Multiple sequence alignment - TraesCS2B01G415200

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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 TraesCS2B01G415200 chr2B 100.000 3499 0 0 1 3499 593657715 593654217 0.000000e+00 6462
1 TraesCS2B01G415200 chr2D 92.641 3044 133 41 507 3499 506146374 506143371 0.000000e+00 4296
2 TraesCS2B01G415200 chr2D 90.619 533 8 14 3 499 506146962 506146436 0.000000e+00 669
3 TraesCS2B01G415200 chr2A 90.977 2560 134 39 1000 3499 650628918 650626396 0.000000e+00 3358
4 TraesCS2B01G415200 chr7B 87.037 108 9 5 381 484 62687452 62687346 2.210000e-22 117
5 TraesCS2B01G415200 chr7D 85.088 114 8 7 379 484 104566716 104566604 1.330000e-19 108
6 TraesCS2B01G415200 chr7A 85.849 106 7 6 379 479 108808882 108808780 4.780000e-19 106


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 TraesCS2B01G415200 chr2B 593654217 593657715 3498 True 6462.0 6462 100.000 1 3499 1 chr2B.!!$R1 3498
1 TraesCS2B01G415200 chr2D 506143371 506146962 3591 True 2482.5 4296 91.630 3 3499 2 chr2D.!!$R1 3496
2 TraesCS2B01G415200 chr2A 650626396 650628918 2522 True 3358.0 3358 90.977 1000 3499 1 chr2A.!!$R1 2499

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
919 1021 0.111639 TAGTTTTTCCCCAAGCCGCT 59.888 50.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2781 2907 0.02877 CTCCTCTCTACTGCTTCGCG 59.971 60.0 0.0 0.0 0.0 5.87 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
21 22 3.756117 GTTGGGACAGTTCAAATCTCCT 58.244 45.455 0.00 0.00 42.39 3.69
207 214 2.125753 GTCGAGCTGCTCCTGGTG 60.126 66.667 22.97 9.39 0.00 4.17
213 220 4.463879 CTGCTCCTGGTGGCGAGG 62.464 72.222 0.00 0.00 0.00 4.63
215 222 3.706373 GCTCCTGGTGGCGAGGAA 61.706 66.667 1.80 0.00 37.88 3.36
220 227 1.078848 CTGGTGGCGAGGAAGGAAG 60.079 63.158 0.00 0.00 0.00 3.46
319 329 1.173913 GTGGTGGTAATTGCAGGTCC 58.826 55.000 0.00 0.00 0.00 4.46
321 331 1.145945 TGGTGGTAATTGCAGGTCCAA 59.854 47.619 0.00 0.00 0.00 3.53
365 397 6.042093 GTCCATGTTCCTCTCTGGTGATAATA 59.958 42.308 0.00 0.00 37.07 0.98
400 432 2.466846 CTGCTTGTTGGTGCTTTTCTG 58.533 47.619 0.00 0.00 0.00 3.02
401 433 2.098614 TGCTTGTTGGTGCTTTTCTGA 58.901 42.857 0.00 0.00 0.00 3.27
403 435 3.054878 GCTTGTTGGTGCTTTTCTGATG 58.945 45.455 0.00 0.00 0.00 3.07
404 436 3.243501 GCTTGTTGGTGCTTTTCTGATGA 60.244 43.478 0.00 0.00 0.00 2.92
406 438 2.886523 TGTTGGTGCTTTTCTGATGAGG 59.113 45.455 0.00 0.00 0.00 3.86
486 523 6.233434 CAGCATCTAAGGTTGGCAATCTATA 58.767 40.000 14.43 7.68 0.00 1.31
487 524 6.883217 CAGCATCTAAGGTTGGCAATCTATAT 59.117 38.462 14.43 4.96 0.00 0.86
488 525 7.065563 CAGCATCTAAGGTTGGCAATCTATATC 59.934 40.741 14.43 1.74 0.00 1.63
489 526 6.881065 GCATCTAAGGTTGGCAATCTATATCA 59.119 38.462 14.43 0.00 0.00 2.15
490 527 7.555554 GCATCTAAGGTTGGCAATCTATATCAT 59.444 37.037 14.43 0.00 0.00 2.45
491 528 9.107177 CATCTAAGGTTGGCAATCTATATCATC 57.893 37.037 14.43 0.00 0.00 2.92
