Multiple sequence alignment - TraesCS4D01G117100

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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 TraesCS4D01G117100 chr4D 100.000 3740 0 0 1 3740 97956926 97960665 0.000000e+00 6907.0
1 TraesCS4D01G117100 chr4D 86.830 896 61 34 819 1681 97508442 97509313 0.000000e+00 948.0
2 TraesCS4D01G117100 chr4D 88.842 717 49 14 990 1681 97605241 97605951 0.000000e+00 852.0
3 TraesCS4D01G117100 chr4D 88.604 702 49 14 990 1675 97720614 97721300 0.000000e+00 824.0
4 TraesCS4D01G117100 chr4D 85.444 529 59 11 2227 2742 97760788 97760265 5.500000e-148 534.0
5 TraesCS4D01G117100 chr4D 86.235 494 58 8 2258 2742 97509918 97510410 9.200000e-146 527.0
6 TraesCS4D01G117100 chr4D 85.628 494 61 8 2258 2742 97606572 97607064 9.270000e-141 510.0
7 TraesCS4D01G117100 chr4D 81.991 422 28 19 13 424 97604372 97604755 7.800000e-82 315.0
8 TraesCS4D01G117100 chr4D 81.991 422 28 19 13 424 97717801 97718184 7.800000e-82 315.0
9 TraesCS4D01G117100 chr4D 83.884 242 16 9 704 928 97604995 97605230 3.790000e-50 209.0
10 TraesCS4D01G117100 chr4D 81.731 208 23 4 704 897 97718424 97718630 3.870000e-35 159.0
11 TraesCS4D01G117100 chr4A 92.624 1871 97 21 1 1853 478220699 478218852 0.000000e+00 2652.0
12 TraesCS4D01G117100 chr4A 91.029 1215 66 33 2201 3386 478218416 478217216 0.000000e+00 1600.0
13 TraesCS4D01G117100 chr4A 85.458 1004 78 35 704 1672 478340330 478339360 0.000000e+00 983.0
14 TraesCS4D01G117100 chr4A 84.946 1023 74 38 708 1685 478303030 478302043 0.000000e+00 963.0
15 TraesCS4D01G117100 chr4A 95.687 371 13 3 3365 3733 478217166 478216797 8.940000e-166 593.0
16 TraesCS4D01G117100 chr4A 86.895 496 53 8 2258 2742 478338855 478338361 2.540000e-151 545.0
17 TraesCS4D01G117100 chr4A 89.858 424 41 2 2341 2764 478300959 478300538 9.140000e-151 544.0
18 TraesCS4D01G117100 chr4A 93.333 225 10 2 1868 2087 478218868 478218644 1.000000e-85 327.0
19 TraesCS4D01G117100 chr4A 77.641 407 32 24 22 424 478303606 478303255 3.810000e-45 193.0
20 TraesCS4D01G117100 chr4A 83.152 184 21 6 1970 2146 478339108 478338928 3.870000e-35 159.0
21 TraesCS4D01G117100 chr4A 94.828 58 3 0 2003 2060 478301799 478301742 1.430000e-14 91.6
22 TraesCS4D01G117100 chr4B 88.629 1539 67 37 1868 3383 139545517 139546970 0.000000e+00 1773.0
23 TraesCS4D01G117100 chr4B 88.999 909 51 17 1 898 139544372 139545242 0.000000e+00 1079.0
24 TraesCS4D01G117100 chr4B 85.545 1010 68 39 704 1679 139398828 139399793 0.000000e+00 985.0
25 TraesCS4D01G117100 chr4B 85.402 1007 68 41 705 1679 139471978 139472937 0.000000e+00 972.0
