Multiple sequence alignment - TraesCS4A01G267700

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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 TraesCS4A01G267700 chr4A 100.000 2942 0 0 893 3834 579866377 579863436 0.000000e+00 5433.0
1 TraesCS4A01G267700 chr4A 100.000 566 0 0 1 566 579867269 579866704 0.000000e+00 1046.0
2 TraesCS4A01G267700 chr4A 84.962 266 34 5 1821 2084 483944891 483944630 8.170000e-67 265.0
3 TraesCS4A01G267700 chr4B 89.424 1787 100 27 2081 3834 34025749 34027479 0.000000e+00 2170.0
4 TraesCS4A01G267700 chr4B 95.755 848 29 4 984 1824 34024905 34025752 0.000000e+00 1360.0
5 TraesCS4A01G267700 chr4B 93.724 478 19 6 893 1370 34018798 34019264 0.000000e+00 706.0
6 TraesCS4A01G267700 chr4B 89.041 584 40 15 1 566 34018184 34018761 0.000000e+00 702.0
7 TraesCS4A01G267700 chr4B 90.541 222 19 2 346 566 34024587 34024807 3.750000e-75 292.0
8 TraesCS4A01G267700 chr4D 96.272 1207 39 4 893 2095 22017416 22018620 0.000000e+00 1975.0
9 TraesCS4A01G267700 chr4D 89.606 1395 81 19 2134 3516 22018613 22019955 0.000000e+00 1714.0
10 TraesCS4A01G267700 chr4D 88.340 506 46 6 1 496 22016545 22017047 2.550000e-166 595.0
11 TraesCS4A01G267700 chr4D 90.994 322 26 3 3516 3834 22021815 22022136 7.610000e-117 431.0
12 TraesCS4A01G267700 chr4D 91.221 262 21 2 1822 2083 428936420 428936161 4.710000e-94 355.0
13 TraesCS4A01G267700 chr4D 95.833 48 2 0 389 436 22016525 22016572 1.140000e-10 78.7
14 TraesCS4A01G267700 chr5D 91.635 263 21 1 1822 2083 440780830 440780568 2.820000e-96 363.0
15 TraesCS4A01G267700 chr5B 89.394 264 25 3 1822 2083 536311659 536311397 2.860000e-86 329.0
16 TraesCS4A01G267700 chr1A 89.434 265 23 4 1822 2084 581437329 581437068 2.860000e-86 329.0
17 TraesCS4A01G267700 chr5A 91.549 213 16 2 1822 2032 556778813 556778601 3.750000e-75 292.0
18 TraesCS4A01G267700 chr1B 85.130 269 34 5 1821 2087 365012213 365011949 1.760000e-68 270.0
19 TraesCS4A01G267700 chr3B 84.962 266 33 6 1821 2083 648742263 648742524 2.940000e-66 263.0


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 TraesCS4A01G267700 chr4A 579863436 579867269 3833 True 3239.50 5433 100.000000 1 3834 2 chr4A.!!$R2 3833
1 TraesCS4A01G267700 chr4B 34024587 34027479 2892 False 1274.00 2170 91.906667 346 3834 3 chr4B.!!$F2 3488
2 TraesCS4A01G267700 chr4B 34018184 34019264 1080 False 704.00 706 91.382500 1 1370 2 chr4B.!!$F1 1369
3 TraesCS4A01G267700 chr4D 22016525 22022136 5611 False 958.74 1975 92.209000 1 3834 5 chr4D.!!$F1 3833

