Multiple sequence alignment - TraesCS1B01G461100

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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 TraesCS1B01G461100 chr1B 100.000 3192 0 0 1 3192 674190674 674187483 0.000000e+00 5895.0
1 TraesCS1B01G461100 chr1B 91.026 936 71 10 2257 3192 30719062 30719984 0.000000e+00 1251.0
2 TraesCS1B01G461100 chr1B 89.989 949 73 12 2260 3192 54303104 54302162 0.000000e+00 1206.0
3 TraesCS1B01G461100 chr1B 87.018 285 32 2 641 925 308316665 308316386 1.850000e-82 316.0
4 TraesCS1B01G461100 chr1B 85.664 286 38 3 2219 2502 689278705 689278421 6.690000e-77 298.0
5 TraesCS1B01G461100 chr1B 78.261 299 37 19 1433 1706 438109625 438109330 1.970000e-37 167.0
6 TraesCS1B01G461100 chr7B 92.549 2899 191 12 316 3192 45503188 45500293 0.000000e+00 4133.0
7 TraesCS1B01G461100 chr7B 94.572 829 44 1 2364 3192 307509762 307508935 0.000000e+00 1280.0
8 TraesCS1B01G461100 chr7B 90.476 399 37 1 1 398 159300067 159300465 2.820000e-145 525.0
9 TraesCS1B01G461100 chr7B 84.221 507 67 13 1865 2365 82315314 82314815 6.190000e-132 481.0
10 TraesCS1B01G461100 chr7B 90.123 324 32 0 1 324 45513311 45512988 3.810000e-114 422.0
11 TraesCS1B01G461100 chr7B 76.082 439 83 20 1662 2092 56907408 56906984 3.230000e-50 209.0
12 TraesCS1B01G461100 chr2A 87.973 3118 307 43 50 3117 216106088 216109187 0.000000e+00 3618.0
13 TraesCS1B01G461100 chr2A 89.263 475 47 4 1890 2362 132124051 132124523 2.740000e-165 592.0
14 TraesCS1B01G461100 chr2A 82.085 307 46 7 1 307 558684391 558684688 1.470000e-63 254.0
15 TraesCS1B01G461100 chr4A 90.304 2434 203 27 466 2877 156392256 156394678 0.000000e+00 3157.0
16 TraesCS1B01G461100 chr4A 87.719 456 45 3 1 455 156384546 156384991 3.650000e-144 521.0
17 TraesCS1B01G461100 chr4A 90.526 95 9 0 234 328 302601905 302601811 3.340000e-25 126.0
18 TraesCS1B01G461100 chr3A 91.693 951 61 10 2257 3192 164466356 164467303 0.000000e+00 1303.0
19 TraesCS1B01G461100 chr3A 84.127 63 9 1 1255 1317 509346290 509346351 3.440000e-05 60.2
20 TraesCS1B01G461100 chr7A 90.632 950 71 11 2257 3192 79311640 79312585 0.000000e+00 1245.0
21 TraesCS1B01G461100 chr7A 95.044 787 37 2 2364 3149 86969038 86969823 0.000000e+00 1236.0
22 TraesCS1B01G461100 chr7A 80.982 163 27 2 1546 1705 304617466 304617627 3.340000e-25 126.0
23 TraesCS1B01G461100 chr7A 84.800 125 16 3 1550 1671 559239522 559239398 4.320000e-24 122.0
24 TraesCS1B01G461100 chr4B 93.614 830 51 2 2363 3192 158182904 158183731 0.000000e+00 1238.0
25 TraesCS1B01G461100 chr6B 90.381 946 72 11 2263 3192 643017857 643016915 0.000000e+00 1225.0
