Multiple sequence alignment - TraesCS3B01G248000

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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 TraesCS3B01G248000 chr3B 100.000 3827 0 0 1 3827 395349678 395353504 0.000000e+00 7068.0
1 TraesCS3B01G248000 chr3D 94.591 2995 91 17 746 3740 323721141 323718218 0.000000e+00 4567.0
2 TraesCS3B01G248000 chr3D 88.764 534 53 5 2 535 323724179 323723653 0.000000e+00 647.0
3 TraesCS3B01G248000 chr3D 93.814 97 3 2 3721 3814 323718201 323718105 3.990000e-30 143.0
4 TraesCS3B01G248000 chr3A 96.288 2209 69 4 851 3054 398736148 398738348 0.000000e+00 3613.0
5 TraesCS3B01G248000 chr3A 93.451 794 20 10 3040 3827 398740126 398740893 0.000000e+00 1149.0
6 TraesCS3B01G248000 chr3A 92.697 178 12 1 519 696 398734109 398734285 4.910000e-64 255.0
7 TraesCS3B01G248000 chr1A 77.876 226 44 5 8 229 97962746 97962969 6.670000e-28 135.0
8 TraesCS3B01G248000 chr1B 100.000 31 0 0 479 509 474461943 474461913 1.480000e-04 58.4


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 TraesCS3B01G248000 chr3B 395349678 395353504 3826 False 7068.000000 7068 100.000000 1 3827 1 chr3B.!!$F1 3826
1 TraesCS3B01G248000 chr3D 323718105 323724179 6074 True 1785.666667 4567 92.389667 2 3814 3 chr3D.!!$R1 3812
2 TraesCS3B01G248000 chr3A 398734109 398740893 6784 False 1672.333333 3613 94.145333 519 3827 3 chr3A.!!$F1 3308

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
39 40 0.031314 ATGACCGCGAGATGCTACAG 59.969 55.0 8.23 0.0 43.27 2.74 F
62 63 0.104671 GCAATGGTGGTTGTTGCAGT 59.895 50.0 4.60 0.0 45.57 4.40 F
309 310 0.173708 GAGCTCGACGAACCTTGGAT 59.826 55.0 0.00 0.0 0.00 3.41 F
338 339 0.179073 CCCTAGAAGCCATGGTGTCG 60.179 60.0 14.67 0.0 0.00 4.35 F
790 3088 0.179108 GTGGACTCGTGGTATCAGCC 60.179 60.0 0.00 0.0 0.00 4.85 F
1800 5834 0.693049 AGATGAGGGTTGAAGGCGTT 59.307 50.0 0.00 0.0 0.00 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1779 5813 0.745845 CGCCTTCAACCCTCATCTGG 60.746 60.000 0.00 0.00 0.0 3.86 R
1922 5956 1.213926 AGTTGATGATTGAGCTCCCCC 59.786 52.381 12.15 0.09 0.0 5.40 R
2032 6066 1.215173 CCCATCCTGCAAATACCCAGA 59.785 52.381 0.00 0.00 0.0 3.86 R
2223 6257 1.630369 TCTATCAGGCCACAAGCAACT 59.370 47.619 5.01 0.00 46.5 3.16 R
