Multiple sequence alignment - TraesCS5D01G318300

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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 TraesCS5D01G318300 chr5D 100.000 2645 0 0 1 2645 411171995 411169351 0.000000e+00 4885.0
1 TraesCS5D01G318300 chr5D 82.079 558 72 16 1000 1546 410843290 410842750 4.010000e-123 451.0
2 TraesCS5D01G318300 chr5D 88.219 365 34 5 1035 1390 410539202 410539566 6.770000e-116 427.0
3 TraesCS5D01G318300 chr5D 81.744 367 52 8 1041 1392 410638161 410637795 2.580000e-75 292.0
4 TraesCS5D01G318300 chr5B 93.092 1549 58 22 204 1719 493631933 493630401 0.000000e+00 2222.0
5 TraesCS5D01G318300 chr5B 84.545 770 63 18 1720 2437 6685585 6684820 0.000000e+00 712.0
6 TraesCS5D01G318300 chr5B 81.720 558 74 17 1000 1546 493160072 493159532 8.690000e-120 440.0
7 TraesCS5D01G318300 chr5B 80.926 367 55 7 1041 1392 493125319 493124953 2.590000e-70 276.0
8 TraesCS5D01G318300 chr5B 81.707 82 13 2 2479 2559 545260728 545260808 1.700000e-07 67.6
9 TraesCS5D01G318300 chr5A 94.352 1328 40 17 397 1719 523016680 523015383 0.000000e+00 2004.0
10 TraesCS5D01G318300 chr5A 88.283 367 34 5 1035 1392 522104293 522104659 5.230000e-117 431.0
11 TraesCS5D01G318300 chr5A 86.579 380 38 10 999 1367 522605563 522605186 8.810000e-110 407.0
12 TraesCS5D01G318300 chr5A 87.465 359 35 6 1034 1382 522082785 522083143 3.170000e-109 405.0
13 TraesCS5D01G318300 chr5A 86.704 361 36 8 1034 1383 522425283 522425642 8.880000e-105 390.0
14 TraesCS5D01G318300 chr5A 79.872 313 32 16 2274 2559 564758161 564758469 1.610000e-47 200.0
15 TraesCS5D01G318300 chr5A 92.632 95 5 1 263 357 523016773 523016681 4.590000e-28 135.0
16 TraesCS5D01G318300 chr7D 97.408 926 15 3 1720 2645 498112928 498113844 0.000000e+00 1568.0
17 TraesCS5D01G318300 chr7D 96.890 611 11 2 1720 2330 498086552 498087154 0.000000e+00 1016.0
18 TraesCS5D01G318300 chr7D 75.763 524 58 27 2093 2563 113012741 113013248 1.610000e-47 200.0
19 TraesCS5D01G318300 chr1B 94.374 942 35 4 1720 2644 558778048 558778988 0.000000e+00 1430.0
20 TraesCS5D01G318300 chr1B 95.500 200 8 1 1 199 36157509 36157708 4.250000e-83 318.0
21 TraesCS5D01G318300 chr7A 94.350 938 35 3 1724 2644 266645786 266644850 0.000000e+00 1423.0
22 TraesCS5D01G318300 chr7A 83.133 415 37 10 1712 2101 4492044 4492450 5.420000e-92 348.0
23 TraesCS5D01G318300 chr1A 94.062 943 38 4 1718 2642 207688130 207687188 0.000000e+00 1415.0
24 TraesCS5D01G318300 chr7B 93.869 946 37 4 1720 2644 288170135 288169190 0.000000e+00 1406.0
25 TraesCS5D01G318300 chr7B 84.635 768 71 20 1714 2437 630128861 630129625 0.000000e+00 721.0
26 TraesCS5D01G318300 chr7B 84.424 764 70 18 1720 2437 607324666 607325426 0.000000e+00 706.0
27 TraesCS5D01G318300 chr7B 94.975 199 10 0 1 199 146002979 146002781 1.980000e-81 313.0
28 TraesCS5D01G318300 chr6A 85.433 762 61 15 1717 2437 426957311 426958063 0.000000e+00 747.0
29 TraesCS5D01G318300 chr2A 84.383 762 72 18 1720 2437 731338712 731337954 0.000000e+00 704.0
30 TraesCS5D01G318300 chr6D 83.596 762 64 21 1720 2439 148007167 148006425 0.000000e+00 658.0
31 TraesCS5D01G318300 chr3A 82.836 402 45 9 1720 2101 681554972 681554575 3.260000e-89 339.0
32 TraesCS5D01G318300 chr3A 92.342 222 16 1 2218 2439 681554248 681554028 5.500000e-82 315.0
