Multiple sequence alignment - TraesCS5A01G199300

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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 TraesCS5A01G199300 chr5A 100.000 3332 0 0 1 3332 404179633 404176302 0.000000e+00 6154.0
1 TraesCS5A01G199300 chr5A 81.081 259 36 11 1307 1560 463452309 463452559 9.430000e-46 195.0
2 TraesCS5A01G199300 chr5A 96.970 33 1 0 2899 2931 589018409 589018441 4.640000e-04 56.5
3 TraesCS5A01G199300 chr5D 92.224 1646 93 27 8 1646 310680365 310678748 0.000000e+00 2298.0
4 TraesCS5A01G199300 chr5D 91.465 1570 91 16 1774 3314 310678475 310676920 0.000000e+00 2117.0
5 TraesCS5A01G199300 chr5D 92.357 157 12 0 1621 1777 310678718 310678562 1.200000e-54 224.0
6 TraesCS5A01G199300 chr5B 95.976 994 31 3 638 1626 356598806 356597817 0.000000e+00 1605.0
7 TraesCS5A01G199300 chr5B 91.019 1080 71 19 1667 2727 356597683 356596611 0.000000e+00 1434.0
8 TraesCS5A01G199300 chr5B 85.714 672 75 17 1 667 356599466 356598811 0.000000e+00 689.0
9 TraesCS5A01G199300 chr5B 85.507 69 9 1 1621 1688 356597759 356597691 1.660000e-08 71.3
10 TraesCS5A01G199300 chr7B 72.065 494 111 18 2846 3323 450676062 450675580 4.510000e-24 122.0
11 TraesCS5A01G199300 chr7B 72.792 419 93 14 2899 3301 625694424 625694011 4.510000e-24 122.0
12 TraesCS5A01G199300 chr6D 72.906 406 86 15 2903 3291 47665815 47666213 5.840000e-23 119.0
13 TraesCS5A01G199300 chr2A 85.542 83 6 5 2859 2940 88088107 88088184 7.660000e-12 82.4
14 TraesCS5A01G199300 chr2D 86.154 65 7 2 3148 3212 353339730 353339668 5.960000e-08 69.4
15 TraesCS5A01G199300 chr4D 100.000 28 0 0 2903 2930 57081276 57081303 6.000000e-03 52.8
16 TraesCS5A01G199300 chr1D 100.000 28 0 0 2903 2930 3997329 3997302 6.000000e-03 52.8


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 TraesCS5A01G199300 chr5A 404176302 404179633 3331 True 6154.000000 6154 100.000000 1 3332 1 chr5A.!!$R1 3331
1 TraesCS5A01G199300 chr5D 310676920 310680365 3445 True 1546.333333 2298 92.015333 8 3314 3 chr5D.!!$R1 3306
2 TraesCS5A01G199300 chr5B 356596611 356599466 2855 True 949.825000 1605 89.554000 1 2727 4 chr5B.!!$R1 2726

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
70 72 0.032130 ATGTTGACACTCACGAGCGT 59.968 50.000 0.00 0.0 0.00 5.07 F
281 287 0.250989 CCGGGCCAACTTTGTCCTTA 60.251 55.000 4.39 0.0 0.00 2.69 F
911 949 1.266989 CTCCGTGTTTCAAAAGGAGGC 59.733 52.381 8.85 0.0 43.42 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1167 1210 1.086696 GCGAGCCTGCAAATACTCAA 58.913 50.0 0.00 0.0 34.15 3.02 R
1258 1301 1.319541 CCGTACATCTCCTCGTCCAT 58.680 55.0 0.00 0.0 0.00 3.41 R
2884 3141 0.036765 GTATCCAGGCGTGTGTGGAA 60.037 55.0 5.57 0.0 46.01 3.53 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
24 25 1.003355 CAGGCGCTCTGGGAGAAAA 60.003 57.895 7.64 0.00 39.76 2.29
