Multiple sequence alignment - TraesCS1B01G355500

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 TraesCS1B01G355500 chr1B 100.000 2552 0 0 1 2552 584797646 584800197 0.000000e+00 4713.0
1 TraesCS1B01G355500 chr1B 98.976 1660 14 1 303 1962 584779159 584780815 0.000000e+00 2968.0
2 TraesCS1B01G355500 chr1B 93.488 1551 52 20 303 1826 584761859 584763387 0.000000e+00 2259.0
3 TraesCS1B01G355500 chr1B 89.108 1570 90 23 303 1826 584620273 584621807 0.000000e+00 1877.0
4 TraesCS1B01G355500 chr1B 89.045 1570 91 26 303 1826 584574912 584576446 0.000000e+00 1871.0
5 TraesCS1B01G355500 chr1B 89.650 1401 91 31 460 1826 584603794 584605174 0.000000e+00 1736.0
6 TraesCS1B01G355500 chr1B 89.096 1394 105 28 460 1826 584654228 584655601 0.000000e+00 1688.0
7 TraesCS1B01G355500 chr1B 91.647 850 51 13 982 1826 584566230 584567064 0.000000e+00 1158.0
8 TraesCS1B01G355500 chr1B 98.167 600 10 1 1954 2552 584783390 584783989 0.000000e+00 1046.0
9 TraesCS1B01G355500 chr1B 97.403 308 3 3 1 307 169938228 169937925 1.050000e-143 520.0
10 TraesCS1B01G355500 chr1A 92.616 1395 65 14 460 1826 531513133 531514517 0.000000e+00 1971.0
11 TraesCS1B01G355500 chr1A 89.149 1410 85 29 460 1826 531561962 531563346 0.000000e+00 1694.0
12 TraesCS1B01G355500 chr1A 89.030 1422 80 31 444 1826 531366990 531368374 0.000000e+00 1692.0
13 TraesCS1B01G355500 chr1A 92.000 75 2 2 331 401 531561888 531561962 4.490000e-18 102.0
14 TraesCS1B01G355500 chr1D 89.270 1575 91 30 303 1826 433092469 433094016 0.000000e+00 1901.0
15 TraesCS1B01G355500 chr1D 90.671 1415 67 24 444 1826 433060542 433061923 0.000000e+00 1821.0
16 TraesCS1B01G355500 chr1D 86.524 935 67 21 917 1826 433143196 433144096 0.000000e+00 974.0
17 TraesCS1B01G355500 chr1D 94.755 286 13 1 462 747 433142789 433142506 6.480000e-121 444.0
18 TraesCS1B01G355500 chr3B 87.200 1250 106 26 481 1697 647943920 647942692 0.000000e+00 1373.0
19 TraesCS1B01G355500 chr3B 98.039 306 4 2 1 304 723494213 723494518 4.830000e-147 531.0
20 TraesCS1B01G355500 chr3B 87.327 434 40 7 481 907 647969327 647968902 1.370000e-132 483.0
21 TraesCS1B01G355500 chr3B 77.839 546 103 12 1993 2533 304405897 304406429 3.170000e-84 322.0
22 TraesCS1B01G355500 chr2B 99.344 305 0 2 1 304 780152637 780152334 3.710000e-153 551.0
23 TraesCS1B01G355500 chr2B 99.013 304 2 1 1 303 70882397 70882700 6.210000e-151 544.0
24 TraesCS1B01G355500 chr2B 97.368 304 3 3 1 303 774393130 774392831 1.750000e-141 512.0
25 TraesCS1B01G355500 chr5B 99.010 303 1 2 1 302 520371249 520370948 2.230000e-150 542.0
26 TraesCS1B01G355500 chr4B 98.684 304 2 2 1 303 664964530 664964832 2.890000e-149 538.0
