Multiple sequence alignment - TraesCS2B01G162600

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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 TraesCS2B01G162600 chr2B 100.000 3202 0 0 1 3202 135125852 135129053 0.000000e+00 5914.0
1 TraesCS2B01G162600 chr2B 92.454 2306 96 38 579 2816 135463367 135465662 0.000000e+00 3223.0
2 TraesCS2B01G162600 chr2B 92.620 1992 79 26 828 2770 135198035 135200007 0.000000e+00 2802.0
3 TraesCS2B01G162600 chr2B 90.634 2050 113 29 828 2825 182153330 182151308 0.000000e+00 2649.0
4 TraesCS2B01G162600 chr2B 88.000 1175 70 30 1679 2816 135513414 135514554 0.000000e+00 1323.0
5 TraesCS2B01G162600 chr2B 90.596 957 69 18 1891 2834 137621211 137620263 0.000000e+00 1249.0
6 TraesCS2B01G162600 chr2B 88.749 951 69 16 1890 2808 182132936 182131992 0.000000e+00 1129.0
7 TraesCS2B01G162600 chr2B 87.959 980 74 21 1891 2834 136813863 136812892 0.000000e+00 1116.0
8 TraesCS2B01G162600 chr2B 91.900 321 15 8 2682 2992 135516444 135516763 3.790000e-119 438.0
9 TraesCS2B01G162600 chr2B 96.341 246 7 1 2856 3099 135515307 135515552 1.380000e-108 403.0
10 TraesCS2B01G162600 chr2B 94.979 239 9 2 2966 3202 182131637 182131400 3.900000e-99 372.0
11 TraesCS2B01G162600 chr2B 93.033 244 9 3 2966 3202 135466009 135466251 1.830000e-92 350.0
12 TraesCS2B01G162600 chr2B 90.909 165 11 3 2830 2992 182132326 182132164 5.380000e-53 219.0
13 TraesCS2B01G162600 chr2B 90.303 165 12 3 2830 2992 135465314 135465476 2.500000e-51 213.0
14 TraesCS2B01G162600 chr2B 91.096 146 10 3 2830 2974 135128328 135128471 9.060000e-46 195.0
15 TraesCS2B01G162600 chr2B 88.235 85 10 0 3013 3097 136812898 136812814 5.650000e-18 102.0
16 TraesCS2B01G162600 chr2B 87.059 85 11 0 3013 3097 137012597 137012513 2.630000e-16 97.1
17 TraesCS2B01G162600 chr2B 87.059 85 11 0 3013 3097 137620269 137620185 2.630000e-16 97.1
18 TraesCS2B01G162600 chr2B 86.765 68 8 1 319 385 254519833 254519766 1.230000e-09 75.0
19 TraesCS2B01G162600 chr2A 89.868 2497 139 30 642 3099 83989925 83992346 0.000000e+00 3105.0
20 TraesCS2B01G162600 chr2A 88.946 2343 142 47 530 2816 83984673 83986954 0.000000e+00 2784.0
21 TraesCS2B01G162600 chr2A 85.977 2175 161 59 703 2816 84143484 84145575 0.000000e+00 2194.0
22 TraesCS2B01G162600 chr2A 90.146 1299 88 13 381 1655 134867966 134866684 0.000000e+00 1653.0
23 TraesCS2B01G162600 chr2A 91.499 647 26 10 2578 3202 84145577 84146216 0.000000e+00 863.0
24 TraesCS2B01G162600 chr2A 96.970 132 4 0 630 761 733423609 733423478 4.160000e-54 222.0
25 TraesCS2B01G162600 chr2A 89.697 165 13 3 2830 2992 84145233 84145395 1.160000e-49 207.0
26 TraesCS2B01G162600 chr2A 88.235 153 14 4 2830 2980 83991732 83991882 2.540000e-41 180.0
