Multiple sequence alignment - TraesCS6B01G025600

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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 TraesCS6B01G025600 chr6B 100.000 3152 0 0 1 3152 15398946 15395795 0.000000e+00 5821.0
1 TraesCS6B01G025600 chr6B 86.186 2179 225 18 980 3152 670592716 670590608 0.000000e+00 2287.0
2 TraesCS6B01G025600 chr6B 89.432 1249 72 26 335 1548 15606927 15605704 0.000000e+00 1520.0
3 TraesCS6B01G025600 chr6B 82.534 1689 247 20 1115 2769 15715098 15713424 0.000000e+00 1441.0
4 TraesCS6B01G025600 chr6B 80.519 1581 239 35 918 2479 16267307 16268837 0.000000e+00 1149.0
5 TraesCS6B01G025600 chr6B 90.645 310 25 3 2847 3152 16238726 16239035 2.930000e-110 409.0
6 TraesCS6B01G025600 chr6B 93.860 114 7 0 3027 3140 16340582 16340695 4.180000e-39 172.0
7 TraesCS6B01G025600 chr6B 94.030 67 3 1 193 259 15606990 15606925 2.000000e-17 100.0
8 TraesCS6B01G025600 chr2B 91.386 2879 199 22 282 3152 709570452 709567615 0.000000e+00 3897.0
9 TraesCS6B01G025600 chr2B 80.401 1296 189 30 1709 2965 89491328 89492597 0.000000e+00 926.0
10 TraesCS6B01G025600 chr2B 77.664 1464 266 35 722 2157 89494359 89495789 0.000000e+00 835.0
11 TraesCS6B01G025600 chr2B 91.961 311 22 3 196 504 89493944 89494253 1.740000e-117 433.0
12 TraesCS6B01G025600 chr2B 81.679 393 43 14 2403 2769 709252383 709251994 1.840000e-77 300.0
13 TraesCS6B01G025600 chr2B 88.112 143 13 2 573 714 757065181 757065042 1.940000e-37 167.0
14 TraesCS6B01G025600 chr5B 89.261 2179 200 19 991 3152 556795758 556793597 0.000000e+00 2697.0
15 TraesCS6B01G025600 chr5B 80.901 466 71 16 2691 3140 621236571 621236108 5.000000e-93 351.0
16 TraesCS6B01G025600 chr6A 90.059 2022 182 8 1129 3146 9355315 9357321 0.000000e+00 2603.0
17 TraesCS6B01G025600 chr6A 86.550 1658 200 18 918 2569 9461385 9463025 0.000000e+00 1805.0
18 TraesCS6B01G025600 chr6A 77.405 1310 254 30 849 2130 30560724 30559429 0.000000e+00 741.0
19 TraesCS6B01G025600 chr6D 86.143 1999 247 22 984 2971 33895036 33897015 0.000000e+00 2130.0
20 TraesCS6B01G025600 chr6D 83.265 1715 236 29 991 2668 8552805 8551105 0.000000e+00 1530.0
21 TraesCS6B01G025600 chr6D 95.643 918 40 0 1451 2368 8568351 8567434 0.000000e+00 1474.0
22 TraesCS6B01G025600 chr6D 83.377 1540 238 13 1040 2569 8987277 8988808 0.000000e+00 1410.0
23 TraesCS6B01G025600 chr6D 90.954 807 35 8 2364 3152 8567307 8566521 0.000000e+00 1051.0
24 TraesCS6B01G025600 chr6D 79.678 1181 221 14 991 2160 8967574 8968746 0.000000e+00 833.0
25 TraesCS6B01G025600 chr6D 78.405 1204 227 29 973 2158 8894030 8895218 0.000000e+00 752.0
26 TraesCS6B01G025600 chr6D 77.597 1165 247 14 993 2150 8397159 8396002 0.000000e+00 693.0
27 TraesCS6B01G025600 chr6D 77.045 1198 239 30 992 2162 9061964 9063152 0.000000e+00 656.0
28 TraesCS6B01G025600 chr6D 84.362 243 28 9 918 1160 33995075 33995307 2.450000e-56 230.0
29 TraesCS6B01G025600 chr6D 98.039 51 1 0 2963 3013 33897023 33897073 4.330000e-14 89.8
30 TraesCS6B01G025600 chr1B 83.528 1627 227 21 951 2562 662152984 662154584 0.000000e+00 1482.0
31 TraesCS6B01G025600 chr5D 80.093 1502 274 11 988 2479 42076051 42077537 0.000000e+00 1094.0
32 TraesCS6B01G025600 chr5D 79.900 602 74 25 2569 3147 42077645 42078222 6.330000e-107 398.0
33 TraesCS6B01G025600 chr5D 83.032 442 56 11 2715 3140 499863241 499862803 1.770000e-102 383.0
34 TraesCS6B01G025600 chrUn 82.418 1257 214 5 1185 2440 95438041 95439291 0.000000e+00 1090.0
