Multiple sequence alignment - TraesCS7B01G301000

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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 TraesCS7B01G301000 chr7B 100.000 4248 0 0 1 4248 538054881 538050634 0.000000e+00 7845.0
1 TraesCS7B01G301000 chr7B 83.580 609 90 9 1046 1646 685361148 685360542 2.870000e-156 562.0
2 TraesCS7B01G301000 chr7D 92.860 2395 92 26 873 3212 509632716 509630346 0.000000e+00 3402.0
3 TraesCS7B01G301000 chr7D 85.172 580 80 6 1051 1628 603583307 603583882 1.320000e-164 590.0
4 TraesCS7B01G301000 chr7D 84.351 262 16 10 3209 3453 509630316 509630063 2.550000e-57 233.0
5 TraesCS7B01G301000 chr7D 87.437 199 14 5 3699 3888 509628623 509628427 7.150000e-53 219.0
6 TraesCS7B01G301000 chr7D 85.784 204 21 4 3484 3682 509628868 509628668 4.300000e-50 209.0
7 TraesCS7B01G301000 chr7D 91.837 49 1 1 4203 4248 509628432 509628384 9.860000e-07 65.8
8 TraesCS7B01G301000 chr7A 94.936 1876 74 10 1358 3212 580633353 580631478 0.000000e+00 2918.0
9 TraesCS7B01G301000 chr7A 92.503 747 25 6 140 871 36659589 36658859 0.000000e+00 1040.0
10 TraesCS7B01G301000 chr7A 93.939 528 27 5 3700 4223 580630075 580629549 0.000000e+00 793.0
11 TraesCS7B01G301000 chr7A 85.931 462 35 10 3209 3644 580631448 580630991 2.310000e-127 466.0
12 TraesCS7B01G301000 chr7A 92.683 287 21 0 1007 1293 580633636 580633350 8.500000e-112 414.0
13 TraesCS7B01G301000 chr7A 94.783 115 6 0 1 115 36659697 36659583 3.370000e-41 180.0
14 TraesCS7B01G301000 chr6D 86.079 2155 234 35 1057 3163 36252670 36254806 0.000000e+00 2257.0
15 TraesCS7B01G301000 chr6D 92.865 883 33 9 1 872 292714499 292715362 0.000000e+00 1254.0
16 TraesCS7B01G301000 chr6B 85.456 2159 240 51 1057 3163 75941544 75943680 0.000000e+00 2180.0
17 TraesCS7B01G301000 chr6B 96.822 881 18 3 1 871 478473632 478474512 0.000000e+00 1463.0
18 TraesCS7B01G301000 chr5D 88.430 1815 160 23 1057 2831 406415459 406417263 0.000000e+00 2143.0
19 TraesCS7B01G301000 chr5D 88.533 593 54 10 1057 1642 417827103 417827688 0.000000e+00 706.0
20 TraesCS7B01G301000 chr5D 89.860 286 28 1 2887 3171 406417285 406417570 2.410000e-97 366.0
21 TraesCS7B01G301000 chr5D 82.063 223 30 7 4032 4246 410346740 410346960 9.380000e-42 182.0
22 TraesCS7B01G301000 chr6A 84.958 2154 259 38 1057 3163 40297975 40300110 0.000000e+00 2122.0
23 TraesCS7B01G301000 chr5A 87.996 1816 172 27 1057 2831 512059560 512061370 0.000000e+00 2104.0
24 TraesCS7B01G301000 chr5A 89.860 286 28 1 2887 3171 512061392 512061677 2.410000e-97 366.0
25 TraesCS7B01G301000 chr5A 83.857 223 26 8 4032 4246 521768588 521768808 2.000000e-48 204.0
26 TraesCS7B01G301000 chr1D 84.523 2171 269 37 1031 3163 440718407 440720548 0.000000e+00 2085.0
