Multiple sequence alignment - TraesCS4B01G056600

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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 TraesCS4B01G056600 chr4B 100.000 3238 0 0 1 3238 46220471 46223708 0.000000e+00 5980
1 TraesCS4B01G056600 chr4D 91.863 3220 133 57 63 3237 32062520 32065655 0.000000e+00 4375
2 TraesCS4B01G056600 chr4A 89.661 3182 161 65 113 3238 570912881 570909812 0.000000e+00 3899
3 TraesCS4B01G056600 chr4A 90.674 193 16 1 117 309 570913616 570913426 4.150000e-64 255


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 TraesCS4B01G056600 chr4B 46220471 46223708 3237 False 5980 5980 100.0000 1 3238 1 chr4B.!!$F1 3237
1 TraesCS4B01G056600 chr4D 32062520 32065655 3135 False 4375 4375 91.8630 63 3237 1 chr4D.!!$F1 3174
2 TraesCS4B01G056600 chr4A 570909812 570913616 3804 True 2077 3899 90.1675 113 3238 2 chr4A.!!$R1 3125

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
355 981 0.039256 CCGGCATTTCACACAACCTG 60.039 55.0 0.00 0.00 0.00 4.00 F
922 1566 0.039708 GGCTGTTTGCTGAGCTTGAC 60.040 55.0 5.83 2.22 42.39 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1905 2583 0.247736 AGTGGATCTTGACGAGCACC 59.752 55.0 0.0 0.0 0.00 5.01 R
2814 3516 0.108138 CAGGCACACCCTACTACTGC 60.108 60.0 0.0 0.0 44.09 4.40 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
70 71 4.581077 TCATCAAGATCAGATGAGGTCG 57.419 45.455 20.53 2.22 44.98 4.79
72 73 2.034878 TCAAGATCAGATGAGGTCGGG 58.965 52.381 0.00 0.00 0.00 5.14
76 77 1.757118 GATCAGATGAGGTCGGGTTCA 59.243 52.381 0.00 0.00 0.00 3.18
79 80 1.550524 CAGATGAGGTCGGGTTCAGAA 59.449 52.381 0.00 0.00 0.00 3.02
83 84 1.003118 TGAGGTCGGGTTCAGAAATGG 59.997 52.381 0.00 0.00 0.00 3.16
85 86 1.916181 AGGTCGGGTTCAGAAATGGAT 59.084 47.619 0.00 0.00 0.00 3.41
87 88 3.716872 AGGTCGGGTTCAGAAATGGATAT 59.283 43.478 0.00 0.00 0.00 1.63
90 91 4.211374 GTCGGGTTCAGAAATGGATATTCG 59.789 45.833 0.00 0.00 32.04 3.34
91 92 4.100344 TCGGGTTCAGAAATGGATATTCGA 59.900 41.667 0.00 0.00 32.04 3.71
94 95 6.495706 GGGTTCAGAAATGGATATTCGAAAC 58.504 40.000 0.00 0.00 31.94 2.78
96 97 7.362574 GGGTTCAGAAATGGATATTCGAAACAA 60.363 37.037 0.00 0.00 33.13 2.83
114 115 9.658475 TCGAAACAATACATTCTTTTTGTGTAG 57.342 29.630 0.00 0.00 32.90 2.74
