Multiple sequence alignment - TraesCS3B01G150800

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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 TraesCS3B01G150800 chr3B 100.000 3263 0 0 1 3263 141865427 141862165 0.000000e+00 6026.0
1 TraesCS3B01G150800 chr3B 88.659 1887 188 15 989 2859 141815700 141813824 0.000000e+00 2276.0
2 TraesCS3B01G150800 chr3B 89.534 1051 106 4 988 2036 141752483 141751435 0.000000e+00 1328.0
3 TraesCS3B01G150800 chr3B 98.367 245 3 1 1 244 222147233 222146989 2.330000e-116 429.0
4 TraesCS3B01G150800 chr3B 82.869 467 47 22 298 761 141753072 141752636 3.950000e-104 388.0
5 TraesCS3B01G150800 chr3B 82.121 330 25 19 298 623 141822103 141821804 5.400000e-63 252.0
6 TraesCS3B01G150800 chr3B 91.045 134 9 2 2860 2990 141745279 141745146 9.300000e-41 178.0
7 TraesCS3B01G150800 chr3B 86.325 117 16 0 3146 3262 141813634 141813518 9.500000e-26 128.0
8 TraesCS3B01G150800 chr3B 89.888 89 9 0 3174 3262 180277541 180277629 7.400000e-22 115.0
9 TraesCS3B01G150800 chr3B 100.000 29 0 0 2860 2888 141862597 141862569 2.000000e-03 54.7
10 TraesCS3B01G150800 chr3D 96.750 1969 45 6 894 2859 92360221 92358269 0.000000e+00 3264.0
11 TraesCS3B01G150800 chr3D 95.696 1975 51 11 894 2859 92125326 92123377 0.000000e+00 3145.0
12 TraesCS3B01G150800 chr3D 87.632 1989 201 24 899 2859 91802886 91800915 0.000000e+00 2268.0
13 TraesCS3B01G150800 chr3D 94.712 1286 54 11 1580 2859 92217228 92215951 0.000000e+00 1986.0
14 TraesCS3B01G150800 chr3D 89.308 1590 143 18 899 2463 91833478 91831891 0.000000e+00 1969.0
15 TraesCS3B01G150800 chr3D 89.011 1547 144 17 899 2431 92264255 92262721 0.000000e+00 1892.0
16 TraesCS3B01G150800 chr3D 90.387 697 45 12 899 1585 92223993 92223309 0.000000e+00 896.0
17 TraesCS3B01G150800 chr3D 90.278 576 21 6 246 814 92125870 92125323 0.000000e+00 721.0
18 TraesCS3B01G150800 chr3D 98.272 405 4 2 2860 3262 92123405 92123002 0.000000e+00 706.0
19 TraesCS3B01G150800 chr3D 96.368 413 4 4 2860 3262 92358297 92357886 0.000000e+00 669.0
20 TraesCS3B01G150800 chr3D 87.500 384 45 2 2478 2859 91831621 91831239 1.070000e-119 440.0
21 TraesCS3B01G150800 chr3D 88.398 362 38 3 2500 2859 92262451 92262092 1.800000e-117 433.0
22 TraesCS3B01G150800 chr3D 88.316 291 21 8 472 761 92224316 92224038 1.450000e-88 337.0
23 TraesCS3B01G150800 chr3D 96.000 175 7 0 290 464 92360601 92360427 5.330000e-73 285.0
24 TraesCS3B01G150800 chr3D 96.753 154 5 0 568 721 92360389 92360236 1.160000e-64 257.0
25 TraesCS3B01G150800 chr3D 76.112 427 63 24 330 739 91803916 91803512 1.550000e-43 187.0
26 TraesCS3B01G150800 chr3D 91.045 134 9 2 2860 2990 91800943 91800810 9.300000e-41 178.0
27 TraesCS3B01G150800 chr3D 85.841 113 16 0 3146 3258 91800811 91800699 1.590000e-23 121.0
28 TraesCS3B01G150800 chr3D 92.857 70 5 0 292 361 92128490 92128421 5.760000e-18 102.0
29 TraesCS3B01G150800 chr3D 96.721 61 2 0 2860 2920 92215979 92215919 5.760000e-18 102.0
30 TraesCS3B01G150800 chr3D 93.023 43 1 2 426 466 91803686 91803644 9.780000e-06 62.1
31 TraesCS3B01G150800 chr3D 100.000 28 0 0 502 529 92360420 92360393 6.000000e-03 52.8
32 TraesCS3B01G150800 chr3A 87.755 1568 159 17 897 2445 545358703 545357150 0.000000e+00 1801.0
33 TraesCS3B01G150800 chr3A 94.326 1075 47 11 1790 2859 545891148 545890083 0.000000e+00 1635.0
34 TraesCS3B01G150800 chr3A 90.257 1129 106 4 894 2020 545892277 545891151 0.000000e+00 1472.0
35 TraesCS3B01G150800 chr3A 86.651 1296 145 17 1436 2707 545364841 545363550 0.000000e+00 1410.0
36 TraesCS3B01G150800 chr3A 91.461 445 36 2 996 1439 545366772 545366329 7.740000e-171 610.0
