Multiple sequence alignment - TraesCS2B01G349200

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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 TraesCS2B01G349200 chr2B 100.000 2510 0 0 1 2510 495953822 495951313 0.000000e+00 4636.0
1 TraesCS2B01G349200 chr2B 82.224 1007 91 36 496 1460 496079252 496078292 0.000000e+00 787.0
2 TraesCS2B01G349200 chr2B 88.283 495 36 12 1046 1530 496087843 496087361 7.790000e-160 573.0
3 TraesCS2B01G349200 chr2B 85.859 495 48 14 1046 1530 496355431 496354949 8.010000e-140 507.0
4 TraesCS2B01G349200 chr2B 85.657 495 49 13 1046 1530 496351117 496350635 3.730000e-138 501.0
5 TraesCS2B01G349200 chr2B 87.715 407 38 7 1052 1449 496542314 496541911 4.890000e-127 464.0
6 TraesCS2B01G349200 chr2B 91.288 264 23 0 2 265 160666580 160666317 6.600000e-96 361.0
7 TraesCS2B01G349200 chr2B 90.943 265 24 0 5 269 164618252 164617988 8.540000e-95 357.0
8 TraesCS2B01G349200 chr2B 90.530 264 24 1 3 265 512346057 512346320 5.140000e-92 348.0
9 TraesCS2B01G349200 chr2B 90.000 260 25 1 7 266 22723176 22723434 4.000000e-88 335.0
10 TraesCS2B01G349200 chrUn 99.886 877 1 0 819 1695 325759926 325760802 0.000000e+00 1615.0
11 TraesCS2B01G349200 chrUn 100.000 635 0 0 1697 2331 471665046 471664412 0.000000e+00 1173.0
12 TraesCS2B01G349200 chrUn 100.000 178 0 0 2333 2510 462537219 462537396 1.860000e-86 329.0
13 TraesCS2B01G349200 chr1A 98.829 854 9 1 1657 2510 516707506 516706654 0.000000e+00 1520.0
14 TraesCS2B01G349200 chr2A 88.072 1333 79 28 285 1580 565323434 565324723 0.000000e+00 1507.0
15 TraesCS2B01G349200 chr2A 86.692 526 45 14 954 1460 565313368 565313887 6.060000e-156 560.0
16 TraesCS2B01G349200 chr2A 87.671 438 36 9 1099 1530 565256258 565256683 6.240000e-136 494.0
17 TraesCS2B01G349200 chr2A 87.081 418 42 7 1052 1460 565234398 565234812 1.760000e-126 462.0
18 TraesCS2B01G349200 chr2A 91.007 278 24 1 1 278 683007972 683008248 8.480000e-100 374.0
19 TraesCS2B01G349200 chr2A 82.463 268 29 9 1272 1530 565270209 565270467 4.200000e-53 219.0
20 TraesCS2B01G349200 chr2A 78.906 128 15 5 444 564 565274380 565274502 2.680000e-10 76.8
21 TraesCS2B01G349200 chr2A 92.683 41 3 0 894 934 565256028 565256068 2.700000e-05 60.2
22 TraesCS2B01G349200 chr2D 86.662 1357 99 35 285 1607 423281085 423279777 0.000000e+00 1428.0
23 TraesCS2B01G349200 chr2D 88.535 471 42 7 1052 1519 423288241 423287780 6.060000e-156 560.0
24 TraesCS2B01G349200 chr2D 89.277 401 37 5 1052 1449 423347736 423347339 4.820000e-137 497.0
25 TraesCS2B01G349200 chr7D 97.222 648 17 1 1625 2272 414423625 414422979 0.000000e+00 1096.0
