Multiple sequence alignment - TraesCS2D01G059400

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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 TraesCS2D01G059400 chr2D 100.000 4547 0 0 666 5212 24705663 24701117 0.000000e+00 8397.0
1 TraesCS2D01G059400 chr2D 84.780 1406 142 30 2993 4361 24560299 24558929 0.000000e+00 1345.0
2 TraesCS2D01G059400 chr2D 89.604 606 48 9 1991 2581 24561301 24560696 0.000000e+00 756.0
3 TraesCS2D01G059400 chr2D 85.996 557 63 8 1213 1764 24562305 24561759 2.700000e-162 582.0
4 TraesCS2D01G059400 chr2D 89.646 367 24 7 2583 2945 24560655 24560299 6.150000e-124 455.0
5 TraesCS2D01G059400 chr2D 82.238 411 55 9 666 1075 24562806 24562413 6.460000e-89 339.0
6 TraesCS2D01G059400 chr2D 87.190 242 23 5 1763 2000 24561700 24561463 8.600000e-68 268.0
7 TraesCS2D01G059400 chr2D 100.000 110 0 0 1 110 24706328 24706219 2.460000e-48 204.0
8 TraesCS2D01G059400 chr2A 94.114 2939 135 20 666 3580 27328052 27330976 0.000000e+00 4434.0
9 TraesCS2D01G059400 chr2A 84.286 1400 143 37 2990 4357 27342249 27343603 0.000000e+00 1295.0
10 TraesCS2D01G059400 chr2A 93.086 781 29 3 3807 4569 27331082 27331855 0.000000e+00 1120.0
11 TraesCS2D01G059400 chr2A 89.274 606 50 9 1991 2581 27341250 27341855 0.000000e+00 745.0
12 TraesCS2D01G059400 chr2A 84.767 558 69 11 1213 1764 27340245 27340792 3.550000e-151 545.0
13 TraesCS2D01G059400 chr2A 95.210 334 15 1 4585 4917 27331923 27332256 1.290000e-145 527.0
14 TraesCS2D01G059400 chr2A 93.960 298 15 3 4916 5212 27332646 27332941 1.030000e-121 448.0
15 TraesCS2D01G059400 chr2A 88.919 370 27 6 2580 2945 27341893 27342252 1.330000e-120 444.0
16 TraesCS2D01G059400 chr2A 80.513 390 58 12 689 1072 27339757 27340134 3.070000e-72 283.0
17 TraesCS2D01G059400 chr2A 97.059 102 3 0 3624 3725 27330983 27331084 6.940000e-39 172.0
18 TraesCS2D01G059400 chr2A 89.815 108 7 4 4370 4474 27343647 27343753 9.100000e-28 135.0
19 TraesCS2D01G059400 chr2B 93.702 2080 83 16 2523 4569 40068490 40070554 0.000000e+00 3072.0
20 TraesCS2D01G059400 chr2B 94.247 1408 56 12 1084 2473 40067091 40068491 0.000000e+00 2128.0
21 TraesCS2D01G059400 chr2B 82.436 1412 164 53 2990 4361 40277614 40278981 0.000000e+00 1157.0
22 TraesCS2D01G059400 chr2B 89.934 606 46 9 1991 2581 40276608 40277213 0.000000e+00 767.0
23 TraesCS2D01G059400 chr2B 93.548 465 28 2 666 1130 40066642 40067104 0.000000e+00 691.0
24 TraesCS2D01G059400 chr2B 88.710 372 31 6 2580 2945 40277251 40277617 1.330000e-120 444.0
25 TraesCS2D01G059400 chr2B 84.410 449 54 13 1325 1764 40275709 40276150 1.340000e-115 427.0
26 TraesCS2D01G059400 chr2B 86.777 242 24 5 1763 2000 40276209 40276446 4.000000e-66 263.0
27 TraesCS2D01G059400 chr2B 85.714 119 17 0 1102 1220 445669129 445669011 5.480000e-25 126.0
28 TraesCS2D01G059400 chr2B 86.916 107 11 3 4370 4474 40279017 40279122 3.300000e-22 117.0
29 TraesCS2D01G059400 chr2B 95.122 41 2 0 4532 4572 40070484 40070524 1.210000e-06 65.8
30 TraesCS2D01G059400 chr5B 77.574 272 26 17 4234 4474 49007512 49007245 1.180000e-26 132.0
31 TraesCS2D01G059400 chr7A 100.000 28 0 0 77 104 87376892 87376865 9.000000e-03 52.8


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 TraesCS2D01G059400 chr2D 24701117 24706328 5211 True 4300.500000 8397 100.000000 1 5212 2 chr2D.!!$R2 5211
1 TraesCS2D01G059400 chr2D 24558929 24562806 3877 True 624.166667 1345 86.575667 666 4361 6 chr2D.!!$R1 3695
2 TraesCS2D01G059400 chr2A 27328052 27332941 4889 False 1340.200000 4434 94.685800 666 5212 5 chr2A.!!$F1 4546
