Multiple sequence alignment - TraesCS5D01G155700

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 TraesCS5D01G155700 chr5D 100.000 3721 0 0 1 3721 243994469 243998189 0.000000e+00 6872.0
1 TraesCS5D01G155700 chr5D 86.503 1919 201 26 807 2693 544457354 544459246 0.000000e+00 2056.0
2 TraesCS5D01G155700 chr5D 89.432 1003 103 2 912 1912 544477785 544478786 0.000000e+00 1262.0
3 TraesCS5D01G155700 chr5D 86.423 847 89 13 1918 2757 544478913 544479740 0.000000e+00 904.0
4 TraesCS5D01G155700 chr5D 87.500 808 44 26 2883 3651 376660793 376661582 0.000000e+00 880.0
5 TraesCS5D01G155700 chr5D 84.710 569 70 9 2016 2579 544371295 544370739 1.510000e-153 553.0
6 TraesCS5D01G155700 chr5A 93.159 3742 142 52 29 3716 328545673 328549354 0.000000e+00 5387.0
7 TraesCS5D01G155700 chr5A 87.946 813 42 18 2883 3646 426300867 426300062 0.000000e+00 907.0
8 TraesCS5D01G155700 chr4A 93.697 1888 99 10 883 2757 624140987 624142867 0.000000e+00 2809.0
9 TraesCS5D01G155700 chr4A 89.349 1906 163 21 881 2757 624227942 624229836 0.000000e+00 2359.0
10 TraesCS5D01G155700 chr4A 86.124 1881 213 18 906 2755 624342813 624344676 0.000000e+00 1984.0
11 TraesCS5D01G155700 chr4A 88.643 995 107 5 925 1915 624355879 624356871 0.000000e+00 1206.0
12 TraesCS5D01G155700 chr4A 87.700 813 44 23 2883 3646 208830595 208829790 0.000000e+00 896.0
13 TraesCS5D01G155700 chr4A 87.469 814 45 19 2883 3646 115287636 115288442 0.000000e+00 885.0
14 TraesCS5D01G155700 chr4A 87.603 726 74 9 1918 2637 624362132 624362847 0.000000e+00 828.0
15 TraesCS5D01G155700 chr4A 85.629 835 46 18 2883 3646 314681417 314680586 0.000000e+00 809.0
16 TraesCS5D01G155700 chr4A 84.424 321 27 13 656 957 624052942 624053258 1.010000e-75 294.0
17 TraesCS5D01G155700 chr4A 84.400 250 18 7 524 752 624227490 624227739 3.740000e-55 226.0
18 TraesCS5D01G155700 chr5B 88.183 1904 172 28 881 2755 686541782 686543661 0.000000e+00 2220.0
19 TraesCS5D01G155700 chr5B 81.831 1420 190 45 1326 2725 686474019 686472648 0.000000e+00 1131.0
20 TraesCS5D01G155700 chr5B 87.439 820 46 22 2883 3653 153896972 153897783 0.000000e+00 891.0
21 TraesCS5D01G155700 chr5B 84.901 404 36 8 387 771 686457144 686457541 5.830000e-103 385.0
22 TraesCS5D01G155700 chrUn 88.526 1438 124 14 519 1918 48437098 48438532 0.000000e+00 1703.0
23 TraesCS5D01G155700 chrUn 84.840 719 92 9 2016 2730 48438676 48439381 0.000000e+00 708.0