2604 6638 0.823356 TTGGTGCTGGCTCAACTTCC 60.823 55.000 0.00 0.00 0.0 3.46 R
2949 6988 0.386113 TTTTTGCCAACGGTAGCACC 59.614 50.000 0.00 0.00 39.1 5.01 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
39 40 0.031314 ATGACCGCGAGATGCTACAG 59.969 55.000 8.23 0.00 43.27 2.74
56 57 3.302344 GCCGGCAATGGTGGTTGT 61.302 61.111 24.80 0.00 0.00 3.32
62 63 0.104671 GCAATGGTGGTTGTTGCAGT 59.895 50.000 4.60 0.00 45.57 4.40
69 70 2.258755 GTGGTTGTTGCAGTTGTTGTC 58.741 47.619 0.00 0.00 0.00 3.18
113 114 0.958876 AAAAGCGGGAATCGACCACC 60.959 55.000 0.00 0.00 42.43 4.61
144 145 5.564048 TGCAACCTACGTTTACAAAAGTT 57.436 34.783 0.00 0.00 32.92 2.66
146 147 5.859824 CAACCTACGTTTACAAAAGTTGC 57.140 39.130 0.00 0.00 32.92 4.17
151 152 4.080969 ACGTTTACAAAAGTTGCGACAA 57.919 36.364 6.90 0.00 0.00 3.18
153 154 5.808403 ACGTTTACAAAAGTTGCGACAATA 58.192 33.333 6.90 0.00 0.00 1.90
154 155 5.905181 ACGTTTACAAAAGTTGCGACAATAG 59.095 36.000 6.90 0.00 0.00 1.73
155 156 5.905181 CGTTTACAAAAGTTGCGACAATAGT 59.095 36.000 6.90 2.40 0.00 2.12
167 168 3.198068 CGACAATAGTGATTGGGGTGAG 58.802 50.000 0.00 0.00 45.83 3.51
169 170 2.301346 CAATAGTGATTGGGGTGAGCC 58.699 52.381 0.00 0.00 39.10 4.70
184 185 2.939022 GCCCGATGCTACAATCGC 59.061 61.111 1.15 0.00 46.38 4.58
191 192 0.670162 ATGCTACAATCGCCAATGGC 59.330 50.000 15.52 15.52 46.75 4.40
220 221 0.794473 GACCGACGTCAACCAATTCC 59.206 55.000 17.16 0.00 38.99 3.01
229 230 0.667184 CAACCAATTCCGCAACCAGC 60.667 55.000 0.00 0.00 40.87 4.85
237 238 2.563798 CCGCAACCAGCCATTGTGT 61.564 57.895 5.38 0.00 41.38 3.72
246 247 2.609459 CCAGCCATTGTGTTACGATCTC 59.391 50.000 0.00 0.00 0.00 2.75
248 249 2.165641 AGCCATTGTGTTACGATCTCGA 59.834 45.455 6.60 0.00 43.02 4.04
262 263 0.735471 TCTCGATCGACAAGGAGCTG 59.265 55.000 15.15 0.94 0.00 4.24
297 298 3.443925 CTCGGTGGCAGAGCTCGA 61.444 66.667 8.37 0.00 0.00 4.04
309 310 0.173708 GAGCTCGACGAACCTTGGAT 59.826 55.000 0.00 0.00 0.00 3.41
311 312 2.032620 AGCTCGACGAACCTTGGATAT 58.967 47.619 0.00 0.00 0.00 1.63
316 317 2.561569 GACGAACCTTGGATATGGTGG 58.438 52.381 0.00 0.00 34.79 4.61
334 335 0.919710 GGTTCCCTAGAAGCCATGGT 59.080 55.000 14.67 0.00 43.32 3.55
338 339 0.179073 CCCTAGAAGCCATGGTGTCG 60.179 60.000 14.67 0.00 0.00 4.35
344 345 3.134127 GCCATGGTGTCGCCCTTC 61.134 66.667 14.67 0.00 36.04 3.46
