Multiple sequence alignment - TraesCS5D01G181800

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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 TraesCS5D01G181800 chr5D 100.000 5519 0 0 1 5519 282844320 282849838 0.000000e+00 10192
1 TraesCS5D01G181800 chr5A 96.431 4735 146 18 797 5519 375247931 375252654 0.000000e+00 7786
2 TraesCS5D01G181800 chr5A 90.107 748 57 11 60 804 375219477 375220210 0.000000e+00 955
3 TraesCS5D01G181800 chr5B 96.733 4469 129 14 796 5256 321125570 321130029 0.000000e+00 7428
4 TraesCS5D01G181800 chr5B 88.372 172 18 2 40 209 309904476 309904647 7.250000e-49 206
5 TraesCS5D01G181800 chr4D 90.341 176 15 2 35 208 126901169 126901344 4.300000e-56 230
6 TraesCS5D01G181800 chr4A 90.286 175 16 1 35 208 121510463 121510637 1.550000e-55 228
7 TraesCS5D01G181800 chr3D 90.643 171 15 1 40 209 460923625 460923795 5.560000e-55 226
8 TraesCS5D01G181800 chr3B 90.643 171 14 2 40 209 611137071 611137240 5.560000e-55 226
9 TraesCS5D01G181800 chr2D 86.036 222 16 9 1 208 136417550 136417770 2.000000e-54 224
10 TraesCS5D01G181800 chr3A 88.827 179 18 2 40 216 468377998 468378176 9.310000e-53 219
11 TraesCS5D01G181800 chr7D 87.500 176 20 1 35 208 253149518 253149693 9.370000e-48 202


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 TraesCS5D01G181800 chr5D 282844320 282849838 5518 False 10192 10192 100.000 1 5519 1 chr5D.!!$F1 5518
1 TraesCS5D01G181800 chr5A 375247931 375252654 4723 False 7786 7786 96.431 797 5519 1 chr5A.!!$F2 4722
2 TraesCS5D01G181800 chr5A 375219477 375220210 733 False 955 955 90.107 60 804 1 chr5A.!!$F1 744
3 TraesCS5D01G181800 chr5B 321125570 321130029 4459 False 7428 7428 96.733 796 5256 1 chr5B.!!$F2 4460

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
799 803 0.175989 GTTTGCCGTCTCTCCCCTAG 59.824 60.000 0.00 0.0 0.00 3.02 F
1707 1712 1.303236 CCGTCCACTGGCCAATTCA 60.303 57.895 7.01 0.0 0.00 2.57 F
1808 1813 0.609131 ATTTCAGTTGGTGCGAGGGG 60.609 55.000 0.00 0.0 0.00 4.79 F
2035 2040 0.912486 AGATGGGTAAGTGTCTGCCC 59.088 55.000 0.00 0.0 41.42 5.36 F
3575 3580 1.317613 ACAGATTGTCTTTTGGCGCA 58.682 45.000 10.83 0.0 0.00 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1787 1792 0.804989 CCTCGCACCAACTGAAATCC 59.195 55.000 0.00 0.0 0.00 3.01 R
3433 3438 0.804989 GGAACAAAGGTCATGCTCGG 59.195 55.000 0.00 0.0 0.00 4.63 R
3796 3801 4.083057 GCCTAGAGCTTTTGAACTTGAAGG 60.083 45.833 0.00 0.0 38.99 3.46 R
3857 3863 8.836413 CACACAAATAAGAACTCTAAAACTCCA 58.164 33.333 0.00 0.0 0.00 3.86 R
5012 5025 0.971386 AACTACATGGACGGTCGGTT 59.029 50.000 1.43 0.0 0.00 4.44 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 4.879295 TTTCCTATGGACCCAATGTGAT 57.121 40.909 0.00 0.00 0.00 3.06
22 23 5.985175 TTTCCTATGGACCCAATGTGATA 57.015 39.130 0.00 0.00 0.00 2.15
23 24 6.529084 TTTCCTATGGACCCAATGTGATAT 57.471 37.500 0.00 0.00 0.00 1.63