35 TraesCS6B01G025600 chr2D 94.712 208 9 2 1 206 6715863 6716070 3.920000e-84 322.0
36 TraesCS6B01G025600 chr2D 89.437 142 12 2 575 714 590279471 590279331 3.230000e-40 176.0
37 TraesCS6B01G025600 chr4B 94.444 198 9 2 1 197 632208254 632208058 1.420000e-78 303.0
38 TraesCS6B01G025600 chr4B 93.939 198 10 2 1 197 632245644 632245448 6.610000e-77 298.0
39 TraesCS6B01G025600 chr1D 94.000 200 11 1 1 199 13677604 13677803 5.110000e-78 302.0
40 TraesCS6B01G025600 chr7D 93.939 198 11 1 1 197 559791634 559791437 6.610000e-77 298.0
41 TraesCS6B01G025600 chr7D 93.532 201 9 4 1 199 93942911 93943109 2.380000e-76 296.0
42 TraesCS6B01G025600 chr7D 93.500 200 11 2 1 199 371261368 371261170 2.380000e-76 296.0
43 TraesCS6B01G025600 chr7D 92.414 145 7 4 573 714 36659734 36659877 1.480000e-48 204.0
44 TraesCS6B01G025600 chr3D 93.939 198 11 1 1 197 574612652 574612849 6.610000e-77 298.0
45 TraesCS6B01G025600 chr3D 91.121 214 16 3 1 212 517443034 517443246 1.430000e-73 287.0
46 TraesCS6B01G025600 chr3D 94.737 114 6 0 3027 3140 582881500 582881613 8.980000e-41 178.0
47 TraesCS6B01G025600 chr3D 89.286 140 8 2 582 714 110222179 110222040 5.410000e-38 169.0
48 TraesCS6B01G025600 chr3B 95.575 113 5 0 3031 3143 778341289 778341177 6.940000e-42 182.0
49 TraesCS6B01G025600 chr5A 88.571 140 14 1 577 714 373424680 373424541 5.410000e-38 169.0
50 TraesCS6B01G025600 chr1A 89.209 139 10 3 577 714 409855167 409855033 5.410000e-38 169.0
51 TraesCS6B01G025600 chr2A 88.406 138 14 2 577 714 418618398 418618263 6.990000e-37 165.0


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 TraesCS6B01G025600 chr6B 15395795 15398946 3151 True 5821.000000 5821 100.0000 1 3152 1 chr6B.!!$R1 3151
1 TraesCS6B01G025600 chr6B 670590608 670592716 2108 True 2287.000000 2287 86.1860 980 3152 1 chr6B.!!$R3 2172
2 TraesCS6B01G025600 chr6B 15713424 15715098 1674 True 1441.000000 1441 82.5340 1115 2769 1 chr6B.!!$R2 1654
3 TraesCS6B01G025600 chr6B 16267307 16268837 1530 False 1149.000000 1149 80.5190 918 2479 1 chr6B.!!$F2 1561
4 TraesCS6B01G025600 chr6B 15605704 15606990 1286 True 810.000000 1520 91.7310 193 1548 2 chr6B.!!$R4 1355
5 TraesCS6B01G025600 chr2B 709567615 709570452 2837 True 3897.000000 3897 91.3860 282 3152 1 chr2B.!!$R2 2870
6 TraesCS6B01G025600 chr2B 89491328 89495789 4461 False 731.333333 926 83.3420 196 2965 3 chr2B.!!$F1 2769
7 TraesCS6B01G025600 chr5B 556793597 556795758 2161 True 2697.000000 2697 89.2610 991 3152 1 chr5B.!!$R1 2161
8 TraesCS6B01G025600 chr6A 9355315 9357321 2006 False 2603.000000 2603 90.0590 1129 3146 1 chr6A.!!$F1 2017
9 TraesCS6B01G025600 chr6A 9461385 9463025 1640 False 1805.000000 1805 86.5500 918 2569 1 chr6A.!!$F2 1651
10 TraesCS6B01G025600 chr6A 30559429 30560724 1295 True 741.000000 741 77.4050 849 2130 1 chr6A.!!$R1 1281
11 TraesCS6B01G025600 chr6D 8551105 8552805 1700 True 1530.000000 1530 83.2650 991 2668 1 chr6D.!!$R2 1677
12 TraesCS6B01G025600 chr6D 8987277 8988808 1531 False 1410.000000 1410 83.3770 1040 2569 1 chr6D.!!$F3 1529
13 TraesCS6B01G025600 chr6D 8566521 8568351 1830 True 1262.500000 1474 93.2985 1451 3152 2 chr6D.!!$R3 1701
14 TraesCS6B01G025600 chr6D 33895036 33897073 2037 False 1109.900000 2130 92.0910 984 3013 2 chr6D.!!$F6 2029
15 TraesCS6B01G025600 chr6D 8967574 8968746 1172 False 833.000000 833 79.6780 991 2160 1 chr6D.!!$F2 1169