3 TraesCS2D01G059400 chr2A 27339757 27343753 3996 False 574.500000 1295 86.262333 689 4474 6 chr2A.!!$F2 3785
4 TraesCS2D01G059400 chr2B 40066642 40070554 3912 False 1489.200000 3072 94.154750 666 4572 4 chr2B.!!$F1 3906
5 TraesCS2D01G059400 chr2B 40275709 40279122 3413 False 529.166667 1157 86.530500 1325 4474 6 chr2B.!!$F2 3149

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
47 48 0.250234 TAGCAGATCTGTGTGTGGGC 59.750 55.000 23.38 6.93 0.00 5.36 F
98 99 0.250727 CTGCTCCCTCCGTTCCAAAA 60.251 55.000 0.00 0.00 0.00 2.44 F
99 100 0.404040 TGCTCCCTCCGTTCCAAAAT 59.596 50.000 0.00 0.00 0.00 1.82 F
100 101 1.631388 TGCTCCCTCCGTTCCAAAATA 59.369 47.619 0.00 0.00 0.00 1.40 F
2084 2395 0.035630 GAGGAGGTTGTGCAGATGCT 60.036 55.000 6.35 0.00 42.66 3.79 F
2333 2644 1.476891 TGTCGGAGTTCCAGATACTGC 59.523 52.381 0.00 0.00 35.14 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1202 1277 0.817654 TCGATCCTTGCGAGACACAT 59.182 50.000 1.22 0.00 33.33 3.21 R
1815 1955 2.359602 CCAGGCTGCTGTCCACAG 60.360 66.667 9.56 2.06 46.40 3.66 R
2084 2395 3.849574 TGAATCTAATTGACCCTCCACCA 59.150 43.478 0.00 0.00 0.00 4.17 R
2144 2455 4.413969 TGCTTGTTCAACATTCATATGCG 58.586 39.130 0.00 0.00 35.03 4.73 R
3074 3448 1.135094 GCTCAGGAGATGGGGATTCA 58.865 55.000 0.00 0.00 0.00 2.57 R
4309 4786 0.470341 GGGCCGCCTATCTCTCTTTT 59.530 55.000 9.86 0.00 0.00 2.27 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
17 18 4.193334 TCGCGTCTCAGGCCGATG 62.193 66.667 5.77 0.00 0.00 3.84
18 19 4.193334 CGCGTCTCAGGCCGATGA 62.193 66.667 0.00 0.00 0.00 2.92
19 20 2.184322 GCGTCTCAGGCCGATGAA 59.816 61.111 0.00 0.00 0.00 2.57
20 21 1.447838 GCGTCTCAGGCCGATGAAA 60.448 57.895 0.00 0.00 0.00 2.69
21 22 0.811616 GCGTCTCAGGCCGATGAAAT 60.812 55.000 0.00 0.00 0.00 2.17
22 23 0.933097 CGTCTCAGGCCGATGAAATG 59.067 55.000 0.00 0.00 0.00 2.32
23 24 1.471501 CGTCTCAGGCCGATGAAATGA 60.472 52.381 0.00 0.00 0.00 2.57
24 25 2.632377 GTCTCAGGCCGATGAAATGAA 58.368 47.619 0.00 0.00 0.00 2.57
25 26 3.209410 GTCTCAGGCCGATGAAATGAAT 58.791 45.455 0.00 0.00 0.00 2.57
26 27 3.249559 GTCTCAGGCCGATGAAATGAATC 59.750 47.826 0.00 0.00 0.00 2.52
27 28 2.212652 TCAGGCCGATGAAATGAATCG 58.787 47.619 0.00 0.00 45.08 3.34
28 29 1.942657 CAGGCCGATGAAATGAATCGT 59.057 47.619 0.00 0.00 44.22 3.73
29 30 3.130633 CAGGCCGATGAAATGAATCGTA 58.869 45.455 0.00 0.00 44.22 3.43
30 31 3.185188 CAGGCCGATGAAATGAATCGTAG 59.815 47.826 0.00 0.00 44.22 3.51
31 32 2.096218 GGCCGATGAAATGAATCGTAGC 60.096 50.000 5.24 2.64 44.22 3.58
32 33 2.543848 GCCGATGAAATGAATCGTAGCA 59.456 45.455 5.24 0.00 44.22 3.49
33 34 3.363378 GCCGATGAAATGAATCGTAGCAG 60.363 47.826 5.24 0.00 44.22 4.24
34 35 4.051237 CCGATGAAATGAATCGTAGCAGA 58.949 43.478 5.24 0.00 44.22 4.26
35 36 4.687948 CCGATGAAATGAATCGTAGCAGAT 59.312 41.667 5.24 0.00 44.22 2.90
36 37 5.164012 CCGATGAAATGAATCGTAGCAGATC 60.164 44.000 5.24 0.00 44.22 2.75
37 38 5.632764 CGATGAAATGAATCGTAGCAGATCT 59.367 40.000 0.00 0.00 41.52 2.75
38 39 6.399775 CGATGAAATGAATCGTAGCAGATCTG 60.400 42.308 18.84 18.84 41.52 2.90
39 40 5.664457 TGAAATGAATCGTAGCAGATCTGT 58.336 37.500 23.38 12.80 0.00 3.41
40 41 5.521372 TGAAATGAATCGTAGCAGATCTGTG 59.479 40.000 23.38 11.46 0.00 3.66
41 42 4.662468 ATGAATCGTAGCAGATCTGTGT 57.338 40.909 23.38 13.77 0.00 3.72
42 43 3.774066 TGAATCGTAGCAGATCTGTGTG 58.226 45.455 23.38 11.45 0.00 3.82
43 44 3.193479 TGAATCGTAGCAGATCTGTGTGT 59.807 43.478 23.38 9.04 0.00 3.72
44 45 2.636768 TCGTAGCAGATCTGTGTGTG 57.363 50.000 23.38 10.47 0.00 3.82
45 46 1.202348 TCGTAGCAGATCTGTGTGTGG 59.798 52.381 23.38 8.99 0.00 4.17
