Multiple sequence alignment - TraesCS5D01G283200

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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 TraesCS5D01G283200 chr5D 100.000 4300 0 0 1 4300 384349161 384344862 0.000000e+00 7941.0
1 TraesCS5D01G283200 chr5D 81.165 515 79 14 3708 4216 464621087 464621589 8.660000e-107 398.0
2 TraesCS5D01G283200 chr5D 79.655 290 56 3 3926 4212 446483253 446482964 5.640000e-49 206.0
3 TraesCS5D01G283200 chr5B 91.847 3753 197 57 112 3807 461142414 461138714 0.000000e+00 5134.0
4 TraesCS5D01G283200 chr5B 81.962 316 43 10 3988 4300 461138623 461138319 5.520000e-64 255.0
5 TraesCS5D01G283200 chr5B 78.523 298 39 12 3708 4003 526540342 526540616 5.720000e-39 172.0
6 TraesCS5D01G283200 chr5B 82.432 148 24 2 1085 1231 267760969 267760823 1.260000e-25 128.0
7 TraesCS5D01G283200 chr5B 88.406 69 7 1 4233 4300 79071043 79070975 9.910000e-12 82.4
8 TraesCS5D01G283200 chr5B 97.222 36 1 0 112 147 55631393 55631428 1.290000e-05 62.1
9 TraesCS5D01G283200 chr5A 90.979 2084 127 25 2265 4300 485206101 485204031 0.000000e+00 2750.0
10 TraesCS5D01G283200 chr5A 91.118 1565 75 27 186 1724 485208070 485206544 0.000000e+00 2061.0
11 TraesCS5D01G283200 chr5A 89.655 319 25 2 1894 2208 485206438 485206124 2.410000e-107 399.0
12 TraesCS5D01G283200 chr5A 79.452 511 84 19 3713 4216 585071285 585071781 4.120000e-90 342.0
13 TraesCS5D01G283200 chr5A 78.149 389 77 7 3829 4212 564202331 564201946 1.550000e-59 241.0
14 TraesCS5D01G283200 chr5A 88.889 63 5 2 4225 4285 564201901 564201839 4.610000e-10 76.8
15 TraesCS5D01G283200 chr5A 97.222 36 1 0 112 147 522364546 522364511 1.290000e-05 62.1
16 TraesCS5D01G283200 chr7D 81.349 504 73 13 3720 4218 12899691 12900178 1.450000e-104 390.0
17 TraesCS5D01G283200 chr7D 82.166 157 23 5 1066 1218 438368463 438368618 3.490000e-26 130.0
18 TraesCS5D01G283200 chr7D 86.842 76 10 0 4225 4300 386922954 386922879 7.660000e-13 86.1
19 TraesCS5D01G283200 chr7D 91.837 49 3 1 4226 4274 17256268 17256315 2.780000e-07 67.6
20 TraesCS5D01G283200 chr2B 77.800 509 105 7 3717 4219 707607667 707608173 1.500000e-79 307.0
21 TraesCS5D01G283200 chr2B 81.333 150 22 3 1084 1230 489418817 489418963 2.720000e-22 117.0
22 TraesCS5D01G283200 chr7A 77.650 434 75 10 3786 4217 204172391 204172804 1.190000e-60 244.0
23 TraesCS5D01G283200 chr7A 83.942 137 19 3 1085 1218 489163067 489163203 1.260000e-25 128.0
24 TraesCS5D01G283200 chr2D 76.667 360 77 6 3864 4218 372607409 372607766 4.390000e-45 193.0
25 TraesCS5D01G283200 chr2D 81.333 150 22 3 1084 1230 417543866 417544012 2.720000e-22 117.0
26 TraesCS5D01G283200 chr3A 96.774 93 3 0 21 113 638068069 638068161 5.760000e-34 156.0
27 TraesCS5D01G283200 chr3A 93.137 102 3 3 17 115 709065486 709065586 3.460000e-31 147.0
28 TraesCS5D01G283200 chr6B 96.774 93 2 1 29 121 471127632 471127541 2.070000e-33 154.0
29 TraesCS5D01G283200 chr6B 90.741 108 8 2 9 114 80083477 80083584 4.480000e-30 143.0
