Multiple sequence alignment - TraesCS2B01G342300

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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 TraesCS2B01G342300 chr2B 100.000 4175 0 0 1 4175 488197610 488193436 0.000000e+00 7710.0
1 TraesCS2B01G342300 chr2D 87.839 1513 109 33 887 2362 414960214 414958740 0.000000e+00 1705.0
2 TraesCS2B01G342300 chr2D 92.931 1061 50 19 784 1838 416397986 416396945 0.000000e+00 1520.0
3 TraesCS2B01G342300 chr2D 87.785 876 58 32 1835 2674 416392351 416391489 0.000000e+00 979.0
4 TraesCS2B01G342300 chr2D 88.207 831 79 14 2708 3530 416391393 416390574 0.000000e+00 974.0
5 TraesCS2B01G342300 chr2D 93.553 667 20 9 3521 4175 414957306 414956651 0.000000e+00 972.0
6 TraesCS2B01G342300 chr2D 85.632 863 62 33 2402 3214 414958628 414957778 0.000000e+00 850.0
7 TraesCS2B01G342300 chr2D 85.231 562 42 18 3521 4068 416390550 416390016 1.320000e-149 540.0
8 TraesCS2B01G342300 chr2D 96.875 320 10 0 3211 3530 414957649 414957330 1.710000e-148 536.0
9 TraesCS2B01G342300 chr2D 85.193 466 26 19 266 704 416398440 416397991 4.960000e-119 438.0
10 TraesCS2B01G342300 chr2D 92.086 139 11 0 1 139 416398867 416398729 3.290000e-46 196.0
11 TraesCS2B01G342300 chr2D 94.444 54 2 1 217 269 416398510 416398457 9.620000e-12 82.4
12 TraesCS2B01G342300 chr2A 89.729 1217 67 30 266 1440 582637210 582636010 0.000000e+00 1502.0
13 TraesCS2B01G342300 chr2A 92.879 660 34 6 3521 4175 581943358 581942707 0.000000e+00 946.0
14 TraesCS2B01G342300 chr2A 88.611 799 55 18 1426 2216 581945920 581945150 0.000000e+00 939.0
15 TraesCS2B01G342300 chr2A 84.012 1032 100 40 2213 3189 581944730 581943709 0.000000e+00 931.0
16 TraesCS2B01G342300 chr2A 89.276 746 51 15 1587 2327 582635952 582635231 0.000000e+00 907.0
17 TraesCS2B01G342300 chr2A 88.703 478 46 7 2708 3182 582634694 582634222 1.010000e-160 577.0
18 TraesCS2B01G342300 chr2A 86.423 383 27 12 887 1248 581959622 581959244 3.020000e-106 396.0
19 TraesCS2B01G342300 chr2A 88.024 334 20 10 3213 3530 581943711 581943382 1.100000e-100 377.0
20 TraesCS2B01G342300 chr2A 92.578 256 13 4 2418 2667 582635050 582634795 3.070000e-96 363.0
21 TraesCS2B01G342300 chr2A 91.573 178 15 0 1244 1421 581950658 581950481 3.220000e-61 246.0
22 TraesCS2B01G342300 chr2A 80.488 123 14 6 1316 1437 416628304 416628191 7.440000e-13 86.1
23 TraesCS2B01G342300 chr6B 85.088 114 8 3 1324 1437 213263036 213262932 1.590000e-19 108.0
24 TraesCS2B01G342300 chrUn 84.956 113 8 3 1324 1436 275301546 275301443 5.710000e-19 106.0
25 TraesCS2B01G342300 chrUn 84.956 113 8 3 1324 1436 308426244 308426347 5.710000e-19 106.0
26 TraesCS2B01G342300 chr4B 84.211 114 9 3 1324 1437 597479775 597479879 7.380000e-18 102.0
27 TraesCS2B01G342300 chr4B 76.056 142 22 8 543 680 601383892 601383759 3.480000e-06 63.9
28 TraesCS2B01G342300 chr4A 96.970 33 1 0 543 575 683869979 683869947 5.830000e-04 56.5


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 TraesCS2B01G342300 chr2B 488193436 488197610 4174 True 7710.00 7710 100.000000 1 4175 1 chr2B.!!$R1 4174
1 TraesCS2B01G342300 chr2D 414956651 414960214 3563 True 1015.75 1705 90.974750 887 4175 4 chr2D.!!$R1 3288
2 TraesCS2B01G342300 chr2D 416390016 416392351 2335 True 831.00 979 87.074333 1835 4068 3 chr2D.!!$R2 2233
3 TraesCS2B01G342300 chr2D 416396945 416398867 1922 True 559.10 1520 91.163500 1 1838 4 chr2D.!!$R3 1837
