Multiple sequence alignment - TraesCS5D01G203500

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 TraesCS5D01G203500 chr5D 100.000 2722 0 0 1 2722 308651349 308648628 0.000000e+00 5027
1 TraesCS5D01G203500 chr5B 90.590 1764 94 40 273 1993 353988332 353986598 0.000000e+00 2272
2 TraesCS5D01G203500 chr5B 86.059 746 66 17 1988 2722 353986560 353985842 0.000000e+00 767
3 TraesCS5D01G203500 chr5B 89.170 277 25 3 1 276 353988710 353988438 9.330000e-90 340
4 TraesCS5D01G203500 chr5A 93.455 1039 45 7 692 1716 389153301 389154330 0.000000e+00 1520
5 TraesCS5D01G203500 chr5A 89.781 274 23 2 3 275 389147206 389147475 2.010000e-91 346
6 TraesCS5D01G203500 chr5A 88.435 294 21 5 273 558 389147581 389147869 2.600000e-90 342
7 TraesCS5D01G203500 chr5A 85.654 237 18 7 1771 1993 389154350 389154584 4.530000e-58 235
8 TraesCS5D01G203500 chr5A 91.358 81 6 1 624 703 389149258 389149338 2.870000e-20 110


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 TraesCS5D01G203500 chr5D 308648628 308651349 2721 True 5027.000000 5027 100.000000 1 2722 1 chr5D.!!$R1 2721
1 TraesCS5D01G203500 chr5B 353985842 353988710 2868 True 1126.333333 2272 88.606333 1 2722 3 chr5B.!!$R1 2721
2 TraesCS5D01G203500 chr5A 389147206 389154584 7378 False 510.600000 1520 89.736600 3 1993 5 chr5A.!!$F1 1990

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
186 188 0.179148 GGACCGCCCGCTAAAAATTG 60.179 55.0 0.0 0.0 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 7414 0.393077 CCCTAGAATTGGCGGTCGAT 59.607 55.0 0.0 0.0 0.0 3.59 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
21 22 0.620556 CCTCCCAACATACACTGGCT 59.379 55.000 0.00 0.00 0.00 4.75
35 36 3.073062 ACACTGGCTAGTTCAACCTTCAT 59.927 43.478 0.00 0.00 34.07 2.57
52 53 9.658799 CAACCTTCATCTTCTTTCTAACTATCA 57.341 33.333 0.00 0.00 0.00 2.15
108 109 5.449297 TCTTCCCATTGATACATTGTCCA 57.551 39.130 0.00 0.00 0.00 4.02
126 128 3.254166 GTCCAAGGACTCGTAGTACAACA 59.746 47.826 11.94 0.00 41.57 3.33
146 148 3.456277 ACACCAATATCCTCCTCAACTCC 59.544 47.826 0.00 0.00 0.00 3.85
147 149 3.455910 CACCAATATCCTCCTCAACTCCA 59.544 47.826 0.00 0.00 0.00 3.86
185 187 0.609681 TGGACCGCCCGCTAAAAATT 60.610 50.000 0.00 0.00 37.93 1.82
186 188 0.179148 GGACCGCCCGCTAAAAATTG 60.179 55.000 0.00 0.00 0.00 2.32
222 224 3.626217 GGTACCTCCTCGCAAATTTTAGG 59.374 47.826 4.06 5.09 0.00 2.69
232 234 3.588955 GCAAATTTTAGGGCCACTTCAG 58.411 45.455 6.18 0.00 0.00 3.02
233 235 3.588955 CAAATTTTAGGGCCACTTCAGC 58.411 45.455 6.18 0.00 0.00 4.26
286 398 4.230657 CACTAAGAGACCACTTCAACTCG 58.769 47.826 0.00 0.00 34.98 4.18
291 403 0.391597 GACCACTTCAACTCGGACCA 59.608 55.000 0.00 0.00 0.00 4.02
