Multiple sequence alignment - TraesCS3A01G179100

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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 TraesCS3A01G179100 chr3A 100.000 2417 0 0 1 2417 205691277 205688861 0.000000e+00 4464.0
1 TraesCS3A01G179100 chr3A 94.099 644 37 1 1775 2417 595929057 595928414 0.000000e+00 977.0
2 TraesCS3A01G179100 chr3A 92.534 509 14 5 352 838 417637081 417637587 0.000000e+00 708.0
3 TraesCS3A01G179100 chr3A 91.137 519 12 8 352 838 417629528 417630044 0.000000e+00 673.0
4 TraesCS3A01G179100 chr3A 78.857 350 49 17 715 1049 167679581 167679920 1.880000e-51 213.0
5 TraesCS3A01G179100 chr3A 78.917 351 47 19 715 1049 167684138 167684477 1.880000e-51 213.0
6 TraesCS3A01G179100 chr1A 93.739 1773 53 28 58 1775 269245328 269243559 0.000000e+00 2606.0
7 TraesCS3A01G179100 chr7B 95.186 644 30 1 1775 2417 24284743 24284100 0.000000e+00 1016.0
8 TraesCS3A01G179100 chr7B 86.680 488 43 16 1301 1781 654668149 654667677 2.750000e-144 521.0
9 TraesCS3A01G179100 chr7B 90.909 88 7 1 697 783 246673972 246674059 1.520000e-22 117.0
10 TraesCS3A01G179100 chr7B 90.909 88 7 1 697 783 246679315 246679402 1.520000e-22 117.0
11 TraesCS3A01G179100 chr7B 95.652 46 2 0 1137 1182 319865935 319865890 9.270000e-10 75.0
12 TraesCS3A01G179100 chr7B 95.652 46 2 0 1137 1182 319870468 319870423 9.270000e-10 75.0
13 TraesCS3A01G179100 chr7B 92.308 52 3 1 939 990 383861436 383861386 3.330000e-09 73.1
14 TraesCS3A01G179100 chr7B 97.561 41 1 0 939 979 383866669 383866629 1.200000e-08 71.3
15 TraesCS3A01G179100 chr7D 91.204 648 55 2 1772 2417 225825561 225824914 0.000000e+00 880.0
16 TraesCS3A01G179100 chr7D 81.227 277 42 10 54 325 604110294 604110565 5.230000e-52 215.0
17 TraesCS3A01G179100 chr1B 94.670 469 25 0 1775 2243 120637898 120638366 0.000000e+00 728.0
18 TraesCS3A01G179100 chr1B 91.534 189 11 3 875 1062 464918855 464918671 3.080000e-64 255.0
19 TraesCS3A01G179100 chr1B 90.052 191 11 5 875 1061 464914198 464914012 8.630000e-60 241.0
20 TraesCS3A01G179100 chr1B 95.000 140 6 1 2279 2417 120638368 120638507 4.050000e-53 219.0
21 TraesCS3A01G179100 chr1B 88.235 170 19 1 515 683 230369088 230369257 4.070000e-48 202.0
22 TraesCS3A01G179100 chr1B 93.939 99 6 0 1044 1142 433240086 433239988 1.500000e-32 150.0
23 TraesCS3A01G179100 chr1B 91.509 106 6 3 697 800 346598619 346598515 2.500000e-30 143.0
24 TraesCS3A01G179100 chr1B 89.908 109 6 4 697 800 346593209 346593101 4.190000e-28 135.0
25 TraesCS3A01G179100 chr1B 97.015 67 2 0 1087 1153 60864391 60864457 1.960000e-21 113.0
26 TraesCS3A01G179100 chr1B 94.030 67 4 0 1087 1153 60859888 60859954 4.250000e-18 102.0