26 TraesCS1B01G461100 chr5B 92.883 829 53 3 2364 3192 280950030 280950852 0.000000e+00 1199.0
27 TraesCS1B01G461100 chr3D 83.990 1218 155 31 910 2111 141118719 141117526 0.000000e+00 1133.0
28 TraesCS1B01G461100 chr5A 83.600 1250 157 38 1897 3117 177848554 177847324 0.000000e+00 1129.0
29 TraesCS1B01G461100 chr2B 84.975 599 82 6 1770 2365 567600753 567601346 4.560000e-168 601.0
30 TraesCS1B01G461100 chr2B 87.420 469 53 4 1890 2355 96045411 96044946 4.690000e-148 534.0
31 TraesCS1B01G461100 chr2B 84.515 536 72 9 1942 2472 215927958 215928487 1.310000e-143 520.0
32 TraesCS1B01G461100 chr6A 84.138 580 87 5 1890 2467 227185252 227184676 1.000000e-154 556.0
33 TraesCS1B01G461100 chr6A 80.426 705 106 20 1651 2345 480948558 480949240 2.840000e-140 508.0
34 TraesCS1B01G461100 chr6A 86.117 461 56 6 1876 2331 498449860 498449403 1.030000e-134 490.0
35 TraesCS1B01G461100 chr6A 86.127 173 15 7 1431 1595 526970639 526970468 9.100000e-41 178.0
36 TraesCS1B01G461100 chr2D 86.639 479 57 7 1783 2256 355837188 355836712 1.010000e-144 523.0
37 TraesCS1B01G461100 chr2D 84.538 498 66 7 1843 2336 80171622 80172112 1.720000e-132 483.0
38 TraesCS1B01G461100 chr2D 85.846 325 42 3 580 903 188182294 188181973 3.050000e-90 342.0
39 TraesCS1B01G461100 chr2D 84.181 177 28 0 749 925 178084739 178084563 4.230000e-39 172.0
40 TraesCS1B01G461100 chr1A 86.304 460 55 8 1783 2237 521480173 521480629 7.950000e-136 494.0
41 TraesCS1B01G461100 chr1A 80.782 307 50 8 1 307 116079035 116079332 6.890000e-57 231.0
42 TraesCS1B01G461100 chr1A 83.439 157 19 6 1550 1703 73198804 73198652 4.290000e-29 139.0
43 TraesCS1B01G461100 chr4D 86.364 440 53 3 1900 2336 205676941 205676506 1.040000e-129 473.0
44 TraesCS1B01G461100 chr4D 84.682 346 50 3 1888 2231 381581065 381580721 3.050000e-90 342.0
45 TraesCS1B01G461100 chr4D 86.538 312 41 1 1894 2205 385563238 385563548 3.050000e-90 342.0
46 TraesCS1B01G461100 chr4D 86.288 299 28 11 2218 2512 490029228 490029517 2.390000e-81 313.0
47 TraesCS1B01G461100 chr4D 89.516 248 21 4 2218 2464 23723195 23722952 3.090000e-80 309.0
48 TraesCS1B01G461100 chr4D 79.762 168 28 6 1664 1828 310643101 310643265 2.010000e-22 117.0
49 TraesCS1B01G461100 chr4D 78.947 171 32 4 1660 1828 312022097 312021929 2.600000e-21 113.0
50 TraesCS1B01G461100 chr6D 86.239 436 54 3 1892 2323 234288149 234287716 4.820000e-128 468.0
51 TraesCS1B01G461100 chr6D 81.818 121 20 2 1680 1799 18310373 18310254 2.030000e-17 100.0
52 TraesCS1B01G461100 chr7D 86.730 422 51 5 1847 2264 267814261 267814681 6.240000e-127 464.0
