Multiple sequence alignment - TraesCS6D01G222500

Loading Multiple Alignment...

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 TraesCS6D01G222500 chr6D 100.000 4949 0 0 1 4949 313284920 313279972 0.000000e+00 9140.0
1 TraesCS6D01G222500 chr6D 92.553 94 7 0 1161 1254 313283670 313283577 8.640000e-28 135.0
2 TraesCS6D01G222500 chr6D 92.553 94 7 0 1251 1344 313283760 313283667 8.640000e-28 135.0
3 TraesCS6D01G222500 chr6A 94.860 4280 127 26 1 4252 450468194 450463980 0.000000e+00 6599.0
4 TraesCS6D01G222500 chr6A 94.713 435 20 1 4518 4949 450463650 450463216 0.000000e+00 673.0
5 TraesCS6D01G222500 chr6A 95.789 95 4 0 1250 1344 450467027 450466933 2.390000e-33 154.0
6 TraesCS6D01G222500 chr6A 88.764 89 9 1 1453 1541 103263953 103264040 1.880000e-19 108.0
7 TraesCS6D01G222500 chr6A 87.000 100 7 2 1161 1254 450466936 450466837 1.880000e-19 108.0
8 TraesCS6D01G222500 chr6A 96.774 31 1 0 3685 3715 144249019 144249049 9.000000e-03 52.8
9 TraesCS6D01G222500 chr6B 94.617 2991 110 22 1258 4224 512871836 512874799 0.000000e+00 4584.0
10 TraesCS6D01G222500 chr6B 93.487 1259 59 7 1 1254 512870676 512871916 0.000000e+00 1849.0
11 TraesCS6D01G222500 chr6B 92.836 335 22 2 4617 4949 512874861 512875195 7.450000e-133 484.0
12 TraesCS6D01G222500 chr6B 96.774 31 1 0 3685 3715 205236226 205236256 9.000000e-03 52.8
13 TraesCS6D01G222500 chr2D 85.852 311 36 6 2932 3235 492509744 492509435 1.720000e-84 324.0
14 TraesCS6D01G222500 chr2D 97.710 131 3 0 4250 4380 245329822 245329952 4.980000e-55 226.0
15 TraesCS6D01G222500 chr2D 89.506 162 17 0 2228 2389 492510808 492510647 6.490000e-49 206.0
16 TraesCS6D01G222500 chr2D 91.216 148 11 2 4243 4389 608656372 608656226 3.020000e-47 200.0
17 TraesCS6D01G222500 chr2B 85.852 311 36 6 2932 3235 578137540 578137231 1.720000e-84 324.0
18 TraesCS6D01G222500 chr2B 89.595 173 16 1 2228 2400 578138610 578138440 8.340000e-53 219.0
19 TraesCS6D01G222500 chr2A 85.852 311 36 6 2932 3235 637678961 637678652 1.720000e-84 324.0
20 TraesCS6D01G222500 chr2A 90.741 162 15 0 2228 2389 637680040 637679879 3.000000e-52 217.0
21 TraesCS6D01G222500 chr5A 87.956 274 29 4 2957 3228 708807354 708807083 2.220000e-83 320.0
22 TraesCS6D01G222500 chr4B 87.956 274 29 4 2957 3228 671632077 671631806 2.220000e-83 320.0
23 TraesCS6D01G222500 chr4B 94.286 140 6 2 4238 4377 142519036 142519173 3.880000e-51 213.0
24 TraesCS6D01G222500 chr4B 88.710 62 4 3 4377 4436 366851343 366851283 6.870000e-09 73.1
25 TraesCS6D01G222500 chrUn 87.591 274 30 4 2957 3228 28396959 28397230 1.030000e-81 315.0
26 TraesCS6D01G222500 chrUn 82.288 271 29 13 4198 4451 128516221 128516489 3.000000e-52 217.0
27 TraesCS6D01G222500 chrUn 94.203 138 8 0 4246 4383 297895072 297895209 1.400000e-50 211.0
28 TraesCS6D01G222500 chr1D 86.667 285 33 4 2952 3233 231465072 231464790 1.340000e-80 311.0
29 TraesCS6D01G222500 chr1D 91.333 150 10 3 4246 4394 406733923 406733776 8.400000e-48 202.0
30 TraesCS6D01G222500 chr1D 84.967 153 21 2 2227 2378 231466171 231466020 2.390000e-33 154.0
31 TraesCS6D01G222500 chr3D 94.286 140 7 1 4242 4381 283321117 283321255 3.880000e-51 213.0
32 TraesCS6D01G222500 chr4D 93.007 143 9 1 4251 4393 99524816 99524675 1.810000e-49 207.0
