Multiple sequence alignment - TraesCS2D01G123200

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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 TraesCS2D01G123200 chr2D 100.000 4542 0 0 1 4542 72161282 72165823 0.000000e+00 8388
1 TraesCS2D01G123200 chr2B 91.102 3495 196 45 444 3887 108794728 108798158 0.000000e+00 4625
2 TraesCS2D01G123200 chr2B 95.263 570 25 2 3929 4498 108798161 108798728 0.000000e+00 902
3 TraesCS2D01G123200 chr2B 78.987 395 49 17 68 445 108793495 108793872 5.870000e-59 239
4 TraesCS2D01G123200 chr2A 91.916 1571 74 17 2177 3726 70975869 70977407 0.000000e+00 2148
5 TraesCS2D01G123200 chr2A 88.618 1766 117 38 472 2190 70974124 70975852 0.000000e+00 2071
6 TraesCS2D01G123200 chr2A 93.839 422 20 5 1 419 70973691 70974109 8.290000e-177 630
7 TraesCS2D01G123200 chr2A 87.719 513 43 8 4035 4533 70977406 70977912 8.470000e-162 580


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 TraesCS2D01G123200 chr2D 72161282 72165823 4541 False 8388.00 8388 100.000000 1 4542 1 chr2D.!!$F1 4541
1 TraesCS2D01G123200 chr2B 108793495 108798728 5233 False 1922.00 4625 88.450667 68 4498 3 chr2B.!!$F1 4430
2 TraesCS2D01G123200 chr2A 70973691 70977912 4221 False 1357.25 2148 90.523000 1 4533 4 chr2A.!!$F1 4532

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
485 1360 0.033796 TATGGACGAAGGACTCCGGT 60.034 55.0 0.00 0.0 0.00 5.28 F
1284 2207 0.598065 GCGGTTGTTCATTGCCTCTT 59.402 50.0 0.00 0.0 0.00 2.85 F
2428 3424 0.108138 AGCACGGATCACTTGCCTAC 60.108 55.0 8.39 0.0 36.91 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1490 2438 0.243636 CTTCCAACCCACAAATCGGC 59.756 55.0 0.00 0.0 0.00 5.54 R
2963 3978 0.809241 CGATCACCTTCTGCAGCTCC 60.809 60.0 9.47 0.0 0.00 4.70 R
3913 4958 0.185901 AGGTTCATGCCACAACTGGT 59.814 50.0 0.00 0.0 40.17 4.00 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
143 153 1.530771 CCCCTTGCAGAGAGATGGG 59.469 63.158 0.00 0.00 34.68 4.00
149 160 1.956869 TGCAGAGAGATGGGAAAGGA 58.043 50.000 0.00 0.00 0.00 3.36
193 204 0.384669 GTATGGACGAGGGACTTCGG 59.615 60.000 8.66 0.00 41.55 4.30
200 211 2.035940 AGGGACTTCGGCGAGAGT 59.964 61.111 19.52 19.52 27.25 3.24
245 259 1.835267 ACCACAGAGGGCACACGTA 60.835 57.895 0.00 0.00 43.89 3.57
290 310 1.933853 GTGGGAAATCAATCGGTCGAG 59.066 52.381 0.00 0.00 0.00 4.04
293 313 2.351726 GGGAAATCAATCGGTCGAGTTG 59.648 50.000 0.00 4.67 0.00 3.16
296 316 4.153475 GGAAATCAATCGGTCGAGTTGAAA 59.847 41.667 15.95 3.00 35.70 2.69
336 357 4.876679 TGGCATATTTCAATTGTTGCATGG 59.123 37.500 5.13 0.00 0.00 3.66
337 358 4.273969 GGCATATTTCAATTGTTGCATGGG 59.726 41.667 5.13 0.00 0.00 4.00
350 371 4.277174 TGTTGCATGGGCGTTAATATAAGG 59.723 41.667 0.00 0.00 45.35 2.69
420 441 0.966179 ATTTGGGAGAAAACCACCGC 59.034 50.000 0.00 0.00 37.82 5.68
422 443 2.281276 GGGAGAAAACCACCGCGT 60.281 61.111 4.92 0.00 0.00 6.01
429 450 3.667360 AGAAAACCACCGCGTATACTTT 58.333 40.909 4.92 0.00 0.00 2.66
433 454 3.042871 ACCACCGCGTATACTTTCAAA 57.957 42.857 4.92 0.00 0.00 2.69
436 457 4.456566 ACCACCGCGTATACTTTCAAATTT 59.543 37.500 4.92 0.00 0.00 1.82
445 466 6.795114 CGTATACTTTCAAATTTGAGCACGTT 59.205 34.615 19.64 8.42 38.61 3.99
