Multiple sequence alignment - TraesCS7D01G042800

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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 TraesCS7D01G042800 chr7D 100.000 4419 0 0 1 4419 21940844 21936426 0.000000e+00 8161.0
1 TraesCS7D01G042800 chr7D 93.011 3162 174 20 725 3881 22038657 22041776 0.000000e+00 4571.0
2 TraesCS7D01G042800 chr7D 87.645 259 30 1 343 601 42220759 42221015 2.580000e-77 300.0
3 TraesCS7D01G042800 chr7D 95.775 71 3 0 3868 3938 22041894 22041964 1.000000e-21 115.0
4 TraesCS7D01G042800 chr7A 90.762 3345 196 50 719 4039 22665744 22668999 0.000000e+00 4361.0
5 TraesCS7D01G042800 chr7A 87.870 3075 273 47 1003 4039 22866728 22869740 0.000000e+00 3520.0
6 TraesCS7D01G042800 chr7A 79.637 992 173 22 2174 3147 24095826 24096806 0.000000e+00 686.0
7 TraesCS7D01G042800 chr7A 80.687 233 42 3 4039 4270 679208091 679207861 1.260000e-40 178.0
8 TraesCS7D01G042800 chr4A 92.507 2509 147 17 1893 4398 711779682 711782152 0.000000e+00 3554.0
9 TraesCS7D01G042800 chr4A 92.467 2509 148 17 1893 4398 711840908 711843378 0.000000e+00 3548.0
10 TraesCS7D01G042800 chr4A 91.706 2532 160 22 1896 4419 704301339 704298850 0.000000e+00 3467.0
11 TraesCS7D01G042800 chr4A 91.105 1158 77 12 728 1874 704302804 704301662 0.000000e+00 1544.0
12 TraesCS7D01G042800 chr4A 93.367 995 66 0 880 1874 711778628 711779622 0.000000e+00 1472.0
13 TraesCS7D01G042800 chr4A 93.367 995 66 0 880 1874 711839854 711840848 0.000000e+00 1472.0
14 TraesCS7D01G042800 chr4A 89.150 682 46 6 16 686 704303925 704303261 0.000000e+00 824.0
15 TraesCS7D01G042800 chr4A 82.110 654 114 1 1174 1827 706499265 706498615 1.390000e-154 556.0
16 TraesCS7D01G042800 chr4A 85.379 383 51 4 4040 4419 740607746 740608126 4.140000e-105 392.0
17 TraesCS7D01G042800 chr4A 88.077 260 26 4 342 599 211380219 211380475 2.000000e-78 303.0
18 TraesCS7D01G042800 chr4A 96.552 58 2 0 628 685 711839505 711839562 3.640000e-16 97.1
19 TraesCS7D01G042800 chr4A 96.491 57 2 0 629 685 711778281 711778337 1.310000e-15 95.3
20 TraesCS7D01G042800 chrUn 92.821 1783 91 14 1896 3671 313746270 313744518 0.000000e+00 2549.0
21 TraesCS7D01G042800 chrUn 95.162 1509 63 3 2168 3671 50547718 50546215 0.000000e+00 2374.0
22 TraesCS7D01G042800 chrUn 91.278 1158 75 12 728 1874 313747735 313746593 0.000000e+00 1555.0
23 TraesCS7D01G042800 chrUn 91.192 1158 76 12 728 1874 50555099 50553957 0.000000e+00 1550.0
24 TraesCS7D01G042800 chrUn 90.585 786 47 11 1896 2679 50553634 50552874 0.000000e+00 1016.0
25 TraesCS7D01G042800 chrUn 90.233 686 57 5 3735 4419 50551951 50551275 0.000000e+00 887.0
26 TraesCS7D01G042800 chrUn 90.233 686 57 5 3735 4419 352755403 352756079 0.000000e+00 887.0
27 TraesCS7D01G042800 chrUn 89.003 682 48 5 16 686 50556194 50555529 0.000000e+00 819.0
28 TraesCS7D01G042800 chrUn 88.856 682 47 7 16 686 436530550 436529887 0.000000e+00 811.0
29 TraesCS7D01G042800 chrUn 93.976 498 25 2 3174 3671 50552456 50551964 0.000000e+00 749.0