37 TraesCS3B01G150800 chr3A 92.506 387 27 2 2475 2859 545357155 545356769 1.320000e-153 553.0
38 TraesCS3B01G150800 chr3A 99.180 244 2 0 1 244 580560375 580560618 1.070000e-119 440.0
39 TraesCS3B01G150800 chr3A 98.770 244 3 0 1 244 431863503 431863260 5.000000e-118 435.0
40 TraesCS3B01G150800 chr3A 84.483 464 46 19 298 761 545359152 545358715 5.000000e-118 435.0
41 TraesCS3B01G150800 chr3A 97.959 245 4 1 1 245 492035238 492035481 1.080000e-114 424.0
42 TraesCS3B01G150800 chr3A 95.816 239 10 0 576 814 545892512 545892274 1.420000e-103 387.0
43 TraesCS3B01G150800 chr3A 86.325 117 16 0 3146 3262 545356665 545356549 9.500000e-26 128.0
44 TraesCS3B01G150800 chr3A 90.244 82 7 1 3174 3254 521717212 521717293 4.450000e-19 106.0
45 TraesCS3B01G150800 chr3A 96.721 61 2 0 2860 2920 545890111 545890051 5.760000e-18 102.0
46 TraesCS3B01G150800 chr5B 98.367 245 3 1 1 244 72093375 72093619 2.330000e-116 429.0
47 TraesCS3B01G150800 chr5B 97.959 245 5 0 1 245 700230505 700230261 3.010000e-115 425.0
48 TraesCS3B01G150800 chr5B 94.079 152 7 1 2989 3140 665744469 665744618 2.530000e-56 230.0
49 TraesCS3B01G150800 chr5B 96.774 93 3 0 813 905 557898140 557898048 4.360000e-34 156.0
50 TraesCS3B01G150800 chr4A 98.367 245 3 1 1 244 674355679 674355435 2.330000e-116 429.0
51 TraesCS3B01G150800 chr2B 98.361 244 4 0 1 244 676743182 676743425 2.330000e-116 429.0
52 TraesCS3B01G150800 chr2B 88.764 89 10 0 3174 3262 399342041 399342129 3.440000e-20 110.0
53 TraesCS3B01G150800 chr2A 98.361 244 4 0 1 244 25350837 25350594 2.330000e-116 429.0
54 TraesCS3B01G150800 chr2A 90.960 177 12 4 2978 3150 79315991 79316167 5.440000e-58 235.0
55 TraesCS3B01G150800 chr2A 95.789 95 4 0 812 906 102029076 102029170 1.570000e-33 154.0
56 TraesCS3B01G150800 chr2D 92.216 167 11 2 2986 3150 79056163 79056329 5.440000e-58 235.0
57 TraesCS3B01G150800 chr2D 95.050 101 4 1 801 900 37535482 37535582 1.210000e-34 158.0
58 TraesCS3B01G150800 chr2D 94.118 102 6 0 812 913 650861479 650861378 4.360000e-34 156.0
59 TraesCS3B01G150800 chr4D 94.118 153 8 1 2989 3140 74079351 74079503 7.040000e-57 231.0
60 TraesCS3B01G150800 chr5D 94.079 152 7 1 2989 3140 528717278 528717427 2.530000e-56 230.0
61 TraesCS3B01G150800 chr5A 94.079 152 7 1 2989 3140 656872285 656872434 2.530000e-56 230.0
62 TraesCS3B01G150800 chr5A 100.000 86 0 0 812 897 272591146 272591231 3.370000e-35 159.0
63 TraesCS3B01G150800 chr5A 96.703 91 2 1 807 897 641680764 641680853 2.030000e-32 150.0
64 TraesCS3B01G150800 chr7B 92.453 159 11 1 2989 3146 505937314 505937472 3.280000e-55 226.0
65 TraesCS3B01G150800 chr7B 94.059 101 4 2 800 900 719465194 719465292 5.640000e-33 152.0
66 TraesCS3B01G150800 chrUn 82.234 197 20 12 358 540 2231128 2230933 4.360000e-34 156.0
67 TraesCS3B01G150800 chr7A 96.809 94 1 2 804 897 41963064 41963155 4.360000e-34 156.0
68 TraesCS3B01G150800 chr1B 95.789 95 2 2 803 897 654313567 654313659 5.640000e-33 152.0
69 TraesCS3B01G150800 chr1B 82.011 189 17 11 334 514 681695428 681695249 9.440000e-31 145.0
70 TraesCS3B01G150800 chr1D 88.430 121 10 3 398 514 488567945 488568065 3.390000e-30 143.0
71 TraesCS3B01G150800 chr7D 81.098 164 13 11 397 554 571253168 571253319 7.400000e-22 115.0
72 TraesCS3B01G150800 chr6D 87.640 89 11 0 3174 3262 126868486 126868574 1.600000e-18 104.0


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 TraesCS3B01G150800 chr3B 141862165 141865427 3262 True 3040.35 6026 100.00000 1 3263 2 chr3B.!!$R6 3262
1 TraesCS3B01G150800 chr3B 141813518 141815700 2182 True 1202.00 2276 87.49200 989 3262 2 chr3B.!!$R5 2273
