Multiple sequence alignment - TraesCS3A01G324600

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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 TraesCS3A01G324600 chr3A 100.000 4088 0 0 1 4088 569239116 569235029 0.000000e+00 7550.0
1 TraesCS3A01G324600 chr3D 89.292 3250 161 78 358 3510 431842288 431839129 0.000000e+00 3901.0
2 TraesCS3A01G324600 chr3D 89.394 528 25 9 3559 4073 431839117 431838608 1.600000e-178 636.0
3 TraesCS3A01G324600 chr3D 86.510 341 24 3 1 339 431842729 431842409 5.030000e-94 355.0
4 TraesCS3A01G324600 chr3D 83.007 153 22 4 361 511 219836353 219836203 7.130000e-28 135.0
5 TraesCS3A01G324600 chr3D 82.759 145 23 2 368 511 125016510 125016653 1.190000e-25 128.0
6 TraesCS3A01G324600 chr3B 88.423 2626 131 73 811 3322 564045840 564043274 0.000000e+00 3005.0
7 TraesCS3A01G324600 chr3B 82.907 743 54 27 3358 4088 564043269 564042588 5.850000e-168 601.0
8 TraesCS3A01G324600 chr3B 83.407 452 31 4 2367 2818 85351813 85351406 2.980000e-101 379.0
9 TraesCS3A01G324600 chr3B 88.261 230 11 6 536 765 564046134 564045921 1.130000e-65 261.0
10 TraesCS3A01G324600 chr3B 89.231 130 12 1 1 128 564046271 564046142 1.180000e-35 161.0
11 TraesCS3A01G324600 chr3B 88.889 99 11 0 2169 2267 85352139 85352041 5.550000e-24 122.0
12 TraesCS3A01G324600 chr7B 86.932 176 23 0 130 305 571836851 571837026 8.960000e-47 198.0
13 TraesCS3A01G324600 chr7B 82.979 141 22 2 361 500 65389952 65389813 4.290000e-25 126.0
14 TraesCS3A01G324600 chr1A 88.024 167 20 0 134 300 204991577 204991743 8.960000e-47 198.0
15 TraesCS3A01G324600 chr7A 85.946 185 25 1 136 319 329474629 329474445 3.220000e-46 196.0
16 TraesCS3A01G324600 chr7A 86.585 82 11 0 430 511 667655155 667655236 1.560000e-14 91.6
17 TraesCS3A01G324600 chr6A 85.946 185 25 1 136 319 384724929 384725113 3.220000e-46 196.0
18 TraesCS3A01G324600 chr6A 85.405 185 26 1 136 319 221456239 221456055 1.500000e-44 191.0
19 TraesCS3A01G324600 chr6A 89.394 66 6 1 447 511 17637222 17637287 9.420000e-12 82.4
20 TraesCS3A01G324600 chr2A 85.946 185 25 1 136 319 752550922 752551106 3.220000e-46 196.0
21 TraesCS3A01G324600 chr2B 85.561 187 22 4 134 318 86541389 86541206 1.500000e-44 191.0
22 TraesCS3A01G324600 chr2B 85.106 188 27 1 132 318 255579663 255579476 1.500000e-44 191.0
23 TraesCS3A01G324600 chr4D 89.855 138 12 2 1267 1404 26926516 26926381 4.200000e-40 176.0
24 TraesCS3A01G324600 chr4D 93.548 93 6 0 1119 1211 26926626 26926534 5.510000e-29 139.0
25 TraesCS3A01G324600 chr4D 85.542 83 11 1 2493 2574 90989970 90989888 7.280000e-13 86.1
26 TraesCS3A01G324600 chr4A 91.964 112 6 1 1119 1230 576565710 576565818 1.970000e-33 154.0
27 TraesCS3A01G324600 chr4A 85.542 83 11 1 2493 2574 502902914 502902832 7.280000e-13 86.1
28 TraesCS3A01G324600 chr4B 91.071 112 7 1 1119 1230 39302622 39302514 9.160000e-32 148.0
29 TraesCS3A01G324600 chr4B 82.500 160 21 6 345 499 119327904 119327747 2.560000e-27 134.0
30 TraesCS3A01G324600 chr5A 86.585 82 11 0 430 511 245673391 245673310 1.560000e-14 91.6
31 TraesCS3A01G324600 chr2D 85.366 82 12 0 430 511 199484948 199485029 7.280000e-13 86.1


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 TraesCS3A01G324600 chr3A 569235029 569239116 4087 True 7550.000000 7550 100.000000 1 4088 1 chr3A.!!$R1 4087
