Multiple sequence alignment - TraesCS6A01G239200

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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 TraesCS6A01G239200 chr6A 100.000 3552 0 0 1 3552 449179746 449183297 0.000000e+00 6560.0
1 TraesCS6A01G239200 chr6A 93.478 46 3 0 196 241 560334460 560334505 6.360000e-08 69.4
2 TraesCS6A01G239200 chr6D 92.600 2865 124 44 714 3552 312557532 312560334 0.000000e+00 4036.0
3 TraesCS6A01G239200 chr6D 95.455 726 27 4 1 720 312556561 312557286 0.000000e+00 1153.0
4 TraesCS6A01G239200 chr6D 93.478 46 3 0 196 241 94849327 94849372 6.360000e-08 69.4
5 TraesCS6A01G239200 chr6B 91.887 2650 101 47 882 3503 514479698 514477135 0.000000e+00 3598.0
6 TraesCS6A01G239200 chr6B 96.057 279 8 3 281 558 514480270 514479994 5.410000e-123 451.0
7 TraesCS6A01G239200 chr6B 86.264 182 15 4 1 172 514480594 514480413 4.680000e-44 189.0
8 TraesCS6A01G239200 chr6B 89.908 109 10 1 585 693 514479993 514479886 4.780000e-29 139.0
9 TraesCS6A01G239200 chr6B 98.039 51 0 1 3503 3552 514476899 514476849 1.760000e-13 87.9
10 TraesCS6A01G239200 chr2A 77.563 673 93 35 1921 2556 635511699 635512350 1.570000e-93 353.0
11 TraesCS6A01G239200 chr2D 86.071 280 35 3 2274 2553 491194222 491194497 7.450000e-77 298.0
12 TraesCS6A01G239200 chr2D 93.478 46 3 0 196 241 290635309 290635354 6.360000e-08 69.4
13 TraesCS6A01G239200 chr2B 81.994 361 53 9 2198 2556 575836419 575836769 2.680000e-76 296.0
14 TraesCS6A01G239200 chr3B 80.383 209 35 6 2292 2497 496615093 496615298 1.710000e-33 154.0
15 TraesCS6A01G239200 chr7B 93.478 46 3 0 196 241 13418884 13418839 6.360000e-08 69.4
16 TraesCS6A01G239200 chr5D 93.478 46 3 0 196 241 10399865 10399910 6.360000e-08 69.4
17 TraesCS6A01G239200 chr5B 93.478 46 3 0 196 241 619572446 619572401 6.360000e-08 69.4
18 TraesCS6A01G239200 chr4D 93.478 46 3 0 196 241 101756635 101756680 6.360000e-08 69.4
19 TraesCS6A01G239200 chr1B 93.478 46 3 0 196 241 61222216 61222261 6.360000e-08 69.4


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 TraesCS6A01G239200 chr6A 449179746 449183297 3551 False 6560.00 6560 100.0000 1 3552 1 chr6A.!!$F1 3551
1 TraesCS6A01G239200 chr6D 312556561 312560334 3773 False 2594.50 4036 94.0275 1 3552 2 chr6D.!!$F2 3551
2 TraesCS6A01G239200 chr6B 514476849 514480594 3745 True 892.98 3598 92.4310 1 3552 5 chr6B.!!$R1 3551
3 TraesCS6A01G239200 chr2A 635511699 635512350 651 False 353.00 353 77.5630 1921 2556 1 chr2A.!!$F1 635

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
649 757 0.102481 AAGTAGTGGCAGTATCGGCG 59.898 55.0 5.16 0.0 0.00 6.46 F