2 TraesCS3B01G150800 chr3B 141751435 141753072 1637 True 858.00 1328 86.20150 298 2036 2 chr3B.!!$R4 1738
3 TraesCS3B01G150800 chr3D 91831239 91833478 2239 True 1204.50 1969 88.40400 899 2859 2 chr3D.!!$R2 1960
4 TraesCS3B01G150800 chr3D 92123002 92128490 5488 True 1168.50 3145 94.27575 246 3262 4 chr3D.!!$R3 3016
5 TraesCS3B01G150800 chr3D 92262092 92264255 2163 True 1162.50 1892 88.70450 899 2859 2 chr3D.!!$R6 1960
6 TraesCS3B01G150800 chr3D 92215919 92217228 1309 True 1044.00 1986 95.71650 1580 2920 2 chr3D.!!$R4 1340
7 TraesCS3B01G150800 chr3D 92357886 92360601 2715 True 905.56 3264 97.17420 290 3262 5 chr3D.!!$R7 2972
8 TraesCS3B01G150800 chr3D 92223309 92224316 1007 True 616.50 896 89.35150 472 1585 2 chr3D.!!$R5 1113
9 TraesCS3B01G150800 chr3D 91800699 91803916 3217 True 563.22 2268 86.73060 330 3258 5 chr3D.!!$R1 2928
10 TraesCS3B01G150800 chr3A 545363550 545366772 3222 True 1010.00 1410 89.05600 996 2707 2 chr3A.!!$R3 1711
11 TraesCS3B01G150800 chr3A 545890051 545892512 2461 True 899.00 1635 94.28000 576 2920 4 chr3A.!!$R4 2344
12 TraesCS3B01G150800 chr3A 545356549 545359152 2603 True 729.25 1801 87.76725 298 3262 4 chr3A.!!$R2 2964

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
563 2968 0.107459 GAATCCCCAGTCAGCCAGTC 60.107 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2546 7826 1.878953 AAACAAGGCAGTACTCGGTG 58.121 50.0 0.0 0.0 0.0 4.94 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
20 21 3.520290 GGCCAACAGGTAAAAATAGGC 57.480 47.619 0.00 0.00 40.08 3.93
21 22 3.096852 GGCCAACAGGTAAAAATAGGCT 58.903 45.455 0.00 0.00 40.61 4.58
22 23 4.274978 GGCCAACAGGTAAAAATAGGCTA 58.725 43.478 0.00 0.00 40.61 3.93
23 24 4.707934 GGCCAACAGGTAAAAATAGGCTAA 59.292 41.667 0.00 0.00 40.61 3.09
25 26 6.295405 GGCCAACAGGTAAAAATAGGCTAAAA 60.295 38.462 0.00 0.00 40.61 1.52
26 27 7.156000 GCCAACAGGTAAAAATAGGCTAAAAA 58.844 34.615 0.00 0.00 37.89 1.94
27 28 7.117236 GCCAACAGGTAAAAATAGGCTAAAAAC 59.883 37.037 0.00 0.00 37.89 2.43
28 29 7.327518 CCAACAGGTAAAAATAGGCTAAAAACG 59.672 37.037 0.00 0.00 0.00 3.60
30 31 6.208007 ACAGGTAAAAATAGGCTAAAAACGCT 59.792 34.615 0.00 0.00 0.00 5.07
32 33 6.431852 AGGTAAAAATAGGCTAAAAACGCTCA 59.568 34.615 0.00 0.00 0.00 4.26
33 34 7.040271 AGGTAAAAATAGGCTAAAAACGCTCAA 60.040 33.333 0.00 0.00 0.00 3.02
35 36 7.581011 AAAAATAGGCTAAAAACGCTCAATG 57.419 32.000 0.00 0.00 0.00 2.82
48 49 2.724349 GCTCAATGCGCAAAATAGGAG 58.276 47.619 17.11 15.51 0.00 3.69
49 50 2.542411 GCTCAATGCGCAAAATAGGAGG 60.542 50.000 17.11 0.00 0.00 4.30
50 51 2.684881 CTCAATGCGCAAAATAGGAGGT 59.315 45.455 17.11 0.00 0.00 3.85
51 52 3.876914 CTCAATGCGCAAAATAGGAGGTA 59.123 43.478 17.11 0.00 0.00 3.08
52 53 3.876914 TCAATGCGCAAAATAGGAGGTAG 59.123 43.478 17.11 0.00 0.00 3.18
53 54 3.838244 ATGCGCAAAATAGGAGGTAGA 57.162 42.857 17.11 0.00 0.00 2.59
54 55 3.838244 TGCGCAAAATAGGAGGTAGAT 57.162 42.857 8.16 0.00 0.00 1.98
55 56 4.150897 TGCGCAAAATAGGAGGTAGATT 57.849 40.909 8.16 0.00 0.00 2.40
58 59 5.163343 TGCGCAAAATAGGAGGTAGATTAGT 60.163 40.000 8.16 0.00 0.00 2.24
59 60 5.177696 GCGCAAAATAGGAGGTAGATTAGTG 59.822 44.000 0.30 0.00 0.00 2.74
60 61 5.696724 CGCAAAATAGGAGGTAGATTAGTGG 59.303 44.000 0.00 0.00 0.00 4.00
61 62 5.998363 GCAAAATAGGAGGTAGATTAGTGGG 59.002 44.000 0.00 0.00 0.00 4.61
62 63 5.827326 AAATAGGAGGTAGATTAGTGGGC 57.173 43.478 0.00 0.00 0.00 5.36
63 64 2.104669 AGGAGGTAGATTAGTGGGCC 57.895 55.000 0.00 0.00 0.00 5.80
64 65 1.581149 AGGAGGTAGATTAGTGGGCCT 59.419 52.381 4.53 0.00 0.00 5.19
65 66 1.694696 GGAGGTAGATTAGTGGGCCTG 59.305 57.143 4.53 0.00 0.00 4.85
66 67 1.694696 GAGGTAGATTAGTGGGCCTGG 59.305 57.143 4.53 0.00 0.00 4.45
