Multiple sequence alignment - TraesCS3A01G149200

Loading Multiple Alignment...

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 TraesCS3A01G149200 chr3A 100.000 2801 0 0 1 2801 134236719 134239519 0.000000e+00 5173.0
1 TraesCS3A01G149200 chr3A 100.000 389 0 0 3329 3717 134240047 134240435 0.000000e+00 719.0
2 TraesCS3A01G149200 chr3A 96.471 85 3 0 1802 1886 685358894 685358810 1.390000e-29 141.0
3 TraesCS3A01G149200 chr3B 92.980 2265 69 27 3 2233 179368615 179370823 0.000000e+00 3219.0
4 TraesCS3A01G149200 chr3B 96.462 424 12 2 2356 2776 179370958 179371381 0.000000e+00 697.0
5 TraesCS3A01G149200 chr3B 90.608 181 12 3 3525 3704 179372996 179373172 6.210000e-58 235.0
6 TraesCS3A01G149200 chr3B 90.000 90 4 2 2238 2323 179370879 179370967 1.090000e-20 111.0
7 TraesCS3A01G149200 chr3D 92.303 1793 75 24 1 1785 125481361 125483098 0.000000e+00 2488.0
8 TraesCS3A01G149200 chr3D 90.295 577 43 7 2238 2801 125483481 125484057 0.000000e+00 743.0
9 TraesCS3A01G149200 chr3D 93.158 380 26 0 3329 3708 125484569 125484948 3.240000e-155 558.0
10 TraesCS3A01G149200 chr3D 90.164 122 11 1 2109 2230 125483299 125483419 1.380000e-34 158.0
11 TraesCS3A01G149200 chr3D 95.238 84 4 0 1804 1887 529790835 529790918 2.330000e-27 134.0
12 TraesCS3A01G149200 chr2A 94.792 192 8 1 1818 2009 695349748 695349937 7.800000e-77 298.0
13 TraesCS3A01G149200 chr2A 90.260 154 12 2 1888 2040 286435084 286434933 8.140000e-47 198.0
14 TraesCS3A01G149200 chr2A 89.308 159 7 8 1858 2009 486497228 486497073 1.360000e-44 191.0
15 TraesCS3A01G149200 chr4A 90.576 191 12 2 1820 2010 635963701 635963885 7.970000e-62 248.0
16 TraesCS3A01G149200 chr4A 91.503 153 11 2 1888 2039 387107503 387107352 3.760000e-50 209.0
17 TraesCS3A01G149200 chr7A 95.489 133 6 0 1888 2020 687928109 687928241 2.910000e-51 213.0
18 TraesCS3A01G149200 chr4B 90.506 158 12 3 1888 2043 448873650 448873806 4.870000e-49 206.0
19 TraesCS3A01G149200 chr7D 91.391 151 9 4 1888 2036 509114850 509114702 1.750000e-48 204.0
20 TraesCS3A01G149200 chr7D 88.889 54 6 0 228 281 427631583 427631636 2.400000e-07 67.6
21 TraesCS3A01G149200 chr6A 91.447 152 7 6 1888 2035 502319150 502319001 1.750000e-48 204.0
22 TraesCS3A01G149200 chr6A 95.455 88 2 2 1801 1886 360513229 360513142 5.010000e-29 139.0
