Multiple sequence alignment - TraesCS4D01G068200

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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 TraesCS4D01G068200 chr4D 100.000 3879 0 0 1 3879 43553146 43557024 0.000000e+00 7164.0
1 TraesCS4D01G068200 chr4A 90.335 3373 176 58 61 3387 556536693 556539961 0.000000e+00 4285.0
2 TraesCS4D01G068200 chr4A 93.204 309 16 3 3423 3728 556539955 556540261 2.130000e-122 449.0
3 TraesCS4D01G068200 chr4A 93.333 150 10 0 3730 3879 556540523 556540672 5.040000e-54 222.0
4 TraesCS4D01G068200 chr4A 86.364 88 12 0 3554 3641 593295054 593295141 3.190000e-16 97.1
5 TraesCS4D01G068200 chr4B 93.694 1348 66 12 2042 3383 63230615 63229281 0.000000e+00 2001.0
6 TraesCS4D01G068200 chr4B 95.683 973 39 1 1000 1972 63231674 63230705 0.000000e+00 1561.0
7 TraesCS4D01G068200 chr4B 87.035 995 63 31 1 981 63232666 63231724 0.000000e+00 1062.0
8 TraesCS4D01G068200 chr4B 90.604 149 12 2 3732 3879 63228764 63228617 3.060000e-46 196.0
9 TraesCS4D01G068200 chr7D 81.818 88 14 2 3557 3642 187108804 187108717 5.380000e-09 73.1
10 TraesCS4D01G068200 chr7B 81.250 96 12 6 3555 3646 490685094 490685187 5.380000e-09 73.1
11 TraesCS4D01G068200 chr6B 84.932 73 5 6 3580 3648 37661063 37660993 6.950000e-08 69.4
12 TraesCS4D01G068200 chr3D 80.460 87 15 2 3559 3643 524301217 524301303 9.000000e-07 65.8
13 TraesCS4D01G068200 chr5D 97.143 35 0 1 3610 3644 482320842 482320875 1.510000e-04 58.4
14 TraesCS4D01G068200 chr7A 100.000 29 0 0 3619 3647 700161207 700161179 2.000000e-03 54.7


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 TraesCS4D01G068200 chr4D 43553146 43557024 3878 False 7164 7164 100.000000 1 3879 1 chr4D.!!$F1 3878
1 TraesCS4D01G068200 chr4A 556536693 556540672 3979 False 1652 4285 92.290667 61 3879 3 chr4A.!!$F2 3818
2 TraesCS4D01G068200 chr4B 63228617 63232666 4049 True 1205 2001 91.754000 1 3879 4 chr4B.!!$R1 3878

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
876 919 1.080501 CGTGCGAGTGATGTGGAGT 60.081 57.895 0.0 0.0 0.00 3.85 F
1317 1411 1.832912 CTCTGCCCAGGTGTATCCC 59.167 63.158 0.0 0.0 36.75 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 1792 1.103398 CATTTCCATCCTCCCCACGC 61.103 60.0 0.0 0.0 0.0 5.34 R
3039 3177 0.898320 ATCCTCCCACTTGACACTCG 59.102 55.0 0.0 0.0 0.0 4.18 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
52 53 3.084039 GAGGAGCAATGGTCAACAATCA 58.916 45.455 14.70 0.00 0.00 2.57
54 55 2.821969 GGAGCAATGGTCAACAATCACT 59.178 45.455 14.70 0.00 0.00 3.41
55 56 3.256631 GGAGCAATGGTCAACAATCACTT 59.743 43.478 14.70 0.00 0.00 3.16
57 58 4.147321 AGCAATGGTCAACAATCACTTCT 58.853 39.130 0.00 0.00 0.00 2.85
59 60 4.217118 GCAATGGTCAACAATCACTTCTCT 59.783 41.667 0.00 0.00 0.00 3.10
