Multiple sequence alignment - TraesCS6D01G056300

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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 TraesCS6D01G056300 chr6D 100.000 5698 0 0 1 5698 27031521 27025824 0.000000e+00 10523.0
1 TraesCS6D01G056300 chr6D 98.201 1112 8 2 1144 2246 413012875 413013983 0.000000e+00 1932.0
2 TraesCS6D01G056300 chr6D 87.457 1451 110 34 4295 5684 26760009 26758570 0.000000e+00 1605.0
3 TraesCS6D01G056300 chr6D 81.789 626 109 3 3307 3928 26761064 26760440 2.350000e-143 520.0
4 TraesCS6D01G056300 chr6D 78.119 553 64 26 569 1109 26761560 26761053 1.200000e-76 298.0
5 TraesCS6D01G056300 chr6D 91.005 189 8 3 1122 1310 27029275 27029454 4.410000e-61 246.0
6 TraesCS6D01G056300 chr6D 90.625 192 9 3 2065 2247 27030209 27030400 4.410000e-61 246.0
7 TraesCS6D01G056300 chr6D 91.018 167 3 4 2068 2225 413013038 413012875 1.240000e-51 215.0
8 TraesCS6D01G056300 chr6D 77.168 346 56 14 772 1100 26589959 26589620 4.540000e-41 180.0
9 TraesCS6D01G056300 chr6A 91.503 2448 107 18 3307 5684 28284367 28281951 0.000000e+00 3275.0
10 TraesCS6D01G056300 chr6A 92.479 944 32 15 176 1105 28285278 28284360 0.000000e+00 1314.0
11 TraesCS6D01G056300 chr6A 89.601 827 65 11 4414 5223 28251958 28251136 0.000000e+00 1031.0
12 TraesCS6D01G056300 chr6A 88.406 690 58 12 4551 5223 28239510 28238826 0.000000e+00 811.0
13 TraesCS6D01G056300 chr6A 87.937 630 39 8 1 612 28317908 28317298 0.000000e+00 708.0
14 TraesCS6D01G056300 chr6A 79.151 801 158 7 3307 4102 28255609 28254813 3.880000e-151 545.0
15 TraesCS6D01G056300 chr6A 89.118 340 20 5 5215 5546 28250979 28250649 1.910000e-109 407.0
16 TraesCS6D01G056300 chr6A 86.471 340 22 5 5215 5546 28238669 28238346 9.080000e-93 351.0
17 TraesCS6D01G056300 chr6A 91.758 182 6 6 1 173 28316497 28316316 1.590000e-60 244.0
18 TraesCS6D01G056300 chr6A 82.234 197 29 4 767 958 31159916 31160111 1.270000e-36 165.0
19 TraesCS6D01G056300 chr6A 92.105 38 2 1 1064 1100 40542976 40542939 1.000000e-02 52.8
20 TraesCS6D01G056300 chr2D 97.993 1096 13 1 1122 2208 544492899 544493994 0.000000e+00 1893.0
21 TraesCS6D01G056300 chr2D 94.651 673 31 3 2268 2935 132975707 132976379 0.000000e+00 1038.0
22 TraesCS6D01G056300 chr2D 95.238 378 17 1 2935 3311 132976706 132977083 1.060000e-166 597.0
23 TraesCS6D01G056300 chr2D 93.691 317 15 2 2414 2725 11455180 11454864 2.400000e-128 470.0
24 TraesCS6D01G056300 chr2D 91.053 190 8 3 2068 2248 544493087 544492898 1.230000e-61 248.0
25 TraesCS6D01G056300 chr2D 95.425 153 7 0 1161 1313 544493994 544493842 1.590000e-60 244.0
26 TraesCS6D01G056300 chr4D 98.590 1064 9 5 2246 3306 403152094 403151034 0.000000e+00 1877.0
27 TraesCS6D01G056300 chr4D 92.522 896 62 5 2414 3305 21189803 21188909 0.000000e+00 1279.0
28 TraesCS6D01G056300 chr4D 92.188 128 6 2 2300 2424 21189949 21189823 1.630000e-40 178.0
