Multiple sequence alignment - TraesCS1A01G041800

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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 TraesCS1A01G041800 chr1A 100.000 4014 0 0 1 4014 22763181 22759168 0.000000e+00 7413.0
1 TraesCS1A01G041800 chr1A 89.621 3141 217 66 924 4014 13271845 13274926 0.000000e+00 3893.0
2 TraesCS1A01G041800 chr1A 85.787 2343 210 62 1593 3882 13212988 13215260 0.000000e+00 2368.0
3 TraesCS1A01G041800 chr1A 85.701 2140 195 46 1593 3674 13229599 13231685 0.000000e+00 2154.0
4 TraesCS1A01G041800 chr1A 85.333 1875 184 46 1022 2879 22818803 22817003 0.000000e+00 1855.0
5 TraesCS1A01G041800 chr1A 86.959 1641 136 28 1593 3193 13009308 13007706 0.000000e+00 1773.0
6 TraesCS1A01G041800 chr1A 88.281 1169 80 16 2086 3229 13005011 13003875 0.000000e+00 1347.0
7 TraesCS1A01G041800 chr1A 85.438 879 97 16 41 897 57298491 57299360 0.000000e+00 885.0
8 TraesCS1A01G041800 chr1A 86.373 477 49 11 3411 3879 13007658 13007190 1.290000e-139 507.0
9 TraesCS1A01G041800 chr1A 80.527 683 72 31 2938 3602 22778864 22778225 6.070000e-128 468.0
10 TraesCS1A01G041800 chr1A 84.564 447 43 5 1654 2090 13005817 13005387 1.730000e-113 420.0
11 TraesCS1A01G041800 chr1A 80.803 573 70 33 1174 1730 13009850 13009302 2.890000e-111 412.0
12 TraesCS1A01G041800 chr1A 82.524 412 56 14 1154 1559 13250410 13250811 8.260000e-92 348.0
13 TraesCS1A01G041800 chr1A 78.835 515 69 33 1232 1730 13229115 13229605 1.080000e-80 311.0
14 TraesCS1A01G041800 chr1A 92.920 113 8 0 3902 4014 13258110 13258222 8.920000e-37 165.0
15 TraesCS1A01G041800 chr1A 90.265 113 7 1 3902 4014 13231690 13231798 1.160000e-30 145.0
16 TraesCS1A01G041800 chr1D 96.223 3627 60 14 427 4014 10929206 10932794 0.000000e+00 5867.0
17 TraesCS1A01G041800 chr1D 86.037 2299 200 48 1639 3879 10775143 10772908 0.000000e+00 2355.0
18 TraesCS1A01G041800 chr1D 89.598 1269 96 17 1625 2879 10763696 10762450 0.000000e+00 1580.0
19 TraesCS1A01G041800 chr1D 87.697 1333 121 16 1508 2826 10836318 10837621 0.000000e+00 1513.0
20 TraesCS1A01G041800 chr1D 88.194 1296 110 23 1593 2873 10844432 10845699 0.000000e+00 1506.0
21 TraesCS1A01G041800 chr1D 85.193 986 93 26 2920 3882 10762302 10761347 0.000000e+00 963.0
22 TraesCS1A01G041800 chr1D 83.778 863 85 28 2920 3771 10845853 10846671 0.000000e+00 767.0
23 TraesCS1A01G041800 chr1D 95.632 435 19 0 1 435 10921589 10922023 0.000000e+00 699.0
24 TraesCS1A01G041800 chr1D 81.013 474 70 15 1154 1624 10776959 10776503 3.810000e-95 359.0
25 TraesCS1A01G041800 chr1D 82.687 387 60 6 1154 1539 10835830 10836210 1.790000e-88 337.0
26 TraesCS1A01G041800 chr1D 79.231 520 75 27 1227 1730 10764214 10763712 8.320000e-87 331.0
