Multiple sequence alignment - TraesCS3B01G492900

Loading Multiple Alignment...

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 TraesCS3B01G492900 chr3B 100.000 2199 0 0 912 3110 738685737 738683539 0.000000e+00 4061.0
1 TraesCS3B01G492900 chr3B 100.000 696 0 0 1 696 738686648 738685953 0.000000e+00 1286.0
2 TraesCS3B01G492900 chr3D 91.274 2166 120 27 970 3110 555454785 555452664 0.000000e+00 2889.0
3 TraesCS3B01G492900 chr3D 79.298 570 63 24 151 696 555455381 555454843 6.380000e-92 348.0
4 TraesCS3B01G492900 chr3D 88.757 169 9 8 1 161 555455583 555455417 6.800000e-47 198.0
5 TraesCS3B01G492900 chr3A 90.909 1837 110 19 991 2793 692607308 692605495 0.000000e+00 2414.0
6 TraesCS3B01G492900 chr3A 79.433 564 71 30 151 696 692607920 692607384 1.060000e-94 357.0
7 TraesCS3B01G492900 chr3A 83.810 315 33 10 2809 3110 692605262 692604953 1.830000e-72 283.0
8 TraesCS3B01G492900 chr3A 81.961 255 32 11 2099 2350 692508884 692508641 1.460000e-48 204.0
9 TraesCS3B01G492900 chr3A 88.820 161 7 3 1 161 692608099 692607950 1.470000e-43 187.0
10 TraesCS3B01G492900 chr3A 90.299 134 12 1 2978 3110 692604772 692604639 1.150000e-39 174.0
11 TraesCS3B01G492900 chr3A 86.047 129 17 1 2983 3110 692604609 692604481 1.500000e-28 137.0
12 TraesCS3B01G492900 chr3A 97.143 35 1 0 2386 2420 692526927 692526893 3.350000e-05 60.2
13 TraesCS3B01G492900 chr2D 77.419 279 45 13 1015 1278 68905018 68904743 1.930000e-32 150.0
14 TraesCS3B01G492900 chr2A 76.792 293 52 10 1000 1278 65814062 65813772 1.930000e-32 150.0
15 TraesCS3B01G492900 chr2B 76.531 294 51 13 1000 1278 101453692 101453982 8.990000e-31 145.0


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 TraesCS3B01G492900 chr3B 738683539 738686648 3109 True 2673.5 4061 100.000 1 3110 2 chr3B.!!$R1 3109
1 TraesCS3B01G492900 chr3D 555452664 555455583 2919 True 1145.0 2889 86.443 1 3110 3 chr3D.!!$R1 3109
2 TraesCS3B01G492900 chr3A 692604481 692608099 3618 True 592.0 2414 86.553 1 3110 6 chr3A.!!$R3 3109

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
523 608 0.321034 GGACCTACGGAAACCACACC 60.321 60.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2459 2564 0.038159 GAACACACCAGACTCTCCGG 60.038 60.0 0.0 0.0 0.0 5.14 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
62 69 1.080329 AGGGAGGCCTTCTCTTTCTCT 59.920 52.381 11.94 0.00 42.10 3.10
63 70 1.484653 GGGAGGCCTTCTCTTTCTCTC 59.515 57.143 11.94 0.00 42.10 3.20
64 71 2.466846 GGAGGCCTTCTCTTTCTCTCT 58.533 52.381 6.77 0.00 42.10 3.10
75 82 2.963101 TCTTTCTCTCTTTCCGGTCACA 59.037 45.455 0.00 0.00 0.00 3.58
