Multiple sequence alignment - TraesCS2B01G146300

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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 TraesCS2B01G146300 chr2B 100.000 2822 0 0 1 2822 112205589 112202768 0.000000e+00 5212.0
1 TraesCS2B01G146300 chr2B 79.797 1084 173 25 1030 2088 113171279 113170217 0.000000e+00 747.0
2 TraesCS2B01G146300 chr2B 87.319 276 24 6 2459 2724 112461780 112461506 3.530000e-79 305.0
3 TraesCS2B01G146300 chr2B 81.586 391 30 25 2440 2815 113163199 113162836 4.600000e-73 285.0
4 TraesCS2B01G146300 chr2B 82.282 333 28 18 2496 2815 112642273 112641959 2.790000e-65 259.0
5 TraesCS2B01G146300 chr2B 82.578 287 35 9 2155 2440 112468904 112468632 3.630000e-59 239.0
6 TraesCS2B01G146300 chr2B 81.569 255 15 19 2573 2815 113028725 113028491 6.210000e-42 182.0
7 TraesCS2B01G146300 chr2D 93.534 1856 98 11 875 2722 73865380 73863539 0.000000e+00 2743.0
8 TraesCS2B01G146300 chr2D 88.966 870 68 11 1 845 73866250 73865384 0.000000e+00 1050.0
9 TraesCS2B01G146300 chr2D 80.441 1089 160 22 1030 2088 73970598 73969533 0.000000e+00 782.0
10 TraesCS2B01G146300 chr2D 83.103 290 37 6 2152 2440 73969495 73969217 1.300000e-63 254.0
11 TraesCS2B01G146300 chr2A 92.424 1452 91 7 875 2311 73300184 73298737 0.000000e+00 2054.0
12 TraesCS2B01G146300 chr2A 87.500 528 44 7 2307 2822 73285750 73285233 8.710000e-165 590.0
13 TraesCS2B01G146300 chr2A 84.536 291 30 11 2440 2724 73376844 73376563 9.960000e-70 274.0
14 TraesCS2B01G146300 chr2A 83.793 290 35 8 2152 2440 73383514 73383236 5.990000e-67 265.0
15 TraesCS2B01G146300 chr2A 82.143 112 12 2 2717 2820 73284781 73284670 3.870000e-14 89.8
16 TraesCS2B01G146300 chr2A 85.542 83 3 3 2741 2815 73376563 73376482 8.380000e-11 78.7
17 TraesCS2B01G146300 chr6D 82.553 235 24 9 251 483 434139780 434139999 1.030000e-44 191.0
18 TraesCS2B01G146300 chr6D 71.736 605 124 28 1061 1647 446149867 446149292 2.950000e-25 126.0
19 TraesCS2B01G146300 chr6D 76.159 151 26 7 2038 2184 446099574 446099718 1.400000e-08 71.3
20 TraesCS2B01G146300 chr6D 100.000 29 0 0 1905 1933 446099429 446099457 1.000000e-03 54.7
21 TraesCS2B01G146300 chr5B 81.166 223 28 9 376 595 576056703 576056914 1.740000e-37 167.0
22 TraesCS2B01G146300 chr1B 83.636 165 20 7 423 583 567197819 567197980 6.300000e-32 148.0
23 TraesCS2B01G146300 chr7A 82.184 174 22 7 414 583 707988601 707988433 1.050000e-29 141.0
24 TraesCS2B01G146300 chr7A 85.714 56 5 3 2038 2092 733669906 733669959 3.930000e-04 56.5
25 TraesCS2B01G146300 chr6B 70.999 831 170 41 1061 1870 674378255 674377475 1.760000e-27 134.0
26 TraesCS2B01G146300 chr6B 86.667 60 7 1 2038 2096 674197122 674197181 6.530000e-07 65.8
27 TraesCS2B01G146300 chr3A 87.179 117 13 2 251 365 60296174 60296058 6.340000e-27 132.0
28 TraesCS2B01G146300 chr3D 85.470 117 15 2 251 365 48069316 48069200 1.370000e-23 121.0