33 TraesCS6D01G222500 chr4D 89.796 49 5 0 4205 4253 379260714 379260666 4.140000e-06 63.9
34 TraesCS6D01G222500 chr3B 91.946 149 10 2 4233 4380 378689147 378689294 1.810000e-49 207.0
35 TraesCS6D01G222500 chr1A 84.615 156 22 2 2224 2378 317812280 317812434 2.390000e-33 154.0
36 TraesCS6D01G222500 chr1B 83.333 156 24 2 2224 2378 365020386 365020540 5.160000e-30 143.0
37 TraesCS6D01G222500 chr5B 97.500 40 1 0 4417 4456 591520986 591521025 8.890000e-08 69.4
38 TraesCS6D01G222500 chr7D 92.500 40 3 0 4205 4244 220639739 220639700 1.920000e-04 58.4
39 TraesCS6D01G222500 chr7B 100.000 31 0 0 4379 4409 41311140 41311170 1.920000e-04 58.4


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 TraesCS6D01G222500 chr6D 313279972 313284920 4948 True 3136.666667 9140 95.035333 1 4949 3 chr6D.!!$R1 4948
1 TraesCS6D01G222500 chr6A 450463216 450468194 4978 True 1883.500000 6599 93.090500 1 4949 4 chr6A.!!$R1 4948
2 TraesCS6D01G222500 chr6B 512870676 512875195 4519 False 2305.666667 4584 93.646667 1 4949 3 chr6B.!!$F2 4948
3 TraesCS6D01G222500 chr2D 492509435 492510808 1373 True 265.000000 324 87.679000 2228 3235 2 chr2D.!!$R2 1007
4 TraesCS6D01G222500 chr2B 578137231 578138610 1379 True 271.500000 324 87.723500 2228 3235 2 chr2B.!!$R1 1007
5 TraesCS6D01G222500 chr2A 637678652 637680040 1388 True 270.500000 324 88.296500 2228 3235 2 chr2A.!!$R1 1007
6 TraesCS6D01G222500 chr1D 231464790 231466171 1381 True 232.500000 311 85.817000 2227 3233 2 chr1D.!!$R2 1006

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
826 835 0.920438 AGAGACGGGAGAGGAGCTTA 59.080 55.000 0.00 0.0 0.00 3.09 F
1339 1361 0.168128 GAACTTCGACCAATTGCCGG 59.832 55.000 15.26 0.0 0.00 6.13 F
1743 1768 0.450583 CTCCTCGATTTCCGTGTCGA 59.549 55.000 0.00 0.0 43.79 4.20 F
1775 1804 0.747283 TCGTCTCGGCTAGAACCTCC 60.747 60.000 0.00 0.0 35.47 4.30 F
2559 2791 1.306141 ATGAGGAAGACCAGGCGGA 60.306 57.895 2.43 0.0 38.94 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2794 3098 0.179108 GCTGGAGGAACGCGATAAGT 60.179 55.000 15.93 0.00 0.00 2.24 R
2842 3170 2.601367 GTGTGGGCTGGCATTGGT 60.601 61.111 2.88 0.00 0.00 3.67 R
3526 4220 0.666880 TTGCGTGCATTGCAATCCAC 60.667 50.000 21.37 21.37 46.62 4.02 R
3533 4227 1.578915 CGATTAAGTTGCGTGCATTGC 59.421 47.619 0.46 0.46 0.00 3.56 R
4478 5176 0.040058 GTTTGGTCCCCCGGGTTTAT 59.960 55.000 21.85 0.00 36.47 1.40 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
425 429 4.207891 TGCTTTCTGTTGGGAGATAGAC 57.792 45.455 0.00 0.00 0.00 2.59
728 737 1.908299 CAGCCCCTTGTTCCCAACC 60.908 63.158 0.00 0.00 0.00 3.77
776 785 2.386661 AGCCGTAAGTCATGTCCTTG 57.613 50.000 9.65 0.00 0.00 3.61
826 835 0.920438 AGAGACGGGAGAGGAGCTTA 59.080 55.000 0.00 0.00 0.00 3.09
964 977 5.995446 ACTAGTGGTAGGTAGTAGTGTACC 58.005 45.833 0.00 0.00 42.68 3.34
993 1006 2.348998 CCACCTGCACTCACTCCC 59.651 66.667 0.00 0.00 0.00 4.30
995 1008 4.008933 ACCTGCACTCACTCCCGC 62.009 66.667 0.00 0.00 0.00 6.13
1058 1071 1.286305 AAGGAAGGTGGTGTGGTGGT 61.286 55.000 0.00 0.00 0.00 4.16
1279 1301 3.838271 GCAGCATCCCGTCTCCGA 61.838 66.667 0.00 0.00 35.63 4.55
1339 1361 0.168128 GAACTTCGACCAATTGCCGG 59.832 55.000 15.26 0.00 0.00 6.13
