Multiple sequence alignment - TraesCS5D01G514300

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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 TraesCS5D01G514300 chr5D 100.000 3311 0 0 1 3311 538042595 538045905 0.000000e+00 6115.0
1 TraesCS5D01G514300 chr5D 89.749 478 31 10 2065 2538 537750271 537749808 2.200000e-166 595.0
2 TraesCS5D01G514300 chr5D 79.830 352 64 5 809 1155 537843646 537843297 1.970000e-62 250.0
3 TraesCS5D01G514300 chr4A 95.533 2664 75 4 571 3228 632230438 632233063 0.000000e+00 4220.0
4 TraesCS5D01G514300 chr4A 92.663 1799 111 10 760 2538 631950409 631948612 0.000000e+00 2571.0
5 TraesCS5D01G514300 chr5B 94.585 1385 66 4 1339 2718 678708580 678707200 0.000000e+00 2134.0
6 TraesCS5D01G514300 chr5B 91.304 667 58 0 1216 1882 678457220 678456554 0.000000e+00 911.0
7 TraesCS5D01G514300 chr5B 91.091 651 55 3 1880 2528 678455901 678455252 0.000000e+00 878.0
8 TraesCS5D01G514300 chr5B 93.996 483 28 1 2753 3234 678707203 678706721 0.000000e+00 730.0
9 TraesCS5D01G514300 chr5B 91.176 374 33 0 717 1090 678708952 678708579 2.950000e-140 508.0
10 TraesCS5D01G514300 chr5B 89.744 273 28 0 802 1074 678487014 678486742 1.890000e-92 350.0
11 TraesCS5D01G514300 chr5B 77.122 271 32 21 317 573 210164802 210165056 2.680000e-26 130.0
12 TraesCS5D01G514300 chr4D 91.724 580 36 3 1 572 6955526 6954951 0.000000e+00 795.0
13 TraesCS5D01G514300 chr4D 82.322 577 82 15 1 569 57685436 57684872 1.790000e-132 483.0
14 TraesCS5D01G514300 chr4D 98.851 87 1 0 3225 3311 372139019 372139105 4.420000e-34 156.0
15 TraesCS5D01G514300 chr4D 100.000 83 0 0 3229 3311 147504669 147504751 1.590000e-33 154.0
16 TraesCS5D01G514300 chr4D 100.000 83 0 0 3229 3311 275075516 275075434 1.590000e-33 154.0
17 TraesCS5D01G514300 chr4D 100.000 83 0 0 3229 3311 372148105 372148187 1.590000e-33 154.0
18 TraesCS5D01G514300 chr4D 95.745 94 2 2 3219 3311 196320905 196320813 2.060000e-32 150.0
19 TraesCS5D01G514300 chr6D 87.326 576 66 3 1 569 433205670 433206245 0.000000e+00 652.0
20 TraesCS5D01G514300 chr6D 87.123 497 60 3 1 494 22102834 22102339 8.020000e-156 560.0
21 TraesCS5D01G514300 chr6D 100.000 83 0 0 3229 3311 403568472 403568554 1.590000e-33 154.0
22 TraesCS5D01G514300 chr6D 100.000 83 0 0 3229 3311 423014785 423014703 1.590000e-33 154.0
23 TraesCS5D01G514300 chr6D 100.000 83 0 0 3229 3311 428556134 428556052 1.590000e-33 154.0
24 TraesCS5D01G514300 chr2A 85.223 582 73 9 1 571 743590799 743591378 1.320000e-163 586.0
25 TraesCS5D01G514300 chr2A 89.333 375 33 3 204 571 19331176 19331550 6.470000e-127 464.0
26 TraesCS5D01G514300 chr2A 92.308 91 3 1 120 206 19311588 19311678 3.470000e-25 126.0