30 TraesCS7D01G042800 chrUn 88.670 609 42 5 89 686 401384532 401383940 0.000000e+00 717.0
31 TraesCS7D01G042800 chrUn 88.406 414 26 11 728 1134 401383510 401383112 3.090000e-131 479.0
32 TraesCS7D01G042800 chrUn 94.286 70 4 0 16 85 403643345 403643276 1.680000e-19 108.0
33 TraesCS7D01G042800 chr1A 88.803 259 27 1 341 599 537981414 537981158 2.570000e-82 316.0
34 TraesCS7D01G042800 chr1A 84.512 297 44 2 4040 4335 314624776 314625071 4.320000e-75 292.0
35 TraesCS7D01G042800 chr2D 88.716 257 26 2 343 599 16177916 16177663 1.190000e-80 311.0
36 TraesCS7D01G042800 chr1B 88.417 259 27 2 342 599 562893903 562894159 4.290000e-80 309.0
37 TraesCS7D01G042800 chr5B 82.432 296 48 4 4040 4333 448876027 448876320 5.670000e-64 255.0
38 TraesCS7D01G042800 chr5A 72.727 528 132 10 2626 3147 607594894 607594373 2.730000e-37 167.0


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 TraesCS7D01G042800 chr7D 21936426 21940844 4418 True 8161.0 8161 100.000000 1 4419 1 chr7D.!!$R1 4418
1 TraesCS7D01G042800 chr7D 22038657 22041964 3307 False 2343.0 4571 94.393000 725 3938 2 chr7D.!!$F2 3213
2 TraesCS7D01G042800 chr7A 22665744 22668999 3255 False 4361.0 4361 90.762000 719 4039 1 chr7A.!!$F1 3320
3 TraesCS7D01G042800 chr7A 22866728 22869740 3012 False 3520.0 3520 87.870000 1003 4039 1 chr7A.!!$F2 3036
4 TraesCS7D01G042800 chr7A 24095826 24096806 980 False 686.0 686 79.637000 2174 3147 1 chr7A.!!$F3 973
5 TraesCS7D01G042800 chr4A 704298850 704303925 5075 True 1945.0 3467 90.653667 16 4419 3 chr4A.!!$R2 4403
6 TraesCS7D01G042800 chr4A 711778281 711782152 3871 False 1707.1 3554 94.121667 629 4398 3 chr4A.!!$F3 3769
7 TraesCS7D01G042800 chr4A 711839505 711843378 3873 False 1705.7 3548 94.128667 628 4398 3 chr4A.!!$F4 3770
8 TraesCS7D01G042800 chr4A 706498615 706499265 650 True 556.0 556 82.110000 1174 1827 1 chr4A.!!$R1 653
9 TraesCS7D01G042800 chrUn 313744518 313747735 3217 True 2052.0 2549 92.049500 728 3671 2 chrUn.!!$R4 2943
10 TraesCS7D01G042800 chrUn 50546215 50556194 9979 True 1232.5 2374 91.691833 16 4419 6 chrUn.!!$R3 4403
11 TraesCS7D01G042800 chrUn 352755403 352756079 676 False 887.0 887 90.233000 3735 4419 1 chrUn.!!$F1 684
12 TraesCS7D01G042800 chrUn 436529887 436530550 663 True 811.0 811 88.856000 16 686 1 chrUn.!!$R2 670
13 TraesCS7D01G042800 chrUn 401383112 401384532 1420 True 598.0 717 88.538000 89 1134 2 chrUn.!!$R5 1045

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
352 353 0.320374 TTGTGCAAGTACTCCCTCCG 59.680 55.0 0.00 0.0 0.00 4.63 F
1800 2320 0.321564 TTGTAGCCGCTGCACATCTT 60.322 50.0 11.04 0.0 41.13 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1988 3082 0.237235 TTTGTCCGCGTGCATCTTTC 59.763 50.0 4.92 0.00 0.0 2.62 R
3427 4552 0.109964 CATGGTTGTAACAACGGCCG 60.110 55.0 26.86 26.86 0.0 6.13 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
