Multiple sequence alignment - TraesCS7D01G218200

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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 TraesCS7D01G218200 chr7D 100.000 6301 0 0 269 6569 178863116 178856816 0.000000e+00 11636.0
1 TraesCS7D01G218200 chr7D 92.769 1466 99 3 1469 2927 178940722 178939257 0.000000e+00 2113.0
2 TraesCS7D01G218200 chr7D 94.937 1264 51 3 3180 4430 178939175 178937912 0.000000e+00 1967.0
3 TraesCS7D01G218200 chr7D 89.175 1552 150 12 1482 3020 179123587 179122041 0.000000e+00 1919.0
4 TraesCS7D01G218200 chr7D 87.916 1142 65 28 4454 5555 178937936 178936828 0.000000e+00 1277.0
5 TraesCS7D01G218200 chr7D 89.320 618 55 7 768 1380 179124245 179123634 0.000000e+00 765.0
6 TraesCS7D01G218200 chr7D 82.650 634 60 21 289 877 178942129 178941501 3.510000e-142 516.0
7 TraesCS7D01G218200 chr7D 76.278 978 198 27 3373 4327 178990013 178989047 2.130000e-134 490.0
8 TraesCS7D01G218200 chr7D 86.316 475 36 6 298 768 179124752 179124303 2.130000e-134 490.0
9 TraesCS7D01G218200 chr7D 87.775 409 34 9 6136 6531 178936213 178935808 1.290000e-126 464.0
10 TraesCS7D01G218200 chr7D 84.524 252 21 7 5605 5856 178936819 178936586 3.960000e-57 233.0
11 TraesCS7D01G218200 chr7D 97.938 97 2 0 3088 3184 179122042 179121946 1.130000e-37 169.0
12 TraesCS7D01G218200 chr7D 88.636 132 14 1 5898 6029 178936498 178936368 6.820000e-35 159.0
13 TraesCS7D01G218200 chr7D 90.090 111 6 1 3180 3290 179121866 179121761 8.880000e-29 139.0
14 TraesCS7D01G218200 chr7D 100.000 37 0 0 1 37 178863384 178863348 1.180000e-07 69.4
15 TraesCS7D01G218200 chr7A 98.057 2831 51 3 355 3184 183310102 183307275 0.000000e+00 4920.0
16 TraesCS7D01G218200 chr7A 97.426 2020 39 3 3180 5186 183307195 183305176 0.000000e+00 3430.0
17 TraesCS7D01G218200 chr7A 92.721 1470 96 6 1467 2927 183483281 183481814 0.000000e+00 2111.0
18 TraesCS7D01G218200 chr7A 95.174 1264 48 3 3180 4430 183654293 183653030 0.000000e+00 1984.0
19 TraesCS7D01G218200 chr7A 94.937 1264 51 3 3180 4430 183481732 183480469 0.000000e+00 1967.0
20 TraesCS7D01G218200 chr7A 88.148 1544 153 12 1482 3020 183655986 183654468 0.000000e+00 1810.0
21 TraesCS7D01G218200 chr7A 89.626 1311 110 9 1460 2760 182856933 182855639 0.000000e+00 1644.0
22 TraesCS7D01G218200 chr7A 94.952 733 37 0 4454 5186 183480493 183479761 0.000000e+00 1149.0
23 TraesCS7D01G218200 chr7A 93.179 733 41 3 4454 5186 183653054 183652331 0.000000e+00 1068.0
24 TraesCS7D01G218200 chr7A 89.130 598 48 6 836 1421 183656588 183655996 0.000000e+00 728.0
