Multiple sequence alignment - TraesCS3A01G139700

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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 TraesCS3A01G139700 chr3A 100.000 2654 0 0 1 2654 118547823 118545170 0.000000e+00 4902
1 TraesCS3A01G139700 chr3B 98.309 769 11 2 1831 2599 8511669 8510903 0.000000e+00 1347
2 TraesCS3A01G139700 chr3B 89.278 970 68 14 851 1812 162639058 162639999 0.000000e+00 1182
3 TraesCS3A01G139700 chr3B 84.337 332 48 3 1057 1384 162688564 162688895 3.300000e-84 322
4 TraesCS3A01G139700 chr3B 91.855 221 15 2 398 617 162638364 162638582 3.320000e-79 305
5 TraesCS3A01G139700 chr3B 88.306 248 22 6 153 396 162637960 162638204 9.290000e-75 291
6 TraesCS3A01G139700 chr3B 100.000 66 0 0 2589 2654 8510934 8510869 3.590000e-24 122
7 TraesCS3A01G139700 chr3D 88.911 983 60 16 851 1813 111955941 111956894 0.000000e+00 1166
8 TraesCS3A01G139700 chr3D 84.135 416 58 6 1057 1465 111963824 111964238 1.910000e-106 396
9 TraesCS3A01G139700 chr3D 88.983 236 19 3 382 617 111955226 111955454 4.320000e-73 285
10 TraesCS3A01G139700 chr3D 90.789 76 6 1 286 360 111955152 111955227 1.680000e-17 100
11 TraesCS3A01G139700 chr1A 86.532 839 83 16 1831 2654 12171799 12172622 0.000000e+00 896
12 TraesCS3A01G139700 chr5B 84.798 842 72 22 1832 2654 325690400 325691204 0.000000e+00 795
13 TraesCS3A01G139700 chr5B 88.028 426 41 5 2238 2654 325786550 325786974 1.830000e-136 496
14 TraesCS3A01G139700 chr6A 84.086 842 84 26 1828 2654 50251217 50252023 0.000000e+00 767
15 TraesCS3A01G139700 chr6A 83.967 842 83 27 1829 2653 50867092 50867898 0.000000e+00 760
16 TraesCS3A01G139700 chr7B 97.297 444 12 0 2211 2654 39927280 39926837 0.000000e+00 754
17 TraesCS3A01G139700 chr7B 98.477 394 5 1 1831 2224 39929298 39928906 0.000000e+00 693


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 TraesCS3A01G139700 chr3A 118545170 118547823 2653 True 4902.000000 4902 100.0000 1 2654 1 chr3A.!!$R1 2653
1 TraesCS3A01G139700 chr3B 8510869 8511669 800 True 734.500000 1347 99.1545 1831 2654 2 chr3B.!!$R1 823
2 TraesCS3A01G139700 chr3B 162637960 162639999 2039 False 592.666667 1182 89.8130 153 1812 3 chr3B.!!$F2 1659
3 TraesCS3A01G139700 chr3D 111955152 111956894 1742 False 517.000000 1166 89.5610 286 1813 3 chr3D.!!$F2 1527
4 TraesCS3A01G139700 chr1A 12171799 12172622 823 False 896.000000 896 86.5320 1831 2654 1 chr1A.!!$F1 823
5 TraesCS3A01G139700 chr5B 325690400 325691204 804 False 795.000000 795 84.7980 1832 2654 1 chr5B.!!$F1 822
6 TraesCS3A01G139700 chr6A 50251217 50252023 806 False 767.000000 767 84.0860 1828 2654 1 chr6A.!!$F1 826
7 TraesCS3A01G139700 chr6A 50867092 50867898 806 False 760.000000 760 83.9670 1829 2653 1 chr6A.!!$F2 824
8 TraesCS3A01G139700 chr7B 39926837 39929298 2461 True 723.500000 754 97.8870 1831 2654 2 chr7B.!!$R1 823

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
135 136 0.036671 AAATCTTGACCCGACCGACC 60.037 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1821 2318 0.597637 CCGAGCGTTCGCCTATGAAT 60.598 55.0 16.81 0.0 45.38 2.57 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