316 428 7.176690 CAGACAAAACCCCATTTTACTCACTAT 59.823 37.037 0.00 0.00 38.50 2.12
376 488 4.274602 TGCCAATGTTTGCTTTGATCAT 57.725 36.364 0.00 0.00 33.22 2.45
377 489 3.997681 TGCCAATGTTTGCTTTGATCATG 59.002 39.130 0.00 0.00 33.22 3.07
412 524 5.872070 CCTCTCCTCTTCTTGTATTCAACAC 59.128 44.000 0.00 0.00 38.00 3.32
436 551 3.845781 ATTTGACGTCTCATAGGCCAT 57.154 42.857 17.92 0.00 0.00 4.40
437 552 2.890808 TTGACGTCTCATAGGCCATC 57.109 50.000 17.92 0.00 0.00 3.51
438 553 1.775385 TGACGTCTCATAGGCCATCA 58.225 50.000 17.92 0.00 0.00 3.07
466 581 2.058798 GCTTGTGATGAAACGTCTCGA 58.941 47.619 0.00 0.00 0.00 4.04
542 664 5.333111 CGAAGCACCTTTGACACTAACTTAC 60.333 44.000 0.00 0.00 0.00 2.34
545 667 6.062095 AGCACCTTTGACACTAACTTACATT 58.938 36.000 0.00 0.00 0.00 2.71
546 668 6.017109 AGCACCTTTGACACTAACTTACATTG 60.017 38.462 0.00 0.00 0.00 2.82
547 669 6.238648 GCACCTTTGACACTAACTTACATTGT 60.239 38.462 0.00 0.00 0.00 2.71
573 695 5.204409 ACACATTGCATATGCTAATTGGG 57.796 39.130 27.13 18.77 42.66 4.12
576 698 5.047872 CACATTGCATATGCTAATTGGGCTA 60.048 40.000 27.13 1.01 42.66 3.93
595 2072 7.461749 TGGGCTAATATCCTTTATTCTCTTGG 58.538 38.462 0.00 0.00 0.00 3.61
596 2073 6.887002 GGGCTAATATCCTTTATTCTCTTGGG 59.113 42.308 0.00 0.00 0.00 4.12
597 2074 7.462590 GGCTAATATCCTTTATTCTCTTGGGT 58.537 38.462 0.00 0.00 0.00 4.51
598 2075 7.945109 GGCTAATATCCTTTATTCTCTTGGGTT 59.055 37.037 0.00 0.00 0.00 4.11
603 2080 9.853177 ATATCCTTTATTCTCTTGGGTTAGTTG 57.147 33.333 0.00 0.00 0.00 3.16
604 2081 7.324388 TCCTTTATTCTCTTGGGTTAGTTGA 57.676 36.000 0.00 0.00 0.00 3.18
605 2082 7.166167 TCCTTTATTCTCTTGGGTTAGTTGAC 58.834 38.462 0.00 0.00 0.00 3.18
606 2083 6.374613 CCTTTATTCTCTTGGGTTAGTTGACC 59.625 42.308 0.00 0.00 39.04 4.02
657 2134 1.630369 TGGGGATCAAGACAACAGAGG 59.370 52.381 0.00 0.00 0.00 3.69
666 2187 6.677781 TCAAGACAACAGAGGTACTTTTTG 57.322 37.500 0.00 0.00 41.55 2.44
826 6322 1.538047 AAGCCCTACAAGACGTCGTA 58.462 50.000 10.46 6.53 0.00 3.43
899 6397 6.419791 CACGTTCTCCTCCTCTATATATCCT 58.580 44.000 0.00 0.00 0.00 3.24
902 6400 6.708949 CGTTCTCCTCCTCTATATATCCTAGC 59.291 46.154 0.00 0.00 0.00 3.42
940 6438 1.738099 CGGAGCAACCACCTCTTCG 60.738 63.158 1.20 0.00 38.90 3.79
981 6479 2.668850 TCCCCTCAAGAAAGATCCCT 57.331 50.000 0.00 0.00 0.00 4.20
1494 6996 2.571653 AGATCGGGTTGATGAACTCCAA 59.428 45.455 0.00 0.00 37.47 3.53
1496 6998 2.710377 TCGGGTTGATGAACTCCAATG 58.290 47.619 0.00 0.00 32.15 2.82
1628 7139 2.236146 AGCATGTCACTTTATCCCACGA 59.764 45.455 0.00 0.00 0.00 4.35
1698 7209 8.791605 CAAGTTTGTGTTATCATCAATTCATCG 58.208 33.333 0.00 0.00 0.00 3.84
