Multiple sequence alignment - TraesCS3A01G032400

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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 TraesCS3A01G032400 chr3A 100.000 3391 0 0 1 3391 18252485 18249095 0.000000e+00 6263.0
1 TraesCS3A01G032400 chr3A 97.609 3262 74 3 134 3391 734137543 734134282 0.000000e+00 5589.0
2 TraesCS3A01G032400 chr3A 97.619 3066 63 6 330 3391 550991818 550994877 0.000000e+00 5249.0
3 TraesCS3A01G032400 chr3A 88.233 2252 239 15 1151 3391 706253112 706255348 0.000000e+00 2667.0
4 TraesCS3A01G032400 chr3A 94.975 199 10 0 136 334 550978207 550978405 2.540000e-81 313.0
5 TraesCS3A01G032400 chr3A 100.000 72 0 0 65 136 643835944 643835873 2.120000e-27 134.0
6 TraesCS3A01G032400 chr3A 98.667 75 1 0 62 136 717635951 717636025 2.120000e-27 134.0
7 TraesCS3A01G032400 chr4A 97.791 3259 69 2 136 3391 584413613 584410355 0.000000e+00 5616.0
8 TraesCS3A01G032400 chr6A 97.639 3262 59 5 134 3391 5066950 5070197 0.000000e+00 5581.0
9 TraesCS3A01G032400 chr2A 97.270 3260 78 6 135 3391 152005306 152002055 0.000000e+00 5517.0
10 TraesCS3A01G032400 chr2A 98.630 73 1 0 64 136 752926529 752926601 2.750000e-26 130.0
11 TraesCS3A01G032400 chr5D 91.069 2273 157 15 1151 3391 432138392 432136134 0.000000e+00 3031.0
12 TraesCS3A01G032400 chr5D 83.654 728 88 20 137 839 432139542 432138821 0.000000e+00 656.0
13 TraesCS3A01G032400 chr5D 83.125 320 32 13 837 1145 432138744 432138436 4.310000e-69 272.0
14 TraesCS3A01G032400 chr5D 86.765 68 6 2 1 65 127199521 127199454 4.690000e-09 73.1
15 TraesCS3A01G032400 chr5D 86.765 68 6 2 1 65 525860915 525860982 4.690000e-09 73.1
16 TraesCS3A01G032400 chr5D 95.000 40 2 0 26 65 287660943 287660904 2.820000e-06 63.9
17 TraesCS3A01G032400 chr5D 88.462 52 6 0 14 65 374722506 374722557 2.820000e-06 63.9
18 TraesCS3A01G032400 chr1D 92.528 1887 121 10 1511 3391 13203606 13201734 0.000000e+00 2686.0
19 TraesCS3A01G032400 chr1D 84.125 737 84 18 133 839 13204483 13203750 0.000000e+00 682.0
20 TraesCS3A01G032400 chr1D 85.912 362 47 3 136 496 316631007 316630649 1.910000e-102 383.0
21 TraesCS3A01G032400 chr1D 85.294 68 7 2 1 65 29873673 29873740 2.180000e-07 67.6
22 TraesCS3A01G032400 chr3B 87.655 2252 251 14 1151 3391 3118209 3115974 0.000000e+00 2593.0
23 TraesCS3A01G032400 chr3B 80.521 729 105 20 134 839 3119490 3118776 3.000000e-145 525.0
24 TraesCS3A01G032400 chr6D 81.507 730 78 31 134 839 325709712 325709016 6.400000e-152 547.0
25 TraesCS3A01G032400 chr6D 82.151 465 42 21 837 1268 325708939 325708483 8.950000e-96 361.0
26 TraesCS3A01G032400 chr6D 95.000 40 2 0 26 65 95588859 95588820 2.820000e-06 63.9
27 TraesCS3A01G032400 chr6B 77.087 515 112 5 1190 1703 183306185 183306694 3.310000e-75 292.0
28 TraesCS3A01G032400 chr6B 83.824 68 8 2 1 65 482985099 482985166 1.020000e-05 62.1
29 TraesCS3A01G032400 chr7A 100.000 71 0 0 66 136 61015325 61015255 7.630000e-27 132.0
