Multiple sequence alignment - TraesCS6A01G039400

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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 TraesCS6A01G039400 chr6A 100.000 2612 0 0 1 2612 20340901 20338290 0.000000e+00 4824.0
1 TraesCS6A01G039400 chr6A 80.157 1270 187 41 964 2186 20310455 20309204 0.000000e+00 889.0
2 TraesCS6A01G039400 chr6A 79.587 1308 202 38 904 2167 20522362 20521076 0.000000e+00 876.0
3 TraesCS6A01G039400 chr6B 88.889 1854 127 36 826 2610 34685452 34683609 0.000000e+00 2209.0
4 TraesCS6A01G039400 chr6B 87.592 814 66 19 17 819 34686533 34685744 0.000000e+00 911.0
5 TraesCS6A01G039400 chr6B 79.491 1336 216 36 879 2171 34341484 34340164 0.000000e+00 896.0
6 TraesCS6A01G039400 chr6B 79.739 1303 203 35 910 2167 35529359 35528073 0.000000e+00 887.0
7 TraesCS6A01G039400 chr6B 84.118 170 21 6 479 648 34686407 34686244 2.690000e-35 159.0
8 TraesCS6A01G039400 chr6D 80.207 1354 206 36 879 2187 20312275 20310939 0.000000e+00 959.0
9 TraesCS6A01G039400 chr6D 79.818 1318 207 35 892 2167 20602636 20601336 0.000000e+00 905.0
10 TraesCS6A01G039400 chrUn 79.700 1335 215 30 879 2171 273854757 273856077 0.000000e+00 913.0
11 TraesCS6A01G039400 chr7D 77.859 1224 214 32 891 2071 632406530 632405321 0.000000e+00 706.0
12 TraesCS6A01G039400 chr1B 80.208 288 34 11 28 304 476928794 476928519 7.380000e-46 195.0
13 TraesCS6A01G039400 chr1B 81.564 179 22 8 479 656 476928681 476928513 1.260000e-28 137.0
14 TraesCS6A01G039400 chr1A 80.328 244 33 13 25 257 454547333 454547094 1.240000e-38 171.0
15 TraesCS6A01G039400 chr1D 81.132 159 20 6 25 175 355098418 355098262 4.570000e-23 119.0
16 TraesCS6A01G039400 chr1D 87.500 80 7 2 612 691 355095320 355095244 3.580000e-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 TraesCS6A01G039400 chr6A 20338290 20340901 2611 True 4824 4824 100.000000 1 2612 1 chr6A.!!$R2 2611
1 TraesCS6A01G039400 chr6A 20309204 20310455 1251 True 889 889 80.157000 964 2186 1 chr6A.!!$R1 1222
2 TraesCS6A01G039400 chr6A 20521076 20522362 1286 True 876 876 79.587000 904 2167 1 chr6A.!!$R3 1263
3 TraesCS6A01G039400 chr6B 34683609 34686533 2924 True 1093 2209 86.866333 17 2610 3 chr6B.!!$R3 2593
4 TraesCS6A01G039400 chr6B 34340164 34341484 1320 True 896 896 79.491000 879 2171 1 chr6B.!!$R1 1292
5 TraesCS6A01G039400 chr6B 35528073 35529359 1286 True 887 887 79.739000 910 2167 1 chr6B.!!$R2 1257
6 TraesCS6A01G039400 chr6D 20310939 20312275 1336 True 959 959 80.207000 879 2187 1 chr6D.!!$R1 1308
7 TraesCS6A01G039400 chr6D 20601336 20602636 1300 True 905 905 79.818000 892 2167 1 chr6D.!!$R2 1275
8 TraesCS6A01G039400 chrUn 273854757 273856077 1320 False 913 913 79.700000 879 2171 1 chrUn.!!$F1 1292
9 TraesCS6A01G039400 chr7D 632405321 632406530 1209 True 706 706 77.859000 891 2071 1 chr7D.!!$R1 1180

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
