Multiple sequence alignment - TraesCS6B01G244400

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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 TraesCS6B01G244400 chr6B 100.000 3894 0 0 1 3894 435835283 435831390 0.000000e+00 7191
1 TraesCS6B01G244400 chr6A 93.018 3896 173 44 4 3851 392196601 392192757 0.000000e+00 5596
2 TraesCS6B01G244400 chr6D 93.460 3318 152 26 575 3851 273924798 273921505 0.000000e+00 4865
3 TraesCS6B01G244400 chr6D 94.105 458 22 4 1 456 273925594 273925140 0.000000e+00 691
4 TraesCS6B01G244400 chr2A 84.848 231 35 0 2662 2892 585212583 585212353 2.340000e-57 233
5 TraesCS6B01G244400 chr2D 84.416 231 36 0 2662 2892 441574416 441574186 1.090000e-55 228
6 TraesCS6B01G244400 chr2B 84.416 231 36 0 2662 2892 519185105 519184875 1.090000e-55 228
7 TraesCS6B01G244400 chr5B 82.212 208 37 0 2685 2892 19790644 19790437 3.090000e-41 180


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 TraesCS6B01G244400 chr6B 435831390 435835283 3893 True 7191 7191 100.0000 1 3894 1 chr6B.!!$R1 3893
1 TraesCS6B01G244400 chr6A 392192757 392196601 3844 True 5596 5596 93.0180 4 3851 1 chr6A.!!$R1 3847
2 TraesCS6B01G244400 chr6D 273921505 273925594 4089 True 2778 4865 93.7825 1 3851 2 chr6D.!!$R1 3850

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
36 37 0.324943 AGTGGCAAGTCTACGGCAAT 59.675 50.000 0.00 0.0 39.64 3.56 F
493 496 0.984995 GTTACAAGCCAGGGAGAGGT 59.015 55.000 0.00 0.0 0.00 3.85 F
953 1181 1.138069 GAGGCCAAGTTAGCTCCTCTC 59.862 57.143 5.01 0.0 40.02 3.20 F
2275 2530 1.310373 CCTACCTTCCGGGAGTCCT 59.690 63.158 9.48 0.0 39.91 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1528 1768 1.081892 GCTGGTACATGTGCTGACAG 58.918 55.0 13.86 12.91 38.20 3.51 R
2264 2519 0.032117 ACATCATCAGGACTCCCGGA 60.032 55.0 0.73 0.00 40.86 5.14 R
2689 2946 0.106268 TTCCTGCTGTTGGCTTTGGA 60.106 50.0 0.00 0.00 42.39 3.53 R
3287 3551 0.178876 TCATTGGGGTCAGGTGAGGA 60.179 55.0 0.00 0.00 0.00 3.71 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
30 31 3.190874 GCAGTATCAGTGGCAAGTCTAC 58.809 50.000 0.00 0.00 0.00 2.59
36 37 0.324943 AGTGGCAAGTCTACGGCAAT 59.675 50.000 0.00 0.00 39.64 3.56
47 48 7.587757 GCAAGTCTACGGCAATAATTAATTGAG 59.412 37.037 11.05 2.01 46.81 3.02
226 229 6.293298 CCACAGATTAGCATCTCAAGCATTAC 60.293 42.308 0.00 0.00 37.71 1.89
230 233 5.490139 TTAGCATCTCAAGCATTACAAGC 57.510 39.130 0.00 0.00 0.00 4.01
242 245 1.491668 TTACAAGCGCTATCCAGGGA 58.508 50.000 12.05 0.00 36.87 4.20
250 253 2.419297 GCGCTATCCAGGGATATCAAGG 60.419 54.545 8.42 3.16 36.62 3.61
256 259 7.147724 CGCTATCCAGGGATATCAAGGTTATTA 60.148 40.741 8.42 0.00 36.62 0.98
260 263 8.150827 TCCAGGGATATCAAGGTTATTATCAG 57.849 38.462 4.83 0.00 0.00 2.90
312 315 1.288633 TCGTCAGGAATACCCCCTACA 59.711 52.381 0.00 0.00 36.73 2.74
325 328 9.465199 GAATACCCCCTACAACTTTTTAACATA 57.535 33.333 0.00 0.00 0.00 2.29
362 365 2.489938 TCCCACCATGCTTACACTTC 57.510 50.000 0.00 0.00 0.00 3.01
365 368 2.749621 CCCACCATGCTTACACTTCTTC 59.250 50.000 0.00 0.00 0.00 2.87
465 468 9.974980 TCTACAATACATAATCGTCATTTAGCA 57.025 29.630 0.00 0.00 0.00 3.49
474 477 8.898792 CATAATCGTCATTTAGCATTTGACATG 58.101 33.333 8.97 0.00 39.75 3.21
475 478 5.878332 TCGTCATTTAGCATTTGACATGT 57.122 34.783 0.00 0.00 39.75 3.21
