Multiple sequence alignment - TraesCS2B01G009600

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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 TraesCS2B01G009600 chr2B 100.000 2382 0 0 740 3121 5578916 5581297 0.000000e+00 4399.0
1 TraesCS2B01G009600 chr2B 100.000 400 0 0 1 400 5578177 5578576 0.000000e+00 739.0
2 TraesCS2B01G009600 chr2A 89.766 1153 70 20 888 2018 4350019 4348893 0.000000e+00 1432.0
3 TraesCS2B01G009600 chr2A 87.574 1014 62 23 2015 2970 4348833 4347826 0.000000e+00 1116.0
4 TraesCS2B01G009600 chr2A 80.488 410 68 7 1 400 4350661 4350254 1.410000e-78 303.0
5 TraesCS2B01G009600 chr2A 86.301 146 14 5 2348 2489 4324836 4324693 1.500000e-33 154.0
6 TraesCS2B01G009600 chr2A 75.936 187 37 5 1374 1559 4617555 4617734 4.290000e-14 89.8
7 TraesCS2B01G009600 chr2D 87.080 983 64 34 1083 2018 5903811 5902845 0.000000e+00 1053.0
8 TraesCS2B01G009600 chr2D 87.667 673 42 13 2015 2646 5902783 5902111 0.000000e+00 745.0
9 TraesCS2B01G009600 chr2D 93.069 404 23 3 1 400 5904499 5904097 1.250000e-163 586.0
10 TraesCS2B01G009600 chr2D 90.345 290 26 1 741 1028 5904090 5903801 2.270000e-101 379.0
11 TraesCS2B01G009600 chr2D 81.922 437 52 15 2348 2764 5916202 5915773 8.290000e-91 344.0
12 TraesCS2B01G009600 chr2D 84.416 154 16 7 2348 2497 5882896 5882747 9.020000e-31 145.0
13 TraesCS2B01G009600 chr1A 91.083 157 14 0 2964 3120 143812255 143812411 2.440000e-51 213.0
14 TraesCS2B01G009600 chr6B 91.026 156 14 0 2964 3119 188831043 188830888 8.770000e-51 211.0
15 TraesCS2B01G009600 chr5D 91.026 156 14 0 2964 3119 393735113 393734958 8.770000e-51 211.0
16 TraesCS2B01G009600 chr4D 91.026 156 12 2 2964 3118 351739559 351739713 3.150000e-50 209.0
17 TraesCS2B01G009600 chr3D 90.506 158 15 0 2964 3121 369414406 369414249 3.150000e-50 209.0
18 TraesCS2B01G009600 chr7B 90.506 158 13 2 2965 3121 449541481 449541637 1.130000e-49 207.0
19 TraesCS2B01G009600 chr1D 90.446 157 15 0 2964 3120 145935484 145935640 1.130000e-49 207.0
20 TraesCS2B01G009600 chr1B 90.446 157 15 0 2964 3120 194786636 194786792 1.130000e-49 207.0
21 TraesCS2B01G009600 chrUn 90.566 159 10 2 2964 3121 75084480 75084326 4.080000e-49 206.0
22 TraesCS2B01G009600 chr3B 87.500 80 10 0 2025 2104 232635930 232636009 3.310000e-15 93.5


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 TraesCS2B01G009600 chr2B 5578177 5581297 3120 False 2569.000000 4399 100.000000 1 3121 2 chr2B.!!$F1 3120
1 TraesCS2B01G009600 chr2A 4347826 4350661 2835 True 950.333333 1432 85.942667 1 2970 3 chr2A.!!$R2 2969
2 TraesCS2B01G009600 chr2D 5902111 5904499 2388 True 690.750000 1053 89.540250 1 2646 4 chr2D.!!$R3 2645

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
