Multiple sequence alignment - TraesCS6D01G243400

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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 TraesCS6D01G243400 chr6D 100.000 3562 0 0 1 3562 345388529 345392090 0.000000e+00 6578.0
1 TraesCS6D01G243400 chr6A 97.541 2196 48 3 1368 3562 486006046 486008236 0.000000e+00 3751.0
2 TraesCS6D01G243400 chr6A 86.864 1081 85 33 334 1362 486004641 486005716 0.000000e+00 1157.0
3 TraesCS6D01G243400 chr6A 89.423 312 19 8 1 306 486004337 486004640 7.220000e-102 381.0
4 TraesCS6D01G243400 chr6B 97.806 1641 27 3 1368 3004 521514610 521516245 0.000000e+00 2822.0
5 TraesCS6D01G243400 chr6B 88.294 1307 97 27 68 1346 521512954 521514232 0.000000e+00 1515.0
6 TraesCS6D01G243400 chr6B 93.774 530 28 2 3034 3562 521516246 521516771 0.000000e+00 791.0
7 TraesCS6D01G243400 chr3D 90.741 216 14 1 1666 1881 32190911 32190702 2.090000e-72 283.0
8 TraesCS6D01G243400 chr3D 85.714 210 24 1 1672 1881 535688248 535688451 2.150000e-52 217.0
9 TraesCS6D01G243400 chr7B 86.574 216 23 1 1666 1881 603666890 603666681 2.140000e-57 233.0
10 TraesCS6D01G243400 chr4A 87.500 88 10 1 2 89 175850082 175850168 2.260000e-17 100.0
11 TraesCS6D01G243400 chr7A 84.286 70 9 2 157 224 575701424 575701355 2.290000e-07 67.6


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 TraesCS6D01G243400 chr6D 345388529 345392090 3561 False 6578.000000 6578 100.000000 1 3562 1 chr6D.!!$F1 3561
1 TraesCS6D01G243400 chr6A 486004337 486008236 3899 False 1763.000000 3751 91.276000 1 3562 3 chr6A.!!$F1 3561
2 TraesCS6D01G243400 chr6B 521512954 521516771 3817 False 1709.333333 2822 93.291333 68 3562 3 chr6B.!!$F1 3494

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
65 66 0.168128 CCAGGCGTTCCGTTTCATTC 59.832 55.0 0.00 0.00 37.47 2.67 F
1158 1198 0.037419 CTGGTTCAAATTTGCCCCGG 60.037 55.0 13.54 14.97 0.00 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1269 1363 0.033894 ACCAACGGACCACCAAAGTT 60.034 50.000 0.0 0.0 35.59 2.66 R
2904 3368 1.534595 CCACTCACAGTGCAAAACAGC 60.535 52.381 0.0 0.0 44.63 4.40 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
43 44 4.636206 GGAGGCATACTCTTTTGTCGAAAT 59.364 41.667 0.00 0.00 45.83 2.17
50 51 4.324267 ACTCTTTTGTCGAAATACCCAGG 58.676 43.478 0.00 0.00 0.00 4.45
58 59 0.392060 GAAATACCCAGGCGTTCCGT 60.392 55.000 0.00 0.00 37.47 4.69
65 66 0.168128 CCAGGCGTTCCGTTTCATTC 59.832 55.000 0.00 0.00 37.47 2.67