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
133 163 0.388659 TTGCATGTGTGAGGGCAAAC 59.611 50.0 0.00 0.0 42.66 2.93 F
1098 1413 0.104462 TCCATCCATCGATTCCCCCT 60.104 55.0 0.00 0.0 0.00 4.79 F
2087 2404 0.037975 GAAACGGCGGGAGTACAAGA 60.038 55.0 13.24 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2069 2386 0.037605 CTCTTGTACTCCCGCCGTTT 60.038 55.0 0.0 0.0 0.0 3.60 R
2574 2894 0.586319 CCGTGACAAATTGAGCGTGT 59.414 50.0 0.0 0.0 0.0 4.49 R
3602 5801 0.827507 ACATCGTTTTTGGCCCAGCT 60.828 50.0 0.0 0.0 0.0 4.24 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
133 163 0.388659 TTGCATGTGTGAGGGCAAAC 59.611 50.000 0.00 0.00 42.66 2.93
144 176 3.501062 GTGAGGGCAAACTGGTAAACTAC 59.499 47.826 0.00 0.00 0.00 2.73
149 181 4.504340 GGGCAAACTGGTAAACTACTCTCA 60.504 45.833 0.00 0.00 0.00 3.27
217 251 1.921869 CGTCCCTGCCCCAAACCTAT 61.922 60.000 0.00 0.00 0.00 2.57
230 264 5.340027 CCCCAAACCTATCACTTCCAATAGT 60.340 44.000 0.00 0.00 0.00 2.12
235 269 2.736670 ATCACTTCCAATAGTGCCCC 57.263 50.000 0.00 0.00 44.10 5.80
237 271 1.922447 TCACTTCCAATAGTGCCCCAT 59.078 47.619 0.00 0.00 44.10 4.00
238 272 2.311542 TCACTTCCAATAGTGCCCCATT 59.688 45.455 0.00 0.00 44.10 3.16
239 273 3.099141 CACTTCCAATAGTGCCCCATTT 58.901 45.455 0.00 0.00 39.12 2.32
247 281 1.014804 AGTGCCCCATTTAATCCCCA 58.985 50.000 0.00 0.00 0.00 4.96
255 289 3.370421 CCCATTTAATCCCCAAAACCAGC 60.370 47.826 0.00 0.00 0.00 4.85
256 290 3.370421 CCATTTAATCCCCAAAACCAGCC 60.370 47.826 0.00 0.00 0.00 4.85
315 349 5.415389 AGTCTCATCATCACCATCTCTATCG 59.585 44.000 0.00 0.00 0.00 2.92
372 410 3.953612 TGGTAGATTCATTGCCATTCCAC 59.046 43.478 0.00 0.00 0.00 4.02
481 519 1.421646 CCACTTTCTCTTGACCCCACT 59.578 52.381 0.00 0.00 0.00 4.00
483 521 2.104792 CACTTTCTCTTGACCCCACTCA 59.895 50.000 0.00 0.00 0.00 3.41
562 863 1.541147 GCAAACCGGTAAAACTACCCC 59.459 52.381 8.00 0.00 36.79 4.95
927 1228 1.674322 CCAAACCTACCACGCCCAG 60.674 63.158 0.00 0.00 0.00 4.45
1089 1390 1.572941 CGCAAGCATCCATCCATCG 59.427 57.895 0.00 0.00 0.00 3.84
1092 1393 1.884579 GCAAGCATCCATCCATCGATT 59.115 47.619 0.00 0.00 0.00 3.34
1098 1413 0.104462 TCCATCCATCGATTCCCCCT 60.104 55.000 0.00 0.00 0.00 4.79
1124 1439 5.420725 TCTCGAAATTTCCTCCAGATTCA 57.579 39.130 12.54 0.00 0.00 2.57
1130 1445 6.350445 CGAAATTTCCTCCAGATTCACCATTT 60.350 38.462 12.54 0.00 0.00 2.32
1139 1454 1.376609 ATTCACCATTTCTCGCGGCC 61.377 55.000 6.13 0.00 0.00 6.13
1475 1791 4.056125 GCTTTTCCGTGGCCCTGC 62.056 66.667 0.00 0.00 0.00 4.85
