Multiple sequence alignment - TraesCS2A01G038600

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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 TraesCS2A01G038600 chr2A 100.000 4407 0 0 1 4407 16129104 16133510 0.000000e+00 8139
1 TraesCS2A01G038600 chr2A 84.055 508 43 11 953 1455 177981869 177982343 5.200000e-124 455
2 TraesCS2A01G038600 chr2A 91.860 86 7 0 4049 4134 26851671 26851586 2.150000e-23 121
3 TraesCS2A01G038600 chr2D 94.796 3017 85 22 864 3835 14085405 14082416 0.000000e+00 4636
4 TraesCS2A01G038600 chr2D 93.906 640 32 4 1 634 14086330 14085692 0.000000e+00 959
5 TraesCS2A01G038600 chr2D 95.070 568 28 0 3836 4403 14046613 14046046 0.000000e+00 894
6 TraesCS2A01G038600 chr2D 91.055 436 25 6 1022 1453 648652164 648652589 1.060000e-160 577
7 TraesCS2A01G038600 chr2D 89.634 164 16 1 651 814 14085707 14085545 1.610000e-49 207
8 TraesCS2A01G038600 chr1B 85.990 2491 274 39 960 3404 100815200 100812739 0.000000e+00 2597
9 TraesCS2A01G038600 chr1B 89.744 507 40 5 953 1455 389086304 389086802 4.810000e-179 638
10 TraesCS2A01G038600 chr1B 89.084 513 36 7 953 1455 389003664 389004166 1.740000e-173 619
11 TraesCS2A01G038600 chr1B 91.011 89 8 0 4046 4134 413494711 413494623 2.150000e-23 121
12 TraesCS2A01G038600 chr2B 94.848 1417 49 5 2436 3835 25580744 25579335 0.000000e+00 2191
13 TraesCS2A01G038600 chr2B 93.660 347 22 0 3872 4218 25574673 25574327 1.820000e-143 520
14 TraesCS2A01G038600 chr2B 85.823 395 53 2 44 435 25586835 25586441 2.450000e-112 416
15 TraesCS2A01G038600 chr2B 81.339 493 56 18 335 826 25586452 25585995 6.960000e-98 368
16 TraesCS2A01G038600 chr1A 83.486 1859 233 43 1578 3402 51678703 51680521 0.000000e+00 1664
17 TraesCS2A01G038600 chr1A 85.630 508 35 10 953 1455 309695264 309695738 2.370000e-137 499
18 TraesCS2A01G038600 chr1D 85.358 1564 155 35 960 2478 51993810 51995344 0.000000e+00 1552
19 TraesCS2A01G038600 chr1D 85.379 896 120 9 2516 3404 51995351 51996242 0.000000e+00 918
20 TraesCS2A01G038600 chr1D 90.395 177 17 0 3228 3404 52128607 52128431 2.650000e-57 233
21 TraesCS2A01G038600 chr1D 91.765 85 7 0 4044 4128 330770297 330770381 7.740000e-23 119
22 TraesCS2A01G038600 chrUn 90.789 456 28 9 953 1404 312292626 312293071 8.160000e-167 597
23 TraesCS2A01G038600 chrUn 84.646 508 40 11 953 1455 13785641 13786115 5.160000e-129 472
24 TraesCS2A01G038600 chr4A 84.158 505 48 7 956 1458 22876220 22875746 1.120000e-125 460
25 TraesCS2A01G038600 chr4A 88.095 84 9 1 416 498 467677351 467677268 1.010000e-16 99
26 TraesCS2A01G038600 chr5D 97.403 77 2 0 4052 4128 352456283 352456359 9.950000e-27 132
27 TraesCS2A01G038600 chr5D 89.888 89 8 1 4046 4134 240084596 240084509 3.600000e-21 113
