Multiple sequence alignment - TraesCS2D01G302500

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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 TraesCS2D01G302500 chr2D 100.000 6143 0 0 1 6143 386247651 386253793 0.000000e+00 11345.0
1 TraesCS2D01G302500 chr2D 87.654 81 10 0 1254 1334 640298895 640298815 1.820000e-15 95.3
2 TraesCS2D01G302500 chr2A 95.511 3408 113 21 894 4287 522072400 522075781 0.000000e+00 5409.0
3 TraesCS2D01G302500 chr2A 96.842 1235 27 7 4287 5511 522076120 522077352 0.000000e+00 2054.0
4 TraesCS2D01G302500 chr2A 92.795 916 41 12 2 899 522071132 522072040 0.000000e+00 1303.0
5 TraesCS2D01G302500 chr2A 96.579 643 14 2 5508 6143 522077431 522078072 0.000000e+00 1059.0
6 TraesCS2D01G302500 chr2A 87.654 81 10 0 1254 1334 765762342 765762262 1.820000e-15 95.3
7 TraesCS2D01G302500 chr2B 93.121 3227 121 45 2 3180 457108077 457111250 0.000000e+00 4636.0
8 TraesCS2D01G302500 chr2B 93.884 1537 54 14 4235 5755 457112464 457113976 0.000000e+00 2281.0
9 TraesCS2D01G302500 chr2B 97.605 1002 20 3 3166 4166 457111270 457112268 0.000000e+00 1714.0
10 TraesCS2D01G302500 chr2B 96.931 391 8 2 5754 6143 457114070 457114457 0.000000e+00 652.0
11 TraesCS2D01G302500 chr2B 87.654 81 10 0 1254 1334 801162567 801162647 1.820000e-15 95.3
12 TraesCS2D01G302500 chr4A 76.045 359 50 19 992 1333 9052559 9052220 2.970000e-33 154.0
13 TraesCS2D01G302500 chr4A 86.364 132 16 2 992 1122 9048282 9048152 6.420000e-30 143.0
14 TraesCS2D01G302500 chr3A 87.619 105 11 2 1230 1333 14278171 14278274 3.010000e-23 121.0
15 TraesCS2D01G302500 chr1A 86.667 105 12 2 1230 1333 540201710 540201813 1.400000e-21 115.0
16 TraesCS2D01G302500 chr4B 85.714 98 14 0 1729 1826 76818443 76818346 3.030000e-18 104.0


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 TraesCS2D01G302500 chr2D 386247651 386253793 6142 False 11345.00 11345 100.00000 1 6143 1 chr2D.!!$F1 6142
1 TraesCS2D01G302500 chr2A 522071132 522078072 6940 False 2456.25 5409 95.43175 2 6143 4 chr2A.!!$F1 6141
2 TraesCS2D01G302500 chr2B 457108077 457114457 6380 False 2320.75 4636 95.38525 2 6143 4 chr2B.!!$F2 6141

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
590 610 0.313672 GCCAAATCAAGCAACACGGA 59.686 50.000 0.00 0.0 0.00 4.69 F
1896 2322 0.315251 GGGGTCAAAAGCTGCACTTC 59.685 55.000 1.02 0.0 37.75 3.01 F
2509 2939 0.107165 GTCCTTTCGGGCCAGCTAAT 60.107 55.000 4.39 0.0 34.39 1.73 F