29 TraesCS2B01G146300 chr1A 79.032 186 28 8 251 434 460972364 460972540 1.780000e-22 117.0
30 TraesCS2B01G146300 chr6A 86.667 60 7 1 2038 2096 592717258 592717317 6.530000e-07 65.8
31 TraesCS2B01G146300 chr7D 92.683 41 2 1 2056 2095 633393580 633393540 1.090000e-04 58.4
32 TraesCS2B01G146300 chr7B 96.970 33 1 0 2056 2088 714316373 714316341 3.930000e-04 56.5
33 TraesCS2B01G146300 chr4A 100.000 29 0 0 2056 2084 704501549 704501577 1.000000e-03 54.7


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 TraesCS2B01G146300 chr2B 112202768 112205589 2821 True 5212.0 5212 100.0000 1 2822 1 chr2B.!!$R1 2821
1 TraesCS2B01G146300 chr2B 113170217 113171279 1062 True 747.0 747 79.7970 1030 2088 1 chr2B.!!$R7 1058
2 TraesCS2B01G146300 chr2D 73863539 73866250 2711 True 1896.5 2743 91.2500 1 2722 2 chr2D.!!$R1 2721
3 TraesCS2B01G146300 chr2D 73969217 73970598 1381 True 518.0 782 81.7720 1030 2440 2 chr2D.!!$R2 1410
4 TraesCS2B01G146300 chr2A 73298737 73300184 1447 True 2054.0 2054 92.4240 875 2311 1 chr2A.!!$R1 1436
5 TraesCS2B01G146300 chr2A 73284670 73285750 1080 True 339.9 590 84.8215 2307 2822 2 chr2A.!!$R3 515

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
88 89 0.109179 GCAACATCGCCAATGCTTCA 60.109 50.000 0.00 0.0 39.12 3.02 F
778 803 0.329596 ATTTCAGTGGACTGGCTCCC 59.670 55.000 6.94 0.0 43.91 4.30 F
1215 1253 1.069358 CCTCTCCTAGGCATCGTTTCC 59.931 57.143 2.96 0.0 38.97 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1561 1617 0.765903 ATGCCATCCTCATCCTCGGT 60.766 55.000 0.00 0.00 0.00 4.69 R
1769 1832 1.390123 CAACAGAAGTATCCGTGTGCG 59.610 52.381 0.00 0.00 37.95 5.34 R
2577 2656 1.538047 ACCAGTACAAGCATGCAAGG 58.462 50.000 21.98 11.05 0.00 3.61 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
60 61 1.311859 ACATCACTGGTGTTGCACTG 58.688 50.000 10.55 0.00 34.54 3.66
67 68 2.040544 GGTGTTGCACTGATCGGGG 61.041 63.158 6.47 2.11 34.40 5.73
76 77 2.513666 TGATCGGGGCGCAACATC 60.514 61.111 10.83 5.31 0.00 3.06
86 87 1.153978 CGCAACATCGCCAATGCTT 60.154 52.632 0.00 0.00 39.12 3.91
87 88 1.135699 CGCAACATCGCCAATGCTTC 61.136 55.000 0.00 0.00 39.12 3.86
88 89 0.109179 GCAACATCGCCAATGCTTCA 60.109 50.000 0.00 0.00 39.12 3.02
140 141 4.570663 CTGGCGACCCGACCGATC 62.571 72.222 0.00 0.00 31.60 3.69
207 208 8.911918 TTTAGTGAAAAGATTACTAAGTGCCA 57.088 30.769 0.00 0.00 37.95 4.92
226 227 1.262950 CAGCGATCGTTTGGACAACAA 59.737 47.619 17.81 0.00 37.28 2.83
273 274 2.552585 TTAGCTACACGCCAGTCGCC 62.553 60.000 0.00 0.00 43.23 5.54
282 283 1.227999 CGCCAGTCGCCTGAAAAAGA 61.228 55.000 0.00 0.00 41.50 2.52
321 322 6.293407 CGATTTGGTAGAGAAGAAAGCAACAA 60.293 38.462 0.00 0.00 30.96 2.83
333 334 4.829492 AGAAAGCAACAACCTTAGAGCATT 59.171 37.500 0.00 0.00 0.00 3.56
342 343 1.211457 CCTTAGAGCATTGAGGCAGGT 59.789 52.381 0.00 0.00 35.83 4.00
347 348 2.097825 GAGCATTGAGGCAGGTTTGAT 58.902 47.619 0.00 0.00 35.83 2.57
353 354 1.347707 TGAGGCAGGTTTGATCTCGTT 59.652 47.619 0.00 0.00 32.40 3.85
