Multiple sequence alignment - TraesCS3D01G381100

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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 TraesCS3D01G381100 chr3D 100.000 2492 0 0 1 2492 497370400 497367909 0.000000e+00 4602.0
1 TraesCS3D01G381100 chr3D 88.776 196 13 3 908 1103 499966934 499966748 5.360000e-57 231.0
2 TraesCS3D01G381100 chr3B 89.981 1577 86 25 380 1932 657344194 657342666 0.000000e+00 1971.0
3 TraesCS3D01G381100 chr3B 92.844 559 37 2 1934 2492 657342635 657342080 0.000000e+00 808.0
4 TraesCS3D01G381100 chr3B 88.175 389 29 6 1 388 657344747 657344375 4.890000e-122 448.0
5 TraesCS3D01G381100 chr3B 93.617 47 3 0 1864 1910 94495178 94495132 1.240000e-08 71.3
6 TraesCS3D01G381100 chr3A 89.798 1137 49 25 733 1820 637292579 637293697 0.000000e+00 1395.0
7 TraesCS3D01G381100 chr3A 89.573 211 15 4 456 659 637292114 637292324 6.840000e-66 261.0
8 TraesCS3D01G381100 chr3A 91.935 62 3 1 657 716 637292524 637292585 4.420000e-13 86.1
9 TraesCS3D01G381100 chr1D 75.161 467 63 25 1952 2415 267982909 267983325 1.190000e-38 171.0
10 TraesCS3D01G381100 chr1D 86.441 59 5 3 1204 1261 362920925 362920981 7.440000e-06 62.1
11 TraesCS3D01G381100 chr6D 79.842 253 34 9 2189 2441 354990496 354990261 4.260000e-38 169.0
12 TraesCS3D01G381100 chr6D 100.000 30 0 0 2454 2483 105587632 105587661 3.460000e-04 56.5
13 TraesCS3D01G381100 chr1A 75.439 228 48 4 2042 2263 66172460 66172235 1.220000e-18 104.0
14 TraesCS3D01G381100 chr1A 87.755 49 5 1 1213 1261 462137162 462137209 3.460000e-04 56.5
15 TraesCS3D01G381100 chr1B 94.286 35 2 0 1227 1261 486158393 486158427 1.000000e-03 54.7


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 TraesCS3D01G381100 chr3D 497367909 497370400 2491 True 4602.000000 4602 100.000000 1 2492 1 chr3D.!!$R1 2491
1 TraesCS3D01G381100 chr3B 657342080 657344747 2667 True 1075.666667 1971 90.333333 1 2492 3 chr3B.!!$R2 2491
2 TraesCS3D01G381100 chr3A 637292114 637293697 1583 False 580.700000 1395 90.435333 456 1820 3 chr3A.!!$F1 1364

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
166 168 0.031010 ACCCCCGAAGCTCCTTATCT 60.031 55.0 0.0 0.0 0.0 1.98 F
963 1385 0.381089 ATCAGTACACTCGTAGCGGC 59.619 55.0 0.0 0.0 0.0 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1131 1559 0.961358 AGGACGAGAGGTTCCTGACG 60.961 60.0 0.0 4.63 0.0 4.35 R
2169 2691 0.388907 CCAAAAGCCATTGTCTGCGG 60.389 55.0 0.0 0.00 0.0 5.69 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