25 TraesCS7D01G218200 chr7A 87.175 577 45 7 269 841 183657247 183656696 4.320000e-176 628.0
26 TraesCS7D01G218200 chr7A 83.255 639 57 21 284 877 183484716 183484083 5.790000e-150 542.0
27 TraesCS7D01G218200 chr7A 91.496 341 22 3 277 612 182858659 182858321 4.640000e-126 462.0
28 TraesCS7D01G218200 chr7A 87.136 412 39 9 5364 5770 183652213 183651811 7.760000e-124 455.0
29 TraesCS7D01G218200 chr7A 96.139 259 10 0 3369 3627 182855638 182855380 2.190000e-114 424.0
30 TraesCS7D01G218200 chr7A 87.164 335 29 7 1143 1467 182857298 182856968 1.040000e-97 368.0
31 TraesCS7D01G218200 chr7A 90.335 269 14 5 6247 6515 182861139 182860883 6.310000e-90 342.0
32 TraesCS7D01G218200 chr7A 83.120 391 35 17 6136 6521 183404917 183404553 1.770000e-85 327.0
33 TraesCS7D01G218200 chr7A 91.213 239 16 5 625 860 182858003 182857767 2.960000e-83 320.0
34 TraesCS7D01G218200 chr7A 85.765 281 29 6 5579 5856 183405555 183405283 3.000000e-73 287.0
35 TraesCS7D01G218200 chr7A 98.969 97 1 0 3088 3184 183654469 183654373 2.430000e-39 174.0
36 TraesCS7D01G218200 chr7A 82.286 175 22 7 894 1061 183483980 183483808 6.870000e-30 143.0
37 TraesCS7D01G218200 chr7A 95.745 47 1 1 5193 5238 183479734 183479688 2.540000e-09 75.0
38 TraesCS7D01G218200 chr7B 94.695 2922 119 22 269 3184 144737874 144734983 0.000000e+00 4505.0
39 TraesCS7D01G218200 chr7B 93.211 2887 137 16 3180 6039 144734903 144732049 0.000000e+00 4191.0
40 TraesCS7D01G218200 chr7B 92.653 1470 97 6 1467 2927 144813428 144811961 0.000000e+00 2106.0
41 TraesCS7D01G218200 chr7B 94.778 1264 53 3 3180 4430 144811879 144810616 0.000000e+00 1956.0
42 TraesCS7D01G218200 chr7B 89.132 1555 152 9 1478 3020 145055224 145053675 0.000000e+00 1919.0
43 TraesCS7D01G218200 chr7B 92.812 1266 71 5 3180 4430 145053500 145052240 0.000000e+00 1816.0
44 TraesCS7D01G218200 chr7B 89.122 1241 86 14 315 1538 145056426 145055218 0.000000e+00 1498.0
45 TraesCS7D01G218200 chr7B 95.225 733 35 0 4454 5186 144810640 144809908 0.000000e+00 1160.0
46 TraesCS7D01G218200 chr7B 94.407 733 32 3 4455 5187 145052263 145051540 0.000000e+00 1118.0
47 TraesCS7D01G218200 chr7B 76.758 981 188 29 3373 4327 145028609 145027643 4.540000e-141 512.0
48 TraesCS7D01G218200 chr7B 86.994 469 42 11 5394 5856 144809699 144809244 1.630000e-140 510.0
49 TraesCS7D01G218200 chr7B 82.927 615 56 24 309 877 144814805 144814194 5.880000e-140 508.0
50 TraesCS7D01G218200 chr7B 86.005 393 36 11 6136 6522 144808874 144808495 2.850000e-108 403.0
