Multiple sequence alignment - TraesCS2D01G552800

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 TraesCS2D01G552800 chr2D 100.000 3816 0 0 1 3816 627918738 627914923 0.000000e+00 7047.0
1 TraesCS2D01G552800 chr2B 88.315 3928 234 103 1 3816 770678194 770674380 0.000000e+00 4503.0
2 TraesCS2D01G552800 chr2B 87.337 845 46 25 828 1672 748355955 748356738 0.000000e+00 911.0
3 TraesCS2D01G552800 chr2B 86.659 847 43 24 828 1672 748202542 748203320 0.000000e+00 874.0
4 TraesCS2D01G552800 chr2B 85.150 835 71 23 2536 3347 748365160 748365964 0.000000e+00 806.0
5 TraesCS2D01G552800 chr2B 85.048 836 73 23 2536 3347 748214184 748214991 0.000000e+00 804.0
6 TraesCS2D01G552800 chr2B 87.147 319 29 9 3441 3756 748366089 748366398 6.070000e-93 351.0
7 TraesCS2D01G552800 chr2B 86.207 319 32 9 3441 3756 748215116 748215425 6.110000e-88 335.0
8 TraesCS2D01G552800 chr2B 83.117 308 27 9 1696 1998 748363963 748364250 1.360000e-64 257.0
9 TraesCS2D01G552800 chr2A 86.903 3436 167 93 1 3348 758395051 758391811 0.000000e+00 3591.0
10 TraesCS2D01G552800 chr2A 94.926 473 18 3 3344 3816 758390220 758389754 0.000000e+00 736.0
11 TraesCS2D01G552800 chr2A 94.715 473 19 3 3344 3816 758391687 758391221 0.000000e+00 730.0
12 TraesCS2D01G552800 chr2A 83.534 498 32 19 2867 3348 758390807 758390344 1.640000e-113 420.0
13 TraesCS2D01G552800 chr7A 75.751 466 51 34 1627 2087 96199431 96199839 1.090000e-40 178.0
14 TraesCS2D01G552800 chr7A 78.469 209 26 14 1412 1619 96199174 96199364 6.700000e-23 119.0
15 TraesCS2D01G552800 chr4B 85.246 122 11 4 1913 2034 413201862 413201976 6.700000e-23 119.0
16 TraesCS2D01G552800 chr4B 85.246 122 11 3 1913 2034 413276816 413276930 6.700000e-23 119.0
17 TraesCS2D01G552800 chr4B 85.246 122 11 4 1913 2034 413307533 413307647 6.700000e-23 119.0
18 TraesCS2D01G552800 chr4B 85.246 122 11 4 1913 2034 413397062 413397176 6.700000e-23 119.0
19 TraesCS2D01G552800 chr4B 86.139 101 8 5 1412 1512 539004315 539004409 1.880000e-18 104.0
20 TraesCS2D01G552800 chr4B 77.778 162 9 18 1627 1777 539004553 539004698 1.470000e-09 75.0
21 TraesCS2D01G552800 chr6B 87.129 101 7 3 1412 1512 201909782 201909876 4.030000e-20 110.0
22 TraesCS2D01G552800 chr6B 77.160 162 10 15 1627 1777 201910020 201910165 6.840000e-08 69.4
23 TraesCS2D01G552800 chr3D 100.000 30 0 0 3471 3500 110244765 110244736 5.330000e-04 56.5
24 TraesCS2D01G552800 chr3B 100.000 30 0 0 3471 3500 161377722 161377693 5.330000e-04 56.5