1 TraesCS3A01G324600 chr3D 431838608 431842729 4121 True 1630.666667 3901 88.398667 1 4073 3 chr3D.!!$R2 4072
2 TraesCS3A01G324600 chr3B 564042588 564046271 3683 True 1007.000000 3005 87.205500 1 4088 4 chr3B.!!$R2 4087
3 TraesCS3A01G324600 chr3B 85351406 85352139 733 True 250.500000 379 86.148000 2169 2818 2 chr3B.!!$R1 649

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
987 1150 0.745845 CTGCGCCTGCCAGAACTAAT 60.746 55.0 4.18 0.0 41.78 1.73 F
2020 2228 0.461961 ACTTGCGGACTCAGGATAGC 59.538 55.0 0.00 0.0 0.00 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2361 2774 0.107897 TCACTGACACACACCCACAC 60.108 55.0 0.0 0.0 0.0 3.82 R
3474 3927 0.107165 GGTGCATTGACCCTACTCCC 60.107 60.0 0.0 0.0 0.0 4.30 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
190 193 3.947196 TCATACATGTCAACTGGGCAATC 59.053 43.478 0.00 0.00 0.00 2.67
198 201 3.507233 GTCAACTGGGCAATCTTGATGAA 59.493 43.478 0.00 0.00 0.00 2.57
203 206 3.760151 CTGGGCAATCTTGATGAAGTGAA 59.240 43.478 0.00 0.00 0.00 3.18
291 294 8.306761 TCTTATACTACTATGTGTCATGCATGG 58.693 37.037 25.97 10.76 0.00 3.66
292 295 4.760530 ACTACTATGTGTCATGCATGGT 57.239 40.909 25.97 15.83 40.35 3.55
300 303 8.570488 ACTATGTGTCATGCATGGTAATAAATG 58.430 33.333 25.97 11.43 36.51 2.32
412 517 9.831737 GCTTTCGCATCATATAGATTTGTTATT 57.168 29.630 0.00 0.00 33.72 1.40
487 593 6.274157 ACTTCAGTCACCTCTAATACACAG 57.726 41.667 0.00 0.00 0.00 3.66
489 595 6.493802 ACTTCAGTCACCTCTAATACACAGAA 59.506 38.462 0.00 0.00 0.00 3.02
530 636 5.579718 AGTAGTAGTACGCATTACAAGCAG 58.420 41.667 2.04 0.00 33.97 4.24
532 638 1.369625 AGTACGCATTACAAGCAGCC 58.630 50.000 0.00 0.00 32.41 4.85
533 639 1.066143 AGTACGCATTACAAGCAGCCT 60.066 47.619 0.00 0.00 32.41 4.58
587 709 2.135581 ACGGTCTCGGGTTGTTCCA 61.136 57.895 0.00 0.00 41.39 3.53
597 719 2.217750 GGGTTGTTCCATTTTGTTGCC 58.782 47.619 0.00 0.00 38.11 4.52
642 764 4.814294 GAGCGCCCACCTGTACCG 62.814 72.222 2.29 0.00 0.00 4.02
691 813 5.066634 TCAACATTTGTTCCTACTCGCAAAA 59.933 36.000 0.00 0.00 35.83 2.44
695 817 3.462483 TGTTCCTACTCGCAAAAGACA 57.538 42.857 0.00 0.00 0.00 3.41
731 855 2.442272 CGGTCCCCGTCTCCATCT 60.442 66.667 0.00 0.00 42.73 2.90
734 858 1.381327 GTCCCCGTCTCCATCTCCA 60.381 63.158 0.00 0.00 0.00 3.86
775 899 3.242349 GCGTCTCGTATCGTATCCATAGG 60.242 52.174 0.00 0.00 0.00 2.57
928 1091 1.402194 CCTCGCTCGCTATCTCAATCC 60.402 57.143 0.00 0.00 0.00 3.01
984 1147 4.711949 CCTGCGCCTGCCAGAACT 62.712 66.667 4.18 0.00 41.78 3.01
985 1148 2.265739 CTGCGCCTGCCAGAACTA 59.734 61.111 4.18 0.00 41.78 2.24
986 1149 1.375908 CTGCGCCTGCCAGAACTAA 60.376 57.895 4.18 0.00 41.78 2.24
987 1150 0.745845 CTGCGCCTGCCAGAACTAAT 60.746 55.000 4.18 0.00 41.78 1.73
1395 1591 2.106683 GTTCCTCAACCCCATCGCG 61.107 63.158 0.00 0.00 0.00 5.87
1827 2032 1.733526 GCACCACCTGTCCAAACAC 59.266 57.895 0.00 0.00 0.00 3.32
1861 2066 1.909376 CATCTGCACTGCATTGCTTC 58.091 50.000 26.72 2.20 43.41 3.86
1872 2080 1.603678 GCATTGCTTCTGTTGGTGGTG 60.604 52.381 0.16 0.00 0.00 4.17
1882 2090 1.149627 TTGGTGGTGGTGGTACTGC 59.850 57.895 0.00 0.00 0.00 4.40
1959 2167 4.843728 TCCTATCCTTTTCGCATTTCAGT 58.156 39.130 0.00 0.00 0.00 3.41