51 TraesCS7D01G218200 chr7B 86.435 317 29 10 5363 5671 145051422 145051112 1.060000e-87 335.0
52 TraesCS7D01G218200 chr7B 96.907 97 3 0 3088 3184 145053676 145053580 5.270000e-36 163.0
53 TraesCS7D01G218200 chr7B 86.207 145 16 2 5898 6039 144809156 144809013 3.170000e-33 154.0
54 TraesCS7D01G218200 chr7B 96.226 53 2 0 5190 5242 145051516 145051464 3.260000e-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 TraesCS7D01G218200 chr7D 178856816 178863384 6568 True 5852.700000 11636 100.000000 1 6569 2 chr7D.!!$R2 6568
1 TraesCS7D01G218200 chr7D 178935808 178942129 6321 True 961.285714 2113 88.458143 289 6531 7 chr7D.!!$R3 6242
2 TraesCS7D01G218200 chr7D 179121761 179124752 2991 True 696.400000 1919 90.567800 298 3290 5 chr7D.!!$R4 2992
3 TraesCS7D01G218200 chr7D 178989047 178990013 966 True 490.000000 490 76.278000 3373 4327 1 chr7D.!!$R1 954
4 TraesCS7D01G218200 chr7A 183305176 183310102 4926 True 4175.000000 4920 97.741500 355 5186 2 chr7A.!!$R2 4831
5 TraesCS7D01G218200 chr7A 183479688 183484716 5028 True 997.833333 2111 90.649333 284 5238 6 chr7A.!!$R4 4954
6 TraesCS7D01G218200 chr7A 183651811 183657247 5436 True 978.142857 1984 91.273000 269 5770 7 chr7A.!!$R5 5501
7 TraesCS7D01G218200 chr7A 182855380 182861139 5759 True 593.333333 1644 90.995500 277 6515 6 chr7A.!!$R1 6238
8 TraesCS7D01G218200 chr7A 183404553 183405555 1002 True 307.000000 327 84.442500 5579 6521 2 chr7A.!!$R3 942
9 TraesCS7D01G218200 chr7B 144732049 144737874 5825 True 4348.000000 4505 93.953000 269 6039 2 chr7B.!!$R2 5770
10 TraesCS7D01G218200 chr7B 145051112 145056426 5314 True 990.985714 1919 92.148714 315 5671 7 chr7B.!!$R4 5356
11 TraesCS7D01G218200 chr7B 144808495 144814805 6310 True 971.000000 2106 89.255571 309 6522 7 chr7B.!!$R3 6213
12 TraesCS7D01G218200 chr7B 145027643 145028609 966 True 512.000000 512 76.758000 3373 4327 1 chr7B.!!$R1 954

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
686 3259 5.855740 ACTAGTTACCCTGTAGAATCTGC 57.144 43.478 0.00 0.00 0.00 4.26 F
1451 4730 1.135960 TGGTCACCATTGGTCTGACA 58.864 50.000 21.49 10.47 32.42 3.58 F
2902 6317 0.603707 CGTCCAACACAGAGTGCCAT 60.604 55.000 0.00 0.00 36.98 4.40 F
3014 6429 1.076332 GGGTGTCGTGTCTAACATGC 58.924 55.000 0.00 0.00 35.17 4.06 F
4686 8207 2.367486 TCTTTCGCATTCATGGCATCA 58.633 42.857 0.00 0.00 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2624 6033 1.579964 TTGTCCTGCTCTGCATTGCG 61.580 55.000 3.84 0.0 38.13 4.85 R
3014 6429 1.134560 GCCTTCTGTAGACCCGTACTG 59.865 57.143 0.00 0.0 0.00 2.74 R