24 TraesCS5D01G155700 chr1A 88.409 811 44 16 2882 3650 581434796 581435598 0.000000e+00 931.0
25 TraesCS5D01G155700 chr4B 88.177 812 48 20 2883 3653 563222144 563222948 0.000000e+00 924.0
26 TraesCS5D01G155700 chr4B 92.553 94 7 0 2756 2849 91488964 91488871 6.480000e-28 135.0
27 TraesCS5D01G155700 chr4B 92.553 94 7 0 2756 2849 99403035 99403128 6.480000e-28 135.0
28 TraesCS5D01G155700 chr4B 92.553 94 7 0 2756 2849 392175388 392175481 6.480000e-28 135.0
29 TraesCS5D01G155700 chr4B 92.553 94 7 0 2756 2849 602942551 602942458 6.480000e-28 135.0
30 TraesCS5D01G155700 chr4D 87.990 816 45 25 2883 3652 175790339 175791147 0.000000e+00 915.0
31 TraesCS5D01G155700 chr4D 93.478 92 6 0 2758 2849 91940727 91940818 1.800000e-28 137.0
32 TraesCS5D01G155700 chr4D 85.915 71 10 0 3651 3721 348134312 348134242 3.990000e-10 76.8
33 TraesCS5D01G155700 chr7A 86.879 846 58 20 2845 3646 216731769 216730933 0.000000e+00 898.0
34 TraesCS5D01G155700 chr3B 87.361 807 55 14 2883 3649 354030577 354031376 0.000000e+00 881.0
35 TraesCS5D01G155700 chr3B 92.708 96 6 1 2755 2849 57357474 57357379 1.800000e-28 137.0
36 TraesCS5D01G155700 chr2A 87.208 813 52 15 2883 3646 724376975 724376166 0.000000e+00 878.0
37 TraesCS5D01G155700 chr2A 93.478 92 6 0 2758 2849 676151743 676151834 1.800000e-28 137.0
38 TraesCS5D01G155700 chr2A 87.324 71 9 0 3651 3721 365316921 365316851 8.570000e-12 82.4
39 TraesCS5D01G155700 chr2B 87.101 814 52 16 2883 3646 365983159 365983969 0.000000e+00 872.0
40 TraesCS5D01G155700 chr2B 88.732 71 8 0 3651 3721 555093237 555093167 1.840000e-13 87.9
41 TraesCS5D01G155700 chr1D 85.258 814 67 19 2883 3650 481041260 481042066 0.000000e+00 789.0
42 TraesCS5D01G155700 chr6D 85.679 810 43 35 2883 3647 78852895 78853676 0.000000e+00 785.0
43 TraesCS5D01G155700 chr2D 93.478 92 6 0 2758 2849 478811589 478811680 1.800000e-28 137.0
44 TraesCS5D01G155700 chr3D 89.706 68 7 0 3651 3718 60546285 60546218 1.840000e-13 87.9
45 TraesCS5D01G155700 chr3D 88.732 71 8 0 3651 3721 237090416 237090346 1.840000e-13 87.9
46 TraesCS5D01G155700 chr3D 89.231 65 7 0 3651 3715 199694708 199694772 8.570000e-12 82.4
47 TraesCS5D01G155700 chr3D 88.710 62 7 0 3651 3712 512018424 512018485 3.990000e-10 76.8
48 TraesCS5D01G155700 chr1B 90.769 65 6 0 3651 3715 613712502 613712566 1.840000e-13 87.9


