Multiple sequence alignment - TraesCS3A01G272400

Loading Multiple Alignment...

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 TraesCS3A01G272400 chr3A 100.000 2732 0 0 1 2732 501720939 501723670 0.000000e+00 5046.0
1 TraesCS3A01G272400 chr3A 82.500 80 14 0 983 1062 575562531 575562452 1.360000e-08 71.3
2 TraesCS3A01G272400 chr7D 97.258 2553 59 4 181 2732 19724912 19722370 0.000000e+00 4316.0
3 TraesCS3A01G272400 chr7D 91.160 181 13 3 1 179 292671837 292672016 2.720000e-60 243.0
4 TraesCS3A01G272400 chr7A 97.145 2557 44 7 181 2732 671196352 671198884 0.000000e+00 4290.0
5 TraesCS3A01G272400 chr7A 90.654 1530 136 5 1207 2732 567708786 567707260 0.000000e+00 2026.0
6 TraesCS3A01G272400 chr7A 82.353 85 14 1 181 264 125254307 125254223 3.770000e-09 73.1
7 TraesCS3A01G272400 chr5A 96.788 2553 63 5 181 2732 52271021 52268487 0.000000e+00 4242.0
8 TraesCS3A01G272400 chr5A 90.588 1530 138 4 1207 2732 631366420 631364893 0.000000e+00 2023.0
9 TraesCS3A01G272400 chr1A 96.568 1486 47 4 1248 2732 589986718 589988200 0.000000e+00 2459.0
10 TraesCS3A01G272400 chr1A 92.818 362 10 5 856 1217 589986376 589986721 6.750000e-141 510.0
11 TraesCS3A01G272400 chr1A 86.413 368 27 10 174 539 589985739 589986085 5.520000e-102 381.0
12 TraesCS3A01G272400 chr1A 91.045 268 16 5 649 909 589986110 589986376 3.350000e-94 355.0
13 TraesCS3A01G272400 chr4A 90.987 1509 134 2 1224 2732 166839143 166837637 0.000000e+00 2032.0
14 TraesCS3A01G272400 chr4A 83.158 95 13 2 181 272 596844307 596844213 1.740000e-12 84.2
15 TraesCS3A01G272400 chr4A 82.500 80 14 0 983 1062 115921341 115921262 1.360000e-08 71.3
16 TraesCS3A01G272400 chr7B 90.588 1530 138 4 1207 2732 710980447 710981974 0.000000e+00 2023.0
17 TraesCS3A01G272400 chr6B 90.570 1527 140 2 1209 2732 324836482 324834957 0.000000e+00 2019.0
18 TraesCS3A01G272400 chr6B 86.364 88 12 0 183 270 706654514 706654427 2.240000e-16 97.1
19 TraesCS3A01G272400 chr6B 81.707 82 11 4 983 1062 2933327 2933406 6.310000e-07 65.8
20 TraesCS3A01G272400 chr1B 88.344 978 83 16 181 1158 611787088 611788034 0.000000e+00 1146.0
21 TraesCS3A01G272400 chr1B 91.111 180 15 1 1 179 271792655 271792834 2.720000e-60 243.0
22 TraesCS3A01G272400 chr6D 89.520 229 19 3 181 405 469942206 469942433 4.450000e-73 285.0
23 TraesCS3A01G272400 chr4D 92.222 180 13 1 1 179 276616824 276616645 1.260000e-63 254.0
24 TraesCS3A01G272400 chr2A 91.667 180 14 1 1 179 495156888 495157067 5.840000e-62 248.0
25 TraesCS3A01G272400 chr5D 91.111 180 15 1 1 179 114874377 114874198 2.720000e-60 243.0
26 TraesCS3A01G272400 chr5D 91.111 180 15 1 1 179 294284731 294284552 2.720000e-60 243.0
27 TraesCS3A01G272400 chr5D 84.146 82 9 4 983 1062 256007743 256007664 2.920000e-10 76.8
28 TraesCS3A01G272400 chr4B 91.111 180 15 1 1 179 520464817 520464638 2.720000e-60 243.0
29 TraesCS3A01G272400 chr3D 91.111 180 15 1 1 179 411572852 411573031 2.720000e-60 243.0
