Multiple sequence alignment - TraesCS1D01G117600

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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 TraesCS1D01G117600 chr1D 100.000 4310 0 0 1 4310 113912600 113908291 0.000000e+00 7960.0
1 TraesCS1D01G117600 chr1A 97.486 3540 67 10 781 4310 122504005 122500478 0.000000e+00 6024.0
2 TraesCS1D01G117600 chr1A 83.359 655 79 13 905 1542 360986360 360987001 2.890000e-161 579.0
3 TraesCS1D01G117600 chr1B 96.529 3400 85 13 630 4007 174104387 174107775 0.000000e+00 5594.0
4 TraesCS1D01G117600 chr1B 97.394 307 7 1 4005 4310 174107897 174108203 4.940000e-144 521.0
5 TraesCS1D01G117600 chr1B 86.783 401 47 3 16 410 174103751 174104151 3.960000e-120 442.0
6 TraesCS1D01G117600 chr1B 85.874 269 34 3 904 1171 653823535 653823270 2.540000e-72 283.0
7 TraesCS1D01G117600 chr5B 83.053 655 82 13 905 1542 591571188 591571830 6.250000e-158 568.0
8 TraesCS1D01G117600 chr2B 80.931 666 95 22 904 1543 482629927 482630586 8.320000e-137 497.0
9 TraesCS1D01G117600 chr2B 80.665 662 75 28 904 1543 725467453 725468083 8.440000e-127 464.0
10 TraesCS1D01G117600 chr2B 79.609 358 52 14 1001 1355 87473287 87473626 2.000000e-58 237.0
11 TraesCS1D01G117600 chr4A 81.882 574 59 18 1005 1542 4251870 4251306 3.960000e-120 442.0
12 TraesCS1D01G117600 chr7B 82.270 282 35 11 930 1211 568667690 568667956 3.350000e-56 230.0
13 TraesCS1D01G117600 chr5D 84.946 186 26 2 936 1121 323560509 323560326 2.050000e-43 187.0
14 TraesCS1D01G117600 chr3D 84.375 192 28 2 930 1121 80578255 80578444 2.050000e-43 187.0
15 TraesCS1D01G117600 chr3A 88.043 92 11 0 1264 1355 628900623 628900714 4.560000e-20 110.0
16 TraesCS1D01G117600 chr3A 88.043 92 11 0 1264 1355 696200047 696200138 4.560000e-20 110.0
17 TraesCS1D01G117600 chr4D 85.714 70 9 1 625 693 372507401 372507332 5.980000e-09 73.1
18 TraesCS1D01G117600 chr6D 76.812 138 16 10 625 749 58006581 58006715 3.600000e-06 63.9


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 TraesCS1D01G117600 chr1D 113908291 113912600 4309 True 7960.000000 7960 100.000000 1 4310 1 chr1D.!!$R1 4309
1 TraesCS1D01G117600 chr1A 122500478 122504005 3527 True 6024.000000 6024 97.486000 781 4310 1 chr1A.!!$R1 3529
2 TraesCS1D01G117600 chr1A 360986360 360987001 641 False 579.000000 579 83.359000 905 1542 1 chr1A.!!$F1 637
3 TraesCS1D01G117600 chr1B 174103751 174108203 4452 False 2185.666667 5594 93.568667 16 4310 3 chr1B.!!$F1 4294
4 TraesCS1D01G117600 chr5B 591571188 591571830 642 False 568.000000 568 83.053000 905 1542 1 chr5B.!!$F1 637