360 363 4.093556 GCAGGTTTGATCTCGTTTCTTAGG 59.906 45.833 0.00 0.00 0.00 2.69
367 370 3.478857 TCTCGTTTCTTAGGGTGCAAA 57.521 42.857 0.00 0.00 0.00 3.68
561 565 3.319198 GCGGTGGGGAGAGGTTGA 61.319 66.667 0.00 0.00 0.00 3.18
565 569 2.124996 TGGGGAGAGGTTGAGGGG 59.875 66.667 0.00 0.00 0.00 4.79
566 570 2.454941 GGGGAGAGGTTGAGGGGA 59.545 66.667 0.00 0.00 0.00 4.81
567 571 1.690985 GGGGAGAGGTTGAGGGGAG 60.691 68.421 0.00 0.00 0.00 4.30
660 664 2.747855 GCAGGCGGTTGGAGGAAG 60.748 66.667 0.00 0.00 0.00 3.46
669 673 1.072331 GGTTGGAGGAAGAAGAGCACA 59.928 52.381 0.00 0.00 0.00 4.57
672 676 0.392327 GGAGGAAGAAGAGCACAGGC 60.392 60.000 0.00 0.00 41.61 4.85
684 688 1.153647 CACAGGCGGCGACAATCTA 60.154 57.895 18.30 0.00 0.00 1.98
778 803 0.329596 ATTTCAGTGGACTGGCTCCC 59.670 55.000 6.94 0.00 43.91 4.30
794 819 2.551504 GCTCCCAGTCGTTCCCTTTTTA 60.552 50.000 0.00 0.00 0.00 1.52
797 822 3.117963 TCCCAGTCGTTCCCTTTTTACAA 60.118 43.478 0.00 0.00 0.00 2.41
799 824 4.082949 CCCAGTCGTTCCCTTTTTACAATC 60.083 45.833 0.00 0.00 0.00 2.67
807 832 6.401796 CGTTCCCTTTTTACAATCTAAGACGG 60.402 42.308 0.00 0.00 0.00 4.79
809 834 7.243604 TCCCTTTTTACAATCTAAGACGGTA 57.756 36.000 0.00 0.00 0.00 4.02
819 844 6.832384 ACAATCTAAGACGGTAGTTAGGATGA 59.168 38.462 15.04 0.00 0.00 2.92
832 858 9.899226 GGTAGTTAGGATGATTTTATGCAATTC 57.101 33.333 0.00 0.00 0.00 2.17
845 871 4.840716 ATGCAATTCACTCCTCTTCTCT 57.159 40.909 0.00 0.00 0.00 3.10
847 873 5.336150 TGCAATTCACTCCTCTTCTCTAG 57.664 43.478 0.00 0.00 0.00 2.43
848 874 4.774726 TGCAATTCACTCCTCTTCTCTAGT 59.225 41.667 0.00 0.00 0.00 2.57
849 875 5.105554 TGCAATTCACTCCTCTTCTCTAGTC 60.106 44.000 0.00 0.00 0.00 2.59
850 876 5.127031 GCAATTCACTCCTCTTCTCTAGTCT 59.873 44.000 0.00 0.00 0.00 3.24
851 877 6.320164 GCAATTCACTCCTCTTCTCTAGTCTA 59.680 42.308 0.00 0.00 0.00 2.59
852 878 7.468631 GCAATTCACTCCTCTTCTCTAGTCTAG 60.469 44.444 0.00 0.00 0.00 2.43
853 879 6.630203 TTCACTCCTCTTCTCTAGTCTAGT 57.370 41.667 6.77 0.00 0.00 2.57
854 880 5.984725 TCACTCCTCTTCTCTAGTCTAGTG 58.015 45.833 6.77 4.80 33.24 2.74
855 881 5.486063 TCACTCCTCTTCTCTAGTCTAGTGT 59.514 44.000 6.77 0.00 33.48 3.55
856 882 5.815740 CACTCCTCTTCTCTAGTCTAGTGTC 59.184 48.000 6.77 0.00 0.00 3.67
857 883 5.486063 ACTCCTCTTCTCTAGTCTAGTGTCA 59.514 44.000 6.77 0.00 0.00 3.58
858 884 6.013206 ACTCCTCTTCTCTAGTCTAGTGTCAA 60.013 42.308 6.77 0.00 0.00 3.18
859 885 6.174760 TCCTCTTCTCTAGTCTAGTGTCAAC 58.825 44.000 6.77 0.00 0.00 3.18
860 886 6.013206 TCCTCTTCTCTAGTCTAGTGTCAACT 60.013 42.308 6.77 0.00 40.67 3.16
861 887 6.093495 CCTCTTCTCTAGTCTAGTGTCAACTG 59.907 46.154 6.77 0.00 37.19 3.16
862 888 6.535540 TCTTCTCTAGTCTAGTGTCAACTGT 58.464 40.000 6.77 0.00 37.19 3.55
863 889 6.999272 TCTTCTCTAGTCTAGTGTCAACTGTT 59.001 38.462 6.77 0.00 37.19 3.16
864 890 8.155510 TCTTCTCTAGTCTAGTGTCAACTGTTA 58.844 37.037 6.77 0.00 37.19 2.41
