Multiple sequence alignment - TraesCS4B01G226800

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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 TraesCS4B01G226800 chr4B 100.000 3820 0 0 1 3820 474377393 474381212 0.000000e+00 7055.0
1 TraesCS4B01G226800 chr4D 91.350 3075 129 55 1 3007 386829990 386832995 0.000000e+00 4078.0
2 TraesCS4B01G226800 chr4D 89.394 792 36 25 3041 3820 386833214 386833969 0.000000e+00 953.0
3 TraesCS4B01G226800 chr4D 97.959 49 0 1 2992 3040 386833141 386833188 2.450000e-12 84.2
4 TraesCS4B01G226800 chr4A 88.402 3242 175 78 7 3150 68140287 68143425 0.000000e+00 3718.0
5 TraesCS4B01G226800 chr4A 86.730 633 50 20 3179 3800 68143427 68144036 0.000000e+00 673.0
6 TraesCS4B01G226800 chr2D 81.743 723 98 26 1157 1853 131777776 131777062 1.190000e-159 573.0
7 TraesCS4B01G226800 chr2D 92.308 39 2 1 2711 2748 131776486 131776448 2.000000e-03 54.7
8 TraesCS4B01G226800 chr2B 81.466 723 100 26 1157 1853 186311856 186312570 2.580000e-156 562.0
9 TraesCS4B01G226800 chr2B 86.007 293 41 0 1561 1853 185776825 185776533 7.970000e-82 315.0
10 TraesCS4B01G226800 chr2B 92.308 39 3 0 2708 2746 186313105 186313143 5.330000e-04 56.5
11 TraesCS4B01G226800 chr2B 96.875 32 1 0 2711 2742 185775988 185775957 2.000000e-03 54.7
12 TraesCS4B01G226800 chr2A 81.025 722 105 25 1157 1853 138827332 138826618 2.590000e-151 545.0
13 TraesCS4B01G226800 chr2A 100.000 29 0 0 2711 2739 138826121 138826093 2.000000e-03 54.7
14 TraesCS4B01G226800 chr5D 74.174 666 126 35 1207 1843 423973283 423973931 6.380000e-58 235.0
15 TraesCS4B01G226800 chr5A 74.251 668 122 40 1207 1843 537615903 537616551 6.380000e-58 235.0
16 TraesCS4B01G226800 chr5B 73.684 665 131 33 1207 1843 511852500 511853148 6.430000e-53 219.0
17 TraesCS4B01G226800 chr6D 72.101 552 97 43 1303 1833 84206903 84207418 3.120000e-21 113.0
18 TraesCS4B01G226800 chr6A 72.122 556 90 43 1303 1833 101428852 101429367 1.450000e-19 108.0
19 TraesCS4B01G226800 chr6B 75.980 204 40 7 1633 1833 159952364 159952561 3.140000e-16 97.1


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 TraesCS4B01G226800 chr4B 474377393 474381212 3819 False 7055.000000 7055 100.0000 1 3820 1 chr4B.!!$F1 3819
1 TraesCS4B01G226800 chr4D 386829990 386833969 3979 False 1705.066667 4078 92.9010 1 3820 3 chr4D.!!$F1 3819
2 TraesCS4B01G226800 chr4A 68140287 68144036 3749 False 2195.500000 3718 87.5660 7 3800 2 chr4A.!!$F1 3793
3 TraesCS4B01G226800 chr2D 131776448 131777776 1328 True 313.850000 573 87.0255 1157 2748 2 chr2D.!!$R1 1591
4 TraesCS4B01G226800 chr2B 186311856 186313143 1287 False 309.250000 562 86.8870 1157 2746 2 chr2B.!!$F1 1589
5 TraesCS4B01G226800 chr2A 138826093 138827332 1239 True 299.850000 545 90.5125 1157 2739 2 chr2A.!!$R1 1582
6 TraesCS4B01G226800 chr5D 423973283 423973931 648 False 235.000000 235 74.1740 1207 1843 1 chr5D.!!$F1 636
7 TraesCS4B01G226800 chr5A 537615903 537616551 648 False 235.000000 235 74.2510 1207 1843 1 chr5A.!!$F1 636
