Multiple sequence alignment - TraesCS4A01G253100

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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 TraesCS4A01G253100 chr4A 100.000 3353 0 0 1 3353 565429040 565432392 0.000000e+00 6192.0
1 TraesCS4A01G253100 chr4D 94.489 1252 57 6 1028 2277 36843926 36842685 0.000000e+00 1919.0
2 TraesCS4A01G253100 chr4D 87.001 1077 69 36 2303 3353 36842579 36841548 0.000000e+00 1147.0
3 TraesCS4A01G253100 chr4D 87.210 993 123 4 2 991 280782464 280783455 0.000000e+00 1127.0
4 TraesCS4A01G253100 chr4D 85.650 446 45 14 2912 3352 36840466 36840035 5.100000e-123 451.0
5 TraesCS4A01G253100 chr5A 97.071 990 29 0 1 990 3046139 3045150 0.000000e+00 1668.0
6 TraesCS4A01G253100 chr1A 89.707 991 100 2 1 990 331274528 331273539 0.000000e+00 1264.0
7 TraesCS4A01G253100 chr1A 93.886 736 45 0 255 990 308905856 308906591 0.000000e+00 1110.0
8 TraesCS4A01G253100 chr1A 98.208 614 11 0 1 614 520794807 520794194 0.000000e+00 1074.0
9 TraesCS4A01G253100 chr1A 89.414 444 40 5 1163 1605 488619043 488619480 1.360000e-153 553.0
10 TraesCS4A01G253100 chr1A 94.154 325 19 0 1 325 308905554 308905878 2.320000e-136 496.0
11 TraesCS4A01G253100 chr7B 88.777 989 111 0 1 989 740027325 740028313 0.000000e+00 1212.0
12 TraesCS4A01G253100 chr7B 86.190 992 134 3 1 990 739553871 739552881 0.000000e+00 1070.0
13 TraesCS4A01G253100 chr1B 87.666 981 121 0 11 991 593506835 593507815 0.000000e+00 1142.0
14 TraesCS4A01G253100 chr1B 89.352 432 40 2 1174 1605 525909971 525909546 3.810000e-149 538.0
15 TraesCS4A01G253100 chr2A 90.937 662 60 0 1 662 655514911 655514250 0.000000e+00 891.0
16 TraesCS4A01G253100 chr4B 90.881 636 51 3 1728 2356 53863741 53863106 0.000000e+00 846.0
17 TraesCS4A01G253100 chr4B 87.387 444 45 6 2912 3352 53859642 53859207 1.800000e-137 499.0
18 TraesCS4A01G253100 chr4B 91.030 301 19 5 3056 3353 53861200 53860905 1.870000e-107 399.0
19 TraesCS4A01G253100 chr4B 89.680 281 23 5 1049 1324 53864402 53864123 1.480000e-93 353.0
20 TraesCS4A01G253100 chr4B 100.000 34 0 0 2357 2390 53862147 53862114 2.790000e-06 63.9


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 TraesCS4A01G253100 chr4A 565429040 565432392 3352 False 6192.000000 6192 100.000000 1 3353 1 chr4A.!!$F1 3352
1 TraesCS4A01G253100 chr4D 36840035 36843926 3891 True 1172.333333 1919 89.046667 1028 3353 3 chr4D.!!$R1 2325
2 TraesCS4A01G253100 chr4D 280782464 280783455 991 False 1127.000000 1127 87.210000 2 991 1 chr4D.!!$F1 989
3 TraesCS4A01G253100 chr5A 3045150 3046139 989 True 1668.000000 1668 97.071000 1 990 1 chr5A.!!$R1 989
4 TraesCS4A01G253100 chr1A 331273539 331274528 989 True 1264.000000 1264 89.707000 1 990 1 chr1A.!!$R1 989