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 TraesCS5D01G155700 chr5D 243994469 243998189 3720 False 6872.0 6872 100.0000 1 3721 1 chr5D.!!$F1 3720
1 TraesCS5D01G155700 chr5D 544457354 544459246 1892 False 2056.0 2056 86.5030 807 2693 1 chr5D.!!$F3 1886
2 TraesCS5D01G155700 chr5D 544477785 544479740 1955 False 1083.0 1262 87.9275 912 2757 2 chr5D.!!$F4 1845
3 TraesCS5D01G155700 chr5D 376660793 376661582 789 False 880.0 880 87.5000 2883 3651 1 chr5D.!!$F2 768
4 TraesCS5D01G155700 chr5D 544370739 544371295 556 True 553.0 553 84.7100 2016 2579 1 chr5D.!!$R1 563
5 TraesCS5D01G155700 chr5A 328545673 328549354 3681 False 5387.0 5387 93.1590 29 3716 1 chr5A.!!$F1 3687
6 TraesCS5D01G155700 chr5A 426300062 426300867 805 True 907.0 907 87.9460 2883 3646 1 chr5A.!!$R1 763
7 TraesCS5D01G155700 chr4A 624140987 624142867 1880 False 2809.0 2809 93.6970 883 2757 1 chr4A.!!$F3 1874
8 TraesCS5D01G155700 chr4A 624342813 624344676 1863 False 1984.0 1984 86.1240 906 2755 1 chr4A.!!$F4 1849
9 TraesCS5D01G155700 chr4A 624227490 624229836 2346 False 1292.5 2359 86.8745 524 2757 2 chr4A.!!$F7 2233
10 TraesCS5D01G155700 chr4A 624355879 624356871 992 False 1206.0 1206 88.6430 925 1915 1 chr4A.!!$F5 990
11 TraesCS5D01G155700 chr4A 208829790 208830595 805 True 896.0 896 87.7000 2883 3646 1 chr4A.!!$R1 763
12 TraesCS5D01G155700 chr4A 115287636 115288442 806 False 885.0 885 87.4690 2883 3646 1 chr4A.!!$F1 763
13 TraesCS5D01G155700 chr4A 624362132 624362847 715 False 828.0 828 87.6030 1918 2637 1 chr4A.!!$F6 719
14 TraesCS5D01G155700 chr4A 314680586 314681417 831 True 809.0 809 85.6290 2883 3646 1 chr4A.!!$R2 763
15 TraesCS5D01G155700 chr5B 686541782 686543661 1879 False 2220.0 2220 88.1830 881 2755 1 chr5B.!!$F3 1874
16 TraesCS5D01G155700 chr5B 686472648 686474019 1371 True 1131.0 1131 81.8310 1326 2725 1 chr5B.!!$R1 1399
17 TraesCS5D01G155700 chr5B 153896972 153897783 811 False 891.0 891 87.4390 2883 3653 1 chr5B.!!$F1 770
18 TraesCS5D01G155700 chrUn 48437098 48439381 2283 False 1205.5 1703 86.6830 519 2730 2 chrUn.!!$F1 2211
19 TraesCS5D01G155700 chr1A 581434796 581435598 802 False 931.0 931 88.4090 2882 3650 1 chr1A.!!$F1 768
20 TraesCS5D01G155700 chr4B 563222144 563222948 804 False 924.0 924 88.1770 2883 3653 1 chr4B.!!$F3 770
21 TraesCS5D01G155700 chr4D 175790339 175791147 808 False 915.0 915 87.9900 2883 3652 1 chr4D.!!$F2 769
22 TraesCS5D01G155700 chr7A 216730933 216731769 836 True 898.0 898 86.8790 2845 3646 1 chr7A.!!$R1 801