25 TraesCS2D01G552800 chr3A 100.000 30 0 0 3471 3500 120224190 120224219 5.330000e-04 56.5


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 TraesCS2D01G552800 chr2D 627914923 627918738 3815 True 7047.000000 7047 100.0000 1 3816 1 chr2D.!!$R1 3815
1 TraesCS2D01G552800 chr2B 770674380 770678194 3814 True 4503.000000 4503 88.3150 1 3816 1 chr2B.!!$R1 3815
2 TraesCS2D01G552800 chr2B 748355955 748356738 783 False 911.000000 911 87.3370 828 1672 1 chr2B.!!$F2 844
3 TraesCS2D01G552800 chr2B 748202542 748203320 778 False 874.000000 874 86.6590 828 1672 1 chr2B.!!$F1 844
4 TraesCS2D01G552800 chr2B 748214184 748215425 1241 False 569.500000 804 85.6275 2536 3756 2 chr2B.!!$F3 1220
5 TraesCS2D01G552800 chr2B 748363963 748366398 2435 False 471.333333 806 85.1380 1696 3756 3 chr2B.!!$F4 2060
6 TraesCS2D01G552800 chr2A 758389754 758395051 5297 True 1369.250000 3591 90.0195 1 3816 4 chr2A.!!$R1 3815

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
918 996 0.318699 TCGACTCGACCTGTGCAAAG 60.319 55.0 0.0 0.0 0.00 2.77 F
1684 1796 0.098376 CTCTGCTCCGCTGAATTTGC 59.902 55.0 0.0 0.0 36.19 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2722 3264 0.807667 ATAGAAAGTCCGCAGCGCTG 60.808 55.0 32.83 32.83 0.00 5.18 R
3376 4105 0.614979 AGCTGTGGTCTGGGACGTAT 60.615 55.0 0.00 0.00 32.65 3.06 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
73 74 5.512788 GTGTTTCAATAATCGAGCAACCATG 59.487 40.000 0.00 0.00 0.00 3.66
130 134 5.934781 AGGCTCTAAAATGATGGTCTAAGG 58.065 41.667 0.00 0.00 0.00 2.69
169 173 3.945346 ACATAACAGCACACCCGATTAA 58.055 40.909 0.00 0.00 0.00 1.40
173 177 4.481368 AACAGCACACCCGATTAAGATA 57.519 40.909 0.00 0.00 0.00 1.98
174 178 4.481368 ACAGCACACCCGATTAAGATAA 57.519 40.909 0.00 0.00 0.00 1.75
175 179 4.442706 ACAGCACACCCGATTAAGATAAG 58.557 43.478 0.00 0.00 0.00 1.73
176 180 4.161565 ACAGCACACCCGATTAAGATAAGA 59.838 41.667 0.00 0.00 0.00 2.10
177 181 4.747108 CAGCACACCCGATTAAGATAAGAG 59.253 45.833 0.00 0.00 0.00 2.85
184 188 5.304871 ACCCGATTAAGATAAGAGAAGGGAC 59.695 44.000 0.00 0.00 38.49 4.46
337 350 1.891919 GAACCGACTGCAACAGCCA 60.892 57.895 0.00 0.00 34.37 4.75
462 495 4.034858 CAGCCACATAGTTAAGCAGTGATG 59.965 45.833 0.00 0.00 32.14 3.07
510 543 2.740826 CGTGATCCCAAACGCCGT 60.741 61.111 0.00 0.00 32.40 5.68
688 753 0.620556 GGGAGCCAAGAGGAATGTGA 59.379 55.000 0.00 0.00 36.89 3.58
689 754 1.407989 GGGAGCCAAGAGGAATGTGAG 60.408 57.143 0.00 0.00 36.89 3.51
690 755 1.556911 GGAGCCAAGAGGAATGTGAGA 59.443 52.381 0.00 0.00 36.89 3.27