85 86 7.233632 TCATTCCAAATGGTCCATCCTAATAG 58.766 38.462 4.39 0.00 37.07 1.73
86 87 4.985538 TCCAAATGGTCCATCCTAATAGC 58.014 43.478 4.39 0.00 37.07 2.97
87 88 4.415179 TCCAAATGGTCCATCCTAATAGCA 59.585 41.667 4.39 0.00 37.07 3.49
88 89 5.074929 TCCAAATGGTCCATCCTAATAGCAT 59.925 40.000 4.39 0.00 37.07 3.79
89 90 6.274436 TCCAAATGGTCCATCCTAATAGCATA 59.726 38.462 4.39 0.00 37.07 3.14
130 133 7.094890 CCACATGCTATTTTATTTGTTTTGGCA 60.095 33.333 0.00 0.00 0.00 4.92
183 191 4.547367 GTCCCTTATGGCGCGGCT 62.547 66.667 33.23 20.43 0.00 5.52
273 282 7.721399 ACCTTAAATGTTGAGACTCACAATCTT 59.279 33.333 4.15 5.50 0.00 2.40
296 305 4.223700 TGCAAAGACATGGTCTGACTCTAT 59.776 41.667 7.85 0.00 42.59 1.98
308 317 3.865383 CTCTATGGGCTGGCCGCA 61.865 66.667 16.08 4.61 41.67 5.69
323 332 1.730451 CCGCAACCAACCCGAAAACT 61.730 55.000 0.00 0.00 0.00 2.66
367 376 3.502979 GGGTGACCGCATAACAAAGTTTA 59.497 43.478 0.00 0.00 43.64 2.01
474 488 6.106673 TCTACCCATCGAGATCAAGAAAAAC 58.893 40.000 0.00 0.00 0.00 2.43
539 553 3.930336 ACATCTTTCGTCTCAATCTGCA 58.070 40.909 0.00 0.00 0.00 4.41
561 575 2.622436 CAGTTCGGGTTCTCAGAATCC 58.378 52.381 6.64 6.64 0.00 3.01
826 860 1.068541 CACGGAACAAAAAGGGCTAGC 60.069 52.381 6.04 6.04 0.00 3.42
847 887 3.088259 GAGTAGCTCTGCTCCGAGA 57.912 57.895 0.00 0.00 40.44 4.04
869 909 1.286260 GCGAGACGACACAGTTCCT 59.714 57.895 0.00 0.00 0.00 3.36
1120 1160 2.430382 TTCTGGTTCGAGGGCGTGAC 62.430 60.000 0.00 0.00 38.98 3.67
1143 1183 4.688021 GAGATATCTCGCTGTTTTCTGGT 58.312 43.478 16.77 0.00 32.78 4.00
1145 1185 5.112686 AGATATCTCGCTGTTTTCTGGTTC 58.887 41.667 0.00 0.00 0.00 3.62
1155 1195 4.195416 TGTTTTCTGGTTCAAATTTGCCC 58.805 39.130 13.54 14.91 0.00 5.36
1158 1198 0.037419 CTGGTTCAAATTTGCCCCGG 60.037 55.000 13.54 14.97 0.00 5.73
1159 1199 0.470080 TGGTTCAAATTTGCCCCGGA 60.470 50.000 13.54 0.00 0.00 5.14
1160 1200 0.901827 GGTTCAAATTTGCCCCGGAT 59.098 50.000 13.54 0.00 0.00 4.18
1161 1201 2.104170 GGTTCAAATTTGCCCCGGATA 58.896 47.619 13.54 0.00 0.00 2.59
1162 1202 2.159156 GGTTCAAATTTGCCCCGGATAC 60.159 50.000 13.54 0.00 0.00 2.24
1163 1203 2.758423 GTTCAAATTTGCCCCGGATACT 59.242 45.455 13.54 0.00 0.00 2.12
1164 1204 3.935818 TCAAATTTGCCCCGGATACTA 57.064 42.857 13.54 0.00 0.00 1.82
1165 1205 3.815809 TCAAATTTGCCCCGGATACTAG 58.184 45.455 13.54 0.00 0.00 2.57
1166 1206 2.884639 CAAATTTGCCCCGGATACTAGG 59.115 50.000 0.73 0.00 0.00 3.02
1167 1207 1.815757 ATTTGCCCCGGATACTAGGT 58.184 50.000 0.73 0.00 0.00 3.08
