Multiple sequence alignment - TraesCS6D01G355700

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 TraesCS6D01G355700 chr6D 100.000 3630 0 0 1 3630 450345725 450342096 0.000000e+00 6704.0
1 TraesCS6D01G355700 chr6D 90.228 614 38 15 958 1553 450488314 450488923 0.000000e+00 782.0
2 TraesCS6D01G355700 chr6D 80.585 376 49 14 2410 2763 450488924 450489297 5.970000e-68 268.0
3 TraesCS6D01G355700 chr6D 92.143 140 11 0 3010 3149 450489434 450489573 7.950000e-47 198.0
4 TraesCS6D01G355700 chr6A 97.011 2743 67 9 857 3591 595769042 595766307 0.000000e+00 4597.0
5 TraesCS6D01G355700 chr6A 88.196 1796 179 13 1148 2915 595892835 595894625 0.000000e+00 2111.0
6 TraesCS6D01G355700 chr6A 91.107 967 68 9 976 1933 595827738 595828695 0.000000e+00 1293.0
7 TraesCS6D01G355700 chr6A 89.905 842 50 16 53 869 595769889 595769058 0.000000e+00 1051.0
8 TraesCS6D01G355700 chr6A 100.000 43 0 0 3588 3630 595766280 595766238 3.000000e-11 80.5
9 TraesCS6D01G355700 chr6B 97.153 2353 62 3 930 3280 683486782 683489131 0.000000e+00 3969.0
10 TraesCS6D01G355700 chr6B 89.761 1719 154 16 976 2678 683647137 683648849 0.000000e+00 2180.0
11 TraesCS6D01G355700 chr6B 88.446 727 56 13 150 865 683499970 683499261 0.000000e+00 852.0
12 TraesCS6D01G355700 chr6B 93.860 342 18 2 3248 3586 683489067 683489408 2.500000e-141 512.0
13 TraesCS6D01G355700 chr6B 91.765 85 5 2 58 140 683500359 683500275 2.290000e-22 117.0
14 TraesCS6D01G355700 chr6B 100.000 43 0 0 3588 3630 683489440 683489482 3.000000e-11 80.5
15 TraesCS6D01G355700 chr1D 75.667 1500 300 44 1019 2496 21148445 21146989 0.000000e+00 688.0
16 TraesCS6D01G355700 chr1B 73.641 1582 303 67 1012 2541 26857179 26855660 1.160000e-139 507.0
17 TraesCS6D01G355700 chr4D 80.274 365 70 2 1593 1956 73966976 73966613 1.280000e-69 274.0
18 TraesCS6D01G355700 chr4D 97.436 39 1 0 3585 3623 419450660 419450698 2.340000e-07 67.6
19 TraesCS6D01G355700 chr3D 75.217 460 84 22 2095 2537 425999127 425998681 1.330000e-44 191.0
20 TraesCS6D01G355700 chr3D 81.884 138 19 4 3443 3578 565803218 565803351 1.070000e-20 111.0
21 TraesCS6D01G355700 chr1A 83.824 204 27 2 2983 3180 36119021 36118818 4.780000e-44 189.0
22 TraesCS6D01G355700 chr3B 73.753 461 96 17 2095 2541 556368977 556369426 1.350000e-34 158.0
23 TraesCS6D01G355700 chr7D 82.857 140 21 2 3454 3591 11616889 11616751 4.920000e-24 122.0
24 TraesCS6D01G355700 chr7D 95.238 42 2 0 3588 3629 11616724 11616683 2.340000e-07 67.6
25 TraesCS6D01G355700 chr3A 97.436 39 1 0 3585 3623 693451448 693451486 2.340000e-07 67.6


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 TraesCS6D01G355700 chr6D 450342096 450345725 3629 True 6704.0 6704 100.000000 1 3630 1 chr6D.!!$R1 3629