4 TraesCS2B01G342300 chr2A 582634222 582637210 2988 True 837.25 1502 90.071500 266 3182 4 chr2A.!!$R5 2916
5 TraesCS2B01G342300 chr2A 581942707 581945920 3213 True 798.25 946 88.381500 1426 4175 4 chr2A.!!$R4 2749

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
711 963 0.471617 TTCCGGTTTGACCCCGTTAA 59.528 50.0 0.00 0.0 43.98 2.01 F
1118 1418 0.325933 CACACATCCCTTGCTCCTCA 59.674 55.0 0.00 0.0 0.00 3.86 F
1344 1660 0.461693 GCCTCATCTTCGAGCTGCTT 60.462 55.0 2.53 0.0 0.00 3.91 F
1884 2216 0.464554 GCCTGTGCTTCCCTGGATAC 60.465 60.0 0.00 0.0 33.53 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 2197 0.464554 GTATCCAGGGAAGCACAGGC 60.465 60.0 0.00 0.0 41.61 4.85 R
1965 2304 0.955428 GCCCATTCAGTGCGAAGTGA 60.955 55.0 0.00 0.0 36.95 3.41 R
2684 3644 1.022735 GCTGCTGTTCCATCATCAGG 58.977 55.0 0.00 0.0 33.75 3.86 R
3744 4970 0.108662 AGATTGCGATCTGTGCGTCA 60.109 50.0 16.02 0.0 41.09 4.35 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
57 58 4.082125 CTCTCTTGTGGGCATAAAAACCT 58.918 43.478 0.00 0.00 0.00 3.50
59 60 5.826643 TCTCTTGTGGGCATAAAAACCTAT 58.173 37.500 0.00 0.00 0.00 2.57
88 89 9.632807 TCGAACCAATACCAAATTAAAATGAAG 57.367 29.630 0.00 0.00 0.00 3.02
91 92 9.500785 AACCAATACCAAATTAAAATGAAGTGG 57.499 29.630 9.21 9.21 0.00 4.00
98 99 8.987890 ACCAAATTAAAATGAAGTGGATTTTCG 58.012 29.630 0.00 0.00 35.25 3.46
99 100 8.442384 CCAAATTAAAATGAAGTGGATTTTCGG 58.558 33.333 0.00 0.00 35.25 4.30
124 125 4.242475 TGTTAGTTCTGCATCTGGTTACG 58.758 43.478 0.00 0.00 0.00 3.18
139 140 4.861210 TGGTTACGCAAATTTGGTTGTAG 58.139 39.130 19.47 0.00 0.00 2.74
140 141 4.579340 TGGTTACGCAAATTTGGTTGTAGA 59.421 37.500 19.47 0.00 0.00 2.59
141 142 5.241949 TGGTTACGCAAATTTGGTTGTAGAT 59.758 36.000 19.47 0.00 0.00 1.98
142 143 5.798434 GGTTACGCAAATTTGGTTGTAGATC 59.202 40.000 19.47 0.00 0.00 2.75
143 144 6.349033 GGTTACGCAAATTTGGTTGTAGATCT 60.349 38.462 19.47 0.00 0.00 2.75
144 145 5.705609 ACGCAAATTTGGTTGTAGATCTT 57.294 34.783 19.47 0.00 0.00 2.40
145 146 5.460646 ACGCAAATTTGGTTGTAGATCTTG 58.539 37.500 19.47 0.00 0.00 3.02
146 147 4.324402 CGCAAATTTGGTTGTAGATCTTGC 59.676 41.667 19.47 0.00 34.69 4.01
147 148 5.229423 GCAAATTTGGTTGTAGATCTTGCA 58.771 37.500 19.47 0.00 37.26 4.08
148 149 5.695816 GCAAATTTGGTTGTAGATCTTGCAA 59.304 36.000 19.47 4.38 37.26 4.08
149 150 6.346838 GCAAATTTGGTTGTAGATCTTGCAAC 60.347 38.462 23.53 23.53 41.02 4.17
155 156 5.438761 GTTGTAGATCTTGCAACCAAGTT 57.561 39.130 22.15 0.00 46.74 2.66
156 157 5.831997 GTTGTAGATCTTGCAACCAAGTTT 58.168 37.500 22.15 0.00 46.74 2.66
157 158 6.273071 GTTGTAGATCTTGCAACCAAGTTTT 58.727 36.000 22.15 0.00 46.74 2.43
158 159 7.422399 GTTGTAGATCTTGCAACCAAGTTTTA 58.578 34.615 22.15 0.00 46.74 1.52
159 160 6.966021 TGTAGATCTTGCAACCAAGTTTTAC 58.034 36.000 0.00 6.01 46.74 2.01
160 161 6.770785 TGTAGATCTTGCAACCAAGTTTTACT 59.229 34.615 0.00 0.00 46.74 2.24
161 162 7.934665 TGTAGATCTTGCAACCAAGTTTTACTA 59.065 33.333 0.00 0.00 46.74 1.82
162 163 7.817418 AGATCTTGCAACCAAGTTTTACTAA 57.183 32.000 0.00 0.00 46.74 2.24
163 164 8.409358 AGATCTTGCAACCAAGTTTTACTAAT 57.591 30.769 0.00 0.00 46.74 1.73
164 165 8.860088 AGATCTTGCAACCAAGTTTTACTAATT 58.140 29.630 0.00 0.00 46.74 1.40
165 166 9.129209 GATCTTGCAACCAAGTTTTACTAATTC 57.871 33.333 0.00 0.00 46.74 2.17
166 167 7.430441 TCTTGCAACCAAGTTTTACTAATTCC 58.570 34.615 0.00 0.00 46.74 3.01
167 168 6.716934 TGCAACCAAGTTTTACTAATTCCA 57.283 33.333 0.00 0.00 0.00 3.53
168 169 6.508777 TGCAACCAAGTTTTACTAATTCCAC 58.491 36.000 0.00 0.00 0.00 4.02
