Multiple sequence alignment - TraesCS5B01G541700

Loading Multiple Alignment...

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 TraesCS5B01G541700 chr5B 100.000 4106 0 0 1 4106 696025937 696030042 0.000000e+00 7583
1 TraesCS5B01G541700 chr4A 94.996 2258 58 11 450 2656 613815935 613818188 0.000000e+00 3493
2 TraesCS5B01G541700 chr4A 94.227 970 47 7 3144 4106 613819197 613820164 0.000000e+00 1472
3 TraesCS5B01G541700 chr4A 97.152 316 7 2 2648 2962 613818863 613819177 2.170000e-147 532
4 TraesCS5B01G541700 chr4A 91.990 387 12 6 1 368 613815551 613815937 3.640000e-145 525
5 TraesCS5B01G541700 chr4A 82.129 263 45 2 262 524 530180732 530180472 1.490000e-54 224
6 TraesCS5B01G541700 chr4A 82.911 158 23 4 723 878 2949116 2948961 5.530000e-29 139
7 TraesCS5B01G541700 chr5D 91.590 654 52 3 2445 3097 554851670 554851019 0.000000e+00 900
8 TraesCS5B01G541700 chr5D 83.703 902 81 23 1536 2400 554853733 554852861 0.000000e+00 791
9 TraesCS5B01G541700 chr5D 90.769 585 43 7 878 1454 554854517 554853936 0.000000e+00 771
10 TraesCS5B01G541700 chr7B 75.442 566 101 22 124 664 616494948 616494396 1.470000e-59 241
11 TraesCS5B01G541700 chr6A 78.723 376 64 10 111 470 599757173 599756798 1.910000e-58 237
12 TraesCS5B01G541700 chr2B 76.225 408 81 14 263 664 73986167 73986564 6.960000e-48 202
13 TraesCS5B01G541700 chr3D 76.533 375 72 9 145 504 316811100 316811473 1.510000e-44 191
14 TraesCS5B01G541700 chr4D 74.790 476 93 14 108 560 65085050 65084579 5.420000e-44 189
15 TraesCS5B01G541700 chr3B 73.116 584 121 22 108 664 720898060 720897486 4.220000e-40 176
16 TraesCS5B01G541700 chr6B 73.321 536 109 16 119 625 720233332 720232802 2.540000e-37 167
17 TraesCS5B01G541700 chr3A 77.736 265 53 6 262 525 635514279 635514538 1.530000e-34 158
18 TraesCS5B01G541700 chr2D 80.380 158 28 3 108 263 119823761 119823605 2.590000e-22 117


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 TraesCS5B01G541700 chr5B 696025937 696030042 4105 False 7583.000000 7583 100.000000 1 4106 1 chr5B.!!$F1 4105
1 TraesCS5B01G541700 chr4A 613815551 613820164 4613 False 1505.500000 3493 94.591250 1 4106 4 chr4A.!!$F1 4105
2 TraesCS5B01G541700 chr5D 554851019 554854517 3498 True 820.666667 900 88.687333 878 3097 3 chr5D.!!$R1 2219
3 TraesCS5B01G541700 chr7B 616494396 616494948 552 True 241.000000 241 75.442000 124 664 1 chr7B.!!$R1 540

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
294 315 0.031585 CTTCACACCCGAGTTCGACA 59.968 55.0 2.59 0.0 43.02 4.35 F
389 410 0.032912 AACCAAACCGGGGAAACACT 60.033 50.0 6.32 0.0 40.22 3.55 F
