Multiple sequence alignment - TraesCS7D01G123500

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 TraesCS7D01G123500 chr7D 100.000 2498 0 0 1 2498 77128263 77125766 0.000000e+00 4614
1 TraesCS7D01G123500 chr7D 87.383 428 39 10 650 1075 77165529 77165115 6.250000e-131 477
2 TraesCS7D01G123500 chr7D 78.184 738 103 31 825 1539 77170659 77169957 3.840000e-113 418
3 TraesCS7D01G123500 chr7D 86.340 388 38 8 1157 1540 77165068 77164692 2.310000e-110 409
4 TraesCS7D01G123500 chr7D 89.262 149 16 0 131 279 7568423 7568275 1.180000e-43 187
5 TraesCS7D01G123500 chr7D 87.821 156 18 1 119 274 153973915 153974069 5.490000e-42 182
6 TraesCS7D01G123500 chr7D 91.489 94 8 0 2405 2498 552703198 552703105 2.020000e-26 130
7 TraesCS7D01G123500 chr7D 91.489 94 8 0 2405 2498 586465961 586466054 2.020000e-26 130
8 TraesCS7D01G123500 chr1D 95.375 973 33 7 1537 2498 416269754 416270725 0.000000e+00 1537
9 TraesCS7D01G123500 chr1D 91.489 94 8 0 2405 2498 483178959 483179052 2.020000e-26 130
10 TraesCS7D01G123500 chr1B 92.905 888 43 12 1538 2408 680990027 680989143 0.000000e+00 1273
11 TraesCS7D01G123500 chr1B 92.553 94 7 0 2405 2498 69665136 69665229 4.330000e-28 135
12 TraesCS7D01G123500 chr7B 82.234 1486 161 45 4 1445 24053616 24052190 0.000000e+00 1186
13 TraesCS7D01G123500 chr7B 88.608 158 17 1 120 276 747358624 747358781 9.120000e-45 191
14 TraesCS7D01G123500 chr7A 78.929 840 80 45 289 1103 80989316 80988549 4.830000e-132 481
15 TraesCS7D01G123500 chr7A 87.047 386 37 7 1157 1539 80988524 80988149 8.260000e-115 424
16 TraesCS7D01G123500 chr7A 82.380 437 61 11 1106 1539 80992269 80991846 1.410000e-97 366
17 TraesCS7D01G123500 chr7A 87.578 161 18 2 120 279 562174661 562174502 4.240000e-43 185
18 TraesCS7D01G123500 chr6A 87.975 158 18 1 120 276 617751684 617751841 4.240000e-43 185
19 TraesCS7D01G123500 chr3B 87.821 156 18 1 120 274 9646994 9646839 5.490000e-42 182
20 TraesCS7D01G123500 chr6B 87.342 158 18 2 120 276 508532838 508532994 1.970000e-41 180
21 TraesCS7D01G123500 chr4D 87.342 158 19 1 120 276 504283285 504283442 1.970000e-41 180
22 TraesCS7D01G123500 chr2D 86.228 167 22 1 113 279 187528963 187528798 1.970000e-41 180
23 TraesCS7D01G123500 chr2D 91.579 95 8 0 2404 2498 340144044 340144138 5.610000e-27 132
24 TraesCS7D01G123500 chr5D 91.489 94 8 0 2405 2498 147221242 147221149 2.020000e-26 130
25 TraesCS7D01G123500 chr4A 91.579 95 7 1 2404 2498 154078688 154078595 2.020000e-26 130