169 170 5.924254 GCAACCAAGTTTTACTAATTCCACC 59.076 40.000 0.00 0.00 0.00 4.61
170 171 6.239204 GCAACCAAGTTTTACTAATTCCACCT 60.239 38.462 0.00 0.00 0.00 4.00
171 172 7.685884 GCAACCAAGTTTTACTAATTCCACCTT 60.686 37.037 0.00 0.00 0.00 3.50
172 173 7.284919 ACCAAGTTTTACTAATTCCACCTTG 57.715 36.000 0.00 0.00 0.00 3.61
173 174 6.837048 ACCAAGTTTTACTAATTCCACCTTGT 59.163 34.615 0.00 0.00 0.00 3.16
174 175 7.343574 ACCAAGTTTTACTAATTCCACCTTGTT 59.656 33.333 0.00 0.00 0.00 2.83
175 176 8.201464 CCAAGTTTTACTAATTCCACCTTGTTT 58.799 33.333 0.00 0.00 0.00 2.83
176 177 9.594478 CAAGTTTTACTAATTCCACCTTGTTTT 57.406 29.630 0.00 0.00 0.00 2.43
177 178 9.594478 AAGTTTTACTAATTCCACCTTGTTTTG 57.406 29.630 0.00 0.00 0.00 2.44
178 179 8.755028 AGTTTTACTAATTCCACCTTGTTTTGT 58.245 29.630 0.00 0.00 0.00 2.83
179 180 9.373603 GTTTTACTAATTCCACCTTGTTTTGTT 57.626 29.630 0.00 0.00 0.00 2.83
180 181 9.945904 TTTTACTAATTCCACCTTGTTTTGTTT 57.054 25.926 0.00 0.00 0.00 2.83
181 182 8.934507 TTACTAATTCCACCTTGTTTTGTTTG 57.065 30.769 0.00 0.00 0.00 2.93
182 183 5.815222 ACTAATTCCACCTTGTTTTGTTTGC 59.185 36.000 0.00 0.00 0.00 3.68
183 184 3.685139 TTCCACCTTGTTTTGTTTGCA 57.315 38.095 0.00 0.00 0.00 4.08
184 185 3.685139 TCCACCTTGTTTTGTTTGCAA 57.315 38.095 0.00 0.00 0.00 4.08
185 186 3.330267 TCCACCTTGTTTTGTTTGCAAC 58.670 40.909 0.00 0.00 33.82 4.17
186 187 3.007398 TCCACCTTGTTTTGTTTGCAACT 59.993 39.130 0.00 0.00 33.82 3.16
187 188 3.124976 CCACCTTGTTTTGTTTGCAACTG 59.875 43.478 0.00 0.00 33.82 3.16
194 195 5.983475 TGTTTTGTTTGCAACTGAGTTTTG 58.017 33.333 0.00 0.00 33.82 2.44
210 211 8.345565 ACTGAGTTTTGCAATAAAGAGTACTTG 58.654 33.333 0.00 0.00 36.39 3.16
211 212 8.445275 TGAGTTTTGCAATAAAGAGTACTTGA 57.555 30.769 0.00 0.00 36.39 3.02
212 213 9.066892 TGAGTTTTGCAATAAAGAGTACTTGAT 57.933 29.630 0.00 0.00 36.39 2.57
213 214 9.334693 GAGTTTTGCAATAAAGAGTACTTGATG 57.665 33.333 0.00 0.00 36.39 3.07
214 215 8.850156 AGTTTTGCAATAAAGAGTACTTGATGT 58.150 29.630 0.00 0.00 36.39 3.06
215 216 9.118236 GTTTTGCAATAAAGAGTACTTGATGTC 57.882 33.333 0.00 0.00 36.39 3.06
220 221 9.677567 GCAATAAAGAGTACTTGATGTCAAAAA 57.322 29.630 0.00 0.00 36.39 1.94
333 547 4.480476 CCCCCAAATCCCAGCCCC 62.480 72.222 0.00 0.00 0.00 5.80
334 548 4.480476 CCCCAAATCCCAGCCCCC 62.480 72.222 0.00 0.00 0.00 5.40
335 549 3.358824 CCCAAATCCCAGCCCCCT 61.359 66.667 0.00 0.00 0.00 4.79
336 550 2.012210 CCCAAATCCCAGCCCCCTA 61.012 63.158 0.00 0.00 0.00 3.53
337 551 1.230212 CCAAATCCCAGCCCCCTAC 59.770 63.158 0.00 0.00 0.00 3.18
338 552 1.152963 CAAATCCCAGCCCCCTACG 60.153 63.158 0.00 0.00 0.00 3.51
339 553 2.383601 AAATCCCAGCCCCCTACGG 61.384 63.158 0.00 0.00 0.00 4.02
447 683 0.838554 TTCATCACCTTCCCGACCCA 60.839 55.000 0.00 0.00 0.00 4.51
662 914 1.365633 CTCAGCGCTCCAGGTATCC 59.634 63.158 7.13 0.00 0.00 2.59
688 940 0.913924 TGAATCCCGTCTAAACCCCC 59.086 55.000 0.00 0.00 0.00 5.40
711 963 0.471617 TTCCGGTTTGACCCCGTTAA 59.528 50.000 0.00 0.00 43.98 2.01
722 1001 5.024785 TGACCCCGTTAAAAGCAATTTTT 57.975 34.783 0.00 0.00 41.68 1.94
779 1065 2.759114 CCTGGCTGCAGGAAGGAA 59.241 61.111 17.12 0.00 45.00 3.36
780 1066 1.378250 CCTGGCTGCAGGAAGGAAG 60.378 63.158 17.12 0.00 45.00 3.46
781 1067 1.378250 CTGGCTGCAGGAAGGAAGG 60.378 63.158 17.12 0.00 0.00 3.46
782 1068 1.845627 CTGGCTGCAGGAAGGAAGGA 61.846 60.000 17.12 0.00 0.00 3.36
867 1159 2.364448 AGTTCGCTCCCCTCCCTC 60.364 66.667 0.00 0.00 0.00 4.30
