Multiple sequence alignment - TraesCS1D01G295700

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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 TraesCS1D01G295700 chr1D 100.000 4541 0 0 1 4541 394182340 394186880 0.000000e+00 8386
1 TraesCS1D01G295700 chr1D 83.854 384 37 18 1200 1564 394183483 394183860 4.350000e-90 342
2 TraesCS1D01G295700 chr1D 83.854 384 37 17 1144 1521 394183539 394183903 4.350000e-90 342
3 TraesCS1D01G295700 chr1B 93.956 2217 79 26 1144 3327 527880122 527877928 0.000000e+00 3301
4 TraesCS1D01G295700 chr1B 86.246 1585 105 45 55 1564 527881292 527879746 0.000000e+00 1615
5 TraesCS1D01G295700 chr1B 85.677 384 33 13 1199 1566 527880163 527879786 7.130000e-103 385
6 TraesCS1D01G295700 chr1B 85.390 308 21 11 1233 1521 527879999 527879697 9.550000e-77 298
7 TraesCS1D01G295700 chr1B 87.259 259 19 9 1316 1566 527880084 527879832 2.670000e-72 283
8 TraesCS1D01G295700 chr5D 98.839 1206 13 1 3336 4541 508120426 508121630 0.000000e+00 2148
9 TraesCS1D01G295700 chr5D 97.010 836 23 2 3337 4171 377963999 377963165 0.000000e+00 1404
10 TraesCS1D01G295700 chr6D 98.309 1183 17 2 3333 4514 291713210 291712030 0.000000e+00 2071
11 TraesCS1D01G295700 chr6D 97.971 1183 23 1 3332 4514 443347473 443348654 0.000000e+00 2050
12 TraesCS1D01G295700 chr3D 97.587 1202 28 1 3340 4541 110747321 110746121 0.000000e+00 2058
13 TraesCS1D01G295700 chr2A 96.432 1205 39 4 3340 4541 12091997 12090794 0.000000e+00 1984
14 TraesCS1D01G295700 chr6B 91.098 820 71 2 3615 4433 558694936 558694118 0.000000e+00 1109
15 TraesCS1D01G295700 chr6B 90.942 817 72 2 3615 4430 558860535 558859720 0.000000e+00 1098
16 TraesCS1D01G295700 chr6B 93.772 289 16 2 3333 3620 558778406 558778119 2.510000e-117 433
17 TraesCS1D01G295700 chr6B 93.640 283 16 2 3339 3620 558861141 558860860 5.430000e-114 422
18 TraesCS1D01G295700 chr6B 89.815 108 11 0 4433 4540 558694071 558693964 6.130000e-29 139
19 TraesCS1D01G295700 chr5B 90.667 825 69 7 3615 4438 339996754 339995937 0.000000e+00 1090
20 TraesCS1D01G295700 chr6A 93.972 282 15 2 3339 3620 453568485 453568206 4.200000e-115 425
21 TraesCS1D01G295700 chr4A 90.833 120 9 2 4423 4540 680328490 680328609 4.700000e-35 159
22 TraesCS1D01G295700 chr5A 90.000 120 10 2 4423 4540 416177220 416177101 2.190000e-33 154


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 TraesCS1D01G295700 chr1D 394182340 394186880 4540 False 3023.333333 8386 89.2360 1 4541 3 chr1D.!!$F1 4540
1 TraesCS1D01G295700 chr1B 527877928 527881292 3364 True 1176.400000 3301 87.7056 55 3327 5 chr1B.!!$R1 3272
2 TraesCS1D01G295700 chr5D 508120426 508121630 1204 False 2148.000000 2148 98.8390 3336 4541 1 chr5D.!!$F1 1205
3 TraesCS1D01G295700 chr5D 377963165 377963999 834 True 1404.000000 1404 97.0100 3337 4171 1 chr5D.!!$R1 834
4 TraesCS1D01G295700 chr6D 291712030 291713210 1180 True 2071.000000 2071 98.3090 3333 4514 1 chr6D.!!$R1 1181
5 TraesCS1D01G295700 chr6D 443347473 443348654 1181 False 2050.000000 2050 97.9710 3332 4514 1 chr6D.!!$F1 1182
6 TraesCS1D01G295700 chr3D 110746121 110747321 1200 True 2058.000000 2058 97.5870 3340 4541 1 chr3D.!!$R1 1201
7 TraesCS1D01G295700 chr2A 12090794 12091997 1203 True 1984.000000 1984 96.4320 3340 4541 1 chr2A.!!$R1 1201
8 TraesCS1D01G295700 chr6B 558859720 558861141 1421 True 760.000000 1098 92.2910 3339 4430 2 chr6B.!!$R3 1091
9 TraesCS1D01G295700 chr6B 558693964 558694936 972 True 624.000000 1109 90.4565 3615 4540 2 chr6B.!!$R2 925
10 TraesCS1D01G295700 chr5B 339995937 339996754 817 True 1090.000000 1090 90.6670 3615 4438 1 chr5B.!!$R1 823

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
112 113 0.036858 GGAAGTGGAGGAGAGTGCAC 60.037 60.0 9.4 9.4 38.97 4.57 F
363 369 0.179004 AACACATGGACTTTGGCGGA 60.179 50.0 0.0 0.0 0.00 5.54 F
1713 1859 0.170561 ATCGTCTCCGTTTCTCCGTG 59.829 55.0 0.0 0.0 35.01 4.94 F
2112 2267 0.179089 CAAGGATCGAGGGCAGTGAG 60.179 60.0 0.0 0.0 0.00 3.51 F