23 TraesCS5D01G155700 chr3B 354030577 354031376 799 False 881.0 881 87.3610 2883 3649 1 chr3B.!!$F1 766
24 TraesCS5D01G155700 chr2A 724376166 724376975 809 True 878.0 878 87.2080 2883 3646 1 chr2A.!!$R2 763
25 TraesCS5D01G155700 chr2B 365983159 365983969 810 False 872.0 872 87.1010 2883 3646 1 chr2B.!!$F1 763
26 TraesCS5D01G155700 chr1D 481041260 481042066 806 False 789.0 789 85.2580 2883 3650 1 chr1D.!!$F1 767
27 TraesCS5D01G155700 chr6D 78852895 78853676 781 False 785.0 785 85.6790 2883 3647 1 chr6D.!!$F1 764

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
137 138 0.817634 CGACAGTTCCCACAGCCAAA 60.818 55.0 0.0 0.0 0.00 3.28 F
1359 1526 1.369091 GCCCACTGTTAGGTGATGCG 61.369 60.0 0.0 0.0 39.34 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 1595 0.368227 GCTGTTGCATCTCTTCGTCG 59.632 55.0 0.00 0.0 39.41 5.12 R
3165 3607 0.035439 GCAATTGGAGAGGTCGGGAA 60.035 55.0 7.72 0.0 0.00 3.97 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
21 22 4.864704 ACGGTTGCCTTAAACATTCATT 57.135 36.364 0.00 0.00 0.00 2.57
22 23 4.805219 ACGGTTGCCTTAAACATTCATTC 58.195 39.130 0.00 0.00 0.00 2.67
23 24 4.173256 CGGTTGCCTTAAACATTCATTCC 58.827 43.478 0.00 0.00 0.00 3.01
24 25 4.321601 CGGTTGCCTTAAACATTCATTCCA 60.322 41.667 0.00 0.00 0.00 3.53
25 26 5.546526 GGTTGCCTTAAACATTCATTCCAA 58.453 37.500 0.00 0.00 0.00 3.53
26 27 5.639082 GGTTGCCTTAAACATTCATTCCAAG 59.361 40.000 0.00 0.00 0.00 3.61
27 28 4.819769 TGCCTTAAACATTCATTCCAAGC 58.180 39.130 0.00 0.00 0.00 4.01
73 74 0.887247 TCGACCGAACCACCGAAATA 59.113 50.000 0.00 0.00 0.00 1.40
85 86 1.349688 ACCGAAATACAGCTTCCCACA 59.650 47.619 0.00 0.00 0.00 4.17
106 107 1.780309 TCGCCAATGGAGGGGAATAAT 59.220 47.619 2.05 0.00 46.25 1.28
109 110 3.092301 GCCAATGGAGGGGAATAATAGC 58.908 50.000 2.05 0.00 0.00 2.97
137 138 0.817634 CGACAGTTCCCACAGCCAAA 60.818 55.000 0.00 0.00 0.00 3.28
183 184 4.340381 GCCATGCCTCTCTGTTCATATTTT 59.660 41.667 0.00 0.00 0.00 1.82
258 263 8.206325 TGCAATGTAAATGTTGAATGTTTTGT 57.794 26.923 0.00 0.00 0.00 2.83
291 296 4.036262 TGTTTTTCTTGCGTGTTATGAGCT 59.964 37.500 0.00 0.00 0.00 4.09
332 337 4.035675 GGTGGTTTTGACAGAGTGAAGAAG 59.964 45.833 0.00 0.00 0.00 2.85
345 350 9.832445 ACAGAGTGAAGAAGTAGTCAAAAATTA 57.168 29.630 0.00 0.00 0.00 1.40
353 358 8.738645 AGAAGTAGTCAAAAATTATAGCCAGG 57.261 34.615 0.00 0.00 0.00 4.45
