Multiple sequence alignment - TraesCS2A01G292300

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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 TraesCS2A01G292300 chr2A 100.000 3190 0 0 1 3190 503453051 503456240 0.000000e+00 5891.0
1 TraesCS2A01G292300 chr2D 92.373 2360 96 25 867 3190 372321804 372324115 0.000000e+00 3284.0
2 TraesCS2A01G292300 chr2D 89.189 222 13 5 245 466 372321107 372321317 1.890000e-67 267.0
3 TraesCS2A01G292300 chr2D 89.286 224 8 5 572 795 372321437 372321644 1.890000e-67 267.0
4 TraesCS2A01G292300 chr2D 86.154 195 14 6 1 194 372320769 372320951 6.980000e-47 198.0
5 TraesCS2A01G292300 chr2D 100.000 51 0 0 459 509 372321338 372321388 9.420000e-16 95.3
6 TraesCS2A01G292300 chr2D 97.917 48 1 0 823 870 372321718 372321765 2.040000e-12 84.2
7 TraesCS2A01G292300 chr2B 89.348 2347 121 56 867 3163 441872873 441875140 0.000000e+00 2830.0
8 TraesCS2A01G292300 chr2B 78.596 570 49 26 243 778 441871871 441872401 3.090000e-80 309.0
9 TraesCS2A01G292300 chr2B 92.754 138 9 1 1 137 441871373 441871510 6.980000e-47 198.0
10 TraesCS2A01G292300 chr2B 100.000 48 0 0 823 870 441872793 441872840 4.380000e-14 89.8


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 TraesCS2A01G292300 chr2A 503453051 503456240 3189 False 5891.00 5891 100.0000 1 3190 1 chr2A.!!$F1 3189
1 TraesCS2A01G292300 chr2D 372320769 372324115 3346 False 699.25 3284 92.4865 1 3190 6 chr2D.!!$F1 3189
2 TraesCS2A01G292300 chr2B 441871373 441875140 3767 False 856.70 2830 90.1745 1 3163 4 chr2B.!!$F1 3162

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
626 1096 0.041047 CCGTTTCCGTTTCCGTTTCC 60.041 55.0 0.0 0.0 0.0 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2503 3404 1.06406 GCGTGTCAGCATCCCAAATAC 59.936 52.381 0.0 0.0 37.05 1.89 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
29 30 8.270799 CAGTTTTTGTAATGATTTCTTGCTGTG 58.729 33.333 0.00 0.00 0.00 3.66
82 83 1.406219 CGACCATGCACGTCTTCTCG 61.406 60.000 12.56 0.00 0.00 4.04
138 144 2.892640 CCGGAGAAGATGACGGCA 59.107 61.111 0.00 0.00 39.85 5.69
166 475 2.478033 CGCCCCTTCCATTAACGCC 61.478 63.158 0.00 0.00 0.00 5.68
183 492 3.091022 CTTCGCGTGCGCCAAAAC 61.091 61.111 9.79 0.00 39.59 2.43
194 503 3.189702 GTGCGCCAAAACAATACTCCTAA 59.810 43.478 4.18 0.00 0.00 2.69
196 505 4.163552 GCGCCAAAACAATACTCCTAAAC 58.836 43.478 0.00 0.00 0.00 2.01
197 506 4.082949 GCGCCAAAACAATACTCCTAAACT 60.083 41.667 0.00 0.00 0.00 2.66
199 508 5.628134 GCCAAAACAATACTCCTAAACTCG 58.372 41.667 0.00 0.00 0.00 4.18
200 509 5.180680 GCCAAAACAATACTCCTAAACTCGT 59.819 40.000 0.00 0.00 0.00 4.18
201 510 6.369615 GCCAAAACAATACTCCTAAACTCGTA 59.630 38.462 0.00 0.00 0.00 3.43
202 511 7.622880 GCCAAAACAATACTCCTAAACTCGTAC 60.623 40.741 0.00 0.00 0.00 3.67
