Multiple sequence alignment - TraesCS7A01G528300

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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 TraesCS7A01G528300 chr7A 100.000 2471 0 0 1 2471 708789070 708791540 0.000000e+00 4564.0
1 TraesCS7A01G528300 chr7A 92.655 354 25 1 1286 1639 122056 122408 2.190000e-140 508.0
2 TraesCS7A01G528300 chr7A 83.158 475 60 13 1518 1981 679164709 679164244 1.370000e-112 416.0
3 TraesCS7A01G528300 chr7A 94.054 185 9 2 2287 2471 122407 122589 1.870000e-71 279.0
4 TraesCS7A01G528300 chr7A 82.886 298 37 7 1693 1981 679175262 679174970 3.150000e-64 255.0
5 TraesCS7A01G528300 chr7A 85.507 69 9 1 2069 2137 127727290 127727357 1.230000e-08 71.3
6 TraesCS7A01G528300 chr7B 94.426 2386 82 18 90 2471 568667121 568664783 0.000000e+00 3622.0
7 TraesCS7A01G528300 chr3B 94.219 2387 85 17 92 2471 460381764 460379424 0.000000e+00 3594.0
8 TraesCS7A01G528300 chr2D 95.732 1312 39 7 90 1399 35056913 35055617 0.000000e+00 2097.0
9 TraesCS7A01G528300 chr2D 94.554 1010 21 9 1462 2471 35055618 35054643 0.000000e+00 1530.0
10 TraesCS7A01G528300 chr2D 87.568 185 17 5 1 184 635109698 635109519 2.490000e-50 209.0
11 TraesCS7A01G528300 chr2D 88.202 178 16 4 1 178 373374859 373375031 8.960000e-50 207.0
12 TraesCS7A01G528300 chr6D 95.801 1286 37 7 115 1399 364892247 364893516 0.000000e+00 2060.0
13 TraesCS7A01G528300 chr6D 94.653 1010 20 13 1462 2471 364893515 364894490 0.000000e+00 1535.0
14 TraesCS7A01G528300 chr6B 94.293 1104 28 19 1369 2471 651217517 651216448 0.000000e+00 1657.0
15 TraesCS7A01G528300 chr6B 90.737 1058 63 14 111 1138 651229595 651228543 0.000000e+00 1378.0
16 TraesCS7A01G528300 chr2B 91.821 1186 58 13 1286 2471 282993757 282992611 0.000000e+00 1616.0
17 TraesCS7A01G528300 chr1D 95.472 530 18 4 475 1003 332594028 332594552 0.000000e+00 841.0
18 TraesCS7A01G528300 chr1D 85.885 418 28 16 90 479 332581277 332581691 1.370000e-112 416.0
19 TraesCS7A01G528300 chrUn 98.582 282 2 2 2190 2471 479143922 479143643 4.750000e-137 497.0
20 TraesCS7A01G528300 chr5D 85.201 473 52 10 1518 1981 199427722 199427259 1.030000e-128 470.0
21 TraesCS7A01G528300 chr5D 91.632 239 18 2 1284 1521 324970542 324970305 1.830000e-86 329.0
22 TraesCS7A01G528300 chr7D 84.211 475 52 14 1518 1981 587258027 587257565 8.110000e-120 440.0
23 TraesCS7A01G528300 chr4A 83.227 471 59 12 1518 1979 107848724 107848265 4.920000e-112 414.0
24 TraesCS7A01G528300 chr5B 90.336 238 23 0 1284 1521 377389077 377388840 1.840000e-81 313.0
25 TraesCS7A01G528300 chr5B 78.981 157 29 3 551 706 348581493 348581646 1.210000e-18 104.0
26 TraesCS7A01G528300 chr5B 90.000 70 4 3 2069 2137 453266291 453266358 1.220000e-13 87.9
27 TraesCS7A01G528300 chr5B 85.507 69 9 1 2069 2137 453295443 453295510 1.230000e-08 71.3
28 TraesCS7A01G528300 chr3D 86.879 282 30 6 1518 1798 164938523 164938248 2.390000e-80 309.0
29 TraesCS7A01G528300 chr3D 87.958 191 17 5 1 191 387347535 387347351 1.150000e-53 220.0