1168 1208 2.475339 TTTGCCCCGGATACTAGGTA 57.525 50.000 0.73 0.00 0.00 3.08
1169 1209 2.005370 TTGCCCCGGATACTAGGTAG 57.995 55.000 0.73 0.00 0.00 3.18
1170 1210 1.151760 TGCCCCGGATACTAGGTAGA 58.848 55.000 0.73 0.00 0.00 2.59
1171 1211 1.500303 TGCCCCGGATACTAGGTAGAA 59.500 52.381 0.73 0.00 0.00 2.10
1172 1212 1.891811 GCCCCGGATACTAGGTAGAAC 59.108 57.143 0.73 0.00 0.00 3.01
1173 1213 2.754186 GCCCCGGATACTAGGTAGAACA 60.754 54.545 0.73 0.00 0.00 3.18
1174 1214 3.775910 CCCCGGATACTAGGTAGAACAT 58.224 50.000 0.73 0.00 0.00 2.71
1175 1215 3.762823 CCCCGGATACTAGGTAGAACATC 59.237 52.174 0.73 0.00 0.00 3.06
1176 1216 4.404640 CCCGGATACTAGGTAGAACATCA 58.595 47.826 0.73 0.00 0.00 3.07
1177 1217 4.831155 CCCGGATACTAGGTAGAACATCAA 59.169 45.833 0.73 0.00 0.00 2.57
1178 1218 5.047943 CCCGGATACTAGGTAGAACATCAAG 60.048 48.000 0.73 0.00 0.00 3.02
1179 1219 5.535406 CCGGATACTAGGTAGAACATCAAGT 59.465 44.000 0.00 0.00 0.00 3.16
1180 1220 6.040616 CCGGATACTAGGTAGAACATCAAGTT 59.959 42.308 0.00 0.00 44.93 2.66
1181 1221 7.230108 CCGGATACTAGGTAGAACATCAAGTTA 59.770 40.741 0.00 0.00 41.51 2.24
1182 1222 8.291032 CGGATACTAGGTAGAACATCAAGTTAG 58.709 40.741 0.00 0.00 41.51 2.34
1183 1223 8.083462 GGATACTAGGTAGAACATCAAGTTAGC 58.917 40.741 0.00 0.00 41.51 3.09
1184 1224 6.852420 ACTAGGTAGAACATCAAGTTAGCA 57.148 37.500 0.00 0.00 41.51 3.49
1185 1225 6.868622 ACTAGGTAGAACATCAAGTTAGCAG 58.131 40.000 0.00 0.00 41.51 4.24
1186 1226 5.746990 AGGTAGAACATCAAGTTAGCAGT 57.253 39.130 0.00 0.00 41.51 4.40
1187 1227 6.115448 AGGTAGAACATCAAGTTAGCAGTT 57.885 37.500 0.00 0.00 41.51 3.16
1188 1228 6.166982 AGGTAGAACATCAAGTTAGCAGTTC 58.833 40.000 0.00 0.00 41.51 3.01
1189 1229 5.932303 GGTAGAACATCAAGTTAGCAGTTCA 59.068 40.000 0.00 0.00 41.51 3.18
1190 1230 5.931441 AGAACATCAAGTTAGCAGTTCAC 57.069 39.130 0.00 0.00 41.51 3.18
1191 1231 4.757149 AGAACATCAAGTTAGCAGTTCACC 59.243 41.667 0.00 0.00 41.51 4.02
1192 1232 4.357918 ACATCAAGTTAGCAGTTCACCT 57.642 40.909 0.00 0.00 0.00 4.00
1193 1233 4.718961 ACATCAAGTTAGCAGTTCACCTT 58.281 39.130 0.00 0.00 0.00 3.50
1210 1250 2.027469 ACCTTGATACGTGGAAACCCTC 60.027 50.000 0.00 0.00 0.00 4.30
1211 1251 2.268298 CTTGATACGTGGAAACCCTCG 58.732 52.381 0.00 0.00 43.89 4.63
1216 1256 3.723348 GTGGAAACCCTCGTGCGC 61.723 66.667 0.00 0.00 0.00 6.09
1217 1257 3.936203 TGGAAACCCTCGTGCGCT 61.936 61.111 9.73 0.00 0.00 5.92
1219 1259 2.665185 GAAACCCTCGTGCGCTGT 60.665 61.111 9.73 0.00 0.00 4.40