30 TraesCS5D01G283200 chr6B 97.222 36 1 0 112 147 80168411 80168446 1.290000e-05 62.1
31 TraesCS5D01G283200 chr6B 97.222 36 1 0 112 147 80181626 80181661 1.290000e-05 62.1
32 TraesCS5D01G283200 chr1B 96.774 93 2 1 24 115 610174434 610174342 2.070000e-33 154.0
33 TraesCS5D01G283200 chr7B 95.789 95 3 1 21 114 446149581 446149487 7.450000e-33 152.0
34 TraesCS5D01G283200 chr7B 90.654 107 8 2 8 113 652932430 652932535 1.610000e-29 141.0
35 TraesCS5D01G283200 chr7B 80.982 163 26 4 1066 1224 455272208 455272047 1.620000e-24 124.0
36 TraesCS5D01G283200 chr7B 97.222 36 1 0 112 147 263668814 263668779 1.290000e-05 62.1
37 TraesCS5D01G283200 chr6A 92.308 104 7 1 12 115 279460446 279460344 3.460000e-31 147.0
38 TraesCS5D01G283200 chr4A 91.509 106 7 2 10 113 43612657 43612762 1.250000e-30 145.0
39 TraesCS5D01G283200 chr2A 81.333 150 22 3 1084 1230 572616091 572615945 2.720000e-22 117.0
40 TraesCS5D01G283200 chr2A 81.818 77 13 1 4225 4300 54469090 54469014 3.590000e-06 63.9
41 TraesCS5D01G283200 chr2A 94.737 38 1 1 116 153 753018976 753019012 1.670000e-04 58.4
42 TraesCS5D01G283200 chr3D 97.222 36 1 0 112 147 310686149 310686184 1.290000e-05 62.1


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 TraesCS5D01G283200 chr5D 384344862 384349161 4299 True 7941.000000 7941 100.0000 1 4300 1 chr5D.!!$R1 4299
1 TraesCS5D01G283200 chr5D 464621087 464621589 502 False 398.000000 398 81.1650 3708 4216 1 chr5D.!!$F1 508
2 TraesCS5D01G283200 chr5B 461138319 461142414 4095 True 2694.500000 5134 86.9045 112 4300 2 chr5B.!!$R3 4188
3 TraesCS5D01G283200 chr5A 485204031 485208070 4039 True 1736.666667 2750 90.5840 186 4300 3 chr5A.!!$R2 4114
4 TraesCS5D01G283200 chr2B 707607667 707608173 506 False 307.000000 307 77.8000 3717 4219 1 chr2B.!!$F2 502

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
403 407 0.386476 CCGGGCAGCGTAATACTGTA 59.614 55.000 0.00 0.0 37.47 2.74 F
837 855 0.506932 CCAGTTTGACGTACACGCAG 59.493 55.000 0.85 0.0 44.43 5.18 F
841 859 1.450905 GTTTGACGTACACGCAGACTC 59.549 52.381 0.85 0.0 44.43 3.36 F
1936 1982 2.102252 TGCACCCTTCAATTTGTTGTCC 59.898 45.455 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1464 1504 0.440371 GCTCTCGAGGAAAAACGCTG 59.560 55.000 13.56 0.00 0.00 5.18 R
2457 2510 0.888619 TCCCGACTAGCTCTTGTGTG 59.111 55.000 0.00 0.00 0.00 3.82 R
2458 2511 1.478510 CATCCCGACTAGCTCTTGTGT 59.521 52.381 0.00 0.00 0.00 3.72 R
3920 4026 0.595310 TCAATGTTGCGTCGTCGACA 60.595 50.000 24.13 6.19 39.71 4.35 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
38 39 5.914033 TCAAATTAAGACATACTCCCTCCG 58.086 41.667 0.00 0.00 0.00 4.63
39 40 5.424252 TCAAATTAAGACATACTCCCTCCGT 59.576 40.000 0.00 0.00 0.00 4.69
40 41 6.608405 TCAAATTAAGACATACTCCCTCCGTA 59.392 38.462 0.00 0.00 0.00 4.02
41 42 7.124599 TCAAATTAAGACATACTCCCTCCGTAA 59.875 37.037 0.00 0.00 0.00 3.18
42 43 7.427989 AATTAAGACATACTCCCTCCGTAAA 57.572 36.000 0.00 0.00 0.00 2.01
