Multiple sequence alignment - TraesCS2D01G118200

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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 TraesCS2D01G118200 chr2D 100.000 2888 0 0 1 2888 67497898 67495011 0.000000e+00 5334
1 TraesCS2D01G118200 chr2D 86.034 179 21 4 1126 1302 367089161 367089337 3.800000e-44 189
2 TraesCS2D01G118200 chr2A 89.815 2818 107 78 1 2757 66847849 66850547 0.000000e+00 3448
3 TraesCS2D01G118200 chr2A 95.556 135 4 2 2755 2888 66850632 66850765 6.270000e-52 215
4 TraesCS2D01G118200 chr2A 86.034 179 21 4 1126 1302 496562925 496563101 3.800000e-44 189
5 TraesCS2D01G118200 chr2B 87.387 1776 71 57 663 2389 103195386 103197057 0.000000e+00 1897
6 TraesCS2D01G118200 chr2B 95.186 457 14 6 1 455 103194137 103194587 0.000000e+00 715
7 TraesCS2D01G118200 chr2B 91.228 228 14 6 2384 2608 103197092 103197316 3.620000e-79 305
8 TraesCS2D01G118200 chr2B 89.302 215 10 9 451 660 103194882 103195088 1.030000e-64 257
9 TraesCS2D01G118200 chr1D 86.325 117 14 2 1147 1262 410072030 410071915 3.020000e-25 126
10 TraesCS2D01G118200 chr6B 82.270 141 23 1 1124 1262 239729254 239729394 1.410000e-23 121
11 TraesCS2D01G118200 chr6A 82.270 141 23 1 1124 1262 183188180 183188320 1.410000e-23 121
12 TraesCS2D01G118200 chr1A 85.470 117 15 2 1147 1262 505925826 505925711 1.410000e-23 121
13 TraesCS2D01G118200 chr1B 84.615 117 16 2 1147 1262 552474242 552474127 6.540000e-22 115


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 TraesCS2D01G118200 chr2D 67495011 67497898 2887 True 5334.0 5334 100.00000 1 2888 1 chr2D.!!$R1 2887
1 TraesCS2D01G118200 chr2A 66847849 66850765 2916 False 1831.5 3448 92.68550 1 2888 2 chr2A.!!$F2 2887
2 TraesCS2D01G118200 chr2B 103194137 103197316 3179 False 793.5 1897 90.77575 1 2608 4 chr2B.!!$F1 2607

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
937 1563 0.250467 GCCAGCCTCACTTCACTTCA 60.25 55.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1999 2656 0.243907 CTACTGCTGCCACGTACTGT 59.756 55.0 0.0 0.0 0.0 3.55 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
82 83 1.072965 AGGCTTGATGCATAGGTAGGC 59.927 52.381 0.00 7.20 45.15 3.93
228 229 5.928976 ACATAGATGCCACAACAAGCTATA 58.071 37.500 0.00 0.00 0.00 1.31
237 238 4.816385 CCACAACAAGCTATACATGTAGGG 59.184 45.833 11.91 7.50 28.03 3.53
242 243 4.844085 ACAAGCTATACATGTAGGGCCATA 59.156 41.667 21.51 0.00 0.00 2.74
243 244 5.488919 ACAAGCTATACATGTAGGGCCATAT 59.511 40.000 21.51 4.47 0.00 1.78