1585 1610 2.029290 TCCAGGTGAGAACGAAACTAGC 60.029 50.000 0.00 0.00 0.00 3.42
1586 1611 2.288825 CCAGGTGAGAACGAAACTAGCA 60.289 50.000 0.00 0.00 0.00 3.49
1603 1628 7.907214 AACTAGCAGTACTGGTAAAAATCTG 57.093 36.000 29.15 19.91 39.56 2.90
1656 1681 1.153901 GAATTCGCCGTCCGTCAGA 60.154 57.895 0.00 0.00 38.35 3.27
1743 1768 0.450583 CTCCTCGATTTCCGTGTCGA 59.549 55.000 0.00 0.00 43.79 4.20
1775 1804 0.747283 TCGTCTCGGCTAGAACCTCC 60.747 60.000 0.00 0.00 35.47 4.30
1872 1907 4.924305 TGCATTGTTTTCTCTGCTCTTT 57.076 36.364 0.00 0.00 35.66 2.52
1873 1908 6.183360 TGTTGCATTGTTTTCTCTGCTCTTTA 60.183 34.615 0.00 0.00 35.66 1.85
1874 1909 5.762045 TGCATTGTTTTCTCTGCTCTTTAC 58.238 37.500 0.00 0.00 35.66 2.01
1878 1913 7.436376 GCATTGTTTTCTCTGCTCTTTACTTTT 59.564 33.333 0.00 0.00 0.00 2.27
1879 1914 8.962111 CATTGTTTTCTCTGCTCTTTACTTTTC 58.038 33.333 0.00 0.00 0.00 2.29
1880 1915 7.865706 TGTTTTCTCTGCTCTTTACTTTTCT 57.134 32.000 0.00 0.00 0.00 2.52
1881 1916 8.958119 TGTTTTCTCTGCTCTTTACTTTTCTA 57.042 30.769 0.00 0.00 0.00 2.10
1920 1955 2.106684 GGTCTCTGGGAAAAGAAGGTGT 59.893 50.000 0.00 0.00 0.00 4.16
1921 1956 3.142174 GTCTCTGGGAAAAGAAGGTGTG 58.858 50.000 0.00 0.00 0.00 3.82
1973 2017 5.746307 TGCTCTGATGAATTAATCTGCAC 57.254 39.130 4.38 0.88 0.00 4.57
2115 2159 5.035443 CCTAGTACTTGTGTGATAGCGTTC 58.965 45.833 0.00 0.00 0.00 3.95
2116 2160 3.846360 AGTACTTGTGTGATAGCGTTCC 58.154 45.455 0.00 0.00 0.00 3.62
2156 2205 1.595311 TGGGATTACCACTCATGCCT 58.405 50.000 0.00 0.00 46.80 4.75
2559 2791 1.306141 ATGAGGAAGACCAGGCGGA 60.306 57.895 2.43 0.00 38.94 5.54
2851 3179 2.601067 CTGCCCACACCAATGCCA 60.601 61.111 0.00 0.00 0.00 4.92
3211 3905 1.604378 CCCCTACTTCCACCAGCTG 59.396 63.158 6.78 6.78 0.00 4.24
3503 4197 5.413309 AACTTTCGAATCTCTCTCCATGT 57.587 39.130 0.00 0.00 0.00 3.21
3508 4202 6.775594 TTCGAATCTCTCTCCATGTAAGAA 57.224 37.500 0.00 0.00 0.00 2.52
3509 4203 6.384258 TCGAATCTCTCTCCATGTAAGAAG 57.616 41.667 0.00 0.00 0.00 2.85
3516 4210 7.382110 TCTCTCTCCATGTAAGAAGTTTTCAG 58.618 38.462 0.00 0.00 0.00 3.02
3525 4219 7.931578 TGTAAGAAGTTTTCAGACTTGGAAA 57.068 32.000 0.00 0.00 39.84 3.13
3750 4447 4.156455 AGAGTTCCAGAAGCACAAAGAA 57.844 40.909 0.00 0.00 0.00 2.52
4023 4720 4.133078 GCTCCCCTCTGTGATTTCATAAG 58.867 47.826 0.00 0.00 0.00 1.73
4052 4749 1.972588 AAACAGGGGAGGTGCTAGAT 58.027 50.000 0.00 0.00 0.00 1.98
4230 4928 4.719273 TCCCTCCATTCCAAAAAGTTTGTT 59.281 37.500 0.00 0.00 0.00 2.83
4234 4932 7.226523 CCCTCCATTCCAAAAAGTTTGTTTTAG 59.773 37.037 0.00 0.00 0.00 1.85
4264 4962 9.977050 TGTCTAGATATATACTCCCTCTATCCT 57.023 37.037 0.00 0.00 0.00 3.24
4275 4973 7.757242 ACTCCCTCTATCCTAAAATTCTTGT 57.243 36.000 0.00 0.00 0.00 3.16
4276 4974 7.797062 ACTCCCTCTATCCTAAAATTCTTGTC 58.203 38.462 0.00 0.00 0.00 3.18
4277 4975 7.625682 ACTCCCTCTATCCTAAAATTCTTGTCT 59.374 37.037 0.00 0.00 0.00 3.41
4278 4976 8.393959 TCCCTCTATCCTAAAATTCTTGTCTT 57.606 34.615 0.00 0.00 0.00 3.01
4279 4977 9.502035 TCCCTCTATCCTAAAATTCTTGTCTTA 57.498 33.333 0.00 0.00 0.00 2.10
4280 4978 9.771534 CCCTCTATCCTAAAATTCTTGTCTTAG 57.228 37.037 0.00 0.00 0.00 2.18
4296 4994 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