26 TraesCS7D01G123500 chr1A 91.489 94 8 0 2405 2498 456809659 456809752 2.020000e-26 130


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 TraesCS7D01G123500 chr7D 77125766 77128263 2497 True 4614.000000 4614 100.000000 1 2498 1 chr7D.!!$R2 2497
1 TraesCS7D01G123500 chr7D 77164692 77165529 837 True 443.000000 477 86.861500 650 1540 2 chr7D.!!$R5 890
2 TraesCS7D01G123500 chr7D 77169957 77170659 702 True 418.000000 418 78.184000 825 1539 1 chr7D.!!$R3 714
3 TraesCS7D01G123500 chr1D 416269754 416270725 971 False 1537.000000 1537 95.375000 1537 2498 1 chr1D.!!$F1 961
4 TraesCS7D01G123500 chr1B 680989143 680990027 884 True 1273.000000 1273 92.905000 1538 2408 1 chr1B.!!$R1 870
5 TraesCS7D01G123500 chr7B 24052190 24053616 1426 True 1186.000000 1186 82.234000 4 1445 1 chr7B.!!$R1 1441
6 TraesCS7D01G123500 chr7A 80988149 80992269 4120 True 423.666667 481 82.785333 289 1539 3 chr7A.!!$R2 1250

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
91 93 0.029167 CAATATGAACGCGCATGGCA 59.971 50.0 5.73 0.0 43.84 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1529 4265 0.511221 CGTCGCACCTTTTCGAATGT 59.489 50.0 0.0 0.0 36.41 2.71 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
39 40 7.835634 TGCAATTAACACGTAACTGATATCA 57.164 32.000 5.07 5.07 0.00 2.15
83 85 3.502191 TTTTCTGCCCAATATGAACGC 57.498 42.857 0.00 0.00 0.00 4.84
87 89 1.100463 TGCCCAATATGAACGCGCAT 61.100 50.000 5.73 5.05 0.00 4.73
88 90 0.661187 GCCCAATATGAACGCGCATG 60.661 55.000 5.73 0.00 0.00 4.06
89 91 0.040157 CCCAATATGAACGCGCATGG 60.040 55.000 5.73 1.75 0.00 3.66
91 93 0.029167 CAATATGAACGCGCATGGCA 59.971 50.000 5.73 0.00 43.84 4.92
92 94 0.029300 AATATGAACGCGCATGGCAC 59.971 50.000 5.73 0.00 43.84 5.01
93 95 2.104770 ATATGAACGCGCATGGCACG 62.105 55.000 5.73 0.00 43.84 5.34
116 118 7.480542 CACGTATGCATTTACTAGTTTGGTTTC 59.519 37.037 3.54 0.00 0.00 2.78
118 120 6.909550 ATGCATTTACTAGTTTGGTTTCCA 57.090 33.333 0.00 0.00 0.00 3.53
122 124 8.207545 TGCATTTACTAGTTTGGTTTCCATTTT 58.792 29.630 0.00 0.00 31.53 1.82
123 125 9.051679 GCATTTACTAGTTTGGTTTCCATTTTT 57.948 29.630 0.00 0.00 31.53 1.94
149 151 7.765695 AGGTGAAAGCTTTTGATCTATTCAA 57.234 32.000 14.05 0.00 46.63 2.69
154 156 8.849168 TGAAAGCTTTTGATCTATTCAACTTCA 58.151 29.630 14.05 0.00 43.99 3.02
157 159 9.852091 AAGCTTTTGATCTATTCAACTTCAATC 57.148 29.630 0.00 0.00 43.99 2.67
172 174 9.047371 TCAACTTCAATCATGTTAGTAAAACGA 57.953 29.630 0.00 0.00 0.00 3.85