27 TraesCS3A01G179100 chr5D 92.360 445 33 1 1974 2417 158789567 158789123 1.220000e-177 632.0
28 TraesCS3A01G179100 chr3B 88.958 480 31 15 1309 1781 409837370 409837834 7.500000e-160 573.0
29 TraesCS3A01G179100 chr3B 88.008 492 34 18 1291 1774 409841874 409842348 2.100000e-155 558.0
30 TraesCS3A01G179100 chr3B 86.475 488 44 17 1301 1781 560057099 560057571 1.280000e-142 516.0
31 TraesCS3A01G179100 chr3B 80.297 269 46 6 58 323 376493963 376493699 1.900000e-46 196.0
32 TraesCS3A01G179100 chr5B 86.708 489 43 17 1300 1781 337435524 337435997 7.660000e-145 523.0
33 TraesCS3A01G179100 chr5B 86.172 499 41 21 1291 1781 293189507 293189985 4.610000e-142 514.0
34 TraesCS3A01G179100 chr5B 86.151 491 41 20 1291 1774 293194009 293194479 2.770000e-139 505.0
35 TraesCS3A01G179100 chr5B 79.255 376 34 27 697 1064 316552204 316552543 3.130000e-54 222.0
36 TraesCS3A01G179100 chr5B 90.000 170 16 1 515 683 412673506 412673675 4.050000e-53 219.0
37 TraesCS3A01G179100 chr5B 89.412 170 17 1 515 683 412678065 412678234 1.880000e-51 213.0
38 TraesCS3A01G179100 chr5B 89.091 165 17 1 520 683 424328526 424328362 1.130000e-48 204.0
39 TraesCS3A01G179100 chr5B 92.784 97 5 2 1087 1182 225404574 225404669 3.240000e-29 139.0
40 TraesCS3A01G179100 chr5B 91.667 96 8 0 1087 1182 225399245 225399340 1.510000e-27 134.0
41 TraesCS3A01G179100 chr4B 86.848 479 36 17 1313 1781 560835571 560836032 5.960000e-141 510.0
42 TraesCS3A01G179100 chr4B 87.500 168 18 3 524 689 534532408 534532242 8.820000e-45 191.0
43 TraesCS3A01G179100 chr6D 81.463 615 89 21 1172 1774 113259259 113259860 4.670000e-132 481.0
44 TraesCS3A01G179100 chr2D 82.031 256 39 6 58 309 279508134 279508386 6.770000e-51 211.0
45 TraesCS3A01G179100 chr2D 90.968 155 12 2 57 210 319352118 319351965 8.760000e-50 207.0
46 TraesCS3A01G179100 chr2D 88.554 166 18 1 1021 1186 251993588 251993424 1.470000e-47 200.0
47 TraesCS3A01G179100 chr2D 90.476 105 9 1 697 800 209705674 209705778 1.170000e-28 137.0
48 TraesCS3A01G179100 chr2D 88.421 95 9 2 697 790 209710283 209710376 1.960000e-21 113.0
49 TraesCS3A01G179100 chr2D 84.615 65 9 1 897 960 276794964 276794900 2.010000e-06 63.9
50 TraesCS3A01G179100 chr2B 82.591 247 33 9 82 324 388225848 388225608 2.430000e-50 209.0
51 TraesCS3A01G179100 chr2B 88.824 170 18 1 515 683 606226907 606227076 8.760000e-50 207.0
52 TraesCS3A01G179100 chr2B 80.812 271 43 8 58 324 556544577 556544312 1.130000e-48 204.0
53 TraesCS3A01G179100 chr2B 74.510 357 68 21 1205 1547 220135039 220134692 1.510000e-27 134.0
54 TraesCS3A01G179100 chr2A 80.934 257 37 10 58 309 498528450 498528699 2.450000e-45 193.0
55 TraesCS3A01G179100 chr6B 82.927 205 32 3 58 261 356445545 356445343 5.310000e-42 182.0