123 133 0.595095 GCAACTGCACAGGAAAGAGG 59.405 55.000 2.21 0.00 41.59 3.69
125 135 2.575532 CAACTGCACAGGAAAGAGGAA 58.424 47.619 2.21 0.00 0.00 3.36
127 137 2.576615 ACTGCACAGGAAAGAGGAAAC 58.423 47.619 2.21 0.00 0.00 2.78
128 138 2.092429 ACTGCACAGGAAAGAGGAAACA 60.092 45.455 2.21 0.00 0.00 2.83
129 139 2.551459 CTGCACAGGAAAGAGGAAACAG 59.449 50.000 0.00 0.00 0.00 3.16
215 272 0.601841 CGTGCGTAGGGTCCACTTTT 60.602 55.000 0.00 0.00 0.00 2.27
216 273 1.601166 GTGCGTAGGGTCCACTTTTT 58.399 50.000 0.00 0.00 0.00 1.94
233 290 0.391130 TTTTGGGAGAGACGATGGCG 60.391 55.000 0.00 0.00 44.79 5.69
248 305 2.505557 GCGTACCCAAGGACGTCG 60.506 66.667 9.92 0.00 41.13 5.12
255 312 1.660560 CCCAAGGACGTCGTATCCGT 61.661 60.000 11.72 0.00 41.52 4.69
258 315 1.135603 CAAGGACGTCGTATCCGTTGA 60.136 52.381 11.72 0.00 41.52 3.18
260 317 0.864797 GGACGTCGTATCCGTTGAGC 60.865 60.000 9.92 0.00 38.92 4.26
261 318 1.192436 GACGTCGTATCCGTTGAGCG 61.192 60.000 0.00 0.00 38.92 5.03
314 371 0.400594 GCCCCACTAACCTGAACAGT 59.599 55.000 1.18 0.00 0.00 3.55
320 377 3.005050 CCACTAACCTGAACAGTACGACA 59.995 47.826 0.00 0.00 0.00 4.35
356 416 3.901797 CTCAACTGTGGGGACGGGC 62.902 68.421 0.00 0.00 0.00 6.13
414 484 2.509336 CCTCGATGACACGTGGGC 60.509 66.667 21.57 12.05 41.31 5.36
415 485 2.573869 CTCGATGACACGTGGGCT 59.426 61.111 21.57 2.82 34.70 5.19
450 520 4.541482 CCACGCGTCATGCATGCC 62.541 66.667 22.25 10.13 46.97 4.40
494 577 3.470567 CACCTGAGAACGACGCGC 61.471 66.667 5.73 0.00 0.00 6.86
495 578 3.973516 ACCTGAGAACGACGCGCA 61.974 61.111 5.73 0.00 0.00 6.09
496 579 2.507102 CCTGAGAACGACGCGCAT 60.507 61.111 5.73 0.00 0.00 4.73
498 581 1.341802 CTGAGAACGACGCGCATTC 59.658 57.895 5.73 7.83 0.00 2.67
499 582 2.313374 GAGAACGACGCGCATTCG 59.687 61.111 22.84 22.84 42.36 3.34
512 597 1.498865 GCATTCGCCATGGACCTACG 61.499 60.000 18.40 9.35 32.81 3.51
513 598 0.880278 CATTCGCCATGGACCTACGG 60.880 60.000 18.40 0.00 0.00 4.02
520 605 1.677820 CCATGGACCTACGGAAACCAC 60.678 57.143 5.56 0.00 33.38 4.16
523 608 0.321034 GGACCTACGGAAACCACACC 60.321 60.000 0.00 0.00 0.00 4.16
528 613 2.590575 CGGAAACCACACCGCACT 60.591 61.111 0.00 0.00 42.55 4.40
539 624 1.669115 ACCGCACTCACTGACATGC 60.669 57.895 0.00 1.72 34.66 4.06
543 628 1.004560 CACTCACTGACATGCGGGT 60.005 57.895 0.00 0.00 0.00 5.28
544 629 0.603707 CACTCACTGACATGCGGGTT 60.604 55.000 0.00 0.00 0.00 4.11
546 631 1.354337 CTCACTGACATGCGGGTTCG 61.354 60.000 0.00 0.00 39.81 3.95
577 662 1.524621 CCCCACGCATCAGCCTTAG 60.525 63.158 0.00 0.00 37.52 2.18
616 701 4.660938 GAAGCACCCCCGCAACCT 62.661 66.667 0.00 0.00 0.00 3.50
674 759 4.547367 GCCCTCCCAACGATCCCG 62.547 72.222 0.00 0.00 42.50 5.14