245 246 7.182026 ACAAGCTATACATGTAGGGCCATATAA 59.818 37.037 21.51 0.00 0.00 0.98
246 247 7.937700 AGCTATACATGTAGGGCCATATAAT 57.062 36.000 21.51 0.00 0.00 1.28
247 248 8.337118 AGCTATACATGTAGGGCCATATAATT 57.663 34.615 21.51 0.00 0.00 1.40
248 249 8.213679 AGCTATACATGTAGGGCCATATAATTG 58.786 37.037 21.51 0.00 0.00 2.32
249 250 8.210946 GCTATACATGTAGGGCCATATAATTGA 58.789 37.037 11.91 0.00 0.00 2.57
252 253 7.090319 ACATGTAGGGCCATATAATTGAAGA 57.910 36.000 6.18 0.00 0.00 2.87
295 301 1.302033 CGGCTCTGGCTTCACAACT 60.302 57.895 0.00 0.00 38.73 3.16
504 808 8.503196 TGTTATTTTCTAGCAACACATACACAG 58.497 33.333 0.00 0.00 0.00 3.66
505 809 8.717821 GTTATTTTCTAGCAACACATACACAGA 58.282 33.333 0.00 0.00 0.00 3.41
510 814 3.743521 AGCAACACATACACAGACACAT 58.256 40.909 0.00 0.00 0.00 3.21
544 848 3.435105 TGTTTGACTGGCACAACATTC 57.565 42.857 7.02 0.00 38.70 2.67
545 849 3.023119 TGTTTGACTGGCACAACATTCT 58.977 40.909 7.02 0.00 38.70 2.40
546 850 3.066621 TGTTTGACTGGCACAACATTCTC 59.933 43.478 7.02 0.00 38.70 2.87
613 917 4.824537 ACACAAGGTGCATACATACAAACA 59.175 37.500 0.00 0.00 36.98 2.83
702 1312 0.952659 ATGTCACTCCCCTCCCCTAT 59.047 55.000 0.00 0.00 0.00 2.57
704 1319 0.264955 GTCACTCCCCTCCCCTATCA 59.735 60.000 0.00 0.00 0.00 2.15
800 1426 1.689273 CCCTCCATAGTGAGCACTACC 59.311 57.143 12.16 0.00 45.61 3.18
801 1427 1.689273 CCTCCATAGTGAGCACTACCC 59.311 57.143 12.16 0.00 45.61 3.69
802 1428 2.388735 CTCCATAGTGAGCACTACCCA 58.611 52.381 12.16 0.00 45.61 4.51
803 1429 2.101582 CTCCATAGTGAGCACTACCCAC 59.898 54.545 12.16 0.00 45.61 4.61
804 1430 1.831106 CCATAGTGAGCACTACCCACA 59.169 52.381 12.16 0.00 45.61 4.17
805 1431 2.418746 CCATAGTGAGCACTACCCACAC 60.419 54.545 12.16 0.00 45.61 3.82
806 1432 2.304221 TAGTGAGCACTACCCACACT 57.696 50.000 6.26 0.00 42.54 3.55
807 1433 2.304221 AGTGAGCACTACCCACACTA 57.696 50.000 0.41 0.00 40.43 2.74
808 1434 1.893801 AGTGAGCACTACCCACACTAC 59.106 52.381 0.41 0.00 40.43 2.73
840 1466 0.886490 CACAGTCTCAGCAACCACCC 60.886 60.000 0.00 0.00 0.00 4.61
849 1475 3.146828 GCAACCACCCCCTCAACCT 62.147 63.158 0.00 0.00 0.00 3.50
850 1476 1.074951 CAACCACCCCCTCAACCTC 59.925 63.158 0.00 0.00 0.00 3.85
851 1477 2.160853 AACCACCCCCTCAACCTCC 61.161 63.158 0.00 0.00 0.00 4.30
852 1478 2.204151 CCACCCCCTCAACCTCCT 60.204 66.667 0.00 0.00 0.00 3.69
853 1479 2.301738 CCACCCCCTCAACCTCCTC 61.302 68.421 0.00 0.00 0.00 3.71
854 1480 1.538876 CACCCCCTCAACCTCCTCA 60.539 63.158 0.00 0.00 0.00 3.86
855 1481 1.133809 CACCCCCTCAACCTCCTCAA 61.134 60.000 0.00 0.00 0.00 3.02
