Multiple sequence alignment - TraesCS2B01G130500

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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 TraesCS2B01G130500 chr2B 100.000 2770 0 0 1 2770 97934921 97932152 0.000000e+00 5116.0
1 TraesCS2B01G130500 chr2B 76.127 821 132 50 1001 1774 98264728 98263925 3.370000e-99 372.0
2 TraesCS2B01G130500 chr2B 80.180 333 52 11 1298 1618 98256762 98256432 1.280000e-58 237.0
3 TraesCS2B01G130500 chr2B 73.756 804 126 57 1047 1774 98286786 98285992 1.280000e-58 237.0
4 TraesCS2B01G130500 chr2B 92.453 106 8 0 1669 1774 98256333 98256228 4.780000e-33 152.0
5 TraesCS2B01G130500 chr2A 88.423 2384 164 61 429 2770 63138787 63136474 0.000000e+00 2771.0
6 TraesCS2B01G130500 chr2A 77.778 765 109 39 1052 1771 63588997 63588249 5.520000e-112 414.0
7 TraesCS2B01G130500 chr2A 87.952 332 22 9 1 320 63139192 63138867 2.600000e-100 375.0
8 TraesCS2B01G130500 chr2A 73.806 775 133 51 1047 1770 63611187 63610432 2.760000e-60 243.0
9 TraesCS2B01G130500 chr2A 78.378 407 52 24 1029 1409 63607276 63606880 5.970000e-57 231.0
10 TraesCS2B01G130500 chr2A 79.412 306 43 13 1477 1771 63606776 63606480 6.050000e-47 198.0
11 TraesCS2B01G130500 chr2D 90.983 1963 108 33 850 2770 62290060 62288125 0.000000e+00 2580.0
12 TraesCS2B01G130500 chr2D 90.400 375 28 4 443 813 62290530 62290160 1.150000e-133 486.0
13 TraesCS2B01G130500 chr2D 77.690 762 113 36 1052 1771 62553298 62552552 1.990000e-111 412.0
14 TraesCS2B01G130500 chr2D 77.449 439 61 27 1001 1409 62559850 62559420 7.720000e-56 228.0
15 TraesCS2B01G130500 chr2D 76.167 407 63 23 1029 1406 62565143 62564742 1.690000e-42 183.0
16 TraesCS2B01G130500 chr2D 77.500 320 44 19 1477 1774 62559263 62558950 1.710000e-37 167.0
17 TraesCS2B01G130500 chr3A 96.970 33 1 0 532 564 659526648 659526616 3.850000e-04 56.5
18 TraesCS2B01G130500 chr1B 100.000 30 0 0 364 393 60473597 60473568 3.850000e-04 56.5
19 TraesCS2B01G130500 chrUn 100.000 28 0 0 367 394 276531742 276531769 5.000000e-03 52.8


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 TraesCS2B01G130500 chr2B 97932152 97934921 2769 True 5116 5116 100.000000 1 2770 1 chr2B.!!$R1 2769
1 TraesCS2B01G130500 chr2B 98263925 98264728 803 True 372 372 76.127000 1001 1774 1 chr2B.!!$R2 773
2 TraesCS2B01G130500 chr2B 98285992 98286786 794 True 237 237 73.756000 1047 1774 1 chr2B.!!$R3 727
3 TraesCS2B01G130500 chr2A 63136474 63139192 2718 True 1573 2771 88.187500 1 2770 2 chr2A.!!$R2 2769
4 TraesCS2B01G130500 chr2A 63588249 63588997 748 True 414 414 77.778000 1052 1771 1 chr2A.!!$R1 719
5 TraesCS2B01G130500 chr2A 63606480 63611187 4707 True 224 243 77.198667 1029 1771 3 chr2A.!!$R3 742
6 TraesCS2B01G130500 chr2D 62288125 62290530 2405 True 1533 2580 90.691500 443 2770 2 chr2D.!!$R3 2327
