Multiple sequence alignment - TraesCS1D01G214800

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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 TraesCS1D01G214800 chr1D 100.000 3920 0 0 1 3920 299932844 299928925 0.000000e+00 7239.0
1 TraesCS1D01G214800 chr1B 90.529 2872 188 25 1084 3919 404517173 404514350 0.000000e+00 3720.0
2 TraesCS1D01G214800 chr1A 91.802 1354 85 11 427 1761 374219921 374218575 0.000000e+00 1862.0
3 TraesCS1D01G214800 chr1A 94.631 1192 42 6 2745 3919 374217528 374216342 0.000000e+00 1827.0
4 TraesCS1D01G214800 chr1A 89.017 956 58 11 1783 2718 374218511 374217583 0.000000e+00 1140.0
5 TraesCS1D01G214800 chr1A 92.556 403 26 3 6 405 374220367 374219966 3.400000e-160 575.0
6 TraesCS1D01G214800 chrUn 89.716 457 40 4 1256 1709 131924519 131924067 9.440000e-161 577.0
7 TraesCS1D01G214800 chr3D 87.527 465 44 7 1256 1710 169728417 169728877 3.470000e-145 525.0
8 TraesCS1D01G214800 chr3D 94.286 35 2 0 1256 1290 141467288 141467322 2.000000e-03 54.7
9 TraesCS1D01G214800 chr5D 88.158 304 33 2 1482 1782 227554668 227554365 3.720000e-95 359.0
10 TraesCS1D01G214800 chr5D 96.471 85 3 0 1260 1344 139281631 139281715 1.470000e-29 141.0
11 TraesCS1D01G214800 chr6D 95.775 71 3 0 1256 1326 436502070 436502000 8.900000e-22 115.0
12 TraesCS1D01G214800 chr7B 100.000 30 0 0 1306 1335 339029100 339029071 5.470000e-04 56.5


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 TraesCS1D01G214800 chr1D 299928925 299932844 3919 True 7239 7239 100.0000 1 3920 1 chr1D.!!$R1 3919
1 TraesCS1D01G214800 chr1B 404514350 404517173 2823 True 3720 3720 90.5290 1084 3919 1 chr1B.!!$R1 2835
2 TraesCS1D01G214800 chr1A 374216342 374220367 4025 True 1351 1862 92.0015 6 3919 4 chr1A.!!$R1 3913

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
528 555 0.035439 CCTTGGCGTGGTCCTACAAT 60.035 55.0 0.0 0.0 0.00 2.71 F
1780 1827 0.034059 CGTTGCCTGGTCTTCTGAGT 59.966 55.0 0.0 0.0 0.00 3.41 F
2600 2738 0.033796 TCGGTATCGAGTCCCCAAGT 60.034 55.0 0.0 0.0 40.88 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 2065 1.069204 CCATCCATGACAGGGTAGACG 59.931 57.143 5.96 0.0 0.00 4.18 R
2770 2936 0.825410 GGGCATGTTCATTGCATCCA 59.175 50.000 0.00 0.0 41.95 3.41 R
3460 3643 1.068588 TGTACACAGCGATCATAGCCC 59.931 52.381 0.00 0.0 34.64 5.19 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
49 50 4.083581 AGTGTAATTTGCTCGCATCAAC 57.916 40.909 0.00 0.00 0.00 3.18
89 90 1.873903 TCACGAAGGTGCTCTTCTTGC 60.874 52.381 16.21 0.00 45.70 4.01
90 91 4.434001 TCACGAAGGTGCTCTTCTTGCA 62.434 50.000 16.21 0.00 45.70 4.08
96 97 0.237761 GTGCTCTTCTTGCAGTGCAG 59.762 55.000 18.81 12.53 42.43 4.41
109 110 1.998315 CAGTGCAGATTCTTGAGACGG 59.002 52.381 0.00 0.00 0.00 4.79
