Multiple sequence alignment - TraesCS7A01G271900

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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 TraesCS7A01G271900 chr7A 100.000 3280 0 0 1 3280 285424133 285427412 0.000000e+00 6058.0
1 TraesCS7A01G271900 chr7A 81.643 207 28 6 3080 3277 24883870 24884075 2.620000e-36 163.0
2 TraesCS7A01G271900 chr7A 81.159 207 29 6 3080 3277 24864432 24864637 1.220000e-34 158.0
3 TraesCS7A01G271900 chr7A 97.297 37 1 0 3070 3106 17098867 17098831 2.730000e-06 63.9
4 TraesCS7A01G271900 chr7B 92.913 2822 130 32 1 2766 241579499 241576692 0.000000e+00 4039.0
5 TraesCS7A01G271900 chr7B 91.228 285 15 4 3005 3280 241575280 241574997 2.390000e-101 379.0
6 TraesCS7A01G271900 chr7B 91.549 142 11 1 2867 3007 241576693 241576552 9.290000e-46 195.0
7 TraesCS7A01G271900 chr7B 84.810 79 10 2 3 79 119714472 119714550 9.760000e-11 78.7
8 TraesCS7A01G271900 chr7D 93.223 2730 121 23 1 2678 262353211 262355928 0.000000e+00 3958.0
9 TraesCS7A01G271900 chr7D 92.933 283 12 4 3005 3280 262358528 262358809 3.940000e-109 405.0
10 TraesCS7A01G271900 chr7D 91.971 137 10 1 2867 3002 262358126 262358262 1.200000e-44 191.0
11 TraesCS7A01G271900 chr7D 96.629 89 3 0 2675 2763 262358036 262358124 7.330000e-32 148.0
12 TraesCS7A01G271900 chr4A 84.703 1935 186 44 715 2600 5832700 5834573 0.000000e+00 1832.0
13 TraesCS7A01G271900 chr4D 89.003 391 42 1 966 1355 464178039 464177649 1.770000e-132 483.0
14 TraesCS7A01G271900 chr4D 89.796 98 10 0 2775 2872 72581093 72580996 3.440000e-25 126.0
15 TraesCS7A01G271900 chr4D 82.812 128 13 3 6 132 505829140 505829021 4.480000e-19 106.0
16 TraesCS7A01G271900 chr4B 83.821 513 45 14 2118 2603 580010882 580010381 1.390000e-123 453.0
17 TraesCS7A01G271900 chr4B 85.714 385 54 1 972 1355 580038172 580037788 3.940000e-109 405.0
18 TraesCS7A01G271900 chr4B 87.342 158 19 1 1178 1335 580033517 580033361 2.600000e-41 180.0
19 TraesCS7A01G271900 chr4B 91.579 95 8 0 2774 2868 598601913 598601819 7.380000e-27 132.0
20 TraesCS7A01G271900 chr4B 76.786 112 21 5 3085 3193 328211144 328211035 1.270000e-04 58.4
21 TraesCS7A01G271900 chr5A 83.732 209 24 6 3077 3277 270152460 270152666 4.320000e-44 189.0
22 TraesCS7A01G271900 chr2D 83.092 207 16 7 3079 3277 573233281 573233476 1.560000e-38 171.0
23 TraesCS7A01G271900 chr2D 94.186 86 5 0 2783 2868 542330515 542330600 7.380000e-27 132.0
24 TraesCS7A01G271900 chr2D 91.398 93 7 1 2776 2868 506449693 506449602 3.440000e-25 126.0
25 TraesCS7A01G271900 chr2D 83.333 90 7 6 33 122 23495390 23495309 3.510000e-10 76.8
26 TraesCS7A01G271900 chr2B 82.039 206 20 6 3079 3277 689300221 689300416 3.390000e-35 159.0
27 TraesCS7A01G271900 chr2B 80.000 120 16 2 6 125 347064972 347065083 7.540000e-12 82.4
