Multiple sequence alignment - TraesCS6B01G005600

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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 TraesCS6B01G005600 chr6B 100.000 2295 0 0 1 2295 4162966 4160672 0.000000e+00 4239.0
1 TraesCS6B01G005600 chr6B 89.084 1649 127 16 3 1627 3871838 3873457 0.000000e+00 1999.0
2 TraesCS6B01G005600 chr6B 100.000 538 0 0 2705 3242 4160262 4159725 0.000000e+00 994.0
3 TraesCS6B01G005600 chr6B 83.585 1060 90 36 1282 2293 4154526 4153503 0.000000e+00 917.0
4 TraesCS6B01G005600 chr6B 84.668 587 51 19 986 1553 4172099 4171533 1.700000e-152 549.0
5 TraesCS6B01G005600 chr6B 85.000 360 40 6 2870 3229 4354488 4354143 1.430000e-93 353.0
6 TraesCS6B01G005600 chr6B 90.351 228 20 1 2068 2293 4170319 4170092 6.800000e-77 298.0
7 TraesCS6B01G005600 chr6B 82.403 233 21 4 1830 2062 3873858 3874070 5.520000e-43 185.0
8 TraesCS6B01G005600 chr6B 93.671 79 4 1 2705 2782 4170077 4169999 2.040000e-22 117.0
9 TraesCS6B01G005600 chr6A 86.450 738 85 10 1 727 687633 686900 0.000000e+00 795.0
10 TraesCS6B01G005600 chr6A 83.189 809 76 33 982 1749 684960 684171 0.000000e+00 686.0
11 TraesCS6B01G005600 chr6A 87.796 549 47 8 2707 3242 731169 730628 2.750000e-175 625.0
12 TraesCS6B01G005600 chr6A 85.329 593 67 8 1597 2183 731846 731268 2.150000e-166 595.0
13 TraesCS6B01G005600 chr6A 90.385 208 20 0 1346 1553 662672 662465 1.150000e-69 274.0
14 TraesCS6B01G005600 chr6A 85.496 131 17 2 148 277 733693 733564 5.640000e-28 135.0
15 TraesCS6B01G005600 chr6A 97.500 40 1 0 753 792 685341 685302 5.800000e-08 69.4
16 TraesCS6B01G005600 chr6D 85.050 602 51 21 971 1553 2169693 2170274 7.800000e-161 577.0
17 TraesCS6B01G005600 chr6D 83.594 512 53 16 1559 2070 2170915 2171395 4.930000e-123 451.0
18 TraesCS6B01G005600 chr6D 80.652 460 49 18 2707 3127 2190860 2191318 1.450000e-83 320.0
19 TraesCS6B01G005600 chr6D 77.925 530 82 16 1251 1766 2240367 2240875 6.800000e-77 298.0
20 TraesCS6B01G005600 chr6D 91.163 215 17 1 2057 2269 2188341 2188555 1.140000e-74 291.0
21 TraesCS6B01G005600 chr6D 77.333 525 92 18 1251 1766 2279322 2278816 5.290000e-73 285.0
22 TraesCS6B01G005600 chr6D 86.192 239 25 3 1828 2062 2188077 2188311 5.370000e-63 252.0
23 TraesCS6B01G005600 chr6D 94.048 84 4 1 2705 2787 2171666 2171749 3.400000e-25 126.0
24 TraesCS6B01G005600 chr6D 83.077 130 21 1 149 277 4204686 4204815 2.040000e-22 117.0
25 TraesCS6B01G005600 chr6D 82.308 130 22 1 149 277 2168430 2168559 9.510000e-21 111.0
26 TraesCS6B01G005600 chrUn 84.722 360 41 6 2870 3229 346747065 346746720 6.660000e-92 348.0
27 TraesCS6B01G005600 chrUn 85.028 354 39 6 2870 3223 350779135 350779474 6.660000e-92 348.0
