Multiple sequence alignment - TraesCS1B01G043200

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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 TraesCS1B01G043200 chr1B 100.000 8787 0 0 1 8787 22700035 22708821 0.000000e+00 16190.0
1 TraesCS1B01G043200 chr1B 96.792 3959 118 6 4833 8787 7992963 7996916 0.000000e+00 6599.0
2 TraesCS1B01G043200 chr1B 97.712 3103 68 2 1568 4669 7989862 7992962 0.000000e+00 5334.0
3 TraesCS1B01G043200 chr1B 92.227 952 24 16 625 1576 7988768 7989669 0.000000e+00 1303.0
4 TraesCS1B01G043200 chr1B 80.609 1707 264 41 5907 7580 144930315 144931987 0.000000e+00 1256.0
5 TraesCS1B01G043200 chr1B 84.076 1256 168 21 1106 2344 7990876 7992116 0.000000e+00 1182.0
6 TraesCS1B01G043200 chr1B 83.745 1255 174 18 2583 3823 22701140 22702378 0.000000e+00 1160.0
7 TraesCS1B01G043200 chr1B 83.745 1255 174 19 1106 2344 22702617 22703857 0.000000e+00 1160.0
8 TraesCS1B01G043200 chr1B 85.494 779 99 5 3056 3823 7989862 7990637 0.000000e+00 800.0
9 TraesCS1B01G043200 chr1B 84.019 851 114 9 5186 6017 22701771 22702618 0.000000e+00 798.0
10 TraesCS1B01G043200 chr1B 84.019 851 114 9 1737 2584 22705220 22706051 0.000000e+00 798.0
11 TraesCS1B01G043200 chr1B 83.666 851 117 9 1737 2584 7993316 7994147 0.000000e+00 782.0
12 TraesCS1B01G043200 chr1B 82.333 600 90 7 5186 5778 7991517 7992107 2.830000e-139 507.0
13 TraesCS1B01G043200 chr1B 81.333 600 96 7 5186 5778 22703258 22703848 2.870000e-129 473.0
14 TraesCS1B01G043200 chr1B 81.333 600 96 7 3224 3814 22705220 22705812 2.870000e-129 473.0
15 TraesCS1B01G043200 chr1B 80.833 600 99 7 3224 3814 7993316 7993908 2.890000e-124 457.0
16 TraesCS1B01G043200 chr1B 90.523 306 24 1 8 313 7987304 7987604 4.940000e-107 399.0
17 TraesCS1B01G043200 chr1B 84.169 379 51 5 1216 1588 144929799 144930174 8.390000e-95 359.0
18 TraesCS1B01G043200 chr1B 81.449 345 57 6 2722 3063 144926617 144926957 8.690000e-70 276.0
19 TraesCS1B01G043200 chr1B 96.753 154 5 0 314 467 7988611 7988764 3.150000e-64 257.0
20 TraesCS1B01G043200 chr1B 84.274 248 29 8 5776 6020 7989899 7990139 5.300000e-57 233.0
21 TraesCS1B01G043200 chr1B 83.594 128 21 0 5172 5299 144930308 144930435 4.310000e-23 121.0
22 TraesCS1B01G043200 chr1B 81.818 110 13 4 8128 8236 459127762 459127865 1.570000e-12 86.1
23 TraesCS1B01G043200 chr1B 81.818 110 13 4 8128 8236 565039803 565039700 1.570000e-12 86.1