28 TraesCS7A01G271900 chr3B 92.553 94 7 0 2775 2868 578274430 578274337 5.710000e-28 135.0
29 TraesCS7A01G271900 chr6D 90.526 95 9 0 2774 2868 50772025 50771931 3.440000e-25 126.0
30 TraesCS7A01G271900 chr3D 80.571 175 22 8 6 178 95832482 95832646 1.240000e-24 124.0
31 TraesCS7A01G271900 chr5D 89.474 95 10 0 2775 2869 422766666 422766760 1.600000e-23 121.0
32 TraesCS7A01G271900 chr5D 80.000 155 17 6 3130 3277 495444541 495444688 5.790000e-18 102.0
33 TraesCS7A01G271900 chr2A 89.474 95 8 2 2776 2870 41607412 41607320 5.750000e-23 119.0
34 TraesCS7A01G271900 chr2A 85.859 99 11 3 2775 2872 45072227 45072131 5.790000e-18 102.0
35 TraesCS7A01G271900 chr2A 94.444 36 1 1 3071 3106 543713744 543713710 2.000000e-03 54.7
36 TraesCS7A01G271900 chr1D 89.362 94 10 0 2775 2868 483405119 483405212 5.750000e-23 119.0
37 TraesCS7A01G271900 chr1D 92.105 38 3 0 3079 3116 304064940 304064977 2.000000e-03 54.7
38 TraesCS7A01G271900 chr5B 87.368 95 10 2 2775 2868 253189215 253189308 1.240000e-19 108.0
39 TraesCS7A01G271900 chr3A 83.186 113 16 3 2760 2870 741361498 741361609 2.080000e-17 100.0
40 TraesCS7A01G271900 chr1A 81.818 121 14 2 6 126 441747678 441747566 9.690000e-16 95.3
41 TraesCS7A01G271900 chr6A 82.828 99 9 2 27 125 445768960 445768870 7.540000e-12 82.4
42 TraesCS7A01G271900 chr6A 100.000 29 0 0 2842 2870 581458323 581458351 2.000000e-03 54.7
43 TraesCS7A01G271900 chrUn 77.857 140 23 7 3145 3277 108385591 108385453 2.710000e-11 80.5
44 TraesCS7A01G271900 chr1B 83.333 96 7 6 2775 2870 860992 860906 2.710000e-11 80.5


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 TraesCS7A01G271900 chr7A 285424133 285427412 3279 False 6058.000000 6058 100.000000 1 3280 1 chr7A.!!$F3 3279
1 TraesCS7A01G271900 chr7B 241574997 241579499 4502 True 1537.666667 4039 91.896667 1 3280 3 chr7B.!!$R1 3279
2 TraesCS7A01G271900 chr7D 262353211 262358809 5598 False 1175.500000 3958 93.689000 1 3280 4 chr7D.!!$F1 3279
3 TraesCS7A01G271900 chr4A 5832700 5834573 1873 False 1832.000000 1832 84.703000 715 2600 1 chr4A.!!$F1 1885
4 TraesCS7A01G271900 chr4B 580010381 580010882 501 True 453.000000 453 83.821000 2118 2603 1 chr4B.!!$R2 485

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
623 668 0.179108 CAAGGTCTACCGCAGTAGCC 60.179 60.0 1.96 7.24 44.87 3.93 F
1221 1285 1.012086 TCGTCTCGGGATACTTCGTG 58.988 55.0 0.00 0.00 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 1882 0.393077 CCCACCTGTTCGTTCTGTCT 59.607 55.0 0.0 0.0 0.00 3.41 R
2889 5121 0.321122 GGCTGCTGCAGTTGTACTCT 60.321 55.0 28.5 0.0 41.91 3.24 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
60 61 4.304939 GCTGAAATTTTGCAAGAAGCTCT 58.695 39.130 0.00 0.00 45.94 4.09
61 62 5.464168 GCTGAAATTTTGCAAGAAGCTCTA 58.536 37.500 0.00 0.00 45.94 2.43
