Multiple sequence alignment - TraesCS1D01G072600

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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 TraesCS1D01G072600 chr1D 100.000 3490 0 0 1 3490 52979009 52975520 0.000000e+00 6445.0
1 TraesCS1D01G072600 chr1B 92.124 2679 90 44 883 3490 84981478 84978850 0.000000e+00 3666.0
2 TraesCS1D01G072600 chr1A 94.772 1970 48 19 1555 3483 52574523 52572568 0.000000e+00 3016.0
3 TraesCS1D01G072600 chr1A 90.511 1507 97 19 1 1491 52576447 52574971 0.000000e+00 1949.0
4 TraesCS1D01G072600 chr2D 81.720 186 33 1 259 444 430002496 430002680 1.680000e-33 154.0
5 TraesCS1D01G072600 chr7D 82.707 133 19 3 314 444 620139976 620140106 7.920000e-22 115.0
6 TraesCS1D01G072600 chr5A 77.717 184 34 7 259 440 601407129 601406951 4.760000e-19 106.0
7 TraesCS1D01G072600 chr3A 82.353 119 17 3 326 444 505670166 505670052 2.220000e-17 100.0
8 TraesCS1D01G072600 chr3D 83.178 107 16 2 349 453 509695017 509695123 2.870000e-16 97.1
9 TraesCS1D01G072600 chr4A 95.745 47 2 0 1645 1691 695467810 695467764 3.740000e-10 76.8


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 TraesCS1D01G072600 chr1D 52975520 52979009 3489 True 6445.0 6445 100.0000 1 3490 1 chr1D.!!$R1 3489
1 TraesCS1D01G072600 chr1B 84978850 84981478 2628 True 3666.0 3666 92.1240 883 3490 1 chr1B.!!$R1 2607
2 TraesCS1D01G072600 chr1A 52572568 52576447 3879 True 2482.5 3016 92.6415 1 3483 2 chr1A.!!$R1 3482

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
384 385 0.027979 CCAGTTCAATGTATGCCGCG 59.972 55.0 0.0 0.0 0.0 6.46 F
1150 1161 0.031111 TGATGTAGGTGGAGGGAGGG 60.031 60.0 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1610 2016 0.487325 TGGAGAGGAAGGAGTGGTCA 59.513 55.0 0.0 0.0 0.0 4.02 R
2559 3001 0.321919 CGGCGATGGATGGATGGATT 60.322 55.0 0.0 0.0 0.0 3.01 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
28 29 9.877178 AGAAATGATATAACGAATGAGTATCCC 57.123 33.333 0.00 0.00 0.00 3.85
64 65 2.277084 GTTATCGTGGTGGGTTGCTAG 58.723 52.381 0.00 0.00 0.00 3.42
91 92 2.481449 CGCATAGGTTAGCTCGAGGTTT 60.481 50.000 23.90 8.91 0.00 3.27
111 112 5.399013 GTTTTGGTTCGAATCACCTTATGG 58.601 41.667 11.46 0.00 35.07 2.74
148 149 8.574196 TTTCTAATTAAGTTGTGCTCTTTTGC 57.426 30.769 0.00 0.00 0.00 3.68
150 151 8.615878 TCTAATTAAGTTGTGCTCTTTTGCTA 57.384 30.769 0.00 0.00 0.00 3.49
154 155 4.558538 AGTTGTGCTCTTTTGCTAACAG 57.441 40.909 0.00 0.00 35.14 3.16