35 36 1.626356 CCTCCCATCCTTGCCGAGAA 61.626 60.000 0.00 0.00 0.00 2.87
36 37 0.471617 CTCCCATCCTTGCCGAGAAT 59.528 55.000 0.00 0.00 0.00 2.40
40 41 1.097232 CATCCTTGCCGAGAATGCAA 58.903 50.000 0.00 0.00 45.83 4.08
81 82 4.245660 TCACATTCACCGAAGATTGAGAC 58.754 43.478 6.13 0.00 0.00 3.36
87 88 1.825474 ACCGAAGATTGAGACGACCAT 59.175 47.619 0.00 0.00 0.00 3.55
91 92 3.679980 CGAAGATTGAGACGACCATTTGT 59.320 43.478 0.00 0.00 0.00 2.83
153 154 0.740868 GAGACGCCATAGCAGCACAA 60.741 55.000 0.00 0.00 39.83 3.33
160 161 2.372264 CCATAGCAGCACAACCAAGAT 58.628 47.619 0.00 0.00 0.00 2.40
163 164 1.080298 GCAGCACAACCAAGATGCC 60.080 57.895 0.00 0.00 40.33 4.40
203 204 2.427095 GAGGAGAGAGGAGAAAGCAGTC 59.573 54.545 0.00 0.00 0.00 3.51
204 205 2.042979 AGGAGAGAGGAGAAAGCAGTCT 59.957 50.000 0.00 0.00 0.00 3.24
206 207 3.088532 GAGAGAGGAGAAAGCAGTCTCA 58.911 50.000 16.00 0.00 45.03 3.27
220 221 2.160615 CAGTCTCATCTCTCACGTCGTT 59.839 50.000 0.00 0.00 0.00 3.85
223 224 1.200252 CTCATCTCTCACGTCGTTGGT 59.800 52.381 0.00 0.00 0.00 3.67
235 236 4.912395 GTTGGTGCCACCCCTGCA 62.912 66.667 12.25 0.00 37.50 4.41
264 265 2.501610 CCTAGCCTTCCAGTCGCC 59.498 66.667 0.00 0.00 0.00 5.54
281 282 2.956964 CAACGCGATCGCCTCCTC 60.957 66.667 32.63 6.30 39.84 3.71
290 291 1.824230 GATCGCCTCCTCTATGCTCAT 59.176 52.381 0.00 0.00 0.00 2.90
317 318 1.374758 GTGGTTGGAGCCTCACGAG 60.375 63.158 0.00 0.00 0.00 4.18
318 319 2.435059 GGTTGGAGCCTCACGAGC 60.435 66.667 0.00 0.00 0.00 5.03
321 322 3.240134 TTGGAGCCTCACGAGCCAC 62.240 63.158 0.00 0.00 0.00 5.01
326 327 2.887568 CCTCACGAGCCACGATGC 60.888 66.667 7.86 0.00 45.77 3.91
351 352 2.561478 TTTGTGCAAGTACTCCCTCC 57.439 50.000 0.00 0.00 0.00 4.30
352 353 0.320374 TTGTGCAAGTACTCCCTCCG 59.680 55.000 0.00 0.00 0.00 4.63
353 354 0.541063 TGTGCAAGTACTCCCTCCGA 60.541 55.000 0.00 0.00 0.00 4.55
354 355 0.824759 GTGCAAGTACTCCCTCCGAT 59.175 55.000 0.00 0.00 0.00 4.18
355 356 1.112113 TGCAAGTACTCCCTCCGATC 58.888 55.000 0.00 0.00 0.00 3.69
356 357 0.389757 GCAAGTACTCCCTCCGATCC 59.610 60.000 0.00 0.00 0.00 3.36
357 358 2.030045 GCAAGTACTCCCTCCGATCCT 61.030 57.143 0.00 0.00 0.00 3.24
358 359 2.389715 CAAGTACTCCCTCCGATCCTT 58.610 52.381 0.00 0.00 0.00 3.36
359 360 2.766828 CAAGTACTCCCTCCGATCCTTT 59.233 50.000 0.00 0.00 0.00 3.11
369 370 3.369471 CCTCCGATCCTTTTTACTCTGCA 60.369 47.826 0.00 0.00 0.00 4.41
379 380 9.638176 ATCCTTTTTACTCTGCATATGAGATTT 57.362 29.630 6.97 0.52 35.66 2.17
381 382 8.680903 CCTTTTTACTCTGCATATGAGATTTGT 58.319 33.333 6.97 4.36 35.66 2.83
399 400 7.047891 AGATTTGTGTCAAGTCAAACTCTACA 58.952 34.615 7.50 0.00 36.58 2.74
401 402 7.624360 TTTGTGTCAAGTCAAACTCTACAAT 57.376 32.000 0.00 0.00 28.68 2.71
402 403 8.725405 TTTGTGTCAAGTCAAACTCTACAATA 57.275 30.769 0.00 0.00 28.68 1.90
563 564 9.924650 GGTCAAAGTAGAGATACTTTAACTTCA 57.075 33.333 11.83 0.00 45.43 3.02
708 778 4.576216 ACACACACACACACAAGAAAAA 57.424 36.364 0.00 0.00 0.00 1.94
709 779 5.132897 ACACACACACACACAAGAAAAAT 57.867 34.783 0.00 0.00 0.00 1.82