482 485 7.541783 TCATTTAGCATTTGACATGTTACAAGC 59.458 33.333 0.00 0.00 0.00 4.01
488 491 1.702401 TGACATGTTACAAGCCAGGGA 59.298 47.619 0.00 0.00 0.00 4.20
490 493 1.985159 ACATGTTACAAGCCAGGGAGA 59.015 47.619 0.00 0.00 0.00 3.71
493 496 0.984995 GTTACAAGCCAGGGAGAGGT 59.015 55.000 0.00 0.00 0.00 3.85
497 504 3.194025 AAGCCAGGGAGAGGTGGGA 62.194 63.158 0.00 0.00 34.06 4.37
502 509 4.825679 GGGAGAGGTGGGAGGGGG 62.826 77.778 0.00 0.00 0.00 5.40
528 535 5.298527 ACTCACCCAAACACTAAGCTTAAAC 59.701 40.000 7.74 0.00 0.00 2.01
529 536 5.442391 TCACCCAAACACTAAGCTTAAACT 58.558 37.500 7.74 0.00 0.00 2.66
530 537 5.298276 TCACCCAAACACTAAGCTTAAACTG 59.702 40.000 7.74 5.87 0.00 3.16
546 553 6.255670 GCTTAAACTGTGTTTGAAGGGAAAAG 59.744 38.462 6.01 1.32 0.00 2.27
629 855 4.934356 TGGGAGATAAGTCAAAAGGCAAT 58.066 39.130 0.00 0.00 0.00 3.56
779 1005 3.910989 GGGTGGACAGCCCTAAATATTT 58.089 45.455 9.33 5.89 42.92 1.40
793 1019 6.027749 CCTAAATATTTCAAGTGACGGCAAC 58.972 40.000 3.39 0.00 0.00 4.17
830 1056 3.625764 GCAGTTTAAAGATACCATGGCGA 59.374 43.478 13.04 0.00 0.00 5.54
876 1102 1.607509 CGAATGGCTCAGCATCTAGGG 60.608 57.143 0.00 0.00 0.00 3.53
953 1181 1.138069 GAGGCCAAGTTAGCTCCTCTC 59.862 57.143 5.01 0.00 40.02 3.20
994 1222 2.028476 CCTCGACACCACCAATTGTAGA 60.028 50.000 4.43 0.00 0.00 2.59
996 1224 4.253685 CTCGACACCACCAATTGTAGATT 58.746 43.478 4.43 0.00 28.63 2.40
997 1225 4.000325 TCGACACCACCAATTGTAGATTG 59.000 43.478 4.43 0.00 0.00 2.67
1257 1485 5.723295 TGATTGGAAATTAAGCTTTCTGCC 58.277 37.500 3.20 1.06 44.23 4.85
1301 1536 2.430465 ACTGCAACTCAAGTGGCTATG 58.570 47.619 10.72 4.22 45.12 2.23
1302 1537 2.224621 ACTGCAACTCAAGTGGCTATGT 60.225 45.455 10.72 4.76 45.12 2.29
1312 1547 1.556911 AGTGGCTATGTCAGGTCAAGG 59.443 52.381 0.00 0.00 0.00 3.61
1321 1556 8.154856 GGCTATGTCAGGTCAAGGTTATTATTA 58.845 37.037 0.00 0.00 0.00 0.98
1337 1577 8.932791 GGTTATTATTATTATGTCAGGTCACCG 58.067 37.037 0.00 0.00 0.00 4.94
1338 1578 8.932791 GTTATTATTATTATGTCAGGTCACCGG 58.067 37.037 0.00 0.00 0.00 5.28
1446 1686 9.561069 TTCACTCTTAAGATTTAAAAGCTGTCT 57.439 29.630 5.44 0.00 0.00 3.41
1482 1722 9.601217 GAGAAAGACCTTTTGCAGTTCTATATA 57.399 33.333 0.00 0.00 32.11 0.86
1519 1759 6.560253 ATCCTATAATGGTGTTCGAATTGC 57.440 37.500 0.00 0.00 0.00 3.56
1540 1780 1.713597 TTCGCTACTGTCAGCACATG 58.286 50.000 0.00 0.00 41.88 3.21
1613 1864 2.097466 GCAATAGGAACATGGAACCACG 59.903 50.000 0.00 0.00 0.00 4.94
1645 1896 6.097270 ACTTCCAGCAATGCATGTTATATGTT 59.903 34.615 8.35 0.00 0.00 2.71
1646 1897 5.834169 TCCAGCAATGCATGTTATATGTTG 58.166 37.500 8.35 1.56 0.00 3.33
1647 1898 5.360429 TCCAGCAATGCATGTTATATGTTGT 59.640 36.000 8.35 0.00 0.00 3.32
1648 1899 5.460748 CCAGCAATGCATGTTATATGTTGTG 59.539 40.000 8.35 0.00 0.00 3.33
1649 1900 6.267070 CAGCAATGCATGTTATATGTTGTGA 58.733 36.000 8.35 0.00 0.00 3.58
1650 1901 6.921307 CAGCAATGCATGTTATATGTTGTGAT 59.079 34.615 8.35 0.00 0.00 3.06
1651 1902 7.436970 CAGCAATGCATGTTATATGTTGTGATT 59.563 33.333 8.35 0.00 0.00 2.57
1652 1903 7.982919 AGCAATGCATGTTATATGTTGTGATTT 59.017 29.630 8.35 0.00 0.00 2.17
1692 1943 2.171003 GCTGGCCAACTTAAGATGGTT 58.829 47.619 27.03 3.09 39.81 3.67
1705 1956 6.599638 ACTTAAGATGGTTCAGAAATAGCACC 59.400 38.462 10.09 0.00 0.00 5.01
1790 2041 4.000331 ACAATTGGATAGCTCAGATCCG 58.000 45.455 10.83 0.00 45.15 4.18