27 TraesCS1B01G355500 chr4B 98.026 304 4 2 1 303 665023935 665024237 6.250000e-146 527.0
28 TraesCS1B01G355500 chr4B 97.368 304 7 1 1 303 115547144 115547447 1.350000e-142 516.0
29 TraesCS1B01G355500 chr4A 82.745 510 78 4 2022 2528 610022750 610023252 1.800000e-121 446.0
30 TraesCS1B01G355500 chr4A 81.382 521 88 4 2022 2540 555803644 555803131 1.410000e-112 416.0
31 TraesCS1B01G355500 chr4D 81.333 525 85 7 2031 2551 435416693 435416178 5.080000e-112 414.0
32 TraesCS1B01G355500 chr5A 78.394 523 97 10 2029 2545 461876838 461876326 2.450000e-85 326.0
33 TraesCS1B01G355500 chr7B 77.442 563 112 9 1991 2548 633943403 633942851 3.170000e-84 322.0
34 TraesCS1B01G355500 chr7D 77.220 518 101 11 2029 2540 21802565 21802059 1.160000e-73 287.0
35 TraesCS1B01G355500 chr7D 77.413 487 97 10 2029 2511 621963099 621963576 6.950000e-71 278.0
36 TraesCS1B01G355500 chr3A 79.787 376 70 6 2161 2533 330739068 330739440 4.190000e-68 268.0
37 TraesCS1B01G355500 chr6A 96.226 53 2 0 303 355 616689218 616689166 1.260000e-13 87.9


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 TraesCS1B01G355500 chr1B 584797646 584800197 2551 False 4713 4713 100.0000 1 2552 1 chr1B.!!$F7 2551
1 TraesCS1B01G355500 chr1B 584761859 584763387 1528 False 2259 2259 93.4880 303 1826 1 chr1B.!!$F6 1523
2 TraesCS1B01G355500 chr1B 584779159 584783989 4830 False 2007 2968 98.5715 303 2552 2 chr1B.!!$F8 2249
3 TraesCS1B01G355500 chr1B 584620273 584621807 1534 False 1877 1877 89.1080 303 1826 1 chr1B.!!$F4 1523
4 TraesCS1B01G355500 chr1B 584574912 584576446 1534 False 1871 1871 89.0450 303 1826 1 chr1B.!!$F2 1523
5 TraesCS1B01G355500 chr1B 584603794 584605174 1380 False 1736 1736 89.6500 460 1826 1 chr1B.!!$F3 1366
6 TraesCS1B01G355500 chr1B 584654228 584655601 1373 False 1688 1688 89.0960 460 1826 1 chr1B.!!$F5 1366
7 TraesCS1B01G355500 chr1B 584566230 584567064 834 False 1158 1158 91.6470 982 1826 1 chr1B.!!$F1 844
8 TraesCS1B01G355500 chr1A 531513133 531514517 1384 False 1971 1971 92.6160 460 1826 1 chr1A.!!$F2 1366
9 TraesCS1B01G355500 chr1A 531366990 531368374 1384 False 1692 1692 89.0300 444 1826 1 chr1A.!!$F1 1382
10 TraesCS1B01G355500 chr1A 531561888 531563346 1458 False 898 1694 90.5745 331 1826 2 chr1A.!!$F3 1495
11 TraesCS1B01G355500 chr1D 433092469 433094016 1547 False 1901 1901 89.2700 303 1826 1 chr1D.!!$F2 1523
12 TraesCS1B01G355500 chr1D 433060542 433061923 1381 False 1821 1821 90.6710 444 1826 1 chr1D.!!$F1 1382
13 TraesCS1B01G355500 chr1D 433143196 433144096 900 False 974 974 86.5240 917 1826 1 chr1D.!!$F3 909