30 TraesCS3A01G272400 chr2D 91.111 180 14 2 1 179 273977733 273977555 2.720000e-60 243.0
31 TraesCS3A01G272400 chr3B 94.286 35 1 1 1186 1219 730167705 730167739 5.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G272400 chr3A 501720939 501723670 2731 False 5046.00 5046 100.000 1 2732 1 chr3A.!!$F1 2731
1 TraesCS3A01G272400 chr7D 19722370 19724912 2542 True 4316.00 4316 97.258 181 2732 1 chr7D.!!$R1 2551
2 TraesCS3A01G272400 chr7A 671196352 671198884 2532 False 4290.00 4290 97.145 181 2732 1 chr7A.!!$F1 2551
3 TraesCS3A01G272400 chr7A 567707260 567708786 1526 True 2026.00 2026 90.654 1207 2732 1 chr7A.!!$R2 1525
4 TraesCS3A01G272400 chr5A 52268487 52271021 2534 True 4242.00 4242 96.788 181 2732 1 chr5A.!!$R1 2551
5 TraesCS3A01G272400 chr5A 631364893 631366420 1527 True 2023.00 2023 90.588 1207 2732 1 chr5A.!!$R2 1525
6 TraesCS3A01G272400 chr1A 589985739 589988200 2461 False 926.25 2459 91.711 174 2732 4 chr1A.!!$F1 2558
7 TraesCS3A01G272400 chr4A 166837637 166839143 1506 True 2032.00 2032 90.987 1224 2732 1 chr4A.!!$R2 1508
8 TraesCS3A01G272400 chr7B 710980447 710981974 1527 False 2023.00 2023 90.588 1207 2732 1 chr7B.!!$F1 1525
9 TraesCS3A01G272400 chr6B 324834957 324836482 1525 True 2019.00 2019 90.570 1209 2732 1 chr6B.!!$R1 1523
10 TraesCS3A01G272400 chr1B 611787088 611788034 946 False 1146.00 1146 88.344 181 1158 1 chr1B.!!$F2 977

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
764 785 0.262876 GCCCCAAATCCTCAATCCCT 59.737 55.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 1895 4.870123 TTGTTGCAAGCCACTTCAATAT 57.13 36.364 0.0 0.0 0.0 1.28 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
24 25 7.746526 GATTTGATGAAGAAAACTGTATGGC 57.253 36.000 0.00 0.00 0.00 4.40
25 26 6.647334 TTTGATGAAGAAAACTGTATGGCA 57.353 33.333 0.00 0.00 0.00 4.92
26 27 6.839124 TTGATGAAGAAAACTGTATGGCAT 57.161 33.333 4.88 4.88 0.00 4.40
27 28 6.839124 TGATGAAGAAAACTGTATGGCATT 57.161 33.333 4.78 0.00 0.00 3.56
28 29 6.623486 TGATGAAGAAAACTGTATGGCATTG 58.377 36.000 4.78 0.00 0.00 2.82
29 30 5.389859 TGAAGAAAACTGTATGGCATTGG 57.610 39.130 4.78 0.00 0.00 3.16
30 31 4.220382 TGAAGAAAACTGTATGGCATTGGG 59.780 41.667 4.78 0.00 0.00 4.12
31 32 2.497273 AGAAAACTGTATGGCATTGGGC 59.503 45.455 4.78 0.00 43.74 5.36
32 33 2.236489 AAACTGTATGGCATTGGGCT 57.764 45.000 4.78 0.00 44.01 5.19
33 34 3.380471 AAACTGTATGGCATTGGGCTA 57.620 42.857 4.78 0.00 44.01 3.93
34 35 3.600448 AACTGTATGGCATTGGGCTAT 57.400 42.857 4.78 0.00 46.46 2.97
35 36 3.146104 ACTGTATGGCATTGGGCTATC 57.854 47.619 4.78 0.00 43.38 2.08
36 37 2.224867 ACTGTATGGCATTGGGCTATCC 60.225 50.000 4.78 0.00 43.38 2.59
37 38 1.779700 TGTATGGCATTGGGCTATCCA 59.220 47.619 4.78 0.00 43.38 3.41
38 39 2.379567 TGTATGGCATTGGGCTATCCAT 59.620 45.455 4.78 0.00 46.52 3.41
39 40 2.226962 ATGGCATTGGGCTATCCATC 57.773 50.000 0.00 0.00 46.52 3.51
40 41 0.852155 TGGCATTGGGCTATCCATCA 59.148 50.000 0.00 0.00 46.52 3.07
