Multiple sequence alignment - TraesCS1D01G117900

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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 TraesCS1D01G117900 chr1D 100.000 2989 0 0 1 2989 114019400 114022388 0.000000e+00 5520.0
1 TraesCS1D01G117900 chr1D 94.357 319 13 1 2419 2737 114046628 114046941 4.480000e-133 484.0
2 TraesCS1D01G117900 chr1B 94.966 1907 71 10 2 1892 174645732 174643835 0.000000e+00 2966.0
3 TraesCS1D01G117900 chr1B 95.960 198 4 2 1899 2096 174643736 174643543 4.810000e-83 318.0
4 TraesCS1D01G117900 chr1B 96.503 143 5 0 2203 2345 174642526 174642384 1.380000e-58 237.0
5 TraesCS1D01G117900 chr1B 92.174 115 6 3 2095 2206 174643461 174643347 3.080000e-35 159.0
6 TraesCS1D01G117900 chr1B 90.698 43 4 0 426 468 47154270 47154228 1.160000e-04 58.4
7 TraesCS1D01G117900 chr1A 87.576 1489 48 31 614 2030 124010612 124012035 0.000000e+00 1598.0
8 TraesCS1D01G117900 chr1A 90.283 566 46 7 54 616 124009663 124010222 0.000000e+00 732.0
9 TraesCS1D01G117900 chr1A 92.157 306 11 2 2042 2347 124016957 124017249 1.280000e-113 420.0
10 TraesCS1D01G117900 chr4B 89.971 1027 46 31 910 1899 496241917 496242923 0.000000e+00 1273.0
11 TraesCS1D01G117900 chr4B 90.448 335 14 6 1903 2224 496242960 496243289 2.750000e-115 425.0
12 TraesCS1D01G117900 chr4B 92.308 65 5 0 2233 2297 496246030 496246094 3.170000e-15 93.5
13 TraesCS1D01G117900 chr7B 87.979 574 60 6 2419 2989 481628118 481627551 0.000000e+00 669.0
14 TraesCS1D01G117900 chr7B 100.000 33 0 0 430 462 732628949 732628917 8.950000e-06 62.1
15 TraesCS1D01G117900 chr7D 82.087 575 91 8 2419 2989 21253669 21253103 5.790000e-132 481.0
16 TraesCS1D01G117900 chr7A 83.592 451 60 8 2540 2989 668000240 667999803 7.710000e-111 411.0
17 TraesCS1D01G117900 chr7A 70.953 451 123 8 211 657 520911088 520911534 1.900000e-17 100.0
18 TraesCS1D01G117900 chr7A 100.000 41 0 0 2109 2149 528226434 528226394 3.190000e-10 76.8
19 TraesCS1D01G117900 chr7A 100.000 41 0 0 2109 2149 576477046 576477086 3.190000e-10 76.8
20 TraesCS1D01G117900 chr6B 91.506 259 12 8 1222 1476 663678647 663678899 6.130000e-92 348.0
21 TraesCS1D01G117900 chr6B 81.579 418 39 16 777 1169 663678236 663678640 8.050000e-81 311.0
22 TraesCS1D01G117900 chr6B 87.037 270 17 5 2095 2347 663679434 663679702 3.770000e-74 289.0
23 TraesCS1D01G117900 chr6B 92.000 200 8 5 1901 2096 663679070 663679265 1.060000e-69 274.0
24 TraesCS1D01G117900 chr6B 82.060 301 41 8 2624 2923 29329136 29329424 8.280000e-61 244.0
25 TraesCS1D01G117900 chr6B 97.059 34 1 0 426 459 69544578 69544611 1.160000e-04 58.4
