Multiple sequence alignment - TraesCS4B01G144200

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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 TraesCS4B01G144200 chr4B 100.000 2607 0 0 1335 3941 193524274 193526880 0.000000e+00 4815.0
1 TraesCS4B01G144200 chr4B 100.000 1025 0 0 1 1025 193522940 193523964 0.000000e+00 1893.0
2 TraesCS4B01G144200 chr4B 96.008 501 17 1 1 501 102704072 102704569 0.000000e+00 811.0
3 TraesCS4B01G144200 chr4B 81.544 298 38 10 2818 3114 289622923 289623204 3.060000e-56 230.0
4 TraesCS4B01G144200 chr4D 93.181 2009 67 21 1335 3289 134547566 134549558 0.000000e+00 2887.0
5 TraesCS4B01G144200 chr4D 90.835 611 36 12 3340 3941 134626832 134627431 0.000000e+00 800.0
6 TraesCS4B01G144200 chr4D 96.533 375 12 1 652 1025 134547157 134547531 1.560000e-173 619.0
7 TraesCS4B01G144200 chr4A 91.581 1259 61 24 2062 3305 424372193 424370965 0.000000e+00 1696.0
8 TraesCS4B01G144200 chr4A 92.717 714 31 6 1335 2029 424372902 424372191 0.000000e+00 1011.0
9 TraesCS4B01G144200 chr4A 92.609 460 21 7 3436 3888 424370588 424370135 0.000000e+00 649.0
10 TraesCS4B01G144200 chr4A 95.000 340 16 1 687 1025 424373278 424372939 2.080000e-147 532.0
11 TraesCS4B01G144200 chr4A 97.727 44 1 0 3898 3941 424369730 424369687 4.220000e-10 76.8
12 TraesCS4B01G144200 chr2B 90.854 492 34 8 1 489 772142394 772142877 0.000000e+00 649.0
13 TraesCS4B01G144200 chr2B 91.250 480 36 6 38 513 777628908 777628431 0.000000e+00 649.0
14 TraesCS4B01G144200 chr2B 90.381 499 37 5 1 498 409928534 409929022 0.000000e+00 645.0
15 TraesCS4B01G144200 chr2B 93.421 304 19 1 1 304 777629213 777628911 2.160000e-122 449.0
16 TraesCS4B01G144200 chr7B 90.702 484 36 7 25 506 136557635 136558111 1.540000e-178 636.0
17 TraesCS4B01G144200 chr7B 89.959 488 42 6 1 486 6932397 6932879 1.200000e-174 623.0
18 TraesCS4B01G144200 chr3B 89.703 505 28 8 1 499 679512152 679511666 1.200000e-174 623.0
19 TraesCS4B01G144200 chr3B 89.200 500 31 6 1 499 299795941 299796418 1.570000e-168 603.0
20 TraesCS4B01G144200 chr3B 78.846 676 84 27 2262 2912 670202325 670202966 6.130000e-108 401.0
21 TraesCS4B01G144200 chr5B 86.534 453 54 5 1 446 687547362 687546910 3.540000e-135 492.0
22 TraesCS4B01G144200 chr6B 82.255 479 57 15 2189 2642 2168213 2167738 4.780000e-104 388.0
23 TraesCS4B01G144200 chr6B 86.006 343 33 9 158 497 247060561 247060891 1.740000e-93 353.0
24 TraesCS4B01G144200 chr6A 81.604 424 52 13 2322 2738 583828871 583829275 1.060000e-85 327.0
25 TraesCS4B01G144200 chr6A 73.444 241 45 15 3333 3559 106666923 106666688 5.460000e-09 73.1
26 TraesCS4B01G144200 chr3A 86.254 291 27 8 3337 3615 659804837 659805126 1.780000e-78 303.0
