Multiple sequence alignment - TraesCS4A01G388500

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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 TraesCS4A01G388500 chr4A 100.000 4989 0 0 409 5397 666118362 666113374 0.000000e+00 9214.0
1 TraesCS4A01G388500 chr4A 100.000 148 0 0 1 148 666118770 666118623 1.920000e-69 274.0
2 TraesCS4A01G388500 chr7A 96.311 4039 114 16 419 4450 54668557 54664547 0.000000e+00 6601.0
3 TraesCS4A01G388500 chr7A 86.667 930 92 19 4447 5366 54664514 54663607 0.000000e+00 1002.0
4 TraesCS4A01G388500 chr7A 86.131 137 5 1 1 137 54668803 54668681 9.430000e-28 135.0
5 TraesCS4A01G388500 chr7D 96.173 4024 114 14 434 4450 51740124 51736134 0.000000e+00 6541.0
6 TraesCS4A01G388500 chr7D 88.889 918 73 11 4480 5397 51736053 51735165 0.000000e+00 1103.0
7 TraesCS4A01G388500 chr7D 79.522 293 40 11 4872 5162 386401579 386401305 1.980000e-44 191.0
8 TraesCS4A01G388500 chr7D 77.778 261 39 11 4914 5164 521687962 521688213 5.630000e-30 143.0
9 TraesCS4A01G388500 chr7D 94.318 88 4 1 62 148 51740588 51740501 3.390000e-27 134.0
10 TraesCS4A01G388500 chr7D 84.848 132 18 1 439 568 603392149 603392280 1.220000e-26 132.0
11 TraesCS4A01G388500 chr3D 80.612 294 47 7 4872 5163 46491268 46490983 9.100000e-53 219.0
12 TraesCS4A01G388500 chr1D 81.992 261 43 3 4909 5169 438367973 438368229 9.100000e-53 219.0
13 TraesCS4A01G388500 chr6B 77.891 294 45 10 4874 5166 439409328 439409602 1.200000e-36 165.0
14 TraesCS4A01G388500 chr3B 87.143 140 16 2 5025 5163 72720991 72720853 2.010000e-34 158.0
15 TraesCS4A01G388500 chr2D 82.386 176 30 1 4904 5079 598801208 598801034 9.360000e-33 152.0
16 TraesCS4A01G388500 chr5B 76.589 299 54 12 4874 5164 259557955 259558245 3.370000e-32 150.0
17 TraesCS4A01G388500 chrUn 88.235 68 5 3 5236 5302 349405791 349405856 1.610000e-10 78.7
18 TraesCS4A01G388500 chr5A 88.235 68 5 3 5236 5302 658923208 658923273 1.610000e-10 78.7
19 TraesCS4A01G388500 chr5A 88.235 68 5 3 5236 5302 658930692 658930757 1.610000e-10 78.7
20 TraesCS4A01G388500 chr5D 77.586 116 18 8 5254 5366 482457102 482456992 4.510000e-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 TraesCS4A01G388500 chr4A 666113374 666118770 5396 True 4744.000000 9214 100.000000 1 5397 2 chr4A.!!$R1 5396
1 TraesCS4A01G388500 chr7A 54663607 54668803 5196 True 2579.333333 6601 89.703000 1 5366 3 chr7A.!!$R1 5365
2 TraesCS4A01G388500 chr7D 51735165 51740588 5423 True 2592.666667 6541 93.126667 62 5397 3 chr7D.!!$R2 5335

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
870 980 0.035458 CGGTGGCCTTTCTCTCAACT 59.965 55.000 3.32 0.0 0.00 3.16 F
1055 1165 0.773644 ACTTGGTTCACAGCCCAGAT 59.226 50.000 0.00 0.0 31.04 2.90 F