167 168 1.523758 CTAACAGGTGGTCTTGTGCC 58.476 55.000 0.00 0.00 34.18 5.01
172 173 1.902918 GGTGGTCTTGTGCCATGCA 60.903 57.895 0.00 0.00 38.40 3.96
185 186 1.575922 CATGCACACACGTCAAGGG 59.424 57.895 0.00 0.00 0.00 3.95
192 193 2.162608 CACACACGTCAAGGGTTTTTCA 59.837 45.455 0.00 0.00 31.20 2.69
194 195 3.066203 ACACACGTCAAGGGTTTTTCATC 59.934 43.478 0.00 0.00 31.20 2.92
219 220 9.665719 TCAGAAAAATAAAATAAAATGAGGGGC 57.334 29.630 0.00 0.00 0.00 5.80
256 257 2.683933 CGCCTAGTCACCACCCCT 60.684 66.667 0.00 0.00 0.00 4.79
258 259 1.299976 GCCTAGTCACCACCCCTTG 59.700 63.158 0.00 0.00 0.00 3.61
269 270 1.271379 CCACCCCTTGGTCACTTACAG 60.271 57.143 0.00 0.00 45.57 2.74
276 277 2.436115 GTCACTTACAGCGGGCCC 60.436 66.667 13.57 13.57 0.00 5.80
277 278 2.606519 TCACTTACAGCGGGCCCT 60.607 61.111 22.43 2.64 0.00 5.19
278 279 2.436646 CACTTACAGCGGGCCCTG 60.437 66.667 22.43 15.46 38.78 4.45
279 280 4.410400 ACTTACAGCGGGCCCTGC 62.410 66.667 25.35 25.35 36.29 4.85
280 281 4.408821 CTTACAGCGGGCCCTGCA 62.409 66.667 31.19 14.83 36.29 4.41
298 299 0.813610 CACCGCTTTGTCACACCTCA 60.814 55.000 0.00 0.00 0.00 3.86
323 324 3.130633 GCTCCGCATGTGTATACAATCA 58.869 45.455 7.25 2.69 40.84 2.57
333 334 9.009327 GCATGTGTATACAATCATGTTTTGTAC 57.991 33.333 25.53 13.82 41.08 2.90
342 343 8.519492 ACAATCATGTTTTGTACTGTATTTGC 57.481 30.769 12.89 0.00 35.91 3.68
344 345 8.427012 CAATCATGTTTTGTACTGTATTTGCAC 58.573 33.333 0.00 0.00 0.00 4.57
352 353 1.336887 ACTGTATTTGCACGCTCGAGT 60.337 47.619 15.13 0.00 0.00 4.18
360 361 0.512952 GCACGCTCGAGTCAAATTGT 59.487 50.000 15.13 0.00 0.00 2.71
363 364 0.179215 CGCTCGAGTCAAATTGTGGC 60.179 55.000 15.13 0.00 0.00 5.01
366 367 1.197721 CTCGAGTCAAATTGTGGCACC 59.802 52.381 16.26 0.00 32.63 5.01
367 368 0.950836 CGAGTCAAATTGTGGCACCA 59.049 50.000 16.26 4.06 32.63 4.17
384 385 0.027979 CCAGTTCAATGTATGCCGCG 59.972 55.000 0.00 0.00 0.00 6.46
397 398 2.658373 TGCCGCGAGTTTTGATACTA 57.342 45.000 8.23 0.00 0.00 1.82
408 409 8.068380 GCGAGTTTTGATACTAAAGTGACTTTT 58.932 33.333 16.49 1.53 35.21 2.27
413 414 8.882415 TTTGATACTAAAGTGACTTTTCTCGT 57.118 30.769 16.49 10.62 35.21 4.18
433 434 2.949644 GTCAAGTTTAAGCACCAGTGGT 59.050 45.455 9.70 9.70 44.00 4.16
482 483 2.315925 ACTATGGTTGAGTGCATCCG 57.684 50.000 0.00 0.00 36.80 4.18
483 484 1.831106 ACTATGGTTGAGTGCATCCGA 59.169 47.619 0.00 0.00 36.80 4.55
508 509 4.023291 GCCCATAAATCAGGAGGTTCAAA 58.977 43.478 0.00 0.00 0.00 2.69