2676 2837 0.248743 TCGACGACAAGTTTCGCACT 60.249 50.0 0.0 0.0 43.06 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1160 1223 0.107831 GCTCTCGCTCCTCCTAGAGA 59.892 60.000 0.00 0.0 38.16 3.10 R
1928 2083 0.109342 CAGCCTGTTCTCCAGTGGTT 59.891 55.000 9.54 0.0 39.74 3.67 R
3001 3162 0.396435 CACCCACTCACACTGGCTTA 59.604 55.000 0.00 0.0 0.00 3.09 R
3051 3212 1.218316 CTACTGGTGCCTCCCGTTC 59.782 63.158 0.00 0.0 35.35 3.95 R
4444 4992 1.101635 CCGTCGTCATCAGGGAGCTA 61.102 60.000 0.00 0.0 0.00 3.32 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
44 45 3.499737 CACGCATCGGGAAGGCAC 61.500 66.667 0.00 0.00 28.17 5.01
45 46 4.015406 ACGCATCGGGAAGGCACA 62.015 61.111 0.00 0.00 0.00 4.57
46 47 2.514592 CGCATCGGGAAGGCACAT 60.515 61.111 0.00 0.00 0.00 3.21
47 48 2.537560 CGCATCGGGAAGGCACATC 61.538 63.158 0.00 0.00 0.00 3.06
48 49 2.189499 GCATCGGGAAGGCACATCC 61.189 63.158 0.00 0.00 46.91 3.51
53 54 3.530067 GGAAGGCACATCCATGGC 58.470 61.111 6.96 0.00 46.84 4.40
74 75 0.759060 GAGGAGAAGGAGGAGGAGGC 60.759 65.000 0.00 0.00 0.00 4.70
79 80 0.985490 GAAGGAGGAGGAGGCCATGT 60.985 60.000 5.01 0.00 0.00 3.21
80 81 0.985490 AAGGAGGAGGAGGCCATGTC 60.985 60.000 5.01 0.00 0.00 3.06
83 84 1.074926 AGGAGGAGGCCATGTCGAT 60.075 57.895 5.01 0.00 0.00 3.59
112 113 0.036858 GGAAGTGGAGGAGAGTGCAC 60.037 60.000 9.40 9.40 38.97 4.57
114 115 0.827925 AAGTGGAGGAGAGTGCACGA 60.828 55.000 12.01 0.00 43.15 4.35
115 116 1.080434 GTGGAGGAGAGTGCACGAC 60.080 63.158 12.01 10.03 0.00 4.34
121 122 1.293498 GAGAGTGCACGACCATGGT 59.707 57.895 19.89 19.89 0.00 3.55
143 144 1.645704 CGAGCGTCGAGGGAGAAAGA 61.646 60.000 7.31 0.00 43.74 2.52
146 147 0.244178 GCGTCGAGGGAGAAAGAAGT 59.756 55.000 7.31 0.00 0.00 3.01
147 148 1.983972 CGTCGAGGGAGAAAGAAGTG 58.016 55.000 0.00 0.00 0.00 3.16
148 149 1.715993 GTCGAGGGAGAAAGAAGTGC 58.284 55.000 0.00 0.00 0.00 4.40
149 150 1.000955 GTCGAGGGAGAAAGAAGTGCA 59.999 52.381 0.00 0.00 0.00 4.57
185 189 1.319541 TCGGGAAGAGAGGATTAGCG 58.680 55.000 0.00 0.00 0.00 4.26
208 212 4.877773 AGAGCAGGAAGAAGATAAGAGGA 58.122 43.478 0.00 0.00 0.00 3.71
212 216 4.551671 CAGGAAGAAGATAAGAGGAGGGA 58.448 47.826 0.00 0.00 0.00 4.20
265 269 2.551912 CCTTGTCGTTGGTGGGTGC 61.552 63.158 0.00 0.00 0.00 5.01
284 288 2.407616 CGTGGCGTATGAGAGCGA 59.592 61.111 0.00 0.00 0.00 4.93
287 293 0.664767 GTGGCGTATGAGAGCGATCC 60.665 60.000 0.00 0.00 0.00 3.36
290 296 0.999228 GCGTATGAGAGCGATCCACG 60.999 60.000 0.00 3.68 45.66 4.94
311 317 1.343506 GACCGACGCAAAGTTCGTAT 58.656 50.000 0.00 0.00 40.59 3.06
312 318 1.058695 GACCGACGCAAAGTTCGTATG 59.941 52.381 0.00 0.00 40.59 2.39
363 369 0.179004 AACACATGGACTTTGGCGGA 60.179 50.000 0.00 0.00 0.00 5.54
364 370 0.179004 ACACATGGACTTTGGCGGAA 60.179 50.000 0.00 0.00 0.00 4.30
440 446 1.645710 ATCTTTCTCCCGTGTGTCCT 58.354 50.000 0.00 0.00 0.00 3.85
451 457 2.135933 CGTGTGTCCTGAGGAAAAGAC 58.864 52.381 0.96 2.55 31.38 3.01
453 459 1.070134 TGTGTCCTGAGGAAAAGACGG 59.930 52.381 0.96 0.00 31.38 4.79
457 463 2.358247 TGAGGAAAAGACGGCCGC 60.358 61.111 28.58 18.62 0.00 6.53
506 512 2.513204 CAGAGGCCGCTGATGTGG 60.513 66.667 30.69 2.35 46.17 4.17
512 518 2.573869 CCGCTGATGTGGTCGTCT 59.426 61.111 0.00 0.00 38.95 4.18
517 523 1.073216 CTGATGTGGTCGTCTCGTGC 61.073 60.000 0.00 0.00 0.00 5.34
670 698 1.734465 CGTCCAGGCAAGATTCTGTTC 59.266 52.381 0.00 0.00 0.00 3.18
710 738 5.105716 TCGAGTCTCCGATTCATTTCTTCTT 60.106 40.000 0.00 0.00 33.14 2.52
728 761 4.307032 TCTTCCCCTCTTGATTTTCCTG 57.693 45.455 0.00 0.00 0.00 3.86
735 768 4.588528 CCCTCTTGATTTTCCTGTTTTGGA 59.411 41.667 0.00 0.00 0.00 3.53
736 769 5.246883 CCCTCTTGATTTTCCTGTTTTGGAT 59.753 40.000 0.00 0.00 35.83 3.41
789 834 4.104383 AGAAGGGAAAGCAAGTGATTGA 57.896 40.909 0.00 0.00 0.00 2.57
793 838 3.571401 AGGGAAAGCAAGTGATTGAACAG 59.429 43.478 0.00 0.00 0.00 3.16
809 854 8.849168 TGATTGAACAGTTGTCTCATTAATTGT 58.151 29.630 0.00 0.00 0.00 2.71
810 855 9.121517 GATTGAACAGTTGTCTCATTAATTGTG 57.878 33.333 0.00 0.00 28.97 3.33
811 856 7.800155 TGAACAGTTGTCTCATTAATTGTGA 57.200 32.000 0.00 0.00 28.97 3.58
812 857 8.394971 TGAACAGTTGTCTCATTAATTGTGAT 57.605 30.769 0.00 0.00 31.03 3.06
