Multiple sequence alignment - TraesCS2B01G395700

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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 TraesCS2B01G395700 chr2B 100.000 2664 0 0 1 2664 561230855 561228192 0.000000e+00 4920
1 TraesCS2B01G395700 chr2B 95.677 347 15 0 459 805 496568861 496568515 2.320000e-155 558
2 TraesCS2B01G395700 chr2D 93.855 1904 74 13 800 2664 478702724 478704623 0.000000e+00 2828
3 TraesCS2B01G395700 chr2D 95.878 558 22 1 253 809 546688779 546688222 0.000000e+00 902
4 TraesCS2B01G395700 chr2D 95.192 104 4 1 150 252 546688986 546688883 2.120000e-36 163
5 TraesCS2B01G395700 chr2A 93.021 1877 92 15 809 2664 621482787 621480929 0.000000e+00 2704
6 TraesCS2B01G395700 chr3A 96.364 550 20 0 253 802 671357395 671357944 0.000000e+00 905
7 TraesCS2B01G395700 chr3A 96.117 103 3 1 151 252 671357189 671357291 1.640000e-37 167
8 TraesCS2B01G395700 chr1D 96.036 555 21 1 253 806 204268838 204269392 0.000000e+00 902
9 TraesCS2B01G395700 chr1D 96.014 552 22 0 253 804 422175153 422175704 0.000000e+00 898
10 TraesCS2B01G395700 chr1D 97.087 103 2 1 150 251 422174946 422175048 3.530000e-39 172
11 TraesCS2B01G395700 chr1D 93.269 104 4 3 150 252 204268633 204268734 1.650000e-32 150
12 TraesCS2B01G395700 chr4D 95.841 553 23 0 253 805 278216229 278215677 0.000000e+00 894
13 TraesCS2B01G395700 chr4D 95.192 104 4 1 150 252 278216436 278216333 2.120000e-36 163
14 TraesCS2B01G395700 chr5D 95.109 552 27 0 253 804 42936806 42937357 0.000000e+00 870
15 TraesCS2B01G395700 chr5D 96.154 104 3 1 150 252 42936599 42936702 4.560000e-38 169
16 TraesCS2B01G395700 chr5B 94.487 526 29 0 278 803 472071937 472072462 0.000000e+00 811
17 TraesCS2B01G395700 chr5B 93.269 104 6 1 150 252 472071711 472071814 4.590000e-33 152
18 TraesCS2B01G395700 chr3D 96.447 394 12 1 414 805 604607877 604607484 0.000000e+00 649
19 TraesCS2B01G395700 chr4A 89.216 102 10 1 152 252 467668728 467668627 2.780000e-25 126


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 TraesCS2B01G395700 chr2B 561228192 561230855 2663 True 4920.0 4920 100.0000 1 2664 1 chr2B.!!$R2 2663
1 TraesCS2B01G395700 chr2D 478702724 478704623 1899 False 2828.0 2828 93.8550 800 2664 1 chr2D.!!$F1 1864
2 TraesCS2B01G395700 chr2D 546688222 546688986 764 True 532.5 902 95.5350 150 809 2 chr2D.!!$R1 659
3 TraesCS2B01G395700 chr2A 621480929 621482787 1858 True 2704.0 2704 93.0210 809 2664 1 chr2A.!!$R1 1855
4 TraesCS2B01G395700 chr3A 671357189 671357944 755 False 536.0 905 96.2405 151 802 2 chr3A.!!$F1 651
5 TraesCS2B01G395700 chr1D 422174946 422175704 758 False 535.0 898 96.5505 150 804 2 chr1D.!!$F2 654
6 TraesCS2B01G395700 chr1D 204268633 204269392 759 False 526.0 902 94.6525 150 806 2 chr1D.!!$F1 656
7 TraesCS2B01G395700 chr4D 278215677 278216436 759 True 528.5 894 95.5165 150 805 2 chr4D.!!$R1 655
8 TraesCS2B01G395700 chr5D 42936599 42937357 758 False 519.5 870 95.6315 150 804 2 chr5D.!!$F1 654