27 TraesCS7B01G301000 chr5B 87.466 1827 167 25 1057 2831 487437659 487439475 0.000000e+00 2049.0
28 TraesCS7B01G301000 chr5B 82.911 907 110 30 1 869 282616328 282615429 0.000000e+00 774.0
29 TraesCS7B01G301000 chr5B 88.571 595 58 7 1057 1646 505378336 505378925 0.000000e+00 713.0
30 TraesCS7B01G301000 chr5B 82.090 201 32 4 4018 4216 699394381 699394579 7.300000e-38 169.0
31 TraesCS7B01G301000 chr1A 84.298 2159 273 38 1044 3166 537347824 537345696 0.000000e+00 2049.0
32 TraesCS7B01G301000 chr1A 92.339 744 30 5 140 871 139901403 139900675 0.000000e+00 1033.0
33 TraesCS7B01G301000 chr1A 92.174 115 9 0 1 115 139901511 139901397 3.400000e-36 163.0
34 TraesCS7B01G301000 chr1B 84.225 2168 275 47 1031 3163 598190635 598192770 0.000000e+00 2047.0
35 TraesCS7B01G301000 chr1B 96.595 881 20 6 1 871 90188684 90189564 0.000000e+00 1452.0
36 TraesCS7B01G301000 chr1B 87.996 908 71 16 1 872 17277252 17278157 0.000000e+00 1038.0
37 TraesCS7B01G301000 chr1B 82.828 198 30 4 4017 4212 20712002 20712197 1.570000e-39 174.0
38 TraesCS7B01G301000 chr2B 96.822 881 18 3 1 871 748593298 748594178 0.000000e+00 1463.0
39 TraesCS7B01G301000 chr2B 88.562 306 16 5 457 744 775004026 775004330 1.880000e-93 353.0
40 TraesCS7B01G301000 chr4A 90.778 694 36 5 188 869 575706466 575705789 0.000000e+00 902.0
41 TraesCS7B01G301000 chr4A 92.437 119 8 1 1 119 575711924 575711807 7.300000e-38 169.0
42 TraesCS7B01G301000 chr4A 98.182 55 0 1 140 193 575711816 575711762 1.260000e-15 95.3
43 TraesCS7B01G301000 chr2D 82.648 219 26 5 4036 4248 613127951 613127739 2.610000e-42 183.0


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 TraesCS7B01G301000 chr7B 538050634 538054881 4247 True 7845.00 7845 100.00000 1 4248 1 chr7B.!!$R1 4247
1 TraesCS7B01G301000 chr7B 685360542 685361148 606 True 562.00 562 83.58000 1046 1646 1 chr7B.!!$R2 600
2 TraesCS7B01G301000 chr7D 509628384 509632716 4332 True 825.76 3402 88.45380 873 4248 5 chr7D.!!$R1 3375
3 TraesCS7B01G301000 chr7D 603583307 603583882 575 False 590.00 590 85.17200 1051 1628 1 chr7D.!!$F1 577
4 TraesCS7B01G301000 chr7A 580629549 580633636 4087 True 1147.75 2918 91.87225 1007 4223 4 chr7A.!!$R2 3216
5 TraesCS7B01G301000 chr7A 36658859 36659697 838 True 610.00 1040 93.64300 1 871 2 chr7A.!!$R1 870
6 TraesCS7B01G301000 chr6D 36252670 36254806 2136 False 2257.00 2257 86.07900 1057 3163 1 chr6D.!!$F1 2106
7 TraesCS7B01G301000 chr6D 292714499 292715362 863 False 1254.00 1254 92.86500 1 872 1 chr6D.!!$F2 871
8 TraesCS7B01G301000 chr6B 75941544 75943680 2136 False 2180.00 2180 85.45600 1057 3163 1 chr6B.!!$F1 2106
9 TraesCS7B01G301000 chr6B 478473632 478474512 880 False 1463.00 1463 96.82200 1 871 1 chr6B.!!$F2 870
