Multiple sequence alignment - TraesCS5D01G474500

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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 TraesCS5D01G474500 chr5D 100.000 4166 0 0 1 4166 514456657 514460822 0.000000e+00 7694.0
1 TraesCS5D01G474500 chr5D 88.519 270 30 1 1594 1862 514519494 514519763 4.020000e-85 326.0
2 TraesCS5D01G474500 chr5D 87.845 181 19 2 3199 3378 514517173 514517351 4.220000e-50 209.0
3 TraesCS5D01G474500 chr5D 82.530 166 15 3 3546 3697 514517565 514517730 2.610000e-27 134.0
4 TraesCS5D01G474500 chr5D 91.525 59 5 0 3110 3168 514432801 514432743 9.600000e-12 82.4
5 TraesCS5D01G474500 chr5A 93.398 3908 143 25 176 4078 642654089 642657886 0.000000e+00 5681.0
6 TraesCS5D01G474500 chr5A 93.220 177 9 2 1 177 642653148 642653321 1.490000e-64 257.0
7 TraesCS5D01G474500 chr5A 94.681 94 5 0 4073 4166 642693699 642693792 3.360000e-31 147.0
8 TraesCS5D01G474500 chr5A 83.673 147 14 4 3464 3603 642713796 642713939 3.380000e-26 130.0
9 TraesCS5D01G474500 chr5A 90.625 96 9 0 1594 1689 642537742 642537837 1.220000e-25 128.0
10 TraesCS5D01G474500 chr5A 92.222 90 7 0 3291 3380 642713599 642713688 1.220000e-25 128.0
11 TraesCS5D01G474500 chr5A 81.481 162 15 5 177 323 642647473 642647634 7.320000e-23 119.0
12 TraesCS5D01G474500 chr5A 83.594 128 10 6 3474 3596 643025116 643025237 4.400000e-20 110.0
13 TraesCS5D01G474500 chr5A 80.000 125 12 7 3482 3599 643201830 643201948 3.450000e-11 80.5
14 TraesCS5D01G474500 chr5B 94.238 1805 65 17 176 1978 646476282 646478049 0.000000e+00 2721.0
15 TraesCS5D01G474500 chr5B 92.895 943 51 9 917 1858 645545948 645545021 0.000000e+00 1356.0
16 TraesCS5D01G474500 chr5B 90.010 1001 55 8 1144 2142 645942541 645941584 0.000000e+00 1253.0
17 TraesCS5D01G474500 chr5B 94.645 803 37 6 1969 2768 646478157 646478956 0.000000e+00 1240.0
18 TraesCS5D01G474500 chr5B 88.807 813 79 7 353 1159 645945397 645944591 0.000000e+00 987.0
19 TraesCS5D01G474500 chr5B 88.107 824 45 21 2866 3666 646478958 646479751 0.000000e+00 929.0
20 TraesCS5D01G474500 chr5B 85.660 530 44 12 3652 4166 646479803 646480315 2.850000e-146 529.0
21 TraesCS5D01G474500 chr5B 85.309 388 37 7 1595 1977 646631029 646631401 2.350000e-102 383.0
22 TraesCS5D01G474500 chr5B 95.041 242 9 2 619 857 645546223 645545982 1.090000e-100 377.0
