Multiple sequence alignment - TraesCS3B01G302000

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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 TraesCS3B01G302000 chr3B 100.000 2539 0 0 1 2539 485534008 485536546 0.000000e+00 4689.0
1 TraesCS3B01G302000 chr3B 86.102 626 53 19 959 1571 790970145 790969541 0.000000e+00 643.0
2 TraesCS3B01G302000 chr3B 83.430 344 28 10 646 965 790970708 790970370 2.470000e-75 292.0
3 TraesCS3B01G302000 chr3B 84.266 286 26 4 1871 2153 790969349 790969080 6.970000e-66 261.0
4 TraesCS3B01G302000 chr3B 83.043 230 30 7 1215 1444 80091204 80091424 1.540000e-47 200.0
5 TraesCS3B01G302000 chr3B 89.873 79 8 0 887 965 80081798 80081876 4.470000e-18 102.0
6 TraesCS3B01G302000 chr5A 82.440 1213 170 29 959 2153 130222881 130221694 0.000000e+00 1020.0
7 TraesCS3B01G302000 chr5A 93.220 649 24 2 1 647 476063819 476064449 0.000000e+00 937.0
8 TraesCS3B01G302000 chr5A 77.554 646 85 38 1446 2055 528894179 528894800 4.050000e-88 335.0
9 TraesCS3B01G302000 chr5A 79.359 281 23 8 646 891 130223547 130223267 5.620000e-37 165.0
10 TraesCS3B01G302000 chr5A 95.082 61 3 0 903 963 130223226 130223166 2.080000e-16 97.1
11 TraesCS3B01G302000 chr5A 96.491 57 2 0 2153 2209 476064449 476064505 7.480000e-16 95.3
12 TraesCS3B01G302000 chr1D 94.915 649 21 5 1 647 417747085 417747723 0.000000e+00 1005.0
13 TraesCS3B01G302000 chr1D 93.548 403 10 5 2153 2539 417747723 417748125 1.010000e-163 586.0
14 TraesCS3B01G302000 chr5D 94.915 649 15 2 1 647 547846133 547845501 0.000000e+00 1000.0
15 TraesCS3B01G302000 chr5D 94.915 649 13 2 1 647 354744224 354744854 0.000000e+00 998.0
16 TraesCS3B01G302000 chr5D 93.548 403 10 5 2153 2539 547845501 547845099 1.010000e-163 586.0
17 TraesCS3B01G302000 chr5D 93.300 403 11 5 2153 2539 354744854 354745256 4.710000e-162 580.0
18 TraesCS3B01G302000 chr5D 87.302 63 5 3 2116 2176 68390809 68390870 4.530000e-08 69.4
19 TraesCS3B01G302000 chr7D 94.607 649 13 2 1 647 449769030 449769658 0.000000e+00 985.0
20 TraesCS3B01G302000 chr7D 93.300 403 11 5 2153 2539 449769658 449770060 4.710000e-162 580.0
21 TraesCS3B01G302000 chr2A 93.837 649 20 6 1 647 23468148 23467518 0.000000e+00 959.0
22 TraesCS3B01G302000 chr2A 93.052 403 12 5 2153 2539 23467518 23467116 2.190000e-160 575.0
23 TraesCS3B01G302000 chr2A 80.593 809 73 43 959 1759 28794149 28794881 4.780000e-152 547.0
24 TraesCS3B01G302000 chr2A 83.430 344 28 10 646 965 28793586 28793924 2.470000e-75 292.0
25 TraesCS3B01G302000 chr2A 84.266 286 26 4 1871 2153 28794916 28795185 6.970000e-66 261.0
26 TraesCS3B01G302000 chr2A 88.298 94 7 3 623 715 394798749 394798839 2.670000e-20 110.0
27 TraesCS3B01G302000 chr2A 88.298 94 7 3 623 715 406410777 406410687 2.670000e-20 110.0