495 532 5.311649 AGGTTGGCAATCTATATCATCCACT 59.688 40.000 12.19 0.00 0.00 4.00
496 533 5.645497 GGTTGGCAATCTATATCATCCACTC 59.355 44.000 1.92 0.00 0.00 3.51
497 534 5.426689 TGGCAATCTATATCATCCACTCC 57.573 43.478 0.00 0.00 0.00 3.85
499 536 5.489997 TGGCAATCTATATCATCCACTCCAT 59.510 40.000 0.00 0.00 0.00 3.41
500 537 5.821470 GGCAATCTATATCATCCACTCCATG 59.179 44.000 0.00 0.00 0.00 3.66
502 539 6.651086 CAATCTATATCATCCACTCCATGCT 58.349 40.000 0.00 0.00 0.00 3.79
503 540 6.887886 ATCTATATCATCCACTCCATGCTT 57.112 37.500 0.00 0.00 0.00 3.91
504 541 6.046290 TCTATATCATCCACTCCATGCTTG 57.954 41.667 0.00 0.00 0.00 4.01
505 542 4.987963 ATATCATCCACTCCATGCTTGA 57.012 40.909 0.22 0.00 0.00 3.02
538 627 1.153369 TCAATAGCTCAGCGGCCAC 60.153 57.895 2.24 0.00 0.00 5.01
616 714 3.460825 TGCCTACCCCTAAGAGTTGAAT 58.539 45.455 0.00 0.00 0.00 2.57
673 771 5.292589 GCCATTGCTAATTGAATTTGGTCTG 59.707 40.000 7.25 0.00 33.53 3.51
705 803 7.566879 AGGACTAGGATATGTTCTGTTCAGAAT 59.433 37.037 16.55 6.29 0.00 2.40
719 817 7.108194 TCTGTTCAGAATATTTGAGATGCACT 58.892 34.615 0.00 0.00 0.00 4.40
720 818 8.260114 TCTGTTCAGAATATTTGAGATGCACTA 58.740 33.333 0.00 0.00 0.00 2.74
721 819 8.969260 TGTTCAGAATATTTGAGATGCACTAT 57.031 30.769 0.00 0.00 0.00 2.12
722 820 8.833493 TGTTCAGAATATTTGAGATGCACTATG 58.167 33.333 0.00 0.00 0.00 2.23
765 863 6.435430 TTGTGCAAGTTATGTGATCCATAC 57.565 37.500 0.00 0.00 35.75 2.39
801 901 5.880332 AGTGATTACTTGGTTATTCGCATGT 59.120 36.000 0.00 0.00 31.66 3.21
880 980 2.352715 GCTGAAACGCTAAATTGGGCTT 60.353 45.455 2.26 0.00 0.00 4.35
919 1021 0.111639 TAGTTTTTCCCCAAGCCGCT 59.888 50.000 0.00 0.00 0.00 5.52
985 1087 4.228899 AACGCTCCACGGTTTGTT 57.771 50.000 0.00 0.00 40.34 2.83
994 1096 1.665735 CCACGGTTTGTTGCAGCATAC 60.666 52.381 14.22 14.22 0.00 2.39
1013 1115 1.522569 GTAAGATGGCCGTGCTCCT 59.477 57.895 0.00 0.00 0.00 3.69
1264 1366 4.617959 TGTCATCGGTAATAGTAGCAAGC 58.382 43.478 0.00 0.00 0.00 4.01
1265 1367 4.098807 TGTCATCGGTAATAGTAGCAAGCA 59.901 41.667 0.00 0.00 0.00 3.91
1266 1368 4.681942 GTCATCGGTAATAGTAGCAAGCAG 59.318 45.833 0.00 0.00 0.00 4.24
1306 1408 5.438761 AACTTTGTTTAGACTGTCCATGC 57.561 39.130 3.76 0.00 0.00 4.06
1421 1523 3.141398 GCTGAAGTGATCAACAGTGGAA 58.859 45.455 19.63 0.00 37.67 3.53
1488 1590 8.229137 CGGTTCCTTTTACGTATGTGATTTTTA 58.771 33.333 0.00 0.00 0.00 1.52
1497 1601 9.900710 TTACGTATGTGATTTTTATTTTGCAGT 57.099 25.926 0.00 0.00 0.00 4.40
1498 1602 8.810652 ACGTATGTGATTTTTATTTTGCAGTT 57.189 26.923 0.00 0.00 0.00 3.16
1499 1603 8.698854 ACGTATGTGATTTTTATTTTGCAGTTG 58.301 29.630 0.00 0.00 0.00 3.16
1519 1623 2.298610 GGTATACTTCCCTTGGCTTGC 58.701 52.381 2.25 0.00 0.00 4.01
1531 1644 1.032014 TGGCTTGCTTTGGTCTGAAC 58.968 50.000 0.00 0.00 0.00 3.18
1533 1646 1.268079 GGCTTGCTTTGGTCTGAACTC 59.732 52.381 0.00 0.00 0.00 3.01
1534 1647 2.225467 GCTTGCTTTGGTCTGAACTCT 58.775 47.619 0.00 0.00 0.00 3.24