938 1029 2.755655 TCTCCTCTCGATCCACAGAAAC 59.244 50.000 0.00 0.00 0.00 2.78
942 1033 1.413767 CTCGATCCACAGAAACCGCG 61.414 60.000 0.00 0.00 0.00 6.46
943 1034 2.785258 GATCCACAGAAACCGCGC 59.215 61.111 0.00 0.00 0.00 6.86
944 1035 2.031919 ATCCACAGAAACCGCGCA 59.968 55.556 8.75 0.00 0.00 6.09
945 1036 1.573829 GATCCACAGAAACCGCGCAA 61.574 55.000 8.75 0.00 0.00 4.85
946 1037 1.577328 ATCCACAGAAACCGCGCAAG 61.577 55.000 8.75 0.00 43.44 4.01
947 1038 2.250939 CCACAGAAACCGCGCAAGA 61.251 57.895 8.75 0.00 43.02 3.02
948 1039 1.646540 CACAGAAACCGCGCAAGAA 59.353 52.632 8.75 0.00 43.02 2.52
949 1040 0.384725 CACAGAAACCGCGCAAGAAG 60.385 55.000 8.75 0.00 43.02 2.85
950 1041 1.441016 CAGAAACCGCGCAAGAAGC 60.441 57.895 8.75 0.00 43.02 3.86
951 1042 1.891919 AGAAACCGCGCAAGAAGCA 60.892 52.632 8.75 0.00 46.13 3.91
952 1043 1.725973 GAAACCGCGCAAGAAGCAC 60.726 57.895 8.75 0.00 46.13 4.40
953 1044 3.194272 AAACCGCGCAAGAAGCACC 62.194 57.895 8.75 0.00 46.13 5.01
957 1048 3.127533 GCGCAAGAAGCACCCGAT 61.128 61.111 0.30 0.00 46.13 4.18
958 1049 3.093278 CGCAAGAAGCACCCGATC 58.907 61.111 0.00 0.00 46.13 3.69
959 1050 2.464459 CGCAAGAAGCACCCGATCC 61.464 63.158 0.00 0.00 46.13 3.36
960 1051 2.115291 GCAAGAAGCACCCGATCCC 61.115 63.158 0.00 0.00 44.79 3.85
961 1052 1.452108 CAAGAAGCACCCGATCCCC 60.452 63.158 0.00 0.00 0.00 4.81
962 1053 2.680370 AAGAAGCACCCGATCCCCC 61.680 63.158 0.00 0.00 0.00 5.40
963 1054 3.407967 GAAGCACCCGATCCCCCA 61.408 66.667 0.00 0.00 0.00 4.96
964 1055 2.938798 AAGCACCCGATCCCCCAA 60.939 61.111 0.00 0.00 0.00 4.12
965 1056 2.893682 GAAGCACCCGATCCCCCAAG 62.894 65.000 0.00 0.00 0.00 3.61
966 1057 4.506255 GCACCCGATCCCCCAAGG 62.506 72.222 0.00 0.00 0.00 3.61
967 1058 4.506255 CACCCGATCCCCCAAGGC 62.506 72.222 0.00 0.00 34.51 4.35
977 1068 2.713967 CCCCAAGGCAAATCGGCAG 61.714 63.158 0.00 0.00 44.47 4.85
978 1069 2.713967 CCCAAGGCAAATCGGCAGG 61.714 63.158 0.00 0.00 44.47 4.85
990 1081 2.586357 GGCAGGAAGATCGCCGTC 60.586 66.667 2.56 0.00 35.79 4.79
991 1082 2.956964 GCAGGAAGATCGCCGTCG 60.957 66.667 2.56 0.00 0.00 5.12
1080 1174 1.144936 CTTCTCGGCCATGGAGGTC 59.855 63.158 18.40 0.00 40.61 3.85
1177 1271 2.338620 CCTGGAACGCGACTGTCA 59.661 61.111 15.93 2.55 0.00 3.58
1188 1282 0.939577 CGACTGTCAGGTTCACCGTG 60.940 60.000 8.73 0.00 42.08 4.94
1191 1285 3.041940 GTCAGGTTCACCGTGCCG 61.042 66.667 0.00 0.00 42.08 5.69
1278 1372 2.187946 GAGGTCCACATCCCGCTG 59.812 66.667 0.00 0.00 0.00 5.18
1281 1375 2.660064 GGTCCACATCCCGCTGTCT 61.660 63.158 0.00 0.00 0.00 3.41
1285 1379 1.593787 CACATCCCGCTGTCTGAGT 59.406 57.895 0.00 0.00 0.00 3.41