28 TraesCS3B01G302000 chr1B 93.374 649 23 5 1 647 497828082 497827452 0.000000e+00 942.0
29 TraesCS3B01G302000 chr1B 93.548 403 10 5 2153 2539 497827452 497827050 1.010000e-163 586.0
30 TraesCS3B01G302000 chr1B 88.393 112 9 3 646 755 131997733 131997624 5.700000e-27 132.0
31 TraesCS3B01G302000 chr4A 93.374 649 22 6 1 647 491456598 491457227 0.000000e+00 941.0
32 TraesCS3B01G302000 chr4A 92.060 403 16 5 2153 2539 491457227 491457629 1.030000e-153 553.0
33 TraesCS3B01G302000 chr4A 84.615 78 11 1 809 886 642396565 642396641 2.710000e-10 76.8
34 TraesCS3B01G302000 chr4B 86.560 811 93 10 959 1759 251869706 251868902 0.000000e+00 880.0
35 TraesCS3B01G302000 chr4B 85.732 813 94 15 959 1759 251533963 251533161 0.000000e+00 839.0
36 TraesCS3B01G302000 chr4B 84.593 344 25 8 646 965 251870262 251869923 1.470000e-82 316.0
37 TraesCS3B01G302000 chr4B 83.430 344 29 7 646 965 251534525 251534186 6.870000e-76 294.0
38 TraesCS3B01G302000 chr4B 84.099 283 30 7 1871 2153 251868867 251868600 2.510000e-65 259.0
39 TraesCS3B01G302000 chr4B 88.333 60 3 4 2103 2158 475278906 475278847 4.530000e-08 69.4
40 TraesCS3B01G302000 chr3A 80.383 1254 164 47 959 2153 362555930 362557160 0.000000e+00 878.0
41 TraesCS3B01G302000 chr3A 82.677 1016 122 32 959 1940 48635597 48634602 0.000000e+00 852.0
42 TraesCS3B01G302000 chr3A 86.286 175 10 5 646 806 48636275 48636101 7.220000e-41 178.0
43 TraesCS3B01G302000 chr3A 80.142 282 21 8 645 891 362555264 362555545 7.220000e-41 178.0
44 TraesCS3B01G302000 chr3A 93.506 77 3 2 895 969 48635951 48635875 2.060000e-21 113.0
45 TraesCS3B01G302000 chr3A 90.141 71 5 2 895 963 362555575 362555645 9.670000e-15 91.6
46 TraesCS3B01G302000 chr3D 97.609 460 10 1 1 460 14356290 14356748 0.000000e+00 787.0
47 TraesCS3B01G302000 chr3D 93.052 403 12 5 2153 2539 14356989 14357391 2.190000e-160 575.0
48 TraesCS3B01G302000 chr3D 95.023 221 8 2 430 647 14356769 14356989 6.720000e-91 344.0
49 TraesCS3B01G302000 chr3D 78.161 609 70 31 1566 2153 578548277 578548843 1.880000e-86 329.0
50 TraesCS3B01G302000 chr6A 84.133 813 110 11 959 1759 445207094 445206289 0.000000e+00 769.0
51 TraesCS3B01G302000 chr6A 83.721 344 28 7 646 965 445207688 445207349 1.480000e-77 300.0
52 TraesCS3B01G302000 chr6A 78.606 416 49 16 1660 2061 140147702 140148091 3.260000e-59 239.0
53 TraesCS3B01G302000 chr6A 81.625 283 36 8 1871 2153 445206254 445205988 1.180000e-53 220.0
54 TraesCS3B01G302000 chr6A 92.241 116 9 0 645 760 140146362 140146477 5.620000e-37 165.0
55 TraesCS3B01G302000 chr2B 93.052 403 12 5 2153 2539 232836369 232836771 2.190000e-160 575.0
56 TraesCS3B01G302000 chr2B 83.951 486 65 8 1453 1929 310623738 310623257 1.070000e-123 453.0
57 TraesCS3B01G302000 chr2B 91.045 335 10 6 315 647 232836053 232836369 3.880000e-118 435.0
