Multiple sequence alignment - TraesCS3A01G242100

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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 TraesCS3A01G242100 chr3A 100.000 6991 0 0 1 6991 454510022 454517012 0.000000e+00 12911.0
1 TraesCS3A01G242100 chr3D 97.358 2839 46 13 4172 6991 337307525 337310353 0.000000e+00 4800.0
2 TraesCS3A01G242100 chr3D 92.657 3146 113 48 1 3063 337303197 337306307 0.000000e+00 4421.0
3 TraesCS3A01G242100 chr3D 95.819 1124 23 7 3055 4172 337306365 337307470 0.000000e+00 1794.0
4 TraesCS3A01G242100 chr3B 95.701 2861 72 27 4172 6991 434984602 434987452 0.000000e+00 4554.0
5 TraesCS3A01G242100 chr3B 90.148 2223 86 33 1 2129 434980008 434982191 0.000000e+00 2769.0
6 TraesCS3A01G242100 chr3B 95.463 1124 22 6 3055 4172 434983422 434984522 0.000000e+00 1766.0
7 TraesCS3A01G242100 chr3B 96.820 912 22 4 2155 3063 434982457 434983364 0.000000e+00 1517.0
8 TraesCS3A01G242100 chrUn 87.629 97 4 5 6729 6823 146902797 146902887 9.590000e-19 106.0
9 TraesCS3A01G242100 chrUn 87.629 97 4 5 6729 6823 146930260 146930350 9.590000e-19 106.0
10 TraesCS3A01G242100 chrUn 88.172 93 3 5 6733 6823 154087980 154088066 3.450000e-18 104.0
11 TraesCS3A01G242100 chrUn 86.598 97 5 5 6729 6823 147063450 147063540 4.460000e-17 100.0
12 TraesCS3A01G242100 chrUn 86.598 97 5 5 6729 6823 147088682 147088772 4.460000e-17 100.0
13 TraesCS3A01G242100 chrUn 87.234 94 4 5 6732 6823 210791169 210791082 4.460000e-17 100.0
14 TraesCS3A01G242100 chr6D 88.172 93 4 3 6732 6823 392273216 392273130 3.450000e-18 104.0
15 TraesCS3A01G242100 chr6D 84.158 101 6 4 3067 3166 41929132 41929041 9.660000e-14 89.8
16 TraesCS3A01G242100 chr6A 82.653 98 8 3 3067 3164 52399501 52399413 2.090000e-10 78.7
17 TraesCS3A01G242100 chr5B 88.136 59 7 0 3062 3120 74996098 74996156 3.500000e-08 71.3
18 TraesCS3A01G242100 chr1D 86.567 67 6 3 6917 6982 116907616 116907552 3.500000e-08 71.3
19 TraesCS3A01G242100 chr1D 100.000 33 0 0 3088 3120 283621941 283621973 2.110000e-05 62.1
20 TraesCS3A01G242100 chr2A 97.561 41 0 1 3081 3120 611102352 611102392 1.260000e-07 69.4
21 TraesCS3A01G242100 chr7D 86.667 60 6 2 6921 6979 551607828 551607770 1.630000e-06 65.8
22 TraesCS3A01G242100 chr5D 84.848 66 6 3 6922 6986 302169091 302169153 5.850000e-06 63.9


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 TraesCS3A01G242100 chr3A 454510022 454517012 6990 False 12911.000000 12911 100.000 1 6991 1 chr3A.!!$F1 6990
