Multiple sequence alignment - TraesCS7D01G331400

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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 TraesCS7D01G331400 chr7D 100.000 3040 0 0 1 3040 422720599 422723638 0.000000e+00 5614.0
1 TraesCS7D01G331400 chr7D 85.269 577 65 10 2478 3037 422859244 422859817 7.310000e-161 577.0
2 TraesCS7D01G331400 chr7D 84.048 583 68 16 2477 3036 422853825 422854405 3.450000e-149 538.0
3 TraesCS7D01G331400 chr7D 97.826 46 0 1 2956 3001 113958734 113958690 9.040000e-11 78.7
4 TraesCS7D01G331400 chr7B 90.209 1481 72 29 614 2071 439994021 439995451 0.000000e+00 1864.0
5 TraesCS7D01G331400 chr7B 95.032 926 39 4 2122 3040 439995776 439996701 0.000000e+00 1448.0
6 TraesCS7D01G331400 chr7B 92.695 616 41 2 1 612 73337133 73337748 0.000000e+00 885.0
7 TraesCS7D01G331400 chr7B 86.240 625 70 10 1 611 151151406 151152028 0.000000e+00 664.0
8 TraesCS7D01G331400 chr7B 86.157 549 49 10 614 1149 439863815 439864349 4.400000e-158 568.0
9 TraesCS7D01G331400 chr7B 85.009 527 64 10 2523 3036 440005159 440005683 3.470000e-144 521.0
10 TraesCS7D01G331400 chr7B 80.132 604 102 14 16 606 357458999 357459597 4.650000e-118 435.0
11 TraesCS7D01G331400 chr7B 95.506 89 3 1 1259 1346 439875686 439875774 1.140000e-29 141.0
12 TraesCS7D01G331400 chr7B 87.069 116 15 0 1148 1263 439873963 439874078 6.840000e-27 132.0
13 TraesCS7D01G331400 chr7A 86.481 1472 118 44 616 2042 510400420 510398985 0.000000e+00 1541.0
14 TraesCS7D01G331400 chr7A 89.339 1135 88 14 741 1851 510467670 510466545 0.000000e+00 1395.0
15 TraesCS7D01G331400 chr7A 89.925 933 64 13 2122 3040 510380781 510379865 0.000000e+00 1175.0
16 TraesCS7D01G331400 chr7A 83.705 583 71 15 2477 3036 510159554 510158973 2.080000e-146 529.0
17 TraesCS7D01G331400 chr5A 94.481 616 29 3 1 612 423735341 423735955 0.000000e+00 944.0
18 TraesCS7D01G331400 chr5D 93.648 614 34 3 4 612 345032017 345031404 0.000000e+00 913.0
19 TraesCS7D01G331400 chr2B 92.496 613 42 3 4 612 184905445 184904833 0.000000e+00 874.0
20 TraesCS7D01G331400 chr6B 91.262 618 45 5 4 612 710339663 710339046 0.000000e+00 833.0
21 TraesCS7D01G331400 chr6A 90.547 603 52 4 6 603 72448902 72449504 0.000000e+00 793.0
22 TraesCS7D01G331400 chr5B 88.448 554 53 8 70 612 653738557 653739110 0.000000e+00 658.0
23 TraesCS7D01G331400 chr6D 97.826 46 0 1 2956 3001 426970139 426970183 9.040000e-11 78.7
24 TraesCS7D01G331400 chr3D 97.826 46 0 1 2956 3001 450037156 450037200 9.040000e-11 78.7


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 TraesCS7D01G331400 chr7D 422720599 422723638 3039 False 5614 5614 100.0000 1 3040 1 chr7D.!!$F1 3039