10 TraesCS7B01G301000 chr5D 406415459 406417570 2111 False 1254.50 2143 89.14500 1057 3171 2 chr5D.!!$F3 2114
11 TraesCS7B01G301000 chr5D 417827103 417827688 585 False 706.00 706 88.53300 1057 1642 1 chr5D.!!$F2 585
12 TraesCS7B01G301000 chr6A 40297975 40300110 2135 False 2122.00 2122 84.95800 1057 3163 1 chr6A.!!$F1 2106
13 TraesCS7B01G301000 chr5A 512059560 512061677 2117 False 1235.00 2104 88.92800 1057 3171 2 chr5A.!!$F2 2114
14 TraesCS7B01G301000 chr1D 440718407 440720548 2141 False 2085.00 2085 84.52300 1031 3163 1 chr1D.!!$F1 2132
15 TraesCS7B01G301000 chr5B 487437659 487439475 1816 False 2049.00 2049 87.46600 1057 2831 1 chr5B.!!$F1 1774
16 TraesCS7B01G301000 chr5B 282615429 282616328 899 True 774.00 774 82.91100 1 869 1 chr5B.!!$R1 868
17 TraesCS7B01G301000 chr5B 505378336 505378925 589 False 713.00 713 88.57100 1057 1646 1 chr5B.!!$F2 589
18 TraesCS7B01G301000 chr1A 537345696 537347824 2128 True 2049.00 2049 84.29800 1044 3166 1 chr1A.!!$R1 2122
19 TraesCS7B01G301000 chr1A 139900675 139901511 836 True 598.00 1033 92.25650 1 871 2 chr1A.!!$R2 870
20 TraesCS7B01G301000 chr1B 598190635 598192770 2135 False 2047.00 2047 84.22500 1031 3163 1 chr1B.!!$F4 2132
21 TraesCS7B01G301000 chr1B 90188684 90189564 880 False 1452.00 1452 96.59500 1 871 1 chr1B.!!$F3 870
22 TraesCS7B01G301000 chr1B 17277252 17278157 905 False 1038.00 1038 87.99600 1 872 1 chr1B.!!$F1 871
23 TraesCS7B01G301000 chr2B 748593298 748594178 880 False 1463.00 1463 96.82200 1 871 1 chr2B.!!$F1 870
24 TraesCS7B01G301000 chr4A 575705789 575706466 677 True 902.00 902 90.77800 188 869 1 chr4A.!!$R1 681

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
753 824 0.467844 TTGTGACATTGCCAGGTGCT 60.468 50.000 0.0 0.0 42.0 4.40 F
901 990 1.984066 TGTAACTTTTCCCCCGTTGG 58.016 50.000 0.0 0.0 0.0 3.77 F
2658 2895 2.401766 CCAGCTCATCACCGGCAAC 61.402 63.158 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1920 2157 0.387622 CGTCGAACAGGAAGCGGTAA 60.388 55.0 0.00 0.0 0.00 2.85 R
2768 3005 0.755079 CCTGATCATCTTCTCCGGCA 59.245 55.0 0.00 0.0 0.00 5.69 R
3953 6305 0.249398 ATTGAAGCCTTCCGCGTAGT 59.751 50.0 4.92 0.0 44.76 2.73 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
34 35 3.456277 AGGGTGGAGTTCCTATCATCAAC 59.544 47.826 0.00 0.00 36.82 3.18
127 130 9.485206 TGTTATTTTGTACTCTTAACAGGTCTC 57.515 33.333 0.00 0.00 31.25 3.36
128 131 8.933807 GTTATTTTGTACTCTTAACAGGTCTCC 58.066 37.037 0.00 0.00 0.00 3.71
129 132 5.479124 TTTGTACTCTTAACAGGTCTCCC 57.521 43.478 0.00 0.00 0.00 4.30
130 133 4.122337 TGTACTCTTAACAGGTCTCCCA 57.878 45.455 0.00 0.00 0.00 4.37
