Multiple sequence alignment - TraesCS5A01G553500

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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 TraesCS5A01G553500 chr5A 100.000 5594 0 0 1 5594 705955849 705950256 0.000000e+00 10331.0
1 TraesCS5A01G553500 chr5A 80.978 368 55 8 62 417 706058763 706059127 1.530000e-70 278.0
2 TraesCS5A01G553500 chr5A 78.880 393 72 6 1402 1783 705952116 705951724 7.190000e-64 255.0
3 TraesCS5A01G553500 chr5A 78.880 393 72 6 3734 4126 705954448 705954067 7.190000e-64 255.0
4 TraesCS5A01G553500 chr5A 80.515 272 37 11 2719 2978 705945618 705945885 1.590000e-45 195.0
5 TraesCS5A01G553500 chr5A 76.000 275 49 12 3721 3979 706066328 706066055 5.880000e-25 126.0
6 TraesCS5A01G553500 chr5A 91.304 46 3 1 2975 3020 12880783 12880827 1.680000e-05 62.1
7 TraesCS5A01G553500 chr5A 91.304 46 3 1 2975 3020 296678486 296678530 1.680000e-05 62.1
8 TraesCS5A01G553500 chrUn 95.986 1171 36 2 1819 2978 108251575 108252745 0.000000e+00 1892.0
9 TraesCS5A01G553500 chrUn 92.727 1045 45 12 3716 4740 108255347 108256380 0.000000e+00 1480.0
10 TraesCS5A01G553500 chrUn 89.756 1064 47 8 809 1819 108250442 108251496 0.000000e+00 1304.0
11 TraesCS5A01G553500 chrUn 94.723 758 33 5 3 754 108249519 108250275 0.000000e+00 1171.0
12 TraesCS5A01G553500 chrUn 79.884 1203 185 31 3734 4920 108300448 108299287 0.000000e+00 828.0
13 TraesCS5A01G553500 chrUn 88.455 589 43 9 817 1398 134300333 134299763 0.000000e+00 688.0
14 TraesCS5A01G553500 chrUn 91.410 454 11 11 2978 3427 108252777 108253206 1.040000e-166 597.0
15 TraesCS5A01G553500 chrUn 80.313 767 109 24 1056 1783 108305135 108304372 4.930000e-150 542.0
16 TraesCS5A01G553500 chrUn 79.916 717 112 15 1089 1774 108430311 108431026 1.080000e-136 497.0
17 TraesCS5A01G553500 chrUn 83.795 469 33 16 4751 5177 108256473 108256940 6.750000e-109 405.0
18 TraesCS5A01G553500 chrUn 83.333 426 43 18 5177 5594 108257100 108257505 8.850000e-98 368.0
19 TraesCS5A01G553500 chrUn 82.619 420 53 7 5 419 134301356 134300952 2.480000e-93 353.0
20 TraesCS5A01G553500 chrUn 80.175 343 50 12 2548 2882 108303402 108303070 2.010000e-59 241.0
21 TraesCS5A01G553500 chrUn 77.212 373 71 6 1819 2178 108431156 108431527 7.350000e-49 206.0
22 TraesCS5A01G553500 chrUn 93.578 109 6 1 416 523 134300922 134300814 1.610000e-35 161.0
23 TraesCS5A01G553500 chrUn 80.198 202 32 4 3961 4162 134261855 134261662 1.620000e-30 145.0
24 TraesCS5A01G553500 chrUn 97.500 40 1 0 2982 3021 108257304 108257343 1.010000e-07 69.4
25 TraesCS5A01G553500 chrUn 96.875 32 1 0 5276 5307 108257229 108257260 3.000000e-03 54.7
26 TraesCS5A01G553500 chr4B 95.383 1083 31 13 4305 5382 665972977 665971909 0.000000e+00 1705.0
27 TraesCS5A01G553500 chr4B 93.304 1150 47 12 2978 4127 665974103 665972984 0.000000e+00 1670.0
28 TraesCS5A01G553500 chr4B 89.710 1069 44 17 809 1819 665976119 665975059 0.000000e+00 1304.0
29 TraesCS5A01G553500 chr4B 94.581 609 27 2 1819 2421 665974980 665974372 0.000000e+00 937.0
30 TraesCS5A01G553500 chr4B 94.699 415 22 0 146 560 665976623 665976209 0.000000e+00 645.0
31 TraesCS5A01G553500 chr4B 80.184 762 113 20 1056 1780 665919819 665920579 2.290000e-148 536.0
32 TraesCS5A01G553500 chr4B 96.460 226 7 1 2753 2978 665974360 665974136 6.840000e-99 372.0
33 TraesCS5A01G553500 chr4B 77.708 637 86 27 3734 4365 625628231 625627646 6.940000e-89 339.0
34 TraesCS5A01G553500 chr4B 91.163 215 18 1 5380 5594 665970567 665970354 1.970000e-74 291.0
35 TraesCS5A01G553500 chr4B 92.965 199 13 1 5382 5580 665971423 665971226 7.090000e-74 289.0
36 TraesCS5A01G553500 chr4B 80.260 385 73 2 1402 1783 665973369 665972985 2.550000e-73 287.0
