Multiple sequence alignment - TraesCS4B01G323800

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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 TraesCS4B01G323800 chr4B 100.000 2336 0 0 1 2336 614160077 614157742 0.000000e+00 4314.0
1 TraesCS4B01G323800 chr4B 100.000 29 0 0 170 198 252326034 252326062 1.000000e-03 54.7
2 TraesCS4B01G323800 chr4D 91.565 1968 79 39 1 1919 483685442 483683513 0.000000e+00 2634.0
3 TraesCS4B01G323800 chr4D 87.069 232 25 4 212 442 483685461 483685234 8.280000e-65 257.0
4 TraesCS4B01G323800 chr4D 86.634 202 17 1 1944 2135 483683313 483683112 5.060000e-52 215.0
5 TraesCS4B01G323800 chr5A 90.182 1487 70 26 659 2079 663727142 663725666 0.000000e+00 1868.0
6 TraesCS4B01G323800 chr5A 78.850 487 56 24 208 649 663727667 663727183 3.800000e-73 285.0
7 TraesCS4B01G323800 chr5A 88.095 168 12 2 2176 2336 663724079 663724245 2.370000e-45 193.0
8 TraesCS4B01G323800 chr2B 91.566 166 8 2 902 1066 130619870 130620030 8.400000e-55 224.0
9 TraesCS4B01G323800 chr6A 89.759 166 11 2 902 1066 277245510 277245670 8.460000e-50 207.0
10 TraesCS4B01G323800 chr6A 89.091 165 12 2 902 1065 75257243 75257084 1.420000e-47 200.0
11 TraesCS4B01G323800 chr3A 88.554 166 13 2 902 1066 683813682 683813522 1.830000e-46 196.0
12 TraesCS4B01G323800 chr2A 87.952 166 14 2 902 1066 580600737 580600897 8.520000e-45 191.0
13 TraesCS4B01G323800 chr6B 87.037 162 16 2 905 1066 148522540 148522384 6.630000e-41 178.0
14 TraesCS4B01G323800 chr7A 88.889 144 10 3 902 1044 292010230 292010368 3.090000e-39 172.0
15 TraesCS4B01G323800 chr3B 97.143 35 1 0 169 203 628116813 628116847 2.510000e-05 60.2
16 TraesCS4B01G323800 chr1D 90.909 44 3 1 170 212 458131176 458131133 9.020000e-05 58.4
17 TraesCS4B01G323800 chr7B 97.059 34 0 1 171 203 485523898 485523931 3.240000e-04 56.5
18 TraesCS4B01G323800 chr3D 90.698 43 3 1 171 212 130722089 130722131 3.240000e-04 56.5
19 TraesCS4B01G323800 chr5D 100.000 29 0 0 170 198 363090846 363090874 1.000000e-03 54.7
20 TraesCS4B01G323800 chr5D 100.000 29 0 0 170 198 440652019 440652047 1.000000e-03 54.7
21 TraesCS4B01G323800 chr2D 100.000 29 0 0 173 201 43090062 43090090 1.000000e-03 54.7


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 TraesCS4B01G323800 chr4B 614157742 614160077 2335 True 4314.000000 4314 100.000000 1 2336 1 chr4B.!!$R1 2335
1 TraesCS4B01G323800 chr4D 483683112 483685461 2349 True 1035.333333 2634 88.422667 1 2135 3 chr4D.!!$R1 2134
2 TraesCS4B01G323800 chr5A 663725666 663727667 2001 True 1076.500000 1868 84.516000 208 2079 2 chr5A.!!$R1 1871

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
813 945 0.108804 CCGCGGTAGAGAAGCAGAAA 60.109 55.0 19.5 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2164 2513 0.25589 TGAATGGAGGCCCTGTTAGC 59.744 55.0 0.0 0.0 0.0 3.09 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
53 73 1.972660 GACGTTCCCCCTCCATCCTG 61.973 65.000 0.00 0.00 0.00 3.86
136 156 7.012704 CGACTCAATCATCCCAACTTATCAAAT 59.987 37.037 0.00 0.00 0.00 2.32
180 209 8.313944 AGTTTTTACCAAAATTGTACTCCCTT 57.686 30.769 0.00 0.00 34.35 3.95
181 210 8.764558 AGTTTTTACCAAAATTGTACTCCCTTT 58.235 29.630 0.00 0.00 34.35 3.11
