Multiple sequence alignment - TraesCS6B01G260600

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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 TraesCS6B01G260600 chr6B 100.000 2492 0 0 1 2492 470842915 470845406 0.000000e+00 4602
1 TraesCS6B01G260600 chr6B 89.013 1438 111 26 310 1719 718648546 718649964 0.000000e+00 1736
2 TraesCS6B01G260600 chr6B 95.882 777 26 6 1718 2492 176322193 176322965 0.000000e+00 1253
3 TraesCS6B01G260600 chr6B 96.000 775 24 5 1719 2492 470851634 470852402 0.000000e+00 1253
4 TraesCS6B01G260600 chr6B 98.649 222 2 1 1 222 524352634 524352414 2.320000e-105 392
5 TraesCS6B01G260600 chr3B 95.427 1509 62 5 215 1719 16284249 16285754 0.000000e+00 2398
6 TraesCS6B01G260600 chr3B 93.775 1510 87 5 215 1719 699150695 699152202 0.000000e+00 2261
7 TraesCS6B01G260600 chr3B 95.630 778 28 5 1719 2492 734724848 734724073 0.000000e+00 1243
8 TraesCS6B01G260600 chr3B 99.535 215 1 0 1 215 151112312 151112526 2.320000e-105 392
9 TraesCS6B01G260600 chr3B 99.065 214 2 0 1 214 801071217 801071430 3.890000e-103 385
10 TraesCS6B01G260600 chr2A 92.489 1531 75 16 215 1719 130798404 130796888 0.000000e+00 2154
11 TraesCS6B01G260600 chr7B 92.216 1516 100 11 215 1719 714403948 714402440 0.000000e+00 2130
12 TraesCS6B01G260600 chr7B 88.016 1527 115 31 215 1719 619074070 619075550 0.000000e+00 1744
13 TraesCS6B01G260600 chr7B 96.129 775 25 4 1719 2492 238280217 238279447 0.000000e+00 1260
14 TraesCS6B01G260600 chr7B 95.882 777 24 7 1718 2491 60062076 60061305 0.000000e+00 1251
15 TraesCS6B01G260600 chr4B 93.162 1404 76 12 322 1719 75650707 75649318 0.000000e+00 2043
16 TraesCS6B01G260600 chr1B 91.165 1528 97 18 215 1719 609855113 609856625 0.000000e+00 2039
17 TraesCS6B01G260600 chr1B 95.903 781 26 6 1715 2492 642107314 642106537 0.000000e+00 1260
18 TraesCS6B01G260600 chr1B 93.952 496 23 5 215 706 502063842 502064334 0.000000e+00 743
19 TraesCS6B01G260600 chr1B 99.535 215 1 0 1 215 33060323 33060537 2.320000e-105 392
20 TraesCS6B01G260600 chr7A 89.100 1523 126 17 216 1719 344655423 344656924 0.000000e+00 1857
21 TraesCS6B01G260600 chr7A 99.070 215 2 0 3 217 502047534 502047748 1.080000e-103 387
22 TraesCS6B01G260600 chr7D 95.683 834 33 1 886 1719 560827597 560826767 0.000000e+00 1338
23 TraesCS6B01G260600 chr3D 95.444 834 37 1 886 1719 305617000 305616168 0.000000e+00 1328
24 TraesCS6B01G260600 chr6D 94.724 834 44 0 886 1719 257992856 257993689 0.000000e+00 1297
25 TraesCS6B01G260600 chr6D 92.173 856 38 6 215 1052 356227378 356226534 0.000000e+00 1182
26 TraesCS6B01G260600 chr2B 95.892 779 24 7 1718 2490 699187770 699188546 0.000000e+00 1254
27 TraesCS6B01G260600 chr2B 95.524 782 27 6 1715 2492 543184311 543183534 0.000000e+00 1243
28 TraesCS6B01G260600 chr5B 95.876 776 26 5 1719 2492 493612499 493611728 0.000000e+00 1251
29 TraesCS6B01G260600 chr6A 99.533 214 1 0 1 214 469150005 469149792 8.360000e-105 390
30 TraesCS6B01G260600 chr1A 99.533 214 1 0 1 214 335528632 335528845 8.360000e-105 390
31 TraesCS6B01G260600 chr1A 99.533 214 1 0 1 214 336520250 336520463 8.360000e-105 390
32 TraesCS6B01G260600 chr1A 99.533 214 1 0 1 214 448849061 448849274 8.360000e-105 390


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 TraesCS6B01G260600 chr6B 470842915 470845406 2491 False 4602 4602 100.000 1 2492 1 chr6B.!!$F2 2491
1 TraesCS6B01G260600 chr6B 718648546 718649964 1418 False 1736 1736 89.013 310 1719 1 chr6B.!!$F4 1409
2 TraesCS6B01G260600 chr6B 176322193 176322965 772 False 1253 1253 95.882 1718 2492 1 chr6B.!!$F1 774