28 TraesCS6B01G005600 chrUn 84.536 291 32 5 2933 3223 199056152 199056429 3.190000e-70 276.0
29 TraesCS6B01G005600 chr3B 77.401 531 95 15 1244 1766 772901217 772900704 3.160000e-75 292.0
30 TraesCS6B01G005600 chr1D 78.241 216 32 8 434 635 30226629 30226415 1.220000e-24 124.0
31 TraesCS6B01G005600 chr5A 87.342 79 7 3 434 511 600425469 600425393 1.600000e-13 87.9


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 TraesCS6B01G005600 chr6B 4159725 4162966 3241 True 2616.500000 4239 100.000000 1 3242 2 chr6B.!!$R3 3241
1 TraesCS6B01G005600 chr6B 3871838 3874070 2232 False 1092.000000 1999 85.743500 3 2062 2 chr6B.!!$F1 2059
2 TraesCS6B01G005600 chr6B 4153503 4154526 1023 True 917.000000 917 83.585000 1282 2293 1 chr6B.!!$R1 1011
3 TraesCS6B01G005600 chr6B 4169999 4172099 2100 True 321.333333 549 89.563333 986 2782 3 chr6B.!!$R4 1796
4 TraesCS6B01G005600 chr6A 684171 687633 3462 True 516.800000 795 89.046333 1 1749 3 chr6A.!!$R2 1748
5 TraesCS6B01G005600 chr6A 730628 733693 3065 True 451.666667 625 86.207000 148 3242 3 chr6A.!!$R3 3094
6 TraesCS6B01G005600 chr6D 2168430 2171749 3319 False 316.250000 577 86.250000 149 2787 4 chr6D.!!$F3 2638
7 TraesCS6B01G005600 chr6D 2240367 2240875 508 False 298.000000 298 77.925000 1251 1766 1 chr6D.!!$F1 515
8 TraesCS6B01G005600 chr6D 2188077 2191318 3241 False 287.666667 320 86.002333 1828 3127 3 chr6D.!!$F4 1299
9 TraesCS6B01G005600 chr6D 2278816 2279322 506 True 285.000000 285 77.333000 1251 1766 1 chr6D.!!$R1 515
10 TraesCS6B01G005600 chr3B 772900704 772901217 513 True 292.000000 292 77.401000 1244 1766 1 chr3B.!!$R1 522

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
417 429 0.179936 GTGCCTCTCATCCTCCCTTG 59.820 60.0 0.0 0.0 0.00 3.61 F
1021 3383 0.172803 GCCGATGTCCGTAGAACACT 59.827 55.0 0.0 0.0 36.31 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1278 3661 0.034960 GGAAGGAGGAGAAGTTGGCC 60.035 60.0 0.00 0.0 0.00 5.36 R
2856 8699 0.107703 TGCAGCTAATAGGCGCTTGT 60.108 50.0 7.64 0.0 33.45 3.16 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
56 58 4.990526 AGCAGATTTATAACATGAGGGGG 58.009 43.478 0.00 0.00 0.00 5.40
111 113 8.633561 GCATAAAGTGGCTAGGATTCTAATTTT 58.366 33.333 0.00 0.00 0.00 1.82
117 119 5.302568 TGGCTAGGATTCTAATTTTGGCATG 59.697 40.000 0.00 0.00 0.00 4.06
134 136 3.065655 GCATGCATTTGCCACAAGTTAA 58.934 40.909 14.21 0.00 41.18 2.01
135 137 3.123959 GCATGCATTTGCCACAAGTTAAG 59.876 43.478 14.21 0.00 41.18 1.85
141 143 7.212976 TGCATTTGCCACAAGTTAAGAATTAA 58.787 30.769 0.00 0.00 38.10 1.40
152 154 9.476202 ACAAGTTAAGAATTAAGTGGCAAAATC 57.524 29.630 0.00 0.00 43.05 2.17