988 1287 0.032952 ACGCTCGAAGCAACCACTTA 59.967 50.0 7.47 0.0 42.58 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2026 2362 0.038892 TTTCACTGGGTACGACGCTC 60.039 55.0 0.0 0.0 31.67 5.03 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
34 35 7.457024 CCTAGCTAGTAGGGAAGAGAAATAC 57.543 44.000 19.31 0.00 44.54 1.89
66 67 6.770303 TGAATTATCGAATCATTAAGGGTGCA 59.230 34.615 0.00 0.00 0.00 4.57
87 88 6.255453 GTGCATTTGACCACGCATAATATTTT 59.745 34.615 0.00 0.00 36.64 1.82
90 91 8.812329 GCATTTGACCACGCATAATATTTTAAA 58.188 29.630 0.00 0.00 0.00 1.52
93 94 9.915629 TTTGACCACGCATAATATTTTAAAACT 57.084 25.926 1.97 0.00 0.00 2.66
94 95 9.915629 TTGACCACGCATAATATTTTAAAACTT 57.084 25.926 1.97 3.10 0.00 2.66
238 247 6.131544 AGTCATGTTTTTATTACCGGATGC 57.868 37.500 9.46 0.00 0.00 3.91
239 248 5.885912 AGTCATGTTTTTATTACCGGATGCT 59.114 36.000 9.46 0.00 0.00 3.79
240 249 5.971202 GTCATGTTTTTATTACCGGATGCTG 59.029 40.000 9.46 0.00 0.00 4.41
241 250 5.650266 TCATGTTTTTATTACCGGATGCTGT 59.350 36.000 9.46 0.00 0.00 4.40
273 282 5.128499 CCAAATATTCATGGGTGGCTTACAA 59.872 40.000 0.00 0.00 32.87 2.41
275 284 6.865834 AATATTCATGGGTGGCTTACAAAA 57.134 33.333 0.00 0.00 0.00 2.44
287 296 6.923508 GGTGGCTTACAAAAATAATAGGCATC 59.076 38.462 0.00 0.00 39.78 3.91
308 317 6.147328 GCATCCCTTATTAGTGGATACGTTTC 59.853 42.308 0.00 0.00 36.76 2.78
312 321 7.289317 TCCCTTATTAGTGGATACGTTTCTCAT 59.711 37.037 5.97 0.00 42.51 2.90
319 328 7.539712 AGTGGATACGTTTCTCATTATGTTG 57.460 36.000 5.97 0.00 42.51 3.33
324 333 8.879759 GGATACGTTTCTCATTATGTTGAAAGA 58.120 33.333 5.97 0.00 0.00 2.52
386 397 0.108396 ACGCATGGCTGCCATATACA 59.892 50.000 32.10 5.08 43.15 2.29
451 462 8.807948 ATTCATGGGTGGCTTACATATATAAC 57.192 34.615 0.00 0.00 0.00 1.89
452 463 7.323052 TCATGGGTGGCTTACATATATAACA 57.677 36.000 0.00 0.00 0.00 2.41
453 464 7.927788 TCATGGGTGGCTTACATATATAACAT 58.072 34.615 0.00 0.00 0.00 2.71
457 468 6.603201 GGGTGGCTTACATATATAACATGCAT 59.397 38.462 0.00 0.00 0.00 3.96
508 519 8.352201 CACTATGTTCAAAGGAAACTCATGAAA 58.648 33.333 0.00 0.00 43.51 2.69
512 523 7.555087 TGTTCAAAGGAAACTCATGAAATTGT 58.445 30.769 0.00 0.00 43.51 2.71
559 570 3.270027 GCACGCATGGCTTCCATATATA 58.730 45.455 0.00 0.00 43.15 0.86
562 573 5.527214 GCACGCATGGCTTCCATATATAATA 59.473 40.000 0.00 0.00 43.15 0.98
563 574 6.293081 GCACGCATGGCTTCCATATATAATAG 60.293 42.308 0.00 0.00 43.15 1.73
564 575 6.763135 CACGCATGGCTTCCATATATAATAGT 59.237 38.462 0.00 0.00 43.15 2.12
565 576 6.986817 ACGCATGGCTTCCATATATAATAGTC 59.013 38.462 0.00 0.00 43.15 2.59
566 577 6.986231 CGCATGGCTTCCATATATAATAGTCA 59.014 38.462 0.00 0.00 43.15 3.41
567 578 7.658982 CGCATGGCTTCCATATATAATAGTCAT 59.341 37.037 0.00 0.00 43.15 3.06
568 579 8.781196 GCATGGCTTCCATATATAATAGTCATG 58.219 37.037 19.95 19.95 43.15 3.07
569 580 8.781196 CATGGCTTCCATATATAATAGTCATGC 58.219 37.037 15.74 0.00 43.15 4.06
570 581 7.282585 TGGCTTCCATATATAATAGTCATGCC 58.717 38.462 0.00 0.00 0.00 4.40
592 603 9.646522 ATGCCTTATTTACTTGATAACATTCCT 57.353 29.630 0.00 0.00 0.00 3.36
