Multiple sequence alignment - TraesCS2A01G357900

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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 TraesCS2A01G357900 chr2A 100.000 5207 0 0 1 5207 602449176 602443970 0 9616
1 TraesCS2A01G357900 chr2D 95.583 3962 117 25 1278 5207 459297455 459293520 0 6294
2 TraesCS2A01G357900 chr2D 85.474 1129 101 29 6 1116 459298702 459297619 0 1118
3 TraesCS2A01G357900 chr2B 93.242 1391 78 8 1342 2720 540432803 540431417 0 2034
4 TraesCS2A01G357900 chr2B 90.265 1130 70 22 1 1116 540435422 540434319 0 1441
5 TraesCS2A01G357900 chr2B 88.578 928 77 19 3530 4439 540430399 540429483 0 1099
6 TraesCS2A01G357900 chr2B 91.267 813 48 11 2724 3521 540431245 540430441 0 1086
7 TraesCS2A01G357900 chr2B 91.399 779 52 10 4444 5207 540429376 540428598 0 1053


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 TraesCS2A01G357900 chr2A 602443970 602449176 5206 True 9616.0 9616 100.0000 1 5207 1 chr2A.!!$R1 5206
1 TraesCS2A01G357900 chr2D 459293520 459298702 5182 True 3706.0 6294 90.5285 6 5207 2 chr2D.!!$R1 5201
2 TraesCS2A01G357900 chr2B 540428598 540435422 6824 True 1342.6 2034 90.9502 1 5207 5 chr2B.!!$R1 5206

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
673 680 0.107081 CCGGGCCGTTATATTGGTCA 59.893 55.0 26.32 0.0 0.0 4.02 F
951 974 0.539051 AACTGGATCTGAAGCTCGGG 59.461 55.0 0.00 0.0 0.0 5.14 F
1171 1194 0.681175 AACTGCCCATTTCACTTGCC 59.319 50.0 0.00 0.0 0.0 4.52 F
2643 4042 0.249398 AAGGCGGCGAACTAATCACT 59.751 50.0 12.98 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2627 4026 0.459585 TGGAGTGATTAGTTCGCCGC 60.460 55.000 0.00 0.0 35.32 6.53 R
2643 4042 4.695606 ACAACTCCCCTCTTACTTATGGA 58.304 43.478 0.00 0.0 0.00 3.41 R
3025 4596 4.522114 TCCATATTTTGAAGCCGATGTCA 58.478 39.130 0.00 0.0 0.00 3.58 R
4593 6335 2.287637 GAACACGCGCCATTCCGTAC 62.288 60.000 5.73 0.0 35.69 3.67 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
45 46 6.644347 TCTGTCAAAATCAGAGGGACTATTC 58.356 40.000 0.00 0.00 41.55 1.75
70 71 1.840635 GAGGCCCCAAGTGATCTAAGT 59.159 52.381 0.00 0.00 0.00 2.24
125 126 9.585099 AAAAATAAATCTTATTGCGCAGATTCA 57.415 25.926 19.20 8.81 38.55 2.57
142 143 7.201591 CGCAGATTCAAAGATACTTTGATCACT 60.202 37.037 21.82 17.92 38.12 3.41
143 144 9.102757 GCAGATTCAAAGATACTTTGATCACTA 57.897 33.333 21.82 11.15 38.12 2.74
187 188 7.270757 TGTGCTTAAACAATACAACACAGAT 57.729 32.000 0.00 0.00 33.27 2.90
208 209 4.412060 TTTTCTCATACCCCACCCATTT 57.588 40.909 0.00 0.00 0.00 2.32
240 241 7.224297 TCCCAATATAATTCTACTTCCACTGC 58.776 38.462 0.00 0.00 0.00 4.40
268 269 5.934625 TCACTTCTACAGCAATTCCTTCTTC 59.065 40.000 0.00 0.00 0.00 2.87