1 TraesCS3A01G242100 chr3D 337303197 337310353 7156 False 3671.666667 4800 95.278 1 6991 3 chr3D.!!$F1 6990
2 TraesCS3A01G242100 chr3B 434980008 434987452 7444 False 2651.500000 4554 94.533 1 6991 4 chr3B.!!$F1 6990


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
377 391 0.322648 CTGGCCATGTGACTGACTGA 59.677 55.000 5.51 0.00 0.0 3.41 F
714 786 0.467290 GCTCCTTGTGTTTGGGTGGA 60.467 55.000 0.00 0.00 0.0 4.02 F
1988 2121 1.132640 GCTACCTTCTTTGTGCGCG 59.867 57.895 0.00 0.00 0.0 6.86 F
1990 2123 0.716108 CTACCTTCTTTGTGCGCGAG 59.284 55.000 12.10 0.00 0.0 5.03 F
3223 3666 3.555966 AGAAACTTGTCCTTTGTCCCAG 58.444 45.455 0.00 0.00 0.0 4.45 F
3580 4027 2.084546 GATTTTGGGCTAGCACGAGTT 58.915 47.619 18.24 3.73 0.0 3.01 F
4134 4581 2.502130 GCAAACCCTTCTAGAGCCTACT 59.498 50.000 0.00 0.00 0.0 2.57 F
4136 4583 3.476485 AACCCTTCTAGAGCCTACTGT 57.524 47.619 0.00 0.00 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1308 1429 0.108615 CAGTTGGACTCCGTAGCTGG 60.109 60.000 0.00 0.0 0.00 4.85 R
1991 2124 0.173481 TTCCGTGAGCTTCTGGATCG 59.827 55.000 3.01 0.0 32.20 3.69 R
2962 3335 1.030488 AGCAAAGCATCAGCAGCGAT 61.030 50.000 0.00 0.0 45.49 4.58 R
3580 4027 2.161855 GTGGGAGTGTCATTGAATGCA 58.838 47.619 0.00 0.0 0.00 3.96 R
5064 5592 3.502119 CCTTCCCTCCATTTTCCTCCAAA 60.502 47.826 0.00 0.0 0.00 3.28 R
5357 5886 1.677576 TCAGCAAGCAAAGTTGAGTGG 59.322 47.619 0.00 0.0 0.00 4.00 R
5848 6378 0.679640 TGCTACATCGGCTTTTGGGG 60.680 55.000 0.00 0.0 0.00 4.96 R
6183 6716 2.996249 TCCTTGGCAGCTAGATCAAG 57.004 50.000 0.00 0.0 37.09 3.02 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
117 122 4.649692 ACCTTATCCTGCTGCTATGAATG 58.350 43.478 0.00 0.00 0.00 2.67
172 177 4.509970 CACCAACCGATAAGATAATTGCGA 59.490 41.667 0.00 0.00 0.00 5.10
173 178 4.510340 ACCAACCGATAAGATAATTGCGAC 59.490 41.667 0.00 0.00 0.00 5.19
246 255 3.680937 CGAACCGCCTACTCATTTTTACA 59.319 43.478 0.00 0.00 0.00 2.41
247 256 4.435121 CGAACCGCCTACTCATTTTTACAC 60.435 45.833 0.00 0.00 0.00 2.90
248 257 4.281898 ACCGCCTACTCATTTTTACACT 57.718 40.909 0.00 0.00 0.00 3.55
249 258 4.000988 ACCGCCTACTCATTTTTACACTG 58.999 43.478 0.00 0.00 0.00 3.66
250 259 3.181510 CCGCCTACTCATTTTTACACTGC 60.182 47.826 0.00 0.00 0.00 4.40
251 260 3.684788 CGCCTACTCATTTTTACACTGCT 59.315 43.478 0.00 0.00 0.00 4.24
252 261 4.436050 CGCCTACTCATTTTTACACTGCTG 60.436 45.833 0.00 0.00 0.00 4.41
253 262 4.455877 GCCTACTCATTTTTACACTGCTGT 59.544 41.667 0.00 0.00 0.00 4.40
254 263 5.642063 GCCTACTCATTTTTACACTGCTGTA 59.358 40.000 0.00 0.00 0.00 2.74