645 656 5.582950 AATAGGCATGCCTTATTAGTGGA 57.417 39.130 42.49 22.74 45.70 4.02
651 662 5.711976 GGCATGCCTTATTAGTGGATAACAT 59.288 40.000 29.98 0.00 0.00 2.71
701 712 9.479549 AATTTTCCAAGAGATATGTACCATGTT 57.520 29.630 0.00 0.00 0.00 2.71
702 713 8.877864 TTTTCCAAGAGATATGTACCATGTTT 57.122 30.769 0.00 0.00 0.00 2.83
703 714 8.506168 TTTCCAAGAGATATGTACCATGTTTC 57.494 34.615 0.00 0.00 0.00 2.78
707 718 8.562892 CCAAGAGATATGTACCATGTTTCAATC 58.437 37.037 0.00 0.00 0.00 2.67
708 719 9.112725 CAAGAGATATGTACCATGTTTCAATCA 57.887 33.333 0.00 0.00 0.00 2.57
709 720 8.668510 AGAGATATGTACCATGTTTCAATCAC 57.331 34.615 0.00 0.00 0.00 3.06
710 721 7.716998 AGAGATATGTACCATGTTTCAATCACC 59.283 37.037 0.00 0.00 0.00 4.02
711 722 6.772716 AGATATGTACCATGTTTCAATCACCC 59.227 38.462 0.00 0.00 0.00 4.61
712 723 3.078097 TGTACCATGTTTCAATCACCCG 58.922 45.455 0.00 0.00 0.00 5.28
713 724 0.887933 ACCATGTTTCAATCACCCGC 59.112 50.000 0.00 0.00 0.00 6.13
716 727 2.288702 CCATGTTTCAATCACCCGCAAA 60.289 45.455 0.00 0.00 0.00 3.68
717 728 3.388308 CATGTTTCAATCACCCGCAAAA 58.612 40.909 0.00 0.00 0.00 2.44
718 729 3.526931 TGTTTCAATCACCCGCAAAAA 57.473 38.095 0.00 0.00 0.00 1.94
788 799 9.997482 GTGAAATAAAGCGAAAAGTCCATATTA 57.003 29.630 0.00 0.00 0.00 0.98
792 803 5.830000 AAGCGAAAAGTCCATATTAACCC 57.170 39.130 0.00 0.00 0.00 4.11
798 809 8.245491 GCGAAAAGTCCATATTAACCCTAAAAA 58.755 33.333 0.00 0.00 0.00 1.94
824 835 8.753497 AATTGTTCTCCATATCTTTACCTTCC 57.247 34.615 0.00 0.00 0.00 3.46
850 1146 9.725019 CAAGAGGTAATATAATACTTGCCATCA 57.275 33.333 0.00 0.00 30.37 3.07
859 1155 1.086067 ACTTGCCATCAGATGACGCG 61.086 55.000 12.41 3.53 0.00 6.01
870 1166 4.438148 TCAGATGACGCGAAATGGATTTA 58.562 39.130 15.93 0.00 0.00 1.40
987 1286 1.222115 GACGCTCGAAGCAACCACTT 61.222 55.000 7.47 0.00 42.58 3.16
988 1287 0.032952 ACGCTCGAAGCAACCACTTA 59.967 50.000 7.47 0.00 42.58 2.24
992 1291 2.866762 GCTCGAAGCAACCACTTATAGG 59.133 50.000 2.53 0.00 41.89 2.57
1008 1307 2.435372 TAGGGCTTACAATGGCAAGG 57.565 50.000 0.00 0.00 0.00 3.61
1053 1355 2.616776 CTATCGTGCTTGTTGCCGCG 62.617 60.000 0.00 0.00 42.00 6.46
1148 1450 2.747822 GCTGGTGCGAGCATCACAG 61.748 63.158 6.97 13.40 38.95 3.66
1154 1456 3.075998 CGAGCATCACAGTGTCGC 58.924 61.111 0.00 4.69 33.17 5.19
1235 1537 2.697751 TCCACAAATTCAACCAAGGTGG 59.302 45.455 0.00 0.00 44.28 4.61
1239 1541 0.827507 AATTCAACCAAGGTGGCGCT 60.828 50.000 7.64 0.00 42.67 5.92
1294 1599 0.809385 GACCGATGAAGAGGTCGACA 59.191 55.000 18.91 0.00 46.08 4.35
1326 1631 4.659172 TGCTCCAACCCCTTGCCG 62.659 66.667 0.00 0.00 0.00 5.69
1394 1699 1.857364 CGCGTGACAACTACCCAAC 59.143 57.895 0.00 0.00 0.00 3.77
1530 1835 1.605710 GGCATCAATTCCATCAGGACG 59.394 52.381 0.00 0.00 45.73 4.79
1567 1891 1.939934 TGACTGCGACAAAGAAAGTGG 59.060 47.619 0.00 0.00 0.00 4.00
1575 1899 2.614983 GACAAAGAAAGTGGCGGTTGTA 59.385 45.455 0.00 0.00 29.75 2.41
1576 1900 3.018149 ACAAAGAAAGTGGCGGTTGTAA 58.982 40.909 0.00 0.00 0.00 2.41