68 69 0.249911 GTAGATTAGTGGGCCTGGCG 60.250 60.000 13.40 0.00 0.00 5.69
69 70 0.689745 TAGATTAGTGGGCCTGGCGT 60.690 55.000 13.40 0.00 0.00 5.68
70 71 1.819632 GATTAGTGGGCCTGGCGTG 60.820 63.158 13.40 0.00 0.00 5.34
94 95 4.643387 GGCCGGCCCGATTAGCAT 62.643 66.667 36.64 0.00 0.00 3.79
95 96 2.345991 GCCGGCCCGATTAGCATA 59.654 61.111 18.11 0.00 0.00 3.14
96 97 2.033194 GCCGGCCCGATTAGCATAC 61.033 63.158 18.11 0.00 0.00 2.39
97 98 1.736645 CCGGCCCGATTAGCATACG 60.737 63.158 3.71 0.00 0.00 3.06
98 99 1.736645 CGGCCCGATTAGCATACGG 60.737 63.158 0.00 0.00 45.24 4.02
101 102 4.278956 CCGATTAGCATACGGGCC 57.721 61.111 0.00 0.00 42.48 5.80
102 103 1.736645 CCGATTAGCATACGGGCCG 60.737 63.158 27.06 27.06 42.48 6.13
103 104 1.006571 CGATTAGCATACGGGCCGT 60.007 57.895 35.91 35.91 44.35 5.68
104 105 1.282248 CGATTAGCATACGGGCCGTG 61.282 60.000 39.80 25.77 41.39 4.94
105 106 1.566018 GATTAGCATACGGGCCGTGC 61.566 60.000 39.80 33.49 41.39 5.34
159 160 2.004733 GGCACGGCCCGTATAATAATC 58.995 52.381 9.25 0.00 44.06 1.75
162 163 2.664568 CACGGCCCGTATAATAATCGTG 59.335 50.000 9.25 0.00 38.32 4.35
164 165 2.004733 GGCCCGTATAATAATCGTGCC 58.995 52.381 0.00 0.00 40.23 5.01
166 167 3.119029 GGCCCGTATAATAATCGTGCCTA 60.119 47.826 0.00 0.00 42.74 3.93
167 168 4.110482 GCCCGTATAATAATCGTGCCTAG 58.890 47.826 0.00 0.00 0.00 3.02
168 169 4.679662 CCCGTATAATAATCGTGCCTAGG 58.320 47.826 3.67 3.67 0.00 3.02
169 170 4.110482 CCGTATAATAATCGTGCCTAGGC 58.890 47.826 27.71 27.71 42.35 3.93
171 172 2.736144 TAATAATCGTGCCTAGGCGG 57.264 50.000 28.28 21.97 45.51 6.13
199 200 1.451936 GGCCAGGCACGATTAGGAT 59.548 57.895 15.19 0.00 0.00 3.24
201 202 0.886490 GCCAGGCACGATTAGGATGG 60.886 60.000 6.55 0.00 0.00 3.51
202 203 0.250467 CCAGGCACGATTAGGATGGG 60.250 60.000 0.00 0.00 0.00 4.00
203 204 0.886490 CAGGCACGATTAGGATGGGC 60.886 60.000 0.00 0.00 0.00 5.36
204 205 1.600916 GGCACGATTAGGATGGGCC 60.601 63.158 0.00 0.00 0.00 5.80
205 206 1.961277 GCACGATTAGGATGGGCCG 60.961 63.158 0.00 0.00 43.43 6.13
207 208 0.880278 CACGATTAGGATGGGCCGTG 60.880 60.000 1.02 0.00 43.43 4.94
244 245 3.513225 CCCGTTTGGCCAGCTATG 58.487 61.111 5.11 0.95 0.00 2.23
245 246 2.774799 CCCGTTTGGCCAGCTATGC 61.775 63.158 5.11 0.00 0.00 3.14
246 247 2.404789 CGTTTGGCCAGCTATGCG 59.595 61.111 5.11 1.87 0.00 4.73
248 249 1.429423 GTTTGGCCAGCTATGCGTC 59.571 57.895 5.11 0.00 0.00 5.19
249 250 2.106074 TTTGGCCAGCTATGCGTCG 61.106 57.895 5.11 0.00 0.00 5.12
266 2642 1.820056 CGGAGGCGAGACTGAGCTA 60.820 63.158 0.00 0.00 0.00 3.32
268 2644 1.730451 GGAGGCGAGACTGAGCTACC 61.730 65.000 0.00 1.38 0.00 3.18
280 2656 3.138798 GCTACCTCTCGCCACGGA 61.139 66.667 0.00 0.00 0.00 4.69
370 2747 1.534235 ACAACCCTCGTGCTCCTCT 60.534 57.895 0.00 0.00 0.00 3.69
556 2961 2.690881 CCCCCGAATCCCCAGTCA 60.691 66.667 0.00 0.00 0.00 3.41
559 2964 2.190578 CCGAATCCCCAGTCAGCC 59.809 66.667 0.00 0.00 0.00 4.85
560 2965 2.669133 CCGAATCCCCAGTCAGCCA 61.669 63.158 0.00 0.00 0.00 4.75
561 2966 1.153289 CGAATCCCCAGTCAGCCAG 60.153 63.158 0.00 0.00 0.00 4.85
562 2967 1.903877 CGAATCCCCAGTCAGCCAGT 61.904 60.000 0.00 0.00 0.00 4.00
563 2968 0.107459 GAATCCCCAGTCAGCCAGTC 60.107 60.000 0.00 0.00 0.00 3.51
814 3810 4.022242 TCTGAAAGTCCTAGTGCACAGTAC 60.022 45.833 21.04 11.22 33.76 2.73
815 3811 3.895656 TGAAAGTCCTAGTGCACAGTACT 59.104 43.478 21.04 13.25 0.00 2.73
816 3812 5.074804 TGAAAGTCCTAGTGCACAGTACTA 58.925 41.667 21.04 0.66 0.00 1.82
817 3813 5.048224 TGAAAGTCCTAGTGCACAGTACTAC 60.048 44.000 21.04 13.26 0.00 2.73
818 3814 3.354467 AGTCCTAGTGCACAGTACTACC 58.646 50.000 21.04 0.00 0.00 3.18
819 3815 3.010361 AGTCCTAGTGCACAGTACTACCT 59.990 47.826 21.04 1.12 0.00 3.08