28 TraesCS2A01G038600 chr4B 94.805 77 4 0 4052 4128 322692942 322693018 2.150000e-23 121
29 TraesCS2A01G038600 chr3D 90.909 88 8 0 4047 4134 66262965 66262878 7.740000e-23 119


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 TraesCS2A01G038600 chr2A 16129104 16133510 4406 False 8139 8139 100.000000 1 4407 1 chr2A.!!$F1 4406
1 TraesCS2A01G038600 chr2D 14082416 14086330 3914 True 1934 4636 92.778667 1 3835 3 chr2D.!!$R2 3834
2 TraesCS2A01G038600 chr2D 14046046 14046613 567 True 894 894 95.070000 3836 4403 1 chr2D.!!$R1 567
3 TraesCS2A01G038600 chr1B 100812739 100815200 2461 True 2597 2597 85.990000 960 3404 1 chr1B.!!$R1 2444
4 TraesCS2A01G038600 chr1B 389003664 389004166 502 False 619 619 89.084000 953 1455 1 chr1B.!!$F1 502
5 TraesCS2A01G038600 chr2B 25579335 25580744 1409 True 2191 2191 94.848000 2436 3835 1 chr2B.!!$R2 1399
6 TraesCS2A01G038600 chr2B 25585995 25586835 840 True 392 416 83.581000 44 826 2 chr2B.!!$R3 782
7 TraesCS2A01G038600 chr1A 51678703 51680521 1818 False 1664 1664 83.486000 1578 3402 1 chr1A.!!$F1 1824
8 TraesCS2A01G038600 chr1D 51993810 51996242 2432 False 1235 1552 85.368500 960 3404 2 chr1D.!!$F2 2444

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
934 1059 0.036671 GACCCTAACAAGACACGGGG 60.037 60.0 0.00 0.0 39.27 5.73 F
1070 1208 0.108585 GGGGCATCATCGGAAGCTTA 59.891 55.0 0.00 0.0 37.84 3.09 F
2128 2414 0.255604 TGGTGCCAATGGATCATCGT 59.744 50.0 2.05 0.0 0.00 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2829 3135 0.894184 ACCAGTCATCGTCTGTCCGT 60.894 55.000 0.00 0.0 0.00 4.69 R
2990 3296 3.087031 CCATGCATGACCTTGAACTCTT 58.913 45.455 28.31 0.0 0.00 2.85 R
4005 4333 1.216990 CCACCTCTTATCCCAAGGCT 58.783 55.000 0.00 0.0 33.21 4.58 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
197 198 3.333898 GCTTCAAGAAGGGCGCAGC 62.334 63.158 10.83 1.52 46.02 5.25
229 230 3.488489 GCGACTTTGCATTAAATCGTGT 58.512 40.909 4.20 0.00 34.62 4.49
316 317 4.223659 CGCCGCTACTTTAAAACATTGTT 58.776 39.130 0.00 0.00 0.00 2.83
439 445 1.884075 TACAGTGAAGCATCGCCGGT 61.884 55.000 1.90 1.07 36.72 5.28
511 517 2.609183 AAGCGTCATCGTCGGCTACC 62.609 60.000 0.00 0.00 39.49 3.18
609 616 2.686816 GCCGCGCCACTATTGTTGT 61.687 57.895 0.00 0.00 0.00 3.32
610 617 1.363145 GCCGCGCCACTATTGTTGTA 61.363 55.000 0.00 0.00 0.00 2.41
614 621 0.650512 CGCCACTATTGTTGTAGCCG 59.349 55.000 0.00 0.00 0.00 5.52
621 628 0.796312 ATTGTTGTAGCCGTGAAGCG 59.204 50.000 0.00 0.00 38.01 4.68
622 629 0.531090 TTGTTGTAGCCGTGAAGCGT 60.531 50.000 0.00 0.00 39.32 5.07
623 630 0.942410 TGTTGTAGCCGTGAAGCGTC 60.942 55.000 0.00 0.00 39.32 5.19
624 631 1.731613 TTGTAGCCGTGAAGCGTCG 60.732 57.895 0.00 0.00 39.32 5.12
625 632 3.542742 GTAGCCGTGAAGCGTCGC 61.543 66.667 9.80 9.80 39.32 5.19