1444 1554 0.914644 CCTCTCCTTCAATGGCCTCA 59.085 55.000 3.32 0.0 0.00 3.86 F
1551 1661 1.702957 CCTTCCCTCACCAACCTAACA 59.297 52.381 0.00 0.0 0.00 2.41 F
2244 2354 2.154854 TCAACAAGTTCTCTGGCTCG 57.845 50.000 0.00 0.0 0.00 5.03 F
3984 4095 0.249120 ATTCATCGAACTGGACCGCA 59.751 50.000 0.00 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1738 1848 1.482182 TGTCATCTCGTGAGGAATGGG 59.518 52.381 3.12 0.0 37.56 4.00 R
3023 3133 0.106519 AGGAATGGCACCATGTAGGC 60.107 55.000 2.19 0.0 43.14 3.93 R
3114 3224 0.966370 GGAGTCCTGCTACCGTGTCT 60.966 60.000 0.41 0.0 0.00 3.41 R
3220 3330 3.181471 CCGCAGAGACCTCTATTGTGAAT 60.181 47.826 0.00 0.0 37.98 2.57 R
4020 4131 0.036010 CTTGCACTGGGGTAGTCAGG 60.036 60.000 0.00 0.0 37.60 3.86 R
5002 5168 0.036875 CGGGCCAGACCTCTTTCTTT 59.963 55.000 4.39 0.0 39.10 2.52 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
26 27 9.039870 GGACTGAATGACTAAAGAATGATGTAG 57.960 37.037 0.00 0.00 0.00 2.74
47 48 7.394016 TGTAGGCTTGAAGAATGAGAAACATA 58.606 34.615 0.00 0.00 38.38 2.29
48 49 7.882791 TGTAGGCTTGAAGAATGAGAAACATAA 59.117 33.333 0.00 0.00 38.38 1.90
49 50 7.765695 AGGCTTGAAGAATGAGAAACATAAA 57.234 32.000 0.00 0.00 38.38 1.40
50 51 7.824672 AGGCTTGAAGAATGAGAAACATAAAG 58.175 34.615 0.00 0.00 38.38 1.85
51 52 7.667219 AGGCTTGAAGAATGAGAAACATAAAGA 59.333 33.333 0.00 0.00 38.38 2.52
52 53 7.967303 GGCTTGAAGAATGAGAAACATAAAGAG 59.033 37.037 0.00 0.00 38.38 2.85
53 54 7.484324 GCTTGAAGAATGAGAAACATAAAGAGC 59.516 37.037 0.00 0.00 38.38 4.09
54 55 8.627208 TTGAAGAATGAGAAACATAAAGAGCT 57.373 30.769 0.00 0.00 38.38 4.09
55 56 9.725019 TTGAAGAATGAGAAACATAAAGAGCTA 57.275 29.630 0.00 0.00 38.38 3.32
56 57 9.725019 TGAAGAATGAGAAACATAAAGAGCTAA 57.275 29.630 0.00 0.00 38.38 3.09
58 59 9.950496 AAGAATGAGAAACATAAAGAGCTAAGA 57.050 29.630 0.00 0.00 38.38 2.10
59 60 9.598517 AGAATGAGAAACATAAAGAGCTAAGAG 57.401 33.333 0.00 0.00 38.38 2.85
60 61 7.784633 ATGAGAAACATAAAGAGCTAAGAGC 57.215 36.000 0.00 0.00 38.35 4.09
79 80 7.801716 AAGAGCACTGAACATTTACTAAACA 57.198 32.000 0.00 0.00 0.00 2.83
119 120 6.112734 ACTAAACTGATGAATTGCGTGGATA 58.887 36.000 0.00 0.00 0.00 2.59
120 121 6.767902 ACTAAACTGATGAATTGCGTGGATAT 59.232 34.615 0.00 0.00 0.00 1.63
427 519 2.027003 AGACACACGAACCCGAAAAA 57.973 45.000 0.00 0.00 39.50 1.94
469 576 3.061260 GACCTGGTACGCGGAGACC 62.061 68.421 12.47 15.51 36.17 3.85
484 591 0.834612 AGACCGAGGACAAACCAACA 59.165 50.000 0.00 0.00 42.04 3.33
524 631 1.219522 CGACGGACAGAAAAACGGCT 61.220 55.000 0.00 0.00 30.83 5.52
525 632 1.787012 GACGGACAGAAAAACGGCTA 58.213 50.000 0.00 0.00 0.00 3.93
552 659 6.206634 AGCCGAATTTAAAAACAGACATCTGA 59.793 34.615 15.76 0.00 46.59 3.27
758 868 4.783667 GGGACGTTGGCAACTACA 57.216 55.556 26.26 0.00 42.89 2.74
