Multiple sequence alignment - TraesCS5B01G369100

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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 TraesCS5B01G369100 chr5B 100.000 3362 0 0 1 3362 548106622 548109983 0.000000e+00 6209
1 TraesCS5B01G369100 chr5B 98.904 1551 16 1 1813 3362 166592777 166594327 0.000000e+00 2769
2 TraesCS5B01G369100 chr5B 78.135 1276 247 28 2098 3360 473172523 473171267 0.000000e+00 782
3 TraesCS5B01G369100 chr4B 89.275 2648 264 16 713 3345 364488672 364491314 0.000000e+00 3299
4 TraesCS5B01G369100 chr7B 95.252 695 32 1 1 694 87182152 87182846 0.000000e+00 1099
5 TraesCS5B01G369100 chr1B 94.942 692 34 1 1 691 6572482 6573173 0.000000e+00 1083
6 TraesCS5B01G369100 chr3D 93.939 693 39 2 4 693 443692065 443691373 0.000000e+00 1044
7 TraesCS5B01G369100 chr3D 93.931 692 21 4 4 694 50545143 50545814 0.000000e+00 1026
8 TraesCS5B01G369100 chr2A 94.872 663 31 2 4 665 752823383 752822723 0.000000e+00 1033
9 TraesCS5B01G369100 chr7D 93.353 692 31 3 4 694 39589196 39588519 0.000000e+00 1009
10 TraesCS5B01G369100 chr7D 75.848 973 222 13 2309 3274 21958055 21959021 1.810000e-132 483
11 TraesCS5B01G369100 chr7D 88.804 393 35 6 26 418 403105414 403105797 1.090000e-129 473
12 TraesCS5B01G369100 chr5D 80.371 1131 205 14 2235 3360 393451694 393450576 0.000000e+00 843
13 TraesCS5B01G369100 chr5D 73.342 799 189 21 2225 3013 346310631 346311415 1.190000e-69 274
14 TraesCS5B01G369100 chr6B 75.713 1017 229 18 2309 3316 159189646 159188639 8.380000e-136 494
15 TraesCS5B01G369100 chr7A 85.161 465 60 8 1 461 650927080 650927539 5.080000e-128 468
16 TraesCS5B01G369100 chr7A 76.575 730 157 14 2310 3032 529446944 529447666 4.070000e-104 388
17 TraesCS5B01G369100 chr6A 76.694 841 189 7 2309 3145 23841916 23841079 8.500000e-126 460
18 TraesCS5B01G369100 chr6D 82.791 430 56 16 4 424 47677974 47677554 5.300000e-98 368
19 TraesCS5B01G369100 chr5A 74.155 917 211 26 2310 3213 73993518 73992615 1.150000e-94 357


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 TraesCS5B01G369100 chr5B 548106622 548109983 3361 False 6209 6209 100.000 1 3362 1 chr5B.!!$F2 3361
1 TraesCS5B01G369100 chr5B 166592777 166594327 1550 False 2769 2769 98.904 1813 3362 1 chr5B.!!$F1 1549
2 TraesCS5B01G369100 chr5B 473171267 473172523 1256 True 782 782 78.135 2098 3360 1 chr5B.!!$R1 1262
3 TraesCS5B01G369100 chr4B 364488672 364491314 2642 False 3299 3299 89.275 713 3345 1 chr4B.!!$F1 2632
4 TraesCS5B01G369100 chr7B 87182152 87182846 694 False 1099 1099 95.252 1 694 1 chr7B.!!$F1 693
5 TraesCS5B01G369100 chr1B 6572482 6573173 691 False 1083 1083 94.942 1 691 1 chr1B.!!$F1 690