26 TraesCS4D01G117100 chr4B 85.402 1007 68 41 705 1679 139510426 139511385 0.000000e+00 972.0
27 TraesCS4D01G117100 chr4B 96.011 376 13 2 3365 3738 139547052 139547427 8.880000e-171 610.0
28 TraesCS4D01G117100 chr4B 87.349 498 34 10 1181 1675 139511506 139511977 9.140000e-151 544.0
29 TraesCS4D01G117100 chr4B 86.437 494 57 8 2258 2742 139400305 139400797 1.980000e-147 532.0
30 TraesCS4D01G117100 chr4B 86.410 493 59 6 2258 2742 139473449 139473941 1.980000e-147 532.0
31 TraesCS4D01G117100 chr4B 81.765 170 25 4 1981 2146 139532005 139532172 1.810000e-28 137.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G117100 chr4D 97956926 97960665 3739 False 6907.000000 6907 100.000000 1 3740 1 chr4D.!!$F1 3739
1 TraesCS4D01G117100 chr4D 97508442 97510410 1968 False 737.500000 948 86.532500 819 2742 2 chr4D.!!$F2 1923
2 TraesCS4D01G117100 chr4D 97760265 97760788 523 True 534.000000 534 85.444000 2227 2742 1 chr4D.!!$R1 515
3 TraesCS4D01G117100 chr4D 97604372 97607064 2692 False 471.500000 852 85.086250 13 2742 4 chr4D.!!$F3 2729
4 TraesCS4D01G117100 chr4D 97717801 97721300 3499 False 432.666667 824 84.108667 13 1675 3 chr4D.!!$F4 1662
5 TraesCS4D01G117100 chr4A 478216797 478220699 3902 True 1293.000000 2652 93.168250 1 3733 4 chr4A.!!$R1 3732
6 TraesCS4D01G117100 chr4A 478338361 478340330 1969 True 562.333333 983 85.168333 704 2742 3 chr4A.!!$R3 2038
7 TraesCS4D01G117100 chr4A 478300538 478303606 3068 True 447.900000 963 86.818250 22 2764 4 chr4A.!!$R2 2742
8 TraesCS4D01G117100 chr4B 139544372 139547427 3055 False 1154.000000 1773 91.213000 1 3738 3 chr4B.!!$F5 3737
9 TraesCS4D01G117100 chr4B 139398828 139400797 1969 False 758.500000 985 85.991000 704 2742 2 chr4B.!!$F2 2038
10 TraesCS4D01G117100 chr4B 139510426 139511977 1551 False 758.000000 972 86.375500 705 1679 2 chr4B.!!$F4 974
11 TraesCS4D01G117100 chr4B 139471978 139473941 1963 False 752.000000 972 85.906000 705 2742 2 chr4B.!!$F3 2037

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
698 754 0.171455 GGCCGGATCGATGTAGCTAG 59.829 60.0 5.05 0.0 0.00 3.42 F
1715 3827 0.039978 TGCACGTTAACCGCCAAATG 60.040 50.0 11.10 0.0 41.42 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2327 5290 0.605319 TGGAACAAGTGATGGGTCGC 60.605 55.0 0.0 0.00 31.92 5.19 R
3110 6269 0.314935 GCCAAACTTTGCTGCTGCTA 59.685 50.0 17.0 6.36 40.48 3.49 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
140 149 3.314635 CCAGTTTCTAAGGATGAGCATGC 59.685 47.826 10.51 10.51 0.00 4.06
153 163 1.413445 GAGCATGCATGGGCCAAATAA 59.587 47.619 27.34 0.00 40.13 1.40
243 264 2.830923 GGATGGTCGGATCATCATCTCT 59.169 50.000 27.45 0.00 41.89 3.10
