Multiple sequence alignment - TraesCS6D01G350700

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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 TraesCS6D01G350700 chr6D 100.000 3242 0 0 1 3242 448060615 448057374 0.000000e+00 5987.0
1 TraesCS6D01G350700 chr6D 93.660 2145 95 7 560 2664 448484902 448487045 0.000000e+00 3169.0
2 TraesCS6D01G350700 chr6D 85.579 1165 142 12 1142 2287 448429029 448430186 0.000000e+00 1197.0
3 TraesCS6D01G350700 chr6D 91.892 518 36 4 2726 3242 448503618 448504130 0.000000e+00 719.0
4 TraesCS6D01G350700 chr6D 81.168 685 118 7 1556 2233 448159824 448159144 1.020000e-149 540.0
5 TraesCS6D01G350700 chr6D 80.389 668 119 5 1600 2255 447914540 447913873 6.250000e-137 497.0
6 TraesCS6D01G350700 chr6D 76.611 714 144 16 1559 2256 448507605 448508311 3.950000e-99 372.0
7 TraesCS6D01G350700 chr6D 86.139 303 23 7 146 445 448483412 448483698 3.140000e-80 309.0
8 TraesCS6D01G350700 chr6D 99.310 145 1 0 1 145 123066749 123066893 2.480000e-66 263.0
9 TraesCS6D01G350700 chr6D 96.753 154 4 1 1 154 301634925 301634773 4.150000e-64 255.0
10 TraesCS6D01G350700 chr6D 80.000 260 33 14 2612 2853 448430554 448430812 1.200000e-39 174.0
11 TraesCS6D01G350700 chr6D 78.788 264 36 8 2920 3172 448432841 448433095 3.350000e-35 159.0
12 TraesCS6D01G350700 chr6D 89.888 89 9 0 720 808 320710317 320710405 7.350000e-22 115.0
13 TraesCS6D01G350700 chr6D 98.387 62 1 0 2658 2719 448503572 448503633 3.420000e-20 110.0
14 TraesCS6D01G350700 chr6B 89.058 2294 120 35 985 3203 678931672 678929435 0.000000e+00 2724.0
15 TraesCS6D01G350700 chr6B 85.911 1164 140 9 1142 2287 679285003 679286160 0.000000e+00 1219.0
16 TraesCS6D01G350700 chr6B 85.911 1164 140 9 1142 2287 679330399 679329242 0.000000e+00 1219.0
17 TraesCS6D01G350700 chr6B 78.062 1094 191 37 1164 2233 679278129 679279197 0.000000e+00 645.0
18 TraesCS6D01G350700 chr6B 93.000 200 12 2 818 1017 678932164 678931967 1.140000e-74 291.0
19 TraesCS6D01G350700 chr6B 82.500 200 32 1 1216 1412 678741343 678741144 4.300000e-39 172.0
20 TraesCS6D01G350700 chr6B 76.923 273 43 8 2919 3180 679288907 679289170 1.570000e-28 137.0
21 TraesCS6D01G350700 chr6B 76.923 273 43 7 2919 3180 679326496 679326233 1.570000e-28 137.0
22 TraesCS6D01G350700 chr6B 97.826 46 1 0 3197 3242 678929222 678929177 2.680000e-11 80.5
23 TraesCS6D01G350700 chr6A 84.914 1107 142 14 1142 2230 594516410 594515311 0.000000e+00 1096.0
24 TraesCS6D01G350700 chr6A 79.231 1093 181 34 1164 2233 594520666 594519597 0.000000e+00 719.0
25 TraesCS6D01G350700 chr6A 78.040 1143 208 25 1138 2257 594530341 594529219 0.000000e+00 680.0
26 TraesCS6D01G350700 chr6A 77.928 666 108 6 1600 2255 594498512 594497876 2.360000e-101 379.0
27 TraesCS6D01G350700 chr6A 76.611 714 144 17 1559 2256 594507509 594506803 3.950000e-99 372.0
28 TraesCS6D01G350700 chr6A 92.135 89 7 0 720 808 458224107 458224195 3.400000e-25 126.0
29 TraesCS6D01G350700 chr2B 86.692 263 32 3 465 725 166592124 166592385 4.090000e-74 289.0
30 TraesCS6D01G350700 chr7B 86.667 255 32 2 465 717 598296154 598296408 6.850000e-72 281.0
31 TraesCS6D01G350700 chr7B 86.694 248 31 2 469 714 63829930 63829683 1.150000e-69 274.0