720 785 1.947456 GTGGATACCTTGCGGGAAATC 59.053 52.381 2.42 5.21 38.76 2.17
725 790 1.220749 CCTTGCGGGAAATCTCGGA 59.779 57.895 4.68 0.00 37.23 4.55
765 838 2.042843 AGAGGGATTCGCCGGAGT 60.043 61.111 5.05 0.00 37.63 3.85
766 839 2.077821 GAGAGGGATTCGCCGGAGTC 62.078 65.000 5.05 0.00 37.63 3.36
767 840 3.486252 GAGGGATTCGCCGGAGTCG 62.486 68.421 5.05 0.00 37.63 4.18
768 841 3.834799 GGGATTCGCCGGAGTCGT 61.835 66.667 5.05 0.00 37.63 4.34
769 842 2.278661 GGATTCGCCGGAGTCGTC 60.279 66.667 5.05 1.89 30.14 4.20
770 843 2.651232 GATTCGCCGGAGTCGTCG 60.651 66.667 5.05 0.00 39.22 5.12
771 844 3.392595 GATTCGCCGGAGTCGTCGT 62.393 63.158 5.05 0.00 38.92 4.34
772 845 3.392595 ATTCGCCGGAGTCGTCGTC 62.393 63.158 5.05 0.00 38.92 4.20
918 996 0.318699 TCGACTCGACCTGTGCAAAG 60.319 55.000 0.00 0.00 0.00 2.77
1003 1089 9.645059 CCATCATCTTATACTGTACTTACATGG 57.355 37.037 0.00 0.00 35.36 3.66
1004 1090 9.144747 CATCATCTTATACTGTACTTACATGGC 57.855 37.037 0.00 0.00 35.36 4.40
1005 1091 7.368059 TCATCTTATACTGTACTTACATGGCG 58.632 38.462 0.00 0.00 35.36 5.69
1006 1092 6.947644 TCTTATACTGTACTTACATGGCGA 57.052 37.500 0.00 0.00 35.36 5.54
1007 1093 6.732154 TCTTATACTGTACTTACATGGCGAC 58.268 40.000 0.00 0.00 35.36 5.19
1610 1722 5.989477 TGGCTTGTATGTACTTAGAGCATT 58.011 37.500 18.17 0.00 0.00 3.56
1613 1725 5.557136 GCTTGTATGTACTTAGAGCATTGCG 60.557 44.000 2.38 0.00 0.00 4.85
1672 1784 1.153588 GGTCTGCTCTGCTCTGCTC 60.154 63.158 0.00 0.00 0.00 4.26
1673 1785 1.153588 GTCTGCTCTGCTCTGCTCC 60.154 63.158 0.00 0.00 0.00 4.70
1674 1786 2.202770 CTGCTCTGCTCTGCTCCG 60.203 66.667 0.00 0.00 0.00 4.63
1675 1787 4.447989 TGCTCTGCTCTGCTCCGC 62.448 66.667 0.00 0.00 0.00 5.54
1676 1788 4.146075 GCTCTGCTCTGCTCCGCT 62.146 66.667 0.00 0.00 0.00 5.52
1684 1796 0.098376 CTCTGCTCCGCTGAATTTGC 59.902 55.000 0.00 0.00 36.19 3.68
1688 1800 1.074872 GCTCCGCTGAATTTGCTTGC 61.075 55.000 3.52 0.00 0.00 4.01
1693 1805 2.602878 CGCTGAATTTGCTTGCAGAAT 58.397 42.857 0.00 0.00 0.00 2.40
1703 1819 1.734465 GCTTGCAGAATTAGCGTCTGT 59.266 47.619 10.19 0.00 43.71 3.41
1717 1833 2.800544 GCGTCTGTCAGTGTAAATGTGT 59.199 45.455 0.00 0.00 31.21 3.72
1727 1843 7.468141 TCAGTGTAAATGTGTACTCTGATCT 57.532 36.000 9.80 0.00 44.02 2.75
1728 1844 7.315890 TCAGTGTAAATGTGTACTCTGATCTG 58.684 38.462 9.80 0.00 44.02 2.90
1729 1845 7.176690 TCAGTGTAAATGTGTACTCTGATCTGA 59.823 37.037 9.80 2.03 44.02 3.27
1730 1846 7.978414 CAGTGTAAATGTGTACTCTGATCTGAT 59.022 37.037 2.43 0.00 43.49 2.90
1737 1853 5.163571 TGTGTACTCTGATCTGATGAGCTTC 60.164 44.000 2.43 0.00 0.00 3.86