509 510 4.651045 GCCCATAAATCAGGAGGTTCAAAT 59.349 41.667 0.00 0.00 0.00 2.32
510 511 5.129320 GCCCATAAATCAGGAGGTTCAAATT 59.871 40.000 0.00 0.00 0.00 1.82
511 512 6.352137 GCCCATAAATCAGGAGGTTCAAATTT 60.352 38.462 0.00 0.00 0.00 1.82
598 599 9.525007 GTACACTTTTTATTGACTCATAACGTG 57.475 33.333 0.00 0.00 0.00 4.49
634 635 2.728690 ATACAAACACTACGACCGCA 57.271 45.000 0.00 0.00 0.00 5.69
657 658 7.524912 GCATACACAATCTCTGCATAATTAGG 58.475 38.462 0.00 0.00 33.13 2.69
674 676 9.188588 CATAATTAGGATGCACAAAACATGATC 57.811 33.333 0.00 0.00 0.00 2.92
685 687 5.351189 CACAAAACATGATCGACACATAGGA 59.649 40.000 0.00 0.00 0.00 2.94
720 722 2.554032 ACGACCTCCAAAATTCTTGCTG 59.446 45.455 0.00 0.00 0.00 4.41
764 766 1.275666 ACCCTCAACATCATCCGACA 58.724 50.000 0.00 0.00 0.00 4.35
765 767 1.208052 ACCCTCAACATCATCCGACAG 59.792 52.381 0.00 0.00 0.00 3.51
792 794 1.734117 GGTGCTTCAACAATGGCGC 60.734 57.895 0.00 0.00 34.89 6.53
803 805 1.330306 CAATGGCGCGTGAAAGAAAG 58.670 50.000 8.43 0.00 0.00 2.62
808 810 1.365699 GCGCGTGAAAGAAAGGGATA 58.634 50.000 8.43 0.00 0.00 2.59
811 813 2.095372 CGCGTGAAAGAAAGGGATAACC 59.905 50.000 0.00 0.00 40.67 2.85
815 817 3.939592 GTGAAAGAAAGGGATAACCGGAG 59.060 47.826 9.46 0.00 46.96 4.63
821 823 1.153229 GGGATAACCGGAGTGTGCC 60.153 63.158 9.46 4.78 36.97 5.01
822 824 1.600107 GGATAACCGGAGTGTGCCA 59.400 57.895 9.46 0.00 0.00 4.92
846 848 0.251916 CGTCAGATGCACCCCCTAAA 59.748 55.000 0.00 0.00 0.00 1.85
854 856 3.054779 TGCACCCCCTAAAGCTAGATA 57.945 47.619 0.00 0.00 0.00 1.98
864 866 5.701290 CCCTAAAGCTAGATAATGGGTTTCG 59.299 44.000 0.00 0.00 40.18 3.46
866 868 3.127425 AGCTAGATAATGGGTTTCGCC 57.873 47.619 0.00 0.00 0.00 5.54
867 869 1.798813 GCTAGATAATGGGTTTCGCCG 59.201 52.381 0.00 0.00 38.44 6.46
874 878 0.393077 ATGGGTTTCGCCGGATAGAG 59.607 55.000 5.05 0.00 38.44 2.43
878 882 0.594284 GTTTCGCCGGATAGAGGACG 60.594 60.000 5.05 0.00 0.00 4.79
881 885 1.299165 CGCCGGATAGAGGACGTTG 60.299 63.158 5.05 0.00 0.00 4.10
959 963 3.741388 GCCAGATACAACCAGCGTAGATT 60.741 47.826 0.00 0.00 0.00 2.40
994 998 2.621055 TCATTCCGGAACCAAACTTGTG 59.379 45.455 21.56 10.71 0.00 3.33
1009 1014 6.348540 CCAAACTTGTGGAGAACTATAACAGC 60.349 42.308 0.00 0.00 41.65 4.40
1024 1029 0.859232 ACAGCGACGTGACAATGTTC 59.141 50.000 0.00 0.00 0.00 3.18
1044 1049 1.411394 CACTTCAAAATGCTGCACGG 58.589 50.000 3.57 0.00 0.00 4.94
1085 1090 4.559643 CCGTAGTGTTCAAACAACAAAACC 59.440 41.667 0.00 0.00 41.21 3.27