14 TraesCS1B01G355500 chr3B 647942692 647943920 1228 True 1373 1373 87.2000 481 1697 1 chr3B.!!$R1 1216
15 TraesCS1B01G355500 chr3B 304405897 304406429 532 False 322 322 77.8390 1993 2533 1 chr3B.!!$F1 540
16 TraesCS1B01G355500 chr4A 610022750 610023252 502 False 446 446 82.7450 2022 2528 1 chr4A.!!$F1 506
17 TraesCS1B01G355500 chr4A 555803131 555803644 513 True 416 416 81.3820 2022 2540 1 chr4A.!!$R1 518
18 TraesCS1B01G355500 chr4D 435416178 435416693 515 True 414 414 81.3330 2031 2551 1 chr4D.!!$R1 520
19 TraesCS1B01G355500 chr5A 461876326 461876838 512 True 326 326 78.3940 2029 2545 1 chr5A.!!$R1 516
20 TraesCS1B01G355500 chr7B 633942851 633943403 552 True 322 322 77.4420 1991 2548 1 chr7B.!!$R1 557
21 TraesCS1B01G355500 chr7D 21802059 21802565 506 True 287 287 77.2200 2029 2540 1 chr7D.!!$R1 511

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
295 296 2.071778 ACATGCAGGTTCCAAAGTGT 57.928 45.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1595 1675 3.957591 ATTTTACCATGCATGCACACA 57.042 38.095 25.37 5.72 0.0 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
22 23 5.814764 GACCTTCTATTGTACTCGTGAGA 57.185 43.478 3.44 0.00 39.12 3.27
23 24 6.192234 GACCTTCTATTGTACTCGTGAGAA 57.808 41.667 3.44 0.00 41.32 2.87
24 25 6.585695 ACCTTCTATTGTACTCGTGAGAAA 57.414 37.500 3.44 0.00 41.32 2.52
25 26 6.989659 ACCTTCTATTGTACTCGTGAGAAAA 58.010 36.000 3.44 0.00 41.32 2.29
26 27 7.612677 ACCTTCTATTGTACTCGTGAGAAAAT 58.387 34.615 3.44 3.40 41.32 1.82
27 28 8.746530 ACCTTCTATTGTACTCGTGAGAAAATA 58.253 33.333 3.44 4.28 41.32 1.40
28 29 9.582431 CCTTCTATTGTACTCGTGAGAAAATAA 57.418 33.333 3.44 0.00 41.32 1.40
33 34 8.786826 ATTGTACTCGTGAGAAAATAAATCCA 57.213 30.769 3.44 0.00 41.32 3.41
34 35 7.591006 TGTACTCGTGAGAAAATAAATCCAC 57.409 36.000 3.44 0.00 41.32 4.02
35 36 7.156000 TGTACTCGTGAGAAAATAAATCCACA 58.844 34.615 3.44 0.00 41.32 4.17
36 37 7.658167 TGTACTCGTGAGAAAATAAATCCACAA 59.342 33.333 3.44 0.00 41.32 3.33
37 38 7.504924 ACTCGTGAGAAAATAAATCCACAAA 57.495 32.000 3.44 0.00 41.32 2.83
38 39 7.936584 ACTCGTGAGAAAATAAATCCACAAAA 58.063 30.769 3.44 0.00 41.32 2.44
39 40 8.410141 ACTCGTGAGAAAATAAATCCACAAAAA 58.590 29.630 3.44 0.00 41.32 1.94
95 96 9.255304 GACAAATTTTTGGCTAAAATAGTGTGA 57.745 29.630 25.81 0.92 43.84 3.58
96 97 9.606631 ACAAATTTTTGGCTAAAATAGTGTGAA 57.393 25.926 22.86 0.00 43.84 3.18
101 102 9.906660 TTTTTGGCTAAAATAGTGTGAATAGTG 57.093 29.630 8.93 0.00 35.82 2.74
102 103 8.856153 TTTGGCTAAAATAGTGTGAATAGTGA 57.144 30.769 0.00 0.00 0.00 3.41
103 104 7.843490 TGGCTAAAATAGTGTGAATAGTGAC 57.157 36.000 0.00 0.00 0.00 3.67
104 105 6.821665 TGGCTAAAATAGTGTGAATAGTGACC 59.178 38.462 0.00 0.00 0.00 4.02