3 TraesCS6B01G260600 chr6B 470851634 470852402 768 False 1253 1253 96.000 1719 2492 1 chr6B.!!$F3 773
4 TraesCS6B01G260600 chr3B 16284249 16285754 1505 False 2398 2398 95.427 215 1719 1 chr3B.!!$F1 1504
5 TraesCS6B01G260600 chr3B 699150695 699152202 1507 False 2261 2261 93.775 215 1719 1 chr3B.!!$F3 1504
6 TraesCS6B01G260600 chr3B 734724073 734724848 775 True 1243 1243 95.630 1719 2492 1 chr3B.!!$R1 773
7 TraesCS6B01G260600 chr2A 130796888 130798404 1516 True 2154 2154 92.489 215 1719 1 chr2A.!!$R1 1504
8 TraesCS6B01G260600 chr7B 714402440 714403948 1508 True 2130 2130 92.216 215 1719 1 chr7B.!!$R3 1504
9 TraesCS6B01G260600 chr7B 619074070 619075550 1480 False 1744 1744 88.016 215 1719 1 chr7B.!!$F1 1504
10 TraesCS6B01G260600 chr7B 238279447 238280217 770 True 1260 1260 96.129 1719 2492 1 chr7B.!!$R2 773
11 TraesCS6B01G260600 chr7B 60061305 60062076 771 True 1251 1251 95.882 1718 2491 1 chr7B.!!$R1 773
12 TraesCS6B01G260600 chr4B 75649318 75650707 1389 True 2043 2043 93.162 322 1719 1 chr4B.!!$R1 1397
13 TraesCS6B01G260600 chr1B 609855113 609856625 1512 False 2039 2039 91.165 215 1719 1 chr1B.!!$F3 1504
14 TraesCS6B01G260600 chr1B 642106537 642107314 777 True 1260 1260 95.903 1715 2492 1 chr1B.!!$R1 777
15 TraesCS6B01G260600 chr7A 344655423 344656924 1501 False 1857 1857 89.100 216 1719 1 chr7A.!!$F1 1503
16 TraesCS6B01G260600 chr7D 560826767 560827597 830 True 1338 1338 95.683 886 1719 1 chr7D.!!$R1 833
17 TraesCS6B01G260600 chr3D 305616168 305617000 832 True 1328 1328 95.444 886 1719 1 chr3D.!!$R1 833
18 TraesCS6B01G260600 chr6D 257992856 257993689 833 False 1297 1297 94.724 886 1719 1 chr6D.!!$F1 833
19 TraesCS6B01G260600 chr6D 356226534 356227378 844 True 1182 1182 92.173 215 1052 1 chr6D.!!$R1 837
20 TraesCS6B01G260600 chr2B 699187770 699188546 776 False 1254 1254 95.892 1718 2490 1 chr2B.!!$F1 772
21 TraesCS6B01G260600 chr2B 543183534 543184311 777 True 1243 1243 95.524 1715 2492 1 chr2B.!!$R1 777
22 TraesCS6B01G260600 chr5B 493611728 493612499 771 True 1251 1251 95.876 1719 2492 1 chr5B.!!$R1 773

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
53 54 0.034896 AGTTTCGGTGCTTGATCGGT 59.965 50.0 0.00 0.0 0.00 4.69 F
159 160 0.106708 TCCCCTCGTTGCTATGCATC 59.893 55.0 0.19 0.0 38.76 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1153 1227 0.606401 CCACGACTTGACTGCCCATT 60.606 55.0 0.0 0.0 0.0 3.16 R
1911 1990 1.570813 CTGAACGTGTGCTGAACTCA 58.429 50.0 0.0 0.0 0.0 3.41 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 3.150895 GAGCTGAACGTGTGCTCG 58.849 61.111 17.59 0.00 42.70 5.03
18 19 1.371758 GAGCTGAACGTGTGCTCGA 60.372 57.895 17.59 0.00 42.70 4.04
19 20 0.939577 GAGCTGAACGTGTGCTCGAA 60.940 55.000 17.59 0.00 42.70 3.71
20 21 1.201825 GCTGAACGTGTGCTCGAAC 59.798 57.895 0.00 0.00 34.70 3.95
21 22 1.215655 GCTGAACGTGTGCTCGAACT 61.216 55.000 0.00 0.00 34.70 3.01
22 23 0.778815 CTGAACGTGTGCTCGAACTC 59.221 55.000 0.00 0.00 34.70 3.01
23 24 0.933047 TGAACGTGTGCTCGAACTCG 60.933 55.000 9.47 9.47 41.49 4.18
24 25 1.606350 GAACGTGTGCTCGAACTCGG 61.606 60.000 14.12 0.00 40.39 4.63
25 26 2.067091 AACGTGTGCTCGAACTCGGA 62.067 55.000 14.12 0.00 40.39 4.55
26 27 1.797933 CGTGTGCTCGAACTCGGAG 60.798 63.158 2.83 2.83 40.29 4.63
27 28 1.444553 GTGTGCTCGAACTCGGAGG 60.445 63.158 10.23 0.00 40.29 4.30
28 29 1.901948 TGTGCTCGAACTCGGAGGT 60.902 57.895 10.23 1.51 40.29 3.85
29 30 1.444553 GTGCTCGAACTCGGAGGTG 60.445 63.158 10.23 0.00 40.29 4.00
30 31 2.507324 GCTCGAACTCGGAGGTGC 60.507 66.667 10.23 0.00 40.29 5.01
31 32 2.182030 CTCGAACTCGGAGGTGCC 59.818 66.667 10.23 0.00 40.29 5.01
