Multiple sequence alignment - TraesCS2D01G100800

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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 TraesCS2D01G100800 chr2D 100.000 3091 0 0 1 3091 52958503 52961593 0.000000e+00 5709.0
1 TraesCS2D01G100800 chr2D 79.750 1279 157 50 845 2064 52851858 52853093 0.000000e+00 833.0
2 TraesCS2D01G100800 chr2D 79.948 1157 144 37 954 2065 52646906 52648019 0.000000e+00 771.0
3 TraesCS2D01G100800 chr2D 78.858 1121 147 41 997 2065 53649010 53650092 0.000000e+00 675.0
4 TraesCS2D01G100800 chr2D 95.094 265 12 1 2536 2799 52960865 52961129 1.710000e-112 416.0
5 TraesCS2D01G100800 chr2D 95.094 265 12 1 2363 2627 52961038 52961301 1.710000e-112 416.0
6 TraesCS2D01G100800 chr2D 87.023 131 12 3 2101 2230 52853395 52853521 3.210000e-30 143.0
7 TraesCS2D01G100800 chr2A 92.342 2037 98 29 323 2341 54139274 54141270 0.000000e+00 2844.0
8 TraesCS2D01G100800 chr2A 94.528 731 37 2 2363 3091 54141257 54141986 0.000000e+00 1125.0
9 TraesCS2D01G100800 chr2A 79.147 1242 167 41 848 2064 54012180 54013354 0.000000e+00 774.0
10 TraesCS2D01G100800 chr2A 78.058 1267 150 59 839 2064 54111747 54112926 0.000000e+00 682.0
11 TraesCS2D01G100800 chr2A 92.669 341 24 1 2460 2799 54141181 54141521 9.960000e-135 490.0
12 TraesCS2D01G100800 chr2A 92.453 265 19 1 2363 2627 54141430 54141693 8.090000e-101 377.0
13 TraesCS2D01G100800 chr2A 92.262 168 12 1 2633 2799 54141181 54141348 1.430000e-58 237.0
14 TraesCS2D01G100800 chr2A 89.706 136 7 2 202 333 54138678 54138810 1.910000e-37 167.0
15 TraesCS2D01G100800 chr2A 88.000 125 12 2 2101 2224 54113213 54113335 8.930000e-31 145.0
16 TraesCS2D01G100800 chr2B 91.409 1618 84 15 738 2343 83210913 83212487 0.000000e+00 2167.0
17 TraesCS2D01G100800 chr2B 79.849 1191 142 46 864 2023 82361148 82362271 0.000000e+00 780.0
18 TraesCS2D01G100800 chr2B 91.713 543 31 7 2554 3091 83212949 83213482 0.000000e+00 741.0
19 TraesCS2D01G100800 chr2B 80.100 1005 135 37 845 1813 82851514 82852489 0.000000e+00 688.0
20 TraesCS2D01G100800 chr2B 79.079 999 124 39 1103 2065 82714082 82715031 2.640000e-170 608.0
21 TraesCS2D01G100800 chr2B 82.553 619 97 9 1016 1632 83369466 83368857 4.540000e-148 534.0
22 TraesCS2D01G100800 chr2B 89.831 413 24 2 264 675 83210481 83210876 5.910000e-142 514.0
23 TraesCS2D01G100800 chr2B 81.157 674 95 21 917 1565 83955492 83954826 2.130000e-141 512.0
24 TraesCS2D01G100800 chr2B 81.745 619 102 9 1016 1632 83324971 83324362 9.890000e-140 507.0
25 TraesCS2D01G100800 chr2B 77.200 807 154 16 839 1632 83416419 83415630 7.870000e-121 444.0
26 TraesCS2D01G100800 chr2B 93.421 228 14 1 2460 2687 83212396 83212622 1.370000e-88 337.0
27 TraesCS2D01G100800 chr2B 90.574 244 15 1 2384 2627 83212952 83213187 1.790000e-82 316.0
28 TraesCS2D01G100800 chr2B 96.129 155 5 1 2363 2517 83212472 83212625 5.120000e-63 252.0
29 TraesCS2D01G100800 chr2B 82.553 235 35 1 1660 1894 83415633 83415405 5.230000e-48 202.0
30 TraesCS2D01G100800 chr2B 82.589 224 33 5 1691 1911 83306675 83306455 3.150000e-45 193.0
31 TraesCS2D01G100800 chr2B 81.897 232 34 6 1691 1916 83329135 83328906 4.070000e-44 189.0
32 TraesCS2D01G100800 chr2B 80.556 252 41 3 1660 1911 83413348 83413105 1.460000e-43 187.0
