Multiple sequence alignment - TraesCS3D01G082900

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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 TraesCS3D01G082900 chr3D 100.000 2213 0 0 1 2213 42091141 42088929 0.000000e+00 4087.0
1 TraesCS3D01G082900 chr3D 100.000 29 0 0 211 239 537391518 537391546 1.000000e-03 54.7
2 TraesCS3D01G082900 chr3B 90.553 1175 48 25 487 1626 65557734 65558880 0.000000e+00 1496.0
3 TraesCS3D01G082900 chr3B 84.116 554 49 16 1624 2161 65558933 65559463 1.180000e-137 499.0
4 TraesCS3D01G082900 chr3B 95.021 241 8 2 247 484 65557305 65557544 2.070000e-100 375.0
5 TraesCS3D01G082900 chr3B 93.413 167 10 1 30 195 65557137 65557303 1.700000e-61 246.0
6 TraesCS3D01G082900 chr3B 78.037 214 22 15 249 454 65556140 65556336 6.460000e-21 111.0
7 TraesCS3D01G082900 chr3A 90.076 1048 43 26 615 1626 53566508 53567530 0.000000e+00 1303.0
8 TraesCS3D01G082900 chr3A 88.702 593 34 12 1624 2210 53567583 53568148 0.000000e+00 693.0
9 TraesCS3D01G082900 chr3A 96.639 238 7 1 247 484 53564366 53564602 5.730000e-106 394.0
10 TraesCS3D01G082900 chr3A 91.018 167 14 1 30 195 53564198 53564364 7.950000e-55 224.0
11 TraesCS3D01G082900 chr3A 94.595 74 3 1 487 560 53566228 53566300 1.800000e-21 113.0
12 TraesCS3D01G082900 chr2A 95.397 239 9 2 247 483 100225764 100226002 1.600000e-101 379.0
13 TraesCS3D01G082900 chr2A 92.771 166 12 0 30 195 100225597 100225762 7.900000e-60 241.0
14 TraesCS3D01G082900 chr2A 80.663 181 35 0 1006 1186 679982439 679982259 8.240000e-30 141.0
15 TraesCS3D01G082900 chr2B 80.663 181 35 0 1006 1186 640085916 640085736 8.240000e-30 141.0
16 TraesCS3D01G082900 chr2D 79.581 191 39 0 996 1186 537448409 537448219 1.070000e-28 137.0
17 TraesCS3D01G082900 chr6B 89.888 89 9 0 100 188 275293274 275293362 4.990000e-22 115.0
18 TraesCS3D01G082900 chr5B 95.000 40 1 1 209 247 437569010 437569049 6.600000e-06 62.1
19 TraesCS3D01G082900 chr4A 97.059 34 1 0 211 244 695134971 695135004 8.530000e-05 58.4
20 TraesCS3D01G082900 chr4B 94.444 36 2 0 211 246 562697112 562697077 3.070000e-04 56.5
21 TraesCS3D01G082900 chr1A 100.000 29 0 0 211 239 287305668 287305640 1.000000e-03 54.7
22 TraesCS3D01G082900 chr1B 100.000 28 0 0 219 246 637934292 637934319 4.000000e-03 52.8


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 TraesCS3D01G082900 chr3D 42088929 42091141 2212 True 4087.0 4087 100.000 1 2213 1 chr3D.!!$R1 2212
1 TraesCS3D01G082900 chr3B 65556140 65559463 3323 False 545.4 1496 88.228 30 2161 5 chr3B.!!$F1 2131
2 TraesCS3D01G082900 chr3A 53564198 53568148 3950 False 545.4 1303 92.206 30 2210 5 chr3A.!!$F1 2180

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