27 TraesCS2B01G162600 chr2A 89.412 85 9 0 3013 3097 85611558 85611474 1.210000e-19 108.0
28 TraesCS2B01G162600 chr2A 92.063 63 5 0 3102 3164 134865420 134865358 4.400000e-14 89.8
29 TraesCS2B01G162600 chr2A 86.667 75 10 0 311 385 679759745 679759819 2.050000e-12 84.2
30 TraesCS2B01G162600 chr2A 97.500 40 1 0 3046 3085 84230363 84230402 5.730000e-08 69.4
31 TraesCS2B01G162600 chr2D 90.337 2401 119 45 450 2770 83187978 83190345 0.000000e+00 3044.0
32 TraesCS2B01G162600 chr2D 91.637 2212 93 47 627 2770 83224974 83227161 0.000000e+00 2976.0
33 TraesCS2B01G162600 chr2D 86.964 1841 141 40 1005 2834 85251744 85249992 0.000000e+00 1978.0
34 TraesCS2B01G162600 chr2D 90.278 1296 80 15 381 1655 127821850 127820580 0.000000e+00 1653.0
35 TraesCS2B01G162600 chr2D 88.272 1134 92 15 1679 2779 127820586 127819461 0.000000e+00 1319.0
36 TraesCS2B01G162600 chr2D 85.054 930 89 14 857 1778 84938015 84937128 0.000000e+00 902.0
37 TraesCS2B01G162600 chr2D 89.964 279 26 2 15 292 127822157 127821880 3.040000e-95 359.0
38 TraesCS2B01G162600 chr2D 83.710 221 23 6 1650 1864 85249007 85248794 2.520000e-46 196.0
39 TraesCS2B01G162600 chr2D 88.550 131 12 2 2864 2992 84778142 84778013 4.280000e-34 156.0
40 TraesCS2B01G162600 chr2D 88.550 131 12 2 2864 2992 84935714 84935585 4.280000e-34 156.0
41 TraesCS2B01G162600 chr2D 92.000 75 6 0 3010 3084 85250001 85249927 4.370000e-19 106.0
42 TraesCS2B01G162600 chr2D 87.209 86 10 1 3012 3097 84935466 84935382 2.630000e-16 97.1
43 TraesCS2B01G162600 chr2D 87.209 86 10 1 3012 3097 85406262 85406178 2.630000e-16 97.1
44 TraesCS2B01G162600 chr2D 89.333 75 8 0 311 385 340277474 340277400 9.460000e-16 95.3
45 TraesCS2B01G162600 chr2D 83.099 71 4 3 3102 3164 127819332 127819262 1.240000e-04 58.4
46 TraesCS2B01G162600 chr5D 93.130 1150 64 5 517 1655 230368712 230369857 0.000000e+00 1672.0
47 TraesCS2B01G162600 chr5D 85.992 257 34 2 36 291 230368396 230368651 1.130000e-69 274.0
48 TraesCS2B01G162600 chr5D 87.143 70 7 2 317 385 232587907 232587975 9.520000e-11 78.7
49 TraesCS2B01G162600 chr5A 93.100 1029 48 8 627 1655 326438151 326437146 0.000000e+00 1485.0
50 TraesCS2B01G162600 chr5A 87.406 1064 71 27 1679 2690 326437152 326436100 0.000000e+00 1164.0
51 TraesCS2B01G162600 chr5A 86.792 212 27 1 102 312 326441546 326441335 5.340000e-58 235.0
52 TraesCS2B01G162600 chr5A 85.714 203 13 9 424 624 326441278 326441090 1.950000e-47 200.0
53 TraesCS2B01G162600 chrUn 91.667 648 34 12 627 1257 362506190 362506834 0.000000e+00 880.0
54 TraesCS2B01G162600 chr5B 87.578 161 17 3 2830 2989 321476677 321476519 1.960000e-42 183.0