856 1482 1.134438 ACCCCCTCAACCTCCTCAAC 61.134 60.000 0.00 0.00 0.00 3.18
857 1483 1.685820 CCCCTCAACCTCCTCAACC 59.314 63.158 0.00 0.00 0.00 3.77
881 1507 1.202359 GCTAGCTAGCTCACACCTCAC 60.202 57.143 33.71 4.79 45.62 3.51
885 1511 0.457509 CTAGCTCACACCTCACAGCG 60.458 60.000 0.00 0.00 36.95 5.18
937 1563 0.250467 GCCAGCCTCACTTCACTTCA 60.250 55.000 0.00 0.00 0.00 3.02
938 1564 1.805869 CCAGCCTCACTTCACTTCAG 58.194 55.000 0.00 0.00 0.00 3.02
939 1565 1.071385 CCAGCCTCACTTCACTTCAGT 59.929 52.381 0.00 0.00 0.00 3.41
940 1566 2.486191 CCAGCCTCACTTCACTTCAGTT 60.486 50.000 0.00 0.00 0.00 3.16
941 1567 2.805099 CAGCCTCACTTCACTTCAGTTC 59.195 50.000 0.00 0.00 0.00 3.01
1084 1710 3.186730 CGTCGTCTCCGAGCGAGA 61.187 66.667 13.05 0.55 45.26 4.04
1397 2026 2.954868 CTCGACCATGCCGTACGC 60.955 66.667 10.49 6.24 38.31 4.42
1891 2532 1.072331 GCTTCCTCTCCCACTGAAACA 59.928 52.381 0.00 0.00 0.00 2.83
1892 2533 2.487265 GCTTCCTCTCCCACTGAAACAA 60.487 50.000 0.00 0.00 0.00 2.83
1906 2547 1.866601 GAAACAACAAATGCACCAGCC 59.133 47.619 0.00 0.00 41.13 4.85
1907 2548 0.829333 AACAACAAATGCACCAGCCA 59.171 45.000 0.00 0.00 41.13 4.75
1908 2549 0.390124 ACAACAAATGCACCAGCCAG 59.610 50.000 0.00 0.00 41.13 4.85
1909 2550 0.947180 CAACAAATGCACCAGCCAGC 60.947 55.000 0.00 0.00 41.13 4.85
1910 2551 1.401318 AACAAATGCACCAGCCAGCA 61.401 50.000 0.00 0.00 45.92 4.41
1914 2555 3.687102 TGCACCAGCCAGCATTGC 61.687 61.111 0.00 0.00 41.13 3.56
1933 2590 0.602060 CTCTCAGTGCTCTGCTGTGA 59.398 55.000 10.95 6.78 41.10 3.58
1934 2591 1.205179 CTCTCAGTGCTCTGCTGTGAT 59.795 52.381 10.95 0.00 41.10 3.06
1939 2596 0.321034 GTGCTCTGCTGTGATCACCA 60.321 55.000 22.85 13.27 29.76 4.17
1943 2600 1.135721 CTCTGCTGTGATCACCATCGA 59.864 52.381 22.85 12.79 0.00 3.59
1944 2601 1.758862 TCTGCTGTGATCACCATCGAT 59.241 47.619 22.85 0.00 0.00 3.59
1947 2604 1.269257 GCTGTGATCACCATCGATCGA 60.269 52.381 21.86 21.86 44.02 3.59
1948 2605 2.389059 CTGTGATCACCATCGATCGAC 58.611 52.381 22.06 6.31 44.02 4.20
1949 2606 1.067060 TGTGATCACCATCGATCGACC 59.933 52.381 22.06 4.54 44.02 4.79
1950 2607 1.067060 GTGATCACCATCGATCGACCA 59.933 52.381 22.06 7.05 44.02 4.02
1951 2608 1.963515 TGATCACCATCGATCGACCAT 59.036 47.619 22.06 7.83 44.02 3.55
1952 2609 3.057526 GTGATCACCATCGATCGACCATA 60.058 47.826 22.06 5.71 44.02 2.74
1953 2610 3.191371 TGATCACCATCGATCGACCATAG 59.809 47.826 22.06 9.83 44.02 2.23
1954 2611 1.269723 TCACCATCGATCGACCATAGC 59.730 52.381 22.06 0.00 0.00 2.97