27 TraesCS1A01G041800 chr1D 93.701 127 8 0 3756 3882 10846714 10846840 1.470000e-44 191.0
28 TraesCS1A01G041800 chr1B 88.592 2095 157 33 1666 3712 39814816 39816876 0.000000e+00 2470.0
29 TraesCS1A01G041800 chr1B 88.443 2042 150 31 1789 3794 16400954 16402945 0.000000e+00 2385.0
30 TraesCS1A01G041800 chr1B 85.077 2352 218 48 1593 3879 16225064 16222781 0.000000e+00 2276.0
31 TraesCS1A01G041800 chr1B 85.268 2111 196 40 1593 3642 23598035 23600091 0.000000e+00 2069.0
32 TraesCS1A01G041800 chr1B 85.268 2111 195 41 1593 3642 23896811 23898866 0.000000e+00 2069.0
33 TraesCS1A01G041800 chr1B 87.754 1478 124 15 1611 3053 39732828 39734283 0.000000e+00 1674.0
34 TraesCS1A01G041800 chr1B 87.689 1389 123 27 1508 2879 23775471 23776828 0.000000e+00 1574.0
35 TraesCS1A01G041800 chr1B 93.048 374 25 1 3642 4014 39816847 39817220 2.730000e-151 545.0
36 TraesCS1A01G041800 chr1B 77.120 861 100 52 3042 3882 23776929 23777712 3.730000e-110 409.0
37 TraesCS1A01G041800 chr1B 86.198 384 43 6 1059 1440 39814095 39814470 1.340000e-109 407.0
38 TraesCS1A01G041800 chr1B 82.108 408 64 7 1156 1561 23774946 23775346 1.380000e-89 340.0
39 TraesCS1A01G041800 chr1B 93.805 113 7 0 3902 4014 39734873 39734985 1.920000e-38 171.0
40 TraesCS1A01G041800 chr1B 93.805 113 7 0 3902 4014 39809208 39809320 1.920000e-38 171.0
41 TraesCS1A01G041800 chr1B 92.920 113 8 0 3902 4014 23600128 23600240 8.920000e-37 165.0
42 TraesCS1A01G041800 chr5B 88.826 877 83 8 1 866 291839534 291838662 0.000000e+00 1062.0
43 TraesCS1A01G041800 chr5B 86.935 819 82 12 1 805 391151801 391150994 0.000000e+00 896.0
44 TraesCS1A01G041800 chr5B 81.868 910 91 45 1 899 370186004 370186850 0.000000e+00 699.0
45 TraesCS1A01G041800 chr5B 81.868 910 91 45 1 899 370236478 370237324 0.000000e+00 699.0
46 TraesCS1A01G041800 chr3A 85.793 908 88 22 1 896 693349530 693348652 0.000000e+00 924.0
47 TraesCS1A01G041800 chr2A 85.323 913 105 14 3 898 692527890 692528790 0.000000e+00 917.0
48 TraesCS1A01G041800 chr6A 87.093 798 85 10 114 898 453118886 453118094 0.000000e+00 887.0
49 TraesCS1A01G041800 chr6A 84.043 470 62 11 435 896 137169439 137169903 1.320000e-119 440.0
50 TraesCS1A01G041800 chr6A 94.118 34 2 0 972 1005 611823194 611823227 7.000000e-03 52.8
51 TraesCS1A01G041800 chr6B 83.557 894 105 23 27 896 216688917 216689792 0.000000e+00 798.0
52 TraesCS1A01G041800 chr6B 92.857 42 3 0 969 1010 42435069 42435110 1.200000e-05 62.1
53 TraesCS1A01G041800 chrUn 92.208 462 34 1 3553 4014 261630582 261630123 0.000000e+00 652.0
54 TraesCS1A01G041800 chr3D 84.681 470 54 11 433 897 309928328 309928784 1.700000e-123 453.0
