Multiple sequence alignment - TraesCS2D01G366600

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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 TraesCS2D01G366600 chr2D 100.000 2910 0 0 1 2910 471067478 471064569 0.000000e+00 5374.0
1 TraesCS2D01G366600 chr2D 97.701 174 3 1 1 173 598709730 598709557 6.100000e-77 298.0
2 TraesCS2D01G366600 chr2D 97.674 172 2 2 1 171 319583694 319583864 7.890000e-76 294.0
3 TraesCS2D01G366600 chr3A 96.116 2111 67 10 169 2268 14061476 14059370 0.000000e+00 3430.0
4 TraesCS2D01G366600 chr3A 97.198 464 11 2 2448 2910 14059301 14058839 0.000000e+00 784.0
5 TraesCS2D01G366600 chr3A 95.050 101 4 1 2267 2366 14059400 14059300 1.080000e-34 158.0
6 TraesCS2D01G366600 chr3B 88.095 1176 120 9 856 2026 813751012 813752172 0.000000e+00 1378.0
7 TraesCS2D01G366600 chr3B 90.369 623 58 2 806 1428 60586477 60585857 0.000000e+00 817.0
8 TraesCS2D01G366600 chr3B 90.508 590 46 8 242 824 813750429 813751015 0.000000e+00 771.0
9 TraesCS2D01G366600 chr3B 81.641 256 36 5 2476 2729 60585688 60585442 4.920000e-48 202.0
10 TraesCS2D01G366600 chr3B 95.506 89 4 0 2361 2449 652296472 652296384 3.020000e-30 143.0
11 TraesCS2D01G366600 chr7B 90.306 980 85 5 806 1778 545984655 545983679 0.000000e+00 1275.0
12 TraesCS2D01G366600 chr7B 93.296 537 29 7 224 754 545985205 545984670 0.000000e+00 785.0
13 TraesCS2D01G366600 chr7B 86.218 312 29 5 2448 2755 545983397 545983096 2.800000e-85 326.0
14 TraesCS2D01G366600 chr7B 91.525 177 15 0 2033 2209 545983683 545983507 8.060000e-61 244.0
15 TraesCS2D01G366600 chr7B 90.141 71 7 0 2832 2902 545983092 545983022 3.090000e-15 93.5
16 TraesCS2D01G366600 chr1D 90.628 971 75 7 820 1778 22558329 22559295 0.000000e+00 1275.0
17 TraesCS2D01G366600 chr1D 93.737 479 26 3 169 645 22557806 22558282 0.000000e+00 715.0
18 TraesCS2D01G366600 chr1D 88.095 462 41 7 2448 2907 22559578 22560027 1.190000e-148 536.0
19 TraesCS2D01G366600 chr1D 90.395 177 17 0 2033 2209 22559291 22559467 1.740000e-57 233.0
20 TraesCS2D01G366600 chr1D 80.000 135 23 3 2448 2581 384138822 384138953 2.390000e-16 97.1
21 TraesCS2D01G366600 chr1D 100.000 31 0 0 2238 2268 22559479 22559509 1.130000e-04 58.4
22 TraesCS2D01G366600 chr1D 100.000 30 0 0 725 754 22558327 22558298 4.050000e-04 56.5
23 TraesCS2D01G366600 chr5B 91.153 859 71 5 206 1060 202930623 202931480 0.000000e+00 1160.0
24 TraesCS2D01G366600 chr5B 86.948 1019 110 9 1055 2072 202940066 202941062 0.000000e+00 1123.0
25 TraesCS2D01G366600 chr5B 87.207 469 35 7 2449 2910 202941278 202941728 7.190000e-141 510.0
26 TraesCS2D01G366600 chr5B 89.333 150 11 1 2119 2268 202941064 202941208 1.780000e-42 183.0
27 TraesCS2D01G366600 chr6B 91.074 829 68 4 954 1778 551954273 551953447 0.000000e+00 1116.0
28 TraesCS2D01G366600 chr6B 83.265 490 43 11 2448 2910 551953164 551952687 5.800000e-112 414.0
29 TraesCS2D01G366600 chr6B 92.014 288 18 4 470 754 551960191 551959906 1.620000e-107 399.0
30 TraesCS2D01G366600 chr6B 93.220 177 12 0 2033 2209 551953451 551953275 8.000000e-66 261.0
31 TraesCS2D01G366600 chr6B 95.763 118 5 0 806 923 551959891 551959774 1.060000e-44 191.0
32 TraesCS2D01G366600 chr7D 80.253 871 137 27 1422 2275 71120805 71121657 8.860000e-175 623.0
33 TraesCS2D01G366600 chr7D 88.298 470 39 6 2449 2910 523435421 523435882 1.520000e-152 549.0
34 TraesCS2D01G366600 chr7D 92.604 338 18 4 213 549 523434812 523435143 2.030000e-131 479.0