1955 2612 1.270826 CACCATCGATCGACCATAGCT 59.729 52.381 22.06 0.00 0.00 3.32
1956 2613 2.488153 CACCATCGATCGACCATAGCTA 59.512 50.000 22.06 0.00 0.00 3.32
1957 2614 2.750166 ACCATCGATCGACCATAGCTAG 59.250 50.000 22.06 0.00 0.00 3.42
1958 2615 2.098280 CCATCGATCGACCATAGCTAGG 59.902 54.545 22.06 7.38 0.00 3.02
1959 2616 2.563261 TCGATCGACCATAGCTAGGT 57.437 50.000 15.15 12.88 43.46 3.08
1960 2617 3.690475 TCGATCGACCATAGCTAGGTA 57.310 47.619 15.15 3.73 40.09 3.08
1971 2628 5.956563 ACCATAGCTAGGTAGTAGTGTTTGT 59.043 40.000 11.74 0.00 37.67 2.83
1974 2631 7.277981 CCATAGCTAGGTAGTAGTGTTTGTTTG 59.722 40.741 7.83 0.00 0.00 2.93
1976 2633 5.306160 AGCTAGGTAGTAGTGTTTGTTTGGA 59.694 40.000 0.00 0.00 0.00 3.53
1982 2639 6.018180 GGTAGTAGTGTTTGTTTGGAGAGTTG 60.018 42.308 0.00 0.00 0.00 3.16
2005 2662 3.946308 TCGATCGATCAGTCACAGTAC 57.054 47.619 24.40 0.00 0.00 2.73
2006 2663 2.284417 TCGATCGATCAGTCACAGTACG 59.716 50.000 24.40 7.25 0.00 3.67
2007 2664 2.030579 CGATCGATCAGTCACAGTACGT 59.969 50.000 24.40 0.00 0.00 3.57
2009 2666 1.467342 TCGATCAGTCACAGTACGTGG 59.533 52.381 14.80 0.00 46.36 4.94
2022 2679 0.530744 TACGTGGCAGCAGTAGAAGG 59.469 55.000 0.00 0.00 0.00 3.46
2026 2683 0.898326 TGGCAGCAGTAGAAGGTCGA 60.898 55.000 0.00 0.00 0.00 4.20
2027 2684 0.461961 GGCAGCAGTAGAAGGTCGAT 59.538 55.000 0.00 0.00 0.00 3.59
2028 2685 1.537135 GGCAGCAGTAGAAGGTCGATC 60.537 57.143 0.00 0.00 0.00 3.69
2029 2686 1.862008 GCAGCAGTAGAAGGTCGATCG 60.862 57.143 9.36 9.36 0.00 3.69
2030 2687 1.671328 CAGCAGTAGAAGGTCGATCGA 59.329 52.381 15.15 15.15 0.00 3.59
2031 2688 1.671845 AGCAGTAGAAGGTCGATCGAC 59.328 52.381 34.70 34.70 43.87 4.20
2032 2689 1.595003 GCAGTAGAAGGTCGATCGACG 60.595 57.143 34.69 22.14 45.41 5.12
2054 2715 4.553547 CGAAGAAGAAGAGTGGCTTGTTTG 60.554 45.833 0.00 0.00 39.89 2.93
2104 2765 5.957771 TCCATGTACTTAGGCTCTTTCAT 57.042 39.130 0.00 0.00 0.00 2.57
2128 2789 4.564940 AGCAGCACTATTACTACGTACC 57.435 45.455 0.00 0.00 0.00 3.34
2130 2791 4.036498 AGCAGCACTATTACTACGTACCAG 59.964 45.833 0.00 0.00 0.00 4.00
2181 2853 7.416964 AGTGACATGCTTAAGTTATCTCTCT 57.583 36.000 4.02 1.34 0.00 3.10
2182 2854 7.488322 AGTGACATGCTTAAGTTATCTCTCTC 58.512 38.462 4.02 0.00 0.00 3.20
2278 2957 2.479049 GGCTCGAGAATGTAGTACGCAA 60.479 50.000 18.75 0.00 0.00 4.85
2284 2963 3.259064 AGAATGTAGTACGCAAACGCAT 58.741 40.909 0.00 0.00 45.53 4.73
2397 3117 3.624777 TCCTACGTACTTACCTGAAGGG 58.375 50.000 0.56 0.00 39.74 3.95