29 TraesCS6D01G056300 chr6B 89.311 1263 88 23 4305 5546 48871511 48870275 0.000000e+00 1541.0
30 TraesCS6D01G056300 chr6B 89.223 1262 91 22 4305 5546 48936004 48934768 0.000000e+00 1535.0
31 TraesCS6D01G056300 chr6B 88.906 1262 92 24 4305 5546 48978869 48977636 0.000000e+00 1511.0
32 TraesCS6D01G056300 chr6B 86.490 681 85 3 3319 3992 49331164 49330484 0.000000e+00 741.0
33 TraesCS6D01G056300 chr6B 90.068 584 29 16 265 834 49231049 49230481 0.000000e+00 730.0
34 TraesCS6D01G056300 chr6B 80.952 987 110 36 2246 3201 56244934 56245873 0.000000e+00 710.0
35 TraesCS6D01G056300 chr6B 84.066 546 72 11 3559 4094 49328817 49328277 3.940000e-141 512.0
36 TraesCS6D01G056300 chr6B 81.499 627 110 4 3307 3928 48937073 48936448 1.420000e-140 510.0
37 TraesCS6D01G056300 chr6B 80.320 625 120 2 3307 3928 49555157 49555781 2.400000e-128 470.0
38 TraesCS6D01G056300 chr6B 82.774 447 74 2 3307 3750 48980117 48979671 4.140000e-106 396.0
39 TraesCS6D01G056300 chr6B 82.550 447 75 2 3307 3750 48872759 48872313 1.920000e-104 390.0
40 TraesCS6D01G056300 chr6B 92.670 191 7 5 1 186 49235697 49235509 9.410000e-68 268.0
41 TraesCS6D01G056300 chr6B 86.264 182 25 0 810 991 48873041 48872860 1.250000e-46 198.0
42 TraesCS6D01G056300 chr6B 86.264 182 25 0 810 991 48937355 48937174 1.250000e-46 198.0
43 TraesCS6D01G056300 chr6B 86.264 182 25 0 810 991 48980399 48980218 1.250000e-46 198.0
44 TraesCS6D01G056300 chr6B 89.634 164 6 6 1 153 49331432 49331269 1.250000e-46 198.0
45 TraesCS6D01G056300 chr6B 80.995 221 34 6 745 959 60593821 60594039 9.820000e-38 169.0
46 TraesCS6D01G056300 chr6B 90.099 101 10 0 1007 1107 49331267 49331167 1.290000e-26 132.0
47 TraesCS6D01G056300 chr6B 91.111 45 3 1 569 612 48980529 48980485 6.170000e-05 60.2
48 TraesCS6D01G056300 chr6B 94.444 36 2 0 1067 1102 49701111 49701076 7.980000e-04 56.5
49 TraesCS6D01G056300 chr6B 100.000 30 0 0 1073 1102 59829251 59829222 7.980000e-04 56.5
50 TraesCS6D01G056300 chr6B 92.105 38 2 1 1064 1100 76177107 76177070 1.000000e-02 52.8
51 TraesCS6D01G056300 chr1D 98.560 764 5 4 2246 3005 59956087 59955326 0.000000e+00 1345.0
52 TraesCS6D01G056300 chr1D 94.568 810 35 6 2247 3049 349269284 349268477 0.000000e+00 1243.0
53 TraesCS6D01G056300 chr1D 98.695 613 4 4 2696 3306 440051393 440050783 0.000000e+00 1085.0
54 TraesCS6D01G056300 chr1D 98.131 428 3 3 2246 2671 440051812 440051388 0.000000e+00 741.0
55 TraesCS6D01G056300 chr1B 89.956 906 68 13 2400 3299 534976797 534977685 0.000000e+00 1147.0
56 TraesCS6D01G056300 chr4B 86.766 1005 97 22 2318 3306 96682944 96683928 0.000000e+00 1086.0
57 TraesCS6D01G056300 chr4B 92.373 118 9 0 1128 1245 579463320 579463437 9.820000e-38 169.0
58 TraesCS6D01G056300 chr5B 83.972 992 87 28 2330 3306 583458388 583459322 0.000000e+00 885.0
59 TraesCS6D01G056300 chr2B 87.548 787 60 19 1486 2248 268012607 268013379 0.000000e+00 876.0