1676 1992 2.872408 TGCCATTTCTGCAGGTAGC 58.128 52.632 15.13 10.65 45.96 3.58
1708 2024 7.282585 TCCTATAAATCCTGATTGTGTTCTGG 58.717 38.462 0.00 0.00 36.38 3.86
1721 2037 4.894784 TGTGTTCTGGGATTAGTTCACTC 58.105 43.478 0.00 0.00 0.00 3.51
1880 2196 9.665719 AATTTGGTCAAAGTCAAACTAAACAAT 57.334 25.926 2.55 0.00 35.97 2.71
1892 2208 7.025485 CAAACTAAACAATGTTTGGCCAAAT 57.975 32.000 32.52 16.26 45.22 2.32
1899 2215 6.799926 ACAATGTTTGGCCAAATTTGTATC 57.200 33.333 36.42 24.23 37.54 2.24
1931 2248 7.972832 TCAACATCTACAAAACCGAAGTTAT 57.027 32.000 0.00 0.00 34.19 1.89
2075 2392 3.619233 TGCAAACTAGAAAGAAACGGC 57.381 42.857 0.00 0.00 0.00 5.68
2087 2404 0.037975 GAAACGGCGGGAGTACAAGA 60.038 55.000 13.24 0.00 0.00 3.02
2106 2423 7.588497 ACAAGAGAAGCTACAAATCCTTTTT 57.412 32.000 0.00 0.00 0.00 1.94
2162 2479 6.147821 GCTAGTTCTTCAGTGTAGCAAATTCA 59.852 38.462 3.91 0.00 36.83 2.57
2164 2481 4.990543 TCTTCAGTGTAGCAAATTCACG 57.009 40.909 0.00 0.00 37.20 4.35
2192 2509 6.712241 TTTGATCGATCTTTGTTCTCTGAC 57.288 37.500 25.02 0.00 0.00 3.51
2194 2511 3.217599 TCGATCTTTGTTCTCTGACGG 57.782 47.619 0.00 0.00 0.00 4.79
2268 2585 4.634443 CGTGCTTGCCTTAAAGTTAGGTAT 59.366 41.667 0.00 0.00 35.13 2.73
2364 2681 0.907486 TGGCAGAGATGGAAGAGGTG 59.093 55.000 0.00 0.00 0.00 4.00
2467 2784 4.338964 TGAACTTGCAAGCTTGATCTTTGA 59.661 37.500 30.39 8.33 0.00 2.69
2492 2809 6.258230 TCTAGCACTCACAAATTGAAATGG 57.742 37.500 0.00 0.00 32.21 3.16
2505 2822 5.760484 ATTGAAATGGGTAAATGGCACTT 57.240 34.783 0.00 0.00 0.00 3.16
2536 2853 5.013079 TGTGGATATCCTGTGTTGAAAGAGT 59.987 40.000 22.35 0.00 36.82 3.24
2539 2856 6.212589 TGGATATCCTGTGTTGAAAGAGTGTA 59.787 38.462 22.35 0.00 36.82 2.90
2541 2858 7.225538 GGATATCCTGTGTTGAAAGAGTGTATG 59.774 40.741 14.97 0.00 0.00 2.39
2543 2860 5.680619 TCCTGTGTTGAAAGAGTGTATGTT 58.319 37.500 0.00 0.00 0.00 2.71
2545 2862 6.601613 TCCTGTGTTGAAAGAGTGTATGTTTT 59.398 34.615 0.00 0.00 0.00 2.43
2546 2863 6.692681 CCTGTGTTGAAAGAGTGTATGTTTTG 59.307 38.462 0.00 0.00 0.00 2.44
2574 2894 3.299503 TGGCTATGTGTATGCTCTCTGA 58.700 45.455 0.00 0.00 0.00 3.27
2593 2913 0.586319 ACACGCTCAATTTGTCACGG 59.414 50.000 11.14 5.23 0.00 4.94
2672 2992 5.598417 GCCATATTCCAAGGTAATTCTGGTT 59.402 40.000 0.00 0.00 0.00 3.67
2673 2993 6.239036 GCCATATTCCAAGGTAATTCTGGTTC 60.239 42.308 0.00 0.00 0.00 3.62
2674 2994 7.062957 CCATATTCCAAGGTAATTCTGGTTCT 58.937 38.462 0.00 0.00 0.00 3.01
2842 3162 1.324736 GGATCATTCTGACAACGACGC 59.675 52.381 0.00 0.00 0.00 5.19