391 412 0.179001 CCAAACCGGGGAAACACTCT 60.179 55.0 6.32 0.0 0.00 3.24 F
1359 1392 0.323451 GGTCATCCACCCCTTGTTCC 60.323 60.0 0.00 0.0 39.69 3.62 F
2259 2454 0.610232 AATGGAGTGGTCAAGCTGCC 60.610 55.0 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1389 1422 0.593128 AACTGCATGCGTTCTTCCAC 59.407 50.000 14.09 0.0 0.00 4.02 R
1803 1967 3.060363 GCGGATAAACAGAACGTGTACAG 59.940 47.826 0.00 0.0 39.03 2.74 R
1810 1974 4.109766 TGAGTATGCGGATAAACAGAACG 58.890 43.478 0.00 0.0 0.00 3.95 R
2966 4998 0.459759 GGACGTCCTTTGGTCCGATC 60.460 60.000 27.64 0.0 42.91 3.69 R
3426 5460 0.680921 GAAGCAAGGCCACCATAGCA 60.681 55.000 5.01 0.0 0.00 3.49 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
61 62 5.009310 CACCATAGTCTAAGCCACGTACATA 59.991 44.000 0.00 0.00 0.00 2.29
69 70 2.550978 AGCCACGTACATACATGCTTC 58.449 47.619 0.00 0.00 0.00 3.86
95 97 1.861982 AAGCCACCTACATACCGACT 58.138 50.000 0.00 0.00 0.00 4.18
106 108 6.886459 ACCTACATACCGACTAGTCAAAACTA 59.114 38.462 22.37 4.42 36.92 2.24
114 116 4.143389 CGACTAGTCAAAACTAAAGCCACG 60.143 45.833 22.37 0.00 37.53 4.94
139 141 1.949465 ACCGACCTGTCAAAACTGAC 58.051 50.000 0.00 0.00 39.15 3.51
254 257 0.325671 CCCCTCACCTCCTCTAGCAA 60.326 60.000 0.00 0.00 0.00 3.91
294 315 0.031585 CTTCACACCCGAGTTCGACA 59.968 55.000 2.59 0.00 43.02 4.35
369 390 3.057174 GGCGAAACCATTACCATTGAACA 60.057 43.478 0.00 0.00 38.86 3.18
372 393 5.107645 GCGAAACCATTACCATTGAACAAAC 60.108 40.000 0.00 0.00 0.00 2.93
375 396 5.878406 ACCATTACCATTGAACAAACCAA 57.122 34.783 0.00 0.00 0.00 3.67
380 401 2.159028 ACCATTGAACAAACCAAACCGG 60.159 45.455 0.00 0.00 42.50 5.28
389 410 0.032912 AACCAAACCGGGGAAACACT 60.033 50.000 6.32 0.00 40.22 3.55
391 412 0.179001 CCAAACCGGGGAAACACTCT 60.179 55.000 6.32 0.00 0.00 3.24
397 418 0.324943 CGGGGAAACACTCTGGACAT 59.675 55.000 0.00 0.00 0.00 3.06
399 420 1.351017 GGGGAAACACTCTGGACATGA 59.649 52.381 0.00 0.00 0.00 3.07
412 433 2.501316 TGGACATGACATCGAACTCCAT 59.499 45.455 0.00 0.00 0.00 3.41
423 444 1.414181 CGAACTCCATATCTGGCACCT 59.586 52.381 0.00 0.00 42.80 4.00
428 449 0.839277 CCATATCTGGCACCTCCACA 59.161 55.000 0.00 0.00 40.72 4.17
429 450 1.422781 CCATATCTGGCACCTCCACAT 59.577 52.381 0.00 0.00 40.72 3.21
430 451 2.501261 CATATCTGGCACCTCCACATG 58.499 52.381 0.00 0.00 40.72 3.21
436 457 1.702401 TGGCACCTCCACATGACTAAA 59.298 47.619 0.00 0.00 40.72 1.85
437 458 2.290260 TGGCACCTCCACATGACTAAAG 60.290 50.000 0.00 0.00 40.72 1.85
448 469 1.250328 TGACTAAAGCGTCGGAGGAA 58.750 50.000 1.18 0.00 36.71 3.36