37 TraesCS5A01G553500 chr4B 77.551 441 64 24 2548 2966 665921559 665921986 3.370000e-57 233.0
38 TraesCS5A01G553500 chr4B 88.618 123 9 3 5177 5296 665970854 665970734 1.620000e-30 145.0
39 TraesCS5A01G553500 chr4B 97.500 40 1 0 2982 3021 665970555 665970516 1.010000e-07 69.4
40 TraesCS5A01G553500 chr4B 100.000 29 0 0 5279 5307 665970722 665970694 3.000000e-03 54.7
41 TraesCS5A01G553500 chr7D 90.556 953 73 8 3719 4671 45838447 45837512 0.000000e+00 1245.0
42 TraesCS5A01G553500 chr7D 88.839 896 59 11 965 1819 45858120 45857225 0.000000e+00 1062.0
43 TraesCS5A01G553500 chr7D 93.071 736 34 4 3 735 45885964 45885243 0.000000e+00 1061.0
44 TraesCS5A01G553500 chr7D 92.402 487 32 2 1822 2304 45857143 45856658 0.000000e+00 689.0
45 TraesCS5A01G553500 chr7D 79.318 938 142 26 874 1783 45838967 45838054 1.330000e-170 610.0
46 TraesCS5A01G553500 chr7D 91.170 453 13 10 2978 3427 45855905 45855477 1.740000e-164 590.0
47 TraesCS5A01G553500 chr7D 83.363 553 46 20 4669 5177 45837277 45836727 2.360000e-128 470.0
48 TraesCS5A01G553500 chr7D 98.444 257 4 0 2362 2618 45856526 45856270 2.380000e-123 453.0
49 TraesCS5A01G553500 chr7D 91.642 335 15 4 2657 2978 45856272 45855938 8.550000e-123 451.0
50 TraesCS5A01G553500 chr7D 85.079 382 52 2 1819 2195 45837933 45837552 8.790000e-103 385.0
51 TraesCS5A01G553500 chr7D 82.436 427 47 19 5177 5594 45836567 45836160 1.150000e-91 348.0
52 TraesCS5A01G553500 chr7D 89.349 169 7 5 809 976 45885251 45885093 9.500000e-48 202.0
53 TraesCS5A01G553500 chr7D 97.500 40 1 0 2982 3021 45836361 45836322 1.010000e-07 69.4
54 TraesCS5A01G553500 chr2D 77.285 1488 243 57 3734 5177 14127570 14126134 0.000000e+00 787.0
55 TraesCS5A01G553500 chr2D 80.803 922 124 17 863 1748 14128127 14127223 0.000000e+00 673.0
56 TraesCS5A01G553500 chr2D 85.075 134 14 4 5177 5307 14125967 14125837 1.260000e-26 132.0
57 TraesCS5A01G553500 chr2B 80.305 919 134 15 873 1748 25844386 25843472 0.000000e+00 651.0
58 TraesCS5A01G553500 chr2B 78.010 1005 172 33 3792 4784 25787920 25786953 2.250000e-163 586.0
59 TraesCS5A01G553500 chr2B 77.111 900 180 17 3714 4607 25843838 25842959 1.080000e-136 497.0
60 TraesCS5A01G553500 chr2B 83.099 355 60 0 1819 2173 25843313 25842959 1.940000e-84 324.0
61 TraesCS5A01G553500 chr2B 83.117 308 52 0 1441 1748 25787936 25787629 1.190000e-71 281.0
62 TraesCS5A01G553500 chr2B 74.510 306 45 21 2647 2937 25779083 25778796 9.910000e-18 102.0
63 TraesCS5A01G553500 chr2B 100.000 33 0 0 5325 5357 25842016 25842048 1.680000e-05 62.1
64 TraesCS5A01G553500 chr4A 76.125 1156 209 40 3735 4870 738742948 738741840 1.370000e-150 544.0
65 TraesCS5A01G553500 chr1B 73.220 1292 233 62 3714 4968 633352266 633353481 1.150000e-96 364.0
66 TraesCS5A01G553500 chr6A 74.480 866 161 36 3721 4578 610477566 610476753 2.510000e-83 320.0
67 TraesCS5A01G553500 chr6A 79.532 342 57 7 1821 2149 617823950 617824291 1.210000e-56 231.0
68 TraesCS5A01G553500 chr6A 90.164 61 2 1 873 933 617814477 617814533 6.010000e-10 76.8
69 TraesCS5A01G553500 chr6D 80.178 338 56 3 1821 2149 471819125 471818790 5.600000e-60 243.0
70 TraesCS5A01G553500 chr6B 75.254 590 96 31 3723 4303 707307312 707306764 9.370000e-58 235.0
71 TraesCS5A01G553500 chr7A 78.947 209 33 8 4492 4699 5049503 5049701 1.260000e-26 132.0
72 TraesCS5A01G553500 chr7A 83.871 124 14 4 4751 4869 5049721 5049843 4.580000e-21 113.0
73 TraesCS5A01G553500 chr7A 81.022 137 19 5 4492 4627 4903491 4903621 9.910000e-18 102.0
74 TraesCS5A01G553500 chr2A 86.869 99 8 4 2738 2832 16495447 16495350 7.660000e-19 106.0
75 TraesCS5A01G553500 chr2A 93.182 44 3 0 2978 3021 24293874 24293831 1.300000e-06 65.8


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 TraesCS5A01G553500 chr5A 705950256 705955849 5593 True 10331.000000 10331 100.000000 1 5594 1 chr5A.!!$R1 5593