1 TraesCS6D01G355700 chr6D 450488314 450489573 1259 False 416.0 782 87.652000 958 3149 3 chr6D.!!$F1 2191
2 TraesCS6D01G355700 chr6A 595892835 595894625 1790 False 2111.0 2111 88.196000 1148 2915 1 chr6A.!!$F2 1767
3 TraesCS6D01G355700 chr6A 595766238 595769889 3651 True 1909.5 4597 95.638667 53 3630 3 chr6A.!!$R1 3577
4 TraesCS6D01G355700 chr6A 595827738 595828695 957 False 1293.0 1293 91.107000 976 1933 1 chr6A.!!$F1 957
5 TraesCS6D01G355700 chr6B 683647137 683648849 1712 False 2180.0 2180 89.761000 976 2678 1 chr6B.!!$F1 1702
6 TraesCS6D01G355700 chr6B 683486782 683489482 2700 False 1520.5 3969 97.004333 930 3630 3 chr6B.!!$F2 2700
7 TraesCS6D01G355700 chr6B 683499261 683500359 1098 True 484.5 852 90.105500 58 865 2 chr6B.!!$R1 807
8 TraesCS6D01G355700 chr1D 21146989 21148445 1456 True 688.0 688 75.667000 1019 2496 1 chr1D.!!$R1 1477
9 TraesCS6D01G355700 chr1B 26855660 26857179 1519 True 507.0 507 73.641000 1012 2541 1 chr1B.!!$R1 1529

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
126 128 0.317160 TCGCGGCCCTATAATCACAG 59.683 55.000 6.13 0.0 0.0 3.66 F
545 851 0.321653 CAGGGGCTGGTAGACACAAC 60.322 60.000 0.00 0.0 0.0 3.32 F
546 852 0.766674 AGGGGCTGGTAGACACAACA 60.767 55.000 0.00 0.0 0.0 3.33 F
1572 1942 1.153628 CTACCGCTTTCCCCACGAG 60.154 63.158 0.00 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1608 1990 1.210478 AGCATGCAGTAGTTACCCAGG 59.790 52.381 21.98 0.0 0.00 4.45 R
2106 2500 3.066760 CGACAAGGAGCTTTTTGAGGTTT 59.933 43.478 15.50 0.0 35.91 3.27 R
2489 2914 4.141869 GCTTGCACCCAGATTGGATTATTT 60.142 41.667 0.00 0.0 40.96 1.40 R
2906 3366 0.184451 AGGTGGTGGGATCATCATGC 59.816 55.000 0.00 0.0 36.28 4.06 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
19 20 2.715749 ATTCGATGGCTGGATGTGAA 57.284 45.000 0.00 0.00 0.00 3.18
20 21 1.737838 TTCGATGGCTGGATGTGAAC 58.262 50.000 0.00 0.00 0.00 3.18
21 22 0.612744 TCGATGGCTGGATGTGAACA 59.387 50.000 0.00 0.00 0.00 3.18
22 23 1.003003 TCGATGGCTGGATGTGAACAA 59.997 47.619 0.00 0.00 0.00 2.83
23 24 1.811965 CGATGGCTGGATGTGAACAAA 59.188 47.619 0.00 0.00 0.00 2.83
24 25 2.424601 CGATGGCTGGATGTGAACAAAT 59.575 45.455 0.00 0.00 0.00 2.32
25 26 3.488047 CGATGGCTGGATGTGAACAAATC 60.488 47.826 0.00 0.00 0.00 2.17
26 27 1.811965 TGGCTGGATGTGAACAAATCG 59.188 47.619 0.00 0.00 0.00 3.34
27 28 1.812571 GGCTGGATGTGAACAAATCGT 59.187 47.619 0.00 0.00 0.00 3.73
28 29 2.414559 GGCTGGATGTGAACAAATCGTG 60.415 50.000 0.00 0.00 0.00 4.35
29 30 2.855180 CTGGATGTGAACAAATCGTGC 58.145 47.619 0.00 0.00 0.00 5.34
30 31 2.225467 TGGATGTGAACAAATCGTGCA 58.775 42.857 0.00 0.00 0.00 4.57