27 28 9.034544 AGGAGTTTGAATTTTCTTTTCGATTTG 57.965 29.630 0.00 0.00 0.00 2.32
28 29 8.275632 GGAGTTTGAATTTTCTTTTCGATTTGG 58.724 33.333 0.00 0.00 0.00 3.28
29 30 8.940768 AGTTTGAATTTTCTTTTCGATTTGGA 57.059 26.923 0.00 0.00 0.00 3.53
30 31 9.377312 AGTTTGAATTTTCTTTTCGATTTGGAA 57.623 25.926 0.00 0.00 0.00 3.53
31 32 9.980780 GTTTGAATTTTCTTTTCGATTTGGAAA 57.019 25.926 0.00 0.00 34.28 3.13
37 38 9.986833 ATTTTCTTTTCGATTTGGAAAAAGTTG 57.013 25.926 14.93 0.00 43.20 3.16
38 39 8.764524 TTTCTTTTCGATTTGGAAAAAGTTGA 57.235 26.923 6.68 0.00 43.20 3.18
39 40 8.940768 TTCTTTTCGATTTGGAAAAAGTTGAT 57.059 26.923 6.68 0.00 43.20 2.57
40 41 8.351495 TCTTTTCGATTTGGAAAAAGTTGATG 57.649 30.769 6.68 0.00 43.20 3.07
41 42 7.437862 TCTTTTCGATTTGGAAAAAGTTGATGG 59.562 33.333 6.68 0.00 43.20 3.51
42 43 6.398234 TTCGATTTGGAAAAAGTTGATGGA 57.602 33.333 0.00 0.00 0.00 3.41
43 44 6.588719 TCGATTTGGAAAAAGTTGATGGAT 57.411 33.333 0.00 0.00 0.00 3.41
44 45 7.695480 TCGATTTGGAAAAAGTTGATGGATA 57.305 32.000 0.00 0.00 0.00 2.59
45 46 8.292444 TCGATTTGGAAAAAGTTGATGGATAT 57.708 30.769 0.00 0.00 0.00 1.63
46 47 8.190122 TCGATTTGGAAAAAGTTGATGGATATG 58.810 33.333 0.00 0.00 0.00 1.78
47 48 8.190122 CGATTTGGAAAAAGTTGATGGATATGA 58.810 33.333 0.00 0.00 0.00 2.15
48 49 9.874205 GATTTGGAAAAAGTTGATGGATATGAA 57.126 29.630 0.00 0.00 0.00 2.57
93 94 9.733556 AAAAAGTTTATGGTTTCAAAGAAAGGT 57.266 25.926 0.00 0.00 0.00 3.50
94 95 9.733556 AAAAGTTTATGGTTTCAAAGAAAGGTT 57.266 25.926 0.00 0.00 0.00 3.50
95 96 8.942338 AAGTTTATGGTTTCAAAGAAAGGTTC 57.058 30.769 0.00 0.00 0.00 3.62
96 97 8.073467 AGTTTATGGTTTCAAAGAAAGGTTCA 57.927 30.769 0.00 0.00 0.00 3.18
97 98 8.197439 AGTTTATGGTTTCAAAGAAAGGTTCAG 58.803 33.333 0.00 0.00 0.00 3.02
98 99 7.889873 TTATGGTTTCAAAGAAAGGTTCAGA 57.110 32.000 0.00 0.00 0.00 3.27
99 100 6.983906 ATGGTTTCAAAGAAAGGTTCAGAT 57.016 33.333 0.00 0.00 0.00 2.90
100 101 9.581289 TTATGGTTTCAAAGAAAGGTTCAGATA 57.419 29.630 0.00 0.00 0.00 1.98
101 102 7.272037 TGGTTTCAAAGAAAGGTTCAGATAC 57.728 36.000 0.00 0.00 0.00 2.24
102 103 6.264518 TGGTTTCAAAGAAAGGTTCAGATACC 59.735 38.462 0.00 0.00 38.53 2.73
112 113 5.957771 AGGTTCAGATACCTAGATTGCAA 57.042 39.130 0.00 0.00 46.65 4.08
113 114 5.923204 AGGTTCAGATACCTAGATTGCAAG 58.077 41.667 4.94 0.00 46.65 4.01
114 115 5.663106 AGGTTCAGATACCTAGATTGCAAGA 59.337 40.000 4.94 0.00 46.65 3.02
115 116 6.156949 AGGTTCAGATACCTAGATTGCAAGAA 59.843 38.462 4.94 0.00 46.65 2.52
116 117 6.823689 GGTTCAGATACCTAGATTGCAAGAAA 59.176 38.462 4.94 0.00 35.23 2.52
117 118 7.336931 GGTTCAGATACCTAGATTGCAAGAAAA 59.663 37.037 4.94 0.00 35.23 2.29
118 119 8.730680 GTTCAGATACCTAGATTGCAAGAAAAA 58.269 33.333 4.94 0.00 0.00 1.94
119 120 9.466497 TTCAGATACCTAGATTGCAAGAAAAAT 57.534 29.630 4.94 0.00 0.00 1.82
120 121 9.113838 TCAGATACCTAGATTGCAAGAAAAATC 57.886 33.333 4.94 0.00 33.77 2.17
121 122 9.118300 CAGATACCTAGATTGCAAGAAAAATCT 57.882 33.333 4.94 4.18 43.71 2.40
122 123 9.692325 AGATACCTAGATTGCAAGAAAAATCTT 57.308 29.630 4.94 0.00 41.97 2.40
132 133 2.423577 AGAAAAATCTTGACCCGACCG 58.576 47.619 0.00 0.00 0.00 4.79