27 TraesCS5D01G514300 chr3D 84.983 586 70 15 1 573 430185559 430186139 2.220000e-161 579.0
28 TraesCS5D01G514300 chr2B 82.837 571 85 11 12 572 363286594 363286027 1.770000e-137 499.0
29 TraesCS5D01G514300 chr7A 82.373 573 86 10 10 571 267423200 267422632 4.970000e-133 484.0
30 TraesCS5D01G514300 chr1B 81.695 590 80 23 1 571 17162211 17162791 1.800000e-127 466.0
31 TraesCS5D01G514300 chr1B 94.643 56 3 0 518 573 585205373 585205318 1.640000e-13 87.9
32 TraesCS5D01G514300 chr6B 96.739 92 0 3 3221 3311 517322845 517322934 2.060000e-32 150.0
33 TraesCS5D01G514300 chr6B 85.455 110 8 6 469 571 693932017 693932125 1.260000e-19 108.0


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 TraesCS5D01G514300 chr5D 538042595 538045905 3310 False 6115.0 6115 100.000000 1 3311 1 chr5D.!!$F1 3310
1 TraesCS5D01G514300 chr4A 632230438 632233063 2625 False 4220.0 4220 95.533000 571 3228 1 chr4A.!!$F1 2657
2 TraesCS5D01G514300 chr4A 631948612 631950409 1797 True 2571.0 2571 92.663000 760 2538 1 chr4A.!!$R1 1778
3 TraesCS5D01G514300 chr5B 678706721 678708952 2231 True 1124.0 2134 93.252333 717 3234 3 chr5B.!!$R3 2517
4 TraesCS5D01G514300 chr5B 678455252 678457220 1968 True 894.5 911 91.197500 1216 2528 2 chr5B.!!$R2 1312
5 TraesCS5D01G514300 chr4D 6954951 6955526 575 True 795.0 795 91.724000 1 572 1 chr4D.!!$R1 571
6 TraesCS5D01G514300 chr4D 57684872 57685436 564 True 483.0 483 82.322000 1 569 1 chr4D.!!$R2 568
7 TraesCS5D01G514300 chr6D 433205670 433206245 575 False 652.0 652 87.326000 1 569 1 chr6D.!!$F2 568
8 TraesCS5D01G514300 chr2A 743590799 743591378 579 False 586.0 586 85.223000 1 571 1 chr2A.!!$F3 570
9 TraesCS5D01G514300 chr3D 430185559 430186139 580 False 579.0 579 84.983000 1 573 1 chr3D.!!$F1 572
10 TraesCS5D01G514300 chr2B 363286027 363286594 567 True 499.0 499 82.837000 12 572 1 chr2B.!!$R1 560
11 TraesCS5D01G514300 chr7A 267422632 267423200 568 True 484.0 484 82.373000 10 571 1 chr7A.!!$R1 561
12 TraesCS5D01G514300 chr1B 17162211 17162791 580 False 466.0 466 81.695000 1 571 1 chr1B.!!$F1 570

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
440 453 0.037734 AATCCGGCTTCGAACCCTTT 59.962 50.0 7.87 0.0 35.61 3.11 F
790 823 0.321653 AAAACCTAGCCTCTGCCGTG 60.322 55.0 0.00 0.0 38.69 4.94 F
900 936 0.680061 ACAACGACCAGGAAGACCTC 59.320 55.0 0.00 0.0 45.94 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 1467 1.521906 CACGTCGGGTTGGAACACA 60.522 57.895 0.0 0.0 39.29 3.72 R
1840 1879 1.638589 CAAAAGAGGGTACATGGGGGA 59.361 52.381 0.0 0.0 0.00 4.81 R
2896 3628 0.038892 GGCTTTGTCGAGTGTCGGTA 60.039 55.000 0.0 0.0 40.88 4.02 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