24 25 6.529084 TTCCTATGGACCCAATGTGATATT 57.471 37.500 0.00 0.00 0.00 1.28
25 26 6.529084 TCCTATGGACCCAATGTGATATTT 57.471 37.500 0.00 0.00 0.00 1.40
26 27 6.306199 TCCTATGGACCCAATGTGATATTTG 58.694 40.000 0.00 0.00 0.00 2.32
27 28 6.102468 TCCTATGGACCCAATGTGATATTTGA 59.898 38.462 0.00 0.00 0.00 2.69
28 29 6.950041 CCTATGGACCCAATGTGATATTTGAT 59.050 38.462 0.00 0.00 0.00 2.57
29 30 6.906157 ATGGACCCAATGTGATATTTGATC 57.094 37.500 0.00 0.00 0.00 2.92
30 31 5.764432 TGGACCCAATGTGATATTTGATCA 58.236 37.500 0.00 0.00 0.00 2.92
31 32 5.593909 TGGACCCAATGTGATATTTGATCAC 59.406 40.000 10.14 10.14 46.28 3.06
32 33 5.829924 GGACCCAATGTGATATTTGATCACT 59.170 40.000 16.35 2.68 46.25 3.41
33 34 6.322201 GGACCCAATGTGATATTTGATCACTT 59.678 38.462 16.35 9.10 46.25 3.16
34 35 7.502226 GGACCCAATGTGATATTTGATCACTTA 59.498 37.037 16.35 0.81 46.25 2.24
35 36 8.455903 ACCCAATGTGATATTTGATCACTTAG 57.544 34.615 16.35 7.63 46.25 2.18
36 37 8.055181 ACCCAATGTGATATTTGATCACTTAGT 58.945 33.333 16.35 7.98 46.25 2.24
37 38 9.559732 CCCAATGTGATATTTGATCACTTAGTA 57.440 33.333 16.35 0.00 46.25 1.82
49 50 9.897744 TTTGATCACTTAGTATTTGAGCTTTTG 57.102 29.630 0.00 0.00 0.00 2.44
62 63 1.150827 GCTTTTGCCAATGTGCTTCC 58.849 50.000 0.00 0.00 40.15 3.46
63 64 1.270465 GCTTTTGCCAATGTGCTTCCT 60.270 47.619 0.00 0.00 40.15 3.36
64 65 2.807837 GCTTTTGCCAATGTGCTTCCTT 60.808 45.455 0.00 0.00 40.15 3.36
65 66 3.554752 GCTTTTGCCAATGTGCTTCCTTA 60.555 43.478 0.00 0.00 40.15 2.69
66 67 3.940209 TTTGCCAATGTGCTTCCTTAG 57.060 42.857 0.00 0.00 0.00 2.18
198 199 4.855340 TCAAAATCACCTGGGGATTAGTC 58.145 43.478 23.79 0.00 34.02 2.59
208 209 2.280628 GGGGATTAGTCGCACTTTCAG 58.719 52.381 4.69 0.00 38.94 3.02
213 214 2.741759 TAGTCGCACTTTCAGCATCA 57.258 45.000 0.00 0.00 0.00 3.07
269 270 5.542251 TGATATTATCGATGTTCTCCCCACA 59.458 40.000 8.54 0.00 0.00 4.17
270 271 3.536956 TTATCGATGTTCTCCCCACAC 57.463 47.619 8.54 0.00 0.00 3.82
293 295 3.667282 CACGACCGTCGGACACCT 61.667 66.667 24.03 0.00 45.59 4.00
299 301 4.308458 CGTCGGACACCTTGCCCA 62.308 66.667 9.10 0.00 0.00 5.36
300 302 2.112297 GTCGGACACCTTGCCCAA 59.888 61.111 2.62 0.00 0.00 4.12
336 338 1.630878 CCCCCTCATAGCCATAGAACC 59.369 57.143 0.00 0.00 0.00 3.62
338 340 2.711009 CCCCTCATAGCCATAGAACCAA 59.289 50.000 0.00 0.00 0.00 3.67
354 356 6.884280 AGAACCAAAACCTAAAGATCACTG 57.116 37.500 0.00 0.00 0.00 3.66
370 372 6.763355 AGATCACTGCCGAAATACATAGATT 58.237 36.000 0.00 0.00 0.00 2.40
397 399 4.778143 CCAAGACCGGGAAGGCGG 62.778 72.222 6.32 0.00 46.52 6.13
400 402 4.698625 AGACCGGGAAGGCGGACT 62.699 66.667 6.32 0.00 46.52 3.85
404 406 3.148279 CGGGAAGGCGGACTAGCT 61.148 66.667 0.00 0.00 37.29 3.32
405 407 2.816012 GGGAAGGCGGACTAGCTC 59.184 66.667 0.00 0.00 37.29 4.09
406 408 2.798364 GGGAAGGCGGACTAGCTCC 61.798 68.421 0.00 0.00 37.29 4.70
427 429 2.213499 CCCCTAAATTAGTGCGAGCAG 58.787 52.381 0.00 0.00 0.00 4.24
