Multiple sequence alignment - TraesCS3A01G433600

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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 TraesCS3A01G433600 chr3A 100.000 2681 0 0 1 2681 675288091 675285411 0.000000e+00 4951.0
1 TraesCS3A01G433600 chr3A 87.921 1010 99 18 1680 2681 464808203 464807209 0.000000e+00 1168.0
2 TraesCS3A01G433600 chr3A 87.413 1001 108 18 1689 2681 194908391 194909381 0.000000e+00 1134.0
3 TraesCS3A01G433600 chr3A 84.226 672 88 18 151 813 95579210 95578548 2.910000e-179 638.0
4 TraesCS3A01G433600 chr3A 84.125 674 84 21 152 813 95568429 95567767 4.870000e-177 630.0
5 TraesCS3A01G433600 chr3A 77.183 916 118 61 152 1036 427800049 427800904 1.460000e-122 449.0
6 TraesCS3A01G433600 chr3A 92.941 85 6 0 1041 1125 295406871 295406787 1.010000e-24 124.0
7 TraesCS3A01G433600 chr4A 93.458 1391 86 5 1293 2681 526176875 526178262 0.000000e+00 2060.0
8 TraesCS3A01G433600 chr4A 96.738 981 30 2 152 1131 526175274 526176253 0.000000e+00 1633.0
9 TraesCS3A01G433600 chr4A 95.825 982 38 3 152 1131 526207464 526208444 0.000000e+00 1583.0
10 TraesCS3A01G433600 chr4A 92.526 776 57 1 1291 2066 526209066 526209840 0.000000e+00 1110.0
11 TraesCS3A01G433600 chr4A 82.947 604 89 13 153 746 375266546 375267145 1.410000e-147 532.0
12 TraesCS3A01G433600 chr4A 90.448 335 32 0 1293 1627 349887409 349887075 2.450000e-120 442.0
13 TraesCS3A01G433600 chr4A 76.856 916 120 59 152 1036 215435427 215436281 1.470000e-117 433.0
14 TraesCS3A01G433600 chr4A 88.451 355 37 3 1291 1642 548861880 548861527 2.470000e-115 425.0
15 TraesCS3A01G433600 chr4A 87.921 356 37 5 1291 1642 548870033 548869680 5.340000e-112 414.0
16 TraesCS3A01G433600 chr4A 87.606 355 40 3 1291 1642 548853724 548853371 2.480000e-110 409.0
17 TraesCS3A01G433600 chr4A 94.709 189 7 2 849 1036 215428265 215428451 9.390000e-75 291.0
18 TraesCS3A01G433600 chr4A 96.000 150 5 1 1128 1277 526176623 526176771 2.670000e-60 243.0
19 TraesCS3A01G433600 chr4A 93.506 154 8 2 1128 1281 526208816 526208967 7.470000e-56 228.0
20 TraesCS3A01G433600 chr4A 91.667 120 6 3 775 894 153655243 153655128 2.140000e-36 163.0
21 TraesCS3A01G433600 chr4A 91.892 111 6 3 1018 1125 512835042 512835152 4.620000e-33 152.0
22 TraesCS3A01G433600 chr4A 85.185 108 12 3 775 881 78898485 78898589 1.010000e-19 108.0
23 TraesCS3A01G433600 chr2A 87.564 981 102 18 1707 2681 462860862 462861828 0.000000e+00 1118.0
24 TraesCS3A01G433600 chr2A 86.066 1055 124 22 1637 2681 577941581 577940540 0.000000e+00 1112.0
25 TraesCS3A01G433600 chr2A 81.674 1386 189 54 1320 2681 384095584 384094240 0.000000e+00 1092.0
26 TraesCS3A01G433600 chr2A 80.678 1387 197 57 1320 2681 384105040 384103700 0.000000e+00 1011.0
27 TraesCS3A01G433600 chr2A 85.841 565 60 16 152 710 350277084 350277634 1.380000e-162 582.0
28 TraesCS3A01G433600 chr2A 88.136 354 39 2 1293 1644 287775945 287776297 4.130000e-113 418.0
29 TraesCS3A01G433600 chr2A 80.174 459 68 18 152 599 169095219 169094773 3.330000e-84 322.0
30 TraesCS3A01G433600 chr2A 80.333 300 38 13 153 439 605558215 605557924 9.730000e-50 207.0
31 TraesCS3A01G433600 chr2A 95.050 101 4 1 1026 1125 445302300 445302400 9.940000e-35 158.0
32 TraesCS3A01G433600 chr2A 88.073 109 10 3 1008 1114 445262774 445262881 2.800000e-25 126.0
33 TraesCS3A01G433600 chr6A 84.348 1150 140 31 1547 2681 223235002 223233878 0.000000e+00 1090.0
