Multiple sequence alignment - TraesCS6B01G362200

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 TraesCS6B01G362200 chr6B 100.000 3550 0 0 1 3550 633899132 633895583 0.000000e+00 6556.0
1 TraesCS6B01G362200 chr6A 92.790 2996 129 49 269 3231 563553038 563550097 0.000000e+00 4255.0
2 TraesCS6B01G362200 chr6A 79.940 1331 203 44 941 2226 563545022 563543711 0.000000e+00 920.0
3 TraesCS6B01G362200 chr6A 97.768 224 4 1 1 224 563553263 563553041 5.560000e-103 385.0
4 TraesCS6B01G362200 chr6A 91.209 273 22 1 3258 3530 563550124 563549854 1.560000e-98 370.0
5 TraesCS6B01G362200 chr6D 91.474 2510 154 36 1 2499 420732149 420729689 0.000000e+00 3395.0
6 TraesCS6B01G362200 chr6D 86.802 985 101 16 941 1905 406622821 406621846 0.000000e+00 1072.0
7 TraesCS6B01G362200 chr6D 92.154 752 45 4 2490 3233 420727901 420727156 0.000000e+00 1050.0
8 TraesCS6B01G362200 chr6D 90.052 573 42 9 1992 2560 406621560 406620999 0.000000e+00 728.0
9 TraesCS6B01G362200 chr6D 89.073 302 22 6 3258 3550 420727185 420726886 7.240000e-97 364.0
10 TraesCS6B01G362200 chr7B 81.315 1643 228 61 941 2556 462240388 462238798 0.000000e+00 1260.0
11 TraesCS6B01G362200 chr7B 85.000 80 8 4 1019 1096 623958435 623958358 1.060000e-10 78.7
12 TraesCS6B01G362200 chr1B 85.253 217 27 4 243 458 673460400 673460188 5.970000e-53 219.0
13 TraesCS6B01G362200 chr1B 84.211 209 27 4 246 450 673551473 673551267 7.770000e-47 198.0
14 TraesCS6B01G362200 chr1B 100.000 32 0 0 2654 2685 465986204 465986173 3.830000e-05 60.2
15 TraesCS6B01G362200 chr7A 79.856 139 17 10 947 1080 657050151 657050019 1.360000e-14 91.6
16 TraesCS6B01G362200 chr7A 78.519 135 18 10 398 528 550314627 550314754 1.060000e-10 78.7
17 TraesCS6B01G362200 chr7A 97.059 34 1 0 2652 2685 704895276 704895243 1.380000e-04 58.4
18 TraesCS6B01G362200 chr3A 100.000 34 0 0 759 792 699759122 699759155 2.960000e-06 63.9
19 TraesCS6B01G362200 chr3A 100.000 28 0 0 2652 2679 6649568 6649595 6.000000e-03 52.8
20 TraesCS6B01G362200 chr2B 100.000 32 0 0 2654 2685 4721033 4721064 3.830000e-05 60.2
21 TraesCS6B01G362200 chr2B 94.286 35 2 0 2654 2688 212024965 212024999 2.000000e-03 54.7
22 TraesCS6B01G362200 chr5D 94.737 38 1 1 760 797 307092764 307092800 1.380000e-04 58.4
23 TraesCS6B01G362200 chr5D 97.059 34 1 0 2659 2692 459221556 459221523 1.380000e-04 58.4
24 TraesCS6B01G362200 chr4A 96.970 33 0 1 760 792 628004533 628004502 2.000000e-03 54.7
25 TraesCS6B01G362200 chr3D 100.000 29 0 0 2657 2685 100553431 100553459 2.000000e-03 54.7


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 TraesCS6B01G362200 chr6B 633895583 633899132 3549 True 6556 6556 100.000000 1 3550 1 chr6B.!!$R1 3549
1 TraesCS6B01G362200 chr6A 563549854 563553263 3409 True 1670 4255 93.922333 1 3530 3 chr6A.!!$R2 3529
2 TraesCS6B01G362200 chr6A 563543711 563545022 1311 True 920 920 79.940000 941 2226 1 chr6A.!!$R1 1285
3 TraesCS6B01G362200 chr6D 420726886 420732149 5263 True 1603 3395 90.900333 1 3550 3 chr6D.!!$R2 3549