33 TraesCS2D01G100800 chr2B 81.466 232 35 6 1691 1916 83373619 83373390 1.890000e-42 183.0
34 TraesCS2D01G100800 chr2B 89.423 104 6 2 2129 2231 82715349 82715448 3.240000e-25 126.0
35 TraesCS2D01G100800 chr1A 98.630 73 1 0 4 76 188185987 188185915 2.500000e-26 130.0
36 TraesCS2D01G100800 chr4B 90.196 51 3 2 19 67 96664868 96664918 7.150000e-07 65.8
37 TraesCS2D01G100800 chr7B 91.304 46 3 1 245 290 427698133 427698177 9.260000e-06 62.1
38 TraesCS2D01G100800 chr7B 94.286 35 2 0 256 290 693970586 693970552 2.000000e-03 54.7
39 TraesCS2D01G100800 chr1B 97.297 37 0 1 254 290 592048012 592048047 9.260000e-06 62.1
40 TraesCS2D01G100800 chr1D 100.000 30 0 0 261 290 487886057 487886028 4.310000e-04 56.5
41 TraesCS2D01G100800 chr3B 96.875 32 1 0 257 288 779567783 779567752 2.000000e-03 54.7


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 TraesCS2D01G100800 chr2D 52958503 52961593 3090 False 2180.333333 5709 96.729333 1 3091 3 chr2D.!!$F4 3090
1 TraesCS2D01G100800 chr2D 52646906 52648019 1113 False 771.000000 771 79.948000 954 2065 1 chr2D.!!$F1 1111
2 TraesCS2D01G100800 chr2D 53649010 53650092 1082 False 675.000000 675 78.858000 997 2065 1 chr2D.!!$F2 1068
3 TraesCS2D01G100800 chr2D 52851858 52853521 1663 False 488.000000 833 83.386500 845 2230 2 chr2D.!!$F3 1385
4 TraesCS2D01G100800 chr2A 54138678 54141986 3308 False 873.333333 2844 92.326667 202 3091 6 chr2A.!!$F3 2889
5 TraesCS2D01G100800 chr2A 54012180 54013354 1174 False 774.000000 774 79.147000 848 2064 1 chr2A.!!$F1 1216
6 TraesCS2D01G100800 chr2A 54111747 54113335 1588 False 413.500000 682 83.029000 839 2224 2 chr2A.!!$F2 1385
7 TraesCS2D01G100800 chr2B 82361148 82362271 1123 False 780.000000 780 79.849000 864 2023 1 chr2B.!!$F1 1159
8 TraesCS2D01G100800 chr2B 83210481 83213482 3001 False 721.166667 2167 92.179500 264 3091 6 chr2B.!!$F4 2827
9 TraesCS2D01G100800 chr2B 82851514 82852489 975 False 688.000000 688 80.100000 845 1813 1 chr2B.!!$F2 968
10 TraesCS2D01G100800 chr2B 83954826 83955492 666 True 512.000000 512 81.157000 917 1565 1 chr2B.!!$R2 648
11 TraesCS2D01G100800 chr2B 82714082 82715448 1366 False 367.000000 608 84.251000 1103 2231 2 chr2B.!!$F3 1128
12 TraesCS2D01G100800 chr2B 83368857 83373619 4762 True 358.500000 534 82.009500 1016 1916 2 chr2B.!!$R4 900
13 TraesCS2D01G100800 chr2B 83324362 83329135 4773 True 348.000000 507 81.821000 1016 1916 2 chr2B.!!$R3 900
14 TraesCS2D01G100800 chr2B 83413105 83416419 3314 True 277.666667 444 80.103000 839 1911 3 chr2B.!!$R5 1072

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
111 112 0.595095 GCCTTCCAGCACTGTTTGAG 59.405 55.0 0.00 0.0 0.00 3.02 F
718 1224 0.745845 AGGACATGCTTAGCCGCTTG 60.746 55.0 0.29 0.0 39.94 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1609 3700 0.442699 GCTCCAACGGTTCAATCGAC 59.557 55.0 0.00 0.0 0.0 4.20 R
2350 8897 0.467290 AGACCCCTCTTGCGCAAAAA 60.467 50.0 25.01 14.1 0.0 1.94 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
82 83 4.075793 AGAGCGGGAGGGTGGCTA 62.076 66.667 0.00 0.00 37.10 3.93
83 84 3.541713 GAGCGGGAGGGTGGCTAG 61.542 72.222 0.00 0.00 37.10 3.42
84 85 4.075793 AGCGGGAGGGTGGCTAGA 62.076 66.667 0.00 0.00 34.75 2.43