60 TraesCS6D01G056300 chr2B 85.934 782 73 18 1486 2243 262481720 262480952 0.000000e+00 800.0
61 TraesCS6D01G056300 chr2B 85.096 785 81 17 1486 2247 262480556 262479785 0.000000e+00 769.0
62 TraesCS6D01G056300 chr2B 85.067 817 53 32 1320 2120 772451400 772452163 0.000000e+00 769.0
63 TraesCS6D01G056300 chr2B 86.702 188 17 3 1133 1313 772451161 772451347 9.680000e-48 202.0
64 TraesCS6D01G056300 chr2B 84.058 207 18 8 2045 2236 772451367 772451161 9.750000e-43 185.0
65 TraesCS6D01G056300 chr2B 94.643 56 2 1 1258 1313 772452163 772452109 1.020000e-12 86.1
66 TraesCS6D01G056300 chr7A 81.130 1097 118 43 2246 3306 117618092 117617049 0.000000e+00 797.0
67 TraesCS6D01G056300 chr7A 80.857 1097 120 44 2246 3306 120749018 120747976 0.000000e+00 780.0
68 TraesCS6D01G056300 chr4A 86.686 353 24 9 1320 1653 72961050 72961398 2.510000e-98 370.0
69 TraesCS6D01G056300 chr4A 87.437 199 18 3 1122 1313 72960798 72960996 7.430000e-54 222.0
70 TraesCS6D01G056300 chr4A 87.629 194 17 2 1127 1313 72961600 72961407 9.610000e-53 219.0
71 TraesCS6D01G056300 chr4A 84.018 219 19 6 2045 2247 72961016 72960798 4.500000e-46 196.0
72 TraesCS6D01G056300 chr4A 83.575 207 18 9 2057 2247 72961399 72961605 4.540000e-41 180.0
73 TraesCS6D01G056300 chr3A 86.119 353 26 9 1320 1653 535574574 535574226 5.430000e-95 359.0
74 TraesCS6D01G056300 chr3A 87.113 194 18 3 1127 1313 535574024 535574217 4.470000e-51 213.0
75 TraesCS6D01G056300 chr3A 83.092 207 19 10 2057 2247 535574225 535574019 2.110000e-39 174.0
76 TraesCS6D01G056300 chrUn 90.800 250 12 3 5305 5546 476313224 476312978 1.980000e-84 324.0
77 TraesCS6D01G056300 chrUn 90.079 252 17 2 4980 5223 480911780 480911529 2.560000e-83 320.0
78 TraesCS6D01G056300 chrUn 84.158 101 14 2 5363 5463 26993663 26993565 4.700000e-16 97.1
79 TraesCS6D01G056300 chr7D 86.131 137 13 4 1119 1250 585726878 585726743 5.950000e-30 143.0
80 TraesCS6D01G056300 chr7D 87.778 90 9 1 2160 2247 585726786 585726875 2.810000e-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 TraesCS6D01G056300 chr6D 27025824 27031521 5697 True 10523.000000 10523 100.000000 1 5698 1 chr6D.!!$R2 5697
1 TraesCS6D01G056300 chr6D 413012875 413013983 1108 False 1932.000000 1932 98.201000 1144 2246 1 chr6D.!!$F1 1102
2 TraesCS6D01G056300 chr6D 26758570 26761560 2990 True 807.666667 1605 82.455000 569 5684 3 chr6D.!!$R4 5115
3 TraesCS6D01G056300 chr6D 27029275 27030400 1125 False 246.000000 246 90.815000 1122 2247 2 chr6D.!!$F2 1125
4 TraesCS6D01G056300 chr6A 28281951 28285278 3327 True 2294.500000 3275 91.991000 176 5684 2 chr6A.!!$R4 5508
5 TraesCS6D01G056300 chr6A 28250649 28255609 4960 True 661.000000 1031 85.956667 3307 5546 3 chr6A.!!$R3 2239
6 TraesCS6D01G056300 chr6A 28238346 28239510 1164 True 581.000000 811 87.438500 4551 5546 2 chr6A.!!$R2 995
