Multiple sequence alignment - TraesCS7D01G245900

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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 TraesCS7D01G245900 chr7D 100.000 3074 0 0 1 3074 214965896 214962823 0.000000e+00 5677.0
1 TraesCS7D01G245900 chr7D 89.730 185 16 3 429 612 214965191 214965009 1.840000e-57 233.0
2 TraesCS7D01G245900 chr7D 89.730 185 16 3 706 888 214965468 214965285 1.840000e-57 233.0
3 TraesCS7D01G245900 chr7D 95.122 41 2 0 639 679 34482379 34482339 7.110000e-07 65.8
4 TraesCS7D01G245900 chr7B 93.819 1456 66 4 796 2229 185391144 185389691 0.000000e+00 2169.0
5 TraesCS7D01G245900 chr7B 93.407 91 5 1 521 610 185391144 185391054 1.920000e-27 134.0
6 TraesCS7D01G245900 chr7B 89.744 78 8 0 2228 2305 185389332 185389255 1.950000e-17 100.0
7 TraesCS7D01G245900 chr7A 90.816 1557 87 22 706 2228 227959252 227957718 0.000000e+00 2032.0
8 TraesCS7D01G245900 chr7A 89.200 250 19 8 706 950 227961521 227961275 3.850000e-79 305.0
9 TraesCS7D01G245900 chr7A 88.889 252 23 5 706 953 227966058 227965808 3.850000e-79 305.0
10 TraesCS7D01G245900 chr7A 88.710 248 24 4 706 950 227960386 227960140 1.790000e-77 300.0
11 TraesCS7D01G245900 chr7A 88.710 248 24 4 706 950 227962654 227962408 1.790000e-77 300.0
12 TraesCS7D01G245900 chr7A 88.492 252 24 5 706 953 227964923 227964673 1.790000e-77 300.0
13 TraesCS7D01G245900 chr7A 87.302 252 27 5 706 953 227963788 227963538 1.800000e-72 283.0
14 TraesCS7D01G245900 chr7A 89.604 202 18 3 413 612 227966074 227965874 1.410000e-63 254.0
15 TraesCS7D01G245900 chr7A 89.216 204 19 3 411 612 227961539 227961337 5.090000e-63 252.0
16 TraesCS7D01G245900 chr7A 89.216 204 19 3 411 612 227962672 227962470 5.090000e-63 252.0
17 TraesCS7D01G245900 chr7A 89.109 202 19 3 411 610 227960404 227960204 6.580000e-62 248.0
18 TraesCS7D01G245900 chr7A 87.745 204 22 3 411 612 227964941 227964739 5.120000e-58 235.0
19 TraesCS7D01G245900 chr7A 85.714 119 15 2 37 154 717979596 717979713 1.160000e-24 124.0
20 TraesCS7D01G245900 chr2B 94.536 787 27 7 2301 3074 762512723 762511940 0.000000e+00 1201.0
21 TraesCS7D01G245900 chr2B 85.714 56 7 1 635 689 561208486 561208541 1.190000e-04 58.4
22 TraesCS7D01G245900 chr1A 94.051 790 26 15 2302 3074 550415738 550414953 0.000000e+00 1179.0
23 TraesCS7D01G245900 chr1A 93.766 786 31 12 2304 3074 294732156 294732938 0.000000e+00 1164.0
24 TraesCS7D01G245900 chr5A 93.257 786 34 7 2302 3074 520646163 520645384 0.000000e+00 1140.0
25 TraesCS7D01G245900 chr4B 92.152 790 43 12 2302 3074 40229570 40228783 0.000000e+00 1098.0
26 TraesCS7D01G245900 chr4B 83.333 354 51 7 2367 2716 514623841 514624190 1.380000e-83 320.0
27 TraesCS7D01G245900 chr3B 81.435 474 56 21 1 446 126568061 126568530 2.910000e-95 359.0
28 TraesCS7D01G245900 chr2A 82.185 421 57 12 41 447 749853287 749852871 2.270000e-91 346.0
29 TraesCS7D01G245900 chr2A 81.481 243 41 4 133 372 608870044 608869803 2.420000e-46 196.0
