Multiple sequence alignment - TraesCS3B01G439600

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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 TraesCS3B01G439600 chr3B 100.000 3720 0 0 1 3720 678547123 678550842 0.000000e+00 6870.0
1 TraesCS3B01G439600 chr3D 89.193 2813 142 66 364 3082 515775599 515778343 0.000000e+00 3362.0
2 TraesCS3B01G439600 chr3D 90.661 514 33 8 3205 3709 515778386 515778893 0.000000e+00 669.0
3 TraesCS3B01G439600 chr3D 88.512 383 28 9 1 370 515775174 515775553 2.040000e-122 449.0
4 TraesCS3B01G439600 chr3A 91.056 1979 83 32 1153 3082 650056166 650058099 0.000000e+00 2588.0
5 TraesCS3B01G439600 chr3A 83.509 1043 51 56 99 1092 650055174 650056144 0.000000e+00 861.0
6 TraesCS3B01G439600 chr3A 86.264 364 30 5 3205 3566 650058163 650058508 9.750000e-101 377.0
7 TraesCS3B01G439600 chr3A 91.463 164 8 3 3547 3705 650059019 650059181 1.740000e-53 220.0
8 TraesCS3B01G439600 chr3A 88.034 117 4 1 1 107 650054285 650054401 3.020000e-26 130.0
9 TraesCS3B01G439600 chr1A 84.882 549 59 17 1174 1704 459188407 459187865 1.970000e-147 532.0
10 TraesCS3B01G439600 chr1A 78.445 283 33 16 2418 2695 459187294 459187035 3.850000e-35 159.0
11 TraesCS3B01G439600 chr1A 88.312 77 7 2 2234 2309 459187451 459187376 1.420000e-14 91.6
12 TraesCS3B01G439600 chr1D 84.630 540 66 16 1174 1705 359666075 359665545 4.260000e-144 521.0
13 TraesCS3B01G439600 chr1D 77.778 477 52 33 2234 2695 359665073 359664636 1.030000e-60 244.0
14 TraesCS3B01G439600 chr1D 78.571 266 41 15 1414 1669 355698592 355698333 1.070000e-35 161.0
15 TraesCS3B01G439600 chr1B 83.948 542 69 16 1174 1705 481542355 481541822 1.540000e-138 503.0
16 TraesCS3B01G439600 chr1B 80.690 290 35 12 2418 2695 481541192 481540912 4.870000e-49 206.0
17 TraesCS3B01G439600 chr4D 90.213 235 21 2 1444 1677 69679958 69679725 4.670000e-79 305.0
18 TraesCS3B01G439600 chr4B 90.213 235 21 2 1444 1677 103056204 103055971 4.670000e-79 305.0
19 TraesCS3B01G439600 chr4A 89.787 235 22 2 1444 1677 521919706 521919473 2.170000e-77 300.0
20 TraesCS3B01G439600 chr2B 75.960 495 88 26 1186 1663 85177909 85177429 3.740000e-55 226.0
21 TraesCS3B01G439600 chr2D 75.813 492 84 28 1186 1660 54317525 54317998 2.250000e-52 217.0
22 TraesCS3B01G439600 chr2D 78.516 256 41 8 1421 1663 175331615 175331869 4.970000e-34 156.0
23 TraesCS3B01G439600 chr6D 87.013 154 12 7 1176 1325 27820282 27820133 2.300000e-37 167.0
24 TraesCS3B01G439600 chr6B 87.013 154 12 7 1176 1325 51580393 51580244 2.300000e-37 167.0
25 TraesCS3B01G439600 chr6A 87.013 154 12 7 1176 1325 30191211 30191062 2.300000e-37 167.0


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 TraesCS3B01G439600 chr3B 678547123 678550842 3719 False 6870.000000 6870 100.000000 1 3720 1 chr3B.!!$F1 3719
1 TraesCS3B01G439600 chr3D 515775174 515778893 3719 False 1493.333333 3362 89.455333 1 3709 3 chr3D.!!$F1 3708