759 869 2.540145 GGGACGTTGGCAACTACAG 58.460 57.895 26.26 14.11 42.89 2.74
868 978 1.302511 GCGGTGGCCTTTCTCTCAA 60.303 57.895 3.32 0.00 0.00 3.02
870 980 0.035458 CGGTGGCCTTTCTCTCAACT 59.965 55.000 3.32 0.00 0.00 3.16
871 981 1.814793 GGTGGCCTTTCTCTCAACTC 58.185 55.000 3.32 0.00 0.00 3.01
872 982 1.349357 GGTGGCCTTTCTCTCAACTCT 59.651 52.381 3.32 0.00 0.00 3.24
873 983 2.614229 GGTGGCCTTTCTCTCAACTCTC 60.614 54.545 3.32 0.00 0.00 3.20
874 984 2.301583 GTGGCCTTTCTCTCAACTCTCT 59.698 50.000 3.32 0.00 0.00 3.10
875 985 3.511934 GTGGCCTTTCTCTCAACTCTCTA 59.488 47.826 3.32 0.00 0.00 2.43
876 986 3.511934 TGGCCTTTCTCTCAACTCTCTAC 59.488 47.826 3.32 0.00 0.00 2.59
877 987 3.118920 GGCCTTTCTCTCAACTCTCTACC 60.119 52.174 0.00 0.00 0.00 3.18
878 988 3.511934 GCCTTTCTCTCAACTCTCTACCA 59.488 47.826 0.00 0.00 0.00 3.25
879 989 4.619628 GCCTTTCTCTCAACTCTCTACCAC 60.620 50.000 0.00 0.00 0.00 4.16
880 990 4.380023 CCTTTCTCTCAACTCTCTACCACG 60.380 50.000 0.00 0.00 0.00 4.94
881 991 2.085320 TCTCTCAACTCTCTACCACGC 58.915 52.381 0.00 0.00 0.00 5.34
882 992 1.133407 CTCTCAACTCTCTACCACGCC 59.867 57.143 0.00 0.00 0.00 5.68
883 993 1.178276 CTCAACTCTCTACCACGCCT 58.822 55.000 0.00 0.00 0.00 5.52
884 994 1.546476 CTCAACTCTCTACCACGCCTT 59.454 52.381 0.00 0.00 0.00 4.35
885 995 1.968493 TCAACTCTCTACCACGCCTTT 59.032 47.619 0.00 0.00 0.00 3.11
886 996 2.029290 TCAACTCTCTACCACGCCTTTC 60.029 50.000 0.00 0.00 0.00 2.62
887 997 1.926108 ACTCTCTACCACGCCTTTCT 58.074 50.000 0.00 0.00 0.00 2.52
888 998 1.819903 ACTCTCTACCACGCCTTTCTC 59.180 52.381 0.00 0.00 0.00 2.87
889 999 2.096248 CTCTCTACCACGCCTTTCTCT 58.904 52.381 0.00 0.00 0.00 3.10
890 1000 2.093106 TCTCTACCACGCCTTTCTCTC 58.907 52.381 0.00 0.00 0.00 3.20
891 1001 1.819288 CTCTACCACGCCTTTCTCTCA 59.181 52.381 0.00 0.00 0.00 3.27
892 1002 2.231478 CTCTACCACGCCTTTCTCTCAA 59.769 50.000 0.00 0.00 0.00 3.02
987 1097 1.756408 ATCTCCTCGCCATCCTGCTG 61.756 60.000 0.00 0.00 0.00 4.41
1055 1165 0.773644 ACTTGGTTCACAGCCCAGAT 59.226 50.000 0.00 0.00 31.04 2.90
1444 1554 0.914644 CCTCTCCTTCAATGGCCTCA 59.085 55.000 3.32 0.00 0.00 3.86
1551 1661 1.702957 CCTTCCCTCACCAACCTAACA 59.297 52.381 0.00 0.00 0.00 2.41
1717 1827 6.729428 ACTAAACTAGGCTACTTAGGACTGA 58.271 40.000 17.05 0.00 0.00 3.41
1728 1838 4.461198 ACTTAGGACTGACCCAAAACTTG 58.539 43.478 0.00 0.00 40.05 3.16
1738 1848 4.038642 TGACCCAAAACTTGCTTATTGGTC 59.961 41.667 0.00 0.00 40.55 4.02
1766 1876 3.131223 CCTCACGAGATGACACACCTTAT 59.869 47.826 0.00 0.00 32.37 1.73
1812 1922 3.003171 CACACAATCAATTCACGTCCACA 59.997 43.478 0.00 0.00 0.00 4.17
1983 2093 4.515191 CCTTTGAGTCTCGGAAATTTGACA 59.485 41.667 0.00 0.00 32.41 3.58
2004 2114 5.363101 ACAATGCTCACATATCTGTACCTG 58.637 41.667 0.00 0.00 34.62 4.00