55 TraesCS2B01G162600 chr5B 84.375 64 10 0 320 383 598759620 598759683 2.670000e-06 63.9
56 TraesCS2B01G162600 chr6D 90.411 73 7 0 313 385 316318018 316318090 2.630000e-16 97.1
57 TraesCS2B01G162600 chr6D 89.333 75 8 0 311 385 379853026 379852952 9.460000e-16 95.3
58 TraesCS2B01G162600 chr4A 85.526 76 9 2 311 385 11074123 11074049 9.520000e-11 78.7
59 TraesCS2B01G162600 chr4D 87.879 66 6 2 318 382 206124859 206124923 3.430000e-10 76.8


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 TraesCS2B01G162600 chr2B 135125852 135129053 3201 False 3054.500000 5914 95.548000 1 3202 2 chr2B.!!$F2 3201
1 TraesCS2B01G162600 chr2B 135198035 135200007 1972 False 2802.000000 2802 92.620000 828 2770 1 chr2B.!!$F1 1942
2 TraesCS2B01G162600 chr2B 182151308 182153330 2022 True 2649.000000 2649 90.634000 828 2825 1 chr2B.!!$R2 1997
3 TraesCS2B01G162600 chr2B 135463367 135466251 2884 False 1262.000000 3223 91.930000 579 3202 3 chr2B.!!$F3 2623
4 TraesCS2B01G162600 chr2B 135513414 135516763 3349 False 721.333333 1323 92.080333 1679 3099 3 chr2B.!!$F4 1420
5 TraesCS2B01G162600 chr2B 137620185 137621211 1026 True 673.050000 1249 88.827500 1891 3097 2 chr2B.!!$R5 1206
6 TraesCS2B01G162600 chr2B 136812814 136813863 1049 True 609.000000 1116 88.097000 1891 3097 2 chr2B.!!$R4 1206
7 TraesCS2B01G162600 chr2B 182131400 182132936 1536 True 573.333333 1129 91.545667 1890 3202 3 chr2B.!!$R6 1312
8 TraesCS2B01G162600 chr2A 83984673 83992346 7673 False 2023.000000 3105 89.016333 530 3099 3 chr2A.!!$F3 2569
9 TraesCS2B01G162600 chr2A 84143484 84146216 2732 False 1088.000000 2194 89.057667 703 3202 3 chr2A.!!$F4 2499
10 TraesCS2B01G162600 chr2A 134865358 134867966 2608 True 871.400000 1653 91.104500 381 3164 2 chr2A.!!$R3 2783
11 TraesCS2B01G162600 chr2D 83187978 83190345 2367 False 3044.000000 3044 90.337000 450 2770 1 chr2D.!!$F1 2320
12 TraesCS2B01G162600 chr2D 83224974 83227161 2187 False 2976.000000 2976 91.637000 627 2770 1 chr2D.!!$F2 2143
13 TraesCS2B01G162600 chr2D 127819262 127822157 2895 True 847.350000 1653 87.903250 15 3164 4 chr2D.!!$R6 3149
14 TraesCS2B01G162600 chr2D 85248794 85251744 2950 True 760.000000 1978 87.558000 1005 3084 3 chr2D.!!$R5 2079
15 TraesCS2B01G162600 chr2D 84935382 84938015 2633 True 385.033333 902 86.937667 857 3097 3 chr2D.!!$R4 2240
16 TraesCS2B01G162600 chr5D 230368396 230369857 1461 False 973.000000 1672 89.561000 36 1655 2 chr5D.!!$F2 1619
17 TraesCS2B01G162600 chr5A 326436100 326441546 5446 True 771.000000 1485 88.253000 102 2690 4 chr5A.!!$R1 2588
18 TraesCS2B01G162600 chrUn 362506190 362506834 644 False 880.000000 880 91.667000 627 1257 1 chrUn.!!$F1 630