865 891 8.687292 TTCTCTAGTCTAGTGTCAACTGTTAA 57.313 34.615 6.77 0.00 37.19 2.01
866 892 8.325421 TCTCTAGTCTAGTGTCAACTGTTAAG 57.675 38.462 6.77 0.00 37.19 1.85
867 893 8.155510 TCTCTAGTCTAGTGTCAACTGTTAAGA 58.844 37.037 6.77 0.00 37.19 2.10
868 894 8.865420 TCTAGTCTAGTGTCAACTGTTAAGAT 57.135 34.615 6.77 0.00 37.19 2.40
869 895 8.731605 TCTAGTCTAGTGTCAACTGTTAAGATG 58.268 37.037 6.77 0.00 37.19 2.90
870 896 7.526142 AGTCTAGTGTCAACTGTTAAGATGA 57.474 36.000 0.00 0.00 37.19 2.92
871 897 8.128322 AGTCTAGTGTCAACTGTTAAGATGAT 57.872 34.615 0.00 0.00 37.52 2.45
872 898 8.589338 AGTCTAGTGTCAACTGTTAAGATGATT 58.411 33.333 0.00 0.00 37.52 2.57
873 899 9.209175 GTCTAGTGTCAACTGTTAAGATGATTT 57.791 33.333 0.00 0.00 37.52 2.17
935 961 4.082300 TCTCTAGTCTAGTGTCGTCTTCGT 60.082 45.833 6.77 0.00 38.33 3.85
962 988 1.604278 GTGAAATATTCCTCCGCTGCC 59.396 52.381 0.00 0.00 0.00 4.85
1015 1041 2.100631 CCAATGGCGTCGACACCTC 61.101 63.158 22.44 5.91 0.00 3.85
1022 1048 3.735029 GTCGACACCTCGCCGTCT 61.735 66.667 11.55 0.00 39.96 4.18
1050 1076 2.801162 CCGACGACACTGCTCACG 60.801 66.667 0.00 0.00 0.00 4.35
1215 1253 1.069358 CCTCTCCTAGGCATCGTTTCC 59.931 57.143 2.96 0.00 38.97 3.13
1218 1256 1.417890 CTCCTAGGCATCGTTTCCCAT 59.582 52.381 2.96 0.00 0.00 4.00
1318 1374 3.175240 CTCACGCCGCTGACTTCG 61.175 66.667 0.00 0.00 0.00 3.79
1372 1428 4.228567 TGCGTGACTTGCGGGACA 62.229 61.111 0.00 0.00 34.24 4.02
1376 1432 3.555324 TGACTTGCGGGACAGCCA 61.555 61.111 0.00 0.00 36.02 4.75
1561 1617 3.311511 TTCCTAGCTCCTCCGGCCA 62.312 63.158 2.24 0.00 0.00 5.36
1575 1631 2.143419 GGCCACCGAGGATGAGGAT 61.143 63.158 0.00 0.00 41.22 3.24
1667 1730 3.127533 GGTGATGGACAGTGGCGC 61.128 66.667 0.00 0.00 0.00 6.53
1824 1887 3.489416 GGCGAACAAAAACAAGTTGATCC 59.511 43.478 10.54 0.00 0.00 3.36
1845 1908 1.734117 CTCGACACACGCAGCATGA 60.734 57.895 0.00 0.00 42.26 3.07
1903 1972 0.540365 ACACAGGTTGCCATTCTGGG 60.540 55.000 0.00 0.00 38.19 4.45
2007 2076 2.028043 GTGCAAACCAGTGGCTGC 59.972 61.111 23.78 23.78 35.98 5.25
2188 2261 1.528586 CAGCTTGAGTGGTTCTTGACG 59.471 52.381 0.00 0.00 0.00 4.35
2251 2324 1.014044 CACCATCGTTGTCTCCACCG 61.014 60.000 0.00 0.00 0.00 4.94
2259 2332 0.966920 TTGTCTCCACCGTCTCTTCC 59.033 55.000 0.00 0.00 0.00 3.46
2279 2352 2.002586 CACATGGTAACCTTGCTCTCG 58.997 52.381 0.00 0.00 32.73 4.04
2289 2363 1.667724 CCTTGCTCTCGGTATTTGCAG 59.332 52.381 0.00 0.00 35.02 4.41
2319 2393 4.081420 ACTTTGCACTCTATAGGACTGTGG 60.081 45.833 0.00 0.00 0.00 4.17
2424 2498 4.025480 GCAATTGAAAAGCTGTGGAACTTG 60.025 41.667 10.34 0.00 38.04 3.16
2467 2541 6.615316 TGTTTCTCATCTTGGGGATATACTCA 59.385 38.462 0.00 0.00 32.64 3.41
2473 2547 7.627311 TCATCTTGGGGATATACTCATCATTG 58.373 38.462 0.00 0.00 32.64 2.82
2475 2549 7.392766 TCTTGGGGATATACTCATCATTGTT 57.607 36.000 0.00 0.00 0.00 2.83
2476 2550 7.815383 TCTTGGGGATATACTCATCATTGTTT 58.185 34.615 0.00 0.00 0.00 2.83
2527 2602 6.127897 GCAGGACCATAATGTTCTATTATGCC 60.128 42.308 12.06 9.65 39.44 4.40