97 110 2.021457 CCTTTGACGTTTTGACCCACT 58.979 47.619 0.00 0.00 0.00 4.00
133 146 5.928264 TCTCACCGCTAAACTAAACTAAACC 59.072 40.000 0.00 0.00 0.00 3.27
148 161 4.562767 ACTAAACCAAAACCCTTCCCAAT 58.437 39.130 0.00 0.00 0.00 3.16
154 171 4.045334 ACCAAAACCCTTCCCAATAGATCA 59.955 41.667 0.00 0.00 0.00 2.92
155 172 5.022787 CCAAAACCCTTCCCAATAGATCAA 58.977 41.667 0.00 0.00 0.00 2.57
157 174 3.953542 ACCCTTCCCAATAGATCAACC 57.046 47.619 0.00 0.00 0.00 3.77
214 242 1.427819 CGGCCACATTTCCTAACGC 59.572 57.895 2.24 0.00 0.00 4.84
215 243 1.302383 CGGCCACATTTCCTAACGCA 61.302 55.000 2.24 0.00 0.00 5.24
406 437 3.005472 TCGTTCACACCTTCTTCCACTAG 59.995 47.826 0.00 0.00 0.00 2.57
407 438 3.665190 GTTCACACCTTCTTCCACTAGG 58.335 50.000 0.00 0.00 35.14 3.02
408 439 3.254093 TCACACCTTCTTCCACTAGGA 57.746 47.619 0.00 0.00 43.93 2.94
409 440 2.897969 TCACACCTTCTTCCACTAGGAC 59.102 50.000 0.00 0.00 45.73 3.85
466 504 3.501548 GTCGACTCCGAGCTCGCT 61.502 66.667 30.49 14.47 46.52 4.93
467 505 3.196394 TCGACTCCGAGCTCGCTC 61.196 66.667 30.49 20.71 40.30 5.03
468 506 3.500642 CGACTCCGAGCTCGCTCA 61.501 66.667 30.49 14.82 42.86 4.26
469 507 2.101380 GACTCCGAGCTCGCTCAC 59.899 66.667 30.49 16.63 42.86 3.51
680 722 2.804931 GCACGCAACAAATCGCCC 60.805 61.111 0.00 0.00 0.00 6.13
830 873 2.618709 CGTTTTCTTGTTCCTCAGCCTT 59.381 45.455 0.00 0.00 0.00 4.35
832 875 4.274950 CGTTTTCTTGTTCCTCAGCCTTTA 59.725 41.667 0.00 0.00 0.00 1.85
871 914 4.002506 TGGCCGTGCGAGTGATGT 62.003 61.111 0.00 0.00 0.00 3.06
872 915 3.490759 GGCCGTGCGAGTGATGTG 61.491 66.667 0.00 0.00 0.00 3.21
876 919 1.080501 CGTGCGAGTGATGTGGAGT 60.081 57.895 0.00 0.00 0.00 3.85
944 987 1.863325 TCCTGCTCTTCAGATCTGCT 58.137 50.000 18.36 0.00 45.72 4.24
963 1011 2.283173 TGGTGAGAGCTGCCGAGA 60.283 61.111 0.00 0.00 0.00 4.04
970 1018 4.443266 AGCTGCCGAGAAGCCGAC 62.443 66.667 0.00 0.00 41.82 4.79
994 1042 4.024893 GTGCTCGTGAACATCTCAAGAAAA 60.025 41.667 0.00 0.00 41.27 2.29
1128 1207 3.923864 ACGGACGAAGCCTGTGCA 61.924 61.111 0.00 0.00 41.13 4.57
1290 1384 3.357079 CTGAACAGTGCGCACCCC 61.357 66.667 35.51 21.68 0.00 4.95
1305 1399 4.154347 CCCTCGACCAGCTCTGCC 62.154 72.222 0.00 0.00 0.00 4.85
1317 1411 1.832912 CTCTGCCCAGGTGTATCCC 59.167 63.158 0.00 0.00 36.75 3.85
1563 1666 1.874019 CGCGAGGTCCTTCATGTCG 60.874 63.158 0.00 0.00 0.00 4.35
1686 1789 2.586245 CCAAGGAGGCGATGCTCA 59.414 61.111 0.00 0.00 0.00 4.26
1689 1792 2.739996 AAGGAGGCGATGCTCAGGG 61.740 63.158 0.00 0.00 0.00 4.45
1773 1876 7.713073 AGAAGGTAGTAAATCTGCTATCTTTGC 59.287 37.037 0.00 0.00 40.21 3.68
1822 1925 9.566331 AGATAGGATCCCATGATAATTGTTCTA 57.434 33.333 8.55 0.00 0.00 2.10
1975 2078 4.415512 CCCCTCATCCCAGGTATTCTTTAA 59.584 45.833 0.00 0.00 0.00 1.52
2029 2146 5.414454 GCACATTTGATACTTTGTAGGGTGA 59.586 40.000 0.00 0.00 0.00 4.02