9 TraesCS2B01G395700 chr5B 472071711 472072462 751 False 481.5 811 93.8780 150 803 2 chr5B.!!$F1 653

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
138 139 0.814457 AAGCGAACAACAAACCAGCA 59.186 45.0 0.0 0.0 0.0 4.41 F
139 140 0.814457 AGCGAACAACAAACCAGCAA 59.186 45.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1050 1157 0.321298 TGGGTTTGTTAGGAGAGCGC 60.321 55.0 0.0 0.0 0.0 5.92 R
1988 2135 0.326264 TCTGGAAGCAAAGGAGAGGC 59.674 55.0 0.0 0.0 0.0 4.70 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 9.533253 TTTTTCTTTGAAACAATGATCCTCTTC 57.467 29.630 0.00 0.00 0.00 2.87
41 42 6.824305 TCTTTGAAACAATGATCCTCTTCC 57.176 37.500 0.00 0.00 0.00 3.46
42 43 6.546484 TCTTTGAAACAATGATCCTCTTCCT 58.454 36.000 0.00 0.00 0.00 3.36
43 44 6.656693 TCTTTGAAACAATGATCCTCTTCCTC 59.343 38.462 0.00 0.00 0.00 3.71
44 45 4.507710 TGAAACAATGATCCTCTTCCTCG 58.492 43.478 0.00 0.00 0.00 4.63
45 46 4.222810 TGAAACAATGATCCTCTTCCTCGA 59.777 41.667 0.00 0.00 0.00 4.04
46 47 5.104776 TGAAACAATGATCCTCTTCCTCGAT 60.105 40.000 0.00 0.00 0.00 3.59
47 48 5.365021 AACAATGATCCTCTTCCTCGATT 57.635 39.130 0.00 0.00 0.00 3.34
48 49 5.365021 ACAATGATCCTCTTCCTCGATTT 57.635 39.130 0.00 0.00 0.00 2.17
49 50 5.363939 ACAATGATCCTCTTCCTCGATTTC 58.636 41.667 0.00 0.00 0.00 2.17
50 51 4.615588 ATGATCCTCTTCCTCGATTTCC 57.384 45.455 0.00 0.00 0.00 3.13
51 52 3.374764 TGATCCTCTTCCTCGATTTCCA 58.625 45.455 0.00 0.00 0.00 3.53
52 53 3.969976 TGATCCTCTTCCTCGATTTCCAT 59.030 43.478 0.00 0.00 0.00 3.41
53 54 4.410228 TGATCCTCTTCCTCGATTTCCATT 59.590 41.667 0.00 0.00 0.00 3.16
54 55 4.142609 TCCTCTTCCTCGATTTCCATTG 57.857 45.455 0.00 0.00 0.00 2.82
55 56 3.774766 TCCTCTTCCTCGATTTCCATTGA 59.225 43.478 0.00 0.00 0.00 2.57
56 57 4.225042 TCCTCTTCCTCGATTTCCATTGAA 59.775 41.667 0.00 0.00 0.00 2.69
57 58 4.574013 CCTCTTCCTCGATTTCCATTGAAG 59.426 45.833 0.00 0.00 0.00 3.02
58 59 5.420725 TCTTCCTCGATTTCCATTGAAGA 57.579 39.130 0.00 0.00 35.63 2.87
59 60 5.804639 TCTTCCTCGATTTCCATTGAAGAA 58.195 37.500 0.00 0.00 35.21 2.52
60 61 6.237901 TCTTCCTCGATTTCCATTGAAGAAA 58.762 36.000 0.00 0.00 35.21 2.52
61 62 6.714810 TCTTCCTCGATTTCCATTGAAGAAAA 59.285 34.615 0.00 0.00 36.83 2.29
62 63 6.254281 TCCTCGATTTCCATTGAAGAAAAC 57.746 37.500 0.00 0.00 36.83 2.43
63 64 5.088739 CCTCGATTTCCATTGAAGAAAACG 58.911 41.667 8.91 8.91 45.36 3.60
64 65 5.334879 CCTCGATTTCCATTGAAGAAAACGT 60.335 40.000 13.17 0.00 44.73 3.99
65 66 5.685841 TCGATTTCCATTGAAGAAAACGTC 58.314 37.500 13.17 0.00 44.73 4.34
66 67 5.237561 TCGATTTCCATTGAAGAAAACGTCA 59.762 36.000 13.17 0.00 44.73 4.35
67 68 6.072728 TCGATTTCCATTGAAGAAAACGTCAT 60.073 34.615 13.17 0.00 44.73 3.06
68 69 6.249260 CGATTTCCATTGAAGAAAACGTCATC 59.751 38.462 7.48 0.00 41.64 2.92
69 70 6.384258 TTTCCATTGAAGAAAACGTCATCA 57.616 33.333 0.00 0.00 32.20 3.07
70 71 6.384258 TTCCATTGAAGAAAACGTCATCAA 57.616 33.333 0.00 0.00 45.35 2.57
71 72 6.000891 TCCATTGAAGAAAACGTCATCAAG 57.999 37.500 0.00 0.00 44.71 3.02