53 55 1.268992 TACCCTAGCCGCCACATGTT 61.269 55.000 0.00 0.00 0.00 2.71
60 62 1.002624 CCGCCACATGTTGTACCCT 60.003 57.895 0.00 0.00 0.00 4.34
63 65 1.616159 GCCACATGTTGTACCCTGTT 58.384 50.000 0.00 0.00 0.00 3.16
121 123 0.804989 CTTTGCCCTTCGTCCACATC 59.195 55.000 0.00 0.00 0.00 3.06
144 146 2.915659 ACTCGCCAAGGACCGTCA 60.916 61.111 0.00 0.00 0.00 4.35
166 168 0.031010 ACCCCCGAAGCTCCTTATCT 60.031 55.000 0.00 0.00 0.00 1.98
171 173 1.134401 CCGAAGCTCCTTATCTGCCAA 60.134 52.381 0.00 0.00 0.00 4.52
176 178 1.613836 CTCCTTATCTGCCAATGCCC 58.386 55.000 0.00 0.00 36.33 5.36
187 189 1.523258 CAATGCCCGAGCTCTGAGG 60.523 63.158 12.85 10.83 40.80 3.86
194 196 0.534412 CCGAGCTCTGAGGTCACATT 59.466 55.000 29.70 0.00 42.53 2.71
223 225 4.401519 CCTTGAAGCTCCATGTTCATCATT 59.598 41.667 0.00 0.00 34.09 2.57
224 226 4.976224 TGAAGCTCCATGTTCATCATTG 57.024 40.909 0.00 0.00 34.09 2.82
232 234 2.905415 TGTTCATCATTGCCTCCCTT 57.095 45.000 0.00 0.00 0.00 3.95
239 241 1.988107 TCATTGCCTCCCTTGAGTTCT 59.012 47.619 0.00 0.00 36.86 3.01
273 275 1.165907 TTGCAGAGCCCGTTGTTGAG 61.166 55.000 0.00 0.00 0.00 3.02
281 283 1.554042 CCCGTTGTTGAGTCCGTTCG 61.554 60.000 0.00 0.00 0.00 3.95
313 315 9.769093 CTATTTCGACCAAATTCGATACTTTTT 57.231 29.630 0.00 0.00 46.94 1.94
319 321 9.632969 CGACCAAATTCGATACTTTTTATAGTG 57.367 33.333 0.00 0.00 41.78 2.74
328 330 3.004862 ACTTTTTATAGTGCCGAACGGG 58.995 45.455 15.01 0.00 39.58 5.28
329 331 2.766345 TTTTATAGTGCCGAACGGGT 57.234 45.000 15.01 0.00 38.44 5.28
330 332 2.766345 TTTATAGTGCCGAACGGGTT 57.234 45.000 15.01 0.00 38.44 4.11
343 345 3.606687 GAACGGGTTGATACCAAGTCAT 58.393 45.455 0.00 0.00 46.96 3.06
372 374 1.260198 CGAGTACGCAGCGGTTATCG 61.260 60.000 21.15 18.04 42.76 2.92
390 581 4.837896 ATCGCTGAGTCTCGAATTATGA 57.162 40.909 11.02 0.00 38.28 2.15
396 587 5.052040 GCTGAGTCTCGAATTATGAAGAACG 60.052 44.000 0.00 0.00 0.00 3.95
398 589 5.800438 TGAGTCTCGAATTATGAAGAACGTG 59.200 40.000 0.00 0.00 0.00 4.49
422 613 1.867233 CTGTGTCCGTTGGAGAAAGTG 59.133 52.381 0.00 0.00 27.04 3.16
427 618 3.759618 TGTCCGTTGGAGAAAGTGTTTTT 59.240 39.130 0.00 0.00 29.39 1.94
430 621 3.129638 CCGTTGGAGAAAGTGTTTTTCCA 59.870 43.478 7.41 7.41 34.55 3.53
433 624 5.474825 GTTGGAGAAAGTGTTTTTCCACAA 58.525 37.500 10.37 4.66 37.82 3.33
435 626 6.293004 TGGAGAAAGTGTTTTTCCACAATT 57.707 33.333 7.41 0.00 36.55 2.32
436 627 6.105333 TGGAGAAAGTGTTTTTCCACAATTG 58.895 36.000 3.24 3.24 35.24 2.32