23 TraesCS3A01G149200 chr7B 97.500 80 2 0 1807 1886 372344665 372344586 1.800000e-28 137.0
24 TraesCS3A01G149200 chr7B 90.000 50 5 0 232 281 445423165 445423214 8.620000e-07 65.8
25 TraesCS3A01G149200 chr4D 95.294 85 3 1 1803 1886 48073641 48073557 2.330000e-27 134.0
26 TraesCS3A01G149200 chr1A 92.473 93 5 2 1796 1886 252517281 252517189 8.380000e-27 132.0


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 TraesCS3A01G149200 chr3A 134236719 134240435 3716 False 2946.00 5173 100.0000 1 3717 2 chr3A.!!$F1 3716
1 TraesCS3A01G149200 chr3B 179368615 179373172 4557 False 1065.50 3219 92.5125 3 3704 4 chr3B.!!$F1 3701
2 TraesCS3A01G149200 chr3D 125481361 125484948 3587 False 986.75 2488 91.4800 1 3708 4 chr3D.!!$F2 3707

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
575 576 0.108424 CGAACTGCTTGGAGGGAGAG 60.108 60.000 0.00 0.00 0.00 3.20 F
578 579 0.411452 ACTGCTTGGAGGGAGAGAGA 59.589 55.000 0.00 0.00 0.00 3.10 F
921 927 0.648441 TAAATTACGAAGCAGCGCCG 59.352 50.000 2.29 1.74 33.86 6.46 F
948 954 1.075151 AGGTAGTAGCAGCTCCCCC 60.075 63.158 0.00 0.00 0.00 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2361 2462 0.189574 TCATGGCCACAGGGGAAAAA 59.810 50.000 8.16 0.00 40.01 1.94 R
2407 2520 1.068055 GCACCCAATTTCTGCAGAGTG 60.068 52.381 21.15 21.15 0.00 3.51 R
2560 2675 7.423199 ACAGAAATATACTTCGCGATGACTTA 58.577 34.615 26.56 14.81 0.00 2.24 R
3355 3470 1.000283 CTAGATAGGAACGGCAGCAGG 60.000 57.143 0.00 0.00 0.00 4.85 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
23 24 5.390613 CAGTCGGTTGAATTTACCAACATC 58.609 41.667 9.83 1.82 44.07 3.06
124 125 3.189287 CCAATCAACATATAGCGAAGGCC 59.811 47.826 0.00 0.00 41.24 5.19
166 167 0.934496 CAAACCACGCGAACAAGAGA 59.066 50.000 15.93 0.00 0.00 3.10
574 575 1.544825 CCGAACTGCTTGGAGGGAGA 61.545 60.000 0.00 0.00 0.00 3.71
575 576 0.108424 CGAACTGCTTGGAGGGAGAG 60.108 60.000 0.00 0.00 0.00 3.20
576 577 1.270907 GAACTGCTTGGAGGGAGAGA 58.729 55.000 0.00 0.00 0.00 3.10
577 578 1.206849 GAACTGCTTGGAGGGAGAGAG 59.793 57.143 0.00 0.00 0.00 3.20
578 579 0.411452 ACTGCTTGGAGGGAGAGAGA 59.589 55.000 0.00 0.00 0.00 3.10
584 585 1.221635 TGGAGGGAGAGAGAGAGAGG 58.778 60.000 0.00 0.00 0.00 3.69
587 588 1.152546 GGGAGAGAGAGAGAGGGGC 60.153 68.421 0.00 0.00 0.00 5.80
618 622 2.430248 TGCTGAGCAATGATGATGGT 57.570 45.000 3.81 0.00 34.76 3.55