30 TraesCS7A01G528300 chr3D 87.027 185 18 5 1 184 597058471 597058650 1.160000e-48 204.0
31 TraesCS7A01G528300 chr5A 88.983 236 25 1 1286 1521 423056746 423056512 8.640000e-75 291.0
32 TraesCS7A01G528300 chr1A 86.911 191 24 1 1 191 287583013 287582824 1.920000e-51 213.0


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 TraesCS7A01G528300 chr7A 708789070 708791540 2470 False 4564.0 4564 100.0000 1 2471 1 chr7A.!!$F2 2470
1 TraesCS7A01G528300 chr7A 122056 122589 533 False 393.5 508 93.3545 1286 2471 2 chr7A.!!$F3 1185
2 TraesCS7A01G528300 chr7B 568664783 568667121 2338 True 3622.0 3622 94.4260 90 2471 1 chr7B.!!$R1 2381
3 TraesCS7A01G528300 chr3B 460379424 460381764 2340 True 3594.0 3594 94.2190 92 2471 1 chr3B.!!$R1 2379
4 TraesCS7A01G528300 chr2D 35054643 35056913 2270 True 1813.5 2097 95.1430 90 2471 2 chr2D.!!$R2 2381
5 TraesCS7A01G528300 chr6D 364892247 364894490 2243 False 1797.5 2060 95.2270 115 2471 2 chr6D.!!$F1 2356
6 TraesCS7A01G528300 chr6B 651216448 651217517 1069 True 1657.0 1657 94.2930 1369 2471 1 chr6B.!!$R1 1102
7 TraesCS7A01G528300 chr6B 651228543 651229595 1052 True 1378.0 1378 90.7370 111 1138 1 chr6B.!!$R2 1027
8 TraesCS7A01G528300 chr2B 282992611 282993757 1146 True 1616.0 1616 91.8210 1286 2471 1 chr2B.!!$R1 1185
9 TraesCS7A01G528300 chr1D 332594028 332594552 524 False 841.0 841 95.4720 475 1003 1 chr1D.!!$F2 528

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
31 32 0.249114 GCCGCGAAAAACCAAGGAAA 60.249 50.0 8.23 0.0 0.0 3.13 F
286 290 0.387202 CGATCTGATCTCCTTGGCGT 59.613 55.0 15.16 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1243 1276 2.044650 CATGGCACCCACCCTCAG 60.045 66.667 0.0 0.0 35.80 3.35 R
2065 2098 1.408683 ACTGAAGCAGCACCAAAGTGA 60.409 47.619 0.0 0.0 46.32 3.41 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
20 21 3.605749 CTTCCCCTCAGCCGCGAAA 62.606 63.158 8.23 0.00 0.00 3.46
21 22 3.185299 TTCCCCTCAGCCGCGAAAA 62.185 57.895 8.23 0.00 0.00 2.29
22 23 2.671619 CCCCTCAGCCGCGAAAAA 60.672 61.111 8.23 0.00 0.00 1.94
23 24 2.561373 CCCTCAGCCGCGAAAAAC 59.439 61.111 8.23 0.00 0.00 2.43
24 25 2.561373 CCTCAGCCGCGAAAAACC 59.439 61.111 8.23 0.00 0.00 3.27
25 26 2.258013 CCTCAGCCGCGAAAAACCA 61.258 57.895 8.23 0.00 0.00 3.67
26 27 1.652012 CTCAGCCGCGAAAAACCAA 59.348 52.632 8.23 0.00 0.00 3.67
27 28 0.385974 CTCAGCCGCGAAAAACCAAG 60.386 55.000 8.23 0.00 0.00 3.61
28 29 1.371635 CAGCCGCGAAAAACCAAGG 60.372 57.895 8.23 0.00 0.00 3.61
29 30 1.527380 AGCCGCGAAAAACCAAGGA 60.527 52.632 8.23 0.00 0.00 3.36
30 31 1.104577 AGCCGCGAAAAACCAAGGAA 61.105 50.000 8.23 0.00 0.00 3.36
31 32 0.249114 GCCGCGAAAAACCAAGGAAA 60.249 50.000 8.23 0.00 0.00 3.13
32 33 1.803252 GCCGCGAAAAACCAAGGAAAA 60.803 47.619 8.23 0.00 0.00 2.29
33 34 1.855978 CCGCGAAAAACCAAGGAAAAC 59.144 47.619 8.23 0.00 0.00 2.43
34 35 1.855978 CGCGAAAAACCAAGGAAAACC 59.144 47.619 0.00 0.00 0.00 3.27
35 36 2.206750 GCGAAAAACCAAGGAAAACCC 58.793 47.619 0.00 0.00 0.00 4.11
36 37 2.828877 CGAAAAACCAAGGAAAACCCC 58.171 47.619 0.00 0.00 34.66 4.95