16 TraesCS6B01G025600 chr6D 8894030 8895218 1188 False 752.000000 752 78.4050 973 2158 1 chr6D.!!$F1 1185
17 TraesCS6B01G025600 chr6D 8396002 8397159 1157 True 693.000000 693 77.5970 993 2150 1 chr6D.!!$R1 1157
18 TraesCS6B01G025600 chr6D 9061964 9063152 1188 False 656.000000 656 77.0450 992 2162 1 chr6D.!!$F4 1170
19 TraesCS6B01G025600 chr1B 662152984 662154584 1600 False 1482.000000 1482 83.5280 951 2562 1 chr1B.!!$F1 1611
20 TraesCS6B01G025600 chr5D 42076051 42078222 2171 False 746.000000 1094 79.9965 988 3147 2 chr5D.!!$F1 2159
21 TraesCS6B01G025600 chrUn 95438041 95439291 1250 False 1090.000000 1090 82.4180 1185 2440 1 chrUn.!!$F1 1255

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
182 183 0.106419 TGAACCGGGATAAATGGCCC 60.106 55.0 6.32 0.0 41.11 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2162 4736 2.037641 AGCACACAGTTACATCAGAGCA 59.962 45.455 0.0 0.0 0.0 4.26 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
29 30 4.384599 GGTGTTACCAACCGGGAC 57.615 61.111 6.32 0.00 38.42 4.46
30 31 1.756665 GGTGTTACCAACCGGGACT 59.243 57.895 6.32 0.00 38.42 3.85
32 33 1.347378 GGTGTTACCAACCGGGACTAA 59.653 52.381 6.32 0.00 38.42 2.24
33 34 2.224499 GGTGTTACCAACCGGGACTAAA 60.224 50.000 6.32 0.00 38.42 1.85
34 35 3.069289 GTGTTACCAACCGGGACTAAAG 58.931 50.000 6.32 0.00 41.15 1.85
35 36 2.038820 TGTTACCAACCGGGACTAAAGG 59.961 50.000 6.32 0.00 41.15 3.11
36 37 2.028561 TACCAACCGGGACTAAAGGT 57.971 50.000 6.32 5.18 41.15 3.50
38 39 0.322187 CCAACCGGGACTAAAGGTGG 60.322 60.000 6.32 0.00 40.01 4.61
39 40 0.688487 CAACCGGGACTAAAGGTGGA 59.312 55.000 6.32 0.00 38.44 4.02
40 41 0.981943 AACCGGGACTAAAGGTGGAG 59.018 55.000 6.32 0.00 38.44 3.86
41 42 0.178912 ACCGGGACTAAAGGTGGAGT 60.179 55.000 6.32 0.00 36.81 3.85
42 43 0.981943 CCGGGACTAAAGGTGGAGTT 59.018 55.000 0.00 0.00 0.00 3.01
43 44 1.066358 CCGGGACTAAAGGTGGAGTTC 60.066 57.143 0.00 0.00 0.00 3.01
49 50 4.771054 GGACTAAAGGTGGAGTTCTAGACA 59.229 45.833 0.00 0.00 0.00 3.41
50 51 5.105675 GGACTAAAGGTGGAGTTCTAGACAG 60.106 48.000 0.00 0.00 0.00 3.51
52 53 1.178276 AGGTGGAGTTCTAGACAGCG 58.822 55.000 0.00 0.00 36.53 5.18
53 54 0.173708 GGTGGAGTTCTAGACAGCGG 59.826 60.000 0.00 0.00 0.00 5.52
54 55 0.458716 GTGGAGTTCTAGACAGCGGC 60.459 60.000 0.00 0.00 0.00 6.53
55 56 1.142097 GGAGTTCTAGACAGCGGCC 59.858 63.158 0.00 0.00 0.00 6.13
57 58 0.458716 GAGTTCTAGACAGCGGCCAC 60.459 60.000 2.24 0.00 0.00 5.01
58 59 1.805945 GTTCTAGACAGCGGCCACG 60.806 63.158 2.24 0.00 44.63 4.94
59 60 2.273179 TTCTAGACAGCGGCCACGT 61.273 57.895 2.24 0.00 43.45 4.49
60 61 2.486636 TTCTAGACAGCGGCCACGTG 62.487 60.000 9.08 9.08 43.45 4.49
61 62 3.989698 CTAGACAGCGGCCACGTGG 62.990 68.421 30.66 30.66 43.45 4.94
69 70 4.309950 GGCCACGTGGACGACCTT 62.310 66.667 38.30 0.00 43.02 3.50
71 72 1.005867 GCCACGTGGACGACCTTTA 60.006 57.895 38.30 0.00 43.02 1.85
81 82 2.956913 GACGACCTTTAGTCCTGGTTC 58.043 52.381 0.00 0.00 43.08 3.62
83 84 1.271656 CGACCTTTAGTCCTGGTTCGT 59.728 52.381 0.00 0.00 43.08 3.85
85 86 2.036862 GACCTTTAGTCCTGGTTCGTGT 59.963 50.000 0.00 0.00 39.84 4.49
86 87 3.233507 ACCTTTAGTCCTGGTTCGTGTA 58.766 45.455 0.00 0.00 0.00 2.90
87 88 3.642848 ACCTTTAGTCCTGGTTCGTGTAA 59.357 43.478 0.00 0.00 0.00 2.41
89 90 4.021719 CCTTTAGTCCTGGTTCGTGTAAGA 60.022 45.833 0.00 0.00 0.00 2.10
90 91 5.510179 CCTTTAGTCCTGGTTCGTGTAAGAA 60.510 44.000 0.00 0.00 0.00 2.52
99 100 4.510038 GTTCGTGTAAGAACCAGGACTA 57.490 45.455 0.00 0.00 43.33 2.59