98 102 2.282251 ACCTGCTCGACTCGGTCA 60.282 61.111 0.00 0.00 32.09 4.02
206 214 2.233605 ATCATTTCCGTCGCACCCGA 62.234 55.000 0.00 0.00 42.01 5.14
249 257 0.694771 ATCCTCTTGCAGCAGTGGAA 59.305 50.000 12.06 0.00 39.37 3.53
440 453 0.037734 AATCCGGCTTCGAACCCTTT 59.962 50.000 7.87 0.00 35.61 3.11
459 472 5.696724 CCCTTTCCGTTATTAGCTGATACTG 59.303 44.000 0.00 0.00 0.00 2.74
621 648 1.520342 GCTGAGACCATGTCCGAGC 60.520 63.158 0.00 0.00 32.70 5.03
649 676 4.138290 TCCTAGTTTTGTTTTGCATCGGA 58.862 39.130 0.00 0.00 0.00 4.55
671 698 2.673368 GTCAGCATCCTAGTTGTTTCCG 59.327 50.000 0.00 0.00 0.00 4.30
790 823 0.321653 AAAACCTAGCCTCTGCCGTG 60.322 55.000 0.00 0.00 38.69 4.94
828 864 1.003355 CATGTCGGGCAGTGGTTCT 60.003 57.895 0.00 0.00 0.00 3.01
892 928 1.002250 CTTCGACGACAACGACCAGG 61.002 60.000 0.00 0.00 42.66 4.45
893 929 1.446516 TTCGACGACAACGACCAGGA 61.447 55.000 0.00 0.00 42.66 3.86
900 936 0.680061 ACAACGACCAGGAAGACCTC 59.320 55.000 0.00 0.00 45.94 3.85
951 987 2.048127 GTCAAGAAGGCGGCGTCT 60.048 61.111 21.24 21.24 0.00 4.18
997 1033 2.675423 CCGACGAGGTGGTCCAGA 60.675 66.667 0.00 0.00 35.89 3.86
1138 1174 0.966920 GACCTTCCTCCACGACTTCA 59.033 55.000 0.00 0.00 0.00 3.02
1142 1178 2.125912 CCTCCACGACTTCAGCCG 60.126 66.667 0.00 0.00 0.00 5.52
1194 1230 1.592669 GTCGCTCCACATGATCCCG 60.593 63.158 0.00 0.00 0.00 5.14
1224 1260 2.046892 CCCTGCTGGAGGTTCACG 60.047 66.667 14.48 0.00 40.87 4.35
1234 1270 3.948719 GGTTCACGGGCCTCACCA 61.949 66.667 0.84 0.00 42.05 4.17
1428 1467 2.049526 TCTTGCGTCGACATGCGT 60.050 55.556 17.16 0.00 41.80 5.24
1449 1488 1.367102 GTTCCAACCCGACGTGGTA 59.633 57.895 8.20 0.00 37.76 3.25
1459 1498 1.058129 CCGACGTGGTATTTTCGTTCG 59.942 52.381 0.00 0.00 37.92 3.95
2595 3308 6.599356 TTTGAACCTCTAGTGCATGTAGTA 57.401 37.500 0.00 0.00 32.45 1.82
2745 3458 3.127376 TGATTGTTGCCATGATTGTCTCG 59.873 43.478 0.00 0.00 0.00 4.04
2811 3524 1.078709 ATCGACACATTTGCCGAGTG 58.921 50.000 0.00 0.00 39.12 3.51
2850 3563 2.818130 TTTTTGCCAGACAATCAGCC 57.182 45.000 0.00 0.00 38.31 4.85
2907 3639 3.413522 GGGAAACTACCGACACTCG 57.586 57.895 0.00 0.00 40.07 4.18
2919 3651 0.166814 GACACTCGACAAAGCCATGC 59.833 55.000 0.00 0.00 0.00 4.06
2982 3714 4.797604 GCACTACATGTCTCTAATCGCCAT 60.798 45.833 0.00 0.00 0.00 4.40
3005 3737 3.438781 GGTTGATGGCGTGTTCTCATTTA 59.561 43.478 0.00 0.00 0.00 1.40
3082 3814 0.755327 GCCCAAGTGTCAACCAGGTT 60.755 55.000 0.00 0.00 0.00 3.50
3085 3817 0.385390 CAAGTGTCAACCAGGTTGCC 59.615 55.000 25.70 16.77 42.55 4.52
3101 3833 3.242518 GTTGCCCTCGCTAAATGTTTTC 58.757 45.455 0.00 0.00 35.36 2.29