72 73 5.530915 TCCATTGAAGAAAACGTCATCAAGT 59.469 36.000 0.00 0.00 44.71 3.16
73 74 6.039270 TCCATTGAAGAAAACGTCATCAAGTT 59.961 34.615 0.00 0.00 44.71 2.66
74 75 6.697019 CCATTGAAGAAAACGTCATCAAGTTT 59.303 34.615 0.00 0.00 44.71 2.66
75 76 7.222611 CCATTGAAGAAAACGTCATCAAGTTTT 59.777 33.333 6.07 6.07 44.71 2.43
76 77 9.232082 CATTGAAGAAAACGTCATCAAGTTTTA 57.768 29.630 6.33 0.00 44.71 1.52
77 78 9.965824 ATTGAAGAAAACGTCATCAAGTTTTAT 57.034 25.926 6.33 1.41 44.71 1.40
79 80 9.872757 TGAAGAAAACGTCATCAAGTTTTATAC 57.127 29.630 6.33 2.91 46.58 1.47
80 81 9.872757 GAAGAAAACGTCATCAAGTTTTATACA 57.127 29.630 6.33 0.00 46.58 2.29
101 102 6.969993 ACAAAAGTTATAGCAAAACAGGGA 57.030 33.333 0.00 0.00 0.00 4.20
102 103 7.354751 ACAAAAGTTATAGCAAAACAGGGAA 57.645 32.000 0.00 0.00 0.00 3.97
103 104 7.787028 ACAAAAGTTATAGCAAAACAGGGAAA 58.213 30.769 0.00 0.00 0.00 3.13
104 105 7.709182 ACAAAAGTTATAGCAAAACAGGGAAAC 59.291 33.333 0.00 0.00 0.00 2.78
105 106 6.969993 AAGTTATAGCAAAACAGGGAAACA 57.030 33.333 0.00 0.00 0.00 2.83
106 107 6.327279 AGTTATAGCAAAACAGGGAAACAC 57.673 37.500 0.00 0.00 0.00 3.32
107 108 5.830991 AGTTATAGCAAAACAGGGAAACACA 59.169 36.000 0.00 0.00 0.00 3.72
108 109 6.493458 AGTTATAGCAAAACAGGGAAACACAT 59.507 34.615 0.00 0.00 0.00 3.21
109 110 3.733443 AGCAAAACAGGGAAACACATC 57.267 42.857 0.00 0.00 0.00 3.06
110 111 2.365293 AGCAAAACAGGGAAACACATCC 59.635 45.455 0.00 0.00 38.86 3.51
111 112 2.862140 GCAAAACAGGGAAACACATCCG 60.862 50.000 0.00 0.00 40.62 4.18
112 113 2.621055 CAAAACAGGGAAACACATCCGA 59.379 45.455 0.00 0.00 40.62 4.55
113 114 2.649531 AACAGGGAAACACATCCGAA 57.350 45.000 0.00 0.00 40.62 4.30
114 115 2.649531 ACAGGGAAACACATCCGAAA 57.350 45.000 0.00 0.00 40.62 3.46
115 116 3.154827 ACAGGGAAACACATCCGAAAT 57.845 42.857 0.00 0.00 40.62 2.17
116 117 3.496331 ACAGGGAAACACATCCGAAATT 58.504 40.909 0.00 0.00 40.62 1.82
117 118 3.506067 ACAGGGAAACACATCCGAAATTC 59.494 43.478 0.00 0.00 40.62 2.17
118 119 3.089284 AGGGAAACACATCCGAAATTCC 58.911 45.455 0.00 0.00 40.62 3.01
119 120 2.823154 GGGAAACACATCCGAAATTCCA 59.177 45.455 4.90 0.00 40.62 3.53
120 121 3.257127 GGGAAACACATCCGAAATTCCAA 59.743 43.478 4.90 0.00 40.62 3.53
121 122 4.485163 GGAAACACATCCGAAATTCCAAG 58.515 43.478 0.00 0.00 37.02 3.61
122 123 3.575965 AACACATCCGAAATTCCAAGC 57.424 42.857 0.00 0.00 0.00 4.01
123 124 1.468520 ACACATCCGAAATTCCAAGCG 59.531 47.619 0.00 0.00 0.00 4.68
124 125 1.737236 CACATCCGAAATTCCAAGCGA 59.263 47.619 0.00 0.00 0.00 4.93
125 126 2.161410 CACATCCGAAATTCCAAGCGAA 59.839 45.455 0.00 0.00 34.14 4.70
126 127 2.161609 ACATCCGAAATTCCAAGCGAAC 59.838 45.455 0.00 0.00 31.79 3.95
127 128 1.885560 TCCGAAATTCCAAGCGAACA 58.114 45.000 0.00 0.00 31.79 3.18
128 129 2.222886 TCCGAAATTCCAAGCGAACAA 58.777 42.857 0.00 0.00 31.79 2.83
129 130 2.031508 TCCGAAATTCCAAGCGAACAAC 60.032 45.455 0.00 0.00 31.79 3.32
130 131 2.287308 CCGAAATTCCAAGCGAACAACA 60.287 45.455 0.00 0.00 31.79 3.33
131 132 3.367607 CGAAATTCCAAGCGAACAACAA 58.632 40.909 0.00 0.00 31.79 2.83