58 TraesCS3B01G302000 chr2B 84.556 259 23 9 646 891 310685442 310685188 9.080000e-60 241.0
59 TraesCS3B01G302000 chr2B 83.951 81 13 0 632 712 408421932 408422012 7.530000e-11 78.7
60 TraesCS3B01G302000 chr2B 83.951 81 13 0 632 712 408423059 408423139 7.530000e-11 78.7
61 TraesCS3B01G302000 chr2B 86.207 58 5 3 1983 2038 25073765 25073709 2.730000e-05 60.2
62 TraesCS3B01G302000 chr7B 78.550 993 120 51 1208 2153 154440166 154439220 3.670000e-158 568.0
63 TraesCS3B01G302000 chr7B 78.261 989 129 45 1208 2153 154464299 154463354 7.930000e-155 556.0
64 TraesCS3B01G302000 chr7B 79.036 892 115 42 1208 2055 138600708 138599845 1.720000e-151 545.0
65 TraesCS3B01G302000 chr7B 85.417 240 31 3 959 1197 484941126 484941362 1.950000e-61 246.0
66 TraesCS3B01G302000 chr7B 85.167 209 30 1 967 1174 138600994 138600786 1.980000e-51 213.0
67 TraesCS3B01G302000 chr5B 76.200 1021 142 52 1077 2055 542827954 542828915 1.790000e-121 446.0
68 TraesCS3B01G302000 chr5B 84.524 84 13 0 809 892 542814244 542814327 1.620000e-12 84.2
69 TraesCS3B01G302000 chr5B 94.118 51 3 0 842 892 84806924 84806874 7.530000e-11 78.7
70 TraesCS3B01G302000 chr7A 78.023 769 101 38 1352 2093 388726842 388727569 3.020000e-114 422.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G302000 chr3B 485534008 485536546 2538 False 4689.000000 4689 100.000000 1 2539 1 chr3B.!!$F3 2538
1 TraesCS3B01G302000 chr3B 790969080 790970708 1628 True 398.666667 643 84.599333 646 2153 3 chr3B.!!$R1 1507
2 TraesCS3B01G302000 chr5A 476063819 476064505 686 False 516.150000 937 94.855500 1 2209 2 chr5A.!!$F2 2208
3 TraesCS3B01G302000 chr5A 130221694 130223547 1853 True 427.366667 1020 85.627000 646 2153 3 chr5A.!!$R1 1507
4 TraesCS3B01G302000 chr5A 528894179 528894800 621 False 335.000000 335 77.554000 1446 2055 1 chr5A.!!$F1 609
5 TraesCS3B01G302000 chr1D 417747085 417748125 1040 False 795.500000 1005 94.231500 1 2539 2 chr1D.!!$F1 2538
6 TraesCS3B01G302000 chr5D 547845099 547846133 1034 True 793.000000 1000 94.231500 1 2539 2 chr5D.!!$R1 2538
7 TraesCS3B01G302000 chr5D 354744224 354745256 1032 False 789.000000 998 94.107500 1 2539 2 chr5D.!!$F2 2538
8 TraesCS3B01G302000 chr7D 449769030 449770060 1030 False 782.500000 985 93.953500 1 2539 2 chr7D.!!$F1 2538
9 TraesCS3B01G302000 chr2A 23467116 23468148 1032 True 767.000000 959 93.444500 1 2539 2 chr2A.!!$R2 2538
10 TraesCS3B01G302000 chr2A 28793586 28795185 1599 False 366.666667 547 82.763000 646 2153 3 chr2A.!!$F2 1507
11 TraesCS3B01G302000 chr1B 497827050 497828082 1032 True 764.000000 942 93.461000 1 2539 2 chr1B.!!$R2 2538
12 TraesCS3B01G302000 chr4A 491456598 491457629 1031 False 747.000000 941 92.717000 1 2539 2 chr4A.!!$F2 2538
13 TraesCS3B01G302000 chr4B 251533161 251534525 1364 True 566.500000 839 84.581000 646 1759 2 chr4B.!!$R2 1113