358 362 6.394809 TGTGCTCTGTTCAATACGATTAGAA 58.605 36.000 0.00 0.00 0.00 2.10
374 378 5.297278 CGATTAGAACTACACTACTGCTCCT 59.703 44.000 0.00 0.00 0.00 3.69
376 380 6.912951 TTAGAACTACACTACTGCTCCTTT 57.087 37.500 0.00 0.00 0.00 3.11
377 381 5.140747 AGAACTACACTACTGCTCCTTTG 57.859 43.478 0.00 0.00 0.00 2.77
379 383 4.957684 ACTACACTACTGCTCCTTTGTT 57.042 40.909 0.00 0.00 0.00 2.83
381 385 3.838244 ACACTACTGCTCCTTTGTTGA 57.162 42.857 0.00 0.00 0.00 3.18
398 402 7.168135 CCTTTGTTGATTCTTTTGACAAGCTAC 59.832 37.037 0.00 0.00 32.50 3.58
422 426 3.503363 TGCTGCTGATTAACCAAAGACTG 59.497 43.478 0.00 0.00 0.00 3.51
453 457 4.379499 CCATCCAAACCTAAGAAAACTCGC 60.379 45.833 0.00 0.00 0.00 5.03
499 503 1.750399 CTCACATGGAAAGGGCGGG 60.750 63.158 0.00 0.00 0.00 6.13
501 505 2.938798 ACATGGAAAGGGCGGGGA 60.939 61.111 0.00 0.00 0.00 4.81
515 519 3.483869 GGGAGGAAGGCCGCAGAT 61.484 66.667 0.00 0.00 39.96 2.90
631 635 2.663196 CCCTCTTTCCCGTTCGCT 59.337 61.111 0.00 0.00 0.00 4.93
670 677 1.969589 GGCCGGGCCGTTATATTGG 60.970 63.158 24.63 7.75 39.62 3.16
671 678 1.228033 GCCGGGCCGTTATATTGGT 60.228 57.895 26.32 0.00 0.00 3.67
672 679 1.232621 GCCGGGCCGTTATATTGGTC 61.233 60.000 26.32 0.00 0.00 4.02
673 680 0.107081 CCGGGCCGTTATATTGGTCA 59.893 55.000 26.32 0.00 0.00 4.02
674 681 1.475392 CCGGGCCGTTATATTGGTCAA 60.475 52.381 26.32 0.00 0.00 3.18
681 694 4.634443 GCCGTTATATTGGTCAACAGAGTT 59.366 41.667 0.00 0.00 0.00 3.01
739 758 2.750888 GGTGTCGCGGCTGAAATCC 61.751 63.158 13.81 1.06 0.00 3.01
857 879 4.736896 GACGCCGCGGACCTTCTT 62.737 66.667 33.48 3.28 0.00 2.52
860 882 2.815647 GCCGCGGACCTTCTTCAG 60.816 66.667 33.48 0.00 0.00 3.02
861 883 2.815647 CCGCGGACCTTCTTCAGC 60.816 66.667 24.07 0.00 33.79 4.26
929 952 3.441290 CTTCCGAGTCCCGAGCGT 61.441 66.667 0.00 0.00 41.76 5.07
947 970 2.693069 CGTTGAACTGGATCTGAAGCT 58.307 47.619 0.00 0.00 0.00 3.74
948 971 2.670414 CGTTGAACTGGATCTGAAGCTC 59.330 50.000 0.00 0.00 0.00 4.09
951 974 0.539051 AACTGGATCTGAAGCTCGGG 59.461 55.000 0.00 0.00 0.00 5.14
953 976 1.306141 TGGATCTGAAGCTCGGGGT 60.306 57.895 0.00 0.00 0.00 4.95
954 977 1.144936 GGATCTGAAGCTCGGGGTG 59.855 63.158 0.00 0.00 0.00 4.61
958 981 1.216710 CTGAAGCTCGGGGTGTCTC 59.783 63.158 0.00 0.00 0.00 3.36
966 989 2.352032 CGGGGTGTCTCCTCAGGTC 61.352 68.421 0.00 0.00 36.19 3.85
1103 1126 2.834549 CCTACATGGTCAGTCCTCTTGT 59.165 50.000 0.00 0.00 37.07 3.16
1116 1139 5.011431 CAGTCCTCTTGTCAGGATATGCATA 59.989 44.000 9.27 9.27 44.75 3.14
1118 1141 5.873712 GTCCTCTTGTCAGGATATGCATATG 59.126 44.000 23.76 11.41 44.75 1.78