872 883 0.604578 TTAAGTAGAGGGCGTTGCGT 59.395 50.0 0.0 0.0 0.0 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2538 2737 0.597072 GGAACACTCCTCGTCTTCGT 59.403 55.0 0.0 0.0 38.88 3.85 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
94 95 2.489073 GGAAGGGAAAGGTGTGTGTCAT 60.489 50.000 0.00 0.00 0.00 3.06
169 172 1.001406 GAGAAGGGGTGGATGCGATAG 59.999 57.143 0.00 0.00 0.00 2.08
273 276 0.834687 AGGTGGACGTTGGGAGCTTA 60.835 55.000 0.00 0.00 0.00 3.09
365 368 0.878416 TGGCCTATGTTCGTTGTTGC 59.122 50.000 3.32 0.00 0.00 4.17
810 820 5.534654 CCTGAAATGTAGACAGGGAAAAACA 59.465 40.000 0.00 0.00 44.96 2.83
816 826 3.775661 AGACAGGGAAAAACAAACACG 57.224 42.857 0.00 0.00 0.00 4.49
819 829 1.923864 CAGGGAAAAACAAACACGTGC 59.076 47.619 17.22 0.00 0.00 5.34
872 883 0.604578 TTAAGTAGAGGGCGTTGCGT 59.395 50.000 0.00 0.00 0.00 5.24
1106 1158 3.450115 GCCTACTCCACCGACGCT 61.450 66.667 0.00 0.00 0.00 5.07
1107 1159 3.003113 GCCTACTCCACCGACGCTT 62.003 63.158 0.00 0.00 0.00 4.68
1256 1325 4.379243 CGCCCACTCGCCTGTTCT 62.379 66.667 0.00 0.00 0.00 3.01
1257 1326 2.743928 GCCCACTCGCCTGTTCTG 60.744 66.667 0.00 0.00 0.00 3.02
1272 1370 1.125566 GTTCTGCGGCGTGTAGTTTAC 59.874 52.381 9.37 2.66 0.00 2.01
1301 1399 0.825425 TGCTAGCTCCTCGATCCTGG 60.825 60.000 17.23 0.00 0.00 4.45
1302 1400 0.538516 GCTAGCTCCTCGATCCTGGA 60.539 60.000 7.70 0.00 0.00 3.86
1303 1401 1.890573 GCTAGCTCCTCGATCCTGGAT 60.891 57.143 9.42 9.42 0.00 3.41
1304 1402 2.091541 CTAGCTCCTCGATCCTGGATC 58.908 57.143 23.93 23.93 35.88 3.36
1328 1426 6.257411 TCGTGTACTCAAATTTTGGTTCGTTA 59.743 34.615 9.18 0.00 0.00 3.18
1329 1427 6.355144 CGTGTACTCAAATTTTGGTTCGTTAC 59.645 38.462 9.18 2.77 0.00 2.50
1330 1428 7.412063 GTGTACTCAAATTTTGGTTCGTTACT 58.588 34.615 9.18 0.00 0.00 2.24
1331 1429 7.911727 GTGTACTCAAATTTTGGTTCGTTACTT 59.088 33.333 9.18 0.00 0.00 2.24
1332 1430 8.124199 TGTACTCAAATTTTGGTTCGTTACTTC 58.876 33.333 9.18 0.00 0.00 3.01
1333 1431 6.196571 ACTCAAATTTTGGTTCGTTACTTCG 58.803 36.000 9.18 0.00 0.00 3.79
1334 1432 6.121613 TCAAATTTTGGTTCGTTACTTCGT 57.878 33.333 9.18 0.00 0.00 3.85
1335 1433 6.553524 TCAAATTTTGGTTCGTTACTTCGTT 58.446 32.000 9.18 0.00 0.00 3.85
1336 1434 7.028361 TCAAATTTTGGTTCGTTACTTCGTTT 58.972 30.769 9.18 0.00 0.00 3.60
1337 1435 8.180267 TCAAATTTTGGTTCGTTACTTCGTTTA 58.820 29.630 9.18 0.00 0.00 2.01
1338 1436 7.897153 AATTTTGGTTCGTTACTTCGTTTAC 57.103 32.000 0.00 0.00 0.00 2.01
1339 1437 6.414408 TTTTGGTTCGTTACTTCGTTTACA 57.586 33.333 0.00 0.00 0.00 2.41
1340 1438 6.601741 TTTGGTTCGTTACTTCGTTTACAT 57.398 33.333 0.00 0.00 0.00 2.29
1341 1439 7.706281 TTTGGTTCGTTACTTCGTTTACATA 57.294 32.000 0.00 0.00 0.00 2.29
1386 1484 6.074648 TGTTTCCAACAAGGTAATGGAGATT 58.925 36.000 0.00 0.00 43.69 2.40
1521 1619 2.445845 CTCCAGGTATCCGGGCCA 60.446 66.667 4.39 0.00 38.75 5.36
1567 1665 2.125912 CGGTTCGCTCCAGAGGTG 60.126 66.667 0.00 0.00 0.00 4.00