1577 1901 3.444388 ACAAAGAAAGTGGCGGTTGTAAA 59.556 39.130 0.00 0.00 0.00 2.01
1667 1991 1.331756 CCATACTTTGCCGATGAGCAC 59.668 52.381 0.00 0.00 43.97 4.40
1695 2019 1.851658 CTTGGTGCCAAAACGAAAGG 58.148 50.000 5.10 0.00 35.33 3.11
1748 2072 2.258726 GCCGCCAAAAGACGAGGTT 61.259 57.895 0.00 0.00 0.00 3.50
2023 2359 0.250858 TTATGCGGCATCCTGATGGG 60.251 55.000 20.34 0.00 39.16 4.00
2161 2510 4.530710 TTCAACGCACACCTAGACTTAT 57.469 40.909 0.00 0.00 0.00 1.73
2203 2552 5.632244 TTATTTTAGGGGTGCGTCTTTTC 57.368 39.130 0.00 0.00 0.00 2.29
2209 2558 3.081804 AGGGGTGCGTCTTTTCTATTTG 58.918 45.455 0.00 0.00 0.00 2.32
2256 2632 2.050077 GTGCCGCTGCTCCAAAAC 60.050 61.111 0.70 0.00 38.71 2.43
2270 2659 7.011499 TGCTCCAAAACCTACTATTAACTGA 57.989 36.000 0.00 0.00 0.00 3.41
2280 2669 9.833917 AACCTACTATTAACTGAGCCTTAATTC 57.166 33.333 0.00 0.00 0.00 2.17
2287 2676 0.180406 TGAGCCTTAATTCTCGCCCC 59.820 55.000 0.00 0.00 32.20 5.80
2288 2677 0.180406 GAGCCTTAATTCTCGCCCCA 59.820 55.000 0.00 0.00 0.00 4.96
2289 2678 0.623723 AGCCTTAATTCTCGCCCCAA 59.376 50.000 0.00 0.00 0.00 4.12
2290 2679 1.215423 AGCCTTAATTCTCGCCCCAAT 59.785 47.619 0.00 0.00 0.00 3.16
2291 2680 2.031870 GCCTTAATTCTCGCCCCAATT 58.968 47.619 0.00 0.00 0.00 2.32
2292 2681 2.430694 GCCTTAATTCTCGCCCCAATTT 59.569 45.455 0.00 0.00 0.00 1.82
2293 2682 3.118775 GCCTTAATTCTCGCCCCAATTTT 60.119 43.478 0.00 0.00 0.00 1.82
2294 2683 4.098807 GCCTTAATTCTCGCCCCAATTTTA 59.901 41.667 0.00 0.00 0.00 1.52
2295 2684 5.221441 GCCTTAATTCTCGCCCCAATTTTAT 60.221 40.000 0.00 0.00 0.00 1.40
2296 2685 6.685368 GCCTTAATTCTCGCCCCAATTTTATT 60.685 38.462 0.00 0.00 0.00 1.40
2297 2686 7.272244 CCTTAATTCTCGCCCCAATTTTATTT 58.728 34.615 0.00 0.00 0.00 1.40
2298 2687 7.438160 CCTTAATTCTCGCCCCAATTTTATTTC 59.562 37.037 0.00 0.00 0.00 2.17
2299 2688 6.544928 AATTCTCGCCCCAATTTTATTTCT 57.455 33.333 0.00 0.00 0.00 2.52
2300 2689 4.981806 TCTCGCCCCAATTTTATTTCTG 57.018 40.909 0.00 0.00 0.00 3.02
2301 2690 3.130340 TCTCGCCCCAATTTTATTTCTGC 59.870 43.478 0.00 0.00 0.00 4.26
2302 2691 3.096092 TCGCCCCAATTTTATTTCTGCT 58.904 40.909 0.00 0.00 0.00 4.24
2303 2692 3.513515 TCGCCCCAATTTTATTTCTGCTT 59.486 39.130 0.00 0.00 0.00 3.91
2304 2693 3.865164 CGCCCCAATTTTATTTCTGCTTC 59.135 43.478 0.00 0.00 0.00 3.86
2305 2694 4.381932 CGCCCCAATTTTATTTCTGCTTCT 60.382 41.667 0.00 0.00 0.00 2.85
2306 2695 5.111989 GCCCCAATTTTATTTCTGCTTCTC 58.888 41.667 0.00 0.00 0.00 2.87
2307 2696 5.337491 GCCCCAATTTTATTTCTGCTTCTCA 60.337 40.000 0.00 0.00 0.00 3.27
2308 2697 6.101997 CCCCAATTTTATTTCTGCTTCTCAC 58.898 40.000 0.00 0.00 0.00 3.51
2309 2698 6.101997 CCCAATTTTATTTCTGCTTCTCACC 58.898 40.000 0.00 0.00 0.00 4.02
2310 2699 5.801947 CCAATTTTATTTCTGCTTCTCACCG 59.198 40.000 0.00 0.00 0.00 4.94
2311 2700 6.381801 CAATTTTATTTCTGCTTCTCACCGT 58.618 36.000 0.00 0.00 0.00 4.83
2312 2701 5.356882 TTTTATTTCTGCTTCTCACCGTG 57.643 39.130 0.00 0.00 0.00 4.94
2313 2702 1.160137 ATTTCTGCTTCTCACCGTGC 58.840 50.000 0.00 0.00 0.00 5.34