32 TraesCS6D01G350700 chr7B 86.454 251 30 2 468 714 574415165 574415415 4.120000e-69 272.0
33 TraesCS6D01G350700 chr1D 86.667 255 30 4 465 716 76970959 76971212 2.460000e-71 279.0
34 TraesCS6D01G350700 chr1D 99.310 145 1 0 1 145 117591362 117591218 2.480000e-66 263.0
35 TraesCS6D01G350700 chr1D 92.553 94 7 0 715 808 32225323 32225416 5.640000e-28 135.0
36 TraesCS6D01G350700 chr5A 85.606 264 33 4 465 724 34841912 34842174 4.120000e-69 272.0
37 TraesCS6D01G350700 chr2D 100.000 145 0 0 1 145 39837436 39837580 5.330000e-68 268.0
38 TraesCS6D01G350700 chr2D 84.644 267 40 1 451 716 37526880 37526614 6.900000e-67 265.0
39 TraesCS6D01G350700 chr2D 99.315 146 1 0 1 146 554821009 554820864 6.900000e-67 265.0
40 TraesCS6D01G350700 chr2D 89.474 95 10 0 714 808 476763857 476763951 1.580000e-23 121.0
41 TraesCS6D01G350700 chr1B 84.701 268 37 3 454 717 12835369 12835102 6.900000e-67 265.0
42 TraesCS6D01G350700 chr4D 98.649 148 2 0 1 148 151814215 151814068 2.480000e-66 263.0
43 TraesCS6D01G350700 chr4D 94.479 163 7 2 1 162 35812147 35812308 1.930000e-62 250.0
44 TraesCS6D01G350700 chr5D 96.774 155 5 0 1 155 394914076 394913922 3.210000e-65 259.0
45 TraesCS6D01G350700 chr7D 95.000 160 8 0 1 160 123272229 123272070 5.370000e-63 252.0
46 TraesCS6D01G350700 chr7D 85.217 115 14 3 720 834 608441429 608441318 7.350000e-22 115.0
47 TraesCS6D01G350700 chr1A 91.398 93 8 0 715 807 514849110 514849018 9.440000e-26 128.0
48 TraesCS6D01G350700 chr1A 91.398 93 8 0 715 807 515105356 515105264 9.440000e-26 128.0
49 TraesCS6D01G350700 chr1A 90.110 91 9 0 715 805 98284058 98284148 5.680000e-23 119.0
50 TraesCS6D01G350700 chr7A 90.426 94 9 0 715 808 38052079 38052172 1.220000e-24 124.0
51 TraesCS6D01G350700 chr7A 88.542 96 8 2 726 821 692898015 692897923 2.640000e-21 113.0
52 TraesCS6D01G350700 chr7A 86.139 101 12 1 715 815 418669595 418669497 1.230000e-19 108.0
53 TraesCS6D01G350700 chr4A 87.129 101 11 2 715 815 454119821 454119919 2.640000e-21 113.0


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 TraesCS6D01G350700 chr6D 448057374 448060615 3241 True 5987.000000 5987 100.000000 1 3242 1 chr6D.!!$R3 3241
1 TraesCS6D01G350700 chr6D 448483412 448487045 3633 False 1739.000000 3169 89.899500 146 2664 2 chr6D.!!$F4 2518
2 TraesCS6D01G350700 chr6D 448159144 448159824 680 True 540.000000 540 81.168000 1556 2233 1 chr6D.!!$R4 677
3 TraesCS6D01G350700 chr6D 448429029 448433095 4066 False 510.000000 1197 81.455667 1142 3172 3 chr6D.!!$F3 2030
4 TraesCS6D01G350700 chr6D 447913873 447914540 667 True 497.000000 497 80.389000 1600 2255 1 chr6D.!!$R2 655
5 TraesCS6D01G350700 chr6D 448503572 448508311 4739 False 400.333333 719 88.963333 1559 3242 3 chr6D.!!$F5 1683
6 TraesCS6D01G350700 chr6B 678929177 678932164 2987 True 1031.833333 2724 93.294667 818 3242 3 chr6B.!!$R2 2424
7 TraesCS6D01G350700 chr6B 679285003 679289170 4167 False 678.000000 1219 81.417000 1142 3180 2 chr6B.!!$F2 2038
8 TraesCS6D01G350700 chr6B 679326233 679330399 4166 True 678.000000 1219 81.417000 1142 3180 2 chr6B.!!$R3 2038
9 TraesCS6D01G350700 chr6B 679278129 679279197 1068 False 645.000000 645 78.062000 1164 2233 1 chr6B.!!$F1 1069