27 TraesCS4B01G144200 chr3A 84.880 291 31 7 3337 3615 659803955 659804244 8.340000e-72 281.0
28 TraesCS4B01G144200 chr2D 84.839 310 31 8 3333 3626 57115883 57115574 8.280000e-77 298.0
29 TraesCS4B01G144200 chr1D 84.589 292 33 5 3333 3614 411784390 411784679 3.000000e-71 279.0
30 TraesCS4B01G144200 chr1D 84.502 271 31 7 3329 3589 11762419 11762688 1.410000e-64 257.0
31 TraesCS4B01G144200 chr1D 80.627 351 50 9 2189 2531 465082492 465082152 5.050000e-64 255.0
32 TraesCS4B01G144200 chr7A 80.769 286 40 10 3333 3606 706968007 706967725 3.990000e-50 209.0
33 TraesCS4B01G144200 chr2A 77.955 313 49 13 3333 3631 592859283 592858977 1.130000e-40 178.0


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 TraesCS4B01G144200 chr4B 193522940 193526880 3940 False 3354.00 4815 100.0000 1 3941 2 chr4B.!!$F3 3940
1 TraesCS4B01G144200 chr4D 134547157 134549558 2401 False 1753.00 2887 94.8570 652 3289 2 chr4D.!!$F2 2637
2 TraesCS4B01G144200 chr4D 134626832 134627431 599 False 800.00 800 90.8350 3340 3941 1 chr4D.!!$F1 601
3 TraesCS4B01G144200 chr4A 424369687 424373278 3591 True 792.96 1696 93.9268 687 3941 5 chr4A.!!$R1 3254
4 TraesCS4B01G144200 chr2B 777628431 777629213 782 True 549.00 649 92.3355 1 513 2 chr2B.!!$R1 512
5 TraesCS4B01G144200 chr3B 670202325 670202966 641 False 401.00 401 78.8460 2262 2912 1 chr3B.!!$F2 650
6 TraesCS4B01G144200 chr3A 659803955 659805126 1171 False 292.00 303 85.5670 3337 3615 2 chr3A.!!$F1 278

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
648 919 0.108233 TGTACGATTTGGGGTACGCC 60.108 55.000 21.62 21.62 41.41 5.68 F
649 920 1.141449 TACGATTTGGGGTACGCCG 59.859 57.895 22.64 13.16 42.25 6.46 F
650 921 1.603236 TACGATTTGGGGTACGCCGT 61.603 55.000 22.64 17.73 42.25 5.68 F
1536 1808 0.614812 GCGGTTTGGGGTTAGGACTA 59.385 55.000 0.00 0.00 0.00 2.59 F
1546 1837 1.134877 GGTTAGGACTAGTGCGTTCCC 60.135 57.143 8.90 4.42 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1451 1723 0.464373 AATCCGCATCAGCAACCGAT 60.464 50.000 0.0 0.0 42.27 4.18 R
1522 1794 0.899720 CGCACTAGTCCTAACCCCAA 59.100 55.000 0.0 0.0 0.00 4.12 R
2237 2537 1.404315 GCTCCTTGAACGACCCACTAG 60.404 57.143 0.0 0.0 0.00 2.57 R
2868 3191 1.137282 GCAGCTCCCTCCTTGTAGTAC 59.863 57.143 0.0 0.0 0.00 2.73 R
3206 3529 1.409790 TGCTTTGCTCATTTGCTGTGT 59.590 42.857 0.0 0.0 0.00 3.72 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
139 408 2.805671 GCTGGGCCAAAATTACAAACAC 59.194 45.455 8.04 0.00 0.00 3.32
145 414 5.233988 GGCCAAAATTACAAACACTATGCA 58.766 37.500 0.00 0.00 0.00 3.96
167 436 5.334337 GCATGCAGCGTATCTGATAAATGAA 60.334 40.000 14.21 0.00 45.72 2.57
174 443 5.334414 GCGTATCTGATAAATGAAGCTTGGG 60.334 44.000 2.10 0.00 0.00 4.12
183 452 1.301716 GAAGCTTGGGCGAGACACA 60.302 57.895 2.10 0.00 44.37 3.72