133 134 2.038033 AGAAAAATCTTGACCCGACCGA 59.962 45.455 0.00 0.00 0.00 4.69
134 135 1.804601 AAAATCTTGACCCGACCGAC 58.195 50.000 0.00 0.00 0.00 4.79
135 136 0.036671 AAATCTTGACCCGACCGACC 60.037 55.000 0.00 0.00 0.00 4.79
136 137 1.189524 AATCTTGACCCGACCGACCA 61.190 55.000 0.00 0.00 0.00 4.02
137 138 0.976073 ATCTTGACCCGACCGACCAT 60.976 55.000 0.00 0.00 0.00 3.55
138 139 1.189524 TCTTGACCCGACCGACCATT 61.190 55.000 0.00 0.00 0.00 3.16
139 140 0.321298 CTTGACCCGACCGACCATTT 60.321 55.000 0.00 0.00 0.00 2.32
140 141 0.320946 TTGACCCGACCGACCATTTC 60.321 55.000 0.00 0.00 0.00 2.17
141 142 1.294138 GACCCGACCGACCATTTCA 59.706 57.895 0.00 0.00 0.00 2.69
142 143 0.107848 GACCCGACCGACCATTTCAT 60.108 55.000 0.00 0.00 0.00 2.57
143 144 0.392461 ACCCGACCGACCATTTCATG 60.392 55.000 0.00 0.00 0.00 3.07
144 145 0.107897 CCCGACCGACCATTTCATGA 60.108 55.000 0.00 0.00 0.00 3.07
145 146 1.677518 CCCGACCGACCATTTCATGAA 60.678 52.381 3.38 3.38 0.00 2.57
146 147 2.080693 CCGACCGACCATTTCATGAAA 58.919 47.619 22.52 22.52 34.46 2.69
147 148 2.486203 CCGACCGACCATTTCATGAAAA 59.514 45.455 23.91 8.65 33.56 2.29
148 149 3.057876 CCGACCGACCATTTCATGAAAAA 60.058 43.478 23.91 3.45 33.56 1.94
149 150 4.380444 CCGACCGACCATTTCATGAAAAAT 60.380 41.667 23.91 12.59 33.56 1.82
150 151 5.163703 CCGACCGACCATTTCATGAAAAATA 60.164 40.000 23.91 2.26 33.56 1.40
151 152 5.965334 CGACCGACCATTTCATGAAAAATAG 59.035 40.000 23.91 14.70 33.56 1.73
186 187 9.183368 TGCATGTATTTCCTATGTAAATGTCAA 57.817 29.630 0.00 0.00 0.00 3.18
225 226 6.035217 TGCATTGATGATATGACCGTTTTTG 58.965 36.000 0.00 0.00 0.00 2.44
236 237 6.597832 ATGACCGTTTTTGATTATTTCCCA 57.402 33.333 0.00 0.00 0.00 4.37
276 277 8.870160 TTGAAAACATACTTTTCAGAACATGG 57.130 30.769 7.96 0.00 45.55 3.66
279 280 9.185192 GAAAACATACTTTTCAGAACATGGAAG 57.815 33.333 0.00 0.00 38.08 3.46
290 293 6.558009 TCAGAACATGGAAGTATACGTACAC 58.442 40.000 5.81 0.00 33.09 2.90
293 296 6.830324 AGAACATGGAAGTATACGTACACCTA 59.170 38.462 5.81 0.00 33.62 3.08
305 308 7.838771 ATACGTACACCTAATCAAAAAGTCC 57.161 36.000 0.00 0.00 0.00 3.85
324 327 5.575019 AGTCCACAACAACGACATAAAAAC 58.425 37.500 0.00 0.00 0.00 2.43
325 328 5.124138 AGTCCACAACAACGACATAAAAACA 59.876 36.000 0.00 0.00 0.00 2.83
362 366 3.382227 TGCAGGCAATTCCACATCATTAG 59.618 43.478 0.00 0.00 37.29 1.73
363 367 3.382546 GCAGGCAATTCCACATCATTAGT 59.617 43.478 0.00 0.00 37.29 2.24
480 642 7.254863 CCCTTCAACCTTCATTTTGAAAATGTG 60.255 37.037 24.86 17.23 40.36 3.21
505 667 0.444260 GCTAAGTTCGTGGCTCTTGC 59.556 55.000 0.00 0.00 38.76 4.01
506 668 1.795768 CTAAGTTCGTGGCTCTTGCA 58.204 50.000 0.00 0.00 41.91 4.08
556 719 9.547753 GCAATTGGAAATCTATTACTCTGTCTA 57.452 33.333 7.72 0.00 0.00 2.59
570 733 5.250200 ACTCTGTCTAGTAGGTCAACTCTG 58.750 45.833 0.00 0.00 0.00 3.35
574 737 6.654161 TCTGTCTAGTAGGTCAACTCTGTTAC 59.346 42.308 0.00 0.00 0.00 2.50
583 746 6.306987 AGGTCAACTCTGTTACCAATTGAAT 58.693 36.000 7.12 0.00 34.29 2.57
584 747 6.777580 AGGTCAACTCTGTTACCAATTGAATT 59.222 34.615 7.12 0.00 34.29 2.17
589 752 9.912634 CAACTCTGTTACCAATTGAATTATTGT 57.087 29.630 7.12 0.00 34.42 2.71
688 851 9.468532 AAAATCAGTTCAGCTAAAGAACATTTC 57.531 29.630 15.47 0.00 45.93 2.17