2115 2225 2.224450 TGGTGATCTGCCATCTAGCATG 60.224 50.000 5.64 0.00 43.09 4.06
2244 2354 2.154854 TCAACAAGTTCTCTGGCTCG 57.845 50.000 0.00 0.00 0.00 5.03
2482 2592 2.487986 CCAGGAAGTTTCAAGGACTGCT 60.488 50.000 0.00 0.00 0.00 4.24
2793 2903 9.469807 CTAGTCAACCTATATTTGCTAGACTTG 57.530 37.037 0.00 0.00 35.23 3.16
2806 2916 8.574251 TTTGCTAGACTTGAGCCAAAATAATA 57.426 30.769 0.00 0.00 39.30 0.98
3003 3113 4.273148 ACTGATTCACCTACAGACAACC 57.727 45.455 0.00 0.00 35.85 3.77
3023 3133 2.947652 CCCTTGATGTCAGCCATAACAG 59.052 50.000 0.00 0.00 32.56 3.16
3220 3330 3.644966 ATTCCTCGGCAGAATGGTTTA 57.355 42.857 0.00 0.00 35.86 2.01
3298 3408 5.242171 TCTGCTGCAAATCATCAGAAAAAGA 59.758 36.000 3.02 0.00 42.87 2.52
3307 3417 9.485206 CAAATCATCAGAAAAAGAACCAAATCT 57.515 29.630 0.00 0.00 0.00 2.40
3325 3435 7.507616 ACCAAATCTTCATGTTAAAAGTGGGTA 59.492 33.333 0.00 0.00 0.00 3.69
3742 3853 5.575157 TGGTTTGCCAATACATAGAAAGGA 58.425 37.500 0.00 0.00 42.83 3.36
3808 3919 3.928727 TTGATTGGCAGAAAAGAGCAG 57.071 42.857 0.00 0.00 0.00 4.24
3827 3938 3.427233 GCAGTTCTCATCAAGGATGTTGC 60.427 47.826 6.15 6.45 40.55 4.17
3984 4095 0.249120 ATTCATCGAACTGGACCGCA 59.751 50.000 0.00 0.00 0.00 5.69
4014 4125 0.249280 CATACGGCTACATCGCACCA 60.249 55.000 0.00 0.00 0.00 4.17
4020 4131 1.287425 GCTACATCGCACCAGGTAAC 58.713 55.000 0.00 0.00 0.00 2.50
4022 4133 1.480954 CTACATCGCACCAGGTAACCT 59.519 52.381 0.00 0.00 37.17 3.50
4036 4147 1.066358 GTAACCTGACTACCCCAGTGC 60.066 57.143 0.00 0.00 37.72 4.40
4039 4150 0.036010 CCTGACTACCCCAGTGCAAG 60.036 60.000 0.00 0.00 37.72 4.01
4091 4202 7.539034 AAAACAATCCCTTGTAACTATGCTT 57.461 32.000 0.00 0.00 44.83 3.91
4535 4697 6.712547 GTCGGAATCAAGAATGAATTCCCTAT 59.287 38.462 2.27 0.00 38.57 2.57
4547 4709 4.141620 TGAATTCCCTATCAAGCTCACCTC 60.142 45.833 2.27 0.00 0.00 3.85
4553 4715 4.101585 CCCTATCAAGCTCACCTCATAACA 59.898 45.833 0.00 0.00 0.00 2.41
4611 4773 3.279434 GACGCATCCCTTTCCAATTAGT 58.721 45.455 0.00 0.00 0.00 2.24
4618 4780 5.466127 TCCCTTTCCAATTAGTAATGGCT 57.534 39.130 0.00 0.00 36.62 4.75
4701 4863 5.278957 GGCACTTTGCTTCTTTTTATCTCCA 60.279 40.000 0.00 0.00 44.28 3.86
4734 4896 1.306739 CGGGGGTAGGGAAGAAGGT 60.307 63.158 0.00 0.00 0.00 3.50
4771 4933 1.405933 GCATTTTGATGGGCCTTGGAC 60.406 52.381 4.53 0.00 0.00 4.02
4782 4944 2.280628 GGCCTTGGACGACAGAAATAG 58.719 52.381 0.00 0.00 0.00 1.73
4828 4990 0.474184 ATCCAAGGTCGGCCCAATAG 59.526 55.000 0.08 0.00 34.66 1.73
4866 5028 3.848917 GCGACTATTCATTCGTAGCGACT 60.849 47.826 0.00 0.00 37.56 4.18
4867 5029 4.280461 CGACTATTCATTCGTAGCGACTT 58.720 43.478 0.00 0.00 34.89 3.01
4868 5030 4.376279 CGACTATTCATTCGTAGCGACTTC 59.624 45.833 0.00 0.00 34.89 3.01
4885 5051 2.203538 CCCATACCTGGCCATGGC 60.204 66.667 29.47 29.47 41.64 4.40