2671 3415 3.056322 AGCTTGCTTGGATTTGTTGGATC 60.056 43.478 0.00 0.00 0.00 3.36
2718 3464 6.842163 AGCAATACAGTACAGTACAAAATGC 58.158 36.000 13.37 14.53 0.00 3.56
2735 3481 3.865011 ATGCGCATGTAACCATTTGAA 57.135 38.095 24.69 0.00 0.00 2.69
2798 3632 4.479158 AGCAATTGGGTTCAAGTCCTAAA 58.521 39.130 7.72 0.00 36.19 1.85
2861 3695 6.643388 AGGAACATTTTGCTGGATTTATTCC 58.357 36.000 0.00 0.00 45.69 3.01
2884 3718 7.214381 TCCAGACATTCCGACGATATTTATTT 58.786 34.615 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 83 4.284829 AGAAGGGAAAGAAGAGAGCTTG 57.715 45.455 0.00 0.00 33.61 4.01
203 204 3.828451 AGCTTGTTGTGGCATCTATGTTT 59.172 39.130 0.00 0.00 0.00 2.83
228 229 7.090319 TCTTCAATTATATGGCCCTACATGT 57.910 36.000 2.69 2.69 32.39 3.21
237 238 7.917505 CCAAGACAAACTCTTCAATTATATGGC 59.082 37.037 0.00 0.00 37.08 4.40
242 243 6.071728 CCTGCCAAGACAAACTCTTCAATTAT 60.072 38.462 0.00 0.00 37.08 1.28
243 244 5.241506 CCTGCCAAGACAAACTCTTCAATTA 59.758 40.000 0.00 0.00 37.08 1.40
245 246 3.571401 CCTGCCAAGACAAACTCTTCAAT 59.429 43.478 0.00 0.00 37.08 2.57
246 247 2.951642 CCTGCCAAGACAAACTCTTCAA 59.048 45.455 0.00 0.00 37.08 2.69
247 248 2.575532 CCTGCCAAGACAAACTCTTCA 58.424 47.619 0.00 0.00 37.08 3.02
248 249 1.882623 CCCTGCCAAGACAAACTCTTC 59.117 52.381 0.00 0.00 37.08 2.87
249 250 1.479389 CCCCTGCCAAGACAAACTCTT 60.479 52.381 0.00 0.00 40.13 2.85
251 252 1.527433 GCCCCTGCCAAGACAAACTC 61.527 60.000 0.00 0.00 0.00 3.01
252 253 1.531602 GCCCCTGCCAAGACAAACT 60.532 57.895 0.00 0.00 0.00 2.66
295 301 7.451566 ACCAGCATATGAGTATATGACACACTA 59.548 37.037 6.97 0.00 45.92 2.74
544 848 2.433970 GGACCAAAGAGATGAGGAGGAG 59.566 54.545 0.00 0.00 0.00 3.69
545 849 2.045047 AGGACCAAAGAGATGAGGAGGA 59.955 50.000 0.00 0.00 0.00 3.71
546 850 2.476199 AGGACCAAAGAGATGAGGAGG 58.524 52.381 0.00 0.00 0.00 4.30
613 917 2.097825 GGAATGGAAAGCTCACTGCAT 58.902 47.619 0.00 0.00 45.94 3.96
702 1312 0.176449 CTGTGGATGAGATGGCGTGA 59.824 55.000 0.00 0.00 0.00 4.35
704 1319 0.107993 CACTGTGGATGAGATGGCGT 60.108 55.000 0.00 0.00 0.00 5.68
800 1426 3.255888 TGAGCTTCTAGTGTGTAGTGTGG 59.744 47.826 0.00 0.00 0.00 4.17
801 1427 4.230657 GTGAGCTTCTAGTGTGTAGTGTG 58.769 47.826 0.00 0.00 0.00 3.82
802 1428 3.889538 TGTGAGCTTCTAGTGTGTAGTGT 59.110 43.478 0.00 0.00 0.00 3.55
803 1429 4.022762 ACTGTGAGCTTCTAGTGTGTAGTG 60.023 45.833 0.00 0.00 0.00 2.74
804 1430 4.145807 ACTGTGAGCTTCTAGTGTGTAGT 58.854 43.478 0.00 0.00 0.00 2.73
805 1431 4.457603 AGACTGTGAGCTTCTAGTGTGTAG 59.542 45.833 2.91 0.00 0.00 2.74