4686 8207 2.096980 CAGCAGCATGATCACGACAATT 59.903 45.455 0.00 0.0 39.69 2.32 R
4967 8488 1.302192 GCCGGTGTGTTTGCTCCTA 60.302 57.895 1.90 0.0 0.00 2.94 R
6110 9782 0.250727 TTGCAGCAGGGGAAGTACAC 60.251 55.000 0.00 0.0 0.00 2.90 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
446 2667 6.209589 TGGTGATAGCAATCAGATCTAGGTAC 59.790 42.308 0.00 0.00 42.80 3.34
447 2668 6.350612 GGTGATAGCAATCAGATCTAGGTACC 60.351 46.154 2.73 2.73 42.80 3.34
686 3259 5.855740 ACTAGTTACCCTGTAGAATCTGC 57.144 43.478 0.00 0.00 0.00 4.26
732 3306 7.862741 TTACTACTTGTCTTATGTGTGTTCG 57.137 36.000 0.00 0.00 0.00 3.95
802 3447 5.949952 ACTTATTTTGGTGGGGTCAGATTAC 59.050 40.000 0.00 0.00 0.00 1.89
1133 4376 7.802251 GTCTATGAACATGAGCTGATAATTTGC 59.198 37.037 0.00 0.00 0.00 3.68
1381 4660 1.580815 GCATAGAGAGCAACCTGAGC 58.419 55.000 0.00 0.00 0.00 4.26
1451 4730 1.135960 TGGTCACCATTGGTCTGACA 58.864 50.000 21.49 10.47 32.42 3.58
1604 5010 4.417437 ACTTCTTGGAGTCCTAGCAGTTA 58.583 43.478 17.50 0.00 30.68 2.24
2177 5586 2.224257 GGCTTTTGGGCTGAAAATGACA 60.224 45.455 0.00 0.00 37.53 3.58
2178 5587 3.062042 GCTTTTGGGCTGAAAATGACAG 58.938 45.455 0.00 0.00 38.27 3.51
2624 6033 0.729140 CTTTCGTGGCCACAAATCGC 60.729 55.000 34.16 6.96 0.00 4.58
2784 6199 2.105477 CCTATAAGGAGCATGCACCTGT 59.895 50.000 33.43 26.15 37.67 4.00
2902 6317 0.603707 CGTCCAACACAGAGTGCCAT 60.604 55.000 0.00 0.00 36.98 4.40
2918 6333 1.487976 GCCATTCTCCAGATGTCCAGA 59.512 52.381 0.00 0.00 0.00 3.86
2920 6335 3.539604 CCATTCTCCAGATGTCCAGAAC 58.460 50.000 0.00 0.00 0.00 3.01
3014 6429 1.076332 GGGTGTCGTGTCTAACATGC 58.924 55.000 0.00 0.00 35.17 4.06
3676 7179 2.908351 GTGGTCCTACTTTCCCTAACCA 59.092 50.000 0.00 0.00 33.13 3.67
3680 7183 3.451540 GTCCTACTTTCCCTAACCAGAGG 59.548 52.174 0.00 0.00 36.23 3.69
4098 7616 7.775120 ACTCAAATTCAGTTTCATTTGTGTCT 58.225 30.769 6.54 0.00 40.51 3.41
4492 8013 3.877508 AGTTGTCGAAGAAGAAAAGGTGG 59.122 43.478 0.00 0.00 39.69 4.61
4686 8207 2.367486 TCTTTCGCATTCATGGCATCA 58.633 42.857 0.00 0.00 0.00 3.07
4967 8488 2.802057 CGAGACGTCCTGAACCTGTTTT 60.802 50.000 13.01 0.00 0.00 2.43
5125 8646 2.983907 TTGACTTGAACACCGGTGTA 57.016 45.000 38.93 23.20 44.13 2.90
5221 8763 1.386533 CTACAAGCAGGCAATGAGGG 58.613 55.000 4.43 0.00 0.00 4.30
5269 8811 3.686726 AGCAAATTCTCGGAGCAACTTAG 59.313 43.478 0.00 0.00 0.00 2.18
5280 8837 6.403049 TCGGAGCAACTTAGTATTTTCATCA 58.597 36.000 0.00 0.00 0.00 3.07
5560 9137 9.356929 GTGTTTTTCGCTTCTTTGATAATTTTG 57.643 29.630 0.00 0.00 0.00 2.44