1220 1260 2.954753 GAAACCCTCGTGCGCTGTG 61.955 63.158 9.73 1.89 0.00 3.66
1237 1331 2.489329 CTGTGGTGCCCATAGACAAAAG 59.511 50.000 11.04 0.00 43.99 2.27
1239 1333 3.073209 TGTGGTGCCCATAGACAAAAGTA 59.927 43.478 0.00 0.00 35.28 2.24
1242 1336 4.532916 TGGTGCCCATAGACAAAAGTACTA 59.467 41.667 0.00 0.00 0.00 1.82
1243 1337 4.874396 GGTGCCCATAGACAAAAGTACTAC 59.126 45.833 0.00 0.00 0.00 2.73
1244 1338 4.565564 GTGCCCATAGACAAAAGTACTACG 59.434 45.833 0.00 0.00 0.00 3.51
1245 1339 4.221262 TGCCCATAGACAAAAGTACTACGT 59.779 41.667 0.00 0.00 0.00 3.57
1246 1340 5.418524 TGCCCATAGACAAAAGTACTACGTA 59.581 40.000 0.00 0.00 0.00 3.57
1261 1355 8.853469 AGTACTACGTATTTATCTGAGTTTGC 57.147 34.615 0.00 0.00 0.00 3.68
1262 1356 8.684520 AGTACTACGTATTTATCTGAGTTTGCT 58.315 33.333 0.00 0.00 0.00 3.91
1265 1359 6.332504 ACGTATTTATCTGAGTTTGCTTCG 57.667 37.500 0.00 0.00 0.00 3.79
1269 1363 7.009265 CGTATTTATCTGAGTTTGCTTCGAAGA 59.991 37.037 28.95 11.00 0.00 2.87
1271 1365 4.999751 ATCTGAGTTTGCTTCGAAGAAC 57.000 40.909 28.95 22.44 45.90 3.01
1296 1394 4.717313 GTCCGTTGGTGGGGGAGC 62.717 72.222 0.00 0.00 0.00 4.70
1346 1444 0.953471 TGTGTACGGCATCTTGGCAC 60.953 55.000 1.91 0.00 43.94 5.01
1362 1460 0.944386 GCACTATGCCATAACGGGTG 59.056 55.000 0.00 0.00 37.42 4.61
1363 1461 1.593196 CACTATGCCATAACGGGTGG 58.407 55.000 0.00 0.00 39.80 4.61
1364 1462 1.134220 CACTATGCCATAACGGGTGGT 60.134 52.381 5.14 0.00 39.01 4.16
1457 1917 5.699458 CAGTTTGATTTAACCTGTCGGTACT 59.301 40.000 0.00 0.00 44.73 2.73
1496 1956 2.513897 GGATCCTCCAAACCCGCG 60.514 66.667 3.84 0.00 36.28 6.46
1522 1982 4.380945 GGCCCATGAAGCACCCCA 62.381 66.667 9.51 0.00 0.00 4.96
1763 2223 1.841302 CTACCAGTGGCCCTGAAGCA 61.841 60.000 19.43 4.22 44.49 3.91
1910 2370 2.556287 GCCTTCAACGCCGTCTTG 59.444 61.111 0.00 0.00 0.00 3.02
1979 2439 6.662663 ACTCGGTACTACTCCTTACATTTTCT 59.337 38.462 0.00 0.00 0.00 2.52
2577 3037 5.991933 TTCCTAATTGCTTTGGTGCATTA 57.008 34.783 0.00 0.00 42.96 1.90
2605 3065 6.395629 TCCAGACTTAATTTCTTGGTACTCG 58.604 40.000 0.00 0.00 0.00 4.18
2727 3190 7.237209 TGTAAGAGATGTATCATCATGGGAG 57.763 40.000 11.47 0.00 0.00 4.30
2851 3315 5.530915 TGAACACTGCATAATGGGCTATTAC 59.469 40.000 5.37 0.00 34.22 1.89
2904 3368 5.414765 GGGTAGTGAAAACTACTGATTTGGG 59.585 44.000 13.97 0.00 41.57 4.12
3109 3573 9.298250 AGTTTCTAGTTGTCATCTTGTAGAGTA 57.702 33.333 0.00 0.00 0.00 2.59
3132 3596 7.934120 AGTACTGACTGTTTAAGAAGCAAGAAT 59.066 33.333 0.00 0.00 33.41 2.40
