Multiple sequence alignment - TraesCS5A01G391400

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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 TraesCS5A01G391400 chr5A 100.000 6265 0 0 1 6265 586598936 586605200 0.000000e+00 11570.0
1 TraesCS5A01G391400 chr5A 89.405 538 37 12 5061 5592 538233016 538232493 0.000000e+00 660.0
2 TraesCS5A01G391400 chr5B 92.917 6353 278 61 1 6265 573220656 573226924 0.000000e+00 9081.0
3 TraesCS5A01G391400 chr5D 94.340 5477 201 41 848 6265 466225786 466231212 0.000000e+00 8296.0
4 TraesCS5A01G391400 chr5D 94.365 834 25 10 1 818 466224897 466225724 0.000000e+00 1260.0
5 TraesCS5A01G391400 chr3A 88.104 538 42 14 5061 5592 380636011 380636532 2.480000e-173 619.0
6 TraesCS5A01G391400 chr6A 87.523 537 47 11 5062 5592 218851049 218850527 2.500000e-168 603.0
7 TraesCS5A01G391400 chr7D 97.222 36 1 0 2071 2106 607448469 607448434 1.890000e-05 62.1


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 TraesCS5A01G391400 chr5A 586598936 586605200 6264 False 11570 11570 100.0000 1 6265 1 chr5A.!!$F1 6264
1 TraesCS5A01G391400 chr5A 538232493 538233016 523 True 660 660 89.4050 5061 5592 1 chr5A.!!$R1 531
2 TraesCS5A01G391400 chr5B 573220656 573226924 6268 False 9081 9081 92.9170 1 6265 1 chr5B.!!$F1 6264
3 TraesCS5A01G391400 chr5D 466224897 466231212 6315 False 4778 8296 94.3525 1 6265 2 chr5D.!!$F1 6264
4 TraesCS5A01G391400 chr3A 380636011 380636532 521 False 619 619 88.1040 5061 5592 1 chr3A.!!$F1 531
5 TraesCS5A01G391400 chr6A 218850527 218851049 522 True 603 603 87.5230 5062 5592 1 chr6A.!!$R1 530

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
514 528 0.170561 ACTTCTGAATCCCGACGACG 59.829 55.000 0.00 0.00 39.43 5.12 F
557 571 0.249031 GGCTATTGATTGGGTTGCGC 60.249 55.000 0.00 0.00 0.00 6.09 F
1544 1623 0.108662 TCAGTACGGACTCGCGTAGA 60.109 55.000 5.77 0.00 40.63 2.59 F
2062 2147 0.401395 ACTCCCTGGTTGTTCCTCCA 60.401 55.000 0.00 0.00 37.07 3.86 F
2548 2638 1.753930 TCCCGCTATGTACTCGTCAA 58.246 50.000 0.00 0.00 0.00 3.18 F
3964 4103 1.342496 TGTCTTCCAGACTGCTGTCAG 59.658 52.381 23.61 16.37 45.27 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1339 1413 0.539438 GGAGCCAAACCATGTGGACA 60.539 55.000 5.96 0.00 38.54 4.02 R