2046 2179 6.089249 AGGGTGATTTTTCTTTGCTAACAG 57.911 37.500 0.00 0.00 0.00 3.16
2271 2404 4.739716 GGTGCTGTACATGTTTGTTTTCTG 59.260 41.667 2.30 0.00 37.28 3.02
2279 2412 6.619801 ACATGTTTGTTTTCTGTCCTCTAC 57.380 37.500 0.00 0.00 29.55 2.59
2281 2414 4.761975 TGTTTGTTTTCTGTCCTCTACGT 58.238 39.130 0.00 0.00 0.00 3.57
2317 2450 3.270877 GAGGTGTCGATGCCTTAATTGT 58.729 45.455 11.29 0.00 34.81 2.71
2369 2502 6.425735 TGATGCCATTCTTTCTTTCCTATGA 58.574 36.000 0.00 0.00 0.00 2.15
2427 2561 4.331168 AGTGAGCACTTCTTAATTCGATGC 59.669 41.667 0.00 0.00 38.83 3.91
2462 2596 6.576662 TCGTGATTCACTTACTCTTTCTCT 57.423 37.500 14.54 0.00 31.34 3.10
2463 2597 6.613233 TCGTGATTCACTTACTCTTTCTCTC 58.387 40.000 14.54 0.00 31.34 3.20
2464 2598 6.431543 TCGTGATTCACTTACTCTTTCTCTCT 59.568 38.462 14.54 0.00 31.34 3.10
2505 2639 1.619827 CAAATGACTTGCCCACCATGT 59.380 47.619 0.00 0.00 34.81 3.21
2519 2653 3.379372 CCACCATGTCTCTGGCTTAAATG 59.621 47.826 0.00 0.00 40.15 2.32
2595 2732 8.757982 AAATATAGTTCTCTGAATTGGCACAT 57.242 30.769 0.00 0.00 39.30 3.21
2641 2778 7.753309 ACACTAGATATAGAAACATCGCTCT 57.247 36.000 0.33 0.00 0.00 4.09
2658 2795 8.230486 ACATCGCTCTTTGTACTTCTATTTTTG 58.770 33.333 0.00 0.00 0.00 2.44
2677 2814 7.979444 TTTTTGTTTCAAACCCAACATGTTA 57.021 28.000 11.53 0.00 32.96 2.41
2682 2819 8.012957 TGTTTCAAACCCAACATGTTACTAAT 57.987 30.769 11.53 0.00 0.00 1.73
2691 2828 9.487790 ACCCAACATGTTACTAATTTTGATTTG 57.512 29.630 11.53 0.00 0.00 2.32
2705 2842 3.988976 TGATTTGTCCCTGGAGAAGAG 57.011 47.619 0.00 0.00 0.00 2.85
2711 2848 1.832366 GTCCCTGGAGAAGAGTAACCC 59.168 57.143 0.00 0.00 0.00 4.11
2713 2850 2.158066 TCCCTGGAGAAGAGTAACCCAA 60.158 50.000 0.00 0.00 0.00 4.12
2714 2851 2.846827 CCCTGGAGAAGAGTAACCCAAT 59.153 50.000 0.00 0.00 0.00 3.16
2716 2853 3.264450 CCTGGAGAAGAGTAACCCAATGT 59.736 47.826 0.00 0.00 0.00 2.71
2764 2901 3.933048 ATGCAGCAGTGTGAGGGGC 62.933 63.158 0.00 0.00 0.00 5.80
2806 2943 1.358725 AACGTTGCGTGGATGATCCG 61.359 55.000 7.03 0.00 39.99 4.18
2833 2970 2.205074 CTCATTGTGACATACGAGGGC 58.795 52.381 0.00 0.00 0.00 5.19
2911 3048 7.363268 CCCCAATTATCACTCTTTTCAGGAAAG 60.363 40.741 0.00 0.00 44.99 2.62
2933 3070 2.542907 AACTCGCCGGCACTTGTTG 61.543 57.895 28.98 8.23 0.00 3.33
2984 3122 4.335315 GGATTGCGAAGTGACAAATATGGA 59.665 41.667 0.00 0.00 0.00 3.41
3010 3148 2.524569 TTGAGCAGTTGATGTGTCGA 57.475 45.000 0.00 0.00 0.00 4.20
3158 3296 4.154347 GCTCAGGAGGGAGTGCGG 62.154 72.222 0.00 0.00 37.24 5.69
3164 3302 2.419739 GGAGGGAGTGCGGAGAGTC 61.420 68.421 0.00 0.00 0.00 3.36
3175 3313 1.668101 CGGAGAGTCGGAAGGGAAGG 61.668 65.000 0.00 0.00 0.00 3.46
3264 3402 4.792521 TTGTACCAAGTGCACAAAAAGT 57.207 36.364 21.04 11.04 0.00 2.66
3269 3407 2.426738 CCAAGTGCACAAAAAGTCTGGA 59.573 45.455 21.04 0.00 0.00 3.86
