Multiple sequence alignment - TraesCS3A01G452500

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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 TraesCS3A01G452500 chr3A 100.000 3505 0 0 1 3505 690856358 690859862 0.000000e+00 6473.0
1 TraesCS3A01G452500 chr3A 93.949 2264 107 10 1267 3505 690785015 690787273 0.000000e+00 3395.0
2 TraesCS3A01G452500 chr3A 91.007 1957 131 20 1257 3172 690896630 690898582 0.000000e+00 2597.0
3 TraesCS3A01G452500 chr3A 100.000 651 0 0 3821 4471 690860178 690860828 0.000000e+00 1203.0
4 TraesCS3A01G452500 chr3A 92.485 652 43 6 3821 4470 690787307 690787954 0.000000e+00 928.0
5 TraesCS3A01G452500 chr3A 82.114 738 74 19 504 1234 690784031 690784717 3.000000e-161 579.0
6 TraesCS3A01G452500 chr3A 80.240 835 86 38 433 1234 690895660 690896448 5.050000e-154 555.0
7 TraesCS3A01G452500 chr3A 85.430 302 36 8 776 1073 690796005 690796302 1.560000e-79 307.0
8 TraesCS3A01G452500 chr3A 82.993 147 15 6 1 146 690894557 690894694 1.690000e-24 124.0
9 TraesCS3A01G452500 chr3A 88.312 77 9 0 3998 4074 690899157 690899233 4.760000e-15 93.5
10 TraesCS3A01G452500 chr3A 91.045 67 5 1 776 842 690752410 690752475 6.160000e-14 89.8
11 TraesCS3A01G452500 chr3B 94.295 2261 102 9 1270 3505 736311018 736313276 0.000000e+00 3435.0
12 TraesCS3A01G452500 chr3B 92.723 1924 99 20 1288 3172 736325041 736326962 0.000000e+00 2739.0
13 TraesCS3A01G452500 chr3B 90.951 652 48 4 3821 4471 736313310 736313951 0.000000e+00 867.0
14 TraesCS3A01G452500 chr3B 84.424 764 84 23 504 1260 736310036 736310771 0.000000e+00 719.0
15 TraesCS3A01G452500 chr3B 81.436 738 74 30 550 1260 736324088 736324789 3.040000e-151 545.0
16 TraesCS3A01G452500 chr3B 84.615 156 16 6 1 153 736323204 736323354 1.000000e-31 148.0
17 TraesCS3A01G452500 chr3B 85.246 122 11 5 629 744 736253604 736253724 7.860000e-23 119.0
18 TraesCS3A01G452500 chr3B 86.598 97 12 1 55 150 736307863 736307959 6.120000e-19 106.0
19 TraesCS3A01G452500 chr3B 95.455 44 1 1 3159 3202 736313031 736313073 8.020000e-08 69.4
20 TraesCS3A01G452500 chr3D 93.795 2240 111 10 1289 3505 554216931 554219165 0.000000e+00 3341.0
21 TraesCS3A01G452500 chr3D 92.587 1929 99 19 1261 3149 554328786 554330710 0.000000e+00 2730.0
22 TraesCS3A01G452500 chr3D 88.755 1076 62 28 160 1218 554316922 554317955 0.000000e+00 1262.0
23 TraesCS3A01G452500 chr3D 92.366 655 43 4 3821 4469 554219199 554219852 0.000000e+00 926.0
24 TraesCS3A01G452500 chr3D 88.131 337 32 5 900 1234 554216330 554216660 1.170000e-105 394.0