740 905 2.880822 GACATGTTGTCGACCACATG 57.119 50.000 39.96 39.96 43.80 3.21
758 923 5.180680 CCACATGACCACATCATCACATATC 59.819 44.000 0.00 0.00 45.52 1.63
796 961 5.125100 GCCAGCAGCATAAATAAGCAATA 57.875 39.130 0.00 0.00 42.97 1.90
832 997 9.679661 TTCAGTGCATTATTTAAAGGAGACATA 57.320 29.630 0.00 0.00 0.00 2.29
844 1009 1.528586 GGAGACATACGTGCATGATGC 59.471 52.381 14.17 11.12 45.29 3.91
859 1024 6.656314 GCATGATGCAATTTTCATCTCAAA 57.344 33.333 13.36 0.69 44.26 2.69
862 1027 8.181573 GCATGATGCAATTTTCATCTCAAAAAT 58.818 29.630 13.36 0.00 44.26 1.82
871 1036 6.409524 TTTCATCTCAAAAATTGCTGGAGT 57.590 33.333 0.00 0.00 0.00 3.85
872 1037 7.523293 TTTCATCTCAAAAATTGCTGGAGTA 57.477 32.000 0.00 0.00 0.00 2.59
873 1038 7.707624 TTCATCTCAAAAATTGCTGGAGTAT 57.292 32.000 0.00 0.00 0.00 2.12
874 1039 8.806429 TTCATCTCAAAAATTGCTGGAGTATA 57.194 30.769 0.00 0.00 0.00 1.47
907 1379 7.383029 CGAAATAGTCGGCATACATACCTAAAA 59.617 37.037 0.00 0.00 46.45 1.52
908 1380 7.958053 AATAGTCGGCATACATACCTAAAAC 57.042 36.000 0.00 0.00 0.00 2.43
909 1381 4.700700 AGTCGGCATACATACCTAAAACC 58.299 43.478 0.00 0.00 0.00 3.27
910 1382 4.407945 AGTCGGCATACATACCTAAAACCT 59.592 41.667 0.00 0.00 0.00 3.50
911 1383 5.599656 AGTCGGCATACATACCTAAAACCTA 59.400 40.000 0.00 0.00 0.00 3.08
912 1384 6.098695 AGTCGGCATACATACCTAAAACCTAA 59.901 38.462 0.00 0.00 0.00 2.69
913 1385 6.762661 GTCGGCATACATACCTAAAACCTAAA 59.237 38.462 0.00 0.00 0.00 1.85
925 1397 6.011981 ACCTAAAACCTAAATGATCTGTCCCA 60.012 38.462 0.00 0.00 0.00 4.37
938 1410 1.004044 CTGTCCCAGCAAGAGAACCAT 59.996 52.381 0.00 0.00 0.00 3.55
939 1411 1.003580 TGTCCCAGCAAGAGAACCATC 59.996 52.381 0.00 0.00 0.00 3.51
941 1413 0.329261 CCCAGCAAGAGAACCATCCA 59.671 55.000 0.00 0.00 0.00 3.41
942 1414 1.272092 CCCAGCAAGAGAACCATCCAA 60.272 52.381 0.00 0.00 0.00 3.53
967 1439 5.560722 TTTTGAGATCACCAACCTGTCTA 57.439 39.130 0.00 0.00 0.00 2.59
976 1448 9.775539 AGATCACCAACCTGTCTACATATATAT 57.224 33.333 0.00 0.00 0.00 0.86
1033 1507 2.365293 TCCACCATGTCCTCATACATCG 59.635 50.000 0.00 0.00 38.01 3.84
1041 1515 1.548973 CCTCATACATCGCGCCGTTC 61.549 60.000 0.00 0.00 0.00 3.95
1042 1516 1.866171 CTCATACATCGCGCCGTTCG 61.866 60.000 0.00 0.00 42.12 3.95
1272 1746 3.141488 ATCGCGCTCTTCCCGTCT 61.141 61.111 5.56 0.00 0.00 4.18
1275 1749 2.445438 CGCGCTCTTCCCGTCTTTC 61.445 63.158 5.56 0.00 0.00 2.62
1389 1863 2.649831 CTGCAAGCACCTGTTCCAT 58.350 52.632 0.00 0.00 0.00 3.41
1407 1881 2.529005 ATCAGGAGTGCGTCGACGTG 62.529 60.000 35.48 25.02 42.22 4.49
1545 2025 0.317160 ACGATGAAACGCTGTCTCCA 59.683 50.000 0.00 0.00 36.70 3.86
1574 2054 2.578981 GTCGTTAGAGCCGTCCGC 60.579 66.667 0.00 0.00 37.98 5.54
1662 2145 1.672881 GAGCGGCAATAGCAGTCATTT 59.327 47.619 1.45 0.00 44.61 2.32
1663 2146 2.094675 AGCGGCAATAGCAGTCATTTT 58.905 42.857 1.45 0.00 44.61 1.82
1666 2149 2.423185 CGGCAATAGCAGTCATTTTCCA 59.577 45.455 0.00 0.00 44.61 3.53
1675 2158 1.279271 AGTCATTTTCCAGGGAGTCCG 59.721 52.381 2.26 0.00 38.33 4.79
1693 2176 3.444388 GTCCGGGACTCCTGTATATGATC 59.556 52.174 19.92 0.00 0.00 2.92