868 1160 3.471806 GTTCGCTCCCCTCCCTCC 61.472 72.222 0.00 0.00 0.00 4.30
914 1206 3.945304 GAATCGTGAACCCGCCCGT 62.945 63.158 0.00 0.00 0.00 5.28
918 1210 4.754667 GTGAACCCGCCCGTCTCC 62.755 72.222 0.00 0.00 0.00 3.71
995 1294 3.522731 CAGGACTCCCGAGGCTCG 61.523 72.222 29.16 29.16 40.07 5.03
1118 1418 0.325933 CACACATCCCTTGCTCCTCA 59.674 55.000 0.00 0.00 0.00 3.86
1135 1435 3.465403 ATCCTCCTGCTCGCGCTT 61.465 61.111 5.56 0.00 36.97 4.68
1159 1475 2.675603 GCCGTTTCTGTTTGGTTTGGTT 60.676 45.455 0.00 0.00 0.00 3.67
1212 1528 1.276421 CCACCAGGTTCGTCTGATTCT 59.724 52.381 0.00 0.00 36.93 2.40
1218 1534 2.234908 AGGTTCGTCTGATTCTCCCTTG 59.765 50.000 0.00 0.00 0.00 3.61
1265 1581 1.520787 GGGCGTTCCCGTACTGATG 60.521 63.158 0.00 0.00 43.94 3.07
1314 1630 0.608640 AAGTTCTCGTTGATCCCGCT 59.391 50.000 0.00 0.00 0.00 5.52
1344 1660 0.461693 GCCTCATCTTCGAGCTGCTT 60.462 55.000 2.53 0.00 0.00 3.91
1470 1795 3.515502 ACTCTGTGAATAGCTGGCAACTA 59.484 43.478 0.00 0.00 37.61 2.24
1497 1822 6.086222 CCCTATAAATTTCGATTCATTGCCG 58.914 40.000 0.00 0.00 0.00 5.69
1661 1992 5.437060 TCCAAGTGGATTTTAGCCATAGAC 58.563 41.667 0.00 0.00 39.78 2.59
1729 2061 2.783135 GAGCACTCTGGGACAATTGAA 58.217 47.619 13.59 0.00 38.70 2.69
1821 2153 3.202818 TGTCCTGTGCCATATCCAGATTT 59.797 43.478 0.00 0.00 0.00 2.17
1830 2162 3.332919 CATATCCAGATTTCCCTGCTCG 58.667 50.000 0.00 0.00 32.97 5.03
1833 2165 1.066143 TCCAGATTTCCCTGCTCGTTC 60.066 52.381 0.00 0.00 32.97 3.95
1845 2177 1.207089 TGCTCGTTCCCTTCAATCGAT 59.793 47.619 0.00 0.00 0.00 3.59
1865 2197 4.438145 CGATCTCCAGTCGATTAGTTTTCG 59.562 45.833 0.00 0.00 41.40 3.46
1884 2216 0.464554 GCCTGTGCTTCCCTGGATAC 60.465 60.000 0.00 0.00 33.53 2.24
1891 2223 1.618837 GCTTCCCTGGATACGATAGCA 59.381 52.381 0.00 0.00 42.67 3.49
1921 2257 5.042593 GCACAAGTCATCTCAGTCTCATAG 58.957 45.833 0.00 0.00 0.00 2.23
1939 2278 9.383519 GTCTCATAGTTTGATATTTCTGTTCCA 57.616 33.333 0.00 0.00 32.72 3.53
1943 2282 6.683974 AGTTTGATATTTCTGTTCCATCGG 57.316 37.500 0.00 0.00 0.00 4.18
1944 2283 6.180472 AGTTTGATATTTCTGTTCCATCGGT 58.820 36.000 0.00 0.00 0.00 4.69
1945 2284 7.335627 AGTTTGATATTTCTGTTCCATCGGTA 58.664 34.615 0.00 0.00 0.00 4.02
1946 2285 7.993183 AGTTTGATATTTCTGTTCCATCGGTAT 59.007 33.333 0.00 0.00 0.00 2.73
1947 2286 8.621286 GTTTGATATTTCTGTTCCATCGGTATT 58.379 33.333 0.00 0.00 0.00 1.89
1952 2291 7.645058 ATTTCTGTTCCATCGGTATTCATTT 57.355 32.000 0.00 0.00 0.00 2.32
1955 2294 9.839817 TTTCTGTTCCATCGGTATTCATTTATA 57.160 29.630 0.00 0.00 0.00 0.98
1957 2296 9.435688 TCTGTTCCATCGGTATTCATTTATATG 57.564 33.333 0.00 0.00 0.00 1.78
1978 2317 3.119029 TGATGATGATCACTTCGCACTGA 60.119 43.478 0.00 0.00 33.40 3.41
1979 2318 3.317603 TGATGATCACTTCGCACTGAA 57.682 42.857 0.00 0.00 34.74 3.02
1980 2319 3.865446 TGATGATCACTTCGCACTGAAT 58.135 40.909 0.00 0.00 35.63 2.57
1981 2320 3.619929 TGATGATCACTTCGCACTGAATG 59.380 43.478 0.00 0.00 35.63 2.67
1982 2321 2.349590 TGATCACTTCGCACTGAATGG 58.650 47.619 0.00 0.00 35.63 3.16
1983 2322 1.667724 GATCACTTCGCACTGAATGGG 59.332 52.381 0.00 0.00 42.62 4.00
1984 2323 0.955428 TCACTTCGCACTGAATGGGC 60.955 55.000 0.00 0.00 42.86 5.36
1985 2324 1.675641 ACTTCGCACTGAATGGGCC 60.676 57.895 0.00 0.00 43.53 5.80
1986 2325 1.377725 CTTCGCACTGAATGGGCCT 60.378 57.895 4.53 0.00 43.53 5.19
1997 2336 4.463891 ACTGAATGGGCCTGTGAATAAAAG 59.536 41.667 4.53 0.00 0.00 2.27
2030 2371 1.131126 CTGACGCTTGATTTCGGCATT 59.869 47.619 0.00 0.00 43.37 3.56