100 101 4.874970 GTTCGTGTAAGAACCAGGACTAA 58.125 43.478 0.00 0.00 43.33 2.24
101 102 5.291971 GTTCGTGTAAGAACCAGGACTAAA 58.708 41.667 0.00 0.00 43.33 1.85
102 103 5.130292 TCGTGTAAGAACCAGGACTAAAG 57.870 43.478 0.00 0.00 0.00 1.85
103 104 4.021719 TCGTGTAAGAACCAGGACTAAAGG 60.022 45.833 0.00 0.00 0.00 3.11
107 108 1.153565 AGAACCAGGACTAAAGGGGGA 59.846 52.381 0.00 0.00 0.00 4.81
108 109 1.560146 GAACCAGGACTAAAGGGGGAG 59.440 57.143 0.00 0.00 0.00 4.30
109 110 0.253207 ACCAGGACTAAAGGGGGAGG 60.253 60.000 0.00 0.00 0.00 4.30
111 112 0.621862 CAGGACTAAAGGGGGAGGCT 60.622 60.000 0.00 0.00 0.00 4.58
112 113 0.121402 AGGACTAAAGGGGGAGGCTT 59.879 55.000 0.00 0.00 0.00 4.35
113 114 1.000496 GGACTAAAGGGGGAGGCTTT 59.000 55.000 0.00 0.00 0.00 3.51
114 115 2.202707 GGACTAAAGGGGGAGGCTTTA 58.797 52.381 0.00 0.00 0.00 1.85
117 118 4.084466 ACTAAAGGGGGAGGCTTTAGTA 57.916 45.455 5.23 0.00 46.00 1.82
118 119 4.441757 ACTAAAGGGGGAGGCTTTAGTAA 58.558 43.478 5.23 0.00 46.00 2.24
119 120 3.733883 AAAGGGGGAGGCTTTAGTAAC 57.266 47.619 0.00 0.00 0.00 2.50
120 121 1.201424 AGGGGGAGGCTTTAGTAACG 58.799 55.000 0.00 0.00 0.00 3.18
121 122 1.197812 GGGGGAGGCTTTAGTAACGA 58.802 55.000 0.00 0.00 0.00 3.85
122 123 1.134580 GGGGGAGGCTTTAGTAACGAC 60.135 57.143 0.00 0.00 0.00 4.34
123 124 1.134580 GGGGAGGCTTTAGTAACGACC 60.135 57.143 0.00 0.00 0.00 4.79
126 127 3.370209 GGGAGGCTTTAGTAACGACCATT 60.370 47.826 0.00 0.00 0.00 3.16
128 129 5.422145 GGAGGCTTTAGTAACGACCATTTA 58.578 41.667 0.00 0.00 0.00 1.40
129 130 5.522824 GGAGGCTTTAGTAACGACCATTTAG 59.477 44.000 0.00 0.00 0.00 1.85
130 131 6.046290 AGGCTTTAGTAACGACCATTTAGT 57.954 37.500 0.00 0.00 0.00 2.24
131 132 6.104665 AGGCTTTAGTAACGACCATTTAGTC 58.895 40.000 0.00 0.00 0.00 2.59
132 133 5.292834 GGCTTTAGTAACGACCATTTAGTCC 59.707 44.000 0.00 0.00 32.91 3.85
133 134 5.292834 GCTTTAGTAACGACCATTTAGTCCC 59.707 44.000 0.00 0.00 32.91 4.46
134 135 3.515330 AGTAACGACCATTTAGTCCCG 57.485 47.619 0.00 0.00 32.91 5.14
135 136 2.167075 AGTAACGACCATTTAGTCCCGG 59.833 50.000 0.00 0.00 32.91 5.73
138 139 1.066645 ACGACCATTTAGTCCCGGTTC 60.067 52.381 0.00 0.00 32.91 3.62
140 141 1.279846 GACCATTTAGTCCCGGTTCCA 59.720 52.381 0.00 0.00 0.00 3.53
142 143 1.557832 CCATTTAGTCCCGGTTCCAGA 59.442 52.381 0.00 0.00 0.00 3.86
143 144 2.026636 CCATTTAGTCCCGGTTCCAGAA 60.027 50.000 0.00 0.00 0.00 3.02
154 155 2.845363 GTTCCAGAACCGGGAGTAAA 57.155 50.000 6.32 0.00 35.46 2.01
155 156 2.696506 GTTCCAGAACCGGGAGTAAAG 58.303 52.381 6.32 0.00 35.46 1.85
157 158 0.392595 CCAGAACCGGGAGTAAAGGC 60.393 60.000 6.32 0.00 0.00 4.35
158 159 0.392595 CAGAACCGGGAGTAAAGGCC 60.393 60.000 6.32 0.00 0.00 5.19
159 160 1.077930 GAACCGGGAGTAAAGGCCC 60.078 63.158 6.32 0.00 41.11 5.80
160 161 1.540617 AACCGGGAGTAAAGGCCCT 60.541 57.895 6.32 0.00 42.40 5.19
162 163 0.252835 ACCGGGAGTAAAGGCCCTTA 60.253 55.000 6.32 0.00 42.40 2.69
163 164 1.137697 CCGGGAGTAAAGGCCCTTAT 58.862 55.000 0.00 0.00 42.40 1.73
164 165 1.202770 CCGGGAGTAAAGGCCCTTATG 60.203 57.143 0.00 0.00 42.40 1.90
165 166 1.766496 CGGGAGTAAAGGCCCTTATGA 59.234 52.381 0.00 0.00 42.40 2.15
166 167 2.171870 CGGGAGTAAAGGCCCTTATGAA 59.828 50.000 0.00 0.00 42.40 2.57
170 171 2.092592 AGTAAAGGCCCTTATGAACCGG 60.093 50.000 0.00 0.00 0.00 5.28
172 173 0.917333 AAGGCCCTTATGAACCGGGA 60.917 55.000 6.32 0.00 40.55 5.14
174 175 1.061546 GGCCCTTATGAACCGGGATA 58.938 55.000 6.32 0.00 40.55 2.59