820 3816 3.377798 GTCCTAGTGCACAGTACTACCTC 59.622 52.174 21.04 0.00 0.00 3.85
821 3817 3.266254 TCCTAGTGCACAGTACTACCTCT 59.734 47.826 21.04 0.00 0.00 3.69
822 3818 3.378742 CCTAGTGCACAGTACTACCTCTG 59.621 52.174 21.04 0.00 37.65 3.35
823 3819 2.877866 AGTGCACAGTACTACCTCTGT 58.122 47.619 21.04 0.00 44.32 3.41
824 3820 4.030314 AGTGCACAGTACTACCTCTGTA 57.970 45.455 21.04 0.00 42.05 2.74
825 3821 4.404640 AGTGCACAGTACTACCTCTGTAA 58.595 43.478 21.04 0.00 42.05 2.41
826 3822 4.831155 AGTGCACAGTACTACCTCTGTAAA 59.169 41.667 21.04 0.00 42.05 2.01
827 3823 4.922103 GTGCACAGTACTACCTCTGTAAAC 59.078 45.833 13.17 0.00 42.05 2.01
828 3824 4.831155 TGCACAGTACTACCTCTGTAAACT 59.169 41.667 0.00 0.00 42.05 2.66
829 3825 6.005823 TGCACAGTACTACCTCTGTAAACTA 58.994 40.000 0.00 0.00 42.05 2.24
830 3826 6.491062 TGCACAGTACTACCTCTGTAAACTAA 59.509 38.462 0.00 0.00 42.05 2.24
831 3827 7.177921 TGCACAGTACTACCTCTGTAAACTAAT 59.822 37.037 0.00 0.00 42.05 1.73
832 3828 8.680903 GCACAGTACTACCTCTGTAAACTAATA 58.319 37.037 0.00 0.00 42.05 0.98
840 3836 9.828852 CTACCTCTGTAAACTAATATAAGAGCG 57.171 37.037 0.00 0.00 0.00 5.03
841 3837 8.235359 ACCTCTGTAAACTAATATAAGAGCGT 57.765 34.615 0.00 0.00 0.00 5.07
842 3838 8.693625 ACCTCTGTAAACTAATATAAGAGCGTT 58.306 33.333 0.00 0.00 0.00 4.84
843 3839 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
891 3887 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
892 3888 7.949434 ACACTCTTATATTAGTTTACGGAGGG 58.051 38.462 0.00 0.00 0.00 4.30
893 3889 7.781693 ACACTCTTATATTAGTTTACGGAGGGA 59.218 37.037 0.00 0.00 0.00 4.20
894 3890 8.298140 CACTCTTATATTAGTTTACGGAGGGAG 58.702 40.741 0.00 0.00 0.00 4.30
895 3891 8.003629 ACTCTTATATTAGTTTACGGAGGGAGT 58.996 37.037 0.00 0.00 0.00 3.85
896 3892 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
1008 4053 4.952262 TCTGCAAAAATCGATGGAGAAG 57.048 40.909 5.59 0.00 40.44 2.85
1019 4064 2.093764 CGATGGAGAAGGCTTCTGTTCT 60.094 50.000 33.05 14.97 40.87 3.01
1069 4114 1.067295 TGATTGGTCCCAGCTTCAGT 58.933 50.000 0.00 0.00 0.00 3.41
1267 4312 1.016627 CCTGCATAACATGTCCACCG 58.983 55.000 0.00 0.00 0.00 4.94
1556 6094 4.326826 CATCTTACACTTGAAGAAGCCCA 58.673 43.478 0.00 0.00 36.54 5.36
1764 6302 3.357166 TTGTTTTATGGTGTTCGTGGC 57.643 42.857 0.00 0.00 0.00 5.01
2349 7146 9.429109 TGGGTATCTATTCATGTTCTGTAGTTA 57.571 33.333 0.00 0.00 0.00 2.24
2396 7193 4.703575 CACAAGTGATCATGTTTCCTCCAT 59.296 41.667 0.00 0.00 0.00 3.41
2397 7194 4.703575 ACAAGTGATCATGTTTCCTCCATG 59.296 41.667 0.00 0.00 40.82 3.66
2398 7195 4.581309 AGTGATCATGTTTCCTCCATGT 57.419 40.909 0.00 0.00 40.43 3.21
2546 7826 3.414549 TGTTTTCAAGGAACACGCTTC 57.585 42.857 0.00 0.00 32.44 3.86
2647 7936 8.576442 GCTTAGCCTTTTATGCTTATTATGGAA 58.424 33.333 0.00 0.00 40.23 3.53
2858 8148 9.608718 ATTATCTCTTTCCTAAGGTACTAGCAT 57.391 33.333 0.00 0.00 38.49 3.79
2859 8149 7.922699 ATCTCTTTCCTAAGGTACTAGCATT 57.077 36.000 0.00 0.00 38.49 3.56
2860 8150 7.735326 TCTCTTTCCTAAGGTACTAGCATTT 57.265 36.000 0.00 0.00 38.49 2.32
2861 8151 8.834004 TCTCTTTCCTAAGGTACTAGCATTTA 57.166 34.615 0.00 0.00 38.49 1.40
2862 8152 9.435570 TCTCTTTCCTAAGGTACTAGCATTTAT 57.564 33.333 0.00 0.00 38.49 1.40
3209 8509 5.529289 ACCATGACTAGGTTTGGAGATCTA 58.471 41.667 12.46 0.00 35.33 1.98
3262 8562 1.627864 TGGGGCTAAAAGGCTTTGTC 58.372 50.000 14.19 3.14 41.09 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.096852 AGCCTATTTTTACCTGTTGGCC 58.903 45.455 0.00 0.00 39.90 5.36
1 2 5.907866 TTAGCCTATTTTTACCTGTTGGC 57.092 39.130 0.00 0.00 39.40 4.52
4 5 6.864685 GCGTTTTTAGCCTATTTTTACCTGTT 59.135 34.615 0.00 0.00 0.00 3.16