43 44 4.732672 AAGACATACTCCCTCCGTAAAC 57.267 45.455 0.00 0.00 0.00 2.01
44 45 3.978610 AGACATACTCCCTCCGTAAACT 58.021 45.455 0.00 0.00 0.00 2.66
45 46 5.121380 AGACATACTCCCTCCGTAAACTA 57.879 43.478 0.00 0.00 0.00 2.24
46 47 5.513233 AGACATACTCCCTCCGTAAACTAA 58.487 41.667 0.00 0.00 0.00 2.24
47 48 6.134754 AGACATACTCCCTCCGTAAACTAAT 58.865 40.000 0.00 0.00 0.00 1.73
48 49 7.293073 AGACATACTCCCTCCGTAAACTAATA 58.707 38.462 0.00 0.00 0.00 0.98
49 50 7.949006 AGACATACTCCCTCCGTAAACTAATAT 59.051 37.037 0.00 0.00 0.00 1.28
50 51 9.236006 GACATACTCCCTCCGTAAACTAATATA 57.764 37.037 0.00 0.00 0.00 0.86
51 52 9.592196 ACATACTCCCTCCGTAAACTAATATAA 57.408 33.333 0.00 0.00 0.00 0.98
54 55 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
55 56 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
56 57 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
57 58 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
58 59 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
59 60 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
109 110 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
137 138 4.225717 ACTCCCACCCTTATTAGCGTTTTA 59.774 41.667 0.00 0.00 0.00 1.52
164 165 8.773033 ACCTATTTTAGAATCAGCAAATGGAT 57.227 30.769 0.00 0.00 0.00 3.41
181 182 7.444299 CAAATGGATGAAATTAATAGTGGGGG 58.556 38.462 0.00 0.00 0.00 5.40
182 183 5.742562 TGGATGAAATTAATAGTGGGGGT 57.257 39.130 0.00 0.00 0.00 4.95
183 184 6.850263 TGGATGAAATTAATAGTGGGGGTA 57.150 37.500 0.00 0.00 0.00 3.69
184 185 6.607019 TGGATGAAATTAATAGTGGGGGTAC 58.393 40.000 0.00 0.00 0.00 3.34
239 240 1.478288 GCATCCAGCAAGGGAGCTAAT 60.478 52.381 0.00 0.00 44.54 1.73
242 243 3.456380 TCCAGCAAGGGAGCTAATTTT 57.544 42.857 0.00 0.00 44.54 1.82
243 244 3.778265 TCCAGCAAGGGAGCTAATTTTT 58.222 40.909 0.00 0.00 44.54 1.94
248 249 7.038373 TCCAGCAAGGGAGCTAATTTTTATTTT 60.038 33.333 0.00 0.00 44.54 1.82
399 403 2.970868 GGCCGGGCAGCGTAATAC 60.971 66.667 25.33 0.00 0.00 1.89
401 405 2.244651 GCCGGGCAGCGTAATACTG 61.245 63.158 15.62 0.00 38.22 2.74
402 406 1.143183 CCGGGCAGCGTAATACTGT 59.857 57.895 0.00 0.00 37.47 3.55
403 407 0.386476 CCGGGCAGCGTAATACTGTA 59.614 55.000 0.00 0.00 37.47 2.74
404 408 1.602165 CCGGGCAGCGTAATACTGTAG 60.602 57.143 0.00 0.00 37.47 2.74
405 409 1.066605 CGGGCAGCGTAATACTGTAGT 59.933 52.381 0.00 0.00 37.47 2.73
406 410 2.480759 CGGGCAGCGTAATACTGTAGTT 60.481 50.000 0.00 0.00 37.47 2.24
456 467 2.814336 AGCAGCGATCGAGATATACACA 59.186 45.455 21.57 0.00 0.00 3.72
457 468 3.441922 AGCAGCGATCGAGATATACACAT 59.558 43.478 21.57 0.00 0.00 3.21
458 469 4.636206 AGCAGCGATCGAGATATACACATA 59.364 41.667 21.57 0.00 0.00 2.29
459 470 5.298026 AGCAGCGATCGAGATATACACATAT 59.702 40.000 21.57 0.00 0.00 1.78
484 499 1.270625 GCACCACTACAGCACCAGTAA 60.271 52.381 0.00 0.00 0.00 2.24
821 839 1.448985 CGGTATTTCACACCCACCAG 58.551 55.000 0.00 0.00 31.96 4.00
832 850 0.831966 ACCCACCAGTTTGACGTACA 59.168 50.000 0.00 0.00 0.00 2.90