35 TraesCS2D01G366600 chr7D 81.135 599 82 19 187 780 536316856 536317428 4.420000e-123 451.0
36 TraesCS2D01G366600 chr7D 83.885 453 66 4 1422 1869 536317475 536317925 2.680000e-115 425.0
37 TraesCS2D01G366600 chr7D 98.266 173 2 1 1 172 182347587 182347415 4.710000e-78 302.0
38 TraesCS2D01G366600 chr7D 86.813 182 19 2 2087 2268 523435175 523435351 6.360000e-47 198.0
39 TraesCS2D01G366600 chr7D 80.000 135 23 3 2448 2581 536327031 536327162 2.390000e-16 97.1
40 TraesCS2D01G366600 chr4D 79.626 908 147 18 1385 2268 488426453 488427346 4.120000e-173 617.0
41 TraesCS2D01G366600 chr4D 81.072 597 86 16 187 780 488425880 488426452 4.420000e-123 451.0
42 TraesCS2D01G366600 chr4D 80.897 602 84 21 187 783 362700256 362699681 2.060000e-121 446.0
43 TraesCS2D01G366600 chr4D 80.000 135 23 3 2448 2581 362698717 362698586 2.390000e-16 97.1
44 TraesCS2D01G366600 chr7A 98.246 171 2 1 1 170 730580006 730579836 6.100000e-77 298.0
45 TraesCS2D01G366600 chr7A 92.632 95 7 0 2355 2449 47050825 47050731 1.410000e-28 137.0
46 TraesCS2D01G366600 chr4B 98.246 171 2 1 1 170 43088890 43088720 6.100000e-77 298.0
47 TraesCS2D01G366600 chr4B 95.506 89 3 1 2361 2449 567009251 567009338 1.090000e-29 141.0
48 TraesCS2D01G366600 chr4B 92.708 96 5 2 2357 2452 567391091 567390998 1.410000e-28 137.0
49 TraesCS2D01G366600 chr3D 97.701 174 3 1 1 173 111256952 111256779 6.100000e-77 298.0
50 TraesCS2D01G366600 chr1B 98.246 171 2 1 1 170 295615016 295614846 6.100000e-77 298.0
51 TraesCS2D01G366600 chr1B 88.288 111 11 2 2365 2474 503352988 503352879 6.540000e-27 132.0
52 TraesCS2D01G366600 chr2B 97.688 173 3 1 1 172 247276608 247276780 2.190000e-76 296.0
53 TraesCS2D01G366600 chr2B 92.784 97 7 0 2353 2449 796526619 796526523 1.090000e-29 141.0
54 TraesCS2D01G366600 chr1A 96.089 179 5 2 1 178 508965989 508965812 1.020000e-74 291.0
55 TraesCS2D01G366600 chr6A 94.505 91 5 0 2359 2449 568938938 568939028 1.090000e-29 141.0
56 TraesCS2D01G366600 chr5D 89.189 111 8 4 2362 2472 395699693 395699587 5.060000e-28 135.0
57 TraesCS2D01G366600 chr5A 91.919 99 5 3 2365 2462 331942336 331942240 5.060000e-28 135.0
58 TraesCS2D01G366600 chr6D 98.611 72 1 0 2755 2826 2091318 2091247 8.460000e-26 128.0


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 TraesCS2D01G366600 chr2D 471064569 471067478 2909 True 5374.000000 5374 100.000000 1 2910 1 chr2D.!!$R1 2909
1 TraesCS2D01G366600 chr3A 14058839 14061476 2637 True 1457.333333 3430 96.121333 169 2910 3 chr3A.!!$R1 2741
2 TraesCS2D01G366600 chr3B 813750429 813752172 1743 False 1074.500000 1378 89.301500 242 2026 2 chr3B.!!$F1 1784
3 TraesCS2D01G366600 chr3B 60585442 60586477 1035 True 509.500000 817 86.005000 806 2729 2 chr3B.!!$R2 1923
4 TraesCS2D01G366600 chr7B 545983022 545985205 2183 True 544.700000 1275 90.297200 224 2902 5 chr7B.!!$R1 2678
5 TraesCS2D01G366600 chr1D 22557806 22560027 2221 False 563.480000 1275 92.571000 169 2907 5 chr1D.!!$F2 2738
6 TraesCS2D01G366600 chr5B 202930623 202931480 857 False 1160.000000 1160 91.153000 206 1060 1 chr5B.!!$F1 854
7 TraesCS2D01G366600 chr5B 202940066 202941728 1662 False 605.333333 1123 87.829333 1055 2910 3 chr5B.!!$F2 1855
8 TraesCS2D01G366600 chr6B 551952687 551954273 1586 True 597.000000 1116 89.186333 954 2910 3 chr6B.!!$R1 1956
9 TraesCS2D01G366600 chr7D 71120805 71121657 852 False 623.000000 623 80.253000 1422 2275 1 chr7D.!!$F1 853