56 TraesCS3A01G179100 chr6B 97.826 46 1 0 1137 1182 272299294 272299339 1.990000e-11 80.5
57 TraesCS3A01G179100 chr6B 97.727 44 1 0 1139 1182 190078392 190078435 2.580000e-10 76.8
58 TraesCS3A01G179100 chr6B 95.652 46 2 0 1137 1182 272295005 272295050 9.270000e-10 75.0
59 TraesCS3A01G179100 chr1D 74.545 220 30 25 745 947 246372194 246371984 3.330000e-09 73.1
60 TraesCS3A01G179100 chr1D 84.722 72 7 4 877 947 246376630 246376562 4.310000e-08 69.4
61 TraesCS3A01G179100 chr3D 92.157 51 3 1 897 947 326347497 326347546 1.200000e-08 71.3


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 TraesCS3A01G179100 chr3A 205688861 205691277 2416 True 4464.0 4464 100.000 1 2417 1 chr3A.!!$R1 2416
1 TraesCS3A01G179100 chr3A 595928414 595929057 643 True 977.0 977 94.099 1775 2417 1 chr3A.!!$R2 642
2 TraesCS3A01G179100 chr3A 417637081 417637587 506 False 708.0 708 92.534 352 838 1 chr3A.!!$F4 486
3 TraesCS3A01G179100 chr3A 417629528 417630044 516 False 673.0 673 91.137 352 838 1 chr3A.!!$F3 486
4 TraesCS3A01G179100 chr1A 269243559 269245328 1769 True 2606.0 2606 93.739 58 1775 1 chr1A.!!$R1 1717
5 TraesCS3A01G179100 chr7B 24284100 24284743 643 True 1016.0 1016 95.186 1775 2417 1 chr7B.!!$R1 642
6 TraesCS3A01G179100 chr7D 225824914 225825561 647 True 880.0 880 91.204 1772 2417 1 chr7D.!!$R1 645
7 TraesCS3A01G179100 chr1B 120637898 120638507 609 False 473.5 728 94.835 1775 2417 2 chr1B.!!$F4 642
8 TraesCS3A01G179100 chr6D 113259259 113259860 601 False 481.0 481 81.463 1172 1774 1 chr6D.!!$F1 602

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
48 49 0.179056 CAACAAGTGACCCACGTCCT 60.179 55.0 0.0 0.0 39.64 3.85 F
49 50 0.544697 AACAAGTGACCCACGTCCTT 59.455 50.0 0.0 0.0 39.64 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1395 1462 0.625849 AGACGCCCTGATTCCCAATT 59.374 50.0 0.0 0.0 0.0 2.32 R
2031 2108 0.693622 TGGGCGGAGGTAAATCACAA 59.306 50.0 0.0 0.0 0.0 3.33 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
29 30 2.712057 CAACAAGTGGACAATCAGCC 57.288 50.000 0.00 0.00 0.00 4.85
30 31 1.955778 CAACAAGTGGACAATCAGCCA 59.044 47.619 0.00 0.00 0.00 4.75
31 32 2.361757 CAACAAGTGGACAATCAGCCAA 59.638 45.455 0.00 0.00 35.63 4.52
32 33 1.956477 ACAAGTGGACAATCAGCCAAC 59.044 47.619 0.00 0.00 35.63 3.77
33 34 1.955778 CAAGTGGACAATCAGCCAACA 59.044 47.619 0.00 0.00 35.63 3.33
34 35 2.361757 CAAGTGGACAATCAGCCAACAA 59.638 45.455 0.00 0.00 35.63 2.83
35 36 2.233271 AGTGGACAATCAGCCAACAAG 58.767 47.619 0.00 0.00 35.63 3.16
36 37 1.956477 GTGGACAATCAGCCAACAAGT 59.044 47.619 0.00 0.00 35.63 3.16
37 38 1.955778 TGGACAATCAGCCAACAAGTG 59.044 47.619 0.00 0.00 0.00 3.16