626 633 3.744719 TAGCCGTGAAGCGTCGCT 61.745 61.111 15.47 15.47 42.56 4.93
627 634 3.964221 TAGCCGTGAAGCGTCGCTG 62.964 63.158 22.50 8.92 39.62 5.18
647 654 4.509737 GGCTACCCGTGCTCCGAC 62.510 72.222 0.00 0.00 39.56 4.79
648 655 3.755628 GCTACCCGTGCTCCGACA 61.756 66.667 0.00 0.00 39.56 4.35
649 656 2.181021 CTACCCGTGCTCCGACAC 59.819 66.667 0.00 0.00 39.56 3.67
650 657 2.598099 TACCCGTGCTCCGACACA 60.598 61.111 4.48 0.00 40.73 3.72
651 658 2.543687 CTACCCGTGCTCCGACACAG 62.544 65.000 4.48 0.00 40.73 3.66
681 688 0.662970 CGGCTCTATCTCAAGCGAGC 60.663 60.000 0.00 0.00 46.06 5.03
683 690 1.274798 GCTCTATCTCAAGCGAGCGC 61.275 60.000 6.78 6.78 39.39 5.92
686 693 3.484742 TATCTCAAGCGAGCGCCCG 62.485 63.158 7.06 7.06 43.17 6.13
708 715 1.079127 ATGGCTGTGACGGTGCTAC 60.079 57.895 0.00 0.00 0.00 3.58
748 755 1.746787 TGTAAAGGTCTATCGCGAGCA 59.253 47.619 16.66 3.69 34.00 4.26
753 760 0.100682 GGTCTATCGCGAGCAAGTGA 59.899 55.000 16.66 3.24 34.92 3.41
776 783 3.417601 CGTGGCTCAGATGGCATG 58.582 61.111 3.81 0.00 44.18 4.06
797 804 3.207677 CATCCTACCGCTGAGATGC 57.792 57.895 0.00 0.00 30.61 3.91
806 813 2.732468 CTGAGATGCGGCCGATCG 60.732 66.667 33.48 8.51 0.00 3.69
809 816 4.286320 AGATGCGGCCGATCGGAC 62.286 66.667 37.64 34.39 40.76 4.79
819 826 4.933064 GATCGGACGGCTCTGCGG 62.933 72.222 0.00 0.00 35.02 5.69
838 945 1.749033 GCGCCTGGCTCTACCTTAT 59.251 57.895 17.92 0.00 40.22 1.73
839 946 0.106894 GCGCCTGGCTCTACCTTATT 59.893 55.000 17.92 0.00 40.22 1.40
841 948 2.224209 GCGCCTGGCTCTACCTTATTAA 60.224 50.000 17.92 0.00 40.22 1.40
842 949 3.391049 CGCCTGGCTCTACCTTATTAAC 58.609 50.000 17.92 0.00 40.22 2.01
845 952 5.221382 CGCCTGGCTCTACCTTATTAACTAA 60.221 44.000 17.92 0.00 40.22 2.24
846 953 5.990386 GCCTGGCTCTACCTTATTAACTAAC 59.010 44.000 12.43 0.00 40.22 2.34
847 954 6.183360 GCCTGGCTCTACCTTATTAACTAACT 60.183 42.308 12.43 0.00 40.22 2.24
850 957 8.370266 TGGCTCTACCTTATTAACTAACTCAA 57.630 34.615 0.00 0.00 40.22 3.02
851 958 8.475639 TGGCTCTACCTTATTAACTAACTCAAG 58.524 37.037 0.00 0.00 40.22 3.02
852 959 8.476447 GGCTCTACCTTATTAACTAACTCAAGT 58.524 37.037 0.00 0.00 34.51 3.16
883 990 3.904824 GTCTCAAACACGTAGACACTACG 59.095 47.826 23.44 23.44 45.44 3.51
893 1000 4.572845 CGTAGACACTACGTAGCTAACAC 58.427 47.826 22.40 13.42 36.31 3.32
918 1025 5.619625 AGTACTACTCAAACACGTAGACC 57.380 43.478 0.00 0.00 37.22 3.85
922 1029 5.072741 ACTACTCAAACACGTAGACCCTAA 58.927 41.667 0.00 0.00 37.22 2.69
934 1059 0.036671 GACCCTAACAAGACACGGGG 60.037 60.000 0.00 0.00 39.27 5.73
972 1097 2.417719 ACTCAAACACGATTCCTGCTC 58.582 47.619 0.00 0.00 0.00 4.26
1017 1150 5.104374 TCGCCGTTTTAAATAAGATCGAGT 58.896 37.500 0.00 0.00 0.00 4.18
1068 1206 2.512896 GGGGCATCATCGGAAGCT 59.487 61.111 0.00 0.00 37.84 3.74