173 175 9.658475 CAACTTCAATCATGTTAGTAAAACGAA 57.342 29.630 0.00 0.00 0.00 3.85
174 176 9.659830 AACTTCAATCATGTTAGTAAAACGAAC 57.340 29.630 0.00 0.00 34.84 3.95
175 177 8.832521 ACTTCAATCATGTTAGTAAAACGAACA 58.167 29.630 7.94 7.94 45.20 3.18
176 178 8.996988 TTCAATCATGTTAGTAAAACGAACAC 57.003 30.769 7.70 0.00 44.24 3.32
177 179 7.577979 TCAATCATGTTAGTAAAACGAACACC 58.422 34.615 7.70 0.00 44.24 4.16
223 225 1.086067 TCGTAGACCACCTAGCGACG 61.086 60.000 0.00 0.00 31.20 5.12
241 243 0.642291 CGACTACATGCACTGAAGCG 59.358 55.000 0.00 0.00 37.31 4.68
292 294 3.947834 CTCCCTGGCATTTACTAGTTTGG 59.052 47.826 0.00 0.00 0.00 3.28
295 297 4.082245 CCCTGGCATTTACTAGTTTGGTTG 60.082 45.833 0.00 0.00 0.00 3.77
443 3111 7.812191 CCGAATATCTTTTGAAACATCCAAACA 59.188 33.333 0.00 0.00 33.74 2.83
641 3319 2.949644 ACAGGGAAAACCGTGAAGAAAG 59.050 45.455 14.38 0.00 46.96 2.62
642 3320 2.949644 CAGGGAAAACCGTGAAGAAAGT 59.050 45.455 0.00 0.00 46.96 2.66
670 3348 6.546772 ACACAAAAAGGGAAAAGGACGTTATA 59.453 34.615 0.00 0.00 0.00 0.98
672 3350 6.999871 ACAAAAAGGGAAAAGGACGTTATAGA 59.000 34.615 0.00 0.00 0.00 1.98
674 3352 8.354426 CAAAAAGGGAAAAGGACGTTATAGAAA 58.646 33.333 0.00 0.00 0.00 2.52
677 3355 9.743581 AAAGGGAAAAGGACGTTATAGAAATTA 57.256 29.630 0.00 0.00 0.00 1.40
787 3466 4.765813 ACGCCTTATAAATGGGTACAGT 57.234 40.909 0.00 0.00 0.00 3.55
958 3659 7.115520 CCACTAGCGAGATATAAATCAACACAG 59.884 40.741 0.00 0.00 34.28 3.66
959 3660 7.862873 CACTAGCGAGATATAAATCAACACAGA 59.137 37.037 0.00 0.00 34.28 3.41
964 3665 7.096271 GCGAGATATAAATCAACACAGACTGAG 60.096 40.741 10.08 3.49 34.28 3.35
968 3669 4.422073 AAATCAACACAGACTGAGGACA 57.578 40.909 10.08 0.00 0.00 4.02
969 3670 4.422073 AATCAACACAGACTGAGGACAA 57.578 40.909 10.08 0.00 0.00 3.18
971 3672 2.499693 TCAACACAGACTGAGGACAACA 59.500 45.455 10.08 0.00 0.00 3.33
983 3684 2.615912 GAGGACAACATATCTGCTTGCC 59.384 50.000 0.00 0.00 0.00 4.52
998 3710 2.675348 GCTTGCCATCTGAAGACACTAC 59.325 50.000 0.00 0.00 0.00 2.73
1098 3810 3.119884 TCTGCATAGCAAAACAATCACCG 60.120 43.478 0.00 0.00 38.41 4.94
1103 3815 3.904136 AGCAAAACAATCACCGAGAAG 57.096 42.857 0.00 0.00 0.00 2.85
1104 3816 2.030805 AGCAAAACAATCACCGAGAAGC 60.031 45.455 0.00 0.00 0.00 3.86
1110 3844 4.002906 ACAATCACCGAGAAGCTTTACA 57.997 40.909 0.00 0.00 0.00 2.41
1119 3853 5.352569 ACCGAGAAGCTTTACAATCAGATTG 59.647 40.000 19.93 19.93 45.59 2.67
1141 3875 4.962362 TGTCTTTAGATCCATAGAGGCACA 59.038 41.667 0.00 0.00 37.29 4.57