26 TraesCS2B01G349200 chr7D 96.234 239 9 0 2272 2510 414416015 414415777 2.340000e-105 392.0
27 TraesCS2B01G349200 chr4A 91.729 266 22 0 1 266 728845797 728846062 1.100000e-98 370.0
28 TraesCS2B01G349200 chr3A 92.742 248 18 0 2 249 404715399 404715646 2.370000e-95 359.0
29 TraesCS2B01G349200 chr6B 93.004 243 17 0 7 249 262047882 262047640 3.070000e-94 355.0
30 TraesCS2B01G349200 chr7B 92.653 245 18 0 5 249 304231351 304231595 1.100000e-93 353.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G349200 chr2B 495951313 495953822 2509 True 4636.0 4636 100.000 1 2510 1 chr2B.!!$R3 2509
1 TraesCS2B01G349200 chr2B 496078292 496079252 960 True 787.0 787 82.224 496 1460 1 chr2B.!!$R4 964
2 TraesCS2B01G349200 chr2B 496350635 496355431 4796 True 504.0 507 85.758 1046 1530 2 chr2B.!!$R7 484
3 TraesCS2B01G349200 chrUn 325759926 325760802 876 False 1615.0 1615 99.886 819 1695 1 chrUn.!!$F1 876
4 TraesCS2B01G349200 chrUn 471664412 471665046 634 True 1173.0 1173 100.000 1697 2331 1 chrUn.!!$R1 634
5 TraesCS2B01G349200 chr1A 516706654 516707506 852 True 1520.0 1520 98.829 1657 2510 1 chr1A.!!$R1 853
6 TraesCS2B01G349200 chr2A 565323434 565324723 1289 False 1507.0 1507 88.072 285 1580 1 chr2A.!!$F3 1295
7 TraesCS2B01G349200 chr2A 565313368 565313887 519 False 560.0 560 86.692 954 1460 1 chr2A.!!$F2 506
8 TraesCS2B01G349200 chr2A 565256028 565256683 655 False 277.1 494 90.177 894 1530 2 chr2A.!!$F5 636
9 TraesCS2B01G349200 chr2D 423279777 423281085 1308 True 1428.0 1428 86.662 285 1607 1 chr2D.!!$R1 1322
10 TraesCS2B01G349200 chr7D 414422979 414423625 646 True 1096.0 1096 97.222 1625 2272 1 chr7D.!!$R2 647

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
591 607 0.038343 GCGGCCAATCATTGTGTTGT 60.038 50.0 2.24 0.0 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2384 5722 1.3382 CCCTCCTGTCTTCCTTGTTCG 60.338 57.143 0.0 0.0 0.0 3.95 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
20 21 4.609018 CAGCCCGGCCCGATACTG 62.609 72.222 3.71 5.05 0.00 2.74
54 55 2.554032 GCTTGAGCCTAGTTTTTGAGCA 59.446 45.455 0.00 0.00 34.31 4.26
55 56 3.610349 GCTTGAGCCTAGTTTTTGAGCAC 60.610 47.826 0.00 0.00 34.31 4.40
56 57 2.143122 TGAGCCTAGTTTTTGAGCACG 58.857 47.619 0.00 0.00 0.00 5.34
57 58 2.224185 TGAGCCTAGTTTTTGAGCACGA 60.224 45.455 0.00 0.00 0.00 4.35
58 59 2.806244 GAGCCTAGTTTTTGAGCACGAA 59.194 45.455 0.00 0.00 0.00 3.85
59 60 2.808543 AGCCTAGTTTTTGAGCACGAAG 59.191 45.455 0.00 0.00 0.00 3.79
60 61 2.095718 GCCTAGTTTTTGAGCACGAAGG 60.096 50.000 0.00 0.00 0.00 3.46
63 64 0.660300 GTTTTTGAGCACGAAGGCCG 60.660 55.000 0.00 0.00 45.44 6.13