115 116 9.445786 CGAAACAATACATTCTTTTTGTGTAGT 57.554 29.630 0.00 0.00 32.90 2.73
283 909 1.847890 CGACGAAACGCCCAACCAAT 61.848 55.000 0.00 0.00 0.00 3.16
284 910 1.158434 GACGAAACGCCCAACCAATA 58.842 50.000 0.00 0.00 0.00 1.90
287 913 1.726571 CGAAACGCCCAACCAATAACG 60.727 52.381 0.00 0.00 0.00 3.18
289 915 0.891904 AACGCCCAACCAATAACGCT 60.892 50.000 0.00 0.00 0.00 5.07
353 979 1.288752 CCCGGCATTTCACACAACC 59.711 57.895 0.00 0.00 0.00 3.77
355 981 0.039256 CCGGCATTTCACACAACCTG 60.039 55.000 0.00 0.00 0.00 4.00
369 995 3.866582 CCTGTGCCCCGATCTCCC 61.867 72.222 0.00 0.00 0.00 4.30
441 1067 0.748005 AGCCAATACCGCAATCGCTT 60.748 50.000 0.00 0.00 35.30 4.68
450 1076 0.740868 CGCAATCGCTTGAGGGAGAA 60.741 55.000 2.58 0.00 40.39 2.87
477 1103 7.228906 AGCGAGAGAGCAATAATGTAAGTAGTA 59.771 37.037 0.00 0.00 40.15 1.82
478 1104 7.324135 GCGAGAGAGCAATAATGTAAGTAGTAC 59.676 40.741 0.00 0.00 37.05 2.73
479 1105 8.561212 CGAGAGAGCAATAATGTAAGTAGTACT 58.439 37.037 0.00 0.00 33.46 2.73
480 1106 9.672086 GAGAGAGCAATAATGTAAGTAGTACTG 57.328 37.037 5.39 0.00 33.46 2.74
481 1107 9.191479 AGAGAGCAATAATGTAAGTAGTACTGT 57.809 33.333 5.39 0.00 33.46 3.55
486 1112 9.460906 GCAATAATGTAAGTAGTACTGTACTCC 57.539 37.037 22.79 12.77 40.14 3.85
487 1113 9.661187 CAATAATGTAAGTAGTACTGTACTCCG 57.339 37.037 22.79 0.00 40.14 4.63
488 1114 8.970859 ATAATGTAAGTAGTACTGTACTCCGT 57.029 34.615 22.79 13.11 40.14 4.69
603 1245 0.984230 TCTGCGGATGAAAGGAAGGT 59.016 50.000 0.00 0.00 0.00 3.50
637 1280 1.254954 AGTTCACACCCGACCTAGAC 58.745 55.000 0.00 0.00 0.00 2.59
658 1301 4.856509 ACCAAGAGGCCTTAAAATAGTCC 58.143 43.478 6.77 0.00 39.06 3.85
761 1404 1.133325 GCTGACCCATCTCTCTCCCTA 60.133 57.143 0.00 0.00 0.00 3.53
766 1409 3.333680 GACCCATCTCTCTCCCTATCTCT 59.666 52.174 0.00 0.00 0.00 3.10
767 1410 3.333680 ACCCATCTCTCTCCCTATCTCTC 59.666 52.174 0.00 0.00 0.00 3.20
768 1411 3.593328 CCCATCTCTCTCCCTATCTCTCT 59.407 52.174 0.00 0.00 0.00 3.10
769 1412 4.568380 CCCATCTCTCTCCCTATCTCTCTG 60.568 54.167 0.00 0.00 0.00 3.35
770 1413 4.043310 CCATCTCTCTCCCTATCTCTCTGT 59.957 50.000 0.00 0.00 0.00 3.41
804 1447 1.338200 CCAAGGTTGGTCTCTCTTCCG 60.338 57.143 0.09 0.00 43.43 4.30
814 1457 6.049955 TGGTCTCTCTTCCGTGATAATTTT 57.950 37.500 0.00 0.00 0.00 1.82
824 1467 4.281525 CGTGATAATTTTTACCCACGGG 57.718 45.455 0.00 0.00 42.23 5.28