1535 1648 2.031333 GCTTGCTTTGGTCTGAACTCTG 60.031 50.000 0.00 0.00 0.00 3.35
1537 1650 3.558931 TGCTTTGGTCTGAACTCTGAA 57.441 42.857 0.00 0.00 0.00 3.02
1539 1652 4.464008 TGCTTTGGTCTGAACTCTGAATT 58.536 39.130 0.00 0.00 0.00 2.17
1540 1653 4.276678 TGCTTTGGTCTGAACTCTGAATTG 59.723 41.667 0.00 0.00 0.00 2.32
1541 1654 4.791974 CTTTGGTCTGAACTCTGAATTGC 58.208 43.478 0.00 0.00 0.00 3.56
1542 1655 3.490439 TGGTCTGAACTCTGAATTGCA 57.510 42.857 0.00 0.00 0.00 4.08
1543 1656 3.819368 TGGTCTGAACTCTGAATTGCAA 58.181 40.909 0.00 0.00 0.00 4.08
1544 1657 3.565482 TGGTCTGAACTCTGAATTGCAAC 59.435 43.478 0.00 0.00 0.00 4.17
1587 1700 1.153349 GATCGGAAGGGTGCCACTC 60.153 63.158 0.00 0.00 0.00 3.51
1634 1747 3.984838 CCAGAGCTCAGATACTGGC 57.015 57.895 17.77 0.00 42.30 4.85
1641 1754 1.202580 GCTCAGATACTGGCGACCATT 60.203 52.381 0.00 0.00 30.82 3.16
1710 1823 2.029623 GCTGCTGGATCCAATGACATT 58.970 47.619 17.00 0.00 0.00 2.71
1711 1824 2.429610 GCTGCTGGATCCAATGACATTT 59.570 45.455 17.00 0.00 0.00 2.32
1729 1842 4.351111 ACATTTTGGAGTACCTCTCACCTT 59.649 41.667 0.00 0.00 44.40 3.50
1761 1874 0.965866 TCGGACGACAGAAGCCTGAT 60.966 55.000 0.00 0.00 43.02 2.90
1789 1902 1.770294 TTTTCAGGACGCCTTGGTTT 58.230 45.000 0.00 0.00 0.00 3.27
1835 1948 1.348064 CCACTCACCCCTAACTCACA 58.652 55.000 0.00 0.00 0.00 3.58
1836 1949 1.276421 CCACTCACCCCTAACTCACAG 59.724 57.143 0.00 0.00 0.00 3.66
1837 1950 1.971357 CACTCACCCCTAACTCACAGT 59.029 52.381 0.00 0.00 0.00 3.55
1838 1951 1.971357 ACTCACCCCTAACTCACAGTG 59.029 52.381 0.00 0.00 0.00 3.66
1840 1953 2.368875 CTCACCCCTAACTCACAGTGTT 59.631 50.000 0.00 0.00 0.00 3.32
1841 1954 2.367567 TCACCCCTAACTCACAGTGTTC 59.632 50.000 0.00 0.00 0.00 3.18
1842 1955 1.697982 ACCCCTAACTCACAGTGTTCC 59.302 52.381 0.00 0.00 0.00 3.62
1843 1956 1.978580 CCCCTAACTCACAGTGTTCCT 59.021 52.381 0.00 0.00 0.00 3.36
1845 1958 3.195825 CCCCTAACTCACAGTGTTCCTAG 59.804 52.174 0.00 0.00 0.00 3.02
1847 1960 3.511934 CCTAACTCACAGTGTTCCTAGCT 59.488 47.826 0.00 0.00 0.00 3.32
1848 1961 4.705507 CCTAACTCACAGTGTTCCTAGCTA 59.294 45.833 0.00 0.00 0.00 3.32
1849 1962 4.792521 AACTCACAGTGTTCCTAGCTAG 57.207 45.455 14.20 14.20 0.00 3.42
1850 1963 3.768878 ACTCACAGTGTTCCTAGCTAGT 58.231 45.455 19.31 0.00 0.00 2.57
1851 1964 3.508012 ACTCACAGTGTTCCTAGCTAGTG 59.492 47.826 19.31 11.89 0.00 2.74
1852 1965 3.759086 CTCACAGTGTTCCTAGCTAGTGA 59.241 47.826 19.31 12.94 34.10 3.41
1853 1966 3.759086 TCACAGTGTTCCTAGCTAGTGAG 59.241 47.826 19.31 8.60 31.81 3.51
1854 1967 3.508012 CACAGTGTTCCTAGCTAGTGAGT 59.492 47.826 19.31 7.41 0.00 3.41
1857 1970 4.944930 CAGTGTTCCTAGCTAGTGAGTAGT 59.055 45.833 19.31 8.84 0.00 2.73
1874 1987 9.490379 AGTGAGTAGTACTGTAATTTTCTTTGG 57.510 33.333 7.76 0.00 0.00 3.28
1907 2020 3.338249 TCTGAGCTTACCATCTTGCAAC 58.662 45.455 0.00 0.00 0.00 4.17
1936 2049 1.155424 AAACGAAGCGGCTGAACGAA 61.155 50.000 23.42 0.00 35.47 3.85
2032 2145 4.410400 CCTGCCGGGGAGTGTTCC 62.410 72.222 14.85 0.00 43.23 3.62