198 467 4.096532 CGAGACACATATATCCTACGCCAT 59.903 45.833 0.00 0.00 0.00 4.40
214 483 5.099042 ACGCCATCCTGTATTTAAAGAGT 57.901 39.130 0.00 0.00 0.00 3.24
256 525 0.954452 AAGAAAAGGAAGTGCAGGCG 59.046 50.000 0.00 0.00 0.00 5.52
263 532 1.377202 GAAGTGCAGGCGGGAATCA 60.377 57.895 0.00 0.00 0.00 2.57
275 544 2.565841 CGGGAATCAAACCTGGATCTC 58.434 52.381 0.00 0.00 0.00 2.75
286 555 3.012153 TGGATCTCCCAGGTGGAAG 57.988 57.895 0.00 0.00 44.57 3.46
327 596 5.991328 ATATTACCGAAGCACTTGTGATG 57.009 39.130 4.79 0.00 0.00 3.07
328 597 1.438651 TACCGAAGCACTTGTGATGC 58.561 50.000 4.79 0.00 43.74 3.91
343 612 6.040504 ACTTGTGATGCAATACGAGACCTATA 59.959 38.462 21.36 0.00 36.36 1.31
359 628 7.201794 CGAGACCTATACCTAATGAACTCAACA 60.202 40.741 0.00 0.00 0.00 3.33
371 640 0.534203 ACTCAACAAACGGCCGATGT 60.534 50.000 35.90 30.72 0.00 3.06
416 687 2.045340 ACTTACCGGTGGCATGGC 60.045 61.111 19.93 13.29 0.00 4.40
433 704 5.279256 GGCATGGCGGGTAAATATTTACAAT 60.279 40.000 30.11 16.80 43.64 2.71
462 733 2.095969 GCAATTTCATGACGGACGACAA 60.096 45.455 0.00 0.00 0.00 3.18
468 739 1.600013 CATGACGGACGACAAAAACCA 59.400 47.619 0.00 0.00 0.00 3.67
480 751 8.822855 GGACGACAAAAACCAAATTTTCTTTAT 58.177 29.630 0.00 0.00 39.70 1.40
641 912 3.567576 TTTGTGCATGTACGATTTGGG 57.432 42.857 9.48 0.00 0.00 4.12
642 913 1.458398 TGTGCATGTACGATTTGGGG 58.542 50.000 9.48 0.00 0.00 4.96
643 914 1.271652 TGTGCATGTACGATTTGGGGT 60.272 47.619 9.48 0.00 0.00 4.95
644 915 2.027100 TGTGCATGTACGATTTGGGGTA 60.027 45.455 9.48 0.00 0.00 3.69
645 916 2.353579 GTGCATGTACGATTTGGGGTAC 59.646 50.000 0.00 0.00 39.50 3.34
646 917 1.595794 GCATGTACGATTTGGGGTACG 59.404 52.381 0.00 0.00 41.41 3.67
647 918 1.595794 CATGTACGATTTGGGGTACGC 59.404 52.381 0.29 0.29 41.41 4.42
648 919 0.108233 TGTACGATTTGGGGTACGCC 60.108 55.000 21.62 21.62 41.41 5.68
649 920 1.141449 TACGATTTGGGGTACGCCG 59.859 57.895 22.64 13.16 42.25 6.46
650 921 1.603236 TACGATTTGGGGTACGCCGT 61.603 55.000 22.64 17.73 42.25 5.68
847 1118 3.770040 CCACAGATCGGACGGCCA 61.770 66.667 8.76 0.00 0.00 5.36
891 1162 2.613223 GGGCTGCTATAAATCCGAGGAC 60.613 54.545 0.00 0.00 0.00 3.85
899 1170 1.885163 AAATCCGAGGACGCCGTCTT 61.885 55.000 17.76 9.88 38.29 3.01
902 1173 2.202492 CGAGGACGCCGTCTTCTG 60.202 66.667 24.01 14.99 36.68 3.02
965 1237 2.347731 GGAGCTCGTTAGGGTTTTCTG 58.652 52.381 7.83 0.00 0.00 3.02
1425 1697 5.413213 GCTTTCGGACTAGCTAGATCTGATA 59.587 44.000 27.45 20.40 34.57 2.15
1451 1723 3.979948 TCGTGAATCGGTTGTTTAGTCA 58.020 40.909 0.00 0.00 40.32 3.41
1522 1794 1.814527 GGTAGATCTCCGTGCGGTT 59.185 57.895 10.60 0.00 36.47 4.44
1536 1808 0.614812 GCGGTTTGGGGTTAGGACTA 59.385 55.000 0.00 0.00 0.00 2.59
1546 1837 1.134877 GGTTAGGACTAGTGCGTTCCC 60.135 57.143 8.90 4.42 0.00 3.97
