Multiple sequence alignment - TraesCS5B01G332000

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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 TraesCS5B01G332000 chr5B 100.000 3371 0 0 1 3371 516065388 516068758 0.000000e+00 6226
1 TraesCS5B01G332000 chr5A 95.440 1513 40 8 885 2372 540385080 540386588 0.000000e+00 2385
2 TraesCS5B01G332000 chr5A 89.868 227 11 3 1 215 540384396 540384622 7.120000e-72 281
3 TraesCS5B01G332000 chr5D 95.458 1431 43 3 964 2372 426288097 426289527 0.000000e+00 2263
4 TraesCS5B01G332000 chr5D 93.598 328 11 5 646 970 426287043 426287363 6.540000e-132 481
5 TraesCS5B01G332000 chr5D 89.003 391 27 6 1 380 426286487 426286872 1.420000e-128 470
6 TraesCS5B01G332000 chr2B 97.899 952 18 2 2422 3371 53200996 53201947 0.000000e+00 1646
7 TraesCS5B01G332000 chr2B 97.899 952 18 2 2422 3371 53222973 53223924 0.000000e+00 1646
8 TraesCS5B01G332000 chr2B 97.558 942 13 4 2432 3371 662370887 662369954 0.000000e+00 1604
9 TraesCS5B01G332000 chr2B 95.421 939 35 6 2438 3371 96165796 96164861 0.000000e+00 1489
10 TraesCS5B01G332000 chr2B 94.921 945 40 6 2432 3371 782557654 782558595 0.000000e+00 1472
11 TraesCS5B01G332000 chr1B 96.921 942 24 5 2432 3371 416751270 416752208 0.000000e+00 1574
12 TraesCS5B01G332000 chr3B 94.974 955 35 10 2423 3371 811892439 811893386 0.000000e+00 1485
13 TraesCS5B01G332000 chr3B 94.869 955 37 9 2423 3371 812042228 812043176 0.000000e+00 1482
14 TraesCS5B01G332000 chr3B 94.660 955 39 9 2423 3371 811973927 811974875 0.000000e+00 1471


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 TraesCS5B01G332000 chr5B 516065388 516068758 3370 False 6226.000000 6226 100.000000 1 3371 1 chr5B.!!$F1 3370
1 TraesCS5B01G332000 chr5A 540384396 540386588 2192 False 1333.000000 2385 92.654000 1 2372 2 chr5A.!!$F1 2371
2 TraesCS5B01G332000 chr5D 426286487 426289527 3040 False 1071.333333 2263 92.686333 1 2372 3 chr5D.!!$F1 2371
3 TraesCS5B01G332000 chr2B 53200996 53201947 951 False 1646.000000 1646 97.899000 2422 3371 1 chr2B.!!$F1 949
4 TraesCS5B01G332000 chr2B 53222973 53223924 951 False 1646.000000 1646 97.899000 2422 3371 1 chr2B.!!$F2 949
5 TraesCS5B01G332000 chr2B 662369954 662370887 933 True 1604.000000 1604 97.558000 2432 3371 1 chr2B.!!$R2 939
6 TraesCS5B01G332000 chr2B 96164861 96165796 935 True 1489.000000 1489 95.421000 2438 3371 1 chr2B.!!$R1 933
7 TraesCS5B01G332000 chr2B 782557654 782558595 941 False 1472.000000 1472 94.921000 2432 3371 1 chr2B.!!$F3 939
8 TraesCS5B01G332000 chr1B 416751270 416752208 938 False 1574.000000 1574 96.921000 2432 3371 1 chr1B.!!$F1 939
9 TraesCS5B01G332000 chr3B 811892439 811893386 947 False 1485.000000 1485 94.974000 2423 3371 1 chr3B.!!$F1 948
10 TraesCS5B01G332000 chr3B 812042228 812043176 948 False 1482.000000 1482 94.869000 2423 3371 1 chr3B.!!$F3 948
11 TraesCS5B01G332000 chr3B 811973927 811974875 948 False 1471.000000 1471 94.660000 2423 3371 1 chr3B.!!$F2 948

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
174 187 0.033504 TCAGTGCCCGTGTTCTTCTC 59.966 55.0 0.0 0.0 0.00 2.87 F