1293 1387 0.243365 CGCTGTCTGAGTTGCTCTCT 59.757 55.000 9.94 0.00 43.13 3.10
1305 1399 3.160047 CTCTCTGGCGCCCCTGAT 61.160 66.667 26.77 0.00 38.26 2.90
1395 1489 3.321111 TCCTCAACTTCTCGTACAAGCTT 59.679 43.478 0.00 0.00 0.00 3.74
1398 1492 3.131396 CAACTTCTCGTACAAGCTTGGT 58.869 45.455 29.18 17.13 0.00 3.67
1404 1498 1.000506 TCGTACAAGCTTGGTGAGGTC 59.999 52.381 29.18 10.53 34.30 3.85
1584 1678 3.066190 CCTCAGTCCGCGTACCCA 61.066 66.667 4.92 0.00 0.00 4.51
1764 1858 3.702048 GTGACGGCCTACCCAGCA 61.702 66.667 0.00 0.00 0.00 4.41
1983 2077 4.928140 GGCATGGGGATGGGCCTG 62.928 72.222 4.53 0.00 43.09 4.85
2111 2205 1.202200 CGGTGGCTTCGACTTCTAGAG 60.202 57.143 0.00 0.00 0.00 2.43
2113 2207 1.202582 GTGGCTTCGACTTCTAGAGCA 59.797 52.381 5.46 0.00 0.00 4.26
2135 2229 3.692101 AGTCGAGGAGGATAAGATATGCG 59.308 47.826 0.00 0.00 0.00 4.73
2157 2251 2.031683 GCAGCACAGTTCTTTTGTACGT 59.968 45.455 0.00 0.00 0.00 3.57
2158 2252 3.844943 GCAGCACAGTTCTTTTGTACGTC 60.845 47.826 0.00 0.00 0.00 4.34
2181 2275 7.255139 CGTCCTTGGTATTTCTTCAGTTCTTTT 60.255 37.037 0.00 0.00 0.00 2.27
2182 2276 8.414003 GTCCTTGGTATTTCTTCAGTTCTTTTT 58.586 33.333 0.00 0.00 0.00 1.94
2183 2277 8.413229 TCCTTGGTATTTCTTCAGTTCTTTTTG 58.587 33.333 0.00 0.00 0.00 2.44
2184 2278 7.169813 CCTTGGTATTTCTTCAGTTCTTTTTGC 59.830 37.037 0.00 0.00 0.00 3.68
2189 2283 4.552166 TCTTCAGTTCTTTTTGCCTTCG 57.448 40.909 0.00 0.00 0.00 3.79
2218 2312 4.834892 CAAAATCGCCGGCGCCTG 62.835 66.667 42.78 29.42 39.59 4.85
2292 2386 9.490663 GATATATTGTGAAACCTTTTTGTCTCG 57.509 33.333 0.00 0.00 34.36 4.04
2301 2395 5.223449 ACCTTTTTGTCTCGATTGGACTA 57.777 39.130 5.08 0.00 35.04 2.59
2335 2429 4.010667 ACTTGGCCGTATTGTCTTTGTA 57.989 40.909 0.00 0.00 0.00 2.41
2346 2440 8.116753 CCGTATTGTCTTTGTACTCATTCATTC 58.883 37.037 0.00 0.00 0.00 2.67
2350 2444 7.905604 TGTCTTTGTACTCATTCATTCGATT 57.094 32.000 0.00 0.00 0.00 3.34
2459 2564 1.202031 GGCGTGACGGTGAATGAATTC 60.202 52.381 7.25 0.00 37.31 2.17
2460 2565 1.202031 GCGTGACGGTGAATGAATTCC 60.202 52.381 7.25 0.00 35.97 3.01
2463 2568 1.276705 TGACGGTGAATGAATTCCGGA 59.723 47.619 0.00 0.00 46.06 5.14
2488 2593 5.930135 AGTCTGGTGTGTTCTTATTGACTT 58.070 37.500 0.00 0.00 0.00 3.01
2497 2602 8.169268 GTGTGTTCTTATTGACTTCTTTATCGG 58.831 37.037 0.00 0.00 0.00 4.18
2503 2608 1.822990 TGACTTCTTTATCGGTCGGCT 59.177 47.619 0.00 0.00 0.00 5.52
2549 2654 3.013219 GAGGAAATTTCTGCTCTGGGTC 58.987 50.000 17.42 0.00 0.00 4.46
2566 2673 1.270893 GGTCAGTGGAAGAGTGGGTTC 60.271 57.143 0.00 0.00 0.00 3.62
2567 2674 1.416401 GTCAGTGGAAGAGTGGGTTCA 59.584 52.381 0.00 0.00 0.00 3.18