619 623 2.021457 TGCTGAGCAATGATGATGGTG 58.979 47.619 3.81 0.00 34.76 4.17
631 635 1.051008 TGATGGTGCTGACAGTGACT 58.949 50.000 3.99 0.00 0.00 3.41
670 674 4.423732 GCCGTCTGCAACATTCATTAAAT 58.576 39.130 0.00 0.00 40.77 1.40
743 748 3.233259 GATCTGGGCTCTAGCGGGC 62.233 68.421 0.00 1.54 43.26 6.13
777 783 3.139077 GGGAAAAACTCGAGAGCTTTCA 58.861 45.455 21.68 0.00 36.26 2.69
778 784 3.187432 GGGAAAAACTCGAGAGCTTTCAG 59.813 47.826 21.68 3.99 36.26 3.02
921 927 0.648441 TAAATTACGAAGCAGCGCCG 59.352 50.000 2.29 1.74 33.86 6.46
948 954 1.075151 AGGTAGTAGCAGCTCCCCC 60.075 63.158 0.00 0.00 0.00 5.40
968 974 1.193323 CAGAGCCACACATCTCTCCT 58.807 55.000 0.00 0.00 37.56 3.69
969 975 2.382882 CAGAGCCACACATCTCTCCTA 58.617 52.381 0.00 0.00 37.56 2.94
1153 1159 3.254903 CGCCCAAAAGGTAATTATAGGCC 59.745 47.826 0.00 0.00 38.26 5.19
1158 1164 5.897250 CCAAAAGGTAATTATAGGCCCAAGT 59.103 40.000 0.00 0.00 0.00 3.16
1161 1167 3.461831 AGGTAATTATAGGCCCAAGTGCA 59.538 43.478 0.00 0.00 0.00 4.57
1210 1219 6.603237 TTCTTGCCGATACAACTATGATTG 57.397 37.500 0.00 0.00 35.59 2.67
1211 1220 5.912892 TCTTGCCGATACAACTATGATTGA 58.087 37.500 0.00 0.00 33.57 2.57
1212 1221 6.524734 TCTTGCCGATACAACTATGATTGAT 58.475 36.000 0.00 0.00 33.57 2.57
1213 1222 7.666623 TCTTGCCGATACAACTATGATTGATA 58.333 34.615 0.00 0.00 33.57 2.15
1214 1223 7.598869 TCTTGCCGATACAACTATGATTGATAC 59.401 37.037 0.00 0.00 33.57 2.24
1215 1224 6.754193 TGCCGATACAACTATGATTGATACA 58.246 36.000 0.00 0.00 33.57 2.29
1216 1225 7.213678 TGCCGATACAACTATGATTGATACAA 58.786 34.615 0.00 0.00 33.57 2.41
1217 1226 7.713073 TGCCGATACAACTATGATTGATACAAA 59.287 33.333 0.00 0.00 33.57 2.83
1218 1227 8.009974 GCCGATACAACTATGATTGATACAAAC 58.990 37.037 0.00 0.00 33.57 2.93
1219 1228 9.261180 CCGATACAACTATGATTGATACAAACT 57.739 33.333 0.00 0.00 33.57 2.66
1323 1334 7.663905 TCTTATCTTTGTGCCTAGCTGTTTTTA 59.336 33.333 0.00 0.00 0.00 1.52
1458 1473 4.427312 GAACAATCTTGCATGCTAAAGGG 58.573 43.478 20.33 10.43 0.00 3.95
1571 1586 5.266733 TGTTTGTACTCGGAGTTACAAGT 57.733 39.130 16.95 0.00 34.46 3.16
1600 1615 3.679824 ACTTGTCTGTACCACTTAGCC 57.320 47.619 0.00 0.00 0.00 3.93
1605 1620 4.154176 TGTCTGTACCACTTAGCCAGTAA 58.846 43.478 0.00 0.00 32.76 2.24
1618 1636 9.988350 CACTTAGCCAGTAACAATTTATTAGTG 57.012 33.333 6.93 6.93 32.76 2.74