2326 2715 1.028330 ACCGTGCGATTCGTCTCCTA 61.028 55.000 8.03 0.00 0.00 2.94
2332 2721 1.859197 GCGATTCGTCTCCTACCGTTC 60.859 57.143 8.03 0.00 0.00 3.95
2356 2745 0.176680 CCTCCCAGATCACCTCAACG 59.823 60.000 0.00 0.00 0.00 4.10
2357 2746 0.176680 CTCCCAGATCACCTCAACGG 59.823 60.000 0.00 0.00 39.35 4.44
2364 2753 2.202236 ATCACCTCAACGGCATGCCT 62.202 55.000 33.07 18.07 35.61 4.75
2366 2755 2.825836 CCTCAACGGCATGCCTCC 60.826 66.667 33.07 8.82 0.00 4.30
2402 2791 2.124403 GCTCCATCAGTGGCAGGG 60.124 66.667 0.00 0.00 45.63 4.45
2480 2869 2.531522 AGTTCCAAATTTGTGCAGGC 57.468 45.000 16.73 1.77 0.00 4.85
2485 2896 0.952010 CAAATTTGTGCAGGCCTGGC 60.952 55.000 33.46 24.58 0.00 4.85
2487 2898 4.892965 TTTGTGCAGGCCTGGCGT 62.893 61.111 33.46 10.89 0.00 5.68
2490 2901 3.204827 GTGCAGGCCTGGCGTATG 61.205 66.667 33.46 12.65 0.00 2.39
2496 2907 3.264897 GCCTGGCGTATGTCAGCG 61.265 66.667 11.23 5.92 46.69 5.18
2504 2915 1.782023 GCGTATGTCAGCGTTCGTTTG 60.782 52.381 2.32 0.00 0.00 2.93
2520 2934 1.792367 GTTTGCCTGGCGAATTGTTTC 59.208 47.619 23.53 6.77 34.24 2.78
2523 2937 0.881118 GCCTGGCGAATTGTTTCTCA 59.119 50.000 1.35 0.00 0.00 3.27
2544 2958 3.947834 CACTCTTCCAACTTGGTTTCACT 59.052 43.478 7.72 0.00 39.03 3.41
2550 2964 1.670811 CAACTTGGTTTCACTCTGCGT 59.329 47.619 0.00 0.00 0.00 5.24
2564 2978 0.529833 CTGCGTCCTGTGTCAGATCT 59.470 55.000 0.00 0.00 32.44 2.75
2567 2981 1.203523 GCGTCCTGTGTCAGATCTTCT 59.796 52.381 0.00 0.00 32.44 2.85
2578 2992 6.870439 TGTGTCAGATCTTCTGTTTCAGTATG 59.130 38.462 0.00 0.00 44.58 2.39
2584 2998 3.748048 TCTTCTGTTTCAGTATGCTGCAC 59.252 43.478 3.57 6.03 42.29 4.57
2585 2999 3.407424 TCTGTTTCAGTATGCTGCACT 57.593 42.857 3.57 0.00 42.29 4.40
2606 3020 4.058817 CTCCCCGTCTTGCTATTGATTAC 58.941 47.826 0.00 0.00 0.00 1.89
2610 3024 5.465724 CCCCGTCTTGCTATTGATTACTTAC 59.534 44.000 0.00 0.00 0.00 2.34
2611 3025 6.281405 CCCGTCTTGCTATTGATTACTTACT 58.719 40.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 4.986054 TCTCTTCCCTACTAGCTAGGAG 57.014 50.000 24.25 24.25 44.88 3.69
9 10 5.728937 TTTCTCTTCCCTACTAGCTAGGA 57.271 43.478 24.35 15.89 44.88 2.94
10 11 7.235804 AGTATTTCTCTTCCCTACTAGCTAGG 58.764 42.308 24.35 9.90 41.96 3.02
11 12 8.700439 AAGTATTTCTCTTCCCTACTAGCTAG 57.300 38.462 19.44 19.44 0.00 3.42
13 14 9.663365 ATTAAGTATTTCTCTTCCCTACTAGCT 57.337 33.333 0.00 0.00 0.00 3.32
14 15 9.917129 GATTAAGTATTTCTCTTCCCTACTAGC 57.083 37.037 0.00 0.00 0.00 3.42
41 42 6.770303 TGCACCCTTAATGATTCGATAATTCA 59.230 34.615 0.00 0.00 0.00 2.57
47 48 5.593909 TCAAATGCACCCTTAATGATTCGAT 59.406 36.000 0.00 0.00 0.00 3.59
50 51 5.105392 TGGTCAAATGCACCCTTAATGATTC 60.105 40.000 0.00 0.00 32.24 2.52
52 53 4.160252 GTGGTCAAATGCACCCTTAATGAT 59.840 41.667 0.00 0.00 32.24 2.45
128 136 7.996644 TCCTTTAAACATAGTGAAAAGTGAGGT 59.003 33.333 0.00 0.00 0.00 3.85
187 196 1.755395 GGAAGCCATGCATGCCAGA 60.755 57.895 21.69 0.00 0.00 3.86
260 269 5.128008 GCCTATTATTTTTGTAAGCCACCCA 59.872 40.000 0.00 0.00 0.00 4.51