1568 1666 2.266055 GGTTCGCTCCAGAGGTGG 59.734 66.667 0.00 0.00 46.63 4.61
1569 1667 2.266055 GTTCGCTCCAGAGGTGGG 59.734 66.667 0.00 0.00 45.11 4.61
1570 1668 3.706373 TTCGCTCCAGAGGTGGGC 61.706 66.667 0.00 0.00 45.11 5.36
1575 1673 3.302347 CTCCAGAGGTGGGCGTGTC 62.302 68.421 0.00 0.00 45.11 3.67
1638 1736 1.394917 GCGTGTCCAAGTGCTCAATAG 59.605 52.381 0.00 0.00 0.00 1.73
1659 1757 8.375506 CAATAGTTGGATTAGGAGCCTTATACA 58.624 37.037 0.00 0.00 30.79 2.29
1692 1790 5.725110 ATATTGTCGAGATTGTTCTGTGC 57.275 39.130 0.00 0.00 30.30 4.57
1696 1800 3.243873 TGTCGAGATTGTTCTGTGCTTCT 60.244 43.478 0.00 0.00 30.30 2.85
1698 1802 3.990469 TCGAGATTGTTCTGTGCTTCTTC 59.010 43.478 0.00 0.00 30.30 2.87
1706 1810 2.799017 TCTGTGCTTCTTCCATTGCAT 58.201 42.857 0.00 0.00 37.76 3.96
1708 1812 3.691118 TCTGTGCTTCTTCCATTGCATAC 59.309 43.478 0.00 0.00 37.76 2.39
1769 1873 7.759489 TCTATTTTATGTTGTGCCTTGAGTT 57.241 32.000 0.00 0.00 0.00 3.01
1912 2017 1.959282 GGATGCCATCCTTGATGTTCC 59.041 52.381 16.71 3.63 46.19 3.62
1936 2041 2.229784 CTGAAGATGGGAAGCACCAAAC 59.770 50.000 0.00 0.00 45.13 2.93
1938 2043 1.915141 AGATGGGAAGCACCAAACAG 58.085 50.000 0.00 0.00 45.13 3.16
1994 2099 1.423395 CACCTCAAGAGAAGACACGC 58.577 55.000 0.00 0.00 0.00 5.34
1996 2101 1.000283 ACCTCAAGAGAAGACACGCTG 60.000 52.381 0.00 0.00 0.00 5.18
2000 2105 3.531538 TCAAGAGAAGACACGCTGTTTT 58.468 40.909 0.00 0.00 0.00 2.43
2001 2106 3.938963 TCAAGAGAAGACACGCTGTTTTT 59.061 39.130 0.00 0.00 0.00 1.94
2030 2200 9.765795 ATTACTCAGAACATAAGTATTACAGCC 57.234 33.333 0.00 0.00 30.46 4.85
2034 2204 8.762481 TCAGAACATAAGTATTACAGCCTCTA 57.238 34.615 0.00 0.00 30.46 2.43
2038 2208 9.982651 GAACATAAGTATTACAGCCTCTATTCA 57.017 33.333 0.00 0.00 30.46 2.57
2084 2254 7.851963 CAGTTCAATTTAAACTGCCAAAATGTG 59.148 33.333 14.40 0.00 44.94 3.21
2108 2278 9.433153 GTGTTATACTTAAAAACAGAGGTAGCT 57.567 33.333 0.00 0.00 34.01 3.32
2163 2351 5.280317 GGAGACCAAAGTAAGTGGGATGTAA 60.280 44.000 0.00 0.00 40.75 2.41
2329 2521 2.498481 TGGGTAGATGAACCTTACACCG 59.502 50.000 0.00 0.00 39.65 4.94
2416 2614 7.647715 ACAAATCAAACTGCAACAACTATGTAC 59.352 33.333 0.00 0.00 39.40 2.90
2445 2643 6.735678 ATTTGAAACTTGTTTTTCCACACC 57.264 33.333 0.06 0.00 35.01 4.16
2477 2675 7.823745 ACATATGCCTTAAGGGACAAATAAG 57.176 36.000 23.06 8.99 38.75 1.73
2481 2679 5.636123 TGCCTTAAGGGACAAATAAGTTCA 58.364 37.500 23.06 4.70 37.23 3.18
2495 2693 7.824779 ACAAATAAGTTCAACTAGGCTAGGAAG 59.175 37.037 24.57 13.79 0.00 3.46
2506 2705 4.273300 AGGCTAGGAAGGAGTAGATGTT 57.727 45.455 0.00 0.00 0.00 2.71
2599 2810 5.871465 TGTAGCAACGATCATTTAGCAAA 57.129 34.783 0.00 0.00 0.00 3.68
2600 2811 6.435430 TGTAGCAACGATCATTTAGCAAAT 57.565 33.333 0.00 0.00 0.00 2.32
2605 2816 7.312154 AGCAACGATCATTTAGCAAATAACAA 58.688 30.769 0.00 0.00 0.00 2.83
2640 2854 1.273327 GGTGCATAACTTTGCCTTGCT 59.727 47.619 0.00 0.00 42.06 3.91
