Multiple sequence alignment - TraesCS4D01G207200

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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 TraesCS4D01G207200 chr4D 100.000 2441 0 0 1 2441 354988144 354985704 0.000000e+00 4508.0
1 TraesCS4D01G207200 chr7D 92.876 1853 96 15 614 2437 272235887 272234042 0.000000e+00 2658.0
2 TraesCS4D01G207200 chr7D 92.726 1856 99 16 616 2441 272281410 272279561 0.000000e+00 2647.0
3 TraesCS4D01G207200 chr7D 94.196 224 13 0 391 614 272236378 272236155 2.320000e-90 342.0
4 TraesCS4D01G207200 chr7D 94.196 224 13 0 391 614 272281782 272281559 2.320000e-90 342.0
5 TraesCS4D01G207200 chr7D 88.832 197 20 2 66 262 272236695 272236501 8.720000e-60 241.0
6 TraesCS4D01G207200 chr7D 88.325 197 21 2 66 262 272282099 272281905 4.060000e-58 235.0
7 TraesCS4D01G207200 chr7D 91.473 129 11 0 260 388 272236285 272236157 6.940000e-41 178.0
8 TraesCS4D01G207200 chr7D 91.473 129 11 0 260 388 272281689 272281561 6.940000e-41 178.0
9 TraesCS4D01G207200 chr7D 100.000 39 0 0 830 868 110887751 110887789 3.370000e-09 73.1
10 TraesCS4D01G207200 chr3B 92.690 1833 122 8 614 2441 85807034 85805209 0.000000e+00 2632.0
11 TraesCS4D01G207200 chr3B 83.900 559 59 16 1907 2441 198128967 198129518 2.800000e-139 505.0
12 TraesCS4D01G207200 chr3B 87.817 197 19 3 66 262 85807512 85807321 2.440000e-55 226.0
13 TraesCS4D01G207200 chr3B 93.519 108 7 0 392 499 85807197 85807090 6.980000e-36 161.0
14 TraesCS4D01G207200 chr3B 94.872 39 1 1 66 104 46946000 46946037 2.620000e-05 60.2
15 TraesCS4D01G207200 chr5B 94.322 1638 74 9 812 2441 237125734 237124108 0.000000e+00 2492.0
16 TraesCS4D01G207200 chr5B 93.474 950 45 7 1496 2441 116641198 116642134 0.000000e+00 1395.0
17 TraesCS4D01G207200 chr5B 89.274 895 56 15 614 1500 116632996 116633858 0.000000e+00 1085.0
18 TraesCS4D01G207200 chr5B 91.111 225 20 0 391 615 116632590 116632814 3.050000e-79 305.0
19 TraesCS4D01G207200 chr5B 94.301 193 11 0 638 830 237125942 237125750 1.840000e-76 296.0
20 TraesCS4D01G207200 chr5B 91.626 203 16 1 60 262 116632266 116632467 1.850000e-71 279.0
21 TraesCS4D01G207200 chr5B 90.863 197 17 1 66 262 237129102 237128907 1.860000e-66 263.0
22 TraesCS4D01G207200 chr5B 88.372 215 25 0 614 828 248649587 248649801 2.410000e-65 259.0
23 TraesCS4D01G207200 chr5B 95.588 136 6 0 391 526 237128783 237128648 4.090000e-53 219.0
24 TraesCS4D01G207200 chr7B 87.358 1495 111 21 893 2350 70066486 70067939 0.000000e+00 1642.0
25 TraesCS4D01G207200 chr7B 87.490 1311 99 14 1074 2350 69830957 69832236 0.000000e+00 1452.0
26 TraesCS4D01G207200 chr7B 87.064 1090 90 15 1293 2350 69990371 69991441 0.000000e+00 1184.0
27 TraesCS4D01G207200 chr7B 84.014 563 54 17 1907 2441 468949502 468948948 2.170000e-140 508.0
28 TraesCS4D01G207200 chr7B 85.783 415 34 8 893 1302 69986369 69986763 1.350000e-112 416.0