204 513 9.630098 CAAAACAATACTCCTAAACTCGTACTA 57.370 33.333 0.00 0.00 0.00 1.82
206 515 8.572855 AACAATACTCCTAAACTCGTACTACT 57.427 34.615 0.00 0.00 0.00 2.57
207 516 9.672673 AACAATACTCCTAAACTCGTACTACTA 57.327 33.333 0.00 0.00 0.00 1.82
208 517 9.103861 ACAATACTCCTAAACTCGTACTACTAC 57.896 37.037 0.00 0.00 0.00 2.73
209 518 9.323985 CAATACTCCTAAACTCGTACTACTACT 57.676 37.037 0.00 0.00 0.00 2.57
211 520 9.974980 ATACTCCTAAACTCGTACTACTACTAC 57.025 37.037 0.00 0.00 0.00 2.73
212 521 8.073467 ACTCCTAAACTCGTACTACTACTACT 57.927 38.462 0.00 0.00 0.00 2.57
213 522 9.191479 ACTCCTAAACTCGTACTACTACTACTA 57.809 37.037 0.00 0.00 0.00 1.82
214 523 9.458374 CTCCTAAACTCGTACTACTACTACTAC 57.542 40.741 0.00 0.00 0.00 2.73
215 524 9.191479 TCCTAAACTCGTACTACTACTACTACT 57.809 37.037 0.00 0.00 0.00 2.57
220 529 8.161699 ACTCGTACTACTACTACTACTACTCC 57.838 42.308 0.00 0.00 0.00 3.85
222 531 9.496873 CTCGTACTACTACTACTACTACTCCTA 57.503 40.741 0.00 0.00 0.00 2.94
223 532 9.275398 TCGTACTACTACTACTACTACTCCTAC 57.725 40.741 0.00 0.00 0.00 3.18
224 533 8.225107 CGTACTACTACTACTACTACTCCTACG 58.775 44.444 0.00 0.00 0.00 3.51
225 534 9.059260 GTACTACTACTACTACTACTCCTACGT 57.941 40.741 0.00 0.00 0.00 3.57
227 536 9.059260 ACTACTACTACTACTACTCCTACGTAC 57.941 40.741 0.00 0.00 0.00 3.67
238 547 8.294954 ACTACTCCTACGTACTACTTACTGTA 57.705 38.462 0.00 0.00 0.00 2.74
239 548 8.919145 ACTACTCCTACGTACTACTTACTGTAT 58.081 37.037 0.00 0.00 0.00 2.29
240 549 9.190858 CTACTCCTACGTACTACTTACTGTATG 57.809 40.741 0.00 0.00 0.00 2.39
241 550 7.560368 ACTCCTACGTACTACTTACTGTATGT 58.440 38.462 10.65 10.65 40.59 2.29
243 552 7.786030 TCCTACGTACTACTTACTGTATGTCT 58.214 38.462 9.33 0.84 39.01 3.41
247 661 8.954950 ACGTACTACTTACTGTATGTCTGTAT 57.045 34.615 9.33 0.80 34.86 2.29
345 759 4.819783 CCAGTGGCTGGCTGTTTA 57.180 55.556 0.00 0.00 45.13 2.01
400 821 3.319198 CTGGTGGGCCCGTACAGT 61.319 66.667 24.49 0.00 35.15 3.55
401 822 1.985662 CTGGTGGGCCCGTACAGTA 60.986 63.158 24.49 1.92 35.15 2.74
403 824 2.285024 GGTGGGCCCGTACAGTACA 61.285 63.158 19.37 0.00 0.00 2.90
404 825 1.217244 GTGGGCCCGTACAGTACAG 59.783 63.158 19.37 0.00 0.00 2.74
405 826 1.985662 TGGGCCCGTACAGTACAGG 60.986 63.158 19.37 9.91 0.00 4.00
406 827 1.683365 GGGCCCGTACAGTACAGGA 60.683 63.158 16.22 0.00 0.00 3.86
427 848 1.743772 CGTTCCTTCCTAGTGCATGGG 60.744 57.143 0.00 0.00 0.00 4.00
429 850 1.524621 CCTTCCTAGTGCATGGGCG 60.525 63.158 0.00 0.00 45.35 6.13
439 860 2.202797 CATGGGCGTCTCGGACTG 60.203 66.667 0.00 0.00 0.00 3.51
440 861 4.148825 ATGGGCGTCTCGGACTGC 62.149 66.667 0.00 10.14 33.75 4.40
548 1015 0.179111 TGCACGACTGCTATGCCTAC 60.179 55.000 0.00 0.00 44.57 3.18
549 1016 1.209275 GCACGACTGCTATGCCTACG 61.209 60.000 0.00 0.00 40.63 3.51