131 134 4.684724 TGTACTCTTAACAGGTCTCCCAT 58.315 43.478 0.00 0.00 0.00 4.00
132 135 5.834460 TGTACTCTTAACAGGTCTCCCATA 58.166 41.667 0.00 0.00 0.00 2.74
133 136 6.441222 TGTACTCTTAACAGGTCTCCCATAT 58.559 40.000 0.00 0.00 0.00 1.78
134 137 5.878406 ACTCTTAACAGGTCTCCCATATG 57.122 43.478 0.00 0.00 0.00 1.78
135 138 4.656112 ACTCTTAACAGGTCTCCCATATGG 59.344 45.833 15.41 15.41 0.00 2.74
136 139 4.631234 TCTTAACAGGTCTCCCATATGGT 58.369 43.478 20.46 1.06 34.77 3.55
137 140 5.784023 TCTTAACAGGTCTCCCATATGGTA 58.216 41.667 20.46 3.62 34.77 3.25
138 141 6.206787 TCTTAACAGGTCTCCCATATGGTAA 58.793 40.000 20.46 7.40 34.77 2.85
139 142 6.849697 TCTTAACAGGTCTCCCATATGGTAAT 59.150 38.462 20.46 0.00 34.77 1.89
140 143 5.994416 AACAGGTCTCCCATATGGTAATT 57.006 39.130 20.46 0.98 34.77 1.40
141 144 5.310409 ACAGGTCTCCCATATGGTAATTG 57.690 43.478 20.46 12.39 34.77 2.32
142 145 4.726825 ACAGGTCTCCCATATGGTAATTGT 59.273 41.667 20.46 12.96 34.77 2.71
348 390 5.104693 TGGTGACCATTTCCATACGAACTAT 60.105 40.000 0.00 0.00 0.00 2.12
513 562 7.734538 TTTGCGCTTGAACTATTTAATAAGC 57.265 32.000 9.73 0.00 37.69 3.09
723 789 2.115427 TGCTGGTAGTGCTATAAGGCA 58.885 47.619 0.00 0.00 40.15 4.75
753 824 0.467844 TTGTGACATTGCCAGGTGCT 60.468 50.000 0.00 0.00 42.00 4.40
775 846 3.268334 TGGTATGTTTCTACCATTGGCCT 59.732 43.478 3.32 0.00 44.87 5.19
819 898 3.181458 GGGCCGTGGTTATCAGAATAGAA 60.181 47.826 0.00 0.00 0.00 2.10
845 933 2.724839 CGTGCAAATTTGGTAGAGACGC 60.725 50.000 19.47 6.73 0.00 5.19
876 964 6.038161 GCATGTGCACATTTACTAGTTCCATA 59.962 38.462 29.48 0.00 41.59 2.74
892 980 9.774742 CTAGTTCCATAAGCATTGTAACTTTTC 57.225 33.333 0.00 0.00 0.00 2.29
893 981 7.602753 AGTTCCATAAGCATTGTAACTTTTCC 58.397 34.615 0.00 0.00 0.00 3.13
896 985 5.395214 CCATAAGCATTGTAACTTTTCCCCC 60.395 44.000 0.00 0.00 0.00 5.40
901 990 1.984066 TGTAACTTTTCCCCCGTTGG 58.016 50.000 0.00 0.00 0.00 3.77
913 1002 3.071892 TCCCCCGTTGGCTACATTAATAG 59.928 47.826 0.00 0.00 0.00 1.73
914 1003 3.181448 CCCCCGTTGGCTACATTAATAGT 60.181 47.826 0.00 0.00 0.00 2.12
918 1007 4.062991 CGTTGGCTACATTAATAGTCCCC 58.937 47.826 0.00 0.00 0.00 4.81
1482 1653 2.839098 CTGCACCAGAACCACCCT 59.161 61.111 0.00 0.00 32.44 4.34
1772 1970 3.083349 CATGGAGGTGGAGGCCGA 61.083 66.667 0.00 0.00 0.00 5.54
1890 2127 2.727544 GCCAAGCTTGCCGTGAAA 59.272 55.556 21.43 0.00 0.00 2.69
2436 2673 3.744719 CGTGGCGAGGAGGACGAA 61.745 66.667 0.00 0.00 33.64 3.85
2658 2895 2.401766 CCAGCTCATCACCGGCAAC 61.402 63.158 0.00 0.00 0.00 4.17
2883 3120 1.152839 GGACGAGGAGGAGGAGGAG 60.153 68.421 0.00 0.00 0.00 3.69
2885 3122 1.928714 GACGAGGAGGAGGAGGAGGT 61.929 65.000 0.00 0.00 0.00 3.85
2913 3162 0.249120 CGTGGGGCACAGACTATGAA 59.751 55.000 0.00 0.00 33.40 2.57