3384 3524 7.817418 ACCAAGTTAAATATCTTGTGTGTGT 57.183 32.000 9.31 0.25 39.25 3.72
3386 3526 7.719633 ACCAAGTTAAATATCTTGTGTGTGTCT 59.280 33.333 9.31 0.00 39.25 3.41
3387 3527 8.230486 CCAAGTTAAATATCTTGTGTGTGTCTC 58.770 37.037 9.31 0.00 39.25 3.36
3390 3530 8.150945 AGTTAAATATCTTGTGTGTGTCTCACT 58.849 33.333 6.60 0.00 46.27 3.41
3391 3531 9.419297 GTTAAATATCTTGTGTGTGTCTCACTA 57.581 33.333 6.60 0.00 46.27 2.74
3392 3532 9.990360 TTAAATATCTTGTGTGTGTCTCACTAA 57.010 29.630 6.60 2.07 46.27 2.24
3393 3533 8.539770 AAATATCTTGTGTGTGTCTCACTAAG 57.460 34.615 6.60 10.11 46.27 2.18
3394 3534 3.717707 TCTTGTGTGTGTCTCACTAAGC 58.282 45.455 6.60 0.00 46.27 3.09
3395 3535 3.384789 TCTTGTGTGTGTCTCACTAAGCT 59.615 43.478 6.60 0.00 46.27 3.74
3396 3536 3.097877 TGTGTGTGTCTCACTAAGCTG 57.902 47.619 6.60 0.00 46.27 4.24
3397 3537 2.693074 TGTGTGTGTCTCACTAAGCTGA 59.307 45.455 6.60 0.00 46.27 4.26
3398 3538 3.321968 TGTGTGTGTCTCACTAAGCTGAT 59.678 43.478 6.60 0.00 46.27 2.90
3399 3539 4.202253 TGTGTGTGTCTCACTAAGCTGATT 60.202 41.667 6.60 0.00 46.27 2.57
3400 3540 5.010617 TGTGTGTGTCTCACTAAGCTGATTA 59.989 40.000 6.60 0.00 46.27 1.75
3401 3541 6.102663 GTGTGTGTCTCACTAAGCTGATTAT 58.897 40.000 6.60 0.00 46.27 1.28
3402 3542 6.254589 GTGTGTGTCTCACTAAGCTGATTATC 59.745 42.308 6.60 0.00 46.27 1.75
3403 3543 5.457148 GTGTGTCTCACTAAGCTGATTATCG 59.543 44.000 0.00 0.00 43.13 2.92
3404 3544 5.125578 TGTGTCTCACTAAGCTGATTATCGT 59.874 40.000 0.00 0.00 35.11 3.73
3405 3545 5.683743 GTGTCTCACTAAGCTGATTATCGTC 59.316 44.000 0.00 0.00 0.00 4.20
3406 3546 5.590663 TGTCTCACTAAGCTGATTATCGTCT 59.409 40.000 0.00 0.00 0.00 4.18
3407 3547 5.912396 GTCTCACTAAGCTGATTATCGTCTG 59.088 44.000 0.00 0.00 0.00 3.51
3408 3548 5.009110 TCTCACTAAGCTGATTATCGTCTGG 59.991 44.000 0.00 0.00 0.00 3.86
3409 3549 4.038042 TCACTAAGCTGATTATCGTCTGGG 59.962 45.833 0.00 0.00 0.00 4.45
3410 3550 4.038042 CACTAAGCTGATTATCGTCTGGGA 59.962 45.833 0.00 0.00 0.00 4.37
3411 3551 4.649674 ACTAAGCTGATTATCGTCTGGGAA 59.350 41.667 0.00 0.00 0.00 3.97
3412 3552 3.742433 AGCTGATTATCGTCTGGGAAG 57.258 47.619 0.00 0.00 0.00 3.46
3413 3553 3.034635 AGCTGATTATCGTCTGGGAAGT 58.965 45.455 0.00 0.00 0.00 3.01
3414 3554 3.126831 GCTGATTATCGTCTGGGAAGTG 58.873 50.000 0.00 0.00 0.00 3.16
3415 3555 3.722147 CTGATTATCGTCTGGGAAGTGG 58.278 50.000 0.00 0.00 0.00 4.00
3416 3556 2.434336 TGATTATCGTCTGGGAAGTGGG 59.566 50.000 0.00 0.00 0.00 4.61
3417 3557 1.200519 TTATCGTCTGGGAAGTGGGG 58.799 55.000 0.00 0.00 0.00 4.96
3418 3558 0.042131 TATCGTCTGGGAAGTGGGGT 59.958 55.000 0.00 0.00 0.00 4.95
3419 3559 1.553690 ATCGTCTGGGAAGTGGGGTG 61.554 60.000 0.00 0.00 0.00 4.61
3420 3560 2.214216 CGTCTGGGAAGTGGGGTGA 61.214 63.158 0.00 0.00 0.00 4.02