550 1017 0.380733 CACGACTGCTATGCCTACGA 59.619 55.000 0.00 0.00 0.00 3.43
551 1018 0.381089 ACGACTGCTATGCCTACGAC 59.619 55.000 0.00 0.00 0.00 4.34
552 1019 0.663688 CGACTGCTATGCCTACGACT 59.336 55.000 0.00 0.00 0.00 4.18
553 1020 1.871676 CGACTGCTATGCCTACGACTA 59.128 52.381 0.00 0.00 0.00 2.59
554 1021 2.349627 CGACTGCTATGCCTACGACTAC 60.350 54.545 0.00 0.00 0.00 2.73
562 1029 0.936600 GCCTACGACTACGAGGACTC 59.063 60.000 0.00 0.00 42.66 3.36
564 1031 2.472816 CCTACGACTACGAGGACTCTC 58.527 57.143 0.00 0.00 42.66 3.20
624 1094 1.377536 TTCCGTTTCCGTTTCCGTTT 58.622 45.000 0.00 0.00 0.00 3.60
625 1095 0.936600 TCCGTTTCCGTTTCCGTTTC 59.063 50.000 0.00 0.00 0.00 2.78
626 1096 0.041047 CCGTTTCCGTTTCCGTTTCC 60.041 55.000 0.00 0.00 0.00 3.13
627 1097 0.383368 CGTTTCCGTTTCCGTTTCCG 60.383 55.000 0.00 0.00 0.00 4.30
628 1098 0.657312 GTTTCCGTTTCCGTTTCCGT 59.343 50.000 0.00 0.00 0.00 4.69
629 1099 1.063912 GTTTCCGTTTCCGTTTCCGTT 59.936 47.619 0.00 0.00 0.00 4.44
630 1100 0.936600 TTCCGTTTCCGTTTCCGTTC 59.063 50.000 0.00 0.00 0.00 3.95
631 1101 1.202320 CCGTTTCCGTTTCCGTTCG 59.798 57.895 0.00 0.00 0.00 3.95
632 1102 1.489881 CCGTTTCCGTTTCCGTTCGT 61.490 55.000 0.00 0.00 0.00 3.85
633 1103 0.111574 CGTTTCCGTTTCCGTTCGTC 60.112 55.000 0.00 0.00 0.00 4.20
673 1143 2.236644 TCCCATCCCAACGAACGAAATA 59.763 45.455 0.14 0.00 0.00 1.40
703 1173 5.574055 ACATGACGCAAACATGATTGAATTC 59.426 36.000 18.88 11.06 45.22 2.17
751 1221 1.865970 CTCCACTAGCGACCTACTACG 59.134 57.143 0.00 0.00 0.00 3.51
788 1567 4.957327 ACTCCTACTACTAAAGCAGAAGGG 59.043 45.833 0.00 0.00 0.00 3.95
789 1568 4.287552 TCCTACTACTAAAGCAGAAGGGG 58.712 47.826 0.00 0.00 0.00 4.79
815 1603 6.071840 GCATAGGAGGGAATACAGTACAGTAG 60.072 46.154 4.36 0.00 0.00 2.57
816 1604 5.728937 AGGAGGGAATACAGTACAGTAGA 57.271 43.478 4.36 0.00 0.00 2.59
817 1605 5.697067 AGGAGGGAATACAGTACAGTAGAG 58.303 45.833 4.36 0.00 0.00 2.43
818 1606 5.194132 AGGAGGGAATACAGTACAGTAGAGT 59.806 44.000 4.36 0.00 0.00 3.24
930 1797 1.286257 GCTTCATTCCCTCCCTTCCTT 59.714 52.381 0.00 0.00 0.00 3.36
931 1798 2.685224 GCTTCATTCCCTCCCTTCCTTC 60.685 54.545 0.00 0.00 0.00 3.46
932 1799 1.596496 TCATTCCCTCCCTTCCTTCC 58.404 55.000 0.00 0.00 0.00 3.46
933 1800 1.082879 TCATTCCCTCCCTTCCTTCCT 59.917 52.381 0.00 0.00 0.00 3.36
934 1801 2.320986 TCATTCCCTCCCTTCCTTCCTA 59.679 50.000 0.00 0.00 0.00 2.94
935 1802 2.265526 TTCCCTCCCTTCCTTCCTAC 57.734 55.000 0.00 0.00 0.00 3.18
961 1828 2.182537 GCCCTCTGCAAAATGCCG 59.817 61.111 0.00 0.00 44.23 5.69
1003 1870 0.958876 GGTTAGTCGCCAAACCCCAG 60.959 60.000 2.29 0.00 39.43 4.45
1005 1872 0.035739 TTAGTCGCCAAACCCCAGAC 59.964 55.000 0.00 0.00 0.00 3.51
1019 1886 1.403687 CCAGACCGATTCCTCCTCCC 61.404 65.000 0.00 0.00 0.00 4.30
