Multiple sequence alignment - TraesCS4B01G205900

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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 TraesCS4B01G205900 chr4B 100.000 4894 0 0 1 4894 438333714 438338607 0.000000e+00 9038
1 TraesCS4B01G205900 chr4B 99.231 130 1 0 4224 4353 120175041 120175170 8.190000e-58 235
2 TraesCS4B01G205900 chr4B 95.205 146 4 3 4223 4366 105342316 105342460 1.370000e-55 228
3 TraesCS4B01G205900 chr4D 97.017 3587 86 8 649 4223 354821325 354824902 0.000000e+00 6011
4 TraesCS4B01G205900 chr4D 95.238 546 14 8 4352 4894 354824906 354825442 0.000000e+00 854
5 TraesCS4B01G205900 chr4D 97.037 270 8 0 56 325 354813991 354814260 5.770000e-124 455
6 TraesCS4B01G205900 chr4D 88.013 317 11 6 321 634 354821051 354821343 2.800000e-92 350
7 TraesCS4B01G205900 chr4A 92.466 1845 110 9 2401 4228 109934933 109933101 0.000000e+00 2610
8 TraesCS4B01G205900 chr4A 94.173 532 21 5 4363 4890 109933092 109932567 0.000000e+00 802
9 TraesCS4B01G205900 chr4A 90.664 557 38 8 1226 1780 109936780 109936236 0.000000e+00 728
10 TraesCS4B01G205900 chr4A 91.992 487 30 3 1791 2268 109936126 109935640 0.000000e+00 675
11 TraesCS4B01G205900 chr4A 89.564 527 17 5 685 1201 109937259 109936761 6.910000e-178 634
12 TraesCS4B01G205900 chr4A 82.852 519 70 15 56 561 109937833 109937321 9.660000e-122 448
13 TraesCS4B01G205900 chr4A 95.070 142 6 1 4224 4365 567877959 567878099 6.380000e-54 222
14 TraesCS4B01G205900 chr5D 99.237 131 1 0 4227 4357 223020788 223020658 2.280000e-58 237
15 TraesCS4B01G205900 chr5D 94.737 95 5 0 998 1092 46040059 46040153 1.100000e-31 148
16 TraesCS4B01G205900 chr1B 96.479 142 5 0 4224 4365 369256130 369255989 8.190000e-58 235
17 TraesCS4B01G205900 chr5A 97.059 136 4 0 4220 4355 145678334 145678469 3.810000e-56 230
18 TraesCS4B01G205900 chr5A 95.789 95 4 0 998 1092 37055880 37055974 2.360000e-33 154
19 TraesCS4B01G205900 chr3A 97.744 133 3 0 4224 4356 681617766 681617898 3.810000e-56 230
20 TraesCS4B01G205900 chr3B 96.403 139 4 1 4218 4355 53574023 53573885 1.370000e-55 228
21 TraesCS4B01G205900 chr1A 95.070 142 6 1 4224 4365 487800125 487799985 6.380000e-54 222
22 TraesCS4B01G205900 chr1A 94.737 95 5 0 998 1092 455031221 455031315 1.100000e-31 148
23 TraesCS4B01G205900 chr5B 95.000 100 4 1 998 1096 47108777 47108876 6.560000e-34 156


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 TraesCS4B01G205900 chr4B 438333714 438338607 4893 False 9038.000000 9038 100.000000 1 4894 1 chr4B.!!$F3 4893
1 TraesCS4B01G205900 chr4D 354821051 354825442 4391 False 2405.000000 6011 93.422667 321 4894 3 chr4D.!!$F2 4573
2 TraesCS4B01G205900 chr4A 109932567 109937833 5266 True 982.833333 2610 90.285167 56 4890 6 chr4A.!!$R1 4834

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
749 779 0.321741 AGAGAGAACGACGGAGAGCA 60.322 55.0 0.00 0.00 0.00 4.26 F
1172 1212 0.958091 CCAATTGTTCACGAAGGGCA 59.042 50.0 4.43 0.00 0.00 5.36 F
1996 2136 1.038280 AAGTCACGACGAGGGAACTT 58.962 50.0 0.00 0.00 44.43 2.66 F
3451 4179 0.867753 CCGAGATCGAGCTGAAACCG 60.868 60.0 8.50 4.61 43.02 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1624 1665 1.546923 TGGCCATCATGAACTGCAAAG 59.453 47.619 0.0 0.0 0.00 2.77 R