446 467 6.991485 ATACTTTCAAATTTGAGCACGTTG 57.009 33.333 19.64 9.33 38.61 4.10
447 468 3.551485 ACTTTCAAATTTGAGCACGTTGC 59.449 39.130 19.64 2.28 45.46 4.17
458 479 2.028484 ACGTTGCGCTCTCCGAAA 59.972 55.556 9.73 0.00 40.02 3.46
459 480 2.022129 ACGTTGCGCTCTCCGAAAG 61.022 57.895 9.73 0.00 34.48 2.62
460 481 1.733041 CGTTGCGCTCTCCGAAAGA 60.733 57.895 9.73 0.00 34.48 2.52
485 1360 0.033796 TATGGACGAAGGACTCCGGT 60.034 55.000 0.00 0.00 0.00 5.28
550 1425 4.751539 GTGTCATGCATGCACGAC 57.248 55.556 33.68 33.68 39.29 4.34
564 1439 3.041940 CGACAGGTGCGGTTGACC 61.042 66.667 0.00 0.00 0.00 4.02
640 1515 2.017783 CCAACTGTTGCATGCACGC 61.018 57.895 22.58 16.81 0.00 5.34
749 1626 8.628882 AGCACGCAAATTAATTTAATCCTTAC 57.371 30.769 12.98 0.05 0.00 2.34
755 1632 7.305763 GCAAATTAATTTAATCCTTACCGTGCG 60.306 37.037 12.98 0.00 0.00 5.34
817 1712 3.682292 AAGCCCGGGAAGATCACGC 62.682 63.158 29.31 4.76 42.99 5.34
819 1714 2.107141 CCCGGGAAGATCACGCTC 59.893 66.667 18.48 0.00 42.99 5.03
820 1715 2.278857 CCGGGAAGATCACGCTCG 60.279 66.667 0.00 0.00 42.99 5.03
821 1716 2.278857 CGGGAAGATCACGCTCGG 60.279 66.667 0.00 0.00 36.07 4.63
823 1718 2.184322 GGAAGATCACGCTCGGCA 59.816 61.111 0.00 0.00 0.00 5.69
824 1719 1.880340 GGAAGATCACGCTCGGCAG 60.880 63.158 0.00 0.00 0.00 4.85
942 1850 1.153745 CTCCCCGCAAGAAGAGTCG 60.154 63.158 0.00 0.00 43.02 4.18
1220 2143 4.558538 AATATCTGCCAGATTCGTTTGC 57.441 40.909 13.32 0.00 36.20 3.68
1228 2151 1.154727 GATTCGTTTGCGTTCGCGT 60.155 52.632 5.77 0.00 43.62 6.01
1282 2205 1.212751 GGCGGTTGTTCATTGCCTC 59.787 57.895 0.00 0.00 42.44 4.70
1283 2206 1.244019 GGCGGTTGTTCATTGCCTCT 61.244 55.000 0.00 0.00 42.44 3.69
1284 2207 0.598065 GCGGTTGTTCATTGCCTCTT 59.402 50.000 0.00 0.00 0.00 2.85
1285 2208 1.401539 GCGGTTGTTCATTGCCTCTTC 60.402 52.381 0.00 0.00 0.00 2.87
1289 2212 4.499696 CGGTTGTTCATTGCCTCTTCTTTT 60.500 41.667 0.00 0.00 0.00 2.27
1309 2232 2.217429 TTTTTCTGCCGTTTCTTGCC 57.783 45.000 0.00 0.00 0.00 4.52
1477 2425 3.868757 AATCTGTTCGGATCTGACGAA 57.131 42.857 2.94 2.24 46.73 3.85
1606 2555 2.028658 TCTGCTCTACTTCAGCTTGGTG 60.029 50.000 0.00 0.00 37.79 4.17
1619 2573 0.823460 CTTGGTGCTTTGGTTGGTGT 59.177 50.000 0.00 0.00 0.00 4.16
1694 2648 4.356405 TGCTCCTGAACTTTCTTCATGA 57.644 40.909 0.00 0.00 0.00 3.07
1748 2702 5.519206 GTCTCGTGTTCTTGTAAGACAGTTT 59.481 40.000 0.00 0.00 34.13 2.66
1755 2709 6.128391 TGTTCTTGTAAGACAGTTTGTGTGTC 60.128 38.462 0.00 0.00 44.02 3.67
1787 2741 3.581101 TCCATTTGTTTTGTCCATCCCA 58.419 40.909 0.00 0.00 0.00 4.37
1810 2764 2.819608 TGGCTGTTTGTGCTTATTCCTC 59.180 45.455 0.00 0.00 0.00 3.71
1889 2846 2.280797 GACAGCCACAACCTCGCA 60.281 61.111 0.00 0.00 0.00 5.10
1927 2884 1.527433 GGCAGCACCCTTTCAGGTTC 61.527 60.000 0.00 0.00 38.39 3.62
1957 2918 2.370445 CCTACCCAGCACTCCCCAG 61.370 68.421 0.00 0.00 0.00 4.45
1958 2919 1.613630 CTACCCAGCACTCCCCAGT 60.614 63.158 0.00 0.00 0.00 4.00
1982 2943 5.221945 TGGTCAGTGGATGTTGTTATTACCA 60.222 40.000 0.00 0.00 0.00 3.25
2003 2964 1.600107 TGGTTACTCCATGGACGGC 59.400 57.895 11.44 1.27 41.93 5.68
2028 2989 2.863809 ACCTGGATCTTGTTGTTGACC 58.136 47.619 0.00 0.00 0.00 4.02