5 6 6.208007 AGCGTTTTTAGCCTATTTTTACCTGT 59.792 34.615 0.00 0.00 34.64 4.00
7 8 6.431852 TGAGCGTTTTTAGCCTATTTTTACCT 59.568 34.615 0.00 0.00 34.64 3.08
8 9 6.614160 TGAGCGTTTTTAGCCTATTTTTACC 58.386 36.000 0.00 0.00 34.64 2.85
9 10 8.583765 CATTGAGCGTTTTTAGCCTATTTTTAC 58.416 33.333 0.00 0.00 34.64 2.01
10 11 7.274686 GCATTGAGCGTTTTTAGCCTATTTTTA 59.725 33.333 0.00 0.00 34.64 1.52
11 12 6.090763 GCATTGAGCGTTTTTAGCCTATTTTT 59.909 34.615 0.00 0.00 34.64 1.94
12 13 5.576774 GCATTGAGCGTTTTTAGCCTATTTT 59.423 36.000 0.00 0.00 34.64 1.82
15 16 4.292977 GCATTGAGCGTTTTTAGCCTAT 57.707 40.909 0.00 0.00 34.64 2.57
16 17 3.757745 GCATTGAGCGTTTTTAGCCTA 57.242 42.857 0.00 0.00 34.64 3.93
17 18 2.636768 GCATTGAGCGTTTTTAGCCT 57.363 45.000 0.00 0.00 34.64 4.58
28 29 2.542411 CCTCCTATTTTGCGCATTGAGC 60.542 50.000 12.75 5.34 40.87 4.26
30 31 2.722094 ACCTCCTATTTTGCGCATTGA 58.278 42.857 12.75 0.00 0.00 2.57
32 33 4.150897 TCTACCTCCTATTTTGCGCATT 57.849 40.909 12.75 1.44 0.00 3.56
33 34 3.838244 TCTACCTCCTATTTTGCGCAT 57.162 42.857 12.75 0.00 0.00 4.73
35 36 5.177696 CACTAATCTACCTCCTATTTTGCGC 59.822 44.000 0.00 0.00 0.00 6.09
37 38 5.998363 CCCACTAATCTACCTCCTATTTTGC 59.002 44.000 0.00 0.00 0.00 3.68
38 39 5.998363 GCCCACTAATCTACCTCCTATTTTG 59.002 44.000 0.00 0.00 0.00 2.44
39 40 5.073280 GGCCCACTAATCTACCTCCTATTTT 59.927 44.000 0.00 0.00 0.00 1.82
40 41 4.597940 GGCCCACTAATCTACCTCCTATTT 59.402 45.833 0.00 0.00 0.00 1.40
42 43 3.406498 AGGCCCACTAATCTACCTCCTAT 59.594 47.826 0.00 0.00 0.00 2.57
43 44 2.795960 AGGCCCACTAATCTACCTCCTA 59.204 50.000 0.00 0.00 0.00 2.94
44 45 1.581149 AGGCCCACTAATCTACCTCCT 59.419 52.381 0.00 0.00 0.00 3.69
45 46 1.694696 CAGGCCCACTAATCTACCTCC 59.305 57.143 0.00 0.00 0.00 4.30
46 47 1.694696 CCAGGCCCACTAATCTACCTC 59.305 57.143 0.00 0.00 0.00 3.85
48 49 0.108774 GCCAGGCCCACTAATCTACC 59.891 60.000 0.00 0.00 0.00 3.18
49 50 0.249911 CGCCAGGCCCACTAATCTAC 60.250 60.000 5.63 0.00 0.00 2.59
50 51 0.689745 ACGCCAGGCCCACTAATCTA 60.690 55.000 5.63 0.00 0.00 1.98
51 52 1.995626 ACGCCAGGCCCACTAATCT 60.996 57.895 5.63 0.00 0.00 2.40
52 53 1.819632 CACGCCAGGCCCACTAATC 60.820 63.158 5.63 0.00 0.00 1.75
53 54 2.272146 CACGCCAGGCCCACTAAT 59.728 61.111 5.63 0.00 0.00 1.73
54 55 4.715523 GCACGCCAGGCCCACTAA 62.716 66.667 5.63 0.00 0.00 2.24
77 78 3.248446 TATGCTAATCGGGCCGGCC 62.248 63.158 38.57 38.57 0.00 6.13
79 80 1.736645 CGTATGCTAATCGGGCCGG 60.737 63.158 27.98 11.17 0.00 6.13
80 81 1.736645 CCGTATGCTAATCGGGCCG 60.737 63.158 22.51 22.51 40.49 6.13
81 82 4.278956 CCGTATGCTAATCGGGCC 57.721 61.111 0.00 0.00 40.49 5.80
84 85 1.736645 CGGCCCGTATGCTAATCGG 60.737 63.158 0.00 0.00 43.30 4.18
85 86 1.006571 ACGGCCCGTATGCTAATCG 60.007 57.895 7.20 0.00 38.73 3.34
86 87 1.566018 GCACGGCCCGTATGCTAATC 61.566 60.000 9.25 0.00 38.32 1.75
87 88 1.597027 GCACGGCCCGTATGCTAAT 60.597 57.895 9.25 0.00 38.32 1.73
141 142 2.664568 CACGATTATTATACGGGCCGTG 59.335 50.000 39.80 22.32 41.39 4.94
146 147 4.679662 CCTAGGCACGATTATTATACGGG 58.320 47.826 0.00 0.00 0.00 5.28
147 148 4.110482 GCCTAGGCACGATTATTATACGG 58.890 47.826 29.33 0.00 41.49 4.02
149 150 4.110482 CCGCCTAGGCACGATTATTATAC 58.890 47.826 32.47 0.00 42.06 1.47
151 152 2.093658 CCCGCCTAGGCACGATTATTAT 60.094 50.000 32.47 0.00 42.06 1.28
152 153 1.274167 CCCGCCTAGGCACGATTATTA 59.726 52.381 32.47 0.00 42.06 0.98
154 155 1.671742 CCCGCCTAGGCACGATTAT 59.328 57.895 32.47 0.00 42.06 1.28
178 179 4.169696 TAATCGTGCCTGGCCCGG 62.170 66.667 22.84 9.24 0.00 5.73
179 180 2.588877 CTAATCGTGCCTGGCCCG 60.589 66.667 17.67 17.67 0.00 6.13
180 181 2.056906 ATCCTAATCGTGCCTGGCCC 62.057 60.000 17.53 2.94 0.00 5.80