1793 2044 4.533919 ATTGGATAGCTCAGATCCGAAG 57.466 45.455 7.84 0.00 45.15 3.79
1811 2062 5.822519 TCCGAAGCATCAAATTATACAAGCT 59.177 36.000 0.00 0.00 0.00 3.74
1869 2120 8.950961 CACATAAGACAAGCAATAAATCAATCG 58.049 33.333 0.00 0.00 0.00 3.34
1907 2158 8.183536 TCAAAGACATATGCATACACAATTCAC 58.816 33.333 8.99 0.00 0.00 3.18
2044 2298 4.553323 CAAGCAATCCAACCAAAAGAGAG 58.447 43.478 0.00 0.00 0.00 3.20
2047 2301 5.574188 AGCAATCCAACCAAAAGAGAGTAT 58.426 37.500 0.00 0.00 0.00 2.12
2074 2328 5.530915 TCATTGGTAAGACCTGAAACACTTG 59.469 40.000 0.00 0.00 39.58 3.16
2082 2336 4.044426 GACCTGAAACACTTGCAATGAAC 58.956 43.478 0.00 0.14 0.00 3.18
2087 2341 4.975502 TGAAACACTTGCAATGAACGATTC 59.024 37.500 0.00 0.00 0.00 2.52
2156 2410 1.774254 AGGTTGGTGACAGACATTCCA 59.226 47.619 0.00 0.00 44.54 3.53
2186 2440 2.509548 AGATGCAAGCTATGGTGGGTTA 59.490 45.455 0.00 0.00 0.00 2.85
2235 2490 7.512297 TCCACGATTTAAATGTTTCGAAGTAC 58.488 34.615 14.12 0.00 35.64 2.73
2269 2524 8.765517 ACATTTATAATATACCTACCTTCCGGG 58.234 37.037 0.00 0.00 41.89 5.73
2275 2530 1.310373 CCTACCTTCCGGGAGTCCT 59.690 63.158 9.48 0.00 39.91 3.85
2293 2548 3.389329 GTCCTGATGATGTCCACACCTAT 59.611 47.826 0.00 0.00 0.00 2.57
2296 2551 5.044919 TCCTGATGATGTCCACACCTATTTT 60.045 40.000 0.00 0.00 0.00 1.82
2306 2561 6.773200 TGTCCACACCTATTTTGTATTGACAA 59.227 34.615 0.00 0.00 43.94 3.18
2360 2615 5.295292 CCCGTAGAGTAAAGATCGACAGTTA 59.705 44.000 0.00 0.00 0.00 2.24
2368 2623 9.953697 GAGTAAAGATCGACAGTTAATCACTAT 57.046 33.333 0.00 0.00 32.76 2.12
2385 2640 6.154203 TCACTATTGAAATGGTGTGCAAAA 57.846 33.333 16.20 0.00 45.00 2.44
2387 2642 7.890515 TCACTATTGAAATGGTGTGCAAAATA 58.109 30.769 16.20 0.00 45.00 1.40
2388 2643 8.530311 TCACTATTGAAATGGTGTGCAAAATAT 58.470 29.630 16.20 0.00 45.00 1.28
2421 2676 8.762481 TTACTCACCATAGACTAGCAATCTAA 57.238 34.615 0.00 0.00 32.50 2.10
2431 2686 7.425224 AGACTAGCAATCTAACACAATAGGT 57.575 36.000 0.00 0.00 0.00 3.08
2435 2690 5.989477 AGCAATCTAACACAATAGGTAGCA 58.011 37.500 0.00 0.00 0.00 3.49
2448 2705 9.935241 CACAATAGGTAGCATATATTTCTGACT 57.065 33.333 0.00 0.00 0.00 3.41
2589 2846 5.934625 ACACCATTGAGATTCTACACTGAAC 59.065 40.000 0.00 0.00 0.00 3.18
2610 2867 4.447290 ACCCAACAAAATGTTTGTAAGCC 58.553 39.130 6.78 0.00 38.77 4.35
2611 2868 4.080863 ACCCAACAAAATGTTTGTAAGCCA 60.081 37.500 6.78 0.00 38.77 4.75
2679 2936 6.464222 ACATTTCAGGAAACGAGATAGTCAA 58.536 36.000 0.00 0.00 32.51 3.18
2887 3144 0.810031 GCGGTGGCAGACGATACATT 60.810 55.000 14.76 0.00 39.62 2.71
2934 3197 5.774690 ACTCTGCAAAAATGAGGGTGAATTA 59.225 36.000 5.07 0.00 32.58 1.40
2936 3199 7.060383 TCTGCAAAAATGAGGGTGAATTAAA 57.940 32.000 0.00 0.00 0.00 1.52
2955 3218 4.866508 AAATGATGATGCATAAGGCCAG 57.133 40.909 5.01 0.00 43.89 4.85
3010 3273 8.969267 CAGCGTAATGTAGTTTAATTCCTAGAG 58.031 37.037 0.00 0.00 0.00 2.43
3122 3386 8.934023 ATGAGGAAAGGTTAAAGTTGATGTAA 57.066 30.769 0.00 0.00 0.00 2.41
3123 3387 8.754991 TGAGGAAAGGTTAAAGTTGATGTAAA 57.245 30.769 0.00 0.00 0.00 2.01
3124 3388 9.191479 TGAGGAAAGGTTAAAGTTGATGTAAAA 57.809 29.630 0.00 0.00 0.00 1.52
3246 3510 3.815809 CAGTGAAAACTGTAAGGTCCCA 58.184 45.455 0.00 0.00 39.30 4.37
3256 3520 1.488705 TAAGGTCCCACAGCCACAGG 61.489 60.000 0.00 0.00 0.00 4.00
3262 3526 0.110486 CCCACAGCCACAGGTTACTT 59.890 55.000 0.00 0.00 0.00 2.24