23 TraesCS5D01G474500 chr5B 93.625 251 14 2 2312 2561 645924357 645924108 1.410000e-99 374.0
24 TraesCS5D01G474500 chr5B 94.091 220 11 2 2554 2772 645923827 645923609 2.400000e-87 333.0
25 TraesCS5D01G474500 chr5B 93.785 177 11 0 1 177 646475326 646475502 2.470000e-67 267.0
26 TraesCS5D01G474500 chr5B 83.548 310 24 7 3473 3768 645544761 645544465 8.880000e-67 265.0
27 TraesCS5D01G474500 chr5B 96.296 162 3 3 1856 2017 645544927 645544769 3.190000e-66 263.0
28 TraesCS5D01G474500 chr5B 92.308 143 11 0 2127 2269 645924495 645924353 1.960000e-48 204.0
29 TraesCS5D01G474500 chr5B 86.486 185 25 0 1594 1778 645989098 645988914 1.960000e-48 204.0
30 TraesCS5D01G474500 chr5B 97.849 93 2 0 492 584 645546319 645546227 1.200000e-35 161.0
31 TraesCS5D01G474500 chr5B 95.000 80 4 0 3803 3882 647347484 647347563 4.370000e-25 126.0
32 TraesCS5D01G474500 chr5B 96.825 63 2 0 2948 3010 645923599 645923537 5.700000e-19 106.0
33 TraesCS5D01G474500 chr5B 95.455 44 2 0 2017 2060 435766679 435766636 2.080000e-08 71.3
34 TraesCS5D01G474500 chr5B 100.000 31 0 0 3109 3139 646268671 646268701 1.620000e-04 58.4


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 TraesCS5D01G474500 chr5D 514456657 514460822 4165 False 7694.00 7694 100.00000 1 4166 1 chr5D.!!$F1 4165
1 TraesCS5D01G474500 chr5D 514517173 514519763 2590 False 223.00 326 86.29800 1594 3697 3 chr5D.!!$F2 2103
2 TraesCS5D01G474500 chr5A 642653148 642657886 4738 False 2969.00 5681 93.30900 1 4078 2 chr5A.!!$F6 4077
3 TraesCS5D01G474500 chr5B 646475326 646480315 4989 False 1137.20 2721 91.28700 1 4166 5 chr5B.!!$F4 4165
4 TraesCS5D01G474500 chr5B 645941584 645945397 3813 True 1120.00 1253 89.40850 353 2142 2 chr5B.!!$R5 1789
5 TraesCS5D01G474500 chr5B 645544465 645546319 1854 True 484.40 1356 93.12580 492 3768 5 chr5B.!!$R3 3276
6 TraesCS5D01G474500 chr5B 645923537 645924495 958 True 254.25 374 94.21225 2127 3010 4 chr5B.!!$R4 883

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
738 1537 1.559682 ACTCAACTTCCCATGCGGTAT 59.440 47.619 0.00 0.0 0.00 2.73 F
1096 1907 0.248907 CCAGCGATATCAACGACCGT 60.249 55.000 3.12 0.0 0.00 4.83 F
2649 6053 1.213013 GGTCGCGTCTGACATGACT 59.787 57.895 21.37 0.0 40.72 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2649 6053 0.249531 TGTCGTCGCCTAGTTTTGCA 60.250 50.0 0.00 0.0 0.00 4.08 R