1566 1857 5.123227 TCCCACGATGGATTTTACTGAATC 58.877 41.667 5.71 0.00 40.96 2.52
1611 1902 2.478831 GATGAGCTTCTGTCGGATTCC 58.521 52.381 0.00 0.00 0.00 3.01
1670 1961 1.887242 TCGATGGCCATGTAAGCGC 60.887 57.895 26.56 5.51 0.00 5.92
1706 1997 2.003658 CTGTGTGCGGTGCTTGGTTT 62.004 55.000 0.00 0.00 0.00 3.27
1805 2096 2.240667 AGCACCTTTCATCTAGGCATGT 59.759 45.455 0.00 0.00 36.17 3.21
1873 2164 3.943381 CAGGCTTGTATCTGCTTTCATGA 59.057 43.478 0.00 0.00 0.00 3.07
1954 2248 5.505780 TGTTTGTATCCTCTATTGGGGTTG 58.494 41.667 0.00 0.00 0.00 3.77
2046 2340 7.714377 TGGATTTGCTTGTGTAAACAATTTCAT 59.286 29.630 0.00 0.00 31.03 2.57
2150 2447 7.342769 TCAACCGTTCATATCTAAAGCTCTA 57.657 36.000 0.00 0.00 0.00 2.43
2151 2448 7.778083 TCAACCGTTCATATCTAAAGCTCTAA 58.222 34.615 0.00 0.00 0.00 2.10
2152 2449 8.255206 TCAACCGTTCATATCTAAAGCTCTAAA 58.745 33.333 0.00 0.00 0.00 1.85
2153 2450 8.543774 CAACCGTTCATATCTAAAGCTCTAAAG 58.456 37.037 0.00 0.00 0.00 1.85
2408 2711 4.038522 TGATGCTCTTGACCTATCTACAGC 59.961 45.833 0.00 0.00 0.00 4.40
2436 2739 3.492383 CACTTGATGATAGTGCTAAGCCG 59.508 47.826 0.00 0.00 36.88 5.52
2439 2742 2.287608 TGATGATAGTGCTAAGCCGTCG 60.288 50.000 0.00 0.00 0.00 5.12
2441 2744 1.202256 TGATAGTGCTAAGCCGTCGTG 60.202 52.381 0.00 0.00 0.00 4.35
2575 2878 1.800805 AGAATGTTGAGTCTGCCACG 58.199 50.000 0.00 0.00 0.00 4.94
2747 3050 5.880054 ATTGAACTTAAATCAGTGACGGG 57.120 39.130 0.00 0.00 0.00 5.28
2786 3098 9.684702 TTTGGGGAAGGTAGTAATAATCTATCT 57.315 33.333 0.00 0.00 31.12 1.98
2942 3265 4.142730 GCTGAAAGAGGTCAAGTGCTAATG 60.143 45.833 0.00 0.00 34.07 1.90
2991 3314 3.681897 CGTCAGTATTTTTGCTCTGCTCT 59.318 43.478 0.00 0.00 0.00 4.09
2992 3315 4.864806 CGTCAGTATTTTTGCTCTGCTCTA 59.135 41.667 0.00 0.00 0.00 2.43
2993 3316 5.521735 CGTCAGTATTTTTGCTCTGCTCTAT 59.478 40.000 0.00 0.00 0.00 1.98
2994 3317 6.509199 CGTCAGTATTTTTGCTCTGCTCTATG 60.509 42.308 0.00 0.00 0.00 2.23
3046 3369 7.712204 TGGTGTCAGTAACTATCAGATGTTA 57.288 36.000 0.00 0.00 0.00 2.41
3054 3377 9.509855 CAGTAACTATCAGATGTTAAGTGTCTC 57.490 37.037 0.00 0.00 31.56 3.36
3077 3400 7.444183 TCTCGAAAACTTTCTGATAATTGTGGT 59.556 33.333 1.03 0.00 35.07 4.16
3146 3469 2.083774 CAATGCCTCGGCTTTTACTCA 58.916 47.619 9.65 0.00 42.51 3.41
3147 3470 2.487762 CAATGCCTCGGCTTTTACTCAA 59.512 45.455 9.65 0.00 42.51 3.02
3150 3473 3.531538 TGCCTCGGCTTTTACTCAATAG 58.468 45.455 9.65 0.00 42.51 1.73
3151 3474 3.055385 TGCCTCGGCTTTTACTCAATAGT 60.055 43.478 9.65 0.00 42.51 2.12
3156 3479 6.148811 CCTCGGCTTTTACTCAATAGTTGAAA 59.851 38.462 0.00 0.00 39.58 2.69
3175 3498 4.202141 TGAAACAAGAGATTTTGCCCTGTG 60.202 41.667 0.00 0.00 0.00 3.66
3208 3531 9.554395 TCAGATTATCTTGTGTCTTTTGTAACA 57.446 29.630 0.00 0.00 0.00 2.41