4297 4995 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
4299 4997 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
4300 4998 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
4307 5005 9.832445 ATTTGTCTAAATACGGATGTATCAAGT 57.168 29.630 0.00 0.00 40.42 3.16
4308 5006 8.867112 TTGTCTAAATACGGATGTATCAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
4309 5007 8.002984 TGTCTAAATACGGATGTATCAAGTCA 57.997 34.615 0.00 0.00 40.42 3.41
4310 5008 7.919091 TGTCTAAATACGGATGTATCAAGTCAC 59.081 37.037 0.00 0.00 40.42 3.67
4311 5009 7.381678 GTCTAAATACGGATGTATCAAGTCACC 59.618 40.741 0.00 0.00 40.42 4.02
4312 5010 5.871396 AATACGGATGTATCAAGTCACCT 57.129 39.130 0.00 0.00 40.42 4.00
4313 5011 5.871396 ATACGGATGTATCAAGTCACCTT 57.129 39.130 0.00 0.00 36.56 3.50
4314 5012 4.553330 ACGGATGTATCAAGTCACCTTT 57.447 40.909 0.00 0.00 0.00 3.11
4315 5013 4.906618 ACGGATGTATCAAGTCACCTTTT 58.093 39.130 0.00 0.00 0.00 2.27
4316 5014 6.045072 ACGGATGTATCAAGTCACCTTTTA 57.955 37.500 0.00 0.00 0.00 1.52
4317 5015 6.106673 ACGGATGTATCAAGTCACCTTTTAG 58.893 40.000 0.00 0.00 0.00 1.85
4318 5016 6.106673 CGGATGTATCAAGTCACCTTTTAGT 58.893 40.000 0.00 0.00 0.00 2.24
4319 5017 7.093640 ACGGATGTATCAAGTCACCTTTTAGTA 60.094 37.037 0.00 0.00 0.00 1.82
4320 5018 7.926555 CGGATGTATCAAGTCACCTTTTAGTAT 59.073 37.037 0.00 0.00 0.00 2.12
4321 5019 9.614792 GGATGTATCAAGTCACCTTTTAGTATT 57.385 33.333 0.00 0.00 0.00 1.89
4332 5030 9.408069 GTCACCTTTTAGTATTAGATACATCCG 57.592 37.037 1.42 0.00 38.21 4.18
4333 5031 9.139734 TCACCTTTTAGTATTAGATACATCCGT 57.860 33.333 1.42 0.00 38.21 4.69
4352 5050 9.001542 ACATCCGTATCTAGACTAATGTAAGAC 57.998 37.037 0.00 0.00 0.00 3.01
4353 5051 9.000486 CATCCGTATCTAGACTAATGTAAGACA 58.000 37.037 0.00 0.00 0.00 3.41
4354 5052 8.969260 TCCGTATCTAGACTAATGTAAGACAA 57.031 34.615 0.00 0.00 0.00 3.18
4355 5053 9.053840 TCCGTATCTAGACTAATGTAAGACAAG 57.946 37.037 0.00 0.00 0.00 3.16
4356 5054 9.053840 CCGTATCTAGACTAATGTAAGACAAGA 57.946 37.037 0.00 0.00 0.00 3.02
4364 5062 9.014297 AGACTAATGTAAGACAAGAATTTTGGG 57.986 33.333 5.68 0.00 0.00 4.12
4365 5063 8.934023 ACTAATGTAAGACAAGAATTTTGGGA 57.066 30.769 5.68 0.00 0.00 4.37
4366 5064 8.793592 ACTAATGTAAGACAAGAATTTTGGGAC 58.206 33.333 5.68 0.00 0.00 4.46
4367 5065 5.682943 TGTAAGACAAGAATTTTGGGACG 57.317 39.130 5.68 0.00 0.00 4.79
4368 5066 4.517453 TGTAAGACAAGAATTTTGGGACGG 59.483 41.667 0.00 0.00 0.00 4.79
4369 5067 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
4370 5068 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
4371 5069 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
4372 5070 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
4373 5071 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
4374 5072 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
4375 5073 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
4376 5074 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
4486 5184 7.659652 TTTCAAAATAGGCAAAATAAACCCG 57.340 32.000 0.00 0.00 0.00 5.28
4487 5185 5.725362 TCAAAATAGGCAAAATAAACCCGG 58.275 37.500 0.00 0.00 0.00 5.73
4488 5186 4.746535 AAATAGGCAAAATAAACCCGGG 57.253 40.909 22.25 22.25 0.00 5.73