813 858 8.849168 TGAACAGTTGTCTCATTAATTGTGATT 58.151 29.630 0.00 0.00 31.03 2.57
816 861 9.725019 ACAGTTGTCTCATTAATTGTGATTAGA 57.275 29.630 0.00 0.00 31.03 2.10
817 862 9.979270 CAGTTGTCTCATTAATTGTGATTAGAC 57.021 33.333 0.00 0.00 31.92 2.59
818 863 8.873830 AGTTGTCTCATTAATTGTGATTAGACG 58.126 33.333 0.00 0.00 33.08 4.18
819 864 7.770801 TGTCTCATTAATTGTGATTAGACGG 57.229 36.000 0.00 0.00 33.08 4.79
820 865 6.257849 TGTCTCATTAATTGTGATTAGACGGC 59.742 38.462 0.00 0.00 33.08 5.68
821 866 5.462068 TCTCATTAATTGTGATTAGACGGCG 59.538 40.000 4.80 4.80 0.00 6.46
822 867 3.936902 TTAATTGTGATTAGACGGCGC 57.063 42.857 6.90 0.00 0.00 6.53
823 868 2.024176 AATTGTGATTAGACGGCGCT 57.976 45.000 6.90 8.04 0.00 5.92
824 869 2.024176 ATTGTGATTAGACGGCGCTT 57.976 45.000 6.90 0.00 0.00 4.68
825 870 2.658373 TTGTGATTAGACGGCGCTTA 57.342 45.000 6.90 0.00 0.00 3.09
826 871 1.917273 TGTGATTAGACGGCGCTTAC 58.083 50.000 6.90 0.00 0.00 2.34
827 872 1.202817 TGTGATTAGACGGCGCTTACA 59.797 47.619 6.90 6.57 0.00 2.41
828 873 2.264813 GTGATTAGACGGCGCTTACAA 58.735 47.619 6.90 0.00 0.00 2.41
829 874 2.281762 GTGATTAGACGGCGCTTACAAG 59.718 50.000 6.90 0.00 0.00 3.16
830 875 2.164827 TGATTAGACGGCGCTTACAAGA 59.835 45.455 6.90 0.00 0.00 3.02
831 876 2.273370 TTAGACGGCGCTTACAAGAG 57.727 50.000 6.90 0.00 0.00 2.85
832 877 0.454600 TAGACGGCGCTTACAAGAGG 59.545 55.000 6.90 0.00 0.00 3.69
833 878 1.080025 GACGGCGCTTACAAGAGGT 60.080 57.895 6.90 0.00 0.00 3.85
834 879 1.352156 GACGGCGCTTACAAGAGGTG 61.352 60.000 6.90 0.00 0.00 4.00
835 880 2.100631 CGGCGCTTACAAGAGGTGG 61.101 63.158 7.64 0.00 0.00 4.61
836 881 1.003718 GGCGCTTACAAGAGGTGGT 60.004 57.895 7.64 0.00 0.00 4.16
837 882 0.605589 GGCGCTTACAAGAGGTGGTT 60.606 55.000 7.64 0.00 0.00 3.67
838 883 0.517316 GCGCTTACAAGAGGTGGTTG 59.483 55.000 0.00 0.00 0.00 3.77
862 907 2.355412 GCAACCGACATTAACCCTACCT 60.355 50.000 0.00 0.00 0.00 3.08
928 977 3.119779 AGAGAAGTCCAGTTCGAATCGAC 60.120 47.826 4.25 7.57 34.89 4.20
950 999 1.280998 GAATTCGTTTCCCTCCCCTCA 59.719 52.381 0.00 0.00 0.00 3.86
952 1001 0.765135 TTCGTTTCCCTCCCCTCACA 60.765 55.000 0.00 0.00 0.00 3.58
1014 1077 6.659668 CCGTCTCTTCCCTATATATTCTGACA 59.340 42.308 0.00 0.00 0.00 3.58
1131 1194 3.426615 TGTGAGTCTTCCTCCTCTCTTC 58.573 50.000 0.00 0.00 39.65 2.87
1132 1195 3.075283 TGTGAGTCTTCCTCCTCTCTTCT 59.925 47.826 0.00 0.00 39.65 2.85
1133 1196 3.694566 GTGAGTCTTCCTCCTCTCTTCTC 59.305 52.174 0.00 0.00 39.65 2.87
1134 1197 3.591527 TGAGTCTTCCTCCTCTCTTCTCT 59.408 47.826 0.00 0.00 39.65 3.10
1135 1198 4.200092 GAGTCTTCCTCCTCTCTTCTCTC 58.800 52.174 0.00 0.00 33.79 3.20
1138 1201 5.016831 GTCTTCCTCCTCTCTTCTCTCTTT 58.983 45.833 0.00 0.00 0.00 2.52
1139 1202 5.125578 GTCTTCCTCCTCTCTTCTCTCTTTC 59.874 48.000 0.00 0.00 0.00 2.62
1140 1203 4.946160 TCCTCCTCTCTTCTCTCTTTCT 57.054 45.455 0.00 0.00 0.00 2.52
1141 1204 6.216662 TCTTCCTCCTCTCTTCTCTCTTTCTA 59.783 42.308 0.00 0.00 0.00 2.10
1142 1205 6.001449 TCCTCCTCTCTTCTCTCTTTCTAG 57.999 45.833 0.00 0.00 0.00 2.43
1143 1206 5.104109 TCCTCCTCTCTTCTCTCTTTCTAGG 60.104 48.000 0.00 0.00 0.00 3.02
1144 1207 5.104109 CCTCCTCTCTTCTCTCTTTCTAGGA 60.104 48.000 0.00 0.00 0.00 2.94
1145 1208 6.001449 TCCTCTCTTCTCTCTTTCTAGGAG 57.999 45.833 0.00 0.00 0.00 3.69
1146 1209 4.580580 CCTCTCTTCTCTCTTTCTAGGAGC 59.419 50.000 0.00 0.00 0.00 4.70
1147 1210 4.196193 TCTCTTCTCTCTTTCTAGGAGCG 58.804 47.826 0.00 0.00 0.00 5.03
1148 1211 3.945285 CTCTTCTCTCTTTCTAGGAGCGT 59.055 47.826 0.00 0.00 0.00 5.07
1149 1212 3.942748 TCTTCTCTCTTTCTAGGAGCGTC 59.057 47.826 0.00 0.00 0.00 5.19
1150 1213 3.637911 TCTCTCTTTCTAGGAGCGTCT 57.362 47.619 0.00 0.00 0.00 4.18
1151 1214 3.537580 TCTCTCTTTCTAGGAGCGTCTC 58.462 50.000 0.00 0.00 0.00 3.36
1152 1215 3.055021 TCTCTCTTTCTAGGAGCGTCTCA 60.055 47.826 8.71 0.00 31.08 3.27
1153 1216 3.882888 CTCTCTTTCTAGGAGCGTCTCAT 59.117 47.826 8.71 4.60 31.08 2.90
1154 1217 4.274147 TCTCTTTCTAGGAGCGTCTCATT 58.726 43.478 8.71 0.55 31.08 2.57
1155 1218 4.336993 TCTCTTTCTAGGAGCGTCTCATTC 59.663 45.833 8.71 0.00 31.08 2.67