2216 3208 0.457443 CAGCCTCTGTCTGCATCGTA 59.543 55.000 0.00 0.00 0.00 3.43
2308 3301 2.475864 GCACTTTGCATCAAATTTGCGA 59.524 40.909 13.54 0.00 44.26 5.10
2360 3355 3.256631 CCATAATGGCCTGGTAATTCTGC 59.743 47.826 3.32 0.00 0.00 4.26
2418 3414 4.742438 TCTTGTTTTTACAGCACGGATC 57.258 40.909 0.00 0.00 0.00 3.36
2421 3417 3.472652 TGTTTTTACAGCACGGATCACT 58.527 40.909 0.00 0.00 0.00 3.41
2422 3418 3.880490 TGTTTTTACAGCACGGATCACTT 59.120 39.130 0.00 0.00 0.00 3.16
2423 3419 4.219033 GTTTTTACAGCACGGATCACTTG 58.781 43.478 0.00 0.00 0.00 3.16
2424 3420 1.438651 TTACAGCACGGATCACTTGC 58.561 50.000 0.00 0.00 36.45 4.01
2425 3421 0.391130 TACAGCACGGATCACTTGCC 60.391 55.000 8.39 0.00 36.91 4.52
2426 3422 1.376424 CAGCACGGATCACTTGCCT 60.376 57.895 8.39 0.00 36.91 4.75
2427 3423 0.108186 CAGCACGGATCACTTGCCTA 60.108 55.000 8.39 0.00 36.91 3.93
2428 3424 0.108138 AGCACGGATCACTTGCCTAC 60.108 55.000 8.39 0.00 36.91 3.18
2429 3425 0.108138 GCACGGATCACTTGCCTACT 60.108 55.000 0.00 0.00 0.00 2.57
2430 3426 1.645034 CACGGATCACTTGCCTACTG 58.355 55.000 0.00 0.00 0.00 2.74
2431 3427 0.537188 ACGGATCACTTGCCTACTGG 59.463 55.000 0.00 0.00 0.00 4.00
2432 3428 0.824109 CGGATCACTTGCCTACTGGA 59.176 55.000 0.00 0.00 34.57 3.86
2433 3429 1.414181 CGGATCACTTGCCTACTGGAT 59.586 52.381 0.00 0.00 34.57 3.41
2434 3430 2.158900 CGGATCACTTGCCTACTGGATT 60.159 50.000 0.00 0.00 34.57 3.01
2435 3431 3.471680 GGATCACTTGCCTACTGGATTC 58.528 50.000 0.00 0.00 34.57 2.52
2436 3432 3.118261 GGATCACTTGCCTACTGGATTCA 60.118 47.826 0.00 0.00 34.57 2.57
2437 3433 4.517285 GATCACTTGCCTACTGGATTCAA 58.483 43.478 0.00 0.00 34.57 2.69
2438 3434 4.574674 TCACTTGCCTACTGGATTCAAT 57.425 40.909 0.00 0.00 34.57 2.57
2439 3435 4.922206 TCACTTGCCTACTGGATTCAATT 58.078 39.130 0.00 0.00 34.57 2.32
2459 3474 7.666623 TCAATTTTCCCCTTCACTAATTGTTC 58.333 34.615 0.00 0.00 35.54 3.18
2460 3475 6.605471 ATTTTCCCCTTCACTAATTGTTCC 57.395 37.500 0.00 0.00 0.00 3.62
2782 3797 4.202151 GGATGGCAAGACAACAAGAAGTTT 60.202 41.667 0.00 0.00 38.74 2.66
2910 3925 2.575532 CAAAGAAGGACCAGCTTGACA 58.424 47.619 0.00 0.00 0.00 3.58
3184 4199 1.411977 CGATCTCAGGAAGCTCACCAT 59.588 52.381 11.59 0.00 0.00 3.55
3253 4268 0.742281 CCCATGGTCGCTCTGTGAAG 60.742 60.000 11.73 0.00 0.00 3.02
3303 4335 2.602738 GCATGATGCAGTCTCTCCG 58.397 57.895 13.36 0.00 44.26 4.63
3375 4407 0.031585 GGGTTTCTTTTGGACCGTGC 59.968 55.000 0.00 0.00 34.22 5.34
3415 4448 6.075949 TCAGGGTTAGCTAGTAGAGAGAAA 57.924 41.667 0.00 0.00 0.00 2.52
3601 4636 4.430137 ACATTTGCTGTTGCTGATACTG 57.570 40.909 0.00 0.00 40.48 2.74
3662 4697 3.368236 GGACGTAAGATGAAACTCTGCAC 59.632 47.826 0.00 0.00 43.62 4.57
3666 4701 2.486472 AGATGAAACTCTGCACCTGG 57.514 50.000 0.00 0.00 0.00 4.45
3668 4703 2.373169 AGATGAAACTCTGCACCTGGAA 59.627 45.455 0.00 0.00 0.00 3.53
3678 4713 1.182667 GCACCTGGAATTGGGGTAAC 58.817 55.000 0.00 0.00 0.00 2.50
3706 4741 4.383173 TGATGAATCATGATGAACTCCGG 58.617 43.478 9.46 0.00 0.00 5.14
3733 4768 7.039313 AGTATTTCGAAGCACTTTCCTTTTT 57.961 32.000 7.66 0.00 31.82 1.94
3737 4772 2.360801 CGAAGCACTTTCCTTTTTGGGA 59.639 45.455 0.00 0.00 36.20 4.37
3784 4825 3.507233 CAGTTGGATTAACATGCCACTGT 59.493 43.478 0.00 0.00 41.88 3.55