1 TraesCS7D01G331400 chr7D 422859244 422859817 573 False 577 577 85.2690 2478 3037 1 chr7D.!!$F3 559
2 TraesCS7D01G331400 chr7D 422853825 422854405 580 False 538 538 84.0480 2477 3036 1 chr7D.!!$F2 559
3 TraesCS7D01G331400 chr7B 439994021 439996701 2680 False 1656 1864 92.6205 614 3040 2 chr7B.!!$F7 2426
4 TraesCS7D01G331400 chr7B 73337133 73337748 615 False 885 885 92.6950 1 612 1 chr7B.!!$F1 611
5 TraesCS7D01G331400 chr7B 151151406 151152028 622 False 664 664 86.2400 1 611 1 chr7B.!!$F2 610
6 TraesCS7D01G331400 chr7B 439863815 439864349 534 False 568 568 86.1570 614 1149 1 chr7B.!!$F4 535
7 TraesCS7D01G331400 chr7B 440005159 440005683 524 False 521 521 85.0090 2523 3036 1 chr7B.!!$F5 513
8 TraesCS7D01G331400 chr7B 357458999 357459597 598 False 435 435 80.1320 16 606 1 chr7B.!!$F3 590
9 TraesCS7D01G331400 chr7A 510398985 510400420 1435 True 1541 1541 86.4810 616 2042 1 chr7A.!!$R3 1426
10 TraesCS7D01G331400 chr7A 510466545 510467670 1125 True 1395 1395 89.3390 741 1851 1 chr7A.!!$R4 1110
11 TraesCS7D01G331400 chr7A 510379865 510380781 916 True 1175 1175 89.9250 2122 3040 1 chr7A.!!$R2 918
12 TraesCS7D01G331400 chr7A 510158973 510159554 581 True 529 529 83.7050 2477 3036 1 chr7A.!!$R1 559
13 TraesCS7D01G331400 chr5A 423735341 423735955 614 False 944 944 94.4810 1 612 1 chr5A.!!$F1 611
14 TraesCS7D01G331400 chr5D 345031404 345032017 613 True 913 913 93.6480 4 612 1 chr5D.!!$R1 608
15 TraesCS7D01G331400 chr2B 184904833 184905445 612 True 874 874 92.4960 4 612 1 chr2B.!!$R1 608
16 TraesCS7D01G331400 chr6B 710339046 710339663 617 True 833 833 91.2620 4 612 1 chr6B.!!$R1 608
17 TraesCS7D01G331400 chr6A 72448902 72449504 602 False 793 793 90.5470 6 603 1 chr6A.!!$F1 597
18 TraesCS7D01G331400 chr5B 653738557 653739110 553 False 658 658 88.4480 70 612 1 chr5B.!!$F1 542

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
646 667 0.518636 CAAAGTCATGTCACAGCCGG 59.481 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2071 2149 0.657312 CACACTGCACACATCGTTGT 59.343 50.0 0.0 0.0 36.15 3.32 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
64 66 2.747855 GTTGCGCCCCCTCAAGAG 60.748 66.667 4.18 0.00 0.00 2.85
74 76 0.676151 CCCTCAAGAGAAGCTGCCAC 60.676 60.000 0.00 0.00 0.00 5.01
109 114 1.486310 ACTTGGAGCTTGACACACAGA 59.514 47.619 0.00 0.00 0.00 3.41
641 662 4.751600 GTCATCAGTCAAAGTCATGTCACA 59.248 41.667 0.00 0.00 0.00 3.58
646 667 0.518636 CAAAGTCATGTCACAGCCGG 59.481 55.000 0.00 0.00 0.00 6.13
663 685 1.447838 GGCTGCTCGGTTGATTCGA 60.448 57.895 0.00 0.00 35.24 3.71
693 729 1.136695 TGGACTTGCTGCAAAACTTGG 59.863 47.619 16.74 6.04 0.00 3.61