85 86 3.541713 GCGGGAGGGTGGCTAGAG 61.542 72.222 0.00 0.00 0.00 2.43
86 87 2.840102 CGGGAGGGTGGCTAGAGG 60.840 72.222 0.00 0.00 0.00 3.69
87 88 3.164977 GGGAGGGTGGCTAGAGGC 61.165 72.222 0.00 0.00 41.50 4.70
88 89 3.541713 GGAGGGTGGCTAGAGGCG 61.542 72.222 0.00 0.00 44.42 5.52
89 90 2.760385 GAGGGTGGCTAGAGGCGT 60.760 66.667 0.00 0.00 44.42 5.68
90 91 2.760385 AGGGTGGCTAGAGGCGTC 60.760 66.667 0.00 0.00 44.42 5.19
91 92 3.851128 GGGTGGCTAGAGGCGTCC 61.851 72.222 2.06 8.07 44.42 4.79
93 94 4.874977 GTGGCTAGAGGCGTCCGC 62.875 72.222 2.45 2.45 44.42 5.54
104 105 4.379243 CGTCCGCCTTCCAGCACT 62.379 66.667 0.00 0.00 0.00 4.40
105 106 2.743928 GTCCGCCTTCCAGCACTG 60.744 66.667 0.00 0.00 0.00 3.66
106 107 3.241530 TCCGCCTTCCAGCACTGT 61.242 61.111 0.00 0.00 0.00 3.55
107 108 2.281761 CCGCCTTCCAGCACTGTT 60.282 61.111 0.00 0.00 0.00 3.16
108 109 1.898574 CCGCCTTCCAGCACTGTTT 60.899 57.895 0.00 0.00 0.00 2.83
109 110 1.283793 CGCCTTCCAGCACTGTTTG 59.716 57.895 0.00 0.00 0.00 2.93
110 111 1.165907 CGCCTTCCAGCACTGTTTGA 61.166 55.000 0.00 0.00 0.00 2.69
111 112 0.595095 GCCTTCCAGCACTGTTTGAG 59.405 55.000 0.00 0.00 0.00 3.02
112 113 1.972872 CCTTCCAGCACTGTTTGAGT 58.027 50.000 0.00 0.00 34.02 3.41
113 114 2.301346 CCTTCCAGCACTGTTTGAGTT 58.699 47.619 0.00 0.00 29.75 3.01
114 115 2.033801 CCTTCCAGCACTGTTTGAGTTG 59.966 50.000 0.00 0.00 29.75 3.16
115 116 2.418368 TCCAGCACTGTTTGAGTTGT 57.582 45.000 0.00 0.00 29.75 3.32
117 118 3.088532 TCCAGCACTGTTTGAGTTGTTT 58.911 40.909 0.00 0.00 29.75 2.83
118 119 3.509575 TCCAGCACTGTTTGAGTTGTTTT 59.490 39.130 0.00 0.00 29.75 2.43
120 121 5.036737 CCAGCACTGTTTGAGTTGTTTTAG 58.963 41.667 0.00 0.00 29.75 1.85
122 123 4.705023 AGCACTGTTTGAGTTGTTTTAGGT 59.295 37.500 0.00 0.00 29.75 3.08
123 124 5.883673 AGCACTGTTTGAGTTGTTTTAGGTA 59.116 36.000 0.00 0.00 29.75 3.08
124 125 6.376018 AGCACTGTTTGAGTTGTTTTAGGTAA 59.624 34.615 0.00 0.00 29.75 2.85
125 126 7.030768 GCACTGTTTGAGTTGTTTTAGGTAAA 58.969 34.615 0.00 0.00 29.75 2.01
126 127 7.542824 GCACTGTTTGAGTTGTTTTAGGTAAAA 59.457 33.333 0.00 0.00 29.75 1.52
127 128 9.413048 CACTGTTTGAGTTGTTTTAGGTAAAAA 57.587 29.630 0.00 0.00 33.03 1.94
153 154 9.454585 AAAAATAGTCATCAATGCAATGATACG 57.545 29.630 16.74 6.37 37.96 3.06
155 156 4.454678 AGTCATCAATGCAATGATACGGT 58.545 39.130 16.74 0.23 37.96 4.83
158 159 4.452114 TCATCAATGCAATGATACGGTAGC 59.548 41.667 16.74 0.00 37.96 3.58
159 160 2.799978 TCAATGCAATGATACGGTAGCG 59.200 45.455 13.69 13.69 0.00 4.26
160 161 2.526304 ATGCAATGATACGGTAGCGT 57.474 45.000 24.61 24.61 0.00 5.07
161 162 3.653539 ATGCAATGATACGGTAGCGTA 57.346 42.857 27.28 27.28 0.00 4.42
162 163 3.653539 TGCAATGATACGGTAGCGTAT 57.346 42.857 33.25 33.25 37.72 3.06
163 164 3.985008 TGCAATGATACGGTAGCGTATT 58.015 40.909 33.17 21.03 35.50 1.89
164 165 3.985279 TGCAATGATACGGTAGCGTATTC 59.015 43.478 33.17 25.89 35.50 1.75
165 166 3.059044 GCAATGATACGGTAGCGTATTCG 59.941 47.826 33.17 23.40 35.50 3.34
166 167 4.224433 CAATGATACGGTAGCGTATTCGT 58.776 43.478 33.17 24.51 35.50 3.85
167 168 3.257745 TGATACGGTAGCGTATTCGTG 57.742 47.619 33.17 0.00 35.50 4.35
168 169 2.871633 TGATACGGTAGCGTATTCGTGA 59.128 45.455 33.17 13.12 35.50 4.35