10 TraesCS2D01G366600 chr7D 536316856 536317925 1069 False 438.000000 451 82.510000 187 1869 2 chr7D.!!$F4 1682
11 TraesCS2D01G366600 chr7D 523434812 523435882 1070 False 408.666667 549 89.238333 213 2910 3 chr7D.!!$F3 2697
12 TraesCS2D01G366600 chr4D 488425880 488427346 1466 False 534.000000 617 80.349000 187 2268 2 chr4D.!!$F1 2081
13 TraesCS2D01G366600 chr4D 362698586 362700256 1670 True 271.550000 446 80.448500 187 2581 2 chr4D.!!$R1 2394

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
847 858 1.349688 CCGGGCTAGCCATAACCATTA 59.65 52.381 34.09 0.0 37.98 1.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2271 2426 0.179192 GCGATGCGACAATTCTTGCA 60.179 50.0 0.0 0.0 42.22 4.08 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
51 52 5.932021 GAAAATACATTTCGTGGTGCATC 57.068 39.130 0.00 0.00 38.21 3.91
52 53 5.640732 GAAAATACATTTCGTGGTGCATCT 58.359 37.500 0.00 0.00 38.21 2.90
53 54 4.621068 AATACATTTCGTGGTGCATCTG 57.379 40.909 0.00 0.00 0.00 2.90
54 55 2.183478 ACATTTCGTGGTGCATCTGA 57.817 45.000 0.00 0.00 0.00 3.27
55 56 2.715046 ACATTTCGTGGTGCATCTGAT 58.285 42.857 0.00 0.00 0.00 2.90
56 57 3.872696 ACATTTCGTGGTGCATCTGATA 58.127 40.909 0.00 0.00 0.00 2.15
57 58 4.260985 ACATTTCGTGGTGCATCTGATAA 58.739 39.130 0.00 0.00 0.00 1.75
58 59 4.883585 ACATTTCGTGGTGCATCTGATAAT 59.116 37.500 0.00 0.00 0.00 1.28
59 60 4.880886 TTTCGTGGTGCATCTGATAATG 57.119 40.909 0.00 0.00 0.00 1.90
60 61 3.541996 TCGTGGTGCATCTGATAATGT 57.458 42.857 0.00 0.00 0.00 2.71
61 62 3.872696 TCGTGGTGCATCTGATAATGTT 58.127 40.909 0.00 0.00 0.00 2.71
62 63 3.871006 TCGTGGTGCATCTGATAATGTTC 59.129 43.478 0.00 0.00 0.00 3.18
63 64 3.622612 CGTGGTGCATCTGATAATGTTCA 59.377 43.478 0.00 0.00 0.00 3.18
64 65 4.274214 CGTGGTGCATCTGATAATGTTCAT 59.726 41.667 0.00 0.00 0.00 2.57
65 66 5.220912 CGTGGTGCATCTGATAATGTTCATT 60.221 40.000 0.00 3.55 0.00 2.57
66 67 6.567050 GTGGTGCATCTGATAATGTTCATTT 58.433 36.000 0.00 0.00 0.00 2.32
67 68 6.694411 GTGGTGCATCTGATAATGTTCATTTC 59.306 38.462 0.00 3.10 0.00 2.17
68 69 6.377712 TGGTGCATCTGATAATGTTCATTTCA 59.622 34.615 0.00 6.74 0.00 2.69
69 70 7.068962 TGGTGCATCTGATAATGTTCATTTCAT 59.931 33.333 0.00 0.00 0.00 2.57
70 71 8.570488 GGTGCATCTGATAATGTTCATTTCATA 58.430 33.333 3.36 2.36 0.00 2.15
123 124 8.276252 AGTTAGTCAAACTTTACAAAGCTTGA 57.724 30.769 13.75 13.75 46.61 3.02
136 137 3.801114 AAGCTTGACTTTGACCAAACC 57.199 42.857 0.00 0.00 33.71 3.27
137 138 3.018423 AGCTTGACTTTGACCAAACCT 57.982 42.857 0.00 0.00 0.00 3.50
138 139 3.365472 AGCTTGACTTTGACCAAACCTT 58.635 40.909 0.00 0.00 0.00 3.50
139 140 4.532834 AGCTTGACTTTGACCAAACCTTA 58.467 39.130 0.00 0.00 0.00 2.69
140 141 5.140454 AGCTTGACTTTGACCAAACCTTAT 58.860 37.500 0.00 0.00 0.00 1.73
141 142 6.303839 AGCTTGACTTTGACCAAACCTTATA 58.696 36.000 0.00 0.00 0.00 0.98
142 143 6.948309 AGCTTGACTTTGACCAAACCTTATAT 59.052 34.615 0.00 0.00 0.00 0.86
143 144 7.029563 GCTTGACTTTGACCAAACCTTATATG 58.970 38.462 0.00 0.00 0.00 1.78
144 145 6.509418 TGACTTTGACCAAACCTTATATGC 57.491 37.500 0.00 0.00 0.00 3.14
145 146 6.007076 TGACTTTGACCAAACCTTATATGCA 58.993 36.000 0.00 0.00 0.00 3.96
146 147 6.150976 TGACTTTGACCAAACCTTATATGCAG 59.849 38.462 0.00 0.00 0.00 4.41
147 148 6.245408 ACTTTGACCAAACCTTATATGCAGA 58.755 36.000 0.00 0.00 0.00 4.26
148 149 6.151144 ACTTTGACCAAACCTTATATGCAGAC 59.849 38.462 0.00 0.00 0.00 3.51
