Multiple sequence alignment - TraesCS6B01G011200

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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 TraesCS6B01G011200 chr6B 100.000 4004 0 0 1 4004 6684152 6680149 0.000000e+00 7395
1 TraesCS6B01G011200 chr6B 95.521 1094 49 0 2219 3312 6605217 6606310 0.000000e+00 1749
2 TraesCS6B01G011200 chr6B 93.488 1121 61 3 930 2040 6602398 6603516 0.000000e+00 1655
3 TraesCS6B01G011200 chr6B 89.106 716 69 8 227 938 6601656 6602366 0.000000e+00 881
4 TraesCS6B01G011200 chr6B 91.685 457 16 12 3568 4004 6606480 6606934 7.350000e-172 614
5 TraesCS6B01G011200 chr6B 88.319 351 40 1 1246 1596 6711269 6710920 1.720000e-113 420
6 TraesCS6B01G011200 chr6B 95.181 166 7 1 3366 3530 6606317 6606482 1.100000e-65 261
7 TraesCS6B01G011200 chr6B 92.623 122 8 1 2099 2220 6605065 6605185 1.480000e-39 174
8 TraesCS6B01G011200 chr6D 93.282 1816 97 10 2099 3893 3317398 3319209 0.000000e+00 2654
9 TraesCS6B01G011200 chr6D 92.360 1034 78 1 1007 2040 3314807 3315839 0.000000e+00 1471
10 TraesCS6B01G011200 chr6D 88.431 752 59 15 3276 4004 3298220 3297474 0.000000e+00 881
11 TraesCS6B01G011200 chr6D 84.706 850 111 17 1 836 52038254 52037410 0.000000e+00 832
12 TraesCS6B01G011200 chr6D 85.714 581 56 8 1004 1580 3311350 3311907 4.460000e-164 588
13 TraesCS6B01G011200 chr6D 98.165 109 2 0 3896 4004 3319624 3319732 1.470000e-44 191
14 TraesCS6B01G011200 chr6D 97.248 109 3 0 3896 4004 3336626 3336734 6.830000e-43 185
15 TraesCS6B01G011200 chr6D 96.330 109 4 0 3896 4004 3324870 3324978 3.180000e-41 180
16 TraesCS6B01G011200 chr6D 95.413 109 5 0 3896 4004 3330745 3330853 1.480000e-39 174
17 TraesCS6B01G011200 chr6D 74.788 353 87 2 2221 2572 449160952 449160601 1.490000e-34 158
18 TraesCS6B01G011200 chr6A 89.857 1814 120 26 2219 4004 2132930 2134707 0.000000e+00 2272
19 TraesCS6B01G011200 chr6A 91.973 1034 78 3 1007 2040 2130307 2131335 0.000000e+00 1445
20 TraesCS6B01G011200 chr6A 89.077 650 62 6 930 1574 2127409 2128054 0.000000e+00 798
21 TraesCS6B01G011200 chr6A 92.623 122 8 1 2099 2220 2132778 2132898 1.480000e-39 174
22 TraesCS6B01G011200 chr4A 85.563 942 119 13 1066 2001 713931220 713932150 0.000000e+00 970
23 TraesCS6B01G011200 chr4A 87.517 729 82 1 2218 2946 713934372 713935091 0.000000e+00 833
24 TraesCS6B01G011200 chr4A 88.786 651 73 0 2225 2875 713894338 713893688 0.000000e+00 798
25 TraesCS6B01G011200 chr4A 82.469 559 72 9 1437 1995 713898481 713897949 2.180000e-127 466
26 TraesCS6B01G011200 chr7D 85.608 938 116 11 1067 2001 18812441 18811520 0.000000e+00 966