255 264 6.402226 GCCTACTCATTTTTACACTGCTGTAC 60.402 42.308 0.00 0.00 32.28 2.90
256 265 6.874134 CCTACTCATTTTTACACTGCTGTACT 59.126 38.462 0.00 0.00 32.28 2.73
257 266 8.033038 CCTACTCATTTTTACACTGCTGTACTA 58.967 37.037 0.00 0.00 32.28 1.82
258 267 7.653767 ACTCATTTTTACACTGCTGTACTAC 57.346 36.000 0.00 0.00 32.28 2.73
273 287 3.949754 TGTACTACTACTCCGTTGGGATG 59.050 47.826 0.00 0.00 42.83 3.51
275 289 2.024655 ACTACTACTCCGTTGGGATGGA 60.025 50.000 0.00 0.00 42.83 3.41
276 290 1.946984 ACTACTCCGTTGGGATGGAA 58.053 50.000 0.00 0.00 42.83 3.53
277 291 2.262637 ACTACTCCGTTGGGATGGAAA 58.737 47.619 0.00 0.00 42.83 3.13
278 292 2.640826 ACTACTCCGTTGGGATGGAAAA 59.359 45.455 0.00 0.00 42.83 2.29
279 293 2.668144 ACTCCGTTGGGATGGAAAAA 57.332 45.000 0.00 0.00 42.83 1.94
280 294 2.514803 ACTCCGTTGGGATGGAAAAAG 58.485 47.619 0.00 0.00 42.83 2.27
281 295 2.107552 ACTCCGTTGGGATGGAAAAAGA 59.892 45.455 0.00 0.00 42.83 2.52
349 363 2.050918 TCCACGCACATCCCCATATTA 58.949 47.619 0.00 0.00 0.00 0.98
350 364 2.642311 TCCACGCACATCCCCATATTAT 59.358 45.455 0.00 0.00 0.00 1.28
374 388 2.042831 GGCTGGCCATGTGACTGAC 61.043 63.158 5.51 0.00 35.81 3.51
375 389 1.002868 GCTGGCCATGTGACTGACT 60.003 57.895 5.51 0.00 0.00 3.41
376 390 1.303799 GCTGGCCATGTGACTGACTG 61.304 60.000 5.51 0.00 0.00 3.51
377 391 0.322648 CTGGCCATGTGACTGACTGA 59.677 55.000 5.51 0.00 0.00 3.41
378 392 0.986527 TGGCCATGTGACTGACTGAT 59.013 50.000 0.00 0.00 0.00 2.90
379 393 1.352017 TGGCCATGTGACTGACTGATT 59.648 47.619 0.00 0.00 0.00 2.57
380 394 2.224843 TGGCCATGTGACTGACTGATTT 60.225 45.455 0.00 0.00 0.00 2.17
422 436 2.731968 CGCAAGCTGAACAAAAGTGTGT 60.732 45.455 0.00 0.00 38.27 3.72
423 437 3.253230 GCAAGCTGAACAAAAGTGTGTT 58.747 40.909 0.00 0.00 44.38 3.32
424 438 4.420168 GCAAGCTGAACAAAAGTGTGTTA 58.580 39.130 0.00 0.00 41.78 2.41
564 581 2.408050 GGATCTCCACGAAATCATCCG 58.592 52.381 0.00 0.00 35.64 4.18
566 583 0.527600 TCTCCACGAAATCATCCGCG 60.528 55.000 0.00 0.00 0.00 6.46
570 587 2.242670 CGAAATCATCCGCGTCGC 59.757 61.111 7.29 7.29 0.00 5.19
572 589 2.882366 GAAATCATCCGCGTCGCCC 61.882 63.158 12.44 0.00 0.00 6.13
618 639 3.243068 GCGGCTGTCAAAAGAAAGAAAGA 60.243 43.478 0.00 0.00 0.00 2.52
684 729 2.874010 ATCGCTCGCACCAGACGAAG 62.874 60.000 0.00 0.00 39.39 3.79
688 733 2.125912 CGCACCAGACGAAGGAGG 60.126 66.667 0.00 0.00 0.00 4.30
712 784 0.954452 GAGCTCCTTGTGTTTGGGTG 59.046 55.000 0.87 0.00 0.00 4.61
713 785 0.468029 AGCTCCTTGTGTTTGGGTGG 60.468 55.000 0.00 0.00 0.00 4.61
714 786 0.467290 GCTCCTTGTGTTTGGGTGGA 60.467 55.000 0.00 0.00 0.00 4.02