7 TraesCS6D01G056300 chr6A 28316316 28317908 1592 True 476.000000 708 89.847500 1 612 2 chr6A.!!$R5 611
8 TraesCS6D01G056300 chr2D 544492899 544493994 1095 False 1893.000000 1893 97.993000 1122 2208 1 chr2D.!!$F1 1086
9 TraesCS6D01G056300 chr2D 132975707 132977083 1376 False 817.500000 1038 94.944500 2268 3311 2 chr2D.!!$F2 1043
10 TraesCS6D01G056300 chr2D 544492898 544493994 1096 True 246.000000 248 93.239000 1161 2248 2 chr2D.!!$R2 1087
11 TraesCS6D01G056300 chr4D 403151034 403152094 1060 True 1877.000000 1877 98.590000 2246 3306 1 chr4D.!!$R1 1060
12 TraesCS6D01G056300 chr4D 21188909 21189949 1040 True 728.500000 1279 92.355000 2300 3305 2 chr4D.!!$R2 1005
13 TraesCS6D01G056300 chr6B 48934768 48937355 2587 True 747.666667 1535 85.662000 810 5546 3 chr6B.!!$R7 4736
14 TraesCS6D01G056300 chr6B 49230481 49231049 568 True 730.000000 730 90.068000 265 834 1 chr6B.!!$R1 569
15 TraesCS6D01G056300 chr6B 56244934 56245873 939 False 710.000000 710 80.952000 2246 3201 1 chr6B.!!$F2 955
16 TraesCS6D01G056300 chr6B 48870275 48873041 2766 True 709.666667 1541 86.041667 810 5546 3 chr6B.!!$R6 4736
17 TraesCS6D01G056300 chr6B 48977636 48980529 2893 True 541.300000 1511 87.263750 569 5546 4 chr6B.!!$R8 4977
18 TraesCS6D01G056300 chr6B 49555157 49555781 624 False 470.000000 470 80.320000 3307 3928 1 chr6B.!!$F1 621
19 TraesCS6D01G056300 chr6B 49328277 49331432 3155 True 395.750000 741 87.572250 1 4094 4 chr6B.!!$R9 4093
20 TraesCS6D01G056300 chr1D 59955326 59956087 761 True 1345.000000 1345 98.560000 2246 3005 1 chr1D.!!$R1 759
21 TraesCS6D01G056300 chr1D 349268477 349269284 807 True 1243.000000 1243 94.568000 2247 3049 1 chr1D.!!$R2 802
22 TraesCS6D01G056300 chr1D 440050783 440051812 1029 True 913.000000 1085 98.413000 2246 3306 2 chr1D.!!$R3 1060
23 TraesCS6D01G056300 chr1B 534976797 534977685 888 False 1147.000000 1147 89.956000 2400 3299 1 chr1B.!!$F1 899
24 TraesCS6D01G056300 chr4B 96682944 96683928 984 False 1086.000000 1086 86.766000 2318 3306 1 chr4B.!!$F1 988
25 TraesCS6D01G056300 chr5B 583458388 583459322 934 False 885.000000 885 83.972000 2330 3306 1 chr5B.!!$F1 976
26 TraesCS6D01G056300 chr2B 268012607 268013379 772 False 876.000000 876 87.548000 1486 2248 1 chr2B.!!$F1 762
27 TraesCS6D01G056300 chr2B 262479785 262481720 1935 True 784.500000 800 85.515000 1486 2247 2 chr2B.!!$R1 761
28 TraesCS6D01G056300 chr2B 772451161 772452163 1002 False 485.500000 769 85.884500 1133 2120 2 chr2B.!!$F2 987
29 TraesCS6D01G056300 chr7A 117617049 117618092 1043 True 797.000000 797 81.130000 2246 3306 1 chr7A.!!$R1 1060
30 TraesCS6D01G056300 chr7A 120747976 120749018 1042 True 780.000000 780 80.857000 2246 3306 1 chr7A.!!$R2 1060
31 TraesCS6D01G056300 chr4A 72960798 72961605 807 False 257.333333 370 85.899333 1122 2247 3 chr4A.!!$F1 1125