2511 2941 0.107214 CCTTTCGGGCCAGCTAATCA 60.107 55.000 4.39 0.0 0.00 2.57 F
2637 3067 1.068434 GCTGGCTCTGAGATAGTGTCC 59.932 57.143 9.28 0.0 0.00 4.02 F
2926 3359 2.125350 CAGCGGTCCCTGCTTCTC 60.125 66.667 0.00 0.0 41.72 2.87 F
4764 5742 0.034059 AAACTCGGGTCAGCTCACTG 59.966 55.000 0.00 0.0 45.95 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 2630 0.468226 GAGAGAGAGAGAGCCGGAGA 59.532 60.000 5.05 0.00 0.00 3.71 R
2924 3357 0.742505 ATTTGGATGGCGTGCATGAG 59.257 50.000 10.93 0.00 0.00 2.90 R
4506 5479 0.760567 TGGGGTCATCAGGATCCTCG 60.761 60.000 12.69 8.09 46.85 4.63 R
4590 5568 6.208599 TGGACCAACCATAAGAAAGTTGAATC 59.791 38.462 3.79 1.86 44.64 2.52 R
4673 5651 1.350684 TGCTTGCAGTCTTGGGATACA 59.649 47.619 0.00 0.00 39.74 2.29 R
4794 5772 8.634335 TTGTTATTCTCTGAAATGATGGTTGA 57.366 30.769 0.00 0.00 0.00 3.18 R
5842 7009 3.516615 TGGTGGAAACTTTCTTTTTGCG 58.483 40.909 1.57 0.00 0.00 4.85 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
65 66 1.216977 CACGTACAAGCCATCCCGA 59.783 57.895 0.00 0.00 0.00 5.14
203 204 8.461222 TCATCATAATCAGCGATGAAAGTTTTT 58.539 29.630 7.76 0.00 41.85 1.94
204 205 8.740369 CATCATAATCAGCGATGAAAGTTTTTC 58.260 33.333 7.76 0.00 39.09 2.29
205 206 7.815641 TCATAATCAGCGATGAAAGTTTTTCA 58.184 30.769 7.76 6.69 0.00 2.69
206 207 7.964559 TCATAATCAGCGATGAAAGTTTTTCAG 59.035 33.333 7.76 0.00 0.00 3.02
207 208 5.695851 ATCAGCGATGAAAGTTTTTCAGT 57.304 34.783 7.76 0.00 0.00 3.41
208 209 5.095691 TCAGCGATGAAAGTTTTTCAGTC 57.904 39.130 0.00 6.98 0.00 3.51
260 261 1.608590 CGTTTTCCACAGTCCAAGCAT 59.391 47.619 0.00 0.00 0.00 3.79
401 418 7.835822 ACTCTCGTCAGTTACTACTTACTCTA 58.164 38.462 0.00 0.00 30.26 2.43
402 419 7.975616 ACTCTCGTCAGTTACTACTTACTCTAG 59.024 40.741 0.00 0.00 30.26 2.43
445 462 4.769859 TTTACTTATTTTGCGGGTGGTC 57.230 40.909 0.00 0.00 0.00 4.02
510 527 2.743553 CAGGGCTCCCTTCAAAATCAT 58.256 47.619 4.34 0.00 45.70 2.45
511 528 2.692041 CAGGGCTCCCTTCAAAATCATC 59.308 50.000 4.34 0.00 45.70 2.92
555 575 1.374758 CAACGGGAGCCAGACTGTC 60.375 63.158 0.00 0.00 0.00 3.51
590 610 0.313672 GCCAAATCAAGCAACACGGA 59.686 50.000 0.00 0.00 0.00 4.69
599 619 1.048601 AGCAACACGGAGAGAAAGGA 58.951 50.000 0.00 0.00 0.00 3.36
644 664 6.016276 GGACCTCACTGTCAATTACAACAAAT 60.016 38.462 0.00 0.00 37.74 2.32
682 703 6.313744 ACAATTAGTTCCGGAGAAAACAAG 57.686 37.500 3.34 0.00 32.58 3.16
802 826 6.894339 ATTAATTAATCGAACCCATCCCAC 57.106 37.500 4.81 0.00 0.00 4.61