10 TraesCS6D01G350700 chr6A 594515311 594520666 5355 True 907.500000 1096 82.072500 1142 2233 2 chr6A.!!$R4 1091
11 TraesCS6D01G350700 chr6A 594529219 594530341 1122 True 680.000000 680 78.040000 1138 2257 1 chr6A.!!$R3 1119
12 TraesCS6D01G350700 chr6A 594497876 594498512 636 True 379.000000 379 77.928000 1600 2255 1 chr6A.!!$R1 655
13 TraesCS6D01G350700 chr6A 594506803 594507509 706 True 372.000000 372 76.611000 1559 2256 1 chr6A.!!$R2 697

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
134 135 0.037326 GAGGACATCTGCCGTGACAA 60.037 55.000 0.0 0.0 0.0 3.18 F
136 137 1.003580 AGGACATCTGCCGTGACAATT 59.996 47.619 0.0 0.0 0.0 2.32 F
1413 4538 0.178947 CCCTCTCCCTAATCCTCGCT 60.179 60.000 0.0 0.0 0.0 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1257 4379 0.617820 AGGAGTAGCCGTGGATGGTT 60.618 55.000 0.0 0.0 43.43 3.67 R
2052 5220 1.078426 GATAGTTGCCACCGTGCCT 60.078 57.895 0.0 0.0 0.00 4.75 R
2983 7443 1.563879 TCCATGAGGGTGTGGGTATTG 59.436 52.381 0.0 0.0 38.11 1.90 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
21 22 4.192429 GTAGGCTTTTACCTTCACCGTA 57.808 45.455 0.00 0.00 41.50 4.02
22 23 3.775261 AGGCTTTTACCTTCACCGTAA 57.225 42.857 0.00 0.00 36.28 3.18
23 24 3.671716 AGGCTTTTACCTTCACCGTAAG 58.328 45.455 0.00 0.00 36.28 2.34
36 37 2.951101 CGTAAGGGGCCGAACCAGT 61.951 63.158 0.00 0.00 42.05 4.00
37 38 1.606885 CGTAAGGGGCCGAACCAGTA 61.607 60.000 0.00 0.00 42.05 2.74
38 39 0.835276 GTAAGGGGCCGAACCAGTAT 59.165 55.000 0.00 0.00 42.05 2.12
41 42 0.835276 AGGGGCCGAACCAGTATAAC 59.165 55.000 0.00 0.00 42.05 1.89
42 43 0.179037 GGGGCCGAACCAGTATAACC 60.179 60.000 0.00 0.00 42.05 2.85
43 44 0.179037 GGGCCGAACCAGTATAACCC 60.179 60.000 0.00 0.00 42.05 4.11
48 49 2.480759 CCGAACCAGTATAACCCTCGTG 60.481 54.545 0.00 0.00 0.00 4.35
49 50 2.165030 CGAACCAGTATAACCCTCGTGT 59.835 50.000 0.00 0.00 0.00 4.49
51 52 3.881937 ACCAGTATAACCCTCGTGTTC 57.118 47.619 0.00 0.00 0.00 3.18
52 53 2.498885 ACCAGTATAACCCTCGTGTTCC 59.501 50.000 0.00 0.00 0.00 3.62
55 56 4.181578 CAGTATAACCCTCGTGTTCCTTG 58.818 47.826 0.00 0.00 0.00 3.61
56 57 3.836562 AGTATAACCCTCGTGTTCCTTGT 59.163 43.478 0.00 0.00 0.00 3.16
59 60 1.003718 CCCTCGTGTTCCTTGTCCC 60.004 63.158 0.00 0.00 0.00 4.46
60 61 1.374252 CCTCGTGTTCCTTGTCCCG 60.374 63.158 0.00 0.00 0.00 5.14
61 62 1.366366 CTCGTGTTCCTTGTCCCGT 59.634 57.895 0.00 0.00 0.00 5.28
64 65 1.411977 TCGTGTTCCTTGTCCCGTTTA 59.588 47.619 0.00 0.00 0.00 2.01
65 66 2.158986 TCGTGTTCCTTGTCCCGTTTAA 60.159 45.455 0.00 0.00 0.00 1.52
68 69 1.881973 GTTCCTTGTCCCGTTTAACCC 59.118 52.381 0.00 0.00 0.00 4.11
70 71 0.402887 CCTTGTCCCGTTTAACCCCT 59.597 55.000 0.00 0.00 0.00 4.79
72 73 2.589720 CTTGTCCCGTTTAACCCCTTT 58.410 47.619 0.00 0.00 0.00 3.11
73 74 3.498301 CCTTGTCCCGTTTAACCCCTTTA 60.498 47.826 0.00 0.00 0.00 1.85
75 76 3.753815 TGTCCCGTTTAACCCCTTTAAG 58.246 45.455 0.00 0.00 31.11 1.85
76 77 2.489329 GTCCCGTTTAACCCCTTTAAGC 59.511 50.000 0.00 0.00 31.11 3.09
78 79 3.159472 CCCGTTTAACCCCTTTAAGCTT 58.841 45.455 3.48 3.48 30.64 3.74
80 81 3.192001 CCGTTTAACCCCTTTAAGCTTCC 59.808 47.826 0.00 0.00 30.64 3.46