31 32 3.142174 CGCTCTGGGAGAAAACTTTCTT 58.858 45.455 6.18 0.00 46.84 2.52
43 45 1.064825 ACTTTCTTCGATGGGGTGGT 58.935 50.000 0.00 0.00 0.00 4.16
48 50 2.167398 CTTCGATGGGGTGGTGACGT 62.167 60.000 0.00 0.00 0.00 4.34
50 52 1.740296 CGATGGGGTGGTGACGTTC 60.740 63.158 0.00 0.00 0.00 3.95
59 61 1.937223 GTGGTGACGTTCATGTTGACA 59.063 47.619 0.00 0.00 0.00 3.58
66 68 2.124122 CGTTCATGTTGACACTCACGA 58.876 47.619 0.00 0.00 30.62 4.35
70 72 0.032130 ATGTTGACACTCACGAGCGT 59.968 50.000 0.00 0.00 0.00 5.07
73 75 0.313987 TTGACACTCACGAGCGTCAT 59.686 50.000 16.34 0.00 46.12 3.06
74 76 0.313987 TGACACTCACGAGCGTCATT 59.686 50.000 12.65 0.00 43.23 2.57
75 77 1.269569 TGACACTCACGAGCGTCATTT 60.270 47.619 12.65 0.00 43.23 2.32
76 78 2.030628 TGACACTCACGAGCGTCATTTA 60.031 45.455 12.65 0.00 43.23 1.40
77 79 2.325761 ACACTCACGAGCGTCATTTAC 58.674 47.619 0.00 0.00 0.00 2.01
78 80 2.030185 ACACTCACGAGCGTCATTTACT 60.030 45.455 0.00 0.00 0.00 2.24
79 81 2.594654 CACTCACGAGCGTCATTTACTC 59.405 50.000 0.00 0.00 0.00 2.59
80 82 2.488545 ACTCACGAGCGTCATTTACTCT 59.511 45.455 0.00 0.00 0.00 3.24
120 124 5.026121 AGAGATTCTTCACACCTGGTATGA 58.974 41.667 3.12 3.12 0.00 2.15
157 161 1.478510 TCGTTGGTTTGCATTTGGTGT 59.521 42.857 0.00 0.00 0.00 4.16
158 162 1.592081 CGTTGGTTTGCATTTGGTGTG 59.408 47.619 0.00 0.00 0.00 3.82
160 164 3.265791 GTTGGTTTGCATTTGGTGTGAA 58.734 40.909 0.00 0.00 0.00 3.18
161 165 3.176552 TGGTTTGCATTTGGTGTGAAG 57.823 42.857 0.00 0.00 0.00 3.02
162 166 2.762887 TGGTTTGCATTTGGTGTGAAGA 59.237 40.909 0.00 0.00 0.00 2.87
163 167 3.196469 TGGTTTGCATTTGGTGTGAAGAA 59.804 39.130 0.00 0.00 0.00 2.52
166 170 3.988379 TGCATTTGGTGTGAAGAACTC 57.012 42.857 0.00 0.00 0.00 3.01
167 171 3.554934 TGCATTTGGTGTGAAGAACTCT 58.445 40.909 0.00 0.00 0.00 3.24
168 172 4.713553 TGCATTTGGTGTGAAGAACTCTA 58.286 39.130 0.00 0.00 0.00 2.43
169 173 5.129634 TGCATTTGGTGTGAAGAACTCTAA 58.870 37.500 0.00 0.00 0.00 2.10
170 174 5.769662 TGCATTTGGTGTGAAGAACTCTAAT 59.230 36.000 0.00 0.00 0.00 1.73
173 177 7.653311 GCATTTGGTGTGAAGAACTCTAATTTT 59.347 33.333 0.00 0.00 0.00 1.82
181 185 8.215050 TGTGAAGAACTCTAATTTTGGTTAGGA 58.785 33.333 0.00 0.00 33.48 2.94
189 193 6.539173 TCTAATTTTGGTTAGGAGTTGCTCA 58.461 36.000 0.00 0.00 33.48 4.26
191 195 3.569194 TTTGGTTAGGAGTTGCTCACA 57.431 42.857 0.00 0.00 31.08 3.58
200 205 0.969149 AGTTGCTCACATCCGAGTCA 59.031 50.000 0.00 0.00 35.33 3.41
219 224 2.825532 TCAGGTTCTATTTTTGCAGGGC 59.174 45.455 0.00 0.00 0.00 5.19
273 279 2.133281 GGTATAAACCGGGCCAACTT 57.867 50.000 6.32 0.00 35.62 2.66
280 286 1.530655 CCGGGCCAACTTTGTCCTT 60.531 57.895 4.39 0.00 0.00 3.36
281 287 0.250989 CCGGGCCAACTTTGTCCTTA 60.251 55.000 4.39 0.00 0.00 2.69
301 307 2.905415 ATGGAATTTCAGGAGCACCA 57.095 45.000 2.07 0.00 38.94 4.17