439 441 1.141881 CGAGCAGCCACCGTCTATT 59.858 57.895 0.00 0.00 0.00 1.73
442 444 0.753262 AGCAGCCACCGTCTATTAGG 59.247 55.000 0.00 0.00 0.00 2.69
452 454 5.290386 CACCGTCTATTAGGAATCCAGAAC 58.710 45.833 0.61 0.00 0.00 3.01
461 463 2.494073 AGGAATCCAGAACGAGAGACAC 59.506 50.000 0.61 0.00 0.00 3.67
463 465 3.306088 GGAATCCAGAACGAGAGACACAA 60.306 47.826 0.00 0.00 0.00 3.33
468 470 4.021104 TCCAGAACGAGAGACACAAATGAT 60.021 41.667 0.00 0.00 0.00 2.45
513 515 4.854587 CTCCGGGAGAGGATAGGG 57.145 66.667 19.57 0.00 39.96 3.53
554 556 2.884639 CAGGGGAAAACAAGGTACACAG 59.115 50.000 0.00 0.00 0.00 3.66
562 564 6.094464 GGAAAACAAGGTACACAGTACTTTGT 59.906 38.462 23.50 23.50 45.49 2.83
575 577 0.810031 ACTTTGTCGACTGTTGCGCT 60.810 50.000 17.92 0.00 0.00 5.92
602 604 1.908299 CTCCTGCAAACCCCAACCC 60.908 63.158 0.00 0.00 0.00 4.11
603 605 2.123077 CCTGCAAACCCCAACCCA 60.123 61.111 0.00 0.00 0.00 4.51
604 606 1.764054 CCTGCAAACCCCAACCCAA 60.764 57.895 0.00 0.00 0.00 4.12
605 607 1.445518 CTGCAAACCCCAACCCAAC 59.554 57.895 0.00 0.00 0.00 3.77
610 612 2.619332 GCAAACCCCAACCCAACTTTTT 60.619 45.455 0.00 0.00 0.00 1.94
634 636 6.937436 TTTAAGGAACAACACTCCTCTTTC 57.063 37.500 0.00 0.00 42.77 2.62
643 645 6.056236 ACAACACTCCTCTTTCTTAAGAACC 58.944 40.000 17.51 0.00 39.80 3.62
671 673 3.391626 GGTAGGAATGGGTTAGGGAGAAG 59.608 52.174 0.00 0.00 0.00 2.85
673 675 2.846827 AGGAATGGGTTAGGGAGAAGTG 59.153 50.000 0.00 0.00 0.00 3.16
682 684 2.031495 AGGGAGAAGTGCTTACTGGT 57.969 50.000 0.00 0.00 0.00 4.00
771 775 7.614124 AAAATGTCATGTGAATAAATTGCCC 57.386 32.000 0.00 0.00 0.00 5.36
779 783 7.329717 TCATGTGAATAAATTGCCCGTAAAAAC 59.670 33.333 0.00 0.00 0.00 2.43
785 789 1.557651 TTGCCCGTAAAAACGTTTGC 58.442 45.000 15.46 12.70 0.00 3.68
799 803 0.175989 GTTTGCCGTCTCTCCCCTAG 59.824 60.000 0.00 0.00 0.00 3.02
814 818 2.484947 CCCCTAGTGCGGTCCTATTTTC 60.485 54.545 0.00 0.00 0.00 2.29
907 912 2.869192 GCGATCCCATCTGACTTTCTTC 59.131 50.000 0.00 0.00 0.00 2.87
908 913 3.462021 CGATCCCATCTGACTTTCTTCC 58.538 50.000 0.00 0.00 0.00 3.46
931 936 1.878102 GCTCCATTCGTGTTCACCACT 60.878 52.381 0.00 0.00 42.20 4.00
1068 1073 3.461773 CGGCCGGTCATGGAGACT 61.462 66.667 20.10 0.00 46.72 3.24
1239 1244 2.692741 CCCTCTCCCAGTTCCCCC 60.693 72.222 0.00 0.00 0.00 5.40
1365 1370 3.351416 GGTGCCGTCGGTTCCAAC 61.351 66.667 13.94 0.95 0.00 3.77
1707 1712 1.303236 CCGTCCACTGGCCAATTCA 60.303 57.895 7.01 0.00 0.00 2.57
1808 1813 0.609131 ATTTCAGTTGGTGCGAGGGG 60.609 55.000 0.00 0.00 0.00 4.79
1867 1872 3.540314 TTGTTGATTTGCAGCCAAAGT 57.460 38.095 0.00 0.00 43.60 2.66
1974 1979 3.266772 TCATTTGGAGGGTGATAGCACTT 59.733 43.478 11.48 0.00 44.52 3.16
2035 2040 0.912486 AGATGGGTAAGTGTCTGCCC 59.088 55.000 0.00 0.00 41.42 5.36
2192 2197 3.211045 TGTTCTGACCTACTTTGTTGGC 58.789 45.455 0.00 0.00 31.94 4.52
2265 2270 6.109156 TGCTAAGAACACTCTCCATGTAAA 57.891 37.500 0.00 0.00 0.00 2.01