2535 2610 8.729756 CATAATGTTCTATTATGCCGGATTTGA 58.270 33.333 5.05 0.00 35.86 2.69
2537 2612 5.680619 TGTTCTATTATGCCGGATTTGAGT 58.319 37.500 5.05 0.00 0.00 3.41
2577 2656 8.865590 TTCTTTGAAGTTATTTTGCCTTGTAC 57.134 30.769 0.00 0.00 0.00 2.90
2592 2671 3.119849 CCTTGTACCTTGCATGCTTGTAC 60.120 47.826 25.04 25.04 33.96 2.90
2593 2672 3.417069 TGTACCTTGCATGCTTGTACT 57.583 42.857 28.40 10.62 34.37 2.73
2595 2674 1.538047 ACCTTGCATGCTTGTACTGG 58.462 50.000 20.33 11.91 0.00 4.00
2596 2675 1.202927 ACCTTGCATGCTTGTACTGGT 60.203 47.619 20.33 12.50 0.00 4.00
2597 2676 1.888512 CCTTGCATGCTTGTACTGGTT 59.111 47.619 20.33 0.00 0.00 3.67
2598 2677 3.081061 CCTTGCATGCTTGTACTGGTTA 58.919 45.455 20.33 0.00 0.00 2.85
2600 2679 4.158394 CCTTGCATGCTTGTACTGGTTATT 59.842 41.667 20.33 0.00 0.00 1.40
2601 2680 5.356751 CCTTGCATGCTTGTACTGGTTATTA 59.643 40.000 20.33 0.00 0.00 0.98
2602 2681 6.039717 CCTTGCATGCTTGTACTGGTTATTAT 59.960 38.462 20.33 0.00 0.00 1.28
2603 2682 6.618287 TGCATGCTTGTACTGGTTATTATC 57.382 37.500 20.33 0.00 0.00 1.75
2604 2683 5.530915 TGCATGCTTGTACTGGTTATTATCC 59.469 40.000 20.33 0.00 0.00 2.59
2605 2684 5.334105 GCATGCTTGTACTGGTTATTATCCG 60.334 44.000 11.37 0.00 0.00 4.18
2623 2702 2.166050 TCCGTCCCAATTGATTGCATTG 59.834 45.455 7.12 0.00 36.48 2.82
2637 2716 6.267817 TGATTGCATTGCTTAGTATCTTTGC 58.732 36.000 10.49 0.00 0.00 3.68
2679 2758 6.977213 TGAAGCACCCAGTATTTTTCTTAAC 58.023 36.000 0.00 0.00 0.00 2.01
2684 2763 6.513720 GCACCCAGTATTTTTCTTAACGTTGA 60.514 38.462 11.99 0.73 0.00 3.18
2698 2777 6.695713 TCTTAACGTTGATTCAGATATGACGG 59.304 38.462 11.99 0.00 33.74 4.79
2708 2787 2.235650 CAGATATGACGGATGCCTCCAT 59.764 50.000 8.86 0.00 42.19 3.41
2722 2801 5.635278 TGCCTCCATTTCTGATTCAGATA 57.365 39.130 16.82 12.65 40.39 1.98
2727 2806 7.222161 CCTCCATTTCTGATTCAGATATGACA 58.778 38.462 31.85 22.15 45.77 3.58
2731 2810 8.680001 CCATTTCTGATTCAGATATGACAAACA 58.320 33.333 31.85 9.90 45.77 2.83
2765 2844 0.536687 ATTGATGCCGCTGGGAGATG 60.537 55.000 0.00 0.00 34.06 2.90
2788 2873 3.166489 ACCTTGACGTTATAGAGCAGC 57.834 47.619 0.00 0.00 0.00 5.25
2813 2899 5.431765 ACTTGGAGCTTATGTACTGGAATG 58.568 41.667 0.00 0.00 0.00 2.67
2814 2900 4.422073 TGGAGCTTATGTACTGGAATGG 57.578 45.455 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.109132 GCTTTGTAGCATGTGGTGGC 60.109 55.000 0.00 0.00 46.95 5.01
26 27 1.442526 GATGTTGCATCCCAGCTCGG 61.443 60.000 0.00 0.00 34.99 4.63
60 61 3.640000 CGATGTTGCGCCCCGATC 61.640 66.667 4.18 0.00 0.00 3.69
76 77 7.392483 AATCATTTGATCTTGAAGCATTGGCG 61.392 38.462 0.00 0.00 38.39 5.69
81 82 6.811665 CACACAATCATTTGATCTTGAAGCAT 59.188 34.615 0.00 0.00 36.64 3.79
82 83 6.153756 CACACAATCATTTGATCTTGAAGCA 58.846 36.000 0.00 0.00 36.64 3.91
86 87 5.323581 TCCCACACAATCATTTGATCTTGA 58.676 37.500 0.00 0.00 36.64 3.02
87 88 5.648178 TCCCACACAATCATTTGATCTTG 57.352 39.130 0.00 0.00 36.64 3.02