25 TraesCS3A01G452500 chr3D 77.371 601 73 36 154 744 554169300 554169847 9.400000e-77 298.0
26 TraesCS3A01G452500 chr3D 91.045 134 11 1 4339 4471 554176253 554176386 3.550000e-41 180.0
27 TraesCS3A01G452500 chr1D 91.118 1700 131 4 1308 2987 78066948 78065249 0.000000e+00 2285.0
28 TraesCS3A01G452500 chr1D 83.893 149 17 4 4327 4469 78111180 78111033 7.800000e-28 135.0
29 TraesCS3A01G452500 chr1B 88.794 1883 162 21 1308 3147 121715424 121713548 0.000000e+00 2263.0
30 TraesCS3A01G452500 chr1A 89.363 1711 155 9 1300 2987 105302965 105304671 0.000000e+00 2126.0
31 TraesCS3A01G452500 chr6D 85.000 80 12 0 4087 4166 17273579 17273500 1.030000e-11 82.4
32 TraesCS3A01G452500 chr6B 96.774 31 1 0 4273 4303 697433467 697433437 8.000000e-03 52.8


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 TraesCS3A01G452500 chr3A 690856358 690860828 4470 False 3838.000000 6473 100.000000 1 4471 2 chr3A.!!$F4 4470
1 TraesCS3A01G452500 chr3A 690784031 690787954 3923 False 1634.000000 3395 89.516000 504 4470 3 chr3A.!!$F3 3966
2 TraesCS3A01G452500 chr3A 690894557 690899233 4676 False 842.375000 2597 85.638000 1 4074 4 chr3A.!!$F5 4073
3 TraesCS3A01G452500 chr3B 736323204 736326962 3758 False 1144.000000 2739 86.258000 1 3172 3 chr3B.!!$F3 3171
4 TraesCS3A01G452500 chr3B 736307863 736313951 6088 False 1039.280000 3435 90.344600 55 4471 5 chr3B.!!$F2 4416
5 TraesCS3A01G452500 chr3D 554328786 554330710 1924 False 2730.000000 2730 92.587000 1261 3149 1 chr3D.!!$F4 1888
6 TraesCS3A01G452500 chr3D 554216330 554219852 3522 False 1553.666667 3341 91.430667 900 4469 3 chr3D.!!$F5 3569
7 TraesCS3A01G452500 chr3D 554316922 554317955 1033 False 1262.000000 1262 88.755000 160 1218 1 chr3D.!!$F3 1058
8 TraesCS3A01G452500 chr3D 554169300 554169847 547 False 298.000000 298 77.371000 154 744 1 chr3D.!!$F1 590
9 TraesCS3A01G452500 chr1D 78065249 78066948 1699 True 2285.000000 2285 91.118000 1308 2987 1 chr1D.!!$R1 1679
10 TraesCS3A01G452500 chr1B 121713548 121715424 1876 True 2263.000000 2263 88.794000 1308 3147 1 chr1B.!!$R1 1839
11 TraesCS3A01G452500 chr1A 105302965 105304671 1706 False 2126.000000 2126 89.363000 1300 2987 1 chr1A.!!$F1 1687

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
588 3105 0.040157 GCGCACTGCAATTTCTCACA 60.040 50.000 0.30 0.00 45.45 3.58 F
929 3486 0.456653 GCATGGTGTTTCATGTCGCC 60.457 55.000 0.00 2.03 44.54 5.54 F
1087 3644 0.585357 TAACTACCGATCGAGAGCGC 59.415 55.000 18.66 0.00 39.12 5.92 F
1339 4212 0.678950 TGCACGAGATGAACCAGACA 59.321 50.000 0.00 0.00 0.00 3.41 F