24 TraesCS1B01G043200 chr1A 94.976 3762 152 13 314 4044 6317088 6320843 0.000000e+00 5866.0
25 TraesCS1B01G043200 chr1A 94.984 2851 99 12 4770 7613 6321582 6324395 0.000000e+00 4433.0
26 TraesCS1B01G043200 chr1A 95.429 1050 41 4 7737 8784 6324392 6325436 0.000000e+00 1666.0
27 TraesCS1B01G043200 chr1A 80.841 1712 256 45 5907 7585 86238590 86240262 0.000000e+00 1279.0
28 TraesCS1B01G043200 chr1A 84.976 1258 154 25 1106 2344 6319374 6320615 0.000000e+00 1243.0
29 TraesCS1B01G043200 chr1A 82.896 1257 183 19 2583 3823 6317895 6319135 0.000000e+00 1101.0
30 TraesCS1B01G043200 chr1A 84.038 852 112 12 5186 6017 6318528 6319375 0.000000e+00 798.0
31 TraesCS1B01G043200 chr1A 94.681 470 14 3 4100 4569 6321121 6321579 0.000000e+00 719.0
32 TraesCS1B01G043200 chr1A 79.747 869 133 27 5183 6020 6319269 6320125 2.730000e-164 590.0
33 TraesCS1B01G043200 chr1A 80.728 742 106 19 5298 6020 6317914 6318637 2.160000e-150 544.0
34 TraesCS1B01G043200 chr1A 81.167 600 96 8 3224 3814 6321981 6322572 4.800000e-127 466.0
35 TraesCS1B01G043200 chr1A 91.640 311 26 0 3 313 6300380 6300690 1.750000e-116 431.0
36 TraesCS1B01G043200 chr1A 81.818 484 61 16 1127 1588 86237971 86238449 1.790000e-101 381.0
37 TraesCS1B01G043200 chr1A 81.341 343 61 3 2722 3063 86235732 86236072 8.690000e-70 276.0
38 TraesCS1B01G043200 chr1A 83.582 134 22 0 5166 5299 86238577 86238710 9.260000e-25 126.0
39 TraesCS1B01G043200 chr1D 97.025 2891 68 7 4726 7613 4824813 4827688 0.000000e+00 4846.0
40 TraesCS1B01G043200 chr1D 95.099 2224 99 4 2393 4607 4822584 4824806 0.000000e+00 3494.0
41 TraesCS1B01G043200 chr1D 95.096 2080 59 13 314 2377 4820546 4822598 0.000000e+00 3236.0
42 TraesCS1B01G043200 chr1D 96.353 1042 32 5 7749 8787 4838014 4839052 0.000000e+00 1709.0
43 TraesCS1B01G043200 chr1D 84.952 1256 156 23 1106 2344 4822776 4824015 0.000000e+00 1242.0
44 TraesCS1B01G043200 chr1D 84.064 1255 170 18 2583 3823 4821327 4822565 0.000000e+00 1182.0
45 TraesCS1B01G043200 chr1D 79.929 1400 200 44 5427 6819 4769091 4770416 0.000000e+00 953.0
46 TraesCS1B01G043200 chr1D 80.659 1153 182 25 6444 7585 90150886 90152008 0.000000e+00 856.0
47 TraesCS1B01G043200 chr1D 84.019 851 114 9 1737 2584 4825274 4826105 0.000000e+00 798.0
48 TraesCS1B01G043200 chr1D 83.075 839 116 14 5186 6017 4821958 4822777 0.000000e+00 739.0
49 TraesCS1B01G043200 chr1D 86.310 672 79 8 6908 7578 4774289 4774948 0.000000e+00 719.0