2569 2676 0.398318 AGTGGAAGAGTGGGTTCAGC 59.602 55.000 0.00 0.00 0.00 4.26
2570 2677 0.606673 GTGGAAGAGTGGGTTCAGCC 60.607 60.000 0.00 0.00 0.00 4.85
2575 2682 1.070786 GAGTGGGTTCAGCCGTTCA 59.929 57.895 0.00 0.00 38.44 3.18
2588 2695 3.066760 CAGCCGTTCAGGAAAGAAACTTT 59.933 43.478 0.00 0.00 45.00 2.66
2652 2760 0.751277 TATGGTGCGCCTTTCCATGG 60.751 55.000 23.73 4.97 41.34 3.66
2653 2761 4.133796 GGTGCGCCTTTCCATGGC 62.134 66.667 9.68 0.00 46.42 4.40
2706 2834 2.615869 GTGCAGACCAGAACTGATCTC 58.384 52.381 3.19 0.00 35.73 2.75
2744 2881 7.831691 TTAAGAAAATGATCCCAACAACAGA 57.168 32.000 0.00 0.00 0.00 3.41
2781 2918 0.036732 CAACTGCTGGCCCTGTTCTA 59.963 55.000 0.00 0.00 0.00 2.10
2793 2930 2.159627 CCCTGTTCTACGCAACAATGTC 59.840 50.000 0.00 0.00 35.83 3.06
2795 2932 3.120546 CCTGTTCTACGCAACAATGTCAG 60.121 47.826 0.00 0.00 35.83 3.51
2801 2939 7.041712 TGTTCTACGCAACAATGTCAGAAAATA 60.042 33.333 0.00 0.00 33.21 1.40
2807 3161 7.274033 ACGCAACAATGTCAGAAAATAATGATG 59.726 33.333 0.00 0.00 0.00 3.07
2838 3192 2.083774 CCCTGAGCTTCGCAACAAATA 58.916 47.619 0.00 0.00 0.00 1.40
2895 3262 3.111853 TGCGAATAGACAGGCCTATTG 57.888 47.619 3.98 0.00 38.91 1.90
2936 3303 0.608640 AAGACAGTCCTGTTAGGGCG 59.391 55.000 0.79 0.00 46.90 6.13
2955 3322 1.227031 TCTCCGTTTGTTCGTGCGT 60.227 52.632 0.00 0.00 0.00 5.24
2973 3340 6.696148 TCGTGCGTAATTTTGTTGGTAAAAAT 59.304 30.769 0.00 0.00 38.54 1.82
3039 3718 7.252708 TGTGTCAATGTTGCTCAATGATATTC 58.747 34.615 4.21 0.00 38.11 1.75
3042 3721 8.525316 TGTCAATGTTGCTCAATGATATTCTTT 58.475 29.630 4.21 0.00 38.11 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 55 3.258228 CGGAAAGAGAGAAAGAGAAGGC 58.742 50.000 0.00 0.00 0.00 4.35
49 56 3.259625 ACCGGAAAGAGAGAAAGAGAAGG 59.740 47.826 9.46 0.00 0.00 3.46
62 69 1.593209 GTGCGTGTGACCGGAAAGA 60.593 57.895 9.46 0.00 0.00 2.52
63 70 1.557443 GAGTGCGTGTGACCGGAAAG 61.557 60.000 9.46 0.00 0.00 2.62
64 71 1.593209 GAGTGCGTGTGACCGGAAA 60.593 57.895 9.46 0.00 0.00 3.13
75 82 2.143925 GCTAAGGAAAAGTGAGTGCGT 58.856 47.619 0.00 0.00 0.00 5.24
120 130 4.467198 TCGTATTCCCTTCTGTTTCCTC 57.533 45.455 0.00 0.00 0.00 3.71
123 133 5.294552 CAGGATTCGTATTCCCTTCTGTTTC 59.705 44.000 0.00 0.00 33.45 2.78
125 135 4.469945 TCAGGATTCGTATTCCCTTCTGTT 59.530 41.667 0.00 0.00 33.45 3.16
127 137 4.372656 GTCAGGATTCGTATTCCCTTCTG 58.627 47.826 0.00 0.00 33.45 3.02
128 138 3.388350 GGTCAGGATTCGTATTCCCTTCT 59.612 47.826 0.00 0.00 33.45 2.85
129 139 3.388350 AGGTCAGGATTCGTATTCCCTTC 59.612 47.826 0.00 0.00 33.45 3.46
215 272 1.218047 CGCCATCGTCTCTCCCAAA 59.782 57.895 0.00 0.00 0.00 3.28
216 273 2.892640 CGCCATCGTCTCTCCCAA 59.107 61.111 0.00 0.00 0.00 4.12