2985 3234 0.250234 TCATCTTCTGGAACCTGCGG 59.750 55.000 0.00 0.00 0.00 5.69
3090 3339 1.737008 GAAGAAGGACGGCGTGGTC 60.737 63.158 21.19 11.84 36.18 4.02
3321 3628 5.390251 CCAGTTCGTTGACTTTGATCATCTG 60.390 44.000 0.00 0.00 0.00 2.90
3325 3632 3.181513 CGTTGACTTTGATCATCTGCAGG 60.182 47.826 15.13 0.00 0.00 4.85
3346 3653 3.306019 GGATTCAAAACCAAATCGTGCCT 60.306 43.478 0.00 0.00 33.57 4.75
3347 3654 2.791383 TCAAAACCAAATCGTGCCTG 57.209 45.000 0.00 0.00 0.00 4.85
3384 3691 1.174712 ATGCTGCGCTTGAGTTGGTT 61.175 50.000 9.73 0.00 0.00 3.67
3399 3706 6.785076 TGAGTTGGTTATCATTCTTGGGTAA 58.215 36.000 0.00 0.00 0.00 2.85
3415 3722 4.721132 TGGGTAAATTTATCCCATCGACC 58.279 43.478 22.21 8.46 45.19 4.79
3416 3723 4.166337 TGGGTAAATTTATCCCATCGACCA 59.834 41.667 22.21 0.93 45.19 4.02
3428 3735 2.816087 CCATCGACCAATGAATCATCCC 59.184 50.000 0.00 0.00 0.00 3.85
3445 3752 1.064463 TCCCTTGGAGTGCATGAATCC 60.064 52.381 0.00 0.06 0.00 3.01
3470 3779 4.000988 TGGATTTCTAAACTCCGAACAGC 58.999 43.478 0.00 0.00 31.36 4.40
3475 3784 2.028112 TCTAAACTCCGAACAGCATGCT 60.028 45.455 16.30 16.30 42.53 3.79
3491 4962 1.795768 TGCTGTCGTGGAGTTTGATC 58.204 50.000 0.00 0.00 0.00 2.92
3510 4987 2.195727 TCAGGGTGCTATGTGAATCCA 58.804 47.619 0.00 0.00 0.00 3.41
3516 4993 3.815401 GGTGCTATGTGAATCCATACCAC 59.185 47.826 7.83 7.83 34.96 4.16
3563 5041 5.867903 TTCTGAATTCAAAAAGGAAGGCA 57.132 34.783 9.88 0.00 0.00 4.75
3566 5044 6.648192 TCTGAATTCAAAAAGGAAGGCAAAA 58.352 32.000 9.88 0.00 0.00 2.44
3567 5045 7.108847 TCTGAATTCAAAAAGGAAGGCAAAAA 58.891 30.769 9.88 0.00 0.00 1.94
3646 5959 3.636231 CAACACCTCCCCGCTCCA 61.636 66.667 0.00 0.00 0.00 3.86
3650 5963 1.146263 CACCTCCCCGCTCCATAAC 59.854 63.158 0.00 0.00 0.00 1.89
3656 5969 1.093496 CCCCGCTCCATAACGAAACC 61.093 60.000 0.00 0.00 0.00 3.27
3677 5990 3.713764 CCACTCCCTCTTTAGTGATCCAT 59.286 47.826 4.11 0.00 44.79 3.41
3682 5995 5.205821 TCCCTCTTTAGTGATCCATAACGA 58.794 41.667 0.00 0.00 0.00 3.85
3683 5996 5.659525 TCCCTCTTTAGTGATCCATAACGAA 59.340 40.000 0.00 0.00 0.00 3.85
3684 5997 6.155565 TCCCTCTTTAGTGATCCATAACGAAA 59.844 38.462 0.00 0.00 0.00 3.46
3686 5999 7.171678 CCCTCTTTAGTGATCCATAACGAAATC 59.828 40.741 0.00 0.00 0.00 2.17
3688 6001 8.420374 TCTTTAGTGATCCATAACGAAATCAC 57.580 34.615 6.28 6.28 45.30 3.06
3691 6004 5.659048 GTGATCCATAACGAAATCACTCC 57.341 43.478 7.00 0.00 42.91 3.85
3692 6005 4.511826 GTGATCCATAACGAAATCACTCCC 59.488 45.833 7.00 0.00 42.91 4.30
3694 6007 4.402056 TCCATAACGAAATCACTCCCTC 57.598 45.455 0.00 0.00 0.00 4.30
3695 6008 4.030913 TCCATAACGAAATCACTCCCTCT 58.969 43.478 0.00 0.00 0.00 3.69
3699 6012 6.480320 CCATAACGAAATCACTCCCTCTTTAG 59.520 42.308 0.00 0.00 0.00 1.85