30 TraesCS3A01G032400 chr7A 97.333 75 2 0 62 136 657689626 657689700 9.880000e-26 128.0
31 TraesCS3A01G032400 chr5A 100.000 71 0 0 66 136 521143436 521143506 7.630000e-27 132.0
32 TraesCS3A01G032400 chr5A 94.118 85 5 0 52 136 76311430 76311346 2.750000e-26 130.0
33 TraesCS3A01G032400 chr5A 98.630 73 1 0 64 136 688173693 688173621 2.750000e-26 130.0
34 TraesCS3A01G032400 chr5A 97.333 75 2 0 62 136 627374470 627374544 9.880000e-26 128.0
35 TraesCS3A01G032400 chr4D 95.000 40 2 0 26 65 415143975 415143936 2.820000e-06 63.9
36 TraesCS3A01G032400 chr2D 88.462 52 6 0 14 65 470109577 470109628 2.820000e-06 63.9


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 TraesCS3A01G032400 chr3A 18249095 18252485 3390 True 6263.000000 6263 100.000000 1 3391 1 chr3A.!!$R1 3390
1 TraesCS3A01G032400 chr3A 734134282 734137543 3261 True 5589.000000 5589 97.609000 134 3391 1 chr3A.!!$R3 3257
2 TraesCS3A01G032400 chr3A 550991818 550994877 3059 False 5249.000000 5249 97.619000 330 3391 1 chr3A.!!$F2 3061
3 TraesCS3A01G032400 chr3A 706253112 706255348 2236 False 2667.000000 2667 88.233000 1151 3391 1 chr3A.!!$F3 2240
4 TraesCS3A01G032400 chr4A 584410355 584413613 3258 True 5616.000000 5616 97.791000 136 3391 1 chr4A.!!$R1 3255
5 TraesCS3A01G032400 chr6A 5066950 5070197 3247 False 5581.000000 5581 97.639000 134 3391 1 chr6A.!!$F1 3257
6 TraesCS3A01G032400 chr2A 152002055 152005306 3251 True 5517.000000 5517 97.270000 135 3391 1 chr2A.!!$R1 3256
7 TraesCS3A01G032400 chr5D 432136134 432139542 3408 True 1319.666667 3031 85.949333 137 3391 3 chr5D.!!$R3 3254
8 TraesCS3A01G032400 chr1D 13201734 13204483 2749 True 1684.000000 2686 88.326500 133 3391 2 chr1D.!!$R2 3258
9 TraesCS3A01G032400 chr3B 3115974 3119490 3516 True 1559.000000 2593 84.088000 134 3391 2 chr3B.!!$R1 3257
10 TraesCS3A01G032400 chr6D 325708483 325709712 1229 True 454.000000 547 81.829000 134 1268 2 chr6D.!!$R2 1134
11 TraesCS3A01G032400 chr6B 183306185 183306694 509 False 292.000000 292 77.087000 1190 1703 1 chr6B.!!$F1 513

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
101 102 0.033781 CCTGTTGTCCCGGTTCGTAA 59.966 55.0 0.00 0.00 0.00 3.18 F
115 116 0.037160 TCGTAAGGGCCTTTTGTCCC 59.963 55.0 26.29 5.03 42.94 4.46 F
128 129 0.107831 TTGTCCCAGTTCCTGAACCG 59.892 55.0 6.41 0.00 42.06 4.44 F
1456 1862 0.478072 ACAGAAAGATGGTGGTGGCA 59.522 50.0 0.00 0.00 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2005 2420 0.179034 GCTAGCTGGTCCAGGATTGG 60.179 60.000 20.72 0.0 46.49 3.16 R
2122 2537 7.365028 CCTCAATGGCTGCATACCTATCTATTA 60.365 40.741 0.50 0.0 0.00 0.98 R
2243 2658 4.074970 CCTTGTTGGCAGTAAAGATGTCT 58.925 43.478 7.28 0.0 0.00 3.41 R
3143 3604 2.294233 CCCCAATTCATTGCTCCATACG 59.706 50.000 0.00 0.0 36.48 3.06 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
39 40 4.596801 TTTGTTTTGCTTGTGATTGTGC 57.403 36.364 0.00 0.00 0.00 4.57