175 176 1.422402 GGCCCTTATGAACCGGGATAA 59.578 52.381 6.32 4.56 40.55 1.75
176 177 2.158579 GGCCCTTATGAACCGGGATAAA 60.159 50.000 6.32 0.00 40.55 1.40
177 178 3.499745 GGCCCTTATGAACCGGGATAAAT 60.500 47.826 6.32 0.00 40.55 1.40
178 179 3.506067 GCCCTTATGAACCGGGATAAATG 59.494 47.826 6.32 1.13 40.55 2.32
179 180 4.079253 CCCTTATGAACCGGGATAAATGG 58.921 47.826 6.32 5.40 40.55 3.16
180 181 3.506067 CCTTATGAACCGGGATAAATGGC 59.494 47.826 6.32 0.00 0.00 4.40
181 182 1.995376 ATGAACCGGGATAAATGGCC 58.005 50.000 6.32 0.00 0.00 5.36
182 183 0.106419 TGAACCGGGATAAATGGCCC 60.106 55.000 6.32 0.00 41.11 5.80
183 184 0.185175 GAACCGGGATAAATGGCCCT 59.815 55.000 6.32 0.00 42.40 5.19
184 185 0.634465 AACCGGGATAAATGGCCCTT 59.366 50.000 6.32 0.00 42.40 3.95
185 186 0.634465 ACCGGGATAAATGGCCCTTT 59.366 50.000 6.32 11.01 42.40 3.11
186 187 1.007842 ACCGGGATAAATGGCCCTTTT 59.992 47.619 11.49 8.52 42.40 2.27
187 188 2.115427 CCGGGATAAATGGCCCTTTTT 58.885 47.619 11.49 3.70 42.40 1.94
189 190 3.031013 CGGGATAAATGGCCCTTTTTCT 58.969 45.455 18.42 4.05 42.40 2.52
190 191 4.211920 CGGGATAAATGGCCCTTTTTCTA 58.788 43.478 18.42 1.10 42.40 2.10
191 192 4.037565 CGGGATAAATGGCCCTTTTTCTAC 59.962 45.833 18.42 12.86 42.40 2.59
192 193 5.208890 GGGATAAATGGCCCTTTTTCTACT 58.791 41.667 18.42 0.00 41.31 2.57
194 195 6.490381 GGGATAAATGGCCCTTTTTCTACTAG 59.510 42.308 18.42 0.00 41.31 2.57
197 198 4.929146 ATGGCCCTTTTTCTACTAGTGT 57.071 40.909 5.39 0.00 0.00 3.55
199 200 4.394729 TGGCCCTTTTTCTACTAGTGTTG 58.605 43.478 5.39 0.00 0.00 3.33
264 2686 1.012841 CAAGGAGCCGAGATCTTTGC 58.987 55.000 8.87 8.87 29.43 3.68
272 2694 1.938577 CCGAGATCTTTGCCACATCTG 59.061 52.381 0.00 0.00 0.00 2.90
298 2720 0.671251 GGCATGTTCCGGACAACAAA 59.329 50.000 12.82 0.00 42.62 2.83
345 2768 4.688597 CGGGGGATAAATGATTGAACCAGA 60.689 45.833 0.00 0.00 0.00 3.86
356 2779 7.893124 ATGATTGAACCAGAAGCTATGATTT 57.107 32.000 0.48 0.00 0.00 2.17
394 2818 3.721087 AGTATTGTTGGGGAGAGTTGG 57.279 47.619 0.00 0.00 0.00 3.77
442 2866 1.157257 TGCAACCATAGCGCCGTATG 61.157 55.000 2.29 6.74 33.85 2.39
456 2880 2.935238 GCCGTATGAACCATGGCGATAT 60.935 50.000 13.04 4.14 35.77 1.63
497 2922 0.950836 CAACACATCAAACTGGCCGA 59.049 50.000 0.00 0.00 0.00 5.54
628 3108 5.348986 TGTAGAGATTTCGCTATGAACCAC 58.651 41.667 0.00 0.00 35.97 4.16
808 3289 6.934645 TGAAAGTGTATTGGAGTAGGAGTTTG 59.065 38.462 0.00 0.00 0.00 2.93
814 3295 5.779241 ATTGGAGTAGGAGTTTGGATTGA 57.221 39.130 0.00 0.00 0.00 2.57
827 3309 8.023706 GGAGTTTGGATTGAAGTAGTCATTTTC 58.976 37.037 0.00 0.00 35.70 2.29
828 3310 8.463930 AGTTTGGATTGAAGTAGTCATTTTCA 57.536 30.769 0.00 0.00 35.70 2.69
1269 3809 2.352032 GGGTCTCTCCACCACCGAG 61.352 68.421 0.00 0.00 38.32 4.63
1314 3854 2.435586 CAGTTCCTCTGCGCCAGG 60.436 66.667 15.00 15.00 37.36 4.45
1853 4427 1.748122 CCAAGGAATCGCTGCAGCT 60.748 57.895 34.22 18.06 39.32 4.24
1966 4540 0.830444 CAGGCCCCGGTACTATGCTA 60.830 60.000 0.00 0.00 0.00 3.49
2162 4736 2.851263 TTCACATAAGCCAAGGACGT 57.149 45.000 0.00 0.00 0.00 4.34
2218 4794 4.681781 GCTGTATGTCTGTTAGATGCTGGT 60.682 45.833 0.00 0.00 0.00 4.00
2408 5124 6.515365 GCCATTCTGAAATGCACCAAAATTTT 60.515 34.615 0.00 0.00 40.85 1.82
2778 5594 6.003950 CCATCGGTCATATTGGAAATACCTT 58.996 40.000 0.00 0.00 39.86 3.50
2779 5595 6.490040 CCATCGGTCATATTGGAAATACCTTT 59.510 38.462 0.00 0.00 39.86 3.11
2797 5621 1.452145 TTTGGGCTGCAGGACGAAAC 61.452 55.000 17.12 0.00 0.00 2.78