449 470 1.201647 TGACTAAAGCGTCGGAGGAAG 59.798 52.381 1.18 0.00 36.71 3.46
450 471 1.471684 GACTAAAGCGTCGGAGGAAGA 59.528 52.381 1.18 0.00 0.00 2.87
473 494 2.303600 ACCATACCTGCCTTTCACGTAA 59.696 45.455 0.00 0.00 0.00 3.18
493 514 8.609176 CACGTAACATAAACCTTAGCACATAAT 58.391 33.333 0.00 0.00 0.00 1.28
505 526 7.230108 ACCTTAGCACATAATCCATCATCTTTG 59.770 37.037 0.00 0.00 0.00 2.77
666 691 1.329906 CATCCTTGCTCGAACAGATGC 59.670 52.381 5.45 0.00 0.00 3.91
720 745 2.052690 CCCCTCATCACCGACGACT 61.053 63.158 0.00 0.00 0.00 4.18
755 780 8.611654 AATTTGACCTAAAACTATACACACGT 57.388 30.769 0.00 0.00 0.00 4.49
757 782 6.330004 TGACCTAAAACTATACACACGTGA 57.670 37.500 25.01 0.00 0.00 4.35
763 789 4.650754 AACTATACACACGTGAGGATCC 57.349 45.455 25.01 2.48 0.00 3.36
765 791 0.744874 ATACACACGTGAGGATCCGG 59.255 55.000 25.01 0.00 33.95 5.14
781 807 2.911143 GGCGACCCACCTCATCAT 59.089 61.111 0.00 0.00 0.00 2.45
782 808 1.744320 CGGCGACCCACCTCATCATA 61.744 60.000 0.00 0.00 0.00 2.15
862 888 3.922171 ATCAAGATCGCCTCTTCCTTT 57.078 42.857 0.00 0.00 42.48 3.11
865 891 3.198635 TCAAGATCGCCTCTTCCTTTGAT 59.801 43.478 0.00 0.00 42.48 2.57
952 981 3.632080 AACCACATCGACGCCCCA 61.632 61.111 0.00 0.00 0.00 4.96
1359 1392 0.323451 GGTCATCCACCCCTTGTTCC 60.323 60.000 0.00 0.00 39.69 3.62
1503 1576 5.643379 ACTTATCCTTTTGTACGTACGGA 57.357 39.130 21.06 19.25 0.00 4.69
1644 1802 4.038080 GTGTTTTCCGCGGGGCAG 62.038 66.667 27.83 0.00 0.00 4.85
1816 1980 5.845985 AATTCACATCTGTACACGTTCTG 57.154 39.130 0.00 0.00 0.00 3.02
1831 1999 4.026804 CACGTTCTGTTTATCCGCATACTC 60.027 45.833 0.00 0.00 0.00 2.59
1907 2075 2.383527 GCGCGTGTTTCCTGGAGAG 61.384 63.158 8.43 0.00 0.00 3.20
2132 2327 5.661056 TTCATCTCACAGGTAGGTAGTTG 57.339 43.478 0.00 0.00 0.00 3.16
2259 2454 0.610232 AATGGAGTGGTCAAGCTGCC 60.610 55.000 0.00 0.00 0.00 4.85
2416 2620 2.285083 GCATAATCTTGGCGTGGTACA 58.715 47.619 0.00 0.00 0.00 2.90
2582 3930 6.334989 TGGTGTTCGTGTATATTCGAGAAAT 58.665 36.000 0.00 0.00 37.38 2.17
2612 3960 1.293963 GGTTGCTCGGGGTACGTTTC 61.294 60.000 0.00 0.00 44.69 2.78
2616 3965 1.202675 TGCTCGGGGTACGTTTCTTTT 60.203 47.619 0.00 0.00 44.69 2.27
2617 3966 1.462283 GCTCGGGGTACGTTTCTTTTC 59.538 52.381 0.00 0.00 44.69 2.29
2684 4715 5.436175 TCAACTTCTGATTGTCAAGAACCA 58.564 37.500 0.00 0.00 0.00 3.67
2803 4834 2.693074 TGCCATGATAGCACTTCTCGTA 59.307 45.455 0.00 0.00 34.69 3.43
2963 4995 2.241160 GCCTCTAAGGGGACTAGCTAC 58.759 57.143 0.00 0.00 42.68 3.58
2966 4998 3.404899 CTCTAAGGGGACTAGCTACTCG 58.595 54.545 0.00 0.00 42.68 4.18
2969 5001 2.572209 AGGGGACTAGCTACTCGATC 57.428 55.000 0.00 0.00 40.61 3.69