27 TraesCS6B01G011200 chr7D 86.158 838 103 12 8 836 617210140 617210973 0.000000e+00 893
28 TraesCS6B01G011200 chr7D 89.058 722 70 1 2225 2946 18809068 18808356 0.000000e+00 887
29 TraesCS6B01G011200 chr7D 84.852 845 111 15 1 836 617227794 617228630 0.000000e+00 835
30 TraesCS6B01G011200 chr7D 84.750 859 96 28 1 836 311938079 311938925 0.000000e+00 828
31 TraesCS6B01G011200 chr7D 84.772 788 89 18 1234 2001 18833674 18834450 0.000000e+00 761
32 TraesCS6B01G011200 chr7A 84.452 939 127 10 1066 1995 19178513 19177585 0.000000e+00 907
33 TraesCS6B01G011200 chr7A 89.094 651 68 1 2225 2875 19175204 19174557 0.000000e+00 806
34 TraesCS6B01G011200 chr7A 81.609 696 102 14 1118 1813 19145620 19146289 1.630000e-153 553
35 TraesCS6B01G011200 chr4D 84.670 848 110 19 1 836 478484569 478483730 0.000000e+00 828
36 TraesCS6B01G011200 chr5D 84.304 841 116 14 3 836 416254057 416254888 0.000000e+00 808
37 TraesCS6B01G011200 chr5D 84.223 843 114 16 3 836 416232017 416232849 0.000000e+00 802
38 TraesCS6B01G011200 chr3B 83.901 851 111 20 1 836 131662279 131661440 0.000000e+00 789
39 TraesCS6B01G011200 chr2B 80.472 635 121 1 2233 2867 727221828 727221197 2.160000e-132 483


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 TraesCS6B01G011200 chr6B 6680149 6684152 4003 True 7395.00 7395 100.00000 1 4004 1 chr6B.!!$R1 4003
1 TraesCS6B01G011200 chr6B 6601656 6606934 5278 False 889.00 1749 92.93400 227 4004 6 chr6B.!!$F1 3777
2 TraesCS6B01G011200 chr6D 3311350 3319732 8382 False 1226.00 2654 92.38025 1004 4004 4 chr6D.!!$F4 3000
3 TraesCS6B01G011200 chr6D 3297474 3298220 746 True 881.00 881 88.43100 3276 4004 1 chr6D.!!$R1 728
4 TraesCS6B01G011200 chr6D 52037410 52038254 844 True 832.00 832 84.70600 1 836 1 chr6D.!!$R2 835
5 TraesCS6B01G011200 chr6A 2127409 2134707 7298 False 1172.25 2272 90.88250 930 4004 4 chr6A.!!$F1 3074
6 TraesCS6B01G011200 chr4A 713931220 713935091 3871 False 901.50 970 86.54000 1066 2946 2 chr4A.!!$F1 1880
7 TraesCS6B01G011200 chr4A 713893688 713898481 4793 True 632.00 798 85.62750 1437 2875 2 chr4A.!!$R1 1438
8 TraesCS6B01G011200 chr7D 18808356 18812441 4085 True 926.50 966 87.33300 1067 2946 2 chr7D.!!$R1 1879
9 TraesCS6B01G011200 chr7D 617210140 617210973 833 False 893.00 893 86.15800 8 836 1 chr7D.!!$F3 828
10 TraesCS6B01G011200 chr7D 617227794 617228630 836 False 835.00 835 84.85200 1 836 1 chr7D.!!$F4 835
11 TraesCS6B01G011200 chr7D 311938079 311938925 846 False 828.00 828 84.75000 1 836 1 chr7D.!!$F2 835
