Multiple sequence alignment - TraesCS4A01G432500

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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 TraesCS4A01G432500 chr4A 100.000 3356 0 0 1 3356 703411762 703408407 0.000000e+00 6198.0
1 TraesCS4A01G432500 chr4A 91.419 606 47 3 1390 1994 703364857 703364256 0.000000e+00 826.0
2 TraesCS4A01G432500 chr4A 94.167 240 14 0 2277 2516 703362879 703362640 1.900000e-97 366.0
3 TraesCS4A01G432500 chr4A 92.469 239 18 0 2278 2516 703430284 703430046 3.210000e-90 342.0
4 TraesCS4A01G432500 chr4A 76.980 404 84 9 1615 2015 703432186 703431789 4.360000e-54 222.0
5 TraesCS4A01G432500 chr7D 91.900 1605 95 23 929 2521 27957629 27956048 0.000000e+00 2211.0
6 TraesCS4A01G432500 chr7D 77.568 477 84 19 1549 2015 28008497 28008034 1.990000e-67 267.0
7 TraesCS4A01G432500 chr7D 78.626 393 74 9 1613 2002 27961258 27960873 5.560000e-63 252.0
8 TraesCS4A01G432500 chr7A 90.179 1395 93 13 899 2253 28171645 28170255 0.000000e+00 1777.0
9 TraesCS4A01G432500 chr7A 98.821 848 10 0 2509 3356 495576056 495576903 0.000000e+00 1511.0
10 TraesCS4A01G432500 chr7A 85.057 870 85 14 1660 2516 28168868 28168031 0.000000e+00 845.0
11 TraesCS4A01G432500 chr7A 95.868 242 9 1 2278 2518 28170270 28170029 1.130000e-104 390.0
12 TraesCS4A01G432500 chr7A 78.079 406 76 11 1615 2015 28255739 28255342 9.300000e-61 244.0
13 TraesCS4A01G432500 chr7A 83.491 212 33 2 1741 1951 28045496 28045286 2.640000e-46 196.0
14 TraesCS4A01G432500 chr6A 99.053 845 7 1 2512 3356 71106397 71107240 0.000000e+00 1515.0
15 TraesCS4A01G432500 chr6A 91.525 59 5 0 2084 2142 91902568 91902510 7.720000e-12 82.4
16 TraesCS4A01G432500 chr2B 99.050 842 8 0 2515 3356 305754751 305755592 0.000000e+00 1511.0
17 TraesCS4A01G432500 chr2B 99.050 842 7 1 2515 3356 325906592 325907432 0.000000e+00 1509.0
18 TraesCS4A01G432500 chr2B 98.932 843 9 0 2514 3356 217834672 217833830 0.000000e+00 1507.0
19 TraesCS4A01G432500 chr2B 99.049 841 7 1 2516 3356 461249366 461248527 0.000000e+00 1507.0
20 TraesCS4A01G432500 chr2B 86.373 477 44 7 11 466 202920917 202921393 5.000000e-138 501.0
21 TraesCS4A01G432500 chr2B 92.857 56 4 0 2085 2140 521974875 521974930 7.720000e-12 82.4
22 TraesCS4A01G432500 chr5B 98.930 841 9 0 2516 3356 581718107 581717267 0.000000e+00 1504.0
23 TraesCS4A01G432500 chr2A 98.931 842 7 1 2515 3356 238721022 238721861 0.000000e+00 1504.0
24 TraesCS4A01G432500 chr2A 88.110 471 35 7 20 469 156667394 156666924 1.060000e-149 540.0