345 346 2.350895 CCATGGTGTCGCCCTTCA 59.649 61.111 2.57 0.00 36.04 3.02
367 368 2.125512 AAGCTCGACGACCATGGC 60.126 61.111 13.04 3.65 0.00 4.40
369 370 4.451150 GCTCGACGACCATGGCCA 62.451 66.667 13.04 8.56 0.00 5.36
377 378 4.344865 ACCATGGCCACGGTGTCC 62.345 66.667 25.57 4.01 33.05 4.02
379 380 4.033776 CATGGCCACGGTGTCCCT 62.034 66.667 8.16 0.00 0.00 4.20
405 406 1.001020 AGGGGAATCACGCAATGCA 60.001 52.632 5.91 0.00 0.00 3.96
414 415 2.126385 CGCAATGCACGTGCCAAT 60.126 55.556 35.72 21.83 38.86 3.16
433 434 3.853355 ATGCGAGGAAGGAGATGATTT 57.147 42.857 0.00 0.00 0.00 2.17
434 435 3.185246 TGCGAGGAAGGAGATGATTTC 57.815 47.619 0.00 0.00 0.00 2.17
436 437 2.748605 CGAGGAAGGAGATGATTTCGG 58.251 52.381 0.00 0.00 0.00 4.30
443 444 1.424638 GAGATGATTTCGGGGAGGGA 58.575 55.000 0.00 0.00 0.00 4.20
477 1353 4.555709 ACGCGGGGCACTCAACAA 62.556 61.111 12.47 0.00 0.00 2.83
502 1378 1.279271 GGAGCTTGAAGCCCAACTCTA 59.721 52.381 14.45 0.00 43.77 2.43
560 1463 2.416202 GCGGGCCAAAATGAAAGAAATG 59.584 45.455 4.39 0.00 0.00 2.32
577 1480 0.188342 ATGACCTTTGGGCCAACAGT 59.812 50.000 20.79 19.04 35.63 3.55
661 1565 3.189287 GCTCCGTCATTGACACTCAAATT 59.811 43.478 16.61 0.00 40.12 1.82
774 3072 0.378257 GCATTGCATAGGTGTCGTGG 59.622 55.000 3.15 0.00 0.00 4.94
790 3088 0.179108 GTGGACTCGTGGTATCAGCC 60.179 60.000 0.00 0.00 0.00 4.85
793 3091 2.279517 CTCGTGGTATCAGCCGGC 60.280 66.667 21.89 21.89 0.00 6.13
816 3114 1.710244 TGGAGCCCATTTCTTTCAGGA 59.290 47.619 0.00 0.00 0.00 3.86
820 3118 4.339530 GGAGCCCATTTCTTTCAGGAATAC 59.660 45.833 0.00 0.00 0.00 1.89
822 3120 4.706962 AGCCCATTTCTTTCAGGAATACAC 59.293 41.667 0.00 0.00 0.00 2.90
823 3121 4.438744 GCCCATTTCTTTCAGGAATACACG 60.439 45.833 0.00 0.00 0.00 4.49
826 3124 6.183360 CCCATTTCTTTCAGGAATACACGTAC 60.183 42.308 0.00 0.00 0.00 3.67
827 3125 6.370442 CCATTTCTTTCAGGAATACACGTACA 59.630 38.462 0.00 0.00 0.00 2.90
828 3126 7.094975 CCATTTCTTTCAGGAATACACGTACAA 60.095 37.037 0.00 0.00 0.00 2.41
829 3127 6.774354 TTCTTTCAGGAATACACGTACAAC 57.226 37.500 0.00 0.00 0.00 3.32
830 3128 6.092955 TCTTTCAGGAATACACGTACAACT 57.907 37.500 0.00 0.00 0.00 3.16
893 4912 5.010617 GGCCCAGTAAAAATGAGAAACAGAA 59.989 40.000 0.00 0.00 0.00 3.02
894 4913 6.152379 GCCCAGTAAAAATGAGAAACAGAAG 58.848 40.000 0.00 0.00 0.00 2.85