1 TraesCS5A01G553500 chr5A 705951724 705954448 2724 True 255.000000 255 78.880000 1402 4126 2 chr5A.!!$R3 2724
2 TraesCS5A01G553500 chrUn 108249519 108257505 7986 False 815.677778 1892 91.789444 3 5594 9 chrUn.!!$F1 5591
3 TraesCS5A01G553500 chrUn 108299287 108305135 5848 True 537.000000 828 80.124000 1056 4920 3 chrUn.!!$R2 3864
4 TraesCS5A01G553500 chrUn 134299763 134301356 1593 True 400.666667 688 88.217333 5 1398 3 chrUn.!!$R3 1393
5 TraesCS5A01G553500 chrUn 108430311 108431527 1216 False 351.500000 497 78.564000 1089 2178 2 chrUn.!!$F2 1089
6 TraesCS5A01G553500 chr4B 665970354 665976623 6269 True 647.425000 1705 92.886917 146 5594 12 chr4B.!!$R2 5448
7 TraesCS5A01G553500 chr4B 665919819 665921986 2167 False 384.500000 536 78.867500 1056 2966 2 chr4B.!!$F1 1910
8 TraesCS5A01G553500 chr4B 625627646 625628231 585 True 339.000000 339 77.708000 3734 4365 1 chr4B.!!$R1 631
9 TraesCS5A01G553500 chr7D 45855477 45858120 2643 True 649.000000 1062 92.499400 965 3427 5 chr7D.!!$R2 2462
10 TraesCS5A01G553500 chr7D 45885093 45885964 871 True 631.500000 1061 91.210000 3 976 2 chr7D.!!$R3 973
11 TraesCS5A01G553500 chr7D 45836160 45838967 2807 True 521.233333 1245 86.375333 874 5594 6 chr7D.!!$R1 4720
12 TraesCS5A01G553500 chr2D 14125837 14128127 2290 True 530.666667 787 81.054333 863 5307 3 chr2D.!!$R1 4444
13 TraesCS5A01G553500 chr2B 25842959 25844386 1427 True 490.666667 651 80.171667 873 4607 3 chr2B.!!$R3 3734
14 TraesCS5A01G553500 chr2B 25786953 25787936 983 True 433.500000 586 80.563500 1441 4784 2 chr2B.!!$R2 3343
15 TraesCS5A01G553500 chr4A 738741840 738742948 1108 True 544.000000 544 76.125000 3735 4870 1 chr4A.!!$R1 1135
16 TraesCS5A01G553500 chr1B 633352266 633353481 1215 False 364.000000 364 73.220000 3714 4968 1 chr1B.!!$F1 1254
17 TraesCS5A01G553500 chr6A 610476753 610477566 813 True 320.000000 320 74.480000 3721 4578 1 chr6A.!!$R1 857
18 TraesCS5A01G553500 chr6B 707306764 707307312 548 True 235.000000 235 75.254000 3723 4303 1 chr6B.!!$R1 580

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
164 165 1.500474 GTGATCCACCCTCTCCATCA 58.500 55.0 0.00 0.00 0.00 3.07 F
1569 2249 0.888619 TGCTGACTTCCGACGAGAAT 59.111 50.0 0.00 0.00 0.00 2.40 F
2178 2966 0.381801 AAGTCTGCACTTGTTTGCCG 59.618 50.0 0.00 0.00 41.64 5.69 F
3196 4031 0.111061 AAGTTGGTGGCTGCTCATGA 59.889 50.0 0.00 0.00 0.00 3.07 F
3197 4032 0.322277 AGTTGGTGGCTGCTCATGAG 60.322 55.0 18.84 18.84 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1877 2659 0.889186 TTTCCGCACCCAAAGAGAGC 60.889 55.000 0.00 0.00 0.00 4.09 R
3184 4019 0.694771 ACTTTCCTCATGAGCAGCCA 59.305 50.000 17.76 0.00 0.00 4.75 R
3695 5911 1.073284 GGGATTGGGCCATGTATACGT 59.927 52.381 7.26 0.00 0.00 3.57 R
4549 7326 1.002990 CAGTGCTGCTCCCATCACA 60.003 57.895 0.00 0.00 39.82 3.58 R
5105 8361 1.438710 CATTATTAGCCGCGCGCAC 60.439 57.895 32.61 22.45 41.38 5.34 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
41 42 4.915158 ACTGTAGCCTACCGAAATAGAC 57.085 45.455 0.00 0.00 0.00 2.59
51 52 3.359950 ACCGAAATAGACGACCCTAACT 58.640 45.455 0.00 0.00 0.00 2.24
73 74 4.853924 AAAACCATCGCAGAATTCACTT 57.146 36.364 8.44 0.00 43.58 3.16
95 96 3.173151 TGAGGTTCATGAGCTTCTACCA 58.827 45.455 19.76 0.74 35.91 3.25
164 165 1.500474 GTGATCCACCCTCTCCATCA 58.500 55.000 0.00 0.00 0.00 3.07
228 233 2.667418 GCTCTGCCTGCCTCTCAA 59.333 61.111 0.00 0.00 0.00 3.02
250 255 2.170607 AGCACCTTATATGTTGCTCCGT 59.829 45.455 5.01 0.00 0.00 4.69
270 275 4.438880 CCGTGTGTAAGATGAAGATCGACT 60.439 45.833 0.00 0.00 33.34 4.18
370 376 9.325198 GGGATCCAAATTGTAAAAATATCAACC 57.675 33.333 15.23 0.00 0.00 3.77
