Multiple sequence alignment - TraesCS2D01G030200

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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 TraesCS2D01G030200 chr2D 100.000 6689 0 0 1 6689 12389611 12382923 0.000000e+00 12353.0
1 TraesCS2D01G030200 chr2D 86.138 2734 333 35 2997 5702 12330070 12332785 0.000000e+00 2907.0
2 TraesCS2D01G030200 chr2D 85.646 2710 342 37 3013 5702 12126923 12129605 0.000000e+00 2806.0
3 TraesCS2D01G030200 chr2D 82.675 785 95 27 1452 2230 12126085 12126834 0.000000e+00 658.0
4 TraesCS2D01G030200 chr2D 92.583 391 26 3 5703 6091 651426300 651425911 5.860000e-155 558.0
5 TraesCS2D01G030200 chr2D 88.435 294 34 0 1616 1909 12329416 12329709 8.250000e-94 355.0
6 TraesCS2D01G030200 chr2D 87.500 232 29 0 1988 2219 12329749 12329980 1.110000e-67 268.0
7 TraesCS2D01G030200 chr2D 78.423 241 43 8 1673 1910 536510288 536510054 1.500000e-31 148.0
8 TraesCS2D01G030200 chr2A 96.562 6195 137 28 512 6689 12965658 12959523 0.000000e+00 10190.0
9 TraesCS2D01G030200 chr2A 85.119 2688 359 33 3033 5702 12739716 12742380 0.000000e+00 2710.0
10 TraesCS2D01G030200 chr2A 86.016 615 71 7 1616 2230 12739008 12739607 0.000000e+00 645.0
11 TraesCS2D01G030200 chr2A 80.081 738 103 19 4430 5153 12524986 12524279 5.980000e-140 508.0
12 TraesCS2D01G030200 chr2A 71.527 1886 430 82 3035 4869 733685731 733683902 6.240000e-110 409.0
13 TraesCS2D01G030200 chr2A 95.600 250 10 1 1 250 12967019 12966771 3.760000e-107 399.0
14 TraesCS2D01G030200 chr2A 93.671 237 11 3 268 502 12966546 12966312 1.070000e-92 351.0
15 TraesCS2D01G030200 chr2A 78.571 238 46 4 1673 1909 679266957 679266724 1.160000e-32 152.0
16 TraesCS2D01G030200 chr2B 94.756 2765 130 8 2949 5702 18713017 18710257 0.000000e+00 4289.0
17 TraesCS2D01G030200 chr2B 94.720 2765 130 8 2949 5702 18722975 18720216 0.000000e+00 4283.0
18 TraesCS2D01G030200 chr2B 92.578 2250 110 23 717 2950 18715256 18713048 0.000000e+00 3177.0
19 TraesCS2D01G030200 chr2B 92.356 2250 115 23 717 2950 18725214 18723006 0.000000e+00 3149.0
20 TraesCS2D01G030200 chr2B 91.892 148 12 0 6103 6250 18710254 18710107 2.440000e-49 207.0
21 TraesCS2D01G030200 chr2B 91.216 148 13 0 6103 6250 18720213 18720066 1.140000e-47 202.0
22 TraesCS2D01G030200 chrUn 86.185 2729 334 32 2998 5702 12443708 12440999 0.000000e+00 2911.0
23 TraesCS2D01G030200 chrUn 91.439 1098 53 11 717 1798 332231923 332232995 0.000000e+00 1469.0
24 TraesCS2D01G030200 chrUn 87.500 432 25 8 6095 6526 12441008 12440606 7.850000e-129 472.0
25 TraesCS2D01G030200 chrUn 88.926 298 31 1 1619 1914 12444626 12444329 3.810000e-97 366.0
26 TraesCS2D01G030200 chrUn 87.500 232 29 0 1988 2219 12444296 12444065 1.110000e-67 268.0