53 TraesCS1B01G461100 chr7D 82.734 278 40 7 570 846 533786684 533786954 1.140000e-59 241.0
54 TraesCS1B01G461100 chr7D 80.156 257 34 4 326 565 533786329 533786585 3.270000e-40 176.0
55 TraesCS1B01G461100 chr7D 80.822 146 21 5 1644 1786 434448956 434448815 1.210000e-19 108.0
56 TraesCS1B01G461100 chr7D 78.723 94 20 0 586 679 452885184 452885091 2.660000e-06 63.9
57 TraesCS1B01G461100 chr1D 85.990 414 51 6 1846 2256 215038765 215038356 1.360000e-118 436.0
58 TraesCS1B01G461100 chr1D 85.526 152 20 2 1962 2111 3666685 3666836 1.190000e-34 158.0
59 TraesCS1B01G461100 chrUn 86.547 223 26 4 1983 2203 448648604 448648824 3.180000e-60 243.0
60 TraesCS1B01G461100 chrUn 85.135 222 26 4 1896 2111 26640937 26641157 1.490000e-53 220.0
61 TraesCS1B01G461100 chrUn 87.591 137 11 3 1955 2091 478928474 478928344 1.530000e-33 154.0
62 TraesCS1B01G461100 chrUn 91.176 102 8 1 2120 2221 91718914 91719014 1.540000e-28 137.0
63 TraesCS1B01G461100 chrUn 89.474 95 9 1 2116 2210 476113653 476113746 5.590000e-23 119.0
64 TraesCS1B01G461100 chrUn 84.298 121 13 4 1675 1792 478928332 478928215 2.600000e-21 113.0
65 TraesCS1B01G461100 chr5D 84.298 121 13 4 1675 1792 471617774 471617657 2.600000e-21 113.0
66 TraesCS1B01G461100 chr5D 79.000 100 21 0 580 679 83706357 83706456 5.710000e-08 69.4
67 TraesCS1B01G461100 chr3B 80.124 161 25 4 1550 1706 82129419 82129262 2.600000e-21 113.0


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 TraesCS1B01G461100 chr1B 674187483 674190674 3191 True 5895.0 5895 100.000 1 3192 1 chr1B.!!$R4 3191
1 TraesCS1B01G461100 chr1B 30719062 30719984 922 False 1251.0 1251 91.026 2257 3192 1 chr1B.!!$F1 935
2 TraesCS1B01G461100 chr1B 54302162 54303104 942 True 1206.0 1206 89.989 2260 3192 1 chr1B.!!$R1 932
3 TraesCS1B01G461100 chr7B 45500293 45503188 2895 True 4133.0 4133 92.549 316 3192 1 chr7B.!!$R1 2876
4 TraesCS1B01G461100 chr7B 307508935 307509762 827 True 1280.0 1280 94.572 2364 3192 1 chr7B.!!$R5 828
5 TraesCS1B01G461100 chr2A 216106088 216109187 3099 False 3618.0 3618 87.973 50 3117 1 chr2A.!!$F2 3067
6 TraesCS1B01G461100 chr4A 156392256 156394678 2422 False 3157.0 3157 90.304 466 2877 1 chr4A.!!$F2 2411
7 TraesCS1B01G461100 chr3A 164466356 164467303 947 False 1303.0 1303 91.693 2257 3192 1 chr3A.!!$F1 935
8 TraesCS1B01G461100 chr7A 79311640 79312585 945 False 1245.0 1245 90.632 2257 3192 1 chr7A.!!$F1 935
9 TraesCS1B01G461100 chr7A 86969038 86969823 785 False 1236.0 1236 95.044 2364 3149 1 chr7A.!!$F2 785
10 TraesCS1B01G461100 chr4B 158182904 158183731 827 False 1238.0 1238 93.614 2363 3192 1 chr4B.!!$F1 829