264 273 6.041523 GGGATGCCTATTATTTTTGTAAGCCA 59.958 38.462 0.00 0.00 0.00 4.75
273 282 9.533831 CCACTAATAAGGGATGCCTATTATTTT 57.466 33.333 6.05 0.00 32.28 1.82
275 284 8.463055 TCCACTAATAAGGGATGCCTATTATT 57.537 34.615 6.05 10.62 33.48 1.40
287 296 6.812998 TGAGAAACGTATCCACTAATAAGGG 58.187 40.000 0.00 0.00 0.00 3.95
345 354 4.994852 GTGCCTGTTATATATGGAAGCGAA 59.005 41.667 0.00 0.00 0.00 4.70
347 356 3.367932 CGTGCCTGTTATATATGGAAGCG 59.632 47.826 0.00 0.00 0.00 4.68
406 417 9.590451 CATGAATATTTGGCAAAAGTGTTATCT 57.410 29.630 17.70 0.00 0.00 1.98
451 462 5.163683 GCTATCCACTAATAAGGCATGCATG 60.164 44.000 22.70 22.70 0.00 4.06
452 463 4.946157 GCTATCCACTAATAAGGCATGCAT 59.054 41.667 21.36 10.32 0.00 3.96
453 464 4.202451 TGCTATCCACTAATAAGGCATGCA 60.202 41.667 21.36 0.00 0.00 3.96
457 468 7.559533 TGAAAAATGCTATCCACTAATAAGGCA 59.440 33.333 0.00 0.00 0.00 4.75
538 549 1.522668 TATATGGAAGCCATGCGTGC 58.477 50.000 9.14 0.00 44.84 5.34
562 573 9.632638 ATGTTATCAAGTAAATAAGGCATGACT 57.367 29.630 0.00 0.00 0.00 3.41
565 576 9.683069 GGAATGTTATCAAGTAAATAAGGCATG 57.317 33.333 0.00 0.00 0.00 4.06
566 577 9.646522 AGGAATGTTATCAAGTAAATAAGGCAT 57.353 29.630 0.00 0.00 0.00 4.40
592 603 9.295825 CTGTAAGCCACCCATGAATATTTATTA 57.704 33.333 0.00 0.00 0.00 0.98
595 606 6.905736 TCTGTAAGCCACCCATGAATATTTA 58.094 36.000 0.00 0.00 0.00 1.40
693 704 2.088423 GCGGGTGATTGAAACATGGTA 58.912 47.619 0.00 0.00 0.00 3.25
697 708 3.742433 TTTTGCGGGTGATTGAAACAT 57.258 38.095 0.00 0.00 0.00 2.71
717 728 5.426504 TGTCATTGAAACATGGTGCTTTTT 58.573 33.333 0.00 0.00 0.00 1.94
718 729 5.021033 TGTCATTGAAACATGGTGCTTTT 57.979 34.783 0.00 0.00 0.00 2.27
719 730 4.341806 TCTGTCATTGAAACATGGTGCTTT 59.658 37.500 0.00 0.00 0.00 3.51
720 731 3.890756 TCTGTCATTGAAACATGGTGCTT 59.109 39.130 0.00 0.00 0.00 3.91
721 732 3.489355 TCTGTCATTGAAACATGGTGCT 58.511 40.909 0.00 0.00 0.00 4.40
722 733 3.921119 TCTGTCATTGAAACATGGTGC 57.079 42.857 0.00 0.00 0.00 5.01
723 734 8.991243 AATTATTCTGTCATTGAAACATGGTG 57.009 30.769 0.00 0.00 0.00 4.17
765 776 9.797556 GGTTAATATGGACTTTTCGCTTTATTT 57.202 29.630 0.00 0.00 0.00 1.40
798 809 9.190317 GGAAGGTAAAGATATGGAGAACAATTT 57.810 33.333 0.00 0.00 0.00 1.82
799 810 8.336235 TGGAAGGTAAAGATATGGAGAACAATT 58.664 33.333 0.00 0.00 0.00 2.32
800 811 7.872138 TGGAAGGTAAAGATATGGAGAACAAT 58.128 34.615 0.00 0.00 0.00 2.71
819 830 9.220767 GCAAGTATTATATTACCTCTTGGAAGG 57.779 37.037 0.00 0.00 42.55 3.46
820 831 9.220767 GGCAAGTATTATATTACCTCTTGGAAG 57.779 37.037 0.00 0.00 37.04 3.46
822 833 8.270137 TGGCAAGTATTATATTACCTCTTGGA 57.730 34.615 0.00 0.00 37.04 3.53
823 834 9.167311 GATGGCAAGTATTATATTACCTCTTGG 57.833 37.037 0.00 0.00 39.83 3.61
824 835 9.725019 TGATGGCAAGTATTATATTACCTCTTG 57.275 33.333 0.00 0.00 35.43 3.02
850 1146 5.056480 TGATAAATCCATTTCGCGTCATCT 58.944 37.500 5.77 0.00 0.00 2.90
859 1155 8.854117 AGTTTCTGCCTATGATAAATCCATTTC 58.146 33.333 0.00 0.00 0.00 2.17
987 1286 3.181434 CCCTTGCCATTGTAAGCCCTATA 60.181 47.826 0.00 0.00 33.33 1.31