2643 2857 1.621107 CATAACTTTGCCTTGCTGCG 58.379 50.000 0.00 0.00 0.00 5.18
2672 2886 3.560503 CTCGGTAGATTGATCTTCTCGC 58.439 50.000 0.00 0.00 38.32 5.03
2674 2888 2.667137 GGTAGATTGATCTTCTCGCCG 58.333 52.381 0.00 0.00 38.32 6.46
2682 2896 2.650813 ATCTTCTCGCCGTCCATGCC 62.651 60.000 0.00 0.00 0.00 4.40
2683 2897 3.376935 CTTCTCGCCGTCCATGCCT 62.377 63.158 0.00 0.00 0.00 4.75
2699 2913 0.393808 GCCTAAGCCGATGGTTTGGA 60.394 55.000 8.73 0.00 44.37 3.53
2701 2915 1.065418 CCTAAGCCGATGGTTTGGACT 60.065 52.381 0.00 0.00 44.37 3.85
2732 2946 8.752005 AATAGCATACACATATGAACCACTTT 57.248 30.769 10.38 0.00 40.75 2.66
2827 3041 1.376683 TGCAATGGTGGCGGAGTAC 60.377 57.895 0.00 0.00 0.00 2.73
2829 3043 0.958382 GCAATGGTGGCGGAGTACAA 60.958 55.000 0.00 0.00 0.00 2.41
2836 3050 0.887387 TGGCGGAGTACAAAAGGTGC 60.887 55.000 0.00 0.00 0.00 5.01
2837 3051 0.887387 GGCGGAGTACAAAAGGTGCA 60.887 55.000 0.00 0.00 34.11 4.57
2838 3052 0.948678 GCGGAGTACAAAAGGTGCAA 59.051 50.000 0.00 0.00 34.11 4.08
2840 3054 2.604614 GCGGAGTACAAAAGGTGCAAAG 60.605 50.000 0.00 0.00 34.11 2.77
2845 3059 3.565902 AGTACAAAAGGTGCAAAGAGAGC 59.434 43.478 0.00 0.00 34.11 4.09
2852 3066 1.024271 GTGCAAAGAGAGCAACACCA 58.976 50.000 0.00 0.00 44.64 4.17
2856 3070 2.564771 CAAAGAGAGCAACACCAGTGA 58.435 47.619 4.48 0.00 0.00 3.41
2868 3098 2.555325 ACACCAGTGATGCTTGTTCATG 59.445 45.455 4.48 0.00 0.00 3.07
2892 3123 5.982516 GCTCTGATCTGATAACAACACTAGG 59.017 44.000 2.43 0.00 0.00 3.02
2929 3160 7.043125 CGTGATCTATGGTTGTTGATGAGTAAG 60.043 40.741 0.00 0.00 0.00 2.34
2960 3191 0.179086 TCAAGTGTCAACAGCTCGCA 60.179 50.000 0.00 0.00 0.00 5.10
2970 3201 7.757173 AGTGTCAACAGCTCGCATATATATAAG 59.243 37.037 0.00 0.00 0.00 1.73
2971 3202 7.009631 GTGTCAACAGCTCGCATATATATAAGG 59.990 40.741 0.00 0.00 0.00 2.69
2972 3203 7.036220 GTCAACAGCTCGCATATATATAAGGT 58.964 38.462 0.00 0.00 0.00 3.50
2973 3204 7.009631 GTCAACAGCTCGCATATATATAAGGTG 59.990 40.741 19.45 19.45 38.02 4.00
2974 3205 6.531503 ACAGCTCGCATATATATAAGGTGT 57.468 37.500 20.28 20.28 39.76 4.16
2975 3206 7.640597 ACAGCTCGCATATATATAAGGTGTA 57.359 36.000 22.48 4.18 41.93 2.90
2976 3207 8.239038 ACAGCTCGCATATATATAAGGTGTAT 57.761 34.615 22.48 9.61 41.93 2.29
2977 3208 8.696374 ACAGCTCGCATATATATAAGGTGTATT 58.304 33.333 22.48 9.16 41.93 1.89
2978 3209 9.534565 CAGCTCGCATATATATAAGGTGTATTT 57.465 33.333 15.93 0.00 0.00 1.40
2979 3210 9.534565 AGCTCGCATATATATAAGGTGTATTTG 57.465 33.333 0.00 0.00 0.00 2.32
2980 3211 9.314321 GCTCGCATATATATAAGGTGTATTTGT 57.686 33.333 0.00 0.00 0.00 2.83
3004 3235 5.368552 TTTTCAAAAGACAAACGAATGCG 57.631 34.783 0.00 0.00 44.79 4.73
3014 3245 4.415490 CGAATGCGTGTTTGACCG 57.585 55.556 0.00 0.00 0.00 4.79
3015 3246 1.856688 CGAATGCGTGTTTGACCGA 59.143 52.632 0.00 0.00 0.00 4.69