37 38 2.800273 CGAAAAACCAAGGAAAACCCCG 60.800 50.000 0.00 0.00 34.66 5.73
38 39 0.466543 AAAACCAAGGAAAACCCCGC 59.533 50.000 0.00 0.00 34.66 6.13
39 40 1.740332 AAACCAAGGAAAACCCCGCG 61.740 55.000 0.00 0.00 34.66 6.46
40 41 2.281900 CCAAGGAAAACCCCGCGA 60.282 61.111 8.23 0.00 34.66 5.87
41 42 1.677633 CCAAGGAAAACCCCGCGAT 60.678 57.895 8.23 0.00 34.66 4.58
42 43 1.654023 CCAAGGAAAACCCCGCGATC 61.654 60.000 8.23 0.00 34.66 3.69
43 44 1.743995 AAGGAAAACCCCGCGATCG 60.744 57.895 11.69 11.69 34.66 3.69
44 45 2.125431 GGAAAACCCCGCGATCGA 60.125 61.111 21.57 0.00 38.10 3.59
45 46 2.171725 GGAAAACCCCGCGATCGAG 61.172 63.158 21.57 16.71 38.10 4.04
46 47 1.447314 GAAAACCCCGCGATCGAGT 60.447 57.895 21.57 7.01 38.10 4.18
47 48 1.419107 GAAAACCCCGCGATCGAGTC 61.419 60.000 21.57 4.10 38.10 3.36
48 49 2.847435 AAAACCCCGCGATCGAGTCC 62.847 60.000 21.57 0.00 38.10 3.85
55 56 2.579787 CGATCGAGTCCCGCACAC 60.580 66.667 10.26 0.00 38.37 3.82
56 57 2.579787 GATCGAGTCCCGCACACG 60.580 66.667 0.00 0.00 40.16 4.49
57 58 4.796231 ATCGAGTCCCGCACACGC 62.796 66.667 0.00 0.00 38.81 5.34
67 68 2.127609 GCACACGCGCAAACTCTC 60.128 61.111 5.73 0.00 0.00 3.20
68 69 2.168621 CACACGCGCAAACTCTCG 59.831 61.111 5.73 0.00 0.00 4.04
69 70 2.279252 ACACGCGCAAACTCTCGT 60.279 55.556 5.73 0.00 35.35 4.18
70 71 2.300787 ACACGCGCAAACTCTCGTC 61.301 57.895 5.73 0.00 32.38 4.20
71 72 3.097728 ACGCGCAAACTCTCGTCG 61.098 61.111 5.73 0.00 0.00 5.12
72 73 3.097728 CGCGCAAACTCTCGTCGT 61.098 61.111 8.75 0.00 0.00 4.34
73 74 1.794785 CGCGCAAACTCTCGTCGTA 60.795 57.895 8.75 0.00 0.00 3.43
74 75 1.332180 CGCGCAAACTCTCGTCGTAA 61.332 55.000 8.75 0.00 0.00 3.18
75 76 0.989890 GCGCAAACTCTCGTCGTAAT 59.010 50.000 0.30 0.00 0.00 1.89
76 77 1.389106 GCGCAAACTCTCGTCGTAATT 59.611 47.619 0.30 0.00 0.00 1.40
77 78 2.595536 GCGCAAACTCTCGTCGTAATTA 59.404 45.455 0.30 0.00 0.00 1.40
78 79 3.059834 GCGCAAACTCTCGTCGTAATTAA 59.940 43.478 0.30 0.00 0.00 1.40
79 80 4.552992 CGCAAACTCTCGTCGTAATTAAC 58.447 43.478 0.00 0.00 0.00 2.01
80 81 4.322804 CGCAAACTCTCGTCGTAATTAACT 59.677 41.667 0.00 0.00 0.00 2.24
81 82 5.539207 GCAAACTCTCGTCGTAATTAACTG 58.461 41.667 0.00 0.00 0.00 3.16
82 83 5.344128 GCAAACTCTCGTCGTAATTAACTGA 59.656 40.000 0.00 0.00 0.00 3.41
83 84 6.452611 GCAAACTCTCGTCGTAATTAACTGAG 60.453 42.308 0.00 0.00 0.00 3.35
84 85 6.492007 AACTCTCGTCGTAATTAACTGAGA 57.508 37.500 11.07 9.33 0.00 3.27
85 86 5.867166 ACTCTCGTCGTAATTAACTGAGAC 58.133 41.667 11.07 5.72 0.00 3.36
90 91 5.770430 GTCGTAATTAACTGAGACGATCG 57.230 43.478 14.88 14.88 43.61 3.69
91 92 5.496387 GTCGTAATTAACTGAGACGATCGA 58.504 41.667 24.34 0.00 43.61 3.59
92 93 5.961843 GTCGTAATTAACTGAGACGATCGAA 59.038 40.000 24.34 2.75 43.61 3.71
93 94 6.467047 GTCGTAATTAACTGAGACGATCGAAA 59.533 38.462 24.34 2.88 43.61 3.46
94 95 7.007725 GTCGTAATTAACTGAGACGATCGAAAA 59.992 37.037 24.34 3.25 43.61 2.29
95 96 7.699391 TCGTAATTAACTGAGACGATCGAAAAT 59.301 33.333 24.34 0.00 37.60 1.82
96 97 8.950961 CGTAATTAACTGAGACGATCGAAAATA 58.049 33.333 24.34 2.98 35.59 1.40