1069 1207 1.152881 GGGGCATCATCGGAAGCTT 60.153 57.895 0.00 0.00 37.84 3.74
1070 1208 0.108585 GGGGCATCATCGGAAGCTTA 59.891 55.000 0.00 0.00 37.84 3.09
1071 1209 1.476833 GGGGCATCATCGGAAGCTTAA 60.477 52.381 0.00 0.00 37.84 1.85
1072 1210 1.876156 GGGCATCATCGGAAGCTTAAG 59.124 52.381 0.00 0.00 37.84 1.85
1073 1211 1.265365 GGCATCATCGGAAGCTTAAGC 59.735 52.381 20.09 20.09 37.84 3.09
1074 1212 1.265365 GCATCATCGGAAGCTTAAGCC 59.735 52.381 23.71 9.44 43.38 4.35
1075 1213 2.564771 CATCATCGGAAGCTTAAGCCA 58.435 47.619 23.71 3.62 43.38 4.75
1076 1214 2.024176 TCATCGGAAGCTTAAGCCAC 57.976 50.000 23.71 16.83 43.38 5.01
1077 1215 1.017387 CATCGGAAGCTTAAGCCACC 58.983 55.000 23.71 23.12 43.38 4.61
1078 1216 0.618458 ATCGGAAGCTTAAGCCACCA 59.382 50.000 28.04 19.66 43.38 4.17
1079 1217 0.321298 TCGGAAGCTTAAGCCACCAC 60.321 55.000 28.04 15.54 43.38 4.16
1080 1218 0.605319 CGGAAGCTTAAGCCACCACA 60.605 55.000 28.04 0.00 43.38 4.17
1081 1219 1.168714 GGAAGCTTAAGCCACCACAG 58.831 55.000 23.71 0.00 43.38 3.66
1082 1220 1.271379 GGAAGCTTAAGCCACCACAGA 60.271 52.381 23.71 0.00 43.38 3.41
1083 1221 1.807142 GAAGCTTAAGCCACCACAGAC 59.193 52.381 23.71 1.96 43.38 3.51
1089 1232 1.402787 AAGCCACCACAGACCAAAAG 58.597 50.000 0.00 0.00 0.00 2.27
1093 1236 2.029918 GCCACCACAGACCAAAAGAATC 60.030 50.000 0.00 0.00 0.00 2.52
1100 1243 4.037208 CACAGACCAAAAGAATCAAGCACT 59.963 41.667 0.00 0.00 0.00 4.40
1960 2135 1.220749 GGGTGCCTATGCGTCTTCA 59.779 57.895 0.00 0.00 41.78 3.02
2097 2383 1.215673 TCGAGGTGGATAGCTCCTCTT 59.784 52.381 14.58 0.00 46.23 2.85
2125 2411 4.147321 GTCTAATGGTGCCAATGGATCAT 58.853 43.478 2.05 0.00 0.00 2.45
2126 2412 4.217118 GTCTAATGGTGCCAATGGATCATC 59.783 45.833 2.05 0.00 0.00 2.92
2127 2413 1.612676 ATGGTGCCAATGGATCATCG 58.387 50.000 2.05 0.00 0.00 3.84
2128 2414 0.255604 TGGTGCCAATGGATCATCGT 59.744 50.000 2.05 0.00 0.00 3.73
2129 2415 0.947244 GGTGCCAATGGATCATCGTC 59.053 55.000 2.05 0.00 0.00 4.20
2130 2416 0.583438 GTGCCAATGGATCATCGTCG 59.417 55.000 2.05 0.00 0.00 5.12
2131 2417 0.532640 TGCCAATGGATCATCGTCGG 60.533 55.000 2.05 0.00 0.00 4.79
2216 2502 3.596214 GCGTACCAGAGATTCTTTTCCA 58.404 45.455 0.00 0.00 0.00 3.53
2258 2546 2.095853 GCAGTTTCCATGACACGTATGG 59.904 50.000 9.21 9.21 45.17 2.74
2451 2751 1.271379 ACCACCAACTCTTTCATCCGG 60.271 52.381 0.00 0.00 0.00 5.14
2616 2922 1.137479 CCATGCCATGGCCTAAACTTG 59.863 52.381 33.44 17.49 44.70 3.16
2677 2983 3.795623 TGGGCGTTAGTGAGAGAATAC 57.204 47.619 0.00 0.00 0.00 1.89
2818 3124 3.704566 AGAGTACAAACTGAGGTGTGACA 59.295 43.478 0.00 0.00 35.56 3.58
2829 3135 1.952133 GTGTGACACGCGTTGGCTA 60.952 57.895 10.22 0.00 36.88 3.93
3096 3402 1.079405 GGCATGGTTCGACGAGGAA 60.079 57.895 0.00 0.00 0.00 3.36