826 850 4.006989 GGGGAAGAAGAAGAAGAAGAAGC 58.993 47.826 0.00 0.00 0.00 3.86
883 917 4.825679 CCCTCCCTCCCTCCCACC 62.826 77.778 0.00 0.00 0.00 4.61
963 1362 3.391665 CTCCGGCCCGATCAAGCTT 62.392 63.158 3.71 0.00 0.00 3.74
966 1365 1.450312 CGGCCCGATCAAGCTTTCT 60.450 57.895 0.00 0.00 0.00 2.52
974 1373 0.607489 ATCAAGCTTTCTGCAGCGGT 60.607 50.000 9.47 2.46 45.24 5.68
1162 1568 2.764128 TCGGGCTCCCCTGTGATC 60.764 66.667 0.00 0.00 42.67 2.92
1169 1575 0.695462 CTCCCCTGTGATCCATCCCA 60.695 60.000 0.00 0.00 0.00 4.37
1173 1579 0.477204 CCTGTGATCCATCCCAGCAT 59.523 55.000 0.00 0.00 31.98 3.79
1205 1629 1.535896 GTCGAGTTTTTCCTTCCTGCC 59.464 52.381 0.00 0.00 0.00 4.85
1373 1798 1.819632 CGGGAGCAATCCTTTCCGG 60.820 63.158 0.00 0.00 37.17 5.14
1380 1805 1.383523 CAATCCTTTCCGGCTTCTCC 58.616 55.000 0.00 0.00 0.00 3.71
1543 1968 0.815615 GGATCGGTCCATTGCCTGTC 60.816 60.000 10.69 0.00 44.42 3.51
1829 2255 6.471519 CGACTTCGGTTACTCAAAGGTAATAG 59.528 42.308 0.00 0.00 34.73 1.73
1896 2322 0.315251 GGGGTCAAAAGCTGCACTTC 59.685 55.000 1.02 0.00 37.75 3.01
2129 2559 1.301479 GAAGCCCAAGTCGACGGTT 60.301 57.895 10.46 7.61 0.00 4.44
2132 2562 2.738480 CCCAAGTCGACGGTTGGA 59.262 61.111 28.87 0.00 45.35 3.53
2194 2624 2.805353 CGACGGCAAGGTCAGTCG 60.805 66.667 2.52 2.52 44.95 4.18
2198 2628 2.432628 GGCAAGGTCAGTCGGTCG 60.433 66.667 0.00 0.00 0.00 4.79
2200 2630 3.048602 CAAGGTCAGTCGGTCGGT 58.951 61.111 0.00 0.00 0.00 4.69
2201 2631 1.080705 CAAGGTCAGTCGGTCGGTC 60.081 63.158 0.00 0.00 0.00 4.79
2202 2632 1.228490 AAGGTCAGTCGGTCGGTCT 60.228 57.895 0.00 0.00 0.00 3.85
2203 2633 1.242665 AAGGTCAGTCGGTCGGTCTC 61.243 60.000 0.00 0.00 0.00 3.36
2204 2634 2.698763 GGTCAGTCGGTCGGTCTCC 61.699 68.421 0.00 0.00 0.00 3.71
2214 2644 2.124487 CGGTCTCCGGCTCTCTCT 60.124 66.667 0.00 0.00 44.15 3.10
2264 2694 1.181741 TTCTGCCTCGTGACTCTGCT 61.182 55.000 0.00 0.00 0.00 4.24
2413 2843 1.529010 CAACCAGCAGCCCTTGTGA 60.529 57.895 0.00 0.00 0.00 3.58
2428 2858 1.678970 GTGAACTGGGTCCATGGGC 60.679 63.158 13.02 10.72 0.00 5.36
2433 2863 3.188903 TGGGTCCATGGGCCACAA 61.189 61.111 35.76 18.57 0.00 3.33
2497 2927 2.369203 GGTCTATAGGCTGGGTCCTTTC 59.631 54.545 3.98 0.00 37.66 2.62
2508 2938 1.298667 GTCCTTTCGGGCCAGCTAA 59.701 57.895 4.39 0.00 34.39 3.09
2509 2939 0.107165 GTCCTTTCGGGCCAGCTAAT 60.107 55.000 4.39 0.00 34.39 1.73