101 1071 0.798389 TTCTCTCGAACGCGCATCTG 60.798 55.0 5.73 2.11 37.46 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1873 4766 0.249741 CGACTCGACACCAAACCCTT 60.25 55.0 0.0 0.0 0.0 3.95 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
23 24 6.908870 CCGTCAAATCATGATGAAGACTTA 57.091 37.500 22.48 0.96 46.22 2.24
24 25 6.941802 CCGTCAAATCATGATGAAGACTTAG 58.058 40.000 22.48 13.21 46.22 2.18
26 27 7.706607 CCGTCAAATCATGATGAAGACTTAGTA 59.293 37.037 22.48 0.04 46.22 1.82
27 28 9.254133 CGTCAAATCATGATGAAGACTTAGTAT 57.746 33.333 22.48 0.00 46.22 2.12
31 32 9.775854 AAATCATGATGAAGACTTAGTATGAGG 57.224 33.333 9.46 0.00 0.00 3.86
58 1027 3.699413 GGTGGTCTGGACTCTACTAGTT 58.301 50.000 0.00 0.00 39.07 2.24
101 1071 0.798389 TTCTCTCGAACGCGCATCTG 60.798 55.000 5.73 2.11 37.46 2.90
131 1101 6.422223 GTGTCATTTTTAGCTACCATCATCG 58.578 40.000 0.00 0.00 0.00 3.84
177 1147 9.490663 CCGAGACAAATTTCAAATTATCAGTAC 57.509 33.333 0.00 0.00 0.00 2.73
197 1167 9.251440 TCAGTACCTATTGTCTAATTGTGTACT 57.749 33.333 0.00 0.00 37.01 2.73
200 1170 9.741647 GTACCTATTGTCTAATTGTGTACTACC 57.258 37.037 0.00 0.00 31.50 3.18
201 1171 8.605325 ACCTATTGTCTAATTGTGTACTACCT 57.395 34.615 0.00 0.00 0.00 3.08
202 1172 9.043548 ACCTATTGTCTAATTGTGTACTACCTT 57.956 33.333 0.00 0.00 0.00 3.50
203 1173 9.530633 CCTATTGTCTAATTGTGTACTACCTTC 57.469 37.037 0.00 0.00 0.00 3.46
204 1174 9.234384 CTATTGTCTAATTGTGTACTACCTTCG 57.766 37.037 0.00 0.00 0.00 3.79
205 1175 6.579666 TGTCTAATTGTGTACTACCTTCGT 57.420 37.500 0.00 0.00 0.00 3.85
206 1176 7.686438 TGTCTAATTGTGTACTACCTTCGTA 57.314 36.000 0.00 0.00 0.00 3.43
207 1177 7.530010 TGTCTAATTGTGTACTACCTTCGTAC 58.470 38.462 0.00 0.00 38.13 3.67
208 1178 6.969473 GTCTAATTGTGTACTACCTTCGTACC 59.031 42.308 0.00 0.00 37.11 3.34
209 1179 5.990120 AATTGTGTACTACCTTCGTACCT 57.010 39.130 0.00 0.00 37.11 3.08
210 1180 8.046708 TCTAATTGTGTACTACCTTCGTACCTA 58.953 37.037 0.00 0.00 37.11 3.08
211 1181 7.466746 AATTGTGTACTACCTTCGTACCTAA 57.533 36.000 0.00 0.00 37.11 2.69
212 1182 6.892658 TTGTGTACTACCTTCGTACCTAAA 57.107 37.500 0.00 0.00 37.11 1.85
213 1183 6.892658 TGTGTACTACCTTCGTACCTAAAA 57.107 37.500 0.00 0.00 37.11 1.52
214 1184 7.283625 TGTGTACTACCTTCGTACCTAAAAA 57.716 36.000 0.00 0.00 37.11 1.94
238 1208 8.904099 AAAGGTCTTATATTTTGATACGGAGG 57.096 34.615 0.00 0.00 0.00 4.30
239 1209 7.613551 AGGTCTTATATTTTGATACGGAGGT 57.386 36.000 0.00 0.00 0.00 3.85
240 1210 8.716674 AGGTCTTATATTTTGATACGGAGGTA 57.283 34.615 0.00 0.00 0.00 3.08
241 1211 9.151177 AGGTCTTATATTTTGATACGGAGGTAA 57.849 33.333 0.00 0.00 31.15 2.85
242 1212 9.939802 GGTCTTATATTTTGATACGGAGGTAAT 57.060 33.333 0.00 0.00 31.15 1.89
308 1278 3.891366 AGGAATCCTTTTTGTGTGGTCAG 59.109 43.478 0.00 0.00 0.00 3.51
361 1331 4.016479 AGGTGTCCTCTTCCTATCCAGTTA 60.016 45.833 0.00 0.00 0.00 2.24
403 1376 5.067805 GTGCCAGCTTAATTAATTAGGTGCT 59.932 40.000 16.16 17.42 0.00 4.40