8 TraesCS4B01G226800 chr5B 511852500 511853148 648 False 219.000000 219 73.6840 1207 1843 1 chr5B.!!$F1 636

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
971 1027 0.396435 TAGTGACCACCAGCACCAAG 59.604 55.0 0.0 0.0 35.67 3.61 F
1871 1979 0.109342 CCATACTCCTGTCCATGCCC 59.891 60.0 0.0 0.0 0.00 5.36 F
2517 2712 0.673333 ATTCATTCGAGCACGCACCA 60.673 50.0 0.0 0.0 39.58 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2494 2689 0.028505 GCGTGCTCGAATGAATGCAT 59.971 50.0 13.13 0.0 39.71 3.96 R
2786 3136 0.247736 GGAGGATGAACAGTGCGAGT 59.752 55.0 0.00 0.0 0.00 4.18 R
3581 4172 0.323087 AGTGCCAATCATCAGCTGCA 60.323 50.0 9.47 0.0 0.00 4.41 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
20 21 4.578913 GCAGCGAGCTGTTCAGTA 57.421 55.556 23.79 0.00 45.24 2.74
32 33 3.753272 GCTGTTCAGTATTTCAGCCTTCA 59.247 43.478 4.90 0.00 44.84 3.02
36 37 5.470098 TGTTCAGTATTTCAGCCTTCACTTC 59.530 40.000 0.00 0.00 0.00 3.01
79 83 3.575687 TCTCTTCACATCAGCAAGTCAGA 59.424 43.478 0.00 0.00 0.00 3.27
87 91 0.866427 CAGCAAGTCAGACTGCACAG 59.134 55.000 20.41 0.00 0.00 3.66
93 97 2.163509 AGTCAGACTGCACAGATACGT 58.836 47.619 0.91 0.00 0.00 3.57
115 119 1.319541 CCGAGATATGACGGTCCAGT 58.680 55.000 5.55 0.00 43.53 4.00
120 124 4.036498 CGAGATATGACGGTCCAGTAAACT 59.964 45.833 5.55 1.68 0.00 2.66
396 409 7.060421 TCTTATCCTTCAATAATCCCCACAAC 58.940 38.462 0.00 0.00 0.00 3.32
479 493 2.171659 TCTGCCAAAAGATACGGCCATA 59.828 45.455 2.24 0.00 45.63 2.74
480 494 2.549754 CTGCCAAAAGATACGGCCATAG 59.450 50.000 2.24 0.00 45.63 2.23
501 515 1.684869 CCAAGCACCAAACCCCGATAT 60.685 52.381 0.00 0.00 0.00 1.63
512 526 4.737855 AACCCCGATATAATCCTGATCG 57.262 45.455 0.00 0.00 41.62 3.69
516 530 3.099267 CGATATAATCCTGATCGGCCC 57.901 52.381 0.00 0.00 38.99 5.80
519 535 2.795231 ATAATCCTGATCGGCCCATG 57.205 50.000 0.00 0.00 0.00 3.66
528 544 0.850100 ATCGGCCCATGGTGGAAATA 59.150 50.000 11.73 0.00 40.96 1.40
562 578 2.491022 CCCTAGACCTTCGCCTCCG 61.491 68.421 0.00 0.00 0.00 4.63
616 632 0.709397 TCCAATCAAGCCCCATTCCA 59.291 50.000 0.00 0.00 0.00 3.53
702 723 0.694444 AATACGGCCATGGAGGGAGT 60.694 55.000 18.40 9.42 38.09 3.85
729 750 2.689034 CCCCTTCTTCCCGCTCCT 60.689 66.667 0.00 0.00 0.00 3.69
730 751 2.736826 CCCCTTCTTCCCGCTCCTC 61.737 68.421 0.00 0.00 0.00 3.71
731 752 2.736826 CCCTTCTTCCCGCTCCTCC 61.737 68.421 0.00 0.00 0.00 4.30
732 753 1.990060 CCTTCTTCCCGCTCCTCCA 60.990 63.158 0.00 0.00 0.00 3.86
733 754 1.219393 CTTCTTCCCGCTCCTCCAC 59.781 63.158 0.00 0.00 0.00 4.02
734 755 1.229209 TTCTTCCCGCTCCTCCACT 60.229 57.895 0.00 0.00 0.00 4.00
739 760 1.227664 CCCGCTCCTCCACTCTCTA 59.772 63.158 0.00 0.00 0.00 2.43
780 813 5.994416 AATCCTGATAGTTTATGGGTGGT 57.006 39.130 0.00 0.00 0.00 4.16
794 832 2.610859 TGGTTGCTCCTCCCTCCC 60.611 66.667 0.80 0.00 37.07 4.30
850 900 5.573219 TCCCACTGCTGTACTAAACTAGTA 58.427 41.667 0.00 0.00 40.14 1.82
851 901 5.651139 TCCCACTGCTGTACTAAACTAGTAG 59.349 44.000 0.00 0.00 41.59 2.57