46 47 1.737029 CGTAGCAGATCTGTGTGTGGG 60.737 57.143 23.38 4.09 0.00 4.61
47 48 0.250234 TAGCAGATCTGTGTGTGGGC 59.750 55.000 23.38 6.93 0.00 5.36
48 49 1.002868 GCAGATCTGTGTGTGGGCT 60.003 57.895 23.38 0.00 0.00 5.19
49 50 1.303799 GCAGATCTGTGTGTGGGCTG 61.304 60.000 23.38 0.00 0.00 4.85
50 51 1.002868 AGATCTGTGTGTGGGCTGC 60.003 57.895 0.00 0.00 0.00 5.25
51 52 2.359107 ATCTGTGTGTGGGCTGCG 60.359 61.111 0.00 0.00 0.00 5.18
52 53 3.182590 ATCTGTGTGTGGGCTGCGT 62.183 57.895 0.00 0.00 0.00 5.24
53 54 2.680974 ATCTGTGTGTGGGCTGCGTT 62.681 55.000 0.00 0.00 0.00 4.84
54 55 3.185082 CTGTGTGTGGGCTGCGTTG 62.185 63.158 0.00 0.00 0.00 4.10
55 56 2.899838 GTGTGTGGGCTGCGTTGA 60.900 61.111 0.00 0.00 0.00 3.18
56 57 2.899838 TGTGTGGGCTGCGTTGAC 60.900 61.111 0.00 0.00 0.00 3.18
57 58 2.591715 GTGTGGGCTGCGTTGACT 60.592 61.111 0.00 0.00 0.00 3.41
58 59 2.280797 TGTGGGCTGCGTTGACTC 60.281 61.111 0.00 0.00 0.00 3.36
59 60 2.031163 GTGGGCTGCGTTGACTCT 59.969 61.111 0.00 0.00 0.00 3.24
60 61 2.029844 GTGGGCTGCGTTGACTCTC 61.030 63.158 0.00 0.00 0.00 3.20
61 62 2.343758 GGGCTGCGTTGACTCTCA 59.656 61.111 0.00 0.00 0.00 3.27
62 63 1.301716 GGGCTGCGTTGACTCTCAA 60.302 57.895 0.00 0.00 33.32 3.02
63 64 0.674895 GGGCTGCGTTGACTCTCAAT 60.675 55.000 0.00 0.00 38.79 2.57
64 65 0.723981 GGCTGCGTTGACTCTCAATC 59.276 55.000 0.00 0.00 38.79 2.67
65 66 1.674221 GGCTGCGTTGACTCTCAATCT 60.674 52.381 0.00 0.00 38.79 2.40
66 67 1.392853 GCTGCGTTGACTCTCAATCTG 59.607 52.381 0.00 0.00 38.79 2.90
67 68 1.392853 CTGCGTTGACTCTCAATCTGC 59.607 52.381 0.00 0.00 38.79 4.26
68 69 0.723981 GCGTTGACTCTCAATCTGCC 59.276 55.000 0.00 0.00 38.79 4.85
69 70 1.941209 GCGTTGACTCTCAATCTGCCA 60.941 52.381 0.00 0.00 38.79 4.92
70 71 2.625737 CGTTGACTCTCAATCTGCCAT 58.374 47.619 0.00 0.00 38.79 4.40
71 72 3.785486 CGTTGACTCTCAATCTGCCATA 58.215 45.455 0.00 0.00 38.79 2.74
72 73 3.801050 CGTTGACTCTCAATCTGCCATAG 59.199 47.826 0.00 0.00 38.79 2.23
73 74 4.679106 CGTTGACTCTCAATCTGCCATAGT 60.679 45.833 0.00 0.00 38.79 2.12
74 75 5.181748 GTTGACTCTCAATCTGCCATAGTT 58.818 41.667 0.00 0.00 38.79 2.24
75 76 6.341316 GTTGACTCTCAATCTGCCATAGTTA 58.659 40.000 0.00 0.00 38.79 2.24
76 77 6.154203 TGACTCTCAATCTGCCATAGTTAG 57.846 41.667 0.00 0.00 0.00 2.34
77 78 5.658634 TGACTCTCAATCTGCCATAGTTAGT 59.341 40.000 0.00 0.00 0.00 2.24
78 79 6.833933 TGACTCTCAATCTGCCATAGTTAGTA 59.166 38.462 0.00 0.00 0.00 1.82
79 80 7.045126 ACTCTCAATCTGCCATAGTTAGTAC 57.955 40.000 0.00 0.00 0.00 2.73
80 81 6.836527 ACTCTCAATCTGCCATAGTTAGTACT 59.163 38.462 0.00 0.00 38.44 2.73
81 82 7.043961 TCTCAATCTGCCATAGTTAGTACTG 57.956 40.000 5.39 0.00 35.78 2.74
82 83 5.601662 TCAATCTGCCATAGTTAGTACTGC 58.398 41.667 5.39 0.00 35.78 4.40
83 84 5.363868 TCAATCTGCCATAGTTAGTACTGCT 59.636 40.000 5.39 6.34 35.78 4.24
84 85 4.920640 TCTGCCATAGTTAGTACTGCTC 57.079 45.455 5.39 0.00 35.78 4.26
85 86 3.637229 TCTGCCATAGTTAGTACTGCTCC 59.363 47.826 5.39 0.00 35.78 4.70
86 87 2.698797 TGCCATAGTTAGTACTGCTCCC 59.301 50.000 5.39 0.00 35.78 4.30
87 88 2.966516 GCCATAGTTAGTACTGCTCCCT 59.033 50.000 5.39 0.00 35.78 4.20
88 89 3.006003 GCCATAGTTAGTACTGCTCCCTC 59.994 52.174 5.39 0.00 35.78 4.30
89 90 3.574826 CCATAGTTAGTACTGCTCCCTCC 59.425 52.174 5.39 0.00 35.78 4.30
90 91 1.765230 AGTTAGTACTGCTCCCTCCG 58.235 55.000 5.39 0.00 31.99 4.63
91 92 1.005687 AGTTAGTACTGCTCCCTCCGT 59.994 52.381 5.39 0.00 31.99 4.69
92 93 1.823610 GTTAGTACTGCTCCCTCCGTT 59.176 52.381 5.39 0.00 0.00 4.44
93 94 1.760192 TAGTACTGCTCCCTCCGTTC 58.240 55.000 5.39 0.00 0.00 3.95
94 95 0.971447 AGTACTGCTCCCTCCGTTCC 60.971 60.000 0.00 0.00 0.00 3.62
