Multiple sequence alignment - TraesCS3D01G365800

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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 TraesCS3D01G365800 chr3D 100.000 2894 0 0 1 2894 480124314 480127207 0.000000e+00 5345.0
1 TraesCS3D01G365800 chr3D 83.956 910 143 3 987 1895 480157916 480158823 0.000000e+00 869.0
2 TraesCS3D01G365800 chr3D 78.790 1207 192 38 796 1982 480366552 480367714 0.000000e+00 752.0
3 TraesCS3D01G365800 chr3D 82.774 685 96 16 805 1480 480836834 480837505 2.480000e-165 592.0
4 TraesCS3D01G365800 chr3D 85.749 407 56 2 1492 1897 480837614 480838019 2.060000e-116 429.0
5 TraesCS3D01G365800 chr3D 100.000 33 0 0 2751 2783 293182975 293182943 8.660000e-06 62.1
6 TraesCS3D01G365800 chr3D 100.000 30 0 0 2753 2782 611200138 611200109 4.030000e-04 56.5
7 TraesCS3D01G365800 chr3B 90.242 1404 121 9 995 2385 640664572 640665972 0.000000e+00 1820.0
8 TraesCS3D01G365800 chr3B 87.968 989 72 12 10 968 640663607 640664578 0.000000e+00 1123.0
9 TraesCS3D01G365800 chr3B 80.480 1209 203 26 796 1982 640700509 640701706 0.000000e+00 894.0
10 TraesCS3D01G365800 chr3B 82.260 1009 153 12 991 1989 640659390 640660382 0.000000e+00 848.0
11 TraesCS3D01G365800 chr3B 91.152 599 40 8 2298 2893 640665927 640666515 0.000000e+00 800.0
12 TraesCS3D01G365800 chr3B 86.585 82 10 1 2783 2864 622284974 622284894 3.970000e-14 89.8
13 TraesCS3D01G365800 chr3A 88.336 1406 123 16 696 2079 623196718 623198104 0.000000e+00 1650.0
14 TraesCS3D01G365800 chr3A 91.877 1108 88 1 968 2075 623200387 623201492 0.000000e+00 1546.0
15 TraesCS3D01G365800 chr3A 81.381 1101 184 14 801 1897 623389452 623390535 0.000000e+00 878.0
16 TraesCS3D01G365800 chr3A 81.176 1105 188 17 796 1895 623354310 623355399 0.000000e+00 870.0
17 TraesCS3D01G365800 chr3A 91.954 348 26 2 2084 2429 623219664 623220011 1.210000e-133 486.0
18 TraesCS3D01G365800 chr3A 85.185 108 12 4 2553 2660 111919081 111918978 1.100000e-19 108.0
19 TraesCS3D01G365800 chr2D 82.326 215 32 5 31 240 572374154 572373941 6.370000e-42 182.0
20 TraesCS3D01G365800 chr2D 100.000 31 0 0 2751 2781 631006774 631006804 1.120000e-04 58.4
21 TraesCS3D01G365800 chr5B 90.385 104 10 0 2558 2661 661308793 661308690 1.400000e-28 137.0
22 TraesCS3D01G365800 chr5B 85.000 120 15 3 2543 2660 590183763 590183645 5.070000e-23 119.0
23 TraesCS3D01G365800 chr1D 84.800 125 18 1 2538 2661 53168549 53168425 1.090000e-24 124.0
24 TraesCS3D01G365800 chr1D 87.850 107 12 1 2558 2663 120536253 120536359 1.090000e-24 124.0
25 TraesCS3D01G365800 chr1D 86.585 82 6 3 2781 2860 298637173 298637095 5.140000e-13 86.1
26 TraesCS3D01G365800 chr5D 87.500 104 13 0 2558 2661 268343044 268343147 1.410000e-23 121.0
27 TraesCS3D01G365800 chr5D 86.275 102 13 1 2559 2660 320886188 320886288 3.050000e-20 110.0
28 TraesCS3D01G365800 chr7D 88.636 88 9 1 2784 2871 1751162 1751248 3.940000e-19 106.0
29 TraesCS3D01G365800 chr7D 85.227 88 12 1 2784 2871 232828526 232828440 3.970000e-14 89.8
30 TraesCS3D01G365800 chr6B 82.031 128 20 3 2549 2675 210275600 210275475 3.940000e-19 106.0