262 295 7.272978 CCTTTCCTTCGTCCAATCTCTTTATA 58.727 38.462 0.00 0.00 0.00 0.98
321 354 4.880696 CCCCATCTCTGATTTTTCTCTCAC 59.119 45.833 0.00 0.00 0.00 3.51
323 356 4.880696 CCATCTCTGATTTTTCTCTCACCC 59.119 45.833 0.00 0.00 0.00 4.61
325 358 4.899502 TCTCTGATTTTTCTCTCACCCAC 58.100 43.478 0.00 0.00 0.00 4.61
458 522 5.490139 AAGACAATATTGCATCCGTCTTG 57.510 39.130 15.48 4.41 41.00 3.02
464 528 7.861630 ACAATATTGCATCCGTCTTGTATTAC 58.138 34.615 15.48 0.00 0.00 1.89
488 552 3.067883 GGACGGGGAGAGTACTTGATAAC 59.932 52.174 0.00 0.00 0.00 1.89
664 771 9.442047 GCCTAATCTACTAGAATGTTTATGCAT 57.558 33.333 3.79 3.79 0.00 3.96
708 817 9.953565 ATTACCTAGTCAAACTAAAATACAGCA 57.046 29.630 0.00 0.00 29.00 4.41
810 942 2.583593 GCCGCGGTAGAGAAGCAG 60.584 66.667 28.70 0.00 0.00 4.24
813 945 0.108804 CCGCGGTAGAGAAGCAGAAA 60.109 55.000 19.50 0.00 0.00 2.52
879 1035 1.408702 CCAACACCCACAGTCCAAAAG 59.591 52.381 0.00 0.00 0.00 2.27
924 1080 2.182030 CTCTCTCGCCCGAACCAC 59.818 66.667 0.00 0.00 0.00 4.16
925 1081 3.685214 CTCTCTCGCCCGAACCACG 62.685 68.421 0.00 0.00 42.18 4.94
998 1154 4.086457 GGAGAAGAGAGAAGAAGGTGAGT 58.914 47.826 0.00 0.00 0.00 3.41
1005 1161 4.163427 AGAGAAGAAGGTGAGTGATGGAA 58.837 43.478 0.00 0.00 0.00 3.53
1007 1163 4.163427 AGAAGAAGGTGAGTGATGGAAGA 58.837 43.478 0.00 0.00 0.00 2.87
1367 1523 4.699522 GTGAACCGCCCGCTCCTT 62.700 66.667 0.00 0.00 0.00 3.36
1427 1585 1.775385 AATTAGGTTGATTGGGCGGG 58.225 50.000 0.00 0.00 0.00 6.13
1432 1590 2.036572 TTGATTGGGCGGGGTTCC 59.963 61.111 0.00 0.00 0.00 3.62
1473 1631 4.158015 CGGTAGGATAGTTGACCCCTATT 58.842 47.826 0.00 0.00 34.21 1.73
1474 1632 4.591924 CGGTAGGATAGTTGACCCCTATTT 59.408 45.833 0.00 0.00 34.21 1.40
1486 1644 1.202651 CCCCTATTTCCGATTGCGAGT 60.203 52.381 0.00 0.00 40.82 4.18
1493 1651 1.145759 TCCGATTGCGAGTCGATTGC 61.146 55.000 18.61 0.00 41.40 3.56
1525 1683 1.402968 CTCAAATTCACGGGATGCTGG 59.597 52.381 0.00 0.00 0.00 4.85
1528 1686 1.033746 AATTCACGGGATGCTGGCAG 61.034 55.000 10.94 10.94 0.00 4.85
1786 1948 7.843490 TTCATTCCGGAGTTTTATACTTCTG 57.157 36.000 3.34 0.00 37.17 3.02
1969 2308 3.334691 TGTAGCACCAGTGAAGCATTAC 58.665 45.455 0.99 4.97 0.00 1.89
1981 2320 8.946085 CCAGTGAAGCATTACAATTTTAGACTA 58.054 33.333 0.00 0.00 0.00 2.59
2000 2339 1.153269 GTCTTAGCAGCAGAGGGGC 60.153 63.158 0.00 0.00 0.00 5.80
2017 2356 5.248020 AGAGGGGCTATCTGTTCTGATTATG 59.752 44.000 0.00 0.00 0.00 1.90
2066 2405 7.446769 TCATCAACAAACTTGCTACCTTACTA 58.553 34.615 0.00 0.00 0.00 1.82
2106 2445 4.096231 TCCATCAATAGGTGACATTTTGCG 59.904 41.667 0.00 0.00 39.72 4.85
2136 2485 8.804204 AGTGATTTACTAGCAACTACAACTAGT 58.196 33.333 7.07 7.07 46.30 2.57
2137 2486 9.420551 GTGATTTACTAGCAACTACAACTAGTT 57.579 33.333 1.12 1.12 43.05 2.24
2147 2496 6.658188 AACTACAACTAGTTGAGAAGCTCT 57.342 37.500 36.14 17.22 41.00 4.09
2148 2497 6.262193 ACTACAACTAGTTGAGAAGCTCTC 57.738 41.667 36.14 6.31 43.65 3.20
2149 2498 4.529109 ACAACTAGTTGAGAAGCTCTCC 57.471 45.455 36.14 0.00 42.73 3.71
2150 2499 3.898123 ACAACTAGTTGAGAAGCTCTCCA 59.102 43.478 36.14 0.00 42.73 3.86
2151 2500 4.530161 ACAACTAGTTGAGAAGCTCTCCAT 59.470 41.667 36.14 11.05 42.73 3.41
2152 2501 5.012561 ACAACTAGTTGAGAAGCTCTCCATT 59.987 40.000 36.14 10.64 42.73 3.16