375 380 1.757682 TGGGTTCAAAGTTTCGCTGT 58.242 45.000 0.00 0.00 0.00 4.40
396 401 1.537990 GCCGCCATGACTTTGTTTTGT 60.538 47.619 0.00 0.00 0.00 2.83
418 423 4.582701 TTTTGCCCACTTCAACATGTAG 57.417 40.909 0.00 0.00 0.00 2.74
438 443 5.427157 TGTAGAACTATGAACCTGGCCATAA 59.573 40.000 5.51 0.00 0.00 1.90
443 448 7.400052 AGAACTATGAACCTGGCCATAATTTTT 59.600 33.333 5.51 0.00 0.00 1.94
483 488 5.604758 TGATCATGTAGGAAGGAGAACAG 57.395 43.478 0.00 0.00 0.00 3.16
634 650 3.204526 CAACTCCTGCATCCATTCTCTC 58.795 50.000 0.00 0.00 0.00 3.20
653 679 4.478699 TCTCGAAAGCTTTTCGACGATTA 58.521 39.130 21.67 11.79 44.76 1.75
839 991 4.574421 CACACTGTAGTTGTGTTTCCATCA 59.426 41.667 0.00 0.00 45.11 3.07
840 992 5.239306 CACACTGTAGTTGTGTTTCCATCAT 59.761 40.000 0.00 0.00 45.11 2.45
841 993 5.470098 ACACTGTAGTTGTGTTTCCATCATC 59.530 40.000 0.00 0.00 45.11 2.92
879 1037 5.578005 TCAGAGTTGGTATGCTGTAGTAC 57.422 43.478 0.00 0.00 0.00 2.73
1180 1347 3.324846 CGATGTCCAGGATTTCCTATCCA 59.675 47.826 0.00 0.00 46.65 3.41
1359 1526 1.369091 GCCCACTGTTAGGTGATGCG 61.369 60.000 0.00 0.00 39.34 4.73
1387 1554 6.970043 CGACAGTGGTTTGTTGAAAGATTTAA 59.030 34.615 0.00 0.00 34.93 1.52
1428 1595 1.272769 ACAAAGACTCTGGACCGTAGC 59.727 52.381 0.00 0.00 0.00 3.58
1523 1692 6.040842 TGCCTCACAAAGCTCTTTCTAAAAAT 59.959 34.615 0.00 0.00 0.00 1.82
2158 2556 3.754188 AAGGAAGCTGTACGTACGTAG 57.246 47.619 27.48 19.72 0.00 3.51
2348 2748 9.436957 GAACTTGATTCCTATGACAGTTCTAAA 57.563 33.333 0.00 0.00 32.85 1.85
2648 3055 1.002366 CGAGATTTCCACGCAAGGAG 58.998 55.000 0.00 0.00 46.39 3.69
2724 3131 9.066892 CGGAGATAATTTTTCATGGATAAGGAA 57.933 33.333 0.00 0.00 0.00 3.36
2734 3143 7.870509 TTCATGGATAAGGAAAGATGACTTG 57.129 36.000 0.00 0.00 36.39 3.16
2742 3151 3.906846 AGGAAAGATGACTTGTCTCAGGT 59.093 43.478 2.35 0.00 36.39 4.00
2759 3168 7.505585 TGTCTCAGGTCAAATAATTTTTGAGGT 59.494 33.333 12.89 4.73 38.88 3.85
2774 3183 2.837947 TGAGGTCATCTTCATCACCCT 58.162 47.619 0.00 0.00 0.00 4.34
2781 3190 1.002134 CTTCATCACCCTGGCGGTT 60.002 57.895 0.00 0.00 45.36 4.44
2784 3193 2.046285 CATCACCCTGGCGGTTTCC 61.046 63.158 0.00 0.00 45.36 3.13
2815 3224 1.348036 GGGAGTAATTCATCCTCGGGG 59.652 57.143 0.00 0.00 35.80 5.73
2816 3225 2.047830 GGAGTAATTCATCCTCGGGGT 58.952 52.381 0.00 0.00 32.51 4.95
2829 3238 1.411612 CTCGGGGTTGAGGGTATGTAC 59.588 57.143 0.00 0.00 32.18 2.90
2852 3261 5.877012 ACCAGTAGCTATGTGTTTGATTCAG 59.123 40.000 0.00 0.00 0.00 3.02