852 902 5.418209 CCCACTGCTGTACTAAACTAGTAGT 59.582 44.000 0.00 0.00 41.59 2.73
939 995 7.394923 GCTGTAATGACACTATATACCTCTCCT 59.605 40.741 0.00 0.00 0.00 3.69
971 1027 0.396435 TAGTGACCACCAGCACCAAG 59.604 55.000 0.00 0.00 35.67 3.61
1027 1083 0.111266 CCAAAGAGTTTGCGTCGTCG 60.111 55.000 0.00 0.00 39.31 5.12
1032 1088 1.818221 GAGTTTGCGTCGTCGTTGCT 61.818 55.000 3.66 0.00 39.49 3.91
1074 1130 4.813161 AGAGGTAATTCGATCGTCGTAGAA 59.187 41.667 15.94 0.58 41.35 2.10
1087 1143 4.152938 TCGTCGTAGAAGAAATCGAGTGAA 59.847 41.667 0.00 0.00 42.98 3.18
1117 1177 6.282199 TGTAGGAGGAGTTCTTGTAATGAC 57.718 41.667 0.00 0.00 0.00 3.06
1718 1811 3.425014 AACACCTGCCACCCCACA 61.425 61.111 0.00 0.00 0.00 4.17
1863 1971 1.584724 CCCAAGGTCCATACTCCTGT 58.415 55.000 0.00 0.00 33.97 4.00
1864 1972 1.486726 CCCAAGGTCCATACTCCTGTC 59.513 57.143 0.00 0.00 33.97 3.51
1866 1974 2.187958 CAAGGTCCATACTCCTGTCCA 58.812 52.381 0.00 0.00 33.97 4.02
1867 1975 2.774234 CAAGGTCCATACTCCTGTCCAT 59.226 50.000 0.00 0.00 33.97 3.41
1868 1976 2.402564 AGGTCCATACTCCTGTCCATG 58.597 52.381 0.00 0.00 32.29 3.66
1869 1977 1.202698 GGTCCATACTCCTGTCCATGC 60.203 57.143 0.00 0.00 0.00 4.06
1870 1978 1.131638 TCCATACTCCTGTCCATGCC 58.868 55.000 0.00 0.00 0.00 4.40
1871 1979 0.109342 CCATACTCCTGTCCATGCCC 59.891 60.000 0.00 0.00 0.00 5.36
1872 1980 0.839277 CATACTCCTGTCCATGCCCA 59.161 55.000 0.00 0.00 0.00 5.36
1873 1981 0.839946 ATACTCCTGTCCATGCCCAC 59.160 55.000 0.00 0.00 0.00 4.61
1874 1982 1.271840 TACTCCTGTCCATGCCCACC 61.272 60.000 0.00 0.00 0.00 4.61
1875 1983 2.531428 TCCTGTCCATGCCCACCA 60.531 61.111 0.00 0.00 0.00 4.17
1876 1984 2.361610 CCTGTCCATGCCCACCAC 60.362 66.667 0.00 0.00 0.00 4.16
1877 1985 2.747460 CTGTCCATGCCCACCACG 60.747 66.667 0.00 0.00 0.00 4.94
1898 2009 2.731027 GCGCCTTAACCACTGCATTTAC 60.731 50.000 0.00 0.00 0.00 2.01
1899 2010 2.747446 CGCCTTAACCACTGCATTTACT 59.253 45.455 0.00 0.00 0.00 2.24
1900 2011 3.936453 CGCCTTAACCACTGCATTTACTA 59.064 43.478 0.00 0.00 0.00 1.82
1913 2024 9.265901 CACTGCATTTACTAATCACTAGCTAAT 57.734 33.333 0.00 0.00 0.00 1.73
1956 2067 1.141645 GTCGTGCGTGGTTAATCACA 58.858 50.000 18.64 0.00 37.50 3.58
2010 2121 2.481276 GGGACACGATCACGATGATGAA 60.481 50.000 5.41 0.00 37.20 2.57
2065 2187 3.118629 GCACTCCATGTCACCTTATCTCA 60.119 47.826 0.00 0.00 0.00 3.27
2160 2288 1.674962 GAGGCTTGGAAGATGATGCAC 59.325 52.381 0.00 0.00 0.00 4.57
2321 2498 2.433318 GTCAGTCGTCAGGGCAGC 60.433 66.667 0.00 0.00 0.00 5.25
2355 2532 5.423015 TCTTATCTTGTGATGAAGTCAGGC 58.577 41.667 0.00 0.00 37.56 4.85
2380 2567 2.162921 GAATGATGGCCGATGTCGCG 62.163 60.000 0.00 0.00 38.18 5.87
2389 2576 1.835121 CCGATGTCGCGATGAAACTA 58.165 50.000 14.06 0.00 38.18 2.24
2469 2664 5.988561 GCTAGATTATGTTTCTCCTGACCTG 59.011 44.000 0.00 0.00 0.00 4.00
2472 2667 6.825610 AGATTATGTTTCTCCTGACCTGATC 58.174 40.000 0.00 0.00 0.00 2.92
2473 2668 3.922171 ATGTTTCTCCTGACCTGATCC 57.078 47.619 0.00 0.00 0.00 3.36