2153 2502 5.083533 ACTAGTTGAGAAGCTCTCCATTG 57.916 43.478 9.71 2.22 42.73 2.82
2154 2503 2.709213 AGTTGAGAAGCTCTCCATTGC 58.291 47.619 9.71 0.00 42.73 3.56
2155 2504 1.742268 GTTGAGAAGCTCTCCATTGCC 59.258 52.381 9.71 0.00 42.73 4.52
2156 2505 0.986527 TGAGAAGCTCTCCATTGCCA 59.013 50.000 9.71 0.00 42.73 4.92
2157 2506 1.562942 TGAGAAGCTCTCCATTGCCAT 59.437 47.619 9.71 0.00 42.73 4.40
2158 2507 2.773661 TGAGAAGCTCTCCATTGCCATA 59.226 45.455 9.71 0.00 42.73 2.74
2159 2508 3.181457 TGAGAAGCTCTCCATTGCCATAG 60.181 47.826 9.71 0.00 42.73 2.23
2160 2509 3.044156 AGAAGCTCTCCATTGCCATAGA 58.956 45.455 0.00 0.00 0.00 1.98
2161 2510 2.926778 AGCTCTCCATTGCCATAGAC 57.073 50.000 0.00 0.00 0.00 2.59
2162 2511 2.121948 AGCTCTCCATTGCCATAGACA 58.878 47.619 0.00 0.00 0.00 3.41
2163 2512 2.104451 AGCTCTCCATTGCCATAGACAG 59.896 50.000 0.00 0.00 0.00 3.51
2164 2513 2.809665 GCTCTCCATTGCCATAGACAGG 60.810 54.545 0.00 0.00 0.00 4.00
2173 2522 2.918712 CCATAGACAGGCTAACAGGG 57.081 55.000 0.00 0.00 31.66 4.45
2174 2523 1.202698 CCATAGACAGGCTAACAGGGC 60.203 57.143 0.00 0.00 31.66 5.19
2180 2529 3.335711 GGCTAACAGGGCCTCCAT 58.664 61.111 0.95 0.00 45.57 3.41
2181 2530 1.615262 GGCTAACAGGGCCTCCATT 59.385 57.895 0.95 0.55 45.57 3.16
2182 2531 0.466372 GGCTAACAGGGCCTCCATTC 60.466 60.000 0.95 0.00 45.57 2.67
2183 2532 0.255890 GCTAACAGGGCCTCCATTCA 59.744 55.000 0.95 0.00 34.83 2.57
2184 2533 1.340991 GCTAACAGGGCCTCCATTCAA 60.341 52.381 0.95 0.00 34.83 2.69
2185 2534 2.687914 GCTAACAGGGCCTCCATTCAAT 60.688 50.000 0.95 0.00 34.83 2.57
2186 2535 3.435026 GCTAACAGGGCCTCCATTCAATA 60.435 47.826 0.95 0.00 34.83 1.90
2187 2536 3.756082 AACAGGGCCTCCATTCAATAA 57.244 42.857 0.95 0.00 34.83 1.40
2188 2537 3.756082 ACAGGGCCTCCATTCAATAAA 57.244 42.857 0.95 0.00 34.83 1.40
2189 2538 4.270317 ACAGGGCCTCCATTCAATAAAT 57.730 40.909 0.95 0.00 34.83 1.40
2190 2539 3.962718 ACAGGGCCTCCATTCAATAAATG 59.037 43.478 0.95 0.00 43.77 2.32
2210 2559 4.453480 TGGAAACAGAAACAGGGATCTT 57.547 40.909 0.00 0.00 35.01 2.40
2211 2560 4.803452 TGGAAACAGAAACAGGGATCTTT 58.197 39.130 0.00 0.00 35.01 2.52
2212 2561 5.208121 TGGAAACAGAAACAGGGATCTTTT 58.792 37.500 0.00 0.00 35.01 2.27
2213 2562 5.660864 TGGAAACAGAAACAGGGATCTTTTT 59.339 36.000 0.00 0.00 35.01 1.94
2231 2580 4.815040 TTTTTAGCGTCGTCCATTTCAA 57.185 36.364 0.00 0.00 0.00 2.69
2232 2581 5.365403 TTTTTAGCGTCGTCCATTTCAAT 57.635 34.783 0.00 0.00 0.00 2.57
2233 2582 6.483385 TTTTTAGCGTCGTCCATTTCAATA 57.517 33.333 0.00 0.00 0.00 1.90
2234 2583 5.712217 TTTAGCGTCGTCCATTTCAATAG 57.288 39.130 0.00 0.00 0.00 1.73
2235 2584 3.520290 AGCGTCGTCCATTTCAATAGA 57.480 42.857 0.00 0.00 0.00 1.98
2236 2585 3.448686 AGCGTCGTCCATTTCAATAGAG 58.551 45.455 0.00 0.00 0.00 2.43
2237 2586 3.130516 AGCGTCGTCCATTTCAATAGAGA 59.869 43.478 0.00 0.00 0.00 3.10
2238 2587 3.487574 GCGTCGTCCATTTCAATAGAGAG 59.512 47.826 0.00 0.00 0.00 3.20
2239 2588 4.733815 GCGTCGTCCATTTCAATAGAGAGA 60.734 45.833 0.00 0.00 0.00 3.10
2240 2589 5.524284 CGTCGTCCATTTCAATAGAGAGAT 58.476 41.667 0.00 0.00 0.00 2.75
2241 2590 6.669278 CGTCGTCCATTTCAATAGAGAGATA 58.331 40.000 0.00 0.00 0.00 1.98
2242 2591 7.139392 CGTCGTCCATTTCAATAGAGAGATAA 58.861 38.462 0.00 0.00 0.00 1.75