367 373 3.055094 AGGGTCTCAGCGTGTAAAATGAT 60.055 43.478 0.00 0.00 0.00 2.45
374 380 4.934602 TCAGCGTGTAAAATGATGATCACA 59.065 37.500 0.00 0.00 35.30 3.58
516 522 3.160679 AGCTGCCACTCTAACCAAATT 57.839 42.857 0.00 0.00 0.00 1.82
517 523 3.084786 AGCTGCCACTCTAACCAAATTC 58.915 45.455 0.00 0.00 0.00 2.17
546 552 3.149005 TCTGTAAATTCACACCACCCC 57.851 47.619 0.00 0.00 0.00 4.95
584 590 4.142038 GCTTCCTCCTTTACACTCCAAAA 58.858 43.478 0.00 0.00 0.00 2.44
596 602 2.359531 CACTCCAAAACTTTACCCGCAA 59.640 45.455 0.00 0.00 0.00 4.85
604 610 1.910671 ACTTTACCCGCAATGTCCCTA 59.089 47.619 0.00 0.00 0.00 3.53
624 630 3.756082 AATCCCCAATTAGGAGTGCAA 57.244 42.857 0.00 0.00 41.22 4.08
626 632 3.534357 TCCCCAATTAGGAGTGCAAAA 57.466 42.857 0.00 0.00 41.22 2.44
627 633 4.059773 TCCCCAATTAGGAGTGCAAAAT 57.940 40.909 0.00 0.00 41.22 1.82
628 634 5.199982 TCCCCAATTAGGAGTGCAAAATA 57.800 39.130 0.00 0.00 41.22 1.40
630 636 6.916909 TCCCCAATTAGGAGTGCAAAATATA 58.083 36.000 0.00 0.00 41.22 0.86
656 662 6.099125 ACAAACCCCAAAAGCTTATTTACAGT 59.901 34.615 0.00 0.00 0.00 3.55
667 705 5.189736 AGCTTATTTACAGTCCAGTCCATCA 59.810 40.000 0.00 0.00 0.00 3.07
679 717 4.715523 CCATCAACCACCGCCGGT 62.716 66.667 1.02 1.02 42.71 5.28
911 949 1.266989 CTCCGTGTTTCAAAAGGAGGC 59.733 52.381 8.85 0.00 43.42 4.70
1148 1191 4.567159 GCGTTCGTTCTTGGAATTCTCTAT 59.433 41.667 5.23 0.00 0.00 1.98
1167 1210 4.935205 TCTATTTGATTGCACTTACACGCT 59.065 37.500 0.00 0.00 0.00 5.07
1258 1301 1.679305 GTGGACGAGGAGCTCCAGA 60.679 63.158 33.90 9.50 37.23 3.86
1599 1642 0.179020 TGATCATCAATCCGGCCACC 60.179 55.000 2.24 0.00 33.01 4.61
1630 1736 8.193438 GCTCATTGCTTAATTAAGTTCAATCCT 58.807 33.333 22.94 5.94 38.95 3.24
1647 1753 9.657419 GTTCAATCCTGGTCAAATTAATTTCAT 57.343 29.630 10.53 0.00 0.00 2.57
1751 1887 7.386025 TCTCTGTAAATAGAATGCGGATTCATG 59.614 37.037 28.21 10.75 40.59 3.07
1764 1900 3.118775 CGGATTCATGAGTAGGGTCACAA 60.119 47.826 0.00 0.00 0.00 3.33
1767 1903 5.123979 GGATTCATGAGTAGGGTCACAAAAC 59.876 44.000 0.00 0.00 0.00 2.43
1777 1913 8.064336 AGTAGGGTCACAAAACAGTATAGTAG 57.936 38.462 0.00 0.00 0.00 2.57
1808 2034 6.712179 ATCTAGTACACCTAGTAAAGTGCC 57.288 41.667 0.00 0.00 43.23 5.01
1817 2043 3.118738 CCTAGTAAAGTGCCCAATCGACT 60.119 47.826 0.00 0.00 0.00 4.18
1825 2051 2.866762 GTGCCCAATCGACTGACTAATC 59.133 50.000 0.00 0.00 0.00 1.75
1830 2056 4.141937 CCCAATCGACTGACTAATCTCCAA 60.142 45.833 0.00 0.00 0.00 3.53
1832 2058 5.464722 CCAATCGACTGACTAATCTCCAATG 59.535 44.000 0.00 0.00 0.00 2.82
1849 2075 5.754782 TCCAATGCTTAGCAAATCCTCTAA 58.245 37.500 12.08 0.00 43.62 2.10
1861 2087 5.446473 GCAAATCCTCTAAATCACTGTCACG 60.446 44.000 0.00 0.00 0.00 4.35
1865 2091 4.768448 TCCTCTAAATCACTGTCACGGTTA 59.232 41.667 0.00 0.00 0.00 2.85