4 TraesCS6B01G362200 chr6D 406620999 406622821 1822 True 900 1072 88.427000 941 2560 2 chr6D.!!$R1 1619
5 TraesCS6B01G362200 chr7B 462238798 462240388 1590 True 1260 1260 81.315000 941 2556 1 chr7B.!!$R1 1615

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
396 398 0.106918 TTTGACCTTGTTGACCGGCT 60.107 50.0 0.0 0.0 0.00 5.52 F
400 402 0.106918 ACCTTGTTGACCGGCTTTGA 60.107 50.0 0.0 0.0 0.00 2.69 F
1063 1091 0.108585 ACCACCACTTGTGCTCGAAT 59.891 50.0 0.0 0.0 44.01 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2146 2432 1.547372 TCGGCAGGTAAGGAGTTACAC 59.453 52.381 0.0 0.0 40.46 2.90 R
2247 2533 3.870633 ACAAGAACCCGAGACAGATAC 57.129 47.619 0.0 0.0 0.00 2.24 R
2559 4648 1.139058 GATGAGGGCAACGGTAGACAT 59.861 52.381 0.0 0.0 37.60 3.06 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
57 58 1.405105 GCTGTTTTGCTGTTGGACTGA 59.595 47.619 0.00 0.00 0.00 3.41
85 86 7.549134 ACTTCTGTGCATCTATTTATTTCGTGA 59.451 33.333 0.00 0.00 0.00 4.35
135 136 3.250040 CCAAACTCTACAAACTTCCGTGG 59.750 47.826 0.00 0.00 0.00 4.94
235 236 6.350906 TGATGTGCAGAGAATGATATGTTGA 58.649 36.000 0.00 0.00 0.00 3.18
267 268 5.324409 AGAAGTGCATATTTCAACCTCCAA 58.676 37.500 10.07 0.00 0.00 3.53
305 306 3.955650 TCTACAGCCCTCAACTGTAAC 57.044 47.619 5.27 0.00 46.88 2.50
329 330 3.431766 CCGTCTAAGAATCAACCCCGAAT 60.432 47.826 0.00 0.00 0.00 3.34
330 331 3.802685 CGTCTAAGAATCAACCCCGAATC 59.197 47.826 0.00 0.00 0.00 2.52
334 335 3.739401 AGAATCAACCCCGAATCCTTT 57.261 42.857 0.00 0.00 0.00 3.11
335 336 4.855298 AGAATCAACCCCGAATCCTTTA 57.145 40.909 0.00 0.00 0.00 1.85
385 387 1.687996 CCCACACCTGGTTTTGACCTT 60.688 52.381 0.00 0.00 35.46 3.50
386 388 1.408702 CCACACCTGGTTTTGACCTTG 59.591 52.381 0.00 0.00 32.03 3.61
387 389 2.099405 CACACCTGGTTTTGACCTTGT 58.901 47.619 0.00 0.00 0.00 3.16
388 390 2.495669 CACACCTGGTTTTGACCTTGTT 59.504 45.455 0.00 0.00 0.00 2.83
389 391 2.495669 ACACCTGGTTTTGACCTTGTTG 59.504 45.455 0.00 0.00 0.00 3.33
390 392 2.757868 CACCTGGTTTTGACCTTGTTGA 59.242 45.455 0.00 0.00 0.00 3.18
391 393 2.758423 ACCTGGTTTTGACCTTGTTGAC 59.242 45.455 0.00 0.00 0.00 3.18
392 394 2.100749 CCTGGTTTTGACCTTGTTGACC 59.899 50.000 0.00 0.00 0.00 4.02
393 395 1.746220 TGGTTTTGACCTTGTTGACCG 59.254 47.619 0.00 0.00 0.00 4.79
394 396 1.066454 GGTTTTGACCTTGTTGACCGG 59.934 52.381 0.00 0.00 0.00 5.28
395 397 0.741915 TTTTGACCTTGTTGACCGGC 59.258 50.000 0.00 0.00 0.00 6.13
396 398 0.106918 TTTGACCTTGTTGACCGGCT 60.107 50.000 0.00 0.00 0.00 5.52
397 399 0.106918 TTGACCTTGTTGACCGGCTT 60.107 50.000 0.00 0.00 0.00 4.35
398 400 0.106918 TGACCTTGTTGACCGGCTTT 60.107 50.000 0.00 0.00 0.00 3.51
399 401 0.310854 GACCTTGTTGACCGGCTTTG 59.689 55.000 0.00 0.00 0.00 2.77
400 402 0.106918 ACCTTGTTGACCGGCTTTGA 60.107 50.000 0.00 0.00 0.00 2.69
401 403 0.310854 CCTTGTTGACCGGCTTTGAC 59.689 55.000 0.00 0.00 0.00 3.18
402 404 0.310854 CTTGTTGACCGGCTTTGACC 59.689 55.000 0.00 0.00 0.00 4.02
572 577 9.425577 GCTTAGTATTGTTTTCTTGACTCTACT 57.574 33.333 0.00 0.00 0.00 2.57
637 643 4.634184 AAATTGAGCAGAGCATCATGAC 57.366 40.909 0.00 0.00 37.82 3.06