609 1034 2.922740 TGCGAGTACCCTTCTTGTTT 57.077 45.000 0.00 0.00 0.00 2.83
616 1042 6.371389 CGAGTACCCTTCTTGTTTGATTTTC 58.629 40.000 0.00 0.00 0.00 2.29
707 1136 7.928307 TCTCCCATTGTTCTTTATTCTTCAG 57.072 36.000 0.00 0.00 0.00 3.02
1158 1822 3.411517 CTGCCCAACCTCCCGGAT 61.412 66.667 0.73 0.00 0.00 4.18
1569 2249 0.888619 TGCTGACTTCCGACGAGAAT 59.111 50.000 0.00 0.00 0.00 2.40
1641 2324 1.994507 CTGCCGTCTTCTCGTCGGAT 61.995 60.000 7.01 0.00 45.40 4.18
1649 2332 1.067212 CTTCTCGTCGGATACAAGGGG 59.933 57.143 0.00 0.00 0.00 4.79
1748 2433 4.261801 TCAGTTTACTGGCCTTTCTATGC 58.738 43.478 3.32 0.00 43.91 3.14
1778 2475 4.201851 ACGCATTATCAAGATCAACACTGC 60.202 41.667 0.00 0.00 0.00 4.40
1877 2659 1.804396 TTTGGGTGCGGCAGAACATG 61.804 55.000 1.18 0.00 0.00 3.21
1892 2674 0.957395 ACATGCTCTCTTTGGGTGCG 60.957 55.000 0.00 0.00 0.00 5.34
2088 2870 2.851263 TGACTGTGCCTTTCCGTATT 57.149 45.000 0.00 0.00 0.00 1.89
2178 2966 0.381801 AAGTCTGCACTTGTTTGCCG 59.618 50.000 0.00 0.00 41.64 5.69
2208 2996 7.341030 AGGAAATGAATGAATGGGATTTTTCC 58.659 34.615 0.00 0.00 39.74 3.13
2450 3238 5.618056 TTATTGAGAGAAAAGCACAGCAG 57.382 39.130 0.00 0.00 0.00 4.24
2622 3410 3.803778 CCATTTTTCTTCCACTGCACAAC 59.196 43.478 0.00 0.00 0.00 3.32
2679 3467 1.133982 TGTTCTTTGTTGTGCGCACAT 59.866 42.857 40.78 0.00 41.52 3.21
2709 3497 6.160576 AGAAATTGGCTTTTAAGTGCTCAA 57.839 33.333 2.60 5.45 0.00 3.02
2718 3506 5.346011 GCTTTTAAGTGCTCAACTATTTGCC 59.654 40.000 0.00 0.00 38.56 4.52
2763 3551 6.719301 TGTTCCCGACCTAATTTTTATGGTA 58.281 36.000 0.00 0.00 32.30 3.25
2863 3655 8.560374 AGAGTTCTGAAAGTAGTTATTGTTTGC 58.440 33.333 0.00 0.00 33.76 3.68
3078 3910 1.000019 ATGCAACAGCAGCAGGGAT 60.000 52.632 0.00 0.00 46.36 3.85
3184 4019 2.787994 CTGCTCATGAGGAAAGTTGGT 58.212 47.619 23.89 0.00 0.00 3.67
3185 4020 2.486982 CTGCTCATGAGGAAAGTTGGTG 59.513 50.000 23.89 3.25 0.00 4.17
3186 4021 1.815003 GCTCATGAGGAAAGTTGGTGG 59.185 52.381 23.89 0.00 0.00 4.61
3187 4022 1.815003 CTCATGAGGAAAGTTGGTGGC 59.185 52.381 15.38 0.00 0.00 5.01
3188 4023 1.425066 TCATGAGGAAAGTTGGTGGCT 59.575 47.619 0.00 0.00 0.00 4.75
3189 4024 1.542915 CATGAGGAAAGTTGGTGGCTG 59.457 52.381 0.00 0.00 0.00 4.85
3190 4025 0.823356 TGAGGAAAGTTGGTGGCTGC 60.823 55.000 0.00 0.00 0.00 5.25
3191 4026 0.538287 GAGGAAAGTTGGTGGCTGCT 60.538 55.000 0.00 0.00 0.00 4.24
3192 4027 0.538287 AGGAAAGTTGGTGGCTGCTC 60.538 55.000 0.00 0.00 0.00 4.26
3193 4028 0.823356 GGAAAGTTGGTGGCTGCTCA 60.823 55.000 0.00 0.00 0.00 4.26
3194 4029 1.251251 GAAAGTTGGTGGCTGCTCAT 58.749 50.000 0.00 0.00 0.00 2.90
3195 4030 0.963962 AAAGTTGGTGGCTGCTCATG 59.036 50.000 0.00 0.00 0.00 3.07
3196 4031 0.111061 AAGTTGGTGGCTGCTCATGA 59.889 50.000 0.00 0.00 0.00 3.07
3197 4032 0.322277 AGTTGGTGGCTGCTCATGAG 60.322 55.000 18.84 18.84 0.00 2.90
3198 4033 1.001764 TTGGTGGCTGCTCATGAGG 60.002 57.895 23.89 9.58 0.00 3.86
3199 4034 1.491274 TTGGTGGCTGCTCATGAGGA 61.491 55.000 23.89 20.40 0.00 3.71
3200 4035 1.300963 GGTGGCTGCTCATGAGGAA 59.699 57.895 23.89 3.82 0.00 3.36
3201 4036 0.322816 GGTGGCTGCTCATGAGGAAA 60.323 55.000 23.89 7.29 0.00 3.13
3202 4037 1.093159 GTGGCTGCTCATGAGGAAAG 58.907 55.000 23.89 11.60 0.00 2.62
3203 4038 0.694771 TGGCTGCTCATGAGGAAAGT 59.305 50.000 23.89 0.00 0.00 2.66
3204 4039 1.074405 TGGCTGCTCATGAGGAAAGTT 59.926 47.619 23.89 0.00 0.00 2.66
3205 4040 1.471684 GGCTGCTCATGAGGAAAGTTG 59.528 52.381 23.89 10.16 0.00 3.16
3206 4041 1.471684 GCTGCTCATGAGGAAAGTTGG 59.528 52.381 23.89 9.46 0.00 3.77
3230 4065 6.389091 GGAATCAACTGCATTTGTTGTGATA 58.611 36.000 15.50 0.00 43.54 2.15
3494 5677 8.193953 TCTTTTGCTTTTAGAAAATCTCCCAT 57.806 30.769 0.00 0.00 0.00 4.00
3559 5746 5.195001 TGAGTTACAAAAACCAATGCCTC 57.805 39.130 0.00 0.00 0.00 4.70