1120 1143 5.873712 CCTCTTGTCAGGATATGCATATGTC 59.126 44.000 23.76 14.71 35.20 3.06
1121 1144 6.295745 CCTCTTGTCAGGATATGCATATGTCT 60.296 42.308 23.76 16.56 35.20 3.41
1122 1145 6.695429 TCTTGTCAGGATATGCATATGTCTC 58.305 40.000 23.76 10.02 0.00 3.36
1124 1147 4.082026 TGTCAGGATATGCATATGTCTCGG 60.082 45.833 23.76 10.70 0.00 4.63
1125 1148 4.081972 GTCAGGATATGCATATGTCTCGGT 60.082 45.833 23.76 0.00 0.00 4.69
1126 1149 4.528206 TCAGGATATGCATATGTCTCGGTT 59.472 41.667 23.76 0.00 0.00 4.44
1127 1150 5.012046 TCAGGATATGCATATGTCTCGGTTT 59.988 40.000 23.76 0.00 0.00 3.27
1131 1154 6.428159 GGATATGCATATGTCTCGGTTTTTCT 59.572 38.462 23.76 0.00 0.00 2.52
1132 1155 7.041098 GGATATGCATATGTCTCGGTTTTTCTT 60.041 37.037 23.76 0.00 0.00 2.52
1133 1156 5.957842 TGCATATGTCTCGGTTTTTCTTT 57.042 34.783 4.29 0.00 0.00 2.52
1134 1157 6.325919 TGCATATGTCTCGGTTTTTCTTTT 57.674 33.333 4.29 0.00 0.00 2.27
1135 1158 6.744112 TGCATATGTCTCGGTTTTTCTTTTT 58.256 32.000 4.29 0.00 0.00 1.94
1153 1176 4.696479 TTTTTATGCCCCAGCTTTTGAA 57.304 36.364 0.00 0.00 40.80 2.69
1154 1177 3.676291 TTTATGCCCCAGCTTTTGAAC 57.324 42.857 0.00 0.00 40.80 3.18
1155 1178 2.603075 TATGCCCCAGCTTTTGAACT 57.397 45.000 0.00 0.00 40.80 3.01
1156 1179 0.971386 ATGCCCCAGCTTTTGAACTG 59.029 50.000 0.00 0.00 40.80 3.16
1157 1180 1.005748 GCCCCAGCTTTTGAACTGC 60.006 57.895 0.00 0.00 35.50 4.40
1158 1181 1.667722 CCCCAGCTTTTGAACTGCC 59.332 57.895 0.00 0.00 32.37 4.85
1159 1182 1.667722 CCCAGCTTTTGAACTGCCC 59.332 57.895 0.00 0.00 32.37 5.36
1160 1183 1.114722 CCCAGCTTTTGAACTGCCCA 61.115 55.000 0.00 0.00 32.37 5.36
1161 1184 0.971386 CCAGCTTTTGAACTGCCCAT 59.029 50.000 0.00 0.00 32.37 4.00
1162 1185 1.345415 CCAGCTTTTGAACTGCCCATT 59.655 47.619 0.00 0.00 32.37 3.16
1171 1194 0.681175 AACTGCCCATTTCACTTGCC 59.319 50.000 0.00 0.00 0.00 4.52
1178 1201 3.954258 GCCCATTTCACTTGCCTATAGTT 59.046 43.478 0.00 0.00 0.00 2.24
1186 1209 7.792374 TTCACTTGCCTATAGTTTGATGATC 57.208 36.000 0.00 0.00 0.00 2.92
1189 1212 7.828717 TCACTTGCCTATAGTTTGATGATCAAA 59.171 33.333 16.04 16.04 43.37 2.69
1242 1314 9.911788 AGTTATCTGATATAAATGCTAATGGGG 57.088 33.333 0.00 0.00 0.00 4.96
1247 1319 7.884877 TCTGATATAAATGCTAATGGGGAACAG 59.115 37.037 0.00 0.00 0.00 3.16
1249 1321 2.834638 AATGCTAATGGGGAACAGCT 57.165 45.000 0.00 0.00 35.05 4.24
1252 1324 3.492102 TGCTAATGGGGAACAGCTATC 57.508 47.619 0.00 0.00 35.05 2.08
1275 1347 4.041723 CCTTTTGTTTCACAACATCGTCC 58.958 43.478 0.00 0.00 42.66 4.79
1276 1348 4.439426 CCTTTTGTTTCACAACATCGTCCA 60.439 41.667 0.00 0.00 42.66 4.02
1277 1349 3.684103 TTGTTTCACAACATCGTCCAC 57.316 42.857 0.00 0.00 42.66 4.02
