Multiple sequence alignment - TraesCS2A01G401000

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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 TraesCS2A01G401000 chr2A 100.000 3460 0 0 1 3460 654876842 654873383 0.000000e+00 6390
1 TraesCS2A01G401000 chr2D 89.367 3301 202 76 238 3455 511529623 511526389 0.000000e+00 4013
2 TraesCS2A01G401000 chr2D 93.048 187 10 2 4 188 511530013 511529828 1.580000e-68 270
3 TraesCS2A01G401000 chr2B 88.219 3319 210 80 217 3455 600710075 600706858 0.000000e+00 3795
4 TraesCS2A01G401000 chr2B 95.062 162 8 0 4 165 600710238 600710077 4.430000e-64 255
5 TraesCS2A01G401000 chr1A 93.179 1510 57 16 1486 2964 12181845 12183339 0.000000e+00 2176
6 TraesCS2A01G401000 chr4A 96.674 902 26 3 1486 2387 453299790 453300687 0.000000e+00 1496
7 TraesCS2A01G401000 chr4A 90.484 599 26 10 2384 2964 453307117 453307702 0.000000e+00 761
8 TraesCS2A01G401000 chr4B 86.400 125 17 0 2038 2162 646974747 646974623 1.670000e-28 137
9 TraesCS2A01G401000 chr5D 82.258 124 17 4 1231 1350 412602064 412601942 6.110000e-18 102


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 TraesCS2A01G401000 chr2A 654873383 654876842 3459 True 6390.0 6390 100.0000 1 3460 1 chr2A.!!$R1 3459
1 TraesCS2A01G401000 chr2D 511526389 511530013 3624 True 2141.5 4013 91.2075 4 3455 2 chr2D.!!$R1 3451
2 TraesCS2A01G401000 chr2B 600706858 600710238 3380 True 2025.0 3795 91.6405 4 3455 2 chr2B.!!$R1 3451
3 TraesCS2A01G401000 chr1A 12181845 12183339 1494 False 2176.0 2176 93.1790 1486 2964 1 chr1A.!!$F1 1478
4 TraesCS2A01G401000 chr4A 453299790 453300687 897 False 1496.0 1496 96.6740 1486 2387 1 chr4A.!!$F1 901
5 TraesCS2A01G401000 chr4A 453307117 453307702 585 False 761.0 761 90.4840 2384 2964 1 chr4A.!!$F2 580

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
710 885 0.178861 ACCCACAGACCCTCCATTCT 60.179 55.0 0.00 0.0 0.0 2.4 F
1436 1623 0.037303 GTGGATCGGATCATGGGCAT 59.963 55.0 18.99 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1947 2141 0.871722 CGACATGGACCGAAGCAAAA 59.128 50.0 0.0 0.0 0.00 2.44 R
2745 2983 0.108186 TCAGCGATGGCAAAGACGAT 60.108 50.0 0.0 0.0 43.41 3.73 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
25 26 5.006358 CCGACAATCTATTGAACCTTAACCG 59.994 44.000 9.60 0.00 40.14 4.44
44 45 1.777819 CGCAACTGAAGCAGACGAG 59.222 57.895 0.82 0.00 35.18 4.18
60 61 1.069513 ACGAGAACGGTTCACATGGAA 59.930 47.619 21.86 0.00 44.46 3.53
165 166 2.545113 GCACTCGCCATCGGAAATACTA 60.545 50.000 0.00 0.00 36.13 1.82
166 167 3.050619 CACTCGCCATCGGAAATACTAC 58.949 50.000 0.00 0.00 36.13 2.73
167 168 2.957006 ACTCGCCATCGGAAATACTACT 59.043 45.455 0.00 0.00 36.13 2.57
168 169 3.383825 ACTCGCCATCGGAAATACTACTT 59.616 43.478 0.00 0.00 36.13 2.24
170 171 4.365723 TCGCCATCGGAAATACTACTTTC 58.634 43.478 0.00 0.00 34.95 2.62
172 173 4.444720 CGCCATCGGAAATACTACTTTCTC 59.555 45.833 0.00 0.00 35.81 2.87
173 174 4.750598 GCCATCGGAAATACTACTTTCTCC 59.249 45.833 0.00 0.00 35.81 3.71
174 175 4.982916 CCATCGGAAATACTACTTTCTCCG 59.017 45.833 1.95 1.95 35.81 4.63
