Multiple sequence alignment - TraesCS6B01G387700

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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 TraesCS6B01G387700 chr6B 100.000 4754 0 0 1 4754 662509678 662514431 0.000000e+00 8780.0
1 TraesCS6B01G387700 chr6D 92.686 2885 134 29 1146 3969 437803464 437806332 0.000000e+00 4087.0
2 TraesCS6B01G387700 chr6D 85.930 1194 94 31 535 1694 437802727 437803880 0.000000e+00 1206.0
3 TraesCS6B01G387700 chr6D 92.985 727 32 3 4022 4748 437806619 437807326 0.000000e+00 1042.0
4 TraesCS6B01G387700 chr6D 85.812 585 50 14 1 585 437802193 437802744 1.470000e-164 590.0
5 TraesCS6B01G387700 chr6A 91.726 2236 103 31 1769 3969 586098224 586100412 0.000000e+00 3029.0
6 TraesCS6B01G387700 chr6A 94.301 737 37 3 4019 4754 586100713 586101445 0.000000e+00 1123.0
7 TraesCS6B01G387700 chr6A 84.289 1203 106 52 535 1702 586096726 586097880 0.000000e+00 1098.0
8 TraesCS6B01G387700 chr6A 88.027 593 60 5 1 585 586096123 586096712 0.000000e+00 691.0
9 TraesCS6B01G387700 chr6A 85.841 565 60 14 1212 1769 586097539 586098090 2.470000e-162 582.0
10 TraesCS6B01G387700 chr7A 100.000 46 0 0 3964 4009 100712929 100712974 8.480000e-13 86.1
11 TraesCS6B01G387700 chr3A 100.000 46 0 0 3964 4009 598939805 598939760 8.480000e-13 86.1
12 TraesCS6B01G387700 chr7D 97.872 47 1 0 3963 4009 616753316 616753362 1.100000e-11 82.4
13 TraesCS6B01G387700 chr5A 97.872 47 1 0 3967 4013 656708144 656708098 1.100000e-11 82.4
14 TraesCS6B01G387700 chr5A 97.674 43 1 0 3967 4009 159863221 159863263 1.830000e-09 75.0
15 TraesCS6B01G387700 chr7B 95.918 49 2 0 3961 4009 661450953 661451001 3.940000e-11 80.5
16 TraesCS6B01G387700 chr7B 100.000 43 0 0 3967 4009 704641673 704641631 3.940000e-11 80.5
17 TraesCS6B01G387700 chr3D 93.878 49 3 0 3961 4009 39329384 39329336 1.830000e-09 75.0
18 TraesCS6B01G387700 chr1A 93.617 47 3 0 3963 4009 521633000 521632954 2.370000e-08 71.3


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 TraesCS6B01G387700 chr6B 662509678 662514431 4753 False 8780.00 8780 100.00000 1 4754 1 chr6B.!!$F1 4753
1 TraesCS6B01G387700 chr6D 437802193 437807326 5133 False 1731.25 4087 89.35325 1 4748 4 chr6D.!!$F1 4747
2 TraesCS6B01G387700 chr6A 586096123 586101445 5322 False 1304.60 3029 88.83680 1 4754 5 chr6A.!!$F1 4753

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
415 436 0.029567 GCATGGTCTCGACTCCGTAG 59.970 60.0 0.0 0.00 37.05 3.51 F
1106 1211 0.103876 AACTTGGAGGAGGAGGGGTT 60.104 55.0 0.0 0.00 0.00 4.11 F
1603 1883 0.250234 TGCCTCCACTGCATGTAGAC 59.750 55.0 18.4 0.58 32.85 2.59 F
3522 3985 0.597637 CGCCATCCACCGTATCTGTC 60.598 60.0 0.0 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1398 1676 0.463833 GCCGTCCCGAATTCCTCAAT 60.464 55.0 0.00 0.00 0.00 2.57 R