251 272 5.404968 GTCGGATCATCATCTCTTTCATGAC 59.595 44.000 0.00 0.00 33.04 3.06
280 301 3.147629 CGGTAGGCAGTAGCTACATACT 58.852 50.000 25.28 19.61 41.70 2.12
295 316 3.215151 ACATACTGATCGAGACGTGGAT 58.785 45.455 0.00 0.00 0.00 3.41
296 317 4.386711 ACATACTGATCGAGACGTGGATA 58.613 43.478 0.00 0.00 0.00 2.59
298 319 5.473846 ACATACTGATCGAGACGTGGATAAT 59.526 40.000 0.00 0.00 0.00 1.28
299 320 4.920640 ACTGATCGAGACGTGGATAATT 57.079 40.909 0.00 0.00 0.00 1.40
300 321 5.263968 ACTGATCGAGACGTGGATAATTT 57.736 39.130 0.00 0.00 0.00 1.82
321 342 3.153919 TCCTTGACATTTGTTGGGTAGC 58.846 45.455 0.00 0.00 0.00 3.58
323 344 1.529226 TGACATTTGTTGGGTAGCGG 58.471 50.000 0.00 0.00 0.00 5.52
414 435 2.415512 GTGTCGCCTTAAAGTCCATGTC 59.584 50.000 0.00 0.00 0.00 3.06
536 576 3.087031 CACAGGAAAGCAACATGAGGAT 58.913 45.455 0.00 0.00 0.00 3.24
547 587 4.302455 CAACATGAGGATACGGAGTCATC 58.698 47.826 0.00 0.00 43.93 2.92
607 663 1.499056 GATTGCACAGTGTCGGCAG 59.501 57.895 8.15 0.00 38.97 4.85
618 674 1.968540 GTCGGCAGGCAGCTTTTCT 60.969 57.895 0.81 0.00 44.79 2.52
696 752 2.920645 CGGCCGGATCGATGTAGCT 61.921 63.158 20.10 0.00 0.00 3.32
697 753 1.583495 CGGCCGGATCGATGTAGCTA 61.583 60.000 20.10 0.00 0.00 3.32
698 754 0.171455 GGCCGGATCGATGTAGCTAG 59.829 60.000 5.05 0.00 0.00 3.42
699 755 0.456995 GCCGGATCGATGTAGCTAGC 60.457 60.000 5.05 6.62 0.00 3.42
700 756 0.881796 CCGGATCGATGTAGCTAGCA 59.118 55.000 18.83 0.00 0.00 3.49
702 758 1.401670 CGGATCGATGTAGCTAGCACC 60.402 57.143 18.83 7.11 0.00 5.01
706 763 1.209275 CGATGTAGCTAGCACCGTGC 61.209 60.000 18.83 16.04 45.46 5.34
812 901 9.682465 TCTAATAATATACGATGGCAGACTAGT 57.318 33.333 0.00 0.00 0.00 2.57
815 904 9.463902 AATAATATACGATGGCAGACTAGTACT 57.536 33.333 0.00 0.00 0.00 2.73
816 905 6.988622 ATATACGATGGCAGACTAGTACTC 57.011 41.667 0.00 0.00 0.00 2.59
817 906 2.299521 ACGATGGCAGACTAGTACTCC 58.700 52.381 0.00 0.00 0.00 3.85
940 2976 6.354130 AGCCACTATCTATCTAGCTAGCTAC 58.646 44.000 20.67 6.24 0.00 3.58
941 2977 6.157994 AGCCACTATCTATCTAGCTAGCTACT 59.842 42.308 20.67 12.94 0.00 2.57
943 2979 7.656137 GCCACTATCTATCTAGCTAGCTACTAG 59.344 44.444 20.67 20.81 38.79 2.57
961 2997 6.913673 GCTACTAGCTAGATAACACACTTGAC 59.086 42.308 27.45 0.00 38.45 3.18
1041 3084 0.324738 TCCTGGTCTCGCTCATCCTT 60.325 55.000 0.00 0.00 0.00 3.36
1302 3356 2.993264 TCCGTCAGGGGGTTCGAC 60.993 66.667 0.00 0.00 38.33 4.20
1321 3375 3.345737 GTCATCGACGCCATCAAGA 57.654 52.632 0.00 0.00 0.00 3.02
1424 3482 7.921786 TGGTAAGTATCCATGCATATAAAGC 57.078 36.000 0.00 0.00 0.00 3.51