169 170 3.312146 TGATACGGTAGCGTATTCGTGAA 59.688 43.478 33.17 16.47 35.50 3.18
170 171 2.634982 ACGGTAGCGTATTCGTGAAA 57.365 45.000 19.91 0.00 39.49 2.69
171 172 2.945278 ACGGTAGCGTATTCGTGAAAA 58.055 42.857 19.91 0.00 39.49 2.29
173 174 2.662637 CGGTAGCGTATTCGTGAAAACA 59.337 45.455 6.07 0.00 39.49 2.83
176 177 4.565564 GGTAGCGTATTCGTGAAAACATCT 59.434 41.667 0.00 0.00 39.49 2.90
177 178 5.745294 GGTAGCGTATTCGTGAAAACATCTA 59.255 40.000 0.00 0.00 39.49 1.98
179 180 7.592533 GGTAGCGTATTCGTGAAAACATCTATA 59.407 37.037 0.00 0.00 39.49 1.31
180 181 9.125906 GTAGCGTATTCGTGAAAACATCTATAT 57.874 33.333 0.00 0.00 39.49 0.86
182 183 9.687210 AGCGTATTCGTGAAAACATCTATATAA 57.313 29.630 0.00 0.00 39.49 0.98
183 184 9.939047 GCGTATTCGTGAAAACATCTATATAAG 57.061 33.333 0.00 0.00 39.49 1.73
189 190 9.489084 TCGTGAAAACATCTATATAAGGATTGG 57.511 33.333 0.00 0.00 0.00 3.16
190 191 9.489084 CGTGAAAACATCTATATAAGGATTGGA 57.511 33.333 0.00 0.00 0.00 3.53
192 193 9.507329 TGAAAACATCTATATAAGGATTGGAGC 57.493 33.333 0.00 0.00 0.00 4.70
193 194 8.553459 AAAACATCTATATAAGGATTGGAGCG 57.447 34.615 0.00 0.00 0.00 5.03
194 195 7.482169 AACATCTATATAAGGATTGGAGCGA 57.518 36.000 0.00 0.00 0.00 4.93
195 196 7.106439 ACATCTATATAAGGATTGGAGCGAG 57.894 40.000 0.00 0.00 0.00 5.03
197 198 7.834681 ACATCTATATAAGGATTGGAGCGAGTA 59.165 37.037 0.00 0.00 0.00 2.59
199 200 8.053026 TCTATATAAGGATTGGAGCGAGTAAC 57.947 38.462 0.00 0.00 0.00 2.50
200 201 6.665992 ATATAAGGATTGGAGCGAGTAACA 57.334 37.500 0.00 0.00 0.00 2.41
234 235 3.047093 TGTCTATGTTCGTGTGTCGTTG 58.953 45.455 0.00 0.00 40.80 4.10
235 236 3.047796 GTCTATGTTCGTGTGTCGTTGT 58.952 45.455 0.00 0.00 40.80 3.32
236 237 3.488310 GTCTATGTTCGTGTGTCGTTGTT 59.512 43.478 0.00 0.00 40.80 2.83
240 241 0.796927 TTCGTGTGTCGTTGTTTGCA 59.203 45.000 0.00 0.00 40.80 4.08
374 854 6.575162 AGTAGCACTGAAATACTTTTTGGG 57.425 37.500 0.00 0.00 0.00 4.12
413 895 6.203530 TGCATCATTAGCAGATTAACACTAGC 59.796 38.462 0.00 0.00 37.02 3.42
438 920 7.201617 GCTTATTACACAGTGGTTATCCAGAAC 60.202 40.741 5.31 0.00 45.24 3.01
516 1001 2.032030 CCCTACATTAATTGGCGCGAAG 60.032 50.000 12.10 0.00 0.00 3.79
544 1029 5.551233 AGGCTAATATTGCGCTATCTTCAA 58.449 37.500 9.73 0.00 0.00 2.69
598 1083 4.496927 CTCAAATTGCGGGGCGGC 62.497 66.667 0.00 0.00 0.00 6.53
646 1131 2.279659 GCGTCAATTTGATCCGCAATTG 59.720 45.455 22.17 0.00 40.27 2.32
655 1140 8.614346 CAATTTGATCCGCAATTGGAAATTATT 58.386 29.630 7.72 0.00 42.46 1.40
708 1214 1.759445 AGCGACTCATTAGGACATGCT 59.241 47.619 0.00 0.00 0.00 3.79
709 1215 2.169352 AGCGACTCATTAGGACATGCTT 59.831 45.455 0.00 0.00 0.00 3.91
710 1216 3.384789 AGCGACTCATTAGGACATGCTTA 59.615 43.478 0.00 0.00 0.00 3.09
711 1217 3.738282 GCGACTCATTAGGACATGCTTAG 59.262 47.826 0.00 0.00 0.00 2.18
712 1218 3.738282 CGACTCATTAGGACATGCTTAGC 59.262 47.826 0.00 0.00 0.00 3.09
713 1219 4.061596 GACTCATTAGGACATGCTTAGCC 58.938 47.826 0.29 0.00 0.00 3.93
714 1220 3.062763 CTCATTAGGACATGCTTAGCCG 58.937 50.000 0.29 0.00 0.00 5.52
715 1221 1.532868 CATTAGGACATGCTTAGCCGC 59.467 52.381 0.29 0.00 0.00 6.53
716 1222 0.830648 TTAGGACATGCTTAGCCGCT 59.169 50.000 0.29 0.00 0.00 5.52
717 1223 0.830648 TAGGACATGCTTAGCCGCTT 59.169 50.000 0.29 0.00 0.00 4.68
