Multiple sequence alignment - TraesCS1A01G053800

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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 TraesCS1A01G053800 chr1A 100.000 1928 0 0 866 2793 35536206 35538133 0.000000e+00 3561
1 TraesCS1A01G053800 chr1A 87.025 1842 175 27 866 2663 35578632 35576811 0.000000e+00 2019
2 TraesCS1A01G053800 chr1A 87.010 1709 160 31 866 2539 35486015 35487696 0.000000e+00 1869
3 TraesCS1A01G053800 chr1A 85.832 1574 171 27 999 2539 35525792 35527346 0.000000e+00 1624
4 TraesCS1A01G053800 chr1A 100.000 642 0 0 1 642 35535341 35535982 0.000000e+00 1186
5 TraesCS1A01G053800 chr1A 95.856 555 23 0 7 561 35514441 35514995 0.000000e+00 898
6 TraesCS1A01G053800 chr1A 87.270 652 55 13 1 640 35484910 35485545 0.000000e+00 719
7 TraesCS1A01G053800 chr1A 87.102 566 56 9 3 561 35579377 35578822 2.360000e-175 625
8 TraesCS1A01G053800 chr1A 76.350 1074 204 33 1138 2174 31032156 31031096 5.300000e-147 531
9 TraesCS1A01G053800 chr1D 89.298 1710 131 26 866 2539 36315623 36317316 0.000000e+00 2097
10 TraesCS1A01G053800 chr1D 92.702 781 57 0 866 1646 36363136 36362356 0.000000e+00 1127
11 TraesCS1A01G053800 chr1D 85.977 1034 85 30 1675 2664 36362365 36361348 0.000000e+00 1051
12 TraesCS1A01G053800 chr1D 86.195 565 56 12 3 561 36363882 36363334 2.400000e-165 592
13 TraesCS1A01G053800 chr1D 89.655 290 28 2 226 514 36314955 36315243 4.390000e-98 368
14 TraesCS1A01G053800 chr1B 88.369 1625 134 25 866 2455 56016975 56018579 0.000000e+00 1903
15 TraesCS1A01G053800 chr1B 94.236 1197 68 1 866 2062 56140938 56139743 0.000000e+00 1827
16 TraesCS1A01G053800 chr1B 91.736 1198 95 2 866 2062 55998323 55999517 0.000000e+00 1661
17 TraesCS1A01G053800 chr1B 91.294 1206 93 3 866 2062 55977056 55978258 0.000000e+00 1635
18 TraesCS1A01G053800 chr1B 86.170 564 58 9 3 559 56141871 56141321 2.400000e-165 592
19 TraesCS1A01G053800 chr1B 76.260 1171 242 30 866 2020 39672090 39673240 8.620000e-165 590
20 TraesCS1A01G053800 chr1B 89.767 430 34 6 131 560 56016177 56016596 2.450000e-150 542
21 TraesCS1A01G053800 chr1B 88.657 432 39 6 131 561 55976421 55976843 4.120000e-143 518
22 TraesCS1A01G053800 chr1B 92.763 304 20 2 1 303 55955792 55956094 3.300000e-119 438
23 TraesCS1A01G053800 chr1B 92.434 304 21 2 1 303 55944539 55944841 1.540000e-117 433
24 TraesCS1A01G053800 chr1B 87.572 346 32 6 217 561 55997571 55997906 9.380000e-105 390