11 TraesCS1B01G461100 chr6B 643016915 643017857 942 True 1225.0 1225 90.381 2263 3192 1 chr6B.!!$R1 929
12 TraesCS1B01G461100 chr5B 280950030 280950852 822 False 1199.0 1199 92.883 2364 3192 1 chr5B.!!$F1 828
13 TraesCS1B01G461100 chr3D 141117526 141118719 1193 True 1133.0 1133 83.990 910 2111 1 chr3D.!!$R1 1201
14 TraesCS1B01G461100 chr5A 177847324 177848554 1230 True 1129.0 1129 83.600 1897 3117 1 chr5A.!!$R1 1220
15 TraesCS1B01G461100 chr2B 567600753 567601346 593 False 601.0 601 84.975 1770 2365 1 chr2B.!!$F2 595
16 TraesCS1B01G461100 chr2B 215927958 215928487 529 False 520.0 520 84.515 1942 2472 1 chr2B.!!$F1 530
17 TraesCS1B01G461100 chr6A 227184676 227185252 576 True 556.0 556 84.138 1890 2467 1 chr6A.!!$R1 577
18 TraesCS1B01G461100 chr6A 480948558 480949240 682 False 508.0 508 80.426 1651 2345 1 chr6A.!!$F1 694
19 TraesCS1B01G461100 chr7D 533786329 533786954 625 False 208.5 241 81.445 326 846 2 chr7D.!!$F2 520

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
24 25 0.038159 CACGACCTGGAAGTGGAGAC 60.038 60.0 15.02 0.0 32.68 3.36 F
744 855 0.172578 CAGCATCGGTTCTACGACCA 59.827 55.0 0.00 0.0 46.64 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1346 1463 0.814457 AGCACAAACAAACGCCTTGA 59.186 45.0 4.94 0.0 38.5 3.02 R
2654 2822 0.032952 CACGTCGGACCCAAAAGAGA 59.967 55.0 1.91 0.0 0.0 3.10 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 2.266055 GAGCCCACGACCTGGAAG 59.734 66.667 0.00 0.00 43.95 3.46
18 19 2.526873 AGCCCACGACCTGGAAGT 60.527 61.111 0.00 0.00 43.95 3.01
22 23 4.996976 CACGACCTGGAAGTGGAG 57.003 61.111 15.02 0.00 32.68 3.86
24 25 0.038159 CACGACCTGGAAGTGGAGAC 60.038 60.000 15.02 0.00 32.68 3.36
25 26 0.469331 ACGACCTGGAAGTGGAGACA 60.469 55.000 0.00 0.00 38.70 3.41
29 30 3.100671 GACCTGGAAGTGGAGACAGTAT 58.899 50.000 0.00 0.00 45.37 2.12
30 31 3.515901 GACCTGGAAGTGGAGACAGTATT 59.484 47.826 0.00 0.00 45.37 1.89
31 32 3.261897 ACCTGGAAGTGGAGACAGTATTG 59.738 47.826 0.00 0.00 45.37 1.90
32 33 3.515502 CCTGGAAGTGGAGACAGTATTGA 59.484 47.826 0.00 0.00 45.37 2.57
33 34 4.499183 CTGGAAGTGGAGACAGTATTGAC 58.501 47.826 0.00 0.00 45.37 3.18
34 35 3.260884 TGGAAGTGGAGACAGTATTGACC 59.739 47.826 0.00 0.00 45.37 4.02
35 36 3.369576 GGAAGTGGAGACAGTATTGACCC 60.370 52.174 0.00 0.00 45.37 4.46
36 37 1.825474 AGTGGAGACAGTATTGACCCG 59.175 52.381 0.00 0.00 43.90 5.28
37 38 1.134788 GTGGAGACAGTATTGACCCGG 60.135 57.143 0.00 0.00 44.46 5.73
38 39 1.192428 GGAGACAGTATTGACCCGGT 58.808 55.000 0.00 0.00 0.00 5.28
39 40 1.136500 GGAGACAGTATTGACCCGGTC 59.864 57.143 10.96 10.96 0.00 4.79