88 89 5.335897 CGTTCCCACACAATCATTTGATCTT 60.336 40.000 0.00 0.00 36.64 2.40
140 141 5.574830 CGTCAACCAACTGATTCTAAGAGAG 59.425 44.000 0.00 0.00 0.00 3.20
207 208 1.263217 GTTGTTGTCCAAACGATCGCT 59.737 47.619 16.60 0.00 34.07 4.93
273 274 5.687285 CGACTGACCCAAATTTCTTTTTCAG 59.313 40.000 8.96 8.96 33.39 3.02
282 283 3.895041 ACCAAATCGACTGACCCAAATTT 59.105 39.130 0.00 0.00 0.00 1.82
321 322 1.211457 CCTGCCTCAATGCTCTAAGGT 59.789 52.381 0.00 0.00 0.00 3.50
333 334 0.976641 ACGAGATCAAACCTGCCTCA 59.023 50.000 0.00 0.00 0.00 3.86
342 343 4.000988 GCACCCTAAGAAACGAGATCAAA 58.999 43.478 0.00 0.00 0.00 2.69
347 348 3.070446 TCTTTGCACCCTAAGAAACGAGA 59.930 43.478 0.00 0.00 31.46 4.04
353 354 1.271926 GCCCTCTTTGCACCCTAAGAA 60.272 52.381 0.56 0.00 33.53 2.52
360 363 2.677875 CCCTGCCCTCTTTGCACC 60.678 66.667 0.00 0.00 34.46 5.01
367 370 1.162085 AACTTCTCCCCTGCCCTCT 59.838 57.895 0.00 0.00 0.00 3.69
479 483 3.321682 CCCTTGAAATTCTCCAGCAAACA 59.678 43.478 0.00 0.00 0.00 2.83
486 490 2.069775 TGGACCCCTTGAAATTCTCCA 58.930 47.619 0.00 0.00 0.00 3.86
509 513 1.227556 CCGGCCATCCCTCTAAACG 60.228 63.158 2.24 0.00 0.00 3.60
545 549 2.660064 CCTCAACCTCTCCCCACCG 61.660 68.421 0.00 0.00 0.00 4.94
551 555 0.689412 CCTCTCCCCTCAACCTCTCC 60.689 65.000 0.00 0.00 0.00 3.71
600 604 3.716195 CATCCCCTGTGGTCGGCA 61.716 66.667 0.00 0.00 34.77 5.69
601 605 4.489771 CCATCCCCTGTGGTCGGC 62.490 72.222 0.00 0.00 34.77 5.54
608 612 2.988839 GCCTGCTTCCATCCCCTGT 61.989 63.158 0.00 0.00 0.00 4.00
647 651 1.021920 GCTCTTCTTCCTCCAACCGC 61.022 60.000 0.00 0.00 0.00 5.68
660 664 4.742201 TCGCCGCCTGTGCTCTTC 62.742 66.667 0.00 0.00 34.43 2.87
669 673 2.038387 AAAATAGATTGTCGCCGCCT 57.962 45.000 0.00 0.00 0.00 5.52
690 694 3.581755 CGTTTCAGATTACGTCTTCCCA 58.418 45.455 0.00 0.00 34.00 4.37
751 776 5.129320 AGCCAGTCCACTGAAATTTCTTTTT 59.871 36.000 18.64 0.00 46.59 1.94
778 803 5.941948 AGATTGTAAAAAGGGAACGACTG 57.058 39.130 0.00 0.00 0.00 3.51
781 806 6.366877 CGTCTTAGATTGTAAAAAGGGAACGA 59.633 38.462 0.00 0.00 0.00 3.85
782 807 6.401796 CCGTCTTAGATTGTAAAAAGGGAACG 60.402 42.308 0.00 0.00 0.00 3.95
783 808 6.429078 ACCGTCTTAGATTGTAAAAAGGGAAC 59.571 38.462 0.00 0.00 0.00 3.62
794 819 6.832384 TCATCCTAACTACCGTCTTAGATTGT 59.168 38.462 0.00 0.00 0.00 2.71
797 822 8.480133 AAATCATCCTAACTACCGTCTTAGAT 57.520 34.615 0.00 0.00 0.00 1.98
809 834 9.193806 AGTGAATTGCATAAAATCATCCTAACT 57.806 29.630 0.00 0.00 0.00 2.24
819 844 7.833183 AGAGAAGAGGAGTGAATTGCATAAAAT 59.167 33.333 0.00 0.00 0.00 1.82
832 858 5.741011 ACACTAGACTAGAGAAGAGGAGTG 58.259 45.833 16.55 4.96 37.42 3.51
845 871 8.631480 TCATCTTAACAGTTGACACTAGACTA 57.369 34.615 0.00 0.00 0.00 2.59
847 873 8.764524 AATCATCTTAACAGTTGACACTAGAC 57.235 34.615 0.00 0.00 32.59 2.59
848 874 9.778741 AAAATCATCTTAACAGTTGACACTAGA 57.221 29.630 0.00 0.00 32.59 2.43
851 877 9.778741 TCTAAAATCATCTTAACAGTTGACACT 57.221 29.630 0.00 0.00 32.59 3.55