3421 3561 1.375326 GTCTGGGAAGTGGGGTGAC 59.625 63.158 0.00 0.00 0.00 3.67
3422 3562 2.214216 TCTGGGAAGTGGGGTGACG 61.214 63.158 0.00 0.00 0.00 4.35
3423 3563 2.446994 TGGGAAGTGGGGTGACGT 60.447 61.111 0.00 0.00 0.00 4.34
3424 3564 2.052047 CTGGGAAGTGGGGTGACGTT 62.052 60.000 0.00 0.00 0.00 3.99
3562 3702 9.974980 GGGAGTATTTTCTAGAGAATTCTACTG 57.025 37.037 18.52 1.49 34.79 2.74
3569 3709 3.817709 AGAGAATTCTACTGCCTCTGC 57.182 47.619 8.25 0.00 33.42 4.26
3583 3723 4.854173 TGCCTCTGCACCAAAATATAAGA 58.146 39.130 0.00 0.00 44.23 2.10
3584 3724 4.640201 TGCCTCTGCACCAAAATATAAGAC 59.360 41.667 0.00 0.00 44.23 3.01
3651 3793 9.573166 TGATATGGAGGGAGTACAAAATAAATG 57.427 33.333 0.00 0.00 0.00 2.32
3710 3855 2.032302 CCATTGAACCAAAACGTCGTCA 59.968 45.455 0.00 0.00 0.00 4.35
3728 3873 3.183172 CGTCATAGATTCCAGCGAATGTG 59.817 47.826 0.00 0.00 38.88 3.21
3761 4179 8.818057 CAAATACTCCCTTTGTCTCTATTTACG 58.182 37.037 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 1.203364 AGGGACATGGGTCAGAGAAGT 60.203 52.381 0.00 0.00 46.17 3.01
54 55 1.573108 GAGGGACATGGGTCAGAGAA 58.427 55.000 0.00 0.00 46.17 2.87
55 56 0.325671 GGAGGGACATGGGTCAGAGA 60.326 60.000 0.00 0.00 46.17 3.10
57 58 1.306997 GGGAGGGACATGGGTCAGA 60.307 63.158 0.00 0.00 46.17 3.27
59 60 1.306997 GAGGGAGGGACATGGGTCA 60.307 63.158 0.00 0.00 46.17 4.02
97 110 1.051008 CGGTGAGATGGGATGATGGA 58.949 55.000 0.00 0.00 0.00 3.41
133 146 5.105351 GGTTGATCTATTGGGAAGGGTTTTG 60.105 44.000 0.00 0.00 0.00 2.44
148 161 0.387929 GATGGACGGCGGTTGATCTA 59.612 55.000 13.24 0.00 0.00 1.98
200 228 0.521242 GCGCTGCGTTAGGAAATGTG 60.521 55.000 24.04 0.00 0.00 3.21
201 229 1.644786 GGCGCTGCGTTAGGAAATGT 61.645 55.000 24.04 0.00 0.00 2.71
203 231 2.461110 CGGCGCTGCGTTAGGAAAT 61.461 57.895 24.04 0.00 0.00 2.17
214 242 1.548973 CCTAGTTTATCGCGGCGCTG 61.549 60.000 30.54 22.35 0.00 5.18
215 243 1.299926 CCTAGTTTATCGCGGCGCT 60.300 57.895 30.54 15.05 0.00 5.92
273 301 2.671396 GCCGGTCTGTATAATATTGCGG 59.329 50.000 1.90 0.00 0.00 5.69
406 437 4.436998 CACCGGAGACCAGCGTCC 62.437 72.222 9.46 0.00 40.12 4.79
407 438 4.436998 CCACCGGAGACCAGCGTC 62.437 72.222 9.46 0.00 39.50 5.19
409 440 4.742201 CACCACCGGAGACCAGCG 62.742 72.222 9.46 0.00 0.00 5.18
478 516 1.875813 GCGTGCGATGAGTCCAGAG 60.876 63.158 0.00 0.00 0.00 3.35
680 722 2.167861 GCAAGAAGCGACCCTAGCG 61.168 63.158 0.00 0.00 40.04 4.26
708 750 4.899239 GCGGGCGTGGAGGATGAG 62.899 72.222 0.00 0.00 0.00 2.90
807 850 2.031944 GGCTGAGGAACAAGAAAACGTC 60.032 50.000 0.00 0.00 0.00 4.34
811 854 4.278419 GCTAAAGGCTGAGGAACAAGAAAA 59.722 41.667 0.00 0.00 38.06 2.29
830 873 2.741759 TCAGCAATCACACGAGCTAA 57.258 45.000 0.00 0.00 35.19 3.09
832 875 1.366679 CATCAGCAATCACACGAGCT 58.633 50.000 0.00 0.00 37.95 4.09
871 914 2.646175 GCTCACCGTGGCTACTCCA 61.646 63.158 0.00 0.00 44.18 3.86