26 TraesCS1D01G117900 chr4A 75.542 507 88 29 2427 2923 631942247 631942727 1.800000e-52 217.0
27 TraesCS1D01G117900 chr6A 100.000 41 0 0 2109 2149 549488516 549488476 3.190000e-10 76.8
28 TraesCS1D01G117900 chr6A 96.970 33 1 0 430 462 77977515 77977483 4.160000e-04 56.5
29 TraesCS1D01G117900 chr3B 84.416 77 12 0 211 287 668078474 668078398 3.190000e-10 76.8
30 TraesCS1D01G117900 chr3B 100.000 41 0 0 2109 2149 712414713 712414673 3.190000e-10 76.8
31 TraesCS1D01G117900 chr3B 100.000 30 0 0 430 459 670307025 670307054 4.160000e-04 56.5
32 TraesCS1D01G117900 chr2B 100.000 41 0 0 2109 2149 98484056 98484016 3.190000e-10 76.8
33 TraesCS1D01G117900 chr2A 84.416 77 12 0 211 287 618995193 618995117 3.190000e-10 76.8


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 TraesCS1D01G117900 chr1D 114019400 114022388 2988 False 5520.000000 5520 100.00000 1 2989 1 chr1D.!!$F1 2988
1 TraesCS1D01G117900 chr1B 174642384 174645732 3348 True 920.000000 2966 94.90075 2 2345 4 chr1B.!!$R2 2343
2 TraesCS1D01G117900 chr1A 124009663 124012035 2372 False 1165.000000 1598 88.92950 54 2030 2 chr1A.!!$F2 1976
3 TraesCS1D01G117900 chr4B 496241917 496246094 4177 False 597.166667 1273 90.90900 910 2297 3 chr4B.!!$F1 1387
4 TraesCS1D01G117900 chr7B 481627551 481628118 567 True 669.000000 669 87.97900 2419 2989 1 chr7B.!!$R1 570
5 TraesCS1D01G117900 chr7D 21253103 21253669 566 True 481.000000 481 82.08700 2419 2989 1 chr7D.!!$R1 570
6 TraesCS1D01G117900 chr6B 663678236 663679702 1466 False 305.500000 348 88.03050 777 2347 4 chr6B.!!$F3 1570

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
993 1426 0.538516 CCATCGTTCCCACCCACAAA 60.539 55.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2663 7102 0.107165 GGCGGCCCAAGAGAAGTAAT 60.107 55.0 8.12 0.0 0.0 1.89 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
35 36 3.286751 GCTTGTGCGCCCACTTCA 61.287 61.111 4.18 0.00 42.54 3.02
36 37 2.629656 GCTTGTGCGCCCACTTCAT 61.630 57.895 4.18 0.00 42.54 2.57
98 100 2.358247 GTTGACCACGTCGGCCAT 60.358 61.111 2.24 0.00 39.03 4.40
121 123 1.276705 GGAGGTTCTTCTGACTGGACC 59.723 57.143 0.35 0.35 0.00 4.46
184 187 2.713967 CCCCAAGCGATGCCCAAAG 61.714 63.158 0.00 0.00 0.00 2.77
200 204 2.488153 CCAAAGGAGACCCGTGAATTTC 59.512 50.000 0.00 0.00 37.58 2.17
243 247 3.147553 AGAAGAGCTGAAAAACCCTCC 57.852 47.619 0.00 0.00 0.00 4.30
272 276 7.724506 ACAGAAGAGGAATAGATACGGTGATAA 59.275 37.037 0.00 0.00 0.00 1.75
314 318 2.202932 CGATGGGAGGAAGCCGTG 60.203 66.667 0.00 0.00 0.00 4.94
378 382 1.315690 CACATCTCATGACCATGGCC 58.684 55.000 13.04 0.00 39.24 5.36