718 1224 0.745845 AGGACATGCTTAGCCGCTTG 60.746 55.000 0.29 0.00 39.94 4.01
719 1225 1.718757 GGACATGCTTAGCCGCTTGG 61.719 60.000 0.29 0.00 38.82 3.61
730 1236 2.440065 CGCTTGGCAGGGGCATTA 60.440 61.111 0.00 0.00 43.71 1.90
731 1237 2.051518 CGCTTGGCAGGGGCATTAA 61.052 57.895 0.00 0.00 43.71 1.40
732 1238 1.394266 CGCTTGGCAGGGGCATTAAT 61.394 55.000 0.00 0.00 43.71 1.40
733 1239 0.832626 GCTTGGCAGGGGCATTAATT 59.167 50.000 0.00 0.00 43.71 1.40
734 1240 1.210234 GCTTGGCAGGGGCATTAATTT 59.790 47.619 0.00 0.00 43.71 1.82
735 1241 2.433970 GCTTGGCAGGGGCATTAATTTA 59.566 45.455 0.00 0.00 43.71 1.40
736 1242 3.741075 GCTTGGCAGGGGCATTAATTTAC 60.741 47.826 0.00 0.00 43.71 2.01
737 1243 3.396685 TGGCAGGGGCATTAATTTACT 57.603 42.857 0.00 0.00 43.71 2.24
738 1244 3.030291 TGGCAGGGGCATTAATTTACTG 58.970 45.455 0.00 0.00 43.71 2.74
739 1245 2.224042 GGCAGGGGCATTAATTTACTGC 60.224 50.000 16.78 16.78 46.54 4.40
758 1264 4.471386 ACTGCCTTGGAATCACTAGTACAT 59.529 41.667 0.00 0.00 0.00 2.29
897 1410 5.882553 TCTTCTAAACCCAAAAACGTTCAC 58.117 37.500 0.00 0.00 0.00 3.18
1153 3184 3.096092 GACTTCTCCTGTCTCATGGTCT 58.904 50.000 0.00 0.00 0.00 3.85
1415 3479 2.586357 GAGATCTTCCGCGGCACC 60.586 66.667 23.51 7.52 0.00 5.01
1586 3661 9.394477 GTACGCAAGAATCTATTTTGTTTTTCT 57.606 29.630 0.00 0.00 43.62 2.52
1622 3723 0.109412 GAGTCGGTCGATTGAACCGT 60.109 55.000 17.90 5.71 46.11 4.83
1675 3793 3.014623 CCTCACATCACATGTCATGCTT 58.985 45.455 9.92 0.00 42.70 3.91
1691 3809 6.211184 TGTCATGCTTGGGATTTGTTTCTTAT 59.789 34.615 0.00 0.00 0.00 1.73
1692 3810 7.099120 GTCATGCTTGGGATTTGTTTCTTATT 58.901 34.615 0.00 0.00 0.00 1.40
1693 3811 7.603784 GTCATGCTTGGGATTTGTTTCTTATTT 59.396 33.333 0.00 0.00 0.00 1.40
1694 3812 8.156165 TCATGCTTGGGATTTGTTTCTTATTTT 58.844 29.630 0.00 0.00 0.00 1.82
1695 3813 8.785946 CATGCTTGGGATTTGTTTCTTATTTTT 58.214 29.630 0.00 0.00 0.00 1.94
1760 3884 3.499737 GTGCAGGACGATTGGGCG 61.500 66.667 0.00 0.00 37.29 6.13
1785 3909 1.021202 CCGGCTGTTGAACAAAGACA 58.979 50.000 0.00 0.00 0.00 3.41
2290 8837 8.753497 ACTATTCCCCTTTTGAATGTTCTATC 57.247 34.615 0.00 0.00 34.43 2.08
2292 8839 7.651027 ATTCCCCTTTTGAATGTTCTATCTG 57.349 36.000 0.00 0.00 31.42 2.90
2304 8851 9.087424 TGAATGTTCTATCTGTTCTATTGTTCG 57.913 33.333 0.00 0.00 0.00 3.95
2332 8879 9.803507 AATCATACATATCATGGTTGATTCAGT 57.196 29.630 10.54 0.00 42.61 3.41
2333 8880 8.837788 TCATACATATCATGGTTGATTCAGTC 57.162 34.615 0.00 0.00 42.61 3.51
2334 8881 8.654094 TCATACATATCATGGTTGATTCAGTCT 58.346 33.333 0.00 0.00 42.61 3.24
2335 8882 9.281371 CATACATATCATGGTTGATTCAGTCTT 57.719 33.333 0.00 0.00 42.61 3.01
2336 8883 7.563888 ACATATCATGGTTGATTCAGTCTTG 57.436 36.000 0.00 0.00 42.61 3.02
2337 8884 6.544931 ACATATCATGGTTGATTCAGTCTTGG 59.455 38.462 0.00 0.00 42.61 3.61
2338 8885 4.371624 TCATGGTTGATTCAGTCTTGGT 57.628 40.909 0.00 0.00 0.00 3.67
2339 8886 4.728772 TCATGGTTGATTCAGTCTTGGTT 58.271 39.130 0.00 0.00 0.00 3.67
2340 8887 5.875224 TCATGGTTGATTCAGTCTTGGTTA 58.125 37.500 0.00 0.00 0.00 2.85
2341 8888 5.705441 TCATGGTTGATTCAGTCTTGGTTAC 59.295 40.000 0.00 0.00 0.00 2.50
2342 8889 5.042463 TGGTTGATTCAGTCTTGGTTACA 57.958 39.130 0.00 0.00 0.00 2.41
2343 8890 5.630121 TGGTTGATTCAGTCTTGGTTACAT 58.370 37.500 0.00 0.00 0.00 2.29