105 106 7.048512 GGCTAAAATAGTGTGAATAGTGACCT 58.951 38.462 0.00 0.00 0.00 3.85
106 107 8.202137 GGCTAAAATAGTGTGAATAGTGACCTA 58.798 37.037 0.00 0.00 0.00 3.08
107 108 9.765795 GCTAAAATAGTGTGAATAGTGACCTAT 57.234 33.333 0.00 0.00 35.33 2.57
114 115 8.478775 AGTGTGAATAGTGACCTATAATAGCA 57.521 34.615 0.00 0.00 32.57 3.49
115 116 8.924303 AGTGTGAATAGTGACCTATAATAGCAA 58.076 33.333 0.00 0.00 32.57 3.91
116 117 9.542462 GTGTGAATAGTGACCTATAATAGCAAA 57.458 33.333 0.00 0.00 32.57 3.68
152 153 6.464895 TTTTTGCTGTGAAGTCAACTTTTG 57.535 33.333 0.00 0.00 36.11 2.44
153 154 4.782019 TTGCTGTGAAGTCAACTTTTGT 57.218 36.364 0.00 0.00 36.11 2.83
154 155 4.782019 TGCTGTGAAGTCAACTTTTGTT 57.218 36.364 0.00 0.00 44.66 2.83
155 156 5.132897 TGCTGTGAAGTCAACTTTTGTTT 57.867 34.783 0.00 0.00 41.35 2.83
156 157 5.537188 TGCTGTGAAGTCAACTTTTGTTTT 58.463 33.333 0.00 0.00 41.35 2.43
157 158 5.988561 TGCTGTGAAGTCAACTTTTGTTTTT 59.011 32.000 0.00 0.00 41.35 1.94
198 199 9.997482 TTTTTACTAGTGCAAAAGTAAGTCAAG 57.003 29.630 17.10 0.00 38.89 3.02
199 200 8.726870 TTTACTAGTGCAAAAGTAAGTCAAGT 57.273 30.769 17.10 0.00 38.89 3.16
200 201 6.604735 ACTAGTGCAAAAGTAAGTCAAGTG 57.395 37.500 0.00 0.00 0.00 3.16
201 202 6.113411 ACTAGTGCAAAAGTAAGTCAAGTGT 58.887 36.000 0.00 0.00 0.00 3.55
202 203 5.897377 AGTGCAAAAGTAAGTCAAGTGTT 57.103 34.783 0.00 0.00 0.00 3.32
203 204 6.267496 AGTGCAAAAGTAAGTCAAGTGTTT 57.733 33.333 0.00 0.00 0.00 2.83
204 205 6.687604 AGTGCAAAAGTAAGTCAAGTGTTTT 58.312 32.000 0.00 0.00 0.00 2.43
205 206 6.586082 AGTGCAAAAGTAAGTCAAGTGTTTTG 59.414 34.615 0.00 0.00 37.74 2.44
206 207 6.364976 GTGCAAAAGTAAGTCAAGTGTTTTGT 59.635 34.615 0.00 0.00 37.26 2.83
207 208 6.584563 TGCAAAAGTAAGTCAAGTGTTTTGTC 59.415 34.615 0.00 0.00 37.26 3.18
208 209 6.584563 GCAAAAGTAAGTCAAGTGTTTTGTCA 59.415 34.615 0.00 0.00 37.26 3.58
209 210 7.115663 GCAAAAGTAAGTCAAGTGTTTTGTCAA 59.884 33.333 0.00 0.00 37.26 3.18
210 211 8.973378 CAAAAGTAAGTCAAGTGTTTTGTCAAA 58.027 29.630 0.00 0.00 32.65 2.69
211 212 9.535878 AAAAGTAAGTCAAGTGTTTTGTCAAAA 57.464 25.926 6.65 6.65 0.00 2.44
212 213 9.705290 AAAGTAAGTCAAGTGTTTTGTCAAAAT 57.295 25.926 13.65 0.00 32.22 1.82
215 216 9.783256 GTAAGTCAAGTGTTTTGTCAAAATAGT 57.217 29.630 13.65 11.04 32.22 2.12
217 218 8.911247 AGTCAAGTGTTTTGTCAAAATAGTTC 57.089 30.769 19.36 12.43 34.29 3.01
218 219 8.739972 AGTCAAGTGTTTTGTCAAAATAGTTCT 58.260 29.630 19.36 13.92 34.29 3.01
219 220 9.353999 GTCAAGTGTTTTGTCAAAATAGTTCTT 57.646 29.630 19.36 11.77 34.29 2.52
222 223 9.797556 AAGTGTTTTGTCAAAATAGTTCTTACC 57.202 29.630 17.46 2.76 31.98 2.85