401 405 4.673580 CGTTCATGCCTGAGAAAATCCAAG 60.674 45.833 0.00 0.00 31.68 3.61
449 453 1.200483 CACTCCACACGATCGTATGC 58.800 55.000 20.84 0.00 0.00 3.14
537 541 1.749063 CACTCATACGCCACTAGGACA 59.251 52.381 0.00 0.00 36.89 4.02
627 1024 2.083167 TTAACCGGTTAGCAAGGACG 57.917 50.000 25.25 0.00 0.00 4.79
642 1045 1.022451 GGACGTTGGCCGCAATCTTA 61.022 55.000 0.00 0.00 41.42 2.10
661 1064 9.445878 CAATCTTATATAGGACATTGCACAGAT 57.554 33.333 0.00 0.00 0.00 2.90
735 1138 5.066764 GCCCAAAATTTAAGCACGTCCTATA 59.933 40.000 0.00 0.00 0.00 1.31
736 1139 6.238925 GCCCAAAATTTAAGCACGTCCTATAT 60.239 38.462 0.00 0.00 0.00 0.86
737 1140 7.040961 GCCCAAAATTTAAGCACGTCCTATATA 60.041 37.037 0.00 0.00 0.00 0.86
738 1141 9.010029 CCCAAAATTTAAGCACGTCCTATATAT 57.990 33.333 0.00 0.00 0.00 0.86
853 1256 1.184431 TGGGGACGCGTGAGTATTTA 58.816 50.000 20.70 0.00 0.00 1.40
993 1426 0.538516 CCATCGTTCCCACCCACAAA 60.539 55.000 0.00 0.00 0.00 2.83
1017 1450 1.344087 ACCCGGTCCACTATCCAGATT 60.344 52.381 0.00 0.00 0.00 2.40
1104 1564 1.000506 GCACCAAGAACCGTCTCTGTA 59.999 52.381 0.00 0.00 30.70 2.74
1149 1610 1.711206 GAGAACCGCGCTCTAGTTTT 58.289 50.000 5.56 0.00 0.00 2.43
1360 1840 1.228894 TGGAGGACTTCTCACCGCT 60.229 57.895 0.00 0.00 44.19 5.52
1532 2066 2.170607 AGCGGCACTCAATATTGGTACT 59.829 45.455 15.36 5.75 0.00 2.73
1534 2068 3.377172 GCGGCACTCAATATTGGTACTTT 59.623 43.478 15.36 0.00 0.00 2.66
1535 2069 4.573201 GCGGCACTCAATATTGGTACTTTA 59.427 41.667 15.36 0.00 0.00 1.85
1852 2395 4.572389 GCTTCAAGAATCGAGCAAATCCTA 59.428 41.667 0.00 0.00 35.29 2.94
1856 2399 2.101582 AGAATCGAGCAAATCCTACGCT 59.898 45.455 0.00 0.00 39.12 5.07
1859 2402 2.268298 TCGAGCAAATCCTACGCTTTC 58.732 47.619 0.00 0.00 35.75 2.62
1921 2594 4.006319 AGTAGTAAGTAGTGGTGTCCGTC 58.994 47.826 0.00 0.00 0.00 4.79
2045 2726 4.072131 AGTGCGTTGGACAAGAATGTATT 58.928 39.130 0.00 0.00 40.74 1.89
2192 3053 3.119280 TGATTGATTGCTGCCATGTTCTG 60.119 43.478 0.00 0.00 0.00 3.02
2210 3904 4.842531 TCTGCATGGGAGTTTAGAATCA 57.157 40.909 0.00 0.00 0.00 2.57
2215 3909 4.455606 CATGGGAGTTTAGAATCAGGGTC 58.544 47.826 0.00 0.00 0.00 4.46
2278 6704 8.918202 TGGATTGGTTTATGATAAGTATGGTC 57.082 34.615 0.00 0.00 0.00 4.02
2353 6790 2.674033 GCCATGGCAGCAGTGTCA 60.674 61.111 32.08 0.00 44.18 3.58
2354 6791 2.270257 GCCATGGCAGCAGTGTCAA 61.270 57.895 32.08 0.00 43.00 3.18
2355 6792 1.808531 GCCATGGCAGCAGTGTCAAA 61.809 55.000 32.08 0.00 43.00 2.69
2356 6793 0.675083 CCATGGCAGCAGTGTCAAAA 59.325 50.000 0.00 0.00 43.00 2.44
2357 6794 1.068895 CCATGGCAGCAGTGTCAAAAA 59.931 47.619 0.00 0.00 43.00 1.94