32 TraesCS6D01G056300 chr4A 72960798 72961600 802 True 207.500000 219 85.823500 1127 2247 2 chr4A.!!$R1 1120
33 TraesCS6D01G056300 chr3A 535574019 535574574 555 True 266.500000 359 84.605500 1320 2247 2 chr3A.!!$R1 927

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
960 1017 0.319297 CCCTCGTCGGTTTCTTCGTT 60.319 55.000 0.00 0.0 0.00 3.85 F
1183 1246 0.036164 CCCATCTGGTTCAACGGACA 59.964 55.000 0.00 0.0 0.00 4.02 F
1232 1295 1.362224 CACCTCCCCTTTCCTTCTCA 58.638 55.000 0.00 0.0 0.00 3.27 F
1997 3570 3.716539 TAGCCCGCGCACATCTGAC 62.717 63.158 8.75 0.0 37.52 3.51 F
3851 8291 0.251634 CTTCTGGAGGAGGAACAGCC 59.748 60.000 0.00 0.0 32.42 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 3383 4.314440 ATGGTGACGGCGCACAGT 62.314 61.111 26.77 16.23 40.52 3.55 R
3312 5433 1.972978 AGGAACTGGTACTCCACGC 59.027 57.895 2.07 0.00 39.03 5.34 R
3384 5505 2.262915 CCCGTGCAGACAGAGTCC 59.737 66.667 0.00 0.00 32.18 3.85 R
3868 8380 0.251297 TTGTTCCCAGCACCCATGAG 60.251 55.000 0.00 0.00 0.00 2.90 R
4999 12146 2.289945 ACTGAAAGCTAGGCACTTGGAG 60.290 50.000 0.00 0.00 37.41 3.86 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
157 165 2.680312 AATGCATGTACTCTGCGACT 57.320 45.000 0.00 2.24 42.62 4.18
158 166 3.801114 AATGCATGTACTCTGCGACTA 57.199 42.857 0.00 0.63 42.62 2.59
159 167 4.327982 AATGCATGTACTCTGCGACTAT 57.672 40.909 0.00 2.55 42.62 2.12
160 168 5.453567 AATGCATGTACTCTGCGACTATA 57.546 39.130 0.00 0.00 42.62 1.31
161 169 5.651387 ATGCATGTACTCTGCGACTATAT 57.349 39.130 0.00 1.72 42.62 0.86
162 170 6.759497 ATGCATGTACTCTGCGACTATATA 57.241 37.500 0.00 0.00 42.62 0.86
163 171 6.759497 TGCATGTACTCTGCGACTATATAT 57.241 37.500 13.79 0.00 42.62 0.86
164 172 7.859325 TGCATGTACTCTGCGACTATATATA 57.141 36.000 13.79 0.00 42.62 0.86
165 173 8.451908 TGCATGTACTCTGCGACTATATATAT 57.548 34.615 13.79 0.00 42.62 0.86
166 174 9.555727 TGCATGTACTCTGCGACTATATATATA 57.444 33.333 13.79 2.49 42.62 0.86
331 348 3.805207 AGACTTAATATTGGTGGTCGCC 58.195 45.455 0.00 0.00 0.00 5.54
334 351 4.196971 ACTTAATATTGGTGGTCGCCTTC 58.803 43.478 0.00 0.00 0.00 3.46
427 444 2.352457 CGGCGACTTCCTCGATCG 60.352 66.667 9.36 9.36 46.14 3.69
475 492 2.172717 GGAGGTGCTTATAAGGGCAAGA 59.827 50.000 14.28 0.00 40.26 3.02
520 547 5.220739 GGATTGAGTGTGTGTGAATATCTGC 60.221 44.000 0.00 0.00 0.00 4.26
619 651 1.078214 CCTGGGCTTCAATCTCGCA 60.078 57.895 0.00 0.00 0.00 5.10
831 888 2.277072 CTCCTCCGCCTCTCTCCA 59.723 66.667 0.00 0.00 0.00 3.86
834 891 1.684049 CCTCCGCCTCTCTCCACTT 60.684 63.158 0.00 0.00 0.00 3.16
960 1017 0.319297 CCCTCGTCGGTTTCTTCGTT 60.319 55.000 0.00 0.00 0.00 3.85
1107 1170 1.227497 GCTCATCTTCCTCGGCCAG 60.227 63.158 2.24 0.00 0.00 4.85
1108 1171 1.445095 CTCATCTTCCTCGGCCAGG 59.555 63.158 13.43 13.43 45.15 4.45
1109 1172 2.037620 CTCATCTTCCTCGGCCAGGG 62.038 65.000 17.89 12.07 43.67 4.45
