Multiple sequence alignment - TraesCS1D01G220100

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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 TraesCS1D01G220100 chr1D 100.000 4012 0 0 1 4012 307835232 307831221 0.000000e+00 7409.0
1 TraesCS1D01G220100 chr1D 95.691 557 24 0 180 736 19874680 19875236 0.000000e+00 896.0
2 TraesCS1D01G220100 chr1D 95.324 556 26 0 181 736 250740831 250741386 0.000000e+00 883.0
3 TraesCS1D01G220100 chr1D 78.100 379 65 12 2457 2820 127504597 127504972 1.450000e-54 224.0
4 TraesCS1D01G220100 chr1A 95.116 2457 65 25 737 3173 387030894 387028473 0.000000e+00 3821.0
5 TraesCS1D01G220100 chr1A 90.827 774 49 11 3246 4012 387028418 387027660 0.000000e+00 1016.0
6 TraesCS1D01G220100 chr1A 78.215 381 65 13 2457 2822 186213064 186213441 1.120000e-55 228.0
7 TraesCS1D01G220100 chr1A 89.189 74 6 2 106 179 387030958 387030887 1.540000e-14 91.6
8 TraesCS1D01G220100 chr1A 97.143 35 1 0 3210 3244 387028469 387028435 4.330000e-05 60.2
9 TraesCS1D01G220100 chr1A 96.774 31 1 0 2192 2222 506541564 506541594 7.000000e-03 52.8
10 TraesCS1D01G220100 chr1B 94.942 2333 60 26 737 3028 416824315 416822000 0.000000e+00 3602.0
11 TraesCS1D01G220100 chr1B 94.719 606 24 4 3347 3950 416821686 416821087 0.000000e+00 935.0
12 TraesCS1D01G220100 chr1B 91.701 241 9 6 3030 3266 416821966 416821733 1.390000e-84 324.0
13 TraesCS1D01G220100 chr1B 77.953 381 66 12 2457 2822 246454724 246455101 5.220000e-54 222.0
14 TraesCS1D01G220100 chr1B 94.915 118 4 2 1 116 654687578 654687695 2.460000e-42 183.0
15 TraesCS1D01G220100 chr1B 92.308 52 3 1 3246 3296 416821738 416821687 5.560000e-09 73.1
16 TraesCS1D01G220100 chr3D 95.683 556 24 0 181 736 579568117 579568672 0.000000e+00 894.0
17 TraesCS1D01G220100 chr3D 95.324 556 26 0 181 736 579562605 579563160 0.000000e+00 883.0
18 TraesCS1D01G220100 chr3D 80.818 391 64 8 2457 2843 136402779 136403162 3.030000e-76 296.0
19 TraesCS1D01G220100 chr3D 76.380 326 65 11 1707 2023 88351400 88351722 8.920000e-37 165.0
20 TraesCS1D01G220100 chr3D 86.486 148 19 1 2479 2625 88352608 88352755 1.150000e-35 161.0
21 TraesCS1D01G220100 chr3D 86.331 139 19 0 2133 2271 88352215 88352353 6.940000e-33 152.0
22 TraesCS1D01G220100 chr2D 95.170 559 26 1 178 735 534494451 534495009 0.000000e+00 881.0
23 TraesCS1D01G220100 chr2D 94.982 558 28 0 181 738 102277371 102277928 0.000000e+00 876.0
24 TraesCS1D01G220100 chr2D 99.029 103 1 0 1 103 605103329 605103227 6.850000e-43 185.0
25 TraesCS1D01G220100 chr2D 94.872 117 3 3 1 114 370198163 370198279 3.190000e-41 180.0
26 TraesCS1D01G220100 chr6D 94.982 558 28 0 180 737 254820552 254819995 0.000000e+00 876.0
27 TraesCS1D01G220100 chr6D 85.915 426 50 8 2442 2865 317006462 317006879 2.840000e-121 446.0
28 TraesCS1D01G220100 chr6D 78.019 414 71 11 1640 2052 317005203 317005597 4.010000e-60 243.0