3785 4826 3.507233 AGTTGGATTAACATGCCACTGTG 59.493 43.478 0.00 0.00 41.88 3.66
3797 4838 6.186957 ACATGCCACTGTGGAAATAGATTAA 58.813 36.000 30.23 2.43 40.96 1.40
3800 4841 6.007076 TGCCACTGTGGAAATAGATTAACAA 58.993 36.000 30.23 0.00 40.96 2.83
3801 4842 6.663093 TGCCACTGTGGAAATAGATTAACAAT 59.337 34.615 30.23 0.00 40.96 2.71
3847 4892 2.202676 GAGGCTGTCTTCGGAGCG 60.203 66.667 0.00 0.00 35.95 5.03
3887 4932 0.909623 AGGTCGGTGATTAGGGTTGG 59.090 55.000 0.00 0.00 0.00 3.77
3889 4934 0.035820 GTCGGTGATTAGGGTTGGCA 60.036 55.000 0.00 0.00 0.00 4.92
3890 4935 0.251916 TCGGTGATTAGGGTTGGCAG 59.748 55.000 0.00 0.00 0.00 4.85
3891 4936 0.748005 CGGTGATTAGGGTTGGCAGG 60.748 60.000 0.00 0.00 0.00 4.85
3892 4937 1.037579 GGTGATTAGGGTTGGCAGGC 61.038 60.000 0.00 0.00 0.00 4.85
3893 4938 1.077787 TGATTAGGGTTGGCAGGCG 60.078 57.895 0.00 0.00 0.00 5.52
3894 4939 1.077716 GATTAGGGTTGGCAGGCGT 60.078 57.895 0.00 0.00 0.00 5.68
3895 4940 1.077716 ATTAGGGTTGGCAGGCGTC 60.078 57.895 0.00 0.00 0.00 5.19
3896 4941 1.847798 ATTAGGGTTGGCAGGCGTCA 61.848 55.000 0.00 0.00 0.00 4.35
3897 4942 1.847798 TTAGGGTTGGCAGGCGTCAT 61.848 55.000 0.00 0.00 0.00 3.06
3898 4943 2.535485 TAGGGTTGGCAGGCGTCATG 62.535 60.000 0.00 0.00 0.00 3.07
3899 4944 3.443045 GGTTGGCAGGCGTCATGG 61.443 66.667 0.00 0.00 0.00 3.66
3900 4945 3.443045 GTTGGCAGGCGTCATGGG 61.443 66.667 0.00 0.00 0.00 4.00
3901 4946 3.645660 TTGGCAGGCGTCATGGGA 61.646 61.111 0.00 0.00 0.00 4.37
3902 4947 3.626996 TTGGCAGGCGTCATGGGAG 62.627 63.158 0.00 0.00 0.00 4.30
3904 4949 4.783621 GCAGGCGTCATGGGAGCA 62.784 66.667 9.45 0.00 0.00 4.26
3905 4950 2.046023 CAGGCGTCATGGGAGCAA 60.046 61.111 9.45 0.00 0.00 3.91
3906 4951 2.110967 CAGGCGTCATGGGAGCAAG 61.111 63.158 9.45 0.00 0.00 4.01
3907 4952 2.268920 GGCGTCATGGGAGCAAGA 59.731 61.111 9.45 0.00 0.00 3.02
3908 4953 1.377202 GGCGTCATGGGAGCAAGAA 60.377 57.895 9.45 0.00 0.00 2.52
3909 4954 1.372087 GGCGTCATGGGAGCAAGAAG 61.372 60.000 9.45 0.00 0.00 2.85
3910 4955 0.391661 GCGTCATGGGAGCAAGAAGA 60.392 55.000 0.00 0.00 0.00 2.87
3911 4956 1.745141 GCGTCATGGGAGCAAGAAGAT 60.745 52.381 0.00 0.00 0.00 2.40
3912 4957 1.938577 CGTCATGGGAGCAAGAAGATG 59.061 52.381 0.00 0.00 0.00 2.90
3913 4958 2.419159 CGTCATGGGAGCAAGAAGATGA 60.419 50.000 0.00 0.00 0.00 2.92
3914 4959 2.941720 GTCATGGGAGCAAGAAGATGAC 59.058 50.000 0.00 0.00 34.64 3.06
3915 4960 2.092753 TCATGGGAGCAAGAAGATGACC 60.093 50.000 0.00 0.00 0.00 4.02
3916 4961 1.361204 TGGGAGCAAGAAGATGACCA 58.639 50.000 0.00 0.00 0.00 4.02
3917 4962 1.280133 TGGGAGCAAGAAGATGACCAG 59.720 52.381 0.00 0.00 0.00 4.00
3918 4963 1.280421 GGGAGCAAGAAGATGACCAGT 59.720 52.381 0.00 0.00 0.00 4.00
3919 4964 2.290577 GGGAGCAAGAAGATGACCAGTT 60.291 50.000 0.00 0.00 0.00 3.16
3920 4965 2.746362 GGAGCAAGAAGATGACCAGTTG 59.254 50.000 0.00 0.00 0.00 3.16
3921 4966 3.406764 GAGCAAGAAGATGACCAGTTGT 58.593 45.455 0.00 0.00 0.00 3.32
3922 4967 3.144506 AGCAAGAAGATGACCAGTTGTG 58.855 45.455 0.00 0.00 0.00 3.33
3934 4979 0.518636 CAGTTGTGGCATGAACCTCG 59.481 55.000 0.00 0.00 0.00 4.63
4096 5142 9.959721 ACTACTTTAGAAGCTATCAAATTTCCA 57.040 29.630 0.00 0.00 0.00 3.53