3198 3930 7.451255 TGACAAACTATTTGAAAGGACATCCAT 59.549 33.333 8.24 0.00 43.26 3.41
3228 3960 6.642707 TTAGGGTTTTGGTGTTAATGACAG 57.357 37.500 0.00 0.00 39.39 3.51
3230 3962 4.959839 AGGGTTTTGGTGTTAATGACAGTT 59.040 37.500 0.00 0.00 39.39 3.16
3234 3966 4.909696 TTGGTGTTAATGACAGTTGTGG 57.090 40.909 0.00 0.00 39.39 4.17
3235 3967 2.621055 TGGTGTTAATGACAGTTGTGGC 59.379 45.455 0.00 0.00 39.39 5.01
3240 3972 2.194597 TGACAGTTGTGGCACCCC 59.805 61.111 16.26 5.30 36.47 4.95
3241 3973 2.978010 GACAGTTGTGGCACCCCG 60.978 66.667 16.26 3.53 0.00 5.73
3242 3974 4.579384 ACAGTTGTGGCACCCCGG 62.579 66.667 16.26 8.59 0.00 5.73
3252 3984 4.020617 CACCCCGGCTCAGAGCAA 62.021 66.667 24.09 0.00 44.75 3.91
3253 3985 4.021925 ACCCCGGCTCAGAGCAAC 62.022 66.667 24.09 6.67 44.75 4.17
3254 3986 4.785453 CCCCGGCTCAGAGCAACC 62.785 72.222 24.09 5.93 44.75 3.77
3257 3989 4.379243 CGGCTCAGAGCAACCGGT 62.379 66.667 24.09 0.00 44.75 5.28
3258 3990 2.032681 GGCTCAGAGCAACCGGTT 59.967 61.111 24.09 15.86 44.75 4.44
3259 3991 1.600916 GGCTCAGAGCAACCGGTTT 60.601 57.895 24.09 3.54 44.75 3.27
3260 3992 0.321298 GGCTCAGAGCAACCGGTTTA 60.321 55.000 24.09 0.00 44.75 2.01
3261 3993 0.796927 GCTCAGAGCAACCGGTTTAC 59.203 55.000 19.55 13.30 41.89 2.01
3262 3994 1.439679 CTCAGAGCAACCGGTTTACC 58.560 55.000 19.55 9.23 0.00 2.85
3263 3995 0.035739 TCAGAGCAACCGGTTTACCC 59.964 55.000 19.55 3.53 0.00 3.69
3264 3996 0.036306 CAGAGCAACCGGTTTACCCT 59.964 55.000 19.55 11.57 0.00 4.34
3265 3997 0.036306 AGAGCAACCGGTTTACCCTG 59.964 55.000 19.55 7.29 0.00 4.45
3266 3998 1.583495 GAGCAACCGGTTTACCCTGC 61.583 60.000 19.55 18.10 34.57 4.85
3267 3999 1.899534 GCAACCGGTTTACCCTGCA 60.900 57.895 19.55 0.00 34.54 4.41
3268 4000 1.248101 GCAACCGGTTTACCCTGCAT 61.248 55.000 19.55 0.00 34.54 3.96
3269 4001 1.253100 CAACCGGTTTACCCTGCATT 58.747 50.000 19.55 0.00 0.00 3.56
3270 4002 1.067915 CAACCGGTTTACCCTGCATTG 60.068 52.381 19.55 0.00 0.00 2.82
3271 4003 1.248101 ACCGGTTTACCCTGCATTGC 61.248 55.000 0.00 0.46 0.00 3.56
3272 4004 1.510844 CGGTTTACCCTGCATTGCC 59.489 57.895 6.12 0.00 0.00 4.52
3273 4005 1.247419 CGGTTTACCCTGCATTGCCA 61.247 55.000 6.12 0.00 0.00 4.92
3274 4006 0.532115 GGTTTACCCTGCATTGCCAG 59.468 55.000 6.12 3.85 0.00 4.85
3275 4007 0.108662 GTTTACCCTGCATTGCCAGC 60.109 55.000 6.12 0.00 0.00 4.85
3276 4008 1.257055 TTTACCCTGCATTGCCAGCC 61.257 55.000 6.12 0.00 0.00 4.85
3277 4009 3.660422 TACCCTGCATTGCCAGCCC 62.660 63.158 6.12 0.00 0.00 5.19
3279 4011 3.458163 CCTGCATTGCCAGCCCAG 61.458 66.667 6.12 0.00 0.00 4.45
3280 4012 2.361992 CTGCATTGCCAGCCCAGA 60.362 61.111 6.12 0.00 0.00 3.86