2981 5013 0.531200 ACTCGATCGGACCAAAGGAC 59.469 55.000 16.41 0.00 0.00 3.85
2982 5014 0.525668 CTCGATCGGACCAAAGGACG 60.526 60.000 16.41 0.00 0.00 4.79
2988 5020 3.154589 GGACCAAAGGACGTCCATC 57.845 57.895 35.00 21.92 46.59 3.51
2997 5029 3.560636 AGGACGTCCATCCCTAAAATG 57.439 47.619 35.00 0.00 39.91 2.32
3003 5035 2.952310 GTCCATCCCTAAAATGCCTGTC 59.048 50.000 0.00 0.00 0.00 3.51
3009 5041 6.239120 CCATCCCTAAAATGCCTGTCTATTTG 60.239 42.308 0.00 0.00 0.00 2.32
3044 5076 8.047310 ACAACTAGTAATATTCTCACCAAAGGG 58.953 37.037 0.00 0.00 41.29 3.95
3081 5113 5.049954 CGTTTATTTGGAAGGTCGTTCTTCA 60.050 40.000 17.31 6.01 43.52 3.02
3087 5119 5.026038 TGGAAGGTCGTTCTTCAAAAGTA 57.974 39.130 17.31 0.89 43.52 2.24
3090 5122 5.469084 GGAAGGTCGTTCTTCAAAAGTATGT 59.531 40.000 17.31 0.00 43.52 2.29
3092 5124 7.172019 GGAAGGTCGTTCTTCAAAAGTATGTAA 59.828 37.037 17.31 0.00 43.52 2.41
3097 5129 9.474249 GTCGTTCTTCAAAAGTATGTAATAAGC 57.526 33.333 0.00 0.00 0.00 3.09
3098 5130 9.431887 TCGTTCTTCAAAAGTATGTAATAAGCT 57.568 29.630 0.00 0.00 0.00 3.74
3099 5131 9.690434 CGTTCTTCAAAAGTATGTAATAAGCTC 57.310 33.333 0.00 0.00 0.00 4.09
3102 5134 8.883731 TCTTCAAAAGTATGTAATAAGCTCAGC 58.116 33.333 0.00 0.00 0.00 4.26
3103 5135 7.234187 TCAAAAGTATGTAATAAGCTCAGCG 57.766 36.000 0.00 0.00 0.00 5.18
3104 5136 5.659048 AAAGTATGTAATAAGCTCAGCGC 57.341 39.130 0.00 0.00 39.57 5.92
3105 5137 4.322080 AGTATGTAATAAGCTCAGCGCA 57.678 40.909 11.47 0.00 42.61 6.09
3106 5138 4.693283 AGTATGTAATAAGCTCAGCGCAA 58.307 39.130 11.47 0.00 42.61 4.85
3107 5139 5.300752 AGTATGTAATAAGCTCAGCGCAAT 58.699 37.500 11.47 0.00 42.61 3.56
3108 5140 6.455647 AGTATGTAATAAGCTCAGCGCAATA 58.544 36.000 11.47 0.00 42.61 1.90
3109 5141 6.929049 AGTATGTAATAAGCTCAGCGCAATAA 59.071 34.615 11.47 0.00 42.61 1.40
3110 5142 6.618287 ATGTAATAAGCTCAGCGCAATAAA 57.382 33.333 11.47 0.00 42.61 1.40
3111 5143 6.429791 TGTAATAAGCTCAGCGCAATAAAA 57.570 33.333 11.47 0.00 42.61 1.52
3112 5144 6.847400 TGTAATAAGCTCAGCGCAATAAAAA 58.153 32.000 11.47 0.00 42.61 1.94
3135 5167 9.490379 AAAAAGTATGTAATAAGCTCCCGATAG 57.510 33.333 0.00 0.00 0.00 2.08
3136 5168 8.418597 AAAGTATGTAATAAGCTCCCGATAGA 57.581 34.615 0.00 0.00 39.76 1.98
3137 5169 7.393841 AGTATGTAATAAGCTCCCGATAGAC 57.606 40.000 0.00 0.00 39.76 2.59
3138 5170 5.662674 ATGTAATAAGCTCCCGATAGACC 57.337 43.478 0.00 0.00 39.76 3.85
3139 5171 4.476297 TGTAATAAGCTCCCGATAGACCA 58.524 43.478 0.00 0.00 39.76 4.02
3140 5172 5.084519 TGTAATAAGCTCCCGATAGACCAT 58.915 41.667 0.00 0.00 39.76 3.55