7 TraesCS2B01G130500 chr2D 62552552 62553298 746 True 412 412 77.690000 1052 1771 1 chr2D.!!$R1 719

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
339 348 0.039074 GATGCGCGCAGGTATAGAGT 60.039 55.0 38.44 19.27 0.00 3.24 F
340 349 0.039074 ATGCGCGCAGGTATAGAGTC 60.039 55.0 38.44 1.80 0.00 3.36 F
754 795 0.181350 GTTGCTGTGCTATAGCCCCT 59.819 55.0 21.84 0.00 40.42 4.79 F
813 854 0.396974 TGGAGCCAAAACCAACAGCT 60.397 50.0 0.00 0.00 36.25 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1250 4165 0.031585 CACCACGAGAGTTCCGAACA 59.968 55.0 13.69 0.0 46.4 3.18 R
1452 4438 0.040692 TGAGCAGTACACGTCGTCAC 60.041 55.0 0.00 0.0 0.0 3.67 R
1657 4699 0.108585 ACAAGCGTCCATGTTCAGGT 59.891 50.0 0.00 0.0 0.0 4.00 R
2161 5214 0.651031 GAGTAAAACGGATGCGAGGC 59.349 55.0 15.49 0.0 0.0 4.70 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
52 53 4.707030 TTGGATGCATAGCTGAAACAAG 57.293 40.909 0.00 0.00 0.00 3.16
56 57 5.709631 TGGATGCATAGCTGAAACAAGTTTA 59.290 36.000 0.00 0.00 32.11 2.01
107 108 4.566004 ACGCAGCTATTAACACTGAGAAA 58.434 39.130 10.53 0.00 35.51 2.52
139 140 8.941977 CCATAGCTGTTGTTTTAGTGTTGTATA 58.058 33.333 0.00 0.00 0.00 1.47
172 173 8.805175 CCAATATATGCATCCATTTAAACTCCA 58.195 33.333 0.19 0.00 32.85 3.86
179 180 1.161843 CATTTAAACTCCACGCGGGT 58.838 50.000 12.47 0.00 38.11 5.28
220 221 1.780503 AATGCTGTATGGCCTTTCCC 58.219 50.000 3.32 0.00 0.00 3.97
221 222 0.630673 ATGCTGTATGGCCTTTCCCA 59.369 50.000 3.32 0.00 39.65 4.37
225 226 1.004745 CTGTATGGCCTTTCCCACTGT 59.995 52.381 3.32 0.00 37.79 3.55
226 227 1.271871 TGTATGGCCTTTCCCACTGTG 60.272 52.381 3.32 0.00 37.79 3.66
229 230 0.260230 TGGCCTTTCCCACTGTGAAA 59.740 50.000 9.86 1.97 0.00 2.69
230 231 0.673985 GGCCTTTCCCACTGTGAAAC 59.326 55.000 9.86 0.00 37.35 2.78
231 232 1.692411 GCCTTTCCCACTGTGAAACT 58.308 50.000 9.86 0.00 38.04 2.66
232 233 1.338020 GCCTTTCCCACTGTGAAACTG 59.662 52.381 9.86 0.00 42.04 3.16
275 277 2.034879 GCTGCACACGCACACCTAT 61.035 57.895 0.00 0.00 45.36 2.57
276 278 1.577328 GCTGCACACGCACACCTATT 61.577 55.000 0.00 0.00 45.36 1.73
290 299 1.004277 ACCTATTGTGTTGCGACCCAT 59.996 47.619 0.45 0.00 0.00 4.00
295 304 0.250684 TGTGTTGCGACCCATGATGT 60.251 50.000 0.45 0.00 0.00 3.06
305 314 0.109179 CCCATGATGTTGTGTTGCCG 60.109 55.000 0.00 0.00 0.00 5.69
307 316 1.269174 CCATGATGTTGTGTTGCCGAA 59.731 47.619 0.00 0.00 0.00 4.30
308 317 2.587956 CATGATGTTGTGTTGCCGAAG 58.412 47.619 0.00 0.00 0.00 3.79
323 332 1.845266 CGAAGGACATGAGGACGATG 58.155 55.000 0.00 0.00 0.00 3.84
324 333 1.576356 GAAGGACATGAGGACGATGC 58.424 55.000 0.00 0.00 0.00 3.91
326 335 2.240500 GGACATGAGGACGATGCGC 61.241 63.158 0.00 0.00 0.00 6.09
328 337 3.993234 CATGAGGACGATGCGCGC 61.993 66.667 27.26 27.26 46.04 6.86
334 343 2.658593 GACGATGCGCGCAGGTAT 60.659 61.111 38.44 23.03 46.04 2.73
335 344 1.371267 GACGATGCGCGCAGGTATA 60.371 57.895 38.44 15.21 46.04 1.47