5 TraesCS1D01G117600 chr2B 482629927 482630586 659 False 497.000000 497 80.931000 904 1543 1 chr2B.!!$F2 639
6 TraesCS1D01G117600 chr2B 725467453 725468083 630 False 464.000000 464 80.665000 904 1543 1 chr2B.!!$F3 639
7 TraesCS1D01G117600 chr4A 4251306 4251870 564 True 442.000000 442 81.882000 1005 1542 1 chr4A.!!$R1 537

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
428 434 0.036732 GCTGAATCAGTGGTGGTGGA 59.963 55.000 12.29 0.0 33.43 4.02 F
441 447 0.531974 TGGTGGATCTAAATCGGCGC 60.532 55.000 0.00 0.0 32.24 6.53 F
1361 1464 1.001520 CACCCTGTGTGTGATCCGTAA 59.998 52.381 0.00 0.0 40.26 3.18 F
1695 1843 0.818296 AGCCTGCCTACTGTTAGTCG 59.182 55.000 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1361 1464 0.896226 GAGCTCAGAGGTTACGGGTT 59.104 55.000 9.40 0.0 0.00 4.11 R
1402 1508 0.934496 TTACAGAAGCACACACACGC 59.066 50.000 0.00 0.0 0.00 5.34 R
2948 3097 0.179040 TTGGAAACCACTCACGGGTC 60.179 55.000 0.00 0.0 37.77 4.46 R
3334 3489 1.275856 ACCAAGCTGAGCAGAGAAGAG 59.724 52.381 7.39 0.0 0.00 2.85 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 2.612285 AGAGGAGTCACATGAGACCA 57.388 50.000 18.21 0.00 39.34 4.02
29 30 6.810911 AGTCACATGAGACCATCTACAATAC 58.189 40.000 18.21 0.00 39.34 1.89
37 38 5.529791 AGACCATCTACAATACGGAAATCG 58.470 41.667 0.00 0.00 45.88 3.34
38 39 4.056050 ACCATCTACAATACGGAAATCGC 58.944 43.478 0.00 0.00 43.89 4.58
39 40 4.055360 CCATCTACAATACGGAAATCGCA 58.945 43.478 0.00 0.00 43.89 5.10
92 97 7.119846 CCCAACAAGTTTAACCAATTTTTCACA 59.880 33.333 0.00 0.00 0.00 3.58
118 123 3.574614 GGGGATTTTGTCGAACATGTTG 58.425 45.455 17.58 8.66 0.00 3.33
137 142 2.106683 CGTGCGGGGATGAAGGAAC 61.107 63.158 0.00 0.00 0.00 3.62
160 166 3.503749 CTGCTAGTCGGAGCGTCT 58.496 61.111 0.00 0.00 45.99 4.18
164 170 0.945813 GCTAGTCGGAGCGTCTATGT 59.054 55.000 0.00 0.00 31.57 2.29
169 175 0.892755 TCGGAGCGTCTATGTTGGTT 59.107 50.000 0.00 0.00 0.00 3.67
171 177 0.727398 GGAGCGTCTATGTTGGTTGC 59.273 55.000 0.00 0.00 0.00 4.17
172 178 1.438651 GAGCGTCTATGTTGGTTGCA 58.561 50.000 0.00 0.00 0.00 4.08
176 182 1.803334 GTCTATGTTGGTTGCACCGA 58.197 50.000 0.00 0.00 42.58 4.69
183 189 1.380403 TTGGTTGCACCGACTGTTGG 61.380 55.000 12.66 12.66 42.58 3.77
189 195 3.566210 ACCGACTGTTGGGGGTGG 61.566 66.667 18.18 0.00 0.00 4.61
215 221 0.106318 GGGTCTCCTACGCCTCCTTA 60.106 60.000 0.00 0.00 35.04 2.69
217 223 1.408340 GGTCTCCTACGCCTCCTTAAC 59.592 57.143 0.00 0.00 0.00 2.01
245 251 1.227674 CTGGTGGCCGAGGCTATTC 60.228 63.158 14.33 5.58 41.60 1.75
247 253 2.499685 GTGGCCGAGGCTATTCGT 59.500 61.111 14.33 0.00 41.60 3.85
268 274 2.726909 CACACAATGCCGGCAACA 59.273 55.556 36.33 11.20 0.00 3.33