3281 4013 2.361992 TGCATTGCCAGCCCAGAG 60.362 61.111 6.12 0.00 0.00 3.35
3282 4014 2.044650 GCATTGCCAGCCCAGAGA 60.045 61.111 0.00 0.00 0.00 3.10
3283 4015 1.455217 GCATTGCCAGCCCAGAGAT 60.455 57.895 0.00 0.00 0.00 2.75
3284 4016 1.453762 GCATTGCCAGCCCAGAGATC 61.454 60.000 0.00 0.00 0.00 2.75
3285 4017 1.147824 ATTGCCAGCCCAGAGATCG 59.852 57.895 0.00 0.00 0.00 3.69
3286 4018 1.340399 ATTGCCAGCCCAGAGATCGA 61.340 55.000 0.00 0.00 0.00 3.59
3287 4019 1.964608 TTGCCAGCCCAGAGATCGAG 61.965 60.000 0.00 0.00 0.00 4.04
3288 4020 2.430610 GCCAGCCCAGAGATCGAGT 61.431 63.158 0.00 0.00 0.00 4.18
3289 4021 1.739049 CCAGCCCAGAGATCGAGTC 59.261 63.158 0.00 0.00 0.00 3.36
3290 4022 0.754957 CCAGCCCAGAGATCGAGTCT 60.755 60.000 0.00 0.00 40.81 3.24
3291 4023 1.110442 CAGCCCAGAGATCGAGTCTT 58.890 55.000 0.00 0.00 37.29 3.01
3292 4024 1.066908 CAGCCCAGAGATCGAGTCTTC 59.933 57.143 0.00 0.00 37.29 2.87
3293 4025 1.064017 AGCCCAGAGATCGAGTCTTCT 60.064 52.381 0.00 0.00 37.29 2.85
3294 4026 1.066908 GCCCAGAGATCGAGTCTTCTG 59.933 57.143 9.86 9.86 37.29 3.02
3295 4027 1.680735 CCCAGAGATCGAGTCTTCTGG 59.319 57.143 21.32 21.32 43.96 3.86
3296 4028 1.066908 CCAGAGATCGAGTCTTCTGGC 59.933 57.143 18.40 0.00 41.26 4.85
3297 4029 1.747924 CAGAGATCGAGTCTTCTGGCA 59.252 52.381 9.24 0.00 37.29 4.92
3298 4030 2.165234 CAGAGATCGAGTCTTCTGGCAA 59.835 50.000 9.24 0.00 37.29 4.52
3299 4031 3.030291 AGAGATCGAGTCTTCTGGCAAT 58.970 45.455 0.00 0.00 37.29 3.56
3300 4032 4.037327 CAGAGATCGAGTCTTCTGGCAATA 59.963 45.833 9.24 0.00 37.29 1.90
3301 4033 4.037446 AGAGATCGAGTCTTCTGGCAATAC 59.963 45.833 0.00 0.00 37.29 1.89
3302 4034 3.701542 AGATCGAGTCTTCTGGCAATACA 59.298 43.478 0.00 0.00 31.47 2.29
3303 4035 3.232213 TCGAGTCTTCTGGCAATACAC 57.768 47.619 0.00 0.00 0.00 2.90
3304 4036 2.560981 TCGAGTCTTCTGGCAATACACA 59.439 45.455 0.00 0.00 0.00 3.72
3305 4037 3.006430 TCGAGTCTTCTGGCAATACACAA 59.994 43.478 0.00 0.00 0.00 3.33
3306 4038 3.123621 CGAGTCTTCTGGCAATACACAAC 59.876 47.826 0.00 0.00 0.00 3.32
3307 4039 4.065088 GAGTCTTCTGGCAATACACAACA 58.935 43.478 0.00 0.00 0.00 3.33
3308 4040 4.460263 AGTCTTCTGGCAATACACAACAA 58.540 39.130 0.00 0.00 0.00 2.83
3309 4041 4.275936 AGTCTTCTGGCAATACACAACAAC 59.724 41.667 0.00 0.00 0.00 3.32
3310 4042 4.036262 GTCTTCTGGCAATACACAACAACA 59.964 41.667 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.518112 TGCGCTCCAAGCAAACCA 60.518 55.556 9.73 0.00 42.58 3.67
45 47 4.265056 AACACGGGTCCCAGGTGC 62.265 66.667 14.16 0.00 35.11 5.01
59 61 2.575532 CAAAAGGTCAGCAGAGGAACA 58.424 47.619 0.00 0.00 0.00 3.18
98 102 2.404083 CACGTTTGTGCTGACCCTT 58.596 52.632 0.00 0.00 39.67 3.95