336 345 1.337817 GACGATGCGCGCAGGTATAG 61.338 60.000 38.44 23.67 46.04 1.31
338 347 1.067743 CGATGCGCGCAGGTATAGAG 61.068 60.000 38.44 18.21 0.00 2.43
339 348 0.039074 GATGCGCGCAGGTATAGAGT 60.039 55.000 38.44 19.27 0.00 3.24
340 349 0.039074 ATGCGCGCAGGTATAGAGTC 60.039 55.000 38.44 1.80 0.00 3.36
342 351 2.030551 CGCGCAGGTATAGAGTCCA 58.969 57.895 8.75 0.00 0.00 4.02
343 352 0.598562 CGCGCAGGTATAGAGTCCAT 59.401 55.000 8.75 0.00 0.00 3.41
345 354 2.545952 CGCGCAGGTATAGAGTCCATTT 60.546 50.000 8.75 0.00 0.00 2.32
346 355 2.802816 GCGCAGGTATAGAGTCCATTTG 59.197 50.000 0.30 0.00 0.00 2.32
347 356 3.741388 GCGCAGGTATAGAGTCCATTTGT 60.741 47.826 0.30 0.00 0.00 2.83
348 357 4.500887 GCGCAGGTATAGAGTCCATTTGTA 60.501 45.833 0.30 0.00 0.00 2.41
350 359 4.982916 GCAGGTATAGAGTCCATTTGTACG 59.017 45.833 0.00 0.00 0.00 3.67
352 361 4.647853 AGGTATAGAGTCCATTTGTACGCA 59.352 41.667 0.00 0.00 0.00 5.24
353 362 5.128171 AGGTATAGAGTCCATTTGTACGCAA 59.872 40.000 0.00 0.00 0.00 4.85
354 363 5.989777 GGTATAGAGTCCATTTGTACGCAAT 59.010 40.000 0.00 0.00 34.18 3.56
356 365 3.674997 AGAGTCCATTTGTACGCAATGT 58.325 40.909 13.71 0.02 34.18 2.71
376 406 5.217978 TGTACTCCCAACGTCTTACATTT 57.782 39.130 0.00 0.00 0.00 2.32
381 411 4.963373 TCCCAACGTCTTACATTTTGAGA 58.037 39.130 0.00 0.00 0.00 3.27
388 418 4.817517 GTCTTACATTTTGAGACGGAGGA 58.182 43.478 0.00 0.00 31.54 3.71
391 421 3.771577 ACATTTTGAGACGGAGGAAGT 57.228 42.857 0.00 0.00 0.00 3.01
392 422 4.884668 ACATTTTGAGACGGAGGAAGTA 57.115 40.909 0.00 0.00 0.00 2.24
393 423 5.422214 ACATTTTGAGACGGAGGAAGTAT 57.578 39.130 0.00 0.00 0.00 2.12
395 425 5.046591 ACATTTTGAGACGGAGGAAGTATCA 60.047 40.000 0.00 0.00 37.96 2.15
396 426 5.677319 TTTTGAGACGGAGGAAGTATCAT 57.323 39.130 0.00 0.00 39.22 2.45
397 427 4.655762 TTGAGACGGAGGAAGTATCATG 57.344 45.455 0.00 0.00 39.22 3.07
398 428 2.959030 TGAGACGGAGGAAGTATCATGG 59.041 50.000 0.00 0.00 35.27 3.66
400 430 3.637229 GAGACGGAGGAAGTATCATGGAA 59.363 47.826 0.00 0.00 30.89 3.53
401 431 3.385111 AGACGGAGGAAGTATCATGGAAC 59.615 47.826 0.00 0.00 0.00 3.62
420 450 2.878520 GCTGACGAGCTCGAGCAC 60.879 66.667 40.58 29.92 45.16 4.40
421 451 2.874019 CTGACGAGCTCGAGCACT 59.126 61.111 40.58 19.74 45.16 4.40
422 452 1.211449 CTGACGAGCTCGAGCACTT 59.789 57.895 40.58 25.63 45.16 3.16
423 453 1.069924 CTGACGAGCTCGAGCACTTG 61.070 60.000 40.58 23.59 45.16 3.16
424 454 1.803519 GACGAGCTCGAGCACTTGG 60.804 63.158 40.58 20.92 45.16 3.61
425 455 3.184683 CGAGCTCGAGCACTTGGC 61.185 66.667 36.87 17.74 45.16 4.52
436 466 1.081242 CACTTGGCACGGACAATGC 60.081 57.895 0.00 0.00 42.62 3.56
483 513 2.597305 CTGCGACCGTGTTATTACTGAC 59.403 50.000 0.00 0.00 0.00 3.51
592 628 9.961266 CTATACGAGACTATGTAATCTTCTTCG 57.039 37.037 0.00 0.00 0.00 3.79
593 629 5.512473 ACGAGACTATGTAATCTTCTTCGC 58.488 41.667 0.00 0.00 0.00 4.70