5561 9138 9.092876 TGTTTTTCGCTTCTTTGATAATTTTGT 57.907 25.926 0.00 0.00 0.00 2.83
5642 9232 5.588648 TGTAGCATTATGAAGTAACCCTTGC 59.411 40.000 0.00 0.00 32.03 4.01
5657 9248 6.575162 AACCCTTGCTTATTTAGAGTGTTG 57.425 37.500 0.00 0.00 0.00 3.33
5671 9262 2.615912 GAGTGTTGCTGAAGCTGTCTTT 59.384 45.455 3.61 0.00 42.66 2.52
5895 9535 1.687123 TCGAGCTTAATGACCTAGCCC 59.313 52.381 0.00 0.00 35.53 5.19
5943 9586 7.652554 ACTCCCTCCATTTGAAATTATAAGGT 58.347 34.615 0.00 0.00 0.00 3.50
5980 9623 8.442605 TTTTGTAAATATAAGCGTGTTTCTGC 57.557 30.769 0.00 0.00 0.00 4.26
6015 9659 5.222631 GTGCAAAGTGTTTAATTCCCTCTG 58.777 41.667 0.00 0.00 0.00 3.35
6025 9675 6.449041 TGTTTAATTCCCTCTGTACCCCTAAT 59.551 38.462 0.00 0.00 0.00 1.73
6063 9735 5.121768 GCTTAGTCTTTCCAATGTTCGCTTA 59.878 40.000 0.00 0.00 0.00 3.09
6065 9737 4.642429 AGTCTTTCCAATGTTCGCTTAGT 58.358 39.130 0.00 0.00 0.00 2.24
6068 9740 4.929808 TCTTTCCAATGTTCGCTTAGTCTC 59.070 41.667 0.00 0.00 0.00 3.36
6072 9744 4.631377 TCCAATGTTCGCTTAGTCTCAATG 59.369 41.667 0.00 0.00 0.00 2.82
6126 9798 3.914426 AATAGTGTACTTCCCCTGCTG 57.086 47.619 0.00 0.00 0.00 4.41
6134 9827 3.105959 ACTTCCCCTGCTGCAAAATAT 57.894 42.857 3.02 0.00 0.00 1.28
6140 9833 3.003689 CCCCTGCTGCAAAATATAAGTCG 59.996 47.826 3.02 0.00 0.00 4.18
6148 9841 7.065204 TGCTGCAAAATATAAGTCGAATGTACA 59.935 33.333 0.00 0.00 0.00 2.90
6161 9854 6.535150 AGTCGAATGTACATATGTTTGACCAG 59.465 38.462 14.77 1.49 36.21 4.00
6199 9896 3.560902 TCTTCGACAACAGCAGAGTAG 57.439 47.619 0.00 0.00 0.00 2.57
6220 9917 8.859236 AGTAGATAGTCATGGCTTAATACGTA 57.141 34.615 4.49 0.00 0.00 3.57
6235 9933 0.867746 ACGTACGTAGTCAAGCACGA 59.132 50.000 21.41 0.00 43.93 4.35
6323 10021 1.496934 CACCGGAAAACAAATGCCAC 58.503 50.000 9.46 0.00 0.00 5.01
6350 10051 1.018226 TCGACGACGAGGAGAAGTCC 61.018 60.000 5.75 0.00 43.81 3.85
6402 10109 3.458163 GACCCCATCGAGCACGGA 61.458 66.667 3.11 0.00 40.21 4.69
6473 10180 2.901840 CAGTGCACCCACGCTGTT 60.902 61.111 14.63 0.00 46.62 3.16
6474 10181 2.901840 AGTGCACCCACGCTGTTG 60.902 61.111 14.63 0.00 46.62 3.33
6522 10240 1.742140 CTCAGGCTCAGCAGTGCAG 60.742 63.158 19.20 9.98 36.01 4.41
6523 10241 2.032223 CAGGCTCAGCAGTGCAGT 59.968 61.111 19.20 0.00 36.01 4.40
6524 10242 2.032223 AGGCTCAGCAGTGCAGTG 59.968 61.111 19.20 17.56 36.01 3.66
6526 10244 2.976350 GCTCAGCAGTGCAGTGCA 60.976 61.111 39.87 24.15 46.60 4.57
6535 10253 3.239464 TGCAGTGCACCCTTCAGA 58.761 55.556 15.37 0.00 31.71 3.27
6536 10254 1.071987 TGCAGTGCACCCTTCAGAG 59.928 57.895 15.37 0.00 31.71 3.35