31 TraesCS3D01G365800 chr4B 95.238 63 3 0 2811 2873 237140195 237140257 1.830000e-17 100.0
32 TraesCS3D01G365800 chr4A 93.651 63 4 0 2811 2873 395027222 395027160 8.540000e-16 95.3
33 TraesCS3D01G365800 chr4A 83.000 100 15 2 2774 2873 144679320 144679417 3.970000e-14 89.8
34 TraesCS3D01G365800 chr4A 81.522 92 11 6 2531 2619 687058001 687057913 1.440000e-08 71.3
35 TraesCS3D01G365800 chr2B 85.714 91 12 1 2784 2873 543480262 543480172 8.540000e-16 95.3
36 TraesCS3D01G365800 chr1A 100.000 29 0 0 2753 2781 280078460 280078488 1.000000e-03 54.7


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 TraesCS3D01G365800 chr3D 480124314 480127207 2893 False 5345.00 5345 100.0000 1 2894 1 chr3D.!!$F1 2893
1 TraesCS3D01G365800 chr3D 480157916 480158823 907 False 869.00 869 83.9560 987 1895 1 chr3D.!!$F2 908
2 TraesCS3D01G365800 chr3D 480366552 480367714 1162 False 752.00 752 78.7900 796 1982 1 chr3D.!!$F3 1186
3 TraesCS3D01G365800 chr3D 480836834 480838019 1185 False 510.50 592 84.2615 805 1897 2 chr3D.!!$F4 1092
4 TraesCS3D01G365800 chr3B 640659390 640666515 7125 False 1147.75 1820 87.9055 10 2893 4 chr3B.!!$F2 2883
5 TraesCS3D01G365800 chr3B 640700509 640701706 1197 False 894.00 894 80.4800 796 1982 1 chr3B.!!$F1 1186
6 TraesCS3D01G365800 chr3A 623196718 623201492 4774 False 1598.00 1650 90.1065 696 2079 2 chr3A.!!$F4 1383
7 TraesCS3D01G365800 chr3A 623389452 623390535 1083 False 878.00 878 81.3810 801 1897 1 chr3A.!!$F3 1096
8 TraesCS3D01G365800 chr3A 623354310 623355399 1089 False 870.00 870 81.1760 796 1895 1 chr3A.!!$F2 1099

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
518 4744 0.319211 GACATGTCCGAACACGTCCA 60.319 55.0 15.31 0.0 41.57 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2366 10220 0.4546 CATGCATGTTGAGGTGAGCC 59.545 55.0 18.91 0.0 0.0 4.7 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
25 4234 2.509336 CGCCTCCGACGCAAGAAT 60.509 61.111 0.00 0.00 43.62 2.40
38 4247 1.451028 AAGAATGCAGAGGCGCTCC 60.451 57.895 7.64 0.00 45.35 4.70
39 4248 2.124983 GAATGCAGAGGCGCTCCA 60.125 61.111 7.64 0.00 45.35 3.86
91 4300 1.522580 GGAGAATGAGACCGCTGCC 60.523 63.158 0.00 0.00 0.00 4.85
92 4301 1.880340 GAGAATGAGACCGCTGCCG 60.880 63.158 0.00 0.00 0.00 5.69
119 4328 2.280797 TGCACCACGTGAAGGAGC 60.281 61.111 19.30 11.55 42.19 4.70
145 4354 1.076339 CCTCCTCCGCCTTCTCTCT 60.076 63.158 0.00 0.00 0.00 3.10
160 4369 3.357203 TCTCTCTGGCTACATTTCGTCT 58.643 45.455 0.00 0.00 0.00 4.18
173 4382 1.595093 TTCGTCTGCATCGGAGAGCA 61.595 55.000 10.63 7.54 43.63 4.26
184 4393 2.427320 GAGAGCAGCACCACCACA 59.573 61.111 0.00 0.00 0.00 4.17
197 4409 1.890979 ACCACAGACGACGACGACT 60.891 57.895 15.32 10.61 43.96 4.18
203 4415 3.081159 GACGACGACGACTCTCCCG 62.081 68.421 15.32 0.00 42.66 5.14
207 4419 3.441290 CGACGACTCTCCCGCCTT 61.441 66.667 0.00 0.00 0.00 4.35
284 4496 1.071471 ACCAAGCGGTGAACTCTGG 59.929 57.895 0.00 0.00 46.79 3.86
287 4499 3.883744 AAGCGGTGAACTCTGGCCG 62.884 63.158 0.00 0.00 46.17 6.13
309 4521 1.876156 CTCCGCCTCTGCATTTTATCC 59.124 52.381 0.00 0.00 37.32 2.59