40 41 3.523606 TGTTTTGCTTGTGATTGTGCT 57.476 38.095 0.00 0.00 0.00 4.40
41 42 3.188492 TGTTTTGCTTGTGATTGTGCTG 58.812 40.909 0.00 0.00 0.00 4.41
42 43 3.189285 GTTTTGCTTGTGATTGTGCTGT 58.811 40.909 0.00 0.00 0.00 4.40
43 44 3.523606 TTTGCTTGTGATTGTGCTGTT 57.476 38.095 0.00 0.00 0.00 3.16
44 45 2.495409 TGCTTGTGATTGTGCTGTTG 57.505 45.000 0.00 0.00 0.00 3.33
45 46 1.067364 TGCTTGTGATTGTGCTGTTGG 59.933 47.619 0.00 0.00 0.00 3.77
46 47 1.067516 GCTTGTGATTGTGCTGTTGGT 59.932 47.619 0.00 0.00 0.00 3.67
47 48 2.734670 CTTGTGATTGTGCTGTTGGTG 58.265 47.619 0.00 0.00 0.00 4.17
48 49 0.385029 TGTGATTGTGCTGTTGGTGC 59.615 50.000 0.00 0.00 0.00 5.01
49 50 0.670162 GTGATTGTGCTGTTGGTGCT 59.330 50.000 0.00 0.00 0.00 4.40
50 51 0.953727 TGATTGTGCTGTTGGTGCTC 59.046 50.000 0.00 0.00 0.00 4.26
51 52 1.242076 GATTGTGCTGTTGGTGCTCT 58.758 50.000 0.00 0.00 0.00 4.09
52 53 1.610522 GATTGTGCTGTTGGTGCTCTT 59.389 47.619 0.00 0.00 0.00 2.85
53 54 1.024271 TTGTGCTGTTGGTGCTCTTC 58.976 50.000 0.00 0.00 0.00 2.87
54 55 0.181114 TGTGCTGTTGGTGCTCTTCT 59.819 50.000 0.00 0.00 0.00 2.85
55 56 1.416030 TGTGCTGTTGGTGCTCTTCTA 59.584 47.619 0.00 0.00 0.00 2.10
56 57 2.072298 GTGCTGTTGGTGCTCTTCTAG 58.928 52.381 0.00 0.00 0.00 2.43
57 58 1.002430 TGCTGTTGGTGCTCTTCTAGG 59.998 52.381 0.00 0.00 0.00 3.02
58 59 1.276421 GCTGTTGGTGCTCTTCTAGGA 59.724 52.381 0.00 0.00 0.00 2.94
59 60 2.933056 GCTGTTGGTGCTCTTCTAGGAC 60.933 54.545 0.00 0.00 45.35 3.85
66 67 4.258702 GTGCTCTTCTAGGACAAAGACA 57.741 45.455 0.00 0.00 45.40 3.41
67 68 3.991121 GTGCTCTTCTAGGACAAAGACAC 59.009 47.826 0.00 0.59 45.40 3.67
68 69 3.898123 TGCTCTTCTAGGACAAAGACACT 59.102 43.478 0.00 0.00 0.00 3.55
69 70 4.241681 GCTCTTCTAGGACAAAGACACTG 58.758 47.826 0.00 0.00 0.00 3.66
70 71 4.815269 CTCTTCTAGGACAAAGACACTGG 58.185 47.826 0.00 0.00 0.00 4.00
71 72 4.223953 TCTTCTAGGACAAAGACACTGGT 58.776 43.478 0.00 0.00 0.00 4.00
72 73 5.391256 TCTTCTAGGACAAAGACACTGGTA 58.609 41.667 0.00 0.00 0.00 3.25
73 74 5.477291 TCTTCTAGGACAAAGACACTGGTAG 59.523 44.000 0.00 0.00 0.00 3.18
74 75 4.994282 TCTAGGACAAAGACACTGGTAGA 58.006 43.478 0.00 0.00 0.00 2.59
75 76 5.391256 TCTAGGACAAAGACACTGGTAGAA 58.609 41.667 0.00 0.00 0.00 2.10
76 77 5.836898 TCTAGGACAAAGACACTGGTAGAAA 59.163 40.000 0.00 0.00 0.00 2.52
77 78 5.367945 AGGACAAAGACACTGGTAGAAAA 57.632 39.130 0.00 0.00 0.00 2.29
78 79 5.751586 AGGACAAAGACACTGGTAGAAAAA 58.248 37.500 0.00 0.00 0.00 1.94
79 80 5.823045 AGGACAAAGACACTGGTAGAAAAAG 59.177 40.000 0.00 0.00 0.00 2.27
80 81 5.008712 GGACAAAGACACTGGTAGAAAAAGG 59.991 44.000 0.00 0.00 0.00 3.11
81 82 4.887655 ACAAAGACACTGGTAGAAAAAGGG 59.112 41.667 0.00 0.00 0.00 3.95
82 83 3.141767 AGACACTGGTAGAAAAAGGGC 57.858 47.619 0.00 0.00 0.00 5.19
83 84 2.160205 GACACTGGTAGAAAAAGGGCC 58.840 52.381 0.00 0.00 0.00 5.80
84 85 1.780919 ACACTGGTAGAAAAAGGGCCT 59.219 47.619 0.00 0.00 0.00 5.19
85 86 2.162681 CACTGGTAGAAAAAGGGCCTG 58.837 52.381 6.92 0.00 0.00 4.85