55 TraesCS1A01G041800 chr6D 84.839 310 40 6 602 905 36823501 36823193 5.040000e-79 305.0
56 TraesCS1A01G041800 chr7D 85.484 62 8 1 852 913 8983489 8983429 3.350000e-06 63.9
57 TraesCS1A01G041800 chr2B 97.059 34 1 0 972 1005 58343955 58343988 1.560000e-04 58.4


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 TraesCS1A01G041800 chr1A 22759168 22763181 4013 True 7413.000000 7413 100.000000 1 4014 1 chr1A.!!$R1 4013
1 TraesCS1A01G041800 chr1A 13271845 13274926 3081 False 3893.000000 3893 89.621000 924 4014 1 chr1A.!!$F4 3090
2 TraesCS1A01G041800 chr1A 13212988 13215260 2272 False 2368.000000 2368 85.787000 1593 3882 1 chr1A.!!$F1 2289
3 TraesCS1A01G041800 chr1A 22817003 22818803 1800 True 1855.000000 1855 85.333000 1022 2879 1 chr1A.!!$R3 1857
4 TraesCS1A01G041800 chr1A 13003875 13009850 5975 True 891.800000 1773 85.396000 1174 3879 5 chr1A.!!$R4 2705
5 TraesCS1A01G041800 chr1A 57298491 57299360 869 False 885.000000 885 85.438000 41 897 1 chr1A.!!$F5 856
6 TraesCS1A01G041800 chr1A 13229115 13231798 2683 False 870.000000 2154 84.933667 1232 4014 3 chr1A.!!$F6 2782
7 TraesCS1A01G041800 chr1A 22778225 22778864 639 True 468.000000 468 80.527000 2938 3602 1 chr1A.!!$R2 664
8 TraesCS1A01G041800 chr1D 10929206 10932794 3588 False 5867.000000 5867 96.223000 427 4014 1 chr1D.!!$F2 3587
9 TraesCS1A01G041800 chr1D 10772908 10776959 4051 True 1357.000000 2355 83.525000 1154 3879 2 chr1D.!!$R2 2725
10 TraesCS1A01G041800 chr1D 10761347 10764214 2867 True 958.000000 1580 84.674000 1227 3882 3 chr1D.!!$R1 2655
11 TraesCS1A01G041800 chr1D 10835830 10837621 1791 False 925.000000 1513 85.192000 1154 2826 2 chr1D.!!$F3 1672
12 TraesCS1A01G041800 chr1D 10844432 10846840 2408 False 821.333333 1506 88.557667 1593 3882 3 chr1D.!!$F4 2289
13 TraesCS1A01G041800 chr1B 16400954 16402945 1991 False 2385.000000 2385 88.443000 1789 3794 1 chr1B.!!$F1 2005
14 TraesCS1A01G041800 chr1B 16222781 16225064 2283 True 2276.000000 2276 85.077000 1593 3879 1 chr1B.!!$R1 2286
15 TraesCS1A01G041800 chr1B 23896811 23898866 2055 False 2069.000000 2069 85.268000 1593 3642 1 chr1B.!!$F2 2049
16 TraesCS1A01G041800 chr1B 39814095 39817220 3125 False 1140.666667 2470 89.279333 1059 4014 3 chr1B.!!$F7 2955
17 TraesCS1A01G041800 chr1B 23598035 23600240 2205 False 1117.000000 2069 89.094000 1593 4014 2 chr1B.!!$F4 2421
18 TraesCS1A01G041800 chr1B 39732828 39734985 2157 False 922.500000 1674 90.779500 1611 4014 2 chr1B.!!$F6 2403
19 TraesCS1A01G041800 chr1B 23774946 23777712 2766 False 774.333333 1574 82.305667 1156 3882 3 chr1B.!!$F5 2726
20 TraesCS1A01G041800 chr5B 291838662 291839534 872 True 1062.000000 1062 88.826000 1 866 1 chr5B.!!$R1 865