3122 3428 3.520290 TGTCATTGACGTATGGAGGAC 57.480 47.619 11.97 0.00 34.95 3.85
3457 3785 6.464222 TGTGCTCTTTGCTTACTACTGTTAT 58.536 36.000 0.00 0.00 43.37 1.89
3459 3787 8.258007 TGTGCTCTTTGCTTACTACTGTTATAT 58.742 33.333 0.00 0.00 43.37 0.86
3556 3884 9.770097 AATGAGATGATATTACGATTGTCAGTT 57.230 29.630 0.00 0.00 0.00 3.16
3570 3898 4.335082 TGTCAGTTCAAGTTTTGTCACG 57.665 40.909 0.00 0.00 0.00 4.35
3598 3926 9.206690 AGAATATATGGATCGGAGACACATAAT 57.793 33.333 0.00 0.00 42.51 1.28
3631 3959 1.474077 GTAGGCCAAGGAGCACATTTG 59.526 52.381 5.01 0.00 0.00 2.32
3789 4117 3.813166 GTCCTTCCTCATCACAAACGAAA 59.187 43.478 0.00 0.00 0.00 3.46
3790 4118 4.274950 GTCCTTCCTCATCACAAACGAAAA 59.725 41.667 0.00 0.00 0.00 2.29
3858 4186 2.816689 TCCCATATAACAACGCAGTCG 58.183 47.619 0.00 0.00 45.00 4.18
3861 4189 3.183754 CCATATAACAACGCAGTCGACA 58.816 45.455 19.50 0.00 45.00 4.35
3893 4221 1.034838 CCCTCGCTGTCAGTAGCTCT 61.035 60.000 0.93 0.00 41.51 4.09
4013 4341 1.915141 ACTCAAATCACAGCCTTGGG 58.085 50.000 0.00 0.00 0.00 4.12
4060 4388 6.556974 AACCACTTAAATACTACTCCCTCC 57.443 41.667 0.00 0.00 0.00 4.30
4066 4394 0.110104 ATACTACTCCCTCCGTCCGG 59.890 60.000 0.00 0.00 0.00 5.14
4087 4415 5.447279 CCGGAAATACTTGTCGAAGAAATGG 60.447 44.000 0.00 0.00 39.69 3.16
4097 4425 8.258007 ACTTGTCGAAGAAATGGATGTATCTAA 58.742 33.333 0.00 0.00 39.69 2.10
4099 4427 9.613428 TTGTCGAAGAAATGGATGTATCTAAAT 57.387 29.630 0.00 0.00 39.69 1.40
4188 4516 5.622346 ACTTCATCTTCTATGACCTTCCC 57.378 43.478 0.00 0.00 0.00 3.97
4284 4612 4.713946 GGCAACCGGATCTTGTCA 57.286 55.556 9.46 0.00 0.00 3.58
4292 4620 0.321564 CGGATCTTGTCAAGCCCACA 60.322 55.000 18.07 0.39 0.00 4.17
4301 4629 0.550914 TCAAGCCCACACCAAGAGTT 59.449 50.000 0.00 0.00 0.00 3.01
4320 4648 5.788014 AGAGTTAACTCCAGATTTTCTCCCT 59.212 40.000 28.05 5.36 43.88 4.20
4403 4731 1.945394 CGCCGAGTGGTATGTAGTACT 59.055 52.381 0.00 0.00 37.67 2.73
4404 4732 2.032204 CGCCGAGTGGTATGTAGTACTC 60.032 54.545 0.00 0.00 37.67 2.59
4405 4733 2.292845 GCCGAGTGGTATGTAGTACTCC 59.707 54.545 0.00 0.00 36.97 3.85
4406 4734 2.883386 CCGAGTGGTATGTAGTACTCCC 59.117 54.545 0.00 0.00 36.97 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 1.563111 CAGTTGCAAAACTGGTGCTG 58.437 50.000 10.21 3.23 44.77 4.41
296 297 4.384547 GCCAACAATGTTTTAAAGTAGCGG 59.615 41.667 0.00 0.00 0.00 5.52
304 305 4.386867 TTGGTCGCCAACAATGTTTTAA 57.613 36.364 7.15 0.00 38.75 1.52
316 317 1.300311 CACACTACGTTGGTCGCCA 60.300 57.895 0.00 0.00 44.19 5.69
499 505 2.442272 AGCAGGGTAGCCGACGAT 60.442 61.111 5.06 0.00 34.23 3.73
549 556 3.554692 CCGCCGACGATGCTTCAC 61.555 66.667 0.00 0.00 43.93 3.18
590 597 3.496131 AACAATAGTGGCGCGGCG 61.496 61.111 28.22 19.62 0.00 6.46