715 787 1.823250 GCTCCTTGTGTTTGGGTGGAT 60.823 52.381 0.00 0.00 0.00 3.41
731 803 1.291184 GGATTTGCCCTTTGCGTTGC 61.291 55.000 0.00 0.00 45.60 4.17
1015 1087 4.147449 CGATGCAGCCGGACCAGA 62.147 66.667 5.05 0.00 0.00 3.86
1162 1251 2.017559 ATGAACCTACCTCGCCTCGC 62.018 60.000 0.00 0.00 0.00 5.03
1260 1377 3.055094 TGGTATCCTGCAACTTCTCTTCC 60.055 47.826 0.00 0.00 0.00 3.46
1308 1429 6.103997 TCCGTATAGTTGAGGTTGTTGATTC 58.896 40.000 0.00 0.00 0.00 2.52
1314 1435 4.072131 GTTGAGGTTGTTGATTCCAGCTA 58.928 43.478 0.00 0.00 0.00 3.32
1335 1456 3.665190 ACGGAGTCCAACTGAATTCTTC 58.335 45.455 10.49 0.00 29.74 2.87
1422 1543 8.561738 TCTCAATTATTAACACAAGGTTCTCC 57.438 34.615 0.00 0.00 40.96 3.71
1870 1997 9.077885 GATATAGATGGTTTTATGCCCAAGAAA 57.922 33.333 0.00 0.00 33.66 2.52
1908 2035 2.203625 TTGGGCCCTTTGTGCTCC 60.204 61.111 25.70 0.00 0.00 4.70
1936 2063 2.680339 GCTGTTTTCCTCATAGCTGGAC 59.320 50.000 0.00 0.00 31.24 4.02
1983 2116 4.262938 GGGAGTTGTAGCTACCTTCTTTGT 60.263 45.833 21.01 0.00 36.54 2.83
1988 2121 1.132640 GCTACCTTCTTTGTGCGCG 59.867 57.895 0.00 0.00 0.00 6.86
1989 2122 1.289109 GCTACCTTCTTTGTGCGCGA 61.289 55.000 12.10 0.00 0.00 5.87
1990 2123 0.716108 CTACCTTCTTTGTGCGCGAG 59.284 55.000 12.10 0.00 0.00 5.03
2029 2162 4.441792 GGAATCCAACTTTTTGTGCTGTT 58.558 39.130 0.00 0.00 0.00 3.16
2030 2163 4.507756 GGAATCCAACTTTTTGTGCTGTTC 59.492 41.667 0.00 0.00 0.00 3.18
2107 2240 5.232463 TGTTCGGTATGAAGTGACCTTTAC 58.768 41.667 0.00 0.00 37.23 2.01
2118 2251 7.038659 TGAAGTGACCTTTACACAAAATTTGG 58.961 34.615 10.71 2.05 40.25 3.28
2225 2598 7.441836 CCTATGTGGCTAGTATGTGTTATCAA 58.558 38.462 0.00 0.00 0.00 2.57
2386 2759 4.233789 TGTGTGTCTTTTGTTTCAGTTGC 58.766 39.130 0.00 0.00 0.00 4.17
2644 3017 4.956700 TCCTCCGTGAGATCAAATTACTCT 59.043 41.667 0.00 0.00 0.00 3.24
2906 3279 5.103000 GCATACAGTTCTCTATTGTCGTGT 58.897 41.667 0.00 0.00 0.00 4.49
3078 3521 3.623960 GGCACTATACGCACATTAACCAA 59.376 43.478 0.00 0.00 0.00 3.67
3083 3526 7.274686 GCACTATACGCACATTAACCAAAATTT 59.725 33.333 0.00 0.00 0.00 1.82
3124 3567 3.681909 CCTAGAGCCTAGGCCCTAG 57.318 63.158 34.45 34.45 45.34 3.02
3207 3650 3.630312 TGGCCGCCATATTTTAGAGAAAC 59.370 43.478 8.43 0.00 0.00 2.78
3223 3666 3.555966 AGAAACTTGTCCTTTGTCCCAG 58.444 45.455 0.00 0.00 0.00 4.45
3258 3701 6.564709 TCTTGTTGATCATTTGTCTTCTGG 57.435 37.500 0.00 0.00 0.00 3.86
3479 3926 9.685276 TTGTCTGTGATCTGACCAATATTTATT 57.315 29.630 10.10 0.00 40.31 1.40
3580 4027 2.084546 GATTTTGGGCTAGCACGAGTT 58.915 47.619 18.24 3.73 0.00 3.01