1965 2173 2.087501 TTTCGCATTTCAGTAGCCGA 57.912 45.000 0.00 0.00 0.00 5.54
1966 2174 1.355971 TTCGCATTTCAGTAGCCGAC 58.644 50.000 0.00 0.00 0.00 4.79
1973 2181 5.447279 CGCATTTCAGTAGCCGACTAAAAAT 60.447 40.000 0.00 0.00 35.64 1.82
1975 2183 6.905609 GCATTTCAGTAGCCGACTAAAAATAC 59.094 38.462 7.82 2.33 35.64 1.89
2006 2214 5.801947 CCTTTTGCAGTCAATATACACTTGC 59.198 40.000 0.00 0.00 31.33 4.01
2020 2228 0.461961 ACTTGCGGACTCAGGATAGC 59.538 55.000 0.00 0.00 0.00 2.97
2030 2238 1.069823 CTCAGGATAGCGCCACTTCAT 59.930 52.381 2.29 0.00 0.00 2.57
2031 2239 1.069204 TCAGGATAGCGCCACTTCATC 59.931 52.381 2.29 0.00 0.00 2.92
2032 2240 1.123077 AGGATAGCGCCACTTCATCA 58.877 50.000 2.29 0.00 0.00 3.07
2034 2242 2.105477 AGGATAGCGCCACTTCATCAAT 59.895 45.455 2.29 0.00 0.00 2.57
2037 2245 4.083802 GGATAGCGCCACTTCATCAATTAC 60.084 45.833 2.29 0.00 0.00 1.89
2040 2248 4.122776 AGCGCCACTTCATCAATTACTAG 58.877 43.478 2.29 0.00 0.00 2.57
2042 2250 4.260375 GCGCCACTTCATCAATTACTAGTG 60.260 45.833 5.39 0.00 34.32 2.74
2157 2393 4.404507 ACAATCTGTGTTTCGATTTCGG 57.595 40.909 0.00 0.00 37.01 4.30
2230 2466 1.205460 TTCACCCCCTCTTGTAGCCC 61.205 60.000 0.00 0.00 0.00 5.19
2353 2766 9.319143 TGGTGTTTGTTTTACTTTTAATGATGG 57.681 29.630 0.00 0.00 0.00 3.51
2359 2772 9.703892 TTGTTTTACTTTTAATGATGGTGATGG 57.296 29.630 0.00 0.00 0.00 3.51
2360 2773 8.865090 TGTTTTACTTTTAATGATGGTGATGGT 58.135 29.630 0.00 0.00 0.00 3.55
2361 2774 9.139174 GTTTTACTTTTAATGATGGTGATGGTG 57.861 33.333 0.00 0.00 0.00 4.17
2362 2775 8.415950 TTTACTTTTAATGATGGTGATGGTGT 57.584 30.769 0.00 0.00 0.00 4.16
2727 3140 0.759060 GCTTCTCCTCCTCCTCCTCC 60.759 65.000 0.00 0.00 0.00 4.30
2728 3141 0.933700 CTTCTCCTCCTCCTCCTCCT 59.066 60.000 0.00 0.00 0.00 3.69
2734 3147 0.338120 CTCCTCCTCCTCCTCCAACT 59.662 60.000 0.00 0.00 0.00 3.16
2735 3148 0.336737 TCCTCCTCCTCCTCCAACTC 59.663 60.000 0.00 0.00 0.00 3.01
2736 3149 0.689412 CCTCCTCCTCCTCCAACTCC 60.689 65.000 0.00 0.00 0.00 3.85
2737 3150 0.338120 CTCCTCCTCCTCCAACTCCT 59.662 60.000 0.00 0.00 0.00 3.69
2738 3151 0.336737 TCCTCCTCCTCCAACTCCTC 59.663 60.000 0.00 0.00 0.00 3.71
2815 3234 4.493747 CCTTCGAGTCCGCCGACC 62.494 72.222 1.30 0.00 40.12 4.79
2820 3239 4.803426 GAGTCCGCCGACCAGCAG 62.803 72.222 1.30 0.00 40.12 4.24
2917 3351 4.410400 GGGAGTTCGTGGGGCAGG 62.410 72.222 0.00 0.00 0.00 4.85
3027 3461 1.672030 CGTGGTCATCTGCAAGCCA 60.672 57.895 0.00 0.00 0.00 4.75
3031 3465 1.064240 TGGTCATCTGCAAGCCATGAT 60.064 47.619 0.00 0.00 0.00 2.45
3032 3466 1.607628 GGTCATCTGCAAGCCATGATC 59.392 52.381 0.00 3.67 0.00 2.92
3033 3467 2.294979 GTCATCTGCAAGCCATGATCA 58.705 47.619 0.00 0.00 0.00 2.92
3034 3468 2.885266 GTCATCTGCAAGCCATGATCAT 59.115 45.455 1.18 1.18 0.00 2.45
3035 3469 3.058155 GTCATCTGCAAGCCATGATCATC 60.058 47.826 4.86 0.00 0.00 2.92
3036 3470 1.589803 TCTGCAAGCCATGATCATCG 58.410 50.000 4.86 0.00 0.00 3.84
3037 3471 1.139455 TCTGCAAGCCATGATCATCGA 59.861 47.619 4.86 0.00 0.00 3.59
3038 3472 1.263484 CTGCAAGCCATGATCATCGAC 59.737 52.381 4.86 0.00 0.00 4.20
3039 3473 0.590195 GCAAGCCATGATCATCGACC 59.410 55.000 4.86 0.00 0.00 4.79
3040 3474 1.233019 CAAGCCATGATCATCGACCC 58.767 55.000 4.86 0.00 0.00 4.46