630 666 4.000557 GCGTGTGTGTGCTGACCG 62.001 66.667 0.00 0.00 0.00 4.79
743 784 3.677648 GGCTGGGCTGTTGCTGTG 61.678 66.667 0.00 0.00 39.59 3.66
751 792 0.659957 GCTGTTGCTGTGCTATAGCC 59.340 55.000 21.84 13.33 40.85 3.93
754 795 0.181350 GTTGCTGTGCTATAGCCCCT 59.819 55.000 21.84 0.00 40.42 4.79
760 801 1.075525 TGCTATAGCCCCTGGTCGT 60.076 57.895 21.84 0.00 41.18 4.34
813 854 0.396974 TGGAGCCAAAACCAACAGCT 60.397 50.000 0.00 0.00 36.25 4.24
815 856 1.541588 GGAGCCAAAACCAACAGCTAG 59.458 52.381 0.00 0.00 32.97 3.42
875 981 2.391389 GGTTTTGGCCGCTCTCTCG 61.391 63.158 0.00 0.00 0.00 4.04
877 983 3.240134 TTTTGGCCGCTCTCTCGCT 62.240 57.895 0.00 0.00 0.00 4.93
925 1032 3.750413 CGATCGCGCTGCTCATCG 61.750 66.667 5.56 10.55 34.50 3.84
932 1039 1.006922 CGCTGCTCATCGGCTCATA 60.007 57.895 0.00 0.00 44.92 2.15
959 1066 1.374758 CAGACCTGCCGACCAAGAC 60.375 63.158 0.00 0.00 0.00 3.01
973 1080 2.237392 ACCAAGACCCTCTTACATCAGC 59.763 50.000 0.00 0.00 33.78 4.26
976 1083 4.566488 CCAAGACCCTCTTACATCAGCTTT 60.566 45.833 0.00 0.00 33.78 3.51
1093 3974 3.841379 GACGACAGCGACCACAGCA 62.841 63.158 0.00 0.00 41.64 4.41
1250 4165 4.022329 CCGTTAATTTCCAGCTTTGGTTCT 60.022 41.667 0.00 0.00 0.00 3.01
1259 4174 1.947456 AGCTTTGGTTCTGTTCGGAAC 59.053 47.619 13.86 13.86 43.24 3.62
1260 4175 1.947456 GCTTTGGTTCTGTTCGGAACT 59.053 47.619 20.53 0.00 43.43 3.01
1296 4255 3.068307 GGAGCTTACTCTGCTTCGGAATA 59.932 47.826 0.00 0.00 42.98 1.75
1419 4397 1.534476 TAACAGCCACGACTCCCCA 60.534 57.895 0.00 0.00 0.00 4.96
1422 4400 1.746615 CAGCCACGACTCCCCATTG 60.747 63.158 0.00 0.00 0.00 2.82
1474 4488 0.596577 ACGACGTGTACTGCTCATGT 59.403 50.000 0.00 0.00 37.68 3.21
1479 4493 3.462982 ACGTGTACTGCTCATGTCAAAA 58.537 40.909 0.00 0.00 30.46 2.44
1544 4558 4.771356 GTGCTCTGCGACGCCGTA 62.771 66.667 18.69 2.36 38.24 4.02
1616 4649 5.245977 TGCCATCAAGAGGTAATCGATGATA 59.754 40.000 0.00 0.00 37.30 2.15
1621 4654 5.481824 TCAAGAGGTAATCGATGATATGCCT 59.518 40.000 0.00 0.64 0.00 4.75
1654 4696 3.320826 GCCGAATAGCCATGGGTTTTATT 59.679 43.478 23.79 15.76 0.00 1.40
1655 4697 4.202212 GCCGAATAGCCATGGGTTTTATTT 60.202 41.667 23.79 8.45 0.00 1.40
1656 4698 5.683770 GCCGAATAGCCATGGGTTTTATTTT 60.684 40.000 23.79 6.69 0.00 1.82
1657 4699 6.461788 GCCGAATAGCCATGGGTTTTATTTTA 60.462 38.462 23.79 0.74 0.00 1.52
1658 4700 6.921307 CCGAATAGCCATGGGTTTTATTTTAC 59.079 38.462 23.79 6.48 0.00 2.01
1675 4717 2.093306 TACCTGAACATGGACGCTTG 57.907 50.000 0.00 0.00 0.00 4.01
1752 4794 2.079158 CCGTCATGATTGTCAAGCAGT 58.921 47.619 9.69 0.00 0.00 4.40
1771 4813 4.943705 GCAGTCCAAGTCCAAGAAATGATA 59.056 41.667 0.00 0.00 0.00 2.15
1792 4834 1.672356 GTCATTGTGGTGCCGAGCT 60.672 57.895 0.00 0.00 0.00 4.09
1806 4848 3.194755 TGCCGAGCTTGTTGTATCTCTTA 59.805 43.478 0.00 0.00 0.00 2.10
1816 4858 9.162764 GCTTGTTGTATCTCTTAGTAAAATCCA 57.837 33.333 0.00 0.00 0.00 3.41