2688 3137 0.245539 ACCTGCACATGATTGCTTGC 59.754 50.0 9.44 3.59 43.41 4.01 R
3562 4025 0.836606 TCCTCGGCAAAGGCATCATA 59.163 50.0 0.00 0.00 43.71 2.15 R
4383 5128 0.615261 GACGAGGAAGGGGAAGAGGT 60.615 60.0 0.00 0.00 0.00 3.85 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
74 75 1.089481 CGCCGCATCCACTATGTTGT 61.089 55.000 0.00 0.00 37.93 3.32
120 121 4.115199 GTCTGCCGCCATCCCCTT 62.115 66.667 0.00 0.00 0.00 3.95
123 124 3.764160 CTGCCGCCATCCCCTTCTC 62.764 68.421 0.00 0.00 0.00 2.87
124 125 3.483869 GCCGCCATCCCCTTCTCT 61.484 66.667 0.00 0.00 0.00 3.10
125 126 2.825264 CCGCCATCCCCTTCTCTC 59.175 66.667 0.00 0.00 0.00 3.20
126 127 2.812619 CCGCCATCCCCTTCTCTCC 61.813 68.421 0.00 0.00 0.00 3.71
127 128 1.764054 CGCCATCCCCTTCTCTCCT 60.764 63.158 0.00 0.00 0.00 3.69
128 129 1.753368 CGCCATCCCCTTCTCTCCTC 61.753 65.000 0.00 0.00 0.00 3.71
129 130 0.399806 GCCATCCCCTTCTCTCCTCT 60.400 60.000 0.00 0.00 0.00 3.69
130 131 1.974197 GCCATCCCCTTCTCTCCTCTT 60.974 57.143 0.00 0.00 0.00 2.85
131 132 2.046292 CCATCCCCTTCTCTCCTCTTC 58.954 57.143 0.00 0.00 0.00 2.87
132 133 2.046292 CATCCCCTTCTCTCCTCTTCC 58.954 57.143 0.00 0.00 0.00 3.46
133 134 1.398799 TCCCCTTCTCTCCTCTTCCT 58.601 55.000 0.00 0.00 0.00 3.36
134 135 1.289530 TCCCCTTCTCTCCTCTTCCTC 59.710 57.143 0.00 0.00 0.00 3.71
165 178 2.269241 GGGTCCAAAGAGCTCGGG 59.731 66.667 8.37 11.69 40.49 5.14
192 206 1.066071 CCAACAATGATGCATGCCCAA 60.066 47.619 16.68 0.00 0.00 4.12
201 215 2.046023 CATGCCCAAGGACGCTCA 60.046 61.111 0.00 0.00 0.00 4.26
210 224 1.133598 CAAGGACGCTCATGGTACGTA 59.866 52.381 8.24 0.00 40.69 3.57
309 330 0.243907 CGACAGAGCTCGGGAAAGAA 59.756 55.000 18.37 0.00 0.00 2.52
323 344 2.573609 AAAGAAGTCCCGGATCGCGG 62.574 60.000 6.13 13.78 0.00 6.46
415 436 0.029567 GCATGGTCTCGACTCCGTAG 59.970 60.000 0.00 0.00 37.05 3.51
437 474 1.134367 TCCTTCATCATCGTCGTCCAC 59.866 52.381 0.00 0.00 0.00 4.02
683 781 1.006571 CAAGGGACGTACGTGCAGT 60.007 57.895 35.38 22.20 38.24 4.40
684 782 1.006571 AAGGGACGTACGTGCAGTG 60.007 57.895 35.38 1.06 38.24 3.66
685 783 3.110178 GGGACGTACGTGCAGTGC 61.110 66.667 35.38 18.23 38.24 4.40
686 784 2.355363 GGACGTACGTGCAGTGCA 60.355 61.111 31.41 15.37 36.45 4.57
692 790 0.382636 GTACGTGCAGTGCAAACGTC 60.383 55.000 29.81 19.79 39.69 4.34
693 791 0.806492 TACGTGCAGTGCAAACGTCA 60.806 50.000 29.81 17.09 39.69 4.35
694 792 1.061729 CGTGCAGTGCAAACGTCAA 59.938 52.632 21.67 0.00 41.47 3.18
695 793 0.925267 CGTGCAGTGCAAACGTCAAG 60.925 55.000 21.67 0.30 41.47 3.02
696 794 1.063972 TGCAGTGCAAACGTCAAGC 59.936 52.632 17.26 0.00 34.76 4.01
697 795 2.645281 TGCAGTGCAAACGTCAAGCG 62.645 55.000 17.26 0.00 40.50 4.68
815 915 3.790437 ACGAGCCCCATCAGCCTG 61.790 66.667 0.00 0.00 0.00 4.85
930 1035 4.547367 CCGTCGCCATCCCTTCCC 62.547 72.222 0.00 0.00 0.00 3.97