117 118 5.622460 GCAGATTCTTGAGACGGAACTTCTA 60.622 44.000 0.00 0.00 36.96 2.10
118 119 5.802956 CAGATTCTTGAGACGGAACTTCTAC 59.197 44.000 0.00 0.00 36.96 2.59
155 156 7.482654 AAATTCATCATCCACACTACATACG 57.517 36.000 0.00 0.00 0.00 3.06
162 163 6.040247 TCATCCACACTACATACGTCAAATC 58.960 40.000 0.00 0.00 0.00 2.17
169 170 6.586463 ACACTACATACGTCAAATCTGAACAG 59.414 38.462 0.00 0.00 31.88 3.16
188 189 3.688185 ACAGAAGACATGCACATCACATC 59.312 43.478 0.00 0.00 0.00 3.06
199 200 4.211584 TGCACATCACATCAAAAATTGCAC 59.788 37.500 0.00 0.00 32.73 4.57
205 206 6.347270 TCACATCAAAAATTGCACACAAAG 57.653 33.333 0.00 0.00 39.77 2.77
227 228 5.916318 AGTGAAAAGGCACATGAAAATCAA 58.084 33.333 0.00 0.00 41.19 2.57
286 289 1.203052 CAGTGAACACATTGGGGATGC 59.797 52.381 7.68 0.00 39.47 3.91
290 293 1.259840 AACACATTGGGGATGCTGGC 61.260 55.000 0.00 0.00 39.47 4.85
302 305 3.712881 GCTGGCGGTTGTGACGAC 61.713 66.667 0.00 0.00 40.49 4.34
339 342 2.124736 TTATGCGGCAGTGGGAGC 60.125 61.111 9.25 0.00 0.00 4.70
351 354 3.451894 GGGAGCGGTGGCCAAATG 61.452 66.667 7.24 0.26 41.24 2.32
387 391 3.901797 GAGGAGTTGGGGCGTGGTG 62.902 68.421 0.00 0.00 0.00 4.17
405 409 4.008933 GGAGGGATCGCCGATGGG 62.009 72.222 3.34 0.00 33.83 4.00
418 422 4.431131 ATGGGCAGGCCTTCGGTG 62.431 66.667 15.38 0.00 36.10 4.94
420 424 3.712907 GGGCAGGCCTTCGGTGTA 61.713 66.667 0.00 0.00 36.10 2.90
421 425 2.125106 GGCAGGCCTTCGGTGTAG 60.125 66.667 0.00 0.00 0.00 2.74
422 426 2.663196 GCAGGCCTTCGGTGTAGT 59.337 61.111 0.00 0.00 0.00 2.73
424 428 1.298859 GCAGGCCTTCGGTGTAGTTG 61.299 60.000 0.00 0.00 0.00 3.16
436 463 2.737252 GGTGTAGTTGCCTTCTTCTTCG 59.263 50.000 0.00 0.00 0.00 3.79
444 471 1.814248 GCCTTCTTCTTCGTGTGGGTT 60.814 52.381 0.00 0.00 0.00 4.11
471 498 2.203070 GCCAATGGATCTCGCGGT 60.203 61.111 6.13 0.00 0.00 5.68
485 512 4.785453 CGGTGGCCTCTTCCCAGC 62.785 72.222 3.32 0.00 45.08 4.85
502 529 2.620112 GCCAGCTTCTTCGCTTGCA 61.620 57.895 4.28 0.00 45.12 4.08
515 542 2.601367 TTGCAGGGAAGCCTTGGC 60.601 61.111 2.97 2.97 30.84 4.52
528 555 0.035439 CCTTGGCGTGGTCCTACAAT 60.035 55.000 0.00 0.00 0.00 2.71
539 566 2.709475 CTACAATGCTTCGCCGGC 59.291 61.111 19.07 19.07 0.00 6.13
580 607 2.210961 GCGGTCCAAGTCCTATAAAGC 58.789 52.381 0.00 0.00 0.00 3.51
591 618 1.499049 CTATAAAGCGGACGGCCTTC 58.501 55.000 5.33 0.00 45.17 3.46
605 632 4.821589 CTTCGGCTCCTCGGCACC 62.822 72.222 0.00 0.00 38.27 5.01
644 672 4.148825 GGCGACTGCTGGGACGAT 62.149 66.667 10.07 0.00 42.25 3.73
650 678 1.267574 ACTGCTGGGACGATGGTCAT 61.268 55.000 10.22 0.00 45.28 3.06
652 680 1.524621 GCTGGGACGATGGTCATGG 60.525 63.158 10.22 0.27 45.28 3.66
653 681 1.524621 CTGGGACGATGGTCATGGC 60.525 63.158 10.22 0.00 45.28 4.40