1108 1113 0.534203 TCTTGGTTCCGTGCCACTTC 60.534 55.000 0.00 0.00 35.46 3.01
1145 1156 2.715749 TGCATTGATGTAGGTGGAGG 57.284 50.000 0.00 0.00 0.00 4.30
1147 1158 1.490490 GCATTGATGTAGGTGGAGGGA 59.510 52.381 0.00 0.00 0.00 4.20
1149 1160 1.879575 TTGATGTAGGTGGAGGGAGG 58.120 55.000 0.00 0.00 0.00 4.30
1150 1161 0.031111 TGATGTAGGTGGAGGGAGGG 60.031 60.000 0.00 0.00 0.00 4.30
1151 1162 1.384643 ATGTAGGTGGAGGGAGGGC 60.385 63.158 0.00 0.00 0.00 5.19
1153 1164 1.615424 GTAGGTGGAGGGAGGGCAA 60.615 63.158 0.00 0.00 0.00 4.52
1154 1165 0.988678 GTAGGTGGAGGGAGGGCAAT 60.989 60.000 0.00 0.00 0.00 3.56
1155 1166 0.645496 TAGGTGGAGGGAGGGCAATA 59.355 55.000 0.00 0.00 0.00 1.90
1156 1167 0.988678 AGGTGGAGGGAGGGCAATAC 60.989 60.000 0.00 0.00 0.00 1.89
1157 1168 1.532238 GTGGAGGGAGGGCAATACC 59.468 63.158 0.00 0.00 37.93 2.73
1168 1179 2.981859 GGCAATACCCTTCGAGAAGA 57.018 50.000 13.90 0.00 40.79 2.87
1169 1180 2.827652 GGCAATACCCTTCGAGAAGAG 58.172 52.381 13.90 3.67 40.79 2.85
1170 1181 2.431057 GGCAATACCCTTCGAGAAGAGA 59.569 50.000 13.90 0.04 40.79 3.10
1171 1182 3.118738 GGCAATACCCTTCGAGAAGAGAA 60.119 47.826 13.90 0.00 40.79 2.87
1288 1299 3.591023 TCCGCGTTGAAACAGATTGATA 58.409 40.909 4.92 0.00 0.00 2.15
1342 1353 3.615155 CCCTCTTGACTTTCCATTCCTC 58.385 50.000 0.00 0.00 0.00 3.71
1986 2401 2.123077 AGGAGGAGGCGGAGATGG 60.123 66.667 0.00 0.00 0.00 3.51
2096 2511 1.851987 GGGAGGAGGGGTCGAGATA 59.148 63.158 0.00 0.00 0.00 1.98
2153 2568 1.360185 GGCAGATGGAGATGGAGGAT 58.640 55.000 0.00 0.00 0.00 3.24
2440 2870 3.966154 TCAATGTTACTCGCTAGCTAGC 58.034 45.455 31.88 31.88 45.62 3.42
2511 2953 9.428097 AGCAAATAATTCTTTCCTCATTTTCAC 57.572 29.630 0.00 0.00 0.00 3.18
2540 2982 8.466798 AGGTCGTAATTTTGGATTCTTAATTGG 58.533 33.333 0.00 0.00 0.00 3.16
2552 2994 5.414789 TTCTTAATTGGTCAGGACGATGA 57.585 39.130 0.00 0.00 0.00 2.92
2553 2995 5.614324 TCTTAATTGGTCAGGACGATGAT 57.386 39.130 0.00 0.00 0.00 2.45
2554 2996 5.601662 TCTTAATTGGTCAGGACGATGATC 58.398 41.667 0.00 0.00 0.00 2.92
2555 2997 2.918712 ATTGGTCAGGACGATGATCC 57.081 50.000 0.00 0.00 39.28 3.36
2556 2998 1.567357 TTGGTCAGGACGATGATCCA 58.433 50.000 0.00 0.00 41.73 3.41
2557 2999 1.793414 TGGTCAGGACGATGATCCAT 58.207 50.000 0.00 0.00 41.73 3.41
2558 3000 1.688735 TGGTCAGGACGATGATCCATC 59.311 52.381 0.00 0.00 41.73 3.51
2559 3001 1.688735 GGTCAGGACGATGATCCATCA 59.311 52.381 7.59 0.00 40.54 3.07