30 TraesCS7D01G245900 chr2A 85.470 117 15 2 1 116 749853374 749853259 1.500000e-23 121.0
31 TraesCS7D01G245900 chr2A 97.222 36 1 0 81 116 33347973 33348008 9.200000e-06 62.1
32 TraesCS7D01G245900 chr2D 86.196 326 31 9 133 446 247847899 247847576 1.060000e-89 340.0
33 TraesCS7D01G245900 chr2D 80.815 417 65 10 37 440 318260664 318261078 2.300000e-81 313.0
34 TraesCS7D01G245900 chr6D 80.303 462 71 15 1 446 149892674 149893131 6.350000e-87 331.0
35 TraesCS7D01G245900 chr3D 80.376 479 58 17 1 445 26645477 26645953 6.350000e-87 331.0
36 TraesCS7D01G245900 chr1D 83.754 357 47 8 2367 2716 427736861 427737213 8.220000e-86 327.0
37 TraesCS7D01G245900 chr1D 88.034 117 12 2 1 116 256080504 256080389 1.490000e-28 137.0
38 TraesCS7D01G245900 chr1B 85.849 318 33 7 133 439 198656603 198656287 8.220000e-86 327.0
39 TraesCS7D01G245900 chr1B 83.427 356 46 11 2367 2716 626701109 626700761 4.950000e-83 318.0
40 TraesCS7D01G245900 chr1B 91.667 108 6 3 1 107 625144091 625144196 2.470000e-31 147.0
41 TraesCS7D01G245900 chrUn 86.466 266 31 5 123 386 363763260 363762998 1.390000e-73 287.0
42 TraesCS7D01G245900 chr5B 86.486 259 31 4 130 386 534913533 534913789 6.490000e-72 281.0
43 TraesCS7D01G245900 chr5D 85.878 262 31 6 133 391 500685289 500685031 1.090000e-69 274.0
44 TraesCS7D01G245900 chr5D 82.840 169 16 8 3 159 507619262 507619429 4.130000e-29 139.0
45 TraesCS7D01G245900 chr4A 81.325 166 17 10 1 154 547310140 547310303 4.160000e-24 122.0
46 TraesCS7D01G245900 chr6B 86.111 108 14 1 1 108 707028864 707028758 6.970000e-22 115.0


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 TraesCS7D01G245900 chr7D 214962823 214965896 3073 True 2047.666667 5677 93.153333 1 3074 3 chr7D.!!$R2 3073
1 TraesCS7D01G245900 chr7B 185389255 185391144 1889 True 801.000000 2169 92.323333 521 2305 3 chr7B.!!$R1 1784
2 TraesCS7D01G245900 chr7A 227957718 227966074 8356 True 422.166667 2032 88.917417 411 2228 12 chr7A.!!$R1 1817
3 TraesCS7D01G245900 chr2B 762511940 762512723 783 True 1201.000000 1201 94.536000 2301 3074 1 chr2B.!!$R1 773
4 TraesCS7D01G245900 chr1A 550414953 550415738 785 True 1179.000000 1179 94.051000 2302 3074 1 chr1A.!!$R1 772
5 TraesCS7D01G245900 chr1A 294732156 294732938 782 False 1164.000000 1164 93.766000 2304 3074 1 chr1A.!!$F1 770
6 TraesCS7D01G245900 chr5A 520645384 520646163 779 True 1140.000000 1140 93.257000 2302 3074 1 chr5A.!!$R1 772
7 TraesCS7D01G245900 chr4B 40228783 40229570 787 True 1098.000000 1098 92.152000 2302 3074 1 chr4B.!!$R1 772
8 TraesCS7D01G245900 chr2A 749852871 749853374 503 True 233.500000 346 83.827500 1 447 2 chr2A.!!$R2 446

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
250 298 0.028374 GTTTCACCCACACGTTTCGG 59.972 55.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2249 9213 0.172578 TCTCCTGCGTAATCACCGTG 59.827 55.0 0.0 0.0 0.0 4.94 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