6 TraesCS5B01G369100 chr3D 443691373 443692065 692 True 1044 1044 93.939 4 693 1 chr3D.!!$R1 689
7 TraesCS5B01G369100 chr3D 50545143 50545814 671 False 1026 1026 93.931 4 694 1 chr3D.!!$F1 690
8 TraesCS5B01G369100 chr2A 752822723 752823383 660 True 1033 1033 94.872 4 665 1 chr2A.!!$R1 661
9 TraesCS5B01G369100 chr7D 39588519 39589196 677 True 1009 1009 93.353 4 694 1 chr7D.!!$R1 690
10 TraesCS5B01G369100 chr7D 21958055 21959021 966 False 483 483 75.848 2309 3274 1 chr7D.!!$F1 965
11 TraesCS5B01G369100 chr5D 393450576 393451694 1118 True 843 843 80.371 2235 3360 1 chr5D.!!$R1 1125
12 TraesCS5B01G369100 chr5D 346310631 346311415 784 False 274 274 73.342 2225 3013 1 chr5D.!!$F1 788
13 TraesCS5B01G369100 chr6B 159188639 159189646 1007 True 494 494 75.713 2309 3316 1 chr6B.!!$R1 1007
14 TraesCS5B01G369100 chr7A 529446944 529447666 722 False 388 388 76.575 2310 3032 1 chr7A.!!$F1 722
15 TraesCS5B01G369100 chr6A 23841079 23841916 837 True 460 460 76.694 2309 3145 1 chr6A.!!$R1 836
16 TraesCS5B01G369100 chr5A 73992615 73993518 903 True 357 357 74.155 2310 3213 1 chr5A.!!$R1 903

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
761 765 0.319555 CCTTCCAGTGACGAGCGAAA 60.320 55.0 0.0 0.0 0.00 3.46 F
1411 1426 0.241749 ACATGCGGTGTTGCTCAATG 59.758 50.0 0.0 0.0 38.01 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 1600 0.394352 CCCTTACCCGCAAGCAATCT 60.394 55.0 0.0 0.0 0.0 2.40 R
2936 2954 0.683973 ACTGCCCTGTCAAGTCTCAG 59.316 55.0 0.0 0.0 0.0 3.35 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
40 42 3.667448 GCATCACGCTCCTATGTCA 57.333 52.632 0.00 0.00 37.77 3.58
67 69 2.416747 CTGAAATCACTGCCGTCTTCA 58.583 47.619 0.00 0.00 0.00 3.02
79 81 1.673033 CCGTCTTCAGCTTTGACCGAT 60.673 52.381 5.31 0.00 0.00 4.18
138 140 2.290641 GCCGAAATTATCCGACTGCAAT 59.709 45.455 0.00 0.00 0.00 3.56
164 166 1.890041 CACCCTGCGTCGTTTTCCA 60.890 57.895 0.00 0.00 0.00 3.53
177 179 0.953471 TTTTCCACCCGCACATCTCG 60.953 55.000 0.00 0.00 0.00 4.04
212 214 1.929169 CGCCCTGTATATGCATGATCG 59.071 52.381 10.16 0.00 0.00 3.69
368 372 1.465689 CGCAATAAAACTGTGCTCCCG 60.466 52.381 0.00 0.00 36.10 5.14
414 418 0.749818 TGTTGTTGTCCATGCCACGT 60.750 50.000 0.00 0.00 0.00 4.49
569 573 6.195600 AGTAACAACCAAGAAATAGTCCCA 57.804 37.500 0.00 0.00 0.00 4.37
578 582 4.554553 AGAAATAGTCCCAGGTAGCCTA 57.445 45.455 0.00 0.00 29.64 3.93
585 589 1.216175 TCCCAGGTAGCCTACACGTAT 59.784 52.381 3.95 0.00 29.64 3.06
684 688 6.702329 TGTTTTCTTTGTTTACCCAACATGT 58.298 32.000 0.00 0.00 45.17 3.21
694 698 3.011566 ACCCAACATGTTCACAACTGA 57.988 42.857 8.48 0.00 0.00 3.41
695 699 2.687935 ACCCAACATGTTCACAACTGAC 59.312 45.455 8.48 0.00 0.00 3.51
696 700 2.034558 CCCAACATGTTCACAACTGACC 59.965 50.000 8.48 0.00 0.00 4.02