149 150 5.435686 TGACCAAACCTTATATGCAGACT 57.564 39.130 0.00 0.00 0.00 3.24
150 151 6.553953 TGACCAAACCTTATATGCAGACTA 57.446 37.500 0.00 0.00 0.00 2.59
151 152 6.953101 TGACCAAACCTTATATGCAGACTAA 58.047 36.000 0.00 0.00 0.00 2.24
152 153 7.398829 TGACCAAACCTTATATGCAGACTAAA 58.601 34.615 0.00 0.00 0.00 1.85
153 154 7.885922 TGACCAAACCTTATATGCAGACTAAAA 59.114 33.333 0.00 0.00 0.00 1.52
154 155 8.644374 ACCAAACCTTATATGCAGACTAAAAA 57.356 30.769 0.00 0.00 0.00 1.94
155 156 8.739972 ACCAAACCTTATATGCAGACTAAAAAG 58.260 33.333 0.00 0.00 0.00 2.27
156 157 8.956426 CCAAACCTTATATGCAGACTAAAAAGA 58.044 33.333 0.00 0.00 0.00 2.52
160 161 8.665685 ACCTTATATGCAGACTAAAAAGAAACG 58.334 33.333 0.00 0.00 0.00 3.60
161 162 8.122952 CCTTATATGCAGACTAAAAAGAAACGG 58.877 37.037 0.00 0.00 0.00 4.44
162 163 8.780846 TTATATGCAGACTAAAAAGAAACGGA 57.219 30.769 0.00 0.00 0.00 4.69
163 164 5.613358 ATGCAGACTAAAAAGAAACGGAG 57.387 39.130 0.00 0.00 0.00 4.63
164 165 3.813166 TGCAGACTAAAAAGAAACGGAGG 59.187 43.478 0.00 0.00 0.00 4.30
165 166 3.188667 GCAGACTAAAAAGAAACGGAGGG 59.811 47.826 0.00 0.00 0.00 4.30
166 167 4.638304 CAGACTAAAAAGAAACGGAGGGA 58.362 43.478 0.00 0.00 0.00 4.20
167 168 4.691216 CAGACTAAAAAGAAACGGAGGGAG 59.309 45.833 0.00 0.00 0.00 4.30
278 280 5.016831 ACTGATCAGTAAAATGGGGGTTTC 58.983 41.667 26.87 0.00 40.43 2.78
280 282 3.905493 TCAGTAAAATGGGGGTTTCCA 57.095 42.857 0.00 0.00 41.60 3.53
281 283 9.627066 ACTGATCAGTAAAATGGGGGTTTCCAT 62.627 40.741 26.87 0.00 43.59 3.41
282 284 4.093011 TCAGTAAAATGGGGGTTTCCATG 58.907 43.478 0.00 0.00 46.05 3.66
283 285 4.093011 CAGTAAAATGGGGGTTTCCATGA 58.907 43.478 0.00 0.00 46.05 3.07
284 286 4.716287 CAGTAAAATGGGGGTTTCCATGAT 59.284 41.667 0.00 0.00 46.05 2.45
285 287 5.896678 CAGTAAAATGGGGGTTTCCATGATA 59.103 40.000 0.00 0.00 46.05 2.15
604 609 8.100791 AGCAGACAAAGTGTATGTAGGAAATTA 58.899 33.333 5.06 0.00 41.30 1.40
757 768 2.151202 GCAGCAAAACAGCCAGTACTA 58.849 47.619 0.00 0.00 34.23 1.82
847 858 1.349688 CCGGGCTAGCCATAACCATTA 59.650 52.381 34.09 0.00 37.98 1.90
1107 1122 5.808366 TCACAAAGAGGTCACTACTGATT 57.192 39.130 0.00 0.00 0.00 2.57
1255 1272 2.503375 GCCAGTGTACGTCGTCGG 60.503 66.667 0.00 0.00 41.85 4.79
1272 1289 6.560433 CGTCGTCGGAAAATTCTAATGATGAG 60.560 42.308 0.00 0.00 0.00 2.90
1315 1332 1.202394 CGGAGCAGTCATGAGAGGAAG 60.202 57.143 0.00 0.00 0.00 3.46
1409 1429 3.698820 GGTCGGGCGTACCAGGTT 61.699 66.667 0.00 0.00 40.22 3.50
1425 1532 3.305608 CCAGGTTGAGGAAATTGTGAAGC 60.306 47.826 0.00 0.00 0.00 3.86
1469 1576 3.056536 CCGAGAAATGTGAGAAGTGGAGA 60.057 47.826 0.00 0.00 0.00 3.71
1653 1775 2.806434 TCCAATGTTTCAGGTGATGGG 58.194 47.619 0.00 0.00 0.00 4.00
1662 1784 1.915489 TCAGGTGATGGGCTATGTTGT 59.085 47.619 0.00 0.00 0.00 3.32
1861 1988 4.577283 TCCGTCATGACATATGAACTCGTA 59.423 41.667 24.93 0.00 0.00 3.43
1872 1999 0.179169 GAACTCGTACTGGGTCGCTC 60.179 60.000 0.00 0.00 0.00 5.03
1895 2022 4.560716 CGAAGGATATGATTGCGGAGGTAA 60.561 45.833 0.00 0.00 0.00 2.85
1996 2132 1.286570 CAGGCGCAATTGTCAGCAA 59.713 52.632 10.83 0.00 39.16 3.91
2039 2180 3.041946 AGAACAGTCTGACCCTTTCTGT 58.958 45.455 6.91 4.40 40.40 3.41
2051 2192 3.655777 ACCCTTTCTGTTAACTGGGATGA 59.344 43.478 19.85 4.14 38.08 2.92
2112 2266 1.502163 GGCGACCATGCATCAGTAGC 61.502 60.000 17.99 17.99 36.28 3.58
2115 2269 2.009051 CGACCATGCATCAGTAGCAAA 58.991 47.619 0.00 0.00 46.27 3.68