966 1071 2.907236 GGCCTGCTCCTTCCTCTC 59.093 66.667 0.00 0.00 0.00 3.20
967 1072 1.688884 GGCCTGCTCCTTCCTCTCT 60.689 63.158 0.00 0.00 0.00 3.10
968 1073 1.685355 GGCCTGCTCCTTCCTCTCTC 61.685 65.000 0.00 0.00 0.00 3.20
969 1074 0.687427 GCCTGCTCCTTCCTCTCTCT 60.687 60.000 0.00 0.00 0.00 3.10
992 1097 1.695465 GGGTCCAGGGTTTTAGGGG 59.305 63.158 0.00 0.00 0.00 4.79
1033 1138 3.145551 GTAGGCCGCGGAGGAAGA 61.146 66.667 33.48 3.59 45.00 2.87
1106 1211 0.103876 AACTTGGAGGAGGAGGGGTT 60.104 55.000 0.00 0.00 0.00 4.11
1107 1212 0.797579 ACTTGGAGGAGGAGGGGTTA 59.202 55.000 0.00 0.00 0.00 2.85
1131 1236 2.124695 GACGGGAATGAGGCCACC 60.125 66.667 5.01 0.00 0.00 4.61
1188 1299 0.459237 CGCTTCCACTGCAGGTAGAG 60.459 60.000 19.93 11.41 0.00 2.43
1189 1300 0.898320 GCTTCCACTGCAGGTAGAGA 59.102 55.000 19.93 4.00 0.00 3.10
1190 1301 1.484240 GCTTCCACTGCAGGTAGAGAT 59.516 52.381 19.93 0.00 0.00 2.75
1238 1359 6.945072 AGATTTTATCGTTGGCGTAGAATTC 58.055 36.000 0.00 0.00 39.49 2.17
1242 1363 4.600012 ATCGTTGGCGTAGAATTCAAAG 57.400 40.909 8.44 0.00 39.49 2.77
1247 1368 6.982141 TCGTTGGCGTAGAATTCAAAGTATAT 59.018 34.615 8.44 0.00 39.49 0.86
1250 1371 5.924254 TGGCGTAGAATTCAAAGTATATCCG 59.076 40.000 8.44 0.00 0.00 4.18
1267 1388 8.750298 AGTATATCCGTTTCTCTTCTTTTGAGA 58.250 33.333 0.00 0.00 38.62 3.27
1273 1394 6.425114 CCGTTTCTCTTCTTTTGAGAGATTCA 59.575 38.462 4.82 0.00 40.99 2.57
1372 1649 5.388164 GGAGATTTTGTCGTTGACGTAGAAC 60.388 44.000 3.25 0.00 40.80 3.01
1382 1659 7.148869 TGTCGTTGACGTAGAACTCAAATTATG 60.149 37.037 3.25 0.00 40.80 1.90
1386 1663 3.869246 ACGTAGAACTCAAATTATGCCCG 59.131 43.478 0.00 0.00 0.00 6.13
1398 1676 8.740123 TCAAATTATGCCCGTTATTTTCTCTA 57.260 30.769 0.00 0.00 0.00 2.43
1437 1715 1.746615 CATCCACACCCCGCTTCTG 60.747 63.158 0.00 0.00 0.00 3.02
1456 1734 5.125367 TCTGCTTCCACTGTAGGTAGATA 57.875 43.478 6.95 0.00 0.00 1.98
1503 1781 0.454452 GGTGGCGCGAAGATTTTGTC 60.454 55.000 12.10 0.00 0.00 3.18
1564 1844 5.880054 TTTTTGAGGAATTCGAGATGACC 57.120 39.130 0.00 0.00 0.00 4.02
1565 1845 2.871182 TGAGGAATTCGAGATGACCG 57.129 50.000 0.00 0.00 0.00 4.79
1591 1871 1.892819 CGCCTCTTCTTCTGCCTCCA 61.893 60.000 0.00 0.00 0.00 3.86
1597 1877 0.694771 TTCTTCTGCCTCCACTGCAT 59.305 50.000 0.00 0.00 38.22 3.96
1603 1883 0.250234 TGCCTCCACTGCATGTAGAC 59.750 55.000 18.40 0.58 32.85 2.59
1606 1886 1.633561 CTCCACTGCATGTAGACGTG 58.366 55.000 18.40 6.26 36.01 4.49
1607 1887 0.966179 TCCACTGCATGTAGACGTGT 59.034 50.000 18.40 0.00 35.38 4.49
2009 2438 2.682494 TCCCACTGGGTCTACGGC 60.682 66.667 14.25 0.00 44.74 5.68
2060 2489 8.651391 TCTTATTTGTACGTGTCTTTCAAAGA 57.349 30.769 0.00 0.00 32.82 2.52
2087 2516 4.220163 ACTCTACCAAGGAAAACTCTACCG 59.780 45.833 0.00 0.00 0.00 4.02
2109 2538 5.396884 CCGAGGAAATCTCTACCAAGGAAAT 60.397 44.000 0.00 0.00 40.30 2.17