2849 5678 7.221838 GCTAAAGAGAGATGCACACTTAACTAG 59.778 40.741 0.00 0.00 0.00 2.57
2863 5692 8.085296 CACACTTAACTAGACATCAAACTCTCT 58.915 37.037 0.00 0.00 0.00 3.10
3015 5911 1.534163 CTCTGCACGATGGCCATATTG 59.466 52.381 20.84 19.17 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.038952 ACCTTTAGTCCCGGTTGGTAAC 59.961 50.000 0.00 0.00 34.77 2.50
16 17 2.038820 CACCTTTAGTCCCGGTTGGTAA 59.961 50.000 0.00 0.00 34.77 2.85
18 19 0.399075 CACCTTTAGTCCCGGTTGGT 59.601 55.000 0.00 0.00 34.77 3.67
19 20 0.322187 CCACCTTTAGTCCCGGTTGG 60.322 60.000 0.00 0.00 0.00 3.77
20 21 0.688487 TCCACCTTTAGTCCCGGTTG 59.312 55.000 0.00 0.00 0.00 3.77
21 22 0.981943 CTCCACCTTTAGTCCCGGTT 59.018 55.000 0.00 0.00 0.00 4.44
22 23 0.178912 ACTCCACCTTTAGTCCCGGT 60.179 55.000 0.00 0.00 0.00 5.28
23 24 0.981943 AACTCCACCTTTAGTCCCGG 59.018 55.000 0.00 0.00 0.00 5.73
24 25 1.900486 AGAACTCCACCTTTAGTCCCG 59.100 52.381 0.00 0.00 0.00 5.14
26 27 4.771054 TGTCTAGAACTCCACCTTTAGTCC 59.229 45.833 0.00 0.00 0.00 3.85
29 30 4.675671 CGCTGTCTAGAACTCCACCTTTAG 60.676 50.000 0.00 0.00 0.00 1.85
30 31 3.192844 CGCTGTCTAGAACTCCACCTTTA 59.807 47.826 0.00 0.00 0.00 1.85
32 33 1.546476 CGCTGTCTAGAACTCCACCTT 59.454 52.381 0.00 0.00 0.00 3.50
33 34 1.178276 CGCTGTCTAGAACTCCACCT 58.822 55.000 0.00 0.00 0.00 4.00
34 35 0.173708 CCGCTGTCTAGAACTCCACC 59.826 60.000 0.00 0.00 0.00 4.61
35 36 0.458716 GCCGCTGTCTAGAACTCCAC 60.459 60.000 0.00 0.00 0.00 4.02
36 37 1.605058 GGCCGCTGTCTAGAACTCCA 61.605 60.000 0.00 0.00 0.00 3.86
38 39 0.458716 GTGGCCGCTGTCTAGAACTC 60.459 60.000 9.68 0.00 0.00 3.01
39 40 1.592223 GTGGCCGCTGTCTAGAACT 59.408 57.895 9.68 0.00 0.00 3.01
40 41 1.805945 CGTGGCCGCTGTCTAGAAC 60.806 63.158 15.69 0.00 0.00 3.01
41 42 2.273179 ACGTGGCCGCTGTCTAGAA 61.273 57.895 15.69 0.00 37.70 2.10
42 43 2.675423 ACGTGGCCGCTGTCTAGA 60.675 61.111 15.69 0.00 37.70 2.43
43 44 2.507102 CACGTGGCCGCTGTCTAG 60.507 66.667 15.69 0.00 37.70 2.43
52 53 2.438951 TAAAGGTCGTCCACGTGGCC 62.439 60.000 30.25 23.65 40.80 5.36
53 54 1.005867 TAAAGGTCGTCCACGTGGC 60.006 57.895 30.25 22.27 40.80 5.01
54 55 0.316204 ACTAAAGGTCGTCCACGTGG 59.684 55.000 29.26 29.26 40.80 4.94
55 56 1.668047 GGACTAAAGGTCGTCCACGTG 60.668 57.143 9.08 9.08 46.98 4.49
57 58 3.413522 GGACTAAAGGTCGTCCACG 57.586 57.895 0.51 0.00 46.98 4.94
61 62 2.670509 CGAACCAGGACTAAAGGTCGTC 60.671 54.545 0.00 0.00 45.35 4.20
62 63 1.271656 CGAACCAGGACTAAAGGTCGT 59.728 52.381 0.00 0.00 45.35 4.34
63 64 1.271656 ACGAACCAGGACTAAAGGTCG 59.728 52.381 0.00 0.00 45.35 4.79
64 65 2.036862 ACACGAACCAGGACTAAAGGTC 59.963 50.000 0.00 0.00 43.79 3.85
65 66 2.044758 ACACGAACCAGGACTAAAGGT 58.955 47.619 0.00 0.00 37.20 3.50
67 68 5.130292 TCTTACACGAACCAGGACTAAAG 57.870 43.478 0.00 0.00 0.00 1.85
68 69 5.291971 GTTCTTACACGAACCAGGACTAAA 58.708 41.667 0.00 0.00 37.82 1.85
69 70 4.874970 GTTCTTACACGAACCAGGACTAA 58.125 43.478 0.00 0.00 37.82 2.24
71 72 3.382048 GTTCTTACACGAACCAGGACT 57.618 47.619 0.00 0.00 37.82 3.85
78 79 3.382048 AGTCCTGGTTCTTACACGAAC 57.618 47.619 0.00 0.00 41.91 3.95
79 80 5.510179 CCTTTAGTCCTGGTTCTTACACGAA 60.510 44.000 0.00 0.00 0.00 3.85
80 81 4.021719 CCTTTAGTCCTGGTTCTTACACGA 60.022 45.833 0.00 0.00 0.00 4.35
81 82 4.243270 CCTTTAGTCCTGGTTCTTACACG 58.757 47.826 0.00 0.00 0.00 4.49
83 84 3.585732 CCCCTTTAGTCCTGGTTCTTACA 59.414 47.826 0.00 0.00 0.00 2.41
85 86 3.181392 TCCCCCTTTAGTCCTGGTTCTTA 60.181 47.826 0.00 0.00 0.00 2.10