223 224 9.185680 AGTGTTTTGTCAAAATAGTTCTTACCT 57.814 29.630 13.65 0.34 32.22 3.08
284 285 7.445121 CCATATAGGGTGTATATACATGCAGG 58.555 42.308 18.27 0.00 38.63 4.85
285 286 7.071196 CCATATAGGGTGTATATACATGCAGGT 59.929 40.741 18.27 9.77 38.63 4.00
286 287 6.952605 ATAGGGTGTATATACATGCAGGTT 57.047 37.500 18.27 0.00 38.63 3.50
287 288 5.228945 AGGGTGTATATACATGCAGGTTC 57.771 43.478 18.27 3.43 38.63 3.62
288 289 4.041691 AGGGTGTATATACATGCAGGTTCC 59.958 45.833 18.27 11.60 38.63 3.62
289 290 4.202419 GGGTGTATATACATGCAGGTTCCA 60.202 45.833 18.27 0.00 38.63 3.53
290 291 5.373222 GGTGTATATACATGCAGGTTCCAA 58.627 41.667 18.27 0.00 38.63 3.53
291 292 5.825679 GGTGTATATACATGCAGGTTCCAAA 59.174 40.000 18.27 0.00 38.63 3.28
292 293 6.017109 GGTGTATATACATGCAGGTTCCAAAG 60.017 42.308 18.27 0.00 38.63 2.77
293 294 6.542370 GTGTATATACATGCAGGTTCCAAAGT 59.458 38.462 18.27 0.00 38.63 2.66
294 295 6.542005 TGTATATACATGCAGGTTCCAAAGTG 59.458 38.462 10.25 0.00 0.00 3.16
295 296 2.071778 ACATGCAGGTTCCAAAGTGT 57.928 45.000 0.00 0.00 0.00 3.55
296 297 3.222173 ACATGCAGGTTCCAAAGTGTA 57.778 42.857 0.00 0.00 0.00 2.90
297 298 3.766545 ACATGCAGGTTCCAAAGTGTAT 58.233 40.909 0.00 0.00 0.00 2.29
298 299 4.151883 ACATGCAGGTTCCAAAGTGTATT 58.848 39.130 0.00 0.00 0.00 1.89
299 300 4.588528 ACATGCAGGTTCCAAAGTGTATTT 59.411 37.500 0.00 0.00 0.00 1.40
300 301 4.846779 TGCAGGTTCCAAAGTGTATTTC 57.153 40.909 0.00 0.00 0.00 2.17
301 302 3.572255 TGCAGGTTCCAAAGTGTATTTCC 59.428 43.478 0.00 0.00 0.00 3.13
439 444 6.428465 TCGAGGTAGATAGCTTCATCTTAGTG 59.572 42.308 4.34 0.00 36.63 2.74
804 839 4.904241 AGCTGATGATTATTAGGGCTGTC 58.096 43.478 0.00 0.00 0.00 3.51
1061 1125 3.435186 GCCGCTCAAGTTCCTGGC 61.435 66.667 0.00 0.00 35.04 4.85
1062 1126 3.121030 CCGCTCAAGTTCCTGGCG 61.121 66.667 0.00 0.00 44.48 5.69
1063 1127 3.793144 CGCTCAAGTTCCTGGCGC 61.793 66.667 0.00 0.00 39.42 6.53
1595 1675 1.872234 CAGCTGCGCACGTACGTAT 60.872 57.895 22.34 0.00 34.88 3.06
1596 1676 1.872234 AGCTGCGCACGTACGTATG 60.872 57.895 22.34 16.94 34.88 2.39
1771 1911 1.530323 GGTTGTGCGGGTCTAATTGT 58.470 50.000 0.00 0.00 0.00 2.71
1897 2042 4.993705 TTGATTGGGTACAGGAACTCTT 57.006 40.909 0.00 0.00 34.60 2.85
2467 5199 3.642848 ACGTACTCCAAAACCTCCAGTAA 59.357 43.478 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.814764 TCTCACGAGTACAATAGAAGGTC 57.185 43.478 0.00 0.00 0.00 3.85
1 2 6.585695 TTTCTCACGAGTACAATAGAAGGT 57.414 37.500 0.00 0.00 0.00 3.50
2 3 9.582431 TTATTTTCTCACGAGTACAATAGAAGG 57.418 33.333 0.00 0.00 0.00 3.46
7 8 9.878667 TGGATTTATTTTCTCACGAGTACAATA 57.121 29.630 0.00 0.00 0.00 1.90
8 9 8.665685 GTGGATTTATTTTCTCACGAGTACAAT 58.334 33.333 0.00 0.00 0.00 2.71