740 1169 7.065324 CACATCCAATTTCCAATTCCAATTCAG 59.935 37.037 0.00 0.00 0.00 3.02
765 1194 1.909376 CGAGAGGTGGTCGTTGTATG 58.091 55.000 0.00 0.00 32.62 2.39
805 1239 8.103935 TGGAAGAGATCTGTCGTATACTCATAT 58.896 37.037 0.00 0.00 0.00 1.78
806 1240 9.602568 GGAAGAGATCTGTCGTATACTCATATA 57.397 37.037 0.00 0.00 0.00 0.86
839 1359 1.298339 GCGGCACATCGGCAATTAC 60.298 57.895 0.00 0.00 41.26 1.89
841 1361 0.662619 CGGCACATCGGCAATTACAT 59.337 50.000 0.00 0.00 41.26 2.29
842 1362 1.870402 CGGCACATCGGCAATTACATA 59.130 47.619 0.00 0.00 41.26 2.29
843 1363 2.349438 CGGCACATCGGCAATTACATAC 60.349 50.000 0.00 0.00 41.26 2.39
844 1364 2.616376 GGCACATCGGCAATTACATACA 59.384 45.455 0.00 0.00 40.76 2.29
845 1365 3.303990 GGCACATCGGCAATTACATACAG 60.304 47.826 0.00 0.00 40.76 2.74
846 1366 3.559655 GCACATCGGCAATTACATACAGA 59.440 43.478 0.00 0.00 0.00 3.41
847 1367 4.552767 GCACATCGGCAATTACATACAGAC 60.553 45.833 0.00 0.00 0.00 3.51
856 1376 7.009631 CGGCAATTACATACAGACAGATATAGC 59.990 40.741 0.00 0.00 0.00 2.97
866 1386 3.248841 AGACAGATATAGCGAGACACACG 59.751 47.826 0.00 0.00 0.00 4.49
867 1387 2.290916 ACAGATATAGCGAGACACACGG 59.709 50.000 0.00 0.00 0.00 4.94
868 1388 1.880675 AGATATAGCGAGACACACGGG 59.119 52.381 0.00 0.00 0.00 5.28
876 1396 3.124921 GACACACGGGGGCGATTG 61.125 66.667 0.00 0.00 0.00 2.67
937 1457 3.617540 ACAAATCGAACGCATTTGTCA 57.382 38.095 20.23 0.00 46.79 3.58
975 1495 0.397941 TCCTCACTTGCAGTTGGAGG 59.602 55.000 15.65 15.65 38.86 4.30
1114 1634 2.536803 GAGTTCAAGTACGACAAACGCA 59.463 45.455 0.00 0.00 46.94 5.24
1281 1801 3.349006 AAGAACTGTGCCGCGCTG 61.349 61.111 5.56 9.07 0.00 5.18
1311 1831 4.660938 GGGGTTGGCAAGACGGCT 62.661 66.667 0.00 0.00 41.89 5.52
1376 1896 3.268603 CACGCTTGTCGGCACACA 61.269 61.111 0.00 0.00 43.86 3.72
1560 2080 4.269523 GGCCCCATAGATGCCGCA 62.270 66.667 0.00 0.00 35.08 5.69
1630 2150 2.569059 CCACGACCTCCGAAGAGTATA 58.431 52.381 0.00 0.00 41.76 1.47
1686 2206 1.226746 GGTTCCAGAAGGTTGTCGTG 58.773 55.000 0.00 0.00 35.89 4.35
1800 2320 0.321564 TTGTAGCCGCTGCACATCTT 60.322 50.000 11.04 0.00 41.13 2.40
1828 2348 4.224433 CCGCTACATTACAGGTACGTATG 58.776 47.826 0.00 0.00 0.00 2.39
1931 3025 9.570468 AGATAACTGATGTATTTGATCATTGCT 57.430 29.630 0.00 0.00 0.00 3.91
1938 3032 2.418368 TTTGATCATTGCTAGGCCGT 57.582 45.000 0.00 0.00 0.00 5.68
1957 3051 4.261197 GCCGTAAATTCCCTGATAAAGCAG 60.261 45.833 0.00 0.00 35.66 4.24
2012 3106 0.313672 ATGCACGCGGACAAACAAAT 59.686 45.000 12.47 0.00 0.00 2.32
2041 3135 3.193479 GGAAATTGTTGTTAGCCCTGGAG 59.807 47.826 0.00 0.00 0.00 3.86
2252 3351 4.119862 CAAGAGGAGAACGACAAGTTGAA 58.880 43.478 10.54 0.00 44.35 2.69
2310 3409 4.644685 GGCCAGGATGAAGCTGTTAATTTA 59.355 41.667 0.00 0.00 39.69 1.40
2575 3688 5.047660 ACACTTTTTGTTTCTAGGCACACAA 60.048 36.000 0.00 0.00 33.09 3.33
2903 4017 5.125578 GGTTTGTGAATCCCAACTATCCTTC 59.874 44.000 0.00 0.00 0.00 3.46