50 TraesCS1B01G043200 chr1D 81.536 742 98 19 5298 6020 4821346 4822067 7.650000e-160 575.0
51 TraesCS1B01G043200 chr1D 81.500 600 95 7 3224 3814 4825274 4825866 6.170000e-131 479.0
52 TraesCS1B01G043200 chr1D 81.658 567 81 12 5900 6447 90150068 90150630 4.840000e-122 449.0
53 TraesCS1B01G043200 chr1D 77.310 736 138 18 6780 7488 10154339 10153606 2.950000e-109 407.0
54 TraesCS1B01G043200 chr1D 81.924 343 59 3 2722 3063 90148873 90149213 4.010000e-73 287.0
55 TraesCS1B01G043200 chr1D 82.051 273 45 2 7215 7483 10070163 10069891 6.860000e-56 230.0
56 TraesCS1B01G043200 chr1D 85.965 114 15 1 5911 6023 4825271 4825384 4.310000e-23 121.0
57 TraesCS1B01G043200 chr1D 95.918 49 2 0 6867 6915 4770415 4770463 7.310000e-11 80.5
58 TraesCS1B01G043200 chr5B 94.074 135 6 1 7606 7740 18076956 18077088 4.160000e-48 204.0
59 TraesCS1B01G043200 chr5B 93.478 138 7 2 7610 7747 20830559 20830424 4.160000e-48 204.0
60 TraesCS1B01G043200 chr5B 92.199 141 8 2 7612 7752 224325536 224325673 6.960000e-46 196.0
61 TraesCS1B01G043200 chr5B 76.382 199 40 7 2 195 548189065 548188869 5.610000e-17 100.0
62 TraesCS1B01G043200 chr5B 76.617 201 36 11 2 195 652823997 652824193 5.610000e-17 100.0
63 TraesCS1B01G043200 chr5B 81.818 110 13 4 8128 8236 101277693 101277590 1.570000e-12 86.1
64 TraesCS1B01G043200 chr5B 94.444 36 1 1 8080 8114 369484058 369484023 4.000000e-03 54.7
65 TraesCS1B01G043200 chr5A 94.697 132 5 1 7609 7740 508283652 508283781 4.160000e-48 204.0
66 TraesCS1B01G043200 chr2A 94.030 134 6 1 7610 7743 221201415 221201284 1.500000e-47 202.0
67 TraesCS1B01G043200 chr7B 93.382 136 7 1 7605 7740 668214062 668214195 5.380000e-47 200.0
68 TraesCS1B01G043200 chr7B 76.000 200 39 9 2 195 687959874 687959678 2.610000e-15 95.3
69 TraesCS1B01G043200 chr3D 91.781 146 7 4 7597 7740 67064769 67064911 1.930000e-46 198.0
70 TraesCS1B01G043200 chr6B 91.549 142 10 1 7603 7744 716890335 716890474 2.500000e-45 195.0
71 TraesCS1B01G043200 chr6B 76.119 201 37 11 2 195 18949871 18950067 2.610000e-15 95.3
72 TraesCS1B01G043200 chr6B 81.651 109 15 2 8128 8236 46222843 46222946 1.570000e-12 86.1
73 TraesCS1B01G043200 chr6B 81.818 110 13 4 8128 8236 512917176 512917073 1.570000e-12 86.1
74 TraesCS1B01G043200 chr6B 81.818 110 13 4 8128 8236 583112441 583112338 1.570000e-12 86.1
75 TraesCS1B01G043200 chr2B 90.000 150 12 2 7604 7752 763632610 763632463 3.240000e-44 191.0