2106 2219 1.606531 GCAGGCTGAACCAGGAGAT 59.393 57.895 20.86 0.00 43.14 2.75
2164 2277 2.775890 GGCATCGTCATGGAGATCATT 58.224 47.619 0.00 0.00 32.92 2.57
2174 2287 0.462581 GGAGATCATTCGGCAGCACA 60.463 55.000 0.00 0.00 0.00 4.57
2188 2301 2.674177 GCAGCACAGTCAATACGGTAGT 60.674 50.000 0.00 0.00 32.39 2.73
2208 2321 6.815142 GGTAGTAGGATTTTCTTTCTTGCGTA 59.185 38.462 0.00 0.00 0.00 4.42
2239 2352 0.034198 TTCGCATTCCGTGGACTGAA 59.966 50.000 10.15 0.00 38.35 3.02
2241 2354 0.165944 CGCATTCCGTGGACTGAAAC 59.834 55.000 10.15 0.00 0.00 2.78
2246 2359 0.834612 TCCGTGGACTGAAACTTGGT 59.165 50.000 0.00 0.00 0.00 3.67
2247 2360 1.202604 TCCGTGGACTGAAACTTGGTC 60.203 52.381 0.00 0.00 0.00 4.02
2248 2361 1.474320 CCGTGGACTGAAACTTGGTCA 60.474 52.381 0.00 0.00 0.00 4.02
2251 2364 2.030805 GTGGACTGAAACTTGGTCATGC 60.031 50.000 0.00 0.00 0.00 4.06
2253 2366 0.593128 ACTGAAACTTGGTCATGCGC 59.407 50.000 0.00 0.00 0.00 6.09
2254 2367 0.592637 CTGAAACTTGGTCATGCGCA 59.407 50.000 14.96 14.96 0.00 6.09
2548 2669 2.483876 CACCGCATCGTGGAATATCTT 58.516 47.619 0.00 0.00 36.58 2.40
2555 2679 2.326428 TCGTGGAATATCTTCTCCCCC 58.674 52.381 0.00 0.00 0.00 5.40
2570 2694 4.038080 CCCCGCGCAACACTTTCC 62.038 66.667 8.75 0.00 0.00 3.13
2654 2779 5.888161 TCTTTTCTTTTTCCTTCTCTGCTGT 59.112 36.000 0.00 0.00 0.00 4.40
2703 2829 3.428452 CCGGAAAGTAGATCGCTGTTGTA 60.428 47.826 0.00 0.00 0.00 2.41
2771 2897 0.166597 CGTACGTGCGGTCTACAGAA 59.833 55.000 18.81 0.00 0.00 3.02
2781 2907 2.860735 CGGTCTACAGAAGTGCATAAGC 59.139 50.000 0.00 0.00 42.57 3.09
2804 2930 3.537580 CGAAGCAGTAGAGAGGAGTAGT 58.462 50.000 0.00 0.00 0.00 2.73
2805 2931 4.695396 CGAAGCAGTAGAGAGGAGTAGTA 58.305 47.826 0.00 0.00 0.00 1.82
2807 2933 4.081322 AGCAGTAGAGAGGAGTAGTAGC 57.919 50.000 0.00 0.00 0.00 3.58
2808 2934 2.803956 GCAGTAGAGAGGAGTAGTAGCG 59.196 54.545 0.00 0.00 0.00 4.26
2809 2935 2.803956 CAGTAGAGAGGAGTAGTAGCGC 59.196 54.545 0.00 0.00 0.00 5.92
2810 2936 2.435069 AGTAGAGAGGAGTAGTAGCGCA 59.565 50.000 11.47 0.00 0.00 6.09
2812 2938 1.065345 AGAGAGGAGTAGTAGCGCACA 60.065 52.381 11.47 0.00 0.00 4.57
2813 2939 1.950909 GAGAGGAGTAGTAGCGCACAT 59.049 52.381 11.47 0.00 0.00 3.21
2814 2940 1.678627 AGAGGAGTAGTAGCGCACATG 59.321 52.381 11.47 0.00 0.00 3.21
2816 2942 0.179111 GGAGTAGTAGCGCACATGCA 60.179 55.000 11.47 0.00 42.21 3.96
2818 2944 2.288213 GGAGTAGTAGCGCACATGCATA 60.288 50.000 11.47 0.00 42.21 3.14
2822 2949 3.614159 AGTAGCGCACATGCATATTTG 57.386 42.857 11.47 0.00 42.21 2.32
2831 2958 4.126437 CACATGCATATTTGACGGGACTA 58.874 43.478 0.00 0.00 0.00 2.59
2841 2968 1.067142 TGACGGGACTATTCTGCACAC 60.067 52.381 0.00 0.00 0.00 3.82
2918 3053 2.415491 CGCAACACTTGGACTCGATCTA 60.415 50.000 0.00 0.00 0.00 1.98
2954 3089 4.053526 TGCCAGGCGCGTACGTAA 62.054 61.111 17.90 0.00 42.08 3.18
3028 3163 2.566765 GTCGTCGTCGTCGTCGTC 60.567 66.667 18.44 11.28 45.27 4.20