1020 1887 1.075151 AGACCGATTCCTCCTCCCC 60.075 63.158 0.00 0.00 0.00 4.81
1021 1888 2.444140 ACCGATTCCTCCTCCCCG 60.444 66.667 0.00 0.00 0.00 5.73
1022 1889 2.444140 CCGATTCCTCCTCCCCGT 60.444 66.667 0.00 0.00 0.00 5.28
1023 1890 2.797278 CCGATTCCTCCTCCCCGTG 61.797 68.421 0.00 0.00 0.00 4.94
1024 1891 2.506472 GATTCCTCCTCCCCGTGC 59.494 66.667 0.00 0.00 0.00 5.34
1025 1892 3.090532 ATTCCTCCTCCCCGTGCC 61.091 66.667 0.00 0.00 0.00 5.01
1060 1927 3.110178 GTGCCTGCACGTACGTCC 61.110 66.667 19.94 10.90 37.19 4.79
1061 1928 3.607661 TGCCTGCACGTACGTCCA 61.608 61.111 19.94 15.88 0.00 4.02
1064 1931 2.803670 CTGCACGTACGTCCACCG 60.804 66.667 19.94 8.20 44.03 4.94
1076 1943 4.077184 CCACCGCCCGACTGCTTA 62.077 66.667 0.00 0.00 0.00 3.09
1077 1944 2.509336 CACCGCCCGACTGCTTAG 60.509 66.667 0.00 0.00 0.00 2.18
1078 1945 2.995574 ACCGCCCGACTGCTTAGT 60.996 61.111 0.00 0.00 0.00 2.24
1444 2311 4.555709 TGCGTGGTGGGCGTCTTT 62.556 61.111 0.00 0.00 0.00 2.52
1867 2734 4.137872 TTCCACGCGATCGACCCC 62.138 66.667 21.57 0.00 39.41 4.95
1937 2804 1.142748 GAGACGAGGCTGTGGATGG 59.857 63.158 0.00 0.00 0.00 3.51
1938 2805 1.305297 AGACGAGGCTGTGGATGGA 60.305 57.895 0.00 0.00 0.00 3.41
1939 2806 1.153549 GACGAGGCTGTGGATGGAC 60.154 63.158 0.00 0.00 0.00 4.02
1990 2857 1.222115 AAAGCGACAAGGAGCACGAC 61.222 55.000 0.00 0.00 35.48 4.34
2071 2938 0.747283 GGTTCTGCCTGCTCATCCAG 60.747 60.000 0.00 0.00 0.00 3.86
2083 2950 0.043183 TCATCCAGGGCTTCAGGAGA 59.957 55.000 0.00 0.00 34.40 3.71
2127 3001 1.004745 ACATTCCGCCACAGGATTTCT 59.995 47.619 0.00 0.00 40.48 2.52
2128 3002 2.094675 CATTCCGCCACAGGATTTCTT 58.905 47.619 0.00 0.00 40.48 2.52
2129 3003 1.821216 TTCCGCCACAGGATTTCTTC 58.179 50.000 0.00 0.00 40.48 2.87
2137 3011 3.445096 CCACAGGATTTCTTCACCAATCC 59.555 47.826 3.14 3.14 46.29 3.01
2165 3039 2.427095 ACTTCTTCTTGGTTTGTGTGCC 59.573 45.455 0.00 0.00 0.00 5.01
2370 3262 4.275689 TGACTGTGAATGTGTTGTGGATTC 59.724 41.667 0.00 0.00 0.00 2.52
2383 3275 7.667635 TGTGTTGTGGATTCCAGAAATATACAA 59.332 33.333 16.22 6.89 38.50 2.41
2407 3305 7.440523 AACAAAGGTTGCAACATTTTGTTTA 57.559 28.000 38.30 6.75 45.36 2.01
2471 3372 4.343526 TGTTTGAGCATGTTTGTATGGGTT 59.656 37.500 0.00 0.00 0.00 4.11
2491 3392 2.580962 TGTGTAAGCTGATTTGCACCA 58.419 42.857 2.48 0.00 41.24 4.17
2503 3404 2.430546 TTGCACCATTAAAACCGCAG 57.569 45.000 0.00 0.00 0.00 5.18
2522 3423 2.352651 CAGTATTTGGGATGCTGACACG 59.647 50.000 0.00 0.00 34.33 4.49
2523 3424 1.064060 GTATTTGGGATGCTGACACGC 59.936 52.381 0.00 0.00 0.00 5.34
2524 3425 0.608856 ATTTGGGATGCTGACACGCA 60.609 50.000 2.70 2.70 45.10 5.24
2525 3426 0.821301 TTTGGGATGCTGACACGCAA 60.821 50.000 4.12 0.00 44.06 4.85