697 701 2.034558 CCAACATGTTCACAACTGACCC 59.965 50.000 8.48 0.00 0.00 4.46
698 702 2.687425 CAACATGTTCACAACTGACCCA 59.313 45.455 8.48 0.00 0.00 4.51
699 703 3.011566 ACATGTTCACAACTGACCCAA 57.988 42.857 0.00 0.00 0.00 4.12
700 704 3.565307 ACATGTTCACAACTGACCCAAT 58.435 40.909 0.00 0.00 0.00 3.16
701 705 3.960102 ACATGTTCACAACTGACCCAATT 59.040 39.130 0.00 0.00 0.00 2.32
702 706 4.037923 ACATGTTCACAACTGACCCAATTC 59.962 41.667 0.00 0.00 0.00 2.17
703 707 3.625853 TGTTCACAACTGACCCAATTCA 58.374 40.909 0.00 0.00 0.00 2.57
704 708 4.214310 TGTTCACAACTGACCCAATTCAT 58.786 39.130 0.00 0.00 0.00 2.57
705 709 4.037803 TGTTCACAACTGACCCAATTCATG 59.962 41.667 0.00 0.00 0.00 3.07
706 710 2.557924 TCACAACTGACCCAATTCATGC 59.442 45.455 0.00 0.00 0.00 4.06
707 711 2.296752 CACAACTGACCCAATTCATGCA 59.703 45.455 0.00 0.00 0.00 3.96
708 712 2.964464 ACAACTGACCCAATTCATGCAA 59.036 40.909 0.00 0.00 0.00 4.08
709 713 3.579586 ACAACTGACCCAATTCATGCAAT 59.420 39.130 0.00 0.00 0.00 3.56
710 714 4.040706 ACAACTGACCCAATTCATGCAATT 59.959 37.500 0.00 0.00 34.79 2.32
711 715 5.245751 ACAACTGACCCAATTCATGCAATTA 59.754 36.000 0.00 0.00 32.48 1.40
712 716 5.329035 ACTGACCCAATTCATGCAATTAC 57.671 39.130 0.00 0.00 32.48 1.89
713 717 4.771577 ACTGACCCAATTCATGCAATTACA 59.228 37.500 0.00 0.00 32.48 2.41
714 718 5.245751 ACTGACCCAATTCATGCAATTACAA 59.754 36.000 0.00 0.00 32.48 2.41
715 719 5.477510 TGACCCAATTCATGCAATTACAAC 58.522 37.500 0.00 0.00 32.48 3.32
716 720 5.245751 TGACCCAATTCATGCAATTACAACT 59.754 36.000 0.00 0.00 32.48 3.16
717 721 5.723295 ACCCAATTCATGCAATTACAACTC 58.277 37.500 0.00 0.00 32.48 3.01
727 731 3.690460 CAATTACAACTCTGCCTCCCTT 58.310 45.455 0.00 0.00 0.00 3.95
744 748 2.357361 CCCTTAGAACTCTCTCGTCCCT 60.357 54.545 0.00 0.00 32.70 4.20
757 761 1.079750 GTCCCTTCCAGTGACGAGC 60.080 63.158 0.00 0.00 0.00 5.03
758 762 2.125912 CCCTTCCAGTGACGAGCG 60.126 66.667 0.00 0.00 0.00 5.03
761 765 0.319555 CCTTCCAGTGACGAGCGAAA 60.320 55.000 0.00 0.00 0.00 3.46
765 769 0.878523 CCAGTGACGAGCGAAACCAA 60.879 55.000 0.00 0.00 0.00 3.67
797 801 0.541863 AATCTGGTGGTCACGATCCC 59.458 55.000 0.00 0.00 0.00 3.85
823 827 2.216898 GCATCCATCCTAGTGTGCTTC 58.783 52.381 0.00 0.00 0.00 3.86
849 854 4.515361 AGCAAGATTCATCTCCTCAACAG 58.485 43.478 0.00 0.00 35.76 3.16
850 855 4.019501 AGCAAGATTCATCTCCTCAACAGT 60.020 41.667 0.00 0.00 35.76 3.55
871 885 1.614241 CCCGTACCCCCAGTTCTCAG 61.614 65.000 0.00 0.00 0.00 3.35
880 895 2.239654 CCCCAGTTCTCAGATTTGGCTA 59.760 50.000 0.27 0.00 0.00 3.93
885 900 3.840666 AGTTCTCAGATTTGGCTACAGGA 59.159 43.478 0.00 0.00 0.00 3.86
901 916 1.001631 GGAAGGGGTGATTTGGGGG 59.998 63.158 0.00 0.00 0.00 5.40