497 3102 4.675063 ATTCCCCTAAACACCAGATTGT 57.325 40.909 0.00 0.00 0.00 2.71
509 3114 5.690865 ACACCAGATTGTTTAGGAACAGAA 58.309 37.500 0.00 0.00 45.80 3.02
513 3118 6.265422 ACCAGATTGTTTAGGAACAGAAAAGG 59.735 38.462 0.00 0.00 45.80 3.11
554 3159 6.902341 TGTGAGACAGAAAAACATGAATAGC 58.098 36.000 0.00 0.00 0.00 2.97
555 3160 6.486320 TGTGAGACAGAAAAACATGAATAGCA 59.514 34.615 0.00 0.00 0.00 3.49
556 3161 7.175467 TGTGAGACAGAAAAACATGAATAGCAT 59.825 33.333 0.00 0.00 37.85 3.79
577 3182 6.684686 GCATGAAGCATGAATGGTATATTGT 58.315 36.000 11.31 0.00 43.81 2.71
578 3183 7.149973 GCATGAAGCATGAATGGTATATTGTT 58.850 34.615 11.31 0.00 43.81 2.83
579 3184 7.115805 GCATGAAGCATGAATGGTATATTGTTG 59.884 37.037 11.31 0.00 43.81 3.33
580 3185 7.878547 TGAAGCATGAATGGTATATTGTTGA 57.121 32.000 0.00 0.00 37.57 3.18
581 3186 7.933396 TGAAGCATGAATGGTATATTGTTGAG 58.067 34.615 0.00 0.00 37.57 3.02
582 3187 7.774625 TGAAGCATGAATGGTATATTGTTGAGA 59.225 33.333 0.00 0.00 37.57 3.27
583 3188 7.502120 AGCATGAATGGTATATTGTTGAGAC 57.498 36.000 0.00 0.00 36.64 3.36
584 3189 7.056006 AGCATGAATGGTATATTGTTGAGACA 58.944 34.615 0.00 0.00 36.64 3.41
585 3190 7.228108 AGCATGAATGGTATATTGTTGAGACAG 59.772 37.037 0.00 0.00 35.35 3.51
586 3191 7.227314 GCATGAATGGTATATTGTTGAGACAGA 59.773 37.037 0.00 0.00 37.04 3.41
587 3192 9.112725 CATGAATGGTATATTGTTGAGACAGAA 57.887 33.333 0.00 0.00 37.04 3.02
588 3193 9.685276 ATGAATGGTATATTGTTGAGACAGAAA 57.315 29.630 0.00 0.00 37.04 2.52
614 3229 2.172679 ACAGCATGCCATGATTGTTGA 58.827 42.857 15.66 0.00 42.53 3.18
616 3231 3.181479 ACAGCATGCCATGATTGTTGATC 60.181 43.478 15.66 0.00 42.53 2.92
622 3414 6.517605 CATGCCATGATTGTTGATCCAATTA 58.482 36.000 0.00 0.00 35.24 1.40
624 3416 7.127012 TGCCATGATTGTTGATCCAATTAAT 57.873 32.000 0.00 0.00 35.24 1.40
684 3478 2.039879 TCCAACCTTTCTAACTGCCTCC 59.960 50.000 0.00 0.00 0.00 4.30
685 3479 2.224769 CCAACCTTTCTAACTGCCTCCA 60.225 50.000 0.00 0.00 0.00 3.86
686 3480 3.486383 CAACCTTTCTAACTGCCTCCAA 58.514 45.455 0.00 0.00 0.00 3.53
687 3481 3.425162 ACCTTTCTAACTGCCTCCAAG 57.575 47.619 0.00 0.00 0.00 3.61
688 3482 2.087646 CCTTTCTAACTGCCTCCAAGC 58.912 52.381 0.00 0.00 0.00 4.01
689 3483 2.290577 CCTTTCTAACTGCCTCCAAGCT 60.291 50.000 0.00 0.00 0.00 3.74
690 3484 2.770164 TTCTAACTGCCTCCAAGCTC 57.230 50.000 0.00 0.00 0.00 4.09
710 3504 1.756538 CCAACTGCCCAAGTGAAAAGT 59.243 47.619 0.00 0.00 39.81 2.66
731 3525 2.299582 TGGTCCATTTTTGGTGCTCATG 59.700 45.455 0.00 0.00 0.00 3.07
737 3531 3.749665 TTTTTGGTGCTCATGAAAGGG 57.250 42.857 0.00 0.00 0.00 3.95
789 3583 1.273886 AGAGAGGCCGTGTTTCTTCTC 59.726 52.381 0.00 1.13 0.00 2.87
799 3593 3.756117 GTGTTTCTTCTCCCTGGAATGT 58.244 45.455 0.00 0.00 0.00 2.71
901 3710 3.594134 ACTGCACAAAGAGATAGACTGC 58.406 45.455 0.00 0.00 0.00 4.40