86 87 1.780919 ACTGGTAGAAAAAGGGCCTGT 59.219 47.619 6.92 0.00 0.00 4.00
87 88 2.177016 ACTGGTAGAAAAAGGGCCTGTT 59.823 45.455 6.92 4.33 0.00 3.16
88 89 2.558359 CTGGTAGAAAAAGGGCCTGTTG 59.442 50.000 10.42 0.00 0.00 3.33
89 90 2.091555 TGGTAGAAAAAGGGCCTGTTGT 60.092 45.455 10.42 7.40 0.00 3.32
90 91 2.557056 GGTAGAAAAAGGGCCTGTTGTC 59.443 50.000 10.42 9.77 0.00 3.18
91 92 1.704641 AGAAAAAGGGCCTGTTGTCC 58.295 50.000 10.42 2.72 0.00 4.02
92 93 0.679505 GAAAAAGGGCCTGTTGTCCC 59.320 55.000 10.42 0.00 42.94 4.46
96 97 4.280019 GGGCCTGTTGTCCCGGTT 62.280 66.667 0.84 0.00 32.00 4.44
97 98 2.671963 GGCCTGTTGTCCCGGTTC 60.672 66.667 0.00 0.00 0.00 3.62
98 99 3.047877 GCCTGTTGTCCCGGTTCG 61.048 66.667 0.00 0.00 0.00 3.95
99 100 2.424302 CCTGTTGTCCCGGTTCGT 59.576 61.111 0.00 0.00 0.00 3.85
100 101 1.667151 CCTGTTGTCCCGGTTCGTA 59.333 57.895 0.00 0.00 0.00 3.43
101 102 0.033781 CCTGTTGTCCCGGTTCGTAA 59.966 55.000 0.00 0.00 0.00 3.18
102 103 1.425412 CTGTTGTCCCGGTTCGTAAG 58.575 55.000 0.00 0.00 0.00 2.34
103 104 0.033781 TGTTGTCCCGGTTCGTAAGG 59.966 55.000 0.00 0.00 38.47 2.69
104 105 0.671472 GTTGTCCCGGTTCGTAAGGG 60.671 60.000 0.00 0.00 46.40 3.95
105 106 2.125391 GTCCCGGTTCGTAAGGGC 60.125 66.667 0.00 0.00 44.70 5.19
106 107 3.393106 TCCCGGTTCGTAAGGGCC 61.393 66.667 0.00 0.00 44.70 5.80
107 108 3.396570 CCCGGTTCGTAAGGGCCT 61.397 66.667 0.00 0.00 38.51 5.19
108 109 2.666812 CCGGTTCGTAAGGGCCTT 59.333 61.111 24.44 24.44 38.47 4.35
109 110 1.002990 CCGGTTCGTAAGGGCCTTT 60.003 57.895 26.29 5.08 38.47 3.11
110 111 0.607217 CCGGTTCGTAAGGGCCTTTT 60.607 55.000 26.29 2.86 38.47 2.27
111 112 0.519961 CGGTTCGTAAGGGCCTTTTG 59.480 55.000 26.29 17.07 38.47 2.44
112 113 1.612676 GGTTCGTAAGGGCCTTTTGT 58.387 50.000 26.29 1.50 38.47 2.83
113 114 1.538512 GGTTCGTAAGGGCCTTTTGTC 59.461 52.381 26.29 11.62 38.47 3.18
114 115 1.538512 GTTCGTAAGGGCCTTTTGTCC 59.461 52.381 26.29 6.64 38.47 4.02
115 116 0.037160 TCGTAAGGGCCTTTTGTCCC 59.963 55.000 26.29 5.03 42.94 4.46
116 117 0.250989 CGTAAGGGCCTTTTGTCCCA 60.251 55.000 26.29 0.34 45.07 4.37
117 118 1.545841 GTAAGGGCCTTTTGTCCCAG 58.454 55.000 26.29 0.00 45.07 4.45
118 119 1.154430 TAAGGGCCTTTTGTCCCAGT 58.846 50.000 26.29 0.00 45.07 4.00
119 120 0.264657 AAGGGCCTTTTGTCCCAGTT 59.735 50.000 14.48 0.00 45.07 3.16
120 121 0.178961 AGGGCCTTTTGTCCCAGTTC 60.179 55.000 0.00 0.00 45.07 3.01
121 122 1.185618 GGGCCTTTTGTCCCAGTTCC 61.186 60.000 0.84 0.00 42.18 3.62
122 123 0.178961 GGCCTTTTGTCCCAGTTCCT 60.179 55.000 0.00 0.00 0.00 3.36
123 124 0.961753 GCCTTTTGTCCCAGTTCCTG 59.038 55.000 0.00 0.00 0.00 3.86
124 125 1.478654 GCCTTTTGTCCCAGTTCCTGA 60.479 52.381 0.00 0.00 32.44 3.86
125 126 2.944129 CCTTTTGTCCCAGTTCCTGAA 58.056 47.619 0.00 0.00 32.44 3.02
126 127 2.623416 CCTTTTGTCCCAGTTCCTGAAC 59.377 50.000 1.75 1.75 41.45 3.18
127 128 2.358322 TTTGTCCCAGTTCCTGAACC 57.642 50.000 6.41 0.00 42.06 3.62