2243 2592 7.648112 CGTCGTCCATTTCAATAGAGAGATAAA 59.352 37.037 0.00 0.00 0.00 1.40
2244 2593 8.973378 GTCGTCCATTTCAATAGAGAGATAAAG 58.027 37.037 0.00 0.00 0.00 1.85
2245 2594 8.914011 TCGTCCATTTCAATAGAGAGATAAAGA 58.086 33.333 0.00 0.00 0.00 2.52
2246 2595 9.534565 CGTCCATTTCAATAGAGAGATAAAGAA 57.465 33.333 0.00 0.00 0.00 2.52
2259 2608 9.403583 AGAGAGATAAAGAACTCTAGAATTCGT 57.596 33.333 8.21 2.44 42.51 3.85
2272 2621 9.666626 ACTCTAGAATTCGTATAAAATCTCACG 57.333 33.333 0.00 0.00 35.78 4.35
2273 2622 9.119329 CTCTAGAATTCGTATAAAATCTCACGG 57.881 37.037 0.00 0.00 35.21 4.94
2274 2623 8.627403 TCTAGAATTCGTATAAAATCTCACGGT 58.373 33.333 0.00 0.00 35.21 4.83
2275 2624 9.245962 CTAGAATTCGTATAAAATCTCACGGTT 57.754 33.333 0.00 0.00 35.21 4.44
2276 2625 7.906160 AGAATTCGTATAAAATCTCACGGTTG 58.094 34.615 0.00 0.00 35.21 3.77
2277 2626 7.762615 AGAATTCGTATAAAATCTCACGGTTGA 59.237 33.333 0.00 0.00 35.21 3.18
2278 2627 8.433421 AATTCGTATAAAATCTCACGGTTGAT 57.567 30.769 0.00 0.00 35.21 2.57
2279 2628 7.837202 TTCGTATAAAATCTCACGGTTGATT 57.163 32.000 0.00 1.64 35.21 2.57
2280 2629 7.229228 TCGTATAAAATCTCACGGTTGATTG 57.771 36.000 6.83 0.00 33.72 2.67
2281 2630 5.901884 CGTATAAAATCTCACGGTTGATTGC 59.098 40.000 6.83 0.00 33.72 3.56
2282 2631 5.895636 ATAAAATCTCACGGTTGATTGCA 57.104 34.783 6.83 0.00 33.72 4.08
2283 2632 4.789012 AAAATCTCACGGTTGATTGCAT 57.211 36.364 6.83 0.00 33.72 3.96
2284 2633 5.895636 AAAATCTCACGGTTGATTGCATA 57.104 34.783 6.83 0.00 33.72 3.14
2285 2634 4.882671 AATCTCACGGTTGATTGCATAC 57.117 40.909 5.63 0.00 32.40 2.39
2286 2635 2.627945 TCTCACGGTTGATTGCATACC 58.372 47.619 0.00 0.00 0.00 2.73
2287 2636 2.027653 TCTCACGGTTGATTGCATACCA 60.028 45.455 0.00 0.00 32.12 3.25
2288 2637 2.746904 CTCACGGTTGATTGCATACCAA 59.253 45.455 0.00 0.00 37.94 3.67
2289 2638 2.486203 TCACGGTTGATTGCATACCAAC 59.514 45.455 14.31 14.31 39.38 3.77
2290 2639 2.487762 CACGGTTGATTGCATACCAACT 59.512 45.455 19.06 5.04 39.84 3.16
2291 2640 3.687212 CACGGTTGATTGCATACCAACTA 59.313 43.478 19.06 0.00 39.84 2.24
2292 2641 4.335315 CACGGTTGATTGCATACCAACTAT 59.665 41.667 19.06 9.82 39.84 2.12
2293 2642 4.335315 ACGGTTGATTGCATACCAACTATG 59.665 41.667 19.06 13.97 39.84 2.23
2294 2643 4.574421 CGGTTGATTGCATACCAACTATGA 59.426 41.667 19.06 0.00 39.84 2.15
2295 2644 5.065859 CGGTTGATTGCATACCAACTATGAA 59.934 40.000 19.06 0.00 39.84 2.57
2296 2645 6.498304 GGTTGATTGCATACCAACTATGAAG 58.502 40.000 19.06 0.00 39.84 3.02
2297 2646 6.095440 GGTTGATTGCATACCAACTATGAAGT 59.905 38.462 19.06 0.00 39.84 3.01
2298 2647 7.282224 GGTTGATTGCATACCAACTATGAAGTA 59.718 37.037 19.06 0.00 39.84 2.24
2299 2648 8.673711 GTTGATTGCATACCAACTATGAAGTAA 58.326 33.333 15.00 0.00 37.69 2.24
2300 2649 8.800370 TGATTGCATACCAACTATGAAGTAAA 57.200 30.769 0.00 0.00 35.06 2.01
2301 2650 9.407380 TGATTGCATACCAACTATGAAGTAAAT 57.593 29.630 0.00 0.00 35.06 1.40
2302 2651 9.669353 GATTGCATACCAACTATGAAGTAAATG 57.331 33.333 0.00 0.00 35.06 2.32
2303 2652 8.800370 TTGCATACCAACTATGAAGTAAATGA 57.200 30.769 0.00 0.00 35.06 2.57
2304 2653 8.437360 TGCATACCAACTATGAAGTAAATGAG 57.563 34.615 0.00 0.00 35.06 2.90
2305 2654 8.046708 TGCATACCAACTATGAAGTAAATGAGT 58.953 33.333 0.00 0.00 35.06 3.41
2306 2655 8.893727 GCATACCAACTATGAAGTAAATGAGTT 58.106 33.333 0.00 0.00 35.06 3.01