1110 1173 3.483869 ATCTTCCTCGGCCAGGGC 61.484 66.667 17.89 1.81 43.67 5.19
1152 1215 1.122019 CCTGCTCCCCGCCTATACTT 61.122 60.000 0.00 0.00 38.05 2.24
1183 1246 0.036164 CCCATCTGGTTCAACGGACA 59.964 55.000 0.00 0.00 0.00 4.02
1232 1295 1.362224 CACCTCCCCTTTCCTTCTCA 58.638 55.000 0.00 0.00 0.00 3.27
1997 3570 3.716539 TAGCCCGCGCACATCTGAC 62.717 63.158 8.75 0.00 37.52 3.51
3214 5333 6.312918 AGTTTGCATCACGTATCGTTTTCTAT 59.687 34.615 0.00 0.00 38.32 1.98
3219 5338 7.148557 TGCATCACGTATCGTTTTCTATTTTCA 60.149 33.333 0.00 0.00 38.32 2.69
3221 5340 9.702726 CATCACGTATCGTTTTCTATTTTCATT 57.297 29.630 0.00 0.00 38.32 2.57
3640 5787 2.300956 ACTGGCTTCTCTCTGACAGA 57.699 50.000 4.78 4.78 0.00 3.41
3713 5860 2.472695 TGAATTTGACGTGGAGAGGG 57.527 50.000 0.00 0.00 0.00 4.30
3771 6101 3.688185 CACACCAAAGACCATGAGATCTG 59.312 47.826 0.00 0.00 0.00 2.90
3791 8231 4.015872 TGTGTGATAACAGAAAGGGGTC 57.984 45.455 0.00 0.00 0.00 4.46
3851 8291 0.251634 CTTCTGGAGGAGGAACAGCC 59.748 60.000 0.00 0.00 32.42 4.85
3885 8397 1.379044 CCTCATGGGTGCTGGGAAC 60.379 63.158 0.00 0.00 0.00 3.62
4027 8545 1.349688 ACGGTCCAGTTTGAGCCATTA 59.650 47.619 0.00 0.00 0.00 1.90
4125 8653 3.840890 TTTCACACGGCATTGTTATCC 57.159 42.857 0.00 0.00 0.00 2.59
4236 8789 7.415206 CCAGGGAAAACTTATAAATTGAGTCCG 60.415 40.741 0.00 0.00 0.00 4.79
4569 11668 2.552031 TCTCGTAGATGTCTCCTCGTG 58.448 52.381 0.00 0.00 33.89 4.35
4577 11676 5.255710 AGATGTCTCCTCGTGTCTATTTG 57.744 43.478 0.00 0.00 0.00 2.32
4587 11686 5.103290 TCGTGTCTATTTGGCTTTTTGTC 57.897 39.130 0.00 0.00 0.00 3.18
4594 11693 2.715737 TTGGCTTTTTGTCGGTATGC 57.284 45.000 0.00 0.00 0.00 3.14
4645 11744 2.279935 AAAACAGGTAATGGCGGTCA 57.720 45.000 0.00 0.00 0.00 4.02
4646 11745 1.530323 AAACAGGTAATGGCGGTCAC 58.470 50.000 0.00 0.00 0.00 3.67
4665 11764 1.022735 CCCTGATGCAGCTGATGTTC 58.977 55.000 20.43 8.22 0.00 3.18
4668 11767 1.400846 CTGATGCAGCTGATGTTCCAC 59.599 52.381 20.43 0.00 0.00 4.02
4669 11768 0.376152 GATGCAGCTGATGTTCCACG 59.624 55.000 20.43 0.00 0.00 4.94
4913 12015 1.527457 CTTCCTCATCCCTTCCCCAT 58.473 55.000 0.00 0.00 0.00 4.00
4999 12146 3.568093 TTTTTGCTTGCCTTCTCGC 57.432 47.368 0.00 0.00 0.00 5.03
5004 12151 1.672356 GCTTGCCTTCTCGCTCCAA 60.672 57.895 0.00 0.00 0.00 3.53
5011 12158 0.532573 CTTCTCGCTCCAAGTGCCTA 59.467 55.000 0.00 0.00 0.00 3.93
5027 12175 3.055747 GTGCCTAGCTTTCAGTTACCTCT 60.056 47.826 0.00 0.00 0.00 3.69
5090 12248 3.309296 TCTTCCTATCGCTCCTCCAATT 58.691 45.455 0.00 0.00 0.00 2.32
5322 12645 2.884639 GTGTAACTTGCATGTTGGTCCT 59.115 45.455 24.00 3.31 0.00 3.85
5328 12660 2.472695 TGCATGTTGGTCCTGTCTAC 57.527 50.000 0.00 0.00 0.00 2.59
5528 12893 5.933790 TGTAATGTTGTCTATCGTTTTGCC 58.066 37.500 0.00 0.00 0.00 4.52
5577 13018 7.617041 ATCATTCTAGTGTTAAGCTGTTTCC 57.383 36.000 0.00 0.00 0.00 3.13
5637 13078 8.988064 AGATATAATTGACCATTAGCTACACG 57.012 34.615 0.00 0.00 30.48 4.49