2859 3268 6.891908 AGCTATGTGTTTGATTCAGGGTTTAT 59.108 34.615 0.00 0.00 0.00 1.40
2860 3269 8.052748 AGCTATGTGTTTGATTCAGGGTTTATA 58.947 33.333 0.00 0.00 0.00 0.98
3007 3446 8.746052 ACATTATGCAATAAAACTAGCCACTA 57.254 30.769 0.00 0.00 42.96 2.74
3029 3468 8.978539 CACTATCTAAATAATTGAGCTACGCAA 58.021 33.333 0.00 0.00 0.00 4.85
3097 3536 3.899981 CTAGCCCAGCACCACGCAA 62.900 63.158 0.00 0.00 46.13 4.85
3138 3579 4.783418 CCCAAATGGCCAGCCTAA 57.217 55.556 13.05 0.00 36.94 2.69
3165 3607 2.377136 CAGCCACTGGAACCCTAGT 58.623 57.895 0.00 0.00 0.00 2.57
3182 3624 1.657804 AGTTCCCGACCTCTCCAATT 58.342 50.000 0.00 0.00 0.00 2.32
3185 3627 0.909610 TCCCGACCTCTCCAATTGCT 60.910 55.000 0.00 0.00 0.00 3.91
3243 3701 1.674057 CCTCTTGTCGCCTTCCACT 59.326 57.895 0.00 0.00 0.00 4.00
3281 3759 1.821332 GCCATGCCTCCTTTCCTCG 60.821 63.158 0.00 0.00 0.00 4.63
3282 3760 1.604378 CCATGCCTCCTTTCCTCGT 59.396 57.895 0.00 0.00 0.00 4.18
3301 3796 4.658063 TCGTTCTCTCTTCCTTCTCTCTT 58.342 43.478 0.00 0.00 0.00 2.85
3315 3810 1.004560 CTCTTGTCTCAAGGCCGCA 60.005 57.895 0.00 0.00 0.00 5.69
3442 3982 3.329889 CAGGGGCTGTGGGTGCTA 61.330 66.667 0.00 0.00 0.00 3.49
3501 4041 1.593426 GTCGCTCGACTCGTATATGC 58.407 55.000 14.42 0.00 41.57 3.14
3578 4139 6.978338 TGTAGTCTACACGAGAAAATGAGTT 58.022 36.000 8.70 0.00 35.37 3.01
3597 4158 0.969149 TGACATCCACTCTGCGACTT 59.031 50.000 0.00 0.00 0.00 3.01
3608 4169 4.073549 ACTCTGCGACTTGTAGACTAGTT 58.926 43.478 0.00 0.00 34.06 2.24
3682 4248 3.191581 TGTCTCTCTCGTGTTCTTGATCC 59.808 47.826 0.00 0.00 0.00 3.36
3687 4253 0.249120 TCGTGTTCTTGATCCGGCAT 59.751 50.000 0.00 0.00 0.00 4.40
3716 4282 3.738830 TGTACCACGAGCTTTGTTAGT 57.261 42.857 0.00 0.00 0.00 2.24
3717 4283 4.852134 TGTACCACGAGCTTTGTTAGTA 57.148 40.909 0.00 0.00 0.00 1.82
3718 4284 4.801891 TGTACCACGAGCTTTGTTAGTAG 58.198 43.478 0.00 0.00 0.00 2.57
3719 4285 4.520111 TGTACCACGAGCTTTGTTAGTAGA 59.480 41.667 0.00 0.00 0.00 2.59
3720 4286 4.175787 ACCACGAGCTTTGTTAGTAGAG 57.824 45.455 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.173256 GGAATGAATGTTTAAGGCAACCG 58.827 43.478 0.00 0.00 37.17 4.44
3 4 5.120674 GCTTGGAATGAATGTTTAAGGCAAC 59.879 40.000 0.00 0.00 0.00 4.17
4 5 5.237048 GCTTGGAATGAATGTTTAAGGCAA 58.763 37.500 0.00 0.00 0.00 4.52
5 6 4.322650 GGCTTGGAATGAATGTTTAAGGCA 60.323 41.667 0.00 0.00 38.58 4.75