902 917 1.685765 GAAGGGGTGATTTGGGGGC 60.686 63.158 0.00 0.00 0.00 5.80
904 919 2.364186 GGGGTGATTTGGGGGCAG 60.364 66.667 0.00 0.00 0.00 4.85
905 920 2.770130 GGGTGATTTGGGGGCAGA 59.230 61.111 0.00 0.00 0.00 4.26
906 921 1.078347 GGGTGATTTGGGGGCAGAA 59.922 57.895 0.00 0.00 0.00 3.02
919 934 2.353109 GGGGCAGAATCTTGTTTGCTTC 60.353 50.000 0.00 0.00 36.79 3.86
946 961 1.253593 TGGCTGTGCGTCAGATCTCT 61.254 55.000 11.97 0.00 46.27 3.10
965 980 4.020751 TCTCTGAAATCTGAGGGTGTGAAG 60.021 45.833 14.80 0.00 40.82 3.02
969 984 1.903877 ATCTGAGGGTGTGAAGGGCG 61.904 60.000 0.00 0.00 0.00 6.13
1020 1035 2.356313 CAGACTCGCGCCAACACT 60.356 61.111 0.00 0.00 0.00 3.55
1037 1052 5.009911 CCAACACTGATTTGACAATGGAGAA 59.990 40.000 0.00 0.00 0.00 2.87
1046 1061 4.387026 TGACAATGGAGAAGGTGGATTT 57.613 40.909 0.00 0.00 0.00 2.17
1056 1071 2.907458 AGGTGGATTTCAAGGGGAAG 57.093 50.000 0.00 0.00 36.72 3.46
1057 1072 2.358258 AGGTGGATTTCAAGGGGAAGA 58.642 47.619 0.00 0.00 36.72 2.87
1164 1179 1.144936 GGACGCCCTCATCTTGGAG 59.855 63.158 0.00 0.00 34.62 3.86
1194 1209 5.831702 ATGAAGCTGATTTGGTGAATCTC 57.168 39.130 0.00 0.00 43.74 2.75
1231 1246 7.898470 ATTGGTAAGGTATTATCCCCACATA 57.102 36.000 0.00 0.00 0.00 2.29
1236 1251 6.688073 AAGGTATTATCCCCACATACTCTG 57.312 41.667 0.00 0.00 0.00 3.35
1260 1275 5.622233 GCATATACAGACTATCATGTCGGCA 60.622 44.000 0.00 0.00 41.47 5.69
1277 1292 0.678048 GCACTTAGACCAGCTTGGGG 60.678 60.000 7.06 0.00 43.37 4.96
1291 1306 2.179427 CTTGGGGGAATCCAAAAGGTC 58.821 52.381 0.09 0.00 45.13 3.85
1293 1308 1.077005 TGGGGGAATCCAAAAGGTCTG 59.923 52.381 0.09 0.00 37.22 3.51
1295 1310 1.357761 GGGGAATCCAAAAGGTCTGGA 59.642 52.381 0.09 0.00 46.86 3.86
1411 1426 0.241749 ACATGCGGTGTTGCTCAATG 59.758 50.000 0.00 0.00 38.01 2.82
1422 1437 4.560035 GTGTTGCTCAATGAATTTGATCCG 59.440 41.667 0.00 0.00 43.30 4.18
1426 1441 4.040376 GCTCAATGAATTTGATCCGAAGC 58.960 43.478 0.00 0.00 43.30 3.86
1452 1468 5.520376 AACCCTCTGATGTTGTTTTCAAG 57.480 39.130 0.00 0.00 40.74 3.02
1459 1475 6.506147 TCTGATGTTGTTTTCAAGACCATTG 58.494 36.000 0.00 0.00 40.74 2.82
1469 1485 2.092158 TCAAGACCATTGTGTTGTGGGA 60.092 45.455 6.69 0.00 44.02 4.37
1483 1499 5.010012 GTGTTGTGGGAAAGAATCATGAACT 59.990 40.000 0.00 0.00 0.00 3.01
1491 1507 6.072452 GGGAAAGAATCATGAACTCTCGTTTT 60.072 38.462 0.00 0.00 32.39 2.43
1509 1525 6.542852 TCGTTTTGAGCTAATGAATAAGCAC 58.457 36.000 0.00 0.00 41.32 4.40
1551 1567 5.979517 AGCGAAAATTGGAAAAGTTGAGAAG 59.020 36.000 0.00 0.00 0.00 2.85
1563 1579 2.028930 AGTTGAGAAGGTGGATGTCGAC 60.029 50.000 9.11 9.11 0.00 4.20
1566 1582 0.898789 AGAAGGTGGATGTCGACGGT 60.899 55.000 11.62 1.47 0.00 4.83
1571 1587 0.736325 GTGGATGTCGACGGTCAAGG 60.736 60.000 18.66 0.00 0.00 3.61