1142 3876 5.425217 TGTCTTTAGATCCATAGAGGCACAA 59.575 40.000 0.00 0.00 37.29 3.33
1143 3877 6.070251 TGTCTTTAGATCCATAGAGGCACAAA 60.070 38.462 0.00 0.00 37.29 2.83
1145 3879 8.150945 GTCTTTAGATCCATAGAGGCACAAATA 58.849 37.037 0.00 0.00 37.29 1.40
1147 3881 8.677148 TTTAGATCCATAGAGGCACAAATAAC 57.323 34.615 0.00 0.00 37.29 1.89
1148 3882 5.625150 AGATCCATAGAGGCACAAATAACC 58.375 41.667 0.00 0.00 37.29 2.85
1149 3883 5.370880 AGATCCATAGAGGCACAAATAACCT 59.629 40.000 0.00 0.00 37.29 3.50
1168 3902 4.461198 ACCTCTTTCCTTTTCATCGTGTT 58.539 39.130 0.00 0.00 0.00 3.32
1181 3915 2.766970 TCGTGTTTTTAAGCAGGCAC 57.233 45.000 0.00 0.00 0.00 5.01
1194 3928 3.052082 GGCACTGCAGCATCGTGT 61.052 61.111 15.27 0.00 35.83 4.49
1200 3934 1.000843 ACTGCAGCATCGTGTAGAACA 59.999 47.619 15.27 0.00 34.50 3.18
1206 3940 3.549471 CAGCATCGTGTAGAACATCAGAC 59.451 47.826 0.00 0.00 0.00 3.51
1257 3993 2.433146 GGGAGGAAGGCCGGAGTAC 61.433 68.421 5.05 0.00 39.96 2.73
1259 3995 0.976590 GGAGGAAGGCCGGAGTACTT 60.977 60.000 5.05 2.76 39.96 2.24
1266 4002 0.735287 GGCCGGAGTACTTCGTGAAC 60.735 60.000 21.82 8.45 0.00 3.18
1267 4003 1.069378 GCCGGAGTACTTCGTGAACG 61.069 60.000 21.82 7.55 41.45 3.95
1270 4006 1.334419 CGGAGTACTTCGTGAACGTGT 60.334 52.381 15.78 6.19 40.80 4.49
1287 4023 1.658409 GTTGAACAACTGCGGCAGC 60.658 57.895 28.80 13.20 45.41 5.25
1292 4028 3.744719 CAACTGCGGCAGCTGCAT 61.745 61.111 37.63 13.17 45.18 3.96
1448 4184 4.506886 AGGTCTTCTTCAACTACGAGTG 57.493 45.455 0.00 0.00 0.00 3.51
1449 4185 3.256136 AGGTCTTCTTCAACTACGAGTGG 59.744 47.826 0.00 0.00 0.00 4.00
1456 4192 3.144657 TCAACTACGAGTGGAGTACCA 57.855 47.619 0.00 0.00 44.76 3.25
1468 4204 4.764050 TGGAGTACCAAGTTCAGTTTCA 57.236 40.909 0.00 0.00 43.91 2.69
1470 4206 4.879545 TGGAGTACCAAGTTCAGTTTCAAC 59.120 41.667 0.00 0.00 43.91 3.18
1488 4224 2.435693 CCCCGTCTCCTCCACCATC 61.436 68.421 0.00 0.00 0.00 3.51
1500 4236 4.280929 TCCTCCACCATCGTATGTTAGATG 59.719 45.833 0.00 0.00 42.71 2.90
1501 4237 4.039245 CCTCCACCATCGTATGTTAGATGT 59.961 45.833 4.98 0.00 41.81 3.06
1502 4238 5.243060 CCTCCACCATCGTATGTTAGATGTA 59.757 44.000 4.98 0.00 41.81 2.29
1503 4239 6.071334 CCTCCACCATCGTATGTTAGATGTAT 60.071 42.308 4.98 0.00 41.81 2.29
1504 4240 7.122204 CCTCCACCATCGTATGTTAGATGTATA 59.878 40.741 4.98 0.00 41.81 1.47
1505 4241 8.411991 TCCACCATCGTATGTTAGATGTATAA 57.588 34.615 4.98 0.00 41.81 0.98