235 241 8.403236 ACCAAAGAAAAACAGTACACAAGTATC 58.597 33.333 0.00 0.00 31.84 2.24
236 242 8.402472 CCAAAGAAAAACAGTACACAAGTATCA 58.598 33.333 0.00 0.00 31.84 2.15
237 243 9.950680 CAAAGAAAAACAGTACACAAGTATCAT 57.049 29.630 0.00 0.00 31.84 2.45
239 245 8.902540 AGAAAAACAGTACACAAGTATCATCA 57.097 30.769 0.00 0.00 31.84 3.07
240 246 9.507329 AGAAAAACAGTACACAAGTATCATCAT 57.493 29.630 0.00 0.00 31.84 2.45
253 270 7.396907 ACAAGTATCATCATTGGGTTCAATTGA 59.603 33.333 3.38 3.38 41.29 2.57
261 278 6.454795 TCATTGGGTTCAATTGAAAGCTAAC 58.545 36.000 22.07 9.58 41.29 2.34
262 279 5.860941 TTGGGTTCAATTGAAAGCTAACA 57.139 34.783 22.07 11.72 35.58 2.41
322 340 1.396301 GCTCAAAGGTCTTCGCAGATG 59.604 52.381 0.00 0.00 35.04 2.90
331 349 2.635229 CTTCGCAGATGGGAGGACGG 62.635 65.000 3.30 0.00 38.26 4.79
366 384 1.219664 CTTCGCCCGTCCACCAATA 59.780 57.895 0.00 0.00 0.00 1.90
423 441 3.020627 CTAGCTTGGCGCATGAGC 58.979 61.111 13.62 13.62 42.61 4.26
439 457 2.426522 TGAGCAGCCAGTGTACAAATC 58.573 47.619 0.00 0.00 0.00 2.17
445 463 1.135689 GCCAGTGTACAAATCTTGCCG 60.136 52.381 0.00 0.00 0.00 5.69
451 469 3.124636 GTGTACAAATCTTGCCGTGGTAG 59.875 47.826 0.00 0.00 0.00 3.18
455 473 3.199071 ACAAATCTTGCCGTGGTAGGATA 59.801 43.478 2.19 0.00 0.00 2.59
464 482 3.788937 CCGTGGTAGGATAATTCAACGT 58.211 45.455 0.00 0.00 0.00 3.99
503 521 2.438021 AGTGTACAAAGTTCTGCCAGGA 59.562 45.455 0.00 0.00 0.00 3.86
623 668 0.179108 CAAGGTCTACCGCAGTAGCC 60.179 60.000 1.96 7.24 44.87 3.93
663 719 7.370383 TCCTTTCATACTTGCATTCTTTTGTC 58.630 34.615 0.00 0.00 0.00 3.18
670 726 2.956132 TGCATTCTTTTGTCTTGGGGA 58.044 42.857 0.00 0.00 0.00 4.81
671 727 3.509442 TGCATTCTTTTGTCTTGGGGAT 58.491 40.909 0.00 0.00 0.00 3.85
672 728 4.671831 TGCATTCTTTTGTCTTGGGGATA 58.328 39.130 0.00 0.00 0.00 2.59
685 741 8.464426 TGTCTTGGGGATAGATAGATAGACTA 57.536 38.462 0.00 0.00 32.75 2.59
692 748 3.655615 AGATAGATAGACTAGGCCCGG 57.344 52.381 0.00 0.00 34.35 5.73
745 802 1.973812 GCCCAACAGTCTTGCCCTC 60.974 63.158 0.00 0.00 0.00 4.30
875 939 1.152226 CTCCTCCTCCCGCCCTAAT 60.152 63.158 0.00 0.00 0.00 1.73
916 980 3.932545 TGTTTAATTGACGCAGCCAAT 57.067 38.095 0.00 0.00 35.92 3.16
955 1019 3.557595 GGCCTGAACTCAGATTCGTATTG 59.442 47.826 8.33 0.00 46.59 1.90
1045 1109 2.740714 GGTGCTGGCGATGACGAAC 61.741 63.158 0.00 0.00 42.66 3.95
1116 1180 3.125573 CTCGACGACCTCTCCGCA 61.126 66.667 0.00 0.00 0.00 5.69
1164 1228 4.849329 CTCACGTACGAGCCGGCC 62.849 72.222 26.15 14.23 0.00 6.13
1221 1285 1.012086 TCGTCTCGGGATACTTCGTG 58.988 55.000 0.00 0.00 0.00 4.35
1599 1666 4.969196 CTGCGTGACCACCTGCGT 62.969 66.667 0.00 0.00 0.00 5.24
1825 1892 0.966920 GGAGGTGGAAGACAGAACGA 59.033 55.000 0.00 0.00 0.00 3.85
1886 1953 0.035458 AAGCTGTGCCTGGTAGTGAC 59.965 55.000 0.00 0.00 0.00 3.67