31 32 2.819019 TGGATGTGAACAAATCGTGCAT 59.181 40.909 0.00 0.00 34.87 3.96
32 33 3.255395 TGGATGTGAACAAATCGTGCATT 59.745 39.130 0.00 0.00 34.87 3.56
33 34 3.609373 GGATGTGAACAAATCGTGCATTG 59.391 43.478 0.00 0.00 34.87 2.82
34 35 3.978718 TGTGAACAAATCGTGCATTGA 57.021 38.095 4.82 0.00 34.87 2.57
35 36 4.502171 TGTGAACAAATCGTGCATTGAT 57.498 36.364 4.82 1.87 34.87 2.57
36 37 4.228317 TGTGAACAAATCGTGCATTGATG 58.772 39.130 4.82 0.00 34.87 3.07
37 38 4.229096 GTGAACAAATCGTGCATTGATGT 58.771 39.130 4.82 0.00 34.87 3.06
38 39 4.321745 GTGAACAAATCGTGCATTGATGTC 59.678 41.667 4.82 2.78 34.87 3.06
39 40 3.121559 ACAAATCGTGCATTGATGTCG 57.878 42.857 4.82 0.00 0.00 4.35
40 41 2.483877 ACAAATCGTGCATTGATGTCGT 59.516 40.909 4.82 1.34 0.00 4.34
41 42 2.811902 AATCGTGCATTGATGTCGTG 57.188 45.000 5.30 0.00 0.00 4.35
42 43 1.725641 ATCGTGCATTGATGTCGTGT 58.274 45.000 3.84 0.00 0.00 4.49
43 44 0.789601 TCGTGCATTGATGTCGTGTG 59.210 50.000 0.00 0.00 0.00 3.82
44 45 0.512518 CGTGCATTGATGTCGTGTGT 59.487 50.000 0.00 0.00 0.00 3.72
45 46 1.724082 CGTGCATTGATGTCGTGTGTA 59.276 47.619 0.00 0.00 0.00 2.90
46 47 2.348362 CGTGCATTGATGTCGTGTGTAT 59.652 45.455 0.00 0.00 0.00 2.29
47 48 3.549873 CGTGCATTGATGTCGTGTGTATA 59.450 43.478 0.00 0.00 0.00 1.47
48 49 4.317348 CGTGCATTGATGTCGTGTGTATAG 60.317 45.833 0.00 0.00 0.00 1.31
49 50 3.555547 TGCATTGATGTCGTGTGTATAGC 59.444 43.478 0.00 0.00 0.00 2.97
50 51 3.555547 GCATTGATGTCGTGTGTATAGCA 59.444 43.478 0.00 0.00 0.00 3.49
51 52 4.318333 GCATTGATGTCGTGTGTATAGCAG 60.318 45.833 0.00 0.00 0.00 4.24
52 53 2.809446 TGATGTCGTGTGTATAGCAGC 58.191 47.619 0.00 0.00 0.00 5.25
53 54 1.781429 GATGTCGTGTGTATAGCAGCG 59.219 52.381 0.00 0.00 0.00 5.18
54 55 0.524414 TGTCGTGTGTATAGCAGCGT 59.476 50.000 0.00 0.00 0.00 5.07
55 56 1.068125 TGTCGTGTGTATAGCAGCGTT 60.068 47.619 0.00 0.00 0.00 4.84
56 57 1.320555 GTCGTGTGTATAGCAGCGTTG 59.679 52.381 0.00 0.00 0.00 4.10
57 58 1.200484 TCGTGTGTATAGCAGCGTTGA 59.800 47.619 2.38 0.00 0.00 3.18
78 79 5.175859 TGAATAGAGATTTTTCGAGCGGTT 58.824 37.500 0.00 0.00 0.00 4.44
126 128 0.317160 TCGCGGCCCTATAATCACAG 59.683 55.000 6.13 0.00 0.00 3.66
128 130 1.797025 GCGGCCCTATAATCACAGAC 58.203 55.000 0.00 0.00 0.00 3.51
143 145 3.056107 TCACAGACGGAGGGAGTAAATTG 60.056 47.826 0.00 0.00 0.00 2.32
242 539 0.924090 CGATAGAGCGACAACAAGGC 59.076 55.000 0.00 0.00 39.76 4.35
303 609 4.989279 AACACTTTGTTGACTGCTCATT 57.011 36.364 0.00 0.00 39.45 2.57
311 617 3.563808 TGTTGACTGCTCATTAACCACAC 59.436 43.478 0.00 0.00 0.00 3.82
337 643 2.559381 AGGTGGCTCTCTACAAGGAT 57.441 50.000 0.00 0.00 0.00 3.24
344 650 6.183360 GGTGGCTCTCTACAAGGATAACAATA 60.183 42.308 0.00 0.00 0.00 1.90