4412 5471 2.811317 GAGCCGAGTTGCACTCCG 60.811 66.667 9.71 3.01 42.12 4.63
4505 5564 0.391927 CTTTGCAACATGGCCCATGG 60.392 55.000 26.79 11.76 45.16 3.66
4533 5592 0.882484 TCCTTTGCAACATGACGCGA 60.882 50.000 15.93 0.00 0.00 5.87
4534 5593 0.453282 CCTTTGCAACATGACGCGAG 60.453 55.000 15.93 1.54 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.293498 CACCGTTGTGGGAGAGGAG 59.707 63.158 0.00 0.00 44.64 3.69
36 37 3.466881 CACCGTTGTGGGAGAGGA 58.533 61.111 0.00 0.00 44.64 3.71
46 47 2.677003 GGCGATGTGACCACCGTTG 61.677 63.158 0.00 0.00 0.00 4.10
130 131 1.956869 TCCTTTCCCATCTCTCTGCA 58.043 50.000 0.00 0.00 0.00 4.41
193 204 3.827302 TCCCTATCATCCTTAACTCTCGC 59.173 47.826 0.00 0.00 0.00 5.03
200 211 4.594920 CAGCCTCTTCCCTATCATCCTTAA 59.405 45.833 0.00 0.00 0.00 1.85
245 259 4.344865 AACCGCCTCCCACGCATT 62.345 61.111 0.00 0.00 0.00 3.56
271 291 1.553248 ACTCGACCGATTGATTTCCCA 59.447 47.619 0.00 0.00 0.00 4.37
290 310 8.583765 GCCAAAGAATATGATAAACGTTTCAAC 58.416 33.333 18.42 10.50 0.00 3.18
293 313 8.856490 ATGCCAAAGAATATGATAAACGTTTC 57.144 30.769 18.42 4.76 0.00 2.78
350 371 9.869757 ATAATTTTCGCCCAATTATATTAAGGC 57.130 29.630 0.00 0.00 35.79 4.35
382 403 7.768120 TCCCAAATTAATGTGAACAATATTGGC 59.232 33.333 19.37 11.25 0.00 4.52
420 441 6.304126 ACGTGCTCAAATTTGAAAGTATACG 58.696 36.000 20.82 21.87 36.64 3.06
422 443 6.580791 GCAACGTGCTCAAATTTGAAAGTATA 59.419 34.615 20.82 2.72 40.96 1.47
429 450 1.752753 CGCAACGTGCTCAAATTTGA 58.247 45.000 19.45 19.45 42.25 2.69
450 471 2.022195 CCATACGACCTCTTTCGGAGA 58.978 52.381 0.00 0.00 44.45 3.71
451 472 2.022195 TCCATACGACCTCTTTCGGAG 58.978 52.381 0.00 0.00 43.58 4.63
475 1350 2.423660 CCTTATCTCTCACCGGAGTCCT 60.424 54.545 9.46 0.00 42.05 3.85
481 1356 1.334243 GTCGTCCTTATCTCTCACCGG 59.666 57.143 0.00 0.00 0.00 5.28
485 1360 2.241430 TCCCTGTCGTCCTTATCTCTCA 59.759 50.000 0.00 0.00 0.00 3.27
519 1394 1.040893 TGACACGTGTCCTCTGTGGT 61.041 55.000 38.12 6.97 44.15 4.16
564 1439 0.855349 CCGATTGATTTCTCGCTCCG 59.145 55.000 0.00 0.00 33.63 4.63
749 1626 2.895372 GATTGTAGGGGCGCACGG 60.895 66.667 10.83 0.00 0.00 4.94
755 1632 0.811616 CAGCTCACGATTGTAGGGGC 60.812 60.000 0.00 0.00 0.00 5.80
797 1692 1.452108 GTGATCTTCCCGGGCTTGG 60.452 63.158 18.49 5.50 0.00 3.61
817 1712 2.802667 CGTTCCGATTGCTGCCGAG 61.803 63.158 0.00 0.00 0.00 4.63
819 1714 4.520846 GCGTTCCGATTGCTGCCG 62.521 66.667 0.00 0.00 0.00 5.69
820 1715 4.179579 GGCGTTCCGATTGCTGCC 62.180 66.667 0.00 0.00 35.04 4.85
821 1716 3.386867 CTGGCGTTCCGATTGCTGC 62.387 63.158 0.00 0.00 34.14 5.25
823 1718 1.741770 GACTGGCGTTCCGATTGCT 60.742 57.895 0.00 0.00 34.14 3.91
824 1719 2.750888 GGACTGGCGTTCCGATTGC 61.751 63.158 0.00 0.00 34.14 3.56
846 1754 1.542187 CCTTTCCGGTTCCTCTCCGT 61.542 60.000 0.00 0.00 45.63 4.69
848 1756 0.981943 TTCCTTTCCGGTTCCTCTCC 59.018 55.000 0.00 0.00 0.00 3.71
849 1757 2.701107 CTTTCCTTTCCGGTTCCTCTC 58.299 52.381 0.00 0.00 0.00 3.20
854 1762 0.241213 GCTGCTTTCCTTTCCGGTTC 59.759 55.000 0.00 0.00 0.00 3.62
1175 2098 1.900016 ACCTGCGTCGTGTGGAGTA 60.900 57.895 7.17 0.00 0.00 2.59
1202 2125 0.729116 CGCAAACGAATCTGGCAGAT 59.271 50.000 24.01 24.01 43.93 2.90