611 678 0.382515 GGAGACGAGAGGGTTGATCG 59.617 60.0 0.0 0.0 42.04 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 2785 0.040204 CAGGTTGGCCAGGAGGATTT 59.960 55.0 5.11 0.0 36.89 2.17 R
2456 3292 0.732538 GGATTTGAAGCAAACCGCCG 60.733 55.0 0.00 0.0 44.04 6.46 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
162 175 6.913170 TCTGAGAAATTATTGTTTCAGTGCC 58.087 36.000 10.94 0.00 39.88 5.01
174 187 0.033504 TCAGTGCCCGTGTTCTTCTC 59.966 55.000 0.00 0.00 0.00 2.87
183 196 2.750166 CCGTGTTCTTCTCTCAGCTCTA 59.250 50.000 0.00 0.00 0.00 2.43
209 222 3.670625 TGCACTAGATTAAACAACGCCT 58.329 40.909 0.00 0.00 0.00 5.52
216 229 0.600557 TTAAACAACGCCTGGCCATG 59.399 50.000 14.12 14.48 0.00 3.66
289 353 4.500887 CCAAGAAAGTCTACGAAGTGTCCA 60.501 45.833 0.00 0.00 45.73 4.02
303 367 1.375523 GTCCATCAACCGCCGTTCT 60.376 57.895 0.00 0.00 0.00 3.01
304 368 1.079405 TCCATCAACCGCCGTTCTC 60.079 57.895 0.00 0.00 0.00 2.87
309 373 3.118454 AACCGCCGTTCTCGCATG 61.118 61.111 0.00 0.00 35.54 4.06
310 374 3.583276 AACCGCCGTTCTCGCATGA 62.583 57.895 0.00 0.00 35.54 3.07
344 408 1.129326 GTAATCCAGATTCGCCGTCG 58.871 55.000 0.00 0.00 32.50 5.12
359 423 3.613737 CGCCGTCGAGGTTTTCTTAATTA 59.386 43.478 4.18 0.00 43.70 1.40
362 426 5.277202 GCCGTCGAGGTTTTCTTAATTATCC 60.277 44.000 4.18 0.00 43.70 2.59
365 429 6.291479 CGTCGAGGTTTTCTTAATTATCCGTC 60.291 42.308 0.00 0.00 0.00 4.79
377 442 8.920174 TCTTAATTATCCGTCCAACTAGATTCA 58.080 33.333 0.00 0.00 0.00 2.57
378 443 9.197694 CTTAATTATCCGTCCAACTAGATTCAG 57.802 37.037 0.00 0.00 0.00 3.02
379 444 6.978674 ATTATCCGTCCAACTAGATTCAGA 57.021 37.500 0.00 0.00 0.00 3.27
380 445 4.657436 ATCCGTCCAACTAGATTCAGAC 57.343 45.455 0.00 0.00 0.00 3.51
383 448 4.527038 TCCGTCCAACTAGATTCAGACTTT 59.473 41.667 0.00 0.00 0.00 2.66
384 449 5.011738 TCCGTCCAACTAGATTCAGACTTTT 59.988 40.000 0.00 0.00 0.00 2.27
385 450 5.701290 CCGTCCAACTAGATTCAGACTTTTT 59.299 40.000 0.00 0.00 0.00 1.94
410 475 7.510549 TTTTTGAGGGAACAACTAGATTCAG 57.489 36.000 0.00 0.00 0.00 3.02
411 476 4.826274 TGAGGGAACAACTAGATTCAGG 57.174 45.455 0.00 0.00 0.00 3.86
432 497 2.562738 GCTTGCATCCTAAGTTTTGGGT 59.437 45.455 0.00 0.00 32.34 4.51
439 504 4.447138 TCCTAAGTTTTGGGTGTGACAT 57.553 40.909 0.00 0.00 32.34 3.06
450 515 0.811281 GTGTGACATAGCAAAGGGGC 59.189 55.000 0.00 0.00 0.00 5.80
498 565 1.671742 GTGGAGAAAGTGGGAGCGA 59.328 57.895 0.00 0.00 0.00 4.93
534 601 2.866028 GCAAAGAGCTGTGAGGCG 59.134 61.111 0.00 0.00 41.15 5.52
535 602 1.669115 GCAAAGAGCTGTGAGGCGA 60.669 57.895 0.00 0.00 41.15 5.54
536 603 1.905922 GCAAAGAGCTGTGAGGCGAC 61.906 60.000 0.00 0.00 41.15 5.19
537 604 1.373497 AAAGAGCTGTGAGGCGACG 60.373 57.895 0.00 0.00 37.29 5.12
538 605 1.806461 AAAGAGCTGTGAGGCGACGA 61.806 55.000 0.00 0.00 37.29 4.20
539 606 2.202544 GAGCTGTGAGGCGACGAG 60.203 66.667 0.00 0.00 37.29 4.18
550 617 3.279183 CGACGAGCAAGGAGACCT 58.721 61.111 0.00 0.00 33.87 3.85
551 618 1.587054 CGACGAGCAAGGAGACCTT 59.413 57.895 0.00 0.00 45.88 3.50
561 628 1.036707 AGGAGACCTTGATAGAGCGC 58.963 55.000 0.00 0.00 0.00 5.92
594 661 4.612412 GTGGTGTTCACCGGCGGA 62.612 66.667 35.78 8.46 40.39 5.54
611 678 0.382515 GGAGACGAGAGGGTTGATCG 59.617 60.000 0.00 0.00 42.04 3.69