1584 1600 1.082766 TCAAGGGAGGGCATCAGGA 59.917 57.895 0.08 0.00 0.00 3.86
1596 1612 0.661552 CATCAGGAGATTGCTTGCGG 59.338 55.000 0.00 0.00 30.20 5.69
1608 1624 1.900545 GCTTGCGGGTAAGGGTCTCT 61.901 60.000 0.00 0.00 0.00 3.10
1654 1670 8.489676 AATGAGATATGTCACTTCCTACTCAT 57.510 34.615 4.42 0.00 41.97 2.90
1671 1687 8.204836 TCCTACTCATTGAAGCTTAAGGATTAC 58.795 37.037 0.00 0.00 0.00 1.89
1683 1699 7.210873 AGCTTAAGGATTACGAAAGGTATGAG 58.789 38.462 4.29 0.00 0.00 2.90
1686 1702 5.277857 AGGATTACGAAAGGTATGAGGTG 57.722 43.478 0.00 0.00 0.00 4.00
1701 1717 7.232534 AGGTATGAGGTGAAATATGAGAGACTC 59.767 40.741 0.00 0.00 0.00 3.36
1719 1735 4.540099 AGACTCCCCCATTATTGTTTCTCA 59.460 41.667 0.00 0.00 0.00 3.27
1725 1741 4.099881 CCCCATTATTGTTTCTCATGTGGG 59.900 45.833 0.00 0.00 42.64 4.61
1731 1747 8.472413 CATTATTGTTTCTCATGTGGGATTCTT 58.528 33.333 0.00 0.00 0.00 2.52
1732 1748 5.710513 TTGTTTCTCATGTGGGATTCTTG 57.289 39.130 0.00 0.00 0.00 3.02
1734 1750 2.425143 TCTCATGTGGGATTCTTGGC 57.575 50.000 0.00 0.00 0.00 4.52
1743 1759 1.283321 GGGATTCTTGGCCACTCTTCT 59.717 52.381 3.88 0.00 0.00 2.85
1749 1765 6.183361 GGATTCTTGGCCACTCTTCTATAGAA 60.183 42.308 3.88 14.42 30.91 2.10
1762 1778 6.537355 TCTTCTATAGAATGCCCAAATCCAG 58.463 40.000 15.47 0.00 33.01 3.86
1773 1789 2.245806 CCCAAATCCAGGAGAAAGGGAT 59.754 50.000 11.90 0.00 43.12 3.85
1800 1816 3.626930 GGGTAAACTCCCATACAATGCA 58.373 45.455 0.00 0.00 46.30 3.96
1865 1881 4.221482 GGGATCAAAATCTGGTCAAAGCTT 59.779 41.667 0.00 0.00 36.83 3.74
2024 2040 7.339466 ACAAGACCAAAGTATGAAACAGAAAGT 59.661 33.333 0.00 0.00 0.00 2.66
2492 2508 1.561643 TGAGGGATTCAAGAGCTCGT 58.438 50.000 8.37 1.01 31.34 4.18
2551 2567 2.234661 CTGTGAGTAGTGATGGCCTGAA 59.765 50.000 3.32 0.00 0.00 3.02
2936 2954 1.166531 GGATGGGCGTAATGTCAGGC 61.167 60.000 0.00 0.00 0.00 4.85
3240 3259 3.445805 TCAACAACCCTTCAAACTTGGAC 59.554 43.478 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 42 1.002366 GCAGTGATTTCAGCGACGAT 58.998 50.000 0.00 0.00 0.00 3.73
67 69 2.103263 GACAGGGATATCGGTCAAAGCT 59.897 50.000 13.02 0.00 0.00 3.74
79 81 1.142262 TCTGACGGATCGACAGGGATA 59.858 52.381 16.48 0.00 45.94 2.59
138 140 1.375908 GACGCAGGGTGAAGCATGA 60.376 57.895 0.00 0.00 0.00 3.07
145 147 1.595929 GGAAAACGACGCAGGGTGA 60.596 57.895 0.00 0.00 0.00 4.02
177 179 1.734117 GGCGTCAAAGCAATGCACC 60.734 57.895 8.35 0.00 39.27 5.01
368 372 9.678941 CAATAAGGAAAGAACTTTTGAGGTTAC 57.321 33.333 1.33 0.00 32.11 2.50
414 418 5.722263 CAATCTGCATGGTTTGGTATTGAA 58.278 37.500 0.00 0.00 0.00 2.69
585 589 2.929641 TGTTGATCTCTTTGCCACACA 58.070 42.857 0.00 0.00 0.00 3.72
684 688 3.005684 GCATGAATTGGGTCAGTTGTGAA 59.994 43.478 0.00 0.00 33.27 3.18