663 691 4.864334 GTCATGGCGGGGAGGCTG 62.864 72.222 0.00 0.00 46.88 4.85
690 718 1.810532 GGCAGTCGAGTCGAGGATT 59.189 57.895 17.12 0.00 36.23 3.01
708 736 0.846015 TTCCTTCCATGGCATCCGAT 59.154 50.000 6.96 0.00 0.00 4.18
715 743 1.069765 ATGGCATCCGATGGTCGTC 59.930 57.895 10.41 0.00 38.40 4.20
723 751 2.202570 GATGGTCGTCGGTGGTCG 60.203 66.667 0.00 0.00 40.90 4.79
724 752 4.430765 ATGGTCGTCGGTGGTCGC 62.431 66.667 0.00 0.00 39.05 5.19
736 764 2.202427 GGTCGCGGCGGAAAATTG 60.202 61.111 23.46 0.00 0.00 2.32
743 771 0.451383 CGGCGGAAAATTGCAGATCA 59.549 50.000 0.00 0.00 0.00 2.92
753 781 3.512516 GCAGATCAGGCGGTTGGC 61.513 66.667 0.00 0.00 42.51 4.52
767 795 1.077357 TTGGCGTTCCCACAGTTGT 60.077 52.632 0.00 0.00 45.34 3.32
795 823 3.438781 TCGTCTTTTGTCTTGTGCTTGTT 59.561 39.130 0.00 0.00 0.00 2.83
872 900 0.618107 TACCCACGGGCTATGGACAA 60.618 55.000 0.69 0.00 39.87 3.18
882 910 2.427095 GGCTATGGACAAATGGTGAACC 59.573 50.000 0.00 0.00 0.00 3.62
908 948 3.475566 AAGTCTAGCTCAAGTTGTGCA 57.524 42.857 26.67 14.42 39.15 4.57
910 950 2.366916 AGTCTAGCTCAAGTTGTGCAGT 59.633 45.455 26.67 13.12 39.15 4.40
958 998 2.669569 GCCGAGCAAAGTGAGCCA 60.670 61.111 0.00 0.00 0.00 4.75
962 1002 1.498865 CGAGCAAAGTGAGCCAACGT 61.499 55.000 0.00 0.00 0.00 3.99
1037 1077 2.876581 CCATAAGGGCCCTTATCCAAC 58.123 52.381 42.39 7.92 44.61 3.77
1064 1104 3.391098 CCACAAAATGGCAGGGGG 58.609 61.111 0.00 0.00 43.24 5.40
1082 1122 1.299468 GTCTCTATCGCACTGCCCG 60.299 63.158 0.00 0.00 0.00 6.13
1418 1462 4.398358 CCTCACACTCGAAATCTACCACTA 59.602 45.833 0.00 0.00 0.00 2.74
1493 1537 3.435186 GTTCTGAAGCTGCGGGGC 61.435 66.667 0.00 0.00 0.00 5.80
1547 1591 4.397417 GCTCAACAGCAGGTAGAAATTCAT 59.603 41.667 0.00 0.00 46.06 2.57
1554 1598 8.579850 ACAGCAGGTAGAAATTCATTCATTTA 57.420 30.769 0.00 0.00 40.72 1.40
1601 1648 1.066716 TCTGCCAGGCATTTCAATTGC 60.067 47.619 16.64 0.00 38.13 3.56
1730 1777 2.048127 GTCGTCGGAAGGCTTGCT 60.048 61.111 16.89 0.00 0.00 3.91
1778 1825 1.301716 GCGTTGCCTGGTCTTCTGA 60.302 57.895 0.00 0.00 0.00 3.27
1779 1826 1.294659 GCGTTGCCTGGTCTTCTGAG 61.295 60.000 0.00 0.00 0.00 3.35
1780 1827 0.034059 CGTTGCCTGGTCTTCTGAGT 59.966 55.000 0.00 0.00 0.00 3.41
1934 2065 4.689612 TTACATGATCTCAAGGTAGGCC 57.310 45.455 0.00 0.00 0.00 5.19
1987 2123 6.036191 GCTACTGCCTGTCATAAACTTTACTC 59.964 42.308 0.00 0.00 0.00 2.59
2032 2169 5.819901 AGTTGCATAAATCTCACTAGGAAGC 59.180 40.000 0.00 0.00 0.00 3.86
2044 2181 2.239150 ACTAGGAAGCTGTCTCGGTCTA 59.761 50.000 0.00 0.00 0.00 2.59
2045 2182 1.465794 AGGAAGCTGTCTCGGTCTAC 58.534 55.000 0.00 0.00 0.00 2.59
2073 2210 4.781775 TGTTCTTCAGGGGTGTTAAGAA 57.218 40.909 0.00 0.00 36.02 2.52
2138 2275 7.037370 TGGTACATATCATTCTGGCCTATTCAT 60.037 37.037 3.32 0.00 0.00 2.57