163 165 9.643693 ATTAAGTGGCAAAATCTTGATTAACTG 57.356 29.630 0.00 0.00 34.14 3.16
310 319 4.380531 CAAGTCTTGCTTCAAGTACTCCA 58.619 43.478 0.00 0.00 41.66 3.86
321 330 5.102953 TCAAGTACTCCATCCATTCCAAG 57.897 43.478 0.00 0.00 0.00 3.61
329 340 8.966868 GTACTCCATCCATTCCAAGAAAAATTA 58.033 33.333 0.00 0.00 0.00 1.40
332 343 9.154847 CTCCATCCATTCCAAGAAAAATTAAAC 57.845 33.333 0.00 0.00 0.00 2.01
355 366 7.404671 ACTTTTTCCATTGTCAAACTACACT 57.595 32.000 0.00 0.00 0.00 3.55
362 373 9.616156 TTCCATTGTCAAACTACACTAACTTTA 57.384 29.630 0.00 0.00 0.00 1.85
413 425 1.494960 AGAAGTGCCTCTCATCCTCC 58.505 55.000 0.00 0.00 0.00 4.30
417 429 0.179936 GTGCCTCTCATCCTCCCTTG 59.820 60.000 0.00 0.00 0.00 3.61
420 432 1.871418 CCTCTCATCCTCCCTTGTCA 58.129 55.000 0.00 0.00 0.00 3.58
426 438 3.114606 TCATCCTCCCTTGTCATAGCAA 58.885 45.455 0.00 0.00 0.00 3.91
458 470 7.630242 TTTTGCGAAAAGGATTCAGATCTAT 57.370 32.000 0.00 0.00 32.66 1.98
514 533 7.647715 CCCCAACATAATAAAAATCACATCGAC 59.352 37.037 0.00 0.00 0.00 4.20
515 534 7.375808 CCCAACATAATAAAAATCACATCGACG 59.624 37.037 0.00 0.00 0.00 5.12
538 557 3.384789 TCCCTAGACCATCGAACAATCAG 59.615 47.826 0.00 0.00 0.00 2.90
602 622 2.105128 GGCCTGACCTCGATGACG 59.895 66.667 0.00 0.00 41.26 4.35
623 643 1.289066 CGGGAAGTCTTCGTGCTCA 59.711 57.895 6.50 0.00 0.00 4.26
624 644 0.319555 CGGGAAGTCTTCGTGCTCAA 60.320 55.000 6.50 0.00 0.00 3.02
628 648 0.394565 AAGTCTTCGTGCTCAAGCCT 59.605 50.000 0.00 0.00 41.18 4.58
675 695 7.048629 TCATTCCTTCTGCTACTCTAGAATG 57.951 40.000 0.00 0.00 40.27 2.67
694 714 5.468072 AGAATGTGAATCATGTCGATAAGGC 59.532 40.000 0.00 0.00 36.81 4.35
695 715 3.466836 TGTGAATCATGTCGATAAGGCC 58.533 45.455 0.00 0.00 32.51 5.19
700 720 1.609072 TCATGTCGATAAGGCCGAGAG 59.391 52.381 0.00 0.00 36.66 3.20
704 724 1.948145 GTCGATAAGGCCGAGAGAGAA 59.052 52.381 0.00 0.00 36.66 2.87
709 729 2.753055 AAGGCCGAGAGAGAAAGAAC 57.247 50.000 0.00 0.00 0.00 3.01
732 767 2.584064 CCGCACACTGGCATCCTA 59.416 61.111 0.00 0.00 0.00 2.94
734 769 2.176273 CGCACACTGGCATCCTAGC 61.176 63.158 0.00 0.00 0.00 3.42
736 771 0.393537 GCACACTGGCATCCTAGCTT 60.394 55.000 0.00 0.00 34.17 3.74
737 772 1.134401 GCACACTGGCATCCTAGCTTA 60.134 52.381 0.00 0.00 34.17 3.09
738 773 2.486191 GCACACTGGCATCCTAGCTTAT 60.486 50.000 0.00 0.00 34.17 1.73
739 774 3.397482 CACACTGGCATCCTAGCTTATC 58.603 50.000 0.00 0.00 34.17 1.75
740 775 2.036475 ACACTGGCATCCTAGCTTATCG 59.964 50.000 0.00 0.00 34.17 2.92
741 776 1.001406 ACTGGCATCCTAGCTTATCGC 59.999 52.381 0.00 0.00 39.57 4.58
792 2632 3.440173 AGAAAATGGCAAGATGTACGTGG 59.560 43.478 0.00 0.00 0.00 4.94