3784 6497 2.859165 ACTGGAACATGATGTCCGTT 57.141 45.000 0.00 0.00 38.20 4.44
3880 6612 2.258013 TTTCGCCTGGCTTGGTTCG 61.258 57.895 17.92 0.00 0.00 3.95
3990 6723 1.149174 CGGAGACATGGGATTGGGG 59.851 63.158 0.00 0.00 0.00 4.96
3993 6726 0.753111 GAGACATGGGATTGGGGCAC 60.753 60.000 0.00 0.00 0.00 5.01
3994 6727 1.217057 AGACATGGGATTGGGGCACT 61.217 55.000 0.00 0.00 0.00 4.40
3995 6728 1.000739 ACATGGGATTGGGGCACTG 59.999 57.895 0.00 0.00 0.00 3.66
3996 6729 1.759299 CATGGGATTGGGGCACTGG 60.759 63.158 0.00 0.00 0.00 4.00
3997 6730 3.012775 ATGGGATTGGGGCACTGGG 62.013 63.158 0.00 0.00 0.00 4.45
3999 6732 4.066139 GGATTGGGGCACTGGGCT 62.066 66.667 0.21 0.00 44.01 5.19
4164 6903 2.372852 TCTACCCTTGCAGGTGGAC 58.627 57.895 7.05 0.00 41.98 4.02
4169 6908 1.106944 CCCTTGCAGGTGGACGTTTT 61.107 55.000 0.00 0.00 31.93 2.43
4209 6951 1.763545 GGGGAGACTAAGGATGGTCAC 59.236 57.143 0.00 0.00 39.36 3.67
4269 7018 2.616765 CCATGTTTGGATCCGTGGTGTA 60.617 50.000 7.39 0.00 46.92 2.90
4338 7091 3.325425 TGAGTGAAGAAATTGGTCGGGTA 59.675 43.478 0.00 0.00 0.00 3.69
4410 7187 7.716998 GGATATGTCTACTTGTCCATGAAATGT 59.283 37.037 0.00 0.00 44.81 2.71
4448 7225 1.279271 ACTCCGCTGCTGGTTCTTATT 59.721 47.619 9.66 0.00 0.00 1.40
4549 7326 1.970640 GGCCTCCTTGTTTGATTGGTT 59.029 47.619 0.00 0.00 0.00 3.67
4691 7719 8.865590 ATTACTTACTTTGTTGACGCAAAATT 57.134 26.923 0.00 0.00 37.82 1.82
4740 7770 2.872858 GGAAGATCGTGCCTTTGTATCC 59.127 50.000 0.00 0.00 0.00 2.59
4742 7772 3.914426 AGATCGTGCCTTTGTATCCTT 57.086 42.857 0.00 0.00 0.00 3.36
4746 7776 3.101437 TCGTGCCTTTGTATCCTTCCTA 58.899 45.455 0.00 0.00 0.00 2.94
4748 7778 3.195661 GTGCCTTTGTATCCTTCCTACG 58.804 50.000 0.00 0.00 0.00 3.51
4750 7780 2.419574 GCCTTTGTATCCTTCCTACGCA 60.420 50.000 0.00 0.00 0.00 5.24
4751 7781 3.869065 CCTTTGTATCCTTCCTACGCAA 58.131 45.455 0.00 0.00 0.00 4.85
4753 7783 4.273480 CCTTTGTATCCTTCCTACGCAATG 59.727 45.833 0.00 0.00 0.00 2.82
4770 7886 5.532406 ACGCAATGGTTATGCTCATAGAAAT 59.468 36.000 0.00 0.00 41.64 2.17
4797 7914 3.391296 AGATGCCTGATAACCGTTGGTAT 59.609 43.478 0.00 0.00 33.12 2.73
5208 9769 7.713764 ACCTGCAATTTATGTTCAGTTTTTC 57.286 32.000 0.00 0.00 0.00 2.29
5209 9770 7.271511 ACCTGCAATTTATGTTCAGTTTTTCA 58.728 30.769 0.00 0.00 0.00 2.69
5210 9771 7.439056 ACCTGCAATTTATGTTCAGTTTTTCAG 59.561 33.333 0.00 0.00 0.00 3.02
5211 9772 7.652909 CCTGCAATTTATGTTCAGTTTTTCAGA 59.347 33.333 0.00 0.00 0.00 3.27
5256 9853 4.121317 TGTTGCAAGAAAGCTGATTTTGG 58.879 39.130 0.00 0.00 34.99 3.28
5259 9856 4.624015 TGCAAGAAAGCTGATTTTGGAAG 58.376 39.130 0.00 0.00 34.99 3.46
5268 9865 3.120511 GCTGATTTTGGAAGTGTCGAGTC 60.121 47.826 0.00 0.00 0.00 3.36
5269 9866 4.058124 CTGATTTTGGAAGTGTCGAGTCA 58.942 43.478 0.00 0.00 0.00 3.41
5270 9867 4.447290 TGATTTTGGAAGTGTCGAGTCAA 58.553 39.130 0.00 0.00 0.00 3.18
5271 9868 4.272504 TGATTTTGGAAGTGTCGAGTCAAC 59.727 41.667 0.00 0.00 0.00 3.18
5272 9869 3.536956 TTTGGAAGTGTCGAGTCAACT 57.463 42.857 0.00 0.00 0.00 3.16
5273 9870 2.509052 TGGAAGTGTCGAGTCAACTG 57.491 50.000 0.00 0.00 0.00 3.16
5277 9905 3.004524 GGAAGTGTCGAGTCAACTGTACT 59.995 47.826 0.00 0.00 0.00 2.73
5307 9937 4.524802 TCGGAGTATAGGACCACCTTAA 57.475 45.455 0.00 0.00 45.36 1.85
5308 9938 5.070823 TCGGAGTATAGGACCACCTTAAT 57.929 43.478 0.00 0.00 45.36 1.40
5309 9939 5.075493 TCGGAGTATAGGACCACCTTAATC 58.925 45.833 0.00 0.00 45.36 1.75
5310 9940 5.078256 CGGAGTATAGGACCACCTTAATCT 58.922 45.833 0.00 0.00 45.36 2.40
5311 9941 5.539193 CGGAGTATAGGACCACCTTAATCTT 59.461 44.000 0.00 0.00 45.36 2.40
5312 9942 6.516860 CGGAGTATAGGACCACCTTAATCTTG 60.517 46.154 0.00 0.00 45.36 3.02
5313 9943 6.326843 GGAGTATAGGACCACCTTAATCTTGT 59.673 42.308 0.00 0.00 45.36 3.16