353 4565 9.886132 ATTATAAGTCCAACGAACTATGTCTTT 57.114 29.630 0.00 0.00 0.00 2.52
355 4567 6.541111 AAGTCCAACGAACTATGTCTTTTC 57.459 37.500 0.00 0.00 0.00 2.29
368 4580 2.151202 GTCTTTTCGGGTCAGATGCAA 58.849 47.619 0.00 0.00 0.00 4.08
381 4593 6.595716 GGGTCAGATGCAATATGTCCTATTAC 59.404 42.308 0.00 0.00 42.22 1.89
394 4606 4.785914 TGTCCTATTACCCATGTGGAGAAA 59.214 41.667 0.00 0.00 37.39 2.52
405 4617 5.221048 CCCATGTGGAGAAATTTATCGTTCC 60.221 44.000 6.73 3.24 37.39 3.62
446 4672 1.889170 TGTTTATGTGCGGGCAAATGA 59.111 42.857 6.58 0.00 0.00 2.57
466 4692 7.956328 AATGACTACTACAGTTGTGGATAGA 57.044 36.000 5.53 0.00 37.72 1.98
467 4693 7.575414 ATGACTACTACAGTTGTGGATAGAG 57.425 40.000 5.53 0.00 37.72 2.43
482 4708 4.943705 TGGATAGAGAAAAATGGACACTGC 59.056 41.667 0.00 0.00 0.00 4.40
493 4719 3.161450 ACACTGCCCGGTCACTGT 61.161 61.111 0.00 0.00 0.00 3.55
496 4722 2.425592 CTGCCCGGTCACTGTCAA 59.574 61.111 0.00 0.00 0.00 3.18
497 4723 1.961277 CTGCCCGGTCACTGTCAAC 60.961 63.158 0.00 0.00 0.00 3.18
517 4743 2.442084 GACATGTCCGAACACGTCC 58.558 57.895 15.31 0.00 41.57 4.79
518 4744 0.319211 GACATGTCCGAACACGTCCA 60.319 55.000 15.31 0.00 41.57 4.02
552 4778 2.096819 GGACTGTTTTTGCGAGTTGTGA 59.903 45.455 0.00 0.00 0.00 3.58
577 4803 6.907853 TGTAGATGCTCTAAGACTGCATAT 57.092 37.500 0.00 0.00 45.90 1.78
620 4846 2.835156 AGTAGAAAACAGAGGAGAGGGC 59.165 50.000 0.00 0.00 0.00 5.19
625 4851 1.264045 AACAGAGGAGAGGGCTCAGC 61.264 60.000 0.00 0.00 43.14 4.26
630 4856 1.834263 GAGGAGAGGGCTCAGCTTTTA 59.166 52.381 0.00 0.00 43.14 1.52
634 4860 2.357323 GAGAGGGCTCAGCTTTTATTGC 59.643 50.000 0.00 0.00 40.96 3.56
649 4875 5.431420 TTTATTGCACGTCTTGTTGATGT 57.569 34.783 0.00 0.00 45.09 3.06
657 4883 3.066203 ACGTCTTGTTGATGTTTTGGTCC 59.934 43.478 0.00 0.00 41.80 4.46
729 4966 7.646526 CCATTGATCAGTACGAGTAAATTACGA 59.353 37.037 0.00 0.00 0.00 3.43
730 4967 8.682895 CATTGATCAGTACGAGTAAATTACGAG 58.317 37.037 0.00 0.00 0.00 4.18
782 5019 4.443913 AACATTGCCGGTAAATTGGTAC 57.556 40.909 9.67 0.00 0.00 3.34
783 5020 3.692690 ACATTGCCGGTAAATTGGTACT 58.307 40.909 9.67 0.00 0.00 2.73
784 5021 3.692593 ACATTGCCGGTAAATTGGTACTC 59.307 43.478 9.67 0.00 0.00 2.59
785 5022 3.706600 TTGCCGGTAAATTGGTACTCT 57.293 42.857 1.06 0.00 0.00 3.24
786 5023 2.980568 TGCCGGTAAATTGGTACTCTG 58.019 47.619 1.90 0.00 0.00 3.35
787 5024 1.669265 GCCGGTAAATTGGTACTCTGC 59.331 52.381 1.90 0.00 0.00 4.26
788 5025 2.937873 GCCGGTAAATTGGTACTCTGCA 60.938 50.000 1.90 0.00 0.00 4.41
789 5026 3.340034 CCGGTAAATTGGTACTCTGCAA 58.660 45.455 0.00 0.00 0.00 4.08
790 5027 3.754323 CCGGTAAATTGGTACTCTGCAAA 59.246 43.478 0.00 0.00 0.00 3.68
791 5028 4.142687 CCGGTAAATTGGTACTCTGCAAAG 60.143 45.833 0.00 0.00 0.00 2.77
792 5029 4.671766 CGGTAAATTGGTACTCTGCAAAGC 60.672 45.833 0.00 0.00 0.00 3.51
793 5030 3.942130 AAATTGGTACTCTGCAAAGCC 57.058 42.857 0.00 0.00 0.00 4.35
794 5031 1.839424 ATTGGTACTCTGCAAAGCCC 58.161 50.000 0.00 0.00 0.00 5.19
823 5060 2.992114 AGGAGCGGACAAGCGACT 60.992 61.111 0.00 0.00 43.00 4.18
900 5144 4.136796 CAAACATACCCGACATCCATCAT 58.863 43.478 0.00 0.00 0.00 2.45