33 TraesCS5D01G318300 chr4D 96.985 199 6 0 1 199 30344865 30345063 4.220000e-88 335.0
34 TraesCS5D01G318300 chrUn 96.482 199 7 0 1 199 155119317 155119515 1.960000e-86 329.0
35 TraesCS5D01G318300 chrUn 96.482 199 7 0 1 199 164220933 164220735 1.960000e-86 329.0
36 TraesCS5D01G318300 chrUn 96.482 199 7 0 1 199 164265858 164265660 1.960000e-86 329.0
37 TraesCS5D01G318300 chrUn 96.482 199 7 0 1 199 385636326 385636524 1.960000e-86 329.0
38 TraesCS5D01G318300 chrUn 95.980 199 8 0 1 199 155204765 155204963 9.130000e-85 324.0
39 TraesCS5D01G318300 chr2D 96.354 192 6 1 3 193 130849128 130849319 5.500000e-82 315.0
40 TraesCS5D01G318300 chr3B 80.144 277 26 10 2315 2563 116123798 116123523 2.090000e-41 180.0


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 TraesCS5D01G318300 chr5D 411169351 411171995 2644 True 4885.0 4885 100.000 1 2645 1 chr5D.!!$R3 2644
1 TraesCS5D01G318300 chr5D 410842750 410843290 540 True 451.0 451 82.079 1000 1546 1 chr5D.!!$R2 546
2 TraesCS5D01G318300 chr5B 493630401 493631933 1532 True 2222.0 2222 93.092 204 1719 1 chr5B.!!$R4 1515
3 TraesCS5D01G318300 chr5B 6684820 6685585 765 True 712.0 712 84.545 1720 2437 1 chr5B.!!$R1 717
4 TraesCS5D01G318300 chr5B 493159532 493160072 540 True 440.0 440 81.720 1000 1546 1 chr5B.!!$R3 546
5 TraesCS5D01G318300 chr5A 523015383 523016773 1390 True 1069.5 2004 93.492 263 1719 2 chr5A.!!$R2 1456
6 TraesCS5D01G318300 chr7D 498112928 498113844 916 False 1568.0 1568 97.408 1720 2645 1 chr7D.!!$F3 925
7 TraesCS5D01G318300 chr7D 498086552 498087154 602 False 1016.0 1016 96.890 1720 2330 1 chr7D.!!$F2 610
8 TraesCS5D01G318300 chr1B 558778048 558778988 940 False 1430.0 1430 94.374 1720 2644 1 chr1B.!!$F2 924
9 TraesCS5D01G318300 chr7A 266644850 266645786 936 True 1423.0 1423 94.350 1724 2644 1 chr7A.!!$R1 920
10 TraesCS5D01G318300 chr1A 207687188 207688130 942 True 1415.0 1415 94.062 1718 2642 1 chr1A.!!$R1 924
11 TraesCS5D01G318300 chr7B 288169190 288170135 945 True 1406.0 1406 93.869 1720 2644 1 chr7B.!!$R2 924
12 TraesCS5D01G318300 chr7B 630128861 630129625 764 False 721.0 721 84.635 1714 2437 1 chr7B.!!$F2 723
13 TraesCS5D01G318300 chr7B 607324666 607325426 760 False 706.0 706 84.424 1720 2437 1 chr7B.!!$F1 717
14 TraesCS5D01G318300 chr6A 426957311 426958063 752 False 747.0 747 85.433 1717 2437 1 chr6A.!!$F1 720
15 TraesCS5D01G318300 chr2A 731337954 731338712 758 True 704.0 704 84.383 1720 2437 1 chr2A.!!$R1 717
16 TraesCS5D01G318300 chr6D 148006425 148007167 742 True 658.0 658 83.596 1720 2439 1 chr6D.!!$R1 719
17 TraesCS5D01G318300 chr3A 681554028 681554972 944 True 327.0 339 87.589 1720 2439 2 chr3A.!!$R1 719

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 0.036105 TCCTACGTGTCGCTAGGTGA 60.036 55.0 0.0 0.0 34.64 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2009 2107 0.179084 CCGCGGGCTAGAGAAATTGA 60.179 55.0 20.1 0.0 0.0 2.57 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
36 37 2.046314 CCGGCGAAGGTTGACCAT 60.046 61.111 9.30 0.00 38.89 3.55
37 38 2.398554 CCGGCGAAGGTTGACCATG 61.399 63.158 9.30 0.00 38.89 3.66
38 39 2.398554 CGGCGAAGGTTGACCATGG 61.399 63.158 11.19 11.19 38.89 3.66
39 40 2.700773 GGCGAAGGTTGACCATGGC 61.701 63.158 13.04 5.35 37.65 4.40
40 41 1.971167 GCGAAGGTTGACCATGGCA 60.971 57.895 13.04 8.31 38.15 4.92
41 42 1.926511 GCGAAGGTTGACCATGGCAG 61.927 60.000 13.04 0.00 38.15 4.85