2326 2675 8.276252 TGAGTTATCAAAAGGTAATGTAAGGC 57.724 34.615 0.00 0.00 30.61 4.35
2327 2676 7.885922 TGAGTTATCAAAAGGTAATGTAAGGCA 59.114 33.333 0.00 0.00 30.61 4.75
2328 2677 8.281212 AGTTATCAAAAGGTAATGTAAGGCAG 57.719 34.615 0.00 0.00 0.00 4.85
2329 2678 8.107095 AGTTATCAAAAGGTAATGTAAGGCAGA 58.893 33.333 0.00 0.00 0.00 4.26
2330 2679 8.903820 GTTATCAAAAGGTAATGTAAGGCAGAT 58.096 33.333 0.00 0.00 0.00 2.90
2331 2680 6.757897 TCAAAAGGTAATGTAAGGCAGATG 57.242 37.500 0.00 0.00 0.00 2.90
2332 2681 5.125417 TCAAAAGGTAATGTAAGGCAGATGC 59.875 40.000 0.00 0.00 41.14 3.91
2333 2682 3.931907 AGGTAATGTAAGGCAGATGCA 57.068 42.857 7.19 0.00 44.36 3.96
2334 2683 4.443978 AGGTAATGTAAGGCAGATGCAT 57.556 40.909 0.00 0.00 44.36 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.423538 GGATGACGGAAAGGGTGAAATG 59.576 50.000 0.00 0.00 0.00 2.32
2 3 1.422024 TGGATGACGGAAAGGGTGAAA 59.578 47.619 0.00 0.00 0.00 2.69
18 38 5.368989 GGAACGTCCATAAAGAGATTGGAT 58.631 41.667 0.00 0.00 41.37 3.41
154 183 8.999905 AGGGAGTACAATTTTGGTAAAAACTA 57.000 30.769 0.00 0.00 38.07 2.24
212 241 8.749354 GGGTGGAATGAGAACTTTACATATTTT 58.251 33.333 0.00 0.00 0.00 1.82
213 242 8.116026 AGGGTGGAATGAGAACTTTACATATTT 58.884 33.333 0.00 0.00 0.00 1.40
214 243 7.643123 AGGGTGGAATGAGAACTTTACATATT 58.357 34.615 0.00 0.00 0.00 1.28
216 245 6.636454 AGGGTGGAATGAGAACTTTACATA 57.364 37.500 0.00 0.00 0.00 2.29
228 261 1.702957 ACGAAGGAAAGGGTGGAATGA 59.297 47.619 0.00 0.00 0.00 2.57
233 266 0.109723 TTGGACGAAGGAAAGGGTGG 59.890 55.000 0.00 0.00 0.00 4.61
262 295 0.267960 AGGATGGAGGGGGAACGTAT 59.732 55.000 0.00 0.00 0.00 3.06
321 354 5.128008 TGAGTTGGTTTTTAGGAAAAGTGGG 59.872 40.000 0.00 0.00 35.53 4.61
323 356 7.167468 CGATTGAGTTGGTTTTTAGGAAAAGTG 59.833 37.037 0.00 0.00 35.53 3.16
325 358 7.200455 ACGATTGAGTTGGTTTTTAGGAAAAG 58.800 34.615 0.00 0.00 35.53 2.27
376 409 7.865706 AACTTCTTGACTTGCTAGAGAAAAA 57.134 32.000 1.04 0.00 30.21 1.94
383 416 7.259290 TGGTAAAAACTTCTTGACTTGCTAG 57.741 36.000 0.00 0.00 0.00 3.42
385 418 6.524101 TTGGTAAAAACTTCTTGACTTGCT 57.476 33.333 0.00 0.00 0.00 3.91
442 478 6.706055 CGTAATACAAGACGGATGCAATAT 57.294 37.500 0.00 0.00 35.43 1.28
458 522 0.957362 CTCTCCCCGTCCCGTAATAC 59.043 60.000 0.00 0.00 0.00 1.89
464 528 1.379576 AAGTACTCTCCCCGTCCCG 60.380 63.158 0.00 0.00 0.00 5.14
564 628 7.566760 TTTACGCAATCACCATGATTTATCT 57.433 32.000 1.25 0.00 44.03 1.98
565 629 8.531530 GTTTTTACGCAATCACCATGATTTATC 58.468 33.333 1.25 0.00 44.03 1.75
617 693 6.638610 AGGCTATGACTGCACATCTATTATC 58.361 40.000 0.00 0.00 0.00 1.75
619 695 7.539034 TTAGGCTATGACTGCACATCTATTA 57.461 36.000 0.00 0.00 0.00 0.98
664 771 3.834013 TTGTCCGTGCGGCAATGGA 62.834 57.895 18.27 18.27 34.68 3.41
665 772 2.211619 AATTGTCCGTGCGGCAATGG 62.212 55.000 23.15 14.57 39.80 3.16
708 817 5.990408 TGTTTTGTTGCGAAAATGTTTTGT 58.010 29.167 0.00 0.00 0.00 2.83
754 864 9.243637 GCATGTATTTTAAATAATTTGCCGAGA 57.756 29.630 12.67 0.00 0.00 4.04
755 865 9.029243 TGCATGTATTTTAAATAATTTGCCGAG 57.971 29.630 17.29 0.20 0.00 4.63
756 866 8.932945 TGCATGTATTTTAAATAATTTGCCGA 57.067 26.923 17.29 5.33 0.00 5.54
810 942 1.433534 CTGCGACTGGGAGTTCTTTC 58.566 55.000 0.00 0.00 0.00 2.62