2676 6080 1.201343 GTATTGTCTCGAGCGCCTTC 58.799 55.0 7.81 0.0 0.00 3.46 R
3755 7250 0.324943 CACGGAGGGGTGTTTGATCT 59.675 55.0 0.00 0.0 33.24 2.75 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
36 37 7.352739 GTTTATCGAGCAAATATGATTTCGGT 58.647 34.615 0.00 0.00 31.58 4.69
121 122 7.454260 AGAAATGTAAGCTAACCTTCCAAAG 57.546 36.000 0.00 0.00 34.95 2.77
179 180 9.788889 TCTGCAATAATCATCTATCATGTTCTT 57.211 29.630 0.00 0.00 0.00 2.52
226 1011 2.733945 CCCAAACCAAACTGGCCG 59.266 61.111 0.00 0.00 42.67 6.13
246 1031 2.094182 CGTAAGCAGGTCTAGGCAGAAA 60.094 50.000 0.00 0.00 30.85 2.52
332 1117 8.255905 ACTGTACAGTAAATCATAGTGTAACCC 58.744 37.037 26.91 0.00 40.43 4.11
589 1386 3.700538 TGCCCATGCTTTGAGTTCTTAT 58.299 40.909 0.00 0.00 38.71 1.73
590 1387 3.696051 TGCCCATGCTTTGAGTTCTTATC 59.304 43.478 0.00 0.00 38.71 1.75
592 1389 4.400567 GCCCATGCTTTGAGTTCTTATCTT 59.599 41.667 0.00 0.00 33.53 2.40
593 1390 5.449725 GCCCATGCTTTGAGTTCTTATCTTC 60.450 44.000 0.00 0.00 33.53 2.87
630 1427 8.407832 CAAAAATCATCTACCATGTTAGCATCA 58.592 33.333 0.00 0.00 31.99 3.07
738 1537 1.559682 ACTCAACTTCCCATGCGGTAT 59.440 47.619 0.00 0.00 0.00 2.73
750 1550 2.580601 GCGGTATGGGCTATCCGGT 61.581 63.158 18.05 0.00 42.71 5.28
804 1604 4.211794 CCTGTATTTTGCTTTTGCCACAAG 59.788 41.667 0.00 0.00 46.87 3.16
932 1743 6.382570 ACTCTGTGCTCCTAATTACTTCTGAT 59.617 38.462 0.00 0.00 0.00 2.90
986 1797 2.104792 ACCAGCAGTTAACAGAGCTTCA 59.895 45.455 14.92 0.00 34.61 3.02
1032 1843 4.394712 CCGTTCTCCGCTGGCCTT 62.395 66.667 3.32 0.00 34.38 4.35
1089 1900 0.250038 GCAGGCTCCAGCGATATCAA 60.250 55.000 3.12 0.00 43.26 2.57
1096 1907 0.248907 CCAGCGATATCAACGACCGT 60.249 55.000 3.12 0.00 0.00 4.83
1159 4035 3.200385 AGTGGTAGACTCTGTATCGGTCT 59.800 47.826 0.00 0.00 42.13 3.85
1160 4036 3.560896 GTGGTAGACTCTGTATCGGTCTC 59.439 52.174 0.00 0.00 40.29 3.36
1161 4037 3.140623 GGTAGACTCTGTATCGGTCTCC 58.859 54.545 0.00 0.00 40.29 3.71
1186 4065 5.193728 TCCTTAATTAGGTGGCCTTTCTGAT 59.806 40.000 3.32 0.00 45.03 2.90
1266 4146 2.802792 CATGGATGGCTTGGCACG 59.197 61.111 0.00 0.00 0.00 5.34
1574 4457 3.131400 AGAGGTGAGTAAAATCGCTCCTC 59.869 47.826 0.00 0.00 43.20 3.71
1637 4520 5.095490 GCATACAAGTGCATTTTACCTCAC 58.905 41.667 0.00 0.00 44.43 3.51