40 41 4.180496 GGAGGTGCCGTAGTTTCG 57.820 61.111 0.00 0.00 0.00 3.46
48 49 3.204505 CCGTAGTTTCGGTGCTTGA 57.795 52.632 0.00 0.00 44.77 3.02
49 50 1.722011 CCGTAGTTTCGGTGCTTGAT 58.278 50.000 0.00 0.00 44.77 2.57
50 51 1.659098 CCGTAGTTTCGGTGCTTGATC 59.341 52.381 0.00 0.00 44.77 2.92
51 52 1.320555 CGTAGTTTCGGTGCTTGATCG 59.679 52.381 0.00 0.00 0.00 3.69
52 53 1.659098 GTAGTTTCGGTGCTTGATCGG 59.341 52.381 0.00 0.00 0.00 4.18
53 54 0.034896 AGTTTCGGTGCTTGATCGGT 59.965 50.000 0.00 0.00 0.00 4.69
54 55 0.872388 GTTTCGGTGCTTGATCGGTT 59.128 50.000 0.00 0.00 0.00 4.44
55 56 0.871722 TTTCGGTGCTTGATCGGTTG 59.128 50.000 0.00 0.00 0.00 3.77
56 57 0.953471 TTCGGTGCTTGATCGGTTGG 60.953 55.000 0.00 0.00 0.00 3.77
57 58 1.375396 CGGTGCTTGATCGGTTGGA 60.375 57.895 0.00 0.00 0.00 3.53
58 59 0.744414 CGGTGCTTGATCGGTTGGAT 60.744 55.000 0.00 0.00 38.35 3.41
66 67 2.579207 GATCGGTTGGATCGTGAAGA 57.421 50.000 0.00 0.00 42.02 2.87
67 68 2.194271 GATCGGTTGGATCGTGAAGAC 58.806 52.381 0.00 0.00 42.02 3.01
69 70 0.388134 CGGTTGGATCGTGAAGACGT 60.388 55.000 0.00 0.00 46.20 4.34
70 71 1.135603 CGGTTGGATCGTGAAGACGTA 60.136 52.381 0.00 0.00 46.20 3.57
71 72 2.257034 GGTTGGATCGTGAAGACGTAC 58.743 52.381 0.00 0.00 46.20 3.67
72 73 1.909532 GTTGGATCGTGAAGACGTACG 59.090 52.381 15.01 15.01 46.20 3.67
78 79 2.677199 TCGTGAAGACGTACGACTACT 58.323 47.619 24.41 6.98 46.20 2.57
79 80 3.059884 TCGTGAAGACGTACGACTACTT 58.940 45.455 24.41 19.15 46.20 2.24
80 81 3.121944 TCGTGAAGACGTACGACTACTTC 59.878 47.826 24.41 25.02 46.20 3.01
81 82 3.723250 CGTGAAGACGTACGACTACTTCC 60.723 52.174 24.41 18.62 42.54 3.46
82 83 3.434984 GTGAAGACGTACGACTACTTCCT 59.565 47.826 24.41 4.54 36.96 3.36
83 84 3.681897 TGAAGACGTACGACTACTTCCTC 59.318 47.826 24.41 14.21 36.96 3.71
84 85 3.608316 AGACGTACGACTACTTCCTCT 57.392 47.619 24.41 7.87 0.00 3.69
85 86 4.727507 AGACGTACGACTACTTCCTCTA 57.272 45.455 24.41 0.00 0.00 2.43
86 87 4.429108 AGACGTACGACTACTTCCTCTAC 58.571 47.826 24.41 0.00 0.00 2.59
87 88 3.182967 ACGTACGACTACTTCCTCTACG 58.817 50.000 24.41 0.00 33.44 3.51
88 89 3.182967 CGTACGACTACTTCCTCTACGT 58.817 50.000 10.44 0.00 36.52 3.57
89 90 3.241784 CGTACGACTACTTCCTCTACGTC 59.758 52.174 10.44 0.00 34.52 4.34
90 91 2.266554 ACGACTACTTCCTCTACGTCG 58.733 52.381 7.91 7.91 46.64 5.12
91 92 2.266554 CGACTACTTCCTCTACGTCGT 58.733 52.381 2.21 2.21 39.30 4.34
92 93 2.029003 CGACTACTTCCTCTACGTCGTG 59.971 54.545 8.47 0.00 39.30 4.35
93 94 2.999355 GACTACTTCCTCTACGTCGTGT 59.001 50.000 8.47 0.00 0.00 4.49
94 95 2.999355 ACTACTTCCTCTACGTCGTGTC 59.001 50.000 8.47 0.00 0.00 3.67
95 96 1.888215 ACTTCCTCTACGTCGTGTCA 58.112 50.000 8.47 0.00 0.00 3.58
96 97 2.434428 ACTTCCTCTACGTCGTGTCAT 58.566 47.619 8.47 0.00 0.00 3.06
97 98 2.419324 ACTTCCTCTACGTCGTGTCATC 59.581 50.000 8.47 0.00 0.00 2.92
98 99 1.004595 TCCTCTACGTCGTGTCATCG 58.995 55.000 8.47 0.00 0.00 3.84
99 100 0.589229 CCTCTACGTCGTGTCATCGC 60.589 60.000 8.47 0.00 0.00 4.58
100 101 0.374063 CTCTACGTCGTGTCATCGCT 59.626 55.000 8.47 0.00 0.00 4.93
101 102 0.800631 TCTACGTCGTGTCATCGCTT 59.199 50.000 8.47 0.00 0.00 4.68
102 103 1.181001 CTACGTCGTGTCATCGCTTC 58.819 55.000 8.47 0.00 0.00 3.86
103 104 0.179181 TACGTCGTGTCATCGCTTCC 60.179 55.000 8.47 0.00 0.00 3.46
104 105 2.497092 CGTCGTGTCATCGCTTCCG 61.497 63.158 0.00 0.00 0.00 4.30
105 106 2.506217 TCGTGTCATCGCTTCCGC 60.506 61.111 0.00 0.00 0.00 5.54
106 107 2.809174 CGTGTCATCGCTTCCGCA 60.809 61.111 0.00 0.00 35.30 5.69
107 108 2.792290 CGTGTCATCGCTTCCGCAG 61.792 63.158 0.00 0.00 35.30 5.18
108 109 1.738099 GTGTCATCGCTTCCGCAGT 60.738 57.895 0.00 0.00 35.30 4.40