1324 2705 5.124776 TGCCCAATGCTGTTTATACAAGTAC 59.875 40.000 0.00 0.00 42.00 2.73
1325 2706 5.357032 GCCCAATGCTGTTTATACAAGTACT 59.643 40.000 0.00 0.00 36.87 2.73
1407 2793 5.287035 GTCATCGTTTGCATGAAGGAATTTC 59.713 40.000 0.00 0.00 31.98 2.17
1523 2920 8.970859 ATCCTTAGGATTCATACTTTTGTCTG 57.029 34.615 8.15 0.00 39.79 3.51
1555 2952 9.942850 TCACTGTATTCTCATTCTGAAAATGTA 57.057 29.630 0.00 0.00 0.00 2.29
1617 3014 5.009210 TGTCCACTACCACTTTATTGTTTGC 59.991 40.000 0.00 0.00 0.00 3.68
1653 3050 2.676121 CATGTTCCCCAGGCGCAA 60.676 61.111 10.83 0.00 0.00 4.85
1722 3119 2.435586 CCTGGCCTGTGAGCTTCG 60.436 66.667 3.32 0.00 0.00 3.79
1750 3147 7.346751 ACTCCTTATTGCTTCAAACTCAAAA 57.653 32.000 0.00 0.00 0.00 2.44
1769 3166 5.514914 TCAAAATTTTCTTGTGACGAACTGC 59.485 36.000 0.00 0.00 0.00 4.40
1919 3316 7.779798 ACTAATGTTATAATGGCAATGGTCTGT 59.220 33.333 0.00 0.00 0.00 3.41
2319 3717 7.432869 TGGTGAAGGTTGTTGATTCATAAAAG 58.567 34.615 0.00 0.00 35.56 2.27
2539 3938 1.620819 TCTTTCTCTCAGTGACTGCCC 59.379 52.381 7.93 0.00 0.00 5.36
2577 3976 7.173907 ACAGTGAACCAACAGATAAATCAAGAG 59.826 37.037 0.00 0.00 0.00 2.85
2627 4026 4.214332 GTCAGTGCTTTAGGTTTGAGAAGG 59.786 45.833 0.00 0.00 0.00 3.46
2630 4029 1.468914 GCTTTAGGTTTGAGAAGGCGG 59.531 52.381 0.00 0.00 0.00 6.13
2643 4042 0.249398 AAGGCGGCGAACTAATCACT 59.751 50.000 12.98 0.00 0.00 3.41
2684 4083 8.041323 GGAGTTGTTTCTGGATCTACTAAATCA 58.959 37.037 0.00 0.00 0.00 2.57
2690 4089 5.891451 TCTGGATCTACTAAATCACACACG 58.109 41.667 0.00 0.00 0.00 4.49
3025 4596 5.766174 TGCAGGTTTTACGGAAGAACTATTT 59.234 36.000 0.00 0.00 0.00 1.40
3101 4672 2.333926 CGTTCGCAATAGTTCTGGTGA 58.666 47.619 0.00 0.00 0.00 4.02
3440 5017 4.465886 TCTTGGTTTAAGCTTTGTGGCTA 58.534 39.130 3.20 0.00 42.24 3.93
3480 5058 2.244695 ACCTGAACACCTCGTATGTGA 58.755 47.619 8.32 0.00 37.18 3.58
3664 5283 6.446318 TCACTTCTGCATAACCAATGTTTTC 58.554 36.000 0.00 0.00 37.93 2.29
3665 5284 6.265196 TCACTTCTGCATAACCAATGTTTTCT 59.735 34.615 0.00 0.00 37.93 2.52
3668 5287 7.439056 ACTTCTGCATAACCAATGTTTTCTTTG 59.561 33.333 0.00 0.00 37.93 2.77
3669 5288 6.815089 TCTGCATAACCAATGTTTTCTTTGT 58.185 32.000 0.00 0.00 37.93 2.83
3670 5289 6.922957 TCTGCATAACCAATGTTTTCTTTGTC 59.077 34.615 0.00 0.00 37.93 3.18
3675 5294 9.919348 CATAACCAATGTTTTCTTTGTCTTTTG 57.081 29.630 0.00 0.00 35.87 2.44
3897 5526 7.331193 TCGCTCTTAAGAAAAGGTTGTCTATTC 59.669 37.037 6.63 0.00 0.00 1.75
4023 5653 2.430367 GTCCCTGCTCCGTTGGTT 59.570 61.111 0.00 0.00 0.00 3.67
4054 5684 2.985896 ACTACACAATCCCATTGGTCG 58.014 47.619 1.20 0.00 44.42 4.79
4071 5701 4.091549 TGGTCGTACTGGTCCTTAATTCT 58.908 43.478 0.00 0.00 0.00 2.40