25 TraesCS1A01G053800 chr1B 77.706 619 77 25 2090 2664 56139746 56139145 3.470000e-84 322
26 TraesCS1A01G053800 chr1B 88.095 126 14 1 2666 2790 56138985 56138860 6.230000e-32 148


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 TraesCS1A01G053800 chr1A 35535341 35538133 2792 False 2373.500000 3561 100.000000 1 2793 2 chr1A.!!$F4 2792
1 TraesCS1A01G053800 chr1A 35525792 35527346 1554 False 1624.000000 1624 85.832000 999 2539 1 chr1A.!!$F2 1540
2 TraesCS1A01G053800 chr1A 35576811 35579377 2566 True 1322.000000 2019 87.063500 3 2663 2 chr1A.!!$R2 2660
3 TraesCS1A01G053800 chr1A 35484910 35487696 2786 False 1294.000000 1869 87.140000 1 2539 2 chr1A.!!$F3 2538
4 TraesCS1A01G053800 chr1A 35514441 35514995 554 False 898.000000 898 95.856000 7 561 1 chr1A.!!$F1 554
5 TraesCS1A01G053800 chr1A 31031096 31032156 1060 True 531.000000 531 76.350000 1138 2174 1 chr1A.!!$R1 1036
6 TraesCS1A01G053800 chr1D 36314955 36317316 2361 False 1232.500000 2097 89.476500 226 2539 2 chr1D.!!$F1 2313
7 TraesCS1A01G053800 chr1D 36361348 36363882 2534 True 923.333333 1127 88.291333 3 2664 3 chr1D.!!$R1 2661
8 TraesCS1A01G053800 chr1B 56016177 56018579 2402 False 1222.500000 1903 89.068000 131 2455 2 chr1B.!!$F6 2324
9 TraesCS1A01G053800 chr1B 55976421 55978258 1837 False 1076.500000 1635 89.975500 131 2062 2 chr1B.!!$F4 1931
10 TraesCS1A01G053800 chr1B 55997571 55999517 1946 False 1025.500000 1661 89.654000 217 2062 2 chr1B.!!$F5 1845
11 TraesCS1A01G053800 chr1B 56138860 56141871 3011 True 722.250000 1827 86.551750 3 2790 4 chr1B.!!$R1 2787
12 TraesCS1A01G053800 chr1B 39672090 39673240 1150 False 590.000000 590 76.260000 866 2020 1 chr1B.!!$F1 1154

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
572 597 0.464036 ACACACGACTTTCTCCTGCA 59.536 50.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2246 2656 0.098376 GTAGTACTGGGCACTCGTCG 59.902 60.0 5.39 0.0 0.0 5.12 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
34 35 2.745884 CGGCGACAGGATTTGGCA 60.746 61.111 0.00 0.00 32.77 4.92
115 121 4.021719 GCAGCAACCTTCCAATATATGCAT 60.022 41.667 3.79 3.79 34.89 3.96
510 535 8.859156 CATTAGTTTTAAAAACGGTGATCCATG 58.141 33.333 1.31 0.00 0.00 3.66
569 594 2.691526 TGTACACACACGACTTTCTCCT 59.308 45.455 0.00 0.00 0.00 3.69
571 596 0.861837 CACACACGACTTTCTCCTGC 59.138 55.000 0.00 0.00 0.00 4.85
572 597 0.464036 ACACACGACTTTCTCCTGCA 59.536 50.000 0.00 0.00 0.00 4.41