33 34 2.738521 CACCCCGTGAGCGTGAAG 60.739 66.667 0.00 0.00 35.23 3.02
49 51 4.175516 CGTGAAGCGTGGGTAATTAACTA 58.824 43.478 0.00 0.00 35.54 2.24
52 54 6.143438 CGTGAAGCGTGGGTAATTAACTATAG 59.857 42.308 0.00 0.00 35.54 1.31
63 65 7.501225 GGGTAATTAACTATAGTTGCCATGTGT 59.499 37.037 25.27 1.08 35.90 3.72
72 74 8.974238 ACTATAGTTGCCATGTGTAGTTAACTA 58.026 33.333 11.38 11.38 34.75 2.24
79 81 6.537301 TGCCATGTGTAGTTAACTATAGTTGC 59.463 38.462 25.27 17.77 38.90 4.17
121 145 5.772672 AGTTGCCATGTGTAACTAATTGGAA 59.227 36.000 13.26 0.00 46.46 3.53
123 147 6.206395 TGCCATGTGTAACTAATTGGAATG 57.794 37.500 0.00 0.00 38.04 2.67
124 148 5.043248 GCCATGTGTAACTAATTGGAATGC 58.957 41.667 0.00 0.00 38.04 3.56
126 150 5.126869 CCATGTGTAACTAATTGGAATGCCA 59.873 40.000 0.00 0.00 39.54 4.92
127 151 5.637006 TGTGTAACTAATTGGAATGCCAC 57.363 39.130 0.00 0.00 40.64 5.01
131 179 2.091541 ACTAATTGGAATGCCACCGTG 58.908 47.619 0.00 0.00 45.94 4.94
162 210 5.046448 ACCATTGTTGCCATGTGTGATTAAT 60.046 36.000 0.00 0.00 0.00 1.40
165 213 7.548427 CCATTGTTGCCATGTGTGATTAATTAA 59.452 33.333 0.00 0.00 0.00 1.40
169 217 9.579768 TGTTGCCATGTGTGATTAATTAATTAC 57.420 29.630 20.61 20.61 34.06 1.89
191 239 4.332543 ACCACATATGCACGATTGTAGTTG 59.667 41.667 1.58 0.00 0.00 3.16
203 251 4.449068 CGATTGTAGTTGCCATCTATCACC 59.551 45.833 0.00 0.00 0.00 4.02
204 252 4.835284 TTGTAGTTGCCATCTATCACCA 57.165 40.909 0.00 0.00 0.00 4.17
207 255 3.939740 AGTTGCCATCTATCACCATGT 57.060 42.857 0.00 0.00 0.00 3.21
212 260 2.410939 CCATCTATCACCATGTGAGCG 58.589 52.381 3.11 0.00 46.04 5.03
214 262 3.461061 CATCTATCACCATGTGAGCGTT 58.539 45.455 3.11 0.00 46.04 4.84
218 266 0.105778 TCACCATGTGAGCGTTGTGA 59.894 50.000 0.00 0.00 37.67 3.58
229 277 1.006102 CGTTGTGAGGGCGAAGAGT 60.006 57.895 0.00 0.00 0.00 3.24
234 282 1.968493 TGTGAGGGCGAAGAGTAGTTT 59.032 47.619 0.00 0.00 0.00 2.66
244 292 2.814280 AGAGTAGTTTCACCCACACG 57.186 50.000 0.00 0.00 0.00 4.49
245 293 2.037144 AGAGTAGTTTCACCCACACGT 58.963 47.619 0.00 0.00 0.00 4.49
250 298 0.028374 GTTTCACCCACACGTTTCGG 59.972 55.000 0.00 0.00 0.00 4.30
251 299 0.107800 TTTCACCCACACGTTTCGGA 60.108 50.000 0.00 0.00 0.00 4.55
271 321 2.704193 GAGCGTCGTGTTCGTTCGG 61.704 63.158 0.00 0.00 38.33 4.30
272 322 3.759828 GCGTCGTGTTCGTTCGGG 61.760 66.667 0.00 0.00 38.33 5.14
302 352 2.414138 GCCGACACATGTGGTACTAAAC 59.586 50.000 28.64 6.95 34.19 2.01
304 354 2.664568 CGACACATGTGGTACTAAACGG 59.335 50.000 28.64 0.23 34.19 4.44
359 409 0.037326 TCGACCCAGATGACAACTGC 60.037 55.000 7.19 0.00 34.47 4.40
394 449 3.485711 GCAAATGAATCGAATCGACTGCA 60.486 43.478 7.77 6.94 39.18 4.41
400 455 1.368641 TCGAATCGACTGCATTTGGG 58.631 50.000 0.00 0.00 0.00 4.12
402 457 1.098050 GAATCGACTGCATTTGGGCT 58.902 50.000 0.00 0.00 34.04 5.19
409 468 3.376859 CGACTGCATTTGGGCTATGTAAA 59.623 43.478 0.00 0.00 34.04 2.01
419 478 1.333619 GGCTATGTAAATGCCACACGG 59.666 52.381 0.00 0.00 45.46 4.94