926 3738 6.826231 CCTAGCTTAGCTGCTATATAGACAGA 59.174 42.308 25.59 11.87 43.54 3.41
928 3740 5.417580 AGCTTAGCTGCTATATAGACAGACC 59.582 44.000 25.59 15.18 42.10 3.85
929 3741 5.184096 GCTTAGCTGCTATATAGACAGACCA 59.816 44.000 25.59 10.29 32.75 4.02
1014 3845 1.203441 AGAAGATGCAGGACTGGGCA 61.203 55.000 1.01 0.00 45.23 5.36
1017 3848 4.437587 ATGCAGGACTGGGCAGGC 62.438 66.667 1.01 0.00 44.24 4.85
1050 3881 1.483827 CTGGTGCTCTTCATCCTGCTA 59.516 52.381 0.00 0.00 0.00 3.49
1271 4102 3.558674 GCTGAACATGTAGCTGGGT 57.441 52.632 12.48 0.00 36.99 4.51
1290 4121 3.704566 GGGTTGGGTTCTCTGAAAGTTTT 59.295 43.478 0.00 0.00 33.76 2.43
1291 4122 4.161565 GGGTTGGGTTCTCTGAAAGTTTTT 59.838 41.667 0.00 0.00 33.76 1.94
1308 4139 6.694877 AGTTTTTAGGGTCTTGTTTCTGTC 57.305 37.500 0.00 0.00 0.00 3.51
1332 4163 5.755375 CGGTTCATGCATAATAGTGTCTCTT 59.245 40.000 0.00 0.00 0.00 2.85
1334 4165 6.425504 GTTCATGCATAATAGTGTCTCTTGC 58.574 40.000 0.00 0.00 0.00 4.01
1388 4219 0.723981 GCGACTGAGGATGAAACTGC 59.276 55.000 0.00 0.00 0.00 4.40
1399 4230 4.022503 AGGATGAAACTGCTTCTTTGCTTC 60.023 41.667 0.00 0.00 34.86 3.86
1411 4242 5.051106 GCTTCTTTGCTTCTAGCTAGATTCG 60.051 44.000 23.81 15.59 42.97 3.34
1468 4299 6.307318 GTGACACTTTTCATCATTCAGATTGC 59.693 38.462 0.00 0.00 33.72 3.56
1561 4396 1.135083 GTCAGATACAGTGTGGTCGGG 60.135 57.143 5.88 3.02 0.00 5.14
1562 4397 0.895530 CAGATACAGTGTGGTCGGGT 59.104 55.000 5.88 0.00 0.00 5.28
1567 4402 0.252103 ACAGTGTGGTCGGGTAGGAT 60.252 55.000 0.00 0.00 0.00 3.24
1642 4532 0.792640 AGAAACGCACAGAGCATTCG 59.207 50.000 0.00 0.00 46.13 3.34
1700 4590 7.721399 TGAGAAAGAAATTTGTTCCTAGCTTCT 59.279 33.333 0.45 0.00 0.00 2.85
1701 4591 9.220767 GAGAAAGAAATTTGTTCCTAGCTTCTA 57.779 33.333 0.45 0.00 0.00 2.10
1702 4592 9.225436 AGAAAGAAATTTGTTCCTAGCTTCTAG 57.775 33.333 0.45 0.00 0.00 2.43
1859 4752 1.541147 CATGTGTCGGGCAAAATGAGT 59.459 47.619 1.35 0.00 0.00 3.41
1866 4759 1.737793 CGGGCAAAATGAGTGTAGGTC 59.262 52.381 0.00 0.00 0.00 3.85
1893 4786 1.068585 GGGTTTGGTGTCGAGTCGT 59.931 57.895 13.12 0.00 0.00 4.34
1901 4794 1.668793 TGTCGAGTCGTGGTAGCGA 60.669 57.895 13.12 0.00 38.68 4.93
1904 4797 2.102553 GAGTCGTGGTAGCGAGCC 59.897 66.667 0.00 0.00 41.85 4.70
1966 4861 1.946283 GCTTTCTGGGTAGTGAGTGGC 60.946 57.143 0.00 0.00 0.00 5.01
1971 4866 2.646175 GGGTAGTGAGTGGCGCAGA 61.646 63.158 10.83 0.00 0.00 4.26
1974 4869 1.071605 GTAGTGAGTGGCGCAGAAAG 58.928 55.000 10.83 0.00 0.00 2.62
2010 4905 1.531423 TAGGTGAGTGTGACCTCGTC 58.469 55.000 0.00 0.00 43.15 4.20
2013 4908 0.110147 GTGAGTGTGACCTCGTCTCG 60.110 60.000 0.00 0.00 34.04 4.04
2044 4939 2.415512 AGGAATAAAAACGTCGCTGCTC 59.584 45.455 0.00 0.00 0.00 4.26
2073 4978 2.550606 GGAACTGGCGTGTGTAAATTGA 59.449 45.455 0.00 0.00 0.00 2.57