1833 4875 0.249447 CCAGAGTTCTGTGTGCGTGA 60.249 55.000 8.23 0.00 42.27 4.35
1834 4876 1.570813 CAGAGTTCTGTGTGCGTGAA 58.429 50.000 0.91 0.00 39.09 3.18
1848 4890 4.101942 GTGCGTGAAAAGTGATGTCAAAA 58.898 39.130 0.00 0.00 0.00 2.44
1855 4901 8.843733 CGTGAAAAGTGATGTCAAAAAGATATG 58.156 33.333 0.00 0.00 0.00 1.78
1952 4999 9.031360 TGTTACTGTATTCAAATATCTTCGAGC 57.969 33.333 0.00 0.00 0.00 5.03
2103 5156 2.472695 TAACAGCGGATGCAGAAGTT 57.527 45.000 0.00 0.00 46.23 2.66
2161 5214 2.840066 CGCCTCTCACCGCTCCTAG 61.840 68.421 0.00 0.00 0.00 3.02
2171 5224 2.341911 GCTCCTAGCCTCGCATCC 59.658 66.667 0.00 0.00 34.48 3.51
2214 5269 6.698766 CCTGAAAATGCAATTGGATACTTAGC 59.301 38.462 13.27 2.41 36.10 3.09
2251 5306 6.045072 ACACTTCCCAATCGACAATAAGTA 57.955 37.500 0.00 0.00 0.00 2.24
2260 5315 6.523201 CCAATCGACAATAAGTAAACACAAGC 59.477 38.462 0.00 0.00 0.00 4.01
2367 5422 0.597377 CGGGCTGAGCAAAAACAACC 60.597 55.000 6.82 0.00 0.00 3.77
2370 5425 2.626840 GGCTGAGCAAAAACAACCAAA 58.373 42.857 6.82 0.00 0.00 3.28
2405 5462 9.655769 CATACACAGATATTGCAAAAGTATGAC 57.344 33.333 1.71 0.00 38.85 3.06
2408 5465 6.690098 CACAGATATTGCAAAAGTATGACTGC 59.310 38.462 1.71 0.00 35.32 4.40
2419 5476 6.807708 AAAGTATGACTGCGAATACTTACG 57.192 37.500 8.13 0.00 44.80 3.18
2422 5479 3.141002 TGACTGCGAATACTTACGGAC 57.859 47.619 0.00 0.00 0.00 4.79
2584 5641 5.649782 AGTAAAATGGGCTCACAGAAATG 57.350 39.130 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 7.594758 TGTTTAAACTTGTTTCAGCTATGCATC 59.405 33.333 18.72 0.00 0.00 3.91
52 53 7.184106 TCGTCAGATGTTTGTCTTGTTTAAAC 58.816 34.615 11.54 11.54 35.46 2.01
56 57 5.116180 TCTCGTCAGATGTTTGTCTTGTTT 58.884 37.500 0.00 0.00 0.00 2.83
107 108 2.113860 AACAACAGCTATGGCATCGT 57.886 45.000 1.65 0.00 41.70 3.73
139 140 8.579850 AAATGGATGCATATATTGGTATTCGT 57.420 30.769 0.00 0.00 0.00 3.85
146 147 8.805175 TGGAGTTTAAATGGATGCATATATTGG 58.195 33.333 0.00 0.00 0.00 3.16
168 169 3.869473 TTTTCGGACCCGCGTGGAG 62.869 63.158 18.79 9.36 39.59 3.86
172 173 3.167822 TTCCTTTTCGGACCCGCGT 62.168 57.895 4.92 0.00 42.97 6.01
179 180 4.062677 TCGAAAGAACTTCCTTTTCGGA 57.937 40.909 18.50 8.65 36.58 4.55
220 221 7.873739 AGAAAAGAAAAACAGTTTCACAGTG 57.126 32.000 0.00 0.00 33.37 3.66
221 222 8.887036 AAAGAAAAGAAAAACAGTTTCACAGT 57.113 26.923 0.00 0.00 33.37 3.55
225 226 9.757227 TCTGAAAAGAAAAGAAAAACAGTTTCA 57.243 25.926 0.00 0.00 33.37 2.69
229 230 9.208022 CCTTTCTGAAAAGAAAAGAAAAACAGT 57.792 29.630 4.18 0.00 43.90 3.55
230 231 9.208022 ACCTTTCTGAAAAGAAAAGAAAAACAG 57.792 29.630 5.78 0.00 43.90 3.16
231 232 8.987890 CACCTTTCTGAAAAGAAAAGAAAAACA 58.012 29.630 5.78 0.00 43.90 2.83
232 233 7.957484 GCACCTTTCTGAAAAGAAAAGAAAAAC 59.043 33.333 5.78 0.00 43.90 2.43
241 243 3.023119 TGCAGCACCTTTCTGAAAAGAA 58.977 40.909 5.78 0.00 43.90 2.52