206 214 5.439721 TGAGCATTTGCATATGAGGTTAGT 58.560 37.500 19.75 0.00 45.16 2.24
212 220 5.473846 AGAGGATTGAGCATTTGCATATGAG 59.526 40.000 19.75 0.00 45.16 2.90
249 257 1.003839 TTCTGCTTCGCCAACGGAT 60.004 52.632 0.00 0.00 40.63 4.18
440 453 6.264518 TGACATCAGTATCAGCTAATAACGGA 59.735 38.462 0.00 0.00 0.00 4.69
459 472 4.685924 CATAACCAAAAGCCCATGACATC 58.314 43.478 0.00 0.00 0.00 3.06
545 572 5.618056 TTTTAGAACGAAGACGCTAGAGA 57.382 39.130 0.00 0.00 43.96 3.10
621 648 4.051237 GCAAAACAAAACTAGGAAGCTGG 58.949 43.478 0.00 0.00 0.00 4.85
649 676 3.617531 CGGAAACAACTAGGATGCTGACT 60.618 47.826 0.00 0.00 0.00 3.41
671 698 1.594269 CGTGTACGTCGACAGCACAC 61.594 60.000 23.91 23.91 36.89 3.82
726 759 0.621082 TTAATGGGATGTGGGCGACA 59.379 50.000 4.40 4.40 39.53 4.35
740 773 2.094675 GATGGCCGATGGGGATTAATG 58.905 52.381 0.00 0.00 38.47 1.90
790 823 1.202615 GGCGGTTAGGTTAGTGGATCC 60.203 57.143 4.20 4.20 0.00 3.36
892 928 1.522580 GCAGGGCGATGAGGTCTTC 60.523 63.158 0.00 0.00 0.00 2.87
893 929 2.249413 CTGCAGGGCGATGAGGTCTT 62.249 60.000 5.57 0.00 0.00 3.01
995 1031 0.033796 CACCCCAATGTCCATGCTCT 60.034 55.000 0.00 0.00 0.00 4.09
997 1033 1.683365 GCACCCCAATGTCCATGCT 60.683 57.895 0.00 0.00 0.00 3.79
1024 1060 4.162690 GATCCCTGGCGGCTCGTT 62.163 66.667 11.43 0.00 0.00 3.85
1028 1064 2.366167 AAGAGATCCCTGGCGGCT 60.366 61.111 11.43 0.00 0.00 5.52
1035 1071 2.381941 GCCCAGGCAAGAGATCCCT 61.382 63.158 3.12 0.00 41.49 4.20
1071 1107 0.670546 CGGCTTCGATGTTGGTCAGT 60.671 55.000 0.00 0.00 35.61 3.41
1142 1178 2.480802 TCGTAGACGAGATAGAGCATGC 59.519 50.000 10.51 10.51 44.22 4.06
1171 1207 0.548031 ATCATGTGGAGCGACCCATT 59.452 50.000 0.00 0.00 38.66 3.16
1224 1260 2.124151 ATGCGAATGGTGAGGCCC 60.124 61.111 0.00 0.00 36.04 5.80
1428 1467 1.521906 CACGTCGGGTTGGAACACA 60.522 57.895 0.00 0.00 39.29 3.72
1459 1498 2.279517 CCAGTAGCCGATGCCGTC 60.280 66.667 0.00 0.00 38.69 4.79
1840 1879 1.638589 CAAAAGAGGGTACATGGGGGA 59.361 52.381 0.00 0.00 0.00 4.81
1974 2668 2.358195 GGAGGCCTGGATGGTGTTATTT 60.358 50.000 12.00 0.00 38.35 1.40
2442 3153 8.197988 ACCTACTAAAGCATACAAATTTCTCG 57.802 34.615 0.00 0.00 0.00 4.04
2601 3314 4.203226 TCACACACAAGCAATCCTAACAA 58.797 39.130 0.00 0.00 0.00 2.83
2602 3315 3.814625 TCACACACAAGCAATCCTAACA 58.185 40.909 0.00 0.00 0.00 2.41
2689 3402 1.818642 AGCAGCCACTCTTGATTGAC 58.181 50.000 0.00 0.00 0.00 3.18
2745 3458 3.629398 AGAGCAAGCCAATACAATAGCAC 59.371 43.478 0.00 0.00 0.00 4.40
2811 3524 4.649088 AAATACTCGGCAAAATTAGGGC 57.351 40.909 0.00 0.00 0.00 5.19
2850 3563 1.550976 ACTCGGTTTAGGAGAGCCTTG 59.449 52.381 0.00 0.00 43.90 3.61
2890 3622 1.267806 TGTCGAGTGTCGGTAGTTTCC 59.732 52.381 0.00 0.00 40.88 3.13