128 129 0.107831 TTGTCCCAGTTCCTGAACCG 59.892 55.000 6.41 0.00 42.06 4.44
129 130 1.003718 GTCCCAGTTCCTGAACCGG 60.004 63.158 0.00 0.00 42.06 5.28
131 132 3.478780 CCAGTTCCTGAACCGGGA 58.521 61.111 6.32 0.00 42.06 5.14
210 213 6.306987 TCCTATGGATATTTTCCTTTGGAGC 58.693 40.000 7.66 0.00 43.71 4.70
314 318 2.643551 CCAGACCTAATGGAAACGCAT 58.356 47.619 0.00 0.00 40.51 4.73
412 425 1.478503 TCCCCCATGGAGAAGGACA 59.521 57.895 15.22 0.00 38.61 4.02
429 442 9.901172 GAGAAGGACAAACCCTAGATTATTTTA 57.099 33.333 0.00 0.00 40.05 1.52
535 566 0.817634 CACAAGGGCTTGACGACCAA 60.818 55.000 0.00 0.00 46.64 3.67
538 569 1.029681 AAGGGCTTGACGACCAAAAC 58.970 50.000 0.00 0.00 46.64 2.43
822 877 1.000731 CTGCTAGCCTGCTAGATGACC 59.999 57.143 26.17 11.00 46.56 4.02
843 1060 3.471680 CTCCTGCATAGCTAAACTTCCC 58.528 50.000 0.00 0.00 0.00 3.97
1259 1665 7.337689 TGTTAAGAGATCATGATGTTCCCAAAG 59.662 37.037 14.30 0.00 0.00 2.77
1434 1840 0.482446 AGTGGTTTTGGCTGGGATCA 59.518 50.000 0.00 0.00 0.00 2.92
1456 1862 0.478072 ACAGAAAGATGGTGGTGGCA 59.522 50.000 0.00 0.00 0.00 4.92
1819 2234 3.005472 CCTGGTGATTCATCCATGCAATC 59.995 47.826 0.00 0.00 33.01 2.67
1989 2404 5.534207 TGGACAGACTTTGCATGAAATTT 57.466 34.783 0.00 0.00 0.00 1.82
2005 2420 7.148755 GCATGAAATTTCACAAGTTGTACATCC 60.149 37.037 22.71 0.56 40.49 3.51
2013 2428 4.156556 CACAAGTTGTACATCCCAATCCTG 59.843 45.833 8.49 0.00 0.00 3.86
2122 2537 3.049344 ACCTGAAACTGAGAAGGGAAGT 58.951 45.455 0.00 0.00 33.87 3.01
2224 2639 1.003233 GTTGGAGGGTCTTTCGATGGT 59.997 52.381 0.00 0.00 0.00 3.55
2239 2654 8.421784 TCTTTCGATGGTAGATATGCTAAAAGT 58.578 33.333 0.00 0.00 0.00 2.66
2654 3087 7.754069 TTCTGCAGTGTTTGACAAAAATAAG 57.246 32.000 14.67 0.00 0.00 1.73
2862 3323 5.073554 TCCATCTGGTACATCCTGCATATTT 59.926 40.000 0.00 0.00 38.20 1.40
2920 3381 7.657354 GCAATGTCATATCTCCATTGTGTAGTA 59.343 37.037 14.97 0.00 44.53 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.180868 AGCACAATCACAAGCAAAACAAAAA 59.819 32.000 0.00 0.00 0.00 1.94
17 18 4.694509 AGCACAATCACAAGCAAAACAAAA 59.305 33.333 0.00 0.00 0.00 2.44
18 19 4.093115 CAGCACAATCACAAGCAAAACAAA 59.907 37.500 0.00 0.00 0.00 2.83
19 20 3.617706 CAGCACAATCACAAGCAAAACAA 59.382 39.130 0.00 0.00 0.00 2.83
20 21 3.188492 CAGCACAATCACAAGCAAAACA 58.812 40.909 0.00 0.00 0.00 2.83
21 22 3.189285 ACAGCACAATCACAAGCAAAAC 58.811 40.909 0.00 0.00 0.00 2.43
22 23 3.523606 ACAGCACAATCACAAGCAAAA 57.476 38.095 0.00 0.00 0.00 2.44
23 24 3.188492 CAACAGCACAATCACAAGCAAA 58.812 40.909 0.00 0.00 0.00 3.68
24 25 2.481622 CCAACAGCACAATCACAAGCAA 60.482 45.455 0.00 0.00 0.00 3.91
25 26 1.067364 CCAACAGCACAATCACAAGCA 59.933 47.619 0.00 0.00 0.00 3.91
26 27 1.067516 ACCAACAGCACAATCACAAGC 59.932 47.619 0.00 0.00 0.00 4.01
27 28 2.734670 CACCAACAGCACAATCACAAG 58.265 47.619 0.00 0.00 0.00 3.16
28 29 1.202394 GCACCAACAGCACAATCACAA 60.202 47.619 0.00 0.00 0.00 3.33