2239 2377 0.532573 TCTCGTCATCAGGTCAAGGC 59.467 55.000 0.00 0.00 0.00 4.35
2287 2425 5.904362 AGGAACTGCAGGACAAATTAATC 57.096 39.130 19.93 0.45 37.18 1.75
2353 2491 6.438763 CACCATTTCCAACTTTAGACAAGAC 58.561 40.000 0.00 0.00 0.00 3.01
2357 2495 6.677781 TTTCCAACTTTAGACAAGACACTG 57.322 37.500 0.00 0.00 0.00 3.66
2358 2496 4.127171 TCCAACTTTAGACAAGACACTGC 58.873 43.478 0.00 0.00 0.00 4.40
2359 2497 3.251004 CCAACTTTAGACAAGACACTGCC 59.749 47.826 0.00 0.00 0.00 4.85
2360 2498 4.130118 CAACTTTAGACAAGACACTGCCT 58.870 43.478 0.00 0.00 0.00 4.75
2361 2499 5.297547 CAACTTTAGACAAGACACTGCCTA 58.702 41.667 0.00 0.00 0.00 3.93
2362 2500 4.884247 ACTTTAGACAAGACACTGCCTAC 58.116 43.478 0.00 0.00 0.00 3.18
2363 2501 4.589374 ACTTTAGACAAGACACTGCCTACT 59.411 41.667 0.00 0.00 0.00 2.57
2364 2502 4.521130 TTAGACAAGACACTGCCTACTG 57.479 45.455 0.00 0.00 0.00 2.74
2365 2503 1.001406 AGACAAGACACTGCCTACTGC 59.999 52.381 0.00 0.00 41.77 4.40
2366 2504 1.001406 GACAAGACACTGCCTACTGCT 59.999 52.381 0.00 0.00 42.00 4.24
2367 2505 2.231478 GACAAGACACTGCCTACTGCTA 59.769 50.000 0.00 0.00 42.00 3.49
2368 2506 2.232452 ACAAGACACTGCCTACTGCTAG 59.768 50.000 0.00 0.00 42.00 3.42
2461 2599 7.774157 ACTTCAATTGACTATGCAATCTCATCT 59.226 33.333 7.89 0.00 37.50 2.90
2475 2613 7.656542 TGCAATCTCATCTTTAGCTCTCTTATG 59.343 37.037 0.00 0.00 0.00 1.90
2480 2618 8.584157 TCTCATCTTTAGCTCTCTTATGGATTC 58.416 37.037 0.00 0.00 0.00 2.52
2560 2698 4.707030 ACGTTATGATGAACCGTCTACA 57.293 40.909 0.00 0.00 0.00 2.74
2585 2723 2.289195 TGATAGCTTTCAACCGTTCGGT 60.289 45.455 11.27 11.27 40.78 4.69
2598 2736 0.819582 GTTCGGTATCGAGTCCCCAA 59.180 55.000 0.00 0.00 46.75 4.12
2600 2738 0.033796 TCGGTATCGAGTCCCCAAGT 60.034 55.000 0.00 0.00 40.88 3.16
2605 2743 1.605058 ATCGAGTCCCCAAGTCCACG 61.605 60.000 0.00 0.00 0.00 4.94
2629 2767 6.425114 CGAGACTCTCTTTTCCAGAAAAATGA 59.575 38.462 6.98 7.01 39.49 2.57
2718 2856 4.213482 GCTGAAACATAGTTTGAACCGTCT 59.787 41.667 0.00 0.00 0.00 4.18
2720 2858 4.024387 TGAAACATAGTTTGAACCGTCTGC 60.024 41.667 0.00 0.00 0.00 4.26
2721 2859 3.120321 ACATAGTTTGAACCGTCTGCA 57.880 42.857 0.00 0.00 0.00 4.41
2722 2860 3.472652 ACATAGTTTGAACCGTCTGCAA 58.527 40.909 0.00 0.00 0.00 4.08
2724 2862 4.083324 ACATAGTTTGAACCGTCTGCAATG 60.083 41.667 0.00 0.00 0.00 2.82
2725 2863 2.571212 AGTTTGAACCGTCTGCAATGA 58.429 42.857 0.00 0.00 0.00 2.57
2726 2864 2.948979 AGTTTGAACCGTCTGCAATGAA 59.051 40.909 0.00 0.00 0.00 2.57
2727 2865 3.569701 AGTTTGAACCGTCTGCAATGAAT 59.430 39.130 0.00 0.00 0.00 2.57
2729 2867 5.415701 AGTTTGAACCGTCTGCAATGAATAT 59.584 36.000 0.00 0.00 0.00 1.28
2730 2868 4.880886 TGAACCGTCTGCAATGAATATG 57.119 40.909 0.00 0.00 0.00 1.78
2732 2870 1.949525 ACCGTCTGCAATGAATATGCC 59.050 47.619 0.00 0.00 43.16 4.40