834 852 0.856641 CCACCAGTTTGACGTACACG 59.143 55.000 0.00 0.00 46.33 4.49
837 855 0.506932 CCAGTTTGACGTACACGCAG 59.493 55.000 0.85 0.00 44.43 5.18
838 856 1.483316 CAGTTTGACGTACACGCAGA 58.517 50.000 0.85 0.00 44.43 4.26
841 859 1.450905 GTTTGACGTACACGCAGACTC 59.549 52.381 0.85 0.00 44.43 3.36
1260 1289 4.965814 TCAGTCAGAAATGTTCTTGAGCT 58.034 39.130 0.00 0.00 38.11 4.09
1261 1290 6.101650 TCAGTCAGAAATGTTCTTGAGCTA 57.898 37.500 0.00 0.00 38.11 3.32
1262 1291 6.162079 TCAGTCAGAAATGTTCTTGAGCTAG 58.838 40.000 0.00 0.00 38.11 3.42
1263 1292 4.934602 AGTCAGAAATGTTCTTGAGCTAGC 59.065 41.667 6.62 6.62 38.11 3.42
1264 1293 4.934602 GTCAGAAATGTTCTTGAGCTAGCT 59.065 41.667 19.45 19.45 38.11 3.32
1265 1294 6.071108 AGTCAGAAATGTTCTTGAGCTAGCTA 60.071 38.462 19.38 1.34 38.11 3.32
1266 1295 6.255453 GTCAGAAATGTTCTTGAGCTAGCTAG 59.745 42.308 19.38 16.84 38.11 3.42
1267 1296 5.006552 CAGAAATGTTCTTGAGCTAGCTAGC 59.993 44.000 33.96 33.96 43.16 3.42
1358 1391 4.591072 CCATGGTTTTGTTTTTCTCCCCTA 59.409 41.667 2.57 0.00 0.00 3.53
1393 1432 6.151691 TGCATAAGCTGTGCTCTTTTAAAAG 58.848 36.000 19.91 19.91 42.92 2.27
1394 1433 6.016360 TGCATAAGCTGTGCTCTTTTAAAAGA 60.016 34.615 25.24 25.24 42.92 2.52
1464 1504 8.581253 AGCTATATAAAAGCCATAAATCACCC 57.419 34.615 6.79 0.00 41.02 4.61
1491 1531 4.736126 TTTTCCTCGAGAGCATATGTGA 57.264 40.909 15.71 0.00 0.00 3.58
1550 1590 8.934023 AATGGTGGATTCTTACAAGTTTAGAA 57.066 30.769 0.00 0.00 32.91 2.10
1621 1661 9.660180 TTAAAAGTTAAAACCTTCATGCTTTGT 57.340 25.926 0.00 0.00 0.00 2.83
1623 1663 6.463995 AGTTAAAACCTTCATGCTTTGTGA 57.536 33.333 0.00 0.00 0.00 3.58
1656 1696 7.069344 TCAAGATTATATGTGTCCCTCTCTCA 58.931 38.462 0.00 0.00 0.00 3.27
1664 1704 2.569404 GTGTCCCTCTCTCATGGTTTCT 59.431 50.000 0.00 0.00 0.00 2.52
1735 1775 2.710902 GGGGAACAGGATTTGCGGC 61.711 63.158 0.00 0.00 0.00 6.53
1764 1804 9.710818 TCTGGTAGTTAGAAACTATTACCATCT 57.289 33.333 11.44 0.00 43.22 2.90
1930 1976 5.540911 AGTTAACATGCACCCTTCAATTTG 58.459 37.500 8.61 0.00 0.00 2.32
1936 1982 2.102252 TGCACCCTTCAATTTGTTGTCC 59.898 45.455 0.00 0.00 0.00 4.02
1945 1991 6.582295 CCTTCAATTTGTTGTCCTTTGATACG 59.418 38.462 0.00 0.00 0.00 3.06
2035 2081 8.510505 TGCTCTTTTGTTTTATTTTGTTTTGCT 58.489 25.926 0.00 0.00 0.00 3.91
2165 2215 8.911918 TTACTAGCAAACAATTAACTGGAAGA 57.088 30.769 0.00 0.00 37.43 2.87
2217 2267 7.958025 CCTAGAATTACGAAAGAGTGCTTTTTC 59.042 37.037 5.45 5.45 44.10 2.29
2224 2274 4.496895 CGAAAGAGTGCTTTTTCAGTTGTG 59.503 41.667 13.26 0.00 44.10 3.33
2225 2275 5.391312 AAAGAGTGCTTTTTCAGTTGTGT 57.609 34.783 0.00 0.00 41.43 3.72
2230 2280 8.220755 AGAGTGCTTTTTCAGTTGTGTTATTA 57.779 30.769 0.00 0.00 0.00 0.98
2231 2281 8.850156 AGAGTGCTTTTTCAGTTGTGTTATTAT 58.150 29.630 0.00 0.00 0.00 1.28
2328 2381 3.895041 AGAAGGCGAAAATGGGAGAAAAA 59.105 39.130 0.00 0.00 0.00 1.94
2355 2408 3.712218 GGTACTTCTTCAGCCTAAGGGAT 59.288 47.826 0.00 0.00 33.58 3.85
2427 2480 2.766828 CTGGAAGACTACGGGGAAAGAT 59.233 50.000 0.00 0.00 34.07 2.40