988 1287 2.424812 CCCTTGCCATTGTAAGCCCTAT 60.425 50.000 0.00 0.00 33.33 2.57
992 1291 1.257055 TGCCCTTGCCATTGTAAGCC 61.257 55.000 0.00 0.00 33.33 4.35
1008 1307 3.621268 TGAGTAGTATCGTTGCAATTGCC 59.379 43.478 26.94 12.00 41.18 4.52
1235 1537 1.154814 GCTTAGCTTGTAGGGAGCGC 61.155 60.000 0.00 0.00 44.71 5.92
1239 1541 2.236395 GTTGAGGCTTAGCTTGTAGGGA 59.764 50.000 3.59 0.00 0.00 4.20
1294 1599 4.729856 GCAGCGACCGTACCCGTT 62.730 66.667 0.00 0.00 0.00 4.44
1326 1631 2.774774 CTCTGCTTCGCGCTGTTC 59.225 61.111 5.56 0.00 40.11 3.18
1342 1647 2.847234 TGTGACCCGGTCTTGGCT 60.847 61.111 18.54 0.00 33.15 4.75
1394 1699 3.982372 ATGCGCCAGTCCACGTACG 62.982 63.158 15.01 15.01 0.00 3.67
1509 1814 2.747467 CGTCCTGATGGAATTGATGCCT 60.747 50.000 0.00 0.00 45.18 4.75
1530 1835 2.079925 GTCAATGACACCAGCTTCCTC 58.920 52.381 8.74 0.00 32.09 3.71
1567 1891 2.910345 TTGCCGCCTTTACAACCGC 61.910 57.895 0.00 0.00 0.00 5.68
1575 1899 3.276642 ATACCGGGTTGCCGCCTTT 62.277 57.895 4.31 0.00 0.00 3.11
1576 1900 3.692370 GATACCGGGTTGCCGCCTT 62.692 63.158 4.31 0.00 0.00 4.35
1577 1901 4.171103 GATACCGGGTTGCCGCCT 62.171 66.667 4.31 0.00 0.00 5.52
1695 2019 1.001597 GTCGATGGTGACGATAGGGTC 60.002 57.143 0.00 0.00 41.62 4.46
1789 2113 2.348666 CGGAATGTCTTCGTGTCAATCC 59.651 50.000 0.00 0.00 32.75 3.01
1791 2115 2.346803 CCGGAATGTCTTCGTGTCAAT 58.653 47.619 0.00 0.00 31.75 2.57
2023 2359 2.045131 ACTGGGTACGACGCTCCTC 61.045 63.158 0.00 0.00 31.67 3.71
2024 2360 2.035312 ACTGGGTACGACGCTCCT 59.965 61.111 0.00 0.00 31.67 3.69
2025 2361 1.870055 TTCACTGGGTACGACGCTCC 61.870 60.000 0.00 0.00 31.67 4.70
2026 2362 0.038892 TTTCACTGGGTACGACGCTC 60.039 55.000 0.00 0.00 31.67 5.03
2118 2460 8.347004 TGAATGTTAATCACATGGTTACACAT 57.653 30.769 0.00 4.43 46.23 3.21
2173 2522 5.105513 ACGCACCCCTAAAATAAAAATGGAG 60.106 40.000 0.00 0.00 0.00 3.86
2174 2523 4.773149 ACGCACCCCTAAAATAAAAATGGA 59.227 37.500 0.00 0.00 0.00 3.41
2176 2525 5.961272 AGACGCACCCCTAAAATAAAAATG 58.039 37.500 0.00 0.00 0.00 2.32
2177 2526 6.599356 AAGACGCACCCCTAAAATAAAAAT 57.401 33.333 0.00 0.00 0.00 1.82
2178 2527 6.408107 AAAGACGCACCCCTAAAATAAAAA 57.592 33.333 0.00 0.00 0.00 1.94
2187 2536 4.020039 TCAAATAGAAAAGACGCACCCCTA 60.020 41.667 0.00 0.00 0.00 3.53
2256 2632 9.699703 GAGAATTAAGGCTCAGTTAATAGTAGG 57.300 37.037 0.00 0.00 31.27 3.18
2270 2659 0.623723 TTGGGGCGAGAATTAAGGCT 59.376 50.000 0.00 0.00 0.00 4.58
2280 2669 3.131046 AGCAGAAATAAAATTGGGGCGAG 59.869 43.478 0.00 0.00 0.00 5.03
2287 2676 6.306356 CACGGTGAGAAGCAGAAATAAAATTG 59.694 38.462 0.74 0.00 0.00 2.32
2288 2677 6.381801 CACGGTGAGAAGCAGAAATAAAATT 58.618 36.000 0.74 0.00 0.00 1.82
2289 2678 5.619981 GCACGGTGAGAAGCAGAAATAAAAT 60.620 40.000 13.29 0.00 0.00 1.82
2290 2679 4.320202 GCACGGTGAGAAGCAGAAATAAAA 60.320 41.667 13.29 0.00 0.00 1.52
2291 2680 3.188460 GCACGGTGAGAAGCAGAAATAAA 59.812 43.478 13.29 0.00 0.00 1.40
2292 2681 2.742053 GCACGGTGAGAAGCAGAAATAA 59.258 45.455 13.29 0.00 0.00 1.40