41 42 1.251251 GGCATTGGGCTATCCATCAC 58.749 55.000 0.00 0.00 46.52 3.06
42 43 1.479205 GGCATTGGGCTATCCATCACA 60.479 52.381 0.00 0.00 46.52 3.58
43 44 1.884579 GCATTGGGCTATCCATCACAG 59.115 52.381 0.00 0.00 46.52 3.66
44 45 2.487805 GCATTGGGCTATCCATCACAGA 60.488 50.000 0.00 0.00 46.52 3.41
45 46 3.813240 GCATTGGGCTATCCATCACAGAT 60.813 47.826 0.00 0.00 46.52 2.90
46 47 3.497103 TTGGGCTATCCATCACAGATG 57.503 47.619 0.07 0.07 46.52 2.90
47 48 1.072806 TGGGCTATCCATCACAGATGC 59.927 52.381 1.52 0.00 41.46 3.91
48 49 1.350351 GGGCTATCCATCACAGATGCT 59.650 52.381 1.52 0.00 35.00 3.79
49 50 2.224719 GGGCTATCCATCACAGATGCTT 60.225 50.000 1.52 0.00 35.00 3.91
50 51 3.484407 GGCTATCCATCACAGATGCTTT 58.516 45.455 1.52 0.00 0.00 3.51
51 52 3.887716 GGCTATCCATCACAGATGCTTTT 59.112 43.478 1.52 0.00 0.00 2.27
52 53 5.065914 GGCTATCCATCACAGATGCTTTTA 58.934 41.667 1.52 0.00 0.00 1.52
53 54 5.709164 GGCTATCCATCACAGATGCTTTTAT 59.291 40.000 1.52 0.00 0.00 1.40
54 55 6.208204 GGCTATCCATCACAGATGCTTTTATT 59.792 38.462 1.52 0.00 0.00 1.40
55 56 7.082602 GCTATCCATCACAGATGCTTTTATTG 58.917 38.462 1.52 0.00 0.00 1.90
56 57 5.252969 TCCATCACAGATGCTTTTATTGC 57.747 39.130 1.52 0.00 0.00 3.56
57 58 4.951715 TCCATCACAGATGCTTTTATTGCT 59.048 37.500 1.52 0.00 0.00 3.91
58 59 6.121590 TCCATCACAGATGCTTTTATTGCTA 58.878 36.000 1.52 0.00 0.00 3.49
59 60 6.261603 TCCATCACAGATGCTTTTATTGCTAG 59.738 38.462 1.52 0.00 0.00 3.42
60 61 6.261603 CCATCACAGATGCTTTTATTGCTAGA 59.738 38.462 0.00 0.00 0.00 2.43
61 62 7.201758 CCATCACAGATGCTTTTATTGCTAGAA 60.202 37.037 0.00 0.00 0.00 2.10
62 63 7.076842 TCACAGATGCTTTTATTGCTAGAAC 57.923 36.000 0.00 0.00 0.00 3.01
63 64 6.094048 TCACAGATGCTTTTATTGCTAGAACC 59.906 38.462 0.00 0.00 0.00 3.62
64 65 5.945784 ACAGATGCTTTTATTGCTAGAACCA 59.054 36.000 0.00 0.00 0.00 3.67
65 66 6.604795 ACAGATGCTTTTATTGCTAGAACCAT 59.395 34.615 0.00 0.00 0.00 3.55
66 67 7.123247 ACAGATGCTTTTATTGCTAGAACCATT 59.877 33.333 0.00 0.00 0.00 3.16
67 68 7.977853 CAGATGCTTTTATTGCTAGAACCATTT 59.022 33.333 0.00 0.00 0.00 2.32
68 69 9.189156 AGATGCTTTTATTGCTAGAACCATTTA 57.811 29.630 0.00 0.00 0.00 1.40
69 70 9.971922 GATGCTTTTATTGCTAGAACCATTTAT 57.028 29.630 0.00 0.00 0.00 1.40
78 79 9.914834 ATTGCTAGAACCATTTATAAAGTACCA 57.085 29.630 3.94 0.00 0.00 3.25
79 80 9.914834 TTGCTAGAACCATTTATAAAGTACCAT 57.085 29.630 3.94 0.00 0.00 3.55
80 81 9.337396 TGCTAGAACCATTTATAAAGTACCATG 57.663 33.333 3.94 0.00 0.00 3.66
81 82 9.555727 GCTAGAACCATTTATAAAGTACCATGA 57.444 33.333 3.94 0.00 0.00 3.07
83 84 8.747538 AGAACCATTTATAAAGTACCATGACC 57.252 34.615 3.94 0.00 0.00 4.02
84 85 7.778382 AGAACCATTTATAAAGTACCATGACCC 59.222 37.037 3.94 0.00 0.00 4.46
85 86 6.975949 ACCATTTATAAAGTACCATGACCCA 58.024 36.000 3.94 0.00 0.00 4.51
86 87 7.591821 ACCATTTATAAAGTACCATGACCCAT 58.408 34.615 3.94 0.00 0.00 4.00
87 88 8.065007 ACCATTTATAAAGTACCATGACCCATT 58.935 33.333 3.94 0.00 0.00 3.16
