Multiple sequence alignment - TraesCS2D01G089000

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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 TraesCS2D01G089000 chr2D 100.000 2987 0 0 1 2987 38783400 38780414 0.000000e+00 5517.0
1 TraesCS2D01G089000 chr2D 96.590 2141 42 12 1 2136 40904006 40901892 0.000000e+00 3520.0
2 TraesCS2D01G089000 chr2D 89.088 1448 80 31 729 2136 38637084 38638493 0.000000e+00 1727.0
3 TraesCS2D01G089000 chr2D 85.629 1684 113 59 412 2061 38678091 38679679 0.000000e+00 1650.0
4 TraesCS2D01G089000 chr2D 91.342 924 69 7 1120 2041 40849917 40850831 0.000000e+00 1253.0
5 TraesCS2D01G089000 chr2D 88.960 625 42 11 1517 2136 38685834 38685232 0.000000e+00 747.0
6 TraesCS2D01G089000 chr2D 85.098 255 35 3 1 254 590024323 590024575 1.060000e-64 257.0
7 TraesCS2D01G089000 chr2D 84.016 244 24 9 2746 2987 40895972 40896202 1.390000e-53 220.0
8 TraesCS2D01G089000 chr2D 88.950 181 8 3 2740 2919 38681408 38681577 2.330000e-51 213.0
9 TraesCS2D01G089000 chr2D 86.066 122 12 3 2137 2256 252347258 252347376 3.130000e-25 126.0
10 TraesCS2D01G089000 chr2D 94.366 71 3 1 2918 2987 38681660 38681730 1.130000e-19 108.0
11 TraesCS2D01G089000 chr2B 87.218 1682 122 46 489 2136 67542265 67540643 0.000000e+00 1829.0
12 TraesCS2D01G089000 chr2B 89.839 1427 88 27 729 2136 67659147 67657759 0.000000e+00 1779.0
13 TraesCS2D01G089000 chr2B 85.459 1733 127 51 400 2099 67464032 67465672 0.000000e+00 1688.0
14 TraesCS2D01G089000 chr2B 87.073 820 51 26 729 1534 67424085 67424863 0.000000e+00 876.0
15 TraesCS2D01G089000 chr2B 83.815 346 30 9 2391 2730 67540511 67540186 3.740000e-79 305.0
16 TraesCS2D01G089000 chr2B 94.767 172 6 1 2740 2911 67426680 67426848 6.350000e-67 265.0
17 TraesCS2D01G089000 chr2B 95.413 109 5 0 2742 2850 67537722 67537614 1.100000e-39 174.0
18 TraesCS2D01G089000 chr2B 76.533 375 44 22 2514 2848 67433495 67433125 6.620000e-37 165.0
19 TraesCS2D01G089000 chr2B 88.785 107 11 1 489 594 67423523 67423629 2.420000e-26 130.0
20 TraesCS2D01G089000 chr2A 86.259 1783 128 57 402 2136 43457876 43459589 0.000000e+00 1827.0
21 TraesCS2D01G089000 chr2A 89.191 1286 97 23 870 2136 43429564 43430826 0.000000e+00 1567.0
22 TraesCS2D01G089000 chr2A 91.559 853 42 13 1284 2136 43484026 43483204 0.000000e+00 1149.0
23 TraesCS2D01G089000 chr2A 87.007 431 43 7 870 1291 43489528 43489102 9.690000e-130 473.0