40 41 2.100989 GAGACAGTATTGACCCGGTCT 58.899 52.381 18.54 1.82 35.72 3.85
41 42 2.099427 GAGACAGTATTGACCCGGTCTC 59.901 54.545 18.54 5.93 39.50 3.36
42 43 1.822990 GACAGTATTGACCCGGTCTCA 59.177 52.381 18.54 5.85 33.15 3.27
43 44 2.431057 GACAGTATTGACCCGGTCTCAT 59.569 50.000 18.54 12.43 33.15 2.90
44 45 2.431057 ACAGTATTGACCCGGTCTCATC 59.569 50.000 18.54 7.10 33.15 2.92
45 46 1.681793 AGTATTGACCCGGTCTCATCG 59.318 52.381 18.54 0.00 33.15 3.84
46 47 0.387929 TATTGACCCGGTCTCATCGC 59.612 55.000 18.54 0.00 33.15 4.58
47 48 2.629050 ATTGACCCGGTCTCATCGCG 62.629 60.000 18.54 0.00 33.15 5.87
61 62 3.414700 CGCGCTGCTTTCCTTCGT 61.415 61.111 5.56 0.00 0.00 3.85
69 70 0.179189 GCTTTCCTTCGTCGGCATTG 60.179 55.000 0.00 0.00 0.00 2.82
210 211 1.470112 GCCTCGCTTCCTCTACTCAAC 60.470 57.143 0.00 0.00 0.00 3.18
303 304 3.797546 GCTGCTGTTCGCCTCTGC 61.798 66.667 0.00 0.00 38.05 4.26
310 311 1.290324 GTTCGCCTCTGCAGAGTCA 59.710 57.895 35.47 19.77 40.48 3.41
332 333 2.289010 CCAGACCCTTTGCAATCAAACC 60.289 50.000 0.00 0.00 37.28 3.27
474 475 4.388499 CCCCCACCAAGTCGTCGG 62.388 72.222 0.00 0.00 0.00 4.79
598 709 1.815421 CTGCGGCGCCTTTGTATCT 60.815 57.895 30.82 0.00 0.00 1.98
619 730 0.735978 CGACTCACCACGCTAATGCA 60.736 55.000 0.00 0.00 39.64 3.96
620 731 1.438651 GACTCACCACGCTAATGCAA 58.561 50.000 0.00 0.00 39.64 4.08
705 816 4.279326 GGTCACTCCGCTCCCTAT 57.721 61.111 0.00 0.00 0.00 2.57
709 820 0.975556 TCACTCCGCTCCCTATTGCA 60.976 55.000 0.00 0.00 0.00 4.08
744 855 0.172578 CAGCATCGGTTCTACGACCA 59.827 55.000 0.00 0.00 46.64 4.02
758 869 1.890894 GACCAAGCTCTGAGCCGTA 59.109 57.895 25.09 0.00 43.77 4.02
772 883 4.111016 CGTAGCCGTCGTGCCTCA 62.111 66.667 2.61 0.00 0.00 3.86
905 1016 2.281484 GTCTTCAACCCGCTGGCA 60.281 61.111 0.00 0.00 33.59 4.92
953 1064 1.609061 CCTCATCTTGCCGTTGTGAGT 60.609 52.381 0.00 0.00 35.66 3.41
1016 1127 3.483954 CCATGAGATGGCCTTCGTT 57.516 52.632 12.65 0.00 44.70 3.85
1024 1135 2.668550 GGCCTTCGTTGAACCGCT 60.669 61.111 0.00 0.00 0.00 5.52
1130 1241 1.066358 TCATGCTCACCTCTGCTTCAG 60.066 52.381 0.00 0.00 0.00 3.02
1193 1304 1.778334 GGCCTTAAACCGCAGTTTTG 58.222 50.000 2.88 0.00 43.82 2.44
1201 1312 0.461339 ACCGCAGTTTTGTGACGAGT 60.461 50.000 0.00 0.00 36.95 4.18
1290 1407 3.832490 ACCAAGCTACTCACATCTGTACA 59.168 43.478 0.00 0.00 0.00 2.90
1342 1459 5.117584 TGAGGCTACAAGTAAACGTTCAAA 58.882 37.500 0.00 0.00 0.00 2.69
1346 1463 6.430000 AGGCTACAAGTAAACGTTCAAATCAT 59.570 34.615 0.00 0.00 0.00 2.45
1385 1502 4.887071 TGCTACTGTTTTCCACTTTGTCAT 59.113 37.500 0.00 0.00 0.00 3.06