1741 7252 9.923143 TCGATCATTAATTAACTAATCGGTGAT 57.077 29.630 24.04 16.58 0.00 3.06
1760 7271 9.554395 TCGGTGATATAGAATCATAGAGAGATC 57.446 37.037 0.00 0.00 0.00 2.75
1789 7300 4.402155 CACCATATATTGCCACAACCTTGT 59.598 41.667 0.00 0.00 43.36 3.16
1804 7315 5.486063 ACAACCTTGTGATGTATACCTACCA 59.514 40.000 0.00 0.00 40.49 3.25
1806 7317 4.407945 ACCTTGTGATGTATACCTACCACC 59.592 45.833 0.00 0.00 0.00 4.61
1807 7318 4.202326 CCTTGTGATGTATACCTACCACCC 60.202 50.000 0.00 0.00 0.00 4.61
1808 7319 4.274794 TGTGATGTATACCTACCACCCT 57.725 45.455 0.00 0.00 0.00 4.34
1809 7320 5.406570 TGTGATGTATACCTACCACCCTA 57.593 43.478 0.00 0.00 0.00 3.53
1810 7321 5.142639 TGTGATGTATACCTACCACCCTAC 58.857 45.833 0.00 0.00 0.00 3.18
1851 7363 5.149977 GTTTTCTTTTCATGAGAGCTTCGG 58.850 41.667 0.00 0.00 0.00 4.30
1898 7410 0.899019 GTTTGGGTGGTGGTGTGTTT 59.101 50.000 0.00 0.00 0.00 2.83
1899 7411 0.898320 TTTGGGTGGTGGTGTGTTTG 59.102 50.000 0.00 0.00 0.00 2.93
1901 7413 0.251832 TGGGTGGTGGTGTGTTTGTT 60.252 50.000 0.00 0.00 0.00 2.83
1902 7414 1.005569 TGGGTGGTGGTGTGTTTGTTA 59.994 47.619 0.00 0.00 0.00 2.41
1950 7473 1.618343 CTCCCGGGCAAATGAAAAGTT 59.382 47.619 18.49 0.00 0.00 2.66
1965 7488 6.701145 TGAAAAGTTAGCACATGTTTGGTA 57.299 33.333 0.00 0.00 0.00 3.25
1993 7516 5.922544 GCACATGGGTAATGCTTGATTAATC 59.077 40.000 8.60 8.60 40.22 1.75
1994 7517 6.449698 CACATGGGTAATGCTTGATTAATCC 58.550 40.000 12.90 0.00 40.22 3.01
1995 7518 6.040729 CACATGGGTAATGCTTGATTAATCCA 59.959 38.462 12.90 4.34 40.22 3.41
1996 7519 6.783977 ACATGGGTAATGCTTGATTAATCCAT 59.216 34.615 12.90 6.45 40.23 3.41
1997 7520 7.949565 ACATGGGTAATGCTTGATTAATCCATA 59.050 33.333 12.90 0.00 38.98 2.74
1999 7522 8.352137 TGGGTAATGCTTGATTAATCCATATG 57.648 34.615 12.90 0.00 31.88 1.78
2003 7567 7.844493 AATGCTTGATTAATCCATATGTGGT 57.156 32.000 12.90 0.00 46.16 4.16
2006 7570 7.062322 TGCTTGATTAATCCATATGTGGTCTT 58.938 34.615 12.90 6.38 46.16 3.01
2008 7572 7.864379 GCTTGATTAATCCATATGTGGTCTTTG 59.136 37.037 12.90 0.00 46.16 2.77
2013 7577 6.933514 AATCCATATGTGGTCTTTGGTTTT 57.066 33.333 8.51 0.00 46.16 2.43
2020 7584 1.289530 TGGTCTTTGGTTTTGGGACCT 59.710 47.619 10.99 0.00 44.60 3.85
2030 7594 1.724148 TTTGGGACCTGGGTGCATGA 61.724 55.000 12.98 0.00 38.24 3.07
2054 7618 1.305802 ACGGGCATCACCTCACCTA 60.306 57.895 0.00 0.00 39.10 3.08
2118 7691 8.147244 AGTTATGGAGGTAGTACTTCACAAAT 57.853 34.615 13.79 5.03 0.00 2.32
2152 7725 0.452987 TTCAGCTGCCATCATTTCGC 59.547 50.000 9.47 0.00 0.00 4.70
2159 7732 2.483106 CTGCCATCATTTCGCTATCCAG 59.517 50.000 0.00 0.00 0.00 3.86
2160 7733 1.198637 GCCATCATTTCGCTATCCAGC 59.801 52.381 0.00 0.00 44.90 4.85