64 65 1.791103 TTTTTGAGCACGAAGGCCGG 61.791 55.000 0.00 0.00 43.93 6.13
95 96 2.126110 CGGGCCCGTCATTTTTGC 60.126 61.111 36.64 0.00 34.35 3.68
96 97 2.925262 CGGGCCCGTCATTTTTGCA 61.925 57.895 36.64 0.00 34.35 4.08
97 98 1.596408 GGGCCCGTCATTTTTGCAT 59.404 52.632 5.69 0.00 0.00 3.96
99 100 1.610363 GGGCCCGTCATTTTTGCATTT 60.610 47.619 5.69 0.00 0.00 2.32
100 101 2.150390 GGCCCGTCATTTTTGCATTTT 58.850 42.857 0.00 0.00 0.00 1.82
101 102 2.551887 GGCCCGTCATTTTTGCATTTTT 59.448 40.909 0.00 0.00 0.00 1.94
102 103 3.364864 GGCCCGTCATTTTTGCATTTTTC 60.365 43.478 0.00 0.00 0.00 2.29
104 105 4.611130 GCCCGTCATTTTTGCATTTTTCTG 60.611 41.667 0.00 0.00 0.00 3.02
105 106 4.749099 CCCGTCATTTTTGCATTTTTCTGA 59.251 37.500 0.00 0.00 0.00 3.27
108 109 6.357198 CGTCATTTTTGCATTTTTCTGAAGG 58.643 36.000 0.00 0.00 0.00 3.46
109 110 6.018832 CGTCATTTTTGCATTTTTCTGAAGGT 60.019 34.615 0.00 0.00 0.00 3.50
110 111 7.347448 GTCATTTTTGCATTTTTCTGAAGGTC 58.653 34.615 0.00 0.00 0.00 3.85
111 112 5.964887 TTTTTGCATTTTTCTGAAGGTCG 57.035 34.783 0.00 0.00 0.00 4.79
112 113 3.641437 TTGCATTTTTCTGAAGGTCGG 57.359 42.857 0.00 0.00 0.00 4.79
113 114 1.885887 TGCATTTTTCTGAAGGTCGGG 59.114 47.619 0.00 0.00 0.00 5.14
114 115 1.402852 GCATTTTTCTGAAGGTCGGGC 60.403 52.381 0.00 0.00 0.00 6.13
115 116 1.202348 CATTTTTCTGAAGGTCGGGCC 59.798 52.381 0.00 0.00 37.58 5.80
117 118 2.741486 TTTTCTGAAGGTCGGGCCGG 62.741 60.000 27.98 8.04 43.70 6.13
147 148 4.629779 CCCGACGGGCTTTTATGT 57.370 55.556 22.37 0.00 35.35 2.29
149 150 0.675522 CCCGACGGGCTTTTATGTGT 60.676 55.000 22.37 0.00 35.35 3.72
150 151 1.161843 CCGACGGGCTTTTATGTGTT 58.838 50.000 5.81 0.00 0.00 3.32
151 152 1.129811 CCGACGGGCTTTTATGTGTTC 59.870 52.381 5.81 0.00 0.00 3.18
152 153 1.201877 CGACGGGCTTTTATGTGTTCG 60.202 52.381 0.00 0.00 0.00 3.95
153 154 1.129811 GACGGGCTTTTATGTGTTCGG 59.870 52.381 0.00 0.00 0.00 4.30
154 155 0.450184 CGGGCTTTTATGTGTTCGGG 59.550 55.000 0.00 0.00 0.00 5.14
155 156 0.172578 GGGCTTTTATGTGTTCGGGC 59.827 55.000 0.00 0.00 0.00 6.13
156 157 0.172578 GGCTTTTATGTGTTCGGGCC 59.827 55.000 0.00 0.00 0.00 5.80
158 159 0.450184 CTTTTATGTGTTCGGGCCGG 59.550 55.000 27.98 7.65 0.00 6.13
159 160 0.961358 TTTTATGTGTTCGGGCCGGG 60.961 55.000 27.98 0.00 0.00 5.73
160 161 3.980442 TTATGTGTTCGGGCCGGGC 62.980 63.158 27.98 22.00 0.00 6.13
176 177 3.056328 GCTCGGGCCCAGAAACAC 61.056 66.667 24.92 6.27 0.00 3.32
177 178 2.429930 CTCGGGCCCAGAAACACA 59.570 61.111 24.92 0.00 0.00 3.72
180 181 2.991540 GGGCCCAGAAACACAGGC 60.992 66.667 19.95 0.00 44.99 4.85
182 183 3.042560 GCCCAGAAACACAGGCAC 58.957 61.111 0.00 0.00 45.07 5.01