1306 1685 0.031314 CTCTGTGCTGAGACGTGTGT 59.969 55.0 0.00 0.0 36.23 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2143 2542 0.317479 CGTCGAGGAGGTTGAAGGTT 59.683 55.0 0.0 0.0 0.00 3.50 R
3042 3504 0.331278 TGGGTAGATTTGGCACAGGG 59.669 55.0 0.0 0.0 42.39 4.45 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
29 31 6.131264 TGATAGACGGTTCTAAATCCCTACA 58.869 40.000 0.00 0.00 37.88 2.74
185 196 0.822811 AACATGCTTGCACCACAACA 59.177 45.000 0.00 0.00 33.68 3.33
196 207 2.664916 CACCACAACAGCATTGCTTAC 58.335 47.619 8.83 0.00 36.40 2.34
203 214 0.179156 CAGCATTGCTTACCGCTTGG 60.179 55.000 8.83 0.00 36.40 3.61
210 221 2.746275 TGCTTACCGCTTGGAACAAGC 61.746 52.381 20.73 20.73 41.57 4.01
231 242 4.186159 GCGGGTAGCTATCTAAAACAACA 58.814 43.478 3.53 0.00 44.04 3.33
572 678 7.442666 GTCAGATAAGAGGGTCAAATTATCACC 59.557 40.741 6.57 0.00 37.19 4.02
649 757 0.102481 AAGTAGTGGCAGTATCGGCG 59.898 55.000 5.16 0.00 0.00 6.46
707 815 3.470645 AAGGTGACCTGTGTCTGTTAC 57.529 47.619 4.15 0.00 42.28 2.50
711 819 3.576648 GTGACCTGTGTCTGTTACTAGC 58.423 50.000 0.00 0.00 42.28 3.42
712 820 3.256136 GTGACCTGTGTCTGTTACTAGCT 59.744 47.826 0.00 0.00 42.28 3.32
723 1086 6.114767 GTCTGTTACTAGCTAGTACTCAGGT 58.885 44.000 34.87 18.07 39.17 4.00
752 1115 8.713971 AGTGGTGAAATGGTATCATTACATCTA 58.286 33.333 0.58 0.00 42.29 1.98
807 1170 9.587772 CATAAGTTGTACATATATACTCCCTGC 57.412 37.037 0.00 0.00 0.00 4.85
818 1181 0.463204 ACTCCCTGCGTCTCATGATG 59.537 55.000 0.00 0.00 0.00 3.07
824 1187 3.379240 CCTGCGTCTCATGATGTAAGAG 58.621 50.000 0.00 0.00 0.00 2.85
849 1212 5.651172 TTTTGACAGTACATCAACGTGAG 57.349 39.130 11.05 0.00 35.82 3.51
868 1231 7.273188 CGTGAGAAAACGTCTTACATTATGA 57.727 36.000 0.00 0.00 41.81 2.15
871 1234 9.314501 GTGAGAAAACGTCTTACATTATGAAAC 57.685 33.333 0.00 0.00 41.45 2.78
879 1242 7.876068 ACGTCTTACATTATGAAACAGAGGAAA 59.124 33.333 0.00 0.00 0.00 3.13
926 1289 4.207165 GGGAACTAGCATCCAAAAGCATA 58.793 43.478 15.11 0.00 38.80 3.14
927 1290 4.276926 GGGAACTAGCATCCAAAAGCATAG 59.723 45.833 15.11 0.00 38.80 2.23
1048 1415 0.038251 GCAAAGCGGGAGAAAAAGGG 60.038 55.000 0.00 0.00 0.00 3.95
1143 1510 3.483869 ATCTCTTCCGCCCCTGCC 61.484 66.667 0.00 0.00 0.00 4.85
1213 1592 0.692756 CCTTTCCCCCTCCTCCTCTC 60.693 65.000 0.00 0.00 0.00 3.20
1215 1594 2.531483 TTTCCCCCTCCTCCTCTCCG 62.531 65.000 0.00 0.00 0.00 4.63
1248 1627 3.999333 TCGTCGTCGTCGTTCGCA 61.999 61.111 11.41 0.00 39.67 5.10
1284 1663 3.071602 CCCTGCAGGTAAGCATACATAGT 59.928 47.826 30.63 0.00 44.68 2.12
1302 1681 0.878416 GTCTCTCTGTGCTGAGACGT 59.122 55.000 7.27 0.00 46.10 4.34