4489 5187 2.146920 TAGGCAAAATAAACCCGGGG 57.853 50.000 27.92 12.73 0.00 5.73
4490 5188 0.616395 AGGCAAAATAAACCCGGGGG 60.616 55.000 27.92 5.70 42.03 5.40
4491 5189 0.615261 GGCAAAATAAACCCGGGGGA 60.615 55.000 27.92 9.91 38.96 4.81
4492 5190 0.533491 GCAAAATAAACCCGGGGGAC 59.467 55.000 27.92 0.00 38.96 4.46
4518 5398 7.305474 CAAACAGTCCATTACATGAAAGGTAC 58.695 38.462 0.00 0.00 30.02 3.34
4519 5399 5.175859 ACAGTCCATTACATGAAAGGTACG 58.824 41.667 0.00 0.00 30.02 3.67
4520 5400 4.034048 CAGTCCATTACATGAAAGGTACGC 59.966 45.833 0.00 0.00 30.02 4.42
4521 5401 4.081087 AGTCCATTACATGAAAGGTACGCT 60.081 41.667 0.00 0.00 30.02 5.07
4522 5402 4.034048 GTCCATTACATGAAAGGTACGCTG 59.966 45.833 0.00 0.00 30.02 5.18
4523 5403 3.242739 CCATTACATGAAAGGTACGCTGC 60.243 47.826 0.00 0.00 30.02 5.25
4597 5487 9.862371 AAATAGTTACATCTGACAGTCTAACAG 57.138 33.333 1.59 0.00 0.00 3.16
4702 5592 6.214191 TGATCTTGCTTAATTCGAGTCTCT 57.786 37.500 0.00 0.00 0.00 3.10
4721 5611 9.752961 GAGTCTCTATGGTATACCTTCTTTTTC 57.247 37.037 22.41 8.18 36.82 2.29
4818 5709 2.500098 AGAAGGAATAAGCGTGCCTACA 59.500 45.455 0.00 0.00 0.00 2.74
4849 5740 2.025605 AGTGGACTAGGGTGTGTCGATA 60.026 50.000 0.00 0.00 34.31 2.92
4876 5768 1.885593 ATTGGGGGCTTGGGGGTTAG 61.886 60.000 0.00 0.00 0.00 2.34
4884 5776 3.140332 GGGCTTGGGGGTTAGAGATTTAT 59.860 47.826 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.113838 GAAATAAAGAGCTATCCATTGTGAAGA 57.886 33.333 0.00 0.00 0.00 2.87
318 322 6.948309 AGGCTGTTTCTTCCATGTTAATAAGT 59.052 34.615 0.00 0.00 0.00 2.24
319 323 7.396540 AGGCTGTTTCTTCCATGTTAATAAG 57.603 36.000 0.00 0.00 0.00 1.73
561 570 5.163468 GGCTGTCTTCACTGATATCTGAGAA 60.163 44.000 15.75 16.59 0.00 2.87
562 571 4.340666 GGCTGTCTTCACTGATATCTGAGA 59.659 45.833 15.75 10.59 0.00 3.27
776 785 2.932614 AGATACAATGAGTGTCGCAAGC 59.067 45.455 0.00 0.00 42.57 4.01
826 835 2.418910 CGCCCATCTCTCTCGGTGT 61.419 63.158 0.00 0.00 0.00 4.16
993 1006 5.551760 AATTCAGTTTGATCTACCTTGCG 57.448 39.130 0.00 0.00 0.00 4.85
995 1008 8.137437 ACACAAAATTCAGTTTGATCTACCTTG 58.863 33.333 6.73 0.00 40.29 3.61
1159 1175 4.996434 GCTGCTGACAGGCACGGT 62.996 66.667 4.26 0.00 44.63 4.83
1379 1401 1.081641 TTCTCGTCGTCGTGGAAGC 60.082 57.895 1.33 0.00 38.33 3.86
1585 1610 5.582665 GGAGAGCAGATTTTTACCAGTACTG 59.417 44.000 16.34 16.34 0.00 2.74
1586 1611 5.338463 GGGAGAGCAGATTTTTACCAGTACT 60.338 44.000 0.00 0.00 0.00 2.73
1603 1628 3.207669 CATTGCGCAGGGGAGAGC 61.208 66.667 11.31 0.00 34.72 4.09
1656 1681 2.034879 CATTTCGCGCAGGACAGGT 61.035 57.895 8.75 0.00 0.00 4.00
1850 1885 4.924305 AAGAGCAGAGAAAACAATGCAA 57.076 36.364 0.00 0.00 41.14 4.08
1872 1907 5.945784 AGTGCATCAATGGCTTAGAAAAGTA 59.054 36.000 0.00 0.00 34.99 2.24
1873 1908 4.768968 AGTGCATCAATGGCTTAGAAAAGT 59.231 37.500 0.00 0.00 34.99 2.66
1874 1909 5.125097 AGAGTGCATCAATGGCTTAGAAAAG 59.875 40.000 0.00 0.00 35.68 2.27
1878 1913 3.538591 CAGAGTGCATCAATGGCTTAGA 58.461 45.455 0.00 0.00 0.00 2.10
1879 1914 2.617308 CCAGAGTGCATCAATGGCTTAG 59.383 50.000 0.00 0.00 0.00 2.18
1880 1915 2.025981 ACCAGAGTGCATCAATGGCTTA 60.026 45.455 9.37 0.00 34.24 3.09
1881 1916 1.272313 ACCAGAGTGCATCAATGGCTT 60.272 47.619 9.37 0.00 34.24 4.35
1920 1955 1.609208 GGAGCAAAAGACTTCCTGCA 58.391 50.000 19.12 0.00 37.26 4.41