619 686 6.889301 ACGAGAGGGTTGATCGTATATAAA 57.111 37.500 0.00 0.00 46.95 1.40
620 687 7.281040 ACGAGAGGGTTGATCGTATATAAAA 57.719 36.000 0.00 0.00 46.95 1.52
621 688 7.719483 ACGAGAGGGTTGATCGTATATAAAAA 58.281 34.615 0.00 0.00 46.95 1.94
706 773 4.814294 GGCTAGCACGTCGGTGGG 62.814 72.222 18.24 0.00 44.54 4.61
780 847 2.095263 ACAAATGATGTAAGCCGCACAC 60.095 45.455 0.00 0.00 41.63 3.82
787 854 2.017782 TGTAAGCCGCACACAGAAAAA 58.982 42.857 0.00 0.00 0.00 1.94
863 931 4.385748 CGAAGGAAGCCAATTTAAAACTGC 59.614 41.667 0.00 0.00 0.00 4.40
911 981 2.074547 ACACATACACGTACACAGCC 57.925 50.000 0.00 0.00 0.00 4.85
912 982 1.341852 ACACATACACGTACACAGCCA 59.658 47.619 0.00 0.00 0.00 4.75
913 983 1.992667 CACATACACGTACACAGCCAG 59.007 52.381 0.00 0.00 0.00 4.85
914 984 1.616865 ACATACACGTACACAGCCAGT 59.383 47.619 0.00 0.00 0.00 4.00
962 1036 4.216731 ACGCGTATTACTGTACATCATCG 58.783 43.478 11.67 0.00 0.00 3.84
1056 1871 1.379916 CATGAGCAACCAGGTCCCA 59.620 57.895 0.00 0.00 44.10 4.37
1128 1943 0.611062 ACGTCCGGGAGATGAACAGA 60.611 55.000 0.00 0.00 35.30 3.41
1158 1973 2.494918 CCGGTCATGGTCTCGGTC 59.505 66.667 0.00 0.00 37.92 4.79
1222 2037 2.666190 GCAAGTGGCTCACGCTCA 60.666 61.111 0.49 0.00 39.50 4.26
1239 2054 2.364448 AGGGACTTCCTCCTCCGC 60.364 66.667 0.00 0.00 44.06 5.54
1488 2303 1.025647 ACTACGACCTGCTCCTCGTC 61.026 60.000 6.43 0.00 42.07 4.20
1578 2393 4.115199 GATGCGGACCAGGGGCTT 62.115 66.667 0.00 0.00 0.00 4.35
1595 2410 3.117888 GGGCTTCTTCACCTCATATCCAA 60.118 47.826 0.00 0.00 0.00 3.53
1785 2621 4.299547 AGCTCGTTCAGGCGCACA 62.300 61.111 10.83 0.00 0.00 4.57
1853 2689 2.432628 CCAGGAGTTCGGCGTCAC 60.433 66.667 6.85 5.25 0.00 3.67
1947 2783 2.742372 GTCATCAACGGCGGCACT 60.742 61.111 13.24 0.00 0.00 4.40
1949 2785 1.017177 GTCATCAACGGCGGCACTAA 61.017 55.000 13.24 0.00 0.00 2.24
1950 2786 0.320858 TCATCAACGGCGGCACTAAA 60.321 50.000 13.24 0.00 0.00 1.85
2124 2960 4.083862 AACGAGGAAGAGGCGGCC 62.084 66.667 12.11 12.11 0.00 6.13
2262 3098 2.571757 CTCAAGCGCGACCACCTA 59.428 61.111 12.10 0.00 0.00 3.08
2325 3161 0.888619 TGCTCTTCGTCTCGGTCATT 59.111 50.000 0.00 0.00 0.00 2.57
2337 3173 1.486310 TCGGTCATTTCTGCTGGCTAT 59.514 47.619 0.00 0.00 0.00 2.97
2372 3208 0.179048 CGCCATTCCTGCACCTGATA 60.179 55.000 0.00 0.00 0.00 2.15
2373 3209 1.602311 GCCATTCCTGCACCTGATAG 58.398 55.000 0.00 0.00 0.00 2.08
2374 3210 1.602311 CCATTCCTGCACCTGATAGC 58.398 55.000 0.00 0.00 0.00 2.97
2375 3211 1.602311 CATTCCTGCACCTGATAGCC 58.398 55.000 0.00 0.00 0.00 3.93
2376 3212 1.134007 CATTCCTGCACCTGATAGCCA 60.134 52.381 0.00 0.00 0.00 4.75
2377 3213 0.991146 TTCCTGCACCTGATAGCCAA 59.009 50.000 0.00 0.00 0.00 4.52
2378 3214 0.543277 TCCTGCACCTGATAGCCAAG 59.457 55.000 0.00 0.00 0.00 3.61
2379 3215 0.543277 CCTGCACCTGATAGCCAAGA 59.457 55.000 0.00 0.00 0.00 3.02
2380 3216 1.142465 CCTGCACCTGATAGCCAAGAT 59.858 52.381 0.00 0.00 0.00 2.40
2381 3217 2.369860 CCTGCACCTGATAGCCAAGATA 59.630 50.000 0.00 0.00 0.00 1.98
2382 3218 3.397482 CTGCACCTGATAGCCAAGATAC 58.603 50.000 0.00 0.00 0.00 2.24
2383 3219 3.041211 TGCACCTGATAGCCAAGATACT 58.959 45.455 0.00 0.00 0.00 2.12