29 TraesCS1D01G220100 chr6D 86.391 169 20 2 2133 2298 317006129 317006297 8.860000e-42 182.0
30 TraesCS1D01G220100 chr7D 94.366 568 32 0 173 740 166222857 166223424 0.000000e+00 872.0
31 TraesCS1D01G220100 chr7D 100.000 103 0 0 1 103 37279605 37279503 1.470000e-44 191.0
32 TraesCS1D01G220100 chr5B 94.973 557 27 1 181 737 318173354 318172799 0.000000e+00 872.0
33 TraesCS1D01G220100 chr5B 96.364 110 3 1 1 110 14710887 14710995 3.190000e-41 180.0
34 TraesCS1D01G220100 chr5B 94.017 117 6 1 1 117 81555339 81555224 4.120000e-40 176.0
35 TraesCS1D01G220100 chr6A 86.385 426 48 7 2442 2865 454648732 454649149 1.310000e-124 457.0
36 TraesCS1D01G220100 chr6A 79.227 414 66 9 1640 2052 454647627 454648021 1.840000e-68 270.0
37 TraesCS1D01G220100 chr6A 85.799 169 21 2 2133 2298 454648399 454648567 4.120000e-40 176.0
38 TraesCS1D01G220100 chr6B 84.633 436 51 11 2442 2868 507593136 507592708 1.720000e-113 420.0
39 TraesCS1D01G220100 chr6B 78.450 413 71 8 1640 2052 507594392 507593998 1.850000e-63 254.0
40 TraesCS1D01G220100 chr6B 90.580 138 13 0 2133 2270 507593469 507593332 2.460000e-42 183.0
41 TraesCS1D01G220100 chr2A 82.078 385 64 5 2482 2865 642910715 642911095 1.390000e-84 324.0
42 TraesCS1D01G220100 chr3B 80.818 391 64 9 2457 2843 194759221 194759604 3.030000e-76 296.0
43 TraesCS1D01G220100 chr3B 77.607 326 61 11 1707 2023 137749914 137750236 1.900000e-43 187.0
44 TraesCS1D01G220100 chr3B 93.443 122 5 3 1 121 817228377 817228258 1.150000e-40 178.0
45 TraesCS1D01G220100 chr3B 85.612 139 20 0 2133 2271 137750706 137750844 3.230000e-31 147.0
46 TraesCS1D01G220100 chr3A 81.132 371 59 8 2457 2823 154032084 154032447 1.820000e-73 287.0
47 TraesCS1D01G220100 chr3A 77.389 314 59 11 1719 2023 105113711 105113401 4.120000e-40 176.0
48 TraesCS1D01G220100 chr3A 86.331 139 19 0 2133 2271 105112952 105112814 6.940000e-33 152.0
49 TraesCS1D01G220100 chr3A 93.023 43 1 1 2429 2469 59431464 59431506 1.200000e-05 62.1
50 TraesCS1D01G220100 chr4D 95.614 114 5 0 1 114 462138089 462138202 2.460000e-42 183.0
51 TraesCS1D01G220100 chr5D 75.495 404 82 15 2457 2853 218190329 218190722 8.860000e-42 182.0
52 TraesCS1D01G220100 chr5A 94.828 116 4 2 1 114 438222689 438222574 3.190000e-41 180.0
53 TraesCS1D01G220100 chr5A 75.321 312 52 21 1717 2014 34262628 34262928 4.210000e-25 126.0
54 TraesCS1D01G220100 chr2B 81.818 165 19 6 2314 2467 69684906 69684742 1.170000e-25 128.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1D01G220100 chr1D 307831221 307835232 4011 True 7409.000000 7409 100.000000 1 4012 1 chr1D.!!$R1 4011
1 TraesCS1D01G220100 chr1D 19874680 19875236 556 False 896.000000 896 95.691000 180 736 1 chr1D.!!$F1 556
2 TraesCS1D01G220100 chr1D 250740831 250741386 555 False 883.000000 883 95.324000 181 736 1 chr1D.!!$F3 555