132 133 3.794028 CGAAATTCCAAGCGAACAACAAA 59.206 39.130 0.00 0.00 31.79 2.83
133 134 4.317069 CGAAATTCCAAGCGAACAACAAAC 60.317 41.667 0.00 0.00 31.79 2.93
134 135 2.570442 TTCCAAGCGAACAACAAACC 57.430 45.000 0.00 0.00 0.00 3.27
135 136 1.464734 TCCAAGCGAACAACAAACCA 58.535 45.000 0.00 0.00 0.00 3.67
136 137 1.403679 TCCAAGCGAACAACAAACCAG 59.596 47.619 0.00 0.00 0.00 4.00
137 138 1.199624 CAAGCGAACAACAAACCAGC 58.800 50.000 0.00 0.00 0.00 4.85
138 139 0.814457 AAGCGAACAACAAACCAGCA 59.186 45.000 0.00 0.00 0.00 4.41
139 140 0.814457 AGCGAACAACAAACCAGCAA 59.186 45.000 0.00 0.00 0.00 3.91
140 141 1.408702 AGCGAACAACAAACCAGCAAT 59.591 42.857 0.00 0.00 0.00 3.56
141 142 2.159114 AGCGAACAACAAACCAGCAATT 60.159 40.909 0.00 0.00 0.00 2.32
142 143 2.218530 GCGAACAACAAACCAGCAATTC 59.781 45.455 0.00 0.00 0.00 2.17
143 144 3.443037 CGAACAACAAACCAGCAATTCA 58.557 40.909 0.00 0.00 0.00 2.57
144 145 3.486841 CGAACAACAAACCAGCAATTCAG 59.513 43.478 0.00 0.00 0.00 3.02
145 146 4.432712 GAACAACAAACCAGCAATTCAGT 58.567 39.130 0.00 0.00 0.00 3.41
146 147 5.587289 GAACAACAAACCAGCAATTCAGTA 58.413 37.500 0.00 0.00 0.00 2.74
147 148 5.186996 ACAACAAACCAGCAATTCAGTAG 57.813 39.130 0.00 0.00 0.00 2.57
148 149 3.923017 ACAAACCAGCAATTCAGTAGC 57.077 42.857 0.00 0.00 0.00 3.58
238 240 1.139058 AGCTGAACTGACTTCGGTTGT 59.861 47.619 8.20 0.00 44.81 3.32
328 433 6.009589 TGACATGGTTAAGGTGAATGTTGAT 58.990 36.000 0.00 0.00 31.82 2.57
615 720 2.672961 TGTAAGCAACTCTCCATCGG 57.327 50.000 0.00 0.00 0.00 4.18
629 734 1.532505 CCATCGGCTTTGCAAAGATCG 60.533 52.381 37.14 33.77 38.28 3.69
893 999 1.823295 GACCGCCAGATTAGCTCCA 59.177 57.895 0.00 0.00 0.00 3.86
945 1051 3.719214 GGCTACTATGCCGTGCAC 58.281 61.111 6.82 6.82 43.04 4.57
955 1061 2.203139 CCGTGCACACCTGAACCA 60.203 61.111 18.64 0.00 0.00 3.67
1045 1152 2.358615 AATCACTCGCCGCAAGCA 60.359 55.556 0.00 0.00 44.04 3.91
1050 1157 3.624300 CTCGCCGCAAGCATCTCG 61.624 66.667 0.00 0.00 44.04 4.04
1069 1176 0.321298 GCGCTCTCCTAACAAACCCA 60.321 55.000 0.00 0.00 0.00 4.51
1074 1181 2.372172 CTCTCCTAACAAACCCACCACT 59.628 50.000 0.00 0.00 0.00 4.00
1125 1232 2.594592 GAACCAACCGGCAGCAGT 60.595 61.111 0.00 0.00 34.57 4.40
1129 1236 2.358615 CAACCGGCAGCAGTAGCA 60.359 61.111 0.00 0.00 45.49 3.49
1233 1355 1.505353 CGCGTTCGACCTAGACCTT 59.495 57.895 0.00 0.00 38.10 3.50
1487 1609 1.410365 CGTCACCAGAGTAGGGGATCT 60.410 57.143 0.00 0.00 44.37 2.75
1658 1780 3.511146 TGACCAGATTTTTGCCAGAATCC 59.489 43.478 0.00 0.00 33.72 3.01
1664 1786 5.649395 CAGATTTTTGCCAGAATCCTGTAGA 59.351 40.000 0.00 0.00 38.74 2.59
1778 1903 1.815817 ATGGACCGGCAAAAAGGCAC 61.816 55.000 0.00 0.00 44.47 5.01
1891 2038 2.224185 TGCAGCAGGACGAGAAAAACTA 60.224 45.455 0.00 0.00 0.00 2.24
1899 2046 6.293462 GCAGGACGAGAAAAACTACAATTTCT 60.293 38.462 0.72 0.72 45.85 2.52
1921 2068 2.028203 TGAAACCATCACTGCTCGATCA 60.028 45.455 0.00 0.00 31.50 2.92
1941 2088 5.999205 TCAAATGTTCAGCCACCAATATT 57.001 34.783 0.00 0.00 0.00 1.28