27 TraesCS2D01G030200 chrUn 86.061 165 22 1 6526 6689 12440523 12440359 6.890000e-40 176.0
28 TraesCS2D01G030200 chr7A 92.640 394 26 3 5703 6095 63333605 63333214 1.260000e-156 564.0
29 TraesCS2D01G030200 chr7D 92.132 394 21 5 5704 6095 579144688 579145073 1.270000e-151 547.0
30 TraesCS2D01G030200 chr3A 91.139 395 29 6 5702 6094 576566756 576566366 1.280000e-146 531.0
31 TraesCS2D01G030200 chr3A 90.380 395 32 6 5702 6094 707104790 707104400 1.290000e-141 514.0
32 TraesCS2D01G030200 chr4D 89.822 393 36 4 5703 6094 322295194 322294805 1.000000e-137 501.0
33 TraesCS2D01G030200 chr5B 89.620 395 35 5 5704 6097 411027172 411027561 1.300000e-136 497.0
34 TraesCS2D01G030200 chr4A 89.500 400 32 7 5703 6099 618878935 618879327 1.300000e-136 497.0
35 TraesCS2D01G030200 chr4A 89.114 395 38 4 5703 6096 495794266 495794656 2.800000e-133 486.0
36 TraesCS2D01G030200 chr6B 72.504 611 131 22 3341 3942 20489016 20489598 5.370000e-36 163.0
37 TraesCS2D01G030200 chr3B 86.441 59 6 2 398 455 17683506 17683563 5.600000e-06 63.9


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 TraesCS2D01G030200 chr2D 12382923 12389611 6688 True 12353.000000 12353 100.000000 1 6689 1 chr2D.!!$R1 6688
1 TraesCS2D01G030200 chr2D 12126085 12129605 3520 False 1732.000000 2806 84.160500 1452 5702 2 chr2D.!!$F1 4250
2 TraesCS2D01G030200 chr2D 12329416 12332785 3369 False 1176.666667 2907 87.357667 1616 5702 3 chr2D.!!$F2 4086
3 TraesCS2D01G030200 chr2A 12959523 12967019 7496 True 3646.666667 10190 95.277667 1 6689 3 chr2A.!!$R4 6688
4 TraesCS2D01G030200 chr2A 12739008 12742380 3372 False 1677.500000 2710 85.567500 1616 5702 2 chr2A.!!$F1 4086
5 TraesCS2D01G030200 chr2A 12524279 12524986 707 True 508.000000 508 80.081000 4430 5153 1 chr2A.!!$R1 723
6 TraesCS2D01G030200 chr2A 733683902 733685731 1829 True 409.000000 409 71.527000 3035 4869 1 chr2A.!!$R3 1834
7 TraesCS2D01G030200 chr2B 18710107 18715256 5149 True 2557.666667 4289 93.075333 717 6250 3 chr2B.!!$R1 5533
8 TraesCS2D01G030200 chr2B 18720066 18725214 5148 True 2544.666667 4283 92.764000 717 6250 3 chr2B.!!$R2 5533
9 TraesCS2D01G030200 chrUn 332231923 332232995 1072 False 1469.000000 1469 91.439000 717 1798 1 chrUn.!!$F1 1081
10 TraesCS2D01G030200 chrUn 12440359 12444626 4267 True 838.600000 2911 87.234400 1619 6689 5 chrUn.!!$R1 5070

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
238 239 0.729116 CCAGTTCATGTGCGGTCATC 59.271 55.000 0.00 0.0 0.00 2.92 F
1043 1906 0.719015 TCCTCTTCCATCCTCCCAGT 59.281 55.000 0.00 0.0 0.00 4.00 F
1800 2674 1.420138 ACTGTAGTGGTTCTTGGGGTG 59.580 52.381 0.00 0.0 0.00 4.61 F
2322 3200 2.622942 CCAGCAAGCAGTCCTGTTTTTA 59.377 45.455 0.00 0.0 31.58 1.52 F
3171 4307 1.412710 TCGTTGTTCAACTCTCCTGCT 59.587 47.619 12.74 0.0 0.00 4.24 F