444 635 8.207521 AGTGTTTTTCCACAATTGGTATTTTG 57.792 30.769 10.83 0.00 44.35 2.44
445 636 8.043710 AGTGTTTTTCCACAATTGGTATTTTGA 58.956 29.630 10.83 0.00 44.35 2.69
446 637 8.835439 GTGTTTTTCCACAATTGGTATTTTGAT 58.165 29.630 10.83 0.00 44.35 2.57
466 657 4.590222 TGATATGCAGAGCAGGATAGTGAA 59.410 41.667 0.00 0.00 43.65 3.18
475 666 3.126831 GCAGGATAGTGAATCGGTTGAG 58.873 50.000 0.00 0.00 35.21 3.02
479 670 4.649674 AGGATAGTGAATCGGTTGAGCTTA 59.350 41.667 0.00 0.00 35.21 3.09
480 671 5.128827 AGGATAGTGAATCGGTTGAGCTTAA 59.871 40.000 0.00 0.00 35.21 1.85
481 672 5.992217 GGATAGTGAATCGGTTGAGCTTAAT 59.008 40.000 0.00 0.00 35.21 1.40
482 673 6.146347 GGATAGTGAATCGGTTGAGCTTAATC 59.854 42.308 0.00 0.00 35.21 1.75
483 674 5.091261 AGTGAATCGGTTGAGCTTAATCT 57.909 39.130 0.00 0.00 0.00 2.40
484 675 5.491982 AGTGAATCGGTTGAGCTTAATCTT 58.508 37.500 0.00 0.00 0.00 2.40
485 676 5.940470 AGTGAATCGGTTGAGCTTAATCTTT 59.060 36.000 0.00 0.00 0.00 2.52
486 677 6.431234 AGTGAATCGGTTGAGCTTAATCTTTT 59.569 34.615 0.00 0.00 0.00 2.27
487 678 6.524586 GTGAATCGGTTGAGCTTAATCTTTTG 59.475 38.462 0.00 0.00 0.00 2.44
488 679 4.419522 TCGGTTGAGCTTAATCTTTTGC 57.580 40.909 0.00 0.00 0.00 3.68
489 680 3.190535 TCGGTTGAGCTTAATCTTTTGCC 59.809 43.478 0.00 0.00 0.00 4.52
490 681 3.057596 CGGTTGAGCTTAATCTTTTGCCA 60.058 43.478 0.00 0.00 0.00 4.92
491 682 4.237724 GGTTGAGCTTAATCTTTTGCCAC 58.762 43.478 0.00 0.00 0.00 5.01
492 683 3.829886 TGAGCTTAATCTTTTGCCACG 57.170 42.857 0.00 0.00 0.00 4.94
493 684 3.407698 TGAGCTTAATCTTTTGCCACGA 58.592 40.909 0.00 0.00 0.00 4.35
513 720 1.376424 CACCAGGAAGCGAGTGCAT 60.376 57.895 0.00 0.00 46.23 3.96
528 735 0.587768 TGCATGCTCGTTCACTGTTG 59.412 50.000 20.33 0.00 0.00 3.33
563 770 3.072038 TCATGCCAGATAAGAGGGTGATG 59.928 47.826 0.00 0.00 0.00 3.07
614 827 4.511454 GCGACAAAGAATCCATATGCACTA 59.489 41.667 0.00 0.00 0.00 2.74
725 1142 4.607025 GGCCCCAACCCACCGAAA 62.607 66.667 0.00 0.00 0.00 3.46
726 1143 3.299977 GCCCCAACCCACCGAAAC 61.300 66.667 0.00 0.00 0.00 2.78
727 1144 2.981350 CCCCAACCCACCGAAACG 60.981 66.667 0.00 0.00 0.00 3.60
754 1171 0.463620 CCAAACCCAACCCAACACAG 59.536 55.000 0.00 0.00 0.00 3.66
829 1251 2.125552 TCATTCTCCACTGCCGCG 60.126 61.111 0.00 0.00 0.00 6.46
927 1349 1.533033 TGAGAACCTCCTCGCCACA 60.533 57.895 0.00 0.00 35.99 4.17
962 1384 1.941294 AGATCAGTACACTCGTAGCGG 59.059 52.381 0.00 0.00 0.00 5.52
963 1385 0.381089 ATCAGTACACTCGTAGCGGC 59.619 55.000 0.00 0.00 0.00 6.53