1780 1897 1.014564 GTGCAGGTGTAAGGCGAGAC 61.015 60.000 0.00 0.00 0.00 3.36
1784 1901 1.448013 GGTGTAAGGCGAGACTGGC 60.448 63.158 0.00 0.00 0.00 4.85
1829 1946 3.324035 GGATGCCGATGAAGCGAC 58.676 61.111 0.00 0.00 0.00 5.19
1876 1997 7.168219 TCAGGTATCACTTGTAAATTGAGCTT 58.832 34.615 0.00 0.00 38.94 3.74
1915 2044 8.338072 TGATACTACATCCTTAGTTAGCTAGC 57.662 38.462 6.62 6.62 34.10 3.42
1916 2045 8.164733 TGATACTACATCCTTAGTTAGCTAGCT 58.835 37.037 23.12 23.12 34.10 3.32
1917 2046 9.669887 GATACTACATCCTTAGTTAGCTAGCTA 57.330 37.037 20.67 20.67 34.10 3.32
1919 2048 8.343168 ACTACATCCTTAGTTAGCTAGCTATG 57.657 38.462 24.69 19.27 0.00 2.23
1967 2097 3.087031 CAGAGTGGCCATTTTCTGTCAT 58.913 45.455 25.24 3.38 33.95 3.06
1981 2115 1.795872 CTGTCATAAACGTGTGCCGAA 59.204 47.619 0.00 0.00 40.70 4.30
1988 2122 0.454196 AACGTGTGCCGAAAGCTTTT 59.546 45.000 14.05 0.00 44.23 2.27
1989 2123 0.454196 ACGTGTGCCGAAAGCTTTTT 59.546 45.000 14.05 0.00 44.23 1.94
2296 2746 3.928992 TGAAGCTTTAAGACATCGCAGAG 59.071 43.478 0.00 0.00 43.63 3.35
2368 2859 4.091365 TCGCAGACTGTTGTGAAAATATCG 59.909 41.667 3.99 0.00 34.85 2.92
2428 2919 5.843673 TGTTGTTGTTCTCTTTTATGGCA 57.156 34.783 0.00 0.00 0.00 4.92
2435 2926 8.296713 TGTTGTTCTCTTTTATGGCAGTTTATC 58.703 33.333 0.00 0.00 0.00 1.75
2490 2981 3.922850 GCCTTTCTTGATAAAAGCTGCAC 59.077 43.478 1.02 0.00 33.33 4.57
2662 3204 3.070446 TCGCTCCAAGTCTTTCAAGGTTA 59.930 43.478 0.00 0.00 0.00 2.85
2663 3205 3.433615 CGCTCCAAGTCTTTCAAGGTTAG 59.566 47.826 0.00 0.00 0.00 2.34
2664 3206 4.390264 GCTCCAAGTCTTTCAAGGTTAGT 58.610 43.478 0.00 0.00 0.00 2.24
2665 3207 4.214332 GCTCCAAGTCTTTCAAGGTTAGTG 59.786 45.833 0.00 0.00 0.00 2.74
2666 3208 5.367945 TCCAAGTCTTTCAAGGTTAGTGT 57.632 39.130 0.00 0.00 0.00 3.55
2667 3209 5.751586 TCCAAGTCTTTCAAGGTTAGTGTT 58.248 37.500 0.00 0.00 0.00 3.32
2668 3210 5.588648 TCCAAGTCTTTCAAGGTTAGTGTTG 59.411 40.000 0.00 0.00 0.00 3.33
2669 3211 5.588648 CCAAGTCTTTCAAGGTTAGTGTTGA 59.411 40.000 0.00 0.00 0.00 3.18
2670 3212 6.094881 CCAAGTCTTTCAAGGTTAGTGTTGAA 59.905 38.462 0.00 0.00 40.16 2.69
2671 3213 7.362574 CCAAGTCTTTCAAGGTTAGTGTTGAAA 60.363 37.037 9.27 9.27 45.78 2.69
2672 3214 7.696992 AGTCTTTCAAGGTTAGTGTTGAAAA 57.303 32.000 10.50 1.90 46.66 2.29
2673 3215 8.117813 AGTCTTTCAAGGTTAGTGTTGAAAAA 57.882 30.769 10.50 0.00 46.66 1.94
2674 3216 8.749354 AGTCTTTCAAGGTTAGTGTTGAAAAAT 58.251 29.630 10.50 1.45 46.66 1.82
2675 3217 8.807581 GTCTTTCAAGGTTAGTGTTGAAAAATG 58.192 33.333 10.50 1.91 46.66 2.32