270 272 0.398696 TGGGTCGCAACACAATAGGT 59.601 50.000 0.00 0.00 35.32 3.08
271 273 1.401552 CATGGGTCGCAACACAATAGG 59.598 52.381 0.00 0.00 43.48 2.57
272 274 2.355197 TCATGGGTCGCAACACAATAG 58.645 47.619 0.00 0.00 43.48 1.73
275 277 0.880441 CATCATGGGTCGCAACACAA 59.120 50.000 0.00 0.00 43.48 3.33
276 278 0.250684 ACATCATGGGTCGCAACACA 60.251 50.000 0.00 0.00 44.62 3.72
283 292 1.401409 GCAACACAACATCATGGGTCG 60.401 52.381 0.00 0.00 35.41 4.79
290 299 0.950836 CCTTCGGCAACACAACATCA 59.049 50.000 0.00 0.00 0.00 3.07
295 304 0.950836 CATGTCCTTCGGCAACACAA 59.049 50.000 0.00 0.00 0.00 3.33
305 314 1.576356 GCATCGTCCTCATGTCCTTC 58.424 55.000 0.00 0.00 0.00 3.46
307 316 1.439228 CGCATCGTCCTCATGTCCT 59.561 57.895 0.00 0.00 0.00 3.85
308 317 2.240500 GCGCATCGTCCTCATGTCC 61.241 63.158 0.30 0.00 0.00 4.02
317 326 1.337817 CTATACCTGCGCGCATCGTC 61.338 60.000 36.48 2.54 41.07 4.20
320 329 0.039074 ACTCTATACCTGCGCGCATC 60.039 55.000 36.48 4.36 0.00 3.91
321 330 0.039074 GACTCTATACCTGCGCGCAT 60.039 55.000 36.48 23.91 0.00 4.73
322 331 1.359117 GACTCTATACCTGCGCGCA 59.641 57.895 34.12 34.12 0.00 6.09
323 332 1.371881 GGACTCTATACCTGCGCGC 60.372 63.158 27.26 27.26 0.00 6.86
324 333 0.598562 ATGGACTCTATACCTGCGCG 59.401 55.000 0.00 0.00 0.00 6.86
326 335 4.060038 ACAAATGGACTCTATACCTGCG 57.940 45.455 0.00 0.00 0.00 5.18
327 336 4.982916 CGTACAAATGGACTCTATACCTGC 59.017 45.833 0.00 0.00 0.00 4.85
328 337 4.982916 GCGTACAAATGGACTCTATACCTG 59.017 45.833 0.00 0.00 0.00 4.00
330 339 4.940463 TGCGTACAAATGGACTCTATACC 58.060 43.478 0.00 0.00 0.00 2.73
334 343 4.827692 ACATTGCGTACAAATGGACTCTA 58.172 39.130 17.86 0.00 39.77 2.43
335 344 3.674997 ACATTGCGTACAAATGGACTCT 58.325 40.909 17.86 0.11 39.77 3.24
347 356 1.273048 ACGTTGGGAGTACATTGCGTA 59.727 47.619 0.00 0.00 0.00 4.42
348 357 0.034337 ACGTTGGGAGTACATTGCGT 59.966 50.000 0.00 0.00 0.00 5.24
350 359 2.094762 AGACGTTGGGAGTACATTGC 57.905 50.000 0.00 0.00 0.00 3.56
352 361 4.877378 TGTAAGACGTTGGGAGTACATT 57.123 40.909 0.00 0.00 0.00 2.71
353 362 5.416271 AATGTAAGACGTTGGGAGTACAT 57.584 39.130 0.00 0.00 34.49 2.29
354 363 4.877378 AATGTAAGACGTTGGGAGTACA 57.123 40.909 0.00 0.00 0.00 2.90
356 365 5.856156 TCAAAATGTAAGACGTTGGGAGTA 58.144 37.500 0.00 0.00 0.00 2.59
359 368 4.753107 GTCTCAAAATGTAAGACGTTGGGA 59.247 41.667 0.00 0.00 31.01 4.37
376 406 3.384789 CCATGATACTTCCTCCGTCTCAA 59.615 47.826 0.00 0.00 0.00 3.02
381 411 3.104512 TGTTCCATGATACTTCCTCCGT 58.895 45.455 0.00 0.00 0.00 4.69
383 413 3.135530 AGCTGTTCCATGATACTTCCTCC 59.864 47.826 0.00 0.00 0.00 4.30
385 415 3.776969 TCAGCTGTTCCATGATACTTCCT 59.223 43.478 14.67 0.00 0.00 3.36
386 416 3.873952 GTCAGCTGTTCCATGATACTTCC 59.126 47.826 14.67 0.00 0.00 3.46
387 417 3.553511 CGTCAGCTGTTCCATGATACTTC 59.446 47.826 14.67 0.00 0.00 3.01
388 418 3.195610 TCGTCAGCTGTTCCATGATACTT 59.804 43.478 14.67 0.00 0.00 2.24