34 TraesCS3A01G433600 chr6A 85.189 1087 129 27 1605 2681 344046658 344047722 0.000000e+00 1086.0
35 TraesCS3A01G433600 chr6A 85.528 1071 117 33 1631 2681 119316501 119317553 0.000000e+00 1085.0
36 TraesCS3A01G433600 chr6A 77.720 763 110 43 302 1036 551828542 551829272 1.920000e-111 412.0
37 TraesCS3A01G433600 chr6A 93.725 255 13 2 775 1029 64356594 64356343 1.950000e-101 379.0
38 TraesCS3A01G433600 chr6A 96.711 152 5 0 1 152 454769380 454769531 1.230000e-63 254.0
39 TraesCS3A01G433600 chr6A 94.444 144 7 1 1132 1275 286434257 286434115 1.250000e-53 220.0
40 TraesCS3A01G433600 chr6A 93.220 59 3 1 971 1028 303771257 303771315 4.760000e-13 86.1
41 TraesCS3A01G433600 chr6A 93.103 58 4 0 971 1028 535656675 535656732 4.760000e-13 86.1
42 TraesCS3A01G433600 chr6A 92.857 56 4 0 881 936 513617492 513617547 6.150000e-12 82.4
43 TraesCS3A01G433600 chr7A 84.183 1138 141 34 1558 2679 310711158 310712272 0.000000e+00 1068.0
44 TraesCS3A01G433600 chr7A 82.388 670 80 27 152 813 107957334 107956695 1.400000e-152 549.0
45 TraesCS3A01G433600 chr7A 83.784 592 81 15 152 737 575069949 575069367 5.050000e-152 547.0
46 TraesCS3A01G433600 chr7A 93.011 186 10 2 850 1034 458351086 458351269 4.400000e-68 268.0
47 TraesCS3A01G433600 chr7A 97.674 43 1 0 804 846 319139205 319139247 1.030000e-09 75.0
48 TraesCS3A01G433600 chr7A 93.023 43 3 0 804 846 319204786 319204828 2.230000e-06 63.9
49 TraesCS3A01G433600 chr5A 85.358 881 106 20 152 1024 219840958 219841823 0.000000e+00 891.0
50 TraesCS3A01G433600 chr5A 94.709 189 7 2 849 1036 404291101 404290915 9.390000e-75 291.0
51 TraesCS3A01G433600 chr5A 94.709 189 7 2 849 1036 404298633 404298447 9.390000e-75 291.0
52 TraesCS3A01G433600 chr5A 94.737 57 3 0 971 1027 164059075 164059019 3.680000e-14 89.8
53 TraesCS3A01G433600 chr5A 88.732 71 7 1 971 1041 60375174 60375105 4.760000e-13 86.1
54 TraesCS3A01G433600 chr1D 97.368 152 4 0 1 152 140603236 140603387 2.650000e-65 259.0
55 TraesCS3A01G433600 chr1D 97.368 152 4 0 1 152 485690816 485690967 2.650000e-65 259.0
56 TraesCS3A01G433600 chr1D 96.711 152 5 0 1 152 60376990 60377141 1.230000e-63 254.0
57 TraesCS3A01G433600 chr1D 96.711 152 5 0 1 152 443122226 443122075 1.230000e-63 254.0
58 TraesCS3A01G433600 chr1D 92.308 130 7 3 1128 1256 340375165 340375292 5.900000e-42 182.0
59 TraesCS3A01G433600 chr3D 97.333 150 4 0 3 152 246612007 246612156 3.430000e-64 255.0
60 TraesCS3A01G433600 chr3D 90.071 141 9 5 1128 1267 274394767 274394631 7.630000e-41 178.0
61 TraesCS3A01G433600 chr3D 90.071 141 9 5 1128 1267 274606641 274606505 7.630000e-41 178.0
62 TraesCS3A01G433600 chr6D 96.711 152 5 0 1 152 380410791 380410942 1.230000e-63 254.0
63 TraesCS3A01G433600 chr6D 92.308 130 7 3 1128 1256 317381837 317381710 5.900000e-42 182.0
64 TraesCS3A01G433600 chr6D 90.071 141 9 5 1128 1267 307412758 307412622 7.630000e-41 178.0
65 TraesCS3A01G433600 chr6D 91.538 130 8 3 1128 1256 317373870 317373743 2.740000e-40 176.0
66 TraesCS3A01G433600 chr6D 90.164 122 11 1 1128 1249 101982483 101982603 9.940000e-35 158.0
67 TraesCS3A01G433600 chr6D 90.164 122 11 1 1128 1249 101997553 101997673 9.940000e-35 158.0
68 TraesCS3A01G433600 chr6D 87.692 65 7 1 1141 1205 315442314 315442251 1.030000e-09 75.0
69 TraesCS3A01G433600 chr6D 87.692 65 7 1 1141 1205 315450359 315450296 1.030000e-09 75.0
70 TraesCS3A01G433600 chr6D 86.441 59 7 1 1141 1199 137079170 137079227 2.230000e-06 63.9