2676 3218 7.491048 TCTTTCAAGGTTAGTGTTGAAAAATGC 59.509 33.333 10.50 0.00 46.66 3.56
2677 3219 6.214191 TCAAGGTTAGTGTTGAAAAATGCA 57.786 33.333 0.00 0.00 29.66 3.96
2678 3220 6.039616 TCAAGGTTAGTGTTGAAAAATGCAC 58.960 36.000 0.00 0.00 29.66 4.57
2679 3221 5.852282 AGGTTAGTGTTGAAAAATGCACT 57.148 34.783 0.00 0.00 43.55 4.40
2680 3222 5.831997 AGGTTAGTGTTGAAAAATGCACTC 58.168 37.500 0.00 0.00 41.67 3.51
2681 3223 5.594317 AGGTTAGTGTTGAAAAATGCACTCT 59.406 36.000 0.00 0.00 41.67 3.24
2682 3224 6.770785 AGGTTAGTGTTGAAAAATGCACTCTA 59.229 34.615 0.00 0.00 41.67 2.43
2683 3225 7.041098 AGGTTAGTGTTGAAAAATGCACTCTAG 60.041 37.037 0.00 0.00 41.67 2.43
2684 3226 7.255139 GGTTAGTGTTGAAAAATGCACTCTAGT 60.255 37.037 0.00 0.00 41.67 2.57
2685 3227 6.699575 AGTGTTGAAAAATGCACTCTAGTT 57.300 33.333 0.00 0.00 37.62 2.24
2688 3230 8.682710 AGTGTTGAAAAATGCACTCTAGTTTTA 58.317 29.630 0.00 0.00 37.62 1.52
2722 3264 1.527696 CAATTGCAGTCGCGTGATTC 58.472 50.000 5.77 0.00 42.97 2.52
2972 3526 9.128107 CTTTGCTCGTTCATTTTAACATTATGT 57.872 29.630 0.00 0.00 0.00 2.29
3051 3615 6.070897 TCATTGTTGTGTCCATGTACTTTG 57.929 37.500 0.00 0.00 0.00 2.77
3068 3632 9.645059 ATGTACTTTGGAACTCGATATATCATG 57.355 33.333 13.11 6.92 0.00 3.07
3114 3678 7.618019 AATTCAGATGTAGGCTATGGAGTTA 57.382 36.000 0.00 0.00 0.00 2.24
3119 3683 8.585881 TCAGATGTAGGCTATGGAGTTATTTAC 58.414 37.037 0.00 0.00 0.00 2.01
3149 3727 3.968265 TCTTTATTGCTTCCCTTCCCAG 58.032 45.455 0.00 0.00 0.00 4.45
3160 3750 3.256704 TCCCTTCCCAGTTGTGAACTAT 58.743 45.455 0.00 0.00 40.46 2.12
3162 3752 4.105697 TCCCTTCCCAGTTGTGAACTATTT 59.894 41.667 0.00 0.00 40.46 1.40
3163 3753 4.459337 CCCTTCCCAGTTGTGAACTATTTC 59.541 45.833 0.00 0.00 40.46 2.17
3226 3824 7.425577 AAGATTAATTTTGAGCCAAACAAGC 57.574 32.000 0.52 0.00 32.79 4.01
3278 3876 4.788100 CGACGCAATTCCTTGATAACTTTG 59.212 41.667 0.00 0.00 34.04 2.77
3350 4079 4.894784 ACCAGCACACGATAATAATAGGG 58.105 43.478 0.00 0.00 0.00 3.53
3460 5654 2.027625 CGCACCTCTTCCCGTTGTC 61.028 63.158 0.00 0.00 0.00 3.18
3581 5775 3.577805 ACCAAGTCATTATAGGGTGCC 57.422 47.619 0.00 0.00 0.00 5.01
3648 5846 0.830648 TCTTCTAGCCATTCCACCGG 59.169 55.000 0.00 0.00 0.00 5.28
3657 5855 0.378257 CATTCCACCGGCATTCGAAG 59.622 55.000 0.00 0.00 42.43 3.79
3661 5859 1.154225 CACCGGCATTCGAAGTTGC 60.154 57.895 14.05 14.05 42.43 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
130 134 2.548875 TGTTTGGACATTTGTTGCTGC 58.451 42.857 0.00 0.00 0.00 5.25
169 173 3.772025 CCACACTGTCCCTTCTCTTATCT 59.228 47.826 0.00 0.00 0.00 1.98