6 7 4.081476 AGGCTTGGAATGAATGTTTAAGGC 60.081 41.667 0.00 0.00 38.88 4.35
7 8 5.665916 AGGCTTGGAATGAATGTTTAAGG 57.334 39.130 0.00 0.00 0.00 2.69
8 9 5.801947 CGAAGGCTTGGAATGAATGTTTAAG 59.198 40.000 3.46 0.00 0.00 1.85
9 10 5.708948 CGAAGGCTTGGAATGAATGTTTAA 58.291 37.500 3.46 0.00 0.00 1.52
10 11 4.380444 GCGAAGGCTTGGAATGAATGTTTA 60.380 41.667 13.81 0.00 35.83 2.01
11 12 3.614870 GCGAAGGCTTGGAATGAATGTTT 60.615 43.478 13.81 0.00 35.83 2.83
12 13 2.094545 GCGAAGGCTTGGAATGAATGTT 60.095 45.455 13.81 0.00 35.83 2.71
13 14 1.474077 GCGAAGGCTTGGAATGAATGT 59.526 47.619 13.81 0.00 35.83 2.71
14 15 2.199291 GCGAAGGCTTGGAATGAATG 57.801 50.000 13.81 0.00 35.83 2.67
73 74 2.045926 GGCGATGTGGGAAGCTGT 60.046 61.111 0.00 0.00 0.00 4.40
85 86 1.444933 TATTCCCCTCCATTGGCGAT 58.555 50.000 0.00 0.00 0.00 4.58
106 107 2.592194 GAACTGTCGTTGTGATCGCTA 58.408 47.619 7.94 0.00 32.39 4.26
109 110 1.068474 GGGAACTGTCGTTGTGATCG 58.932 55.000 0.00 0.00 32.39 3.69
137 138 3.383698 TCAAGACGAGAGGGGACTTAT 57.616 47.619 0.00 0.00 44.43 1.73
332 337 7.973944 CCAAACCTGGCTATAATTTTTGACTAC 59.026 37.037 0.00 0.00 35.39 2.73
345 350 2.990740 TTGAACCCAAACCTGGCTAT 57.009 45.000 0.00 0.00 41.99 2.97
353 358 2.857748 CAGCGAAACTTTGAACCCAAAC 59.142 45.455 0.00 0.00 37.36 2.93
375 380 0.749649 AAAACAAAGTCATGGCGGCA 59.250 45.000 16.34 16.34 0.00 5.69
396 401 3.902881 ACATGTTGAAGTGGGCAAAAA 57.097 38.095 0.00 0.00 0.00 1.94
418 423 6.715347 AAATTATGGCCAGGTTCATAGTTC 57.285 37.500 13.05 0.00 29.55 3.01
468 473 4.273148 TGCTTTCTGTTCTCCTTCCTAC 57.727 45.455 0.00 0.00 0.00 3.18
634 650 3.322755 CGTAATCGTCGAAAAGCTTTCG 58.677 45.455 13.10 16.71 42.74 3.46
653 679 4.699735 TGAAAAGTATGCATCAATCCACGT 59.300 37.500 0.19 0.00 0.00 4.49
768 822 0.742990 TTGCCGCTACAGTACCATGC 60.743 55.000 0.00 0.00 0.00 4.06
839 991 7.830099 ACTCTGAAACTTTGAATTCCAAGAT 57.170 32.000 22.38 10.59 35.94 2.40
840 992 7.416664 CCAACTCTGAAACTTTGAATTCCAAGA 60.417 37.037 22.38 2.98 35.94 3.02
841 993 6.698766 CCAACTCTGAAACTTTGAATTCCAAG 59.301 38.462 15.77 15.77 35.94 3.61
879 1037 7.585573 GCGTGAAAATTGCTTGATTATCTCTAG 59.414 37.037 0.00 0.00 0.00 2.43
1359 1526 4.272504 TCTTTCAACAAACCACTGTCGATC 59.727 41.667 0.00 0.00 0.00 3.69
1387 1554 4.125703 GTCTCATCAAGAATGCCGAGATT 58.874 43.478 0.00 0.00 36.55 2.40
1428 1595 0.368227 GCTGTTGCATCTCTTCGTCG 59.632 55.000 0.00 0.00 39.41 5.12
1523 1692 4.646945 TGTCCAATTTGTCAAAGCCTACAA 59.353 37.500 4.03 0.00 33.92 2.41