2028 2113 0.790814 GGAGTAACAAGTCGCAGTGC 59.209 55.000 4.58 4.58 0.00 4.40 R
3252 3373 4.644103 ATGGCATACAGAATCAAACTGC 57.356 40.909 0.00 0.00 38.74 4.40 R
3825 3964 0.768221 TGGACAAGGGAGCAGGAAGT 60.768 55.000 0.00 0.00 0.00 3.01 R
4514 4658 3.113260 ACTGGAAGAAGGTTTCACTCG 57.887 47.619 0.00 0.00 37.43 4.18 R
5930 6094 2.086869 ACAACCATGGATCTTGAAGCG 58.913 47.619 21.47 0.00 0.00 4.68 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
51 52 1.672356 GGATGGCGACTGTGCAAGT 60.672 57.895 0.00 0.00 43.85 3.16
128 142 1.000171 GTTGCCCTTGCTCTTCTTTGG 60.000 52.381 0.00 0.00 38.71 3.28
183 197 6.446318 GGATGCAATGTCACTTAACTGAAAA 58.554 36.000 0.00 0.00 0.00 2.29
213 227 1.077787 CGGTTTGCTGGATAGGCCA 60.078 57.895 5.01 0.00 46.96 5.36
514 528 0.170561 ACTTCTGAATCCCGACGACG 59.829 55.000 0.00 0.00 39.43 5.12
527 541 3.812019 CGACGGGTGTCCTCGAGG 61.812 72.222 26.32 26.32 42.37 4.63
541 555 2.883828 CGAGGTGTGAACCAGGGCT 61.884 63.158 0.00 0.00 0.00 5.19
557 571 0.249031 GGCTATTGATTGGGTTGCGC 60.249 55.000 0.00 0.00 0.00 6.09
711 727 1.080705 ACGGCAACTCTACGAGTGC 60.081 57.895 0.00 4.10 42.59 4.40
718 734 1.352056 CTCTACGAGTGCGCGATGA 59.648 57.895 12.10 0.00 42.48 2.92
805 822 6.146837 CGTTCAGTCTGATTTGAGATTCTTGT 59.853 38.462 2.68 0.00 0.00 3.16
814 831 9.212641 CTGATTTGAGATTCTTGTTCTTCTGTA 57.787 33.333 0.00 0.00 0.00 2.74
857 897 6.183360 GCAGTTTGCAGAGTATACTACACTTG 60.183 42.308 5.09 1.51 44.26 3.16
866 909 8.297426 CAGAGTATACTACACTTGTGTGAAGAA 58.703 37.037 15.72 0.00 46.55 2.52
867 910 8.857098 AGAGTATACTACACTTGTGTGAAGAAA 58.143 33.333 15.72 2.48 46.55 2.52
961 1034 0.813610 CGTTGCTGGACCAGTTGTGA 60.814 55.000 22.58 2.24 33.43 3.58
1280 1354 2.770048 CGATCCCCTTCCCTGGCT 60.770 66.667 0.00 0.00 0.00 4.75
1388 1467 1.276138 TCTCGCCTTCAAATCTCTGCA 59.724 47.619 0.00 0.00 0.00 4.41
1389 1468 1.396301 CTCGCCTTCAAATCTCTGCAC 59.604 52.381 0.00 0.00 0.00 4.57
1395 1474 3.318839 CCTTCAAATCTCTGCACACCAAA 59.681 43.478 0.00 0.00 0.00 3.28
1409 1488 2.443255 ACACCAAACCTGTCAGATCCTT 59.557 45.455 0.00 0.00 0.00 3.36
1523 1602 2.582436 GAATTCCACGCCTCCCGA 59.418 61.111 0.00 0.00 41.02 5.14
1543 1622 0.301088 CTCAGTACGGACTCGCGTAG 59.699 60.000 5.77 4.90 40.63 3.51
1544 1623 0.108662 TCAGTACGGACTCGCGTAGA 60.109 55.000 5.77 0.00 40.63 2.59