175 176 5.221185 CCATCGGAAATACTACTTTCTCCGA 60.221 44.000 12.84 12.84 35.13 4.55
176 177 6.448006 CATCGGAAATACTACTTTCTCCGAT 58.552 40.000 15.96 15.96 38.69 4.18
179 181 5.398711 CGGAAATACTACTTTCTCCGATTCG 59.601 44.000 2.19 0.00 35.81 3.34
188 190 7.980099 ACTACTTTCTCCGATTCGTAAATTGAT 59.020 33.333 5.20 0.00 0.00 2.57
189 191 9.459640 CTACTTTCTCCGATTCGTAAATTGATA 57.540 33.333 5.20 0.00 0.00 2.15
193 195 7.034685 TCTCCGATTCGTAAATTGATACTGA 57.965 36.000 5.20 0.00 0.00 3.41
196 198 8.657074 TCCGATTCGTAAATTGATACTGATTT 57.343 30.769 5.20 0.00 0.00 2.17
197 199 9.752961 TCCGATTCGTAAATTGATACTGATTTA 57.247 29.630 5.20 0.00 0.00 1.40
211 213 9.653287 TGATACTGATTTAGTACAACTTTCTGG 57.347 33.333 0.00 0.00 44.30 3.86
212 214 9.871238 GATACTGATTTAGTACAACTTTCTGGA 57.129 33.333 0.00 0.00 44.30 3.86
213 215 9.877178 ATACTGATTTAGTACAACTTTCTGGAG 57.123 33.333 0.00 0.00 44.30 3.86
214 216 7.736893 ACTGATTTAGTACAACTTTCTGGAGT 58.263 34.615 0.00 0.00 38.04 3.85
227 300 6.827727 ACTTTCTGGAGTAGTAGCTTTCAAA 58.172 36.000 0.00 0.00 0.00 2.69
250 407 1.280066 AACGACGTAAACAACAGCGT 58.720 45.000 0.00 0.00 40.44 5.07
298 455 1.269448 GCATGGCCAGAAACTTTTCGA 59.731 47.619 13.05 0.00 41.92 3.71
310 467 7.599998 CCAGAAACTTTTCGAAATGATTTCCAT 59.400 33.333 25.41 14.41 41.92 3.41
389 562 5.764686 ACATCATATGCCAAATACACACGAT 59.235 36.000 0.00 0.00 0.00 3.73
391 564 6.779115 TCATATGCCAAATACACACGATAC 57.221 37.500 0.00 0.00 0.00 2.24
453 626 3.202818 ACAATCCTACCATGCATCTGGAA 59.797 43.478 13.35 0.00 39.73 3.53
454 627 4.141088 ACAATCCTACCATGCATCTGGAAT 60.141 41.667 13.35 1.55 39.73 3.01
455 628 4.736611 ATCCTACCATGCATCTGGAATT 57.263 40.909 13.35 0.00 39.73 2.17
456 629 4.090761 TCCTACCATGCATCTGGAATTC 57.909 45.455 13.35 0.00 39.73 2.17
457 630 3.718434 TCCTACCATGCATCTGGAATTCT 59.282 43.478 13.35 0.00 39.73 2.40
458 631 3.819337 CCTACCATGCATCTGGAATTCTG 59.181 47.826 13.35 0.00 39.73 3.02
459 632 2.662866 ACCATGCATCTGGAATTCTGG 58.337 47.619 13.35 3.73 39.73 3.86
460 633 2.242965 ACCATGCATCTGGAATTCTGGA 59.757 45.455 13.35 7.89 39.73 3.86
497 670 1.568612 AAACATCAGTGTCGCCAGCG 61.569 55.000 5.50 5.50 37.67 5.18
535 708 7.394641 GGTTGGTTGATTCTAAAGAAAGGATCT 59.605 37.037 0.00 0.00 41.32 2.75
538 711 6.183360 GGTTGATTCTAAAGAAAGGATCTGCC 60.183 42.308 0.00 0.00 38.79 4.85
587 762 9.284968 TCACCTTTATTAAGCTGATTATAAGCC 57.715 33.333 0.00 0.00 41.82 4.35
588 763 9.066892 CACCTTTATTAAGCTGATTATAAGCCA 57.933 33.333 0.00 0.00 41.82 4.75
606 781 4.642429 AGCCACTAATAATTTAGCCGGAG 58.358 43.478 5.05 0.00 38.74 4.63
614 789 1.749334 ATTTAGCCGGAGAGAGCCCG 61.749 60.000 5.05 0.00 46.10 6.13
648 823 1.662629 CGTAGCATCAAGTGAGCCAAG 59.337 52.381 0.00 0.00 0.00 3.61
664 839 3.017442 GCCAAGGGGTCAACTTCTAATC 58.983 50.000 0.00 0.00 36.17 1.75
681 856 0.735287 ATCGCGCCATCATCATCTCG 60.735 55.000 0.00 0.00 0.00 4.04
707 882 0.475632 TGAACCCACAGACCCTCCAT 60.476 55.000 0.00 0.00 0.00 3.41
708 883 0.698818 GAACCCACAGACCCTCCATT 59.301 55.000 0.00 0.00 0.00 3.16
709 884 0.698818 AACCCACAGACCCTCCATTC 59.301 55.000 0.00 0.00 0.00 2.67