226 283 1.520787 GTCCTTGGGTACGCCATCG 60.521 63.158 7.55 1.36 42.43 3.84
233 290 1.066152 GGATACGACGTCCTTGGGTAC 59.934 57.143 10.58 1.77 32.85 3.34
234 291 1.392589 GGATACGACGTCCTTGGGTA 58.607 55.000 10.58 6.35 32.85 3.69
295 352 0.400594 ACTGTTCAGGTTAGTGGGGC 59.599 55.000 4.82 0.00 0.00 5.80
298 355 3.005050 TGTCGTACTGTTCAGGTTAGTGG 59.995 47.826 4.82 0.00 0.00 4.00
314 371 6.432783 AGGGTGAATGAATTGAAATTGTCGTA 59.567 34.615 0.00 0.00 0.00 3.43
320 377 7.156673 CAGTTGAGGGTGAATGAATTGAAATT 58.843 34.615 0.00 0.00 0.00 1.82
471 554 0.031721 GTCGTTCTCAGGTGGTTCGT 59.968 55.000 0.00 0.00 0.00 3.85
472 555 1.002250 CGTCGTTCTCAGGTGGTTCG 61.002 60.000 0.00 0.00 0.00 3.95
473 556 1.282930 GCGTCGTTCTCAGGTGGTTC 61.283 60.000 0.00 0.00 0.00 3.62
478 561 2.765250 AATGCGCGTCGTTCTCAGGT 62.765 55.000 8.43 0.00 0.00 4.00
479 562 2.014093 GAATGCGCGTCGTTCTCAGG 62.014 60.000 20.74 0.00 37.64 3.86
494 577 2.605094 CGTAGGTCCATGGCGAATG 58.395 57.895 6.96 0.00 35.89 2.67
512 597 1.525077 TGAGTGCGGTGTGGTTTCC 60.525 57.895 0.00 0.00 0.00 3.13
513 598 0.814010 AGTGAGTGCGGTGTGGTTTC 60.814 55.000 0.00 0.00 0.00 2.78
520 605 1.904852 GCATGTCAGTGAGTGCGGTG 61.905 60.000 13.01 0.00 0.00 4.94
524 609 2.393768 CCCGCATGTCAGTGAGTGC 61.394 63.158 16.71 16.71 0.00 4.40
525 610 0.603707 AACCCGCATGTCAGTGAGTG 60.604 55.000 0.00 0.00 0.00 3.51
526 611 0.320771 GAACCCGCATGTCAGTGAGT 60.321 55.000 0.00 0.00 0.00 3.41
527 612 1.354337 CGAACCCGCATGTCAGTGAG 61.354 60.000 0.00 0.00 0.00 3.51
528 613 1.374125 CGAACCCGCATGTCAGTGA 60.374 57.895 0.00 0.00 0.00 3.41
559 644 1.524621 CTAAGGCTGATGCGTGGGG 60.525 63.158 0.00 0.00 40.82 4.96
577 662 1.883084 CACGCGGATACTTGGCCTC 60.883 63.158 12.47 0.00 0.00 4.70
586 671 2.055633 TGCTTCTCCCACGCGGATA 61.056 57.895 12.47 0.00 41.00 2.59
608 693 4.821589 GAGCGGAGGAGGTTGCGG 62.822 72.222 0.00 0.00 32.14 5.69
674 759 3.587797 TGTATCCGAAGACTTGGTGAC 57.412 47.619 0.00 0.00 0.00 3.67
942 1033 2.115291 GGGATCGGGTGCTTCTTGC 61.115 63.158 0.00 0.00 43.25 4.01
943 1034 1.452108 GGGGATCGGGTGCTTCTTG 60.452 63.158 0.00 0.00 0.00 3.02
944 1035 2.680370 GGGGGATCGGGTGCTTCTT 61.680 63.158 0.00 0.00 0.00 2.52
945 1036 3.090532 GGGGGATCGGGTGCTTCT 61.091 66.667 0.00 0.00 0.00 2.85
946 1037 2.893682 CTTGGGGGATCGGGTGCTTC 62.894 65.000 0.00 0.00 0.00 3.86
947 1038 2.938798 TTGGGGGATCGGGTGCTT 60.939 61.111 0.00 0.00 0.00 3.91
948 1039 3.411517 CTTGGGGGATCGGGTGCT 61.412 66.667 0.00 0.00 0.00 4.40
949 1040 4.506255 CCTTGGGGGATCGGGTGC 62.506 72.222 0.00 0.00 37.23 5.01
950 1041 4.506255 GCCTTGGGGGATCGGGTG 62.506 72.222 0.00 0.00 37.23 4.61