38 39 2.229792 GGACAATCAGCCAACAAGTGA 58.770 47.619 0.00 0.00 0.00 3.41
39 40 2.030805 GGACAATCAGCCAACAAGTGAC 60.031 50.000 0.00 0.00 0.00 3.67
40 41 1.956477 ACAATCAGCCAACAAGTGACC 59.044 47.619 0.00 0.00 0.00 4.02
41 42 1.270550 CAATCAGCCAACAAGTGACCC 59.729 52.381 0.00 0.00 0.00 4.46
42 43 0.478072 ATCAGCCAACAAGTGACCCA 59.522 50.000 0.00 0.00 0.00 4.51
43 44 0.465460 TCAGCCAACAAGTGACCCAC 60.465 55.000 0.00 0.00 34.10 4.61
44 45 1.525995 AGCCAACAAGTGACCCACG 60.526 57.895 0.00 0.00 39.64 4.94
45 46 1.822186 GCCAACAAGTGACCCACGT 60.822 57.895 0.00 0.00 39.64 4.49
46 47 1.782028 GCCAACAAGTGACCCACGTC 61.782 60.000 0.00 0.00 39.64 4.34
47 48 1.164041 CCAACAAGTGACCCACGTCC 61.164 60.000 0.00 0.00 39.64 4.79
48 49 0.179056 CAACAAGTGACCCACGTCCT 60.179 55.000 0.00 0.00 39.64 3.85
49 50 0.544697 AACAAGTGACCCACGTCCTT 59.455 50.000 0.00 0.00 39.64 3.36
50 51 0.179056 ACAAGTGACCCACGTCCTTG 60.179 55.000 14.53 14.53 44.45 3.61
51 52 0.884704 CAAGTGACCCACGTCCTTGG 60.885 60.000 10.88 0.00 40.24 3.61
78 79 3.723260 TGATCGTTTGTAAGTGCAGTGA 58.277 40.909 0.00 0.00 0.00 3.41
118 119 1.001706 CGAGTGTCGTGTTCTCCTCAA 60.002 52.381 0.00 0.00 34.72 3.02
174 175 2.729882 GCTAGGTAACGCGGTTCATATG 59.270 50.000 12.47 0.00 46.39 1.78
233 234 7.499895 AGGATGACAACAAAGAAAATGCAAAAT 59.500 29.630 0.00 0.00 0.00 1.82
262 263 5.723887 AGGGTAGATTCAGATTTGACTCAGT 59.276 40.000 6.40 0.00 35.94 3.41
375 378 4.615588 TCACCAACATGTATGTCACAGA 57.384 40.909 0.00 0.00 41.51 3.41
451 454 7.169645 GCAGTACACATGTGAAATGAAACAAAT 59.830 33.333 31.94 7.39 0.00 2.32
843 907 2.498726 GAAGAGGAGGAGCAGCGG 59.501 66.667 0.00 0.00 0.00 5.52
863 927 1.480498 GCAGGAAGGGAAAGGGAACAA 60.480 52.381 0.00 0.00 0.00 2.83
966 1030 2.183555 GGGGTTCAGAGTACGCCG 59.816 66.667 0.00 0.00 38.59 6.46
1000 1064 0.820226 CAGTAGGAGCAGCAGTAGCA 59.180 55.000 0.00 0.00 45.49 3.49
1028 1092 3.632145 GTGAGGAAGAAGAAAGGCAACAA 59.368 43.478 0.00 0.00 41.41 2.83
1035 1099 2.877043 AGAAAGGCAACAACAGCAAG 57.123 45.000 0.00 0.00 41.41 4.01
1076 1140 3.727258 CAGGGGCGTGGGGATCAA 61.727 66.667 0.00 0.00 0.00 2.57
1100 1164 2.821810 GGCGCAAGGAGAAGGAGC 60.822 66.667 10.83 0.00 38.28 4.70
1122 1186 1.589414 AAGGGAATAGGAGCAGCAGT 58.411 50.000 0.00 0.00 0.00 4.40
1368 1435 2.203938 TGGAGAAGGAAGCGGGGT 60.204 61.111 0.00 0.00 0.00 4.95
1388 1455 3.500289 GGTAGAGAGGAGATGGAGATGCT 60.500 52.174 0.00 0.00 0.00 3.79
1395 1462 2.558575 GGAGATGGAGATGCTAGGCCTA 60.559 54.545 13.09 13.09 0.00 3.93
1409 1479 1.500736 AGGCCTAATTGGGAATCAGGG 59.499 52.381 12.81 0.00 36.00 4.45
1538 1612 4.504858 TGGATACTTCTTTTCTTCTCGCC 58.495 43.478 0.00 0.00 37.61 5.54
1781 1858 5.044846 AGGAAATGTACTTATCAGTTGCCCT 60.045 40.000 0.00 0.00 33.22 5.19