1303 1682 0.877743 TCTCTCTGTGCTGAGACGTG 59.122 55.000 0.00 0.00 38.08 4.49
1304 1683 0.595588 CTCTCTGTGCTGAGACGTGT 59.404 55.000 0.00 0.00 38.08 4.49
1305 1684 0.312102 TCTCTGTGCTGAGACGTGTG 59.688 55.000 0.00 0.00 38.08 3.82
1306 1685 0.031314 CTCTGTGCTGAGACGTGTGT 59.969 55.000 0.00 0.00 36.23 3.72
1307 1686 1.266989 CTCTGTGCTGAGACGTGTGTA 59.733 52.381 0.00 0.00 36.23 2.90
1346 1727 3.574826 ACGGTTTCTAGCAAGAGAGAAGT 59.425 43.478 0.00 0.00 33.38 3.01
1347 1728 3.923461 CGGTTTCTAGCAAGAGAGAAGTG 59.077 47.826 0.00 0.00 33.38 3.16
1565 1958 2.430610 GGAGCTCTGCGAGGTGGAT 61.431 63.158 14.64 0.00 40.67 3.41
1571 1964 1.067821 CTCTGCGAGGTGGATAAGGAC 59.932 57.143 0.00 0.00 0.00 3.85
1580 1973 1.153229 GGATAAGGACGGCGGCTTT 60.153 57.895 16.23 16.23 0.00 3.51
1706 2099 0.601841 ACCTGCCGGTAAGACGTTTG 60.602 55.000 1.90 0.00 43.29 2.93
1712 2105 2.610232 GCCGGTAAGACGTTTGACCTTA 60.610 50.000 10.77 0.61 0.00 2.69
1718 2111 6.183360 CGGTAAGACGTTTGACCTTATTTCTC 60.183 42.308 10.77 0.00 0.00 2.87
1720 2113 7.063191 GGTAAGACGTTTGACCTTATTTCTCTC 59.937 40.741 5.33 0.00 0.00 3.20
1726 2119 6.206829 CGTTTGACCTTATTTCTCTCCCTTTT 59.793 38.462 0.00 0.00 0.00 2.27
2187 2619 1.165907 CCACGCACCAAGAGCAAGAA 61.166 55.000 0.00 0.00 0.00 2.52
2207 2639 1.678101 ACAAGAAGTCCAAGCACAAGC 59.322 47.619 0.00 0.00 42.56 4.01
2683 3138 7.452501 TGTTGCCCTACTACTAGAAAGAACTTA 59.547 37.037 0.00 0.00 0.00 2.24
2685 3140 8.235359 TGCCCTACTACTAGAAAGAACTTATC 57.765 38.462 0.00 0.00 0.00 1.75
2742 3197 5.658190 GTGTTAGGTGTAGGGATTACCACTA 59.342 44.000 0.00 0.00 43.89 2.74
2766 3221 6.396450 ACTCTACTAAGCTTTCGGTTTTAGG 58.604 40.000 3.20 0.00 32.30 2.69
2839 3294 2.665794 CGGGAAGAAAGCTTTTCGAAGC 60.666 50.000 14.05 0.62 45.81 3.86
2933 3395 4.261783 GCTAGCTGCCTTGTTTTTCTTTCT 60.262 41.667 7.70 0.00 35.15 2.52
2947 3409 3.340814 TCTTTCTAGGAAGCTGCCAAG 57.659 47.619 15.05 7.91 0.00 3.61
2970 3432 4.455606 CCCATGGTTCCAGAAGAATACTC 58.544 47.826 11.73 0.00 36.69 2.59
2980 3442 5.652891 TCCAGAAGAATACTCTGTCTGGTAC 59.347 44.000 21.33 0.00 45.52 3.34
2985 3447 8.770322 AGAAGAATACTCTGTCTGGTACTAGTA 58.230 37.037 6.10 0.00 34.15 1.82
2996 3458 3.558033 TGGTACTAGTATCATGGCGTGA 58.442 45.455 11.96 12.53 42.06 4.35
3021 3483 2.093235 CCCCTCTTCCTCTTCACATCAC 60.093 54.545 0.00 0.00 0.00 3.06
3022 3484 2.836981 CCCTCTTCCTCTTCACATCACT 59.163 50.000 0.00 0.00 0.00 3.41
3023 3485 4.026744 CCCTCTTCCTCTTCACATCACTA 58.973 47.826 0.00 0.00 0.00 2.74
3024 3486 4.142049 CCCTCTTCCTCTTCACATCACTAC 60.142 50.000 0.00 0.00 0.00 2.73