1988 2135 0.038159 GGTTCCTCAGTCACCACTCG 60.038 60.000 0.00 0.00 0.00 4.18
2053 2200 1.338337 CTCTATTCGTCGCCATCTGGT 59.662 52.381 0.00 0.00 37.57 4.00
2119 2266 7.171630 ACTACCGATGAAGTTTCAGTATCTT 57.828 36.000 0.74 0.00 41.08 2.40
2316 2463 9.884465 GATATGAAATCACTAGGTAAAATGCAC 57.116 33.333 0.00 0.00 0.00 4.57
2514 2665 4.428294 TCATTAGAGGCAGGGATTCTTG 57.572 45.455 0.00 0.00 0.00 3.02
2548 2699 7.630242 AGCACAGCTTTAATATTTCTGCTAA 57.370 32.000 0.00 0.00 33.89 3.09
2616 2767 1.672881 GAGGCCATCAATGTTCCTTCG 59.327 52.381 5.01 0.00 31.70 3.79
2636 2787 1.827578 CACGCGATTGAAGAGATCGA 58.172 50.000 15.93 0.00 46.93 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.533253 GAAGAGGATCATTGTTTCAAAGAAAAA 57.467 29.630 0.00 0.00 37.82 1.94
15 16 8.143835 GGAAGAGGATCATTGTTTCAAAGAAAA 58.856 33.333 0.00 0.00 37.82 2.29
16 17 7.506938 AGGAAGAGGATCATTGTTTCAAAGAAA 59.493 33.333 0.00 0.00 37.82 2.52
17 18 7.006509 AGGAAGAGGATCATTGTTTCAAAGAA 58.993 34.615 0.00 0.00 37.82 2.52
18 19 6.546484 AGGAAGAGGATCATTGTTTCAAAGA 58.454 36.000 0.00 0.00 37.82 2.52
19 20 6.402983 CGAGGAAGAGGATCATTGTTTCAAAG 60.403 42.308 0.00 0.00 37.82 2.77
20 21 5.412594 CGAGGAAGAGGATCATTGTTTCAAA 59.587 40.000 0.00 0.00 37.82 2.69
21 22 4.937620 CGAGGAAGAGGATCATTGTTTCAA 59.062 41.667 0.00 0.00 37.82 2.69
22 23 4.222810 TCGAGGAAGAGGATCATTGTTTCA 59.777 41.667 0.00 0.00 37.82 2.69
23 24 4.759782 TCGAGGAAGAGGATCATTGTTTC 58.240 43.478 0.00 0.00 37.82 2.78
24 25 4.826274 TCGAGGAAGAGGATCATTGTTT 57.174 40.909 0.00 0.00 37.82 2.83
25 26 5.365021 AATCGAGGAAGAGGATCATTGTT 57.635 39.130 0.00 0.00 37.82 2.83
26 27 5.363939 GAAATCGAGGAAGAGGATCATTGT 58.636 41.667 0.00 0.00 37.82 2.71
27 28 4.754114 GGAAATCGAGGAAGAGGATCATTG 59.246 45.833 0.00 0.00 37.82 2.82
28 29 4.410228 TGGAAATCGAGGAAGAGGATCATT 59.590 41.667 0.00 0.00 37.82 2.57
29 30 3.969976 TGGAAATCGAGGAAGAGGATCAT 59.030 43.478 0.00 0.00 37.82 2.45
30 31 3.374764 TGGAAATCGAGGAAGAGGATCA 58.625 45.455 0.00 0.00 37.82 2.92
31 32 4.615588 ATGGAAATCGAGGAAGAGGATC 57.384 45.455 0.00 0.00 0.00 3.36
32 33 4.410228 TCAATGGAAATCGAGGAAGAGGAT 59.590 41.667 0.00 0.00 0.00 3.24
33 34 3.774766 TCAATGGAAATCGAGGAAGAGGA 59.225 43.478 0.00 0.00 0.00 3.71
34 35 4.142609 TCAATGGAAATCGAGGAAGAGG 57.857 45.455 0.00 0.00 0.00 3.69
35 36 5.423015 TCTTCAATGGAAATCGAGGAAGAG 58.577 41.667 0.00 0.00 35.63 2.85
36 37 5.420725 TCTTCAATGGAAATCGAGGAAGA 57.579 39.130 0.00 0.00 37.52 2.87
37 38 6.500684 TTTCTTCAATGGAAATCGAGGAAG 57.499 37.500 0.00 0.00 31.35 3.46
38 39 6.567701 CGTTTTCTTCAATGGAAATCGAGGAA 60.568 38.462 11.64 0.00 42.98 3.36
39 40 5.106712 CGTTTTCTTCAATGGAAATCGAGGA 60.107 40.000 11.64 0.00 42.98 3.71
40 41 5.088739 CGTTTTCTTCAATGGAAATCGAGG 58.911 41.667 11.64 0.00 42.98 4.63
41 42 5.689819 ACGTTTTCTTCAATGGAAATCGAG 58.310 37.500 19.33 4.18 42.98 4.04
42 43 5.237561 TGACGTTTTCTTCAATGGAAATCGA 59.762 36.000 19.33 0.00 42.98 3.59
43 44 5.448438 TGACGTTTTCTTCAATGGAAATCG 58.552 37.500 14.06 14.06 44.42 3.34