2120 2274 3.194116 CCATGCATCAGTAGCAAAAAGGT 59.806 43.478 0.00 0.00 46.27 3.50
2225 2380 1.668628 GGGTTACATGCCAAAACAGCG 60.669 52.381 0.00 0.00 0.00 5.18
2271 2426 4.778143 GGCATCGCCGGACAACCT 62.778 66.667 5.05 0.00 39.62 3.50
2272 2427 3.499737 GCATCGCCGGACAACCTG 61.500 66.667 5.05 0.00 0.00 4.00
2273 2428 3.499737 CATCGCCGGACAACCTGC 61.500 66.667 5.05 0.00 41.83 4.85
2274 2429 4.015406 ATCGCCGGACAACCTGCA 62.015 61.111 5.05 0.00 44.73 4.41
2275 2430 3.545124 ATCGCCGGACAACCTGCAA 62.545 57.895 5.05 0.00 44.73 4.08
2276 2431 3.726517 CGCCGGACAACCTGCAAG 61.727 66.667 5.05 0.00 44.73 4.01
2277 2432 2.281484 GCCGGACAACCTGCAAGA 60.281 61.111 5.05 0.00 44.08 3.02
2278 2433 1.896660 GCCGGACAACCTGCAAGAA 60.897 57.895 5.05 0.00 44.08 2.52
2279 2434 1.244019 GCCGGACAACCTGCAAGAAT 61.244 55.000 5.05 0.00 44.08 2.40
2280 2435 1.247567 CCGGACAACCTGCAAGAATT 58.752 50.000 0.00 0.00 34.07 2.17
2291 2446 3.224955 CAAGAATTGTCGCATCGCC 57.775 52.632 0.00 0.00 42.34 5.54
2292 2447 0.587242 CAAGAATTGTCGCATCGCCG 60.587 55.000 0.00 0.00 42.34 6.46
2293 2448 1.705337 AAGAATTGTCGCATCGCCGG 61.705 55.000 0.00 0.00 0.00 6.13
2294 2449 2.125310 AATTGTCGCATCGCCGGA 60.125 55.556 5.05 0.00 0.00 5.14
2295 2450 2.361427 GAATTGTCGCATCGCCGGAC 62.361 60.000 5.05 0.00 0.00 4.79
2296 2451 2.852495 AATTGTCGCATCGCCGGACT 62.852 55.000 5.05 0.00 0.00 3.85
2373 2529 8.546083 AGAGAAACATGTATGATACTTCCTCT 57.454 34.615 0.00 4.92 0.00 3.69
2374 2530 8.420222 AGAGAAACATGTATGATACTTCCTCTG 58.580 37.037 0.00 0.00 0.00 3.35
2375 2531 8.083828 AGAAACATGTATGATACTTCCTCTGT 57.916 34.615 0.00 0.00 0.00 3.41
2376 2532 9.201989 AGAAACATGTATGATACTTCCTCTGTA 57.798 33.333 0.00 0.00 0.00 2.74
2377 2533 9.817809 GAAACATGTATGATACTTCCTCTGTAA 57.182 33.333 0.00 0.00 0.00 2.41
2379 2535 9.601217 AACATGTATGATACTTCCTCTGTAAAC 57.399 33.333 0.00 0.00 0.00 2.01
2380 2536 8.982723 ACATGTATGATACTTCCTCTGTAAACT 58.017 33.333 0.00 0.00 0.00 2.66
2392 2548 9.400638 CTTCCTCTGTAAACTAATATAAGAGCG 57.599 37.037 0.00 0.00 0.00 5.03
2393 2549 8.461249 TCCTCTGTAAACTAATATAAGAGCGT 57.539 34.615 0.00 0.00 0.00 5.07
2394 2550 8.910944 TCCTCTGTAAACTAATATAAGAGCGTT 58.089 33.333 0.00 0.00 0.00 4.84
2395 2551 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2444 2600 9.965902 AATGCTCTTATATTAGTTTATGGAGGG 57.034 33.333 0.00 0.00 0.00 4.30
2445 2601 8.736097 TGCTCTTATATTAGTTTATGGAGGGA 57.264 34.615 0.00 0.00 0.00 4.20
2446 2602 8.816894 TGCTCTTATATTAGTTTATGGAGGGAG 58.183 37.037 0.00 0.00 0.00 4.30
2447 2603 8.817876 GCTCTTATATTAGTTTATGGAGGGAGT 58.182 37.037 0.00 0.00 0.00 3.85
2548 2704 9.204570 AGTGTAAACTAGCTGTATTTGTAACTG 57.795 33.333 0.00 0.00 0.00 3.16
2697 2862 6.170506 TGTCACTGAACTTGACTGTAAACTT 58.829 36.000 4.27 0.00 43.30 2.66
2863 3055 3.579709 GACCACTGTATCGCTCATATGG 58.420 50.000 2.13 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 8.342634 GCACCACGAAATGTATTTTCATACTAT 58.657 33.333 0.00 0.00 43.32 2.12
23 24 7.334671 TGCACCACGAAATGTATTTTCATACTA 59.665 33.333 0.00 0.00 43.32 1.82
24 25 6.150307 TGCACCACGAAATGTATTTTCATACT 59.850 34.615 0.00 0.00 43.32 2.12
25 26 6.318628 TGCACCACGAAATGTATTTTCATAC 58.681 36.000 0.00 0.00 43.32 2.39
26 27 6.502136 TGCACCACGAAATGTATTTTCATA 57.498 33.333 0.00 0.00 43.32 2.15
27 28 5.384063 TGCACCACGAAATGTATTTTCAT 57.616 34.783 0.00 0.00 43.32 2.57
28 29 4.837896 TGCACCACGAAATGTATTTTCA 57.162 36.364 0.00 0.00 43.32 2.69