2733 2871 1.267806 CCGTCTGCAATGAATATGCCC 59.732 52.381 0.00 0.00 43.16 5.36
2768 2934 0.114364 ACAACAGTTCCCATTCCCCC 59.886 55.000 0.00 0.00 0.00 5.40
2840 3009 9.842775 TGATCTATCTTTTCTGTATCTGCATTT 57.157 29.630 0.00 0.00 0.00 2.32
2908 3077 2.938869 GCAGATTGCTGGAGACAAAAC 58.061 47.619 0.00 0.00 42.53 2.43
2945 3128 6.228995 TCAAGAATCAGCTGTCCATATGATC 58.771 40.000 14.67 0.00 31.31 2.92
3036 3219 4.659172 CAAGCCGGGGGAAGTGCA 62.659 66.667 2.18 0.00 0.00 4.57
3113 3296 2.232941 CAGGAATGGTGCAGAGCAAAAT 59.767 45.455 0.00 0.00 41.47 1.82
3128 3311 1.665679 CAAAATGCATAGGCGACGACT 59.334 47.619 8.97 8.97 45.35 4.18
3146 3329 2.812591 GACTACCAGAATCCTCGCGATA 59.187 50.000 10.36 0.38 0.00 2.92
3179 3362 2.436542 CCATGGGAATGCCATGACAAAT 59.563 45.455 31.31 0.00 45.40 2.32
3248 3431 2.686405 GAGCAGGAATGCATTGATCACA 59.314 45.455 18.59 0.00 37.25 3.58
3249 3432 2.688446 AGCAGGAATGCATTGATCACAG 59.312 45.455 18.59 0.74 37.25 3.66
3393 3576 0.253044 GATTAGCCACTGCACCAGGA 59.747 55.000 0.00 0.00 41.13 3.86
3460 3643 2.187073 GCCTTGCCAATCTGGTGAG 58.813 57.895 0.00 0.00 40.46 3.51
3474 3657 0.320247 GGTGAGGGCTATGATCGCTG 60.320 60.000 0.00 0.00 0.00 5.18
3606 3789 9.976511 CATGCCACATATGATTTCTTTTCTATT 57.023 29.630 10.38 0.00 0.00 1.73
3827 4011 9.730420 GCAATATTTCAGTAAAATGTCGGTAAT 57.270 29.630 0.00 0.00 38.08 1.89
3838 4022 9.931210 GTAAAATGTCGGTAATTATCTTTGGAG 57.069 33.333 0.00 0.00 0.00 3.86
3843 4027 4.879545 TCGGTAATTATCTTTGGAGGCAAC 59.120 41.667 0.00 0.00 0.00 4.17
3846 4030 6.349777 CGGTAATTATCTTTGGAGGCAACAAA 60.350 38.462 6.47 6.47 41.41 2.83
3919 4103 1.001293 GATGCGTCCATCTGATAGCCA 59.999 52.381 0.00 0.00 43.62 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 5.671329 GCGAGCAAATTACACTACCAAAGAG 60.671 44.000 0.00 0.00 0.00 2.85
49 50 4.081406 TGACATGGAAGATGAGGGTTTTG 58.919 43.478 0.00 0.00 0.00 2.44
89 90 1.998315 CCGTCTCAAGAATCTGCACTG 59.002 52.381 0.00 0.00 0.00 3.66
90 91 1.895798 TCCGTCTCAAGAATCTGCACT 59.104 47.619 0.00 0.00 0.00 4.40
96 97 5.802956 CAGTAGAAGTTCCGTCTCAAGAATC 59.197 44.000 0.00 0.00 0.00 2.52
134 135 5.126384 TGACGTATGTAGTGTGGATGATGAA 59.874 40.000 0.00 0.00 0.00 2.57
155 156 5.049198 TGCATGTCTTCTGTTCAGATTTGAC 60.049 40.000 16.32 16.32 31.71 3.18
162 163 3.749609 TGATGTGCATGTCTTCTGTTCAG 59.250 43.478 0.00 0.00 0.00 3.02
169 170 4.690184 TTGATGTGATGTGCATGTCTTC 57.310 40.909 0.00 0.00 0.00 2.87
188 189 6.523893 CCTTTTCACTTTGTGTGCAATTTTTG 59.476 34.615 0.00 0.00 45.81 2.44
199 200 4.044336 TCATGTGCCTTTTCACTTTGTG 57.956 40.909 0.00 0.00 37.81 3.33
205 206 6.479660 TCTTTGATTTTCATGTGCCTTTTCAC 59.520 34.615 0.00 0.00 37.48 3.18
260 263 3.573538 CCCCAATGTGTTCACTGAAATGA 59.426 43.478 4.59 0.00 0.00 2.57