173 177 1.059913 CCCACACTGTCCCTTCTCTT 58.940 55.000 0.00 0.00 0.00 2.85
174 178 1.484444 GCCCACACTGTCCCTTCTCT 61.484 60.000 0.00 0.00 0.00 3.10
175 179 1.003233 GCCCACACTGTCCCTTCTC 60.003 63.158 0.00 0.00 0.00 2.87
176 180 1.062488 AAGCCCACACTGTCCCTTCT 61.062 55.000 0.00 0.00 0.00 2.85
177 181 0.690762 TAAGCCCACACTGTCCCTTC 59.309 55.000 0.00 0.00 0.00 3.46
276 289 3.295093 TCCGAAGAGAGCTGATCTGATT 58.705 45.455 0.00 0.00 38.84 2.57
324 337 2.912624 GCAGGTGGCTGTTGCAGTC 61.913 63.158 0.00 0.00 41.91 3.51
337 350 4.673375 CAAGGGCTGGCAGCAGGT 62.673 66.667 37.49 20.29 44.75 4.00
462 495 1.468914 GTTTGATGAAACGCCTCTCCC 59.531 52.381 0.00 0.00 32.49 4.30
583 616 2.814183 ATCGGTTCGACTGCGGTGTC 62.814 60.000 0.80 0.00 39.18 3.67
584 617 2.814183 GATCGGTTCGACTGCGGTGT 62.814 60.000 0.80 0.00 39.18 4.16
585 618 2.126071 ATCGGTTCGACTGCGGTG 60.126 61.111 0.80 0.00 39.18 4.94
587 620 2.158959 GTGATCGGTTCGACTGCGG 61.159 63.158 0.00 0.00 39.18 5.69
588 621 1.406219 CTGTGATCGGTTCGACTGCG 61.406 60.000 0.00 0.00 39.18 5.18
688 753 0.912486 GTATCCACCCCTGTGCTTCT 59.088 55.000 0.00 0.00 41.35 2.85
689 754 0.107165 GGTATCCACCCCTGTGCTTC 60.107 60.000 0.00 0.00 41.35 3.86
690 755 1.999346 GGTATCCACCCCTGTGCTT 59.001 57.895 0.00 0.00 41.35 3.91
744 809 2.731571 CCGGCGAATCCCTCTCCAA 61.732 63.158 9.30 0.00 0.00 3.53
745 810 3.154473 CCGGCGAATCCCTCTCCA 61.154 66.667 9.30 0.00 0.00 3.86
765 838 2.125229 CTCCTCCTCCGACGACGA 60.125 66.667 9.28 0.00 42.66 4.20
766 839 3.203412 CCTCCTCCTCCGACGACG 61.203 72.222 0.00 0.00 39.43 5.12
767 840 3.519930 GCCTCCTCCTCCGACGAC 61.520 72.222 0.00 0.00 0.00 4.34
918 996 5.400066 ACATATAGGGTGGTTTTTGCAAC 57.600 39.130 0.00 0.00 0.00 4.17
1041 1127 3.847602 CAGGCGAGGGAGCAGGAG 61.848 72.222 0.00 0.00 39.27 3.69
1121 1207 2.838225 CCCGTATCTCCACCGCCT 60.838 66.667 0.00 0.00 0.00 5.52
1672 1784 0.241749 TCTGCAAGCAAATTCAGCGG 59.758 50.000 0.00 0.00 37.01 5.52
1673 1785 2.054687 TTCTGCAAGCAAATTCAGCG 57.945 45.000 0.00 0.00 37.01 5.18
1674 1786 4.032558 GCTAATTCTGCAAGCAAATTCAGC 59.967 41.667 14.10 15.29 36.26 4.26
1675 1787 4.264614 CGCTAATTCTGCAAGCAAATTCAG 59.735 41.667 8.00 11.91 35.98 3.02
1676 1788 4.168014 CGCTAATTCTGCAAGCAAATTCA 58.832 39.130 8.00 5.74 35.98 2.57
1684 1796 2.995939 TGACAGACGCTAATTCTGCAAG 59.004 45.455 0.24 0.00 43.79 4.01
1688 1800 3.579709 ACACTGACAGACGCTAATTCTG 58.420 45.455 10.08 0.00 45.21 3.02
1693 1805 4.684242 CACATTTACACTGACAGACGCTAA 59.316 41.667 10.08 0.00 0.00 3.09