2031 2372 2.351418 CTGACGCTTGATTTCGGCATTA 59.649 45.455 0.00 0.00 43.37 1.90
2124 2465 8.912988 TCCCTTGGAATTATGCTTAAATAGTTG 58.087 33.333 0.00 0.00 0.00 3.16
2146 2487 8.856490 GTTGATGTTTGTTATTTCAACTGAGT 57.144 30.769 6.80 0.00 41.69 3.41
2169 2511 5.048713 GTGTTGACTACCTTTGCAGCTTTAT 60.049 40.000 0.00 0.00 0.00 1.40
2229 2994 2.368548 AGTTATCACCGCATATGAGCCA 59.631 45.455 6.97 0.00 0.00 4.75
2376 3207 8.240883 CAGCTAGTACTGTTCGTTTCTTAATT 57.759 34.615 5.39 0.00 32.78 1.40
2378 3209 8.923683 AGCTAGTACTGTTCGTTTCTTAATTTC 58.076 33.333 5.39 0.00 0.00 2.17
2379 3210 8.923683 GCTAGTACTGTTCGTTTCTTAATTTCT 58.076 33.333 5.39 0.00 0.00 2.52
2582 3531 1.500474 AAGATAGGCCTGCTGTGCTA 58.500 50.000 17.99 0.00 0.00 3.49
2600 3549 7.809806 GCTGTGCTAAAATATTTCAGTCAGTTT 59.190 33.333 18.14 0.38 0.00 2.66
2657 3610 3.945981 TCGTAGTAGTGTCAATGGCAA 57.054 42.857 0.00 0.00 0.00 4.52
2712 3731 2.653726 TGGAACAGCAGCTTTCTTCAA 58.346 42.857 13.63 0.00 0.00 2.69
2718 3737 4.625028 ACAGCAGCTTTCTTCAATTTTCC 58.375 39.130 0.00 0.00 0.00 3.13
2763 3782 5.503927 TGCTATAATAGTACTACGGGGAGG 58.496 45.833 4.31 0.00 0.00 4.30
2785 3804 5.535043 GCCAAAATGCCAAAACTAGATTG 57.465 39.130 0.00 1.24 0.00 2.67
2833 3862 5.556355 AACAGTGTAATGATGCATCACAG 57.444 39.130 30.92 17.15 40.03 3.66
3001 4033 0.744874 CAGCTGCCCCTTGAATGATG 59.255 55.000 0.00 0.00 0.00 3.07
3008 4040 3.006752 TGCCCCTTGAATGATGTGTTTTC 59.993 43.478 0.00 0.00 0.00 2.29
3111 4143 1.926511 GCTTGCCAATGTCGGAGGTG 61.927 60.000 0.00 0.00 0.00 4.00
3135 4167 4.454678 TCAGACTTGCAGTGATGAACTTT 58.545 39.130 0.00 0.00 36.83 2.66
3286 4453 9.670719 CAAAAACTAGTCTCTGAATTTTCCTTC 57.329 33.333 0.00 0.00 0.00 3.46
3345 4522 5.023533 AGCGTATGTAGTGTCATCCAAAT 57.976 39.130 0.00 0.00 0.00 2.32
3382 4559 9.604626 GAAGTTCAATATATCATGTTAGCTTGC 57.395 33.333 0.00 0.00 0.00 4.01
3591 4810 6.012337 TGGTCTGCAATATTTATCCCTCAA 57.988 37.500 0.00 0.00 0.00 3.02
3624 4843 3.627395 TTCTTGACCACTCACACACTT 57.373 42.857 0.00 0.00 0.00 3.16
3685 4908 3.868661 CCATGATGTCCGACGAAAATACA 59.131 43.478 0.00 0.00 0.00 2.29
3744 4970 1.922447 TGCCATCATCCACCTAGGTTT 59.078 47.619 13.15 0.00 39.02 3.27
3746 4972 2.092429 GCCATCATCCACCTAGGTTTGA 60.092 50.000 13.15 15.72 39.02 2.69
3750 4976 0.981183 ATCCACCTAGGTTTGACGCA 59.019 50.000 13.15 0.00 39.02 5.24
3880 5107 6.008960 TCCCTTAAATTTTGCAATTGCCATT 58.991 32.000 26.94 18.33 41.18 3.16
3938 5167 6.970043 TCGTGTATGGTTCAAACTTTTCTTTG 59.030 34.615 0.00 0.00 33.14 2.77
3955 5184 5.970317 TCTTTGTGAGTTGATCATGCATT 57.030 34.783 0.00 0.00 40.92 3.56
3975 5206 9.754382 ATGCATTTTTAGATAGCAATAAAGGTG 57.246 29.630 0.00 0.00 38.85 4.00
3986 5217 5.981174 AGCAATAAAGGTGAAAATGATGGG 58.019 37.500 0.00 0.00 0.00 4.00
3994 5225 3.195610 GGTGAAAATGATGGGAAGGTTCC 59.804 47.826 0.00 0.00 46.82 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.957395 CCCACAAGAGAGCGCAACAT 60.957 55.000 11.47 0.00 0.00 2.71
28 29 1.597854 CCCACAAGAGAGCGCAACA 60.598 57.895 11.47 0.00 0.00 3.33
59 60 9.579768 CATTTTAATTTGGTATTGGTTCGATGA 57.420 29.630 0.00 0.00 0.00 2.92
88 89 5.912955 CAGAACTAACAAACCGAAAATCCAC 59.087 40.000 0.00 0.00 0.00 4.02
91 92 5.516090 TGCAGAACTAACAAACCGAAAATC 58.484 37.500 0.00 0.00 0.00 2.17
98 99 3.821033 ACCAGATGCAGAACTAACAAACC 59.179 43.478 0.00 0.00 0.00 3.27
99 100 5.438761 AACCAGATGCAGAACTAACAAAC 57.561 39.130 0.00 0.00 0.00 2.93
124 125 5.229423 TGCAAGATCTACAACCAAATTTGC 58.771 37.500 12.92 0.00 38.95 3.68