3278 3542 5.715279 AGGTTACTTGTGTCATAGTGCTAGA 59.285 40.000 0.00 0.00 0.00 2.43
3287 3551 7.217200 TGTGTCATAGTGCTAGAAGTCTTTTT 58.783 34.615 0.00 0.00 0.00 1.94
3288 3552 7.385205 TGTGTCATAGTGCTAGAAGTCTTTTTC 59.615 37.037 0.00 0.00 0.00 2.29
3289 3553 6.874134 TGTCATAGTGCTAGAAGTCTTTTTCC 59.126 38.462 0.00 0.00 0.00 3.13
3370 3635 1.213182 GAATTCAGAACCCTCTCCCCC 59.787 57.143 0.00 0.00 0.00 5.40
3413 3678 0.257328 TCCACCAACACCAGCAAAGA 59.743 50.000 0.00 0.00 0.00 2.52
3414 3679 1.133513 TCCACCAACACCAGCAAAGAT 60.134 47.619 0.00 0.00 0.00 2.40
3443 3708 4.319118 GCGTAGAAGCAGATCATTAAAGGC 60.319 45.833 0.00 0.00 37.05 4.35
3444 3709 4.811024 CGTAGAAGCAGATCATTAAAGGCA 59.189 41.667 0.00 0.00 0.00 4.75
3463 3728 3.259123 GGCATAAATCCAAATAGCCCTGG 59.741 47.826 0.00 0.00 34.71 4.45
3476 3741 1.250154 GCCCTGGCATGTTAGTGCAA 61.250 55.000 2.58 0.00 46.81 4.08
3548 3815 1.331214 CTTTTCCTGCCTGCCTTTGA 58.669 50.000 0.00 0.00 0.00 2.69
3564 3831 4.125703 CCTTTGATAGACAGGCTTAGCAG 58.874 47.826 6.53 0.00 0.00 4.24
3589 3856 2.171448 CAGGAAGGGAATCAGGTACCTG 59.829 54.545 32.61 32.61 44.86 4.00
3646 3913 0.171231 GCCCGGCTTTGAATGAAGTC 59.829 55.000 0.71 0.00 0.00 3.01
3681 3948 2.516906 TCTGCTTTTGCCATGACATGA 58.483 42.857 17.24 0.00 46.87 3.07
3693 3960 6.840527 TGCCATGACATGATAAGATAAAGGA 58.159 36.000 17.24 0.00 0.00 3.36
3773 4040 1.808945 CAGAACTGGCATCACACTTCC 59.191 52.381 0.00 0.00 0.00 3.46
3787 4054 0.921896 ACTTCCCACAGCATAGGCAT 59.078 50.000 0.67 0.00 44.61 4.40
3789 4056 2.509548 ACTTCCCACAGCATAGGCATAA 59.490 45.455 0.67 0.00 44.61 1.90
3791 4058 3.660970 TCCCACAGCATAGGCATAAAA 57.339 42.857 0.67 0.00 44.61 1.52
3820 4087 2.357517 GTCGGTCAGTGGCAGTGG 60.358 66.667 21.53 6.60 0.00 4.00
3862 4129 4.659172 CAAGCCGCCTGAACCCCA 62.659 66.667 0.00 0.00 0.00 4.96
3863 4130 4.660938 AAGCCGCCTGAACCCCAC 62.661 66.667 0.00 0.00 0.00 4.61
3866 4133 3.636231 CCGCCTGAACCCCACTGA 61.636 66.667 0.00 0.00 0.00 3.41
3867 4134 2.429930 CGCCTGAACCCCACTGAA 59.570 61.111 0.00 0.00 0.00 3.02
3868 4135 1.228124 CGCCTGAACCCCACTGAAA 60.228 57.895 0.00 0.00 0.00 2.69
3869 4136 1.515521 CGCCTGAACCCCACTGAAAC 61.516 60.000 0.00 0.00 0.00 2.78
3870 4137 0.178990 GCCTGAACCCCACTGAAACT 60.179 55.000 0.00 0.00 0.00 2.66
3871 4138 1.609208 CCTGAACCCCACTGAAACTG 58.391 55.000 0.00 0.00 0.00 3.16
3872 4139 1.133792 CCTGAACCCCACTGAAACTGT 60.134 52.381 0.00 0.00 0.00 3.55
3873 4140 2.105821 CCTGAACCCCACTGAAACTGTA 59.894 50.000 0.00 0.00 0.00 2.74
3874 4141 3.139077 CTGAACCCCACTGAAACTGTAC 58.861 50.000 0.00 0.00 0.00 2.90
3875 4142 2.506231 TGAACCCCACTGAAACTGTACA 59.494 45.455 0.00 0.00 0.00 2.90
3876 4143 2.930826 ACCCCACTGAAACTGTACAG 57.069 50.000 21.44 21.44 39.65 2.74
3877 4144 1.420138 ACCCCACTGAAACTGTACAGG 59.580 52.381 26.12 10.81 38.30 4.00
3878 4145 1.697432 CCCCACTGAAACTGTACAGGA 59.303 52.381 26.12 6.87 38.30 3.86
3879 4146 2.289694 CCCCACTGAAACTGTACAGGAG 60.290 54.545 26.12 17.13 38.30 3.69
3880 4147 2.632996 CCCACTGAAACTGTACAGGAGA 59.367 50.000 26.12 6.87 38.30 3.71
3881 4148 3.306364 CCCACTGAAACTGTACAGGAGAG 60.306 52.174 26.12 17.12 38.30 3.20
3882 4149 3.321497 CACTGAAACTGTACAGGAGAGC 58.679 50.000 26.12 11.26 38.30 4.09
3883 4150 2.965831 ACTGAAACTGTACAGGAGAGCA 59.034 45.455 26.12 14.76 38.30 4.26