42 43 1.885871 GAAGGTTGACCATGGCAGC 59.114 57.895 13.04 12.65 38.89 5.25
43 44 1.926511 GAAGGTTGACCATGGCAGCG 61.927 60.000 13.04 0.00 38.89 5.18
44 45 3.443045 GGTTGACCATGGCAGCGG 61.443 66.667 13.04 4.27 35.64 5.52
45 46 3.443045 GTTGACCATGGCAGCGGG 61.443 66.667 13.04 5.96 0.00 6.13
46 47 4.738998 TTGACCATGGCAGCGGGG 62.739 66.667 13.04 3.56 0.00 5.73
48 49 4.864334 GACCATGGCAGCGGGGAG 62.864 72.222 13.04 0.00 0.00 4.30
50 51 4.559063 CCATGGCAGCGGGGAGAG 62.559 72.222 0.00 0.00 0.00 3.20
51 52 3.473647 CATGGCAGCGGGGAGAGA 61.474 66.667 0.00 0.00 0.00 3.10
52 53 3.160047 ATGGCAGCGGGGAGAGAG 61.160 66.667 0.00 0.00 0.00 3.20
53 54 3.686098 ATGGCAGCGGGGAGAGAGA 62.686 63.158 0.00 0.00 0.00 3.10
54 55 3.535962 GGCAGCGGGGAGAGAGAG 61.536 72.222 0.00 0.00 0.00 3.20
55 56 2.441164 GCAGCGGGGAGAGAGAGA 60.441 66.667 0.00 0.00 0.00 3.10
56 57 2.489275 GCAGCGGGGAGAGAGAGAG 61.489 68.421 0.00 0.00 0.00 3.20
57 58 1.225983 CAGCGGGGAGAGAGAGAGA 59.774 63.158 0.00 0.00 0.00 3.10
58 59 1.101049 CAGCGGGGAGAGAGAGAGAC 61.101 65.000 0.00 0.00 0.00 3.36
59 60 2.184167 GCGGGGAGAGAGAGAGACG 61.184 68.421 0.00 0.00 0.00 4.18
60 61 1.523046 CGGGGAGAGAGAGAGACGA 59.477 63.158 0.00 0.00 0.00 4.20
61 62 0.531974 CGGGGAGAGAGAGAGACGAG 60.532 65.000 0.00 0.00 0.00 4.18
62 63 0.818040 GGGGAGAGAGAGAGACGAGC 60.818 65.000 0.00 0.00 0.00 5.03
63 64 1.157870 GGGAGAGAGAGAGACGAGCG 61.158 65.000 0.00 0.00 0.00 5.03
64 65 0.179094 GGAGAGAGAGAGACGAGCGA 60.179 60.000 0.00 0.00 0.00 4.93
65 66 0.928229 GAGAGAGAGAGACGAGCGAC 59.072 60.000 0.00 0.00 0.00 5.19
75 76 2.875485 CGAGCGACGGGAAGAAGA 59.125 61.111 0.00 0.00 38.46 2.87
76 77 1.226435 CGAGCGACGGGAAGAAGAG 60.226 63.158 0.00 0.00 38.46 2.85
77 78 1.645704 CGAGCGACGGGAAGAAGAGA 61.646 60.000 0.00 0.00 38.46 3.10
78 79 0.526662 GAGCGACGGGAAGAAGAGAA 59.473 55.000 0.00 0.00 0.00 2.87
79 80 0.966920 AGCGACGGGAAGAAGAGAAA 59.033 50.000 0.00 0.00 0.00 2.52
80 81 1.069255 GCGACGGGAAGAAGAGAAAC 58.931 55.000 0.00 0.00 0.00 2.78
81 82 1.604693 GCGACGGGAAGAAGAGAAACA 60.605 52.381 0.00 0.00 0.00 2.83
82 83 2.329379 CGACGGGAAGAAGAGAAACAG 58.671 52.381 0.00 0.00 0.00 3.16
83 84 2.689646 GACGGGAAGAAGAGAAACAGG 58.310 52.381 0.00 0.00 0.00 4.00
84 85 2.299297 GACGGGAAGAAGAGAAACAGGA 59.701 50.000 0.00 0.00 0.00 3.86
85 86 2.300437 ACGGGAAGAAGAGAAACAGGAG 59.700 50.000 0.00 0.00 0.00 3.69
86 87 2.354203 CGGGAAGAAGAGAAACAGGAGG 60.354 54.545 0.00 0.00 0.00 4.30
87 88 2.026729 GGGAAGAAGAGAAACAGGAGGG 60.027 54.545 0.00 0.00 0.00 4.30
88 89 2.907042 GGAAGAAGAGAAACAGGAGGGA 59.093 50.000 0.00 0.00 0.00 4.20
89 90 3.055458 GGAAGAAGAGAAACAGGAGGGAG 60.055 52.174 0.00 0.00 0.00 4.30
90 91 3.551635 AGAAGAGAAACAGGAGGGAGA 57.448 47.619 0.00 0.00 0.00 3.71
91 92 3.863086 AGAAGAGAAACAGGAGGGAGAA 58.137 45.455 0.00 0.00 0.00 2.87
92 93 3.837731 AGAAGAGAAACAGGAGGGAGAAG 59.162 47.826 0.00 0.00 0.00 2.85
93 94 3.551635 AGAGAAACAGGAGGGAGAAGA 57.448 47.619 0.00 0.00 0.00 2.87
94 95 3.169908 AGAGAAACAGGAGGGAGAAGAC 58.830 50.000 0.00 0.00 0.00 3.01
95 96 1.896465 AGAAACAGGAGGGAGAAGACG 59.104 52.381 0.00 0.00 0.00 4.18
96 97 1.619332 GAAACAGGAGGGAGAAGACGT 59.381 52.381 0.00 0.00 0.00 4.34
97 98 2.599408 AACAGGAGGGAGAAGACGTA 57.401 50.000 0.00 0.00 0.00 3.57
98 99 1.836802 ACAGGAGGGAGAAGACGTAC 58.163 55.000 0.00 0.00 0.00 3.67
