Multiple sequence alignment - TraesCS2D01G530300

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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 TraesCS2D01G530300 chr2D 100.000 4794 0 0 1 4794 616948164 616952957 0.000000e+00 8853.0
1 TraesCS2D01G530300 chr2D 91.111 360 23 1 3239 3589 616951225 616951584 3.360000e-131 479.0
2 TraesCS2D01G530300 chr2D 91.111 360 23 1 3062 3421 616951402 616951752 3.360000e-131 479.0
3 TraesCS2D01G530300 chr2D 88.525 183 12 1 3416 3589 616951225 616951407 3.760000e-51 213.0
4 TraesCS2D01G530300 chr2D 88.525 183 12 1 3062 3244 616951579 616951752 3.760000e-51 213.0
5 TraesCS2D01G530300 chr2A 91.598 4523 247 62 341 4791 746964695 746969156 0.000000e+00 6124.0
6 TraesCS2D01G530300 chr2A 91.944 360 20 1 3239 3589 746967424 746967783 3.330000e-136 496.0
7 TraesCS2D01G530300 chr2A 90.556 360 25 1 3062 3421 746967601 746967951 7.260000e-128 468.0
8 TraesCS2D01G530300 chr2A 87.789 303 16 6 3 290 746964243 746964539 7.690000e-88 335.0
9 TraesCS2D01G530300 chr2A 84.444 270 21 6 40 288 746945230 746945499 3.710000e-61 246.0
10 TraesCS2D01G530300 chr2A 89.617 183 10 1 3416 3589 746967424 746967606 1.740000e-54 224.0
11 TraesCS2D01G530300 chr2A 88.525 183 12 6 3062 3244 746967778 746967951 3.760000e-51 213.0
12 TraesCS2D01G530300 chr2A 95.833 48 2 0 274 321 746964557 746964604 1.430000e-10 78.7
13 TraesCS2D01G530300 chr2B 96.576 2716 76 12 2081 4791 752488167 752490870 0.000000e+00 4484.0
14 TraesCS2D01G530300 chr2B 94.741 1312 53 10 774 2082 752486775 752488073 0.000000e+00 2026.0
15 TraesCS2D01G530300 chr2B 92.570 996 56 9 1 992 752415859 752416840 0.000000e+00 1413.0
16 TraesCS2D01G530300 chr2B 91.389 360 22 1 3239 3589 752489148 752489507 7.210000e-133 484.0
17 TraesCS2D01G530300 chr2B 90.833 360 24 1 3062 3421 752489325 752489675 1.560000e-129 473.0
18 TraesCS2D01G530300 chr2B 91.304 184 16 0 1082 1265 752459430 752459613 7.960000e-63 252.0
19 TraesCS2D01G530300 chr2B 89.071 183 11 1 3416 3589 752489148 752489330 8.080000e-53 219.0
20 TraesCS2D01G530300 chr2B 88.525 183 12 1 3062 3244 752489502 752489675 3.760000e-51 213.0
21 TraesCS2D01G530300 chr2B 80.088 226 39 5 2539 2758 752488772 752488997 3.840000e-36 163.0
22 TraesCS2D01G530300 chr2B 76.176 340 45 22 1 321 752486060 752486382 3.870000e-31 147.0


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 TraesCS2D01G530300 chr2D 616948164 616952957 4793 False 2047.400 8853 91.854400 1 4794 5 chr2D.!!$F1 4793