88 89 8.923270 CCATTTATAAAGTACCATGACCCATTT 58.077 33.333 3.94 0.00 0.00 2.32
94 95 5.888982 AGTACCATGACCCATTTAGTAGG 57.111 43.478 0.00 0.00 0.00 3.18
95 96 5.286221 AGTACCATGACCCATTTAGTAGGT 58.714 41.667 0.00 0.00 36.31 3.08
96 97 5.729718 AGTACCATGACCCATTTAGTAGGTT 59.270 40.000 0.00 0.00 32.81 3.50
97 98 5.530176 ACCATGACCCATTTAGTAGGTTT 57.470 39.130 0.00 0.00 32.81 3.27
98 99 6.645884 ACCATGACCCATTTAGTAGGTTTA 57.354 37.500 0.00 0.00 32.81 2.01
99 100 7.220890 ACCATGACCCATTTAGTAGGTTTAT 57.779 36.000 0.00 0.00 32.81 1.40
100 101 7.648770 ACCATGACCCATTTAGTAGGTTTATT 58.351 34.615 0.00 0.00 32.81 1.40
101 102 8.783903 ACCATGACCCATTTAGTAGGTTTATTA 58.216 33.333 0.00 0.00 32.81 0.98
102 103 9.284968 CCATGACCCATTTAGTAGGTTTATTAG 57.715 37.037 0.00 0.00 32.81 1.73
103 104 9.847224 CATGACCCATTTAGTAGGTTTATTAGT 57.153 33.333 0.00 0.00 32.81 2.24
143 144 9.638239 TTCCAGTATTAAGCAAATTCACATTTC 57.362 29.630 0.00 0.00 29.41 2.17
144 145 8.801299 TCCAGTATTAAGCAAATTCACATTTCA 58.199 29.630 0.00 0.00 29.41 2.69
145 146 9.590451 CCAGTATTAAGCAAATTCACATTTCAT 57.410 29.630 0.00 0.00 29.41 2.57
149 150 7.565450 TTAAGCAAATTCACATTTCATGTCG 57.435 32.000 0.00 0.00 42.70 4.35
150 151 5.375417 AGCAAATTCACATTTCATGTCGA 57.625 34.783 0.00 0.00 42.70 4.20
151 152 5.771469 AGCAAATTCACATTTCATGTCGAA 58.229 33.333 0.00 5.03 42.70 3.71
152 153 6.392354 AGCAAATTCACATTTCATGTCGAAT 58.608 32.000 0.00 7.90 42.70 3.34
153 154 7.537715 AGCAAATTCACATTTCATGTCGAATA 58.462 30.769 11.56 0.00 42.70 1.75
154 155 7.699391 AGCAAATTCACATTTCATGTCGAATAG 59.301 33.333 11.56 9.76 42.70 1.73
155 156 7.485913 GCAAATTCACATTTCATGTCGAATAGT 59.514 33.333 11.56 4.93 42.70 2.12
156 157 9.345517 CAAATTCACATTTCATGTCGAATAGTT 57.654 29.630 11.56 5.15 42.70 2.24
157 158 8.900511 AATTCACATTTCATGTCGAATAGTTG 57.099 30.769 11.56 0.00 42.70 3.16
158 159 7.433708 TTCACATTTCATGTCGAATAGTTGT 57.566 32.000 0.00 0.00 42.70 3.32
159 160 7.433708 TCACATTTCATGTCGAATAGTTGTT 57.566 32.000 0.00 0.00 42.70 2.83
160 161 7.870826 TCACATTTCATGTCGAATAGTTGTTT 58.129 30.769 0.00 0.00 42.70 2.83
161 162 7.802720 TCACATTTCATGTCGAATAGTTGTTTG 59.197 33.333 0.00 0.00 42.70 2.93
162 163 6.582295 ACATTTCATGTCGAATAGTTGTTTGC 59.418 34.615 0.00 0.00 39.92 3.68
163 164 5.681337 TTCATGTCGAATAGTTGTTTGCA 57.319 34.783 0.00 0.00 0.00 4.08
164 165 5.681337 TCATGTCGAATAGTTGTTTGCAA 57.319 34.783 0.00 0.00 0.00 4.08
165 166 6.252967 TCATGTCGAATAGTTGTTTGCAAT 57.747 33.333 0.00 0.00 36.92 3.56
166 167 6.676950 TCATGTCGAATAGTTGTTTGCAATT 58.323 32.000 0.00 0.00 36.92 2.32
167 168 7.144661 TCATGTCGAATAGTTGTTTGCAATTT 58.855 30.769 0.00 0.00 36.92 1.82
168 169 6.984740 TGTCGAATAGTTGTTTGCAATTTC 57.015 33.333 0.00 0.00 36.92 2.17
169 170 6.499172 TGTCGAATAGTTGTTTGCAATTTCA 58.501 32.000 0.00 0.00 36.92 2.69
170 171 7.144661 TGTCGAATAGTTGTTTGCAATTTCAT 58.855 30.769 0.00 0.00 36.92 2.57
171 172 8.293157 TGTCGAATAGTTGTTTGCAATTTCATA 58.707 29.630 0.00 0.00 36.92 2.15