700 736 2.027745 TGCTGCAAAACTTGGAAACCAA 60.028 40.909 0.00 3.21 41.69 3.67
782 818 1.065854 CCAGCCGAGAAGTCAAATCCT 60.066 52.381 0.00 0.00 0.00 3.24
862 908 8.689251 TCTGCTGCGTCTATATATATTTCAAC 57.311 34.615 0.00 0.00 0.00 3.18
903 949 3.043713 CGAGCAGCACGGAAAGCA 61.044 61.111 4.04 0.00 0.00 3.91
904 950 2.558313 GAGCAGCACGGAAAGCAC 59.442 61.111 0.00 0.00 0.00 4.40
905 951 2.970974 GAGCAGCACGGAAAGCACC 61.971 63.158 0.00 0.00 0.00 5.01
906 952 2.980233 GCAGCACGGAAAGCACCT 60.980 61.111 0.00 0.00 0.00 4.00
910 956 2.328099 GCACGGAAAGCACCTCCTG 61.328 63.158 0.00 0.00 0.00 3.86
911 957 1.371183 CACGGAAAGCACCTCCTGA 59.629 57.895 0.00 0.00 0.00 3.86
915 961 1.757118 CGGAAAGCACCTCCTGATCTA 59.243 52.381 0.00 0.00 0.00 1.98
917 963 2.484594 GGAAAGCACCTCCTGATCTAGC 60.485 54.545 0.00 0.00 0.00 3.42
1053 1114 3.744559 GCCGACAACTTCAAGGCA 58.255 55.556 0.00 0.00 46.48 4.75
1059 1120 2.546795 CGACAACTTCAAGGCAGAGTCT 60.547 50.000 0.00 0.00 0.00 3.24
1529 1590 4.986645 TCCGGACGACGTGGACGA 62.987 66.667 4.58 0.00 43.02 4.20
1530 1591 3.807538 CCGGACGACGTGGACGAT 61.808 66.667 4.58 0.00 43.02 3.73
1802 1868 4.394920 CCAGGCTGTTTAACGATAACACAT 59.605 41.667 14.43 0.00 32.46 3.21
1808 1874 6.474819 TGTTTAACGATAACACATGACCAG 57.525 37.500 0.00 0.00 30.96 4.00
1812 1878 0.657840 GATAACACATGACCAGCCGC 59.342 55.000 0.00 0.00 0.00 6.53
1813 1879 1.089481 ATAACACATGACCAGCCGCG 61.089 55.000 0.00 0.00 0.00 6.46
1899 1970 8.071177 AGTGGCTAAAAGCATTCATCTTATTT 57.929 30.769 0.78 0.00 44.75 1.40
1900 1971 7.977853 AGTGGCTAAAAGCATTCATCTTATTTG 59.022 33.333 0.78 0.00 44.75 2.32
1901 1972 7.761249 GTGGCTAAAAGCATTCATCTTATTTGT 59.239 33.333 0.78 0.00 44.75 2.83
1902 1973 8.965819 TGGCTAAAAGCATTCATCTTATTTGTA 58.034 29.630 0.78 0.00 44.75 2.41
1912 1983 6.710597 TCATCTTATTTGTAGTAGGAGCGT 57.289 37.500 0.00 0.00 0.00 5.07
1917 1988 8.737168 TCTTATTTGTAGTAGGAGCGTAAGTA 57.263 34.615 0.00 0.00 41.68 2.24
1922 1993 6.764308 TGTAGTAGGAGCGTAAGTACATTT 57.236 37.500 0.00 0.00 41.68 2.32
1923 1994 6.558009 TGTAGTAGGAGCGTAAGTACATTTG 58.442 40.000 0.00 0.00 41.68 2.32
1970 2048 8.082242 TGGATATGATGTATACGTGACTTTCTG 58.918 37.037 1.31 0.00 0.00 3.02
1971 2049 7.062371 GGATATGATGTATACGTGACTTTCTGC 59.938 40.741 1.31 0.00 0.00 4.26
1973 2051 5.102313 TGATGTATACGTGACTTTCTGCTG 58.898 41.667 1.31 0.00 0.00 4.41
1974 2052 4.776795 TGTATACGTGACTTTCTGCTGA 57.223 40.909 0.00 0.00 0.00 4.26
1975 2053 5.128992 TGTATACGTGACTTTCTGCTGAA 57.871 39.130 0.00 1.33 0.00 3.02
1976 2054 4.921515 TGTATACGTGACTTTCTGCTGAAC 59.078 41.667 5.41 0.00 31.02 3.18
1978 2056 3.728076 ACGTGACTTTCTGCTGAACTA 57.272 42.857 5.41 0.00 31.02 2.24