901 5145 3.685139 ACATACCCGACATCCATCATC 57.315 47.619 0.00 0.00 0.00 2.92
902 5146 2.972021 ACATACCCGACATCCATCATCA 59.028 45.455 0.00 0.00 0.00 3.07
903 5147 3.007290 ACATACCCGACATCCATCATCAG 59.993 47.826 0.00 0.00 0.00 2.90
908 5152 3.321968 CCCGACATCCATCATCAGAACTA 59.678 47.826 0.00 0.00 0.00 2.24
962 5220 3.876341 AGTCTCTACTCCTTCCTGTACG 58.124 50.000 0.00 0.00 0.00 3.67
965 5223 2.614983 CTCTACTCCTTCCTGTACGAGC 59.385 54.545 0.00 0.00 0.00 5.03
986 5263 2.423898 GCTAGCCAGGTACGCTCCA 61.424 63.158 2.29 0.00 37.79 3.86
1032 5309 1.851304 CTCTCACTCTCCTCCAGCTT 58.149 55.000 0.00 0.00 0.00 3.74
1047 5324 2.967946 GCTTACCGCCACCCTCCTT 61.968 63.158 0.00 0.00 0.00 3.36
1146 5423 2.435938 ACATGCGCGTCCGGAAAT 60.436 55.556 5.23 0.00 38.61 2.17
1185 5462 0.400594 CTTTCCTCCCCAAGTTCGGT 59.599 55.000 0.00 0.00 0.00 4.69
1269 5546 1.028868 GCCAGAGCAAGGACATCCAC 61.029 60.000 0.00 0.00 39.53 4.02
1305 5582 1.551329 GGTGTCAAGGTCCTCCTCTCT 60.551 57.143 0.00 0.00 44.35 3.10
1488 5765 1.178276 AGTTCTGGAACGATCTCGCT 58.822 50.000 7.67 0.00 45.50 4.93
1515 5889 5.935206 GGACCTGAAGAACTTAGGAAAGAAG 59.065 44.000 13.04 0.00 36.50 2.85
1520 5894 5.844516 TGAAGAACTTAGGAAAGAAGGGAGA 59.155 40.000 0.00 0.00 36.50 3.71
1584 9363 2.359850 GAGTGGGACGGCAATGCA 60.360 61.111 7.79 0.00 0.00 3.96
1599 9378 1.315257 ATGCAATCAACACGGGGCTC 61.315 55.000 0.00 0.00 0.00 4.70
1641 9420 1.416243 TCTACAACAACCCGGAGTGT 58.584 50.000 0.73 3.00 0.00 3.55
1674 9453 2.032634 GCGTGGAGCGTTCATGGAA 61.033 57.895 0.53 0.00 43.66 3.53
1897 9676 2.715046 TCAAGAGCCATGTGTGATTCC 58.285 47.619 0.00 0.00 0.00 3.01
1930 9725 4.211374 GCTTGGCCTAGTATTTATGTGTCG 59.789 45.833 15.85 0.00 0.00 4.35
1946 9745 2.290641 GTGTCGCTTGTCCTGTTTCATT 59.709 45.455 0.00 0.00 0.00 2.57
1973 9772 6.493449 TCATGCGTTAATTGTTTGAGATGA 57.507 33.333 0.00 0.00 0.00 2.92
2082 9884 9.778741 TCTAAGCTAAGTCCCATAATACAATTG 57.221 33.333 3.24 3.24 0.00 2.32
2089 9891 4.887071 GTCCCATAATACAATTGAGCACCA 59.113 41.667 13.59 0.00 0.00 4.17
2104 9906 6.048732 TGAGCACCATGACATACTTTTCTA 57.951 37.500 0.00 0.00 0.00 2.10
2162 9971 8.903820 AGTTATAATCTTACATTTGGCAACCTC 58.096 33.333 0.00 0.00 0.00 3.85
2165 9974 6.610075 AATCTTACATTTGGCAACCTCAAT 57.390 33.333 0.00 0.00 0.00 2.57
2188 9998 3.857157 ATAACATCCGGTATGCAGGTT 57.143 42.857 0.00 0.00 39.39 3.50
2191 10001 1.299541 CATCCGGTATGCAGGTTCAC 58.700 55.000 0.00 0.00 0.00 3.18
2192 10002 0.180406 ATCCGGTATGCAGGTTCACC 59.820 55.000 0.00 0.00 0.00 4.02
2216 10026 6.091849 CCATATTCTCATGGTCTAAAGATGCG 59.908 42.308 0.00 0.00 40.62 4.73
2218 10028 4.736126 TCTCATGGTCTAAAGATGCGAA 57.264 40.909 0.00 0.00 0.00 4.70
2224 10034 5.712217 TGGTCTAAAGATGCGAATAAACG 57.288 39.130 0.00 0.00 0.00 3.60
2228 10038 7.331440 TGGTCTAAAGATGCGAATAAACGTTAA 59.669 33.333 0.00 0.00 35.59 2.01
2231 10041 8.164153 TCTAAAGATGCGAATAAACGTTAACAC 58.836 33.333 0.00 0.00 35.59 3.32
2240 10050 8.706035 GCGAATAAACGTTAACACATCCTATAT 58.294 33.333 0.00 0.00 35.59 0.86
2270 10080 9.796180 GATCTAAGTAGTTAATCTCCACTCCTA 57.204 37.037 0.00 0.00 0.00 2.94