2173 7746 3.732721 GCTATCCAGCGCAAATTTCAATC 59.267 43.478 11.47 0.00 38.22 2.67
2178 7751 4.217334 TCCAGCGCAAATTTCAATCTACAA 59.783 37.500 11.47 0.00 0.00 2.41
2187 7760 9.045223 GCAAATTTCAATCTACAACCTTCTTTT 57.955 29.630 0.00 0.00 0.00 2.27
2198 7771 3.982576 ACCTTCTTTTGGTACTTTGCG 57.017 42.857 0.00 0.00 35.80 4.85
2199 7772 3.547746 ACCTTCTTTTGGTACTTTGCGA 58.452 40.909 0.00 0.00 35.80 5.10
2211 7784 2.162681 ACTTTGCGAAAGAGGGGAATG 58.837 47.619 13.35 0.00 41.02 2.67
2317 7890 7.612244 TGTAGGCTAAATAAGTGCAAAACCATA 59.388 33.333 0.00 0.00 0.00 2.74
2361 7934 7.232330 CCAGGAAGATGATGTAGTTAGAGATCA 59.768 40.741 0.00 0.00 0.00 2.92
2383 7957 9.291664 GATCACAACTTCAAGTATACACTAGAC 57.708 37.037 5.50 0.00 33.48 2.59
2385 7959 6.033619 CACAACTTCAAGTATACACTAGACGC 59.966 42.308 5.50 0.00 33.48 5.19
2391 7965 2.681848 AGTATACACTAGACGCGCAGTT 59.318 45.455 5.73 1.55 31.45 3.16
2396 7970 1.136611 CACTAGACGCGCAGTTTTGTC 60.137 52.381 5.73 5.38 0.00 3.18
2397 7971 1.269621 ACTAGACGCGCAGTTTTGTCT 60.270 47.619 15.89 15.89 43.62 3.41
2398 7972 2.030540 ACTAGACGCGCAGTTTTGTCTA 60.031 45.455 16.34 16.34 41.60 2.59
2406 7980 3.611113 GCGCAGTTTTGTCTATCGAAGTA 59.389 43.478 0.30 0.00 0.00 2.24
2434 8008 3.256285 CGAAGCGTGTCTACTATCTCC 57.744 52.381 0.00 0.00 0.00 3.71
2435 8009 2.873472 CGAAGCGTGTCTACTATCTCCT 59.127 50.000 0.00 0.00 0.00 3.69
2436 8010 3.059461 CGAAGCGTGTCTACTATCTCCTC 60.059 52.174 0.00 0.00 0.00 3.71
2437 8011 2.853705 AGCGTGTCTACTATCTCCTCC 58.146 52.381 0.00 0.00 0.00 4.30
2438 8012 2.440253 AGCGTGTCTACTATCTCCTCCT 59.560 50.000 0.00 0.00 0.00 3.69
2439 8013 3.117813 AGCGTGTCTACTATCTCCTCCTT 60.118 47.826 0.00 0.00 0.00 3.36
2440 8014 3.633065 GCGTGTCTACTATCTCCTCCTTT 59.367 47.826 0.00 0.00 0.00 3.11
2441 8015 4.498345 GCGTGTCTACTATCTCCTCCTTTG 60.498 50.000 0.00 0.00 0.00 2.77
2442 8016 4.498345 CGTGTCTACTATCTCCTCCTTTGC 60.498 50.000 0.00 0.00 0.00 3.68
2443 8017 3.632604 TGTCTACTATCTCCTCCTTTGCG 59.367 47.826 0.00 0.00 0.00 4.85
2444 8018 3.884091 GTCTACTATCTCCTCCTTTGCGA 59.116 47.826 0.00 0.00 0.00 5.10
2448 8022 3.572255 ACTATCTCCTCCTTTGCGAGATC 59.428 47.826 2.23 0.00 41.38 2.75
2462 8036 3.479505 CGAGATCTCGTGAACAGTTCT 57.520 47.619 32.23 0.00 46.99 3.01
2471 8045 2.030457 CGTGAACAGTTCTTCAAAGCGT 59.970 45.455 14.51 0.00 31.90 5.07
2472 8046 3.244345 CGTGAACAGTTCTTCAAAGCGTA 59.756 43.478 14.51 0.00 31.90 4.42
2473 8047 4.606232 CGTGAACAGTTCTTCAAAGCGTAG 60.606 45.833 14.51 0.00 31.90 3.51
2474 8048 4.270325 GTGAACAGTTCTTCAAAGCGTAGT 59.730 41.667 14.51 0.00 31.90 2.73
2475 8049 4.270084 TGAACAGTTCTTCAAAGCGTAGTG 59.730 41.667 14.51 0.00 0.00 2.74