3025 3487 4.464244 CCTCTTCCTCTTCACATCACTACA 59.536 45.833 0.00 0.00 0.00 2.74
3026 3488 5.128499 CCTCTTCCTCTTCACATCACTACAT 59.872 44.000 0.00 0.00 0.00 2.29
3027 3489 6.214191 TCTTCCTCTTCACATCACTACATC 57.786 41.667 0.00 0.00 0.00 3.06
3028 3490 5.716703 TCTTCCTCTTCACATCACTACATCA 59.283 40.000 0.00 0.00 0.00 3.07
3029 3491 5.588958 TCCTCTTCACATCACTACATCAG 57.411 43.478 0.00 0.00 0.00 2.90
3030 3492 5.264395 TCCTCTTCACATCACTACATCAGA 58.736 41.667 0.00 0.00 0.00 3.27
3031 3493 5.716703 TCCTCTTCACATCACTACATCAGAA 59.283 40.000 0.00 0.00 0.00 3.02
3032 3494 6.211384 TCCTCTTCACATCACTACATCAGAAA 59.789 38.462 0.00 0.00 0.00 2.52
3033 3495 7.046652 CCTCTTCACATCACTACATCAGAAAT 58.953 38.462 0.00 0.00 0.00 2.17
3034 3496 7.551974 CCTCTTCACATCACTACATCAGAAATT 59.448 37.037 0.00 0.00 0.00 1.82
3035 3497 8.484641 TCTTCACATCACTACATCAGAAATTC 57.515 34.615 0.00 0.00 0.00 2.17
3036 3498 8.096414 TCTTCACATCACTACATCAGAAATTCA 58.904 33.333 0.00 0.00 0.00 2.57
3037 3499 7.838771 TCACATCACTACATCAGAAATTCAG 57.161 36.000 0.00 0.00 0.00 3.02
3038 3500 6.314648 TCACATCACTACATCAGAAATTCAGC 59.685 38.462 0.00 0.00 0.00 4.26
3039 3501 6.093082 CACATCACTACATCAGAAATTCAGCA 59.907 38.462 0.00 0.00 0.00 4.41
3040 3502 6.827251 ACATCACTACATCAGAAATTCAGCAT 59.173 34.615 0.00 0.00 0.00 3.79
3041 3503 6.915544 TCACTACATCAGAAATTCAGCATC 57.084 37.500 0.00 0.00 0.00 3.91
3042 3504 5.819379 TCACTACATCAGAAATTCAGCATCC 59.181 40.000 0.00 0.00 0.00 3.51
3097 3561 1.407979 CGGCCCTTCGTCATTACTACT 59.592 52.381 0.00 0.00 0.00 2.57
3098 3562 2.620115 CGGCCCTTCGTCATTACTACTA 59.380 50.000 0.00 0.00 0.00 1.82
3099 3563 3.549625 CGGCCCTTCGTCATTACTACTAC 60.550 52.174 0.00 0.00 0.00 2.73
3151 3616 2.073816 CACATCGGGTACAAACAGGAC 58.926 52.381 0.00 0.00 0.00 3.85
3198 3663 5.657745 TCCATCTACGACACCCAAATTACTA 59.342 40.000 0.00 0.00 0.00 1.82
3209 3674 6.071952 ACACCCAAATTACTACTGCATTCAAG 60.072 38.462 0.00 0.00 0.00 3.02
3236 3701 1.076192 AGTAGACTAGGCCACGGGG 60.076 63.158 5.01 0.00 37.18 5.73
3252 3717 0.892063 GGGGTTGCGAGCCAAAAATA 59.108 50.000 23.51 0.00 45.46 1.40
3271 3736 8.786898 CAAAAATATTCACAAGAGTCCTGAAGA 58.213 33.333 0.00 0.00 0.00 2.87
3275 3740 5.455056 TTCACAAGAGTCCTGAAGAGTAC 57.545 43.478 0.00 0.00 0.00 2.73
3295 3760 4.151258 ACACGAGAAGAATGCAATTGTG 57.849 40.909 7.40 0.00 36.07 3.33
3309 3774 4.454847 TGCAATTGTGTATTTGCATTTGGG 59.545 37.500 7.40 0.00 30.55 4.12
3378 3843 1.296056 AATGGCGCGCGAGTTACTTT 61.296 50.000 37.18 17.20 0.00 2.66
3388 3853 3.060740 CGCGAGTTACTTTGAAAGAACGT 60.061 43.478 12.53 2.95 0.00 3.99
3389 3854 4.549489 CGCGAGTTACTTTGAAAGAACGTT 60.549 41.667 12.53 0.00 0.00 3.99