2306 2311 7.707624 TTCCTTTTGAAATCTGTGCAGATAT 57.292 32.000 14.24 3.76 46.75 1.63
2345 2350 5.347012 TCGTCGATTTTGGTTTTCCTAAC 57.653 39.130 0.00 0.00 41.38 2.34
2391 2396 8.685838 ATGCTTAGTTTACTTTTGGACAGTTA 57.314 30.769 0.00 0.00 0.00 2.24
2395 2400 8.685838 TTAGTTTACTTTTGGACAGTTATGCT 57.314 30.769 0.00 0.00 0.00 3.79
2694 2699 1.762957 TGGCCCAGAGTAAGTAGCATC 59.237 52.381 0.00 0.00 0.00 3.91
2806 2811 3.751518 ACACTCCCGCTGTTCTTAAATT 58.248 40.909 0.00 0.00 0.00 1.82
3019 3024 4.965814 TGCAGACATCATCTATTTCCTCC 58.034 43.478 0.00 0.00 35.15 4.30
3290 3295 8.621532 AGTAAATGTTTTAATCACAGCTGAGA 57.378 30.769 23.35 19.61 0.00 3.27
3374 3379 4.747108 CGTGGATCTGCTCTTTTATCGAAT 59.253 41.667 0.00 0.00 0.00 3.34
3433 3438 6.768381 AGAAAGCAGCCAATATAAGAGGTAAC 59.232 38.462 0.00 0.00 0.00 2.50
3575 3580 1.317613 ACAGATTGTCTTTTGGCGCA 58.682 45.000 10.83 0.00 0.00 6.09
3770 3775 6.214615 TCACATAATAGGGGAAGTGACAAAGA 59.785 38.462 0.00 0.00 31.72 2.52
3979 3986 7.990314 TGGAGGTATTCGATCATTTTACATCAA 59.010 33.333 0.00 0.00 0.00 2.57
4041 4048 3.066760 GGTTTGGCCATCGGAATAGAAAG 59.933 47.826 6.09 0.00 37.17 2.62
4167 4175 1.304381 TGCCACCTTGGAAGCCATC 60.304 57.895 0.00 0.00 40.96 3.51
4237 4245 5.678583 CCTGATGGTAGGATGCTTATATGG 58.321 45.833 0.00 0.00 40.42 2.74
4243 4251 7.806680 TGGTAGGATGCTTATATGGTTGATA 57.193 36.000 0.00 0.00 0.00 2.15
4248 4256 8.585471 AGGATGCTTATATGGTTGATATTTGG 57.415 34.615 0.00 0.00 0.00 3.28
4356 4366 4.925054 TGCGTTCTTGTACTTATGTGGTAC 59.075 41.667 0.00 0.00 39.70 3.34
4644 4655 7.610305 AGGTTAATTTCATAACGTGGAACTGAT 59.390 33.333 0.00 0.00 36.78 2.90
4660 4671 5.395682 AACTGATGTGTGATTTTGATGGG 57.604 39.130 0.00 0.00 0.00 4.00
4707 4720 6.575132 GTTTGAAGCATATATGATTTTGCGC 58.425 36.000 16.84 0.00 36.41 6.09
4762 4775 7.390718 ACCTATCATAACCATTCGCTATTTTCC 59.609 37.037 0.00 0.00 0.00 3.13
4846 4859 9.285770 CGTAAATTAAGTTTTCCTCTAATTGGC 57.714 33.333 0.00 0.00 0.00 4.52
4877 4890 4.635223 TCTGTAGCATTACATCATCTGGC 58.365 43.478 0.00 0.00 39.00 4.85
4960 4973 8.318167 GCAAAGTGTAATTAACAAACAACAGTC 58.682 33.333 0.00 0.00 40.63 3.51
4984 4997 5.246307 CGTTTCCTTTAAAGAGGACCTCAT 58.754 41.667 23.60 9.06 45.30 2.90
5012 5025 5.975693 AACCACAAACTCTTGTCAAAGAA 57.024 34.783 2.91 0.00 44.15 2.52
5024 5037 0.464870 TCAAAGAAACCGACCGTCCA 59.535 50.000 0.00 0.00 0.00 4.02
5094 5109 3.237268 TCCAAATGTGCCTACCTTGTT 57.763 42.857 0.00 0.00 0.00 2.83
5200 5217 7.192852 TCTTCATCTTCAATAAGCCTCTCTT 57.807 36.000 0.00 0.00 38.79 2.85
5257 5275 5.901552 TCACCTTCCTCATTTTTGTGTTTC 58.098 37.500 0.00 0.00 0.00 2.78
5296 5314 6.437162 ACTGAAATCACTAGCTTCTCTTCTCT 59.563 38.462 0.00 0.00 0.00 3.10
5310 5328 5.319453 TCTCTTCTCTGTGCATTCCATTTT 58.681 37.500 0.00 0.00 0.00 1.82
5365 5383 1.670295 TCATGCCGTGATTGATTTCCG 59.330 47.619 0.00 0.00 0.00 4.30
5397 5415 3.395210 CACCTAGGTTGTGTGTGCA 57.605 52.632 13.15 0.00 0.00 4.57