1962 2035 2.437281 GAGATGGGAGAAGAAGATGGCA 59.563 50.000 0.00 0.00 0.00 4.92
2025 2098 3.609256 ATACTCAGGGATCTCTGCTCA 57.391 47.619 18.41 5.06 34.91 4.26
2093 2166 3.555956 TGAAATCGCTCGCTTAATTCTCC 59.444 43.478 0.00 0.00 0.00 3.71
2098 2171 2.930040 CGCTCGCTTAATTCTCCTTCAA 59.070 45.455 0.00 0.00 0.00 2.69
2115 2188 7.878127 TCTCCTTCAAATCTTCGTTACAATCTT 59.122 33.333 0.00 0.00 0.00 2.40
2181 2273 0.730840 GTACGATTTTTGGAGGGGCG 59.269 55.000 0.00 0.00 0.00 6.13
2240 2332 7.497925 ACAAGAAGTTTTCAAGTATGAGTCC 57.502 36.000 0.00 0.00 36.78 3.85
2286 2378 9.219603 TCGATGAAAACAAAATCTAGACTGATT 57.780 29.630 0.00 0.00 38.19 2.57
2298 2392 5.610398 TCTAGACTGATTGACACTGCAAAA 58.390 37.500 0.00 0.00 0.00 2.44
2316 2410 4.832019 CAAAATTTGCGTTTTGGAAGACC 58.168 39.130 11.67 0.00 42.51 3.85
2319 2413 1.448922 TTGCGTTTTGGAAGACCCGG 61.449 55.000 0.00 0.00 37.93 5.73
2369 2470 3.488778 TCTACTCTCCGTATCCTGGTC 57.511 52.381 0.00 0.00 0.00 4.02
2418 2527 7.149973 AGGAAACAACAAATCTTGATGATGTG 58.850 34.615 3.96 0.00 44.16 3.21
2488 2605 4.095782 TCATTTATTAACACCGCTTCAGGC 59.904 41.667 0.00 0.00 37.64 4.85
2498 2615 2.831526 ACCGCTTCAGGCCAATAAATTT 59.168 40.909 5.01 0.00 37.74 1.82
2501 2618 3.062504 CGCTTCAGGCCAATAAATTTTGC 59.937 43.478 5.01 0.00 37.74 3.68
2620 2741 6.282199 ACAGGTATGAGATAAACGAGTTGT 57.718 37.500 0.00 0.00 0.00 3.32
2623 2744 6.255887 CAGGTATGAGATAAACGAGTTGTTCC 59.744 42.308 0.00 0.00 40.84 3.62
2634 2755 3.243643 ACGAGTTGTTCCGTTCGTTAAAG 59.756 43.478 0.00 0.00 42.99 1.85
2646 2767 5.007039 CGTTCGTTAAAGTCGTGATCATTG 58.993 41.667 0.00 0.00 0.00 2.82
2666 2787 2.121009 GAAGCTCGGTTCGATAAGCTC 58.879 52.381 10.54 3.62 34.70 4.09
2715 4947 1.343506 CTCACGTGTACCGGTAAAGC 58.656 55.000 17.78 4.66 42.24 3.51
2738 4970 4.573900 TGGAAACAACACAAAAGCATTGT 58.426 34.783 2.38 2.38 37.44 2.71
2777 5009 9.588096 AAATTTTAACATGTACTCCTTCTTCCT 57.412 29.630 0.00 0.00 0.00 3.36
2778 5010 9.588096 AATTTTAACATGTACTCCTTCTTCCTT 57.412 29.630 0.00 0.00 0.00 3.36
2779 5011 8.617290 TTTTAACATGTACTCCTTCTTCCTTC 57.383 34.615 0.00 0.00 0.00 3.46
2780 5012 7.554959 TTAACATGTACTCCTTCTTCCTTCT 57.445 36.000 0.00 0.00 0.00 2.85
2781 5013 5.413309 ACATGTACTCCTTCTTCCTTCTG 57.587 43.478 0.00 0.00 0.00 3.02
2782 5014 4.841246 ACATGTACTCCTTCTTCCTTCTGT 59.159 41.667 0.00 0.00 0.00 3.41
2783 5015 5.308237 ACATGTACTCCTTCTTCCTTCTGTT 59.692 40.000 0.00 0.00 0.00 3.16
2784 5016 5.888982 TGTACTCCTTCTTCCTTCTGTTT 57.111 39.130 0.00 0.00 0.00 2.83
2785 5017 5.855045 TGTACTCCTTCTTCCTTCTGTTTC 58.145 41.667 0.00 0.00 0.00 2.78
2786 5018 5.365605 TGTACTCCTTCTTCCTTCTGTTTCA 59.634 40.000 0.00 0.00 0.00 2.69
2787 5019 5.373812 ACTCCTTCTTCCTTCTGTTTCAA 57.626 39.130 0.00 0.00 0.00 2.69
2788 5020 5.755849 ACTCCTTCTTCCTTCTGTTTCAAA 58.244 37.500 0.00 0.00 0.00 2.69