964 1386 0.956902 TCAGTACACTCGTAGCGGCA 60.957 55.000 1.45 0.00 0.00 5.69
965 1387 0.523546 CAGTACACTCGTAGCGGCAG 60.524 60.000 1.45 0.00 0.00 4.85
966 1388 1.872679 GTACACTCGTAGCGGCAGC 60.873 63.158 0.00 0.00 45.58 5.25
1008 1430 2.925162 GAAGCGGGAGGATGAACGGG 62.925 65.000 0.00 0.00 0.00 5.28
1150 1578 0.961358 CGTCAGGAACCTCTCGTCCT 60.961 60.000 0.00 0.00 0.00 3.85
1168 1596 3.382832 CCTCCCAGAGGTTCGCGT 61.383 66.667 5.77 0.00 44.25 6.01
1424 1873 1.810532 ACGAGATCGGCAAGGAGAC 59.189 57.895 7.22 0.00 44.95 3.36
1534 1988 2.505407 TGGATTCAAGATCCATGGACGT 59.495 45.455 18.99 0.80 42.81 4.34
1666 2128 1.153647 CACGTGAGCTCGGCCATTA 60.154 57.895 10.90 0.00 34.94 1.90
1682 2144 3.701040 GCCATTAAATGTGGTCCTGACAT 59.299 43.478 0.00 0.00 39.01 3.06
1791 2272 3.567797 GGATCCGCTGCGCACTTC 61.568 66.667 18.00 9.56 0.00 3.01
1839 2323 1.604278 GACTCGCAGCTCAAAAGGTTT 59.396 47.619 0.00 0.00 0.00 3.27
1841 2325 1.334869 CTCGCAGCTCAAAAGGTTTGT 59.665 47.619 0.98 0.00 0.00 2.83
1850 2343 4.747810 CTCAAAAGGTTTGTTCAAGCAGT 58.252 39.130 0.98 0.00 35.10 4.40
1864 2357 5.929697 TCAAGCAGTAGTTTTGATGTGAG 57.070 39.130 0.00 0.00 0.00 3.51
1900 2393 1.073923 ACTTGACAAATCCGGCTCCTT 59.926 47.619 0.00 0.00 0.00 3.36
1904 2397 3.963129 TGACAAATCCGGCTCCTTAAAT 58.037 40.909 0.00 0.00 0.00 1.40
1905 2398 3.694072 TGACAAATCCGGCTCCTTAAATG 59.306 43.478 0.00 0.00 0.00 2.32
1911 2404 0.179067 CGGCTCCTTAAATGCCCGTA 60.179 55.000 0.00 0.00 43.42 4.02
1913 2406 2.371306 GGCTCCTTAAATGCCCGTAAA 58.629 47.619 0.00 0.00 40.71 2.01
1915 2408 3.383505 GGCTCCTTAAATGCCCGTAAAAT 59.616 43.478 0.00 0.00 40.71 1.82
1966 2488 4.899457 TCGTGTACCTCATATTTCATCCCT 59.101 41.667 0.00 0.00 0.00 4.20
1975 2497 9.305555 ACCTCATATTTCATCCCTTAAATCATG 57.694 33.333 0.00 0.00 0.00 3.07
1976 2498 9.305555 CCTCATATTTCATCCCTTAAATCATGT 57.694 33.333 0.00 0.00 0.00 3.21
2000 2522 7.593273 TGTAAACCATGCAAAAGAATTCTTACG 59.407 33.333 20.76 15.14 34.61 3.18
2003 2525 6.608610 ACCATGCAAAAGAATTCTTACGTAC 58.391 36.000 20.76 9.72 34.61 3.67
2026 2548 2.179427 ACTCTGTACACCATGCTAGCA 58.821 47.619 21.85 21.85 0.00 3.49
2095 2617 4.729856 GGTAGTTGGGCGCGTCGT 62.730 66.667 8.43 0.00 0.00 4.34
2127 2649 5.398603 ACTCCTCTTCATCCATATAAGCG 57.601 43.478 0.00 0.00 0.00 4.68
2146 2668 4.194720 GCATCTCGTCGACGCCCT 62.195 66.667 32.19 15.75 39.60 5.19
2182 2704 3.113745 CATCCCGCAGACAATGGC 58.886 61.111 0.00 0.00 0.00 4.40