3136 3600 7.861630 TGACTGTTTAAGAAGCAAGAATACAC 58.138 34.615 0.00 0.00 0.00 2.90
3283 3748 7.437713 AGGCCTTGCAGCTTGTATATATATA 57.562 36.000 0.00 0.00 0.00 0.86
3284 3749 8.038862 AGGCCTTGCAGCTTGTATATATATAT 57.961 34.615 0.00 10.10 0.00 0.86
3285 3750 9.159254 AGGCCTTGCAGCTTGTATATATATATA 57.841 33.333 0.00 8.16 0.00 0.86
3286 3751 9.950496 GGCCTTGCAGCTTGTATATATATATAT 57.050 33.333 17.37 17.37 33.68 0.86
3336 3801 4.329296 TGTACAAAACCGCATTACATCG 57.671 40.909 0.00 0.00 0.00 3.84
3342 3807 2.115348 ACCGCATTACATCGAGTACG 57.885 50.000 0.00 0.00 41.26 3.67
3343 3808 1.268896 ACCGCATTACATCGAGTACGG 60.269 52.381 14.84 14.84 42.42 4.02
3389 3854 2.540265 AGAACACAGAGCCTGAACAG 57.460 50.000 8.91 0.00 35.18 3.16
3427 3892 9.249457 CTCTTAATCTACTTGCGAATTGTGATA 57.751 33.333 0.00 0.00 0.00 2.15
3486 3951 8.100135 TCCCAAATTTTTAATTATGCCATCCT 57.900 30.769 0.00 0.00 0.00 3.24
3513 3978 6.405278 AGAGGTCAACCATTGTTTAAAAGG 57.595 37.500 1.33 0.00 38.89 3.11
3529 3994 3.292492 AAAGGAAAGAGGTCAACCGTT 57.708 42.857 0.00 0.00 42.08 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.308069 TGCCTCCAGCGATTTTGCTC 61.308 55.000 0.00 0.00 45.23 4.26
58 59 4.686891 AGGATGGACCATTTGGAATGAAA 58.313 39.130 8.78 0.00 42.04 2.69
65 66 4.728772 TGCTATTAGGATGGACCATTTGG 58.271 43.478 8.78 0.00 42.04 3.28
85 86 1.134946 GGGTTGGTGTTCATGCTATGC 59.865 52.381 0.00 0.00 0.00 3.14
86 87 2.164219 GTGGGTTGGTGTTCATGCTATG 59.836 50.000 0.00 0.00 0.00 2.23
87 88 2.224992 TGTGGGTTGGTGTTCATGCTAT 60.225 45.455 0.00 0.00 0.00 2.97
88 89 1.143889 TGTGGGTTGGTGTTCATGCTA 59.856 47.619 0.00 0.00 0.00 3.49
89 90 0.106268 TGTGGGTTGGTGTTCATGCT 60.106 50.000 0.00 0.00 0.00 3.79
273 282 2.369860 AGAGTCAGACCATGTCTTTGCA 59.630 45.455 0.00 0.00 41.37 4.08
279 288 2.224161 GCCCATAGAGTCAGACCATGTC 60.224 54.545 0.00 0.00 0.00 3.06
345 354 1.530323 ACTTTGTTATGCGGTCACCC 58.470 50.000 0.00 0.00 0.00 4.61
432 442 2.240162 GATTCTCTGCGGTCCCGGTT 62.240 60.000 7.97 0.00 40.19 4.44
474 488 0.742281 CAACAGCGATGGGTGAGAGG 60.742 60.000 14.16 0.00 44.37 3.69
539 553 1.420430 TTCTGAGAACCCGAACTGGT 58.580 50.000 0.00 0.00 41.55 4.00
561 575 4.797743 TCTCCCGATGATAGGATAGATGG 58.202 47.826 0.00 0.00 0.00 3.51
714 741 1.258982 GACTTGTGACTTGTGACGCTG 59.741 52.381 0.00 0.00 0.00 5.18
715 742 1.571919 GACTTGTGACTTGTGACGCT 58.428 50.000 0.00 0.00 0.00 5.07
719 746 1.538204 GCGAGGACTTGTGACTTGTGA 60.538 52.381 0.00 0.00 0.00 3.58