3424 4560 2.795175 TCGGAATATCTCGGCACTTC 57.205 50.000 0.00 0.0 0.00 3.01 F
4761 5957 2.229062 TGAGTTCTACTCCGAGCAAGTG 59.771 50.000 4.52 0.0 44.44 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1158 2021 1.746615 GGAGGCTGAGCATGCGAAA 60.747 57.895 13.01 0.58 0.00 3.46 R
2781 3663 2.381911 CCTGGAGCTTGTGGCAAATAT 58.618 47.619 0.00 0.00 44.79 1.28 R
3171 4307 1.079057 TAATACAGCGGCCGTTGCA 60.079 52.632 37.57 28.43 40.13 4.08 R
4060 5222 2.042162 TGTTCCTCTTACGGTCTAGGGT 59.958 50.000 0.00 0.00 0.00 4.34 R
4648 5830 0.602638 TACACCAGCGCTGTTTCAGG 60.603 55.000 33.75 21.01 31.21 3.86 R
4827 6024 3.058914 AGTGCTTTGTAACATCGCAGTTC 60.059 43.478 0.00 0.00 30.68 3.01 R
6642 7960 1.269723 TGCAGTGACTCGGTCAAGTAG 59.730 52.381 8.09 1.79 44.49 2.57 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
49 50 8.899771 GGCCAAGTTAATTAGCAACTTCTATTA 58.100 33.333 0.00 0.00 42.79 0.98
90 91 3.880490 TGGTTAGTCGCATGTGTCTTTTT 59.120 39.130 11.21 0.00 0.00 1.94
152 153 7.489757 GCAGTATTAGACTTTCTCAGTTACCTG 59.510 40.741 0.00 0.00 35.64 4.00
159 160 8.880991 AGACTTTCTCAGTTACCTGACTAATA 57.119 34.615 0.00 0.00 42.80 0.98
237 238 1.308069 GCCAGTTCATGTGCGGTCAT 61.308 55.000 0.00 0.00 0.00 3.06
238 239 0.729116 CCAGTTCATGTGCGGTCATC 59.271 55.000 0.00 0.00 0.00 2.92
243 244 1.478631 TCATGTGCGGTCATCTCTCT 58.521 50.000 0.00 0.00 0.00 3.10
250 251 1.873591 GCGGTCATCTCTCTCTCTCTC 59.126 57.143 0.00 0.00 0.00 3.20
251 252 2.485479 GCGGTCATCTCTCTCTCTCTCT 60.485 54.545 0.00 0.00 0.00 3.10
252 253 3.393800 CGGTCATCTCTCTCTCTCTCTC 58.606 54.545 0.00 0.00 0.00 3.20
253 254 3.070159 CGGTCATCTCTCTCTCTCTCTCT 59.930 52.174 0.00 0.00 0.00 3.10
254 255 4.636249 GGTCATCTCTCTCTCTCTCTCTC 58.364 52.174 0.00 0.00 0.00 3.20
255 256 4.346418 GGTCATCTCTCTCTCTCTCTCTCT 59.654 50.000 0.00 0.00 0.00 3.10
256 257 5.510520 GGTCATCTCTCTCTCTCTCTCTCTC 60.511 52.000 0.00 0.00 0.00 3.20
257 258 5.304101 GTCATCTCTCTCTCTCTCTCTCTCT 59.696 48.000 0.00 0.00 0.00 3.10
258 259 5.538053 TCATCTCTCTCTCTCTCTCTCTCTC 59.462 48.000 0.00 0.00 0.00 3.20
259 260 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
260 261 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
261 262 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
262 263 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
263 264 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
264 265 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
265 266 4.219115 TCTCTCTCTCTCTCTCTCTCTCC 58.781 52.174 0.00 0.00 0.00 3.71
266 267 3.309296 TCTCTCTCTCTCTCTCTCTCCC 58.691 54.545 0.00 0.00 0.00 4.30
290 498 9.078753 CCCCGTAATTTAATTTACATTTGTCAC 57.921 33.333 16.45 0.00 32.69 3.67
363 571 6.414408 AATTAGCTCAAATCGTCACTTCAG 57.586 37.500 0.00 0.00 0.00 3.02