872 915 1.889530 AAGCTCACCGTGGCTACTCC 61.890 60.000 12.97 0.00 37.87 3.85
876 919 0.685097 AGAAAAGCTCACCGTGGCTA 59.315 50.000 12.97 0.00 37.87 3.93
882 925 3.370366 CAGATCTCAAGAAAAGCTCACCG 59.630 47.826 0.00 0.00 0.00 4.94
944 987 2.917227 TCGGCAGCTCTCACCACA 60.917 61.111 0.00 0.00 0.00 4.17
970 1018 1.388093 CTTGAGATGTTCACGAGCACG 59.612 52.381 0.76 0.76 45.75 5.34
981 1029 9.312904 TCCTCCATTTTTATTTTCTTGAGATGT 57.687 29.630 0.00 0.00 0.00 3.06
994 1042 4.119155 TCCTCCACCTCCTCCATTTTTAT 58.881 43.478 0.00 0.00 0.00 1.40
1110 1189 3.414700 GCACAGGCTTCGTCCGTG 61.415 66.667 0.00 0.00 36.96 4.94
1128 1207 2.106684 GGAGACCACCTTCCTGAACTTT 59.893 50.000 0.00 0.00 0.00 2.66
1290 1384 3.368190 CTGGGCAGAGCTGGTCGAG 62.368 68.421 0.00 0.00 0.00 4.04
1305 1399 2.941415 GCTGTTTCTGGGATACACCTGG 60.941 54.545 0.00 0.00 38.98 4.45
1317 1411 2.156917 TCCAGAATGCTGCTGTTTCTG 58.843 47.619 22.28 22.28 43.75 3.02
1563 1666 1.404391 CTGCCATCCATGCTCAAAGAC 59.596 52.381 0.00 0.00 0.00 3.01
1689 1792 1.103398 CATTTCCATCCTCCCCACGC 61.103 60.000 0.00 0.00 0.00 5.34
1773 1876 9.909644 ATCTTGAATCAAAAGAATCAGAAACAG 57.090 29.630 0.00 0.00 37.22 3.16
1804 1907 7.888514 AGGGTATAGAACAATTATCATGGGA 57.111 36.000 0.00 0.00 0.00 4.37
1822 1925 5.440610 CAACTTCCTGCTGAAATAGGGTAT 58.559 41.667 0.00 0.00 34.76 2.73
1849 1952 5.243207 GGGAACTTTAATCGTCCTCTTCAA 58.757 41.667 0.00 0.00 0.00 2.69
1950 2053 1.981495 GAATACCTGGGATGAGGGGAG 59.019 57.143 0.00 0.00 37.45 4.30
2271 2404 3.058363 GGATACCGAATCACGTAGAGGAC 60.058 52.174 0.00 0.00 40.78 3.85
2279 2412 2.035961 ACCTCATGGATACCGAATCACG 59.964 50.000 0.00 0.00 36.20 4.35
2281 2414 3.038280 ACACCTCATGGATACCGAATCA 58.962 45.455 0.00 0.00 36.20 2.57
2337 2470 2.827800 AGAATGGCATCATCGACGAT 57.172 45.000 4.05 4.05 32.24 3.73
2342 2475 4.337555 AGGAAAGAAAGAATGGCATCATCG 59.662 41.667 0.00 0.00 32.24 3.84
2409 2543 4.864916 TCTGCATCGAATTAAGAAGTGC 57.135 40.909 0.00 0.00 0.00 4.40
2427 2561 3.423536 GTGAATCACGATAGCACGATCTG 59.576 47.826 0.00 0.00 42.67 2.90
2433 2567 5.583495 AGAGTAAGTGAATCACGATAGCAC 58.417 41.667 7.83 1.62 39.64 4.40
2576 2713 5.999044 AGATATGTGCCAATTCAGAGAACT 58.001 37.500 0.00 0.00 0.00 3.01
2621 2758 9.894783 GTACAAAGAGCGATGTTTCTATATCTA 57.105 33.333 0.00 0.00 0.00 1.98
2622 2759 8.634444 AGTACAAAGAGCGATGTTTCTATATCT 58.366 33.333 0.00 0.00 0.00 1.98
2636 2773 8.782533 AAACAAAAATAGAAGTACAAAGAGCG 57.217 30.769 0.00 0.00 0.00 5.03
2658 2795 8.880878 AATTAGTAACATGTTGGGTTTGAAAC 57.119 30.769 21.42 7.72 0.00 2.78
2677 2814 6.552008 TCTCCAGGGACAAATCAAAATTAGT 58.448 36.000 0.00 0.00 0.00 2.24
2682 2819 5.060427 TCTTCTCCAGGGACAAATCAAAA 57.940 39.130 0.00 0.00 0.00 2.44
2691 2828 1.832366 GGGTTACTCTTCTCCAGGGAC 59.168 57.143 0.00 0.00 0.00 4.46