3141 5173 6.250711 TGTAATAAGCTCCCGATAGACCATA 58.749 40.000 0.00 0.00 39.76 2.74
3142 5174 6.895756 TGTAATAAGCTCCCGATAGACCATAT 59.104 38.462 0.00 0.00 39.76 1.78
3212 5244 7.274447 AGAGAGAAAATCAGCTCTTTATCCAG 58.726 38.462 0.00 0.00 41.33 3.86
3230 5262 2.229784 CCAGACATCTCCCAAACTTTGC 59.770 50.000 0.00 0.00 0.00 3.68
3255 5287 6.453791 CGTCATACAAGTCGAAACACCATAAG 60.454 42.308 0.00 0.00 0.00 1.73
3317 5349 2.412870 TGCTTACCAGAATGTCACGTG 58.587 47.619 9.94 9.94 0.00 4.49
3326 5358 4.274950 CCAGAATGTCACGTGGTAAAAAGT 59.725 41.667 17.00 0.00 0.00 2.66
3406 5440 1.068434 CATCAACCCCACCAACACAAC 59.932 52.381 0.00 0.00 0.00 3.32
3410 5444 0.396556 ACCCCACCAACACAACTTCC 60.397 55.000 0.00 0.00 0.00 3.46
3426 5460 7.160726 CACAACTTCCCATCCAACAAATAAAT 58.839 34.615 0.00 0.00 0.00 1.40
3467 5501 9.609346 GCTTCTCTTATGTTTAGGGTTATTGTA 57.391 33.333 0.00 0.00 0.00 2.41
3510 5544 9.990360 GACTCTCTTTCCCTTTTATAGAATAGG 57.010 37.037 0.00 0.00 34.46 2.57
3527 5561 7.354751 AGAATAGGATTAAGAGCGAGACTTT 57.645 36.000 0.00 0.00 0.00 2.66
3565 5599 3.872511 TGGGCAAAATCATTGTAGCAG 57.127 42.857 0.00 0.00 0.00 4.24
3693 5729 6.766429 ACTAAAATCAGAAGTACCCTCGTTT 58.234 36.000 0.00 0.00 0.00 3.60
3710 5746 6.038936 CCCTCGTTTCCGATAATATTTTTGGT 59.961 38.462 10.88 0.00 43.27 3.67
3833 5869 8.888716 GTTTCCCAAATTATGTTTTGAAGTGTT 58.111 29.630 4.31 0.00 38.58 3.32
3847 5883 5.856126 TGAAGTGTTTCGTATGTGAATCC 57.144 39.130 0.00 0.00 36.04 3.01
3914 5950 6.544650 AGTCAGAGTCTTCTTACTAGGAACA 58.455 40.000 0.00 0.00 36.40 3.18
3916 5952 7.672239 AGTCAGAGTCTTCTTACTAGGAACATT 59.328 37.037 0.00 0.00 36.40 2.71
4096 6134 7.445707 GCCCAACATTTTTAAGGTCCATTTTTA 59.554 33.333 0.00 0.00 0.00 1.52
4100 6138 9.907229 AACATTTTTAAGGTCCATTTTTAACCA 57.093 25.926 0.00 0.00 35.43 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 3.007614 ACGTGGCTTAGACTATGGTGTTT 59.992 43.478 0.00 0.00 0.00 2.83
46 47 3.717707 AGCATGTATGTACGTGGCTTAG 58.282 45.455 12.80 0.00 42.12 2.18
95 97 5.599732 TGTACGTGGCTTTAGTTTTGACTA 58.400 37.500 0.00 0.00 0.00 2.59
106 108 1.404583 GGTCGGTATGTACGTGGCTTT 60.405 52.381 0.00 0.00 0.00 3.51
114 116 4.387862 CAGTTTTGACAGGTCGGTATGTAC 59.612 45.833 0.00 0.00 0.00 2.90
139 141 4.929808 AGAGACTAGTGTTTTGTTATGCGG 59.070 41.667 0.00 0.00 0.00 5.69
254 257 2.151202 GTGATCCATCGTTTGTGGTGT 58.849 47.619 0.00 0.00 37.96 4.16
294 315 1.159285 CATATCAATGATGGCGCCGT 58.841 50.000 24.16 24.16 34.84 5.68
369 390 0.825410 GTGTTTCCCCGGTTTGGTTT 59.175 50.000 0.00 0.00 35.15 3.27
372 393 0.179001 AGAGTGTTTCCCCGGTTTGG 60.179 55.000 0.00 0.00 37.55 3.28