1696 2179 2.826128 GGGACTCCTGTATATGATCGCA 59.174 50.000 0.00 0.00 0.00 5.10
1762 2259 1.152902 AGAGCTTGTTGGCAGCACA 60.153 52.632 2.60 0.00 34.17 4.57
1776 2273 3.574614 GCAGCACACATTTTATTCGGTT 58.425 40.909 0.00 0.00 0.00 4.44
1778 2275 4.545610 CAGCACACATTTTATTCGGTTGT 58.454 39.130 0.00 0.00 0.00 3.32
1779 2276 4.981674 CAGCACACATTTTATTCGGTTGTT 59.018 37.500 0.00 0.00 0.00 2.83
1813 2310 1.164411 TTGCGACCCTAACTTGCATG 58.836 50.000 0.00 0.00 35.20 4.06
1814 2311 0.676466 TGCGACCCTAACTTGCATGG 60.676 55.000 4.44 0.00 0.00 3.66
1815 2312 1.376609 GCGACCCTAACTTGCATGGG 61.377 60.000 4.44 6.18 44.89 4.00
1816 2313 1.376609 CGACCCTAACTTGCATGGGC 61.377 60.000 4.44 0.00 43.25 5.36
1817 2314 1.376609 GACCCTAACTTGCATGGGCG 61.377 60.000 4.44 0.00 45.35 6.13
1818 2315 2.774799 CCCTAACTTGCATGGGCGC 61.775 63.158 0.00 0.00 45.35 6.53
1819 2316 1.750399 CCTAACTTGCATGGGCGCT 60.750 57.895 7.64 0.00 45.35 5.92
1820 2317 1.315257 CCTAACTTGCATGGGCGCTT 61.315 55.000 7.64 0.00 45.35 4.68
1821 2318 1.378531 CTAACTTGCATGGGCGCTTA 58.621 50.000 7.64 0.00 45.35 3.09
1822 2319 1.949525 CTAACTTGCATGGGCGCTTAT 59.050 47.619 7.64 0.00 45.35 1.73
1823 2320 1.185315 AACTTGCATGGGCGCTTATT 58.815 45.000 7.64 0.00 45.35 1.40
1824 2321 0.740737 ACTTGCATGGGCGCTTATTC 59.259 50.000 7.64 0.00 45.35 1.75
1825 2322 0.740149 CTTGCATGGGCGCTTATTCA 59.260 50.000 7.64 0.00 45.35 2.57
1826 2323 1.338973 CTTGCATGGGCGCTTATTCAT 59.661 47.619 7.64 1.15 45.35 2.57
2011 2522 6.410942 TCATCACATCTCATCGGATAAGTT 57.589 37.500 0.00 0.00 0.00 2.66
2139 2650 1.559682 GGGGAGCTGGTCTACATCAAA 59.440 52.381 6.83 0.00 0.00 2.69
2413 4568 1.734465 GTGCAGTACAAGCTGATGGAC 59.266 52.381 10.98 0.00 38.70 4.02
2463 4618 1.588239 TCTGGATTGCTGGATCTGGT 58.412 50.000 0.00 0.00 0.00 4.00
2583 4772 5.344743 TGTTGTTATTTTTGCTGGAACCA 57.655 34.783 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.034544 CAAATCGAAAAGAAAATTCAAACTCCT 57.965 29.630 0.00 0.00 0.00 3.69
2 3 8.275632 CCAAATCGAAAAGAAAATTCAAACTCC 58.724 33.333 0.00 0.00 0.00 3.85
3 4 9.030301 TCCAAATCGAAAAGAAAATTCAAACTC 57.970 29.630 0.00 0.00 0.00 3.01
4 5 8.940768 TCCAAATCGAAAAGAAAATTCAAACT 57.059 26.923 0.00 0.00 0.00 2.66
5 6 9.980780 TTTCCAAATCGAAAAGAAAATTCAAAC 57.019 25.926 0.00 0.00 0.00 2.93
11 12 9.986833 CAACTTTTTCCAAATCGAAAAGAAAAT 57.013 25.926 12.99 0.00 41.45 1.82
12 13 9.209175 TCAACTTTTTCCAAATCGAAAAGAAAA 57.791 25.926 12.99 10.03 41.45 2.29
13 14 8.764524 TCAACTTTTTCCAAATCGAAAAGAAA 57.235 26.923 12.99 5.19 41.45 2.52
14 15 8.816144 CATCAACTTTTTCCAAATCGAAAAGAA 58.184 29.630 12.99 0.00 41.45 2.52
15 16 7.437862 CCATCAACTTTTTCCAAATCGAAAAGA 59.562 33.333 12.99 0.91 41.45 2.52
16 17 7.437862 TCCATCAACTTTTTCCAAATCGAAAAG 59.562 33.333 0.00 6.33 41.45 2.27
17 18 7.268586 TCCATCAACTTTTTCCAAATCGAAAA 58.731 30.769 0.00 0.00 39.39 2.29
18 19 6.810911 TCCATCAACTTTTTCCAAATCGAAA 58.189 32.000 0.00 0.00 0.00 3.46
19 20 6.398234 TCCATCAACTTTTTCCAAATCGAA 57.602 33.333 0.00 0.00 0.00 3.71
20 21 6.588719 ATCCATCAACTTTTTCCAAATCGA 57.411 33.333 0.00 0.00 0.00 3.59
21 22 8.190122 TCATATCCATCAACTTTTTCCAAATCG 58.810 33.333 0.00 0.00 0.00 3.34