694 698 5.481473 AGAGTTGTAATTGCATGAATTGGGT 59.519 36.000 0.00 0.00 35.74 4.51
695 699 5.808540 CAGAGTTGTAATTGCATGAATTGGG 59.191 40.000 0.00 0.00 35.74 4.12
696 700 5.290158 GCAGAGTTGTAATTGCATGAATTGG 59.710 40.000 0.00 0.00 35.74 3.16
697 701 5.290158 GGCAGAGTTGTAATTGCATGAATTG 59.710 40.000 0.00 0.00 38.27 2.32
698 702 5.186409 AGGCAGAGTTGTAATTGCATGAATT 59.814 36.000 0.00 2.74 38.27 2.17
699 703 4.708421 AGGCAGAGTTGTAATTGCATGAAT 59.292 37.500 0.00 0.00 38.27 2.57
700 704 4.081406 AGGCAGAGTTGTAATTGCATGAA 58.919 39.130 0.00 0.00 38.27 2.57
701 705 3.689347 AGGCAGAGTTGTAATTGCATGA 58.311 40.909 0.00 0.00 38.27 3.07
702 706 3.181493 GGAGGCAGAGTTGTAATTGCATG 60.181 47.826 0.00 0.00 38.27 4.06
703 707 3.019564 GGAGGCAGAGTTGTAATTGCAT 58.980 45.455 0.00 0.00 38.27 3.96
704 708 2.436417 GGAGGCAGAGTTGTAATTGCA 58.564 47.619 0.00 0.00 38.27 4.08
705 709 1.745653 GGGAGGCAGAGTTGTAATTGC 59.254 52.381 0.00 0.00 35.87 3.56
706 710 3.356529 AGGGAGGCAGAGTTGTAATTG 57.643 47.619 0.00 0.00 0.00 2.32
707 711 4.783227 TCTAAGGGAGGCAGAGTTGTAATT 59.217 41.667 0.00 0.00 0.00 1.40
708 712 4.362677 TCTAAGGGAGGCAGAGTTGTAAT 58.637 43.478 0.00 0.00 0.00 1.89
709 713 3.786553 TCTAAGGGAGGCAGAGTTGTAA 58.213 45.455 0.00 0.00 0.00 2.41
710 714 3.468071 TCTAAGGGAGGCAGAGTTGTA 57.532 47.619 0.00 0.00 0.00 2.41
711 715 2.303311 GTTCTAAGGGAGGCAGAGTTGT 59.697 50.000 0.00 0.00 0.00 3.32
712 716 2.569404 AGTTCTAAGGGAGGCAGAGTTG 59.431 50.000 0.00 0.00 0.00 3.16
713 717 2.835156 GAGTTCTAAGGGAGGCAGAGTT 59.165 50.000 0.00 0.00 0.00 3.01
714 718 2.043801 AGAGTTCTAAGGGAGGCAGAGT 59.956 50.000 0.00 0.00 0.00 3.24
715 719 2.693074 GAGAGTTCTAAGGGAGGCAGAG 59.307 54.545 0.00 0.00 0.00 3.35
716 720 2.313342 AGAGAGTTCTAAGGGAGGCAGA 59.687 50.000 0.00 0.00 0.00 4.26
717 721 2.693074 GAGAGAGTTCTAAGGGAGGCAG 59.307 54.545 0.00 0.00 32.53 4.85
727 731 2.307980 TGGAAGGGACGAGAGAGTTCTA 59.692 50.000 0.00 0.00 32.53 2.10
744 748 0.599204 GGTTTCGCTCGTCACTGGAA 60.599 55.000 0.00 0.00 0.00 3.53
757 761 1.966451 AAGCCTCGCCTTGGTTTCG 60.966 57.895 0.00 0.00 0.00 3.46
758 762 1.581447 CAAGCCTCGCCTTGGTTTC 59.419 57.895 0.00 0.00 38.78 2.78
761 765 3.790416 TTGCAAGCCTCGCCTTGGT 62.790 57.895 0.00 0.00 41.88 3.67
765 769 1.748122 CAGATTGCAAGCCTCGCCT 60.748 57.895 11.83 0.00 0.00 5.52
797 801 2.224137 ACACTAGGATGGATGCACGATG 60.224 50.000 0.00 0.00 0.00 3.84
823 827 4.267536 TGAGGAGATGAATCTTGCTTTGG 58.732 43.478 0.00 0.00 37.25 3.28
829 833 5.353678 GGAACTGTTGAGGAGATGAATCTTG 59.646 44.000 0.00 0.00 37.25 3.02
834 838 2.028112 CGGGAACTGTTGAGGAGATGAA 60.028 50.000 0.00 0.00 0.00 2.57
849 854 1.196766 AGAACTGGGGGTACGGGAAC 61.197 60.000 0.00 0.00 0.00 3.62