109 110 1.446099 TGTCATCGCTTCCGCAGTC 60.446 57.895 0.00 0.00 35.30 3.51
110 111 2.202610 TCATCGCTTCCGCAGTCG 60.203 61.111 0.00 0.00 35.30 4.18
122 123 2.490217 CAGTCGGTCTGCGTAGGG 59.510 66.667 0.00 0.00 37.36 3.53
123 124 2.035312 AGTCGGTCTGCGTAGGGT 59.965 61.111 0.00 0.00 0.00 4.34
124 125 1.028330 CAGTCGGTCTGCGTAGGGTA 61.028 60.000 0.00 0.00 37.36 3.69
125 126 1.028868 AGTCGGTCTGCGTAGGGTAC 61.029 60.000 0.00 0.00 0.00 3.34
138 139 5.335827 CGTAGGGTACGTAGACAATACTC 57.664 47.826 0.00 0.00 46.41 2.59
139 140 5.053145 CGTAGGGTACGTAGACAATACTCT 58.947 45.833 0.00 0.00 46.41 3.24
140 141 5.525378 CGTAGGGTACGTAGACAATACTCTT 59.475 44.000 0.00 0.00 46.41 2.85
141 142 6.292596 CGTAGGGTACGTAGACAATACTCTTC 60.293 46.154 0.00 0.00 46.41 2.87
142 143 4.886489 AGGGTACGTAGACAATACTCTTCC 59.114 45.833 0.00 0.00 0.00 3.46
143 144 4.037327 GGGTACGTAGACAATACTCTTCCC 59.963 50.000 0.00 0.00 0.00 3.97
144 145 4.037327 GGTACGTAGACAATACTCTTCCCC 59.963 50.000 0.00 0.00 0.00 4.81
145 146 3.978610 ACGTAGACAATACTCTTCCCCT 58.021 45.455 0.00 0.00 0.00 4.79
146 147 3.952967 ACGTAGACAATACTCTTCCCCTC 59.047 47.826 0.00 0.00 0.00 4.30
147 148 3.003482 CGTAGACAATACTCTTCCCCTCG 59.997 52.174 0.00 0.00 0.00 4.63
148 149 3.103080 AGACAATACTCTTCCCCTCGT 57.897 47.619 0.00 0.00 0.00 4.18
149 150 3.442076 AGACAATACTCTTCCCCTCGTT 58.558 45.455 0.00 0.00 0.00 3.85
150 151 3.195825 AGACAATACTCTTCCCCTCGTTG 59.804 47.826 0.00 0.00 0.00 4.10
151 152 2.280628 CAATACTCTTCCCCTCGTTGC 58.719 52.381 0.00 0.00 0.00 4.17
152 153 1.867363 ATACTCTTCCCCTCGTTGCT 58.133 50.000 0.00 0.00 0.00 3.91
153 154 2.519771 TACTCTTCCCCTCGTTGCTA 57.480 50.000 0.00 0.00 0.00 3.49
154 155 1.867363 ACTCTTCCCCTCGTTGCTAT 58.133 50.000 0.00 0.00 0.00 2.97
155 156 1.482593 ACTCTTCCCCTCGTTGCTATG 59.517 52.381 0.00 0.00 0.00 2.23
156 157 0.178068 TCTTCCCCTCGTTGCTATGC 59.822 55.000 0.00 0.00 0.00 3.14
157 158 0.107703 CTTCCCCTCGTTGCTATGCA 60.108 55.000 0.00 0.00 36.47 3.96
158 159 0.546122 TTCCCCTCGTTGCTATGCAT 59.454 50.000 3.79 3.79 38.76 3.96
159 160 0.106708 TCCCCTCGTTGCTATGCATC 59.893 55.000 0.19 0.00 38.76 3.91
160 161 0.179048 CCCCTCGTTGCTATGCATCA 60.179 55.000 0.19 0.00 38.76 3.07
161 162 0.940126 CCCTCGTTGCTATGCATCAC 59.060 55.000 0.19 0.00 38.76 3.06
162 163 1.655484 CCTCGTTGCTATGCATCACA 58.345 50.000 0.19 0.00 38.76 3.58
163 164 2.216046 CCTCGTTGCTATGCATCACAT 58.784 47.619 0.19 0.00 43.18 3.21
164 165 2.032290 CCTCGTTGCTATGCATCACATG 60.032 50.000 0.19 0.00 40.06 3.21
165 166 2.867975 CTCGTTGCTATGCATCACATGA 59.132 45.455 0.19 3.61 40.06 3.07
166 167 3.469739 TCGTTGCTATGCATCACATGAT 58.530 40.909 0.19 0.00 40.06 2.45
167 168 3.495753 TCGTTGCTATGCATCACATGATC 59.504 43.478 0.19 0.00 40.06 2.92
168 169 3.364664 CGTTGCTATGCATCACATGATCC 60.365 47.826 0.19 0.00 40.06 3.36
169 170 3.782656 TGCTATGCATCACATGATCCT 57.217 42.857 0.19 0.00 40.06 3.24
170 171 3.408634 TGCTATGCATCACATGATCCTG 58.591 45.455 0.19 0.00 40.06 3.86
171 172 3.181448 TGCTATGCATCACATGATCCTGT 60.181 43.478 0.19 0.00 40.06 4.00
172 173 3.188667 GCTATGCATCACATGATCCTGTG 59.811 47.826 21.26 21.26 46.34 3.66
173 174 2.793288 TGCATCACATGATCCTGTGT 57.207 45.000 24.67 13.23 45.40 3.72
174 175 2.361789 TGCATCACATGATCCTGTGTG 58.638 47.619 24.67 21.71 45.40 3.82
175 176 1.065102 GCATCACATGATCCTGTGTGC 59.935 52.381 26.11 26.11 45.40 4.57
176 177 1.329599 CATCACATGATCCTGTGTGCG 59.670 52.381 24.67 13.83 45.40 5.34
177 178 1.020861 TCACATGATCCTGTGTGCGC 61.021 55.000 24.67 0.00 45.40 6.09
178 179 1.003476 ACATGATCCTGTGTGCGCA 60.003 52.632 5.66 5.66 0.00 6.09