1979 2057 3.381949 ACGTGACTTTCTGCTGAACTAC 58.618 45.455 5.41 2.71 31.02 2.73
1980 2058 3.068307 ACGTGACTTTCTGCTGAACTACT 59.932 43.478 5.41 0.00 31.02 2.57
1984 2062 6.183360 CGTGACTTTCTGCTGAACTACTATTG 60.183 42.308 5.41 0.00 31.02 1.90
1985 2063 5.639506 TGACTTTCTGCTGAACTACTATTGC 59.360 40.000 5.41 0.00 31.02 3.56
1986 2064 5.551233 ACTTTCTGCTGAACTACTATTGCA 58.449 37.500 5.41 0.00 31.02 4.08
1987 2065 6.176183 ACTTTCTGCTGAACTACTATTGCAT 58.824 36.000 5.41 0.00 31.02 3.96
1988 2066 6.656693 ACTTTCTGCTGAACTACTATTGCATT 59.343 34.615 5.41 0.00 31.02 3.56
1989 2067 7.175641 ACTTTCTGCTGAACTACTATTGCATTT 59.824 33.333 5.41 0.00 31.02 2.32
1990 2068 8.560355 TTTCTGCTGAACTACTATTGCATTTA 57.440 30.769 5.41 0.00 31.02 1.40
2015 2093 6.769608 ATTTGAAAAACAGAAAATCCGAGC 57.230 33.333 0.00 0.00 0.00 5.03
2016 2094 4.237349 TGAAAAACAGAAAATCCGAGCC 57.763 40.909 0.00 0.00 0.00 4.70
2079 2157 6.539649 TTTTAGAAGAGGTTGACAACGATG 57.460 37.500 12.07 0.00 0.00 3.84
2080 2158 3.753294 AGAAGAGGTTGACAACGATGT 57.247 42.857 12.07 0.00 44.25 3.06
2083 2161 2.483876 AGAGGTTGACAACGATGTGTG 58.516 47.619 12.07 0.00 40.74 3.82
2084 2162 0.944386 AGGTTGACAACGATGTGTGC 59.056 50.000 12.07 0.00 40.74 4.57
2085 2163 0.660488 GGTTGACAACGATGTGTGCA 59.340 50.000 12.07 0.00 40.74 4.57
2086 2164 1.334059 GGTTGACAACGATGTGTGCAG 60.334 52.381 12.07 0.00 40.74 4.41
2087 2165 1.330521 GTTGACAACGATGTGTGCAGT 59.669 47.619 1.86 0.00 40.74 4.40
2088 2166 0.936600 TGACAACGATGTGTGCAGTG 59.063 50.000 1.86 0.00 40.74 3.66
2089 2167 0.937304 GACAACGATGTGTGCAGTGT 59.063 50.000 1.86 0.00 40.74 3.55
2090 2168 0.657312 ACAACGATGTGTGCAGTGTG 59.343 50.000 0.00 0.00 38.69 3.82
2091 2169 0.658244 CAACGATGTGTGCAGTGTGC 60.658 55.000 0.00 0.00 45.29 4.57
2141 2498 7.183112 TGAAGGGAAGGGAATACTATGTTTACA 59.817 37.037 0.00 0.00 0.00 2.41
2164 2521 2.665165 TGAAGTGCAATTCAAGGGTGT 58.335 42.857 25.91 0.00 36.28 4.16
2165 2522 2.622942 TGAAGTGCAATTCAAGGGTGTC 59.377 45.455 25.91 0.00 36.28 3.67
2167 2524 2.949447 AGTGCAATTCAAGGGTGTCTT 58.051 42.857 0.00 0.00 35.79 3.01
2168 2525 3.299503 AGTGCAATTCAAGGGTGTCTTT 58.700 40.909 0.00 0.00 32.41 2.52
2169 2526 4.469657 AGTGCAATTCAAGGGTGTCTTTA 58.530 39.130 0.00 0.00 32.41 1.85
2170 2527 4.278419 AGTGCAATTCAAGGGTGTCTTTAC 59.722 41.667 0.00 0.00 32.41 2.01
2171 2528 4.037446 GTGCAATTCAAGGGTGTCTTTACA 59.963 41.667 0.00 0.00 32.41 2.41
2172 2529 4.832266 TGCAATTCAAGGGTGTCTTTACAT 59.168 37.500 0.00 0.00 38.08 2.29
2211 2571 3.193903 TGAGCTGCACATAAGGTACGTAA 59.806 43.478 1.02 0.00 0.00 3.18
2263 2626 8.842777 CATTTTTGTTTCAAAAACAGCAGAAAG 58.157 29.630 18.26 0.00 32.67 2.62
2266 2629 2.888834 TCAAAAACAGCAGAAAGGGC 57.111 45.000 0.00 0.00 0.00 5.19