1156 1219 3.065510 TCTTTCTAGGAGCGTCTCATTCG 59.934 47.826 8.71 0.00 31.08 3.34
1157 1220 2.327200 TCTAGGAGCGTCTCATTCGA 57.673 50.000 8.71 0.00 31.08 3.71
1158 1221 2.640184 TCTAGGAGCGTCTCATTCGAA 58.360 47.619 0.00 0.00 31.08 3.71
1159 1222 3.215151 TCTAGGAGCGTCTCATTCGAAT 58.785 45.455 4.39 4.39 31.08 3.34
1160 1223 2.969628 AGGAGCGTCTCATTCGAATT 57.030 45.000 8.21 0.00 31.08 2.17
1161 1224 2.815478 AGGAGCGTCTCATTCGAATTC 58.185 47.619 8.21 1.43 31.08 2.17
1162 1225 2.428890 AGGAGCGTCTCATTCGAATTCT 59.571 45.455 8.21 0.00 31.08 2.40
1163 1226 2.792116 GGAGCGTCTCATTCGAATTCTC 59.208 50.000 8.21 8.02 31.08 2.87
1164 1227 3.490078 GGAGCGTCTCATTCGAATTCTCT 60.490 47.826 8.21 0.19 31.08 3.10
1165 1228 4.261238 GGAGCGTCTCATTCGAATTCTCTA 60.261 45.833 8.21 0.00 31.08 2.43
1166 1229 4.854399 AGCGTCTCATTCGAATTCTCTAG 58.146 43.478 8.21 1.81 0.00 2.43
1167 1230 3.978217 GCGTCTCATTCGAATTCTCTAGG 59.022 47.826 8.21 0.00 0.00 3.02
1191 1254 1.063327 CGAGAGCGAGCGTCTCATT 59.937 57.895 17.79 1.76 40.56 2.57
1310 1400 6.791303 TCGAATTATTTGCTGACCCAAATAC 58.209 36.000 6.79 0.00 43.52 1.89
1315 1405 4.582701 TTTGCTGACCCAAATACTTGTG 57.417 40.909 0.00 0.00 30.28 3.33
1320 1410 1.130561 GACCCAAATACTTGTGCGAGC 59.869 52.381 0.00 0.00 0.00 5.03
1360 1454 7.701539 ATTTGCTGATCCAAATACTTGTACA 57.298 32.000 7.83 0.00 42.04 2.90
1369 1463 4.201910 CCAAATACTTGTACAAGCATCGGG 60.202 45.833 30.97 23.29 41.99 5.14
1375 1469 7.835805 TACTTGTACAAGCATCGGGTTCGAG 62.836 48.000 30.97 7.61 44.24 4.04
1457 1597 2.499197 TCCAAATACTTGTGCGAGCAA 58.501 42.857 0.00 0.00 0.00 3.91
1547 1693 4.895224 AATACTTCGTACGAGCATCTGA 57.105 40.909 18.64 0.38 0.00 3.27
1704 1850 0.813210 GTCCGGTAGATCGTCTCCGT 60.813 60.000 0.00 0.00 36.29 4.69
1713 1859 0.170561 ATCGTCTCCGTTTCTCCGTG 59.829 55.000 0.00 0.00 35.01 4.94
1738 1884 0.958091 CAAGAAATGGCACGGGTTCA 59.042 50.000 0.00 0.00 0.00 3.18
1740 1886 1.463674 AGAAATGGCACGGGTTCATC 58.536 50.000 0.00 0.00 0.00 2.92
1741 1887 1.173043 GAAATGGCACGGGTTCATCA 58.827 50.000 0.00 0.00 0.00 3.07
1751 1897 1.000717 CGGGTTCATCAAACAACACCC 60.001 52.381 0.00 0.00 39.81 4.61
1754 1900 2.296190 GGTTCATCAAACAACACCCTCC 59.704 50.000 0.00 0.00 39.81 4.30
1756 1902 3.140325 TCATCAAACAACACCCTCCTC 57.860 47.619 0.00 0.00 0.00 3.71
1757 1903 1.806542 CATCAAACAACACCCTCCTCG 59.193 52.381 0.00 0.00 0.00 4.63
1770 1922 0.814457 CTCCTCGTCTTCCTCCACTG 59.186 60.000 0.00 0.00 0.00 3.66
1779 1931 3.775654 CCTCCACTGCTCCCGTCC 61.776 72.222 0.00 0.00 0.00 4.79
1792 1944 2.125673 CGTCCTTGGTGCTACCGG 60.126 66.667 0.00 0.00 42.58 5.28
1897 2052 2.673368 GCAAGTTTCTGTGGATCCTACG 59.327 50.000 14.23 6.58 0.00 3.51
1927 2082 1.404391 GGTTCGTCCTCGCTCTTGATA 59.596 52.381 0.00 0.00 36.96 2.15
1928 2083 2.159282 GGTTCGTCCTCGCTCTTGATAA 60.159 50.000 0.00 0.00 36.96 1.75
1938 2093 2.932614 CGCTCTTGATAAACCACTGGAG 59.067 50.000 0.71 0.00 0.00 3.86
2005 2160 2.435938 CGACAATGGTGGACGGGG 60.436 66.667 0.00 0.00 0.00 5.73
2006 2161 2.949909 CGACAATGGTGGACGGGGA 61.950 63.158 0.00 0.00 0.00 4.81
2034 2189 1.418334 ATATCCGAGTTGAGGCAGCT 58.582 50.000 0.00 0.00 0.00 4.24
2040 2195 0.534412 GAGTTGAGGCAGCTGCTCTA 59.466 55.000 35.82 23.69 41.70 2.43
2101 2256 2.052766 GCGCGATTGCAAGGATCG 60.053 61.111 12.10 14.93 46.75 3.69
2108 2263 0.465097 ATTGCAAGGATCGAGGGCAG 60.465 55.000 4.94 0.00 35.68 4.85
2112 2267 0.179089 CAAGGATCGAGGGCAGTGAG 60.179 60.000 0.00 0.00 0.00 3.51
2115 2270 1.112113 GGATCGAGGGCAGTGAGTTA 58.888 55.000 0.00 0.00 0.00 2.24
2158 2313 2.046892 CCAAGGAGCACTGGACGG 60.047 66.667 0.00 0.00 0.00 4.79
2187 2342 3.415237 GGATCTCATCCGATCGCAG 57.585 57.895 10.32 2.46 40.52 5.18
2359 2520 0.471211 TGAGGAACACCCGGAGAACT 60.471 55.000 0.73 0.00 40.87 3.01
2451 2612 2.522836 ATCAAGATGAGCCTACGCAG 57.477 50.000 0.00 0.00 37.52 5.18
2590 2751 3.188667 GTCGGACCATGAGTTTTTCCTTC 59.811 47.826 0.00 0.00 0.00 3.46
2670 2831 2.557056 TGAGGATCTCGACGACAAGTTT 59.443 45.455 0.00 0.00 34.92 2.66
2676 2837 0.248743 TCGACGACAAGTTTCGCACT 60.249 50.000 0.00 0.00 43.06 4.40