825 1468 3.487879 CGTGATAATTTTTACCCACGGGC 60.488 47.826 0.69 0.00 42.23 6.13
826 1469 3.444388 GTGATAATTTTTACCCACGGGCA 59.556 43.478 0.69 0.00 39.32 5.36
827 1470 3.697045 TGATAATTTTTACCCACGGGCAG 59.303 43.478 0.69 0.00 39.32 4.85
854 1497 2.437200 TGCTATGTGTTTGCTTTGCC 57.563 45.000 0.00 0.00 0.00 4.52
872 1515 0.737219 CCCAATGCTAACTGCTCTGC 59.263 55.000 0.00 0.00 43.37 4.26
886 1529 0.111089 CTCTGCTTTCGTGCGTGTTC 60.111 55.000 0.00 0.00 35.36 3.18
910 1553 1.281867 TGATCAGGATTCCGGCTGTTT 59.718 47.619 0.00 0.00 0.00 2.83
912 1555 0.960364 TCAGGATTCCGGCTGTTTGC 60.960 55.000 0.00 0.00 41.94 3.68
921 1565 2.334307 GGCTGTTTGCTGAGCTTGA 58.666 52.632 5.83 0.00 42.39 3.02
922 1566 0.039708 GGCTGTTTGCTGAGCTTGAC 60.040 55.000 5.83 2.22 42.39 3.18
960 1608 4.722700 TTGGCTTGGAGGCGAGGC 62.723 66.667 0.00 0.00 44.78 4.70
971 1619 4.430765 GCGAGGCGTTTCGAGGGA 62.431 66.667 13.56 0.00 43.03 4.20
1074 1722 1.377987 CGGGTGTAATGGTGTGGGG 60.378 63.158 0.00 0.00 0.00 4.96
1075 1723 1.680989 GGGTGTAATGGTGTGGGGC 60.681 63.158 0.00 0.00 0.00 5.80
1079 1727 2.112815 GTAATGGTGTGGGGCGAGC 61.113 63.158 0.00 0.00 0.00 5.03
1101 1755 1.172812 GGTGGCTGACTGGTTGTTCC 61.173 60.000 0.00 0.00 0.00 3.62
1137 1791 2.711922 GGTGATGGACGAGCCGAGT 61.712 63.158 1.50 0.00 40.66 4.18
1488 2166 1.075659 GAAGCCCAAGCAGGAGGTT 59.924 57.895 0.00 0.00 43.56 3.50
2017 2695 0.251297 CAATGTGCTCCCCTTCACCA 60.251 55.000 0.00 0.00 32.51 4.17
2083 2761 6.460676 CCAATCATCTCCACTTCTTAATTGCC 60.461 42.308 0.00 0.00 0.00 4.52
2098 2776 8.700439 TCTTAATTGCCCCATAATTTACTACC 57.300 34.615 0.00 0.00 0.00 3.18
2099 2777 8.282982 TCTTAATTGCCCCATAATTTACTACCA 58.717 33.333 0.00 0.00 0.00 3.25
2100 2778 6.976934 AATTGCCCCATAATTTACTACCAG 57.023 37.500 0.00 0.00 0.00 4.00
2101 2779 5.459982 TTGCCCCATAATTTACTACCAGT 57.540 39.130 0.00 0.00 0.00 4.00
2102 2780 6.578313 TTGCCCCATAATTTACTACCAGTA 57.422 37.500 0.00 0.00 0.00 2.74
2103 2781 5.932455 TGCCCCATAATTTACTACCAGTAC 58.068 41.667 0.00 0.00 28.93 2.73
2104 2782 5.429109 TGCCCCATAATTTACTACCAGTACA 59.571 40.000 0.00 0.00 28.93 2.90
2105 2783 6.102027 TGCCCCATAATTTACTACCAGTACAT 59.898 38.462 0.00 0.00 28.93 2.29
2106 2784 6.430000 GCCCCATAATTTACTACCAGTACATG 59.570 42.308 0.00 0.00 28.93 3.21