813 945 2.948720 GCCTGCGACTGGGAGTTCT 61.949 63.158 0.00 0.00 30.99 3.01
975 1131 3.085533 TCACCTTCTTCTCTCTTCTCCG 58.914 50.000 0.00 0.00 0.00 4.63
976 1132 4.082245 CACTCACCTTCTTCTCTCTTCTCC 60.082 50.000 0.00 0.00 0.00 3.71
977 1133 4.764823 TCACTCACCTTCTTCTCTCTTCTC 59.235 45.833 0.00 0.00 0.00 2.87
978 1134 4.735369 TCACTCACCTTCTTCTCTCTTCT 58.265 43.478 0.00 0.00 0.00 2.85
979 1135 5.410067 CATCACTCACCTTCTTCTCTCTTC 58.590 45.833 0.00 0.00 0.00 2.87
998 1154 4.161295 CCGCCGCCTCTTCCATCA 62.161 66.667 0.00 0.00 0.00 3.07
1367 1523 5.186942 TCGAACGGAAAATAAATGATGGGA 58.813 37.500 0.00 0.00 0.00 4.37
1427 1585 1.761198 ACCCTAGCTATTCACGGAACC 59.239 52.381 0.00 0.00 0.00 3.62
1432 1590 1.593006 CGCAAACCCTAGCTATTCACG 59.407 52.381 0.00 0.00 0.00 4.35
1473 1631 1.277326 CAATCGACTCGCAATCGGAA 58.723 50.000 0.00 0.00 40.05 4.30
1474 1632 1.145759 GCAATCGACTCGCAATCGGA 61.146 55.000 0.00 0.00 40.05 4.55
1525 1683 5.065474 ACAGATCTAGACTCTAAACGTCTGC 59.935 44.000 12.09 0.00 41.52 4.26
1528 1686 7.909641 GGTTTACAGATCTAGACTCTAAACGTC 59.090 40.741 16.93 3.19 33.12 4.34
1784 1946 9.467258 AAATATTCACATTTGACAACTCAACAG 57.533 29.630 0.00 0.00 36.06 3.16
1785 1947 9.814899 AAAATATTCACATTTGACAACTCAACA 57.185 25.926 0.00 0.00 36.06 3.33
1947 2274 2.566833 ATGCTTCACTGGTGCTACAA 57.433 45.000 0.00 0.00 0.00 2.41
1948 2275 2.566833 AATGCTTCACTGGTGCTACA 57.433 45.000 0.00 0.00 0.00 2.74
1951 2290 2.566833 TGTAATGCTTCACTGGTGCT 57.433 45.000 0.00 0.00 0.00 4.40
1955 2294 7.820648 AGTCTAAAATTGTAATGCTTCACTGG 58.179 34.615 0.00 0.00 0.00 4.00
1969 2308 7.761704 TCTGCTGCTAAGACTAGTCTAAAATTG 59.238 37.037 25.42 11.83 39.39 2.32
1981 2320 1.621672 GCCCCTCTGCTGCTAAGACT 61.622 60.000 0.00 0.00 0.00 3.24
2017 2356 9.301153 TGAAGCTTTTCTTTTCTAATTCAACAC 57.699 29.630 0.00 0.00 34.56 3.32
2045 2384 7.602644 TGAGATAGTAAGGTAGCAAGTTTGTTG 59.397 37.037 0.00 0.00 0.00 3.33
2046 2385 7.676947 TGAGATAGTAAGGTAGCAAGTTTGTT 58.323 34.615 0.00 0.00 0.00 2.83
2066 2405 3.448093 TGGAGACACAGAGACTGAGAT 57.552 47.619 5.76 0.00 35.18 2.75
2106 2445 8.654215 GTTGTAGTTGCTAGTAAATCACTAACC 58.346 37.037 0.00 0.00 39.28 2.85
2135 2484 1.742268 GGCAATGGAGAGCTTCTCAAC 59.258 52.381 13.06 1.03 45.12 3.18
2136 2485 1.352017 TGGCAATGGAGAGCTTCTCAA 59.648 47.619 13.06 4.61 45.12 3.02
2137 2486 0.986527 TGGCAATGGAGAGCTTCTCA 59.013 50.000 13.06 1.84 45.12 3.27
2138 2487 2.345124 ATGGCAATGGAGAGCTTCTC 57.655 50.000 0.00 0.00 42.66 2.87
2139 2488 3.044156 TCTATGGCAATGGAGAGCTTCT 58.956 45.455 0.00 0.00 0.00 2.85
2140 2489 3.137533 GTCTATGGCAATGGAGAGCTTC 58.862 50.000 0.00 0.00 0.00 3.86
2141 2490 2.507058 TGTCTATGGCAATGGAGAGCTT 59.493 45.455 0.00 0.00 0.00 3.74
2142 2491 2.104451 CTGTCTATGGCAATGGAGAGCT 59.896 50.000 0.00 0.00 29.73 4.09
2143 2492 2.492012 CTGTCTATGGCAATGGAGAGC 58.508 52.381 0.00 0.00 29.73 4.09
2144 2493 3.123157 CCTGTCTATGGCAATGGAGAG 57.877 52.381 4.72 4.72 35.25 3.20
2154 2503 1.202698 GCCCTGTTAGCCTGTCTATGG 60.203 57.143 0.00 0.00 0.00 2.74
2155 2504 2.246719 GCCCTGTTAGCCTGTCTATG 57.753 55.000 0.00 0.00 0.00 2.23
2164 2513 0.255890 TGAATGGAGGCCCTGTTAGC 59.744 55.000 0.00 0.00 0.00 3.09
2165 2514 2.806945 TTGAATGGAGGCCCTGTTAG 57.193 50.000 0.00 0.00 0.00 2.34