12 TraesCS6B01G011200 chr7D 18833674 18834450 776 False 761.00 761 84.77200 1234 2001 1 chr7D.!!$F1 767
13 TraesCS6B01G011200 chr7A 19174557 19178513 3956 True 856.50 907 86.77300 1066 2875 2 chr7A.!!$R1 1809
14 TraesCS6B01G011200 chr7A 19145620 19146289 669 False 553.00 553 81.60900 1118 1813 1 chr7A.!!$F1 695
15 TraesCS6B01G011200 chr4D 478483730 478484569 839 True 828.00 828 84.67000 1 836 1 chr4D.!!$R1 835
16 TraesCS6B01G011200 chr5D 416254057 416254888 831 False 808.00 808 84.30400 3 836 1 chr5D.!!$F2 833
17 TraesCS6B01G011200 chr5D 416232017 416232849 832 False 802.00 802 84.22300 3 836 1 chr5D.!!$F1 833
18 TraesCS6B01G011200 chr3B 131661440 131662279 839 True 789.00 789 83.90100 1 836 1 chr3B.!!$R1 835
19 TraesCS6B01G011200 chr2B 727221197 727221828 631 True 483.00 483 80.47200 2233 2867 1 chr2B.!!$R1 634

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
868 902 0.113776 AGGTGGGTGACTCGTTCCTA 59.886 55.0 0.00 0.0 0.0 2.94 F
1159 7523 0.178987 CTCCTTCTAGCGCTCCCCTA 60.179 60.0 16.34 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2449 13963 0.472734 AGAAGTGTGGGAGGCTGAGT 60.473 55.000 0.0 0.0 0.0 3.41 R
3092 14606 1.336755 ACCTGTTTCCGTTGCATTCAC 59.663 47.619 0.0 0.0 0.0 3.18 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
54 57 6.930164 TGCATCATTTGACAGCTTTGTATTTT 59.070 30.769 7.92 0.00 31.94 1.82
122 130 2.879756 GCAATGGGAGAGGTGCTTTGTA 60.880 50.000 0.00 0.00 34.13 2.41
125 133 3.806949 TGGGAGAGGTGCTTTGTAATT 57.193 42.857 0.00 0.00 0.00 1.40
139 147 6.922957 TGCTTTGTAATTGGTTCAATCTTGTC 59.077 34.615 0.00 0.00 32.43 3.18
158 166 1.006102 GTGTCCTCACCCAGTGACG 60.006 63.158 0.00 0.00 37.67 4.35
195 206 7.852454 CGAGACACATATTGTATTGTTTCCATG 59.148 37.037 0.00 0.00 39.17 3.66
246 259 9.964408 TCATATTGATTGGATCTATCCCTCTAT 57.036 33.333 6.54 8.15 46.59 1.98
288 303 9.709495 TTAAGGCGTTACTCTGTTTTTATCTTA 57.291 29.630 0.00 0.00 0.00 2.10
345 361 6.264744 TGTGTGGAGTAATAGTAGTAGATGCC 59.735 42.308 0.00 0.00 0.00 4.40
355 371 0.978146 AGTAGATGCCGGCAGGAGTT 60.978 55.000 35.36 18.34 41.02 3.01
360 376 4.329545 GCCGGCAGGAGTTGGTCA 62.330 66.667 24.80 0.00 41.02 4.02
365 381 1.471676 CGGCAGGAGTTGGTCATACTC 60.472 57.143 0.00 0.00 41.00 2.59
402 418 3.439476 GCTCATATTCATGATCACTGCCC 59.561 47.826 0.00 0.00 40.40 5.36
471 488 9.500785 AGAAATTTGTTTACCCACAATATTTGG 57.499 29.630 0.00 8.77 36.54 3.28
473 490 9.634021 AAATTTGTTTACCCACAATATTTGGTT 57.366 25.926 12.67 4.73 36.54 3.67
476 493 8.664211 TTGTTTACCCACAATATTTGGTTTTC 57.336 30.769 12.67 4.24 31.48 2.29
511 528 4.290942 CTCTAGTGAAACCTATGACCCCT 58.709 47.826 0.00 0.00 37.80 4.79