183 184 2.908073 GCCCAGAAACACAGGCACG 61.908 63.158 0.00 0.00 45.07 5.34
185 186 0.606401 CCCAGAAACACAGGCACGAT 60.606 55.000 0.00 0.00 0.00 3.73
186 187 0.518636 CCAGAAACACAGGCACGATG 59.481 55.000 0.00 0.00 0.00 3.84
188 189 1.210155 GAAACACAGGCACGATGGC 59.790 57.895 0.00 0.00 44.10 4.40
234 235 1.439644 TTTTTGTGTCGGGCTTGGC 59.560 52.632 0.00 0.00 0.00 4.52
235 236 1.040339 TTTTTGTGTCGGGCTTGGCT 61.040 50.000 0.00 0.00 0.00 4.75
236 237 0.179015 TTTTGTGTCGGGCTTGGCTA 60.179 50.000 0.00 0.00 0.00 3.93
238 239 2.125106 GTGTCGGGCTTGGCTAGG 60.125 66.667 0.00 0.00 0.00 3.02
251 252 4.835891 CTAGGCCCGACCCGAGGT 62.836 72.222 0.00 0.00 40.58 3.85
252 253 4.387343 TAGGCCCGACCCGAGGTT 62.387 66.667 0.00 0.00 40.58 3.50
253 254 3.910784 TAGGCCCGACCCGAGGTTT 62.911 63.158 0.00 0.00 40.58 3.27
259 260 2.359975 GACCCGAGGTTTGGCCAG 60.360 66.667 5.11 0.00 40.61 4.85
260 261 3.920093 GACCCGAGGTTTGGCCAGG 62.920 68.421 5.11 4.14 40.61 4.45
261 262 3.966543 CCCGAGGTTTGGCCAGGT 61.967 66.667 5.11 0.00 40.61 4.00
263 264 1.607612 CCGAGGTTTGGCCAGGTAT 59.392 57.895 5.11 0.00 40.61 2.73
264 265 0.834612 CCGAGGTTTGGCCAGGTATA 59.165 55.000 5.11 0.00 40.61 1.47
269 270 1.208776 GGTTTGGCCAGGTATACTCGT 59.791 52.381 5.11 0.00 37.17 4.18
270 271 2.277084 GTTTGGCCAGGTATACTCGTG 58.723 52.381 5.11 0.00 0.00 4.35
272 273 1.299926 GGCCAGGTATACTCGTGCG 60.300 63.158 0.00 0.00 0.00 5.34
273 274 1.436336 GCCAGGTATACTCGTGCGT 59.564 57.895 2.25 0.00 0.00 5.24
274 275 0.664761 GCCAGGTATACTCGTGCGTA 59.335 55.000 2.25 0.00 0.00 4.42
275 276 1.268899 GCCAGGTATACTCGTGCGTAT 59.731 52.381 2.25 0.00 34.63 3.06
276 277 2.288030 GCCAGGTATACTCGTGCGTATT 60.288 50.000 2.25 0.00 32.63 1.89
280 281 4.675565 CAGGTATACTCGTGCGTATTCAAG 59.324 45.833 2.25 0.00 32.63 3.02
281 282 4.577693 AGGTATACTCGTGCGTATTCAAGA 59.422 41.667 2.25 0.00 32.63 3.02
282 283 5.066893 AGGTATACTCGTGCGTATTCAAGAA 59.933 40.000 2.25 0.00 32.63 2.52
298 299 6.395426 TTCAAGAAAATTGATGAGCAGTGT 57.605 33.333 0.00 0.00 0.00 3.55
304 305 4.978083 AATTGATGAGCAGTGTCATTCC 57.022 40.909 8.85 0.92 37.29 3.01
313 315 4.495422 AGCAGTGTCATTCCTACGTAAAG 58.505 43.478 0.00 0.00 0.00 1.85
336 338 5.293079 AGGTTTTACGTACTTTTTACGCACA 59.707 36.000 0.00 0.00 43.97 4.57
339 341 5.709011 TTACGTACTTTTTACGCACACAA 57.291 34.783 0.00 0.00 43.97 3.33
345 347 3.437395 ACTTTTTACGCACACAACACTCA 59.563 39.130 0.00 0.00 0.00 3.41
350 352 1.009222 GCACACAACACTCAGCAGC 60.009 57.895 0.00 0.00 0.00 5.25
352 354 1.889105 ACACAACACTCAGCAGCGG 60.889 57.895 0.00 0.00 0.00 5.52
353 355 1.595109 CACAACACTCAGCAGCGGA 60.595 57.895 0.00 0.00 0.00 5.54