2379 6816 3.788937 ACGTCTTAACATTATGGGACGG 58.211 45.455 23.35 13.20 46.80 4.79
2380 6817 3.128349 CGTCTTAACATTATGGGACGGG 58.872 50.000 17.16 0.00 41.50 5.28
2381 6818 3.473625 GTCTTAACATTATGGGACGGGG 58.526 50.000 0.00 0.00 0.00 5.73
2382 6819 2.440253 TCTTAACATTATGGGACGGGGG 59.560 50.000 0.00 0.00 0.00 5.40
2383 6820 2.193566 TAACATTATGGGACGGGGGA 57.806 50.000 0.00 0.00 0.00 4.81
2384 6821 0.843984 AACATTATGGGACGGGGGAG 59.156 55.000 0.00 0.00 0.00 4.30
2385 6822 0.327191 ACATTATGGGACGGGGGAGT 60.327 55.000 0.00 0.00 0.00 3.85
2386 6823 1.061967 ACATTATGGGACGGGGGAGTA 60.062 52.381 0.00 0.00 0.00 2.59
2387 6824 1.623811 CATTATGGGACGGGGGAGTAG 59.376 57.143 0.00 0.00 0.00 2.57
2388 6825 0.638292 TTATGGGACGGGGGAGTAGT 59.362 55.000 0.00 0.00 0.00 2.73
2389 6826 0.638292 TATGGGACGGGGGAGTAGTT 59.362 55.000 0.00 0.00 0.00 2.24
2390 6827 0.253020 ATGGGACGGGGGAGTAGTTT 60.253 55.000 0.00 0.00 0.00 2.66
2391 6828 1.196104 TGGGACGGGGGAGTAGTTTG 61.196 60.000 0.00 0.00 0.00 2.93
2392 6829 1.078637 GGACGGGGGAGTAGTTTGC 60.079 63.158 0.00 0.00 0.00 3.68
2393 6830 1.551019 GGACGGGGGAGTAGTTTGCT 61.551 60.000 0.00 0.00 0.00 3.91
2394 6831 0.391263 GACGGGGGAGTAGTTTGCTG 60.391 60.000 0.00 0.00 0.00 4.41
2395 6832 1.745489 CGGGGGAGTAGTTTGCTGC 60.745 63.158 0.00 0.00 0.00 5.25
2396 6833 1.378646 GGGGGAGTAGTTTGCTGCC 60.379 63.158 0.00 0.00 42.73 4.85
2397 6834 1.378762 GGGGAGTAGTTTGCTGCCA 59.621 57.895 6.99 0.00 44.86 4.92
2398 6835 0.960861 GGGGAGTAGTTTGCTGCCAC 60.961 60.000 6.99 0.00 44.86 5.01
2399 6836 1.298859 GGGAGTAGTTTGCTGCCACG 61.299 60.000 0.00 0.00 42.94 4.94
2400 6837 0.602905 GGAGTAGTTTGCTGCCACGT 60.603 55.000 0.00 0.00 0.00 4.49
2401 6838 0.790814 GAGTAGTTTGCTGCCACGTC 59.209 55.000 0.00 0.00 0.00 4.34
2402 6839 0.393077 AGTAGTTTGCTGCCACGTCT 59.607 50.000 0.00 0.00 0.00 4.18
2403 6840 0.790814 GTAGTTTGCTGCCACGTCTC 59.209 55.000 0.00 0.00 0.00 3.36
2404 6841 0.666274 TAGTTTGCTGCCACGTCTCG 60.666 55.000 0.00 0.00 0.00 4.04
2405 6842 3.345808 TTTGCTGCCACGTCTCGC 61.346 61.111 0.00 0.00 0.00 5.03
2406 6843 4.600576 TTGCTGCCACGTCTCGCA 62.601 61.111 0.00 1.91 0.00 5.10
2448 6885 4.253685 CCCTCTTACTCGATTCAAGCAAA 58.746 43.478 0.00 0.00 0.00 3.68
2471 6908 0.249911 GGCGAATTACAGGCGGATCT 60.250 55.000 0.00 0.00 0.00 2.75
2472 6909 1.583054 GCGAATTACAGGCGGATCTT 58.417 50.000 0.00 0.00 0.00 2.40
2484 6921 1.679032 GCGGATCTTGCTAGGGTTTGT 60.679 52.381 0.00 0.00 0.00 2.83
2499 6937 0.777446 TTTGTGAGGGAGAAAGGGGG 59.223 55.000 0.00 0.00 0.00 5.40