375 681 6.619744 TGTGCAACCACACTTATTATTCATG 58.380 36.000 0.00 0.00 46.51 3.07
376 682 6.432472 TGTGCAACCACACTTATTATTCATGA 59.568 34.615 0.00 0.00 46.51 3.07
383 689 9.113838 ACCACACTTATTATTCATGAATGAGTC 57.886 33.333 27.59 0.00 38.19 3.36
384 690 8.562892 CCACACTTATTATTCATGAATGAGTCC 58.437 37.037 27.59 0.00 38.19 3.85
419 725 4.519350 CACTAGCGTCTCCATCCACTATTA 59.481 45.833 0.00 0.00 0.00 0.98
420 726 5.009710 CACTAGCGTCTCCATCCACTATTAA 59.990 44.000 0.00 0.00 0.00 1.40
446 752 2.704572 GACAGAACCCATGAAGACCTG 58.295 52.381 0.00 0.00 0.00 4.00
448 754 1.630369 CAGAACCCATGAAGACCTGGA 59.370 52.381 0.00 0.00 34.45 3.86
467 773 1.337071 GATGGCTGGATTAGACGACGA 59.663 52.381 0.00 0.00 37.17 4.20
543 849 2.592993 GCAGGGGCTGGTAGACACA 61.593 63.158 0.00 0.00 36.96 3.72
545 851 0.321653 CAGGGGCTGGTAGACACAAC 60.322 60.000 0.00 0.00 0.00 3.32
546 852 0.766674 AGGGGCTGGTAGACACAACA 60.767 55.000 0.00 0.00 0.00 3.33
573 880 3.067601 TCACAATATAGTCGACGCCACAT 59.932 43.478 10.46 2.73 0.00 3.21
650 957 7.497909 GGTAGCAACACAAGGATATTTAGCTAA 59.502 37.037 0.86 0.86 33.31 3.09
709 1016 8.356000 TCAGGTCCAACTAAGAAAAAGAAAAA 57.644 30.769 0.00 0.00 0.00 1.94
747 1054 7.487189 CGTGTCCAATACTTACTAGAAAACGAT 59.513 37.037 0.00 0.00 0.00 3.73
766 1073 4.208460 ACGATCCAATTACAACGCTAATCG 59.792 41.667 0.00 0.00 45.38 3.34
769 1076 6.346598 CGATCCAATTACAACGCTAATCGAAT 60.347 38.462 0.00 0.00 41.67 3.34
772 1079 7.184106 TCCAATTACAACGCTAATCGAATTTC 58.816 34.615 0.00 0.00 41.67 2.17
795 1102 4.156008 CCTTTTTGCAGGTAAGCTAATCGT 59.844 41.667 0.00 0.00 34.99 3.73
797 1104 6.417191 TTTTTGCAGGTAAGCTAATCGTAG 57.583 37.500 0.00 0.00 34.99 3.51
810 1128 5.536916 AGCTAATCGTAGATGTTTAGGAGCT 59.463 40.000 0.00 0.00 45.12 4.09
811 1129 6.715718 AGCTAATCGTAGATGTTTAGGAGCTA 59.284 38.462 0.00 0.00 45.12 3.32
817 1135 6.430308 TCGTAGATGTTTAGGAGCTATACCAG 59.570 42.308 0.00 0.00 0.00 4.00
820 1138 6.621394 AGATGTTTAGGAGCTATACCAGGTA 58.379 40.000 0.39 0.39 34.30 3.08
826 1144 3.705072 AGGAGCTATACCAGGTAACACAC 59.295 47.826 2.53 0.00 34.30 3.82
1474 1844 2.678580 TCGACCACCTGATCGCCA 60.679 61.111 0.00 0.00 38.24 5.69
1504 1874 1.925888 GCATGGGGAGTGGAGGATT 59.074 57.895 0.00 0.00 0.00 3.01
1572 1942 1.153628 CTACCGCTTTCCCCACGAG 60.154 63.158 0.00 0.00 0.00 4.18
1608 1990 3.435186 GGCCTTCGCAGCTTGACC 61.435 66.667 0.00 0.00 36.38 4.02
1787 2172 1.951510 CACATGACTGTGTGGTGGC 59.048 57.895 0.00 0.00 46.33 5.01
2489 2914 3.694043 TGATGAAATGGTCGTGAGGAA 57.306 42.857 0.00 0.00 0.00 3.36
2567 2992 0.316204 GCTTGGCATTGCAGACTTGT 59.684 50.000 11.39 0.00 0.00 3.16
2599 3025 0.033504 GGGATATTCGGCTTCGCTGA 59.966 55.000 0.00 0.00 42.66 4.26