29 30 0.385029 GCACCAACAGCACAATCACA 59.615 50.000 0.00 0.00 0.00 3.58
30 31 0.670162 AGCACCAACAGCACAATCAC 59.330 50.000 0.00 0.00 0.00 3.06
31 32 0.953727 GAGCACCAACAGCACAATCA 59.046 50.000 0.00 0.00 0.00 2.57
32 33 1.242076 AGAGCACCAACAGCACAATC 58.758 50.000 0.00 0.00 0.00 2.67
33 34 1.610522 GAAGAGCACCAACAGCACAAT 59.389 47.619 0.00 0.00 0.00 2.71
34 35 1.024271 GAAGAGCACCAACAGCACAA 58.976 50.000 0.00 0.00 0.00 3.33
35 36 0.181114 AGAAGAGCACCAACAGCACA 59.819 50.000 0.00 0.00 0.00 4.57
36 37 2.072298 CTAGAAGAGCACCAACAGCAC 58.928 52.381 0.00 0.00 0.00 4.40
37 38 1.002430 CCTAGAAGAGCACCAACAGCA 59.998 52.381 0.00 0.00 0.00 4.41
38 39 1.276421 TCCTAGAAGAGCACCAACAGC 59.724 52.381 0.00 0.00 0.00 4.40
39 40 2.300152 TGTCCTAGAAGAGCACCAACAG 59.700 50.000 0.00 0.00 0.00 3.16
40 41 2.325484 TGTCCTAGAAGAGCACCAACA 58.675 47.619 0.00 0.00 0.00 3.33
41 42 3.402628 TTGTCCTAGAAGAGCACCAAC 57.597 47.619 0.00 0.00 0.00 3.77
42 43 3.646162 TCTTTGTCCTAGAAGAGCACCAA 59.354 43.478 0.00 0.00 0.00 3.67
43 44 3.006967 GTCTTTGTCCTAGAAGAGCACCA 59.993 47.826 0.00 0.00 32.91 4.17
44 45 3.006967 TGTCTTTGTCCTAGAAGAGCACC 59.993 47.826 0.00 0.00 32.91 5.01
45 46 3.991121 GTGTCTTTGTCCTAGAAGAGCAC 59.009 47.826 0.00 1.07 32.91 4.40
46 47 3.898123 AGTGTCTTTGTCCTAGAAGAGCA 59.102 43.478 0.00 0.00 32.91 4.26
47 48 4.241681 CAGTGTCTTTGTCCTAGAAGAGC 58.758 47.826 0.00 0.00 32.91 4.09
48 49 4.282195 ACCAGTGTCTTTGTCCTAGAAGAG 59.718 45.833 0.00 0.00 32.91 2.85
49 50 4.223953 ACCAGTGTCTTTGTCCTAGAAGA 58.776 43.478 0.00 0.00 0.00 2.87
50 51 4.608948 ACCAGTGTCTTTGTCCTAGAAG 57.391 45.455 0.00 0.00 0.00 2.85
51 52 5.391256 TCTACCAGTGTCTTTGTCCTAGAA 58.609 41.667 0.00 0.00 0.00 2.10
52 53 4.994282 TCTACCAGTGTCTTTGTCCTAGA 58.006 43.478 0.00 0.00 0.00 2.43
53 54 5.723672 TTCTACCAGTGTCTTTGTCCTAG 57.276 43.478 0.00 0.00 0.00 3.02
54 55 6.488769 TTTTCTACCAGTGTCTTTGTCCTA 57.511 37.500 0.00 0.00 0.00 2.94
55 56 5.367945 TTTTCTACCAGTGTCTTTGTCCT 57.632 39.130 0.00 0.00 0.00 3.85
56 57 5.008712 CCTTTTTCTACCAGTGTCTTTGTCC 59.991 44.000 0.00 0.00 0.00 4.02
57 58 5.008712 CCCTTTTTCTACCAGTGTCTTTGTC 59.991 44.000 0.00 0.00 0.00 3.18
58 59 4.887655 CCCTTTTTCTACCAGTGTCTTTGT 59.112 41.667 0.00 0.00 0.00 2.83
59 60 4.261614 GCCCTTTTTCTACCAGTGTCTTTG 60.262 45.833 0.00 0.00 0.00 2.77
60 61 3.889538 GCCCTTTTTCTACCAGTGTCTTT 59.110 43.478 0.00 0.00 0.00 2.52
61 62 3.487372 GCCCTTTTTCTACCAGTGTCTT 58.513 45.455 0.00 0.00 0.00 3.01
62 63 2.224793 GGCCCTTTTTCTACCAGTGTCT 60.225 50.000 0.00 0.00 0.00 3.41
63 64 2.160205 GGCCCTTTTTCTACCAGTGTC 58.840 52.381 0.00 0.00 0.00 3.67
64 65 1.780919 AGGCCCTTTTTCTACCAGTGT 59.219 47.619 0.00 0.00 0.00 3.55
65 66 2.162681 CAGGCCCTTTTTCTACCAGTG 58.837 52.381 0.00 0.00 0.00 3.66
66 67 1.780919 ACAGGCCCTTTTTCTACCAGT 59.219 47.619 0.00 0.00 0.00 4.00
67 68 2.558359 CAACAGGCCCTTTTTCTACCAG 59.442 50.000 0.00 0.00 0.00 4.00
68 69 2.091555 ACAACAGGCCCTTTTTCTACCA 60.092 45.455 0.00 0.00 0.00 3.25