2107 2785 7.514721 CCCCATAATTTACTACCAGTACATGT 58.485 38.462 2.69 2.69 28.93 3.21
2108 2786 8.653191 CCCCATAATTTACTACCAGTACATGTA 58.347 37.037 0.08 0.08 28.93 2.29
2119 2797 9.223099 ACTACCAGTACATGTAATAAAAACCAC 57.777 33.333 7.25 0.00 0.00 4.16
2269 2958 7.624549 TGCTCCTCAACAAGTCTAATTTAGAT 58.375 34.615 9.28 0.00 37.13 1.98
2341 3031 4.291249 TGGGGCTAATGAGTTTTAGGTTCT 59.709 41.667 0.00 0.00 31.19 3.01
2356 3046 3.551496 TTCTTCCCCGCTGGTGCTG 62.551 63.158 0.00 0.00 36.97 4.41
2357 3047 4.020617 CTTCCCCGCTGGTGCTGA 62.021 66.667 0.00 0.00 36.97 4.26
2414 3105 3.225940 CCCTCAAAGATAGCCATTTCCC 58.774 50.000 0.00 0.00 0.00 3.97
2415 3106 3.373001 CCCTCAAAGATAGCCATTTCCCA 60.373 47.826 0.00 0.00 0.00 4.37
2417 3108 3.631250 TCAAAGATAGCCATTTCCCACC 58.369 45.455 0.00 0.00 0.00 4.61
2444 3135 1.004679 CCCATGGGTGCAGCAAAAC 60.005 57.895 23.93 0.08 0.00 2.43
2452 3143 1.681264 GGTGCAGCAAAACCACTAGTT 59.319 47.619 11.86 0.00 41.81 2.24
2473 3164 6.754178 AGTTAATTACTTCTACCCTCTCCCT 58.246 40.000 0.00 0.00 31.29 4.20
2624 3315 6.590656 TCATTTCTCCCCTACACCAATATT 57.409 37.500 0.00 0.00 0.00 1.28
2712 3408 1.852157 TTGCCGGCCTCTCAAATCCT 61.852 55.000 26.77 0.00 0.00 3.24
2717 3413 1.417890 CGGCCTCTCAAATCCTACCAT 59.582 52.381 0.00 0.00 0.00 3.55
2760 3459 5.999205 AATATCTGTGGACAAAAATGGCA 57.001 34.783 0.00 0.00 0.00 4.92
2814 3516 3.005050 TGCAAGCCTTTGATTCAGAAGTG 59.995 43.478 0.00 2.90 36.36 3.16
2867 3578 2.736531 CAAGCTGGTTGGTTGGCC 59.263 61.111 11.59 0.00 46.85 5.36
2868 3579 2.524148 AAGCTGGTTGGTTGGCCC 60.524 61.111 0.00 0.00 34.77 5.80
2869 3580 3.387609 AAGCTGGTTGGTTGGCCCA 62.388 57.895 0.00 0.00 43.27 5.36
2870 3581 3.305516 GCTGGTTGGTTGGCCCAG 61.306 66.667 0.00 0.00 46.31 4.45
2871 3582 3.305516 CTGGTTGGTTGGCCCAGC 61.306 66.667 0.00 0.00 46.31 4.85
2872 3583 4.149019 TGGTTGGTTGGCCCAGCA 62.149 61.111 4.28 4.28 45.76 4.41
2873 3584 3.305516 GGTTGGTTGGCCCAGCAG 61.306 66.667 8.88 0.00 45.76 4.24
2874 3585 3.994853 GTTGGTTGGCCCAGCAGC 61.995 66.667 8.88 7.97 46.31 5.25
2894 3606 2.037641 GCTTGGATGAACCCTTTGCTTT 59.962 45.455 0.00 0.00 38.00 3.51
2902 3614 6.239317 GGATGAACCCTTTGCTTTTAGTTTCT 60.239 38.462 0.00 0.00 0.00 2.52
2950 3667 5.590663 TCAAGATTGTAGCTCGATCTGTACT 59.409 40.000 13.48 0.65 44.12 2.73