3016 3247 0.179250 CGAATGCGTGTTTGACCGAG 60.179 55.000 0.00 0.00 0.00 4.63
3017 3248 0.865769 GAATGCGTGTTTGACCGAGT 59.134 50.000 0.00 0.00 0.00 4.18
3018 3249 1.263217 GAATGCGTGTTTGACCGAGTT 59.737 47.619 0.00 0.00 0.00 3.01
3019 3250 1.305201 ATGCGTGTTTGACCGAGTTT 58.695 45.000 0.00 0.00 0.00 2.66
3020 3251 0.653636 TGCGTGTTTGACCGAGTTTC 59.346 50.000 0.00 0.00 0.00 2.78
3021 3252 0.935196 GCGTGTTTGACCGAGTTTCT 59.065 50.000 0.00 0.00 0.00 2.52
3022 3253 2.129607 GCGTGTTTGACCGAGTTTCTA 58.870 47.619 0.00 0.00 0.00 2.10
3023 3254 2.155155 GCGTGTTTGACCGAGTTTCTAG 59.845 50.000 0.00 0.00 0.00 2.43
3024 3255 2.729882 CGTGTTTGACCGAGTTTCTAGG 59.270 50.000 0.00 0.00 32.46 3.02
3025 3256 3.551454 CGTGTTTGACCGAGTTTCTAGGA 60.551 47.826 3.15 0.00 30.74 2.94
3026 3257 4.374399 GTGTTTGACCGAGTTTCTAGGAA 58.626 43.478 3.15 0.00 30.74 3.36
3027 3258 4.812626 GTGTTTGACCGAGTTTCTAGGAAA 59.187 41.667 3.15 0.00 30.74 3.13
3028 3259 5.295045 GTGTTTGACCGAGTTTCTAGGAAAA 59.705 40.000 3.15 1.71 30.74 2.29
3029 3260 6.017357 GTGTTTGACCGAGTTTCTAGGAAAAT 60.017 38.462 3.15 0.00 30.74 1.82
3030 3261 6.204108 TGTTTGACCGAGTTTCTAGGAAAATC 59.796 38.462 9.48 9.48 30.74 2.17
3031 3262 5.740290 TGACCGAGTTTCTAGGAAAATCT 57.260 39.130 15.11 2.18 30.74 2.40
3032 3263 6.845758 TGACCGAGTTTCTAGGAAAATCTA 57.154 37.500 15.11 1.54 30.74 1.98
3033 3264 7.419711 TGACCGAGTTTCTAGGAAAATCTAT 57.580 36.000 15.11 6.16 30.74 1.98
3034 3265 7.490000 TGACCGAGTTTCTAGGAAAATCTATC 58.510 38.462 15.11 12.72 30.74 2.08
3035 3266 7.123697 TGACCGAGTTTCTAGGAAAATCTATCA 59.876 37.037 15.11 14.40 30.74 2.15
3036 3267 7.848128 ACCGAGTTTCTAGGAAAATCTATCAA 58.152 34.615 15.11 0.00 30.74 2.57
3037 3268 8.487028 ACCGAGTTTCTAGGAAAATCTATCAAT 58.513 33.333 15.11 0.00 30.74 2.57
3038 3269 9.982651 CCGAGTTTCTAGGAAAATCTATCAATA 57.017 33.333 15.11 0.00 0.00 1.90
3084 3315 8.322906 TCATTTGATTCATCACGAAAAGTAGT 57.677 30.769 0.00 0.00 37.12 2.73
3085 3316 8.783093 TCATTTGATTCATCACGAAAAGTAGTT 58.217 29.630 0.00 0.00 37.12 2.24
3086 3317 9.398170 CATTTGATTCATCACGAAAAGTAGTTT 57.602 29.630 0.00 0.00 37.12 2.66
3087 3318 9.612620 ATTTGATTCATCACGAAAAGTAGTTTC 57.387 29.630 0.00 0.00 37.12 2.78
3088 3319 7.722795 TGATTCATCACGAAAAGTAGTTTCA 57.277 32.000 0.00 0.00 45.15 2.69
3089 3320 8.322906 TGATTCATCACGAAAAGTAGTTTCAT 57.677 30.769 0.00 0.00 45.15 2.57
3090 3321 9.430623 TGATTCATCACGAAAAGTAGTTTCATA 57.569 29.630 0.00 0.00 45.15 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 6.239204 CCGAGGTAATGTTTTCCCTTTTCTTT 60.239 38.462 0.00 0.00 0.00 2.52
23 24 5.243060 CCGAGGTAATGTTTTCCCTTTTCTT 59.757 40.000 0.00 0.00 0.00 2.52
94 95 2.710377 GGTGCACCAACATCACTGATA 58.290 47.619 31.23 0.00 35.64 2.15
365 368 4.785453 GACAAGGGGGAGCGGCAG 62.785 72.222 1.45 0.00 0.00 4.85
739 749 3.795688 AAGTGGCCAATTCAAGAGAGA 57.204 42.857 13.79 0.00 0.00 3.10