2516 6954 1.309006 GGTCGGGAGGTAGGAGGAA 59.691 63.158 0.00 0.00 0.00 3.36
2517 6955 0.756070 GGTCGGGAGGTAGGAGGAAG 60.756 65.000 0.00 0.00 0.00 3.46
2518 6956 0.756070 GTCGGGAGGTAGGAGGAAGG 60.756 65.000 0.00 0.00 0.00 3.46
2519 6957 1.457831 CGGGAGGTAGGAGGAAGGG 60.458 68.421 0.00 0.00 0.00 3.95
2551 6990 1.064825 GGAAACAGAGGAAGGGGACA 58.935 55.000 0.00 0.00 0.00 4.02
2554 6993 1.068121 AACAGAGGAAGGGGACAAGG 58.932 55.000 0.00 0.00 0.00 3.61
2560 6999 0.840722 GGAAGGGGACAAGGAGTGGA 60.841 60.000 0.00 0.00 0.00 4.02
2573 7012 7.202047 GGACAAGGAGTGGATTCAGTCTATTAT 60.202 40.741 8.77 0.00 41.76 1.28
2586 7025 9.939802 ATTCAGTCTATTATAATTTCGTACCCC 57.060 33.333 2.68 0.00 0.00 4.95
2587 7026 7.596494 TCAGTCTATTATAATTTCGTACCCCG 58.404 38.462 2.68 0.00 38.13 5.73
2614 7053 0.322322 CCACCGTGGGCTACTTAACA 59.678 55.000 9.99 0.00 32.67 2.41
2636 7075 1.296715 CGCTTACAGCTCCCAGGTT 59.703 57.895 0.00 0.00 39.60 3.50
2648 7087 3.642938 CCAGGTTGATGGGTCGAAA 57.357 52.632 0.00 0.00 36.64 3.46
2707 7146 3.386237 GCTCGTGGGCTCTGGACT 61.386 66.667 0.00 0.00 0.00 3.85
2711 7150 2.985456 GTGGGCTCTGGACTGGAG 59.015 66.667 0.00 0.00 0.00 3.86
2721 7160 2.431683 GACTGGAGGCTGGTGCAA 59.568 61.111 0.00 0.00 41.91 4.08
2815 7255 0.827368 GCTCGAAGAAGTCCTCCCAT 59.173 55.000 0.00 0.00 34.09 4.00
2820 7260 0.905357 AAGAAGTCCTCCCATGACGG 59.095 55.000 0.00 0.00 37.80 4.79
2850 7290 2.658707 GCTGCGACGACCACTTGAC 61.659 63.158 0.00 0.00 0.00 3.18
2859 7299 1.230324 GACCACTTGACCAGCACTTC 58.770 55.000 0.00 0.00 0.00 3.01
2876 7316 4.256920 CACTTCAGGGATCTTCGATTTGT 58.743 43.478 0.00 0.00 0.00 2.83
2973 7413 3.729356 CTGATACTGTGTCAGCGCT 57.271 52.632 19.37 2.64 36.95 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 0.987294 CTCCAACTCCAGGACACCAT 59.013 55.000 0.00 0.00 0.00 3.55
36 37 0.399949 ACTCCAACTCCAGGACACCA 60.400 55.000 0.00 0.00 0.00 4.17
98 100 2.158310 TCCAGTCAGAAGAACCTCCAGA 60.158 50.000 0.00 0.00 0.00 3.86
130 133 1.646189 GAGGCGTTGATCAAGAGGAC 58.354 55.000 8.80 3.53 0.00 3.85
143 146 3.374402 CAGACGAGGTGGAGGCGT 61.374 66.667 0.00 0.00 41.45 5.68
184 187 2.491675 AAGGAAATTCACGGGTCTCC 57.508 50.000 0.00 0.00 0.00 3.71
200 204 3.722728 AGCAAGCTCAACAAGAAAAGG 57.277 42.857 0.00 0.00 0.00 3.11
243 247 5.067936 ACCGTATCTATTCCTCTTCTGTGTG 59.932 44.000 0.00 0.00 0.00 3.82
272 276 0.250513 GCTTCGACAGGGTGATCCTT 59.749 55.000 0.00 0.00 45.47 3.36
309 313 3.788766 GGCGATGTGTCACACGGC 61.789 66.667 26.01 26.01 39.37 5.68
314 318 1.442769 ACTGAATGGCGATGTGTCAC 58.557 50.000 0.00 0.00 32.94 3.67
378 382 2.749076 TGGATTTTCTCAGGCATGAACG 59.251 45.455 1.37 0.00 34.23 3.95