1877 2103 3.244596 TGTCACGGTTATCCCAAATCACA 60.245 43.478 0.00 0.00 0.00 3.58
1878 2104 3.126343 GTCACGGTTATCCCAAATCACAC 59.874 47.826 0.00 0.00 0.00 3.82
1886 2112 4.970662 ATCCCAAATCACACGAATTCAG 57.029 40.909 6.22 0.00 0.00 3.02
1892 2118 5.149273 CAAATCACACGAATTCAGACAAGG 58.851 41.667 6.22 0.00 0.00 3.61
1920 2146 1.229428 CCTTGATAATGACCGCGCAT 58.771 50.000 8.75 0.00 0.00 4.73
1979 2205 2.344203 CCAAGGAGTCGTCGGAGCT 61.344 63.158 0.00 0.00 0.00 4.09
2034 2260 2.112297 GGTGTCCCAGCCGTTGAA 59.888 61.111 0.00 0.00 0.00 2.69
2127 2353 2.120718 AGCCCGGAGTCCAACTCT 59.879 61.111 10.49 0.00 44.46 3.24
2131 2357 0.535797 CCCGGAGTCCAACTCTTACC 59.464 60.000 10.49 0.00 44.46 2.85
2163 2389 1.674651 CTCACCTCCGTCGTCCTCA 60.675 63.158 0.00 0.00 0.00 3.86
2336 2562 1.137872 GTGGTTCTGGAGCTGATCGAT 59.862 52.381 0.00 0.00 0.00 3.59
2337 2563 1.137675 TGGTTCTGGAGCTGATCGATG 59.862 52.381 0.54 0.00 0.00 3.84
2338 2564 1.410517 GGTTCTGGAGCTGATCGATGA 59.589 52.381 0.54 0.00 0.00 2.92
2349 2575 3.828786 CTGATCGATGAGAGAGCATCAG 58.171 50.000 5.92 0.00 43.76 2.90
2368 2594 6.264067 GCATCAGGAAAATTAGCAATACTCCT 59.736 38.462 0.00 0.00 34.22 3.69
2380 2606 0.108804 ATACTCCTTGTGGACGTGCG 60.109 55.000 1.60 0.00 37.46 5.34
2381 2607 2.758770 TACTCCTTGTGGACGTGCGC 62.759 60.000 14.24 14.24 37.46 6.09
2398 2624 3.023119 TGCGCCATGTTTAATCCAATCT 58.977 40.909 4.18 0.00 0.00 2.40
2469 2697 5.521735 GCAGTGAGTAGTGAATTAGTGATGG 59.478 44.000 0.00 0.00 0.00 3.51
2470 2698 6.634805 CAGTGAGTAGTGAATTAGTGATGGT 58.365 40.000 0.00 0.00 0.00 3.55
2471 2699 7.630728 GCAGTGAGTAGTGAATTAGTGATGGTA 60.631 40.741 0.00 0.00 0.00 3.25
2475 2703 8.977412 TGAGTAGTGAATTAGTGATGGTAATGA 58.023 33.333 0.00 0.00 0.00 2.57
2640 2874 2.035632 TGGAGACCATTTTGGCGTTTT 58.964 42.857 0.00 0.00 42.67 2.43
2649 2883 5.697178 ACCATTTTGGCGTTTTAATTACCAC 59.303 36.000 0.00 0.00 42.67 4.16
2736 2970 6.481313 TGCTAGAAGTATGACATGAAGCAATC 59.519 38.462 0.00 0.00 34.75 2.67
2822 3063 3.999051 GAGCATCTACCGTCACGC 58.001 61.111 0.00 0.00 0.00 5.34
2832 3073 3.861113 TCTACCGTCACGCATAACAAATC 59.139 43.478 0.00 0.00 0.00 2.17
2835 3076 1.392168 CGTCACGCATAACAAATCCGT 59.608 47.619 0.00 0.00 0.00 4.69
2836 3077 2.534150 CGTCACGCATAACAAATCCGTC 60.534 50.000 0.00 0.00 0.00 4.79
2845 3086 1.905637 ACAAATCCGTCCCCTCAAAC 58.094 50.000 0.00 0.00 0.00 2.93
2856 3113 2.452813 CCTCAAACATCCGCGGACG 61.453 63.158 33.75 27.50 39.67 4.79
2896 3153 1.997669 TTTTTGTTTCCACACACGCC 58.002 45.000 0.00 0.00 30.32 5.68
2926 3183 5.185828 ACCTCAATTAGCAAACCTCAAATCC 59.814 40.000 0.00 0.00 0.00 3.01
2931 3190 8.980596 TCAATTAGCAAACCTCAAATCCATATT 58.019 29.630 0.00 0.00 0.00 1.28
2940 3199 5.536161 ACCTCAAATCCATATTACACATGCC 59.464 40.000 0.00 0.00 0.00 4.40
2951 3210 0.467290 ACACATGCCCCGTCAACTTT 60.467 50.000 0.00 0.00 0.00 2.66