354 356 0.952497 CACAACACTCAGCAGCGGAT 60.952 55.000 0.00 0.00 0.00 4.18
355 357 0.952497 ACAACACTCAGCAGCGGATG 60.952 55.000 0.00 0.00 0.00 3.51
357 359 2.116983 AACACTCAGCAGCGGATGGT 62.117 55.000 1.43 0.00 41.36 3.55
358 360 1.376424 CACTCAGCAGCGGATGGTT 60.376 57.895 1.43 0.00 37.60 3.67
359 361 0.108186 CACTCAGCAGCGGATGGTTA 60.108 55.000 1.43 0.00 37.60 2.85
374 376 1.626321 TGGTTAGCAAAGATCACGGGA 59.374 47.619 0.00 0.00 0.00 5.14
395 397 6.044682 GGGATGGTTGCAATCTAAAAATCAG 58.955 40.000 11.73 0.00 0.00 2.90
406 408 7.041712 GCAATCTAAAAATCAGCTAGTCCCTAC 60.042 40.741 0.00 0.00 0.00 3.18
554 558 0.379669 CGGTCTACGCCGTTATGTCT 59.620 55.000 0.00 0.00 46.11 3.41
587 603 1.072116 CAACGCGGCCAATCATTGTG 61.072 55.000 12.47 0.00 0.00 3.33
588 604 1.523154 AACGCGGCCAATCATTGTGT 61.523 50.000 12.47 0.00 0.00 3.72
589 605 1.212490 CGCGGCCAATCATTGTGTT 59.788 52.632 2.24 0.00 0.00 3.32
590 606 1.072116 CGCGGCCAATCATTGTGTTG 61.072 55.000 2.24 0.00 0.00 3.33
591 607 0.038343 GCGGCCAATCATTGTGTTGT 60.038 50.000 2.24 0.00 0.00 3.32
592 608 1.700523 CGGCCAATCATTGTGTTGTG 58.299 50.000 2.24 0.00 0.00 3.33
667 684 6.403200 CGTTTACTACATGCATGGCTACTTTT 60.403 38.462 29.41 9.36 0.00 2.27
736 756 3.193614 CTGCTGCTGCTGCTACGG 61.194 66.667 27.67 13.92 40.48 4.02
795 815 3.625897 CTGCTCCCACACCCACGA 61.626 66.667 0.00 0.00 0.00 4.35
2405 5743 0.402121 AACAAGGAAGACAGGAGGGC 59.598 55.000 0.00 0.00 0.00 5.19
2409 5747 2.291043 GGAAGACAGGAGGGCCGAA 61.291 63.158 0.00 0.00 39.96 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.554032 TGCTCAAAAACTAGGCTCAAGC 59.446 45.455 0.00 0.00 41.14 4.01
34 35 3.364366 CGTGCTCAAAAACTAGGCTCAAG 60.364 47.826 0.00 0.00 0.00 3.02
35 36 2.548057 CGTGCTCAAAAACTAGGCTCAA 59.452 45.455 0.00 0.00 0.00 3.02
36 37 2.143122 CGTGCTCAAAAACTAGGCTCA 58.857 47.619 0.00 0.00 0.00 4.26
37 38 2.413837 TCGTGCTCAAAAACTAGGCTC 58.586 47.619 0.00 0.00 0.00 4.70
38 39 2.543777 TCGTGCTCAAAAACTAGGCT 57.456 45.000 0.00 0.00 0.00 4.58
40 41 2.095718 GCCTTCGTGCTCAAAAACTAGG 60.096 50.000 0.00 0.00 0.00 3.02
41 42 2.095718 GGCCTTCGTGCTCAAAAACTAG 60.096 50.000 0.00 0.00 0.00 2.57
42 43 1.877443 GGCCTTCGTGCTCAAAAACTA 59.123 47.619 0.00 0.00 0.00 2.24
43 44 0.668535 GGCCTTCGTGCTCAAAAACT 59.331 50.000 0.00 0.00 0.00 2.66
44 45 0.660300 CGGCCTTCGTGCTCAAAAAC 60.660 55.000 0.00 0.00 0.00 2.43
45 46 1.652012 CGGCCTTCGTGCTCAAAAA 59.348 52.632 0.00 0.00 0.00 1.94
46 47 2.258013 CCGGCCTTCGTGCTCAAAA 61.258 57.895 0.00 0.00 37.11 2.44
47 48 2.668212 CCGGCCTTCGTGCTCAAA 60.668 61.111 0.00 0.00 37.11 2.69