2789 5021 6.187682 ACTCCTTCTTCCTTCTGTTTCAAAA 58.812 36.000 0.00 0.00 0.00 2.44
2790 5022 6.836007 ACTCCTTCTTCCTTCTGTTTCAAAAT 59.164 34.615 0.00 0.00 0.00 1.82
2791 5023 7.998964 ACTCCTTCTTCCTTCTGTTTCAAAATA 59.001 33.333 0.00 0.00 0.00 1.40
2792 5024 8.760980 TCCTTCTTCCTTCTGTTTCAAAATAA 57.239 30.769 0.00 0.00 0.00 1.40
2793 5025 9.196139 TCCTTCTTCCTTCTGTTTCAAAATAAA 57.804 29.630 0.00 0.00 0.00 1.40
2794 5026 9.987272 CCTTCTTCCTTCTGTTTCAAAATAAAT 57.013 29.630 0.00 0.00 0.00 1.40
2797 5029 9.965824 TCTTCCTTCTGTTTCAAAATAAATGAC 57.034 29.630 0.00 0.00 0.00 3.06
2798 5030 9.971922 CTTCCTTCTGTTTCAAAATAAATGACT 57.028 29.630 0.00 0.00 0.00 3.41
2799 5031 9.965824 TTCCTTCTGTTTCAAAATAAATGACTC 57.034 29.630 0.00 0.00 0.00 3.36
2800 5032 9.130661 TCCTTCTGTTTCAAAATAAATGACTCA 57.869 29.630 0.00 0.00 0.00 3.41
2801 5033 9.748708 CCTTCTGTTTCAAAATAAATGACTCAA 57.251 29.630 0.00 0.00 0.00 3.02
2859 5091 8.996024 AAATTGGGTCATCTATTTTAAAACGG 57.004 30.769 1.97 0.00 0.00 4.44
2860 5092 7.948034 ATTGGGTCATCTATTTTAAAACGGA 57.052 32.000 1.97 5.09 0.00 4.69
2861 5093 6.995511 TGGGTCATCTATTTTAAAACGGAG 57.004 37.500 1.97 1.74 0.00 4.63
2862 5094 5.883673 TGGGTCATCTATTTTAAAACGGAGG 59.116 40.000 1.97 6.55 0.00 4.30
2863 5095 6.117488 GGGTCATCTATTTTAAAACGGAGGA 58.883 40.000 1.97 8.66 0.00 3.71
2864 5096 6.600427 GGGTCATCTATTTTAAAACGGAGGAA 59.400 38.462 15.79 4.22 0.00 3.36
2865 5097 7.201705 GGGTCATCTATTTTAAAACGGAGGAAG 60.202 40.741 15.79 4.66 0.00 3.46
2869 5101 7.838771 TCTATTTTAAAACGGAGGAAGTAGC 57.161 36.000 1.97 0.00 0.00 3.58
2889 5121 7.262772 AGTAGCGAATAGTTAAACATGTAGCA 58.737 34.615 0.00 0.00 0.00 3.49
2895 5127 8.744011 CGAATAGTTAAACATGTAGCAGAGTAC 58.256 37.037 0.00 0.00 0.00 2.73
3152 6664 9.577110 CACACTATGCAAACTTTGATCATATTT 57.423 29.630 5.65 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 8.316640 ACATTAGACAAGCTCTCACTAAAAAG 57.683 34.615 0.00 0.00 0.00 2.27
141 143 9.337396 TGTACTACATCTGAGTTTGTCAAAAAT 57.663 29.630 0.00 0.00 33.60 1.82
145 147 7.050970 AGTGTACTACATCTGAGTTTGTCAA 57.949 36.000 0.00 0.00 33.60 3.18
146 148 6.567891 CGAGTGTACTACATCTGAGTTTGTCA 60.568 42.308 0.00 0.00 0.00 3.58
147 149 5.795939 CGAGTGTACTACATCTGAGTTTGTC 59.204 44.000 0.00 0.00 0.00 3.18
149 151 5.939457 TCGAGTGTACTACATCTGAGTTTG 58.061 41.667 0.00 0.00 0.00 2.93
151 153 5.489249 TCTCGAGTGTACTACATCTGAGTT 58.511 41.667 13.13 0.00 0.00 3.01
152 154 5.087391 TCTCGAGTGTACTACATCTGAGT 57.913 43.478 13.13 0.00 0.00 3.41
153 155 6.128661 GCTATCTCGAGTGTACTACATCTGAG 60.129 46.154 13.13 1.18 0.00 3.35
154 156 5.697178 GCTATCTCGAGTGTACTACATCTGA 59.303 44.000 13.13 0.00 0.00 3.27
155 157 5.106869 GGCTATCTCGAGTGTACTACATCTG 60.107 48.000 13.13 0.00 0.00 2.90
156 158 4.998672 GGCTATCTCGAGTGTACTACATCT 59.001 45.833 13.13 0.00 0.00 2.90