81 82 4.077108 CGTTTAACCCCTTTAAGCTTCCT 58.923 43.478 0.00 0.00 30.64 3.36
83 84 5.353400 CGTTTAACCCCTTTAAGCTTCCTAG 59.647 44.000 0.00 0.00 30.64 3.02
92 93 2.663188 GCTTCCTAGCGGCGATGG 60.663 66.667 12.98 6.20 37.71 3.51
93 94 2.663188 CTTCCTAGCGGCGATGGC 60.663 66.667 12.98 0.00 38.90 4.40
94 95 3.154473 TTCCTAGCGGCGATGGCT 61.154 61.111 12.98 0.00 44.35 4.75
95 96 3.151958 TTCCTAGCGGCGATGGCTC 62.152 63.158 12.98 0.00 41.80 4.70
98 99 4.221422 TAGCGGCGATGGCTCCAC 62.221 66.667 12.98 0.00 41.80 4.02
102 103 4.148825 GGCGATGGCTCCACGACT 62.149 66.667 12.62 0.00 39.81 4.18
103 104 2.782222 GGCGATGGCTCCACGACTA 61.782 63.158 12.62 0.00 39.81 2.59
104 105 1.141019 GCGATGGCTCCACGACTAA 59.859 57.895 12.62 0.00 35.83 2.24
106 107 0.456221 CGATGGCTCCACGACTAAGT 59.544 55.000 0.00 0.00 0.00 2.24
107 108 1.534175 CGATGGCTCCACGACTAAGTC 60.534 57.143 0.00 0.00 0.00 3.01
108 109 0.824759 ATGGCTCCACGACTAAGTCC 59.175 55.000 0.00 0.00 0.00 3.85
109 110 0.251653 TGGCTCCACGACTAAGTCCT 60.252 55.000 0.00 0.00 0.00 3.85
111 112 2.097825 GGCTCCACGACTAAGTCCTAA 58.902 52.381 0.00 0.00 0.00 2.69
113 114 2.490903 GCTCCACGACTAAGTCCTAACA 59.509 50.000 0.00 0.00 0.00 2.41
114 115 3.672781 GCTCCACGACTAAGTCCTAACAC 60.673 52.174 0.00 0.00 0.00 3.32
115 116 2.485426 TCCACGACTAAGTCCTAACACG 59.515 50.000 0.00 0.00 0.00 4.49
117 118 3.425892 CCACGACTAAGTCCTAACACGAG 60.426 52.174 0.00 0.00 0.00 4.18
126 127 1.476891 TCCTAACACGAGGACATCTGC 59.523 52.381 0.00 0.00 40.89 4.26
127 128 1.471676 CCTAACACGAGGACATCTGCC 60.472 57.143 0.00 0.00 39.15 4.85
128 129 0.172578 TAACACGAGGACATCTGCCG 59.827 55.000 0.00 0.00 0.00 5.69
129 130 1.816863 AACACGAGGACATCTGCCGT 61.817 55.000 0.00 0.00 0.00 5.68
130 131 1.807165 CACGAGGACATCTGCCGTG 60.807 63.158 0.00 0.00 43.24 4.94
133 134 1.591703 GAGGACATCTGCCGTGACA 59.408 57.895 0.00 0.00 0.00 3.58
134 135 0.037326 GAGGACATCTGCCGTGACAA 60.037 55.000 0.00 0.00 0.00 3.18
136 137 1.003580 AGGACATCTGCCGTGACAATT 59.996 47.619 0.00 0.00 0.00 2.32
137 138 1.398390 GGACATCTGCCGTGACAATTC 59.602 52.381 0.00 0.00 0.00 2.17
138 139 1.398390 GACATCTGCCGTGACAATTCC 59.602 52.381 0.00 0.00 0.00 3.01
139 140 1.271325 ACATCTGCCGTGACAATTCCA 60.271 47.619 0.00 0.00 0.00 3.53
164 165 9.796120 CACGACAAAAATGGTTATATTTATGGT 57.204 29.630 0.00 0.00 30.47 3.55
198 199 3.435105 TTTTCAAACTCACATGCGCTT 57.565 38.095 9.73 0.00 0.00 4.68
199 200 2.404265 TTCAAACTCACATGCGCTTG 57.596 45.000 20.60 20.60 0.00 4.01
207 208 2.931969 CTCACATGCGCTTGTTATCAGA 59.068 45.455 24.68 17.09 0.00 3.27
208 209 3.333804 TCACATGCGCTTGTTATCAGAA 58.666 40.909 24.68 3.89 0.00 3.02
212 213 5.574055 CACATGCGCTTGTTATCAGAAAAAT 59.426 36.000 24.68 0.00 0.00 1.82
223 224 6.206634 TGTTATCAGAAAAATCGTTTCAGCCT 59.793 34.615 2.00 0.00 0.00 4.58
283 284 2.039746 ACAAATCTTCGATGTGTGGGGA 59.960 45.455 0.00 0.00 0.00 4.81
300 301 5.423610 TGTGGGGATTTTTGTTTGAAGAAGA 59.576 36.000 0.00 0.00 0.00 2.87
303 304 7.335673 GTGGGGATTTTTGTTTGAAGAAGAAAA 59.664 33.333 0.00 0.00 0.00 2.29
318 319 4.775253 AGAAGAAAACCACCAAGGAAACAA 59.225 37.500 0.00 0.00 41.22 2.83
348 349 4.637534 GTCCATCATCACACTTGCAACTAT 59.362 41.667 0.00 0.00 0.00 2.12