172 173 9.289303 GTCGAATAGTTGTTTGCAATTTCATAT 57.711 29.630 0.00 0.00 36.92 1.78
173 174 9.502145 TCGAATAGTTGTTTGCAATTTCATATC 57.498 29.630 0.00 0.00 36.92 1.63
174 175 9.288124 CGAATAGTTGTTTGCAATTTCATATCA 57.712 29.630 0.00 0.00 36.92 2.15
176 177 9.590451 AATAGTTGTTTGCAATTTCATATCAGG 57.410 29.630 0.00 0.00 36.92 3.86
177 178 5.870978 AGTTGTTTGCAATTTCATATCAGGC 59.129 36.000 0.00 0.00 36.92 4.85
178 179 5.402997 TGTTTGCAATTTCATATCAGGCA 57.597 34.783 0.00 0.00 0.00 4.75
179 180 5.979993 TGTTTGCAATTTCATATCAGGCAT 58.020 33.333 0.00 0.00 0.00 4.40
318 320 0.380378 GTGCGAGCTGAAACCAAACA 59.620 50.000 0.00 0.00 0.00 2.83
411 413 3.210012 ATCCGCCACCAGCCAAGTT 62.210 57.895 0.00 0.00 38.78 2.66
446 448 2.300967 GGCCCACCACTGGATCTCA 61.301 63.158 0.71 0.00 40.55 3.27
612 629 1.281960 GCAGCAACACACTGAGCAG 59.718 57.895 0.00 0.00 37.32 4.24
726 743 0.695347 CCTTCTCCTGCACTCCCTTT 59.305 55.000 0.00 0.00 0.00 3.11
727 744 1.074566 CCTTCTCCTGCACTCCCTTTT 59.925 52.381 0.00 0.00 0.00 2.27
764 785 0.262876 GCCCCAAATCCTCAATCCCT 59.737 55.000 0.00 0.00 0.00 4.20
767 788 2.785857 CCCCAAATCCTCAATCCCTAGT 59.214 50.000 0.00 0.00 0.00 2.57
963 1041 3.476552 ACGGTGAACTGATGAACACATT 58.523 40.909 0.00 0.00 35.33 2.71
964 1042 3.882888 ACGGTGAACTGATGAACACATTT 59.117 39.130 0.00 0.00 35.33 2.32
965 1043 5.060506 ACGGTGAACTGATGAACACATTTA 58.939 37.500 0.00 0.00 35.33 1.40
966 1044 5.049680 ACGGTGAACTGATGAACACATTTAC 60.050 40.000 0.00 0.00 35.33 2.01
967 1045 5.049749 CGGTGAACTGATGAACACATTTACA 60.050 40.000 0.00 0.00 35.33 2.41
968 1046 6.142817 GGTGAACTGATGAACACATTTACAC 58.857 40.000 0.00 0.00 35.33 2.90
969 1047 6.238621 GGTGAACTGATGAACACATTTACACA 60.239 38.462 0.00 0.00 35.33 3.72
970 1048 7.362662 GTGAACTGATGAACACATTTACACAT 58.637 34.615 0.00 0.00 34.05 3.21
1017 1095 3.814504 AGAATGAAGAGGGCAGGAAAA 57.185 42.857 0.00 0.00 0.00 2.29
1052 1130 1.135170 TGCGAGACATGCTCAGAAGAG 60.135 52.381 14.69 0.00 44.15 2.85
1376 1457 6.088016 TGCACATAACTTTGAAGCAAGAAT 57.912 33.333 0.00 0.00 31.76 2.40
1495 1577 7.642669 TGTATGCTTCTTGTTCAAAGAGAAAG 58.357 34.615 0.00 0.00 38.13 2.62
1555 1637 5.893824 GGTGGTTGGAGAAATTGGAATAGAT 59.106 40.000 0.00 0.00 0.00 1.98
1732 1815 8.934507 GAAGTATTCACTTAGATGCTTGTAGT 57.065 34.615 0.00 0.00 45.18 2.73
1793 1878 6.691754 TGAAAGTGAACAATCTAGCAACAA 57.308 33.333 0.00 0.00 0.00 2.83
1810 1895 4.037923 GCAACAAGGGAAACTTCATTGAGA 59.962 41.667 11.45 0.00 37.29 3.27
1928 2013 9.985730 ACAAAATCAGATTATTCAATGTTGTGT 57.014 25.926 0.00 0.00 31.59 3.72
2047 2132 5.682943 AGCTCTATGTTTGCGTTTTGTTA 57.317 34.783 0.00 0.00 0.00 2.41
2233 2319 7.941919 AGGAGAAATTAAAGGACTGAAAACAC 58.058 34.615 0.00 0.00 0.00 3.32
2322 2408 1.134551 GTTGCTGTTGCCAAGGGAAAA 60.135 47.619 0.00 0.00 38.71 2.29
2337 2423 5.762179 AGGGAAAAGATGACTGTGTATGA 57.238 39.130 0.00 0.00 0.00 2.15