99 100 0.733729 CAGGAGGGAGAAGACGTACG 59.266 60.000 15.01 15.01 0.00 3.67
100 101 0.327591 AGGAGGGAGAAGACGTACGT 59.672 55.000 23.04 23.04 0.00 3.57
101 102 0.450983 GGAGGGAGAAGACGTACGTG 59.549 60.000 28.16 0.00 0.00 4.49
102 103 0.450983 GAGGGAGAAGACGTACGTGG 59.549 60.000 28.16 0.00 0.00 4.94
103 104 0.964358 AGGGAGAAGACGTACGTGGG 60.964 60.000 28.16 0.00 0.00 4.61
104 105 1.153881 GGAGAAGACGTACGTGGGC 60.154 63.158 28.16 11.83 0.00 5.36
105 106 1.513586 GAGAAGACGTACGTGGGCG 60.514 63.158 28.16 2.59 44.93 6.13
106 107 2.505557 GAAGACGTACGTGGGCGG 60.506 66.667 28.16 0.00 43.45 6.13
107 108 3.976902 GAAGACGTACGTGGGCGGG 62.977 68.421 28.16 0.00 43.45 6.13
126 127 2.812499 CCCCCATCCTACGTGTCG 59.188 66.667 0.00 0.00 0.00 4.35
127 128 2.106332 CCCCATCCTACGTGTCGC 59.894 66.667 0.00 0.00 0.00 5.19
128 129 2.423898 CCCCATCCTACGTGTCGCT 61.424 63.158 0.00 0.00 0.00 4.93
129 130 1.105167 CCCCATCCTACGTGTCGCTA 61.105 60.000 0.00 0.00 0.00 4.26
130 131 0.311165 CCCATCCTACGTGTCGCTAG 59.689 60.000 0.00 0.00 0.00 3.42
131 132 0.311165 CCATCCTACGTGTCGCTAGG 59.689 60.000 0.00 0.00 34.48 3.02
132 133 1.022735 CATCCTACGTGTCGCTAGGT 58.977 55.000 0.00 0.00 34.64 3.08
133 134 1.022735 ATCCTACGTGTCGCTAGGTG 58.977 55.000 0.00 0.00 34.64 4.00
134 135 0.036105 TCCTACGTGTCGCTAGGTGA 60.036 55.000 0.00 0.00 34.64 4.02
135 136 0.377554 CCTACGTGTCGCTAGGTGAG 59.622 60.000 0.00 0.00 31.32 3.51
136 137 1.085091 CTACGTGTCGCTAGGTGAGT 58.915 55.000 0.00 0.00 0.00 3.41
137 138 1.062294 CTACGTGTCGCTAGGTGAGTC 59.938 57.143 0.00 0.00 0.00 3.36
138 139 1.226046 CGTGTCGCTAGGTGAGTCG 60.226 63.158 0.00 0.00 0.00 4.18
139 140 1.514443 GTGTCGCTAGGTGAGTCGC 60.514 63.158 0.00 0.00 0.00 5.19
140 141 1.674651 TGTCGCTAGGTGAGTCGCT 60.675 57.895 3.25 0.00 0.00 4.93
141 142 1.062845 GTCGCTAGGTGAGTCGCTC 59.937 63.158 3.25 0.58 0.00 5.03
142 143 2.023461 CGCTAGGTGAGTCGCTCG 59.977 66.667 3.25 0.00 32.35 5.03
143 144 2.409651 GCTAGGTGAGTCGCTCGG 59.590 66.667 3.25 0.00 32.35 4.63
144 145 2.408241 GCTAGGTGAGTCGCTCGGT 61.408 63.158 3.25 0.00 32.35 4.69
145 146 1.094073 GCTAGGTGAGTCGCTCGGTA 61.094 60.000 3.25 0.00 32.35 4.02
146 147 0.656785 CTAGGTGAGTCGCTCGGTAC 59.343 60.000 3.25 0.00 32.35 3.34
160 161 3.820164 GTACGTTCGCGCGTGGAC 61.820 66.667 30.98 21.20 45.33 4.02
200 201 4.265056 GGTGCCCCGTGGTGAAGT 62.265 66.667 0.00 0.00 0.00 3.01
201 202 2.203294 GTGCCCCGTGGTGAAGTT 60.203 61.111 0.00 0.00 0.00 2.66
202 203 1.826487 GTGCCCCGTGGTGAAGTTT 60.826 57.895 0.00 0.00 0.00 2.66
203 204 0.535553 GTGCCCCGTGGTGAAGTTTA 60.536 55.000 0.00 0.00 0.00 2.01
204 205 0.402504 TGCCCCGTGGTGAAGTTTAT 59.597 50.000 0.00 0.00 0.00 1.40
205 206 1.202952 TGCCCCGTGGTGAAGTTTATT 60.203 47.619 0.00 0.00 0.00 1.40
206 207 1.201414 GCCCCGTGGTGAAGTTTATTG 59.799 52.381 0.00 0.00 0.00 1.90
207 208 2.785562 CCCCGTGGTGAAGTTTATTGA 58.214 47.619 0.00 0.00 0.00 2.57
208 209 2.486592 CCCCGTGGTGAAGTTTATTGAC 59.513 50.000 0.00 0.00 0.00 3.18
209 210 3.408634 CCCGTGGTGAAGTTTATTGACT 58.591 45.455 0.00 0.00 0.00 3.41
210 211 3.818773 CCCGTGGTGAAGTTTATTGACTT 59.181 43.478 0.00 0.00 42.31 3.01
234 235 8.600449 TTGAAAAATACATCCCAACAAACATC 57.400 30.769 0.00 0.00 0.00 3.06
240 241 3.569701 ACATCCCAACAAACATCACAGTC 59.430 43.478 0.00 0.00 0.00 3.51
243 244 1.334960 CCAACAAACATCACAGTCGGC 60.335 52.381 0.00 0.00 0.00 5.54