29 TraesCS4D01G207200 chr7B 90.233 215 21 0 614 828 205197863 205197649 5.140000e-72 281.0
30 TraesCS4D01G207200 chr7B 94.565 92 5 0 393 484 87061985 87061894 2.530000e-30 143.0
31 TraesCS4D01G207200 chr6B 87.688 1064 83 11 1317 2350 548946289 548947334 0.000000e+00 1195.0
32 TraesCS4D01G207200 chr6B 82.216 1119 136 31 827 1897 685331419 685332522 0.000000e+00 905.0
33 TraesCS4D01G207200 chr6B 85.912 433 33 4 897 1324 548945452 548945861 1.040000e-118 436.0
34 TraesCS4D01G207200 chr6B 90.909 55 5 0 851 905 549026261 549026315 9.360000e-10 75.0
35 TraesCS4D01G207200 chr6D 84.105 1101 125 27 832 1897 451161889 451162974 0.000000e+00 1018.0
36 TraesCS4D01G207200 chr6A 83.700 1092 125 33 832 1897 596895335 596896399 0.000000e+00 981.0
37 TraesCS4D01G207200 chr4A 86.097 597 77 5 898 1493 127333155 127333746 2.650000e-179 638.0
38 TraesCS4D01G207200 chr4A 94.565 92 5 0 393 484 718517602 718517693 2.530000e-30 143.0
39 TraesCS4D01G207200 chr4A 90.698 43 3 1 66 108 732389446 732389487 3.390000e-04 56.5
40 TraesCS4D01G207200 chrUn 83.692 558 57 17 1907 2441 22424155 22424701 1.690000e-136 496.0
41 TraesCS4D01G207200 chr1B 90.233 215 21 0 614 828 633782290 633782504 5.140000e-72 281.0
42 TraesCS4D01G207200 chr1B 94.565 92 5 0 393 484 133078724 133078633 2.530000e-30 143.0
43 TraesCS4D01G207200 chr7A 87.442 215 23 1 614 828 715756962 715757172 6.740000e-61 244.0
44 TraesCS4D01G207200 chr7A 94.565 92 5 0 393 484 729956469 729956560 2.530000e-30 143.0
45 TraesCS4D01G207200 chr7A 97.727 44 1 0 825 868 116015020 116015063 2.600000e-10 76.8
46 TraesCS4D01G207200 chr1A 95.122 41 0 2 66 105 256963058 256963019 2.030000e-06 63.9
47 TraesCS4D01G207200 chr3D 94.444 36 2 0 71 106 268128215 268128180 3.390000e-04 56.5


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 TraesCS4D01G207200 chr4D 354985704 354988144 2440 True 4508.000000 4508 100.000000 1 2441 1 chr4D.!!$R1 2440
1 TraesCS4D01G207200 chr7D 272234042 272236695 2653 True 854.750000 2658 91.844250 66 2437 4 chr7D.!!$R1 2371
2 TraesCS4D01G207200 chr7D 272279561 272282099 2538 True 850.500000 2647 91.680000 66 2441 4 chr7D.!!$R2 2375
3 TraesCS4D01G207200 chr3B 85805209 85807512 2303 True 1006.333333 2632 91.342000 66 2441 3 chr3B.!!$R1 2375
4 TraesCS4D01G207200 chr3B 198128967 198129518 551 False 505.000000 505 83.900000 1907 2441 1 chr3B.!!$F2 534
5 TraesCS4D01G207200 chr5B 116641198 116642134 936 False 1395.000000 1395 93.474000 1496 2441 1 chr5B.!!$F1 945
6 TraesCS4D01G207200 chr5B 237124108 237129102 4994 True 817.500000 2492 93.768500 66 2441 4 chr5B.!!$R1 2375
7 TraesCS4D01G207200 chr5B 116632266 116633858 1592 False 556.333333 1085 90.670333 60 1500 3 chr5B.!!$F3 1440
8 TraesCS4D01G207200 chr7B 70066486 70067939 1453 False 1642.000000 1642 87.358000 893 2350 1 chr7B.!!$F2 1457