3838 4285 6.371548 TGTTGTGTTTGCTAGGATATCTTGTC 59.628 38.462 2.05 0.00 0.00 3.18
4134 4581 2.502130 GCAAACCCTTCTAGAGCCTACT 59.498 50.000 0.00 0.00 0.00 2.57
4135 4582 3.680196 GCAAACCCTTCTAGAGCCTACTG 60.680 52.174 0.00 0.00 0.00 2.74
4136 4583 3.476485 AACCCTTCTAGAGCCTACTGT 57.524 47.619 0.00 0.00 0.00 3.55
4137 4584 3.476485 ACCCTTCTAGAGCCTACTGTT 57.524 47.619 0.00 0.00 0.00 3.16
4138 4585 3.792515 ACCCTTCTAGAGCCTACTGTTT 58.207 45.455 0.00 0.00 0.00 2.83
4139 4586 3.515901 ACCCTTCTAGAGCCTACTGTTTG 59.484 47.826 0.00 0.00 0.00 2.93
4140 4587 3.769844 CCCTTCTAGAGCCTACTGTTTGA 59.230 47.826 0.00 0.00 0.00 2.69
4141 4588 4.142049 CCCTTCTAGAGCCTACTGTTTGAG 60.142 50.000 0.00 0.00 0.00 3.02
4425 4952 4.261197 GGGTACGCTTTTCCATTCATGATC 60.261 45.833 2.05 0.00 0.00 2.92
4664 5191 8.100508 AGGCAAGTGTTTCTAGATAAAACTTC 57.899 34.615 14.97 11.64 37.48 3.01
4966 5494 6.479331 GGTTTTTACCATAAGATCTCCTCGAC 59.521 42.308 0.00 0.00 0.00 4.20
5357 5886 4.577693 TGGCATGATAATTTCAGAGACTGC 59.422 41.667 0.00 0.00 37.89 4.40
5848 6378 2.362077 CCTATTACATGCCAAAGGGTGC 59.638 50.000 0.00 0.00 36.17 5.01
6183 6716 1.200948 GCAAAGACAACATCCTGCCTC 59.799 52.381 0.00 0.00 32.72 4.70
6577 7110 0.533308 GTTGGCTCAACCGTGGTACA 60.533 55.000 6.76 0.00 43.94 2.90
6589 7122 5.680594 ACCGTGGTACATATTAAACCAGA 57.319 39.130 0.00 0.00 43.73 3.86
6657 7190 9.309516 CTGATCATTTCCAAATTAACTGAATGG 57.690 33.333 0.00 0.00 0.00 3.16
6681 7227 6.127619 GGCTAGCCTTGTCATAAAAGTTTGAT 60.128 38.462 27.17 0.00 0.00 2.57
6682 7228 6.749118 GCTAGCCTTGTCATAAAAGTTTGATG 59.251 38.462 2.29 6.61 0.00 3.07
6712 7272 8.122330 TCAATATATCAACGTTTGCTTCATCAC 58.878 33.333 0.00 0.00 0.00 3.06
6719 7279 6.416455 TCAACGTTTGCTTCATCACAAAATAC 59.584 34.615 0.00 0.00 37.50 1.89
6737 7302 8.380743 CAAAATACATTTGGTATCTGTTCACG 57.619 34.615 0.00 0.00 43.85 4.35
6750 7315 9.477484 GGTATCTGTTCACGAATATAAGATGTT 57.523 33.333 0.00 0.00 0.00 2.71
6815 7381 6.561737 TGAGTGAACAAACACACTAAAACA 57.438 33.333 0.00 0.00 45.54 2.83
6890 7458 6.708949 GGGAGTAGAACTTGTATTTGTGAACA 59.291 38.462 0.00 0.00 0.00 3.18
6904 7472 2.622942 TGTGAACAAAGGGAGTGCATTC 59.377 45.455 0.00 0.00 0.00 2.67
6938 7507 0.396139 ATACTAGAACGGTGGGCGGA 60.396 55.000 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 6.017109 TCCATCTTCTTTTTCTTTCCTCGTTG 60.017 38.462 0.00 0.00 0.00 4.10
9 10 6.372659 TCATCCATCTTCTTTTTCTTTCCTCG 59.627 38.462 0.00 0.00 0.00 4.63
18 19 8.306761 GTGGTGTTAATCATCCATCTTCTTTTT 58.693 33.333 0.00 0.00 32.83 1.94