95 96 1.077805 TACTGCTCCCTCCGTTCCA 59.922 57.895 0.00 0.00 0.00 3.53
96 97 0.543410 TACTGCTCCCTCCGTTCCAA 60.543 55.000 0.00 0.00 0.00 3.53
97 98 1.374947 CTGCTCCCTCCGTTCCAAA 59.625 57.895 0.00 0.00 0.00 3.28
98 99 0.250727 CTGCTCCCTCCGTTCCAAAA 60.251 55.000 0.00 0.00 0.00 2.44
99 100 0.404040 TGCTCCCTCCGTTCCAAAAT 59.596 50.000 0.00 0.00 0.00 1.82
100 101 1.631388 TGCTCCCTCCGTTCCAAAATA 59.369 47.619 0.00 0.00 0.00 1.40
101 102 2.289565 GCTCCCTCCGTTCCAAAATAG 58.710 52.381 0.00 0.00 0.00 1.73
102 103 2.093128 GCTCCCTCCGTTCCAAAATAGA 60.093 50.000 0.00 0.00 0.00 1.98
103 104 3.433740 GCTCCCTCCGTTCCAAAATAGAT 60.434 47.826 0.00 0.00 0.00 1.98
104 105 4.781934 CTCCCTCCGTTCCAAAATAGATT 58.218 43.478 0.00 0.00 0.00 2.40
105 106 5.686650 GCTCCCTCCGTTCCAAAATAGATTA 60.687 44.000 0.00 0.00 0.00 1.75
106 107 5.925509 TCCCTCCGTTCCAAAATAGATTAG 58.074 41.667 0.00 0.00 0.00 1.73
107 108 5.664006 TCCCTCCGTTCCAAAATAGATTAGA 59.336 40.000 0.00 0.00 0.00 2.10
108 109 6.329197 TCCCTCCGTTCCAAAATAGATTAGAT 59.671 38.462 0.00 0.00 0.00 1.98
109 110 6.428159 CCCTCCGTTCCAAAATAGATTAGATG 59.572 42.308 0.00 0.00 0.00 2.90
788 789 5.711506 TCAAACATATTGTGATGCTTCAGGT 59.288 36.000 1.91 0.00 30.85 4.00
789 790 5.571784 AACATATTGTGATGCTTCAGGTG 57.428 39.130 1.91 1.28 30.85 4.00
833 847 6.992063 ATCATAATGTGGTGTCTGTTTCTC 57.008 37.500 0.00 0.00 0.00 2.87
947 962 6.289064 TCCTTTTAACCTTCACTTCTCTGAC 58.711 40.000 0.00 0.00 0.00 3.51
959 974 4.869297 CACTTCTCTGACTAGATTTGGCTG 59.131 45.833 0.00 0.00 31.21 4.85
1167 1242 4.142816 CCCTCAGAACTTAATGTTGCTTCG 60.143 45.833 0.00 0.00 39.30 3.79
1184 1259 3.737047 GCTTCGGTTGATGATAGTTCCGA 60.737 47.826 0.00 0.00 43.93 4.55
1202 1277 3.119137 TCCGATGAAGAAGATTCTCGCAA 60.119 43.478 0.00 0.00 36.28 4.85
1315 1390 2.153401 CAGTGTGGGGGTCTTGGGA 61.153 63.158 0.00 0.00 0.00 4.37
1417 1492 3.604875 AGGCGAAAAGAAAGACGGATA 57.395 42.857 0.00 0.00 0.00 2.59
1478 1556 9.956640 ATCAACAAAGAGAGATGAAATTAGTCT 57.043 29.630 0.00 0.00 0.00 3.24
1815 1955 5.277538 GCATCAGTTTCCCATCGAAGATAAC 60.278 44.000 0.00 0.00 45.12 1.89
1902 2045 5.692814 CATTTGTATGACAGTGTGGAACAG 58.307 41.667 0.00 0.00 40.25 3.16
2084 2395 0.035630 GAGGAGGTTGTGCAGATGCT 60.036 55.000 6.35 0.00 42.66 3.79
2144 2455 8.962679 TGGTGTGAAAACAAAGGATATATTACC 58.037 33.333 0.00 0.00 0.00 2.85
2269 2580 9.720769 GGCTAGAAAATATAGTTTATGGTGCTA 57.279 33.333 3.20 0.00 0.00 3.49
2316 2627 6.704512 TGTTTTGAAACAAAAGCTTCTGTC 57.295 33.333 5.76 0.00 45.17 3.51
2333 2644 1.476891 TGTCGGAGTTCCAGATACTGC 59.523 52.381 0.00 0.00 35.14 4.40
2342 2653 2.103373 TCCAGATACTGCTGTGACTCC 58.897 52.381 6.48 0.00 34.06 3.85
2343 2654 1.827344 CCAGATACTGCTGTGACTCCA 59.173 52.381 6.48 0.00 34.06 3.86
2349 2675 1.486310 ACTGCTGTGACTCCAACAGAA 59.514 47.619 7.72 0.00 33.65 3.02
2359 2685 5.758296 GTGACTCCAACAGAAGTTTCACATA 59.242 40.000 0.00 0.00 39.67 2.29
2394 2720 2.438434 GCCAACATGGAGGGGTCG 60.438 66.667 0.00 0.00 40.96 4.79
2412 2738 4.511826 GGGTCGTCAAAGGATATGAATCAC 59.488 45.833 0.00 0.00 33.41 3.06
2581 2946 8.746052 TCCTGAAGAAACACAAGAAATTTCTA 57.254 30.769 20.76 0.30 40.85 2.10
2855 3227 6.932356 ATCTATGCCATCTGTAGTGTTTTG 57.068 37.500 0.00 0.00 0.00 2.44
2856 3228 5.804639 TCTATGCCATCTGTAGTGTTTTGT 58.195 37.500 0.00 0.00 0.00 2.83
2964 3338 8.058667 TGAAGATTGTGATGCAAGTAATCAAT 57.941 30.769 14.59 9.46 40.86 2.57
3074 3448 5.685728 AGCAAAGGAGTTCTTAAGTCAACT 58.314 37.500 8.82 8.82 35.48 3.16
3097 3471 0.267054 TCCCCATCTCCTGAGCTGAT 59.733 55.000 0.00 0.00 0.00 2.90