1534 3609 0.991920 GTTGGGAGGTGAAGATGGGA 59.008 55.000 0.00 0.00 0.00 4.37
1682 3763 4.324408 CCCTCTCAGGTAGTACTACACACT 60.324 50.000 29.38 17.22 37.78 3.55
1715 3827 0.039978 TGCACGTTAACCGCCAAATG 60.040 50.000 11.10 0.00 41.42 2.32
1856 4017 6.509418 TGCAGTCTTAATAACCAACATTCC 57.491 37.500 0.00 0.00 0.00 3.01
1858 4019 5.163550 GCAGTCTTAATAACCAACATTCCCC 60.164 44.000 0.00 0.00 0.00 4.81
1859 4020 6.187682 CAGTCTTAATAACCAACATTCCCCT 58.812 40.000 0.00 0.00 0.00 4.79
1861 4022 7.832187 CAGTCTTAATAACCAACATTCCCCTAA 59.168 37.037 0.00 0.00 0.00 2.69
1867 4028 8.499288 AATAACCAACATTCCCCTAAAAAGAA 57.501 30.769 0.00 0.00 0.00 2.52
1868 4029 6.419484 AACCAACATTCCCCTAAAAAGAAG 57.581 37.500 0.00 0.00 0.00 2.85
1869 4030 5.464069 ACCAACATTCCCCTAAAAAGAAGT 58.536 37.500 0.00 0.00 0.00 3.01
1870 4031 5.538813 ACCAACATTCCCCTAAAAAGAAGTC 59.461 40.000 0.00 0.00 0.00 3.01
1872 4033 6.267699 CCAACATTCCCCTAAAAAGAAGTCTT 59.732 38.462 0.00 0.00 37.91 3.01
1873 4034 7.450323 CCAACATTCCCCTAAAAAGAAGTCTTA 59.550 37.037 0.00 0.00 34.61 2.10
1874 4035 8.856103 CAACATTCCCCTAAAAAGAAGTCTTAA 58.144 33.333 0.00 0.00 34.61 1.85
2083 4351 8.581253 ACCTTTTCTCAGGATTAACCAAATAG 57.419 34.615 0.00 0.00 42.04 1.73
2114 4532 7.057894 ACAAGTGGTGAATTAGAAAGTTGGTA 58.942 34.615 0.00 0.00 0.00 3.25
2115 4533 7.228706 ACAAGTGGTGAATTAGAAAGTTGGTAG 59.771 37.037 0.00 0.00 0.00 3.18
2116 4534 6.838382 AGTGGTGAATTAGAAAGTTGGTAGT 58.162 36.000 0.00 0.00 0.00 2.73
2192 4611 9.502091 ACTATAGATAACAACAGCAAAAACTGA 57.498 29.630 6.78 0.00 40.25 3.41
2195 4614 7.516198 AGATAACAACAGCAAAAACTGATCT 57.484 32.000 0.00 0.00 40.25 2.75
2196 4615 7.945134 AGATAACAACAGCAAAAACTGATCTT 58.055 30.769 0.00 0.00 40.25 2.40
2197 4616 8.416329 AGATAACAACAGCAAAAACTGATCTTT 58.584 29.630 0.00 0.00 40.25 2.52
2198 4617 6.892310 AACAACAGCAAAAACTGATCTTTC 57.108 33.333 0.00 0.00 40.25 2.62
2199 4618 6.212888 ACAACAGCAAAAACTGATCTTTCT 57.787 33.333 0.00 0.00 40.25 2.52
2200 4619 6.268566 ACAACAGCAAAAACTGATCTTTCTC 58.731 36.000 0.00 0.00 40.25 2.87
2201 4620 6.127647 ACAACAGCAAAAACTGATCTTTCTCA 60.128 34.615 0.00 0.00 40.25 3.27
2202 4621 6.455360 ACAGCAAAAACTGATCTTTCTCAA 57.545 33.333 0.00 0.00 40.25 3.02
2208 4627 8.442384 GCAAAAACTGATCTTTCTCAAAACAAA 58.558 29.630 0.00 0.00 0.00 2.83
2249 4669 6.254157 GCTCCGTGATCACTTAAAATACGTAA 59.746 38.462 22.95 0.00 0.00 3.18
2324 5287 6.168389 AGAGTAACCATTTAACGGTAACCTG 58.832 40.000 0.00 0.00 34.99 4.00
2326 5289 5.934043 AGTAACCATTTAACGGTAACCTGAC 59.066 40.000 0.00 0.00 34.99 3.51
2327 5290 3.328505 ACCATTTAACGGTAACCTGACG 58.671 45.455 0.00 0.00 34.02 4.35