391 394 5.710099 ACAAGCGAAAAAGATATTCCTTCCA 59.290 36.000 0.00 0.00 0.00 3.53
393 396 7.093771 ACAAGCGAAAAAGATATTCCTTCCATT 60.094 33.333 0.00 0.00 0.00 3.16
410 413 6.239289 CCTTCCATTCCAAAATATATGGCGTT 60.239 38.462 0.00 0.00 37.92 4.84
412 415 6.068010 TCCATTCCAAAATATATGGCGTTCT 58.932 36.000 0.00 0.00 37.92 3.01
447 450 4.742438 TCTTTGATGCACGACTTTAACC 57.258 40.909 0.00 0.00 0.00 2.85
448 451 4.130857 TCTTTGATGCACGACTTTAACCA 58.869 39.130 0.00 0.00 0.00 3.67
517 1580 5.649557 TGGTCAAAGTCAAACATTGTGAAG 58.350 37.500 0.00 0.00 29.78 3.02
691 1786 9.770097 TTTGATTTCAAACAAACCTTATATGCA 57.230 25.926 1.66 0.00 40.55 3.96
701 1796 9.691362 AACAAACCTTATATGCACAGTAAAAAG 57.309 29.630 0.00 0.00 0.00 2.27
702 1797 8.303876 ACAAACCTTATATGCACAGTAAAAAGG 58.696 33.333 0.00 0.00 38.54 3.11
712 1807 4.131596 CACAGTAAAAAGGAACGAAGGGA 58.868 43.478 0.00 0.00 0.00 4.20
718 1813 3.521947 AAAGGAACGAAGGGAGTATCG 57.478 47.619 0.00 0.00 44.33 2.92
837 1945 9.189156 ACATTCATTATAGCCAAAGTTATGTGT 57.811 29.630 0.00 0.00 0.00 3.72
853 1961 1.227321 TGTCGAACGGTTGTGACCC 60.227 57.895 16.00 0.00 43.42 4.46
871 1979 2.308690 CCCCCTAAAAACACGTTTGGA 58.691 47.619 0.00 0.00 32.36 3.53
876 1984 6.377712 CCCCCTAAAAACACGTTTGGATTATA 59.622 38.462 0.00 0.00 32.36 0.98
950 2058 4.022762 CCTGAGGATATCTGTTACGGAGTG 60.023 50.000 2.05 0.00 45.73 3.51
974 2082 5.215160 GTTTTCACCTTAGACATGCAACAG 58.785 41.667 0.00 0.00 0.00 3.16
1039 2475 1.853319 GTCACGGACTGTTTGAGCG 59.147 57.895 0.00 0.00 0.00 5.03
1059 2495 2.220313 GATCTGCTCCATCTTCTTGCC 58.780 52.381 0.00 0.00 0.00 4.52
1060 2496 1.283347 TCTGCTCCATCTTCTTGCCT 58.717 50.000 0.00 0.00 0.00 4.75
1108 2550 4.849329 CCTCGTCGCCCGTAGCAC 62.849 72.222 0.00 0.00 44.04 4.40
1374 4499 1.301623 CCCCAACGGCATAACCTCA 59.698 57.895 0.00 0.00 35.61 3.86
1413 4538 0.178947 CCCTCTCCCTAATCCTCGCT 60.179 60.000 0.00 0.00 0.00 4.93
1437 4562 3.723348 GTCAAGGCGGCGGTGAAC 61.723 66.667 17.66 9.99 0.00 3.18
1548 4679 0.317854 GGTGTTGCTTCTTCAACCGC 60.318 55.000 4.46 0.00 44.15 5.68
2052 5220 1.469703 CTGTGTGGGTACATCGACGTA 59.530 52.381 0.00 0.00 39.39 3.57
2077 5245 1.805120 CGGTGGCAACTATCCTTACGG 60.805 57.143 0.00 0.00 37.61 4.02
2187 5355 2.299013 TGACGGCTTACAACATCTGAGT 59.701 45.455 0.00 0.00 0.00 3.41
2194 5362 0.033920 ACAACATCTGAGTGCGAGCA 59.966 50.000 0.00 0.00 0.00 4.26
2403 5690 5.393124 TCGCTTGTTTTAGCATCAATCTTG 58.607 37.500 0.00 0.00 41.28 3.02
2482 5784 7.531857 TTTGCATTGGATGTTTCTTTACCTA 57.468 32.000 0.00 0.00 0.00 3.08
2483 5785 7.531857 TTGCATTGGATGTTTCTTTACCTAA 57.468 32.000 0.00 0.00 0.00 2.69
2541 5843 8.341173 GCTACATGATTTCACCTTATCTTTCTG 58.659 37.037 0.00 0.00 0.00 3.02
2558 5860 5.928839 TCTTTCTGTGAGATGCAAGTAGTTC 59.071 40.000 0.00 0.00 0.00 3.01
2659 5961 4.834357 TCAACTGGACATGTTGATGTTG 57.166 40.909 19.51 19.51 45.77 3.33
2712 6058 7.587037 TCAGGATGAGAAGTCAAAATTGTTT 57.413 32.000 0.00 0.00 42.56 2.83
2713 6059 7.651808 TCAGGATGAGAAGTCAAAATTGTTTC 58.348 34.615 0.00 0.32 42.56 2.78
2714 6060 7.503566 TCAGGATGAGAAGTCAAAATTGTTTCT 59.496 33.333 12.20 12.20 42.56 2.52
2715 6061 8.139989 CAGGATGAGAAGTCAAAATTGTTTCTT 58.860 33.333 13.03 8.08 39.69 2.52
2716 6062 9.354673 AGGATGAGAAGTCAAAATTGTTTCTTA 57.645 29.630 13.03 10.83 35.88 2.10