1581 1660 6.693113 CGATTCTCATCAATCTCTCGTTGTTA 59.307 38.462 0.00 0.00 31.48 2.41
1585 1664 5.410924 TCATCAATCTCTCGTTGTTACTGG 58.589 41.667 0.00 0.00 0.00 4.00
1791 1870 3.798202 AGTGTGAGTTTCAGGTGTTCTC 58.202 45.455 0.00 0.00 0.00 2.87
1861 1940 4.297299 GATTGTTGATCGTGCCATCAAT 57.703 40.909 6.21 0.00 43.17 2.57
2028 2113 7.981789 AGATTATATATGGAGTACAATGTGCCG 59.018 37.037 0.00 0.00 0.00 5.69
2058 2143 2.943036 TGTTACTCCCTGGTTGTTCC 57.057 50.000 0.00 0.00 0.00 3.62
2062 2147 0.401395 ACTCCCTGGTTGTTCCTCCA 60.401 55.000 0.00 0.00 37.07 3.86
2244 2331 7.979444 TCACTTCTCTTTTAATAACCACCTG 57.021 36.000 0.00 0.00 0.00 4.00
2413 2500 2.044492 TCATCCTCCCTACCACTTGTCT 59.956 50.000 0.00 0.00 0.00 3.41
2442 2531 9.994432 CTTTACTTAAAACATGATCTGGCTAAG 57.006 33.333 0.00 0.00 0.00 2.18
2448 2537 2.238144 ACATGATCTGGCTAAGCAGTGT 59.762 45.455 0.00 0.00 0.00 3.55
2502 2591 5.453567 TCATAATCTCCTGTGTCCATACG 57.546 43.478 0.00 0.00 0.00 3.06
2548 2638 1.753930 TCCCGCTATGTACTCGTCAA 58.246 50.000 0.00 0.00 0.00 3.18
2549 2639 2.304092 TCCCGCTATGTACTCGTCAAT 58.696 47.619 0.00 0.00 0.00 2.57
2550 2640 3.479489 TCCCGCTATGTACTCGTCAATA 58.521 45.455 0.00 0.00 0.00 1.90
2660 2750 9.684448 CTGTAAGCTTCTATGATTCTATCGAAA 57.316 33.333 0.00 0.00 31.91 3.46
2943 3059 4.515191 TCAGAAAGTGGGATTTCGACAAAG 59.485 41.667 0.00 0.00 42.73 2.77
3067 3183 2.875296 TGGCATAGGTTTGCTGTCTTT 58.125 42.857 0.00 0.00 42.38 2.52
3073 3189 6.972901 GGCATAGGTTTGCTGTCTTTTTATAC 59.027 38.462 0.00 0.00 42.38 1.47
3074 3190 7.362574 GGCATAGGTTTGCTGTCTTTTTATACA 60.363 37.037 0.00 0.00 42.38 2.29
3208 3329 2.912956 AGGCAGGTGTGAGGATTAAAGA 59.087 45.455 0.00 0.00 0.00 2.52
3252 3373 4.478206 TCTATTCCTTGCAGTCTTCCTG 57.522 45.455 0.00 0.00 44.53 3.86
3482 3603 7.148474 TGTGCTCTTTCGTATATTTGTTTCTCC 60.148 37.037 0.00 0.00 0.00 3.71
3621 3742 4.821805 CCGTATGGTTTTGATATTCTGGCT 59.178 41.667 0.00 0.00 0.00 4.75
3665 3786 7.881912 TGGTAGGGCCAAAATATCTATCTAA 57.118 36.000 6.18 0.00 45.94 2.10
3666 3787 8.463055 TGGTAGGGCCAAAATATCTATCTAAT 57.537 34.615 6.18 0.00 45.94 1.73
3667 3788 9.569074 TGGTAGGGCCAAAATATCTATCTAATA 57.431 33.333 6.18 0.00 45.94 0.98
3807 3946 6.620678 AGTCCCATTTTGTTGATATGTTTCG 58.379 36.000 0.00 0.00 0.00 3.46