2550 2603 1.195115 ACTGGGTCATGCACGAGTAT 58.805 50.000 0.00 0.00 0.00 2.12
2592 2645 5.163550 GGCCTCCAAATCAAACAAGGTATAC 60.164 44.000 0.00 0.00 0.00 1.47
2604 2657 5.552870 ACAAGGTATACATGACATCCCTC 57.447 43.478 13.13 0.00 0.00 4.30
2605 2658 4.968719 ACAAGGTATACATGACATCCCTCA 59.031 41.667 13.13 0.00 0.00 3.86
2616 2669 7.156673 ACATGACATCCCTCAAATTTTTCTTG 58.843 34.615 0.00 0.00 0.00 3.02
2618 2671 4.559153 ACATCCCTCAAATTTTTCTTGCG 58.441 39.130 0.00 0.00 0.00 4.85
2623 2676 4.996758 CCCTCAAATTTTTCTTGCGGAATT 59.003 37.500 0.00 0.00 31.53 2.17
2658 2721 5.100751 GCTAAGCGATTGCATGATTAACT 57.899 39.130 7.90 0.00 46.23 2.24
2659 2722 6.228273 GCTAAGCGATTGCATGATTAACTA 57.772 37.500 7.90 0.00 46.23 2.24
2661 2724 7.132213 GCTAAGCGATTGCATGATTAACTAAA 58.868 34.615 7.90 0.00 46.23 1.85
2662 2725 7.643764 GCTAAGCGATTGCATGATTAACTAAAA 59.356 33.333 7.90 0.00 46.23 1.52
2664 2727 7.919313 AGCGATTGCATGATTAACTAAAATG 57.081 32.000 7.90 0.00 46.23 2.32
2667 2730 7.096477 GCGATTGCATGATTAACTAAAATGACC 60.096 37.037 0.00 0.00 42.15 4.02
2668 2731 7.112009 CGATTGCATGATTAACTAAAATGACCG 59.888 37.037 0.00 0.00 0.00 4.79
2669 2732 6.993786 TGCATGATTAACTAAAATGACCGA 57.006 33.333 0.00 0.00 0.00 4.69
2693 2761 9.763979 CGAATTTTTCATTTTAACTTGAACTCG 57.236 29.630 0.00 3.53 31.87 4.18
3078 3161 4.408821 TCCTCCACCACGCCATGC 62.409 66.667 0.00 0.00 0.00 4.06
3464 3560 1.519408 TTCAGGTTAGCTTTGGTCGC 58.481 50.000 0.00 0.00 0.00 5.19
3482 3582 1.375523 CCCGCCTTGTACACAGACC 60.376 63.158 0.00 0.00 0.00 3.85
3589 3694 1.202313 TGTGCCAAAGTTAAACGTGCC 60.202 47.619 0.00 0.00 0.00 5.01
3592 3697 1.066454 GCCAAAGTTAAACGTGCCTGT 59.934 47.619 0.00 0.00 0.00 4.00
3595 3700 3.428316 CCAAAGTTAAACGTGCCTGTTGT 60.428 43.478 0.00 0.00 31.10 3.32
3641 3746 0.713883 CGGAGTTCACCACGAATTCG 59.286 55.000 25.64 25.64 40.38 3.34
3656 3761 0.181350 ATTCGGGCCTCAATGGAGAC 59.819 55.000 0.84 0.00 44.26 3.36
3856 3962 2.365105 CGGGGCCTTCCTCTACCA 60.365 66.667 0.84 0.00 35.33 3.25
3859 3965 1.684734 GGGCCTTCCTCTACCACGA 60.685 63.158 0.84 0.00 0.00 4.35
3865 3971 0.325933 TTCCTCTACCACGACTCCGA 59.674 55.000 0.00 0.00 39.50 4.55
3897 4003 3.134127 GGCGATCCACAAGGGTGC 61.134 66.667 0.00 0.00 43.88 5.01
4007 4113 3.580319 GGGGGTGTGGCTCCAGTT 61.580 66.667 0.00 0.00 40.42 3.16
4027 4133 2.358984 GCGGTTTCCCTACGGCAA 60.359 61.111 0.00 0.00 42.09 4.52
4030 4136 0.885596 CGGTTTCCCTACGGCAAACA 60.886 55.000 2.25 0.00 33.93 2.83
4033 4139 2.433436 GTTTCCCTACGGCAAACATCT 58.567 47.619 0.00 0.00 33.18 2.90
4057 4163 2.120909 GGGCATGTTGGATGACGGG 61.121 63.158 0.00 0.00 0.00 5.28
4111 4219 2.468831 GTGAATTTGCCAACGAAAGCA 58.531 42.857 0.00 0.00 37.18 3.91
4171 4280 1.081242 GGCGTCGTTACCTCGTTCA 60.081 57.895 0.00 0.00 0.00 3.18
4215 4325 0.890996 CCTGTGTGCTCCAGGGAAAC 60.891 60.000 12.76 0.00 44.77 2.78
4235 4374 0.934496 CCTTTTCTGTTCGTGCGTCA 59.066 50.000 0.00 0.00 0.00 4.35