221 227 6.115446 ACCCAATGATGATACTTGTGTACTG 58.885 40.000 0.00 0.00 0.00 2.74
235 241 5.484715 AGCTTTCAATTGAACCCAATGATG 58.515 37.500 20.35 1.24 41.84 3.07
236 242 5.750352 AGCTTTCAATTGAACCCAATGAT 57.250 34.783 20.35 3.46 41.84 2.45
237 243 6.041409 TGTTAGCTTTCAATTGAACCCAATGA 59.959 34.615 20.35 3.48 41.84 2.57
238 244 6.222389 TGTTAGCTTTCAATTGAACCCAATG 58.778 36.000 20.35 7.92 41.84 2.82
239 245 6.418057 TGTTAGCTTTCAATTGAACCCAAT 57.582 33.333 20.35 7.85 44.38 3.16
240 246 5.860941 TGTTAGCTTTCAATTGAACCCAA 57.139 34.783 20.35 9.44 36.61 4.12
253 270 3.244112 ACCAGCGTAGAGTTGTTAGCTTT 60.244 43.478 0.00 0.00 32.05 3.51
261 278 0.438830 GCGAAACCAGCGTAGAGTTG 59.561 55.000 0.00 0.00 0.00 3.16
262 279 0.669625 GGCGAAACCAGCGTAGAGTT 60.670 55.000 0.00 0.00 38.86 3.01
357 375 3.571590 AGCAAAAGTGGTTATTGGTGGA 58.428 40.909 0.00 0.00 33.88 4.02
360 378 4.736473 ACCTAGCAAAAGTGGTTATTGGT 58.264 39.130 0.00 0.00 38.26 3.67
366 384 1.544759 CCGGACCTAGCAAAAGTGGTT 60.545 52.381 0.00 0.00 36.66 3.67
423 441 2.095059 GGCAAGATTTGTACACTGGCTG 60.095 50.000 10.29 1.35 31.96 4.85
439 457 3.804036 TGAATTATCCTACCACGGCAAG 58.196 45.455 0.00 0.00 0.00 4.01
445 463 8.031848 TGTTTTACGTTGAATTATCCTACCAC 57.968 34.615 0.00 0.00 0.00 4.16
451 469 5.511729 GCAGCTGTTTTACGTTGAATTATCC 59.488 40.000 16.64 0.00 0.00 2.59
455 473 3.067461 TGGCAGCTGTTTTACGTTGAATT 59.933 39.130 16.64 0.00 0.00 2.17
503 521 6.546772 GCTGTCTAGTATAGGACTTTAGGTGT 59.453 42.308 0.00 0.00 39.78 4.16
518 536 6.160684 TGAATAAAACTTGCGCTGTCTAGTA 58.839 36.000 9.73 0.00 0.00 1.82
663 719 6.775629 GCCTAGTCTATCTATCTATCCCCAAG 59.224 46.154 0.00 0.00 0.00 3.61
670 726 4.727841 ACCGGGCCTAGTCTATCTATCTAT 59.272 45.833 6.32 0.00 0.00 1.98
671 727 4.110072 ACCGGGCCTAGTCTATCTATCTA 58.890 47.826 6.32 0.00 0.00 1.98
672 728 2.920941 ACCGGGCCTAGTCTATCTATCT 59.079 50.000 6.32 0.00 0.00 1.98
712 768 1.227973 GGGCCGTTGGATGAGGATC 60.228 63.158 0.00 0.00 0.00 3.36
713 769 1.570857 TTGGGCCGTTGGATGAGGAT 61.571 55.000 0.00 0.00 0.00 3.24
716 773 1.303236 TGTTGGGCCGTTGGATGAG 60.303 57.895 0.00 0.00 0.00 2.90
748 805 0.596083 CTACGATCAGAAGGCTGCGG 60.596 60.000 0.00 0.00 42.01 5.69
875 939 0.804544 CGGCGAAATAACTGCGAGGA 60.805 55.000 0.00 0.00 0.00 3.71
916 980 1.605058 GCCAGAAGAGACCGGCTACA 61.605 60.000 0.00 0.00 41.50 2.74
937 1001 3.055458 TGGGCAATACGAATCTGAGTTCA 60.055 43.478 0.00 0.00 0.00 3.18
1164 1228 2.734673 GCAGTGAAGCGCCGAGAAG 61.735 63.158 2.29 0.00 0.00 2.85
1815 1882 0.393077 CCCACCTGTTCGTTCTGTCT 59.607 55.000 0.00 0.00 0.00 3.41
1825 1892 4.974721 CTTGCCCGCCCACCTGTT 62.975 66.667 0.00 0.00 0.00 3.16
1886 1953 4.227134 CCGCCTCCTCATCCACGG 62.227 72.222 0.00 0.00 0.00 4.94
1962 2035 3.578716 TCCCGAGATTCTTCAAGTTCACT 59.421 43.478 0.00 0.00 0.00 3.41