2110 2539 6.183360 CCGAGGAAATCTCTACCAAGGAAATA 60.183 42.308 0.00 0.00 40.30 1.40
2231 2675 2.702592 TGGTAATTGGGAGGTAAGCG 57.297 50.000 0.00 0.00 0.00 4.68
2250 2695 3.432252 AGCGATTTCCTTGTGTTAACTCG 59.568 43.478 7.22 5.54 0.00 4.18
2417 2865 3.130340 GCTTGTCTGGGAAGTTTTGAACA 59.870 43.478 0.00 0.00 0.00 3.18
2465 2913 6.217294 GTCCAGTGGTTAGATATTACTGCTC 58.783 44.000 9.54 0.00 37.89 4.26
2528 2976 5.886960 ACTGATGGTTAGTTCTTGCAATC 57.113 39.130 0.00 0.00 0.00 2.67
2616 3065 2.040544 GTTGTCTCGGCCACCCATG 61.041 63.158 2.24 0.00 0.00 3.66
2632 3081 3.084786 CCCATGTTCTTTCAAGAGACCC 58.915 50.000 0.00 0.00 36.22 4.46
2688 3137 1.270550 GCACCAGATTTCACTTGTGGG 59.729 52.381 0.64 0.00 35.17 4.61
2805 3254 2.741517 TGTCGCTGTGATTTATGGTGTG 59.258 45.455 0.00 0.00 0.00 3.82
2866 3318 4.671377 TGCTGCTAGTTGTTTCTGTTTTG 58.329 39.130 0.00 0.00 0.00 2.44
2994 3448 7.985634 TTTTGAAAAGCTTATTCAGTGTGAC 57.014 32.000 17.54 0.00 38.01 3.67
3027 3481 0.674895 AGCTGAGCCGACAACCAATC 60.675 55.000 0.00 0.00 0.00 2.67
3078 3532 8.951243 GGATCCATAAGCTCTATATTTGGAAAC 58.049 37.037 6.95 0.00 35.57 2.78
3187 3644 2.730382 AGCATCATCAGCCATTGAACA 58.270 42.857 0.00 0.00 39.77 3.18
3329 3792 5.524646 CAGATGTCCAAGCAAAAATTGTTGT 59.475 36.000 10.07 0.00 0.00 3.32
3431 3894 2.434336 TCTTAAGCGATACACATGCCCT 59.566 45.455 0.00 0.00 0.00 5.19
3486 3949 4.246458 GAGTGGACTCGTTTAGCAATCTT 58.754 43.478 0.00 0.00 32.78 2.40
3522 3985 0.597637 CGCCATCCACCGTATCTGTC 60.598 60.000 0.00 0.00 0.00 3.51
3562 4025 1.376037 GCTGCAGGCGAAGTAGGTT 60.376 57.895 17.12 0.00 0.00 3.50
3682 4148 2.093106 TCTCTAGAAAGGAGTCCGTGC 58.907 52.381 2.76 0.00 33.06 5.34
3816 4290 2.260844 TGAGGAACTGTGCCTTCTTG 57.739 50.000 9.19 0.00 41.55 3.02
3850 4324 2.235650 GTCCCCTGTCTGTAACTTACCC 59.764 54.545 0.00 0.00 0.00 3.69
3889 4363 1.006805 TGAAATTTGCGCAACCCCG 60.007 52.632 24.99 0.00 0.00 5.73
3914 4388 7.568861 CGTTTCGCTGTTCTTACTACATTTCTT 60.569 37.037 0.00 0.00 0.00 2.52
3969 4443 2.169769 TCCAACAAGCCGATACTAAGGG 59.830 50.000 0.00 0.00 0.00 3.95
3974 4448 2.134092 GCCGATACTAAGGGCCTGT 58.866 57.895 6.92 3.82 41.01 4.00
3975 4449 0.468648 GCCGATACTAAGGGCCTGTT 59.531 55.000 6.92 0.00 41.01 3.16
3976 4450 1.540580 GCCGATACTAAGGGCCTGTTC 60.541 57.143 6.92 1.84 41.01 3.18
3977 4451 1.269621 CCGATACTAAGGGCCTGTTCG 60.270 57.143 6.92 12.96 0.00 3.95
3978 4452 1.269621 CGATACTAAGGGCCTGTTCGG 60.270 57.143 6.92 0.00 0.00 4.30
3987 4461 3.787001 CCTGTTCGGCCCTCCTCC 61.787 72.222 0.00 0.00 0.00 4.30
3996 4470 3.775654 CCCTCCTCCGCTCCACAC 61.776 72.222 0.00 0.00 0.00 3.82
3998 4472 2.716017 CCTCCTCCGCTCCACACTC 61.716 68.421 0.00 0.00 0.00 3.51
4001 4475 2.487428 CTCCGCTCCACACTCTCG 59.513 66.667 0.00 0.00 0.00 4.04
4003 4477 3.753434 CCGCTCCACACTCTCGCT 61.753 66.667 0.00 0.00 0.00 4.93