2476 2671 3.103742 GTTTCTCCTGACCTGATCCTCT 58.896 50.000 0.00 0.00 0.00 3.69
2494 2689 4.757657 TCCTCTTTTATTTTACTGCACGCA 59.242 37.500 0.00 0.00 0.00 5.24
2511 2706 1.474017 GCATGCATTCATTCGAGCAC 58.526 50.000 14.21 0.00 40.14 4.40
2512 2707 1.738432 CATGCATTCATTCGAGCACG 58.262 50.000 0.00 0.00 40.14 5.34
2517 2712 0.673333 ATTCATTCGAGCACGCACCA 60.673 50.000 0.00 0.00 39.58 4.17
2551 2747 4.339247 TGATCGTGAACTCAGCTCATCATA 59.661 41.667 0.00 0.00 0.00 2.15
2808 3158 1.296715 GCACTGTTCATCCTCCGGT 59.703 57.895 0.00 0.00 0.00 5.28
2843 3193 8.674263 AGCATCAAATTAAGATCAGTAGAAGG 57.326 34.615 0.00 0.00 0.00 3.46
2852 3202 3.012959 AGATCAGTAGAAGGGAAGGACCA 59.987 47.826 0.00 0.00 41.20 4.02
2862 3212 1.140312 GGAAGGACCAGCCATATCCA 58.860 55.000 0.00 0.00 40.02 3.41
3067 3614 6.495872 CCATTGTAAAATCCATCCATCCATCT 59.504 38.462 0.00 0.00 0.00 2.90
3068 3615 7.015877 CCATTGTAAAATCCATCCATCCATCTT 59.984 37.037 0.00 0.00 0.00 2.40
3070 3617 7.976414 TGTAAAATCCATCCATCCATCTTTT 57.024 32.000 0.00 0.00 0.00 2.27
3072 3619 8.477256 TGTAAAATCCATCCATCCATCTTTTTC 58.523 33.333 0.00 0.00 0.00 2.29
3073 3620 7.499200 AAAATCCATCCATCCATCTTTTTCA 57.501 32.000 0.00 0.00 0.00 2.69
3077 3630 7.499200 TCCATCCATCCATCTTTTTCATTTT 57.501 32.000 0.00 0.00 0.00 1.82
3125 3684 9.530633 GTGGAGTACAAAGGAAATATACTACTG 57.469 37.037 0.00 0.00 29.51 2.74
3151 3710 5.705609 AAAAAGATTCTTACACGCATGGT 57.294 34.783 0.00 0.00 0.00 3.55
3152 3711 6.811253 AAAAAGATTCTTACACGCATGGTA 57.189 33.333 0.00 0.00 0.00 3.25
3153 3712 5.796350 AAAGATTCTTACACGCATGGTAC 57.204 39.130 0.00 0.00 0.00 3.34
3154 3713 4.737855 AGATTCTTACACGCATGGTACT 57.262 40.909 0.00 0.00 0.00 2.73
3155 3714 5.847111 AGATTCTTACACGCATGGTACTA 57.153 39.130 0.00 0.00 0.00 1.82
3156 3715 5.833082 AGATTCTTACACGCATGGTACTAG 58.167 41.667 0.00 0.00 0.00 2.57
3157 3716 5.593095 AGATTCTTACACGCATGGTACTAGA 59.407 40.000 0.00 0.00 0.00 2.43
3158 3717 5.648178 TTCTTACACGCATGGTACTAGAA 57.352 39.130 0.00 0.00 0.00 2.10
3159 3718 5.648178 TCTTACACGCATGGTACTAGAAA 57.352 39.130 0.00 0.00 0.00 2.52
3160 3719 6.216801 TCTTACACGCATGGTACTAGAAAT 57.783 37.500 0.00 0.00 0.00 2.17
3161 3720 6.636705 TCTTACACGCATGGTACTAGAAATT 58.363 36.000 0.00 0.00 0.00 1.82
3162 3721 6.755141 TCTTACACGCATGGTACTAGAAATTC 59.245 38.462 0.00 0.00 0.00 2.17
3163 3722 3.863424 ACACGCATGGTACTAGAAATTCG 59.137 43.478 0.00 0.00 0.00 3.34
3164 3723 4.109766 CACGCATGGTACTAGAAATTCGA 58.890 43.478 0.00 0.00 0.00 3.71
3165 3724 4.565166 CACGCATGGTACTAGAAATTCGAA 59.435 41.667 0.00 0.00 0.00 3.71
3166 3725 5.234329 CACGCATGGTACTAGAAATTCGAAT 59.766 40.000 4.39 4.39 0.00 3.34
3167 3726 5.234329 ACGCATGGTACTAGAAATTCGAATG 59.766 40.000 12.25 0.84 0.00 2.67
3168 3727 5.333339 CGCATGGTACTAGAAATTCGAATGG 60.333 44.000 12.25 3.00 0.00 3.16
3169 3728 5.527582 GCATGGTACTAGAAATTCGAATGGT 59.472 40.000 12.25 2.57 0.00 3.55
3170 3729 6.511767 GCATGGTACTAGAAATTCGAATGGTG 60.512 42.308 12.25 3.68 0.00 4.17
3171 3730 5.424757 TGGTACTAGAAATTCGAATGGTGG 58.575 41.667 12.25 4.11 0.00 4.61