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
332 351 0.107017 CCTGGCCGATCCAAACAGAT 60.107 55.0 0.00 0.00 46.01 2.90 F
352 371 0.112309 GAAAAACGAACAAAGCGCGC 60.112 50.0 26.66 26.66 0.00 6.86 F
842 3847 0.742281 AATGAGCGCGTGAGATTGCT 60.742 50.0 8.43 0.00 38.10 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1742 4760 1.878656 GCAGTGGTGTAGAGCCGACT 61.879 60.000 0.00 0.0 0.0 4.18 R
1847 5471 2.031157 CGATTGGTTTTGCTTCGGAACT 60.031 45.455 0.00 0.0 0.0 3.01 R
2446 6109 0.388134 TACTCGTCGGAAACTGCAGC 60.388 55.000 15.27 0.0 0.0 5.25 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
17 18 3.142917 ATGATGGGGAGAGGGGGT 58.857 61.111 0.00 0.00 0.00 4.95
28 29 2.365635 AGGGGGTGAGGTCATCGG 60.366 66.667 0.00 0.00 0.00 4.18
54 55 3.986006 GCGACAGGGACCGTGTGA 61.986 66.667 23.99 0.00 0.00 3.58
64 65 2.034066 CCGTGTGATGCACCCCTT 59.966 61.111 0.00 0.00 44.97 3.95
74 75 4.290622 CACCCCTTGCCAGCCACT 62.291 66.667 0.00 0.00 0.00 4.00
93 94 0.678684 TGGGACGACGAGCTATGACA 60.679 55.000 0.00 0.00 0.00 3.58
94 95 0.454600 GGGACGACGAGCTATGACAA 59.545 55.000 0.00 0.00 0.00 3.18
99 100 1.321743 CGACGAGCTATGACAACAAGC 59.678 52.381 0.00 0.76 36.48 4.01
106 107 1.281867 CTATGACAACAAGCCCCCTCA 59.718 52.381 0.00 0.00 0.00 3.86
118 119 2.191375 CCCTCATGCCTCGCACAT 59.809 61.111 0.00 0.00 43.04 3.21
172 174 0.888619 GTCCTCATCTGTCGTGGTCA 59.111 55.000 0.00 0.00 0.00 4.02
205 207 2.341176 GGTCGTGCTACAACCGGT 59.659 61.111 0.00 0.00 0.00 5.28
221 223 2.342279 GTGACCAGCCGTGCTACA 59.658 61.111 0.00 0.00 36.40 2.74
233 235 1.705256 GTGCTACAATCAACGACCGA 58.295 50.000 0.00 0.00 0.00 4.69
235 237 2.281762 GTGCTACAATCAACGACCGATC 59.718 50.000 0.00 0.00 0.00 3.69
312 331 3.188786 GCGAGGTAGCTGCAACCG 61.189 66.667 0.00 4.83 42.15 4.44
313 332 3.188786 CGAGGTAGCTGCAACCGC 61.189 66.667 0.00 0.56 42.15 5.68
315 334 3.316573 GAGGTAGCTGCAACCGCCT 62.317 63.158 0.00 0.34 42.15 5.52
316 335 3.127533 GGTAGCTGCAACCGCCTG 61.128 66.667 3.61 0.00 37.32 4.85
317 336 3.127533 GTAGCTGCAACCGCCTGG 61.128 66.667 1.02 0.00 42.84 4.45
327 346 4.794648 CCGCCTGGCCGATCCAAA 62.795 66.667 14.12 0.00 46.01 3.28
328 347 3.508840 CGCCTGGCCGATCCAAAC 61.509 66.667 14.12 0.00 46.01 2.93
329 348 2.361104 GCCTGGCCGATCCAAACA 60.361 61.111 7.66 0.00 46.01 2.83
330 349 2.409870 GCCTGGCCGATCCAAACAG 61.410 63.158 7.66 0.00 46.01 3.16
331 350 1.299648 CCTGGCCGATCCAAACAGA 59.700 57.895 0.00 0.00 46.01 3.41
332 351 0.107017 CCTGGCCGATCCAAACAGAT 60.107 55.000 0.00 0.00 46.01 2.90
333 352 1.019673 CTGGCCGATCCAAACAGATG 58.980 55.000 0.00 0.00 46.01 2.90
334 353 0.617935 TGGCCGATCCAAACAGATGA 59.382 50.000 0.00 0.00 43.21 2.92
335 354 1.004161 TGGCCGATCCAAACAGATGAA 59.996 47.619 0.00 0.00 43.21 2.57