2720 6066 9.130661 TGAGAAGTCAAAATTGTTTCTTATCCA 57.869 29.630 13.03 7.22 35.23 3.41
2721 6067 9.965824 GAGAAGTCAAAATTGTTTCTTATCCAA 57.034 29.630 13.03 0.00 35.23 3.53
2983 7443 7.390027 ACTCTGCAGGATATGGTATAACAATC 58.610 38.462 15.13 0.00 0.00 2.67
2998 7458 3.366052 ACAATCAATACCCACACCCTC 57.634 47.619 0.00 0.00 0.00 4.30
2999 7459 2.647299 ACAATCAATACCCACACCCTCA 59.353 45.455 0.00 0.00 0.00 3.86
3000 7460 3.269381 ACAATCAATACCCACACCCTCAT 59.731 43.478 0.00 0.00 0.00 2.90
3015 7478 4.026052 ACCCTCATGGATTTGGTGATTTC 58.974 43.478 0.00 0.00 38.00 2.17
3136 8900 1.822990 CTGTTTACCAGAGGAGGCGTA 59.177 52.381 0.00 0.00 44.49 4.42
3139 8903 2.226962 TTACCAGAGGAGGCGTAACT 57.773 50.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.049708 ACGGTGAAGGTAAAAGCCTAC 57.950 47.619 0.00 0.00 38.03 3.18
5 6 3.340928 CCCCTTACGGTGAAGGTAAAAG 58.659 50.000 10.90 0.00 44.02 2.27
6 7 2.552809 GCCCCTTACGGTGAAGGTAAAA 60.553 50.000 10.90 0.00 44.02 1.52
8 9 0.614812 GCCCCTTACGGTGAAGGTAA 59.385 55.000 10.90 0.00 44.02 2.85
10 11 2.599757 GGCCCCTTACGGTGAAGGT 61.600 63.158 10.90 0.00 44.02 3.50
11 12 2.271173 GGCCCCTTACGGTGAAGG 59.729 66.667 0.00 6.14 44.96 3.46
12 13 2.125269 CGGCCCCTTACGGTGAAG 60.125 66.667 0.00 0.00 0.00 3.02
14 15 2.604079 TTCGGCCCCTTACGGTGA 60.604 61.111 0.00 0.00 0.00 4.02
17 18 3.675619 CTGGTTCGGCCCCTTACGG 62.676 68.421 0.00 0.00 36.04 4.02
18 19 1.606885 TACTGGTTCGGCCCCTTACG 61.607 60.000 0.00 0.00 36.04 3.18
21 22 1.211212 GTTATACTGGTTCGGCCCCTT 59.789 52.381 0.00 0.00 36.04 3.95
22 23 0.835276 GTTATACTGGTTCGGCCCCT 59.165 55.000 0.00 0.00 36.04 4.79
23 24 0.179037 GGTTATACTGGTTCGGCCCC 60.179 60.000 0.00 0.00 36.04 5.80
24 25 0.179037 GGGTTATACTGGTTCGGCCC 60.179 60.000 0.00 0.00 36.04 5.80
25 26 0.835276 AGGGTTATACTGGTTCGGCC 59.165 55.000 0.00 0.00 37.90 6.13
26 27 1.537562 CGAGGGTTATACTGGTTCGGC 60.538 57.143 0.00 0.00 0.00 5.54
30 31 3.055602 GGAACACGAGGGTTATACTGGTT 60.056 47.826 0.00 0.00 0.00 3.67
31 32 2.498885 GGAACACGAGGGTTATACTGGT 59.501 50.000 0.00 0.00 0.00 4.00
34 35 3.836562 ACAAGGAACACGAGGGTTATACT 59.163 43.478 0.00 0.00 0.00 2.12
36 37 3.196254 GGACAAGGAACACGAGGGTTATA 59.804 47.826 0.00 0.00 0.00 0.98
37 38 2.027469 GGACAAGGAACACGAGGGTTAT 60.027 50.000 0.00 0.00 0.00 1.89
38 39 1.345415 GGACAAGGAACACGAGGGTTA 59.655 52.381 0.00 0.00 0.00 2.85
41 42 1.003718 GGGACAAGGAACACGAGGG 60.004 63.158 0.00 0.00 0.00 4.30
42 43 1.374252 CGGGACAAGGAACACGAGG 60.374 63.158 0.00 0.00 34.69 4.63
43 44 0.249741 AACGGGACAAGGAACACGAG 60.250 55.000 0.00 0.00 36.71 4.18
48 49 1.881973 GGGTTAAACGGGACAAGGAAC 59.118 52.381 0.00 0.00 0.00 3.62
49 50 1.202915 GGGGTTAAACGGGACAAGGAA 60.203 52.381 0.00 0.00 0.00 3.36
51 52 0.402887 AGGGGTTAAACGGGACAAGG 59.597 55.000 0.00 0.00 0.00 3.61
52 53 2.281539 AAGGGGTTAAACGGGACAAG 57.718 50.000 0.00 0.00 0.00 3.16
55 56 2.489329 GCTTAAAGGGGTTAAACGGGAC 59.511 50.000 0.00 0.00 31.22 4.46
56 57 2.376181 AGCTTAAAGGGGTTAAACGGGA 59.624 45.455 0.00 0.00 31.22 5.14
59 60 4.077108 AGGAAGCTTAAAGGGGTTAAACG 58.923 43.478 0.00 0.00 31.22 3.60
60 61 5.125097 GCTAGGAAGCTTAAAGGGGTTAAAC 59.875 44.000 0.00 0.00 45.85 2.01