895 4914 6.016276 GCCCAGTAAAAATGAGAAACAGAAGA 60.016 38.462 0.00 0.00 0.00 2.87
896 4915 7.470009 GCCCAGTAAAAATGAGAAACAGAAGAA 60.470 37.037 0.00 0.00 0.00 2.52
897 4916 8.413229 CCCAGTAAAAATGAGAAACAGAAGAAA 58.587 33.333 0.00 0.00 0.00 2.52
945 4964 5.163693 CCATTAGTCCGTTAAACATCAACCC 60.164 44.000 0.00 0.00 0.00 4.11
1521 5555 1.300697 GGACAACTTCGTCGTGCCT 60.301 57.895 0.00 0.00 36.73 4.75
1548 5582 1.819632 GAAGTCATGCGCCGGGATT 60.820 57.895 4.18 0.00 0.00 3.01
1620 5654 4.300803 GGTTCATGGAATGCGTATACGTA 58.699 43.478 25.04 21.85 46.21 3.57
1779 5813 5.503031 CGATGATGCTGTGGAATTGTTCTAC 60.503 44.000 0.00 0.00 41.05 2.59
1800 5834 0.693049 AGATGAGGGTTGAAGGCGTT 59.307 50.000 0.00 0.00 0.00 4.84
1842 5876 2.833943 TCTTAGCCTTCTGTCTGCATCA 59.166 45.455 0.00 0.00 0.00 3.07
1859 5893 2.479566 TCAGCCGATTTTGAAGCTCT 57.520 45.000 0.00 0.00 31.93 4.09
1917 5951 1.750018 TGGCTTGGCGATGGATGTG 60.750 57.895 0.00 0.00 0.00 3.21
1922 5956 2.797087 GCTTGGCGATGGATGTGATTTG 60.797 50.000 0.00 0.00 0.00 2.32
2032 6066 6.753279 CGCTGTTACATGGAATTTGATGATTT 59.247 34.615 0.00 0.00 0.00 2.17
2223 6257 2.886523 CAACCTTGAATCAGACCAAGCA 59.113 45.455 8.29 0.00 38.65 3.91
2295 6329 3.853330 CGCCGGCTGTTCGATGTG 61.853 66.667 26.68 0.00 0.00 3.21
2467 6501 7.432545 CAGCTTTTATGAAGAATGAGCAGATTG 59.567 37.037 0.00 0.00 0.00 2.67
2500 6534 7.039152 CCCTAGAGATCTTCAATGAGATGCTAA 60.039 40.741 0.00 0.00 36.54 3.09
2586 6620 1.438651 TGCACTGCGAGGTAATGAAC 58.561 50.000 0.00 0.00 0.00 3.18
2625 6659 1.458639 AAGTTGAGCCAGCACCAAGC 61.459 55.000 0.00 0.00 46.19 4.01
2640 6674 2.035832 ACCAAGCCCAACAATTTTCTCG 59.964 45.455 0.00 0.00 0.00 4.04
2742 6776 3.913548 TTGTTGTCCAAATCCGTGATG 57.086 42.857 0.00 0.00 0.00 3.07
2745 6779 1.902938 TGTCCAAATCCGTGATGCAA 58.097 45.000 0.00 0.00 0.00 4.08
2780 6814 3.402110 TGTATGGCAGTTTCAGTGACAG 58.598 45.455 0.00 0.00 40.44 3.51
2782 6816 2.708216 TGGCAGTTTCAGTGACAGAA 57.292 45.000 0.00 0.00 30.01 3.02
2783 6817 2.288666 TGGCAGTTTCAGTGACAGAAC 58.711 47.619 0.00 0.00 30.01 3.01
2847 6881 1.640428 TAACGCAGCTGCACATAGTC 58.360 50.000 36.03 6.57 42.21 2.59
2871 6910 5.903530 CACATTACATAGCGTTTGCACATAG 59.096 40.000 0.00 0.00 46.23 2.23
2888 6927 6.479990 TGCACATAGTATCAACTTGCTCATAC 59.520 38.462 0.00 0.00 37.70 2.39