25 TraesCS4A01G432500 chr2A 91.667 60 5 0 2085 2144 27640981 27640922 2.150000e-12 84.2
26 TraesCS4A01G432500 chr6B 98.472 851 13 0 2506 3356 21248830 21249680 0.000000e+00 1500.0
27 TraesCS4A01G432500 chr6B 87.692 65 6 2 2085 2147 415861589 415861653 1.290000e-09 75.0
28 TraesCS4A01G432500 chr3B 90.849 907 55 14 1 900 703848428 703847543 0.000000e+00 1190.0
29 TraesCS4A01G432500 chr3A 90.698 903 62 13 1 900 451664545 451665428 0.000000e+00 1182.0
30 TraesCS4A01G432500 chr3A 90.397 906 61 13 1 901 259838605 259837721 0.000000e+00 1168.0
31 TraesCS4A01G432500 chr3A 90.312 898 65 12 1 895 451658480 451657602 0.000000e+00 1157.0
32 TraesCS4A01G432500 chr5A 90.387 905 61 13 1 900 525733940 525733057 0.000000e+00 1166.0
33 TraesCS4A01G432500 chr5A 93.220 59 4 0 2085 2143 705906124 705906182 1.660000e-13 87.9
34 TraesCS4A01G432500 chr2D 87.421 477 39 7 11 466 145363417 145363893 2.290000e-146 529.0
35 TraesCS4A01G432500 chr4D 77.239 949 129 54 4 895 164107271 164106353 3.030000e-130 475.0
36 TraesCS4A01G432500 chr5D 92.857 56 4 0 2085 2140 555061006 555061061 7.720000e-12 82.4


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 TraesCS4A01G432500 chr4A 703408407 703411762 3355 True 6198.0 6198 100.0000 1 3356 1 chr4A.!!$R1 3355
1 TraesCS4A01G432500 chr4A 703362640 703364857 2217 True 596.0 826 92.7930 1390 2516 2 chr4A.!!$R2 1126
2 TraesCS4A01G432500 chr4A 703430046 703432186 2140 True 282.0 342 84.7245 1615 2516 2 chr4A.!!$R3 901
3 TraesCS4A01G432500 chr7D 27956048 27961258 5210 True 1231.5 2211 85.2630 929 2521 2 chr7D.!!$R2 1592
4 TraesCS4A01G432500 chr7A 495576056 495576903 847 False 1511.0 1511 98.8210 2509 3356 1 chr7A.!!$F1 847
5 TraesCS4A01G432500 chr7A 28168031 28171645 3614 True 1004.0 1777 90.3680 899 2518 3 chr7A.!!$R3 1619
6 TraesCS4A01G432500 chr6A 71106397 71107240 843 False 1515.0 1515 99.0530 2512 3356 1 chr6A.!!$F1 844
7 TraesCS4A01G432500 chr2B 305754751 305755592 841 False 1511.0 1511 99.0500 2515 3356 1 chr2B.!!$F2 841
8 TraesCS4A01G432500 chr2B 325906592 325907432 840 False 1509.0 1509 99.0500 2515 3356 1 chr2B.!!$F3 841
9 TraesCS4A01G432500 chr2B 217833830 217834672 842 True 1507.0 1507 98.9320 2514 3356 1 chr2B.!!$R1 842
10 TraesCS4A01G432500 chr2B 461248527 461249366 839 True 1507.0 1507 99.0490 2516 3356 1 chr2B.!!$R2 840
11 TraesCS4A01G432500 chr5B 581717267 581718107 840 True 1504.0 1504 98.9300 2516 3356 1 chr5B.!!$R1 840
12 TraesCS4A01G432500 chr2A 238721022 238721861 839 False 1504.0 1504 98.9310 2515 3356 1 chr2A.!!$F1 841