2987 4101 2.936498 GCGCTTCAAGCCTGAACTTATA 59.064 45.455 3.08 0.00 38.18 0.98
3228 4353 4.156190 TGTCCAGTTTTTAACGCTTCAACA 59.844 37.500 0.00 0.00 36.23 3.33
3277 4402 1.637553 AGAAGGTGGGTGCAGAATCAT 59.362 47.619 0.00 0.00 0.00 2.45
3427 4552 6.039493 AGTTGGCAGATCAATGAGATGATTTC 59.961 38.462 0.00 0.00 40.08 2.17
3437 4562 1.737793 GAGATGATTTCGGCCGTTGTT 59.262 47.619 27.15 8.78 0.00 2.83
3466 4591 7.058525 ACCATGATAGATGAAGAAAGATGCAA 58.941 34.615 0.00 0.00 0.00 4.08
3485 4610 6.245115 TGCAAGCTCATACATAATGCATAC 57.755 37.500 0.00 0.00 37.40 2.39
3486 4611 5.999600 TGCAAGCTCATACATAATGCATACT 59.000 36.000 0.00 0.00 37.40 2.12
3487 4612 6.148315 TGCAAGCTCATACATAATGCATACTC 59.852 38.462 0.00 0.00 37.40 2.59
3864 5143 5.011431 CCATGGTACTCAGATAAGATCAGCA 59.989 44.000 2.57 0.00 0.00 4.41
3915 5194 2.777692 TCTTCTTCACACCCTTGTCCTT 59.222 45.455 0.00 0.00 31.66 3.36
3931 5210 2.299867 GTCCTTACCGTGGAAGTTACCA 59.700 50.000 0.00 0.00 35.10 3.25
3952 5231 2.000447 GTGGAACTGACAATACTCGGC 59.000 52.381 0.00 0.00 0.00 5.54
3953 5232 1.278238 GGAACTGACAATACTCGGCG 58.722 55.000 0.00 0.00 0.00 6.46
3954 5233 1.135199 GGAACTGACAATACTCGGCGA 60.135 52.381 10.14 10.14 0.00 5.54
3955 5234 2.481449 GGAACTGACAATACTCGGCGAT 60.481 50.000 11.27 3.37 0.00 4.58
3956 5235 3.243301 GGAACTGACAATACTCGGCGATA 60.243 47.826 11.27 5.77 0.00 2.92
3986 5265 0.179000 ATCGACCTGCAGGATCCAAC 59.821 55.000 39.19 19.07 38.94 3.77
3990 5269 1.687612 CCTGCAGGATCCAACAGGT 59.312 57.895 31.22 4.22 43.86 4.00
3991 5270 0.038744 CCTGCAGGATCCAACAGGTT 59.961 55.000 31.22 3.53 43.86 3.50
4005 5284 1.157751 AGGTTCCCTCGTCTTCCCA 59.842 57.895 0.00 0.00 0.00 4.37
4043 5322 7.065085 GTGACTCTTAACATACGGTCTACACTA 59.935 40.741 0.00 0.00 0.00 2.74
4054 5333 4.525487 ACGGTCTACACTACTGGAATTTCA 59.475 41.667 0.00 0.00 0.00 2.69
4064 5343 6.481976 CACTACTGGAATTTCATTATACGCCA 59.518 38.462 0.00 0.00 0.00 5.69
4065 5344 7.011950 CACTACTGGAATTTCATTATACGCCAA 59.988 37.037 0.00 0.00 0.00 4.52
4097 5376 0.456824 TCGCTGAGAGCTAAAGCACG 60.457 55.000 13.42 2.60 45.16 5.34
4152 5431 2.912025 CGGCAACAGGGGCAACTT 60.912 61.111 0.00 0.00 0.00 2.66
4194 5473 2.363788 GAGTCATACTCGGCAACACA 57.636 50.000 0.00 0.00 35.28 3.72
4196 5475 3.262420 GAGTCATACTCGGCAACACATT 58.738 45.455 0.00 0.00 35.28 2.71
4235 5514 0.314935 ATTTGCCGACAGCCAAACAG 59.685 50.000 0.00 0.00 42.71 3.16
4237 5516 4.043200 GCCGACAGCCAAACAGCC 62.043 66.667 0.00 0.00 34.35 4.85
4241 5520 2.954753 GACAGCCAAACAGCCGTCG 61.955 63.158 0.00 0.00 31.01 5.12
4354 5634 0.519077 CCGGCTCTCAGCAAAACTTC 59.481 55.000 0.00 0.00 44.75 3.01
4356 5636 1.808945 CGGCTCTCAGCAAAACTTCAT 59.191 47.619 0.00 0.00 44.75 2.57
4383 5663 1.667724 CTTGCCCAGAGATAAGCAACG 59.332 52.381 0.00 0.00 40.13 4.10
4387 5667 1.202580 CCCAGAGATAAGCAACGGGAG 60.203 57.143 0.00 0.00 33.83 4.30
4410 5690 6.053650 AGCGGTTTAAATAGTTGGATAGTCC 58.946 40.000 0.00 0.00 36.96 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.320247 GAGGACTGGCACACACAGAG 60.320 60.000 0.00 0.00 39.24 3.35