1506 4242 8.862085 TCCACCATCGTATGTTAGATGTATAAA 58.138 33.333 4.98 0.00 41.81 1.40
1507 4243 9.483916 CCACCATCGTATGTTAGATGTATAAAA 57.516 33.333 4.98 0.00 41.81 1.52
1533 4269 8.339344 TGCGAATAAATGATATCATGGACATT 57.661 30.769 18.85 14.23 36.56 2.71
1534 4270 8.453320 TGCGAATAAATGATATCATGGACATTC 58.547 33.333 18.85 19.38 36.56 2.67
1535 4271 7.637519 GCGAATAAATGATATCATGGACATTCG 59.362 37.037 31.02 31.02 40.84 3.34
1551 4287 4.424430 CGAAAAGGTGCGACGGCG 62.424 66.667 6.12 6.12 44.10 6.46
1646 4382 0.250295 AGTCGTTTGCAGGCTTAGCA 60.250 50.000 6.53 0.00 40.85 3.49
1687 4423 4.717629 CGAGCAACAGCGACGGGA 62.718 66.667 0.00 0.00 32.61 5.14
1688 4424 2.811317 GAGCAACAGCGACGGGAG 60.811 66.667 0.00 0.00 0.00 4.30
1689 4425 4.379243 AGCAACAGCGACGGGAGG 62.379 66.667 0.00 0.00 0.00 4.30
1690 4426 4.681978 GCAACAGCGACGGGAGGT 62.682 66.667 0.00 0.00 0.00 3.85
1787 4538 0.174389 AGCAGCACTGATAGGTGACG 59.826 55.000 0.81 0.00 39.34 4.35
1867 4618 1.429148 GCATACTGTGGCGTGTAGGC 61.429 60.000 5.56 5.56 46.95 3.93
2003 4757 5.341617 CAAGCCAAAAGTTACCGTTTTACA 58.658 37.500 0.00 0.00 0.00 2.41
2060 4814 3.746492 GCCCATCTATCGTTGTGGTTATC 59.254 47.826 0.00 0.00 0.00 1.75
2096 4850 1.209621 AATACGGAGGGCAAAGGCTA 58.790 50.000 0.00 0.00 40.87 3.93
2360 5117 2.818274 CGCGGGTCTTGGGCTAAC 60.818 66.667 0.00 0.00 0.00 2.34
2409 5166 3.763897 GTGGTCTGATTGCCATTTTAGGT 59.236 43.478 0.00 0.00 37.09 3.08
2413 5170 3.696051 TCTGATTGCCATTTTAGGTGCTC 59.304 43.478 0.00 0.00 0.00 4.26
2419 5176 2.825532 GCCATTTTAGGTGCTCTTTGGA 59.174 45.455 0.00 0.00 0.00 3.53
2422 5179 4.201950 CCATTTTAGGTGCTCTTTGGATCG 60.202 45.833 0.00 0.00 0.00 3.69
2450 5207 0.107945 TTTGCCAAAGGTTGCCACAC 60.108 50.000 0.00 0.00 0.00 3.82
2451 5208 0.975040 TTGCCAAAGGTTGCCACACT 60.975 50.000 0.00 0.00 0.00 3.55
2461 5218 3.137728 AGGTTGCCACACTTAAGGTTAGT 59.862 43.478 7.53 0.00 0.00 2.24
2462 5219 3.501062 GGTTGCCACACTTAAGGTTAGTC 59.499 47.826 7.53 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 68 1.436195 GCGCGTTCATATTGGGCAGA 61.436 55.000 8.43 0.00 40.80 4.26
91 93 7.361457 GGAAACCAAACTAGTAAATGCATACGT 60.361 37.037 0.00 0.00 0.00 3.57
92 94 6.964934 GGAAACCAAACTAGTAAATGCATACG 59.035 38.462 0.00 0.00 0.00 3.06
93 95 7.822658 TGGAAACCAAACTAGTAAATGCATAC 58.177 34.615 0.00 0.00 0.00 2.39
122 124 9.295825 TGAATAGATCAAAAGCTTTCACCTAAA 57.704 29.630 13.10 0.00 34.30 1.85
123 125 8.862325 TGAATAGATCAAAAGCTTTCACCTAA 57.138 30.769 13.10 0.00 34.30 2.69