3701 6014 5.941555 ACGAAATCACTCCCTCTTTAGAT 57.058 39.130 0.00 0.00 0.00 1.98
3703 6016 7.604657 ACGAAATCACTCCCTCTTTAGATAT 57.395 36.000 0.00 0.00 0.00 1.63
3774 6120 0.238289 AACTTCTCGGCATTGCGTTG 59.762 50.000 1.91 0.00 0.00 4.10
3883 6233 7.755373 GGTAAGTCAGGAATGATAAAAACAAGC 59.245 37.037 0.00 0.00 0.00 4.01
3890 6240 5.994668 GGAATGATAAAAACAAGCCCACAAA 59.005 36.000 0.00 0.00 0.00 2.83
3926 6276 0.811281 GGGCTCCGATGAACCTTTTG 59.189 55.000 0.00 0.00 0.00 2.44
3927 6277 0.171231 GGCTCCGATGAACCTTTTGC 59.829 55.000 0.00 0.00 0.00 3.68
3993 6346 1.283905 GGGGGAAGGGAAAAGATCGAA 59.716 52.381 0.00 0.00 0.00 3.71
3998 6351 3.381590 GGAAGGGAAAAGATCGAATTGGG 59.618 47.826 0.00 0.00 0.00 4.12
4015 6368 1.265454 GGGAATCCACGGAGACCACT 61.265 60.000 0.09 0.00 0.00 4.00
4180 6533 2.930019 CCCCTCCTCTGGCACACA 60.930 66.667 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 3.063861 TGCATTTGAATGTACAGCTAGCG 59.936 43.478 9.55 7.05 38.65 4.26
131 134 9.127277 GGGTGCTTTATAAAGACAATTACCATA 57.873 33.333 26.00 0.00 38.28 2.74
132 135 7.839200 AGGGTGCTTTATAAAGACAATTACCAT 59.161 33.333 26.00 16.82 38.28 3.55
133 136 7.179269 AGGGTGCTTTATAAAGACAATTACCA 58.821 34.615 26.00 10.68 38.28 3.25
134 137 7.640597 AGGGTGCTTTATAAAGACAATTACC 57.359 36.000 26.00 19.81 38.28 2.85
137 140 9.646522 ATCATAGGGTGCTTTATAAAGACAATT 57.353 29.630 26.00 11.72 38.28 2.32
255 295 6.273071 ACCAATTTGCACTTTACTGAAAGAC 58.727 36.000 4.50 0.00 44.23 3.01
348 390 5.006165 CAGAAAAACGGCAAGCAAACAATAA 59.994 36.000 0.00 0.00 0.00 1.40
513 562 6.566197 AGTAAATTCAGAAGGCTTGAACAG 57.434 37.500 3.46 0.00 0.00 3.16
723 789 1.967319 ATGTCACAAACTCTGGCGTT 58.033 45.000 0.00 0.00 0.00 4.84
731 802 1.682854 CACCTGGCAATGTCACAAACT 59.317 47.619 0.00 0.00 0.00 2.66
831 919 1.665679 CAATGCGCGTCTCTACCAAAT 59.334 47.619 8.43 0.00 0.00 2.32
876 964 2.560981 CGGGGGAAAAGTTACAATGCTT 59.439 45.455 0.00 0.00 0.00 3.91
892 980 2.358322 ATTAATGTAGCCAACGGGGG 57.642 50.000 0.00 0.00 37.04 5.40
893 981 4.062991 GACTATTAATGTAGCCAACGGGG 58.937 47.826 0.00 0.00 40.85 5.73
896 985 4.062991 GGGGACTATTAATGTAGCCAACG 58.937 47.826 0.00 0.00 0.00 4.10
901 990 5.652518 GATCGAGGGGACTATTAATGTAGC 58.347 45.833 0.00 0.00 44.43 3.58
913 1002 1.960612 CAGATCCGATCGAGGGGAC 59.039 63.158 18.66 1.85 34.58 4.46
914 1003 1.903890 GCAGATCCGATCGAGGGGA 60.904 63.158 18.66 9.42 36.61 4.81
918 1007 2.429907 GGCGCAGATCCGATCGAG 60.430 66.667 18.66 6.99 0.00 4.04
1789 2002 2.818714 CTTCTGCTCAGCCGGCTG 60.819 66.667 44.24 44.24 44.86 4.85
1797 2013 1.004560 CACCTTCGGCTTCTGCTCA 60.005 57.895 0.00 0.00 39.59 4.26
1881 2118 1.741401 CTCCAGCGATTTCACGGCA 60.741 57.895 0.00 0.00 0.00 5.69
1890 2127 0.935898 CGTAGTACGTCTCCAGCGAT 59.064 55.000 14.62 0.00 36.74 4.58