1 TraesCS2D01G530300 chr2A 746964243 746969156 4913 False 1134.100 6124 90.837429 3 4791 7 chr2A.!!$F2 4788
2 TraesCS2D01G530300 chr2B 752415859 752416840 981 False 1413.000 1413 92.570000 1 992 1 chr2B.!!$F1 991
3 TraesCS2D01G530300 chr2B 752486060 752490870 4810 False 1026.125 4484 88.424875 1 4791 8 chr2B.!!$F3 4790

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
737 882 0.536233 AGTGTAAACATGGTGCCGCA 60.536 50.0 0.0 0.0 0.00 5.69 F
1431 1579 0.595095 CACCTGAGCTTTGAAGTGCC 59.405 55.0 0.0 0.0 0.00 5.01 F
2546 2827 0.108186 TGCAAGCTCTGGTGATACCG 60.108 55.0 0.0 0.0 42.58 4.02 F
2562 2861 0.830444 ACCGTACCTGCTCCAACAGA 60.830 55.0 0.0 0.0 40.25 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2512 2793 0.036732 TTGCAGAATTCTCGGGTGCT 59.963 50.000 4.57 0.0 35.11 4.40 R
2873 3175 0.676782 GATGTGGTGGTGGTGTAGGC 60.677 60.000 0.00 0.0 0.00 3.93 R
3643 3945 1.015109 AGCTGAGATTTGCATCTGCG 58.985 50.000 10.16 0.0 45.83 5.18 R
4201 4505 2.030371 TGCTTGGCAAACATGTCTTCA 58.970 42.857 0.00 0.0 34.76 3.02 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
26 27 1.207089 TGAATGGGTAGGCTCTTCGTG 59.793 52.381 0.00 0.00 0.00 4.35
42 46 6.508721 GCTCTTCGTGAACTATTGATTAGTGC 60.509 42.308 0.00 0.00 40.37 4.40
275 297 3.658709 AGCAGAGTAACTTCAAGTCAGC 58.341 45.455 0.00 0.00 0.00 4.26
330 466 5.482908 GACTTGCCAGTTCAAGAAGAGATA 58.517 41.667 10.10 0.00 44.61 1.98
331 467 5.486526 ACTTGCCAGTTCAAGAAGAGATAG 58.513 41.667 10.10 0.00 44.61 2.08
332 468 5.247110 ACTTGCCAGTTCAAGAAGAGATAGA 59.753 40.000 10.10 0.00 44.61 1.98
333 469 5.336150 TGCCAGTTCAAGAAGAGATAGAG 57.664 43.478 0.00 0.00 0.00 2.43
334 470 5.019470 TGCCAGTTCAAGAAGAGATAGAGA 58.981 41.667 0.00 0.00 0.00 3.10
335 471 5.481824 TGCCAGTTCAAGAAGAGATAGAGAA 59.518 40.000 0.00 0.00 0.00 2.87
336 472 6.155910 TGCCAGTTCAAGAAGAGATAGAGAAT 59.844 38.462 0.00 0.00 0.00 2.40
337 473 7.047271 GCCAGTTCAAGAAGAGATAGAGAATT 58.953 38.462 0.00 0.00 0.00 2.17
354 490 7.658525 AGAGAATTAGAGATGACTGTCACAT 57.341 36.000 13.50 4.37 0.00 3.21
363 499 6.379417 AGAGATGACTGTCACATCACTTCATA 59.621 38.462 13.50 0.00 44.29 2.15
577 721 5.401531 AGCCAGTCTTCTTGTAACGAATA 57.598 39.130 0.00 0.00 0.00 1.75
608 752 6.355747 TGGCCATGAATTAATTGATTTTCCC 58.644 36.000 0.00 1.38 0.00 3.97
616 760 8.150945 TGAATTAATTGATTTTCCCGGTCAAAA 58.849 29.630 5.17 9.31 35.70 2.44
617 761 8.546597 AATTAATTGATTTTCCCGGTCAAAAG 57.453 30.769 8.34 0.00 35.70 2.27
618 762 5.799827 AATTGATTTTCCCGGTCAAAAGA 57.200 34.783 8.34 1.65 35.70 2.52