2901 6940 6.828788 ACTTGCTCATACTCATCATCAGATT 58.171 36.000 0.00 0.00 30.20 2.40
2949 6988 5.980698 ATCAGAAAATGAGCGAGTACATG 57.019 39.130 0.00 0.00 42.53 3.21
2957 6996 0.460311 AGCGAGTACATGGTGCTACC 59.540 55.000 0.00 0.00 39.22 3.18
3088 8919 1.434188 TGAGTCTCTGGCCCTTTTGA 58.566 50.000 0.00 0.00 0.00 2.69
3136 8967 2.664402 AGATTTGCTGGGCGGATTAT 57.336 45.000 0.00 0.00 0.00 1.28
3138 8969 2.624838 AGATTTGCTGGGCGGATTATTG 59.375 45.455 0.00 0.00 0.00 1.90
3139 8970 0.459489 TTTGCTGGGCGGATTATTGC 59.541 50.000 0.00 0.00 0.00 3.56
3143 8974 1.148310 CTGGGCGGATTATTGCTACG 58.852 55.000 0.00 0.00 0.00 3.51
3144 8975 0.466543 TGGGCGGATTATTGCTACGT 59.533 50.000 0.00 0.00 0.00 3.57
3146 8977 2.300723 TGGGCGGATTATTGCTACGTAT 59.699 45.455 0.00 0.00 0.00 3.06
3147 8978 3.510753 TGGGCGGATTATTGCTACGTATA 59.489 43.478 0.00 0.00 0.00 1.47
3148 8979 4.021280 TGGGCGGATTATTGCTACGTATAA 60.021 41.667 0.00 0.00 0.00 0.98
3149 8980 4.931002 GGGCGGATTATTGCTACGTATAAA 59.069 41.667 0.00 0.00 0.00 1.40
3150 8981 5.163923 GGGCGGATTATTGCTACGTATAAAC 60.164 44.000 0.00 0.00 0.00 2.01
3151 8982 5.406175 GGCGGATTATTGCTACGTATAAACA 59.594 40.000 0.00 0.00 0.00 2.83
3178 9009 9.988350 ATAACTGCAAACTGTAATATTCTTTCG 57.012 29.630 0.00 0.00 0.00 3.46
3312 9145 9.284968 TCATTTATCTACATCGATCACTGTCTA 57.715 33.333 0.00 0.00 0.00 2.59
3393 9226 4.157840 CAGTTTATCCTTGGCAACTTACCC 59.842 45.833 0.00 0.00 37.61 3.69
3408 9241 0.818852 TACCCGATCGACGCCACATA 60.819 55.000 18.66 0.00 41.07 2.29
3577 9411 1.064824 ATGATGGAAGGAGGGGAGCC 61.065 60.000 0.00 0.00 0.00 4.70
3578 9412 2.368878 ATGGAAGGAGGGGAGCCC 60.369 66.667 0.00 0.00 45.90 5.19
3589 9423 4.410400 GGAGCCCCCAACCGAGTG 62.410 72.222 0.00 0.00 34.14 3.51
3594 9428 3.953775 CCCCAACCGAGTGCACCT 61.954 66.667 14.63 0.04 0.00 4.00
3595 9429 2.669569 CCCAACCGAGTGCACCTG 60.670 66.667 14.63 6.04 0.00 4.00
3596 9430 2.111043 CCAACCGAGTGCACCTGT 59.889 61.111 14.63 5.38 0.00 4.00
3681 9515 2.225491 GAGCGATCGATTAGTCTCTGCT 59.775 50.000 21.57 0.51 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.553248 TGGTTCCAACTCTATGGTCGG 59.447 52.381 0.00 0.00 41.46 4.79
12 13 1.375396 CTCGCGGTCATGGTTCCAA 60.375 57.895 6.13 0.00 0.00 3.53
39 40 2.866726 AACAACCACCATTGCCGGC 61.867 57.895 22.73 22.73 32.47 6.13