3164 3538 4.277423 TCACAAAGGCAGATGCATGATATG 59.723 41.667 2.46 0.00 44.36 1.78
3233 3607 5.744490 AGTTTAGTGGACGAAAATTTGTCG 58.256 37.500 7.43 7.43 41.53 4.35
3272 3646 3.640967 TGCTTCCCAATTTTAACACTGCT 59.359 39.130 0.00 0.00 0.00 4.24
3282 3656 4.623932 TTTAACACTGCTGAGGTGAGAT 57.376 40.909 0.00 0.00 38.01 2.75
3337 3711 4.916983 TTGATTTTACTGCTGTGCAACT 57.083 36.364 6.48 0.00 38.41 3.16
3475 3855 2.975732 TCCTGTCAGCTGCTTCTATG 57.024 50.000 9.47 0.00 0.00 2.23
3614 4005 8.050778 GGTTCTCATGTAAACCATATGTTTGA 57.949 34.615 20.19 0.00 46.50 2.69
3802 4242 2.812591 CTGAAGTTCACAGCTGCTTGAT 59.187 45.455 15.27 0.00 0.00 2.57
3890 4330 1.067250 GAGAGCAGCATCCGAGGAC 59.933 63.158 0.00 0.00 0.00 3.85
4184 4656 5.169295 GTGTTTAGTGATGTACAGACCTCC 58.831 45.833 0.33 0.00 0.00 4.30
4261 4733 9.423061 AGGCAATTTTGTTGTAATAAGTTGATC 57.577 29.630 0.00 0.00 0.00 2.92
4512 5041 2.019984 GCCATGTGGATTCCTCTGTTC 58.980 52.381 2.55 0.00 37.39 3.18
4569 5098 5.843673 TTAGCCATGACACTGTTTTTGAA 57.156 34.783 0.00 0.00 0.00 2.69
4570 5099 4.942761 AGCCATGACACTGTTTTTGAAT 57.057 36.364 0.00 0.00 0.00 2.57
4571 5100 5.280654 AGCCATGACACTGTTTTTGAATT 57.719 34.783 0.00 0.00 0.00 2.17
4572 5101 5.051816 AGCCATGACACTGTTTTTGAATTG 58.948 37.500 0.00 0.00 0.00 2.32
4573 5102 4.318974 GCCATGACACTGTTTTTGAATTGC 60.319 41.667 0.00 0.00 0.00 3.56
4574 5103 5.051816 CCATGACACTGTTTTTGAATTGCT 58.948 37.500 0.00 0.00 0.00 3.91
4575 5104 5.050634 CCATGACACTGTTTTTGAATTGCTG 60.051 40.000 0.00 0.00 0.00 4.41
4576 5105 4.431809 TGACACTGTTTTTGAATTGCTGG 58.568 39.130 0.00 0.00 0.00 4.85
4578 5107 4.183101 ACACTGTTTTTGAATTGCTGGTG 58.817 39.130 0.00 0.00 0.00 4.17
4579 5108 3.001533 CACTGTTTTTGAATTGCTGGTGC 59.998 43.478 0.00 0.00 40.20 5.01
4581 5110 1.070643 GTTTTTGAATTGCTGGTGCGC 60.071 47.619 0.00 0.00 43.34 6.09
4582 5111 0.103755 TTTTGAATTGCTGGTGCGCA 59.896 45.000 5.66 5.66 43.34 6.09
4583 5112 0.597118 TTTGAATTGCTGGTGCGCAC 60.597 50.000 32.15 32.15 43.34 5.34
4610 5191 3.278574 GGGGTCAATCGTTCATCATTCA 58.721 45.455 0.00 0.00 0.00 2.57
4644 5225 4.406003 TCTTGGGCTGAGAGTAGAAATACC 59.594 45.833 0.00 0.00 0.00 2.73
4708 5289 8.758633 TCTGTAAAAGTATTGTTCTGACTAGC 57.241 34.615 0.00 0.00 0.00 3.42
4744 5325 3.157087 AGGCACTTCATAAAGTTGTGGG 58.843 45.455 0.00 0.00 43.28 4.61
4745 5326 3.153919 GGCACTTCATAAAGTTGTGGGA 58.846 45.455 0.00 0.00 43.28 4.37
4759 5340 5.630121 AGTTGTGGGATCTAAATTGTGACA 58.370 37.500 0.00 0.00 0.00 3.58
4790 5372 7.393515 GTGGTTAGAGGGAAAACATGAGTTATT 59.606 37.037 0.00 0.00 36.84 1.40
5012 5985 7.602517 ACGATTTTCCTAATTCTGAGTTGAG 57.397 36.000 0.00 0.00 0.00 3.02
5029 6002 8.092521 TGAGTTGAGTGAGATTTTTGATTCTC 57.907 34.615 0.00 0.00 39.07 2.87
5030 6003 7.716560 TGAGTTGAGTGAGATTTTTGATTCTCA 59.283 33.333 0.00 0.00 44.55 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 0.811616 ATTTCATCGGCCTGAGACGC 60.812 55.000 0.00 0.00 0.00 5.19
3 4 0.933097 CATTTCATCGGCCTGAGACG 59.067 55.000 0.00 0.00 0.00 4.18
5 6 3.470709 GATTCATTTCATCGGCCTGAGA 58.529 45.455 0.00 0.00 0.00 3.27
7 8 2.212652 CGATTCATTTCATCGGCCTGA 58.787 47.619 0.00 0.00 39.94 3.86
8 9 1.942657 ACGATTCATTTCATCGGCCTG 59.057 47.619 0.00 0.00 46.44 4.85
9 10 2.332063 ACGATTCATTTCATCGGCCT 57.668 45.000 0.00 0.00 46.44 5.19
10 11 2.096218 GCTACGATTCATTTCATCGGCC 60.096 50.000 7.20 0.00 46.44 6.13
11 12 2.543848 TGCTACGATTCATTTCATCGGC 59.456 45.455 7.20 2.71 46.44 5.54
12 13 4.051237 TCTGCTACGATTCATTTCATCGG 58.949 43.478 7.20 0.00 46.44 4.18
14 15 6.423302 ACAGATCTGCTACGATTCATTTCATC 59.577 38.462 22.83 0.00 0.00 2.92