181 182 0.886490 CATCCTAATCGTGCCTGGCC 60.886 60.000 17.53 6.66 0.00 5.36
182 183 0.886490 CCATCCTAATCGTGCCTGGC 60.886 60.000 12.87 12.87 0.00 4.85
184 185 0.886490 GCCCATCCTAATCGTGCCTG 60.886 60.000 0.00 0.00 0.00 4.85
186 187 1.600916 GGCCCATCCTAATCGTGCC 60.601 63.158 0.00 0.00 0.00 5.01
187 188 1.961277 CGGCCCATCCTAATCGTGC 60.961 63.158 0.00 0.00 0.00 5.34
188 189 0.880278 CACGGCCCATCCTAATCGTG 60.880 60.000 0.00 0.00 41.09 4.35
189 190 1.445942 CACGGCCCATCCTAATCGT 59.554 57.895 0.00 0.00 0.00 3.73
191 192 1.600916 GGCACGGCCCATCCTAATC 60.601 63.158 0.00 0.00 44.06 1.75
227 228 2.774799 GCATAGCTGGCCAAACGGG 61.775 63.158 7.01 0.00 40.85 5.28
229 230 2.309764 GACGCATAGCTGGCCAAACG 62.310 60.000 7.01 7.03 0.00 3.60
231 232 2.106074 CGACGCATAGCTGGCCAAA 61.106 57.895 7.01 0.00 0.00 3.28
234 235 4.221422 TCCGACGCATAGCTGGCC 62.221 66.667 0.00 0.00 0.00 5.36
237 238 2.659897 GCCTCCGACGCATAGCTG 60.660 66.667 0.00 0.00 0.00 4.24
244 245 4.838486 CAGTCTCGCCTCCGACGC 62.838 72.222 0.00 0.00 38.82 5.19
245 246 3.102107 CTCAGTCTCGCCTCCGACG 62.102 68.421 0.00 0.00 38.82 5.12
246 247 2.795297 CTCAGTCTCGCCTCCGAC 59.205 66.667 0.00 0.00 38.82 4.79
248 249 1.820056 TAGCTCAGTCTCGCCTCCG 60.820 63.158 0.00 0.00 0.00 4.63
249 250 1.730451 GGTAGCTCAGTCTCGCCTCC 61.730 65.000 0.00 0.00 0.00 4.30
280 2656 1.095600 TCGCAAGAGCTATGTCTCGT 58.904 50.000 0.00 0.00 45.01 4.18
321 2697 1.219393 GTGGAGGTGGTAGCAGAGC 59.781 63.158 0.00 0.00 0.00 4.09
402 2799 0.874175 CGAGTTTCACGTGCTCACCA 60.874 55.000 11.67 0.00 0.00 4.17
556 2961 2.741145 CTGAACCCTACTAGACTGGCT 58.259 52.381 0.00 0.00 0.00 4.75
559 2964 2.691011 GGAGCTGAACCCTACTAGACTG 59.309 54.545 0.00 0.00 0.00 3.51
560 2965 2.358405 GGGAGCTGAACCCTACTAGACT 60.358 54.545 0.00 0.00 43.65 3.24
561 2966 2.033372 GGGAGCTGAACCCTACTAGAC 58.967 57.143 0.00 0.00 43.65 2.59
562 2967 1.409802 CGGGAGCTGAACCCTACTAGA 60.410 57.143 7.35 0.00 44.72 2.43
563 2968 1.033574 CGGGAGCTGAACCCTACTAG 58.966 60.000 7.35 0.00 44.72 2.57
725 3146 4.027782 ACCTAGGAATCCTCCCAGAAAT 57.972 45.455 17.98 0.00 43.64 2.17
814 3810 9.828852 CGCTCTTATATTAGTTTACAGAGGTAG 57.171 37.037 0.00 0.00 0.00 3.18
815 3811 9.347240 ACGCTCTTATATTAGTTTACAGAGGTA 57.653 33.333 0.00 0.00 0.00 3.08
816 3812 8.235359 ACGCTCTTATATTAGTTTACAGAGGT 57.765 34.615 0.00 0.00 0.00 3.85
817 3813 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
865 3861 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
866 3862 8.419442 CCCTCCGTAAACTAATATAAGAGTGTT 58.581 37.037 0.00 0.00 0.00 3.32
867 3863 7.781693 TCCCTCCGTAAACTAATATAAGAGTGT 59.218 37.037 0.00 0.00 0.00 3.55
868 3864 8.174733 TCCCTCCGTAAACTAATATAAGAGTG 57.825 38.462 0.00 0.00 0.00 3.51
869 3865 8.003629 ACTCCCTCCGTAAACTAATATAAGAGT 58.996 37.037 0.00 0.00 0.00 3.24
870 3866 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
875 3871 9.377238 AGAAATACTCCCTCCGTAAACTAATAT 57.623 33.333 0.00 0.00 0.00 1.28
876 3872 8.636213 CAGAAATACTCCCTCCGTAAACTAATA 58.364 37.037 0.00 0.00 0.00 0.98
877 3873 7.343833 TCAGAAATACTCCCTCCGTAAACTAAT 59.656 37.037 0.00 0.00 0.00 1.73
878 3874 6.664816 TCAGAAATACTCCCTCCGTAAACTAA 59.335 38.462 0.00 0.00 0.00 2.24
879 3875 6.189859 TCAGAAATACTCCCTCCGTAAACTA 58.810 40.000 0.00 0.00 0.00 2.24
880 3876 5.021458 TCAGAAATACTCCCTCCGTAAACT 58.979 41.667 0.00 0.00 0.00 2.66
881 3877 5.334724 TCAGAAATACTCCCTCCGTAAAC 57.665 43.478 0.00 0.00 0.00 2.01
882 3878 6.013984 ACTTTCAGAAATACTCCCTCCGTAAA 60.014 38.462 0.00 0.00 0.00 2.01
883 3879 5.482878 ACTTTCAGAAATACTCCCTCCGTAA 59.517 40.000 0.00 0.00 0.00 3.18
884 3880 5.021458 ACTTTCAGAAATACTCCCTCCGTA 58.979 41.667 0.00 0.00 0.00 4.02