2338 2424 6.319048 AGGGAAAAGATGACTGTGTATGAT 57.681 37.500 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.315142 TGCCATACAGTTTTCTTCATCAAATC 58.685 34.615 0.00 0.00 0.00 2.17
2 3 6.647334 TGCCATACAGTTTTCTTCATCAAA 57.353 33.333 0.00 0.00 0.00 2.69
3 4 6.839124 ATGCCATACAGTTTTCTTCATCAA 57.161 33.333 0.00 0.00 0.00 2.57
4 5 6.350361 CCAATGCCATACAGTTTTCTTCATCA 60.350 38.462 0.00 0.00 0.00 3.07
5 6 6.038356 CCAATGCCATACAGTTTTCTTCATC 58.962 40.000 0.00 0.00 0.00 2.92
6 7 5.105228 CCCAATGCCATACAGTTTTCTTCAT 60.105 40.000 0.00 0.00 0.00 2.57
7 8 4.220382 CCCAATGCCATACAGTTTTCTTCA 59.780 41.667 0.00 0.00 0.00 3.02
8 9 4.747810 CCCAATGCCATACAGTTTTCTTC 58.252 43.478 0.00 0.00 0.00 2.87
9 10 3.055891 GCCCAATGCCATACAGTTTTCTT 60.056 43.478 0.00 0.00 0.00 2.52
10 11 2.497273 GCCCAATGCCATACAGTTTTCT 59.503 45.455 0.00 0.00 0.00 2.52
11 12 2.497273 AGCCCAATGCCATACAGTTTTC 59.503 45.455 0.00 0.00 42.71 2.29
12 13 2.539302 AGCCCAATGCCATACAGTTTT 58.461 42.857 0.00 0.00 42.71 2.43
13 14 2.236489 AGCCCAATGCCATACAGTTT 57.764 45.000 0.00 0.00 42.71 2.66
14 15 3.490348 GATAGCCCAATGCCATACAGTT 58.510 45.455 0.00 0.00 42.71 3.16
15 16 2.224867 GGATAGCCCAATGCCATACAGT 60.225 50.000 0.00 0.00 42.71 3.55
16 17 2.224843 TGGATAGCCCAATGCCATACAG 60.225 50.000 0.00 0.00 43.29 2.74
17 18 1.779700 TGGATAGCCCAATGCCATACA 59.220 47.619 0.00 0.00 43.29 2.29
18 19 2.584835 TGGATAGCCCAATGCCATAC 57.415 50.000 0.00 0.00 43.29 2.39
28 29 1.350351 AGCATCTGTGATGGATAGCCC 59.650 52.381 9.24 0.00 0.00 5.19
29 30 2.855209 AGCATCTGTGATGGATAGCC 57.145 50.000 9.24 0.00 0.00 3.93
30 31 6.814506 ATAAAAGCATCTGTGATGGATAGC 57.185 37.500 9.24 0.00 0.00 2.97
31 32 7.040617 AGCAATAAAAGCATCTGTGATGGATAG 60.041 37.037 9.24 0.00 0.00 2.08
32 33 6.774170 AGCAATAAAAGCATCTGTGATGGATA 59.226 34.615 9.24 0.00 0.00 2.59
33 34 5.597182 AGCAATAAAAGCATCTGTGATGGAT 59.403 36.000 9.24 0.00 0.00 3.41
34 35 4.951715 AGCAATAAAAGCATCTGTGATGGA 59.048 37.500 9.24 0.00 0.00 3.41
35 36 5.258456 AGCAATAAAAGCATCTGTGATGG 57.742 39.130 9.24 0.00 0.00 3.51
36 37 7.255491 TCTAGCAATAAAAGCATCTGTGATG 57.745 36.000 3.42 3.42 0.00 3.07
37 38 7.201767 GGTTCTAGCAATAAAAGCATCTGTGAT 60.202 37.037 0.00 0.00 0.00 3.06
38 39 6.094048 GGTTCTAGCAATAAAAGCATCTGTGA 59.906 38.462 0.00 0.00 0.00 3.58
39 40 6.127925 TGGTTCTAGCAATAAAAGCATCTGTG 60.128 38.462 0.00 0.00 0.00 3.66
40 41 5.945784 TGGTTCTAGCAATAAAAGCATCTGT 59.054 36.000 0.00 0.00 0.00 3.41
41 42 6.441093 TGGTTCTAGCAATAAAAGCATCTG 57.559 37.500 0.00 0.00 0.00 2.90
42 43 7.651027 AATGGTTCTAGCAATAAAAGCATCT 57.349 32.000 5.16 0.00 38.49 2.90
43 44 9.971922 ATAAATGGTTCTAGCAATAAAAGCATC 57.028 29.630 5.16 0.00 38.49 3.91
52 53 9.914834 TGGTACTTTATAAATGGTTCTAGCAAT 57.085 29.630 0.00 0.00 0.00 3.56
53 54 9.914834 ATGGTACTTTATAAATGGTTCTAGCAA 57.085 29.630 0.00 0.00 0.00 3.91
54 55 9.337396 CATGGTACTTTATAAATGGTTCTAGCA 57.663 33.333 0.00 0.00 0.00 3.49
55 56 9.555727 TCATGGTACTTTATAAATGGTTCTAGC 57.444 33.333 0.00 0.00 0.00 3.42