1620 1638 8.801882 TTAGCCAGTAACAATTTATTAGTGCT 57.198 30.769 7.93 9.99 33.41 4.40
1693 1713 7.929941 AATAGTTTGTCTCCTTTGAGGATTC 57.070 36.000 0.00 0.00 44.81 2.52
1711 1731 3.720949 TTCTGTGATATTCGGTACCGG 57.279 47.619 32.80 15.32 40.25 5.28
1736 1756 8.977505 GGTAGTTAAATGACGCCGTATTATTAA 58.022 33.333 0.00 0.00 0.00 1.40
1811 1836 8.178313 GCAGAATGACTACTCCAAAAAGTTATC 58.822 37.037 0.00 0.00 39.69 1.75
1812 1837 9.219603 CAGAATGACTACTCCAAAAAGTTATCA 57.780 33.333 0.00 0.00 39.69 2.15
1813 1838 9.793259 AGAATGACTACTCCAAAAAGTTATCAA 57.207 29.630 0.00 0.00 30.39 2.57
1815 1840 8.918202 ATGACTACTCCAAAAAGTTATCAACA 57.082 30.769 0.00 0.00 30.39 3.33
1816 1841 8.740123 TGACTACTCCAAAAAGTTATCAACAA 57.260 30.769 0.00 0.00 0.00 2.83
1882 1907 4.959210 AGGCTAGAGCTGAAACTCATAAGA 59.041 41.667 0.00 0.00 39.26 2.10
2049 2074 6.875753 ACATGCAAAATAAATTGACAACACG 58.124 32.000 0.00 0.00 31.84 4.49
2156 2199 4.217550 CCGAATCCTCTGCAAACCTTTAAA 59.782 41.667 0.00 0.00 0.00 1.52
2174 2217 2.640316 AAGCCTCCTGTTTTTCTCGT 57.360 45.000 0.00 0.00 0.00 4.18
2233 2276 2.050934 GTCGAACCCTAGGTCGCCT 61.051 63.158 15.21 3.87 33.12 5.52
2235 2278 2.783288 CGAACCCTAGGTCGCCTCC 61.783 68.421 8.29 0.00 33.12 4.30
2255 2352 3.010027 TCCTGTTTCTCAATGTATGGGCA 59.990 43.478 0.00 0.00 0.00 5.36
2300 2401 4.763793 ACATTATCCATCTGCCTACATTGC 59.236 41.667 0.00 0.00 0.00 3.56
2328 2429 6.912591 GGAATGCACCTTTCGATTTTATACTG 59.087 38.462 0.00 0.00 0.00 2.74
2337 2438 4.448210 TCGATTTTATACTGGTTGCTCCC 58.552 43.478 0.00 0.00 34.77 4.30
2340 2441 6.042781 TCGATTTTATACTGGTTGCTCCCTAT 59.957 38.462 0.00 0.00 34.77 2.57
2353 2454 2.002586 CTCCCTATTGTTGCAGTGTCG 58.997 52.381 0.00 0.00 0.00 4.35
2359 2460 4.024048 CCTATTGTTGCAGTGTCGTTTTCT 60.024 41.667 0.00 0.00 0.00 2.52
2361 2462 5.689383 ATTGTTGCAGTGTCGTTTTCTAT 57.311 34.783 0.00 0.00 0.00 1.98
2364 2465 5.885881 TGTTGCAGTGTCGTTTTCTATTTT 58.114 33.333 0.00 0.00 0.00 1.82
2365 2466 6.326375 TGTTGCAGTGTCGTTTTCTATTTTT 58.674 32.000 0.00 0.00 0.00 1.94
2400 2513 7.710907 GCCATGAGAAGTTACTACATCACAATA 59.289 37.037 0.00 0.00 29.04 1.90
2407 2520 8.888579 AAGTTACTACATCACAATATGGCTAC 57.111 34.615 0.00 0.00 0.00 3.58
2441 2556 9.474313 AGAAATTGGGTGCTAACAGAAATAATA 57.526 29.630 0.00 0.00 0.00 0.98
2560 2675 2.711009 TGTCTCATGTTTTCCTCCAGGT 59.289 45.455 0.00 0.00 36.34 4.00