449 453 5.006746 GCGGTTAAGTTAGACATGATGAAGG 59.993 44.000 0.00 0.00 0.00 3.46
537 541 6.846505 TCAAGGGGAGACTTATCACTGATAAT 59.153 38.462 11.20 3.56 34.57 1.28
581 585 9.784531 AATGTGTTCTACCCATTATTATCTCTG 57.215 33.333 0.00 0.00 0.00 3.35
627 1024 4.392138 GTCCTATATAAGATTGCGGCCAAC 59.608 45.833 2.24 0.00 32.95 3.77
642 1045 9.017509 CCAATTAATCTGTGCAATGTCCTATAT 57.982 33.333 0.00 0.00 0.00 0.86
661 1064 4.142556 GCGTGCTTAGTTTAGGCCAATTAA 60.143 41.667 5.01 0.00 0.00 1.40
735 1138 1.299165 GCGACGGTCGTGCTCATAT 60.299 57.895 28.75 0.00 42.81 1.78
736 1139 2.101575 GCGACGGTCGTGCTCATA 59.898 61.111 28.75 0.00 42.81 2.15
853 1256 2.119029 TCGTGCCAGATCGGACGAT 61.119 57.895 12.05 6.95 40.25 3.73
1104 1564 3.502237 CTACAAACGGTAGCACGGT 57.498 52.632 0.00 0.00 42.81 4.83
1149 1610 5.305128 AGATGAAAAAGGGTTGCAGATCAAA 59.695 36.000 0.00 0.00 36.26 2.69
1360 1840 1.754380 CTTGACGAGGTCCCACCACA 61.754 60.000 0.00 0.00 41.95 4.17
1532 2066 4.764823 GTGGACAGTGAATTGGGTGATAAA 59.235 41.667 0.00 0.00 0.00 1.40
1534 2068 3.618752 CGTGGACAGTGAATTGGGTGATA 60.619 47.826 0.00 0.00 0.00 2.15
1535 2069 2.795329 GTGGACAGTGAATTGGGTGAT 58.205 47.619 0.00 0.00 0.00 3.06
1852 2395 1.670406 CTGCAGGCAGAGAAAGCGT 60.670 57.895 16.02 0.00 46.30 5.07
1856 2399 1.817357 CATCACTGCAGGCAGAGAAA 58.183 50.000 26.63 9.62 44.28 2.52
2045 2726 5.588648 GCAATAACAAGGGTGCATTCTACTA 59.411 40.000 0.00 0.00 36.97 1.82
2103 2961 7.321745 ACGCATCTTTATCTTTAGAAAAGGG 57.678 36.000 0.00 0.00 32.33 3.95
2192 3053 3.217626 CCCTGATTCTAAACTCCCATGC 58.782 50.000 0.00 0.00 0.00 4.06
2278 6704 6.641169 TCAGTGTATATAGCTGAGGTGAAG 57.359 41.667 11.04 0.00 34.72 3.02
2354 6791 6.348704 CCGTCCCATAATGTTAAGACGTTTTT 60.349 38.462 9.20 0.00 44.06 1.94
2355 6792 5.122711 CCGTCCCATAATGTTAAGACGTTTT 59.877 40.000 9.20 0.00 44.06 2.43
2356 6793 4.632688 CCGTCCCATAATGTTAAGACGTTT 59.367 41.667 9.20 0.00 44.06 3.60
2357 6794 4.186159 CCGTCCCATAATGTTAAGACGTT 58.814 43.478 9.20 0.00 44.06 3.99
2358 6795 3.431207 CCCGTCCCATAATGTTAAGACGT 60.431 47.826 9.20 0.00 44.06 4.34
2359 6796 3.128349 CCCGTCCCATAATGTTAAGACG 58.872 50.000 3.52 3.52 44.88 4.18
2360 6797 3.473625 CCCCGTCCCATAATGTTAAGAC 58.526 50.000 0.00 0.00 0.00 3.01
2361 6798 2.440253 CCCCCGTCCCATAATGTTAAGA 59.560 50.000 0.00 0.00 0.00 2.10
2362 6799 2.440253 TCCCCCGTCCCATAATGTTAAG 59.560 50.000 0.00 0.00 0.00 1.85
2363 6800 2.440253 CTCCCCCGTCCCATAATGTTAA 59.560 50.000 0.00 0.00 0.00 2.01
2364 6801 2.051692 CTCCCCCGTCCCATAATGTTA 58.948 52.381 0.00 0.00 0.00 2.41
2365 6802 0.843984 CTCCCCCGTCCCATAATGTT 59.156 55.000 0.00 0.00 0.00 2.71