4005 4479 2.183046 GCTCCACACTCTCGCTCC 59.817 66.667 0.00 0.00 0.00 4.70
4006 4480 2.487428 CTCCACACTCTCGCTCCG 59.513 66.667 0.00 0.00 0.00 4.63
4039 4783 8.138074 TGTTTATGACACTAGTAGATCAGATGC 58.862 37.037 3.59 2.41 32.00 3.91
4046 4790 1.350351 AGTAGATCAGATGCCATGGCC 59.650 52.381 33.44 19.25 41.09 5.36
4052 4796 0.681887 CAGATGCCATGGCCACTTCA 60.682 55.000 33.44 14.74 41.09 3.02
4169 4914 5.065218 CCATACATCTGCAACAAACCTAGAC 59.935 44.000 0.00 0.00 0.00 2.59
4700 5445 3.814842 CACTAGAACAATGCACAGGTCAA 59.185 43.478 7.88 0.00 0.00 3.18
4701 5446 4.456911 CACTAGAACAATGCACAGGTCAAT 59.543 41.667 7.88 0.00 0.00 2.57
4702 5447 5.048504 CACTAGAACAATGCACAGGTCAATT 60.049 40.000 7.88 0.00 0.00 2.32
4711 5456 7.651704 ACAATGCACAGGTCAATTTAAGTTAAC 59.348 33.333 0.00 0.00 0.00 2.01
4713 5458 5.527951 TGCACAGGTCAATTTAAGTTAACGA 59.472 36.000 0.00 0.00 0.00 3.85
4748 5493 1.772836 ATGCTTGATTTCAGGCCTCC 58.227 50.000 0.00 0.00 46.80 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 2.282816 CCGGGGGCAACAACATCA 60.283 61.111 0.00 0.00 39.74 3.07
107 108 3.468326 GAGAGAAGGGGATGGCGGC 62.468 68.421 0.00 0.00 0.00 6.53
120 121 1.850345 GAGGAGGAGGAAGAGGAGAGA 59.150 57.143 0.00 0.00 0.00 3.10
123 124 1.568597 TCAGAGGAGGAGGAAGAGGAG 59.431 57.143 0.00 0.00 0.00 3.69
124 125 1.568597 CTCAGAGGAGGAGGAAGAGGA 59.431 57.143 0.00 0.00 37.51 3.71
125 126 2.028996 GCTCAGAGGAGGAGGAAGAGG 61.029 61.905 0.00 0.00 41.67 3.69
126 127 1.402787 GCTCAGAGGAGGAGGAAGAG 58.597 60.000 0.00 0.00 41.67 2.85
127 128 0.032615 GGCTCAGAGGAGGAGGAAGA 60.033 60.000 0.00 0.00 41.67 2.87
128 129 1.048160 GGGCTCAGAGGAGGAGGAAG 61.048 65.000 0.00 0.00 41.67 3.46
129 130 1.002274 GGGCTCAGAGGAGGAGGAA 59.998 63.158 0.00 0.00 41.67 3.36
130 131 2.693017 GGGCTCAGAGGAGGAGGA 59.307 66.667 0.00 0.00 41.67 3.71
131 132 2.837291 CGGGCTCAGAGGAGGAGG 60.837 72.222 0.00 0.00 41.67 4.30
132 133 2.837291 CCGGGCTCAGAGGAGGAG 60.837 72.222 0.00 0.00 41.67 3.69
133 134 4.465446 CCCGGGCTCAGAGGAGGA 62.465 72.222 8.08 0.00 41.67 3.71
134 135 4.787280 ACCCGGGCTCAGAGGAGG 62.787 72.222 24.08 0.00 41.67 4.30
165 178 1.434696 CATCATTGTTGGCGAGCCC 59.565 57.895 12.05 0.00 34.56 5.19
192 206 0.737219 GTACGTACCATGAGCGTCCT 59.263 55.000 15.00 0.00 39.64 3.85
201 215 0.458669 CCAAGGAGCGTACGTACCAT 59.541 55.000 25.56 16.30 0.00 3.55
251 265 1.160329 GGTCGCCACCTACATGATGC 61.160 60.000 0.00 0.00 40.00 3.91
304 325 1.153628 CGCGATCCGGGACTTCTTT 60.154 57.895 0.00 0.00 42.31 2.52
385 406 1.729131 GACCATGCGGCAAAACACG 60.729 57.895 6.82 0.00 34.57 4.49
415 436 1.536284 GGACGACGATGATGAAGGACC 60.536 57.143 0.00 0.00 0.00 4.46
416 437 1.134367 TGGACGACGATGATGAAGGAC 59.866 52.381 0.00 0.00 0.00 3.85
417 438 1.134367 GTGGACGACGATGATGAAGGA 59.866 52.381 0.00 0.00 0.00 3.36
418 439 1.560923 GTGGACGACGATGATGAAGG 58.439 55.000 0.00 0.00 0.00 3.46