5 TraesCS4A01G253100 chr1A 520794194 520794807 613 True 1074.000000 1074 98.208000 1 614 1 chr1A.!!$R2 613
6 TraesCS4A01G253100 chr1A 308905554 308906591 1037 False 803.000000 1110 94.020000 1 990 2 chr1A.!!$F2 989
7 TraesCS4A01G253100 chr7B 740027325 740028313 988 False 1212.000000 1212 88.777000 1 989 1 chr7B.!!$F1 988
8 TraesCS4A01G253100 chr7B 739552881 739553871 990 True 1070.000000 1070 86.190000 1 990 1 chr7B.!!$R1 989
9 TraesCS4A01G253100 chr1B 593506835 593507815 980 False 1142.000000 1142 87.666000 11 991 1 chr1B.!!$F1 980
10 TraesCS4A01G253100 chr2A 655514250 655514911 661 True 891.000000 891 90.937000 1 662 1 chr2A.!!$R1 661
11 TraesCS4A01G253100 chr4B 53859207 53864402 5195 True 432.180000 846 91.795600 1049 3353 5 chr4B.!!$R1 2304


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
145 146 2.110006 GGAGCTTCCCATCTCCGC 59.890 66.667 0.0 0.0 39.43 5.54 F
998 1048 2.825836 CCAGCCATCCCGCAAGTC 60.826 66.667 0.0 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1015 1065 0.112412 TGGGGCTTCTTGGAACCTTC 59.888 55.0 0.0 0.0 0.0 3.46 R
2828 4609 0.250793 CCCAACCCGCATACACTGTA 59.749 55.0 0.0 0.0 0.0 2.74 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
145 146 2.110006 GGAGCTTCCCATCTCCGC 59.890 66.667 0.00 0.00 39.43 5.54
325 374 3.198853 GGTGGCTTCTCTTTGGATCTAGT 59.801 47.826 0.00 0.00 0.00 2.57
889 939 4.193334 CAGCACGATCCGGAGCGA 62.193 66.667 44.86 5.95 43.75 4.93
998 1048 2.825836 CCAGCCATCCCGCAAGTC 60.826 66.667 0.00 0.00 0.00 3.01
999 1049 3.197790 CAGCCATCCCGCAAGTCG 61.198 66.667 0.00 0.00 38.08 4.18
1013 1063 5.127371 CGCAAGTCGGAATAACTAAACTC 57.873 43.478 0.00 0.00 33.78 3.01
1014 1064 4.259292 CGCAAGTCGGAATAACTAAACTCG 60.259 45.833 0.00 0.00 33.78 4.18
1015 1065 4.032558 GCAAGTCGGAATAACTAAACTCGG 59.967 45.833 0.00 0.00 0.00 4.63
1016 1066 5.404946 CAAGTCGGAATAACTAAACTCGGA 58.595 41.667 0.00 0.00 0.00 4.55
1017 1067 5.649782 AGTCGGAATAACTAAACTCGGAA 57.350 39.130 0.00 0.00 0.00 4.30
1018 1068 5.648572 AGTCGGAATAACTAAACTCGGAAG 58.351 41.667 0.00 0.00 0.00 3.46
1019 1069 4.802563 GTCGGAATAACTAAACTCGGAAGG 59.197 45.833 0.00 0.00 0.00 3.46
1020 1070 4.463891 TCGGAATAACTAAACTCGGAAGGT 59.536 41.667 0.00 0.00 0.00 3.50
1021 1071 5.047092 TCGGAATAACTAAACTCGGAAGGTT 60.047 40.000 0.00 0.00 36.14 3.50
1022 1072 5.290400 CGGAATAACTAAACTCGGAAGGTTC 59.710 44.000 0.00 0.00 33.42 3.62
1023 1073 5.583854 GGAATAACTAAACTCGGAAGGTTCC 59.416 44.000 0.00 0.00 44.05 3.62
1061 1111 1.261619 CTCGACTGCTGTTGTTGGTTC 59.738 52.381 10.46 0.00 0.00 3.62
1068 1118 2.159254 TGCTGTTGTTGGTTCTCTTTGC 60.159 45.455 0.00 0.00 0.00 3.68