1228 2151 3.395702 AATCCAGTACCCGCGCCA 61.396 61.111 0.00 0.00 0.00 5.69
1309 2232 3.257561 CTCCGCCGCAGTTCATCG 61.258 66.667 0.00 0.00 0.00 3.84
1477 2425 1.512156 AATCGGCAAACCTCGCGTTT 61.512 50.000 5.77 0.00 45.83 3.60
1490 2438 0.243636 CTTCCAACCCACAAATCGGC 59.756 55.000 0.00 0.00 0.00 5.54
1492 2440 1.200020 GCTCTTCCAACCCACAAATCG 59.800 52.381 0.00 0.00 0.00 3.34
1572 2521 2.124778 GCAGAGAAGAGGCCAGGC 60.125 66.667 5.01 1.26 0.00 4.85
1573 2522 0.977108 AGAGCAGAGAAGAGGCCAGG 60.977 60.000 5.01 0.00 0.00 4.45
1574 2523 1.408702 GTAGAGCAGAGAAGAGGCCAG 59.591 57.143 5.01 0.00 0.00 4.85
1575 2524 1.006519 AGTAGAGCAGAGAAGAGGCCA 59.993 52.381 5.01 0.00 0.00 5.36
1576 2525 1.775385 AGTAGAGCAGAGAAGAGGCC 58.225 55.000 0.00 0.00 0.00 5.19
1606 2555 2.350772 CGAGAATCACACCAACCAAAGC 60.351 50.000 0.00 0.00 33.17 3.51
1645 2599 2.917227 AAGGCGTTGGCAAAGGGG 60.917 61.111 14.83 0.32 42.47 4.79
1669 2623 3.822735 TGAAGAAAGTTCAGGAGCATTGG 59.177 43.478 0.00 0.00 0.00 3.16
1694 2648 6.042437 AGCCAACAAAAGAGAAGATTTGGAAT 59.958 34.615 1.63 0.00 40.09 3.01
1787 2741 3.834231 AGGAATAAGCACAAACAGCCAAT 59.166 39.130 0.00 0.00 0.00 3.16
1810 2764 8.310382 TCTCTTCTTCTTACCTTCAGAAATCAG 58.690 37.037 0.00 0.00 29.74 2.90
1889 2846 2.610859 AGCCATGGGGACGTCCTT 60.611 61.111 32.52 15.99 35.59 3.36
1957 2918 5.123344 GGTAATAACAACATCCACTGACCAC 59.877 44.000 0.00 0.00 0.00 4.16
1958 2919 5.221945 TGGTAATAACAACATCCACTGACCA 60.222 40.000 0.00 0.00 0.00 4.02
1959 2920 5.250200 TGGTAATAACAACATCCACTGACC 58.750 41.667 0.00 0.00 0.00 4.02
1960 2921 6.374333 ACATGGTAATAACAACATCCACTGAC 59.626 38.462 0.00 0.00 0.00 3.51
1961 2922 6.374053 CACATGGTAATAACAACATCCACTGA 59.626 38.462 0.00 0.00 0.00 3.41
1962 2923 6.404623 CCACATGGTAATAACAACATCCACTG 60.405 42.308 0.00 0.00 0.00 3.66
1963 2924 5.652014 CCACATGGTAATAACAACATCCACT 59.348 40.000 0.00 0.00 0.00 4.00
2003 2964 3.146104 ACAACAAGATCCAGGTTCAGG 57.854 47.619 0.14 0.00 0.00 3.86
2308 3301 5.300792 TGCATCACAAGATTGCATATGTCAT 59.699 36.000 4.29 0.00 35.13 3.06
2418 3414 5.649782 AAATTGAATCCAGTAGGCAAGTG 57.350 39.130 0.00 0.00 33.74 3.16
2421 3417 4.466015 GGGAAAATTGAATCCAGTAGGCAA 59.534 41.667 7.31 0.00 37.46 4.52
2422 3418 4.023291 GGGAAAATTGAATCCAGTAGGCA 58.977 43.478 7.31 0.00 37.46 4.75
2423 3419 3.384789 GGGGAAAATTGAATCCAGTAGGC 59.615 47.826 7.31 0.00 37.46 3.93
2424 3420 4.871822 AGGGGAAAATTGAATCCAGTAGG 58.128 43.478 7.31 0.00 37.46 3.18
2425 3421 5.951747 TGAAGGGGAAAATTGAATCCAGTAG 59.048 40.000 7.31 0.00 37.46 2.57
2426 3422 5.714806 GTGAAGGGGAAAATTGAATCCAGTA 59.285 40.000 7.31 0.00 37.46 2.74
2427 3423 4.528206 GTGAAGGGGAAAATTGAATCCAGT 59.472 41.667 7.31 0.00 37.46 4.00
2428 3424 4.774200 AGTGAAGGGGAAAATTGAATCCAG 59.226 41.667 7.31 0.00 37.46 3.86
2429 3425 4.750941 AGTGAAGGGGAAAATTGAATCCA 58.249 39.130 7.31 0.00 37.46 3.41
2430 3426 6.850752 TTAGTGAAGGGGAAAATTGAATCC 57.149 37.500 0.00 0.00 34.85 3.01
2431 3427 8.314021 ACAATTAGTGAAGGGGAAAATTGAATC 58.686 33.333 11.36 0.00 37.61 2.52
2432 3428 8.206126 ACAATTAGTGAAGGGGAAAATTGAAT 57.794 30.769 11.36 0.00 37.61 2.57
2433 3429 7.610580 ACAATTAGTGAAGGGGAAAATTGAA 57.389 32.000 11.36 0.00 37.61 2.69