76 TraesCS1B01G043200 chr5D 82.297 209 32 4 7260 7465 59223122 59222916 9.070000e-40 176.0
77 TraesCS1B01G043200 chr5D 74.522 157 25 5 8080 8235 319252939 319252797 4.000000e-03 54.7
78 TraesCS1B01G043200 chr6A 76.617 201 36 11 2 195 8219049 8219245 5.610000e-17 100.0
79 TraesCS1B01G043200 chr3A 76.617 201 36 11 2 195 177081336 177081532 5.610000e-17 100.0
80 TraesCS1B01G043200 chr4B 76.119 201 37 11 2 195 476877125 476877321 2.610000e-15 95.3
81 TraesCS1B01G043200 chr3B 81.416 113 19 2 8125 8236 148524499 148524388 3.380000e-14 91.6


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 TraesCS1B01G043200 chr1B 22700035 22708821 8786 False 16190.000000 16190 100.000000 1 8787 1 chr1B.!!$F1 8786
1 TraesCS1B01G043200 chr1B 7987304 7996916 9612 False 1623.000000 6599 88.607545 8 8787 11 chr1B.!!$F3 8779
2 TraesCS1B01G043200 chr1B 22701140 22706051 4911 False 810.333333 1160 83.032333 1106 6017 6 chr1B.!!$F4 4911
3 TraesCS1B01G043200 chr1B 144926617 144931987 5370 False 503.000000 1256 82.455250 1216 7580 4 chr1B.!!$F5 6364
4 TraesCS1B01G043200 chr1A 6317088 6325436 8348 False 1742.600000 5866 87.362200 314 8784 10 chr1A.!!$F2 8470
5 TraesCS1B01G043200 chr1A 86235732 86240262 4530 False 515.500000 1279 81.895500 1127 7585 4 chr1A.!!$F3 6458
6 TraesCS1B01G043200 chr1D 4838014 4839052 1038 False 1709.000000 1709 96.353000 7749 8787 1 chr1D.!!$F1 1038
7 TraesCS1B01G043200 chr1D 4820546 4827688 7142 False 1671.200000 4846 87.233100 314 7613 10 chr1D.!!$F3 7299
8 TraesCS1B01G043200 chr1D 4769091 4774948 5857 False 584.166667 953 87.385667 5427 7578 3 chr1D.!!$F2 2151
9 TraesCS1B01G043200 chr1D 90148873 90152008 3135 False 530.666667 856 81.413667 2722 7585 3 chr1D.!!$F4 4863
10 TraesCS1B01G043200 chr1D 10153606 10154339 733 True 407.000000 407 77.310000 6780 7488 1 chr1D.!!$R2 708

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
93 94 0.179111 CGTGGCATGACATCTACCGT 60.179 55.000 3.50 0.0 0.00 4.83 F
265 266 0.321653 GGGTTCACAGAAGATGGCGT 60.322 55.000 0.00 0.0 0.00 5.68 F
269 270 0.969149 TCACAGAAGATGGCGTCAGT 59.031 50.000 9.78 0.0 0.00 3.41 F
308 309 1.153046 TATTAGGCGGCCTGGTTGC 60.153 57.895 31.26 0.0 34.61 4.17 F
6391 11785 0.331278 CCAACCCTCCAGCACCATTA 59.669 55.000 0.00 0.0 0.00 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
6083 11455 6.986231 TCTTTCAGCATACGTACATTCATGAT 59.014 34.615 0.00 0.00 0.00 2.45 R