9 TraesCS4D01G207200 chr7B 69830957 69832236 1279 False 1452.000000 1452 87.490000 1074 2350 1 chr7B.!!$F1 1276
10 TraesCS4D01G207200 chr7B 69986369 69991441 5072 False 800.000000 1184 86.423500 893 2350 2 chr7B.!!$F3 1457
11 TraesCS4D01G207200 chr7B 468948948 468949502 554 True 508.000000 508 84.014000 1907 2441 1 chr7B.!!$R3 534
12 TraesCS4D01G207200 chr6B 685331419 685332522 1103 False 905.000000 905 82.216000 827 1897 1 chr6B.!!$F2 1070
13 TraesCS4D01G207200 chr6B 548945452 548947334 1882 False 815.500000 1195 86.800000 897 2350 2 chr6B.!!$F3 1453
14 TraesCS4D01G207200 chr6D 451161889 451162974 1085 False 1018.000000 1018 84.105000 832 1897 1 chr6D.!!$F1 1065
15 TraesCS4D01G207200 chr6A 596895335 596896399 1064 False 981.000000 981 83.700000 832 1897 1 chr6A.!!$F1 1065
16 TraesCS4D01G207200 chr4A 127333155 127333746 591 False 638.000000 638 86.097000 898 1493 1 chr4A.!!$F1 595
17 TraesCS4D01G207200 chrUn 22424155 22424701 546 False 496.000000 496 83.692000 1907 2441 1 chrUn.!!$F1 534

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
333 334 0.033504 TGAAGTTGCAGGTCCTCGTC 59.966 55.0 0.0 0.0 0.0 4.20 F
655 3477 0.671796 CCGGGTGTGTTTTTCTTCCC 59.328 55.0 0.0 0.0 0.0 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1335 8332 0.874390 CGTGTACACCTGCAAATGCT 59.126 50.000 20.11 0.0 42.66 3.79 R
1775 8807 1.477295 CCAGGAGTCTAGGACGTTTCC 59.523 57.143 0.00 0.0 43.22 3.13 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
18 19 3.175976 AAAAAGCGCGACCACGGTG 62.176 57.895 12.10 0.00 44.08 4.94
19 20 4.595538 AAAGCGCGACCACGGTGA 62.596 61.111 12.10 0.00 44.08 4.02
25 26 3.991051 CGACCACGGTGAGCAGGT 61.991 66.667 10.28 0.00 37.00 4.00
26 27 2.357517 GACCACGGTGAGCAGGTG 60.358 66.667 10.28 0.00 33.77 4.00
27 28 3.161450 ACCACGGTGAGCAGGTGT 61.161 61.111 10.28 0.00 32.04 4.16
28 29 2.666190 CCACGGTGAGCAGGTGTG 60.666 66.667 10.28 0.00 0.00 3.82
89 90 0.378962 GCATAAATGCCCGTGCGTTA 59.621 50.000 3.47 0.00 45.88 3.18
126 127 9.643693 AAAATAATGAGGTGCTGATGTTAAAAG 57.356 29.630 0.00 0.00 0.00 2.27
131 132 3.127548 AGGTGCTGATGTTAAAAGCGATG 59.872 43.478 0.00 0.00 39.88 3.84
238 239 7.385267 GTGTATCCATGCATCTATCTTCTCTT 58.615 38.462 0.00 0.00 0.00 2.85
252 253 3.779183 TCTTCTCTTGGCCTTCTGATCAT 59.221 43.478 3.32 0.00 0.00 2.45
262 263 6.899089 TGGCCTTCTGATCATAATCTAACAA 58.101 36.000 3.32 0.00 32.75 2.83
263 264 7.345691 TGGCCTTCTGATCATAATCTAACAAA 58.654 34.615 3.32 0.00 32.75 2.83
264 265 7.833682 TGGCCTTCTGATCATAATCTAACAAAA 59.166 33.333 3.32 0.00 32.75 2.44
278 279 8.566008 AATCTAACAAAAATATGATCGCAAGC 57.434 30.769 0.00 0.00 37.18 4.01
280 281 6.966632 TCTAACAAAAATATGATCGCAAGCAC 59.033 34.615 0.00 0.00 37.18 4.40
281 282 5.058149 ACAAAAATATGATCGCAAGCACA 57.942 34.783 0.00 0.00 37.18 4.57