283 289 1.434555 CAACACCGACCGAAGCAATA 58.565 50.000 0.00 0.00 0.00 1.90
296 302 2.593134 GCAATAGCGGCTCAGCTCG 61.593 63.158 5.39 0.00 45.67 5.03
315 321 2.807895 CCGCGTTGGTCGTTCGAT 60.808 61.111 4.92 0.00 42.13 3.59
318 324 0.918619 CGCGTTGGTCGTTCGATAAT 59.081 50.000 0.00 0.00 42.13 1.28
330 336 3.394719 GTTCGATAATCCCTCCAAGCTC 58.605 50.000 0.00 0.00 0.00 4.09
331 337 1.971357 TCGATAATCCCTCCAAGCTCC 59.029 52.381 0.00 0.00 0.00 4.70
336 342 4.479993 CCCTCCAAGCTCCGGCAG 62.480 72.222 0.00 0.00 41.70 4.85
352 358 2.623889 CGGCAGCCAGTAGTTCTACTAT 59.376 50.000 13.30 0.40 32.65 2.12
359 365 4.501743 GCCAGTAGTTCTACTATGGAAGGC 60.502 50.000 17.00 16.33 34.31 4.35
363 369 0.387929 TTCTACTATGGAAGGCGGCG 59.612 55.000 0.51 0.51 0.00 6.46
419 425 3.987404 GCCAACGGCTGAATCAGT 58.013 55.556 12.29 0.00 46.69 3.41
420 426 1.503542 GCCAACGGCTGAATCAGTG 59.496 57.895 12.29 7.53 46.69 3.66
421 427 1.926511 GCCAACGGCTGAATCAGTGG 61.927 60.000 12.29 12.05 46.69 4.00
422 428 0.606401 CCAACGGCTGAATCAGTGGT 60.606 55.000 12.29 7.26 33.43 4.16
423 429 0.518636 CAACGGCTGAATCAGTGGTG 59.481 55.000 12.29 9.84 33.43 4.17
424 430 0.606401 AACGGCTGAATCAGTGGTGG 60.606 55.000 12.29 0.11 33.43 4.61
425 431 1.003355 CGGCTGAATCAGTGGTGGT 60.003 57.895 12.29 0.00 33.43 4.16
426 432 1.300971 CGGCTGAATCAGTGGTGGTG 61.301 60.000 12.29 0.00 33.43 4.17
427 433 0.962356 GGCTGAATCAGTGGTGGTGG 60.962 60.000 12.29 0.00 33.43 4.61
428 434 0.036732 GCTGAATCAGTGGTGGTGGA 59.963 55.000 12.29 0.00 33.43 4.02
429 435 1.340405 GCTGAATCAGTGGTGGTGGAT 60.340 52.381 12.29 0.00 33.43 3.41
430 436 2.636830 CTGAATCAGTGGTGGTGGATC 58.363 52.381 1.31 0.00 0.00 3.36
431 437 2.238144 CTGAATCAGTGGTGGTGGATCT 59.762 50.000 1.31 0.00 0.00 2.75
432 438 3.449918 TGAATCAGTGGTGGTGGATCTA 58.550 45.455 0.00 0.00 0.00 1.98
433 439 3.843619 TGAATCAGTGGTGGTGGATCTAA 59.156 43.478 0.00 0.00 0.00 2.10
434 440 4.288366 TGAATCAGTGGTGGTGGATCTAAA 59.712 41.667 0.00 0.00 0.00 1.85
435 441 5.044919 TGAATCAGTGGTGGTGGATCTAAAT 60.045 40.000 0.00 0.00 0.00 1.40
436 442 4.487714 TCAGTGGTGGTGGATCTAAATC 57.512 45.455 0.00 0.00 0.00 2.17
437 443 3.118775 TCAGTGGTGGTGGATCTAAATCG 60.119 47.826 0.00 0.00 32.24 3.34
438 444 2.170607 AGTGGTGGTGGATCTAAATCGG 59.829 50.000 0.00 0.00 32.24 4.18
439 445 1.134220 TGGTGGTGGATCTAAATCGGC 60.134 52.381 0.00 0.00 32.24 5.54
440 446 1.217882 GTGGTGGATCTAAATCGGCG 58.782 55.000 0.00 0.00 32.24 6.46
441 447 0.531974 TGGTGGATCTAAATCGGCGC 60.532 55.000 0.00 0.00 32.24 6.53
442 448 1.557443 GGTGGATCTAAATCGGCGCG 61.557 60.000 0.00 0.00 32.24 6.86
443 449 1.954146 TGGATCTAAATCGGCGCGC 60.954 57.895 25.94 25.94 32.24 6.86