1837 1914 2.410322 TTTCTGGCCAGCACATCGGT 62.410 55.000 28.91 0.00 0.00 4.69
1841 1918 3.188786 GCCAGCACATCGGTCGTC 61.189 66.667 0.00 0.00 0.00 4.20
1935 2012 2.824341 GTCCGAAAACCCACTCTAGAGA 59.176 50.000 26.57 0.00 0.00 3.10
1972 2049 0.941463 GAGTATGCGGATCGTGCTGG 60.941 60.000 9.60 0.00 0.00 4.85
2006 2083 3.554960 CGTTTGTCCATCTCCAAGAGACA 60.555 47.826 0.00 0.00 41.76 3.41
2019 2096 0.546267 AGAGACAGTGTCCAGCCCAT 60.546 55.000 19.71 0.00 32.18 4.00
2031 2108 1.695597 AGCCCATTGCCTAGCTCCT 60.696 57.895 0.00 0.00 42.71 3.69
2067 2144 1.477558 CCCAAAGTGCAGTGAACTCCT 60.478 52.381 3.60 0.00 0.00 3.69
2198 2275 0.764369 AGGTGTTCTGGAGGCTGACA 60.764 55.000 0.00 0.00 0.00 3.58
2318 2395 0.609662 GCATGTCCAAACCAAGCCAT 59.390 50.000 0.00 0.00 0.00 4.40
2319 2396 1.824230 GCATGTCCAAACCAAGCCATA 59.176 47.619 0.00 0.00 0.00 2.74
2339 2416 5.072329 CCATAGTTTACTCCCATCAGTCCAT 59.928 44.000 0.00 0.00 0.00 3.41
2410 2487 1.838611 ATGATCCCTAGGCCACCAAT 58.161 50.000 5.01 0.00 0.00 3.16
2412 2489 1.494721 TGATCCCTAGGCCACCAATTC 59.505 52.381 5.01 0.00 0.00 2.17
2413 2490 1.494721 GATCCCTAGGCCACCAATTCA 59.505 52.381 5.01 0.00 0.00 2.57
2414 2491 0.918983 TCCCTAGGCCACCAATTCAG 59.081 55.000 5.01 0.00 0.00 3.02
2415 2492 0.625849 CCCTAGGCCACCAATTCAGT 59.374 55.000 5.01 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.748493 TCCACTTGTTGGCTGTTTGTC 59.252 47.619 0.00 0.00 46.47 3.18
1 2 1.476488 GTCCACTTGTTGGCTGTTTGT 59.524 47.619 0.00 0.00 46.47 2.83
2 3 1.476085 TGTCCACTTGTTGGCTGTTTG 59.524 47.619 0.00 0.00 46.47 2.93
3 4 1.846007 TGTCCACTTGTTGGCTGTTT 58.154 45.000 0.00 0.00 46.47 2.83
4 5 1.846007 TTGTCCACTTGTTGGCTGTT 58.154 45.000 0.00 0.00 46.47 3.16
5 6 1.956477 GATTGTCCACTTGTTGGCTGT 59.044 47.619 0.00 0.00 46.47 4.40
6 7 1.955778 TGATTGTCCACTTGTTGGCTG 59.044 47.619 0.00 0.00 46.47 4.85
7 8 2.233271 CTGATTGTCCACTTGTTGGCT 58.767 47.619 0.00 0.00 46.47 4.75
8 9 1.336240 GCTGATTGTCCACTTGTTGGC 60.336 52.381 0.00 0.00 46.47 4.52
10 11 1.955778 TGGCTGATTGTCCACTTGTTG 59.044 47.619 0.00 0.00 0.00 3.33
11 12 2.362077 GTTGGCTGATTGTCCACTTGTT 59.638 45.455 0.00 0.00 30.97 2.83
12 13 1.956477 GTTGGCTGATTGTCCACTTGT 59.044 47.619 0.00 0.00 30.97 3.16
13 14 1.955778 TGTTGGCTGATTGTCCACTTG 59.044 47.619 0.00 0.00 30.97 3.16
14 15 2.363306 TGTTGGCTGATTGTCCACTT 57.637 45.000 0.00 0.00 30.97 3.16
15 16 2.233271 CTTGTTGGCTGATTGTCCACT 58.767 47.619 0.00 0.00 30.97 4.00
16 17 1.956477 ACTTGTTGGCTGATTGTCCAC 59.044 47.619 0.00 0.00 30.97 4.02
17 18 1.955778 CACTTGTTGGCTGATTGTCCA 59.044 47.619 0.00 0.00 0.00 4.02
18 19 2.030805 GTCACTTGTTGGCTGATTGTCC 60.031 50.000 0.00 0.00 0.00 4.02