2751 2912 4.301505 CGTGGTGACATGGGAAGG 57.698 61.111 0.00 0.00 46.14 3.46
2838 2999 1.810030 GCGCAAGTTCCCTCCTACG 60.810 63.158 0.30 0.00 41.68 3.51
2839 3000 1.153628 CGCAAGTTCCCTCCTACGG 60.154 63.158 0.00 0.00 0.00 4.02
2947 3108 2.627699 CCACTAGGGCACACAAAAACAT 59.372 45.455 0.00 0.00 0.00 2.71
2970 3131 2.748461 TAACGTGCTGCAAACTGTTC 57.252 45.000 2.77 0.00 0.00 3.18
3018 3179 0.321653 GGTAAGCCAGTGTGAGTGGG 60.322 60.000 0.00 0.00 39.13 4.61
3051 3212 6.039829 GCTCTAGTTAAGAAAATGGAATGGGG 59.960 42.308 0.00 0.00 32.46 4.96
3135 3297 3.378742 TCGTATGTTGTTTTGTTGCAGGT 59.621 39.130 0.00 0.00 0.00 4.00
3212 3374 5.549742 AACCTTTTCTGGATCAATGCAAA 57.450 34.783 0.00 0.00 0.00 3.68
3235 3397 1.757118 TCCAATTCGGGTTTGTTTGCA 59.243 42.857 0.00 0.00 34.36 4.08
3263 3425 2.930950 ACAGTTGGTGCTTGTACATGT 58.069 42.857 2.69 2.69 0.00 3.21
3276 3438 2.029380 TGTACATGTAACGCTCAGCTGT 60.029 45.455 14.67 0.00 0.00 4.40
3295 3457 4.500887 GCTGTGAATGAATAGGCATGCATT 60.501 41.667 21.36 11.64 42.27 3.56
3323 3485 6.817765 TTTTGGTTGGAGATGTCATAACTC 57.182 37.500 8.46 0.00 0.00 3.01
3327 3489 6.640518 TGGTTGGAGATGTCATAACTCTTAC 58.359 40.000 8.46 0.00 0.00 2.34
3328 3490 6.440647 TGGTTGGAGATGTCATAACTCTTACT 59.559 38.462 8.46 0.00 0.00 2.24
3329 3491 6.981559 GGTTGGAGATGTCATAACTCTTACTC 59.018 42.308 8.46 0.00 0.00 2.59
3330 3492 6.716934 TGGAGATGTCATAACTCTTACTCC 57.283 41.667 0.00 0.00 40.89 3.85
4291 4792 2.291540 CCCTCCTCTCCATAGCTCCTAG 60.292 59.091 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.928769 CGATGCGTGCCGACATGG 61.929 66.667 0.00 0.82 42.50 3.66
19 20 3.928769 CCGATGCGTGCCGACATG 61.929 66.667 0.00 0.00 35.78 3.21
23 24 4.812476 CTTCCCGATGCGTGCCGA 62.812 66.667 0.00 0.00 0.00 5.54
27 28 3.499737 GTGCCTTCCCGATGCGTG 61.500 66.667 0.00 0.00 0.00 5.34
28 29 3.329542 ATGTGCCTTCCCGATGCGT 62.330 57.895 0.00 0.00 0.00 5.24
29 30 2.514592 ATGTGCCTTCCCGATGCG 60.515 61.111 0.00 0.00 0.00 4.73
30 31 2.189499 GGATGTGCCTTCCCGATGC 61.189 63.158 0.00 0.00 0.00 3.91
31 32 0.179009 ATGGATGTGCCTTCCCGATG 60.179 55.000 0.00 0.00 37.63 3.84
32 33 0.179009 CATGGATGTGCCTTCCCGAT 60.179 55.000 0.00 0.00 37.63 4.18
33 34 1.224315 CATGGATGTGCCTTCCCGA 59.776 57.895 0.00 0.00 37.63 5.14
34 35 1.825191 CCATGGATGTGCCTTCCCG 60.825 63.158 5.56 0.00 37.63 5.14
35 36 2.129785 GCCATGGATGTGCCTTCCC 61.130 63.158 18.40 0.00 37.63 3.97
36 37 2.484062 CGCCATGGATGTGCCTTCC 61.484 63.158 18.40 0.00 37.63 3.46
37 38 2.484062 CCGCCATGGATGTGCCTTC 61.484 63.158 18.40 0.00 42.00 3.46
38 39 2.440796 CCGCCATGGATGTGCCTT 60.441 61.111 18.40 0.00 42.00 4.35
39 40 3.410628 TCCGCCATGGATGTGCCT 61.411 61.111 18.40 0.00 43.74 4.75
47 48 2.037620 CTCCTTCTCCTCCGCCATGG 62.038 65.000 7.63 7.63 40.09 3.66
48 49 1.445095 CTCCTTCTCCTCCGCCATG 59.555 63.158 0.00 0.00 0.00 3.66
49 50 1.764054 CCTCCTTCTCCTCCGCCAT 60.764 63.158 0.00 0.00 0.00 4.40
50 51 2.364317 CCTCCTTCTCCTCCGCCA 60.364 66.667 0.00 0.00 0.00 5.69
51 52 2.042843 TCCTCCTTCTCCTCCGCC 60.043 66.667 0.00 0.00 0.00 6.13
52 53 2.131067 CCTCCTCCTTCTCCTCCGC 61.131 68.421 0.00 0.00 0.00 5.54
53 54 0.467290 CTCCTCCTCCTTCTCCTCCG 60.467 65.000 0.00 0.00 0.00 4.63
61 62 0.985490 GACATGGCCTCCTCCTCCTT 60.985 60.000 3.32 0.00 0.00 3.36
74 75 1.509703 CCTGATGCTCATCGACATGG 58.490 55.000 0.00 0.20 40.63 3.66
79 80 1.137675 CACTTCCCTGATGCTCATCGA 59.862 52.381 5.51 0.00 40.63 3.59
80 81 1.579698 CACTTCCCTGATGCTCATCG 58.420 55.000 5.51 1.33 40.63 3.84
83 84 0.907486 CTCCACTTCCCTGATGCTCA 59.093 55.000 0.00 0.00 0.00 4.26
91 92 0.907230 GCACTCTCCTCCACTTCCCT 60.907 60.000 0.00 0.00 0.00 4.20
112 113 2.880879 CGCTCGTCACCATGGTCG 60.881 66.667 16.53 17.15 0.00 4.79
114 115 2.261671 GACGCTCGTCACCATGGT 59.738 61.111 13.00 13.00 44.02 3.55
115 116 2.880879 CGACGCTCGTCACCATGG 60.881 66.667 20.35 11.19 44.77 3.66
121 122 3.125573 CTCCCTCGACGCTCGTCA 61.126 66.667 20.35 8.34 44.77 4.35
136 137 2.157738 ACATGGCTGCACTTCTTTCTC 58.842 47.619 0.50 0.00 0.00 2.87
169 173 2.030274 GCTCTCGCTAATCCTCTCTTCC 60.030 54.545 0.00 0.00 0.00 3.46
171 175 2.622942 CTGCTCTCGCTAATCCTCTCTT 59.377 50.000 0.00 0.00 36.97 2.85