710 885 0.178861 ACCCACAGACCCTCCATTCT 60.179 55.000 0.00 0.00 0.00 2.40
711 886 0.995024 CCCACAGACCCTCCATTCTT 59.005 55.000 0.00 0.00 0.00 2.52
796 975 2.158534 AGGCGGCCAATATTTGTCCATA 60.159 45.455 23.09 0.00 0.00 2.74
799 978 4.236935 GCGGCCAATATTTGTCCATATTG 58.763 43.478 2.24 6.48 42.94 1.90
831 1011 7.988547 ACGAAATAATAAAACAAGAAACACGC 58.011 30.769 0.00 0.00 0.00 5.34
832 1012 7.644551 ACGAAATAATAAAACAAGAAACACGCA 59.355 29.630 0.00 0.00 0.00 5.24
852 1032 4.457466 GCATAGATTAAAAACCCTCGGGA 58.543 43.478 9.43 0.00 38.96 5.14
857 1037 9.127277 CATAGATTAAAAACCCTCGGGATAAAA 57.873 33.333 9.43 0.00 38.96 1.52
866 1046 2.356135 CTCGGGATAAAACCACCACAG 58.644 52.381 0.00 0.00 0.00 3.66
885 1068 0.310854 GAGGCTCCAAACAAACACCG 59.689 55.000 2.15 0.00 0.00 4.94
908 1091 1.697772 CTCCAGTCGTCGTCTCCTCG 61.698 65.000 0.00 0.00 0.00 4.63
944 1127 0.586319 ACGATTGTGTTTGCACCGAG 59.414 50.000 0.00 0.00 44.65 4.63
967 1150 3.437795 CAGCAGCCAAGAAGCGGG 61.438 66.667 0.00 0.00 38.01 6.13
992 1178 2.818274 GGGCGTGGGTTCATCGAC 60.818 66.667 0.00 0.00 0.00 4.20
1213 1399 2.560861 CCAACGTGGCCATGTTCG 59.439 61.111 35.39 27.38 38.39 3.95
1233 1419 3.441222 TCGTCGTGGTCATGTACTACAAT 59.559 43.478 10.64 0.00 39.44 2.71
1242 1428 3.118408 TCATGTACTACAATGACTGCCCC 60.118 47.826 0.00 0.00 0.00 5.80
1374 1560 4.898265 CACAGATATCTTCTCTCTTCCCCA 59.102 45.833 1.33 0.00 29.93 4.96
1378 1564 0.614979 TCTTCTCTCTTCCCCACCGG 60.615 60.000 0.00 0.00 0.00 5.28
1382 1568 4.148825 CTCTTCCCCACCGGCTCG 62.149 72.222 0.00 0.00 0.00 5.03
1418 1604 2.455674 TGCTTGCTTGTACTCATCGT 57.544 45.000 0.00 0.00 0.00 3.73
1423 1610 3.165058 TGCTTGTACTCATCGTGGATC 57.835 47.619 0.00 0.00 0.00 3.36
1436 1623 0.037303 GTGGATCGGATCATGGGCAT 59.963 55.000 18.99 0.00 0.00 4.40
1626 1817 1.887707 GGATTCTGTAAGCGCCCGG 60.888 63.158 2.29 0.00 0.00 5.73
1947 2141 2.946329 CTCGTCTCTGCCACTACTGTAT 59.054 50.000 0.00 0.00 0.00 2.29
1982 2185 3.026630 TGTCGAACACCTTCTGACATC 57.973 47.619 0.00 0.00 36.19 3.06
2199 2405 0.872388 CAAAGTCCAAGTACACGGCC 59.128 55.000 0.00 0.00 0.00 6.13
2271 2482 0.096976 CGCCGGTGCAAGATACAAAG 59.903 55.000 0.00 0.00 37.32 2.77
2303 2514 9.888878 ATTCAGATTCTACAAAATGAATATGCG 57.111 29.630 0.00 0.00 39.97 4.73
2306 2517 8.337532 CAGATTCTACAAAATGAATATGCGTCA 58.662 33.333 0.00 0.00 35.88 4.35
2316 2527 4.119136 TGAATATGCGTCATGTGTGGTAG 58.881 43.478 0.00 0.00 0.00 3.18
2325 2536 4.566759 CGTCATGTGTGGTAGTTAATCTGG 59.433 45.833 0.00 0.00 0.00 3.86
2484 2703 9.959721 AATAAAAATAAGAGGAGAACAGCTGTA 57.040 29.630 22.01 0.34 0.00 2.74
2505 2724 0.036164 AGACAAACGTGCTGCCCATA 59.964 50.000 0.00 0.00 0.00 2.74
2528 2747 4.523943 ACAGATAATTGCTTCAGTTTGGCA 59.476 37.500 0.00 0.00 0.00 4.92
2529 2748 5.186409 ACAGATAATTGCTTCAGTTTGGCAT 59.814 36.000 0.00 0.00 35.84 4.40
2663 2901 3.632145 ACTCTGGTTTGTTTGTGGCTAAG 59.368 43.478 0.00 0.00 0.00 2.18
2702 2940 2.095372 GGTTTTACATAGCCAGTCGCAC 59.905 50.000 0.00 0.00 41.38 5.34
2720 2958 3.424039 CGCACTTGCAATGTTCAGAGTAG 60.424 47.826 0.00 0.00 42.21 2.57