1902 4775 0.806868 CTGCTGCGGATTGTGAACAT 59.193 50.000 1.17 0.00 0.00 2.71 F
2610 5512 1.069823 CGGTGGAGATCATCTTCCAGG 59.930 57.143 1.76 0.00 32.30 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2343 5244 0.333312 ACGATGGTCTCTGGACTCCT 59.667 55.000 0.0 0.0 41.82 3.69 R
2687 5589 0.111639 TCTTGGGGTTGTAGTTGCCC 59.888 55.000 0.0 0.0 41.62 5.36 R
2740 5642 3.414700 GCACCGTGTTCCTCAGCG 61.415 66.667 0.0 0.0 0.00 5.18 R
3154 6092 4.079970 CTGACACTGAACCCTACTAGACA 58.920 47.826 0.0 0.0 0.00 3.41 R
3308 6285 7.437565 GGGACAGTAGGATTTAGATTAAACGAC 59.562 40.741 0.0 0.0 0.00 4.34 R
3979 6961 0.756903 AGTGCCCACTTTACGTGACT 59.243 50.000 0.0 0.0 46.81 3.41 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 41 5.126061 AGCATCTGTTACCAATGAAACATCC 59.874 40.000 2.48 0.00 35.21 3.51
53 55 4.287067 TGAAACATCCTAAGTCAGGCTCTT 59.713 41.667 0.00 0.00 45.10 2.85
65 67 0.687757 AGGCTCTTACCGATGCTGGA 60.688 55.000 0.00 0.00 33.69 3.86
74 76 1.837439 ACCGATGCTGGATTGGTAGAA 59.163 47.619 18.47 0.00 46.04 2.10
78 80 4.442893 CCGATGCTGGATTGGTAGAAGTTA 60.443 45.833 7.25 0.00 31.27 2.24
83 85 4.770795 CTGGATTGGTAGAAGTTAGTGGG 58.229 47.826 0.00 0.00 0.00 4.61
92 94 2.829120 AGAAGTTAGTGGGCAGAGAGTC 59.171 50.000 0.00 0.00 0.00 3.36
101 103 2.507058 TGGGCAGAGAGTCTTTGCATAT 59.493 45.455 30.32 0.00 42.33 1.78
211 2103 1.745087 TGGACGCCTAACTAGGTTACG 59.255 52.381 4.72 2.79 45.42 3.18
287 2183 2.907910 AGTCAAGCGATGCAATGTTC 57.092 45.000 0.00 0.00 0.00 3.18
424 2929 4.103469 TCAGGTATTGTGGTTGTTGGTAGT 59.897 41.667 0.00 0.00 0.00 2.73
545 3053 4.221342 CGTGATTTGATGTGGTGAACTTG 58.779 43.478 0.00 0.00 0.00 3.16
588 3105 0.040157 GCGCACTGCAATTTCTCACA 60.040 50.000 0.30 0.00 45.45 3.58
589 3106 1.678360 CGCACTGCAATTTCTCACAC 58.322 50.000 1.11 0.00 0.00 3.82
652 3169 1.665679 CATAGCCGCGATTGACTTGTT 59.334 47.619 8.23 0.00 0.00 2.83
695 3221 2.867975 CGTGCTAAACTAATTACCCCGG 59.132 50.000 0.00 0.00 0.00 5.73
746 3280 1.718711 CCGGCGCAACAAAAAGTATTG 59.281 47.619 10.83 0.00 36.37 1.90
853 3387 4.352600 GCTAAGCTAATAGCCATGCATG 57.647 45.455 20.19 20.19 43.77 4.06
855 3389 2.281539 AGCTAATAGCCATGCATGCA 57.718 45.000 25.04 25.04 43.77 3.96
856 3390 2.803956 AGCTAATAGCCATGCATGCAT 58.196 42.857 27.46 27.46 43.77 3.96
858 3392 4.533815 AGCTAATAGCCATGCATGCATAT 58.466 39.130 31.73 21.88 43.77 1.78
859 3393 4.338400 AGCTAATAGCCATGCATGCATATG 59.662 41.667 31.73 24.94 43.77 1.78
861 3395 5.297527 GCTAATAGCCATGCATGCATATGTA 59.702 40.000 31.73 21.57 34.30 2.29