21 TraesCS1A01G041800 chr5B 391150994 391151801 807 True 896.000000 896 86.935000 1 805 1 chr5B.!!$R2 804
22 TraesCS1A01G041800 chr5B 370186004 370186850 846 False 699.000000 699 81.868000 1 899 1 chr5B.!!$F1 898
23 TraesCS1A01G041800 chr5B 370236478 370237324 846 False 699.000000 699 81.868000 1 899 1 chr5B.!!$F2 898
24 TraesCS1A01G041800 chr3A 693348652 693349530 878 True 924.000000 924 85.793000 1 896 1 chr3A.!!$R1 895
25 TraesCS1A01G041800 chr2A 692527890 692528790 900 False 917.000000 917 85.323000 3 898 1 chr2A.!!$F1 895
26 TraesCS1A01G041800 chr6A 453118094 453118886 792 True 887.000000 887 87.093000 114 898 1 chr6A.!!$R1 784
27 TraesCS1A01G041800 chr6B 216688917 216689792 875 False 798.000000 798 83.557000 27 896 1 chr6B.!!$F2 869

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
51 52 0.532862 CGCGTCTTGATTAGGCCCAT 60.533 55.0 0.0 0.0 0.0 4.00 F
1861 3598 1.194781 AGCGTCTGTCCCTCCAATGT 61.195 55.0 0.0 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1972 3709 2.166870 TGACACGGCCGTAGACATTTAT 59.833 45.455 33.7 7.67 0.0 1.40 R
3397 5337 1.974957 TCACATTCGGGAAGGAGAACA 59.025 47.619 0.0 0.00 0.0 3.18 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
25 26 2.494918 GTCTGCCGCGTCCTATGT 59.505 61.111 4.92 0.00 0.00 2.29
50 51 1.153449 CGCGTCTTGATTAGGCCCA 60.153 57.895 0.00 0.00 0.00 5.36
51 52 0.532862 CGCGTCTTGATTAGGCCCAT 60.533 55.000 0.00 0.00 0.00 4.00
78 79 4.262808 CCGCATCTCTCCTTCATCCTTATT 60.263 45.833 0.00 0.00 0.00 1.40
81 82 6.532826 GCATCTCTCCTTCATCCTTATTTCT 58.467 40.000 0.00 0.00 0.00 2.52
89 90 5.823045 CCTTCATCCTTATTTCTGTGGTACC 59.177 44.000 4.43 4.43 0.00 3.34
95 98 4.263771 CCTTATTTCTGTGGTACCCTGGTT 60.264 45.833 10.07 0.00 0.00 3.67
124 127 5.967088 TCTGTTTCTGTAGCTACTTCCATC 58.033 41.667 23.84 10.88 0.00 3.51
125 128 5.480422 TCTGTTTCTGTAGCTACTTCCATCA 59.520 40.000 23.84 14.22 0.00 3.07
229 232 1.271871 TGGCCACCCACAACTTATCTG 60.272 52.381 0.00 0.00 35.79 2.90
232 235 3.560453 GGCCACCCACAACTTATCTGTTA 60.560 47.826 0.00 0.00 0.00 2.41
340 345 4.090057 GGTGACGAAGCAAGCGGC 62.090 66.667 0.00 0.00 45.30 6.53
385 391 3.702048 CGTGATGGGGTGACGGGT 61.702 66.667 0.00 0.00 33.58 5.28
410 416 1.229209 TCTCCTCCCTCACCACCAC 60.229 63.158 0.00 0.00 0.00 4.16
414 420 4.567597 TCCCTCACCACCACCCGT 62.568 66.667 0.00 0.00 0.00 5.28
428 434 4.429212 CCGTCGGGTGCATGTCGA 62.429 66.667 2.34 0.00 0.00 4.20
559 573 8.049117 AGGAAGATTTCTGCAACATTAGTCATA 58.951 33.333 0.00 0.00 0.00 2.15
657 679 7.277760 AGTTTTTCAGCAACAATACCTTTGTTC 59.722 33.333 0.94 0.00 40.30 3.18
658 680 6.463995 TTTCAGCAACAATACCTTTGTTCT 57.536 33.333 0.94 0.67 40.30 3.01
871 925 4.421058 GCGGCGGATCTTTTTAAAAGATT 58.579 39.130 27.12 15.07 37.14 2.40