592 599 0.650512 CTACAACAATAGTGGCGCGG 59.349 55.000 8.83 0.00 0.00 6.46
599 606 3.000727 GCTTCACGGCTACAACAATAGT 58.999 45.455 0.00 0.00 0.00 2.12
602 609 0.796312 CGCTTCACGGCTACAACAAT 59.204 50.000 0.00 0.00 38.44 2.71
630 637 4.509737 GTCGGAGCACGGGTAGCC 62.510 72.222 0.00 0.00 44.45 3.93
631 638 3.755628 TGTCGGAGCACGGGTAGC 61.756 66.667 0.96 0.00 44.45 3.58
632 639 2.181021 GTGTCGGAGCACGGGTAG 59.819 66.667 0.96 0.00 44.45 3.18
633 640 2.598099 TGTGTCGGAGCACGGGTA 60.598 61.111 0.96 0.00 44.45 3.69
634 641 3.991051 CTGTGTCGGAGCACGGGT 61.991 66.667 10.04 0.00 44.45 5.28
639 646 4.724602 GAGCGCTGTGTCGGAGCA 62.725 66.667 18.48 0.00 37.99 4.26
683 690 2.436646 GTCACAGCCATGTCCGGG 60.437 66.667 0.00 0.00 37.65 5.73
686 693 2.034879 CACCGTCACAGCCATGTCC 61.035 63.158 0.00 0.00 37.65 4.02
687 694 2.680913 GCACCGTCACAGCCATGTC 61.681 63.158 0.00 0.00 37.65 3.06
688 695 1.826340 TAGCACCGTCACAGCCATGT 61.826 55.000 0.00 0.00 41.57 3.21
690 697 1.079127 GTAGCACCGTCACAGCCAT 60.079 57.895 0.00 0.00 0.00 4.40
691 698 2.342279 GTAGCACCGTCACAGCCA 59.658 61.111 0.00 0.00 0.00 4.75
748 755 4.235762 AGCCACGCACGGTCACTT 62.236 61.111 0.00 0.00 0.00 3.16
753 760 3.695606 ATCTGAGCCACGCACGGT 61.696 61.111 0.00 0.00 0.00 4.83
776 783 0.390860 ATCTCAGCGGTAGGATGCAC 59.609 55.000 0.00 0.00 30.27 4.57
819 826 1.759459 ATAAGGTAGAGCCAGGCGCC 61.759 60.000 21.89 21.89 40.61 6.53
820 827 0.106894 AATAAGGTAGAGCCAGGCGC 59.893 55.000 7.17 7.17 40.61 6.53
821 828 3.069729 AGTTAATAAGGTAGAGCCAGGCG 59.930 47.826 5.55 0.00 40.61 5.52
822 829 4.691326 AGTTAATAAGGTAGAGCCAGGC 57.309 45.455 1.84 1.84 40.61 4.85
839 946 9.962783 GAGACTTTGAGTTACTTGAGTTAGTTA 57.037 33.333 0.00 0.00 0.00 2.24
841 948 8.008513 TGAGACTTTGAGTTACTTGAGTTAGT 57.991 34.615 0.00 0.00 0.00 2.24
842 949 8.873215 TTGAGACTTTGAGTTACTTGAGTTAG 57.127 34.615 0.00 0.00 0.00 2.34
845 952 7.064728 GTGTTTGAGACTTTGAGTTACTTGAGT 59.935 37.037 0.00 0.00 0.00 3.41
846 953 7.402640 GTGTTTGAGACTTTGAGTTACTTGAG 58.597 38.462 0.00 0.00 0.00 3.02
847 954 6.035650 CGTGTTTGAGACTTTGAGTTACTTGA 59.964 38.462 0.00 0.00 0.00 3.02
850 957 5.416947 ACGTGTTTGAGACTTTGAGTTACT 58.583 37.500 0.00 0.00 0.00 2.24
851 958 5.713822 ACGTGTTTGAGACTTTGAGTTAC 57.286 39.130 0.00 0.00 0.00 2.50
852 959 6.694411 GTCTACGTGTTTGAGACTTTGAGTTA 59.306 38.462 7.94 0.00 37.27 2.24
853 960 5.519206 GTCTACGTGTTTGAGACTTTGAGTT 59.481 40.000 7.94 0.00 37.27 3.01
854 961 5.041940 GTCTACGTGTTTGAGACTTTGAGT 58.958 41.667 7.94 0.00 37.27 3.41
855 962 5.041287 TGTCTACGTGTTTGAGACTTTGAG 58.959 41.667 14.67 0.00 40.26 3.02
856 963 4.802039 GTGTCTACGTGTTTGAGACTTTGA 59.198 41.667 14.67 0.00 40.26 2.69
857 964 4.804139 AGTGTCTACGTGTTTGAGACTTTG 59.196 41.667 14.67 0.00 40.26 2.77