391 421 2.481969 GCTCGTCAGCTGTTCCATGATA 60.482 50.000 14.67 0.00 43.09 2.15
392 422 1.741732 GCTCGTCAGCTGTTCCATGAT 60.742 52.381 14.67 0.00 43.09 2.45
393 423 0.390340 GCTCGTCAGCTGTTCCATGA 60.390 55.000 14.67 4.23 43.09 3.07
395 425 4.606071 GCTCGTCAGCTGTTCCAT 57.394 55.556 14.67 0.00 43.09 3.41
404 434 1.069924 CAAGTGCTCGAGCTCGTCAG 61.070 60.000 35.27 25.21 42.66 3.51
407 437 2.259818 CCAAGTGCTCGAGCTCGT 59.740 61.111 35.27 27.38 42.66 4.18
408 438 3.184683 GCCAAGTGCTCGAGCTCG 61.185 66.667 35.27 30.03 42.66 5.03
409 439 2.047844 TGCCAAGTGCTCGAGCTC 60.048 61.111 35.27 31.34 42.66 4.09
410 440 2.358003 GTGCCAAGTGCTCGAGCT 60.358 61.111 35.27 16.24 42.66 4.09
415 445 1.237285 ATTGTCCGTGCCAAGTGCTC 61.237 55.000 0.00 0.00 42.00 4.26
417 447 1.081242 CATTGTCCGTGCCAAGTGC 60.081 57.895 0.00 0.00 41.77 4.40
418 448 1.081242 GCATTGTCCGTGCCAAGTG 60.081 57.895 0.00 0.00 36.61 3.16
419 449 0.895100 ATGCATTGTCCGTGCCAAGT 60.895 50.000 0.00 0.00 41.83 3.16
420 450 0.457166 CATGCATTGTCCGTGCCAAG 60.457 55.000 0.00 0.00 41.83 3.61
421 451 1.585517 CATGCATTGTCCGTGCCAA 59.414 52.632 0.00 0.00 41.83 4.52
422 452 2.992273 GCATGCATTGTCCGTGCCA 61.992 57.895 14.21 0.00 41.83 4.92
423 453 2.202650 GCATGCATTGTCCGTGCC 60.203 61.111 14.21 0.00 41.83 5.01
424 454 1.515519 CAGCATGCATTGTCCGTGC 60.516 57.895 21.98 0.00 43.70 5.34
425 455 4.777781 CAGCATGCATTGTCCGTG 57.222 55.556 21.98 2.32 0.00 4.94
436 466 0.179181 CGGTTACAAGCAGCAGCATG 60.179 55.000 3.17 3.98 44.59 4.06
483 513 1.159713 TCCGATTATTGCAGCAGCGG 61.160 55.000 11.18 11.18 46.23 5.52
592 628 6.356190 CACGCTTTACTTTTAAGTTGTACAGC 59.644 38.462 0.72 0.72 40.37 4.40
593 629 7.372396 CACACGCTTTACTTTTAAGTTGTACAG 59.628 37.037 0.00 0.00 40.37 2.74
630 666 3.065371 ACAAGCGCAGTAAGATAATTGCC 59.935 43.478 11.47 0.00 33.10 4.52
680 719 3.125316 CCGTGACCGTTAGTTTTTCAGA 58.875 45.455 0.00 0.00 0.00 3.27
743 784 1.335145 TAACGACCAGGGGCTATAGC 58.665 55.000 16.78 16.78 41.14 2.97
754 795 1.220749 GGCTGCTGGATAACGACCA 59.779 57.895 0.00 0.00 35.96 4.02
813 854 0.890090 CCCCGGTTTTCGTTTGGCTA 60.890 55.000 0.00 0.00 37.11 3.93
815 856 2.337170 CCCCGGTTTTCGTTTGGC 59.663 61.111 0.00 0.00 37.11 4.52
888 994 2.158957 CGAGGGGCGTATATATTGGCAT 60.159 50.000 11.78 2.53 34.64 4.40
925 1032 3.829601 AGGTCTGCTATGTAGTATGAGCC 59.170 47.826 0.00 0.00 33.87 4.70
959 1066 3.691609 GGAACAAAGCTGATGTAAGAGGG 59.308 47.826 5.89 0.00 0.00 4.30
973 1080 3.344904 CAGACAGTGCAAGGAACAAAG 57.655 47.619 0.00 0.00 0.00 2.77
1229 4122 5.842907 ACAGAACCAAAGCTGGAAATTAAC 58.157 37.500 0.00 0.00 46.92 2.01
1250 4165 0.031585 CACCACGAGAGTTCCGAACA 59.968 55.000 13.69 0.00 46.40 3.18
1259 4174 0.389166 GCTCCAGTTCACCACGAGAG 60.389 60.000 0.00 0.00 34.27 3.20
1260 4175 0.827925 AGCTCCAGTTCACCACGAGA 60.828 55.000 0.00 0.00 0.00 4.04