3821 3960 7.149307 TGATATGTTTCGAGTGTTAACTGACA 58.851 34.615 7.22 2.23 36.52 3.58
3825 3964 5.408909 TGTTTCGAGTGTTAACTGACAAACA 59.591 36.000 7.22 11.74 36.52 2.83
3964 4103 1.342496 TGTCTTCCAGACTGCTGTCAG 59.658 52.381 23.61 16.37 45.27 3.51
4045 4187 9.533253 CTTATCTTGGAACTTGATTTGTTGTTT 57.467 29.630 0.00 0.00 0.00 2.83
4100 4242 4.785376 AGGAGGAAGCTTGAAGGAATTCTA 59.215 41.667 2.10 0.00 0.00 2.10
4514 4658 7.642071 ATGCAACAACAAAATTCACTGATAC 57.358 32.000 0.00 0.00 0.00 2.24
4562 4711 6.761714 ACAGTCTTATGATTTTATCCCGTGTC 59.238 38.462 0.00 0.00 0.00 3.67
4569 4718 6.159299 TGATTTTATCCCGTGTCCGTAATA 57.841 37.500 0.00 0.00 0.00 0.98
4621 4770 4.355543 TTCAAAAACTCCATATCTGCGC 57.644 40.909 0.00 0.00 0.00 6.09
4640 4790 1.000506 GCCACCTTGTCGACTCTAACA 59.999 52.381 17.92 0.00 0.00 2.41
4670 4820 2.627699 TGCTCCATTGTTCCAAAAGGTC 59.372 45.455 0.00 0.00 0.00 3.85
4774 4924 6.420903 CGGTTCTTTTTCCTGAAGATTTTTCC 59.579 38.462 0.00 0.00 33.48 3.13
4789 4939 9.794685 GAAGATTTTTCCTCCTGAAATATTCAC 57.205 33.333 9.31 0.00 42.38 3.18
4918 5068 0.921896 ACATCCCCCAACAGATCAGG 59.078 55.000 0.00 0.00 0.00 3.86
4930 5080 2.452823 ACAGATCAGGCTAGGGAGGTAT 59.547 50.000 0.00 0.00 0.00 2.73
5028 5178 5.410746 CACTTGTAGTTGCTTGTCTGATCAT 59.589 40.000 0.00 0.00 0.00 2.45
5029 5179 6.591448 CACTTGTAGTTGCTTGTCTGATCATA 59.409 38.462 0.00 0.00 0.00 2.15
5030 5180 6.591834 ACTTGTAGTTGCTTGTCTGATCATAC 59.408 38.462 4.34 4.34 0.00 2.39
5031 5181 5.102313 TGTAGTTGCTTGTCTGATCATACG 58.898 41.667 6.73 0.00 0.00 3.06
5032 5182 4.193826 AGTTGCTTGTCTGATCATACGT 57.806 40.909 6.73 0.00 0.00 3.57
5033 5183 4.177026 AGTTGCTTGTCTGATCATACGTC 58.823 43.478 6.73 0.00 0.00 4.34
5034 5184 3.866883 TGCTTGTCTGATCATACGTCA 57.133 42.857 6.73 2.28 0.00 4.35
5078 5228 3.709987 ACAAGAGTTTGACTGCAATTGC 58.290 40.909 23.69 23.69 37.73 3.56
5090 5240 4.558538 CTGCAATTGCTGTATACCTTCC 57.441 45.455 29.37 0.00 42.66 3.46
5091 5241 3.947196 CTGCAATTGCTGTATACCTTCCA 59.053 43.478 29.37 5.11 42.66 3.53
5335 5492 0.254178 GCAATTCTGGAGCCAGGAGA 59.746 55.000 16.06 4.03 43.75 3.71
5415 5577 7.156876 TCATGGCTGGAAAATAGTTTAACAG 57.843 36.000 12.76 12.76 36.01 3.16
5531 5693 6.533723 TGTTAAATACATGTAGGAGCTCAACG 59.466 38.462 17.19 4.19 0.00 4.10