4074 5704 4.159135 GTCGTACTGGTCCTTAATTCTCCA 59.841 45.833 0.00 0.00 0.00 3.86
4212 5842 6.262273 CACAAAGGTTCATGTGGTAGTTTAGT 59.738 38.462 0.00 0.00 42.46 2.24
4256 5886 1.069823 CTCCAGTGTTCAGTCACAGCT 59.930 52.381 0.00 0.00 40.37 4.24
4369 6001 8.967552 ACTAGTGTTCTTATGAGTTTAAGTCG 57.032 34.615 0.00 0.00 32.21 4.18
4372 6004 8.882415 AGTGTTCTTATGAGTTTAAGTCGAAA 57.118 30.769 0.00 0.00 32.21 3.46
4545 6285 6.142139 GCAAAAATTTGAATTGTACAAGGCC 58.858 36.000 14.65 0.00 40.55 5.19
4648 6391 6.795590 AGTCCAGGCAGAGTATATACTACAT 58.204 40.000 15.42 3.69 36.50 2.29
4714 6462 7.987268 TCTTATACAAGTCGACAATGCTTAG 57.013 36.000 19.50 11.28 33.20 2.18
4948 6696 3.617540 TCGTGTTCGACAAAAATGCAT 57.382 38.095 0.00 0.00 41.35 3.96
5026 6776 3.508845 AAGCAGTCAATAACCCAGTGT 57.491 42.857 0.00 0.00 0.00 3.55
5196 6946 9.130312 CTTATTCAGTATATCCTCGTTTACTGC 57.870 37.037 4.48 0.00 40.72 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
116 117 6.904011 GTGATCAAAGTATCTTTGAATCTGCG 59.096 38.462 22.64 0.00 41.16 5.18
142 143 9.899661 AGCACATTGGTCTTACAATAATAAGTA 57.100 29.630 0.00 0.00 38.94 2.24
143 144 8.807948 AGCACATTGGTCTTACAATAATAAGT 57.192 30.769 0.00 0.00 38.94 2.24
153 154 8.293867 TGTATTGTTTAAGCACATTGGTCTTAC 58.706 33.333 0.00 0.00 0.00 2.34
187 188 4.412060 AAATGGGTGGGGTATGAGAAAA 57.588 40.909 0.00 0.00 0.00 2.29
197 198 2.225117 GGGATCTGATAAATGGGTGGGG 60.225 54.545 0.00 0.00 0.00 4.96
240 241 4.081198 AGGAATTGCTGTAGAAGTGAGGAG 60.081 45.833 0.00 0.00 0.00 3.69
285 289 6.072618 TCGCTATTTGTAGCTAGACATAGGAC 60.073 42.308 19.94 8.19 40.75 3.85
318 322 1.329292 GCACAGCACGTACAGTTGAAA 59.671 47.619 6.23 0.00 0.00 2.69
358 362 4.344102 TCAACAAAGGAGCAGTAGTGTAGT 59.656 41.667 0.00 0.00 0.00 2.73
374 378 6.978080 GGTAGCTTGTCAAAAGAATCAACAAA 59.022 34.615 0.00 0.00 30.16 2.83
376 380 5.827797 AGGTAGCTTGTCAAAAGAATCAACA 59.172 36.000 0.00 0.00 0.00 3.33
377 381 6.145535 CAGGTAGCTTGTCAAAAGAATCAAC 58.854 40.000 0.00 0.00 0.00 3.18
379 383 4.216257 GCAGGTAGCTTGTCAAAAGAATCA 59.784 41.667 0.00 0.00 41.15 2.57
381 385 4.773323 GCAGGTAGCTTGTCAAAAGAAT 57.227 40.909 0.00 0.00 41.15 2.40
398 402 3.084039 TCTTTGGTTAATCAGCAGCAGG 58.916 45.455 0.00 0.00 33.34 4.85
453 457 1.490574 ACTCTTCTTCTCCCCCATCG 58.509 55.000 0.00 0.00 0.00 3.84
499 503 1.524849 GAATCTGCGGCCTTCCTCC 60.525 63.158 0.00 0.00 0.00 4.30
501 505 1.524482 GAGAATCTGCGGCCTTCCT 59.476 57.895 0.00 0.00 0.00 3.36
566 570 0.263172 TCTCCCACCCTCTGATCTCC 59.737 60.000 0.00 0.00 0.00 3.71
662 669 5.943416 CCCACAACTCTGTTGACCAATATAA 59.057 40.000 16.04 0.00 31.64 0.98
664 671 4.335416 CCCACAACTCTGTTGACCAATAT 58.665 43.478 16.04 0.00 31.64 1.28