1091 1141 3.248363 TGTTGCTGAACAATCGAACTGAG 59.752 43.478 4.99 0.00 41.27 3.35
1141 1192 1.489230 ACTTTACCCCATCCGTCCATC 59.511 52.381 0.00 0.00 0.00 3.51
1200 1251 2.675348 GGAAGAACTGATGAAGGAAGCG 59.325 50.000 0.00 0.00 0.00 4.68
1269 1320 1.111277 TAAGCACGCTCCAGCATCTA 58.889 50.000 0.00 0.00 42.21 1.98
1297 1354 2.501222 CGACCAAGACCGACGACG 60.501 66.667 0.00 0.00 39.43 5.12
1298 1355 2.949106 GACCAAGACCGACGACGA 59.051 61.111 9.28 0.00 42.66 4.20
1299 1356 1.154263 GACCAAGACCGACGACGAG 60.154 63.158 9.28 1.47 42.66 4.18
1445 1502 0.983378 ATGGAGAAGGACCTTCCCCG 60.983 60.000 27.38 0.00 40.57 5.73
1511 1568 4.640855 CGTGGTGCTGGTCGTCGT 62.641 66.667 0.00 0.00 0.00 4.34
1541 1598 1.599047 CGGTGATCTGGTTCTGCCT 59.401 57.895 0.00 0.00 38.35 4.75
1542 1599 0.460987 CGGTGATCTGGTTCTGCCTC 60.461 60.000 0.00 0.00 38.35 4.70
1562 1619 4.637489 CGGAGGCGAGCGATGGAG 62.637 72.222 0.00 0.00 0.00 3.86
1695 1753 3.182572 CCGACGAAGAAACAAGAACAGAG 59.817 47.826 0.00 0.00 0.00 3.35
1722 1780 0.764890 TGGAGGGACACAACTGGAAG 59.235 55.000 0.00 0.00 42.29 3.46
1726 1784 2.368875 GAGGGACACAACTGGAAGAGAA 59.631 50.000 0.00 0.00 37.43 2.87
1771 2136 3.580022 TGGCAGTCATCGATTCCAGATAT 59.420 43.478 0.00 0.00 0.00 1.63
1813 2178 2.391879 GCAAGTTCTACTTCGACGTGT 58.608 47.619 4.57 0.00 36.03 4.49
1816 2181 1.538950 AGTTCTACTTCGACGTGTCCC 59.461 52.381 4.57 0.00 0.00 4.46
1830 2195 4.377760 TCCCCCTCGAAGCTCGGT 62.378 66.667 5.87 0.00 40.88 4.69
1885 2250 3.628646 ATGGACACCAAGGGAGCGC 62.629 63.158 0.00 0.00 36.95 5.92
1928 2293 2.514824 GGCGTTCCCTCATCTGGC 60.515 66.667 0.00 0.00 0.00 4.85
1972 2337 3.554129 CCTGTTCGTCATCGCCCATAATA 60.554 47.826 0.00 0.00 36.96 0.98
1973 2338 3.649073 TGTTCGTCATCGCCCATAATAG 58.351 45.455 0.00 0.00 36.96 1.73
2043 2411 0.389391 CCAAGGTGGATCGCGTCTAT 59.611 55.000 5.77 0.00 40.96 1.98
2046 2414 1.621992 AGGTGGATCGCGTCTATGAT 58.378 50.000 5.77 0.00 0.00 2.45
2141 2510 2.579873 TGTCTACTATCTGGGCCGTAC 58.420 52.381 0.00 0.00 0.00 3.67
2180 2549 3.110178 GCCGGAGACAAACGTCGG 61.110 66.667 5.05 5.32 38.51 4.79
2344 2799 0.937304 CCGGGATATGTTTGTGCTCG 59.063 55.000 0.00 0.00 0.00 5.03
2353 2808 7.387948 GGGATATGTTTGTGCTCGTCTAATTAT 59.612 37.037 0.00 0.00 0.00 1.28
2390 3803 8.980481 TCCCCTTTCTTCAAATCAGTATATTC 57.020 34.615 0.00 0.00 0.00 1.75
2391 3804 7.998964 TCCCCTTTCTTCAAATCAGTATATTCC 59.001 37.037 0.00 0.00 0.00 3.01
2392 3805 7.041098 CCCCTTTCTTCAAATCAGTATATTCCG 60.041 40.741 0.00 0.00 0.00 4.30
2393 3806 7.041098 CCCTTTCTTCAAATCAGTATATTCCGG 60.041 40.741 0.00 0.00 0.00 5.14
2394 3807 7.041098 CCTTTCTTCAAATCAGTATATTCCGGG 60.041 40.741 0.00 0.00 0.00 5.73
2395 3808 6.740944 TCTTCAAATCAGTATATTCCGGGA 57.259 37.500 0.00 0.00 0.00 5.14