5002 5168 2.352388 GGCCTGTCGTATTTGCAGTTA 58.648 47.619 0.00 0.00 0.00 2.24
5006 5172 4.153475 GCCTGTCGTATTTGCAGTTAAAGA 59.847 41.667 0.00 0.00 0.00 2.52
5023 5196 1.079057 GAAAGAGGTCTGGCCCGAC 60.079 63.158 18.35 18.35 38.26 4.79
5116 5289 1.079503 CTCGTGCCTAGGTTTTCTGC 58.920 55.000 11.31 0.00 0.00 4.26
5117 5290 0.394938 TCGTGCCTAGGTTTTCTGCA 59.605 50.000 11.31 0.00 0.00 4.41
5120 5293 2.716217 GTGCCTAGGTTTTCTGCATCT 58.284 47.619 11.31 0.00 34.04 2.90
5123 5296 2.619074 GCCTAGGTTTTCTGCATCTGGT 60.619 50.000 11.31 0.00 0.00 4.00
5128 5301 3.960102 AGGTTTTCTGCATCTGGTTTTGA 59.040 39.130 0.00 0.00 0.00 2.69
5170 5343 0.836400 ATGGCCAGGTATACTCCCCG 60.836 60.000 13.05 0.00 0.00 5.73
5201 5374 1.079543 CTGCAGCGAGCCAGTAGTT 60.080 57.895 0.00 0.00 44.83 2.24
5239 5412 1.350193 GTGATCTCGTCACGCATGTT 58.650 50.000 0.00 0.00 46.99 2.71
5241 5414 1.992667 TGATCTCGTCACGCATGTTTC 59.007 47.619 0.00 0.00 0.00 2.78
5247 5420 4.149922 TCTCGTCACGCATGTTTCTTTTAG 59.850 41.667 0.00 0.00 0.00 1.85
5350 5524 7.223582 ACAACAGATCTAGAAGATGTAAATGCG 59.776 37.037 0.00 0.00 34.53 4.73
5359 5533 6.817184 AGAAGATGTAAATGCGGTGTATACT 58.183 36.000 4.17 0.00 0.00 2.12
5366 5540 7.911343 TGTAAATGCGGTGTATACTAATGTTG 58.089 34.615 4.17 0.00 0.00 3.33
5391 5565 7.020602 GGCACAATTTATAAAAACCACATTGC 58.979 34.615 1.21 3.41 0.00 3.56
5393 5567 8.072567 GCACAATTTATAAAAACCACATTGCAA 58.927 29.630 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 7.820648 TCTTTATGTTTCTCATTCTTCAAGCC 58.179 34.615 0.00 0.00 37.91 4.35
47 48 4.342862 TGTTCAGTGCTCTTAGCTCTTT 57.657 40.909 0.00 0.00 41.75 2.52
48 49 4.550076 ATGTTCAGTGCTCTTAGCTCTT 57.450 40.909 0.00 0.00 41.75 2.85
49 50 4.550076 AATGTTCAGTGCTCTTAGCTCT 57.450 40.909 0.00 0.00 44.91 4.09
50 51 5.872070 AGTAAATGTTCAGTGCTCTTAGCTC 59.128 40.000 0.00 0.00 42.97 4.09
51 52 5.799213 AGTAAATGTTCAGTGCTCTTAGCT 58.201 37.500 0.00 0.00 42.97 3.32
52 53 7.596749 TTAGTAAATGTTCAGTGCTCTTAGC 57.403 36.000 0.00 0.00 42.82 3.09
53 54 8.988934 TGTTTAGTAAATGTTCAGTGCTCTTAG 58.011 33.333 0.00 0.00 0.00 2.18
54 55 8.896320 TGTTTAGTAAATGTTCAGTGCTCTTA 57.104 30.769 0.00 0.00 0.00 2.10
55 56 7.715249 TCTGTTTAGTAAATGTTCAGTGCTCTT 59.285 33.333 0.00 0.00 0.00 2.85
56 57 7.217200 TCTGTTTAGTAAATGTTCAGTGCTCT 58.783 34.615 0.00 0.00 0.00 4.09
57 58 7.421530 TCTGTTTAGTAAATGTTCAGTGCTC 57.578 36.000 0.00 0.00 0.00 4.26
58 59 7.094634 CCATCTGTTTAGTAAATGTTCAGTGCT 60.095 37.037 0.00 0.00 0.00 4.40
59 60 7.023575 CCATCTGTTTAGTAAATGTTCAGTGC 58.976 38.462 0.00 0.00 0.00 4.40
60 61 8.322906 TCCATCTGTTTAGTAAATGTTCAGTG 57.677 34.615 0.00 3.65 0.00 3.66
408 416 1.667212 GTTTTTCGGGTTCGTGTGTCT 59.333 47.619 0.00 0.00 37.69 3.41