139 140 9.129209 GAATTAGTAAAACTTGGTTGCAAGATC 57.871 33.333 0.00 0.00 36.16 2.75
140 141 8.088365 GGAATTAGTAAAACTTGGTTGCAAGAT 58.912 33.333 0.00 0.00 36.16 2.40
141 142 7.068839 TGGAATTAGTAAAACTTGGTTGCAAGA 59.931 33.333 0.00 0.00 36.16 3.02
142 143 7.169140 GTGGAATTAGTAAAACTTGGTTGCAAG 59.831 37.037 0.00 0.00 38.11 4.01
143 144 6.981559 GTGGAATTAGTAAAACTTGGTTGCAA 59.018 34.615 0.00 0.00 0.00 4.08
144 145 6.461788 GGTGGAATTAGTAAAACTTGGTTGCA 60.462 38.462 0.00 0.00 0.00 4.08
145 146 5.924254 GGTGGAATTAGTAAAACTTGGTTGC 59.076 40.000 0.00 0.00 0.00 4.17
146 147 7.284919 AGGTGGAATTAGTAAAACTTGGTTG 57.715 36.000 0.00 0.00 0.00 3.77
147 148 7.343574 ACAAGGTGGAATTAGTAAAACTTGGTT 59.656 33.333 12.51 0.00 37.64 3.67
148 149 6.837048 ACAAGGTGGAATTAGTAAAACTTGGT 59.163 34.615 12.51 0.04 37.64 3.67
149 150 7.284919 ACAAGGTGGAATTAGTAAAACTTGG 57.715 36.000 12.51 0.00 37.64 3.61
150 151 9.594478 AAAACAAGGTGGAATTAGTAAAACTTG 57.406 29.630 8.06 8.06 38.85 3.16
151 152 9.594478 CAAAACAAGGTGGAATTAGTAAAACTT 57.406 29.630 0.00 0.00 0.00 2.66
152 153 8.755028 ACAAAACAAGGTGGAATTAGTAAAACT 58.245 29.630 0.00 0.00 0.00 2.66
153 154 8.936070 ACAAAACAAGGTGGAATTAGTAAAAC 57.064 30.769 0.00 0.00 0.00 2.43
154 155 9.945904 AAACAAAACAAGGTGGAATTAGTAAAA 57.054 25.926 0.00 0.00 0.00 1.52
155 156 9.372369 CAAACAAAACAAGGTGGAATTAGTAAA 57.628 29.630 0.00 0.00 0.00 2.01
156 157 7.492994 GCAAACAAAACAAGGTGGAATTAGTAA 59.507 33.333 0.00 0.00 0.00 2.24
157 158 6.981559 GCAAACAAAACAAGGTGGAATTAGTA 59.018 34.615 0.00 0.00 0.00 1.82
158 159 5.815222 GCAAACAAAACAAGGTGGAATTAGT 59.185 36.000 0.00 0.00 0.00 2.24
159 160 5.814705 TGCAAACAAAACAAGGTGGAATTAG 59.185 36.000 0.00 0.00 0.00 1.73
160 161 5.734720 TGCAAACAAAACAAGGTGGAATTA 58.265 33.333 0.00 0.00 0.00 1.40
161 162 4.583871 TGCAAACAAAACAAGGTGGAATT 58.416 34.783 0.00 0.00 0.00 2.17
162 163 4.213564 TGCAAACAAAACAAGGTGGAAT 57.786 36.364 0.00 0.00 0.00 3.01
163 164 3.685139 TGCAAACAAAACAAGGTGGAA 57.315 38.095 0.00 0.00 0.00 3.53
164 165 3.685139 TTGCAAACAAAACAAGGTGGA 57.315 38.095 0.00 0.00 31.21 4.02
182 183 8.345565 AGTACTCTTTATTGCAAAACTCAGTTG 58.654 33.333 1.71 0.00 0.00 3.16
183 184 8.451908 AGTACTCTTTATTGCAAAACTCAGTT 57.548 30.769 1.71 0.00 0.00 3.16
184 185 8.345565 CAAGTACTCTTTATTGCAAAACTCAGT 58.654 33.333 1.71 6.11 0.00 3.41
185 186 8.559536 TCAAGTACTCTTTATTGCAAAACTCAG 58.440 33.333 1.71 0.00 0.00 3.35
186 187 8.445275 TCAAGTACTCTTTATTGCAAAACTCA 57.555 30.769 1.71 0.00 0.00 3.41
187 188 9.334693 CATCAAGTACTCTTTATTGCAAAACTC 57.665 33.333 1.71 0.00 0.00 3.01
194 195 9.677567 TTTTTGACATCAAGTACTCTTTATTGC 57.322 29.630 0.00 0.00 37.15 3.56
220 221 3.688673 TGGTTAACGAACGAGGTGTTTTT 59.311 39.130 0.14 0.00 42.09 1.94
221 222 3.269178 TGGTTAACGAACGAGGTGTTTT 58.731 40.909 0.14 0.00 42.09 2.43
222 223 2.903798 TGGTTAACGAACGAGGTGTTT 58.096 42.857 0.14 0.00 42.09 2.83
223 224 2.600470 TGGTTAACGAACGAGGTGTT 57.400 45.000 0.14 0.00 45.61 3.32
320 534 1.152963 CGTAGGGGGCTGGGATTTG 60.153 63.158 0.00 0.00 0.00 2.32
334 548 4.157120 CCGTGGAAGGGGCCGTAG 62.157 72.222 0.00 0.00 38.48 3.51
362 591 0.589223 GTAGGCCTCGAGATCAGTCG 59.411 60.000 9.68 0.00 41.51 4.18
447 683 0.260523 GAGTAGGGCAGAGGAGACCT 59.739 60.000 0.00 0.00 36.03 3.85
662 914 1.403814 TAGACGGGATTCAGAGGCTG 58.596 55.000 0.00 0.00 0.00 4.85
741 1020 3.554752 GGCAGCCAGAGCATGTTTAAAAA 60.555 43.478 6.55 0.00 43.56 1.94
746 1025 1.076192 AGGCAGCCAGAGCATGTTT 59.924 52.632 15.80 0.00 43.56 2.83