859 885 9.708222 CCGTTTGATCTAAAATCATCTTAACAG 57.292 33.333 0.00 0.00 0.00 3.16
860 886 8.181573 GCCGTTTGATCTAAAATCATCTTAACA 58.818 33.333 0.00 0.00 0.00 2.41
861 887 8.181573 TGCCGTTTGATCTAAAATCATCTTAAC 58.818 33.333 0.00 0.00 0.00 2.01
862 888 8.181573 GTGCCGTTTGATCTAAAATCATCTTAA 58.818 33.333 0.00 0.00 0.00 1.85
863 889 7.465379 CGTGCCGTTTGATCTAAAATCATCTTA 60.465 37.037 0.00 0.00 0.00 2.10
864 890 6.555315 GTGCCGTTTGATCTAAAATCATCTT 58.445 36.000 0.00 0.00 0.00 2.40
865 891 5.220662 CGTGCCGTTTGATCTAAAATCATCT 60.221 40.000 0.00 0.00 0.00 2.90
866 892 4.963953 CGTGCCGTTTGATCTAAAATCATC 59.036 41.667 0.00 0.00 0.00 2.92
867 893 4.394920 ACGTGCCGTTTGATCTAAAATCAT 59.605 37.500 0.00 0.00 36.35 2.45
868 894 3.749088 ACGTGCCGTTTGATCTAAAATCA 59.251 39.130 0.00 0.00 36.35 2.57
869 895 4.336532 ACGTGCCGTTTGATCTAAAATC 57.663 40.909 0.00 0.00 36.35 2.17
898 924 2.165845 ACTAGAGAACGAATGAACGGGG 59.834 50.000 0.00 0.00 37.61 5.73
899 925 3.128938 AGACTAGAGAACGAATGAACGGG 59.871 47.826 0.00 0.00 37.61 5.28
935 961 2.223971 GGAGGAATATTTCACTCGCCGA 60.224 50.000 0.00 0.00 31.70 5.54
962 988 2.035321 GGATAGGGTTTCTCTCGCTCTG 59.965 54.545 0.00 0.00 0.00 3.35
1050 1076 1.737201 GAGAAGCTCCTCGGGTAGC 59.263 63.158 0.00 0.00 39.08 3.58
1120 1146 1.002011 GGAAGGAGACCCAGGCAAC 60.002 63.158 0.00 0.00 33.88 4.17
1215 1253 1.366366 GTACCGGTGGGATCGATGG 59.634 63.158 19.93 0.00 36.97 3.51
1218 1256 1.755395 CAGGTACCGGTGGGATCGA 60.755 63.158 19.93 0.00 36.97 3.59
1311 1367 1.372997 GAAGGAGCACGCGAAGTCA 60.373 57.895 15.93 0.00 0.00 3.41
1318 1374 4.475135 GGGGAGGAAGGAGCACGC 62.475 72.222 0.00 0.00 0.00 5.34
1372 1428 1.680651 CAGAGAGGAGGACGTGGCT 60.681 63.158 0.00 0.00 0.00 4.75
1376 1432 2.752238 CGCCAGAGAGGAGGACGT 60.752 66.667 0.00 0.00 41.22 4.34
1561 1617 0.765903 ATGCCATCCTCATCCTCGGT 60.766 55.000 0.00 0.00 0.00 4.69
1575 1631 5.732633 CAAATAACCCTGAATGAAATGCCA 58.267 37.500 0.00 0.00 0.00 4.92
1667 1730 3.554524 CCAATTGTCAAGTGTAACAGCG 58.445 45.455 11.74 0.00 41.43 5.18
1728 1791 3.062639 CACAAGTACGATTCTGGCATGAC 59.937 47.826 0.00 0.00 0.00 3.06
1732 1795 1.943968 GCCACAAGTACGATTCTGGCA 60.944 52.381 14.45 0.00 42.09 4.92
1739 1802 2.495366 TTCGCGGCCACAAGTACGAT 62.495 55.000 6.13 0.00 0.00 3.73
1769 1832 1.390123 CAACAGAAGTATCCGTGTGCG 59.610 52.381 0.00 0.00 37.95 5.34
1845 1908 4.263639 TGGGAGATTGACAGCAGAGAAATT 60.264 41.667 0.00 0.00 0.00 1.82
1903 1972 4.448976 GCCTTCCTTCCCCTGCCC 62.449 72.222 0.00 0.00 0.00 5.36
2007 2076 3.568430 GGTAAACTGAACCTTCCTTGTGG 59.432 47.826 0.00 0.00 33.97 4.17
2188 2261 3.931578 ACCTATGTTGCTGAACTGAGAC 58.068 45.455 0.00 0.00 32.79 3.36
2251 2324 3.983044 AGGTTACCATGTGGAAGAGAC 57.017 47.619 3.51 0.00 38.94 3.36
2259 2332 2.002586 CGAGAGCAAGGTTACCATGTG 58.997 52.381 8.45 2.25 0.00 3.21
2279 2352 5.154222 GCAAAGTACAAGTCTGCAAATACC 58.846 41.667 0.00 0.00 33.19 2.73