2745 2983 8.755977 AGAATAGGTTATACTTGAAGAACCGAA 58.244 33.333 0.00 0.00 44.99 4.30
2747 2985 9.543783 AATAGGTTATACTTGAAGAACCGAATC 57.456 33.333 0.00 0.00 44.99 2.52
2748 2986 6.040878 AGGTTATACTTGAAGAACCGAATCG 58.959 40.000 0.00 0.00 44.99 3.34
2750 2988 6.020041 GGTTATACTTGAAGAACCGAATCGTC 60.020 42.308 0.00 0.00 32.57 4.20
2751 2989 3.662247 ACTTGAAGAACCGAATCGTCT 57.338 42.857 0.00 0.00 0.00 4.18
2752 2990 3.991367 ACTTGAAGAACCGAATCGTCTT 58.009 40.909 8.01 8.01 0.00 3.01
2753 2991 4.377897 ACTTGAAGAACCGAATCGTCTTT 58.622 39.130 9.37 0.00 0.00 2.52
2754 2992 4.211374 ACTTGAAGAACCGAATCGTCTTTG 59.789 41.667 9.37 6.55 0.00 2.77
2803 3051 4.171416 GCGCTAGGCTGCTTGCAC 62.171 66.667 0.00 0.00 45.15 4.57
2841 3101 3.498777 TCGTTGGAATGCGATTGTGTTAA 59.501 39.130 0.00 0.00 31.76 2.01
2865 3129 1.795768 TCAGTCATCTTCCACGCAAC 58.204 50.000 0.00 0.00 0.00 4.17
2975 3239 9.618890 ATCATCCTATAACAAATATCAATCCGG 57.381 33.333 0.00 0.00 0.00 5.14
3008 3272 0.919710 ATGGAAGAGGTGTAAGGGCC 59.080 55.000 0.00 0.00 0.00 5.80
3012 3276 1.073284 GAAGAGGTGTAAGGGCCACAA 59.927 52.381 6.18 0.00 34.46 3.33
3018 3282 1.751924 GTGTAAGGGCCACAAAACACA 59.248 47.619 6.18 0.00 37.69 3.72
3033 3297 7.592533 CCACAAAACACATAGAAAGAATCACAG 59.407 37.037 0.00 0.00 0.00 3.66
3034 3298 8.344831 CACAAAACACATAGAAAGAATCACAGA 58.655 33.333 0.00 0.00 0.00 3.41
3035 3299 8.345565 ACAAAACACATAGAAAGAATCACAGAC 58.654 33.333 0.00 0.00 0.00 3.51
3036 3300 8.562892 CAAAACACATAGAAAGAATCACAGACT 58.437 33.333 0.00 0.00 0.00 3.24
3037 3301 7.897575 AACACATAGAAAGAATCACAGACTC 57.102 36.000 0.00 0.00 0.00 3.36
3038 3302 6.096036 ACACATAGAAAGAATCACAGACTCG 58.904 40.000 0.00 0.00 0.00 4.18
3040 3304 3.667497 AGAAAGAATCACAGACTCGCA 57.333 42.857 0.00 0.00 0.00 5.10
3041 3305 3.583806 AGAAAGAATCACAGACTCGCAG 58.416 45.455 0.00 0.00 0.00 5.18
3042 3306 1.719600 AAGAATCACAGACTCGCAGC 58.280 50.000 0.00 0.00 0.00 5.25
3043 3307 0.605083 AGAATCACAGACTCGCAGCA 59.395 50.000 0.00 0.00 0.00 4.41
3044 3308 1.001293 AGAATCACAGACTCGCAGCAA 59.999 47.619 0.00 0.00 0.00 3.91
3045 3309 1.392853 GAATCACAGACTCGCAGCAAG 59.607 52.381 0.00 0.00 0.00 4.01
3051 3315 0.389166 AGACTCGCAGCAAGCAGTAC 60.389 55.000 0.00 0.00 46.13 2.73
3059 3323 2.263077 CAGCAAGCAGTACCTAACTCG 58.737 52.381 0.00 0.00 35.76 4.18
3062 3326 3.508793 AGCAAGCAGTACCTAACTCGTTA 59.491 43.478 0.00 0.00 35.76 3.18
3070 3334 7.338957 AGCAGTACCTAACTCGTTACTAAAGAT 59.661 37.037 0.00 0.00 35.76 2.40
3076 3340 6.471519 CCTAACTCGTTACTAAAGATCCAACG 59.528 42.308 0.00 0.00 42.38 4.10
3081 3345 6.392354 TCGTTACTAAAGATCCAACGATGTT 58.608 36.000 3.96 0.00 44.10 2.71
3105 3372 7.023197 TGTAGAAAATAAAGCTATTTCCGCC 57.977 36.000 9.35 2.05 36.84 6.13
3110 3377 6.715347 AAATAAAGCTATTTCCGCCTCAAT 57.285 33.333 0.00 0.00 33.26 2.57
3111 3378 5.948992 ATAAAGCTATTTCCGCCTCAATC 57.051 39.130 0.00 0.00 0.00 2.67
3167 3434 5.279156 CCAAAAGACTCAAAATCAGGGGAAG 60.279 44.000 0.00 0.00 0.00 3.46
3179 3468 4.855298 TCAGGGGAAGGGTTATAAACAG 57.145 45.455 2.32 0.00 0.00 3.16