336 355 2.091541 GGCCGATCCAAACAGATGAAA 58.908 47.619 0.00 0.00 34.01 2.69
337 356 2.491693 GGCCGATCCAAACAGATGAAAA 59.508 45.455 0.00 0.00 34.01 2.29
338 357 3.056891 GGCCGATCCAAACAGATGAAAAA 60.057 43.478 0.00 0.00 34.01 1.94
339 358 3.920412 GCCGATCCAAACAGATGAAAAAC 59.080 43.478 0.00 0.00 0.00 2.43
340 359 4.158384 CCGATCCAAACAGATGAAAAACG 58.842 43.478 0.00 0.00 0.00 3.60
341 360 4.083537 CCGATCCAAACAGATGAAAAACGA 60.084 41.667 0.00 0.00 0.00 3.85
342 361 5.448438 CGATCCAAACAGATGAAAAACGAA 58.552 37.500 0.00 0.00 0.00 3.85
343 362 5.339611 CGATCCAAACAGATGAAAAACGAAC 59.660 40.000 0.00 0.00 0.00 3.95
344 363 5.568685 TCCAAACAGATGAAAAACGAACA 57.431 34.783 0.00 0.00 0.00 3.18
345 364 5.955488 TCCAAACAGATGAAAAACGAACAA 58.045 33.333 0.00 0.00 0.00 2.83
346 365 6.390721 TCCAAACAGATGAAAAACGAACAAA 58.609 32.000 0.00 0.00 0.00 2.83
347 366 6.529829 TCCAAACAGATGAAAAACGAACAAAG 59.470 34.615 0.00 0.00 0.00 2.77
348 367 5.949233 AACAGATGAAAAACGAACAAAGC 57.051 34.783 0.00 0.00 0.00 3.51
349 368 4.035017 ACAGATGAAAAACGAACAAAGCG 58.965 39.130 0.00 0.00 0.00 4.68
350 369 3.042887 AGATGAAAAACGAACAAAGCGC 58.957 40.909 0.00 0.00 0.00 5.92
351 370 1.184349 TGAAAAACGAACAAAGCGCG 58.816 45.000 0.00 0.00 0.00 6.86
352 371 0.112309 GAAAAACGAACAAAGCGCGC 60.112 50.000 26.66 26.66 0.00 6.86
353 372 1.793480 AAAAACGAACAAAGCGCGCG 61.793 50.000 28.44 28.44 0.00 6.86
354 373 2.906416 AAAACGAACAAAGCGCGCGT 62.906 50.000 32.35 21.73 36.68 6.01
355 374 3.833176 AACGAACAAAGCGCGCGTC 62.833 57.895 32.35 22.88 33.66 5.19
360 379 4.659874 CAAAGCGCGCGTCCGTTT 62.660 61.111 32.35 21.22 36.67 3.60
361 380 4.659874 AAAGCGCGCGTCCGTTTG 62.660 61.111 32.35 0.04 36.67 2.93
374 393 4.676586 GTTTGGGTCGGCGCGTTG 62.677 66.667 8.43 0.00 0.00 4.10
395 414 1.227556 GTTGCTCTGACGGGTGTGT 60.228 57.895 0.00 0.00 0.00 3.72
398 417 3.138625 CTCTGACGGGTGTGTGGT 58.861 61.111 0.00 0.00 0.00 4.16
458 477 4.333633 CTTCTCTTTCGGAAGCACATTC 57.666 45.455 0.00 0.00 34.66 2.67
463 482 4.245660 TCTTTCGGAAGCACATTCAGTAG 58.754 43.478 0.00 0.00 39.91 2.57
472 495 4.985538 AGCACATTCAGTAGAGGGAAAAA 58.014 39.130 0.00 0.00 0.00 1.94
475 498 6.494835 AGCACATTCAGTAGAGGGAAAAATTT 59.505 34.615 0.00 0.00 0.00 1.82
477 500 8.303876 GCACATTCAGTAGAGGGAAAAATTTTA 58.696 33.333 3.34 0.00 0.00 1.52
556 581 7.221067 CAGTAGAGGTCAAATTTAGTAGCTTCG 59.779 40.741 0.00 0.00 0.00 3.79
568 593 7.618502 TTTAGTAGCTTCGGAAATTTATGCA 57.381 32.000 0.00 0.00 0.00 3.96
572 597 7.196331 AGTAGCTTCGGAAATTTATGCAATTC 58.804 34.615 0.00 0.00 33.60 2.17
624 650 0.961019 TCATTTTGGGCTGTGCTCAC 59.039 50.000 0.00 0.00 39.49 3.51
625 651 0.963962 CATTTTGGGCTGTGCTCACT 59.036 50.000 1.47 0.00 39.49 3.41