3884 4151 3.388024 ACTGAAACTGTACAGGAGAGCAA 59.612 43.478 26.12 4.99 38.30 3.91
3885 4152 3.993081 CTGAAACTGTACAGGAGAGCAAG 59.007 47.826 26.12 10.46 0.00 4.01
3886 4153 3.244215 TGAAACTGTACAGGAGAGCAAGG 60.244 47.826 26.12 0.00 0.00 3.61
3887 4154 2.310779 ACTGTACAGGAGAGCAAGGA 57.689 50.000 26.12 0.00 0.00 3.36
3888 4155 1.896465 ACTGTACAGGAGAGCAAGGAC 59.104 52.381 26.12 0.00 0.00 3.85
3889 4156 2.175202 CTGTACAGGAGAGCAAGGACT 58.825 52.381 15.49 0.00 0.00 3.85
3890 4157 2.165437 CTGTACAGGAGAGCAAGGACTC 59.835 54.545 15.49 0.00 36.91 3.36
3891 4158 2.171840 GTACAGGAGAGCAAGGACTCA 58.828 52.381 0.00 0.00 39.26 3.41
3892 4159 1.722034 ACAGGAGAGCAAGGACTCAA 58.278 50.000 0.00 0.00 39.26 3.02
3893 4160 1.346068 ACAGGAGAGCAAGGACTCAAC 59.654 52.381 0.00 0.00 39.26 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.108138 GCCGTAGACTTGCCACTGAT 60.108 55.000 0.00 0.00 0.00 2.90
226 229 2.234661 TGATATCCCTGGATAGCGCTTG 59.765 50.000 18.68 0.83 43.91 4.01
230 233 2.834549 ACCTTGATATCCCTGGATAGCG 59.165 50.000 14.77 5.45 43.91 4.26
242 245 9.941325 CTTCTGCTCTGATAATAACCTTGATAT 57.059 33.333 0.00 0.00 0.00 1.63
250 253 6.045318 TGCTGTCTTCTGCTCTGATAATAAC 58.955 40.000 0.00 0.00 38.91 1.89
256 259 3.413846 TTTGCTGTCTTCTGCTCTGAT 57.586 42.857 0.00 0.00 38.91 2.90
282 285 5.246429 GGGTATTCCTGACGAATCTATCCTT 59.754 44.000 0.00 0.00 40.51 3.36
283 286 4.773149 GGGTATTCCTGACGAATCTATCCT 59.227 45.833 0.00 0.00 40.51 3.24
293 296 1.784358 TGTAGGGGGTATTCCTGACG 58.216 55.000 0.00 0.00 35.92 4.35
325 328 6.501805 TGGTGGGATGAGAATATTATACTGCT 59.498 38.462 0.00 0.00 0.00 4.24
342 345 2.578021 AGAAGTGTAAGCATGGTGGGAT 59.422 45.455 0.00 0.00 0.00 3.85
362 365 0.798776 GCATGGTGTTCCGTCAGAAG 59.201 55.000 0.00 0.00 34.29 2.85
365 368 1.732259 GTAAGCATGGTGTTCCGTCAG 59.268 52.381 0.00 0.00 36.30 3.51
457 460 7.201461 GGCTTGTAACATGTCAAATGCTAAATG 60.201 37.037 0.00 0.00 0.00 2.32
458 461 6.813152 GGCTTGTAACATGTCAAATGCTAAAT 59.187 34.615 0.00 0.00 0.00 1.40
461 464 4.764308 TGGCTTGTAACATGTCAAATGCTA 59.236 37.500 0.00 0.00 0.00 3.49
462 465 3.573538 TGGCTTGTAACATGTCAAATGCT 59.426 39.130 0.00 0.00 0.00 3.79
463 466 3.911868 TGGCTTGTAACATGTCAAATGC 58.088 40.909 0.00 1.08 0.00 3.56
464 467 4.487948 CCTGGCTTGTAACATGTCAAATG 58.512 43.478 0.00 0.00 0.00 2.32
465 468 3.511146 CCCTGGCTTGTAACATGTCAAAT 59.489 43.478 0.00 0.00 0.00 2.32
468 471 1.702401 TCCCTGGCTTGTAACATGTCA 59.298 47.619 0.00 0.00 0.00 3.58
474 477 0.984995 ACCTCTCCCTGGCTTGTAAC 59.015 55.000 0.00 0.00 0.00 2.50
475 478 0.984230 CACCTCTCCCTGGCTTGTAA 59.016 55.000 0.00 0.00 0.00 2.41
482 485 2.366167 CCTCCCACCTCTCCCTGG 60.366 72.222 0.00 0.00 0.00 4.45
502 509 2.152016 GCTTAGTGTTTGGGTGAGTCC 58.848 52.381 0.00 0.00 0.00 3.85
518 525 6.123651 TCCCTTCAAACACAGTTTAAGCTTA 58.876 36.000 0.86 0.86 0.00 3.09
528 535 3.447229 ACACCTTTTCCCTTCAAACACAG 59.553 43.478 0.00 0.00 0.00 3.66
529 536 3.436243 ACACCTTTTCCCTTCAAACACA 58.564 40.909 0.00 0.00 0.00 3.72
530 537 4.399934 TGTACACCTTTTCCCTTCAAACAC 59.600 41.667 0.00 0.00 0.00 3.32
546 553 2.841881 TCCCACCCTCTTTATGTACACC 59.158 50.000 0.00 0.00 0.00 4.16
779 1005 0.687920 TATGGGTTGCCGTCACTTGA 59.312 50.000 0.00 0.00 0.00 3.02
793 1019 8.034215 TCTTTAAACTGCAAACAATGATATGGG 58.966 33.333 0.00 0.00 0.00 4.00