124 126 8.862325 TTGAATAGATCAAAAGCTTTCACCTA 57.138 30.769 13.10 11.59 44.94 3.08
149 151 8.832521 TGTTCGTTTTACTAACATGATTGAAGT 58.167 29.630 0.00 0.00 30.26 3.01
154 156 7.442969 TCTGGTGTTCGTTTTACTAACATGATT 59.557 33.333 0.00 0.00 36.42 2.57
156 158 6.282167 TCTGGTGTTCGTTTTACTAACATGA 58.718 36.000 0.00 0.00 36.42 3.07
157 159 6.533819 TCTGGTGTTCGTTTTACTAACATG 57.466 37.500 0.00 0.00 36.42 3.21
198 200 2.688958 GCTAGGTGGTCTACGAATCTGT 59.311 50.000 0.00 0.00 0.00 3.41
199 201 2.287069 CGCTAGGTGGTCTACGAATCTG 60.287 54.545 0.00 0.00 0.00 2.90
209 211 0.376502 GTAGTCGTCGCTAGGTGGTC 59.623 60.000 0.00 0.00 0.00 4.02
210 212 0.321919 TGTAGTCGTCGCTAGGTGGT 60.322 55.000 0.00 0.00 0.00 4.16
212 214 1.860399 GCATGTAGTCGTCGCTAGGTG 60.860 57.143 0.00 0.00 0.00 4.00
223 225 1.996292 TCGCTTCAGTGCATGTAGTC 58.004 50.000 0.00 0.00 0.00 2.59
241 243 3.723348 GTGGCACGCCTTCGGTTC 61.723 66.667 9.92 0.00 40.69 3.62
256 258 2.181021 GGAGTGGCTACGACGGTG 59.819 66.667 0.00 0.00 0.00 4.94
257 259 3.066814 GGGAGTGGCTACGACGGT 61.067 66.667 0.00 0.00 0.00 4.83
258 260 2.754658 AGGGAGTGGCTACGACGG 60.755 66.667 0.00 0.00 0.00 4.79
434 3102 7.727331 TTGCCTTTTAAGAAATGTTTGGATG 57.273 32.000 0.00 0.00 0.00 3.51
608 3285 2.358322 TTCCCTGTTTGTTCCCTGTC 57.642 50.000 0.00 0.00 0.00 3.51
610 3287 2.102420 GGTTTTCCCTGTTTGTTCCCTG 59.898 50.000 0.00 0.00 0.00 4.45
611 3288 2.394632 GGTTTTCCCTGTTTGTTCCCT 58.605 47.619 0.00 0.00 0.00 4.20
612 3289 1.067974 CGGTTTTCCCTGTTTGTTCCC 59.932 52.381 0.00 0.00 36.42 3.97
613 3290 1.752498 ACGGTTTTCCCTGTTTGTTCC 59.248 47.619 0.00 0.00 36.42 3.62
621 3299 2.949644 ACTTTCTTCACGGTTTTCCCTG 59.050 45.455 0.00 0.00 36.42 4.45
623 3301 5.163632 TGTTTACTTTCTTCACGGTTTTCCC 60.164 40.000 0.00 0.00 36.42 3.97
641 3319 5.517411 CGTCCTTTTCCCTTTTTGTGTTTAC 59.483 40.000 0.00 0.00 0.00 2.01
642 3320 5.185442 ACGTCCTTTTCCCTTTTTGTGTTTA 59.815 36.000 0.00 0.00 0.00 2.01
787 3466 9.837681 TGATTGAGATATAAGGTATAACTCCCA 57.162 33.333 0.00 4.15 38.85 4.37
958 3659 4.399004 AGCAGATATGTTGTCCTCAGTC 57.601 45.455 0.00 0.00 0.00 3.51
959 3660 4.511527 CAAGCAGATATGTTGTCCTCAGT 58.488 43.478 0.00 0.00 0.00 3.41
964 3665 2.368439 TGGCAAGCAGATATGTTGTCC 58.632 47.619 5.30 6.84 0.00 4.02
968 3669 4.160642 TCAGATGGCAAGCAGATATGTT 57.839 40.909 0.00 0.00 0.00 2.71
969 3670 3.851458 TCAGATGGCAAGCAGATATGT 57.149 42.857 0.00 0.00 0.00 2.29
971 3672 4.141551 TGTCTTCAGATGGCAAGCAGATAT 60.142 41.667 0.00 0.00 0.00 1.63