2102 2251 1.787012 GCTGACCCAAGCAAACATTG 58.213 50.000 0.0 0.0 43.01 2.82 R
3848 4576 0.328926 TGGCAGCATTCAGATCCACA 59.671 50.000 0.0 0.0 0.00 4.17 R
4358 5101 0.326927 TCCAAATCTCGAACCCCCAC 59.673 55.000 0.0 0.0 0.00 4.61 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
21 22 4.569719 CATAACTACTCCACAAACCCCT 57.430 45.455 0.00 0.00 0.00 4.79
22 23 4.514401 CATAACTACTCCACAAACCCCTC 58.486 47.826 0.00 0.00 0.00 4.30
23 24 2.112279 ACTACTCCACAAACCCCTCA 57.888 50.000 0.00 0.00 0.00 3.86
24 25 2.414612 ACTACTCCACAAACCCCTCAA 58.585 47.619 0.00 0.00 0.00 3.02
25 26 2.781174 ACTACTCCACAAACCCCTCAAA 59.219 45.455 0.00 0.00 0.00 2.69
26 27 2.838637 ACTCCACAAACCCCTCAAAA 57.161 45.000 0.00 0.00 0.00 2.44
27 28 3.108847 ACTCCACAAACCCCTCAAAAA 57.891 42.857 0.00 0.00 0.00 1.94
63 64 5.105716 CCACAAGGGATATACAGTATCCTCG 60.106 48.000 12.43 5.63 42.34 4.63
141 142 5.358922 TGGTTTTCATTGGCTTTCTTTCAG 58.641 37.500 0.00 0.00 0.00 3.02
151 152 6.530019 TGGCTTTCTTTCAGTTTTCTTTCT 57.470 33.333 0.00 0.00 0.00 2.52
186 188 9.971922 ATTCTCTGTTTTGTTTATTCTTTCCAG 57.028 29.630 0.00 0.00 0.00 3.86
228 230 7.524717 ACCTAAATTACTCATGCAACACTTT 57.475 32.000 0.00 0.00 0.00 2.66
229 231 7.593825 ACCTAAATTACTCATGCAACACTTTC 58.406 34.615 0.00 0.00 0.00 2.62
245 247 9.543018 GCAACACTTTCTGTATATAGTTTGAAC 57.457 33.333 0.00 0.00 30.51 3.18
295 297 6.806249 TCTCCAAATGCACGTTGAATAATTTC 59.194 34.615 12.45 0.00 0.00 2.17
481 507 6.478512 AAACTTCTTCTTAAATGGGCACAA 57.521 33.333 0.00 0.00 0.00 3.33
562 592 7.647715 ACCTTTTTAAGACATGTGAACATTTCG 59.352 33.333 1.15 0.00 37.92 3.46
582 612 5.753713 TCGTTTGTGTTGTGAACATTTTG 57.246 34.783 0.00 0.00 44.35 2.44
749 779 0.321741 AGAGAGAACGACGGAGAGCA 60.322 55.000 0.00 0.00 0.00 4.26
1122 1162 4.780815 TCCCTTCTGATTTTGCGTATCAT 58.219 39.130 0.00 0.00 32.00 2.45
1172 1212 0.958091 CCAATTGTTCACGAAGGGCA 59.042 50.000 4.43 0.00 0.00 5.36
1183 1223 5.092554 TCACGAAGGGCAACATTATCTTA 57.907 39.130 0.00 0.00 43.25 2.10
1211 1251 9.468532 GCTATCATTTCTCTTTTGACAAAAGTT 57.531 29.630 30.36 14.75 46.18 2.66
1336 1376 1.987807 ATCTGGCCAAGGTGCGCTAT 61.988 55.000 7.01 0.00 0.00 2.97
1498 1538 4.314440 GGCAGCGACACCACTCCA 62.314 66.667 0.00 0.00 0.00 3.86
1501 1541 1.367471 CAGCGACACCACTCCAGAA 59.633 57.895 0.00 0.00 0.00 3.02
1559 1599 2.660064 CCCAAGGTCTGTAGGCGCT 61.660 63.158 7.64 0.00 0.00 5.92
1574 1615 1.871039 GGCGCTTGTAAACTCAGTTCA 59.129 47.619 7.64 0.00 0.00 3.18
1596 1637 3.281727 TTGTCTTTCCTGTGCTTCTGT 57.718 42.857 0.00 0.00 0.00 3.41
1605 1646 2.413239 CCTGTGCTTCTGTTGTTATGCG 60.413 50.000 0.00 0.00 0.00 4.73
1664 1705 2.258013 CGGTGCATTGGTCCGTGTT 61.258 57.895 4.61 0.00 39.51 3.32
1724 1765 2.792290 CGTCGATGGCAGCTTCGTG 61.792 63.158 15.02 7.94 36.74 4.35
1756 1797 5.548056 ACGGGAAGGTATGGATCTGATATTT 59.452 40.000 0.00 0.00 0.00 1.40
1996 2136 1.038280 AAGTCACGACGAGGGAACTT 58.962 50.000 0.00 0.00 44.43 2.66
2024 2164 4.496673 CGTAAGTTGCTTTGGCTTGTGTTA 60.497 41.667 0.00 0.00 39.59 2.41
2102 2251 4.156008 ACCATTTCCTAATGCAAAGTCGAC 59.844 41.667 7.70 7.70 39.87 4.20
2116 2265 1.608590 AGTCGACAATGTTTGCTTGGG 59.391 47.619 19.50 0.00 0.00 4.12
2209 2358 1.339610 ACTATCTCGATGAGCCTGCAC 59.660 52.381 0.00 0.00 0.00 4.57