99 100 9.968743 AATTAACTGAGACGATCGAAAATAAAC 57.031 29.630 24.34 4.72 0.00 2.01
100 101 6.404712 AACTGAGACGATCGAAAATAAACC 57.595 37.500 24.34 0.89 0.00 3.27
101 102 5.475719 ACTGAGACGATCGAAAATAAACCA 58.524 37.500 24.34 5.29 0.00 3.67
102 103 6.106673 ACTGAGACGATCGAAAATAAACCAT 58.893 36.000 24.34 0.00 0.00 3.55
103 104 6.255887 ACTGAGACGATCGAAAATAAACCATC 59.744 38.462 24.34 3.86 0.00 3.51
104 105 5.231357 TGAGACGATCGAAAATAAACCATCG 59.769 40.000 24.34 0.00 39.20 3.84
105 106 5.345702 AGACGATCGAAAATAAACCATCGA 58.654 37.500 24.34 0.00 46.81 3.59
106 107 5.459107 AGACGATCGAAAATAAACCATCGAG 59.541 40.000 24.34 0.00 46.09 4.04
107 108 4.025979 ACGATCGAAAATAAACCATCGAGC 60.026 41.667 24.34 2.55 46.09 5.03
108 109 5.403897 GATCGAAAATAAACCATCGAGCA 57.596 39.130 7.32 0.00 46.49 4.26
109 110 4.593597 TCGAAAATAAACCATCGAGCAC 57.406 40.909 0.00 0.00 39.19 4.40
223 227 0.902516 GCCCTAGATCAGATCCCGCT 60.903 60.000 6.80 0.00 0.00 5.52
286 290 0.387202 CGATCTGATCTCCTTGGCGT 59.613 55.000 15.16 0.00 0.00 5.68
363 395 2.043852 ACTCCTCCGCGACCTCAT 60.044 61.111 8.23 0.00 0.00 2.90
445 477 1.837051 ACTCCTTCGTGGCCTCACA 60.837 57.895 3.32 0.00 43.79 3.58
500 532 0.978146 ATGACTTCCCCTCCCTGACG 60.978 60.000 0.00 0.00 0.00 4.35
623 656 2.338620 CAGTCCTTGCGACGGTGA 59.661 61.111 0.00 0.00 46.92 4.02
729 762 1.078356 ACGACAGCGAGCTAGGAGA 60.078 57.895 0.00 0.00 41.64 3.71
730 763 1.092921 ACGACAGCGAGCTAGGAGAG 61.093 60.000 0.00 0.00 41.64 3.20
761 794 0.388649 GACGCCCTACTGACTGTGTG 60.389 60.000 0.00 0.00 0.00 3.82
765 798 1.633774 CCCTACTGACTGTGTGGTCT 58.366 55.000 0.00 0.00 37.16 3.85
891 924 1.817447 GGCTCTGCTCTGCAATTTCTT 59.183 47.619 0.00 0.00 38.41 2.52
935 968 2.795329 ACTCATGGATGGTTGGTTCAC 58.205 47.619 0.00 0.00 0.00 3.18
980 1013 3.767673 AGGAGAGCACGTTGGAAATAGTA 59.232 43.478 0.00 0.00 0.00 1.82
1115 1148 3.772932 TGCCGTGGTTTATACTCTTACG 58.227 45.455 0.00 0.00 0.00 3.18
1138 1171 5.106555 CGACTTGTTATCAATTCACTTGGCT 60.107 40.000 5.16 0.00 34.36 4.75
1174 1207 6.547141 CCATGCAAGATTATCACTTTCCCTTA 59.453 38.462 0.00 0.00 0.00 2.69
1175 1208 7.068593 CCATGCAAGATTATCACTTTCCCTTAA 59.931 37.037 0.00 0.00 0.00 1.85
1176 1209 7.630242 TGCAAGATTATCACTTTCCCTTAAG 57.370 36.000 0.00 0.00 0.00 1.85
1177 1210 6.095440 TGCAAGATTATCACTTTCCCTTAAGC 59.905 38.462 0.00 0.00 0.00 3.09
1178 1211 6.319911 GCAAGATTATCACTTTCCCTTAAGCT 59.680 38.462 0.00 0.00 0.00 3.74
1179 1212 7.148000 GCAAGATTATCACTTTCCCTTAAGCTT 60.148 37.037 3.48 3.48 30.92 3.74
1243 1276 4.072131 TGGTCTTTGGTTCTGTGATTAGC 58.928 43.478 0.00 0.00 0.00 3.09
1305 1338 4.154737 CACGATCACATCTTCCACATGTTT 59.845 41.667 0.00 0.00 31.83 2.83
1346 1379 3.564053 TGTGGAAGGGTTACGTTTTCT 57.436 42.857 0.00 0.00 0.00 2.52
1384 1417 7.610580 TTTGACCATTGTTTTAGAGGGATTT 57.389 32.000 0.00 0.00 0.00 2.17
1913 1946 7.573710 ACATATGGGATGCTTTGTTAGTTCTA 58.426 34.615 7.80 0.00 0.00 2.10
2065 2098 9.646427 TTGTGATTAAACTTTGTTGCTTTTACT 57.354 25.926 0.00 0.00 0.00 2.24
2088 2121 0.740149 TTTGGTGCTGCTTCAGTGTG 59.260 50.000 0.00 0.00 33.43 3.82