15 16 6.202379 CACAGATCTGCTACGATTCATTTCAT 59.798 38.462 22.83 0.00 0.00 2.57
16 17 5.521372 CACAGATCTGCTACGATTCATTTCA 59.479 40.000 22.83 0.00 0.00 2.69
17 18 5.521735 ACACAGATCTGCTACGATTCATTTC 59.478 40.000 22.83 0.00 0.00 2.17
18 19 5.292834 CACACAGATCTGCTACGATTCATTT 59.707 40.000 22.83 0.00 0.00 2.32
19 20 4.807834 CACACAGATCTGCTACGATTCATT 59.192 41.667 22.83 0.00 0.00 2.57
20 21 4.142071 ACACACAGATCTGCTACGATTCAT 60.142 41.667 22.83 0.00 0.00 2.57
21 22 3.193479 ACACACAGATCTGCTACGATTCA 59.807 43.478 22.83 0.00 0.00 2.57
22 23 3.549471 CACACACAGATCTGCTACGATTC 59.451 47.826 22.83 0.00 0.00 2.52
23 24 3.515630 CACACACAGATCTGCTACGATT 58.484 45.455 22.83 0.00 0.00 3.34
24 25 2.159184 CCACACACAGATCTGCTACGAT 60.159 50.000 22.83 0.00 0.00 3.73
25 26 1.202348 CCACACACAGATCTGCTACGA 59.798 52.381 22.83 0.00 0.00 3.43
26 27 1.633561 CCACACACAGATCTGCTACG 58.366 55.000 22.83 11.06 0.00 3.51
27 28 2.009042 GCCCACACACAGATCTGCTAC 61.009 57.143 22.83 0.39 0.00 3.58
28 29 0.250234 GCCCACACACAGATCTGCTA 59.750 55.000 22.83 0.00 0.00 3.49
29 30 1.002868 GCCCACACACAGATCTGCT 60.003 57.895 22.83 7.28 0.00 4.24
30 31 1.002868 AGCCCACACACAGATCTGC 60.003 57.895 22.83 5.96 0.00 4.26
31 32 1.303799 GCAGCCCACACACAGATCTG 61.304 60.000 21.37 21.37 0.00 2.90
32 33 1.002868 GCAGCCCACACACAGATCT 60.003 57.895 0.00 0.00 0.00 2.75
33 34 2.393768 CGCAGCCCACACACAGATC 61.394 63.158 0.00 0.00 0.00 2.75
34 35 2.359107 CGCAGCCCACACACAGAT 60.359 61.111 0.00 0.00 0.00 2.90
35 36 3.399105 AACGCAGCCCACACACAGA 62.399 57.895 0.00 0.00 0.00 3.41
36 37 2.901840 AACGCAGCCCACACACAG 60.902 61.111 0.00 0.00 0.00 3.66
37 38 3.208383 CAACGCAGCCCACACACA 61.208 61.111 0.00 0.00 0.00 3.72
38 39 2.899838 TCAACGCAGCCCACACAC 60.900 61.111 0.00 0.00 0.00 3.82
39 40 2.899838 GTCAACGCAGCCCACACA 60.900 61.111 0.00 0.00 0.00 3.72
40 41 2.591715 AGTCAACGCAGCCCACAC 60.592 61.111 0.00 0.00 0.00 3.82
41 42 2.280797 GAGTCAACGCAGCCCACA 60.281 61.111 0.00 0.00 0.00 4.17
42 43 2.029844 GAGAGTCAACGCAGCCCAC 61.030 63.158 0.00 0.00 0.00 4.61
43 44 2.038814 TTGAGAGTCAACGCAGCCCA 62.039 55.000 0.00 0.00 30.26 5.36
44 45 0.674895 ATTGAGAGTCAACGCAGCCC 60.675 55.000 0.00 0.00 39.45 5.19
45 46 0.723981 GATTGAGAGTCAACGCAGCC 59.276 55.000 0.00 0.00 39.45 4.85
46 47 1.392853 CAGATTGAGAGTCAACGCAGC 59.607 52.381 0.00 0.00 39.45 5.25
47 48 1.392853 GCAGATTGAGAGTCAACGCAG 59.607 52.381 0.00 0.00 39.45 5.18
48 49 1.432514 GCAGATTGAGAGTCAACGCA 58.567 50.000 0.00 0.00 39.45 5.24
49 50 0.723981 GGCAGATTGAGAGTCAACGC 59.276 55.000 0.00 0.00 39.45 4.84
50 51 2.084610 TGGCAGATTGAGAGTCAACG 57.915 50.000 0.00 0.00 39.45 4.10
51 52 4.764172 ACTATGGCAGATTGAGAGTCAAC 58.236 43.478 0.00 0.00 39.45 3.18
52 53 5.426689 AACTATGGCAGATTGAGAGTCAA 57.573 39.130 0.00 0.00 41.09 3.18
53 54 5.658634 ACTAACTATGGCAGATTGAGAGTCA 59.341 40.000 0.00 0.00 0.00 3.41
54 55 6.155475 ACTAACTATGGCAGATTGAGAGTC 57.845 41.667 0.00 0.00 0.00 3.36
55 56 6.836527 AGTACTAACTATGGCAGATTGAGAGT 59.163 38.462 0.00 0.00 32.84 3.24
56 57 7.144661 CAGTACTAACTATGGCAGATTGAGAG 58.855 42.308 0.00 0.00 33.48 3.20
57 58 6.461648 GCAGTACTAACTATGGCAGATTGAGA 60.462 42.308 0.00 0.00 33.48 3.27
58 59 5.694006 GCAGTACTAACTATGGCAGATTGAG 59.306 44.000 0.00 0.00 33.48 3.02
59 60 5.363868 AGCAGTACTAACTATGGCAGATTGA 59.636 40.000 0.00 0.00 33.48 2.57
60 61 5.605534 AGCAGTACTAACTATGGCAGATTG 58.394 41.667 0.00 0.00 33.48 2.67
61 62 5.221541 GGAGCAGTACTAACTATGGCAGATT 60.222 44.000 0.00 0.00 33.48 2.40
62 63 4.282195 GGAGCAGTACTAACTATGGCAGAT 59.718 45.833 0.00 0.00 33.48 2.90