1920 2157 0.387622 CGTCGAACAGGAAGCGGTAA 60.388 55.000 0.00 0.00 0.00 2.85
2287 2524 0.905337 AAGAGGACCTTGTAGCGCCT 60.905 55.000 2.29 0.00 32.92 5.52
2436 2673 2.341543 CACTGCAGCTCCGACACT 59.658 61.111 15.27 0.00 0.00 3.55
2651 2888 3.353836 CACGAAGGGTGTTGCCGG 61.354 66.667 0.00 0.00 41.89 6.13
2658 2895 2.417924 CCTCATCTTCTCACGAAGGGTG 60.418 54.545 0.00 3.18 45.36 4.61
2768 3005 0.755079 CCTGATCATCTTCTCCGGCA 59.245 55.000 0.00 0.00 0.00 5.69
2900 3149 3.555139 GCAGATCACTTCATAGTCTGTGC 59.445 47.826 0.00 0.00 30.92 4.57
2913 3162 3.054802 CCCTAAACTTCTGGCAGATCACT 60.055 47.826 19.50 6.48 0.00 3.41
2985 3234 0.594284 CCGGCGTCGATTTAGAGTCC 60.594 60.000 12.93 0.00 39.00 3.85
3090 3339 0.182537 TCATAATGGCCTCGGGGTTG 59.817 55.000 1.62 0.00 34.45 3.77
3121 3370 3.129502 CTGGTACTCGTCGCCGGA 61.130 66.667 5.05 0.00 33.95 5.14
3176 3425 1.208614 CTTGCAAACAGAGGCGAGC 59.791 57.895 0.00 0.00 34.96 5.03
3242 3530 2.640184 AGCGTACTCCTTAATTTGCCC 58.360 47.619 0.00 0.00 0.00 5.36
3308 3615 4.851843 TGAATCCTGCAGATGATCAAAGT 58.148 39.130 17.39 0.00 34.56 2.66
3321 3628 3.674753 CACGATTTGGTTTTGAATCCTGC 59.325 43.478 0.00 0.00 0.00 4.85
3325 3632 3.674753 CAGGCACGATTTGGTTTTGAATC 59.325 43.478 0.00 0.00 0.00 2.52
3370 3677 3.375299 AGAATGATAACCAACTCAAGCGC 59.625 43.478 0.00 0.00 0.00 5.92
3371 3678 5.327091 CAAGAATGATAACCAACTCAAGCG 58.673 41.667 0.00 0.00 0.00 4.68
3399 3706 6.777091 TGATTCATTGGTCGATGGGATAAATT 59.223 34.615 0.00 0.00 0.00 1.82
3412 3719 3.887716 CTCCAAGGGATGATTCATTGGTC 59.112 47.826 16.05 0.00 39.50 4.02
3415 3722 3.067742 GCACTCCAAGGGATGATTCATTG 59.932 47.826 0.00 0.00 0.00 2.82
3416 3723 3.294214 GCACTCCAAGGGATGATTCATT 58.706 45.455 0.00 0.00 0.00 2.57
3445 3752 6.494893 TGTTCGGAGTTTAGAAATCCATTG 57.505 37.500 7.77 0.00 32.31 2.82
3453 3760 2.742053 GCATGCTGTTCGGAGTTTAGAA 59.258 45.455 11.37 0.00 0.00 2.10
3470 3779 1.511850 TCAAACTCCACGACAGCATG 58.488 50.000 0.00 0.00 46.00 4.06
3475 3784 1.001974 CCCTGATCAAACTCCACGACA 59.998 52.381 0.00 0.00 0.00 4.35
3491 4962 2.715749 TGGATTCACATAGCACCCTG 57.284 50.000 0.00 0.00 0.00 4.45
3510 4987 6.489603 TCAATTACAAGGATGGTTGTGGTAT 58.510 36.000 0.00 0.00 40.89 2.73
3516 4993 6.528537 TCCATTCAATTACAAGGATGGTTG 57.471 37.500 0.00 0.00 0.00 3.77
3566 5044 9.594478 ACATCTTTTCCGTAAAACTGAATTTTT 57.406 25.926 0.00 0.00 40.99 1.94
3567 5045 9.594478 AACATCTTTTCCGTAAAACTGAATTTT 57.406 25.926 0.00 0.00 43.18 1.82
3571 5049 8.989653 AAAAACATCTTTTCCGTAAAACTGAA 57.010 26.923 0.00 0.00 31.37 3.02
3599 5080 2.939103 CAACTCGAATGGCTCCCTTAAG 59.061 50.000 0.00 0.00 0.00 1.85
3600 5081 2.569853 TCAACTCGAATGGCTCCCTTAA 59.430 45.455 0.00 0.00 0.00 1.85