778 788 5.414765 CCTGTCTACATTTCAGGGGTTAAAC 59.585 44.000 0.00 0.00 43.30 2.01
810 820 4.893424 AAATGTAGAGTTGCACGTGTTT 57.107 36.364 18.38 2.53 0.00 2.83
846 856 6.457799 CGCAACGCCCTCTACTTAATTTAAAT 60.458 38.462 0.00 0.00 0.00 1.40
955 1002 4.281182 GGCGAGAAGAAGAATATCCCAGTA 59.719 45.833 0.00 0.00 0.00 2.74
1026 1075 2.681778 AGTGGAGCGGAGGTGGAG 60.682 66.667 0.00 0.00 39.88 3.86
1106 1158 2.666862 ACGCGCCATCGTTGGAAA 60.667 55.556 16.83 0.00 46.92 3.13
1107 1159 3.418913 CACGCGCCATCGTTGGAA 61.419 61.111 16.83 0.00 46.92 3.53
1251 1320 0.531090 AAACTACACGCCGCAGAACA 60.531 50.000 0.00 0.00 0.00 3.18
1255 1324 0.730155 TCGTAAACTACACGCCGCAG 60.730 55.000 0.00 0.00 39.23 5.18
1256 1325 0.109179 ATCGTAAACTACACGCCGCA 60.109 50.000 0.00 0.00 39.23 5.69
1257 1326 0.569349 GATCGTAAACTACACGCCGC 59.431 55.000 0.00 0.00 39.23 6.53
1259 1328 3.141002 TCAGATCGTAAACTACACGCC 57.859 47.619 0.00 0.00 39.23 5.68
1261 1330 4.438145 GCAGATCAGATCGTAAACTACACG 59.562 45.833 4.67 0.00 40.72 4.49
1262 1331 5.583495 AGCAGATCAGATCGTAAACTACAC 58.417 41.667 4.67 0.00 0.00 2.90
1272 1370 2.161855 AGGAGCTAGCAGATCAGATCG 58.838 52.381 18.83 1.81 30.96 3.69
1301 1399 5.788531 CGAACCAAAATTTGAGTACACGATC 59.211 40.000 7.37 0.00 0.00 3.69
1302 1400 5.237779 ACGAACCAAAATTTGAGTACACGAT 59.762 36.000 7.37 1.50 0.00 3.73
1303 1401 4.571580 ACGAACCAAAATTTGAGTACACGA 59.428 37.500 7.37 0.00 0.00 4.35
1304 1402 4.839796 ACGAACCAAAATTTGAGTACACG 58.160 39.130 7.37 11.50 0.00 4.49
1305 1403 7.412063 AGTAACGAACCAAAATTTGAGTACAC 58.588 34.615 7.37 4.48 0.00 2.90
1306 1404 7.556733 AGTAACGAACCAAAATTTGAGTACA 57.443 32.000 7.37 0.00 0.00 2.90
1307 1405 7.319615 CGAAGTAACGAACCAAAATTTGAGTAC 59.680 37.037 7.37 0.00 35.09 2.73
1308 1406 7.011295 ACGAAGTAACGAACCAAAATTTGAGTA 59.989 33.333 7.37 0.00 41.94 2.59
1437 1535 0.963962 AAATGCTGTGCCAGAACCTG 59.036 50.000 6.40 0.00 32.44 4.00
1438 1536 1.251251 GAAATGCTGTGCCAGAACCT 58.749 50.000 6.40 0.00 32.44 3.50
1459 1557 0.178990 AGGTTCCACTTCCAGGCAAC 60.179 55.000 0.00 0.00 0.00 4.17
1521 1619 1.275573 GTAAGAAGGCCGTCTCCTTGT 59.724 52.381 22.08 8.33 45.92 3.16
1560 1658 1.374758 GAAGACACGCCCACCTCTG 60.375 63.158 0.00 0.00 0.00 3.35
1567 1665 3.400255 AGAAACTAAAGAAGACACGCCC 58.600 45.455 0.00 0.00 0.00 6.13
1568 1666 4.750598 AGAAGAAACTAAAGAAGACACGCC 59.249 41.667 0.00 0.00 0.00 5.68
1569 1667 5.908916 AGAAGAAACTAAAGAAGACACGC 57.091 39.130 0.00 0.00 0.00 5.34
1570 1668 7.685594 ACAAAGAAGAAACTAAAGAAGACACG 58.314 34.615 0.00 0.00 0.00 4.49
1638 1736 6.998673 ACATTGTATAAGGCTCCTAATCCAAC 59.001 38.462 0.00 0.00 0.00 3.77
1686 1784 2.275134 TGCAATGGAAGAAGCACAGA 57.725 45.000 0.00 0.00 31.05 3.41
1688 1786 3.419943 TGTATGCAATGGAAGAAGCACA 58.580 40.909 0.00 0.00 40.14 4.57