2397 3810 8.430573 TCTTCAAATCAGTATATTCCGGGATA 57.569 34.615 4.49 4.49 0.00 2.59
2399 3812 9.102757 CTTCAAATCAGTATATTCCGGGATATG 57.897 37.037 23.53 10.18 0.00 1.78
2403 3816 8.792830 AATCAGTATATTCCGGGATATGTTTG 57.207 34.615 23.53 17.44 0.00 2.93
2429 3852 7.594758 GTGCACATTGAGTTTAGCTTTCATTTA 59.405 33.333 13.17 0.00 0.00 1.40
2456 4218 4.862641 TTATTTCTGAGGGAAAGGGGAG 57.137 45.455 0.00 0.00 45.61 4.30
2457 4219 2.133858 TTTCTGAGGGAAAGGGGAGT 57.866 50.000 0.00 0.00 38.81 3.85
2458 4220 2.133858 TTCTGAGGGAAAGGGGAGTT 57.866 50.000 0.00 0.00 0.00 3.01
2459 4221 3.285290 TTCTGAGGGAAAGGGGAGTTA 57.715 47.619 0.00 0.00 0.00 2.24
2466 4228 3.587951 AGGGAAAGGGGAGTTAGAGTTTC 59.412 47.826 0.00 0.00 0.00 2.78
2515 4278 4.029520 AGACAGTTCTACCATGATCTGCT 58.970 43.478 0.00 0.00 37.31 4.24
2522 4285 2.906691 ACCATGATCTGCTACTCTGC 57.093 50.000 0.00 0.00 0.00 4.26
2524 4287 2.770802 ACCATGATCTGCTACTCTGCTT 59.229 45.455 0.00 0.00 0.00 3.91
2555 4318 6.873605 CCTGGAAATTTTCATAGGAACAAACC 59.126 38.462 19.30 0.00 37.60 3.27
2563 4333 1.672529 TAGGAACAAACCCCCTACCC 58.327 55.000 0.00 0.00 0.00 3.69
2576 4346 2.360423 CCCCTACCCACCATAAGACTCT 60.360 54.545 0.00 0.00 0.00 3.24
2607 4377 9.512588 CTCTAAAATAAGATGACCATAAGGCAT 57.487 33.333 0.00 0.00 39.06 4.40
2611 4381 7.693969 AATAAGATGACCATAAGGCATAAGC 57.306 36.000 0.00 0.00 39.06 3.09
2633 4403 2.066393 CCGATCCAGGGCCTCAGAA 61.066 63.158 0.95 0.00 0.00 3.02
2634 4404 1.445095 CGATCCAGGGCCTCAGAAG 59.555 63.158 0.95 0.00 0.00 2.85
2636 4406 1.433121 GATCCAGGGCCTCAGAAGAT 58.567 55.000 0.95 0.70 0.00 2.40
2637 4407 1.347378 GATCCAGGGCCTCAGAAGATC 59.653 57.143 0.95 7.16 0.00 2.75
2638 4408 1.045350 TCCAGGGCCTCAGAAGATCG 61.045 60.000 0.95 0.00 0.00 3.69
2639 4409 1.445095 CAGGGCCTCAGAAGATCGG 59.555 63.158 0.95 0.00 0.00 4.18
2641 4411 2.066999 GGGCCTCAGAAGATCGGGT 61.067 63.158 0.84 0.00 0.00 5.28
2642 4412 1.144936 GGCCTCAGAAGATCGGGTG 59.855 63.158 0.00 0.00 0.00 4.61
2645 4415 0.103937 CCTCAGAAGATCGGGTGAGC 59.896 60.000 13.04 0.00 35.99 4.26
2646 4416 0.820226 CTCAGAAGATCGGGTGAGCA 59.180 55.000 7.91 0.00 31.29 4.26
2647 4417 0.532573 TCAGAAGATCGGGTGAGCAC 59.467 55.000 0.00 0.00 31.29 4.40
2648 4418 0.247460 CAGAAGATCGGGTGAGCACA 59.753 55.000 2.75 0.00 31.29 4.57
2649 4419 1.134580 CAGAAGATCGGGTGAGCACAT 60.135 52.381 2.75 0.00 31.29 3.21
2650 4420 1.137872 AGAAGATCGGGTGAGCACATC 59.862 52.381 2.75 0.00 31.29 3.06
2651 4421 0.179100 AAGATCGGGTGAGCACATCG 60.179 55.000 2.75 6.18 31.29 3.84
2652 4422 1.141881 GATCGGGTGAGCACATCGT 59.858 57.895 12.64 4.17 33.52 3.73
2653 4423 0.384309 GATCGGGTGAGCACATCGTA 59.616 55.000 12.64 4.15 33.52 3.43