2396 2760 4.338400 GGACCAATATAAACTCCAACCAGC 59.662 45.833 0.00 0.00 0.00 4.85
2409 2773 2.944349 CCAACCAGCACAAGCAATTTTT 59.056 40.909 0.00 0.00 45.49 1.94
2427 2791 5.651172 TTTTTCACGTCTCATGTAGTGTG 57.349 39.130 0.00 0.00 36.16 3.82
2634 3019 7.414222 AATAATGTTTGCCTGAGATGACATT 57.586 32.000 0.00 0.00 39.94 2.71
2845 3238 7.157347 GCTCACATGTAAATGATCTATCCTCA 58.843 38.462 0.00 0.00 0.00 3.86
2862 3255 0.035317 TCAAGCTCGCCAGTGATTGT 59.965 50.000 0.00 0.00 38.12 2.71
2870 3263 4.322049 GCTCGCCAGTGATTGTAGGTATAT 60.322 45.833 0.00 0.00 0.00 0.86
2953 3346 5.125900 TGCACCAACATTCATTGAAGGATAG 59.874 40.000 17.21 1.97 0.00 2.08
3004 3399 8.594550 TGGTATAGTTCAAGAGTTAGCTTCTTT 58.405 33.333 0.00 0.00 0.00 2.52
3022 3417 6.294843 GCTTCTTTAGACTAGGTGAGTTCTGT 60.295 42.308 0.00 0.00 39.06 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 62 2.759795 GGGGTGGCAGCTTCTCTT 59.240 61.111 17.16 0.00 0.00 2.85
612 633 6.014242 ACATGACTTTGACTGATGACCTTAGA 60.014 38.462 0.00 0.00 0.00 2.10
646 667 2.002127 CTCGAATCAACCGAGCAGC 58.998 57.895 0.00 0.00 45.37 5.25
663 685 2.943199 GCAGCAAGTCCAAAGCCTATCT 60.943 50.000 0.00 0.00 0.00 1.98
749 785 1.146930 GGCTGGATTCGGAGATGCA 59.853 57.895 0.00 0.00 35.04 3.96
782 818 4.395854 TCGTAGGTGCAGTATTTTCGACTA 59.604 41.667 0.00 0.00 0.00 2.59
845 890 9.088512 CCTGCTTCCGTTGAAATATATATAGAC 57.911 37.037 0.00 0.00 0.00 2.59
862 908 3.382803 CTCTGGAGGCCTGCTTCCG 62.383 68.421 25.93 11.00 44.11 4.30
903 949 3.329520 ACGATAGAGCTAGATCAGGAGGT 59.670 47.826 11.20 0.00 41.38 3.85
904 950 3.950397 ACGATAGAGCTAGATCAGGAGG 58.050 50.000 11.20 0.00 41.38 4.30
905 951 5.116180 CCTACGATAGAGCTAGATCAGGAG 58.884 50.000 11.20 4.62 41.38 3.69
906 952 4.080807 CCCTACGATAGAGCTAGATCAGGA 60.081 50.000 11.20 0.00 41.38 3.86
910 956 3.625764 CAGCCCTACGATAGAGCTAGATC 59.374 52.174 0.00 0.00 41.38 2.75
911 957 3.616219 CAGCCCTACGATAGAGCTAGAT 58.384 50.000 0.00 0.00 41.38 1.98
915 961 1.182385 GGCAGCCCTACGATAGAGCT 61.182 60.000 0.00 0.00 41.38 4.09
917 963 0.315568 GTGGCAGCCCTACGATAGAG 59.684 60.000 9.64 0.00 41.38 2.43
1053 1114 1.589113 GCAGAAGACGGCAGACTCT 59.411 57.895 0.00 0.00 37.19 3.24
1059 1120 1.219124 GATCTGGCAGAAGACGGCA 59.781 57.895 22.84 0.00 38.87 5.69
1158 1219 2.678580 TCCTCGGCGGTCATGTCA 60.679 61.111 7.21 0.00 0.00 3.58
1323 1384 1.101635 CGAGGTAGGCGATGGAGTCA 61.102 60.000 0.00 0.00 0.00 3.41
1517 1578 1.346365 CATGAAATCGTCCACGTCGT 58.654 50.000 0.00 0.00 40.80 4.34
1529 1590 1.683943 CCGCACCATCTCCATGAAAT 58.316 50.000 0.00 0.00 30.57 2.17
1530 1591 1.031571 GCCGCACCATCTCCATGAAA 61.032 55.000 0.00 0.00 30.57 2.69