179 180 0.393402 ACATGATCCTGTGTGCGCAT 60.393 50.000 15.91 0.00 0.00 4.73
180 181 1.134431 ACATGATCCTGTGTGCGCATA 60.134 47.619 15.91 8.59 0.00 3.14
181 182 1.529865 CATGATCCTGTGTGCGCATAG 59.470 52.381 15.91 16.35 34.18 2.23
188 189 3.492421 CTGTGTGCGCATAGGAAAATT 57.508 42.857 15.91 0.00 31.27 1.82
189 190 3.836949 CTGTGTGCGCATAGGAAAATTT 58.163 40.909 15.91 0.00 31.27 1.82
190 191 4.236935 CTGTGTGCGCATAGGAAAATTTT 58.763 39.130 15.91 2.28 31.27 1.82
191 192 4.626042 TGTGTGCGCATAGGAAAATTTTT 58.374 34.783 15.91 0.00 0.00 1.94
192 193 4.447054 TGTGTGCGCATAGGAAAATTTTTG 59.553 37.500 15.91 0.46 0.00 2.44
193 194 4.683781 GTGTGCGCATAGGAAAATTTTTGA 59.316 37.500 15.91 0.00 0.00 2.69
194 195 5.176590 GTGTGCGCATAGGAAAATTTTTGAA 59.823 36.000 15.91 0.00 0.00 2.69
195 196 5.755375 TGTGCGCATAGGAAAATTTTTGAAA 59.245 32.000 15.91 0.00 0.00 2.69
196 197 6.426328 TGTGCGCATAGGAAAATTTTTGAAAT 59.574 30.769 15.91 0.00 0.00 2.17
197 198 7.041508 TGTGCGCATAGGAAAATTTTTGAAATT 60.042 29.630 15.91 0.00 0.00 1.82
198 199 8.439286 GTGCGCATAGGAAAATTTTTGAAATTA 58.561 29.630 15.91 0.00 0.00 1.40
199 200 8.439286 TGCGCATAGGAAAATTTTTGAAATTAC 58.561 29.630 5.66 0.00 0.00 1.89
200 201 8.655970 GCGCATAGGAAAATTTTTGAAATTACT 58.344 29.630 0.30 0.00 0.00 2.24
210 211 9.819267 AAATTTTTGAAATTACTACGAAACCCA 57.181 25.926 0.00 0.00 0.00 4.51
211 212 9.819267 AATTTTTGAAATTACTACGAAACCCAA 57.181 25.926 0.00 0.00 0.00 4.12
212 213 8.631676 TTTTTGAAATTACTACGAAACCCAAC 57.368 30.769 0.00 0.00 0.00 3.77
213 214 6.939132 TTGAAATTACTACGAAACCCAACA 57.061 33.333 0.00 0.00 0.00 3.33
277 280 7.389053 TGTGAAAGCAAAACCATTTACAAAAGT 59.611 29.630 0.00 0.00 0.00 2.66
509 540 2.536803 TCTACGTCGCTTGAAACACAAC 59.463 45.455 0.00 0.00 34.56 3.32
603 638 6.935741 AACACAAGTACTGCACATAAAAGA 57.064 33.333 0.00 0.00 0.00 2.52
677 713 5.157940 TGCTAGTGCTCTCTCTGATTTTT 57.842 39.130 0.00 0.00 40.48 1.94
902 959 2.076863 CTAGTGTGCTTAGGTGGTTGC 58.923 52.381 0.00 0.00 0.00 4.17
939 996 5.292101 CCTGTATTTACTGTGCTACTTGCTC 59.708 44.000 0.00 0.00 43.37 4.26
1136 1210 4.794003 GCAAAAAGTCAGTGTTGCTGCTAT 60.794 41.667 7.86 0.00 44.66 2.97
1416 1491 4.347583 TCCTTGCAGATGGGTTTTTCAATT 59.652 37.500 3.24 0.00 0.00 2.32
1453 1528 2.109304 AGGAAGGATTTGAAAACCGGGA 59.891 45.455 6.32 0.00 0.00 5.14
1529 1604 1.340017 CGGAGGGGCAGAAAAGATTCA 60.340 52.381 0.00 0.00 38.06 2.57
1728 1806 5.010282 GTGATCTACTTTGTGTTGGGGAAT 58.990 41.667 0.00 0.00 0.00 3.01
1735 1813 5.313712 ACTTTGTGTTGGGGAATGTAGTAG 58.686 41.667 0.00 0.00 0.00 2.57
1808 1887 1.203364 AGAGGGGAGAGTGTTGTCCAT 60.203 52.381 0.00 0.00 38.50 3.41
1911 1990 0.886490 ACCGAACGTACGACACCTCT 60.886 55.000 24.41 0.00 35.09 3.69
2020 2099 5.163416 TGTGGTGACGATGATGATGTTCTAT 60.163 40.000 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.067416 TTCGAGCACACGTTCAGCT 59.933 52.632 5.90 5.90 42.17 4.24
5 6 1.606350 CCGAGTTCGAGCACACGTTC 61.606 60.000 1.01 0.00 43.02 3.95
6 7 1.660575 CCGAGTTCGAGCACACGTT 60.661 57.895 1.01 0.00 43.02 3.99
7 8 2.050351 CCGAGTTCGAGCACACGT 60.050 61.111 1.01 0.00 43.02 4.49
8 9 1.797933 CTCCGAGTTCGAGCACACG 60.798 63.158 1.01 0.89 43.02 4.49
9 10 1.444553 CCTCCGAGTTCGAGCACAC 60.445 63.158 1.01 0.00 43.02 3.82
10 11 1.901948 ACCTCCGAGTTCGAGCACA 60.902 57.895 1.01 0.00 43.02 4.57
11 12 1.444553 CACCTCCGAGTTCGAGCAC 60.445 63.158 1.01 0.00 43.02 4.40
12 13 2.962569 CACCTCCGAGTTCGAGCA 59.037 61.111 1.01 0.00 43.02 4.26
13 14 2.507324 GCACCTCCGAGTTCGAGC 60.507 66.667 2.59 0.00 43.02 5.03
14 15 2.182030 GGCACCTCCGAGTTCGAG 59.818 66.667 2.59 0.00 43.02 4.04