2434 3430 7.256154 GGAACAATTAGTGAAGGGGAAAATTGA 60.256 37.037 11.36 0.00 37.61 2.57
2435 3431 6.873605 GGAACAATTAGTGAAGGGGAAAATTG 59.126 38.462 0.00 0.00 39.21 2.32
2436 3432 6.013725 GGGAACAATTAGTGAAGGGGAAAATT 60.014 38.462 0.00 0.00 0.00 1.82
2437 3433 5.483937 GGGAACAATTAGTGAAGGGGAAAAT 59.516 40.000 0.00 0.00 0.00 1.82
2438 3434 4.836175 GGGAACAATTAGTGAAGGGGAAAA 59.164 41.667 0.00 0.00 0.00 2.29
2439 3435 4.107311 AGGGAACAATTAGTGAAGGGGAAA 59.893 41.667 0.00 0.00 0.00 3.13
2459 3474 1.827344 GCAATCAAAGGGAAGGAAGGG 59.173 52.381 0.00 0.00 0.00 3.95
2460 3475 2.494870 CTGCAATCAAAGGGAAGGAAGG 59.505 50.000 0.00 0.00 0.00 3.46
2549 3564 4.490959 CGCTTCTTGTAGTACATTTCAGCG 60.491 45.833 21.92 21.92 35.77 5.18
2782 3797 1.490490 AGCACAGTGAGTTGGAGGAAA 59.510 47.619 4.15 0.00 0.00 3.13
2881 3896 2.674380 CCTTCTTTGCCGCTGCCT 60.674 61.111 0.00 0.00 36.33 4.75
2910 3925 1.085091 CGCATGAGCTCTGCTTCTTT 58.915 50.000 25.44 0.00 39.88 2.52
2963 3978 0.809241 CGATCACCTTCTGCAGCTCC 60.809 60.000 9.47 0.00 0.00 4.70
3184 4199 2.154798 CTTCGCCGAGAACAGGTCCA 62.155 60.000 0.00 0.00 34.66 4.02
3215 4230 1.580845 GACCAGAATGCTTGCGCTGT 61.581 55.000 9.73 0.00 36.97 4.40
3253 4268 4.389374 TCTTCATCACCAAAACTCACTCC 58.611 43.478 0.00 0.00 0.00 3.85
3303 4335 4.100653 TCTCATGGATCTGGATGTCAAGAC 59.899 45.833 0.00 0.00 0.00 3.01
3375 4407 0.698238 TGAACAAGGATGGGACCAGG 59.302 55.000 0.00 0.00 0.00 4.45
3450 4483 9.988815 TGGCTATACTACTACTACTTACTACAC 57.011 37.037 0.00 0.00 0.00 2.90
3546 4579 2.725312 ATCGCACAGGACCGCTGAT 61.725 57.895 0.00 0.00 0.00 2.90
3581 4616 3.119602 AGCAGTATCAGCAACAGCAAATG 60.120 43.478 0.00 0.00 32.31 2.32
3597 4632 4.551702 TGATGGCACTTCTAAAGCAGTA 57.448 40.909 0.00 0.00 0.00 2.74
3601 4636 4.637534 TCTTGATGATGGCACTTCTAAAGC 59.362 41.667 0.00 0.00 0.00 3.51
3641 4676 3.368236 GGTGCAGAGTTTCATCTTACGTC 59.632 47.826 0.00 0.00 0.00 4.34
3678 4713 5.936372 AGTTCATCATGATTCATCATACGGG 59.064 40.000 5.16 0.00 45.23 5.28
3784 4825 5.896678 CCCCACCATTGTTAATCTATTTCCA 59.103 40.000 0.00 0.00 0.00 3.53
3785 4826 5.304357 CCCCCACCATTGTTAATCTATTTCC 59.696 44.000 0.00 0.00 0.00 3.13
3815 4860 4.148825 CTCCCCGCCTTCACCTCG 62.149 72.222 0.00 0.00 0.00 4.63
3853 4898 4.489771 CCTCCACCATCCACGGCC 62.490 72.222 0.00 0.00 0.00 6.13
3887 4932 4.783621 TGCTCCCATGACGCCTGC 62.784 66.667 0.00 0.00 0.00 4.85
3889 4934 1.841302 TTCTTGCTCCCATGACGCCT 61.841 55.000 0.00 0.00 0.00 5.52
3890 4935 1.372087 CTTCTTGCTCCCATGACGCC 61.372 60.000 0.00 0.00 0.00 5.68
3891 4936 0.391661 TCTTCTTGCTCCCATGACGC 60.392 55.000 0.00 0.00 0.00 5.19
3892 4937 1.938577 CATCTTCTTGCTCCCATGACG 59.061 52.381 0.00 0.00 0.00 4.35
3893 4938 2.941720 GTCATCTTCTTGCTCCCATGAC 59.058 50.000 0.00 0.00 34.92 3.06
3894 4939 2.092753 GGTCATCTTCTTGCTCCCATGA 60.093 50.000 0.00 0.00 0.00 3.07
3895 4940 2.295885 GGTCATCTTCTTGCTCCCATG 58.704 52.381 0.00 0.00 0.00 3.66
3896 4941 1.918262 TGGTCATCTTCTTGCTCCCAT 59.082 47.619 0.00 0.00 0.00 4.00
3897 4942 1.280133 CTGGTCATCTTCTTGCTCCCA 59.720 52.381 0.00 0.00 0.00 4.37
3898 4943 1.280421 ACTGGTCATCTTCTTGCTCCC 59.720 52.381 0.00 0.00 0.00 4.30