2906 3366 1.153168 CGCCAACCTACATCCTGGG 60.153 63.158 0.00 0.00 0.00 4.45
2973 3433 1.734465 GGCAGCCTCGACATATAATGC 59.266 52.381 3.29 0.00 0.00 3.56
3008 3468 1.369839 TTTGGAACGCGCACACAGAA 61.370 50.000 5.73 0.00 0.00 3.02
3227 3687 2.330216 AGGCACTCTTGGTTAGACACT 58.670 47.619 0.00 0.00 0.00 3.55
3272 3762 6.650120 TGGTTAGACACTCTCTTCTTTTGTT 58.350 36.000 0.00 0.00 0.00 2.83
3273 3763 7.110155 TGGTTAGACACTCTCTTCTTTTGTTT 58.890 34.615 0.00 0.00 0.00 2.83
3274 3764 7.610305 TGGTTAGACACTCTCTTCTTTTGTTTT 59.390 33.333 0.00 0.00 0.00 2.43
3275 3765 8.459635 GGTTAGACACTCTCTTCTTTTGTTTTT 58.540 33.333 0.00 0.00 0.00 1.94
3299 3789 9.936759 TTTTTGTTGGTTAGACATTTTCTTCTT 57.063 25.926 0.00 0.00 35.55 2.52
3300 3790 9.936759 TTTTGTTGGTTAGACATTTTCTTCTTT 57.063 25.926 0.00 0.00 35.55 2.52
3301 3791 9.936759 TTTGTTGGTTAGACATTTTCTTCTTTT 57.063 25.926 0.00 0.00 35.55 2.27
3302 3792 8.925161 TGTTGGTTAGACATTTTCTTCTTTTG 57.075 30.769 0.00 0.00 35.55 2.44
3303 3793 8.527810 TGTTGGTTAGACATTTTCTTCTTTTGT 58.472 29.630 0.00 0.00 35.55 2.83
3312 3802 9.567848 GACATTTTCTTCTTTTGTTGTCTTGTA 57.432 29.630 0.00 0.00 31.78 2.41
3345 3835 5.761726 GTGAGATCAATGATATGCTGGAACA 59.238 40.000 0.00 0.00 0.00 3.18
3346 3836 6.261603 GTGAGATCAATGATATGCTGGAACAA 59.738 38.462 0.00 0.00 38.70 2.83
3390 3880 6.017400 ACTGAATTCCACACAAATGCTTAG 57.983 37.500 2.27 0.00 0.00 2.18
3391 3881 5.047802 ACTGAATTCCACACAAATGCTTAGG 60.048 40.000 2.27 0.00 0.00 2.69
3392 3882 4.832266 TGAATTCCACACAAATGCTTAGGT 59.168 37.500 2.27 0.00 0.00 3.08
3393 3883 6.007076 TGAATTCCACACAAATGCTTAGGTA 58.993 36.000 2.27 0.00 0.00 3.08
3394 3884 5.897377 ATTCCACACAAATGCTTAGGTAC 57.103 39.130 0.00 0.00 0.00 3.34
3447 3941 6.532657 CACATTATCAGCCATTGTTCTTTTCC 59.467 38.462 0.00 0.00 0.00 3.13
3451 3945 5.200368 TCAGCCATTGTTCTTTTCCTTTC 57.800 39.130 0.00 0.00 0.00 2.62
3452 3946 4.039124 TCAGCCATTGTTCTTTTCCTTTCC 59.961 41.667 0.00 0.00 0.00 3.13
3580 4074 5.499004 TCAGTTCTACCAAAACTAGCCAT 57.501 39.130 0.00 0.00 35.25 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.003003 TGTTCACATCCAGCCATCGAA 59.997 47.619 0.00 0.00 0.00 3.71
6 7 1.811965 CGATTTGTTCACATCCAGCCA 59.188 47.619 0.00 0.00 0.00 4.75
10 11 2.225467 TGCACGATTTGTTCACATCCA 58.775 42.857 0.00 0.00 0.00 3.41
11 12 2.987413 TGCACGATTTGTTCACATCC 57.013 45.000 0.00 0.00 0.00 3.51
12 13 4.475028 TCAATGCACGATTTGTTCACATC 58.525 39.130 0.00 0.00 0.00 3.06
13 14 4.502171 TCAATGCACGATTTGTTCACAT 57.498 36.364 0.00 0.00 0.00 3.21
14 15 3.978718 TCAATGCACGATTTGTTCACA 57.021 38.095 0.00 0.00 0.00 3.58
15 16 4.229096 ACATCAATGCACGATTTGTTCAC 58.771 39.130 0.00 0.00 0.00 3.18