2762 2877 5.234329 CACTTACATAACATGTTCTAGGCCG 59.766 44.000 15.85 2.49 41.63 6.13
2764 2879 1.873591 CATAACATGTTCTAGGCCGGC 59.126 52.381 21.18 21.18 0.00 6.13
2791 2906 4.003648 CTGGTTTAGTGTTGGATCTGTCC 58.996 47.826 0.00 0.00 45.31 4.02
3355 3470 7.439655 AGGATGAATGTACTTTCGCTAGATTTC 59.560 37.037 14.67 4.18 0.00 2.17
3373 3488 0.687757 TCCTGCTGCCGTTCCTATCT 60.688 55.000 0.00 0.00 0.00 1.98
3400 3515 4.143543 TCATGATTGCAGGTGTCTGAAAA 58.856 39.130 0.00 0.00 41.56 2.29
3432 3547 2.082231 CAGTTGCCATCTCTTCACAGG 58.918 52.381 0.00 0.00 0.00 4.00
3441 3556 4.334759 CCATCTCTTCACAGGTTTATGCTG 59.665 45.833 0.00 0.00 0.00 4.41
3476 3591 2.681344 GCCAAATCGTCGATAAAAGGGT 59.319 45.455 8.43 0.00 0.00 4.34
3496 3611 4.394920 GGGTAACTTGATGATTTCGAAGCA 59.605 41.667 0.00 1.33 0.00 3.91
3497 3612 5.066505 GGGTAACTTGATGATTTCGAAGCAT 59.933 40.000 13.38 13.38 40.80 3.79
3519 3634 6.923508 GCATATTTTTGGCCTGTTTAGTATCC 59.076 38.462 3.32 0.00 0.00 2.59
3557 4549 5.345702 CAATTTGATGCGTTCATGGAGATT 58.654 37.500 0.00 0.00 33.34 2.40
3574 4566 3.243336 AGATTTCTTGTACTGCGTCGAC 58.757 45.455 5.18 5.18 0.00 4.20
3680 4672 0.250467 CCCTGGGCTTATGTGATCCG 60.250 60.000 0.00 0.00 0.00 4.18
3704 4696 6.092122 CGCACAAGTAGGAATATGAAAGAACA 59.908 38.462 0.00 0.00 0.00 3.18
3708 4700 8.462016 ACAAGTAGGAATATGAAAGAACATTGC 58.538 33.333 0.00 0.00 0.00 3.56
3709 4701 8.680903 CAAGTAGGAATATGAAAGAACATTGCT 58.319 33.333 0.00 0.00 34.12 3.91
3710 4702 8.218338 AGTAGGAATATGAAAGAACATTGCTG 57.782 34.615 0.00 0.00 32.30 4.41
3711 4703 6.461110 AGGAATATGAAAGAACATTGCTGG 57.539 37.500 0.00 0.00 29.27 4.85
3712 4704 5.954150 AGGAATATGAAAGAACATTGCTGGT 59.046 36.000 0.00 0.00 29.27 4.00
3713 4705 6.438425 AGGAATATGAAAGAACATTGCTGGTT 59.562 34.615 0.00 0.00 29.27 3.67
3714 4706 7.038799 AGGAATATGAAAGAACATTGCTGGTTT 60.039 33.333 0.00 0.00 29.27 3.27
3715 4707 7.603784 GGAATATGAAAGAACATTGCTGGTTTT 59.396 33.333 0.00 0.00 0.00 2.43
3716 4708 8.907222 AATATGAAAGAACATTGCTGGTTTTT 57.093 26.923 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.010582 GAGGCTCGCTGTGGGTAGAG 62.011 65.000 0.00 0.00 0.00 2.43
124 125 2.731721 TACTGTGTTCCGCGCGTG 60.732 61.111 29.95 19.95 0.00 5.34
166 167 1.895886 ATCCCCTGCTCAGACCCTCT 61.896 60.000 0.00 0.00 0.00 3.69
574 575 1.011595 TTACCTGCCCCTCTCTCTCT 58.988 55.000 0.00 0.00 0.00 3.10