23 24 1.447314 CCGAAACTACGGCACCTCC 60.447 63.158 0.00 0.00 46.20 4.30
24 25 4.180496 CCGAAACTACGGCACCTC 57.820 61.111 0.00 0.00 46.20 3.85
31 32 1.320555 CGATCAAGCACCGAAACTACG 59.679 52.381 0.00 0.00 0.00 3.51
32 33 1.659098 CCGATCAAGCACCGAAACTAC 59.341 52.381 0.00 0.00 0.00 2.73
33 34 1.274167 ACCGATCAAGCACCGAAACTA 59.726 47.619 0.00 0.00 0.00 2.24
34 35 0.034896 ACCGATCAAGCACCGAAACT 59.965 50.000 0.00 0.00 0.00 2.66
35 36 0.872388 AACCGATCAAGCACCGAAAC 59.128 50.000 0.00 0.00 0.00 2.78
36 37 0.871722 CAACCGATCAAGCACCGAAA 59.128 50.000 0.00 0.00 0.00 3.46
37 38 0.953471 CCAACCGATCAAGCACCGAA 60.953 55.000 0.00 0.00 0.00 4.30
38 39 1.375396 CCAACCGATCAAGCACCGA 60.375 57.895 0.00 0.00 0.00 4.69
39 40 0.744414 ATCCAACCGATCAAGCACCG 60.744 55.000 0.00 0.00 0.00 4.94
40 41 1.017387 GATCCAACCGATCAAGCACC 58.983 55.000 0.00 0.00 45.92 5.01
41 42 0.652592 CGATCCAACCGATCAAGCAC 59.347 55.000 0.00 0.00 46.85 4.40
42 43 0.249120 ACGATCCAACCGATCAAGCA 59.751 50.000 0.00 0.00 46.85 3.91
43 44 0.652592 CACGATCCAACCGATCAAGC 59.347 55.000 0.00 0.00 46.85 4.01
44 45 2.293677 TCACGATCCAACCGATCAAG 57.706 50.000 0.00 0.00 46.85 3.02
45 46 2.232696 TCTTCACGATCCAACCGATCAA 59.767 45.455 0.00 0.00 46.85 2.57
46 47 1.822371 TCTTCACGATCCAACCGATCA 59.178 47.619 0.00 0.00 46.85 2.92
47 48 2.194271 GTCTTCACGATCCAACCGATC 58.806 52.381 0.00 0.00 43.58 3.69
48 49 2.295253 GTCTTCACGATCCAACCGAT 57.705 50.000 0.00 0.00 0.00 4.18
49 50 3.806591 GTCTTCACGATCCAACCGA 57.193 52.632 0.00 0.00 0.00 4.69
60 61 3.434984 AGGAAGTAGTCGTACGTCTTCAC 59.565 47.826 27.06 19.30 37.67 3.18
61 62 3.668447 AGGAAGTAGTCGTACGTCTTCA 58.332 45.455 27.06 11.79 37.67 3.02
62 63 3.932089 AGAGGAAGTAGTCGTACGTCTTC 59.068 47.826 19.61 21.62 41.24 2.87
63 64 3.936564 AGAGGAAGTAGTCGTACGTCTT 58.063 45.455 19.61 16.11 37.67 3.01
64 65 3.608316 AGAGGAAGTAGTCGTACGTCT 57.392 47.619 18.54 18.54 37.67 4.18
65 66 3.241784 CGTAGAGGAAGTAGTCGTACGTC 59.758 52.174 16.05 10.06 37.04 4.34
66 67 3.182967 CGTAGAGGAAGTAGTCGTACGT 58.817 50.000 16.05 0.00 33.97 3.57
67 68 3.182967 ACGTAGAGGAAGTAGTCGTACG 58.817 50.000 9.53 9.53 37.23 3.67
68 69 3.241784 CGACGTAGAGGAAGTAGTCGTAC 59.758 52.174 7.52 0.00 44.10 3.67
69 70 3.439293 CGACGTAGAGGAAGTAGTCGTA 58.561 50.000 7.52 0.00 44.10 3.43
70 71 2.266554 CGACGTAGAGGAAGTAGTCGT 58.733 52.381 7.52 0.00 44.10 4.34
71 72 2.994716 CGACGTAGAGGAAGTAGTCG 57.005 55.000 1.51 1.51 43.79 4.18
72 73 2.999355 ACACGACGTAGAGGAAGTAGTC 59.001 50.000 0.00 0.00 0.00 2.59
73 74 2.999355 GACACGACGTAGAGGAAGTAGT 59.001 50.000 0.00 0.00 0.00 2.73
74 75 2.998670 TGACACGACGTAGAGGAAGTAG 59.001 50.000 0.00 0.00 0.00 2.57
75 76 3.044235 TGACACGACGTAGAGGAAGTA 57.956 47.619 0.00 0.00 0.00 2.24
76 77 1.888215 TGACACGACGTAGAGGAAGT 58.112 50.000 0.00 0.00 0.00 3.01
77 78 2.537128 CGATGACACGACGTAGAGGAAG 60.537 54.545 0.00 0.00 35.09 3.46
78 79 1.395954 CGATGACACGACGTAGAGGAA 59.604 52.381 0.00 0.00 35.09 3.36
79 80 1.004595 CGATGACACGACGTAGAGGA 58.995 55.000 0.00 0.00 35.09 3.71
80 81 0.589229 GCGATGACACGACGTAGAGG 60.589 60.000 0.00 0.00 35.09 3.69
81 82 0.374063 AGCGATGACACGACGTAGAG 59.626 55.000 0.00 0.00 35.09 2.43
82 83 0.800631 AAGCGATGACACGACGTAGA 59.199 50.000 0.00 0.00 35.09 2.59
83 84 1.181001 GAAGCGATGACACGACGTAG 58.819 55.000 0.00 0.00 35.09 3.51
84 85 0.179181 GGAAGCGATGACACGACGTA 60.179 55.000 0.00 0.00 35.09 3.57
85 86 1.443872 GGAAGCGATGACACGACGT 60.444 57.895 0.00 0.00 35.09 4.34
86 87 2.497092 CGGAAGCGATGACACGACG 61.497 63.158 0.00 0.00 35.09 5.12
87 88 3.374330 CGGAAGCGATGACACGAC 58.626 61.111 0.00 0.00 35.09 4.34