839 863 0.620556 GAGGGGAGGTTGAATGCTGA 59.379 55.000 0.00 0.00 0.00 4.26
850 874 3.907894 TGAATGCTGACCGGTTTTAAC 57.092 42.857 9.42 0.00 0.00 2.01
898 922 8.621286 GGTATTATTGTTGAGGGTTGTAGATTG 58.379 37.037 0.00 0.00 0.00 2.67
1031 1059 9.289303 AGATGTGAATTATTTAAAATCACGTGC 57.711 29.630 11.67 12.83 38.16 5.34
1063 1091 0.108585 ACCACCACTTGTGCTCGAAT 59.891 50.000 0.00 0.00 44.01 3.34
1250 1278 4.445453 TGCAATCTTGATCATCGTAGCTT 58.555 39.130 0.00 0.00 0.00 3.74
1281 1309 2.820197 GGTCTGGGCTAAACTTCCAAAG 59.180 50.000 0.00 0.00 0.00 2.77
1602 1662 5.059161 TGTAGTGAGATGATGGCTAATTGC 58.941 41.667 0.00 0.00 41.94 3.56
1659 1723 1.226030 CCCACCGAAACAGGTCGTTC 61.226 60.000 0.00 0.00 43.89 3.95
2064 2346 7.852945 GCATTACAACTTCTCCATTCTATTTCG 59.147 37.037 0.00 0.00 0.00 3.46
2146 2432 5.392380 GCATGAACTTCTATGGTGAAACTGG 60.392 44.000 0.00 0.00 36.74 4.00
2237 2523 5.454966 AGGTACATCTTTCCCTGTTTTGTT 58.545 37.500 0.00 0.00 0.00 2.83
2247 2533 5.261209 TCCCTGTTTTGTTGTCTCATTTG 57.739 39.130 0.00 0.00 0.00 2.32
2291 2579 8.914011 TGTTGTCTAGATATATATCCATTCGGG 58.086 37.037 17.44 3.09 33.17 5.14
2298 2586 2.276732 ATATCCATTCGGGGTGCTTG 57.723 50.000 0.00 0.00 37.22 4.01
2459 2751 7.225145 TGAATTTGCACTGAAAAGAATTTGGAG 59.775 33.333 0.00 0.00 39.02 3.86
2559 4648 4.583489 GGCAACTCCAGTAGTGCTATACTA 59.417 45.833 3.93 0.00 38.88 1.82
2585 4674 1.361668 CCGTTGCCCTCATCTCGTTG 61.362 60.000 0.00 0.00 0.00 4.10
2680 4777 6.014242 AGCGACAATTAATATGGATCAGAGGA 60.014 38.462 0.00 0.00 0.00 3.71
2937 5035 7.234661 ACTTTCTAGAAGACAGAGGGTAAAG 57.765 40.000 5.12 0.00 0.00 1.85
3034 5132 1.340991 ACTCCAACGCATAAGGGCATT 60.341 47.619 0.00 0.00 0.00 3.56
3035 5133 1.066002 CTCCAACGCATAAGGGCATTG 59.934 52.381 0.00 0.00 0.00 2.82
3036 5134 0.528249 CCAACGCATAAGGGCATTGC 60.528 55.000 0.00 0.00 0.00 3.56
3061 5159 3.346631 CTGGCCAACAAGGATGCGC 62.347 63.158 7.01 0.00 41.22 6.09
3071 5169 2.279120 GGATGCGCCTCGACTGAG 60.279 66.667 4.18 0.00 42.18 3.35
3094 5192 3.817647 GTCAGTCACCTTCAAAGAGCAAT 59.182 43.478 0.00 0.00 0.00 3.56
3103 5201 5.763204 ACCTTCAAAGAGCAATAACTCGAAA 59.237 36.000 0.00 0.00 41.77 3.46
3156 5254 4.279169 TCTTGATTGCTGAAAAGAGTTGGG 59.721 41.667 0.00 0.00 0.00 4.12
3157 5255 2.892852 TGATTGCTGAAAAGAGTTGGGG 59.107 45.455 0.00 0.00 0.00 4.96
3187 5285 2.288886 GCAAACTAGGACGACCTCAAGT 60.289 50.000 10.44 6.62 46.43 3.16
3218 5316 1.549170 ACTGGACTTACCCGTGACATC 59.451 52.381 0.00 0.00 34.86 3.06
3224 5322 2.756760 ACTTACCCGTGACATCGTACAT 59.243 45.455 0.00 0.00 0.00 2.29
3225 5323 3.947196 ACTTACCCGTGACATCGTACATA 59.053 43.478 0.00 0.00 0.00 2.29
3226 5324 4.036027 ACTTACCCGTGACATCGTACATAG 59.964 45.833 0.00 0.00 0.00 2.23
3227 5325 2.372264 ACCCGTGACATCGTACATAGT 58.628 47.619 0.00 0.00 0.00 2.12
3228 5326 2.098607 ACCCGTGACATCGTACATAGTG 59.901 50.000 0.00 0.00 0.00 2.74
3229 5327 2.098607 CCCGTGACATCGTACATAGTGT 59.901 50.000 0.00 0.00 0.00 3.55
3230 5328 3.360533 CCGTGACATCGTACATAGTGTC 58.639 50.000 8.94 8.94 40.93 3.67
3231 5329 3.360533 CGTGACATCGTACATAGTGTCC 58.639 50.000 11.83 5.54 40.07 4.02