71 TraesCS3A01G433600 chr5D 96.711 152 5 0 1 152 436748244 436748395 1.230000e-63 254.0
72 TraesCS3A01G433600 chr5D 90.780 141 8 5 1128 1267 292280485 292280349 1.640000e-42 183.0
73 TraesCS3A01G433600 chr5D 90.780 141 8 5 1128 1267 315070345 315070209 1.640000e-42 183.0
74 TraesCS3A01G433600 chr5D 89.362 141 10 5 1128 1267 516244934 516245070 3.550000e-39 172.0
75 TraesCS3A01G433600 chr4D 96.711 152 5 0 1 152 45855527 45855678 1.230000e-63 254.0
76 TraesCS3A01G433600 chr4D 91.538 130 8 3 1128 1256 134309425 134309552 2.740000e-40 176.0
77 TraesCS3A01G433600 chr4D 90.164 122 11 1 1128 1249 165123104 165122984 9.940000e-35 158.0
78 TraesCS3A01G433600 chr4D 89.831 118 12 0 1132 1249 232248556 232248673 4.620000e-33 152.0
79 TraesCS3A01G433600 chr4D 94.565 92 4 1 1128 1219 165115120 165115030 1.000000e-29 141.0
80 TraesCS3A01G433600 chr1A 88.571 105 4 7 880 982 441203306 441203208 1.300000e-23 121.0
81 TraesCS3A01G433600 chr1A 92.500 80 4 2 880 958 97148733 97148811 2.180000e-21 113.0
82 TraesCS3A01G433600 chr1A 100.000 43 0 0 880 922 447757609 447757651 2.210000e-11 80.5
83 TraesCS3A01G433600 chrUn 88.136 59 6 1 1141 1199 371407364 371407421 4.790000e-08 69.4


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 TraesCS3A01G433600 chr3A 675285411 675288091 2680 True 4951.000000 4951 100.000000 1 2681 1 chr3A.!!$R5 2680
1 TraesCS3A01G433600 chr3A 464807209 464808203 994 True 1168.000000 1168 87.921000 1680 2681 1 chr3A.!!$R4 1001
2 TraesCS3A01G433600 chr3A 194908391 194909381 990 False 1134.000000 1134 87.413000 1689 2681 1 chr3A.!!$F1 992
3 TraesCS3A01G433600 chr3A 95578548 95579210 662 True 638.000000 638 84.226000 151 813 1 chr3A.!!$R2 662
4 TraesCS3A01G433600 chr3A 95567767 95568429 662 True 630.000000 630 84.125000 152 813 1 chr3A.!!$R1 661
5 TraesCS3A01G433600 chr3A 427800049 427800904 855 False 449.000000 449 77.183000 152 1036 1 chr3A.!!$F2 884
6 TraesCS3A01G433600 chr4A 526175274 526178262 2988 False 1312.000000 2060 95.398667 152 2681 3 chr4A.!!$F6 2529
7 TraesCS3A01G433600 chr4A 526207464 526209840 2376 False 973.666667 1583 93.952333 152 2066 3 chr4A.!!$F7 1914
8 TraesCS3A01G433600 chr4A 375266546 375267145 599 False 532.000000 532 82.947000 153 746 1 chr4A.!!$F4 593
9 TraesCS3A01G433600 chr4A 215435427 215436281 854 False 433.000000 433 76.856000 152 1036 1 chr4A.!!$F3 884
10 TraesCS3A01G433600 chr2A 462860862 462861828 966 False 1118.000000 1118 87.564000 1707 2681 1 chr2A.!!$F5 974
11 TraesCS3A01G433600 chr2A 577940540 577941581 1041 True 1112.000000 1112 86.066000 1637 2681 1 chr2A.!!$R4 1044
12 TraesCS3A01G433600 chr2A 384094240 384095584 1344 True 1092.000000 1092 81.674000 1320 2681 1 chr2A.!!$R2 1361
13 TraesCS3A01G433600 chr2A 384103700 384105040 1340 True 1011.000000 1011 80.678000 1320 2681 1 chr2A.!!$R3 1361
14 TraesCS3A01G433600 chr2A 350277084 350277634 550 False 582.000000 582 85.841000 152 710 1 chr2A.!!$F2 558
15 TraesCS3A01G433600 chr6A 223233878 223235002 1124 True 1090.000000 1090 84.348000 1547 2681 1 chr6A.!!$R2 1134
16 TraesCS3A01G433600 chr6A 344046658 344047722 1064 False 1086.000000 1086 85.189000 1605 2681 1 chr6A.!!$F3 1076
17 TraesCS3A01G433600 chr6A 119316501 119317553 1052 False 1085.000000 1085 85.528000 1631 2681 1 chr6A.!!$F1 1050
18 TraesCS3A01G433600 chr6A 551828542 551829272 730 False 412.000000 412 77.720000 302 1036 1 chr6A.!!$F7 734