646 679 0.320073 TTGCGAGTAACCGTGAAGGG 60.320 55.000 0.00 0.00 46.96 3.95
656 689 1.142060 ACCGTGAAGGGATTGACAACA 59.858 47.619 0.00 0.00 46.96 3.33
697 731 6.083630 GCAAGTATTTATTCGTTTGTGCAGA 58.916 36.000 0.00 0.00 0.00 4.26
727 761 6.998074 ACTATTGGAGATTTGTGTGTTTCTCA 59.002 34.615 0.00 0.00 37.04 3.27
837 871 5.886960 ACGAAAGCTCAAGAAATAGCAAT 57.113 34.783 0.00 0.00 41.32 3.56
844 878 3.554934 TCAAGAAATAGCAATCCGCCAT 58.445 40.909 0.00 0.00 44.04 4.40
868 902 0.113776 AGGTGGGTGACTCGTTCCTA 59.886 55.000 0.00 0.00 0.00 2.94
886 920 4.251169 TCCTATCCCTAAGCCCAATCATT 58.749 43.478 0.00 0.00 0.00 2.57
924 958 1.620822 AAGCCCAATCATAATCCGCC 58.379 50.000 0.00 0.00 0.00 6.13
952 1025 7.376866 CGTTTGACATTTGGCATACATAATCTC 59.623 37.037 7.59 0.00 35.16 2.75
953 1026 8.408601 GTTTGACATTTGGCATACATAATCTCT 58.591 33.333 2.57 0.00 35.47 3.10
964 1037 9.727627 GGCATACATAATCTCTGAAAAGAAAAG 57.272 33.333 0.00 0.00 0.00 2.27
977 1050 7.119116 TCTGAAAAGAAAAGCATACATAAGCGA 59.881 33.333 0.00 0.00 35.48 4.93
1021 1102 5.049543 ACGAAATACTACTCCGCTAGCTAAG 60.050 44.000 13.93 12.03 0.00 2.18
1029 1112 3.182967 CTCCGCTAGCTAAGTGAACAAG 58.817 50.000 13.93 0.00 37.99 3.16
1069 4606 0.322975 ATTCCTCTTCACACAGCGCT 59.677 50.000 2.64 2.64 0.00 5.92
1092 4629 4.845580 CGATGCAGCTCGCCCCTT 62.846 66.667 0.00 0.00 41.33 3.95
1144 7505 1.758440 TTCGTGTGCCTCTTGCTCCT 61.758 55.000 0.00 0.00 42.00 3.69
1156 7517 1.961180 TTGCTCCTTCTAGCGCTCCC 61.961 60.000 16.34 0.00 45.85 4.30
1159 7523 0.178987 CTCCTTCTAGCGCTCCCCTA 60.179 60.000 16.34 0.00 0.00 3.53
1179 7543 1.752198 CTGAACCCCAACTCCGTCA 59.248 57.895 0.00 0.00 0.00 4.35
1841 8214 0.968901 ACATCCAGTTCGACGGGCTA 60.969 55.000 0.00 0.00 33.25 3.93
1982 8373 0.779997 AGGTCAACATCAAGGGCCTT 59.220 50.000 14.48 14.48 0.00 4.35
2024 8423 0.824109 CCTCGCCTACACTTCCATCA 59.176 55.000 0.00 0.00 0.00 3.07
2040 8439 3.008266 TCCATCATGTTCTCAACAGCTGA 59.992 43.478 23.35 0.00 45.95 4.26
2041 8440 3.945921 CCATCATGTTCTCAACAGCTGAT 59.054 43.478 23.35 5.41 45.95 2.90
2042 8441 5.104817 TCCATCATGTTCTCAACAGCTGATA 60.105 40.000 23.35 3.88 45.95 2.15
2043 8442 5.763698 CCATCATGTTCTCAACAGCTGATAT 59.236 40.000 23.35 2.84 45.95 1.63
2044 8443 6.932960 CCATCATGTTCTCAACAGCTGATATA 59.067 38.462 23.35 0.00 45.95 0.86
2045 8444 7.606839 CCATCATGTTCTCAACAGCTGATATAT 59.393 37.037 23.35 0.00 45.95 0.86
2046 8445 9.649167 CATCATGTTCTCAACAGCTGATATATA 57.351 33.333 23.35 0.00 45.95 0.86
2095 8502 3.452755 ACCGCATCATCTAATCGAACA 57.547 42.857 0.00 0.00 0.00 3.18
2097 8504 4.380531 ACCGCATCATCTAATCGAACAAT 58.619 39.130 0.00 0.00 0.00 2.71