3138 3856 3.861840 ACGATCTTGTATGTTGTCCTGG 58.138 45.455 0.00 0.00 0.00 4.45
3186 3904 8.103935 TGTATTACCTGTCCACAAATCAATACA 58.896 33.333 0.00 0.00 35.25 2.29
3188 3906 5.964958 ACCTGTCCACAAATCAATACAAG 57.035 39.130 0.00 0.00 0.00 3.16
3190 3908 6.248433 ACCTGTCCACAAATCAATACAAGAT 58.752 36.000 0.00 0.00 0.00 2.40
3191 3909 6.721208 ACCTGTCCACAAATCAATACAAGATT 59.279 34.615 0.00 0.00 37.30 2.40
3194 3912 9.726232 CTGTCCACAAATCAATACAAGATTATG 57.274 33.333 0.00 0.00 34.78 1.90
3195 3913 9.241919 TGTCCACAAATCAATACAAGATTATGT 57.758 29.630 0.00 0.00 34.78 2.29
3207 3928 0.179045 GATTATGTGGGCGGCACTCT 60.179 55.000 12.47 2.46 0.00 3.24
3217 3938 1.810151 GGCGGCACTCTTTTGTTCATA 59.190 47.619 3.07 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 9.506018 TCATCTGATCTTGATGAACAGTAAAAA 57.494 29.630 21.26 3.99 44.79 1.94
40 41 9.159364 CTCATCTGATCTTGATGAACAGTAAAA 57.841 33.333 22.64 7.10 46.30 1.52
41 42 7.767659 CCTCATCTGATCTTGATGAACAGTAAA 59.232 37.037 22.64 7.57 46.30 2.01
42 43 7.093156 ACCTCATCTGATCTTGATGAACAGTAA 60.093 37.037 22.64 8.06 46.30 2.24
46 47 5.668471 GACCTCATCTGATCTTGATGAACA 58.332 41.667 22.64 9.51 46.30 3.18
47 48 4.744137 CGACCTCATCTGATCTTGATGAAC 59.256 45.833 22.64 17.58 46.30 3.18
48 49 4.202192 CCGACCTCATCTGATCTTGATGAA 60.202 45.833 22.64 12.84 46.30 2.57
49 50 3.320256 CCGACCTCATCTGATCTTGATGA 59.680 47.826 21.75 21.75 45.33 2.92
50 51 3.554544 CCCGACCTCATCTGATCTTGATG 60.555 52.174 17.42 17.42 41.75 3.07
51 52 2.632028 CCCGACCTCATCTGATCTTGAT 59.368 50.000 0.00 0.00 0.00 2.57
52 53 2.034878 CCCGACCTCATCTGATCTTGA 58.965 52.381 0.00 0.00 0.00 3.02
53 54 1.759445 ACCCGACCTCATCTGATCTTG 59.241 52.381 0.00 0.00 0.00 3.02
54 55 2.166907 ACCCGACCTCATCTGATCTT 57.833 50.000 0.00 0.00 0.00 2.40
55 56 2.035632 GAACCCGACCTCATCTGATCT 58.964 52.381 0.00 0.00 0.00 2.75
57 58 1.759445 CTGAACCCGACCTCATCTGAT 59.241 52.381 0.00 0.00 0.00 2.90
59 60 1.186200 TCTGAACCCGACCTCATCTG 58.814 55.000 0.00 0.00 0.00 2.90
60 61 1.938585 TTCTGAACCCGACCTCATCT 58.061 50.000 0.00 0.00 0.00 2.90
61 62 2.762535 TTTCTGAACCCGACCTCATC 57.237 50.000 0.00 0.00 0.00 2.92
62 63 2.356125 CCATTTCTGAACCCGACCTCAT 60.356 50.000 0.00 0.00 0.00 2.90
63 64 1.003118 CCATTTCTGAACCCGACCTCA 59.997 52.381 0.00 0.00 0.00 3.86