2344 8891 6.068010 TGGTTGATTCAGTCTTGGTTACATT 58.932 36.000 0.00 0.00 0.00 2.71
2345 8892 6.549364 TGGTTGATTCAGTCTTGGTTACATTT 59.451 34.615 0.00 0.00 0.00 2.32
2346 8893 7.069331 TGGTTGATTCAGTCTTGGTTACATTTT 59.931 33.333 0.00 0.00 0.00 1.82
2347 8894 7.926018 GGTTGATTCAGTCTTGGTTACATTTTT 59.074 33.333 0.00 0.00 0.00 1.94
2545 9092 1.075374 TGGTTGATTCAGGGGTCTTGG 59.925 52.381 0.00 0.00 0.00 3.61
2594 9428 1.964933 GTTTGTTTCCCAATCCCCGAA 59.035 47.619 0.00 0.00 31.81 4.30
2664 9498 7.610580 TGAACTATTCCCCTTTTGAATGTTT 57.389 32.000 0.00 0.00 34.43 2.83
2763 9598 2.717390 TGTGTTTGTATCCCAATCCCG 58.283 47.619 0.00 0.00 31.81 5.14
2804 9639 5.587443 ACCAAGCAAACTATACCGAAATACC 59.413 40.000 0.00 0.00 0.00 2.73
2932 9767 9.513906 CAATGGTTTCAAAATTATAGGGGTTTT 57.486 29.630 0.00 0.00 0.00 2.43
2964 9799 5.952526 ACCCGTTTGTTAAATGGTTCTAG 57.047 39.130 10.65 0.00 44.44 2.43
3069 9906 8.472007 TCTCTGCCCTTTTTATTTTTAGTTCA 57.528 30.769 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 4.075793 TAGCCACCCTCCCGCTCT 62.076 66.667 0.00 0.00 34.03 4.09
67 68 4.075793 TCTAGCCACCCTCCCGCT 62.076 66.667 0.00 0.00 36.63 5.52
69 70 2.840102 CCTCTAGCCACCCTCCCG 60.840 72.222 0.00 0.00 0.00 5.14
70 71 3.164977 GCCTCTAGCCACCCTCCC 61.165 72.222 0.00 0.00 34.35 4.30
72 73 2.760385 ACGCCTCTAGCCACCCTC 60.760 66.667 0.00 0.00 38.78 4.30
73 74 2.760385 GACGCCTCTAGCCACCCT 60.760 66.667 0.00 0.00 38.78 4.34
74 75 3.851128 GGACGCCTCTAGCCACCC 61.851 72.222 0.00 0.00 38.78 4.61
76 77 4.874977 GCGGACGCCTCTAGCCAC 62.875 72.222 5.20 0.00 38.78 5.01
87 88 4.379243 AGTGCTGGAAGGCGGACG 62.379 66.667 0.00 0.00 34.52 4.79
88 89 2.743928 CAGTGCTGGAAGGCGGAC 60.744 66.667 0.00 0.00 34.52 4.79
89 90 2.337879 AAACAGTGCTGGAAGGCGGA 62.338 55.000 4.11 0.00 34.52 5.54
90 91 1.898574 AAACAGTGCTGGAAGGCGG 60.899 57.895 4.11 0.00 34.52 6.13
91 92 1.165907 TCAAACAGTGCTGGAAGGCG 61.166 55.000 4.11 0.00 34.52 5.52
93 94 1.972872 ACTCAAACAGTGCTGGAAGG 58.027 50.000 4.11 0.00 32.26 3.46
97 98 3.508744 AAACAACTCAAACAGTGCTGG 57.491 42.857 4.11 0.00 34.56 4.85
98 99 5.036737 CCTAAAACAACTCAAACAGTGCTG 58.963 41.667 0.00 0.00 34.56 4.41
99 100 4.705023 ACCTAAAACAACTCAAACAGTGCT 59.295 37.500 0.00 0.00 34.56 4.40
101 102 8.973835 TTTTACCTAAAACAACTCAAACAGTG 57.026 30.769 0.00 0.00 30.87 3.66
127 128 9.454585 CGTATCATTGCATTGATGACTATTTTT 57.545 29.630 26.68 6.76 36.97 1.94
128 129 8.077991 CCGTATCATTGCATTGATGACTATTTT 58.922 33.333 26.68 7.36 36.97 1.82
129 130 7.229306 ACCGTATCATTGCATTGATGACTATTT 59.771 33.333 26.68 7.96 36.97 1.40
132 133 5.610398 ACCGTATCATTGCATTGATGACTA 58.390 37.500 26.68 10.08 36.97 2.59
133 134 4.454678 ACCGTATCATTGCATTGATGACT 58.545 39.130 26.68 10.08 36.97 3.41
135 136 4.452114 GCTACCGTATCATTGCATTGATGA 59.548 41.667 26.68 16.20 36.97 2.92
137 138 3.433274 CGCTACCGTATCATTGCATTGAT 59.567 43.478 23.42 23.42 39.60 2.57
138 139 2.799978 CGCTACCGTATCATTGCATTGA 59.200 45.455 13.30 13.30 0.00 2.57
139 140 3.173399 CGCTACCGTATCATTGCATTG 57.827 47.619 2.08 2.08 0.00 2.82
152 153 2.662637 TGTTTTCACGAATACGCTACCG 59.337 45.455 0.00 0.00 43.96 4.02
153 154 4.565564 AGATGTTTTCACGAATACGCTACC 59.434 41.667 0.00 0.00 43.96 3.18