2 TraesCS3B01G439600 chr3A 650054285 650059181 4896 False 835.200000 2588 88.065200 1 3705 5 chr3A.!!$F1 3704
3 TraesCS3B01G439600 chr1A 459187035 459188407 1372 True 260.866667 532 83.879667 1174 2695 3 chr1A.!!$R1 1521
4 TraesCS3B01G439600 chr1D 359664636 359666075 1439 True 382.500000 521 81.204000 1174 2695 2 chr1D.!!$R2 1521
5 TraesCS3B01G439600 chr1B 481540912 481542355 1443 True 354.500000 503 82.319000 1174 2695 2 chr1B.!!$R1 1521

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
558 1461 0.104090 AGACCTACCAACCCCCAACT 60.104 55.0 0.00 0.0 0.00 3.16 F
1054 1992 0.036199 AGCAGCAGCAGAAGAGAAGG 60.036 55.0 3.17 0.0 45.49 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1877 2973 1.002659 CAACAATCCACTGTACCCCGA 59.997 52.381 0.0 0.0 0.0 5.14 R
2857 4116 0.673644 CGCCACCTTCCAATCTTCGT 60.674 55.000 0.0 0.0 0.0 3.85 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
67 68 1.088340 CAGCACGCCATCTCTTCTGG 61.088 60.000 0.00 0.00 36.81 3.86
208 1000 1.074951 GGGCATATTCCTTCCCCCG 59.925 63.158 0.00 0.00 32.60 5.73
209 1001 1.603739 GGCATATTCCTTCCCCCGC 60.604 63.158 0.00 0.00 0.00 6.13
210 1002 1.966451 GCATATTCCTTCCCCCGCG 60.966 63.158 0.00 0.00 0.00 6.46
211 1003 1.966451 CATATTCCTTCCCCCGCGC 60.966 63.158 0.00 0.00 0.00 6.86
212 1004 3.530910 ATATTCCTTCCCCCGCGCG 62.531 63.158 25.67 25.67 0.00 6.86
235 1035 2.345991 GGACAGTGGGCGCACTTA 59.654 61.111 31.65 0.00 32.26 2.24
240 1040 1.071071 ACAGTGGGCGCACTTACTTTA 59.929 47.619 31.65 0.00 32.26 1.85
308 1112 0.600255 CTCGTGTCGGTTTTCTGCCT 60.600 55.000 0.00 0.00 0.00 4.75
314 1118 2.380410 CGGTTTTCTGCCTCGGTCG 61.380 63.158 0.00 0.00 0.00 4.79
315 1119 1.005394 GGTTTTCTGCCTCGGTCGA 60.005 57.895 0.00 0.00 0.00 4.20
347 1160 1.446272 CGAACCAAGAGAGGCGGTC 60.446 63.158 0.00 0.00 30.91 4.79
358 1171 0.876342 GAGGCGGTCGATTGATGGAC 60.876 60.000 0.00 0.00 35.16 4.02
372 1237 0.600557 ATGGACTGATCGATCGAGCC 59.399 55.000 28.63 19.66 0.00 4.70
373 1238 0.466372 TGGACTGATCGATCGAGCCT 60.466 55.000 28.63 14.98 0.00 4.58
388 1253 2.822561 CGAGCCTGCTGGAATCTATCTA 59.177 50.000 14.77 0.00 34.57 1.98
404 1273 5.942961 TCTATCTATCCTATCCGTCCATCC 58.057 45.833 0.00 0.00 0.00 3.51
405 1274 3.000684 TCTATCCTATCCGTCCATCCG 57.999 52.381 0.00 0.00 0.00 4.18
411 1280 1.461091 TATCCGTCCATCCGTCTGCC 61.461 60.000 0.00 0.00 0.00 4.85
452 1321 1.301637 CATGCCATGCCATGCCATG 60.302 57.895 13.50 13.50 41.71 3.66
453 1322 3.177194 ATGCCATGCCATGCCATGC 62.177 57.895 11.13 7.49 40.92 4.06
454 1323 4.619227 GCCATGCCATGCCATGCC 62.619 66.667 11.13 0.00 40.92 4.40
468 1345 0.391597 CATGCCATGGATCCAAAGCC 59.608 55.000 27.57 12.70 0.00 4.35
484 1361 4.834453 CCGCAGGCAGCTCCTCAG 62.834 72.222 0.00 0.75 45.52 3.35
507 1384 2.957006 AGAATACCCTAGCACTGTACCG 59.043 50.000 0.00 0.00 0.00 4.02
509 1386 3.582998 ATACCCTAGCACTGTACCGTA 57.417 47.619 0.00 0.00 0.00 4.02
510 1387 1.467920 ACCCTAGCACTGTACCGTAC 58.532 55.000 1.40 1.40 0.00 3.67
511 1388 0.743097 CCCTAGCACTGTACCGTACC 59.257 60.000 6.23 0.00 0.00 3.34