747 1026 1.677966 CAGGCAGCCAGAGCATGTT 60.678 57.895 15.80 0.00 43.56 2.71
914 1206 2.683933 GTTGGGGAGAGCCGGAGA 60.684 66.667 5.05 0.00 33.83 3.71
919 1211 3.732849 CAGGGGTTGGGGAGAGCC 61.733 72.222 0.00 0.00 0.00 4.70
920 1212 2.936032 ACAGGGGTTGGGGAGAGC 60.936 66.667 0.00 0.00 0.00 4.09
929 1227 2.778899 CTGGGAGAAGACAGGGGTT 58.221 57.895 0.00 0.00 0.00 4.11
935 1233 0.906756 CTGGAGCCTGGGAGAAGACA 60.907 60.000 0.00 0.00 0.00 3.41
995 1294 3.798954 CTCTCGCCGGCCATCTTCC 62.799 68.421 23.46 0.00 0.00 3.46
1135 1435 1.666054 AACCAAACAGAAACGGCGTA 58.334 45.000 15.20 0.00 0.00 4.42
1159 1475 2.349590 CGAATGTTGCTCACATCCTGA 58.650 47.619 2.97 0.00 46.23 3.86
1218 1534 1.370051 GCTCCAAACGAAACCGTGC 60.370 57.895 0.00 0.00 40.55 5.34
1265 1581 1.152963 AGCAGAACCACACACACCC 60.153 57.895 0.00 0.00 0.00 4.61
1267 1583 1.356624 GCAGCAGAACCACACACAC 59.643 57.895 0.00 0.00 0.00 3.82
1314 1630 0.393132 AGATGAGGCTCTCGTCACGA 60.393 55.000 16.72 0.00 45.82 4.35
1470 1795 6.294731 GCAATGAATCGAAATTTATAGGGCCT 60.295 38.462 12.58 12.58 0.00 5.19
1497 1822 1.194772 GCCAAGCACGAGAACTGTAAC 59.805 52.381 0.00 0.00 0.00 2.50
1661 1992 5.431765 AGATAAGTTACCAACATGCCTCTG 58.568 41.667 0.00 0.00 0.00 3.35
1729 2061 2.716017 GGAGCGCAGACCAGCTAGT 61.716 63.158 11.47 0.00 44.69 2.57
1821 2153 1.125093 TTGAAGGGAACGAGCAGGGA 61.125 55.000 0.00 0.00 0.00 4.20
1830 2162 3.118592 ACTGGAGATCGATTGAAGGGAAC 60.119 47.826 0.00 0.00 0.00 3.62
1833 2165 2.544694 CGACTGGAGATCGATTGAAGGG 60.545 54.545 0.00 0.00 42.25 3.95
1845 2177 3.508762 GCGAAAACTAATCGACTGGAGA 58.491 45.455 0.00 0.00 42.76 3.71
1865 2197 0.464554 GTATCCAGGGAAGCACAGGC 60.465 60.000 0.00 0.00 41.61 4.85
1891 2223 5.555017 ACTGAGATGACTTGTGCAACTAAT 58.445 37.500 0.00 0.00 38.04 1.73
1947 2286 8.876790 GCGAAGTGATCATCATCATATAAATGA 58.123 33.333 0.00 4.24 46.01 2.57
1952 2291 6.810182 CAGTGCGAAGTGATCATCATCATATA 59.190 38.462 0.00 0.00 41.26 0.86
1955 2294 3.808174 CAGTGCGAAGTGATCATCATCAT 59.192 43.478 0.00 0.00 41.26 2.45
1956 2295 3.119029 TCAGTGCGAAGTGATCATCATCA 60.119 43.478 0.00 0.00 36.62 3.07
1957 2296 3.451526 TCAGTGCGAAGTGATCATCATC 58.548 45.455 0.00 0.00 0.00 2.92
1964 2303 1.742761 CCCATTCAGTGCGAAGTGAT 58.257 50.000 0.56 0.00 36.95 3.06
1965 2304 0.955428 GCCCATTCAGTGCGAAGTGA 60.955 55.000 0.00 0.00 36.95 3.41
1978 2317 3.790126 ACCTTTTATTCACAGGCCCATT 58.210 40.909 0.00 0.00 0.00 3.16
1979 2318 3.473113 ACCTTTTATTCACAGGCCCAT 57.527 42.857 0.00 0.00 0.00 4.00
1980 2319 2.990740 ACCTTTTATTCACAGGCCCA 57.009 45.000 0.00 0.00 0.00 5.36
1981 2320 3.964411 AGTACCTTTTATTCACAGGCCC 58.036 45.455 0.00 0.00 0.00 5.80
1982 2321 6.095021 CCTTAAGTACCTTTTATTCACAGGCC 59.905 42.308 0.00 0.00 0.00 5.19
1983 2322 6.882678 TCCTTAAGTACCTTTTATTCACAGGC 59.117 38.462 0.97 0.00 0.00 4.85
1984 2323 9.110502 GATCCTTAAGTACCTTTTATTCACAGG 57.889 37.037 0.97 0.00 0.00 4.00
1985 2324 9.892130 AGATCCTTAAGTACCTTTTATTCACAG 57.108 33.333 0.97 0.00 0.00 3.66
1986 2325 9.667107 CAGATCCTTAAGTACCTTTTATTCACA 57.333 33.333 0.97 0.00 0.00 3.58
1997 2336 4.113354 CAAGCGTCAGATCCTTAAGTACC 58.887 47.826 0.97 0.00 0.00 3.34
2012 2352 3.242739 ACATAATGCCGAAATCAAGCGTC 60.243 43.478 0.00 0.00 0.00 5.19
2030 2371 5.249780 TCCCTTTTGAAACAGCCTACATA 57.750 39.130 0.00 0.00 0.00 2.29
2031 2372 4.082125 CTCCCTTTTGAAACAGCCTACAT 58.918 43.478 0.00 0.00 0.00 2.29
2124 2465 8.856490 AACACTCAGTTGAAATAACAAACATC 57.144 30.769 0.00 0.00 39.49 3.06