2166 2515 4.871871 TTATTGAATGGAGGCCCTGTTA 57.128 40.909 0.00 0.00 0.00 2.41
2167 2516 3.756082 TTATTGAATGGAGGCCCTGTT 57.244 42.857 0.00 0.00 0.00 3.16
2168 2517 3.756082 TTTATTGAATGGAGGCCCTGT 57.244 42.857 0.00 0.00 0.00 4.00
2169 2518 4.595762 CATTTATTGAATGGAGGCCCTG 57.404 45.455 0.00 0.00 41.19 4.45
2178 2527 8.928733 CCTGTTTCTGTTTCCATTTATTGAATG 58.071 33.333 0.00 0.00 43.89 2.67
2179 2528 8.096414 CCCTGTTTCTGTTTCCATTTATTGAAT 58.904 33.333 0.00 0.00 0.00 2.57
2180 2529 7.288852 TCCCTGTTTCTGTTTCCATTTATTGAA 59.711 33.333 0.00 0.00 0.00 2.69
2181 2530 6.780031 TCCCTGTTTCTGTTTCCATTTATTGA 59.220 34.615 0.00 0.00 0.00 2.57
2182 2531 6.991938 TCCCTGTTTCTGTTTCCATTTATTG 58.008 36.000 0.00 0.00 0.00 1.90
2183 2532 7.675619 AGATCCCTGTTTCTGTTTCCATTTATT 59.324 33.333 0.00 0.00 0.00 1.40
2184 2533 7.184862 AGATCCCTGTTTCTGTTTCCATTTAT 58.815 34.615 0.00 0.00 0.00 1.40
2185 2534 6.552008 AGATCCCTGTTTCTGTTTCCATTTA 58.448 36.000 0.00 0.00 0.00 1.40
2186 2535 5.397360 AGATCCCTGTTTCTGTTTCCATTT 58.603 37.500 0.00 0.00 0.00 2.32
2187 2536 5.003096 AGATCCCTGTTTCTGTTTCCATT 57.997 39.130 0.00 0.00 0.00 3.16
2188 2537 4.664688 AGATCCCTGTTTCTGTTTCCAT 57.335 40.909 0.00 0.00 0.00 3.41
2189 2538 4.453480 AAGATCCCTGTTTCTGTTTCCA 57.547 40.909 0.00 0.00 0.00 3.53
2190 2539 5.791336 AAAAGATCCCTGTTTCTGTTTCC 57.209 39.130 0.00 0.00 0.00 3.13
2210 2559 4.815040 TTGAAATGGACGACGCTAAAAA 57.185 36.364 0.00 0.00 0.00 1.94
2211 2560 5.870433 TCTATTGAAATGGACGACGCTAAAA 59.130 36.000 0.00 0.00 0.00 1.52
2212 2561 5.412640 TCTATTGAAATGGACGACGCTAAA 58.587 37.500 0.00 0.00 0.00 1.85
2213 2562 5.001237 TCTATTGAAATGGACGACGCTAA 57.999 39.130 0.00 0.00 0.00 3.09
2214 2563 4.337274 TCTCTATTGAAATGGACGACGCTA 59.663 41.667 0.00 0.00 0.00 4.26
2215 2564 3.130516 TCTCTATTGAAATGGACGACGCT 59.869 43.478 0.00 0.00 0.00 5.07
2216 2565 3.444916 TCTCTATTGAAATGGACGACGC 58.555 45.455 0.00 0.00 0.00 5.19
2217 2566 4.921547 TCTCTCTATTGAAATGGACGACG 58.078 43.478 0.00 0.00 0.00 5.12
2218 2567 8.873215 TTTATCTCTCTATTGAAATGGACGAC 57.127 34.615 0.00 0.00 0.00 4.34
2219 2568 8.914011 TCTTTATCTCTCTATTGAAATGGACGA 58.086 33.333 0.00 0.00 0.00 4.20
2220 2569 9.534565 TTCTTTATCTCTCTATTGAAATGGACG 57.465 33.333 0.00 0.00 0.00 4.79
2233 2582 9.403583 ACGAATTCTAGAGTTCTTTATCTCTCT 57.596 33.333 21.49 0.00 40.78 3.10
2246 2595 9.666626 CGTGAGATTTTATACGAATTCTAGAGT 57.333 33.333 3.52 0.00 38.72 3.24
2247 2596 9.119329 CCGTGAGATTTTATACGAATTCTAGAG 57.881 37.037 3.52 0.00 38.72 2.43
2248 2597 8.627403 ACCGTGAGATTTTATACGAATTCTAGA 58.373 33.333 3.52 0.00 38.72 2.43
2249 2598 8.798748 ACCGTGAGATTTTATACGAATTCTAG 57.201 34.615 3.52 0.00 38.72 2.43
2250 2599 9.027129 CAACCGTGAGATTTTATACGAATTCTA 57.973 33.333 3.52 0.00 38.72 2.10
2251 2600 7.762615 TCAACCGTGAGATTTTATACGAATTCT 59.237 33.333 3.52 0.00 38.72 2.40
2252 2601 7.902032 TCAACCGTGAGATTTTATACGAATTC 58.098 34.615 0.00 0.00 38.72 2.17
2253 2602 7.837202 TCAACCGTGAGATTTTATACGAATT 57.163 32.000 0.00 0.00 38.72 2.17
2254 2603 8.335356 CAATCAACCGTGAGATTTTATACGAAT 58.665 33.333 0.00 0.00 37.14 3.34
2255 2604 7.675403 GCAATCAACCGTGAGATTTTATACGAA 60.675 37.037 0.00 0.00 37.14 3.85
2256 2605 6.237996 GCAATCAACCGTGAGATTTTATACGA 60.238 38.462 0.00 0.00 37.14 3.43