24 TraesCS2D01G089000 chr2A 91.961 311 14 6 2679 2987 43480831 43480530 2.750000e-115 425.0
25 TraesCS2D01G089000 chr2A 87.430 358 27 7 2251 2607 43481173 43480833 2.160000e-106 396.0
26 TraesCS2D01G089000 chr2A 85.984 371 31 11 2634 2985 43433625 43433993 7.820000e-101 377.0
27 TraesCS2D01G089000 chr2A 81.053 285 18 19 2446 2730 43460038 43460286 8.450000e-46 195.0
28 TraesCS2D01G089000 chr2A 77.246 334 40 21 372 683 43429133 43429452 2.380000e-36 163.0
29 TraesCS2D01G089000 chr2A 88.235 136 14 2 384 519 43489957 43489824 8.570000e-36 161.0
30 TraesCS2D01G089000 chr2A 80.631 222 21 11 2509 2712 43463432 43463649 5.160000e-33 152.0
31 TraesCS2D01G089000 chr2A 80.090 221 18 16 2771 2987 43472388 43472586 1.120000e-29 141.0
32 TraesCS2D01G089000 chr2A 82.394 142 19 5 2251 2391 54816814 54816950 5.230000e-23 119.0
33 TraesCS2D01G089000 chr2A 78.182 220 21 10 258 461 44073310 44073102 6.770000e-22 115.0
34 TraesCS2D01G089000 chr2A 93.333 75 4 1 2914 2987 43460620 43460694 3.150000e-20 110.0
35 TraesCS2D01G089000 chr2A 98.039 51 1 0 2859 2909 43460412 43460462 4.100000e-14 89.8
36 TraesCS2D01G089000 chr2A 97.222 36 0 1 2728 2762 43468887 43468922 3.220000e-05 60.2
37 TraesCS2D01G089000 chr7D 87.843 255 28 2 1 254 386362895 386363147 2.250000e-76 296.0
38 TraesCS2D01G089000 chr5D 87.843 255 27 4 1 254 437980073 437979822 2.250000e-76 296.0
39 TraesCS2D01G089000 chr5D 82.979 141 20 2 2251 2391 176106918 176107054 1.120000e-24 124.0
40 TraesCS2D01G089000 chr1D 87.449 247 20 6 14 255 240596634 240596874 1.050000e-69 274.0
41 TraesCS2D01G089000 chr6D 85.771 253 32 3 3 254 418311899 418311650 6.350000e-67 265.0
42 TraesCS2D01G089000 chr4A 85.039 254 35 2 1 253 461710144 461709893 3.820000e-64 255.0
43 TraesCS2D01G089000 chr1B 84.030 263 38 4 1 262 549722733 549722474 1.780000e-62 250.0
44 TraesCS2D01G089000 chr6A 83.984 256 38 3 1 255 76696658 76696405 2.970000e-60 243.0
45 TraesCS2D01G089000 chr5A 83.916 143 14 6 2251 2391 145666032 145666167 8.690000e-26 128.0
46 TraesCS2D01G089000 chr5A 82.394 142 20 4 2251 2391 651751719 651751856 5.230000e-23 119.0
47 TraesCS2D01G089000 chr3A 83.824 136 16 6 2257 2391 36649398 36649268 1.120000e-24 124.0
48 TraesCS2D01G089000 chr3A 83.582 134 16 6 2257 2389 412937116 412936988 1.450000e-23 121.0
49 TraesCS2D01G089000 chr6B 83.099 142 16 7 2251 2390 340074856 340074991 4.040000e-24 122.0