22 23 9.874205 TTCATATCCATCAACTTTTTCCAAATC 57.126 29.630 0.00 0.00 0.00 2.17
67 68 9.733556 ACCTTTCTTTGAAACCATAAACTTTTT 57.266 25.926 0.00 0.00 0.00 1.94
68 69 9.733556 AACCTTTCTTTGAAACCATAAACTTTT 57.266 25.926 0.00 0.00 0.00 2.27
69 70 9.378551 GAACCTTTCTTTGAAACCATAAACTTT 57.621 29.630 0.00 0.00 0.00 2.66
70 71 8.536175 TGAACCTTTCTTTGAAACCATAAACTT 58.464 29.630 0.00 0.00 0.00 2.66
71 72 8.073467 TGAACCTTTCTTTGAAACCATAAACT 57.927 30.769 0.00 0.00 0.00 2.66
72 73 8.194769 TCTGAACCTTTCTTTGAAACCATAAAC 58.805 33.333 0.00 0.00 0.00 2.01
73 74 8.299990 TCTGAACCTTTCTTTGAAACCATAAA 57.700 30.769 0.00 0.00 0.00 1.40
74 75 7.889873 TCTGAACCTTTCTTTGAAACCATAA 57.110 32.000 0.00 0.00 0.00 1.90
75 76 9.010029 GTATCTGAACCTTTCTTTGAAACCATA 57.990 33.333 0.00 0.00 0.00 2.74
76 77 6.983906 ATCTGAACCTTTCTTTGAAACCAT 57.016 33.333 0.00 0.00 0.00 3.55
77 78 6.264518 GGTATCTGAACCTTTCTTTGAAACCA 59.735 38.462 0.00 0.00 36.53 3.67
78 79 6.678878 GGTATCTGAACCTTTCTTTGAAACC 58.321 40.000 2.91 0.00 36.53 3.27
91 92 5.918608 TCTTGCAATCTAGGTATCTGAACC 58.081 41.667 0.00 2.10 40.06 3.62
92 93 7.849804 TTTCTTGCAATCTAGGTATCTGAAC 57.150 36.000 0.00 0.00 0.00 3.18
93 94 8.862325 TTTTTCTTGCAATCTAGGTATCTGAA 57.138 30.769 0.00 0.00 0.00 3.02
94 95 9.113838 GATTTTTCTTGCAATCTAGGTATCTGA 57.886 33.333 0.00 0.00 0.00 3.27
95 96 9.118300 AGATTTTTCTTGCAATCTAGGTATCTG 57.882 33.333 0.00 0.00 37.87 2.90
96 97 9.692325 AAGATTTTTCTTGCAATCTAGGTATCT 57.308 29.630 0.00 0.61 38.55 1.98
97 98 9.727627 CAAGATTTTTCTTGCAATCTAGGTATC 57.272 33.333 0.00 0.00 38.55 2.24
98 99 9.466497 TCAAGATTTTTCTTGCAATCTAGGTAT 57.534 29.630 0.00 0.00 44.82 2.73
99 100 8.730680 GTCAAGATTTTTCTTGCAATCTAGGTA 58.269 33.333 0.00 0.00 44.82 3.08
100 101 7.309438 GGTCAAGATTTTTCTTGCAATCTAGGT 60.309 37.037 0.00 0.00 44.82 3.08
101 102 7.031975 GGTCAAGATTTTTCTTGCAATCTAGG 58.968 38.462 0.00 0.00 44.82 3.02
102 103 7.031975 GGGTCAAGATTTTTCTTGCAATCTAG 58.968 38.462 0.00 0.00 44.82 2.43
103 104 6.349280 CGGGTCAAGATTTTTCTTGCAATCTA 60.349 38.462 0.00 0.00 44.82 1.98
104 105 5.565439 CGGGTCAAGATTTTTCTTGCAATCT 60.565 40.000 0.00 0.00 44.82 2.40
105 106 4.622740 CGGGTCAAGATTTTTCTTGCAATC 59.377 41.667 0.00 0.00 44.82 2.67
106 107 4.280677 TCGGGTCAAGATTTTTCTTGCAAT 59.719 37.500 0.00 0.00 44.82 3.56
107 108 3.634448 TCGGGTCAAGATTTTTCTTGCAA 59.366 39.130 10.19 0.00 44.82 4.08
108 109 3.004315 GTCGGGTCAAGATTTTTCTTGCA 59.996 43.478 10.19 0.00 44.82 4.08
109 110 3.565516 GTCGGGTCAAGATTTTTCTTGC 58.434 45.455 10.19 6.32 44.82 4.01
110 111 3.364964 CGGTCGGGTCAAGATTTTTCTTG 60.365 47.826 9.00 9.00 46.11 3.02
111 112 2.812011 CGGTCGGGTCAAGATTTTTCTT 59.188 45.455 0.00 0.00 0.00 2.52
112 113 2.038033 TCGGTCGGGTCAAGATTTTTCT 59.962 45.455 0.00 0.00 0.00 2.52
113 114 2.159037 GTCGGTCGGGTCAAGATTTTTC 59.841 50.000 0.00 0.00 0.00 2.29
114 115 2.148768 GTCGGTCGGGTCAAGATTTTT 58.851 47.619 0.00 0.00 0.00 1.94
115 116 1.609841 GGTCGGTCGGGTCAAGATTTT 60.610 52.381 0.00 0.00 0.00 1.82
116 117 0.036671 GGTCGGTCGGGTCAAGATTT 60.037 55.000 0.00 0.00 0.00 2.17
117 118 1.189524 TGGTCGGTCGGGTCAAGATT 61.190 55.000 0.00 0.00 0.00 2.40