48 49 4.697756 CCCGGCCTTCGTGCTCAA 62.698 66.667 0.00 0.00 37.11 3.02
76 77 2.678580 AAAAATGACGGGCCCGGG 60.679 61.111 44.99 22.37 44.69 5.73
77 78 2.571231 CAAAAATGACGGGCCCGG 59.429 61.111 44.99 28.13 44.69 5.73
78 79 2.126110 GCAAAAATGACGGGCCCG 60.126 61.111 42.17 42.17 46.03 6.13
79 80 0.036483 AATGCAAAAATGACGGGCCC 60.036 50.000 13.57 13.57 0.00 5.80
80 81 1.807139 AAATGCAAAAATGACGGGCC 58.193 45.000 0.00 0.00 0.00 5.80
83 84 5.903764 TCAGAAAAATGCAAAAATGACGG 57.096 34.783 0.00 0.00 0.00 4.79
84 85 6.018832 ACCTTCAGAAAAATGCAAAAATGACG 60.019 34.615 0.00 0.00 0.00 4.35
85 86 7.250445 ACCTTCAGAAAAATGCAAAAATGAC 57.750 32.000 0.00 0.00 0.00 3.06
86 87 6.200665 CGACCTTCAGAAAAATGCAAAAATGA 59.799 34.615 0.00 0.00 0.00 2.57
87 88 6.357198 CGACCTTCAGAAAAATGCAAAAATG 58.643 36.000 0.00 0.00 0.00 2.32
89 90 4.808364 CCGACCTTCAGAAAAATGCAAAAA 59.192 37.500 0.00 0.00 0.00 1.94
90 91 4.367450 CCGACCTTCAGAAAAATGCAAAA 58.633 39.130 0.00 0.00 0.00 2.44
91 92 3.243704 CCCGACCTTCAGAAAAATGCAAA 60.244 43.478 0.00 0.00 0.00 3.68
95 96 1.202348 GGCCCGACCTTCAGAAAAATG 59.798 52.381 0.00 0.00 34.51 2.32
96 97 1.545841 GGCCCGACCTTCAGAAAAAT 58.454 50.000 0.00 0.00 34.51 1.82
97 98 0.887387 CGGCCCGACCTTCAGAAAAA 60.887 55.000 0.00 0.00 35.61 1.94
99 100 2.345991 CGGCCCGACCTTCAGAAA 59.654 61.111 0.00 0.00 35.61 2.52
100 101 3.702048 CCGGCCCGACCTTCAGAA 61.702 66.667 3.71 0.00 35.61 3.02
133 134 1.129811 CCGAACACATAAAAGCCCGTC 59.870 52.381 0.00 0.00 0.00 4.79
135 136 0.450184 CCCGAACACATAAAAGCCCG 59.550 55.000 0.00 0.00 0.00 6.13
137 138 0.172578 GGCCCGAACACATAAAAGCC 59.827 55.000 0.00 0.00 0.00 4.35
138 139 0.179174 CGGCCCGAACACATAAAAGC 60.179 55.000 0.00 0.00 0.00 3.51
141 142 1.377463 CCCGGCCCGAACACATAAA 60.377 57.895 3.71 0.00 0.00 1.40
142 143 2.269562 CCCGGCCCGAACACATAA 59.730 61.111 3.71 0.00 0.00 1.90
143 144 4.476752 GCCCGGCCCGAACACATA 62.477 66.667 3.71 0.00 0.00 2.29
159 160 3.056328 GTGTTTCTGGGCCCGAGC 61.056 66.667 19.37 13.75 38.76 5.03
160 161 1.672356 CTGTGTTTCTGGGCCCGAG 60.672 63.158 19.37 15.85 0.00 4.63
161 162 2.429930 CTGTGTTTCTGGGCCCGA 59.570 61.111 19.37 14.97 0.00 5.14
166 167 0.606401 ATCGTGCCTGTGTTTCTGGG 60.606 55.000 0.00 0.00 35.96 4.45
167 168 0.518636 CATCGTGCCTGTGTTTCTGG 59.481 55.000 0.00 0.00 38.06 3.86
168 169 0.518636 CCATCGTGCCTGTGTTTCTG 59.481 55.000 0.00 0.00 0.00 3.02
170 171 1.210155 GCCATCGTGCCTGTGTTTC 59.790 57.895 0.00 0.00 0.00 2.78
216 217 1.040339 AGCCAAGCCCGACACAAAAA 61.040 50.000 0.00 0.00 0.00 1.94
217 218 0.179015 TAGCCAAGCCCGACACAAAA 60.179 50.000 0.00 0.00 0.00 2.44
218 219 0.605319 CTAGCCAAGCCCGACACAAA 60.605 55.000 0.00 0.00 0.00 2.83