3232 5330 3.064958 CGTGACATCGTACATAGTGTCCT 59.935 47.826 11.83 0.00 40.07 3.85
3233 5331 4.271776 CGTGACATCGTACATAGTGTCCTA 59.728 45.833 11.83 0.00 40.07 2.94
3234 5332 5.508872 GTGACATCGTACATAGTGTCCTAC 58.491 45.833 11.83 4.28 40.07 3.18
3235 5333 5.296283 GTGACATCGTACATAGTGTCCTACT 59.704 44.000 11.83 0.00 40.07 2.57
3236 5334 5.296035 TGACATCGTACATAGTGTCCTACTG 59.704 44.000 11.83 0.00 40.65 2.74
3237 5335 5.191426 ACATCGTACATAGTGTCCTACTGT 58.809 41.667 0.00 0.00 40.65 3.55
3238 5336 5.296283 ACATCGTACATAGTGTCCTACTGTC 59.704 44.000 0.00 0.00 40.65 3.51
3239 5337 4.194640 TCGTACATAGTGTCCTACTGTCC 58.805 47.826 0.00 0.00 40.65 4.02
3240 5338 4.080695 TCGTACATAGTGTCCTACTGTCCT 60.081 45.833 0.00 0.00 40.65 3.85
3241 5339 4.639310 CGTACATAGTGTCCTACTGTCCTT 59.361 45.833 0.00 0.00 40.65 3.36
3242 5340 5.448768 CGTACATAGTGTCCTACTGTCCTTG 60.449 48.000 0.00 0.00 40.65 3.61
3243 5341 4.673968 ACATAGTGTCCTACTGTCCTTGA 58.326 43.478 0.00 0.00 40.65 3.02
3244 5342 4.463186 ACATAGTGTCCTACTGTCCTTGAC 59.537 45.833 0.00 0.00 40.65 3.18
3245 5343 1.887198 AGTGTCCTACTGTCCTTGACG 59.113 52.381 0.00 0.00 38.49 4.35
3246 5344 1.884579 GTGTCCTACTGTCCTTGACGA 59.115 52.381 0.00 0.00 34.95 4.20
3247 5345 2.295349 GTGTCCTACTGTCCTTGACGAA 59.705 50.000 0.00 0.00 34.95 3.85
3248 5346 2.295349 TGTCCTACTGTCCTTGACGAAC 59.705 50.000 0.00 0.00 34.95 3.95
3249 5347 2.295349 GTCCTACTGTCCTTGACGAACA 59.705 50.000 0.00 0.00 34.95 3.18
3250 5348 2.960384 TCCTACTGTCCTTGACGAACAA 59.040 45.455 0.00 0.00 34.95 2.83
3251 5349 3.576982 TCCTACTGTCCTTGACGAACAAT 59.423 43.478 0.00 0.00 37.88 2.71
3252 5350 3.927142 CCTACTGTCCTTGACGAACAATC 59.073 47.826 0.00 0.00 37.88 2.67
3253 5351 2.767505 ACTGTCCTTGACGAACAATCC 58.232 47.619 0.00 0.00 37.88 3.01
3254 5352 2.104111 ACTGTCCTTGACGAACAATCCA 59.896 45.455 0.00 0.00 37.88 3.41
3255 5353 3.138304 CTGTCCTTGACGAACAATCCAA 58.862 45.455 0.00 0.00 37.88 3.53
3256 5354 3.546724 TGTCCTTGACGAACAATCCAAA 58.453 40.909 0.00 0.00 37.88 3.28
3257 5355 3.948473 TGTCCTTGACGAACAATCCAAAA 59.052 39.130 0.00 0.00 37.88 2.44
3258 5356 4.201970 TGTCCTTGACGAACAATCCAAAAC 60.202 41.667 0.00 0.00 37.88 2.43
3259 5357 4.036380 GTCCTTGACGAACAATCCAAAACT 59.964 41.667 0.00 0.00 37.88 2.66
3260 5358 4.642885 TCCTTGACGAACAATCCAAAACTT 59.357 37.500 0.00 0.00 37.88 2.66
3261 5359 5.823570 TCCTTGACGAACAATCCAAAACTTA 59.176 36.000 0.00 0.00 37.88 2.24
3262 5360 5.912955 CCTTGACGAACAATCCAAAACTTAC 59.087 40.000 0.00 0.00 37.88 2.34
3263 5361 5.427036 TGACGAACAATCCAAAACTTACC 57.573 39.130 0.00 0.00 0.00 2.85
3264 5362 4.276431 TGACGAACAATCCAAAACTTACCC 59.724 41.667 0.00 0.00 0.00 3.69
3265 5363 3.251487 ACGAACAATCCAAAACTTACCCG 59.749 43.478 0.00 0.00 0.00 5.28
3266 5364 3.251487 CGAACAATCCAAAACTTACCCGT 59.749 43.478 0.00 0.00 0.00 5.28
3267 5365 4.542735 GAACAATCCAAAACTTACCCGTG 58.457 43.478 0.00 0.00 0.00 4.94
3268 5366 3.822940 ACAATCCAAAACTTACCCGTGA 58.177 40.909 0.00 0.00 0.00 4.35
3269 5367 3.566742 ACAATCCAAAACTTACCCGTGAC 59.433 43.478 0.00 0.00 0.00 3.67