885 3881 3.838903 ACTTTCAGAAATACTCCCTCCGT 59.161 43.478 0.00 0.00 0.00 4.69
886 3882 4.434520 GACTTTCAGAAATACTCCCTCCG 58.565 47.826 0.00 0.00 0.00 4.63
887 3883 4.471747 AGGACTTTCAGAAATACTCCCTCC 59.528 45.833 0.00 0.00 0.00 4.30
888 3884 5.685520 AGGACTTTCAGAAATACTCCCTC 57.314 43.478 0.00 0.00 0.00 4.30
889 3885 6.455690 AAAGGACTTTCAGAAATACTCCCT 57.544 37.500 0.00 0.00 0.00 4.20
890 3886 6.570571 GCAAAAGGACTTTCAGAAATACTCCC 60.571 42.308 0.00 0.00 31.45 4.30
891 3887 6.016276 TGCAAAAGGACTTTCAGAAATACTCC 60.016 38.462 0.00 1.71 31.45 3.85
892 3888 6.970484 TGCAAAAGGACTTTCAGAAATACTC 58.030 36.000 0.00 0.00 31.45 2.59
893 3889 6.547510 ACTGCAAAAGGACTTTCAGAAATACT 59.452 34.615 15.98 0.00 31.75 2.12
894 3890 6.739112 ACTGCAAAAGGACTTTCAGAAATAC 58.261 36.000 15.98 0.00 31.75 1.89
895 3891 6.772716 AGACTGCAAAAGGACTTTCAGAAATA 59.227 34.615 15.98 0.00 31.75 1.40
896 3892 5.595952 AGACTGCAAAAGGACTTTCAGAAAT 59.404 36.000 15.98 0.16 31.75 2.17
1008 4053 3.308323 GTGAATCATCGAGAACAGAAGCC 59.692 47.826 0.00 0.00 0.00 4.35
1019 4064 3.742327 GCTCCAATCTGGTGAATCATCGA 60.742 47.826 0.00 0.00 39.03 3.59
1267 4312 2.475487 GAGTGACGTGGTAAAGCTTGTC 59.525 50.000 0.00 2.27 0.00 3.18
1556 6094 5.782845 ACAACCCTCTCATAGAAGAAGAAGT 59.217 40.000 0.00 0.00 0.00 3.01
1764 6302 6.294620 GGTTAATAGAATCTACCTGACCCTCG 60.295 46.154 0.00 0.00 0.00 4.63
1920 6698 6.319048 ACACATTCTGTTATCCCATTCTCT 57.681 37.500 0.00 0.00 0.00 3.10
2349 7146 4.504858 CGATTACAAAGGTCTAACTGGCT 58.495 43.478 0.00 0.00 0.00 4.75
2396 7193 6.649141 CCTAAGTGCATAGTTACACAAGAACA 59.351 38.462 0.00 0.00 39.30 3.18
2397 7194 6.402226 GCCTAAGTGCATAGTTACACAAGAAC 60.402 42.308 0.00 0.00 39.30 3.01
2398 7195 5.642063 GCCTAAGTGCATAGTTACACAAGAA 59.358 40.000 0.00 0.00 39.30 2.52
2473 7708 8.370182 GGATAGGTTTATACCCGAAACATCTAA 58.630 37.037 0.00 0.00 46.28 2.10
2546 7826 1.878953 AAACAAGGCAGTACTCGGTG 58.121 50.000 0.00 0.00 0.00 4.94
2861 8151 9.608718 ATGCTAGTACCTTAGGAAAGAGATAAT 57.391 33.333 4.77 0.00 34.37 1.28
2864 8154 9.608718 ATTATGCTAGTACCTTAGGAAAGAGAT 57.391 33.333 4.77 0.00 34.37 2.75
2865 8155 8.861086 CATTATGCTAGTACCTTAGGAAAGAGA 58.139 37.037 4.77 0.00 34.37 3.10
2866 8156 8.643324 ACATTATGCTAGTACCTTAGGAAAGAG 58.357 37.037 4.77 0.00 34.37 2.85
2867 8157 8.548880 ACATTATGCTAGTACCTTAGGAAAGA 57.451 34.615 4.77 0.00 34.37 2.52
2868 8158 9.614792 AAACATTATGCTAGTACCTTAGGAAAG 57.385 33.333 4.77 0.00 0.00 2.62
2869 8159 9.969001 AAAACATTATGCTAGTACCTTAGGAAA 57.031 29.630 4.77 0.00 0.00 3.13
2870 8160 9.391006 CAAAACATTATGCTAGTACCTTAGGAA 57.609 33.333 4.77 0.00 0.00 3.36
2871 8161 8.764558 TCAAAACATTATGCTAGTACCTTAGGA 58.235 33.333 4.77 0.00 0.00 2.94
2872 8162 8.958119 TCAAAACATTATGCTAGTACCTTAGG 57.042 34.615 0.00 0.00 0.00 2.69
2875 8165 9.461312 TCATTCAAAACATTATGCTAGTACCTT 57.539 29.630 0.00 0.00 0.00 3.50
2876 8166 9.632638 ATCATTCAAAACATTATGCTAGTACCT 57.367 29.630 0.00 0.00 0.00 3.08
2877 8167 9.884465 GATCATTCAAAACATTATGCTAGTACC 57.116 33.333 0.00 0.00 0.00 3.34
2878 8168 9.884465 GGATCATTCAAAACATTATGCTAGTAC 57.116 33.333 0.00 0.00 0.00 2.73
2879 8169 9.851686 AGGATCATTCAAAACATTATGCTAGTA 57.148 29.630 0.00 0.00 0.00 1.82
2880 8170 8.757982 AGGATCATTCAAAACATTATGCTAGT 57.242 30.769 0.00 0.00 0.00 2.57
2980 8272 5.126061 TGTGAACCGAGGAAGTAATAGTACC 59.874 44.000 0.00 0.00 0.00 3.34
3171 8471 3.041940 GGTTCTGGCACGTGGACG 61.042 66.667 18.88 0.00 46.33 4.79
3209 8509 7.349859 TGGGGTAGGATATAGTTGAAACTCATT 59.650 37.037 0.00 0.00 40.37 2.57


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

AutoCloner maintained by Alex Coulton.