19 TraesCS3A01G433600 chr7A 310711158 310712272 1114 False 1068.000000 1068 84.183000 1558 2679 1 chr7A.!!$F1 1121
20 TraesCS3A01G433600 chr7A 107956695 107957334 639 True 549.000000 549 82.388000 152 813 1 chr7A.!!$R1 661
21 TraesCS3A01G433600 chr7A 575069367 575069949 582 True 547.000000 547 83.784000 152 737 1 chr7A.!!$R2 585
22 TraesCS3A01G433600 chr5A 219840958 219841823 865 False 891.000000 891 85.358000 152 1024 1 chr5A.!!$F1 872

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
67 68 0.106519 GATAGCAGCCACCCCATGTT 60.107 55.0 0.00 0.00 0.0 2.71 F
68 69 0.396139 ATAGCAGCCACCCCATGTTG 60.396 55.0 0.00 0.00 0.0 3.33 F
1231 1674 0.742990 CGTCAAGGCCGGCAAGATTA 60.743 55.0 30.85 4.91 0.0 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1230 1673 0.033781 ACTTGGCGCCGTTGTAGTTA 59.966 50.0 23.90 0.0 0.00 2.24 R
1609 2142 0.108041 TGTCCGTAGATTTTCGGGGC 60.108 55.0 1.45 0.0 45.79 5.80 R
2497 3065 0.665369 ACAAACGGGCGTAGTCGAAG 60.665 55.0 0.00 0.0 39.71 3.79 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
22 23 4.736896 GCCGTCGTCCCTGTCACC 62.737 72.222 0.00 0.00 0.00 4.02
23 24 4.415332 CCGTCGTCCCTGTCACCG 62.415 72.222 0.00 0.00 0.00 4.94
24 25 3.359523 CGTCGTCCCTGTCACCGA 61.360 66.667 0.00 0.00 0.00 4.69
25 26 2.257676 GTCGTCCCTGTCACCGAC 59.742 66.667 0.00 0.00 42.22 4.79
26 27 2.987547 TCGTCCCTGTCACCGACC 60.988 66.667 0.00 0.00 0.00 4.79
27 28 4.065281 CGTCCCTGTCACCGACCC 62.065 72.222 0.00 0.00 0.00 4.46
28 29 3.703127 GTCCCTGTCACCGACCCC 61.703 72.222 0.00 0.00 0.00 4.95
31 32 3.391382 CCTGTCACCGACCCCCTC 61.391 72.222 0.00 0.00 0.00 4.30
32 33 3.391382 CTGTCACCGACCCCCTCC 61.391 72.222 0.00 0.00 0.00 4.30
40 41 4.437587 GACCCCCTCCGACCTCGA 62.438 72.222 0.00 0.00 43.02 4.04
41 42 3.735251 GACCCCCTCCGACCTCGAT 62.735 68.421 0.00 0.00 43.02 3.59
42 43 2.913060 CCCCCTCCGACCTCGATC 60.913 72.222 0.00 0.00 43.02 3.69
43 44 3.288290 CCCCTCCGACCTCGATCG 61.288 72.222 9.36 9.36 43.02 3.69
44 45 2.203167 CCCTCCGACCTCGATCGA 60.203 66.667 18.32 18.32 45.13 3.59
45 46 2.255172 CCCTCCGACCTCGATCGAG 61.255 68.421 33.32 33.32 45.13 4.04
55 56 2.610219 CTCGATCGAGGTGATAGCAG 57.390 55.000 32.81 8.16 37.47 4.24
56 57 0.593618 TCGATCGAGGTGATAGCAGC 59.406 55.000 15.15 0.98 42.72 5.25
57 58 0.387878 CGATCGAGGTGATAGCAGCC 60.388 60.000 10.26 0.00 43.41 4.85
58 59 0.676184 GATCGAGGTGATAGCAGCCA 59.324 55.000 6.55 0.00 43.41 4.75
59 60 0.390860 ATCGAGGTGATAGCAGCCAC 59.609 55.000 6.55 0.83 43.41 5.01
62 63 2.193248 GGTGATAGCAGCCACCCC 59.807 66.667 7.86 0.00 45.30 4.95
63 64 2.679342 GGTGATAGCAGCCACCCCA 61.679 63.158 7.86 0.00 45.30 4.96
64 65 1.533711 GTGATAGCAGCCACCCCAT 59.466 57.895 0.00 0.00 0.00 4.00
65 66 0.820891 GTGATAGCAGCCACCCCATG 60.821 60.000 0.00 0.00 0.00 3.66
66 67 1.281199 TGATAGCAGCCACCCCATGT 61.281 55.000 0.00 0.00 0.00 3.21
67 68 0.106519 GATAGCAGCCACCCCATGTT 60.107 55.000 0.00 0.00 0.00 2.71
68 69 0.396139 ATAGCAGCCACCCCATGTTG 60.396 55.000 0.00 0.00 0.00 3.33
69 70 1.788518 TAGCAGCCACCCCATGTTGT 61.789 55.000 0.00 0.00 0.00 3.32
70 71 2.209315 GCAGCCACCCCATGTTGTT 61.209 57.895 0.00 0.00 0.00 2.83
71 72 0.897863 GCAGCCACCCCATGTTGTTA 60.898 55.000 0.00 0.00 0.00 2.41
72 73 1.626686 CAGCCACCCCATGTTGTTAA 58.373 50.000 0.00 0.00 0.00 2.01
73 74 2.178580 CAGCCACCCCATGTTGTTAAT 58.821 47.619 0.00 0.00 0.00 1.40
74 75 2.566724 CAGCCACCCCATGTTGTTAATT 59.433 45.455 0.00 0.00 0.00 1.40
75 76 3.007831 CAGCCACCCCATGTTGTTAATTT 59.992 43.478 0.00 0.00 0.00 1.82