3270 5368 3.495434 ATCCAAAACTTACCCGTGACA 57.505 42.857 0.00 0.00 0.00 3.58
3271 5369 3.495434 TCCAAAACTTACCCGTGACAT 57.505 42.857 0.00 0.00 0.00 3.06
3272 5370 3.404899 TCCAAAACTTACCCGTGACATC 58.595 45.455 0.00 0.00 0.00 3.06
3273 5371 3.142951 CCAAAACTTACCCGTGACATCA 58.857 45.455 0.00 0.00 0.00 3.07
3274 5372 3.756434 CCAAAACTTACCCGTGACATCAT 59.244 43.478 0.00 0.00 0.00 2.45
3275 5373 4.938832 CCAAAACTTACCCGTGACATCATA 59.061 41.667 0.00 0.00 0.00 2.15
3276 5374 5.163794 CCAAAACTTACCCGTGACATCATAC 60.164 44.000 0.00 0.00 0.00 2.39
3277 5375 4.811969 AACTTACCCGTGACATCATACA 57.188 40.909 0.00 0.00 0.00 2.29
3341 5439 2.434702 AGGAACACGAACAAAGACCTCT 59.565 45.455 0.00 0.00 0.00 3.69
3349 5447 3.669536 GAACAAAGACCTCTCTCCCAAG 58.330 50.000 0.00 0.00 0.00 3.61
3373 5471 1.336517 GGAACGATGTCAAGGACGTCA 60.337 52.381 18.91 0.00 45.67 4.35
3405 5503 6.212235 TGATGCGAATCAGAATCTAGACTTC 58.788 40.000 0.51 0.78 0.00 3.01
3438 5536 6.495181 AGATAACCAAACAAGTGAGAGAGAGA 59.505 38.462 0.00 0.00 0.00 3.10
3439 5537 4.599047 ACCAAACAAGTGAGAGAGAGAG 57.401 45.455 0.00 0.00 0.00 3.20
3440 5538 3.244044 ACCAAACAAGTGAGAGAGAGAGC 60.244 47.826 0.00 0.00 0.00 4.09
3441 5539 3.244009 CCAAACAAGTGAGAGAGAGAGCA 60.244 47.826 0.00 0.00 0.00 4.26
3442 5540 4.375272 CAAACAAGTGAGAGAGAGAGCAA 58.625 43.478 0.00 0.00 0.00 3.91
3443 5541 4.679373 AACAAGTGAGAGAGAGAGCAAA 57.321 40.909 0.00 0.00 0.00 3.68
3484 5582 1.817740 CGCCTCCAAGAAAGGGAAACA 60.818 52.381 0.00 0.00 34.26 2.83
3485 5583 2.529632 GCCTCCAAGAAAGGGAAACAT 58.470 47.619 0.00 0.00 34.26 2.71
3488 5586 4.347607 CCTCCAAGAAAGGGAAACATCAT 58.652 43.478 0.00 0.00 33.11 2.45
3503 5601 3.819368 ACATCATCCACAGTTGTTGTCA 58.181 40.909 0.00 0.00 38.16 3.58
3514 5612 3.084039 AGTTGTTGTCATCGATGGCATT 58.916 40.909 31.49 13.27 42.67 3.56
3522 5620 2.423185 TCATCGATGGCATTGACCAAAC 59.577 45.455 24.61 0.00 44.65 2.93
3524 5622 1.811965 TCGATGGCATTGACCAAACAG 59.188 47.619 13.49 0.00 44.65 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 136 4.357918 ACACCATCAGGCAAGGTATATC 57.642 45.455 0.00 0.00 39.06 1.63
235 236 9.846248 GTTGAAATATGCACTTCTCTTTAACAT 57.154 29.630 0.00 0.00 0.00 2.71
267 268 5.767670 TGTAGATTAGACTAGGGCAAGAGT 58.232 41.667 0.00 0.00 0.00 3.24
305 306 2.629051 GGGGTTGATTCTTAGACGGTG 58.371 52.381 0.00 0.00 0.00 4.94
329 330 2.946785 TCTTGGCCGGTTTTTAAAGGA 58.053 42.857 1.90 0.00 0.00 3.36
330 331 3.953712 ATCTTGGCCGGTTTTTAAAGG 57.046 42.857 1.90 0.00 0.00 3.11
334 335 3.006003 GGTTGAATCTTGGCCGGTTTTTA 59.994 43.478 1.90 0.00 0.00 1.52
335 336 2.224185 GGTTGAATCTTGGCCGGTTTTT 60.224 45.455 1.90 0.00 0.00 1.94
385 387 0.817634 CAGGTCAAAGCCGGTCAACA 60.818 55.000 1.90 0.00 0.00 3.33
386 388 0.818040 ACAGGTCAAAGCCGGTCAAC 60.818 55.000 1.90 0.00 31.39 3.18
387 389 0.106918 AACAGGTCAAAGCCGGTCAA 60.107 50.000 1.90 0.00 35.95 3.18
388 390 0.817634 CAACAGGTCAAAGCCGGTCA 60.818 55.000 1.90 0.00 35.95 4.02
389 391 0.534203 TCAACAGGTCAAAGCCGGTC 60.534 55.000 1.90 0.00 35.95 4.79
390 392 0.818040 GTCAACAGGTCAAAGCCGGT 60.818 55.000 1.90 0.00 38.55 5.28