5314 9944 7.125792 AGTATAGGACCACCTTAATCTTGTG 57.874 40.000 0.00 0.00 45.36 3.33
5315 9945 6.672657 AGTATAGGACCACCTTAATCTTGTGT 59.327 38.462 0.00 0.00 45.36 3.72
5316 9946 4.287766 AGGACCACCTTAATCTTGTGTC 57.712 45.455 0.00 0.00 45.36 3.67
5317 9947 3.910627 AGGACCACCTTAATCTTGTGTCT 59.089 43.478 0.00 0.00 45.36 3.41
5318 9948 4.351111 AGGACCACCTTAATCTTGTGTCTT 59.649 41.667 0.00 0.00 45.36 3.01
5319 9949 5.546499 AGGACCACCTTAATCTTGTGTCTTA 59.454 40.000 0.00 0.00 45.36 2.10
5320 9950 6.043938 AGGACCACCTTAATCTTGTGTCTTAA 59.956 38.462 0.00 0.00 45.36 1.85
5321 9951 6.884836 GGACCACCTTAATCTTGTGTCTTAAT 59.115 38.462 0.00 0.00 0.00 1.40
5322 9952 7.065923 GGACCACCTTAATCTTGTGTCTTAATC 59.934 40.741 0.00 0.00 0.00 1.75
5323 9953 7.458397 ACCACCTTAATCTTGTGTCTTAATCA 58.542 34.615 0.00 0.00 0.00 2.57
5324 9954 8.109634 ACCACCTTAATCTTGTGTCTTAATCAT 58.890 33.333 0.00 0.00 0.00 2.45
5325 9955 8.960591 CCACCTTAATCTTGTGTCTTAATCATT 58.039 33.333 0.00 0.00 0.00 2.57
5335 9965 9.282247 CTTGTGTCTTAATCATTAATCTTGTGC 57.718 33.333 0.00 0.00 0.00 4.57
5336 9966 8.334263 TGTGTCTTAATCATTAATCTTGTGCA 57.666 30.769 0.00 0.00 0.00 4.57
5337 9967 8.791675 TGTGTCTTAATCATTAATCTTGTGCAA 58.208 29.630 0.00 0.00 0.00 4.08
5338 9968 9.624697 GTGTCTTAATCATTAATCTTGTGCAAA 57.375 29.630 0.00 0.00 0.00 3.68
5345 9975 9.807649 AATCATTAATCTTGTGCAAATTCTACC 57.192 29.630 0.00 0.00 0.00 3.18
5346 9976 7.771183 TCATTAATCTTGTGCAAATTCTACCC 58.229 34.615 0.00 0.00 0.00 3.69
5347 9977 7.615365 TCATTAATCTTGTGCAAATTCTACCCT 59.385 33.333 0.00 0.00 0.00 4.34
5348 9978 7.775053 TTAATCTTGTGCAAATTCTACCCTT 57.225 32.000 0.00 0.00 0.00 3.95
5349 9979 6.670695 AATCTTGTGCAAATTCTACCCTTT 57.329 33.333 0.00 0.00 0.00 3.11
5350 9980 5.452078 TCTTGTGCAAATTCTACCCTTTG 57.548 39.130 0.00 0.00 35.84 2.77
5351 9981 4.280677 TCTTGTGCAAATTCTACCCTTTGG 59.719 41.667 0.00 0.00 33.85 3.28
5365 9995 2.483538 CCCTTTGGTGCAAGAAACTTGG 60.484 50.000 12.36 0.00 0.00 3.61
5382 10107 5.410355 ACTTGGTGCGTTTCCTAGTTATA 57.590 39.130 4.68 0.00 37.67 0.98
5383 10108 5.985911 ACTTGGTGCGTTTCCTAGTTATAT 58.014 37.500 4.68 0.00 37.67 0.86
5388 10113 7.531716 TGGTGCGTTTCCTAGTTATATTTTTG 58.468 34.615 0.00 0.00 0.00 2.44
5389 10114 6.970613 GGTGCGTTTCCTAGTTATATTTTTGG 59.029 38.462 0.00 0.00 0.00 3.28
5411 10140 4.741676 GGAAGAACAGAATTGCACAAGTTG 59.258 41.667 0.00 0.00 0.00 3.16
5425 10154 4.669318 CACAAGTTGCATCCTGAATCATC 58.331 43.478 1.81 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 2.606272 GCGATGGTTTTAGTTAGGGTCG 59.394 50.000 0.00 0.00 0.00 4.79
51 52 5.957842 AAGTGAATTCTGCGATGGTTTTA 57.042 34.783 7.05 0.00 0.00 1.52
73 74 3.582647 TGGTAGAAGCTCATGAACCTCAA 59.417 43.478 12.14 0.00 0.00 3.02
95 96 6.942976 TCAACTTCTTCGGTACCATAAGATT 58.057 36.000 21.42 13.88 0.00 2.40
154 155 8.743085 TTGAAGATTATTTCTTGATGGAGAGG 57.257 34.615 0.00 0.00 44.88 3.69
185 186 5.174037 TGCTAAATTACCTAAGGTGCAGT 57.826 39.130 0.00 0.00 36.19 4.40
186 187 5.741388 CTGCTAAATTACCTAAGGTGCAG 57.259 43.478 0.00 0.00 36.19 4.41
187 188 4.941263 CACTGCTAAATTACCTAAGGTGCA 59.059 41.667 0.00 0.00 36.19 4.57
228 233 3.206150 CGGAGCAACATATAAGGTGCTT 58.794 45.455 20.61 5.89 32.34 3.91
250 255 5.048013 ACACAGTCGATCTTCATCTTACACA 60.048 40.000 0.00 0.00 0.00 3.72
270 275 0.303191 CGCACAACAACGATCACACA 59.697 50.000 0.00 0.00 0.00 3.72
435 475 1.336240 GCTTTGGGATGCTGTGTTGTC 60.336 52.381 0.00 0.00 0.00 3.18
740 1171 7.875327 AAAACTCCTAGCAGTTACTCAAAAA 57.125 32.000 0.00 0.00 35.45 1.94
741 1172 7.875327 AAAAACTCCTAGCAGTTACTCAAAA 57.125 32.000 0.00 0.00 35.45 2.44
804 1235 8.805175 TGTGTGCACCTAGTACTACTATAAAAA 58.195 33.333 15.69 0.00 33.54 1.94
806 1237 7.943079 TGTGTGCACCTAGTACTACTATAAA 57.057 36.000 15.69 0.00 33.54 1.40