862 3396 5.830000 AATAGCCATGCATGCATATGTAG 57.170 39.130 31.73 18.92 36.65 2.74
863 3397 1.816835 AGCCATGCATGCATATGTAGC 59.183 47.619 31.73 25.57 36.65 3.58
929 3486 0.456653 GCATGGTGTTTCATGTCGCC 60.457 55.000 0.00 2.03 44.54 5.54
957 3514 2.561478 TTAGCCTGGTCAAGTCAACC 57.439 50.000 0.00 0.00 37.31 3.77
993 3550 1.367840 GATGCCGACGCCTAATCCT 59.632 57.895 0.00 0.00 0.00 3.24
1016 3573 4.940463 TCGAGTGTATAAATAGGCCACAC 58.060 43.478 5.01 9.00 39.78 3.82
1054 3611 1.372087 CCCTTCCATTGAGCAGCGAC 61.372 60.000 0.00 0.00 0.00 5.19
1066 3623 3.065510 TGAGCAGCGACTTAACTAGCTAG 59.934 47.826 19.44 19.44 37.94 3.42
1067 3624 2.121009 GCAGCGACTTAACTAGCTAGC 58.879 52.381 20.91 6.62 37.94 3.42
1068 3625 2.223618 GCAGCGACTTAACTAGCTAGCT 60.224 50.000 23.12 23.12 37.94 3.32
1069 3626 3.003482 GCAGCGACTTAACTAGCTAGCTA 59.997 47.826 22.85 22.85 37.94 3.32
1085 3642 1.874872 AGCTAACTACCGATCGAGAGC 59.125 52.381 18.66 12.33 0.00 4.09
1087 3644 0.585357 TAACTACCGATCGAGAGCGC 59.415 55.000 18.66 0.00 39.12 5.92
1108 3676 2.417933 CCATAGCACTGAGTTTGCAGAC 59.582 50.000 0.00 0.00 42.83 3.51
1127 3696 1.202976 ACCAAGCAAGCATGGAGAAGT 60.203 47.619 21.67 0.00 38.11 3.01
1159 3728 2.281484 ACCATGTTCTGCGCCGTT 60.281 55.556 4.18 0.00 0.00 4.44
1165 3734 2.357034 TTCTGCGCCGTTGTCCTC 60.357 61.111 4.18 0.00 0.00 3.71
1230 3799 4.578928 GGAACACACCTTTGTTGTGAGTAT 59.421 41.667 9.38 0.00 39.88 2.12
1234 3803 7.817418 ACACACCTTTGTTGTGAGTATAATT 57.183 32.000 9.38 0.00 36.08 1.40
1235 3804 8.911918 ACACACCTTTGTTGTGAGTATAATTA 57.088 30.769 9.38 0.00 36.08 1.40
1236 3805 9.344772 ACACACCTTTGTTGTGAGTATAATTAA 57.655 29.630 9.38 0.00 36.08 1.40
1282 4147 8.618240 TCTTTATCCTCCTGATTGGTTAACTA 57.382 34.615 5.42 0.00 34.76 2.24
1286 4153 5.590818 TCCTCCTGATTGGTTAACTAGACT 58.409 41.667 5.42 0.00 37.07 3.24
1306 4176 9.999009 CTAGACTAATCAGTTACGTATTTGACA 57.001 33.333 10.59 3.50 34.21 3.58
1315 4188 9.425577 TCAGTTACGTATTTGACAAATGATGTA 57.574 29.630 21.21 16.61 44.12 2.29
1339 4212 0.678950 TGCACGAGATGAACCAGACA 59.321 50.000 0.00 0.00 0.00 3.41
1576 4449 1.483316 TGTACAGCTTCAACGTCACG 58.517 50.000 0.00 0.00 0.00 4.35
1582 4455 1.890041 CTTCAACGTCACGGGCCAA 60.890 57.895 4.39 0.00 0.00 4.52
1902 4775 0.806868 CTGCTGCGGATTGTGAACAT 59.193 50.000 1.17 0.00 0.00 2.71
1950 4823 3.049674 CGCTGGGCACACGTTCAT 61.050 61.111 3.22 0.00 0.00 2.57
1987 4860 1.312815 GGTACTACCTGACGCCGTAT 58.687 55.000 0.00 0.00 34.73 3.06
2045 4926 3.716539 GACGTGCTCATGGCCGCTA 62.717 63.158 0.00 0.00 40.92 4.26
2156 5037 3.908081 TTCGCTACGCCGGATCCC 61.908 66.667 5.05 0.00 0.00 3.85