2526 3427 1.236616 TTGGGATGCTGACACGCAAG 61.237 55.000 4.12 0.00 44.06 4.01
2527 3428 1.375908 GGGATGCTGACACGCAAGA 60.376 57.895 4.12 0.00 44.06 3.02
2656 3563 1.739929 CCGCGCACACAACCATAGA 60.740 57.895 8.75 0.00 0.00 1.98
2684 3591 2.852413 CGACGTCGATTGTGAGCTTTAT 59.148 45.455 33.35 0.00 43.02 1.40
2685 3592 4.033019 CGACGTCGATTGTGAGCTTTATA 58.967 43.478 33.35 0.00 43.02 0.98
2758 3665 1.545651 GGGCCCCTCTCAATTATTCCG 60.546 57.143 12.23 0.00 0.00 4.30
2777 3684 0.107945 GGGACATGACTGCCACTCTC 60.108 60.000 0.00 0.00 0.00 3.20
2779 3686 1.674221 GGACATGACTGCCACTCTCAC 60.674 57.143 0.00 0.00 0.00 3.51
2826 3733 4.344679 AGAAGCAAATGAAACATGGTCCAA 59.655 37.500 0.00 0.00 0.00 3.53
2833 3740 3.142951 TGAAACATGGTCCAACCTTACG 58.857 45.455 0.00 0.00 39.58 3.18
2887 3815 7.713073 GTGGGATTCTGAAAAACAAAACCAATA 59.287 33.333 0.00 0.00 0.00 1.90
2964 3913 3.494626 GCATAAATTCAGGATTCGCTCGA 59.505 43.478 0.00 0.00 0.00 4.04
3081 4041 3.455469 GCCATTCACCTGCCTGCC 61.455 66.667 0.00 0.00 0.00 4.85
3107 4067 4.081420 AGGTCAACATGTTAGGCTAGTGAG 60.081 45.833 11.53 0.00 0.00 3.51
3164 4126 5.479306 GGATTCACAGTAGCACAAGAGTAA 58.521 41.667 0.00 0.00 0.00 2.24
3166 4128 3.897325 TCACAGTAGCACAAGAGTAACG 58.103 45.455 0.00 0.00 0.00 3.18
3167 4129 2.987149 CACAGTAGCACAAGAGTAACGG 59.013 50.000 0.00 0.00 0.00 4.44
3174 4136 2.866460 GCACAAGAGTAACGGCTTCAGA 60.866 50.000 0.00 0.00 0.00 3.27
3179 4141 3.067833 AGAGTAACGGCTTCAGAAAAGC 58.932 45.455 1.16 1.16 42.30 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.437862 GGACACAGCAAGAAATCATTACAAAAA 59.562 33.333 0.00 0.00 0.00 1.94
29 30 3.185188 CGTGATGGAATGAATGATCGGAC 59.815 47.826 0.00 0.00 0.00 4.79
89 91 2.989422 CACAAACTCCGTGGATTTCC 57.011 50.000 0.00 0.00 0.00 3.13
166 475 3.091022 GTTTTGGCGCACGCGAAG 61.091 61.111 15.93 5.94 39.76 3.79
183 492 9.323985 AGTAGTAGTACGAGTTTAGGAGTATTG 57.676 37.037 2.04 0.00 33.97 1.90
194 503 8.626526 GGAGTAGTAGTAGTAGTAGTACGAGTT 58.373 40.741 18.28 6.73 39.29 3.01
196 505 8.391075 AGGAGTAGTAGTAGTAGTAGTACGAG 57.609 42.308 18.28 0.00 39.29 4.18
197 506 9.275398 GTAGGAGTAGTAGTAGTAGTAGTACGA 57.725 40.741 18.28 8.56 39.29 3.43
199 508 9.059260 ACGTAGGAGTAGTAGTAGTAGTAGTAC 57.941 40.741 17.28 17.28 35.87 2.73
201 510 9.059260 GTACGTAGGAGTAGTAGTAGTAGTAGT 57.941 40.741 0.00 0.12 0.00 2.73
202 511 9.280174 AGTACGTAGGAGTAGTAGTAGTAGTAG 57.720 40.741 0.00 0.00 0.00 2.57
204 513 9.059260 GTAGTACGTAGGAGTAGTAGTAGTAGT 57.941 40.741 0.00 0.00 34.33 2.73
206 515 9.629878 AAGTAGTACGTAGGAGTAGTAGTAGTA 57.370 37.037 0.00 0.00 35.97 1.82
207 516 8.528044 AAGTAGTACGTAGGAGTAGTAGTAGT 57.472 38.462 0.00 0.00 35.97 2.73
208 517 9.887406 GTAAGTAGTACGTAGGAGTAGTAGTAG 57.113 40.741 0.00 0.00 35.97 2.57
209 518 9.629878 AGTAAGTAGTACGTAGGAGTAGTAGTA 57.370 37.037 0.00 0.00 35.97 1.82