3209 3532 9.599322 CAGATTATCTTGTGTCTTTTGTAACAC 57.401 33.333 0.00 0.00 44.75 3.32
3302 3650 8.849168 TGATGAGTTTCACTTAATTGATGTGTT 58.151 29.630 0.00 0.00 35.28 3.32
3306 3654 9.774742 GAGTTTCACTTAATTGATGTGTTATCC 57.225 33.333 0.00 0.00 35.28 2.59
3323 3671 8.471609 TGTGTTATCCTAAATACACATCGAGAA 58.528 33.333 0.00 0.00 44.10 2.87
3325 3673 8.909923 TGTTATCCTAAATACACATCGAGAAGA 58.090 33.333 0.00 0.00 0.00 2.87
3326 3674 9.745880 GTTATCCTAAATACACATCGAGAAGAA 57.254 33.333 0.00 0.00 0.00 2.52
3329 3677 9.838339 ATCCTAAATACACATCGAGAAGAAAAT 57.162 29.630 0.00 0.00 0.00 1.82
3334 3682 9.449719 AAATACACATCGAGAAGAAAATAGGTT 57.550 29.630 0.00 0.00 0.00 3.50
3335 3683 6.969828 ACACATCGAGAAGAAAATAGGTTC 57.030 37.500 0.00 0.00 0.00 3.62
3392 4913 7.698628 TCAGACTCTAAATACACATCGAGAAG 58.301 38.462 0.00 0.00 0.00 2.85
3397 4920 9.706691 ACTCTAAATACACATCGAGAAGAAAAA 57.293 29.630 0.00 0.00 0.00 1.94
3634 5161 1.215423 GGGTGGGAGCACAATATTCCT 59.785 52.381 0.00 0.00 0.00 3.36
3646 5173 7.019388 AGCACAATATTCCTCTATAGAAGGGA 58.981 38.462 3.57 5.30 0.00 4.20
3647 5174 7.038658 AGCACAATATTCCTCTATAGAAGGGAC 60.039 40.741 9.68 0.00 0.00 4.46
3648 5175 7.616313 CACAATATTCCTCTATAGAAGGGACC 58.384 42.308 9.68 0.00 0.00 4.46
3655 5182 4.282195 CCTCTATAGAAGGGACCATGACAC 59.718 50.000 3.57 0.00 0.00 3.67
3686 5213 4.829492 CCTCTCAATCCCTTCTTTGTGTTT 59.171 41.667 0.00 0.00 0.00 2.83
3687 5214 6.003950 CCTCTCAATCCCTTCTTTGTGTTTA 58.996 40.000 0.00 0.00 0.00 2.01
3692 5223 9.546428 CTCAATCCCTTCTTTGTGTTTATTTTT 57.454 29.630 0.00 0.00 0.00 1.94
3907 5836 4.973168 ACACAAGTTTGATGCCTTCTCTA 58.027 39.130 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 364 7.976175 CAGCTTTTCTCTGTTTAACTTTTTCCT 59.024 33.333 0.00 0.00 0.00 3.36
96 365 7.222805 CCAGCTTTTCTCTGTTTAACTTTTTCC 59.777 37.037 0.00 0.00 0.00 3.13
97 366 7.222805 CCCAGCTTTTCTCTGTTTAACTTTTTC 59.777 37.037 0.00 0.00 0.00 2.29
139 408 2.680577 TCAGATACGCTGCATGCATAG 58.319 47.619 22.97 19.75 44.52 2.23
145 414 5.106791 GCTTCATTTATCAGATACGCTGCAT 60.107 40.000 0.00 0.00 44.52 3.96
152 421 5.334414 CGCCCAAGCTTCATTTATCAGATAC 60.334 44.000 0.00 0.00 36.60 2.24
167 436 0.833287 ATATGTGTCTCGCCCAAGCT 59.167 50.000 0.00 0.00 36.60 3.74
174 443 3.427243 GCGTAGGATATATGTGTCTCGC 58.573 50.000 0.00 0.00 0.00 5.03
183 452 7.676683 AAATACAGGATGGCGTAGGATATAT 57.323 36.000 0.00 0.00 43.62 0.86
246 515 0.539438 TTTGATTCCCGCCTGCACTT 60.539 50.000 0.00 0.00 0.00 3.16
249 518 1.976474 GGTTTGATTCCCGCCTGCA 60.976 57.895 0.00 0.00 0.00 4.41
256 525 2.423517 GGGAGATCCAGGTTTGATTCCC 60.424 54.545 0.47 0.00 37.91 3.97
275 544 2.674220 GCCCTCTCTTCCACCTGGG 61.674 68.421 0.00 0.00 37.76 4.45