2343 5244 2.942796 AAGACATGCGAGCGTGGGA 61.943 57.895 19.79 0.00 37.27 4.37
2351 5252 2.680352 GAGCGTGGGAGGAGTCCA 60.680 66.667 12.86 0.00 46.07 4.02
2610 5512 1.069823 CGGTGGAGATCATCTTCCAGG 59.930 57.143 1.76 0.00 32.30 4.45
2669 5571 2.093447 CCTCCATGGCTACGACTTCTTT 60.093 50.000 6.96 0.00 0.00 2.52
2687 5589 4.436998 GTCCTCGCCACGGGACTG 62.437 72.222 15.73 0.00 45.99 3.51
2740 5642 1.951602 GTTCAACTACCACAACCCACC 59.048 52.381 0.00 0.00 0.00 4.61
2807 5709 1.366366 CTTCGTCACCGACAACCCT 59.634 57.895 0.00 0.00 44.13 4.34
3091 6027 8.908786 TCATTGTATTGAGGATGATTCTTACC 57.091 34.615 0.00 0.00 0.00 2.85
3092 6028 8.493607 TCATTGTATTGAGGATGATTCTTACCA 58.506 33.333 0.00 0.00 0.00 3.25
3101 6037 9.753674 TGAGGATGATTCTTACCATAAAAAGTT 57.246 29.630 0.00 0.00 0.00 2.66
3103 6039 9.753674 AGGATGATTCTTACCATAAAAAGTTGA 57.246 29.630 0.00 0.00 0.00 3.18
3154 6092 7.173218 CCATTGTAATGTGTGAACTGTAAGTCT 59.827 37.037 4.12 0.00 39.81 3.24
3247 6185 4.333649 CGAACTGGCTGATATCACAAACAT 59.666 41.667 0.00 0.00 0.00 2.71
3304 6281 3.054361 AGTGTGTCAAACTCAAACCTCCT 60.054 43.478 0.00 0.00 0.00 3.69
3308 6285 2.623416 GTCAAACTCAAACCTCCTTGGG 59.377 50.000 0.00 0.00 41.11 4.12
3347 6324 5.132648 TCCTACTGTCCCAAATCATATTGCT 59.867 40.000 0.00 0.00 0.00 3.91
3408 6385 4.957327 AGAAGAAGTCGACTTAGCCCTATT 59.043 41.667 29.79 11.37 36.11 1.73
3469 6446 8.726988 TGGTTAGATTTGTTATGTACTTTGCTC 58.273 33.333 0.00 0.00 0.00 4.26
3979 6961 3.206964 TCCGCCATAATTCGCAAACATA 58.793 40.909 0.00 0.00 0.00 2.29
4017 7190 1.419012 CTCTCCATTGCATAGCCCTCA 59.581 52.381 0.00 0.00 0.00 3.86
4019 7192 2.160205 CTCCATTGCATAGCCCTCATG 58.840 52.381 0.00 0.00 0.00 3.07
4044 7218 8.675504 TGAAAACTCTGTAATTGGTTCGTAAAA 58.324 29.630 0.00 0.00 0.00 1.52
4078 7253 7.179338 GTGATATACCTCTACAAGTGGGATCAT 59.821 40.741 0.00 0.00 34.44 2.45
4098 7273 8.486210 GGATCATATTATGTTATACAGAGGCCA 58.514 37.037 5.01 0.00 0.00 5.36
4214 7390 7.707464 TGACTTTACTCTTTGTCGACATGTTTA 59.293 33.333 20.80 0.00 32.64 2.01
4245 7421 7.695480 ATGTTAGTGTTGGTTGTATGCATTA 57.305 32.000 3.54 0.00 0.00 1.90
4273 7449 2.960384 TGTAAAGTTCACGGAGAGGACA 59.040 45.455 0.00 0.00 0.00 4.02
4294 7470 6.861055 GGACAGGTATGTGTTTATTGTGTTTG 59.139 38.462 0.00 0.00 40.68 2.93
4307 7483 8.456471 GTTTATTGTGTTTGTATCCCCTACTTC 58.544 37.037 0.00 0.00 0.00 3.01
4310 7486 4.595781 TGTGTTTGTATCCCCTACTTCTGT 59.404 41.667 0.00 0.00 0.00 3.41
4375 7551 9.875691 CGATGTCCTAGATTTAATCCATGAATA 57.124 33.333 0.78 0.00 0.00 1.75