793 2633 2.779755 AATGGCAAGATGTACGTGGA 57.220 45.000 0.00 0.00 0.00 4.02
794 2634 2.024176 ATGGCAAGATGTACGTGGAC 57.976 50.000 0.00 0.00 0.00 4.02
795 2635 0.682292 TGGCAAGATGTACGTGGACA 59.318 50.000 0.00 0.00 0.00 4.02
833 2833 6.208402 TGAGTTTGCCAAAGTGCTCAATATTA 59.792 34.615 1.42 0.00 31.14 0.98
972 2973 4.261072 GCTACTCATTGCATTCATCACCAG 60.261 45.833 0.00 0.00 0.00 4.00
1019 3381 0.821517 ATGCCGATGTCCGTAGAACA 59.178 50.000 0.00 0.00 36.31 3.18
1021 3383 0.172803 GCCGATGTCCGTAGAACACT 59.827 55.000 0.00 0.00 36.31 3.55
1023 3385 2.793933 GCCGATGTCCGTAGAACACTAC 60.794 54.545 0.00 0.00 36.31 2.73
1155 3532 2.128507 GCCCCGATCTCTCGTCCTT 61.129 63.158 0.00 0.00 43.49 3.36
1455 3838 2.526873 ACCCAGGACCGTCAGCTT 60.527 61.111 0.00 0.00 0.00 3.74
1525 3908 3.391382 GCGTGCCCAGGGACTACT 61.391 66.667 10.89 0.00 36.02 2.57
1539 3922 1.864082 GACTACTCCTACTACGGCGAC 59.136 57.143 16.62 0.00 0.00 5.19
1557 4782 3.834610 CGACAGGACCAAGTAAGTAGTG 58.165 50.000 0.00 0.00 0.00 2.74
1560 4791 5.336531 CGACAGGACCAAGTAAGTAGTGATT 60.337 44.000 0.00 0.00 0.00 2.57
1592 4839 4.074526 TGTCCGGCTGCTGCTCTC 62.075 66.667 15.64 4.89 39.59 3.20
1622 4906 2.367030 TGCGATTTTTCCATTGCTGG 57.633 45.000 0.00 0.00 44.64 4.85
1639 4923 4.195334 GAGGGACGCCATGGCCAT 62.195 66.667 30.79 19.51 37.98 4.40
1640 4924 4.511246 AGGGACGCCATGGCCATG 62.511 66.667 34.82 34.82 37.98 3.66
1673 4957 3.644719 CAGAGGCTGGATCCTGCT 58.355 61.111 34.20 23.46 40.14 4.24
1696 4980 1.014044 CAGAACGTCACCACCATCGG 61.014 60.000 0.00 0.00 0.00 4.18
1749 5036 4.069232 CCGTGCTCGCCTTCCTCA 62.069 66.667 1.89 0.00 35.54 3.86
1797 5084 2.092103 AGCAAAGTCTACCAACCAACCA 60.092 45.455 0.00 0.00 0.00 3.67
1807 5094 0.860533 CAACCAACCAAATTGCTGCG 59.139 50.000 0.00 0.00 36.93 5.18
1840 5359 5.302568 ACACATGTGGCCCATAATTGATTAG 59.697 40.000 28.64 0.00 34.19 1.73
1948 5471 2.613223 GGCTGTCAACTTCTACCAGACC 60.613 54.545 0.00 0.00 0.00 3.85
1966 5489 3.264193 AGACCACCAATCTTGATGTAGCA 59.736 43.478 0.00 0.00 0.00 3.49
2034 5560 2.147150 GCTCAACAAACAGGAGGAGAC 58.853 52.381 0.00 0.00 0.00 3.36
2038 5564 2.528041 ACAAACAGGAGGAGACGTTC 57.472 50.000 0.00 0.00 0.00 3.95
2040 5566 2.368875 ACAAACAGGAGGAGACGTTCAT 59.631 45.455 0.00 0.00 0.00 2.57
2054 5580 6.438259 AGACGTTCATCCTATATGGTATCG 57.562 41.667 0.00 0.00 37.07 2.92
2178 5745 2.159184 TGCAATTGCCGAGTTTGTTTCA 60.159 40.909 26.94 0.87 41.18 2.69
2193 5760 2.223923 TGTTTCAGCCAACAAAATCCCG 60.224 45.455 0.00 0.00 33.60 5.14
2216 5783 2.501316 TGATCACATACCACCCTCACAG 59.499 50.000 0.00 0.00 0.00 3.66
2261 5828 7.094420 TGTTTGATAATCCGATCAAGAAGCAAA 60.094 33.333 0.00 0.00 44.51 3.68