163 164 9.489084 CCAATCCTTATATAGATGTTTTCACGA 57.511 33.333 0.00 0.00 0.00 4.35
164 165 9.489084 TCCAATCCTTATATAGATGTTTTCACG 57.511 33.333 0.00 0.00 0.00 4.35
166 167 9.507329 GCTCCAATCCTTATATAGATGTTTTCA 57.493 33.333 0.00 0.00 0.00 2.69
167 168 8.660373 CGCTCCAATCCTTATATAGATGTTTTC 58.340 37.037 0.00 0.00 0.00 2.29
168 169 8.375506 TCGCTCCAATCCTTATATAGATGTTTT 58.624 33.333 0.00 0.00 0.00 2.43
169 170 7.907389 TCGCTCCAATCCTTATATAGATGTTT 58.093 34.615 0.00 0.00 0.00 2.83
170 171 7.179338 ACTCGCTCCAATCCTTATATAGATGTT 59.821 37.037 0.00 0.00 0.00 2.71
171 172 6.665680 ACTCGCTCCAATCCTTATATAGATGT 59.334 38.462 0.00 0.00 0.00 3.06
173 174 8.688151 GTTACTCGCTCCAATCCTTATATAGAT 58.312 37.037 0.00 0.00 0.00 1.98
176 177 7.309621 GGTGTTACTCGCTCCAATCCTTATATA 60.310 40.741 0.00 0.00 0.00 0.86
177 178 6.456501 GTGTTACTCGCTCCAATCCTTATAT 58.543 40.000 0.00 0.00 0.00 0.86
179 180 4.443034 GGTGTTACTCGCTCCAATCCTTAT 60.443 45.833 0.00 0.00 0.00 1.73
180 181 3.118884 GGTGTTACTCGCTCCAATCCTTA 60.119 47.826 0.00 0.00 0.00 2.69
182 183 1.207329 GGTGTTACTCGCTCCAATCCT 59.793 52.381 0.00 0.00 0.00 3.24
183 184 1.207329 AGGTGTTACTCGCTCCAATCC 59.793 52.381 0.00 0.00 0.00 3.01
184 185 2.674796 AGGTGTTACTCGCTCCAATC 57.325 50.000 0.00 0.00 0.00 2.67
185 186 3.243434 CGATAGGTGTTACTCGCTCCAAT 60.243 47.826 0.00 0.00 0.00 3.16
187 188 1.674441 CGATAGGTGTTACTCGCTCCA 59.326 52.381 0.00 0.00 0.00 3.86
188 189 2.402640 CGATAGGTGTTACTCGCTCC 57.597 55.000 0.00 0.00 0.00 4.70
413 895 8.041323 AGTTCTGGATAACCACTGTGTAATAAG 58.959 37.037 7.08 0.00 41.77 1.73
438 920 7.715265 AATCGTTGGTTGCTAATGATACTAG 57.285 36.000 1.41 0.00 33.78 2.57
516 1001 5.582665 AGATAGCGCAATATTAGCCTAAAGC 59.417 40.000 11.47 5.50 44.25 3.51
544 1029 0.318784 GGAGATAGCGCCGAAATCGT 60.319 55.000 2.29 0.00 37.74 3.73
598 1083 2.544267 GGGCGATATCTCCGTTTGAAAG 59.456 50.000 5.66 0.00 0.00 2.62
603 1088 1.111116 TCCGGGCGATATCTCCGTTT 61.111 55.000 23.53 0.00 41.98 3.60
620 1105 2.719798 CGGATCAAATTGACGCAATCC 58.280 47.619 0.00 0.00 32.43 3.01
655 1140 6.686630 CATCCAGTGTTAATAGGTTGCAAAA 58.313 36.000 0.00 0.00 0.00 2.44
713 1219 1.394266 ATTAATGCCCCTGCCAAGCG 61.394 55.000 0.00 0.00 36.33 4.68
714 1220 0.832626 AATTAATGCCCCTGCCAAGC 59.167 50.000 0.00 0.00 36.33 4.01
715 1221 3.706086 AGTAAATTAATGCCCCTGCCAAG 59.294 43.478 0.00 0.00 36.33 3.61
716 1222 3.450457 CAGTAAATTAATGCCCCTGCCAA 59.550 43.478 0.00 0.00 36.33 4.52
717 1223 3.030291 CAGTAAATTAATGCCCCTGCCA 58.970 45.455 0.00 0.00 36.33 4.92
718 1224 2.224042 GCAGTAAATTAATGCCCCTGCC 60.224 50.000 13.72 0.00 43.36 4.85
719 1225 3.097877 GCAGTAAATTAATGCCCCTGC 57.902 47.619 13.72 4.93 43.36 4.85
726 1232 7.775120 AGTGATTCCAAGGCAGTAAATTAATG 58.225 34.615 0.00 0.00 0.00 1.90
727 1233 7.961326 AGTGATTCCAAGGCAGTAAATTAAT 57.039 32.000 0.00 0.00 0.00 1.40
728 1234 8.107095 ACTAGTGATTCCAAGGCAGTAAATTAA 58.893 33.333 0.00 0.00 0.00 1.40
729 1235 7.630082 ACTAGTGATTCCAAGGCAGTAAATTA 58.370 34.615 0.00 0.00 0.00 1.40
730 1236 6.485171 ACTAGTGATTCCAAGGCAGTAAATT 58.515 36.000 0.00 0.00 0.00 1.82
731 1237 6.067217 ACTAGTGATTCCAAGGCAGTAAAT 57.933 37.500 0.00 0.00 0.00 1.40
732 1238 5.499004 ACTAGTGATTCCAAGGCAGTAAA 57.501 39.130 0.00 0.00 0.00 2.01