282 283 5.653507 ACAAAAATATGATCGCAAGCACAT 58.346 33.333 0.00 0.00 36.91 3.21
283 284 5.517411 ACAAAAATATGATCGCAAGCACATG 59.483 36.000 0.00 0.00 35.35 3.21
285 286 3.891056 ATATGATCGCAAGCACATGTG 57.109 42.857 21.83 21.83 35.35 3.21
286 287 0.736636 ATGATCGCAAGCACATGTGG 59.263 50.000 26.55 11.74 33.28 4.17
287 288 0.606130 TGATCGCAAGCACATGTGGT 60.606 50.000 24.37 24.37 44.00 4.16
289 290 0.321919 ATCGCAAGCACATGTGGTCT 60.322 50.000 29.22 14.97 40.87 3.85
290 291 1.208358 CGCAAGCACATGTGGTCTG 59.792 57.895 29.22 25.93 40.87 3.51
291 292 1.229975 CGCAAGCACATGTGGTCTGA 61.230 55.000 29.22 0.00 40.87 3.27
293 294 1.542915 GCAAGCACATGTGGTCTGATT 59.457 47.619 29.22 11.97 40.87 2.57
294 295 2.749076 GCAAGCACATGTGGTCTGATTA 59.251 45.455 29.22 0.00 40.87 1.75
295 296 3.181503 GCAAGCACATGTGGTCTGATTAG 60.182 47.826 29.22 14.33 40.87 1.73
297 298 5.178061 CAAGCACATGTGGTCTGATTAGTA 58.822 41.667 29.22 0.00 40.87 1.82
298 299 5.620738 AGCACATGTGGTCTGATTAGTAT 57.379 39.130 24.37 0.00 36.44 2.12
299 300 5.363101 AGCACATGTGGTCTGATTAGTATG 58.637 41.667 24.37 0.00 36.44 2.39
300 301 5.104776 AGCACATGTGGTCTGATTAGTATGT 60.105 40.000 24.37 0.00 36.44 2.29
301 302 6.098266 AGCACATGTGGTCTGATTAGTATGTA 59.902 38.462 24.37 0.00 36.44 2.29
302 303 6.931281 GCACATGTGGTCTGATTAGTATGTAT 59.069 38.462 26.55 0.00 0.00 2.29
303 304 7.095481 GCACATGTGGTCTGATTAGTATGTATG 60.095 40.741 26.55 0.00 0.00 2.39
304 305 6.931281 ACATGTGGTCTGATTAGTATGTATGC 59.069 38.462 0.00 0.00 0.00 3.14
305 306 5.528870 TGTGGTCTGATTAGTATGTATGCG 58.471 41.667 0.00 0.00 0.00 4.73
306 307 5.300792 TGTGGTCTGATTAGTATGTATGCGA 59.699 40.000 0.00 0.00 0.00 5.10
307 308 5.859114 GTGGTCTGATTAGTATGTATGCGAG 59.141 44.000 0.00 0.00 0.00 5.03
308 309 5.535030 TGGTCTGATTAGTATGTATGCGAGT 59.465 40.000 0.00 0.00 0.00 4.18
309 310 6.087522 GGTCTGATTAGTATGTATGCGAGTC 58.912 44.000 0.00 0.00 0.00 3.36
313 314 7.014326 TCTGATTAGTATGTATGCGAGTCCTTT 59.986 37.037 0.00 0.00 0.00 3.11
314 315 7.497595 TGATTAGTATGTATGCGAGTCCTTTT 58.502 34.615 0.00 0.00 0.00 2.27
316 317 5.339008 AGTATGTATGCGAGTCCTTTTGA 57.661 39.130 0.00 0.00 0.00 2.69
317 318 5.730550 AGTATGTATGCGAGTCCTTTTGAA 58.269 37.500 0.00 0.00 0.00 2.69
318 319 5.812642 AGTATGTATGCGAGTCCTTTTGAAG 59.187 40.000 0.00 0.00 0.00 3.02
319 320 4.002906 TGTATGCGAGTCCTTTTGAAGT 57.997 40.909 0.00 0.00 0.00 3.01
322 323 1.333619 TGCGAGTCCTTTTGAAGTTGC 59.666 47.619 0.00 0.00 0.00 4.17
323 324 1.333619 GCGAGTCCTTTTGAAGTTGCA 59.666 47.619 0.00 0.00 0.00 4.08
324 325 2.603173 GCGAGTCCTTTTGAAGTTGCAG 60.603 50.000 0.00 0.00 0.00 4.41
325 326 2.031682 CGAGTCCTTTTGAAGTTGCAGG 60.032 50.000 0.00 0.00 0.00 4.85
326 327 2.952310 GAGTCCTTTTGAAGTTGCAGGT 59.048 45.455 0.00 0.00 0.00 4.00
327 328 2.952310 AGTCCTTTTGAAGTTGCAGGTC 59.048 45.455 0.00 0.00 0.00 3.85