842 3847 0.742281 AATGAGCGCGTGAGATTGCT 60.742 50.000 8.43 0.00 38.10 3.91
904 3910 2.413837 CGACAGTTCCAATCCGAGTTT 58.586 47.619 0.00 0.00 0.00 2.66
1301 4313 3.121030 CAAGAACTCCGCCGCCAG 61.121 66.667 0.00 0.00 0.00 4.85
1742 4760 2.162681 GCTTCCAAGGCTTGCTCTTTA 58.837 47.619 21.77 1.99 0.00 1.85
2281 5940 2.336667 CTCGCCGCAAAATCCAAAATT 58.663 42.857 0.00 0.00 0.00 1.82
2379 6041 2.159085 GCCTAGCGTTTGGAGACTATGT 60.159 50.000 3.55 0.00 0.00 2.29
2446 6109 2.163818 TGGCGTCTTGGTGAGTTAAG 57.836 50.000 0.00 0.00 0.00 1.85
2447 6110 0.796927 GGCGTCTTGGTGAGTTAAGC 59.203 55.000 0.00 0.00 0.00 3.09
2623 6414 6.183360 GCAGAGCATTTGAGTAATCTTTTTGC 60.183 38.462 0.00 0.00 0.00 3.68
2670 6468 2.230266 TGGCTTCTTAAAACATTCCGGC 59.770 45.455 0.00 0.00 0.00 6.13
2672 6470 2.095415 GCTTCTTAAAACATTCCGGCGT 60.095 45.455 6.01 0.00 0.00 5.68
2782 12696 4.218417 ACCATGTTTGGAACAGTTATCAGC 59.782 41.667 0.00 0.00 46.92 4.26
2818 12735 5.428253 TGGTTTGAGATACAGCAATCTACC 58.572 41.667 6.99 6.99 36.33 3.18
2846 12765 4.517285 AGAATGTGAACTCTTGTGTGTGT 58.483 39.130 0.00 0.00 0.00 3.72
2847 12766 5.670485 AGAATGTGAACTCTTGTGTGTGTA 58.330 37.500 0.00 0.00 0.00 2.90
3085 13492 6.966066 GCTTTTCTCAGATCATGTTAGCTTTC 59.034 38.462 0.00 0.00 0.00 2.62
3174 13721 4.611807 CGCTCCAAGTATCTATCTCGTGAC 60.612 50.000 0.00 0.00 0.00 3.67
3188 13735 2.354821 CTCGTGACACTATCATCGGTCA 59.645 50.000 3.68 0.00 40.28 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.386485 CACCCCCTCTCCCCATCAT 60.386 63.158 0.00 0.00 0.00 2.45
1 2 2.042762 CACCCCCTCTCCCCATCA 59.957 66.667 0.00 0.00 0.00 3.07
2 3 1.768077 CTCACCCCCTCTCCCCATC 60.768 68.421 0.00 0.00 0.00 3.51
3 4 2.374342 CTCACCCCCTCTCCCCAT 59.626 66.667 0.00 0.00 0.00 4.00
4 5 4.024984 CCTCACCCCCTCTCCCCA 62.025 72.222 0.00 0.00 0.00 4.96
5 6 4.026357 ACCTCACCCCCTCTCCCC 62.026 72.222 0.00 0.00 0.00 4.81
6 7 2.365768 GACCTCACCCCCTCTCCC 60.366 72.222 0.00 0.00 0.00 4.30
7 8 1.003573 ATGACCTCACCCCCTCTCC 59.996 63.158 0.00 0.00 0.00 3.71
8 9 1.395826 CGATGACCTCACCCCCTCTC 61.396 65.000 0.00 0.00 0.00 3.20
9 10 1.381872 CGATGACCTCACCCCCTCT 60.382 63.158 0.00 0.00 0.00 3.69
10 11 2.435693 CCGATGACCTCACCCCCTC 61.436 68.421 0.00 0.00 0.00 4.30
11 12 2.365635 CCGATGACCTCACCCCCT 60.366 66.667 0.00 0.00 0.00 4.79
12 13 4.176752 GCCGATGACCTCACCCCC 62.177 72.222 0.00 0.00 0.00 5.40
13 14 2.746375 ATGCCGATGACCTCACCCC 61.746 63.158 0.00 0.00 0.00 4.95
17 18 2.745308 CCCCATGCCGATGACCTCA 61.745 63.158 0.00 0.00 0.00 3.86
37 38 3.296709 ATCACACGGTCCCTGTCGC 62.297 63.158 0.00 0.00 0.00 5.19
39 40 1.741770 GCATCACACGGTCCCTGTC 60.742 63.158 0.00 0.00 0.00 3.51