619 763 6.358974 AATTGATTTTCCCGGTCAAAAGAT 57.641 33.333 8.34 3.53 35.70 2.40
647 792 4.797471 TCTTTGCCGATCTTTTGTCATTG 58.203 39.130 0.00 0.00 0.00 2.82
654 799 5.390613 CCGATCTTTTGTCATTGTGGTTAC 58.609 41.667 0.00 0.00 0.00 2.50
658 803 8.286800 CGATCTTTTGTCATTGTGGTTACTTTA 58.713 33.333 0.00 0.00 0.00 1.85
710 855 8.150827 ACCCATCTGTGCATATACAAGTATAT 57.849 34.615 6.87 6.87 38.81 0.86
737 882 0.536233 AGTGTAAACATGGTGCCGCA 60.536 50.000 0.00 0.00 0.00 5.69
744 889 1.102809 ACATGGTGCCGCATGTATGG 61.103 55.000 14.82 0.00 39.91 2.74
750 895 4.777384 CCGCATGTATGGCAGCTA 57.223 55.556 0.00 0.00 0.00 3.32
765 910 3.037941 GCTATGGCTCTCCGGTCTA 57.962 57.895 0.00 0.00 35.22 2.59
766 911 0.599060 GCTATGGCTCTCCGGTCTAC 59.401 60.000 0.00 0.00 35.22 2.59
839 984 5.471797 TGCAAGCAACATAGTTACTGCTAAA 59.528 36.000 0.00 0.00 44.18 1.85
963 1110 2.673775 TTCCAGAATCCAAGCAACCA 57.326 45.000 0.00 0.00 0.00 3.67
1015 1162 2.036731 AGATGTCGTCCCGGTCCA 59.963 61.111 0.00 0.00 0.00 4.02
1146 1293 1.169661 TGGGCGGCAACAACTACAAG 61.170 55.000 12.47 0.00 0.00 3.16
1152 1299 2.230660 GGCAACAACTACAAGAGGCTT 58.769 47.619 0.00 0.00 0.00 4.35
1167 1314 1.451028 GCTTCCCTACCTGCTGCTG 60.451 63.158 0.00 0.00 0.00 4.41
1307 1454 1.244816 CGCCTCGAGGTATGGATACA 58.755 55.000 31.43 0.00 45.47 2.29
1322 1469 1.678101 GATACAGTTTCTGGCATGCCC 59.322 52.381 33.44 17.70 35.51 5.36
1431 1579 0.595095 CACCTGAGCTTTGAAGTGCC 59.405 55.000 0.00 0.00 0.00 5.01
1463 1611 7.299246 TCTAACCAGTAAGCTGAGTTTAGTT 57.701 36.000 0.00 0.00 45.28 2.24
1501 1649 3.055747 TGACGTCACATAAATGTAGCCCA 60.056 43.478 15.76 0.00 39.39 5.36
1502 1650 3.267483 ACGTCACATAAATGTAGCCCAC 58.733 45.455 0.00 0.00 39.39 4.61
1616 1771 4.163078 AGTGGATGAAAGAGTCCTACATGG 59.837 45.833 0.00 0.00 35.49 3.66
1669 1824 7.129109 TCTAACCTCGATTTTCAATCAACAC 57.871 36.000 0.00 0.00 0.00 3.32
1757 1914 4.635765 GTGGCTTGTGCAAATACTCATAGA 59.364 41.667 0.00 0.00 41.91 1.98
1792 1949 6.587990 CAGAAGTACAGATAGAACACAACTGG 59.412 42.308 0.00 0.00 33.57 4.00
1838 1996 4.644103 AGTCCAACAATGAGCATAATGC 57.356 40.909 0.00 0.00 45.46 3.56
1858 2016 5.937540 AATGCCAAATATGGAATCATGCATG 59.062 36.000 21.07 21.07 45.03 4.06
2179 2460 4.806640 TGGCCAGAATGAAAAGGAAATC 57.193 40.909 0.00 0.00 39.69 2.17
2263 2544 5.104941 TGAGAGGACAGAACTGAAGAACAAA 60.105 40.000 8.87 0.00 0.00 2.83
2398 2679 1.997874 AGGGCCTGACCAGATGTCC 60.998 63.158 4.50 0.00 43.78 4.02
2466 2747 0.886490 AAGACCAAGTTCAGCGGCAG 60.886 55.000 1.45 0.00 0.00 4.85