391 393 1.515521 GGTCAACAGGTCAAAGCCGG 61.516 60.000 0.00 0.00 0.00 6.13
392 394 0.817634 TGGTCAACAGGTCAAAGCCG 60.818 55.000 0.00 0.00 0.00 5.52
393 395 1.541588 GATGGTCAACAGGTCAAAGCC 59.458 52.381 0.00 0.00 0.00 4.35
394 396 1.541588 GGATGGTCAACAGGTCAAAGC 59.458 52.381 0.00 0.00 0.00 3.51
395 397 2.816087 CTGGATGGTCAACAGGTCAAAG 59.184 50.000 0.00 0.00 0.00 2.77
396 398 2.174639 ACTGGATGGTCAACAGGTCAAA 59.825 45.455 9.63 0.00 36.57 2.69
397 399 1.774254 ACTGGATGGTCAACAGGTCAA 59.226 47.619 9.63 0.00 36.57 3.18
398 400 1.347707 GACTGGATGGTCAACAGGTCA 59.652 52.381 9.63 0.00 36.57 4.02
399 401 1.347707 TGACTGGATGGTCAACAGGTC 59.652 52.381 9.63 0.00 42.35 3.85
400 402 1.349026 CTGACTGGATGGTCAACAGGT 59.651 52.381 9.63 0.00 44.24 4.00
401 403 1.947678 GCTGACTGGATGGTCAACAGG 60.948 57.143 0.00 0.00 44.24 4.00
402 404 1.271001 TGCTGACTGGATGGTCAACAG 60.271 52.381 0.00 0.00 44.24 3.16
529 534 5.385198 ACTAAGCATTCTGGGAAAGTTGAA 58.615 37.500 0.00 0.00 0.00 2.69
756 777 2.174210 CCCATTGACCATCCAGTCAGAT 59.826 50.000 0.00 0.00 46.90 2.90
839 863 0.250424 CCCCGACTGTTAAAACCGGT 60.250 55.000 0.00 0.00 38.61 5.28
850 874 3.522553 GTCTAAGAATCAACCCCGACTG 58.477 50.000 0.00 0.00 0.00 3.51
898 922 2.117051 CCCCAACTCTTACCCTAGTCC 58.883 57.143 0.00 0.00 0.00 3.85
1031 1059 0.839277 TGGTGGTGGCTGAGGATATG 59.161 55.000 0.00 0.00 0.00 1.78
1063 1091 7.254761 CGCCAATATAGAAAGCAATGACTTACA 60.255 37.037 0.00 0.00 0.00 2.41
1225 1253 5.530171 AGCTACGATGATCAAGATTGCAATT 59.470 36.000 14.33 0.00 0.00 2.32
1250 1278 2.935481 CCCAGACCTGCTCCCCAA 60.935 66.667 0.00 0.00 0.00 4.12
1281 1309 5.575218 CCGGCCAATATTTGTAACAACTTTC 59.425 40.000 2.24 0.00 0.00 2.62
1602 1662 5.860182 TCTGAAACGGTAGATAAAGTCAACG 59.140 40.000 0.00 0.00 0.00 4.10
1659 1723 2.615493 GGTACAGTTCCAGTGTCCCATG 60.615 54.545 0.00 0.00 33.15 3.66
2021 2296 9.236006 GTTGTAATGCCTTGGATAGATTATGAT 57.764 33.333 0.00 0.00 0.00 2.45
2022 2297 8.439971 AGTTGTAATGCCTTGGATAGATTATGA 58.560 33.333 0.00 0.00 0.00 2.15
2023 2298 8.627208 AGTTGTAATGCCTTGGATAGATTATG 57.373 34.615 0.00 0.00 0.00 1.90
2064 2346 3.118371 CCTCCAATCCCAACCTAGTACAC 60.118 52.174 0.00 0.00 0.00 2.90
2146 2432 1.547372 TCGGCAGGTAAGGAGTTACAC 59.453 52.381 0.00 0.00 40.46 2.90
2237 2523 4.142160 CCCGAGACAGATACAAATGAGACA 60.142 45.833 0.00 0.00 0.00 3.41
2247 2533 3.870633 ACAAGAACCCGAGACAGATAC 57.129 47.619 0.00 0.00 0.00 2.24
2291 2579 8.707938 AGAAAGAAAATATTAATGCAAGCACC 57.292 30.769 0.00 0.00 0.00 5.01
2559 4648 1.139058 GATGAGGGCAACGGTAGACAT 59.861 52.381 0.00 0.00 37.60 3.06
2937 5035 3.750652 GGAGCTTGCCTATATTCTTGAGC 59.249 47.826 0.00 0.00 0.00 4.26
3036 5134 2.521465 TTGTTGGCCAGTGCAGGG 60.521 61.111 5.11 0.00 40.13 4.45
3040 5138 1.588082 CATCCTTGTTGGCCAGTGC 59.412 57.895 5.11 0.78 35.26 4.40
3071 5169 2.147150 GCTCTTTGAAGGTGACTGACC 58.853 52.381 0.00 0.00 46.58 4.02
3083 5181 6.612247 TTGTTTCGAGTTATTGCTCTTTGA 57.388 33.333 0.00 0.00 33.55 2.69
3094 5192 5.048991 GGCAAGGAGATTTTGTTTCGAGTTA 60.049 40.000 0.00 0.00 0.00 2.24