2075 4980 4.393680 GGAACTGGCGTGTGTAAATTGATA 59.606 41.667 0.00 0.00 0.00 2.15
2104 5009 7.670009 AGTGATTCAGATAATAATGCAGAGC 57.330 36.000 0.00 0.00 0.00 4.09
2105 5010 7.451732 AGTGATTCAGATAATAATGCAGAGCT 58.548 34.615 0.00 0.00 0.00 4.09
2106 5011 7.388224 AGTGATTCAGATAATAATGCAGAGCTG 59.612 37.037 0.00 0.00 0.00 4.24
2129 5040 1.077123 CTGCTGCTGCTTCAGTGTAG 58.923 55.000 17.00 0.00 40.48 2.74
2174 5085 8.980596 AGTGATTCAGAGAGTTATTCAGAGAAT 58.019 33.333 0.00 0.00 0.00 2.40
2210 5121 1.470632 CGGTGAAAGAGCTGAGCCTAG 60.471 57.143 0.00 0.00 0.00 3.02
2211 5122 1.552792 GGTGAAAGAGCTGAGCCTAGT 59.447 52.381 0.00 0.00 0.00 2.57
2212 5123 2.418060 GGTGAAAGAGCTGAGCCTAGTC 60.418 54.545 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.808042 AAGTCTTCATCATGATTTGACGG 57.192 39.130 5.16 0.00 37.11 4.79
1 2 7.531280 ACTAAGTCTTCATCATGATTTGACG 57.469 36.000 5.16 0.84 37.11 4.35
7 8 8.489676 ACCTCATACTAAGTCTTCATCATGAT 57.510 34.615 1.18 1.18 0.00 2.45
9 10 8.824781 CAAACCTCATACTAAGTCTTCATCATG 58.175 37.037 0.00 0.00 0.00 3.07
10 11 7.497249 GCAAACCTCATACTAAGTCTTCATCAT 59.503 37.037 0.00 0.00 0.00 2.45
11 12 6.818644 GCAAACCTCATACTAAGTCTTCATCA 59.181 38.462 0.00 0.00 0.00 3.07
12 13 6.019479 CGCAAACCTCATACTAAGTCTTCATC 60.019 42.308 0.00 0.00 0.00 2.92
14 15 5.168569 CGCAAACCTCATACTAAGTCTTCA 58.831 41.667 0.00 0.00 0.00 3.02
15 16 4.567159 CCGCAAACCTCATACTAAGTCTTC 59.433 45.833 0.00 0.00 0.00 2.87
16 17 4.020485 ACCGCAAACCTCATACTAAGTCTT 60.020 41.667 0.00 0.00 0.00 3.01
17 18 3.514309 ACCGCAAACCTCATACTAAGTCT 59.486 43.478 0.00 0.00 0.00 3.24
18 19 3.617263 CACCGCAAACCTCATACTAAGTC 59.383 47.826 0.00 0.00 0.00 3.01
19 20 3.596214 CACCGCAAACCTCATACTAAGT 58.404 45.455 0.00 0.00 0.00 2.24
20 21 2.936498 CCACCGCAAACCTCATACTAAG 59.064 50.000 0.00 0.00 0.00 2.18
23 24 0.690762 ACCACCGCAAACCTCATACT 59.309 50.000 0.00 0.00 0.00 2.12
24 25 1.084289 GACCACCGCAAACCTCATAC 58.916 55.000 0.00 0.00 0.00 2.39
26 27 0.606401 CAGACCACCGCAAACCTCAT 60.606 55.000 0.00 0.00 0.00 2.90
27 28 1.227823 CAGACCACCGCAAACCTCA 60.228 57.895 0.00 0.00 0.00 3.86
28 29 1.966451 CCAGACCACCGCAAACCTC 60.966 63.158 0.00 0.00 0.00 3.85
31 32 1.227853 AGTCCAGACCACCGCAAAC 60.228 57.895 0.00 0.00 0.00 2.93
58 1027 7.707624 ATGAAAGAAGATGGTTAAAGCATGA 57.292 32.000 0.00 0.00 36.31 3.07
101 1071 5.028375 GGTAGCTAAAAATGACACGCAATC 58.972 41.667 0.00 0.00 0.00 2.67
131 1101 3.060339 CGGTGAAAAGCAAAAGCATGAAC 60.060 43.478 0.00 0.00 0.00 3.18
177 1147 9.530633 GAAGGTAGTACACAATTAGACAATAGG 57.469 37.037 2.06 0.00 0.00 2.57
212 1182 9.338622 CCTCCGTATCAAAATATAAGACCTTTT 57.661 33.333 0.00 0.00 0.00 2.27
213 1183 8.491958 ACCTCCGTATCAAAATATAAGACCTTT 58.508 33.333 0.00 0.00 0.00 3.11
214 1184 8.030913 ACCTCCGTATCAAAATATAAGACCTT 57.969 34.615 0.00 0.00 0.00 3.50