513 1390 1.404391 CCTAGCACTGTACCGTACCTG 59.596 57.143 6.23 3.19 0.00 4.00
514 1391 0.813184 TAGCACTGTACCGTACCTGC 59.187 55.000 15.85 15.85 33.71 4.85
515 1392 1.447314 GCACTGTACCGTACCTGCC 60.447 63.158 13.83 1.94 0.00 4.85
516 1393 1.153901 CACTGTACCGTACCTGCCG 60.154 63.158 6.23 0.00 0.00 5.69
558 1461 0.104090 AGACCTACCAACCCCCAACT 60.104 55.000 0.00 0.00 0.00 3.16
615 1525 1.671328 TCGTCTCATCATCGTCCTCAC 59.329 52.381 0.00 0.00 0.00 3.51
888 1823 4.394712 GGCTCCACGTGTCCCAGG 62.395 72.222 15.65 0.00 0.00 4.45
1029 1965 2.328589 CCTCTCCTCCCTCCTCCCA 61.329 68.421 0.00 0.00 0.00 4.37
1030 1966 1.075600 CTCTCCTCCCTCCTCCCAC 60.076 68.421 0.00 0.00 0.00 4.61
1031 1967 2.041405 CTCCTCCCTCCTCCCACC 60.041 72.222 0.00 0.00 0.00 4.61
1049 1987 0.822811 CCTAGAGCAGCAGCAGAAGA 59.177 55.000 3.17 0.00 45.49 2.87
1054 1992 0.036199 AGCAGCAGCAGAAGAGAAGG 60.036 55.000 3.17 0.00 45.49 3.46
1056 1994 1.610102 GCAGCAGCAGAAGAGAAGGAA 60.610 52.381 0.00 0.00 41.58 3.36
1075 2013 7.604545 AGAAGGAAAATTCAGTAGCAGTAGAAC 59.395 37.037 0.00 0.00 0.00 3.01
1086 2024 1.906757 CAGTAGAACTCAGAGCAGCG 58.093 55.000 0.00 0.00 0.00 5.18
1088 2026 0.804156 GTAGAACTCAGAGCAGCGGC 60.804 60.000 0.00 0.00 41.61 6.53
1129 2067 0.811915 TCCAGCGAGAGAACTACAGC 59.188 55.000 0.00 0.00 0.00 4.40
1134 2072 1.088306 CGAGAGAACTACAGCGAGGT 58.912 55.000 0.00 0.00 0.00 3.85
1136 2074 2.095161 CGAGAGAACTACAGCGAGGTTT 60.095 50.000 0.00 0.00 0.00 3.27
1147 2085 1.794222 CGAGGTTTGTTGGATCGCC 59.206 57.895 0.00 0.00 0.00 5.54
1151 2089 1.500396 GTTTGTTGGATCGCCGACC 59.500 57.895 0.00 0.00 46.45 4.79
1357 2326 2.753966 CCAATCCTCCACGCGCTTG 61.754 63.158 5.73 6.96 0.00 4.01
1372 2359 1.789506 GCTTGATCCGTCCAGCTATC 58.210 55.000 0.00 0.00 39.40 2.08
1532 2522 1.218316 GTCAGGGTACTGGAAGGCG 59.782 63.158 0.00 0.00 44.99 5.52
1535 2525 2.183555 GGGTACTGGAAGGCGACG 59.816 66.667 0.00 0.00 39.30 5.12
1730 2726 2.107750 ATCCATGTCAGCCTCGCG 59.892 61.111 0.00 0.00 0.00 5.87
1750 2758 3.248602 GCGGCAGTAATTCCAGTATCTTG 59.751 47.826 0.00 0.00 0.00 3.02
1815 2911 4.270566 CGTAGATAGATTAGATCGACGGGG 59.729 50.000 9.51 0.00 44.01 5.73
1839 2935 7.339466 GGGGATATTTTAGTGCGATATTTCCAT 59.661 37.037 0.00 0.00 0.00 3.41
1857 2953 2.221749 CCATGATCTGGCAATTACGACG 59.778 50.000 0.00 0.00 38.47 5.12
1858 2954 1.934589 TGATCTGGCAATTACGACGG 58.065 50.000 0.00 0.00 0.00 4.79
1859 2955 0.582005 GATCTGGCAATTACGACGGC 59.418 55.000 0.00 0.00 0.00 5.68
1860 2956 0.107897 ATCTGGCAATTACGACGGCA 60.108 50.000 0.00 0.00 0.00 5.69
1861 2957 1.017177 TCTGGCAATTACGACGGCAC 61.017 55.000 0.00 0.00 0.00 5.01
1862 2958 1.295357 CTGGCAATTACGACGGCACA 61.295 55.000 0.00 0.00 0.00 4.57
1863 2959 1.295357 TGGCAATTACGACGGCACAG 61.295 55.000 0.00 0.00 0.00 3.66
1864 2960 1.296056 GGCAATTACGACGGCACAGT 61.296 55.000 0.00 0.00 0.00 3.55
1865 2961 1.352114 GCAATTACGACGGCACAGTA 58.648 50.000 0.00 0.00 0.00 2.74