3390 3855 5.260900 GCGAGTTACTTTGAAAGAACGTTT 58.739 37.500 12.53 0.00 0.00 3.60
3391 3856 5.391721 GCGAGTTACTTTGAAAGAACGTTTC 59.608 40.000 12.53 0.00 0.00 2.78
3392 3857 6.702897 CGAGTTACTTTGAAAGAACGTTTCT 58.297 36.000 12.53 0.00 43.15 2.52
3393 3858 7.515684 GCGAGTTACTTTGAAAGAACGTTTCTA 60.516 37.037 12.53 0.00 39.61 2.10
3394 3859 7.786572 CGAGTTACTTTGAAAGAACGTTTCTAC 59.213 37.037 12.53 0.00 39.61 2.59
3408 3873 5.693814 ACGTTTCTACTTTCTACGGTACTG 58.306 41.667 0.00 0.00 36.60 2.74
3500 3968 4.564940 AATATACTCCGTTCGGACAGAC 57.435 45.455 10.00 0.00 0.00 3.51
3506 4213 0.879765 CCGTTCGGACAGACTAGTGT 59.120 55.000 0.00 0.00 0.00 3.55
3507 4214 1.401148 CCGTTCGGACAGACTAGTGTG 60.401 57.143 17.93 17.93 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 31 2.549754 CGAGTTGTGATCTGTTTGGCTT 59.450 45.455 0.00 0.00 0.00 4.35
64 72 1.619654 TCGGGTCGACAAACCTTCTA 58.380 50.000 18.91 0.00 39.42 2.10
76 84 3.051392 GCCTTGCCAAATCGGGTCG 62.051 63.158 0.00 0.00 34.06 4.79
210 221 6.292168 CGATTGTTGTTTTAGATAGCTACCCG 60.292 42.308 0.00 0.00 0.00 5.28
227 238 1.978097 CAATGCCGTTGTCGATTGTTG 59.022 47.619 0.00 0.00 39.71 3.33
231 242 0.881118 AAGCAATGCCGTTGTCGATT 59.119 45.000 0.00 0.00 40.07 3.34
617 724 6.598064 ACTGCCACTACTTATTTGTATTGGTC 59.402 38.462 11.01 6.03 42.00 4.02
632 739 0.870307 CACGCCGATACTGCCACTAC 60.870 60.000 0.00 0.00 0.00 2.73
649 757 4.111916 GAGCATCTCTAAGCTTGACTCAC 58.888 47.826 9.86 0.00 42.04 3.51
707 815 4.336993 CCACTTGACCTGAGTACTAGCTAG 59.663 50.000 19.44 19.44 0.00 3.42
711 819 4.079970 TCACCACTTGACCTGAGTACTAG 58.920 47.826 0.00 0.00 0.00 2.57
712 820 4.108501 TCACCACTTGACCTGAGTACTA 57.891 45.455 0.00 0.00 0.00 1.82
723 1086 7.171653 TGTAATGATACCATTTCACCACTTGA 58.828 34.615 0.00 0.00 42.56 3.02
789 1152 5.646793 TGAGACGCAGGGAGTATATATGTAC 59.353 44.000 1.55 1.55 0.00 2.90
791 1154 4.663334 TGAGACGCAGGGAGTATATATGT 58.337 43.478 0.00 0.00 0.00 2.29
792 1155 5.358160 TCATGAGACGCAGGGAGTATATATG 59.642 44.000 0.00 0.00 0.00 1.78
793 1156 5.510430 TCATGAGACGCAGGGAGTATATAT 58.490 41.667 0.00 0.00 0.00 0.86
794 1157 4.918588 TCATGAGACGCAGGGAGTATATA 58.081 43.478 0.00 0.00 0.00 0.86
795 1158 3.767711 TCATGAGACGCAGGGAGTATAT 58.232 45.455 0.00 0.00 0.00 0.86
796 1159 3.223674 TCATGAGACGCAGGGAGTATA 57.776 47.619 0.00 0.00 0.00 1.47
797 1160 2.073252 TCATGAGACGCAGGGAGTAT 57.927 50.000 0.00 0.00 0.00 2.12
798 1161 1.683385 CATCATGAGACGCAGGGAGTA 59.317 52.381 0.09 0.00 0.00 2.59
799 1162 0.463204 CATCATGAGACGCAGGGAGT 59.537 55.000 0.09 0.00 0.00 3.85