9 10 7.658167 TGTGGATTTATTTTCTCACGAGTACAA 59.342 33.333 0.00 0.00 0.00 2.41
10 11 7.156000 TGTGGATTTATTTTCTCACGAGTACA 58.844 34.615 0.00 0.00 0.00 2.90
11 12 7.591006 TGTGGATTTATTTTCTCACGAGTAC 57.409 36.000 0.00 0.00 0.00 2.73
12 13 8.610248 TTTGTGGATTTATTTTCTCACGAGTA 57.390 30.769 0.00 0.00 0.00 2.59
13 14 7.504924 TTTGTGGATTTATTTTCTCACGAGT 57.495 32.000 0.00 0.00 0.00 4.18
14 15 8.795786 TTTTTGTGGATTTATTTTCTCACGAG 57.204 30.769 0.00 0.00 0.00 4.18
67 68 9.830975 ACACTATTTTAGCCAAAAATTTGTCTT 57.169 25.926 11.38 0.00 43.75 3.01
68 69 9.260002 CACACTATTTTAGCCAAAAATTTGTCT 57.740 29.630 11.38 0.28 43.75 3.41
69 70 9.255304 TCACACTATTTTAGCCAAAAATTTGTC 57.745 29.630 11.38 0.00 43.75 3.18
70 71 9.606631 TTCACACTATTTTAGCCAAAAATTTGT 57.393 25.926 11.38 11.68 43.75 2.83
75 76 9.906660 CACTATTCACACTATTTTAGCCAAAAA 57.093 29.630 0.00 0.00 41.21 1.94
76 77 9.290988 TCACTATTCACACTATTTTAGCCAAAA 57.709 29.630 0.00 0.00 38.00 2.44
77 78 8.726988 GTCACTATTCACACTATTTTAGCCAAA 58.273 33.333 0.00 0.00 0.00 3.28
78 79 7.335924 GGTCACTATTCACACTATTTTAGCCAA 59.664 37.037 0.00 0.00 0.00 4.52
79 80 6.821665 GGTCACTATTCACACTATTTTAGCCA 59.178 38.462 0.00 0.00 0.00 4.75
80 81 7.048512 AGGTCACTATTCACACTATTTTAGCC 58.951 38.462 0.00 0.00 0.00 3.93
81 82 9.765795 ATAGGTCACTATTCACACTATTTTAGC 57.234 33.333 0.00 0.00 36.51 3.09
88 89 9.582648 TGCTATTATAGGTCACTATTCACACTA 57.417 33.333 1.12 0.00 40.35 2.74
89 90 8.478775 TGCTATTATAGGTCACTATTCACACT 57.521 34.615 1.12 0.00 40.35 3.55
90 91 9.542462 TTTGCTATTATAGGTCACTATTCACAC 57.458 33.333 1.12 0.00 40.35 3.82
129 130 5.988561 ACAAAAGTTGACTTCACAGCAAAAA 59.011 32.000 0.00 0.00 34.61 1.94
130 131 5.537188 ACAAAAGTTGACTTCACAGCAAAA 58.463 33.333 0.00 0.00 34.61 2.44
131 132 5.132897 ACAAAAGTTGACTTCACAGCAAA 57.867 34.783 0.00 0.00 34.61 3.68
132 133 4.782019 ACAAAAGTTGACTTCACAGCAA 57.218 36.364 0.00 0.00 34.61 3.91
133 134 4.782019 AACAAAAGTTGACTTCACAGCA 57.218 36.364 0.00 0.00 34.61 4.41
134 135 6.466308 AAAAACAAAAGTTGACTTCACAGC 57.534 33.333 0.00 0.00 34.61 4.40
172 173 9.997482 CTTGACTTACTTTTGCACTAGTAAAAA 57.003 29.630 16.44 12.59 38.55 1.94
173 174 9.169592 ACTTGACTTACTTTTGCACTAGTAAAA 57.830 29.630 16.44 0.00 36.66 1.52
174 175 8.609176 CACTTGACTTACTTTTGCACTAGTAAA 58.391 33.333 16.44 1.77 36.66 2.01
175 176 7.767198 ACACTTGACTTACTTTTGCACTAGTAA 59.233 33.333 15.40 15.40 35.96 2.24
176 177 7.270047 ACACTTGACTTACTTTTGCACTAGTA 58.730 34.615 0.00 3.57 0.00 1.82
177 178 6.113411 ACACTTGACTTACTTTTGCACTAGT 58.887 36.000 5.34 5.34 0.00 2.57
178 179 6.604735 ACACTTGACTTACTTTTGCACTAG 57.395 37.500 0.00 0.00 0.00 2.57