1122 1185 3.207669 GATTGGCTCTGCGGGCAG 61.208 66.667 14.36 14.36 44.86 4.85
1389 1457 3.447586 CACCCGGTTCTTTCTCAGAGATA 59.552 47.826 0.00 0.00 31.12 1.98
1861 3598 1.194781 AGCGTCTGTCCCTCCAATGT 61.195 55.000 0.00 0.00 0.00 2.71
1870 3607 3.197766 TGTCCCTCCAATGTGATACACTC 59.802 47.826 0.00 0.00 35.11 3.51
1871 3608 2.771943 TCCCTCCAATGTGATACACTCC 59.228 50.000 0.00 0.00 35.11 3.85
1872 3609 2.505407 CCCTCCAATGTGATACACTCCA 59.495 50.000 0.00 0.00 35.11 3.86
1873 3610 3.054434 CCCTCCAATGTGATACACTCCAA 60.054 47.826 0.00 0.00 35.11 3.53
1874 3611 4.385643 CCCTCCAATGTGATACACTCCAAT 60.386 45.833 0.00 0.00 35.11 3.16
1875 3612 4.577693 CCTCCAATGTGATACACTCCAATG 59.422 45.833 0.00 0.00 35.11 2.82
1876 3613 3.947196 TCCAATGTGATACACTCCAATGC 59.053 43.478 0.00 0.00 35.11 3.56
1877 3614 3.242837 CCAATGTGATACACTCCAATGCG 60.243 47.826 0.00 0.00 35.11 4.73
1878 3615 3.541996 ATGTGATACACTCCAATGCGA 57.458 42.857 0.00 0.00 35.11 5.10
1879 3616 3.541996 TGTGATACACTCCAATGCGAT 57.458 42.857 0.00 0.00 35.11 4.58
1880 3617 4.664150 TGTGATACACTCCAATGCGATA 57.336 40.909 0.00 0.00 35.11 2.92
1881 3618 4.368315 TGTGATACACTCCAATGCGATAC 58.632 43.478 0.00 0.00 35.11 2.24
1882 3619 4.142049 TGTGATACACTCCAATGCGATACA 60.142 41.667 0.00 0.00 35.11 2.29
1883 3620 4.209288 GTGATACACTCCAATGCGATACAC 59.791 45.833 0.00 0.00 0.00 2.90
1884 3621 4.099419 TGATACACTCCAATGCGATACACT 59.901 41.667 0.00 0.00 0.00 3.55
1897 3634 7.923414 ATGCGATACACTGATAGTATCTACA 57.077 36.000 11.40 9.02 43.48 2.74
1972 3709 1.839994 CCTCAGATGTAGGCTTCCCAA 59.160 52.381 0.00 0.00 0.00 4.12
2466 4244 6.239373 CCGAGTACTGTCTAGAGAGGAAGATA 60.239 46.154 20.13 1.43 0.00 1.98
2875 4653 2.084546 GAAGTTCGGATTCAGGGTTGG 58.915 52.381 0.00 0.00 0.00 3.77
2981 4898 6.374417 AGTGATGTGGTCCACTAAGTTATT 57.626 37.500 22.56 0.00 41.38 1.40
3126 5060 3.489813 GCACTTGGCGTTTTAAGGG 57.510 52.632 0.00 0.00 0.00 3.95
3127 5061 0.955905 GCACTTGGCGTTTTAAGGGA 59.044 50.000 0.00 0.00 28.68 4.20
3128 5062 1.335597 GCACTTGGCGTTTTAAGGGAC 60.336 52.381 0.00 0.00 28.68 4.46
3129 5063 1.950909 CACTTGGCGTTTTAAGGGACA 59.049 47.619 0.00 0.00 28.68 4.02
3130 5064 2.556622 CACTTGGCGTTTTAAGGGACAT 59.443 45.455 0.00 0.00 28.68 3.06
3131 5065 3.754323 CACTTGGCGTTTTAAGGGACATA 59.246 43.478 0.00 0.00 28.68 2.29
3132 5066 4.398044 CACTTGGCGTTTTAAGGGACATAT 59.602 41.667 0.00 0.00 28.68 1.78
3133 5067 5.587043 CACTTGGCGTTTTAAGGGACATATA 59.413 40.000 0.00 0.00 28.68 0.86
3134 5068 6.262273 CACTTGGCGTTTTAAGGGACATATAT 59.738 38.462 0.00 0.00 28.68 0.86
3135 5069 7.442969 CACTTGGCGTTTTAAGGGACATATATA 59.557 37.037 0.00 0.00 28.68 0.86
3136 5070 8.161425 ACTTGGCGTTTTAAGGGACATATATAT 58.839 33.333 0.00 0.00 0.00 0.86