211 520 8.410141 ACAGTAAGTAGTACGTAGGAGTAGTAG 58.590 40.741 0.00 0.00 37.81 2.57
212 521 8.294954 ACAGTAAGTAGTACGTAGGAGTAGTA 57.705 38.462 0.00 0.00 37.81 1.82
213 522 7.176589 ACAGTAAGTAGTACGTAGGAGTAGT 57.823 40.000 0.00 0.00 37.81 2.73
214 523 9.190858 CATACAGTAAGTAGTACGTAGGAGTAG 57.809 40.741 0.00 0.00 37.81 2.57
215 524 8.696374 ACATACAGTAAGTAGTACGTAGGAGTA 58.304 37.037 0.00 1.75 37.81 2.59
216 525 7.560368 ACATACAGTAAGTAGTACGTAGGAGT 58.440 38.462 0.00 0.00 37.81 3.85
217 526 7.925483 AGACATACAGTAAGTAGTACGTAGGAG 59.075 40.741 0.00 0.00 37.81 3.69
218 527 7.708322 CAGACATACAGTAAGTAGTACGTAGGA 59.292 40.741 0.00 0.00 37.81 2.94
219 528 7.493971 ACAGACATACAGTAAGTAGTACGTAGG 59.506 40.741 0.00 0.00 37.81 3.18
220 529 8.417780 ACAGACATACAGTAAGTAGTACGTAG 57.582 38.462 0.00 0.00 37.81 3.51
222 531 8.954950 ATACAGACATACAGTAAGTAGTACGT 57.045 34.615 0.00 0.00 37.81 3.57
239 548 8.397906 GCTTTGCAGATTTTGTATATACAGACA 58.602 33.333 14.96 4.73 37.52 3.41
240 549 7.857885 GGCTTTGCAGATTTTGTATATACAGAC 59.142 37.037 14.96 8.54 37.52 3.51
241 550 7.013274 GGGCTTTGCAGATTTTGTATATACAGA 59.987 37.037 14.96 8.73 37.52 3.41
243 552 6.238621 CGGGCTTTGCAGATTTTGTATATACA 60.239 38.462 11.62 11.62 0.00 2.29
247 661 3.181491 GCGGGCTTTGCAGATTTTGTATA 60.181 43.478 0.00 0.00 0.00 1.47
342 756 1.663695 GGCCATGCGCTACTCTTAAA 58.336 50.000 9.73 0.00 37.74 1.52
343 757 0.529773 CGGCCATGCGCTACTCTTAA 60.530 55.000 9.73 0.00 37.74 1.85
345 759 2.202932 CGGCCATGCGCTACTCTT 60.203 61.111 9.73 0.00 37.74 2.85
372 793 1.914764 CCCACCAGCCAAGGCAAAT 60.915 57.895 14.40 0.00 44.88 2.32
405 826 2.271800 CATGCACTAGGAAGGAACGTC 58.728 52.381 0.00 0.00 35.71 4.34
406 827 1.066143 CCATGCACTAGGAAGGAACGT 60.066 52.381 0.00 0.00 0.00 3.99
427 848 4.838486 CCGAGCAGTCCGAGACGC 62.838 72.222 10.43 10.43 37.67 5.19
429 850 3.444805 AGCCGAGCAGTCCGAGAC 61.445 66.667 0.00 0.00 0.00 3.36
439 860 3.322318 AAAGAGAGGGCAGCCGAGC 62.322 63.158 5.00 0.00 0.00 5.03
440 861 1.153469 GAAAGAGAGGGCAGCCGAG 60.153 63.158 5.00 0.00 0.00 4.63
532 999 0.381089 GTCGTAGGCATAGCAGTCGT 59.619 55.000 0.00 0.00 0.00 4.34
533 1000 0.663688 AGTCGTAGGCATAGCAGTCG 59.336 55.000 0.00 0.00 0.00 4.18
569 1036 3.067684 ACATGGGTAAACGGAAGGAAG 57.932 47.619 0.00 0.00 0.00 3.46
624 1094 3.884581 CTGCGAACGGACGAACGGA 62.885 63.158 7.62 4.24 38.39 4.69
625 1095 3.467119 CTGCGAACGGACGAACGG 61.467 66.667 7.62 0.49 38.39 4.44
626 1096 2.297912 AACTGCGAACGGACGAACG 61.298 57.895 7.62 4.95 40.31 3.95
627 1097 1.200839 CAACTGCGAACGGACGAAC 59.799 57.895 7.62 0.00 35.09 3.95
628 1098 1.952133 CCAACTGCGAACGGACGAA 60.952 57.895 7.62 0.00 35.09 3.85
629 1099 2.352704 TTCCAACTGCGAACGGACGA 62.353 55.000 7.62 0.00 35.09 4.20