74 75 0.678684 TGTCATAGCTCGTCGTCCCA 60.679 55.000 0.00 0.00 0.00 4.37
93 94 2.037847 GGCATGAGGGGGCTTGTT 59.962 61.111 0.00 0.00 0.00 2.83
94 95 2.943265 AGGCATGAGGGGGCTTGT 60.943 61.111 0.00 0.00 38.04 3.16
99 100 4.864334 GTGCGAGGCATGAGGGGG 62.864 72.222 0.00 0.00 41.91 5.40
106 107 1.598517 TGTCTCATGTGCGAGGCAT 59.401 52.632 0.00 0.00 42.57 4.40
115 116 0.976641 ACGGTCATGGTGTCTCATGT 59.023 50.000 0.00 0.00 43.52 3.21
118 119 1.005037 GCACGGTCATGGTGTCTCA 60.005 57.895 0.00 0.00 37.70 3.27
172 174 2.185350 CCCTTCAGAGCGCGTGAT 59.815 61.111 15.09 0.00 0.00 3.06
205 207 0.391130 GATTGTAGCACGGCTGGTCA 60.391 55.000 8.44 3.40 40.10 4.02
233 235 1.524393 TCATGGCTTGCATCGCGAT 60.524 52.632 17.62 17.62 0.00 4.58
235 237 2.023741 GTCATGGCTTGCATCGCG 59.976 61.111 0.00 0.00 0.00 5.87
295 314 3.188786 CGGTTGCAGCTACCTCGC 61.189 66.667 21.76 0.00 33.35 5.03
316 335 1.750193 TTCATCTGTTTGGATCGGCC 58.250 50.000 0.00 0.00 37.10 6.13
317 336 3.848272 TTTTCATCTGTTTGGATCGGC 57.152 42.857 0.00 0.00 0.00 5.54
318 337 4.083537 TCGTTTTTCATCTGTTTGGATCGG 60.084 41.667 0.00 0.00 0.00 4.18
322 341 5.568685 TGTTCGTTTTTCATCTGTTTGGA 57.431 34.783 0.00 0.00 0.00 3.53
323 342 6.639671 TTTGTTCGTTTTTCATCTGTTTGG 57.360 33.333 0.00 0.00 0.00 3.28
324 343 6.177822 GCTTTGTTCGTTTTTCATCTGTTTG 58.822 36.000 0.00 0.00 0.00 2.93
325 344 5.004345 CGCTTTGTTCGTTTTTCATCTGTTT 59.996 36.000 0.00 0.00 0.00 2.83
326 345 4.499040 CGCTTTGTTCGTTTTTCATCTGTT 59.501 37.500 0.00 0.00 0.00 3.16
327 346 4.035017 CGCTTTGTTCGTTTTTCATCTGT 58.965 39.130 0.00 0.00 0.00 3.41
328 347 3.121696 GCGCTTTGTTCGTTTTTCATCTG 60.122 43.478 0.00 0.00 0.00 2.90
329 348 3.042887 GCGCTTTGTTCGTTTTTCATCT 58.957 40.909 0.00 0.00 0.00 2.90
330 349 2.160285 CGCGCTTTGTTCGTTTTTCATC 60.160 45.455 5.56 0.00 0.00 2.92
331 350 1.778591 CGCGCTTTGTTCGTTTTTCAT 59.221 42.857 5.56 0.00 0.00 2.57
332 351 1.184349 CGCGCTTTGTTCGTTTTTCA 58.816 45.000 5.56 0.00 0.00 2.69
333 352 0.112309 GCGCGCTTTGTTCGTTTTTC 60.112 50.000 26.67 0.00 0.00 2.29
334 353 1.793480 CGCGCGCTTTGTTCGTTTTT 61.793 50.000 30.48 0.00 0.00 1.94
335 354 2.283058 CGCGCGCTTTGTTCGTTTT 61.283 52.632 30.48 0.00 0.00 2.43
336 355 2.720750 CGCGCGCTTTGTTCGTTT 60.721 55.556 30.48 0.00 0.00 3.60
337 356 3.833176 GACGCGCGCTTTGTTCGTT 62.833 57.895 32.58 5.66 33.21 3.85
338 357 4.349871 GACGCGCGCTTTGTTCGT 62.350 61.111 32.58 17.67 35.98 3.85
343 362 4.659874 AAACGGACGCGCGCTTTG 62.660 61.111 32.58 19.69 0.00 2.77
344 363 4.659874 CAAACGGACGCGCGCTTT 62.660 61.111 32.58 19.12 0.00 3.51
357 376 4.676586 CAACGCGCCGACCCAAAC 62.677 66.667 5.73 0.00 0.00 2.93
368 387 3.726517 CAGAGCAACCCCAACGCG 61.727 66.667 3.53 3.53 0.00 6.01