3207 3342 1.380515 CTCTCCCTCTTCGCCTCCA 60.381 63.158 0.00 0.00 0.00 3.86
3297 3445 2.420568 CCCGCCTCCACGTAGCTTA 61.421 63.158 0.00 0.00 0.00 3.09
3301 3449 0.806492 GCCTCCACGTAGCTTACAGC 60.806 60.000 0.00 0.00 42.84 4.40
3341 3504 3.456280 CATGCAGTAGCTTCTCTTCTCC 58.544 50.000 0.00 0.00 42.74 3.71
3403 3566 3.532155 GCTCGCTCCGGGATCAGT 61.532 66.667 0.00 0.00 0.00 3.41
3412 3575 2.632028 CTCCGGGATCAGTTGAGATCAT 59.368 50.000 0.00 0.00 44.89 2.45
3417 3580 4.636249 GGGATCAGTTGAGATCATACCAC 58.364 47.826 6.32 0.00 44.89 4.16
3470 3644 5.762179 TGTTTCTATGTCCAGGATCACTT 57.238 39.130 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.753797 GAGGAGATTTGAACTGTCCCAAC 59.246 47.826 0.00 0.00 0.00 3.77
1 2 3.652869 AGAGGAGATTTGAACTGTCCCAA 59.347 43.478 0.00 0.00 0.00 4.12
21 22 3.657634 GTCATGTCTGACTGCTTCAAGA 58.342 45.455 9.51 0.00 46.84 3.02
207 214 2.736826 CCCTCCTTCCTTCCTCGCC 61.737 68.421 0.00 0.00 0.00 5.54
212 219 0.326713 AGCTACCCCTCCTTCCTTCC 60.327 60.000 0.00 0.00 0.00 3.46
213 220 0.833949 CAGCTACCCCTCCTTCCTTC 59.166 60.000 0.00 0.00 0.00 3.46
214 221 0.417841 TCAGCTACCCCTCCTTCCTT 59.582 55.000 0.00 0.00 0.00 3.36
215 222 0.417841 TTCAGCTACCCCTCCTTCCT 59.582 55.000 0.00 0.00 0.00 3.36
220 227 2.431419 GAGTAACTTCAGCTACCCCTCC 59.569 54.545 0.00 0.00 0.00 4.30
319 329 0.671781 CTGCGGAGAGGTTGGACTTG 60.672 60.000 0.00 0.00 0.00 3.16
321 331 1.228894 TCTGCGGAGAGGTTGGACT 60.229 57.895 0.98 0.00 0.00 3.85
365 397 1.538047 AGCAGCACATCGAAAATGGT 58.462 45.000 0.00 0.00 0.00 3.55
400 432 0.886563 AGCAAAGCAACAGCCTCATC 59.113 50.000 0.00 0.00 0.00 2.92
401 433 1.335145 AAGCAAAGCAACAGCCTCAT 58.665 45.000 0.00 0.00 0.00 2.90
403 435 1.202452 ACAAAGCAAAGCAACAGCCTC 60.202 47.619 0.00 0.00 0.00 4.70
404 436 0.826062 ACAAAGCAAAGCAACAGCCT 59.174 45.000 0.00 0.00 0.00 4.58
406 438 1.325338 CACACAAAGCAAAGCAACAGC 59.675 47.619 0.00 0.00 0.00 4.40
459 496 1.272092 TGCCAACCTTAGATGCTGCTT 60.272 47.619 0.00 0.00 0.00 3.91
486 523 3.878237 ATCAAGCATGGAGTGGATGAT 57.122 42.857 0.00 0.00 0.00 2.45
487 524 4.987963 ATATCAAGCATGGAGTGGATGA 57.012 40.909 0.00 0.00 0.00 2.92
488 525 5.301045 ACAAATATCAAGCATGGAGTGGATG 59.699 40.000 0.00 0.00 0.00 3.51
489 526 5.301045 CACAAATATCAAGCATGGAGTGGAT 59.699 40.000 0.00 0.00 0.00 3.41
490 527 4.641541 CACAAATATCAAGCATGGAGTGGA 59.358 41.667 0.00 0.00 0.00 4.02
491 528 4.400251 ACACAAATATCAAGCATGGAGTGG 59.600 41.667 0.00 0.00 0.00 4.00
495 532 6.658816 ACAACTACACAAATATCAAGCATGGA 59.341 34.615 0.00 0.00 0.00 3.41
496 533 6.855836 ACAACTACACAAATATCAAGCATGG 58.144 36.000 0.00 0.00 0.00 3.66
497 534 7.529158 TGACAACTACACAAATATCAAGCATG 58.471 34.615 0.00 0.00 0.00 4.06
499 536 7.503521 TTGACAACTACACAAATATCAAGCA 57.496 32.000 0.00 0.00 0.00 3.91
500 537 9.708222 CTATTGACAACTACACAAATATCAAGC 57.292 33.333 0.00 0.00 0.00 4.01
502 539 9.448438 AGCTATTGACAACTACACAAATATCAA 57.552 29.630 0.00 0.00 0.00 2.57