1491 1611 4.692625 CACAGGACAAGTTGATAAGGACAG 59.307 45.833 10.54 0.00 0.00 3.51
1507 1627 2.980233 AGCCAAGTTCAGTGCGCC 60.980 61.111 4.18 0.00 0.00 6.53
1508 1628 3.286751 GCCAAGTTCAGTGCGCCA 61.287 61.111 4.18 0.00 0.00 5.69
1514 1637 1.300931 GTTCAGTGCGCCACTCAGA 60.301 57.895 4.18 0.56 43.43 3.27
1656 1783 3.826729 TCTGTCTGCAAACAGCTACTCTA 59.173 43.478 15.58 0.00 45.12 2.43
1678 1805 2.661504 TTGCGATATTTTCCGATGCG 57.338 45.000 0.00 0.00 0.00 4.73
1765 1893 0.747644 CGCCAGCATCCAACCATACA 60.748 55.000 0.00 0.00 0.00 2.29
1789 1917 2.929531 TGTTCAACAAATGTGTGCGT 57.070 40.000 0.00 0.00 38.27 5.24
1822 1950 2.606551 CGTGCAGCTCGATCTACATCAT 60.607 50.000 11.47 0.00 0.00 2.45
1888 2019 0.379669 CCACTGCTGCGATTGATTCC 59.620 55.000 0.00 0.00 0.00 3.01
1983 2114 5.716228 TGATTTCAGCTTCACCATGGTAATT 59.284 36.000 19.28 2.71 0.00 1.40
2105 2242 1.251251 GCTTGCAAGTTCTCCCATGT 58.749 50.000 26.55 0.00 0.00 3.21
2179 2316 1.063806 CTCAAAGTCGCCTTGAGACG 58.936 55.000 12.83 0.00 42.97 4.18
2324 2466 6.248433 AGGCTTTGAAAACTCTCAATATCCA 58.752 36.000 0.00 0.00 35.31 3.41
2393 2550 1.592543 GGTTGCCAAAAAGAACTTGCG 59.407 47.619 0.00 0.00 0.00 4.85
2424 2581 3.191669 CGCGGTTCAAACATAGGTATCA 58.808 45.455 0.00 0.00 0.00 2.15
2576 2744 7.015877 GTCGTATTCAAACCAAAGAGAACATC 58.984 38.462 0.00 0.00 0.00 3.06
2577 2745 6.708502 TCGTATTCAAACCAAAGAGAACATCA 59.291 34.615 0.00 0.00 0.00 3.07
2771 2940 6.959639 TTCAAACCAAAGAGAACATAGCTT 57.040 33.333 0.00 0.00 0.00 3.74
2890 3065 9.607988 TCATATACGAATCAGAAGCCTTAAAAA 57.392 29.630 0.00 0.00 0.00 1.94
3046 3237 2.846206 TCATCTAGGTGGAAGCATTGGT 59.154 45.455 2.43 0.00 36.26 3.67
3080 3271 3.681593 GGTTATCACCCTAACTGCACAA 58.318 45.455 0.00 0.00 37.03 3.33
3155 3346 2.283173 GACCCACCCTGGCTTTGG 60.283 66.667 0.00 0.00 35.79 3.28
3187 3378 4.432712 GCCAGGGCATATGTTGTTTAAAG 58.567 43.478 5.20 0.00 41.49 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.244994 CTGTCTCCACTTCCAGGTCG 59.755 60.000 0.00 0.00 0.00 4.79
8 9 1.343069 ACTGTCTCCACTTCCAGGTC 58.657 55.000 0.00 0.00 0.00 3.85
9 10 2.696526 TACTGTCTCCACTTCCAGGT 57.303 50.000 0.00 0.00 0.00 4.00
10 11 3.515502 TCAATACTGTCTCCACTTCCAGG 59.484 47.826 0.00 0.00 0.00 4.45
11 12 4.499183 GTCAATACTGTCTCCACTTCCAG 58.501 47.826 0.00 0.00 0.00 3.86
14 15 3.676324 CGGGTCAATACTGTCTCCACTTC 60.676 52.174 0.00 0.00 0.00 3.01
15 16 2.233922 CGGGTCAATACTGTCTCCACTT 59.766 50.000 0.00 0.00 0.00 3.16
16 17 1.825474 CGGGTCAATACTGTCTCCACT 59.175 52.381 0.00 0.00 0.00 4.00
17 18 1.134788 CCGGGTCAATACTGTCTCCAC 60.135 57.143 0.00 0.00 0.00 4.02