44 45 7.083858 TGATGACGTTTTCTTCAATGGAAATC 58.916 34.615 0.00 0.00 35.88 2.17
45 46 6.980593 TGATGACGTTTTCTTCAATGGAAAT 58.019 32.000 0.00 0.00 35.88 2.17
46 47 6.384258 TGATGACGTTTTCTTCAATGGAAA 57.616 33.333 0.00 0.00 35.88 3.13
47 48 6.039270 ACTTGATGACGTTTTCTTCAATGGAA 59.961 34.615 0.00 0.00 43.72 3.53
48 49 5.530915 ACTTGATGACGTTTTCTTCAATGGA 59.469 36.000 0.00 0.00 43.72 3.41
49 50 5.762045 ACTTGATGACGTTTTCTTCAATGG 58.238 37.500 0.00 0.00 43.72 3.16
50 51 7.684062 AAACTTGATGACGTTTTCTTCAATG 57.316 32.000 0.00 0.00 43.72 2.82
51 52 9.965824 ATAAAACTTGATGACGTTTTCTTCAAT 57.034 25.926 2.89 0.00 43.72 2.57
53 54 9.872757 GTATAAAACTTGATGACGTTTTCTTCA 57.127 29.630 2.89 0.00 41.07 3.02
54 55 9.872757 TGTATAAAACTTGATGACGTTTTCTTC 57.127 29.630 2.89 0.00 41.07 2.87
75 76 9.742144 TCCCTGTTTTGCTATAACTTTTGTATA 57.258 29.630 0.00 0.00 0.00 1.47
76 77 8.644374 TCCCTGTTTTGCTATAACTTTTGTAT 57.356 30.769 0.00 0.00 0.00 2.29
77 78 8.466617 TTCCCTGTTTTGCTATAACTTTTGTA 57.533 30.769 0.00 0.00 0.00 2.41
78 79 6.969993 TCCCTGTTTTGCTATAACTTTTGT 57.030 33.333 0.00 0.00 0.00 2.83
79 80 7.708752 TGTTTCCCTGTTTTGCTATAACTTTTG 59.291 33.333 0.00 0.00 0.00 2.44
80 81 7.709182 GTGTTTCCCTGTTTTGCTATAACTTTT 59.291 33.333 0.00 0.00 0.00 2.27
81 82 7.147811 TGTGTTTCCCTGTTTTGCTATAACTTT 60.148 33.333 0.00 0.00 0.00 2.66
82 83 6.322712 TGTGTTTCCCTGTTTTGCTATAACTT 59.677 34.615 0.00 0.00 0.00 2.66
83 84 5.830991 TGTGTTTCCCTGTTTTGCTATAACT 59.169 36.000 0.00 0.00 0.00 2.24
84 85 6.079424 TGTGTTTCCCTGTTTTGCTATAAC 57.921 37.500 0.00 0.00 0.00 1.89
85 86 6.071616 GGATGTGTTTCCCTGTTTTGCTATAA 60.072 38.462 0.00 0.00 0.00 0.98
86 87 5.417580 GGATGTGTTTCCCTGTTTTGCTATA 59.582 40.000 0.00 0.00 0.00 1.31
87 88 4.220602 GGATGTGTTTCCCTGTTTTGCTAT 59.779 41.667 0.00 0.00 0.00 2.97
88 89 3.572255 GGATGTGTTTCCCTGTTTTGCTA 59.428 43.478 0.00 0.00 0.00 3.49
89 90 2.365293 GGATGTGTTTCCCTGTTTTGCT 59.635 45.455 0.00 0.00 0.00 3.91
90 91 2.754472 GGATGTGTTTCCCTGTTTTGC 58.246 47.619 0.00 0.00 0.00 3.68
91 92 2.621055 TCGGATGTGTTTCCCTGTTTTG 59.379 45.455 0.00 0.00 31.61 2.44
92 93 2.938838 TCGGATGTGTTTCCCTGTTTT 58.061 42.857 0.00 0.00 31.61 2.43
93 94 2.649531 TCGGATGTGTTTCCCTGTTT 57.350 45.000 0.00 0.00 31.61 2.83
94 95 2.649531 TTCGGATGTGTTTCCCTGTT 57.350 45.000 0.00 0.00 31.61 3.16
95 96 2.649531 TTTCGGATGTGTTTCCCTGT 57.350 45.000 0.00 0.00 31.61 4.00
96 97 3.119495 GGAATTTCGGATGTGTTTCCCTG 60.119 47.826 0.00 0.00 31.61 4.45
97 98 3.089284 GGAATTTCGGATGTGTTTCCCT 58.911 45.455 0.00 0.00 31.61 4.20
98 99 2.823154 TGGAATTTCGGATGTGTTTCCC 59.177 45.455 0.00 0.00 33.30 3.97
99 100 4.485163 CTTGGAATTTCGGATGTGTTTCC 58.515 43.478 0.00 0.00 34.54 3.13
100 101 3.920412 GCTTGGAATTTCGGATGTGTTTC 59.080 43.478 0.00 0.00 0.00 2.78
101 102 3.611530 CGCTTGGAATTTCGGATGTGTTT 60.612 43.478 0.00 0.00 0.00 2.83
102 103 2.095263 CGCTTGGAATTTCGGATGTGTT 60.095 45.455 0.00 0.00 0.00 3.32
103 104 1.468520 CGCTTGGAATTTCGGATGTGT 59.531 47.619 0.00 0.00 0.00 3.72