1646 4529 6.595716 AGTGCATTTTACCTCACAGAATACTC 59.404 38.462 0.00 0.00 32.25 2.59
1806 4689 5.582269 CGGTGAGTTGACATCAGTTCATTAT 59.418 40.000 2.10 0.00 0.00 1.28
1950 4929 5.832539 TCTCCCTTGTTTTCATCTCTCTT 57.167 39.130 0.00 0.00 0.00 2.85
1951 4930 5.799213 TCTCCCTTGTTTTCATCTCTCTTC 58.201 41.667 0.00 0.00 0.00 2.87
1958 4937 3.902881 TTTCATCTCTCTTCCTGCCTC 57.097 47.619 0.00 0.00 0.00 4.70
2190 5287 7.993238 CGTAATCGGTATCAAATATGCTTTG 57.007 36.000 0.00 0.00 0.00 2.77
2191 5288 7.572759 CGTAATCGGTATCAAATATGCTTTGT 58.427 34.615 0.00 0.00 0.00 2.83
2192 5289 7.530525 CGTAATCGGTATCAAATATGCTTTGTG 59.469 37.037 0.00 0.00 0.00 3.33
2193 5290 5.168526 TCGGTATCAAATATGCTTTGTGC 57.831 39.130 0.00 0.00 43.25 4.57
2194 5291 4.881273 TCGGTATCAAATATGCTTTGTGCT 59.119 37.500 0.00 0.00 43.37 4.40
2195 5292 5.356751 TCGGTATCAAATATGCTTTGTGCTT 59.643 36.000 0.00 0.00 43.37 3.91
2196 5293 5.456497 CGGTATCAAATATGCTTTGTGCTTG 59.544 40.000 0.00 0.00 43.37 4.01
2197 5294 5.232838 GGTATCAAATATGCTTTGTGCTTGC 59.767 40.000 0.00 0.00 43.37 4.01
2198 5295 3.587923 TCAAATATGCTTTGTGCTTGCC 58.412 40.909 0.00 0.00 43.37 4.52
2199 5296 3.258872 TCAAATATGCTTTGTGCTTGCCT 59.741 39.130 0.00 0.00 43.37 4.75
2200 5297 4.462132 TCAAATATGCTTTGTGCTTGCCTA 59.538 37.500 0.00 0.00 43.37 3.93
2201 5298 5.127519 TCAAATATGCTTTGTGCTTGCCTAT 59.872 36.000 0.00 0.00 43.37 2.57
2202 5299 5.603170 AATATGCTTTGTGCTTGCCTATT 57.397 34.783 0.00 0.00 43.37 1.73
2203 5300 6.713762 AATATGCTTTGTGCTTGCCTATTA 57.286 33.333 0.00 0.00 43.37 0.98
2317 5432 8.293157 TCTTAGAAGCGTCTCTGTTATATGATG 58.707 37.037 5.11 0.00 35.12 3.07
2542 5659 4.213059 GCAGCCTAGAATAAGCACATCTTC 59.787 45.833 0.00 0.00 36.25 2.87
2561 5965 4.456911 TCTTCATTAAAGTGCTGCTCCTTG 59.543 41.667 0.00 0.00 36.31 3.61
2649 6053 1.213013 GGTCGCGTCTGACATGACT 59.787 57.895 21.37 0.00 40.72 3.41
2754 6159 8.038944 GCATTGGCTAAATTCCATATGAATCAT 58.961 33.333 3.65 0.00 38.79 2.45
2850 6255 3.129300 CGGGCTCGCTATCTCCAA 58.871 61.111 0.00 0.00 0.00 3.53
2851 6256 1.441729 CGGGCTCGCTATCTCCAAA 59.558 57.895 0.00 0.00 0.00 3.28
2852 6257 0.179084 CGGGCTCGCTATCTCCAAAA 60.179 55.000 0.00 0.00 0.00 2.44
2853 6258 1.742411 CGGGCTCGCTATCTCCAAAAA 60.742 52.381 0.00 0.00 0.00 1.94
2914 6319 5.523438 TGGAGTTTTCGCTTTGGTTTTAT 57.477 34.783 0.00 0.00 0.00 1.40