2510 2940 0.180406 TCCTTTCGGGCCAGCTAATC 59.820 55.000 4.39 0.00 34.39 1.75
2511 2941 0.107214 CCTTTCGGGCCAGCTAATCA 60.107 55.000 4.39 0.00 0.00 2.57
2512 2942 1.303309 CTTTCGGGCCAGCTAATCAG 58.697 55.000 4.39 0.00 0.00 2.90
2637 3067 1.068434 GCTGGCTCTGAGATAGTGTCC 59.932 57.143 9.28 0.00 0.00 4.02
2924 3357 3.553095 AACCAGCGGTCCCTGCTTC 62.553 63.158 0.69 0.00 41.72 3.86
2926 3359 2.125350 CAGCGGTCCCTGCTTCTC 60.125 66.667 0.00 0.00 41.72 2.87
3018 3451 5.048294 AGTGGTCACGAGTTCTTTTTGTTTT 60.048 36.000 0.00 0.00 36.20 2.43
3020 3453 5.859648 TGGTCACGAGTTCTTTTTGTTTTTC 59.140 36.000 0.00 0.00 0.00 2.29
3084 3518 4.826556 TGGTTTAATTTATTGTGGCCTGC 58.173 39.130 3.32 0.00 0.00 4.85
3164 3598 8.910351 AATTAGATACCCTATTTCTGCACTTC 57.090 34.615 0.00 0.00 0.00 3.01
3171 3639 6.583562 ACCCTATTTCTGCACTTCATACTAC 58.416 40.000 0.00 0.00 0.00 2.73
3555 4025 7.963981 TGAAACGAACAGATTAGCTAATTGAG 58.036 34.615 19.77 14.32 0.00 3.02
3602 4072 4.488879 CAATCCTTTTCAAGTAGCCTTGC 58.511 43.478 0.00 0.00 46.33 4.01
3789 4259 3.084786 GTTACATCTTGGCTTTCCAGCT 58.915 45.455 0.00 0.00 46.44 4.24
3882 4352 3.198409 TGGATAGCATAGCAACCAGTG 57.802 47.619 0.00 0.00 0.00 3.66
3921 4391 5.530176 TTCTAGGCCAACCCTTTTAAGAT 57.470 39.130 5.01 0.00 43.06 2.40
4009 4479 8.924691 GCATTTTGTCTGCTTTCACATTAAATA 58.075 29.630 0.00 0.00 36.68 1.40
4013 4483 8.984891 TTGTCTGCTTTCACATTAAATAATGG 57.015 30.769 15.51 6.68 45.54 3.16
4200 4670 8.360390 CAGGTGTGATTACTATATGTAGCTCAA 58.640 37.037 0.00 0.00 31.22 3.02
4298 5270 8.669243 GCACTTGAAGCTTTATGTACTATTTCT 58.331 33.333 9.09 0.00 0.00 2.52
4315 5287 8.007821 ACTATTTCTGCATTTATGATCGTACG 57.992 34.615 9.53 9.53 0.00 3.67
4335 5307 6.890870 CGTACGTCTTAAATTGGTTATGTTCG 59.109 38.462 7.22 0.00 0.00 3.95
4429 5402 9.786105 TGTTATGTGTTCTAACATATTTGCATG 57.214 29.630 9.87 0.00 41.46 4.06
4494 5467 3.181465 CCCTTTATGTGATGCTAGTCGGT 60.181 47.826 0.00 0.00 0.00 4.69
4506 5479 2.676176 GCTAGTCGGTGGTTACCCTTTC 60.676 54.545 0.00 0.00 44.53 2.62
4673 5651 5.416271 ACAAAATACCAGAGTACGTCCAT 57.584 39.130 0.00 0.00 0.00 3.41
4712 5690 3.838120 GCAACTCCTTGCCAGTATTTTC 58.162 45.455 0.00 0.00 46.27 2.29
4764 5742 0.034059 AAACTCGGGTCAGCTCACTG 59.966 55.000 0.00 0.00 45.95 3.66
4794 5772 4.755411 TCATCGTCGGCTTATTCTTTTCT 58.245 39.130 0.00 0.00 0.00 2.52
5063 6041 1.627834 CAAGAAGCCAGAGGAGGAAGT 59.372 52.381 0.00 0.00 0.00 3.01
5228 6206 7.438564 AGTTTGTAGTTTGTGGTTTTGTTCTT 58.561 30.769 0.00 0.00 0.00 2.52