830 1056 5.776744 ACGACCGAAACTATTACTTCTGTT 58.223 37.500 0.00 0.00 0.00 3.16
859 1085 0.767446 AGCCCTAGATGCTGAGCCAT 60.767 55.000 0.23 0.00 37.76 4.40
876 1102 6.459573 GCCTGTGCTCTATATATACTCTCAGC 60.460 46.154 0.00 0.00 33.53 4.26
953 1181 6.073167 TCGAGGAGATTAAGTACTATTGCTCG 60.073 42.308 19.76 19.76 43.35 5.03
967 1195 2.225382 TGGTGGTGTCGAGGAGATTA 57.775 50.000 0.00 0.00 0.00 1.75
994 1222 1.288633 TGGATCCCTTGACATGGCAAT 59.711 47.619 15.95 0.00 0.00 3.56
996 1224 0.034186 GTGGATCCCTTGACATGGCA 60.034 55.000 9.90 0.00 0.00 4.92
997 1225 0.257039 AGTGGATCCCTTGACATGGC 59.743 55.000 9.90 0.00 0.00 4.40
1257 1485 9.581099 AGTAATCACTGTTTTGTTTGGTTAAAG 57.419 29.630 0.00 0.00 32.25 1.85
1290 1525 2.768253 TGACCTGACATAGCCACTTG 57.232 50.000 0.00 0.00 0.00 3.16
1312 1547 8.932791 CCGGTGACCTGACATAATAATAATAAC 58.067 37.037 0.00 0.00 0.00 1.89
1321 1556 3.713826 AAACCGGTGACCTGACATAAT 57.286 42.857 8.52 0.00 0.00 1.28
1388 1628 4.383335 CCTTCCAGTTTAATGGGCGTACTA 60.383 45.833 0.00 0.00 41.01 1.82
1394 1634 1.555967 TGCCTTCCAGTTTAATGGGC 58.444 50.000 0.00 0.00 41.01 5.36
1446 1686 2.639065 AGGTCTTTCTCACGCAACAAA 58.361 42.857 0.00 0.00 0.00 2.83
1519 1759 1.783284 TGTGCTGACAGTAGCGAAAG 58.217 50.000 3.99 0.00 46.61 2.62
1528 1768 1.081892 GCTGGTACATGTGCTGACAG 58.918 55.000 13.86 12.91 38.20 3.51
1566 1817 9.314321 CGAATCTAGACCAATGTGTATAACTTT 57.686 33.333 0.00 0.00 0.00 2.66
1589 1840 3.013921 GGTTCCATGTTCCTATTGCGAA 58.986 45.455 0.00 0.00 0.00 4.70
1613 1864 2.754552 TGCATTGCTGGAAGTAACCATC 59.245 45.455 10.49 0.00 42.67 3.51
1645 1896 6.475504 AGTACATGGATCTTCACAAATCACA 58.524 36.000 0.00 0.00 0.00 3.58
1646 1897 6.992063 AGTACATGGATCTTCACAAATCAC 57.008 37.500 0.00 0.00 0.00 3.06
1647 1898 7.575532 GCAAAGTACATGGATCTTCACAAATCA 60.576 37.037 0.00 0.00 0.00 2.57
1648 1899 6.749118 GCAAAGTACATGGATCTTCACAAATC 59.251 38.462 0.00 0.00 0.00 2.17
1649 1900 6.435277 AGCAAAGTACATGGATCTTCACAAAT 59.565 34.615 0.00 0.00 0.00 2.32
1650 1901 5.769662 AGCAAAGTACATGGATCTTCACAAA 59.230 36.000 0.00 0.00 0.00 2.83
1651 1902 5.181811 CAGCAAAGTACATGGATCTTCACAA 59.818 40.000 0.00 0.00 0.00 3.33
1652 1903 4.696877 CAGCAAAGTACATGGATCTTCACA 59.303 41.667 0.00 0.00 0.00 3.58
1692 1943 4.537135 AGTTTCTCGGTGCTATTTCTGA 57.463 40.909 0.00 0.00 0.00 3.27
1758 2009 9.995003 TGAGCTATCCAATTGTTTAATGTTTTT 57.005 25.926 4.43 0.00 0.00 1.94
1759 2010 9.643693 CTGAGCTATCCAATTGTTTAATGTTTT 57.356 29.630 4.43 0.00 0.00 2.43
1760 2011 9.023962 TCTGAGCTATCCAATTGTTTAATGTTT 57.976 29.630 4.43 0.00 0.00 2.83
1761 2012 8.579850 TCTGAGCTATCCAATTGTTTAATGTT 57.420 30.769 4.43 0.00 0.00 2.71
1762 2013 8.757982 ATCTGAGCTATCCAATTGTTTAATGT 57.242 30.769 4.43 0.00 0.00 2.71
1778 2029 2.310538 TGATGCTTCGGATCTGAGCTA 58.689 47.619 19.89 11.23 0.00 3.32
1847 2098 8.335356 GCTACGATTGATTTATTGCTTGTCTTA 58.665 33.333 0.00 0.00 0.00 2.10
1869 2120 7.541783 TGCATATGTCTTTGAAATGTTTGCTAC 59.458 33.333 4.29 0.00 0.00 3.58
1871 2122 6.457355 TGCATATGTCTTTGAAATGTTTGCT 58.543 32.000 4.29 0.00 0.00 3.91
1996 2250 1.139853 GGTGAGTCAGGATCCACCATC 59.860 57.143 15.82 7.28 46.13 3.51
2044 2298 7.606456 TGTTTCAGGTCTTACCAATGAAGATAC 59.394 37.037 0.00 0.00 41.95 2.24
2047 2301 5.763204 GTGTTTCAGGTCTTACCAATGAAGA 59.237 40.000 0.00 0.00 41.95 2.87