3172 3731 4.272748 GGTACTAGAAATTCGAATGGTGGC 59.727 45.833 12.25 0.00 0.00 5.01
3173 3732 4.222124 ACTAGAAATTCGAATGGTGGCT 57.778 40.909 12.25 7.44 0.00 4.75
3174 3733 4.192317 ACTAGAAATTCGAATGGTGGCTC 58.808 43.478 12.25 2.47 0.00 4.70
3175 3734 3.356529 AGAAATTCGAATGGTGGCTCT 57.643 42.857 12.25 4.64 0.00 4.09
3176 3735 3.690460 AGAAATTCGAATGGTGGCTCTT 58.310 40.909 12.25 0.00 0.00 2.85
3177 3736 3.441572 AGAAATTCGAATGGTGGCTCTTG 59.558 43.478 12.25 0.00 0.00 3.02
3281 3868 4.873827 GGCGAACAAACTATAACCTGATCA 59.126 41.667 0.00 0.00 0.00 2.92
3294 3883 5.841957 AACCTGATCAATGCACTTATTCC 57.158 39.130 0.00 0.00 0.00 3.01
3321 3910 1.606885 GCTCTCAGCTGTCAGAGGCT 61.607 60.000 25.68 0.00 38.45 4.58
3352 3941 4.984785 GTCAAGCTATGATATGCACGAAGA 59.015 41.667 0.00 0.00 40.97 2.87
3493 4084 5.126869 TGATTTGCCATAACCATAACCAGTG 59.873 40.000 0.00 0.00 0.00 3.66
3525 4116 2.163010 CAGTTCCATCCATTGTCACTGC 59.837 50.000 0.00 0.00 30.77 4.40
3581 4172 4.815846 GGAACATTCACCAAACATTTGCTT 59.184 37.500 0.00 0.00 36.86 3.91
3596 4191 0.815095 TGCTTGCAGCTGATGATTGG 59.185 50.000 20.43 0.47 42.97 3.16
3672 4267 1.434696 GCGGCATGGACTGGAAATG 59.565 57.895 0.00 0.00 0.00 2.32
3699 4294 0.966920 ACCACTCCTACCACGACAAG 59.033 55.000 0.00 0.00 0.00 3.16
3707 4302 3.054878 CCTACCACGACAAGTTGTACAC 58.945 50.000 8.88 0.00 30.73 2.90
3708 4303 2.973694 ACCACGACAAGTTGTACACT 57.026 45.000 8.88 0.00 37.30 3.55
3710 4305 3.709987 ACCACGACAAGTTGTACACTAC 58.290 45.455 8.88 0.00 32.94 2.73
3711 4306 3.130869 ACCACGACAAGTTGTACACTACA 59.869 43.478 8.88 0.00 32.94 2.74
3712 4307 4.114073 CCACGACAAGTTGTACACTACAA 58.886 43.478 8.88 0.00 45.66 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 5.703130 AGAAGTGAAGGCTGAAATACTGAAC 59.297 40.000 0.00 0.00 0.00 3.18
20 21 3.005155 GTGCAAGAAGTGAAGGCTGAAAT 59.995 43.478 0.00 0.00 0.00 2.17
27 28 4.843220 AATTCAGTGCAAGAAGTGAAGG 57.157 40.909 8.57 0.00 41.54 3.46
32 33 6.543831 AGTCAAGTTAATTCAGTGCAAGAAGT 59.456 34.615 8.57 8.28 0.00 3.01
36 37 6.426328 AGAGAGTCAAGTTAATTCAGTGCAAG 59.574 38.462 0.00 0.00 0.00 4.01
79 83 3.814577 GGTGACGTATCTGTGCAGT 57.185 52.632 0.00 0.00 0.00 4.40
108 112 3.003378 GTGTGCTTCAAGTTTACTGGACC 59.997 47.826 0.00 0.00 0.00 4.46
115 119 4.435425 ACGTACTGTGTGCTTCAAGTTTA 58.565 39.130 0.00 0.00 0.00 2.01
120 124 2.588027 TGACGTACTGTGTGCTTCAA 57.412 45.000 0.00 0.00 0.00 2.69
324 332 7.111247 TGAAAATCTTGTTGACAATCTTGGT 57.889 32.000 0.00 0.00 35.02 3.67
325 333 6.145048 GCTGAAAATCTTGTTGACAATCTTGG 59.855 38.462 0.00 0.00 35.02 3.61
326 334 6.698329 TGCTGAAAATCTTGTTGACAATCTTG 59.302 34.615 0.00 0.00 35.02 3.02
327 335 6.808829 TGCTGAAAATCTTGTTGACAATCTT 58.191 32.000 0.00 0.00 35.02 2.40
328 336 6.395426 TGCTGAAAATCTTGTTGACAATCT 57.605 33.333 0.00 0.00 35.02 2.40
329 337 6.145048 CCTTGCTGAAAATCTTGTTGACAATC 59.855 38.462 0.00 0.00 35.02 2.67
330 338 5.987347 CCTTGCTGAAAATCTTGTTGACAAT 59.013 36.000 0.00 0.00 35.02 2.71