573 598 1.134521 ACACACGACTTTCTCCTGCAA 60.135 47.619 0.00 0.00 0.00 4.08
574 599 1.939934 CACACGACTTTCTCCTGCAAA 59.060 47.619 0.00 0.00 0.00 3.68
912 1212 1.177401 CAGATCTCGTCCTCACCACA 58.823 55.000 0.00 0.00 0.00 4.17
913 1213 1.753649 CAGATCTCGTCCTCACCACAT 59.246 52.381 0.00 0.00 0.00 3.21
914 1214 2.028130 AGATCTCGTCCTCACCACATC 58.972 52.381 0.00 0.00 0.00 3.06
915 1215 1.751351 GATCTCGTCCTCACCACATCA 59.249 52.381 0.00 0.00 0.00 3.07
916 1216 1.177401 TCTCGTCCTCACCACATCAG 58.823 55.000 0.00 0.00 0.00 2.90
917 1217 1.177401 CTCGTCCTCACCACATCAGA 58.823 55.000 0.00 0.00 0.00 3.27
918 1218 1.753649 CTCGTCCTCACCACATCAGAT 59.246 52.381 0.00 0.00 0.00 2.90
919 1219 1.751351 TCGTCCTCACCACATCAGATC 59.249 52.381 0.00 0.00 0.00 2.75
920 1220 1.534805 CGTCCTCACCACATCAGATCG 60.535 57.143 0.00 0.00 0.00 3.69
921 1221 1.478510 GTCCTCACCACATCAGATCGT 59.521 52.381 0.00 0.00 0.00 3.73
990 1301 1.883084 GATCGTGGGTGCGACATCC 60.883 63.158 2.57 2.57 43.99 3.51
1009 1320 1.000896 CCCCTGACCATGGTGAACC 60.001 63.158 25.52 8.41 0.00 3.62
1110 1421 1.227176 GGTAGATCCAACGCCGTCC 60.227 63.158 0.00 0.00 35.97 4.79
1136 1447 0.467384 CATCGAGGGAGGCTGATGTT 59.533 55.000 0.00 0.00 34.83 2.71
1506 1818 1.480137 CTCAAGAGGCCACGATTCTCT 59.520 52.381 5.01 0.00 39.31 3.10
1773 2098 3.708631 CAGATCAACATGGAGTCCTACCT 59.291 47.826 11.33 0.00 0.00 3.08
1799 2124 0.535335 GGACAATCGCTGACCCTGTA 59.465 55.000 0.00 0.00 34.14 2.74
1810 2135 3.630312 GCTGACCCTGTAAACTCAACAAA 59.370 43.478 0.00 0.00 0.00 2.83
1905 2230 7.148573 CCATTGTTAGCTACATAATCCATCGAC 60.149 40.741 0.00 0.00 36.44 4.20
1907 2232 6.447162 TGTTAGCTACATAATCCATCGACTG 58.553 40.000 0.00 0.00 0.00 3.51
1969 2294 5.003804 CACCAGGAAACTAGTTGTAAGCAT 58.996 41.667 9.34 0.00 40.21 3.79
2041 2396 8.803235 TGATAGTCATTTCCGTAATAGCACTAT 58.197 33.333 0.00 0.00 0.00 2.12
2102 2457 6.125029 AGGACGTAATGTGGTGTACTAGTAT 58.875 40.000 5.75 0.00 0.00 2.12
2105 2460 7.433425 GGACGTAATGTGGTGTACTAGTATTTC 59.567 40.741 5.75 0.17 0.00 2.17
2106 2461 7.829725 ACGTAATGTGGTGTACTAGTATTTCA 58.170 34.615 5.75 2.27 0.00 2.69
2107 2462 7.756722 ACGTAATGTGGTGTACTAGTATTTCAC 59.243 37.037 5.75 13.76 0.00 3.18
2145 2529 6.071560 TCCAGTTAGTATGTTCGTTGATGTCT 60.072 38.462 0.00 0.00 0.00 3.41
2150 2551 5.844004 AGTATGTTCGTTGATGTCTATCCC 58.156 41.667 0.00 0.00 32.09 3.85
2151 2552 3.536956 TGTTCGTTGATGTCTATCCCC 57.463 47.619 0.00 0.00 32.09 4.81