387 595 6.830324 AGAGTGTTATGTGGATATTTGCATGT 59.170 34.615 0.00 0.00 0.00 3.21
395 603 5.034152 GTGGATATTTGCATGTTGTTACCG 58.966 41.667 0.00 0.00 0.00 4.02
424 634 6.121776 AGTCCACTTGGTGAACATATGTTA 57.878 37.500 20.83 2.83 35.23 2.41
506 716 9.816787 AGAACTCCTAACCAAATTTTTATACCA 57.183 29.630 0.00 0.00 0.00 3.25
544 1398 4.098914 TCTTGGCTAAAGTGACCAACAT 57.901 40.909 0.00 0.00 38.52 2.71
550 1404 6.186957 TGGCTAAAGTGACCAACATGATAAT 58.813 36.000 0.00 0.00 0.00 1.28
558 1412 7.475015 AGTGACCAACATGATAATTTTGATCG 58.525 34.615 0.00 0.00 0.00 3.69
607 1461 7.129457 ACTTAGAGATTGATGTGGCAAGATA 57.871 36.000 0.00 0.00 0.00 1.98
720 1574 2.963599 TTTTCCCGGGAAGCTAAGTT 57.036 45.000 33.64 0.00 35.38 2.66
805 1659 1.370778 GGGTTGGCAAACGCGTAAC 60.371 57.895 14.46 13.11 39.16 2.50
1043 1906 0.719015 TCCTCTTCCATCCTCCCAGT 59.281 55.000 0.00 0.00 0.00 4.00
1286 2149 2.628178 GCTTTGCTAGGGTGGACTTTTT 59.372 45.455 0.00 0.00 0.00 1.94
1359 2226 3.153919 TGTTCTCTGTTTACCAATGCCC 58.846 45.455 0.00 0.00 0.00 5.36
1360 2227 3.153919 GTTCTCTGTTTACCAATGCCCA 58.846 45.455 0.00 0.00 0.00 5.36
1368 2235 6.268847 TCTGTTTACCAATGCCCAAAACTTAT 59.731 34.615 0.00 0.00 32.57 1.73
1369 2236 7.451877 TCTGTTTACCAATGCCCAAAACTTATA 59.548 33.333 0.00 0.00 32.57 0.98
1370 2237 7.379750 TGTTTACCAATGCCCAAAACTTATAC 58.620 34.615 0.00 0.00 32.57 1.47
1657 2531 5.888161 AGGCTAGAATACAAAAACATCTGGG 59.112 40.000 0.00 0.00 0.00 4.45
1800 2674 1.420138 ACTGTAGTGGTTCTTGGGGTG 59.580 52.381 0.00 0.00 0.00 4.61
2219 3093 5.827797 AGCTGAGAAGGTGTGTAATGAAAAA 59.172 36.000 0.00 0.00 0.00 1.94
2322 3200 2.622942 CCAGCAAGCAGTCCTGTTTTTA 59.377 45.455 0.00 0.00 31.58 1.52
2922 3804 7.562088 TGTTTTTCTAATTTACTGTTCAGGGGT 59.438 33.333 4.82 0.00 0.00 4.95
3171 4307 1.412710 TCGTTGTTCAACTCTCCTGCT 59.587 47.619 12.74 0.00 0.00 4.24
3424 4560 2.795175 TCGGAATATCTCGGCACTTC 57.205 50.000 0.00 0.00 0.00 3.01
3670 4819 8.243961 TCAAAATTCCATGTCTCCTAACAAAA 57.756 30.769 0.00 0.00 31.81 2.44
3676 4825 8.477419 TTCCATGTCTCCTAACAAAAATTCTT 57.523 30.769 0.00 0.00 31.81 2.52
3700 4849 5.897377 TTTGCCCTTGATTTTACTAGCTC 57.103 39.130 0.00 0.00 0.00 4.09
3843 4992 8.321005 GCTTCAAAACTATGTTTGTCAGAAAAC 58.679 33.333 0.00 0.00 39.16 2.43
4060 5222 5.798125 TCCATTTTATGCAACTGTGGAAA 57.202 34.783 8.25 0.00 31.81 3.13
4062 5224 4.690280 CCATTTTATGCAACTGTGGAAACC 59.310 41.667 0.00 0.00 0.00 3.27
4690 5881 8.252417 TGTATTATGCTTTGCAAATGAGTCATT 58.748 29.630 13.23 12.75 43.62 2.57
4709 5905 5.047802 GTCATTCTTCCTGCTTTTCCAATGA 60.048 40.000 0.00 0.00 0.00 2.57
4761 5957 2.229062 TGAGTTCTACTCCGAGCAAGTG 59.771 50.000 4.52 0.00 44.44 3.16
4827 6024 3.373439 GAGAAATGGCTTCTGCAGTACAG 59.627 47.826 14.67 9.57 44.82 2.74
5736 6963 3.466836 CTGCACACGGGTACATATGAAT 58.533 45.455 10.38 0.00 0.00 2.57