733 1239 5.482526 TGTACTAGTGATTCCAAGGCAGTAA 59.517 40.000 5.39 0.00 0.00 2.24
734 1240 5.020795 TGTACTAGTGATTCCAAGGCAGTA 58.979 41.667 5.39 0.00 0.00 2.74
735 1241 3.838317 TGTACTAGTGATTCCAAGGCAGT 59.162 43.478 5.39 0.00 0.00 4.40
736 1242 4.471904 TGTACTAGTGATTCCAAGGCAG 57.528 45.455 5.39 0.00 0.00 4.85
737 1243 4.469586 TGATGTACTAGTGATTCCAAGGCA 59.530 41.667 5.39 0.00 0.00 4.75
738 1244 5.023533 TGATGTACTAGTGATTCCAAGGC 57.976 43.478 5.39 0.00 0.00 4.35
739 1245 9.613428 TTTAATGATGTACTAGTGATTCCAAGG 57.387 33.333 5.39 0.00 0.00 3.61
897 1410 4.818546 AGAGATGTGAAGAGGTGTTTTGTG 59.181 41.667 0.00 0.00 0.00 3.33
1153 3184 2.431419 TGTTGTTGAGGTTGACGTAGGA 59.569 45.455 0.00 0.00 0.00 2.94
1609 3700 0.442699 GCTCCAACGGTTCAATCGAC 59.557 55.000 0.00 0.00 0.00 4.20
1692 3810 9.280174 ACAACACGAGGAGAATAAGAAATAAAA 57.720 29.630 0.00 0.00 0.00 1.52
1693 3811 8.842358 ACAACACGAGGAGAATAAGAAATAAA 57.158 30.769 0.00 0.00 0.00 1.40
1694 3812 8.842358 AACAACACGAGGAGAATAAGAAATAA 57.158 30.769 0.00 0.00 0.00 1.40
1695 3813 8.842358 AAACAACACGAGGAGAATAAGAAATA 57.158 30.769 0.00 0.00 0.00 1.40
1696 3814 7.745620 AAACAACACGAGGAGAATAAGAAAT 57.254 32.000 0.00 0.00 0.00 2.17
1760 3884 1.299850 GTTCAACAGCCGGCAAACC 60.300 57.895 31.54 5.39 0.00 3.27
1775 3899 1.154225 CGCGGCCATGTCTTTGTTC 60.154 57.895 2.24 0.00 0.00 3.18
1785 3909 2.438254 TGCATTCTTCGCGGCCAT 60.438 55.556 6.13 0.00 0.00 4.40
2008 6472 0.882042 CAGATGCTCCATGTACGGCC 60.882 60.000 0.00 0.00 0.00 6.13
2013 6477 0.752658 CGGGTCAGATGCTCCATGTA 59.247 55.000 0.00 0.00 0.00 2.29
2249 8796 5.305585 GGAATAGTTCGGCTCCATCAATAA 58.694 41.667 0.00 0.00 0.00 1.40
2262 8809 5.897377 ACATTCAAAAGGGGAATAGTTCG 57.103 39.130 0.00 0.00 33.40 3.95
2317 8864 4.371624 ACCAAGACTGAATCAACCATGA 57.628 40.909 0.00 0.00 40.57 3.07
2350 8897 0.467290 AGACCCCTCTTGCGCAAAAA 60.467 50.000 25.01 14.10 0.00 1.94
2351 8898 0.467290 AAGACCCCTCTTGCGCAAAA 60.467 50.000 25.01 10.74 35.24 2.44
2352 8899 1.150536 AAGACCCCTCTTGCGCAAA 59.849 52.632 25.01 13.79 35.24 3.68
2353 8900 1.600636 CAAGACCCCTCTTGCGCAA 60.601 57.895 23.48 23.48 45.43 4.85
2354 8901 2.032528 CAAGACCCCTCTTGCGCA 59.967 61.111 5.66 5.66 45.43 6.09
2359 8906 3.256704 TCATGTAACCAAGACCCCTCTT 58.743 45.455 0.00 0.00 37.19 2.85
2360 8907 2.915869 TCATGTAACCAAGACCCCTCT 58.084 47.619 0.00 0.00 0.00 3.69
2361 8908 3.933861 ATCATGTAACCAAGACCCCTC 57.066 47.619 0.00 0.00 0.00 4.30
2362 8909 4.371681 ACTATCATGTAACCAAGACCCCT 58.628 43.478 0.00 0.00 0.00 4.79
2363 8910 4.772886 ACTATCATGTAACCAAGACCCC 57.227 45.455 0.00 0.00 0.00 4.95
2545 9092 3.508762 CAGGACGGTACTGTCATGTAAC 58.491 50.000 31.74 16.83 43.59 2.50
2683 9517 7.435305 TGAATCAACCATGGCATGTATTATTG 58.565 34.615 24.80 18.61 0.00 1.90
2687 9521 4.342951 CCTGAATCAACCATGGCATGTATT 59.657 41.667 24.80 17.38 0.00 1.89
2763 9598 2.341318 GGTAAACACATTTGCCGTCC 57.659 50.000 0.00 0.00 40.25 4.79
2804 9639 4.928615 TGGGCGCTTCAAAATCTTTAAATG 59.071 37.500 7.64 0.00 0.00 2.32
2932 9767 7.094549 CCATTTAACAAACGGGTAGAGAAATCA 60.095 37.037 0.00 0.00 0.00 2.57
2964 9799 1.192428 ACCATCCGGACCACTACTTC 58.808 55.000 6.12 0.00 35.59 3.01


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

AutoCloner maintained by Alex Coulton.