3 TraesCS1D01G220100 chr1A 387027660 387030958 3298 True 1247.200000 3821 93.068750 106 4012 4 chr1A.!!$R1 3906
4 TraesCS1D01G220100 chr1B 416821087 416824315 3228 True 1233.525000 3602 93.417500 737 3950 4 chr1B.!!$R1 3213
5 TraesCS1D01G220100 chr3D 579568117 579568672 555 False 894.000000 894 95.683000 181 736 1 chr3D.!!$F3 555
6 TraesCS1D01G220100 chr3D 579562605 579563160 555 False 883.000000 883 95.324000 181 736 1 chr3D.!!$F2 555
7 TraesCS1D01G220100 chr2D 534494451 534495009 558 False 881.000000 881 95.170000 178 735 1 chr2D.!!$F3 557
8 TraesCS1D01G220100 chr2D 102277371 102277928 557 False 876.000000 876 94.982000 181 738 1 chr2D.!!$F1 557
9 TraesCS1D01G220100 chr6D 254819995 254820552 557 True 876.000000 876 94.982000 180 737 1 chr6D.!!$R1 557
10 TraesCS1D01G220100 chr6D 317005203 317006879 1676 False 290.333333 446 83.441667 1640 2865 3 chr6D.!!$F1 1225
11 TraesCS1D01G220100 chr7D 166222857 166223424 567 False 872.000000 872 94.366000 173 740 1 chr7D.!!$F1 567
12 TraesCS1D01G220100 chr5B 318172799 318173354 555 True 872.000000 872 94.973000 181 737 1 chr5B.!!$R2 556
13 TraesCS1D01G220100 chr6A 454647627 454649149 1522 False 301.000000 457 83.803667 1640 2865 3 chr6A.!!$F1 1225
14 TraesCS1D01G220100 chr6B 507592708 507594392 1684 True 285.666667 420 84.554333 1640 2868 3 chr6B.!!$R1 1228

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
142 143 0.030101 TCGGCAAACAAAGCGGAAAG 59.970 50.0 0.00 0.0 38.21 2.62 F
987 1015 0.250467 GACAAGGAGTCAGCCAAGCA 60.250 55.0 0.00 0.0 46.77 3.91 F
2085 2129 1.085091 CTTGCAGCTGATCTGTGGAC 58.915 55.0 20.43 0.0 44.66 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 2129 0.039617 TGCTTGGAACGCGAATTTGG 60.040 50.000 15.93 0.0 0.0 3.28 R
2116 2180 2.126463 TGAGCGAACGAGCGAAGG 60.126 61.111 5.91 0.0 43.0 3.46 R
3311 4135 0.322546 AATCTTTCGGCAGACCCCAC 60.323 55.000 0.00 0.0 0.0 4.61 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
72 73 4.572985 ACTTTTAAAGTTAACGTGGCCC 57.427 40.909 4.30 0.00 39.04 5.80
73 74 3.318839 ACTTTTAAAGTTAACGTGGCCCC 59.681 43.478 4.30 0.00 39.04 5.80
74 75 1.521580 TTAAAGTTAACGTGGCCCCG 58.478 50.000 5.91 5.91 0.00 5.73
75 76 0.396060 TAAAGTTAACGTGGCCCCGT 59.604 50.000 7.70 7.70 44.23 5.28
99 100 3.782042 GCACGGGCGTTCTTCTAG 58.218 61.111 0.00 0.00 0.00 2.43
100 101 1.080025 GCACGGGCGTTCTTCTAGT 60.080 57.895 0.00 0.00 0.00 2.57
101 102 0.171903 GCACGGGCGTTCTTCTAGTA 59.828 55.000 0.00 0.00 0.00 1.82
102 103 1.403249 GCACGGGCGTTCTTCTAGTAA 60.403 52.381 0.00 0.00 0.00 2.24
103 104 2.737679 GCACGGGCGTTCTTCTAGTAAT 60.738 50.000 0.00 0.00 0.00 1.89
104 105 2.858344 CACGGGCGTTCTTCTAGTAATG 59.142 50.000 0.00 0.00 0.00 1.90
121 122 9.364653 TCTAGTAATGTATAAGAAGGAAGTCCC 57.635 37.037 0.00 0.00 36.42 4.46
122 123 7.989947 AGTAATGTATAAGAAGGAAGTCCCA 57.010 36.000 0.00 0.00 37.41 4.37