575 576 1.867363 TTTACCTGCCCCTCTCTCTC 58.133 55.000 0.00 0.00 0.00 3.20
576 577 2.344093 TTTTACCTGCCCCTCTCTCT 57.656 50.000 0.00 0.00 0.00 3.10
577 578 3.653835 AATTTTACCTGCCCCTCTCTC 57.346 47.619 0.00 0.00 0.00 3.20
578 579 4.089361 CAAAATTTTACCTGCCCCTCTCT 58.911 43.478 2.44 0.00 0.00 3.10
584 585 3.588955 CTCAGCAAAATTTTACCTGCCC 58.411 45.455 18.77 0.14 35.33 5.36
617 621 3.371102 TGTCTTAGTCACTGTCAGCAC 57.629 47.619 0.00 0.00 0.00 4.40
618 622 3.306294 CCATGTCTTAGTCACTGTCAGCA 60.306 47.826 0.00 0.00 0.00 4.41
619 623 3.257393 CCATGTCTTAGTCACTGTCAGC 58.743 50.000 0.00 0.00 0.00 4.26
631 635 1.148273 GCCGATGGCCCATGTCTTA 59.852 57.895 0.00 0.00 44.06 2.10
670 674 0.623723 AGAATTTAAGAGGGCCGCCA 59.376 50.000 12.58 0.00 0.00 5.69
759 765 5.180304 GGATTCTGAAAGCTCTCGAGTTTTT 59.820 40.000 13.13 11.18 41.00 1.94
777 783 4.662179 TGATGGCATAGAAGGAAGGATTCT 59.338 41.667 0.00 0.00 46.56 2.40
778 784 4.978099 TGATGGCATAGAAGGAAGGATTC 58.022 43.478 0.00 0.00 46.67 2.52
853 859 3.656045 GCCGGTTTGGTGTGTCGG 61.656 66.667 1.90 0.00 43.13 4.79
854 860 2.892334 CTGCCGGTTTGGTGTGTCG 61.892 63.158 1.90 0.00 41.21 4.35
855 861 3.030652 CTGCCGGTTTGGTGTGTC 58.969 61.111 1.90 0.00 41.21 3.67
921 927 1.035932 TGCTACTACCTGGAGACCGC 61.036 60.000 0.00 0.00 0.00 5.68
948 954 0.177604 GGAGAGATGTGTGGCTCTGG 59.822 60.000 0.00 0.00 41.33 3.86
950 956 2.383855 GTAGGAGAGATGTGTGGCTCT 58.616 52.381 0.00 0.00 43.78 4.09
951 957 1.066303 CGTAGGAGAGATGTGTGGCTC 59.934 57.143 0.00 0.00 0.00 4.70
952 958 1.107114 CGTAGGAGAGATGTGTGGCT 58.893 55.000 0.00 0.00 0.00 4.75
953 959 0.818296 ACGTAGGAGAGATGTGTGGC 59.182 55.000 0.00 0.00 0.00 5.01
954 960 1.469940 GCACGTAGGAGAGATGTGTGG 60.470 57.143 0.00 0.00 36.40 4.17
955 961 1.474478 AGCACGTAGGAGAGATGTGTG 59.526 52.381 0.00 0.00 36.40 3.82
956 962 1.474478 CAGCACGTAGGAGAGATGTGT 59.526 52.381 0.00 0.00 36.40 3.72
968 974 1.018148 CAACCAACCAACAGCACGTA 58.982 50.000 0.00 0.00 0.00 3.57
969 975 1.662438 CCAACCAACCAACAGCACGT 61.662 55.000 0.00 0.00 0.00 4.49
1153 1159 1.442520 CCAAACGCGATGCACTTGG 60.443 57.895 15.93 11.36 34.93 3.61
1158 1164 2.281139 TCCACCAAACGCGATGCA 60.281 55.556 15.93 0.00 0.00 3.96
1161 1167 2.740826 CGGTCCACCAAACGCGAT 60.741 61.111 15.93 0.00 35.14 4.58