1624 1685 3.044059 GCTGCTTCACGATGTGGCC 62.044 63.158 0.00 0.00 33.87 5.36
1660 1721 2.509336 CGTCGGCTTCGGCTCATT 60.509 61.111 0.00 0.00 41.44 2.57
1779 1840 3.749088 TGTGTTATCGTTAAACAGCCTGG 59.251 43.478 0.00 0.00 37.51 4.45
1812 1878 2.665519 GCTATTATTGCAACATCGGCCG 60.666 50.000 22.12 22.12 0.00 6.13
1813 1879 2.351738 GGCTATTATTGCAACATCGGCC 60.352 50.000 15.38 15.38 0.00 6.13
1815 1881 2.884012 TGGGCTATTATTGCAACATCGG 59.116 45.455 0.00 0.00 0.00 4.18
1816 1882 4.566545 TTGGGCTATTATTGCAACATCG 57.433 40.909 0.00 0.00 0.00 3.84
1817 1883 4.746611 GCTTTGGGCTATTATTGCAACATC 59.253 41.667 0.00 0.00 38.06 3.06
1818 1884 4.161942 TGCTTTGGGCTATTATTGCAACAT 59.838 37.500 0.00 0.00 42.39 2.71
1867 1933 7.938140 TGAATGCTTTTAGCCACTAATTAGT 57.062 32.000 12.50 12.50 41.51 2.24
1868 1934 8.844244 AGATGAATGCTTTTAGCCACTAATTAG 58.156 33.333 11.05 11.05 41.51 1.73
1870 1936 7.651027 AGATGAATGCTTTTAGCCACTAATT 57.349 32.000 0.00 0.00 41.51 1.40
1871 1937 7.651027 AAGATGAATGCTTTTAGCCACTAAT 57.349 32.000 0.00 0.00 41.51 1.73
1872 1938 8.752005 ATAAGATGAATGCTTTTAGCCACTAA 57.248 30.769 0.00 0.00 41.51 2.24
1899 1970 6.151648 ACAAATGTACTTACGCTCCTACTACA 59.848 38.462 0.00 0.00 0.00 2.74
1900 1971 6.558909 ACAAATGTACTTACGCTCCTACTAC 58.441 40.000 0.00 0.00 0.00 2.73
1901 1972 6.600822 AGACAAATGTACTTACGCTCCTACTA 59.399 38.462 0.00 0.00 0.00 1.82
1902 1973 5.418209 AGACAAATGTACTTACGCTCCTACT 59.582 40.000 0.00 0.00 0.00 2.57
1912 1983 9.158233 GGCACATACTTAAGACAAATGTACTTA 57.842 33.333 10.09 0.00 0.00 2.24
1917 1988 5.351465 CGAGGCACATACTTAAGACAAATGT 59.649 40.000 10.09 9.97 0.00 2.71
1922 1993 3.762288 AGTCGAGGCACATACTTAAGACA 59.238 43.478 10.09 0.00 0.00 3.41
1923 1994 4.106197 CAGTCGAGGCACATACTTAAGAC 58.894 47.826 10.09 0.00 0.00 3.01
1936 2014 4.727507 ATACATCATATCCAGTCGAGGC 57.272 45.455 0.00 0.00 0.00 4.70
1989 2067 9.567848 GCTCGGATTTTCTGTTTTTCAAATATA 57.432 29.630 0.00 0.00 0.00 0.86
1990 2068 7.545615 GGCTCGGATTTTCTGTTTTTCAAATAT 59.454 33.333 0.00 0.00 0.00 1.28
2000 2078 3.191371 GTCAATGGCTCGGATTTTCTGTT 59.809 43.478 0.00 0.00 0.00 3.16
2013 2091 5.643379 ATTCATACAAAACGTCAATGGCT 57.357 34.783 0.00 0.00 0.00 4.75
2014 2092 7.804614 TTAATTCATACAAAACGTCAATGGC 57.195 32.000 0.00 0.00 0.00 4.40
2071 2149 0.657312 CACACTGCACACATCGTTGT 59.343 50.000 0.00 0.00 36.15 3.32
2073 2151 1.648720 GCACACTGCACACATCGTT 59.351 52.632 0.00 0.00 44.26 3.85
2074 2152 3.333414 GCACACTGCACACATCGT 58.667 55.556 0.00 0.00 44.26 3.73
2083 2161 9.586435 TTACATCTATATATGTATGCACACTGC 57.414 33.333 10.72 0.00 40.93 4.40
2086 2164 9.020813 CGGTTACATCTATATATGTATGCACAC 57.979 37.037 10.72 6.63 40.93 3.82