2955 3214 0.035439 ATGCCCCGTCAACTTTCGAT 60.035 50.000 0.00 0.00 0.00 3.59
2997 3256 1.211703 ACATCAATACATGCCACCGGA 59.788 47.619 9.46 0.00 0.00 5.14
3006 3265 2.173782 ACATGCCACCGGATTACCAATA 59.826 45.455 9.46 0.00 35.59 1.90
3034 3293 9.674068 TTGGCATGTTCTACATACATACTAAAA 57.326 29.630 0.00 0.00 36.53 1.52
3075 3334 2.874086 CGGTTGATATTGCTGCTCATGA 59.126 45.455 0.00 0.00 0.00 3.07
3085 3344 1.532868 GCTGCTCATGACGTCTTTGTT 59.467 47.619 17.92 0.00 0.00 2.83
3140 3399 2.202932 CGGATCCACTCCTTGCCG 60.203 66.667 13.41 0.00 42.47 5.69
3177 3436 2.774234 TCAATGTCCCCATTCTCCTCTC 59.226 50.000 0.00 0.00 39.28 3.20
3192 3451 1.229951 TCTCTTGGGGGCAGTCCAT 60.230 57.895 0.00 0.00 37.22 3.41
3223 3482 4.741781 CGCCCACGCTTGCTTTCG 62.742 66.667 0.00 0.00 0.00 3.46
3253 3512 2.383527 GCGTGTTCCTTCTCTGCCG 61.384 63.158 0.00 0.00 0.00 5.69
3257 3516 0.108585 TGTTCCTTCTCTGCCGCTTT 59.891 50.000 0.00 0.00 0.00 3.51
3302 3561 4.669842 TCTTCTGCAGCAGCGCGT 62.670 61.111 18.43 0.00 46.23 6.01
3323 3582 4.925861 GCTGCCTCCGCCTCCATC 62.926 72.222 0.00 0.00 0.00 3.51
3324 3583 3.473647 CTGCCTCCGCCTCCATCA 61.474 66.667 0.00 0.00 0.00 3.07
3325 3584 3.746949 CTGCCTCCGCCTCCATCAC 62.747 68.421 0.00 0.00 0.00 3.06
3326 3585 3.785859 GCCTCCGCCTCCATCACA 61.786 66.667 0.00 0.00 0.00 3.58
3327 3586 3.112205 GCCTCCGCCTCCATCACAT 62.112 63.158 0.00 0.00 0.00 3.21
3328 3587 1.070445 CCTCCGCCTCCATCACATC 59.930 63.158 0.00 0.00 0.00 3.06
3329 3588 1.300465 CTCCGCCTCCATCACATCG 60.300 63.158 0.00 0.00 0.00 3.84
3330 3589 2.021068 CTCCGCCTCCATCACATCGT 62.021 60.000 0.00 0.00 0.00 3.73
3331 3590 1.592669 CCGCCTCCATCACATCGTC 60.593 63.158 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.003355 TTTTCTCCCAGAGCGCCTG 60.003 57.895 16.22 16.22 42.55 4.85
14 15 4.154918 CCATCGAAGAAAGTTTTCTCCCAG 59.845 45.833 7.52 1.38 46.22 4.45
24 25 1.064825 ACCACCCCATCGAAGAAAGT 58.935 50.000 0.00 0.00 43.58 2.66
31 32 2.162338 GAACGTCACCACCCCATCGA 62.162 60.000 0.00 0.00 0.00 3.59
43 45 2.863740 GTGAGTGTCAACATGAACGTCA 59.136 45.455 0.00 0.00 0.00 4.35
48 50 2.135139 GCTCGTGAGTGTCAACATGAA 58.865 47.619 0.00 0.00 32.76 2.57
50 52 0.436150 CGCTCGTGAGTGTCAACATG 59.564 55.000 2.28 0.00 34.41 3.21
59 61 2.488545 AGAGTAAATGACGCTCGTGAGT 59.511 45.455 0.00 0.00 31.72 3.41
66 68 3.511934 ACCTCTGAAGAGTAAATGACGCT 59.488 43.478 6.59 0.00 40.35 5.07
70 72 6.174720 ACAACACCTCTGAAGAGTAAATGA 57.825 37.500 6.59 0.00 40.48 2.57
73 75 5.984725 TCAACAACACCTCTGAAGAGTAAA 58.015 37.500 6.59 0.00 40.48 2.01
74 76 5.607939 TCAACAACACCTCTGAAGAGTAA 57.392 39.130 6.59 0.00 40.48 2.24
75 77 5.362717 TCTTCAACAACACCTCTGAAGAGTA 59.637 40.000 8.82 0.00 45.43 2.59
76 78 4.162320 TCTTCAACAACACCTCTGAAGAGT 59.838 41.667 8.82 0.00 45.43 3.24