219 220 1.003839 CTAGCCAAGCCCGACACAA 60.004 57.895 0.00 0.00 0.00 3.33
220 221 2.662596 CTAGCCAAGCCCGACACA 59.337 61.111 0.00 0.00 0.00 3.72
221 222 2.125106 CCTAGCCAAGCCCGACAC 60.125 66.667 0.00 0.00 0.00 3.67
222 223 4.096003 GCCTAGCCAAGCCCGACA 62.096 66.667 0.00 0.00 0.00 4.35
234 235 4.835891 ACCTCGGGTCGGGCCTAG 62.836 72.222 0.84 0.00 37.43 3.02
235 236 3.910784 AAACCTCGGGTCGGGCCTA 62.911 63.158 0.84 0.00 33.12 3.93
242 243 2.359975 CTGGCCAAACCTCGGGTC 60.360 66.667 7.01 0.00 40.22 4.46
243 244 3.966543 CCTGGCCAAACCTCGGGT 61.967 66.667 7.01 0.00 40.22 5.28
244 245 1.921869 ATACCTGGCCAAACCTCGGG 61.922 60.000 7.01 4.92 40.22 5.14
245 246 0.834612 TATACCTGGCCAAACCTCGG 59.165 55.000 7.01 5.79 40.22 4.63
247 248 2.483188 CGAGTATACCTGGCCAAACCTC 60.483 54.545 7.01 5.72 40.22 3.85
248 249 1.485066 CGAGTATACCTGGCCAAACCT 59.515 52.381 7.01 0.00 40.22 3.50
249 250 1.208776 ACGAGTATACCTGGCCAAACC 59.791 52.381 7.01 0.00 39.84 3.27
250 251 2.277084 CACGAGTATACCTGGCCAAAC 58.723 52.381 7.01 0.00 0.00 2.93
251 252 1.406341 GCACGAGTATACCTGGCCAAA 60.406 52.381 7.01 0.00 0.00 3.28
252 253 0.177141 GCACGAGTATACCTGGCCAA 59.823 55.000 7.01 0.00 0.00 4.52
253 254 1.820581 GCACGAGTATACCTGGCCA 59.179 57.895 4.71 4.71 0.00 5.36
254 255 1.299926 CGCACGAGTATACCTGGCC 60.300 63.158 0.00 0.00 0.00 5.36
255 256 0.664761 TACGCACGAGTATACCTGGC 59.335 55.000 0.00 0.00 0.00 4.85
257 258 4.219143 TGAATACGCACGAGTATACCTG 57.781 45.455 0.00 0.00 36.39 4.00
259 260 4.852138 TCTTGAATACGCACGAGTATACC 58.148 43.478 0.00 0.00 36.39 2.73
260 261 6.801367 TTTCTTGAATACGCACGAGTATAC 57.199 37.500 0.00 0.00 36.39 1.47
261 262 7.997107 ATTTTCTTGAATACGCACGAGTATA 57.003 32.000 0.00 0.00 36.39 1.47
263 264 6.366604 TCAATTTTCTTGAATACGCACGAGTA 59.633 34.615 0.00 0.00 0.00 2.59
264 265 5.178623 TCAATTTTCTTGAATACGCACGAGT 59.821 36.000 0.00 0.00 0.00 4.18
269 270 6.029607 GCTCATCAATTTTCTTGAATACGCA 58.970 36.000 0.00 0.00 31.55 5.24
270 271 6.029607 TGCTCATCAATTTTCTTGAATACGC 58.970 36.000 0.00 0.00 31.55 4.42
272 273 8.025445 ACACTGCTCATCAATTTTCTTGAATAC 58.975 33.333 0.00 0.00 31.55 1.89
273 274 8.114331 ACACTGCTCATCAATTTTCTTGAATA 57.886 30.769 0.00 0.00 31.55 1.75
274 275 6.989659 ACACTGCTCATCAATTTTCTTGAAT 58.010 32.000 0.00 0.00 31.55 2.57
275 276 6.039605 TGACACTGCTCATCAATTTTCTTGAA 59.960 34.615 0.00 0.00 31.55 2.69
276 277 5.532032 TGACACTGCTCATCAATTTTCTTGA 59.468 36.000 0.00 0.00 0.00 3.02
280 281 5.803967 GGAATGACACTGCTCATCAATTTTC 59.196 40.000 0.00 0.00 30.12 2.29
281 282 5.479375 AGGAATGACACTGCTCATCAATTTT 59.521 36.000 0.00 0.00 30.12 1.82