5651 13092 2.094390 GCTACACGTCATTCCACTGGTA 60.094 50.000 0.00 0.00 0.00 3.25
5652 13093 3.615592 GCTACACGTCATTCCACTGGTAA 60.616 47.826 0.00 0.00 0.00 2.85
5684 13125 4.748892 TCTGTCTGTAGCTATGCTTTGTC 58.251 43.478 0.00 0.00 40.44 3.18
5685 13126 3.861840 TGTCTGTAGCTATGCTTTGTCC 58.138 45.455 0.00 0.00 40.44 4.02
5686 13127 3.260632 TGTCTGTAGCTATGCTTTGTCCA 59.739 43.478 0.00 0.00 40.44 4.02
5687 13128 3.619038 GTCTGTAGCTATGCTTTGTCCAC 59.381 47.826 0.00 0.00 40.44 4.02
5688 13129 3.515502 TCTGTAGCTATGCTTTGTCCACT 59.484 43.478 0.00 0.00 40.44 4.00
5689 13130 4.709886 TCTGTAGCTATGCTTTGTCCACTA 59.290 41.667 0.00 0.00 40.44 2.74
5690 13131 4.755411 TGTAGCTATGCTTTGTCCACTAC 58.245 43.478 0.00 0.00 40.44 2.73
5691 13132 3.981071 AGCTATGCTTTGTCCACTACA 57.019 42.857 0.00 0.00 33.89 2.74
5692 13133 3.866651 AGCTATGCTTTGTCCACTACAG 58.133 45.455 0.00 0.00 39.87 2.74
5693 13134 3.261897 AGCTATGCTTTGTCCACTACAGT 59.738 43.478 0.00 0.00 39.87 3.55
5694 13135 3.619038 GCTATGCTTTGTCCACTACAGTC 59.381 47.826 0.00 0.00 39.87 3.51
5695 13136 4.621747 GCTATGCTTTGTCCACTACAGTCT 60.622 45.833 0.00 0.00 39.87 3.24
5696 13137 5.394224 GCTATGCTTTGTCCACTACAGTCTA 60.394 44.000 0.00 0.00 39.87 2.59
5697 13138 4.521130 TGCTTTGTCCACTACAGTCTAG 57.479 45.455 0.00 0.00 39.87 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
316 333 3.279434 GAAGAAGGCGACCACCAATATT 58.721 45.455 0.00 0.00 0.00 1.28
334 351 7.374491 GCGAAAGATCTGAAATAAATTCCGAAG 59.626 37.037 0.00 0.00 35.31 3.79
391 408 0.725784 GCAGACGCATTTGTTGTCGG 60.726 55.000 0.00 0.00 37.69 4.79
427 444 1.734117 GAGCCGGCACAACATTTGC 60.734 57.895 31.54 0.00 39.41 3.68
495 516 5.295292 CAGATATTCACACACACTCAATCCC 59.705 44.000 0.00 0.00 0.00 3.85
564 592 4.165760 GGCCCATATACTGGTAGTTAGGT 58.834 47.826 0.00 0.00 44.30 3.08
782 836 1.478510 GATCTTCCTCTTCCAGCGACA 59.521 52.381 0.00 0.00 0.00 4.35
1047 1110 0.107017 GCATCTGGCTGCCTTCCTTA 60.107 55.000 21.03 0.00 40.25 2.69
1089 1152 1.227497 CTGGCCGAGGAAGATGAGC 60.227 63.158 0.00 0.00 0.00 4.26
1115 1178 4.101448 CAAGCCCGGTCCCTCAGG 62.101 72.222 0.00 0.00 0.00 3.86
1116 1179 4.785453 GCAAGCCCGGTCCCTCAG 62.785 72.222 0.00 0.00 0.00 3.35
1152 1215 1.383109 AGATGGGAGCACGGATGGA 60.383 57.895 0.00 0.00 0.00 3.41
1183 1246 4.776837 TGGGCCTTCACATAAAACAATCAT 59.223 37.500 4.53 0.00 0.00 2.45
1232 1295 2.338500 GGACGAAGAAAAGAGACGCAT 58.662 47.619 0.00 0.00 0.00 4.73
1822 3383 4.314440 ATGGTGACGGCGCACAGT 62.314 61.111 26.77 16.23 40.52 3.55
3312 5433 1.972978 AGGAACTGGTACTCCACGC 59.027 57.895 2.07 0.00 39.03 5.34
3384 5505 2.262915 CCCGTGCAGACAGAGTCC 59.737 66.667 0.00 0.00 32.18 3.85
3640 5787 1.313812 CCTCAGTTAGGCTCGTCGGT 61.314 60.000 0.00 0.00 38.97 4.69
3713 5860 0.802607 CGTTCCACGCTTAGGCTCTC 60.803 60.000 0.00 0.00 33.65 3.20
3771 6101 3.000727 CGACCCCTTTCTGTTATCACAC 58.999 50.000 0.00 0.00 0.00 3.82