2098 8505 4.212004 ACCGCATCATCTAATCGAACAATG 59.788 41.667 0.00 0.00 0.00 2.82
2102 13547 6.572621 CGCATCATCTAATCGAACAATGAAAG 59.427 38.462 0.00 0.00 30.76 2.62
2119 13564 5.963176 TGAAAGCTGATTTGCATGTCTTA 57.037 34.783 0.00 0.00 34.99 2.10
2124 13569 5.191426 AGCTGATTTGCATGTCTTATGAGT 58.809 37.500 0.00 0.00 34.99 3.41
2159 13619 6.332103 AGCTGGATGCATATATTGGATATCCT 59.668 38.462 22.35 6.03 45.94 3.24
2198 13662 6.070538 AGTCCACTCTTGAATACATACAAGCT 60.071 38.462 0.00 0.00 41.91 3.74
2596 14110 0.893727 AATTTCGGCCAGAGCGGTTT 60.894 50.000 2.24 0.00 41.24 3.27
2627 14141 4.891727 CGGCCAAGATCGACCCGG 62.892 72.222 2.24 0.00 35.54 5.73
2653 14167 4.283212 GGGAACAATTTTGAACTGATCCCA 59.717 41.667 11.16 0.00 42.84 4.37
2821 14335 4.016706 CCCAAGACCGTCCCGCTT 62.017 66.667 0.00 0.00 0.00 4.68
2884 14398 6.311445 ACACATGATTGTTCGTATCTCAGAAC 59.689 38.462 0.00 1.80 44.93 3.01
2897 14411 2.812011 TCTCAGAACTTCGTGACGATCA 59.188 45.455 9.08 0.00 35.23 2.92
3023 14537 4.695217 AAACATGTACCTACATTTGGCG 57.305 40.909 0.00 0.00 43.99 5.69
3036 14550 4.079253 ACATTTGGCGGTCAAAAGAGTAT 58.921 39.130 16.14 0.00 46.93 2.12
3092 14606 4.827304 TCACTATCGATCTCTCAAGCAG 57.173 45.455 0.00 0.00 0.00 4.24
3202 14720 6.405538 TGAAAGCACAAAAGGTTCTTGAAAT 58.594 32.000 0.00 0.00 33.11 2.17
3233 14751 5.836024 AATTTCTGGAAGGGTGTACAGTA 57.164 39.130 0.00 0.00 32.92 2.74
3239 14757 5.104444 TCTGGAAGGGTGTACAGTAAAAACA 60.104 40.000 0.00 0.00 32.92 2.83
3289 14834 1.118838 CCAAGTTGGTTGCCCTTTGA 58.881 50.000 14.21 0.00 34.45 2.69
3400 14945 3.702792 AGTGCTAGCAGAGGAAAGTCTA 58.297 45.455 20.03 0.00 0.00 2.59
3535 15081 0.323269 TTGCCGATCATGCTTTGGGA 60.323 50.000 5.88 0.00 0.00 4.37
3638 15185 2.250939 TCGGCAAAGTGCGGAGTTG 61.251 57.895 6.41 0.00 45.71 3.16
3639 15186 2.050077 GGCAAAGTGCGGAGTTGC 60.050 61.111 14.65 14.65 46.21 4.17
3640 15187 2.555547 GGCAAAGTGCGGAGTTGCT 61.556 57.895 20.05 0.00 46.21 3.91
3641 15188 1.370900 GCAAAGTGCGGAGTTGCTG 60.371 57.895 15.43 5.16 43.40 4.41
3642 15189 1.785041 GCAAAGTGCGGAGTTGCTGA 61.785 55.000 15.43 0.00 43.40 4.26
3648 15195 2.053627 GTGCGGAGTTGCTGAATTTTG 58.946 47.619 0.00 0.00 35.36 2.44
3770 15340 6.482835 CGATAAAATGAACTCGGCAAACATA 58.517 36.000 0.00 0.00 0.00 2.29
3798 15369 5.707298 CACTGACCAAAGTTGTGGATTAGAT 59.293 40.000 10.03 0.00 41.65 1.98
3801 15372 7.390718 ACTGACCAAAGTTGTGGATTAGATTAC 59.609 37.037 10.03 0.00 41.65 1.89
3883 15455 6.746120 ACATAGGTTATGCTTTAGGTACTCG 58.254 40.000 0.00 0.00 38.84 4.18
3884 15456 4.056092 AGGTTATGCTTTAGGTACTCGC 57.944 45.455 0.00 0.00 41.75 5.03