1689 1787 4.644103 ATGTATGCAATGGAAGAAGCAC 57.356 40.909 0.00 0.00 40.14 4.40
1745 1849 7.665559 AGAACTCAAGGCACAACATAAAATAGA 59.334 33.333 0.00 0.00 0.00 1.98
1746 1850 7.820648 AGAACTCAAGGCACAACATAAAATAG 58.179 34.615 0.00 0.00 0.00 1.73
1748 1852 6.655078 AGAACTCAAGGCACAACATAAAAT 57.345 33.333 0.00 0.00 0.00 1.82
1756 1860 4.365514 TCCATAAGAACTCAAGGCACAA 57.634 40.909 0.00 0.00 0.00 3.33
1769 1873 9.904198 TGTGATGTTAAATCAGAATCCATAAGA 57.096 29.630 0.00 0.00 0.00 2.10
1912 2017 2.237143 TGGTGCTTCCCATCTTCAGTAG 59.763 50.000 0.00 0.00 34.77 2.57
1936 2041 4.113354 GTCTGGAATCCTTACGCTTACTG 58.887 47.826 0.00 0.00 0.00 2.74
1938 2043 4.119442 TGTCTGGAATCCTTACGCTTAC 57.881 45.455 0.00 0.00 0.00 2.34
2134 2304 4.506625 CCCACTTACTTTGGTCTCCATCAA 60.507 45.833 0.00 0.00 31.53 2.57
2135 2305 3.009033 CCCACTTACTTTGGTCTCCATCA 59.991 47.826 0.00 0.00 31.53 3.07
2201 2389 3.425758 GCGCCACAACCAGTAAAAGATAC 60.426 47.826 0.00 0.00 0.00 2.24
2210 2398 4.189580 ACAGGCGCCACAACCAGT 62.190 61.111 31.54 11.88 0.00 4.00
2329 2521 5.163663 TGGCTAATTGCACAACTAGTTATGC 60.164 40.000 27.98 27.98 42.84 3.14
2416 2614 6.201806 TGGAAAAACAAGTTTCAAATATGCCG 59.798 34.615 0.00 0.00 38.93 5.69
2445 2643 4.083324 CCCTTAAGGCATATGTAATGCGTG 60.083 45.833 16.70 0.00 45.41 5.34
2477 2675 3.770388 ACTCCTTCCTAGCCTAGTTGAAC 59.230 47.826 0.00 0.00 0.00 3.18
2481 2679 5.103430 ACATCTACTCCTTCCTAGCCTAGTT 60.103 44.000 0.00 0.00 0.00 2.24
2495 2693 1.927895 CTGCCGTCAACATCTACTCC 58.072 55.000 0.00 0.00 0.00 3.85
2538 2737 0.597072 GGAACACTCCTCGTCTTCGT 59.403 55.000 0.00 0.00 38.88 3.85
2549 2748 3.609853 TGGATACATGCAAGGAACACTC 58.390 45.455 0.00 0.00 46.17 3.51
2584 2795 8.620416 TGCTATTGTTATTTGCTAAATGATCGT 58.380 29.630 4.89 0.00 32.38 3.73
2599 2810 7.040755 TGCACCGCTAAATATTGCTATTGTTAT 60.041 33.333 0.00 0.00 34.18 1.89
2600 2811 6.261158 TGCACCGCTAAATATTGCTATTGTTA 59.739 34.615 0.00 0.00 34.18 2.41
2605 2816 6.655003 AGTTATGCACCGCTAAATATTGCTAT 59.345 34.615 0.00 0.00 34.18 2.97
2643 2857 0.811616 CAATCTACCGAGCAGGGTGC 60.812 60.000 8.81 0.00 46.96 5.01
2651 2865 3.560503 GCGAGAAGATCAATCTACCGAG 58.439 50.000 11.39 1.26 35.76 4.63
2672 2886 2.383245 ATCGGCTTAGGCATGGACGG 62.383 60.000 6.60 0.00 40.87 4.79
2674 2888 0.886490 CCATCGGCTTAGGCATGGAC 60.886 60.000 22.70 0.00 38.22 4.02
2682 2896 2.403252 AGTCCAAACCATCGGCTTAG 57.597 50.000 0.00 0.00 0.00 2.18
2683 2897 2.871096 AAGTCCAAACCATCGGCTTA 57.129 45.000 0.00 0.00 0.00 3.09
2701 2915 9.448438 GGTTCATATGTGTATGCTATTCCATAA 57.552 33.333 1.90 0.00 38.05 1.90
2790 3004 4.728917 GCACAATGCATGTATCTCTCTC 57.271 45.455 0.00 0.00 44.26 3.20
2827 3041 3.118542 GTTGCTCTCTTTGCACCTTTTG 58.881 45.455 0.00 0.00 40.40 2.44
2829 3043 2.099756 GTGTTGCTCTCTTTGCACCTTT 59.900 45.455 0.00 0.00 40.40 3.11
2836 3050 2.564771 TCACTGGTGTTGCTCTCTTTG 58.435 47.619 0.53 0.00 0.00 2.77