76 77 4.221703 CAGCCACCCCATGTTGTTAATTTA 59.778 41.667 0.00 0.00 0.00 1.40
77 78 4.841246 AGCCACCCCATGTTGTTAATTTAA 59.159 37.500 0.00 0.00 0.00 1.52
78 79 5.487131 AGCCACCCCATGTTGTTAATTTAAT 59.513 36.000 0.00 0.00 0.00 1.40
79 80 6.012945 AGCCACCCCATGTTGTTAATTTAATT 60.013 34.615 0.00 0.00 0.00 1.40
80 81 6.657117 GCCACCCCATGTTGTTAATTTAATTT 59.343 34.615 0.00 0.00 0.00 1.82
81 82 7.824779 GCCACCCCATGTTGTTAATTTAATTTA 59.175 33.333 0.00 0.00 0.00 1.40
82 83 9.377312 CCACCCCATGTTGTTAATTTAATTTAG 57.623 33.333 0.00 0.00 0.00 1.85
83 84 9.377312 CACCCCATGTTGTTAATTTAATTTAGG 57.623 33.333 0.00 0.00 0.00 2.69
84 85 9.106977 ACCCCATGTTGTTAATTTAATTTAGGT 57.893 29.630 0.00 0.00 0.00 3.08
116 117 9.686683 AGGTGTTTAATCTTAGAATAATGCAGT 57.313 29.630 0.00 0.00 0.00 4.40
124 125 8.854614 ATCTTAGAATAATGCAGTATGAACCC 57.145 34.615 7.55 0.00 39.69 4.11
125 126 8.034313 TCTTAGAATAATGCAGTATGAACCCT 57.966 34.615 7.55 3.57 39.69 4.34
126 127 9.154632 TCTTAGAATAATGCAGTATGAACCCTA 57.845 33.333 7.55 2.71 39.69 3.53
127 128 9.429359 CTTAGAATAATGCAGTATGAACCCTAG 57.571 37.037 7.55 0.00 39.69 3.02
128 129 7.380423 AGAATAATGCAGTATGAACCCTAGT 57.620 36.000 7.55 0.00 39.69 2.57
129 130 7.806180 AGAATAATGCAGTATGAACCCTAGTT 58.194 34.615 7.55 0.00 39.69 2.24
130 131 8.934697 AGAATAATGCAGTATGAACCCTAGTTA 58.065 33.333 7.55 0.00 39.69 2.24
131 132 9.726438 GAATAATGCAGTATGAACCCTAGTTAT 57.274 33.333 7.55 0.00 39.69 1.89
132 133 9.507329 AATAATGCAGTATGAACCCTAGTTATG 57.493 33.333 7.55 0.00 39.69 1.90
133 134 6.747414 ATGCAGTATGAACCCTAGTTATGA 57.253 37.500 0.00 0.00 39.69 2.15
134 135 6.747414 TGCAGTATGAACCCTAGTTATGAT 57.253 37.500 0.00 0.00 39.69 2.45
135 136 6.759272 TGCAGTATGAACCCTAGTTATGATC 58.241 40.000 0.00 0.00 39.69 2.92
136 137 5.864474 GCAGTATGAACCCTAGTTATGATCG 59.136 44.000 0.00 0.00 39.69 3.69
137 138 6.294564 GCAGTATGAACCCTAGTTATGATCGA 60.295 42.308 0.00 0.00 39.69 3.59
138 139 7.658261 CAGTATGAACCCTAGTTATGATCGAA 58.342 38.462 0.00 0.00 39.69 3.71
139 140 8.307483 CAGTATGAACCCTAGTTATGATCGAAT 58.693 37.037 0.00 0.00 39.69 3.34
140 141 8.524487 AGTATGAACCCTAGTTATGATCGAATC 58.476 37.037 0.00 0.00 35.94 2.52
141 142 6.724893 TGAACCCTAGTTATGATCGAATCA 57.275 37.500 0.00 0.00 39.05 2.57
162 163 2.028130 TGTTCAAAATTGTGACGCCCT 58.972 42.857 0.00 0.00 0.00 5.19
925 992 1.595058 ATCCCTCGACCTCTCCCCTT 61.595 60.000 0.00 0.00 0.00 3.95
1046 1114 4.168291 CCTCGCCCAGCTCTTCCC 62.168 72.222 0.00 0.00 0.00 3.97
1108 1176 2.646719 CGGTTCCTTGGTCGTCGA 59.353 61.111 0.00 0.00 0.00 4.20
1230 1673 2.040544 CGTCAAGGCCGGCAAGATT 61.041 57.895 30.85 14.18 0.00 2.40
1231 1674 0.742990 CGTCAAGGCCGGCAAGATTA 60.743 55.000 30.85 4.91 0.00 1.75
1236 1679 2.327200 AGGCCGGCAAGATTAACTAC 57.673 50.000 30.85 5.70 0.00 2.73
1277 1720 0.869730 CGACGACCGTTTTGGGATTT 59.130 50.000 0.00 0.00 44.64 2.17
1278 1721 1.136169 CGACGACCGTTTTGGGATTTC 60.136 52.381 0.00 0.00 44.64 2.17
1279 1722 1.874872 GACGACCGTTTTGGGATTTCA 59.125 47.619 0.00 0.00 44.64 2.69
1281 1724 1.877443 CGACCGTTTTGGGATTTCACT 59.123 47.619 0.00 0.00 44.64 3.41
1284 1727 3.418047 ACCGTTTTGGGATTTCACTAGG 58.582 45.455 0.00 0.00 44.64 3.02
1285 1728 3.181437 ACCGTTTTGGGATTTCACTAGGT 60.181 43.478 0.00 0.00 44.64 3.08
1286 1729 4.041938 ACCGTTTTGGGATTTCACTAGGTA 59.958 41.667 0.00 0.00 44.64 3.08
1287 1730 5.190677 CCGTTTTGGGATTTCACTAGGTAT 58.809 41.667 0.00 0.00 0.00 2.73