5405 5423 1.533756 GGTTGTGTGTGCATGTGTGTC 60.534 52.381 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.102468 TCAAATATCACATTGGGTCCATAGGA 59.898 38.462 0.00 0.00 0.00 2.94
4 5 7.666804 TGATCAAATATCACATTGGGTCCATAG 59.333 37.037 0.00 0.00 0.00 2.23
6 7 6.266103 GTGATCAAATATCACATTGGGTCCAT 59.734 38.462 12.12 0.00 45.61 3.41
7 8 5.593909 GTGATCAAATATCACATTGGGTCCA 59.406 40.000 12.12 0.00 45.61 4.02
8 9 6.076981 GTGATCAAATATCACATTGGGTCC 57.923 41.667 12.12 0.00 45.61 4.46
23 24 9.897744 CAAAAGCTCAAATACTAAGTGATCAAA 57.102 29.630 0.00 0.00 0.00 2.69
24 25 8.023128 GCAAAAGCTCAAATACTAAGTGATCAA 58.977 33.333 0.00 0.00 0.00 2.57
25 26 7.362056 GGCAAAAGCTCAAATACTAAGTGATCA 60.362 37.037 0.00 0.00 0.00 2.92
26 27 6.969473 GGCAAAAGCTCAAATACTAAGTGATC 59.031 38.462 0.00 0.00 0.00 2.92
27 28 6.434028 TGGCAAAAGCTCAAATACTAAGTGAT 59.566 34.615 0.00 0.00 0.00 3.06
28 29 5.767665 TGGCAAAAGCTCAAATACTAAGTGA 59.232 36.000 0.00 0.00 0.00 3.41
29 30 6.012658 TGGCAAAAGCTCAAATACTAAGTG 57.987 37.500 0.00 0.00 0.00 3.16
30 31 6.648879 TTGGCAAAAGCTCAAATACTAAGT 57.351 33.333 0.00 0.00 0.00 2.24
31 32 7.062605 CACATTGGCAAAAGCTCAAATACTAAG 59.937 37.037 3.01 0.00 0.00 2.18
32 33 6.867816 CACATTGGCAAAAGCTCAAATACTAA 59.132 34.615 3.01 0.00 0.00 2.24
33 34 6.389091 CACATTGGCAAAAGCTCAAATACTA 58.611 36.000 3.01 0.00 0.00 1.82
34 35 5.232463 CACATTGGCAAAAGCTCAAATACT 58.768 37.500 3.01 0.00 0.00 2.12
35 36 4.143052 GCACATTGGCAAAAGCTCAAATAC 60.143 41.667 3.01 0.00 0.00 1.89
36 37 3.995705 GCACATTGGCAAAAGCTCAAATA 59.004 39.130 3.01 0.00 0.00 1.40
37 38 2.809696 GCACATTGGCAAAAGCTCAAAT 59.190 40.909 3.01 0.00 0.00 2.32
38 39 2.158928 AGCACATTGGCAAAAGCTCAAA 60.159 40.909 15.68 0.00 35.83 2.69
39 40 1.413445 AGCACATTGGCAAAAGCTCAA 59.587 42.857 15.68 0.00 35.83 3.02
40 41 1.042229 AGCACATTGGCAAAAGCTCA 58.958 45.000 15.68 0.00 35.83 4.26
41 42 2.064014 GAAGCACATTGGCAAAAGCTC 58.936 47.619 19.83 12.24 35.83 4.09
42 43 1.270465 GGAAGCACATTGGCAAAAGCT 60.270 47.619 15.68 15.68 35.83 3.74
43 44 1.150827 GGAAGCACATTGGCAAAAGC 58.849 50.000 3.01 8.90 35.83 3.51
44 45 2.825861 AGGAAGCACATTGGCAAAAG 57.174 45.000 3.01 2.40 35.83 2.27
45 46 4.255833 CTAAGGAAGCACATTGGCAAAA 57.744 40.909 3.01 0.00 35.83 2.44
46 47 3.940209 CTAAGGAAGCACATTGGCAAA 57.060 42.857 3.01 0.00 35.83 3.68
58 59 3.701664 ACCCCTCAAAATGCTAAGGAAG 58.298 45.455 0.00 0.00 0.00 3.46
59 60 3.825908 ACCCCTCAAAATGCTAAGGAA 57.174 42.857 0.00 0.00 0.00 3.36
60 61 3.075283 TGAACCCCTCAAAATGCTAAGGA 59.925 43.478 0.00 0.00 0.00 3.36
61 62 3.193479 GTGAACCCCTCAAAATGCTAAGG 59.807 47.826 0.00 0.00 35.22 2.69
62 63 3.826157 TGTGAACCCCTCAAAATGCTAAG 59.174 43.478 0.00 0.00 35.22 2.18
63 64 3.838565 TGTGAACCCCTCAAAATGCTAA 58.161 40.909 0.00 0.00 35.22 3.09
64 65 3.517296 TGTGAACCCCTCAAAATGCTA 57.483 42.857 0.00 0.00 35.22 3.49