806 1432 4.399219 AGACTGTGAGCTTCTAGTGTGTA 58.601 43.478 2.91 0.00 0.00 2.90
807 1433 3.226777 AGACTGTGAGCTTCTAGTGTGT 58.773 45.455 2.91 0.00 0.00 3.72
808 1434 3.254411 TGAGACTGTGAGCTTCTAGTGTG 59.746 47.826 2.91 0.00 0.00 3.82
840 1466 1.952621 TAGGTTGAGGAGGTTGAGGG 58.047 55.000 0.00 0.00 0.00 4.30
849 1475 2.959707 GCTAGCTAGCTTAGGTTGAGGA 59.040 50.000 33.71 0.00 45.62 3.71
850 1476 3.378911 GCTAGCTAGCTTAGGTTGAGG 57.621 52.381 33.71 1.00 45.62 3.86
885 1511 1.818785 CTGCTCCAGCCTAGCTTGC 60.819 63.158 0.00 0.00 40.73 4.01
896 1522 4.399219 CTGGCTACTATACTACTGCTCCA 58.601 47.826 0.00 0.00 0.00 3.86
1170 1796 2.330745 GTCGGGTCGCGTATCTCC 59.669 66.667 5.77 2.31 0.00 3.71
1459 2100 4.162690 CTGGTGGTAGCCGAGGCC 62.163 72.222 10.95 0.00 43.17 5.19
1460 2101 4.840005 GCTGGTGGTAGCCGAGGC 62.840 72.222 5.89 5.89 37.73 4.70
1461 2102 3.376935 CTGCTGGTGGTAGCCGAGG 62.377 68.421 0.00 0.00 43.02 4.63
1462 2103 2.185350 CTGCTGGTGGTAGCCGAG 59.815 66.667 0.00 0.00 43.02 4.63
1463 2104 3.390521 CCTGCTGGTGGTAGCCGA 61.391 66.667 0.51 0.00 43.02 5.54
1464 2105 4.473520 CCCTGCTGGTGGTAGCCG 62.474 72.222 9.00 0.00 43.02 5.52
1465 2106 4.803908 GCCCTGCTGGTGGTAGCC 62.804 72.222 9.00 0.00 43.02 3.93
1466 2107 4.803908 GGCCCTGCTGGTGGTAGC 62.804 72.222 9.00 4.17 43.95 3.58
1467 2108 4.115199 GGGCCCTGCTGGTGGTAG 62.115 72.222 17.04 0.00 36.04 3.18
1749 2390 3.136123 CAGAAGCCGGCCACCATG 61.136 66.667 26.15 11.67 0.00 3.66
1891 2532 1.368579 GCTGGCTGGTGCATTTGTT 59.631 52.632 0.00 0.00 41.91 2.83
1892 2533 1.189524 ATGCTGGCTGGTGCATTTGT 61.190 50.000 0.00 0.00 46.29 2.83
1908 2549 0.727970 CAGAGCACTGAGAGCAATGC 59.272 55.000 5.03 0.00 46.94 3.56
1909 2550 0.727970 GCAGAGCACTGAGAGCAATG 59.272 55.000 15.88 3.51 46.03 2.82
1910 2551 0.614294 AGCAGAGCACTGAGAGCAAT 59.386 50.000 15.88 0.00 46.03 3.56
1912 2553 1.292541 CAGCAGAGCACTGAGAGCA 59.707 57.895 15.88 0.00 46.03 4.26
1914 2555 0.602060 TCACAGCAGAGCACTGAGAG 59.398 55.000 15.88 5.92 46.03 3.20
1933 2590 2.094494 GCTATGGTCGATCGATGGTGAT 60.094 50.000 22.50 11.03 0.00 3.06
1934 2591 1.269723 GCTATGGTCGATCGATGGTGA 59.730 52.381 22.50 5.38 0.00 4.02
1939 2596 3.074675 ACCTAGCTATGGTCGATCGAT 57.925 47.619 22.50 8.10 31.03 3.59
1943 2600 5.221884 ACACTACTACCTAGCTATGGTCGAT 60.222 44.000 15.48 7.67 38.88 3.59
1944 2601 4.102210 ACACTACTACCTAGCTATGGTCGA 59.898 45.833 15.48 2.66 38.88 4.20
1947 2604 5.956563 ACAAACACTACTACCTAGCTATGGT 59.043 40.000 16.07 16.07 41.28 3.55
1948 2605 6.466885 ACAAACACTACTACCTAGCTATGG 57.533 41.667 0.00 0.53 0.00 2.74