375 396 1.057851 TCCAGAGTGTTTCCCCGGTT 61.058 55.000 0.00 0.00 0.00 4.44
380 401 2.224523 TGTCATGTCCAGAGTGTTTCCC 60.225 50.000 0.00 0.00 0.00 3.97
389 410 2.166459 GGAGTTCGATGTCATGTCCAGA 59.834 50.000 0.00 0.00 0.00 3.86
391 412 1.899142 TGGAGTTCGATGTCATGTCCA 59.101 47.619 0.00 0.00 0.00 4.02
397 418 3.243873 GCCAGATATGGAGTTCGATGTCA 60.244 47.826 11.49 0.00 0.00 3.58
399 420 2.700371 TGCCAGATATGGAGTTCGATGT 59.300 45.455 11.49 0.00 0.00 3.06
423 444 1.403647 CCGACGCTTTAGTCATGTGGA 60.404 52.381 0.00 0.00 40.98 4.02
428 449 1.471119 TCCTCCGACGCTTTAGTCAT 58.529 50.000 0.00 0.00 40.98 3.06
429 450 1.201647 CTTCCTCCGACGCTTTAGTCA 59.798 52.381 0.00 0.00 40.98 3.41
430 451 1.471684 TCTTCCTCCGACGCTTTAGTC 59.528 52.381 0.00 0.00 37.76 2.59
436 457 1.292541 GGTTTCTTCCTCCGACGCT 59.707 57.895 0.00 0.00 0.00 5.07
437 458 0.391263 ATGGTTTCTTCCTCCGACGC 60.391 55.000 0.00 0.00 0.00 5.19
448 469 3.421844 GTGAAAGGCAGGTATGGTTTCT 58.578 45.455 0.00 0.00 0.00 2.52
449 470 2.161609 CGTGAAAGGCAGGTATGGTTTC 59.838 50.000 0.00 0.00 0.00 2.78
450 471 2.159382 CGTGAAAGGCAGGTATGGTTT 58.841 47.619 0.00 0.00 0.00 3.27
473 494 7.998383 TGATGGATTATGTGCTAAGGTTTATGT 59.002 33.333 0.00 0.00 0.00 2.29
505 526 0.603172 ATCAGCATCGGCAGCATCTC 60.603 55.000 0.00 0.00 44.61 2.75
609 632 0.673644 GTGGTGGTGGACCTGATTCG 60.674 60.000 0.00 0.00 46.32 3.34
626 649 3.118454 GGTGGTGATGCCGTCGTG 61.118 66.667 0.00 0.00 41.21 4.35
705 730 0.805614 AGTCAGTCGTCGGTGATGAG 59.194 55.000 0.00 0.00 0.00 2.90
755 780 4.770362 TGGGTCGCCGGATCCTCA 62.770 66.667 5.05 0.00 44.38 3.86
763 789 1.744320 TATGATGAGGTGGGTCGCCG 61.744 60.000 0.00 0.00 39.30 6.46
765 791 1.040646 TCTATGATGAGGTGGGTCGC 58.959 55.000 0.00 0.00 0.00 5.19
817 843 2.579738 GTCGCCAGGGAGTTCCTC 59.420 66.667 0.00 0.00 46.12 3.71
838 864 2.430546 AAGAGGCGATCTTGATAGCG 57.569 50.000 9.02 0.00 46.80 4.26
1359 1392 2.029020 TGTCCCTGACAATCTTCAGTCG 60.029 50.000 0.00 0.00 41.40 4.18
1389 1422 0.593128 AACTGCATGCGTTCTTCCAC 59.407 50.000 14.09 0.00 0.00 4.02
1644 1802 3.195698 GCATTCACCGGACCGAGC 61.196 66.667 17.49 2.29 0.00 5.03
1696 1854 7.645058 CCTCATCAAGGTAAATTACAATGGT 57.355 36.000 5.45 0.00 40.67 3.55
1793 1951 5.758296 ACAGAACGTGTACAGATGTGAATTT 59.242 36.000 0.00 0.00 37.75 1.82
1797 1961 4.316205 AACAGAACGTGTACAGATGTGA 57.684 40.909 0.00 0.00 39.03 3.58
1803 1967 3.060363 GCGGATAAACAGAACGTGTACAG 59.940 47.826 0.00 0.00 39.03 2.74
1810 1974 4.109766 TGAGTATGCGGATAAACAGAACG 58.890 43.478 0.00 0.00 0.00 3.95