268 271 1.203052 CAGCATCCCCAATGTGTTCAC 59.797 52.381 0.00 0.00 37.71 3.18
286 289 3.403057 CGTCGTCACAACCGCCAG 61.403 66.667 0.00 0.00 0.00 4.85
290 293 3.033764 CACCCGTCGTCACAACCG 61.034 66.667 0.00 0.00 0.00 4.44
302 305 3.667282 ACGGACAGACGTCACCCG 61.667 66.667 28.98 28.98 45.08 5.28
321 324 2.472909 GCTCCCACTGCCGCATAAC 61.473 63.158 0.00 0.00 0.00 1.89
387 391 4.008933 CCATCGGCGATCCCTCCC 62.009 72.222 21.25 0.00 0.00 4.30
421 425 1.264288 CCACACGAAGAAGAAGGCAAC 59.736 52.381 0.00 0.00 0.00 4.17
422 426 1.593196 CCACACGAAGAAGAAGGCAA 58.407 50.000 0.00 0.00 0.00 4.52
424 428 0.250338 ACCCACACGAAGAAGAAGGC 60.250 55.000 0.00 0.00 0.00 4.35
444 471 2.458969 ATCCATTGGCCAGGGTTGCA 62.459 55.000 21.19 6.32 0.00 4.08
502 529 4.351054 CCACGCCAAGGCTTCCCT 62.351 66.667 9.73 0.00 45.77 4.20
515 542 0.999406 CGAAGCATTGTAGGACCACG 59.001 55.000 0.00 0.00 0.00 4.94
550 577 4.572571 TGGACCGCCACCAACCAC 62.573 66.667 0.00 0.00 39.92 4.16
562 589 2.433239 TCCGCTTTATAGGACTTGGACC 59.567 50.000 0.00 0.00 0.00 4.46
640 668 4.175337 CCCCGCCATGACCATCGT 62.175 66.667 0.00 0.00 0.00 3.73
643 671 3.492353 CCTCCCCGCCATGACCAT 61.492 66.667 0.00 0.00 0.00 3.55
690 718 0.109153 CATCGGATGCCATGGAAGGA 59.891 55.000 18.40 4.47 0.00 3.36
723 751 0.867329 GATCTGCAATTTTCCGCCGC 60.867 55.000 0.00 0.00 0.00 6.53
724 752 0.451383 TGATCTGCAATTTTCCGCCG 59.549 50.000 0.00 0.00 0.00 6.46
736 764 3.512516 GCCAACCGCCTGATCTGC 61.513 66.667 0.00 0.00 0.00 4.26
767 795 4.728534 CACAAGACAAAAGACGAAAACCA 58.271 39.130 0.00 0.00 0.00 3.67
795 823 9.463902 GCTACAGGAGTGATATATTTAGGTCTA 57.536 37.037 0.00 0.00 0.00 2.59
859 887 1.024271 CACCATTTGTCCATAGCCCG 58.976 55.000 0.00 0.00 0.00 6.13
864 892 3.509575 GCTTGGTTCACCATTTGTCCATA 59.490 43.478 0.00 0.00 46.97 2.74
872 900 3.299503 AGACTTTGCTTGGTTCACCATT 58.700 40.909 0.00 0.00 46.97 3.16
882 910 4.274459 ACAACTTGAGCTAGACTTTGCTTG 59.726 41.667 0.00 2.16 39.91 4.01
908 948 2.420022 GCACGATCAAGGCATACAAACT 59.580 45.455 0.00 0.00 0.00 2.66
910 950 2.710377 AGCACGATCAAGGCATACAAA 58.290 42.857 0.00 0.00 0.00 2.83
942 982 1.576421 GTTGGCTCACTTTGCTCGG 59.424 57.895 0.00 0.00 0.00 4.63
958 998 2.032987 CCTGGGCCCGTTAACGTT 59.967 61.111 25.15 5.88 37.74 3.99
962 1002 1.844289 AGTCACCTGGGCCCGTTAA 60.844 57.895 19.37 0.00 0.00 2.01
1037 1077 2.702261 CCATTTTGTGGCTGGATTTGG 58.298 47.619 0.00 0.00 42.12 3.28
1062 1102 1.068250 GGCAGTGCGATAGAGACCC 59.932 63.158 9.45 0.00 39.76 4.46
1063 1103 1.068250 GGGCAGTGCGATAGAGACC 59.932 63.158 9.45 0.00 39.76 3.85
1064 1104 1.299468 CGGGCAGTGCGATAGAGAC 60.299 63.158 9.45 0.00 39.76 3.36
1092 1134 4.776647 GCGGTTGCCATGGCGAAC 62.777 66.667 29.64 29.64 45.51 3.95
1418 1462 3.041940 CCGAACGGAGCAAAGCGT 61.042 61.111 7.53 0.00 37.50 5.07