57 58 9.841295 GGTCATGGTACTTTATAAATGGTTCTA 57.159 33.333 0.00 0.00 0.00 2.10
58 59 7.778382 GGGTCATGGTACTTTATAAATGGTTCT 59.222 37.037 0.00 0.00 0.00 3.01
59 60 7.558444 TGGGTCATGGTACTTTATAAATGGTTC 59.442 37.037 0.00 0.00 0.00 3.62
60 61 7.415086 TGGGTCATGGTACTTTATAAATGGTT 58.585 34.615 0.00 0.00 0.00 3.67
61 62 6.975949 TGGGTCATGGTACTTTATAAATGGT 58.024 36.000 0.00 0.00 0.00 3.55
62 63 8.477419 AATGGGTCATGGTACTTTATAAATGG 57.523 34.615 0.00 0.00 0.00 3.16
68 69 8.437575 CCTACTAAATGGGTCATGGTACTTTAT 58.562 37.037 0.00 0.00 0.00 1.40
69 70 7.403813 ACCTACTAAATGGGTCATGGTACTTTA 59.596 37.037 0.00 0.00 37.76 1.85
70 71 6.216868 ACCTACTAAATGGGTCATGGTACTTT 59.783 38.462 0.00 0.00 37.76 2.66
71 72 5.729718 ACCTACTAAATGGGTCATGGTACTT 59.270 40.000 0.00 0.00 37.76 2.24
72 73 5.286221 ACCTACTAAATGGGTCATGGTACT 58.714 41.667 0.00 0.00 37.76 2.73
73 74 5.625568 ACCTACTAAATGGGTCATGGTAC 57.374 43.478 0.00 0.00 37.76 3.34
74 75 6.645884 AAACCTACTAAATGGGTCATGGTA 57.354 37.500 0.00 0.00 42.53 3.25
75 76 5.530176 AAACCTACTAAATGGGTCATGGT 57.470 39.130 0.00 0.00 42.53 3.55
76 77 9.284968 CTAATAAACCTACTAAATGGGTCATGG 57.715 37.037 0.00 0.00 42.53 3.66
77 78 9.847224 ACTAATAAACCTACTAAATGGGTCATG 57.153 33.333 0.00 0.00 42.53 3.07
117 118 9.638239 GAAATGTGAATTTGCTTAATACTGGAA 57.362 29.630 0.00 0.00 0.00 3.53
118 119 8.801299 TGAAATGTGAATTTGCTTAATACTGGA 58.199 29.630 0.00 0.00 0.00 3.86
119 120 8.984891 TGAAATGTGAATTTGCTTAATACTGG 57.015 30.769 0.00 0.00 0.00 4.00
139 140 6.676950 TGCAAACAACTATTCGACATGAAAT 58.323 32.000 0.00 0.00 40.71 2.17
140 141 6.066054 TGCAAACAACTATTCGACATGAAA 57.934 33.333 0.00 0.00 40.71 2.69
141 142 5.681337 TGCAAACAACTATTCGACATGAA 57.319 34.783 0.00 0.00 41.81 2.57
142 143 5.681337 TTGCAAACAACTATTCGACATGA 57.319 34.783 0.00 0.00 0.00 3.07
143 144 6.932901 AATTGCAAACAACTATTCGACATG 57.067 33.333 1.71 0.00 38.99 3.21
144 145 7.144661 TGAAATTGCAAACAACTATTCGACAT 58.855 30.769 1.71 0.00 38.99 3.06
145 146 6.499172 TGAAATTGCAAACAACTATTCGACA 58.501 32.000 1.71 0.00 38.99 4.35
146 147 6.984740 TGAAATTGCAAACAACTATTCGAC 57.015 33.333 1.71 0.00 38.99 4.20
147 148 9.502145 GATATGAAATTGCAAACAACTATTCGA 57.498 29.630 1.71 0.00 38.99 3.71
148 149 9.288124 TGATATGAAATTGCAAACAACTATTCG 57.712 29.630 1.71 0.00 38.99 3.34
150 151 9.590451 CCTGATATGAAATTGCAAACAACTATT 57.410 29.630 1.71 0.00 38.99 1.73
151 152 7.707893 GCCTGATATGAAATTGCAAACAACTAT 59.292 33.333 1.71 0.00 38.99 2.12
152 153 7.035004 GCCTGATATGAAATTGCAAACAACTA 58.965 34.615 1.71 0.00 38.99 2.24
153 154 5.870978 GCCTGATATGAAATTGCAAACAACT 59.129 36.000 1.71 0.00 38.99 3.16
154 155 5.638657 TGCCTGATATGAAATTGCAAACAAC 59.361 36.000 1.71 0.00 38.99 3.32
155 156 5.791666 TGCCTGATATGAAATTGCAAACAA 58.208 33.333 1.71 0.00 40.87 2.83
156 157 5.402997 TGCCTGATATGAAATTGCAAACA 57.597 34.783 1.71 4.97 0.00 2.83
157 158 7.168637 CACTATGCCTGATATGAAATTGCAAAC 59.831 37.037 1.71 0.00 0.00 2.93
158 159 7.204604 CACTATGCCTGATATGAAATTGCAAA 58.795 34.615 1.71 0.00 0.00 3.68