59 60 2.610374 TGACGCCAAATAACCTAATCGC 59.390 45.455 0.00 0.00 0.00 4.58
117 122 4.134379 TCTTCCATCTCATCTCAACAGC 57.866 45.455 0.00 0.00 0.00 4.40
172 177 2.029290 GGGCCGTGATACGATAAGATGT 60.029 50.000 2.52 0.00 46.05 3.06
173 178 2.607187 GGGCCGTGATACGATAAGATG 58.393 52.381 2.52 0.00 46.05 2.90
246 255 3.347077 ACGGAGTAGTAGTACAGCAGT 57.653 47.619 10.33 5.72 41.94 4.40
247 256 3.181499 CCAACGGAGTAGTAGTACAGCAG 60.181 52.174 10.33 5.16 45.00 4.24
248 257 2.751259 CCAACGGAGTAGTAGTACAGCA 59.249 50.000 10.33 0.00 45.00 4.41
249 258 2.098770 CCCAACGGAGTAGTAGTACAGC 59.901 54.545 10.33 1.85 45.00 4.40
250 259 3.614092 TCCCAACGGAGTAGTAGTACAG 58.386 50.000 10.33 3.88 45.00 2.74
251 260 3.719268 TCCCAACGGAGTAGTAGTACA 57.281 47.619 10.33 0.00 45.00 2.90
252 261 3.317430 CCATCCCAACGGAGTAGTAGTAC 59.683 52.174 0.00 0.00 45.00 2.73
253 262 3.202818 TCCATCCCAACGGAGTAGTAGTA 59.797 47.826 0.00 0.00 45.00 1.82
254 263 2.024655 TCCATCCCAACGGAGTAGTAGT 60.025 50.000 0.00 0.00 45.00 2.73
255 264 2.662866 TCCATCCCAACGGAGTAGTAG 58.337 52.381 0.00 0.00 45.00 2.57
256 265 2.832643 TCCATCCCAACGGAGTAGTA 57.167 50.000 0.00 0.00 45.00 1.82
257 266 1.946984 TTCCATCCCAACGGAGTAGT 58.053 50.000 0.00 0.00 45.00 2.73
258 267 3.343941 TTTTCCATCCCAACGGAGTAG 57.656 47.619 0.00 0.00 45.00 2.57
294 308 1.247567 ATCTCAACCCAACGGCTTTG 58.752 50.000 0.00 0.00 34.63 2.77
374 388 6.251376 GCTTATTTTGTGGCGACTTAAATCAG 59.749 38.462 12.92 12.64 0.00 2.90
375 389 6.090129 GCTTATTTTGTGGCGACTTAAATCA 58.910 36.000 12.92 5.36 0.00 2.57
376 390 6.033513 GTGCTTATTTTGTGGCGACTTAAATC 59.966 38.462 12.92 4.27 0.00 2.17
377 391 5.861787 GTGCTTATTTTGTGGCGACTTAAAT 59.138 36.000 13.66 13.66 0.00 1.40
378 392 5.216648 GTGCTTATTTTGTGGCGACTTAAA 58.783 37.500 0.00 1.61 0.00 1.52
379 393 4.611807 CGTGCTTATTTTGTGGCGACTTAA 60.612 41.667 0.00 0.00 0.00 1.85
380 394 3.120477 CGTGCTTATTTTGTGGCGACTTA 60.120 43.478 0.00 0.00 0.00 2.24
554 571 2.626455 GGCGACGCGGATGATTTC 59.374 61.111 14.61 0.00 0.00 2.17
564 581 3.576356 CCATGTGATGGGCGACGC 61.576 66.667 12.43 12.43 46.86 5.19
618 639 5.407502 ACGTTAAAAAGAAGTGCTTGCTTT 58.592 33.333 0.00 0.00 36.80 3.51
712 784 1.291184 GCAACGCAAAGGGCAAATCC 61.291 55.000 0.00 0.00 45.17 3.01
713 785 1.291184 GGCAACGCAAAGGGCAAATC 61.291 55.000 0.00 0.00 45.17 2.17
714 786 1.301637 GGCAACGCAAAGGGCAAAT 60.302 52.632 0.00 0.00 45.17 2.32
715 787 2.107953 GGCAACGCAAAGGGCAAA 59.892 55.556 0.00 0.00 45.17 3.68
916 988 1.956477 GAGGGAGAGATCTCTGTCTGC 59.044 57.143 29.81 14.29 42.48 4.26