1811 1975 7.891183 ATATGAGTATGCGGATAAACAGAAC 57.109 36.000 0.00 0.00 0.00 3.01
1907 2075 4.520874 TGACGATCTTGTCTCCTCCATATC 59.479 45.833 0.00 0.00 39.64 1.63
2533 3881 2.299993 TGTTGCCGAGATAAGAGCAG 57.700 50.000 0.00 0.00 36.44 4.24
2534 3882 2.554142 CATGTTGCCGAGATAAGAGCA 58.446 47.619 0.00 0.00 0.00 4.26
2582 3930 0.676466 CGAGCAACCTGGCCACATAA 60.676 55.000 0.00 0.00 0.00 1.90
2616 3965 7.390718 GCAGGAAGAGAAGTGTAAATTAAAGGA 59.609 37.037 0.00 0.00 0.00 3.36
2617 3966 7.174946 TGCAGGAAGAGAAGTGTAAATTAAAGG 59.825 37.037 0.00 0.00 0.00 3.11
2963 4995 0.525668 CGTCCTTTGGTCCGATCGAG 60.526 60.000 18.66 6.99 0.00 4.04
2966 4998 0.459759 GGACGTCCTTTGGTCCGATC 60.460 60.000 27.64 0.00 42.91 3.69
2981 5013 1.949525 CAGGCATTTTAGGGATGGACG 59.050 52.381 0.00 0.00 0.00 4.79
2982 5014 2.952310 GACAGGCATTTTAGGGATGGAC 59.048 50.000 0.00 0.00 0.00 4.02
2988 5020 4.342092 CCCAAATAGACAGGCATTTTAGGG 59.658 45.833 0.00 0.00 0.00 3.53
2997 5029 2.489938 TGACACCCAAATAGACAGGC 57.510 50.000 0.00 0.00 0.00 4.85
3003 5035 6.877611 ACTAGTTGTTTGACACCCAAATAG 57.122 37.500 14.50 14.50 45.48 1.73
3009 5041 8.788325 AGAATATTACTAGTTGTTTGACACCC 57.212 34.615 0.00 0.00 0.00 4.61
3071 5103 9.474249 GCTTATTACATACTTTTGAAGAACGAC 57.526 33.333 0.00 0.00 0.00 4.34
3081 5113 6.049263 GCGCTGAGCTTATTACATACTTTT 57.951 37.500 1.78 0.00 44.04 2.27
3109 5141 9.490379 CTATCGGGAGCTTATTACATACTTTTT 57.510 33.333 0.00 0.00 0.00 1.94
3110 5142 8.867097 TCTATCGGGAGCTTATTACATACTTTT 58.133 33.333 0.00 0.00 0.00 2.27
3111 5143 8.305317 GTCTATCGGGAGCTTATTACATACTTT 58.695 37.037 0.00 0.00 0.00 2.66
3112 5144 7.093858 GGTCTATCGGGAGCTTATTACATACTT 60.094 40.741 0.00 0.00 0.00 2.24
3113 5145 6.377712 GGTCTATCGGGAGCTTATTACATACT 59.622 42.308 0.00 0.00 0.00 2.12
3114 5146 6.152323 TGGTCTATCGGGAGCTTATTACATAC 59.848 42.308 0.00 0.00 35.11 2.39
3115 5147 6.250711 TGGTCTATCGGGAGCTTATTACATA 58.749 40.000 0.00 0.00 35.11 2.29
3116 5148 5.084519 TGGTCTATCGGGAGCTTATTACAT 58.915 41.667 0.00 0.00 35.11 2.29
3117 5149 4.476297 TGGTCTATCGGGAGCTTATTACA 58.524 43.478 0.00 0.00 35.11 2.41
3118 5150 5.662674 ATGGTCTATCGGGAGCTTATTAC 57.337 43.478 0.00 0.00 35.11 1.89
3119 5151 9.078990 CATATATGGTCTATCGGGAGCTTATTA 57.921 37.037 4.68 0.00 36.34 0.98
3120 5152 7.785028 TCATATATGGTCTATCGGGAGCTTATT 59.215 37.037 12.78 4.34 36.34 1.40
3121 5153 7.298374 TCATATATGGTCTATCGGGAGCTTAT 58.702 38.462 12.78 0.00 37.60 1.73
3122 5154 6.669631 TCATATATGGTCTATCGGGAGCTTA 58.330 40.000 12.78 0.00 35.11 3.09
3123 5155 5.519808 TCATATATGGTCTATCGGGAGCTT 58.480 41.667 12.78 0.00 35.11 3.74