328 329 2.034685 GTCCTTTTGAAGTTGCAGGTCC 59.965 50.000 0.00 0.00 0.00 4.46
330 331 2.294512 CCTTTTGAAGTTGCAGGTCCTC 59.705 50.000 0.00 0.00 0.00 3.71
331 332 1.593196 TTTGAAGTTGCAGGTCCTCG 58.407 50.000 0.00 0.00 0.00 4.63
332 333 0.468226 TTGAAGTTGCAGGTCCTCGT 59.532 50.000 0.00 0.00 0.00 4.18
333 334 0.033504 TGAAGTTGCAGGTCCTCGTC 59.966 55.000 0.00 0.00 0.00 4.20
334 335 1.006102 AAGTTGCAGGTCCTCGTCG 60.006 57.895 0.00 0.00 0.00 5.12
335 336 1.461091 AAGTTGCAGGTCCTCGTCGA 61.461 55.000 0.00 0.00 0.00 4.20
336 337 1.733399 GTTGCAGGTCCTCGTCGAC 60.733 63.158 5.18 5.18 0.00 4.20
337 338 3.263503 TTGCAGGTCCTCGTCGACG 62.264 63.158 31.30 31.30 41.45 5.12
338 339 4.477975 GCAGGTCCTCGTCGACGG 62.478 72.222 35.05 24.95 40.29 4.79
339 340 4.477975 CAGGTCCTCGTCGACGGC 62.478 72.222 35.05 22.05 40.29 5.68
340 341 4.719106 AGGTCCTCGTCGACGGCT 62.719 66.667 35.05 16.16 40.29 5.52
341 342 4.477975 GGTCCTCGTCGACGGCTG 62.478 72.222 35.05 24.15 40.29 4.85
342 343 4.477975 GTCCTCGTCGACGGCTGG 62.478 72.222 35.05 30.42 40.29 4.85
344 345 4.778415 CCTCGTCGACGGCTGGTG 62.778 72.222 35.05 18.18 40.29 4.17
345 346 4.039357 CTCGTCGACGGCTGGTGT 62.039 66.667 35.05 0.00 40.29 4.16
347 348 2.503375 CGTCGACGGCTGGTGTAC 60.503 66.667 29.70 0.00 35.37 2.90
350 351 1.007038 TCGACGGCTGGTGTACAAC 60.007 57.895 3.20 3.20 0.00 3.32
351 352 1.300311 CGACGGCTGGTGTACAACA 60.300 57.895 14.09 14.09 0.00 3.33
360 361 2.281208 TGTACAACAGCCGCCACC 60.281 61.111 0.00 0.00 0.00 4.61
484 485 0.745486 CATGCTCGACTGCCCATGAA 60.745 55.000 0.00 0.00 37.78 2.57
636 907 4.083003 TCACCAATGCAGAACCGATTTAAC 60.083 41.667 0.00 0.00 0.00 2.01
646 3468 1.525941 CCGATTTAACCGGGTGTGTT 58.474 50.000 0.00 0.00 43.05 3.32
655 3477 0.671796 CCGGGTGTGTTTTTCTTCCC 59.328 55.000 0.00 0.00 0.00 3.97
1352 8349 3.133141 TGTAGCATTTGCAGGTGTACA 57.867 42.857 5.20 0.00 45.16 2.90
1500 8501 1.021390 CACCGTCTTCATGCCAGTCC 61.021 60.000 0.00 0.00 0.00 3.85
1704 8732 5.654603 TGCCTCGACTAACTGAGAAATAA 57.345 39.130 0.00 0.00 34.04 1.40
1731 8759 7.480760 AAGTAAATGATGCTTACCCAAATGT 57.519 32.000 0.00 0.00 31.59 2.71
1826 8858 9.887862 ATTTATTCCTGATGATTGGGTATCTTT 57.112 29.630 0.00 0.00 34.17 2.52
2095 9139 1.993956 TTGCAGCTGGGCTAAAGAAA 58.006 45.000 17.12 0.00 36.40 2.52
2135 9200 8.202137 ACCACGAAGTAAGTATAATAAGCACAT 58.798 33.333 0.00 0.00 41.61 3.21
2308 9375 5.867903 ATTCACACAAAAGTTCATTGGGA 57.132 34.783 0.00 0.00 34.77 4.37
2410 9477 7.172532 AGTCACTGACGAGCAATTTTATAACAA 59.827 33.333 3.46 0.00 37.67 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.898343 ACCGTGGTCGCGCTTTTT 60.898 55.556 5.56 0.00 35.54 1.94
1 2 3.645975 CACCGTGGTCGCGCTTTT 61.646 61.111 5.56 0.00 35.54 2.27
8 9 3.991051 ACCTGCTCACCGTGGTCG 61.991 66.667 0.00 0.00 0.00 4.79
9 10 2.357517 CACCTGCTCACCGTGGTC 60.358 66.667 0.00 0.00 0.00 4.02