61 62 5.258841 GCTAGGAAGCTTAAAGGGGTTAAA 58.741 41.667 0.00 0.00 45.85 1.52
64 65 3.367646 GCTAGGAAGCTTAAAGGGGTT 57.632 47.619 0.00 0.00 45.85 4.11
75 76 2.663188 CCATCGCCGCTAGGAAGC 60.663 66.667 0.00 0.00 45.86 3.86
76 77 2.663188 GCCATCGCCGCTAGGAAG 60.663 66.667 0.00 0.00 41.02 3.46
78 79 3.606662 GAGCCATCGCCGCTAGGA 61.607 66.667 0.00 0.00 41.02 2.94
80 81 3.916544 TGGAGCCATCGCCGCTAG 61.917 66.667 0.00 0.00 36.48 3.42
81 82 4.221422 GTGGAGCCATCGCCGCTA 62.221 66.667 0.00 0.00 39.23 4.26
85 86 2.292794 TTAGTCGTGGAGCCATCGCC 62.293 60.000 0.00 0.00 34.57 5.54
86 87 0.872021 CTTAGTCGTGGAGCCATCGC 60.872 60.000 0.00 0.00 0.00 4.58
88 89 1.202428 GGACTTAGTCGTGGAGCCATC 60.202 57.143 6.27 0.00 32.65 3.51
89 90 0.824759 GGACTTAGTCGTGGAGCCAT 59.175 55.000 6.27 0.00 32.65 4.40
92 93 2.490903 TGTTAGGACTTAGTCGTGGAGC 59.509 50.000 16.60 1.96 32.77 4.70
93 94 3.425892 CGTGTTAGGACTTAGTCGTGGAG 60.426 52.174 16.60 1.79 32.77 3.86
94 95 2.485426 CGTGTTAGGACTTAGTCGTGGA 59.515 50.000 16.60 3.80 32.77 4.02
95 96 2.485426 TCGTGTTAGGACTTAGTCGTGG 59.515 50.000 16.60 2.72 32.77 4.94
98 99 3.005554 TCCTCGTGTTAGGACTTAGTCG 58.994 50.000 6.27 0.00 40.86 4.18
106 107 1.476891 GCAGATGTCCTCGTGTTAGGA 59.523 52.381 0.00 0.00 43.58 2.94
107 108 1.471676 GGCAGATGTCCTCGTGTTAGG 60.472 57.143 0.00 0.00 38.06 2.69
108 109 1.799181 CGGCAGATGTCCTCGTGTTAG 60.799 57.143 0.00 0.00 0.00 2.34
109 110 0.172578 CGGCAGATGTCCTCGTGTTA 59.827 55.000 0.00 0.00 0.00 2.41
111 112 2.276116 ACGGCAGATGTCCTCGTGT 61.276 57.895 0.00 0.00 32.60 4.49
113 114 1.977009 TCACGGCAGATGTCCTCGT 60.977 57.895 0.00 0.00 34.19 4.18
114 115 1.517257 GTCACGGCAGATGTCCTCG 60.517 63.158 0.00 0.00 0.00 4.63
115 116 0.037326 TTGTCACGGCAGATGTCCTC 60.037 55.000 0.00 0.00 0.00 3.71
117 118 1.398390 GAATTGTCACGGCAGATGTCC 59.602 52.381 0.00 0.00 0.00 4.02
120 121 1.131126 GTGGAATTGTCACGGCAGATG 59.869 52.381 0.00 0.00 0.00 2.90
121 122 1.453155 GTGGAATTGTCACGGCAGAT 58.547 50.000 0.00 0.00 0.00 2.90
122 123 2.927004 GTGGAATTGTCACGGCAGA 58.073 52.632 0.00 0.00 0.00 4.26
128 129 4.444056 CCATTTTTGTCGTGGAATTGTCAC 59.556 41.667 0.00 0.00 34.94 3.67
129 130 4.098654 ACCATTTTTGTCGTGGAATTGTCA 59.901 37.500 0.00 0.00 36.82 3.58
130 131 4.616953 ACCATTTTTGTCGTGGAATTGTC 58.383 39.130 0.00 0.00 36.82 3.18
133 134 9.936759 AAATATAACCATTTTTGTCGTGGAATT 57.063 25.926 0.00 0.00 36.82 2.17
137 138 9.243637 CCATAAATATAACCATTTTTGTCGTGG 57.756 33.333 0.00 0.00 38.96 4.94
138 139 9.796120 ACCATAAATATAACCATTTTTGTCGTG 57.204 29.630 0.00 0.00 29.81 4.35
175 176 5.119931 AGCGCATGTGAGTTTGAAAAATA 57.880 34.783 11.47 0.00 0.00 1.40
198 199 6.206634 AGGCTGAAACGATTTTTCTGATAACA 59.793 34.615 7.56 0.00 31.61 2.41
199 200 6.612306 AGGCTGAAACGATTTTTCTGATAAC 58.388 36.000 7.56 0.00 31.61 1.89
207 208 3.550030 CCGTCAAGGCTGAAACGATTTTT 60.550 43.478 15.48 0.00 31.88 1.94
208 209 2.031157 CCGTCAAGGCTGAAACGATTTT 60.031 45.455 15.48 0.00 31.88 1.82
212 213 0.599204 GTCCGTCAAGGCTGAAACGA 60.599 55.000 15.48 2.75 40.77 3.85
283 284 7.663493 TGGTGGTTTTCTTCTTCAAACAAAAAT 59.337 29.630 0.00 0.00 35.01 1.82
300 301 3.944650 GCAATTGTTTCCTTGGTGGTTTT 59.055 39.130 7.40 0.00 37.07 2.43