2275 10085 9.892130 AAGTAGTTAATCTCCACTCCTAAATTG 57.108 33.333 0.00 0.00 0.00 2.32
2282 10092 6.042638 TCTCCACTCCTAAATTGTCTCAAG 57.957 41.667 0.00 0.00 0.00 3.02
2285 10095 6.409704 TCCACTCCTAAATTGTCTCAAGATG 58.590 40.000 0.00 0.00 0.00 2.90
2309 10162 5.744345 GCACACATACTACATCACTACTCAC 59.256 44.000 0.00 0.00 0.00 3.51
2319 10172 0.532573 CACTACTCACGCCACCTCAT 59.467 55.000 0.00 0.00 0.00 2.90
2366 10220 2.719739 ACTCATGCCACCTCATCAAAG 58.280 47.619 0.00 0.00 0.00 2.77
2369 10223 0.333993 ATGCCACCTCATCAAAGGCT 59.666 50.000 0.00 0.00 45.42 4.58
2384 10238 0.330604 AGGCTCACCTCAACATGCAT 59.669 50.000 0.00 0.00 46.34 3.96
2450 10304 4.960938 TCAACATGCACATATCCTACCTC 58.039 43.478 0.00 0.00 0.00 3.85
2459 10313 5.698545 GCACATATCCTACCTCATCAAAGAC 59.301 44.000 0.00 0.00 0.00 3.01
2482 10336 4.763073 TCACCACAACATGCATTGAAAAA 58.237 34.783 7.04 0.00 33.57 1.94
2578 10432 6.743575 AAGAATTACTTGTCTCGGAAATGG 57.256 37.500 0.00 0.00 37.45 3.16
2603 10457 8.689069 GGATGTATCTAGACGTATTTTTCGTTC 58.311 37.037 0.00 0.00 41.64 3.95
2612 10466 8.612233 AGACGTATTTTTCGTTCTAGATACAC 57.388 34.615 0.00 0.00 41.64 2.90
2624 10478 7.042335 CGTTCTAGATACACCCATTTCTTTCT 58.958 38.462 0.00 0.00 0.00 2.52
2634 10488 6.155827 CACCCATTTCTTTCTATTTTTGCGA 58.844 36.000 0.00 0.00 0.00 5.10
2644 10498 9.959749 TCTTTCTATTTTTGCGACAAGTAATTT 57.040 25.926 0.00 0.00 0.00 1.82
2645 10499 9.993881 CTTTCTATTTTTGCGACAAGTAATTTG 57.006 29.630 0.00 0.00 42.68 2.32
2754 10610 4.944962 TGAAATATTGCAGTGACTTCCG 57.055 40.909 0.00 0.00 0.00 4.30
2764 10620 3.345808 GACTTCCGCAGCAACGCA 61.346 61.111 0.00 0.00 0.00 5.24
2776 10632 2.358247 AACGCACGGGGTGTCATC 60.358 61.111 0.00 0.00 39.93 2.92
2779 10635 1.226974 CGCACGGGGTGTCATCTAG 60.227 63.158 0.00 0.00 35.75 2.43
2857 10713 3.364460 TGGGTCTATCCAACACCATTG 57.636 47.619 0.00 0.00 38.11 2.82
2883 10739 2.223340 GCTAACAATGTCGGCATCCTTG 60.223 50.000 1.37 0.82 33.50 3.61
2893 10749 1.399440 CGGCATCCTTGTCACATTGAG 59.601 52.381 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.093278 CATTCTTGCGTCGGAGGC 58.907 61.111 15.31 15.31 0.00 4.70
10 11 3.093278 GCATTCTTGCGTCGGAGG 58.907 61.111 0.00 0.00 39.49 4.30
102 4311 2.280797 GCTCCTTCACGTGGTGCA 60.281 61.111 17.00 0.00 41.91 4.57
138 4347 3.764434 AGACGAAATGTAGCCAGAGAGAA 59.236 43.478 0.00 0.00 0.00 2.87
139 4348 3.129462 CAGACGAAATGTAGCCAGAGAGA 59.871 47.826 0.00 0.00 0.00 3.10
145 4354 2.279741 GATGCAGACGAAATGTAGCCA 58.720 47.619 0.00 0.00 32.34 4.75
160 4369 2.125391 GTGCTGCTCTCCGATGCA 60.125 61.111 0.00 0.00 37.63 3.96
173 4382 2.421739 GTCGTCTGTGGTGGTGCT 59.578 61.111 0.00 0.00 0.00 4.40
184 4393 1.741032 GGGAGAGTCGTCGTCGTCT 60.741 63.158 1.35 1.35 38.04 4.18
203 4415 1.883084 CCCTGTACGCATCGAAGGC 60.883 63.158 2.57 2.57 0.00 4.35
207 4419 1.077285 TCCTCCCTGTACGCATCGA 60.077 57.895 0.00 0.00 0.00 3.59
244 4456 4.659172 CCCTTGCCCTTGCGGTCA 62.659 66.667 0.00 0.00 41.78 4.02
272 4484 2.432628 GTCGGCCAGAGTTCACCG 60.433 66.667 2.24 0.00 46.97 4.94
287 4499 2.024176 TAAAATGCAGAGGCGGAGTC 57.976 50.000 0.00 0.00 45.35 3.36