331 339 5.105392 ACCTTGCTGAAAATCTTGTTGACAA 60.105 36.000 0.00 0.00 0.00 3.18
332 340 4.402155 ACCTTGCTGAAAATCTTGTTGACA 59.598 37.500 0.00 0.00 0.00 3.58
333 341 4.936891 ACCTTGCTGAAAATCTTGTTGAC 58.063 39.130 0.00 0.00 0.00 3.18
334 342 5.451798 GGAACCTTGCTGAAAATCTTGTTGA 60.452 40.000 0.00 0.00 0.00 3.18
396 409 1.134521 TGGCTATGGCTTAACCGACAG 60.135 52.381 0.00 0.00 43.94 3.51
479 493 2.524148 GGGGTTTGGTGCTTGGCT 60.524 61.111 0.00 0.00 0.00 4.75
480 494 3.989787 CGGGGTTTGGTGCTTGGC 61.990 66.667 0.00 0.00 0.00 4.52
501 515 0.692476 CCATGGGCCGATCAGGATTA 59.308 55.000 2.85 0.00 45.00 1.75
512 526 0.396974 TGCTATTTCCACCATGGGCC 60.397 55.000 18.09 0.00 38.32 5.80
513 527 1.035139 CTGCTATTTCCACCATGGGC 58.965 55.000 18.09 7.57 38.32 5.36
514 528 1.696063 CCTGCTATTTCCACCATGGG 58.304 55.000 18.09 4.89 38.32 4.00
515 529 1.215173 TCCCTGCTATTTCCACCATGG 59.785 52.381 11.19 11.19 39.43 3.66
516 530 2.689983 GTTCCCTGCTATTTCCACCATG 59.310 50.000 0.00 0.00 0.00 3.66
519 535 2.507407 TGTTCCCTGCTATTTCCACC 57.493 50.000 0.00 0.00 0.00 4.61
528 544 3.596362 GGGCTAATTGTTCCCTGCT 57.404 52.632 4.73 0.00 37.08 4.24
616 632 8.225603 TGCTTTCACTTTACTGAAGAAAGAAT 57.774 30.769 15.11 0.00 44.78 2.40
702 723 1.561542 GGAAGAAGGGGAATCTGAGCA 59.438 52.381 0.00 0.00 0.00 4.26
729 750 0.396417 GGCAGAGGCTAGAGAGTGGA 60.396 60.000 0.00 0.00 40.87 4.02
730 751 0.396974 AGGCAGAGGCTAGAGAGTGG 60.397 60.000 0.00 0.00 40.87 4.00
731 752 1.032014 GAGGCAGAGGCTAGAGAGTG 58.968 60.000 0.00 0.00 38.98 3.51
732 753 0.926293 AGAGGCAGAGGCTAGAGAGT 59.074 55.000 0.00 0.00 38.98 3.24
733 754 1.133823 TGAGAGGCAGAGGCTAGAGAG 60.134 57.143 0.00 0.00 38.98 3.20
734 755 0.922626 TGAGAGGCAGAGGCTAGAGA 59.077 55.000 0.00 0.00 38.98 3.10
739 760 0.560193 TAGGATGAGAGGCAGAGGCT 59.440 55.000 0.00 0.00 42.48 4.58
780 813 2.285668 CCTGGGAGGGAGGAGCAA 60.286 66.667 0.00 0.00 31.48 3.91
794 832 3.583024 GAGGTAGAGAAGTCTCGGCCTG 61.583 59.091 22.61 0.00 45.10 4.85
850 900 1.889530 GCAACTCCGGCTCCAGTACT 61.890 60.000 0.00 0.00 0.00 2.73
851 901 1.448013 GCAACTCCGGCTCCAGTAC 60.448 63.158 0.00 0.00 0.00 2.73
852 902 1.609501 AGCAACTCCGGCTCCAGTA 60.610 57.895 0.00 0.00 36.81 2.74
939 995 0.392461 GTCACTAATGGCGAGGGCAA 60.392 55.000 0.00 0.00 42.43 4.52
971 1027 2.101770 GAAGCAATGCAGCTCGGC 59.898 61.111 8.35 0.00 45.89 5.54
1027 1083 3.629398 AGGCATATACAAAGCAGAGCAAC 59.371 43.478 0.00 0.00 0.00 4.17
1032 1088 4.202295 CCTCTCAGGCATATACAAAGCAGA 60.202 45.833 0.00 0.00 0.00 4.26
1074 1130 6.591834 CCTACAATCAACTTCACTCGATTTCT 59.408 38.462 0.00 0.00 0.00 2.52
1087 1143 5.308237 ACAAGAACTCCTCCTACAATCAACT 59.692 40.000 0.00 0.00 0.00 3.16
1117 1177 5.193216 CAAATACGATGTCAATTCAGCTCG 58.807 41.667 0.00 0.00 0.00 5.03
1580 1658 4.379243 CGCAGGTTCAGGTCCGCT 62.379 66.667 0.00 0.00 0.00 5.52
1869 1977 3.428282 GTTAAGGCGCGTGGTGGG 61.428 66.667 8.43 0.00 0.00 4.61
1870 1978 3.428282 GGTTAAGGCGCGTGGTGG 61.428 66.667 8.43 0.00 0.00 4.61