508 545 2.125106 GTGGACGTGGATGCCTCC 60.125 66.667 0.00 0.22 42.45 4.30
683 781 2.515057 ACCCGCTTGACGTTTGCA 60.515 55.556 0.00 0.00 41.42 4.08
684 782 2.051345 CACCCGCTTGACGTTTGC 60.051 61.111 0.00 0.00 41.42 3.68
685 783 2.637025 CCACCCGCTTGACGTTTG 59.363 61.111 0.00 0.00 41.42 2.93
686 784 3.284449 GCCACCCGCTTGACGTTT 61.284 61.111 0.00 0.00 41.42 3.60
778 878 3.530910 AAGGTTGGTGAGGGACGCG 62.531 63.158 3.53 3.53 0.00 6.01
779 879 1.671379 GAAGGTTGGTGAGGGACGC 60.671 63.158 0.00 0.00 0.00 5.19
791 891 1.299976 GATGGGGCTCGTGAAGGTT 59.700 57.895 0.00 0.00 0.00 3.50
913 1018 4.547367 GGGAAGGGATGGCGACGG 62.547 72.222 0.00 0.00 0.00 4.79
916 1021 2.768344 GGAGGGAAGGGATGGCGA 60.768 66.667 0.00 0.00 0.00 5.54
919 1024 0.769873 CAGATGGAGGGAAGGGATGG 59.230 60.000 0.00 0.00 0.00 3.51
921 1026 2.630232 GATCAGATGGAGGGAAGGGAT 58.370 52.381 0.00 0.00 0.00 3.85
922 1027 1.415126 GGATCAGATGGAGGGAAGGGA 60.415 57.143 0.00 0.00 0.00 4.20
923 1028 1.063183 GGATCAGATGGAGGGAAGGG 58.937 60.000 0.00 0.00 0.00 3.95
924 1029 0.683973 CGGATCAGATGGAGGGAAGG 59.316 60.000 0.00 0.00 0.00 3.46
925 1030 1.709578 TCGGATCAGATGGAGGGAAG 58.290 55.000 0.00 0.00 0.00 3.46
930 1035 0.529833 CGGGATCGGATCAGATGGAG 59.470 60.000 18.99 0.49 0.00 3.86
1017 1122 2.833582 CTCTTCCTCCGCGGCCTA 60.834 66.667 23.51 1.50 0.00 3.93
1087 1192 0.103876 AACCCCTCCTCCTCCAAGTT 60.104 55.000 0.00 0.00 0.00 2.66
1088 1193 0.797579 TAACCCCTCCTCCTCCAAGT 59.202 55.000 0.00 0.00 0.00 3.16
1090 1195 2.680439 AATAACCCCTCCTCCTCCAA 57.320 50.000 0.00 0.00 0.00 3.53
1106 1211 1.616865 CCTCATTCCCGTCGCCTAATA 59.383 52.381 0.00 0.00 0.00 0.98
1107 1212 0.393077 CCTCATTCCCGTCGCCTAAT 59.607 55.000 0.00 0.00 0.00 1.73
1131 1236 2.158959 CGTCCTAACGCGCTTCTGG 61.159 63.158 5.73 2.02 42.82 3.86
1188 1299 9.895138 TTCATAGTAAACTACTAAAACCCCATC 57.105 33.333 0.00 0.00 43.82 3.51
1189 1300 9.901172 CTTCATAGTAAACTACTAAAACCCCAT 57.099 33.333 0.00 0.00 43.82 4.00
1190 1301 9.103582 TCTTCATAGTAAACTACTAAAACCCCA 57.896 33.333 0.00 0.00 43.82 4.96
1238 1359 9.760660 CAAAAGAAGAGAAACGGATATACTTTG 57.239 33.333 0.00 0.00 0.00 2.77
1242 1363 8.928270 TCTCAAAAGAAGAGAAACGGATATAC 57.072 34.615 0.00 0.00 39.07 1.47
1247 1368 5.531122 TCTCTCAAAAGAAGAGAAACGGA 57.469 39.130 0.49 0.00 44.76 4.69
1267 1388 2.815308 CTACGCCGCCCTGAATCT 59.185 61.111 0.00 0.00 0.00 2.40
1341 1475 0.999406 CGACAAAATCTCCGCGTCAT 59.001 50.000 4.92 0.00 0.00 3.06
1349 1483 5.401674 AGTTCTACGTCAACGACAAAATCTC 59.598 40.000 9.88 0.00 43.02 2.75
1372 1649 7.707104 AGAGAAAATAACGGGCATAATTTGAG 58.293 34.615 0.00 0.00 0.00 3.02
1382 1659 5.365619 TCCTCAATAGAGAAAATAACGGGC 58.634 41.667 0.00 0.00 44.98 6.13
1386 1663 8.560374 CCCGAATTCCTCAATAGAGAAAATAAC 58.440 37.037 0.00 0.00 44.98 1.89