2150 2548 6.264832 TCAACAAATATACCACCTACGTACG 58.735 40.000 15.01 15.01 0.00 3.67
2151 2549 8.652810 ATTCAACAAATATACCACCTACGTAC 57.347 34.615 0.00 0.00 0.00 3.67
2152 2550 9.669887 AAATTCAACAAATATACCACCTACGTA 57.330 29.630 0.00 0.00 0.00 3.57
2153 2551 8.455682 CAAATTCAACAAATATACCACCTACGT 58.544 33.333 0.00 0.00 0.00 3.57
2158 2556 9.651913 AATGTCAAATTCAACAAATATACCACC 57.348 29.630 0.00 0.00 0.00 4.61
2348 2748 5.072741 ACCTGTATTTGTGTGAGCAATTCT 58.927 37.500 0.00 0.00 0.00 2.40
2648 3055 1.202818 ACAACCACTTCTTGCTCCTCC 60.203 52.381 0.00 0.00 0.00 4.30
2724 3131 4.963318 TTGACCTGAGACAAGTCATCTT 57.037 40.909 2.72 0.00 40.06 2.40
2734 3143 7.886338 ACCTCAAAAATTATTTGACCTGAGAC 58.114 34.615 15.04 0.00 34.06 3.36
2759 3168 0.178767 CGCCAGGGTGATGAAGATGA 59.821 55.000 0.00 0.00 0.00 2.92
2771 3180 2.046285 GTCATGGAAACCGCCAGGG 61.046 63.158 0.00 0.00 42.15 4.45
2774 3183 1.024046 CATCGTCATGGAAACCGCCA 61.024 55.000 0.00 0.00 43.23 5.69
2781 3190 1.866015 ACTCCCTCATCGTCATGGAA 58.134 50.000 0.00 0.00 0.00 3.53
2784 3193 4.948847 TGAATTACTCCCTCATCGTCATG 58.051 43.478 0.00 0.00 0.00 3.07
2815 3224 3.705072 AGCTACTGGTACATACCCTCAAC 59.295 47.826 5.62 0.00 45.87 3.18
2816 3225 3.990369 AGCTACTGGTACATACCCTCAA 58.010 45.455 5.62 0.00 45.87 3.02
2829 3238 5.295292 CCTGAATCAAACACATAGCTACTGG 59.705 44.000 0.00 0.00 0.00 4.00
2842 3251 7.461918 GTCGACTTATAAACCCTGAATCAAAC 58.538 38.462 8.70 0.00 0.00 2.93
2903 3325 9.028284 AGTACCATGTTAACTAGTTAGCACTAA 57.972 33.333 27.87 14.70 38.68 2.24
3025 3464 2.216750 CTTGGGCCCAGAACATTGCG 62.217 60.000 26.87 2.33 0.00 4.85
3029 3468 1.077265 CCACTTGGGCCCAGAACAT 59.923 57.895 26.87 7.06 0.00 2.71
3138 3579 3.010144 CAGTGGCTGGGGGCTAAT 58.990 61.111 0.00 0.00 41.46 1.73
3165 3607 0.035439 GCAATTGGAGAGGTCGGGAA 60.035 55.000 7.72 0.00 0.00 3.97
3281 3759 5.476945 AGACAAGAGAGAAGGAAGAGAGAAC 59.523 44.000 0.00 0.00 0.00 3.01
3282 3760 5.640147 AGACAAGAGAGAAGGAAGAGAGAA 58.360 41.667 0.00 0.00 0.00 2.87
3426 3961 3.011517 CTAGCACCCACAGCCCCT 61.012 66.667 0.00 0.00 0.00 4.79
3528 4089 3.458163 TCGAGCCGTGGATGGACC 61.458 66.667 0.00 0.00 39.54 4.46
3578 4139 0.969149 AAGTCGCAGAGTGGATGTCA 59.031 50.000 0.00 0.00 40.67 3.58
3682 4248 2.987149 GTGGTACATCGAGATTATGCCG 59.013 50.000 0.00 0.00 44.52 5.69


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

AutoCloner maintained by Alex Coulton.