4408 7584 5.756347 TGAATGGATTAAATAGTTCGGGTCG 59.244 40.000 0.00 0.00 0.00 4.79
4458 7634 1.016627 GCCTTGCATGCGAATCACTA 58.983 50.000 14.09 0.00 0.00 2.74
4459 7635 1.605710 GCCTTGCATGCGAATCACTAT 59.394 47.619 14.09 0.00 0.00 2.12
4460 7636 2.350197 GCCTTGCATGCGAATCACTATC 60.350 50.000 14.09 0.00 0.00 2.08
4461 7637 3.136763 CCTTGCATGCGAATCACTATCT 58.863 45.455 14.09 0.00 0.00 1.98
4462 7638 3.059120 CCTTGCATGCGAATCACTATCTG 60.059 47.826 14.09 0.00 0.00 2.90
4463 7639 3.457610 TGCATGCGAATCACTATCTGA 57.542 42.857 14.09 0.00 0.00 3.27
4464 7640 3.126073 TGCATGCGAATCACTATCTGAC 58.874 45.455 14.09 0.00 0.00 3.51
4470 7646 6.349973 TGCGAATCACTATCTGACATTTTC 57.650 37.500 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 41 3.797184 GCATCGGTAAGAGCCTGACTTAG 60.797 52.174 0.00 0.00 31.75 2.18
48 50 1.869767 CAATCCAGCATCGGTAAGAGC 59.130 52.381 0.00 0.00 0.00 4.09
53 55 2.673258 TCTACCAATCCAGCATCGGTA 58.327 47.619 0.00 0.00 0.00 4.02
65 67 3.844211 TCTGCCCACTAACTTCTACCAAT 59.156 43.478 0.00 0.00 0.00 3.16
74 76 2.614134 AGACTCTCTGCCCACTAACT 57.386 50.000 0.00 0.00 0.00 2.24
78 80 0.036022 GCAAAGACTCTCTGCCCACT 59.964 55.000 0.00 0.00 0.00 4.00
83 85 7.206687 ACTAGTAATATGCAAAGACTCTCTGC 58.793 38.462 0.00 0.00 36.60 4.26
146 152 3.976793 TGGTCGGCTCGTAGTATTAAG 57.023 47.619 0.00 0.00 0.00 1.85
147 153 4.924305 ATTGGTCGGCTCGTAGTATTAA 57.076 40.909 0.00 0.00 0.00 1.40
149 155 3.714391 GAATTGGTCGGCTCGTAGTATT 58.286 45.455 0.00 0.00 0.00 1.89
173 862 0.738975 CATGAAGTGGGCATCAGCTG 59.261 55.000 7.63 7.63 41.70 4.24
174 863 0.395311 CCATGAAGTGGGCATCAGCT 60.395 55.000 0.00 0.00 44.79 4.24
211 2103 3.325716 TGGAGGGAGTGTACCACTTTTAC 59.674 47.826 0.00 0.00 45.44 2.01
398 2895 3.826157 CCAACAACCACAATACCTGACAT 59.174 43.478 0.00 0.00 0.00 3.06
402 2899 4.394729 ACTACCAACAACCACAATACCTG 58.605 43.478 0.00 0.00 0.00 4.00
437 2942 8.524870 AGTGCAAAGATTGATCAAATTTGTAC 57.475 30.769 33.81 33.81 41.35 2.90
453 2958 7.566760 TCTCAAAAGTCAAATAGTGCAAAGA 57.433 32.000 0.00 0.00 0.00 2.52
487 2995 9.553064 CCTCTTCAAAAGAATGCTACAGTATAT 57.447 33.333 0.00 0.00 37.02 0.86
501 3009 4.022242 CGTACTCTCACCCTCTTCAAAAGA 60.022 45.833 0.00 0.00 35.87 2.52
545 3053 2.239201 GAGTTAACGCGGCATCAAAAC 58.761 47.619 12.47 3.81 0.00 2.43
579 3087 1.674817 CCTAACCGGCGTGTGAGAAAT 60.675 52.381 6.01 0.00 0.00 2.17
588 3105 1.888736 GAGACTTCCTAACCGGCGT 59.111 57.895 6.01 0.00 0.00 5.68
589 3106 1.226603 CGAGACTTCCTAACCGGCG 60.227 63.158 0.00 0.00 0.00 6.46
652 3169 7.258441 CACGACTTGTTAATCCAGAGAGAATA 58.742 38.462 0.00 0.00 0.00 1.75