3899 4944 2.746362 CAACTGGTCATCTTCTTGCTCC 59.254 50.000 0.00 0.00 0.00 4.70
3900 4945 3.188048 CACAACTGGTCATCTTCTTGCTC 59.812 47.826 0.00 0.00 0.00 4.26
3901 4946 3.144506 CACAACTGGTCATCTTCTTGCT 58.855 45.455 0.00 0.00 0.00 3.91
3902 4947 2.227388 CCACAACTGGTCATCTTCTTGC 59.773 50.000 0.00 0.00 32.03 4.01
3903 4948 2.227388 GCCACAACTGGTCATCTTCTTG 59.773 50.000 0.00 0.00 40.17 3.02
3904 4949 2.158623 TGCCACAACTGGTCATCTTCTT 60.159 45.455 0.00 0.00 40.17 2.52
3905 4950 1.421268 TGCCACAACTGGTCATCTTCT 59.579 47.619 0.00 0.00 40.17 2.85
3906 4951 1.896220 TGCCACAACTGGTCATCTTC 58.104 50.000 0.00 0.00 40.17 2.87
3907 4952 2.165167 CATGCCACAACTGGTCATCTT 58.835 47.619 0.00 0.00 40.17 2.40
3908 4953 1.352017 TCATGCCACAACTGGTCATCT 59.648 47.619 0.00 0.00 40.17 2.90
3909 4954 1.825090 TCATGCCACAACTGGTCATC 58.175 50.000 0.00 0.00 40.17 2.92
3910 4955 1.888512 GTTCATGCCACAACTGGTCAT 59.111 47.619 0.00 0.00 40.17 3.06
3911 4956 1.317613 GTTCATGCCACAACTGGTCA 58.682 50.000 0.00 0.00 40.17 4.02
3912 4957 0.598065 GGTTCATGCCACAACTGGTC 59.402 55.000 0.00 0.00 40.17 4.02
3913 4958 0.185901 AGGTTCATGCCACAACTGGT 59.814 50.000 0.00 0.00 40.17 4.00
3914 4959 0.883833 GAGGTTCATGCCACAACTGG 59.116 55.000 0.00 0.00 41.13 4.00
3915 4960 0.518636 CGAGGTTCATGCCACAACTG 59.481 55.000 0.00 0.00 0.00 3.16
3916 4961 1.237285 GCGAGGTTCATGCCACAACT 61.237 55.000 0.00 0.00 0.00 3.16
3917 4962 1.210155 GCGAGGTTCATGCCACAAC 59.790 57.895 0.00 0.00 0.00 3.32
3918 4963 1.228094 TGCGAGGTTCATGCCACAA 60.228 52.632 0.00 0.00 0.00 3.33
3919 4964 1.672030 CTGCGAGGTTCATGCCACA 60.672 57.895 0.00 0.00 0.00 4.17
3920 4965 1.237285 AACTGCGAGGTTCATGCCAC 61.237 55.000 0.00 0.00 0.00 5.01
3921 4966 1.073025 AACTGCGAGGTTCATGCCA 59.927 52.632 0.00 0.00 0.00 4.92
3922 4967 1.503542 CAACTGCGAGGTTCATGCC 59.496 57.895 0.00 0.00 0.00 4.40
3923 4968 0.955428 TCCAACTGCGAGGTTCATGC 60.955 55.000 0.00 0.00 0.00 4.06
3924 4969 1.399440 CATCCAACTGCGAGGTTCATG 59.601 52.381 0.00 0.00 0.00 3.07
3925 4970 1.278985 TCATCCAACTGCGAGGTTCAT 59.721 47.619 0.00 0.00 0.00 2.57
3926 4971 0.684535 TCATCCAACTGCGAGGTTCA 59.315 50.000 0.00 0.00 0.00 3.18
3927 4972 1.734465 CTTCATCCAACTGCGAGGTTC 59.266 52.381 0.00 0.00 0.00 3.62
3934 4979 1.674962 GCCAGATCTTCATCCAACTGC 59.325 52.381 0.00 0.00 0.00 4.40
4028 5073 1.418637 TGTGGACCAGTGGAACCTAAC 59.581 52.381 18.40 13.43 37.80 2.34
4096 5142 2.632996 TCTCACTCTCCATCAAACCGTT 59.367 45.455 0.00 0.00 0.00 4.44
4110 5156 4.314121 AGTTGCAGAGTTTCATCTCACTC 58.686 43.478 0.00 0.00 39.92 3.51
4193 5239 9.537192 CCAACAATTGATCAACTATTGCATAAT 57.463 29.630 13.59 0.00 42.38 1.28
4251 5310 6.044682 GGCAAATTCGATCAAATCATTTCCT 58.955 36.000 0.00 0.00 0.00 3.36
4298 5357 5.453648 AGAGAACGAACGACTATCATATGC 58.546 41.667 0.00 0.00 0.00 3.14
4301 5360 6.286758 AGGTAGAGAACGAACGACTATCATA 58.713 40.000 0.14 0.00 0.00 2.15
4350 5409 2.987149 CAATAGCTATGCTACGAACGGG 59.013 50.000 7.09 0.00 44.24 5.28
4505 5564 0.315251 GTTGCAAAGGAGCTTCCCAC 59.685 55.000 0.00 0.00 37.19 4.61
4508 5567 1.888512 TCATGTTGCAAAGGAGCTTCC 59.111 47.619 0.00 0.00 36.58 3.46


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

AutoCloner maintained by Alex Coulton.