2891 3623 2.693797 TGTCGAGTGTCGGTAGTTTC 57.306 50.000 0.00 0.00 40.88 2.78
2892 3624 3.378339 CTTTGTCGAGTGTCGGTAGTTT 58.622 45.455 0.00 0.00 40.88 2.66
2893 3625 2.861360 GCTTTGTCGAGTGTCGGTAGTT 60.861 50.000 0.00 0.00 40.88 2.24
2894 3626 1.335689 GCTTTGTCGAGTGTCGGTAGT 60.336 52.381 0.00 0.00 40.88 2.73
2895 3627 1.337821 GCTTTGTCGAGTGTCGGTAG 58.662 55.000 0.00 0.00 40.88 3.18
2896 3628 0.038892 GGCTTTGTCGAGTGTCGGTA 60.039 55.000 0.00 0.00 40.88 4.02
2897 3629 1.300697 GGCTTTGTCGAGTGTCGGT 60.301 57.895 0.00 0.00 40.88 4.69
2898 3630 0.670546 ATGGCTTTGTCGAGTGTCGG 60.671 55.000 0.00 0.00 40.88 4.79
2899 3631 0.439985 CATGGCTTTGTCGAGTGTCG 59.560 55.000 0.00 0.00 42.10 4.35
2900 3632 0.166814 GCATGGCTTTGTCGAGTGTC 59.833 55.000 0.00 0.00 0.00 3.67
2901 3633 0.250467 AGCATGGCTTTGTCGAGTGT 60.250 50.000 0.00 0.00 33.89 3.55
2902 3634 2.548178 AGCATGGCTTTGTCGAGTG 58.452 52.632 0.00 0.00 33.89 3.51
2953 3685 7.363431 CGATTAGAGACATGTAGTGCTTCATA 58.637 38.462 0.00 0.00 0.00 2.15
2982 3714 0.107643 TGAGAACACGCCATCAACCA 59.892 50.000 0.00 0.00 0.00 3.67
3005 3737 7.122055 TCCAAATATTGCCTAAAAACACTCGAT 59.878 33.333 0.00 0.00 0.00 3.59
3082 3814 1.466950 CGAAAACATTTAGCGAGGGCA 59.533 47.619 0.00 0.00 43.41 5.36
3085 3817 3.058501 ACAACCGAAAACATTTAGCGAGG 60.059 43.478 0.00 0.00 0.00 4.63
3235 3967 4.020617 TTGCTCTGAGCCGGGGTG 62.021 66.667 25.61 0.00 41.51 4.61
3236 3968 4.021925 GTTGCTCTGAGCCGGGGT 62.022 66.667 25.61 0.00 41.51 4.95
3237 3969 4.785453 GGTTGCTCTGAGCCGGGG 62.785 72.222 25.61 0.00 41.51 5.73
3240 3972 3.883744 AACCGGTTGCTCTGAGCCG 62.884 63.158 25.61 20.57 41.51 5.52
3241 3973 0.321298 TAAACCGGTTGCTCTGAGCC 60.321 55.000 23.08 11.85 41.51 4.70
3242 3974 0.796927 GTAAACCGGTTGCTCTGAGC 59.203 55.000 23.08 22.38 42.82 4.26
3243 3975 1.439679 GGTAAACCGGTTGCTCTGAG 58.560 55.000 23.08 0.00 0.00 3.35
3244 3976 0.035739 GGGTAAACCGGTTGCTCTGA 59.964 55.000 23.08 0.00 36.71 3.27
3245 3977 0.036306 AGGGTAAACCGGTTGCTCTG 59.964 55.000 23.08 0.00 46.96 3.35
3246 3978 0.036306 CAGGGTAAACCGGTTGCTCT 59.964 55.000 23.08 19.01 46.96 4.09
3247 3979 1.583495 GCAGGGTAAACCGGTTGCTC 61.583 60.000 23.08 16.92 46.96 4.26
3248 3980 1.602605 GCAGGGTAAACCGGTTGCT 60.603 57.895 23.08 8.92 46.96 3.91
3249 3981 1.248101 ATGCAGGGTAAACCGGTTGC 61.248 55.000 23.08 19.99 46.96 4.17
3250 3982 1.067915 CAATGCAGGGTAAACCGGTTG 60.068 52.381 23.08 9.21 46.96 3.77
3251 3983 1.253100 CAATGCAGGGTAAACCGGTT 58.747 50.000 15.86 15.86 46.96 4.44
3252 3984 1.248101 GCAATGCAGGGTAAACCGGT 61.248 55.000 0.00 0.00 46.96 5.28
3253 3985 1.510844 GCAATGCAGGGTAAACCGG 59.489 57.895 0.00 0.00 46.96 5.28