282 283 5.014858 AGGAATGACACTGCTCATCAATTT 58.985 37.500 0.00 0.00 30.12 1.82
298 299 6.949578 CGTAAAACCTTTACGTAGGAATGA 57.050 37.500 18.78 0.00 41.79 2.57
313 315 5.392297 GTGTGCGTAAAAAGTACGTAAAACC 59.608 40.000 0.00 0.00 42.35 3.27
336 338 0.952497 CATCCGCTGCTGAGTGTTGT 60.952 55.000 0.00 0.00 0.00 3.32
339 341 2.116983 AACCATCCGCTGCTGAGTGT 62.117 55.000 0.00 0.00 0.00 3.55
345 347 0.322456 TTTGCTAACCATCCGCTGCT 60.322 50.000 0.00 0.00 0.00 4.24
350 352 2.285220 CGTGATCTTTGCTAACCATCCG 59.715 50.000 0.00 0.00 0.00 4.18
352 354 2.614057 CCCGTGATCTTTGCTAACCATC 59.386 50.000 0.00 0.00 0.00 3.51
353 355 2.238646 TCCCGTGATCTTTGCTAACCAT 59.761 45.455 0.00 0.00 0.00 3.55
354 356 1.626321 TCCCGTGATCTTTGCTAACCA 59.374 47.619 0.00 0.00 0.00 3.67
355 357 2.396590 TCCCGTGATCTTTGCTAACC 57.603 50.000 0.00 0.00 0.00 2.85
357 359 2.238646 ACCATCCCGTGATCTTTGCTAA 59.761 45.455 0.00 0.00 0.00 3.09
358 360 1.837439 ACCATCCCGTGATCTTTGCTA 59.163 47.619 0.00 0.00 0.00 3.49
359 361 0.620556 ACCATCCCGTGATCTTTGCT 59.379 50.000 0.00 0.00 0.00 3.91
374 376 6.290294 AGCTGATTTTTAGATTGCAACCAT 57.710 33.333 0.00 0.00 0.00 3.55
395 397 1.067071 ACGCAAACTGTAGGGACTAGC 60.067 52.381 0.00 0.00 44.14 3.42
406 408 6.192360 GCTAATGTTATTCCTACGCAAACTG 58.808 40.000 0.00 0.00 0.00 3.16
423 425 5.049612 CAGCTCAATCAATGATCGCTAATGT 60.050 40.000 12.14 0.00 37.44 2.71
547 551 1.519234 CTCGCCGCTGCAGACATAA 60.519 57.895 20.43 0.00 37.32 1.90
587 603 4.158384 CGATCACAAAGGCATTACACAAC 58.842 43.478 0.00 0.00 0.00 3.32
588 604 3.190327 CCGATCACAAAGGCATTACACAA 59.810 43.478 0.00 0.00 0.00 3.33
589 605 2.746904 CCGATCACAAAGGCATTACACA 59.253 45.455 0.00 0.00 0.00 3.72
590 606 3.006940 TCCGATCACAAAGGCATTACAC 58.993 45.455 0.00 0.00 0.00 2.90
591 607 3.055458 TCTCCGATCACAAAGGCATTACA 60.055 43.478 0.00 0.00 0.00 2.41
592 608 3.531538 TCTCCGATCACAAAGGCATTAC 58.468 45.455 0.00 0.00 0.00 1.89
667 684 2.113774 CTGCCCACCAACTGAGCA 59.886 61.111 0.00 0.00 0.00 4.26
732 752 0.030235 CGATCCAACGCAGATCCGTA 59.970 55.000 0.00 0.00 41.16 4.02
734 754 1.951130 CCGATCCAACGCAGATCCG 60.951 63.158 4.81 0.00 37.45 4.18
735 755 0.876342 GACCGATCCAACGCAGATCC 60.876 60.000 4.81 0.00 37.45 3.36
736 756 0.876342 GGACCGATCCAACGCAGATC 60.876 60.000 0.00 0.96 45.47 2.75
795 815 0.250295 ATACACACGCAAGCAGTGGT 60.250 50.000 15.83 13.57 46.91 4.16
2384 5722 1.338200 CCCTCCTGTCTTCCTTGTTCG 60.338 57.143 0.00 0.00 0.00 3.95
2405 5743 3.291101 TTCTTCGGCGTCCCTTCGG 62.291 63.158 6.85 0.00 0.00 4.30
2409 5747 4.083862 GGCTTCTTCGGCGTCCCT 62.084 66.667 6.85 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.