2645 3369 1.202952 TGACCACGCCAATTTACCCTT 60.203 47.619 0.00 0.00 0.00 3.95
2656 3380 7.558444 ACGCCAATTTACCCTTAATTGATAGAA 59.442 33.333 9.26 0.00 42.72 2.10
2934 3662 2.319472 GCGAAATGCAAGAAGGTTGTC 58.681 47.619 0.00 0.00 45.45 3.18
3019 3747 3.877559 TCAGATTCAGGCTTGTGGTATG 58.122 45.455 0.00 0.00 0.00 2.39
3280 4008 7.090173 TGGTTTTAGCTGTTATGATTGCTTTC 58.910 34.615 0.00 0.00 37.02 2.62
3358 4086 1.134640 TGCAGGTACGTGTTCTGTTGT 60.135 47.619 16.36 0.00 0.00 3.32
3451 4179 0.867753 CCGAGATCGAGCTGAAACCG 60.868 60.000 8.50 4.61 43.02 4.44
3617 4345 5.240623 TGCAGGATTGTTCTTAATTCGTTGT 59.759 36.000 0.00 0.00 0.00 3.32
3848 4576 5.075493 ACAATGCAGGAACTTGATCTTTCT 58.925 37.500 4.06 0.00 34.60 2.52
4022 4751 6.884295 TCCATTTGTCCTTCCTATACAAAGTG 59.116 38.462 0.00 0.00 43.92 3.16
4023 4752 6.659242 CCATTTGTCCTTCCTATACAAAGTGT 59.341 38.462 0.00 0.00 43.92 3.55
4089 4828 0.317160 TAGCGTGAACCTGTGAGTGG 59.683 55.000 0.00 0.00 0.00 4.00
4191 4931 3.860930 AAAACATCGCCGTGGCCCT 62.861 57.895 5.08 0.00 37.98 5.19
4228 4971 1.199558 GGGCACGACTCTCGGATATAC 59.800 57.143 0.00 0.00 45.59 1.47
4229 4972 2.152830 GGCACGACTCTCGGATATACT 58.847 52.381 0.00 0.00 45.59 2.12
4230 4973 2.160022 GGCACGACTCTCGGATATACTC 59.840 54.545 0.00 0.00 45.59 2.59
4231 4974 2.160022 GCACGACTCTCGGATATACTCC 59.840 54.545 0.00 0.00 45.59 3.85
4232 4975 2.743126 CACGACTCTCGGATATACTCCC 59.257 54.545 0.00 0.00 45.59 4.30
4233 4976 2.638855 ACGACTCTCGGATATACTCCCT 59.361 50.000 0.00 0.00 45.59 4.20
4234 4977 3.264104 CGACTCTCGGATATACTCCCTC 58.736 54.545 0.00 0.00 41.49 4.30
4235 4978 3.613030 GACTCTCGGATATACTCCCTCC 58.387 54.545 0.00 0.00 41.49 4.30
4240 4983 1.817447 CGGATATACTCCCTCCGTTCC 59.183 57.143 3.95 0.00 45.30 3.62
4241 4984 1.817447 GGATATACTCCCTCCGTTCCG 59.183 57.143 0.00 0.00 38.19 4.30
4242 4985 2.553904 GGATATACTCCCTCCGTTCCGA 60.554 54.545 0.00 0.00 38.19 4.55
4243 4986 2.734755 TATACTCCCTCCGTTCCGAA 57.265 50.000 0.00 0.00 0.00 4.30
4244 4987 2.083628 ATACTCCCTCCGTTCCGAAT 57.916 50.000 0.00 0.00 0.00 3.34
4245 4988 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
4246 4989 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
4247 4990 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
4248 4991 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
4249 4992 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
4250 4993 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
4251 4994 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
4252 4995 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
4253 4996 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
4254 4997 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
4255 4998 3.991773 TCCGTTCCGAATTACTTGTCTTG 59.008 43.478 0.00 0.00 0.00 3.02
4256 4999 3.124636 CCGTTCCGAATTACTTGTCTTGG 59.875 47.826 0.00 0.00 0.00 3.61
4257 5000 3.991773 CGTTCCGAATTACTTGTCTTGGA 59.008 43.478 0.00 0.00 0.00 3.53
4258 5001 4.630069 CGTTCCGAATTACTTGTCTTGGAT 59.370 41.667 0.00 0.00 0.00 3.41
4259 5002 5.121768 CGTTCCGAATTACTTGTCTTGGATT 59.878 40.000 0.00 0.00 0.00 3.01
4260 5003 6.348213 CGTTCCGAATTACTTGTCTTGGATTT 60.348 38.462 0.00 0.00 0.00 2.17