411 419 0.029700 GGGTTTTTCGGGTTCGTGTG 59.970 55.000 0.00 0.00 37.69 3.82
413 421 0.739561 TTGGGTTTTTCGGGTTCGTG 59.260 50.000 0.00 0.00 37.69 4.35
414 422 0.740149 GTTGGGTTTTTCGGGTTCGT 59.260 50.000 0.00 0.00 37.69 3.85
415 423 0.739561 TGTTGGGTTTTTCGGGTTCG 59.260 50.000 0.00 0.00 37.82 3.95
416 424 2.963548 TTGTTGGGTTTTTCGGGTTC 57.036 45.000 0.00 0.00 0.00 3.62
417 425 5.354842 TTTATTGTTGGGTTTTTCGGGTT 57.645 34.783 0.00 0.00 0.00 4.11
447 554 2.807895 CCGCGTACCAGGTCGTTG 60.808 66.667 4.92 0.00 0.00 4.10
448 555 2.985282 TCCGCGTACCAGGTCGTT 60.985 61.111 4.92 0.00 0.00 3.85
469 576 1.278637 GCGTGTTGGTTTGTCCTCG 59.721 57.895 0.00 0.00 37.07 4.63
484 591 2.370281 ATTCACACGAATCTCTGCGT 57.630 45.000 0.00 0.00 37.25 5.24
509 616 1.732809 GCTCTAGCCGTTTTTCTGTCC 59.267 52.381 0.00 0.00 34.31 4.02
524 631 7.606456 AGATGTCTGTTTTTAAATTCGGCTCTA 59.394 33.333 0.00 0.00 0.00 2.43
525 632 6.431234 AGATGTCTGTTTTTAAATTCGGCTCT 59.569 34.615 0.00 0.00 0.00 4.09
868 978 1.819903 GAGAAAGGCGTGGTAGAGAGT 59.180 52.381 0.00 0.00 0.00 3.24
870 980 2.093106 GAGAGAAAGGCGTGGTAGAGA 58.907 52.381 0.00 0.00 0.00 3.10
871 981 1.819288 TGAGAGAAAGGCGTGGTAGAG 59.181 52.381 0.00 0.00 0.00 2.43
872 982 1.919240 TGAGAGAAAGGCGTGGTAGA 58.081 50.000 0.00 0.00 0.00 2.59
873 983 2.028930 AGTTGAGAGAAAGGCGTGGTAG 60.029 50.000 0.00 0.00 0.00 3.18
874 984 1.968493 AGTTGAGAGAAAGGCGTGGTA 59.032 47.619 0.00 0.00 0.00 3.25
875 985 0.759346 AGTTGAGAGAAAGGCGTGGT 59.241 50.000 0.00 0.00 0.00 4.16
876 986 1.001406 AGAGTTGAGAGAAAGGCGTGG 59.999 52.381 0.00 0.00 0.00 4.94
877 987 2.029470 AGAGAGTTGAGAGAAAGGCGTG 60.029 50.000 0.00 0.00 0.00 5.34
878 988 2.243810 AGAGAGTTGAGAGAAAGGCGT 58.756 47.619 0.00 0.00 0.00 5.68
879 989 3.428316 GGTAGAGAGTTGAGAGAAAGGCG 60.428 52.174 0.00 0.00 0.00 5.52
880 990 3.511934 TGGTAGAGAGTTGAGAGAAAGGC 59.488 47.826 0.00 0.00 0.00 4.35
881 991 4.524714 TGTGGTAGAGAGTTGAGAGAAAGG 59.475 45.833 0.00 0.00 0.00 3.11
882 992 5.713792 TGTGGTAGAGAGTTGAGAGAAAG 57.286 43.478 0.00 0.00 0.00 2.62
883 993 6.948886 ACTATGTGGTAGAGAGTTGAGAGAAA 59.051 38.462 0.00 0.00 34.38 2.52
884 994 6.486056 ACTATGTGGTAGAGAGTTGAGAGAA 58.514 40.000 0.00 0.00 34.38 2.87
885 995 6.068461 ACTATGTGGTAGAGAGTTGAGAGA 57.932 41.667 0.00 0.00 34.38 3.10
886 996 6.261381 GGTACTATGTGGTAGAGAGTTGAGAG 59.739 46.154 0.00 0.00 34.38 3.20
887 997 6.120905 GGTACTATGTGGTAGAGAGTTGAGA 58.879 44.000 0.00 0.00 34.38 3.27
888 998 5.886474 TGGTACTATGTGGTAGAGAGTTGAG 59.114 44.000 0.00 0.00 34.38 3.02
889 999 5.651139 GTGGTACTATGTGGTAGAGAGTTGA 59.349 44.000 0.00 0.00 34.38 3.18
890 1000 5.163540 GGTGGTACTATGTGGTAGAGAGTTG 60.164 48.000 0.00 0.00 34.38 3.16
891 1001 4.954826 GGTGGTACTATGTGGTAGAGAGTT 59.045 45.833 0.00 0.00 34.38 3.01