3791 8231 1.790623 CGTGAGTAAACCAAGTCCACG 59.209 52.381 0.00 0.00 0.00 4.94
3851 8291 3.480505 TGAGGTATCACCATCATGCTG 57.519 47.619 0.00 0.00 41.95 4.41
3868 8380 0.251297 TTGTTCCCAGCACCCATGAG 60.251 55.000 0.00 0.00 0.00 2.90
3885 8397 8.954350 AGAGAAGATTGTCCAATTCAATAGTTG 58.046 33.333 0.00 0.00 35.94 3.16
4027 8545 5.440610 ACATTGTGAAGTTTCTTGACCTCT 58.559 37.500 0.00 0.00 0.00 3.69
4103 8631 4.219507 TGGATAACAATGCCGTGTGAAAAT 59.780 37.500 0.00 0.00 0.00 1.82
4111 8639 1.677576 CAGCATGGATAACAATGCCGT 59.322 47.619 8.64 0.00 40.63 5.68
4149 8677 9.703892 TTCGAACAAATTTGACATTATGGATTT 57.296 25.926 24.64 3.72 0.00 2.17
4172 8700 6.548441 TGGACTTGGTACTTGTAAATTTCG 57.452 37.500 0.00 0.00 0.00 3.46
4272 8825 8.280084 TCCTAAGTCCTAGCTACTCAGATTTAA 58.720 37.037 0.00 0.00 0.00 1.52
4335 8891 1.492599 TGTTCCATGCCATATCGGGAA 59.507 47.619 0.00 0.00 39.40 3.97
4383 8939 6.820656 CACTCAGACTATTTAGCTGGTCAAAT 59.179 38.462 0.00 0.00 32.26 2.32
4560 11659 2.457598 AGCCAAATAGACACGAGGAGA 58.542 47.619 0.00 0.00 0.00 3.71
4569 11668 4.499037 ACCGACAAAAAGCCAAATAGAC 57.501 40.909 0.00 0.00 0.00 2.59
4577 11676 0.885196 TGGCATACCGACAAAAAGCC 59.115 50.000 0.00 0.00 39.70 4.35
4587 11686 3.311486 AACAACCAAAATGGCATACCG 57.689 42.857 0.00 0.00 42.67 4.02
4594 11693 5.659463 TCAGAAGTCAAACAACCAAAATGG 58.341 37.500 0.00 0.00 45.02 3.16
4645 11744 0.330604 AACATCAGCTGCATCAGGGT 59.669 50.000 9.47 0.00 31.21 4.34
4646 11745 1.022735 GAACATCAGCTGCATCAGGG 58.977 55.000 9.47 0.00 31.21 4.45
4669 11768 5.340667 CAGACAATCTTCTTAAGCGTTTTGC 59.659 40.000 0.00 0.00 46.98 3.68
4684 11783 9.650539 GTGCATCATATATCTAACAGACAATCT 57.349 33.333 0.00 0.00 0.00 2.40
4913 12015 4.935578 TGAGGAAGATAACAGAGAGGTGA 58.064 43.478 0.00 0.00 0.00 4.02
4999 12146 2.289945 ACTGAAAGCTAGGCACTTGGAG 60.290 50.000 0.00 0.00 37.41 3.86
5004 12151 3.336138 GGTAACTGAAAGCTAGGCACT 57.664 47.619 0.00 0.00 40.02 4.40
5027 12175 3.447950 GAACTGGGGGAGTACTAAGGAA 58.552 50.000 0.00 0.00 33.09 3.36
5090 12248 4.832266 TCCTACTTAACCAAACCACGAGTA 59.168 41.667 0.00 0.00 0.00 2.59
5298 12621 4.083484 GGACCAACATGCAAGTTACACTAC 60.083 45.833 7.05 0.00 0.00 2.73
5322 12645 7.762159 TGTTATGATCAATTACTTGCGTAGACA 59.238 33.333 0.00 0.00 32.11 3.41
5328 12660 7.433131 AGCAATTGTTATGATCAATTACTTGCG 59.567 33.333 18.33 0.00 41.58 4.85
5396 12736 7.501559 AGAAGCAATGTGAAATGTCATAGCTAT 59.498 33.333 0.00 0.00 35.80 2.97
5528 12893 7.609760 TGTCCATAAACTACAATAACTGCAG 57.390 36.000 13.48 13.48 0.00 4.41
5577 13018 4.942852 TGCAAATTTAGTGGACAACAAGG 58.057 39.130 0.00 0.00 0.00 3.61
5637 13078 4.825085 TGGACTTTTTACCAGTGGAATGAC 59.175 41.667 18.40 2.84 0.00 3.06
5651 13092 5.625150 AGCTACAGACAGATTGGACTTTTT 58.375 37.500 0.00 0.00 0.00 1.94
5652 13093 5.234466 AGCTACAGACAGATTGGACTTTT 57.766 39.130 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.