2705 2842 5.508200 TTTGTGTTCAGACATTGGGTTAC 57.492 39.130 0.00 0.00 38.23 2.50
2711 2848 4.446385 CCTGCATTTTGTGTTCAGACATTG 59.554 41.667 0.00 0.00 38.23 2.82
2713 2850 3.006110 CCCTGCATTTTGTGTTCAGACAT 59.994 43.478 0.00 0.00 38.23 3.06
2714 2851 2.361757 CCCTGCATTTTGTGTTCAGACA 59.638 45.455 0.00 0.00 0.00 3.41
2716 2853 1.962807 CCCCTGCATTTTGTGTTCAGA 59.037 47.619 0.00 0.00 0.00 3.27
2806 2943 3.060940 CGTATGTCACAATGAGCATCGAC 60.061 47.826 0.00 0.00 38.61 4.20
2833 2970 3.783377 CATTCGCGTATGGTTATGTTCG 58.217 45.455 16.99 0.00 0.00 3.95
2887 3024 7.542025 CCTTTCCTGAAAAGAGTGATAATTGG 58.458 38.462 0.00 0.00 46.18 3.16
2888 3025 7.031975 GCCTTTCCTGAAAAGAGTGATAATTG 58.968 38.462 0.00 0.00 46.18 2.32
2889 3026 6.153510 GGCCTTTCCTGAAAAGAGTGATAATT 59.846 38.462 0.00 0.00 46.18 1.40
2933 3070 1.140816 GAGAACAACGCAGTCTGTCC 58.859 55.000 0.93 0.00 45.00 4.02
2984 3122 4.525487 ACACATCAACTGCTCAAATGGATT 59.475 37.500 0.00 0.00 0.00 3.01
3010 3148 1.492176 CATGTAGGTCAGGAGGCCAAT 59.508 52.381 5.01 0.00 0.00 3.16
3039 3177 0.898320 ATCCTCCCACTTGACACTCG 59.102 55.000 0.00 0.00 0.00 4.18
3114 3252 8.560124 AATCTCAGGTTTCCTATCTAACATCT 57.440 34.615 0.00 0.00 29.64 2.90
3158 3296 2.025898 CTACCTTCCCTTCCGACTCTC 58.974 57.143 0.00 0.00 0.00 3.20
3164 3302 3.279434 CCAATTTCTACCTTCCCTTCCG 58.721 50.000 0.00 0.00 0.00 4.30
3175 3313 6.207417 CACACATATCATCCCCCAATTTCTAC 59.793 42.308 0.00 0.00 0.00 2.59
3316 3456 2.563179 CTGGAGGTACAACTACACAGCT 59.437 50.000 0.00 0.00 0.00 4.24
3318 3458 2.353803 GCCTGGAGGTACAACTACACAG 60.354 54.545 0.00 0.00 37.57 3.66
3322 3462 2.458620 AGAGCCTGGAGGTACAACTAC 58.541 52.381 0.00 0.00 37.57 2.73
3323 3463 2.921834 AGAGCCTGGAGGTACAACTA 57.078 50.000 0.00 0.00 37.57 2.24
3324 3464 2.741145 CTAGAGCCTGGAGGTACAACT 58.259 52.381 0.00 0.00 37.57 3.16
3384 3524 5.009110 CCAGACGATAATCAGCTTAGTGAGA 59.991 44.000 0.00 0.00 0.00 3.27
3386 3526 4.038042 CCCAGACGATAATCAGCTTAGTGA 59.962 45.833 0.00 0.00 0.00 3.41
3387 3527 4.038042 TCCCAGACGATAATCAGCTTAGTG 59.962 45.833 0.00 0.00 0.00 2.74
3390 3530 4.649674 ACTTCCCAGACGATAATCAGCTTA 59.350 41.667 0.00 0.00 0.00 3.09
3391 3531 3.452627 ACTTCCCAGACGATAATCAGCTT 59.547 43.478 0.00 0.00 0.00 3.74
3392 3532 3.034635 ACTTCCCAGACGATAATCAGCT 58.965 45.455 0.00 0.00 0.00 4.24
3393 3533 3.126831 CACTTCCCAGACGATAATCAGC 58.873 50.000 0.00 0.00 0.00 4.26
3394 3534 3.493350 CCCACTTCCCAGACGATAATCAG 60.493 52.174 0.00 0.00 0.00 2.90
3395 3535 2.434336 CCCACTTCCCAGACGATAATCA 59.566 50.000 0.00 0.00 0.00 2.57
3396 3536 2.224305 CCCCACTTCCCAGACGATAATC 60.224 54.545 0.00 0.00 0.00 1.75
3397 3537 1.768870 CCCCACTTCCCAGACGATAAT 59.231 52.381 0.00 0.00 0.00 1.28
3398 3538 1.200519 CCCCACTTCCCAGACGATAA 58.799 55.000 0.00 0.00 0.00 1.75