1866 2962 1.323534 GCAATTACGACGGCACAGTAG 59.676 52.381 0.00 0.00 0.00 2.57
1867 2963 2.871133 CAATTACGACGGCACAGTAGA 58.129 47.619 0.00 0.00 0.00 2.59
1868 2964 3.444916 CAATTACGACGGCACAGTAGAT 58.555 45.455 0.00 0.00 0.00 1.98
1869 2965 3.795623 ATTACGACGGCACAGTAGATT 57.204 42.857 0.00 0.00 0.00 2.40
1870 2966 3.581024 TTACGACGGCACAGTAGATTT 57.419 42.857 0.00 0.00 0.00 2.17
1871 2967 2.450609 ACGACGGCACAGTAGATTTT 57.549 45.000 0.00 0.00 0.00 1.82
1872 2968 2.762745 ACGACGGCACAGTAGATTTTT 58.237 42.857 0.00 0.00 0.00 1.94
1905 3001 2.948979 ACAGTGGATTGTTGCTTTCGAA 59.051 40.909 0.00 0.00 0.00 3.71
2129 3307 2.298610 CTGTACCGGTAGAGAGCATCA 58.701 52.381 30.04 13.99 37.82 3.07
2177 3355 6.881065 TGCTAAAATAATGAAGCTGTCAGAGT 59.119 34.615 3.32 0.00 40.43 3.24
2187 3382 2.098934 AGCTGTCAGAGTGATCGTCATC 59.901 50.000 3.32 0.00 0.00 2.92
2702 3960 0.875059 AGCCGTTCTAAGCAGCAAAC 59.125 50.000 0.00 0.00 0.00 2.93
2713 3971 0.237235 GCAGCAAACAAACCGATCGA 59.763 50.000 18.66 0.00 0.00 3.59
2857 4116 0.728129 GTGCTTGATGACGACGACGA 60.728 55.000 15.32 0.00 42.66 4.20
2914 4173 3.073735 CGGGCTCTCTCACCAGCT 61.074 66.667 0.00 0.00 35.82 4.24
3034 4310 4.287067 GGATGGGTGTACATACATGGAGAT 59.713 45.833 16.84 0.00 38.63 2.75
3082 4358 5.359576 TGCTGTTTCTTGATTGGTTAGTTGT 59.640 36.000 0.00 0.00 0.00 3.32
3083 4359 6.544197 TGCTGTTTCTTGATTGGTTAGTTGTA 59.456 34.615 0.00 0.00 0.00 2.41
3084 4360 7.067615 TGCTGTTTCTTGATTGGTTAGTTGTAA 59.932 33.333 0.00 0.00 0.00 2.41
3085 4361 8.082242 GCTGTTTCTTGATTGGTTAGTTGTAAT 58.918 33.333 0.00 0.00 0.00 1.89
3151 4429 4.617253 TGATACCATACCATACCAGTGC 57.383 45.455 0.00 0.00 0.00 4.40
3152 4430 4.231273 TGATACCATACCATACCAGTGCT 58.769 43.478 0.00 0.00 0.00 4.40
3153 4431 5.399113 TGATACCATACCATACCAGTGCTA 58.601 41.667 0.00 0.00 0.00 3.49
3154 4432 5.480422 TGATACCATACCATACCAGTGCTAG 59.520 44.000 0.00 0.00 0.00 3.42
3155 4433 2.368875 ACCATACCATACCAGTGCTAGC 59.631 50.000 8.10 8.10 0.00 3.42
3156 4434 2.289694 CCATACCATACCAGTGCTAGCC 60.290 54.545 13.29 3.49 0.00 3.93
3157 4435 1.037493 TACCATACCAGTGCTAGCCG 58.963 55.000 13.29 0.13 0.00 5.52
3158 4436 1.595382 CCATACCAGTGCTAGCCGC 60.595 63.158 13.29 5.21 39.77 6.53
3159 4437 1.595382 CATACCAGTGCTAGCCGCC 60.595 63.158 13.29 0.00 38.05 6.13
3160 4438 3.151958 ATACCAGTGCTAGCCGCCG 62.152 63.158 13.29 0.00 38.05 6.46
3196 4474 3.572632 AGCTGTAGTCCGATGGTAGTA 57.427 47.619 0.00 0.00 0.00 1.82
3197 4475 3.478509 AGCTGTAGTCCGATGGTAGTAG 58.521 50.000 0.00 0.00 0.00 2.57
3198 4476 3.117963 AGCTGTAGTCCGATGGTAGTAGT 60.118 47.826 0.00 0.00 0.00 2.73
3199 4477 3.003482 GCTGTAGTCCGATGGTAGTAGTG 59.997 52.174 0.00 0.00 0.00 2.74
3200 4478 4.197750 CTGTAGTCCGATGGTAGTAGTGT 58.802 47.826 0.00 0.00 0.00 3.55
3201 4479 5.357742 TGTAGTCCGATGGTAGTAGTGTA 57.642 43.478 0.00 0.00 0.00 2.90
3202 4480 5.744171 TGTAGTCCGATGGTAGTAGTGTAA 58.256 41.667 0.00 0.00 0.00 2.41
3203 4481 5.586243 TGTAGTCCGATGGTAGTAGTGTAAC 59.414 44.000 0.00 0.00 0.00 2.50