4274 4413 4.042809 TCATCTTTGGGGTTGTACATCAGT 59.957 41.667 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 6.992715 CGGAGGGAGTATGTCTTAATTTGATT 59.007 38.462 0.00 0.00 0.00 2.57
14 15 6.099845 ACGGAGGGAGTATGTCTTAATTTGAT 59.900 38.462 0.00 0.00 0.00 2.57
16 17 5.671493 ACGGAGGGAGTATGTCTTAATTTG 58.329 41.667 0.00 0.00 0.00 2.32
18 19 7.125356 AGTTTACGGAGGGAGTATGTCTTAATT 59.875 37.037 0.00 0.00 0.00 1.40
19 20 6.610425 AGTTTACGGAGGGAGTATGTCTTAAT 59.390 38.462 0.00 0.00 0.00 1.40
20 21 5.954150 AGTTTACGGAGGGAGTATGTCTTAA 59.046 40.000 0.00 0.00 0.00 1.85
21 22 5.513233 AGTTTACGGAGGGAGTATGTCTTA 58.487 41.667 0.00 0.00 0.00 2.10
22 23 4.351127 AGTTTACGGAGGGAGTATGTCTT 58.649 43.478 0.00 0.00 0.00 3.01
23 24 3.978610 AGTTTACGGAGGGAGTATGTCT 58.021 45.455 0.00 0.00 0.00 3.41
24 25 5.841957 TTAGTTTACGGAGGGAGTATGTC 57.158 43.478 0.00 0.00 0.00 3.06
25 26 9.592196 TTATATTAGTTTACGGAGGGAGTATGT 57.408 33.333 0.00 0.00 0.00 2.29
28 29 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
29 30 8.003629 ACTCTTATATTAGTTTACGGAGGGAGT 58.996 37.037 0.00 0.00 0.00 3.85
30 31 8.298140 CACTCTTATATTAGTTTACGGAGGGAG 58.702 40.741 0.00 0.00 0.00 4.30
31 32 7.781693 ACACTCTTATATTAGTTTACGGAGGGA 59.218 37.037 0.00 0.00 0.00 4.20
32 33 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
33 34 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
83 84 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
85 86 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
91 92 9.134055 GAGTGTACTCCCTCTGTAAACTAATAT 57.866 37.037 0.48 0.00 38.25 1.28
92 93 8.517062 GAGTGTACTCCCTCTGTAAACTAATA 57.483 38.462 0.48 0.00 38.25 0.98
93 94 7.407393 GAGTGTACTCCCTCTGTAAACTAAT 57.593 40.000 0.48 0.00 38.25 1.73
94 95 6.830873 GAGTGTACTCCCTCTGTAAACTAA 57.169 41.667 0.48 0.00 38.25 2.24
108 109 4.202233 GCTAATAAGGGTGGGAGTGTACTC 60.202 50.000 3.43 3.43 42.14 2.59
109 110 3.710165 GCTAATAAGGGTGGGAGTGTACT 59.290 47.826 0.00 0.00 0.00 2.73
110 111 3.492137 CGCTAATAAGGGTGGGAGTGTAC 60.492 52.174 0.00 0.00 0.00 2.90
137 138 9.034800 TCCATTTGCTGATTCTAAAATAGGTTT 57.965 29.630 0.00 0.00 0.00 3.27
151 152 9.976511 CACTATTAATTTCATCCATTTGCTGAT 57.023 29.630 0.00 0.00 0.00 2.90
152 153 8.415553 CCACTATTAATTTCATCCATTTGCTGA 58.584 33.333 0.00 0.00 0.00 4.26
155 156 6.930722 CCCCACTATTAATTTCATCCATTTGC 59.069 38.462 0.00 0.00 0.00 3.68
164 165 8.808240 AGATAGTACCCCCACTATTAATTTCA 57.192 34.615 0.00 0.00 40.92 2.69
181 182 7.278203 GGTCTTCCTGCAAAGTTAAGATAGTAC 59.722 40.741 0.00 0.00 0.00 2.73
182 183 7.328737 GGTCTTCCTGCAAAGTTAAGATAGTA 58.671 38.462 0.00 0.00 0.00 1.82
183 184 6.174049 GGTCTTCCTGCAAAGTTAAGATAGT 58.826 40.000 0.00 0.00 0.00 2.12
184 185 5.586643 GGGTCTTCCTGCAAAGTTAAGATAG 59.413 44.000 0.00 0.00 0.00 2.08
393 397 7.693951 CCAGTGTACGTGTAACTACAGTATTAC 59.306 40.741 0.00 6.20 34.57 1.89
394 398 7.626240 GCCAGTGTACGTGTAACTACAGTATTA 60.626 40.741 0.00 0.00 34.57 0.98
399 403 3.240069 GCCAGTGTACGTGTAACTACAG 58.760 50.000 0.00 0.00 36.78 2.74