2147 2180 8.922058 ATTTTGCTTTATAGTCATTCAGCTTG 57.078 30.769 0.00 0.00 0.00 4.01
2148 2181 5.490139 TGCTTTATAGTCATTCAGCTTGC 57.510 39.130 0.00 0.00 0.00 4.01
2149 2182 5.188434 TGCTTTATAGTCATTCAGCTTGCT 58.812 37.500 0.00 0.00 0.00 3.91
2150 2183 5.649395 TGCTTTATAGTCATTCAGCTTGCTT 59.351 36.000 0.00 0.00 0.00 3.91
2151 2184 6.183360 TGCTTTATAGTCATTCAGCTTGCTTC 60.183 38.462 0.00 0.00 0.00 3.86
2152 2185 6.183360 GCTTTATAGTCATTCAGCTTGCTTCA 60.183 38.462 0.00 0.00 0.00 3.02
2153 2186 6.915544 TTATAGTCATTCAGCTTGCTTCAG 57.084 37.500 0.00 0.00 0.00 3.02
2154 2187 3.137446 AGTCATTCAGCTTGCTTCAGT 57.863 42.857 0.00 0.00 0.00 3.41
2155 2188 2.812591 AGTCATTCAGCTTGCTTCAGTG 59.187 45.455 0.00 0.00 0.00 3.66
2156 2189 2.551459 GTCATTCAGCTTGCTTCAGTGT 59.449 45.455 0.00 0.00 0.00 3.55
2157 2190 2.551032 TCATTCAGCTTGCTTCAGTGTG 59.449 45.455 0.00 0.00 0.00 3.82
2158 2191 2.330440 TTCAGCTTGCTTCAGTGTGA 57.670 45.000 0.00 0.00 0.00 3.58
2159 2192 2.556144 TCAGCTTGCTTCAGTGTGAT 57.444 45.000 0.00 0.00 0.00 3.06
2160 2193 3.683365 TCAGCTTGCTTCAGTGTGATA 57.317 42.857 0.00 0.00 0.00 2.15
2161 2194 4.212143 TCAGCTTGCTTCAGTGTGATAT 57.788 40.909 0.00 0.00 0.00 1.63
2162 2195 3.937079 TCAGCTTGCTTCAGTGTGATATG 59.063 43.478 0.00 0.00 0.00 1.78
2163 2196 3.688185 CAGCTTGCTTCAGTGTGATATGT 59.312 43.478 0.00 0.00 0.00 2.29
2164 2197 4.872124 CAGCTTGCTTCAGTGTGATATGTA 59.128 41.667 0.00 0.00 0.00 2.29
2165 2198 4.872691 AGCTTGCTTCAGTGTGATATGTAC 59.127 41.667 0.00 0.00 0.00 2.90
2166 2199 4.872691 GCTTGCTTCAGTGTGATATGTACT 59.127 41.667 0.00 0.00 0.00 2.73
2167 2200 5.006165 GCTTGCTTCAGTGTGATATGTACTC 59.994 44.000 0.00 0.00 0.00 2.59
2168 2201 5.659440 TGCTTCAGTGTGATATGTACTCA 57.341 39.130 0.00 0.00 0.00 3.41
2169 2202 5.410924 TGCTTCAGTGTGATATGTACTCAC 58.589 41.667 6.76 6.76 42.68 3.51
2170 2203 5.185828 TGCTTCAGTGTGATATGTACTCACT 59.814 40.000 13.14 0.00 42.78 3.41
2171 2204 6.102663 GCTTCAGTGTGATATGTACTCACTT 58.897 40.000 13.14 1.96 42.78 3.16
2183 2216 4.641396 TGTACTCACTTTGGTTCATGAGG 58.359 43.478 0.00 0.00 42.39 3.86
2448 2489 9.224267 GTGATATGCAGTATAAAACATCTCCAT 57.776 33.333 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.605749 TTTCGCGGCTGAGGGGAAG 62.606 63.158 6.13 0.00 37.59 3.46
5 6 2.671619 TTTTTCGCGGCTGAGGGG 60.672 61.111 6.13 0.00 0.00 4.79
6 7 2.561373 GTTTTTCGCGGCTGAGGG 59.439 61.111 6.13 0.00 0.00 4.30
7 8 1.791103 TTGGTTTTTCGCGGCTGAGG 61.791 55.000 6.13 0.00 0.00 3.86
8 9 0.385974 CTTGGTTTTTCGCGGCTGAG 60.386 55.000 6.13 0.00 0.00 3.35
9 10 1.652012 CTTGGTTTTTCGCGGCTGA 59.348 52.632 6.13 0.00 0.00 4.26
11 12 1.104577 TTCCTTGGTTTTTCGCGGCT 61.105 50.000 6.13 0.00 0.00 5.52
12 13 0.249114 TTTCCTTGGTTTTTCGCGGC 60.249 50.000 6.13 0.00 0.00 6.53
13 14 1.855978 GTTTTCCTTGGTTTTTCGCGG 59.144 47.619 6.13 0.00 0.00 6.46
16 17 2.800273 CGGGGTTTTCCTTGGTTTTTCG 60.800 50.000 0.00 0.00 40.46 3.46
17 18 2.828877 CGGGGTTTTCCTTGGTTTTTC 58.171 47.619 0.00 0.00 40.46 2.29
20 21 1.740332 CGCGGGGTTTTCCTTGGTTT 61.740 55.000 0.00 0.00 40.46 3.27