334 4546 4.143179 CCGAAAAGACATAGTTCGTTGGAC 60.143 45.833 4.56 0.00 41.91 4.02
335 4547 3.991773 CCGAAAAGACATAGTTCGTTGGA 59.008 43.478 4.56 0.00 41.91 3.53
338 4550 3.992427 GACCCGAAAAGACATAGTTCGTT 59.008 43.478 4.56 0.00 41.91 3.85
340 4552 3.581755 TGACCCGAAAAGACATAGTTCG 58.418 45.455 0.00 0.00 42.85 3.95
353 4565 3.466836 GACATATTGCATCTGACCCGAA 58.533 45.455 0.00 0.00 0.00 4.30
355 4567 2.146342 GGACATATTGCATCTGACCCG 58.854 52.381 0.00 0.00 0.00 5.28
368 4580 6.331032 TCTCCACATGGGTAATAGGACATAT 58.669 40.000 0.00 0.00 38.11 1.78
381 4593 5.221048 GGAACGATAAATTTCTCCACATGGG 60.221 44.000 0.00 0.00 35.41 4.00
394 4606 8.908786 ATGTAGATCAACATGGAACGATAAAT 57.091 30.769 0.00 0.00 38.65 1.40
428 4640 2.166829 AGTCATTTGCCCGCACATAAA 58.833 42.857 0.00 0.00 0.00 1.40
429 4641 1.832883 AGTCATTTGCCCGCACATAA 58.167 45.000 0.00 0.00 0.00 1.90
431 4643 1.094785 GTAGTCATTTGCCCGCACAT 58.905 50.000 0.00 0.00 0.00 3.21
432 4644 0.036164 AGTAGTCATTTGCCCGCACA 59.964 50.000 0.00 0.00 0.00 4.57
446 4672 8.418597 TTTTCTCTATCCACAACTGTAGTAGT 57.581 34.615 0.00 0.00 42.89 2.73
466 4692 1.247567 CGGGCAGTGTCCATTTTTCT 58.752 50.000 15.51 0.00 0.00 2.52
467 4693 0.243636 CCGGGCAGTGTCCATTTTTC 59.756 55.000 15.51 0.00 0.00 2.29
482 4708 2.357034 CCGTTGACAGTGACCGGG 60.357 66.667 6.32 0.00 35.11 5.73
514 4740 1.609210 CCCCCAAACACCCATGGAC 60.609 63.158 15.22 0.00 39.12 4.02
517 4743 0.899717 CAGTCCCCCAAACACCCATG 60.900 60.000 0.00 0.00 0.00 3.66
518 4744 1.368268 ACAGTCCCCCAAACACCCAT 61.368 55.000 0.00 0.00 0.00 4.00
577 4803 0.542938 AGAGTACCAGGCAGAGCACA 60.543 55.000 0.00 0.00 0.00 4.57
620 4846 4.153986 CAAGACGTGCAATAAAAGCTGAG 58.846 43.478 0.00 0.00 0.00 3.35
625 4851 5.914635 ACATCAACAAGACGTGCAATAAAAG 59.085 36.000 0.00 0.00 0.00 2.27
630 4856 3.988379 AACATCAACAAGACGTGCAAT 57.012 38.095 0.00 0.00 0.00 3.56
634 4860 4.027572 ACCAAAACATCAACAAGACGTG 57.972 40.909 0.00 0.00 0.00 4.49
649 4875 0.250553 CCTACCGTGCTGGACCAAAA 60.251 55.000 0.00 0.00 42.00 2.44
657 4883 2.358247 AAACGCCCTACCGTGCTG 60.358 61.111 0.00 0.00 41.90 4.41
715 4952 8.127954 GGTAATCTCTTCTCGTAATTTACTCGT 58.872 37.037 5.11 0.00 0.00 4.18
729 4966 1.471119 TGCGGTCGGTAATCTCTTCT 58.529 50.000 0.00 0.00 0.00 2.85
730 4967 2.288961 TTGCGGTCGGTAATCTCTTC 57.711 50.000 0.00 0.00 0.00 2.87
782 5019 3.426695 CGTCTAAATTGGGCTTTGCAGAG 60.427 47.826 0.00 0.00 0.00 3.35
783 5020 2.487762 CGTCTAAATTGGGCTTTGCAGA 59.512 45.455 0.00 0.00 0.00 4.26
784 5021 2.867429 CGTCTAAATTGGGCTTTGCAG 58.133 47.619 0.00 0.00 0.00 4.41
785 5022 1.067915 GCGTCTAAATTGGGCTTTGCA 60.068 47.619 0.00 0.00 0.00 4.08
786 5023 1.067915 TGCGTCTAAATTGGGCTTTGC 60.068 47.619 0.00 0.00 0.00 3.68
787 5024 2.415893 CCTGCGTCTAAATTGGGCTTTG 60.416 50.000 0.00 0.00 0.00 2.77
788 5025 1.818674 CCTGCGTCTAAATTGGGCTTT 59.181 47.619 0.00 0.00 0.00 3.51
789 5026 1.004277 TCCTGCGTCTAAATTGGGCTT 59.996 47.619 0.00 0.00 0.00 4.35
790 5027 0.618458 TCCTGCGTCTAAATTGGGCT 59.382 50.000 0.00 0.00 0.00 5.19
791 5028 1.017387 CTCCTGCGTCTAAATTGGGC 58.983 55.000 0.00 0.00 0.00 5.36