2152 2553 3.104512 TGTTCGTTGATGTCTATCCCCT 58.895 45.455 0.00 0.00 32.09 4.79
2153 2554 4.283337 TGTTCGTTGATGTCTATCCCCTA 58.717 43.478 0.00 0.00 32.09 3.53
2154 2555 4.899457 TGTTCGTTGATGTCTATCCCCTAT 59.101 41.667 0.00 0.00 32.09 2.57
2155 2556 5.365605 TGTTCGTTGATGTCTATCCCCTATT 59.634 40.000 0.00 0.00 32.09 1.73
2156 2557 5.468540 TCGTTGATGTCTATCCCCTATTG 57.531 43.478 0.00 0.00 32.09 1.90
2157 2558 3.997021 CGTTGATGTCTATCCCCTATTGC 59.003 47.826 0.00 0.00 32.09 3.56
2158 2559 4.503123 CGTTGATGTCTATCCCCTATTGCA 60.503 45.833 0.00 0.00 32.09 4.08
2159 2560 5.376625 GTTGATGTCTATCCCCTATTGCAA 58.623 41.667 0.00 0.00 32.09 4.08
2160 2561 5.848286 TGATGTCTATCCCCTATTGCAAT 57.152 39.130 17.56 17.56 32.09 3.56
2161 2562 5.809001 TGATGTCTATCCCCTATTGCAATC 58.191 41.667 16.86 0.00 32.09 2.67
2162 2563 5.549228 TGATGTCTATCCCCTATTGCAATCT 59.451 40.000 16.86 0.00 32.09 2.40
2163 2564 5.912149 TGTCTATCCCCTATTGCAATCTT 57.088 39.130 16.86 0.00 0.00 2.40
2164 2565 7.237471 TGATGTCTATCCCCTATTGCAATCTTA 59.763 37.037 16.86 0.00 32.09 2.10
2165 2566 7.387265 TGTCTATCCCCTATTGCAATCTTAA 57.613 36.000 16.86 0.00 0.00 1.85
2166 2567 7.988937 TGTCTATCCCCTATTGCAATCTTAAT 58.011 34.615 16.86 7.26 0.00 1.40
2167 2568 7.884877 TGTCTATCCCCTATTGCAATCTTAATG 59.115 37.037 16.86 1.39 0.00 1.90
2168 2569 5.990120 ATCCCCTATTGCAATCTTAATGC 57.010 39.130 16.86 0.00 44.08 3.56
2169 2570 5.065613 TCCCCTATTGCAATCTTAATGCT 57.934 39.130 16.86 0.00 44.14 3.79
2170 2571 6.199557 TCCCCTATTGCAATCTTAATGCTA 57.800 37.500 16.86 0.00 44.14 3.49
2171 2572 6.240894 TCCCCTATTGCAATCTTAATGCTAG 58.759 40.000 16.86 4.13 44.14 3.42
2172 2573 6.006449 CCCCTATTGCAATCTTAATGCTAGT 58.994 40.000 16.86 0.00 44.14 2.57
2173 2574 7.017155 TCCCCTATTGCAATCTTAATGCTAGTA 59.983 37.037 16.86 0.00 44.14 1.82
2174 2575 7.831193 CCCCTATTGCAATCTTAATGCTAGTAT 59.169 37.037 16.86 0.00 44.14 2.12
2175 2576 9.236006 CCCTATTGCAATCTTAATGCTAGTATT 57.764 33.333 16.86 11.02 44.14 1.89
2244 2654 9.646427 TTTCTTGCTATTCTTTCTCTAGAAGAC 57.354 33.333 0.00 0.00 37.55 3.01
2246 2656 5.583495 TGCTATTCTTTCTCTAGAAGACGC 58.417 41.667 0.00 0.00 37.55 5.19
2247 2657 4.673311 GCTATTCTTTCTCTAGAAGACGCG 59.327 45.833 3.53 3.53 37.55 6.01
2248 2658 4.966965 ATTCTTTCTCTAGAAGACGCGA 57.033 40.909 15.93 0.00 37.55 5.87
2249 2659 3.743567 TCTTTCTCTAGAAGACGCGAC 57.256 47.619 15.93 6.86 35.21 5.19