3317 4604 2.048597 CGAGCTGCGGTTGTGGTA 60.049 61.111 0.00 0.00 36.03 3.25
3320 4607 0.108138 GAGCTGCGGTTGTGGTATCT 60.108 55.000 0.00 0.00 0.00 1.98
3331 4618 5.163754 CGGTTGTGGTATCTGGAGAAAAATC 60.164 44.000 0.00 0.00 0.00 2.17
3342 4629 6.001460 TCTGGAGAAAAATCGGTGTGTAAAT 58.999 36.000 0.00 0.00 0.00 1.40
3371 4658 4.822685 TTCTTGGCGTATTTACCCACTA 57.177 40.909 0.00 0.00 0.00 2.74
3394 4681 0.320771 AAAGAGCACGCTTCACCGAT 60.321 50.000 0.00 0.00 0.00 4.18
3395 4682 0.320771 AAGAGCACGCTTCACCGATT 60.321 50.000 0.00 0.00 0.00 3.34
3398 4685 0.517316 AGCACGCTTCACCGATTTTC 59.483 50.000 0.00 0.00 0.00 2.29
3399 4686 0.517316 GCACGCTTCACCGATTTTCT 59.483 50.000 0.00 0.00 0.00 2.52
3400 4687 1.069227 GCACGCTTCACCGATTTTCTT 60.069 47.619 0.00 0.00 0.00 2.52
3401 4688 2.574322 CACGCTTCACCGATTTTCTTG 58.426 47.619 0.00 0.00 0.00 3.02
3402 4689 1.535462 ACGCTTCACCGATTTTCTTGG 59.465 47.619 0.00 0.00 0.00 3.61
3403 4690 1.804151 CGCTTCACCGATTTTCTTGGA 59.196 47.619 0.00 0.00 31.98 3.53
3404 4691 2.159653 CGCTTCACCGATTTTCTTGGAG 60.160 50.000 0.00 0.00 31.98 3.86
3471 4758 2.600122 GAAACGTGTTTGTGGCCGCA 62.600 55.000 16.89 16.89 32.11 5.69
3502 4789 0.618981 GGAGGAGGGGAAAACGTGAT 59.381 55.000 0.00 0.00 0.00 3.06
3522 4809 2.282391 AAATCAGCGGTGCAGGCA 60.282 55.556 10.38 0.00 0.00 4.75
3683 5504 1.300465 CGGATGGATCACGCTGGAG 60.300 63.158 0.00 0.00 0.00 3.86
3705 5526 1.736586 CTCGTGCTTATCGCCTCCT 59.263 57.895 0.00 0.00 38.05 3.69
3709 5530 0.175760 GTGCTTATCGCCTCCTGTCA 59.824 55.000 0.00 0.00 38.05 3.58
3710 5531 0.461548 TGCTTATCGCCTCCTGTCAG 59.538 55.000 0.00 0.00 38.05 3.51
3711 5532 0.878086 GCTTATCGCCTCCTGTCAGC 60.878 60.000 0.00 0.00 0.00 4.26
3712 5533 0.749649 CTTATCGCCTCCTGTCAGCT 59.250 55.000 0.00 0.00 0.00 4.24
3713 5534 0.461548 TTATCGCCTCCTGTCAGCTG 59.538 55.000 7.63 7.63 0.00 4.24
3714 5535 1.395045 TATCGCCTCCTGTCAGCTGG 61.395 60.000 15.13 0.00 35.32 4.85
3715 5536 4.463879 CGCCTCCTGTCAGCTGGG 62.464 72.222 15.13 7.58 34.83 4.45
3716 5537 4.792804 GCCTCCTGTCAGCTGGGC 62.793 72.222 15.13 13.75 34.83 5.36
3717 5538 3.007920 CCTCCTGTCAGCTGGGCT 61.008 66.667 15.13 0.00 40.77 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.351435 CGACCGCGCGTTTGTTTT 60.351 55.556 29.95 2.98 0.00 2.43
67 68 4.754667 GCGTGAGGTCCCCGGAAC 62.755 72.222 0.73 0.00 0.00 3.62
347 1160 2.913590 CGATCGATCAGTCCATCAATCG 59.086 50.000 24.40 4.06 41.69 3.34
358 1171 0.663867 CAGCAGGCTCGATCGATCAG 60.664 60.000 24.40 19.63 0.00 2.90
372 1237 6.016360 CGGATAGGATAGATAGATTCCAGCAG 60.016 46.154 0.00 0.00 31.65 4.24
373 1238 5.830457 CGGATAGGATAGATAGATTCCAGCA 59.170 44.000 0.00 0.00 31.65 4.41
388 1253 1.075698 AGACGGATGGACGGATAGGAT 59.924 52.381 0.00 0.00 38.39 3.24
404 1273 2.745884 TGGAAATGCGGGCAGACG 60.746 61.111 0.00 0.00 0.00 4.18
405 1274 1.315257 ATGTGGAAATGCGGGCAGAC 61.315 55.000 0.00 0.00 0.00 3.51
411 1280 1.809207 GGGTGATGTGGAAATGCGG 59.191 57.895 0.00 0.00 0.00 5.69