6271 11665 1.961394 ACGATATATGTGCTCCGGTGT 59.039 47.619 0.00 0.00 0.00 4.16 R
6391 11785 1.754745 TTGCAAAGAGCCTCCGACT 59.245 52.632 0.00 0.00 44.83 4.18 R
6404 11798 1.732917 CGTTGTCCAAGGCTTGCAA 59.267 52.632 21.77 17.32 0.00 4.08 R
8311 17846 0.460311 ATTCATCGACCTCACCGACC 59.540 55.000 0.00 0.00 38.97 4.79 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
75 76 2.747855 GAGGGCAAGGAAGTGGCG 60.748 66.667 0.00 0.00 44.73 5.69
76 77 3.553095 GAGGGCAAGGAAGTGGCGT 62.553 63.158 0.00 0.00 44.73 5.68
77 78 3.365265 GGGCAAGGAAGTGGCGTG 61.365 66.667 0.00 0.00 44.73 5.34
78 79 3.365265 GGCAAGGAAGTGGCGTGG 61.365 66.667 0.00 0.00 34.03 4.94
79 80 4.043200 GCAAGGAAGTGGCGTGGC 62.043 66.667 0.00 0.00 0.00 5.01
93 94 0.179111 CGTGGCATGACATCTACCGT 60.179 55.000 3.50 0.00 0.00 4.83
99 100 2.451132 CATGACATCTACCGTGTCGAC 58.549 52.381 9.11 9.11 46.89 4.20
140 141 1.493311 GAGCAACAGTTTCTCGGCG 59.507 57.895 0.00 0.00 0.00 6.46
149 150 1.302112 TTTCTCGGCGTTGGATGCA 60.302 52.632 6.85 0.00 0.00 3.96
158 159 1.605232 GCGTTGGATGCATGATGATGA 59.395 47.619 2.46 0.00 0.00 2.92
168 169 0.654160 ATGATGATGAACGTGCGCAG 59.346 50.000 12.22 7.95 0.00 5.18
179 180 2.030412 TGCGCAGATCGGTTGTGT 59.970 55.556 5.66 0.00 38.94 3.72
195 196 3.712881 GTTGTCTGGCGTCGTGGC 61.713 66.667 0.00 0.00 45.12 5.01
252 253 5.218959 TGATCTATCCTGAAGATGGGTTCA 58.781 41.667 0.00 0.00 36.33 3.18
259 260 3.008375 CCTGAAGATGGGTTCACAGAAGA 59.992 47.826 0.00 0.00 34.88 2.87
260 261 4.324099 CCTGAAGATGGGTTCACAGAAGAT 60.324 45.833 0.00 0.00 34.88 2.40
265 266 0.321653 GGGTTCACAGAAGATGGCGT 60.322 55.000 0.00 0.00 0.00 5.68
268 269 1.728971 GTTCACAGAAGATGGCGTCAG 59.271 52.381 9.78 0.00 0.00 3.51
269 270 0.969149 TCACAGAAGATGGCGTCAGT 59.031 50.000 9.78 0.00 0.00 3.41
280 281 1.279840 GCGTCAGTGGTTTGTGCTC 59.720 57.895 0.00 0.00 0.00 4.26
294 295 1.830847 TGCTCCCGGCTCGCTATTA 60.831 57.895 0.00 0.00 42.39 0.98
308 309 1.153046 TATTAGGCGGCCTGGTTGC 60.153 57.895 31.26 0.00 34.61 4.17
345 1352 7.683704 GCGATGGAAGAAAACTGATACTACCTA 60.684 40.741 0.00 0.00 0.00 3.08
544 1551 7.448748 AAACCTACAAGCGATTCTACAAAAT 57.551 32.000 0.00 0.00 0.00 1.82
547 1554 6.093633 ACCTACAAGCGATTCTACAAAATTCC 59.906 38.462 0.00 0.00 0.00 3.01
549 1556 6.325919 ACAAGCGATTCTACAAAATTCCAA 57.674 33.333 0.00 0.00 0.00 3.53
550 1557 6.924111 ACAAGCGATTCTACAAAATTCCAAT 58.076 32.000 0.00 0.00 0.00 3.16
605 1614 7.915397 CCGAATTGGAATTTAGGTTATTCACTG 59.085 37.037 0.00 0.00 42.00 3.66