2328 5291 2.094734 CCATTTAACGGTAACCTGACGC 59.905 50.000 0.00 0.00 0.00 5.19
2635 5793 2.358372 TACATCGGCAGCCAGAGCA 61.358 57.895 13.30 0.00 43.56 4.26
2665 5823 1.078426 GACTTCGTGGTGGGGATGG 60.078 63.158 0.00 0.00 0.00 3.51
2989 6148 2.612200 GCCTACAGCACGACAACAA 58.388 52.632 0.00 0.00 42.97 2.83
3023 6182 5.957842 TTTTCGCAACTGAAGAACCATAT 57.042 34.783 0.00 0.00 0.00 1.78
3024 6183 7.441890 TTTTTCGCAACTGAAGAACCATATA 57.558 32.000 0.00 0.00 0.00 0.86
3025 6184 7.441890 TTTTCGCAACTGAAGAACCATATAA 57.558 32.000 0.00 0.00 0.00 0.98
3026 6185 7.624360 TTTCGCAACTGAAGAACCATATAAT 57.376 32.000 0.00 0.00 0.00 1.28
3027 6186 6.844696 TCGCAACTGAAGAACCATATAATC 57.155 37.500 0.00 0.00 0.00 1.75
3028 6187 6.345298 TCGCAACTGAAGAACCATATAATCA 58.655 36.000 0.00 0.00 0.00 2.57
3065 6224 0.038159 GTGACCCTCTGGAACGACAG 60.038 60.000 0.00 0.00 39.84 3.51
3109 6268 7.148272 GCAGAAGATCATAGAATAAATGGAGGC 60.148 40.741 0.00 0.00 0.00 4.70
3110 6269 8.102047 CAGAAGATCATAGAATAAATGGAGGCT 58.898 37.037 0.00 0.00 0.00 4.58
3111 6270 9.331466 AGAAGATCATAGAATAAATGGAGGCTA 57.669 33.333 0.00 0.00 0.00 3.93
3112 6271 9.598517 GAAGATCATAGAATAAATGGAGGCTAG 57.401 37.037 0.00 0.00 0.00 3.42
3113 6272 7.563906 AGATCATAGAATAAATGGAGGCTAGC 58.436 38.462 6.04 6.04 0.00 3.42
3121 6311 1.918467 ATGGAGGCTAGCAGCAGCAA 61.918 55.000 18.24 0.00 44.75 3.91
3144 6334 3.702048 GGCCGCCTGGACACACTA 61.702 66.667 0.71 0.00 45.78 2.74
3304 6495 6.498304 CCAATAATTGACTTGGCACATCTAC 58.502 40.000 0.00 0.00 39.30 2.59
3358 6549 5.392703 GCACAATCTGAGAGCATCAAAATCA 60.393 40.000 0.00 0.00 37.52 2.57
3416 6707 6.482524 ACATCAAGCCTCATATGAATAGCAT 58.517 36.000 18.89 8.66 41.08 3.79
3420 6711 6.429078 TCAAGCCTCATATGAATAGCATCAAC 59.571 38.462 18.89 0.00 38.44 3.18
3423 6714 6.598457 AGCCTCATATGAATAGCATCAACATC 59.402 38.462 18.89 0.00 38.44 3.06
3446 6737 5.291858 TCGTGCAATGTAATTCTCATCAGAC 59.708 40.000 0.00 0.00 31.22 3.51
3539 6831 2.032178 GCATTTCCGACAGAATGGTAGC 59.968 50.000 0.00 0.00 43.62 3.58
3733 7026 3.429822 CGAAAGGGTCGCCAATAGAACTA 60.430 47.826 0.00 0.00 44.14 2.24
3738 7031 0.748450 TCGCCAATAGAACTACCCGG 59.252 55.000 0.00 0.00 0.00 5.73
3739 7032 0.462789 CGCCAATAGAACTACCCGGT 59.537 55.000 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.908601 TTCTCTCCTCAAGGCAACATAA 57.091 40.909 0.00 0.00 41.41 1.90
25 26 3.679389 GTGAATTCTCTCCTCAAGGCAA 58.321 45.455 7.05 0.00 34.44 4.52
140 149 1.272212 GGCGGTATTATTTGGCCCATG 59.728 52.381 0.00 0.00 37.82 3.66
175 188 4.188247 TCAAGTTTCGAGGACATACAGG 57.812 45.455 4.19 0.00 0.00 4.00
243 264 3.118555 CCTACCGGTACATGGTCATGAAA 60.119 47.826 11.16 2.93 41.20 2.69