56 57 2.223249 GCTTTCTCGACAACAACTGCAA 60.223 45.455 0.00 0.00 0.00 4.08
62 63 4.624024 CGGTTATAGCTTTCTCGACAACAA 59.376 41.667 0.00 0.00 0.00 2.83
69 70 2.218953 TGCCGGTTATAGCTTTCTCG 57.781 50.000 1.90 0.00 0.00 4.04
93 94 0.168128 GTGGTCGATTCCCGCTTTTG 59.832 55.000 0.00 0.00 38.37 2.44
100 101 1.409427 CTCTACTGGTGGTCGATTCCC 59.591 57.143 0.00 0.00 0.00 3.97
113 114 3.861131 AAACGTAGGTTGCAGCTCTACTG 60.861 47.826 19.27 16.08 41.86 2.74
144 145 1.280710 ACCCCAATCACTATTGTCGCA 59.719 47.619 0.00 0.00 40.84 5.10
146 147 3.198068 CTCACCCCAATCACTATTGTCG 58.802 50.000 0.00 0.00 40.84 4.35
167 168 2.607892 GGCGATTGTAGCATCGGGC 61.608 63.158 6.33 0.00 45.30 6.13
169 170 1.069703 CATTGGCGATTGTAGCATCGG 60.070 52.381 6.33 0.00 40.33 4.18
171 172 1.335324 GCCATTGGCGATTGTAGCATC 60.335 52.381 12.82 0.00 39.62 3.91
184 185 4.763593 CGTAGCAAACGCCATTGG 57.236 55.556 0.00 0.00 46.10 3.16
205 206 0.589223 TTGCGGAATTGGTTGACGTC 59.411 50.000 9.11 9.11 0.00 4.34
206 207 0.309612 GTTGCGGAATTGGTTGACGT 59.690 50.000 0.00 0.00 0.00 4.34
220 221 0.595588 TAACACAATGGCTGGTTGCG 59.404 50.000 0.00 0.00 44.05 4.85
229 230 4.956034 GATCGAGATCGTAACACAATGG 57.044 45.455 1.70 0.00 40.80 3.16
246 247 2.226896 CGCAGCTCCTTGTCGATCG 61.227 63.158 9.36 9.36 0.00 3.69
248 249 0.249238 GATCGCAGCTCCTTGTCGAT 60.249 55.000 0.00 0.00 38.80 3.59
262 263 1.130613 GCACTGTTGTGTCGATCGC 59.869 57.895 11.09 6.41 45.44 4.58
297 298 1.913419 ACCACCATATCCAAGGTTCGT 59.087 47.619 0.00 0.00 35.52 3.85
316 317 1.282157 ACACCATGGCTTCTAGGGAAC 59.718 52.381 13.04 0.00 0.00 3.62
344 345 3.524759 GTCGTCGAGCTTCGCGTG 61.525 66.667 5.77 1.17 40.21 5.34
345 346 4.755614 GGTCGTCGAGCTTCGCGT 62.756 66.667 16.89 0.00 40.21 6.01
350 351 2.125512 GCCATGGTCGTCGAGCTT 60.126 61.111 23.53 15.52 0.00 3.74
367 368 1.823295 CCTGATAGGGACACCGTGG 59.177 63.158 3.03 0.00 43.47 4.94
377 378 1.981495 GTGATTCCCCTCCCTGATAGG 59.019 57.143 0.00 0.00 34.30 2.57
379 380 1.717032 CGTGATTCCCCTCCCTGATA 58.283 55.000 0.00 0.00 0.00 2.15
386 387 1.031571 TGCATTGCGTGATTCCCCTC 61.032 55.000 3.84 0.00 0.00 4.30
405 406 2.031919 TTCCTCGCATTGGCACGT 59.968 55.556 0.00 0.00 41.24 4.49
414 415 2.481969 CGAAATCATCTCCTTCCTCGCA 60.482 50.000 0.00 0.00 0.00 5.10
459 1335 4.980805 TGTTGAGTGCCCCGCGTC 62.981 66.667 4.92 0.00 0.00 5.19