2501 2782 5.236047 GCCACAAACAATGAAAATGCAACTA 59.764 36.000 0.00 0.00 0.00 2.24
2506 2787 7.927629 ACAAACAATGAAAATGCAACTACTGAT 59.072 29.630 0.00 0.00 0.00 2.90
2512 2793 9.448438 AATGAAAATGCAACTACTGATACTGTA 57.552 29.630 0.00 0.00 0.00 2.74
2546 2827 0.108186 TGCAAGCTCTGGTGATACCG 60.108 55.000 0.00 0.00 42.58 4.02
2560 2859 1.479323 GATACCGTACCTGCTCCAACA 59.521 52.381 0.00 0.00 0.00 3.33
2561 2860 0.892755 TACCGTACCTGCTCCAACAG 59.107 55.000 0.00 0.00 37.42 3.16
2562 2861 0.830444 ACCGTACCTGCTCCAACAGA 60.830 55.000 0.00 0.00 40.25 3.41
2674 2973 2.697229 TGATGCTGTGATACCTGAGGAG 59.303 50.000 4.99 0.00 0.00 3.69
2679 2978 3.935828 GCTGTGATACCTGAGGAGAAAAC 59.064 47.826 4.99 0.00 0.00 2.43
2683 2982 5.763204 TGTGATACCTGAGGAGAAAACAAAC 59.237 40.000 4.99 0.00 0.00 2.93
2729 3031 2.376808 AGAACTGCATTCTGACGAGG 57.623 50.000 9.65 0.00 46.44 4.63
2740 3042 2.512515 GACGAGGCCACTGCATCC 60.513 66.667 5.01 0.00 45.24 3.51
2812 3114 2.224042 TGCTGTAACTCCTGACACTGTG 60.224 50.000 6.19 6.19 0.00 3.66
2837 3139 2.287608 GGTGAGGAAAAAGCAAACTCCG 60.288 50.000 0.00 0.00 32.91 4.63
2880 3182 2.481952 CAGAAGAACTGCAAGCCTACAC 59.518 50.000 0.00 0.00 39.86 2.90
2888 3190 1.454104 CAAGCCTACACCACCACCA 59.546 57.895 0.00 0.00 0.00 4.17
2912 3214 1.593196 CGAGAGCAACCACCAAGAAA 58.407 50.000 0.00 0.00 0.00 2.52
2915 3217 3.751175 CGAGAGCAACCACCAAGAAAATA 59.249 43.478 0.00 0.00 0.00 1.40
2931 3233 7.413438 CCAAGAAAATAGTTCATCAGAAGGTCG 60.413 40.741 0.00 0.00 33.63 4.79
2932 3234 6.936279 AGAAAATAGTTCATCAGAAGGTCGA 58.064 36.000 0.00 0.00 33.63 4.20
2959 3261 8.428186 TTGTAAAGTTCACAACTAACTTCGAT 57.572 30.769 2.02 0.00 44.35 3.59
3010 3312 3.411446 TGCCAATCAAAGTTCAGACGAT 58.589 40.909 0.00 0.00 0.00 3.73
3038 3340 1.068055 CAAAGGGCACACATTCAGAGC 60.068 52.381 0.00 0.00 0.00 4.09
3115 3417 4.402616 TGGGAGAAAACAATTGGAGGAT 57.597 40.909 10.83 0.00 0.00 3.24
3643 3945 2.991540 GAACCTGTTGCCAGCCCC 60.992 66.667 0.00 0.00 37.38 5.80
3655 3957 2.043652 AGCCCCGCAGATGCAAAT 60.044 55.556 5.55 0.00 42.21 2.32
3683 3985 4.038642 GCTTGTCCACAAATAACAGGGAAA 59.961 41.667 0.00 0.00 35.15 3.13
3745 4047 2.701551 TCCAAAAGGAGGAAGAGGACA 58.298 47.619 0.00 0.00 30.71 4.02
4110 4414 1.573108 ACACCTAGCTGCATGGTAGT 58.427 50.000 14.49 12.25 43.23 2.73
4345 4649 7.201478 CGCAGAAAAGGTACAAACAAAATTGAA 60.201 33.333 0.00 0.00 34.38 2.69
4352 4656 8.920509 AGGTACAAACAAAATTGAACAACTAC 57.079 30.769 0.00 0.00 34.38 2.73
4603 4911 5.009631 TGCAAGTTATGAAGCCATGTACTT 58.990 37.500 0.00 0.00 38.43 2.24