2093 2166 9.831737 AATGAAGATTGTAACGAAGATTTGAAG 57.168 29.630 0.00 0.00 0.00 3.02
2115 2188 3.000041 ACACTTCGCTTGCGAATAATGA 59.000 40.909 26.79 7.64 0.00 2.57
2181 2273 1.067821 CACGGGGACTTCTGCTATCTC 59.932 57.143 0.00 0.00 0.00 2.75
2298 2392 1.000717 CGGGTCTTCCAAAACGCAAAT 60.001 47.619 0.00 0.00 34.36 2.32
2316 2410 5.269505 AGATTGACAATTCTAGAGACCGG 57.730 43.478 0.00 0.00 0.00 5.28
2319 2413 6.593382 ACTGCAAGATTGACAATTCTAGAGAC 59.407 38.462 1.39 0.00 37.43 3.36
2369 2470 1.989165 CTCACGAAAAAGAGAGGCTCG 59.011 52.381 9.22 0.00 35.36 5.03
2418 2527 4.941873 AGACGGAGGTAATTGAATTTGTCC 59.058 41.667 0.00 0.00 0.00 4.02
2498 2615 8.991026 CATCTGAATTCCAACAAAATTTAGCAA 58.009 29.630 2.27 0.00 32.61 3.91
2501 2618 8.537049 TGCATCTGAATTCCAACAAAATTTAG 57.463 30.769 2.27 0.00 33.38 1.85
2620 2741 3.077229 TCACGACTTTAACGAACGGAA 57.923 42.857 0.00 0.00 34.70 4.30
2623 2744 4.817987 ATGATCACGACTTTAACGAACG 57.182 40.909 0.00 0.00 34.70 3.95
2634 2755 1.590238 CCGAGCTTCAATGATCACGAC 59.410 52.381 0.00 0.00 0.00 4.34
2646 2767 2.121009 GAGCTTATCGAACCGAGCTTC 58.879 52.381 13.86 6.55 39.91 3.86
2666 2787 8.492748 TCAACTTAATGAGTGTTAGCTTTAACG 58.507 33.333 0.00 0.00 39.00 3.18
2715 4947 4.630940 ACAATGCTTTTGTGTTGTTTCCAG 59.369 37.500 5.03 0.00 31.20 3.86
2763 4995 5.855045 TGAAACAGAAGGAAGAAGGAGTAC 58.145 41.667 0.00 0.00 0.00 2.73
2764 4996 6.494666 TTGAAACAGAAGGAAGAAGGAGTA 57.505 37.500 0.00 0.00 0.00 2.59
2765 4997 5.373812 TTGAAACAGAAGGAAGAAGGAGT 57.626 39.130 0.00 0.00 0.00 3.85
2766 4998 6.699575 TTTTGAAACAGAAGGAAGAAGGAG 57.300 37.500 0.00 0.00 0.00 3.69
2767 4999 8.760980 TTATTTTGAAACAGAAGGAAGAAGGA 57.239 30.769 0.00 0.00 0.00 3.36
2768 5000 9.987272 ATTTATTTTGAAACAGAAGGAAGAAGG 57.013 29.630 0.00 0.00 0.00 3.46
2771 5003 9.965824 GTCATTTATTTTGAAACAGAAGGAAGA 57.034 29.630 0.00 0.00 0.00 2.87
2772 5004 9.971922 AGTCATTTATTTTGAAACAGAAGGAAG 57.028 29.630 0.00 0.00 0.00 3.46
2773 5005 9.965824 GAGTCATTTATTTTGAAACAGAAGGAA 57.034 29.630 0.00 0.00 0.00 3.36
2774 5006 9.130661 TGAGTCATTTATTTTGAAACAGAAGGA 57.869 29.630 0.00 0.00 0.00 3.36
2775 5007 9.748708 TTGAGTCATTTATTTTGAAACAGAAGG 57.251 29.630 0.00 0.00 0.00 3.46
2833 5065 9.430623 CCGTTTTAAAATAGATGACCCAATTTT 57.569 29.630 3.52 0.00 36.04 1.82
2834 5066 8.808092 TCCGTTTTAAAATAGATGACCCAATTT 58.192 29.630 3.52 0.00 0.00 1.82
2835 5067 8.356000 TCCGTTTTAAAATAGATGACCCAATT 57.644 30.769 3.52 0.00 0.00 2.32
2836 5068 7.068226 CCTCCGTTTTAAAATAGATGACCCAAT 59.932 37.037 3.52 0.00 0.00 3.16
2837 5069 6.376018 CCTCCGTTTTAAAATAGATGACCCAA 59.624 38.462 3.52 0.00 0.00 4.12
2838 5070 5.883673 CCTCCGTTTTAAAATAGATGACCCA 59.116 40.000 3.52 0.00 0.00 4.51
2839 5071 6.117488 TCCTCCGTTTTAAAATAGATGACCC 58.883 40.000 3.52 0.00 0.00 4.46
2840 5072 7.336176 ACTTCCTCCGTTTTAAAATAGATGACC 59.664 37.037 3.52 0.00 0.00 4.02