2121 2375 2.030540 CCAACCTGTGTGAAATGCTCAG 60.031 50.000 0.00 0.00 33.60 3.35
2124 2378 1.682854 CACCAACCTGTGTGAAATGCT 59.317 47.619 0.00 0.00 34.37 3.79
2129 2383 1.557371 TCTGTCACCAACCTGTGTGAA 59.443 47.619 0.00 0.00 42.67 3.18
2156 2410 4.579340 CCATAGCTTGCATCTGTTGATTCT 59.421 41.667 0.00 0.00 0.00 2.40
2186 2440 6.625532 AACAATATGCAAAAGGAAGGGAAT 57.374 33.333 0.00 0.00 0.00 3.01
2262 2517 1.069823 CATCATCAGGACTCCCGGAAG 59.930 57.143 0.73 0.00 40.02 3.46
2264 2519 0.032117 ACATCATCAGGACTCCCGGA 60.032 55.000 0.73 0.00 40.86 5.14
2265 2520 0.390860 GACATCATCAGGACTCCCGG 59.609 60.000 0.00 0.00 37.58 5.73
2269 2524 2.419297 GGTGTGGACATCATCAGGACTC 60.419 54.545 0.00 0.00 0.00 3.36
2275 2530 5.569355 ACAAAATAGGTGTGGACATCATCA 58.431 37.500 0.00 0.00 0.00 3.07
2329 2584 6.703607 TCGATCTTTACTCTACGGGTAAGTAG 59.296 42.308 0.00 0.00 43.97 2.57
2334 2589 4.769688 TGTCGATCTTTACTCTACGGGTA 58.230 43.478 0.00 0.00 0.00 3.69
2336 2591 3.626670 ACTGTCGATCTTTACTCTACGGG 59.373 47.826 0.00 0.00 0.00 5.28
2339 2594 9.224058 GTGATTAACTGTCGATCTTTACTCTAC 57.776 37.037 0.00 0.00 0.00 2.59
2360 2615 5.981088 TGCACACCATTTCAATAGTGATT 57.019 34.783 5.27 0.00 33.21 2.57
2408 2663 7.382759 GCTACCTATTGTGTTAGATTGCTAGTC 59.617 40.741 0.00 0.00 0.00 2.59
2410 2665 7.210174 TGCTACCTATTGTGTTAGATTGCTAG 58.790 38.462 0.00 0.00 0.00 3.42
2421 2676 9.712305 GTCAGAAATATATGCTACCTATTGTGT 57.288 33.333 0.00 0.00 0.00 3.72
2431 2686 9.851686 AAATGTGGAAGTCAGAAATATATGCTA 57.148 29.630 0.00 0.00 0.00 3.49
2565 2822 5.745312 TCAGTGTAGAATCTCAATGGTGT 57.255 39.130 9.12 0.00 31.83 4.16
2589 2846 4.446371 TGGCTTACAAACATTTTGTTGGG 58.554 39.130 9.44 2.85 40.14 4.12
2610 2867 6.578020 CAAGTTATGCAATATTGTGCCTTG 57.422 37.500 16.61 15.47 44.26 3.61
2653 2910 7.782049 TGACTATCTCGTTTCCTGAAATGTAT 58.218 34.615 10.68 8.72 38.22 2.29
2655 2912 6.037786 TGACTATCTCGTTTCCTGAAATGT 57.962 37.500 10.68 0.00 38.22 2.71
2679 2936 2.876550 GTTGGCTTTGGACTTTCGTAGT 59.123 45.455 0.00 0.00 40.71 2.73
2689 2946 0.106268 TTCCTGCTGTTGGCTTTGGA 60.106 50.000 0.00 0.00 42.39 3.53
2755 3012 4.210331 GTCTCCATCCTGGTGCATAAATT 58.790 43.478 0.00 0.00 39.03 1.82
2887 3144 3.008923 TGGAATGCACCAGTTGTCATCTA 59.991 43.478 0.00 0.00 34.77 1.98
2934 3197 3.576982 CCTGGCCTTATGCATCATCATTT 59.423 43.478 0.19 0.00 43.89 2.32
2936 3199 2.803956 CCTGGCCTTATGCATCATCAT 58.196 47.619 0.19 0.00 43.89 2.45
2965 3228 1.312371 GCACCATACACAACGCCCAT 61.312 55.000 0.00 0.00 0.00 4.00
3010 3273 6.477033 CAGTGCCTGTACATGAGATAAAGTAC 59.523 42.308 0.00 0.00 37.82 2.73
3107 3371 9.869757 ATTGCCCTATTTTACATCAACTTTAAC 57.130 29.630 0.00 0.00 0.00 2.01
3122 3386 7.810260 AGATCTTTACTCTCATTGCCCTATTT 58.190 34.615 0.00 0.00 0.00 1.40
3123 3387 7.292120 AGAGATCTTTACTCTCATTGCCCTATT 59.708 37.037 0.00 0.00 40.14 1.73
3124 3388 6.786959 AGAGATCTTTACTCTCATTGCCCTAT 59.213 38.462 0.00 0.00 40.14 2.57
3176 3440 6.540551 TCTGCAGTTTATCATTTATTGGCGTA 59.459 34.615 14.67 0.00 0.00 4.42
3246 3510 1.211949 ACACAAGTAACCTGTGGCTGT 59.788 47.619 10.43 0.00 37.83 4.40
3256 3520 7.091443 ACTTCTAGCACTATGACACAAGTAAC 58.909 38.462 0.00 0.00 0.00 2.50
3262 3526 5.984695 AAGACTTCTAGCACTATGACACA 57.015 39.130 0.00 0.00 0.00 3.72
3278 3542 3.435169 GGGTCAGGTGAGGAAAAAGACTT 60.435 47.826 0.00 0.00 0.00 3.01