1547 1591 8.777413 CACAGAGAAGAGAACAACATAAATGAA 58.223 33.333 0.00 0.00 0.00 2.57
1554 1598 3.406764 GGCACAGAGAAGAGAACAACAT 58.593 45.455 0.00 0.00 0.00 2.71
1601 1648 1.512734 GGAGCAGCAAATTCACGCG 60.513 57.895 3.53 3.53 0.00 6.01
1679 1726 2.113433 GGACTGCGGCGTCTCTCTA 61.113 63.158 19.02 0.00 34.38 2.43
1730 1777 4.680237 CTGTCGGCCGCTTGGACA 62.680 66.667 23.51 18.45 43.14 4.02
1763 1810 2.303022 CCTAACTCAGAAGACCAGGCAA 59.697 50.000 0.00 0.00 0.00 4.52
1767 1814 3.007398 ACAAGCCTAACTCAGAAGACCAG 59.993 47.826 0.00 0.00 0.00 4.00
1771 1818 3.181455 TGCAACAAGCCTAACTCAGAAGA 60.181 43.478 0.00 0.00 44.83 2.87
1773 1820 3.141398 CTGCAACAAGCCTAACTCAGAA 58.859 45.455 0.00 0.00 44.83 3.02
1778 1825 2.348411 ACACTGCAACAAGCCTAACT 57.652 45.000 0.00 0.00 44.83 2.24
1779 1826 2.618709 AGAACACTGCAACAAGCCTAAC 59.381 45.455 0.00 0.00 44.83 2.34
1780 1827 2.930950 AGAACACTGCAACAAGCCTAA 58.069 42.857 0.00 0.00 44.83 2.69
1934 2065 1.069204 CCATCCATGACAGGGTAGACG 59.931 57.143 5.96 0.00 0.00 4.18
1968 2099 4.501071 TCGGAGTAAAGTTTATGACAGGC 58.499 43.478 0.00 0.00 0.00 4.85
2013 2150 6.815089 AGACAGCTTCCTAGTGAGATTTATG 58.185 40.000 0.00 0.00 0.00 1.90
2032 2169 3.191581 ACATGAGTTGTAGACCGAGACAG 59.808 47.826 0.00 0.00 36.57 3.51
2044 2181 2.443255 ACCCCTGAAGAACATGAGTTGT 59.557 45.455 0.00 0.00 41.53 3.32
2045 2182 2.816087 CACCCCTGAAGAACATGAGTTG 59.184 50.000 0.00 0.00 38.30 3.16
2073 2210 2.023414 TTTGTCGTCACGGGCAGACT 62.023 55.000 12.32 0.00 34.92 3.24
2138 2275 4.398673 ACACACAAAAGCCGGTAAAAAGTA 59.601 37.500 1.90 0.00 0.00 2.24
2239 2377 3.452474 CCTAGGAAGAACAATCTGAGCG 58.548 50.000 1.05 0.00 35.59 5.03
2287 2425 1.421382 CATCTTGCCTTGGTTTTGCG 58.579 50.000 0.00 0.00 0.00 4.85
2333 2471 6.238759 GCAGTGTCTTGTCTAAAGTTGGAAAT 60.239 38.462 0.00 0.00 0.00 2.17
2353 2491 4.927978 ATTCTACTAGCAGTAGGCAGTG 57.072 45.455 17.67 0.00 46.25 3.66
2357 2495 6.579865 TGGTTAAATTCTACTAGCAGTAGGC 58.420 40.000 17.67 0.00 46.25 3.93
2358 2496 9.046296 CAATGGTTAAATTCTACTAGCAGTAGG 57.954 37.037 17.67 5.54 46.25 3.18
2360 2498 9.378551 CACAATGGTTAAATTCTACTAGCAGTA 57.621 33.333 0.00 0.00 0.00 2.74
2361 2499 7.883311 ACACAATGGTTAAATTCTACTAGCAGT 59.117 33.333 0.00 0.00 0.00 4.40
2362 2500 8.268850 ACACAATGGTTAAATTCTACTAGCAG 57.731 34.615 0.00 0.00 0.00 4.24
2363 2501 8.630054 AACACAATGGTTAAATTCTACTAGCA 57.370 30.769 0.00 0.00 0.00 3.49
2364 2502 8.947115 AGAACACAATGGTTAAATTCTACTAGC 58.053 33.333 0.00 0.00 0.00 3.42
2366 2504 9.787435 ACAGAACACAATGGTTAAATTCTACTA 57.213 29.630 0.00 0.00 0.00 1.82
2367 2505 8.691661 ACAGAACACAATGGTTAAATTCTACT 57.308 30.769 0.00 0.00 0.00 2.57
2461 2599 9.373450 AGATACAGAATCCATAAGAGAGCTAAA 57.627 33.333 0.00 0.00 34.90 1.85