700 1709 5.775701 TCCCTCCAATCCGTTTTAAATTTCA 59.224 36.000 0.00 0.00 0.00 2.69
799 1808 1.933519 GTAGAGCAGACGCGTACGC 60.934 63.158 29.83 29.83 45.53 4.42
859 1882 2.649034 GAGTGGTCGAGCGGTTCA 59.351 61.111 10.46 0.00 0.00 3.18
860 1883 1.733399 GAGTGGTCGAGCGGTTCAC 60.733 63.158 10.46 1.89 0.00 3.18
896 1924 7.578310 AGTTGAGTAGTTCACACTTGTAGTA 57.422 36.000 0.00 0.00 34.94 1.82
929 1957 3.244249 GGCCTCTTCTGACACAGTTTAGT 60.244 47.826 0.00 0.00 32.61 2.24
6083 11455 2.418197 GGCAAAGATACGGCTACACAGA 60.418 50.000 0.00 0.00 0.00 3.41
6391 11785 0.331278 CCAACCCTCCAGCACCATTA 59.669 55.000 0.00 0.00 0.00 1.90
6404 11798 1.482593 CACCATTAGTCGGAGGCTCTT 59.517 52.381 15.23 0.78 40.46 2.85
6525 12180 8.970859 TGGGAAATTACATGTTTTTGTTGAAT 57.029 26.923 2.30 0.00 0.00 2.57
6696 12351 0.320247 CTCGCAGCAAGGTCTCTGTT 60.320 55.000 0.00 0.00 33.09 3.16
6986 16479 1.142314 CGAATTGCAGGGCATTGGG 59.858 57.895 0.00 0.00 38.76 4.12
7007 16500 2.456000 GAGCTCGTCGATTTTGCCA 58.544 52.632 0.00 0.00 0.00 4.92
7066 16559 2.038033 CCTGGTCTTCGAACCCAAGTTA 59.962 50.000 11.78 0.00 38.65 2.24
7192 16691 8.018520 GGTAAGTCTGTGATAGTTAGATCATCG 58.981 40.741 0.00 0.00 38.11 3.84
7621 17155 7.989947 AATGATTTAAGTAGTACTCCCTCCA 57.010 36.000 2.58 0.70 0.00 3.86
7625 17159 5.745988 TTAAGTAGTACTCCCTCCATCCT 57.254 43.478 2.58 0.00 0.00 3.24
7679 17213 9.845214 AGGGGATGTATCTAGATGTATTTTAGT 57.155 33.333 15.79 0.00 0.00 2.24
7704 17238 4.526970 TCTAGATGCATCCCTTTTTGTCC 58.473 43.478 23.06 0.00 0.00 4.02
7710 17244 5.815233 TGCATCCCTTTTTGTCCATTTTA 57.185 34.783 0.00 0.00 0.00 1.52
7931 17465 8.405531 GCTTAACATCAATTGCACTCCTTATAA 58.594 33.333 0.00 0.00 0.00 0.98
8139 17673 5.781818 TCCCAGATTCATATGCATCTAGACA 59.218 40.000 16.13 0.76 0.00 3.41
8209 17743 8.617809 AGTCAATAGTGAAAAAGCTAAAAACGA 58.382 29.630 0.00 0.00 34.87 3.85
8311 17846 0.946221 GAGTCCTCACTGTGGTTGCG 60.946 60.000 8.11 0.00 30.63 4.85
8333 17868 0.175760 CGGTGAGGTCGATGAATGGT 59.824 55.000 0.00 0.00 0.00 3.55
8357 17893 2.280552 GGTAGACGGCTCCACACCA 61.281 63.158 0.00 0.00 0.00 4.17
8370 17906 1.620589 ACACCAGAGGGCCCATCAT 60.621 57.895 27.56 1.40 37.90 2.45
8430 17966 2.249413 CTCCTTGATGTGCGGCTCCT 62.249 60.000 0.00 0.00 0.00 3.69
8466 18003 4.056125 CGGCAGTGCTCCTCGACA 62.056 66.667 16.11 0.00 0.00 4.35
8559 18096 1.320344 ATGTAGTCCTCTTCGGCGCA 61.320 55.000 10.83 0.00 0.00 6.09