431 490 2.046700 ACACGGGTGGGCGTTATG 60.047 61.111 0.00 0.00 34.19 1.90
504 563 3.492011 AGTGTTTTTGTTAGTCCGTAGCG 59.508 43.478 0.00 0.00 0.00 4.26
510 569 1.475280 TGTTAGTCCGTAGCGAGCATT 59.525 47.619 0.00 0.00 0.00 3.56
514 573 1.141019 TCCGTAGCGAGCATTGACC 59.859 57.895 0.00 0.00 0.00 4.02
519 578 0.175760 TAGCGAGCATTGACCCAGTC 59.824 55.000 0.00 0.00 0.00 3.51
534 594 4.277476 ACCCAGTCAGAAAAACAATGACA 58.723 39.130 7.25 0.00 44.59 3.58
542 602 7.223387 AGTCAGAAAAACAATGACAGAAATTGC 59.777 33.333 7.25 0.00 44.59 3.56
549 609 1.678970 GACAGAAATTGCCCCCGCT 60.679 57.895 0.00 0.00 35.36 5.52
556 616 2.069165 AATTGCCCCCGCTCCCTATC 62.069 60.000 0.00 0.00 35.36 2.08
599 660 1.069823 CTATCCATCCGCTCACAGCTT 59.930 52.381 0.00 0.00 39.60 3.74
612 1801 2.612115 AGCTTCCCCACTCCCCAG 60.612 66.667 0.00 0.00 0.00 4.45
628 1817 1.990060 CAGTCCCCACCCATCTCGT 60.990 63.158 0.00 0.00 0.00 4.18
629 1818 1.229529 AGTCCCCACCCATCTCGTT 60.230 57.895 0.00 0.00 0.00 3.85
631 1820 1.537889 TCCCCACCCATCTCGTTGT 60.538 57.895 0.00 0.00 0.00 3.32
632 1821 0.252330 TCCCCACCCATCTCGTTGTA 60.252 55.000 0.00 0.00 0.00 2.41
633 1822 0.616371 CCCCACCCATCTCGTTGTAA 59.384 55.000 0.00 0.00 0.00 2.41
639 2404 4.273480 CCACCCATCTCGTTGTAATCAATC 59.727 45.833 0.00 0.00 35.92 2.67
641 2406 5.235186 CACCCATCTCGTTGTAATCAATCTC 59.765 44.000 0.00 0.00 35.92 2.75
642 2407 4.445718 CCCATCTCGTTGTAATCAATCTCG 59.554 45.833 0.00 0.00 35.92 4.04
646 2411 4.862574 TCTCGTTGTAATCAATCTCGTTGG 59.137 41.667 0.00 0.00 38.39 3.77
648 2413 4.992319 TCGTTGTAATCAATCTCGTTGGTT 59.008 37.500 0.00 0.00 43.42 3.67
679 2444 9.886132 TTATAGTCAAACTTAGATCTGGGAAAC 57.114 33.333 5.18 0.00 0.00 2.78
680 2445 5.238583 AGTCAAACTTAGATCTGGGAAACG 58.761 41.667 5.18 0.00 0.00 3.60
682 2447 2.295253 ACTTAGATCTGGGAAACGCG 57.705 50.000 3.53 3.53 0.00 6.01
687 2452 2.822764 AGATCTGGGAAACGCGAATAC 58.177 47.619 15.93 0.20 0.00 1.89
689 2454 1.717194 TCTGGGAAACGCGAATACAC 58.283 50.000 15.93 2.59 0.00 2.90
690 2455 0.368907 CTGGGAAACGCGAATACACG 59.631 55.000 15.93 0.00 0.00 4.49
691 2456 0.319727 TGGGAAACGCGAATACACGT 60.320 50.000 15.93 0.00 46.07 4.49
692 2457 0.094046 GGGAAACGCGAATACACGTG 59.906 55.000 15.93 15.48 42.68 4.49
693 2458 0.094046 GGAAACGCGAATACACGTGG 59.906 55.000 21.57 2.06 46.02 4.94
694 2459 1.062258 GAAACGCGAATACACGTGGA 58.938 50.000 21.57 13.01 46.02 4.02
698 2463 1.273688 CGCGAATACACGTGGAATGA 58.726 50.000 21.57 0.00 39.60 2.57
700 2465 2.285026 CGCGAATACACGTGGAATGAAG 60.285 50.000 21.57 4.19 39.60 3.02
701 2466 2.030457 GCGAATACACGTGGAATGAAGG 59.970 50.000 21.57 0.44 35.59 3.46
702 2467 2.607635 CGAATACACGTGGAATGAAGGG 59.392 50.000 21.57 0.00 0.00 3.95
704 2469 3.543680 ATACACGTGGAATGAAGGGAG 57.456 47.619 21.57 0.00 0.00 4.30
715 3902 7.509546 GTGGAATGAAGGGAGTATCATTTAGA 58.490 38.462 2.87 0.00 44.15 2.10
717 3904 8.159447 TGGAATGAAGGGAGTATCATTTAGATG 58.841 37.037 2.87 0.00 44.15 2.90