401 405 3.287312 TGCCAGTGTACGTGTAACTAC 57.713 47.619 0.00 0.00 31.75 2.73
402 406 3.840468 CATGCCAGTGTACGTGTAACTA 58.160 45.455 0.00 0.00 31.75 2.24
403 407 2.683968 CATGCCAGTGTACGTGTAACT 58.316 47.619 0.00 0.00 31.75 2.24
404 408 1.127951 GCATGCCAGTGTACGTGTAAC 59.872 52.381 6.36 0.00 0.00 2.50
405 409 1.270358 TGCATGCCAGTGTACGTGTAA 60.270 47.619 16.68 0.00 0.00 2.41
406 410 0.318762 TGCATGCCAGTGTACGTGTA 59.681 50.000 16.68 0.00 0.00 2.90
456 467 5.248248 TGGTGCTGTAGTGGTGCATATATAT 59.752 40.000 0.00 0.00 39.00 0.86
457 468 4.591072 TGGTGCTGTAGTGGTGCATATATA 59.409 41.667 0.00 0.00 39.00 0.86
458 469 3.390967 TGGTGCTGTAGTGGTGCATATAT 59.609 43.478 0.00 0.00 39.00 0.86
459 470 2.769095 TGGTGCTGTAGTGGTGCATATA 59.231 45.455 0.00 0.00 39.00 0.86
821 839 1.450905 GAGTCTGCGTGTACGTCAAAC 59.549 52.381 6.27 2.42 42.22 2.93
832 850 3.753434 CTGGAGCCGAGTCTGCGT 61.753 66.667 0.50 0.00 0.00 5.24
1233 1262 7.055667 TCAAGAACATTTCTGACTGAGTAGT 57.944 36.000 0.00 0.00 40.59 2.73
1234 1263 6.090628 GCTCAAGAACATTTCTGACTGAGTAG 59.909 42.308 13.69 0.00 40.59 2.57
1260 1289 1.136774 CACTGACGTGCGCTAGCTA 59.863 57.895 13.93 0.00 45.42 3.32
1261 1290 2.126307 CACTGACGTGCGCTAGCT 60.126 61.111 13.93 0.00 45.42 3.32
1358 1391 0.458669 GCTTATGCATGCTGCTTGGT 59.541 50.000 20.33 0.00 45.31 3.67
1393 1432 6.895040 CGCGTATGAAGTCTAGTCAATTTTTC 59.105 38.462 0.00 0.00 0.00 2.29
1394 1433 6.672357 GCGCGTATGAAGTCTAGTCAATTTTT 60.672 38.462 8.43 0.00 0.00 1.94
1459 1499 0.882927 CGAGGAAAAACGCTGGGTGA 60.883 55.000 0.00 0.00 0.00 4.02
1464 1504 0.440371 GCTCTCGAGGAAAAACGCTG 59.560 55.000 13.56 0.00 0.00 5.18
1491 1531 6.753913 TTATCTATGCATGAAGTCCTCCTT 57.246 37.500 10.16 0.00 35.59 3.36
1556 1596 7.820044 TGTGTTCAACCAAAATTTCTACAAC 57.180 32.000 0.00 0.00 0.00 3.32
1595 1635 9.660180 ACAAAGCATGAAGGTTTTAACTTTTAA 57.340 25.926 0.00 0.00 45.06 1.52
1596 1636 9.092876 CACAAAGCATGAAGGTTTTAACTTTTA 57.907 29.630 0.00 0.00 45.06 1.52
1599 1639 6.872920 TCACAAAGCATGAAGGTTTTAACTT 58.127 32.000 0.00 0.00 45.06 2.66
1601 1641 6.701400 ACATCACAAAGCATGAAGGTTTTAAC 59.299 34.615 0.00 0.00 45.06 2.01
1616 1656 5.852738 AATCTTGAGACGACATCACAAAG 57.147 39.130 0.00 0.00 37.44 2.77
1621 1661 7.716612 ACACATATAATCTTGAGACGACATCA 58.283 34.615 0.00 0.00 0.00 3.07
1623 1663 7.148641 GGACACATATAATCTTGAGACGACAT 58.851 38.462 0.00 0.00 0.00 3.06
1764 1804 8.099537 ACCATGCAAACATCCAATTAATTGTTA 58.900 29.630 23.24 13.44 33.23 2.41
1908 1954 5.296748 ACAAATTGAAGGGTGCATGTTAAC 58.703 37.500 0.00 0.00 0.00 2.01
1930 1976 6.362283 CCAAACAAATCGTATCAAAGGACAAC 59.638 38.462 0.00 0.00 0.00 3.32
1936 1982 7.305474 AGCTAACCAAACAAATCGTATCAAAG 58.695 34.615 0.00 0.00 0.00 2.77
1945 1991 6.086871 GTGCTAGAAGCTAACCAAACAAATC 58.913 40.000 0.00 0.00 42.97 2.17
2163 2213 7.736881 ATGCATACATGGAGAGAATAGATCT 57.263 36.000 0.00 0.00 36.62 2.75
2165 2215 8.256605 GTGTATGCATACATGGAGAGAATAGAT 58.743 37.037 35.33 0.00 44.25 1.98