3287 3551 0.178876 TCATTGGGGTCAGGTGAGGA 60.179 55.000 0.00 0.00 0.00 3.71
3288 3552 0.921896 ATCATTGGGGTCAGGTGAGG 59.078 55.000 0.00 0.00 0.00 3.86
3289 3553 2.814805 AATCATTGGGGTCAGGTGAG 57.185 50.000 0.00 0.00 0.00 3.51
3370 3635 1.208776 TGAGAGCATGACTGGTGGATG 59.791 52.381 0.00 0.00 31.99 3.51
3432 3697 9.933723 GCTATTTGGATTTATGCCTTTAATGAT 57.066 29.630 0.00 0.00 0.00 2.45
3443 3708 3.896888 TGCCAGGGCTATTTGGATTTATG 59.103 43.478 12.19 0.00 42.51 1.90
3444 3709 4.197559 TGCCAGGGCTATTTGGATTTAT 57.802 40.909 12.19 0.00 42.51 1.40
3463 3728 2.094675 ACCAGGATTGCACTAACATGC 58.905 47.619 0.00 0.00 46.32 4.06
3476 3741 2.301296 CGGAGCATAATCTGACCAGGAT 59.699 50.000 0.00 0.00 0.00 3.24
3548 3815 1.691434 GCTCCTGCTAAGCCTGTCTAT 59.309 52.381 0.00 0.00 33.53 1.98
3564 3831 0.182299 CCTGATTCCCTTCCTGCTCC 59.818 60.000 0.00 0.00 0.00 4.70
3589 3856 7.714377 AGATGGTCATATTCTCTGTTGTCATTC 59.286 37.037 0.00 0.00 0.00 2.67
3646 3913 4.445452 AAGCAGATGCATTTTGTGTAGG 57.555 40.909 0.00 0.00 45.16 3.18
3693 3960 7.094032 CCTTGAAAATTGGAAACAGATAGCTCT 60.094 37.037 0.00 0.00 44.54 4.09
3787 4054 3.994392 GACCGACTCTGACAAGCATTTTA 59.006 43.478 0.00 0.00 0.00 1.52
3789 4056 2.224281 TGACCGACTCTGACAAGCATTT 60.224 45.455 0.00 0.00 0.00 2.32
3791 4058 0.969149 TGACCGACTCTGACAAGCAT 59.031 50.000 0.00 0.00 0.00 3.79
3851 4118 0.178990 AGTTTCAGTGGGGTTCAGGC 60.179 55.000 0.00 0.00 0.00 4.85
3852 4119 1.133792 ACAGTTTCAGTGGGGTTCAGG 60.134 52.381 0.00 0.00 0.00 3.86
3853 4120 2.348411 ACAGTTTCAGTGGGGTTCAG 57.652 50.000 0.00 0.00 0.00 3.02
3854 4121 2.506231 TGTACAGTTTCAGTGGGGTTCA 59.494 45.455 0.00 0.00 0.00 3.18
3855 4122 3.139077 CTGTACAGTTTCAGTGGGGTTC 58.861 50.000 15.06 0.00 0.00 3.62
3856 4123 2.158667 CCTGTACAGTTTCAGTGGGGTT 60.159 50.000 21.18 0.00 0.00 4.11
3857 4124 1.420138 CCTGTACAGTTTCAGTGGGGT 59.580 52.381 21.18 0.00 0.00 4.95
3858 4125 1.697432 TCCTGTACAGTTTCAGTGGGG 59.303 52.381 21.18 3.23 0.00 4.96
3859 4126 2.632996 TCTCCTGTACAGTTTCAGTGGG 59.367 50.000 21.18 4.46 0.00 4.61
3860 4127 3.862642 GCTCTCCTGTACAGTTTCAGTGG 60.863 52.174 21.18 4.70 0.00 4.00
3861 4128 3.243873 TGCTCTCCTGTACAGTTTCAGTG 60.244 47.826 21.18 12.28 0.00 3.66
3862 4129 2.965831 TGCTCTCCTGTACAGTTTCAGT 59.034 45.455 21.18 0.00 0.00 3.41
3863 4130 3.667497 TGCTCTCCTGTACAGTTTCAG 57.333 47.619 21.18 11.92 0.00 3.02
3864 4131 3.244215 CCTTGCTCTCCTGTACAGTTTCA 60.244 47.826 21.18 8.85 0.00 2.69
3865 4132 3.006967 TCCTTGCTCTCCTGTACAGTTTC 59.993 47.826 21.18 6.53 0.00 2.78
3866 4133 2.972713 TCCTTGCTCTCCTGTACAGTTT 59.027 45.455 21.18 0.00 0.00 2.66
3867 4134 2.300437 GTCCTTGCTCTCCTGTACAGTT 59.700 50.000 21.18 0.00 0.00 3.16
3868 4135 1.896465 GTCCTTGCTCTCCTGTACAGT 59.104 52.381 21.18 0.00 0.00 3.55
3869 4136 2.165437 GAGTCCTTGCTCTCCTGTACAG 59.835 54.545 16.34 16.34 32.99 2.74
3870 4137 2.171840 GAGTCCTTGCTCTCCTGTACA 58.828 52.381 0.00 0.00 32.99 2.90
3871 4138 2.171840 TGAGTCCTTGCTCTCCTGTAC 58.828 52.381 0.00 0.00 36.51 2.90
3872 4139 2.563179 GTTGAGTCCTTGCTCTCCTGTA 59.437 50.000 0.00 0.00 36.51 2.74
3873 4140 1.346068 GTTGAGTCCTTGCTCTCCTGT 59.654 52.381 0.00 0.00 36.51 4.00
3874 4141 2.091852 GTTGAGTCCTTGCTCTCCTG 57.908 55.000 0.00 0.00 36.51 3.86


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

AutoCloner maintained by Alex Coulton.