14 TraesCS3B01G302000 chr4B 251868600 251870262 1662 True 485.000000 880 85.084000 646 2153 3 chr4B.!!$R3 1507
15 TraesCS3B01G302000 chr3A 362555264 362557160 1896 False 382.533333 878 83.555333 645 2153 3 chr3A.!!$F1 1508
16 TraesCS3B01G302000 chr3A 48634602 48636275 1673 True 381.000000 852 87.489667 646 1940 3 chr3A.!!$R1 1294
17 TraesCS3B01G302000 chr3D 14356290 14357391 1101 False 568.666667 787 95.228000 1 2539 3 chr3D.!!$F2 2538
18 TraesCS3B01G302000 chr3D 578548277 578548843 566 False 329.000000 329 78.161000 1566 2153 1 chr3D.!!$F1 587
19 TraesCS3B01G302000 chr6A 445205988 445207688 1700 True 429.666667 769 83.159667 646 2153 3 chr6A.!!$R1 1507
20 TraesCS3B01G302000 chr6A 140146362 140148091 1729 False 202.000000 239 85.423500 645 2061 2 chr6A.!!$F1 1416
21 TraesCS3B01G302000 chr2B 232836053 232836771 718 False 505.000000 575 92.048500 315 2539 2 chr2B.!!$F1 2224
22 TraesCS3B01G302000 chr7B 154439220 154440166 946 True 568.000000 568 78.550000 1208 2153 1 chr7B.!!$R1 945
23 TraesCS3B01G302000 chr7B 154463354 154464299 945 True 556.000000 556 78.261000 1208 2153 1 chr7B.!!$R2 945
24 TraesCS3B01G302000 chr7B 138599845 138600994 1149 True 379.000000 545 82.101500 967 2055 2 chr7B.!!$R3 1088
25 TraesCS3B01G302000 chr5B 542827954 542828915 961 False 446.000000 446 76.200000 1077 2055 1 chr5B.!!$F2 978
26 TraesCS3B01G302000 chr7A 388726842 388727569 727 False 422.000000 422 78.023000 1352 2093 1 chr7A.!!$F1 741

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
874 997 0.036164 TCCAATTCCACCCACACGAG 59.964 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 2653 0.716108 GTTGAGATGACCTTGTCGCG 59.284 55.0 0.0 0.0 34.95 5.87 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
105 106 9.733556 TGTTATACCTCTTATTTGCTTCAAAGA 57.266 29.630 0.00 0.00 36.76 2.52
226 227 3.696051 AGCGACCAAGTGCATCAAATAAT 59.304 39.130 0.00 0.00 0.00 1.28
376 377 6.866480 AGTGTTTGACAATGATTTCACAGTT 58.134 32.000 0.00 0.00 0.00 3.16
528 602 4.063689 GCCATATCACAGAGTGAGATTGG 58.936 47.826 15.66 15.66 46.04 3.16
597 671 6.027482 TCAAGTAACCTAGATTGTACCCCTT 58.973 40.000 0.00 0.00 0.00 3.95
643 717 3.141398 CATTGTCATATCCTTGACCCCG 58.859 50.000 2.43 0.00 44.37 5.73
648 722 2.823747 TCATATCCTTGACCCCGTATCG 59.176 50.000 0.00 0.00 0.00 2.92
712 786 3.819337 GACATGCAAGCTATCCACATCAT 59.181 43.478 0.00 0.00 0.00 2.45
741 815 4.408270 ACTCTCATACAGCCACATCATCTT 59.592 41.667 0.00 0.00 0.00 2.40
780 869 1.884464 CGTGCCTCCATGTCATCCG 60.884 63.158 0.00 0.00 0.00 4.18
816 937 3.119280 GCCCCGTGCTTTTGTTATTATGT 60.119 43.478 0.00 0.00 36.87 2.29
831 952 2.139323 TATGTCTGGGCTGTACGTCT 57.861 50.000 0.00 0.00 0.00 4.18
833 954 1.913778 TGTCTGGGCTGTACGTCTTA 58.086 50.000 0.00 0.00 0.00 2.10