630 1100 1.886861 CTTCCAACTGCGAACGGACG 61.887 60.000 0.00 0.00 0.00 4.79
631 1101 1.860078 CTTCCAACTGCGAACGGAC 59.140 57.895 0.00 0.00 0.00 4.79
632 1102 1.959226 GCTTCCAACTGCGAACGGA 60.959 57.895 0.00 0.00 0.00 4.69
633 1103 2.556287 GCTTCCAACTGCGAACGG 59.444 61.111 0.00 0.00 0.00 4.44
673 1143 3.314913 TCATGTTTGCGTCATGTTCTTGT 59.685 39.130 12.76 0.00 42.03 3.16
714 1184 1.463444 GGAGAACAAATTCGACGGGTG 59.537 52.381 0.00 0.00 40.04 4.61
718 1188 3.060895 GCTAGTGGAGAACAAATTCGACG 59.939 47.826 0.00 0.00 40.04 5.12
719 1189 3.060895 CGCTAGTGGAGAACAAATTCGAC 59.939 47.826 0.00 0.00 40.04 4.20
788 1567 2.339769 ACTGTATTCCCTCCTATGCCC 58.660 52.381 0.00 0.00 0.00 5.36
789 1568 3.901844 TGTACTGTATTCCCTCCTATGCC 59.098 47.826 0.00 0.00 0.00 4.40
815 1603 3.197333 GGTTTCCCCTCCAACTACTACTC 59.803 52.174 0.00 0.00 0.00 2.59
816 1604 3.179685 GGTTTCCCCTCCAACTACTACT 58.820 50.000 0.00 0.00 0.00 2.57
817 1605 3.623906 GGTTTCCCCTCCAACTACTAC 57.376 52.381 0.00 0.00 0.00 2.73
932 1799 4.208686 GAGGGCGACGGGCAGTAG 62.209 72.222 0.00 0.00 46.16 2.57
933 1800 4.753662 AGAGGGCGACGGGCAGTA 62.754 66.667 0.00 0.00 46.16 2.74
1003 1870 2.499827 CGGGGAGGAGGAATCGGTC 61.500 68.421 0.00 0.00 0.00 4.79
1005 1872 2.444140 ACGGGGAGGAGGAATCGG 60.444 66.667 0.00 0.00 0.00 4.18
1059 1926 4.077184 TAAGCAGTCGGGCGGTGG 62.077 66.667 0.00 0.00 39.27 4.61
1060 1927 2.509336 CTAAGCAGTCGGGCGGTG 60.509 66.667 0.00 0.00 39.27 4.94
1061 1928 2.995574 ACTAAGCAGTCGGGCGGT 60.996 61.111 0.00 0.00 39.27 5.68
1064 1931 2.820037 GCCACTAAGCAGTCGGGC 60.820 66.667 0.00 0.00 36.87 6.13
1065 1932 2.662596 TGCCACTAAGCAGTCGGG 59.337 61.111 0.00 0.00 38.00 5.14
1072 1939 1.065126 AGGTCCTTCATGCCACTAAGC 60.065 52.381 0.00 0.00 0.00 3.09
1075 1942 0.911769 CCAGGTCCTTCATGCCACTA 59.088 55.000 0.00 0.00 0.00 2.74
1076 1943 1.136329 ACCAGGTCCTTCATGCCACT 61.136 55.000 0.00 0.00 0.00 4.00
1077 1944 0.962356 CACCAGGTCCTTCATGCCAC 60.962 60.000 0.00 0.00 0.00 5.01
1078 1945 1.379916 CACCAGGTCCTTCATGCCA 59.620 57.895 0.00 0.00 0.00 4.92
1531 2398 4.521062 ATGTCGCCGAGCAGGAGC 62.521 66.667 2.12 0.00 45.00 4.70
1867 2734 3.522731 CTGGACGAGGAGGCGGAG 61.523 72.222 0.00 0.00 35.12 4.63
1972 2839 1.664965 GTCGTGCTCCTTGTCGCTT 60.665 57.895 0.00 0.00 0.00 4.68
2083 2950 2.122768 GATCAGGTGGTCTTGGAGGAT 58.877 52.381 0.00 0.00 0.00 3.24
2094 2961 2.826428 CGGAATGTACAGATCAGGTGG 58.174 52.381 0.33 0.00 0.00 4.61
2127 3001 4.714632 AGAAGTCGAAAAGGATTGGTGAA 58.285 39.130 0.00 0.00 0.00 3.18
2128 3002 4.351874 AGAAGTCGAAAAGGATTGGTGA 57.648 40.909 0.00 0.00 0.00 4.02
2129 3003 4.757149 AGAAGAAGTCGAAAAGGATTGGTG 59.243 41.667 0.00 0.00 0.00 4.17
2137 3011 5.739161 CACAAACCAAGAAGAAGTCGAAAAG 59.261 40.000 0.00 0.00 0.00 2.27