104 105 1.737236 TCGCTTGGAATTTCGGATGTG 59.263 47.619 0.00 0.00 0.00 3.21
105 106 2.107950 TCGCTTGGAATTTCGGATGT 57.892 45.000 0.00 0.00 0.00 3.06
106 107 2.161410 TGTTCGCTTGGAATTTCGGATG 59.839 45.455 0.00 0.00 36.92 3.51
107 108 2.432444 TGTTCGCTTGGAATTTCGGAT 58.568 42.857 0.00 0.00 36.92 4.18
108 109 1.885560 TGTTCGCTTGGAATTTCGGA 58.114 45.000 0.00 0.00 36.92 4.55
109 110 2.287308 TGTTGTTCGCTTGGAATTTCGG 60.287 45.455 0.00 0.00 36.92 4.30
110 111 2.993545 TGTTGTTCGCTTGGAATTTCG 58.006 42.857 0.00 0.00 36.92 3.46
111 112 4.026062 GGTTTGTTGTTCGCTTGGAATTTC 60.026 41.667 0.00 0.00 36.92 2.17
112 113 3.868661 GGTTTGTTGTTCGCTTGGAATTT 59.131 39.130 0.00 0.00 36.92 1.82
113 114 3.118956 TGGTTTGTTGTTCGCTTGGAATT 60.119 39.130 0.00 0.00 36.92 2.17
114 115 2.428890 TGGTTTGTTGTTCGCTTGGAAT 59.571 40.909 0.00 0.00 36.92 3.01
115 116 1.819288 TGGTTTGTTGTTCGCTTGGAA 59.181 42.857 0.00 0.00 0.00 3.53
116 117 1.403679 CTGGTTTGTTGTTCGCTTGGA 59.596 47.619 0.00 0.00 0.00 3.53
117 118 1.838913 CTGGTTTGTTGTTCGCTTGG 58.161 50.000 0.00 0.00 0.00 3.61
118 119 1.199624 GCTGGTTTGTTGTTCGCTTG 58.800 50.000 0.00 0.00 0.00 4.01
119 120 0.814457 TGCTGGTTTGTTGTTCGCTT 59.186 45.000 0.00 0.00 0.00 4.68
120 121 0.814457 TTGCTGGTTTGTTGTTCGCT 59.186 45.000 0.00 0.00 0.00 4.93
121 122 1.851658 ATTGCTGGTTTGTTGTTCGC 58.148 45.000 0.00 0.00 0.00 4.70
122 123 3.443037 TGAATTGCTGGTTTGTTGTTCG 58.557 40.909 0.00 0.00 0.00 3.95
123 124 4.432712 ACTGAATTGCTGGTTTGTTGTTC 58.567 39.130 0.00 0.00 0.00 3.18
124 125 4.470334 ACTGAATTGCTGGTTTGTTGTT 57.530 36.364 0.00 0.00 0.00 2.83
125 126 4.499696 GCTACTGAATTGCTGGTTTGTTGT 60.500 41.667 0.00 0.00 0.00 3.32
126 127 3.983344 GCTACTGAATTGCTGGTTTGTTG 59.017 43.478 0.00 0.00 0.00 3.33
127 128 3.636300 TGCTACTGAATTGCTGGTTTGTT 59.364 39.130 0.00 0.00 0.00 2.83
128 129 3.221771 TGCTACTGAATTGCTGGTTTGT 58.778 40.909 0.00 0.00 0.00 2.83
129 130 3.921119 TGCTACTGAATTGCTGGTTTG 57.079 42.857 0.00 0.00 0.00 2.93
130 131 4.022849 GTCTTGCTACTGAATTGCTGGTTT 60.023 41.667 0.00 0.00 0.00 3.27
131 132 3.503748 GTCTTGCTACTGAATTGCTGGTT 59.496 43.478 0.00 0.00 0.00 3.67
132 133 3.077359 GTCTTGCTACTGAATTGCTGGT 58.923 45.455 0.00 0.00 0.00 4.00
133 134 3.076621 TGTCTTGCTACTGAATTGCTGG 58.923 45.455 0.00 0.00 0.00 4.85
134 135 3.126514 CCTGTCTTGCTACTGAATTGCTG 59.873 47.826 0.00 0.00 0.00 4.41
135 136 3.244700 ACCTGTCTTGCTACTGAATTGCT 60.245 43.478 0.00 0.00 0.00 3.91
136 137 3.077359 ACCTGTCTTGCTACTGAATTGC 58.923 45.455 0.00 0.00 0.00 3.56
137 138 4.391216 CAGACCTGTCTTGCTACTGAATTG 59.609 45.833 0.00 0.00 37.98 2.32
138 139 4.564406 CCAGACCTGTCTTGCTACTGAATT 60.564 45.833 0.00 0.00 37.98 2.17
139 140 3.055530 CCAGACCTGTCTTGCTACTGAAT 60.056 47.826 0.00 0.00 37.98 2.57
140 141 2.300152 CCAGACCTGTCTTGCTACTGAA 59.700 50.000 0.00 0.00 37.98 3.02
141 142 1.895798 CCAGACCTGTCTTGCTACTGA 59.104 52.381 0.00 0.00 37.98 3.41
142 143 1.066573 CCCAGACCTGTCTTGCTACTG 60.067 57.143 0.00 0.00 37.98 2.74
143 144 1.270907 CCCAGACCTGTCTTGCTACT 58.729 55.000 0.00 0.00 37.98 2.57