4261 5004 6.494893 TCCGAATTACTTGTCTTGGATTTG 57.505 37.500 0.00 0.00 0.00 2.32
4262 5005 6.001460 TCCGAATTACTTGTCTTGGATTTGT 58.999 36.000 0.00 0.00 0.00 2.83
4263 5006 6.148811 TCCGAATTACTTGTCTTGGATTTGTC 59.851 38.462 0.00 0.00 0.00 3.18
4264 5007 6.149474 CCGAATTACTTGTCTTGGATTTGTCT 59.851 38.462 0.00 0.00 0.00 3.41
4265 5008 7.333423 CCGAATTACTTGTCTTGGATTTGTCTA 59.667 37.037 0.00 0.00 0.00 2.59
4266 5009 8.383619 CGAATTACTTGTCTTGGATTTGTCTAG 58.616 37.037 0.00 0.00 0.00 2.43
4267 5010 9.436957 GAATTACTTGTCTTGGATTTGTCTAGA 57.563 33.333 0.00 0.00 0.00 2.43
4268 5011 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
4270 5013 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
4271 5014 7.036220 ACTTGTCTTGGATTTGTCTAGATACG 58.964 38.462 0.00 0.00 0.00 3.06
4272 5015 5.902681 TGTCTTGGATTTGTCTAGATACGG 58.097 41.667 0.00 0.00 0.00 4.02
4273 5016 5.655090 TGTCTTGGATTTGTCTAGATACGGA 59.345 40.000 0.00 0.00 0.00 4.69
4274 5017 6.323996 TGTCTTGGATTTGTCTAGATACGGAT 59.676 38.462 0.00 0.00 0.00 4.18
4275 5018 6.642950 GTCTTGGATTTGTCTAGATACGGATG 59.357 42.308 0.00 0.00 0.00 3.51
4276 5019 6.323996 TCTTGGATTTGTCTAGATACGGATGT 59.676 38.462 0.00 0.00 0.00 3.06
4277 5020 7.504574 TCTTGGATTTGTCTAGATACGGATGTA 59.495 37.037 0.00 0.00 34.45 2.29
4278 5021 7.776618 TGGATTTGTCTAGATACGGATGTAT 57.223 36.000 0.00 0.00 43.97 2.29
4292 5035 8.988064 ATACGGATGTATCTAGCACTAAAATG 57.012 34.615 0.00 0.00 36.56 2.32
4293 5036 7.050970 ACGGATGTATCTAGCACTAAAATGA 57.949 36.000 0.00 0.00 0.00 2.57
4294 5037 7.148641 ACGGATGTATCTAGCACTAAAATGAG 58.851 38.462 0.00 0.00 0.00 2.90
4295 5038 7.148641 CGGATGTATCTAGCACTAAAATGAGT 58.851 38.462 0.00 0.00 0.00 3.41
4296 5039 7.327275 CGGATGTATCTAGCACTAAAATGAGTC 59.673 40.741 0.00 0.00 0.00 3.36
4297 5040 8.364142 GGATGTATCTAGCACTAAAATGAGTCT 58.636 37.037 0.00 0.00 0.00 3.24
4300 5043 9.628500 TGTATCTAGCACTAAAATGAGTCTAGA 57.372 33.333 11.59 11.59 38.76 2.43
4304 5047 9.628500 TCTAGCACTAAAATGAGTCTAGATACA 57.372 33.333 0.00 0.00 34.65 2.29
4307 5050 8.364142 AGCACTAAAATGAGTCTAGATACATCC 58.636 37.037 12.66 0.00 0.00 3.51
4308 5051 7.327275 GCACTAAAATGAGTCTAGATACATCCG 59.673 40.741 12.66 6.68 0.00 4.18
4309 5052 8.353684 CACTAAAATGAGTCTAGATACATCCGT 58.646 37.037 12.66 7.10 0.00 4.69
4310 5053 9.570468 ACTAAAATGAGTCTAGATACATCCGTA 57.430 33.333 12.66 6.93 0.00 4.02
4327 5070 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
4328 5071 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
4329 5072 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
4330 5073 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
4331 5074 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
4332 5075 8.407064 CCGTATCTAGACAAATCTAAGACAAGT 58.593 37.037 0.00 0.00 36.98 3.16
4339 5082 8.480643 AGACAAATCTAAGACAAGTAATTCGG 57.519 34.615 0.00 0.00 31.46 4.30
4340 5083 8.311836 AGACAAATCTAAGACAAGTAATTCGGA 58.688 33.333 0.00 0.00 31.46 4.55
4341 5084 8.842358 ACAAATCTAAGACAAGTAATTCGGAA 57.158 30.769 0.00 0.00 0.00 4.30
4342 5085 8.718734 ACAAATCTAAGACAAGTAATTCGGAAC 58.281 33.333 0.00 0.00 0.00 3.62
4360 5103 5.388408 GGAACGGAGGGAGTATAATAGTG 57.612 47.826 0.00 0.00 0.00 2.74
4397 5140 6.825944 TGGACAGAGAGAATAGATATTCCG 57.174 41.667 8.61 0.00 42.29 4.30