5242 6220 8.147704 TGGTTTTGTTCTTGAGTTTTTCTCTTT 58.852 29.630 0.00 0.00 43.13 2.52
5480 6463 8.885693 ATTATATGATCAGAGTGGTGCTACTA 57.114 34.615 0.09 0.00 0.00 1.82
5525 6590 7.201947 CCATGTACTACTTCTGAATCCTGATGA 60.202 40.741 0.00 0.00 0.00 2.92
5594 6659 9.571816 TGCAGATATTTCCAAATGTATCATGTA 57.428 29.630 0.00 0.00 0.00 2.29
5842 7009 5.695851 ATCATCGCAAACAATCTAATCCC 57.304 39.130 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.933021 TCAGTGAACCTACCGATGGT 58.067 50.000 0.00 0.00 40.16 3.55
65 66 4.175337 CCATCGGCGTCATGGGGT 62.175 66.667 17.33 0.00 37.71 4.95
160 161 3.717913 TGATGATGATGATGTGGAAGGGA 59.282 43.478 0.00 0.00 0.00 4.20
203 204 0.992695 TTCTCCTCTCTCGGGACTGA 59.007 55.000 0.00 0.00 0.00 3.41
204 205 1.474879 GTTTCTCCTCTCTCGGGACTG 59.525 57.143 0.00 0.00 0.00 3.51
205 206 1.842052 GTTTCTCCTCTCTCGGGACT 58.158 55.000 0.00 0.00 0.00 3.85
206 207 0.452585 CGTTTCTCCTCTCTCGGGAC 59.547 60.000 0.00 0.00 0.00 4.46
207 208 0.037877 ACGTTTCTCCTCTCTCGGGA 59.962 55.000 0.00 0.00 0.00 5.14
208 209 0.171455 CACGTTTCTCCTCTCTCGGG 59.829 60.000 0.00 0.00 0.00 5.14
293 296 4.142622 CCAACTGAAATGAATTGCTCGCTA 60.143 41.667 0.00 0.00 0.00 4.26
296 299 3.057315 ACCCAACTGAAATGAATTGCTCG 60.057 43.478 0.00 0.00 0.00 5.03
445 462 3.781846 CGGTTGCGGTCAAATAATAAACG 59.218 43.478 0.00 0.00 33.37 3.60
590 610 3.694926 CATTGGGAGCTTTCCTTTCTCT 58.305 45.455 8.27 0.00 0.00 3.10
599 619 1.342174 CTTGTGTGCATTGGGAGCTTT 59.658 47.619 0.00 0.00 0.00 3.51
644 664 5.127491 ACTAATTGTCGTTTGGACCTTTGA 58.873 37.500 0.00 0.00 45.46 2.69
682 703 1.020861 TGACATGGCGTGCTCATGAC 61.021 55.000 21.86 17.77 43.25 3.06
765 786 5.499139 TTAATTAATACCACTGCTGCAGC 57.501 39.130 31.89 31.89 42.50 5.25
802 826 2.567615 TCTTCTTCTTCTTCTTCCCCGG 59.432 50.000 0.00 0.00 0.00 5.73
826 850 3.681313 GCTTAAAGGAGAAGGAGAGGCTG 60.681 52.174 0.00 0.00 0.00 4.85
883 917 3.734834 TTCGTCGCGGCGAGATGAG 62.735 63.158 35.11 18.12 42.10 2.90
984 1383 4.880426 ATGGATCCCGGGCCGAGT 62.880 66.667 30.79 12.87 0.00 4.18
1205 1629 1.320555 CACTCCGTCACTAAATTCGCG 59.679 52.381 0.00 0.00 0.00 5.87
1373 1798 1.811679 CTTCTTCGGCCGGAGAAGC 60.812 63.158 46.73 2.58 43.40 3.86
1380 1805 2.382519 CGTTATACTCTTCTTCGGCCG 58.617 52.381 22.12 22.12 0.00 6.13
1382 1807 3.705043 TCCGTTATACTCTTCTTCGGC 57.295 47.619 0.00 0.00 36.99 5.54
2198 2628 0.818040 GAGAGAGAGAGCCGGAGACC 60.818 65.000 5.05 0.00 0.00 3.85