64 65 1.278127 TCCATTTCTGAACCCGACCTC 59.722 52.381 0.00 0.00 0.00 3.85
66 67 2.420058 ATCCATTTCTGAACCCGACC 57.580 50.000 0.00 0.00 0.00 4.79
67 68 4.211374 CGAATATCCATTTCTGAACCCGAC 59.789 45.833 0.00 0.00 0.00 4.79
70 71 6.094881 TGTTTCGAATATCCATTTCTGAACCC 59.905 38.462 0.00 0.00 0.00 4.11
87 88 8.918961 ACACAAAAAGAATGTATTGTTTCGAA 57.081 26.923 0.00 0.00 32.87 3.71
136 760 6.840780 ATGTGATATGAGATGGTGTATCGA 57.159 37.500 0.00 0.00 40.86 3.59
137 761 7.538575 TGTATGTGATATGAGATGGTGTATCG 58.461 38.462 0.00 0.00 40.86 2.92
187 813 7.707624 TTTGGAGATTTTGCATATCAGAAGT 57.292 32.000 10.80 0.00 0.00 3.01
201 827 7.105588 GCCACTTGGATTTTATTTGGAGATTT 58.894 34.615 0.00 0.00 37.39 2.17
207 833 4.222588 TGAGGCCACTTGGATTTTATTTGG 59.777 41.667 5.01 0.00 37.39 3.28
287 913 1.391826 GTTCTTGTCGCTTCTGCTAGC 59.608 52.381 8.10 8.10 37.80 3.42
289 915 1.337823 GGGTTCTTGTCGCTTCTGCTA 60.338 52.381 0.00 0.00 36.97 3.49
353 979 2.370445 AAGGGAGATCGGGGCACAG 61.370 63.158 0.00 0.00 0.00 3.66
355 981 2.190578 CAAGGGAGATCGGGGCAC 59.809 66.667 0.00 0.00 0.00 5.01
362 988 3.135348 TCATGGTGATGTCAAGGGAGATC 59.865 47.826 0.00 0.00 42.56 2.75
369 995 5.882000 TGGATTACTTCATGGTGATGTCAAG 59.118 40.000 0.00 0.00 36.38 3.02
441 1067 1.468985 CTCTCTCGCTTTCTCCCTCA 58.531 55.000 0.00 0.00 0.00 3.86
450 1076 5.665459 ACTTACATTATTGCTCTCTCGCTT 58.335 37.500 0.00 0.00 0.00 4.68
483 1109 4.060900 AGCATTATGTCAAGCATACGGAG 58.939 43.478 0.00 0.00 39.57 4.63
484 1110 4.071961 AGCATTATGTCAAGCATACGGA 57.928 40.909 0.00 0.00 39.57 4.69
485 1111 4.991056 AGTAGCATTATGTCAAGCATACGG 59.009 41.667 0.00 0.00 39.57 4.02
486 1112 5.119279 GGAGTAGCATTATGTCAAGCATACG 59.881 44.000 0.00 0.00 39.57 3.06
487 1113 5.991606 TGGAGTAGCATTATGTCAAGCATAC 59.008 40.000 0.00 0.00 39.57 2.39
488 1114 6.173427 TGGAGTAGCATTATGTCAAGCATA 57.827 37.500 0.00 0.00 38.94 3.14
603 1245 0.683504 GAACTACTCGGCCTCCCTCA 60.684 60.000 0.00 0.00 0.00 3.86
637 1280 4.207955 GGGACTATTTTAAGGCCTCTTGG 58.792 47.826 5.23 0.00 44.97 3.61
668 1311 4.474113 GACCTTATATAACCTCTGCGACG 58.526 47.826 0.00 0.00 0.00 5.12
761 1404 4.346418 GGAGAGAGAGAGAGACAGAGAGAT 59.654 50.000 0.00 0.00 0.00 2.75
766 1409 2.556766 TGGGAGAGAGAGAGAGACAGA 58.443 52.381 0.00 0.00 0.00 3.41
767 1410 3.282021 CTTGGGAGAGAGAGAGAGACAG 58.718 54.545 0.00 0.00 0.00 3.51