2889 3342 6.755141 GCATGACTTTGCATGATCAATTAACT 59.245 34.615 0.00 0.00 46.64 2.24
2902 3355 5.929697 TCAATTAACTCATCCATCGATGC 57.070 39.130 20.25 0.00 44.83 3.91
2914 3375 2.481854 CATCGATGCTGCTAGCTTCTT 58.518 47.619 17.23 5.65 42.97 2.52
2986 3450 1.831389 CTCACAACGTGGGTTCTGCG 61.831 60.000 0.00 0.00 32.98 5.18
3005 3469 5.179182 TCTGCGTACATACATGCATTATTGG 59.821 40.000 0.00 0.00 36.64 3.16
3228 3696 3.243367 TGCTTTGCTTTGCTTATCGTGTT 60.243 39.130 0.00 0.00 0.00 3.32
3270 3738 4.202040 TGCTTGTATATGTTTGCCTGATGC 60.202 41.667 0.00 0.00 41.77 3.91
3366 3843 6.074782 GCTAGATAGTGCTTGTTTGACGATAC 60.075 42.308 0.00 0.00 0.00 2.24
3368 3845 5.807520 AGATAGTGCTTGTTTGACGATACTG 59.192 40.000 0.00 0.00 0.00 2.74
3430 3912 7.016153 TGAAGGTATGACAAGTATGAAACCT 57.984 36.000 0.00 0.00 37.71 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 8.056407 TGATGTTCTATAGGGATACTCATTCG 57.944 38.462 0.00 0.00 0.00 3.34
64 65 1.327764 GAGCTAACCTATGCGTGTTGC 59.672 52.381 0.00 0.00 46.70 4.17
148 149 1.202758 TGGCACAAGACCACCTGTTAG 60.203 52.381 0.00 0.00 31.92 2.34
150 151 1.612513 TGGCACAAGACCACCTGTT 59.387 52.632 0.00 0.00 31.92 3.16
167 168 1.165907 ACCCTTGACGTGTGTGCATG 61.166 55.000 0.00 0.00 37.62 4.06
172 173 2.438411 TGAAAAACCCTTGACGTGTGT 58.562 42.857 0.00 0.00 0.00 3.72
173 174 3.066064 TGATGAAAAACCCTTGACGTGTG 59.934 43.478 0.00 0.00 0.00 3.82
194 195 9.671279 AGCCCCTCATTTTATTTTATTTTTCTG 57.329 29.630 0.00 0.00 0.00 3.02
201 202 8.601546 TGTGAAAAGCCCCTCATTTTATTTTAT 58.398 29.630 0.00 0.00 0.00 1.40
202 203 7.967908 TGTGAAAAGCCCCTCATTTTATTTTA 58.032 30.769 0.00 0.00 0.00 1.52
203 204 6.836242 TGTGAAAAGCCCCTCATTTTATTTT 58.164 32.000 0.00 0.00 0.00 1.82
207 208 5.878406 TTTGTGAAAAGCCCCTCATTTTA 57.122 34.783 0.00 0.00 0.00 1.52
210 211 4.769345 TTTTTGTGAAAAGCCCCTCATT 57.231 36.364 0.00 0.00 31.41 2.57
262 263 4.410400 GCAGGGCCCGCTGTAAGT 62.410 66.667 25.40 0.55 35.30 2.24
276 277 1.009675 GTGTGACAAAGCGGTGCAG 60.010 57.895 0.00 0.00 0.00 4.41
277 278 2.477176 GGTGTGACAAAGCGGTGCA 61.477 57.895 0.00 0.00 0.00 4.57
278 279 2.117941 GAGGTGTGACAAAGCGGTGC 62.118 60.000 0.00 0.00 0.00 5.01
279 280 0.813610 TGAGGTGTGACAAAGCGGTG 60.814 55.000 0.00 0.00 0.00 4.94
280 281 0.108585 ATGAGGTGTGACAAAGCGGT 59.891 50.000 0.00 0.00 0.00 5.68
282 283 1.462283 CTGATGAGGTGTGACAAAGCG 59.538 52.381 0.00 0.00 0.00 4.68
283 284 1.198637 GCTGATGAGGTGTGACAAAGC 59.801 52.381 0.00 0.00 0.00 3.51