124 125 8.652290 AGTAATGTATAAGAAGGAAGTCCCATC 58.348 37.037 0.00 0.00 37.41 3.51
125 126 5.531122 TGTATAAGAAGGAAGTCCCATCG 57.469 43.478 0.00 0.00 37.41 3.84
139 140 1.578926 CATCGGCAAACAAAGCGGA 59.421 52.632 0.00 0.00 43.85 5.54
141 142 0.671251 ATCGGCAAACAAAGCGGAAA 59.329 45.000 0.00 0.00 43.13 3.13
142 143 0.030101 TCGGCAAACAAAGCGGAAAG 59.970 50.000 0.00 0.00 38.21 2.62
535 536 4.165926 CCTAGCTCTCAGGCGCTA 57.834 61.111 7.64 0.00 37.68 4.26
548 549 1.616865 AGGCGCTACACACTGACTTAA 59.383 47.619 7.64 0.00 0.00 1.85
591 592 2.438254 CGCTGGCCAGGCATGTAA 60.438 61.111 33.46 0.00 0.00 2.41
606 607 1.753930 TGTAACGCCTATCCGTGAGA 58.246 50.000 0.00 0.00 41.90 3.27
607 608 2.304092 TGTAACGCCTATCCGTGAGAT 58.696 47.619 0.00 0.00 41.90 2.75
704 705 6.908820 CGGACAGTTCATTATGTGATTTGATG 59.091 38.462 0.00 0.00 36.54 3.07
740 741 7.875554 GGTTAAATTTGTCAATTTTGCCCTAGA 59.124 33.333 13.29 0.00 39.19 2.43
741 742 8.708742 GTTAAATTTGTCAATTTTGCCCTAGAC 58.291 33.333 13.29 0.00 39.19 2.59
742 743 6.418057 AATTTGTCAATTTTGCCCTAGACA 57.582 33.333 0.00 0.00 34.54 3.41
743 744 4.846779 TTGTCAATTTTGCCCTAGACAC 57.153 40.909 0.00 0.00 35.92 3.67
744 745 3.826524 TGTCAATTTTGCCCTAGACACA 58.173 40.909 0.00 0.00 31.72 3.72
745 746 3.568007 TGTCAATTTTGCCCTAGACACAC 59.432 43.478 0.00 0.00 31.72 3.82
746 747 3.057526 GTCAATTTTGCCCTAGACACACC 60.058 47.826 0.00 0.00 0.00 4.16
747 748 2.215942 ATTTTGCCCTAGACACACCC 57.784 50.000 0.00 0.00 0.00 4.61
748 749 0.847373 TTTTGCCCTAGACACACCCA 59.153 50.000 0.00 0.00 0.00 4.51
749 750 0.400213 TTTGCCCTAGACACACCCAG 59.600 55.000 0.00 0.00 0.00 4.45
750 751 2.124507 TTGCCCTAGACACACCCAGC 62.125 60.000 0.00 0.00 0.00 4.85
751 752 2.990479 CCCTAGACACACCCAGCC 59.010 66.667 0.00 0.00 0.00 4.85
752 753 1.918293 CCCTAGACACACCCAGCCA 60.918 63.158 0.00 0.00 0.00 4.75
753 754 1.599047 CCTAGACACACCCAGCCAG 59.401 63.158 0.00 0.00 0.00 4.85
754 755 1.194781 CCTAGACACACCCAGCCAGT 61.195 60.000 0.00 0.00 0.00 4.00
755 756 1.557099 CTAGACACACCCAGCCAGTA 58.443 55.000 0.00 0.00 0.00 2.74
756 757 1.204941 CTAGACACACCCAGCCAGTAC 59.795 57.143 0.00 0.00 0.00 2.73
771 772 6.548622 CCAGCCAGTACTACCACTATTACTAA 59.451 42.308 0.00 0.00 0.00 2.24
809 817 1.442526 GCCCTGCCATCATTGTCTCG 61.443 60.000 0.00 0.00 0.00 4.04
810 818 1.442526 CCCTGCCATCATTGTCTCGC 61.443 60.000 0.00 0.00 0.00 5.03
811 819 0.745486 CCTGCCATCATTGTCTCGCA 60.745 55.000 0.00 0.00 0.00 5.10
813 821 0.804364 TGCCATCATTGTCTCGCAAC 59.196 50.000 0.00 0.00 40.28 4.17
814 822 0.804364 GCCATCATTGTCTCGCAACA 59.196 50.000 0.00 0.00 40.28 3.33
826 834 1.933181 CTCGCAACACACACAAGAGAA 59.067 47.619 0.00 0.00 0.00 2.87
827 835 1.933181 TCGCAACACACACAAGAGAAG 59.067 47.619 0.00 0.00 0.00 2.85
898 917 1.880027 GTTGTGTGATTGTGTCCCCTC 59.120 52.381 0.00 0.00 0.00 4.30
987 1015 0.250467 GACAAGGAGTCAGCCAAGCA 60.250 55.000 0.00 0.00 46.77 3.91