2183 2705 1.452651 CATCCCGCAGACAATGGCT 60.453 57.895 0.00 0.00 0.00 4.75
2251 2773 2.439156 GCTCCGCCTGCAAATCCT 60.439 61.111 0.00 0.00 0.00 3.24
2252 2774 2.476320 GCTCCGCCTGCAAATCCTC 61.476 63.158 0.00 0.00 0.00 3.71
2253 2775 2.125147 TCCGCCTGCAAATCCTCG 60.125 61.111 0.00 0.00 0.00 4.63
2264 2786 2.420466 AAATCCTCGGCCCCAACGTT 62.420 55.000 0.00 0.00 0.00 3.99
2288 2810 1.254284 CGTCCTCCTTGTGCTCCTCT 61.254 60.000 0.00 0.00 0.00 3.69
2297 2819 0.616111 TGTGCTCCTCTTCCTCCTCC 60.616 60.000 0.00 0.00 0.00 4.30
2298 2820 0.325203 GTGCTCCTCTTCCTCCTCCT 60.325 60.000 0.00 0.00 0.00 3.69
2299 2821 0.032615 TGCTCCTCTTCCTCCTCCTC 60.033 60.000 0.00 0.00 0.00 3.71
2300 2822 0.759060 GCTCCTCTTCCTCCTCCTCC 60.759 65.000 0.00 0.00 0.00 4.30
2323 2845 1.687493 CCTCCTCTCCCACCACCTC 60.687 68.421 0.00 0.00 0.00 3.85
2348 2870 0.252467 CCACCTCCAAGTCCTCCTCT 60.252 60.000 0.00 0.00 0.00 3.69
2352 2874 1.343884 CCTCCAAGTCCTCCTCTGGAT 60.344 57.143 0.00 0.00 38.52 3.41
2417 2939 0.819259 TTGCCCGGATATGCTCAAGC 60.819 55.000 0.73 0.00 42.50 4.01
2428 2950 3.800863 CTCAAGCAGCTGCAGCCG 61.801 66.667 38.24 26.32 45.16 5.52
2458 2980 3.243535 GGCGTTAGGTATGGGTACACTAC 60.244 52.174 0.00 0.00 32.25 2.73
2474 2996 3.159858 TACCGCGGGAATGCCTAGC 62.160 63.158 31.76 0.00 35.49 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 55 2.228480 GGAGGGGCAACAGGGTACA 61.228 63.158 0.00 0.00 39.74 2.90
60 62 2.840753 GGTCAAGGGAGGGGCAACA 61.841 63.158 0.00 0.00 39.74 3.33
88 90 4.351054 AAAGAGGGCGGTGGCAGG 62.351 66.667 0.00 0.00 42.47 4.85
89 91 3.058160 CAAAGAGGGCGGTGGCAG 61.058 66.667 0.00 0.00 42.47 4.85
93 95 3.868200 AAGGGCAAAGAGGGCGGTG 62.868 63.158 0.00 0.00 0.00 4.94
94 96 3.569200 GAAGGGCAAAGAGGGCGGT 62.569 63.158 0.00 0.00 0.00 5.68
134 136 2.298661 GGGGGTGATGACGGTCCTT 61.299 63.158 5.55 0.00 0.00 3.36
144 146 0.326238 TAAGGAGCTTCGGGGGTGAT 60.326 55.000 0.00 0.00 0.00 3.06
166 168 3.720601 AGAGCTCGGGCATTGGCA 61.721 61.111 11.40 0.00 43.71 4.92
171 173 2.364842 ACCTCAGAGCTCGGGCAT 60.365 61.111 11.40 0.00 41.70 4.40
176 178 1.203287 TCAATGTGACCTCAGAGCTCG 59.797 52.381 8.37 3.55 0.00 5.03
187 189 2.476854 GCTTCAAGGCGATCAATGTGAC 60.477 50.000 0.00 0.00 0.00 3.67
194 196 0.543277 ATGGAGCTTCAAGGCGATCA 59.457 50.000 0.00 0.00 37.29 2.92
223 225 1.544825 CCGAGAACTCAAGGGAGGCA 61.545 60.000 2.78 0.00 45.81 4.75
224 226 1.219393 CCGAGAACTCAAGGGAGGC 59.781 63.158 2.78 0.00 45.81 4.70