800 1163 0.463204 ACATCATGAGACGCAGGGAG 59.537 55.000 0.09 0.00 0.00 4.30
802 1165 2.101415 TCTTACATCATGAGACGCAGGG 59.899 50.000 0.09 0.00 0.00 4.45
804 1167 4.039151 ACTCTTACATCATGAGACGCAG 57.961 45.455 0.09 0.00 33.61 5.18
805 1168 4.456280 AACTCTTACATCATGAGACGCA 57.544 40.909 0.09 0.00 33.61 5.24
806 1169 5.786401 AAAACTCTTACATCATGAGACGC 57.214 39.130 0.09 0.00 33.61 5.19
844 1207 7.273188 TCATAATGTAAGACGTTTTCTCACG 57.727 36.000 0.00 0.00 46.04 4.35
847 1210 9.530129 CTGTTTCATAATGTAAGACGTTTTCTC 57.470 33.333 0.00 0.00 31.02 2.87
848 1211 9.268268 TCTGTTTCATAATGTAAGACGTTTTCT 57.732 29.630 0.00 0.00 35.32 2.52
849 1212 9.530129 CTCTGTTTCATAATGTAAGACGTTTTC 57.470 33.333 0.00 0.00 0.00 2.29
890 1253 4.811557 GCTAGTTCCCGGATGAATATATGC 59.188 45.833 0.73 0.00 0.00 3.14
977 1340 9.112725 CCATTTCTTTTTCCTGTCAAGAAAAAT 57.887 29.630 18.12 5.39 46.51 1.82
983 1350 6.211515 CACTCCATTTCTTTTTCCTGTCAAG 58.788 40.000 0.00 0.00 0.00 3.02
1143 1510 1.673665 AGAGGAAAAGGCAGCAGCG 60.674 57.895 0.00 0.00 43.41 5.18
1231 1610 3.999333 TGCGAACGACGACGACGA 61.999 61.111 25.15 0.25 45.77 4.20
1232 1611 3.798776 GTGCGAACGACGACGACG 61.799 66.667 17.60 17.60 45.77 5.12
1233 1612 2.723271 TGTGCGAACGACGACGAC 60.723 61.111 15.32 6.72 45.77 4.34
1284 1663 0.877743 CACGTCTCAGCACAGAGAGA 59.122 55.000 4.08 0.00 44.76 3.10
1302 1681 3.118956 TCTCACACACACACACATACACA 60.119 43.478 0.00 0.00 0.00 3.72
1303 1682 3.245284 GTCTCACACACACACACATACAC 59.755 47.826 0.00 0.00 0.00 2.90
1304 1683 3.453424 GTCTCACACACACACACATACA 58.547 45.455 0.00 0.00 0.00 2.29
1305 1684 2.471370 CGTCTCACACACACACACATAC 59.529 50.000 0.00 0.00 0.00 2.39
1306 1685 2.544903 CCGTCTCACACACACACACATA 60.545 50.000 0.00 0.00 0.00 2.29
1307 1686 1.570813 CGTCTCACACACACACACAT 58.429 50.000 0.00 0.00 0.00 3.21
1346 1727 2.029964 GTTCCCGCACGAGAACCA 59.970 61.111 6.20 0.00 37.08 3.67
1347 1728 2.027625 CAGTTCCCGCACGAGAACC 61.028 63.158 12.90 0.00 42.73 3.62
1373 1760 1.032014 GCACCCACAGAAAGAGCAAA 58.968 50.000 0.00 0.00 0.00 3.68
1565 1958 1.217244 GAGAAAGCCGCCGTCCTTA 59.783 57.895 0.00 0.00 0.00 2.69
1601 1994 1.222113 CTTTTCCTCCTCCTCGGCC 59.778 63.158 0.00 0.00 0.00 6.13
1613 2006 1.239347 GGGAGTCACTGCACTTTTCC 58.761 55.000 0.00 0.00 0.00 3.13
1706 2099 5.354513 CGGAAAAAGGGAGAGAAATAAGGTC 59.645 44.000 0.00 0.00 0.00 3.85
1712 2105 2.447443 GCCGGAAAAAGGGAGAGAAAT 58.553 47.619 5.05 0.00 0.00 2.17
1718 2111 0.960861 GTCTGGCCGGAAAAAGGGAG 60.961 60.000 18.11 0.00 0.00 4.30
1720 2113 2.332654 CGTCTGGCCGGAAAAAGGG 61.333 63.158 18.11 0.00 0.00 3.95
1912 2305 3.741476 GGCACAGCGCTTTCCTGG 61.741 66.667 7.50 0.00 41.91 4.45