444 450 2.668280 GGATCTAAATCGGCGCGCC 61.668 63.158 39.82 39.82 32.24 6.53
445 451 1.954146 GATCTAAATCGGCGCGCCA 60.954 57.895 45.26 33.00 35.37 5.69
446 452 1.495584 GATCTAAATCGGCGCGCCAA 61.496 55.000 45.26 33.96 35.37 4.52
447 453 1.772063 ATCTAAATCGGCGCGCCAAC 61.772 55.000 45.26 22.78 35.37 3.77
448 454 3.767066 CTAAATCGGCGCGCCAACG 62.767 63.158 45.26 32.55 44.07 4.10
490 496 1.188219 CGATGGGGTCAGGGATCGAT 61.188 60.000 0.00 0.00 40.06 3.59
526 532 1.202545 GGCGACTACCAGGGAGAAATC 60.203 57.143 5.34 0.00 0.00 2.17
530 536 2.758979 GACTACCAGGGAGAAATCGTCA 59.241 50.000 5.34 0.00 0.00 4.35
531 537 2.761208 ACTACCAGGGAGAAATCGTCAG 59.239 50.000 5.34 0.00 0.00 3.51
564 572 2.179517 GGAGGAGCGACTGTGACG 59.820 66.667 0.00 0.00 0.00 4.35
618 626 1.136169 GCGACGCGAATTGGTTTTACT 60.136 47.619 15.93 0.00 0.00 2.24
621 629 1.461897 ACGCGAATTGGTTTTACTCGG 59.538 47.619 15.93 0.00 0.00 4.63
622 630 1.727880 CGCGAATTGGTTTTACTCGGA 59.272 47.619 0.00 0.00 0.00 4.55
627 635 2.618442 TTGGTTTTACTCGGACGGTT 57.382 45.000 0.00 0.00 0.00 4.44
639 676 5.535333 ACTCGGACGGTTATGTATATTTGG 58.465 41.667 0.00 0.00 0.00 3.28
642 679 6.761312 TCGGACGGTTATGTATATTTGGATT 58.239 36.000 0.00 0.00 0.00 3.01
681 750 8.645814 TTTTACATCTAGAGTAGAACCAGTGA 57.354 34.615 0.00 0.00 38.50 3.41
682 751 8.645814 TTTACATCTAGAGTAGAACCAGTGAA 57.354 34.615 0.00 0.00 38.50 3.18
712 781 2.645802 ACTGTTGGAGCACCGTTTTTA 58.354 42.857 0.00 0.00 39.42 1.52
731 800 9.187455 CGTTTTTAGGCATTTGTACTGTAAAAT 57.813 29.630 0.00 0.00 0.00 1.82
791 860 2.859165 TTAGCTTTGAGGGACTGGTG 57.141 50.000 0.00 0.00 41.55 4.17
1129 1203 1.607148 ACTCAAAACCCTAGCGCAAAC 59.393 47.619 11.47 0.00 0.00 2.93
1178 1265 2.046023 CCGGTGAATGGCAGCTGA 60.046 61.111 20.43 0.00 42.75 4.26
1361 1464 1.001520 CACCCTGTGTGTGATCCGTAA 59.998 52.381 0.00 0.00 40.26 3.18
1402 1508 7.172190 AGCTCAATACCTTCGAATTGATATGTG 59.828 37.037 11.26 2.90 40.37 3.21
1403 1509 7.189693 TCAATACCTTCGAATTGATATGTGC 57.810 36.000 7.63 0.00 37.23 4.57
1404 1510 5.845985 ATACCTTCGAATTGATATGTGCG 57.154 39.130 0.00 0.00 0.00 5.34
1405 1511 3.531538 ACCTTCGAATTGATATGTGCGT 58.468 40.909 0.00 0.00 0.00 5.24
1491 1639 1.444895 CGCTTGCTTTGGTGGATGC 60.445 57.895 0.00 0.00 0.00 3.91
1494 1642 1.164411 CTTGCTTTGGTGGATGCGTA 58.836 50.000 0.00 0.00 0.00 4.42
1564 1712 1.839424 AGAAGGGTTGCATGCCTAAC 58.161 50.000 16.68 13.65 0.00 2.34
1672 1820 6.150976 CCAATTCTTCTATTACACCTTGCACA 59.849 38.462 0.00 0.00 0.00 4.57
1695 1843 0.818296 AGCCTGCCTACTGTTAGTCG 59.182 55.000 0.00 0.00 0.00 4.18