2384 3220 3.070159 TGCACCTGATAGCCAAGATACTC 59.930 47.826 0.00 0.00 0.00 2.59
2385 3221 3.070159 GCACCTGATAGCCAAGATACTCA 59.930 47.826 0.00 0.00 0.00 3.41
2386 3222 4.262808 GCACCTGATAGCCAAGATACTCAT 60.263 45.833 0.00 0.00 0.00 2.90
2387 3223 5.236282 CACCTGATAGCCAAGATACTCATG 58.764 45.833 0.00 0.00 0.00 3.07
2388 3224 4.252073 CCTGATAGCCAAGATACTCATGC 58.748 47.826 0.00 0.00 0.00 4.06
2389 3225 4.262765 CCTGATAGCCAAGATACTCATGCA 60.263 45.833 0.00 0.00 0.00 3.96
2390 3226 5.294734 TGATAGCCAAGATACTCATGCAA 57.705 39.130 0.00 0.00 0.00 4.08
2391 3227 5.059161 TGATAGCCAAGATACTCATGCAAC 58.941 41.667 0.00 0.00 0.00 4.17
2392 3228 3.354948 AGCCAAGATACTCATGCAACA 57.645 42.857 0.00 0.00 0.00 3.33
2393 3229 3.276857 AGCCAAGATACTCATGCAACAG 58.723 45.455 0.00 0.00 0.00 3.16
2394 3230 3.012518 GCCAAGATACTCATGCAACAGT 58.987 45.455 6.21 6.21 0.00 3.55
2395 3231 3.064545 GCCAAGATACTCATGCAACAGTC 59.935 47.826 4.25 0.00 0.00 3.51
2396 3232 4.511527 CCAAGATACTCATGCAACAGTCT 58.488 43.478 4.25 0.00 0.00 3.24
2397 3233 4.569966 CCAAGATACTCATGCAACAGTCTC 59.430 45.833 4.25 5.21 0.00 3.36
2398 3234 5.417811 CAAGATACTCATGCAACAGTCTCT 58.582 41.667 4.25 7.20 29.66 3.10
2399 3235 5.008619 AGATACTCATGCAACAGTCTCTG 57.991 43.478 12.78 0.00 37.52 3.35
2401 3237 5.654209 AGATACTCATGCAACAGTCTCTGTA 59.346 40.000 12.78 0.00 44.62 2.74
2402 3238 4.607293 ACTCATGCAACAGTCTCTGTAA 57.393 40.909 2.80 0.00 44.62 2.41
2403 3239 4.960938 ACTCATGCAACAGTCTCTGTAAA 58.039 39.130 2.80 0.00 44.62 2.01
2404 3240 5.555017 ACTCATGCAACAGTCTCTGTAAAT 58.445 37.500 2.80 0.00 44.62 1.40
2405 3241 6.701340 ACTCATGCAACAGTCTCTGTAAATA 58.299 36.000 2.80 0.00 44.62 1.40
2406 3242 7.161404 ACTCATGCAACAGTCTCTGTAAATAA 58.839 34.615 2.80 0.00 44.62 1.40
2407 3243 7.118390 ACTCATGCAACAGTCTCTGTAAATAAC 59.882 37.037 2.80 0.00 44.62 1.89
2408 3244 6.371548 TCATGCAACAGTCTCTGTAAATAACC 59.628 38.462 2.80 0.00 44.62 2.85
2409 3245 5.865085 TGCAACAGTCTCTGTAAATAACCT 58.135 37.500 2.80 0.00 44.62 3.50
2410 3246 5.700832 TGCAACAGTCTCTGTAAATAACCTG 59.299 40.000 2.80 0.00 44.62 4.00
2411 3247 5.701290 GCAACAGTCTCTGTAAATAACCTGT 59.299 40.000 2.80 0.00 44.62 4.00
2412 3248 6.347725 GCAACAGTCTCTGTAAATAACCTGTG 60.348 42.308 2.80 0.00 44.62 3.66
2413 3249 6.665992 ACAGTCTCTGTAAATAACCTGTGA 57.334 37.500 0.27 0.00 43.46 3.58
2414 3250 6.456501 ACAGTCTCTGTAAATAACCTGTGAC 58.543 40.000 0.27 0.00 43.46 3.67
2415 3251 6.041637 ACAGTCTCTGTAAATAACCTGTGACA 59.958 38.462 0.27 0.00 43.46 3.58
2416 3252 6.366332 CAGTCTCTGTAAATAACCTGTGACAC 59.634 42.308 0.00 0.00 31.88 3.67
2417 3253 6.041637 AGTCTCTGTAAATAACCTGTGACACA 59.958 38.462 8.26 8.26 31.88 3.72
2418 3254 6.145696 GTCTCTGTAAATAACCTGTGACACAC 59.854 42.308 3.56 0.00 34.56 3.82
2419 3255 6.041637 TCTCTGTAAATAACCTGTGACACACT 59.958 38.462 3.56 0.00 35.11 3.55
2420 3256 6.220930 TCTGTAAATAACCTGTGACACACTC 58.779 40.000 3.56 0.00 35.11 3.51
2429 3265 3.748048 CCTGTGACACACTCCATTAACAG 59.252 47.826 3.56 0.00 35.11 3.16
2456 3292 3.460857 AAATCTATCCAGCAGTCGACC 57.539 47.619 13.01 0.00 0.00 4.79
2695 3533 1.408822 GGGCCTGTCCATTCGAATCTT 60.409 52.381 7.92 0.00 36.21 2.40