21 22 2.197605 CGCGGGGTTTTCCTTGGTT 61.198 57.895 0.00 0.00 40.46 3.67
22 23 2.420466 ATCGCGGGGTTTTCCTTGGT 62.420 55.000 6.13 0.00 40.46 3.67
23 24 1.654023 GATCGCGGGGTTTTCCTTGG 61.654 60.000 6.13 0.00 40.46 3.61
24 25 1.800681 GATCGCGGGGTTTTCCTTG 59.199 57.895 6.13 0.00 40.46 3.61
25 26 1.743995 CGATCGCGGGGTTTTCCTT 60.744 57.895 6.13 0.00 40.46 3.36
26 27 2.125269 CGATCGCGGGGTTTTCCT 60.125 61.111 6.13 0.00 40.46 3.36
27 28 2.125431 TCGATCGCGGGGTTTTCC 60.125 61.111 11.09 0.00 38.28 3.13
28 29 1.419107 GACTCGATCGCGGGGTTTTC 61.419 60.000 11.09 0.00 43.99 2.29
29 30 1.447314 GACTCGATCGCGGGGTTTT 60.447 57.895 11.09 0.00 43.99 2.43
30 31 2.183555 GACTCGATCGCGGGGTTT 59.816 61.111 11.09 0.00 43.99 3.27
31 32 3.834799 GGACTCGATCGCGGGGTT 61.835 66.667 11.09 0.00 43.99 4.11
38 39 2.579787 GTGTGCGGGACTCGATCG 60.580 66.667 9.36 9.36 42.43 3.69
39 40 2.579787 CGTGTGCGGGACTCGATC 60.580 66.667 17.26 0.00 42.85 3.69
40 41 4.796231 GCGTGTGCGGGACTCGAT 62.796 66.667 24.49 0.00 42.85 3.59
50 51 2.127609 GAGAGTTTGCGCGTGTGC 60.128 61.111 8.43 0.00 37.91 4.57
51 52 2.168621 CGAGAGTTTGCGCGTGTG 59.831 61.111 8.43 0.00 0.00 3.82
52 53 2.279252 ACGAGAGTTTGCGCGTGT 60.279 55.556 8.43 0.00 46.40 4.49
63 64 4.956778 CGTCTCAGTTAATTACGACGAGAG 59.043 45.833 0.00 9.08 44.81 3.20
64 65 4.627035 TCGTCTCAGTTAATTACGACGAGA 59.373 41.667 15.21 10.68 45.35 4.04
65 66 4.890378 TCGTCTCAGTTAATTACGACGAG 58.110 43.478 15.21 9.23 45.35 4.18
67 68 4.372235 CGATCGTCTCAGTTAATTACGACG 59.628 45.833 7.03 12.15 44.34 5.12
68 69 5.496387 TCGATCGTCTCAGTTAATTACGAC 58.504 41.667 15.94 0.00 44.34 4.34
69 70 5.723492 TCGATCGTCTCAGTTAATTACGA 57.277 39.130 15.94 0.00 45.44 3.43
70 71 6.785633 TTTCGATCGTCTCAGTTAATTACG 57.214 37.500 15.94 0.00 34.99 3.18
73 74 9.968743 GTTTATTTTCGATCGTCTCAGTTAATT 57.031 29.630 15.94 0.00 0.00 1.40
74 75 8.601476 GGTTTATTTTCGATCGTCTCAGTTAAT 58.399 33.333 15.94 6.92 0.00 1.40
75 76 7.599621 TGGTTTATTTTCGATCGTCTCAGTTAA 59.400 33.333 15.94 0.00 0.00 2.01
76 77 7.092079 TGGTTTATTTTCGATCGTCTCAGTTA 58.908 34.615 15.94 0.00 0.00 2.24
77 78 5.929992 TGGTTTATTTTCGATCGTCTCAGTT 59.070 36.000 15.94 0.00 0.00 3.16
78 79 5.475719 TGGTTTATTTTCGATCGTCTCAGT 58.524 37.500 15.94 0.72 0.00 3.41
79 80 6.560433 CGATGGTTTATTTTCGATCGTCTCAG 60.560 42.308 15.94 0.00 37.45 3.35
80 81 5.231357 CGATGGTTTATTTTCGATCGTCTCA 59.769 40.000 15.94 0.00 37.45 3.27
81 82 5.457799 TCGATGGTTTATTTTCGATCGTCTC 59.542 40.000 15.94 0.00 40.90 3.36
82 83 5.345702 TCGATGGTTTATTTTCGATCGTCT 58.654 37.500 15.94 1.09 40.90 4.18
83 84 5.630896 TCGATGGTTTATTTTCGATCGTC 57.369 39.130 15.94 0.00 40.90 4.20
84 85 4.025979 GCTCGATGGTTTATTTTCGATCGT 60.026 41.667 15.94 0.00 40.90 3.73
85 86 4.026062 TGCTCGATGGTTTATTTTCGATCG 60.026 41.667 9.36 9.36 39.59 3.69
86 87 5.198274 GTGCTCGATGGTTTATTTTCGATC 58.802 41.667 0.00 0.00 39.59 3.69
87 88 4.634004 TGTGCTCGATGGTTTATTTTCGAT 59.366 37.500 0.00 0.00 39.59 3.59
88 89 3.997681 TGTGCTCGATGGTTTATTTTCGA 59.002 39.130 0.00 0.00 38.20 3.71