4632 5377 7.361799 CCATAGTGGTTAACTAAAACTTGCCTC 60.362 40.741 5.42 0.00 44.57 4.70
4655 5400 2.834638 AACTGCTTTATCCAGGCCAT 57.165 45.000 5.01 0.00 34.65 4.40
4679 5424 4.778143 AACGGCGTGGGCTCCATC 62.778 66.667 15.70 0.00 39.81 3.51
4681 5426 4.552365 CGGCGTGGGCTCCATCAT 62.552 66.667 0.00 0.00 39.81 2.45
4875 5622 5.253330 AGCAGATATCCTTTTTCGTTGGAA 58.747 37.500 0.00 0.00 33.20 3.53
4884 5631 5.828859 TCCTTTTTCGTTGGAACCAATCTAA 59.171 36.000 9.53 2.60 38.28 2.10
4886 5633 7.014808 TCCTTTTTCGTTGGAACCAATCTAATT 59.985 33.333 9.53 0.00 38.28 1.40
4887 5634 8.301002 CCTTTTTCGTTGGAACCAATCTAATTA 58.699 33.333 9.53 0.00 38.28 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.019681 TGAGGGGTTTGTGGAGTAGTTATG 60.020 45.833 0.00 0.00 0.00 1.90
1 2 4.172807 TGAGGGGTTTGTGGAGTAGTTAT 58.827 43.478 0.00 0.00 0.00 1.89
2 3 3.589641 TGAGGGGTTTGTGGAGTAGTTA 58.410 45.455 0.00 0.00 0.00 2.24
3 4 2.414612 TGAGGGGTTTGTGGAGTAGTT 58.585 47.619 0.00 0.00 0.00 2.24
4 5 2.112279 TGAGGGGTTTGTGGAGTAGT 57.888 50.000 0.00 0.00 0.00 2.73
5 6 3.502123 TTTGAGGGGTTTGTGGAGTAG 57.498 47.619 0.00 0.00 0.00 2.57
6 7 3.955524 TTTTGAGGGGTTTGTGGAGTA 57.044 42.857 0.00 0.00 0.00 2.59
7 8 2.838637 TTTTGAGGGGTTTGTGGAGT 57.161 45.000 0.00 0.00 0.00 3.85
95 96 0.179073 CAGAATGTCCGGCCCACTAG 60.179 60.000 0.00 0.00 0.00 2.57
107 108 5.786311 CCAATGAAAACCATCACAGAATGT 58.214 37.500 0.00 0.00 42.96 2.71
205 207 7.752239 CAGAAAGTGTTGCATGAGTAATTTAGG 59.248 37.037 0.00 0.00 0.00 2.69
215 217 9.448438 AAACTATATACAGAAAGTGTTGCATGA 57.552 29.630 0.00 0.00 40.94 3.07
219 221 9.543018 GTTCAAACTATATACAGAAAGTGTTGC 57.457 33.333 0.00 0.00 40.94 4.17
258 260 7.064847 ACGTGCATTTGGAGAATATTTAACGTA 59.935 33.333 0.00 0.00 36.39 3.57
261 263 7.753132 TCAACGTGCATTTGGAGAATATTTAAC 59.247 33.333 10.24 0.00 0.00 2.01
266 268 5.895636 TTCAACGTGCATTTGGAGAATAT 57.104 34.783 10.24 0.00 0.00 1.28
271 273 6.034898 GGAAATTATTCAACGTGCATTTGGAG 59.965 38.462 10.24 0.00 37.29 3.86
273 275 5.063312 GGGAAATTATTCAACGTGCATTTGG 59.937 40.000 10.24 0.00 37.29 3.28
357 359 8.454570 AAAGGTCATGCAATTTTTGAGAAATT 57.545 26.923 0.00 0.00 0.00 1.82
464 490 4.255833 TGCTTTGTGCCCATTTAAGAAG 57.744 40.909 0.00 0.00 42.00 2.85
530 559 9.191995 GTTCACATGTCTTAAAAAGGTAAATGG 57.808 33.333 0.00 0.00 0.00 3.16
562 592 7.472798 CGTTAACAAAATGTTCACAACACAAAC 59.527 33.333 6.39 0.00 45.50 2.93
653 683 9.052759 GCTCCCTTTTCATCGTATATTTCTAAA 57.947 33.333 0.00 0.00 0.00 1.85
654 684 7.384115 CGCTCCCTTTTCATCGTATATTTCTAA 59.616 37.037 0.00 0.00 0.00 2.10
655 685 6.866770 CGCTCCCTTTTCATCGTATATTTCTA 59.133 38.462 0.00 0.00 0.00 2.10
1122 1162 2.874014 TCCAGCAACATTTCCATGTGA 58.126 42.857 0.00 0.00 43.34 3.58
1208 1248 5.355350 GGCTTCAGAGTTATGCATTGTAACT 59.645 40.000 12.15 12.15 43.17 2.24
1211 1251 4.842574 TGGCTTCAGAGTTATGCATTGTA 58.157 39.130 3.54 0.00 0.00 2.41
1344 1384 2.178580 CATATGGTGTTTGCAGGGGTT 58.821 47.619 0.00 0.00 0.00 4.11
1395 1435 7.609532 AGATTCACGAGAATTTTGAGATCCTTT 59.390 33.333 9.51 0.00 44.30 3.11
1396 1436 7.108847 AGATTCACGAGAATTTTGAGATCCTT 58.891 34.615 9.51 0.00 44.30 3.36
1397 1437 6.648192 AGATTCACGAGAATTTTGAGATCCT 58.352 36.000 9.51 0.00 44.30 3.24