3254 3986 1.247419 TGGCAATGCAGGGTAAACCG 61.247 55.000 7.79 0.00 46.96 4.44
3255 3987 0.532115 CTGGCAATGCAGGGTAAACC 59.468 55.000 7.79 0.00 40.67 3.27
3256 3988 0.108662 GCTGGCAATGCAGGGTAAAC 60.109 55.000 7.79 0.00 0.00 2.01
3257 3989 1.257055 GGCTGGCAATGCAGGGTAAA 61.257 55.000 7.79 0.00 0.00 2.01
3258 3990 1.682005 GGCTGGCAATGCAGGGTAA 60.682 57.895 7.79 0.00 0.00 2.85
3259 3991 2.044053 GGCTGGCAATGCAGGGTA 60.044 61.111 7.79 0.00 0.00 3.69
3262 3994 3.458163 CTGGGCTGGCAATGCAGG 61.458 66.667 7.79 0.00 0.00 4.85
3263 3995 2.361992 TCTGGGCTGGCAATGCAG 60.362 61.111 7.79 3.93 0.00 4.41
3264 3996 2.219449 ATCTCTGGGCTGGCAATGCA 62.219 55.000 7.79 0.00 0.00 3.96
3265 3997 1.453762 GATCTCTGGGCTGGCAATGC 61.454 60.000 2.88 0.00 0.00 3.56
3266 3998 1.164662 CGATCTCTGGGCTGGCAATG 61.165 60.000 2.88 0.00 0.00 2.82
3267 3999 1.147824 CGATCTCTGGGCTGGCAAT 59.852 57.895 2.88 0.00 0.00 3.56
3268 4000 1.964608 CTCGATCTCTGGGCTGGCAA 61.965 60.000 2.88 0.00 0.00 4.52
3269 4001 2.364186 TCGATCTCTGGGCTGGCA 60.364 61.111 2.88 0.00 0.00 4.92
3270 4002 2.362329 GACTCGATCTCTGGGCTGGC 62.362 65.000 0.00 0.00 0.00 4.85
3271 4003 0.754957 AGACTCGATCTCTGGGCTGG 60.755 60.000 0.00 0.00 28.16 4.85
3272 4004 1.066908 GAAGACTCGATCTCTGGGCTG 59.933 57.143 0.00 0.00 36.27 4.85
3273 4005 1.064017 AGAAGACTCGATCTCTGGGCT 60.064 52.381 0.00 0.00 36.27 5.19
3274 4006 1.066908 CAGAAGACTCGATCTCTGGGC 59.933 57.143 0.00 0.00 36.27 5.36
3275 4007 1.680735 CCAGAAGACTCGATCTCTGGG 59.319 57.143 15.46 7.47 42.84 4.45
3276 4008 1.066908 GCCAGAAGACTCGATCTCTGG 59.933 57.143 17.88 17.88 45.87 3.86
3277 4009 1.747924 TGCCAGAAGACTCGATCTCTG 59.252 52.381 1.39 1.39 36.27 3.35
3278 4010 2.136298 TGCCAGAAGACTCGATCTCT 57.864 50.000 0.00 0.00 36.27 3.10
3279 4011 2.949451 TTGCCAGAAGACTCGATCTC 57.051 50.000 0.00 0.00 36.27 2.75
3280 4012 3.701542 TGTATTGCCAGAAGACTCGATCT 59.298 43.478 0.00 0.00 40.46 2.75
3281 4013 3.799420 GTGTATTGCCAGAAGACTCGATC 59.201 47.826 0.00 0.00 0.00 3.69
3282 4014 3.195610 TGTGTATTGCCAGAAGACTCGAT 59.804 43.478 0.00 0.00 0.00 3.59
3283 4015 2.560981 TGTGTATTGCCAGAAGACTCGA 59.439 45.455 0.00 0.00 0.00 4.04
3284 4016 2.959516 TGTGTATTGCCAGAAGACTCG 58.040 47.619 0.00 0.00 0.00 4.18
3285 4017 4.065088 TGTTGTGTATTGCCAGAAGACTC 58.935 43.478 0.00 0.00 0.00 3.36
3286 4018 4.085357 TGTTGTGTATTGCCAGAAGACT 57.915 40.909 0.00 0.00 0.00 3.24
3287 4019 4.036262 TGTTGTTGTGTATTGCCAGAAGAC 59.964 41.667 0.00 0.00 0.00 3.01
3288 4020 4.203226 TGTTGTTGTGTATTGCCAGAAGA 58.797 39.130 0.00 0.00 0.00 2.87
3289 4021 4.566545 TGTTGTTGTGTATTGCCAGAAG 57.433 40.909 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.