503 540 9.098355 GAGCTATTGACAACTACACAAATATCA 57.902 33.333 0.00 0.00 0.00 2.15
504 541 9.098355 TGAGCTATTGACAACTACACAAATATC 57.902 33.333 0.00 0.00 0.00 1.63
505 542 9.102757 CTGAGCTATTGACAACTACACAAATAT 57.897 33.333 0.00 0.00 0.00 1.28
566 655 3.254629 GCTTGACTTGCCATGGAGA 57.745 52.632 18.40 0.95 0.00 3.71
673 771 6.778559 ACAGAACATATCCTAGTCCTACTTCC 59.221 42.308 0.00 0.00 0.00 3.46
705 803 7.071069 AGGTCATCATAGTGCATCTCAAATA 57.929 36.000 0.00 0.00 0.00 1.40
765 863 9.561069 AACCAAGTAATCACTAATTAGGCATAG 57.439 33.333 16.73 1.91 33.48 2.23
801 901 9.657419 ACAATCAAGCATCGAATATCACATATA 57.343 29.630 0.00 0.00 0.00 0.86
815 915 8.986477 AAAAGGTAAACATACAATCAAGCATC 57.014 30.769 0.00 0.00 0.00 3.91
856 956 3.181397 CCCAATTTAGCGTTTCAGCATG 58.819 45.455 0.00 0.00 40.15 4.06
896 997 2.423538 CGGCTTGGGGAAAAACTATGAG 59.576 50.000 0.00 0.00 0.00 2.90
919 1021 2.436646 GCGCCAAGCCTCTTAGCA 60.437 61.111 0.00 0.00 40.81 3.49
982 1084 2.935849 CCATCTTACGTATGCTGCAACA 59.064 45.455 6.36 0.00 0.00 3.33
983 1085 2.286418 GCCATCTTACGTATGCTGCAAC 60.286 50.000 6.36 5.69 0.00 4.17
984 1086 1.939934 GCCATCTTACGTATGCTGCAA 59.060 47.619 6.36 0.00 0.00 4.08
985 1087 1.581934 GCCATCTTACGTATGCTGCA 58.418 50.000 4.13 4.13 0.00 4.41
994 1096 1.883084 GGAGCACGGCCATCTTACG 60.883 63.158 2.24 0.00 0.00 3.18
1264 1366 9.390795 CAAAGTTTCTCATGAAAACTCATACTG 57.609 33.333 23.89 16.43 42.94 2.74
1265 1367 9.125026 ACAAAGTTTCTCATGAAAACTCATACT 57.875 29.630 23.89 13.15 42.94 2.12
1266 1368 9.736023 AACAAAGTTTCTCATGAAAACTCATAC 57.264 29.630 23.89 4.97 42.94 2.39
1306 1408 7.017645 CACCAAGACATTTTCGTCAGATAAAG 58.982 38.462 0.00 0.00 38.43 1.85
1421 1523 4.327680 GAAGAACCAGAAGCATAGTTGGT 58.672 43.478 0.00 0.00 45.47 3.67
1488 1590 5.580022 AGGGAAGTATACCAACTGCAAAAT 58.420 37.500 0.00 0.00 0.00 1.82
1492 1596 3.308117 CCAAGGGAAGTATACCAACTGCA 60.308 47.826 0.00 0.00 0.00 4.41
1493 1597 3.279434 CCAAGGGAAGTATACCAACTGC 58.721 50.000 0.00 0.00 0.00 4.40
1495 1599 3.190439 AGCCAAGGGAAGTATACCAACT 58.810 45.455 0.00 0.00 0.00 3.16
1496 1600 3.646736 AGCCAAGGGAAGTATACCAAC 57.353 47.619 0.00 0.00 0.00 3.77
1497 1601 3.876156 GCAAGCCAAGGGAAGTATACCAA 60.876 47.826 0.00 0.00 0.00 3.67
1498 1602 2.356741 GCAAGCCAAGGGAAGTATACCA 60.357 50.000 0.00 0.00 0.00 3.25
1499 1603 2.092375 AGCAAGCCAAGGGAAGTATACC 60.092 50.000 0.00 0.00 0.00 2.73
1519 1623 4.276678 TGCAATTCAGAGTTCAGACCAAAG 59.723 41.667 0.00 0.00 0.00 2.77
1531 1644 5.981315 ACATTTTCACAGTTGCAATTCAGAG 59.019 36.000 0.59 0.00 0.00 3.35
1533 1646 5.050634 CCACATTTTCACAGTTGCAATTCAG 60.051 40.000 0.59 0.00 0.00 3.02
1534 1647 4.809958 CCACATTTTCACAGTTGCAATTCA 59.190 37.500 0.59 0.00 0.00 2.57
1535 1648 4.810491 ACCACATTTTCACAGTTGCAATTC 59.190 37.500 0.59 0.00 0.00 2.17
1537 1650 4.405116 ACCACATTTTCACAGTTGCAAT 57.595 36.364 0.59 0.00 0.00 3.56
1539 1652 3.519579 CAACCACATTTTCACAGTTGCA 58.480 40.909 0.00 0.00 0.00 4.08