1398 1438 6.917217 AGATTCACGAGAATTTTGAGATCC 57.083 37.500 9.51 0.00 44.30 3.36
1404 1444 9.270576 CATAACTGAAGATTCACGAGAATTTTG 57.729 33.333 14.45 5.65 44.30 2.44
1498 1538 3.118112 CCTTGCTGATACCCAGATGTTCT 60.118 47.826 0.00 0.00 45.78 3.01
1501 1541 2.437281 CTCCTTGCTGATACCCAGATGT 59.563 50.000 0.00 0.00 45.78 3.06
1511 1551 3.195610 TCGACATTGTACTCCTTGCTGAT 59.804 43.478 0.00 0.00 0.00 2.90
1559 1599 8.188139 GGAAAGACAAATGAACTGAGTTTACAA 58.812 33.333 0.00 0.00 0.00 2.41
1574 1615 4.210331 ACAGAAGCACAGGAAAGACAAAT 58.790 39.130 0.00 0.00 0.00 2.32
1605 1646 4.823790 AAGTCACATTTTACGGTGAACC 57.176 40.909 0.00 0.00 44.83 3.62
1624 1665 1.546923 TGGCCATCATGAACTGCAAAG 59.453 47.619 0.00 0.00 0.00 2.77
1724 1765 3.004862 CCATACCTTCCCGTTGTTGTAC 58.995 50.000 0.00 0.00 0.00 2.90
1756 1797 5.045668 TGTTTAACAGTAGTATCGCGTCA 57.954 39.130 5.77 0.00 0.00 4.35
1796 1936 8.250332 GCATTACCAAAGAAGGAAATGTGAATA 58.750 33.333 0.00 0.00 0.00 1.75
1996 2136 4.202245 AGCCAAAGCAACTTACGAGATA 57.798 40.909 0.00 0.00 43.56 1.98
2024 2164 6.774170 TGATTATTGAGCAGCAACCAGAATAT 59.226 34.615 0.00 0.00 39.78 1.28
2102 2251 1.787012 GCTGACCCAAGCAAACATTG 58.213 50.000 0.00 0.00 43.01 2.82
2116 2265 3.118261 TCCTCCAGTCCATATTTGCTGAC 60.118 47.826 0.00 0.00 0.00 3.51
2422 3146 5.738909 TCATGTTGTTTGTTTCACCCATTT 58.261 33.333 0.00 0.00 0.00 2.32
2438 3162 5.823209 TTATCTGTCATGGCTTCATGTTG 57.177 39.130 0.00 0.00 46.19 3.33
2460 3184 9.447157 CAAACCCCAATGTATTTATTGTCAAAT 57.553 29.630 0.00 0.00 36.54 2.32
2499 3223 5.679734 ATGTGGCGATCAGATGTTAATTC 57.320 39.130 0.00 0.00 0.00 2.17
2934 3662 2.437281 AGGCAAGTATGAGGGATCACAG 59.563 50.000 0.00 0.00 0.00 3.66
3280 4008 6.064846 ACTAAACAAGACAGCTCATGTTTG 57.935 37.500 15.52 10.04 44.28 2.93
3358 4086 0.847670 CAACGTTGTGAGCGTACGAA 59.152 50.000 21.65 0.00 42.10 3.85
3725 4453 9.463443 AATATTGACGTTTTGAAAGAAAGGAAG 57.537 29.630 0.00 0.00 0.00 3.46
3848 4576 0.328926 TGGCAGCATTCAGATCCACA 59.671 50.000 0.00 0.00 0.00 4.17
3937 4665 5.414360 CCATCTATGAACGAATCGATGGAT 58.586 41.667 10.55 2.72 46.73 3.41
3974 4702 4.095946 AGCCCAAAAGCAAGAAATGGATA 58.904 39.130 0.00 0.00 32.82 2.59
4022 4751 8.668353 TCGACGTATATAAATCCATGGTACTAC 58.332 37.037 12.58 4.80 0.00 2.73
4023 4752 8.791327 TCGACGTATATAAATCCATGGTACTA 57.209 34.615 12.58 1.80 0.00 1.82
4089 4828 5.839621 AGCATAGATGAACAATGCAATTCC 58.160 37.500 8.99 0.00 46.66 3.01
4175 4915 3.385749 CTAGGGCCACGGCGATGTT 62.386 63.158 16.62 0.00 43.06 2.71
4176 4916 3.849951 CTAGGGCCACGGCGATGT 61.850 66.667 16.62 0.00 43.06 3.06
4191 4931 2.021441 TGCCCTTCTTCCCCTTATCCTA 60.021 50.000 0.00 0.00 0.00 2.94
4236 4979 6.496338 AATCCAAGACAAGTAATTCGGAAC 57.504 37.500 0.00 0.00 0.00 3.62
4237 4980 6.488683 ACAAATCCAAGACAAGTAATTCGGAA 59.511 34.615 0.00 0.00 0.00 4.30
4238 4981 6.001460 ACAAATCCAAGACAAGTAATTCGGA 58.999 36.000 0.00 0.00 0.00 4.55
4239 4982 6.149474 AGACAAATCCAAGACAAGTAATTCGG 59.851 38.462 0.00 0.00 0.00 4.30
4240 4983 7.133891 AGACAAATCCAAGACAAGTAATTCG 57.866 36.000 0.00 0.00 0.00 3.34
4241 4984 9.436957 TCTAGACAAATCCAAGACAAGTAATTC 57.563 33.333 0.00 0.00 0.00 2.17
4242 4985 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
4244 4987 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