251 272 1.340248 CTACTGCCTACCGGTACATGG 59.660 57.143 11.16 12.20 34.16 3.66
295 316 6.739331 ACCCAACAAATGTCAAGGAAATTA 57.261 33.333 4.14 0.00 0.00 1.40
296 317 5.628797 ACCCAACAAATGTCAAGGAAATT 57.371 34.783 4.14 0.00 0.00 1.82
298 319 4.038642 GCTACCCAACAAATGTCAAGGAAA 59.961 41.667 4.14 0.00 0.00 3.13
299 320 3.572255 GCTACCCAACAAATGTCAAGGAA 59.428 43.478 4.14 0.00 0.00 3.36
300 321 3.153919 GCTACCCAACAAATGTCAAGGA 58.846 45.455 4.14 0.00 0.00 3.36
321 342 2.346099 ATTTTTGCATCACCGTTCCG 57.654 45.000 0.00 0.00 0.00 4.30
343 364 9.023967 GCACGCTGATGATTTTCTTAATTAAAT 57.976 29.630 0.00 0.00 0.00 1.40
344 365 8.243426 AGCACGCTGATGATTTTCTTAATTAAA 58.757 29.630 0.00 0.00 0.00 1.52
362 383 2.860735 GGAAGAGTACATTAGCACGCTG 59.139 50.000 0.72 0.00 0.00 5.18
446 482 5.065988 GCTAGCTACTCTACATAGCATCTCC 59.934 48.000 7.70 0.00 46.27 3.71
536 576 1.473257 GCTTGCATGGATGACTCCGTA 60.473 52.381 4.18 0.00 45.37 4.02
607 663 3.726291 TTTTGGTGTAGAAAAGCTGCC 57.274 42.857 0.00 0.00 0.00 4.85
635 691 1.783140 ACGTCGTAGCTCGTGAAAAAC 59.217 47.619 0.00 0.00 40.80 2.43
706 763 2.949478 CGCATTAGAATAACGCGTTTCG 59.051 45.455 31.50 14.49 40.99 3.46
798 874 2.577700 AGGAGTACTAGTCTGCCATCG 58.422 52.381 0.00 0.00 0.00 3.84
812 901 6.834451 GGCCATGATTATACTAGCTAGGAGTA 59.166 42.308 24.35 11.30 34.01 2.59
813 902 5.659079 GGCCATGATTATACTAGCTAGGAGT 59.341 44.000 24.35 9.27 0.00 3.85
814 903 5.221145 CGGCCATGATTATACTAGCTAGGAG 60.221 48.000 24.35 2.78 0.00 3.69
815 904 4.645136 CGGCCATGATTATACTAGCTAGGA 59.355 45.833 24.35 17.51 0.00 2.94
816 905 4.202161 CCGGCCATGATTATACTAGCTAGG 60.202 50.000 24.35 7.13 0.00 3.02
817 906 4.737946 GCCGGCCATGATTATACTAGCTAG 60.738 50.000 18.11 19.44 0.00 3.42
885 979 1.002069 TTGCTGGATGGTGGAGGAAT 58.998 50.000 0.00 0.00 0.00 3.01
940 2976 6.037281 TCGAGTCAAGTGTGTTATCTAGCTAG 59.963 42.308 15.01 15.01 0.00 3.42
941 2977 5.878669 TCGAGTCAAGTGTGTTATCTAGCTA 59.121 40.000 0.00 0.00 0.00 3.32
943 2979 4.982999 TCGAGTCAAGTGTGTTATCTAGC 58.017 43.478 0.00 0.00 0.00 3.42
944 2980 5.904630 CGATCGAGTCAAGTGTGTTATCTAG 59.095 44.000 10.26 0.00 0.00 2.43
945 2981 5.583457 TCGATCGAGTCAAGTGTGTTATCTA 59.417 40.000 15.15 0.00 0.00 1.98
947 2983 4.659088 TCGATCGAGTCAAGTGTGTTATC 58.341 43.478 15.15 0.00 0.00 1.75
948 2984 4.696899 TCGATCGAGTCAAGTGTGTTAT 57.303 40.909 15.15 0.00 0.00 1.89
949 2985 4.155280 TGATCGATCGAGTCAAGTGTGTTA 59.845 41.667 23.84 0.00 0.00 2.41
950 2986 3.057526 TGATCGATCGAGTCAAGTGTGTT 60.058 43.478 23.84 1.18 0.00 3.32
951 2987 2.488153 TGATCGATCGAGTCAAGTGTGT 59.512 45.455 23.84 1.76 0.00 3.72