452 1321 3.122850 CGGCTTTGGATCCATGGC 58.877 61.111 23.31 23.31 0.00 4.40
453 1322 1.731433 CTGCGGCTTTGGATCCATGG 61.731 60.000 17.06 12.41 0.00 3.66
454 1323 1.731433 CCTGCGGCTTTGGATCCATG 61.731 60.000 17.06 12.84 0.00 3.66
484 1361 2.990066 ACAGTGCTAGGGTATTCTGC 57.010 50.000 0.00 0.00 0.00 4.26
490 1367 2.643551 GTACGGTACAGTGCTAGGGTA 58.356 52.381 13.25 0.00 0.00 3.69
513 1390 2.682856 TGGAAAAGACTATGCAATCGGC 59.317 45.455 0.00 0.00 45.13 5.54
514 1391 3.065371 GGTGGAAAAGACTATGCAATCGG 59.935 47.826 0.00 0.00 0.00 4.18
515 1392 3.065371 GGGTGGAAAAGACTATGCAATCG 59.935 47.826 0.00 0.00 0.00 3.34
516 1393 4.016444 TGGGTGGAAAAGACTATGCAATC 58.984 43.478 0.00 0.00 0.00 2.67
530 1433 1.422402 GTTGGTAGGTCTTGGGTGGAA 59.578 52.381 0.00 0.00 0.00 3.53
558 1461 0.597118 GTGTGTTGGGCGTACGTGTA 60.597 55.000 17.90 0.01 0.00 2.90
822 1757 2.775032 TTACGTCAGGGCGCTTGGAC 62.775 60.000 7.64 11.36 34.88 4.02
1029 1965 0.536260 CTTCTGCTGCTGCTCTAGGT 59.464 55.000 17.00 0.00 40.48 3.08
1030 1966 0.822811 TCTTCTGCTGCTGCTCTAGG 59.177 55.000 17.00 3.11 40.48 3.02
1031 1967 1.750206 TCTCTTCTGCTGCTGCTCTAG 59.250 52.381 17.00 10.35 40.48 2.43
1049 1987 7.246171 TCTACTGCTACTGAATTTTCCTTCT 57.754 36.000 0.00 0.00 0.00 2.85
1054 1992 7.815068 TCTGAGTTCTACTGCTACTGAATTTTC 59.185 37.037 0.00 0.00 0.00 2.29
1056 1994 7.233389 TCTGAGTTCTACTGCTACTGAATTT 57.767 36.000 0.00 0.00 0.00 1.82
1075 2013 4.754667 TGCTGCCGCTGCTCTGAG 62.755 66.667 21.13 0.00 38.71 3.35
1094 2032 2.510238 GATCAGCTCGCCGCAGTT 60.510 61.111 0.00 0.00 42.61 3.16
1095 2033 4.521062 GGATCAGCTCGCCGCAGT 62.521 66.667 0.00 0.00 42.61 4.40
1096 2034 4.519437 TGGATCAGCTCGCCGCAG 62.519 66.667 0.00 0.00 42.61 5.18
1097 2035 4.519437 CTGGATCAGCTCGCCGCA 62.519 66.667 0.00 0.00 42.61 5.69
1118 2056 3.027974 ACAAACCTCGCTGTAGTTCTC 57.972 47.619 0.00 0.00 0.00 2.87
1124 2062 2.695359 GATCCAACAAACCTCGCTGTA 58.305 47.619 0.00 0.00 0.00 2.74
1129 2067 1.794222 GGCGATCCAACAAACCTCG 59.206 57.895 0.00 0.00 0.00 4.63
1134 2072 1.673009 GGGTCGGCGATCCAACAAA 60.673 57.895 33.11 0.00 32.11 2.83
1136 2074 4.444838 CGGGTCGGCGATCCAACA 62.445 66.667 35.73 0.00 31.02 3.33
1147 2085 2.827190 TCATCTCCGGTCGGGTCG 60.827 66.667 9.68 0.00 37.00 4.79
1150 2088 4.271816 CGCTCATCTCCGGTCGGG 62.272 72.222 9.68 0.00 35.59 5.14
1151 2089 4.271816 CCGCTCATCTCCGGTCGG 62.272 72.222 0.00 2.52 39.67 4.79
1172 2141 1.220206 CGGCAGATTCAGCTCCTGT 59.780 57.895 0.86 0.00 32.61 4.00
1357 2326 3.460857 AAACAGATAGCTGGACGGATC 57.539 47.619 13.45 0.00 46.60 3.36
1397 2387 3.124128 CACAACAGATCACGAGAACATGG 59.876 47.826 0.00 0.00 0.00 3.66
1517 2507 2.348888 CGTCGCCTTCCAGTACCCT 61.349 63.158 0.00 0.00 0.00 4.34
1670 2660 1.745489 GTTCTTCTTGCGGGCGGAT 60.745 57.895 0.00 0.00 0.00 4.18
1711 2701 2.541120 GCGAGGCTGACATGGATGC 61.541 63.158 0.00 0.00 0.00 3.91
1730 2726 6.583562 AGTACAAGATACTGGAATTACTGCC 58.416 40.000 0.00 0.00 0.00 4.85
1767 2775 9.758470 CGGCGATTTCAATTTAATTAATTAACG 57.242 29.630 18.16 15.87 34.69 3.18