2263 5830 5.296780 TGATAATCCGATCAAGAAGCAAACC 59.703 40.000 0.00 0.00 32.84 3.27
2265 5837 2.426522 TCCGATCAAGAAGCAAACCAG 58.573 47.619 0.00 0.00 0.00 4.00
2271 5843 1.000938 CAAGAAGCAAACCAGTCCTGC 60.001 52.381 0.00 0.00 36.29 4.85
2742 6316 8.292444 AGAATTGATTGAACGGAATGGAAATA 57.708 30.769 0.00 0.00 0.00 1.40
2750 6324 6.442952 TGAACGGAATGGAAATACTTGTTTG 58.557 36.000 0.00 0.00 0.00 2.93
2807 8638 1.268539 CCCAACACGCTGAACAGTTTC 60.269 52.381 3.77 0.00 0.00 2.78
2813 8644 3.311596 ACACGCTGAACAGTTTCCTTAAC 59.688 43.478 3.77 0.00 36.99 2.01
2814 8645 3.311322 CACGCTGAACAGTTTCCTTAACA 59.689 43.478 3.77 0.00 39.30 2.41
2816 8647 4.396790 ACGCTGAACAGTTTCCTTAACAAA 59.603 37.500 3.77 0.00 39.30 2.83
2827 8661 8.928733 CAGTTTCCTTAACAAATGAATGGAATG 58.071 33.333 0.00 0.00 39.30 2.67
2841 8675 1.901159 TGGAATGGAATGCTTGTTGGG 59.099 47.619 0.00 0.00 0.00 4.12
2843 8677 2.094026 GGAATGGAATGCTTGTTGGGAC 60.094 50.000 0.00 0.00 0.00 4.46
2844 8678 2.610438 ATGGAATGCTTGTTGGGACT 57.390 45.000 0.00 0.00 0.00 3.85
2851 8694 1.427368 TGCTTGTTGGGACTAATGGGT 59.573 47.619 0.00 0.00 0.00 4.51
2855 8698 0.039035 GTTGGGACTAATGGGTGGCA 59.961 55.000 0.00 0.00 0.00 4.92
2856 8699 0.780637 TTGGGACTAATGGGTGGCAA 59.219 50.000 0.00 0.00 0.00 4.52
2903 8772 0.799393 GCCTCTGGTTTTCTTCTCGC 59.201 55.000 0.00 0.00 0.00 5.03
2972 8841 6.094603 ACCAATGACAAGCTCAATCATTAGTC 59.905 38.462 15.74 0.00 40.30 2.59
3058 8927 8.093927 TGATTTTCATGAGTAAAAATTGGGGAC 58.906 33.333 4.92 0.00 35.72 4.46
3074 8943 8.837099 AATTGGGGACATTATGAGTTTATGAA 57.163 30.769 0.00 0.00 42.32 2.57
3095 8964 3.334691 ACATGGGTCGTATTGTTGAGTG 58.665 45.455 0.00 0.00 0.00 3.51
3131 9000 8.506437 TGAGTACTTCTATGCTTCAAACATTTG 58.494 33.333 0.00 0.00 39.48 2.32
3133 9002 8.507249 AGTACTTCTATGCTTCAAACATTTGTC 58.493 33.333 4.36 0.00 39.18 3.18
3184 9053 3.620488 GATAGGGCACAAGTTCATTGGA 58.380 45.455 0.00 0.00 43.68 3.53
3201 9070 0.103208 GGATCAGCGTAGGTCCACAG 59.897 60.000 3.98 0.00 33.74 3.66
3232 9101 1.361668 GATGTCGCACGCTGACCAAT 61.362 55.000 10.12 1.19 35.46 3.16
3233 9102 1.638388 ATGTCGCACGCTGACCAATG 61.638 55.000 10.12 0.00 35.46 2.82
3238 9107 2.434884 ACGCTGACCAATGCTCCG 60.435 61.111 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 34 5.456619 CCCCCTCATGTTATAAATCTGCTCA 60.457 44.000 0.00 0.00 0.00 4.26
34 36 4.990526 CCCCCTCATGTTATAAATCTGCT 58.009 43.478 0.00 0.00 0.00 4.24
58 60 1.618343 CTTCCATTTTGTGACACCCCC 59.382 52.381 2.45 0.00 0.00 5.40
59 61 2.316108 ACTTCCATTTTGTGACACCCC 58.684 47.619 2.45 0.00 0.00 4.95
60 62 4.119136 CAAACTTCCATTTTGTGACACCC 58.881 43.478 2.45 0.00 0.00 4.61