1 2 1.748403 GAGGACTGGCACACACAGA 59.252 57.895 0.00 0.00 39.24 3.41
3 4 2.818169 GGGAGGACTGGCACACACA 61.818 63.158 0.00 0.00 0.00 3.72
4 5 2.032681 GGGAGGACTGGCACACAC 59.967 66.667 0.00 0.00 0.00 3.82
5 6 1.841302 GATGGGAGGACTGGCACACA 61.841 60.000 0.00 0.00 0.00 3.72
6 7 1.078143 GATGGGAGGACTGGCACAC 60.078 63.158 0.00 0.00 0.00 3.82
7 8 2.300967 GGATGGGAGGACTGGCACA 61.301 63.158 0.00 0.00 0.00 4.57
8 9 1.566298 AAGGATGGGAGGACTGGCAC 61.566 60.000 0.00 0.00 0.00 5.01
9 10 1.229951 AAGGATGGGAGGACTGGCA 60.230 57.895 0.00 0.00 0.00 4.92
10 11 1.225704 CAAGGATGGGAGGACTGGC 59.774 63.158 0.00 0.00 0.00 4.85
11 12 1.225704 GCAAGGATGGGAGGACTGG 59.774 63.158 0.00 0.00 0.00 4.00
12 13 1.225704 GGCAAGGATGGGAGGACTG 59.774 63.158 0.00 0.00 0.00 3.51
13 14 2.370445 CGGCAAGGATGGGAGGACT 61.370 63.158 0.00 0.00 0.00 3.85
14 15 2.190578 CGGCAAGGATGGGAGGAC 59.809 66.667 0.00 0.00 0.00 3.85
35 36 0.035630 GTCAGAGGAGGCAGTTGCAT 60.036 55.000 6.43 0.00 44.36 3.96
36 37 1.372683 GTCAGAGGAGGCAGTTGCA 59.627 57.895 6.43 0.00 44.36 4.08
81 82 2.584791 GCTAGCACAAACAAATGGTCG 58.415 47.619 10.63 0.00 0.00 4.79
153 154 1.178534 CGGTGTTTGGGCATCTTGGT 61.179 55.000 0.00 0.00 0.00 3.67
160 161 1.969064 CGGATTCGGTGTTTGGGCA 60.969 57.895 0.00 0.00 0.00 5.36
203 204 1.200252 ACCAACGACGTGAGAGATGAG 59.800 52.381 0.00 0.00 0.00 2.90
204 205 1.068541 CACCAACGACGTGAGAGATGA 60.069 52.381 0.00 0.00 32.77 2.92
206 207 0.388649 GCACCAACGACGTGAGAGAT 60.389 55.000 0.00 0.00 32.77 2.75
209 210 2.028484 GGCACCAACGACGTGAGA 59.972 61.111 0.00 0.00 32.77 3.27
223 224 1.304381 GATTTCTGCAGGGGTGGCA 60.304 57.895 15.13 0.00 39.32 4.92
235 236 3.717392 GGAAGGCTAGGGTTAGGATTTCT 59.283 47.826 0.00 0.00 0.00 2.52
264 265 2.060004 TAGAGGAGGCGATCGCGTTG 62.060 60.000 32.84 0.00 43.06 4.10
281 282 2.478370 CCACGCAAAACCATGAGCATAG 60.478 50.000 0.00 0.00 0.00 2.23
290 291 2.010582 GCTCCAACCACGCAAAACCA 62.011 55.000 0.00 0.00 0.00 3.67
340 341 2.850695 AAAGGATCGGAGGGAGTACT 57.149 50.000 0.00 0.00 0.00 2.73
347 348 3.198872 GCAGAGTAAAAAGGATCGGAGG 58.801 50.000 0.00 0.00 0.00 4.30
348 349 3.861840 TGCAGAGTAAAAAGGATCGGAG 58.138 45.455 0.00 0.00 0.00 4.63
349 350 3.973206 TGCAGAGTAAAAAGGATCGGA 57.027 42.857 0.00 0.00 0.00 4.55
350 351 5.991606 TCATATGCAGAGTAAAAAGGATCGG 59.008 40.000 0.00 0.00 0.00 4.18
351 352 6.925718 TCTCATATGCAGAGTAAAAAGGATCG 59.074 38.462 0.00 0.00 34.73 3.69
352 353 8.845413 ATCTCATATGCAGAGTAAAAAGGATC 57.155 34.615 0.00 0.00 34.73 3.36
353 354 9.638176 AAATCTCATATGCAGAGTAAAAAGGAT 57.362 29.630 0.00 0.00 34.73 3.24
354 355 8.896744 CAAATCTCATATGCAGAGTAAAAAGGA 58.103 33.333 0.00 0.00 34.73 3.36
355 356 8.680903 ACAAATCTCATATGCAGAGTAAAAAGG 58.319 33.333 0.00 0.00 34.73 3.11
356 357 9.499585 CACAAATCTCATATGCAGAGTAAAAAG 57.500 33.333 0.00 0.00 34.73 2.27
357 358 9.013229 ACACAAATCTCATATGCAGAGTAAAAA 57.987 29.630 0.00 0.00 34.73 1.94