106 107 1.028868 GTACCCTACGCAGACCGACT 61.029 60.000 0.00 0.00 41.02 4.18
107 108 1.431036 GTACCCTACGCAGACCGAC 59.569 63.158 0.00 0.00 41.02 4.79
108 109 2.108514 CGTACCCTACGCAGACCGA 61.109 63.158 0.00 0.00 45.81 4.69
109 110 2.406401 CGTACCCTACGCAGACCG 59.594 66.667 0.00 0.00 45.81 4.79
117 118 6.017523 GGAAGAGTATTGTCTACGTACCCTAC 60.018 46.154 0.00 0.00 0.00 3.18
118 119 6.058183 GGAAGAGTATTGTCTACGTACCCTA 58.942 44.000 0.00 0.00 0.00 3.53
119 120 4.886489 GGAAGAGTATTGTCTACGTACCCT 59.114 45.833 0.00 0.00 0.00 4.34
120 121 4.037327 GGGAAGAGTATTGTCTACGTACCC 59.963 50.000 0.00 0.00 0.00 3.69
121 122 4.037327 GGGGAAGAGTATTGTCTACGTACC 59.963 50.000 0.00 0.00 0.00 3.34
122 123 4.886489 AGGGGAAGAGTATTGTCTACGTAC 59.114 45.833 0.00 0.00 0.00 3.67
123 124 5.121380 AGGGGAAGAGTATTGTCTACGTA 57.879 43.478 0.00 0.00 0.00 3.57
124 125 3.952967 GAGGGGAAGAGTATTGTCTACGT 59.047 47.826 0.00 0.00 0.00 3.57
125 126 3.003482 CGAGGGGAAGAGTATTGTCTACG 59.997 52.174 0.00 0.00 0.00 3.51
126 127 3.952967 ACGAGGGGAAGAGTATTGTCTAC 59.047 47.826 0.00 0.00 0.00 2.59
127 128 4.246712 ACGAGGGGAAGAGTATTGTCTA 57.753 45.455 0.00 0.00 0.00 2.59
128 129 3.103080 ACGAGGGGAAGAGTATTGTCT 57.897 47.619 0.00 0.00 0.00 3.41
129 130 3.522553 CAACGAGGGGAAGAGTATTGTC 58.477 50.000 0.00 0.00 0.00 3.18
130 131 2.354805 GCAACGAGGGGAAGAGTATTGT 60.355 50.000 0.00 0.00 0.00 2.71
131 132 2.093447 AGCAACGAGGGGAAGAGTATTG 60.093 50.000 0.00 0.00 0.00 1.90
132 133 2.188817 AGCAACGAGGGGAAGAGTATT 58.811 47.619 0.00 0.00 0.00 1.89
133 134 1.867363 AGCAACGAGGGGAAGAGTAT 58.133 50.000 0.00 0.00 0.00 2.12
134 135 2.519771 TAGCAACGAGGGGAAGAGTA 57.480 50.000 0.00 0.00 0.00 2.59
135 136 1.482593 CATAGCAACGAGGGGAAGAGT 59.517 52.381 0.00 0.00 0.00 3.24
136 137 1.808133 GCATAGCAACGAGGGGAAGAG 60.808 57.143 0.00 0.00 0.00 2.85
137 138 0.178068 GCATAGCAACGAGGGGAAGA 59.822 55.000 0.00 0.00 0.00 2.87
138 139 0.107703 TGCATAGCAACGAGGGGAAG 60.108 55.000 0.00 0.00 34.76 3.46
139 140 0.546122 ATGCATAGCAACGAGGGGAA 59.454 50.000 0.00 0.00 43.62 3.97
140 141 0.106708 GATGCATAGCAACGAGGGGA 59.893 55.000 0.00 0.00 43.62 4.81
141 142 0.179048 TGATGCATAGCAACGAGGGG 60.179 55.000 0.00 0.00 43.62 4.79
142 143 0.940126 GTGATGCATAGCAACGAGGG 59.060 55.000 0.00 0.00 43.62 4.30
143 144 1.655484 TGTGATGCATAGCAACGAGG 58.345 50.000 0.00 0.00 43.62 4.63
144 145 2.867975 TCATGTGATGCATAGCAACGAG 59.132 45.455 0.00 0.00 43.62 4.18
145 146 2.903798 TCATGTGATGCATAGCAACGA 58.096 42.857 0.00 0.66 43.62 3.85
146 147 3.364664 GGATCATGTGATGCATAGCAACG 60.365 47.826 0.00 0.00 43.62 4.10
147 148 3.819337 AGGATCATGTGATGCATAGCAAC 59.181 43.478 15.41 0.00 44.10 4.17
148 149 3.818773 CAGGATCATGTGATGCATAGCAA 59.181 43.478 15.41 0.00 44.10 3.91
149 150 3.181448 ACAGGATCATGTGATGCATAGCA 60.181 43.478 13.05 1.62 44.10 3.49
150 151 3.409570 ACAGGATCATGTGATGCATAGC 58.590 45.455 13.05 0.00 44.10 2.97
160 161 0.393402 ATGCGCACACAGGATCATGT 60.393 50.000 14.90 7.30 0.00 3.21
161 162 1.529865 CTATGCGCACACAGGATCATG 59.470 52.381 14.90 5.68 0.00 3.07
162 163 1.541889 CCTATGCGCACACAGGATCAT 60.542 52.381 23.60 3.55 0.00 2.45
163 164 0.179076 CCTATGCGCACACAGGATCA 60.179 55.000 23.60 0.00 0.00 2.92
164 165 0.104855 TCCTATGCGCACACAGGATC 59.895 55.000 25.53 0.00 32.20 3.36
165 166 0.541392 TTCCTATGCGCACACAGGAT 59.459 50.000 28.20 9.92 37.06 3.24
166 167 0.323302 TTTCCTATGCGCACACAGGA 59.677 50.000 25.53 25.53 35.38 3.86
167 168 1.164411 TTTTCCTATGCGCACACAGG 58.836 50.000 22.50 22.50 0.00 4.00
168 169 3.492421 AATTTTCCTATGCGCACACAG 57.508 42.857 14.90 10.62 0.00 3.66
169 170 3.932545 AAATTTTCCTATGCGCACACA 57.067 38.095 14.90 0.00 0.00 3.72