3124 5156 5.130705 TCATATATGGTCTATCGGGAGCT 57.869 43.478 12.78 0.00 35.11 4.09
3125 5157 5.854010 TTCATATATGGTCTATCGGGAGC 57.146 43.478 12.78 0.00 0.00 4.70
3126 5158 8.094548 TGTTTTTCATATATGGTCTATCGGGAG 58.905 37.037 12.78 0.00 0.00 4.30
3127 5159 7.969004 TGTTTTTCATATATGGTCTATCGGGA 58.031 34.615 12.78 0.00 0.00 5.14
3128 5160 8.615878 TTGTTTTTCATATATGGTCTATCGGG 57.384 34.615 12.78 0.00 0.00 5.14
3129 5161 8.230486 GCTTGTTTTTCATATATGGTCTATCGG 58.770 37.037 12.78 0.75 0.00 4.18
3130 5162 8.773645 TGCTTGTTTTTCATATATGGTCTATCG 58.226 33.333 12.78 0.00 0.00 2.92
3132 5164 9.851686 TCTGCTTGTTTTTCATATATGGTCTAT 57.148 29.630 12.78 0.00 0.00 1.98
3133 5165 9.679661 TTCTGCTTGTTTTTCATATATGGTCTA 57.320 29.630 12.78 0.00 0.00 2.59
3134 5166 8.579850 TTCTGCTTGTTTTTCATATATGGTCT 57.420 30.769 12.78 0.00 0.00 3.85
3135 5167 9.455847 GATTCTGCTTGTTTTTCATATATGGTC 57.544 33.333 12.78 0.95 0.00 4.02
3136 5168 8.970020 TGATTCTGCTTGTTTTTCATATATGGT 58.030 29.630 12.78 0.00 0.00 3.55
3137 5169 9.976511 ATGATTCTGCTTGTTTTTCATATATGG 57.023 29.630 12.78 0.00 0.00 2.74
3141 5173 9.932207 TGAAATGATTCTGCTTGTTTTTCATAT 57.068 25.926 0.00 0.00 36.48 1.78
3142 5174 9.761504 TTGAAATGATTCTGCTTGTTTTTCATA 57.238 25.926 0.00 0.00 36.48 2.15
3212 5244 1.880027 ACGCAAAGTTTGGGAGATGTC 59.120 47.619 32.17 7.45 45.47 3.06
3230 5262 3.054166 TGGTGTTTCGACTTGTATGACG 58.946 45.455 0.00 0.00 0.00 4.35
3296 5328 2.805671 CACGTGACATTCTGGTAAGCAA 59.194 45.455 10.90 0.00 0.00 3.91
3306 5338 6.201425 TCACTACTTTTTACCACGTGACATTC 59.799 38.462 19.30 0.00 0.00 2.67
3406 5440 5.981174 AGCATTTATTTGTTGGATGGGAAG 58.019 37.500 0.00 0.00 0.00 3.46
3410 5444 6.702723 CACCATAGCATTTATTTGTTGGATGG 59.297 38.462 0.00 0.00 36.89 3.51
3426 5460 0.680921 GAAGCAAGGCCACCATAGCA 60.681 55.000 5.01 0.00 0.00 3.49
3485 5519 9.731001 TCCTATTCTATAAAAGGGAAAGAGAGT 57.269 33.333 0.00 0.00 0.00 3.24
3506 5540 6.969993 AGAAAGTCTCGCTCTTAATCCTAT 57.030 37.500 0.00 0.00 0.00 2.57
3509 5543 5.980715 CCTAAGAAAGTCTCGCTCTTAATCC 59.019 44.000 0.00 0.00 32.67 3.01
3510 5544 6.566141 ACCTAAGAAAGTCTCGCTCTTAATC 58.434 40.000 0.00 0.00 32.67 1.75
3527 5561 4.016444 GCCCATGAATTGACAACCTAAGA 58.984 43.478 0.00 0.00 0.00 2.10
3693 5729 9.463902 TGTTAGGAAACCAAAAATATTATCGGA 57.536 29.630 4.44 0.00 34.49 4.55
3822 5858 7.012894 AGGATTCACATACGAAACACTTCAAAA 59.987 33.333 0.00 0.00 0.00 2.44
3847 5883 5.592688 CCTAGGAGAGTAAGAAGAAGGTGAG 59.407 48.000 1.05 0.00 0.00 3.51
4062 6098 5.466393 CCTTAAAAATGTTGGGCACTTCTTG 59.534 40.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.