695 3221 0.392595 CCACCTAACCCTTCGCCTTC 60.393 60.000 0.00 0.00 0.00 3.46
746 3280 3.736252 AGATTAGCATCATTCGCACGTAC 59.264 43.478 0.00 0.00 0.00 3.67
853 3387 4.533919 AGATCACTCCTGCTACATATGC 57.466 45.455 1.58 0.00 0.00 3.14
855 3389 6.208402 CACAGTAGATCACTCCTGCTACATAT 59.792 42.308 0.00 0.00 34.16 1.78
856 3390 5.532779 CACAGTAGATCACTCCTGCTACATA 59.467 44.000 0.00 0.00 34.16 2.29
858 3392 3.696548 CACAGTAGATCACTCCTGCTACA 59.303 47.826 0.00 0.00 34.16 2.74
859 3393 3.490078 GCACAGTAGATCACTCCTGCTAC 60.490 52.174 0.00 0.00 36.00 3.58
861 3395 1.480137 GCACAGTAGATCACTCCTGCT 59.520 52.381 0.00 0.00 36.00 4.24
862 3396 1.480137 AGCACAGTAGATCACTCCTGC 59.520 52.381 0.00 6.05 37.89 4.85
863 3397 3.519579 CAAGCACAGTAGATCACTCCTG 58.480 50.000 0.00 0.00 36.40 3.86
864 3398 2.093764 GCAAGCACAGTAGATCACTCCT 60.094 50.000 0.00 0.00 34.26 3.69
916 3473 1.336440 CAAACCAGGCGACATGAAACA 59.664 47.619 0.00 0.00 0.00 2.83
929 3486 3.071874 TGACCAGGCTAATCAAACCAG 57.928 47.619 0.00 0.00 0.00 4.00
957 3514 1.136565 CCTACGGCCGTTTGCAATG 59.863 57.895 38.94 11.28 43.89 2.82
993 3550 5.353938 GTGTGGCCTATTTATACACTCGAA 58.646 41.667 3.32 0.00 38.76 3.71
1016 3573 0.598065 GTGGTTTGCTAAGCCTGTGG 59.402 55.000 7.60 0.00 0.00 4.17
1054 3611 6.857777 TCGGTAGTTAGCTAGCTAGTTAAG 57.142 41.667 25.14 15.52 41.97 1.85
1066 3623 1.398705 CGCTCTCGATCGGTAGTTAGC 60.399 57.143 16.41 10.71 38.10 3.09
1067 3624 1.398705 GCGCTCTCGATCGGTAGTTAG 60.399 57.143 16.41 3.96 38.10 2.34
1068 3625 0.585357 GCGCTCTCGATCGGTAGTTA 59.415 55.000 16.41 0.00 38.10 2.24
1069 3626 1.355916 GCGCTCTCGATCGGTAGTT 59.644 57.895 16.41 0.00 38.10 2.24
1085 3642 0.097674 GCAAACTCAGTGCTATGGCG 59.902 55.000 0.00 0.00 42.25 5.69
1087 3644 2.417933 GTCTGCAAACTCAGTGCTATGG 59.582 50.000 0.00 0.00 42.69 2.74
1108 3676 1.542492 ACTTCTCCATGCTTGCTTGG 58.458 50.000 18.00 18.00 0.00 3.61
1250 4115 9.265862 ACCAATCAGGAGGATAAAGATAGATAG 57.734 37.037 0.00 0.00 41.22 2.08
1251 4116 9.621239 AACCAATCAGGAGGATAAAGATAGATA 57.379 33.333 0.00 0.00 41.22 1.98
1253 4118 7.937700 AACCAATCAGGAGGATAAAGATAGA 57.062 36.000 0.00 0.00 41.22 1.98
1256 4121 8.107196 AGTTAACCAATCAGGAGGATAAAGAT 57.893 34.615 0.88 0.00 41.22 2.40
1282 4147 9.701098 TTTGTCAAATACGTAACTGATTAGTCT 57.299 29.630 11.74 0.00 35.69 3.24
1305 4175 2.741517 TCGTGCACCTGTACATCATTTG 59.258 45.455 12.15 0.00 0.00 2.32
1306 4176 3.002791 CTCGTGCACCTGTACATCATTT 58.997 45.455 12.15 0.00 0.00 2.32
1315 4188 0.320771 GGTTCATCTCGTGCACCTGT 60.321 55.000 12.15 0.00 40.51 4.00