232 234 3.071892 ACATTTTGGTACCCGAGAACTCA 59.928 43.478 10.07 0.00 0.00 3.41
239 241 1.883275 CTGCAACATTTTGGTACCCGA 59.117 47.619 10.07 0.00 32.81 5.14
259 261 2.027625 CGGACTCAACAACGGGCTC 61.028 63.158 0.00 0.00 0.00 4.70
273 275 1.844962 GAAATAGTCGCTCGAACGGAC 59.155 52.381 8.55 5.29 0.00 4.79
295 297 8.403236 GGCACTATAAAAAGTATCGAATTTGGT 58.597 33.333 0.00 0.00 0.00 3.67
301 303 6.020440 CGTTCGGCACTATAAAAAGTATCGAA 60.020 38.462 0.00 8.49 39.01 3.71
303 305 5.332055 CCGTTCGGCACTATAAAAAGTATCG 60.332 44.000 0.00 0.00 0.00 2.92
305 307 4.812626 CCCGTTCGGCACTATAAAAAGTAT 59.187 41.667 5.66 0.00 0.00 2.12
313 315 1.184431 TCAACCCGTTCGGCACTATA 58.816 50.000 5.66 0.00 33.26 1.31
316 318 0.390735 GTATCAACCCGTTCGGCACT 60.391 55.000 5.66 0.00 33.26 4.40
319 321 0.674269 TTGGTATCAACCCGTTCGGC 60.674 55.000 5.66 0.00 46.16 5.54
343 345 4.902308 CGTACTCGCCATGTCCAA 57.098 55.556 0.00 0.00 0.00 3.53
369 371 4.837896 TCATAATTCGAGACTCAGCGAT 57.162 40.909 2.82 0.00 36.31 4.58
372 374 5.052040 CGTTCTTCATAATTCGAGACTCAGC 60.052 44.000 2.82 0.00 0.00 4.26
373 375 6.021074 CACGTTCTTCATAATTCGAGACTCAG 60.021 42.308 2.82 0.00 0.00 3.35
390 581 1.014352 GGACACAGCAACACGTTCTT 58.986 50.000 0.00 0.00 0.00 2.52
396 587 1.092921 TCCAACGGACACAGCAACAC 61.093 55.000 0.00 0.00 0.00 3.32
398 589 0.531974 TCTCCAACGGACACAGCAAC 60.532 55.000 0.00 0.00 0.00 4.17
430 621 7.147863 TGCTCTGCATATCAAAATACCAATTGT 60.148 33.333 4.43 0.00 31.71 2.71
433 624 6.015688 CCTGCTCTGCATATCAAAATACCAAT 60.016 38.462 0.00 0.00 38.13 3.16
435 626 4.823442 CCTGCTCTGCATATCAAAATACCA 59.177 41.667 0.00 0.00 38.13 3.25
436 627 5.065914 TCCTGCTCTGCATATCAAAATACC 58.934 41.667 0.00 0.00 38.13 2.73
444 635 4.797800 TCACTATCCTGCTCTGCATATC 57.202 45.455 0.00 0.00 38.13 1.63
445 636 5.624052 CGATTCACTATCCTGCTCTGCATAT 60.624 44.000 0.00 0.00 38.13 1.78
446 637 4.321527 CGATTCACTATCCTGCTCTGCATA 60.322 45.833 0.00 0.00 38.13 3.14
466 657 4.142381 GGCAAAAGATTAAGCTCAACCGAT 60.142 41.667 0.00 0.00 0.00 4.18
475 666 2.519963 GCTCGTGGCAAAAGATTAAGC 58.480 47.619 0.00 0.00 41.35 3.09
487 678 2.743928 CTTCCTGGTGCTCGTGGC 60.744 66.667 0.00 0.00 42.22 5.01
488 679 2.743928 GCTTCCTGGTGCTCGTGG 60.744 66.667 7.08 0.00 0.00 4.94
489 680 3.114616 CGCTTCCTGGTGCTCGTG 61.115 66.667 11.24 0.00 0.00 4.35
490 681 3.288308 CTCGCTTCCTGGTGCTCGT 62.288 63.158 11.24 0.00 0.00 4.18
491 682 2.507992 CTCGCTTCCTGGTGCTCG 60.508 66.667 11.24 4.20 0.00 5.03