768 1411 2.025416 CCTTGGGAGAGAGAGAGAGACA 60.025 54.545 0.00 0.00 0.00 3.41
769 1412 2.025321 ACCTTGGGAGAGAGAGAGAGAC 60.025 54.545 0.00 0.00 0.00 3.36
770 1413 2.283834 ACCTTGGGAGAGAGAGAGAGA 58.716 52.381 0.00 0.00 0.00 3.10
804 1447 3.444388 TGCCCGTGGGTAAAAATTATCAC 59.556 43.478 6.82 0.00 37.65 3.06
814 1457 4.028490 CAGCCTGCCCGTGGGTAA 62.028 66.667 6.82 0.00 37.65 2.85
824 1467 0.248907 CACATAGCAATGCAGCCTGC 60.249 55.000 10.45 10.45 45.29 4.85
825 1468 1.100510 ACACATAGCAATGCAGCCTG 58.899 50.000 8.35 1.42 36.50 4.85
826 1469 1.843368 AACACATAGCAATGCAGCCT 58.157 45.000 8.35 0.00 36.50 4.58
827 1470 2.264813 CAAACACATAGCAATGCAGCC 58.735 47.619 8.35 0.00 36.50 4.85
872 1515 1.858458 TCAGAAGAACACGCACGAAAG 59.142 47.619 0.00 0.00 0.00 2.62
886 1529 1.415659 AGCCGGAATCCTGATCAGAAG 59.584 52.381 24.62 8.47 0.00 2.85
939 1586 1.301677 CTCGCCTCCAAGCCAAAGAC 61.302 60.000 0.00 0.00 0.00 3.01
960 1608 2.881352 GCTCGCTCCCTCGAAACG 60.881 66.667 0.00 0.00 38.08 3.60
970 1618 0.921347 TAAAAATCGCTCGCTCGCTC 59.079 50.000 0.00 0.00 0.00 5.03
971 1619 0.924090 CTAAAAATCGCTCGCTCGCT 59.076 50.000 0.00 0.00 0.00 4.93
1075 1723 3.699894 AGTCAGCCACCCAGCTCG 61.700 66.667 0.00 0.00 42.61 5.03
1079 1727 1.601759 CAACCAGTCAGCCACCCAG 60.602 63.158 0.00 0.00 0.00 4.45
1101 1755 3.198236 CTGCACGCCACCAAACCAG 62.198 63.158 0.00 0.00 0.00 4.00
1507 2185 1.301716 GCTTGACCTGCTGGAACGA 60.302 57.895 17.64 8.66 37.04 3.85
1609 2287 3.775654 CTTCTCCCGGCGCTTCCT 61.776 66.667 7.64 0.00 0.00 3.36
1905 2583 0.247736 AGTGGATCTTGACGAGCACC 59.752 55.000 0.00 0.00 0.00 5.01
2017 2695 1.115467 GTGATGTCGATGGAGGAGGT 58.885 55.000 0.00 0.00 0.00 3.85
2134 2812 7.871973 GCATCAGATTAACATATCAGTCAGACT 59.128 37.037 0.00 0.00 0.00 3.24
2139 2817 6.128336 GCCTGCATCAGATTAACATATCAGTC 60.128 42.308 0.00 0.00 32.44 3.51
2143 2821 4.093998 CGGCCTGCATCAGATTAACATATC 59.906 45.833 0.00 0.00 32.44 1.63
2145 2823 3.402110 CGGCCTGCATCAGATTAACATA 58.598 45.455 0.00 0.00 32.44 2.29
2146 2824 2.224606 CGGCCTGCATCAGATTAACAT 58.775 47.619 0.00 0.00 32.44 2.71
2147 2825 1.667236 CGGCCTGCATCAGATTAACA 58.333 50.000 0.00 0.00 32.44 2.41
2148 2826 0.947244 CCGGCCTGCATCAGATTAAC 59.053 55.000 0.00 0.00 32.44 2.01