13 TraesCS4A01G432500 chr6B 21248830 21249680 850 False 1500.0 1500 98.4720 2506 3356 1 chr6B.!!$F1 850
14 TraesCS4A01G432500 chr3B 703847543 703848428 885 True 1190.0 1190 90.8490 1 900 1 chr3B.!!$R1 899
15 TraesCS4A01G432500 chr3A 451664545 451665428 883 False 1182.0 1182 90.6980 1 900 1 chr3A.!!$F1 899
16 TraesCS4A01G432500 chr3A 259837721 259838605 884 True 1168.0 1168 90.3970 1 901 1 chr3A.!!$R1 900
17 TraesCS4A01G432500 chr3A 451657602 451658480 878 True 1157.0 1157 90.3120 1 895 1 chr3A.!!$R2 894
18 TraesCS4A01G432500 chr5A 525733057 525733940 883 True 1166.0 1166 90.3870 1 900 1 chr5A.!!$R1 899
19 TraesCS4A01G432500 chr4D 164106353 164107271 918 True 475.0 475 77.2390 4 895 1 chr4D.!!$R1 891

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
614 678 0.106519 CGATTTGGGAAGGCTGGGAT 60.107 55.0 0.00 0.0 0.0 3.85 F
624 688 0.106519 AGGCTGGGATGCGCTAATTT 60.107 50.0 9.73 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 5439 0.457853 TCATTCACGAGCAGGCGTAC 60.458 55.000 0.0 0.0 43.59 3.67 R
2479 7600 1.135915 GCTGATCCGTGAGACACATCT 59.864 52.381 0.0 0.0 38.15 2.90 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
194 203 2.962569 CCGAGTTGCAGACCTCGA 59.037 61.111 24.99 0.00 41.24 4.04
198 207 1.634702 GAGTTGCAGACCTCGATGAC 58.365 55.000 0.00 0.00 0.00 3.06
256 265 2.101415 CTCGTGGAAGCCTATGATGTGA 59.899 50.000 0.00 0.00 0.00 3.58
284 295 3.706373 GGGAGGAGAAGGCGCACA 61.706 66.667 10.83 0.00 0.00 4.57
371 385 3.948719 GTGCACCCCCTGGTCGAA 61.949 66.667 5.22 0.00 45.57 3.71
372 386 3.948719 TGCACCCCCTGGTCGAAC 61.949 66.667 0.00 0.00 45.57 3.95
373 387 4.717313 GCACCCCCTGGTCGAACC 62.717 72.222 0.00 0.00 45.57 3.62
409 433 4.864334 CGGAGCCCATCCCAGCAC 62.864 72.222 0.00 0.00 46.50 4.40
458 482 1.139095 GTCTACCTCCTGGAACGCG 59.861 63.158 3.53 3.53 37.04 6.01
471 522 4.280494 ACGCGTCCTCGTTGCTGT 62.280 61.111 5.58 0.00 40.07 4.40
492 543 2.721167 TTCCTCCTGCCGTCGATGG 61.721 63.158 19.87 19.87 0.00 3.51
548 599 1.311059 GGAGGATTTGGGGGCATGT 59.689 57.895 0.00 0.00 0.00 3.21
608 672 2.750237 ACCGCGATTTGGGAAGGC 60.750 61.111 8.23 0.00 0.00 4.35
614 678 0.106519 CGATTTGGGAAGGCTGGGAT 60.107 55.000 0.00 0.00 0.00 3.85
624 688 0.106519 AGGCTGGGATGCGCTAATTT 60.107 50.000 9.73 0.00 0.00 1.82
625 689 1.142870 AGGCTGGGATGCGCTAATTTA 59.857 47.619 9.73 0.00 0.00 1.40
641 705 6.070767 CGCTAATTTAGGGATGGGATTAGAGA 60.071 42.308 13.68 0.00 40.83 3.10
662 726 3.179443 TGAGAGGTTAGCGCTAATTGG 57.821 47.619 30.90 0.00 0.00 3.16