1398 1676 0.463833 GCCGTCCCGAATTCCTCAAT 60.464 55.000 0.00 0.00 0.00 2.57
1437 1715 3.574826 CCCTATCTACCTACAGTGGAAGC 59.425 52.174 0.00 0.00 39.70 3.86
1456 1734 2.152680 TACTAAAACCCCCAACCCCT 57.847 50.000 0.00 0.00 0.00 4.79
1556 1836 2.105128 CGGTGGCTCGGTCATCTC 59.895 66.667 0.00 0.00 0.00 2.75
1557 1837 4.148825 GCGGTGGCTCGGTCATCT 62.149 66.667 3.41 0.00 35.83 2.90
1591 1871 0.679505 ACCACACGTCTACATGCAGT 59.320 50.000 0.00 0.00 0.00 4.40
1597 1877 0.677288 CCCTGAACCACACGTCTACA 59.323 55.000 0.00 0.00 0.00 2.74
1603 1883 2.567985 ACTAAAACCCTGAACCACACG 58.432 47.619 0.00 0.00 0.00 4.49
1632 1912 8.116753 CCAACGACAAAATCTATCTGTCATTAC 58.883 37.037 0.00 0.00 39.56 1.89
1636 1916 4.391830 GCCAACGACAAAATCTATCTGTCA 59.608 41.667 0.00 0.00 39.56 3.58
1643 1923 4.177165 TCTACGCCAACGACAAAATCTA 57.823 40.909 0.00 0.00 43.93 1.98
2060 2489 7.501559 GGTAGAGTTTTCCTTGGTAGAGTTTTT 59.498 37.037 0.00 0.00 0.00 1.94
2087 2516 8.655901 AGATATTTCCTTGGTAGAGATTTCCTC 58.344 37.037 0.00 0.00 42.28 3.71
2109 2538 1.760613 CAGAACGGCCCTTGGTAGATA 59.239 52.381 0.00 0.00 0.00 1.98
2110 2539 0.541863 CAGAACGGCCCTTGGTAGAT 59.458 55.000 0.00 0.00 0.00 1.98
2231 2675 6.980051 ATACCGAGTTAACACAAGGAAATC 57.020 37.500 8.61 0.00 0.00 2.17
2417 2865 9.138596 GACCTCTATCTTACTCTTAAGACCATT 57.861 37.037 0.00 0.00 45.26 3.16
2536 2985 9.128107 GATTGATCGATACACAAACAAACAATT 57.872 29.630 0.00 0.00 0.00 2.32
2553 3002 6.511605 CGTTTGAGGCAATAATGATTGATCGA 60.512 38.462 7.00 1.24 44.59 3.59
2555 3004 6.728200 TCGTTTGAGGCAATAATGATTGATC 58.272 36.000 7.00 4.50 44.59 2.92
2616 3065 4.257731 GAGGATGGGTCTCTTGAAAGAAC 58.742 47.826 0.00 0.00 34.03 3.01
2632 3081 6.573664 TGTATGTTTTCTTGGTTGAGGATG 57.426 37.500 0.00 0.00 0.00 3.51
2688 3137 0.245539 ACCTGCACATGATTGCTTGC 59.754 50.000 9.44 3.59 43.41 4.01
2805 3254 4.236935 CAATACAAAGGCACAACACATCC 58.763 43.478 0.00 0.00 0.00 3.51
2908 3360 5.311265 CCTCCTGCATTCAGAGCATTTATA 58.689 41.667 0.00 0.00 42.95 0.98
2909 3361 4.142790 CCTCCTGCATTCAGAGCATTTAT 58.857 43.478 0.00 0.00 42.95 1.40
2994 3448 2.115595 CTCAGCTCATTTAGTCGCTCG 58.884 52.381 0.00 0.00 0.00 5.03
3055 3509 7.147213 TGGGTTTCCAAATATAGAGCTTATGGA 60.147 37.037 0.00 0.00 40.73 3.41
3078 3532 1.079888 GCCGGCACTTTCATTTGGG 60.080 57.895 24.80 0.00 0.00 4.12
3136 3593 1.882623 CCTTTGGACCACTGAAGAAGC 59.117 52.381 6.04 0.00 0.00 3.86
3187 3644 6.783482 GTCTGAAGAAGGGGATACTTACCTAT 59.217 42.308 0.00 0.00 33.37 2.57
3329 3792 6.790232 AATTGAGGTTCCTTTGTTCTTGAA 57.210 33.333 0.00 0.00 0.00 2.69
3475 3938 6.677920 GCGCCTTTCTCAATAAGATTGCTAAA 60.678 38.462 0.00 0.00 32.82 1.85
3484 3947 1.267732 CGCAGCGCCTTTCTCAATAAG 60.268 52.381 2.29 0.00 0.00 1.73
3486 3949 2.383170 CGCAGCGCCTTTCTCAATA 58.617 52.632 2.29 0.00 0.00 1.90
3522 3985 2.401766 GGTGTCATTGCGCTCAGGG 61.402 63.158 9.73 0.00 0.00 4.45