10 11 3.161450 ACACCTGCTCACCGTGGT 61.161 61.111 0.00 0.00 0.00 4.16
11 12 2.666190 CACACCTGCTCACCGTGG 60.666 66.667 0.00 0.00 0.00 4.94
12 13 3.349006 GCACACCTGCTCACCGTG 61.349 66.667 0.00 0.00 40.63 4.94
13 14 3.814615 CTGCACACCTGCTCACCGT 62.815 63.158 0.00 0.00 44.57 4.83
14 15 2.994387 TTCTGCACACCTGCTCACCG 62.994 60.000 0.00 0.00 44.57 4.94
15 16 1.227943 TTCTGCACACCTGCTCACC 60.228 57.895 0.00 0.00 44.57 4.02
16 17 1.849976 GCTTCTGCACACCTGCTCAC 61.850 60.000 0.00 0.00 44.57 3.51
17 18 1.598962 GCTTCTGCACACCTGCTCA 60.599 57.895 0.00 0.00 44.57 4.26
18 19 1.598962 TGCTTCTGCACACCTGCTC 60.599 57.895 0.00 0.00 45.31 4.26
19 20 2.512397 TGCTTCTGCACACCTGCT 59.488 55.556 0.00 0.00 45.31 4.24
73 74 1.197264 GTTGTAACGCACGGGCATTTA 59.803 47.619 11.77 3.08 41.24 1.40
89 90 5.183140 CACCTCATTATTTTTCTCCCGTTGT 59.817 40.000 0.00 0.00 0.00 3.32
126 127 5.679734 ATCATTCTCAATTGGTACATCGC 57.320 39.130 5.42 0.00 39.30 4.58
131 132 7.706159 TGTGCATAATCATTCTCAATTGGTAC 58.294 34.615 5.42 0.00 0.00 3.34
238 239 6.499106 TGTTAGATTATGATCAGAAGGCCA 57.501 37.500 5.01 0.00 34.60 5.36
252 253 9.663904 GCTTGCGATCATATTTTTGTTAGATTA 57.336 29.630 0.00 0.00 0.00 1.75
262 263 5.038683 CACATGTGCTTGCGATCATATTTT 58.961 37.500 13.94 0.00 0.00 1.82
263 264 4.498513 CCACATGTGCTTGCGATCATATTT 60.499 41.667 20.81 0.00 0.00 1.40
264 265 3.004002 CCACATGTGCTTGCGATCATATT 59.996 43.478 20.81 0.00 0.00 1.28
266 267 1.941975 CCACATGTGCTTGCGATCATA 59.058 47.619 20.81 0.00 0.00 2.15
267 268 0.736636 CCACATGTGCTTGCGATCAT 59.263 50.000 20.81 0.00 0.00 2.45
268 269 0.606130 ACCACATGTGCTTGCGATCA 60.606 50.000 20.81 0.00 0.00 2.92
269 270 0.097674 GACCACATGTGCTTGCGATC 59.902 55.000 20.81 4.88 0.00 3.69
270 271 0.321919 AGACCACATGTGCTTGCGAT 60.322 50.000 20.81 0.00 0.00 4.58
271 272 1.071299 AGACCACATGTGCTTGCGA 59.929 52.632 20.81 0.00 0.00 5.10
272 273 1.208358 CAGACCACATGTGCTTGCG 59.792 57.895 20.81 8.84 0.00 4.85
273 274 1.171308 ATCAGACCACATGTGCTTGC 58.829 50.000 20.81 8.61 0.00 4.01
274 275 4.005650 ACTAATCAGACCACATGTGCTTG 58.994 43.478 20.81 16.29 0.00 4.01
275 276 4.292186 ACTAATCAGACCACATGTGCTT 57.708 40.909 20.81 9.13 0.00 3.91
276 277 3.988976 ACTAATCAGACCACATGTGCT 57.011 42.857 20.81 6.88 0.00 4.40
277 278 5.118990 ACATACTAATCAGACCACATGTGC 58.881 41.667 20.81 7.84 0.00 4.57
278 279 7.095481 GCATACATACTAATCAGACCACATGTG 60.095 40.741 19.31 19.31 0.00 3.21
280 281 6.089954 CGCATACATACTAATCAGACCACATG 59.910 42.308 0.00 0.00 0.00 3.21
281 282 6.015434 TCGCATACATACTAATCAGACCACAT 60.015 38.462 0.00 0.00 0.00 3.21
282 283 5.300792 TCGCATACATACTAATCAGACCACA 59.699 40.000 0.00 0.00 0.00 4.17
283 284 5.769367 TCGCATACATACTAATCAGACCAC 58.231 41.667 0.00 0.00 0.00 4.16
285 286 6.015027 ACTCGCATACATACTAATCAGACC 57.985 41.667 0.00 0.00 0.00 3.85