3893 15466 0.391661 TAGGTACTCGCTCCGTTCGT 60.392 55.000 0.00 0.00 41.75 3.85
3894 15878 0.391661 AGGTACTCGCTCCGTTCGTA 60.392 55.000 0.00 0.00 0.00 3.43
3988 15972 3.181445 TGGAAGTCATAGCACCACTTTGT 60.181 43.478 0.00 0.00 30.32 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 8.252417 ACAAAGCTGTCAAATGATGCATATAAA 58.748 29.630 0.00 0.00 0.00 1.40
34 36 7.148918 CGGAGAAAAATACAAAGCTGTCAAATG 60.149 37.037 0.00 0.00 36.96 2.32
54 57 6.318648 CCAAACCAAATCAATAGATCGGAGAA 59.681 38.462 0.00 0.00 43.58 2.87
89 93 5.105064 CCTCTCCCATTGCAAGAAAAATCAT 60.105 40.000 4.94 0.00 0.00 2.45
122 130 4.023193 GGACACGACAAGATTGAACCAATT 60.023 41.667 0.00 0.00 33.90 2.32
125 133 2.104111 AGGACACGACAAGATTGAACCA 59.896 45.455 0.00 0.00 0.00 3.67
139 147 1.006102 GTCACTGGGTGAGGACACG 60.006 63.158 0.27 0.00 43.57 4.49
158 166 1.255667 TGTGTCTCGCTACCCTTCCC 61.256 60.000 0.00 0.00 0.00 3.97
160 168 4.051922 CAATATGTGTCTCGCTACCCTTC 58.948 47.826 0.00 0.00 0.00 3.46
162 172 3.031736 ACAATATGTGTCTCGCTACCCT 58.968 45.455 0.00 0.00 34.38 4.34
207 218 9.889388 TCCAATCAATATGAAATAAACCCCATA 57.111 29.630 0.00 0.00 29.06 2.74
246 259 5.302059 ACGCCTTAAGCTAGATGACAAGATA 59.698 40.000 0.00 0.00 40.39 1.98
250 263 3.887621 ACGCCTTAAGCTAGATGACAA 57.112 42.857 0.00 0.00 40.39 3.18
259 272 3.679824 AACAGAGTAACGCCTTAAGCT 57.320 42.857 0.00 0.00 40.39 3.74
280 293 9.273016 GCCTGCATCTAGTGTATTTAAGATAAA 57.727 33.333 0.00 0.00 0.00 1.40
288 303 3.455910 TCCTGCCTGCATCTAGTGTATTT 59.544 43.478 0.00 0.00 0.00 1.40
345 361 0.537188 AGTATGACCAACTCCTGCCG 59.463 55.000 0.00 0.00 0.00 5.69
355 371 0.806868 GTCCGTGACGAGTATGACCA 59.193 55.000 6.54 0.00 0.00 4.02
382 398 4.987963 AGGGCAGTGATCATGAATATGA 57.012 40.909 0.00 0.00 46.67 2.15
429 446 9.545105 AACAAATTTCTGTTGAGCAATTGATAA 57.455 25.926 10.34 0.00 38.12 1.75
447 464 9.634021 AACCAAATATTGTGGGTAAACAAATTT 57.366 25.926 16.24 0.00 42.98 1.82
468 485 3.117512 AGGCTTCTCTCTTGGAAAACCAA 60.118 43.478 0.00 0.00 0.00 3.67
471 488 4.014569 AGAGGCTTCTCTCTTGGAAAAC 57.985 45.455 0.00 0.00 43.99 2.43
473 490 4.221703 CACTAGAGGCTTCTCTCTTGGAAA 59.778 45.833 0.00 0.00 43.99 3.13
476 493 3.360867 TCACTAGAGGCTTCTCTCTTGG 58.639 50.000 0.00 0.00 43.99 3.61
620 651 1.274167 ACGGTTACTCGCAAGGATGAA 59.726 47.619 0.00 0.00 38.47 2.57
646 679 7.867403 ACCAAATGTGATAAAGTGTTGTCAATC 59.133 33.333 0.00 0.00 36.72 2.67
683 717 6.985188 ATAGTAACATCTGCACAAACGAAT 57.015 33.333 0.00 0.00 0.00 3.34
686 720 5.121611 TCCAATAGTAACATCTGCACAAACG 59.878 40.000 0.00 0.00 0.00 3.60