304 573 5.465390 GCATCACAAGTGCTTCGGTAATATA 59.535 40.000 0.00 0.00 39.45 0.86
305 574 4.273480 GCATCACAAGTGCTTCGGTAATAT 59.727 41.667 0.00 0.00 39.45 1.28
308 577 1.804151 GCATCACAAGTGCTTCGGTAA 59.196 47.619 0.00 0.00 39.45 2.85
313 582 3.125146 TCGTATTGCATCACAAGTGCTTC 59.875 43.478 0.00 0.00 42.87 3.86
327 596 7.154435 TCATTAGGTATAGGTCTCGTATTGC 57.846 40.000 0.00 0.00 0.00 3.56
328 597 8.794553 AGTTCATTAGGTATAGGTCTCGTATTG 58.205 37.037 0.00 0.00 0.00 1.90
343 612 3.252458 GCCGTTTGTTGAGTTCATTAGGT 59.748 43.478 0.00 0.00 0.00 3.08
359 628 1.808390 GTCGCTACATCGGCCGTTT 60.808 57.895 27.15 11.61 0.00 3.60
386 657 2.874086 CCGGTAAGTCAAAAACGGTTCT 59.126 45.455 0.00 0.00 36.78 3.01
387 658 3.257745 CCGGTAAGTCAAAAACGGTTC 57.742 47.619 0.00 0.00 36.78 3.62
390 661 1.264826 CCACCGGTAAGTCAAAAACGG 59.735 52.381 6.87 0.00 46.16 4.44
416 687 7.430441 CCCCTGAAATTGTAAATATTTACCCG 58.570 38.462 27.56 13.02 41.72 5.28
419 690 9.830975 ATTGCCCCTGAAATTGTAAATATTTAC 57.169 29.630 25.18 25.18 42.51 2.01
433 704 2.230992 CGTCATGAAATTGCCCCTGAAA 59.769 45.455 0.00 0.00 0.00 2.69
619 890 4.302455 CCCAAATCGTACATGCACAAAAA 58.698 39.130 0.00 0.00 0.00 1.94
620 891 3.305676 CCCCAAATCGTACATGCACAAAA 60.306 43.478 0.00 0.00 0.00 2.44
621 892 2.230025 CCCCAAATCGTACATGCACAAA 59.770 45.455 0.00 0.00 0.00 2.83
622 893 1.815613 CCCCAAATCGTACATGCACAA 59.184 47.619 0.00 0.00 0.00 3.33
623 894 1.271652 ACCCCAAATCGTACATGCACA 60.272 47.619 0.00 0.00 0.00 4.57
624 895 1.459450 ACCCCAAATCGTACATGCAC 58.541 50.000 0.00 0.00 0.00 4.57
625 896 2.634600 GTACCCCAAATCGTACATGCA 58.365 47.619 0.00 0.00 35.86 3.96
626 897 1.595794 CGTACCCCAAATCGTACATGC 59.404 52.381 0.00 0.00 35.59 4.06
627 898 1.595794 GCGTACCCCAAATCGTACATG 59.404 52.381 0.00 0.00 35.59 3.21
628 899 1.473788 GGCGTACCCCAAATCGTACAT 60.474 52.381 0.00 0.00 35.59 2.29
629 900 0.108233 GGCGTACCCCAAATCGTACA 60.108 55.000 0.00 0.00 35.59 2.90
630 901 1.147557 CGGCGTACCCCAAATCGTAC 61.148 60.000 0.00 0.00 33.08 3.67
631 902 1.141449 CGGCGTACCCCAAATCGTA 59.859 57.895 0.00 0.00 0.00 3.43
632 903 2.125431 CGGCGTACCCCAAATCGT 60.125 61.111 0.00 0.00 0.00 3.73
633 904 2.125431 ACGGCGTACCCCAAATCG 60.125 61.111 12.58 0.00 0.00 3.34
634 905 1.078988 TGACGGCGTACCCCAAATC 60.079 57.895 14.74 0.00 0.00 2.17
635 906 1.376295 GTGACGGCGTACCCCAAAT 60.376 57.895 14.74 0.00 0.00 2.32
636 907 2.030862 GTGACGGCGTACCCCAAA 59.969 61.111 14.74 0.00 0.00 3.28
637 908 4.006357 GGTGACGGCGTACCCCAA 62.006 66.667 14.74 0.00 0.00 4.12
638 909 3.582242 TAGGTGACGGCGTACCCCA 62.582 63.158 24.87 13.43 37.70 4.96
639 910 2.755469 TAGGTGACGGCGTACCCC 60.755 66.667 24.87 19.44 37.70 4.95
640 911 2.803479 CTAGGTGACGGCGTACCC 59.197 66.667 24.87 21.46 37.70 3.69