185 189 4.892934 TCCTCTTATCTTCTTCCTGCTCTC 59.107 45.833 0.00 0.00 0.00 3.20
190 194 4.551671 TCCCTCCTCTTATCTTCTTCCTG 58.448 47.826 0.00 0.00 0.00 3.86
192 196 4.346709 CCTTCCCTCCTCTTATCTTCTTCC 59.653 50.000 0.00 0.00 0.00 3.46
203 207 1.829261 CGCATATCCCTTCCCTCCTCT 60.829 57.143 0.00 0.00 0.00 3.69
208 212 1.418908 CCCACGCATATCCCTTCCCT 61.419 60.000 0.00 0.00 0.00 4.20
212 216 2.515901 GGCCCACGCATATCCCTT 59.484 61.111 0.00 0.00 36.38 3.95
242 246 4.555709 ACCAACGACAAGGCGCCA 62.556 61.111 31.54 0.00 33.86 5.69
249 253 2.897846 CGCACCCACCAACGACAA 60.898 61.111 0.00 0.00 0.00 3.18
307 313 0.249280 TACATCTGGCACGCCATACG 60.249 55.000 11.97 0.00 46.15 3.06
311 317 1.295357 CGTTTACATCTGGCACGCCA 61.295 55.000 10.95 10.95 45.02 5.69
312 318 1.296056 ACGTTTACATCTGGCACGCC 61.296 55.000 0.00 0.00 34.14 5.68
346 352 1.176527 ATTCCGCCAAAGTCCATGTG 58.823 50.000 0.00 0.00 0.00 3.21
363 369 8.700439 TTTAGCCCTCTAACTTTGTGTTAATT 57.300 30.769 0.00 0.00 40.24 1.40
364 370 8.879427 ATTTAGCCCTCTAACTTTGTGTTAAT 57.121 30.769 0.00 0.00 40.24 1.40
420 426 1.978580 AGGACACACGGGAGAAAGATT 59.021 47.619 0.00 0.00 0.00 2.40
440 446 2.358247 GCGGCCGTCTTTTCCTCA 60.358 61.111 28.70 0.00 0.00 3.86
543 549 2.890474 GAATCACACGCGCCCGAT 60.890 61.111 5.73 1.84 38.29 4.18
710 738 4.469469 AAACAGGAAAATCAAGAGGGGA 57.531 40.909 0.00 0.00 0.00 4.81
793 838 8.116753 CCGTCTAATCACAATTAATGAGACAAC 58.883 37.037 10.53 2.52 30.87 3.32
809 854 2.164827 TCTTGTAAGCGCCGTCTAATCA 59.835 45.455 2.29 0.00 0.00 2.57
810 855 2.789893 CTCTTGTAAGCGCCGTCTAATC 59.210 50.000 2.29 0.00 0.00 1.75
811 856 2.481449 CCTCTTGTAAGCGCCGTCTAAT 60.481 50.000 2.29 0.00 0.00 1.73
812 857 1.135199 CCTCTTGTAAGCGCCGTCTAA 60.135 52.381 2.29 0.00 0.00 2.10
813 858 0.454600 CCTCTTGTAAGCGCCGTCTA 59.545 55.000 2.29 0.00 0.00 2.59
814 859 1.215647 CCTCTTGTAAGCGCCGTCT 59.784 57.895 2.29 0.00 0.00 4.18
815 860 1.080025 ACCTCTTGTAAGCGCCGTC 60.080 57.895 2.29 0.00 0.00 4.79
816 861 1.374252 CACCTCTTGTAAGCGCCGT 60.374 57.895 2.29 0.00 0.00 5.68
817 862 2.100631 CCACCTCTTGTAAGCGCCG 61.101 63.158 2.29 0.00 0.00 6.46
818 863 0.605589 AACCACCTCTTGTAAGCGCC 60.606 55.000 2.29 0.00 0.00 6.53
819 864 0.517316 CAACCACCTCTTGTAAGCGC 59.483 55.000 0.00 0.00 0.00 5.92
820 865 0.517316 GCAACCACCTCTTGTAAGCG 59.483 55.000 0.00 0.00 0.00 4.68
821 866 0.881796 GGCAACCACCTCTTGTAAGC 59.118 55.000 0.00 0.00 0.00 3.09
822 867 1.156736 CGGCAACCACCTCTTGTAAG 58.843 55.000 0.00 0.00 0.00 2.34
823 868 0.887387 GCGGCAACCACCTCTTGTAA 60.887 55.000 0.00 0.00 0.00 2.41
824 869 1.302192 GCGGCAACCACCTCTTGTA 60.302 57.895 0.00 0.00 0.00 2.41
825 870 2.594592 GCGGCAACCACCTCTTGT 60.595 61.111 0.00 0.00 0.00 3.16
826 871 2.192861 TTGCGGCAACCACCTCTTG 61.193 57.895 12.11 0.00 0.00 3.02
827 872 2.193536 GTTGCGGCAACCACCTCTT 61.194 57.895 30.48 0.00 38.30 2.85
828 873 2.594592 GTTGCGGCAACCACCTCT 60.595 61.111 30.48 0.00 38.30 3.69
835 880 0.238817 TTAATGTCGGTTGCGGCAAC 59.761 50.000 32.15 32.15 42.89 4.17
836 881 0.238817 GTTAATGTCGGTTGCGGCAA 59.761 50.000 12.11 12.11 0.00 4.52
837 882 1.579084 GGTTAATGTCGGTTGCGGCA 61.579 55.000 0.00 0.00 0.00 5.69
838 883 1.135939 GGTTAATGTCGGTTGCGGC 59.864 57.895 0.00 0.00 0.00 6.53
928 977 0.746923 GGGGAGGGAAACGAATTCGG 60.747 60.000 29.79 13.35 44.95 4.30
987 1050 5.361285 CAGAATATATAGGGAAGAGACGGGG 59.639 48.000 0.00 0.00 0.00 5.73
994 1057 6.630131 TGGGTGTCAGAATATATAGGGAAGA 58.370 40.000 0.00 0.00 0.00 2.87
1096 1159 0.926155 CTCACATCATCAGCCGAACG 59.074 55.000 0.00 0.00 0.00 3.95
1099 1162 1.478631 AGACTCACATCATCAGCCGA 58.521 50.000 0.00 0.00 0.00 5.54
1131 1194 3.275143 TGAGACGCTCCTAGAAAGAGAG 58.725 50.000 0.00 0.00 37.22 3.20
1132 1195 3.351794 TGAGACGCTCCTAGAAAGAGA 57.648 47.619 0.00 0.00 32.86 3.10
1133 1196 4.606961 GAATGAGACGCTCCTAGAAAGAG 58.393 47.826 0.00 0.00 0.00 2.85
1134 1197 3.065510 CGAATGAGACGCTCCTAGAAAGA 59.934 47.826 0.00 0.00 0.00 2.52
1135 1198 3.065510 TCGAATGAGACGCTCCTAGAAAG 59.934 47.826 0.00 0.00 0.00 2.62