1214 1223 8.393366 CAGTACAGGATCACAAATCATAGTTTG 58.607 37.037 0.00 0.00 43.11 2.93
1215 1224 8.321353 TCAGTACAGGATCACAAATCATAGTTT 58.679 33.333 0.00 0.00 0.00 2.66
1216 1225 7.851228 TCAGTACAGGATCACAAATCATAGTT 58.149 34.615 0.00 0.00 0.00 2.24
1217 1226 7.423844 TCAGTACAGGATCACAAATCATAGT 57.576 36.000 0.00 0.00 0.00 2.12
1218 1227 7.440556 CCTTCAGTACAGGATCACAAATCATAG 59.559 40.741 0.00 0.00 32.41 2.23
1219 1228 7.092891 ACCTTCAGTACAGGATCACAAATCATA 60.093 37.037 4.80 0.00 35.14 2.15
1220 1229 6.118170 CCTTCAGTACAGGATCACAAATCAT 58.882 40.000 0.00 0.00 32.41 2.45
1280 1291 6.441222 AGATAAGATTACTCAGTGGTGGGTA 58.559 40.000 0.00 0.00 38.75 3.69
1323 1334 1.995542 AGTCCCACAATTGTCCATCCT 59.004 47.619 8.48 0.00 0.00 3.24
1444 1459 5.940617 AGTATGTATCCCTTTAGCATGCAA 58.059 37.500 21.98 9.44 0.00 4.08
1458 1473 8.958119 TCTACCATCCAACAAAAGTATGTATC 57.042 34.615 0.00 0.00 32.02 2.24
1571 1586 5.597182 AGTGGTACAGACAAGTAGTTTCAGA 59.403 40.000 0.00 0.00 41.80 3.27
1600 1615 7.277981 ACCTCGAGCACTAATAAATTGTTACTG 59.722 37.037 6.99 0.00 0.00 2.74
1605 1620 8.732746 AATTACCTCGAGCACTAATAAATTGT 57.267 30.769 6.99 0.00 0.00 2.71
1618 1636 2.093128 TCAAAGGGGAATTACCTCGAGC 60.093 50.000 6.68 0.00 45.50 5.03
1620 1638 4.644163 TTTCAAAGGGGAATTACCTCGA 57.356 40.909 6.68 2.16 45.50 4.04
1693 1713 3.567164 ACTACCGGTACCGAATATCACAG 59.433 47.826 35.41 17.06 42.83 3.66
1736 1756 9.180678 CGAACATATTTTAGACAAGTTGCTTTT 57.819 29.630 1.81 0.00 0.00 2.27
1738 1758 7.871853 ACGAACATATTTTAGACAAGTTGCTT 58.128 30.769 1.81 0.00 0.00 3.91
1761 1781 5.201713 AGATAACACATATCCACCTGACG 57.798 43.478 0.00 0.00 41.23 4.35
1811 1836 4.903016 GCTTTGTTGTTGTTGTTGTTGTTG 59.097 37.500 0.00 0.00 0.00 3.33
1812 1837 4.024472 GGCTTTGTTGTTGTTGTTGTTGTT 60.024 37.500 0.00 0.00 0.00 2.83
1813 1838 3.496507 GGCTTTGTTGTTGTTGTTGTTGT 59.503 39.130 0.00 0.00 0.00 3.32
1815 1840 4.001618 AGGCTTTGTTGTTGTTGTTGTT 57.998 36.364 0.00 0.00 0.00 2.83
1816 1841 3.676291 AGGCTTTGTTGTTGTTGTTGT 57.324 38.095 0.00 0.00 0.00 3.32
1882 1907 6.077322 TGGAGATGAAACCCAAAAGAAAGAT 58.923 36.000 0.00 0.00 0.00 2.40
2049 2074 6.226052 TGTCATGACATAATAGGTGCATCTC 58.774 40.000 24.56 0.00 36.21 2.75
2100 2141 5.200368 TCAGCTACTATTGATTGCATCGA 57.800 39.130 0.00 0.00 0.00 3.59
2101 2142 5.234972 TGTTCAGCTACTATTGATTGCATCG 59.765 40.000 0.00 0.00 0.00 3.84