2200 2630 0.468226 GAGAGAGAGAGAGCCGGAGA 59.532 60.000 5.05 0.00 0.00 3.71
2201 2631 0.469917 AGAGAGAGAGAGAGCCGGAG 59.530 60.000 5.05 0.00 0.00 4.63
2202 2632 0.468226 GAGAGAGAGAGAGAGCCGGA 59.532 60.000 5.05 0.00 0.00 5.14
2203 2633 0.469917 AGAGAGAGAGAGAGAGCCGG 59.530 60.000 0.00 0.00 0.00 6.13
2204 2634 1.414181 AGAGAGAGAGAGAGAGAGCCG 59.586 57.143 0.00 0.00 0.00 5.52
2205 2635 2.703007 AGAGAGAGAGAGAGAGAGAGCC 59.297 54.545 0.00 0.00 0.00 4.70
2206 2636 3.244044 GGAGAGAGAGAGAGAGAGAGAGC 60.244 56.522 0.00 0.00 0.00 4.09
2207 2637 3.005261 CGGAGAGAGAGAGAGAGAGAGAG 59.995 56.522 0.00 0.00 0.00 3.20
2212 2642 0.468226 GGCGGAGAGAGAGAGAGAGA 59.532 60.000 0.00 0.00 0.00 3.10
2213 2643 0.880278 CGGCGGAGAGAGAGAGAGAG 60.880 65.000 0.00 0.00 0.00 3.20
2214 2644 1.145156 CGGCGGAGAGAGAGAGAGA 59.855 63.158 0.00 0.00 0.00 3.10
2413 2843 2.863484 TGGCCCATGGACCCAGTT 60.863 61.111 15.42 0.00 0.00 3.16
2428 2858 0.518636 CGCTGAATGGAGTGTTGTGG 59.481 55.000 0.00 0.00 0.00 4.17
2508 2938 2.964464 CCACCAGTCAGAGATAGCTGAT 59.036 50.000 0.00 0.00 45.75 2.90
2509 2939 2.024941 TCCACCAGTCAGAGATAGCTGA 60.025 50.000 0.00 0.00 42.31 4.26
2510 2940 2.382882 TCCACCAGTCAGAGATAGCTG 58.617 52.381 0.00 0.00 37.24 4.24
2511 2941 2.836636 TCCACCAGTCAGAGATAGCT 57.163 50.000 0.00 0.00 0.00 3.32
2512 2942 3.551863 CGAATCCACCAGTCAGAGATAGC 60.552 52.174 0.00 0.00 0.00 2.97
2513 2943 3.005261 CCGAATCCACCAGTCAGAGATAG 59.995 52.174 0.00 0.00 0.00 2.08
2514 2944 2.959030 CCGAATCCACCAGTCAGAGATA 59.041 50.000 0.00 0.00 0.00 1.98
2515 2945 1.759445 CCGAATCCACCAGTCAGAGAT 59.241 52.381 0.00 0.00 0.00 2.75
2637 3067 4.112341 GCAGCAAGCCAAGCGAGG 62.112 66.667 0.00 0.00 37.23 4.63
2663 3096 3.435601 GGGAATCTAATCACCTGCCACAT 60.436 47.826 0.00 0.00 0.00 3.21
2742 3175 4.751767 TTCAACAAAATCCACTGCCTTT 57.248 36.364 0.00 0.00 0.00 3.11
2914 3347 1.364626 CGTGCATGAGAAGCAGGGAC 61.365 60.000 0.00 0.00 44.68 4.46
2916 3349 2.758089 GCGTGCATGAGAAGCAGGG 61.758 63.158 10.93 0.00 45.21 4.45
2924 3357 0.742505 ATTTGGATGGCGTGCATGAG 59.257 50.000 10.93 0.00 0.00 2.90
2926 3359 1.149361 GCATTTGGATGGCGTGCATG 61.149 55.000 0.47 0.09 35.93 4.06
2990 3423 6.149807 ACAAAAAGAACTCGTGACCACTTAAA 59.850 34.615 0.00 0.00 0.00 1.52
2993 3426 4.007659 ACAAAAAGAACTCGTGACCACTT 58.992 39.130 0.00 0.00 0.00 3.16
3018 3451 1.272490 ACTCTTGATGTTCTCGCGGAA 59.728 47.619 6.13 6.05 0.00 4.30