86 87 1.993301 CCCCCTTTAGTCCTGGTTCTT 59.007 52.381 0.00 0.00 0.00 2.52
87 88 1.153565 TCCCCCTTTAGTCCTGGTTCT 59.846 52.381 0.00 0.00 0.00 3.01
89 90 1.670059 CTCCCCCTTTAGTCCTGGTT 58.330 55.000 0.00 0.00 0.00 3.67
90 91 0.253207 CCTCCCCCTTTAGTCCTGGT 60.253 60.000 0.00 0.00 0.00 4.00
91 92 1.636769 GCCTCCCCCTTTAGTCCTGG 61.637 65.000 0.00 0.00 0.00 4.45
92 93 0.621862 AGCCTCCCCCTTTAGTCCTG 60.622 60.000 0.00 0.00 0.00 3.86
93 94 0.121402 AAGCCTCCCCCTTTAGTCCT 59.879 55.000 0.00 0.00 0.00 3.85
95 96 3.562343 CTAAAGCCTCCCCCTTTAGTC 57.438 52.381 11.01 0.00 43.17 2.59
99 100 2.026542 CGTTACTAAAGCCTCCCCCTTT 60.027 50.000 0.00 0.00 36.55 3.11
100 101 1.558294 CGTTACTAAAGCCTCCCCCTT 59.442 52.381 0.00 0.00 0.00 3.95
101 102 1.201424 CGTTACTAAAGCCTCCCCCT 58.799 55.000 0.00 0.00 0.00 4.79
102 103 1.134580 GTCGTTACTAAAGCCTCCCCC 60.135 57.143 0.00 0.00 0.00 5.40
103 104 1.134580 GGTCGTTACTAAAGCCTCCCC 60.135 57.143 0.00 0.00 0.00 4.81
107 108 6.046290 ACTAAATGGTCGTTACTAAAGCCT 57.954 37.500 0.00 0.00 0.00 4.58
108 109 5.292834 GGACTAAATGGTCGTTACTAAAGCC 59.707 44.000 0.00 0.00 37.12 4.35
109 110 5.292834 GGGACTAAATGGTCGTTACTAAAGC 59.707 44.000 0.00 0.00 37.12 3.51
111 112 5.410067 CGGGACTAAATGGTCGTTACTAAA 58.590 41.667 0.00 0.00 37.12 1.85
112 113 4.142182 CCGGGACTAAATGGTCGTTACTAA 60.142 45.833 0.00 0.00 37.12 2.24
113 114 3.381272 CCGGGACTAAATGGTCGTTACTA 59.619 47.826 0.00 0.00 37.12 1.82
114 115 2.167075 CCGGGACTAAATGGTCGTTACT 59.833 50.000 0.00 0.00 37.12 2.24
117 118 0.978907 ACCGGGACTAAATGGTCGTT 59.021 50.000 6.32 0.00 37.12 3.85
118 119 0.978907 AACCGGGACTAAATGGTCGT 59.021 50.000 6.32 0.00 37.12 4.34
119 120 1.648504 GAACCGGGACTAAATGGTCG 58.351 55.000 6.32 0.00 37.12 4.79
120 121 1.279846 TGGAACCGGGACTAAATGGTC 59.720 52.381 6.32 0.00 32.37 4.02
121 122 1.280998 CTGGAACCGGGACTAAATGGT 59.719 52.381 6.32 0.00 35.90 3.55
122 123 1.557832 TCTGGAACCGGGACTAAATGG 59.442 52.381 6.32 0.00 0.00 3.16
123 124 3.007635 GTTCTGGAACCGGGACTAAATG 58.992 50.000 6.32 0.00 35.36 2.32
135 136 2.614734 CCTTTACTCCCGGTTCTGGAAC 60.615 54.545 0.00 5.02 40.45 3.62
138 139 0.392595 GCCTTTACTCCCGGTTCTGG 60.393 60.000 0.00 0.00 0.00 3.86
140 141 1.559965 GGGCCTTTACTCCCGGTTCT 61.560 60.000 0.84 0.00 32.00 3.01
142 143 3.084304 GGGCCTTTACTCCCGGTT 58.916 61.111 0.84 0.00 32.00 4.44
147 148 3.552875 GGTTCATAAGGGCCTTTACTCC 58.447 50.000 26.29 16.19 0.00 3.85
148 149 3.203716 CGGTTCATAAGGGCCTTTACTC 58.796 50.000 26.29 11.28 0.00 2.59
152 153 0.033503 CCCGGTTCATAAGGGCCTTT 60.034 55.000 26.29 5.08 38.51 3.11
154 155 0.697854 ATCCCGGTTCATAAGGGCCT 60.698 55.000 0.00 0.00 44.70 5.19
155 156 1.061546 TATCCCGGTTCATAAGGGCC 58.938 55.000 0.00 0.00 44.70 5.80
157 158 4.079253 CCATTTATCCCGGTTCATAAGGG 58.921 47.826 0.00 2.73 46.40 3.95
158 159 3.506067 GCCATTTATCCCGGTTCATAAGG 59.494 47.826 0.00 0.54 0.00 2.69
159 160 3.506067 GGCCATTTATCCCGGTTCATAAG 59.494 47.826 0.00 0.00 0.00 1.73
160 161 3.492337 GGCCATTTATCCCGGTTCATAA 58.508 45.455 0.00 0.00 0.00 1.90
162 163 1.480498 GGGCCATTTATCCCGGTTCAT 60.480 52.381 4.39 0.00 32.00 2.57
163 164 0.106419 GGGCCATTTATCCCGGTTCA 60.106 55.000 4.39 0.00 32.00 3.18
164 165 2.728397 GGGCCATTTATCCCGGTTC 58.272 57.895 4.39 0.00 32.00 3.62
170 171 7.013369 CACTAGTAGAAAAAGGGCCATTTATCC 59.987 40.741 17.01 8.26 0.00 2.59
172 173 7.410991 ACACTAGTAGAAAAAGGGCCATTTAT 58.589 34.615 17.01 8.03 0.00 1.40
174 175 5.641155 ACACTAGTAGAAAAAGGGCCATTT 58.359 37.500 10.16 10.16 0.00 2.32