1703 1819 7.176690 TCAGATCAGAGTACACATTTACACTGA 59.823 37.037 11.24 11.24 46.78 3.41
1717 1833 4.827304 CGAAGCTCATCAGATCAGAGTA 57.173 45.455 0.00 0.00 0.00 2.59
1780 1897 1.301716 CGGTATCCCCAATCGCCAG 60.302 63.158 0.00 0.00 0.00 4.85
1784 1901 2.357034 CGGCGGTATCCCCAATCG 60.357 66.667 0.00 0.00 0.00 3.34
1829 1946 4.540715 AGGAAATTTGGGAGCTATCCTTG 58.459 43.478 0.00 0.00 45.85 3.61
1876 1997 8.243426 GGATGTAGTATCATGAACAAGCAAAAA 58.757 33.333 0.00 0.00 0.00 1.94
1914 2043 8.629158 TCCAATTCATAAACAATACACCATAGC 58.371 33.333 0.00 0.00 0.00 2.97
1917 2046 8.423349 CCATCCAATTCATAAACAATACACCAT 58.577 33.333 0.00 0.00 0.00 3.55
1918 2047 7.632462 GCCATCCAATTCATAAACAATACACCA 60.632 37.037 0.00 0.00 0.00 4.17
1919 2048 6.701400 GCCATCCAATTCATAAACAATACACC 59.299 38.462 0.00 0.00 0.00 4.16
1967 2097 1.301423 AAGCTTTCGGCACACGTTTA 58.699 45.000 0.00 0.00 44.79 2.01
1981 2115 9.842775 ACTTACTACCTAGTTAACAAAAAGCTT 57.157 29.630 8.61 0.00 37.73 3.74
1988 2122 8.482852 ACCTGAACTTACTACCTAGTTAACAA 57.517 34.615 8.61 0.00 37.73 2.83
1989 2123 8.362639 CAACCTGAACTTACTACCTAGTTAACA 58.637 37.037 8.61 0.00 37.73 2.41
2066 2353 3.244700 GGCTCATGGTCAGGCATACTAAT 60.245 47.826 2.01 0.00 36.45 1.73
2296 2746 3.988819 TGGGCAGTTCAAAAGCATTAAC 58.011 40.909 0.00 0.00 0.00 2.01
2346 2837 4.143115 ACGATATTTTCACAACAGTCTGCG 60.143 41.667 0.00 0.00 0.00 5.18
2368 2859 1.131883 CAGAGCCAAGCTATGCACAAC 59.868 52.381 9.75 0.00 40.91 3.32
2490 2981 0.895530 TCAGAGGCAGGAAGGTTACG 59.104 55.000 0.00 0.00 0.00 3.18
2662 3204 6.699575 AACTAGAGTGCATTTTTCAACACT 57.300 33.333 0.00 0.00 45.66 3.55
2663 3205 7.755582 AAAACTAGAGTGCATTTTTCAACAC 57.244 32.000 0.00 0.00 0.00 3.32
2664 3206 7.647715 GCTAAAACTAGAGTGCATTTTTCAACA 59.352 33.333 0.00 0.00 0.00 3.33
2665 3207 7.647715 TGCTAAAACTAGAGTGCATTTTTCAAC 59.352 33.333 0.00 0.00 0.00 3.18
2666 3208 7.711846 TGCTAAAACTAGAGTGCATTTTTCAA 58.288 30.769 0.00 0.00 0.00 2.69
2667 3209 7.270757 TGCTAAAACTAGAGTGCATTTTTCA 57.729 32.000 0.00 0.00 0.00 2.69
2668 3210 8.748380 AATGCTAAAACTAGAGTGCATTTTTC 57.252 30.769 10.53 0.00 45.13 2.29
2673 3215 7.415989 CCATGAAATGCTAAAACTAGAGTGCAT 60.416 37.037 0.00 2.41 44.97 3.96
2674 3216 6.127925 CCATGAAATGCTAAAACTAGAGTGCA 60.128 38.462 0.00 0.00 44.97 4.57
2675 3217 6.127897 ACCATGAAATGCTAAAACTAGAGTGC 60.128 38.462 0.00 0.00 44.97 4.40
2676 3218 7.383102 ACCATGAAATGCTAAAACTAGAGTG 57.617 36.000 0.00 0.00 44.97 3.51
2677 3219 7.121315 GGAACCATGAAATGCTAAAACTAGAGT 59.879 37.037 0.00 0.00 44.97 3.24