792 5029 1.017387 GCTCCTGCGTCTAAATTGGG 58.983 55.000 0.00 0.00 0.00 4.12
900 5144 7.284489 AGGTGCACTTTGTATTTTTAGTTCTGA 59.716 33.333 17.98 0.00 0.00 3.27
901 5145 7.425606 AGGTGCACTTTGTATTTTTAGTTCTG 58.574 34.615 17.98 0.00 0.00 3.02
902 5146 7.255486 GGAGGTGCACTTTGTATTTTTAGTTCT 60.255 37.037 17.98 0.00 0.00 3.01
903 5147 6.861572 GGAGGTGCACTTTGTATTTTTAGTTC 59.138 38.462 17.98 0.00 0.00 3.01
908 5152 4.892934 TGAGGAGGTGCACTTTGTATTTTT 59.107 37.500 17.98 0.00 0.00 1.94
917 5161 1.056700 ACTGGTGAGGAGGTGCACTT 61.057 55.000 17.98 9.59 35.43 3.16
920 5164 1.152247 AGACTGGTGAGGAGGTGCA 60.152 57.895 0.00 0.00 0.00 4.57
965 5223 0.594110 GAGCGTACCTGGCTAGCTAG 59.406 60.000 20.50 20.50 41.72 3.42
986 5263 2.765969 CCATGGCTGGGGTCAAGT 59.234 61.111 0.00 0.00 39.04 3.16
1032 5309 2.203877 ACAAGGAGGGTGGCGGTA 60.204 61.111 0.00 0.00 0.00 4.02
1083 5360 3.012119 TGGCCCCAATAGACGGCA 61.012 61.111 0.00 0.00 44.90 5.69
1092 5369 4.323477 CCGTCGTTCTGGCCCCAA 62.323 66.667 0.00 0.00 0.00 4.12
1146 5423 4.574674 AGCCAGGATGACAAACTCATAA 57.425 40.909 0.00 0.00 39.96 1.90
1488 5765 4.038271 TCCTAAGTTCTTCAGGTCCGTA 57.962 45.455 0.00 0.00 0.00 4.02
1515 5889 1.235281 GCAGGACGGTTTTGTCTCCC 61.235 60.000 0.00 0.00 38.91 4.30
1520 5894 1.166531 GCTCAGCAGGACGGTTTTGT 61.167 55.000 0.00 0.00 0.00 2.83
1584 9363 0.673644 CGAAGAGCCCCGTGTTGATT 60.674 55.000 0.00 0.00 0.00 2.57
1599 9378 1.278238 GCACCCATACGAAGTCGAAG 58.722 55.000 7.87 0.00 43.93 3.79
1674 9453 2.681976 CGACTCCCATCTTTTCCATGCT 60.682 50.000 0.00 0.00 0.00 3.79
1897 9676 0.618458 TAGGCCAAGCACACTAAGGG 59.382 55.000 5.01 0.00 0.00 3.95
1930 9725 5.627499 TGATACAATGAAACAGGACAAGC 57.373 39.130 0.00 0.00 0.00 4.01
1946 9745 7.371126 TCTCAAACAATTAACGCATGATACA 57.629 32.000 0.00 0.00 0.00 2.29
1973 9772 7.205992 CGGTATGCTAGCTATCAATATGATGT 58.794 38.462 17.23 0.00 37.70 3.06
1984 9783 3.493334 TGTACACCGGTATGCTAGCTAT 58.507 45.455 17.23 10.27 0.00 2.97
2053 9855 9.832445 TTGTATTATGGGACTTAGCTTAGAAAG 57.168 33.333 6.76 0.00 0.00 2.62
2081 9883 4.910195 AGAAAAGTATGTCATGGTGCTCA 58.090 39.130 0.00 0.00 0.00 4.26
2082 9884 6.109359 ACTAGAAAAGTATGTCATGGTGCTC 58.891 40.000 0.00 0.00 36.36 4.26
2113 9915 8.732746 ACTGGGTGATCATAAAAGTAACATAC 57.267 34.615 0.00 0.00 0.00 2.39
2142 9944 6.014327 ACATTGAGGTTGCCAAATGTAAGATT 60.014 34.615 13.81 0.00 39.54 2.40
2145 9954 5.138125 ACATTGAGGTTGCCAAATGTAAG 57.862 39.130 13.81 0.00 39.54 2.34
2147 9956 7.394641 TGTTATACATTGAGGTTGCCAAATGTA 59.605 33.333 19.36 19.36 43.09 2.29
2162 9971 5.122239 CCTGCATACCGGATGTTATACATTG 59.878 44.000 9.46 0.00 39.27 2.82
2165 9974 3.644265 ACCTGCATACCGGATGTTATACA 59.356 43.478 9.46 0.00 37.90 2.29
2192 10002 6.870439 TCGCATCTTTAGACCATGAGAATATG 59.130 38.462 0.00 0.00 0.00 1.78
2244 10054 8.700439 AGGAGTGGAGATTAACTACTTAGATC 57.300 38.462 0.00 0.00 33.61 2.75
2250 10060 9.047947 ACAATTTAGGAGTGGAGATTAACTACT 57.952 33.333 0.00 0.00 40.74 2.57
2251 10061 9.315525 GACAATTTAGGAGTGGAGATTAACTAC 57.684 37.037 0.00 0.00 0.00 2.73
2252 10062 9.268282 AGACAATTTAGGAGTGGAGATTAACTA 57.732 33.333 0.00 0.00 0.00 2.24