2654 4424 0.385751 ATCGGGTGAGCACATCGTAG 59.614 55.000 12.64 0.00 33.52 3.51
2655 4425 1.878522 CGGGTGAGCACATCGTAGC 60.879 63.158 2.75 0.00 0.00 3.58
2670 4440 2.094700 TCGTAGCGCTGTTGAGAAATCT 60.095 45.455 22.90 0.00 0.00 2.40
2680 4450 5.964168 GCTGTTGAGAAATCTGATTGAATCG 59.036 40.000 3.22 0.00 0.00 3.34
2693 4471 0.249955 TGAATCGTGCATGGAGCTCA 59.750 50.000 17.19 1.87 45.94 4.26
2740 4518 2.919666 AAATGACGGTATGCAGCAAC 57.080 45.000 0.00 0.00 0.00 4.17
2753 4531 0.739462 CAGCAACGATTACGCTCCCA 60.739 55.000 0.00 0.00 43.96 4.37
2758 4536 2.440539 ACGATTACGCTCCCATCATC 57.559 50.000 0.00 0.00 43.96 2.92
2785 4566 2.044806 ATCATACCTGACCCTGCCGC 62.045 60.000 0.00 0.00 33.22 6.53
2805 4586 1.077644 CCGTCCGAGGAGAAGGAGA 60.078 63.158 0.00 0.00 37.58 3.71
2809 4590 1.407258 GTCCGAGGAGAAGGAGACATG 59.593 57.143 0.00 0.00 37.18 3.21
2828 4609 2.733956 TGTTTTTCTGAGGGCACAACT 58.266 42.857 0.00 0.00 0.00 3.16
2832 4613 2.839486 TTCTGAGGGCACAACTACAG 57.161 50.000 0.00 0.00 0.00 2.74
2839 4620 1.737793 GGGCACAACTACAGTGTATGC 59.262 52.381 15.28 15.28 39.17 3.14
2842 4623 1.999735 CACAACTACAGTGTATGCGGG 59.000 52.381 2.82 0.00 32.44 6.13
2894 4675 8.267894 TCTATTTTTCCCTGTCCTGAATTCTAG 58.732 37.037 7.05 2.75 0.00 2.43
2901 4682 6.903534 TCCCTGTCCTGAATTCTAGAACTTAT 59.096 38.462 7.48 0.00 0.00 1.73
2992 4773 5.244755 TGAGATGACAATGATGAAACGGAA 58.755 37.500 0.00 0.00 0.00 4.30
2993 4774 5.122239 TGAGATGACAATGATGAAACGGAAC 59.878 40.000 0.00 0.00 0.00 3.62
3017 4798 1.737838 TGCACCAGATTTAAGAGGCG 58.262 50.000 0.00 0.00 0.00 5.52
3022 4803 2.832129 ACCAGATTTAAGAGGCGAGTGA 59.168 45.455 0.00 0.00 0.00 3.41
3068 4849 1.002773 TCCTTGAGAACTTAACCGGGC 59.997 52.381 6.32 0.00 0.00 6.13
3131 4912 2.894387 GGCGTGCTCCTCTCATGC 60.894 66.667 0.00 0.00 43.66 4.06
3239 5020 3.653344 GAGCCTTCCATGAAACCAAAAC 58.347 45.455 0.00 0.00 0.00 2.43
3312 5093 8.087982 TGAGAAAACAGCAGAACATAGTTAAG 57.912 34.615 0.00 0.00 0.00 1.85
3341 5122 0.109226 GGCGTAGAAGCTCTTGTCGT 60.109 55.000 0.00 0.00 37.29 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 146 0.669318 TAACGTCTGGAAGCGCAAGG 60.669 55.000 11.47 0.00 37.05 3.61
325 374 2.009186 ATCCCCCACAAATCCCCTTA 57.991 50.000 0.00 0.00 0.00 2.69
889 939 2.037367 TCTGGCTGCGTAGGGAGT 59.963 61.111 1.76 0.00 33.52 3.85
992 1042 4.032558 CCGAGTTTAGTTATTCCGACTTGC 59.967 45.833 0.00 0.00 0.00 4.01
993 1043 5.404946 TCCGAGTTTAGTTATTCCGACTTG 58.595 41.667 0.00 0.00 0.00 3.16
994 1044 5.649782 TCCGAGTTTAGTTATTCCGACTT 57.350 39.130 0.00 0.00 0.00 3.01
995 1045 5.393896 CCTTCCGAGTTTAGTTATTCCGACT 60.394 44.000 0.00 0.00 0.00 4.18
996 1046 4.802563 CCTTCCGAGTTTAGTTATTCCGAC 59.197 45.833 0.00 0.00 0.00 4.79