63 64 3.637229 GGAGCAGTACTAACTATGGCAGA 59.363 47.826 0.00 0.00 33.48 4.26
64 65 3.243907 GGGAGCAGTACTAACTATGGCAG 60.244 52.174 0.00 0.00 33.48 4.85
65 66 2.698797 GGGAGCAGTACTAACTATGGCA 59.301 50.000 0.00 0.00 33.48 4.92
66 67 2.966516 AGGGAGCAGTACTAACTATGGC 59.033 50.000 0.00 0.00 33.48 4.40
67 68 3.574826 GGAGGGAGCAGTACTAACTATGG 59.425 52.174 0.00 0.00 33.48 2.74
68 69 3.253677 CGGAGGGAGCAGTACTAACTATG 59.746 52.174 0.00 0.00 33.48 2.23
69 70 3.117587 ACGGAGGGAGCAGTACTAACTAT 60.118 47.826 0.00 0.00 33.48 2.12
70 71 2.240667 ACGGAGGGAGCAGTACTAACTA 59.759 50.000 0.00 0.00 33.48 2.24
71 72 1.005687 ACGGAGGGAGCAGTACTAACT 59.994 52.381 0.00 0.00 35.91 2.24
72 73 1.472188 ACGGAGGGAGCAGTACTAAC 58.528 55.000 0.00 0.00 0.00 2.34
73 74 2.097825 GAACGGAGGGAGCAGTACTAA 58.902 52.381 0.00 0.00 0.00 2.24
74 75 1.684248 GGAACGGAGGGAGCAGTACTA 60.684 57.143 0.00 0.00 0.00 1.82
75 76 0.971447 GGAACGGAGGGAGCAGTACT 60.971 60.000 0.00 0.00 0.00 2.73
76 77 1.255667 TGGAACGGAGGGAGCAGTAC 61.256 60.000 0.00 0.00 0.00 2.73
77 78 0.543410 TTGGAACGGAGGGAGCAGTA 60.543 55.000 0.00 0.00 0.00 2.74
78 79 1.415672 TTTGGAACGGAGGGAGCAGT 61.416 55.000 0.00 0.00 0.00 4.40
79 80 0.250727 TTTTGGAACGGAGGGAGCAG 60.251 55.000 0.00 0.00 0.00 4.24
80 81 0.404040 ATTTTGGAACGGAGGGAGCA 59.596 50.000 0.00 0.00 0.00 4.26
81 82 2.093128 TCTATTTTGGAACGGAGGGAGC 60.093 50.000 0.00 0.00 0.00 4.70
82 83 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
83 84 4.855298 AATCTATTTTGGAACGGAGGGA 57.145 40.909 0.00 0.00 0.00 4.20
84 85 5.925509 TCTAATCTATTTTGGAACGGAGGG 58.074 41.667 0.00 0.00 0.00 4.30
85 86 7.426929 CATCTAATCTATTTTGGAACGGAGG 57.573 40.000 0.00 0.00 0.00 4.30
710 711 6.811170 CGTAAGAGAGCAGAAGAAGAAGAAAT 59.189 38.462 0.00 0.00 43.02 2.17
714 715 5.303747 TCGTAAGAGAGCAGAAGAAGAAG 57.696 43.478 0.00 0.00 45.01 2.85
780 781 4.479619 CAAGCATCTTTTACACCTGAAGC 58.520 43.478 0.00 0.00 0.00 3.86
788 789 7.998580 TGATATTCATGCAAGCATCTTTTACA 58.001 30.769 4.24 0.28 33.90 2.41
904 919 2.424956 GGATCCCTGCAGACATGAAAAC 59.575 50.000 17.39 3.04 0.00 2.43
947 962 4.098349 TGCCTTATTTGCAGCCAAATCTAG 59.902 41.667 4.45 4.62 45.99 2.43
959 974 4.708726 ACAGATTGAGTGCCTTATTTGC 57.291 40.909 0.00 0.00 0.00 3.68
1167 1242 5.601662 TCTTCATCGGAACTATCATCAACC 58.398 41.667 0.00 0.00 0.00 3.77
1184 1259 4.940046 ACACATTGCGAGAATCTTCTTCAT 59.060 37.500 0.00 0.00 37.73 2.57
1202 1277 0.817654 TCGATCCTTGCGAGACACAT 59.182 50.000 1.22 0.00 33.33 3.21
1315 1390 6.486657 TCAACTTCCTCGTTTGATCTTTCAAT 59.513 34.615 0.00 0.00 41.38 2.57
1417 1492 3.928005 AGCATGTGGAGAAGATGATGT 57.072 42.857 0.00 0.00 31.04 3.06
1478 1556 6.105397 ACTCGAATAGGGAAGTTTGTACAA 57.895 37.500 3.59 3.59 0.00 2.41
1815 1955 2.359602 CCAGGCTGCTGTCCACAG 60.360 66.667 9.56 2.06 46.40 3.66
2084 2395 3.849574 TGAATCTAATTGACCCTCCACCA 59.150 43.478 0.00 0.00 0.00 4.17
2144 2455 4.413969 TGCTTGTTCAACATTCATATGCG 58.586 39.130 0.00 0.00 35.03 4.73
2269 2580 5.532406 ACTTCCGCTGCACATTATTATTCAT 59.468 36.000 0.00 0.00 0.00 2.57
2308 2619 0.603569 TCTGGAACTCCGACAGAAGC 59.396 55.000 0.00 0.00 38.22 3.86
2316 2627 1.478510 ACAGCAGTATCTGGAACTCCG 59.521 52.381 0.00 0.00 38.36 4.63
2333 2644 4.034510 GTGAAACTTCTGTTGGAGTCACAG 59.965 45.833 4.58 4.58 38.79 3.66
2342 2653 6.079763 CGACCATTATGTGAAACTTCTGTTG 58.920 40.000 0.00 0.00 38.04 3.33
2343 2654 5.334879 GCGACCATTATGTGAAACTTCTGTT 60.335 40.000 0.00 0.00 38.04 3.16
2349 2675 3.055094 AGAGGCGACCATTATGTGAAACT 60.055 43.478 0.00 0.00 38.04 2.66
2359 2685 1.679032 GGCAAGTAAGAGGCGACCATT 60.679 52.381 0.00 0.00 0.00 3.16