2250 2660 2.093941 TCTTTCTCTAGAAGACGCGACG 59.906 50.000 15.93 0.00 35.21 5.12
2251 2661 1.718396 TTCTCTAGAAGACGCGACGA 58.282 50.000 15.93 0.00 32.27 4.20
2252 2662 1.279152 TCTCTAGAAGACGCGACGAG 58.721 55.000 15.93 8.65 0.00 4.18
2254 2664 0.720027 TCTAGAAGACGCGACGAGTG 59.280 55.000 15.93 0.00 0.00 3.51
2255 2665 0.858135 CTAGAAGACGCGACGAGTGC 60.858 60.000 15.93 1.06 0.00 4.40
2289 2718 0.461339 CCGCGTTATAGCTGGTTGGT 60.461 55.000 4.92 0.00 34.40 3.67
2291 2720 0.377203 GCGTTATAGCTGGTTGGTGC 59.623 55.000 0.00 0.00 0.00 5.01
2316 2745 1.917872 CCCGGGATCAAAAGGTTTCA 58.082 50.000 18.48 0.00 0.00 2.69
2322 2751 5.112686 CGGGATCAAAAGGTTTCAAAAACA 58.887 37.500 5.07 0.00 0.00 2.83
2363 2792 2.226912 GCTGTGGGTGTTGCGTAATTTA 59.773 45.455 0.00 0.00 0.00 1.40
2367 2796 4.702612 TGTGGGTGTTGCGTAATTTATCAT 59.297 37.500 0.00 0.00 0.00 2.45
2368 2797 5.880887 TGTGGGTGTTGCGTAATTTATCATA 59.119 36.000 0.00 0.00 0.00 2.15
2390 2819 2.370519 TGTTTCCTGATTTCTCGTGGGA 59.629 45.455 0.00 0.00 0.00 4.37
2399 2828 3.499737 CTCGTGGGATTGGCGTGC 61.500 66.667 0.00 0.00 0.00 5.34
2434 2863 7.374272 CCGAGTGAGATAGTTGAATGACATAT 58.626 38.462 0.00 0.00 0.00 1.78
2498 2927 1.373435 CCAGGGTTTGGTGACGCTA 59.627 57.895 0.00 0.00 42.41 4.26
2502 2931 0.250166 GGGTTTGGTGACGCTACACT 60.250 55.000 9.33 0.00 40.22 3.55
2524 2961 0.991355 TTTCTGGGTGTGAGTGGGGT 60.991 55.000 0.00 0.00 0.00 4.95
2534 2971 0.770166 TGAGTGGGGTTGGTGGATGA 60.770 55.000 0.00 0.00 0.00 2.92
2539 2976 1.678970 GGGTTGGTGGATGAGCACC 60.679 63.158 0.00 0.00 41.64 5.01
2541 2978 2.040544 GTTGGTGGATGAGCACCGG 61.041 63.158 0.00 0.00 44.07 5.28
2735 3340 2.624838 CCTAGCCATCCGATTTTGCAAT 59.375 45.455 0.00 0.00 0.00 3.56
2763 3368 7.905604 TTGCCAAGATTGATAGATTATACCG 57.094 36.000 0.00 0.00 0.00 4.02
2777 3382 6.932947 AGATTATACCGATAACCCTAACAGC 58.067 40.000 0.00 0.00 30.24 4.40
2778 3383 6.724905 AGATTATACCGATAACCCTAACAGCT 59.275 38.462 0.00 0.00 30.24 4.24
2781 3386 3.039011 ACCGATAACCCTAACAGCTCAT 58.961 45.455 0.00 0.00 0.00 2.90
2790 3395 4.896482 ACCCTAACAGCTCATCTACCTTAG 59.104 45.833 0.00 0.00 0.00 2.18
2791 3396 4.896482 CCCTAACAGCTCATCTACCTTAGT 59.104 45.833 0.00 0.00 0.00 2.24
2792 3397 5.364157 CCCTAACAGCTCATCTACCTTAGTT 59.636 44.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 121 0.684805 AAAAACAGGGCACAACCGGA 60.685 50.000 9.46 0.00 40.62 5.14
355 372 1.364626 AAGCTTCATTCGGCAGCGAG 61.365 55.000 0.00 0.00 38.66 5.03