2146 2487 2.638480 AGCTGCAAAGGTAGTCAACA 57.362 45.000 1.02 0.00 0.00 3.33
2151 2492 4.321974 GCCAAATAAAGCTGCAAAGGTAGT 60.322 41.667 1.02 0.00 0.00 2.73
2169 2511 4.130857 TCTTGAGACGTATGTTTGCCAAA 58.869 39.130 0.00 0.00 0.00 3.28
2229 2994 5.409826 GTGCTCAGCTTACTTTATCAACAGT 59.590 40.000 0.00 0.00 0.00 3.55
2351 3123 7.813852 ATTAAGAAACGAACAGTACTAGCTG 57.186 36.000 0.00 0.00 41.92 4.24
2564 3513 1.500474 TTAGCACAGCAGGCCTATCT 58.500 50.000 3.98 2.17 0.00 1.98
2605 3554 5.547258 CGTATTCAACGTGCCTAGCTTAGG 61.547 50.000 0.00 0.00 46.72 2.69
2683 3643 1.407851 GCTGCTGTTCCATCATCAGGA 60.408 52.381 0.00 0.00 33.75 3.86
2684 3644 1.022735 GCTGCTGTTCCATCATCAGG 58.977 55.000 0.00 0.00 33.75 3.86
2688 3648 3.083122 AGAAAGCTGCTGTTCCATCAT 57.917 42.857 1.35 0.00 0.00 2.45
2694 3654 5.176406 GGAAAATTGAAGAAAGCTGCTGTTC 59.824 40.000 1.35 9.43 0.00 3.18
2700 3660 5.205759 AGGTGGAAAATTGAAGAAAGCTG 57.794 39.130 0.00 0.00 0.00 4.24
2704 3664 5.393866 AGCCTAGGTGGAAAATTGAAGAAA 58.606 37.500 11.31 0.00 38.35 2.52
2706 3666 4.657814 AGCCTAGGTGGAAAATTGAAGA 57.342 40.909 11.31 0.00 38.35 2.87
2712 3731 4.475016 ACATGACTAGCCTAGGTGGAAAAT 59.525 41.667 11.31 0.00 38.35 1.82
2718 3737 4.471904 TTCAACATGACTAGCCTAGGTG 57.528 45.455 11.31 0.84 0.00 4.00
2763 3782 4.996758 ACAATCTAGTTTTGGCATTTTGGC 59.003 37.500 11.20 0.00 44.03 4.52
2785 3804 7.031372 TCATCTGCATTTCAGCTGAAAAATAC 58.969 34.615 37.81 27.32 42.87 1.89
2817 3838 6.624352 ACATTACCTGTGATGCATCATTAC 57.376 37.500 30.89 19.05 39.30 1.89
2893 3922 5.290386 AGCTAGTCGTTAACTTGGATATGC 58.710 41.667 3.71 0.00 39.55 3.14
3001 4033 9.313118 ACTGAAATAAAAATGACAGGAAAACAC 57.687 29.630 0.00 0.00 0.00 3.32
3008 4040 8.359642 TCAAAGGACTGAAATAAAAATGACAGG 58.640 33.333 0.00 0.00 0.00 4.00
3286 4453 8.678199 ACTTTCAGGAAAAGAAAAACTACTCTG 58.322 33.333 4.64 0.00 46.18 3.35
3345 4522 8.553153 TGATATATTGAACTTCAACCAGGGTTA 58.447 33.333 6.35 0.00 39.45 2.85
3442 4624 2.445905 ACTCAATGCCCCATGATGAGAT 59.554 45.455 11.72 0.00 39.85 2.75
3563 4779 5.354234 GGGATAAATATTGCAGACCATACGG 59.646 44.000 0.00 0.00 38.77 4.02
3591 4810 8.717717 TGAGTGGTCAAGAATATATGGAAATCT 58.282 33.333 0.00 0.00 0.00 2.40
3624 4843 3.890756 CCTATATGCTTGGTGCCAATCAA 59.109 43.478 10.91 2.97 42.00 2.57
3674 4897 5.584442 ACTTTTGTGGGTTGTATTTTCGTC 58.416 37.500 0.00 0.00 0.00 4.20
3744 4970 0.108662 AGATTGCGATCTGTGCGTCA 60.109 50.000 16.02 0.00 41.09 4.35
3746 4972 0.174389 AGAGATTGCGATCTGTGCGT 59.826 50.000 21.56 0.00 42.66 5.24
3750 4976 5.752472 CACAAGATAAGAGATTGCGATCTGT 59.248 40.000 21.56 14.64 42.66 3.41
3938 5167 9.661187 CTATCTAAAAATGCATGATCAACTCAC 57.339 33.333 0.00 0.00 36.48 3.51
3986 5217 3.818773 TCGTTCTTGGATTTGGAACCTTC 59.181 43.478 0.00 0.00 36.85 3.46
3994 5225 6.672147 AGAATTCAACTCGTTCTTGGATTTG 58.328 36.000 8.44 0.00 28.54 2.32
3995 5226 6.884280 AGAATTCAACTCGTTCTTGGATTT 57.116 33.333 8.44 0.00 28.54 2.17
3996 5227 6.934645 TGTAGAATTCAACTCGTTCTTGGATT 59.065 34.615 8.44 0.00 34.33 3.01
3997 5228 6.464222 TGTAGAATTCAACTCGTTCTTGGAT 58.536 36.000 8.44 0.00 34.33 3.41
3998 5229 5.849510 TGTAGAATTCAACTCGTTCTTGGA 58.150 37.500 8.44 0.00 34.33 3.53
3999 5230 6.368791 TGATGTAGAATTCAACTCGTTCTTGG 59.631 38.462 8.44 0.00 34.33 3.61
4000 5231 7.329471 TCTGATGTAGAATTCAACTCGTTCTTG 59.671 37.037 8.44 0.00 34.33 3.02


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

AutoCloner maintained by Alex Coulton.