701 765 1.975660 CCAAACGAACCTTTCCTCCA 58.024 50.000 0.00 0.00 0.00 3.86
735 799 0.179040 AGTTTTCGTCCGCCCAGAAA 60.179 50.000 0.00 0.00 32.76 2.52
759 823 4.579270 AAATGCTAAGCGTACTTTCGAC 57.421 40.909 0.00 0.00 37.33 4.20
768 832 1.860326 CGTACTTTCGACGTGGGTTTT 59.140 47.619 0.00 0.00 35.58 2.43
795 861 8.664798 TGTAATCTTGACGGTTAGATCAAATTG 58.335 33.333 0.00 0.00 34.52 2.32
901 969 6.763135 TGCTTGTTTAATAGCAGTAGAGATGG 59.237 38.462 0.00 0.00 42.12 3.51
902 970 6.986817 GCTTGTTTAATAGCAGTAGAGATGGA 59.013 38.462 0.00 0.00 37.35 3.41
903 971 7.659390 GCTTGTTTAATAGCAGTAGAGATGGAT 59.341 37.037 0.00 0.00 37.35 3.41
904 972 9.553064 CTTGTTTAATAGCAGTAGAGATGGATT 57.447 33.333 0.00 0.00 0.00 3.01
905 973 9.905713 TTGTTTAATAGCAGTAGAGATGGATTT 57.094 29.630 0.00 0.00 0.00 2.17
906 974 9.905713 TGTTTAATAGCAGTAGAGATGGATTTT 57.094 29.630 0.00 0.00 0.00 1.82
932 1000 7.523293 TTTTAAGAAGAATGAACTGCATGGA 57.477 32.000 0.00 0.00 37.28 3.41
1003 3705 2.139811 CAACGCGCGATCTGCAAAC 61.140 57.895 39.36 0.00 46.97 2.93
1159 3869 3.019003 ATCCGGCTCCCACGTCTTG 62.019 63.158 0.00 0.00 0.00 3.02
1177 3887 1.095600 TGAGGATCGAGGAGTTCACG 58.904 55.000 0.00 0.00 38.61 4.35
1256 3974 1.745489 GGCCACGACTGGTTCATCC 60.745 63.158 0.00 0.00 40.17 3.51
1266 3984 1.656587 TGGTTCATCCAGTGCTACCT 58.343 50.000 0.00 0.00 41.93 3.08
1313 4031 3.268034 ACCATATCTCCCTCTTCCTCC 57.732 52.381 0.00 0.00 0.00 4.30
1314 4032 2.524440 ACCATATCTCCCTCTTCCTCCA 59.476 50.000 0.00 0.00 0.00 3.86
1327 4045 2.267006 CTCCAGCACGACAGCCAT 59.733 61.111 0.00 0.00 34.23 4.40
1359 4077 1.421410 GATGCCACGGCGACTTACAG 61.421 60.000 16.62 0.00 45.51 2.74
1387 4105 2.743636 TACTCGACAAGGCCTTGAAG 57.256 50.000 44.50 35.50 42.93 3.02
1388 4106 0.759346 ACTCGACAAGGCCTTGAAGT 59.241 50.000 44.50 36.04 42.93 3.01
1411 4129 4.091365 TCATCGTGCACTAAATTCGAACAG 59.909 41.667 16.19 0.45 34.38 3.16
1651 4384 4.894201 GGGGACGGAGAGACGATA 57.106 61.111 0.00 0.00 37.61 2.92
1717 5417 3.984749 GATCTCGCCCTCGCCTCC 61.985 72.222 0.00 0.00 35.26 4.30
1810 5510 2.190325 GGTTCATCTACACCGACTCG 57.810 55.000 0.00 0.00 0.00 4.18
2054 5990 4.322101 CGTGAGCAACCAATTAGTACAC 57.678 45.455 0.00 0.00 0.00 2.90
2074 6010 8.838365 AGTACACGTGTATTTTGAATTTACCAA 58.162 29.630 29.58 1.57 32.54 3.67
2101 6037 2.377073 AGCTACTTCCTCCGTTCCTAC 58.623 52.381 0.00 0.00 0.00 3.18
2107 6043 6.127952 GCTACTTCCTCCGTTCCTACATATAG 60.128 46.154 0.00 0.00 0.00 1.31
2188 7298 1.577328 AATGCACACACCAGTAGCGC 61.577 55.000 0.00 0.00 32.46 5.92