3103 5201 3.323751 GCATTGGCAAGGAGATTTTGT 57.676 42.857 17.10 0.00 40.72 2.83
3156 5254 1.304134 CTAGTTTGCCACCCACCCC 60.304 63.158 0.00 0.00 0.00 4.95
3157 5255 1.304134 CCTAGTTTGCCACCCACCC 60.304 63.158 0.00 0.00 0.00 4.61
3187 5285 4.218417 GGGTAAGTCCAGTACAACGACTTA 59.782 45.833 18.21 18.21 43.31 2.24
3195 5293 1.888512 GTCACGGGTAAGTCCAGTACA 59.111 52.381 0.00 0.00 42.43 2.90
3218 5316 4.197750 AGGACAGTAGGACACTATGTACG 58.802 47.826 0.00 0.00 36.00 3.67
3224 5322 3.079578 CGTCAAGGACAGTAGGACACTA 58.920 50.000 0.00 0.00 34.98 2.74
3225 5323 1.887198 CGTCAAGGACAGTAGGACACT 59.113 52.381 0.00 0.00 38.32 3.55
3226 5324 1.884579 TCGTCAAGGACAGTAGGACAC 59.115 52.381 0.00 0.00 32.09 3.67
3227 5325 2.281539 TCGTCAAGGACAGTAGGACA 57.718 50.000 0.00 0.00 32.09 4.02
3228 5326 2.295349 TGTTCGTCAAGGACAGTAGGAC 59.705 50.000 0.00 0.00 32.09 3.85
3229 5327 2.589720 TGTTCGTCAAGGACAGTAGGA 58.410 47.619 0.00 0.00 32.09 2.94
3230 5328 3.380479 TTGTTCGTCAAGGACAGTAGG 57.620 47.619 0.00 0.00 32.09 3.18
3231 5329 3.927142 GGATTGTTCGTCAAGGACAGTAG 59.073 47.826 0.00 0.00 39.55 2.57
3232 5330 3.322541 TGGATTGTTCGTCAAGGACAGTA 59.677 43.478 0.00 0.00 39.55 2.74
3233 5331 2.104111 TGGATTGTTCGTCAAGGACAGT 59.896 45.455 0.00 0.00 39.55 3.55
3234 5332 2.766313 TGGATTGTTCGTCAAGGACAG 58.234 47.619 0.00 0.00 39.55 3.51
3235 5333 2.920724 TGGATTGTTCGTCAAGGACA 57.079 45.000 0.00 0.00 39.55 4.02
3236 5334 4.036380 AGTTTTGGATTGTTCGTCAAGGAC 59.964 41.667 2.92 0.00 39.55 3.85
3237 5335 4.204012 AGTTTTGGATTGTTCGTCAAGGA 58.796 39.130 2.92 0.00 39.55 3.36
3238 5336 4.568152 AGTTTTGGATTGTTCGTCAAGG 57.432 40.909 2.92 0.00 39.55 3.61
3239 5337 5.912955 GGTAAGTTTTGGATTGTTCGTCAAG 59.087 40.000 2.92 0.00 39.55 3.02
3240 5338 5.221087 GGGTAAGTTTTGGATTGTTCGTCAA 60.221 40.000 0.00 0.00 40.53 3.18
3241 5339 4.276431 GGGTAAGTTTTGGATTGTTCGTCA 59.724 41.667 0.00 0.00 0.00 4.35
3242 5340 4.612033 CGGGTAAGTTTTGGATTGTTCGTC 60.612 45.833 0.00 0.00 0.00 4.20
3243 5341 3.251487 CGGGTAAGTTTTGGATTGTTCGT 59.749 43.478 0.00 0.00 0.00 3.85
3244 5342 3.251487 ACGGGTAAGTTTTGGATTGTTCG 59.749 43.478 0.00 0.00 0.00 3.95
3245 5343 4.276431 TCACGGGTAAGTTTTGGATTGTTC 59.724 41.667 0.00 0.00 0.00 3.18
3246 5344 4.037089 GTCACGGGTAAGTTTTGGATTGTT 59.963 41.667 0.00 0.00 0.00 2.83
3247 5345 3.566742 GTCACGGGTAAGTTTTGGATTGT 59.433 43.478 0.00 0.00 0.00 2.71
3248 5346 3.566322 TGTCACGGGTAAGTTTTGGATTG 59.434 43.478 0.00 0.00 0.00 2.67
3249 5347 3.822940 TGTCACGGGTAAGTTTTGGATT 58.177 40.909 0.00 0.00 0.00 3.01
3250 5348 3.495434 TGTCACGGGTAAGTTTTGGAT 57.505 42.857 0.00 0.00 0.00 3.41
3251 5349 3.181453 TGATGTCACGGGTAAGTTTTGGA 60.181 43.478 0.00 0.00 0.00 3.53
3252 5350 3.142951 TGATGTCACGGGTAAGTTTTGG 58.857 45.455 0.00 0.00 0.00 3.28
3253 5351 5.410132 TGTATGATGTCACGGGTAAGTTTTG 59.590 40.000 0.00 0.00 0.00 2.44
3254 5352 5.553123 TGTATGATGTCACGGGTAAGTTTT 58.447 37.500 0.00 0.00 0.00 2.43
3255 5353 5.155278 TGTATGATGTCACGGGTAAGTTT 57.845 39.130 0.00 0.00 0.00 2.66
3256 5354 4.811969 TGTATGATGTCACGGGTAAGTT 57.188 40.909 0.00 0.00 0.00 2.66