401 421 7.067859 CACATTTACCTTCATGTCCAATGATCT 59.932 37.037 0.00 0.00 30.90 2.75
409 429 7.047891 TGATCTACACATTTACCTTCATGTCC 58.952 38.462 0.00 0.00 30.90 4.02
510 535 3.914426 TTTCTCCCTCTAGACCATTGC 57.086 47.619 0.00 0.00 0.00 3.56
912 1212 2.175931 AGTGAGAGGGGTACGATCTGAT 59.824 50.000 0.00 0.00 0.00 2.90
913 1213 1.564818 AGTGAGAGGGGTACGATCTGA 59.435 52.381 0.00 0.00 0.00 3.27
914 1214 1.678627 CAGTGAGAGGGGTACGATCTG 59.321 57.143 0.00 0.00 0.00 2.90
915 1215 2.024825 GCAGTGAGAGGGGTACGATCT 61.025 57.143 0.00 0.00 0.00 2.75
916 1216 0.386113 GCAGTGAGAGGGGTACGATC 59.614 60.000 0.00 0.00 0.00 3.69
917 1217 1.043673 GGCAGTGAGAGGGGTACGAT 61.044 60.000 0.00 0.00 0.00 3.73
918 1218 1.681327 GGCAGTGAGAGGGGTACGA 60.681 63.158 0.00 0.00 0.00 3.43
919 1219 2.893398 GGCAGTGAGAGGGGTACG 59.107 66.667 0.00 0.00 0.00 3.67
920 1220 2.893398 CGGCAGTGAGAGGGGTAC 59.107 66.667 0.00 0.00 0.00 3.34
921 1221 3.075005 GCGGCAGTGAGAGGGGTA 61.075 66.667 0.00 0.00 0.00 3.69
990 1301 1.000896 GTTCACCATGGTCAGGGGG 60.001 63.158 16.53 2.34 36.92 5.40
997 1308 4.715523 CGCCGGGTTCACCATGGT 62.716 66.667 13.00 13.00 40.22 3.55
1136 1447 0.815095 CTTGAGCATTGATGGCAGCA 59.185 50.000 0.00 0.00 0.00 4.41
1506 1818 2.405143 CTCCGCGGAGAGTGATACA 58.595 57.895 45.28 12.76 44.53 2.29
1773 2098 4.015406 AGCGATTGTCCGGCACCA 62.015 61.111 0.00 0.00 0.00 4.17
1799 2124 1.404035 GTGGAGGCGTTTGTTGAGTTT 59.596 47.619 0.00 0.00 0.00 2.66
1810 2135 1.412453 TTACTGTTGGGTGGAGGCGT 61.412 55.000 0.00 0.00 0.00 5.68
1907 2232 6.756074 CCAACTCTGACTCTATCTGAACAATC 59.244 42.308 0.00 0.00 35.10 2.67
1969 2294 5.745312 ATCACTAACAGGTCATCACTTGA 57.255 39.130 0.00 0.00 33.76 3.02
2020 2347 6.482308 ACCAATAGTGCTATTACGGAAATGAC 59.518 38.462 12.47 0.00 34.27 3.06
2041 2396 3.002038 ACCAAAGTAACGAACCACCAA 57.998 42.857 0.00 0.00 0.00 3.67
2102 2457 1.066858 GGAGCATCGAGGACAGTGAAA 60.067 52.381 0.00 0.00 34.37 2.69
2105 2460 0.179116 CTGGAGCATCGAGGACAGTG 60.179 60.000 0.00 0.00 37.29 3.66
2106 2461 0.613292 ACTGGAGCATCGAGGACAGT 60.613 55.000 14.00 14.00 46.07 3.55
2107 2462 0.534412 AACTGGAGCATCGAGGACAG 59.466 55.000 0.00 8.24 46.07 3.51
2145 2529 6.793478 AGCATTAAGATTGCAATAGGGGATA 58.207 36.000 12.97 0.00 42.62 2.59
2154 2555 8.786898 GGATGAATACTAGCATTAAGATTGCAA 58.213 33.333 0.00 0.00 42.62 4.08
2155 2556 8.159447 AGGATGAATACTAGCATTAAGATTGCA 58.841 33.333 2.59 0.00 42.62 4.08