3077 6482 7.819900 GTCCTTCATATGGACCAGATGTATTAC 59.180 40.741 24.74 16.30 46.01 1.89
3078 6483 7.512402 TCCTTCATATGGACCAGATGTATTACA 59.488 37.037 24.74 5.54 35.01 2.41
3169 6583 0.895100 TGGCCTGTCCATTTGAGTGC 60.895 55.000 3.32 0.00 40.72 4.40
3175 6589 2.417933 CTGTCCATTTGAGTGCTACTGC 59.582 50.000 0.00 0.00 40.20 4.40
3193 6607 2.737376 AACCGAACCGAAGCGAGC 60.737 61.111 0.00 0.00 0.00 5.03
3240 6654 3.190535 AGAAACAAGGTTGTGTCACACAC 59.809 43.478 11.09 6.05 45.76 3.82
3253 6667 5.168526 TGTCACACACAATTAAGCTCAAC 57.831 39.130 0.00 0.00 29.30 3.18
3255 6669 5.299028 TGTCACACACAATTAAGCTCAACAT 59.701 36.000 0.00 0.00 29.30 2.71
3256 6670 6.484977 TGTCACACACAATTAAGCTCAACATA 59.515 34.615 0.00 0.00 29.30 2.29
3283 6697 0.394938 TCCTTTGCGTCAGGCTTGTA 59.605 50.000 0.00 0.00 44.05 2.41
3284 6698 1.202710 TCCTTTGCGTCAGGCTTGTAA 60.203 47.619 0.00 0.00 44.05 2.41
3296 6710 1.343506 GCTTGTAACGTACGGAGTGG 58.656 55.000 21.06 6.17 45.73 4.00
3339 6753 3.075148 GGAGGTTGGAGAAAGTTGTAGC 58.925 50.000 0.00 0.00 0.00 3.58
3343 6757 3.477530 GTTGGAGAAAGTTGTAGCCTGT 58.522 45.455 0.00 0.00 0.00 4.00
3349 6763 4.833390 AGAAAGTTGTAGCCTGTATGGAC 58.167 43.478 0.00 0.00 38.35 4.02
3407 6821 4.300189 TCATTTGGTTCAACCGAAAGTG 57.700 40.909 13.59 8.42 44.37 3.16
3411 6825 0.030235 GGTTCAACCGAAAGTGCCAC 59.970 55.000 0.00 0.00 31.43 5.01
3416 6830 2.159310 TCAACCGAAAGTGCCACAAAAG 60.159 45.455 0.00 0.00 0.00 2.27
3435 6850 6.254804 ACAAAAGAACCAAAGTTAACGAATGC 59.745 34.615 0.00 0.00 35.94 3.56
3471 6886 2.577700 TGTACAAGTCCGCCAAATGTT 58.422 42.857 0.00 0.00 0.00 2.71
3550 6965 9.531942 TTGAATTAGCATGTTAGGCATTTTATG 57.468 29.630 0.00 0.00 35.19 1.90
3658 7153 5.466819 ACAGATCGTACGAGTGATTCAAAA 58.533 37.500 27.99 2.79 0.00 2.44
3721 7216 7.518848 GCAATATCTATCTTTGAACATGACGCA 60.519 37.037 0.00 0.00 0.00 5.24
3727 7222 3.876914 TCTTTGAACATGACGCAGAAAGT 59.123 39.130 0.00 0.00 0.00 2.66
3912 7408 2.365293 AGCGCCAGGAAACAAGAAAATT 59.635 40.909 2.29 0.00 0.00 1.82
4021 7531 2.002586 CAACACCTCAGGTATTCTGCG 58.997 52.381 0.00 0.00 43.06 5.18
4069 7579 5.768980 ATGGATATCAGGTATTCAGGTGG 57.231 43.478 4.83 0.00 31.78 4.61
4087 7597 6.012858 TCAGGTGGTGTTATATCTCCAAACTT 60.013 38.462 6.24 0.00 33.66 2.66
4103 7613 6.379386 TCCAAACTTGAGATATATAGCGTCG 58.621 40.000 0.00 0.00 0.00 5.12