5739 6966 3.057019 CACACGGGTACATATGAATCCG 58.943 50.000 23.07 23.07 42.69 4.18
5764 6991 7.061027 GCCTTTCAAAAATGTACTTTTAACGC 58.939 34.615 7.12 1.56 36.01 4.84
5906 7133 8.895932 ACAAATTTTAGTGCTTCTAAATAGCG 57.104 30.769 12.70 7.43 44.72 4.26
5907 7134 8.512138 ACAAATTTTAGTGCTTCTAAATAGCGT 58.488 29.630 12.70 7.85 44.72 5.07
5908 7135 9.341899 CAAATTTTAGTGCTTCTAAATAGCGTT 57.658 29.630 12.70 0.00 44.72 4.84
5909 7136 9.908152 AAATTTTAGTGCTTCTAAATAGCGTTT 57.092 25.926 12.70 0.00 44.72 3.60
5910 7137 9.556030 AATTTTAGTGCTTCTAAATAGCGTTTC 57.444 29.630 12.70 0.00 44.72 2.78
5911 7138 7.661127 TTTAGTGCTTCTAAATAGCGTTTCA 57.339 32.000 9.43 0.00 41.80 2.69
5912 7139 5.532025 AGTGCTTCTAAATAGCGTTTCAC 57.468 39.130 0.00 0.00 41.54 3.18
5913 7140 4.091509 AGTGCTTCTAAATAGCGTTTCACG 59.908 41.667 0.00 0.00 45.88 4.35
5914 7141 3.369756 TGCTTCTAAATAGCGTTTCACGG 59.630 43.478 0.00 0.00 42.82 4.94
5915 7142 3.784525 GCTTCTAAATAGCGTTTCACGGC 60.785 47.826 0.00 0.00 42.82 5.68
5916 7143 1.921887 TCTAAATAGCGTTTCACGGCG 59.078 47.619 4.80 4.80 42.82 6.46
5926 7153 2.026272 CGTTTCACGGCGCAATATTTTG 59.974 45.455 10.83 0.00 38.08 2.44
5981 7208 4.998671 TTTCCATGAAACTTTCTGCACA 57.001 36.364 0.00 0.00 0.00 4.57
5994 7221 7.312657 ACTTTCTGCACACACATAGAATATG 57.687 36.000 0.00 0.00 0.00 1.78
6092 7323 1.667724 CGAGTTCATCCATGCACTTCC 59.332 52.381 0.00 0.00 34.48 3.46
6150 7381 6.969043 TGGATGACAAGGAAATATACCAAGT 58.031 36.000 0.00 0.00 0.00 3.16
6153 7384 7.012421 GGATGACAAGGAAATATACCAAGTGAC 59.988 40.741 0.00 0.00 0.00 3.67
6154 7385 6.774673 TGACAAGGAAATATACCAAGTGACA 58.225 36.000 0.00 0.00 0.00 3.58
6187 7418 5.753438 TGCGACAGTAATCATATGAACCTTC 59.247 40.000 9.99 3.26 0.00 3.46
6214 7445 3.767131 TGAATCACTCACCGGTATCTGAA 59.233 43.478 6.87 0.00 0.00 3.02
6330 7561 3.744660 AGCTCGAGGTGATGTTTTTCTT 58.255 40.909 17.85 0.00 0.00 2.52
6336 7567 4.161333 GAGGTGATGTTTTTCTTGCGATG 58.839 43.478 0.00 0.00 0.00 3.84
6358 7589 8.538856 CGATGCTTTTGTCAAAAACTTTATTGA 58.461 29.630 11.73 0.00 31.94 2.57
6419 7654 7.092716 AGCAATCAATCGAAGCTACAAATTTT 58.907 30.769 0.00 0.00 35.53 1.82
6506 7741 5.931146 ACAGCTACAAATTTCTCAGTCTCAG 59.069 40.000 0.00 0.00 0.00 3.35
6517 7752 3.766051 TCTCAGTCTCAGCTCTGCATTAA 59.234 43.478 0.00 0.00 0.00 1.40
6642 7960 1.165270 ATTTGGTTGAGGCGCTACAC 58.835 50.000 7.64 0.00 0.00 2.90
6647 7965 1.067071 GGTTGAGGCGCTACACTACTT 60.067 52.381 7.64 0.00 0.00 2.24
6652 7970 0.801067 GGCGCTACACTACTTGACCG 60.801 60.000 7.64 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.610509 TGGCCGGCAGCTGAAATTAA 60.611 50.000 30.85 0.00 43.05 1.40
49 50 2.494059 CACCCACTTCAGTCGAACAAT 58.506 47.619 0.00 0.00 0.00 2.71
90 91 7.392393 GCAAACACTCTCTTTTATACCCCTAAA 59.608 37.037 0.00 0.00 0.00 1.85