215 1185 7.613551 ACCTCCGTATCAAAATATAAGACCT 57.386 36.000 0.00 0.00 0.00 3.85
216 1186 9.939802 ATTACCTCCGTATCAAAATATAAGACC 57.060 33.333 0.00 0.00 0.00 3.85
224 1194 9.760077 CAACTACTATTACCTCCGTATCAAAAT 57.240 33.333 0.00 0.00 0.00 1.82
225 1195 8.199449 CCAACTACTATTACCTCCGTATCAAAA 58.801 37.037 0.00 0.00 0.00 2.44
226 1196 7.342799 ACCAACTACTATTACCTCCGTATCAAA 59.657 37.037 0.00 0.00 0.00 2.69
227 1197 6.835488 ACCAACTACTATTACCTCCGTATCAA 59.165 38.462 0.00 0.00 0.00 2.57
228 1198 6.367983 ACCAACTACTATTACCTCCGTATCA 58.632 40.000 0.00 0.00 0.00 2.15
229 1199 6.890979 ACCAACTACTATTACCTCCGTATC 57.109 41.667 0.00 0.00 0.00 2.24
230 1200 7.779798 TGTTACCAACTACTATTACCTCCGTAT 59.220 37.037 0.00 0.00 0.00 3.06
231 1201 7.116075 TGTTACCAACTACTATTACCTCCGTA 58.884 38.462 0.00 0.00 0.00 4.02
232 1202 5.951747 TGTTACCAACTACTATTACCTCCGT 59.048 40.000 0.00 0.00 0.00 4.69
233 1203 6.455360 TGTTACCAACTACTATTACCTCCG 57.545 41.667 0.00 0.00 0.00 4.63
234 1204 7.124750 TCCTTGTTACCAACTACTATTACCTCC 59.875 40.741 0.00 0.00 0.00 4.30
235 1205 8.071177 TCCTTGTTACCAACTACTATTACCTC 57.929 38.462 0.00 0.00 0.00 3.85
236 1206 8.316946 GTTCCTTGTTACCAACTACTATTACCT 58.683 37.037 0.00 0.00 0.00 3.08
237 1207 8.316946 AGTTCCTTGTTACCAACTACTATTACC 58.683 37.037 0.00 0.00 0.00 2.85
238 1208 9.716531 AAGTTCCTTGTTACCAACTACTATTAC 57.283 33.333 0.00 0.00 0.00 1.89
239 1209 9.715121 CAAGTTCCTTGTTACCAACTACTATTA 57.285 33.333 0.00 0.00 36.79 0.98
240 1210 7.174426 GCAAGTTCCTTGTTACCAACTACTATT 59.826 37.037 5.92 0.00 42.77 1.73
241 1211 6.653740 GCAAGTTCCTTGTTACCAACTACTAT 59.346 38.462 5.92 0.00 42.77 2.12
242 1212 5.993441 GCAAGTTCCTTGTTACCAACTACTA 59.007 40.000 5.92 0.00 42.77 1.82
243 1213 4.820173 GCAAGTTCCTTGTTACCAACTACT 59.180 41.667 5.92 0.00 42.77 2.57
244 1214 4.820173 AGCAAGTTCCTTGTTACCAACTAC 59.180 41.667 5.92 0.00 42.77 2.73
245 1215 5.043737 AGCAAGTTCCTTGTTACCAACTA 57.956 39.130 5.92 0.00 42.77 2.24
273 1243 8.522830 CAAAAAGGATTCCTGATAAAACAGCTA 58.477 33.333 5.84 0.00 36.67 3.32
361 1331 3.319122 GGCACTTCAAAGTCAGACCAATT 59.681 43.478 0.00 0.00 37.08 2.32
485 1458 5.690865 TCTGTTCCTAAACAATCTGGTGTT 58.309 37.500 0.00 0.00 44.53 3.32
497 3102 6.916360 ATTCATGCCTTTTCTGTTCCTAAA 57.084 33.333 0.00 0.00 0.00 1.85
554 3159 8.354426 TCAACAATATACCATTCATGCTTCATG 58.646 33.333 0.59 0.59 42.60 3.07
555 3160 8.467963 TCAACAATATACCATTCATGCTTCAT 57.532 30.769 0.00 0.00 0.00 2.57
556 3161 7.774625 TCTCAACAATATACCATTCATGCTTCA 59.225 33.333 0.00 0.00 0.00 3.02
557 3162 8.072567 GTCTCAACAATATACCATTCATGCTTC 58.927 37.037 0.00 0.00 0.00 3.86
558 3163 7.557358 TGTCTCAACAATATACCATTCATGCTT 59.443 33.333 0.00 0.00 30.70 3.91
559 3164 7.056006 TGTCTCAACAATATACCATTCATGCT 58.944 34.615 0.00 0.00 30.70 3.79