1774 1922 5.426504 TGTGACAGCAAACAATTCCATTTT 58.573 33.333 0.00 0.00 0.00 1.82
1798 1946 4.448537 TGTGTAGTTTTGTGCTTTGCTT 57.551 36.364 0.00 0.00 0.00 3.91
1845 1993 7.651704 GGGTGGAAATTTATAACCATGAAATCG 59.348 37.037 14.87 0.00 34.87 3.34
1872 2021 3.394606 TGAAAAGGAGGCTTACTTGACCT 59.605 43.478 0.00 0.00 36.19 3.85
2221 2370 6.432581 TCTGAGGCTACTACTTTCAATCCTA 58.567 40.000 0.00 0.00 0.00 2.94
2222 2371 7.069986 TCTGAGGCTACTACTTTCAATCCTAT 58.930 38.462 0.00 0.00 0.00 2.57
2264 2413 3.401182 GAGATGAGATGGTTGAGGCATC 58.599 50.000 0.00 0.00 34.02 3.91
2307 2456 2.334977 TGTCAGGACACCTTGTACCAT 58.665 47.619 0.00 0.00 36.21 3.55
2391 2540 1.787847 GGTCACGCCTGAAACATCG 59.212 57.895 0.00 0.00 0.00 3.84
2502 2651 1.202698 CGTGATTCCTCCCCTGGATTC 60.203 57.143 0.00 0.00 37.15 2.52
2679 2828 6.561614 AGCATTTTGTAGCTTTGATGATCAG 58.438 36.000 0.09 0.00 38.01 2.90
2687 2836 3.380637 AGCTTTGATGATCAGCATGGTTC 59.619 43.478 15.50 0.00 37.34 3.62
2740 2889 3.074390 TGATGTTGAGACCACTTTGGGAT 59.926 43.478 0.00 0.00 43.37 3.85
2767 2916 5.852282 ACCACACAATACAAGAAAGCTTT 57.148 34.783 12.53 12.53 30.14 3.51
2948 3097 4.452733 GAGGCGTCGGGGTCTTGG 62.453 72.222 0.00 0.00 0.00 3.61
3035 3184 1.606737 GGAGTGTCCTCAGTCTGTTGC 60.607 57.143 0.00 0.00 42.03 4.17
3795 3952 9.007901 GGCAATATTCTGTTAGCTCTTGAATAT 57.992 33.333 13.62 13.62 40.12 1.28
4147 4429 6.113411 CGGAAGTAATACCAAAGGAAGATGT 58.887 40.000 0.00 0.00 0.00 3.06
4180 4462 5.591877 CAGAGATCTTCCCAAACATTTAGGG 59.408 44.000 0.00 0.00 44.22 3.53
4216 4498 1.063266 GTCTGATCTGGGAGGAGAGGT 60.063 57.143 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.612285 TGGTCTCATGTGACTCCTCT 57.388 50.000 23.17 0.00 37.16 3.69
1 2 3.030291 AGATGGTCTCATGTGACTCCTC 58.970 50.000 23.17 17.23 37.16 3.71
2 3 3.113191 AGATGGTCTCATGTGACTCCT 57.887 47.619 23.17 15.69 37.16 3.69
3 4 3.701542 TGTAGATGGTCTCATGTGACTCC 59.298 47.826 23.17 11.52 37.16 3.85
4 5 4.991153 TGTAGATGGTCTCATGTGACTC 57.009 45.455 23.17 15.54 37.16 3.36
6 7 5.687730 CGTATTGTAGATGGTCTCATGTGAC 59.312 44.000 17.64 17.64 32.98 3.67
7 8 5.221244 CCGTATTGTAGATGGTCTCATGTGA 60.221 44.000 0.00 0.00 32.98 3.58
8 9 4.984785 CCGTATTGTAGATGGTCTCATGTG 59.015 45.833 0.00 0.00 32.98 3.21
9 10 4.893524 TCCGTATTGTAGATGGTCTCATGT 59.106 41.667 0.00 0.00 32.98 3.21
10 11 5.453567 TCCGTATTGTAGATGGTCTCATG 57.546 43.478 0.00 0.00 32.98 3.07
11 12 6.479972 TTTCCGTATTGTAGATGGTCTCAT 57.520 37.500 0.00 0.00 36.09 2.90
12 13 5.925506 TTTCCGTATTGTAGATGGTCTCA 57.074 39.130 0.00 0.00 0.00 3.27
13 14 5.629849 CGATTTCCGTATTGTAGATGGTCTC 59.370 44.000 0.00 0.00 0.00 3.36