850 855 0.906282 GAGAACTGGGGGTACGGGAA 60.906 60.000 0.00 0.00 0.00 3.97
871 885 1.285078 ACCCCTTCCTGTAGCCAAATC 59.715 52.381 0.00 0.00 0.00 2.17
880 895 0.409484 CCCAAATCACCCCTTCCTGT 59.591 55.000 0.00 0.00 0.00 4.00
885 900 2.449777 GCCCCCAAATCACCCCTT 59.550 61.111 0.00 0.00 0.00 3.95
901 916 2.297033 TGGGAAGCAAACAAGATTCTGC 59.703 45.455 0.00 0.00 34.50 4.26
902 917 3.305608 GGTGGGAAGCAAACAAGATTCTG 60.306 47.826 0.00 0.00 34.50 3.02
904 919 2.029020 GGGTGGGAAGCAAACAAGATTC 60.029 50.000 0.00 0.00 33.36 2.52
905 920 1.970640 GGGTGGGAAGCAAACAAGATT 59.029 47.619 0.00 0.00 0.00 2.40
906 921 1.632589 GGGTGGGAAGCAAACAAGAT 58.367 50.000 0.00 0.00 0.00 2.40
946 961 2.040278 CCCTTCACACCCTCAGATTTCA 59.960 50.000 0.00 0.00 0.00 2.69
952 967 2.046892 CGCCCTTCACACCCTCAG 60.047 66.667 0.00 0.00 0.00 3.35
965 980 2.897350 CGCTCCTCAAATCCGCCC 60.897 66.667 0.00 0.00 0.00 6.13
969 984 1.432270 CTTCGCCGCTCCTCAAATCC 61.432 60.000 0.00 0.00 0.00 3.01
998 1013 4.819761 TGGCGCGAGTCTGCATCC 62.820 66.667 12.10 0.00 36.07 3.51
1006 1021 0.884704 AAATCAGTGTTGGCGCGAGT 60.885 50.000 12.10 0.00 0.00 4.18
1020 1035 4.081406 CCACCTTCTCCATTGTCAAATCA 58.919 43.478 0.00 0.00 0.00 2.57
1037 1052 2.041755 GTCTTCCCCTTGAAATCCACCT 59.958 50.000 0.00 0.00 31.06 4.00
1046 1061 3.702048 CCGCGGTCTTCCCCTTGA 61.702 66.667 19.50 0.00 0.00 3.02
1056 1071 4.699522 ACCAGCTTTCCCGCGGTC 62.700 66.667 26.12 7.43 33.66 4.79
1057 1072 4.699522 GACCAGCTTTCCCGCGGT 62.700 66.667 26.12 0.43 38.72 5.68
1062 1077 3.894547 TTCGCCGACCAGCTTTCCC 62.895 63.158 0.00 0.00 0.00 3.97
1099 1114 2.638855 GCTCCATCATCTCCCTGATCTT 59.361 50.000 0.00 0.00 33.59 2.40
1102 1117 0.975135 CGCTCCATCATCTCCCTGAT 59.025 55.000 0.00 0.00 36.29 2.90
1164 1179 4.643784 ACCAAATCAGCTTCATTCTCATCC 59.356 41.667 0.00 0.00 0.00 3.51
1165 1180 5.356190 TCACCAAATCAGCTTCATTCTCATC 59.644 40.000 0.00 0.00 0.00 2.92
1231 1246 7.361628 CGACATGATAGTCTGTATATGCAGAGT 60.362 40.741 27.49 27.49 45.03 3.24
1236 1251 4.800993 GCCGACATGATAGTCTGTATATGC 59.199 45.833 0.00 0.00 36.38 3.14
1260 1275 0.178873 TCCCCCAAGCTGGTCTAAGT 60.179 55.000 0.00 0.00 35.17 2.24
1293 1308 3.123050 GTTTGACACTGGTTTTGCATCC 58.877 45.455 0.00 0.00 0.00 3.51
1295 1310 3.883830 TGTTTGACACTGGTTTTGCAT 57.116 38.095 0.00 0.00 0.00 3.96
1411 1426 4.415735 GGTTTCTGCTTCGGATCAAATTC 58.584 43.478 0.00 0.00 0.00 2.17
1439 1454 5.976458 ACACAATGGTCTTGAAAACAACAT 58.024 33.333 0.00 0.00 0.00 2.71
1452 1468 2.955660 TCTTTCCCACAACACAATGGTC 59.044 45.455 0.00 0.00 33.80 4.02
1459 1475 5.010012 AGTTCATGATTCTTTCCCACAACAC 59.990 40.000 0.00 0.00 0.00 3.32
1483 1499 6.593770 TGCTTATTCATTAGCTCAAAACGAGA 59.406 34.615 0.00 0.00 45.45 4.04