1419 4397 1.789078 GATCGAGCAATGCGGCCAAT 61.789 55.000 2.24 0.00 0.00 3.16
1422 4400 2.890109 CTGATCGAGCAATGCGGCC 61.890 63.158 4.32 0.00 0.00 6.13
1452 4438 0.040692 TGAGCAGTACACGTCGTCAC 60.041 55.000 0.00 0.00 0.00 3.67
1474 4488 1.106351 ACCATGCACCTGCGTTTTGA 61.106 50.000 0.00 0.00 45.83 2.69
1479 4493 2.189191 ATCAGACCATGCACCTGCGT 62.189 55.000 0.00 0.00 45.83 5.24
1544 4558 3.923864 TCGGCGTGGTGCTTGTCT 61.924 61.111 6.85 0.00 45.43 3.41
1654 4696 2.811431 CAAGCGTCCATGTTCAGGTAAA 59.189 45.455 0.00 0.00 0.00 2.01
1655 4697 2.224426 ACAAGCGTCCATGTTCAGGTAA 60.224 45.455 0.00 0.00 0.00 2.85
1656 4698 1.346395 ACAAGCGTCCATGTTCAGGTA 59.654 47.619 0.00 0.00 0.00 3.08
1657 4699 0.108585 ACAAGCGTCCATGTTCAGGT 59.891 50.000 0.00 0.00 0.00 4.00
1658 4700 1.069022 CAACAAGCGTCCATGTTCAGG 60.069 52.381 0.00 0.00 37.66 3.86
1675 4717 1.508088 CCGAGAAATGCCCTGCAAC 59.492 57.895 0.00 0.00 43.62 4.17
1752 4794 4.191544 CGCTATCATTTCTTGGACTTGGA 58.808 43.478 0.00 0.00 0.00 3.53
1771 4813 3.049674 CGGCACCACAATGACGCT 61.050 61.111 0.00 0.00 45.71 5.07
1784 4826 1.550524 AGAGATACAACAAGCTCGGCA 59.449 47.619 0.00 0.00 32.80 5.69
1816 4858 2.309528 TTTCACGCACACAGAACTCT 57.690 45.000 0.00 0.00 0.00 3.24
1848 4890 5.234752 TGCGACACTGTTTACACATATCTT 58.765 37.500 0.00 0.00 30.39 2.40
1855 4901 3.783943 CAGTTTTGCGACACTGTTTACAC 59.216 43.478 11.50 0.00 36.44 2.90
1949 4996 6.535508 GGATTATTATCTATGGTCGTTGGCTC 59.464 42.308 0.00 0.00 0.00 4.70
1950 4997 6.013725 TGGATTATTATCTATGGTCGTTGGCT 60.014 38.462 0.00 0.00 0.00 4.75
1951 4998 6.170506 TGGATTATTATCTATGGTCGTTGGC 58.829 40.000 0.00 0.00 0.00 4.52
1952 4999 7.878127 ACTTGGATTATTATCTATGGTCGTTGG 59.122 37.037 0.00 0.00 0.00 3.77
2103 5156 4.909696 TCTTCAAATTTTGTCTTCGCCA 57.090 36.364 8.89 0.00 0.00 5.69
2118 5171 4.834496 AGCCATGGTCTTCAAATTCTTCAA 59.166 37.500 14.67 0.00 0.00 2.69
2156 5209 1.327690 AAACGGATGCGAGGCTAGGA 61.328 55.000 15.49 0.00 0.00 2.94
2161 5214 0.651031 GAGTAAAACGGATGCGAGGC 59.349 55.000 15.49 0.00 0.00 4.70
2171 5224 3.751175 TCAGGCCAAATCAGAGTAAAACG 59.249 43.478 5.01 0.00 0.00 3.60
2214 5269 4.701651 TGGGAAGTGTTCATTGCTCTTATG 59.298 41.667 0.00 0.00 0.00 1.90
2251 5306 9.062524 TGTAATATAACTCTTGTGCTTGTGTTT 57.937 29.630 0.00 0.00 0.00 2.83
2260 5315 9.469807 GTCTCCTGATGTAATATAACTCTTGTG 57.530 37.037 0.00 0.00 0.00 3.33
2370 5425 9.448438 TTGCAATATCTGTGTATGAAACTTACT 57.552 29.630 0.00 0.00 0.00 2.24
2383 5438 6.690098 GCAGTCATACTTTTGCAATATCTGTG 59.310 38.462 0.00 0.00 36.59 3.66
2405 5462 0.844503 GCGTCCGTAAGTATTCGCAG 59.155 55.000 0.00 0.00 42.54 5.18
2408 5465 0.844503 GCTGCGTCCGTAAGTATTCG 59.155 55.000 0.00 0.00 0.00 3.34
2584 5641 6.645700 TTTTGACACAACTGATTGCTTTTC 57.354 33.333 0.00 0.00 39.66 2.29


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

AutoCloner maintained by Alex Coulton.