14 15 5.529791 CGATTTCCGTATTGTAGATGGTCT 58.470 41.667 0.00 0.00 0.00 3.85
15 16 4.150098 GCGATTTCCGTATTGTAGATGGTC 59.850 45.833 0.00 0.00 41.15 4.02
16 17 4.056050 GCGATTTCCGTATTGTAGATGGT 58.944 43.478 0.00 0.00 41.15 3.55
17 18 4.055360 TGCGATTTCCGTATTGTAGATGG 58.945 43.478 0.00 0.00 41.15 3.51
18 19 5.651172 TTGCGATTTCCGTATTGTAGATG 57.349 39.130 0.00 0.00 41.15 2.90
19 20 5.989168 TGATTGCGATTTCCGTATTGTAGAT 59.011 36.000 0.00 0.00 41.15 1.98
29 30 4.335082 TGTAGTTTGATTGCGATTTCCG 57.665 40.909 0.00 0.00 42.21 4.30
37 38 4.092821 TGCACGTAGATGTAGTTTGATTGC 59.907 41.667 0.00 0.00 0.00 3.56
38 39 5.778161 TGCACGTAGATGTAGTTTGATTG 57.222 39.130 0.00 0.00 0.00 2.67
39 40 6.795098 TTTGCACGTAGATGTAGTTTGATT 57.205 33.333 0.00 0.00 0.00 2.57
98 103 2.986479 GCAACATGTTCGACAAAATCCC 59.014 45.455 8.48 0.00 0.00 3.85
114 119 3.834013 TTCATCCCCGCACGCAACA 62.834 57.895 0.00 0.00 0.00 3.33
118 123 3.969250 TTCCTTCATCCCCGCACGC 62.969 63.158 0.00 0.00 0.00 5.34
169 175 4.263572 CCCCCAACAGTCGGTGCA 62.264 66.667 0.00 0.00 0.00 4.57
171 177 2.281484 CACCCCCAACAGTCGGTG 60.281 66.667 0.00 0.00 39.85 4.94
172 178 3.566210 CCACCCCCAACAGTCGGT 61.566 66.667 0.00 0.00 0.00 4.69
189 195 2.582978 GTAGGAGACCCAACCGCC 59.417 66.667 0.00 0.00 33.88 6.13
239 245 1.094785 ATTGTGTGGCCACGAATAGC 58.905 50.000 30.07 15.57 44.92 2.97
240 246 1.202177 GCATTGTGTGGCCACGAATAG 60.202 52.381 30.07 21.64 44.92 1.73
263 269 1.852067 ATTGCTTCGGTCGGTGTTGC 61.852 55.000 0.00 0.00 0.00 4.17
268 274 1.518572 CGCTATTGCTTCGGTCGGT 60.519 57.895 0.00 0.00 36.97 4.69
271 277 1.491505 GAGCCGCTATTGCTTCGGTC 61.492 60.000 0.00 0.00 44.58 4.79
300 306 1.257155 GGATTATCGAACGACCAACGC 59.743 52.381 0.00 0.00 46.94 4.84
315 321 1.696097 GCCGGAGCTTGGAGGGATTA 61.696 60.000 5.05 0.00 35.50 1.75
330 336 0.179108 GTAGAACTACTGGCTGCCGG 60.179 60.000 25.62 25.62 35.68 6.13
331 337 0.818296 AGTAGAACTACTGGCTGCCG 59.182 55.000 14.98 11.36 44.11 5.69
336 342 4.501743 GCCTTCCATAGTAGAACTACTGGC 60.502 50.000 20.46 18.49 45.25 4.85
363 369 0.662085 GATGTCTCCCGTACCTCGTC 59.338 60.000 0.00 0.00 37.94 4.20
369 375 0.179081 GCCCTTGATGTCTCCCGTAC 60.179 60.000 0.00 0.00 0.00 3.67
374 380 1.817099 CAGCGCCCTTGATGTCTCC 60.817 63.158 2.29 0.00 0.00 3.71
410 416 2.238144 AGATCCACCACCACTGATTCAG 59.762 50.000 12.17 12.17 37.52 3.02
411 417 2.269023 AGATCCACCACCACTGATTCA 58.731 47.619 0.00 0.00 0.00 2.57
412 418 4.487714 TTAGATCCACCACCACTGATTC 57.512 45.455 0.00 0.00 0.00 2.52
413 419 4.927267 TTTAGATCCACCACCACTGATT 57.073 40.909 0.00 0.00 0.00 2.57
414 420 4.443457 CGATTTAGATCCACCACCACTGAT 60.443 45.833 0.00 0.00 0.00 2.90