1921 1956 0.884514 GGGAGCAAAAGACTTCCTGC 59.115 55.000 12.26 12.26 34.96 4.85
1973 2017 1.680651 ACTGTCAGCGGGAGAGAGG 60.681 63.158 11.55 0.00 39.20 3.69
2137 2181 1.595311 AGGCATGAGTGGTAATCCCA 58.405 50.000 0.00 0.00 42.51 4.37
2138 2182 2.173569 AGAAGGCATGAGTGGTAATCCC 59.826 50.000 0.00 0.00 0.00 3.85
2542 2774 2.119611 TCCGCCTGGTCTTCCTCA 59.880 61.111 0.00 0.00 36.30 3.86
2794 3098 0.179108 GCTGGAGGAACGCGATAAGT 60.179 55.000 15.93 0.00 0.00 2.24
2842 3170 2.601367 GTGTGGGCTGGCATTGGT 60.601 61.111 2.88 0.00 0.00 3.67
3394 4088 4.925861 GGCGGGGCATCTGAGCTC 62.926 72.222 6.82 6.82 34.17 4.09
3503 4197 7.067008 CCACTTTCCAAGTCTGAAAACTTCTTA 59.933 37.037 0.00 0.00 40.46 2.10
3508 4202 4.855340 TCCACTTTCCAAGTCTGAAAACT 58.145 39.130 0.00 0.00 40.46 2.66
3509 4203 5.774498 ATCCACTTTCCAAGTCTGAAAAC 57.226 39.130 0.00 0.00 40.46 2.43
3516 4210 4.240096 CATTGCAATCCACTTTCCAAGTC 58.760 43.478 9.53 0.00 40.46 3.01
3525 4219 1.213537 GCGTGCATTGCAATCCACT 59.786 52.632 26.60 0.00 41.47 4.00
3526 4220 0.666880 TTGCGTGCATTGCAATCCAC 60.667 50.000 21.37 21.37 46.62 4.02
3527 4221 1.664306 TTGCGTGCATTGCAATCCA 59.336 47.368 21.10 3.28 46.62 3.41
3528 4222 4.575076 TTGCGTGCATTGCAATCC 57.425 50.000 21.10 0.00 46.62 3.01
3532 4226 2.594321 GATTAAGTTGCGTGCATTGCA 58.406 42.857 7.38 7.38 41.38 4.08
3533 4227 1.578915 CGATTAAGTTGCGTGCATTGC 59.421 47.619 0.46 0.46 0.00 3.56
4023 4720 2.027100 CCTCCCCTGTTTTCCAGTCTAC 60.027 54.545 0.00 0.00 39.74 2.59
4052 4749 5.774690 ACTTGCTGTTTGGGATTTCTATTGA 59.225 36.000 0.00 0.00 0.00 2.57
4147 4844 1.064003 TAGGCAAAACAGAGGCTCCA 58.936 50.000 11.71 0.00 41.29 3.86
4252 4950 8.028652 AGACAAGAATTTTAGGATAGAGGGAG 57.971 38.462 0.00 0.00 0.00 4.30
4253 4951 7.996758 AGACAAGAATTTTAGGATAGAGGGA 57.003 36.000 0.00 0.00 0.00 4.20
4254 4952 9.771534 CTAAGACAAGAATTTTAGGATAGAGGG 57.228 37.037 0.00 0.00 0.00 4.30
4270 4968 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
4271 4969 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
4273 4971 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
4274 4972 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
4281 4979 9.832445 ACTTGATACATCCGTATTTAGACAAAT 57.168 29.630 0.00 0.00 38.48 2.32
4282 4980 9.309516 GACTTGATACATCCGTATTTAGACAAA 57.690 33.333 0.00 0.00 38.48 2.83
4283 4981 8.471609 TGACTTGATACATCCGTATTTAGACAA 58.528 33.333 0.00 0.00 38.48 3.18
4284 4982 7.919091 GTGACTTGATACATCCGTATTTAGACA 59.081 37.037 0.00 0.00 38.48 3.41
4285 4983 7.381678 GGTGACTTGATACATCCGTATTTAGAC 59.618 40.741 0.00 0.00 38.48 2.59
4286 4984 7.287005 AGGTGACTTGATACATCCGTATTTAGA 59.713 37.037 0.00 0.00 36.25 2.10
4287 4985 7.434492 AGGTGACTTGATACATCCGTATTTAG 58.566 38.462 0.00 0.00 36.25 1.85
4288 4986 7.356089 AGGTGACTTGATACATCCGTATTTA 57.644 36.000 0.00 0.00 36.25 1.40
4289 4987 6.235231 AGGTGACTTGATACATCCGTATTT 57.765 37.500 0.00 0.00 36.25 1.40
4290 4988 5.871396 AGGTGACTTGATACATCCGTATT 57.129 39.130 0.00 0.00 36.25 1.89
4306 5004 9.408069 CGGATGTATCTAATACTAAAAGGTGAC 57.592 37.037 0.00 0.00 36.70 3.67
4307 5005 9.139734 ACGGATGTATCTAATACTAAAAGGTGA 57.860 33.333 0.00 0.00 36.70 4.02