159 160 6.239092 CCACTATGCCTGATATGAAATTGCAA 60.239 38.462 0.00 0.00 0.00 4.08
160 161 5.242171 CCACTATGCCTGATATGAAATTGCA 59.758 40.000 0.00 0.00 0.00 4.08
161 162 5.706916 CCACTATGCCTGATATGAAATTGC 58.293 41.667 0.00 0.00 0.00 3.56
162 163 5.618418 CGCCACTATGCCTGATATGAAATTG 60.618 44.000 0.00 0.00 0.00 2.32
163 164 4.456911 CGCCACTATGCCTGATATGAAATT 59.543 41.667 0.00 0.00 0.00 1.82
164 165 4.005650 CGCCACTATGCCTGATATGAAAT 58.994 43.478 0.00 0.00 0.00 2.17
165 166 3.402110 CGCCACTATGCCTGATATGAAA 58.598 45.455 0.00 0.00 0.00 2.69
166 167 2.289631 CCGCCACTATGCCTGATATGAA 60.290 50.000 0.00 0.00 0.00 2.57
167 168 1.276138 CCGCCACTATGCCTGATATGA 59.724 52.381 0.00 0.00 0.00 2.15
168 169 1.276138 TCCGCCACTATGCCTGATATG 59.724 52.381 0.00 0.00 0.00 1.78
169 170 1.552337 CTCCGCCACTATGCCTGATAT 59.448 52.381 0.00 0.00 0.00 1.63
170 171 0.969149 CTCCGCCACTATGCCTGATA 59.031 55.000 0.00 0.00 0.00 2.15
171 172 1.750930 CTCCGCCACTATGCCTGAT 59.249 57.895 0.00 0.00 0.00 2.90
172 173 3.094062 GCTCCGCCACTATGCCTGA 62.094 63.158 0.00 0.00 0.00 3.86
173 174 2.590007 GCTCCGCCACTATGCCTG 60.590 66.667 0.00 0.00 0.00 4.85
318 320 0.321653 GGAGAGGATGTGCCGTGTTT 60.322 55.000 0.00 0.00 43.43 2.83
436 438 1.014804 AGGGAGGTCTGAGATCCAGT 58.985 55.000 4.62 0.00 43.38 4.00
446 448 0.971447 GTCAGCCGTTAGGGAGGTCT 60.971 60.000 0.00 0.00 38.47 3.85
600 617 2.664185 CGCTGCTGCTCAGTGTGT 60.664 61.111 14.03 0.00 45.73 3.72
726 743 2.621929 GGCCAGTACCTCTCTCTCTCAA 60.622 54.545 0.00 0.00 0.00 3.02
727 744 1.064314 GGCCAGTACCTCTCTCTCTCA 60.064 57.143 0.00 0.00 0.00 3.27
764 785 8.644374 ACAAATTTAACTGAAATAGGCCACTA 57.356 30.769 5.01 0.00 36.71 2.74
767 788 8.207545 ACAAACAAATTTAACTGAAATAGGCCA 58.792 29.630 5.01 0.00 36.71 5.36
919 989 7.063074 CCGTTCATCTACTAGTTTGTTAACAGG 59.937 40.741 8.56 4.23 36.70 4.00
965 1043 9.709495 AATTCTGCAAAATTTATGTGTATGTGT 57.291 25.926 0.00 0.00 0.00 3.72
1017 1095 2.627699 TCTCGCAAAAAGGGAAGCAATT 59.372 40.909 0.00 0.00 38.87 2.32
1052 1130 3.188492 GGCGTACTAGCTTTCTTCCTTC 58.812 50.000 0.00 0.00 37.29 3.46
1376 1457 7.996066 TGAATGATCGAAACCTATTCCCAATTA 59.004 33.333 0.00 0.00 0.00 1.40
1495 1577 5.494390 TTAGTTCCCTTCCCACTAGTTTC 57.506 43.478 0.00 0.00 0.00 2.78
1729 1812 6.375455 GCCAATCCTTGATGAAGAAGAAACTA 59.625 38.462 0.00 0.00 0.00 2.24
1732 1815 5.078949 TGCCAATCCTTGATGAAGAAGAAA 58.921 37.500 0.00 0.00 0.00 2.52
1793 1878 8.517062 CTTCAATATCTCAATGAAGTTTCCCT 57.483 34.615 6.59 0.00 43.11 4.20
1810 1895 4.870123 TTGTTGCAAGCCACTTCAATAT 57.130 36.364 0.00 0.00 0.00 1.28
1943 2028 9.258826 CATCACCAACTTGTTCAATAATTTGAA 57.741 29.630 0.00 0.00 46.88 2.69
2047 2132 6.350103 GCTCACTTAGCCTTCCTACTTTATT 58.650 40.000 0.00 0.00 46.25 1.40
2233 2319 5.581479 CAGAAGGTGACTCTTTCATGATCAG 59.419 44.000 0.09 0.00 42.68 2.90


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

AutoCloner maintained by Alex Coulton.