2678 3220 7.121168 TGGAACCATGAAATGCTAAAACTAGAG 59.879 37.037 0.00 0.00 44.97 2.43
2679 3221 6.945435 TGGAACCATGAAATGCTAAAACTAGA 59.055 34.615 0.00 0.00 44.97 2.43
2680 3222 7.156876 TGGAACCATGAAATGCTAAAACTAG 57.843 36.000 0.00 0.00 44.97 2.57
2681 3223 7.531857 TTGGAACCATGAAATGCTAAAACTA 57.468 32.000 0.00 0.00 44.97 2.24
2682 3224 6.418057 TTGGAACCATGAAATGCTAAAACT 57.582 33.333 0.00 0.00 44.97 2.66
2683 3225 7.520686 CAATTGGAACCATGAAATGCTAAAAC 58.479 34.615 0.00 0.00 44.97 2.43
2684 3226 6.149142 GCAATTGGAACCATGAAATGCTAAAA 59.851 34.615 7.72 0.00 44.97 1.52
2685 3227 5.642919 GCAATTGGAACCATGAAATGCTAAA 59.357 36.000 7.72 0.00 44.97 1.85
2688 3230 3.008157 TGCAATTGGAACCATGAAATGCT 59.992 39.130 7.72 0.00 44.97 3.79
2722 3264 0.807667 ATAGAAAGTCCGCAGCGCTG 60.808 55.000 32.83 32.83 0.00 5.18
2862 3415 8.400947 CACAAGCTATACATACATTTCTTGCTT 58.599 33.333 0.00 0.00 37.49 3.91
2972 3526 5.123502 GTCAACGGAAGATCTCTGTACACTA 59.876 44.000 0.00 0.00 43.28 2.74
2982 3536 4.601084 TCTAAGGAGTCAACGGAAGATCT 58.399 43.478 0.00 0.00 0.00 2.75
3119 3683 5.893824 AGGGAAGCAATAAAGATTAACCCAG 59.106 40.000 0.00 0.00 36.44 4.45
3162 3752 8.704668 CCAATGCCAGTATATATGGTATAGTGA 58.295 37.037 9.82 0.69 41.64 3.41
3163 3753 8.486210 ACCAATGCCAGTATATATGGTATAGTG 58.514 37.037 9.82 6.76 41.64 2.74
3169 3759 9.600432 AATAAAACCAATGCCAGTATATATGGT 57.400 29.630 8.32 5.09 41.23 3.55
3174 3764 8.995027 TCTGAATAAAACCAATGCCAGTATAT 57.005 30.769 0.00 0.00 0.00 0.86
3175 3765 8.995027 ATCTGAATAAAACCAATGCCAGTATA 57.005 30.769 0.00 0.00 0.00 1.47
3225 3823 6.645790 AATCACATTTCCTTCATATCCAGC 57.354 37.500 0.00 0.00 0.00 4.85
3226 3824 8.472413 ACAAAATCACATTTCCTTCATATCCAG 58.528 33.333 0.00 0.00 0.00 3.86
3278 3876 4.809426 GCCACACCTATCATACTGTGTTAC 59.191 45.833 0.00 0.00 39.78 2.50
3295 3893 2.433868 TGTCTTTCTAGTCGCCACAC 57.566 50.000 0.00 0.00 0.00 3.82
3328 3926 4.591498 TCCCTATTATTATCGTGTGCTGGT 59.409 41.667 0.00 0.00 0.00 4.00
3330 3928 5.171476 CCTCCCTATTATTATCGTGTGCTG 58.829 45.833 0.00 0.00 0.00 4.41
3376 4105 0.614979 AGCTGTGGTCTGGGACGTAT 60.615 55.000 0.00 0.00 32.65 3.06
3460 5654 3.176708 CCCACGATGAACTACAACTACG 58.823 50.000 0.00 0.00 0.00 3.51
3498 5692 7.992180 AAAATGTGACATTCAGTTTGACTTC 57.008 32.000 11.70 0.00 33.08 3.01
3581 5775 7.309770 AGTTAGATAGAAGAAGCCATAAGGG 57.690 40.000 0.00 0.00 40.85 3.95
3648 5846 2.907910 ACATGAGCAACTTCGAATGC 57.092 45.000 14.48 14.48 42.87 3.56


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

AutoCloner maintained by Alex Coulton.