29 30 5.512788 CAGATGCACCACGAAATGTATTTTC 59.487 40.000 0.00 0.00 40.34 2.29
30 31 5.182950 TCAGATGCACCACGAAATGTATTTT 59.817 36.000 0.00 0.00 0.00 1.82
31 32 4.699735 TCAGATGCACCACGAAATGTATTT 59.300 37.500 0.00 0.00 0.00 1.40
32 33 4.260985 TCAGATGCACCACGAAATGTATT 58.739 39.130 0.00 0.00 0.00 1.89
33 34 3.872696 TCAGATGCACCACGAAATGTAT 58.127 40.909 0.00 0.00 0.00 2.29
34 35 3.326836 TCAGATGCACCACGAAATGTA 57.673 42.857 0.00 0.00 0.00 2.29
35 36 2.183478 TCAGATGCACCACGAAATGT 57.817 45.000 0.00 0.00 0.00 2.71
36 37 4.880886 TTATCAGATGCACCACGAAATG 57.119 40.909 0.00 0.00 0.00 2.32
37 38 4.883585 ACATTATCAGATGCACCACGAAAT 59.116 37.500 0.00 0.00 0.00 2.17
38 39 4.260985 ACATTATCAGATGCACCACGAAA 58.739 39.130 0.00 0.00 0.00 3.46
39 40 3.872696 ACATTATCAGATGCACCACGAA 58.127 40.909 0.00 0.00 0.00 3.85
40 41 3.541996 ACATTATCAGATGCACCACGA 57.458 42.857 0.00 0.00 0.00 4.35
41 42 3.622612 TGAACATTATCAGATGCACCACG 59.377 43.478 0.00 0.00 0.00 4.94
42 43 5.762825 ATGAACATTATCAGATGCACCAC 57.237 39.130 0.00 0.00 31.76 4.16
43 44 6.377712 TGAAATGAACATTATCAGATGCACCA 59.622 34.615 0.00 0.00 31.76 4.17
44 45 6.798482 TGAAATGAACATTATCAGATGCACC 58.202 36.000 0.00 0.00 31.76 5.01
116 117 3.365472 AGGTTTGGTCAAAGTCAAGCTT 58.635 40.909 0.00 0.00 39.52 3.74
117 118 3.018423 AGGTTTGGTCAAAGTCAAGCT 57.982 42.857 0.00 0.00 0.00 3.74
118 119 3.801114 AAGGTTTGGTCAAAGTCAAGC 57.199 42.857 0.00 0.00 0.00 4.01
119 120 7.029563 GCATATAAGGTTTGGTCAAAGTCAAG 58.970 38.462 0.00 0.00 0.00 3.02
120 121 6.491745 TGCATATAAGGTTTGGTCAAAGTCAA 59.508 34.615 0.00 0.00 0.00 3.18
121 122 6.007076 TGCATATAAGGTTTGGTCAAAGTCA 58.993 36.000 0.00 0.00 0.00 3.41
122 123 6.374333 TCTGCATATAAGGTTTGGTCAAAGTC 59.626 38.462 0.00 0.00 0.00 3.01
123 124 6.151144 GTCTGCATATAAGGTTTGGTCAAAGT 59.849 38.462 0.00 0.00 0.00 2.66
124 125 6.375455 AGTCTGCATATAAGGTTTGGTCAAAG 59.625 38.462 0.00 0.00 0.00 2.77
125 126 6.245408 AGTCTGCATATAAGGTTTGGTCAAA 58.755 36.000 0.00 0.00 0.00 2.69
126 127 5.815581 AGTCTGCATATAAGGTTTGGTCAA 58.184 37.500 0.00 0.00 0.00 3.18
127 128 5.435686 AGTCTGCATATAAGGTTTGGTCA 57.564 39.130 0.00 0.00 0.00 4.02
128 129 7.859325 TTTAGTCTGCATATAAGGTTTGGTC 57.141 36.000 0.00 0.00 0.00 4.02
129 130 8.644374 TTTTTAGTCTGCATATAAGGTTTGGT 57.356 30.769 0.00 0.00 0.00 3.67
130 131 8.956426 TCTTTTTAGTCTGCATATAAGGTTTGG 58.044 33.333 0.00 0.00 0.00 3.28
134 135 8.665685 CGTTTCTTTTTAGTCTGCATATAAGGT 58.334 33.333 0.00 0.00 0.00 3.50
135 136 8.122952 CCGTTTCTTTTTAGTCTGCATATAAGG 58.877 37.037 0.00 0.00 0.00 2.69
136 137 8.879759 TCCGTTTCTTTTTAGTCTGCATATAAG 58.120 33.333 0.00 0.00 0.00 1.73
137 138 8.780846 TCCGTTTCTTTTTAGTCTGCATATAA 57.219 30.769 0.00 0.00 0.00 0.98
138 139 7.494625 CCTCCGTTTCTTTTTAGTCTGCATATA 59.505 37.037 0.00 0.00 0.00 0.86
139 140 6.316390 CCTCCGTTTCTTTTTAGTCTGCATAT 59.684 38.462 0.00 0.00 0.00 1.78
140 141 5.642063 CCTCCGTTTCTTTTTAGTCTGCATA 59.358 40.000 0.00 0.00 0.00 3.14
141 142 4.455877 CCTCCGTTTCTTTTTAGTCTGCAT 59.544 41.667 0.00 0.00 0.00 3.96
142 143 3.813166 CCTCCGTTTCTTTTTAGTCTGCA 59.187 43.478 0.00 0.00 0.00 4.41
143 144 3.188667 CCCTCCGTTTCTTTTTAGTCTGC 59.811 47.826 0.00 0.00 0.00 4.26
144 145 4.638304 TCCCTCCGTTTCTTTTTAGTCTG 58.362 43.478 0.00 0.00 0.00 3.51
145 146 4.347292 ACTCCCTCCGTTTCTTTTTAGTCT 59.653 41.667 0.00 0.00 0.00 3.24
146 147 4.639334 ACTCCCTCCGTTTCTTTTTAGTC 58.361 43.478 0.00 0.00 0.00 2.59