858 965 5.007385 AGTGTCTACGTGTTTGAGACTTT 57.993 39.130 14.67 2.82 40.26 2.66
859 966 4.650754 AGTGTCTACGTGTTTGAGACTT 57.349 40.909 14.67 3.11 40.26 3.01
860 967 4.319333 CGTAGTGTCTACGTGTTTGAGACT 60.319 45.833 17.53 14.05 40.26 3.24
861 968 3.904824 CGTAGTGTCTACGTGTTTGAGAC 59.095 47.826 17.53 8.22 40.07 3.36
862 969 4.137849 CGTAGTGTCTACGTGTTTGAGA 57.862 45.455 17.53 0.00 36.31 3.27
883 990 7.856145 TTGAGTAGTACTAGGTGTTAGCTAC 57.144 40.000 1.87 0.00 32.25 3.58
893 1000 6.183360 GGTCTACGTGTTTGAGTAGTACTAGG 60.183 46.154 1.87 0.00 40.69 3.02
918 1025 1.740296 CGCCCCGTGTCTTGTTAGG 60.740 63.158 0.00 0.00 0.00 2.69
934 1059 2.041686 TTACATCCGGTTTGGGCGC 61.042 57.895 0.00 0.00 38.76 6.53
946 1071 5.671329 GCAGGAATCGTGTTTGAGTTACATC 60.671 44.000 4.81 0.00 0.00 3.06
949 1074 3.746492 AGCAGGAATCGTGTTTGAGTTAC 59.254 43.478 4.81 0.00 0.00 2.50
1068 1206 2.738587 TTTGGTCTGTGGTGGCTTAA 57.261 45.000 0.00 0.00 0.00 1.85
1069 1207 2.173782 TCTTTTGGTCTGTGGTGGCTTA 59.826 45.455 0.00 0.00 0.00 3.09
1070 1208 1.064017 TCTTTTGGTCTGTGGTGGCTT 60.064 47.619 0.00 0.00 0.00 4.35
1071 1209 0.550914 TCTTTTGGTCTGTGGTGGCT 59.449 50.000 0.00 0.00 0.00 4.75
1072 1210 1.398692 TTCTTTTGGTCTGTGGTGGC 58.601 50.000 0.00 0.00 0.00 5.01
1073 1211 3.221771 TGATTCTTTTGGTCTGTGGTGG 58.778 45.455 0.00 0.00 0.00 4.61
1074 1212 4.794003 GCTTGATTCTTTTGGTCTGTGGTG 60.794 45.833 0.00 0.00 0.00 4.17
1075 1213 3.319122 GCTTGATTCTTTTGGTCTGTGGT 59.681 43.478 0.00 0.00 0.00 4.16
1076 1214 3.318839 TGCTTGATTCTTTTGGTCTGTGG 59.681 43.478 0.00 0.00 0.00 4.17
1077 1215 4.037208 AGTGCTTGATTCTTTTGGTCTGTG 59.963 41.667 0.00 0.00 0.00 3.66
1078 1216 4.210331 AGTGCTTGATTCTTTTGGTCTGT 58.790 39.130 0.00 0.00 0.00 3.41
1079 1217 4.843220 AGTGCTTGATTCTTTTGGTCTG 57.157 40.909 0.00 0.00 0.00 3.51
1080 1218 5.006386 CCTAGTGCTTGATTCTTTTGGTCT 58.994 41.667 0.00 0.00 0.00 3.85
1081 1219 5.003804 TCCTAGTGCTTGATTCTTTTGGTC 58.996 41.667 0.00 0.00 0.00 4.02
1082 1220 4.985538 TCCTAGTGCTTGATTCTTTTGGT 58.014 39.130 0.00 0.00 0.00 3.67
1083 1221 5.220739 CGATCCTAGTGCTTGATTCTTTTGG 60.221 44.000 0.00 0.00 0.00 3.28
1089 1232 3.993081 CCATCGATCCTAGTGCTTGATTC 59.007 47.826 0.00 0.00 0.00 2.52
1093 1236 1.506493 GCCATCGATCCTAGTGCTTG 58.494 55.000 0.00 0.00 0.00 4.01
1100 1243 4.357947 GCGCCGCCATCGATCCTA 62.358 66.667 0.00 0.00 38.10 2.94
2011 2220 2.900106 AACAGAGCTGCTCCCACCC 61.900 63.158 25.09 0.51 0.00 4.61
2065 2351 4.426112 CCTCGACTGCAGCTGCGA 62.426 66.667 32.11 21.77 45.83 5.10
2097 2383 3.500448 TTGGCACCATTAGACAGACAA 57.500 42.857 0.00 0.00 0.00 3.18
2125 2411 4.188247 ACATGATTTTCTTCTCCGACGA 57.812 40.909 0.00 0.00 0.00 4.20
2126 2412 4.490959 CGAACATGATTTTCTTCTCCGACG 60.491 45.833 0.00 0.00 0.00 5.12