284 285 2.740981 GAGCTGATGAGGTGTGACAAAG 59.259 50.000 0.00 0.00 0.00 2.77
285 286 2.550855 GGAGCTGATGAGGTGTGACAAA 60.551 50.000 0.00 0.00 0.00 2.83
286 287 1.002430 GGAGCTGATGAGGTGTGACAA 59.998 52.381 0.00 0.00 0.00 3.18
323 324 4.915085 GCGTGCAAATACAGTACAAAACAT 59.085 37.500 0.00 0.00 0.00 2.71
333 334 1.321743 GACTCGAGCGTGCAAATACAG 59.678 52.381 13.61 0.00 0.00 2.74
341 342 0.512952 ACAATTTGACTCGAGCGTGC 59.487 50.000 13.61 0.00 0.00 5.34
342 343 1.136252 CCACAATTTGACTCGAGCGTG 60.136 52.381 13.61 8.37 0.00 5.34
344 345 0.179215 GCCACAATTTGACTCGAGCG 60.179 55.000 13.61 0.00 0.00 5.03
352 353 2.382882 TGAACTGGTGCCACAATTTGA 58.617 42.857 2.79 0.00 0.00 2.69
360 361 1.818060 GCATACATTGAACTGGTGCCA 59.182 47.619 0.00 0.00 0.00 4.92
363 364 1.202177 GCGGCATACATTGAACTGGTG 60.202 52.381 0.00 0.00 0.00 4.17
366 367 1.004610 CTCGCGGCATACATTGAACTG 60.005 52.381 6.13 0.00 0.00 3.16
367 368 1.290203 CTCGCGGCATACATTGAACT 58.710 50.000 6.13 0.00 0.00 3.01
397 398 6.496338 AAACTTGACGAGAAAAGTCACTTT 57.504 33.333 0.00 0.00 46.81 2.66
408 409 3.181469 ACTGGTGCTTAAACTTGACGAGA 60.181 43.478 0.00 0.00 0.00 4.04
413 414 3.290948 ACCACTGGTGCTTAAACTTGA 57.709 42.857 0.00 0.00 32.98 3.02
454 455 7.136822 TGCACTCAACCATAGTTAATCCTAT 57.863 36.000 0.00 0.00 33.27 2.57
482 483 1.074566 CCTCCTGATTTATGGGCCCTC 59.925 57.143 25.70 12.61 0.00 4.30
483 484 1.152649 CCTCCTGATTTATGGGCCCT 58.847 55.000 25.70 11.37 0.00 5.19
565 566 7.776030 TGAGTCAATAAAAAGTGTACTTTCCCA 59.224 33.333 10.16 0.53 44.69 4.37
614 615 3.029320 TGCGGTCGTAGTGTTTGTATT 57.971 42.857 0.00 0.00 0.00 1.89
615 616 2.728690 TGCGGTCGTAGTGTTTGTAT 57.271 45.000 0.00 0.00 0.00 2.29
634 635 9.445878 CATCCTAATTATGCAGAGATTGTGTAT 57.554 33.333 0.00 0.00 0.00 2.29
657 658 3.848019 GTGTCGATCATGTTTTGTGCATC 59.152 43.478 0.00 0.00 0.00 3.91
665 666 6.406370 TCTTTCCTATGTGTCGATCATGTTT 58.594 36.000 13.71 0.00 0.00 2.83
701 703 4.853924 TTCAGCAAGAATTTTGGAGGTC 57.146 40.909 0.00 0.00 0.00 3.85
704 706 6.927381 AGTTCATTTCAGCAAGAATTTTGGAG 59.073 34.615 0.00 0.00 35.83 3.86
708 710 9.034544 GTTGTAGTTCATTTCAGCAAGAATTTT 57.965 29.630 0.00 0.00 35.83 1.82
720 722 6.208644 ACTGTTGCATGTTGTAGTTCATTTC 58.791 36.000 0.00 0.00 0.00 2.17
764 766 3.620488 TGTTGAAGCACCTTTTCTCACT 58.380 40.909 0.00 0.00 0.00 3.41
765 767 4.370364 TTGTTGAAGCACCTTTTCTCAC 57.630 40.909 0.00 0.00 0.00 3.51
792 794 2.676342 CCGGTTATCCCTTTCTTTCACG 59.324 50.000 0.00 0.00 0.00 4.35