50 TraesCS2D01G089000 chr7A 83.088 136 17 6 2257 2391 174707298 174707168 5.230000e-23 119.0
51 TraesCS2D01G089000 chr5B 89.474 95 9 1 2253 2347 265295781 265295874 5.230000e-23 119.0


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 TraesCS2D01G089000 chr2D 38780414 38783400 2986 True 5517.000000 5517 100.000000 1 2987 1 chr2D.!!$R2 2986
1 TraesCS2D01G089000 chr2D 40901892 40904006 2114 True 3520.000000 3520 96.590000 1 2136 1 chr2D.!!$R3 2135
2 TraesCS2D01G089000 chr2D 38637084 38638493 1409 False 1727.000000 1727 89.088000 729 2136 1 chr2D.!!$F1 1407
3 TraesCS2D01G089000 chr2D 40849917 40850831 914 False 1253.000000 1253 91.342000 1120 2041 1 chr2D.!!$F2 921
4 TraesCS2D01G089000 chr2D 38685232 38685834 602 True 747.000000 747 88.960000 1517 2136 1 chr2D.!!$R1 619
5 TraesCS2D01G089000 chr2D 38678091 38681730 3639 False 657.000000 1650 89.648333 412 2987 3 chr2D.!!$F6 2575
6 TraesCS2D01G089000 chr2B 67657759 67659147 1388 True 1779.000000 1779 89.839000 729 2136 1 chr2B.!!$R2 1407
7 TraesCS2D01G089000 chr2B 67464032 67465672 1640 False 1688.000000 1688 85.459000 400 2099 1 chr2B.!!$F1 1699
8 TraesCS2D01G089000 chr2B 67537614 67542265 4651 True 769.333333 1829 88.815333 489 2850 3 chr2B.!!$R3 2361
9 TraesCS2D01G089000 chr2B 67423523 67426848 3325 False 423.666667 876 90.208333 489 2911 3 chr2B.!!$F2 2422
10 TraesCS2D01G089000 chr2A 43429133 43433993 4860 False 702.333333 1567 84.140333 372 2985 3 chr2A.!!$F2 2613
11 TraesCS2D01G089000 chr2A 43480530 43484026 3496 True 656.666667 1149 90.316667 1284 2987 3 chr2A.!!$R2 1703
12 TraesCS2D01G089000 chr2A 43457876 43463649 5773 False 474.760000 1827 87.863000 402 2987 5 chr2A.!!$F3 2585
13 TraesCS2D01G089000 chr2A 43489102 43489957 855 True 317.000000 473 87.621000 384 1291 2 chr2A.!!$R3 907

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
123 124 1.961277 GGCGTCACCTCACACCTTG 60.961 63.158 0.0 0.0 34.51 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 2542 0.656785 CTCGAGCACGTACTACCCTC 59.343 60.0 0.0 0.0 40.69 4.3 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
48 49 2.427095 ACGATTGACGATCATGTCCAGA 59.573 45.455 3.57 0.00 45.77 3.86
81 82 4.761739 TCCATCTGTTCCATTCTTTGTCAC 59.238 41.667 0.00 0.00 0.00 3.67
98 99 4.900684 TGTCACCGTCCAGATATTTTTGA 58.099 39.130 0.00 0.00 0.00 2.69