2087 2165 8.962679 TCGGTTACATCTATATATGTATGCACA 58.037 33.333 10.72 0.00 40.93 4.57
2088 2166 9.797556 TTCGGTTACATCTATATATGTATGCAC 57.202 33.333 10.72 7.18 40.93 4.57
2095 2452 9.534565 CCCTTCATTCGGTTACATCTATATATG 57.465 37.037 0.00 0.00 0.00 1.78
2098 2455 7.792364 TCCCTTCATTCGGTTACATCTATAT 57.208 36.000 0.00 0.00 0.00 0.86
2102 2459 4.384208 CCTTCCCTTCATTCGGTTACATCT 60.384 45.833 0.00 0.00 0.00 2.90
2103 2460 3.877508 CCTTCCCTTCATTCGGTTACATC 59.122 47.826 0.00 0.00 0.00 3.06
2110 2467 2.736670 ATTCCCTTCCCTTCATTCGG 57.263 50.000 0.00 0.00 0.00 4.30
2116 2473 7.571025 TGTAAACATAGTATTCCCTTCCCTTC 58.429 38.462 0.00 0.00 0.00 3.46
2117 2474 7.519347 TGTAAACATAGTATTCCCTTCCCTT 57.481 36.000 0.00 0.00 0.00 3.95
2118 2475 7.519347 TTGTAAACATAGTATTCCCTTCCCT 57.481 36.000 0.00 0.00 0.00 4.20
2119 2476 8.630037 CATTTGTAAACATAGTATTCCCTTCCC 58.370 37.037 0.00 0.00 0.00 3.97
2120 2477 9.403583 TCATTTGTAAACATAGTATTCCCTTCC 57.596 33.333 0.00 0.00 0.00 3.46
2141 2498 4.101430 ACACCCTTGAATTGCACTTCATTT 59.899 37.500 18.85 2.95 35.20 2.32
2169 2526 9.000486 CAGCTCAACTTCATATGATATTCATGT 58.000 33.333 6.17 0.00 37.70 3.21
2170 2527 7.963465 GCAGCTCAACTTCATATGATATTCATG 59.037 37.037 6.17 1.34 37.70 3.07
2171 2528 7.664318 TGCAGCTCAACTTCATATGATATTCAT 59.336 33.333 6.17 0.00 40.72 2.57
2172 2529 6.993902 TGCAGCTCAACTTCATATGATATTCA 59.006 34.615 6.17 0.00 0.00 2.57
2211 2571 4.768448 TCATGTCATGCCAATCTTTGAACT 59.232 37.500 8.03 0.00 0.00 3.01
2224 2584 5.600908 AACAAAAATGCTTCATGTCATGC 57.399 34.783 8.03 0.00 0.00 4.06
2263 2626 1.866601 GCACAAAACTTGATGTTGCCC 59.133 47.619 0.00 0.00 39.13 5.36
2266 2629 2.540931 GGCTGCACAAAACTTGATGTTG 59.459 45.455 0.50 0.00 39.13 3.33
2396 2760 4.350346 TGAGACGTGAAAAATTGCTTGTG 58.650 39.130 0.00 0.00 0.00 3.33
2409 2773 3.554259 GTCACACTACATGAGACGTGA 57.446 47.619 0.00 4.22 38.83 4.35
2427 2791 2.000447 GTGCCATTCTGGTAGAACGTC 59.000 52.381 0.00 0.00 40.46 4.34
2634 3019 7.178097 TGAAATTACATGGAATCACACATTGGA 59.822 33.333 2.92 0.00 0.00 3.53
2845 3238 1.406069 CCTACAATCACTGGCGAGCTT 60.406 52.381 0.00 0.00 0.00 3.74
2875 3268 1.396648 TGCCAGCGTGAATATCAAACG 59.603 47.619 0.00 0.00 40.22 3.60
2876 3269 3.485947 TTGCCAGCGTGAATATCAAAC 57.514 42.857 0.00 0.00 0.00 2.93
2885 3278 2.887783 TCCTTTTTATTTGCCAGCGTGA 59.112 40.909 0.00 0.00 0.00 4.35
2886 3279 3.296322 TCCTTTTTATTTGCCAGCGTG 57.704 42.857 0.00 0.00 0.00 5.34
2953 3346 4.792521 ATATGGTCTTCTCCGTAGCATC 57.207 45.455 0.00 0.00 33.23 3.91
3004 3399 6.215023 TCTTCCTACAGAACTCACCTAGTCTA 59.785 42.308 0.00 0.00 37.50 2.59


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

AutoCloner maintained by Alex Coulton.