835 956 2.829720 TGTCTGGGCTGTACGTCTTATT 59.170 45.455 0.00 0.00 0.00 1.40
874 997 0.036164 TCCAATTCCACCCACACGAG 59.964 55.000 0.00 0.00 0.00 4.18
893 1045 2.816087 GAGCAGATCAAAAGCCACTTCA 59.184 45.455 0.00 0.00 0.00 3.02
901 1054 8.896744 CAGATCAAAAGCCACTTCATCTTATTA 58.103 33.333 0.00 0.00 0.00 0.98
1041 1556 1.661821 GTCGATTGATCCGCCGGAG 60.662 63.158 13.12 0.00 34.05 4.63
1104 1619 1.052124 CCGGGCCATTAGTCCCAGTA 61.052 60.000 4.39 0.00 42.75 2.74
1109 1624 2.504175 GGCCATTAGTCCCAGTAAGACA 59.496 50.000 0.00 0.00 36.68 3.41
1307 1934 1.444553 GCGTGTCGGAGAAGACCTG 60.445 63.158 0.00 0.00 39.69 4.00
1309 1936 1.666011 GTGTCGGAGAAGACCTGCA 59.334 57.895 0.00 0.00 39.69 4.41
1337 1973 0.250081 GATGAGATGGGGTTCCTCGC 60.250 60.000 0.00 0.00 0.00 5.03
1462 2142 2.082231 GCATGATCCATCCATTCCTCG 58.918 52.381 0.00 0.00 0.00 4.63
1477 2157 1.694150 TCCTCGAGCCATTAATCCCTG 59.306 52.381 6.99 0.00 0.00 4.45
1532 2217 4.012374 CTCCTTTGATTACAGGTGCACAT 58.988 43.478 20.43 9.24 0.00 3.21
1548 2255 1.656587 ACATAAGTGAGGCCAGGACA 58.343 50.000 5.01 0.00 0.00 4.02
1553 2260 0.548682 AGTGAGGCCAGGACAAGGAT 60.549 55.000 5.01 0.00 0.00 3.24
1582 2290 3.181458 GGCGGTGGACTGGATATTTTCTA 60.181 47.826 0.00 0.00 0.00 2.10
1606 2320 4.817464 TCTGTTAATAGCGTCTCTCTCTCC 59.183 45.833 0.00 0.00 0.00 3.71
1607 2321 4.524053 TGTTAATAGCGTCTCTCTCTCCA 58.476 43.478 0.00 0.00 0.00 3.86
1649 2374 8.026607 CCTCTCTGTTAACTTTCTCTCTGTTAG 58.973 40.741 7.22 0.00 0.00 2.34
1655 2380 8.142551 TGTTAACTTTCTCTCTGTTAGTTCTCC 58.857 37.037 7.22 0.00 31.94 3.71
1661 2386 6.918067 TCTCTCTGTTAGTTCTCCATGAAA 57.082 37.500 0.00 0.00 36.30 2.69
1726 2478 1.968017 CAGTGGGCATGTGCGACTT 60.968 57.895 5.77 0.00 43.26 3.01
1750 2506 2.427453 TCCTACAGCTTCGTCCAATCTC 59.573 50.000 0.00 0.00 0.00 2.75
1798 2562 5.924356 TCTCAAGTGAGTGTTATGAACCAA 58.076 37.500 8.14 0.00 42.60 3.67
1800 2564 6.650807 TCTCAAGTGAGTGTTATGAACCAATC 59.349 38.462 8.14 0.00 42.60 2.67
1820 2584 7.833682 ACCAATCACATAATAACAATCTGTGGA 59.166 33.333 0.00 0.00 38.16 4.02
1885 2658 0.872021 GACCACCATCTCATCGCGAC 60.872 60.000 12.93 0.00 0.00 5.19
1886 2659 1.141665 CCACCATCTCATCGCGACA 59.858 57.895 12.93 0.00 0.00 4.35
1914 2688 9.342308 GGTCATCTCAACAAATTATCCATCTTA 57.658 33.333 0.00 0.00 0.00 2.10
1942 2718 9.679661 ATCCTTTCAACCAAATACAAAGTTTTT 57.320 25.926 0.00 0.00 0.00 1.94
1973 2749 5.755849 ACAAAGTTGGCTAGCTATAACCAT 58.244 37.500 15.72 7.25 27.30 3.55
2069 2866 2.430610 GGCAAACCAAGTGCACCCA 61.431 57.895 14.63 0.00 44.07 4.51
2199 2997 6.040391 AGTCTCCATAGATTCAAGCAGTACTC 59.960 42.308 0.00 0.00 33.30 2.59
2230 3044 0.251341 CCACCTTCAAGAACCCCAGG 60.251 60.000 0.00 0.00 0.00 4.45
2257 3071 8.051901 AGTACTCCTCAATTTTTATTTTCCCG 57.948 34.615 0.00 0.00 0.00 5.14
2277 3091 3.002451 CCGTCCGACAAATTAACACAACA 59.998 43.478 0.00 0.00 0.00 3.33