170 171 4.683781 TCAAAAATTTTCCTATGCGCACAC 59.316 37.500 14.90 0.00 0.00 3.82
171 172 4.876125 TCAAAAATTTTCCTATGCGCACA 58.124 34.783 14.90 0.00 0.00 4.57
172 173 5.837586 TTCAAAAATTTTCCTATGCGCAC 57.162 34.783 14.90 0.00 0.00 5.34
173 174 7.432350 AATTTCAAAAATTTTCCTATGCGCA 57.568 28.000 14.96 14.96 0.00 6.09
174 175 8.655970 AGTAATTTCAAAAATTTTCCTATGCGC 58.344 29.630 3.41 0.00 0.00 6.09
184 185 9.819267 TGGGTTTCGTAGTAATTTCAAAAATTT 57.181 25.926 3.24 0.00 0.00 1.82
185 186 9.819267 TTGGGTTTCGTAGTAATTTCAAAAATT 57.181 25.926 3.43 3.43 0.00 1.82
186 187 9.251792 GTTGGGTTTCGTAGTAATTTCAAAAAT 57.748 29.630 0.00 0.00 0.00 1.82
187 188 8.248945 TGTTGGGTTTCGTAGTAATTTCAAAAA 58.751 29.630 0.00 0.00 0.00 1.94
188 189 7.769220 TGTTGGGTTTCGTAGTAATTTCAAAA 58.231 30.769 0.00 0.00 0.00 2.44
189 190 7.330900 TGTTGGGTTTCGTAGTAATTTCAAA 57.669 32.000 0.00 0.00 0.00 2.69
190 191 6.939132 TGTTGGGTTTCGTAGTAATTTCAA 57.061 33.333 0.00 0.00 0.00 2.69
191 192 6.711194 TCATGTTGGGTTTCGTAGTAATTTCA 59.289 34.615 0.00 0.00 0.00 2.69
192 193 7.136289 TCATGTTGGGTTTCGTAGTAATTTC 57.864 36.000 0.00 0.00 0.00 2.17
193 194 7.392113 TCATCATGTTGGGTTTCGTAGTAATTT 59.608 33.333 3.98 0.00 0.00 1.82
194 195 6.882140 TCATCATGTTGGGTTTCGTAGTAATT 59.118 34.615 3.98 0.00 0.00 1.40
195 196 6.411376 TCATCATGTTGGGTTTCGTAGTAAT 58.589 36.000 3.98 0.00 0.00 1.89
196 197 5.795972 TCATCATGTTGGGTTTCGTAGTAA 58.204 37.500 3.98 0.00 0.00 2.24
197 198 5.408880 TCATCATGTTGGGTTTCGTAGTA 57.591 39.130 3.98 0.00 0.00 1.82
198 199 4.280436 TCATCATGTTGGGTTTCGTAGT 57.720 40.909 3.98 0.00 0.00 2.73
199 200 4.875536 TCATCATCATGTTGGGTTTCGTAG 59.124 41.667 3.98 0.00 0.00 3.51
200 201 4.634004 GTCATCATCATGTTGGGTTTCGTA 59.366 41.667 3.98 0.00 0.00 3.43
201 202 3.440173 GTCATCATCATGTTGGGTTTCGT 59.560 43.478 3.98 0.00 0.00 3.85
202 203 3.439825 TGTCATCATCATGTTGGGTTTCG 59.560 43.478 3.98 0.00 0.00 3.46
203 204 5.047802 ACTTGTCATCATCATGTTGGGTTTC 60.048 40.000 3.98 0.00 0.00 2.78
204 205 4.834496 ACTTGTCATCATCATGTTGGGTTT 59.166 37.500 3.98 0.00 0.00 3.27
205 206 4.410099 ACTTGTCATCATCATGTTGGGTT 58.590 39.130 3.98 0.00 0.00 4.11
206 207 4.038271 ACTTGTCATCATCATGTTGGGT 57.962 40.909 3.98 0.00 0.00 4.51
207 208 4.219070 ACAACTTGTCATCATCATGTTGGG 59.781 41.667 20.23 0.00 46.00 4.12
208 209 5.158494 CACAACTTGTCATCATCATGTTGG 58.842 41.667 20.23 11.04 46.00 3.77
209 210 5.765176 ACACAACTTGTCATCATCATGTTG 58.235 37.500 16.97 16.97 46.54 3.33
210 211 6.210796 CAACACAACTTGTCATCATCATGTT 58.789 36.000 0.00 0.00 37.51 2.71
211 212 5.765176 CAACACAACTTGTCATCATCATGT 58.235 37.500 0.00 0.00 37.51 3.21
212 213 4.619760 GCAACACAACTTGTCATCATCATG 59.380 41.667 0.00 0.00 37.51 3.07
213 214 4.278919 TGCAACACAACTTGTCATCATCAT 59.721 37.500 0.00 0.00 37.51 2.45
277 280 8.356657 CCACTATTGAAACAACATACCTTTCAA 58.643 33.333 7.12 7.12 44.11 2.69
509 540 2.163010 AGTGTGTTCCGTATCCACGTAG 59.837 50.000 0.00 0.00 46.96 3.51
603 638 4.888326 ATTATGGGCAACAATGTTGTGT 57.112 36.364 24.71 12.25 41.31 3.72
677 713 7.541091 GTCATTAAGATCGAGCATATTTACGGA 59.459 37.037 2.38 0.00 0.00 4.69
1136 1210 4.272489 CCCATTTGTCTCCATTGCTTCTA 58.728 43.478 0.00 0.00 0.00 2.10
1153 1227 0.606401 CCACGACTTGACTGCCCATT 60.606 55.000 0.00 0.00 0.00 3.16
1529 1604 4.334759 GCTCAACAATGTCATCTAGCACAT 59.665 41.667 0.00 0.00 34.58 3.21
1911 1990 1.570813 CTGAACGTGTGCTGAACTCA 58.429 50.000 0.00 0.00 0.00 3.41
1994 2073 2.234661 ACATCATCATCGTCACCACACT 59.765 45.455 0.00 0.00 0.00 3.55
2442 2529 2.613474 CGGGTGATTTCGGAGTAAACCA 60.613 50.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.