77 79 4.697514 TCTTCAACAACACCTCTGAAGAG 58.302 43.478 8.82 0.00 45.43 2.85
79 81 4.697514 TCTCTTCAACAACACCTCTGAAG 58.302 43.478 4.63 4.63 43.97 3.02
80 82 4.753516 TCTCTTCAACAACACCTCTGAA 57.246 40.909 0.00 0.00 0.00 3.02
115 117 5.662456 GACCTTAGGTCCAAAGAGTCATAC 58.338 45.833 20.11 0.00 46.19 2.39
116 118 5.934402 GACCTTAGGTCCAAAGAGTCATA 57.066 43.478 20.11 0.00 46.19 2.15
117 119 4.828072 GACCTTAGGTCCAAAGAGTCAT 57.172 45.455 20.11 0.00 46.19 3.06
139 143 2.898705 TCACACCAAATGCAAACCAAC 58.101 42.857 0.00 0.00 0.00 3.77
141 145 2.762887 TCTTCACACCAAATGCAAACCA 59.237 40.909 0.00 0.00 0.00 3.67
157 161 8.437575 ACTCCTAACCAAAATTAGAGTTCTTCA 58.562 33.333 0.00 0.00 34.59 3.02
158 162 8.850007 ACTCCTAACCAAAATTAGAGTTCTTC 57.150 34.615 0.00 0.00 34.59 2.87
160 164 7.175119 GCAACTCCTAACCAAAATTAGAGTTCT 59.825 37.037 0.00 0.00 34.21 3.01
161 165 7.175119 AGCAACTCCTAACCAAAATTAGAGTTC 59.825 37.037 0.00 0.00 34.21 3.01
162 166 7.004691 AGCAACTCCTAACCAAAATTAGAGTT 58.995 34.615 0.00 0.00 35.38 3.01
163 167 6.543735 AGCAACTCCTAACCAAAATTAGAGT 58.456 36.000 0.00 0.00 34.59 3.24
166 170 6.206634 TGTGAGCAACTCCTAACCAAAATTAG 59.793 38.462 0.00 0.00 32.78 1.73
167 171 6.065374 TGTGAGCAACTCCTAACCAAAATTA 58.935 36.000 0.00 0.00 0.00 1.40
168 172 4.892934 TGTGAGCAACTCCTAACCAAAATT 59.107 37.500 0.00 0.00 0.00 1.82
169 173 4.469657 TGTGAGCAACTCCTAACCAAAAT 58.530 39.130 0.00 0.00 0.00 1.82
170 174 3.892284 TGTGAGCAACTCCTAACCAAAA 58.108 40.909 0.00 0.00 0.00 2.44
173 177 2.027192 GGATGTGAGCAACTCCTAACCA 60.027 50.000 0.00 0.00 0.00 3.67
181 185 0.969149 TGACTCGGATGTGAGCAACT 59.031 50.000 0.00 0.00 39.68 3.16
189 193 5.422214 AAAATAGAACCTGACTCGGATGT 57.578 39.130 0.00 0.00 0.00 3.06
191 195 4.636206 GCAAAAATAGAACCTGACTCGGAT 59.364 41.667 0.00 0.00 0.00 4.18
200 205 3.175438 AGCCCTGCAAAAATAGAACCT 57.825 42.857 0.00 0.00 0.00 3.50
252 258 1.355043 AGTTGGCCCGGTTTATACCAA 59.645 47.619 0.00 1.36 45.31 3.67
255 261 2.821378 ACAAAGTTGGCCCGGTTTATAC 59.179 45.455 0.00 0.00 0.00 1.47
280 286 4.314522 TGGTGCTCCTGAAATTCCATTA 57.685 40.909 6.34 0.00 34.23 1.90
281 287 3.173953 TGGTGCTCCTGAAATTCCATT 57.826 42.857 6.34 0.00 34.23 3.16
290 296 2.169978 CTCATCAAGATGGTGCTCCTGA 59.830 50.000 9.96 1.68 39.24 3.86
327 333 9.747898 TGAGACCCTAATAAAAATAGCAAAAGA 57.252 29.630 0.00 0.00 0.00 2.52
331 337 6.260050 CGCTGAGACCCTAATAAAAATAGCAA 59.740 38.462 0.00 0.00 0.00 3.91
332 338 5.758296 CGCTGAGACCCTAATAAAAATAGCA 59.242 40.000 0.00 0.00 0.00 3.49
367 373 7.039011 GGTATTCCACCTAGTCATATGTGATCA 60.039 40.741 1.90 0.00 44.79 2.92
516 522 6.206634 GGTGTGAATTTACAGAAATGTCCTGA 59.793 38.462 2.84 0.00 35.38 3.86
517 523 6.016360 TGGTGTGAATTTACAGAAATGTCCTG 60.016 38.462 2.84 0.00 35.38 3.86
546 552 5.184892 AGGAAGCATTATATAGGCCCAAG 57.815 43.478 0.00 0.00 0.00 3.61