16 17 4.475028 GACATCAATGCACGATTTGTTCA 58.525 39.130 0.00 0.00 0.00 3.18
17 18 3.539563 CGACATCAATGCACGATTTGTTC 59.460 43.478 0.00 0.00 34.53 3.18
18 19 3.058293 ACGACATCAATGCACGATTTGTT 60.058 39.130 14.00 0.00 35.80 2.83
19 20 2.483877 ACGACATCAATGCACGATTTGT 59.516 40.909 14.00 0.00 35.80 2.83
20 21 2.841907 CACGACATCAATGCACGATTTG 59.158 45.455 14.00 0.00 35.80 2.32
21 22 2.483877 ACACGACATCAATGCACGATTT 59.516 40.909 14.00 0.00 35.80 2.17
22 23 2.076100 ACACGACATCAATGCACGATT 58.924 42.857 14.00 0.00 35.80 3.34
23 24 1.394572 CACACGACATCAATGCACGAT 59.605 47.619 14.00 0.00 35.80 3.73
24 25 0.789601 CACACGACATCAATGCACGA 59.210 50.000 14.00 0.00 35.80 4.35
25 26 0.512518 ACACACGACATCAATGCACG 59.487 50.000 0.00 8.06 37.09 5.34
26 27 4.550831 GCTATACACACGACATCAATGCAC 60.551 45.833 0.00 0.00 0.00 4.57
27 28 3.555547 GCTATACACACGACATCAATGCA 59.444 43.478 0.00 0.00 0.00 3.96
28 29 3.555547 TGCTATACACACGACATCAATGC 59.444 43.478 0.00 0.00 0.00 3.56
29 30 4.318333 GCTGCTATACACACGACATCAATG 60.318 45.833 0.00 0.00 0.00 2.82
30 31 3.804325 GCTGCTATACACACGACATCAAT 59.196 43.478 0.00 0.00 0.00 2.57
31 32 3.186909 GCTGCTATACACACGACATCAA 58.813 45.455 0.00 0.00 0.00 2.57
32 33 2.794631 CGCTGCTATACACACGACATCA 60.795 50.000 0.00 0.00 0.00 3.07
33 34 1.781429 CGCTGCTATACACACGACATC 59.219 52.381 0.00 0.00 0.00 3.06
34 35 1.134367 ACGCTGCTATACACACGACAT 59.866 47.619 0.00 0.00 0.00 3.06
35 36 0.524414 ACGCTGCTATACACACGACA 59.476 50.000 0.00 0.00 0.00 4.35
36 37 1.320555 CAACGCTGCTATACACACGAC 59.679 52.381 0.00 0.00 0.00 4.34
37 38 1.200484 TCAACGCTGCTATACACACGA 59.800 47.619 0.00 0.00 0.00 4.35
38 39 1.624487 TCAACGCTGCTATACACACG 58.376 50.000 0.00 0.00 0.00 4.49
39 40 5.041287 TCTATTCAACGCTGCTATACACAC 58.959 41.667 0.00 0.00 0.00 3.82
40 41 5.067283 TCTCTATTCAACGCTGCTATACACA 59.933 40.000 0.00 0.00 0.00 3.72
41 42 5.520632 TCTCTATTCAACGCTGCTATACAC 58.479 41.667 0.00 0.00 0.00 2.90
42 43 5.767816 TCTCTATTCAACGCTGCTATACA 57.232 39.130 0.00 0.00 0.00 2.29
43 44 7.644986 AAATCTCTATTCAACGCTGCTATAC 57.355 36.000 0.00 0.00 0.00 1.47
44 45 8.662781 AAAAATCTCTATTCAACGCTGCTATA 57.337 30.769 0.00 0.00 0.00 1.31
45 46 7.517417 CGAAAAATCTCTATTCAACGCTGCTAT 60.517 37.037 0.00 0.00 0.00 2.97
46 47 6.237835 CGAAAAATCTCTATTCAACGCTGCTA 60.238 38.462 0.00 0.00 0.00 3.49
47 48 5.446473 CGAAAAATCTCTATTCAACGCTGCT 60.446 40.000 0.00 0.00 0.00 4.24
48 49 4.725754 CGAAAAATCTCTATTCAACGCTGC 59.274 41.667 0.00 0.00 0.00 5.25
49 50 6.094739 TCGAAAAATCTCTATTCAACGCTG 57.905 37.500 0.00 0.00 0.00 5.18
50 51 5.220491 GCTCGAAAAATCTCTATTCAACGCT 60.220 40.000 0.00 0.00 0.00 5.07
51 52 4.958563 GCTCGAAAAATCTCTATTCAACGC 59.041 41.667 0.00 0.00 0.00 4.84