3192 3481 8.270030 AGGGTTATAAACAGGGATACAACTAAC 58.730 37.037 2.32 0.00 39.74 2.34
3232 3521 4.915667 GGTAGCTTCCAAAATGTTTTCGTC 59.084 41.667 4.19 0.00 0.00 4.20
3237 3526 4.136517 TCCAAAATGTTTTCGTCGCTAC 57.863 40.909 0.00 0.00 0.00 3.58
3258 3547 4.392940 ACAAGTATTTTCTCAGCACTGCT 58.607 39.130 0.00 0.00 40.77 4.24
3305 3594 1.065251 GAGTAGTCCACCGAATCGACC 59.935 57.143 3.36 0.00 0.00 4.79
3375 3664 1.600636 CAGTTCCTTCTGGGCGCAA 60.601 57.895 10.83 0.00 34.39 4.85
3420 3709 1.896220 TCAAACAGGTCACATCTGCC 58.104 50.000 0.00 0.00 35.78 4.85
3435 3724 2.076100 TCTGCCACAAGTAGAAATGCG 58.924 47.619 0.00 0.00 33.83 4.73
3436 3725 1.131126 CTGCCACAAGTAGAAATGCGG 59.869 52.381 0.00 0.00 0.00 5.69
3445 3734 5.581085 ACAAGTAGAAATGCGGTCAGTTATC 59.419 40.000 0.00 0.00 29.77 1.75
3451 3740 3.735237 ATGCGGTCAGTTATCAGGTAG 57.265 47.619 0.00 0.00 0.00 3.18
3452 3741 1.136305 TGCGGTCAGTTATCAGGTAGC 59.864 52.381 0.00 0.00 0.00 3.58
3453 3742 1.409427 GCGGTCAGTTATCAGGTAGCT 59.591 52.381 0.00 0.00 0.00 3.32
3454 3743 2.544069 GCGGTCAGTTATCAGGTAGCTC 60.544 54.545 0.00 0.00 0.00 4.09
3455 3744 2.952978 CGGTCAGTTATCAGGTAGCTCT 59.047 50.000 0.00 0.00 0.00 4.09
3456 3745 3.381908 CGGTCAGTTATCAGGTAGCTCTT 59.618 47.826 0.00 0.00 0.00 2.85
3457 3746 4.142138 CGGTCAGTTATCAGGTAGCTCTTT 60.142 45.833 0.00 0.00 0.00 2.52
3458 3747 5.624738 CGGTCAGTTATCAGGTAGCTCTTTT 60.625 44.000 0.00 0.00 0.00 2.27
3459 3748 6.405508 CGGTCAGTTATCAGGTAGCTCTTTTA 60.406 42.308 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.878669 GGTTAAGGTTCAATAGATTGTCGGT 59.121 40.000 2.32 0.00 38.84 4.69
1 2 5.006358 CGGTTAAGGTTCAATAGATTGTCGG 59.994 44.000 2.32 0.00 38.84 4.79
2 3 5.501897 GCGGTTAAGGTTCAATAGATTGTCG 60.502 44.000 2.32 0.00 38.84 4.35
9 10 2.004017 TGCGCGGTTAAGGTTCAATAG 58.996 47.619 8.83 0.00 0.00 1.73
25 26 2.171940 CGTCTGCTTCAGTTGCGC 59.828 61.111 0.00 0.00 32.61 6.09
165 166 7.980099 AGTATCAATTTACGAATCGGAGAAAGT 59.020 33.333 7.80 1.01 43.58 2.66
166 167 8.269424 CAGTATCAATTTACGAATCGGAGAAAG 58.731 37.037 7.80 0.00 43.58 2.62
167 168 7.977293 TCAGTATCAATTTACGAATCGGAGAAA 59.023 33.333 7.80 4.92 43.58 2.52
168 169 7.485810 TCAGTATCAATTTACGAATCGGAGAA 58.514 34.615 7.80 0.00 43.58 2.87
170 171 7.875316 ATCAGTATCAATTTACGAATCGGAG 57.125 36.000 7.80 0.00 0.00 4.63
188 190 8.867097 ACTCCAGAAAGTTGTACTAAATCAGTA 58.133 33.333 0.00 0.00 38.80 2.74
189 191 7.736893 ACTCCAGAAAGTTGTACTAAATCAGT 58.263 34.615 0.00 0.00 41.62 3.41
196 198 7.173722 AGCTACTACTCCAGAAAGTTGTACTA 58.826 38.462 0.00 0.00 36.74 1.82
197 199 6.011481 AGCTACTACTCCAGAAAGTTGTACT 58.989 40.000 0.00 0.00 36.74 2.73
198 200 6.270156 AGCTACTACTCCAGAAAGTTGTAC 57.730 41.667 0.00 0.00 36.74 2.90
199 201 6.912951 AAGCTACTACTCCAGAAAGTTGTA 57.087 37.500 0.00 0.00 36.74 2.41
201 203 6.223852 TGAAAGCTACTACTCCAGAAAGTTG 58.776 40.000 0.00 0.00 0.00 3.16
202 204 6.420913 TGAAAGCTACTACTCCAGAAAGTT 57.579 37.500 0.00 0.00 0.00 2.66
204 206 6.128795 CGTTTGAAAGCTACTACTCCAGAAAG 60.129 42.308 0.00 0.00 0.00 2.62
206 208 5.221382 ACGTTTGAAAGCTACTACTCCAGAA 60.221 40.000 0.00 0.00 0.00 3.02