1160 1188 2.829043 TTCCGCTTCGACATGGACGG 62.829 60.000 12.97 8.75 41.92 4.79
1161 1189 3.554692 CGCTTCGACATGGACGGC 61.555 66.667 12.97 9.23 0.00 5.68
1162 1190 3.554692 GCTTCGACATGGACGGCG 61.555 66.667 4.80 4.80 0.00 6.46
1163 1191 2.885644 CTTCGACATGGACGGCGG 60.886 66.667 13.24 0.00 0.00 6.13
2085 2129 1.085091 CTTGCAGCTGATCTGTGGAC 58.915 55.000 20.43 0.00 44.66 4.02
2115 2179 2.485426 CGTTCCAAGCATGTGACATTCT 59.515 45.455 0.00 0.00 0.00 2.40
2116 2180 3.425359 CGTTCCAAGCATGTGACATTCTC 60.425 47.826 0.00 0.00 0.00 2.87
2943 3711 2.928801 TTACAACAGCAGCAAGAGGA 57.071 45.000 0.00 0.00 0.00 3.71
2944 3712 2.169832 TACAACAGCAGCAAGAGGAC 57.830 50.000 0.00 0.00 0.00 3.85
2987 3755 1.209019 CATGTGGAGTCTGGAGGGAAG 59.791 57.143 0.00 0.00 0.00 3.46
3121 3927 4.471386 AGCTCCATAGTGTCAGTATTTGGT 59.529 41.667 7.06 0.90 0.00 3.67
3181 3987 5.731686 GCTTTCCTGAGCTTGTATAACATGC 60.732 44.000 9.24 9.24 46.03 4.06
3190 3996 6.867662 GCTTGTATAACATGCTAATCAGGT 57.132 37.500 9.84 0.00 43.42 4.00
3191 3997 6.892691 GCTTGTATAACATGCTAATCAGGTC 58.107 40.000 9.84 0.00 43.42 3.85
3192 3998 6.483307 GCTTGTATAACATGCTAATCAGGTCA 59.517 38.462 9.84 0.00 43.42 4.02
3199 4005 0.833287 GCTAATCAGGTCAGGCCTCA 59.167 55.000 0.00 0.00 46.96 3.86
3244 4051 6.942976 AGTGAAATTCATGCATTCCAAAGAT 58.057 32.000 0.00 0.00 0.00 2.40
3300 4124 1.699634 TCAAACCCAGTGCTAGAAGCT 59.300 47.619 0.00 0.00 42.97 3.74
3303 4127 0.252467 ACCCAGTGCTAGAAGCTCCT 60.252 55.000 0.00 0.00 42.97 3.69
3304 4128 0.463620 CCCAGTGCTAGAAGCTCCTC 59.536 60.000 0.00 0.00 42.97 3.71
3305 4129 0.463620 CCAGTGCTAGAAGCTCCTCC 59.536 60.000 0.00 0.00 42.97 4.30
3306 4130 1.189752 CAGTGCTAGAAGCTCCTCCA 58.810 55.000 0.00 0.00 42.97 3.86
3307 4131 1.134848 CAGTGCTAGAAGCTCCTCCAC 60.135 57.143 0.00 0.00 42.97 4.02
3308 4132 0.176910 GTGCTAGAAGCTCCTCCACC 59.823 60.000 0.00 0.00 42.97 4.61
3309 4133 0.252239 TGCTAGAAGCTCCTCCACCA 60.252 55.000 0.00 0.00 42.97 4.17
3310 4134 0.463620 GCTAGAAGCTCCTCCACCAG 59.536 60.000 0.00 0.00 38.45 4.00
3311 4135 1.118838 CTAGAAGCTCCTCCACCAGG 58.881 60.000 0.00 0.00 45.15 4.45
3312 4136 0.413832 TAGAAGCTCCTCCACCAGGT 59.586 55.000 0.00 0.00 43.95 4.00
3313 4137 1.197430 AGAAGCTCCTCCACCAGGTG 61.197 60.000 13.35 13.35 43.95 4.00
3326 4150 2.852075 AGGTGGGGTCTGCCGAAA 60.852 61.111 0.00 0.00 34.97 3.46
3334 4158 3.181458 TGGGGTCTGCCGAAAGATTATAC 60.181 47.826 0.00 0.00 34.97 1.47
3341 4165 3.244078 TGCCGAAAGATTATACGAGGCAT 60.244 43.478 1.35 0.00 46.94 4.40
3343 4167 4.563184 GCCGAAAGATTATACGAGGCATAG 59.437 45.833 0.00 0.00 42.57 2.23
3344 4168 5.621555 GCCGAAAGATTATACGAGGCATAGA 60.622 44.000 0.00 0.00 42.57 1.98
3377 4201 9.185192 CCTCGGCAAATTCTTATATGATTTTTC 57.815 33.333 6.00 3.04 0.00 2.29
3438 4262 4.039124 CAGGAAAACCCACTGCTTGTATTT 59.961 41.667 0.00 0.00 37.41 1.40