3041 3475 0.109342 AAGCCATGATCATCGACCCC 59.891 55.000 4.86 0.00 0.00 4.95
3042 3476 1.056125 AGCCATGATCATCGACCCCA 61.056 55.000 4.86 0.00 0.00 4.96
3043 3477 0.037303 GCCATGATCATCGACCCCAT 59.963 55.000 4.86 0.00 0.00 4.00
3080 3518 5.814705 CGAGCTTCTCTGAATTAACCATTCT 59.185 40.000 0.00 0.00 41.91 2.40
3100 3539 2.169832 TTTTCTCTCTCGGTTGCCTG 57.830 50.000 0.00 0.00 0.00 4.85
3101 3540 0.320771 TTTCTCTCTCGGTTGCCTGC 60.321 55.000 0.00 0.00 0.00 4.85
3102 3541 2.125350 CTCTCTCGGTTGCCTGCC 60.125 66.667 0.00 0.00 0.00 4.85
3103 3542 2.922503 TCTCTCGGTTGCCTGCCA 60.923 61.111 0.00 0.00 0.00 4.92
3172 3612 2.900273 TGGTAGCATCGGCCAGAC 59.100 61.111 2.24 0.00 42.56 3.51
3187 3627 1.127951 CCAGACGCGTTTTGTCCATAC 59.872 52.381 15.53 0.00 37.04 2.39
3233 3673 1.299468 CGTGTAGGAGCTGATCGCC 60.299 63.158 0.00 0.00 40.39 5.54
3236 3676 0.395724 TGTAGGAGCTGATCGCCTCA 60.396 55.000 12.70 0.00 41.47 3.86
3295 3735 3.248602 GCTAATTTGCTAGACGACATGGG 59.751 47.826 4.53 0.00 0.00 4.00
3298 3738 2.962253 GCTAGACGACATGGGCGC 60.962 66.667 0.00 0.00 0.00 6.53
3326 3766 1.196808 CGATTGCTTTTGGTACGTGCT 59.803 47.619 3.01 0.00 0.00 4.40
3329 3769 1.225376 TGCTTTTGGTACGTGCTCCG 61.225 55.000 3.01 0.00 44.03 4.63
3342 3782 2.724839 CGTGCTCCGTTTTGTTGATAGC 60.725 50.000 0.00 0.00 0.00 2.97
3394 3842 1.897398 CTTGCGTTGTGTACCCTCGC 61.897 60.000 12.44 12.44 45.70 5.03
3395 3843 2.048503 GCGTTGTGTACCCTCGCT 60.049 61.111 12.18 0.00 42.88 4.93
3407 3855 2.821366 CTCGCTGCATGGACACCC 60.821 66.667 0.00 0.00 0.00 4.61
3422 3870 3.305539 GGACACCCGAACAAATTTTACCC 60.306 47.826 0.00 0.00 0.00 3.69
3437 3886 1.032794 TACCCGTAGCAGAGCATCAG 58.967 55.000 0.00 0.00 37.82 2.90
3439 3892 1.680522 CCCGTAGCAGAGCATCAGGT 61.681 60.000 0.00 0.00 37.82 4.00
3453 3906 4.081198 AGCATCAGGTTTCAAGAGAGGTAG 60.081 45.833 0.00 0.00 0.00 3.18
3464 3917 4.707448 TCAAGAGAGGTAGAAAGTGCCTAG 59.293 45.833 0.00 0.00 42.38 3.02
3465 3918 4.325084 AGAGAGGTAGAAAGTGCCTAGT 57.675 45.455 0.00 0.00 42.38 2.57
3466 3919 5.453866 AGAGAGGTAGAAAGTGCCTAGTA 57.546 43.478 0.00 0.00 42.38 1.82
3468 3921 5.830991 AGAGAGGTAGAAAGTGCCTAGTATG 59.169 44.000 0.00 0.00 42.38 2.39
3469 3922 5.520751 AGAGGTAGAAAGTGCCTAGTATGT 58.479 41.667 0.00 0.00 42.38 2.29
3471 3924 6.440965 AGAGGTAGAAAGTGCCTAGTATGTTT 59.559 38.462 0.00 0.00 42.38 2.83
3472 3925 6.407202 AGGTAGAAAGTGCCTAGTATGTTTG 58.593 40.000 0.00 0.00 40.05 2.93
3473 3926 6.013639 AGGTAGAAAGTGCCTAGTATGTTTGT 60.014 38.462 0.00 0.00 40.05 2.83
3474 3927 6.092259 GGTAGAAAGTGCCTAGTATGTTTGTG 59.908 42.308 0.00 0.00 0.00 3.33
3529 3982 1.825474 AGTGCAGCTGTACTCCGTATT 59.175 47.619 29.16 8.15 36.19 1.89
3531 3984 2.348666 GTGCAGCTGTACTCCGTATTTG 59.651 50.000 25.57 0.00 0.00 2.32
3534 3987 3.262420 CAGCTGTACTCCGTATTTGCTT 58.738 45.455 5.25 0.00 0.00 3.91
3538 3991 1.326548 GTACTCCGTATTTGCTTGCCG 59.673 52.381 0.00 0.00 0.00 5.69
3545 3998 1.065551 GTATTTGCTTGCCGGCCTAAG 59.934 52.381 26.77 22.54 0.00 2.18
3568 4022 2.088423 AGAGAGAGGCGTAGAGTTGTG 58.912 52.381 0.00 0.00 0.00 3.33
3658 4113 7.927629 TGCATATTTATTTTCAAATCCTGCTCC 59.072 33.333 12.96 0.00 37.46 4.70
3729 4185 6.183361 ACCTCCATTGCCTGTTTCAAAAATTA 60.183 34.615 0.00 0.00 0.00 1.40
3777 4237 2.597805 AGCCACTGACTCGTCCGT 60.598 61.111 0.00 0.00 0.00 4.69