3137 5071 7.915293 TGGCGTTTTAAGGGACATATATATG 57.085 36.000 19.21 19.21 39.55 1.78
3309 5247 6.144175 GCATTGCATTTTGTTGCTGTTATTT 58.856 32.000 3.15 0.00 43.18 1.40
3332 5270 6.882610 TTGAACTAACTTCTGATGCACAAT 57.117 33.333 0.00 0.00 0.00 2.71
3396 5336 4.422073 TCTCAGTTCTGAACCACATGTT 57.578 40.909 16.48 0.00 40.81 2.71
3397 5337 4.780815 TCTCAGTTCTGAACCACATGTTT 58.219 39.130 16.48 0.00 37.29 2.83
3398 5338 4.576053 TCTCAGTTCTGAACCACATGTTTG 59.424 41.667 16.48 6.40 37.29 2.93
3521 5481 1.911357 TGATCTTCCAGACACCATGCT 59.089 47.619 0.00 0.00 0.00 3.79
3528 5488 1.487976 CCAGACACCATGCTACCAGAT 59.512 52.381 0.00 0.00 0.00 2.90
3557 5521 7.014326 ACCTTTTCTTCCCATGTTCTCTTTTAC 59.986 37.037 0.00 0.00 0.00 2.01
3586 5553 0.038166 TGGTTCTGGGATTCTGGCAC 59.962 55.000 0.00 0.00 0.00 5.01
3587 5554 0.329596 GGTTCTGGGATTCTGGCACT 59.670 55.000 0.00 0.00 0.00 4.40
3588 5555 1.457346 GTTCTGGGATTCTGGCACTG 58.543 55.000 0.00 0.00 0.00 3.66
3685 5695 7.974482 ATAACCTAGGGCATACGTTTATTTC 57.026 36.000 14.81 0.00 0.00 2.17
3730 5743 7.726033 ACCTAGTGCCTTTCCTATCATATAG 57.274 40.000 0.00 0.00 0.00 1.31
3772 5841 8.330302 CCAAAGACAAACAACTCATGATTTTTC 58.670 33.333 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.463056 CTAATCAAGACGCGTGGCAAA 59.537 47.619 20.70 0.00 0.00 3.68
50 51 2.388735 TGAAGGAGAGATGCGGTGTAT 58.611 47.619 0.00 0.00 0.00 2.29
51 52 1.847328 TGAAGGAGAGATGCGGTGTA 58.153 50.000 0.00 0.00 0.00 2.90
89 90 6.535508 GCTACAGAAACAGATTAGTAACCAGG 59.464 42.308 0.00 0.00 0.00 4.45
95 98 8.684520 GGAAGTAGCTACAGAAACAGATTAGTA 58.315 37.037 25.28 0.00 0.00 1.82
124 127 0.464373 ACAGGTGACCAGTTGCAGTG 60.464 55.000 3.63 0.00 0.00 3.66
125 128 0.255890 AACAGGTGACCAGTTGCAGT 59.744 50.000 11.83 0.00 0.00 4.40
220 223 6.181908 ACGGAGAGAGACTAACAGATAAGTT 58.818 40.000 0.00 0.00 35.55 2.66
221 224 5.747342 ACGGAGAGAGACTAACAGATAAGT 58.253 41.667 0.00 0.00 0.00 2.24
229 232 6.708949 AGATAAGATGACGGAGAGAGACTAAC 59.291 42.308 0.00 0.00 0.00 2.34
232 235 5.071788 AGAGATAAGATGACGGAGAGAGACT 59.928 44.000 0.00 0.00 0.00 3.24
340 345 1.924320 GACGAGTGACAGACCTCCGG 61.924 65.000 0.00 0.00 0.00 5.14
370 375 3.326578 CCACCCGTCACCCCATCA 61.327 66.667 0.00 0.00 0.00 3.07
378 383 3.371063 GAGAGTCGCCACCCGTCA 61.371 66.667 0.00 0.00 38.35 4.35
385 391 2.043852 GAGGGAGGAGAGTCGCCA 60.044 66.667 15.88 0.00 0.00 5.69
390 396 1.079438 GGTGGTGAGGGAGGAGAGT 59.921 63.158 0.00 0.00 0.00 3.24
414 420 3.366915 TCGTCGACATGCACCCGA 61.367 61.111 17.16 0.93 0.00 5.14
428 434 1.153369 CCATCCTTGCCATCGTCGT 60.153 57.895 0.00 0.00 0.00 4.34
1389 1457 3.056821 TCGTTGATGTCAAAGACGGAGAT 60.057 43.478 7.19 0.00 38.93 2.75