983 3684 4.403752 TCTCCATGGTAGTGTCTTCAGATG 59.596 45.833 12.58 0.00 0.00 2.90
998 3710 1.164662 CGCTGGCTTGATCTCCATGG 61.165 60.000 4.97 4.97 0.00 3.66
1119 3853 5.537300 TGTGCCTCTATGGATCTAAAGAC 57.463 43.478 0.00 0.00 38.35 3.01
1123 3857 7.072454 AGGTTATTTGTGCCTCTATGGATCTAA 59.928 37.037 0.00 0.00 38.35 2.10
1127 3861 5.625150 GAGGTTATTTGTGCCTCTATGGAT 58.375 41.667 0.00 0.00 43.93 3.41
1134 3868 4.336280 AGGAAAGAGGTTATTTGTGCCTC 58.664 43.478 0.00 0.00 46.75 4.70
1141 3875 7.230712 ACACGATGAAAAGGAAAGAGGTTATTT 59.769 33.333 0.00 0.00 0.00 1.40
1142 3876 6.715264 ACACGATGAAAAGGAAAGAGGTTATT 59.285 34.615 0.00 0.00 0.00 1.40
1143 3877 6.238648 ACACGATGAAAAGGAAAGAGGTTAT 58.761 36.000 0.00 0.00 0.00 1.89
1145 3879 4.461198 ACACGATGAAAAGGAAAGAGGTT 58.539 39.130 0.00 0.00 0.00 3.50
1147 3881 5.438761 AAACACGATGAAAAGGAAAGAGG 57.561 39.130 0.00 0.00 0.00 3.69
1148 3882 8.850454 TTAAAAACACGATGAAAAGGAAAGAG 57.150 30.769 0.00 0.00 0.00 2.85
1149 3883 7.434013 GCTTAAAAACACGATGAAAAGGAAAGA 59.566 33.333 0.00 0.00 0.00 2.52
1150 3884 7.221838 TGCTTAAAAACACGATGAAAAGGAAAG 59.778 33.333 0.00 0.00 0.00 2.62
1181 3915 1.713597 TGTTCTACACGATGCTGCAG 58.286 50.000 10.11 10.11 0.00 4.41
1189 3923 5.134202 ACAATGTCTGATGTTCTACACGA 57.866 39.130 0.00 0.00 0.00 4.35
1190 3924 5.177511 ACAACAATGTCTGATGTTCTACACG 59.822 40.000 0.00 0.00 37.77 4.49
1206 3940 2.069273 GTCTCCGTCTGGACAACAATG 58.931 52.381 1.63 0.00 40.17 2.82
1216 3950 2.119655 CCGGGTAGGTCTCCGTCTG 61.120 68.421 0.00 0.00 44.32 3.51
1217 3951 1.643475 ATCCGGGTAGGTCTCCGTCT 61.643 60.000 0.00 0.00 44.32 4.18
1218 3952 1.152798 ATCCGGGTAGGTCTCCGTC 60.153 63.158 0.00 0.00 44.32 4.79
1251 3987 2.412421 ACACGTTCACGAAGTACTCC 57.588 50.000 6.30 0.00 41.61 3.85
1253 3989 3.425577 TCAACACGTTCACGAAGTACT 57.574 42.857 6.30 0.00 41.61 2.73
1255 3991 3.509740 TGTTCAACACGTTCACGAAGTA 58.490 40.909 6.30 0.00 41.61 2.24
1257 3993 3.088552 GTTGTTCAACACGTTCACGAAG 58.911 45.455 6.30 0.82 43.02 3.79
1259 3995 2.092995 CAGTTGTTCAACACGTTCACGA 59.907 45.455 16.31 0.00 43.02 4.35
1266 4002 1.654137 GCCGCAGTTGTTCAACACG 60.654 57.895 16.31 17.06 0.00 4.49
1267 4003 0.592247 CTGCCGCAGTTGTTCAACAC 60.592 55.000 12.54 8.12 0.00 3.32
1270 4006 1.823470 AGCTGCCGCAGTTGTTCAA 60.823 52.632 21.29 0.00 39.10 2.69
1287 4023 1.150827 TCACGTTCTTCTGCATGCAG 58.849 50.000 36.80 36.80 44.86 4.41
1292 4028 1.220529 CAGCTTCACGTTCTTCTGCA 58.779 50.000 0.00 0.00 0.00 4.41