2476 8050 3.131396 ACAGTTCTTCAAAGCGTAGTGG 58.869 45.455 0.00 0.00 0.00 4.00
2477 8051 2.096218 CAGTTCTTCAAAGCGTAGTGGC 60.096 50.000 0.00 0.00 0.00 5.01
2478 8052 1.197036 GTTCTTCAAAGCGTAGTGGCC 59.803 52.381 0.00 0.00 0.00 5.36
2516 8090 5.587289 TGTACAAAATTGAAGTGAGTTGGC 58.413 37.500 0.00 0.00 0.00 4.52
2517 8091 3.705604 ACAAAATTGAAGTGAGTTGGCG 58.294 40.909 0.00 0.00 0.00 5.69
2521 8095 3.056328 GAAGTGAGTTGGCGGGCC 61.056 66.667 1.86 1.86 0.00 5.80
2546 8120 1.461127 GCTAGCAACTCCGAACAACAG 59.539 52.381 10.63 0.00 0.00 3.16
2547 8121 2.069273 CTAGCAACTCCGAACAACAGG 58.931 52.381 0.00 0.00 0.00 4.00
2552 8126 0.249911 ACTCCGAACAACAGGTCAGC 60.250 55.000 0.00 0.00 0.00 4.26
2577 8151 2.285868 GGCACCCTAGGGCTCCTA 59.714 66.667 28.88 1.60 39.32 2.94
2583 8157 1.082365 ACCCTAGGGCTCCTAAAACCT 59.918 52.381 28.88 0.00 35.49 3.50
2584 8158 1.490910 CCCTAGGGCTCCTAAAACCTG 59.509 57.143 16.90 0.00 35.49 4.00
2585 8159 1.134068 CCTAGGGCTCCTAAAACCTGC 60.134 57.143 0.00 0.00 35.49 4.85
2586 8160 1.559682 CTAGGGCTCCTAAAACCTGCA 59.440 52.381 0.00 0.00 35.49 4.41
2641 8216 4.717313 GTTCGGTGCACCCCCTCC 62.717 72.222 29.95 9.90 0.00 4.30
2649 8224 0.623723 TGCACCCCCTCCACTATTTC 59.376 55.000 0.00 0.00 0.00 2.17
2655 8230 2.339769 CCCCTCCACTATTTCCCCTAG 58.660 57.143 0.00 0.00 0.00 3.02
2686 8261 1.474330 CCAAATTAGCCCGCTCCTTT 58.526 50.000 0.00 0.00 0.00 3.11
2712 8287 3.420893 TCCTTCGGATTGCATCTGTTTT 58.579 40.909 0.00 0.00 36.98 2.43
2718 8293 4.218200 TCGGATTGCATCTGTTTTGACATT 59.782 37.500 0.00 0.00 36.98 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 9.490379 GTTAGAAAGAAGATGAAGGTTGAACTA 57.510 33.333 0.00 0.00 0.00 2.24
35 36 8.902540 TGCAACTTTGATAGTTAGAAAGAAGA 57.097 30.769 0.00 0.00 45.29 2.87
108 109 3.225104 TGGTGTTGTACTACGAGTCCTT 58.775 45.455 3.03 0.00 0.00 3.36
126 128 3.736094 TGGAGTTGAGGAGGATATTGGT 58.264 45.455 0.00 0.00 0.00 3.67
146 148 5.529060 GTCCACTATTGCTTAGGAGGAATTG 59.471 44.000 0.00 0.46 40.56 2.32
147 149 5.398012 GGTCCACTATTGCTTAGGAGGAATT 60.398 44.000 0.00 0.00 40.56 2.17
185 187 1.340600 GGTACCAAGCATTAGCCACCA 60.341 52.381 7.15 0.00 43.56 4.17
186 188 1.064685 AGGTACCAAGCATTAGCCACC 60.065 52.381 15.94 0.00 43.56 4.61
222 224 1.986575 GATGAAGCGCTGAAGTGGCC 61.987 60.000 12.58 0.00 0.00 5.36
232 234 1.486644 GCGGAGAGAAGATGAAGCGC 61.487 60.000 0.00 0.00 0.00 5.92
233 235 0.102120 AGCGGAGAGAAGATGAAGCG 59.898 55.000 0.00 0.00 0.00 4.68
268 270 2.036089 GTCCGAGTTGAAGTGGTCTCTT 59.964 50.000 0.00 0.00 0.00 2.85
286 398 2.009681 AATGGGGTTTTGTCTGGTCC 57.990 50.000 0.00 0.00 0.00 4.46
291 403 5.454966 AGTGAGTAAAATGGGGTTTTGTCT 58.545 37.500 0.00 0.00 40.17 3.41