4121 7631 3.673052 CGTCGGAACCCACGAACTAAATA 60.673 47.826 5.14 0.00 42.55 1.40
4124 7634 4.704540 TCGGAACCCACGAACTAAATACTA 59.295 41.667 0.00 0.00 37.42 1.82
4142 7652 3.240302 ACTATTGGTATCGAAGGAGGGG 58.760 50.000 0.00 0.00 0.00 4.79
4144 7654 2.257391 TTGGTATCGAAGGAGGGGAA 57.743 50.000 0.00 0.00 0.00 3.97
4159 7669 4.651045 GGAGGGGAAATGTATTGCAGAAAT 59.349 41.667 0.00 0.00 0.00 2.17
4160 7670 5.221322 GGAGGGGAAATGTATTGCAGAAATC 60.221 44.000 0.00 0.00 0.00 2.17
4161 7671 5.271598 AGGGGAAATGTATTGCAGAAATCA 58.728 37.500 0.00 0.00 0.00 2.57
4162 7672 5.361857 AGGGGAAATGTATTGCAGAAATCAG 59.638 40.000 0.00 0.00 0.00 2.90
4163 7673 5.360714 GGGGAAATGTATTGCAGAAATCAGA 59.639 40.000 0.00 0.00 0.00 3.27
4165 7675 7.418254 GGGGAAATGTATTGCAGAAATCAGATT 60.418 37.037 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.490962 AAATCATATTTGCTCGATAAACCGA 57.509 32.000 0.00 0.00 37.03 4.69
10 11 6.797033 CCGAAATCATATTTGCTCGATAAACC 59.203 38.462 0.00 0.00 0.00 3.27
36 37 4.113815 CCGGGCCATGAAGCAGGA 62.114 66.667 4.39 0.00 35.01 3.86
182 183 9.490379 GGTATTTCTCAGAGAAGTTTTGTTAGA 57.510 33.333 13.03 0.00 35.37 2.10
183 184 8.722394 GGGTATTTCTCAGAGAAGTTTTGTTAG 58.278 37.037 13.03 0.00 35.37 2.34
197 982 3.449746 TGGTTTGGGGGTATTTCTCAG 57.550 47.619 0.00 0.00 0.00 3.35
226 1011 3.611766 TTTCTGCCTAGACCTGCTTAC 57.388 47.619 0.00 0.00 31.21 2.34
246 1031 9.933723 AAAGAAATTGCAGCTATCTTGTTATTT 57.066 25.926 6.82 0.00 31.14 1.40
307 1092 8.475639 AGGGTTACACTATGATTTACTGTACAG 58.524 37.037 21.44 21.44 0.00 2.74
308 1093 8.255206 CAGGGTTACACTATGATTTACTGTACA 58.745 37.037 0.00 0.00 0.00 2.90
309 1094 8.255905 ACAGGGTTACACTATGATTTACTGTAC 58.744 37.037 0.00 0.00 33.10 2.90
589 1386 9.458727 AGATGATTTTTGCAGAAGAATAGAAGA 57.541 29.630 0.00 0.00 0.00 2.87
592 1389 9.113838 GGTAGATGATTTTTGCAGAAGAATAGA 57.886 33.333 0.00 0.00 0.00 1.98
593 1390 8.896744 TGGTAGATGATTTTTGCAGAAGAATAG 58.103 33.333 0.00 0.00 0.00 1.73
630 1427 4.018484 AGAAAGAACTGCATCTTGCTCT 57.982 40.909 4.90 2.43 40.65 4.09
673 1472 5.579119 TGAACTGCATGTTTACACGGTATAG 59.421 40.000 0.00 0.00 39.30 1.31
704 1503 0.747852 TTGAGTCCGTGTACTGTGCA 59.252 50.000 0.00 0.00 0.00 4.57
738 1537 0.762842 ACATAGCACCGGATAGCCCA 60.763 55.000 9.46 0.37 34.14 5.36
804 1604 4.535526 ATTGGTTATTGGGCAGTCAAAC 57.464 40.909 0.00 0.00 0.00 2.93