892 1002 4.534797 GGTGGTACTATGTGGTAGAGAGT 58.465 47.826 0.00 0.00 34.38 3.24
927 1037 1.875576 GCAGGAGTAGCCATGGATTCG 60.876 57.143 18.40 0.00 40.02 3.34
957 1067 1.406065 CGAGGAGATGGAGCCATGGT 61.406 60.000 14.67 0.00 36.70 3.55
987 1097 1.373570 CGAACATGGAAGGGAGAAGC 58.626 55.000 0.00 0.00 0.00 3.86
1551 1661 7.118971 GTGAACAGACTTAAATCTCTGAGCAAT 59.881 37.037 0.00 0.00 37.85 3.56
1717 1827 3.323691 GGACCAATAAGCAAGTTTTGGGT 59.676 43.478 7.91 0.00 42.34 4.51
1728 1838 2.952310 GTGAGGAATGGGACCAATAAGC 59.048 50.000 0.00 0.00 0.00 3.09
1738 1848 1.482182 TGTCATCTCGTGAGGAATGGG 59.518 52.381 3.12 0.00 37.56 4.00
1766 1876 7.598869 GTGATATCATGAGCACGGTAAGATTAA 59.401 37.037 9.02 0.00 0.00 1.40
1812 1922 1.927487 TTGTGATTGCTGCAGGGATT 58.073 45.000 17.12 0.00 0.00 3.01
1983 2093 5.620738 ACAGGTACAGATATGTGAGCATT 57.379 39.130 6.90 0.00 36.58 3.56
2004 2114 3.057734 CCCAGACAAGTTGTTCTCGTAC 58.942 50.000 10.45 0.00 0.00 3.67
2482 2592 3.031013 TGTCGAGGATGATTAAGGAGCA 58.969 45.455 0.00 0.00 0.00 4.26
2793 2903 8.284945 TGCATCCAGATATATTATTTTGGCTC 57.715 34.615 0.00 0.00 0.00 4.70
2815 2925 3.640498 TGACCAATGTTTTGAGGAATGCA 59.360 39.130 0.00 0.00 34.60 3.96
3003 3113 2.357009 GCTGTTATGGCTGACATCAAGG 59.643 50.000 0.00 0.00 41.03 3.61
3023 3133 0.106519 AGGAATGGCACCATGTAGGC 60.107 55.000 2.19 0.00 43.14 3.93
3114 3224 0.966370 GGAGTCCTGCTACCGTGTCT 60.966 60.000 0.41 0.00 0.00 3.41
3220 3330 3.181471 CCGCAGAGACCTCTATTGTGAAT 60.181 47.826 0.00 0.00 37.98 2.57
3298 3408 7.147567 ACCCACTTTTAACATGAAGATTTGGTT 60.148 33.333 0.00 0.00 0.00 3.67
3325 3435 5.580022 AGTAATAGCCACAAAAACAGGGAT 58.420 37.500 0.00 0.00 0.00 3.85
3742 3853 2.246067 TCAGGATTGAGGCTAGACTCCT 59.754 50.000 23.17 10.79 36.66 3.69
3808 3919 2.476854 GCGCAACATCCTTGATGAGAAC 60.477 50.000 0.30 0.00 42.09 3.01
3827 3938 3.802685 GTGTAGGTAGGAAATAGCTTGCG 59.197 47.826 0.00 0.00 42.26 4.85
3921 4032 1.593196 CAAAGTCCGAGACAAAGGCA 58.407 50.000 6.78 0.00 34.60 4.75
3984 4095 3.467226 CCGTATGTCCCCGCCAGT 61.467 66.667 0.00 0.00 0.00 4.00
4014 4125 1.435959 ACTGGGGTAGTCAGGTTACCT 59.564 52.381 0.00 0.00 40.36 3.08
4020 4131 0.036010 CTTGCACTGGGGTAGTCAGG 60.036 60.000 0.00 0.00 37.60 3.86
4022 4133 1.127567 AGCTTGCACTGGGGTAGTCA 61.128 55.000 0.00 0.00 37.60 3.41
4023 4134 0.674895 CAGCTTGCACTGGGGTAGTC 60.675 60.000 0.00 0.00 37.60 2.59
4036 4147 7.088589 AGCTATGTAATTAACCAACAGCTTG 57.911 36.000 8.55 0.00 0.00 4.01
4039 4150 5.823045 AGGAGCTATGTAATTAACCAACAGC 59.177 40.000 0.00 0.00 0.00 4.40
4296 4407 5.221461 ACCGATATTAGCCGATTGATATCCC 60.221 44.000 0.00 0.00 31.07 3.85
4399 4510 2.172293 GCAACTCAGGGAATCAGGATCT 59.828 50.000 0.00 0.00 0.00 2.75
4535 4697 3.327757 AGGTTGTTATGAGGTGAGCTTGA 59.672 43.478 0.00 0.00 0.00 3.02