19 20 2.030805 GGTCACTTGTTGGCTGATTGTC 60.031 50.000 0.00 0.00 0.00 3.18
20 21 1.956477 GGTCACTTGTTGGCTGATTGT 59.044 47.619 0.00 0.00 0.00 2.71
21 22 1.270550 GGGTCACTTGTTGGCTGATTG 59.729 52.381 0.00 0.00 0.00 2.67
22 23 1.133513 TGGGTCACTTGTTGGCTGATT 60.134 47.619 0.00 0.00 0.00 2.57
23 24 0.478072 TGGGTCACTTGTTGGCTGAT 59.522 50.000 0.00 0.00 0.00 2.90
24 25 0.465460 GTGGGTCACTTGTTGGCTGA 60.465 55.000 0.00 0.00 0.00 4.26
25 26 1.785041 CGTGGGTCACTTGTTGGCTG 61.785 60.000 0.00 0.00 31.34 4.85
26 27 1.525995 CGTGGGTCACTTGTTGGCT 60.526 57.895 0.00 0.00 31.34 4.75
27 28 1.782028 GACGTGGGTCACTTGTTGGC 61.782 60.000 0.00 0.00 42.91 4.52
28 29 1.164041 GGACGTGGGTCACTTGTTGG 61.164 60.000 0.00 0.00 45.28 3.77
29 30 0.179056 AGGACGTGGGTCACTTGTTG 60.179 55.000 0.00 0.00 45.28 3.33
30 31 0.544697 AAGGACGTGGGTCACTTGTT 59.455 50.000 0.00 0.00 45.28 2.83
31 32 0.179056 CAAGGACGTGGGTCACTTGT 60.179 55.000 0.00 0.00 45.28 3.16
32 33 0.884704 CCAAGGACGTGGGTCACTTG 60.885 60.000 0.00 13.67 45.28 3.16
33 34 1.450211 CCAAGGACGTGGGTCACTT 59.550 57.895 0.00 0.00 45.28 3.16
34 35 3.148084 CCAAGGACGTGGGTCACT 58.852 61.111 0.00 0.00 45.28 3.41
40 41 2.113139 AGCAACCCAAGGACGTGG 59.887 61.111 0.00 0.00 38.51 4.94
41 42 0.606401 ATCAGCAACCCAAGGACGTG 60.606 55.000 0.00 0.00 0.00 4.49
42 43 0.321653 GATCAGCAACCCAAGGACGT 60.322 55.000 0.00 0.00 0.00 4.34
43 44 1.361668 CGATCAGCAACCCAAGGACG 61.362 60.000 0.00 0.00 0.00 4.79
44 45 0.321653 ACGATCAGCAACCCAAGGAC 60.322 55.000 0.00 0.00 0.00 3.85
45 46 0.400213 AACGATCAGCAACCCAAGGA 59.600 50.000 0.00 0.00 0.00 3.36
46 47 1.068333 CAAACGATCAGCAACCCAAGG 60.068 52.381 0.00 0.00 0.00 3.61
47 48 1.608590 ACAAACGATCAGCAACCCAAG 59.391 47.619 0.00 0.00 0.00 3.61
48 49 1.686355 ACAAACGATCAGCAACCCAA 58.314 45.000 0.00 0.00 0.00 4.12
49 50 2.552599 TACAAACGATCAGCAACCCA 57.447 45.000 0.00 0.00 0.00 4.51
50 51 2.812011 ACTTACAAACGATCAGCAACCC 59.188 45.455 0.00 0.00 0.00 4.11
51 52 3.810373 CACTTACAAACGATCAGCAACC 58.190 45.455 0.00 0.00 0.00 3.77
52 53 3.226347 GCACTTACAAACGATCAGCAAC 58.774 45.455 0.00 0.00 0.00 4.17
53 54 2.875317 TGCACTTACAAACGATCAGCAA 59.125 40.909 0.00 0.00 0.00 3.91
54 55 2.480037 CTGCACTTACAAACGATCAGCA 59.520 45.455 0.00 0.00 0.00 4.41
55 56 2.480419 ACTGCACTTACAAACGATCAGC 59.520 45.455 0.00 0.00 0.00 4.26
56 57 3.740832 TCACTGCACTTACAAACGATCAG 59.259 43.478 0.00 0.00 0.00 2.90
78 79 2.549329 CGTAGTTTGGGCGTAAAAACCT 59.451 45.455 5.67 0.00 37.04 3.50
233 234 6.156949 AGTCAAATCTGAATCTACCCTTGCTA 59.843 38.462 0.00 0.00 31.88 3.49
538 562 2.263945 TCGTAGTTGTGTGTGTGTGTG 58.736 47.619 0.00 0.00 0.00 3.82
539 563 2.658373 TCGTAGTTGTGTGTGTGTGT 57.342 45.000 0.00 0.00 0.00 3.72