666 673 2.586425 CCCACAACTCTGTTGACCAAT 58.414 47.619 16.04 0.00 31.64 3.16
667 674 2.021723 GCCCACAACTCTGTTGACCAA 61.022 52.381 16.04 0.00 31.64 3.67
670 677 0.179018 AGGCCCACAACTCTGTTGAC 60.179 55.000 16.04 4.00 31.64 3.18
671 678 0.179020 CAGGCCCACAACTCTGTTGA 60.179 55.000 16.04 0.00 31.64 3.18
672 679 1.799258 GCAGGCCCACAACTCTGTTG 61.799 60.000 0.00 8.66 31.64 3.33
673 680 1.529244 GCAGGCCCACAACTCTGTT 60.529 57.895 0.00 0.00 31.64 3.16
674 681 2.113986 GCAGGCCCACAACTCTGT 59.886 61.111 0.00 0.00 35.63 3.41
739 758 2.363795 TCAGGCTAGACCGGTGGG 60.364 66.667 14.63 2.17 46.52 4.61
817 839 2.202570 CGAGTTCGCCGGTGGTAG 60.203 66.667 16.49 0.00 0.00 3.18
850 872 1.407989 GCTATGCAGGCTGAAGAAGGT 60.408 52.381 20.86 0.00 0.00 3.50
857 879 1.144716 CGGAAGCTATGCAGGCTGA 59.855 57.895 20.86 3.68 40.19 4.26
860 882 0.744414 TTGTCGGAAGCTATGCAGGC 60.744 55.000 6.36 6.36 0.00 4.85
861 883 1.398390 GTTTGTCGGAAGCTATGCAGG 59.602 52.381 0.00 0.00 0.00 4.85
929 952 2.354103 CCGAGCTTCAGATCCAGTTCAA 60.354 50.000 0.00 0.00 0.00 2.69
947 970 2.037367 CCTGAGGAGACACCCCGA 59.963 66.667 0.00 0.00 40.05 5.14
948 971 2.283966 ACCTGAGGAGACACCCCG 60.284 66.667 4.99 0.00 40.05 5.73
951 974 2.352032 CCCGACCTGAGGAGACACC 61.352 68.421 4.99 0.00 39.35 4.16
953 976 0.898789 GAACCCGACCTGAGGAGACA 60.899 60.000 4.99 0.00 0.00 3.41
954 977 1.605971 GGAACCCGACCTGAGGAGAC 61.606 65.000 4.99 0.00 0.00 3.36
1092 1115 3.133542 TGCATATCCTGACAAGAGGACTG 59.866 47.826 0.00 0.00 45.20 3.51
1103 1126 4.089361 ACCGAGACATATGCATATCCTGA 58.911 43.478 16.46 0.00 0.00 3.86
1132 1155 4.102367 AGTTCAAAAGCTGGGGCATAAAAA 59.898 37.500 0.00 0.00 41.70 1.94
1133 1156 3.645687 AGTTCAAAAGCTGGGGCATAAAA 59.354 39.130 0.00 0.00 41.70 1.52
1134 1157 3.006752 CAGTTCAAAAGCTGGGGCATAAA 59.993 43.478 0.00 0.00 41.70 1.40
1135 1158 2.562298 CAGTTCAAAAGCTGGGGCATAA 59.438 45.455 0.00 0.00 41.70 1.90
1136 1159 2.170166 CAGTTCAAAAGCTGGGGCATA 58.830 47.619 0.00 0.00 41.70 3.14
1137 1160 0.971386 CAGTTCAAAAGCTGGGGCAT 59.029 50.000 0.00 0.00 41.70 4.40
1138 1161 1.747325 GCAGTTCAAAAGCTGGGGCA 61.747 55.000 0.00 0.00 41.70 5.36
1139 1162 1.005748 GCAGTTCAAAAGCTGGGGC 60.006 57.895 0.00 0.00 39.06 5.80
1140 1163 1.667722 GGCAGTTCAAAAGCTGGGG 59.332 57.895 0.00 0.00 33.62 4.96
1141 1164 1.114722 TGGGCAGTTCAAAAGCTGGG 61.115 55.000 0.00 0.00 33.62 4.45
1142 1165 0.971386 ATGGGCAGTTCAAAAGCTGG 59.029 50.000 0.00 0.00 33.62 4.85
1143 1166 2.825861 AATGGGCAGTTCAAAAGCTG 57.174 45.000 0.00 0.00 35.93 4.24
1144 1167 2.699846 TGAAATGGGCAGTTCAAAAGCT 59.300 40.909 0.00 0.00 41.62 3.74