560 3165 7.227314 TCTGTCTCAACAATATACCATTCATGC 59.773 37.037 0.00 0.00 34.24 4.06
561 3166 8.667076 TCTGTCTCAACAATATACCATTCATG 57.333 34.615 0.00 0.00 34.24 3.07
562 3167 9.685276 TTTCTGTCTCAACAATATACCATTCAT 57.315 29.630 0.00 0.00 34.24 2.57
563 3168 8.946085 GTTTCTGTCTCAACAATATACCATTCA 58.054 33.333 0.00 0.00 34.24 2.57
564 3169 8.946085 TGTTTCTGTCTCAACAATATACCATTC 58.054 33.333 0.00 0.00 34.24 2.67
565 3170 8.862325 TGTTTCTGTCTCAACAATATACCATT 57.138 30.769 0.00 0.00 34.24 3.16
566 3171 8.896744 CATGTTTCTGTCTCAACAATATACCAT 58.103 33.333 0.00 0.00 36.50 3.55
567 3172 8.100164 TCATGTTTCTGTCTCAACAATATACCA 58.900 33.333 0.00 0.00 36.50 3.25
568 3173 8.492673 TCATGTTTCTGTCTCAACAATATACC 57.507 34.615 0.00 0.00 36.50 2.73
569 3174 9.760660 GTTCATGTTTCTGTCTCAACAATATAC 57.239 33.333 0.00 0.00 36.50 1.47
570 3175 9.500785 TGTTCATGTTTCTGTCTCAACAATATA 57.499 29.630 0.00 0.00 36.50 0.86
571 3176 8.394971 TGTTCATGTTTCTGTCTCAACAATAT 57.605 30.769 0.00 0.00 36.50 1.28
572 3177 7.520453 GCTGTTCATGTTTCTGTCTCAACAATA 60.520 37.037 0.00 0.00 36.50 1.90
573 3178 6.698008 TGTTCATGTTTCTGTCTCAACAAT 57.302 33.333 0.00 0.00 36.50 2.71
574 3179 5.449041 GCTGTTCATGTTTCTGTCTCAACAA 60.449 40.000 0.00 0.00 36.50 2.83
575 3180 4.035558 GCTGTTCATGTTTCTGTCTCAACA 59.964 41.667 0.00 0.00 37.31 3.33
576 3181 4.035558 TGCTGTTCATGTTTCTGTCTCAAC 59.964 41.667 0.00 0.00 0.00 3.18
577 3182 4.198530 TGCTGTTCATGTTTCTGTCTCAA 58.801 39.130 0.00 0.00 0.00 3.02
578 3183 3.807553 TGCTGTTCATGTTTCTGTCTCA 58.192 40.909 0.00 0.00 0.00 3.27
579 3184 4.720090 CATGCTGTTCATGTTTCTGTCTC 58.280 43.478 0.00 0.00 45.79 3.36
580 3185 4.761235 CATGCTGTTCATGTTTCTGTCT 57.239 40.909 0.00 0.00 45.79 3.41
667 3461 2.553247 GCTTGGAGGCAGTTAGAAAGGT 60.553 50.000 0.00 0.00 0.00 3.50
684 3478 0.825010 ACTTGGGCAGTTGGAGCTTG 60.825 55.000 0.00 0.00 27.32 4.01
685 3479 0.825010 CACTTGGGCAGTTGGAGCTT 60.825 55.000 0.00 0.00 30.92 3.74
686 3480 1.228367 CACTTGGGCAGTTGGAGCT 60.228 57.895 0.00 0.00 30.92 4.09
687 3481 0.823356 TTCACTTGGGCAGTTGGAGC 60.823 55.000 0.00 0.00 30.92 4.70
688 3482 1.691196 TTTCACTTGGGCAGTTGGAG 58.309 50.000 0.00 0.00 30.92 3.86
689 3483 2.031120 CTTTTCACTTGGGCAGTTGGA 58.969 47.619 0.00 0.00 30.92 3.53
690 3484 1.756538 ACTTTTCACTTGGGCAGTTGG 59.243 47.619 0.00 0.00 30.92 3.77
710 3504 2.079170 TGAGCACCAAAAATGGACCA 57.921 45.000 0.00 0.00 0.00 4.02
789 3583 1.958579 CACATGCCATACATTCCAGGG 59.041 52.381 0.00 0.00 36.64 4.45
799 3593 4.738243 GCTTTCATTCATGCACATGCCATA 60.738 41.667 5.73 0.00 41.18 2.74
926 3738 1.070445 GCTCTGACACACTGCTGGT 59.930 57.895 0.00 0.00 0.00 4.00
928 3740 1.998315 GTATGCTCTGACACACTGCTG 59.002 52.381 0.00 0.00 0.00 4.41
929 3741 1.898472 AGTATGCTCTGACACACTGCT 59.102 47.619 0.00 0.00 0.00 4.24