2143 2542 0.317479 CGTCGAGGAGGTTGAAGGTT 59.683 55.000 0.00 0.00 0.00 3.50
2187 2619 1.678101 GCTTGTGCTTGGACTTCTTGT 59.322 47.619 0.00 0.00 36.03 3.16
2683 3138 7.672239 AGACTCCTACTGAAACTACTTTCTGAT 59.328 37.037 8.15 0.00 38.24 2.90
2685 3140 7.222000 AGACTCCTACTGAAACTACTTTCTG 57.778 40.000 0.00 0.00 39.84 3.02
2698 3153 5.124645 ACACGACCTAATAGACTCCTACTG 58.875 45.833 0.00 0.00 0.00 2.74
2742 3197 6.014755 ACCTAAAACCGAAAGCTTAGTAGAGT 60.015 38.462 0.00 0.00 0.00 3.24
2766 3221 4.035208 CGGCAATATCCTAACAGACCAAAC 59.965 45.833 0.00 0.00 0.00 2.93
2839 3294 1.469703 TGCCTCGCATGATTCAAACAG 59.530 47.619 0.00 0.00 31.71 3.16
2933 3395 1.574526 ATGGGCTTGGCAGCTTCCTA 61.575 55.000 3.45 0.00 46.44 2.94
2947 3409 2.149973 ATTCTTCTGGAACCATGGGC 57.850 50.000 18.09 7.56 36.70 5.36
2948 3410 4.164988 AGAGTATTCTTCTGGAACCATGGG 59.835 45.833 18.09 0.00 36.70 4.00
2949 3411 5.121811 CAGAGTATTCTTCTGGAACCATGG 58.878 45.833 11.19 11.19 36.70 3.66
2950 3412 5.738909 ACAGAGTATTCTTCTGGAACCATG 58.261 41.667 7.13 0.00 36.70 3.66
2951 3413 5.723887 AGACAGAGTATTCTTCTGGAACCAT 59.276 40.000 7.13 0.00 36.70 3.55
2952 3414 5.047021 CAGACAGAGTATTCTTCTGGAACCA 60.047 44.000 14.26 0.00 36.28 3.67
2953 3415 5.415221 CAGACAGAGTATTCTTCTGGAACC 58.585 45.833 14.26 0.00 36.28 3.62
2970 3432 4.320567 CGCCATGATACTAGTACCAGACAG 60.321 50.000 4.31 0.00 0.00 3.51
2980 3442 3.997021 GGGAATTCACGCCATGATACTAG 59.003 47.826 7.93 0.00 37.11 2.57
2985 3447 0.552848 AGGGGAATTCACGCCATGAT 59.447 50.000 7.93 0.00 43.85 2.45
2996 3458 3.260205 TGTGAAGAGGAAGAGGGGAATT 58.740 45.455 0.00 0.00 0.00 2.17
3021 3483 4.518211 GGGGATGCTGAATTTCTGATGTAG 59.482 45.833 7.40 0.00 0.00 2.74
3022 3484 4.166725 AGGGGATGCTGAATTTCTGATGTA 59.833 41.667 7.40 0.00 0.00 2.29
3023 3485 3.053095 AGGGGATGCTGAATTTCTGATGT 60.053 43.478 7.40 0.00 0.00 3.06
3024 3486 3.318275 CAGGGGATGCTGAATTTCTGATG 59.682 47.826 7.40 0.00 0.00 3.07
3025 3487 3.053095 ACAGGGGATGCTGAATTTCTGAT 60.053 43.478 7.40 0.00 0.00 2.90
3026 3488 2.309755 ACAGGGGATGCTGAATTTCTGA 59.690 45.455 7.40 0.00 0.00 3.27
3027 3489 2.426024 CACAGGGGATGCTGAATTTCTG 59.574 50.000 0.00 0.00 0.00 3.02
3028 3490 2.731572 CACAGGGGATGCTGAATTTCT 58.268 47.619 0.00 0.00 0.00 2.52
3029 3491 1.135721 GCACAGGGGATGCTGAATTTC 59.864 52.381 0.00 0.00 40.08 2.17
3030 3492 1.188863 GCACAGGGGATGCTGAATTT 58.811 50.000 0.00 0.00 40.08 1.82
3031 3493 0.685458 GGCACAGGGGATGCTGAATT 60.685 55.000 0.00 0.00 42.93 2.17
3032 3494 1.076485 GGCACAGGGGATGCTGAAT 60.076 57.895 0.00 0.00 42.93 2.57