358 359 8.565896 ACACAAATCTCATATGCAGAGTAAAA 57.434 30.769 0.00 0.00 34.73 1.52
359 360 7.823799 TGACACAAATCTCATATGCAGAGTAAA 59.176 33.333 0.00 0.00 34.73 2.01
369 370 8.627208 AGTTTGACTTGACACAAATCTCATAT 57.373 30.769 0.00 0.00 38.09 1.78
379 380 8.902540 AATATTGTAGAGTTTGACTTGACACA 57.097 30.769 0.00 0.00 0.00 3.72
381 382 9.554395 TCAAATATTGTAGAGTTTGACTTGACA 57.446 29.630 0.00 0.00 36.11 3.58
575 576 6.189859 TCTCCGGTCCTTTTTAGTCTGTATA 58.810 40.000 0.00 0.00 0.00 1.47
579 580 3.368531 CCTCTCCGGTCCTTTTTAGTCTG 60.369 52.174 0.00 0.00 0.00 3.51
626 638 0.036732 CAGACTAAACCTGCAGCCCA 59.963 55.000 8.66 0.00 0.00 5.36
708 778 7.347748 TGGAATTGGAAATTGGATGTGGATTAT 59.652 33.333 0.00 0.00 0.00 1.28
709 779 6.671340 TGGAATTGGAAATTGGATGTGGATTA 59.329 34.615 0.00 0.00 0.00 1.75
740 1169 0.389948 ACGACCACCTCTCGCAAATC 60.390 55.000 0.00 0.00 34.34 2.17
805 1239 5.119694 TGTGCCGCACAAGATGTATTTATA 58.880 37.500 23.80 0.00 41.69 0.98
806 1240 3.944650 TGTGCCGCACAAGATGTATTTAT 59.055 39.130 23.80 0.00 41.69 1.40
839 1359 6.073003 TGTGTCTCGCTATATCTGTCTGTATG 60.073 42.308 0.00 0.00 0.00 2.39
841 1361 5.236695 GTGTGTCTCGCTATATCTGTCTGTA 59.763 44.000 0.00 0.00 0.00 2.74
842 1362 4.035792 GTGTGTCTCGCTATATCTGTCTGT 59.964 45.833 0.00 0.00 0.00 3.41
843 1363 4.532276 GTGTGTCTCGCTATATCTGTCTG 58.468 47.826 0.00 0.00 0.00 3.51
844 1364 3.248841 CGTGTGTCTCGCTATATCTGTCT 59.751 47.826 0.00 0.00 0.00 3.41
845 1365 3.546617 CGTGTGTCTCGCTATATCTGTC 58.453 50.000 0.00 0.00 0.00 3.51
846 1366 2.290916 CCGTGTGTCTCGCTATATCTGT 59.709 50.000 0.00 0.00 0.00 3.41
847 1367 2.350868 CCCGTGTGTCTCGCTATATCTG 60.351 54.545 0.00 0.00 0.00 2.90
866 1386 0.463833 AAAGATCGTCAATCGCCCCC 60.464 55.000 0.00 0.00 39.55 5.40
867 1387 0.657840 CAAAGATCGTCAATCGCCCC 59.342 55.000 0.00 0.00 39.55 5.80
868 1388 1.062587 CACAAAGATCGTCAATCGCCC 59.937 52.381 0.00 0.00 39.55 6.13
876 1396 0.166814 GGTGCAGCACAAAGATCGTC 59.833 55.000 26.78 2.36 35.86 4.20
900 1420 4.932268 TTTGTTTCGATACGATTCCACC 57.068 40.909 1.52 0.00 35.23 4.61
930 1450 6.888632 AGAAGAATATGAAGGTGCTGACAAAT 59.111 34.615 0.00 0.00 0.00 2.32
937 1457 5.190528 TGAGGAAGAAGAATATGAAGGTGCT 59.809 40.000 0.00 0.00 0.00 4.40
975 1495 5.587043 AGCTACTGTACTATATGATCGAGCC 59.413 44.000 0.00 0.00 0.00 4.70
1114 1634 2.800629 CGTTGTAGTTGGTGTCCGAAGT 60.801 50.000 0.00 0.00 0.00 3.01
1311 1831 2.812499 GCGAGGCCCTCAACGATA 59.188 61.111 12.13 0.00 0.00 2.92
1376 1896 1.339055 CCATGTCAACCTCCACGATGT 60.339 52.381 0.00 0.00 0.00 3.06
1467 1987 4.082523 TTGCCTTCCGCCTCCTCG 62.083 66.667 0.00 0.00 36.24 4.63
1486 2006 4.639135 TCTCGTCGATGAACAAGATGAT 57.361 40.909 8.98 0.00 30.62 2.45
1560 2080 2.040544 CGCCGGCTTGAGGATGTTT 61.041 57.895 26.68 0.00 0.00 2.83
1686 2206 1.001641 ATGCACAGTTGGCTCCTCC 60.002 57.895 0.00 0.00 0.00 4.30
1828 2348 7.061752 AGTAAACTGATTTCTTGACGTATGC 57.938 36.000 0.00 0.00 0.00 3.14
1911 3005 6.349115 GGCCTAGCAATGATCAAATACATCAG 60.349 42.308 0.00 0.00 33.74 2.90