952 1043 2.588029 ATTTGCCTTGGGGGATCGGG 62.588 60.000 0.00 0.00 37.23 5.14
953 1044 1.076044 ATTTGCCTTGGGGGATCGG 60.076 57.895 0.00 0.00 37.23 4.18
954 1045 1.447317 CGATTTGCCTTGGGGGATCG 61.447 60.000 0.00 0.00 34.56 3.69
955 1046 1.109323 CCGATTTGCCTTGGGGGATC 61.109 60.000 0.00 0.00 37.23 3.36
956 1047 1.076044 CCGATTTGCCTTGGGGGAT 60.076 57.895 0.00 0.00 37.23 3.85
957 1048 2.358619 CCGATTTGCCTTGGGGGA 59.641 61.111 0.00 0.00 37.23 4.81
958 1049 3.460868 GCCGATTTGCCTTGGGGG 61.461 66.667 0.00 0.00 38.36 5.40
959 1050 2.679642 TGCCGATTTGCCTTGGGG 60.680 61.111 0.00 0.00 0.00 4.96
960 1051 2.713967 CCTGCCGATTTGCCTTGGG 61.714 63.158 0.00 0.00 0.00 4.12
961 1052 1.250154 TTCCTGCCGATTTGCCTTGG 61.250 55.000 0.00 0.00 0.00 3.61
962 1053 0.171903 CTTCCTGCCGATTTGCCTTG 59.828 55.000 0.00 0.00 0.00 3.61
963 1054 0.038166 TCTTCCTGCCGATTTGCCTT 59.962 50.000 0.00 0.00 0.00 4.35
964 1055 0.257039 ATCTTCCTGCCGATTTGCCT 59.743 50.000 0.00 0.00 0.00 4.75
965 1056 0.665298 GATCTTCCTGCCGATTTGCC 59.335 55.000 0.00 0.00 0.00 4.52
966 1057 0.305922 CGATCTTCCTGCCGATTTGC 59.694 55.000 0.00 0.00 0.00 3.68
967 1058 0.305922 GCGATCTTCCTGCCGATTTG 59.694 55.000 0.00 0.00 0.00 2.32
968 1059 0.815615 GGCGATCTTCCTGCCGATTT 60.816 55.000 0.00 0.00 39.30 2.17
977 1068 2.651232 CGACGACGGCGATCTTCC 60.651 66.667 22.49 0.00 41.64 3.46
978 1069 1.933519 GACGACGACGGCGATCTTC 60.934 63.158 32.70 13.40 44.46 2.87
1317 1411 1.069378 GGTAGGCGACGAACTTGACG 61.069 60.000 0.00 0.00 0.00 4.35
1709 1803 1.072505 GGCTTTCCTGACGGACCAA 59.927 57.895 0.00 0.00 39.60 3.67
1875 1969 3.387947 CCGCCGTACCCTCCTTGT 61.388 66.667 0.00 0.00 0.00 3.16
1923 2017 1.443407 CTGCTGCTGGTAGCCGTAT 59.557 57.895 8.09 0.00 41.51 3.06
2103 2197 1.946768 CCTCCTCGACTGCTCTAGAAG 59.053 57.143 0.00 0.00 0.00 2.85
2111 2205 4.676723 GCATATCTTATCCTCCTCGACTGC 60.677 50.000 0.00 0.00 0.00 4.40
2113 2207 3.692101 CGCATATCTTATCCTCCTCGACT 59.308 47.826 0.00 0.00 0.00 4.18
2118 2212 2.499289 CTGCCGCATATCTTATCCTCCT 59.501 50.000 0.00 0.00 0.00 3.69
2135 2229 2.602217 CGTACAAAAGAACTGTGCTGCC 60.602 50.000 0.00 0.00 0.00 4.85
2157 2251 8.413229 CAAAAAGAACTGAAGAAATACCAAGGA 58.587 33.333 0.00 0.00 0.00 3.36
2158 2252 7.169813 GCAAAAAGAACTGAAGAAATACCAAGG 59.830 37.037 0.00 0.00 0.00 3.61
2189 2283 3.182182 GGCGATTTTGAGCAGAAAATCC 58.818 45.455 19.58 14.59 44.37 3.01
2218 2312 2.859273 ATCACACTAGCTGCGCCCAC 62.859 60.000 4.18 0.00 0.00 4.61
2221 2315 1.143305 CATATCACACTAGCTGCGCC 58.857 55.000 4.18 0.00 0.00 6.53
2277 2371 4.887655 AGTCCAATCGAGACAAAAAGGTTT 59.112 37.500 6.13 0.00 36.68 3.27