865 1434 2.301870 ACGCAATAGTCCAAGACTCCAA 59.698 45.455 0.00 0.00 42.40 3.53
866 1435 1.899814 ACGCAATAGTCCAAGACTCCA 59.100 47.619 0.00 0.00 42.40 3.86
867 1436 2.674796 ACGCAATAGTCCAAGACTCC 57.325 50.000 0.00 0.00 42.40 3.85
868 1437 4.106029 TGTACGCAATAGTCCAAGACTC 57.894 45.455 0.00 0.00 42.40 3.36
869 1438 4.433615 CATGTACGCAATAGTCCAAGACT 58.566 43.478 2.38 2.38 45.54 3.24
870 1439 3.555956 CCATGTACGCAATAGTCCAAGAC 59.444 47.826 0.00 0.00 0.00 3.01
871 1440 3.431626 CCCATGTACGCAATAGTCCAAGA 60.432 47.826 0.00 0.00 0.00 3.02
1641 2324 2.855014 ACGGCCCAACCCCTTGTA 60.855 61.111 0.00 0.00 33.26 2.41
1714 2399 2.370849 AGTAAACTGAACCGTCCACCAT 59.629 45.455 0.00 0.00 0.00 3.55
1748 2433 2.821546 TCTTGATAATGCGTCCTTCGG 58.178 47.619 0.00 0.00 40.26 4.30
1877 2659 0.889186 TTTCCGCACCCAAAGAGAGC 60.889 55.000 0.00 0.00 0.00 4.09
1887 2669 1.029947 ACCCGATCAATTTCCGCACC 61.030 55.000 0.00 0.00 0.00 5.01
1892 2674 1.933853 CGAGTGACCCGATCAATTTCC 59.066 52.381 0.00 0.00 39.72 3.13
2178 2966 5.123227 TCCCATTCATTCATTTCCTCGTAC 58.877 41.667 0.00 0.00 0.00 3.67
2238 3026 8.929260 ACCAGATATTATTTTGCATCATCAGA 57.071 30.769 0.00 0.00 0.00 3.27
2346 3134 6.770746 ATGCAACATCTTCTAGCAGAATTT 57.229 33.333 0.00 0.00 38.75 1.82
2450 3238 8.888579 TTATAATTACTTTCCAGAGCTAGCAC 57.111 34.615 18.83 11.32 0.00 4.40
2520 3308 9.646522 AGTAATATGCATAAAGGGATTCTTGTT 57.353 29.630 11.13 0.00 35.55 2.83
2709 3497 7.334858 CCTAAGAAGAAGAAGAGGCAAATAGT 58.665 38.462 0.00 0.00 0.00 2.12
2718 3506 8.147704 GGAACATATCCCTAAGAAGAAGAAGAG 58.852 40.741 0.00 0.00 43.00 2.85
2763 3551 5.721232 AGTATAACAAGTCGCAACTAAGCT 58.279 37.500 0.00 0.00 33.48 3.74
3078 3910 3.978217 CCTCTTTCGCAAAAACGCAAATA 59.022 39.130 0.00 0.00 0.00 1.40
3184 4019 0.694771 ACTTTCCTCATGAGCAGCCA 59.305 50.000 17.76 0.00 0.00 4.75
3185 4020 1.471684 CAACTTTCCTCATGAGCAGCC 59.528 52.381 17.76 0.00 0.00 4.85
3186 4021 1.471684 CCAACTTTCCTCATGAGCAGC 59.528 52.381 17.76 0.00 0.00 5.25
3187 4022 2.089980 CCCAACTTTCCTCATGAGCAG 58.910 52.381 17.76 13.97 0.00 4.24
3188 4023 1.704628 TCCCAACTTTCCTCATGAGCA 59.295 47.619 17.76 0.00 0.00 4.26
3189 4024 2.496899 TCCCAACTTTCCTCATGAGC 57.503 50.000 17.76 0.00 0.00 4.26
3190 4025 4.592942 TGATTCCCAACTTTCCTCATGAG 58.407 43.478 16.24 16.24 0.00 2.90
3191 4026 4.656100 TGATTCCCAACTTTCCTCATGA 57.344 40.909 0.00 0.00 0.00 3.07
3203 4038 4.686191 AACAAATGCAGTTGATTCCCAA 57.314 36.364 31.51 0.00 32.59 4.12
3230 4065 8.409358 AAAGCAAGTATCCTTTGTACAAATCT 57.591 30.769 20.83 11.10 30.61 2.40
3288 4123 3.711086 CAGACTCACGGTATCATTCTGG 58.289 50.000 0.00 0.00 0.00 3.86
3689 5905 2.028476 TGGGCCATGTATACGTGATAGC 60.028 50.000 23.87 18.13 34.90 2.97
3695 5911 1.073284 GGGATTGGGCCATGTATACGT 59.927 52.381 7.26 0.00 0.00 3.57
3784 6497 3.965258 ATGGGGTTCACGGCAGCA 61.965 61.111 0.00 0.00 0.00 4.41
3880 6612 1.287730 CCTCACAAGACAGCAGACGC 61.288 60.000 0.00 0.00 38.99 5.19
4164 6903 3.980775 CCTTGTAATTGCACCTCAAAACG 59.019 43.478 0.00 0.00 38.34 3.60
4169 6908 2.161855 CAGCCTTGTAATTGCACCTCA 58.838 47.619 0.00 0.00 0.00 3.86
4269 7018 4.547886 AATCCCAATTCCATCACCATCT 57.452 40.909 0.00 0.00 0.00 2.90
4410 7187 3.393278 GGAGTATGCCAACAGGGGTAATA 59.607 47.826 0.00 0.00 37.04 0.98
4448 7225 4.289410 TCTTGATGGTCTCCAATGAAAGGA 59.711 41.667 0.00 0.00 36.95 3.36
4549 7326 1.002990 CAGTGCTGCTCCCATCACA 60.003 57.895 0.00 0.00 39.82 3.58
4683 7708 8.556194 TGCCAACTAAGTAGATATAATTTTGCG 58.444 33.333 0.00 0.00 0.00 4.85
4740 7770 3.206150 AGCATAACCATTGCGTAGGAAG 58.794 45.455 0.00 0.00 44.16 3.46
4742 7772 2.169561 TGAGCATAACCATTGCGTAGGA 59.830 45.455 0.00 0.00 44.82 2.94
4746 7776 4.071961 TCTATGAGCATAACCATTGCGT 57.928 40.909 0.00 0.00 44.82 5.24