2257 2606 5.901884 GCAATCAACCGTGAGATTTTATACG 59.098 40.000 0.00 0.00 37.14 3.06
2258 2607 6.781138 TGCAATCAACCGTGAGATTTTATAC 58.219 36.000 0.00 0.00 37.14 1.47
2259 2608 6.993786 TGCAATCAACCGTGAGATTTTATA 57.006 33.333 0.00 0.00 37.14 0.98
2260 2609 5.895636 TGCAATCAACCGTGAGATTTTAT 57.104 34.783 0.00 0.00 37.14 1.40
2261 2610 5.895636 ATGCAATCAACCGTGAGATTTTA 57.104 34.783 0.00 0.00 37.14 1.52
2262 2611 4.789012 ATGCAATCAACCGTGAGATTTT 57.211 36.364 0.00 0.00 37.14 1.82
2263 2612 4.096382 GGTATGCAATCAACCGTGAGATTT 59.904 41.667 0.00 0.00 37.14 2.17
2264 2613 3.627577 GGTATGCAATCAACCGTGAGATT 59.372 43.478 0.00 0.00 37.14 2.40
2265 2614 3.206150 GGTATGCAATCAACCGTGAGAT 58.794 45.455 0.00 0.00 37.14 2.75
2266 2615 2.027653 TGGTATGCAATCAACCGTGAGA 60.028 45.455 0.00 0.00 37.14 3.27
2267 2616 2.355197 TGGTATGCAATCAACCGTGAG 58.645 47.619 0.00 0.00 37.14 3.51
2268 2617 2.481289 TGGTATGCAATCAACCGTGA 57.519 45.000 0.00 0.00 38.41 4.35
2269 2618 2.487762 AGTTGGTATGCAATCAACCGTG 59.512 45.455 19.56 0.00 40.96 4.94
2270 2619 2.790433 AGTTGGTATGCAATCAACCGT 58.210 42.857 19.56 6.42 40.96 4.83
2271 2620 4.574421 TCATAGTTGGTATGCAATCAACCG 59.426 41.667 19.56 12.42 40.96 4.44
2272 2621 6.095440 ACTTCATAGTTGGTATGCAATCAACC 59.905 38.462 19.56 12.85 40.96 3.77
2273 2622 7.088589 ACTTCATAGTTGGTATGCAATCAAC 57.911 36.000 17.07 17.07 38.82 3.18
2274 2623 8.800370 TTACTTCATAGTTGGTATGCAATCAA 57.200 30.769 0.00 0.00 38.82 2.57
2275 2624 8.800370 TTTACTTCATAGTTGGTATGCAATCA 57.200 30.769 0.00 0.00 38.82 2.57
2276 2625 9.669353 CATTTACTTCATAGTTGGTATGCAATC 57.331 33.333 0.00 0.00 38.82 2.67
2277 2626 9.407380 TCATTTACTTCATAGTTGGTATGCAAT 57.593 29.630 0.00 0.00 38.82 3.56
2278 2627 8.800370 TCATTTACTTCATAGTTGGTATGCAA 57.200 30.769 0.00 0.00 38.82 4.08
2279 2628 8.046708 ACTCATTTACTTCATAGTTGGTATGCA 58.953 33.333 0.00 0.00 38.82 3.96
2280 2629 8.438676 ACTCATTTACTTCATAGTTGGTATGC 57.561 34.615 0.00 0.00 38.82 3.14
2300 2649 8.903820 GCCTTACATTACCTTTTGATAACTCAT 58.096 33.333 0.00 0.00 0.00 2.90
2301 2650 7.885922 TGCCTTACATTACCTTTTGATAACTCA 59.114 33.333 0.00 0.00 0.00 3.41
2302 2651 8.276252 TGCCTTACATTACCTTTTGATAACTC 57.724 34.615 0.00 0.00 0.00 3.01
2303 2652 8.107095 TCTGCCTTACATTACCTTTTGATAACT 58.893 33.333 0.00 0.00 0.00 2.24
2304 2653 8.276252 TCTGCCTTACATTACCTTTTGATAAC 57.724 34.615 0.00 0.00 0.00 1.89
2305 2654 8.902806 CATCTGCCTTACATTACCTTTTGATAA 58.097 33.333 0.00 0.00 0.00 1.75
2306 2655 7.013274 GCATCTGCCTTACATTACCTTTTGATA 59.987 37.037 0.00 0.00 34.31 2.15
2307 2656 6.183360 GCATCTGCCTTACATTACCTTTTGAT 60.183 38.462 0.00 0.00 34.31 2.57
2308 2657 5.125417 GCATCTGCCTTACATTACCTTTTGA 59.875 40.000 0.00 0.00 34.31 2.69
2309 2658 5.105797 TGCATCTGCCTTACATTACCTTTTG 60.106 40.000 0.00 0.00 41.18 2.44
2310 2659 5.016173 TGCATCTGCCTTACATTACCTTTT 58.984 37.500 0.00 0.00 41.18 2.27
2311 2660 4.599041 TGCATCTGCCTTACATTACCTTT 58.401 39.130 0.00 0.00 41.18 3.11
2312 2661 4.235079 TGCATCTGCCTTACATTACCTT 57.765 40.909 0.00 0.00 41.18 3.50
2313 2662 3.931907 TGCATCTGCCTTACATTACCT 57.068 42.857 0.00 0.00 41.18 3.08


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

AutoCloner maintained by Alex Coulton.