1815 2911 8.946085 TCATGGAAATATCGCACTAAAATATCC 58.054 33.333 0.00 0.00 0.00 2.59
1839 2935 1.934589 CCGTCGTAATTGCCAGATCA 58.065 50.000 0.00 0.00 0.00 2.92
1843 2939 1.295357 TGTGCCGTCGTAATTGCCAG 61.295 55.000 0.00 0.00 0.00 4.85
1846 2942 1.323534 CTACTGTGCCGTCGTAATTGC 59.676 52.381 0.00 0.00 0.00 3.56
1873 2969 3.150767 CAATCCACTGTACCCCGAAAAA 58.849 45.455 0.00 0.00 0.00 1.94
1874 2970 2.106857 ACAATCCACTGTACCCCGAAAA 59.893 45.455 0.00 0.00 0.00 2.29
1875 2971 1.700739 ACAATCCACTGTACCCCGAAA 59.299 47.619 0.00 0.00 0.00 3.46
1876 2972 1.354101 ACAATCCACTGTACCCCGAA 58.646 50.000 0.00 0.00 0.00 4.30
1877 2973 1.002659 CAACAATCCACTGTACCCCGA 59.997 52.381 0.00 0.00 0.00 5.14
1878 2974 1.448985 CAACAATCCACTGTACCCCG 58.551 55.000 0.00 0.00 0.00 5.73
1879 2975 1.173913 GCAACAATCCACTGTACCCC 58.826 55.000 0.00 0.00 0.00 4.95
1880 2976 2.200373 AGCAACAATCCACTGTACCC 57.800 50.000 0.00 0.00 0.00 3.69
1883 2979 3.734463 TCGAAAGCAACAATCCACTGTA 58.266 40.909 0.00 0.00 0.00 2.74
1905 3001 1.613255 CCGCCTATCCGCCCATTTATT 60.613 52.381 0.00 0.00 0.00 1.40
2177 3355 3.696051 TCACAGATCACAGATGACGATCA 59.304 43.478 14.79 0.00 37.79 2.92
2187 3382 4.091075 CAGACAAACGATCACAGATCACAG 59.909 45.833 7.67 0.00 0.00 3.66
2340 3568 4.133373 CACCATGGCCCCAGGAGG 62.133 72.222 13.04 1.49 0.00 4.30
2341 3569 3.016971 TCACCATGGCCCCAGGAG 61.017 66.667 13.04 4.50 0.00 3.69
2342 3570 3.016971 CTCACCATGGCCCCAGGA 61.017 66.667 13.04 0.00 0.00 3.86
2713 3971 0.747283 AGGTACTCGCTTCGACCGAT 60.747 55.000 7.69 2.61 33.83 4.18
2857 4116 0.673644 CGCCACCTTCCAATCTTCGT 60.674 55.000 0.00 0.00 0.00 3.85
2901 4160 2.233186 TCATGTCAAGCTGGTGAGAGAG 59.767 50.000 0.00 0.00 0.00 3.20
2902 4161 2.028658 GTCATGTCAAGCTGGTGAGAGA 60.029 50.000 0.00 0.00 0.00 3.10
2914 4173 2.047655 GGGCGTCGGTCATGTCAA 60.048 61.111 0.00 0.00 0.00 3.18
2990 4254 1.661341 TATACACGCACATGCATGCA 58.339 45.000 26.53 25.04 46.47 3.96
3000 4264 1.765904 ACACCCATCCATATACACGCA 59.234 47.619 0.00 0.00 0.00 5.24
3002 4266 4.594123 TGTACACCCATCCATATACACG 57.406 45.455 0.00 0.00 0.00 4.49
3034 4310 1.452110 CTGCACCGAACCAATCATGA 58.548 50.000 0.00 0.00 0.00 3.07
3094 4370 2.359531 CCTTACAACTCACCCGCAAAAA 59.640 45.455 0.00 0.00 0.00 1.94
3095 4371 1.950909 CCTTACAACTCACCCGCAAAA 59.049 47.619 0.00 0.00 0.00 2.44
3096 4372 1.600023 CCTTACAACTCACCCGCAAA 58.400 50.000 0.00 0.00 0.00 3.68
3097 4373 0.250553 CCCTTACAACTCACCCGCAA 60.251 55.000 0.00 0.00 0.00 4.85
3098 4374 1.373435 CCCTTACAACTCACCCGCA 59.627 57.895 0.00 0.00 0.00 5.69
3099 4375 0.250597 AACCCTTACAACTCACCCGC 60.251 55.000 0.00 0.00 0.00 6.13
3100 4376 2.265589 AAACCCTTACAACTCACCCG 57.734 50.000 0.00 0.00 0.00 5.28
3101 4377 5.318630 TCAATAAACCCTTACAACTCACCC 58.681 41.667 0.00 0.00 0.00 4.61
3102 4378 8.570068 TTATCAATAAACCCTTACAACTCACC 57.430 34.615 0.00 0.00 0.00 4.02
3103 4379 9.227777 ACTTATCAATAAACCCTTACAACTCAC 57.772 33.333 0.00 0.00 0.00 3.51