2475 2613 7.253684 CGAAAACGAAGTGTAGATACAGAATCC 60.254 40.741 0.00 0.00 45.00 3.01
2480 2618 6.312487 TCTCGAAAACGAAGTGTAGATACAG 58.688 40.000 0.00 0.00 45.00 2.74
2560 2698 5.390613 CGAACGGTTGAAAGCTATCAAAAT 58.609 37.500 0.00 0.00 40.76 1.82
2585 2723 1.481871 GTGGACTTGGGGACTCGATA 58.518 55.000 0.00 0.00 0.00 2.92
2600 2738 2.558795 CTGGAAAAGAGAGTCTCGTGGA 59.441 50.000 14.47 0.00 35.36 4.02
2605 2743 7.736447 TCATTTTTCTGGAAAAGAGAGTCTC 57.264 36.000 12.54 12.54 40.35 3.36
2655 2793 5.523552 TCCGCGAATGGAAATATGCATATAG 59.476 40.000 19.39 5.59 36.48 1.31
2672 2810 2.232941 AGTTATTTCCTGTCTCCGCGAA 59.767 45.455 8.23 0.00 0.00 4.70
2675 2813 2.096013 GCAAGTTATTTCCTGTCTCCGC 59.904 50.000 0.00 0.00 0.00 5.54
2698 2836 4.024387 TGCAGACGGTTCAAACTATGTTTC 60.024 41.667 0.00 0.00 0.00 2.78
2740 2878 7.039293 GGGAATGGGAACTGTTGTAAATTAACT 60.039 37.037 0.00 0.00 0.00 2.24
2741 2879 7.094631 GGGAATGGGAACTGTTGTAAATTAAC 58.905 38.462 0.00 0.00 0.00 2.01
2742 2880 6.211785 GGGGAATGGGAACTGTTGTAAATTAA 59.788 38.462 0.00 0.00 0.00 1.40
2768 2934 1.202486 GGCATGTTCATTGCATCCAGG 60.202 52.381 0.00 0.00 41.95 4.45
2770 2936 0.825410 GGGCATGTTCATTGCATCCA 59.175 50.000 0.00 0.00 41.95 3.41
2908 3077 6.316640 AGCTGATTCTTGATTCATTCTGACTG 59.683 38.462 0.00 0.00 0.00 3.51
2945 3128 8.407832 TGTAAAGGTTTGATATGCTTCATCATG 58.592 33.333 0.00 0.00 32.63 3.07
3020 3203 4.351054 CTGCACTTCCCCCGGCTT 62.351 66.667 0.00 0.00 0.00 4.35
3036 3219 4.015084 CAAACAATGCTTGAGAGGGATCT 58.985 43.478 0.00 0.00 0.00 2.75
3062 3245 1.139734 CGTGAGGGTGATGGACTCG 59.860 63.158 0.00 0.00 34.03 4.18
3113 3296 1.033202 TGGTAGTCGTCGCCTATGCA 61.033 55.000 0.00 0.00 37.32 3.96
3128 3311 1.884579 GGTATCGCGAGGATTCTGGTA 59.115 52.381 16.66 0.00 36.55 3.25
3179 3362 2.760092 GCTTGGGATTGTTGGAATGCTA 59.240 45.455 0.00 0.00 0.00 3.49
3215 3398 4.711949 CTGCTCCCACCGCTTGCT 62.712 66.667 0.00 0.00 0.00 3.91
3248 3431 2.262915 CTCGCCTTCTCAACGGCT 59.737 61.111 0.00 0.00 44.11 5.52
3249 3432 2.815647 CCTCGCCTTCTCAACGGC 60.816 66.667 0.00 0.00 42.86 5.68
3393 3576 1.810412 GCGACCTGAGAAACAAGGTGT 60.810 52.381 0.00 0.00 32.90 4.16
3460 3643 1.068588 TGTACACAGCGATCATAGCCC 59.931 52.381 0.00 0.00 34.64 5.19
3474 3657 3.797039 TCATGGAGCTGCTAATGTACAC 58.203 45.455 18.83 0.00 0.00 2.90
3606 3789 6.578944 ACGACCACAATATATACTTGAGCAA 58.421 36.000 10.16 0.00 0.00 3.91
3827 4011 6.348950 CGTATGTTTGTTGCCTCCAAAGATAA 60.349 38.462 9.66 0.00 38.77 1.75
3838 4022 3.636282 AACCTTCGTATGTTTGTTGCC 57.364 42.857 0.00 0.00 0.00 4.52
3843 4027 6.816640 TCCATTCTCTAACCTTCGTATGTTTG 59.183 38.462 0.00 0.00 0.00 2.93
3846 4030 5.452077 GCTCCATTCTCTAACCTTCGTATGT 60.452 44.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.