562 568 3.418684 TTGGAGTGTAAAGGAGGAAGC 57.581 47.619 0.00 0.00 0.00 3.86
584 590 0.696501 AGGGACATTGCGGGTAAAGT 59.303 50.000 0.00 0.00 0.00 2.66
604 610 3.756082 TTGCACTCCTAATTGGGGATT 57.244 42.857 8.14 0.00 39.16 3.01
621 627 6.429692 AGCTTTTGGGGTTTGTTATATTTTGC 59.570 34.615 0.00 0.00 0.00 3.68
628 634 8.652290 TGTAAATAAGCTTTTGGGGTTTGTTAT 58.348 29.630 3.20 0.00 0.00 1.89
630 636 6.890293 TGTAAATAAGCTTTTGGGGTTTGTT 58.110 32.000 3.20 0.00 0.00 2.83
656 662 1.676968 CGGTGGTTGATGGACTGGA 59.323 57.895 0.00 0.00 0.00 3.86
679 717 3.706373 GGTGGCCGGAGAAGCTGA 61.706 66.667 5.05 0.00 0.00 4.26
944 982 5.473504 CCCTATCTTGCGGCACTAAAATTAT 59.526 40.000 0.05 0.00 0.00 1.28
945 983 4.819630 CCCTATCTTGCGGCACTAAAATTA 59.180 41.667 0.05 0.00 0.00 1.40
946 984 3.632145 CCCTATCTTGCGGCACTAAAATT 59.368 43.478 0.05 0.00 0.00 1.82
1148 1191 3.313803 TCAAGCGTGTAAGTGCAATCAAA 59.686 39.130 0.00 0.00 0.00 2.69
1167 1210 1.086696 GCGAGCCTGCAAATACTCAA 58.913 50.000 0.00 0.00 34.15 3.02
1258 1301 1.319541 CCGTACATCTCCTCGTCCAT 58.680 55.000 0.00 0.00 0.00 3.41
1610 1653 6.945435 TGACCAGGATTGAACTTAATTAAGCA 59.055 34.615 22.45 12.13 36.79 3.91
1751 1887 6.932947 ACTATACTGTTTTGTGACCCTACTC 58.067 40.000 0.00 0.00 0.00 2.59
1808 2034 4.655762 TGGAGATTAGTCAGTCGATTGG 57.344 45.455 8.17 0.00 0.00 3.16
1817 2043 5.357742 TGCTAAGCATTGGAGATTAGTCA 57.642 39.130 0.00 0.00 39.14 3.41
1825 2051 4.205587 AGAGGATTTGCTAAGCATTGGAG 58.794 43.478 0.00 0.00 38.76 3.86
1830 2056 7.013083 CAGTGATTTAGAGGATTTGCTAAGCAT 59.987 37.037 0.00 0.00 38.76 3.79
1832 2058 6.317391 ACAGTGATTTAGAGGATTTGCTAAGC 59.683 38.462 0.00 0.00 0.00 3.09
1849 2075 2.569853 TGGGATAACCGTGACAGTGATT 59.430 45.455 0.00 0.00 44.64 2.57
1861 2087 5.124776 TGAATTCGTGTGATTTGGGATAACC 59.875 40.000 0.04 0.00 40.81 2.85
1865 2091 4.396166 GTCTGAATTCGTGTGATTTGGGAT 59.604 41.667 0.04 0.00 0.00 3.85
1877 2103 2.154462 CAAGGCCTTGTCTGAATTCGT 58.846 47.619 33.46 0.00 35.92 3.85
1878 2104 2.907910 CAAGGCCTTGTCTGAATTCG 57.092 50.000 33.46 7.51 35.92 3.34
1892 2118 3.378427 GGTCATTATCAAGGTGACAAGGC 59.622 47.826 7.00 0.00 43.01 4.35
1904 2130 1.941072 GCATGCGCGGTCATTATCA 59.059 52.632 8.83 0.00 0.00 2.15
2148 2374 1.674980 GTCTGAGGACGACGGAGGT 60.675 63.158 0.00 0.00 32.47 3.85
2223 2449 1.589196 GTCGAGCATGGCGTACTCC 60.589 63.158 1.36 0.00 0.00 3.85
2336 2562 5.121811 GCTAATTTTCCTGATGCTCTCTCA 58.878 41.667 0.00 0.00 0.00 3.27
2337 2563 5.121811 TGCTAATTTTCCTGATGCTCTCTC 58.878 41.667 0.00 0.00 0.00 3.20
2338 2564 5.108187 TGCTAATTTTCCTGATGCTCTCT 57.892 39.130 0.00 0.00 0.00 3.10
2349 2575 6.377146 TCCACAAGGAGTATTGCTAATTTTCC 59.623 38.462 0.00 0.00 39.61 3.13
2368 2594 3.353029 CATGGCGCACGTCCACAA 61.353 61.111 10.83 0.00 36.26 3.33
2380 2606 7.067494 ACACTTCTAGATTGGATTAAACATGGC 59.933 37.037 0.00 0.00 0.00 4.40