2280 2374 5.479306 TCTAGTCCAATCGAGACAAAAAGG 58.521 41.667 6.13 0.00 36.68 3.11
2292 2386 9.474920 CAAGTTATCAGAGATTCTAGTCCAATC 57.525 37.037 0.00 0.00 0.00 2.67
2301 2395 3.452627 ACGGCCAAGTTATCAGAGATTCT 59.547 43.478 2.24 0.00 0.00 2.40
2335 2429 6.313658 TGATCAAACGAATCGAATGAATGAGT 59.686 34.615 10.55 0.00 31.87 3.41
2459 2564 0.038159 GAACACACCAGACTCTCCGG 60.038 60.000 0.00 0.00 0.00 5.14
2460 2565 0.962489 AGAACACACCAGACTCTCCG 59.038 55.000 0.00 0.00 0.00 4.63
2463 2568 5.305644 AGTCAATAAGAACACACCAGACTCT 59.694 40.000 0.00 0.00 0.00 3.24
2488 2593 0.174845 CACCAGCCGACCGATAAAGA 59.825 55.000 0.00 0.00 0.00 2.52
2497 2602 0.526211 GGAAAATTCCACCAGCCGAC 59.474 55.000 7.32 0.00 46.76 4.79
2519 2624 7.120285 CAGAGCAGAAATTTCCTCACAAGATAA 59.880 37.037 20.05 0.00 0.00 1.75
2520 2625 6.596888 CAGAGCAGAAATTTCCTCACAAGATA 59.403 38.462 20.05 0.00 0.00 1.98
2549 2654 1.879796 GCTGAACCCACTCTTCCACTG 60.880 57.143 0.00 0.00 0.00 3.66
2566 2673 2.222027 AGTTTCTTTCCTGAACGGCTG 58.778 47.619 0.00 0.00 0.00 4.85
2567 2674 2.640316 AGTTTCTTTCCTGAACGGCT 57.360 45.000 0.00 0.00 0.00 5.52
2569 2676 3.303791 CCGAAAGTTTCTTTCCTGAACGG 60.304 47.826 13.56 9.06 0.00 4.44
2570 2677 3.311596 ACCGAAAGTTTCTTTCCTGAACG 59.688 43.478 13.56 4.85 0.00 3.95
2575 2682 3.800531 TCGAACCGAAAGTTTCTTTCCT 58.199 40.909 13.56 2.62 39.40 3.36
2660 2768 1.815866 GCAGTTGGCACCAAACAGT 59.184 52.632 3.10 0.00 43.97 3.55
2662 2770 1.683707 TGGCAGTTGGCACCAAACA 60.684 52.632 3.10 0.00 46.12 2.83
2781 2918 6.676950 TCATTATTTTCTGACATTGTTGCGT 58.323 32.000 0.00 0.00 0.00 5.24
2793 2930 9.512435 GGAGATTGTTCACATCATTATTTTCTG 57.488 33.333 0.00 0.00 0.00 3.02
2795 2932 8.689972 AGGGAGATTGTTCACATCATTATTTTC 58.310 33.333 0.00 0.00 0.00 2.29
2801 2939 5.183530 TCAGGGAGATTGTTCACATCATT 57.816 39.130 0.00 0.00 0.00 2.57
2807 3161 2.777832 AGCTCAGGGAGATTGTTCAC 57.222 50.000 0.00 0.00 0.00 3.18
2838 3192 4.145052 GGACAGTTCAGATCCTTTTTGGT 58.855 43.478 0.00 0.00 37.07 3.67
2867 3234 4.202050 GGCCTGTCTATTCGCATCATTTTT 60.202 41.667 0.00 0.00 0.00 1.94
2936 3303 1.200839 CGCACGAACAAACGGAGAC 59.799 57.895 0.00 0.00 37.61 3.36
2973 3340 8.089115 TGTATTTTGTTGACGACATGAACATA 57.911 30.769 0.00 0.00 38.26 2.29
3011 3378 1.677942 TGAGCAACATTGACACAGCA 58.322 45.000 0.00 0.00 0.00 4.41
3013 3380 4.492791 TCATTGAGCAACATTGACACAG 57.507 40.909 0.00 0.00 35.06 3.66
3039 3718 5.863935 GGCAGCCATGTTAGTTTTCTTAAAG 59.136 40.000 6.55 0.00 0.00 1.85
3042 3721 3.761752 GGGCAGCCATGTTAGTTTTCTTA 59.238 43.478 15.19 0.00 0.00 2.10
3059 3738 0.535102 AGACGAAAACACAGGGGCAG 60.535 55.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.