1931 3025 5.617252 CTTTATCAGGGAATTTACGGCCTA 58.383 41.667 0.00 0.00 0.00 3.93
1938 3032 8.055181 AGATCAACTGCTTTATCAGGGAATTTA 58.945 33.333 0.00 0.00 38.36 1.40
1957 3051 4.082895 GCATGCCTCATCCATAAGATCAAC 60.083 45.833 6.36 0.00 30.59 3.18
1988 3082 0.237235 TTTGTCCGCGTGCATCTTTC 59.763 50.000 4.92 0.00 0.00 2.62
2012 3106 3.003897 GCTAACAACAATTTCCACGGTCA 59.996 43.478 0.00 0.00 0.00 4.02
2041 3135 1.755380 AGGACTTACCCGTGCTACATC 59.245 52.381 0.00 0.00 40.05 3.06
2184 3283 0.321564 TCCATCGGCTCACAACCTTG 60.322 55.000 0.00 0.00 0.00 3.61
2871 3984 4.081406 TGGGATTCACAAACCTGATTCAG 58.919 43.478 6.70 6.70 0.00 3.02
2903 4017 1.927174 CTTGCCAATCGAGGACGTTAG 59.073 52.381 0.00 0.00 40.69 2.34
3228 4353 3.437795 CGCCGTCCACCTACGAGT 61.438 66.667 0.00 0.00 45.68 4.18
3427 4552 0.109964 CATGGTTGTAACAACGGCCG 60.110 55.000 26.86 26.86 0.00 6.13
3437 4562 9.551734 CATCTTTCTTCATCTATCATGGTTGTA 57.448 33.333 0.00 0.00 0.00 2.41
3466 4591 5.414360 CCGAGTATGCATTATGTATGAGCT 58.586 41.667 3.54 0.00 36.26 4.09
3485 4610 4.307443 TCTGTCTACATTACATGCCGAG 57.693 45.455 0.00 0.00 0.00 4.63
3486 4611 4.159693 ACTTCTGTCTACATTACATGCCGA 59.840 41.667 0.00 0.00 0.00 5.54
3487 4612 4.268644 CACTTCTGTCTACATTACATGCCG 59.731 45.833 0.00 0.00 0.00 5.69
3529 4669 7.312154 GCACTTGTCATTACATTCATTAACCA 58.688 34.615 0.00 0.00 34.97 3.67
3652 4797 4.503741 TTGCTGAGAAATTCCGGAAAAG 57.496 40.909 23.08 12.54 0.00 2.27
3710 4855 9.847224 TGAAATTTTCCTTGAGTTACTAGTTCT 57.153 29.630 0.00 0.00 0.00 3.01
3864 5143 2.296073 TTTATGTTTGTTCCCGGGCT 57.704 45.000 18.49 0.00 0.00 5.19
3915 5194 1.619827 CCACTGGTAACTTCCACGGTA 59.380 52.381 0.00 0.00 33.55 4.02
3931 5210 2.353803 GCCGAGTATTGTCAGTTCCACT 60.354 50.000 0.00 0.00 0.00 4.00
3990 5269 0.981277 GGGATGGGAAGACGAGGGAA 60.981 60.000 0.00 0.00 0.00 3.97
3991 5270 1.382695 GGGATGGGAAGACGAGGGA 60.383 63.158 0.00 0.00 0.00 4.20
4043 5322 5.885912 ACTTGGCGTATAATGAAATTCCAGT 59.114 36.000 0.00 0.00 37.87 4.00
4054 5333 1.967319 CCTGGCACTTGGCGTATAAT 58.033 50.000 0.00 0.00 46.16 1.28
4113 5392 1.823797 AGGTACTCTCGGTGTCTGTC 58.176 55.000 0.00 0.00 0.00 3.51
4152 5431 3.762823 TCAGCAATATCATGTGTTTGCCA 59.237 39.130 18.67 8.80 44.21 4.92
4186 5465 0.238289 CCGAGTGTCAATGTGTTGCC 59.762 55.000 0.00 0.00 35.26 4.52
4194 5473 0.537143 TGCCTTTGCCGAGTGTCAAT 60.537 50.000 0.00 0.00 36.33 2.57
4196 5475 1.891919 GTGCCTTTGCCGAGTGTCA 60.892 57.895 0.00 0.00 36.33 3.58
4278 5557 1.293267 CCGTGACCGTGCCGTTATTT 61.293 55.000 0.00 0.00 0.00 1.40
4354 5634 0.682209 CTCTGGGCAAGGTGGGAATG 60.682 60.000 0.00 0.00 0.00 2.67
4356 5636 0.846427 ATCTCTGGGCAAGGTGGGAA 60.846 55.000 0.00 0.00 0.00 3.97
4383 5663 3.613030 TCCAACTATTTAAACCGCTCCC 58.387 45.455 0.00 0.00 0.00 4.30
4387 5667 5.818857 TGGACTATCCAACTATTTAAACCGC 59.181 40.000 0.00 0.00 45.00 5.68


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

AutoCloner maintained by Alex Coulton.