4326 5024 9.001542 GTCTTACATTAGTCTAGATACGGATGT 57.998 37.037 0.00 5.71 35.45 3.06
4327 5025 9.000486 TGTCTTACATTAGTCTAGATACGGATG 58.000 37.037 0.00 0.00 0.00 3.51
4328 5026 9.570468 TTGTCTTACATTAGTCTAGATACGGAT 57.430 33.333 0.00 0.00 0.00 4.18
4329 5027 8.969260 TTGTCTTACATTAGTCTAGATACGGA 57.031 34.615 0.00 0.00 0.00 4.69
4330 5028 9.053840 TCTTGTCTTACATTAGTCTAGATACGG 57.946 37.037 0.00 0.00 0.00 4.02
4338 5036 9.014297 CCCAAAATTCTTGTCTTACATTAGTCT 57.986 33.333 0.00 0.00 0.00 3.24
4339 5037 9.010029 TCCCAAAATTCTTGTCTTACATTAGTC 57.990 33.333 0.00 0.00 0.00 2.59
4340 5038 8.793592 GTCCCAAAATTCTTGTCTTACATTAGT 58.206 33.333 0.00 0.00 0.00 2.24
4341 5039 7.962918 CGTCCCAAAATTCTTGTCTTACATTAG 59.037 37.037 0.00 0.00 0.00 1.73
4342 5040 7.094549 CCGTCCCAAAATTCTTGTCTTACATTA 60.095 37.037 0.00 0.00 0.00 1.90
4343 5041 6.294508 CCGTCCCAAAATTCTTGTCTTACATT 60.295 38.462 0.00 0.00 0.00 2.71
4344 5042 5.183140 CCGTCCCAAAATTCTTGTCTTACAT 59.817 40.000 0.00 0.00 0.00 2.29
4345 5043 4.517453 CCGTCCCAAAATTCTTGTCTTACA 59.483 41.667 0.00 0.00 0.00 2.41
4346 5044 4.758165 TCCGTCCCAAAATTCTTGTCTTAC 59.242 41.667 0.00 0.00 0.00 2.34
4347 5045 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
4348 5046 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
4349 5047 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
4350 5048 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
4351 5049 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
4352 5050 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
4353 5051 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
4354 5052 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
4355 5053 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
4356 5054 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
4357 5055 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
4358 5056 1.557832 CATACTCCCTCCGTCCCAAAA 59.442 52.381 0.00 0.00 0.00 2.44
4359 5057 1.200519 CATACTCCCTCCGTCCCAAA 58.799 55.000 0.00 0.00 0.00 3.28
4360 5058 0.042131 ACATACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
4361 5059 0.928505 TACATACTCCCTCCGTCCCA 59.071 55.000 0.00 0.00 0.00 4.37
4362 5060 2.169330 GATACATACTCCCTCCGTCCC 58.831 57.143 0.00 0.00 0.00 4.46
4363 5061 3.157750 AGATACATACTCCCTCCGTCC 57.842 52.381 0.00 0.00 0.00 4.79
4364 5062 4.937015 GTCTAGATACATACTCCCTCCGTC 59.063 50.000 0.00 0.00 0.00 4.79
4365 5063 4.350225 TGTCTAGATACATACTCCCTCCGT 59.650 45.833 0.00 0.00 0.00 4.69
4366 5064 4.696402 GTGTCTAGATACATACTCCCTCCG 59.304 50.000 14.20 0.00 0.00 4.63
4367 5065 5.632118 TGTGTCTAGATACATACTCCCTCC 58.368 45.833 17.43 0.00 0.00 4.30
4368 5066 7.768807 AATGTGTCTAGATACATACTCCCTC 57.231 40.000 28.78 0.00 41.35 4.30
4369 5067 8.554490 AAAATGTGTCTAGATACATACTCCCT 57.446 34.615 28.78 13.98 41.35 4.20
4460 5158 9.372369 CGGGTTTATTTTGCCTATTTTGAAATA 57.628 29.630 0.00 0.00 0.00 1.40
4461 5159 7.335673 CCGGGTTTATTTTGCCTATTTTGAAAT 59.664 33.333 0.00 0.00 0.00 2.17
4462 5160 6.651225 CCGGGTTTATTTTGCCTATTTTGAAA 59.349 34.615 0.00 0.00 0.00 2.69
4463 5161 6.166982 CCGGGTTTATTTTGCCTATTTTGAA 58.833 36.000 0.00 0.00 0.00 2.69
4464 5162 5.337652 CCCGGGTTTATTTTGCCTATTTTGA 60.338 40.000 14.18 0.00 0.00 2.69