61 63 5.004922 TCAAACTTCCATTTTGTGACACC 57.995 39.130 2.45 0.00 35.75 4.16
62 64 5.043248 CCTCAAACTTCCATTTTGTGACAC 58.957 41.667 0.00 0.00 35.75 3.67
63 65 4.441356 GCCTCAAACTTCCATTTTGTGACA 60.441 41.667 0.00 0.00 35.75 3.58
64 66 4.051237 GCCTCAAACTTCCATTTTGTGAC 58.949 43.478 0.00 0.00 35.75 3.67
75 77 3.507622 AGCCACTTTATGCCTCAAACTTC 59.492 43.478 0.00 0.00 0.00 3.01
86 88 9.956720 CAAAATTAGAATCCTAGCCACTTTATG 57.043 33.333 0.00 0.00 0.00 1.90
97 99 6.982160 ATGCATGCCAAAATTAGAATCCTA 57.018 33.333 16.68 0.00 0.00 2.94
117 119 7.384932 ACTTAATTCTTAACTTGTGGCAAATGC 59.615 33.333 0.00 0.00 41.14 3.56
141 143 6.655078 ACAGTTAATCAAGATTTTGCCACT 57.345 33.333 0.02 0.00 34.21 4.00
204 207 5.631119 AGATAAGCCCAAAGTAGTTTGTGT 58.369 37.500 19.25 2.08 41.44 3.72
248 257 9.425577 GACCAAATACTGCCTTATCTATAGAAC 57.574 37.037 6.52 0.00 0.00 3.01
299 308 4.782691 TCTTGGAATGGATGGAGTACTTGA 59.217 41.667 0.00 0.00 0.00 3.02
329 340 8.311109 AGTGTAGTTTGACAATGGAAAAAGTTT 58.689 29.630 0.00 0.00 0.00 2.66
332 343 9.233232 GTTAGTGTAGTTTGACAATGGAAAAAG 57.767 33.333 0.00 0.00 0.00 2.27
338 349 9.659830 GTTAAAGTTAGTGTAGTTTGACAATGG 57.340 33.333 0.00 0.00 31.12 3.16
394 405 1.494960 GGAGGATGAGAGGCACTTCT 58.505 55.000 0.00 0.00 41.55 2.85
399 410 0.252881 ACAAGGGAGGATGAGAGGCA 60.253 55.000 0.00 0.00 0.00 4.75
403 414 2.968574 GCTATGACAAGGGAGGATGAGA 59.031 50.000 0.00 0.00 0.00 3.27
413 425 2.486951 GCAGCATTGCTATGACAAGG 57.513 50.000 11.55 0.00 46.95 3.61
426 438 2.137523 CCTTTTCGCAAAAAGCAGCAT 58.862 42.857 4.25 0.00 46.63 3.79
479 491 9.605951 ATTTTTATTATGTTGGGGATGCTCTAT 57.394 29.630 0.00 0.00 0.00 1.98
514 533 1.100510 TGTTCGATGGTCTAGGGACG 58.899 55.000 0.00 0.00 42.97 4.79
515 534 3.132289 TGATTGTTCGATGGTCTAGGGAC 59.868 47.826 0.00 0.00 41.43 4.46
538 557 1.505353 CTCGTCCTGGTCGTGGTAC 59.495 63.158 12.76 0.00 0.00 3.34
602 622 2.434359 CACGAAGACTTCCCGGGC 60.434 66.667 18.49 0.36 0.00 6.13
628 648 2.567615 GGAAGGTCACAAGAGCCTTAGA 59.432 50.000 0.00 0.00 42.13 2.10
642 662 3.013219 GCAGAAGGAATGAAGGAAGGTC 58.987 50.000 0.00 0.00 0.00 3.85
675 695 2.476619 CGGCCTTATCGACATGATTCAC 59.523 50.000 0.00 0.00 38.57 3.18
694 714 2.898705 CCATGGTTCTTTCTCTCTCGG 58.101 52.381 2.57 0.00 0.00 4.63
695 715 2.275318 GCCATGGTTCTTTCTCTCTCG 58.725 52.381 14.67 0.00 0.00 4.04
700 720 0.960364 TGCGGCCATGGTTCTTTCTC 60.960 55.000 14.67 0.00 0.00 2.87
704 724 2.115052 TGTGCGGCCATGGTTCTT 59.885 55.556 14.67 0.00 0.00 2.52
734 769 5.696724 CCTTAGGAACCATGTTAGCGATAAG 59.303 44.000 0.00 0.00 0.00 1.73
736 771 4.897076 TCCTTAGGAACCATGTTAGCGATA 59.103 41.667 0.00 0.00 0.00 2.92
737 772 3.709653 TCCTTAGGAACCATGTTAGCGAT 59.290 43.478 0.00 0.00 0.00 4.58