2194 7304 2.809601 CACCAGTAGCGCCGTGTC 60.810 66.667 2.29 0.00 0.00 3.67
2204 7314 2.738521 GCCGTGTCGCATCACACT 60.739 61.111 8.48 0.00 43.97 3.55
2205 7315 2.317609 GCCGTGTCGCATCACACTT 61.318 57.895 8.48 0.00 43.97 3.16
2206 7316 1.011968 GCCGTGTCGCATCACACTTA 61.012 55.000 8.48 0.00 43.97 2.24
2207 7317 1.424403 CCGTGTCGCATCACACTTAA 58.576 50.000 8.48 0.00 43.97 1.85
2208 7318 1.795872 CCGTGTCGCATCACACTTAAA 59.204 47.619 8.48 0.00 43.97 1.52
2209 7319 2.411031 CCGTGTCGCATCACACTTAAAC 60.411 50.000 8.48 0.00 43.97 2.01
2210 7320 2.219903 CGTGTCGCATCACACTTAAACA 59.780 45.455 8.48 0.00 43.97 2.83
2211 7321 3.120683 CGTGTCGCATCACACTTAAACAT 60.121 43.478 8.48 0.00 43.97 2.71
2212 7322 4.610456 CGTGTCGCATCACACTTAAACATT 60.610 41.667 8.48 0.00 43.97 2.71
2213 7323 5.212194 GTGTCGCATCACACTTAAACATTT 58.788 37.500 3.83 0.00 43.00 2.32
2250 7371 5.579718 GGATGACTCTTCATGCTTGAATTG 58.420 41.667 14.72 12.46 44.95 2.32
2254 7375 6.210796 TGACTCTTCATGCTTGAATTGTTTG 58.789 36.000 14.72 3.58 40.95 2.93
2258 7379 7.010738 ACTCTTCATGCTTGAATTGTTTGTTTG 59.989 33.333 14.72 1.01 40.95 2.93
2261 7382 7.375106 TCATGCTTGAATTGTTTGTTTGTTT 57.625 28.000 0.00 0.00 0.00 2.83
2262 7383 7.814642 TCATGCTTGAATTGTTTGTTTGTTTT 58.185 26.923 0.00 0.00 0.00 2.43
2263 7384 8.295288 TCATGCTTGAATTGTTTGTTTGTTTTT 58.705 25.926 0.00 0.00 0.00 1.94
2264 7385 8.577110 CATGCTTGAATTGTTTGTTTGTTTTTC 58.423 29.630 0.00 0.00 0.00 2.29
2265 7386 7.869800 TGCTTGAATTGTTTGTTTGTTTTTCT 58.130 26.923 0.00 0.00 0.00 2.52
2266 7387 8.348507 TGCTTGAATTGTTTGTTTGTTTTTCTT 58.651 25.926 0.00 0.00 0.00 2.52
2267 7388 9.179552 GCTTGAATTGTTTGTTTGTTTTTCTTT 57.820 25.926 0.00 0.00 0.00 2.52
2401 7522 9.678941 ACTGTATATATGACTTGTTGTATGTCG 57.321 33.333 0.00 0.00 36.52 4.35
2496 9618 5.000012 ACTTTAGATGTGTCTCACGGATC 58.000 43.478 0.00 0.00 37.14 3.36
2625 9747 5.450818 TGGGGTGCTCTAATTAGAAACAT 57.549 39.130 21.10 0.00 0.00 2.71
2990 10112 2.302260 CACTATCCTTGCTCCTCGAGA 58.698 52.381 15.71 0.00 0.00 4.04
3128 10250 1.247567 CAAAGTCAAGACCCGCCATT 58.752 50.000 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
194 203 1.291877 GGCGTGCTCAACTTCGTCAT 61.292 55.000 0.00 0.00 0.00 3.06
198 207 3.777925 CCGGCGTGCTCAACTTCG 61.778 66.667 6.01 0.00 0.00 3.79
256 265 2.461300 TCTCCTCCCTTCATCGTGAT 57.539 50.000 0.00 0.00 0.00 3.06
371 385 2.047061 TCAAGAAGGTGTACTGCTGGT 58.953 47.619 0.00 0.00 34.35 4.00
372 386 2.417719 GTCAAGAAGGTGTACTGCTGG 58.582 52.381 0.00 0.00 34.35 4.85