147 148 4.701651 ACTCCCTCCGTTTCTTTTTAGT 57.298 40.909 0.00 0.00 0.00 2.24
148 149 7.683437 AAATACTCCCTCCGTTTCTTTTTAG 57.317 36.000 0.00 0.00 0.00 1.85
149 150 7.095102 CGAAAATACTCCCTCCGTTTCTTTTTA 60.095 37.037 0.00 0.00 0.00 1.52
150 151 6.293790 CGAAAATACTCCCTCCGTTTCTTTTT 60.294 38.462 0.00 0.00 0.00 1.94
151 152 5.180680 CGAAAATACTCCCTCCGTTTCTTTT 59.819 40.000 0.00 0.00 0.00 2.27
152 153 4.694037 CGAAAATACTCCCTCCGTTTCTTT 59.306 41.667 0.00 0.00 0.00 2.52
153 154 4.251268 CGAAAATACTCCCTCCGTTTCTT 58.749 43.478 0.00 0.00 0.00 2.52
154 155 3.260128 ACGAAAATACTCCCTCCGTTTCT 59.740 43.478 0.00 0.00 0.00 2.52
155 156 3.593096 ACGAAAATACTCCCTCCGTTTC 58.407 45.455 0.00 0.00 0.00 2.78
156 157 3.690475 ACGAAAATACTCCCTCCGTTT 57.310 42.857 0.00 0.00 0.00 3.60
157 158 4.442472 CCATACGAAAATACTCCCTCCGTT 60.442 45.833 0.00 0.00 0.00 4.44
158 159 3.069158 CCATACGAAAATACTCCCTCCGT 59.931 47.826 0.00 0.00 0.00 4.69
159 160 3.319972 TCCATACGAAAATACTCCCTCCG 59.680 47.826 0.00 0.00 0.00 4.63
160 161 4.262506 CCTCCATACGAAAATACTCCCTCC 60.263 50.000 0.00 0.00 0.00 4.30
161 162 4.344390 ACCTCCATACGAAAATACTCCCTC 59.656 45.833 0.00 0.00 0.00 4.30
162 163 4.296056 ACCTCCATACGAAAATACTCCCT 58.704 43.478 0.00 0.00 0.00 4.20
163 164 4.684484 ACCTCCATACGAAAATACTCCC 57.316 45.455 0.00 0.00 0.00 4.30
164 165 6.402456 ACTACCTCCATACGAAAATACTCC 57.598 41.667 0.00 0.00 0.00 3.85
165 166 8.164058 ACTACTACCTCCATACGAAAATACTC 57.836 38.462 0.00 0.00 0.00 2.59
166 167 8.411683 CAACTACTACCTCCATACGAAAATACT 58.588 37.037 0.00 0.00 0.00 2.12
167 168 8.193438 ACAACTACTACCTCCATACGAAAATAC 58.807 37.037 0.00 0.00 0.00 1.89
376 379 1.683943 CCAGGGCATGGTTATCTGTG 58.316 55.000 10.66 0.00 44.91 3.66
604 609 1.074405 ACTGACCAAGCATCCACACAT 59.926 47.619 0.00 0.00 0.00 3.21
847 858 3.884895 TCACCACAAGTCAGTGACAATT 58.115 40.909 24.73 8.90 42.05 2.32
1018 1032 3.964688 TGTAGAAAGGTTCTGGAGTGACA 59.035 43.478 0.70 0.00 40.94 3.58
1107 1122 1.662517 ACTGTCGCACAAACACATGA 58.337 45.000 0.00 0.00 0.00 3.07
1226 1243 3.666902 CGTACACTGGCACAACAATTAGC 60.667 47.826 0.00 0.00 38.70 3.09
1315 1332 4.244066 TGCATGTTGTTCAATGGCAATAC 58.756 39.130 0.00 0.00 32.02 1.89
1425 1532 2.753989 TCGTTGTGTCTTGCAATGTG 57.246 45.000 0.00 0.00 35.16 3.21
1469 1576 3.137544 TGGTCACCTTGTAATCAACCACT 59.862 43.478 0.00 0.00 0.00 4.00
1653 1775 3.232213 TCTCCTTCACGACAACATAGC 57.768 47.619 0.00 0.00 0.00 2.97
1662 1784 1.404717 GCTTCAGCATCTCCTTCACGA 60.405 52.381 0.00 0.00 41.59 4.35
1861 1988 0.395311 TATCCTTCGAGCGACCCAGT 60.395 55.000 0.00 0.00 0.00 4.00
1872 1999 2.289072 ACCTCCGCAATCATATCCTTCG 60.289 50.000 0.00 0.00 0.00 3.79
1895 2022 2.028112 TCTTGTTTCAGCTAGCGGTGAT 60.028 45.455 14.70 0.00 46.03 3.06
2039 2180 3.010027 TCCAGCATGTTCATCCCAGTTAA 59.990 43.478 0.00 0.00 0.00 2.01
2051 2192 0.399454 AGCAGACAGTCCAGCATGTT 59.601 50.000 15.76 0.00 0.00 2.71
2112 2266 5.243207 AGTCCTTCATACGGTACCTTTTTG 58.757 41.667 10.90 2.68 0.00 2.44
2115 2269 5.718607 ACTTAGTCCTTCATACGGTACCTTT 59.281 40.000 10.90 0.00 0.00 3.11
2120 2274 7.615365 TCCTTTTACTTAGTCCTTCATACGGTA 59.385 37.037 0.00 0.00 0.00 4.02
2209 2364 0.515127 CGACGCTGTTTTGGCATGTA 59.485 50.000 0.00 0.00 0.00 2.29
2268 2423 1.470098 GATGCGACAATTCTTGCAGGT 59.530 47.619 1.97 0.00 41.19 4.00
2269 2424 1.530441 CGATGCGACAATTCTTGCAGG 60.530 52.381 1.97 0.00 41.19 4.85
2270 2425 1.806511 CGATGCGACAATTCTTGCAG 58.193 50.000 1.97 0.00 41.19 4.41