2907 3227 1.683943 AGGGATGATTGATGGTTGCG 58.316 50.000 0.00 0.00 0.00 4.85
2971 3292 4.234530 AGACTCTGTTGCTGAAAAATGC 57.765 40.909 0.00 0.00 0.00 3.56
2972 3293 3.005155 AGACTCTGTTGCTGAAAAATGCC 59.995 43.478 0.00 0.00 0.00 4.40
2980 3301 1.468520 GCTGAAAAATGCCGAGCTACA 59.531 47.619 0.00 0.00 0.00 2.74
2981 3302 2.476854 GCTGAAAAATGCCGAGCTACAG 60.477 50.000 0.00 0.00 0.00 2.74
3210 3535 5.346551 TGTCGTCGTAAAAATGGTATGAGTG 59.653 40.000 0.00 0.00 0.00 3.51
3211 3536 4.865925 TCGTCGTAAAAATGGTATGAGTGG 59.134 41.667 0.00 0.00 0.00 4.00
3213 3538 3.942748 TCGTAAAAATGGTATGAGTGGCC 59.057 43.478 0.00 0.00 0.00 5.36
3214 3539 3.692101 CGTAAAAATGGTATGAGTGGCCA 59.308 43.478 0.00 0.00 36.64 5.36
3215 3540 4.156922 CGTAAAAATGGTATGAGTGGCCAA 59.843 41.667 7.24 0.00 35.74 4.52
3216 3541 5.336055 CGTAAAAATGGTATGAGTGGCCAAA 60.336 40.000 7.24 0.00 35.74 3.28
3217 3542 4.806640 AAAATGGTATGAGTGGCCAAAG 57.193 40.909 7.24 0.00 35.74 2.77
3218 3543 3.737559 AATGGTATGAGTGGCCAAAGA 57.262 42.857 7.24 0.00 35.74 2.52
3219 3544 3.737559 ATGGTATGAGTGGCCAAAGAA 57.262 42.857 7.24 0.00 35.74 2.52
3220 3545 3.737559 TGGTATGAGTGGCCAAAGAAT 57.262 42.857 7.24 1.34 0.00 2.40
3221 3546 3.620488 TGGTATGAGTGGCCAAAGAATC 58.380 45.455 7.24 1.20 0.00 2.52
3222 3547 3.266772 TGGTATGAGTGGCCAAAGAATCT 59.733 43.478 7.24 0.00 0.00 2.40
3223 3548 4.473196 TGGTATGAGTGGCCAAAGAATCTA 59.527 41.667 7.24 0.00 0.00 1.98
3224 3549 5.132648 TGGTATGAGTGGCCAAAGAATCTAT 59.867 40.000 7.24 0.00 0.00 1.98
3225 3550 5.471456 GGTATGAGTGGCCAAAGAATCTATG 59.529 44.000 7.24 0.00 0.00 2.23
3226 3551 3.282021 TGAGTGGCCAAAGAATCTATGC 58.718 45.455 7.24 0.00 0.00 3.14
3283 3608 3.804873 GGCCAAAGATGTCGAAGATAGTC 59.195 47.826 0.00 0.00 40.67 2.59
3284 3609 4.433615 GCCAAAGATGTCGAAGATAGTCA 58.566 43.478 0.00 0.00 40.67 3.41
3285 3610 4.870426 GCCAAAGATGTCGAAGATAGTCAA 59.130 41.667 0.00 0.00 40.67 3.18
3286 3611 5.351465 GCCAAAGATGTCGAAGATAGTCAAA 59.649 40.000 0.00 0.00 40.67 2.69
3287 3612 6.128282 GCCAAAGATGTCGAAGATAGTCAAAA 60.128 38.462 0.00 0.00 40.67 2.44
3288 3613 7.459486 CCAAAGATGTCGAAGATAGTCAAAAG 58.541 38.462 0.00 0.00 40.67 2.27
3289 3614 7.331934 CCAAAGATGTCGAAGATAGTCAAAAGA 59.668 37.037 0.00 0.00 40.67 2.52
3290 3615 8.712363 CAAAGATGTCGAAGATAGTCAAAAGAA 58.288 33.333 0.00 0.00 40.67 2.52
3291 3616 8.472683 AAGATGTCGAAGATAGTCAAAAGAAG 57.527 34.615 0.00 0.00 40.67 2.85
3292 3617 7.831753 AGATGTCGAAGATAGTCAAAAGAAGA 58.168 34.615 0.00 0.00 40.67 2.87