932 1743 2.851263 AATGGTGCTGTCTACGGAAA 57.149 45.000 0.00 0.00 0.00 3.13
986 1797 1.067295 TGCCATGGAAGAGGAGTTGT 58.933 50.000 18.40 0.00 0.00 3.32
1032 1843 1.110518 GCGGAAACCCAAGGGAAACA 61.111 55.000 13.15 0.00 38.96 2.83
1089 1900 0.033504 AAATGAGAGTGCACGGTCGT 59.966 50.000 12.01 10.61 0.00 4.34
1096 1907 2.290450 TGCCTGATGAAATGAGAGTGCA 60.290 45.455 0.00 0.00 23.63 4.57
1177 4056 5.259632 AGACAATTCCTTCCATCAGAAAGG 58.740 41.667 0.00 0.00 32.88 3.11
1186 4065 5.248477 AGCTACAGTAAGACAATTCCTTCCA 59.752 40.000 0.00 0.00 0.00 3.53
1464 4347 5.728471 AGATGATGTTCAGTACAGTTCCAG 58.272 41.667 0.00 0.00 40.83 3.86
1637 4520 4.135306 AGCATGGCATGAAGAGTATTCTG 58.865 43.478 30.69 1.27 32.79 3.02
1646 4529 2.159282 GGAAGACAAGCATGGCATGAAG 60.159 50.000 30.69 19.69 36.86 3.02
1958 4937 2.293318 TAGTCAGCTGTGCAGGGGG 61.293 63.158 14.67 0.00 0.00 5.40
2201 5298 8.987890 GCAGCCTGAAACAAGATTTTTAAATAA 58.012 29.630 0.00 0.00 0.00 1.40
2202 5299 7.328249 CGCAGCCTGAAACAAGATTTTTAAATA 59.672 33.333 0.00 0.00 0.00 1.40
2203 5300 6.146021 CGCAGCCTGAAACAAGATTTTTAAAT 59.854 34.615 0.00 0.00 0.00 1.40
2272 5387 7.553334 TCTAAGAATAGAAACGGCACATAGTT 58.447 34.615 0.00 0.00 35.21 2.24
2317 5432 8.336801 ACTGTACCCAAAAATTATTGTCTCTC 57.663 34.615 0.00 0.00 0.00 3.20
2439 5556 1.874299 ATCCAATCACCCCGGCCTTT 61.874 55.000 0.00 0.00 0.00 3.11
2542 5659 4.510038 AACAAGGAGCAGCACTTTAATG 57.490 40.909 0.00 0.00 0.00 1.90
2561 5965 6.494842 TGTCAGACAAGCTTAATGTTCAAAC 58.505 36.000 0.00 0.00 0.00 2.93
2649 6053 0.249531 TGTCGTCGCCTAGTTTTGCA 60.250 50.000 0.00 0.00 0.00 4.08
2676 6080 1.201343 GTATTGTCTCGAGCGCCTTC 58.799 55.000 7.81 0.00 0.00 3.46
2714 6119 5.039920 AGCCAATGCAGATGATTACTACA 57.960 39.130 3.95 0.00 41.13 2.74
2850 6255 7.916977 GCCATTGCAAGATTTTCTTTTCTTTTT 59.083 29.630 4.94 0.00 33.78 1.94
2851 6256 7.067251 TGCCATTGCAAGATTTTCTTTTCTTTT 59.933 29.630 4.94 0.00 46.66 2.27
2852 6257 6.543100 TGCCATTGCAAGATTTTCTTTTCTTT 59.457 30.769 4.94 0.00 46.66 2.52
2853 6258 6.056884 TGCCATTGCAAGATTTTCTTTTCTT 58.943 32.000 4.94 0.00 46.66 2.52
2854 6259 5.613329 TGCCATTGCAAGATTTTCTTTTCT 58.387 33.333 4.94 0.00 46.66 2.52
2855 6260 5.927954 TGCCATTGCAAGATTTTCTTTTC 57.072 34.783 4.94 0.00 46.66 2.29
2914 6319 2.596346 TCCATCAGCAAGAAAAGGCAA 58.404 42.857 0.00 0.00 0.00 4.52