344 456 2.128771 ACATTGGCAAGGCTTACGAT 57.871 45.000 12.40 0.00 0.00 3.73
390 502 5.243060 TCGTGTTGAATACAAGAAGAGGAGA 59.757 40.000 0.00 0.00 41.36 3.71
412 524 3.001330 GGCCTATGAGACGTCAAATTTCG 59.999 47.826 19.50 0.22 35.88 3.46
466 581 7.014615 AGGTTATTTCAAAGAGTGCTTTCATGT 59.985 33.333 0.00 0.00 42.27 3.21
542 664 6.037726 AGCATATGCAATGTGTTGTACAATG 58.962 36.000 28.62 6.67 42.84 2.82
545 667 6.749923 TTAGCATATGCAATGTGTTGTACA 57.250 33.333 28.62 0.00 45.16 2.90
546 668 7.167968 CCAATTAGCATATGCAATGTGTTGTAC 59.832 37.037 28.62 0.00 45.16 2.90
547 669 7.201835 CCAATTAGCATATGCAATGTGTTGTA 58.798 34.615 28.62 6.92 45.16 2.41
573 695 8.926092 AACCCAAGAGAATAAAGGATATTAGC 57.074 34.615 0.00 0.00 0.00 3.09
612 2089 7.663043 AGGTCAAATAACCCTGTGTTAAAAA 57.337 32.000 0.00 0.00 42.51 1.94
613 2090 7.418025 CCAAGGTCAAATAACCCTGTGTTAAAA 60.418 37.037 0.00 0.00 42.51 1.52
614 2091 6.041069 CCAAGGTCAAATAACCCTGTGTTAAA 59.959 38.462 0.00 0.00 42.51 1.52
615 2092 5.536916 CCAAGGTCAAATAACCCTGTGTTAA 59.463 40.000 0.00 0.00 42.51 2.01
616 2093 5.074115 CCAAGGTCAAATAACCCTGTGTTA 58.926 41.667 0.00 0.00 43.35 2.41
617 2094 3.895041 CCAAGGTCAAATAACCCTGTGTT 59.105 43.478 0.00 0.00 40.42 3.32
618 2095 3.496331 CCAAGGTCAAATAACCCTGTGT 58.504 45.455 0.00 0.00 40.42 3.72
619 2096 2.825532 CCCAAGGTCAAATAACCCTGTG 59.174 50.000 0.00 0.00 40.42 3.66
620 2097 2.225267 CCCCAAGGTCAAATAACCCTGT 60.225 50.000 0.00 0.00 40.42 4.00
621 2098 2.042433 TCCCCAAGGTCAAATAACCCTG 59.958 50.000 0.00 0.00 40.42 4.45
622 2099 2.364190 TCCCCAAGGTCAAATAACCCT 58.636 47.619 0.00 0.00 40.42 4.34
623 2100 2.911552 TCCCCAAGGTCAAATAACCC 57.088 50.000 0.00 0.00 40.42 4.11
657 2134 6.426025 ACCTCTGTTCGGATAACAAAAAGTAC 59.574 38.462 0.00 0.00 0.00 2.73
666 2187 7.384387 GTGGAATAATACCTCTGTTCGGATAAC 59.616 40.741 0.00 0.00 0.00 1.89
826 6322 3.487202 CGCCACGCACGCAGTAAT 61.487 61.111 0.00 0.00 41.61 1.89
899 6397 4.189580 GCCCCCAATGCGAGGCTA 62.190 66.667 0.00 0.00 42.34 3.93
940 6438 2.165998 AGATCTTCCTTGTTGCTTGGC 58.834 47.619 0.00 0.00 0.00 4.52
1007 6505 7.728847 AACTAAATTCAACTTGCCAAAATCC 57.271 32.000 0.00 0.00 0.00 3.01
1271 6773 2.125552 CGCGCAGTTCTCCATGGA 60.126 61.111 15.27 15.27 0.00 3.41
1613 7124 4.658063 ACCAAATTCGTGGGATAAAGTGA 58.342 39.130 1.33 0.00 43.56 3.41
1616 7127 6.347321 GCAAAAACCAAATTCGTGGGATAAAG 60.347 38.462 1.33 0.00 43.56 1.85
1623 7134 1.524776 CCGCAAAAACCAAATTCGTGG 59.475 47.619 0.00 0.00 44.92 4.94
1624 7135 1.070909 GCCGCAAAAACCAAATTCGTG 60.071 47.619 0.00 0.00 0.00 4.35
1628 7139 1.067821 TCTCGCCGCAAAAACCAAATT 59.932 42.857 0.00 0.00 0.00 1.82
1698 7209 8.770438 AATGATCGATCTAAGCTTAATTCCTC 57.230 34.615 25.02 6.62 0.00 3.71