3104 4380 9.802039 AACTTATCAATAAACCCTTACAACTCA 57.198 29.630 0.00 0.00 0.00 3.41
3106 4382 9.802039 TCAACTTATCAATAAACCCTTACAACT 57.198 29.630 0.00 0.00 0.00 3.16
3137 4413 1.618837 CGGCTAGCACTGGTATGGTAT 59.381 52.381 18.24 0.00 32.39 2.73
3160 4438 3.121030 CTAGCCAGCACCACGCAC 61.121 66.667 0.00 0.00 46.13 5.34
3170 4448 1.000827 CATCGGACTACAGCTAGCCAG 60.001 57.143 12.13 9.04 0.00 4.85
3171 4449 1.032794 CATCGGACTACAGCTAGCCA 58.967 55.000 12.13 0.00 0.00 4.75
3172 4450 0.315568 CCATCGGACTACAGCTAGCC 59.684 60.000 12.13 0.00 0.00 3.93
3173 4451 1.033574 ACCATCGGACTACAGCTAGC 58.966 55.000 6.62 6.62 0.00 3.42
3174 4452 3.478509 ACTACCATCGGACTACAGCTAG 58.521 50.000 0.00 0.00 0.00 3.42
3196 4474 5.804639 TGATGAATGGCTTACAGTTACACT 58.195 37.500 0.00 0.00 0.00 3.55
3197 4475 6.494893 TTGATGAATGGCTTACAGTTACAC 57.505 37.500 0.00 0.00 0.00 2.90
3198 4476 7.392953 TCATTTGATGAATGGCTTACAGTTACA 59.607 33.333 0.00 0.00 44.30 2.41
3199 4477 7.761409 TCATTTGATGAATGGCTTACAGTTAC 58.239 34.615 0.00 0.00 44.30 2.50
3200 4478 7.936496 TCATTTGATGAATGGCTTACAGTTA 57.064 32.000 0.00 0.00 44.30 2.24
3201 4479 6.839124 TCATTTGATGAATGGCTTACAGTT 57.161 33.333 0.00 0.00 44.30 3.16
3202 4480 6.839124 TTCATTTGATGAATGGCTTACAGT 57.161 33.333 0.00 0.00 43.84 3.55
3238 4516 2.755103 CAAGTGGAGGGGCAAGAATAAC 59.245 50.000 0.00 0.00 0.00 1.89
3317 4604 4.021102 ACACACCGATTTTTCTCCAGAT 57.979 40.909 0.00 0.00 0.00 2.90
3320 4607 6.938030 ACTATTTACACACCGATTTTTCTCCA 59.062 34.615 0.00 0.00 0.00 3.86
3331 4618 7.021196 CCAAGAAAATCACTATTTACACACCG 58.979 38.462 0.00 0.00 34.12 4.94
3342 4629 6.316890 GGGTAAATACGCCAAGAAAATCACTA 59.683 38.462 0.00 0.00 33.54 2.74
3371 4658 0.663153 GTGAAGCGTGCTCTTTTGGT 59.337 50.000 0.00 0.00 0.00 3.67
3394 4681 2.489329 GCATGCAGCTACTCCAAGAAAA 59.511 45.455 14.21 0.00 41.15 2.29
3395 4682 2.086869 GCATGCAGCTACTCCAAGAAA 58.913 47.619 14.21 0.00 41.15 2.52
3398 4685 2.012237 CGCATGCAGCTACTCCAAG 58.988 57.895 19.57 0.00 42.61 3.61
3399 4686 2.108514 GCGCATGCAGCTACTCCAA 61.109 57.895 19.57 0.00 42.61 3.53
3400 4687 2.512286 GCGCATGCAGCTACTCCA 60.512 61.111 19.57 0.00 42.61 3.86
3401 4688 2.202987 AGCGCATGCAGCTACTCC 60.203 61.111 27.57 5.25 44.05 3.85
3402 4689 2.243264 GGAGCGCATGCAGCTACTC 61.243 63.158 28.28 20.04 46.13 2.59
3403 4690 2.202987 GGAGCGCATGCAGCTACT 60.203 61.111 28.28 14.36 46.13 2.57
3404 4691 2.512286 TGGAGCGCATGCAGCTAC 60.512 61.111 28.62 28.62 46.13 3.58
3429 4716 3.285484 TCCGTACGAAAGCTTATCTCCT 58.715 45.455 18.76 0.00 0.00 3.69
3502 4789 1.675310 CCTGCACCGCTGATTTCCA 60.675 57.895 0.00 0.00 0.00 3.53
3522 4809 5.241728 GTCCAAGGTTAAAAGTCTGCTCAAT 59.758 40.000 0.00 0.00 0.00 2.57
3665 5481 1.300465 CTCCAGCGTGATCCATCCG 60.300 63.158 0.00 0.00 0.00 4.18
3678 5499 2.796383 CGATAAGCACGAGGTTCTCCAG 60.796 54.545 0.00 0.00 36.70 3.86


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

AutoCloner maintained by Alex Coulton.