286 287 6.072397 AGGACTCGCATACATACTAATCAGAC 60.072 42.308 0.00 0.00 0.00 3.51
287 288 6.004574 AGGACTCGCATACATACTAATCAGA 58.995 40.000 0.00 0.00 0.00 3.27
289 290 6.650427 AAGGACTCGCATACATACTAATCA 57.350 37.500 0.00 0.00 0.00 2.57
290 291 7.652105 TCAAAAGGACTCGCATACATACTAATC 59.348 37.037 0.00 0.00 0.00 1.75
291 292 7.497595 TCAAAAGGACTCGCATACATACTAAT 58.502 34.615 0.00 0.00 0.00 1.73
293 294 6.459670 TCAAAAGGACTCGCATACATACTA 57.540 37.500 0.00 0.00 0.00 1.82
294 295 5.339008 TCAAAAGGACTCGCATACATACT 57.661 39.130 0.00 0.00 0.00 2.12
295 296 5.581085 ACTTCAAAAGGACTCGCATACATAC 59.419 40.000 0.00 0.00 0.00 2.39
297 298 4.579869 ACTTCAAAAGGACTCGCATACAT 58.420 39.130 0.00 0.00 0.00 2.29
298 299 4.002906 ACTTCAAAAGGACTCGCATACA 57.997 40.909 0.00 0.00 0.00 2.29
299 300 4.712763 CAACTTCAAAAGGACTCGCATAC 58.287 43.478 0.00 0.00 0.00 2.39
300 301 3.188460 GCAACTTCAAAAGGACTCGCATA 59.812 43.478 0.00 0.00 0.00 3.14
301 302 2.030805 GCAACTTCAAAAGGACTCGCAT 60.031 45.455 0.00 0.00 0.00 4.73
302 303 1.333619 GCAACTTCAAAAGGACTCGCA 59.666 47.619 0.00 0.00 0.00 5.10
303 304 1.333619 TGCAACTTCAAAAGGACTCGC 59.666 47.619 0.00 0.00 0.00 5.03
304 305 2.031682 CCTGCAACTTCAAAAGGACTCG 60.032 50.000 0.00 0.00 0.00 4.18
305 306 2.952310 ACCTGCAACTTCAAAAGGACTC 59.048 45.455 0.00 0.00 0.00 3.36
306 307 2.952310 GACCTGCAACTTCAAAAGGACT 59.048 45.455 0.00 0.00 0.00 3.85
307 308 2.034685 GGACCTGCAACTTCAAAAGGAC 59.965 50.000 0.00 0.00 0.00 3.85
308 309 2.091885 AGGACCTGCAACTTCAAAAGGA 60.092 45.455 0.00 0.00 0.00 3.36
309 310 2.294512 GAGGACCTGCAACTTCAAAAGG 59.705 50.000 0.00 0.00 0.00 3.11
313 314 0.468226 ACGAGGACCTGCAACTTCAA 59.532 50.000 0.00 0.00 0.00 2.69
314 315 0.033504 GACGAGGACCTGCAACTTCA 59.966 55.000 0.00 0.00 0.00 3.02
316 317 1.006102 CGACGAGGACCTGCAACTT 60.006 57.895 0.00 0.00 0.00 2.66
317 318 1.901948 TCGACGAGGACCTGCAACT 60.902 57.895 0.00 0.00 0.00 3.16
318 319 1.733399 GTCGACGAGGACCTGCAAC 60.733 63.158 0.00 0.00 0.00 4.17
319 320 2.649034 GTCGACGAGGACCTGCAA 59.351 61.111 0.00 0.00 0.00 4.08
322 323 4.477975 GCCGTCGACGAGGACCTG 62.478 72.222 37.65 20.24 43.02 4.00
323 324 4.719106 AGCCGTCGACGAGGACCT 62.719 66.667 37.65 20.99 43.02 3.85
324 325 4.477975 CAGCCGTCGACGAGGACC 62.478 72.222 37.65 19.25 43.02 4.46
325 326 4.477975 CCAGCCGTCGACGAGGAC 62.478 72.222 37.65 22.75 43.02 3.85
327 328 4.778415 CACCAGCCGTCGACGAGG 62.778 72.222 37.65 32.79 43.02 4.63
328 329 2.683859 TACACCAGCCGTCGACGAG 61.684 63.158 37.65 26.91 43.02 4.18
330 331 2.503375 GTACACCAGCCGTCGACG 60.503 66.667 30.33 30.33 39.44 5.12
331 332 1.007038 TTGTACACCAGCCGTCGAC 60.007 57.895 5.18 5.18 0.00 4.20
332 333 1.007038 GTTGTACACCAGCCGTCGA 60.007 57.895 0.00 0.00 0.00 4.20
333 334 1.282248 CTGTTGTACACCAGCCGTCG 61.282 60.000 7.54 0.00 0.00 5.12
334 335 1.566018 GCTGTTGTACACCAGCCGTC 61.566 60.000 29.35 7.02 46.55 4.79