3033 3495 2.079088 TTGGCACAGGGGATGCTGAA 62.079 55.000 0.00 0.00 42.39 3.02
3034 3496 2.079088 TTTGGCACAGGGGATGCTGA 62.079 55.000 0.00 0.00 42.39 4.26
3035 3497 0.974010 ATTTGGCACAGGGGATGCTG 60.974 55.000 0.00 0.00 42.39 4.41
3036 3498 0.685458 GATTTGGCACAGGGGATGCT 60.685 55.000 0.00 0.00 42.39 3.79
3037 3499 0.685458 AGATTTGGCACAGGGGATGC 60.685 55.000 0.00 0.00 42.39 3.91
3038 3500 2.301346 GTAGATTTGGCACAGGGGATG 58.699 52.381 0.00 0.00 42.39 3.51
3039 3501 1.215423 GGTAGATTTGGCACAGGGGAT 59.785 52.381 0.00 0.00 42.39 3.85
3040 3502 0.623723 GGTAGATTTGGCACAGGGGA 59.376 55.000 0.00 0.00 42.39 4.81
3041 3503 0.395724 GGGTAGATTTGGCACAGGGG 60.396 60.000 0.00 0.00 42.39 4.79
3042 3504 0.331278 TGGGTAGATTTGGCACAGGG 59.669 55.000 0.00 0.00 42.39 4.45
3099 3563 6.302549 CCATTAATCAGATACGTACGAGTTCG 59.697 42.308 24.41 7.32 46.33 3.95
3151 3616 2.277084 GTAACGGTGCAGTTATCAGGG 58.723 52.381 2.28 0.00 38.63 4.45
3198 3663 1.133513 TGGTTCCACCTTGAATGCAGT 60.134 47.619 0.00 0.00 39.58 4.40
3209 3674 1.481363 GCCTAGTCTACTGGTTCCACC 59.519 57.143 0.00 0.00 39.22 4.61
3236 3701 4.233789 TGTGAATATTTTTGGCTCGCAAC 58.766 39.130 0.00 0.00 0.00 4.17
3241 3706 6.151817 AGGACTCTTGTGAATATTTTTGGCTC 59.848 38.462 0.00 0.00 0.00 4.70
3252 3717 5.540337 TGTACTCTTCAGGACTCTTGTGAAT 59.460 40.000 0.00 0.00 33.99 2.57
3271 3736 4.997395 ACAATTGCATTCTTCTCGTGTACT 59.003 37.500 5.05 0.00 0.00 2.73
3275 3740 4.151258 ACACAATTGCATTCTTCTCGTG 57.849 40.909 5.05 0.00 0.00 4.35
3295 3760 3.348647 AAAGGGCCCAAATGCAAATAC 57.651 42.857 27.56 0.00 0.00 1.89
3309 3774 0.823356 TGCTGACTGGTGAAAAGGGC 60.823 55.000 0.00 0.00 0.00 5.19
3344 3809 2.107141 ATTCGCTACGCTCTGCCC 59.893 61.111 0.00 0.00 0.00 5.36
3388 3853 5.972107 AGCAGTACCGTAGAAAGTAGAAA 57.028 39.130 0.00 0.00 0.00 2.52
3389 3854 6.093219 CAGTAGCAGTACCGTAGAAAGTAGAA 59.907 42.308 0.00 0.00 0.00 2.10
3390 3855 5.583854 CAGTAGCAGTACCGTAGAAAGTAGA 59.416 44.000 0.00 0.00 0.00 2.59
3391 3856 5.220815 CCAGTAGCAGTACCGTAGAAAGTAG 60.221 48.000 0.00 0.00 0.00 2.57
3392 3857 4.637534 CCAGTAGCAGTACCGTAGAAAGTA 59.362 45.833 0.00 0.00 0.00 2.24
3393 3858 3.442977 CCAGTAGCAGTACCGTAGAAAGT 59.557 47.826 0.00 0.00 0.00 2.66
3394 3859 3.734293 GCCAGTAGCAGTACCGTAGAAAG 60.734 52.174 0.00 0.00 42.97 2.62
3408 3873 0.469917 TAGCTCCAATGGCCAGTAGC 59.530 55.000 18.13 18.13 42.60 3.58
3500 3968 1.335324 GCTGCAACCAAAGCACACTAG 60.335 52.381 0.00 0.00 39.31 2.57
3506 4213 4.283403 GCCGCTGCAACCAAAGCA 62.283 61.111 0.00 0.00 39.47 3.91


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

AutoCloner maintained by Alex Coulton.