69 70 2.557056 GACAACAGGCCCTTTTTCTACC 59.443 50.000 0.00 0.00 0.00 3.18
70 71 2.557056 GGACAACAGGCCCTTTTTCTAC 59.443 50.000 0.00 0.00 0.00 2.59
71 72 2.490168 GGGACAACAGGCCCTTTTTCTA 60.490 50.000 0.00 0.00 41.31 2.10
72 73 1.704641 GGACAACAGGCCCTTTTTCT 58.295 50.000 0.00 0.00 0.00 2.52
73 74 0.679505 GGGACAACAGGCCCTTTTTC 59.320 55.000 0.00 0.00 41.31 2.29
74 75 1.112916 CGGGACAACAGGCCCTTTTT 61.113 55.000 4.64 0.00 42.40 1.94
75 76 1.530655 CGGGACAACAGGCCCTTTT 60.531 57.895 4.64 0.00 42.40 2.27
76 77 2.115266 CGGGACAACAGGCCCTTT 59.885 61.111 4.64 0.00 42.40 3.11
77 78 3.966543 CCGGGACAACAGGCCCTT 61.967 66.667 4.64 0.00 42.40 3.95
79 80 4.280019 AACCGGGACAACAGGCCC 62.280 66.667 6.32 0.00 41.11 5.80
80 81 2.671963 GAACCGGGACAACAGGCC 60.672 66.667 6.32 0.00 0.00 5.19
81 82 2.438951 TACGAACCGGGACAACAGGC 62.439 60.000 6.32 0.00 0.00 4.85
82 83 0.033781 TTACGAACCGGGACAACAGG 59.966 55.000 6.32 0.00 0.00 4.00
83 84 1.425412 CTTACGAACCGGGACAACAG 58.575 55.000 6.32 0.00 0.00 3.16
84 85 0.033781 CCTTACGAACCGGGACAACA 59.966 55.000 6.32 0.00 0.00 3.33
85 86 0.671472 CCCTTACGAACCGGGACAAC 60.671 60.000 6.32 0.00 40.55 3.32
86 87 1.672898 CCCTTACGAACCGGGACAA 59.327 57.895 6.32 0.00 40.55 3.18
87 88 2.946346 GCCCTTACGAACCGGGACA 61.946 63.158 6.32 0.00 40.55 4.02
88 89 2.125391 GCCCTTACGAACCGGGAC 60.125 66.667 6.32 0.00 40.55 4.46
89 90 3.393106 GGCCCTTACGAACCGGGA 61.393 66.667 6.32 0.00 40.55 5.14
90 91 2.473891 AAAGGCCCTTACGAACCGGG 62.474 60.000 6.32 0.00 41.06 5.73
91 92 0.607217 AAAAGGCCCTTACGAACCGG 60.607 55.000 0.00 0.00 0.00 5.28
92 93 0.519961 CAAAAGGCCCTTACGAACCG 59.480 55.000 0.00 0.00 0.00 4.44
93 94 1.538512 GACAAAAGGCCCTTACGAACC 59.461 52.381 0.00 0.00 0.00 3.62
94 95 1.538512 GGACAAAAGGCCCTTACGAAC 59.461 52.381 0.00 0.00 0.00 3.95
95 96 1.546099 GGGACAAAAGGCCCTTACGAA 60.546 52.381 0.00 0.00 41.31 3.85
96 97 0.037160 GGGACAAAAGGCCCTTACGA 59.963 55.000 0.00 0.00 41.31 3.43
97 98 0.250989 TGGGACAAAAGGCCCTTACG 60.251 55.000 8.08 0.00 44.96 3.18
98 99 1.203013 ACTGGGACAAAAGGCCCTTAC 60.203 52.381 8.08 0.00 44.96 2.34
99 100 1.154430 ACTGGGACAAAAGGCCCTTA 58.846 50.000 8.08 0.00 44.96 2.69
100 101 0.264657 AACTGGGACAAAAGGCCCTT 59.735 50.000 8.08 0.00 44.96 3.95
101 102 0.178961 GAACTGGGACAAAAGGCCCT 60.179 55.000 8.08 0.00 44.96 5.19
102 103 1.185618 GGAACTGGGACAAAAGGCCC 61.186 60.000 0.00 0.00 44.93 5.80
103 104 0.178961 AGGAACTGGGACAAAAGGCC 60.179 55.000 0.00 0.00 38.70 5.19
104 105 3.439440 AGGAACTGGGACAAAAGGC 57.561 52.632 0.00 0.00 38.70 4.35
116 117 1.900486 CTTAGTCCCGGTTCAGGAACT 59.100 52.381 11.56 0.00 40.94 3.01
117 118 1.066358 CCTTAGTCCCGGTTCAGGAAC 60.066 57.143 0.00 3.58 40.45 3.62
118 119 1.272807 CCTTAGTCCCGGTTCAGGAA 58.727 55.000 0.00 0.00 34.43 3.36
119 120 1.262640 GCCTTAGTCCCGGTTCAGGA 61.263 60.000 0.00 0.00 0.00 3.86
120 121 1.221021 GCCTTAGTCCCGGTTCAGG 59.779 63.158 0.00 0.00 0.00 3.86