5617 5781 8.911918 TTCAACCAAAGTATTTAAGCTGTAGA 57.088 30.769 0.00 0.00 35.03 2.59
5819 5983 6.696583 CACTGCACATATCAAAGTTCACAAAA 59.303 34.615 0.00 0.00 0.00 2.44
5820 5984 7.383029 CACTGCACATATCAAAGTTCACAAAAT 59.617 33.333 0.00 0.00 0.00 1.82
5821 5985 7.596248 ACTGCACATATCAAAGTTCACAAAATC 59.404 33.333 0.00 0.00 0.00 2.17
5823 5987 7.924947 TGCACATATCAAAGTTCACAAAATCAA 59.075 29.630 0.00 0.00 0.00 2.57
5824 5988 8.216453 GCACATATCAAAGTTCACAAAATCAAC 58.784 33.333 0.00 0.00 0.00 3.18
5825 5989 9.247126 CACATATCAAAGTTCACAAAATCAACA 57.753 29.630 0.00 0.00 0.00 3.33
5826 5990 9.985730 ACATATCAAAGTTCACAAAATCAACAT 57.014 25.926 0.00 0.00 0.00 2.71
5829 5993 8.945481 ATCAAAGTTCACAAAATCAACATCAA 57.055 26.923 0.00 0.00 0.00 2.57
5830 5994 8.945481 TCAAAGTTCACAAAATCAACATCAAT 57.055 26.923 0.00 0.00 0.00 2.57
5909 6073 5.659440 CATTATGTGCTTACCCCACTTTT 57.341 39.130 0.00 0.00 34.38 2.27
5930 6094 2.822561 TCGATCACTATCCAGATCAGCC 59.177 50.000 0.00 0.00 40.45 4.85
5984 6148 0.614812 GAACCCATTTGGCCAGCATT 59.385 50.000 5.11 0.00 37.83 3.56
6014 6178 0.741326 GCTCGGTGTAGATCTCAGCA 59.259 55.000 18.17 7.50 33.61 4.41
6065 6229 6.959639 ATGGTGCTCGTAATTATCCAAAAT 57.040 33.333 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 8.974060 TGACCACTATAATTTTTATCTGACCC 57.026 34.615 0.00 0.00 0.00 4.46
128 142 6.109359 ACTCATCAGGCAATCTAAACACTAC 58.891 40.000 0.00 0.00 0.00 2.73
183 197 2.422276 GCAAACCGCTTTCAGATTGT 57.578 45.000 0.00 0.00 37.77 2.71
213 227 7.530426 ACAGCTGTTATTTTCAAGGAGATTT 57.470 32.000 15.25 0.00 0.00 2.17
313 327 3.873812 GATACCCCTGGGCCGTGG 61.874 72.222 7.39 8.26 39.32 4.94
514 528 1.469335 TTCACACCTCGAGGACACCC 61.469 60.000 37.69 0.00 38.94 4.61
527 541 2.489938 TCAATAGCCCTGGTTCACAC 57.510 50.000 0.00 0.00 0.00 3.82
541 555 2.822561 TCTTTGCGCAACCCAATCAATA 59.177 40.909 24.99 2.62 0.00 1.90
557 571 0.319405 CCCAAAGGGCTTGCTCTTTG 59.681 55.000 30.38 30.38 45.44 2.77
582 596 7.701501 CAGCTACACATATGATACATCAGCTAG 59.298 40.741 10.38 5.08 40.64 3.42
630 644 1.988107 AGCTCCTCCTCAACCATCAAA 59.012 47.619 0.00 0.00 0.00 2.69
746 763 3.866651 ACCACCTGAGAATTGATCGAAG 58.133 45.455 0.00 0.00 0.00 3.79
836 853 6.645003 CACACAAGTGTAGTATACTCTGCAAA 59.355 38.462 9.12 0.00 43.88 3.68
961 1034 2.049063 GAGAGCGCCGTCACAAGT 60.049 61.111 2.29 0.00 0.00 3.16