110 111 9.777297 TCTAATACTGCTTATCATATGCAAACA 57.223 29.630 6.68 0.00 38.21 2.83
152 153 4.686554 GTGCCAGATGACCGAATATTAGTC 59.313 45.833 10.00 10.00 0.00 2.59
159 160 2.019249 CAATGTGCCAGATGACCGAAT 58.981 47.619 0.00 0.00 0.00 3.34
237 238 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
238 239 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
243 244 4.219115 GGAGAGAGAGAGAGAGAGAGAGA 58.781 52.174 0.00 0.00 0.00 3.10
250 251 0.837272 ACGGGGAGAGAGAGAGAGAG 59.163 60.000 0.00 0.00 0.00 3.20
251 252 2.177811 TACGGGGAGAGAGAGAGAGA 57.822 55.000 0.00 0.00 0.00 3.10
252 253 3.502123 ATTACGGGGAGAGAGAGAGAG 57.498 52.381 0.00 0.00 0.00 3.20
253 254 3.955524 AATTACGGGGAGAGAGAGAGA 57.044 47.619 0.00 0.00 0.00 3.10
254 255 6.658188 ATTAAATTACGGGGAGAGAGAGAG 57.342 41.667 0.00 0.00 0.00 3.20
255 256 7.433537 AAATTAAATTACGGGGAGAGAGAGA 57.566 36.000 0.00 0.00 0.00 3.10
256 257 8.202137 TGTAAATTAAATTACGGGGAGAGAGAG 58.798 37.037 8.52 0.00 38.37 3.20
257 258 8.081517 TGTAAATTAAATTACGGGGAGAGAGA 57.918 34.615 8.52 0.00 38.37 3.10
258 259 8.904099 ATGTAAATTAAATTACGGGGAGAGAG 57.096 34.615 8.52 0.00 38.37 3.20
259 260 9.689501 AAATGTAAATTAAATTACGGGGAGAGA 57.310 29.630 8.52 0.00 38.37 3.10
260 261 9.730420 CAAATGTAAATTAAATTACGGGGAGAG 57.270 33.333 8.52 0.00 38.37 3.20
261 262 9.245481 ACAAATGTAAATTAAATTACGGGGAGA 57.755 29.630 8.52 0.00 38.37 3.71
262 263 9.511144 GACAAATGTAAATTAAATTACGGGGAG 57.489 33.333 8.52 1.74 38.37 4.30
263 264 9.021807 TGACAAATGTAAATTAAATTACGGGGA 57.978 29.630 8.52 0.00 38.37 4.81
264 265 9.078753 GTGACAAATGTAAATTAAATTACGGGG 57.921 33.333 8.52 2.27 38.37 5.73
265 266 9.849166 AGTGACAAATGTAAATTAAATTACGGG 57.151 29.630 8.52 1.99 38.37 5.28
290 498 9.509855 TTGTACACTTTGCTTTAACATTTACAG 57.490 29.630 0.00 0.00 0.00 2.74
330 538 7.697691 ACGATTTGAGCTAATTTCATTTCGAT 58.302 30.769 13.35 1.99 35.29 3.59
343 551 4.218635 ACTCTGAAGTGACGATTTGAGCTA 59.781 41.667 0.00 0.00 33.32 3.32
363 571 7.031226 ACATGCAAATATCCACATAACACTC 57.969 36.000 0.00 0.00 0.00 3.51
387 595 3.705051 AGTGGACTATCTCCGGTAACAA 58.295 45.455 0.00 0.00 43.03 2.83
395 603 3.260884 TGTTCACCAAGTGGACTATCTCC 59.739 47.826 3.83 0.00 42.16 3.71
472 682 8.507524 AATTTGGTTAGGAGTTCTACTATTGC 57.492 34.615 0.00 0.00 0.00 3.56
503 713 7.831193 GCCAAGATATGATCCAATACTATTGGT 59.169 37.037 22.22 12.81 40.40 3.67
504 714 8.051535 AGCCAAGATATGATCCAATACTATTGG 58.948 37.037 18.60 18.60 40.87 3.16
509 719 8.664079 ACTTTAGCCAAGATATGATCCAATACT 58.336 33.333 0.26 0.00 36.21 2.12
522 1376 4.098914 TGTTGGTCACTTTAGCCAAGAT 57.901 40.909 0.26 0.00 42.20 2.40
576 1430 7.014134 TGCCACATCAATCTCTAAGTTTTTCAA 59.986 33.333 0.00 0.00 0.00 2.69
607 1461 4.853007 ACTGATCAAATTAGAGCAAGCCT 58.147 39.130 0.00 0.00 32.97 4.58