738 773 3.101437 TCCTTAGGAACCATGTTAGCGA 58.899 45.455 0.00 0.00 0.00 4.93
739 774 3.536956 TCCTTAGGAACCATGTTAGCG 57.463 47.619 0.00 0.00 0.00 4.26
750 785 1.070445 TGAAACGCGGTTCCTTAGGAA 59.930 47.619 32.26 10.01 39.66 3.36
792 2632 6.202954 GGCAAACTCATATATGTGGTACTGTC 59.797 42.308 16.87 6.56 0.00 3.51
793 2633 6.055588 GGCAAACTCATATATGTGGTACTGT 58.944 40.000 16.87 0.00 0.00 3.55
794 2634 6.054941 TGGCAAACTCATATATGTGGTACTG 58.945 40.000 16.87 9.17 0.00 2.74
795 2635 6.247229 TGGCAAACTCATATATGTGGTACT 57.753 37.500 16.87 0.00 0.00 2.73
833 2833 4.333372 CCAATTTTGTTTCTTGCTTGCTGT 59.667 37.500 0.00 0.00 0.00 4.40
878 2879 4.528596 TCCAAAGTCCAAACAGAAAAACCA 59.471 37.500 0.00 0.00 0.00 3.67
1019 3381 5.011227 GGAGACTTTGAGGACTTTGAGTAGT 59.989 44.000 0.00 0.00 0.00 2.73
1021 3383 4.022242 CGGAGACTTTGAGGACTTTGAGTA 60.022 45.833 0.00 0.00 0.00 2.59
1023 3385 3.321497 CGGAGACTTTGAGGACTTTGAG 58.679 50.000 0.00 0.00 0.00 3.02
1155 3532 2.043852 GTGGCGAGGAGGAGGAGA 60.044 66.667 0.00 0.00 0.00 3.71
1278 3661 0.034960 GGAAGGAGGAGAAGTTGGCC 60.035 60.000 0.00 0.00 0.00 5.36
1525 3908 0.745845 GTCCTGTCGCCGTAGTAGGA 60.746 60.000 0.00 0.00 35.29 2.94
1539 3922 6.287589 AGAATCACTACTTACTTGGTCCTG 57.712 41.667 0.00 0.00 0.00 3.86
1557 4782 4.203226 GGACAGGGGAATGAAGAAGAATC 58.797 47.826 0.00 0.00 0.00 2.52
1560 4791 1.555075 CGGACAGGGGAATGAAGAAGA 59.445 52.381 0.00 0.00 0.00 2.87
1590 4837 3.575858 AAATCGCAACGATGATTCGAG 57.424 42.857 2.87 0.00 46.30 4.04
1592 4839 3.478516 GGAAAAATCGCAACGATGATTCG 59.521 43.478 2.87 0.00 46.30 3.34
1594 4841 4.433186 TGGAAAAATCGCAACGATGATT 57.567 36.364 2.87 2.13 46.30 2.57
1622 4906 4.195334 ATGGCCATGGCGTCCCTC 62.195 66.667 29.90 15.60 43.06 4.30
1636 4920 2.242043 GGGATATCCAAGCAACCATGG 58.758 52.381 23.27 11.19 37.91 3.66
1637 4921 2.889045 CTGGGATATCCAAGCAACCATG 59.111 50.000 23.27 0.00 46.51 3.66
1638 4922 2.785269 TCTGGGATATCCAAGCAACCAT 59.215 45.455 23.27 0.00 46.51 3.55
1639 4923 2.173356 CTCTGGGATATCCAAGCAACCA 59.827 50.000 23.27 9.00 46.51 3.67
1640 4924 2.487986 CCTCTGGGATATCCAAGCAACC 60.488 54.545 23.27 4.62 46.51 3.77
1641 4925 2.856222 CCTCTGGGATATCCAAGCAAC 58.144 52.381 23.27 5.34 46.51 4.17
1643 4927 0.767375 GCCTCTGGGATATCCAAGCA 59.233 55.000 23.27 11.09 46.51 3.91
1673 4957 1.522806 GGTGGTGACGTTCTGCACA 60.523 57.895 7.33 0.00 36.76 4.57
1696 4980 0.665972 GATGATCTTCTCGGCCTCGC 60.666 60.000 0.00 0.00 36.13 5.03
1816 5103 3.098774 TCAATTATGGGCCACATGTGT 57.901 42.857 23.79 8.06 40.82 3.72
1869 5392 1.527034 GGCAAGCTCATCACTGTGAA 58.473 50.000 15.31 0.00 0.00 3.18