2271 2426 0.179192 GCGATGCGACAATTCTTGCA 60.179 50.000 0.00 0.00 42.22 4.08
2272 2427 0.863119 GGCGATGCGACAATTCTTGC 60.863 55.000 0.00 0.00 33.63 4.01
2273 2428 0.587242 CGGCGATGCGACAATTCTTG 60.587 55.000 0.00 0.00 32.52 3.02
2274 2429 1.705337 CCGGCGATGCGACAATTCTT 61.705 55.000 9.30 0.00 32.52 2.52
2275 2430 2.173669 CCGGCGATGCGACAATTCT 61.174 57.895 9.30 0.00 32.52 2.40
2276 2431 2.171079 TCCGGCGATGCGACAATTC 61.171 57.895 9.30 0.00 32.52 2.17
2277 2432 2.125310 TCCGGCGATGCGACAATT 60.125 55.556 9.30 0.00 32.52 2.32
2278 2433 2.890474 GTCCGGCGATGCGACAAT 60.890 61.111 9.30 0.00 32.52 2.71
2279 2434 3.982372 GAGTCCGGCGATGCGACAA 62.982 63.158 9.30 0.00 32.52 3.18
2280 2435 4.492160 GAGTCCGGCGATGCGACA 62.492 66.667 9.30 0.00 32.52 4.35
2295 2450 0.792640 GTGCATGAAGTGTGACGGAG 59.207 55.000 0.00 0.00 0.00 4.63
2296 2451 0.602638 GGTGCATGAAGTGTGACGGA 60.603 55.000 0.00 0.00 0.00 4.69
2366 2522 9.400638 CGCTCTTATATTAGTTTACAGAGGAAG 57.599 37.037 0.00 0.00 0.00 3.46
2367 2523 8.910944 ACGCTCTTATATTAGTTTACAGAGGAA 58.089 33.333 0.00 0.00 0.00 3.36
2368 2524 8.461249 ACGCTCTTATATTAGTTTACAGAGGA 57.539 34.615 0.00 0.00 0.00 3.71
2369 2525 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2418 2574 9.965902 CCCTCCATAAACTAATATAAGAGCATT 57.034 33.333 0.00 0.00 0.00 3.56
2419 2575 9.338968 TCCCTCCATAAACTAATATAAGAGCAT 57.661 33.333 0.00 0.00 0.00 3.79
2420 2576 8.736097 TCCCTCCATAAACTAATATAAGAGCA 57.264 34.615 0.00 0.00 0.00 4.26
2421 2577 8.817876 ACTCCCTCCATAAACTAATATAAGAGC 58.182 37.037 0.00 0.00 0.00 4.09
2427 2583 9.900112 AGAGTTACTCCCTCCATAAACTAATAT 57.100 33.333 8.96 0.00 0.00 1.28
2428 2584 9.144298 CAGAGTTACTCCCTCCATAAACTAATA 57.856 37.037 8.96 0.00 0.00 0.98
2429 2585 7.844779 TCAGAGTTACTCCCTCCATAAACTAAT 59.155 37.037 8.96 0.00 0.00 1.73
2430 2586 7.186972 TCAGAGTTACTCCCTCCATAAACTAA 58.813 38.462 8.96 0.00 0.00 2.24
2431 2587 6.738635 TCAGAGTTACTCCCTCCATAAACTA 58.261 40.000 8.96 0.00 0.00 2.24
2432 2588 5.590818 TCAGAGTTACTCCCTCCATAAACT 58.409 41.667 8.96 0.00 0.00 2.66
2433 2589 5.934402 TCAGAGTTACTCCCTCCATAAAC 57.066 43.478 8.96 0.00 0.00 2.01
2434 2590 7.510675 AATTCAGAGTTACTCCCTCCATAAA 57.489 36.000 8.96 0.00 0.00 1.40
2435 2591 7.510675 AAATTCAGAGTTACTCCCTCCATAA 57.489 36.000 8.96 0.00 0.00 1.90
2436 2592 7.510675 AAAATTCAGAGTTACTCCCTCCATA 57.489 36.000 8.96 0.00 0.00 2.74
2437 2593 6.394345 AAAATTCAGAGTTACTCCCTCCAT 57.606 37.500 8.96 0.00 0.00 3.41
2438 2594 5.843019 AAAATTCAGAGTTACTCCCTCCA 57.157 39.130 8.96 0.00 0.00 3.86
2439 2595 5.811100 CGTAAAATTCAGAGTTACTCCCTCC 59.189 44.000 8.96 0.00 0.00 4.30
2440 2596 6.396450 ACGTAAAATTCAGAGTTACTCCCTC 58.604 40.000 8.96 0.00 0.00 4.30
2441 2597 6.356186 ACGTAAAATTCAGAGTTACTCCCT 57.644 37.500 8.96 0.00 0.00 4.20
2442 2598 7.430992 AAACGTAAAATTCAGAGTTACTCCC 57.569 36.000 8.96 0.00 0.00 4.30
2443 2599 8.553696 TCAAAACGTAAAATTCAGAGTTACTCC 58.446 33.333 8.96 0.00 0.00 3.85
2444 2600 9.582223 CTCAAAACGTAAAATTCAGAGTTACTC 57.418 33.333 3.85 3.85 0.00 2.59
2445 2601 9.321562 TCTCAAAACGTAAAATTCAGAGTTACT 57.678 29.630 0.00 0.00 0.00 2.24
2446 2602 9.925268 TTCTCAAAACGTAAAATTCAGAGTTAC 57.075 29.630 0.00 0.00 0.00 2.50
2625 2785 1.614903 TCAGCAGGTGCAAATTGGAAG 59.385 47.619 4.48 0.00 45.16 3.46
2863 3055 7.968405 AGCTTACGAATTTGAATACATTTGACC 59.032 33.333 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.