4676 4984 0.756903 ACCTGTATGGCCGGTCATAC 59.243 55.000 40.01 40.01 45.76 2.39
4698 5006 4.514441 ACCTGTAGTCGATGTACCTTATCG 59.486 45.833 7.55 7.55 46.45 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.207089 CACGAAGAGCCTACCCATTCA 59.793 52.381 0.00 0.00 0.00 2.57
26 27 6.310467 TCAACAGACGCACTAATCAATAGTTC 59.690 38.462 0.00 0.00 42.31 3.01
42 46 3.940852 TGATTCCCATCAATCAACAGACG 59.059 43.478 0.00 0.00 39.37 4.18
202 213 9.060347 CCTTGAATATCTCTGCTGCTTTAAATA 57.940 33.333 0.00 0.00 0.00 1.40
330 466 7.341512 TGATGTGACAGTCATCTCTAATTCTCT 59.658 37.037 6.51 0.00 41.30 3.10
331 467 7.434897 GTGATGTGACAGTCATCTCTAATTCTC 59.565 40.741 6.51 0.00 41.30 2.87
332 468 7.123997 AGTGATGTGACAGTCATCTCTAATTCT 59.876 37.037 6.51 0.00 41.31 2.40
333 469 7.264221 AGTGATGTGACAGTCATCTCTAATTC 58.736 38.462 6.51 0.00 41.31 2.17
334 470 7.180322 AGTGATGTGACAGTCATCTCTAATT 57.820 36.000 6.51 0.00 41.31 1.40
335 471 6.788598 AGTGATGTGACAGTCATCTCTAAT 57.211 37.500 6.51 0.00 41.31 1.73
336 472 6.209391 TGAAGTGATGTGACAGTCATCTCTAA 59.791 38.462 6.51 0.00 41.84 2.10
337 473 5.711976 TGAAGTGATGTGACAGTCATCTCTA 59.288 40.000 6.51 0.00 41.84 2.43
354 490 5.732331 AAGAATCCCCCAATATGAAGTGA 57.268 39.130 0.00 0.00 0.00 3.41
363 499 4.746466 TGTACACAAAAGAATCCCCCAAT 58.254 39.130 0.00 0.00 0.00 3.16
442 578 8.383175 ACTGATCTGGACTATTTTTAAGTGGAA 58.617 33.333 4.49 0.00 0.00 3.53
542 686 9.499479 CAAGAAGACTGGCTACATGAATAATAT 57.501 33.333 0.00 0.00 0.00 1.28
583 727 6.999871 GGGAAAATCAATTAATTCATGGCCAT 59.000 34.615 14.09 14.09 0.00 4.40
633 777 9.612620 CTAAAGTAACCACAATGACAAAAGATC 57.387 33.333 0.00 0.00 0.00 2.75
647 792 4.998033 AGAGAAAGCTGCTAAAGTAACCAC 59.002 41.667 0.90 0.00 0.00 4.16
710 855 3.743911 CACCATGTTTACACTCTGCGTTA 59.256 43.478 0.00 0.00 0.00 3.18
747 892 0.599060 GTAGACCGGAGAGCCATAGC 59.401 60.000 9.46 0.00 40.32 2.97
750 895 0.820074 CTCGTAGACCGGAGAGCCAT 60.820 60.000 9.46 0.00 37.11 4.40
758 903 0.456312 GAAGTGTGCTCGTAGACCGG 60.456 60.000 0.00 0.00 37.11 5.28
759 904 0.522180 AGAAGTGTGCTCGTAGACCG 59.478 55.000 0.00 0.00 38.13 4.79
760 905 1.540267 TCAGAAGTGTGCTCGTAGACC 59.460 52.381 0.00 0.00 0.00 3.85
761 906 2.991434 TCAGAAGTGTGCTCGTAGAC 57.009 50.000 0.00 0.00 0.00 2.59
762 907 3.081804 TGATCAGAAGTGTGCTCGTAGA 58.918 45.455 0.00 0.00 0.00 2.59
763 908 3.494045 TGATCAGAAGTGTGCTCGTAG 57.506 47.619 0.00 0.00 0.00 3.51
765 910 2.820059 TTGATCAGAAGTGTGCTCGT 57.180 45.000 0.00 0.00 0.00 4.18