1138 1201 2.327200 TCGAATGAGACGCTCCTAGA 57.673 50.000 0.00 0.00 0.00 2.43
1139 1202 3.634568 ATTCGAATGAGACGCTCCTAG 57.365 47.619 10.50 0.00 0.00 3.02
1140 1203 3.632604 AGAATTCGAATGAGACGCTCCTA 59.367 43.478 12.25 0.00 0.00 2.94
1141 1204 2.428890 AGAATTCGAATGAGACGCTCCT 59.571 45.455 12.25 0.00 0.00 3.69
1142 1205 2.792116 GAGAATTCGAATGAGACGCTCC 59.208 50.000 12.25 0.00 0.00 4.70
1143 1206 3.701241 AGAGAATTCGAATGAGACGCTC 58.299 45.455 12.25 11.22 0.00 5.03
1144 1207 3.791973 AGAGAATTCGAATGAGACGCT 57.208 42.857 12.25 8.11 0.00 5.07
1145 1208 3.978217 CCTAGAGAATTCGAATGAGACGC 59.022 47.826 12.25 6.05 0.00 5.19
1146 1209 5.425577 TCCTAGAGAATTCGAATGAGACG 57.574 43.478 12.25 0.00 0.00 4.18
1147 1210 5.533154 TCCTCCTAGAGAATTCGAATGAGAC 59.467 44.000 12.25 4.30 0.00 3.36
1148 1211 5.696030 TCCTCCTAGAGAATTCGAATGAGA 58.304 41.667 12.25 0.80 0.00 3.27
1149 1212 5.564651 GCTCCTCCTAGAGAATTCGAATGAG 60.565 48.000 12.25 11.34 35.82 2.90
1150 1213 4.279671 GCTCCTCCTAGAGAATTCGAATGA 59.720 45.833 12.25 1.68 35.82 2.57
1151 1214 4.555262 GCTCCTCCTAGAGAATTCGAATG 58.445 47.826 12.25 0.00 35.82 2.67
1152 1215 3.254657 CGCTCCTCCTAGAGAATTCGAAT 59.745 47.826 4.39 4.39 35.82 3.34
1153 1216 2.619177 CGCTCCTCCTAGAGAATTCGAA 59.381 50.000 0.00 0.00 35.82 3.71
1154 1217 2.158798 TCGCTCCTCCTAGAGAATTCGA 60.159 50.000 0.00 0.00 35.82 3.71
1155 1218 2.222886 TCGCTCCTCCTAGAGAATTCG 58.777 52.381 0.00 0.00 35.82 3.34
1156 1219 3.482436 TCTCGCTCCTCCTAGAGAATTC 58.518 50.000 0.00 0.00 36.88 2.17
1157 1220 3.486383 CTCTCGCTCCTCCTAGAGAATT 58.514 50.000 0.00 0.00 39.00 2.17
1158 1221 2.814097 GCTCTCGCTCCTCCTAGAGAAT 60.814 54.545 0.00 0.00 39.00 2.40
1159 1222 1.476110 GCTCTCGCTCCTCCTAGAGAA 60.476 57.143 0.00 0.00 39.00 2.87
1160 1223 0.107831 GCTCTCGCTCCTCCTAGAGA 59.892 60.000 0.00 0.00 38.16 3.10
1161 1224 1.227999 CGCTCTCGCTCCTCCTAGAG 61.228 65.000 0.00 0.00 38.79 2.43
1162 1225 1.227704 CGCTCTCGCTCCTCCTAGA 60.228 63.158 0.00 0.00 0.00 2.43
1163 1226 1.227704 TCGCTCTCGCTCCTCCTAG 60.228 63.158 0.00 0.00 35.26 3.02
1164 1227 1.227704 CTCGCTCTCGCTCCTCCTA 60.228 63.158 0.00 0.00 35.26 2.94
1165 1228 2.515991 CTCGCTCTCGCTCCTCCT 60.516 66.667 0.00 0.00 35.26 3.69
1166 1229 4.264638 GCTCGCTCTCGCTCCTCC 62.265 72.222 0.00 0.00 35.26 4.30
1167 1230 4.605967 CGCTCGCTCTCGCTCCTC 62.606 72.222 0.00 0.00 35.26 3.71
1310 1400 1.091771 AATCCGATGGCTCGCACAAG 61.092 55.000 1.56 0.00 43.66 3.16
1315 1405 0.946221 ATTCGAATCCGATGGCTCGC 60.946 55.000 4.39 0.00 45.10 5.03
1320 1410 5.049474 TCAGCAAATAATTCGAATCCGATGG 60.049 40.000 11.83 1.55 45.10 3.51
1336 1426 7.701539 TGTACAAGTATTTGGATCAGCAAAT 57.298 32.000 12.64 12.64 38.66 2.32
1337 1427 7.517614 TTGTACAAGTATTTGGATCAGCAAA 57.482 32.000 3.59 0.00 38.66 3.68
1341 1435 6.741992 TGCTTGTACAAGTATTTGGATCAG 57.258 37.500 30.90 7.61 40.45 2.90
1360 1454 2.754946 TAAACTCGAACCCGATGCTT 57.245 45.000 0.00 0.00 44.62 3.91
1369 1463 6.183360 TGGATCATCAGCAAATAAACTCGAAC 60.183 38.462 0.00 0.00 0.00 3.95
1375 1469 9.807649 AAGTATTTGGATCATCAGCAAATAAAC 57.192 29.630 12.71 7.14 29.12 2.01
1547 1693 9.674824 GATCAGAAATCAGCAAATAATTCGAAT 57.325 29.630 4.39 4.39 0.00 3.34
1662 1808 4.379243 AGGCGGGAGAGCACAACG 62.379 66.667 0.00 0.00 39.27 4.10
1704 1850 2.992124 TCTTGTTGACCACGGAGAAA 57.008 45.000 0.00 0.00 0.00 2.52
1713 1859 1.335872 CCGTGCCATTTCTTGTTGACC 60.336 52.381 0.00 0.00 0.00 4.02
1738 1884 1.420138 ACGAGGAGGGTGTTGTTTGAT 59.580 47.619 0.00 0.00 0.00 2.57
1740 1886 1.202651 AGACGAGGAGGGTGTTGTTTG 60.203 52.381 0.00 0.00 0.00 2.93
1741 1887 1.129058 AGACGAGGAGGGTGTTGTTT 58.871 50.000 0.00 0.00 0.00 2.83
1751 1897 0.814457 CAGTGGAGGAAGACGAGGAG 59.186 60.000 0.00 0.00 0.00 3.69
1754 1900 0.172352 GAGCAGTGGAGGAAGACGAG 59.828 60.000 0.00 0.00 0.00 4.18
1756 1902 1.216710 GGAGCAGTGGAGGAAGACG 59.783 63.158 0.00 0.00 0.00 4.18
1757 1903 1.599576 GGGAGCAGTGGAGGAAGAC 59.400 63.158 0.00 0.00 0.00 3.01
1770 1922 2.656069 TAGCACCAAGGACGGGAGC 61.656 63.158 0.00 0.00 41.60 4.70
1792 1944 1.220477 GAGGGTGCTCTGGAGAAGC 59.780 63.158 1.35 0.34 33.72 3.86