720 3907 7.437713 TGAAGGGAGTATCATTTAGATGTGT 57.562 36.000 0.00 0.00 37.57 3.72
722 3909 7.987458 TGAAGGGAGTATCATTTAGATGTGTTC 59.013 37.037 0.00 0.00 37.57 3.18
816 5137 7.869800 AGTCAGAAGAAACAATGACAGAAATC 58.130 34.615 6.91 0.00 43.55 2.17
824 5145 1.910580 ATGACAGAAATCGCCCCCGT 61.911 55.000 0.00 0.00 35.54 5.28
870 5192 0.894141 CTCCCTATCCATCCGCTCAG 59.106 60.000 0.00 0.00 0.00 3.35
876 6333 1.470996 ATCCATCCGCTCAGAGCTCC 61.471 60.000 20.39 0.00 39.60 4.70
886 6343 4.423209 AGAGCTCCCCCACTCCCC 62.423 72.222 10.93 0.00 33.18 4.81
937 6394 2.383170 CCAACATGGGATGACGTCG 58.617 57.895 11.62 0.00 32.67 5.12
939 6396 0.391130 CAACATGGGATGACGTCGGT 60.391 55.000 11.62 1.47 0.00 4.69
951 6408 1.347221 CGTCGGTCGCAAAATAGGC 59.653 57.895 0.00 0.00 0.00 3.93
958 7515 3.899700 GCAAAATAGGCGCCCCCG 61.900 66.667 26.15 7.20 39.21 5.73
1199 7772 2.261671 CAACGACCCTGGTCTCCG 59.738 66.667 14.10 4.72 42.54 4.63
1204 7777 2.203788 ACCCTGGTCTCCGCTTCA 60.204 61.111 0.00 0.00 0.00 3.02
1288 7861 1.079057 GCCGAGTTCAACCTCCTCC 60.079 63.158 0.00 0.00 0.00 4.30
1734 8307 1.959226 GCCACGCTCCGACAAGAAA 60.959 57.895 0.00 0.00 0.00 2.52
1760 8339 1.023513 AGCAAAGCAGATGTCTCGCC 61.024 55.000 0.00 0.00 0.00 5.54
1837 8437 0.955428 GCAACTGGAGGCGATGAACA 60.955 55.000 0.00 0.00 0.00 3.18
1846 8446 1.153745 GCGATGAACACGGAGAGCT 60.154 57.895 0.00 0.00 0.00 4.09
2130 8730 2.143008 TGCTGCAGTGCTGATTTTTG 57.857 45.000 24.47 2.62 0.00 2.44
2155 8758 7.673504 TGGATTTTGGATTGGAATAAGAACAGA 59.326 33.333 0.00 0.00 0.00 3.41
2158 8761 5.178096 TGGATTGGAATAAGAACAGAGCA 57.822 39.130 0.00 0.00 0.00 4.26
2173 8776 6.881065 AGAACAGAGCAAATTCAGTAGCATTA 59.119 34.615 0.00 0.00 0.00 1.90
2287 9251 6.008960 AGGAGATCAGGGCAAATGATTTATC 58.991 40.000 0.00 0.00 37.52 1.75
2294 9258 6.040054 TCAGGGCAAATGATTTATCATCTGTG 59.960 38.462 5.73 6.27 46.22 3.66
2299 9263 6.921307 GCAAATGATTTATCATCTGTGCATGA 59.079 34.615 20.07 0.00 46.22 3.07
2322 9286 2.163010 ACTAGTTAGTATGCACGTGCGT 59.837 45.455 35.14 35.14 43.64 5.24
2546 9525 4.456662 ACCACACCATACCCTAACAAAA 57.543 40.909 0.00 0.00 0.00 2.44
2616 9595 7.506328 ACTTGGAGTAACATGGAAAACTAAC 57.494 36.000 0.00 0.00 0.00 2.34
2810 9796 5.830799 TCAATGGTCTATCATAGGCACAT 57.169 39.130 0.00 0.00 30.24 3.21
2895 9881 2.359354 TTGCATACGCCCGCAGTT 60.359 55.556 0.00 0.00 39.75 3.16
2929 9915 2.366590 CACTCACATGCATCCTAGCCTA 59.633 50.000 0.00 0.00 0.00 3.93
2967 9955 8.511604 TTTAAGAACATGGGAATTTTGCAAAA 57.488 26.923 25.76 25.76 0.00 2.44
2968 9956 6.375945 AAGAACATGGGAATTTTGCAAAAC 57.624 33.333 26.05 14.51 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 5.049886 GGCAACTATAGTTAATTACCCACGC 60.050 44.000 17.62 12.12 36.32 5.34
34 35 6.050432 TGGCAACTATAGTTAATTACCCACG 58.950 40.000 17.62 3.23 36.32 4.94
35 36 7.501225 ACATGGCAACTATAGTTAATTACCCAC 59.499 37.037 17.62 2.33 36.32 4.61
36 37 7.500892 CACATGGCAACTATAGTTAATTACCCA 59.499 37.037 17.62 15.52 36.32 4.51