766 911 3.320626 TCTTTGATCAGAAGTGTGCTCG 58.679 45.455 13.69 0.00 0.00 5.03
772 917 9.543783 TGATGAAGATATCTTTGATCAGAAGTG 57.456 33.333 24.10 0.00 36.11 3.16
839 984 6.094186 GGTTTGTCTCTCTCTTTGACTTTTGT 59.906 38.462 0.00 0.00 0.00 2.83
963 1110 5.046663 TGTGAAGAAACTTGGCCTTCTTTTT 60.047 36.000 16.40 4.12 40.98 1.94
1080 1227 3.515562 ACTACCTCCATCCATCTCCATC 58.484 50.000 0.00 0.00 0.00 3.51
1132 1279 1.897560 AGCCTCTTGTAGTTGTTGCC 58.102 50.000 0.00 0.00 0.00 4.52
1146 1293 1.524482 CAGCAGGTAGGGAAGCCTC 59.476 63.158 0.00 0.00 31.73 4.70
1152 1299 2.284921 AGCAGCAGCAGGTAGGGA 60.285 61.111 3.17 0.00 45.49 4.20
1307 1454 4.428845 CAGGGCATGCCAGAAACT 57.571 55.556 36.56 21.67 37.98 2.66
1322 1469 1.338973 AGCAAACCAGTTGTGATGCAG 59.661 47.619 7.45 0.00 40.98 4.41
1330 1477 4.024556 CACAGAGAAGTAGCAAACCAGTTG 60.025 45.833 0.00 0.00 40.50 3.16
1389 1537 1.047801 AATCACCAAAGTGGGGCAAC 58.952 50.000 0.00 0.00 41.90 4.17
1419 1567 1.502190 GCGTAGGGCACTTCAAAGC 59.498 57.895 0.00 0.00 42.87 3.51
1422 1570 1.192146 AGAGGCGTAGGGCACTTCAA 61.192 55.000 11.84 0.00 46.16 2.69
1431 1579 2.223758 GCTTACTGGTTAGAGGCGTAGG 60.224 54.545 0.00 0.00 0.00 3.18
1463 1611 6.093404 GTGACGTCATTCAGTGAATAAGAGA 58.907 40.000 23.12 8.57 38.90 3.10
1616 1771 3.277807 GCTACAGCCTGCATGATTGCC 62.278 57.143 0.00 0.00 40.83 4.52
1669 1824 4.876107 GGTACTTGTAATCTGTGACCATGG 59.124 45.833 11.19 11.19 0.00 3.66
1722 1879 0.966875 CAAGCCACATGCCAAGCCTA 60.967 55.000 0.00 0.00 42.71 3.93
1838 1996 4.888917 TGCATGCATGATTCCATATTTGG 58.111 39.130 30.64 0.00 45.15 3.28
1858 2016 9.831737 ATTCTTTTACGATATTGAATGCTATGC 57.168 29.630 0.00 0.00 0.00 3.14
2005 2164 8.700973 TGGTAGTGCTACAAGAATATCATTGTA 58.299 33.333 10.98 10.60 40.09 2.41
2098 2379 8.527567 TTTACTTTGAAAAACAGGTTTGTGAG 57.472 30.769 0.00 0.00 37.67 3.51
2179 2460 6.593382 CCACTTTTCTCCTCATCTCTTTACTG 59.407 42.308 0.00 0.00 0.00 2.74
2263 2544 5.010012 GGTGGTTGTTTCTGAATTCATGACT 59.990 40.000 8.96 0.00 0.00 3.41
2398 2679 4.391830 TGTTGCAGGAGTTCTTTTATAGCG 59.608 41.667 0.00 0.00 0.00 4.26
2501 2782 2.025155 CTCGGGTGCTACAGTATCAGT 58.975 52.381 0.00 0.00 0.00 3.41
2506 2787 3.130516 CAGAATTCTCGGGTGCTACAGTA 59.869 47.826 4.57 0.00 0.00 2.74
2512 2793 0.036732 TTGCAGAATTCTCGGGTGCT 59.963 50.000 4.57 0.00 35.11 4.40
2546 2827 3.006967 TCTTCTTCTGTTGGAGCAGGTAC 59.993 47.826 0.00 0.00 37.12 3.34
2560 2859 8.207545 GTGGTGTTATAGGAATGATCTTCTTCT 58.792 37.037 0.00 0.00 0.00 2.85
2561 2860 8.207545 AGTGGTGTTATAGGAATGATCTTCTTC 58.792 37.037 0.00 0.00 0.00 2.87