123 124 1.961277 GGCGTCACCTCACACCTTG 60.961 63.158 0.00 0.00 34.51 3.61
191 192 9.916360 AAAATAGGGGTATTCTAGACGAATTTT 57.084 29.630 0.00 0.00 42.26 1.82
256 257 7.193595 GGGGTAAAATATGAAATTCACTCACG 58.806 38.462 0.00 0.00 0.00 4.35
699 1088 4.410400 GGTGAGGGGCGGGTCAAG 62.410 72.222 0.00 0.00 0.00 3.02
1080 1535 2.902419 CGCCACCAACGACAATGCA 61.902 57.895 0.00 0.00 0.00 3.96
1878 2390 2.420138 GCTGAGAGCGGGAGACATA 58.580 57.895 0.00 0.00 0.00 2.29
2019 2538 1.308069 CCGATTGAGGTGCAGTTGGG 61.308 60.000 0.00 0.00 34.83 4.12
2020 2539 0.606401 CGATTGAGGTGCAGTTGGGT 60.606 55.000 0.00 0.00 0.00 4.51
2021 2540 1.620822 GATTGAGGTGCAGTTGGGTT 58.379 50.000 0.00 0.00 0.00 4.11
2022 2541 1.270550 GATTGAGGTGCAGTTGGGTTG 59.729 52.381 0.00 0.00 0.00 3.77
2023 2542 0.754957 TTGAGGTGCAGTTGGGTTGG 60.755 55.000 0.00 0.00 0.00 3.77
2137 2670 1.348064 TAGCTTGGCACTAGTGGTGT 58.652 50.000 23.95 2.76 46.86 4.16
2139 2672 1.909302 AGCTTGGCACTAGTGGTGTAT 59.091 47.619 23.95 0.00 46.86 2.29
2142 2675 4.019681 AGCTTGGCACTAGTGGTGTATTAA 60.020 41.667 23.95 0.00 46.86 1.40
2144 2677 5.220854 GCTTGGCACTAGTGGTGTATTAATG 60.221 44.000 23.95 0.00 46.86 1.90
2147 2680 6.288294 TGGCACTAGTGGTGTATTAATGATC 58.712 40.000 23.95 2.20 46.86 2.92
2148 2681 5.701290 GGCACTAGTGGTGTATTAATGATCC 59.299 44.000 23.95 7.71 46.86 3.36
2149 2682 6.288294 GCACTAGTGGTGTATTAATGATCCA 58.712 40.000 23.95 1.09 46.86 3.41
2152 2685 5.975988 AGTGGTGTATTAATGATCCAGGT 57.024 39.130 0.00 0.00 0.00 4.00
2153 2686 6.327386 AGTGGTGTATTAATGATCCAGGTT 57.673 37.500 0.00 0.00 0.00 3.50
2160 2693 8.975439 GTGTATTAATGATCCAGGTTAGTAACG 58.025 37.037 6.94 0.00 0.00 3.18
2161 2694 8.916062 TGTATTAATGATCCAGGTTAGTAACGA 58.084 33.333 6.94 0.00 0.00 3.85
2165 2698 9.675464 TTAATGATCCAGGTTAGTAACGAAAAT 57.325 29.630 6.94 0.00 0.00 1.82
2168 2701 9.675464 ATGATCCAGGTTAGTAACGAAAATAAA 57.325 29.630 6.94 0.00 0.00 1.40
2169 2702 9.504708 TGATCCAGGTTAGTAACGAAAATAAAA 57.495 29.630 6.94 0.00 0.00 1.52
2180 2713 9.522804 AGTAACGAAAATAAAAATTGACTTGCA 57.477 25.926 0.00 0.00 0.00 4.08
2185 2718 8.119226 CGAAAATAAAAATTGACTTGCAAACCA 58.881 29.630 0.00 0.00 40.48 3.67
2186 2719 9.437045 GAAAATAAAAATTGACTTGCAAACCAG 57.563 29.630 0.00 0.00 40.48 4.00
2187 2720 8.504812 AAATAAAAATTGACTTGCAAACCAGT 57.495 26.923 0.00 0.00 40.48 4.00
2188 2721 7.713764 ATAAAAATTGACTTGCAAACCAGTC 57.286 32.000 8.97 8.97 40.48 3.51