89 90 4.335082 TGTGCTCGATGGTTTATTTTCG 57.665 40.909 0.00 0.00 0.00 3.46
90 91 5.344933 GGTTTGTGCTCGATGGTTTATTTTC 59.655 40.000 0.00 0.00 0.00 2.29
91 92 5.227152 GGTTTGTGCTCGATGGTTTATTTT 58.773 37.500 0.00 0.00 0.00 1.82
92 93 4.614993 CGGTTTGTGCTCGATGGTTTATTT 60.615 41.667 0.00 0.00 0.00 1.40
93 94 3.119990 CGGTTTGTGCTCGATGGTTTATT 60.120 43.478 0.00 0.00 0.00 1.40
94 95 2.418628 CGGTTTGTGCTCGATGGTTTAT 59.581 45.455 0.00 0.00 0.00 1.40
95 96 1.801771 CGGTTTGTGCTCGATGGTTTA 59.198 47.619 0.00 0.00 0.00 2.01
96 97 0.591170 CGGTTTGTGCTCGATGGTTT 59.409 50.000 0.00 0.00 0.00 3.27
97 98 0.250124 TCGGTTTGTGCTCGATGGTT 60.250 50.000 0.00 0.00 0.00 3.67
98 99 0.949105 GTCGGTTTGTGCTCGATGGT 60.949 55.000 0.00 0.00 35.35 3.55
99 100 0.948623 TGTCGGTTTGTGCTCGATGG 60.949 55.000 0.00 0.00 35.35 3.51
100 101 0.865111 TTGTCGGTTTGTGCTCGATG 59.135 50.000 0.00 0.00 35.35 3.84
101 102 1.588674 TTTGTCGGTTTGTGCTCGAT 58.411 45.000 0.00 0.00 35.35 3.59
102 103 1.370609 TTTTGTCGGTTTGTGCTCGA 58.629 45.000 0.00 0.00 0.00 4.04
103 104 2.181426 TTTTTGTCGGTTTGTGCTCG 57.819 45.000 0.00 0.00 0.00 5.03
104 105 5.051307 GGTTAATTTTTGTCGGTTTGTGCTC 60.051 40.000 0.00 0.00 0.00 4.26
105 106 4.806775 GGTTAATTTTTGTCGGTTTGTGCT 59.193 37.500 0.00 0.00 0.00 4.40
106 107 4.567159 TGGTTAATTTTTGTCGGTTTGTGC 59.433 37.500 0.00 0.00 0.00 4.57
107 108 5.276631 GCTGGTTAATTTTTGTCGGTTTGTG 60.277 40.000 0.00 0.00 0.00 3.33
108 109 4.806775 GCTGGTTAATTTTTGTCGGTTTGT 59.193 37.500 0.00 0.00 0.00 2.83
109 110 4.085312 CGCTGGTTAATTTTTGTCGGTTTG 60.085 41.667 0.00 0.00 0.00 2.93
145 148 1.070175 GTACGCACGCACAATCTTGTT 60.070 47.619 0.00 0.00 39.91 2.83
223 227 2.680352 GAGGAGGGGCAGTCGTCA 60.680 66.667 3.87 0.00 0.00 4.35
357 389 1.546476 GAGAGGACGACAACATGAGGT 59.454 52.381 0.00 0.00 0.00 3.85
363 395 0.596577 CGAAGGAGAGGACGACAACA 59.403 55.000 0.00 0.00 0.00 3.33
445 477 4.467107 GAGGGAGAGGAGGGCGGT 62.467 72.222 0.00 0.00 0.00 5.68
482 514 1.609501 CGTCAGGGAGGGGAAGTCA 60.610 63.158 0.00 0.00 0.00 3.41
500 532 1.652012 CCTCTCTCCGTCAGATCGC 59.348 63.158 0.00 0.00 0.00 4.58
729 762 1.823041 GGCGTCTACCTCGTAGGCT 60.823 63.158 0.00 0.00 38.45 4.58
730 763 2.720605 GGCGTCTACCTCGTAGGC 59.279 66.667 0.00 0.00 39.63 3.93
761 794 1.832912 CCATGTGGAGGCCTAGACC 59.167 63.158 4.42 2.86 37.39 3.85
801 834 5.009010 GTGATCAAGGACATGACAAACAACT 59.991 40.000 0.00 0.00 30.82 3.16
891 924 3.648067 AGGTTCTCCACAATGTTCTCTCA 59.352 43.478 0.00 0.00 35.89 3.27
935 968 6.592607 CCTTGTCATCAATTCATCCCAAAAAG 59.407 38.462 0.00 0.00 32.82 2.27
980 1013 0.323908 CCTCTCCCGTCTCCACTTCT 60.324 60.000 0.00 0.00 0.00 2.85
1115 1148 6.088824 CAGCCAAGTGAATTGATAACAAGTC 58.911 40.000 6.26 6.26 46.78 3.01
1175 1208 9.247861 ACTAATCCAGAAATTATTGAACAAGCT 57.752 29.630 0.00 0.00 0.00 3.74
1176 1209 9.508567 GACTAATCCAGAAATTATTGAACAAGC 57.491 33.333 0.00 0.00 0.00 4.01
1179 1212 9.739276 AGTGACTAATCCAGAAATTATTGAACA 57.261 29.630 0.00 0.00 0.00 3.18
1243 1276 2.044650 CATGGCACCCACCCTCAG 60.045 66.667 0.00 0.00 35.80 3.35