179 180 6.995511 AACACTTGACTTACTTTTGCACTA 57.004 33.333 0.00 0.00 0.00 2.74
180 181 5.897377 AACACTTGACTTACTTTTGCACT 57.103 34.783 0.00 0.00 0.00 4.40
181 182 6.364976 ACAAAACACTTGACTTACTTTTGCAC 59.635 34.615 0.00 0.00 33.72 4.57
182 183 6.451393 ACAAAACACTTGACTTACTTTTGCA 58.549 32.000 0.00 0.00 33.72 4.08
183 184 6.584563 TGACAAAACACTTGACTTACTTTTGC 59.415 34.615 0.00 0.00 33.72 3.68
184 185 8.514136 TTGACAAAACACTTGACTTACTTTTG 57.486 30.769 0.00 0.00 35.61 2.44
185 186 9.535878 TTTTGACAAAACACTTGACTTACTTTT 57.464 25.926 9.30 0.00 0.00 2.27
186 187 9.705290 ATTTTGACAAAACACTTGACTTACTTT 57.295 25.926 15.36 0.00 32.37 2.66
189 190 9.783256 ACTATTTTGACAAAACACTTGACTTAC 57.217 29.630 15.36 0.00 32.37 2.34
191 192 9.353999 GAACTATTTTGACAAAACACTTGACTT 57.646 29.630 15.36 0.00 32.37 3.01
192 193 8.739972 AGAACTATTTTGACAAAACACTTGACT 58.260 29.630 15.36 7.03 32.37 3.41
193 194 8.911247 AGAACTATTTTGACAAAACACTTGAC 57.089 30.769 15.36 5.14 32.37 3.18
196 197 9.797556 GGTAAGAACTATTTTGACAAAACACTT 57.202 29.630 15.36 15.89 32.37 3.16
197 198 9.185680 AGGTAAGAACTATTTTGACAAAACACT 57.814 29.630 15.36 3.23 32.37 3.55
259 260 7.071196 ACCTGCATGTATATACACCCTATATGG 59.929 40.741 17.69 13.09 39.30 2.74
260 261 8.023021 ACCTGCATGTATATACACCCTATATG 57.977 38.462 17.69 11.11 39.30 1.78
261 262 8.624019 AACCTGCATGTATATACACCCTATAT 57.376 34.615 17.69 0.00 39.30 0.86
262 263 7.125204 GGAACCTGCATGTATATACACCCTATA 59.875 40.741 17.69 1.71 39.30 1.31
263 264 6.070194 GGAACCTGCATGTATATACACCCTAT 60.070 42.308 17.69 0.00 39.30 2.57
264 265 5.247564 GGAACCTGCATGTATATACACCCTA 59.752 44.000 17.69 4.59 39.30 3.53
265 266 4.041691 GGAACCTGCATGTATATACACCCT 59.958 45.833 17.69 0.00 39.30 4.34
266 267 4.202419 TGGAACCTGCATGTATATACACCC 60.202 45.833 17.69 11.73 39.30 4.61
267 268 4.968259 TGGAACCTGCATGTATATACACC 58.032 43.478 17.69 11.85 39.30 4.16
268 269 6.542370 ACTTTGGAACCTGCATGTATATACAC 59.458 38.462 17.69 7.09 39.30 2.90
269 270 6.542005 CACTTTGGAACCTGCATGTATATACA 59.458 38.462 17.65 17.65 40.98 2.29
270 271 6.542370 ACACTTTGGAACCTGCATGTATATAC 59.458 38.462 5.89 5.89 0.00 1.47
271 272 6.658849 ACACTTTGGAACCTGCATGTATATA 58.341 36.000 0.00 0.00 0.00 0.86
272 273 5.509498 ACACTTTGGAACCTGCATGTATAT 58.491 37.500 0.00 0.00 0.00 0.86
273 274 4.917385 ACACTTTGGAACCTGCATGTATA 58.083 39.130 0.00 0.00 0.00 1.47
274 275 3.766545 ACACTTTGGAACCTGCATGTAT 58.233 40.909 0.00 0.00 0.00 2.29
275 276 3.222173 ACACTTTGGAACCTGCATGTA 57.778 42.857 0.00 0.00 0.00 2.29
276 277 2.071778 ACACTTTGGAACCTGCATGT 57.928 45.000 0.00 0.00 0.00 3.21
277 278 4.789012 AATACACTTTGGAACCTGCATG 57.211 40.909 0.00 0.00 0.00 4.06