1280 1354 0.251653 AGTTCTGGTAGCGGTGGAGA 60.252 55.000 0.00 0.00 0.00 3.71
1339 1413 0.539438 GGAGCCAAACCATGTGGACA 60.539 55.000 5.96 0.00 38.54 4.02
1388 1467 2.057922 AGGATCTGACAGGTTTGGTGT 58.942 47.619 1.81 0.00 0.00 4.16
1389 1468 2.867109 AGGATCTGACAGGTTTGGTG 57.133 50.000 1.81 0.00 0.00 4.17
1395 1474 1.273098 ACCGGTAAGGATCTGACAGGT 60.273 52.381 4.49 9.82 45.00 4.00
1523 1602 1.670406 ACGCGAGTCCGTACTGAGT 60.670 57.895 15.93 0.00 44.19 3.41
1535 1614 1.352156 GCCAGTTTGGTCTACGCGAG 61.352 60.000 15.93 6.12 40.46 5.03
1543 1622 2.003301 GAGAATCGAGCCAGTTTGGTC 58.997 52.381 0.00 0.00 40.46 4.02
1544 1623 1.347707 TGAGAATCGAGCCAGTTTGGT 59.652 47.619 0.00 0.00 37.74 3.67
1581 1660 4.012374 CCAAACTGATTAGCATGACCAGT 58.988 43.478 0.00 0.00 39.49 4.00
1585 1664 4.498682 GCATCCCAAACTGATTAGCATGAC 60.499 45.833 0.00 0.00 0.00 3.06
1791 1870 3.374988 TGTCACTCACACAGCAAAGAAAG 59.625 43.478 0.00 0.00 0.00 2.62
1861 1940 5.987953 GCACTTGAAGAGTATGCAGATATCA 59.012 40.000 5.32 0.00 36.65 2.15
2002 2081 7.981789 CGGCACATTGTACTCCATATATAATCT 59.018 37.037 0.00 0.00 0.00 2.40
2009 2088 2.158827 TGCGGCACATTGTACTCCATAT 60.159 45.455 0.00 0.00 0.00 1.78
2010 2089 1.208293 TGCGGCACATTGTACTCCATA 59.792 47.619 0.00 0.00 0.00 2.74
2015 2094 1.577328 GCAGTGCGGCACATTGTACT 61.577 55.000 32.29 9.36 38.23 2.73
2028 2113 0.790814 GGAGTAACAAGTCGCAGTGC 59.209 55.000 4.58 4.58 0.00 4.40
2131 2216 5.249163 TCATGGAGAAATGAAGACCTCAAGA 59.751 40.000 0.00 0.00 37.67 3.02
2346 2433 9.206848 AGTTAAGTAACGGCATGGGACAAGATA 62.207 40.741 0.00 0.00 41.17 1.98
2413 2500 7.039784 AGCCAGATCATGTTTTAAGTAAAGCAA 60.040 33.333 4.73 0.00 39.28 3.91
2457 2546 5.551760 TGCTCTAAATGTCTGCTAAAAGC 57.448 39.130 0.00 0.00 42.82 3.51
2548 2638 8.877864 TCACCAAACTGGAACAATAAAGATAT 57.122 30.769 0.00 0.00 40.96 1.63
2549 2639 8.739039 CATCACCAAACTGGAACAATAAAGATA 58.261 33.333 0.00 0.00 40.96 1.98
2550 2640 7.309990 CCATCACCAAACTGGAACAATAAAGAT 60.310 37.037 0.00 0.00 40.96 2.40
2864 2954 6.370994 ACTGAACATTGACTTGCTAAGAGATG 59.629 38.462 3.37 6.29 0.00 2.90
2921 3037 4.787598 CTTTGTCGAAATCCCACTTTCTG 58.212 43.478 0.00 0.00 33.80 3.02
2960 3076 9.676861 ATGAATTCTCATTACTCTTTCACATGA 57.323 29.630 7.05 0.00 39.36 3.07