2381 2607 8.511604 ACACTTCTAGATTGGATTAAACATGG 57.488 34.615 0.00 0.00 0.00 3.66
2398 2624 6.533723 CACCGAGCAAATATGTAACACTTCTA 59.466 38.462 0.00 0.00 0.00 2.10
2506 2735 2.819608 TGCAGTTTCAGCCTAAACATCC 59.180 45.455 12.51 3.10 40.97 3.51
2606 2835 4.886496 GGTCTCCACCAAAACTAGTACT 57.114 45.455 0.00 0.00 43.17 2.73
2640 2874 9.938670 GATTGTTAATATTGTGCGTGGTAATTA 57.061 29.630 0.00 0.00 0.00 1.40
2649 2883 4.545823 ACCGGATTGTTAATATTGTGCG 57.454 40.909 9.46 0.00 0.00 5.34
2655 2889 7.034685 GGTTGCTAAACCGGATTGTTAATAT 57.965 36.000 9.46 0.00 46.32 1.28
2700 2934 8.864087 TGTCATACTTCTAGCATCATCTGTAAT 58.136 33.333 0.00 0.00 0.00 1.89
2791 3032 9.640963 ACGGTAGATGCTCTTACATAATTTATC 57.359 33.333 0.00 0.00 0.00 1.75
2815 3056 1.392168 ACGGATTTGTTATGCGTGACG 59.608 47.619 0.00 0.00 44.07 4.35
2816 3057 2.222953 GGACGGATTTGTTATGCGTGAC 60.223 50.000 8.98 0.00 45.64 3.67
2822 3063 3.275617 TGAGGGGACGGATTTGTTATG 57.724 47.619 0.00 0.00 0.00 1.90
2832 3073 1.449601 CGGATGTTTGAGGGGACGG 60.450 63.158 0.00 0.00 0.00 4.79
2835 3076 2.267642 CGCGGATGTTTGAGGGGA 59.732 61.111 0.00 0.00 0.00 4.81
2836 3077 2.824041 CCGCGGATGTTTGAGGGG 60.824 66.667 24.07 0.00 0.00 4.79
2881 3138 1.821759 CCAGGCGTGTGTGGAAACA 60.822 57.895 5.57 0.00 35.67 2.83
2884 3141 0.036765 GTATCCAGGCGTGTGTGGAA 60.037 55.000 5.57 0.00 46.01 3.53
2894 3151 3.492102 TGCTAATTGAGGTATCCAGGC 57.508 47.619 0.00 0.00 0.00 4.85
2895 3152 4.580580 GGTTTGCTAATTGAGGTATCCAGG 59.419 45.833 0.00 0.00 0.00 4.45
2896 3153 5.440610 AGGTTTGCTAATTGAGGTATCCAG 58.559 41.667 0.00 0.00 0.00 3.86
2926 3183 2.844946 TGACGGGGCATGTGTAATATG 58.155 47.619 0.00 0.00 38.61 1.78
2931 3190 0.398696 AAGTTGACGGGGCATGTGTA 59.601 50.000 0.00 0.00 0.00 2.90
2940 3199 1.659098 GCTGTATCGAAAGTTGACGGG 59.341 52.381 0.00 0.00 0.00 5.28
2951 3210 1.450848 AGACGTCCGGCTGTATCGA 60.451 57.895 13.01 0.00 28.47 3.59
3006 3265 9.845740 TTAGTATGTATGTAGAACATGCCAAAT 57.154 29.630 2.83 0.00 39.94 2.32
3034 3293 4.103153 ACCGTGGATGATCTTTGTGGATAT 59.897 41.667 0.00 0.00 0.00 1.63
3075 3334 2.132762 CTACTTCCGCAACAAAGACGT 58.867 47.619 0.00 0.00 0.00 4.34
3085 3344 0.109272 CTTCGAGTGCTACTTCCGCA 60.109 55.000 0.00 0.00 34.52 5.69
3144 3403 2.819595 CATTGACGGGGCGGACAG 60.820 66.667 0.00 0.00 0.00 3.51
3177 3436 1.941403 ATGGATGGACTGCCCCCAAG 61.941 60.000 0.00 0.00 38.73 3.61
3253 3512 0.965363 TGCCGGAATCCTCCAAAAGC 60.965 55.000 5.05 0.00 42.58 3.51
3257 3516 1.832719 TTCGTGCCGGAATCCTCCAA 61.833 55.000 5.05 0.00 42.58 3.53
3274 3533 2.159407 GCTGCAGAAGAGGAAGCAATTC 60.159 50.000 20.43 0.00 36.44 2.17
3278 3537 0.321387 CTGCTGCAGAAGAGGAAGCA 60.321 55.000 24.88 3.32 41.36 3.91
3314 3573 4.018609 GACGATGTGATGGAGGCG 57.981 61.111 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.