207 209 4.280174 ACGTTTGAAAGCTACTACTCCAGA 59.720 41.667 0.00 0.00 0.00 3.86
208 210 4.557205 ACGTTTGAAAGCTACTACTCCAG 58.443 43.478 0.00 0.00 0.00 3.86
209 211 4.595762 ACGTTTGAAAGCTACTACTCCA 57.404 40.909 0.00 0.00 0.00 3.86
210 212 5.060200 CGTTACGTTTGAAAGCTACTACTCC 59.940 44.000 0.00 0.00 0.00 3.85
211 213 5.853282 TCGTTACGTTTGAAAGCTACTACTC 59.147 40.000 4.24 0.00 0.00 2.59
212 214 5.626955 GTCGTTACGTTTGAAAGCTACTACT 59.373 40.000 4.24 0.00 0.00 2.57
213 215 5.440714 CGTCGTTACGTTTGAAAGCTACTAC 60.441 44.000 4.24 0.00 44.21 2.73
214 216 4.612614 CGTCGTTACGTTTGAAAGCTACTA 59.387 41.667 4.24 0.00 44.21 1.82
275 432 3.320626 GAAAAGTTTCTGGCCATGCTTC 58.679 45.455 5.51 0.00 34.41 3.86
298 455 8.854117 GGTCTCAGCTTATTATGGAAATCATTT 58.146 33.333 0.00 0.00 37.30 2.32
310 467 3.932710 CGCTTGTTGGTCTCAGCTTATTA 59.067 43.478 0.00 0.00 0.00 0.98
370 543 5.932303 GGAGTATCGTGTGTATTTGGCATAT 59.068 40.000 0.00 0.00 34.37 1.78
430 603 3.144506 CCAGATGCATGGTAGGATTGTC 58.855 50.000 2.46 0.00 35.47 3.18
433 606 4.736611 ATTCCAGATGCATGGTAGGATT 57.263 40.909 2.46 0.00 41.43 3.01
471 644 2.159787 GCGACACTGATGTTTGCTACTG 60.160 50.000 0.00 0.00 39.95 2.74
477 650 0.110056 GCTGGCGACACTGATGTTTG 60.110 55.000 0.00 0.00 39.95 2.93
497 670 1.338020 CAACCAACCAACTGGAAGCTC 59.662 52.381 1.86 0.00 38.96 4.09
535 708 0.391793 TTTACACGCATGGATCGGCA 60.392 50.000 0.00 0.00 0.00 5.69
538 711 5.403897 AATACTTTTACACGCATGGATCG 57.596 39.130 0.00 0.00 0.00 3.69
586 761 6.097915 TCTCTCCGGCTAAATTATTAGTGG 57.902 41.667 0.00 0.00 40.59 4.00
587 762 5.635700 GCTCTCTCCGGCTAAATTATTAGTG 59.364 44.000 0.00 0.00 40.59 2.74
588 763 5.279556 GGCTCTCTCCGGCTAAATTATTAGT 60.280 44.000 0.00 0.00 40.59 2.24
606 781 0.318275 CGAGCTGTATTCGGGCTCTC 60.318 60.000 11.47 0.00 46.96 3.20
614 789 1.268589 TGCTACGCTCGAGCTGTATTC 60.269 52.381 32.88 25.09 40.76 1.75
624 799 1.195347 CTCACTTGATGCTACGCTCG 58.805 55.000 0.00 0.00 0.00 5.03
648 823 1.287425 CGCGATTAGAAGTTGACCCC 58.713 55.000 0.00 0.00 0.00 4.95
664 839 1.372128 TCGAGATGATGATGGCGCG 60.372 57.895 0.00 0.00 0.00 6.86
681 856 1.270893 GGTCTGTGGGTTCAAGGAGTC 60.271 57.143 0.00 0.00 0.00 3.36
707 882 7.535139 CGGGAAGTTTTATATGCAAGAAAGAA 58.465 34.615 0.00 0.00 0.00 2.52
708 883 6.404293 GCGGGAAGTTTTATATGCAAGAAAGA 60.404 38.462 0.00 0.00 0.00 2.52
709 884 5.743872 GCGGGAAGTTTTATATGCAAGAAAG 59.256 40.000 0.00 0.00 0.00 2.62
710 885 5.393678 GGCGGGAAGTTTTATATGCAAGAAA 60.394 40.000 0.00 0.00 0.00 2.52
711 886 4.097286 GGCGGGAAGTTTTATATGCAAGAA 59.903 41.667 0.00 0.00 0.00 2.52
831 1011 8.685838 TTTATCCCGAGGGTTTTTAATCTATG 57.314 34.615 8.20 0.00 36.47 2.23
832 1012 9.128404 GTTTTATCCCGAGGGTTTTTAATCTAT 57.872 33.333 8.20 0.00 36.47 1.98
852 1032 2.290960 GGAGCCTCTGTGGTGGTTTTAT 60.291 50.000 0.00 0.00 38.35 1.40
857 1037 1.352622 TTTGGAGCCTCTGTGGTGGT 61.353 55.000 0.00 0.00 38.35 4.16
866 1046 0.310854 CGGTGTTTGTTTGGAGCCTC 59.689 55.000 0.00 0.00 0.00 4.70
885 1068 1.646624 GAGACGACGACTGGAGACCC 61.647 65.000 4.18 0.00 0.00 4.46