2787 3626 1.079405 GAATCCGCGGTGAGGAACA 60.079 57.895 27.15 2.48 41.69 3.18
2825 3665 3.593442 TTCCTTCCTCTTTTTGCTCCA 57.407 42.857 0.00 0.00 0.00 3.86
3340 4182 7.981789 TGTTTTATGTTGGTTTTGTTAGATGCA 59.018 29.630 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 173 1.016653 GCTGAGAGAAGAACACGGGC 61.017 60.000 0.00 0.00 0.00 6.13
162 175 1.543802 AGAGCTGAGAGAAGAACACGG 59.456 52.381 0.00 0.00 0.00 4.94
174 187 3.944650 TCTAGTGCAGAGTTAGAGCTGAG 59.055 47.826 0.00 0.00 34.06 3.35
183 196 5.107065 GCGTTGTTTAATCTAGTGCAGAGTT 60.107 40.000 0.00 0.00 36.48 3.01
209 222 1.758280 GCAAAATCTCCATCATGGCCA 59.242 47.619 8.56 8.56 37.47 5.36
216 229 0.665298 GAGCCGGCAAAATCTCCATC 59.335 55.000 31.54 9.44 0.00 3.51
289 353 2.813908 GCGAGAACGGCGGTTGAT 60.814 61.111 15.03 2.75 36.24 2.57
303 367 3.576078 AAATTGGGGAGTATCATGCGA 57.424 42.857 0.00 0.00 36.25 5.10
304 368 4.389374 ACTAAATTGGGGAGTATCATGCG 58.611 43.478 0.00 0.00 36.25 4.73
309 373 7.974504 TCTGGATTACTAAATTGGGGAGTATC 58.025 38.462 0.00 0.00 0.00 2.24
310 374 7.947782 TCTGGATTACTAAATTGGGGAGTAT 57.052 36.000 0.00 0.00 0.00 2.12
344 408 7.336176 AGTTGGACGGATAATTAAGAAAACCTC 59.664 37.037 0.00 0.00 0.00 3.85
359 423 4.282496 AGTCTGAATCTAGTTGGACGGAT 58.718 43.478 0.00 0.00 0.00 4.18
362 426 6.787085 AAAAAGTCTGAATCTAGTTGGACG 57.213 37.500 0.00 0.00 0.00 4.79
386 451 6.490040 CCTGAATCTAGTTGTTCCCTCAAAAA 59.510 38.462 0.00 0.00 0.00 1.94
387 452 6.003950 CCTGAATCTAGTTGTTCCCTCAAAA 58.996 40.000 0.00 0.00 0.00 2.44
388 453 5.560724 CCTGAATCTAGTTGTTCCCTCAAA 58.439 41.667 0.00 0.00 0.00 2.69
389 454 4.565652 GCCTGAATCTAGTTGTTCCCTCAA 60.566 45.833 0.00 0.00 0.00 3.02
390 455 3.055094 GCCTGAATCTAGTTGTTCCCTCA 60.055 47.826 0.00 0.00 0.00 3.86
391 456 3.198853 AGCCTGAATCTAGTTGTTCCCTC 59.801 47.826 0.00 0.00 0.00 4.30
392 457 3.185455 AGCCTGAATCTAGTTGTTCCCT 58.815 45.455 0.00 0.00 0.00 4.20
393 458 3.636153 AGCCTGAATCTAGTTGTTCCC 57.364 47.619 0.00 0.00 0.00 3.97
394 459 3.127721 GCAAGCCTGAATCTAGTTGTTCC 59.872 47.826 0.00 0.00 0.00 3.62
395 460 3.753272 TGCAAGCCTGAATCTAGTTGTTC 59.247 43.478 0.00 0.00 0.00 3.18
396 461 3.754965 TGCAAGCCTGAATCTAGTTGTT 58.245 40.909 0.00 0.00 0.00 2.83
397 462 3.423539 TGCAAGCCTGAATCTAGTTGT 57.576 42.857 0.00 0.00 0.00 3.32
398 463 3.314635 GGATGCAAGCCTGAATCTAGTTG 59.685 47.826 3.23 0.00 41.12 3.16
399 464 3.549794 GGATGCAAGCCTGAATCTAGTT 58.450 45.455 3.23 0.00 41.12 2.24
400 465 3.205784 GGATGCAAGCCTGAATCTAGT 57.794 47.619 3.23 0.00 41.12 2.57
411 476 2.562738 ACCCAAAACTTAGGATGCAAGC 59.437 45.455 0.00 0.00 0.00 4.01
432 497 0.403655 TGCCCCTTTGCTATGTCACA 59.596 50.000 0.00 0.00 0.00 3.58
439 504 0.771127 ACTGTTCTGCCCCTTTGCTA 59.229 50.000 0.00 0.00 0.00 3.49
450 515 2.253452 GCAGCCGCAACTGTTCTG 59.747 61.111 5.01 3.37 39.96 3.02
470 537 1.574702 CTTTCTCCACGGTTTCGCCC 61.575 60.000 0.00 0.00 40.63 6.13
477 544 2.058675 CTCCCACTTTCTCCACGGT 58.941 57.895 0.00 0.00 0.00 4.83
481 548 0.321671 CTTCGCTCCCACTTTCTCCA 59.678 55.000 0.00 0.00 0.00 3.86
527 594 2.811317 CCTTGCTCGTCGCCTCAC 60.811 66.667 0.00 0.00 38.05 3.51