1305 1338 2.189191 GATCAGCCACTCCAGCACCA 62.189 60.000 0.00 0.00 0.00 4.17
1346 1379 6.494491 ACAATGGTCAAAATCCATGAGAAGAA 59.506 34.615 0.00 0.00 43.85 2.52
1384 1417 7.620491 TGTACTAACTACCAGAACCATTATCCA 59.380 37.037 0.00 0.00 0.00 3.41
1543 1576 2.093128 GGAATTCCAAGACCTCGGCTAA 60.093 50.000 20.04 0.00 35.64 3.09
1572 1605 6.854381 CCGTTAAATGAGTTCACTTGTTTACC 59.146 38.462 0.00 0.00 0.00 2.85
1931 1964 8.407832 CCATTATCATAGCTCATCAACACAAAA 58.592 33.333 0.00 0.00 0.00 2.44
2065 2098 1.408683 ACTGAAGCAGCACCAAAGTGA 60.409 47.619 0.00 0.00 46.32 3.41
2137 2170 2.551032 TCACACTGAAGCAAGCTGAATG 59.449 45.455 0.00 0.00 0.00 2.67
2138 2171 2.854963 TCACACTGAAGCAAGCTGAAT 58.145 42.857 0.00 0.00 0.00 2.57
2139 2172 2.330440 TCACACTGAAGCAAGCTGAA 57.670 45.000 0.00 0.00 0.00 3.02
2140 2173 2.556144 ATCACACTGAAGCAAGCTGA 57.444 45.000 0.00 0.00 0.00 4.26
2141 2174 3.688185 ACATATCACACTGAAGCAAGCTG 59.312 43.478 0.00 0.00 0.00 4.24
2142 2175 3.947868 ACATATCACACTGAAGCAAGCT 58.052 40.909 0.00 0.00 0.00 3.74
2143 2176 4.872691 AGTACATATCACACTGAAGCAAGC 59.127 41.667 0.00 0.00 0.00 4.01
2144 2177 6.035435 GTGAGTACATATCACACTGAAGCAAG 59.965 42.308 8.45 0.00 45.18 4.01
2145 2178 5.869344 GTGAGTACATATCACACTGAAGCAA 59.131 40.000 8.45 0.00 45.18 3.91
2146 2179 5.410924 GTGAGTACATATCACACTGAAGCA 58.589 41.667 8.45 0.00 45.18 3.91
2147 2180 5.957910 GTGAGTACATATCACACTGAAGC 57.042 43.478 8.45 0.00 45.18 3.86
2155 2188 7.549134 TCATGAACCAAAGTGAGTACATATCAC 59.451 37.037 5.77 5.77 46.01 3.06
2156 2189 7.619965 TCATGAACCAAAGTGAGTACATATCA 58.380 34.615 0.00 0.00 0.00 2.15
2157 2190 7.225538 CCTCATGAACCAAAGTGAGTACATATC 59.774 40.741 0.00 0.00 37.08 1.63
2158 2191 7.050377 CCTCATGAACCAAAGTGAGTACATAT 58.950 38.462 0.00 0.00 37.08 1.78
2159 2192 6.212589 TCCTCATGAACCAAAGTGAGTACATA 59.787 38.462 0.00 0.00 37.08 2.29
2160 2193 5.013079 TCCTCATGAACCAAAGTGAGTACAT 59.987 40.000 0.00 0.00 37.08 2.29
2161 2194 4.346709 TCCTCATGAACCAAAGTGAGTACA 59.653 41.667 0.00 0.00 37.08 2.90
2162 2195 4.894784 TCCTCATGAACCAAAGTGAGTAC 58.105 43.478 0.00 0.00 37.08 2.73
2163 2196 4.838423 TCTCCTCATGAACCAAAGTGAGTA 59.162 41.667 0.00 0.00 37.08 2.59
2164 2197 3.648067 TCTCCTCATGAACCAAAGTGAGT 59.352 43.478 0.00 0.00 37.08 3.41
2165 2198 4.277515 TCTCCTCATGAACCAAAGTGAG 57.722 45.455 0.00 0.00 38.20 3.51
2166 2199 4.705110 TTCTCCTCATGAACCAAAGTGA 57.295 40.909 0.00 0.00 0.00 3.41
2167 2200 4.380233 GCATTCTCCTCATGAACCAAAGTG 60.380 45.833 0.00 0.00 0.00 3.16
2168 2201 3.760684 GCATTCTCCTCATGAACCAAAGT 59.239 43.478 0.00 0.00 0.00 2.66
2169 2202 4.015084 AGCATTCTCCTCATGAACCAAAG 58.985 43.478 0.00 0.00 0.00 2.77
2170 2203 3.760151 CAGCATTCTCCTCATGAACCAAA 59.240 43.478 0.00 0.00 0.00 3.28
2171 2204 3.009363 TCAGCATTCTCCTCATGAACCAA 59.991 43.478 0.00 0.00 0.00 3.67
2320 2360 4.246712 ACTACTTGTTCCTCCGATCCTA 57.753 45.455 0.00 0.00 0.00 2.94
2448 2489 5.913137 TGCTCACCAAAGAAGAAGAAAAA 57.087 34.783 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.