843 907 0.112412 TGTTCCCTTTCCCTTCCTGC 59.888 55.000 0.00 0.00 0.00 4.85
863 927 1.643286 TCCCTCTCTCCACATCTCTGT 59.357 52.381 0.00 0.00 35.44 3.41
941 1005 1.366319 ACTCTGAACCCCATTCTGCT 58.634 50.000 0.00 0.00 38.25 4.24
966 1030 1.208293 CTACTGCCCTTCTTCTCCCAC 59.792 57.143 0.00 0.00 0.00 4.61
1000 1064 3.265479 CCTTTCTTCTTCCTCACCTCCAT 59.735 47.826 0.00 0.00 0.00 3.41
1028 1092 2.057922 TCTTCTTCTTCCCCTTGCTGT 58.942 47.619 0.00 0.00 0.00 4.40
1035 1099 2.619332 GCCTTCCTTCTTCTTCTTCCCC 60.619 54.545 0.00 0.00 0.00 4.81
1076 1140 3.710722 CTCCTTGCGCCTCCCTGT 61.711 66.667 4.18 0.00 0.00 4.00
1100 1164 2.686915 CTGCTGCTCCTATTCCCTTTTG 59.313 50.000 0.00 0.00 0.00 2.44
1122 1186 3.202373 TCCCTCGTCTCTGAATCTCCTTA 59.798 47.826 0.00 0.00 0.00 2.69
1368 1435 4.018506 CCTAGCATCTCCATCTCCTCTCTA 60.019 50.000 0.00 0.00 0.00 2.43
1388 1455 2.716424 CCCTGATTCCCAATTAGGCCTA 59.284 50.000 8.91 8.91 41.88 3.93
1395 1462 0.625849 AGACGCCCTGATTCCCAATT 59.374 50.000 0.00 0.00 0.00 2.32
1409 1479 2.937149 GAGGTCAAAAATCCCTAGACGC 59.063 50.000 0.00 0.00 0.00 5.19
1538 1612 2.362632 AGAGAACGAGGGACCCGG 60.363 66.667 4.40 3.77 29.95 5.73
1595 1671 7.486232 GCAAAGGCACTATAAACTTCAAGATTC 59.514 37.037 0.00 0.00 38.49 2.52
1704 1780 2.979814 TGTGATCCGACGATCCATTT 57.020 45.000 0.00 0.00 43.82 2.32
1811 1888 3.170362 CTGGCCAGAAAGGGGTGA 58.830 61.111 29.88 0.00 38.09 4.02
1837 1914 0.884704 GCTTGGAAGGTGCAAGACGA 60.885 55.000 12.96 0.00 46.92 4.20
1841 1918 0.879765 CTCTGCTTGGAAGGTGCAAG 59.120 55.000 5.25 5.25 46.72 4.01
1917 1994 3.254892 GCTTCTCTAGAGTGGGTTTTCG 58.745 50.000 19.21 0.91 0.00 3.46
1935 2012 6.712547 GCATACTCTATACAATTTGAGGGCTT 59.287 38.462 2.79 0.00 0.00 4.35
1972 2049 1.940613 GGACAAACGATGGCATCTACC 59.059 52.381 23.97 13.63 39.66 3.18
2006 2083 2.036256 GGCAATGGGCTGGACACT 59.964 61.111 0.00 0.00 44.01 3.55
2019 2096 3.439857 AAATCACAAGGAGCTAGGCAA 57.560 42.857 0.00 0.00 0.00 4.52
2031 2108 0.693622 TGGGCGGAGGTAAATCACAA 59.306 50.000 0.00 0.00 0.00 3.33
2136 2213 5.048013 ACTGCACCAGGAAAAACTTAATAGC 60.048 40.000 0.00 0.00 35.51 2.97
2139 2216 4.501400 GCACTGCACCAGGAAAAACTTAAT 60.501 41.667 0.00 0.00 35.51 1.40
2308 2385 3.332485 TGGGAGTAAACTATGGCTTGGTT 59.668 43.478 0.00 0.00 0.00 3.67
2318 2395 5.030147 ACATGGACTGATGGGAGTAAACTA 58.970 41.667 0.00 0.00 0.00 2.24
2319 2396 3.846588 ACATGGACTGATGGGAGTAAACT 59.153 43.478 0.00 0.00 0.00 2.66
2339 2416 1.684386 CCAGGTGGCTTTGGCAAACA 61.684 55.000 8.93 3.74 40.46 2.83
2375 2452 1.090728 TCATAAATCTTGCGGCGCAA 58.909 45.000 40.21 40.21 46.80 4.85


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

AutoCloner maintained by Alex Coulton.