908 1091 1.367471 GTTTGCTGGTTGGCTTCCC 59.633 57.895 0.00 0.00 0.00 3.97
975 1158 2.818274 GTCGATGAACCCACGCCC 60.818 66.667 0.00 0.00 0.00 6.13
992 1178 2.511600 GGTTCGACATGGCCTCGG 60.512 66.667 12.42 0.36 0.00 4.63
1183 1369 3.297620 GTTGGCCAGCACCACCAG 61.298 66.667 15.64 0.00 40.19 4.00
1213 1399 4.561606 GTCATTGTAGTACATGACCACGAC 59.438 45.833 22.35 7.93 34.04 4.34
1397 1583 2.738846 ACGATGAGTACAAGCAAGCAAG 59.261 45.455 0.00 0.00 0.00 4.01
1398 1584 2.480037 CACGATGAGTACAAGCAAGCAA 59.520 45.455 0.00 0.00 0.00 3.91
1399 1585 2.068519 CACGATGAGTACAAGCAAGCA 58.931 47.619 0.00 0.00 0.00 3.91
1418 1604 0.037160 CATGCCCATGATCCGATCCA 59.963 55.000 5.91 0.00 41.20 3.41
1423 1610 3.359523 CGCCATGCCCATGATCCG 61.360 66.667 9.73 5.87 41.20 4.18
1937 2130 4.092968 GGACCGAAGCAAAATACAGTAGTG 59.907 45.833 0.00 0.00 0.00 2.74
1947 2141 0.871722 CGACATGGACCGAAGCAAAA 59.128 50.000 0.00 0.00 0.00 2.44
1982 2185 1.127951 GCAGACGGTGTTTACATTCGG 59.872 52.381 11.26 1.42 32.54 4.30
2199 2405 1.440893 CAGGAGGACGATCTGGCAG 59.559 63.158 8.58 8.58 0.00 4.85
2257 2463 6.902341 TGAATGAAGACTTTGTATCTTGCAC 58.098 36.000 0.00 0.00 36.53 4.57
2298 2509 3.603158 AACTACCACACATGACGCATA 57.397 42.857 0.00 0.00 0.00 3.14
2299 2510 2.472695 AACTACCACACATGACGCAT 57.527 45.000 0.00 0.00 0.00 4.73
2303 2514 5.730550 TCCAGATTAACTACCACACATGAC 58.269 41.667 0.00 0.00 0.00 3.06
2306 2517 4.384208 GGCTCCAGATTAACTACCACACAT 60.384 45.833 0.00 0.00 0.00 3.21
2316 2527 3.019564 ACAAGCATGGCTCCAGATTAAC 58.980 45.455 0.00 0.00 38.25 2.01
2325 2536 1.729149 GCGTACAAACAAGCATGGCTC 60.729 52.381 0.00 0.00 38.25 4.70
2354 2570 1.064003 ACACCATCAGCAACCCTACA 58.936 50.000 0.00 0.00 0.00 2.74
2484 2703 1.598130 GGGCAGCACGTTTGTCTCT 60.598 57.895 0.00 0.00 0.00 3.10
2505 2724 4.523943 TGCCAAACTGAAGCAATTATCTGT 59.476 37.500 0.00 0.00 32.56 3.41
2618 2856 9.974750 GAGTGAATTACAGAGCTTTAATAACAC 57.025 33.333 15.90 15.90 31.97 3.32
2638 2876 2.165437 GCCACAAACAAACCAGAGTGAA 59.835 45.455 0.00 0.00 0.00 3.18
2663 2901 3.092334 ACCAAAGAATGAACAAACGCC 57.908 42.857 0.00 0.00 0.00 5.68
2702 2940 6.820656 ACCTATTCTACTCTGAACATTGCAAG 59.179 38.462 4.94 0.00 0.00 4.01
2720 2958 8.937634 TTCGGTTCTTCAAGTATAACCTATTC 57.062 34.615 5.26 0.00 39.39 1.75
2745 2983 0.108186 TCAGCGATGGCAAAGACGAT 60.108 50.000 0.00 0.00 43.41 3.73
2747 2985 0.729116 ATTCAGCGATGGCAAAGACG 59.271 50.000 0.00 0.00 43.41 4.18
2748 2986 1.739466 TCATTCAGCGATGGCAAAGAC 59.261 47.619 0.00 0.00 43.41 3.01
2750 2988 2.925578 TTCATTCAGCGATGGCAAAG 57.074 45.000 0.00 0.00 43.41 2.77
2751 2989 3.513662 CAATTCATTCAGCGATGGCAAA 58.486 40.909 0.00 0.00 43.41 3.68
2752 2990 2.159212 CCAATTCATTCAGCGATGGCAA 60.159 45.455 0.00 0.00 43.41 4.52
2753 2991 1.406180 CCAATTCATTCAGCGATGGCA 59.594 47.619 0.00 0.00 43.41 4.92
2754 2992 1.406539 ACCAATTCATTCAGCGATGGC 59.593 47.619 0.00 0.00 40.37 4.40
2803 3051 5.948588 TCCAACGATACCATTTCATGTTTG 58.051 37.500 0.00 0.00 0.00 2.93
2826 3074 5.470098 ACTGAAGTCTTAACACAATCGCATT 59.530 36.000 0.00 0.00 0.00 3.56