144 145 0.977395 ACCCAGACCTGTCTTGCTAC 59.023 55.000 0.00 0.00 37.98 3.58
145 146 1.267121 GACCCAGACCTGTCTTGCTA 58.733 55.000 0.00 0.00 37.98 3.49
146 147 0.764369 TGACCCAGACCTGTCTTGCT 60.764 55.000 0.00 0.00 37.98 3.91
147 148 0.108585 TTGACCCAGACCTGTCTTGC 59.891 55.000 0.00 0.00 37.98 4.01
148 149 2.867109 ATTGACCCAGACCTGTCTTG 57.133 50.000 0.00 0.00 37.98 3.02
328 433 1.525197 GTGTCGACGTGAAAAGATGCA 59.475 47.619 11.62 0.00 0.00 3.96
565 670 1.171308 CTGCAACATCTGGTCCTTGG 58.829 55.000 0.00 0.00 0.00 3.61
615 720 1.068333 TGAAGGCGATCTTTGCAAAGC 60.068 47.619 30.35 20.79 35.50 3.51
629 734 3.254166 TCTCTGAAACAATGCTTGAAGGC 59.746 43.478 0.00 0.00 0.00 4.35
805 910 6.983890 GGGTTTTTCTTTTACTGAATTGCTGA 59.016 34.615 0.00 0.00 0.00 4.26
818 923 5.878116 GGTTTAGTTGCTGGGTTTTTCTTTT 59.122 36.000 0.00 0.00 0.00 2.27
822 927 4.665833 AGGTTTAGTTGCTGGGTTTTTC 57.334 40.909 0.00 0.00 0.00 2.29
828 933 2.823747 GGGTTTAGGTTTAGTTGCTGGG 59.176 50.000 0.00 0.00 0.00 4.45
893 999 2.355481 GGTTCGTCACGTTCGCCT 60.355 61.111 0.00 0.00 0.00 5.52
939 1045 0.040157 CATTGGTTCAGGTGTGCACG 60.040 55.000 13.13 0.00 0.00 5.34
945 1051 2.162681 GGTTCTCCATTGGTTCAGGTG 58.837 52.381 1.86 0.00 0.00 4.00
955 1061 5.011023 GTGGAATCTTGTTTGGTTCTCCATT 59.989 40.000 0.00 0.00 43.91 3.16
992 1099 2.440796 CCATTGCCATGGCGGAGT 60.441 61.111 30.87 14.14 43.95 3.85
1045 1152 1.103803 TTGTTAGGAGAGCGCGAGAT 58.896 50.000 12.10 0.00 0.00 2.75
1050 1157 0.321298 TGGGTTTGTTAGGAGAGCGC 60.321 55.000 0.00 0.00 0.00 5.92
1069 1176 3.400054 GCTCGGGGGCTTAGTGGT 61.400 66.667 0.00 0.00 0.00 4.16
1074 1181 2.595095 CCATTGCTCGGGGGCTTA 59.405 61.111 0.00 0.00 0.00 3.09
1125 1232 2.125391 CTTCTGCCGCTGCTGCTA 60.125 61.111 16.81 2.87 38.71 3.49
1129 1236 4.774503 GCTCCTTCTGCCGCTGCT 62.775 66.667 0.70 0.00 38.71 4.24
1443 1565 3.083293 GTTGAAGAGGTCGGAGTAGAGT 58.917 50.000 0.00 0.00 0.00 3.24
1510 1632 1.671328 CATGAGCAATGTCAGAGGCTG 59.329 52.381 0.00 0.00 36.59 4.85
1658 1780 2.094894 CGAGCCAGTGCAAAATCTACAG 59.905 50.000 0.00 0.00 41.13 2.74
1664 1786 0.729116 CGATCGAGCCAGTGCAAAAT 59.271 50.000 10.26 0.00 41.13 1.82
1891 2038 5.069516 AGCAGTGATGGTTTCAAGAAATTGT 59.930 36.000 0.00 0.00 35.70 2.71
1899 2046 2.542020 TCGAGCAGTGATGGTTTCAA 57.458 45.000 0.00 0.00 35.70 2.69
1921 2068 5.105228 CCTGAATATTGGTGGCTGAACATTT 60.105 40.000 0.00 0.00 0.00 2.32
1988 2135 0.326264 TCTGGAAGCAAAGGAGAGGC 59.674 55.000 0.00 0.00 0.00 4.70
2119 2266 1.649321 AAGCAGGTCACAGATGAGGA 58.351 50.000 0.00 0.00 34.75 3.71
2360 2509 2.561478 TGGTAAGTTCTTCCAGGTGC 57.439 50.000 0.00 0.00 0.00 5.01
2548 2699 7.891712 TCCACCTATGATCAATGCATAATTCAT 59.108 33.333 17.27 17.27 0.00 2.57
2596 2747 1.672881 CGAAGGAACATTGATGGCCTC 59.327 52.381 3.32 0.00 36.22 4.70
2616 2767 0.228238 CGATCTCTTCAATCGCGTGC 59.772 55.000 5.77 0.00 39.50 5.34
2636 2787 6.916360 TTTCTTCCAGGCTCAAAATAACAT 57.084 33.333 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.