1927 2082 0.846693 AGCCTGTTCTCCAGTGGTTT 59.153 50.000 9.54 0.00 39.74 3.27
1928 2083 0.109342 CAGCCTGTTCTCCAGTGGTT 59.891 55.000 9.54 0.00 39.74 3.67
1944 2099 2.032178 GCCGGAGAATATGTTGAACAGC 59.968 50.000 5.05 0.00 0.00 4.40
2005 2160 4.733850 TCAACTCGGATATATCGTGCATC 58.266 43.478 6.64 0.00 0.00 3.91
2006 2161 4.380973 CCTCAACTCGGATATATCGTGCAT 60.381 45.833 6.64 0.00 0.00 3.96
2034 2189 1.381191 TGGCGACCCTGATAGAGCA 60.381 57.895 0.00 0.00 0.00 4.26
2040 2195 1.599047 CAGAACTGGCGACCCTGAT 59.401 57.895 0.00 0.00 34.43 2.90
2101 2256 1.474143 GCCAGATAACTCACTGCCCTC 60.474 57.143 0.00 0.00 33.40 4.30
2108 2263 3.012518 AGTGCAATGCCAGATAACTCAC 58.987 45.455 1.53 0.00 0.00 3.51
2112 2267 3.254166 CCCATAGTGCAATGCCAGATAAC 59.746 47.826 1.53 0.00 0.00 1.89
2115 2270 1.496001 TCCCATAGTGCAATGCCAGAT 59.504 47.619 1.53 0.00 0.00 2.90
2158 2313 2.502295 GATGAGATCCCAGTCAATGCC 58.498 52.381 0.00 0.00 0.00 4.40
2180 2335 4.670478 CGTGTATATCCAGACTCTGCGATC 60.670 50.000 11.28 0.00 0.00 3.69
2182 2337 2.548480 CGTGTATATCCAGACTCTGCGA 59.452 50.000 0.00 0.64 0.00 5.10
2187 2342 4.278669 ACCACATCGTGTATATCCAGACTC 59.721 45.833 0.00 0.00 0.00 3.36
2359 2520 2.422597 CAAATACCGCTGGACTGTCAA 58.577 47.619 10.38 0.00 0.00 3.18
2418 2579 5.121105 TCATCTTGATACTTGAGCACCATG 58.879 41.667 0.00 0.00 0.00 3.66
2451 2612 2.743928 CGCACAGAGGAAGTGGGC 60.744 66.667 0.00 0.00 41.86 5.36
2504 2665 2.035632 CATCCTCAGGGTACTCTGGAC 58.964 57.143 22.59 0.00 35.58 4.02
2590 2751 3.005472 CCAATGAATATGAGCTTGGCCTG 59.995 47.826 3.32 0.00 30.85 4.85
2676 2837 5.795772 GTCGTAGAAGAAAATGGACACTCCA 60.796 44.000 0.00 0.00 46.59 3.86
2838 2999 3.864789 ACATATCAGTGAATCCACCCC 57.135 47.619 0.00 0.00 44.22 4.95
2839 3000 4.576463 GTCAACATATCAGTGAATCCACCC 59.424 45.833 0.00 0.00 44.22 4.61
2937 3098 5.283717 GCAGCACGTTATCTATGTTTTTGTG 59.716 40.000 0.00 0.00 0.00 3.33
2938 3099 5.049060 TGCAGCACGTTATCTATGTTTTTGT 60.049 36.000 0.00 0.00 0.00 2.83
2939 3100 5.389778 TGCAGCACGTTATCTATGTTTTTG 58.610 37.500 0.00 0.00 0.00 2.44
2940 3101 5.621197 TGCAGCACGTTATCTATGTTTTT 57.379 34.783 0.00 0.00 0.00 1.94
2941 3102 5.621197 TTGCAGCACGTTATCTATGTTTT 57.379 34.783 0.00 0.00 0.00 2.43
2942 3103 5.181245 AGTTTGCAGCACGTTATCTATGTTT 59.819 36.000 0.00 0.00 0.00 2.83
2943 3104 4.695455 AGTTTGCAGCACGTTATCTATGTT 59.305 37.500 0.00 0.00 0.00 2.71
2947 3108 3.659786 ACAGTTTGCAGCACGTTATCTA 58.340 40.909 0.00 0.00 0.00 1.98
2970 3131 2.271800 CGGTCTTTTGCCTGCTAGTAG 58.728 52.381 0.00 0.00 0.00 2.57
3001 3162 0.396435 CACCCACTCACACTGGCTTA 59.604 55.000 0.00 0.00 0.00 3.09
3018 3179 5.924475 TTTCTTAACTAGAGCAGCAACAC 57.076 39.130 0.00 0.00 33.51 3.32
3051 3212 1.218316 CTACTGGTGCCTCCCGTTC 59.782 63.158 0.00 0.00 35.35 3.95
3067 3228 5.278266 CCAGCCAAAACTGTTTTTCGATCTA 60.278 40.000 15.41 0.00 35.83 1.98
3099 3260 3.849911 ACATACGAGGACACACATGAAG 58.150 45.455 0.00 0.00 0.00 3.02
3198 3360 4.524316 TTGGAAGTTTGCATTGATCCAG 57.476 40.909 10.50 0.00 38.14 3.86
3212 3374 3.739830 GCAAACAAACCCGAATTGGAAGT 60.740 43.478 0.00 0.00 42.00 3.01
3235 3397 2.687935 CAAGCACCAACTGTTACCAACT 59.312 45.455 0.00 0.00 0.00 3.16
3263 3425 2.741759 TCATTCACAGCTGAGCGTTA 57.258 45.000 23.35 0.00 0.00 3.18
3276 3438 5.601583 AACAATGCATGCCTATTCATTCA 57.398 34.783 16.68 0.00 29.47 2.57
3295 3457 8.519526 GTTATGACATCTCCAACCAAAATAACA 58.480 33.333 0.00 0.00 30.72 2.41
3327 3489 9.523168 GGGCATTCTACTAGTATATATAGGGAG 57.477 40.741 2.33 0.00 0.00 4.30
3328 3490 8.162085 CGGGCATTCTACTAGTATATATAGGGA 58.838 40.741 2.33 0.00 0.00 4.20
3329 3491 7.943447 ACGGGCATTCTACTAGTATATATAGGG 59.057 40.741 2.33 0.00 0.00 3.53
3330 3492 8.784994 CACGGGCATTCTACTAGTATATATAGG 58.215 40.741 2.33 0.00 0.00 2.57
3427 3589 6.992063 ATTGTGATCGTGCTATCTTTTCTT 57.008 33.333 0.00 0.00 0.00 2.52
4259 4760 1.766864 GAGGAGGGTTAGGAGGGCC 60.767 68.421 0.00 0.00 0.00 5.80
4291 4792 1.555075 TGAGCACCCACTGATAACCTC 59.445 52.381 0.00 0.00 0.00 3.85
4444 4992 1.101635 CCGTCGTCATCAGGGAGCTA 61.102 60.000 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.