2156 2557 8.558973 AGGATGAATACTAGCATTAAGATTGC 57.441 34.615 0.00 0.00 40.45 3.56
2160 2561 9.658799 GCAATAGGATGAATACTAGCATTAAGA 57.341 33.333 0.00 0.00 0.00 2.10
2161 2562 9.440773 TGCAATAGGATGAATACTAGCATTAAG 57.559 33.333 0.00 0.00 0.00 1.85
2162 2563 9.791801 TTGCAATAGGATGAATACTAGCATTAA 57.208 29.630 0.00 0.00 28.33 1.40
2163 2564 9.964354 ATTGCAATAGGATGAATACTAGCATTA 57.036 29.630 11.02 0.00 28.33 1.90
2164 2565 8.874744 ATTGCAATAGGATGAATACTAGCATT 57.125 30.769 11.02 0.00 28.33 3.56
2165 2566 8.327271 AGATTGCAATAGGATGAATACTAGCAT 58.673 33.333 12.97 0.00 28.33 3.79
2166 2567 7.683578 AGATTGCAATAGGATGAATACTAGCA 58.316 34.615 12.97 0.00 0.00 3.49
2167 2568 7.821359 TGAGATTGCAATAGGATGAATACTAGC 59.179 37.037 12.97 0.00 0.00 3.42
2168 2569 9.368674 CTGAGATTGCAATAGGATGAATACTAG 57.631 37.037 12.97 0.00 0.00 2.57
2169 2570 8.874156 ACTGAGATTGCAATAGGATGAATACTA 58.126 33.333 12.97 0.00 0.00 1.82
2170 2571 7.660617 CACTGAGATTGCAATAGGATGAATACT 59.339 37.037 12.97 0.46 0.00 2.12
2171 2572 7.572724 GCACTGAGATTGCAATAGGATGAATAC 60.573 40.741 12.97 0.00 39.93 1.89
2172 2573 6.429078 GCACTGAGATTGCAATAGGATGAATA 59.571 38.462 12.97 0.00 39.93 1.75
2173 2574 5.241064 GCACTGAGATTGCAATAGGATGAAT 59.759 40.000 12.97 0.00 39.93 2.57
2174 2575 4.577693 GCACTGAGATTGCAATAGGATGAA 59.422 41.667 12.97 0.00 39.93 2.57
2175 2576 4.132336 GCACTGAGATTGCAATAGGATGA 58.868 43.478 12.97 0.00 39.93 2.92
2176 2577 4.135306 AGCACTGAGATTGCAATAGGATG 58.865 43.478 12.97 8.64 42.83 3.51
2177 2578 4.434545 AGCACTGAGATTGCAATAGGAT 57.565 40.909 12.97 0.00 42.83 3.24
2178 2579 3.920231 AGCACTGAGATTGCAATAGGA 57.080 42.857 12.97 0.00 42.83 2.94
2244 2654 4.111016 TACTGGGCACTCGTCGCG 62.111 66.667 0.00 0.00 0.00 5.87
2246 2656 0.098376 GTAGTACTGGGCACTCGTCG 59.902 60.000 5.39 0.00 0.00 5.12
2247 2657 1.461559 AGTAGTACTGGGCACTCGTC 58.538 55.000 5.39 0.00 0.00 4.20
2248 2658 1.544691 CAAGTAGTACTGGGCACTCGT 59.455 52.381 5.39 0.00 0.00 4.18
2249 2659 1.135083 CCAAGTAGTACTGGGCACTCG 60.135 57.143 10.95 0.00 31.40 4.18
2250 2660 2.674796 CCAAGTAGTACTGGGCACTC 57.325 55.000 10.95 0.00 31.40 3.51
2255 2665 1.153429 GCGGCCAAGTAGTACTGGG 60.153 63.158 18.40 18.40 42.46 4.45
2291 2720 3.929334 TTTTGATCCCGGGCCCACG 62.929 63.158 24.92 11.14 0.00 4.94
2304 2733 4.693095 GCCAGTGTTTTTGAAACCTTTTGA 59.307 37.500 1.53 0.00 0.00 2.69
2316 2745 2.411290 CGCGGTGCCAGTGTTTTT 59.589 55.556 0.00 0.00 0.00 1.94