52 53 5.183919 CGCTCGAAAAATCTCTATTCAACG 58.816 41.667 0.00 0.00 0.00 4.10
53 54 5.063564 ACCGCTCGAAAAATCTCTATTCAAC 59.936 40.000 0.00 0.00 0.00 3.18
54 55 5.175859 ACCGCTCGAAAAATCTCTATTCAA 58.824 37.500 0.00 0.00 0.00 2.69
55 56 4.755411 ACCGCTCGAAAAATCTCTATTCA 58.245 39.130 0.00 0.00 0.00 2.57
56 57 5.720261 AACCGCTCGAAAAATCTCTATTC 57.280 39.130 0.00 0.00 0.00 1.75
57 58 7.605410 TTAAACCGCTCGAAAAATCTCTATT 57.395 32.000 0.00 0.00 0.00 1.73
126 128 4.732672 AGTACAATTTACTCCCTCCGTC 57.267 45.455 0.00 0.00 0.00 4.79
128 130 8.502105 AAAAATAGTACAATTTACTCCCTCCG 57.498 34.615 0.00 0.00 0.00 4.63
242 539 2.365635 AGGGAGATGGGGTGGACG 60.366 66.667 0.00 0.00 0.00 4.79
243 540 0.264955 TAGAGGGAGATGGGGTGGAC 59.735 60.000 0.00 0.00 0.00 4.02
303 609 2.370349 CCACCTTTGTGTGTGTGGTTA 58.630 47.619 0.00 0.00 42.61 2.85
311 617 2.224281 TGTAGAGAGCCACCTTTGTGTG 60.224 50.000 0.00 0.00 41.09 3.82
375 681 0.924090 GTCATGTCGCGGACTCATTC 59.076 55.000 6.13 0.00 33.15 2.67
376 682 0.246360 TGTCATGTCGCGGACTCATT 59.754 50.000 6.13 0.00 35.11 2.57
383 689 1.413767 GCTAGTGTGTCATGTCGCGG 61.414 60.000 6.13 0.00 0.00 6.46
384 690 1.733416 CGCTAGTGTGTCATGTCGCG 61.733 60.000 0.00 0.00 0.00 5.87
419 725 1.167851 CATGGGTTCTGTCGCACATT 58.832 50.000 0.00 0.00 33.39 2.71
420 726 0.324614 TCATGGGTTCTGTCGCACAT 59.675 50.000 0.00 0.00 33.39 3.21
446 752 1.603172 CGTCGTCTAATCCAGCCATCC 60.603 57.143 0.00 0.00 0.00 3.51
448 754 1.067212 GTCGTCGTCTAATCCAGCCAT 59.933 52.381 0.00 0.00 0.00 4.40
467 773 5.221009 GGTTTTAGATCCGATACTCGACAGT 60.221 44.000 0.00 0.00 43.74 3.55
543 849 6.807708 GTCGACTATATTGTGACGATTGTT 57.192 37.500 8.70 0.00 33.78 2.83
573 880 1.134367 GTGACCGATTGTCCTCGATCA 59.866 52.381 0.00 0.00 43.78 2.92
747 1054 6.671614 AATTCGATTAGCGTTGTAATTGGA 57.328 33.333 0.00 0.00 41.80 3.53
766 1073 5.541845 AGCTTACCTGCAAAAAGGAAATTC 58.458 37.500 0.00 0.00 40.02 2.17
769 1076 6.569610 CGATTAGCTTACCTGCAAAAAGGAAA 60.570 38.462 0.00 0.00 40.02 3.13
772 1079 4.156008 ACGATTAGCTTACCTGCAAAAAGG 59.844 41.667 0.00 0.00 43.57 3.11
795 1102 6.621394 ACCTGGTATAGCTCCTAAACATCTA 58.379 40.000 0.00 0.00 0.00 1.98
797 1104 5.810080 ACCTGGTATAGCTCCTAAACATC 57.190 43.478 0.00 0.00 0.00 3.06
810 1128 3.164268 ACCACGTGTGTTACCTGGTATA 58.836 45.455 15.65 0.00 43.89 1.47
811 1129 1.972795 ACCACGTGTGTTACCTGGTAT 59.027 47.619 15.65 0.00 43.89 2.73
817 1135 1.868469 TGCTTACCACGTGTGTTACC 58.132 50.000 15.65 4.71 0.00 2.85
820 1138 2.946329 TGAATTGCTTACCACGTGTGTT 59.054 40.909 15.65 0.52 0.00 3.32
826 1144 5.390567 GGAGTAGTTTGAATTGCTTACCACG 60.391 44.000 0.00 0.00 0.00 4.94
1463 1833 4.457496 CTGCGGTGGCGATCAGGT 62.457 66.667 0.00 0.00 44.10 4.00