803 805 1.153229 GGCACACTCCGGTTATCCC 60.153 63.158 0.00 0.00 0.00 3.85
846 848 2.548067 CGGCGAAACCCATTATCTAGCT 60.548 50.000 0.00 0.00 33.26 3.32
854 856 0.834612 TCTATCCGGCGAAACCCATT 59.165 50.000 9.30 0.00 33.26 3.16
864 866 1.067582 CCAACGTCCTCTATCCGGC 59.932 63.158 0.00 0.00 0.00 6.13
866 868 0.384669 GTCCCAACGTCCTCTATCCG 59.615 60.000 0.00 0.00 0.00 4.18
867 869 1.481871 TGTCCCAACGTCCTCTATCC 58.518 55.000 0.00 0.00 0.00 2.59
874 878 2.825861 TAGAGTTTGTCCCAACGTCC 57.174 50.000 0.00 0.00 0.00 4.79
878 882 4.988540 GGCATTTTTAGAGTTTGTCCCAAC 59.011 41.667 0.00 0.00 0.00 3.77
881 885 4.082190 GGAGGCATTTTTAGAGTTTGTCCC 60.082 45.833 0.00 0.00 0.00 4.46
959 963 6.363167 TCCGGAATGAAAACTTTAGGTCTA 57.637 37.500 0.00 0.00 0.00 2.59
994 998 3.106672 CACGTCGCTGTTATAGTTCTCC 58.893 50.000 0.00 0.00 0.00 3.71
1009 1014 1.497991 AGTGGAACATTGTCACGTCG 58.502 50.000 3.73 0.00 44.52 5.12
1024 1029 1.411394 CGTGCAGCATTTTGAAGTGG 58.589 50.000 0.00 0.00 0.00 4.00
1044 1049 1.079503 GGACTTGGAAGACACGATGC 58.920 55.000 0.00 0.00 0.00 3.91
1056 1061 3.199677 TGTTTGAACACTACGGACTTGG 58.800 45.455 0.00 0.00 33.17 3.61
1108 1113 3.270027 TGCATATCCAGTCCAGAAAACG 58.730 45.455 0.00 0.00 0.00 3.60
1149 1160 2.431057 TCTCTTCTCGAAGGGTATTGCC 59.569 50.000 6.45 0.00 39.84 4.52
1150 1161 3.802948 TCTCTTCTCGAAGGGTATTGC 57.197 47.619 6.45 0.00 39.84 3.56
1151 1162 5.358442 TCTCTTCTCTTCTCGAAGGGTATTG 59.642 44.000 6.45 0.00 39.46 1.90
1153 1164 5.118729 TCTCTTCTCTTCTCGAAGGGTAT 57.881 43.478 6.45 0.00 39.46 2.73
1154 1165 4.571369 TCTCTTCTCTTCTCGAAGGGTA 57.429 45.455 6.45 0.00 39.46 3.69
1155 1166 3.443145 TCTCTTCTCTTCTCGAAGGGT 57.557 47.619 6.45 0.00 39.46 4.34
1156 1167 4.013728 TCTTCTCTTCTCTTCTCGAAGGG 58.986 47.826 6.81 3.58 39.73 3.95
1157 1168 4.941263 TCTCTTCTCTTCTCTTCTCGAAGG 59.059 45.833 6.81 0.00 38.66 3.46
1159 1170 6.234920 TCTTCTCTTCTCTTCTCTTCTCGAA 58.765 40.000 0.00 0.00 0.00 3.71
1160 1171 5.800296 TCTTCTCTTCTCTTCTCTTCTCGA 58.200 41.667 0.00 0.00 0.00 4.04
1161 1172 5.065218 CCTCTTCTCTTCTCTTCTCTTCTCG 59.935 48.000 0.00 0.00 0.00 4.04
1162 1173 6.180472 TCCTCTTCTCTTCTCTTCTCTTCTC 58.820 44.000 0.00 0.00 0.00 2.87
1163 1174 6.012508 TCTCCTCTTCTCTTCTCTTCTCTTCT 60.013 42.308 0.00 0.00 0.00 2.85
1164 1175 6.094186 GTCTCCTCTTCTCTTCTCTTCTCTTC 59.906 46.154 0.00 0.00 0.00 2.87
1165 1176 5.946377 GTCTCCTCTTCTCTTCTCTTCTCTT 59.054 44.000 0.00 0.00 0.00 2.85