3601 5082 2.168521 CTCAACTCGAATGGCTCCCTTA 59.831 50.000 0.00 0.00 0.00 2.69
3646 5959 4.635699 AAAGAGGGAGTGGTTTCGTTAT 57.364 40.909 0.00 0.00 0.00 1.89
3650 5963 3.006537 TCACTAAAGAGGGAGTGGTTTCG 59.993 47.826 2.44 0.00 42.77 3.46
3656 5969 6.284459 GTTATGGATCACTAAAGAGGGAGTG 58.716 44.000 0.00 0.00 38.94 3.51
3677 5990 6.845758 TCTAAAGAGGGAGTGATTTCGTTA 57.154 37.500 0.00 0.00 0.00 3.18
3682 5995 7.934120 CGGAAATATCTAAAGAGGGAGTGATTT 59.066 37.037 0.00 0.00 0.00 2.17
3683 5996 7.445945 CGGAAATATCTAAAGAGGGAGTGATT 58.554 38.462 0.00 0.00 0.00 2.57
3684 5997 6.014156 CCGGAAATATCTAAAGAGGGAGTGAT 60.014 42.308 0.00 0.00 0.00 3.06
3686 5999 5.070580 ACCGGAAATATCTAAAGAGGGAGTG 59.929 44.000 9.46 0.00 0.00 3.51
3688 6001 5.279556 GGACCGGAAATATCTAAAGAGGGAG 60.280 48.000 9.46 0.00 0.00 4.30
3689 6002 4.591924 GGACCGGAAATATCTAAAGAGGGA 59.408 45.833 9.46 0.00 0.00 4.20
3690 6003 4.593634 AGGACCGGAAATATCTAAAGAGGG 59.406 45.833 9.46 0.00 0.00 4.30
3691 6004 5.810080 AGGACCGGAAATATCTAAAGAGG 57.190 43.478 9.46 0.00 0.00 3.69
3692 6005 9.425577 GATTAAGGACCGGAAATATCTAAAGAG 57.574 37.037 9.46 0.00 0.00 2.85
3694 6007 8.154856 TGGATTAAGGACCGGAAATATCTAAAG 58.845 37.037 9.46 0.00 0.00 1.85
3695 6008 7.935210 GTGGATTAAGGACCGGAAATATCTAAA 59.065 37.037 9.46 0.00 0.00 1.85
3699 6012 4.689345 CGTGGATTAAGGACCGGAAATATC 59.311 45.833 9.46 2.98 0.00 1.63
3701 6014 3.181463 CCGTGGATTAAGGACCGGAAATA 60.181 47.826 9.46 0.00 37.66 1.40
3703 6016 1.065998 CCGTGGATTAAGGACCGGAAA 60.066 52.381 9.46 0.00 37.66 3.13
3751 6093 0.455633 GCAATGCCGAGAAGTTGCAG 60.456 55.000 0.00 0.00 44.63 4.41
3759 6101 0.882484 TTGACAACGCAATGCCGAGA 60.882 50.000 0.00 0.00 0.00 4.04
3774 6120 4.217550 TGAAAGGTTCGGATGGAATTTGAC 59.782 41.667 0.00 0.00 36.92 3.18
3827 6173 0.869880 AACTTGCGCTCGTTTTTGGC 60.870 50.000 9.73 0.00 0.00 4.52
3883 6233 3.332034 CTTAGTTACCGAGGTTTGTGGG 58.668 50.000 0.00 0.00 0.00 4.61
3916 6266 4.182339 GTTTAAAACGGGCAAAAGGTTCA 58.818 39.130 0.00 0.00 0.00 3.18
3945 6297 0.525668 CTTCCGCGTAGTTGCTCGAT 60.526 55.000 4.92 0.00 0.00 3.59
3953 6305 0.249398 ATTGAAGCCTTCCGCGTAGT 59.751 50.000 4.92 0.00 44.76 2.73
3954 6306 0.652592 CATTGAAGCCTTCCGCGTAG 59.347 55.000 4.92 1.38 44.76 3.51
3955 6307 0.742990 CCATTGAAGCCTTCCGCGTA 60.743 55.000 4.92 0.00 44.76 4.42
3993 6346 0.546598 GGTCTCCGTGGATTCCCAAT 59.453 55.000 0.00 0.00 45.59 3.16
3998 6351 0.741221 GCAGTGGTCTCCGTGGATTC 60.741 60.000 0.00 0.00 0.00 2.52
4015 6368 0.613260 AGAAGTAGCGTTCCATGGCA 59.387 50.000 6.96 0.00 0.00 4.92
4130 6483 2.887568 CATCTCCGTGGTGCGCTC 60.888 66.667 9.73 4.47 39.71 5.03


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

AutoCloner maintained by Alex Coulton.