1504 1874 2.429930 CCTGGCAACGACCTCCAA 59.570 61.111 0.00 0.00 42.51 3.53
1608 1990 1.210478 AGCATGCAGTAGTTACCCAGG 59.790 52.381 21.98 0.00 0.00 4.45
2105 2499 4.440112 CGACAAGGAGCTTTTTGAGGTTTT 60.440 41.667 15.50 0.00 35.91 2.43
2106 2500 3.066760 CGACAAGGAGCTTTTTGAGGTTT 59.933 43.478 15.50 0.00 35.91 3.27
2489 2914 4.141869 GCTTGCACCCAGATTGGATTATTT 60.142 41.667 0.00 0.00 40.96 1.40
2567 2992 4.833380 CCGAATATCCCTTCCAACTCTCTA 59.167 45.833 0.00 0.00 0.00 2.43
2599 3025 3.067601 GGTCGTTTCATTCAAACCTTGGT 59.932 43.478 0.00 0.00 41.40 3.67
2818 3278 1.807742 TGCTAATTTTTGCTACCGCGT 59.192 42.857 4.92 0.00 39.65 6.01
2825 3285 4.248058 GCTCAATGGTGCTAATTTTTGCT 58.752 39.130 0.00 0.00 0.00 3.91
2906 3366 0.184451 AGGTGGTGGGATCATCATGC 59.816 55.000 0.00 0.00 36.28 4.06
2973 3433 2.888513 CAAAGCATGGAAGTGTCGAG 57.111 50.000 0.00 0.00 0.00 4.04
3008 3468 6.400568 CCAGATGAACATTTTGCATTTAGGT 58.599 36.000 0.00 0.00 0.00 3.08
3191 3651 2.813754 GTGCCTAACTGCAACAAGATGA 59.186 45.455 0.00 0.00 44.11 2.92
3227 3687 5.710099 ACCAACAAGACAACAAAAGAAGAGA 59.290 36.000 0.00 0.00 0.00 3.10
3273 3763 9.936759 AAGAAGAAAATGTCTAACCAACAAAAA 57.063 25.926 0.00 0.00 34.56 1.94
3274 3764 9.936759 AAAGAAGAAAATGTCTAACCAACAAAA 57.063 25.926 0.00 0.00 34.56 2.44
3275 3765 9.936759 AAAAGAAGAAAATGTCTAACCAACAAA 57.063 25.926 0.00 0.00 34.56 2.83
3276 3766 9.364989 CAAAAGAAGAAAATGTCTAACCAACAA 57.635 29.630 0.00 0.00 34.56 2.83
3277 3767 8.527810 ACAAAAGAAGAAAATGTCTAACCAACA 58.472 29.630 0.00 0.00 34.56 3.33
3278 3768 8.926715 ACAAAAGAAGAAAATGTCTAACCAAC 57.073 30.769 0.00 0.00 34.56 3.77
3279 3769 9.364989 CAACAAAAGAAGAAAATGTCTAACCAA 57.635 29.630 0.00 0.00 34.56 3.67
3280 3770 8.527810 ACAACAAAAGAAGAAAATGTCTAACCA 58.472 29.630 0.00 0.00 34.56 3.67
3281 3771 8.926715 ACAACAAAAGAAGAAAATGTCTAACC 57.073 30.769 0.00 0.00 34.56 2.85
3282 3772 9.788960 AGACAACAAAAGAAGAAAATGTCTAAC 57.211 29.630 3.47 0.00 43.07 2.34
3284 3774 9.787532 CAAGACAACAAAAGAAGAAAATGTCTA 57.212 29.630 5.62 0.00 43.82 2.59
3285 3775 8.306761 ACAAGACAACAAAAGAAGAAAATGTCT 58.693 29.630 0.00 0.00 45.83 3.41
3286 3776 8.466086 ACAAGACAACAAAAGAAGAAAATGTC 57.534 30.769 0.00 0.00 36.95 3.06
3302 3792 7.169035 TCTCACGTTGTTAATACAAGACAAC 57.831 36.000 8.17 8.17 44.53 3.32
3303 3793 7.654116 TGATCTCACGTTGTTAATACAAGACAA 59.346 33.333 0.00 0.00 44.53 3.18
3312 3802 8.285394 GCATATCATTGATCTCACGTTGTTAAT 58.715 33.333 1.55 0.00 0.00 1.40
3380 3870 8.087750 TGAAATCCTTTTGTACCTAAGCATTTG 58.912 33.333 9.46 0.00 25.45 2.32
3580 4074 9.917129 TTCGAGAAACTTGTATTACTGATTGTA 57.083 29.630 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.