3794 4254 4.109050 GTCCGTTTTCAAAATTGTGCTGA 58.891 39.130 0.00 0.00 0.00 4.26
3795 4255 4.564769 GTCCGTTTTCAAAATTGTGCTGAA 59.435 37.500 0.00 0.00 0.00 3.02
3845 4318 3.196207 ATGGCACGTCCTTGGCTGT 62.196 57.895 0.00 0.00 42.50 4.40
3858 4331 2.501128 GCTGTGGCCAGATCGCTA 59.499 61.111 5.11 0.00 41.50 4.26
3859 4332 1.884926 GCTGTGGCCAGATCGCTAC 60.885 63.158 5.11 2.75 41.50 3.58
3860 4333 1.819229 CTGTGGCCAGATCGCTACT 59.181 57.895 5.11 0.00 41.50 2.57
3913 4386 6.074569 GCTCTTTTCTACGTATCAATGCTCTC 60.075 42.308 0.00 0.00 0.00 3.20
3923 4396 5.005203 CGTATCAATGCTCTCTTCTGTTGAC 59.995 44.000 0.00 0.00 0.00 3.18
4005 4478 4.767255 GCAGCGCCCTGTAGCACT 62.767 66.667 2.29 0.00 41.26 4.40
4007 4480 1.519455 CAGCGCCCTGTAGCACTAC 60.519 63.158 2.29 0.70 34.31 2.73
4008 4481 2.582498 GCGCCCTGTAGCACTACG 60.582 66.667 0.00 0.00 38.85 3.51
4009 4482 2.582498 CGCCCTGTAGCACTACGC 60.582 66.667 3.52 0.66 38.85 4.42
4026 4499 2.701006 CCGGAGCGCGTAAATGTG 59.299 61.111 8.43 0.00 0.00 3.21
4059 4532 1.268640 GCCGTCGGTTTGCTAAAACAA 60.269 47.619 13.94 0.00 46.30 2.83
4060 4533 2.795331 GCCGTCGGTTTGCTAAAACAAA 60.795 45.455 13.94 0.00 46.30 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 2.772568 TTTTGTTGCCTCACGACATG 57.227 45.000 0.00 0.00 42.43 3.21
128 131 4.067896 CCATTACGAAGAGCCTTATGCAT 58.932 43.478 3.79 3.79 44.83 3.96
129 132 3.466836 CCATTACGAAGAGCCTTATGCA 58.533 45.455 0.00 0.00 44.83 3.96
140 143 7.658261 TCAACTATGATACTCCCATTACGAAG 58.342 38.462 0.00 0.00 0.00 3.79
141 144 7.591421 TCAACTATGATACTCCCATTACGAA 57.409 36.000 0.00 0.00 0.00 3.85
172 175 2.559668 CAAGATTGCCCAGTTGACATGT 59.440 45.455 0.00 0.00 0.00 3.21
177 180 3.438216 TCATCAAGATTGCCCAGTTGA 57.562 42.857 0.00 0.00 33.61 3.18
183 186 4.789012 TTTCACTTCATCAAGATTGCCC 57.211 40.909 0.00 0.00 33.34 5.36
266 269 8.090831 ACCATGCATGACACATAGTAGTATAAG 58.909 37.037 28.31 6.79 0.00 1.73
463 568 6.151312 TCTGTGTATTAGAGGTGACTGAAGTC 59.849 42.308 3.41 3.41 44.43 3.01
500 606 7.031372 TGTAATGCGTACTACTACTCCTTTTG 58.969 38.462 0.00 0.00 33.46 2.44
501 607 7.161773 TGTAATGCGTACTACTACTCCTTTT 57.838 36.000 0.00 0.00 33.46 2.27
504 610 5.221009 GCTTGTAATGCGTACTACTACTCCT 60.221 44.000 0.00 0.00 33.46 3.69
511 617 2.284417 GGCTGCTTGTAATGCGTACTAC 59.716 50.000 0.00 0.00 40.34 2.73
512 618 2.167693 AGGCTGCTTGTAATGCGTACTA 59.832 45.455 0.00 0.00 40.34 1.82
513 619 1.066143 AGGCTGCTTGTAATGCGTACT 60.066 47.619 0.00 0.00 40.34 2.73
514 620 1.062587 CAGGCTGCTTGTAATGCGTAC 59.937 52.381 0.00 0.00 40.34 3.67
532 638 4.368808 CGGGCGCGTGTGTTTCAG 62.369 66.667 15.94 0.00 0.00 3.02
566 688 0.942884 GAACAACCCGAGACCGTGAC 60.943 60.000 0.00 0.00 0.00 3.67
587 709 6.754193 CCCATAATTATACGGGCAACAAAAT 58.246 36.000 7.71 0.00 39.74 1.82
597 719 1.375551 GGGCGCCCATAATTATACGG 58.624 55.000 40.73 10.16 35.81 4.02
649 771 2.096248 TGAATTGTAAATGGGGACGCC 58.904 47.619 0.53 0.53 0.00 5.68
650 772 3.057174 TGTTGAATTGTAAATGGGGACGC 60.057 43.478 0.00 0.00 0.00 5.19
691 813 1.990060 CGGGGTGAGGGTGATGTCT 60.990 63.158 0.00 0.00 0.00 3.41
731 855 0.326927 GGGAGATTGGTTTCGGTGGA 59.673 55.000 0.00 0.00 0.00 4.02
734 858 0.249398 CTCGGGAGATTGGTTTCGGT 59.751 55.000 0.00 0.00 38.80 4.69