2127 2413 4.201724 CCGAACATGATTTTCTTCTCCGAC 60.202 45.833 0.00 0.00 0.00 4.79
2128 2414 3.932710 CCGAACATGATTTTCTTCTCCGA 59.067 43.478 0.00 0.00 0.00 4.55
2129 2415 3.485877 GCCGAACATGATTTTCTTCTCCG 60.486 47.826 0.00 0.00 0.00 4.63
2130 2416 3.440173 TGCCGAACATGATTTTCTTCTCC 59.560 43.478 0.00 0.00 0.00 3.71
2131 2417 4.406943 GTGCCGAACATGATTTTCTTCTC 58.593 43.478 0.00 0.00 0.00 2.87
2139 2425 2.406616 GCCCGTGCCGAACATGATT 61.407 57.895 0.00 0.00 37.49 2.57
2616 2922 2.356667 CCAAAGCTCCACCTCCCC 59.643 66.667 0.00 0.00 0.00 4.81
2677 2983 2.473816 TGCGTCTCTCTTGACTTGTTG 58.526 47.619 0.00 0.00 35.00 3.33
2829 3135 0.894184 ACCAGTCATCGTCTGTCCGT 60.894 55.000 0.00 0.00 0.00 4.69
2990 3296 3.087031 CCATGCATGACCTTGAACTCTT 58.913 45.455 28.31 0.00 0.00 2.85
3096 3402 5.586243 CCTCCATACGTCAATGACATTCTTT 59.414 40.000 14.24 0.00 32.09 2.52
3122 3428 1.476833 CCCCGTCCATTATGTCCTTGG 60.477 57.143 0.00 0.00 0.00 3.61
3556 3884 7.279981 CCATATATTCTCCGTGACAAAACTTGA 59.720 37.037 0.00 0.00 0.00 3.02
3570 3898 5.419155 TGTGTCTCCGATCCATATATTCTCC 59.581 44.000 0.00 0.00 0.00 3.71
3598 3926 4.721211 TTGGCCTACAAGTGCTTCAGCA 62.721 50.000 3.32 0.00 40.78 4.41
3858 4186 2.258726 GGGCGGTGGTCAACTTGTC 61.259 63.158 0.00 0.00 0.00 3.18
3861 4189 2.430367 GAGGGCGGTGGTCAACTT 59.570 61.111 0.00 0.00 0.00 2.66
3893 4221 3.333219 CCAAGGGAGGCCAGCTCA 61.333 66.667 5.01 0.00 0.00 4.26
3981 4309 8.462016 GCTGTGATTTGAGTATAATTTTGGACT 58.538 33.333 0.00 0.00 0.00 3.85
4005 4333 1.216990 CCACCTCTTATCCCAAGGCT 58.783 55.000 0.00 0.00 33.21 4.58
4038 4366 4.648307 CGGAGGGAGTAGTATTTAAGTGGT 59.352 45.833 0.00 0.00 0.00 4.16
4042 4370 4.023365 CGGACGGAGGGAGTAGTATTTAAG 60.023 50.000 0.00 0.00 0.00 1.85
4060 4388 2.267188 TCGACAAGTATTTCCGGACG 57.733 50.000 1.83 0.27 0.00 4.79
4066 4394 7.752695 ACATCCATTTCTTCGACAAGTATTTC 58.247 34.615 0.00 0.00 0.00 2.17
4122 4450 8.811017 ACATGTGATGGGTTTTGTATGAAAATA 58.189 29.630 0.00 0.00 33.60 1.40
4123 4451 7.678837 ACATGTGATGGGTTTTGTATGAAAAT 58.321 30.769 0.00 0.00 33.60 1.82
4139 4467 7.805542 TGTACGTCCAAATTAAAACATGTGATG 59.194 33.333 0.00 0.00 0.00 3.07
4140 4468 7.877003 TGTACGTCCAAATTAAAACATGTGAT 58.123 30.769 0.00 0.00 0.00 3.06
4188 4516 2.170607 ACCCACGGTGATTAGATTGAGG 59.829 50.000 10.28 0.41 32.98 3.86
4246 4574 2.890311 CCATACTCTCATCTTCGGCTCT 59.110 50.000 0.00 0.00 0.00 4.09
4284 4612 2.174854 AGTTAACTCTTGGTGTGGGCTT 59.825 45.455 1.12 0.00 0.00 4.35
4292 4620 6.842676 AGAAAATCTGGAGTTAACTCTTGGT 58.157 36.000 29.66 18.29 42.48 3.67
4301 4629 5.726308 TCATGAGGGAGAAAATCTGGAGTTA 59.274 40.000 0.00 0.00 0.00 2.24
4320 4648 0.676466 GACGTTGGGTGGCATCATGA 60.676 55.000 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.