3208 3329 5.605540 AAAATCATATGCAGATAGGGGGT 57.394 39.130 0.00 0.00 0.00 4.95
3252 3373 4.644103 ATGGCATACAGAATCAAACTGC 57.356 40.909 0.00 0.00 38.74 4.40
3492 3613 8.132362 TGTACGTTTCAAATAGCAATTCAGTTT 58.868 29.630 0.00 0.00 0.00 2.66
3621 3742 8.221944 CCTACCATGGAACCAAATTTATAGGTA 58.778 37.037 21.47 0.00 34.63 3.08
3821 3960 1.215423 ACAAGGGAGCAGGAAGTGTTT 59.785 47.619 0.00 0.00 0.00 2.83
3825 3964 0.768221 TGGACAAGGGAGCAGGAAGT 60.768 55.000 0.00 0.00 0.00 3.01
3964 4103 4.456911 TGACCTTCAGATGACAATTGAAGC 59.543 41.667 13.59 2.65 43.96 3.86
4062 4204 3.237746 TCCTCCTATCTGAAGCAGGATG 58.762 50.000 6.51 5.00 37.82 3.51
4100 4242 3.569701 CCTTGTGCAAGTAACATCTGGTT 59.430 43.478 10.56 0.00 38.24 3.67
4171 4313 8.999431 CATAGCCATAAAGTTATTGGAATACGT 58.001 33.333 7.94 0.00 0.00 3.57
4245 4389 9.294030 GCCATTTTGTAAGAAAGATATTGTGAG 57.706 33.333 0.00 0.00 0.00 3.51
4514 4658 3.113260 ACTGGAAGAAGGTTTCACTCG 57.887 47.619 0.00 0.00 37.43 4.18
4523 4667 4.608948 AAGACTGTGTACTGGAAGAAGG 57.391 45.455 0.00 0.00 37.43 3.46
4621 4770 2.927014 GCTGTTAGAGTCGACAAGGTGG 60.927 54.545 19.50 3.35 0.00 4.61
4670 4820 3.265791 GACCAGGTGAAAGCAGTCATAG 58.734 50.000 0.00 0.00 38.99 2.23
4735 4885 7.066645 GGAAAAAGAACCGGCTATTAACTACAT 59.933 37.037 0.00 0.00 0.00 2.29
4918 5068 6.782988 TGCAATCCTATATATACCTCCCTAGC 59.217 42.308 0.00 0.00 0.00 3.42
5028 5178 3.811083 ACCAAGGTGATTGTTTGACGTA 58.189 40.909 0.00 0.00 37.17 3.57
5029 5179 2.650322 ACCAAGGTGATTGTTTGACGT 58.350 42.857 0.00 0.00 37.17 4.34
5030 5180 5.049060 TGAATACCAAGGTGATTGTTTGACG 60.049 40.000 1.07 0.00 37.17 4.35
5031 5181 6.149633 GTGAATACCAAGGTGATTGTTTGAC 58.850 40.000 1.07 0.00 37.17 3.18
5032 5182 5.830457 TGTGAATACCAAGGTGATTGTTTGA 59.170 36.000 1.07 0.00 37.17 2.69
5033 5183 6.083098 TGTGAATACCAAGGTGATTGTTTG 57.917 37.500 1.07 0.00 37.17 2.93
5034 5184 6.097554 TGTTGTGAATACCAAGGTGATTGTTT 59.902 34.615 1.07 0.00 37.17 2.83
5078 5228 6.293626 GCAATGCAGTAATGGAAGGTATACAG 60.294 42.308 0.00 0.00 0.00 2.74
5087 5237 4.842574 TGAGTAGCAATGCAGTAATGGAA 58.157 39.130 8.35 0.00 0.00 3.53
5155 5307 6.999272 TCTAACAGGTTGCCTTTACACATTAA 59.001 34.615 0.00 0.00 0.00 1.40
5158 5310 4.980573 TCTAACAGGTTGCCTTTACACAT 58.019 39.130 0.00 0.00 0.00 3.21