790 914 3.374402 CGAGGTGAGAGGTGCGGT 61.374 66.667 0.00 0.00 0.00 5.68
791 915 4.135153 CCGAGGTGAGAGGTGCGG 62.135 72.222 0.00 0.00 0.00 5.69
972 1135 1.718757 CCGCATTAGTTCTGGCAGGC 61.719 60.000 15.73 7.12 0.00 4.85
973 1136 0.392998 ACCGCATTAGTTCTGGCAGG 60.393 55.000 15.73 0.00 0.00 4.85
974 1137 0.729116 CACCGCATTAGTTCTGGCAG 59.271 55.000 8.58 8.58 0.00 4.85
975 1138 0.323302 TCACCGCATTAGTTCTGGCA 59.677 50.000 0.00 0.00 0.00 4.92
976 1139 0.727398 GTCACCGCATTAGTTCTGGC 59.273 55.000 0.00 0.00 0.00 4.85
977 1140 2.271800 GAGTCACCGCATTAGTTCTGG 58.728 52.381 0.00 0.00 0.00 3.86
978 1141 2.668457 GTGAGTCACCGCATTAGTTCTG 59.332 50.000 12.54 0.00 0.00 3.02
980 1143 2.000447 GGTGAGTCACCGCATTAGTTC 59.000 52.381 26.12 0.00 44.95 3.01
981 1144 2.094762 GGTGAGTCACCGCATTAGTT 57.905 50.000 26.12 0.00 44.95 2.24
982 1145 3.834732 GGTGAGTCACCGCATTAGT 57.165 52.632 26.12 0.00 44.95 2.24
1036 1202 4.957684 CATCTCCTGCGCGCGGAT 62.958 66.667 40.01 27.35 0.00 4.18
1234 1430 1.471676 GGTCACGATGGATGACAGTCC 60.472 57.143 7.38 0.00 46.89 3.85
1235 1431 1.204704 TGGTCACGATGGATGACAGTC 59.795 52.381 7.38 0.00 46.89 3.51
1236 1432 1.266178 TGGTCACGATGGATGACAGT 58.734 50.000 7.38 0.00 46.89 3.55
1242 1438 1.815421 GCGCTTGGTCACGATGGAT 60.815 57.895 0.00 0.00 0.00 3.41
1785 1990 4.365111 AGCGCCTCCCATTTGCCA 62.365 61.111 2.29 0.00 0.00 4.92
1818 2023 1.507141 CCTCACCTGCGTGTTTGGAC 61.507 60.000 0.00 0.00 41.09 4.02
1827 2032 1.890979 GATGCCATCCTCACCTGCG 60.891 63.158 0.00 0.00 0.00 5.18
1841 2046 4.088421 GCAATGCAGTGCAGATGC 57.912 55.556 32.30 30.87 43.65 3.91
1861 2066 0.472471 AGTACCACCACCACCAACAG 59.528 55.000 0.00 0.00 0.00 3.16
1872 2080 1.476891 TCGATCTGAAGCAGTACCACC 59.523 52.381 0.00 0.00 32.61 4.61
1882 2090 0.179134 GTGTCCGGGTCGATCTGAAG 60.179 60.000 5.94 0.00 0.00 3.02
1906 2114 1.962100 GGTACCCTGAAGATCTACCGG 59.038 57.143 0.00 0.00 0.00 5.28
1907 2115 2.662866 TGGTACCCTGAAGATCTACCG 58.337 52.381 10.07 0.00 31.10 4.02
1927 2135 5.123979 GCGAAAAGGATAGGAGTGACATTTT 59.876 40.000 0.00 0.00 0.00 1.82
1928 2136 4.636206 GCGAAAAGGATAGGAGTGACATTT 59.364 41.667 0.00 0.00 0.00 2.32
1934 2142 4.635765 TGAAATGCGAAAAGGATAGGAGTG 59.364 41.667 0.00 0.00 0.00 3.51
1959 2167 4.931002 GTGGTGTGTATTTTTAGTCGGCTA 59.069 41.667 0.00 0.00 0.00 3.93
1965 2173 6.127310 TGCAAAAGGTGGTGTGTATTTTTAGT 60.127 34.615 0.00 0.00 0.00 2.24
1966 2174 6.276847 TGCAAAAGGTGGTGTGTATTTTTAG 58.723 36.000 0.00 0.00 0.00 1.85
1973 2181 2.294074 GACTGCAAAAGGTGGTGTGTA 58.706 47.619 0.00 0.00 0.00 2.90
1975 2183 1.102154 TGACTGCAAAAGGTGGTGTG 58.898 50.000 0.00 0.00 0.00 3.82
2006 2214 2.336809 GGCGCTATCCTGAGTCCG 59.663 66.667 7.64 0.00 0.00 4.79
2020 2228 4.260375 GCACTAGTAATTGATGAAGTGGCG 60.260 45.833 0.00 0.00 35.89 5.69
2030 2238 7.338710 AGCTAGAAAATGGCACTAGTAATTGA 58.661 34.615 10.47 0.00 38.00 2.57
2031 2239 7.280876 TGAGCTAGAAAATGGCACTAGTAATTG 59.719 37.037 10.47 0.00 38.00 2.32
2032 2240 7.338710 TGAGCTAGAAAATGGCACTAGTAATT 58.661 34.615 10.47 0.00 38.00 1.40
2034 2242 6.294361 TGAGCTAGAAAATGGCACTAGTAA 57.706 37.500 10.47 0.00 38.00 2.24
2037 2245 6.500684 TTTTGAGCTAGAAAATGGCACTAG 57.499 37.500 0.00 5.71 38.00 2.57
2078 2287 2.409948 ACTGAAACCTATGCCAGCTC 57.590 50.000 0.00 0.00 0.00 4.09