1760 7271 5.833406 TGTGGCAATATATGGTGAAACTG 57.167 39.130 0.00 0.00 36.74 3.16
1789 7300 4.449672 GGGTAGGGTGGTAGGTATACATCA 60.450 50.000 5.01 0.00 33.21 3.07
1796 7307 1.652843 ACATGGGTAGGGTGGTAGGTA 59.347 52.381 0.00 0.00 0.00 3.08
1797 7308 0.420272 ACATGGGTAGGGTGGTAGGT 59.580 55.000 0.00 0.00 0.00 3.08
1798 7309 2.326428 CTACATGGGTAGGGTGGTAGG 58.674 57.143 0.00 0.00 42.71 3.18
1851 7363 2.203266 GCTATGCTGTGGAGGGGC 60.203 66.667 0.00 0.00 0.00 5.80
1898 7410 2.684001 AGAATTGGCGGTCGATAACA 57.316 45.000 0.00 0.00 0.00 2.41
1899 7411 3.057734 CCTAGAATTGGCGGTCGATAAC 58.942 50.000 0.00 0.00 0.00 1.89
1901 7413 1.616865 CCCTAGAATTGGCGGTCGATA 59.383 52.381 0.00 0.00 0.00 2.92
1902 7414 0.393077 CCCTAGAATTGGCGGTCGAT 59.607 55.000 0.00 0.00 0.00 3.59
1950 7473 4.339530 TGTGCTTTTACCAAACATGTGCTA 59.660 37.500 0.00 0.00 0.00 3.49
1994 7517 4.526262 TCCCAAAACCAAAGACCACATATG 59.474 41.667 0.00 0.00 0.00 1.78
1995 7518 4.526650 GTCCCAAAACCAAAGACCACATAT 59.473 41.667 0.00 0.00 0.00 1.78
1996 7519 3.892588 GTCCCAAAACCAAAGACCACATA 59.107 43.478 0.00 0.00 0.00 2.29
1997 7520 2.698274 GTCCCAAAACCAAAGACCACAT 59.302 45.455 0.00 0.00 0.00 3.21
1999 7522 1.411246 GGTCCCAAAACCAAAGACCAC 59.589 52.381 2.68 0.00 45.20 4.16
2002 7566 1.686587 CCAGGTCCCAAAACCAAAGAC 59.313 52.381 0.00 0.00 42.12 3.01
2003 7567 1.412361 CCCAGGTCCCAAAACCAAAGA 60.412 52.381 0.00 0.00 42.12 2.52
2006 7570 0.397816 CACCCAGGTCCCAAAACCAA 60.398 55.000 0.00 0.00 42.12 3.67
2008 7572 2.207229 GCACCCAGGTCCCAAAACC 61.207 63.158 0.00 0.00 39.80 3.27
2013 7577 2.531428 TCATGCACCCAGGTCCCA 60.531 61.111 0.00 0.00 0.00 4.37
2087 7660 9.263446 TGAAGTACTACCTCCATAACTAAACAT 57.737 33.333 0.00 0.00 0.00 2.71
2089 7662 8.526147 TGTGAAGTACTACCTCCATAACTAAAC 58.474 37.037 0.00 0.00 0.00 2.01
2092 7665 8.654485 TTTGTGAAGTACTACCTCCATAACTA 57.346 34.615 0.00 0.00 0.00 2.24
2135 7708 1.302366 TAGCGAAATGATGGCAGCTG 58.698 50.000 10.11 10.11 34.79 4.24
2152 7725 5.179045 AGATTGAAATTTGCGCTGGATAG 57.821 39.130 9.73 0.00 0.00 2.08
2159 7732 4.485163 AGGTTGTAGATTGAAATTTGCGC 58.515 39.130 0.00 0.00 0.00 6.09
2160 7733 6.381801 AGAAGGTTGTAGATTGAAATTTGCG 58.618 36.000 0.00 0.00 0.00 4.85
2173 7746 6.206498 GCAAAGTACCAAAAGAAGGTTGTAG 58.794 40.000 0.00 0.00 40.54 2.74
2178 7751 3.547746 TCGCAAAGTACCAAAAGAAGGT 58.452 40.909 0.00 0.00 43.14 3.50
2187 7760 1.271163 CCCCTCTTTCGCAAAGTACCA 60.271 52.381 8.01 0.00 39.52 3.25
2198 7771 3.941704 AGGTGATCATTCCCCTCTTTC 57.058 47.619 0.00 0.00 0.00 2.62
2199 7772 4.682021 AAAGGTGATCATTCCCCTCTTT 57.318 40.909 0.00 0.00 0.00 2.52