65 66 2.380064 TGTGAACCCCTCAAAATGCT 57.620 45.000 0.00 0.00 35.22 3.79
66 67 2.094026 GGATGTGAACCCCTCAAAATGC 60.094 50.000 0.00 0.00 35.22 3.56
176 177 4.625324 CGACTAATCCCCAGGTGATTTTGA 60.625 45.833 2.06 0.00 34.43 2.69
177 178 3.627577 CGACTAATCCCCAGGTGATTTTG 59.372 47.826 2.06 0.00 34.43 2.44
187 188 1.626321 TGAAAGTGCGACTAATCCCCA 59.374 47.619 0.00 0.00 0.00 4.96
188 189 2.280628 CTGAAAGTGCGACTAATCCCC 58.719 52.381 0.00 0.00 0.00 4.81
189 190 1.666189 GCTGAAAGTGCGACTAATCCC 59.334 52.381 0.00 0.00 35.30 3.85
198 199 3.362831 GTGAATTTGATGCTGAAAGTGCG 59.637 43.478 0.00 0.00 35.30 5.34
208 209 4.082787 TCGGGAAGAAAGTGAATTTGATGC 60.083 41.667 0.00 0.00 0.00 3.91
213 214 4.100279 AGGTCGGGAAGAAAGTGAATTT 57.900 40.909 0.00 0.00 0.00 1.82
293 295 3.119637 GCTATTTTAAGCTCGTTGGGCAA 60.120 43.478 0.00 0.00 39.50 4.52
298 300 2.357952 GGGGGCTATTTTAAGCTCGTTG 59.642 50.000 0.00 0.00 44.41 4.10
299 301 2.651455 GGGGGCTATTTTAAGCTCGTT 58.349 47.619 0.00 0.00 44.41 3.85
300 302 2.343484 GGGGGCTATTTTAAGCTCGT 57.657 50.000 0.00 0.00 44.41 4.18
336 338 3.751175 TCGGCAGTGATCTTTAGGTTTTG 59.249 43.478 0.00 0.00 0.00 2.44
338 340 3.695830 TCGGCAGTGATCTTTAGGTTT 57.304 42.857 0.00 0.00 0.00 3.27
354 356 5.995897 AGTGGGTTAATCTATGTATTTCGGC 59.004 40.000 0.00 0.00 0.00 5.54
370 372 1.269012 CCGGTCTTGGTAGTGGGTTA 58.731 55.000 0.00 0.00 0.00 2.85
406 408 1.134220 TGCTCGCACTAATTTAGGGGG 60.134 52.381 14.81 14.81 42.92 5.40
416 418 4.435436 CGGTGGCTGCTCGCACTA 62.435 66.667 0.00 0.00 41.67 2.74
427 429 2.367567 TGGATTCCTAATAGACGGTGGC 59.632 50.000 3.95 0.00 0.00 5.01
439 441 3.695060 GTGTCTCTCGTTCTGGATTCCTA 59.305 47.826 3.95 0.00 0.00 2.94
442 444 3.577649 TGTGTCTCTCGTTCTGGATTC 57.422 47.619 0.00 0.00 0.00 2.52
452 454 5.611796 TTTTGGATCATTTGTGTCTCTCG 57.388 39.130 0.00 0.00 0.00 4.04
481 483 1.000506 CCGGAGTTTCTTCGGTGAGAA 59.999 52.381 8.19 0.00 46.70 2.87
483 485 3.123674 CCGGAGTTTCTTCGGTGAG 57.876 57.895 8.19 0.00 46.70 3.51
488 490 0.173708 CCTCTCCCGGAGTTTCTTCG 59.826 60.000 14.36 0.00 40.30 3.79
513 515 2.186125 CCCGGCGACTTAGGGTTC 59.814 66.667 9.30 0.00 40.27 3.62
528 530 0.541998 CCTTGTTTTCCCCTGGTCCC 60.542 60.000 0.00 0.00 0.00 4.46
533 535 2.884639 CTGTGTACCTTGTTTTCCCCTG 59.115 50.000 0.00 0.00 0.00 4.45
535 537 2.940158 ACTGTGTACCTTGTTTTCCCC 58.060 47.619 0.00 0.00 0.00 4.81
554 556 1.396815 GCGCAACAGTCGACAAAGTAC 60.397 52.381 19.50 8.19 0.00 2.73
562 564 0.808060 TCAACAAGCGCAACAGTCGA 60.808 50.000 11.47 0.00 0.00 4.20
575 577 2.627699 GGGTTTGCAGGAGATTCAACAA 59.372 45.455 0.00 0.00 0.00 2.83
610 612 7.116736 AGAAAGAGGAGTGTTGTTCCTTAAAA 58.883 34.615 0.00 0.00 45.00 1.52
611 613 6.659824 AGAAAGAGGAGTGTTGTTCCTTAAA 58.340 36.000 0.00 0.00 45.00 1.52
612 614 6.248569 AGAAAGAGGAGTGTTGTTCCTTAA 57.751 37.500 0.00 0.00 45.00 1.85
613 615 5.888982 AGAAAGAGGAGTGTTGTTCCTTA 57.111 39.130 0.00 0.00 45.00 2.69