997 1047 4.463891 ACCTTCCGAGTTTAGTTATTCCGA 59.536 41.667 0.00 0.00 0.00 4.55
998 1048 4.752146 ACCTTCCGAGTTTAGTTATTCCG 58.248 43.478 0.00 0.00 0.00 4.30
999 1049 5.583854 GGAACCTTCCGAGTTTAGTTATTCC 59.416 44.000 0.00 0.00 37.65 3.01
1000 1050 6.659361 GGAACCTTCCGAGTTTAGTTATTC 57.341 41.667 0.00 0.00 37.65 1.75
1015 1065 0.112412 TGGGGCTTCTTGGAACCTTC 59.888 55.000 0.00 0.00 0.00 3.46
1016 1066 0.113190 CTGGGGCTTCTTGGAACCTT 59.887 55.000 0.00 0.00 0.00 3.50
1017 1067 1.770324 CTGGGGCTTCTTGGAACCT 59.230 57.895 0.00 0.00 0.00 3.50
1018 1068 1.979155 GCTGGGGCTTCTTGGAACC 60.979 63.158 0.00 0.00 35.22 3.62
1019 1069 3.686760 GCTGGGGCTTCTTGGAAC 58.313 61.111 0.00 0.00 35.22 3.62
1040 1090 0.464036 ACCAACAACAGCAGTCGAGA 59.536 50.000 0.00 0.00 0.00 4.04
1041 1091 1.261619 GAACCAACAACAGCAGTCGAG 59.738 52.381 0.00 0.00 0.00 4.04
1042 1092 1.134521 AGAACCAACAACAGCAGTCGA 60.135 47.619 0.00 0.00 0.00 4.20
1044 1094 2.565841 AGAGAACCAACAACAGCAGTC 58.434 47.619 0.00 0.00 0.00 3.51
1045 1095 2.717639 AGAGAACCAACAACAGCAGT 57.282 45.000 0.00 0.00 0.00 4.40
1061 1111 3.425577 TTGTTCAGCAACAGCAAAGAG 57.574 42.857 0.00 0.00 43.54 2.85
1068 1118 3.248363 TCAGTTCGATTGTTCAGCAACAG 59.752 43.478 0.00 0.00 43.54 3.16
1091 1141 6.533012 TGAGATCGATCTTGATTCTGTTCAAC 59.467 38.462 27.90 11.03 37.25 3.18
1269 1320 3.927163 CTTGGTCGCCGCCGTTAGT 62.927 63.158 0.00 0.00 35.54 2.24
1311 1368 1.444553 CCAGCACCTCGTCGTCTTC 60.445 63.158 0.00 0.00 0.00 2.87
1436 1493 2.411765 CTTGCAGTTCCGGGGAAGGT 62.412 60.000 0.00 0.00 34.49 3.50
1440 1497 2.429930 CACTTGCAGTTCCGGGGA 59.570 61.111 0.00 0.00 0.00 4.81
1445 1502 1.900498 AGCAGGCACTTGCAGTTCC 60.900 57.895 7.53 0.00 44.36 3.62
1526 1583 0.532573 GACGAGGCAGAACCAGATCA 59.467 55.000 0.00 0.00 43.14 2.92
1556 1613 0.528684 GTACTCGTGCCTGCTCCATC 60.529 60.000 0.00 0.00 0.00 3.51
1562 1619 0.592754 GATCTCGTACTCGTGCCTGC 60.593 60.000 0.00 0.00 38.33 4.85
1695 1753 3.008049 AGTTGTGTCCCTCCAAGATGTAC 59.992 47.826 0.00 0.00 0.00 2.90
1722 1780 4.444720 CCGTCGCTTGGTATTCTTATTCTC 59.555 45.833 0.00 0.00 0.00 2.87
1726 1784 2.805657 GCCCGTCGCTTGGTATTCTTAT 60.806 50.000 0.00 0.00 0.00 1.73
1788 2153 1.068055 TCGAAGTAGAACTTGCCGTCC 60.068 52.381 0.00 0.00 38.80 4.79
1813 2178 4.377760 ACCGAGCTTCGAGGGGGA 62.378 66.667 7.07 0.00 43.74 4.81
1816 2181 2.182030 GACACCGAGCTTCGAGGG 59.818 66.667 7.07 2.22 43.74 4.30
1830 2195 1.677966 CGGGAGGAAGTCGAGGACA 60.678 63.158 0.00 0.00 34.60 4.02
1885 2250 0.877649 CAGGAATCCCATGCGACTCG 60.878 60.000 0.00 0.00 33.88 4.18
2075 2443 1.063649 GCAGAATACGACGCCGAGA 59.936 57.895 0.00 0.00 39.50 4.04
2077 2445 0.869880 CATGCAGAATACGACGCCGA 60.870 55.000 0.00 0.00 39.50 5.54