2328 2381 2.896039 AGGCTGAAGAAGTACCACTCT 58.104 47.619 0.00 0.00 0.00 3.24
2355 2408 3.751246 CCGGTCGGGTACTTGCGA 61.751 66.667 0.74 0.00 0.00 5.10
2427 2480 2.684943 TGCCCGGTGAATATCTCCTTA 58.315 47.619 0.00 0.00 0.00 2.69
2457 2510 0.888619 TCCCGACTAGCTCTTGTGTG 59.111 55.000 0.00 0.00 0.00 3.82
2458 2511 1.478510 CATCCCGACTAGCTCTTGTGT 59.521 52.381 0.00 0.00 0.00 3.72
2592 2645 6.091713 GCAAGAAAAATTTGAGGGATGTCATG 59.908 38.462 0.00 0.00 0.00 3.07
2604 2657 9.875675 TTATGAAAATTCCGCAAGAAAAATTTG 57.124 25.926 0.00 0.00 38.21 2.32
2616 2669 3.551485 AGCGCAAATTATGAAAATTCCGC 59.449 39.130 11.47 14.94 38.93 5.54
2618 2671 6.640137 GCTTAGCGCAAATTATGAAAATTCC 58.360 36.000 11.47 0.00 38.92 3.01
2662 2725 9.757227 TCAAGTTAAAATGAAAAATTCGGTCAT 57.243 25.926 0.00 0.00 33.41 3.06
2664 2727 9.843874 GTTCAAGTTAAAATGAAAAATTCGGTC 57.156 29.630 5.92 0.00 37.31 4.79
2667 2730 9.763979 CGAGTTCAAGTTAAAATGAAAAATTCG 57.236 29.630 5.92 8.85 37.31 3.34
2682 2750 9.612620 GAAACATTAATTGATCGAGTTCAAGTT 57.387 29.630 6.99 3.16 38.90 2.66
2696 2764 8.917088 ACCCATTCATCCTAGAAACATTAATTG 58.083 33.333 0.00 0.00 0.00 2.32
2697 2765 8.917088 CACCCATTCATCCTAGAAACATTAATT 58.083 33.333 0.00 0.00 0.00 1.40
2698 2766 7.506938 CCACCCATTCATCCTAGAAACATTAAT 59.493 37.037 0.00 0.00 0.00 1.40
2699 2767 6.833416 CCACCCATTCATCCTAGAAACATTAA 59.167 38.462 0.00 0.00 0.00 1.40
2700 2768 6.069088 ACCACCCATTCATCCTAGAAACATTA 60.069 38.462 0.00 0.00 0.00 1.90
3464 3560 1.375523 GGTCTGTGTACAAGGCGGG 60.376 63.158 0.00 0.00 0.00 6.13
3482 3582 1.127951 CGCAGTTAGGTAAGGCAAACG 59.872 52.381 0.00 0.00 0.00 3.60
3561 3666 4.724697 CTTTGGCACAGACGCGCG 62.725 66.667 30.96 30.96 42.39 6.86
3589 3694 5.611796 TCGATTTCAGAAATCCACAACAG 57.388 39.130 24.39 12.32 43.39 3.16
3592 3697 6.980593 ACAAATCGATTTCAGAAATCCACAA 58.019 32.000 24.39 11.87 43.39 3.33
3641 3746 0.681243 GGTTGTCTCCATTGAGGCCC 60.681 60.000 0.00 0.00 42.81 5.80
3656 3761 1.205893 GAGGGCTCTGTCACTAGGTTG 59.794 57.143 0.00 0.00 0.00 3.77
3913 4019 4.016629 CGTCGTCGACACCGGACA 62.017 66.667 24.13 0.00 39.71 4.02
3920 4026 0.595310 TCAATGTTGCGTCGTCGACA 60.595 50.000 24.13 6.19 39.71 4.35
4057 4163 2.253403 GACCACCGGATCAACCTCCC 62.253 65.000 9.46 0.00 36.31 4.30
4111 4219 0.904865 TCTGTCCGAGGCTGAACCAT 60.905 55.000 0.00 0.00 43.14 3.55
4146 4255 4.362476 GTAACGACGCCCACGGGT 62.362 66.667 3.54 0.00 46.04 5.28
4151 4260 2.476534 GAACGAGGTAACGACGCCCA 62.477 60.000 0.00 0.00 42.87 5.36
4171 4280 1.745827 CGAATCGCCCCATAACACCTT 60.746 52.381 0.00 0.00 0.00 3.50
4212 4322 1.064952 CGCACGAACAGAAAAGGGTTT 59.935 47.619 0.00 0.00 0.00 3.27
4215 4325 0.234884 GACGCACGAACAGAAAAGGG 59.765 55.000 0.00 0.00 0.00 3.95
4223 4344 1.666553 GGGTGATGACGCACGAACA 60.667 57.895 0.00 0.00 39.66 3.18
4274 4413 0.107831 CCAAACACTTGTCCCTCCGA 59.892 55.000 0.00 0.00 0.00 4.55


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

AutoCloner maintained by Alex Coulton.