697 731 8.635765 AACACACAAATCTCCAATAGTAACAT 57.364 30.769 0.00 0.00 0.00 2.71
727 761 6.831664 AGAACCAAGGTATCAATCCAGTAT 57.168 37.500 0.00 0.00 0.00 2.12
780 814 4.935578 TGAAGAGAGAAGGGTGATGTAGA 58.064 43.478 0.00 0.00 0.00 2.59
783 817 3.906846 ACTTGAAGAGAGAAGGGTGATGT 59.093 43.478 0.00 0.00 0.00 3.06
794 828 5.064707 TCGTTGGTTTTTCACTTGAAGAGAG 59.935 40.000 0.00 0.00 35.21 3.20
837 871 2.350895 CCACCTGAACATGGCGGA 59.649 61.111 0.00 0.00 0.00 5.54
844 878 1.046472 ACGAGTCACCCACCTGAACA 61.046 55.000 0.00 0.00 0.00 3.18
868 902 4.324563 CGGATAATGATTGGGCTTAGGGAT 60.325 45.833 0.00 0.00 0.00 3.85
886 920 3.625764 GCTTAAGTCAAACATGGCGGATA 59.374 43.478 4.02 0.00 0.00 2.59
924 958 3.894920 TGTATGCCAAATGTCAAACGTG 58.105 40.909 0.00 0.00 0.00 4.49
952 1025 7.243487 TCGCTTATGTATGCTTTTCTTTTCAG 58.757 34.615 0.00 0.00 0.00 3.02
953 1026 7.139896 TCGCTTATGTATGCTTTTCTTTTCA 57.860 32.000 0.00 0.00 0.00 2.69
964 1037 5.639506 AGTACATGGATTCGCTTATGTATGC 59.360 40.000 0.00 0.00 38.04 3.14
1029 1112 2.727647 CGTGATAGAGCTCGCGGC 60.728 66.667 6.13 9.11 43.52 6.53
1042 1125 3.181470 TGTGTGAAGAGGAATGAACGTGA 60.181 43.478 0.00 0.00 0.00 4.35
1089 4626 3.353836 CGGGTCGGTGCACAAAGG 61.354 66.667 20.43 4.62 0.00 3.11
1092 4629 2.589442 GAACGGGTCGGTGCACAA 60.589 61.111 20.43 2.67 0.00 3.33
1144 7505 0.755698 CAGGTAGGGGAGCGCTAGAA 60.756 60.000 11.50 0.00 29.74 2.10
1156 7517 0.618981 GGAGTTGGGGTTCAGGTAGG 59.381 60.000 0.00 0.00 0.00 3.18
1159 7523 1.768888 ACGGAGTTGGGGTTCAGGT 60.769 57.895 0.00 0.00 37.78 4.00
1841 8214 2.113986 GCCAGCCACTTGGTGACT 59.886 61.111 0.00 0.00 45.48 3.41
1898 8277 2.915659 TCCACGAAGTCCAGGCGT 60.916 61.111 0.00 0.00 41.61 5.68
1982 8373 1.209621 GGTGGGGGCTTACAGTGATA 58.790 55.000 0.00 0.00 0.00 2.15
2056 8455 9.677567 GATGCGGTAATTAATCACAAATAATGT 57.322 29.630 0.00 0.00 45.34 2.71
2057 8456 9.676195 TGATGCGGTAATTAATCACAAATAATG 57.324 29.630 0.00 0.00 0.00 1.90
2065 8464 8.110612 CGATTAGATGATGCGGTAATTAATCAC 58.889 37.037 0.70 0.00 32.18 3.06
2095 8502 5.401531 AGACATGCAAATCAGCTTTCATT 57.598 34.783 0.00 0.00 34.99 2.57
2097 8504 4.859304 AAGACATGCAAATCAGCTTTCA 57.141 36.364 0.00 0.00 34.99 2.69
2098 8505 6.558009 TCATAAGACATGCAAATCAGCTTTC 58.442 36.000 0.00 0.00 34.99 2.62
2102 13547 5.065602 TGACTCATAAGACATGCAAATCAGC 59.934 40.000 0.00 0.00 0.00 4.26
2119 13564 2.234661 TCCAGCTTTCATCGTGACTCAT 59.765 45.455 0.00 0.00 0.00 2.90
2124 13569 1.338960 TGCATCCAGCTTTCATCGTGA 60.339 47.619 0.00 0.00 45.94 4.35
2159 13619 5.143369 AGAGTGGACTATCTATCATGCACA 58.857 41.667 0.00 0.00 0.00 4.57