4547 4709 2.614057 GCGAAGATCCCAGGTTGTTATG 59.386 50.000 0.00 0.00 0.00 1.90
4553 4715 2.998949 GGGCGAAGATCCCAGGTT 59.001 61.111 0.00 0.00 43.37 3.50
4611 4773 3.347216 GAGAGCCAAGACAAAGCCATTA 58.653 45.455 0.00 0.00 0.00 1.90
4618 4780 1.149101 AAGGGGAGAGCCAAGACAAA 58.851 50.000 0.00 0.00 35.15 2.83
4771 4933 4.396166 ACAATGGGCTTTCTATTTCTGTCG 59.604 41.667 0.00 0.00 0.00 4.35
4782 4944 1.337167 GGCTGTGAACAATGGGCTTTC 60.337 52.381 0.00 0.00 0.00 2.62
4819 4981 2.363359 CTGCTGAATTTCCTATTGGGCC 59.637 50.000 0.00 0.00 34.39 5.80
4828 4990 0.392998 TCGCTCCCTGCTGAATTTCC 60.393 55.000 0.00 0.00 40.11 3.13
4847 5009 4.499357 GGGAAGTCGCTACGAATGAATAGT 60.499 45.833 0.00 0.00 37.72 2.12
4848 5010 3.982058 GGGAAGTCGCTACGAATGAATAG 59.018 47.826 0.00 0.00 37.72 1.73
4849 5011 3.382227 TGGGAAGTCGCTACGAATGAATA 59.618 43.478 0.00 0.00 37.72 1.75
4850 5012 2.167693 TGGGAAGTCGCTACGAATGAAT 59.832 45.455 0.00 0.00 37.72 2.57
4851 5013 1.546923 TGGGAAGTCGCTACGAATGAA 59.453 47.619 0.00 0.00 37.72 2.57
4852 5014 1.179152 TGGGAAGTCGCTACGAATGA 58.821 50.000 0.00 0.00 37.72 2.57
4853 5015 2.225068 ATGGGAAGTCGCTACGAATG 57.775 50.000 0.00 0.00 37.72 2.67
4885 5051 4.517934 CCATCTGGGCCTGGCTGG 62.518 72.222 19.68 13.96 39.35 4.85
4977 5143 0.108329 CAAATACGACAGGCCCGAGT 60.108 55.000 6.90 0.00 0.00 4.18
5002 5168 0.036875 CGGGCCAGACCTCTTTCTTT 59.963 55.000 4.39 0.00 39.10 2.52
5006 5172 2.943978 CGTCGGGCCAGACCTCTTT 61.944 63.158 27.38 0.00 37.85 2.52
5035 5208 1.184970 CCCGGCCCAACAGTCAAAAT 61.185 55.000 0.00 0.00 0.00 1.82
5076 5249 2.357517 GGCACGGCCCTATCATCG 60.358 66.667 0.00 0.00 44.06 3.84
5101 5274 2.618816 CCAGATGCAGAAAACCTAGGCA 60.619 50.000 9.30 0.00 39.03 4.75
5116 5289 1.949525 CGGGCCTATCAAAACCAGATG 59.050 52.381 0.84 0.00 0.00 2.90
5117 5290 1.133792 CCGGGCCTATCAAAACCAGAT 60.134 52.381 0.84 0.00 0.00 2.90
5120 5293 1.379309 GCCGGGCCTATCAAAACCA 60.379 57.895 8.12 0.00 0.00 3.67
5201 5374 1.136695 ACGTTGTTACTCGACCAACCA 59.863 47.619 7.36 0.00 36.06 3.67
5204 5377 2.867287 TCACGTTGTTACTCGACCAA 57.133 45.000 7.36 0.00 0.00 3.67
5210 5383 3.818387 TGACGAGATCACGTTGTTACTC 58.182 45.455 19.13 5.60 46.52 2.59
5320 5494 9.645059 TTTACATCTTCTAGATCTGTTGTGAAG 57.355 33.333 5.18 10.71 31.32 3.02
5330 5504 5.986135 ACACCGCATTTACATCTTCTAGATC 59.014 40.000 0.00 0.00 31.32 2.75
5333 5507 8.082852 AGTATACACCGCATTTACATCTTCTAG 58.917 37.037 5.50 0.00 0.00 2.43
5350 5524 6.693315 ATTGTGCCAACATTAGTATACACC 57.307 37.500 5.50 0.00 35.83 4.16
5359 5533 9.778741 TGGTTTTTATAAATTGTGCCAACATTA 57.221 25.926 0.00 0.00 35.83 1.90
5366 5540 7.020602 GCAATGTGGTTTTTATAAATTGTGCC 58.979 34.615 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.