2364 3178 3.487372 ACTTGGCCTCTTTAACAACCTC 58.513 45.455 3.32 0.00 0.00 3.85
2409 3223 5.125097 CAGCAGCCAAAAGAGATATCAACTT 59.875 40.000 5.32 7.35 0.00 2.66
2501 3315 5.870433 TGCATTACCAAATCAAATTCTGCAG 59.130 36.000 7.63 7.63 32.64 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 4.690748 CGTCAACCATGTGTATTGACTCTT 59.309 41.667 19.00 0.00 46.52 2.85
376 377 9.738832 GTTTTGCTTAAACATGTTCCTAGTTTA 57.261 29.630 12.39 0.00 44.49 2.01
528 602 1.672881 GCCATGTGCTTGTCATAGTCC 59.327 52.381 0.00 0.00 36.87 3.85
597 671 7.726291 TGGTTCTAACATGAAAGGAAAATACCA 59.274 33.333 0.00 0.00 0.00 3.25
648 722 9.668497 GTGGGGATGAACTATTTAGGTATTATC 57.332 37.037 0.00 0.00 0.00 1.75
712 786 2.028112 GTGGCTGTATGAGAGTGGTTGA 60.028 50.000 0.00 0.00 0.00 3.18
741 815 7.708752 GGCACGAATAAAATTATTTGGGATCAA 59.291 33.333 16.23 0.00 39.33 2.57
780 869 1.648467 CGGGGCAGTAGAGCAAAAGC 61.648 60.000 0.00 0.00 35.83 3.51
816 937 4.020928 TGAAAATAAGACGTACAGCCCAGA 60.021 41.667 0.00 0.00 0.00 3.86
831 952 7.549488 GGAGGAGACGAAGAGAATTGAAAATAA 59.451 37.037 0.00 0.00 0.00 1.40
833 954 5.877564 GGAGGAGACGAAGAGAATTGAAAAT 59.122 40.000 0.00 0.00 0.00 1.82
835 956 4.283467 TGGAGGAGACGAAGAGAATTGAAA 59.717 41.667 0.00 0.00 0.00 2.69
874 997 3.442977 AGATGAAGTGGCTTTTGATCTGC 59.557 43.478 0.00 0.00 0.00 4.26
901 1054 7.605259 CGTCACAACGTTTGTTTCAATAAAAT 58.395 30.769 0.00 0.00 43.23 1.82
918 1071 2.232941 TCAGGATAGGGAACGTCACAAC 59.767 50.000 0.00 0.00 0.00 3.32
924 1077 2.176247 ACCATCAGGATAGGGAACGT 57.824 50.000 0.00 0.00 38.69 3.99
1041 1556 8.814235 TCTTCGAGAAAAATAATATGAACCGAC 58.186 33.333 0.00 0.00 0.00 4.79
1194 1725 3.376078 CCACCAGCACCACCATGC 61.376 66.667 0.00 0.00 46.50 4.06
1195 1726 1.676635 CTCCACCAGCACCACCATG 60.677 63.158 0.00 0.00 0.00 3.66
1196 1727 2.156098 ACTCCACCAGCACCACCAT 61.156 57.895 0.00 0.00 0.00 3.55
1238 1850 2.665000 CCAGCCACGACATGTCCT 59.335 61.111 20.03 8.32 0.00 3.85
1307 1934 3.112205 ATCTCATCCACCGCCCTGC 62.112 63.158 0.00 0.00 0.00 4.85
1309 1936 2.446848 CCATCTCATCCACCGCCCT 61.447 63.158 0.00 0.00 0.00 5.19
1347 1983 3.458163 GGGATCCCGTCAGCGTCA 61.458 66.667 17.02 0.00 36.15 4.35
1392 2057 0.893727 GGAAATGGAAGCCGGTGTGT 60.894 55.000 1.90 0.00 0.00 3.72
1477 2157 0.671472 GTGCCCTGCAATCAAAAGGC 60.671 55.000 0.00 0.00 41.47 4.35
1532 2217 0.984230 CCTTGTCCTGGCCTCACTTA 59.016 55.000 3.32 0.00 0.00 2.24
1544 2229 1.069935 GCCGCCTAGATCCTTGTCC 59.930 63.158 0.00 0.00 0.00 4.02
1548 2255 2.444140 ACCGCCGCCTAGATCCTT 60.444 61.111 0.00 0.00 0.00 3.36
1553 2260 4.753662 AGTCCACCGCCGCCTAGA 62.754 66.667 0.00 0.00 0.00 2.43
1582 2290 5.472137 GGAGAGAGAGACGCTATTAACAGAT 59.528 44.000 0.00 0.00 0.00 2.90
1606 2320 7.102346 ACAGAGAGGAGACAGAAATTTATGTG 58.898 38.462 22.36 7.77 31.94 3.21