1448 4184 4.275196 GGTTGAAACTGAACTTGGTACTCC 59.725 45.833 0.00 0.00 0.00 3.85
1449 4185 4.275196 GGGTTGAAACTGAACTTGGTACTC 59.725 45.833 0.00 0.00 0.00 2.59
1456 4192 2.092592 AGACGGGGTTGAAACTGAACTT 60.093 45.455 0.00 0.00 0.00 2.66
1464 4200 0.765135 TGGAGGAGACGGGGTTGAAA 60.765 55.000 0.00 0.00 0.00 2.69
1468 4204 2.606826 GGTGGAGGAGACGGGGTT 60.607 66.667 0.00 0.00 0.00 4.11
1470 4206 2.365635 ATGGTGGAGGAGACGGGG 60.366 66.667 0.00 0.00 0.00 5.73
1504 4240 9.630098 GTCCATGATATCATTTATTCGCATTTT 57.370 29.630 15.74 0.00 33.61 1.82
1505 4241 8.795513 TGTCCATGATATCATTTATTCGCATTT 58.204 29.630 15.74 0.00 33.61 2.32
1506 4242 8.339344 TGTCCATGATATCATTTATTCGCATT 57.661 30.769 15.74 0.00 33.61 3.56
1507 4243 7.926674 TGTCCATGATATCATTTATTCGCAT 57.073 32.000 15.74 0.00 33.61 4.73
1529 4265 0.511221 CGTCGCACCTTTTCGAATGT 59.489 50.000 0.00 0.00 36.41 2.71
1533 4269 3.039588 GCCGTCGCACCTTTTCGA 61.040 61.111 0.00 0.00 34.03 3.71
1534 4270 4.424430 CGCCGTCGCACCTTTTCG 62.424 66.667 0.00 0.00 34.03 3.46
1535 4271 3.039588 TCGCCGTCGCACCTTTTC 61.040 61.111 0.00 0.00 35.26 2.29
1687 4423 1.133009 CATGCTACTCCCTCCCTACCT 60.133 57.143 0.00 0.00 0.00 3.08
1688 4424 1.343069 CATGCTACTCCCTCCCTACC 58.657 60.000 0.00 0.00 0.00 3.18
1689 4425 0.682292 GCATGCTACTCCCTCCCTAC 59.318 60.000 11.37 0.00 0.00 3.18
1690 4426 0.827925 CGCATGCTACTCCCTCCCTA 60.828 60.000 17.13 0.00 0.00 3.53
1787 4538 0.526662 ACGCCACAGTACTAGTGCTC 59.473 55.000 10.90 0.00 35.69 4.26
2003 4757 3.719268 TCCACAGTTCAAGGCATACAT 57.281 42.857 0.00 0.00 0.00 2.29
2060 4814 2.754946 ATTTTGCATGCAGGGAACAG 57.245 45.000 21.50 0.00 0.00 3.16
2096 4850 2.272146 CCGCACCCTGCCATACTT 59.728 61.111 0.00 0.00 41.12 2.24
2203 4959 2.763039 TGGCAGGATTCCATCTACTGA 58.237 47.619 5.29 0.00 0.00 3.41
2360 5117 1.386748 CGTGTTGTCACATCGCTACAG 59.613 52.381 0.00 0.00 44.02 2.74
2409 5166 3.258372 AGTTAGTCACGATCCAAAGAGCA 59.742 43.478 0.00 0.00 0.00 4.26
2413 5170 4.378459 GGCAAAGTTAGTCACGATCCAAAG 60.378 45.833 0.00 0.00 0.00 2.77
2419 5176 3.502211 CCTTTGGCAAAGTTAGTCACGAT 59.498 43.478 31.68 0.00 36.77 3.73
2422 5179 4.359706 CAACCTTTGGCAAAGTTAGTCAC 58.640 43.478 31.68 0.00 36.77 3.67
2461 5218 7.936847 ACACTCACCTATGTTAGTCAAATTTGA 59.063 33.333 16.91 16.91 34.20 2.69
2462 5219 8.099364 ACACTCACCTATGTTAGTCAAATTTG 57.901 34.615 12.15 12.15 26.29 2.32


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

AutoCloner maintained by Alex Coulton.