1339 4212 1.752694 GGTGGTGTTGCACAGGTGT 60.753 57.895 0.91 0.00 35.86 4.16
1562 4435 2.665185 GCCCGTGACGTTGAAGCT 60.665 61.111 3.64 0.00 0.00 3.74
1582 4455 2.901840 CACCACAGCGTGCCAACT 60.902 61.111 3.56 0.00 31.34 3.16
1902 4775 0.389426 GTACTCCGAAAAGAGCGCCA 60.389 55.000 2.29 0.00 37.39 5.69
1987 4860 0.528924 CGGTCACCATGTCCGTCTTA 59.471 55.000 6.37 0.00 42.56 2.10
2157 5038 4.754667 GAGTGGCGTCGGAACCCC 62.755 72.222 0.00 0.00 0.00 4.95
2158 5039 3.310860 ATGAGTGGCGTCGGAACCC 62.311 63.158 0.00 0.00 0.00 4.11
2162 5063 4.451150 GGCATGAGTGGCGTCGGA 62.451 66.667 0.00 0.00 41.35 4.55
2171 5072 3.654143 TGCTGGCTGGGCATGAGT 61.654 61.111 0.00 0.00 34.56 3.41
2343 5244 0.333312 ACGATGGTCTCTGGACTCCT 59.667 55.000 0.00 0.00 41.82 3.69
2687 5589 0.111639 TCTTGGGGTTGTAGTTGCCC 59.888 55.000 0.00 0.00 41.62 5.36
2740 5642 3.414700 GCACCGTGTTCCTCAGCG 61.415 66.667 0.00 0.00 0.00 5.18
3126 6063 4.724399 ACAGTTCACACATTACAATGGGA 58.276 39.130 11.09 1.03 42.45 4.37
3154 6092 4.079970 CTGACACTGAACCCTACTAGACA 58.920 47.826 0.00 0.00 0.00 3.41
3158 6096 7.453752 ACTTATTTCTGACACTGAACCCTACTA 59.546 37.037 0.00 0.00 0.00 1.82
3304 6281 7.767198 CAGTAGGATTTAGATTAAACGACCCAA 59.233 37.037 0.00 0.00 0.00 4.12
3308 6285 7.437565 GGGACAGTAGGATTTAGATTAAACGAC 59.562 40.741 0.00 0.00 0.00 4.34
3979 6961 0.756903 AGTGCCCACTTTACGTGACT 59.243 50.000 0.00 0.00 46.81 3.41
3995 6977 1.142465 AGGGCTATGCAATGGAGAGTG 59.858 52.381 0.00 0.00 0.00 3.51
3999 6981 2.160205 CATGAGGGCTATGCAATGGAG 58.840 52.381 0.00 0.00 0.00 3.86
4017 7190 6.877611 ACGAACCAATTACAGAGTTTTCAT 57.122 33.333 0.00 0.00 0.00 2.57
4019 7192 9.166126 CTTTTACGAACCAATTACAGAGTTTTC 57.834 33.333 0.00 0.00 0.00 2.29
4044 7218 7.624077 ACTTGTAGAGGTATATCACTTTTCCCT 59.376 37.037 0.00 0.00 0.00 4.20
4078 7253 7.849322 TGTCTGGCCTCTGTATAACATAATA 57.151 36.000 3.32 0.00 0.00 0.98
4214 7390 9.906660 CATACAACCAACACTAACATACAAATT 57.093 29.630 0.00 0.00 0.00 1.82
4245 7421 8.701895 TCCTCTCCGTGAACTTTACATAATTAT 58.298 33.333 0.00 0.00 0.00 1.28
4273 7449 8.736244 GGATACAAACACAATAAACACATACCT 58.264 33.333 0.00 0.00 0.00 3.08
4294 7470 9.490379 CAATATTTACACAGAAGTAGGGGATAC 57.510 37.037 0.00 0.00 34.30 2.24
4307 7483 8.506168 TCCTAGCCTTTTCAATATTTACACAG 57.494 34.615 0.00 0.00 0.00 3.66
4310 7486 9.528489 AAACTCCTAGCCTTTTCAATATTTACA 57.472 29.630 0.00 0.00 0.00 2.41
4408 7584 2.032799 CCACAGCGTCTATCTGAGAGAC 59.967 54.545 19.74 19.74 40.02 3.36


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

AutoCloner maintained by Alex Coulton.