3505 4329 7.467623 ACCTATTACAGAAAACGTAGTAGTCG 58.532 38.462 0.00 0.00 45.00 4.18
3530 4354 4.486125 AAGTTCAAGCAACACCCAATTT 57.514 36.364 0.00 0.00 37.48 1.82
3531 4355 4.486125 AGTTCAAGCAACACCCAATTTT 57.514 36.364 0.00 0.00 37.48 1.82
3637 4462 1.503542 CAATGACTGTGGCCGAAGC 59.496 57.895 0.00 0.00 38.76 3.86
3772 4604 1.296715 CAGGTTCAGGAGGGGTTCG 59.703 63.158 0.00 0.00 0.00 3.95
3887 4719 0.183492 TCCATGGGAGGTTAGCATGC 59.817 55.000 13.02 10.51 0.00 4.06
3889 4721 1.602311 CATGGGAGGTTAGCATGCTC 58.398 55.000 26.57 11.06 0.00 4.26
3952 4784 1.081892 CCATGTTGTCTTGCTCCTCG 58.918 55.000 0.00 0.00 0.00 4.63
3958 4790 1.515304 GTCTTGCTCCTCGAGACGC 60.515 63.158 15.71 15.90 44.03 5.19
3964 4796 3.119709 CTCCTCGAGACGCTCCAGC 62.120 68.421 15.71 0.00 37.78 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 3.318839 GGGGCCACGTTAACTTTAAAAGT 59.681 43.478 4.39 0.00 45.46 2.66
52 53 3.609879 CGGGGCCACGTTAACTTTAAAAG 60.610 47.826 22.33 0.00 0.00 2.27
53 54 2.292845 CGGGGCCACGTTAACTTTAAAA 59.707 45.455 22.33 0.00 0.00 1.52
54 55 1.878734 CGGGGCCACGTTAACTTTAAA 59.121 47.619 22.33 0.00 0.00 1.52
55 56 1.202746 ACGGGGCCACGTTAACTTTAA 60.203 47.619 31.47 0.00 46.25 1.52
56 57 0.396060 ACGGGGCCACGTTAACTTTA 59.604 50.000 31.47 0.00 46.25 1.85
57 58 1.148949 ACGGGGCCACGTTAACTTT 59.851 52.632 31.47 1.71 46.25 2.66
58 59 2.831043 ACGGGGCCACGTTAACTT 59.169 55.556 31.47 2.70 46.25 2.66
82 83 0.171903 TACTAGAAGAACGCCCGTGC 59.828 55.000 0.00 0.00 0.00 5.34
83 84 2.642139 TTACTAGAAGAACGCCCGTG 57.358 50.000 0.00 0.00 0.00 4.94
84 85 2.494870 ACATTACTAGAAGAACGCCCGT 59.505 45.455 0.00 0.00 0.00 5.28
85 86 3.160777 ACATTACTAGAAGAACGCCCG 57.839 47.619 0.00 0.00 0.00 6.13
86 87 7.655490 TCTTATACATTACTAGAAGAACGCCC 58.345 38.462 0.00 0.00 0.00 6.13
87 88 9.182933 CTTCTTATACATTACTAGAAGAACGCC 57.817 37.037 0.00 0.00 42.68 5.68
88 89 9.182933 CCTTCTTATACATTACTAGAAGAACGC 57.817 37.037 10.76 0.00 42.68 4.84
95 96 9.364653 GGGACTTCCTTCTTATACATTACTAGA 57.635 37.037 0.00 0.00 35.95 2.43
96 97 9.144298 TGGGACTTCCTTCTTATACATTACTAG 57.856 37.037 0.00 0.00 36.20 2.57
97 98 9.670442 ATGGGACTTCCTTCTTATACATTACTA 57.330 33.333 0.00 0.00 36.20 1.82
98 99 7.989947 TGGGACTTCCTTCTTATACATTACT 57.010 36.000 0.00 0.00 36.20 2.24
99 100 7.599245 CGATGGGACTTCCTTCTTATACATTAC 59.401 40.741 0.00 0.00 37.50 1.89
100 101 7.256190 CCGATGGGACTTCCTTCTTATACATTA 60.256 40.741 0.00 0.00 37.50 1.90
101 102 6.464465 CCGATGGGACTTCCTTCTTATACATT 60.464 42.308 0.00 0.00 37.50 2.71
102 103 5.012148 CCGATGGGACTTCCTTCTTATACAT 59.988 44.000 0.00 0.00 37.50 2.29
103 104 4.344102 CCGATGGGACTTCCTTCTTATACA 59.656 45.833 0.00 0.00 37.50 2.29
104 105 4.799917 GCCGATGGGACTTCCTTCTTATAC 60.800 50.000 0.00 0.00 37.50 1.47
119 120 1.444212 CGCTTTGTTTGCCGATGGG 60.444 57.895 0.00 0.00 0.00 4.00
121 122 0.039617 TTCCGCTTTGTTTGCCGATG 60.040 50.000 0.00 0.00 0.00 3.84