961 2997 1.712877 CGTTGCTGATGATCGATCGAG 59.287 52.381 23.84 15.69 33.17 4.04
1321 3375 3.441290 CTCCTTCTCGACGGCCGT 61.441 66.667 34.89 34.89 39.75 5.68
1516 3591 0.991920 GTCCCATCTTCACCTCCCAA 59.008 55.000 0.00 0.00 0.00 4.12
1534 3609 2.745492 GTCGTCGAGTCCCTCCGT 60.745 66.667 0.00 0.00 0.00 4.69
1794 3955 3.140325 TGATGGAGTGGGAACAGAAAC 57.860 47.619 0.00 0.00 44.46 2.78
1867 4028 8.308931 TCACGACTTATGTTGGTTATTAAGACT 58.691 33.333 0.00 0.00 31.91 3.24
1868 4029 8.470040 TCACGACTTATGTTGGTTATTAAGAC 57.530 34.615 0.00 0.00 31.91 3.01
1869 4030 9.309516 GATCACGACTTATGTTGGTTATTAAGA 57.690 33.333 0.00 0.00 31.91 2.10
1870 4031 9.093970 TGATCACGACTTATGTTGGTTATTAAG 57.906 33.333 0.00 0.00 31.91 1.85
1872 4033 8.415192 GTGATCACGACTTATGTTGGTTATTA 57.585 34.615 10.69 0.00 31.91 0.98
1873 4034 7.303634 GTGATCACGACTTATGTTGGTTATT 57.696 36.000 10.69 0.00 31.91 1.40
1874 4035 6.903883 GTGATCACGACTTATGTTGGTTAT 57.096 37.500 10.69 0.00 31.91 1.89
1937 4154 6.665992 TTAACAGTGTGGAGAAGTAGTCAT 57.334 37.500 0.00 0.00 0.00 3.06
1996 4252 0.796312 CAGTTCCGTTGGTTGATCCG 59.204 55.000 0.00 0.00 39.52 4.18
2092 4360 6.838382 ACTACCAACTTTCTAATTCACCACT 58.162 36.000 0.00 0.00 0.00 4.00
2114 4532 7.827729 GGTTCAGGTCAATGGTAATTAGTTACT 59.172 37.037 7.92 0.00 40.06 2.24
2115 4533 7.827729 AGGTTCAGGTCAATGGTAATTAGTTAC 59.172 37.037 0.00 0.00 39.57 2.50
2116 4534 7.924541 AGGTTCAGGTCAATGGTAATTAGTTA 58.075 34.615 0.00 0.00 0.00 2.24
2174 4593 7.771183 AGAAAGATCAGTTTTTGCTGTTGTTA 58.229 30.769 0.00 0.00 37.70 2.41
2176 4595 6.127647 TGAGAAAGATCAGTTTTTGCTGTTGT 60.128 34.615 0.00 0.00 37.70 3.32
2177 4596 6.267817 TGAGAAAGATCAGTTTTTGCTGTTG 58.732 36.000 0.00 0.00 37.70 3.33
2179 4598 6.455360 TTGAGAAAGATCAGTTTTTGCTGT 57.545 33.333 0.00 0.00 37.70 4.40
2180 4599 7.276218 TGTTTTGAGAAAGATCAGTTTTTGCTG 59.724 33.333 0.00 0.00 37.81 4.41
2181 4600 7.322664 TGTTTTGAGAAAGATCAGTTTTTGCT 58.677 30.769 0.00 0.00 0.00 3.91
2182 4601 7.524294 TGTTTTGAGAAAGATCAGTTTTTGC 57.476 32.000 0.00 0.00 0.00 3.68
2186 4605 9.487790 TGTTTTTGTTTTGAGAAAGATCAGTTT 57.512 25.926 0.00 0.00 0.00 2.66
2187 4606 9.487790 TTGTTTTTGTTTTGAGAAAGATCAGTT 57.512 25.926 0.00 0.00 0.00 3.16
2188 4607 9.487790 TTTGTTTTTGTTTTGAGAAAGATCAGT 57.512 25.926 0.00 0.00 0.00 3.41
2199 4618 9.339492 GCAGATCAATTTTTGTTTTTGTTTTGA 57.661 25.926 0.00 0.00 0.00 2.69
2200 4619 9.344309 AGCAGATCAATTTTTGTTTTTGTTTTG 57.656 25.926 0.00 0.00 0.00 2.44
2201 4620 9.558648 GAGCAGATCAATTTTTGTTTTTGTTTT 57.441 25.926 0.00 0.00 0.00 2.43
2202 4621 8.183536 GGAGCAGATCAATTTTTGTTTTTGTTT 58.816 29.630 0.00 0.00 0.00 2.83