118 119 0.976073 ATGGTCGGTCGGGTCAAGAT 60.976 55.000 0.00 0.00 0.00 2.40
119 120 1.189524 AATGGTCGGTCGGGTCAAGA 61.190 55.000 0.00 0.00 0.00 3.02
120 121 0.321298 AAATGGTCGGTCGGGTCAAG 60.321 55.000 0.00 0.00 0.00 3.02
121 122 0.320946 GAAATGGTCGGTCGGGTCAA 60.321 55.000 0.00 0.00 0.00 3.18
122 123 1.294138 GAAATGGTCGGTCGGGTCA 59.706 57.895 0.00 0.00 0.00 4.02
123 124 0.107848 ATGAAATGGTCGGTCGGGTC 60.108 55.000 0.00 0.00 0.00 4.46
124 125 0.392461 CATGAAATGGTCGGTCGGGT 60.392 55.000 0.00 0.00 41.79 5.28
125 126 0.107897 TCATGAAATGGTCGGTCGGG 60.108 55.000 0.00 0.00 46.73 5.14
126 127 1.732941 TTCATGAAATGGTCGGTCGG 58.267 50.000 5.45 0.00 46.73 4.79
127 128 3.822594 TTTTCATGAAATGGTCGGTCG 57.177 42.857 21.10 0.00 46.73 4.79
128 129 6.852664 ACTATTTTTCATGAAATGGTCGGTC 58.147 36.000 21.10 0.00 46.73 4.79
129 130 6.834168 ACTATTTTTCATGAAATGGTCGGT 57.166 33.333 21.10 12.28 46.73 4.69
192 193 9.970395 GGTCATATCATCAATGCAAATTTTCTA 57.030 29.630 0.00 0.00 0.00 2.10
193 194 7.650504 CGGTCATATCATCAATGCAAATTTTCT 59.349 33.333 0.00 0.00 0.00 2.52
194 195 7.436080 ACGGTCATATCATCAATGCAAATTTTC 59.564 33.333 0.00 0.00 0.00 2.29
201 202 5.833406 AAAACGGTCATATCATCAATGCA 57.167 34.783 0.00 0.00 0.00 3.96
202 203 6.264832 TCAAAAACGGTCATATCATCAATGC 58.735 36.000 0.00 0.00 0.00 3.56
252 253 8.231692 TCCATGTTCTGAAAAGTATGTTTTCA 57.768 30.769 13.96 13.96 0.00 2.69
253 254 9.185192 CTTCCATGTTCTGAAAAGTATGTTTTC 57.815 33.333 7.75 7.75 0.00 2.29
275 276 8.931385 TTTTGATTAGGTGTACGTATACTTCC 57.069 34.615 19.98 5.96 32.00 3.46
279 280 8.811378 GGACTTTTTGATTAGGTGTACGTATAC 58.189 37.037 13.54 13.54 0.00 1.47
284 285 5.467399 TGTGGACTTTTTGATTAGGTGTACG 59.533 40.000 0.00 0.00 0.00 3.67
290 293 5.685511 CGTTGTTGTGGACTTTTTGATTAGG 59.314 40.000 0.00 0.00 0.00 2.69
293 296 5.099575 GTCGTTGTTGTGGACTTTTTGATT 58.900 37.500 0.00 0.00 0.00 2.57
305 308 6.804534 ACATGTTTTTATGTCGTTGTTGTG 57.195 33.333 0.00 0.00 36.60 3.33
324 327 2.587956 CTGCACGAATGGTCAAACATG 58.412 47.619 0.00 0.00 0.00 3.21
325 328 1.541147 CCTGCACGAATGGTCAAACAT 59.459 47.619 0.00 0.00 0.00 2.71
362 366 8.589335 TTGATATAAACTAATCTCTTCGCCAC 57.411 34.615 0.00 0.00 0.00 5.01
363 367 8.421784 ACTTGATATAAACTAATCTCTTCGCCA 58.578 33.333 0.00 0.00 0.00 5.69
365 369 9.464714 TCACTTGATATAAACTAATCTCTTCGC 57.535 33.333 0.00 0.00 0.00 4.70
396 400 9.360901 AGATGCTTCTTGACTTGAGATATACTA 57.639 33.333 0.00 0.00 0.00 1.82
416 578 3.051940 TCCATTGGAGGTAGAGATGCT 57.948 47.619 0.00 0.00 0.00 3.79
480 642 2.671888 GAGCCACGAACTTAGCTTTACC 59.328 50.000 0.00 0.00 35.23 2.85
544 707 7.554835 CAGAGTTGACCTACTAGACAGAGTAAT 59.445 40.741 0.00 0.00 31.57 1.89
686 849 9.944376 GCCCAGTATATTTCAGTAGATTATGAA 57.056 33.333 0.00 0.00 33.73 2.57
688 851 9.725019 TTGCCCAGTATATTTCAGTAGATTATG 57.275 33.333 0.00 0.00 0.00 1.90
697 860 5.560966 ACGTTTTGCCCAGTATATTTCAG 57.439 39.130 0.00 0.00 0.00 3.02
700 863 5.241949 TGTCAACGTTTTGCCCAGTATATTT 59.758 36.000 0.00 0.00 32.17 1.40
709 874 1.857837 CAACATGTCAACGTTTTGCCC 59.142 47.619 0.00 0.00 32.17 5.36
758 923 6.373495 TGCTGCTGGCTAATCAATAGATTATG 59.627 38.462 0.00 0.00 43.71 1.90