6537 10255 1.673665 GCAGTGCACCCTTCAGAGG 60.674 63.158 14.63 0.00 43.15 3.69
6538 10256 1.757306 CAGTGCACCCTTCAGAGGT 59.243 57.895 14.63 0.00 41.85 3.85
6543 10261 3.793060 ACCCTTCAGAGGTGACCG 58.207 61.111 0.00 0.00 41.85 4.79
6544 10262 1.152312 ACCCTTCAGAGGTGACCGT 60.152 57.895 0.00 0.00 41.85 4.83
6545 10263 1.186267 ACCCTTCAGAGGTGACCGTC 61.186 60.000 0.00 0.00 41.85 4.79
6546 10264 1.213013 CCTTCAGAGGTGACCGTCG 59.787 63.158 0.00 0.00 38.32 5.12
6547 10265 1.444553 CTTCAGAGGTGACCGTCGC 60.445 63.158 3.31 3.31 30.10 5.19
6548 10266 3.263503 TTCAGAGGTGACCGTCGCG 62.264 63.158 0.00 0.00 30.10 5.87
6549 10267 3.733960 CAGAGGTGACCGTCGCGA 61.734 66.667 3.71 3.71 0.00 5.87
6550 10268 2.750637 AGAGGTGACCGTCGCGAT 60.751 61.111 14.06 0.00 0.00 4.58
6551 10269 2.579787 GAGGTGACCGTCGCGATG 60.580 66.667 21.42 21.42 0.00 3.84
6552 10270 3.338126 GAGGTGACCGTCGCGATGT 62.338 63.158 25.56 19.37 0.00 3.06
6553 10271 2.879462 GGTGACCGTCGCGATGTC 60.879 66.667 25.56 25.70 0.00 3.06
6554 10272 2.178521 GTGACCGTCGCGATGTCT 59.821 61.111 29.61 16.39 0.00 3.41
6555 10273 2.152699 GTGACCGTCGCGATGTCTG 61.153 63.158 29.61 18.23 0.00 3.51
6556 10274 3.248171 GACCGTCGCGATGTCTGC 61.248 66.667 25.56 9.03 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
446 2667 6.665248 AGATATTTCCCTTTGTTTTCTCTGGG 59.335 38.462 0.00 0.00 36.14 4.45
447 2668 7.363268 CCAGATATTTCCCTTTGTTTTCTCTGG 60.363 40.741 0.00 0.00 39.02 3.86
732 3306 4.216411 TCTTCCAACTGCTATTACCACC 57.784 45.455 0.00 0.00 0.00 4.61
802 3447 9.650371 CATATACATGATTGAACTTTACCGTTG 57.350 33.333 0.00 0.00 33.67 4.10
1007 4205 8.511321 TGTTAAAAGACGAAAGCATATTGTCAT 58.489 29.630 0.00 0.00 32.08 3.06
1163 4407 2.026636 TGCCTGTTAGACCCCACAATAC 60.027 50.000 0.00 0.00 0.00 1.89
1280 4552 7.725397 TCAAGGATAATTCAAGGATGGTTATGG 59.275 37.037 0.00 0.00 0.00 2.74
1381 4660 3.119919 GCTCTCTGACTGAAATTGCAAGG 60.120 47.826 4.94 0.00 0.00 3.61
1451 4730 0.951558 GCCTCGTGGTGTTGATGTTT 59.048 50.000 5.26 0.00 35.27 2.83
1604 5010 3.701205 TCCAGCATTGTATGTCACACT 57.299 42.857 0.00 0.00 36.69 3.55
2177 5586 5.126061 CCAAATGCAGCTTATTAGAACCACT 59.874 40.000 0.00 0.00 0.00 4.00
2178 5587 5.343249 CCAAATGCAGCTTATTAGAACCAC 58.657 41.667 0.00 0.00 0.00 4.16
2624 6033 1.579964 TTGTCCTGCTCTGCATTGCG 61.580 55.000 3.84 0.00 38.13 4.85
2768 6183 1.279496 TCTACAGGTGCATGCTCCTT 58.721 50.000 33.31 25.54 37.79 3.36
2902 6317 2.248248 ACGTTCTGGACATCTGGAGAA 58.752 47.619 0.00 0.00 0.00 2.87
2918 6333 2.489329 CCTCATCCATTTCTGCAACGTT 59.511 45.455 0.00 0.00 0.00 3.99