1540 1653 2.865551 CCAACCACATTTTCACAGTTGC 59.134 45.455 0.00 0.00 34.64 4.17
1541 1654 3.118811 ACCCAACCACATTTTCACAGTTG 60.119 43.478 0.00 0.00 35.51 3.16
1542 1655 3.103742 ACCCAACCACATTTTCACAGTT 58.896 40.909 0.00 0.00 0.00 3.16
1543 1656 2.745968 ACCCAACCACATTTTCACAGT 58.254 42.857 0.00 0.00 0.00 3.55
1544 1657 3.456280 CAACCCAACCACATTTTCACAG 58.544 45.455 0.00 0.00 0.00 3.66
1587 1700 2.015736 AGTAGCTGATTTGCTGTCCG 57.984 50.000 0.00 0.00 43.87 4.79
1634 1747 1.032114 GGCTTTCTCCCCAATGGTCG 61.032 60.000 0.00 0.00 34.77 4.79
1681 1794 2.599645 GATCCAGCAGCCACCGTGAT 62.600 60.000 0.00 0.00 0.00 3.06
1729 1842 0.389817 CGTCCGAAGAATGGCACTGA 60.390 55.000 0.00 0.00 0.00 3.41
1789 1902 3.765381 TCAGATGAAATGCCAACTTGGA 58.235 40.909 12.37 0.00 40.96 3.53
1835 1948 5.182169 ACTACTCACTAGCTAGGAACACT 57.818 43.478 24.35 0.00 0.00 3.55
1836 1949 6.037391 CAGTACTACTCACTAGCTAGGAACAC 59.963 46.154 24.35 10.56 0.00 3.32
1837 1950 6.114089 CAGTACTACTCACTAGCTAGGAACA 58.886 44.000 24.35 8.41 0.00 3.18
1838 1951 6.114767 ACAGTACTACTCACTAGCTAGGAAC 58.885 44.000 24.35 12.41 0.00 3.62
1840 1953 5.954153 ACAGTACTACTCACTAGCTAGGA 57.046 43.478 24.35 16.54 0.00 2.94
1841 1954 8.680039 AATTACAGTACTACTCACTAGCTAGG 57.320 38.462 24.35 13.33 0.00 3.02
1845 1958 9.857957 AAGAAAATTACAGTACTACTCACTAGC 57.142 33.333 0.00 0.00 0.00 3.42
1848 1961 9.490379 CCAAAGAAAATTACAGTACTACTCACT 57.510 33.333 0.00 0.00 0.00 3.41
1849 1962 9.269453 ACCAAAGAAAATTACAGTACTACTCAC 57.731 33.333 0.00 0.00 0.00 3.51
1850 1963 9.841295 AACCAAAGAAAATTACAGTACTACTCA 57.159 29.630 0.00 0.00 0.00 3.41
1853 1966 9.177304 GCAAACCAAAGAAAATTACAGTACTAC 57.823 33.333 0.00 0.00 0.00 2.73
1854 1967 9.127277 AGCAAACCAAAGAAAATTACAGTACTA 57.873 29.630 0.00 0.00 0.00 1.82
1857 1970 7.430441 GGAGCAAACCAAAGAAAATTACAGTA 58.570 34.615 0.00 0.00 0.00 2.74
1936 2049 1.633945 ACAAATTTCCTAGCCCCGAGT 59.366 47.619 0.00 0.00 0.00 4.18
2023 2136 2.031163 ACAGCTGCGGAACACTCC 59.969 61.111 15.27 0.00 38.52 3.85
2032 2145 1.206072 GAGCTTGTTCACAGCTGCG 59.794 57.895 15.27 3.95 39.21 5.18
2035 2148 1.226686 CGCAGAGCTTGTTCACAGCT 61.227 55.000 0.00 0.00 42.13 4.24
2125 2238 0.105224 CGTGGGTGTTGGTGTAGACA 59.895 55.000 0.00 0.00 0.00 3.41
2164 2277 0.735978 CGTATTGACTGTGCTGCCGA 60.736 55.000 0.00 0.00 0.00 5.54
2174 2287 7.657023 AGAAAATCCTACTACCGTATTGACT 57.343 36.000 0.00 0.00 0.00 3.41
2188 2301 5.121768 GCAGTACGCAAGAAAGAAAATCCTA 59.878 40.000 5.07 0.00 41.79 2.94
2217 2330 2.046700 TCCACGGAATGCGAACCC 60.047 61.111 0.00 0.00 0.00 4.11
2228 2341 1.226746 GACCAAGTTTCAGTCCACGG 58.773 55.000 0.00 0.00 0.00 4.94
2239 2352 0.601576 TACGTGCGCATGACCAAGTT 60.602 50.000 34.95 13.88 0.00 2.66
2241 2354 1.695893 CCTACGTGCGCATGACCAAG 61.696 60.000 34.95 22.85 0.00 3.61
2246 2359 1.348538 CGAAACCTACGTGCGCATGA 61.349 55.000 34.95 17.49 0.00 3.07
2247 2360 1.058748 CGAAACCTACGTGCGCATG 59.941 57.895 27.53 27.53 0.00 4.06