772 937 3.819368 TGCTTATTTATGCTGCTGGCTA 58.181 40.909 0.00 0.00 42.39 3.93
814 979 8.559536 CATGCACGTATGTCTCCTTTAAATAAT 58.440 33.333 0.00 0.00 0.00 1.28
824 989 1.528586 GCATCATGCACGTATGTCTCC 59.471 52.381 4.20 0.00 44.26 3.71
863 1028 9.642343 ACTATTTCGGATATATATACTCCAGCA 57.358 33.333 15.60 4.98 0.00 4.41
925 1397 5.813513 AAATTTTGGATGGTTCTCTTGCT 57.186 34.783 0.00 0.00 0.00 3.91
938 1410 5.602145 AGGTTGGTGATCTCAAAATTTTGGA 59.398 36.000 26.45 21.97 38.66 3.53
939 1411 5.697633 CAGGTTGGTGATCTCAAAATTTTGG 59.302 40.000 26.45 18.26 38.66 3.28
941 1413 6.324770 AGACAGGTTGGTGATCTCAAAATTTT 59.675 34.615 0.00 0.00 0.00 1.82
942 1414 5.835280 AGACAGGTTGGTGATCTCAAAATTT 59.165 36.000 0.00 0.00 0.00 1.82
1335 1809 3.507009 GTCTCCCCCTCGTCGACG 61.507 72.222 31.30 31.30 41.45 5.12
1389 1863 2.976350 ACGTCGACGCACTCCTGA 60.976 61.111 35.92 0.00 44.43 3.86
1407 1881 3.050275 GCGTTGGACAGGAGCCAC 61.050 66.667 0.00 0.00 34.56 5.01
1515 1995 2.469147 CGTTTCATCGTCCATCATCTCG 59.531 50.000 0.00 0.00 0.00 4.04
1556 2036 2.277120 CGGACGGCTCTAACGACG 60.277 66.667 0.00 0.00 34.93 5.12
1557 2037 2.578981 GCGGACGGCTCTAACGAC 60.579 66.667 0.00 0.00 39.11 4.34
1558 2038 4.170062 CGCGGACGGCTCTAACGA 62.170 66.667 0.00 0.00 40.44 3.85
1662 2145 2.284405 GTCCCGGACTCCCTGGAA 60.284 66.667 10.59 0.00 45.73 3.53
1663 2146 3.273654 AGTCCCGGACTCCCTGGA 61.274 66.667 14.84 0.00 38.71 3.86
1675 2158 2.826128 TGCGATCATATACAGGAGTCCC 59.174 50.000 5.25 0.00 0.00 4.46
1677 2160 3.188667 TCGTGCGATCATATACAGGAGTC 59.811 47.826 0.00 0.00 0.00 3.36
1693 2176 1.920574 CCTACTTCAACAGATCGTGCG 59.079 52.381 0.00 0.00 0.00 5.34
1696 2179 3.762288 TGCTACCTACTTCAACAGATCGT 59.238 43.478 0.00 0.00 0.00 3.73
1762 2259 7.416022 TCGTTTACAACAACCGAATAAAATGT 58.584 30.769 0.00 0.00 0.00 2.71
1776 2273 4.924462 TCGCAATACTGATCGTTTACAACA 59.076 37.500 0.00 0.00 0.00 3.33
1778 2275 4.327898 GGTCGCAATACTGATCGTTTACAA 59.672 41.667 0.00 0.00 0.00 2.41
1779 2276 3.861113 GGTCGCAATACTGATCGTTTACA 59.139 43.478 0.00 0.00 0.00 2.41
1792 2289 2.772077 TGCAAGTTAGGGTCGCAATA 57.228 45.000 0.00 0.00 0.00 1.90
1813 2310 2.162716 CGCCTATGAATAAGCGCCC 58.837 57.895 2.29 0.00 42.31 6.13
1817 2314 2.135933 AGCGTTCGCCTATGAATAAGC 58.864 47.619 13.54 0.00 0.00 3.09
1818 2315 2.405357 CGAGCGTTCGCCTATGAATAAG 59.595 50.000 9.17 0.00 40.36 1.73
1819 2316 2.390938 CGAGCGTTCGCCTATGAATAA 58.609 47.619 9.17 0.00 40.36 1.40
1820 2317 1.335597 CCGAGCGTTCGCCTATGAATA 60.336 52.381 16.81 0.00 45.38 1.75
1821 2318 0.597637 CCGAGCGTTCGCCTATGAAT 60.598 55.000 16.81 0.00 45.38 2.57
1822 2319 1.226859 CCGAGCGTTCGCCTATGAA 60.227 57.895 16.81 0.00 45.38 2.57
1823 2320 2.411701 CCGAGCGTTCGCCTATGA 59.588 61.111 16.81 0.00 45.38 2.15
1824 2321 3.330853 GCCGAGCGTTCGCCTATG 61.331 66.667 16.81 3.29 45.38 2.23
1825 2322 4.587189 GGCCGAGCGTTCGCCTAT 62.587 66.667 16.81 0.00 45.38 2.57
2011 2522 0.613260 CAAAGTCGGGAGGTGGATGA 59.387 55.000 0.00 0.00 0.00 2.92
2139 2650 0.838122 CCCTCCGCCTCCCAATATCT 60.838 60.000 0.00 0.00 0.00 1.98
2463 4618 4.799564 AAAGACACTTGTTCCAGCAAAA 57.200 36.364 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.