1949 2606 7.277981 CCAAACAAACACTACTACCTAGCTATG 59.722 40.741 0.00 0.00 0.00 2.23
1950 2607 7.179694 TCCAAACAAACACTACTACCTAGCTAT 59.820 37.037 0.00 0.00 0.00 2.97
1951 2608 6.494491 TCCAAACAAACACTACTACCTAGCTA 59.506 38.462 0.00 0.00 0.00 3.32
1952 2609 5.306160 TCCAAACAAACACTACTACCTAGCT 59.694 40.000 0.00 0.00 0.00 3.32
1953 2610 5.544650 TCCAAACAAACACTACTACCTAGC 58.455 41.667 0.00 0.00 0.00 3.42
1954 2611 6.989659 TCTCCAAACAAACACTACTACCTAG 58.010 40.000 0.00 0.00 0.00 3.02
1955 2612 6.552350 ACTCTCCAAACAAACACTACTACCTA 59.448 38.462 0.00 0.00 0.00 3.08
1956 2613 5.365895 ACTCTCCAAACAAACACTACTACCT 59.634 40.000 0.00 0.00 0.00 3.08
1957 2614 5.608449 ACTCTCCAAACAAACACTACTACC 58.392 41.667 0.00 0.00 0.00 3.18
1958 2615 6.018180 CCAACTCTCCAAACAAACACTACTAC 60.018 42.308 0.00 0.00 0.00 2.73
1959 2616 6.053005 CCAACTCTCCAAACAAACACTACTA 58.947 40.000 0.00 0.00 0.00 1.82
1960 2617 4.881850 CCAACTCTCCAAACAAACACTACT 59.118 41.667 0.00 0.00 0.00 2.57
1971 2628 2.758423 TCGATCGATCCAACTCTCCAAA 59.242 45.455 19.51 0.00 0.00 3.28
1974 2631 3.210358 GATCGATCGATCCAACTCTCC 57.790 52.381 36.97 17.01 43.71 3.71
1999 2656 0.243907 CTACTGCTGCCACGTACTGT 59.756 55.000 0.00 0.00 0.00 3.55
2000 2657 0.526211 TCTACTGCTGCCACGTACTG 59.474 55.000 0.00 0.00 0.00 2.74
2001 2658 1.202582 CTTCTACTGCTGCCACGTACT 59.797 52.381 0.00 0.00 0.00 2.73
2002 2659 1.630148 CTTCTACTGCTGCCACGTAC 58.370 55.000 0.00 0.00 0.00 3.67
2003 2660 0.530744 CCTTCTACTGCTGCCACGTA 59.469 55.000 0.00 0.00 0.00 3.57
2004 2661 1.293498 CCTTCTACTGCTGCCACGT 59.707 57.895 0.00 0.00 0.00 4.49
2005 2662 0.737715 GACCTTCTACTGCTGCCACG 60.738 60.000 0.00 0.00 0.00 4.94
2006 2663 0.737715 CGACCTTCTACTGCTGCCAC 60.738 60.000 0.00 0.00 0.00 5.01
2007 2664 0.898326 TCGACCTTCTACTGCTGCCA 60.898 55.000 0.00 0.00 0.00 4.92
2008 2665 0.461961 ATCGACCTTCTACTGCTGCC 59.538 55.000 0.00 0.00 0.00 4.85
2009 2666 1.846541 GATCGACCTTCTACTGCTGC 58.153 55.000 0.00 0.00 0.00 5.25
2010 2667 1.671328 TCGATCGACCTTCTACTGCTG 59.329 52.381 15.15 0.00 0.00 4.41
2011 2668 1.671845 GTCGATCGACCTTCTACTGCT 59.328 52.381 33.06 0.00 39.08 4.24
2012 2669 1.595003 CGTCGATCGACCTTCTACTGC 60.595 57.143 35.48 12.87 41.76 4.40
2013 2670 1.931841 TCGTCGATCGACCTTCTACTG 59.068 52.381 35.48 21.82 44.01 2.74
2026 2683 2.416162 GCCACTCTTCTTCTTCGTCGAT 60.416 50.000 0.00 0.00 0.00 3.59
2027 2684 1.068472 GCCACTCTTCTTCTTCGTCGA 60.068 52.381 0.00 0.00 0.00 4.20