1910 5433 1.574702 GCCCGGTACAAGCTGTTGAC 61.575 60.000 0.00 0.00 37.10 3.18
1948 5471 4.157289 AGCTTTGCTACATCAAGATTGGTG 59.843 41.667 4.28 4.28 44.73 4.17
1966 5489 1.407618 GGGTCAACGTGGAAAAGCTTT 59.592 47.619 5.69 5.69 0.00 3.51
2034 5560 6.316640 AGAGACGATACCATATAGGATGAACG 59.683 42.308 0.00 0.00 41.22 3.95
2038 5564 8.740123 AGTTAGAGACGATACCATATAGGATG 57.260 38.462 0.00 0.00 41.22 3.51
2040 5566 7.120873 GCAAGTTAGAGACGATACCATATAGGA 59.879 40.741 0.00 0.00 41.22 2.94
2054 5580 6.809630 AGAAATGGAAAGCAAGTTAGAGAC 57.190 37.500 0.00 0.00 0.00 3.36
2149 5716 4.133796 GGCAATTGCAGACGCCCC 62.134 66.667 30.32 7.97 44.36 5.80
2178 5745 1.698506 TCAACGGGATTTTGTTGGCT 58.301 45.000 5.38 0.00 44.28 4.75
2193 5760 3.270877 GTGAGGGTGGTATGTGATCAAC 58.729 50.000 0.00 0.00 0.00 3.18
2227 5794 3.639561 TCGGATTATCAAACATCGGAGGA 59.360 43.478 0.00 0.00 0.00 3.71
2717 6290 6.588719 TTTCCATTCCGTTCAATCAATTCT 57.411 33.333 0.00 0.00 0.00 2.40
2742 6316 4.021280 TGCATTGCATCCATACAAACAAGT 60.021 37.500 7.38 0.00 31.71 3.16
2750 6324 3.108144 GTTCGTTGCATTGCATCCATAC 58.892 45.455 12.95 6.26 38.76 2.39
2807 8638 7.011669 GCATTCCATTCCATTCATTTGTTAAGG 59.988 37.037 0.00 0.00 0.00 2.69
2813 8644 5.878116 ACAAGCATTCCATTCCATTCATTTG 59.122 36.000 0.00 0.00 0.00 2.32
2814 8645 6.057321 ACAAGCATTCCATTCCATTCATTT 57.943 33.333 0.00 0.00 0.00 2.32
2816 8647 5.424757 CAACAAGCATTCCATTCCATTCAT 58.575 37.500 0.00 0.00 0.00 2.57
2827 8661 3.131046 CCATTAGTCCCAACAAGCATTCC 59.869 47.826 0.00 0.00 0.00 3.01
2841 8675 1.202348 GCTTGTTGCCACCCATTAGTC 59.798 52.381 0.00 0.00 35.15 2.59
2843 8677 0.171007 CGCTTGTTGCCACCCATTAG 59.829 55.000 0.00 0.00 38.78 1.73
2844 8678 1.872197 GCGCTTGTTGCCACCCATTA 61.872 55.000 0.00 0.00 38.78 1.90
2855 8698 1.017387 GCAGCTAATAGGCGCTTGTT 58.983 50.000 7.64 7.13 33.45 2.83
2856 8699 0.107703 TGCAGCTAATAGGCGCTTGT 60.108 50.000 7.64 0.00 33.45 3.16
2866 8709 4.823989 AGAGGCGATTTATTTGCAGCTAAT 59.176 37.500 7.27 7.27 36.33 1.73
2903 8772 6.038161 ACACATCACATTATGGGTATTTCACG 59.962 38.462 0.00 0.00 41.71 4.35
2943 8812 6.198650 TGATTGAGCTTGTCATTGGTATTG 57.801 37.500 0.00 0.00 34.17 1.90
2991 8860 3.625764 ACTCGTTACATTGCAACTGTGTT 59.374 39.130 18.73 3.13 0.00 3.32
3058 8927 7.012327 ACGACCCATGTTCATAAACTCATAATG 59.988 37.037 0.00 0.00 36.30 1.90
3074 8943 3.244422 ACACTCAACAATACGACCCATGT 60.244 43.478 0.00 0.00 0.00 3.21
3095 8964 8.034058 AGCATAGAAGTACTCATGTTTTTGAC 57.966 34.615 0.00 0.00 0.00 3.18
3184 9053 1.557099 TTCTGTGGACCTACGCTGAT 58.443 50.000 0.00 0.00 0.00 2.90
3201 9070 4.024438 CGTGCGACATCATTCAAGAATTC 58.976 43.478 0.00 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.