2190 2723 4.942761 AATTGACTTGCAAACCAGTCAT 57.057 36.364 17.37 3.70 40.39 3.06
2194 3474 5.843673 TGACTTGCAAACCAGTCATTAAA 57.156 34.783 13.67 0.00 36.51 1.52
2226 3506 8.736244 TCTTCATACCTGTAATTTAAGTTTGGC 58.264 33.333 0.00 0.00 0.00 4.52
2227 3507 7.399245 TCATACCTGTAATTTAAGTTTGGCC 57.601 36.000 0.00 0.00 0.00 5.36
2228 3508 7.179269 TCATACCTGTAATTTAAGTTTGGCCT 58.821 34.615 3.32 0.00 0.00 5.19
2229 3509 7.672239 TCATACCTGTAATTTAAGTTTGGCCTT 59.328 33.333 3.32 0.00 0.00 4.35
2230 3510 6.096673 ACCTGTAATTTAAGTTTGGCCTTG 57.903 37.500 3.32 0.00 0.00 3.61
2231 3511 5.600898 ACCTGTAATTTAAGTTTGGCCTTGT 59.399 36.000 3.32 0.00 0.00 3.16
2232 3512 6.778559 ACCTGTAATTTAAGTTTGGCCTTGTA 59.221 34.615 3.32 0.00 0.00 2.41
2233 3513 7.453439 ACCTGTAATTTAAGTTTGGCCTTGTAT 59.547 33.333 3.32 0.00 0.00 2.29
2234 3514 8.962679 CCTGTAATTTAAGTTTGGCCTTGTATA 58.037 33.333 3.32 0.00 0.00 1.47
2263 5602 5.011090 TGGAGAGACTACCATTGAATTCG 57.989 43.478 0.04 0.00 0.00 3.34
2305 5644 2.099427 TGGTATAAATTTTTCGCCCGCC 59.901 45.455 0.00 0.00 0.00 6.13
2306 5645 2.377880 GTATAAATTTTTCGCCCGCCG 58.622 47.619 0.00 0.00 38.61 6.46
2307 5646 0.812549 ATAAATTTTTCGCCCGCCGT 59.187 45.000 0.00 0.00 38.35 5.68
2309 5648 0.169451 AAATTTTTCGCCCGCCGTAG 59.831 50.000 0.00 0.00 38.35 3.51
2334 5673 9.337396 AGTCGGCTACATTGATTAAATTTATGA 57.663 29.630 0.00 0.00 0.00 2.15
2358 5697 9.906660 TGATCAAACTTAAATATCAAAAAGCGT 57.093 25.926 0.00 0.00 0.00 5.07
2360 5699 8.514136 TCAAACTTAAATATCAAAAAGCGTGG 57.486 30.769 0.00 0.00 0.00 4.94
2361 5700 8.353684 TCAAACTTAAATATCAAAAAGCGTGGA 58.646 29.630 0.00 0.00 0.00 4.02
2362 5701 8.424731 CAAACTTAAATATCAAAAAGCGTGGAC 58.575 33.333 0.00 0.00 0.00 4.02
2366 5705 5.895636 AATATCAAAAAGCGTGGACATGA 57.104 34.783 0.00 0.00 0.00 3.07
2382 5721 9.869757 CGTGGACATGAACTATATTATATGGAA 57.130 33.333 0.00 0.00 0.00 3.53
2398 5738 2.875296 TGGAATGAAGGGACAAAGTGG 58.125 47.619 0.00 0.00 0.00 4.00
2406 5756 1.896660 GGACAAAGTGGCGCAGGAA 60.897 57.895 10.83 0.00 0.00 3.36
2459 5809 0.580104 CGAACCGTTGAGTGTTGGAC 59.420 55.000 0.00 0.00 0.00 4.02
2461 5811 0.108041 AACCGTTGAGTGTTGGACGT 60.108 50.000 0.00 0.00 33.95 4.34
2492 5849 0.530650 CACTGTGCAGTTCAGTCGGT 60.531 55.000 5.53 0.00 43.14 4.69
2608 5975 1.066858 CCAGATGCAGTTGGAGTACGT 60.067 52.381 12.72 0.00 36.55 3.57
2629 7833 2.741517 TGACGCGAATGTCACATCAATT 59.258 40.909 15.93 0.00 43.62 2.32