2028 2685 1.068194 AGCCACTCTTCTTCTTCGTCG 60.068 52.381 0.00 0.00 0.00 5.12
2029 2686 2.734079 CAAGCCACTCTTCTTCTTCGTC 59.266 50.000 0.00 0.00 31.27 4.20
2030 2687 2.103263 ACAAGCCACTCTTCTTCTTCGT 59.897 45.455 0.00 0.00 31.27 3.85
2031 2688 2.760374 ACAAGCCACTCTTCTTCTTCG 58.240 47.619 0.00 0.00 31.27 3.79
2032 2689 4.261363 CCAAACAAGCCACTCTTCTTCTTC 60.261 45.833 0.00 0.00 31.27 2.87
2033 2690 3.633986 CCAAACAAGCCACTCTTCTTCTT 59.366 43.478 0.00 0.00 31.27 2.52
2034 2691 3.217626 CCAAACAAGCCACTCTTCTTCT 58.782 45.455 0.00 0.00 31.27 2.85
2128 2789 7.148423 TGCATGCATGAAAAGTTACTAGTACTG 60.148 37.037 30.64 0.00 0.00 2.74
2130 2791 6.961554 GTGCATGCATGAAAAGTTACTAGTAC 59.038 38.462 30.64 6.85 0.00 2.73
2139 2800 1.881973 ACTCGTGCATGCATGAAAAGT 59.118 42.857 35.31 28.06 40.88 2.66
2140 2801 2.095617 TCACTCGTGCATGCATGAAAAG 60.096 45.455 35.31 27.50 40.88 2.27
2278 2957 3.674997 AGGATCAACAACAGTATGCGTT 58.325 40.909 0.00 0.00 42.53 4.84
2284 2963 7.338196 TGAAACTTTCAAGGATCAACAACAGTA 59.662 33.333 1.47 0.00 36.59 2.74
2397 3117 6.294620 CCGTGTACTATTCCCCTTATCTTCTC 60.295 46.154 0.00 0.00 0.00 2.87
2434 3154 1.897133 TGTCAAGGCGTAGTACCACAT 59.103 47.619 0.00 0.00 0.00 3.21
2435 3155 1.271379 CTGTCAAGGCGTAGTACCACA 59.729 52.381 0.00 0.00 0.00 4.17
2438 3159 2.029649 TGAACTGTCAAGGCGTAGTACC 60.030 50.000 0.00 0.00 0.00 3.34
2699 3443 4.308265 TGCGCATTTTGTACTGTACTGTA 58.692 39.130 17.98 8.40 0.00 2.74
2701 3445 3.804518 TGCGCATTTTGTACTGTACTG 57.195 42.857 17.98 9.50 0.00 2.74
2703 3447 4.078363 ACATGCGCATTTTGTACTGTAC 57.922 40.909 22.81 10.98 0.00 2.90
2704 3448 5.391097 GGTTACATGCGCATTTTGTACTGTA 60.391 40.000 22.81 15.87 0.00 2.74
2705 3449 4.472286 GTTACATGCGCATTTTGTACTGT 58.528 39.130 22.81 16.98 0.00 3.55
2706 3450 3.851403 GGTTACATGCGCATTTTGTACTG 59.149 43.478 22.81 11.27 0.00 2.74
2707 3451 3.504134 TGGTTACATGCGCATTTTGTACT 59.496 39.130 22.81 0.00 0.00 2.73
2708 3452 3.827625 TGGTTACATGCGCATTTTGTAC 58.172 40.909 22.81 14.88 0.00 2.90
2709 3453 4.710423 ATGGTTACATGCGCATTTTGTA 57.290 36.364 22.81 18.97 35.57 2.41
2710 3454 3.591196 ATGGTTACATGCGCATTTTGT 57.409 38.095 22.81 20.12 35.57 2.83
2711 3455 4.388165 TCAAATGGTTACATGCGCATTTTG 59.612 37.500 24.98 24.98 37.40 2.44
2712 3456 4.564041 TCAAATGGTTACATGCGCATTTT 58.436 34.783 22.81 14.00 37.40 1.82
2718 3464 7.490725 TCCAATAAATTCAAATGGTTACATGCG 59.509 33.333 0.00 0.00 37.40 4.73
2861 3695 9.193133 ACTAAATAAATATCGTCGGAATGTCTG 57.807 33.333 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.