122 123 0.671251 TTTCCGCTTTGTTTGCCGAT 59.329 45.000 0.00 0.00 0.00 4.18
124 125 0.030101 TCTTTCCGCTTTGTTTGCCG 59.970 50.000 0.00 0.00 0.00 5.69
125 126 2.328473 GATCTTTCCGCTTTGTTTGCC 58.672 47.619 0.00 0.00 0.00 4.52
139 140 1.648467 GCTTCCGCGCTTGGATCTTT 61.648 55.000 5.56 0.00 38.00 2.52
141 142 2.512515 GCTTCCGCGCTTGGATCT 60.513 61.111 5.56 0.00 38.00 2.75
142 143 2.817423 CTGCTTCCGCGCTTGGATC 61.817 63.158 5.56 1.70 38.00 3.36
203 204 6.206438 TCATTCTGTGATTTGATTTCGTCCAA 59.794 34.615 0.00 0.00 0.00 3.53
309 310 1.676529 GTGTAGCGCCTATCTGTGAGA 59.323 52.381 2.29 0.00 0.00 3.27
435 436 3.006672 GTGCAACCACTAGTGCAGT 57.993 52.632 17.86 8.14 38.93 4.40
535 536 7.972832 TCCGAAAATTATTAAGTCAGTGTGT 57.027 32.000 0.00 0.00 0.00 3.72
548 549 3.625764 CACCCGTGTGATCCGAAAATTAT 59.374 43.478 0.00 0.00 45.76 1.28
591 592 1.112113 AACATCTCACGGATAGGCGT 58.888 50.000 0.00 0.00 32.64 5.68
641 642 1.400494 GCTGACCTTTTTGTGTGACGT 59.600 47.619 0.00 0.00 0.00 4.34
704 705 9.705290 AATTGACAAATTTAACCTATGGACAAC 57.295 29.630 0.00 0.00 31.76 3.32
740 741 0.974383 GTAGTACTGGCTGGGTGTGT 59.026 55.000 5.39 0.00 0.00 3.72
741 742 0.249398 GGTAGTACTGGCTGGGTGTG 59.751 60.000 5.39 0.00 0.00 3.82
742 743 0.178915 TGGTAGTACTGGCTGGGTGT 60.179 55.000 5.39 0.00 0.00 4.16
743 744 0.249398 GTGGTAGTACTGGCTGGGTG 59.751 60.000 5.39 0.00 0.00 4.61
744 745 0.116541 AGTGGTAGTACTGGCTGGGT 59.883 55.000 5.39 0.00 0.00 4.51
745 746 2.154567 TAGTGGTAGTACTGGCTGGG 57.845 55.000 5.39 0.00 32.19 4.45
746 747 4.894114 AGTAATAGTGGTAGTACTGGCTGG 59.106 45.833 5.39 0.00 38.36 4.85
747 748 7.578310 TTAGTAATAGTGGTAGTACTGGCTG 57.422 40.000 5.39 0.00 39.72 4.85
748 749 9.294614 GTATTAGTAATAGTGGTAGTACTGGCT 57.705 37.037 5.39 0.89 39.72 4.75
749 750 9.294614 AGTATTAGTAATAGTGGTAGTACTGGC 57.705 37.037 5.39 0.00 39.72 4.85
752 753 9.294614 GGCAGTATTAGTAATAGTGGTAGTACT 57.705 37.037 27.61 0.00 42.46 2.73
753 754 9.294614 AGGCAGTATTAGTAATAGTGGTAGTAC 57.705 37.037 27.61 15.79 42.46 2.73
754 755 9.512588 GAGGCAGTATTAGTAATAGTGGTAGTA 57.487 37.037 27.61 0.00 42.46 1.82
755 756 7.174599 CGAGGCAGTATTAGTAATAGTGGTAGT 59.825 40.741 27.61 2.30 42.46 2.73
756 757 7.528307 CGAGGCAGTATTAGTAATAGTGGTAG 58.472 42.308 27.61 11.79 42.46 3.18
771 772 1.760086 AGAGCAGGCGAGGCAGTAT 60.760 57.895 0.00 0.00 0.00 2.12
809 817 3.623060 TCTTCTTCTCTTGTGTGTGTTGC 59.377 43.478 0.00 0.00 0.00 4.17
810 818 5.582269 TCTTCTTCTTCTCTTGTGTGTGTTG 59.418 40.000 0.00 0.00 0.00 3.33
811 819 5.734720 TCTTCTTCTTCTCTTGTGTGTGTT 58.265 37.500 0.00 0.00 0.00 3.32
813 821 6.045318 TCTTCTTCTTCTTCTCTTGTGTGTG 58.955 40.000 0.00 0.00 0.00 3.82
814 822 6.227298 TCTTCTTCTTCTTCTCTTGTGTGT 57.773 37.500 0.00 0.00 0.00 3.72
826 834 1.271102 AGCGCGTCTTCTTCTTCTTCT 59.729 47.619 8.43 0.00 0.00 2.85
827 835 1.651631 GAGCGCGTCTTCTTCTTCTTC 59.348 52.381 8.43 0.00 0.00 2.87