8568 18105 3.302347 CTTCGGCGCACTCCCTCTT 62.302 63.158 10.83 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.038892 AGAACGGCACATAACGTCGT 60.039 50.000 0.00 0.00 43.31 4.34
1 2 0.638746 GAGAACGGCACATAACGTCG 59.361 55.000 0.00 0.00 43.31 5.12
2 3 0.997196 GGAGAACGGCACATAACGTC 59.003 55.000 0.00 0.00 43.31 4.34
3 4 0.390735 GGGAGAACGGCACATAACGT 60.391 55.000 0.00 0.00 46.48 3.99
4 5 0.108329 AGGGAGAACGGCACATAACG 60.108 55.000 0.00 0.00 0.00 3.18
5 6 1.653151 GAGGGAGAACGGCACATAAC 58.347 55.000 0.00 0.00 0.00 1.89
6 7 0.539986 GGAGGGAGAACGGCACATAA 59.460 55.000 0.00 0.00 0.00 1.90
13 14 3.622514 CCTCAGGAGGGAGAACGG 58.377 66.667 7.48 0.00 44.87 4.44
75 76 1.290203 CACGGTAGATGTCATGCCAC 58.710 55.000 0.00 0.00 0.00 5.01
76 77 0.901827 ACACGGTAGATGTCATGCCA 59.098 50.000 0.00 0.00 0.00 4.92
77 78 1.571919 GACACGGTAGATGTCATGCC 58.428 55.000 0.00 0.00 44.87 4.40
78 79 1.200483 CGACACGGTAGATGTCATGC 58.800 55.000 6.01 0.00 45.64 4.06
79 80 2.451132 GTCGACACGGTAGATGTCATG 58.549 52.381 11.55 0.00 45.64 3.07
99 100 2.805353 CGCCAAGACCTGTCGTCG 60.805 66.667 0.00 0.00 46.92 5.12
130 131 1.134694 GCATCCAACGCCGAGAAAC 59.865 57.895 0.00 0.00 0.00 2.78
132 133 1.078497 ATGCATCCAACGCCGAGAA 60.078 52.632 0.00 0.00 0.00 2.87
140 141 3.065786 ACGTTCATCATCATGCATCCAAC 59.934 43.478 0.00 0.00 0.00 3.77
149 150 0.654160 CTGCGCACGTTCATCATCAT 59.346 50.000 5.66 0.00 0.00 2.45
158 159 2.357034 AACCGATCTGCGCACGTT 60.357 55.556 5.66 3.54 39.11 3.99
168 169 0.517316 GCCAGACAACACAACCGATC 59.483 55.000 0.00 0.00 0.00 3.69
201 202 1.601759 CCTTGTCAGGCCAGGTGTG 60.602 63.158 5.01 0.00 31.53 3.82
207 208 1.391157 GCAAACACCTTGTCAGGCCA 61.391 55.000 5.01 0.00 45.56 5.36
252 253 0.036952 CCACTGACGCCATCTTCTGT 60.037 55.000 0.00 0.00 0.00 3.41
259 260 1.795170 GCACAAACCACTGACGCCAT 61.795 55.000 0.00 0.00 0.00 4.40
260 261 2.477176 GCACAAACCACTGACGCCA 61.477 57.895 0.00 0.00 0.00 5.69
265 266 1.227823 CGGGAGCACAAACCACTGA 60.228 57.895 0.00 0.00 0.00 3.41
268 269 3.670377 GCCGGGAGCACAAACCAC 61.670 66.667 2.18 0.00 42.97 4.16
280 281 2.048127 GCCTAATAGCGAGCCGGG 60.048 66.667 2.18 0.00 0.00 5.73
308 309 3.891400 CCATCGCCAATGTGCCCG 61.891 66.667 0.00 0.00 33.13 6.13
605 1614 6.932356 TCATTTCATAGCAGGAGATTCAAC 57.068 37.500 0.00 0.00 0.00 3.18
733 1742 6.998802 ACTCCCTCTGATCCTAAATAATTCG 58.001 40.000 0.00 0.00 0.00 3.34
832 1841 3.243434 CGCTCGACCACTCCAACTATATT 60.243 47.826 0.00 0.00 0.00 1.28