2165 3039 6.095440 ACATCGACCCTAAATTTCATTTCCAG 59.905 38.462 0.00 0.00 33.82 3.86
2183 3057 5.980116 AGCATCAATCAGTAAGTACATCGAC 59.020 40.000 0.00 0.00 0.00 4.20
2185 3059 5.176406 CCAGCATCAATCAGTAAGTACATCG 59.824 44.000 0.00 0.00 0.00 3.84
2370 3262 7.151308 TGCAACCTTTGTTTGTATATTTCTGG 58.849 34.615 0.00 0.00 30.42 3.86
2383 3275 5.956068 AACAAAATGTTGCAACCTTTGTT 57.044 30.435 36.86 36.86 42.61 2.83
2407 3305 4.119136 CAATGAAAAGGAGCAAACGGTTT 58.881 39.130 0.00 0.00 0.00 3.27
2471 3372 2.580962 TGGTGCAAATCAGCTTACACA 58.419 42.857 0.00 0.00 43.32 3.72
2491 3392 5.681179 GCATCCCAAATACTGCGGTTTTAAT 60.681 40.000 1.99 0.00 0.00 1.40
2503 3404 1.064060 GCGTGTCAGCATCCCAAATAC 59.936 52.381 0.00 0.00 37.05 1.89
2522 3423 5.113502 ACTTGCTTGTTTATCACTCTTGC 57.886 39.130 0.00 0.00 0.00 4.01
2523 3424 8.559536 TCTTAACTTGCTTGTTTATCACTCTTG 58.440 33.333 0.72 0.00 0.00 3.02
2524 3425 8.677148 TCTTAACTTGCTTGTTTATCACTCTT 57.323 30.769 0.72 0.00 0.00 2.85
2525 3426 8.677148 TTCTTAACTTGCTTGTTTATCACTCT 57.323 30.769 0.72 0.00 0.00 3.24
2526 3427 9.730420 TTTTCTTAACTTGCTTGTTTATCACTC 57.270 29.630 0.72 0.00 0.00 3.51
2527 3428 9.516314 GTTTTCTTAACTTGCTTGTTTATCACT 57.484 29.630 0.72 0.00 0.00 3.41
2565 3472 1.528824 CATCTCCACCCGGCTTGAT 59.471 57.895 0.00 0.00 0.00 2.57
2656 3563 1.872234 CAATCGACGTCGGCGATGT 60.872 57.895 34.68 32.65 46.67 3.06
2685 3592 8.994429 TGATATGTCAAACACAAGTTTTGTTT 57.006 26.923 13.17 13.17 45.32 2.83
2737 3644 1.203063 GGAATAATTGAGAGGGGCCCC 60.203 57.143 35.90 35.90 0.00 5.80
2741 3648 2.054799 TCCCGGAATAATTGAGAGGGG 58.945 52.381 0.73 4.33 37.98 4.79
2758 3665 0.107945 GAGAGTGGCAGTCATGTCCC 60.108 60.000 23.46 2.77 0.00 4.46
2777 3684 1.320344 TGGGACCTCTCGGATTCGTG 61.320 60.000 0.00 0.00 37.69 4.35
2779 3686 0.535335 TTTGGGACCTCTCGGATTCG 59.465 55.000 0.00 0.00 37.82 3.34
2796 3703 6.927381 CCATGTTTCATTTGCTTCTTCTCTTT 59.073 34.615 0.00 0.00 0.00 2.52
2826 3733 3.576982 TCAGAATTCCACACTCGTAAGGT 59.423 43.478 0.65 0.00 38.47 3.50
2833 3740 6.738114 TGTTTCATTTCAGAATTCCACACTC 58.262 36.000 0.65 0.00 0.00 3.51
2899 3848 2.295909 TCCCCAAGTCTTTTTGCAATCG 59.704 45.455 0.00 0.00 0.00 3.34
2907 3856 4.077108 GGATAAACGTCCCCAAGTCTTTT 58.923 43.478 0.00 0.00 31.82 2.27
2964 3913 1.608283 GCCACTAGCGACTCTGGTTTT 60.608 52.381 0.00 0.00 33.93 2.43
3081 4041 5.003804 ACTAGCCTAACATGTTGACCTTTG 58.996 41.667 21.42 11.42 0.00 2.77
3107 4067 4.505808 GGTTAGTTGGGCTAGTTCTCTTC 58.494 47.826 0.00 0.00 0.00 2.87
3153 4115 1.461127 CTGAAGCCGTTACTCTTGTGC 59.539 52.381 0.00 0.00 0.00 4.57
3167 4129 3.342377 ACTAGGAGGCTTTTCTGAAGC 57.658 47.619 2.27 2.27 42.30 3.86


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

AutoCloner maintained by Alex Coulton.