720 747 0.861837 GCGAGGACTTGTGACTTGTG 59.138 55.000 0.00 0.00 0.00 3.33
721 748 0.753262 AGCGAGGACTTGTGACTTGT 59.247 50.000 0.00 0.00 0.00 3.16
723 750 1.067495 GCTAGCGAGGACTTGTGACTT 60.067 52.381 0.00 0.00 0.00 3.01
799 833 0.312416 TTTTTGTTCCGTGCCGATGG 59.688 50.000 0.00 0.00 0.00 3.51
847 887 1.783031 AACTGTGTCGTCTCGCGTCT 61.783 55.000 5.77 0.00 42.13 4.18
869 909 1.152860 TGTGGAAAAGAGGCCGCAA 60.153 52.632 9.88 0.00 41.35 4.85
1009 1049 3.037249 GTTGCCGTTGCCGTCGTA 61.037 61.111 0.00 0.00 36.33 3.43
1138 1178 0.965439 CGGGGCAAATTTGAACCAGA 59.035 50.000 22.31 0.00 0.00 3.86
1141 1181 0.901827 ATCCGGGGCAAATTTGAACC 59.098 50.000 22.31 20.26 0.00 3.62
1143 1183 3.094484 AGTATCCGGGGCAAATTTGAA 57.906 42.857 22.31 0.00 0.00 2.69
1145 1185 2.884639 CCTAGTATCCGGGGCAAATTTG 59.115 50.000 14.03 14.03 0.00 2.32
1155 1195 5.535406 ACTTGATGTTCTACCTAGTATCCGG 59.465 44.000 0.00 0.00 0.00 5.14
1158 1198 8.630917 TGCTAACTTGATGTTCTACCTAGTATC 58.369 37.037 0.00 0.00 39.89 2.24
1159 1199 8.534954 TGCTAACTTGATGTTCTACCTAGTAT 57.465 34.615 0.00 0.00 39.89 2.12
1160 1200 7.614583 ACTGCTAACTTGATGTTCTACCTAGTA 59.385 37.037 0.00 0.00 39.89 1.82
1161 1201 6.437793 ACTGCTAACTTGATGTTCTACCTAGT 59.562 38.462 0.00 0.00 39.89 2.57
1162 1202 6.868622 ACTGCTAACTTGATGTTCTACCTAG 58.131 40.000 0.00 0.00 39.89 3.02
1163 1203 6.852420 ACTGCTAACTTGATGTTCTACCTA 57.148 37.500 0.00 0.00 39.89 3.08
1164 1204 5.746990 ACTGCTAACTTGATGTTCTACCT 57.253 39.130 0.00 0.00 39.89 3.08
1165 1205 5.932303 TGAACTGCTAACTTGATGTTCTACC 59.068 40.000 0.00 0.00 39.89 3.18
1166 1206 6.128526 GGTGAACTGCTAACTTGATGTTCTAC 60.129 42.308 0.00 0.00 39.89 2.59
1167 1207 5.932303 GGTGAACTGCTAACTTGATGTTCTA 59.068 40.000 0.00 0.00 39.89 2.10
1168 1208 4.757149 GGTGAACTGCTAACTTGATGTTCT 59.243 41.667 0.00 0.00 39.89 3.01
1169 1209 4.757149 AGGTGAACTGCTAACTTGATGTTC 59.243 41.667 0.00 0.00 39.89 3.18
1170 1210 4.718961 AGGTGAACTGCTAACTTGATGTT 58.281 39.130 0.00 0.00 42.31 2.71
1171 1211 4.357918 AGGTGAACTGCTAACTTGATGT 57.642 40.909 0.00 0.00 0.00 3.06
1172 1212 4.756642 TCAAGGTGAACTGCTAACTTGATG 59.243 41.667 0.00 0.00 39.29 3.07
1173 1213 4.973168 TCAAGGTGAACTGCTAACTTGAT 58.027 39.130 0.00 0.00 39.29 2.57
1174 1214 4.415881 TCAAGGTGAACTGCTAACTTGA 57.584 40.909 0.00 0.00 41.16 3.02
1175 1215 5.163953 CGTATCAAGGTGAACTGCTAACTTG 60.164 44.000 0.00 0.00 37.31 3.16
1176 1216 4.929808 CGTATCAAGGTGAACTGCTAACTT 59.070 41.667 0.00 0.00 0.00 2.66