2344 2773 4.072839 TGATAAATTACGCAACACCCACA 58.927 39.130 0.00 0.00 0.00 4.17
2363 2792 6.484643 CCACGAGAAATCAGGAAACATATGAT 59.515 38.462 10.38 0.00 35.21 2.45
2367 2796 4.224147 TCCCACGAGAAATCAGGAAACATA 59.776 41.667 0.00 0.00 0.00 2.29
2368 2797 3.009033 TCCCACGAGAAATCAGGAAACAT 59.991 43.478 0.00 0.00 0.00 2.71
2381 2810 2.264480 CACGCCAATCCCACGAGA 59.736 61.111 0.00 0.00 0.00 4.04
2390 2819 3.329889 TCTCCCTGGCACGCCAAT 61.330 61.111 12.67 0.00 46.63 3.16
2399 2828 2.037367 TCACTCGGGTCTCCCTGG 59.963 66.667 3.25 0.00 42.67 4.45
2401 2830 1.144093 CTATCTCACTCGGGTCTCCCT 59.856 57.143 3.25 0.00 42.67 4.20
2434 2863 6.502863 GGGACCACCTAGGGTTCAAATATATA 59.497 42.308 14.81 0.00 42.53 0.86
2441 2870 2.781631 GGGACCACCTAGGGTTCAA 58.218 57.895 14.81 0.00 42.53 2.69
2490 2919 2.221055 CCAGAAAACAGTGTAGCGTCAC 59.779 50.000 0.00 6.27 38.46 3.67
2498 2927 2.026262 ACTCACACCCAGAAAACAGTGT 60.026 45.455 0.00 0.00 43.99 3.55
2502 2931 1.409521 CCCACTCACACCCAGAAAACA 60.410 52.381 0.00 0.00 0.00 2.83
2534 2971 0.249398 AGAGATTAAACGCCGGTGCT 59.751 50.000 16.69 0.00 34.43 4.40
2539 2976 1.062587 CCAGCAAGAGATTAAACGCCG 59.937 52.381 0.00 0.00 0.00 6.46
2541 2978 1.468520 TGCCAGCAAGAGATTAAACGC 59.531 47.619 0.00 0.00 0.00 4.84
2567 3013 2.485814 GCTCAGCAGTAACCTTTTCCTG 59.514 50.000 0.00 0.00 0.00 3.86
2664 3110 8.519799 TGGACTAAGGAATTAATCAAACCATC 57.480 34.615 0.00 0.00 0.00 3.51
2676 3280 7.504911 CCAAGATCATTGATGGACTAAGGAATT 59.495 37.037 3.32 0.00 34.82 2.17
2684 3288 2.423947 GGGCCAAGATCATTGATGGACT 60.424 50.000 4.39 0.00 40.97 3.85
2685 3289 1.959282 GGGCCAAGATCATTGATGGAC 59.041 52.381 4.39 2.82 40.42 4.02
2699 3304 0.620556 CTAGGAGAGCAAAGGGCCAA 59.379 55.000 6.18 0.00 46.50 4.52
2700 3305 2.300996 CTAGGAGAGCAAAGGGCCA 58.699 57.895 6.18 0.00 46.50 5.36
2735 3340 9.453572 GTATAATCTATCAATCTTGGCAATCCA 57.546 33.333 0.00 0.00 41.55 3.41
2749 3354 9.758021 TGTTAGGGTTATCGGTATAATCTATCA 57.242 33.333 0.00 0.00 30.59 2.15
2751 3356 8.693625 GCTGTTAGGGTTATCGGTATAATCTAT 58.306 37.037 0.00 0.00 30.59 1.98
2757 3362 5.387788 TGAGCTGTTAGGGTTATCGGTATA 58.612 41.667 0.00 0.00 0.00 1.47
2758 3363 4.220724 TGAGCTGTTAGGGTTATCGGTAT 58.779 43.478 0.00 0.00 0.00 2.73
2763 3368 5.540719 AGGTAGATGAGCTGTTAGGGTTATC 59.459 44.000 0.00 0.00 33.53 1.75


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

AutoCloner maintained by Alex Coulton.