2366 6803 0.327191 ACTCCCCCGTCCCATAATGT 60.327 55.000 0.00 0.00 0.00 2.71
2367 6804 1.623811 CTACTCCCCCGTCCCATAATG 59.376 57.143 0.00 0.00 0.00 1.90
2368 6805 1.222298 ACTACTCCCCCGTCCCATAAT 59.778 52.381 0.00 0.00 0.00 1.28
2369 6806 0.638292 ACTACTCCCCCGTCCCATAA 59.362 55.000 0.00 0.00 0.00 1.90
2370 6807 0.638292 AACTACTCCCCCGTCCCATA 59.362 55.000 0.00 0.00 0.00 2.74
2371 6808 0.253020 AAACTACTCCCCCGTCCCAT 60.253 55.000 0.00 0.00 0.00 4.00
2372 6809 1.159184 AAACTACTCCCCCGTCCCA 59.841 57.895 0.00 0.00 0.00 4.37
2373 6810 1.600638 CAAACTACTCCCCCGTCCC 59.399 63.158 0.00 0.00 0.00 4.46
2374 6811 1.078637 GCAAACTACTCCCCCGTCC 60.079 63.158 0.00 0.00 0.00 4.79
2375 6812 0.391263 CAGCAAACTACTCCCCCGTC 60.391 60.000 0.00 0.00 0.00 4.79
2376 6813 1.677552 CAGCAAACTACTCCCCCGT 59.322 57.895 0.00 0.00 0.00 5.28
2377 6814 1.745489 GCAGCAAACTACTCCCCCG 60.745 63.158 0.00 0.00 0.00 5.73
2378 6815 1.378646 GGCAGCAAACTACTCCCCC 60.379 63.158 0.00 0.00 0.00 5.40
2379 6816 0.960861 GTGGCAGCAAACTACTCCCC 60.961 60.000 0.00 0.00 0.00 4.81
2380 6817 1.298859 CGTGGCAGCAAACTACTCCC 61.299 60.000 0.00 0.00 0.00 4.30
2381 6818 0.602905 ACGTGGCAGCAAACTACTCC 60.603 55.000 0.00 0.00 0.00 3.85
2382 6819 0.790814 GACGTGGCAGCAAACTACTC 59.209 55.000 0.00 0.00 0.00 2.59
2383 6820 0.393077 AGACGTGGCAGCAAACTACT 59.607 50.000 0.00 0.00 0.00 2.57
2384 6821 0.790814 GAGACGTGGCAGCAAACTAC 59.209 55.000 0.00 0.00 0.00 2.73
2385 6822 0.666274 CGAGACGTGGCAGCAAACTA 60.666 55.000 0.00 0.00 0.00 2.24
2386 6823 1.956170 CGAGACGTGGCAGCAAACT 60.956 57.895 0.00 0.00 0.00 2.66
2387 6824 2.551270 CGAGACGTGGCAGCAAAC 59.449 61.111 0.00 0.00 0.00 2.93
2388 6825 3.345808 GCGAGACGTGGCAGCAAA 61.346 61.111 0.00 0.00 0.00 3.68
2389 6826 4.600576 TGCGAGACGTGGCAGCAA 62.601 61.111 0.00 0.00 31.56 3.91
2393 6830 3.295273 ACTCTGCGAGACGTGGCA 61.295 61.111 11.64 0.00 35.85 4.92
2394 6831 2.807045 CACTCTGCGAGACGTGGC 60.807 66.667 11.64 0.00 33.32 5.01
2395 6832 2.807045 GCACTCTGCGAGACGTGG 60.807 66.667 11.64 0.00 31.71 4.94
2404 6841 0.795085 GTGACAGTGATGCACTCTGC 59.205 55.000 14.26 9.87 43.43 4.26
2405 6842 1.066136 CGTGACAGTGATGCACTCTG 58.934 55.000 0.00 13.31 43.43 3.35
2406 6843 0.961753 TCGTGACAGTGATGCACTCT 59.038 50.000 0.00 0.00 43.43 3.24
2407 6844 1.063806 GTCGTGACAGTGATGCACTC 58.936 55.000 0.00 0.00 43.43 3.51
2408 6845 0.319900 GGTCGTGACAGTGATGCACT 60.320 55.000 0.00 0.00 46.51 4.40
2409 6846 1.291877 GGGTCGTGACAGTGATGCAC 61.292 60.000 0.00 1.29 34.10 4.57
2410 6847 1.005037 GGGTCGTGACAGTGATGCA 60.005 57.895 0.00 0.00 0.00 3.96