278 279 4.220602 GGAAATACACTTTGGAACCTGCAT 59.779 41.667 0.00 0.00 0.00 3.96
279 280 3.572255 GGAAATACACTTTGGAACCTGCA 59.428 43.478 0.00 0.00 0.00 4.41
280 281 3.056821 GGGAAATACACTTTGGAACCTGC 60.057 47.826 0.00 0.00 0.00 4.85
281 282 3.509967 GGGGAAATACACTTTGGAACCTG 59.490 47.826 0.00 0.00 0.00 4.00
282 283 3.401342 AGGGGAAATACACTTTGGAACCT 59.599 43.478 0.00 0.00 0.00 3.50
283 284 3.762288 GAGGGGAAATACACTTTGGAACC 59.238 47.826 0.00 0.00 0.00 3.62
284 285 3.439129 CGAGGGGAAATACACTTTGGAAC 59.561 47.826 0.00 0.00 0.00 3.62
285 286 3.328343 TCGAGGGGAAATACACTTTGGAA 59.672 43.478 0.00 0.00 0.00 3.53
286 287 2.907696 TCGAGGGGAAATACACTTTGGA 59.092 45.455 0.00 0.00 0.00 3.53
287 288 3.270877 CTCGAGGGGAAATACACTTTGG 58.729 50.000 3.91 0.00 0.00 3.28
288 289 3.684788 CACTCGAGGGGAAATACACTTTG 59.315 47.826 18.41 0.00 0.00 2.77
289 290 3.326880 ACACTCGAGGGGAAATACACTTT 59.673 43.478 20.91 0.00 0.00 2.66
290 291 2.904434 ACACTCGAGGGGAAATACACTT 59.096 45.455 20.91 0.00 0.00 3.16
291 292 2.496470 GACACTCGAGGGGAAATACACT 59.504 50.000 20.91 0.00 0.00 3.55
292 293 2.418334 GGACACTCGAGGGGAAATACAC 60.418 54.545 20.91 0.00 0.00 2.90
293 294 1.829222 GGACACTCGAGGGGAAATACA 59.171 52.381 20.91 0.00 0.00 2.29
294 295 1.829222 TGGACACTCGAGGGGAAATAC 59.171 52.381 20.91 0.00 0.00 1.89
295 296 1.829222 GTGGACACTCGAGGGGAAATA 59.171 52.381 20.91 0.00 0.00 1.40
296 297 0.613777 GTGGACACTCGAGGGGAAAT 59.386 55.000 20.91 0.00 0.00 2.17
297 298 1.477685 GGTGGACACTCGAGGGGAAA 61.478 60.000 20.91 0.00 0.00 3.13
298 299 1.911766 GGTGGACACTCGAGGGGAA 60.912 63.158 20.91 0.21 0.00 3.97
299 300 1.503401 TAGGTGGACACTCGAGGGGA 61.503 60.000 20.91 0.00 0.00 4.81
300 301 0.397254 ATAGGTGGACACTCGAGGGG 60.397 60.000 20.91 12.20 0.00 4.79
301 302 2.359981 TATAGGTGGACACTCGAGGG 57.640 55.000 14.61 14.61 0.00 4.30
439 444 1.273455 CTTGCGTGCTTGCTTGCTTC 61.273 55.000 9.97 0.00 35.36 3.86
559 565 1.661463 TCTCCAGTGGCCAGAAAGAT 58.339 50.000 5.11 0.00 0.00 2.40
560 566 1.556911 GATCTCCAGTGGCCAGAAAGA 59.443 52.381 5.11 7.67 0.00 2.52
804 839 1.153289 CCAGGAGGACGGAAGCATG 60.153 63.158 0.00 0.00 36.89 4.06
1028 1092 4.821589 GCTCGGAGGCGTTGGAGG 62.822 72.222 7.20 0.00 0.00 4.30
1595 1675 3.957591 ATTTTACCATGCATGCACACA 57.042 38.095 25.37 5.72 0.00 3.72
1596 1676 4.142859 CCAAATTTTACCATGCATGCACAC 60.143 41.667 25.37 0.00 0.00 3.82
1897 2042 4.458989 GTCCAGCAACTTGTAATCCATGAA 59.541 41.667 0.00 0.00 0.00 2.57
2245 4976 5.513233 TCAGGGAGTAACTTACTTATCCGT 58.487 41.667 2.91 0.13 39.59 4.69
2467 5199 4.653341 AGGCTACAGTGATGATAGAAAGCT 59.347 41.667 0.00 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.