2289 2363 6.752815 GTCCTATAGAGTGCAAAGTACAAGTC 59.247 42.308 0.00 0.00 0.00 3.01
2347 2421 6.726230 ACTGACATAGCACACTACTAATACG 58.274 40.000 0.00 0.00 0.00 3.06
2353 2427 9.534565 CAATTATTACTGACATAGCACACTACT 57.465 33.333 0.00 0.00 0.00 2.57
2354 2428 9.314321 ACAATTATTACTGACATAGCACACTAC 57.686 33.333 0.00 0.00 0.00 2.73
2424 2498 7.987458 TGAGAAACATATACTTCTTGATGTCCC 59.013 37.037 1.19 0.00 32.01 4.46
2487 2561 9.586732 TTATGGTCCTGCTTTGCTTATAATTAT 57.413 29.630 2.97 2.97 0.00 1.28
2491 2565 6.833416 ACATTATGGTCCTGCTTTGCTTATAA 59.167 34.615 0.00 0.00 0.00 0.98
2492 2566 6.364701 ACATTATGGTCCTGCTTTGCTTATA 58.635 36.000 0.00 0.00 0.00 0.98
2527 2602 7.772332 AGTAGCTAATACAAACTCAAATCCG 57.228 36.000 0.00 0.00 36.79 4.18
2577 2656 1.538047 ACCAGTACAAGCATGCAAGG 58.462 50.000 21.98 11.05 0.00 3.61
2592 2671 5.373222 TCAATTGGGACGGATAATAACCAG 58.627 41.667 5.42 0.00 0.00 4.00
2593 2672 5.375283 TCAATTGGGACGGATAATAACCA 57.625 39.130 5.42 0.00 0.00 3.67
2595 2674 6.149633 GCAATCAATTGGGACGGATAATAAC 58.850 40.000 5.42 0.00 38.21 1.89
2596 2675 5.830457 TGCAATCAATTGGGACGGATAATAA 59.170 36.000 5.42 0.00 38.21 1.40
2597 2676 5.380900 TGCAATCAATTGGGACGGATAATA 58.619 37.500 5.42 0.00 38.21 0.98
2598 2677 4.214310 TGCAATCAATTGGGACGGATAAT 58.786 39.130 5.42 0.00 38.21 1.28
2600 2679 3.289407 TGCAATCAATTGGGACGGATA 57.711 42.857 5.42 0.00 38.21 2.59
2601 2680 2.142356 TGCAATCAATTGGGACGGAT 57.858 45.000 5.42 0.00 38.21 4.18
2602 2681 2.142356 ATGCAATCAATTGGGACGGA 57.858 45.000 5.42 0.00 38.21 4.69
2603 2682 2.542597 CAATGCAATCAATTGGGACGG 58.457 47.619 5.42 0.00 38.21 4.79
2604 2683 1.928503 GCAATGCAATCAATTGGGACG 59.071 47.619 5.42 0.00 38.21 4.79
2605 2684 3.255969 AGCAATGCAATCAATTGGGAC 57.744 42.857 8.35 0.00 38.21 4.46
2652 2731 3.942130 AAAATACTGGGTGCTTCAAGC 57.058 42.857 1.04 1.04 42.82 4.01
2655 2734 6.293735 CGTTAAGAAAAATACTGGGTGCTTCA 60.294 38.462 0.00 0.00 0.00 3.02
2656 2735 6.084277 CGTTAAGAAAAATACTGGGTGCTTC 58.916 40.000 0.00 0.00 0.00 3.86
2659 2738 5.366829 ACGTTAAGAAAAATACTGGGTGC 57.633 39.130 0.00 0.00 0.00 5.01
2679 2758 4.143242 GCATCCGTCATATCTGAATCAACG 60.143 45.833 0.00 0.00 31.85 4.10
2684 2763 3.055530 GGAGGCATCCGTCATATCTGAAT 60.056 47.826 0.00 0.00 35.37 2.57
2698 2777 4.458397 TCTGAATCAGAAATGGAGGCATC 58.542 43.478 10.99 0.00 37.57 3.91
2708 2787 9.676861 AGATGTTTGTCATATCTGAATCAGAAA 57.323 29.630 17.59 2.88 39.28 2.52
2722 2801 5.233083 TCAGAACTGGAGATGTTTGTCAT 57.767 39.130 1.93 0.00 39.77 3.06
2727 2806 7.013083 GCATCAATATCAGAACTGGAGATGTTT 59.987 37.037 0.00 0.00 34.43 2.83
2731 2810 5.558818 GGCATCAATATCAGAACTGGAGAT 58.441 41.667 1.93 0.00 0.00 2.75
2732 2811 4.502087 CGGCATCAATATCAGAACTGGAGA 60.502 45.833 1.93 0.00 0.00 3.71
2765 2844 4.033014 GCTGCTCTATAACGTCAAGGTTTC 59.967 45.833 0.00 0.00 0.00 2.78
2788 2873 4.832248 TCCAGTACATAAGCTCCAAGTTG 58.168 43.478 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.