2920 6335 2.358957 TCCTCATCCATTTCTGCAACG 58.641 47.619 0.00 0.00 0.00 4.10
3014 6429 1.134560 GCCTTCTGTAGACCCGTACTG 59.865 57.143 0.00 0.00 0.00 2.74
3073 6488 2.898729 ATGGGTCATACTCTTGCTCG 57.101 50.000 0.00 0.00 0.00 5.03
3111 6526 4.397730 ACATACCGCACATGCTATTTTCAA 59.602 37.500 1.82 0.00 39.32 2.69
3676 7179 3.008485 CAGTTCCCTAGAGCAAAACCTCT 59.992 47.826 0.00 0.00 44.12 3.69
3680 7183 2.485814 CTGCAGTTCCCTAGAGCAAAAC 59.514 50.000 5.25 0.00 34.45 2.43
4492 8013 5.293079 GCATCAGATACTTGTGTCTCTTTCC 59.707 44.000 0.00 0.00 28.78 3.13
4686 8207 2.096980 CAGCAGCATGATCACGACAATT 59.903 45.455 0.00 0.00 39.69 2.32
4967 8488 1.302192 GCCGGTGTGTTTGCTCCTA 60.302 57.895 1.90 0.00 0.00 2.94
5125 8646 2.816087 CAAGAACATACAACAGGCAGCT 59.184 45.455 0.00 0.00 0.00 4.24
5589 9178 0.687427 AAAGCCTTGGTGTGCCAGTT 60.687 50.000 0.00 0.00 46.91 3.16
5642 9232 6.148480 ACAGCTTCAGCAACACTCTAAATAAG 59.852 38.462 0.75 0.00 45.16 1.73
5657 9248 5.808042 TCATCATAAAAGACAGCTTCAGC 57.192 39.130 0.00 0.00 42.49 4.26
5671 9262 9.033711 TGATTCTTGGGAAACATTTCATCATAA 57.966 29.630 6.68 3.50 38.92 1.90
5885 9525 0.981183 ACAATGTTCGGGCTAGGTCA 59.019 50.000 0.00 0.00 0.00 4.02
5886 9526 2.109425 AACAATGTTCGGGCTAGGTC 57.891 50.000 0.00 0.00 0.00 3.85
5895 9535 1.539388 TGCCTAGCCAAACAATGTTCG 59.461 47.619 0.00 0.00 0.00 3.95
5973 9616 3.308530 CACCGGAAAATGAAGCAGAAAC 58.691 45.455 9.46 0.00 0.00 2.78
5979 9622 2.061028 CTTTGCACCGGAAAATGAAGC 58.939 47.619 9.46 0.00 0.00 3.86
5980 9623 3.052036 CACTTTGCACCGGAAAATGAAG 58.948 45.455 9.46 6.97 0.00 3.02
5982 9625 2.028130 ACACTTTGCACCGGAAAATGA 58.972 42.857 9.46 0.00 0.00 2.57
6015 9659 3.089284 ACAAGCAAAGCATTAGGGGTAC 58.911 45.455 0.00 0.00 0.00 3.34
6025 9675 4.389374 AGACTAAGCTAACAAGCAAAGCA 58.611 39.130 0.00 0.00 38.75 3.91
6047 9718 4.637276 TGAGACTAAGCGAACATTGGAAA 58.363 39.130 0.00 0.00 0.00 3.13
6050 9721 4.728882 GCATTGAGACTAAGCGAACATTGG 60.729 45.833 0.00 0.00 0.00 3.16
6063 9735 1.884579 CAGTTGCCTTGCATTGAGACT 59.115 47.619 0.00 0.00 38.76 3.24
6065 9737 1.985473 ACAGTTGCCTTGCATTGAGA 58.015 45.000 7.73 0.00 38.76 3.27
6068 9740 7.650890 TGAATATATACAGTTGCCTTGCATTG 58.349 34.615 0.00 0.00 38.76 2.82
6072 9744 9.831737 CTATTTGAATATATACAGTTGCCTTGC 57.168 33.333 0.00 0.00 0.00 4.01
6105 9777 3.622455 GCAGCAGGGGAAGTACACTATTT 60.622 47.826 0.00 0.00 0.00 1.40
6106 9778 2.092914 GCAGCAGGGGAAGTACACTATT 60.093 50.000 0.00 0.00 0.00 1.73
6107 9779 1.486726 GCAGCAGGGGAAGTACACTAT 59.513 52.381 0.00 0.00 0.00 2.12