37 38 7.501225 ACACATGGCAACTATAGTTAATTACCC 59.499 37.037 17.62 11.24 36.32 3.69
49 51 9.982651 CTATAGTTAACTACACATGGCAACTAT 57.017 33.333 17.45 8.59 39.65 2.12
52 54 8.388103 CAACTATAGTTAACTACACATGGCAAC 58.612 37.037 17.45 0.00 36.32 4.17
63 65 7.842982 TCACACATGGCAACTATAGTTAACTA 58.157 34.615 17.62 17.41 36.32 2.24
65 67 6.978343 TCACACATGGCAACTATAGTTAAC 57.022 37.500 17.62 13.40 36.32 2.01
72 74 7.466746 AAAGTTAATCACACATGGCAACTAT 57.533 32.000 0.00 0.00 37.61 2.12
79 81 6.092748 GGCAACTAAAGTTAATCACACATGG 58.907 40.000 0.00 0.00 36.32 3.66
162 210 7.561021 ACAATCGTGCATATGTGGTAATTAA 57.439 32.000 4.29 0.00 0.00 1.40
165 213 6.288294 ACTACAATCGTGCATATGTGGTAAT 58.712 36.000 4.29 0.00 36.00 1.89
168 216 4.137116 ACTACAATCGTGCATATGTGGT 57.863 40.909 4.29 0.00 33.40 4.16
169 217 4.786292 GCAACTACAATCGTGCATATGTGG 60.786 45.833 4.29 0.00 0.00 4.17
181 229 5.368145 TGGTGATAGATGGCAACTACAATC 58.632 41.667 6.64 3.13 37.61 2.67
183 231 4.835284 TGGTGATAGATGGCAACTACAA 57.165 40.909 6.64 0.00 37.61 2.41
185 233 4.512944 CACATGGTGATAGATGGCAACTAC 59.487 45.833 6.64 0.00 35.23 2.73
191 239 2.149578 GCTCACATGGTGATAGATGGC 58.850 52.381 0.00 0.00 41.94 4.40
203 251 1.915614 GCCCTCACAACGCTCACATG 61.916 60.000 0.00 0.00 0.00 3.21
204 252 1.672356 GCCCTCACAACGCTCACAT 60.672 57.895 0.00 0.00 0.00 3.21
207 255 3.158537 TTCGCCCTCACAACGCTCA 62.159 57.895 0.00 0.00 0.00 4.26
212 260 1.272769 ACTACTCTTCGCCCTCACAAC 59.727 52.381 0.00 0.00 0.00 3.32
214 262 1.629043 AACTACTCTTCGCCCTCACA 58.371 50.000 0.00 0.00 0.00 3.58
218 266 1.275573 GGTGAAACTACTCTTCGCCCT 59.724 52.381 4.18 0.00 44.36 5.19
229 277 2.203401 CGAAACGTGTGGGTGAAACTA 58.797 47.619 0.00 0.00 36.74 2.24
234 282 1.227321 GTCCGAAACGTGTGGGTGA 60.227 57.895 6.67 0.00 0.00 4.02
257 305 3.759828 CGCCCGAACGAACACGAC 61.760 66.667 0.00 0.00 34.06 4.34
284 334 3.656559 ACCGTTTAGTACCACATGTGTC 58.343 45.455 23.79 13.61 0.00 3.67
289 339 3.253230 GCGTTACCGTTTAGTACCACAT 58.747 45.455 0.00 0.00 36.15 3.21
302 352 3.107661 GTCGTGTGGGCGTTACCG 61.108 66.667 0.00 0.00 40.62 4.02
304 354 3.770424 GCGTCGTGTGGGCGTTAC 61.770 66.667 0.00 0.00 0.00 2.50
325 375 1.071567 GTCGAGAGCCACGTAAGCAC 61.072 60.000 11.84 5.88 45.62 4.40
327 377 1.516603 GGTCGAGAGCCACGTAAGC 60.517 63.158 1.59 1.59 45.62 3.09
400 455 1.333619 CCCGTGTGGCATTTACATAGC 59.666 52.381 0.00 0.00 0.00 2.97
402 457 2.360844 CACCCGTGTGGCATTTACATA 58.639 47.619 0.00 0.00 38.90 2.29
419 478 2.927028 ACCTAAATCATAACGCCCACC 58.073 47.619 0.00 0.00 0.00 4.61
494 553 0.179134 GTCAATGCTCGCTACGGACT 60.179 55.000 0.00 0.00 0.00 3.85
495 554 1.146358 GGTCAATGCTCGCTACGGAC 61.146 60.000 0.00 0.00 0.00 4.79
497 556 1.883084 GGGTCAATGCTCGCTACGG 60.883 63.158 0.00 0.00 0.00 4.02
504 563 2.479566 TTCTGACTGGGTCAATGCTC 57.520 50.000 2.04 0.00 42.26 4.26
510 569 4.338118 GTCATTGTTTTTCTGACTGGGTCA 59.662 41.667 0.43 0.43 40.50 4.02
514 573 5.756195 TCTGTCATTGTTTTTCTGACTGG 57.244 39.130 8.34 1.12 39.94 4.00