2635 7839 6.020984 CGCGAATGTCACATCAATTTAAGAA 58.979 36.000 0.00 0.00 0.00 2.52
2708 9081 1.271163 GCTTGGTAACCAGTGGCTGTA 60.271 52.381 9.78 0.00 33.81 2.74
2825 11698 3.049674 CTCGGCGGCAGAGCAAAA 61.050 61.111 16.82 0.00 39.27 2.44
2837 11710 3.181497 GCAGAGCAAAACAGTGACTTTGA 60.181 43.478 19.77 0.00 35.03 2.69
2912 11789 5.063564 GCAAGTGGCAATACAAGTAGAGTAC 59.936 44.000 0.00 0.00 43.97 2.73
2964 12079 0.733223 GAAGAACGGCGGACTGACTC 60.733 60.000 13.24 1.16 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 5.762179 TGGAACAGATGGACAATAGAAGT 57.238 39.130 0.00 0.00 0.00 3.01
81 82 4.436852 CGGTGTTCAAAAATATCTGGACGG 60.437 45.833 0.00 0.00 0.00 4.79
98 99 4.309950 GAGGTGACGCCCGGTGTT 62.310 66.667 4.79 0.00 38.26 3.32
123 124 2.854963 TCTGATGCATGTCCATTAGGC 58.145 47.619 2.46 0.00 31.75 3.93
148 149 5.952347 CCTATTTTAGAAGCTTTGGACCCTT 59.048 40.000 0.00 0.00 0.00 3.95
191 192 5.186215 TGACACTAATTATCCCGTTGAGTGA 59.814 40.000 6.16 0.00 37.01 3.41
256 257 8.252964 AGTTCGTAGATCTTGTTGGTAAAATC 57.747 34.615 0.00 0.00 31.76 2.17
467 485 1.337167 TGTGCTCCAAGTCGTGATCAG 60.337 52.381 0.00 0.00 0.00 2.90
699 1088 1.273327 CTGGTTTTGATTGTCCTGGGC 59.727 52.381 0.00 0.00 0.00 5.36
786 1192 1.737008 GGCACCGTCTTCGTCTTCC 60.737 63.158 0.00 0.00 35.01 3.46
1072 1521 4.487412 GGCGGCAGCTGCATTGTC 62.487 66.667 37.63 24.75 44.36 3.18
1411 1893 2.032681 GCTCTTGGTTCCCGCACT 59.967 61.111 0.00 0.00 0.00 4.40
1413 1895 4.697756 CCGCTCTTGGTTCCCGCA 62.698 66.667 0.00 0.00 0.00 5.69
1419 1901 4.722700 ATGCCGCCGCTCTTGGTT 62.723 61.111 0.00 0.00 35.36 3.67
1789 2301 3.443925 CTCCTCAGCGCTCACCGA 61.444 66.667 7.13 0.00 40.02 4.69
1800 2312 1.984570 CGCCTTCTCCACCTCCTCA 60.985 63.158 0.00 0.00 0.00 3.86
1893 2405 3.382803 CTCCTCGCTGGCCAGGAAG 62.383 68.421 33.46 21.06 38.39 3.46
2009 2528 1.903404 CCCTCCAACCCAACTGCAC 60.903 63.158 0.00 0.00 0.00 4.57
2019 2538 0.893447 AGCACGTACTACCCTCCAAC 59.107 55.000 0.00 0.00 0.00 3.77
2020 2539 1.180029 GAGCACGTACTACCCTCCAA 58.820 55.000 0.00 0.00 0.00 3.53
2021 2540 1.028330 CGAGCACGTACTACCCTCCA 61.028 60.000 0.00 0.00 34.56 3.86
2022 2541 0.745845 TCGAGCACGTACTACCCTCC 60.746 60.000 2.86 0.00 40.69 4.30
2023 2542 0.656785 CTCGAGCACGTACTACCCTC 59.343 60.000 0.00 0.00 40.69 4.30
2139 2672 9.675464 ATTTTCGTTACTAACCTGGATCATTAA 57.325 29.630 0.00 0.00 0.00 1.40
2142 2675 9.675464 TTTATTTTCGTTACTAACCTGGATCAT 57.325 29.630 0.00 0.00 0.00 2.45