6109 9781 1.127567 TGCAGCAGGGGAAGTACACT 61.128 55.000 0.00 0.00 0.00 3.55
6110 9782 0.250727 TTGCAGCAGGGGAAGTACAC 60.251 55.000 0.00 0.00 0.00 2.90
6113 9785 2.603075 ATTTTGCAGCAGGGGAAGTA 57.397 45.000 0.00 0.00 0.00 2.24
6114 9786 2.603075 TATTTTGCAGCAGGGGAAGT 57.397 45.000 0.00 0.00 0.00 3.01
6119 9791 3.876914 TCGACTTATATTTTGCAGCAGGG 59.123 43.478 0.00 0.00 0.00 4.45
6120 9792 5.484173 TTCGACTTATATTTTGCAGCAGG 57.516 39.130 0.00 0.00 0.00 4.85
6122 9794 6.435430 ACATTCGACTTATATTTTGCAGCA 57.565 33.333 0.00 0.00 0.00 4.41
6134 9827 8.035984 TGGTCAAACATATGTACATTCGACTTA 58.964 33.333 14.77 0.00 0.00 2.24
6140 9833 7.391148 AACCTGGTCAAACATATGTACATTC 57.609 36.000 14.77 0.51 0.00 2.67
6191 9888 4.599047 AAGCCATGACTATCTACTCTGC 57.401 45.455 0.00 0.00 0.00 4.26
6199 9896 6.376978 ACGTACGTATTAAGCCATGACTATC 58.623 40.000 21.41 0.00 0.00 2.08
6220 9917 4.565564 GGAAAATATCGTGCTTGACTACGT 59.434 41.667 0.00 0.00 40.87 3.57
6347 10048 2.095469 GTCGACGTCGTCTCGGAC 59.905 66.667 34.40 21.54 40.80 4.79
6402 10109 3.168528 ACCACCAACCAGCGGTCT 61.169 61.111 0.69 0.00 33.12 3.85
6469 10176 3.300009 GCTTTGACATTTCGTCCAACAG 58.700 45.455 0.00 0.00 44.71 3.16
6470 10177 2.034053 GGCTTTGACATTTCGTCCAACA 59.966 45.455 0.00 0.00 44.71 3.33
6471 10178 2.034053 TGGCTTTGACATTTCGTCCAAC 59.966 45.455 0.00 0.00 44.71 3.77
6473 10180 1.879380 CTGGCTTTGACATTTCGTCCA 59.121 47.619 0.00 0.00 44.71 4.02
6474 10181 1.401539 GCTGGCTTTGACATTTCGTCC 60.402 52.381 0.00 0.00 44.71 4.79
6491 10209 1.447489 CCTGAGAGCGTCAAGGCTG 60.447 63.158 1.33 0.00 44.93 4.85
6529 10247 1.444553 GCGACGGTCACCTCTGAAG 60.445 63.158 9.10 0.00 0.00 3.02
6530 10248 2.649034 GCGACGGTCACCTCTGAA 59.351 61.111 9.10 0.00 0.00 3.02
6531 10249 3.733960 CGCGACGGTCACCTCTGA 61.734 66.667 0.00 0.00 0.00 3.27
6532 10250 3.052620 ATCGCGACGGTCACCTCTG 62.053 63.158 12.93 0.00 0.00 3.35
6533 10251 2.750637 ATCGCGACGGTCACCTCT 60.751 61.111 12.93 0.00 0.00 3.69
6534 10252 2.579787 CATCGCGACGGTCACCTC 60.580 66.667 12.93 0.00 0.00 3.85
6535 10253 3.338126 GACATCGCGACGGTCACCT 62.338 63.158 28.07 3.49 0.00 4.00
6536 10254 2.879462 GACATCGCGACGGTCACC 60.879 66.667 28.07 9.99 0.00 4.02
6537 10255 2.152699 CAGACATCGCGACGGTCAC 61.153 63.158 31.85 15.84 34.04 3.67
6538 10256 2.178273 CAGACATCGCGACGGTCA 59.822 61.111 31.85 5.51 34.04 4.02
6539 10257 3.248171 GCAGACATCGCGACGGTC 61.248 66.667 26.60 26.60 0.00 4.79


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

AutoCloner maintained by Alex Coulton.