2562 2861 7.989741 CAGTGGTGTTATAGGAATGATCTTCTT 59.010 37.037 0.00 0.00 0.00 2.52
2674 2973 5.514274 TGGAATCACTGGAGTTTGTTTTC 57.486 39.130 0.00 0.00 0.00 2.29
2679 2978 2.165030 GGCATGGAATCACTGGAGTTTG 59.835 50.000 0.00 0.00 0.00 2.93
2683 2982 1.676746 CAGGCATGGAATCACTGGAG 58.323 55.000 0.00 0.00 0.00 3.86
2722 3024 2.265739 GATGCAGTGGCCTCGTCA 59.734 61.111 3.32 4.31 40.13 4.35
2728 3030 2.202987 CTCTCGGATGCAGTGGCC 60.203 66.667 0.00 0.00 40.13 5.36
2729 3031 2.894387 GCTCTCGGATGCAGTGGC 60.894 66.667 0.00 0.00 41.68 5.01
2740 3042 1.081892 CATCTTGGTGGTTGCTCTCG 58.918 55.000 0.00 0.00 0.00 4.04
2812 3114 5.106118 GGAGTTTGCTTTTTCCTCACCTATC 60.106 44.000 0.00 0.00 0.00 2.08
2873 3175 0.676782 GATGTGGTGGTGGTGTAGGC 60.677 60.000 0.00 0.00 0.00 3.93
2880 3182 1.219124 CTCTCGGATGTGGTGGTGG 59.781 63.158 0.00 0.00 0.00 4.61
2888 3190 1.296715 GGTGGTTGCTCTCGGATGT 59.703 57.895 0.00 0.00 0.00 3.06
2912 3214 7.106239 ACAAATCGACCTTCTGATGAACTATT 58.894 34.615 0.00 0.00 0.00 1.73
2915 3217 4.899502 ACAAATCGACCTTCTGATGAACT 58.100 39.130 0.00 0.00 0.00 3.01
2931 3233 9.155053 CGAAGTTAGTTGTGAACTTTACAAATC 57.845 33.333 2.99 0.00 45.02 2.17
2932 3234 8.885722 TCGAAGTTAGTTGTGAACTTTACAAAT 58.114 29.630 4.97 4.97 45.02 2.32
2959 3261 6.003326 TGTTTTCTCTTGTAAGGCATCATCA 58.997 36.000 0.00 0.00 0.00 3.07
3115 3417 1.192146 AGCTGACTTCGCCTTGGGTA 61.192 55.000 0.00 0.00 0.00 3.69
3321 3623 5.047660 TCCTTCTCAAGCAGTTTACTCTCTC 60.048 44.000 0.00 0.00 0.00 3.20
3331 3633 2.617532 GCCATCTTCCTTCTCAAGCAGT 60.618 50.000 0.00 0.00 0.00 4.40
3643 3945 1.015109 AGCTGAGATTTGCATCTGCG 58.985 50.000 10.16 0.00 45.83 5.18
3655 3957 4.713553 TGTTATTTGTGGACAAGCTGAGA 58.286 39.130 0.00 0.00 37.15 3.27
3683 3985 3.734902 CGCCTCTTGCTTGTTTCTTTTGT 60.735 43.478 0.00 0.00 38.05 2.83
3823 4126 7.275888 TGTATTGCAGTGTTTCTTCAAATCT 57.724 32.000 0.00 0.00 33.56 2.40
3835 4138 4.400251 CCTTCCATCATTGTATTGCAGTGT 59.600 41.667 0.00 0.00 36.38 3.55
3905 4208 3.564053 TTCAGCATATGCCAGTGATCA 57.436 42.857 23.96 5.05 43.38 2.92
4201 4505 2.030371 TGCTTGGCAAACATGTCTTCA 58.970 42.857 0.00 0.00 34.76 3.02
4258 4562 4.122046 GCCTGCTGTGAGAAAATTGTTTT 58.878 39.130 0.00 0.00 35.12 2.43
4676 4984 4.753610 TCGATAAGGTACATCGACTACAGG 59.246 45.833 11.50 0.00 46.80 4.00
4698 5006 3.689161 TGTTTATGCTGGCATGTGTAGTC 59.311 43.478 17.09 3.17 37.82 2.59


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

AutoCloner maintained by Alex Coulton.