641 912 2.103736 GCTAGGTGACGGCGTACC 59.896 66.667 14.74 20.05 37.23 3.34
642 913 2.277756 CGCTAGGTGACGGCGTAC 60.278 66.667 14.74 11.67 46.45 3.67
811 1082 3.058501 GTGGGTATGTTTCAGTTGAACGG 60.059 47.826 0.00 0.00 33.13 4.44
945 1217 2.289506 ACAGAAAACCCTAACGAGCTCC 60.290 50.000 8.47 0.00 0.00 4.70
1376 1648 4.141287 TCAGATCTAGCTTCTAGCCAGTC 58.859 47.826 0.00 0.00 43.77 3.51
1425 1697 1.878953 ACAACCGATTCACGAAAGCT 58.121 45.000 0.00 0.00 45.77 3.74
1451 1723 0.464373 AATCCGCATCAGCAACCGAT 60.464 50.000 0.00 0.00 42.27 4.18
1522 1794 0.899720 CGCACTAGTCCTAACCCCAA 59.100 55.000 0.00 0.00 0.00 4.12
1536 1808 1.899437 ATCCATCGTGGGAACGCACT 61.899 55.000 17.16 0.32 41.12 4.40
1546 1837 5.295292 AGCAGATTCAGTAAAATCCATCGTG 59.705 40.000 0.00 0.00 36.49 4.35
1566 1857 1.661178 GCGACACATCAAACACAGCAG 60.661 52.381 0.00 0.00 0.00 4.24
1593 1884 1.561643 AGGAATCCGACAGAAGCTCA 58.438 50.000 0.00 0.00 0.00 4.26
1706 1997 4.679639 GCACGTGATCTACCAAGATAACCA 60.680 45.833 22.23 0.00 42.73 3.67
1873 2164 6.091713 GCACAATATAACAAGGACTAACACGT 59.908 38.462 0.00 0.00 0.00 4.49
1954 2248 4.956075 ACATACCAATCAATCCAAACCTCC 59.044 41.667 0.00 0.00 0.00 4.30
2046 2340 5.237561 TGTGTGCGCAATAACTTTTAGAAGA 59.762 36.000 14.00 0.00 36.69 2.87
2063 2357 1.463056 ACGGTTGATAATGTGTGTGCG 59.537 47.619 0.00 0.00 0.00 5.34
2150 2447 2.267174 ATGTGCAGTGTGAGAGCTTT 57.733 45.000 0.00 0.00 0.00 3.51
2151 2448 2.267174 AATGTGCAGTGTGAGAGCTT 57.733 45.000 0.00 0.00 0.00 3.74
2152 2449 2.301296 AGTAATGTGCAGTGTGAGAGCT 59.699 45.455 0.00 0.00 0.00 4.09
2153 2450 2.693069 AGTAATGTGCAGTGTGAGAGC 58.307 47.619 0.00 0.00 0.00 4.09
2154 2451 5.468072 AGAAAAGTAATGTGCAGTGTGAGAG 59.532 40.000 0.00 0.00 0.00 3.20
2155 2452 5.368145 AGAAAAGTAATGTGCAGTGTGAGA 58.632 37.500 0.00 0.00 0.00 3.27
2156 2453 5.679734 AGAAAAGTAATGTGCAGTGTGAG 57.320 39.130 0.00 0.00 0.00 3.51
2237 2537 1.404315 GCTCCTTGAACGACCCACTAG 60.404 57.143 0.00 0.00 0.00 2.57
2575 2878 6.257630 CCTTGAGCTTGCTAAGAAGATACTTC 59.742 42.308 0.00 0.00 0.00 3.01
2796 3108 2.032924 ACACCAGTTTTAGAACTTGCGC 59.967 45.455 0.00 0.00 43.48 6.09
2868 3191 1.137282 GCAGCTCCCTCCTTGTAGTAC 59.863 57.143 0.00 0.00 0.00 2.73
2947 3270 4.881850 CGACCCCAAAGATTTTAGCATACT 59.118 41.667 0.00 0.00 0.00 2.12
2962 3285 2.554893 GCAAAAATACTGACGACCCCAA 59.445 45.455 0.00 0.00 0.00 4.12
2965 3288 3.125316 CAGAGCAAAAATACTGACGACCC 59.875 47.826 0.00 0.00 32.90 4.46
3046 3369 8.608844 ATTATCAGAAAGTTTTCGAGACACTT 57.391 30.769 4.19 2.70 41.92 3.16
3054 3377 9.840427 AATACCACAATTATCAGAAAGTTTTCG 57.160 29.630 0.00 0.00 41.92 3.46
3077 3400 8.270080 TCACGATTACCATTACAAAGCAAATA 57.730 30.769 0.00 0.00 0.00 1.40
3146 3469 7.015584 AGGGCAAAATCTCTTGTTTCAACTATT 59.984 33.333 0.00 0.00 0.00 1.73