373 387 2.061773 CGTCAAGAAGGTGTACTGCTG 58.938 52.381 0.00 0.00 34.35 4.41
375 389 1.000506 TCCGTCAAGAAGGTGTACTGC 59.999 52.381 2.06 0.00 0.00 4.40
376 390 2.927014 GCTCCGTCAAGAAGGTGTACTG 60.927 54.545 2.06 0.00 0.00 2.74
379 393 0.606604 GGCTCCGTCAAGAAGGTGTA 59.393 55.000 2.06 0.00 0.00 2.90
380 394 1.371558 GGCTCCGTCAAGAAGGTGT 59.628 57.895 2.06 0.00 0.00 4.16
381 395 1.376037 GGGCTCCGTCAAGAAGGTG 60.376 63.158 2.06 1.32 0.00 4.00
439 463 1.313812 CGCGTTCCAGGAGGTAGACT 61.314 60.000 0.00 0.00 35.89 3.24
443 467 2.345760 GGACGCGTTCCAGGAGGTA 61.346 63.158 15.53 0.00 45.10 3.08
458 482 0.586802 GGAACAACAGCAACGAGGAC 59.413 55.000 0.00 0.00 0.00 3.85
471 522 1.541310 ATCGACGGCAGGAGGAACAA 61.541 55.000 0.00 0.00 0.00 2.83
532 583 0.413037 TTCACATGCCCCCAAATCCT 59.587 50.000 0.00 0.00 0.00 3.24
583 634 1.424493 CCAAATCGCGGTCTCAGCTC 61.424 60.000 6.13 0.00 0.00 4.09
608 672 2.154462 CCCTAAATTAGCGCATCCCAG 58.846 52.381 11.47 0.00 0.00 4.45
614 678 1.771854 TCCCATCCCTAAATTAGCGCA 59.228 47.619 11.47 0.00 0.00 6.09
624 688 5.281979 CCTCTCATCTCTAATCCCATCCCTA 60.282 48.000 0.00 0.00 0.00 3.53
625 689 4.512574 CCTCTCATCTCTAATCCCATCCCT 60.513 50.000 0.00 0.00 0.00 4.20
641 705 3.495100 CCCAATTAGCGCTAACCTCTCAT 60.495 47.826 30.92 11.57 0.00 2.90
662 726 1.675552 CAACGACATAATCCCACCCC 58.324 55.000 0.00 0.00 0.00 4.95
740 804 2.182825 CGTCGAAAGTACGCTTAGCAT 58.817 47.619 4.70 0.00 33.95 3.79
756 820 4.024725 TCAAGATTACAAAAACCCACGTCG 60.025 41.667 0.00 0.00 0.00 5.12
759 823 4.215965 CGTCAAGATTACAAAAACCCACG 58.784 43.478 0.00 0.00 0.00 4.94
768 832 8.786826 ATTTGATCTAACCGTCAAGATTACAA 57.213 30.769 0.00 0.00 35.91 2.41
795 861 1.689273 AGCCTCCCGATCAGATAACAC 59.311 52.381 0.00 0.00 0.00 3.32
852 918 7.676338 GCAAACATATTTATCACTACGTGCACT 60.676 37.037 16.19 4.64 32.98 4.40
907 975 7.950512 TCCATGCAGTTCATTCTTCTTAAAAA 58.049 30.769 0.00 0.00 31.79 1.94
908 976 7.523293 TCCATGCAGTTCATTCTTCTTAAAA 57.477 32.000 0.00 0.00 31.79 1.52
909 977 7.707624 ATCCATGCAGTTCATTCTTCTTAAA 57.292 32.000 0.00 0.00 31.79 1.52
910 978 7.394077 TCAATCCATGCAGTTCATTCTTCTTAA 59.606 33.333 0.00 0.00 31.79 1.85
911 979 6.885918 TCAATCCATGCAGTTCATTCTTCTTA 59.114 34.615 0.00 0.00 31.79 2.10
912 980 5.713389 TCAATCCATGCAGTTCATTCTTCTT 59.287 36.000 0.00 0.00 31.79 2.52
913 981 5.258841 TCAATCCATGCAGTTCATTCTTCT 58.741 37.500 0.00 0.00 31.79 2.85
914 982 5.571784 TCAATCCATGCAGTTCATTCTTC 57.428 39.130 0.00 0.00 31.79 2.87
915 983 5.479375 ACTTCAATCCATGCAGTTCATTCTT 59.521 36.000 0.00 0.00 30.91 2.52