2208 4627 4.984161 CACGGAGCAGATCAATTTTTGTTT 59.016 37.500 0.00 0.00 0.00 2.83
2249 4669 1.530323 ACTTCCGTAATTGGCGCTTT 58.470 45.000 7.64 1.36 0.00 3.51
2324 5287 0.949105 AACAAGTGATGGGTCGCGTC 60.949 55.000 5.77 0.00 39.83 5.19
2326 5289 1.635663 GGAACAAGTGATGGGTCGCG 61.636 60.000 0.00 0.00 39.83 5.87
2327 5290 0.605319 TGGAACAAGTGATGGGTCGC 60.605 55.000 0.00 0.00 31.92 5.19
2328 5291 1.442769 CTGGAACAAGTGATGGGTCG 58.557 55.000 0.00 0.00 38.70 4.79
2844 6002 1.141053 ACGAGAGGAAACCACAAGCTT 59.859 47.619 0.00 0.00 0.00 3.74
2985 6144 8.357402 AGTTGCGAAAAATAAGGTTATCTTGTT 58.643 29.630 0.00 0.00 38.24 2.83
2989 6148 7.681939 TCAGTTGCGAAAAATAAGGTTATCT 57.318 32.000 0.00 0.00 0.00 1.98
3023 6182 5.163163 ACAGCTTCTTCATGGCCTATGATTA 60.163 40.000 15.69 7.09 44.90 1.75
3024 6183 4.142790 CAGCTTCTTCATGGCCTATGATT 58.857 43.478 15.69 0.59 44.90 2.57
3025 6184 3.137913 ACAGCTTCTTCATGGCCTATGAT 59.862 43.478 15.69 0.00 44.90 2.45
3026 6185 2.507058 ACAGCTTCTTCATGGCCTATGA 59.493 45.455 3.32 9.06 43.92 2.15
3027 6186 2.617308 CACAGCTTCTTCATGGCCTATG 59.383 50.000 3.32 6.57 38.17 2.23
3028 6187 2.507058 TCACAGCTTCTTCATGGCCTAT 59.493 45.455 3.32 0.00 0.00 2.57
3065 6224 3.309682 TCTGCACGCAATGATAAAGTAGC 59.690 43.478 0.00 0.00 0.00 3.58
3109 6268 1.668047 GCCAAACTTTGCTGCTGCTAG 60.668 52.381 17.00 15.10 40.48 3.42
3110 6269 0.314935 GCCAAACTTTGCTGCTGCTA 59.685 50.000 17.00 6.36 40.48 3.49
3111 6270 1.068585 GCCAAACTTTGCTGCTGCT 59.931 52.632 17.00 0.00 40.48 4.24
3112 6271 1.957695 GGCCAAACTTTGCTGCTGC 60.958 57.895 8.89 8.89 40.20 5.25
3113 6272 1.662446 CGGCCAAACTTTGCTGCTG 60.662 57.895 2.24 0.00 0.00 4.41
3121 6311 2.597510 GTCCAGGCGGCCAAACTT 60.598 61.111 23.09 0.00 0.00 2.66
3141 6331 4.660771 AGGGCATGCCTAAGAATAGTTAGT 59.339 41.667 34.70 1.25 36.10 2.24
3142 6332 5.234466 AGGGCATGCCTAAGAATAGTTAG 57.766 43.478 34.70 0.00 36.10 2.34
3143 6333 5.104109 ACAAGGGCATGCCTAAGAATAGTTA 60.104 40.000 34.70 0.00 36.10 2.24
3144 6334 4.210331 CAAGGGCATGCCTAAGAATAGTT 58.790 43.478 34.70 12.14 36.10 2.24
3182 6372 3.181397 TCGCAACGTGCTAAGGTAATAC 58.819 45.455 8.07 0.00 42.25 1.89
3304 6495 4.614284 GTGTTCTGTTCTGATTGATTTGCG 59.386 41.667 0.00 0.00 0.00 4.85
3358 6549 4.282195 GGATAGTAGTAACAGCTGGCAGAT 59.718 45.833 20.86 9.84 0.00 2.90
3416 6707 5.411053 TGAGAATTACATTGCACGATGTTGA 59.589 36.000 9.22 0.54 40.54 3.18
3420 6711 6.018507 TCTGATGAGAATTACATTGCACGATG 60.019 38.462 0.00 0.00 0.00 3.84
3423 6714 5.496387 GTCTGATGAGAATTACATTGCACG 58.504 41.667 0.00 0.00 0.00 5.34
3539 6831 2.508867 CGTCTTCGTTGATGCAAATGG 58.491 47.619 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.