528 595 2.989253 TCCTTGCTCGTCGCCTCA 60.989 61.111 0.00 0.00 38.05 3.86
529 596 2.202676 CTCCTTGCTCGTCGCCTC 60.203 66.667 0.00 0.00 38.05 4.70
532 599 2.493907 AAGGTCTCCTTGCTCGTCGC 62.494 60.000 0.00 0.00 42.96 5.19
533 600 1.587054 AAGGTCTCCTTGCTCGTCG 59.413 57.895 0.00 0.00 42.96 5.12
541 608 1.410882 GCGCTCTATCAAGGTCTCCTT 59.589 52.381 0.00 0.00 45.88 3.36
542 609 1.036707 GCGCTCTATCAAGGTCTCCT 58.963 55.000 0.00 0.00 33.87 3.69
543 610 0.032815 GGCGCTCTATCAAGGTCTCC 59.967 60.000 7.64 0.00 0.00 3.71
544 611 0.318275 CGGCGCTCTATCAAGGTCTC 60.318 60.000 7.64 0.00 0.00 3.36
545 612 0.752009 TCGGCGCTCTATCAAGGTCT 60.752 55.000 7.64 0.00 0.00 3.85
546 613 0.595310 GTCGGCGCTCTATCAAGGTC 60.595 60.000 7.64 0.00 0.00 3.85
547 614 1.437986 GTCGGCGCTCTATCAAGGT 59.562 57.895 7.64 0.00 0.00 3.50
548 615 1.658717 CGTCGGCGCTCTATCAAGG 60.659 63.158 7.64 0.00 0.00 3.61
549 616 1.658717 CCGTCGGCGCTCTATCAAG 60.659 63.158 2.51 0.00 36.67 3.02
550 617 1.940883 AACCGTCGGCGCTCTATCAA 61.941 55.000 12.28 0.00 36.67 2.57
551 618 2.332362 GAACCGTCGGCGCTCTATCA 62.332 60.000 12.28 0.00 36.67 2.15
552 619 1.657794 GAACCGTCGGCGCTCTATC 60.658 63.158 12.28 0.00 36.67 2.08
553 620 2.412112 GAACCGTCGGCGCTCTAT 59.588 61.111 12.28 0.00 36.67 1.98
554 621 4.170062 CGAACCGTCGGCGCTCTA 62.170 66.667 12.28 0.00 43.81 2.43
591 658 0.382515 GATCAACCCTCTCGTCTCCG 59.617 60.000 0.00 0.00 0.00 4.63
592 659 0.382515 CGATCAACCCTCTCGTCTCC 59.617 60.000 0.00 0.00 0.00 3.71
593 660 1.096416 ACGATCAACCCTCTCGTCTC 58.904 55.000 0.00 0.00 41.42 3.36
594 661 2.414994 TACGATCAACCCTCTCGTCT 57.585 50.000 0.00 0.00 43.88 4.18
622 689 7.206687 TCAGGCGTCAATTTTACAGAATTTTT 58.793 30.769 0.00 0.00 0.00 1.94
623 690 6.744112 TCAGGCGTCAATTTTACAGAATTTT 58.256 32.000 0.00 0.00 0.00 1.82
624 691 6.325919 TCAGGCGTCAATTTTACAGAATTT 57.674 33.333 0.00 0.00 0.00 1.82
625 692 5.957842 TCAGGCGTCAATTTTACAGAATT 57.042 34.783 0.00 0.00 0.00 2.17
626 693 5.647658 TGATCAGGCGTCAATTTTACAGAAT 59.352 36.000 0.00 0.00 0.00 2.40
627 694 5.000591 TGATCAGGCGTCAATTTTACAGAA 58.999 37.500 0.00 0.00 0.00 3.02
628 695 4.574892 TGATCAGGCGTCAATTTTACAGA 58.425 39.130 0.00 0.00 0.00 3.41
629 696 4.944962 TGATCAGGCGTCAATTTTACAG 57.055 40.909 0.00 0.00 0.00 2.74
630 697 5.895636 ATTGATCAGGCGTCAATTTTACA 57.104 34.783 9.11 0.00 42.08 2.41
636 703 2.726821 ACCAATTGATCAGGCGTCAAT 58.273 42.857 7.12 9.11 45.53 2.57
637 704 2.198827 ACCAATTGATCAGGCGTCAA 57.801 45.000 7.12 5.69 39.65 3.18
638 705 2.198827 AACCAATTGATCAGGCGTCA 57.801 45.000 7.12 0.00 0.00 4.35
639 706 2.159379 GGAAACCAATTGATCAGGCGTC 60.159 50.000 7.12 0.00 0.00 5.19
640 707 1.818674 GGAAACCAATTGATCAGGCGT 59.181 47.619 7.12 0.00 0.00 5.68
641 708 1.202177 CGGAAACCAATTGATCAGGCG 60.202 52.381 7.12 0.00 0.00 5.52
642 709 1.469767 GCGGAAACCAATTGATCAGGC 60.470 52.381 7.12 6.27 0.00 4.85
643 710 2.094675 AGCGGAAACCAATTGATCAGG 58.905 47.619 7.12 0.00 0.00 3.86
644 711 2.489329 ACAGCGGAAACCAATTGATCAG 59.511 45.455 7.12 4.54 0.00 2.90
706 773 3.639561 GGTCAGTATTCTTCCTCCCTCTC 59.360 52.174 0.00 0.00 0.00 3.20
766 833 1.890876 TTTCTGTGTGCGGCTTACAT 58.109 45.000 0.00 0.00 0.00 2.29