2116 2484 3.572682 CGGCCCAGATAGTAGACATTACA 59.427 47.826 0.00 0.00 0.00 2.41
2141 2510 0.941463 AGAACACGTTGAGCAGCTCG 60.941 55.000 17.81 9.14 32.35 5.03
2180 2549 1.153369 TATGCAGTTGGAGCGAGGC 60.153 57.895 0.00 0.00 33.85 4.70
2390 3803 1.458398 TGTGCACAAACATATCCCGG 58.542 50.000 19.28 0.00 0.00 5.73
2391 3804 3.128415 TCAATGTGCACAAACATATCCCG 59.872 43.478 25.72 3.11 39.89 5.14
2392 3805 4.158394 ACTCAATGTGCACAAACATATCCC 59.842 41.667 25.72 0.00 39.89 3.85
2393 3806 5.314923 ACTCAATGTGCACAAACATATCC 57.685 39.130 25.72 0.00 39.89 2.59
2394 3807 7.008628 GCTAAACTCAATGTGCACAAACATATC 59.991 37.037 25.72 3.56 39.89 1.63
2395 3808 6.808212 GCTAAACTCAATGTGCACAAACATAT 59.192 34.615 25.72 10.27 39.89 1.78
2397 3810 4.984161 GCTAAACTCAATGTGCACAAACAT 59.016 37.500 25.72 3.79 42.62 2.71
2399 3812 4.610945 AGCTAAACTCAATGTGCACAAAC 58.389 39.130 25.72 0.00 0.00 2.93
2403 3816 4.858935 TGAAAGCTAAACTCAATGTGCAC 58.141 39.130 10.75 10.75 0.00 4.57
2429 3852 8.351414 TCCCCTTTCCCTCAGAAATAAATAAAT 58.649 33.333 0.00 0.00 43.50 1.40
2433 4195 5.256389 ACTCCCCTTTCCCTCAGAAATAAAT 59.744 40.000 0.00 0.00 43.50 1.40
2441 4203 2.769095 CTCTAACTCCCCTTTCCCTCAG 59.231 54.545 0.00 0.00 0.00 3.35
2444 4206 3.293215 AACTCTAACTCCCCTTTCCCT 57.707 47.619 0.00 0.00 0.00 4.20
2445 4207 3.329814 TGAAACTCTAACTCCCCTTTCCC 59.670 47.826 0.00 0.00 0.00 3.97
2446 4208 4.635699 TGAAACTCTAACTCCCCTTTCC 57.364 45.455 0.00 0.00 0.00 3.13
2447 4209 6.372937 CAGAATGAAACTCTAACTCCCCTTTC 59.627 42.308 0.00 0.00 39.69 2.62
2448 4210 6.044404 TCAGAATGAAACTCTAACTCCCCTTT 59.956 38.462 0.00 0.00 45.97 3.11
2449 4211 5.548056 TCAGAATGAAACTCTAACTCCCCTT 59.452 40.000 0.00 0.00 45.97 3.95
2466 4228 4.913924 GCACAGCTTGTTAACTTCAGAATG 59.086 41.667 7.22 5.87 37.54 2.67
2515 4278 0.984230 CCAGGGACCAAAGCAGAGTA 59.016 55.000 0.00 0.00 0.00 2.59
2522 4285 4.953940 TGAAAATTTCCAGGGACCAAAG 57.046 40.909 3.00 0.00 0.00 2.77
2524 4287 5.022787 CCTATGAAAATTTCCAGGGACCAA 58.977 41.667 12.93 0.00 30.94 3.67
2555 4318 2.047830 GAGTCTTATGGTGGGTAGGGG 58.952 57.143 0.00 0.00 0.00 4.79
2563 4333 9.829507 ATTTTAGAGATCAAGAGTCTTATGGTG 57.170 33.333 4.74 0.00 0.00 4.17
2604 4374 0.947244 CTGGATCGGTTGGCTTATGC 59.053 55.000 0.00 0.00 38.76 3.14
2607 4377 1.912220 CCCTGGATCGGTTGGCTTA 59.088 57.895 0.00 0.00 0.00 3.09
2608 4378 2.677228 CCCTGGATCGGTTGGCTT 59.323 61.111 0.00 0.00 0.00 4.35
2611 4381 3.406595 GAGGCCCTGGATCGGTTGG 62.407 68.421 0.00 0.00 0.00 3.77
2612 4382 2.190578 GAGGCCCTGGATCGGTTG 59.809 66.667 0.00 0.00 0.00 3.77
2633 4403 1.323271 ACGATGTGCTCACCCGATCT 61.323 55.000 16.04 0.00 33.05 2.75
2634 4404 0.384309 TACGATGTGCTCACCCGATC 59.616 55.000 16.04 4.53 33.05 3.69