916 984 5.014858 ACTTCAATCCATGCAGTTCATTCT 58.985 37.500 0.00 0.00 30.91 2.40
917 985 5.320549 ACTTCAATCCATGCAGTTCATTC 57.679 39.130 0.00 0.00 30.91 2.67
918 986 5.163581 GCTACTTCAATCCATGCAGTTCATT 60.164 40.000 0.00 0.00 36.82 2.57
919 987 4.337555 GCTACTTCAATCCATGCAGTTCAT 59.662 41.667 0.00 0.00 36.82 2.57
920 988 3.691118 GCTACTTCAATCCATGCAGTTCA 59.309 43.478 0.00 0.00 36.82 3.18
921 989 3.065925 GGCTACTTCAATCCATGCAGTTC 59.934 47.826 0.00 0.00 36.82 3.01
922 990 3.019564 GGCTACTTCAATCCATGCAGTT 58.980 45.455 0.00 0.00 36.82 3.16
923 991 2.025981 TGGCTACTTCAATCCATGCAGT 60.026 45.455 0.00 0.00 39.03 4.40
924 992 2.646930 TGGCTACTTCAATCCATGCAG 58.353 47.619 0.00 0.00 0.00 4.41
925 993 2.804986 TGGCTACTTCAATCCATGCA 57.195 45.000 0.00 0.00 0.00 3.96
926 994 4.136796 TGTATGGCTACTTCAATCCATGC 58.863 43.478 3.10 2.53 39.46 4.06
927 995 4.758674 CCTGTATGGCTACTTCAATCCATG 59.241 45.833 3.10 0.00 39.46 3.66
928 996 4.660303 TCCTGTATGGCTACTTCAATCCAT 59.340 41.667 0.00 0.00 41.71 3.41
929 997 4.037222 TCCTGTATGGCTACTTCAATCCA 58.963 43.478 0.00 0.00 35.26 3.41
930 998 4.141711 TGTCCTGTATGGCTACTTCAATCC 60.142 45.833 0.00 0.00 35.26 3.01
931 999 4.811557 GTGTCCTGTATGGCTACTTCAATC 59.188 45.833 0.00 0.00 35.26 2.67
932 1000 4.680708 CGTGTCCTGTATGGCTACTTCAAT 60.681 45.833 0.00 0.00 35.26 2.57
1003 3705 2.074729 AGGAGAAGATCACCTACGGG 57.925 55.000 0.00 0.00 35.66 5.28
1016 3718 1.423921 GGGTTGACCAAGGAAGGAGAA 59.576 52.381 2.12 0.00 39.85 2.87
1048 3751 3.179265 GACGTGGACATGACGCGG 61.179 66.667 23.81 11.74 45.29 6.46
1050 3753 3.179265 CGGACGTGGACATGACGC 61.179 66.667 0.00 0.00 40.56 5.19
1052 3755 0.108804 ATCACGGACGTGGACATGAC 60.109 55.000 22.71 0.00 45.43 3.06
1053 3756 0.172578 GATCACGGACGTGGACATGA 59.827 55.000 22.71 4.71 45.43 3.07
1134 3844 3.161450 GGGAGCCGGATGCCTGTA 61.161 66.667 24.55 0.00 42.71 2.74
1136 3846 4.864334 GTGGGAGCCGGATGCCTG 62.864 72.222 31.06 0.00 42.71 4.85
1159 3869 0.248702 GCGTGAACTCCTCGATCCTC 60.249 60.000 0.00 0.00 33.99 3.71
1177 3887 2.105466 CAGCTTCTCCCTTGCTCGC 61.105 63.158 0.00 0.00 34.51 5.03
1211 3921 1.226974 CGAACGGGCTCGACATGAT 60.227 57.895 15.95 0.00 41.44 2.45
1256 3974 2.094659 CGCCGTTCAGGTAGCACTG 61.095 63.158 0.00 0.00 43.70 3.66
1352 4070 4.036971 GTCGAGTATGCTCATCCTGTAAGT 59.963 45.833 11.58 0.00 41.71 2.24
1359 4077 2.748605 CCTTGTCGAGTATGCTCATCC 58.251 52.381 11.58 0.00 41.71 3.51
1387 4105 4.143200 TGTTCGAATTTAGTGCACGATGAC 60.143 41.667 12.01 0.14 33.25 3.06