2160 2693 9.437045 CTGGTTTGCAAGTCAATTTTTATTTTC 57.563 29.630 0.00 0.00 34.12 2.29
2161 2694 8.955388 ACTGGTTTGCAAGTCAATTTTTATTTT 58.045 25.926 0.00 0.00 34.12 1.82
2163 2696 8.141835 GACTGGTTTGCAAGTCAATTTTTATT 57.858 30.769 10.70 0.00 43.55 1.40
2173 2706 7.713764 AAATTTAATGACTGGTTTGCAAGTC 57.286 32.000 8.97 8.97 44.18 3.01
2174 2707 9.777297 ATAAAATTTAATGACTGGTTTGCAAGT 57.223 25.926 0.00 0.00 0.00 3.16
2176 2709 9.995003 AGATAAAATTTAATGACTGGTTTGCAA 57.005 25.926 0.00 0.00 0.00 4.08
2177 2710 9.995003 AAGATAAAATTTAATGACTGGTTTGCA 57.005 25.926 0.00 0.00 0.00 4.08
2201 3481 7.973944 GGCCAAACTTAAATTACAGGTATGAAG 59.026 37.037 0.00 0.00 0.00 3.02
2205 3485 7.453439 ACAAGGCCAAACTTAAATTACAGGTAT 59.547 33.333 5.01 0.00 0.00 2.73
2208 3488 6.096673 ACAAGGCCAAACTTAAATTACAGG 57.903 37.500 5.01 0.00 0.00 4.00
2211 3491 9.797556 CCTTATACAAGGCCAAACTTAAATTAC 57.202 33.333 5.01 0.00 44.90 1.89
2227 3507 6.739331 AGTCTCTCCATTCCCTTATACAAG 57.261 41.667 0.00 0.00 0.00 3.16
2228 3508 6.553852 GGTAGTCTCTCCATTCCCTTATACAA 59.446 42.308 0.00 0.00 0.00 2.41
2229 3509 6.075984 GGTAGTCTCTCCATTCCCTTATACA 58.924 44.000 0.00 0.00 0.00 2.29
2230 3510 6.075984 TGGTAGTCTCTCCATTCCCTTATAC 58.924 44.000 0.00 0.00 0.00 1.47
2231 3511 6.289482 TGGTAGTCTCTCCATTCCCTTATA 57.711 41.667 0.00 0.00 0.00 0.98
2232 3512 5.157770 TGGTAGTCTCTCCATTCCCTTAT 57.842 43.478 0.00 0.00 0.00 1.73
2233 3513 4.620086 TGGTAGTCTCTCCATTCCCTTA 57.380 45.455 0.00 0.00 0.00 2.69
2234 3514 3.491766 TGGTAGTCTCTCCATTCCCTT 57.508 47.619 0.00 0.00 0.00 3.95
2235 3515 3.715648 ATGGTAGTCTCTCCATTCCCT 57.284 47.619 4.27 0.00 41.02 4.20
2241 3521 4.466370 ACGAATTCAATGGTAGTCTCTCCA 59.534 41.667 6.22 0.11 38.14 3.86
2243 3523 7.113684 CGAATACGAATTCAATGGTAGTCTCTC 59.886 40.741 6.22 0.00 41.44 3.20
2245 3525 6.916387 TCGAATACGAATTCAATGGTAGTCTC 59.084 38.462 6.22 0.00 45.74 3.36
2262 5601 7.075741 ACCATTGAAAACTTCTTTCGAATACG 58.924 34.615 0.00 0.00 41.26 3.06
2278 5617 6.531948 CGGGCGAAAAATTTATACCATTGAAA 59.468 34.615 0.00 0.00 0.00 2.69
2281 5620 4.208253 GCGGGCGAAAAATTTATACCATTG 59.792 41.667 0.00 0.00 0.00 2.82
2292 5631 1.363885 GACTACGGCGGGCGAAAAAT 61.364 55.000 31.03 10.17 0.00 1.82
2294 5633 2.432972 GACTACGGCGGGCGAAAA 60.433 61.111 31.03 13.77 0.00 2.29
2332 5671 9.906660 ACGCTTTTTGATATTTAAGTTTGATCA 57.093 25.926 0.00 0.00 0.00 2.92