614 616 4.779993 AGAAAGAGGAGTGTTGTTCCTT 57.220 40.909 0.00 0.00 45.00 3.36
616 618 6.289064 TCTTAAGAAAGAGGAGTGTTGTTCC 58.711 40.000 1.68 0.00 36.80 3.62
617 619 7.254829 GGTTCTTAAGAAAGAGGAGTGTTGTTC 60.255 40.741 19.30 1.67 42.60 3.18
626 628 6.003950 CCAACATGGTTCTTAAGAAAGAGGA 58.996 40.000 19.30 2.92 42.60 3.71
643 645 4.207165 CCTAACCCATTCCTACCAACATG 58.793 47.826 0.00 0.00 0.00 3.21
660 662 3.261137 ACCAGTAAGCACTTCTCCCTAAC 59.739 47.826 0.00 0.00 30.46 2.34
748 752 5.811613 CGGGCAATTTATTCACATGACATTT 59.188 36.000 0.00 0.00 0.00 2.32
749 753 5.105392 ACGGGCAATTTATTCACATGACATT 60.105 36.000 0.00 0.00 0.00 2.71
750 754 4.402155 ACGGGCAATTTATTCACATGACAT 59.598 37.500 0.00 0.00 0.00 3.06
751 755 3.761218 ACGGGCAATTTATTCACATGACA 59.239 39.130 0.00 0.00 0.00 3.58
752 756 4.370364 ACGGGCAATTTATTCACATGAC 57.630 40.909 0.00 0.00 0.00 3.06
754 758 7.452231 GTTTTTACGGGCAATTTATTCACATG 58.548 34.615 0.00 0.00 0.00 3.21
755 759 6.309251 CGTTTTTACGGGCAATTTATTCACAT 59.691 34.615 0.00 0.00 0.00 3.21
756 760 5.629849 CGTTTTTACGGGCAATTTATTCACA 59.370 36.000 0.00 0.00 0.00 3.58
757 761 5.630264 ACGTTTTTACGGGCAATTTATTCAC 59.370 36.000 2.61 0.00 37.45 3.18
766 770 1.557651 GCAAACGTTTTTACGGGCAA 58.442 45.000 11.66 0.00 37.45 4.52
785 789 2.482333 CGCACTAGGGGAGAGACGG 61.482 68.421 0.00 0.00 0.00 4.79
799 803 2.835027 CCCTAGAAAATAGGACCGCAC 58.165 52.381 2.43 0.00 36.85 5.34
814 818 2.436646 CTTGTGTGGGCGCCCTAG 60.437 66.667 43.34 27.08 36.94 3.02
907 912 0.389817 TGAACACGAATGGAGCGAGG 60.390 55.000 0.00 0.00 0.00 4.63
908 913 0.716108 GTGAACACGAATGGAGCGAG 59.284 55.000 0.00 0.00 0.00 5.03
931 936 1.909781 GGAGACGGGTGTGGTGGTA 60.910 63.158 0.00 0.00 0.00 3.25
1068 1073 2.110213 GCGTGGTTGTGGAGGACA 59.890 61.111 0.00 0.00 0.00 4.02
1204 1209 1.212229 GGTGGAGGAAGTCGACGAC 59.788 63.158 20.25 20.25 34.78 4.34
1729 1734 2.005451 GCCTGACAACACATCTAGCAG 58.995 52.381 0.00 0.00 0.00 4.24
1734 1739 0.952497 CTGCGCCTGACAACACATCT 60.952 55.000 4.18 0.00 0.00 2.90
1787 1792 0.804989 CCTCGCACCAACTGAAATCC 59.195 55.000 0.00 0.00 0.00 3.01
1808 1813 4.063689 CTGCCTCATATTGTCCTCATGAC 58.936 47.826 0.00 0.00 44.72 3.06
1842 1847 1.987770 GGCTGCAAATCAACAATGTCG 59.012 47.619 0.50 0.00 0.00 4.35
1867 1872 1.454201 TCAACGTTGTTCAGCACCAA 58.546 45.000 26.47 1.47 0.00 3.67
1974 1979 2.566833 AGCACTGTTCATTAGCACCA 57.433 45.000 0.00 0.00 0.00 4.17
2035 2040 4.346734 AGCATGCAGAAAGAAACATACG 57.653 40.909 21.98 0.00 0.00 3.06
2171 2176 3.118038 AGCCAACAAAGTAGGTCAGAACA 60.118 43.478 0.00 0.00 0.00 3.18
2192 2197 7.821595 TTCGTATTGTGGATAGTACAACAAG 57.178 36.000 0.00 0.00 40.47 3.16
2297 2302 5.532406 TGCTTGGGAAGAATAATATCTGCAC 59.468 40.000 0.00 0.00 0.00 4.57
2306 2311 3.621268 CGACGAATGCTTGGGAAGAATAA 59.379 43.478 0.00 0.00 0.00 1.40
2345 2350 5.050499 GCATACCTCACGAGAAATGAAGATG 60.050 44.000 10.84 0.00 0.00 2.90