3257 5355 5.597182 ACTATGTATGATGTCACGGGTAAGT 59.403 40.000 0.00 0.00 0.00 2.24
3258 5356 5.920840 CACTATGTATGATGTCACGGGTAAG 59.079 44.000 0.00 0.00 0.00 2.34
3259 5357 5.361571 ACACTATGTATGATGTCACGGGTAA 59.638 40.000 0.00 0.00 0.00 2.85
3260 5358 4.891168 ACACTATGTATGATGTCACGGGTA 59.109 41.667 0.00 0.00 0.00 3.69
3261 5359 3.704566 ACACTATGTATGATGTCACGGGT 59.295 43.478 0.00 0.00 0.00 5.28
3262 5360 4.299155 GACACTATGTATGATGTCACGGG 58.701 47.826 0.00 0.00 40.95 5.28
3263 5361 4.038042 AGGACACTATGTATGATGTCACGG 59.962 45.833 5.66 0.00 42.66 4.94
3264 5362 5.188327 AGGACACTATGTATGATGTCACG 57.812 43.478 5.66 0.00 42.66 4.35
3265 5363 6.477033 GTCAAGGACACTATGTATGATGTCAC 59.523 42.308 5.66 0.00 42.66 3.67
3266 5364 6.573434 GTCAAGGACACTATGTATGATGTCA 58.427 40.000 5.66 0.00 42.66 3.58
3267 5365 5.687730 CGTCAAGGACACTATGTATGATGTC 59.312 44.000 0.00 0.00 40.62 3.06
3268 5366 5.359860 TCGTCAAGGACACTATGTATGATGT 59.640 40.000 0.00 0.00 31.79 3.06
3269 5367 5.831997 TCGTCAAGGACACTATGTATGATG 58.168 41.667 0.00 0.00 31.42 3.07
3270 5368 6.127451 TGTTCGTCAAGGACACTATGTATGAT 60.127 38.462 0.00 0.00 32.09 2.45
3271 5369 5.184287 TGTTCGTCAAGGACACTATGTATGA 59.816 40.000 0.00 0.00 32.09 2.15
3272 5370 5.407502 TGTTCGTCAAGGACACTATGTATG 58.592 41.667 0.00 0.00 32.09 2.39
3273 5371 5.654603 TGTTCGTCAAGGACACTATGTAT 57.345 39.130 0.00 0.00 32.09 2.29
3274 5372 5.456548 TTGTTCGTCAAGGACACTATGTA 57.543 39.130 0.00 0.00 32.09 2.29
3275 5373 4.330944 TTGTTCGTCAAGGACACTATGT 57.669 40.909 0.00 0.00 32.09 2.29
3276 5374 4.330074 GGATTGTTCGTCAAGGACACTATG 59.670 45.833 0.00 0.00 39.55 2.23
3277 5375 4.020573 TGGATTGTTCGTCAAGGACACTAT 60.021 41.667 0.00 0.00 39.55 2.12
3341 5439 2.103373 CATCGTTCCTCTCTTGGGAGA 58.897 52.381 0.00 0.00 45.30 3.71
3349 5447 2.732597 CGTCCTTGACATCGTTCCTCTC 60.733 54.545 0.00 0.00 32.09 3.20
3405 5503 4.929808 ACTTGTTTGGTTATCTCTACGCAG 59.070 41.667 0.00 0.00 0.00 5.18
3438 5536 2.186826 GGTGTGTCGGCACTTTGCT 61.187 57.895 22.43 0.00 44.28 3.91
3439 5537 2.331451 GGTGTGTCGGCACTTTGC 59.669 61.111 22.43 8.69 45.44 3.68
3440 5538 1.355210 GTGGTGTGTCGGCACTTTG 59.645 57.895 22.43 0.00 45.44 2.77
3441 5539 0.465460 ATGTGGTGTGTCGGCACTTT 60.465 50.000 22.43 0.00 45.44 2.66
3442 5540 0.884704 GATGTGGTGTGTCGGCACTT 60.885 55.000 22.43 0.00 45.44 3.16
3443 5541 1.301716 GATGTGGTGTGTCGGCACT 60.302 57.895 22.43 0.00 45.44 4.40
3484 5582 3.686241 CGATGACAACAACTGTGGATGAT 59.314 43.478 0.00 0.00 38.84 2.45
3485 5583 3.066380 CGATGACAACAACTGTGGATGA 58.934 45.455 0.00 0.00 38.84 2.92
3488 5586 2.900716 TCGATGACAACAACTGTGGA 57.099 45.000 0.00 0.00 38.84 4.02
3503 5601 2.424601 CTGTTTGGTCAATGCCATCGAT 59.575 45.455 0.00 0.00 38.48 3.59
3514 5612 4.715534 TTTGGATACTCCTGTTTGGTCA 57.284 40.909 0.00 0.00 37.46 4.02
3522 5620 4.363999 GTGAGACGATTTGGATACTCCTG 58.636 47.826 0.00 0.00 37.46 3.86
3524 5622 3.385111 AGGTGAGACGATTTGGATACTCC 59.615 47.826 0.00 0.00 36.96 3.85


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

AutoCloner maintained by Alex Coulton.