461 1337 3.055719 ATTGTTGAGTGCCCCGCG 61.056 61.111 0.00 0.00 0.00 6.46
477 1353 2.439156 GGCTTCAAGCTCCGCCAT 60.439 61.111 9.83 0.00 41.99 4.40
521 1397 1.756430 GCCTAGCCTTCCCTCAAAAG 58.244 55.000 0.00 0.00 0.00 2.27
560 1463 1.989706 TTACTGTTGGCCCAAAGGTC 58.010 50.000 0.00 0.00 38.73 3.85
601 1505 1.259840 GCCATGACCTGCCCAACATT 61.260 55.000 0.00 0.00 0.00 2.71
623 1527 1.003718 AGCTACAACAAGGCCGGAC 60.004 57.895 5.05 0.00 0.00 4.79
750 3048 1.039233 ACACCTATGCAATGCTGGCC 61.039 55.000 6.82 0.00 0.00 5.36
774 3072 1.065928 CCGGCTGATACCACGAGTC 59.934 63.158 0.00 0.00 0.00 3.36
802 3100 5.880054 ACGTGTATTCCTGAAAGAAATGG 57.120 39.130 0.00 0.00 34.07 3.16
849 3540 8.648698 TGGGCCTTATATATTAGTTGTACGTA 57.351 34.615 4.53 0.00 0.00 3.57
945 4964 1.564483 TAAAGGGGTAAGGGCCGTGG 61.564 60.000 0.90 0.00 0.00 4.94
1192 5226 4.139234 GTACACCTCCGGGCCGAC 62.139 72.222 30.79 12.18 35.63 4.79
1521 5555 1.078201 CGCATGACTTCAGCACGCTA 61.078 55.000 0.00 0.00 0.00 4.26
1620 5654 1.001641 GTCCACCAGGCTGCTCAAT 60.002 57.895 9.56 0.00 33.74 2.57
1779 5813 0.745845 CGCCTTCAACCCTCATCTGG 60.746 60.000 0.00 0.00 0.00 3.86
1842 5876 2.783135 TCAAGAGCTTCAAAATCGGCT 58.217 42.857 0.00 0.00 37.77 5.52
1859 5893 2.006748 CCCTGCCTACCCCAATCAA 58.993 57.895 0.00 0.00 0.00 2.57
1917 5951 2.442236 TGATTGAGCTCCCCCAAATC 57.558 50.000 12.15 13.28 0.00 2.17
1922 5956 1.213926 AGTTGATGATTGAGCTCCCCC 59.786 52.381 12.15 0.09 0.00 5.40
2032 6066 1.215173 CCCATCCTGCAAATACCCAGA 59.785 52.381 0.00 0.00 0.00 3.86
2223 6257 1.630369 TCTATCAGGCCACAAGCAACT 59.370 47.619 5.01 0.00 46.50 3.16
2295 6329 2.935201 GACCATGTCTCTGCAACTCATC 59.065 50.000 0.00 0.00 0.00 2.92
2322 6356 5.988092 GCATAAGCAGAAATCATCACTCTC 58.012 41.667 0.00 0.00 41.58 3.20
2467 6501 3.505386 TGAAGATCTCTAGGGCCTCATC 58.495 50.000 10.74 7.97 0.00 2.92
2500 6534 5.208463 AGATTTGGGCGTGTTTTTGTTAT 57.792 34.783 0.00 0.00 0.00 1.89
2604 6638 0.823356 TTGGTGCTGGCTCAACTTCC 60.823 55.000 0.00 0.00 0.00 3.46
2610 6644 4.666253 GGGCTTGGTGCTGGCTCA 62.666 66.667 0.00 0.00 42.39 4.26
2625 6659 1.669795 GCTGCCGAGAAAATTGTTGGG 60.670 52.381 0.00 0.00 0.00 4.12
2670 6704 3.429492 TGCCTTTCCATATTGCACTGAA 58.571 40.909 0.00 0.00 0.00 3.02