1177 1217 4.021368 ACGTATCAAGGTGAACTGCTAACT 60.021 41.667 0.00 0.00 0.00 2.24
1178 1218 4.091509 CACGTATCAAGGTGAACTGCTAAC 59.908 45.833 0.00 0.00 42.77 2.34
1179 1219 4.242475 CACGTATCAAGGTGAACTGCTAA 58.758 43.478 0.00 0.00 42.77 3.09
1180 1220 3.368013 CCACGTATCAAGGTGAACTGCTA 60.368 47.826 0.00 0.00 42.77 3.49
1181 1221 2.612972 CCACGTATCAAGGTGAACTGCT 60.613 50.000 0.00 0.00 42.77 4.24
1182 1222 1.732259 CCACGTATCAAGGTGAACTGC 59.268 52.381 0.00 0.00 42.77 4.40
1183 1223 3.313012 TCCACGTATCAAGGTGAACTG 57.687 47.619 0.00 0.00 42.77 3.16
1184 1224 4.062991 GTTTCCACGTATCAAGGTGAACT 58.937 43.478 0.00 0.00 42.77 3.01
1185 1225 3.187842 GGTTTCCACGTATCAAGGTGAAC 59.812 47.826 0.00 0.00 42.77 3.18
1186 1226 3.404899 GGTTTCCACGTATCAAGGTGAA 58.595 45.455 0.00 0.00 42.77 3.18
1187 1227 2.289819 GGGTTTCCACGTATCAAGGTGA 60.290 50.000 0.00 0.00 42.77 4.02
1188 1228 2.081462 GGGTTTCCACGTATCAAGGTG 58.919 52.381 0.00 0.00 40.42 4.00
1189 1229 1.982958 AGGGTTTCCACGTATCAAGGT 59.017 47.619 0.00 0.00 34.83 3.50
1190 1230 2.629051 GAGGGTTTCCACGTATCAAGG 58.371 52.381 0.00 0.00 34.83 3.61
1191 1231 2.268298 CGAGGGTTTCCACGTATCAAG 58.732 52.381 0.00 0.00 41.23 3.02
1192 1232 2.373540 CGAGGGTTTCCACGTATCAA 57.626 50.000 0.00 0.00 41.23 2.57
1222 1262 4.221262 ACGTAGTACTTTTGTCTATGGGCA 59.779 41.667 0.00 0.00 41.94 5.36
1223 1263 4.752146 ACGTAGTACTTTTGTCTATGGGC 58.248 43.478 0.00 0.00 41.94 5.36
1242 1336 6.097356 TCGAAGCAAACTCAGATAAATACGT 58.903 36.000 0.00 0.00 0.00 3.57
1243 1337 6.569228 TCGAAGCAAACTCAGATAAATACG 57.431 37.500 0.00 0.00 0.00 3.06
1244 1338 8.186178 TCTTCGAAGCAAACTCAGATAAATAC 57.814 34.615 20.56 0.00 0.00 1.89
1245 1339 8.656849 GTTCTTCGAAGCAAACTCAGATAAATA 58.343 33.333 20.56 0.00 0.00 1.40
1246 1340 7.389053 AGTTCTTCGAAGCAAACTCAGATAAAT 59.611 33.333 20.70 4.69 0.00 1.40
1254 1348 4.201920 ACCAAAGTTCTTCGAAGCAAACTC 60.202 41.667 24.41 10.93 0.00 3.01
1259 1353 1.946768 CCACCAAAGTTCTTCGAAGCA 59.053 47.619 20.56 6.89 0.00 3.91
1261 1355 2.548480 GGACCACCAAAGTTCTTCGAAG 59.452 50.000 19.35 19.35 35.97 3.79
1262 1356 2.567985 GGACCACCAAAGTTCTTCGAA 58.432 47.619 0.00 0.00 35.97 3.71
1265 1359 1.963172 ACGGACCACCAAAGTTCTTC 58.037 50.000 0.00 0.00 35.59 2.87
1269 1363 0.033894 ACCAACGGACCACCAAAGTT 60.034 50.000 0.00 0.00 35.59 2.66
1271 1365 1.452145 CCACCAACGGACCACCAAAG 61.452 60.000 0.00 0.00 35.59 2.77
1346 1444 2.341846 AACCACCCGTTATGGCATAG 57.658 50.000 7.35 0.00 41.31 2.23