1166 1177 5.501156 GTCTCCTCTTCTCTTCTCTTCTCT 58.499 45.833 0.00 0.00 0.00 3.10
1167 1178 4.332819 CGTCTCCTCTTCTCTTCTCTTCTC 59.667 50.000 0.00 0.00 0.00 2.87
1168 1179 4.261801 CGTCTCCTCTTCTCTTCTCTTCT 58.738 47.826 0.00 0.00 0.00 2.85
1169 1180 3.181500 GCGTCTCCTCTTCTCTTCTCTTC 60.181 52.174 0.00 0.00 0.00 2.87
1170 1181 2.752903 GCGTCTCCTCTTCTCTTCTCTT 59.247 50.000 0.00 0.00 0.00 2.85
1171 1182 2.365582 GCGTCTCCTCTTCTCTTCTCT 58.634 52.381 0.00 0.00 0.00 3.10
1288 1299 3.517500 AGAGAGAAAGAGGCGAGGAAATT 59.482 43.478 0.00 0.00 0.00 1.82
1342 1353 1.498576 TGAGAGAGAGAGAGATGGGGG 59.501 57.143 0.00 0.00 0.00 5.40
1610 2016 0.487325 TGGAGAGGAAGGAGTGGTCA 59.513 55.000 0.00 0.00 0.00 4.02
1986 2401 3.519930 GCCCTCCTCCTCGTCGAC 61.520 72.222 5.18 5.18 0.00 4.20
2440 2870 3.713764 AGGAGGGTGAATCCATGAAGTAG 59.286 47.826 0.00 0.00 39.47 2.57
2511 2953 4.189231 AGAATCCAAAATTACGACCTCGG 58.811 43.478 0.00 0.00 44.95 4.63
2540 2982 3.459232 TTGATGGATCATCGTCCTGAC 57.541 47.619 0.00 0.00 43.14 3.51
2552 2994 4.627984 CGATGGATGGATGGATTGATGGAT 60.628 45.833 0.00 0.00 0.00 3.41
2553 2995 3.307904 CGATGGATGGATGGATTGATGGA 60.308 47.826 0.00 0.00 0.00 3.41
2554 2996 3.014623 CGATGGATGGATGGATTGATGG 58.985 50.000 0.00 0.00 0.00 3.51
2555 2997 2.422479 GCGATGGATGGATGGATTGATG 59.578 50.000 0.00 0.00 0.00 3.07
2556 2998 2.619849 GGCGATGGATGGATGGATTGAT 60.620 50.000 0.00 0.00 0.00 2.57
2557 2999 1.271543 GGCGATGGATGGATGGATTGA 60.272 52.381 0.00 0.00 0.00 2.57
2558 3000 1.171308 GGCGATGGATGGATGGATTG 58.829 55.000 0.00 0.00 0.00 2.67
2559 3001 0.321919 CGGCGATGGATGGATGGATT 60.322 55.000 0.00 0.00 0.00 3.01
2902 3355 3.446873 TGAGGAGAAGAAGAAGCTAGCAG 59.553 47.826 18.83 0.00 0.00 4.24
2914 3375 4.080695 CCTTGTGGAATGATGAGGAGAAGA 60.081 45.833 0.00 0.00 34.57 2.87
2969 3433 0.876777 TACGCAGAACCCACGTTGTG 60.877 55.000 0.00 0.00 44.15 3.33
2986 3450 8.647143 AAAAAGCCAATAATGCATGTATGTAC 57.353 30.769 0.00 0.00 0.00 2.90
3097 3564 4.442472 GCAAATCTCTTTAGGGCATGCAAT 60.442 41.667 21.36 9.68 0.00 3.56
3179 3646 2.952245 CAGCTGCACTTGACTGCC 59.048 61.111 0.00 0.00 36.21 4.85
3228 3696 2.142220 GGGCATCGATACCCTTCCA 58.858 57.895 24.43 0.00 43.36 3.53
3340 3817 3.926527 CGTCAAACAAGCACTATCTAGCA 59.073 43.478 0.00 0.00 0.00 3.49
3430 3912 1.740585 GTACACACTGTGTTGGTGCAA 59.259 47.619 19.77 0.00 45.08 4.08


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

AutoCloner maintained by Alex Coulton.