2412 2738 6.481976 TGTCAACATTCACTGTACCACTTAAG 59.518 38.462 0.00 0.00 36.98 1.85
2581 2946 0.679960 GACGCCCTAGTTTGCCCATT 60.680 55.000 0.00 0.00 0.00 3.16
2964 3338 5.008613 GCTTGTTTGTTGTCTGAGGTAATGA 59.991 40.000 0.00 0.00 0.00 2.57
3074 3448 1.135094 GCTCAGGAGATGGGGATTCA 58.865 55.000 0.00 0.00 0.00 2.57
3097 3471 7.012327 CAGTGTCCAAAAGAACAGATGAACTTA 59.988 37.037 0.00 0.00 0.00 2.24
3164 3538 1.749634 AGATTTGCTGCAATGCTCTCC 59.250 47.619 16.77 1.19 0.00 3.71
3404 3781 7.526608 TCTTAAATACATCTTTTTGTGCTCCG 58.473 34.615 0.00 0.00 0.00 4.63
3607 3998 6.201517 CGTGTGATCTTTTCAGTTCAAACAT 58.798 36.000 0.00 0.00 37.01 2.71
3614 4005 2.851195 AGGCGTGTGATCTTTTCAGTT 58.149 42.857 0.00 0.00 34.17 3.16
3700 4114 7.018249 ACCTAATTCAGAGGGAAAAAGGTAGAA 59.982 37.037 10.29 0.00 45.59 2.10
3802 4242 2.111384 GAGTTGGGCCTCATCTACTCA 58.889 52.381 4.53 0.00 33.86 3.41
3890 4330 3.600388 AGTTCTCTCCACCTTTAATGCG 58.400 45.455 0.00 0.00 0.00 4.73
4000 4446 9.561069 AGTTCAGAAAACACTTCAATACTATGT 57.439 29.630 0.00 0.00 0.00 2.29
4184 4656 2.515523 CCCTCGCATGCAGAAGGG 60.516 66.667 26.63 26.63 0.00 3.95
4261 4733 8.861033 TCTTGTTTGATTCTTCATTGTCAAAG 57.139 30.769 0.00 0.00 40.16 2.77
4309 4786 0.470341 GGGCCGCCTATCTCTCTTTT 59.530 55.000 9.86 0.00 0.00 2.27
4367 4848 5.923684 GGACTCTAGCATCTAAACATACAGC 59.076 44.000 0.00 0.00 0.00 4.40
4512 5041 4.333649 CCACAAACATAGTGTCATGGCTAG 59.666 45.833 0.00 0.00 35.24 3.42
4571 5100 2.357396 CTGTAGTGCGCACCAGCA 60.357 61.111 35.51 27.65 45.96 4.41
4572 5101 3.121030 CCTGTAGTGCGCACCAGC 61.121 66.667 35.51 24.84 37.71 4.85
4573 5102 2.434884 CCCTGTAGTGCGCACCAG 60.435 66.667 35.51 31.78 0.00 4.00
4574 5103 4.015406 CCCCTGTAGTGCGCACCA 62.015 66.667 35.51 25.44 0.00 4.17
4575 5104 4.778143 CCCCCTGTAGTGCGCACC 62.778 72.222 35.51 22.20 0.00 5.01
4576 5105 3.952628 GACCCCCTGTAGTGCGCAC 62.953 68.421 32.79 32.79 0.00 5.34
4578 5107 2.536997 ATTGACCCCCTGTAGTGCGC 62.537 60.000 0.00 0.00 0.00 6.09
4579 5108 0.462047 GATTGACCCCCTGTAGTGCG 60.462 60.000 0.00 0.00 0.00 5.34
4581 5110 0.902531 ACGATTGACCCCCTGTAGTG 59.097 55.000 0.00 0.00 0.00 2.74
4582 5111 1.553704 GAACGATTGACCCCCTGTAGT 59.446 52.381 0.00 0.00 0.00 2.73
4583 5112 1.553248 TGAACGATTGACCCCCTGTAG 59.447 52.381 0.00 0.00 0.00 2.74
4697 5278 4.923871 TGAATTCAACGAGCTAGTCAGAAC 59.076 41.667 5.45 6.45 0.00 3.01
4701 5282 5.179368 CCTTTTGAATTCAACGAGCTAGTCA 59.821 40.000 20.35 0.00 35.28 3.41
4706 5287 2.622942 TGCCTTTTGAATTCAACGAGCT 59.377 40.909 20.35 0.00 35.28 4.09
4708 5289 4.228912 AGTGCCTTTTGAATTCAACGAG 57.771 40.909 20.35 18.80 35.28 4.18
4744 5325 4.095483 CCACTGGCTGTCACAATTTAGATC 59.905 45.833 0.00 0.00 0.00 2.75
4745 5326 4.012374 CCACTGGCTGTCACAATTTAGAT 58.988 43.478 0.00 0.00 0.00 1.98
4759 5340 1.742308 TTTCCCTCTAACCACTGGCT 58.258 50.000 0.00 0.00 0.00 4.75
4850 5432 8.499162 GCACAGTTAGTTATCATCATCAATACC 58.501 37.037 0.00 0.00 0.00 2.73
4851 5433 9.045223 TGCACAGTTAGTTATCATCATCAATAC 57.955 33.333 0.00 0.00 0.00 1.89
4857 5439 5.371526 CCCTGCACAGTTAGTTATCATCAT 58.628 41.667 0.00 0.00 0.00 2.45
4974 5947 7.915293 AGGAAAATCGTTACACATATTCACA 57.085 32.000 0.00 0.00 0.00 3.58
4989 5962 7.331934 TCACTCAACTCAGAATTAGGAAAATCG 59.668 37.037 0.00 0.00 0.00 3.34
5029 6002 7.475015 TCACTTTTCAAAGTTGATTGAGACTG 58.525 34.615 2.01 0.00 46.52 3.51
5030 6003 7.630242 TCACTTTTCAAAGTTGATTGAGACT 57.370 32.000 2.01 0.00 46.52 3.24
5115 6088 6.691754 TTCAGTGAAAAGTGTATCTTGCAA 57.308 33.333 2.20 0.00 36.40 4.08


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

AutoCloner maintained by Alex Coulton.