787 854 7.778470 TTTTGTAATTGCCGTTTCATTTCTT 57.222 28.000 0.00 0.00 0.00 2.52
788 855 7.961325 ATTTTGTAATTGCCGTTTCATTTCT 57.039 28.000 0.00 0.00 0.00 2.52
798 865 5.403766 TGTGCACTTAATTTTGTAATTGCCG 59.596 36.000 19.41 0.00 38.31 5.69
799 866 6.777526 TGTGCACTTAATTTTGTAATTGCC 57.222 33.333 19.41 0.00 38.31 4.52
804 871 8.747666 GTCGAATTTGTGCACTTAATTTTGTAA 58.252 29.630 22.58 4.00 0.00 2.41
849 917 5.051106 CGTTCCTGTTGCAGTTTTAAATTGG 60.051 40.000 2.57 0.00 0.00 3.16
911 981 5.504392 TGTATATACGTACGACAAGCACTG 58.496 41.667 24.41 0.00 0.00 3.66
912 982 5.525012 TCTGTATATACGTACGACAAGCACT 59.475 40.000 24.41 0.00 0.00 4.40
913 983 5.741425 TCTGTATATACGTACGACAAGCAC 58.259 41.667 24.41 12.19 0.00 4.40
914 984 5.989551 TCTGTATATACGTACGACAAGCA 57.010 39.130 24.41 11.83 0.00 3.91
962 1036 2.808543 CTCAGTTCTGTGTGGTTAAGGC 59.191 50.000 0.00 0.00 0.00 4.35
998 1813 1.931906 CAGCATGTCGTAGTGCATCT 58.068 50.000 10.28 0.00 43.63 2.90
1158 1973 2.189521 GACATGTGGTAGGGCCCG 59.810 66.667 18.44 0.95 36.04 6.13
1214 2029 1.228894 AGGAAGTCCCTGAGCGTGA 60.229 57.895 0.00 0.00 45.61 4.35
1488 2303 1.115467 AGTAGGGCATCTGGTTCTCG 58.885 55.000 0.00 0.00 0.00 4.04
1578 2393 6.213397 TGAAGAAGTTGGATATGAGGTGAAGA 59.787 38.462 0.00 0.00 0.00 2.87
1595 2410 2.740055 CGCGCAGGCTGAAGAAGT 60.740 61.111 20.86 0.00 36.88 3.01
1674 2489 0.905337 GGTGGAGCAGGTGGTAGACT 60.905 60.000 0.00 0.00 0.00 3.24
1768 2604 4.299547 TGTGCGCCTGAACGAGCT 62.300 61.111 4.18 0.00 34.06 4.09
1853 2689 0.737715 CGAGGGCTTCTCCTTGAACG 60.738 60.000 0.00 0.00 40.07 3.95
1947 2783 2.000048 AGGTTGGCCAGGAGGATTTTA 59.000 47.619 5.11 0.00 36.89 1.52
1949 2785 0.040204 CAGGTTGGCCAGGAGGATTT 59.960 55.000 5.11 0.00 36.89 2.17
1950 2786 1.142688 ACAGGTTGGCCAGGAGGATT 61.143 55.000 5.11 0.00 36.89 3.01
2124 2960 1.630244 CGAGCTGGTTGAAGAAGGCG 61.630 60.000 0.00 0.00 0.00 5.52
2325 3161 2.424601 GCAAATCACATAGCCAGCAGAA 59.575 45.455 0.00 0.00 0.00 3.02
2337 3173 2.395360 GCGGTAGCGGCAAATCACA 61.395 57.895 17.08 0.00 0.00 3.58
2372 3208 3.276857 CTGTTGCATGAGTATCTTGGCT 58.723 45.455 0.00 0.00 40.31 4.75
2373 3209 3.012518 ACTGTTGCATGAGTATCTTGGC 58.987 45.455 0.00 0.00 40.31 4.52
2374 3210 4.511527 AGACTGTTGCATGAGTATCTTGG 58.488 43.478 0.00 0.00 40.31 3.61
2375 3211 5.291371 CAGAGACTGTTGCATGAGTATCTTG 59.709 44.000 16.27 10.48 38.43 3.02
2376 3212 5.046735 ACAGAGACTGTTGCATGAGTATCTT 60.047 40.000 16.27 8.55 42.59 2.40
2377 3213 4.465660 ACAGAGACTGTTGCATGAGTATCT 59.534 41.667 14.10 14.10 42.59 1.98
2378 3214 4.753233 ACAGAGACTGTTGCATGAGTATC 58.247 43.478 10.74 10.74 42.59 2.24
2379 3215 4.815533 ACAGAGACTGTTGCATGAGTAT 57.184 40.909 0.00 0.00 42.59 2.12
2380 3216 5.722021 TTACAGAGACTGTTGCATGAGTA 57.278 39.130 9.63 0.00 42.59 2.59
2381 3217 4.607293 TTACAGAGACTGTTGCATGAGT 57.393 40.909 9.63 0.00 42.59 3.41
2382 3218 7.413438 GGTTATTTACAGAGACTGTTGCATGAG 60.413 40.741 9.63 0.00 42.59 2.90
2383 3219 6.371548 GGTTATTTACAGAGACTGTTGCATGA 59.628 38.462 9.63 0.00 42.59 3.07
2384 3220 6.372659 AGGTTATTTACAGAGACTGTTGCATG 59.627 38.462 9.63 0.00 42.59 4.06
2385 3221 6.372659 CAGGTTATTTACAGAGACTGTTGCAT 59.627 38.462 9.63 3.41 42.59 3.96