1145 1168 2.802247 GTGAAATGGGCAGTTCAAAAGC 59.198 45.455 0.00 0.00 45.26 3.51
1146 1169 4.326504 AGTGAAATGGGCAGTTCAAAAG 57.673 40.909 0.00 0.00 45.26 2.27
1147 1170 4.440880 CAAGTGAAATGGGCAGTTCAAAA 58.559 39.130 0.00 0.00 45.26 2.44
1148 1171 3.740764 GCAAGTGAAATGGGCAGTTCAAA 60.741 43.478 0.00 0.00 45.26 2.69
1149 1172 2.224018 GCAAGTGAAATGGGCAGTTCAA 60.224 45.455 0.00 0.00 45.26 2.69
1150 1173 1.340889 GCAAGTGAAATGGGCAGTTCA 59.659 47.619 0.00 0.00 42.21 3.18
1151 1174 1.337167 GGCAAGTGAAATGGGCAGTTC 60.337 52.381 0.00 0.00 36.10 3.01
1152 1175 0.681175 GGCAAGTGAAATGGGCAGTT 59.319 50.000 0.00 0.00 0.00 3.16
1153 1176 0.178953 AGGCAAGTGAAATGGGCAGT 60.179 50.000 0.00 0.00 0.00 4.40
1154 1177 1.838112 TAGGCAAGTGAAATGGGCAG 58.162 50.000 0.00 0.00 0.00 4.85
1155 1178 2.530460 ATAGGCAAGTGAAATGGGCA 57.470 45.000 0.00 0.00 0.00 5.36
1156 1179 3.555966 ACTATAGGCAAGTGAAATGGGC 58.444 45.455 4.43 0.00 0.00 5.36
1157 1180 5.652014 TCAAACTATAGGCAAGTGAAATGGG 59.348 40.000 4.43 0.00 0.00 4.00
1158 1181 6.757897 TCAAACTATAGGCAAGTGAAATGG 57.242 37.500 4.43 0.00 0.00 3.16
1159 1182 7.988737 TCATCAAACTATAGGCAAGTGAAATG 58.011 34.615 4.43 0.00 0.00 2.32
1160 1183 8.757982 ATCATCAAACTATAGGCAAGTGAAAT 57.242 30.769 4.43 0.00 0.00 2.17
1161 1184 7.828717 TGATCATCAAACTATAGGCAAGTGAAA 59.171 33.333 4.43 0.00 0.00 2.69
1162 1185 7.337938 TGATCATCAAACTATAGGCAAGTGAA 58.662 34.615 4.43 0.00 0.00 3.18
1226 1249 5.952387 AGCTGTTCCCCATTAGCATTTATA 58.048 37.500 0.00 0.00 38.59 0.98
1242 1314 5.461526 GTGAAACAAAAGGGATAGCTGTTC 58.538 41.667 0.00 0.00 36.32 3.18
1275 1347 2.937591 AGCGTCATTGCAATTTCAGTG 58.062 42.857 9.83 0.00 37.31 3.66
1276 1348 3.243501 ACAAGCGTCATTGCAATTTCAGT 60.244 39.130 9.83 0.00 37.31 3.41
1277 1349 3.311106 ACAAGCGTCATTGCAATTTCAG 58.689 40.909 9.83 3.00 37.31 3.02
1340 2721 8.707449 ACCAATGCTACCATATCAATGAAAATT 58.293 29.630 0.00 0.00 34.84 1.82
1345 2726 6.604171 AGAACCAATGCTACCATATCAATGA 58.396 36.000 0.00 0.00 34.84 2.57
1356 2737 2.684881 CCCACATGAGAACCAATGCTAC 59.315 50.000 0.00 0.00 0.00 3.58
1431 2823 3.914312 TCCGCAGAACTCAACTTTCTAG 58.086 45.455 0.00 0.00 31.86 2.43
1457 2849 0.311165 CCTCACGTCGCCGAATCTAT 59.689 55.000 0.00 0.00 37.88 1.98
1470 2867 1.323412 AGCTCTACCTATGCCTCACG 58.677 55.000 0.00 0.00 0.00 4.35
1594 2991 5.240844 AGCAAACAATAAAGTGGTAGTGGAC 59.759 40.000 0.00 0.00 0.00 4.02
1617 3014 9.007901 GGAACATGGAATATCTCATCCTAAAAG 57.992 37.037 0.00 0.00 36.64 2.27
1653 3050 3.055094 AGAAATCTCCACGGCAATAGTGT 60.055 43.478 0.00 0.00 37.88 3.55
1722 3119 6.874134 TGAGTTTGAAGCAATAAGGAGTAGTC 59.126 38.462 0.00 0.00 0.00 2.59