519 578 6.293027 GGGCAATTTCTGTCATTGTTTTTCTG 60.293 38.462 0.00 0.00 34.58 3.02
534 594 2.043953 GGAGCGGGGGCAATTTCT 60.044 61.111 0.00 0.00 0.00 2.52
549 609 0.267960 GGTGAAGAGGGGGATAGGGA 59.732 60.000 0.00 0.00 0.00 4.20
556 616 2.153401 TGTGTGGGTGAAGAGGGGG 61.153 63.158 0.00 0.00 0.00 5.40
599 660 4.348495 GGGACTGGGGAGTGGGGA 62.348 72.222 0.00 0.00 0.00 4.81
612 1801 1.078426 CAACGAGATGGGTGGGGAC 60.078 63.158 0.00 0.00 0.00 4.46
654 2419 8.195436 CGTTTCCCAGATCTAAGTTTGACTATA 58.805 37.037 0.00 0.00 0.00 1.31
658 2423 4.142881 GCGTTTCCCAGATCTAAGTTTGAC 60.143 45.833 0.00 0.00 0.00 3.18
660 2425 3.181520 CGCGTTTCCCAGATCTAAGTTTG 60.182 47.826 0.00 0.00 0.00 2.93
661 2426 3.000727 CGCGTTTCCCAGATCTAAGTTT 58.999 45.455 0.00 0.00 0.00 2.66
662 2427 2.232941 TCGCGTTTCCCAGATCTAAGTT 59.767 45.455 5.77 0.00 0.00 2.66
663 2428 1.822990 TCGCGTTTCCCAGATCTAAGT 59.177 47.619 5.77 0.00 0.00 2.24
664 2429 2.579207 TCGCGTTTCCCAGATCTAAG 57.421 50.000 5.77 0.00 0.00 2.18
665 2430 3.536956 ATTCGCGTTTCCCAGATCTAA 57.463 42.857 5.77 0.00 0.00 2.10
666 2431 3.382227 TGTATTCGCGTTTCCCAGATCTA 59.618 43.478 5.77 0.00 0.00 1.98
667 2432 2.167693 TGTATTCGCGTTTCCCAGATCT 59.832 45.455 5.77 0.00 0.00 2.75
669 2434 2.277084 GTGTATTCGCGTTTCCCAGAT 58.723 47.619 5.77 0.00 0.00 2.90
670 2435 1.717194 GTGTATTCGCGTTTCCCAGA 58.283 50.000 5.77 0.00 0.00 3.86
671 2436 0.368907 CGTGTATTCGCGTTTCCCAG 59.631 55.000 5.77 0.00 41.80 4.45
672 2437 2.447408 CGTGTATTCGCGTTTCCCA 58.553 52.632 5.77 0.00 41.80 4.37
680 2445 2.030457 CCTTCATTCCACGTGTATTCGC 59.970 50.000 15.65 0.00 0.00 4.70
682 2447 3.869065 TCCCTTCATTCCACGTGTATTC 58.131 45.455 15.65 0.00 0.00 1.75
687 2452 3.118775 TGATACTCCCTTCATTCCACGTG 60.119 47.826 9.08 9.08 0.00 4.49
689 2454 3.819564 TGATACTCCCTTCATTCCACG 57.180 47.619 0.00 0.00 0.00 4.94
690 2455 7.509546 TCTAAATGATACTCCCTTCATTCCAC 58.490 38.462 0.00 0.00 40.70 4.02
691 2456 7.690454 TCTAAATGATACTCCCTTCATTCCA 57.310 36.000 0.00 0.00 40.70 3.53
692 2457 8.160106 ACATCTAAATGATACTCCCTTCATTCC 58.840 37.037 0.00 0.00 40.70 3.01
693 2458 8.997323 CACATCTAAATGATACTCCCTTCATTC 58.003 37.037 0.00 0.00 40.70 2.67
694 2459 8.497745 ACACATCTAAATGATACTCCCTTCATT 58.502 33.333 0.00 0.00 42.77 2.57
698 2463 7.861629 TGAACACATCTAAATGATACTCCCTT 58.138 34.615 0.00 0.00 36.67 3.95
700 2465 7.552687 TGTTGAACACATCTAAATGATACTCCC 59.447 37.037 0.00 0.00 36.67 4.30
701 2466 8.492673 TGTTGAACACATCTAAATGATACTCC 57.507 34.615 0.00 0.00 36.67 3.85
702 2467 9.926751 CATGTTGAACACATCTAAATGATACTC 57.073 33.333 0.00 0.00 43.17 2.59
768 5088 2.418197 GGTCAATGCTTGCTACGGAGTA 60.418 50.000 0.00 0.00 45.11 2.59
770 5090 1.009829 GGTCAATGCTTGCTACGGAG 58.990 55.000 0.00 0.00 0.00 4.63
771 5091 0.613260 AGGTCAATGCTTGCTACGGA 59.387 50.000 0.00 0.00 0.00 4.69
773 5093 2.860735 GACTAGGTCAATGCTTGCTACG 59.139 50.000 0.00 0.00 32.09 3.51
774 5094 3.861840 TGACTAGGTCAATGCTTGCTAC 58.138 45.455 0.00 0.00 39.78 3.58