1871 1979 2.666862 TGGTTAAGGCGCGTGGTG 60.667 61.111 8.43 0.00 0.00 4.17
1872 1980 2.667199 GTGGTTAAGGCGCGTGGT 60.667 61.111 8.43 0.00 0.00 4.16
1873 1981 2.358247 AGTGGTTAAGGCGCGTGG 60.358 61.111 8.43 0.00 0.00 4.94
1874 1982 2.860293 CAGTGGTTAAGGCGCGTG 59.140 61.111 8.43 0.00 0.00 5.34
1875 1983 3.047877 GCAGTGGTTAAGGCGCGT 61.048 61.111 8.43 0.00 0.00 6.01
1876 1984 1.922135 AATGCAGTGGTTAAGGCGCG 61.922 55.000 0.00 0.00 0.00 6.86
1877 1985 0.243636 AAATGCAGTGGTTAAGGCGC 59.756 50.000 0.00 0.00 0.00 6.53
1878 1986 2.747446 AGTAAATGCAGTGGTTAAGGCG 59.253 45.455 0.00 0.00 0.00 5.52
1879 1987 5.890424 TTAGTAAATGCAGTGGTTAAGGC 57.110 39.130 0.00 0.00 0.00 4.35
1932 2043 2.068837 TTAACCACGCACGACCTAAG 57.931 50.000 0.00 0.00 0.00 2.18
1933 2044 2.029200 TGATTAACCACGCACGACCTAA 60.029 45.455 0.00 0.00 0.00 2.69
1956 2067 0.241749 CAGTGCGTGCAAATCATGGT 59.758 50.000 0.00 0.00 32.31 3.55
2010 2121 0.033208 ACCAACCATCCATGCCGATT 60.033 50.000 0.00 0.00 0.00 3.34
2065 2187 3.825308 CACTCGCAAGCATTTTGTATGT 58.175 40.909 0.00 0.00 37.18 2.29
2160 2288 4.468765 AACTCCAGACTGATCATCACAG 57.531 45.455 3.32 0.00 40.68 3.66
2194 2327 6.384015 ACATGAATGAGACATCTACTACCCAA 59.616 38.462 0.00 0.00 0.00 4.12
2321 2498 6.169419 TCACAAGATAAGAAAATGACTGCG 57.831 37.500 0.00 0.00 0.00 5.18
2355 2532 4.505556 CGACATCGGCCATCATTCATATAG 59.494 45.833 2.24 0.00 35.37 1.31
2380 2567 6.453396 CGCTAAAGTGTTACGGTAGTTTCATC 60.453 42.308 0.00 0.00 0.00 2.92
2389 2576 2.818130 TTCCGCTAAAGTGTTACGGT 57.182 45.000 0.00 0.00 44.17 4.83
2436 2631 7.313951 AGAAACATAATCTAGCACTGAAAGC 57.686 36.000 0.00 0.00 37.60 3.51
2448 2643 6.183361 GGATCAGGTCAGGAGAAACATAATCT 60.183 42.308 0.00 0.00 0.00 2.40
2469 2664 5.965918 GCGTGCAGTAAAATAAAAGAGGATC 59.034 40.000 0.00 0.00 0.00 3.36
2472 2667 5.041951 TGCGTGCAGTAAAATAAAAGAGG 57.958 39.130 0.00 0.00 0.00 3.69
2473 2668 6.544620 CATGCGTGCAGTAAAATAAAAGAG 57.455 37.500 0.00 0.00 0.00 2.85
2494 2689 0.028505 GCGTGCTCGAATGAATGCAT 59.971 50.000 13.13 0.00 39.71 3.96
2517 2712 2.744202 GTTCACGATCAATGCTCCAACT 59.256 45.455 0.00 0.00 0.00 3.16
2551 2747 2.993899 CACACGAAAAGAATAGCGGAGT 59.006 45.455 0.00 0.00 0.00 3.85
2786 3136 0.247736 GGAGGATGAACAGTGCGAGT 59.752 55.000 0.00 0.00 0.00 4.18
2825 3175 7.147461 GGTCCTTCCCTTCTACTGATCTTAATT 60.147 40.741 0.00 0.00 0.00 1.40
2826 3176 6.327887 GGTCCTTCCCTTCTACTGATCTTAAT 59.672 42.308 0.00 0.00 0.00 1.40
2827 3177 5.661759 GGTCCTTCCCTTCTACTGATCTTAA 59.338 44.000 0.00 0.00 0.00 1.85
2828 3178 5.209659 GGTCCTTCCCTTCTACTGATCTTA 58.790 45.833 0.00 0.00 0.00 2.10
2829 3179 4.034410 GGTCCTTCCCTTCTACTGATCTT 58.966 47.826 0.00 0.00 0.00 2.40
2830 3180 3.012959 TGGTCCTTCCCTTCTACTGATCT 59.987 47.826 0.00 0.00 34.77 2.75
2831 3181 3.375699 TGGTCCTTCCCTTCTACTGATC 58.624 50.000 0.00 0.00 34.77 2.92
2834 3184 1.208293 GCTGGTCCTTCCCTTCTACTG 59.792 57.143 0.00 0.00 34.77 2.74
2836 3186 0.542333 GGCTGGTCCTTCCCTTCTAC 59.458 60.000 0.00 0.00 34.77 2.59