306 307 0.386476 AACAGGCGTAGTCGTTCACA 59.614 50.000 0.00 0.00 36.95 3.58
392 393 5.525378 CGCTAATCCAGAAGCTTTGAACTAT 59.475 40.000 0.00 0.00 36.56 2.12
468 469 2.664916 CGTGCTGTCCTTTTCATTTGG 58.335 47.619 0.00 0.00 0.00 3.28
491 492 0.242286 CTCAGTCGACAGTGGGTGAG 59.758 60.000 19.50 16.09 0.00 3.51
492 493 0.467474 TCAGTCGACAGTGGGTGAGT 60.467 55.000 19.50 0.00 0.00 3.41
493 494 0.319040 CAGTCGACAGTGGGTGAGTG 60.319 60.000 19.50 0.00 0.00 3.51
494 495 0.755698 AGTCGACAGTGGGTGAGTGT 60.756 55.000 19.50 0.00 41.26 3.55
495 496 0.597637 GTCGACAGTGGGTGAGTGTG 60.598 60.000 11.55 0.00 38.44 3.82
496 497 0.753848 TCGACAGTGGGTGAGTGTGA 60.754 55.000 0.00 0.00 38.44 3.58
587 606 1.073199 CCAACAGGGCTCCGAAAGT 59.927 57.895 0.00 0.00 0.00 2.66
653 672 1.069978 TGCTTGGATGTGAAGTGTCGA 59.930 47.619 0.00 0.00 0.00 4.20
729 751 1.080298 GCTTGTCCTTGCATGTGGC 60.080 57.895 0.00 0.00 45.13 5.01
783 805 2.094417 GGCGTTCAAGCTAATGTCACTC 59.906 50.000 0.00 0.00 37.29 3.51
894 918 3.365265 CAACCAAGCCTCACCGCC 61.365 66.667 0.00 0.00 0.00 6.13
1010 1048 2.459421 GATCGATCGATGGACGCCGT 62.459 60.000 33.86 8.66 42.26 5.68
1517 1564 3.023119 TGTTGAATGAGCACTGGTTTGT 58.977 40.909 0.00 0.00 0.00 2.83
1524 1571 1.210155 GCACTGGTTTGTCGGCATC 59.790 57.895 0.00 0.00 0.00 3.91
1647 1694 4.280174 TGGAGCTACTTGTTCGACTAAAGT 59.720 41.667 0.00 10.43 37.82 2.66
1657 1704 9.591792 ACTTGTTCGACTAAAGTAGTTAAAAGT 57.408 29.630 5.08 0.00 39.59 2.66
1693 1748 5.794894 TCTCTCTTCTGTTCCACCAAATAC 58.205 41.667 0.00 0.00 0.00 1.89
1707 1762 3.265995 ACCAAATACGGGAGGAAACAGAT 59.734 43.478 0.00 0.00 0.00 2.90
1730 1785 8.875168 AGATGGGGATATTTTTCTCTACTACTG 58.125 37.037 0.00 0.00 0.00 2.74
1846 1901 2.910688 AATCGAACGGCCTGTATCAT 57.089 45.000 0.00 0.00 0.00 2.45
2009 2107 3.646162 TGGATGCTCCGTATCCAGTATTT 59.354 43.478 9.21 0.00 46.75 1.40
2276 2652 3.128589 GGGAATTTTGCTGCGTGAGAATA 59.871 43.478 0.00 0.00 0.00 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.046314 ATGGTCAACCTTCGCCGG 60.046 61.111 0.00 0.00 36.82 6.13
20 21 2.398554 CCATGGTCAACCTTCGCCG 61.399 63.158 2.57 0.00 36.82 6.46
21 22 2.700773 GCCATGGTCAACCTTCGCC 61.701 63.158 14.67 0.00 36.82 5.54
22 23 1.926511 CTGCCATGGTCAACCTTCGC 61.927 60.000 14.67 0.00 36.82 4.70
23 24 1.926511 GCTGCCATGGTCAACCTTCG 61.927 60.000 14.67 0.61 36.82 3.79
24 25 1.885871 GCTGCCATGGTCAACCTTC 59.114 57.895 14.67 0.00 36.82 3.46
25 26 1.973281 CGCTGCCATGGTCAACCTT 60.973 57.895 14.67 0.00 36.82 3.50
26 27 2.360350 CGCTGCCATGGTCAACCT 60.360 61.111 14.67 0.00 36.82 3.50
27 28 3.443045 CCGCTGCCATGGTCAACC 61.443 66.667 14.67 5.25 0.00 3.77
28 29 3.443045 CCCGCTGCCATGGTCAAC 61.443 66.667 14.67 6.56 0.00 3.18
29 30 4.738998 CCCCGCTGCCATGGTCAA 62.739 66.667 14.67 0.00 0.00 3.18
31 32 4.864334 CTCCCCGCTGCCATGGTC 62.864 72.222 14.67 6.41 0.00 4.02
33 34 4.559063 CTCTCCCCGCTGCCATGG 62.559 72.222 7.63 7.63 0.00 3.66
34 35 3.457625 CTCTCTCCCCGCTGCCATG 62.458 68.421 0.00 0.00 0.00 3.66
35 36 3.160047 CTCTCTCCCCGCTGCCAT 61.160 66.667 0.00 0.00 0.00 4.40
36 37 4.382541 TCTCTCTCCCCGCTGCCA 62.383 66.667 0.00 0.00 0.00 4.92
37 38 3.535962 CTCTCTCTCCCCGCTGCC 61.536 72.222 0.00 0.00 0.00 4.85
38 39 2.441164 TCTCTCTCTCCCCGCTGC 60.441 66.667 0.00 0.00 0.00 5.25
39 40 1.101049 GTCTCTCTCTCTCCCCGCTG 61.101 65.000 0.00 0.00 0.00 5.18