2198 13662 5.080731 CACGTTAAGTGTTTTCGTGTGAAA 58.919 37.500 7.65 0.00 45.51 2.69
2441 13955 4.767255 GAGGCTGAGTGGCGTGGG 62.767 72.222 0.00 0.00 46.88 4.61
2449 13963 0.472734 AGAAGTGTGGGAGGCTGAGT 60.473 55.000 0.00 0.00 0.00 3.41
2581 14095 3.311110 AGAAACCGCTCTGGCCGA 61.311 61.111 0.00 0.00 43.94 5.54
2627 14141 4.664150 TCAGTTCAAAATTGTTCCCCAC 57.336 40.909 0.00 0.00 0.00 4.61
2641 14155 1.462616 CGCCAAATGGGATCAGTTCA 58.537 50.000 0.90 0.00 40.01 3.18
2653 14167 1.451387 CCTTCTACCGGCGCCAAAT 60.451 57.895 28.98 13.56 0.00 2.32
2821 14335 2.263540 GGCTTGACGACGGCCTTA 59.736 61.111 0.00 0.00 42.31 2.69
2851 14365 1.748950 ACAATCATGTGTATGCGGCA 58.251 45.000 4.58 4.58 38.69 5.69
3019 14533 4.095782 GCAATTATACTCTTTTGACCGCCA 59.904 41.667 0.00 0.00 0.00 5.69
3023 14537 6.759497 ACAGGCAATTATACTCTTTTGACC 57.241 37.500 0.00 0.00 0.00 4.02
3036 14550 6.369340 TCGTTCTCGATAAAAACAGGCAATTA 59.631 34.615 0.00 0.00 41.35 1.40
3074 14588 4.827304 TCACTGCTTGAGAGATCGATAG 57.173 45.455 0.00 0.00 0.00 2.08
3092 14606 1.336755 ACCTGTTTCCGTTGCATTCAC 59.663 47.619 0.00 0.00 0.00 3.18
3187 14705 9.685276 ATTTTTGGAAGATTTCAAGAACCTTTT 57.315 25.926 0.00 0.00 0.00 2.27
3233 14751 1.005569 GGCCTAGCCTAGGGTGTTTTT 59.994 52.381 23.91 0.00 46.69 1.94
3289 14834 0.034670 GCTTTCCAGCAGGAGGATGT 60.035 55.000 0.00 0.00 46.74 3.06
3400 14945 2.098607 TGACACGTCGAGAAGTCTTTGT 59.901 45.455 0.00 0.00 32.56 2.83
3535 15081 1.207329 GGCTCCATTTACCGAGTGTCT 59.793 52.381 0.00 0.00 0.00 3.41
3638 15185 5.173131 CCAAGTACACGAAACAAAATTCAGC 59.827 40.000 0.00 0.00 0.00 4.26
3639 15186 5.173131 GCCAAGTACACGAAACAAAATTCAG 59.827 40.000 0.00 0.00 0.00 3.02
3640 15187 5.038033 GCCAAGTACACGAAACAAAATTCA 58.962 37.500 0.00 0.00 0.00 2.57
3641 15188 5.038033 TGCCAAGTACACGAAACAAAATTC 58.962 37.500 0.00 0.00 0.00 2.17
3642 15189 5.000012 TGCCAAGTACACGAAACAAAATT 58.000 34.783 0.00 0.00 0.00 1.82
3648 15195 3.955771 TCTTTGCCAAGTACACGAAAC 57.044 42.857 0.00 0.00 0.00 2.78
3770 15340 1.750778 CACAACTTTGGTCAGTGCCTT 59.249 47.619 5.39 0.00 0.00 4.35
3798 15369 7.652105 GTCGTATTTCTAATGGATGCTCAGTAA 59.348 37.037 0.00 0.00 0.00 2.24
3801 15372 5.985530 TGTCGTATTTCTAATGGATGCTCAG 59.014 40.000 0.00 0.00 0.00 3.35
3842 15414 6.803642 ACCTATGTCCTCACGTATTTTAGAC 58.196 40.000 0.00 0.00 0.00 2.59
3857 15429 7.063934 AGTACCTAAAGCATAACCTATGTCC 57.936 40.000 0.00 0.00 38.43 4.02
3883 15455 2.602878 TGAGATTGTTACGAACGGAGC 58.397 47.619 0.00 0.00 0.00 4.70
3884 15456 5.103000 AGAATGAGATTGTTACGAACGGAG 58.897 41.667 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.