121 122 1.221021 GGCCTTAGTCCCGGTTCAG 59.779 63.158 0.00 0.00 0.00 3.02
122 123 0.912487 ATGGCCTTAGTCCCGGTTCA 60.912 55.000 3.32 0.00 0.00 3.18
123 124 0.463833 CATGGCCTTAGTCCCGGTTC 60.464 60.000 3.32 0.00 0.00 3.62
124 125 1.205460 ACATGGCCTTAGTCCCGGTT 61.205 55.000 3.32 0.00 0.00 4.44
125 126 1.205460 AACATGGCCTTAGTCCCGGT 61.205 55.000 3.32 0.00 0.00 5.28
126 127 0.463833 GAACATGGCCTTAGTCCCGG 60.464 60.000 3.32 0.00 0.00 5.73
127 128 0.810031 CGAACATGGCCTTAGTCCCG 60.810 60.000 3.32 4.02 0.00 5.14
128 129 0.463833 CCGAACATGGCCTTAGTCCC 60.464 60.000 3.32 0.00 0.00 4.46
129 130 0.463833 CCCGAACATGGCCTTAGTCC 60.464 60.000 3.32 0.00 0.00 3.85
130 131 0.539986 TCCCGAACATGGCCTTAGTC 59.460 55.000 3.32 0.00 0.00 2.59
131 132 0.252197 GTCCCGAACATGGCCTTAGT 59.748 55.000 3.32 0.00 0.00 2.24
164 165 6.013984 AGGAAAGGAAAGTTGTACGATTCCTA 60.014 38.462 15.54 0.00 43.57 2.94
210 213 2.293399 CTCTTTCCTTTGTCCCAAACGG 59.707 50.000 0.00 0.00 0.00 4.44
314 318 1.214589 GCGGCGACTCTGTTTCCTA 59.785 57.895 12.98 0.00 0.00 2.94
412 425 4.514066 CCGCGCTAAAATAATCTAGGGTTT 59.486 41.667 5.56 0.00 32.27 3.27
429 442 1.078497 TCCATGTTGATTCCGCGCT 60.078 52.632 5.56 0.00 0.00 5.92
535 566 3.680777 TCTTGACTTCCCCCAAAGTTT 57.319 42.857 0.00 0.00 39.55 2.66
538 569 4.411013 AGATTTCTTGACTTCCCCCAAAG 58.589 43.478 0.00 0.00 0.00 2.77
680 724 4.997905 AACATTCTCAATCTGTGTGACG 57.002 40.909 0.00 0.00 29.55 4.35
822 877 3.471680 GGGAAGTTTAGCTATGCAGGAG 58.528 50.000 0.00 0.00 0.00 3.69
843 1060 8.905660 ATATCCTGTAGTAGTATATGCTACCG 57.094 38.462 22.75 11.71 44.12 4.02
981 1341 9.502091 TTTTATCTCTTTACTACAAGCACACAT 57.498 29.630 0.00 0.00 0.00 3.21
1047 1407 7.450074 TGTGGTATTGAAGGCAGGTAATATAG 58.550 38.462 0.00 0.00 0.00 1.31
1136 1504 4.459852 AAAGTGCATATTAGGGCTCCAT 57.540 40.909 0.00 0.00 0.00 3.41
1259 1665 1.062258 CATGCATTTTGTGTGCGGTC 58.938 50.000 0.00 0.00 45.37 4.79
1434 1840 2.881403 GCCACCACCATCTTTCTGTCAT 60.881 50.000 0.00 0.00 0.00 3.06
1456 1862 1.762708 CAGCCCAAACATTATCGGGT 58.237 50.000 0.00 0.00 41.11 5.28
1763 2178 1.270839 GGTGTAGGTGTGTGCAGATGT 60.271 52.381 0.00 0.00 0.00 3.06
1819 2234 7.388776 TGTTTTCACTATCCTCTTCAATGTCAG 59.611 37.037 0.00 0.00 0.00 3.51
1989 2404 4.042809 AGGATTGGGATGTACAACTTGTGA 59.957 41.667 0.00 0.00 0.00 3.58
2005 2420 0.179034 GCTAGCTGGTCCAGGATTGG 60.179 60.000 20.72 0.00 46.49 3.16
2122 2537 7.365028 CCTCAATGGCTGCATACCTATCTATTA 60.365 40.741 0.50 0.00 0.00 0.98
2243 2658 4.074970 CCTTGTTGGCAGTAAAGATGTCT 58.925 43.478 7.28 0.00 0.00 3.41
2654 3087 7.224167 GGTTGTACTGTACTCCACTTAATATGC 59.776 40.741 17.98 0.00 0.00 3.14
2941 3402 7.713507 ACAAGTTGATACAGTTGTAGCTTGTTA 59.286 33.333 10.54 0.00 38.45 2.41
3143 3604 2.294233 CCCCAATTCATTGCTCCATACG 59.706 50.000 0.00 0.00 36.48 3.06


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

AutoCloner maintained by Alex Coulton.