40 41 1.226262 GTCTCTCTCTCTCCCCGCT 59.774 63.158 0.00 0.00 0.00 5.52
41 42 2.184167 CGTCTCTCTCTCTCCCCGC 61.184 68.421 0.00 0.00 0.00 6.13
42 43 0.531974 CTCGTCTCTCTCTCTCCCCG 60.532 65.000 0.00 0.00 0.00 5.73
43 44 0.818040 GCTCGTCTCTCTCTCTCCCC 60.818 65.000 0.00 0.00 0.00 4.81
44 45 1.157870 CGCTCGTCTCTCTCTCTCCC 61.158 65.000 0.00 0.00 0.00 4.30
45 46 0.179094 TCGCTCGTCTCTCTCTCTCC 60.179 60.000 0.00 0.00 0.00 3.71
46 47 0.928229 GTCGCTCGTCTCTCTCTCTC 59.072 60.000 0.00 0.00 0.00 3.20
47 48 0.804544 CGTCGCTCGTCTCTCTCTCT 60.805 60.000 0.00 0.00 34.52 3.10
48 49 1.634225 CGTCGCTCGTCTCTCTCTC 59.366 63.158 0.00 0.00 34.52 3.20
49 50 1.812093 CCGTCGCTCGTCTCTCTCT 60.812 63.158 0.00 0.00 37.94 3.10
50 51 2.704616 CCGTCGCTCGTCTCTCTC 59.295 66.667 0.00 0.00 37.94 3.20
51 52 2.799814 TTCCCGTCGCTCGTCTCTCT 62.800 60.000 0.00 0.00 37.94 3.10
52 53 2.312398 CTTCCCGTCGCTCGTCTCTC 62.312 65.000 0.00 0.00 37.94 3.20
53 54 2.359602 TTCCCGTCGCTCGTCTCT 60.360 61.111 0.00 0.00 37.94 3.10
54 55 1.919956 TTCTTCCCGTCGCTCGTCTC 61.920 60.000 0.00 0.00 37.94 3.36
55 56 1.924320 CTTCTTCCCGTCGCTCGTCT 61.924 60.000 0.00 0.00 37.94 4.18
56 57 1.514443 CTTCTTCCCGTCGCTCGTC 60.514 63.158 0.00 0.00 37.94 4.20
57 58 1.924320 CTCTTCTTCCCGTCGCTCGT 61.924 60.000 0.00 0.00 37.94 4.18
58 59 1.226435 CTCTTCTTCCCGTCGCTCG 60.226 63.158 0.00 0.00 39.52 5.03
59 60 0.526662 TTCTCTTCTTCCCGTCGCTC 59.473 55.000 0.00 0.00 0.00 5.03
60 61 0.966920 TTTCTCTTCTTCCCGTCGCT 59.033 50.000 0.00 0.00 0.00 4.93
61 62 1.069255 GTTTCTCTTCTTCCCGTCGC 58.931 55.000 0.00 0.00 0.00 5.19
62 63 2.329379 CTGTTTCTCTTCTTCCCGTCG 58.671 52.381 0.00 0.00 0.00 5.12
63 64 2.299297 TCCTGTTTCTCTTCTTCCCGTC 59.701 50.000 0.00 0.00 0.00 4.79
64 65 2.300437 CTCCTGTTTCTCTTCTTCCCGT 59.700 50.000 0.00 0.00 0.00 5.28
65 66 2.354203 CCTCCTGTTTCTCTTCTTCCCG 60.354 54.545 0.00 0.00 0.00 5.14
66 67 2.026729 CCCTCCTGTTTCTCTTCTTCCC 60.027 54.545 0.00 0.00 0.00 3.97
67 68 2.907042 TCCCTCCTGTTTCTCTTCTTCC 59.093 50.000 0.00 0.00 0.00 3.46
68 69 3.835395 TCTCCCTCCTGTTTCTCTTCTTC 59.165 47.826 0.00 0.00 0.00 2.87
69 70 3.863086 TCTCCCTCCTGTTTCTCTTCTT 58.137 45.455 0.00 0.00 0.00 2.52
70 71 3.551635 TCTCCCTCCTGTTTCTCTTCT 57.448 47.619 0.00 0.00 0.00 2.85
71 72 3.835395 TCTTCTCCCTCCTGTTTCTCTTC 59.165 47.826 0.00 0.00 0.00 2.87
72 73 3.580895 GTCTTCTCCCTCCTGTTTCTCTT 59.419 47.826 0.00 0.00 0.00 2.85
73 74 3.169908 GTCTTCTCCCTCCTGTTTCTCT 58.830 50.000 0.00 0.00 0.00 3.10
74 75 2.094442 CGTCTTCTCCCTCCTGTTTCTC 60.094 54.545 0.00 0.00 0.00 2.87
75 76 1.896465 CGTCTTCTCCCTCCTGTTTCT 59.104 52.381 0.00 0.00 0.00 2.52
76 77 1.619332 ACGTCTTCTCCCTCCTGTTTC 59.381 52.381 0.00 0.00 0.00 2.78
77 78 1.718280 ACGTCTTCTCCCTCCTGTTT 58.282 50.000 0.00 0.00 0.00 2.83
78 79 2.169330 GTACGTCTTCTCCCTCCTGTT 58.831 52.381 0.00 0.00 0.00 3.16
79 80 1.836802 GTACGTCTTCTCCCTCCTGT 58.163 55.000 0.00 0.00 0.00 4.00
80 81 0.733729 CGTACGTCTTCTCCCTCCTG 59.266 60.000 7.22 0.00 0.00 3.86
81 82 0.327591 ACGTACGTCTTCTCCCTCCT 59.672 55.000 16.72 0.00 0.00 3.69
82 83 0.450983 CACGTACGTCTTCTCCCTCC 59.549 60.000 19.94 0.00 0.00 4.30
83 84 0.450983 CCACGTACGTCTTCTCCCTC 59.549 60.000 19.94 0.00 0.00 4.30
84 85 0.964358 CCCACGTACGTCTTCTCCCT 60.964 60.000 19.94 0.00 0.00 4.20
85 86 1.509923 CCCACGTACGTCTTCTCCC 59.490 63.158 19.94 0.00 0.00 4.30