2157 2393 5.164158 CGCAGTTATTGTGATTTGTGAAAGC 60.164 40.000 0.00 0.00 39.74 3.51
2230 2466 4.801891 CAGAAAACATGGGAGTGATTGTG 58.198 43.478 0.00 0.00 0.00 3.33
2353 2766 0.465460 ACACACCCACACACCATCAC 60.465 55.000 0.00 0.00 0.00 3.06
2356 2769 0.465460 GACACACACCCACACACCAT 60.465 55.000 0.00 0.00 0.00 3.55
2357 2770 1.078072 GACACACACCCACACACCA 60.078 57.895 0.00 0.00 0.00 4.17
2358 2771 1.078072 TGACACACACCCACACACC 60.078 57.895 0.00 0.00 0.00 4.16
2359 2772 0.392461 ACTGACACACACCCACACAC 60.392 55.000 0.00 0.00 0.00 3.82
2360 2773 0.392327 CACTGACACACACCCACACA 60.392 55.000 0.00 0.00 0.00 3.72
2361 2774 0.107897 TCACTGACACACACCCACAC 60.108 55.000 0.00 0.00 0.00 3.82
2362 2775 0.107897 GTCACTGACACACACCCACA 60.108 55.000 4.17 0.00 32.09 4.17
2727 3140 1.944177 TCTTGGAGGAGGAGTTGGAG 58.056 55.000 0.00 0.00 0.00 3.86
2728 3141 2.260822 CTTCTTGGAGGAGGAGTTGGA 58.739 52.381 0.00 0.00 0.00 3.53
3000 3434 1.450312 GATGACCACGAAGCAGGGG 60.450 63.158 0.00 0.00 41.48 4.79
3003 3437 0.671472 TGCAGATGACCACGAAGCAG 60.671 55.000 0.00 0.00 0.00 4.24
3027 3461 1.352352 GGGAATGGGGTCGATGATCAT 59.648 52.381 8.25 8.25 0.00 2.45
3031 3465 3.101796 GCGGGAATGGGGTCGATGA 62.102 63.158 0.00 0.00 0.00 2.92
3032 3466 2.591715 GCGGGAATGGGGTCGATG 60.592 66.667 0.00 0.00 0.00 3.84
3033 3467 4.235762 CGCGGGAATGGGGTCGAT 62.236 66.667 0.00 0.00 0.00 3.59
3036 3470 3.394635 TTAGCGCGGGAATGGGGTC 62.395 63.158 8.83 0.00 34.22 4.46
3037 3471 3.404438 TTAGCGCGGGAATGGGGT 61.404 61.111 8.83 0.00 36.45 4.95
3038 3472 2.900337 GTTAGCGCGGGAATGGGG 60.900 66.667 8.83 0.00 0.00 4.96
3039 3473 2.900337 GGTTAGCGCGGGAATGGG 60.900 66.667 8.83 0.00 0.00 4.00
3040 3474 3.269347 CGGTTAGCGCGGGAATGG 61.269 66.667 8.83 0.00 0.00 3.16
3041 3475 2.202824 TCGGTTAGCGCGGGAATG 60.203 61.111 8.83 0.00 0.00 2.67
3042 3476 2.106332 CTCGGTTAGCGCGGGAAT 59.894 61.111 8.83 0.00 0.00 3.01
3043 3477 4.807039 GCTCGGTTAGCGCGGGAA 62.807 66.667 8.83 0.00 42.53 3.97
3062 3496 9.799106 AGAGAAAAAGAATGGTTAATTCAGAGA 57.201 29.630 1.30 0.00 46.21 3.10
3064 3498 9.799106 AGAGAGAAAAAGAATGGTTAATTCAGA 57.201 29.630 1.30 0.00 46.21 3.27
3067 3501 8.178313 CCGAGAGAGAAAAAGAATGGTTAATTC 58.822 37.037 0.00 0.00 44.44 2.17
3080 3518 2.494059 CAGGCAACCGAGAGAGAAAAA 58.506 47.619 0.00 0.00 37.17 1.94
3100 3539 0.875059 GTTAACAGAGTGGCAGTGGC 59.125 55.000 10.30 10.30 40.13 5.01
3101 3540 1.148310 CGTTAACAGAGTGGCAGTGG 58.852 55.000 0.00 0.00 0.00 4.00
3102 3541 1.865865 ACGTTAACAGAGTGGCAGTG 58.134 50.000 0.00 0.00 0.00 3.66
3103 3542 2.612212 CAAACGTTAACAGAGTGGCAGT 59.388 45.455 0.00 0.00 0.00 4.40
3156 3596 2.279517 CGTCTGGCCGATGCTACC 60.280 66.667 0.00 0.00 37.74 3.18
3172 3612 1.393539 CAGGAGTATGGACAAAACGCG 59.606 52.381 3.53 3.53 0.00 6.01
3187 3627 3.062639 GCATTCACGTACATTCACAGGAG 59.937 47.826 0.00 0.00 0.00 3.69
3233 3673 0.872388 CGGGAAAGGAAAACGGTGAG 59.128 55.000 0.00 0.00 0.00 3.51
3236 3676 4.486887 CCGGGAAAGGAAAACGGT 57.513 55.556 0.00 0.00 39.70 4.83
3310 3750 1.225376 CGGAGCACGTACCAAAAGCA 61.225 55.000 0.00 0.00 37.93 3.91
3326 3766 3.334691 CTCCTGCTATCAACAAAACGGA 58.665 45.455 0.00 0.00 0.00 4.69
3329 3769 2.729156 GCGCTCCTGCTATCAACAAAAC 60.729 50.000 0.00 0.00 36.97 2.43