4748 7778 7.211966 AGATTTCTATGAGCATAACCATTGC 57.788 36.000 0.00 0.00 40.45 3.56
4770 7886 5.116180 CAACGGTTATCAGGCATCTAAAGA 58.884 41.667 0.00 0.00 0.00 2.52
5104 8360 1.594293 ATTATTAGCCGCGCGCACT 60.594 52.632 32.61 28.12 41.38 4.40
5105 8361 1.438710 CATTATTAGCCGCGCGCAC 60.439 57.895 32.61 22.45 41.38 5.34
5208 9769 8.425577 AGGTGATCTTATACGACAATTTTCTG 57.574 34.615 0.00 0.00 0.00 3.02
5209 9770 8.883731 CAAGGTGATCTTATACGACAATTTTCT 58.116 33.333 0.00 0.00 33.68 2.52
5210 9771 8.665685 ACAAGGTGATCTTATACGACAATTTTC 58.334 33.333 0.00 0.00 33.68 2.29
5211 9772 8.561738 ACAAGGTGATCTTATACGACAATTTT 57.438 30.769 0.00 0.00 33.68 1.82
5256 9853 4.220572 GAGTACAGTTGACTCGACACTTC 58.779 47.826 0.00 0.00 34.41 3.01
5259 9856 3.556513 CTGAGTACAGTTGACTCGACAC 58.443 50.000 0.00 0.00 45.29 3.67
5272 9869 6.318144 CCTATACTCCGAAGAAACTGAGTACA 59.682 42.308 0.00 0.00 0.00 2.90
5273 9870 6.541641 TCCTATACTCCGAAGAAACTGAGTAC 59.458 42.308 0.00 0.00 0.00 2.73
5277 9905 4.643784 GGTCCTATACTCCGAAGAAACTGA 59.356 45.833 0.00 0.00 0.00 3.41
5309 9939 9.282247 GCACAAGATTAATGATTAAGACACAAG 57.718 33.333 3.83 0.00 0.00 3.16
5310 9940 8.791675 TGCACAAGATTAATGATTAAGACACAA 58.208 29.630 3.83 0.00 0.00 3.33
5311 9941 8.334263 TGCACAAGATTAATGATTAAGACACA 57.666 30.769 3.83 0.00 0.00 3.72
5312 9942 9.624697 TTTGCACAAGATTAATGATTAAGACAC 57.375 29.630 3.83 0.00 0.00 3.67
5319 9949 9.807649 GGTAGAATTTGCACAAGATTAATGATT 57.192 29.630 0.00 0.00 0.00 2.57
5320 9950 8.416329 GGGTAGAATTTGCACAAGATTAATGAT 58.584 33.333 0.00 0.00 0.00 2.45
5321 9951 7.615365 AGGGTAGAATTTGCACAAGATTAATGA 59.385 33.333 0.00 0.00 0.00 2.57
5322 9952 7.775120 AGGGTAGAATTTGCACAAGATTAATG 58.225 34.615 0.00 0.00 0.00 1.90
5323 9953 7.961326 AGGGTAGAATTTGCACAAGATTAAT 57.039 32.000 0.00 0.00 0.00 1.40
5324 9954 7.775053 AAGGGTAGAATTTGCACAAGATTAA 57.225 32.000 0.00 0.00 0.00 1.40
5325 9955 7.309744 CCAAAGGGTAGAATTTGCACAAGATTA 60.310 37.037 0.00 0.00 35.53 1.75
5326 9956 6.458210 CAAAGGGTAGAATTTGCACAAGATT 58.542 36.000 0.00 0.00 30.37 2.40
5327 9957 5.047092 CCAAAGGGTAGAATTTGCACAAGAT 60.047 40.000 0.00 0.00 35.53 2.40
5328 9958 4.280677 CCAAAGGGTAGAATTTGCACAAGA 59.719 41.667 0.00 0.00 35.53 3.02
5329 9959 4.559153 CCAAAGGGTAGAATTTGCACAAG 58.441 43.478 0.00 0.00 35.53 3.16
5330 9960 4.599047 CCAAAGGGTAGAATTTGCACAA 57.401 40.909 0.00 0.00 35.53 3.33
5344 9974 2.483538 CCAAGTTTCTTGCACCAAAGGG 60.484 50.000 4.22 0.00 41.29 3.95
5345 9975 2.168313 ACCAAGTTTCTTGCACCAAAGG 59.832 45.455 4.22 0.00 0.00 3.11
5346 9976 3.189285 CACCAAGTTTCTTGCACCAAAG 58.811 45.455 4.22 0.00 0.00 2.77
5347 9977 2.676463 GCACCAAGTTTCTTGCACCAAA 60.676 45.455 4.22 0.00 34.97 3.28
5348 9978 1.134848 GCACCAAGTTTCTTGCACCAA 60.135 47.619 4.22 0.00 34.97 3.67
5349 9979 0.459489 GCACCAAGTTTCTTGCACCA 59.541 50.000 4.22 0.00 34.97 4.17
5350 9980 0.594796 CGCACCAAGTTTCTTGCACC 60.595 55.000 4.22 0.00 34.49 5.01
5351 9981 0.100503 ACGCACCAAGTTTCTTGCAC 59.899 50.000 4.22 0.00 34.49 4.57
5361 9991 6.920569 AATATAACTAGGAAACGCACCAAG 57.079 37.500 0.00 0.00 0.00 3.61
5365 9995 7.754625 TCCAAAAATATAACTAGGAAACGCAC 58.245 34.615 0.00 0.00 0.00 5.34
5382 10107 6.347696 TGTGCAATTCTGTTCTTCCAAAAAT 58.652 32.000 0.00 0.00 0.00 1.82
5383 10108 5.728471 TGTGCAATTCTGTTCTTCCAAAAA 58.272 33.333 0.00 0.00 0.00 1.94
5388 10113 4.574599 ACTTGTGCAATTCTGTTCTTCC 57.425 40.909 0.00 0.00 0.00 3.46
5389 10114 5.878261 CAACTTGTGCAATTCTGTTCTTC 57.122 39.130 0.00 0.00 0.00 2.87
5411 10140 0.590195 GGTGCGATGATTCAGGATGC 59.410 55.000 0.00 0.00 34.76 3.91
5447 10176 4.245660 TCAAATCAGCGTCTTACTCTTGG 58.754 43.478 0.00 0.00 0.00 3.61
5453 10182 7.470289 AATCTACATCAAATCAGCGTCTTAC 57.530 36.000 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.