1750 3147 3.627577 ACAGCAGTTCGTCACAAGAAAAT 59.372 39.130 0.00 0.00 0.00 1.82
1919 3316 1.774254 AGGTCATGGACAAGAACACCA 59.226 47.619 0.00 0.00 38.09 4.17
1972 3369 2.205022 AGCATAAGCAGTTGCCTTCA 57.795 45.000 0.00 0.00 45.49 3.02
2319 3717 1.474077 GATGTGGGGCACTGAACATTC 59.526 52.381 4.38 0.00 33.51 2.67
2539 3938 4.635223 TGGTTCACTGTTCTCATCAGAAG 58.365 43.478 0.00 0.00 39.45 2.85
2627 4026 0.459585 TGGAGTGATTAGTTCGCCGC 60.460 55.000 0.00 0.00 35.32 6.53
2630 4029 7.201145 TCTTACTTATGGAGTGATTAGTTCGC 58.799 38.462 0.00 0.00 39.48 4.70
2643 4042 4.695606 ACAACTCCCCTCTTACTTATGGA 58.304 43.478 0.00 0.00 0.00 3.41
3025 4596 4.522114 TCCATATTTTGAAGCCGATGTCA 58.478 39.130 0.00 0.00 0.00 3.58
3101 4672 8.537728 TTCCAGATTATAAATGCTCCAAATGT 57.462 30.769 0.00 0.00 0.00 2.71
4071 5701 3.916359 TTGCCATTACCGATTACTGGA 57.084 42.857 5.05 0.00 33.15 3.86
4074 5704 4.644685 AGCAATTTGCCATTACCGATTACT 59.355 37.500 17.51 0.00 46.52 2.24
4212 5842 6.096705 AGTTGGTCACTTGTCAATTTCATCAA 59.903 34.615 0.00 0.00 27.32 2.57
4278 5908 8.268850 TCATTGTAGTTCTAATTTCTCCAAGC 57.731 34.615 0.00 0.00 0.00 4.01
4324 5954 2.579410 ATACACACAAACTGACCCCC 57.421 50.000 0.00 0.00 0.00 5.40
4369 6001 6.924111 TCTTCAAATCCAAGCACCTATTTTC 58.076 36.000 0.00 0.00 0.00 2.29
4372 6004 5.819991 TCTCTTCAAATCCAAGCACCTATT 58.180 37.500 0.00 0.00 0.00 1.73
4376 6008 4.268359 AGATCTCTTCAAATCCAAGCACC 58.732 43.478 0.00 0.00 0.00 5.01
4414 6047 4.020662 ACAAAACAACTCACATTTGGGTGT 60.021 37.500 0.00 0.00 36.16 4.16
4477 6212 5.454045 GGTTCAATTTTGTTTTAGCCTGGGA 60.454 40.000 0.00 0.00 0.00 4.37
4545 6285 4.675190 ACTCATTTCTTCAGTCATTGCG 57.325 40.909 0.00 0.00 0.00 4.85
4593 6335 2.287637 GAACACGCGCCATTCCGTAC 62.288 60.000 5.73 0.00 35.69 3.67
4670 6413 4.163427 AGATTCAGGAAGAGACTGGAACA 58.837 43.478 0.00 0.00 36.62 3.18
4671 6414 4.817318 AGATTCAGGAAGAGACTGGAAC 57.183 45.455 0.00 0.00 36.62 3.62
4672 6415 7.619698 TGTATAAGATTCAGGAAGAGACTGGAA 59.380 37.037 0.00 0.00 36.62 3.53
4673 6416 7.126061 TGTATAAGATTCAGGAAGAGACTGGA 58.874 38.462 0.00 0.00 36.62 3.86
4674 6417 7.353414 TGTATAAGATTCAGGAAGAGACTGG 57.647 40.000 0.00 0.00 36.62 4.00
4714 6462 7.277098 TCTGTGTGTGTAGTTTTAGAAACTGTC 59.723 37.037 14.50 9.01 0.00 3.51
4827 6575 2.503331 TGATGCACGTTGACCTTGAAT 58.497 42.857 0.00 0.00 0.00 2.57
4831 6579 2.095768 CGATTTGATGCACGTTGACCTT 60.096 45.455 0.00 0.00 0.00 3.50
4902 6650 3.189287 GCTGAAATCTGTACAGGGTTGTG 59.811 47.826 22.48 10.42 38.23 3.33
5026 6776 7.394816 CAGAAGGGTCTCTTTAAACCATCTTA 58.605 38.462 0.00 0.00 37.28 2.10


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

AutoCloner maintained by Alex Coulton.