175 176 5.256806 ACACTAGTAGAAAAAGGGCCATT 57.743 39.130 6.18 0.00 0.00 3.16
176 177 4.929146 ACACTAGTAGAAAAAGGGCCAT 57.071 40.909 6.18 0.00 0.00 4.40
177 178 4.141344 ACAACACTAGTAGAAAAAGGGCCA 60.141 41.667 6.18 0.00 0.00 5.36
178 179 4.215613 CACAACACTAGTAGAAAAAGGGCC 59.784 45.833 3.59 0.00 0.00 5.80
179 180 4.215613 CCACAACACTAGTAGAAAAAGGGC 59.784 45.833 3.59 0.00 0.00 5.19
180 181 4.215613 GCCACAACACTAGTAGAAAAAGGG 59.784 45.833 3.59 0.21 0.00 3.95
181 182 5.049405 CAGCCACAACACTAGTAGAAAAAGG 60.049 44.000 3.59 0.09 0.00 3.11
182 183 5.560953 GCAGCCACAACACTAGTAGAAAAAG 60.561 44.000 3.59 0.00 0.00 2.27
183 184 4.274950 GCAGCCACAACACTAGTAGAAAAA 59.725 41.667 3.59 0.00 0.00 1.94
184 185 3.813166 GCAGCCACAACACTAGTAGAAAA 59.187 43.478 3.59 0.00 0.00 2.29
185 186 3.071023 AGCAGCCACAACACTAGTAGAAA 59.929 43.478 3.59 0.00 0.00 2.52
186 187 2.632996 AGCAGCCACAACACTAGTAGAA 59.367 45.455 3.59 0.00 0.00 2.10
187 188 2.029020 CAGCAGCCACAACACTAGTAGA 60.029 50.000 3.59 0.00 0.00 2.59
189 190 1.001974 CCAGCAGCCACAACACTAGTA 59.998 52.381 0.00 0.00 0.00 1.82
190 191 0.250467 CCAGCAGCCACAACACTAGT 60.250 55.000 0.00 0.00 0.00 2.57
191 192 1.580845 GCCAGCAGCCACAACACTAG 61.581 60.000 0.00 0.00 34.35 2.57
192 193 1.600636 GCCAGCAGCCACAACACTA 60.601 57.895 0.00 0.00 34.35 2.74
194 195 2.908940 AGCCAGCAGCCACAACAC 60.909 61.111 0.00 0.00 45.47 3.32
197 198 2.595463 GTGAGCCAGCAGCCACAA 60.595 61.111 12.32 0.00 45.47 3.33
199 200 2.744768 AAGAGTGAGCCAGCAGCCAC 62.745 60.000 10.37 10.37 45.47 5.01
226 2648 6.072649 TCCTTGTTCACGACCTATATATGGA 58.927 40.000 0.00 0.00 0.00 3.41
264 2686 4.864334 GCCGGCCCTCAGATGTGG 62.864 72.222 18.11 0.00 0.00 4.17
298 2720 1.478510 CCTGATTCAGTCGCAGGTACT 59.521 52.381 12.54 0.00 43.25 2.73
345 2768 3.181446 GCCTCTCCTCCAAATCATAGCTT 60.181 47.826 0.00 0.00 0.00 3.74
356 2779 1.930914 ACTAACCTAGCCTCTCCTCCA 59.069 52.381 0.00 0.00 0.00 3.86
433 2857 3.022287 CCATGGTTCATACGGCGC 58.978 61.111 6.90 0.00 0.00 6.53
442 2866 4.194640 AGCATCATATATCGCCATGGTTC 58.805 43.478 14.67 0.00 0.00 3.62
456 2880 1.933181 CTTCGCACCGAAAGCATCATA 59.067 47.619 1.59 0.00 45.23 2.15
497 2922 4.790766 GCATTTTTATGCAGCTGCTACGAT 60.791 41.667 36.61 24.48 46.25 3.73
808 3289 7.308435 CCAACTGAAAATGACTACTTCAATCC 58.692 38.462 0.00 0.00 37.92 3.01
814 3295 4.022849 GCTGCCAACTGAAAATGACTACTT 60.023 41.667 0.00 0.00 0.00 2.24
827 3309 1.400846 GTCATCTCATGCTGCCAACTG 59.599 52.381 0.00 0.00 0.00 3.16
828 3310 1.747709 GTCATCTCATGCTGCCAACT 58.252 50.000 0.00 0.00 0.00 3.16
1314 3854 2.671682 GCCAGGGTCCTCTCAACC 59.328 66.667 0.00 0.00 35.97 3.77
1966 4540 5.644188 TCCATTTTCCTTGAGAAACCTCAT 58.356 37.500 0.00 0.00 44.20 2.90
2162 4736 2.037641 AGCACACAGTTACATCAGAGCA 59.962 45.455 0.00 0.00 0.00 4.26
2218 4794 3.607741 TCACTCGTTAACAACCACCAAA 58.392 40.909 6.39 0.00 0.00 3.28
2458 5175 3.131046 GCATTACCCACAAATGAAGGAGG 59.869 47.826 0.18 0.00 36.61 4.30
2778 5594 1.152860 TTTCGTCCTGCAGCCCAAA 60.153 52.632 8.66 1.25 0.00 3.28
2779 5595 1.896660 GTTTCGTCCTGCAGCCCAA 60.897 57.895 8.66 0.00 0.00 4.12
2797 5621 1.275291 ACCAGATGTGAACCCTGTACG 59.725 52.381 0.00 0.00 0.00 3.67
2849 5678 6.227298 TCCTCCATAAGAGAGTTTGATGTC 57.773 41.667 0.00 0.00 46.50 3.06
2863 5692 2.580322 TGATGCCAAACCTCCTCCATAA 59.420 45.455 0.00 0.00 0.00 1.90
3050 5948 5.481105 CAAAAATCTTAAGCTGCCATCCAA 58.519 37.500 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.