2837 3051 3.144506 CATCACTGGTGTTGCTCTCTTT 58.855 45.455 0.53 0.00 0.00 2.52
2838 3052 2.775890 CATCACTGGTGTTGCTCTCTT 58.224 47.619 0.53 0.00 0.00 2.85
2840 3054 0.801251 GCATCACTGGTGTTGCTCTC 59.199 55.000 22.02 2.10 46.90 3.20
2845 3059 2.358582 TGAACAAGCATCACTGGTGTTG 59.641 45.455 7.26 7.26 30.69 3.33
2849 3063 1.542915 GCATGAACAAGCATCACTGGT 59.457 47.619 0.00 0.00 32.01 4.00
2852 3066 2.747989 CAGAGCATGAACAAGCATCACT 59.252 45.455 0.00 0.00 0.00 3.41
2856 3070 3.628032 CAGATCAGAGCATGAACAAGCAT 59.372 43.478 0.00 0.00 42.53 3.79
2868 3098 5.982516 CCTAGTGTTGTTATCAGATCAGAGC 59.017 44.000 0.00 0.00 0.00 4.09
2940 3171 0.937304 GCGAGCTGTTGACACTTGAA 59.063 50.000 0.00 0.00 0.00 2.69
2981 3212 5.780192 CGCATTCGTTTGTCTTTTGAAAAA 58.220 33.333 0.00 0.00 33.54 1.94
2982 3213 5.368552 CGCATTCGTTTGTCTTTTGAAAA 57.631 34.783 0.00 0.00 0.00 2.29
2997 3228 0.179250 CTCGGTCAAACACGCATTCG 60.179 55.000 0.00 0.00 42.43 3.34
2998 3229 0.865769 ACTCGGTCAAACACGCATTC 59.134 50.000 0.00 0.00 0.00 2.67
2999 3230 1.305201 AACTCGGTCAAACACGCATT 58.695 45.000 0.00 0.00 0.00 3.56
3000 3231 1.263217 GAAACTCGGTCAAACACGCAT 59.737 47.619 0.00 0.00 0.00 4.73
3001 3232 0.653636 GAAACTCGGTCAAACACGCA 59.346 50.000 0.00 0.00 0.00 5.24
3002 3233 0.935196 AGAAACTCGGTCAAACACGC 59.065 50.000 0.00 0.00 0.00 5.34
3003 3234 2.729882 CCTAGAAACTCGGTCAAACACG 59.270 50.000 0.00 0.00 0.00 4.49
3004 3235 3.986277 TCCTAGAAACTCGGTCAAACAC 58.014 45.455 0.00 0.00 0.00 3.32
3005 3236 4.675976 TTCCTAGAAACTCGGTCAAACA 57.324 40.909 0.00 0.00 0.00 2.83
3006 3237 5.996669 TTTTCCTAGAAACTCGGTCAAAC 57.003 39.130 0.00 0.00 0.00 2.93
3007 3238 6.531021 AGATTTTCCTAGAAACTCGGTCAAA 58.469 36.000 0.00 0.00 0.00 2.69
3008 3239 6.110411 AGATTTTCCTAGAAACTCGGTCAA 57.890 37.500 0.00 0.00 0.00 3.18
3009 3240 5.740290 AGATTTTCCTAGAAACTCGGTCA 57.260 39.130 0.00 0.00 0.00 4.02
3010 3241 7.490000 TGATAGATTTTCCTAGAAACTCGGTC 58.510 38.462 0.00 5.53 0.00 4.79
3011 3242 7.419711 TGATAGATTTTCCTAGAAACTCGGT 57.580 36.000 0.00 0.00 0.00 4.69
3012 3243 8.894768 ATTGATAGATTTTCCTAGAAACTCGG 57.105 34.615 0.00 0.00 0.00 4.63
3058 3289 8.950210 ACTACTTTTCGTGATGAATCAAATGAT 58.050 29.630 0.00 0.00 38.75 2.45
3059 3290 8.322906 ACTACTTTTCGTGATGAATCAAATGA 57.677 30.769 0.00 0.00 38.75 2.57
3060 3291 8.955061 AACTACTTTTCGTGATGAATCAAATG 57.045 30.769 0.00 0.00 38.75 2.32
3061 3292 9.612620 GAAACTACTTTTCGTGATGAATCAAAT 57.387 29.630 0.00 0.00 35.08 2.32
3062 3293 8.616942 TGAAACTACTTTTCGTGATGAATCAAA 58.383 29.630 0.00 0.00 45.96 2.69
3063 3294 8.148807 TGAAACTACTTTTCGTGATGAATCAA 57.851 30.769 0.00 0.00 45.96 2.57
3064 3295 7.722795 TGAAACTACTTTTCGTGATGAATCA 57.277 32.000 0.00 0.00 45.96 2.57


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

AutoCloner maintained by Alex Coulton.