2253 10063 8.152023 AGACAATTTAGGAGTGGAGATTAACT 57.848 34.615 0.00 0.00 0.00 2.24
2254 10064 8.041323 TGAGACAATTTAGGAGTGGAGATTAAC 58.959 37.037 0.00 0.00 0.00 2.01
2256 10066 7.733773 TGAGACAATTTAGGAGTGGAGATTA 57.266 36.000 0.00 0.00 0.00 1.75
2257 10067 6.627087 TGAGACAATTTAGGAGTGGAGATT 57.373 37.500 0.00 0.00 0.00 2.40
2262 10072 5.065731 GCATCTTGAGACAATTTAGGAGTGG 59.934 44.000 0.00 0.00 0.00 4.00
2267 10077 5.181811 TGTGTGCATCTTGAGACAATTTAGG 59.818 40.000 0.00 0.00 0.00 2.69
2270 10080 5.717078 ATGTGTGCATCTTGAGACAATTT 57.283 34.783 0.00 0.00 0.00 1.82
2275 10085 5.410924 TGTAGTATGTGTGCATCTTGAGAC 58.589 41.667 0.00 0.00 36.58 3.36
2282 10092 6.507900 AGTAGTGATGTAGTATGTGTGCATC 58.492 40.000 0.00 0.00 36.58 3.91
2285 10095 5.744345 GTGAGTAGTGATGTAGTATGTGTGC 59.256 44.000 0.00 0.00 0.00 4.57
2309 10162 2.409870 GGCCTTTGATGAGGTGGCG 61.410 63.158 0.00 0.00 44.07 5.69
2366 10220 0.454600 CATGCATGTTGAGGTGAGCC 59.545 55.000 18.91 0.00 0.00 4.70
2410 10264 9.270640 GCATGTTGAGATAAATAGAGAAGTGAT 57.729 33.333 0.00 0.00 0.00 3.06
2411 10265 8.260114 TGCATGTTGAGATAAATAGAGAAGTGA 58.740 33.333 0.00 0.00 0.00 3.41
2412 10266 8.333908 GTGCATGTTGAGATAAATAGAGAAGTG 58.666 37.037 0.00 0.00 0.00 3.16
2413 10267 8.043113 TGTGCATGTTGAGATAAATAGAGAAGT 58.957 33.333 0.00 0.00 0.00 3.01
2414 10268 8.429493 TGTGCATGTTGAGATAAATAGAGAAG 57.571 34.615 0.00 0.00 0.00 2.85
2415 10269 8.969260 ATGTGCATGTTGAGATAAATAGAGAA 57.031 30.769 0.00 0.00 0.00 2.87
2435 10289 5.698545 GTCTTTGATGAGGTAGGATATGTGC 59.301 44.000 0.00 0.00 0.00 4.57
2450 10304 4.790878 CATGTTGTGGTGAGTCTTTGATG 58.209 43.478 0.00 0.00 0.00 3.07
2459 10313 3.646611 TTCAATGCATGTTGTGGTGAG 57.353 42.857 0.00 0.00 0.00 3.51
2571 10425 9.490379 AAAATACGTCTAGATACATCCATTTCC 57.510 33.333 0.00 0.00 0.00 3.13
2578 10432 9.448294 AGAACGAAAAATACGTCTAGATACATC 57.552 33.333 0.00 0.00 43.16 3.06
2612 10466 6.155827 TGTCGCAAAAATAGAAAGAAATGGG 58.844 36.000 0.00 0.00 0.00 4.00
2624 10478 6.864165 GTCCCAAATTACTTGTCGCAAAAATA 59.136 34.615 0.00 0.00 32.65 1.40
2630 10484 1.801771 CGTCCCAAATTACTTGTCGCA 59.198 47.619 0.00 0.00 32.65 5.10
2634 10488 3.071892 TCACTCCGTCCCAAATTACTTGT 59.928 43.478 0.00 0.00 32.65 3.16
2644 10498 2.812836 TGTATACTCACTCCGTCCCA 57.187 50.000 4.17 0.00 0.00 4.37
2645 10499 5.243283 ACATATTGTATACTCACTCCGTCCC 59.757 44.000 4.17 0.00 0.00 4.46
2731 10585 5.677091 GCGGAAGTCACTGCAATATTTCAAT 60.677 40.000 0.00 0.00 41.27 2.57
2746 10602 3.345808 GCGTTGCTGCGGAAGTCA 61.346 61.111 0.00 0.00 0.00 3.41
2764 10620 5.391256 TCATATAACTAGATGACACCCCGT 58.609 41.667 0.00 0.00 29.77 5.28
2811 10667 8.060931 ACTTATGATATACTGCGAGATCACAT 57.939 34.615 0.00 0.00 31.41 3.21
2812 10668 7.454260 ACTTATGATATACTGCGAGATCACA 57.546 36.000 0.00 0.00 31.41 3.58
2819 10675 5.538813 AGACCCAACTTATGATATACTGCGA 59.461 40.000 0.00 0.00 0.00 5.10
2820 10676 5.784177 AGACCCAACTTATGATATACTGCG 58.216 41.667 0.00 0.00 0.00 5.18
2857 10713 1.804151 TGCCGACATTGTTAGCAGAAC 59.196 47.619 9.78 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.