2156 2199 1.694696 AGACGAGAAAAACAGGAGGCT 59.305 47.619 0.00 0.00 0.00 4.58
2174 2217 1.076187 TGGACAAGAGGAGCTGAGAGA 59.924 52.381 0.00 0.00 0.00 3.10
2233 2276 3.010027 TGCCCATACATTGAGAAACAGGA 59.990 43.478 0.00 0.00 0.00 3.86
2235 2278 5.587388 ATTGCCCATACATTGAGAAACAG 57.413 39.130 0.00 0.00 0.00 3.16
2300 2401 3.788333 AATCGAAAGGTGCATTCCATG 57.212 42.857 0.00 0.00 0.00 3.66
2328 2429 1.474077 CTGCAACAATAGGGAGCAACC 59.526 52.381 0.00 0.00 34.45 3.77
2337 2438 5.095691 AGAAAACGACACTGCAACAATAG 57.904 39.130 0.00 0.00 0.00 1.73
2340 2441 5.493133 AATAGAAAACGACACTGCAACAA 57.507 34.783 0.00 0.00 0.00 2.83
2353 2454 4.562757 GGCCACAGGGGAAAAATAGAAAAC 60.563 45.833 0.00 0.00 40.01 2.43
2359 2460 2.043664 TCATGGCCACAGGGGAAAAATA 59.956 45.455 8.16 0.00 40.01 1.40
2361 2462 0.189574 TCATGGCCACAGGGGAAAAA 59.810 50.000 8.16 0.00 40.01 1.94
2364 2465 1.139498 TTCTCATGGCCACAGGGGAA 61.139 55.000 8.16 10.14 44.83 3.97
2365 2466 1.541118 TTCTCATGGCCACAGGGGA 60.541 57.895 8.16 2.79 35.83 4.81
2400 2513 3.641434 ATTTCTGCAGAGTGTAGCCAT 57.359 42.857 17.43 0.00 29.77 4.40
2402 2515 2.421424 CCAATTTCTGCAGAGTGTAGCC 59.579 50.000 17.43 0.00 29.77 3.93
2407 2520 1.068055 GCACCCAATTTCTGCAGAGTG 60.068 52.381 21.15 21.15 0.00 3.51
2441 2556 9.214957 TGAAACAAACTGATCGTGACTAATATT 57.785 29.630 0.00 0.00 0.00 1.28
2560 2675 7.423199 ACAGAAATATACTTCGCGATGACTTA 58.577 34.615 26.56 14.81 0.00 2.24
3355 3470 1.000283 CTAGATAGGAACGGCAGCAGG 60.000 57.143 0.00 0.00 0.00 4.85
3373 3488 4.696877 CAGACACCTGCAATCATGAAACTA 59.303 41.667 0.00 0.00 33.07 2.24
3400 3515 0.593128 GGCAACTGTTCATGCGACTT 59.407 50.000 0.00 0.00 43.47 3.01
3432 3547 5.572896 GCACAGAACAATTACCAGCATAAAC 59.427 40.000 0.00 0.00 0.00 2.01
3441 3556 4.165779 CGATTTGGCACAGAACAATTACC 58.834 43.478 0.00 0.00 42.39 2.85
3496 3611 7.057894 TCGGATACTAAACAGGCCAAAAATAT 58.942 34.615 5.01 0.00 0.00 1.28
3497 3612 6.416415 TCGGATACTAAACAGGCCAAAAATA 58.584 36.000 5.01 0.00 0.00 1.40
3519 3634 3.127376 TCAAATTGCACATGTCAGGATCG 59.873 43.478 0.00 0.00 0.00 3.69
3574 4566 3.496130 AGACAAGACAAGAAACATCAGCG 59.504 43.478 0.00 0.00 0.00 5.18
3680 4672 7.377766 TGTTCTTTCATATTCCTACTTGTGC 57.622 36.000 0.00 0.00 0.00 4.57
3685 4677 7.284034 CCAGCAATGTTCTTTCATATTCCTACT 59.716 37.037 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.