2411 6848 0.737715 GAGGGTCGTGACAGTGATGC 60.738 60.000 0.00 0.00 0.00 3.91
2412 6849 0.891373 AGAGGGTCGTGACAGTGATG 59.109 55.000 0.00 0.00 0.00 3.07
2413 6850 1.633774 AAGAGGGTCGTGACAGTGAT 58.366 50.000 0.00 0.00 0.00 3.06
2414 6851 1.884579 GTAAGAGGGTCGTGACAGTGA 59.115 52.381 0.00 0.00 0.00 3.41
2415 6852 1.887198 AGTAAGAGGGTCGTGACAGTG 59.113 52.381 2.00 0.00 0.00 3.66
2416 6853 2.161030 GAGTAAGAGGGTCGTGACAGT 58.839 52.381 2.00 0.00 0.00 3.55
2417 6854 1.130749 CGAGTAAGAGGGTCGTGACAG 59.869 57.143 2.00 0.00 0.00 3.51
2448 6885 1.095228 CCGCCTGTAATTCGCCATGT 61.095 55.000 0.00 0.00 0.00 3.21
2471 6908 1.351017 CTCCCTCACAAACCCTAGCAA 59.649 52.381 0.00 0.00 0.00 3.91
2472 6909 0.984230 CTCCCTCACAAACCCTAGCA 59.016 55.000 0.00 0.00 0.00 3.49
2484 6921 1.612442 CGACCCCCTTTCTCCCTCA 60.612 63.158 0.00 0.00 0.00 3.86
2499 6937 0.756070 CCTTCCTCCTACCTCCCGAC 60.756 65.000 0.00 0.00 0.00 4.79
2516 6954 1.243230 TTCCCTGTATCCCCTCCCCT 61.243 60.000 0.00 0.00 0.00 4.79
2517 6955 0.328158 TTTCCCTGTATCCCCTCCCC 60.328 60.000 0.00 0.00 0.00 4.81
2518 6956 0.844660 GTTTCCCTGTATCCCCTCCC 59.155 60.000 0.00 0.00 0.00 4.30
2519 6957 1.490910 CTGTTTCCCTGTATCCCCTCC 59.509 57.143 0.00 0.00 0.00 4.30
2560 6999 9.939802 GGGGTACGAAATTATAATAGACTGAAT 57.060 33.333 0.00 0.00 0.00 2.57
2585 7024 4.742201 CACGGTGGAGTGGAGCGG 62.742 72.222 0.00 0.00 38.62 5.52
2636 7075 2.270352 ACAAGCTTTTCGACCCATCA 57.730 45.000 0.00 0.00 0.00 3.07
2663 7102 0.107165 GGCGGCCCAAGAGAAGTAAT 60.107 55.000 8.12 0.00 0.00 1.89
2666 7105 4.035102 GGGCGGCCCAAGAGAAGT 62.035 66.667 32.90 0.00 44.65 3.01
2690 7129 3.386237 AGTCCAGAGCCCACGAGC 61.386 66.667 0.00 0.00 0.00 5.03
2693 7132 2.997315 TCCAGTCCAGAGCCCACG 60.997 66.667 0.00 0.00 0.00 4.94
2707 7146 0.918258 TGATATTGCACCAGCCTCCA 59.082 50.000 0.00 0.00 41.13 3.86
2721 7160 1.696097 GGGGGTGTCACGGCTGATAT 61.696 60.000 0.00 0.00 0.00 1.63
2744 7184 2.738521 TCAAGCCGCGTCTGAAGC 60.739 61.111 4.92 5.46 0.00 3.86
2836 7276 2.022129 GCTGGTCAAGTGGTCGTCG 61.022 63.158 0.00 0.00 0.00 5.12
2850 7290 1.741732 CGAAGATCCCTGAAGTGCTGG 60.742 57.143 0.00 0.00 35.50 4.85
2859 7299 5.182001 ACAAAAGACAAATCGAAGATCCCTG 59.818 40.000 0.00 0.00 45.12 4.45
2876 7316 2.489938 AGGCGCCTGATTACAAAAGA 57.510 45.000 32.33 0.00 0.00 2.52
2955 7395 1.554392 GAGCGCTGACACAGTATCAG 58.446 55.000 18.48 4.29 45.40 2.90
2959 7399 2.265904 ACCGAGCGCTGACACAGTA 61.266 57.895 18.48 0.00 33.43 2.74
2962 7402 4.662961 CCACCGAGCGCTGACACA 62.663 66.667 18.48 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.