1352 1450 6.149807 ACAAACAGTATAAACCACCCGTTATG 59.850 38.462 0.00 0.00 33.05 1.90
1353 1451 6.240145 ACAAACAGTATAAACCACCCGTTAT 58.760 36.000 0.00 0.00 33.05 1.89
1362 1460 6.017687 ACGAACTCCAACAAACAGTATAAACC 60.018 38.462 0.00 0.00 0.00 3.27
1363 1461 6.951643 ACGAACTCCAACAAACAGTATAAAC 58.048 36.000 0.00 0.00 0.00 2.01
1364 1462 6.203338 GGACGAACTCCAACAAACAGTATAAA 59.797 38.462 0.00 0.00 39.21 1.40
1457 1917 4.996122 CCTGCAATTTACAATTGGAAAGCA 59.004 37.500 22.06 22.06 0.00 3.91
1496 1956 0.897621 CTTCATGGGCCAAGGAAACC 59.102 55.000 11.89 0.00 0.00 3.27
1522 1982 0.872388 CTTAACCGGAGCGCTTTGTT 59.128 50.000 13.26 17.40 0.00 2.83
1910 2370 7.099120 ACTTTTGGGCATTGAGAAAATATGAC 58.901 34.615 0.00 0.00 0.00 3.06
2577 3037 9.588096 AGTACCAAGAAATTAAGTCTGGAAAAT 57.412 29.630 5.85 0.00 0.00 1.82
2727 3190 5.853936 ACTTTTGCCTTCTTATTTCCCAAC 58.146 37.500 0.00 0.00 0.00 3.77
2851 3315 2.535331 CAAACCGAACCAAACCAACAG 58.465 47.619 0.00 0.00 0.00 3.16
2904 3368 1.534595 CCACTCACAGTGCAAAACAGC 60.535 52.381 0.00 0.00 44.63 4.40
3109 3573 7.715249 TGTATTCTTGCTTCTTAAACAGTCAGT 59.285 33.333 0.00 0.00 0.00 3.41
3132 3596 7.989416 AGGAAAAAGACATTTATTCCGTGTA 57.011 32.000 0.00 0.00 38.82 2.90
3136 3600 9.855021 ACATAAAGGAAAAAGACATTTATTCCG 57.145 29.630 0.00 0.00 38.82 4.30
3153 3618 3.396276 TGGTCTGTGGGAAACATAAAGGA 59.604 43.478 0.00 0.00 38.39 3.36
3154 3619 3.761897 TGGTCTGTGGGAAACATAAAGG 58.238 45.455 0.00 0.00 38.39 3.11
3197 3662 5.317808 TGCCTTTTAACCAAGTATGTGCTA 58.682 37.500 0.00 0.00 0.00 3.49
3283 3748 9.986157 ATGGGATATAGAGCACAAAATTCATAT 57.014 29.630 0.00 0.00 0.00 1.78
3284 3749 9.234827 CATGGGATATAGAGCACAAAATTCATA 57.765 33.333 0.00 0.00 0.00 2.15
3285 3750 7.177921 CCATGGGATATAGAGCACAAAATTCAT 59.822 37.037 2.85 0.00 0.00 2.57
3286 3751 6.491062 CCATGGGATATAGAGCACAAAATTCA 59.509 38.462 2.85 0.00 0.00 2.57
3367 3832 5.016831 TCTGTTCAGGCTCTGTGTTCTATA 58.983 41.667 0.00 0.00 32.61 1.31
3374 3839 4.511527 ACATATTCTGTTCAGGCTCTGTG 58.488 43.478 0.00 0.00 32.90 3.66
3449 3914 5.945144 AAAATTTGGGAGCTGCTCATAAT 57.055 34.783 28.95 20.31 31.08 1.28
3486 3951 7.411486 TTTAAACAATGGTTGACCTCTTTGA 57.589 32.000 13.91 0.00 37.30 2.69
3513 3978 2.143925 CCTCAACGGTTGACCTCTTTC 58.856 52.381 19.07 0.00 35.46 2.62
3529 3994 7.256296 CCTTACATCATACACATATGGACCTCA 60.256 40.741 7.80 0.00 39.04 3.86


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

AutoCloner maintained by Alex Coulton.