2171 2857 3.243569 CCTTGACAGACAACGAGAAGTCT 60.244 47.826 0.00 0.00 45.46 3.24
2251 2937 8.734386 AGCCAAAGATCTAAATTAGACTTGTTG 58.266 33.333 4.66 7.49 37.69 3.33
2253 2942 8.870075 AAGCCAAAGATCTAAATTAGACTTGT 57.130 30.769 4.66 0.00 37.69 3.16
2269 2958 2.489073 GGAGGGAAACAGAAGCCAAAGA 60.489 50.000 0.00 0.00 0.00 2.52
2309 2999 1.142870 TCATTAGCCCCAAATCCTCGG 59.857 52.381 0.00 0.00 0.00 4.63
2356 3046 2.410939 TGCAAGCGAGCTATCATCATC 58.589 47.619 0.00 0.00 34.99 2.92
2357 3047 2.224233 ACTGCAAGCGAGCTATCATCAT 60.224 45.455 0.00 0.00 37.60 2.45
2444 3135 8.536340 AGAGGGTAGAAGTAATTAACTAGTGG 57.464 38.462 0.00 0.00 37.50 4.00
2452 3143 8.458951 AAAAAGGGAGAGGGTAGAAGTAATTA 57.541 34.615 0.00 0.00 0.00 1.40
2498 3189 0.254178 CTCCCAGGAACATGGAGTGG 59.746 60.000 7.08 0.00 43.57 4.00
2544 3235 5.783875 TGGTAACTAGCCCTAGAAAAAGACT 59.216 40.000 9.20 0.00 36.97 3.24
2624 3315 1.872773 AAAACAGGGTGAAAAGGGCA 58.127 45.000 0.00 0.00 0.00 5.36
2646 3337 3.437795 GTCCGGCCTCTCGTCGAA 61.438 66.667 0.00 0.00 0.00 3.71
2786 3487 4.370917 TGAATCAAAGGCTTGCAAAAGTC 58.629 39.130 0.00 0.00 32.14 3.01
2814 3516 0.108138 CAGGCACACCCTACTACTGC 60.108 60.000 0.00 0.00 44.09 4.40
2845 3547 0.249155 CAACCAACCAGCTTGCACTG 60.249 55.000 0.00 0.00 37.42 3.66
2867 3578 1.318158 GGGTTCATCCAAGCTGCTGG 61.318 60.000 1.35 7.37 38.11 4.85
2868 3579 0.323178 AGGGTTCATCCAAGCTGCTG 60.323 55.000 1.35 0.00 38.11 4.41
2869 3580 0.407139 AAGGGTTCATCCAAGCTGCT 59.593 50.000 0.00 0.00 38.11 4.24
2870 3581 1.067354 CAAAGGGTTCATCCAAGCTGC 60.067 52.381 0.00 0.00 38.11 5.25
2871 3582 1.067354 GCAAAGGGTTCATCCAAGCTG 60.067 52.381 0.00 0.00 38.11 4.24
2872 3583 1.203100 AGCAAAGGGTTCATCCAAGCT 60.203 47.619 0.00 0.00 38.11 3.74
2873 3584 1.260544 AGCAAAGGGTTCATCCAAGC 58.739 50.000 0.00 0.00 38.11 4.01
2874 3585 4.341366 AAAAGCAAAGGGTTCATCCAAG 57.659 40.909 0.00 0.00 38.11 3.61
2902 3614 8.696374 TGATCCTGTTACAACAAAAACCATAAA 58.304 29.630 0.00 0.00 38.66 1.40
3087 3804 7.067008 ACGATTCTGGTCCATAAACAAATTAGG 59.933 37.037 0.00 0.00 0.00 2.69
3186 3904 2.793831 GTGCCGCCCACATAATCTT 58.206 52.632 0.26 0.00 44.06 2.40
3194 3912 1.734388 AACAAAAGAGTGCCGCCCAC 61.734 55.000 0.00 0.00 45.01 4.61
3195 3913 1.452145 GAACAAAAGAGTGCCGCCCA 61.452 55.000 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.