3086 6500 7.553334 AGTCAAGTCTTCAAGTACACTAACAA 58.447 34.615 0.00 0.00 0.00 2.83
3169 6583 1.068474 CTTCGGTTCGGTTGCAGTAG 58.932 55.000 0.00 0.00 0.00 2.57
3175 6589 3.011760 GCTCGCTTCGGTTCGGTTG 62.012 63.158 0.00 0.00 0.00 3.77
3214 6628 5.295787 GTGTGACACAACCTTGTTTCTCATA 59.704 40.000 10.50 0.14 40.88 2.15
3249 6663 3.696051 GCAAAGGAATGGAGCTATGTTGA 59.304 43.478 0.00 0.00 0.00 3.18
3253 6667 2.289002 GACGCAAAGGAATGGAGCTATG 59.711 50.000 0.00 0.00 0.00 2.23
3255 6669 1.277842 TGACGCAAAGGAATGGAGCTA 59.722 47.619 0.00 0.00 0.00 3.32
3256 6670 0.036732 TGACGCAAAGGAATGGAGCT 59.963 50.000 0.00 0.00 0.00 4.09
3264 6678 0.394938 TACAAGCCTGACGCAAAGGA 59.605 50.000 2.95 0.00 41.38 3.36
3283 6697 0.807496 GAGTAGCCACTCCGTACGTT 59.193 55.000 15.21 0.00 44.72 3.99
3284 6698 2.475666 GAGTAGCCACTCCGTACGT 58.524 57.895 15.21 0.00 44.72 3.57
3296 6710 4.691216 CCCTGTAAAGAACACAAGAGTAGC 59.309 45.833 0.00 0.00 33.45 3.58
3339 6753 7.055667 ACATACTACTGAATGTCCATACAGG 57.944 40.000 0.00 0.00 39.49 4.00
3343 6757 8.094548 GCCAATACATACTACTGAATGTCCATA 58.905 37.037 0.00 0.00 37.50 2.74
3349 6763 7.065085 GCTATGGCCAATACATACTACTGAATG 59.935 40.741 10.96 0.00 0.00 2.67
3407 6821 4.266739 CGTTAACTTTGGTTCTTTTGTGGC 59.733 41.667 3.71 0.00 36.92 5.01
3411 6825 6.254589 TGCATTCGTTAACTTTGGTTCTTTTG 59.745 34.615 3.71 0.00 36.92 2.44
3416 6830 6.691388 GGATATGCATTCGTTAACTTTGGTTC 59.309 38.462 3.54 0.00 36.92 3.62
3471 6886 4.469657 AGACAAAGGACAGCCAAAACATA 58.530 39.130 0.00 0.00 36.29 2.29
3550 6965 3.289525 AGGCACTCTACGGACAGC 58.710 61.111 0.00 0.00 0.00 4.40
3563 6978 3.898123 AGTTCACTTCTTCAGTAGAGGCA 59.102 43.478 0.00 0.00 33.42 4.75
3642 7071 6.801377 TGAATGCAATTTTGAATCACTCGTAC 59.199 34.615 0.00 0.00 36.07 3.67
3658 7153 6.032956 TCAGCTCTGAATTTTGAATGCAAT 57.967 33.333 0.00 0.00 36.53 3.56
3755 7250 0.324943 CACGGAGGGGTGTTTGATCT 59.675 55.000 0.00 0.00 33.24 2.75
3801 7296 6.481976 TGCAAAATCTTCTCGAGTTCTAAACA 59.518 34.615 13.13 0.00 0.00 2.83
4087 7597 3.693085 GGGTTCCGACGCTATATATCTCA 59.307 47.826 0.00 0.00 35.94 3.27
4103 7613 6.259387 CCAATAGTATTTAGTTCGTGGGTTCC 59.741 42.308 0.00 0.00 0.00 3.62
4121 7631 3.116862 TCCCCTCCTTCGATACCAATAGT 60.117 47.826 0.00 0.00 0.00 2.12
4124 7634 2.489528 TCCCCTCCTTCGATACCAAT 57.510 50.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.