2841 3101 2.353208 GCGTGGAAGATGACTGAAGTCT 60.353 50.000 11.55 0.00 44.99 3.24
2858 3119 6.632834 GCAATATAAACCATTCTAGTTGCGTG 59.367 38.462 0.00 0.00 31.57 5.34
2865 3129 9.208022 TCGATCTTGCAATATAAACCATTCTAG 57.792 33.333 0.00 0.00 0.00 2.43
2999 3263 2.145397 TGTGTTTTGTGGCCCTTACA 57.855 45.000 0.00 0.00 0.00 2.41
3000 3264 4.076394 TCTATGTGTTTTGTGGCCCTTAC 58.924 43.478 0.00 0.00 0.00 2.34
3001 3265 4.374689 TCTATGTGTTTTGTGGCCCTTA 57.625 40.909 0.00 0.00 0.00 2.69
3008 3272 8.344831 TCTGTGATTCTTTCTATGTGTTTTGTG 58.655 33.333 0.00 0.00 0.00 3.33
3012 3276 7.116948 CGAGTCTGTGATTCTTTCTATGTGTTT 59.883 37.037 0.00 0.00 0.00 2.83
3018 3282 5.330455 TGCGAGTCTGTGATTCTTTCTAT 57.670 39.130 0.00 0.00 0.00 1.98
3033 3297 1.355066 GGTACTGCTTGCTGCGAGTC 61.355 60.000 17.76 10.76 46.63 3.36
3034 3298 1.374758 GGTACTGCTTGCTGCGAGT 60.375 57.895 17.76 8.40 46.63 4.18
3035 3299 0.173481 TAGGTACTGCTTGCTGCGAG 59.827 55.000 12.66 12.66 46.63 5.03
3036 3300 0.606096 TTAGGTACTGCTTGCTGCGA 59.394 50.000 0.00 0.00 46.63 5.10
3037 3301 0.721718 GTTAGGTACTGCTTGCTGCG 59.278 55.000 0.00 0.00 46.63 5.18
3038 3302 2.003301 GAGTTAGGTACTGCTTGCTGC 58.997 52.381 0.00 0.00 41.52 5.25
3040 3304 1.893801 ACGAGTTAGGTACTGCTTGCT 59.106 47.619 0.00 0.00 41.52 3.91
3041 3305 2.365408 ACGAGTTAGGTACTGCTTGC 57.635 50.000 0.00 0.00 41.52 4.01
3042 3306 5.056894 AGTAACGAGTTAGGTACTGCTTG 57.943 43.478 0.00 0.00 42.52 4.01
3043 3307 6.824305 TTAGTAACGAGTTAGGTACTGCTT 57.176 37.500 5.09 0.00 43.75 3.91
3044 3308 6.656693 TCTTTAGTAACGAGTTAGGTACTGCT 59.343 38.462 5.09 0.00 43.75 4.24
3045 3309 6.846350 TCTTTAGTAACGAGTTAGGTACTGC 58.154 40.000 5.09 0.00 43.75 4.40
3051 3315 6.471519 CGTTGGATCTTTAGTAACGAGTTAGG 59.528 42.308 0.00 0.00 44.76 2.69
3059 3323 7.360575 ACAACATCGTTGGATCTTTAGTAAC 57.639 36.000 11.26 0.00 0.00 2.50
3062 3326 6.931838 TCTACAACATCGTTGGATCTTTAGT 58.068 36.000 11.26 0.00 0.00 2.24
3070 3334 7.174253 AGCTTTATTTTCTACAACATCGTTGGA 59.826 33.333 11.26 1.75 0.00 3.53
3081 3345 6.826741 AGGCGGAAATAGCTTTATTTTCTACA 59.173 34.615 0.00 0.00 30.51 2.74
3105 3372 6.817641 GGGATTAGCACTGATATCAGATTGAG 59.182 42.308 34.16 19.55 46.59 3.02
3110 3377 4.774726 GGAGGGATTAGCACTGATATCAGA 59.225 45.833 34.16 15.43 46.59 3.27
3167 3434 7.500227 GGTTAGTTGTATCCCTGTTTATAACCC 59.500 40.741 0.00 0.00 34.82 4.11
3192 3481 4.223032 AGCTACCATTAACATCGGGATAGG 59.777 45.833 0.00 0.00 0.00 2.57
3199 3488 5.811399 TTTGGAAGCTACCATTAACATCG 57.189 39.130 0.00 0.00 39.82 3.84
3232 3521 4.627467 AGTGCTGAGAAAATACTTGTAGCG 59.373 41.667 0.00 0.00 32.88 4.26
3237 3526 5.049198 TCAAGCAGTGCTGAGAAAATACTTG 60.049 40.000 20.55 8.54 39.62 3.16
3258 3547 1.344438 ACGACAGTGAGCCTGAATCAA 59.656 47.619 0.00 0.00 44.49 2.57
3305 3594 0.818296 AAGGCTGTACAGGTAGCTCG 59.182 55.000 23.95 0.00 39.80 5.03
3375 3664 1.768275 TGTTGGAGATGGACCGCATAT 59.232 47.619 0.00 0.00 0.00 1.78
3420 3709 3.067106 ACTGACCGCATTTCTACTTGTG 58.933 45.455 0.00 0.00 0.00 3.33
3435 3724 5.346181 AAAGAGCTACCTGATAACTGACC 57.654 43.478 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.