3020 3453 1.656095 GAACTCTTGATGTTCTCGCGG 59.344 52.381 6.13 0.00 40.23 6.46
3084 3518 8.848474 TTTCTCCAGGAAATCTAACTTTACTG 57.152 34.615 2.44 2.44 43.74 2.74
3156 3590 4.177026 AGCTTTCGTAGTATGAAGTGCAG 58.823 43.478 22.67 12.80 31.53 4.41
3529 3999 7.963981 TCAATTAGCTAATCTGTTCGTTTCAG 58.036 34.615 19.11 0.00 0.00 3.02
3540 4010 6.711277 TGTGACAACCTCAATTAGCTAATCT 58.289 36.000 19.11 7.28 0.00 2.40
3555 4025 2.554032 CAGATGGACCTTTGTGACAACC 59.446 50.000 0.00 0.00 0.00 3.77
3602 4072 3.246619 GCCAACGAGAAGTTCAGTCTAG 58.753 50.000 5.50 0.00 42.02 2.43
3656 4126 5.523013 GGACAACGAGAGAAAAAGAGATG 57.477 43.478 0.00 0.00 0.00 2.90
3882 4352 6.456584 GGCCTAGAAACGAACAATAAAGTAGC 60.457 42.308 0.00 0.00 0.00 3.58
3921 4391 4.344679 AGGGAAATCAATGACACTTTGCAA 59.655 37.500 0.00 0.00 0.00 4.08
4009 4479 3.064820 GTCGAGACAAACACAACACCATT 59.935 43.478 0.00 0.00 0.00 3.16
4013 4483 2.277084 AGGTCGAGACAAACACAACAC 58.723 47.619 5.55 0.00 0.00 3.32
4137 4607 6.677913 CAGTTGTTATTTGGGGAAGTAACAG 58.322 40.000 0.00 0.00 38.04 3.16
4149 4619 7.647318 TGTTGTGTTCTATGCAGTTGTTATTTG 59.353 33.333 0.00 0.00 0.00 2.32
4186 4656 8.449397 GCTGGAAATGATTTGAGCTACATATAG 58.551 37.037 9.97 0.00 0.00 1.31
4210 4680 6.976934 TTGAACTTAAATCTTTTCCCTGCT 57.023 33.333 0.00 0.00 0.00 4.24
4298 5270 7.758613 TTTAAGACGTACGATCATAAATGCA 57.241 32.000 24.41 0.00 0.00 3.96
4315 5287 9.620660 ACATTTCGAACATAACCAATTTAAGAC 57.379 29.630 0.00 0.00 0.00 3.01
4429 5402 2.609459 CGGCTGTCTGAACCATCAATAC 59.391 50.000 0.00 0.00 34.49 1.89
4506 5479 0.760567 TGGGGTCATCAGGATCCTCG 60.761 60.000 12.69 8.09 46.85 4.63
4590 5568 6.208599 TGGACCAACCATAAGAAAGTTGAATC 59.791 38.462 3.79 1.86 44.64 2.52
4661 5639 3.308035 TGGGATACATGGACGTACTCT 57.692 47.619 0.00 0.00 39.74 3.24
4673 5651 1.350684 TGCTTGCAGTCTTGGGATACA 59.649 47.619 0.00 0.00 39.74 2.29
4794 5772 8.634335 TTGTTATTCTCTGAAATGATGGTTGA 57.366 30.769 0.00 0.00 0.00 3.18
5063 6041 0.408309 TTCCTCGTCTTCCTCCTCCA 59.592 55.000 0.00 0.00 0.00 3.86
5242 6220 3.055891 TGCAGAATCGGAGACAAGAATGA 60.056 43.478 0.00 0.00 42.51 2.57
5368 6346 4.723309 ACAGGAAAGAGAAGTGCAAGAAT 58.277 39.130 0.00 0.00 0.00 2.40
5480 6463 1.612726 GGACATCAACAAGGAGCTGCT 60.613 52.381 0.00 0.00 0.00 4.24
5525 6590 2.246091 AGCTAGAGAGGGAAGTTGCT 57.754 50.000 0.00 0.00 0.00 3.91
5842 7009 3.516615 TGGTGGAAACTTTCTTTTTGCG 58.483 40.909 1.57 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.