3342 3782 2.202570 GCATGCAAAGCGCTCCTG 60.203 61.111 12.06 13.08 43.06 3.86
3394 3842 0.888736 TTGTTCGGGTGTCCATGCAG 60.889 55.000 0.00 0.00 0.00 4.41
3395 3843 0.466372 TTTGTTCGGGTGTCCATGCA 60.466 50.000 0.00 0.00 0.00 3.96
3407 3855 4.152759 TCTGCTACGGGTAAAATTTGTTCG 59.847 41.667 0.00 0.00 0.00 3.95
3422 3870 1.929836 GAAACCTGATGCTCTGCTACG 59.070 52.381 0.00 0.00 0.00 3.51
3437 3886 4.452795 GCACTTTCTACCTCTCTTGAAACC 59.547 45.833 0.00 0.00 0.00 3.27
3439 3892 4.348168 AGGCACTTTCTACCTCTCTTGAAA 59.652 41.667 0.00 0.00 27.25 2.69
3453 3906 4.156008 CCCACAAACATACTAGGCACTTTC 59.844 45.833 0.00 0.00 41.75 2.62
3464 3917 3.262405 TGACCCTACTCCCACAAACATAC 59.738 47.826 0.00 0.00 0.00 2.39
3465 3918 3.522759 TGACCCTACTCCCACAAACATA 58.477 45.455 0.00 0.00 0.00 2.29
3466 3919 2.344592 TGACCCTACTCCCACAAACAT 58.655 47.619 0.00 0.00 0.00 2.71
3468 3921 2.943036 TTGACCCTACTCCCACAAAC 57.057 50.000 0.00 0.00 0.00 2.93
3469 3922 2.554344 GCATTGACCCTACTCCCACAAA 60.554 50.000 0.00 0.00 0.00 2.83
3471 3924 0.618458 GCATTGACCCTACTCCCACA 59.382 55.000 0.00 0.00 0.00 4.17
3472 3925 0.618458 TGCATTGACCCTACTCCCAC 59.382 55.000 0.00 0.00 0.00 4.61
3473 3926 0.618458 GTGCATTGACCCTACTCCCA 59.382 55.000 0.00 0.00 0.00 4.37
3474 3927 0.107165 GGTGCATTGACCCTACTCCC 60.107 60.000 0.00 0.00 0.00 4.30
3529 3982 2.361104 CCTTAGGCCGGCAAGCAA 60.361 61.111 30.85 14.47 0.00 3.91
3545 3998 0.750182 ACTCTACGCCTCTCTCTGCC 60.750 60.000 0.00 0.00 0.00 4.85
3551 4004 2.726832 AACACAACTCTACGCCTCTC 57.273 50.000 0.00 0.00 0.00 3.20
3568 4022 7.892731 CGAAAAGTCAGACAAACATTTGAAAAC 59.107 33.333 11.24 4.23 40.55 2.43
3658 4113 0.892755 ACATTCAATGCACAGCCCTG 59.107 50.000 0.00 0.00 0.00 4.45
3665 4120 2.486982 AGTCAGAGCACATTCAATGCAC 59.513 45.455 0.00 0.00 45.92 4.57
3729 4185 2.992114 AGTGAGAGCCGCCGAACT 60.992 61.111 0.00 0.00 0.00 3.01
3794 4254 6.041296 CCTTGGCTATCCATAAGATTTGCTTT 59.959 38.462 0.00 0.00 43.05 3.51
3795 4255 5.537674 CCTTGGCTATCCATAAGATTTGCTT 59.462 40.000 0.00 0.00 43.05 3.91
3808 4278 3.282920 GCTGCGCCTTGGCTATCC 61.283 66.667 4.18 0.00 0.00 2.59
3845 4318 0.750850 GGTAAGTAGCGATCTGGCCA 59.249 55.000 4.71 4.71 0.00 5.36
3849 4322 1.409064 TGGCTGGTAAGTAGCGATCTG 59.591 52.381 0.00 0.00 42.03 2.90
3857 4330 1.762957 GGCTCAGATGGCTGGTAAGTA 59.237 52.381 0.00 0.00 42.53 2.24
3858 4331 0.543749 GGCTCAGATGGCTGGTAAGT 59.456 55.000 0.00 0.00 42.53 2.24
3859 4332 0.531532 CGGCTCAGATGGCTGGTAAG 60.532 60.000 0.00 0.00 42.53 2.34
3860 4333 0.975556 TCGGCTCAGATGGCTGGTAA 60.976 55.000 0.00 0.00 42.53 2.85
3913 4386 1.860950 CCACAGACACGTCAACAGAAG 59.139 52.381 0.00 0.00 0.00 2.85
3983 4456 4.765449 TACAGGGCGCTGCAGCAG 62.765 66.667 36.03 27.94 42.21 4.24
4008 4481 3.192922 ACATTTACGCGCTCCGGC 61.193 61.111 5.73 0.00 42.52 6.13
4009 4482 2.701006 CACATTTACGCGCTCCGG 59.299 61.111 5.73 0.00 42.52 5.14
4022 4495 1.286880 GCAAACAGGAAGCGCACAT 59.713 52.632 11.47 0.00 0.00 3.21
4026 4499 3.595108 GACGGCAAACAGGAAGCGC 62.595 63.158 0.00 0.00 0.00 5.92
4059 4532 1.892209 ATGGCCGACGAACTTTCTTT 58.108 45.000 0.00 0.00 0.00 2.52
4060 4533 1.535462 CAATGGCCGACGAACTTTCTT 59.465 47.619 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.