1491 1507 4.454678 CCCAGTGCTTATTCATTAGCTCA 58.545 43.478 0.00 0.00 38.22 4.26
1529 1545 6.198966 CACCTTCTCAACTTTTCCAATTTTCG 59.801 38.462 0.00 0.00 0.00 3.46
1551 1567 0.736325 CTTGACCGTCGACATCCACC 60.736 60.000 17.16 0.00 0.00 4.61
1563 1579 2.190578 GATGCCCTCCCTTGACCG 59.809 66.667 0.00 0.00 0.00 4.79
1566 1582 0.984961 CTCCTGATGCCCTCCCTTGA 60.985 60.000 0.00 0.00 0.00 3.02
1571 1587 0.536915 GCAATCTCCTGATGCCCTCC 60.537 60.000 0.00 0.00 32.44 4.30
1584 1600 0.394352 CCCTTACCCGCAAGCAATCT 60.394 55.000 0.00 0.00 0.00 2.40
1596 1612 5.601313 TGTTATATCCACAGAGACCCTTACC 59.399 44.000 0.00 0.00 0.00 2.85
1627 1643 9.072375 TGAGTAGGAAGTGACATATCTCATTAG 57.928 37.037 0.00 0.00 0.00 1.73
1630 1646 8.366401 CAATGAGTAGGAAGTGACATATCTCAT 58.634 37.037 0.00 0.00 40.35 2.90
1654 1670 6.235664 ACCTTTCGTAATCCTTAAGCTTCAA 58.764 36.000 0.00 0.00 0.00 2.69
1671 1687 7.210174 TCTCATATTTCACCTCATACCTTTCG 58.790 38.462 0.00 0.00 0.00 3.46
1683 1699 3.071747 GGGGGAGTCTCTCATATTTCACC 59.928 52.174 1.23 0.00 31.08 4.02
1686 1702 5.574970 AATGGGGGAGTCTCTCATATTTC 57.425 43.478 5.60 0.00 31.08 2.17
1701 1717 4.099881 CCACATGAGAAACAATAATGGGGG 59.900 45.833 0.00 0.00 38.02 5.40
1719 1735 3.288099 GTGGCCAAGAATCCCACAT 57.712 52.632 7.24 0.00 46.38 3.21
1725 1741 6.412362 TCTATAGAAGAGTGGCCAAGAATC 57.588 41.667 7.24 4.14 0.00 2.52
1731 1747 4.342862 GCATTCTATAGAAGAGTGGCCA 57.657 45.455 19.51 0.00 41.15 5.36
1734 1750 4.963318 TGGGCATTCTATAGAAGAGTGG 57.037 45.455 19.51 8.41 41.15 4.00
1743 1759 4.913355 TCTCCTGGATTTGGGCATTCTATA 59.087 41.667 0.00 0.00 0.00 1.31
1749 1765 2.625087 CCTTTCTCCTGGATTTGGGCAT 60.625 50.000 0.00 0.00 0.00 4.40
1762 1778 1.147153 CCTCGGCATCCCTTTCTCC 59.853 63.158 0.00 0.00 0.00 3.71
1773 1789 3.395630 GGGAGTTTACCCTCGGCA 58.604 61.111 0.00 0.00 45.90 5.69
1794 1810 8.407832 TCCTTCATACATAATTTGTCTGCATTG 58.592 33.333 0.00 0.00 39.87 2.82
1797 1813 6.543465 CCTCCTTCATACATAATTTGTCTGCA 59.457 38.462 0.00 0.00 39.87 4.41
1799 1815 8.206867 TCTCCTCCTTCATACATAATTTGTCTG 58.793 37.037 0.00 0.00 39.87 3.51
1800 1816 8.324191 TCTCCTCCTTCATACATAATTTGTCT 57.676 34.615 0.00 0.00 39.87 3.41
1865 1881 1.630369 AGCTTCTACCACTGGATTGCA 59.370 47.619 0.71 0.00 0.00 4.08
2024 2040 5.636123 TCACCTTCCCAAGCTTTTGTATAA 58.364 37.500 0.00 0.00 0.00 0.98
2492 2508 3.772387 TCCCAACTGCCACATGAATTTA 58.228 40.909 0.00 0.00 0.00 1.40
2551 2567 2.242043 CAAAACAGAACCAGCCTCCAT 58.758 47.619 0.00 0.00 0.00 3.41
2936 2954 0.683973 ACTGCCCTGTCAAGTCTCAG 59.316 55.000 0.00 0.00 0.00 3.35
3240 3259 3.412386 ACCGAACCAAAAGATTCTCTGG 58.588 45.455 11.46 11.46 34.95 3.86


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

AutoCloner maintained by Alex Coulton.