18 19 1.191535 CCGGGTCAATACTGTCTCCA 58.808 55.000 0.00 0.00 0.00 3.86
20 21 2.099427 GAGACCGGGTCAATACTGTCTC 59.901 54.545 27.87 10.32 37.92 3.36
21 22 2.100989 GAGACCGGGTCAATACTGTCT 58.899 52.381 27.87 4.70 34.60 3.41
22 23 1.822990 TGAGACCGGGTCAATACTGTC 59.177 52.381 27.87 15.24 34.60 3.51
24 25 2.543861 CGATGAGACCGGGTCAATACTG 60.544 54.545 27.87 9.96 34.60 2.74
25 26 1.681793 CGATGAGACCGGGTCAATACT 59.318 52.381 27.87 7.78 34.60 2.12
29 30 2.577059 GCGATGAGACCGGGTCAA 59.423 61.111 27.87 16.42 34.60 3.18
30 31 3.822192 CGCGATGAGACCGGGTCA 61.822 66.667 27.87 10.47 34.60 4.02
35 36 4.862092 AGCAGCGCGATGAGACCG 62.862 66.667 30.90 0.00 0.00 4.79
36 37 2.029904 GAAAGCAGCGCGATGAGACC 62.030 60.000 30.90 10.39 0.00 3.85
37 38 1.346538 GAAAGCAGCGCGATGAGAC 59.653 57.895 30.90 10.81 0.00 3.36
38 39 1.811266 GGAAAGCAGCGCGATGAGA 60.811 57.895 30.90 0.00 0.00 3.27
39 40 1.364626 AAGGAAAGCAGCGCGATGAG 61.365 55.000 30.90 2.02 0.00 2.90
40 41 1.361668 GAAGGAAAGCAGCGCGATGA 61.362 55.000 30.90 0.00 0.00 2.92
41 42 1.061570 GAAGGAAAGCAGCGCGATG 59.938 57.895 22.00 22.00 0.00 3.84
42 43 2.456119 CGAAGGAAAGCAGCGCGAT 61.456 57.895 12.10 0.00 0.00 4.58
43 44 3.112075 CGAAGGAAAGCAGCGCGA 61.112 61.111 12.10 0.00 0.00 5.87
44 45 3.354499 GACGAAGGAAAGCAGCGCG 62.354 63.158 0.00 0.00 0.00 6.86
45 46 2.476499 GACGAAGGAAAGCAGCGC 59.524 61.111 0.00 0.00 0.00 5.92
46 47 2.730672 CCGACGAAGGAAAGCAGCG 61.731 63.158 0.00 0.00 0.00 5.18
47 48 3.028366 GCCGACGAAGGAAAGCAGC 62.028 63.158 0.00 0.00 0.00 5.25
48 49 1.021390 ATGCCGACGAAGGAAAGCAG 61.021 55.000 0.00 0.00 33.10 4.24
61 62 2.751436 GCCCAGAAGCAATGCCGA 60.751 61.111 0.00 0.00 0.00 5.54
125 126 2.508887 GCAGCTCAGAGGCGACAG 60.509 66.667 0.00 0.00 37.29 3.51
187 188 3.528370 TAGAGGAAGCGAGGCGGC 61.528 66.667 0.00 0.00 0.00 6.53
198 199 3.730215 AGAGCAGAGTTGAGTAGAGGA 57.270 47.619 0.00 0.00 0.00 3.71
310 311 2.365293 GTTTGATTGCAAAGGGTCTGGT 59.635 45.455 1.71 0.00 44.12 4.00
332 333 1.129326 GTCTGTCTCGGTTGTTGTCG 58.871 55.000 0.00 0.00 0.00 4.35
413 414 3.407967 GAATGGACCTGCCGGGGA 61.408 66.667 2.18 0.00 40.66 4.81
462 463 1.215647 GATGAGCCGACGACTTGGT 59.784 57.895 0.00 0.00 0.00 3.67
466 467 2.711922 GGTGGATGAGCCGACGACT 61.712 63.158 0.00 0.00 40.66 4.18
541 559 3.818787 GCGATGTGGCTGGCTTGG 61.819 66.667 2.00 0.00 0.00 3.61
548 566 2.115052 TTTGGTGGCGATGTGGCT 59.885 55.556 0.00 0.00 45.14 4.75
614 725 0.964358 GCTGAGCTGGAGGTTGCATT 60.964 55.000 0.00 0.00 0.00 3.56
705 816 2.669569 GCGTGAAGGAGGCTGCAA 60.670 61.111 9.23 0.00 32.41 4.08
744 855 2.896443 GGCTACGGCTCAGAGCTT 59.104 61.111 21.99 11.78 41.99 3.74