369 388 2.281484 TCAGAGCAACCCCAACGC 60.281 61.111 0.00 0.00 0.00 4.84
370 389 2.317609 CGTCAGAGCAACCCCAACG 61.318 63.158 0.00 0.00 0.00 4.10
371 390 1.966451 CCGTCAGAGCAACCCCAAC 60.966 63.158 0.00 0.00 0.00 3.77
372 391 2.429930 CCGTCAGAGCAACCCCAA 59.570 61.111 0.00 0.00 0.00 4.12
373 392 3.636231 CCCGTCAGAGCAACCCCA 61.636 66.667 0.00 0.00 0.00 4.96
374 393 3.637273 ACCCGTCAGAGCAACCCC 61.637 66.667 0.00 0.00 0.00 4.95
375 394 2.358737 CACCCGTCAGAGCAACCC 60.359 66.667 0.00 0.00 0.00 4.11
376 395 1.961277 CACACCCGTCAGAGCAACC 60.961 63.158 0.00 0.00 0.00 3.77
377 396 1.227556 ACACACCCGTCAGAGCAAC 60.228 57.895 0.00 0.00 0.00 4.17
378 397 1.227527 CACACACCCGTCAGAGCAA 60.228 57.895 0.00 0.00 0.00 3.91
379 398 2.421314 CACACACCCGTCAGAGCA 59.579 61.111 0.00 0.00 0.00 4.26
383 402 1.594293 GACACCACACACCCGTCAG 60.594 63.158 0.00 0.00 0.00 3.51
398 417 2.449518 TCCTGGTGCCCTTGGACA 60.450 61.111 0.00 0.00 0.00 4.02
411 430 2.354003 GCAAAAATGGTCATGGGTCCTG 60.354 50.000 0.00 0.00 0.00 3.86
412 431 1.901833 GCAAAAATGGTCATGGGTCCT 59.098 47.619 0.00 0.00 0.00 3.85
420 439 1.344114 GAAGCCCAGCAAAAATGGTCA 59.656 47.619 0.00 0.00 35.96 4.02
624 650 7.812648 TCGGTGGTACAAAAATCAATCTTAAG 58.187 34.615 0.00 0.00 44.16 1.85
625 651 7.747155 TCGGTGGTACAAAAATCAATCTTAA 57.253 32.000 0.00 0.00 44.16 1.85
842 3847 1.669115 GAACTTGAGCTCGGCTGCA 60.669 57.895 9.64 0.00 39.88 4.41
904 3910 1.209019 GAGAGCTCCTGATTCTTGCCA 59.791 52.381 10.93 0.00 0.00 4.92
1301 4313 4.489771 CCTCCATGGTGGACGCCC 62.490 72.222 25.90 0.00 42.67 6.13
1742 4760 1.878656 GCAGTGGTGTAGAGCCGACT 61.879 60.000 0.00 0.00 0.00 4.18
1847 5471 2.031157 CGATTGGTTTTGCTTCGGAACT 60.031 45.455 0.00 0.00 0.00 3.01
2379 6041 8.522830 CCAAGATTAATTTTACAAGAGAGCCAA 58.477 33.333 0.00 0.00 0.00 4.52
2446 6109 0.388134 TACTCGTCGGAAACTGCAGC 60.388 55.000 15.27 0.00 0.00 5.25
2447 6110 1.719780 GTTACTCGTCGGAAACTGCAG 59.280 52.381 13.48 13.48 0.00 4.41
2670 6468 3.119637 ACAACACTTTTCCAACCAGAACG 60.120 43.478 0.00 0.00 0.00 3.95
2672 6470 4.399934 GGTACAACACTTTTCCAACCAGAA 59.600 41.667 0.00 0.00 0.00 3.02
2846 12765 3.411446 CTCAAGGCTTCACCAACACATA 58.589 45.455 0.00 0.00 43.14 2.29
2847 12766 2.233271 CTCAAGGCTTCACCAACACAT 58.767 47.619 0.00 0.00 43.14 3.21
2877 13275 7.122650 ACAACTTGATATTTGGTACATTGAGGG 59.877 37.037 0.00 0.00 39.30 4.30
2940 13338 0.886563 GCTCTGCACAAATTCAGGCT 59.113 50.000 0.00 0.00 0.00 4.58
3085 13492 6.127897 GGAGTCTGAAAATGTAATCCAAGTGG 60.128 42.308 0.00 0.00 0.00 4.00
3174 13721 5.991606 ACCAATAACATGACCGATGATAGTG 59.008 40.000 0.00 0.00 35.99 2.74


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

AutoCloner maintained by Alex Coulton.