3293 3618 8.307483 AGATGTCGAAGATAGTCAAAAGAAGAA 58.693 33.333 0.00 0.00 40.67 2.52
3294 3619 8.833231 ATGTCGAAGATAGTCAAAAGAAGAAA 57.167 30.769 0.00 0.00 40.67 2.52
3295 3620 8.833231 TGTCGAAGATAGTCAAAAGAAGAAAT 57.167 30.769 0.00 0.00 40.67 2.17
3326 3651 5.520376 AATTTCATGCCTGGTACTATTGC 57.480 39.130 0.00 0.00 0.00 3.56
3329 3654 1.949525 CATGCCTGGTACTATTGCACC 59.050 52.381 5.85 0.00 34.33 5.01
3347 3672 5.192927 TGCACCCAACATAATTCTTCTAGG 58.807 41.667 0.00 0.00 0.00 3.02
3388 3713 3.128632 TATGCCGACACTACCCGCG 62.129 63.158 0.00 0.00 0.00 6.46
3397 3722 0.368907 CACTACCCGCGTGATTTTCG 59.631 55.000 4.92 0.00 34.35 3.46
3456 3794 6.811665 CGAGTGTCTGGATCAGTAAAATGTTA 59.188 38.462 0.00 0.00 32.61 2.41
3477 3815 8.800370 TGTTATCTTATACACATCCTTTTGCA 57.200 30.769 0.00 0.00 0.00 4.08
3493 3831 5.522460 CCTTTTGCAATAAGATCTTGCCATG 59.478 40.000 18.47 11.65 46.61 3.66
3544 5742 6.527423 ACAAGTTGAAATCAGAAATGCCAAT 58.473 32.000 10.54 0.00 0.00 3.16
3624 5823 2.924880 GCTGGGCCAAAAACGATGTAAC 60.925 50.000 8.04 0.00 0.00 2.50
3633 5832 5.008217 CCAAAAACGATGTAACAGTCCAAGA 59.992 40.000 0.00 0.00 0.00 3.02
3700 5921 2.494530 GCCGGGCAAACAGAAACCA 61.495 57.895 15.62 0.00 0.00 3.67
3708 5931 2.099756 GCAAACAGAAACCAGTCTTGCT 59.900 45.455 0.00 0.00 29.86 3.91
3711 5934 4.423625 AACAGAAACCAGTCTTGCTAGT 57.576 40.909 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 41 3.937814 TCATCGACAACTAGTGGCAAAT 58.062 40.909 0.00 0.00 33.13 2.32
98 120 5.068198 CACATGCAAGCCTGGTTAAATCTAT 59.932 40.000 0.00 0.00 0.00 1.98
133 163 2.416972 GCCCGTGAGAGTAGTTTACCAG 60.417 54.545 0.00 0.00 0.00 4.00
200 233 0.551377 TGATAGGTTTGGGGCAGGGA 60.551 55.000 0.00 0.00 0.00 4.20
230 264 2.573915 GTTTTGGGGATTAAATGGGGCA 59.426 45.455 0.00 0.00 0.00 5.36
235 269 3.370421 GGGCTGGTTTTGGGGATTAAATG 60.370 47.826 0.00 0.00 0.00 2.32
237 271 2.261729 GGGCTGGTTTTGGGGATTAAA 58.738 47.619 0.00 0.00 0.00 1.52
238 272 1.553651 GGGGCTGGTTTTGGGGATTAA 60.554 52.381 0.00 0.00 0.00 1.40
239 273 0.041982 GGGGCTGGTTTTGGGGATTA 59.958 55.000 0.00 0.00 0.00 1.75
265 299 2.666596 CTAGCCTTCCCATCGTGGCC 62.667 65.000 0.00 0.00 45.94 5.36
271 305 1.115930 TCTCGCCTAGCCTTCCCATC 61.116 60.000 0.00 0.00 0.00 3.51
315 349 4.799564 TCCATTTCCCATTACTTTGTGC 57.200 40.909 0.00 0.00 0.00 4.57
385 423 0.239879 CGTTGGTTGAACCGGAATGG 59.760 55.000 9.46 0.00 42.58 3.16
387 425 1.202722 AGACGTTGGTTGAACCGGAAT 60.203 47.619 9.46 0.00 42.58 3.01
506 776 4.157840 TCGCTGCAAGTCTAGTAAATCTGA 59.842 41.667 0.00 0.00 35.30 3.27