86 87 1.153881 GCCCACGTACGTCTTCTCC 60.154 63.158 19.94 0.14 0.00 3.71
87 88 1.513586 CGCCCACGTACGTCTTCTC 60.514 63.158 19.94 5.34 33.53 2.87
88 89 2.564975 CGCCCACGTACGTCTTCT 59.435 61.111 19.94 0.00 33.53 2.85
89 90 2.505557 CCGCCCACGTACGTCTTC 60.506 66.667 19.94 8.97 37.70 2.87
90 91 4.060038 CCCGCCCACGTACGTCTT 62.060 66.667 19.94 0.00 37.70 3.01
109 110 2.812499 CGACACGTAGGATGGGGG 59.188 66.667 0.00 0.00 0.00 5.40
110 111 1.105167 TAGCGACACGTAGGATGGGG 61.105 60.000 0.00 0.00 0.00 4.96
111 112 0.311165 CTAGCGACACGTAGGATGGG 59.689 60.000 0.00 0.00 0.00 4.00
112 113 0.311165 CCTAGCGACACGTAGGATGG 59.689 60.000 0.00 0.00 38.54 3.51
113 114 1.022735 ACCTAGCGACACGTAGGATG 58.977 55.000 18.54 0.00 38.54 3.51
114 115 1.022735 CACCTAGCGACACGTAGGAT 58.977 55.000 18.54 0.00 38.54 3.24
115 116 0.036105 TCACCTAGCGACACGTAGGA 60.036 55.000 18.54 3.68 38.54 2.94
116 117 0.377554 CTCACCTAGCGACACGTAGG 59.622 60.000 13.63 13.63 41.58 3.18
117 118 1.062294 GACTCACCTAGCGACACGTAG 59.938 57.143 0.00 0.00 0.00 3.51
118 119 1.081892 GACTCACCTAGCGACACGTA 58.918 55.000 0.00 0.00 0.00 3.57
119 120 1.874562 GACTCACCTAGCGACACGT 59.125 57.895 0.00 0.00 0.00 4.49
120 121 1.226046 CGACTCACCTAGCGACACG 60.226 63.158 0.00 0.00 0.00 4.49
121 122 1.514443 GCGACTCACCTAGCGACAC 60.514 63.158 0.00 0.00 0.00 3.67
122 123 1.645704 GAGCGACTCACCTAGCGACA 61.646 60.000 0.00 0.00 34.34 4.35
123 124 1.062845 GAGCGACTCACCTAGCGAC 59.937 63.158 0.00 0.00 34.34 5.19
124 125 2.461945 CGAGCGACTCACCTAGCGA 61.462 63.158 7.47 0.00 34.34 4.93
125 126 2.023461 CGAGCGACTCACCTAGCG 59.977 66.667 7.47 0.00 34.34 4.26
126 127 1.094073 TACCGAGCGACTCACCTAGC 61.094 60.000 7.47 0.00 0.00 3.42
127 128 0.656785 GTACCGAGCGACTCACCTAG 59.343 60.000 7.47 0.00 0.00 3.02
128 129 1.086067 CGTACCGAGCGACTCACCTA 61.086 60.000 7.47 0.00 0.00 3.08
129 130 2.396955 CGTACCGAGCGACTCACCT 61.397 63.158 7.47 0.00 0.00 4.00
130 131 2.099831 CGTACCGAGCGACTCACC 59.900 66.667 7.47 0.00 0.00 4.02
131 132 0.792356 GAACGTACCGAGCGACTCAC 60.792 60.000 0.00 0.00 0.00 3.51
132 133 1.499056 GAACGTACCGAGCGACTCA 59.501 57.895 0.00 0.00 0.00 3.41
133 134 1.579626 CGAACGTACCGAGCGACTC 60.580 63.158 4.50 0.00 31.70 3.36
134 135 2.477845 CGAACGTACCGAGCGACT 59.522 61.111 4.50 0.00 31.70 4.18
135 136 3.236137 GCGAACGTACCGAGCGAC 61.236 66.667 13.43 0.00 31.70 5.19
136 137 4.799473 CGCGAACGTACCGAGCGA 62.799 66.667 0.00 0.00 44.71 4.93
143 144 3.820164 GTCCACGCGCGAACGTAC 61.820 66.667 39.36 21.38 46.34 3.67
184 185 0.535553 TAAACTTCACCACGGGGCAC 60.536 55.000 1.73 0.00 37.90 5.01
185 186 0.402504 ATAAACTTCACCACGGGGCA 59.597 50.000 1.73 0.00 37.90 5.36
186 187 1.201414 CAATAAACTTCACCACGGGGC 59.799 52.381 1.73 0.00 37.90 5.80
187 188 2.486592 GTCAATAAACTTCACCACGGGG 59.513 50.000 0.00 0.00 41.29 5.73
188 189 3.408634 AGTCAATAAACTTCACCACGGG 58.591 45.455 0.00 0.00 0.00 5.28
189 190 4.513692 TCAAGTCAATAAACTTCACCACGG 59.486 41.667 0.00 0.00 37.38 4.94
190 191 5.666969 TCAAGTCAATAAACTTCACCACG 57.333 39.130 0.00 0.00 37.38 4.94
191 192 8.696410 TTTTTCAAGTCAATAAACTTCACCAC 57.304 30.769 0.00 0.00 37.38 4.16
199 200 9.921637 TGGGATGTATTTTTCAAGTCAATAAAC 57.078 29.630 0.00 0.00 0.00 2.01
201 202 9.921637 GTTGGGATGTATTTTTCAAGTCAATAA 57.078 29.630 0.00 0.00 0.00 1.40
202 203 9.083422 TGTTGGGATGTATTTTTCAAGTCAATA 57.917 29.630 0.00 0.00 0.00 1.90