2334 5673 9.139174 CCACGCTTTTTGATATTTAAGTTTGAT 57.861 29.630 0.00 0.00 0.00 2.57
2335 5674 8.353684 TCCACGCTTTTTGATATTTAAGTTTGA 58.646 29.630 0.00 0.00 0.00 2.69
2337 5676 8.138712 TGTCCACGCTTTTTGATATTTAAGTTT 58.861 29.630 0.00 0.00 0.00 2.66
2340 5679 7.967854 TCATGTCCACGCTTTTTGATATTTAAG 59.032 33.333 0.00 0.00 0.00 1.85
2341 5680 7.821652 TCATGTCCACGCTTTTTGATATTTAA 58.178 30.769 0.00 0.00 0.00 1.52
2342 5681 7.384439 TCATGTCCACGCTTTTTGATATTTA 57.616 32.000 0.00 0.00 0.00 1.40
2344 5683 5.895636 TCATGTCCACGCTTTTTGATATT 57.104 34.783 0.00 0.00 0.00 1.28
2345 5684 5.415701 AGTTCATGTCCACGCTTTTTGATAT 59.584 36.000 0.00 0.00 0.00 1.63
2346 5685 4.759693 AGTTCATGTCCACGCTTTTTGATA 59.240 37.500 0.00 0.00 0.00 2.15
2348 5687 2.948979 AGTTCATGTCCACGCTTTTTGA 59.051 40.909 0.00 0.00 0.00 2.69
2349 5688 3.354089 AGTTCATGTCCACGCTTTTTG 57.646 42.857 0.00 0.00 0.00 2.44
2350 5689 7.391148 AATATAGTTCATGTCCACGCTTTTT 57.609 32.000 0.00 0.00 0.00 1.94
2351 5690 8.677148 ATAATATAGTTCATGTCCACGCTTTT 57.323 30.769 0.00 0.00 0.00 2.27
2352 5691 9.944376 ATATAATATAGTTCATGTCCACGCTTT 57.056 29.630 0.00 0.00 0.00 3.51
2353 5692 9.371136 CATATAATATAGTTCATGTCCACGCTT 57.629 33.333 0.00 0.00 0.00 4.68
2354 5693 7.981789 CCATATAATATAGTTCATGTCCACGCT 59.018 37.037 0.00 0.00 0.00 5.07
2355 5694 7.979537 TCCATATAATATAGTTCATGTCCACGC 59.020 37.037 0.00 0.00 0.00 5.34
2356 5695 9.869757 TTCCATATAATATAGTTCATGTCCACG 57.130 33.333 0.00 0.00 0.00 4.94
2382 5721 1.244019 GCGCCACTTTGTCCCTTCAT 61.244 55.000 0.00 0.00 0.00 2.57
2406 5756 2.104281 GCCCCGAACAGGAATGTACTAT 59.896 50.000 0.00 0.00 45.00 2.12
2459 5809 0.032130 ACAGTGTGTCAGTGGCTACG 59.968 55.000 0.00 0.00 38.94 3.51
2461 5811 0.249868 GCACAGTGTGTCAGTGGCTA 60.250 55.000 23.73 0.00 38.94 3.93
2512 5869 3.617540 ATCGCAAACACACGATGAAAA 57.382 38.095 0.00 0.00 46.56 2.29
2608 5975 3.505808 TGATGTGACATTCGCGTCA 57.494 47.368 5.77 7.41 46.87 4.35
2629 7833 3.454375 GCCCAGATCGAATCGTTCTTAA 58.546 45.455 12.91 0.00 34.32 1.85
2635 7839 1.443407 CTGGCCCAGATCGAATCGT 59.557 57.895 4.15 0.00 32.44 3.73
2708 9081 8.036575 CCAATGTCAAACAGATCCAATAAACAT 58.963 33.333 0.00 0.00 0.00 2.71
2825 11698 8.561738 TTTCTAAACTTCTTCAAAGTCACTGT 57.438 30.769 0.00 0.00 0.00 3.55
2964 12079 4.088823 GCACTGGCAAAGTCTTAATCTG 57.911 45.455 0.00 0.00 36.83 2.90


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

AutoCloner maintained by Alex Coulton.