3562 4025 0.836606 TCCTCGGCAAAGGCATCATA 59.163 50.000 0.00 0.00 43.71 2.15
3660 4123 3.884091 GCACGGACTCCTTTCTAGAGATA 59.116 47.826 0.00 0.00 35.27 1.98
3682 4148 0.396811 AGGTTCTCAAACAGACCCGG 59.603 55.000 0.00 0.00 38.79 5.73
3703 4169 1.131693 CATAGACGGTATGCGGCGATA 59.868 52.381 12.98 2.75 0.00 2.92
3850 4324 2.549754 AGTTGTTGCCAAATGAGAGTCG 59.450 45.455 0.00 0.00 30.94 4.18
3889 4363 7.118422 AGAAATGTAGTAAGAACAGCGAAAC 57.882 36.000 0.00 0.00 0.00 2.78
3914 4388 3.391296 AGGCCAACAGAGAAACTACTGAA 59.609 43.478 5.01 0.00 37.54 3.02
3921 4395 1.876156 CTCACAGGCCAACAGAGAAAC 59.124 52.381 5.01 0.00 0.00 2.78
3970 4444 3.787001 GGAGGAGGGCCGAACAGG 61.787 72.222 0.00 0.00 44.97 4.00
3979 4453 3.775654 GTGTGGAGCGGAGGAGGG 61.776 72.222 0.00 0.00 0.00 4.30
3980 4454 2.681778 AGTGTGGAGCGGAGGAGG 60.682 66.667 0.00 0.00 0.00 4.30
3981 4455 1.662438 GAGAGTGTGGAGCGGAGGAG 61.662 65.000 0.00 0.00 0.00 3.69
3982 4456 1.679305 GAGAGTGTGGAGCGGAGGA 60.679 63.158 0.00 0.00 0.00 3.71
3983 4457 2.888863 GAGAGTGTGGAGCGGAGG 59.111 66.667 0.00 0.00 0.00 4.30
3984 4458 2.487428 CGAGAGTGTGGAGCGGAG 59.513 66.667 0.00 0.00 0.00 4.63
3985 4459 3.749064 GCGAGAGTGTGGAGCGGA 61.749 66.667 0.00 0.00 0.00 5.54
3986 4460 3.691744 GAGCGAGAGTGTGGAGCGG 62.692 68.421 0.00 0.00 0.00 5.52
3987 4461 2.202544 GAGCGAGAGTGTGGAGCG 60.203 66.667 0.00 0.00 0.00 5.03
3988 4462 2.183046 GGAGCGAGAGTGTGGAGC 59.817 66.667 0.00 0.00 0.00 4.70
3989 4463 2.487428 CGGAGCGAGAGTGTGGAG 59.513 66.667 0.00 0.00 0.00 3.86
3991 4465 4.135153 CCCGGAGCGAGAGTGTGG 62.135 72.222 0.73 0.00 0.00 4.17
3992 4466 4.803426 GCCCGGAGCGAGAGTGTG 62.803 72.222 0.73 0.00 0.00 3.82
4001 4475 1.748493 TCATAAACAAATGCCCGGAGC 59.252 47.619 0.73 5.29 44.14 4.70
4003 4477 2.490115 GTGTCATAAACAAATGCCCGGA 59.510 45.455 0.73 0.00 40.31 5.14
4005 4479 3.848272 AGTGTCATAAACAAATGCCCG 57.152 42.857 0.00 0.00 40.31 6.13
4006 4480 5.897377 ACTAGTGTCATAAACAAATGCCC 57.103 39.130 0.00 0.00 40.31 5.36
4039 4783 5.341872 TTCATATTTTGAAGTGGCCATGG 57.658 39.130 9.72 7.63 39.44 3.66
4066 4810 0.033781 TTTGCCAGCCACTGCAATTC 59.966 50.000 0.00 0.00 41.13 2.17
4069 4813 1.336131 TATTTTGCCAGCCACTGCAA 58.664 45.000 0.00 0.00 41.13 4.08
4169 4914 5.116983 GCATGTTTTATTGTTCCTGTTCGTG 59.883 40.000 0.00 0.00 0.00 4.35
4383 5128 0.615261 GACGAGGAAGGGGAAGAGGT 60.615 60.000 0.00 0.00 0.00 3.85
4621 5366 5.638657 TGCCAAATTTGCATCATAAGTTGAC 59.361 36.000 12.92 0.56 37.11 3.18
4627 5372 8.449397 GTTATTGTTGCCAAATTTGCATCATAA 58.551 29.630 12.92 12.23 38.01 1.90
4711 5456 9.988350 ATCAAGCATTAAACACTAACTTTATCG 57.012 29.630 0.00 0.00 0.00 2.92
4728 5473 2.105766 GGAGGCCTGAAATCAAGCATT 58.894 47.619 12.00 0.00 35.10 3.56


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

AutoCloner maintained by Alex Coulton.