2676 6710 3.182341 TGCATTGCCTTTCCATATTGC 57.818 42.857 6.12 0.00 0.00 3.56
2745 6779 3.117550 TGCCATACATGTTTAGCAGGGAT 60.118 43.478 2.30 0.00 31.65 3.85
2780 6814 5.866092 CCTAGTAAACTTTCTACCGTGGTTC 59.134 44.000 0.00 0.00 0.00 3.62
2782 6816 4.322273 GCCTAGTAAACTTTCTACCGTGGT 60.322 45.833 0.00 0.00 0.00 4.16
2783 6817 4.081807 AGCCTAGTAAACTTTCTACCGTGG 60.082 45.833 0.00 0.00 0.00 4.94
2847 6881 4.077063 TGTGCAAACGCTATGTAATGTG 57.923 40.909 0.00 0.00 0.00 3.21
2871 6910 7.654923 TGATGATGAGTATGAGCAAGTTGATAC 59.345 37.037 7.16 6.10 0.00 2.24
2888 6927 9.878667 ATCTAAGAATAGCAATCTGATGATGAG 57.121 33.333 0.00 0.00 32.44 2.90
2901 6940 6.384015 TGGAACCTTCTGATCTAAGAATAGCA 59.616 38.462 9.23 0.00 35.67 3.49
2911 6950 5.768980 TTCTGATTGGAACCTTCTGATCT 57.231 39.130 0.00 0.00 0.00 2.75
2949 6988 0.386113 TTTTTGCCAACGGTAGCACC 59.614 50.000 0.00 0.00 39.10 5.01
2957 6996 3.414549 ACTGTACACTTTTTGCCAACG 57.585 42.857 0.00 0.00 0.00 4.10
3088 8919 3.069586 TGTCGTGTCTTCTCACAAATCCT 59.930 43.478 0.00 0.00 38.12 3.24
3136 8967 7.598189 TGCAGTTATTGTTTATACGTAGCAA 57.402 32.000 0.08 4.48 0.00 3.91
3138 8969 8.173130 AGTTTGCAGTTATTGTTTATACGTAGC 58.827 33.333 0.08 0.00 0.00 3.58
3139 8970 9.472995 CAGTTTGCAGTTATTGTTTATACGTAG 57.527 33.333 0.08 0.00 0.00 3.51
3178 9009 1.472480 AGGGACGCATGTATTTGCAAC 59.528 47.619 0.00 0.00 42.91 4.17
3316 9149 1.372872 AAACAAAAGCATCGGCCGC 60.373 52.632 23.51 6.64 42.56 6.53
3393 9226 2.661675 CCTAATTATGTGGCGTCGATCG 59.338 50.000 9.36 9.36 43.12 3.69
3408 9241 3.549794 GATGAGAGTTGGCAGCCTAATT 58.450 45.455 14.15 2.10 0.00 1.40
3577 9411 3.953775 AGGTGCACTCGGTTGGGG 61.954 66.667 17.98 0.00 0.00 4.96
3578 9412 2.669569 CAGGTGCACTCGGTTGGG 60.670 66.667 17.98 0.00 0.00 4.12
3579 9413 1.961277 GACAGGTGCACTCGGTTGG 60.961 63.158 17.98 1.43 0.00 3.77
3580 9414 1.227527 TGACAGGTGCACTCGGTTG 60.228 57.895 17.98 10.02 0.00 3.77
3581 9415 1.227556 GTGACAGGTGCACTCGGTT 60.228 57.895 17.98 0.00 33.57 4.44
3582 9416 2.421739 GTGACAGGTGCACTCGGT 59.578 61.111 17.98 13.32 33.57 4.69
3583 9417 2.357517 GGTGACAGGTGCACTCGG 60.358 66.667 17.98 10.12 36.53 4.63
3584 9418 2.421314 TGGTGACAGGTGCACTCG 59.579 61.111 17.98 10.59 36.53 4.18
3681 9515 5.239306 AGAACAGAACAGAATCGCATCAAAA 59.761 36.000 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.