335 336 1.597027 GCTGTTGTACACCAGCCGT 60.597 57.895 29.35 0.00 46.55 5.68
336 337 3.253955 GCTGTTGTACACCAGCCG 58.746 61.111 29.35 4.09 46.55 5.52
339 340 2.325082 GGCGGCTGTTGTACACCAG 61.325 63.158 15.57 15.57 0.00 4.00
340 341 2.281208 GGCGGCTGTTGTACACCA 60.281 61.111 0.00 0.00 0.00 4.17
341 342 2.281208 TGGCGGCTGTTGTACACC 60.281 61.111 11.43 0.00 0.00 4.16
342 343 2.613506 GGTGGCGGCTGTTGTACAC 61.614 63.158 11.43 0.00 0.00 2.90
344 345 3.419759 CGGTGGCGGCTGTTGTAC 61.420 66.667 11.43 0.00 0.00 2.90
345 346 4.690719 CCGGTGGCGGCTGTTGTA 62.691 66.667 11.43 0.00 0.00 2.41
373 374 2.892425 GAAGATCGGCCTGCGTGG 60.892 66.667 0.00 0.00 39.35 4.94
374 375 3.257561 CGAAGATCGGCCTGCGTG 61.258 66.667 0.00 0.00 36.00 5.34
383 384 2.604046 AATTCACCTCCCGAAGATCG 57.396 50.000 0.00 0.00 40.07 3.69
385 386 4.717280 AGACTTAATTCACCTCCCGAAGAT 59.283 41.667 0.00 0.00 0.00 2.40
386 387 4.081642 CAGACTTAATTCACCTCCCGAAGA 60.082 45.833 0.00 0.00 0.00 2.87
387 388 4.081642 TCAGACTTAATTCACCTCCCGAAG 60.082 45.833 0.00 0.00 0.00 3.79
388 389 3.835978 TCAGACTTAATTCACCTCCCGAA 59.164 43.478 0.00 0.00 0.00 4.30
389 390 3.194968 GTCAGACTTAATTCACCTCCCGA 59.805 47.826 0.00 0.00 0.00 5.14
507 508 4.517832 TCGCGTACATACTAATCAGACCAT 59.482 41.667 5.77 0.00 0.00 3.55
540 541 0.456312 GCGACGAGGACCTACAACTG 60.456 60.000 0.00 0.00 0.00 3.16
636 907 0.671796 GGGAAGAAAAACACACCCGG 59.328 55.000 0.00 0.00 0.00 5.73
646 3468 7.410174 TGAGATTATAAGCCAAGGGAAGAAAA 58.590 34.615 0.00 0.00 0.00 2.29
655 3477 6.352516 ACCACTCTTGAGATTATAAGCCAAG 58.647 40.000 18.26 18.26 36.49 3.61
782 3604 6.266168 AGCGAATTAACCATTTCATGTTCA 57.734 33.333 0.00 0.00 0.00 3.18
802 3624 1.657594 CTCATGCGAGGCAATATAGCG 59.342 52.381 0.00 0.00 43.62 4.26
1252 4173 4.189580 ACGCTTGGCACCTGGTGT 62.190 61.111 26.48 3.34 35.75 4.16
1323 8320 4.022676 CCTGCAAATGCTACATCATATGCA 60.023 41.667 6.97 0.00 42.66 3.96
1335 8332 0.874390 CGTGTACACCTGCAAATGCT 59.126 50.000 20.11 0.00 42.66 3.79
1500 8501 2.366972 ATTCACCGGGGGAGAGGG 60.367 66.667 2.42 0.00 0.00 4.30
1680 8708 4.537135 TTTCTCAGTTAGTCGAGGCATT 57.463 40.909 0.00 0.00 0.00 3.56
1704 8732 6.909550 TTGGGTAAGCATCATTTACTTTGT 57.090 33.333 0.00 0.00 32.81 2.83
1775 8807 1.477295 CCAGGAGTCTAGGACGTTTCC 59.523 57.143 0.00 0.00 43.22 3.13
1825 8857 5.072055 CCACCATGGATCTGCATACATTAA 58.928 41.667 21.47 0.00 40.96 1.40
1826 8858 4.350520 TCCACCATGGATCTGCATACATTA 59.649 41.667 21.47 0.00 42.67 1.90
1888 8921 3.892284 TGTGTGTACATTTCCAAGGTGT 58.108 40.909 0.00 0.00 0.00 4.16
2095 9139 6.628919 ACTTCGTGGTTTGTTATTTAGCTT 57.371 33.333 0.00 0.00 0.00 3.74
2289 9356 5.599732 TCATTCCCAATGAACTTTTGTGTG 58.400 37.500 0.00 0.00 44.47 3.82
2340 9407 5.993106 AAAGTGAACTAGCAGACAAACTC 57.007 39.130 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.