1388 4106 3.991121 TGTTCGAATTTAGTGCACGATGA 59.009 39.130 12.01 1.15 33.25 2.92
1411 4129 4.785453 CCCCTGAAGTGGCGCTCC 62.785 72.222 7.64 0.00 0.00 4.70
1429 4147 2.111878 GTCCAGCCCCATCCATCG 59.888 66.667 0.00 0.00 0.00 3.84
1581 4314 4.880537 AGATGGCTTCCGCGAGCG 62.881 66.667 8.23 10.86 43.62 5.03
1582 4315 3.267860 CAGATGGCTTCCGCGAGC 61.268 66.667 8.23 9.98 41.96 5.03
1613 4346 1.153628 GGTGGATCTTCACGTCCGG 60.154 63.158 0.00 0.00 38.46 5.14
1623 4356 2.442272 CGTCCCCGAGGTGGATCT 60.442 66.667 0.00 0.00 42.00 2.75
1717 5417 3.276091 TCAGCGGTGGCGTTGTTG 61.276 61.111 15.67 0.00 46.35 3.33
1739 5439 0.457853 TCATTCACGAGCAGGCGTAC 60.458 55.000 0.00 0.00 43.59 3.67
1814 5514 4.838486 CGTCTCGAGCTCGGTGGC 62.838 72.222 33.98 25.80 40.29 5.01
1926 5626 1.736645 ACGGAGTTGGCGTCGATTG 60.737 57.895 0.00 0.00 37.78 2.67
2032 5968 2.739913 TGTACTAATTGGTTGCTCACGC 59.260 45.455 0.00 0.00 0.00 5.34
2034 5970 3.744426 ACGTGTACTAATTGGTTGCTCAC 59.256 43.478 0.00 4.83 0.00 3.51
2053 5989 7.168469 GCAGTTTGGTAAATTCAAAATACACGT 59.832 33.333 0.00 0.00 36.11 4.49
2054 5990 7.381139 AGCAGTTTGGTAAATTCAAAATACACG 59.619 33.333 0.00 0.00 36.11 4.49
2074 6010 1.751924 CGGAGGAAGTAGCTAGCAGTT 59.248 52.381 18.83 11.76 0.00 3.16
2142 7252 4.447389 GCATTGCCGAAACATAAAGTTGTT 59.553 37.500 0.00 0.00 41.19 2.83
2174 7284 3.612681 ACGGCGCTACTGGTGTGT 61.613 61.111 6.90 0.00 0.00 3.72
2266 7387 9.553064 AACAATACAAGCATGAAACCATAAAAA 57.447 25.926 0.00 0.00 0.00 1.94
2268 7389 9.632807 GTAACAATACAAGCATGAAACCATAAA 57.367 29.630 0.00 0.00 32.02 1.40
2269 7390 9.019656 AGTAACAATACAAGCATGAAACCATAA 57.980 29.630 0.00 0.00 34.29 1.90
2270 7391 8.574251 AGTAACAATACAAGCATGAAACCATA 57.426 30.769 0.00 0.00 34.29 2.74
2271 7392 7.466746 AGTAACAATACAAGCATGAAACCAT 57.533 32.000 0.00 0.00 34.29 3.55
2272 7393 6.348132 CGAGTAACAATACAAGCATGAAACCA 60.348 38.462 0.00 0.00 34.29 3.67
2273 7394 6.021596 CGAGTAACAATACAAGCATGAAACC 58.978 40.000 0.00 0.00 34.29 3.27
2274 7395 6.599437 ACGAGTAACAATACAAGCATGAAAC 58.401 36.000 0.00 0.00 34.29 2.78
2401 7522 8.931385 AAAACACAAGCATATCAAATGGTATC 57.069 30.769 0.00 0.00 0.00 2.24
2479 7600 1.135915 GCTGATCCGTGAGACACATCT 59.864 52.381 0.00 0.00 38.15 2.90
2974 10096 1.691196 CTCTCTCGAGGAGCAAGGAT 58.309 55.000 13.56 0.00 41.60 3.24
2990 10112 3.177228 AGAACATTGTGTCCCTAGCTCT 58.823 45.455 0.00 0.00 0.00 4.09
3128 10250 2.013563 GCGAGCCTGATTTGTGGATCA 61.014 52.381 0.00 0.00 38.54 2.92


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

AutoCloner maintained by Alex Coulton.