910 930 3.189287 CGGGAGGATGACAAAAGAAGTTG 59.811 47.826 0.00 0.00 34.52 3.16
914 934 3.502123 AACGGGAGGATGACAAAAGAA 57.498 42.857 0.00 0.00 0.00 2.52
987 1015 1.812922 CTGCATCGCTCGCTCCTTT 60.813 57.895 0.00 0.00 0.00 3.11
1189 1217 1.113517 TCCTCCTTATCCTTCGCGGG 61.114 60.000 6.13 0.00 0.00 6.13
1749 1783 1.318158 GGTACACCGTCCCGATGTCT 61.318 60.000 0.00 0.00 0.00 3.41
2085 2129 0.039617 TGCTTGGAACGCGAATTTGG 60.040 50.000 15.93 0.00 0.00 3.28
2115 2179 2.178521 GAGCGAACGAGCGAAGGA 59.821 61.111 5.91 0.00 43.00 3.36
2116 2180 2.126463 TGAGCGAACGAGCGAAGG 60.126 61.111 5.91 0.00 43.00 3.46
2987 3755 5.736486 AAAAGAACTCAAAGTCGAGGAAC 57.264 39.130 0.00 0.00 37.34 3.62
3199 4005 1.272425 TGAAAATCCCCTGTTCGGCAT 60.272 47.619 0.00 0.00 0.00 4.40
3204 4010 5.529581 TTTCACTTGAAAATCCCCTGTTC 57.470 39.130 1.81 0.00 40.68 3.18
3280 4104 1.699634 AGCTTCTAGCACTGGGTTTGA 59.300 47.619 1.09 0.00 45.56 2.69
3305 4129 4.351054 GGCAGACCCCACCTGGTG 62.351 72.222 20.01 20.01 39.24 4.17
3308 4132 3.190738 TTTCGGCAGACCCCACCTG 62.191 63.158 0.00 0.00 34.88 4.00
3309 4133 2.852075 TTTCGGCAGACCCCACCT 60.852 61.111 0.00 0.00 0.00 4.00
3310 4134 2.198304 ATCTTTCGGCAGACCCCACC 62.198 60.000 0.00 0.00 0.00 4.61
3311 4135 0.322546 AATCTTTCGGCAGACCCCAC 60.323 55.000 0.00 0.00 0.00 4.61
3312 4136 1.281419 TAATCTTTCGGCAGACCCCA 58.719 50.000 0.00 0.00 0.00 4.96
3313 4137 2.640316 ATAATCTTTCGGCAGACCCC 57.360 50.000 0.00 0.00 0.00 4.95
3314 4138 3.057734 CGTATAATCTTTCGGCAGACCC 58.942 50.000 0.00 0.00 0.00 4.46
3321 4145 5.800941 GTCTATGCCTCGTATAATCTTTCGG 59.199 44.000 0.00 0.00 0.00 4.30
3323 4147 7.148722 GCAAGTCTATGCCTCGTATAATCTTTC 60.149 40.741 0.00 0.00 40.49 2.62
3326 4150 5.715070 GCAAGTCTATGCCTCGTATAATCT 58.285 41.667 0.00 0.00 40.49 2.40
3377 4201 9.553064 ACTCATAATCTGCCTACTATTTTCAAG 57.447 33.333 0.00 0.00 0.00 3.02
3392 4216 5.812127 TGGTGAACATCGAACTCATAATCTG 59.188 40.000 0.00 0.00 0.00 2.90
3398 4222 2.567169 TCCTGGTGAACATCGAACTCAT 59.433 45.455 0.00 0.00 0.00 2.90
3401 4225 3.485463 TTTCCTGGTGAACATCGAACT 57.515 42.857 0.00 0.00 31.05 3.01
3438 4262 5.013079 CCCCATAGCTTGTATTCAGGTATGA 59.987 44.000 16.90 0.00 42.94 2.15
3480 4304 7.467623 CGACTACTACGTTTTCTGTAATAGGT 58.532 38.462 0.00 0.00 28.57 3.08
3505 4329 1.334689 GGGTGTTGCTTGAACTTACGC 60.335 52.381 0.00 0.00 35.37 4.42
3531 4355 5.173535 TGCTTGGGCTTTTCTCTGAAGAAA 61.174 41.667 0.00 0.00 42.54 2.52
3584 4409 3.565482 AGATGAAGCAACACGTTTGATGT 59.435 39.130 12.62 0.00 0.00 3.06
3748 4580 0.838122 CCCTCCTGAACCTGGAGTGT 60.838 60.000 15.56 0.00 44.60 3.55
3772 4604 5.416013 CCAGAAGAAGTAATCCCAACCTTTC 59.584 44.000 0.00 0.00 0.00 2.62
3952 4784 4.838486 CGACGGCTGGAGCGTCTC 62.838 72.222 16.20 0.00 43.26 3.36


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

AutoCloner maintained by Alex Coulton.