2841 5073 8.265165 ACTTCCTCCGTTTTAAAATAGATGAC 57.735 34.615 3.52 0.00 0.00 3.06
2842 5074 9.595823 CTACTTCCTCCGTTTTAAAATAGATGA 57.404 33.333 3.52 4.41 0.00 2.92
2843 5075 8.336080 GCTACTTCCTCCGTTTTAAAATAGATG 58.664 37.037 3.52 2.26 0.00 2.90
2844 5076 7.224167 CGCTACTTCCTCCGTTTTAAAATAGAT 59.776 37.037 3.52 0.00 0.00 1.98
2845 5077 6.532657 CGCTACTTCCTCCGTTTTAAAATAGA 59.467 38.462 3.52 3.61 0.00 1.98
2846 5078 6.532657 TCGCTACTTCCTCCGTTTTAAAATAG 59.467 38.462 3.52 1.99 0.00 1.73
2847 5079 6.397272 TCGCTACTTCCTCCGTTTTAAAATA 58.603 36.000 3.52 0.00 0.00 1.40
2848 5080 5.240121 TCGCTACTTCCTCCGTTTTAAAAT 58.760 37.500 3.52 0.00 0.00 1.82
2849 5081 4.630111 TCGCTACTTCCTCCGTTTTAAAA 58.370 39.130 0.00 0.00 0.00 1.52
2850 5082 4.255833 TCGCTACTTCCTCCGTTTTAAA 57.744 40.909 0.00 0.00 0.00 1.52
2851 5083 3.940209 TCGCTACTTCCTCCGTTTTAA 57.060 42.857 0.00 0.00 0.00 1.52
2852 5084 3.940209 TTCGCTACTTCCTCCGTTTTA 57.060 42.857 0.00 0.00 0.00 1.52
2853 5085 2.825861 TTCGCTACTTCCTCCGTTTT 57.174 45.000 0.00 0.00 0.00 2.43
2854 5086 3.446516 ACTATTCGCTACTTCCTCCGTTT 59.553 43.478 0.00 0.00 0.00 3.60
2855 5087 3.022406 ACTATTCGCTACTTCCTCCGTT 58.978 45.455 0.00 0.00 0.00 4.44
2856 5088 2.652590 ACTATTCGCTACTTCCTCCGT 58.347 47.619 0.00 0.00 0.00 4.69
2857 5089 3.712091 AACTATTCGCTACTTCCTCCG 57.288 47.619 0.00 0.00 0.00 4.63
2858 5090 6.335777 TGTTTAACTATTCGCTACTTCCTCC 58.664 40.000 0.00 0.00 0.00 4.30
2859 5091 7.491696 ACATGTTTAACTATTCGCTACTTCCTC 59.508 37.037 0.00 0.00 0.00 3.71
2860 5092 7.328737 ACATGTTTAACTATTCGCTACTTCCT 58.671 34.615 0.00 0.00 0.00 3.36
2861 5093 7.535489 ACATGTTTAACTATTCGCTACTTCC 57.465 36.000 0.00 0.00 0.00 3.46
2862 5094 8.267367 GCTACATGTTTAACTATTCGCTACTTC 58.733 37.037 2.30 0.00 0.00 3.01
2863 5095 7.762615 TGCTACATGTTTAACTATTCGCTACTT 59.237 33.333 2.30 0.00 0.00 2.24
2864 5096 7.262772 TGCTACATGTTTAACTATTCGCTACT 58.737 34.615 2.30 0.00 0.00 2.57
2865 5097 7.434307 TCTGCTACATGTTTAACTATTCGCTAC 59.566 37.037 2.30 0.00 0.00 3.58
2869 5101 7.757097 ACTCTGCTACATGTTTAACTATTCG 57.243 36.000 2.30 0.00 0.00 3.34
2889 5121 0.321122 GGCTGCTGCAGTTGTACTCT 60.321 55.000 28.50 0.00 41.91 3.24
2895 5127 1.288127 GGAAAGGCTGCTGCAGTTG 59.712 57.895 28.50 9.56 41.91 3.16
2903 5135 2.837532 TCAATTTTGGGAAAGGCTGC 57.162 45.000 0.00 0.00 0.00 5.25
2906 5138 5.588246 TGAAAGTTTCAATTTTGGGAAAGGC 59.412 36.000 15.92 0.00 36.59 4.35
2971 5204 9.643693 GACTAATCATTGATGTTCAAACCATTT 57.356 29.630 0.00 0.00 40.12 2.32
2972 5205 8.805175 TGACTAATCATTGATGTTCAAACCATT 58.195 29.630 0.00 0.00 40.12 3.16
3067 6577 4.362677 TGGAGGAAGTATGACTTTAGGCT 58.637 43.478 0.00 0.00 38.80 4.58
3118 6630 6.449635 AAGTTTGCATAGTGTGACTTTTGA 57.550 33.333 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.