415 421 3.118775 CGATTTAGATCCACCACCACTGA 60.119 47.826 0.00 0.00 0.00 3.41
416 422 3.198068 CGATTTAGATCCACCACCACTG 58.802 50.000 0.00 0.00 0.00 3.66
417 423 2.170607 CCGATTTAGATCCACCACCACT 59.829 50.000 0.00 0.00 0.00 4.00
418 424 2.561569 CCGATTTAGATCCACCACCAC 58.438 52.381 0.00 0.00 0.00 4.16
419 425 1.134220 GCCGATTTAGATCCACCACCA 60.134 52.381 0.00 0.00 0.00 4.17
420 426 1.594331 GCCGATTTAGATCCACCACC 58.406 55.000 0.00 0.00 0.00 4.61
421 427 1.217882 CGCCGATTTAGATCCACCAC 58.782 55.000 0.00 0.00 0.00 4.16
422 428 0.531974 GCGCCGATTTAGATCCACCA 60.532 55.000 0.00 0.00 0.00 4.17
423 429 1.557443 CGCGCCGATTTAGATCCACC 61.557 60.000 0.00 0.00 0.00 4.61
424 430 1.853319 CGCGCCGATTTAGATCCAC 59.147 57.895 0.00 0.00 0.00 4.02
425 431 1.954146 GCGCGCCGATTTAGATCCA 60.954 57.895 23.24 0.00 0.00 3.41
426 432 2.668280 GGCGCGCCGATTTAGATCC 61.668 63.158 37.24 7.16 0.00 3.36
427 433 1.495584 TTGGCGCGCCGATTTAGATC 61.496 55.000 41.73 17.23 39.42 2.75
428 434 1.522806 TTGGCGCGCCGATTTAGAT 60.523 52.632 41.73 0.00 39.42 1.98
429 435 2.125472 TTGGCGCGCCGATTTAGA 60.125 55.556 41.73 22.75 39.42 2.10
430 436 2.022762 GTTGGCGCGCCGATTTAG 59.977 61.111 40.71 0.00 39.42 1.85
431 437 3.855589 CGTTGGCGCGCCGATTTA 61.856 61.111 40.71 23.49 39.42 1.40
443 449 4.796231 CGTCGGAGGCCTCGTTGG 62.796 72.222 26.36 15.01 39.35 3.77
444 450 4.796231 CCGTCGGAGGCCTCGTTG 62.796 72.222 26.36 18.05 0.00 4.10
465 471 3.790437 CTGACCCCATCGCCAGCT 61.790 66.667 0.00 0.00 0.00 4.24
473 479 1.130054 CCATCGATCCCTGACCCCAT 61.130 60.000 0.00 0.00 0.00 4.00
520 526 0.976641 TCCCACTGCTGACGATTTCT 59.023 50.000 0.00 0.00 0.00 2.52
564 572 4.832608 CAGCCGGTACCTTCCCGC 62.833 72.222 10.90 3.65 44.13 6.13
578 586 4.043200 GAACGCCCAACTGCCAGC 62.043 66.667 0.00 0.00 0.00 4.85
597 605 0.866427 TAAAACCAATTCGCGTCGCA 59.134 45.000 18.75 0.00 0.00 5.10
603 611 2.473376 CGTCCGAGTAAAACCAATTCGC 60.473 50.000 0.00 0.00 0.00 4.70
607 615 2.845363 ACCGTCCGAGTAAAACCAAT 57.155 45.000 0.00 0.00 0.00 3.16
618 626 5.787953 TCCAAATATACATAACCGTCCGA 57.212 39.130 0.00 0.00 0.00 4.55
621 629 8.836268 TGGTAATCCAAATATACATAACCGTC 57.164 34.615 0.00 0.00 41.25 4.79
689 758 2.335316 AACGGTGCTCCAACAGTAAA 57.665 45.000 5.52 0.00 0.00 2.01
690 759 2.335316 AAACGGTGCTCCAACAGTAA 57.665 45.000 5.52 0.00 0.00 2.24
705 774 8.563289 TTTTACAGTACAAATGCCTAAAAACG 57.437 30.769 0.00 0.00 0.00 3.60
712 781 5.538433 ACCACATTTTACAGTACAAATGCCT 59.462 36.000 18.50 6.73 42.01 4.75
743 812 6.014327 TGCAGAGCATGTCCAATATAGATGTA 60.014 38.462 0.00 0.00 31.71 2.29
773 842 1.347707 CACACCAGTCCCTCAAAGCTA 59.652 52.381 0.00 0.00 0.00 3.32