303 304 2.114616 TGCAATTGTTTCCTTGGTGGT 58.885 42.857 7.40 0.00 37.07 4.16
318 319 3.628008 AGTGTGATGATGGACATGCAAT 58.372 40.909 0.00 0.00 39.56 3.56
391 394 7.285401 AGTCAAGAACGCCATATATTTTGGAAT 59.715 33.333 8.24 0.00 36.26 3.01
393 396 6.119536 AGTCAAGAACGCCATATATTTTGGA 58.880 36.000 8.24 0.00 36.26 3.53
410 413 6.617879 CATCAAAGATCATGCAAAGTCAAGA 58.382 36.000 0.00 0.00 0.00 3.02
412 415 5.165676 GCATCAAAGATCATGCAAAGTCAA 58.834 37.500 10.09 0.00 44.18 3.18
495 1558 5.650543 ACTTCACAATGTTTGACTTTGACC 58.349 37.500 11.98 0.00 36.91 4.02
509 1572 9.295825 TCTATAATGTTGGACAAACTTCACAAT 57.704 29.630 0.00 0.00 39.70 2.71
691 1786 4.141551 ACTCCCTTCGTTCCTTTTTACTGT 60.142 41.667 0.00 0.00 0.00 3.55
701 1796 2.426381 ACTTCGATACTCCCTTCGTTCC 59.574 50.000 0.00 0.00 36.74 3.62
702 1797 3.779271 ACTTCGATACTCCCTTCGTTC 57.221 47.619 0.00 0.00 36.74 3.95
812 1909 9.669353 GACACATAACTTTGGCTATAATGAATG 57.331 33.333 0.00 0.00 0.00 2.67
853 1961 8.899771 AGATATAATCCAAACGTGTTTTTAGGG 58.100 33.333 0.00 0.00 0.00 3.53
876 1984 7.014326 TCGTGCTTATCCATGAGTTAGTTAGAT 59.986 37.037 0.00 0.00 0.00 1.98
950 2058 4.037446 TGTTGCATGTCTAAGGTGAAAACC 59.963 41.667 0.00 0.00 0.00 3.27
974 2082 0.932585 GTCTAGATCTGCTGCGCGTC 60.933 60.000 8.43 0.00 0.00 5.19
1039 2475 2.158784 AGGCAAGAAGATGGAGCAGATC 60.159 50.000 0.00 0.00 0.00 2.75
1059 2495 1.597461 GTGGAAGGGGAGGAACGAG 59.403 63.158 0.00 0.00 0.00 4.18
1060 2496 1.916777 GGTGGAAGGGGAGGAACGA 60.917 63.158 0.00 0.00 0.00 3.85
1257 4379 0.617820 AGGAGTAGCCGTGGATGGTT 60.618 55.000 0.00 0.00 43.43 3.67
1374 4499 3.746409 GACGTAATCCGCGACCGCT 62.746 63.158 8.23 0.00 41.42 5.52
1413 4538 1.741401 CGCCGCCTTGACATCTTCA 60.741 57.895 0.00 0.00 0.00 3.02
1982 5150 1.608055 CATGTCAAACCTGTCAGCCA 58.392 50.000 0.00 0.00 0.00 4.75
2052 5220 1.078426 GATAGTTGCCACCGTGCCT 60.078 57.895 0.00 0.00 0.00 4.75
2260 5433 4.399004 AAGACAGCTAGCTCATTACCAG 57.601 45.455 16.15 3.33 0.00 4.00
2403 5690 3.777478 CCATGACATTCAGAAACCATGC 58.223 45.455 13.30 0.00 32.43 4.06
2541 5843 3.664107 TGTGGAACTACTTGCATCTCAC 58.336 45.455 0.00 0.00 38.04 3.51
2558 5860 7.464577 CGTGACATTACTGACAGAATAATGTGG 60.465 40.741 25.00 15.24 45.21 4.17
2646 5948 3.250762 CGAGACAACCAACATCAACATGT 59.749 43.478 0.00 0.00 45.89 3.21
2659 5961 7.307811 GCAGGGAAATAATATAACGAGACAACC 60.308 40.741 0.00 0.00 0.00 3.77
2808 6154 5.830912 TGCAAAGTGTGAAATTTACAGGAG 58.169 37.500 0.00 0.00 0.00 3.69
2959 7419 7.389232 TGATTGTTATACCATATCCTGCAGAG 58.611 38.462 17.39 5.49 0.00 3.35
2983 7443 1.563879 TCCATGAGGGTGTGGGTATTG 59.436 52.381 0.00 0.00 38.11 1.90
2998 7458 4.082300 TGTTCCGAAATCACCAAATCCATG 60.082 41.667 0.00 0.00 0.00 3.66
2999 7459 4.085733 TGTTCCGAAATCACCAAATCCAT 58.914 39.130 0.00 0.00 0.00 3.41
3000 7460 3.491342 TGTTCCGAAATCACCAAATCCA 58.509 40.909 0.00 0.00 0.00 3.41
3015 7478 2.028420 TCATGATGCCTTCTGTTCCG 57.972 50.000 0.00 0.00 0.00 4.30
3139 8903 9.309516 CTTGTAATATGACTAGCCTTAACGAAA 57.690 33.333 0.00 0.00 0.00 3.46
3175 8939 2.520982 TCGAGGTAGCATCCCCCG 60.521 66.667 0.00 0.00 0.00 5.73


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

AutoCloner maintained by Alex Coulton.