720 1574 2.379634 CGCTGATGTTTCGACGGCA 61.380 57.895 4.86 0.00 35.91 5.69
805 1659 1.270839 ACTTCAGGAACATGACCACCG 60.271 52.381 0.00 0.00 0.00 4.94
1043 1906 2.731571 GGTGCCTGCCGTCCAGATA 61.732 63.158 2.22 0.00 44.64 1.98
1158 2021 1.746615 GGAGGCTGAGCATGCGAAA 60.747 57.895 13.01 0.58 0.00 3.46
1286 2149 9.908152 GCAAGGAAAGTAGCTTAAGAAAAATAA 57.092 29.630 6.67 0.00 0.00 1.40
1359 2226 7.174253 TCCCAAGCACAAGTAGTATAAGTTTTG 59.826 37.037 0.00 0.00 0.00 2.44
1360 2227 7.228590 TCCCAAGCACAAGTAGTATAAGTTTT 58.771 34.615 0.00 0.00 0.00 2.43
1368 2235 3.009033 AGCAATCCCAAGCACAAGTAGTA 59.991 43.478 0.00 0.00 0.00 1.82
1369 2236 2.162681 GCAATCCCAAGCACAAGTAGT 58.837 47.619 0.00 0.00 0.00 2.73
1370 2237 2.440409 AGCAATCCCAAGCACAAGTAG 58.560 47.619 0.00 0.00 0.00 2.57
1657 2531 3.691609 AGATGGCGAGAATTCAGGTTTTC 59.308 43.478 8.44 0.00 0.00 2.29
1800 2674 4.598062 GCTAATAAGCCGAATTGGTTGAC 58.402 43.478 0.00 0.00 43.40 3.18
2219 3093 4.516698 GTGCTACACTAATATGGCAGCATT 59.483 41.667 0.00 0.00 41.17 3.56
2510 3388 5.010282 ACATCTTAAAACGCTTCTCCCATT 58.990 37.500 0.00 0.00 0.00 3.16
2781 3663 2.381911 CCTGGAGCTTGTGGCAAATAT 58.618 47.619 0.00 0.00 44.79 1.28
2922 3804 2.534396 CCCAGGCCAACTACACCCA 61.534 63.158 5.01 0.00 0.00 4.51
3022 4158 4.159135 ACCAGCCAATCTAAATTGAAGCAG 59.841 41.667 0.00 0.00 44.25 4.24
3171 4307 1.079057 TAATACAGCGGCCGTTGCA 60.079 52.632 37.57 28.43 40.13 4.08
3676 4825 6.295067 GGAGCTAGTAAAATCAAGGGCAAAAA 60.295 38.462 0.00 0.00 0.00 1.94
3843 4992 6.051717 ACTTATGTTCTCCAGGATCAATTCG 58.948 40.000 0.00 0.00 0.00 3.34
4060 5222 2.042162 TGTTCCTCTTACGGTCTAGGGT 59.958 50.000 0.00 0.00 0.00 4.34
4062 5224 4.401519 TCAATGTTCCTCTTACGGTCTAGG 59.598 45.833 0.00 0.00 0.00 3.02
4203 5374 3.233507 ACACAGCCTGATCCAACATTTT 58.766 40.909 0.00 0.00 0.00 1.82
4204 5375 2.821969 GACACAGCCTGATCCAACATTT 59.178 45.455 0.00 0.00 0.00 2.32
4482 5664 4.127907 GAGCATCAGAGAATTCATGAGCA 58.872 43.478 22.12 5.88 33.17 4.26
4648 5830 0.602638 TACACCAGCGCTGTTTCAGG 60.603 55.000 33.75 21.01 31.21 3.86
4690 5881 4.834496 ACAATCATTGGAAAAGCAGGAAGA 59.166 37.500 1.58 0.00 34.12 2.87
4827 6024 3.058914 AGTGCTTTGTAACATCGCAGTTC 60.059 43.478 0.00 0.00 30.68 3.01
5736 6963 5.523438 AAAGTACATTTTTGAAAGGCGGA 57.477 34.783 0.00 0.00 0.00 5.54
5739 6966 7.061027 GCGTTAAAAGTACATTTTTGAAAGGC 58.939 34.615 0.83 4.05 41.40 4.35
5906 7133 2.983803 ACAAAATATTGCGCCGTGAAAC 59.016 40.909 4.18 0.00 40.34 2.78
5907 7134 3.057876 AGACAAAATATTGCGCCGTGAAA 60.058 39.130 4.18 0.00 40.34 2.69
5908 7135 2.486203 AGACAAAATATTGCGCCGTGAA 59.514 40.909 4.18 0.00 40.34 3.18
5909 7136 2.080693 AGACAAAATATTGCGCCGTGA 58.919 42.857 4.18 0.00 40.34 4.35
5910 7137 2.542766 AGACAAAATATTGCGCCGTG 57.457 45.000 4.18 0.00 40.34 4.94