775 844 1.518903 GCACACCAGTCCCTCAAAGC 61.519 60.000 0.00 0.00 0.00 3.51
791 860 2.097250 GCTCTGTTTTTCGCAAATGCAC 60.097 45.455 6.18 0.00 42.21 4.57
1129 1203 0.441145 GAACCAAACGAATCGACGGG 59.559 55.000 10.55 9.54 37.61 5.28
1361 1464 0.896226 GAGCTCAGAGGTTACGGGTT 59.104 55.000 9.40 0.00 0.00 4.11
1402 1508 0.934496 TTACAGAAGCACACACACGC 59.066 50.000 0.00 0.00 0.00 5.34
1403 1509 2.159973 CGATTACAGAAGCACACACACG 60.160 50.000 0.00 0.00 0.00 4.49
1404 1510 2.411547 GCGATTACAGAAGCACACACAC 60.412 50.000 0.00 0.00 0.00 3.82
1405 1511 1.798223 GCGATTACAGAAGCACACACA 59.202 47.619 0.00 0.00 0.00 3.72
1466 1605 1.069227 CACCAAAGCAAGCGTCCTAAC 60.069 52.381 0.00 0.00 0.00 2.34
1491 1639 4.210328 TGGCACAAGCGTAATAATGATACG 59.790 41.667 1.99 1.99 41.99 3.06
1494 1642 3.565482 CCTGGCACAAGCGTAATAATGAT 59.435 43.478 0.00 0.00 43.41 2.45
1564 1712 8.751242 AGAGAGATCCACTATGATAATGACATG 58.249 37.037 0.00 0.00 0.00 3.21
1672 1820 1.827969 CTAACAGTAGGCAGGCTCAGT 59.172 52.381 0.00 0.00 0.00 3.41
1695 1843 1.717194 TTCTACACCGAATTGTCGCC 58.283 50.000 0.00 0.00 46.28 5.54
1774 1922 4.097741 AGCAAAGCACAAAACTACACATGA 59.902 37.500 0.00 0.00 0.00 3.07
1798 1946 2.423185 CCTAAACGAAATGCAGGCATGA 59.577 45.455 7.64 0.00 36.68 3.07
1845 1993 4.505324 AGTAAGCCTCCTTTTCATACCC 57.495 45.455 0.00 0.00 32.47 3.69
1889 2038 6.538945 TGGTACATGAGCATAGACAAACTA 57.461 37.500 0.00 0.00 35.42 2.24
2221 2370 4.220382 TCCAGCGGAATTTTCATTGACAAT 59.780 37.500 0.00 0.00 0.00 2.71
2222 2371 3.571828 TCCAGCGGAATTTTCATTGACAA 59.428 39.130 0.00 0.00 0.00 3.18
2264 2413 1.728971 GACTTGTGTGAGCATCCTTCG 59.271 52.381 0.00 0.00 0.00 3.79
2307 2456 9.077885 ACTTCTTTTGAGTGGCATTTCTTTATA 57.922 29.630 0.00 0.00 0.00 0.98
2391 2540 8.177663 CACTTTATGTATTCACCAGTGTCAATC 58.822 37.037 0.00 0.00 0.00 2.67
2679 2828 4.125703 CAGGATGACTAAGAGAACCATGC 58.874 47.826 0.00 0.00 39.69 4.06
2740 2889 7.165485 AGCTTTCTTGTATTGTGTGGTATGTA 58.835 34.615 0.00 0.00 0.00 2.29
2767 2916 2.373169 ACTCATCAGAACTTGGCCTTGA 59.627 45.455 3.32 0.00 0.00 3.02
2948 3097 0.179040 TTGGAAACCACTCACGGGTC 60.179 55.000 0.00 0.00 37.77 4.46
3334 3489 1.275856 ACCAAGCTGAGCAGAGAAGAG 59.724 52.381 7.39 0.00 0.00 2.85
3795 3952 6.707440 AACACCATCTTGTTTGTTGTGATA 57.293 33.333 0.00 0.00 36.22 2.15
4147 4429 1.755959 GGAAGATCTCTGCAGCTCTGA 59.244 52.381 9.47 4.96 0.00 3.27
4180 4462 1.065854 CAGACCAGATGAACCAGACCC 60.066 57.143 0.00 0.00 0.00 4.46
4216 4498 5.013704 TCTGGTTCTGGTCTTTAGGCATAAA 59.986 40.000 3.23 3.23 0.00 1.40


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

AutoCloner maintained by Alex Coulton.