904 1205 0.953960 GCGTGGTAGGTTTGGGACAG 60.954 60.000 0.00 0.00 42.39 3.51
907 1208 2.751688 GGCGTGGTAGGTTTGGGA 59.248 61.111 0.00 0.00 0.00 4.37
1056 1357 1.348538 TTGCGCGTACCATGTTCTCG 61.349 55.000 8.43 0.00 0.00 4.04
1089 1390 3.560636 TTTCGAGATTGAGGGGGAATC 57.439 47.619 0.00 0.00 0.00 2.52
1092 1393 3.371595 GGAAATTTCGAGATTGAGGGGGA 60.372 47.826 11.95 0.00 0.00 4.81
1098 1413 5.420725 TCTGGAGGAAATTTCGAGATTGA 57.579 39.130 11.95 3.76 0.00 2.57
1124 1439 3.717294 AGGGCCGCGAGAAATGGT 61.717 61.111 8.23 0.00 0.00 3.55
1153 1468 0.958876 GGTCACCGGATCCCAAACAC 60.959 60.000 9.46 0.00 0.00 3.32
1561 1877 3.318275 GCCTCTCCTTGTCGATGTACATA 59.682 47.826 8.71 0.00 0.00 2.29
1676 1992 6.652481 ACAATCAGGATTTATAGGATGCGAAG 59.348 38.462 0.00 0.00 0.00 3.79
1708 2024 6.702282 GGCAACTATACTGAGTGAACTAATCC 59.298 42.308 0.00 0.00 0.00 3.01
1721 2037 0.459585 ACACGGCGGCAACTATACTG 60.460 55.000 13.24 0.00 0.00 2.74
1880 2196 7.630242 TTTTTGATACAAATTTGGCCAAACA 57.370 28.000 32.62 20.48 32.51 2.83
1899 2215 9.619316 TCGGTTTTGTAGATGTTGATATTTTTG 57.381 29.630 0.00 0.00 0.00 2.44
2004 2321 8.766000 TTGCAATGTTCGACTAACTTTATAGA 57.234 30.769 0.00 0.00 38.99 1.98
2049 2366 7.328493 GCCGTTTCTTTCTAGTTTGCATAAAAT 59.672 33.333 0.00 0.00 0.00 1.82
2052 2369 5.615984 CGCCGTTTCTTTCTAGTTTGCATAA 60.616 40.000 0.00 0.00 0.00 1.90
2053 2370 4.142988 CGCCGTTTCTTTCTAGTTTGCATA 60.143 41.667 0.00 0.00 0.00 3.14
2064 2381 1.073964 GTACTCCCGCCGTTTCTTTC 58.926 55.000 0.00 0.00 0.00 2.62
2069 2386 0.037605 CTCTTGTACTCCCGCCGTTT 60.038 55.000 0.00 0.00 0.00 3.60
2075 2392 2.753452 TGTAGCTTCTCTTGTACTCCCG 59.247 50.000 0.00 0.00 0.00 5.14
2162 2479 5.862924 ACAAAGATCGATCAAATGAACGT 57.137 34.783 26.47 9.25 40.52 3.99
2164 2481 7.691463 CAGAGAACAAAGATCGATCAAATGAAC 59.309 37.037 26.47 17.68 0.00 3.18
2192 2509 3.382832 ACTCCGTCTTCCCTGCCG 61.383 66.667 0.00 0.00 0.00 5.69
2194 2511 2.435059 GCACTCCGTCTTCCCTGC 60.435 66.667 0.00 0.00 0.00 4.85
2268 2585 3.153919 GCCATTGAACTTACCTTCACCA 58.846 45.455 0.00 0.00 29.62 4.17
2325 2642 3.679980 CCACCACGTCTCAAATTCAGTAG 59.320 47.826 0.00 0.00 0.00 2.57
2364 2681 4.453819 CACATCCACTTCTTGTTCTTCCTC 59.546 45.833 0.00 0.00 0.00 3.71
2423 2740 2.573462 ACTCACCTGTTGCATATCCAGT 59.427 45.455 0.00 0.00 0.00 4.00
2467 2784 7.318141 CCATTTCAATTTGTGAGTGCTAGAAT 58.682 34.615 0.00 0.00 37.61 2.40
2522 2839 7.250569 ACAAAACATACACTCTTTCAACACAG 58.749 34.615 0.00 0.00 0.00 3.66
2536 2853 7.010645 CACATAGCCATACGTACAAAACATACA 59.989 37.037 0.00 0.00 0.00 2.29