1289 1732 5.006358 CGTTTTGGGATTTCACTAGGTATCG 59.994 44.000 0.00 0.00 0.00 2.92
1300 1831 4.619140 GGTATCGCGGACCCGTCG 62.619 72.222 17.39 13.31 42.09 5.12
1378 1909 2.302733 GGTTTTACCGAGTACCCCTTCA 59.697 50.000 0.00 0.00 0.00 3.02
1390 1921 5.892348 AGTACCCCTTCATTTTGTCAAGAT 58.108 37.500 0.00 0.00 0.00 2.40
1391 1922 6.314917 AGTACCCCTTCATTTTGTCAAGATT 58.685 36.000 0.00 0.00 0.00 2.40
1453 1984 4.341806 TGTACCAAGTACCTCTTCGTTTCA 59.658 41.667 2.63 0.00 38.14 2.69
1455 1986 3.387050 ACCAAGTACCTCTTCGTTTCAGT 59.613 43.478 0.00 0.00 33.63 3.41
1609 2142 0.790207 CGTCAAGTTCCGTGTCATGG 59.210 55.000 4.52 4.52 0.00 3.66
1617 2150 2.359354 CGTGTCATGGCCCCGAAA 60.359 61.111 0.00 0.00 0.00 3.46
1981 2531 0.535553 GTTGTCGTGGCACCCCTTTA 60.536 55.000 12.86 0.00 0.00 1.85
1993 2543 0.037734 CCCCTTTAGTTTCCGCCACT 59.962 55.000 0.00 0.00 0.00 4.00
2153 2711 6.011481 AGGGATTTACCGGAATTGTTGTTTA 58.989 36.000 9.46 0.00 40.11 2.01
2161 2719 9.557338 TTACCGGAATTGTTGTTTATTATTTCG 57.443 29.630 9.46 0.00 0.00 3.46
2163 2721 7.094291 ACCGGAATTGTTGTTTATTATTTCGGA 60.094 33.333 9.46 0.00 45.77 4.55
2216 2775 0.107703 TTATGCTCCACCTCTTGCCG 60.108 55.000 0.00 0.00 0.00 5.69
2267 2828 7.043788 GGGTACATAAACGAGATCGAACTAAAC 60.044 40.741 9.58 0.00 43.02 2.01
2350 2915 6.443934 TGTAGTATTGTTTGTGCACTTTGT 57.556 33.333 19.41 2.03 0.00 2.83
2497 3065 1.477685 TTCCGGAGTTGTGAGGACCC 61.478 60.000 3.34 0.00 31.69 4.46
2547 3115 2.616842 GGACTCGTTCTTTTTCCTTGCA 59.383 45.455 0.00 0.00 0.00 4.08
2558 3126 0.914644 TTCCTTGCAGGATCTCAGGG 59.085 55.000 0.00 0.00 45.34 4.45
2599 3167 6.873605 TCGAAATCACTTCTATCTTTGCTTGA 59.126 34.615 0.00 0.00 31.20 3.02
2646 3220 2.862921 GCGCTACCTACCACTTGCTATC 60.863 54.545 0.00 0.00 0.00 2.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.736896 GGTGACAGGGACGACGGC 62.737 72.222 0.00 0.00 0.00 5.68
6 7 4.415332 CGGTGACAGGGACGACGG 62.415 72.222 0.00 0.00 0.00 4.79
7 8 3.359523 TCGGTGACAGGGACGACG 61.360 66.667 0.00 0.00 0.00 5.12
8 9 2.257676 GTCGGTGACAGGGACGAC 59.742 66.667 0.00 0.00 46.89 4.34
9 10 2.987547 GGTCGGTGACAGGGACGA 60.988 66.667 0.00 0.00 33.68 4.20
10 11 4.065281 GGGTCGGTGACAGGGACG 62.065 72.222 0.00 0.00 33.68 4.79
11 12 3.703127 GGGGTCGGTGACAGGGAC 61.703 72.222 0.00 0.00 33.68 4.46
14 15 3.391382 GAGGGGGTCGGTGACAGG 61.391 72.222 0.00 0.00 33.68 4.00
15 16 3.391382 GGAGGGGGTCGGTGACAG 61.391 72.222 0.00 0.00 33.68 3.51
23 24 3.735251 ATCGAGGTCGGAGGGGGTC 62.735 68.421 0.00 0.00 40.29 4.46
24 25 3.735251 GATCGAGGTCGGAGGGGGT 62.735 68.421 0.00 0.00 40.29 4.95
25 26 2.913060 GATCGAGGTCGGAGGGGG 60.913 72.222 0.00 0.00 40.29 5.40
26 27 3.288290 CGATCGAGGTCGGAGGGG 61.288 72.222 10.26 0.00 40.29 4.79
27 28 2.203167 TCGATCGAGGTCGGAGGG 60.203 66.667 15.15 0.00 41.74 4.30
28 29 3.335513 CTCGATCGAGGTCGGAGG 58.664 66.667 32.81 9.62 41.74 4.30
36 37 1.400888 GCTGCTATCACCTCGATCGAG 60.401 57.143 33.32 33.32 41.63 4.04
37 38 0.593618 GCTGCTATCACCTCGATCGA 59.406 55.000 18.32 18.32 35.39 3.59
38 39 0.387878 GGCTGCTATCACCTCGATCG 60.388 60.000 9.36 9.36 35.39 3.69
39 40 0.676184 TGGCTGCTATCACCTCGATC 59.324 55.000 0.00 0.00 35.39 3.69
40 41 0.390860 GTGGCTGCTATCACCTCGAT 59.609 55.000 0.00 0.00 38.21 3.59
41 42 1.816537 GTGGCTGCTATCACCTCGA 59.183 57.895 0.00 0.00 0.00 4.04
42 43 4.427394 GTGGCTGCTATCACCTCG 57.573 61.111 0.00 0.00 0.00 4.63
46 47 0.820891 CATGGGGTGGCTGCTATCAC 60.821 60.000 0.00 0.00 0.00 3.06
47 48 1.281199 ACATGGGGTGGCTGCTATCA 61.281 55.000 0.00 0.00 0.00 2.15