772 883 2.914289 GGGCCATAGCAGCTCAGT 59.086 61.111 4.39 0.00 42.56 3.41
905 1016 0.469144 ACGGTGGGTCAAAGGCAAAT 60.469 50.000 0.00 0.00 0.00 2.32
1009 1120 1.569493 CACAGCGGTTCAACGAAGG 59.431 57.895 0.00 0.00 35.47 3.46
1016 1127 4.680237 CGAGGCCACAGCGGTTCA 62.680 66.667 5.01 0.00 41.24 3.18
1024 1135 1.891919 GTTTGACAGCGAGGCCACA 60.892 57.895 5.01 0.00 0.00 4.17
1096 1207 1.737735 CATGACGGCAGCTCAACGA 60.738 57.895 0.00 0.00 0.00 3.85
1179 1290 2.277969 TCGTCACAAAACTGCGGTTTA 58.722 42.857 23.51 5.66 43.90 2.01
1180 1291 1.063469 CTCGTCACAAAACTGCGGTTT 59.937 47.619 18.05 18.05 46.27 3.27
1189 1300 1.771073 CGCCAGCACTCGTCACAAAA 61.771 55.000 0.00 0.00 0.00 2.44
1193 1304 2.807045 CTCGCCAGCACTCGTCAC 60.807 66.667 0.00 0.00 0.00 3.67
1342 1459 3.641648 CACAAACAAACGCCTTGATGAT 58.358 40.909 4.94 0.00 38.50 2.45
1346 1463 0.814457 AGCACAAACAAACGCCTTGA 59.186 45.000 4.94 0.00 38.50 3.02
1385 1502 2.635915 ACCAACTCGATTGACCCTTGTA 59.364 45.455 8.56 0.00 41.23 2.41
1461 1579 7.012894 CCTTATCAACTTGTCCTGTGTAAACAA 59.987 37.037 0.00 0.00 0.00 2.83
1491 1611 3.286751 TGGCGCACTGAACTTGGC 61.287 61.111 10.83 0.00 0.00 4.52
1508 1628 9.865321 CCAATTTTAAATGAATCATGTCTGAGT 57.135 29.630 0.00 0.00 34.12 3.41
1656 1783 3.974401 CGCATCGGAAAATATCGCAAAAT 59.026 39.130 0.00 0.00 0.00 1.82
1765 1893 3.556775 GCACACATTTGTTGAACAATGCT 59.443 39.130 20.24 4.88 38.00 3.79
1822 1950 1.377202 GGGCATGGTTTCAGCGAGA 60.377 57.895 0.00 0.00 0.00 4.04
1983 2114 4.021559 TCCACCGCGGAGTTGATA 57.978 55.556 35.90 8.64 39.64 2.15
2105 2242 5.533903 GTGATATAGACCGGTTCAAGTCCTA 59.466 44.000 9.42 3.64 33.29 2.94
2179 2316 0.957395 CATGTCATCATAGCCCCCGC 60.957 60.000 0.00 0.00 32.47 6.13
2324 2466 3.827722 TCTTGAACCGGGATTTTGAACT 58.172 40.909 6.32 0.00 0.00 3.01
2393 2550 4.256090 GAACCGCGCATCATGGCC 62.256 66.667 8.75 0.00 0.00 5.36
2576 2744 3.363970 CGATCAAAAGGGTTTCGACAGTG 60.364 47.826 0.00 0.00 0.00 3.66
2577 2745 2.806244 CGATCAAAAGGGTTTCGACAGT 59.194 45.455 0.00 0.00 0.00 3.55
2616 2784 1.807814 ACGATCAAGAAGCCCCCTAT 58.192 50.000 0.00 0.00 0.00 2.57
2654 2822 0.032952 CACGTCGGACCCAAAAGAGA 59.967 55.000 1.91 0.00 0.00 3.10
2805 2980 4.694339 GAATACGATCATATAGCCCCCAC 58.306 47.826 0.00 0.00 0.00 4.61
2909 3098 7.262048 GTCTCAAGTCAAACCCAAAATTGTTA 58.738 34.615 0.00 0.00 0.00 2.41
2982 3173 5.790593 ACTTATAGTCAAAAGTCAAGCCGA 58.209 37.500 0.00 0.00 30.08 5.54
3080 3271 2.626266 TGTACTGTCGGTTCACATGACT 59.374 45.455 0.00 0.00 33.81 3.41
3126 3317 3.578716 CAGGGTGGGTCGTAATATCTCAT 59.421 47.826 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.