859 1882 2.888594 ACTCAACTATATGCGTTGCGT 58.111 42.857 12.36 10.46 41.05 5.24
860 1883 4.042398 ACTACTCAACTATATGCGTTGCG 58.958 43.478 12.36 9.98 41.05 4.85
861 1884 5.518847 TGAACTACTCAACTATATGCGTTGC 59.481 40.000 12.36 0.00 41.05 4.17
862 1885 6.530181 TGTGAACTACTCAACTATATGCGTTG 59.470 38.462 11.41 11.41 42.27 4.10
863 1886 6.530534 GTGTGAACTACTCAACTATATGCGTT 59.469 38.462 0.00 0.00 35.22 4.84
896 1924 3.330701 TCAGAAGAGGCCACTTGGTTTAT 59.669 43.478 20.95 0.00 37.57 1.40
6083 11455 6.986231 TCTTTCAGCATACGTACATTCATGAT 59.014 34.615 0.00 0.00 0.00 2.45
6271 11665 1.961394 ACGATATATGTGCTCCGGTGT 59.039 47.619 0.00 0.00 0.00 4.16
6391 11785 1.754745 TTGCAAAGAGCCTCCGACT 59.245 52.632 0.00 0.00 44.83 4.18
6404 11798 1.732917 CGTTGTCCAAGGCTTGCAA 59.267 52.632 21.77 17.32 0.00 4.08
6525 12180 2.397597 TGTGCCTCCTGCTCATACATA 58.602 47.619 0.00 0.00 38.48 2.29
6755 12413 2.640184 GAATTACCCGGCTACTTTGCT 58.360 47.619 0.00 0.00 0.00 3.91
7039 16532 1.553706 GTTCGAAGACCAGGTAGGGA 58.446 55.000 0.00 0.00 43.89 4.20
7066 16559 2.230508 CTGCTGCACATTGGATTTGTCT 59.769 45.455 0.00 0.00 0.00 3.41
7192 16691 1.539388 TGGAACCGTGCATGATCAAAC 59.461 47.619 7.72 0.00 0.00 2.93
7474 16991 8.325421 TCCGTTCATAGTTGCAAATTTAGTTA 57.675 30.769 4.05 0.00 0.00 2.24
7621 17155 9.246670 TCATTTTGATGACAAGTATTTCAGGAT 57.753 29.630 0.00 0.00 37.32 3.24
7653 17187 9.845214 ACTAAAATACATCTAGATACATCCCCT 57.155 33.333 4.54 0.00 0.00 4.79
7679 17213 5.324409 ACAAAAAGGGATGCATCTAGAACA 58.676 37.500 25.28 0.00 0.00 3.18
7704 17238 8.785101 CGTCGGAAAATACTTGTCATTAAAATG 58.215 33.333 0.00 0.00 37.75 2.32
7710 17244 4.571919 TCCGTCGGAAAATACTTGTCATT 58.428 39.130 12.68 0.00 0.00 2.57
7854 17388 7.790027 AGATATGCCCATAGAGCAAAGTATAG 58.210 38.462 0.00 0.00 44.83 1.31
8117 17651 9.833917 AATATGTCTAGATGCATATGAATCTGG 57.166 33.333 29.65 27.13 40.58 3.86
8209 17743 7.226059 ACTCCCTCCATTCCAAAATATAAGT 57.774 36.000 0.00 0.00 0.00 2.24
8311 17846 0.460311 ATTCATCGACCTCACCGACC 59.540 55.000 0.00 0.00 38.97 4.79
8357 17893 2.446848 CGGTGATGATGGGCCCTCT 61.447 63.158 25.70 10.73 0.00 3.69
8430 17966 1.008875 GCACGTGAAGATGAGACGCA 61.009 55.000 22.23 0.00 36.56 5.24
8559 18096 1.048601 TTTGCGTCTCAAGAGGGAGT 58.951 50.000 0.00 0.00 35.84 3.85
8689 18226 1.734137 GAGTCGAGGCGCTTCCATA 59.266 57.895 14.49 0.00 37.29 2.74


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

AutoCloner maintained by Alex Coulton.