3019 3024 4.202202 CCTGCTGAAGATTACTACCTCCAG 60.202 50.000 0.00 0.00 0.00 3.86
3290 3295 4.651045 TGACATCTCATACAGCATAGGTGT 59.349 41.667 7.06 7.06 46.27 4.16
3374 3379 8.722394 TCGATATTTAATGCAAAAGTACACACA 58.278 29.630 0.00 0.00 0.00 3.72
3433 3438 0.804989 GGAACAAAGGTCATGCTCGG 59.195 55.000 0.00 0.00 0.00 4.63
3796 3801 4.083057 GCCTAGAGCTTTTGAACTTGAAGG 60.083 45.833 0.00 0.00 38.99 3.46
3857 3863 8.836413 CACACAAATAAGAACTCTAAAACTCCA 58.164 33.333 0.00 0.00 0.00 3.86
4041 4048 3.128242 AGCTTTGTAGATGTTGCTGATGC 59.872 43.478 0.00 0.00 40.20 3.91
4124 4132 9.132521 CACTTTGACCATCTAAAATTGTTGATC 57.867 33.333 0.00 0.00 0.00 2.92
4167 4175 7.985476 CAATGTAGGTAGTTTTAGACATTGGG 58.015 38.462 14.71 0.00 45.21 4.12
4237 4245 5.914898 AAGCCAACCTACCAAATATCAAC 57.085 39.130 0.00 0.00 0.00 3.18
4243 4251 7.179269 TGATAAAGTAAGCCAACCTACCAAAT 58.821 34.615 0.00 0.00 0.00 2.32
4248 4256 6.877322 TCTGTTGATAAAGTAAGCCAACCTAC 59.123 38.462 0.00 0.00 37.04 3.18
4356 4366 8.487176 GTGCCATAAGAAACAAAACATTTACAG 58.513 33.333 0.00 0.00 0.00 2.74
4633 4644 4.024133 TCAAAATCACACATCAGTTCCACG 60.024 41.667 0.00 0.00 0.00 4.94
4644 4655 8.759481 TTATATAAGCCCATCAAAATCACACA 57.241 30.769 0.00 0.00 0.00 3.72
4740 4753 5.763204 ACGGAAAATAGCGAATGGTTATGAT 59.237 36.000 0.00 0.00 0.00 2.45
4762 4775 3.731089 TGGGTTACTAACTGGTTGAACG 58.269 45.455 0.00 0.00 0.00 3.95
4824 4837 8.967918 GGTAGCCAATTAGAGGAAAACTTAATT 58.032 33.333 0.00 0.00 0.00 1.40
4825 4838 8.336987 AGGTAGCCAATTAGAGGAAAACTTAAT 58.663 33.333 0.00 0.00 0.00 1.40
4828 4841 6.140968 AGGTAGCCAATTAGAGGAAAACTT 57.859 37.500 0.00 0.00 0.00 2.66
4831 4844 5.772393 TGAGGTAGCCAATTAGAGGAAAA 57.228 39.130 0.00 0.00 0.00 2.29
4846 4859 7.436933 TGATGTAATGCTACAGATTGAGGTAG 58.563 38.462 0.00 0.00 41.33 3.18
4948 4961 2.718563 AGGAAACGGACTGTTGTTTGT 58.281 42.857 14.25 2.59 40.84 2.83
4960 4973 4.001652 GAGGTCCTCTTTAAAGGAAACGG 58.998 47.826 15.13 8.29 46.90 4.44
5012 5025 0.971386 AACTACATGGACGGTCGGTT 59.029 50.000 1.43 0.00 0.00 4.44
5024 5037 5.768164 CCAGGTTACAGGAAACAAACTACAT 59.232 40.000 0.00 0.00 0.00 2.29
5155 5171 5.132502 AGAAAAGGGCAAGGAAATTTTTGG 58.867 37.500 5.08 0.00 0.00 3.28
5200 5217 3.168035 TGCTCAAGGGCAAGGAATTAA 57.832 42.857 0.00 0.00 39.43 1.40
5257 5275 5.523552 GTGATTTCAGTTTTGGGGTTTGAAG 59.476 40.000 0.00 0.00 0.00 3.02
5296 5314 1.054231 TGGCCAAAATGGAATGCACA 58.946 45.000 0.61 0.00 40.96 4.57
5365 5383 3.259625 ACCTAGGTGCAAGAAGAAGAGAC 59.740 47.826 15.42 0.00 0.00 3.36
5397 5415 4.097135 CGAGTATTGGAGAGAGACACACAT 59.903 45.833 0.00 0.00 0.00 3.21
5405 5423 3.702045 AGTTTCCCGAGTATTGGAGAGAG 59.298 47.826 0.00 0.00 45.05 3.20
5449 5467 7.044181 TGATCCACTAGCACAGATTCTAAAAG 58.956 38.462 0.00 0.00 0.00 2.27
5465 5483 7.875327 GGCTAAACCTAAAAATGATCCACTA 57.125 36.000 0.00 0.00 34.51 2.74


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

AutoCloner maintained by Alex Coulton.