2636 4406 1.807226 CTACGATGTGCTCACCCGA 59.193 57.895 16.04 3.34 33.05 5.14
2637 4407 1.878522 GCTACGATGTGCTCACCCG 60.879 63.158 9.81 9.81 34.27 5.28
2638 4408 1.878522 CGCTACGATGTGCTCACCC 60.879 63.158 0.00 0.00 0.00 4.61
2639 4409 2.517450 GCGCTACGATGTGCTCACC 61.517 63.158 0.00 0.00 40.01 4.02
2648 4418 2.363788 TTTCTCAACAGCGCTACGAT 57.636 45.000 10.99 0.00 0.00 3.73
2649 4419 2.094700 AGATTTCTCAACAGCGCTACGA 60.095 45.455 10.99 5.96 0.00 3.43
2650 4420 2.028523 CAGATTTCTCAACAGCGCTACG 59.971 50.000 10.99 0.00 0.00 3.51
2651 4421 3.254060 TCAGATTTCTCAACAGCGCTAC 58.746 45.455 10.99 0.00 0.00 3.58
2652 4422 3.592898 TCAGATTTCTCAACAGCGCTA 57.407 42.857 10.99 0.00 0.00 4.26
2653 4423 2.462456 TCAGATTTCTCAACAGCGCT 57.538 45.000 2.64 2.64 0.00 5.92
2654 4424 3.125829 TCAATCAGATTTCTCAACAGCGC 59.874 43.478 0.00 0.00 0.00 5.92
2655 4425 4.934075 TCAATCAGATTTCTCAACAGCG 57.066 40.909 0.00 0.00 0.00 5.18
2670 4440 1.672363 GCTCCATGCACGATTCAATCA 59.328 47.619 0.00 0.00 42.31 2.57
2680 4450 0.675837 TGAAGCTGAGCTCCATGCAC 60.676 55.000 7.72 15.14 45.94 4.57
2709 4487 8.178964 TGCATACCGTCATTTATTCTTTTGTAC 58.821 33.333 0.00 0.00 0.00 2.90
2740 4518 1.673033 GGGATGATGGGAGCGTAATCG 60.673 57.143 0.00 0.00 40.37 3.34
2753 4531 7.127955 GGGTCAGGTATGATATTAAGGGATGAT 59.872 40.741 0.00 0.00 37.87 2.45
2758 4536 5.571658 GCAGGGTCAGGTATGATATTAAGGG 60.572 48.000 0.00 0.00 37.87 3.95
2785 4566 3.148279 CCTTCTCCTCGGACGGGG 61.148 72.222 3.76 3.76 37.02 5.73
2805 4586 2.665165 TGTGCCCTCAGAAAAACATGT 58.335 42.857 0.00 0.00 0.00 3.21
2809 4590 3.630312 TGTAGTTGTGCCCTCAGAAAAAC 59.370 43.478 0.00 0.00 0.00 2.43
2828 4609 0.250793 CCCAACCCGCATACACTGTA 59.749 55.000 0.00 0.00 0.00 2.74
2832 4613 1.470051 AATTCCCAACCCGCATACAC 58.530 50.000 0.00 0.00 0.00 2.90
2839 4620 0.823460 CATCCCAAATTCCCAACCCG 59.177 55.000 0.00 0.00 0.00 5.28
2842 4623 5.948742 TTATTCCATCCCAAATTCCCAAC 57.051 39.130 0.00 0.00 0.00 3.77
2931 4712 9.234384 CAAATCTTTGCTTGATCTGATATTGTC 57.766 33.333 0.00 0.00 0.00 3.18
2933 4714 9.020813 CACAAATCTTTGCTTGATCTGATATTG 57.979 33.333 2.63 0.00 41.79 1.90
2992 4773 4.520492 CCTCTTAAATCTGGTGCAACTTGT 59.480 41.667 2.04 0.00 36.74 3.16
2993 4774 4.616835 GCCTCTTAAATCTGGTGCAACTTG 60.617 45.833 2.04 0.00 36.74 3.16
3112 4893 1.521010 CATGAGAGGAGCACGCCAG 60.521 63.158 0.00 0.00 0.00 4.85
3131 4912 5.986135 ACAAGAACAAGTAGCTAGTGTTGAG 59.014 40.000 21.70 14.79 35.67 3.02
3239 5020 9.846248 CTTTTACAAGAGGAATTACAAGGATTG 57.154 33.333 0.00 0.00 41.72 2.67
3312 5093 1.897398 CTTCTACGCCGTGGTTGCAC 61.897 60.000 0.00 0.00 0.00 4.57



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

AutoCloner maintained by Alex Coulton.