2211 7784 7.066766 AGAGCAAATGTAGATGAAAAGGTGATC 59.933 37.037 0.00 0.00 0.00 2.92
2270 7843 5.030147 ACATGGTTCCCTACATCTACTTGA 58.970 41.667 0.00 0.00 0.00 3.02
2361 7934 6.091437 GCGTCTAGTGTATACTTGAAGTTGT 58.909 40.000 1.97 0.00 39.70 3.32
2383 7957 0.989164 TCGATAGACAAAACTGCGCG 59.011 50.000 0.00 0.00 42.67 6.86
2396 7970 3.965292 TCGCCAACTCTACTTCGATAG 57.035 47.619 0.00 0.00 0.00 2.08
2397 7971 3.488721 GCTTCGCCAACTCTACTTCGATA 60.489 47.826 0.00 0.00 0.00 2.92
2398 7972 2.735762 GCTTCGCCAACTCTACTTCGAT 60.736 50.000 0.00 0.00 0.00 3.59
2406 7980 1.664965 GACACGCTTCGCCAACTCT 60.665 57.895 0.00 0.00 0.00 3.24
2419 7993 4.498345 GCAAAGGAGGAGATAGTAGACACG 60.498 50.000 0.00 0.00 0.00 4.49
2428 8002 3.823873 GAGATCTCGCAAAGGAGGAGATA 59.176 47.826 7.04 0.00 45.06 1.98
2432 8006 0.741326 CGAGATCTCGCAAAGGAGGA 59.259 55.000 30.41 0.00 46.50 3.71
2433 8007 3.264666 CGAGATCTCGCAAAGGAGG 57.735 57.895 30.41 3.19 46.50 4.30
2443 8017 4.799678 TGAAGAACTGTTCACGAGATCTC 58.200 43.478 21.50 13.05 31.31 2.75
2444 8018 4.855715 TGAAGAACTGTTCACGAGATCT 57.144 40.909 21.50 0.00 31.31 2.75
2448 8022 3.602491 CGCTTTGAAGAACTGTTCACGAG 60.602 47.826 21.50 15.61 36.15 4.18
2451 8025 3.675467 ACGCTTTGAAGAACTGTTCAC 57.325 42.857 21.50 14.91 36.15 3.18
2461 8035 0.517316 GTGGCCACTACGCTTTGAAG 59.483 55.000 29.12 0.00 0.00 3.02
2462 8036 0.179043 TGTGGCCACTACGCTTTGAA 60.179 50.000 34.75 9.34 0.00 2.69
2471 8045 1.057275 TGGAGGTGTTGTGGCCACTA 61.057 55.000 34.75 26.28 33.31 2.74
2472 8046 2.382770 TGGAGGTGTTGTGGCCACT 61.383 57.895 34.75 15.34 33.31 4.00
2473 8047 2.193536 GTGGAGGTGTTGTGGCCAC 61.194 63.158 29.67 29.67 41.77 5.01
2474 8048 2.005606 ATGTGGAGGTGTTGTGGCCA 62.006 55.000 0.00 0.00 0.00 5.36
2475 8049 1.228552 ATGTGGAGGTGTTGTGGCC 60.229 57.895 0.00 0.00 0.00 5.36
2476 8050 0.823356 ACATGTGGAGGTGTTGTGGC 60.823 55.000 0.00 0.00 0.00 5.01
2477 8051 2.151202 GTACATGTGGAGGTGTTGTGG 58.849 52.381 9.11 0.00 0.00 4.17
2478 8052 2.844946 TGTACATGTGGAGGTGTTGTG 58.155 47.619 9.11 0.00 0.00 3.33
2538 8112 0.947244 CACCTGCTGACCTGTTGTTC 59.053 55.000 0.00 0.00 0.00 3.18
2546 8120 3.640407 TGCCTCCACCTGCTGACC 61.640 66.667 0.00 0.00 0.00 4.02
2547 8121 2.359230 GTGCCTCCACCTGCTGAC 60.359 66.667 0.00 0.00 35.92 3.51
2574 8148 2.267045 GCAGGGTGCAGGTTTTAGG 58.733 57.895 0.00 0.00 44.26 2.69
2584 8158 0.324275 TAAAAGGATGGGCAGGGTGC 60.324 55.000 0.00 0.00 44.08 5.01
2585 8159 2.459555 ATAAAAGGATGGGCAGGGTG 57.540 50.000 0.00 0.00 0.00 4.61
2586 8160 3.791545 TCTTATAAAAGGATGGGCAGGGT 59.208 43.478 0.00 0.00 33.22 4.34
2655 8230 2.101415 GCTAATTTGGCCTTGATCCCAC 59.899 50.000 3.32 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.