3399 3539 0.042131 ACCCCACTTCCCAGACGATA 59.958 55.000 0.00 0.00 0.00 2.92
3400 3540 1.229529 ACCCCACTTCCCAGACGAT 60.230 57.895 0.00 0.00 0.00 3.73
3401 3541 2.203182 ACCCCACTTCCCAGACGA 59.797 61.111 0.00 0.00 0.00 4.20
3402 3542 2.214216 TCACCCCACTTCCCAGACG 61.214 63.158 0.00 0.00 0.00 4.18
3403 3543 1.375326 GTCACCCCACTTCCCAGAC 59.625 63.158 0.00 0.00 0.00 3.51
3404 3544 2.214216 CGTCACCCCACTTCCCAGA 61.214 63.158 0.00 0.00 0.00 3.86
3405 3545 2.052047 AACGTCACCCCACTTCCCAG 62.052 60.000 0.00 0.00 0.00 4.45
3406 3546 2.047213 GAACGTCACCCCACTTCCCA 62.047 60.000 0.00 0.00 0.00 4.37
3407 3547 1.302271 GAACGTCACCCCACTTCCC 60.302 63.158 0.00 0.00 0.00 3.97
3408 3548 0.320508 GAGAACGTCACCCCACTTCC 60.321 60.000 0.00 0.00 0.00 3.46
3409 3549 0.680061 AGAGAACGTCACCCCACTTC 59.320 55.000 0.00 0.00 0.00 3.01
3410 3550 1.070289 GAAGAGAACGTCACCCCACTT 59.930 52.381 0.00 0.00 0.00 3.16
3411 3551 0.680061 GAAGAGAACGTCACCCCACT 59.320 55.000 0.00 0.00 0.00 4.00
3412 3552 0.391597 TGAAGAGAACGTCACCCCAC 59.608 55.000 0.00 0.00 30.40 4.61
3413 3553 1.124780 TTGAAGAGAACGTCACCCCA 58.875 50.000 0.00 0.00 34.62 4.96
3414 3554 2.474410 ATTGAAGAGAACGTCACCCC 57.526 50.000 0.00 0.00 34.62 4.95
3415 3555 4.174762 GACTATTGAAGAGAACGTCACCC 58.825 47.826 0.00 0.00 34.62 4.61
3416 3556 4.806330 TGACTATTGAAGAGAACGTCACC 58.194 43.478 0.00 0.00 34.62 4.02
3417 3557 4.324936 GCTGACTATTGAAGAGAACGTCAC 59.675 45.833 0.00 0.00 34.62 3.67
3418 3558 4.218635 AGCTGACTATTGAAGAGAACGTCA 59.781 41.667 0.00 0.00 33.21 4.35
3419 3559 4.739195 AGCTGACTATTGAAGAGAACGTC 58.261 43.478 0.00 0.00 0.00 4.34
3420 3560 4.673061 CGAGCTGACTATTGAAGAGAACGT 60.673 45.833 0.00 0.00 0.00 3.99
3421 3561 3.788694 CGAGCTGACTATTGAAGAGAACG 59.211 47.826 0.00 0.00 0.00 3.95
3422 3562 4.739195 ACGAGCTGACTATTGAAGAGAAC 58.261 43.478 0.00 0.00 0.00 3.01
3423 3563 5.392767 AACGAGCTGACTATTGAAGAGAA 57.607 39.130 0.00 0.00 0.00 2.87
3424 3564 5.048013 TCAAACGAGCTGACTATTGAAGAGA 60.048 40.000 0.00 0.00 0.00 3.10
3562 3702 4.260784 CGTCTTATATTTTGGTGCAGAGGC 60.261 45.833 0.00 0.00 41.68 4.70
3612 3754 9.502091 CTCCCTCCATATCAAAATATAAAACGA 57.498 33.333 0.00 0.00 0.00 3.85
3613 3755 9.284968 ACTCCCTCCATATCAAAATATAAAACG 57.715 33.333 0.00 0.00 0.00 3.60
3665 3807 9.474313 TGGCTTTCCATGTATTAGTAGATTTTT 57.526 29.630 0.00 0.00 37.47 1.94
3696 3841 3.930848 GGAATCTATGACGACGTTTTGGT 59.069 43.478 0.13 0.00 0.00 3.67
3710 3855 4.100035 TGTCTCACATTCGCTGGAATCTAT 59.900 41.667 0.00 0.00 40.90 1.98
3761 4179 2.504367 ACCATGAACAAGTGTAGCCAC 58.496 47.619 0.00 0.00 42.17 5.01
3853 4271 7.961855 TGCGATTAATTTTTGACCATCAATTG 58.038 30.769 0.00 0.00 36.11 2.32


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

AutoCloner maintained by Alex Coulton.