2248 2361 1.076533 CTCGAAACCTACGTGCGCAT 61.077 55.000 15.91 0.00 0.00 4.73
2251 2364 0.797249 CTCCTCGAAACCTACGTGCG 60.797 60.000 0.00 0.00 0.00 5.34
2253 2366 0.458025 GCCTCCTCGAAACCTACGTG 60.458 60.000 0.00 0.00 0.00 4.49
2254 2367 1.888736 GCCTCCTCGAAACCTACGT 59.111 57.895 0.00 0.00 0.00 3.57
2525 2646 1.087202 TATTCCACGATGCGGTGCAC 61.087 55.000 8.80 8.80 43.04 4.57
2568 2692 3.620286 CGTTTGAAGACGTGCGGA 58.380 55.556 0.00 0.00 38.19 5.54
2669 2795 0.039165 CTTTCCGGCCTTCACAAAGC 60.039 55.000 0.00 0.00 0.00 3.51
2703 2829 3.497262 GTCGTTCCGAATTGTTCCTTTCT 59.503 43.478 0.00 0.00 37.72 2.52
2771 2897 1.699656 CTGCTTCGCGCTTATGCACT 61.700 55.000 5.56 0.00 40.11 4.40
2781 2907 0.028770 CTCCTCTCTACTGCTTCGCG 59.971 60.000 0.00 0.00 0.00 5.87
2798 2924 1.858091 ATGCATGTGCGCTACTACTC 58.142 50.000 9.73 0.00 45.83 2.59
2801 2927 4.211164 GTCAAATATGCATGTGCGCTACTA 59.789 41.667 10.16 0.00 45.83 1.82
2802 2928 3.002656 GTCAAATATGCATGTGCGCTACT 59.997 43.478 10.16 0.00 45.83 2.57
2803 2929 3.291585 GTCAAATATGCATGTGCGCTAC 58.708 45.455 10.16 5.95 45.83 3.58
2804 2930 2.032979 CGTCAAATATGCATGTGCGCTA 60.033 45.455 10.16 0.00 45.83 4.26
2805 2931 1.268184 CGTCAAATATGCATGTGCGCT 60.268 47.619 10.16 0.00 45.83 5.92
2807 2933 1.597690 CCCGTCAAATATGCATGTGCG 60.598 52.381 10.16 11.64 45.83 5.34
2808 2934 1.675483 TCCCGTCAAATATGCATGTGC 59.325 47.619 10.16 0.00 42.50 4.57
2809 2935 2.945008 AGTCCCGTCAAATATGCATGTG 59.055 45.455 10.16 4.99 0.00 3.21
2810 2936 3.281727 AGTCCCGTCAAATATGCATGT 57.718 42.857 10.16 0.00 0.00 3.21
2812 2938 5.702670 CAGAATAGTCCCGTCAAATATGCAT 59.297 40.000 3.79 3.79 0.00 3.96
2813 2939 5.056480 CAGAATAGTCCCGTCAAATATGCA 58.944 41.667 0.00 0.00 0.00 3.96
2814 2940 4.083802 GCAGAATAGTCCCGTCAAATATGC 60.084 45.833 0.00 0.00 0.00 3.14
2816 2942 5.057149 GTGCAGAATAGTCCCGTCAAATAT 58.943 41.667 0.00 0.00 0.00 1.28
2818 2944 3.270877 GTGCAGAATAGTCCCGTCAAAT 58.729 45.455 0.00 0.00 0.00 2.32
2822 2949 1.641577 GTGTGCAGAATAGTCCCGTC 58.358 55.000 0.00 0.00 0.00 4.79
2881 3016 2.522638 GCGCGCATATATACCCGCC 61.523 63.158 29.10 10.40 43.16 6.13
2954 3089 3.411517 CCCGCCTCCATGGAAGGT 61.412 66.667 23.28 0.00 38.35 3.50
3281 3425 0.525668 CTGTAAGCTACGTGGAGGCG 60.526 60.000 1.81 0.00 37.94 5.52
3297 3445 0.250901 ACGGAAGAATGGCAAGCTGT 60.251 50.000 0.00 0.00 0.00 4.40
3301 3449 1.135315 CGCACGGAAGAATGGCAAG 59.865 57.895 0.00 0.00 0.00 4.01
3303 3451 3.430862 GCGCACGGAAGAATGGCA 61.431 61.111 0.30 0.00 0.00 4.92
3304 3452 2.764314 ATGCGCACGGAAGAATGGC 61.764 57.895 14.90 0.00 0.00 4.40
3403 3566 6.293004 TGTGTACATGTGGTATGATCTCAA 57.707 37.500 9.11 0.00 33.76 3.02
3412 3575 3.515901 TGTATGGCTGTGTACATGTGGTA 59.484 43.478 9.11 0.00 0.00 3.25
3417 3580 6.482973 TGAACATATGTATGGCTGTGTACATG 59.517 38.462 9.21 0.00 40.63 3.21
3470 3644 1.609208 GAAGAAACCCAAGCAGCAGA 58.391 50.000 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.