4245 4988 8.188799 CGTATCTAGACAAATCCAAGACAAGTA 58.811 37.037 0.00 0.00 0.00 2.24
4246 4989 7.036220 CGTATCTAGACAAATCCAAGACAAGT 58.964 38.462 0.00 0.00 0.00 3.16
4247 4990 6.477033 CCGTATCTAGACAAATCCAAGACAAG 59.523 42.308 0.00 0.00 0.00 3.16
4248 4991 6.153851 TCCGTATCTAGACAAATCCAAGACAA 59.846 38.462 0.00 0.00 0.00 3.18
4249 4992 5.655090 TCCGTATCTAGACAAATCCAAGACA 59.345 40.000 0.00 0.00 0.00 3.41
4250 4993 6.145338 TCCGTATCTAGACAAATCCAAGAC 57.855 41.667 0.00 0.00 0.00 3.01
4251 4994 6.323996 ACATCCGTATCTAGACAAATCCAAGA 59.676 38.462 0.00 0.00 0.00 3.02
4252 4995 6.516718 ACATCCGTATCTAGACAAATCCAAG 58.483 40.000 0.00 0.00 0.00 3.61
4253 4996 6.479972 ACATCCGTATCTAGACAAATCCAA 57.520 37.500 0.00 0.00 0.00 3.53
4254 4997 7.776618 ATACATCCGTATCTAGACAAATCCA 57.223 36.000 0.00 0.00 32.66 3.41
4267 5010 8.803235 TCATTTTAGTGCTAGATACATCCGTAT 58.197 33.333 0.00 0.00 41.16 3.06
4268 5011 8.173542 TCATTTTAGTGCTAGATACATCCGTA 57.826 34.615 0.00 0.00 0.00 4.02
4269 5012 7.050970 TCATTTTAGTGCTAGATACATCCGT 57.949 36.000 0.00 0.00 0.00 4.69
4270 5013 7.148641 ACTCATTTTAGTGCTAGATACATCCG 58.851 38.462 0.00 0.00 0.00 4.18
4271 5014 8.364142 AGACTCATTTTAGTGCTAGATACATCC 58.636 37.037 0.00 0.00 0.00 3.51
4274 5017 9.628500 TCTAGACTCATTTTAGTGCTAGATACA 57.372 33.333 0.00 0.00 34.69 2.29
4278 5021 9.628500 TGTATCTAGACTCATTTTAGTGCTAGA 57.372 33.333 0.00 0.00 38.76 2.43
4281 5024 8.364142 GGATGTATCTAGACTCATTTTAGTGCT 58.636 37.037 11.25 0.00 0.00 4.40
4282 5025 7.327275 CGGATGTATCTAGACTCATTTTAGTGC 59.673 40.741 11.25 0.00 0.00 4.40
4283 5026 8.353684 ACGGATGTATCTAGACTCATTTTAGTG 58.646 37.037 11.25 3.85 0.00 2.74
4284 5027 8.466617 ACGGATGTATCTAGACTCATTTTAGT 57.533 34.615 11.25 7.70 0.00 2.24
4301 5044 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
4302 5045 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
4303 5046 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
4304 5047 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
4305 5048 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
4306 5049 8.407064 ACTTGTCTTAGATTTGTCTAGATACGG 58.593 37.037 0.00 0.00 0.00 4.02
4313 5056 9.582431 CCGAATTACTTGTCTTAGATTTGTCTA 57.418 33.333 0.00 0.00 0.00 2.59
4314 5057 8.311836 TCCGAATTACTTGTCTTAGATTTGTCT 58.688 33.333 0.00 0.00 0.00 3.41
4315 5058 8.475331 TCCGAATTACTTGTCTTAGATTTGTC 57.525 34.615 0.00 0.00 0.00 3.18
4316 5059 8.718734 GTTCCGAATTACTTGTCTTAGATTTGT 58.281 33.333 0.00 0.00 0.00 2.83
4317 5060 7.898309 CGTTCCGAATTACTTGTCTTAGATTTG 59.102 37.037 0.00 0.00 0.00 2.32
4318 5061 7.064253 CCGTTCCGAATTACTTGTCTTAGATTT 59.936 37.037 0.00 0.00 0.00 2.17
4319 5062 6.534079 CCGTTCCGAATTACTTGTCTTAGATT 59.466 38.462 0.00 0.00 0.00 2.40
4320 5063 6.040878 CCGTTCCGAATTACTTGTCTTAGAT 58.959 40.000 0.00 0.00 0.00 1.98
4321 5064 5.183713 TCCGTTCCGAATTACTTGTCTTAGA 59.816 40.000 0.00 0.00 0.00 2.10
4322 5065 5.404946 TCCGTTCCGAATTACTTGTCTTAG 58.595 41.667 0.00 0.00 0.00 2.18
4323 5066 5.389859 TCCGTTCCGAATTACTTGTCTTA 57.610 39.130 0.00 0.00 0.00 2.10
4324 5067 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
4325 5068 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