950 3769 3.955551 CTCCTCCTCCTAAGGTAGAACAC 59.044 52.174 0.00 0.00 43.82 3.32
1014 3845 1.599047 CAGAGGGATGAACACGCCT 59.401 57.895 0.00 0.00 0.00 5.52
1017 3848 1.021390 GCACCAGAGGGATGAACACG 61.021 60.000 0.00 0.00 38.05 4.49
1271 4102 5.596772 CCCTAAAAACTTTCAGAGAACCCAA 59.403 40.000 0.00 0.00 0.00 4.12
1290 4121 2.701951 ACCGACAGAAACAAGACCCTAA 59.298 45.455 0.00 0.00 0.00 2.69
1291 4122 2.322658 ACCGACAGAAACAAGACCCTA 58.677 47.619 0.00 0.00 0.00 3.53
1308 4139 5.292765 AGAGACACTATTATGCATGAACCG 58.707 41.667 10.16 0.00 0.00 4.44
1388 4219 5.051106 GCGAATCTAGCTAGAAGCAAAGAAG 60.051 44.000 28.80 15.74 45.56 2.85
1399 4230 5.239744 TCTTGAGGTAAGCGAATCTAGCTAG 59.760 44.000 15.01 15.01 45.31 3.42
1411 4242 8.555361 CAGAGCTTTATTTATCTTGAGGTAAGC 58.445 37.037 0.00 0.00 36.31 3.09
1468 4299 0.971386 AGGCACAAGGGAAATGCAAG 59.029 50.000 0.00 0.00 41.27 4.01
1552 4383 1.354101 AACAATCCTACCCGACCACA 58.646 50.000 0.00 0.00 0.00 4.17
1553 4384 2.081462 CAAACAATCCTACCCGACCAC 58.919 52.381 0.00 0.00 0.00 4.16
1554 4385 1.003812 CCAAACAATCCTACCCGACCA 59.996 52.381 0.00 0.00 0.00 4.02
1561 4396 3.751518 ACTCCACACCAAACAATCCTAC 58.248 45.455 0.00 0.00 0.00 3.18
1562 4397 3.556213 CGACTCCACACCAAACAATCCTA 60.556 47.826 0.00 0.00 0.00 2.94
1567 4402 1.433053 CGCGACTCCACACCAAACAA 61.433 55.000 0.00 0.00 0.00 2.83
1642 4532 0.398318 ACCAGGCTCAGTTCTTCACC 59.602 55.000 0.00 0.00 0.00 4.02
1700 4590 6.544197 CAGAGGTGACTGAATCTTAGCTACTA 59.456 42.308 0.00 0.00 44.43 1.82
1701 4591 5.359576 CAGAGGTGACTGAATCTTAGCTACT 59.640 44.000 0.00 0.00 44.43 2.57
1702 4592 5.358442 TCAGAGGTGACTGAATCTTAGCTAC 59.642 44.000 0.00 0.00 44.43 3.58
1808 4698 3.431725 CCTTGTTTCCTCGGCGCC 61.432 66.667 19.07 19.07 0.00 6.53
1859 4752 4.204012 CAAACCCTTCTTTGTGACCTACA 58.796 43.478 0.00 0.00 37.56 2.74
1866 4759 2.223479 CGACACCAAACCCTTCTTTGTG 60.223 50.000 0.00 0.00 30.33 3.33
1873 4766 0.249741 CGACTCGACACCAAACCCTT 60.250 55.000 0.00 0.00 0.00 3.95
1893 4786 3.774528 CAGCAGGGCTCGCTACCA 61.775 66.667 2.62 0.00 37.72 3.25
1904 4797 2.821969 AGATAAAAGCCAACACAGCAGG 59.178 45.455 0.00 0.00 0.00 4.85
1966 4861 2.295909 TGGATTTTGTTCCCTTTCTGCG 59.704 45.455 0.00 0.00 34.67 5.18
1971 4866 4.528206 CCTAAGCTGGATTTTGTTCCCTTT 59.472 41.667 0.00 0.00 34.67 3.11
1974 4869 3.193479 CACCTAAGCTGGATTTTGTTCCC 59.807 47.826 0.00 0.00 34.67 3.97
2010 4905 6.577427 CGTTTTTATTCCTGTTCCTTTTCGAG 59.423 38.462 0.00 0.00 0.00 4.04
2013 4908 6.358822 CGACGTTTTTATTCCTGTTCCTTTTC 59.641 38.462 0.00 0.00 0.00 2.29
2107 5012 1.966972 ACTGAAGCAGCAGCAGCAG 60.967 57.895 12.92 17.46 45.49 4.24
2108 5013 2.112507 ACTGAAGCAGCAGCAGCA 59.887 55.556 12.92 0.00 45.49 4.41
2191 5102 1.552792 ACTAGGCTCAGCTCTTTCACC 59.447 52.381 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.