2843 3193 1.140312 TGGATATGGCTGGTCCTTCC 58.860 55.000 0.00 0.00 35.26 3.46
2852 3202 4.474303 TTTTGGATGGATGGATATGGCT 57.526 40.909 0.00 0.00 0.00 4.75
2885 3247 4.398044 TCTGTTCAACTTCTGACCAAAACC 59.602 41.667 0.00 0.00 32.21 3.27
2938 3300 3.626680 CTCGCTTTCGCTCCGGTGA 62.627 63.158 7.92 0.00 35.26 4.02
3070 3617 7.221838 CCGTGCAAACTAGAAAAAGAAAATGAA 59.778 33.333 0.00 0.00 0.00 2.57
3072 3619 6.562086 GCCGTGCAAACTAGAAAAAGAAAATG 60.562 38.462 0.00 0.00 0.00 2.32
3073 3620 5.462068 GCCGTGCAAACTAGAAAAAGAAAAT 59.538 36.000 0.00 0.00 0.00 1.82
3077 3630 3.003275 CAGCCGTGCAAACTAGAAAAAGA 59.997 43.478 0.00 0.00 0.00 2.52
3129 3688 5.705609 ACCATGCGTGTAAGAATCTTTTT 57.294 34.783 0.00 0.00 0.00 1.94
3150 3709 5.116882 AGCCACCATTCGAATTTCTAGTAC 58.883 41.667 8.21 0.00 0.00 2.73
3151 3710 5.128827 AGAGCCACCATTCGAATTTCTAGTA 59.871 40.000 8.21 0.00 0.00 1.82
3152 3711 4.080863 AGAGCCACCATTCGAATTTCTAGT 60.081 41.667 8.21 0.00 0.00 2.57
3153 3712 4.446371 AGAGCCACCATTCGAATTTCTAG 58.554 43.478 8.21 0.00 0.00 2.43
3154 3713 4.487714 AGAGCCACCATTCGAATTTCTA 57.512 40.909 8.21 0.00 0.00 2.10
3155 3714 3.356529 AGAGCCACCATTCGAATTTCT 57.643 42.857 8.21 1.25 0.00 2.52
3156 3715 3.440173 TCAAGAGCCACCATTCGAATTTC 59.560 43.478 8.21 0.32 0.00 2.17
3157 3716 3.420893 TCAAGAGCCACCATTCGAATTT 58.579 40.909 8.21 0.00 0.00 1.82
3158 3717 3.071874 TCAAGAGCCACCATTCGAATT 57.928 42.857 8.21 0.00 0.00 2.17
3159 3718 2.787473 TCAAGAGCCACCATTCGAAT 57.213 45.000 4.39 4.39 0.00 3.34
3160 3719 2.027285 TCATCAAGAGCCACCATTCGAA 60.027 45.455 0.00 0.00 0.00 3.71
3161 3720 1.554617 TCATCAAGAGCCACCATTCGA 59.445 47.619 0.00 0.00 0.00 3.71
3162 3721 1.938577 CTCATCAAGAGCCACCATTCG 59.061 52.381 0.00 0.00 37.59 3.34
3173 3732 3.797353 GGGCCGGGCTCATCAAGA 61.797 66.667 28.80 0.00 0.00 3.02
3281 3868 3.181476 GCAAATCCCGGAATAAGTGCATT 60.181 43.478 0.73 0.00 0.00 3.56
3294 3883 0.392193 ACAGCTGAGAGCAAATCCCG 60.392 55.000 23.35 0.00 45.56 5.14
3321 3910 5.997746 GCATATCATAGCTTGACCAGGTTTA 59.002 40.000 0.00 0.00 37.11 2.01
3352 3941 5.489792 TGTGAACTTGAGCCTAATCTTCT 57.510 39.130 0.00 0.00 0.00 2.85
3410 4000 4.744137 CACTACAGAGCAGAGATAACATGC 59.256 45.833 0.00 0.00 40.29 4.06
3518 4109 3.432517 CAGCTAGACTGGCAGTGAC 57.567 57.895 27.45 11.87 43.19 3.67
3581 4172 0.323087 AGTGCCAATCATCAGCTGCA 60.323 50.000 9.47 0.00 0.00 4.41
3596 4191 4.216257 TCCTTTTAGCTGTTGATTGAGTGC 59.784 41.667 0.00 0.00 0.00 4.40
3672 4267 3.004524 CGTGGTAGGAGTGGTATTCTAGC 59.995 52.174 0.00 0.00 0.00 3.42
3718 4313 3.068448 TCTGCACGGTACTGACTTGTAAA 59.932 43.478 9.17 0.00 0.00 2.01
3719 4314 2.624364 TCTGCACGGTACTGACTTGTAA 59.376 45.455 9.17 0.00 0.00 2.41
3720 4315 2.232399 TCTGCACGGTACTGACTTGTA 58.768 47.619 9.17 0.00 0.00 2.41
3721 4316 1.037493 TCTGCACGGTACTGACTTGT 58.963 50.000 9.17 0.00 0.00 3.16
3722 4317 2.370281 ATCTGCACGGTACTGACTTG 57.630 50.000 9.17 0.00 0.00 3.16
3732 4327 2.711311 CGCCATCAATCTGCACGG 59.289 61.111 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.