4465 5163 4.873259 CCCGGGTTTATTTTGCCTATTTTG 59.127 41.667 14.18 0.00 0.00 2.44
4466 5164 4.080807 CCCCGGGTTTATTTTGCCTATTTT 60.081 41.667 21.85 0.00 0.00 1.82
4467 5165 3.452990 CCCCGGGTTTATTTTGCCTATTT 59.547 43.478 21.85 0.00 0.00 1.40
4468 5166 3.035363 CCCCGGGTTTATTTTGCCTATT 58.965 45.455 21.85 0.00 0.00 1.73
4469 5167 2.673258 CCCCGGGTTTATTTTGCCTAT 58.327 47.619 21.85 0.00 0.00 2.57
4470 5168 1.342175 CCCCCGGGTTTATTTTGCCTA 60.342 52.381 21.85 0.00 0.00 3.93
4471 5169 0.616395 CCCCCGGGTTTATTTTGCCT 60.616 55.000 21.85 0.00 0.00 4.75
4472 5170 0.615261 TCCCCCGGGTTTATTTTGCC 60.615 55.000 21.85 0.00 36.47 4.52
4473 5171 0.533491 GTCCCCCGGGTTTATTTTGC 59.467 55.000 21.85 0.00 36.47 3.68
4474 5172 1.187974 GGTCCCCCGGGTTTATTTTG 58.812 55.000 21.85 0.03 36.47 2.44
4475 5173 0.785141 TGGTCCCCCGGGTTTATTTT 59.215 50.000 21.85 0.00 36.47 1.82
4476 5174 0.785141 TTGGTCCCCCGGGTTTATTT 59.215 50.000 21.85 0.00 36.47 1.40
4477 5175 0.785141 TTTGGTCCCCCGGGTTTATT 59.215 50.000 21.85 0.00 36.47 1.40
4478 5176 0.040058 GTTTGGTCCCCCGGGTTTAT 59.960 55.000 21.85 0.00 36.47 1.40
4479 5177 1.358830 TGTTTGGTCCCCCGGGTTTA 61.359 55.000 21.85 0.15 36.47 2.01
4480 5178 2.199257 GTTTGGTCCCCCGGGTTT 59.801 61.111 21.85 0.00 36.47 3.27
4481 5179 3.104568 TGTTTGGTCCCCCGGGTT 61.105 61.111 21.85 0.00 36.47 4.11
4482 5180 3.576259 CTGTTTGGTCCCCCGGGT 61.576 66.667 21.85 0.00 36.47 5.28
4483 5181 3.562732 GACTGTTTGGTCCCCCGGG 62.563 68.421 15.80 15.80 0.00 5.73
4484 5182 2.033602 GACTGTTTGGTCCCCCGG 59.966 66.667 0.00 0.00 0.00 5.73
4490 5188 5.957842 TTCATGTAATGGACTGTTTGGTC 57.042 39.130 0.00 0.00 46.73 4.02
4491 5189 5.243730 CCTTTCATGTAATGGACTGTTTGGT 59.756 40.000 0.00 0.00 46.73 3.67
4492 5190 5.243730 ACCTTTCATGTAATGGACTGTTTGG 59.756 40.000 13.22 0.00 46.73 3.28
4493 5191 6.331369 ACCTTTCATGTAATGGACTGTTTG 57.669 37.500 13.22 0.00 46.73 2.93
4494 5192 6.148811 CGTACCTTTCATGTAATGGACTGTTT 59.851 38.462 13.22 0.00 46.73 2.83
4495 5193 5.642063 CGTACCTTTCATGTAATGGACTGTT 59.358 40.000 13.22 0.00 46.73 3.16
4496 5194 5.175859 CGTACCTTTCATGTAATGGACTGT 58.824 41.667 13.22 0.00 46.73 3.55
4497 5195 4.034048 GCGTACCTTTCATGTAATGGACTG 59.966 45.833 13.22 4.55 46.73 3.51
4498 5196 4.081087 AGCGTACCTTTCATGTAATGGACT 60.081 41.667 13.22 5.79 46.73 3.85
4499 5197 4.034048 CAGCGTACCTTTCATGTAATGGAC 59.966 45.833 13.22 5.19 46.73 4.02
4500 5198 4.188462 CAGCGTACCTTTCATGTAATGGA 58.812 43.478 13.22 0.00 46.73 3.41
4574 5464 7.094334 CCACTGTTAGACTGTCAGATGTAACTA 60.094 40.741 10.88 0.00 33.93 2.24
4597 5487 2.930826 TCCAGGAAGTTTCAGTCCAC 57.069 50.000 0.00 0.00 36.28 4.02
4622 5512 2.224314 GCATCTAGCCGCTTGATTAACC 59.776 50.000 13.78 1.50 37.23 2.85
4671 5561 6.144563 TCGAATTAAGCAAGATCAATCTAGCG 59.855 38.462 0.00 0.00 35.76 4.26
4721 5611 7.655328 GTCTTGTTAAGGAGGATCATAGACATG 59.345 40.741 0.00 0.00 36.25 3.21
4818 5709 2.305927 CCCTAGTCCACTTGACCATGTT 59.694 50.000 0.00 0.00 45.68 2.71
4849 5740 2.091333 CCCAAGCCCCCAATACACTTAT 60.091 50.000 0.00 0.00 0.00 1.73
4884 5776 8.920174 TGTAAGTAGGCTAACATTCTGCTTATA 58.080 33.333 0.00 0.00 37.77 0.98


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

AutoCloner maintained by Alex Coulton.