48 49 0.106519 AACATGGGGTGGCTGCTATC 60.107 55.000 0.00 0.00 0.00 2.08
49 50 0.396139 CAACATGGGGTGGCTGCTAT 60.396 55.000 0.00 0.00 0.00 2.97
50 51 1.001020 CAACATGGGGTGGCTGCTA 60.001 57.895 0.00 0.00 0.00 3.49
51 52 2.283388 CAACATGGGGTGGCTGCT 60.283 61.111 0.00 0.00 0.00 4.24
52 53 0.897863 TAACAACATGGGGTGGCTGC 60.898 55.000 0.00 0.00 0.00 5.25
53 54 1.626686 TTAACAACATGGGGTGGCTG 58.373 50.000 0.00 0.00 0.00 4.85
54 55 2.621556 ATTAACAACATGGGGTGGCT 57.378 45.000 0.00 0.00 0.00 4.75
55 56 3.694043 AAATTAACAACATGGGGTGGC 57.306 42.857 0.00 0.00 0.00 5.01
56 57 9.377312 CTAAATTAAATTAACAACATGGGGTGG 57.623 33.333 0.00 0.00 0.00 4.61
57 58 9.377312 CCTAAATTAAATTAACAACATGGGGTG 57.623 33.333 0.00 0.00 0.00 4.61
58 59 9.106977 ACCTAAATTAAATTAACAACATGGGGT 57.893 29.630 0.00 0.00 0.00 4.95
90 91 9.686683 ACTGCATTATTCTAAGATTAAACACCT 57.313 29.630 0.00 0.00 0.00 4.00
98 99 9.289782 GGGTTCATACTGCATTATTCTAAGATT 57.710 33.333 0.00 0.00 0.00 2.40
99 100 8.664079 AGGGTTCATACTGCATTATTCTAAGAT 58.336 33.333 0.00 0.00 0.00 2.40
100 101 8.034313 AGGGTTCATACTGCATTATTCTAAGA 57.966 34.615 0.00 0.00 0.00 2.10
101 102 9.429359 CTAGGGTTCATACTGCATTATTCTAAG 57.571 37.037 0.00 0.00 0.00 2.18
102 103 8.934697 ACTAGGGTTCATACTGCATTATTCTAA 58.065 33.333 0.00 0.00 0.00 2.10
103 104 8.492415 ACTAGGGTTCATACTGCATTATTCTA 57.508 34.615 0.00 0.00 0.00 2.10
104 105 7.380423 ACTAGGGTTCATACTGCATTATTCT 57.620 36.000 0.00 0.00 0.00 2.40
105 106 9.726438 ATAACTAGGGTTCATACTGCATTATTC 57.274 33.333 0.00 0.00 36.92 1.75
106 107 9.507329 CATAACTAGGGTTCATACTGCATTATT 57.493 33.333 0.00 0.00 36.92 1.40
107 108 8.880244 TCATAACTAGGGTTCATACTGCATTAT 58.120 33.333 0.00 0.00 36.92 1.28
108 109 8.257602 TCATAACTAGGGTTCATACTGCATTA 57.742 34.615 0.00 0.00 36.92 1.90
109 110 7.136822 TCATAACTAGGGTTCATACTGCATT 57.863 36.000 0.00 0.00 36.92 3.56
110 111 6.747414 TCATAACTAGGGTTCATACTGCAT 57.253 37.500 0.00 0.00 36.92 3.96
111 112 6.516693 CGATCATAACTAGGGTTCATACTGCA 60.517 42.308 0.00 0.00 36.92 4.41
112 113 5.864474 CGATCATAACTAGGGTTCATACTGC 59.136 44.000 0.00 0.00 36.92 4.40
113 114 7.215719 TCGATCATAACTAGGGTTCATACTG 57.784 40.000 0.00 0.00 36.92 2.74
114 115 7.834881 TTCGATCATAACTAGGGTTCATACT 57.165 36.000 0.00 0.00 36.92 2.12
115 116 8.304596 TGATTCGATCATAACTAGGGTTCATAC 58.695 37.037 0.00 0.00 34.19 2.39
116 117 8.417273 TGATTCGATCATAACTAGGGTTCATA 57.583 34.615 0.00 0.00 34.19 2.15
117 118 7.303182 TGATTCGATCATAACTAGGGTTCAT 57.697 36.000 0.00 0.00 34.19 2.57
118 119 6.724893 TGATTCGATCATAACTAGGGTTCA 57.275 37.500 0.00 0.00 34.19 3.18
131 132 7.538334 GTCACAATTTTGAACATGATTCGATCA 59.462 33.333 0.00 0.00 44.55 2.92
132 133 7.253092 CGTCACAATTTTGAACATGATTCGATC 60.253 37.037 0.00 0.00 0.00 3.69
133 134 6.524239 CGTCACAATTTTGAACATGATTCGAT 59.476 34.615 0.00 0.00 0.00 3.59
134 135 5.850653 CGTCACAATTTTGAACATGATTCGA 59.149 36.000 0.00 0.00 0.00 3.71
135 136 5.441872 GCGTCACAATTTTGAACATGATTCG 60.442 40.000 0.00 0.00 0.00 3.34
136 137 5.164061 GGCGTCACAATTTTGAACATGATTC 60.164 40.000 0.00 0.12 0.00 2.52
137 138 4.685628 GGCGTCACAATTTTGAACATGATT 59.314 37.500 0.00 0.00 0.00 2.57
138 139 4.236935 GGCGTCACAATTTTGAACATGAT 58.763 39.130 0.00 0.00 0.00 2.45
139 140 3.551863 GGGCGTCACAATTTTGAACATGA 60.552 43.478 0.00 0.00 0.00 3.07
140 141 2.730928 GGGCGTCACAATTTTGAACATG 59.269 45.455 0.00 0.00 0.00 3.21
141 142 2.627699 AGGGCGTCACAATTTTGAACAT 59.372 40.909 0.00 0.00 0.00 2.71