1015 1087 2.348998 CTTCCTCCGCTGCTGGTT 59.651 61.111 9.66 0.00 0.00 3.67
1162 1251 6.084326 TCAAAAAGAAAAAGAATCCTCCCG 57.916 37.500 0.00 0.00 0.00 5.14
1215 1332 4.736126 TGGCAAGAGATAATTCTGACGA 57.264 40.909 0.00 0.00 30.30 4.20
1260 1377 0.249398 AGGAATTGTCGACGGAAGGG 59.751 55.000 11.62 0.00 0.00 3.95
1308 1429 0.108615 CAGTTGGACTCCGTAGCTGG 60.109 60.000 0.00 0.00 0.00 4.85
1314 1435 3.665190 GAAGAATTCAGTTGGACTCCGT 58.335 45.455 8.44 0.00 46.62 4.69
1335 1456 7.274250 CCTTTTTCGCAATAAGAAATGGAAGAG 59.726 37.037 0.00 0.00 37.43 2.85
1485 1606 8.472007 TTTATAGAGGGACAAAGCAAGAAAAA 57.528 30.769 0.00 0.00 0.00 1.94
1539 1660 7.265673 TGAGTATTCAACTACTAGCATGGAAC 58.734 38.462 0.00 0.00 39.07 3.62
1870 1997 7.068716 GCCCAAGAATGACTATTTAAGGATGTT 59.931 37.037 0.00 0.00 0.00 2.71
1908 2035 4.553547 GCTATGAGGAAAACAGCGCTTATG 60.554 45.833 7.50 0.00 0.00 1.90
1936 2063 0.454957 CGATGCAAAACTCCTTGGCG 60.455 55.000 0.00 0.00 0.00 5.69
1976 2109 1.955529 GATCGCTCGCGCACAAAGAA 61.956 55.000 8.75 0.00 39.59 2.52
1983 2116 4.128388 TTCTGGATCGCTCGCGCA 62.128 61.111 8.75 0.00 39.59 6.09
1989 2122 1.140589 CGTGAGCTTCTGGATCGCT 59.859 57.895 0.00 0.00 38.54 4.93
1990 2123 1.880340 CCGTGAGCTTCTGGATCGC 60.880 63.158 0.00 0.00 37.48 4.58
1991 2124 0.173481 TTCCGTGAGCTTCTGGATCG 59.827 55.000 3.01 0.00 32.20 3.69
2004 2137 2.794350 GCACAAAAAGTTGGATTCCGTG 59.206 45.455 0.00 0.00 39.22 4.94
2107 2240 6.073657 CCTCAATACAACAGCCAAATTTTGTG 60.074 38.462 8.26 3.72 34.15 3.33
2142 2275 4.293671 CCAGGTTTTCCGCCCCCA 62.294 66.667 0.00 0.00 46.35 4.96
2145 2278 0.540133 TAAACCCAGGTTTTCCGCCC 60.540 55.000 19.35 0.00 44.84 6.13
2148 2281 3.887110 AGAAGTTAAACCCAGGTTTTCCG 59.113 43.478 19.35 0.00 44.84 4.30
2218 2591 4.862371 TGGATAAACCCCAGGTTGATAAC 58.138 43.478 0.00 0.00 46.20 1.89
2225 2598 2.364190 TCCTTTGGATAAACCCCAGGT 58.636 47.619 0.00 0.00 37.81 4.00
2386 2759 0.447801 CGCAATGGAGAACCTTTCCG 59.552 55.000 0.00 0.00 37.54 4.30
2644 3017 6.956435 ACTATATCAGGATGTCTCAATAGGCA 59.044 38.462 0.00 0.00 42.75 4.75
2879 3252 7.649705 CACGACAATAGAGAACTGTATGCTAAT 59.350 37.037 0.00 0.00 0.00 1.73
2927 3300 8.694696 AGGGTATGGATAAAATACCTACTCCTA 58.305 37.037 11.35 0.00 46.01 2.94
2962 3335 1.030488 AGCAAAGCATCAGCAGCGAT 61.030 50.000 0.00 0.00 45.49 4.58
3078 3521 3.865164 GCAAAATGCCTAGCGCTAAATTT 59.135 39.130 19.37 19.25 37.42 1.82
3083 3526 2.613026 TAGCAAAATGCCTAGCGCTA 57.387 45.000 17.75 17.75 46.52 4.26
3207 3650 4.911390 ACTAATCTGGGACAAAGGACAAG 58.089 43.478 0.00 0.00 38.70 3.16