2539 2856 5.878116 ACACATAGCCATACGTACAAAACAT 59.122 36.000 0.00 0.00 0.00 2.71
2541 2858 5.789710 ACACATAGCCATACGTACAAAAC 57.210 39.130 0.00 0.00 0.00 2.43
2543 2860 5.464057 GCATACACATAGCCATACGTACAAA 59.536 40.000 0.00 0.00 0.00 2.83
2545 2862 4.279922 AGCATACACATAGCCATACGTACA 59.720 41.667 0.00 0.00 0.00 2.90
2546 2863 4.806330 AGCATACACATAGCCATACGTAC 58.194 43.478 0.00 0.00 0.00 3.67
2574 2894 0.586319 CCGTGACAAATTGAGCGTGT 59.414 50.000 0.00 0.00 0.00 4.49
2672 2992 2.575532 CTGAAGTTGCACCTTGGAAGA 58.424 47.619 0.00 0.00 0.00 2.87
2673 2993 1.000938 GCTGAAGTTGCACCTTGGAAG 60.001 52.381 0.00 0.00 0.00 3.46
2674 2994 1.032014 GCTGAAGTTGCACCTTGGAA 58.968 50.000 0.00 0.00 0.00 3.53
2695 3015 5.538118 TGGGTATAATCTGCGTGAACATAG 58.462 41.667 0.00 0.00 0.00 2.23
2842 3162 1.374758 GGAACTCCAGGCAGTCGTG 60.375 63.158 0.00 0.00 35.64 4.35
2907 3227 3.975035 GTCAACGAAACAAAAGATCCAGC 59.025 43.478 0.00 0.00 0.00 4.85
2971 3292 2.417515 GGAGAAGGTTTCTGTAGCTCGG 60.418 54.545 0.00 0.00 40.87 4.63
2972 3293 2.417515 GGGAGAAGGTTTCTGTAGCTCG 60.418 54.545 0.00 0.00 40.87 5.03
2980 3301 3.009584 GGAACATCTGGGAGAAGGTTTCT 59.990 47.826 0.00 0.00 44.21 2.52
2981 3302 3.348119 GGAACATCTGGGAGAAGGTTTC 58.652 50.000 0.00 0.00 29.66 2.78
3154 3479 2.910688 TTCTTGACCGAAGAAGCACT 57.089 45.000 0.00 0.00 44.32 4.40
3183 3508 6.767080 TCATACCATTTTTACGACGACATTG 58.233 36.000 0.00 0.00 0.00 2.82
3326 3651 6.001449 TCCCTAGAAGAATTATGTTGGGTG 57.999 41.667 0.00 0.00 31.10 4.61
3329 3654 6.763610 GTGTCTCCCTAGAAGAATTATGTTGG 59.236 42.308 0.00 0.00 32.16 3.77
3397 3722 7.923878 TCCCTGTTAGTGTTTTTATTTTCTTGC 59.076 33.333 0.00 0.00 0.00 4.01
3406 3731 7.041916 CGTGTGTTATCCCTGTTAGTGTTTTTA 60.042 37.037 0.00 0.00 0.00 1.52
3417 3743 2.743636 CACTCGTGTGTTATCCCTGT 57.256 50.000 9.42 0.00 39.24 4.00
3477 3815 6.322969 TCATTTCAGCATGGCAAGATCTTATT 59.677 34.615 7.86 0.00 36.16 1.40
3493 3831 3.428589 GGCTCCATGAACTTCATTTCAGC 60.429 47.826 13.55 13.55 38.87 4.26
3582 5780 6.080406 CAGCTAGTGCAGTTTTAGTTTTAGC 58.920 40.000 0.00 0.00 42.74 3.09
3602 5801 0.827507 ACATCGTTTTTGGCCCAGCT 60.828 50.000 0.00 0.00 0.00 4.24
3693 5914 4.573900 CATCACTAGCAAGACTGGTTTCT 58.426 43.478 0.00 0.00 38.17 2.52
3700 5921 1.404717 CGGTGCATCACTAGCAAGACT 60.405 52.381 0.00 0.00 44.64 3.24
3708 5931 4.830765 GGCGGCGGTGCATCACTA 62.831 66.667 9.78 0.00 36.28 2.74


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

AutoCloner maintained by Alex Coulton.