142 143 2.028130 AGGGCGTCACAATTTTGAACA 58.972 42.857 0.00 0.00 0.00 3.18
143 144 2.793278 AGGGCGTCACAATTTTGAAC 57.207 45.000 0.00 0.00 0.00 3.18
144 145 4.023536 GTCTTAGGGCGTCACAATTTTGAA 60.024 41.667 0.00 0.00 0.00 2.69
145 146 3.500680 GTCTTAGGGCGTCACAATTTTGA 59.499 43.478 0.00 0.00 0.00 2.69
146 147 3.365969 GGTCTTAGGGCGTCACAATTTTG 60.366 47.826 0.00 0.00 0.00 2.44
147 148 2.817844 GGTCTTAGGGCGTCACAATTTT 59.182 45.455 0.00 0.00 0.00 1.82
148 149 2.433436 GGTCTTAGGGCGTCACAATTT 58.567 47.619 0.00 0.00 0.00 1.82
149 150 1.674817 CGGTCTTAGGGCGTCACAATT 60.675 52.381 0.00 0.00 0.00 2.32
162 163 1.137086 GCATCTGAAGCTCCGGTCTTA 59.863 52.381 0.00 0.00 0.00 2.10
759 806 2.318908 CTGCTGCTATCTCTCCCTCTT 58.681 52.381 0.00 0.00 0.00 2.85
925 992 4.090588 GTCGTGGGGATCGGGCAA 62.091 66.667 0.00 0.00 0.00 4.52
1230 1673 0.033781 ACTTGGCGCCGTTGTAGTTA 59.966 50.000 23.90 0.00 0.00 2.24
1231 1674 0.816421 AACTTGGCGCCGTTGTAGTT 60.816 50.000 23.90 20.65 0.00 2.24
1236 1679 3.283684 TGGAACTTGGCGCCGTTG 61.284 61.111 22.23 16.48 0.00 4.10
1277 1720 0.820891 GGGTCCGCGATACCTAGTGA 60.821 60.000 23.96 1.57 37.18 3.41
1278 1721 1.658673 GGGTCCGCGATACCTAGTG 59.341 63.158 23.96 0.00 37.18 2.74
1279 1722 1.895707 CGGGTCCGCGATACCTAGT 60.896 63.158 23.96 0.00 37.18 2.57
1281 1724 1.893808 GACGGGTCCGCGATACCTA 60.894 63.158 23.96 0.00 44.19 3.08
1284 1727 3.518293 CTCGACGGGTCCGCGATAC 62.518 68.421 21.59 5.16 42.82 2.24
1285 1728 2.642996 TACTCGACGGGTCCGCGATA 62.643 60.000 21.59 15.41 42.82 2.92
1287 1730 4.758251 TACTCGACGGGTCCGCGA 62.758 66.667 20.65 20.65 44.19 5.87
1289 1732 2.981560 TTGTACTCGACGGGTCCGC 61.982 63.158 2.15 0.00 44.19 5.54
1300 1831 1.595794 CAACGTGGTGTGGTTGTACTC 59.404 52.381 0.00 0.00 38.89 2.59
1340 1871 1.348064 ACCATGTTCTTCGGAGGTCA 58.652 50.000 0.00 0.00 0.00 4.02
1378 1909 5.835280 AGGGACTTGACAATCTTGACAAAAT 59.165 36.000 8.66 1.84 40.96 1.82
1453 1984 0.827925 TCAGACTTGCCGGTCTCACT 60.828 55.000 1.90 0.00 43.75 3.41
1455 1986 0.318441 CTTCAGACTTGCCGGTCTCA 59.682 55.000 1.90 0.00 43.75 3.27
1609 2142 0.108041 TGTCCGTAGATTTTCGGGGC 60.108 55.000 1.45 0.00 45.79 5.80
1617 2150 4.639310 AGTAGTCGTTCATGTCCGTAGATT 59.361 41.667 0.00 0.00 0.00 2.40
1852 2399 2.300967 GGATGGTGGGGTGCTCTCA 61.301 63.158 0.00 0.00 0.00 3.27
1854 2401 1.542375 AAGGATGGTGGGGTGCTCT 60.542 57.895 0.00 0.00 0.00 4.09
1981 2531 2.851263 TTGTCATAGTGGCGGAAACT 57.149 45.000 0.00 0.00 0.00 2.66
2129 2687 4.042271 ACAACAATTCCGGTAAATCCCT 57.958 40.909 0.00 0.00 0.00 4.20
2153 2711 7.973944 GCAAGTTTAAATGAGGTCCGAAATAAT 59.026 33.333 0.00 0.00 0.00 1.28
2161 2719 6.584185 TTTAGGCAAGTTTAAATGAGGTCC 57.416 37.500 0.00 0.00 0.00 4.46
2163 2721 7.539034 ACATTTAGGCAAGTTTAAATGAGGT 57.461 32.000 18.77 2.00 44.34 3.85
2267 2828 4.454161 TGACGGAACACCATATTCAACTTG 59.546 41.667 0.00 0.00 0.00 3.16
2350 2915 7.988028 TGTCCGGTTAAAATATGTATGACATGA 59.012 33.333 0.00 0.00 39.53 3.07
2497 3065 0.665369 ACAAACGGGCGTAGTCGAAG 60.665 55.000 0.00 0.00 39.71 3.79
2547 3115 2.022625 TGGTCATCTTCCCTGAGATCCT 60.023 50.000 0.00 0.00 34.20 3.24
2558 3126 4.402056 TTTCGAGGGTATGGTCATCTTC 57.598 45.455 0.00 0.00 0.00 2.87
2599 3167 5.406780 GCATAGCAATAGAGCGAACAACTAT 59.593 40.000 0.00 0.00 40.15 2.12
2646 3220 1.202964 TGGCAATATGGGAGGCATGAG 60.203 52.381 0.00 0.00 32.54 2.90


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

AutoCloner maintained by Alex Coulton.