3258 3701 8.392612 CAATGAAAGGCCAAATATCAAAATCAC 58.607 33.333 5.01 0.00 0.00 3.06
3479 3926 7.134163 CGATGATAAACATTAGCTGCAATCAA 58.866 34.615 1.02 0.00 39.56 2.57
3580 4027 2.161855 GTGGGAGTGTCATTGAATGCA 58.838 47.619 0.00 0.00 0.00 3.96
3726 4173 6.283694 TCTAGTAGCAACATAATCCTGCAAG 58.716 40.000 0.00 0.00 38.58 4.01
3838 4285 4.730613 GCATGTTTATGTGGAAAGTAGCGG 60.731 45.833 0.00 0.00 36.65 5.52
4048 4495 8.969260 TCTAGTAGTCGTATGAACCTTGAATA 57.031 34.615 0.00 0.00 0.00 1.75
4134 4581 6.428465 TCTGTAGTTGTGAAAACACTCAAACA 59.572 34.615 0.00 0.00 0.00 2.83
4135 4582 6.837992 TCTGTAGTTGTGAAAACACTCAAAC 58.162 36.000 0.00 0.00 0.00 2.93
4136 4583 6.653320 ACTCTGTAGTTGTGAAAACACTCAAA 59.347 34.615 0.00 0.00 29.00 2.69
4137 4584 6.170506 ACTCTGTAGTTGTGAAAACACTCAA 58.829 36.000 0.00 0.00 29.00 3.02
4138 4585 5.730550 ACTCTGTAGTTGTGAAAACACTCA 58.269 37.500 0.00 0.00 29.00 3.41
4139 4586 7.948278 ATACTCTGTAGTTGTGAAAACACTC 57.052 36.000 0.00 0.00 37.15 3.51
4140 4587 9.424319 CATATACTCTGTAGTTGTGAAAACACT 57.576 33.333 0.00 0.00 37.15 3.55
4141 4588 8.169268 GCATATACTCTGTAGTTGTGAAAACAC 58.831 37.037 0.00 0.00 37.15 3.32
4425 4952 5.940617 TGGATACCTTACTTTGGATCATGG 58.059 41.667 0.00 0.00 0.00 3.66
4664 5191 9.150348 AGTTTTTAACACCTGTTTTTGAATCTG 57.850 29.630 0.00 0.00 39.31 2.90
4707 5234 6.569035 CGCCTGATTATGATGTGCACATAAAT 60.569 38.462 31.45 26.90 41.42 1.40
5064 5592 3.502119 CCTTCCCTCCATTTTCCTCCAAA 60.502 47.826 0.00 0.00 0.00 3.28
5357 5886 1.677576 TCAGCAAGCAAAGTTGAGTGG 59.322 47.619 0.00 0.00 0.00 4.00
5524 6053 8.996655 AGGATATATACATGTCATATTGGTGCT 58.003 33.333 0.00 3.46 0.00 4.40
5848 6378 0.679640 TGCTACATCGGCTTTTGGGG 60.680 55.000 0.00 0.00 0.00 4.96
6183 6716 2.996249 TCCTTGGCAGCTAGATCAAG 57.004 50.000 0.00 0.00 37.09 3.02
6589 7122 9.256228 TGTTTCTACTGTTCCTCTATATCAACT 57.744 33.333 0.00 0.00 0.00 3.16
6657 7190 6.254281 TCAAACTTTTATGACAAGGCTAGC 57.746 37.500 6.04 6.04 0.00 3.42
6681 7227 7.609760 AGCAAACGTTGATATATTGACTTCA 57.390 32.000 0.00 0.00 0.00 3.02
6682 7228 8.175069 TGAAGCAAACGTTGATATATTGACTTC 58.825 33.333 0.00 11.48 36.21 3.01
6712 7272 8.233868 TCGTGAACAGATACCAAATGTATTTTG 58.766 33.333 0.00 0.00 40.31 2.44
6862 7430 4.189231 CAAATACAAGTTCTACTCCCCGG 58.811 47.826 0.00 0.00 0.00 5.73
6890 7458 3.222603 AGTTTTCGAATGCACTCCCTTT 58.777 40.909 0.00 0.00 0.00 3.11
6904 7472 8.371053 CCGTTCTAGTATTTGACTAAGTTTTCG 58.629 37.037 0.00 0.00 40.23 3.46



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

AutoCloner maintained by Alex Coulton.