3147 3470 6.494835 AGGGCAAAATCTCTTGTTTCAACTAT 59.505 34.615 0.00 0.00 0.00 2.12
3150 3473 4.746611 CAGGGCAAAATCTCTTGTTTCAAC 59.253 41.667 0.00 0.00 0.00 3.18
3151 3474 4.405358 ACAGGGCAAAATCTCTTGTTTCAA 59.595 37.500 0.00 0.00 0.00 2.69
3156 3479 3.228188 TCACAGGGCAAAATCTCTTGT 57.772 42.857 0.00 0.00 0.00 3.16
3206 3529 1.409790 TGCTTTGCTCATTTGCTGTGT 59.590 42.857 0.00 0.00 0.00 3.72
3207 3530 2.143008 TGCTTTGCTCATTTGCTGTG 57.857 45.000 0.00 0.00 0.00 3.66
3208 3531 2.894763 TTGCTTTGCTCATTTGCTGT 57.105 40.000 0.00 0.00 0.00 4.40
3209 3532 4.212425 TCATTTTGCTTTGCTCATTTGCTG 59.788 37.500 0.00 0.00 0.00 4.41
3210 3533 4.382291 TCATTTTGCTTTGCTCATTTGCT 58.618 34.783 0.00 0.00 0.00 3.91
3211 3534 4.735662 TCATTTTGCTTTGCTCATTTGC 57.264 36.364 0.00 0.00 0.00 3.68
3214 3537 6.876789 TGATTGATCATTTTGCTTTGCTCATT 59.123 30.769 0.00 0.00 0.00 2.57
3215 3538 6.403049 TGATTGATCATTTTGCTTTGCTCAT 58.597 32.000 0.00 0.00 0.00 2.90
3309 3657 9.099454 GAACCTATTTTCTTCTCGATGTGTATT 57.901 33.333 0.00 0.00 0.00 1.89
3310 3658 8.258007 TGAACCTATTTTCTTCTCGATGTGTAT 58.742 33.333 0.00 0.00 0.00 2.29
3311 3659 7.544566 GTGAACCTATTTTCTTCTCGATGTGTA 59.455 37.037 0.00 0.00 0.00 2.90
3314 3662 6.464222 TGTGAACCTATTTTCTTCTCGATGT 58.536 36.000 0.00 0.00 0.00 3.06
3315 3663 6.968131 TGTGAACCTATTTTCTTCTCGATG 57.032 37.500 0.00 0.00 0.00 3.84
3316 3664 6.595716 CCTTGTGAACCTATTTTCTTCTCGAT 59.404 38.462 0.00 0.00 0.00 3.59
3317 3665 5.932303 CCTTGTGAACCTATTTTCTTCTCGA 59.068 40.000 0.00 0.00 0.00 4.04
3318 3666 5.932303 TCCTTGTGAACCTATTTTCTTCTCG 59.068 40.000 0.00 0.00 0.00 4.04
3319 3667 7.745620 TTCCTTGTGAACCTATTTTCTTCTC 57.254 36.000 0.00 0.00 0.00 2.87
3321 3669 7.886338 ACATTCCTTGTGAACCTATTTTCTTC 58.114 34.615 0.00 0.00 37.11 2.87
3380 4901 6.677781 TTTCACTTTTTCTTCTCGATGTGT 57.322 33.333 0.00 0.00 0.00 3.72
3386 4907 8.633408 CATGCTAAATTTCACTTTTTCTTCTCG 58.367 33.333 0.00 0.00 0.00 4.04
3397 4920 8.565896 TGACACTATTCATGCTAAATTTCACT 57.434 30.769 0.00 0.00 0.00 3.41
3481 5004 6.323739 AGGTCCAAACTTGAAATGTACATTGT 59.676 34.615 21.46 12.03 0.00 2.71
3512 5035 4.702131 GGAATGTGACTGCAACCTCTAAAT 59.298 41.667 0.00 0.00 0.00 1.40
3634 5161 4.078571 AGGTGTCATGGTCCCTTCTATAGA 60.079 45.833 0.00 0.00 0.00 1.98
3646 5173 0.415429 AGGGAGAGAGGTGTCATGGT 59.585 55.000 0.00 0.00 0.00 3.55
3647 5174 1.118838 GAGGGAGAGAGGTGTCATGG 58.881 60.000 0.00 0.00 0.00 3.66
3648 5175 2.031120 GAGAGGGAGAGAGGTGTCATG 58.969 57.143 0.00 0.00 0.00 3.07
3655 5182 1.220236 AGGGATTGAGAGGGAGAGAGG 59.780 57.143 0.00 0.00 0.00 3.69
3907 5836 8.466798 GTTATTGTAGCTGGATTTGTTTACCAT 58.533 33.333 0.00 0.00 33.08 3.55


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

AutoCloner maintained by Alex Coulton.