492 683 1.739562 CACTCGCTTCCTGGTGCTC 60.740 63.158 11.24 0.00 0.00 4.26
493 684 2.345244 CACTCGCTTCCTGGTGCT 59.655 61.111 11.24 0.00 0.00 4.40
513 720 0.880278 GCTCCAACAGTGAACGAGCA 60.880 55.000 18.63 0.00 44.26 4.26
528 735 1.358046 GCATGAATTCAGGCGCTCC 59.642 57.895 27.10 4.24 43.83 4.70
563 770 0.379316 GACGTGTCACCAACCAAACC 59.621 55.000 0.00 0.00 0.00 3.27
614 827 1.672881 GGAATTGCTGCGCTACAATCT 59.327 47.619 22.71 15.21 35.49 2.40
636 849 1.593006 GTGACGCCAATTCGTATCCAG 59.407 52.381 0.00 0.00 43.42 3.86
681 1098 2.478746 CGTCCAATTTGACCGCCG 59.521 61.111 4.21 0.00 31.35 6.46
722 1139 2.981350 TTTGGGGCGAGCCGTTTC 60.981 61.111 8.14 0.00 36.85 2.78
723 1140 3.292159 GTTTGGGGCGAGCCGTTT 61.292 61.111 8.14 0.00 36.85 3.60
727 1144 4.986708 TTGGGTTTGGGGCGAGCC 62.987 66.667 5.37 5.37 0.00 4.70
728 1145 3.680786 GTTGGGTTTGGGGCGAGC 61.681 66.667 0.00 0.00 0.00 5.03
729 1146 2.989253 GGTTGGGTTTGGGGCGAG 60.989 66.667 0.00 0.00 0.00 5.03
774 1196 0.610174 TGTGAGTGTGAGATCAGCCC 59.390 55.000 0.00 0.00 0.00 5.19
829 1251 3.117171 CTCGTCAGCAGCAGCACC 61.117 66.667 3.17 0.00 45.49 5.01
834 1256 2.050077 CGTCACTCGTCAGCAGCA 60.050 61.111 0.00 0.00 34.52 4.41
969 1391 3.359523 TTTCCGCTGCTGCTGCTG 61.360 61.111 25.43 20.27 40.48 4.41
970 1392 3.360340 GTTTCCGCTGCTGCTGCT 61.360 61.111 25.43 0.00 40.48 4.24
971 1393 3.360340 AGTTTCCGCTGCTGCTGC 61.360 61.111 19.94 19.94 36.97 5.25
972 1394 1.509644 TTCAGTTTCCGCTGCTGCTG 61.510 55.000 14.03 7.35 36.49 4.41
984 1406 0.984230 TCATCCTCCCGCTTCAGTTT 59.016 50.000 0.00 0.00 0.00 2.66
1008 1430 2.508663 GAGGCGAGGTTGCGGTAC 60.509 66.667 0.00 0.00 35.06 3.34
1131 1559 0.961358 AGGACGAGAGGTTCCTGACG 60.961 60.000 0.00 4.63 0.00 4.35
1231 1662 3.801997 CCGCATGGAGAAGGCCCT 61.802 66.667 0.00 0.00 37.49 5.19
1346 1777 1.093159 CACCTGATGCTTCTTCTGCC 58.907 55.000 0.88 0.00 0.00 4.85
1424 1873 2.563179 TGACCCCTCTTCTTCTTCTTCG 59.437 50.000 0.00 0.00 0.00 3.79
1534 1988 3.318839 CCAAAACAGAGGCACATCAAGAA 59.681 43.478 0.00 0.00 0.00 2.52
1666 2128 2.109834 TCCCAATGTCAGGACCACATTT 59.890 45.455 7.32 0.00 41.58 2.32
1682 2144 1.229145 CATGCCCCCAAAGTCCCAA 60.229 57.895 0.00 0.00 0.00 4.12
1758 2239 2.827921 GGATCCATGGCCACAAATATCC 59.172 50.000 8.16 12.91 0.00 2.59
1839 2323 5.588246 TCACATCAAAACTACTGCTTGAACA 59.412 36.000 0.00 0.00 33.08 3.18
1841 2325 6.054941 TCTCACATCAAAACTACTGCTTGAA 58.945 36.000 0.00 0.00 33.08 2.69
1864 2357 4.710423 TCAAGTCTGACAGTAGATGCTC 57.290 45.455 10.88 0.00 0.00 4.26