1861 3598 4.099419 AGTGTATCGCATTGGAGTGTATCA 59.901 41.667 0.00 0.00 0.00 2.15
1870 3607 6.625362 AGATACTATCAGTGTATCGCATTGG 58.375 40.000 0.00 0.00 46.34 3.16
1871 3608 8.237267 TGTAGATACTATCAGTGTATCGCATTG 58.763 37.037 0.00 0.00 46.34 2.82
1872 3609 8.336801 TGTAGATACTATCAGTGTATCGCATT 57.663 34.615 0.00 0.00 46.34 3.56
1873 3610 7.923414 TGTAGATACTATCAGTGTATCGCAT 57.077 36.000 0.00 0.00 46.34 4.73
1874 3611 7.739498 TTGTAGATACTATCAGTGTATCGCA 57.261 36.000 0.00 0.00 46.34 5.10
1875 3612 8.504815 TCTTTGTAGATACTATCAGTGTATCGC 58.495 37.037 0.00 0.00 46.34 4.58
1897 3634 8.332487 AGAGTCTTCTAGCCCAAATTAATCTTT 58.668 33.333 0.00 0.00 0.00 2.52
1903 3640 4.225042 TGCAGAGTCTTCTAGCCCAAATTA 59.775 41.667 0.00 0.00 30.73 1.40
1972 3709 2.166870 TGACACGGCCGTAGACATTTAT 59.833 45.455 33.70 7.67 0.00 1.40
2466 4244 3.326880 AGGGTTTCACTTCTAACCACGAT 59.673 43.478 0.00 0.00 44.48 3.73
2875 4653 5.073311 TGACTAAGTCACAGGATTACAGC 57.927 43.478 0.00 0.00 37.67 4.40
3131 5065 9.959721 ATTTCCGCCTAATAAAGTGACATATAT 57.040 29.630 0.00 0.00 0.00 0.86
3133 5067 9.959721 ATATTTCCGCCTAATAAAGTGACATAT 57.040 29.630 0.00 0.00 0.00 1.78
3134 5068 9.214957 CATATTTCCGCCTAATAAAGTGACATA 57.785 33.333 0.00 0.00 0.00 2.29
3135 5069 7.936847 TCATATTTCCGCCTAATAAAGTGACAT 59.063 33.333 0.00 0.00 0.00 3.06
3136 5070 7.276658 TCATATTTCCGCCTAATAAAGTGACA 58.723 34.615 0.00 0.00 0.00 3.58
3137 5071 7.724305 TCATATTTCCGCCTAATAAAGTGAC 57.276 36.000 0.00 0.00 0.00 3.67
3138 5072 7.771361 TGTTCATATTTCCGCCTAATAAAGTGA 59.229 33.333 0.00 0.00 0.00 3.41
3139 5073 7.925993 TGTTCATATTTCCGCCTAATAAAGTG 58.074 34.615 0.00 0.00 0.00 3.16
3140 5074 8.691661 ATGTTCATATTTCCGCCTAATAAAGT 57.308 30.769 0.00 0.00 0.00 2.66
3309 5247 6.882610 ATTGTGCATCAGAAGTTAGTTCAA 57.117 33.333 2.45 0.00 37.67 2.69
3332 5270 5.425539 CCTCCTAGTTGAACCATCTTCCTAA 59.574 44.000 0.00 0.00 0.00 2.69
3396 5336 2.370519 TCACATTCGGGAAGGAGAACAA 59.629 45.455 0.00 0.00 0.00 2.83
3397 5337 1.974957 TCACATTCGGGAAGGAGAACA 59.025 47.619 0.00 0.00 0.00 3.18
3398 5338 2.028020 AGTCACATTCGGGAAGGAGAAC 60.028 50.000 0.00 0.00 0.00 3.01
3521 5481 4.847512 TGGGAAGAAAAGGTACATCTGGTA 59.152 41.667 0.00 0.00 0.00 3.25
3528 5488 5.073144 AGAGAACATGGGAAGAAAAGGTACA 59.927 40.000 0.00 0.00 0.00 2.90
3557 5521 2.315176 TCCCAGAACCAACACCATTTG 58.685 47.619 0.00 0.00 0.00 2.32
3586 5553 2.090400 ATGCATATGTAGAGGCGCAG 57.910 50.000 10.83 0.00 32.10 5.18
3587 5554 3.524541 CATATGCATATGTAGAGGCGCA 58.475 45.455 30.55 0.00 36.31 6.09
3730 5743 4.016444 TCTTTGGGCTAATGACATTCACC 58.984 43.478 3.36 7.35 0.00 4.02
3900 5978 5.528320 CCAAGTCAGCAATTCCAACATTTTT 59.472 36.000 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.