203 204 7.961351 TGTTGGGATGTATTTTTCAAGTCAAT 58.039 30.769 0.00 0.00 0.00 2.57
204 205 7.353414 TGTTGGGATGTATTTTTCAAGTCAA 57.647 32.000 0.00 0.00 0.00 3.18
205 206 6.968263 TGTTGGGATGTATTTTTCAAGTCA 57.032 33.333 0.00 0.00 0.00 3.41
206 207 7.708752 TGTTTGTTGGGATGTATTTTTCAAGTC 59.291 33.333 0.00 0.00 0.00 3.01
207 208 7.560368 TGTTTGTTGGGATGTATTTTTCAAGT 58.440 30.769 0.00 0.00 0.00 3.16
208 209 8.606040 ATGTTTGTTGGGATGTATTTTTCAAG 57.394 30.769 0.00 0.00 0.00 3.02
209 210 8.206867 TGATGTTTGTTGGGATGTATTTTTCAA 58.793 29.630 0.00 0.00 0.00 2.69
210 211 7.655328 GTGATGTTTGTTGGGATGTATTTTTCA 59.345 33.333 0.00 0.00 0.00 2.69
221 222 2.217750 CGACTGTGATGTTTGTTGGGA 58.782 47.619 0.00 0.00 0.00 4.37
250 251 2.504367 CGAGTCATCAACAACCCCTTT 58.496 47.619 0.00 0.00 0.00 3.11
253 254 0.605319 TGCGAGTCATCAACAACCCC 60.605 55.000 0.00 0.00 0.00 4.95
257 258 4.930963 ACATTTTTGCGAGTCATCAACAA 58.069 34.783 0.00 0.00 0.00 2.83
258 259 4.566545 ACATTTTTGCGAGTCATCAACA 57.433 36.364 0.00 0.00 0.00 3.33
306 307 3.371965 ACCCGTTATAGTCTCACCACAT 58.628 45.455 0.00 0.00 0.00 3.21
392 393 2.981859 GAAAAGATCCAGGGCTACGA 57.018 50.000 0.00 0.00 0.00 3.43
450 451 3.068024 GTGACCAAATGAAAAGGACAGCA 59.932 43.478 0.00 0.00 0.00 4.41
468 469 0.039074 CCCACTGTCGACTGAGTGAC 60.039 60.000 28.32 0.00 41.90 3.67
491 492 1.409064 TCCTCACACTCACACTCACAC 59.591 52.381 0.00 0.00 0.00 3.82
492 493 1.775385 TCCTCACACTCACACTCACA 58.225 50.000 0.00 0.00 0.00 3.58
493 494 2.748605 CTTCCTCACACTCACACTCAC 58.251 52.381 0.00 0.00 0.00 3.51
494 495 1.069204 GCTTCCTCACACTCACACTCA 59.931 52.381 0.00 0.00 0.00 3.41
495 496 1.069204 TGCTTCCTCACACTCACACTC 59.931 52.381 0.00 0.00 0.00 3.51
496 497 1.069823 CTGCTTCCTCACACTCACACT 59.930 52.381 0.00 0.00 0.00 3.55
537 538 1.334992 CGACGTAACTGTGCCACGAG 61.335 60.000 14.26 6.38 38.96 4.18
539 540 2.995450 GCGACGTAACTGTGCCACG 61.995 63.158 0.00 7.91 41.32 4.94
653 672 6.084925 CGTCGAACAAGTATCTTAGTTGAGT 58.915 40.000 8.65 0.00 40.68 3.41
729 751 1.534163 CATCTGGCCACATAATCTGCG 59.466 52.381 0.00 0.00 0.00 5.18
768 790 1.061711 GCGCTGAGTGACATTAGCTTG 59.938 52.381 0.00 0.00 34.13 4.01
894 918 0.686224 GATGGATGCTGGAGAGAGGG 59.314 60.000 0.00 0.00 0.00 4.30
1654 1701 7.659390 CAGAAGAGAGAAACCATCTACAAACTT 59.341 37.037 0.00 0.00 38.96 2.66
1655 1702 7.158021 CAGAAGAGAGAAACCATCTACAAACT 58.842 38.462 0.00 0.00 38.96 2.66
1656 1703 6.931840 ACAGAAGAGAGAAACCATCTACAAAC 59.068 38.462 0.00 0.00 38.96 2.93
1657 1704 7.067496 ACAGAAGAGAGAAACCATCTACAAA 57.933 36.000 0.00 0.00 38.96 2.83
1658 1705 6.672266 ACAGAAGAGAGAAACCATCTACAA 57.328 37.500 0.00 0.00 38.96 2.41
1659 1706 6.295349 GGAACAGAAGAGAGAAACCATCTACA 60.295 42.308 0.00 0.00 38.96 2.74
1660 1707 6.103330 GGAACAGAAGAGAGAAACCATCTAC 58.897 44.000 0.00 0.00 38.96 2.59
1693 1748 1.224592 CCCCATCTGTTTCCTCCCG 59.775 63.158 0.00 0.00 0.00 5.14
1707 1762 7.989947 ACAGTAGTAGAGAAAAATATCCCCA 57.010 36.000 0.00 0.00 0.00 4.96
1846 1901 2.975536 GTGGGTGACGAATCCGGA 59.024 61.111 6.61 6.61 40.78 5.14
1865 1920 2.559231 GTTTTCAGGTTTGGCGGGATTA 59.441 45.455 0.00 0.00 0.00 1.75
2009 2107 0.179084 CCGCGGGCTAGAGAAATTGA 60.179 55.000 20.10 0.00 0.00 2.57
2511 2888 6.481643 ACCACAACCTACAGTATAAGCATTT 58.518 36.000 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.