4326 5069 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
4327 5070 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
4328 5071 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
4329 5072 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
4330 5073 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
4331 5074 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
4332 5075 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
4333 5076 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
4334 5077 2.083628 ATACTCCCTCCGTTCCGAAT 57.916 50.000 0.00 0.00 0.00 3.34
4335 5078 2.734755 TATACTCCCTCCGTTCCGAA 57.265 50.000 0.00 0.00 0.00 4.30
4336 5079 2.734755 TTATACTCCCTCCGTTCCGA 57.265 50.000 0.00 0.00 0.00 4.55
4337 5080 4.077822 ACTATTATACTCCCTCCGTTCCG 58.922 47.826 0.00 0.00 0.00 4.30
4338 5081 4.220163 CCACTATTATACTCCCTCCGTTCC 59.780 50.000 0.00 0.00 0.00 3.62
4339 5082 4.220163 CCCACTATTATACTCCCTCCGTTC 59.780 50.000 0.00 0.00 0.00 3.95
4340 5083 4.158015 CCCACTATTATACTCCCTCCGTT 58.842 47.826 0.00 0.00 0.00 4.44
4341 5084 3.501751 CCCCACTATTATACTCCCTCCGT 60.502 52.174 0.00 0.00 0.00 4.69
4342 5085 3.097614 CCCCACTATTATACTCCCTCCG 58.902 54.545 0.00 0.00 0.00 4.63
4343 5086 3.181398 ACCCCCACTATTATACTCCCTCC 60.181 52.174 0.00 0.00 0.00 4.30
4344 5087 4.143406 ACCCCCACTATTATACTCCCTC 57.857 50.000 0.00 0.00 0.00 4.30
4345 5088 4.500452 GAACCCCCACTATTATACTCCCT 58.500 47.826 0.00 0.00 0.00 4.20
4346 5089 3.260128 CGAACCCCCACTATTATACTCCC 59.740 52.174 0.00 0.00 0.00 4.30
4347 5090 4.154942 TCGAACCCCCACTATTATACTCC 58.845 47.826 0.00 0.00 0.00 3.85
4348 5091 5.075493 TCTCGAACCCCCACTATTATACTC 58.925 45.833 0.00 0.00 0.00 2.59
4349 5092 5.070823 TCTCGAACCCCCACTATTATACT 57.929 43.478 0.00 0.00 0.00 2.12
4350 5093 5.997384 ATCTCGAACCCCCACTATTATAC 57.003 43.478 0.00 0.00 0.00 1.47
4351 5094 6.239772 CCAAATCTCGAACCCCCACTATTATA 60.240 42.308 0.00 0.00 0.00 0.98
4352 5095 5.456186 CCAAATCTCGAACCCCCACTATTAT 60.456 44.000 0.00 0.00 0.00 1.28
4353 5096 4.141574 CCAAATCTCGAACCCCCACTATTA 60.142 45.833 0.00 0.00 0.00 0.98
4354 5097 3.371595 CCAAATCTCGAACCCCCACTATT 60.372 47.826 0.00 0.00 0.00 1.73
4355 5098 2.172717 CCAAATCTCGAACCCCCACTAT 59.827 50.000 0.00 0.00 0.00 2.12
4356 5099 1.557832 CCAAATCTCGAACCCCCACTA 59.442 52.381 0.00 0.00 0.00 2.74
4357 5100 0.328258 CCAAATCTCGAACCCCCACT 59.672 55.000 0.00 0.00 0.00 4.00
4358 5101 0.326927 TCCAAATCTCGAACCCCCAC 59.673 55.000 0.00 0.00 0.00 4.61
4359 5102 0.326927 GTCCAAATCTCGAACCCCCA 59.673 55.000 0.00 0.00 0.00 4.96
4360 5103 0.326927 TGTCCAAATCTCGAACCCCC 59.673 55.000 0.00 0.00 0.00 5.40
4397 5140 3.967987 AGGACAATAGGTAGATGGACACC 59.032 47.826 0.00 0.00 34.86 4.16
4543 5286 6.093909 GGCCTGAATTATTTGAAAACCCAATG 59.906 38.462 0.00 0.00 0.00 2.82
4632 5377 3.953612 TGGCCTGGATAAAGCAGTTTATG 59.046 43.478 3.32 0.00 38.70 1.90
4655 5400 1.962306 GCCCACGCCGTTTTCTGTA 60.962 57.895 0.00 0.00 0.00 2.74
4679 5424 8.411683 CCTTTGATCCTTTTCCTTCAATCTATG 58.588 37.037 0.00 0.00 0.00 2.23
4680 5425 8.118600 ACCTTTGATCCTTTTCCTTCAATCTAT 58.881 33.333 0.00 0.00 0.00 1.98
4681 5426 7.470192 ACCTTTGATCCTTTTCCTTCAATCTA 58.530 34.615 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.