2293 2682 2.346803 GCACGGTGAGAAGCAGAAATA 58.653 47.619 13.29 0.00 0.00 1.40
2294 2683 1.160137 GCACGGTGAGAAGCAGAAAT 58.840 50.000 13.29 0.00 0.00 2.17
2295 2684 1.221466 CGCACGGTGAGAAGCAGAAA 61.221 55.000 13.29 0.00 0.00 2.52
2296 2685 1.664649 CGCACGGTGAGAAGCAGAA 60.665 57.895 13.29 0.00 0.00 3.02
2297 2686 1.877576 ATCGCACGGTGAGAAGCAGA 61.878 55.000 18.22 2.26 28.16 4.26
2298 2687 1.016130 AATCGCACGGTGAGAAGCAG 61.016 55.000 18.22 0.00 28.16 4.24
2299 2688 1.005037 AATCGCACGGTGAGAAGCA 60.005 52.632 18.22 0.00 28.16 3.91
2300 2689 1.710339 GAATCGCACGGTGAGAAGC 59.290 57.895 18.22 9.63 28.16 3.86
2301 2690 0.732880 ACGAATCGCACGGTGAGAAG 60.733 55.000 18.22 14.24 34.93 2.85
2302 2691 0.731514 GACGAATCGCACGGTGAGAA 60.732 55.000 18.22 2.89 34.93 2.87
2303 2692 1.154093 GACGAATCGCACGGTGAGA 60.154 57.895 16.74 16.74 34.93 3.27
2304 2693 1.134530 GAGACGAATCGCACGGTGAG 61.135 60.000 13.29 9.22 34.93 3.51
2305 2694 1.154093 GAGACGAATCGCACGGTGA 60.154 57.895 13.29 0.00 34.93 4.02
2306 2695 2.158959 GGAGACGAATCGCACGGTG 61.159 63.158 1.15 3.15 34.93 4.94
2307 2696 1.028330 TAGGAGACGAATCGCACGGT 61.028 55.000 1.15 0.00 34.93 4.83
2308 2697 0.591741 GTAGGAGACGAATCGCACGG 60.592 60.000 1.15 0.00 34.93 4.94
2309 2698 0.591741 GGTAGGAGACGAATCGCACG 60.592 60.000 1.15 0.00 0.00 5.34
2310 2699 0.591741 CGGTAGGAGACGAATCGCAC 60.592 60.000 1.15 0.00 0.00 5.34
2311 2700 1.028330 ACGGTAGGAGACGAATCGCA 61.028 55.000 1.15 0.00 0.00 5.10
2312 2701 0.100146 AACGGTAGGAGACGAATCGC 59.900 55.000 1.15 0.00 0.00 4.58
2313 2702 1.268437 GGAACGGTAGGAGACGAATCG 60.268 57.143 0.00 0.00 0.00 3.34
2326 2715 0.473117 TCTGGGAGGAAAGGAACGGT 60.473 55.000 0.00 0.00 0.00 4.83
2332 2721 1.488393 GAGGTGATCTGGGAGGAAAGG 59.512 57.143 0.00 0.00 0.00 3.11
2375 2764 3.838271 GATGGAGCCGGAGTGCGA 61.838 66.667 5.05 0.00 36.02 5.10
2442 2831 5.629435 GGAACTTTGGATTAAGTTTTCTGCG 59.371 40.000 0.00 0.00 45.68 5.18
2472 2861 3.716195 ATACGCCAGGCCTGCACA 61.716 61.111 28.39 11.94 0.00 4.57
2480 2869 1.421410 GAACGCTGACATACGCCAGG 61.421 60.000 0.00 0.00 0.00 4.45
2485 2896 1.782023 GCAAACGAACGCTGACATACG 60.782 52.381 0.00 0.00 0.00 3.06
2487 2898 0.793861 GGCAAACGAACGCTGACATA 59.206 50.000 0.00 0.00 0.00 2.29
2490 2901 1.082756 CAGGCAAACGAACGCTGAC 60.083 57.895 0.00 0.00 0.00 3.51
2496 2907 3.027292 TTCGCCAGGCAAACGAAC 58.973 55.556 13.30 0.00 40.56 3.95
2504 2915 0.881118 TGAGAAACAATTCGCCAGGC 59.119 50.000 0.00 0.00 40.63 4.85
2520 2934 4.035675 GTGAAACCAAGTTGGAAGAGTGAG 59.964 45.833 28.80 0.00 40.96 3.51
2523 2937 4.080299 AGAGTGAAACCAAGTTGGAAGAGT 60.080 41.667 28.80 11.25 40.96 3.24
2544 2958 0.528017 GATCTGACACAGGACGCAGA 59.472 55.000 0.00 0.00 41.14 4.26
2578 2992 2.743928 CAAGACGGGGAGTGCAGC 60.744 66.667 0.00 0.00 0.00 5.25
2584 2998 2.918712 ATCAATAGCAAGACGGGGAG 57.081 50.000 0.00 0.00 0.00 4.30
2585 2999 3.709653 AGTAATCAATAGCAAGACGGGGA 59.290 43.478 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.