2386 3222 5.700832 CAGGTTATTTACAGAGACTGTTGCA 59.299 40.000 9.63 0.00 42.59 4.08
2387 3223 5.701290 ACAGGTTATTTACAGAGACTGTTGC 59.299 40.000 9.63 0.00 42.59 4.17
2388 3224 6.929049 TCACAGGTTATTTACAGAGACTGTTG 59.071 38.462 9.63 2.78 42.59 3.33
2389 3225 6.929606 GTCACAGGTTATTTACAGAGACTGTT 59.070 38.462 9.63 0.00 42.59 3.16
2391 3227 6.366332 GTGTCACAGGTTATTTACAGAGACTG 59.634 42.308 0.00 0.00 37.52 3.51
2392 3228 6.041637 TGTGTCACAGGTTATTTACAGAGACT 59.958 38.462 0.18 0.00 30.76 3.24
2393 3229 6.145696 GTGTGTCACAGGTTATTTACAGAGAC 59.854 42.308 5.74 0.00 34.08 3.36
2394 3230 6.041637 AGTGTGTCACAGGTTATTTACAGAGA 59.958 38.462 5.74 0.00 36.74 3.10
2395 3231 6.223852 AGTGTGTCACAGGTTATTTACAGAG 58.776 40.000 5.74 0.00 36.74 3.35
2396 3232 6.169557 AGTGTGTCACAGGTTATTTACAGA 57.830 37.500 5.74 0.00 36.74 3.41
2397 3233 5.408604 GGAGTGTGTCACAGGTTATTTACAG 59.591 44.000 5.74 0.00 36.74 2.74
2398 3234 5.163290 TGGAGTGTGTCACAGGTTATTTACA 60.163 40.000 5.74 0.00 36.74 2.41
2399 3235 5.302360 TGGAGTGTGTCACAGGTTATTTAC 58.698 41.667 5.74 0.00 36.74 2.01
2400 3236 5.554437 TGGAGTGTGTCACAGGTTATTTA 57.446 39.130 5.74 0.00 36.74 1.40
2401 3237 4.431416 TGGAGTGTGTCACAGGTTATTT 57.569 40.909 5.74 0.00 36.74 1.40
2402 3238 4.640771 ATGGAGTGTGTCACAGGTTATT 57.359 40.909 5.74 0.00 36.74 1.40
2403 3239 4.640771 AATGGAGTGTGTCACAGGTTAT 57.359 40.909 5.74 0.00 36.74 1.89
2404 3240 5.163290 TGTTAATGGAGTGTGTCACAGGTTA 60.163 40.000 5.74 0.00 36.74 2.85
2405 3241 4.134563 GTTAATGGAGTGTGTCACAGGTT 58.865 43.478 5.74 0.00 36.74 3.50
2406 3242 3.135712 TGTTAATGGAGTGTGTCACAGGT 59.864 43.478 5.74 0.00 36.74 4.00
2407 3243 3.738982 TGTTAATGGAGTGTGTCACAGG 58.261 45.455 5.74 0.00 36.74 4.00
2408 3244 4.631131 TCTGTTAATGGAGTGTGTCACAG 58.369 43.478 5.74 0.00 36.74 3.66
2409 3245 4.681074 TCTGTTAATGGAGTGTGTCACA 57.319 40.909 0.18 0.18 36.74 3.58
2410 3246 4.084537 CGTTCTGTTAATGGAGTGTGTCAC 60.085 45.833 0.00 0.00 34.10 3.67
2411 3247 4.055360 CGTTCTGTTAATGGAGTGTGTCA 58.945 43.478 0.00 0.00 0.00 3.58
2412 3248 4.304110 TCGTTCTGTTAATGGAGTGTGTC 58.696 43.478 0.00 0.00 0.00 3.67
2413 3249 4.330944 TCGTTCTGTTAATGGAGTGTGT 57.669 40.909 0.00 0.00 0.00 3.72
2414 3250 6.961359 TTATCGTTCTGTTAATGGAGTGTG 57.039 37.500 0.00 0.00 0.00 3.82
2415 3251 8.041323 AGATTTATCGTTCTGTTAATGGAGTGT 58.959 33.333 0.00 0.00 0.00 3.55
2416 3252 8.425577 AGATTTATCGTTCTGTTAATGGAGTG 57.574 34.615 0.00 0.00 0.00 3.51
2419 3255 9.706691 GGATAGATTTATCGTTCTGTTAATGGA 57.293 33.333 0.00 0.00 37.20 3.41
2420 3256 9.489084 TGGATAGATTTATCGTTCTGTTAATGG 57.511 33.333 0.00 0.00 37.20 3.16
2429 3265 5.343593 CGACTGCTGGATAGATTTATCGTTC 59.656 44.000 0.00 0.00 37.20 3.95
2456 3292 0.732538 GGATTTGAAGCAAACCGCCG 60.733 55.000 0.00 0.00 44.04 6.46
2695 3533 4.144727 GGGGAGGGGAGCGAGAGA 62.145 72.222 0.00 0.00 0.00 3.10
2720 3558 4.235762 ACCAGCAGCAACCGTCGT 62.236 61.111 0.00 0.00 0.00 4.34
2787 3626 2.380571 AAAACAGGGGCGGGGAATGT 62.381 55.000 0.00 0.00 0.00 2.71
3340 4182 6.041979 ACAAAAGCCTAATCAATGGACAAACT 59.958 34.615 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.