5159 5311 4.425180 TCTAACAGGTTGCCTTTACACA 57.575 40.909 0.00 0.00 0.00 3.72
5160 5312 4.820173 ACTTCTAACAGGTTGCCTTTACAC 59.180 41.667 0.00 0.00 0.00 2.90
5161 5313 4.819630 CACTTCTAACAGGTTGCCTTTACA 59.180 41.667 0.00 0.00 0.00 2.41
5162 5314 5.061179 TCACTTCTAACAGGTTGCCTTTAC 58.939 41.667 0.00 0.00 0.00 2.01
5163 5315 5.298989 TCACTTCTAACAGGTTGCCTTTA 57.701 39.130 0.00 0.00 0.00 1.85
5164 5316 4.164843 TCACTTCTAACAGGTTGCCTTT 57.835 40.909 0.00 0.00 0.00 3.11
5531 5693 8.754230 AGTAAAGTGTTAAAAGATACGACCTC 57.246 34.615 0.00 0.00 0.00 3.85
5616 5780 6.073222 CGAACATATGGGCTTGTACCTAATTC 60.073 42.308 7.80 0.00 0.00 2.17
5617 5781 5.763204 CGAACATATGGGCTTGTACCTAATT 59.237 40.000 7.80 0.00 0.00 1.40
5622 5786 2.870411 GACGAACATATGGGCTTGTACC 59.130 50.000 7.80 0.00 0.00 3.34
5819 5983 6.682113 GCAGGTAATGAGCAATTGATGTTGAT 60.682 38.462 10.34 0.00 0.00 2.57
5820 5984 5.393352 GCAGGTAATGAGCAATTGATGTTGA 60.393 40.000 10.34 0.00 0.00 3.18
5821 5985 4.802039 GCAGGTAATGAGCAATTGATGTTG 59.198 41.667 10.34 0.00 0.00 3.33
5823 5987 4.018490 TGCAGGTAATGAGCAATTGATGT 58.982 39.130 10.34 0.00 34.97 3.06
5824 5988 4.642445 TGCAGGTAATGAGCAATTGATG 57.358 40.909 10.34 0.00 34.97 3.07
5825 5989 5.664294 TTTGCAGGTAATGAGCAATTGAT 57.336 34.783 10.34 1.34 46.32 2.57
5826 5990 5.465532 TTTTGCAGGTAATGAGCAATTGA 57.534 34.783 10.34 0.00 46.32 2.57
5827 5991 6.103997 AGATTTTGCAGGTAATGAGCAATTG 58.896 36.000 0.00 0.00 46.32 2.32
5828 5992 6.071221 TGAGATTTTGCAGGTAATGAGCAATT 60.071 34.615 0.00 0.00 46.32 2.32
5829 5993 5.419788 TGAGATTTTGCAGGTAATGAGCAAT 59.580 36.000 0.00 0.00 46.32 3.56
5830 5994 4.766373 TGAGATTTTGCAGGTAATGAGCAA 59.234 37.500 0.00 0.00 45.53 3.91
5909 6073 2.822561 GGCTGATCTGGATAGTGATCGA 59.177 50.000 1.46 0.00 41.24 3.59
5930 6094 2.086869 ACAACCATGGATCTTGAAGCG 58.913 47.619 21.47 0.00 0.00 4.68
5993 6157 0.309302 CTGAGATCTACACCGAGCGG 59.691 60.000 7.48 7.48 42.03 5.52
6014 6178 2.076863 GCGCTGTTCTTCATGTACCTT 58.923 47.619 0.00 0.00 0.00 3.50
6050 6214 5.579384 TCGCGGTATTTTGGATAATTACG 57.421 39.130 6.13 0.00 0.00 3.18
6166 6330 5.373812 TTTTCTCTGGAAGGTTGAGAAGT 57.626 39.130 0.00 0.00 44.35 3.01
6230 6394 8.500753 ACAAGACAAAGTACAAATTCTACACA 57.499 30.769 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.