785 5106 6.183360 TGTCATTGTTTCTTCTGACTAGGTCA 60.183 38.462 0.00 0.43 40.50 4.02
789 5110 7.953158 TTCTGTCATTGTTTCTTCTGACTAG 57.047 36.000 0.00 0.00 38.98 2.57
790 5111 8.908786 ATTTCTGTCATTGTTTCTTCTGACTA 57.091 30.769 0.00 0.00 38.98 2.59
794 5115 5.566774 GCGATTTCTGTCATTGTTTCTTCTG 59.433 40.000 0.00 0.00 0.00 3.02
824 5145 0.398098 GTGAAGACGGGGATAGGGGA 60.398 60.000 0.00 0.00 0.00 4.81
836 5158 0.250338 GGGAGTGTGTGGGTGAAGAC 60.250 60.000 0.00 0.00 0.00 3.01
870 5192 4.741239 TGGGGAGTGGGGGAGCTC 62.741 72.222 4.71 4.71 0.00 4.09
876 6333 3.420482 GATGGGTGGGGAGTGGGG 61.420 72.222 0.00 0.00 0.00 4.96
958 7515 2.885113 GGGGCTTTGATTGGTCGC 59.115 61.111 0.00 0.00 0.00 5.19
1039 7612 2.676121 CACCTTGGCCCGCATCAA 60.676 61.111 0.00 0.00 0.00 2.57
1199 7772 1.162800 GCGGATGGAGATGGTGAAGC 61.163 60.000 0.00 0.00 0.00 3.86
1204 7777 4.241555 GGCGCGGATGGAGATGGT 62.242 66.667 8.83 0.00 0.00 3.55
1288 7861 1.144936 GAGATCCGGAGTTGGCAGG 59.855 63.158 11.34 0.00 0.00 4.85
1377 7950 2.757099 GTACGGGGCGGAGGAGAA 60.757 66.667 0.00 0.00 0.00 2.87
1723 8296 2.218603 GCTGTCCTTTTTCTTGTCGGA 58.781 47.619 0.00 0.00 0.00 4.55
1734 8307 2.555757 GACATCTGCTTTGCTGTCCTTT 59.444 45.455 0.00 0.00 33.51 3.11
1936 8536 1.078848 AGAACCCGTGATGCAGCTC 60.079 57.895 2.53 0.00 0.00 4.09
1940 8540 2.264480 CCGAGAACCCGTGATGCA 59.736 61.111 0.00 0.00 0.00 3.96
2098 8698 1.168407 TGCAGCAACCAAGAGTGAGC 61.168 55.000 0.00 0.00 0.00 4.26
2130 8730 8.066612 TCTGTTCTTATTCCAATCCAAAATCC 57.933 34.615 0.00 0.00 0.00 3.01
2155 8758 4.191544 TCGCTAATGCTACTGAATTTGCT 58.808 39.130 0.00 0.00 37.66 3.91
2158 8761 4.446371 AGCTCGCTAATGCTACTGAATTT 58.554 39.130 0.00 0.00 37.81 1.82
2173 8776 1.068434 GCTCCAGATTTCTAGCTCGCT 59.932 52.381 0.00 0.00 32.18 4.93
2237 9201 1.832883 TCACCGTGCTGGCAATATTT 58.167 45.000 0.00 0.00 43.94 1.40
2239 9203 2.057137 AATCACCGTGCTGGCAATAT 57.943 45.000 0.00 0.00 43.94 1.28
2242 9206 1.295357 CGTAATCACCGTGCTGGCAA 61.295 55.000 0.00 0.00 43.94 4.52
2243 9207 1.739929 CGTAATCACCGTGCTGGCA 60.740 57.895 0.00 0.00 43.94 4.92
2249 9213 0.172578 TCTCCTGCGTAATCACCGTG 59.827 55.000 0.00 0.00 0.00 4.94
2287 9251 9.351570 CATACTAACTAGTATCATGCACAGATG 57.648 37.037 12.46 0.00 45.16 2.90
2294 9258 6.088217 CACGTGCATACTAACTAGTATCATGC 59.912 42.308 17.93 17.93 45.16 4.06
2465 9444 8.197988 AGGATACGATTGATTTTGTCTTGTAC 57.802 34.615 0.00 0.00 46.39 2.90
2680 9666 9.241317 GTGATGCTTATTATTTTGTTCCATCAG 57.759 33.333 0.00 0.00 37.71 2.90
2844 9830 8.340618 TCTTTTGCTTCAATGTTAGATAGCTT 57.659 30.769 0.00 0.00 0.00 3.74
2895 9881 0.313043 GTGAGTGTCCGAAGTCCGAA 59.687 55.000 0.00 0.00 41.76 4.30
2929 9915 6.127730 CCATGTTCTTAAAATTAGCCGAGGTT 60.128 38.462 0.00 0.00 0.00 3.50
3050 10038 3.354397 GCTTGTAAGCGAAAATCGATGG 58.646 45.455 0.00 0.00 43.74 3.51


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

AutoCloner maintained by Alex Coulton.