1876 2369 1.347707 AGCCGGATTTGTCAAGTCTGA 59.652 47.619 16.36 0.00 0.00 3.27
1878 2371 1.339151 GGAGCCGGATTTGTCAAGTCT 60.339 52.381 5.05 0.00 0.00 3.24
1884 2377 3.489229 GCATTTAAGGAGCCGGATTTGTC 60.489 47.826 5.05 0.00 0.00 3.18
1900 2393 6.017770 CGTCCAATCTATTTTACGGGCATTTA 60.018 38.462 0.00 0.00 0.00 1.40
1904 2397 3.199677 CGTCCAATCTATTTTACGGGCA 58.800 45.455 0.00 0.00 0.00 5.36
1905 2398 3.001939 CACGTCCAATCTATTTTACGGGC 59.998 47.826 9.90 0.00 32.60 6.13
1946 2468 9.793259 GATTTAAGGGATGAAATATGAGGTACA 57.207 33.333 0.00 0.00 0.00 2.90
1975 2497 7.593644 ACGTAAGAATTCTTTTGCATGGTTTAC 59.406 33.333 25.02 11.65 43.62 2.01
1976 2498 7.653647 ACGTAAGAATTCTTTTGCATGGTTTA 58.346 30.769 25.02 0.52 43.62 2.01
2000 2522 3.128242 AGCATGGTGTACAGAGTACGTAC 59.872 47.826 18.10 18.10 39.75 3.67
2003 2525 2.941453 AGCATGGTGTACAGAGTACG 57.059 50.000 0.00 0.00 0.00 3.67
2026 2548 4.978083 TCGACGAGGAAGCTTAGTTTAT 57.022 40.909 0.00 0.00 0.00 1.40
2095 2617 1.850998 TGAAGAGGAGTCGGATCCCTA 59.149 52.381 6.06 0.00 40.53 3.53
2169 2691 0.388907 CCAAAAGCCATTGTCTGCGG 60.389 55.000 0.00 0.00 0.00 5.69
2170 2692 1.010419 GCCAAAAGCCATTGTCTGCG 61.010 55.000 0.00 0.00 34.35 5.18
2198 2720 1.103803 TTCTCTCCGGTCGGAATCAG 58.896 55.000 13.36 9.35 44.66 2.90
2241 2763 2.830370 GGGGCCGAGGATTTGCAG 60.830 66.667 0.00 0.00 0.00 4.41
2264 2786 2.879233 GCACAAGGAGGACGTGGGA 61.879 63.158 0.00 0.00 33.42 4.37
2288 2810 1.002274 GGAGCTGGAGGAGGAGGAA 59.998 63.158 0.00 0.00 0.00 3.36
2297 2819 1.457455 GGGAGAGGAGGAGCTGGAG 60.457 68.421 0.00 0.00 0.00 3.86
2298 2820 2.249125 TGGGAGAGGAGGAGCTGGA 61.249 63.158 0.00 0.00 0.00 3.86
2299 2821 2.063378 GTGGGAGAGGAGGAGCTGG 61.063 68.421 0.00 0.00 0.00 4.85
2300 2822 2.063378 GGTGGGAGAGGAGGAGCTG 61.063 68.421 0.00 0.00 0.00 4.24
2323 2845 1.268283 GGACTTGGAGGTGGAGGAGG 61.268 65.000 0.00 0.00 0.00 4.30
2348 2870 0.541392 CTTCGGATGTGGTGGATCCA 59.459 55.000 11.44 11.44 45.01 3.41
2352 2874 1.191535 CTACCTTCGGATGTGGTGGA 58.808 55.000 7.73 0.00 34.81 4.02
2433 2955 1.069668 GTACCCATACCTAACGCCTGG 59.930 57.143 0.00 0.00 0.00 4.45
2435 2957 1.758862 GTGTACCCATACCTAACGCCT 59.241 52.381 0.00 0.00 0.00 5.52
2458 2980 4.545706 TGCTAGGCATTCCCGCGG 62.546 66.667 21.04 21.04 39.21 6.46
2462 2984 4.567318 CCACTGCTAGGCATTCCC 57.433 61.111 0.00 0.00 38.13 3.97
2474 2996 2.281208 TTTTCCCGTCCGCCACTG 60.281 61.111 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.