5911 7138 3.569250 AAAGACAAAATATTGCGCCGT 57.431 38.095 4.18 0.00 40.34 5.68
5912 7139 4.901866 AAAAAGACAAAATATTGCGCCG 57.098 36.364 4.18 0.00 40.34 6.46
5950 7177 9.283768 AGAAAGTTTCATGGAAAAACAACTTTT 57.716 25.926 17.65 3.42 40.03 2.27
5953 7180 6.313658 GCAGAAAGTTTCATGGAAAAACAACT 59.686 34.615 17.65 4.67 38.73 3.16
5981 7208 5.233225 CGCACATCTCCATATTCTATGTGT 58.767 41.667 13.45 0.00 45.79 3.72
6037 7268 7.878127 TGAACCCACTTTGAAAAACACATTTTA 59.122 29.630 0.00 0.00 41.27 1.52
6043 7274 6.983890 ACATATGAACCCACTTTGAAAAACAC 59.016 34.615 10.38 0.00 0.00 3.32
6092 7323 7.205515 AGGATAATAGCATAAGGAATCCTGG 57.794 40.000 0.90 0.00 40.11 4.45
6150 7381 3.990092 ACTGTCGCATTTACTCTTGTCA 58.010 40.909 0.00 0.00 0.00 3.58
6153 7384 6.647212 TGATTACTGTCGCATTTACTCTTG 57.353 37.500 0.00 0.00 0.00 3.02
6154 7385 8.982685 CATATGATTACTGTCGCATTTACTCTT 58.017 33.333 0.00 0.00 0.00 2.85
6187 7418 2.436417 ACCGGTGAGTGATTCATTTGG 58.564 47.619 6.12 0.00 38.29 3.28
6293 7524 3.132111 TCGAGCTAACTATGCCATTGACA 59.868 43.478 0.00 0.00 0.00 3.58
6330 7561 3.779759 AGTTTTTGACAAAAGCATCGCA 58.220 36.364 23.89 3.16 34.50 5.10
6336 7567 7.683746 TGCTCAATAAAGTTTTTGACAAAAGC 58.316 30.769 17.01 17.01 32.32 3.51
6358 7589 2.301346 GGCATACCAGCTTACAATGCT 58.699 47.619 15.69 0.00 42.01 3.79
6419 7654 5.947228 AAATGCTCGATTTGAAGACTGAA 57.053 34.783 0.00 0.00 32.69 3.02
6454 7689 2.827921 GGGGAAATGTGCAAAGAGTCAT 59.172 45.455 0.00 0.00 0.00 3.06
6455 7690 2.238521 GGGGAAATGTGCAAAGAGTCA 58.761 47.619 0.00 0.00 0.00 3.41
6456 7691 2.029918 GTGGGGAAATGTGCAAAGAGTC 60.030 50.000 0.00 0.00 0.00 3.36
6457 7692 1.963515 GTGGGGAAATGTGCAAAGAGT 59.036 47.619 0.00 0.00 0.00 3.24
6458 7693 2.029649 CAGTGGGGAAATGTGCAAAGAG 60.030 50.000 0.00 0.00 0.00 2.85
6459 7694 1.962807 CAGTGGGGAAATGTGCAAAGA 59.037 47.619 0.00 0.00 0.00 2.52
6460 7695 1.962807 TCAGTGGGGAAATGTGCAAAG 59.037 47.619 0.00 0.00 0.00 2.77
6461 7696 2.079170 TCAGTGGGGAAATGTGCAAA 57.921 45.000 0.00 0.00 0.00 3.68
6468 7703 2.683211 AGCTGTTTCAGTGGGGAAAT 57.317 45.000 0.00 0.00 38.86 2.17
6506 7741 8.883731 TGAAAACTAGATACTTTAATGCAGAGC 58.116 33.333 0.00 0.00 0.00 4.09
6578 7896 6.488683 TGGTGTTCGGTTGATCTTTTATTCTT 59.511 34.615 0.00 0.00 0.00 2.52
6611 7929 5.050295 GCCTCAACCAAATACTATAGCGAAC 60.050 44.000 0.00 0.00 0.00 3.95
6615 7933 3.186613 GCGCCTCAACCAAATACTATAGC 59.813 47.826 0.00 0.00 0.00 2.97
6619 7937 3.196039 TGTAGCGCCTCAACCAAATACTA 59.804 43.478 2.29 0.00 0.00 1.82
6642 7960 1.269723 TGCAGTGACTCGGTCAAGTAG 59.730 52.381 8.09 1.79 44.49 2.57
6647 7965 3.856309 ACTGCAGTGACTCGGTCA 58.144 55.556 20.97 3.02 40.50 4.02


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

AutoCloner maintained by Alex Coulton.