1607 2321 7.251321 ACAGAGAGGAGACAGAAATTTATGT 57.749 36.000 17.91 17.91 34.95 2.29
1661 2386 8.057623 AGTCTGGGATTCACAATCTATTGATTT 58.942 33.333 9.60 0.00 40.61 2.17
1726 2478 4.649674 AGATTGGACGAAGCTGTAGGATAA 59.350 41.667 0.00 0.00 0.00 1.75
1774 2531 6.114187 TGGTTCATAACACTCACTTGAGAT 57.886 37.500 13.27 1.93 44.74 2.75
1880 2653 0.716108 GTTGAGATGACCTTGTCGCG 59.284 55.000 0.00 0.00 34.95 5.87
1885 2658 7.395190 TGGATAATTTGTTGAGATGACCTTG 57.605 36.000 0.00 0.00 0.00 3.61
1886 2659 8.057623 AGATGGATAATTTGTTGAGATGACCTT 58.942 33.333 0.00 0.00 0.00 3.50
1940 2716 6.490040 AGCTAGCCAACTTTGTATCAGAAAAA 59.510 34.615 12.13 0.00 0.00 1.94
1941 2717 6.003950 AGCTAGCCAACTTTGTATCAGAAAA 58.996 36.000 12.13 0.00 0.00 2.29
1942 2718 5.560724 AGCTAGCCAACTTTGTATCAGAAA 58.439 37.500 12.13 0.00 0.00 2.52
1943 2719 5.165961 AGCTAGCCAACTTTGTATCAGAA 57.834 39.130 12.13 0.00 0.00 3.02
1944 2720 4.826274 AGCTAGCCAACTTTGTATCAGA 57.174 40.909 12.13 0.00 0.00 3.27
1945 2721 7.171678 GGTTATAGCTAGCCAACTTTGTATCAG 59.828 40.741 12.13 0.00 0.00 2.90
1946 2722 6.990349 GGTTATAGCTAGCCAACTTTGTATCA 59.010 38.462 12.13 0.00 0.00 2.15
1947 2723 6.990349 TGGTTATAGCTAGCCAACTTTGTATC 59.010 38.462 12.13 0.37 35.51 2.24
1948 2724 6.895782 TGGTTATAGCTAGCCAACTTTGTAT 58.104 36.000 12.13 2.62 35.51 2.29
1949 2725 6.302535 TGGTTATAGCTAGCCAACTTTGTA 57.697 37.500 12.13 0.00 35.51 2.41
1950 2726 5.174037 TGGTTATAGCTAGCCAACTTTGT 57.826 39.130 12.13 0.00 35.51 2.83
1951 2727 6.699575 AATGGTTATAGCTAGCCAACTTTG 57.300 37.500 12.13 0.00 41.03 2.77
1952 2728 8.996651 ATAAATGGTTATAGCTAGCCAACTTT 57.003 30.769 12.13 12.27 41.03 2.66
1953 2729 8.440771 AGATAAATGGTTATAGCTAGCCAACTT 58.559 33.333 12.13 13.85 41.03 2.66
1954 2730 7.978925 AGATAAATGGTTATAGCTAGCCAACT 58.021 34.615 12.13 9.80 41.03 3.16
1955 2731 8.622948 AAGATAAATGGTTATAGCTAGCCAAC 57.377 34.615 12.13 12.93 41.03 3.77
1956 2732 8.660435 AGAAGATAAATGGTTATAGCTAGCCAA 58.340 33.333 12.13 0.00 41.03 4.52
1957 2733 8.207350 AGAAGATAAATGGTTATAGCTAGCCA 57.793 34.615 12.13 14.33 41.78 4.75
1963 2739 8.677148 TGGTTGAGAAGATAAATGGTTATAGC 57.323 34.615 0.00 0.00 29.69 2.97
2107 2905 4.143052 GCTGCGGTACTTGTTACGTATTTT 60.143 41.667 0.00 0.00 0.00 1.82
2111 2909 1.269174 TGCTGCGGTACTTGTTACGTA 59.731 47.619 0.00 0.00 0.00 3.57
2199 2997 7.315890 GTTCTTGAAGGTGGATGGATTTTTAG 58.684 38.462 0.00 0.00 0.00 1.85
2230 3044 9.856488 GGGAAAATAAAAATTGAGGAGTACTTC 57.144 33.333 0.00 0.00 0.00 3.01
2257 3071 6.031471 AGTTTGTTGTGTTAATTTGTCGGAC 58.969 36.000 0.00 0.00 0.00 4.79
2315 3129 6.923670 TCTCTGTTATCCTAGATTGTACCCT 58.076 40.000 0.00 0.00 0.00 4.34
2364 3178 6.927381 TGCTGACATCACATGTTCTATCATAG 59.073 38.462 0.00 0.00 45.03 2.23
2501 3315 6.545504 TTTCTTAGCTTGTGTTGAGATGAC 57.454 37.500 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.