Multiple sequence alignment - TraesCS5A01G165500

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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 TraesCS5A01G165500 chr5A 100.000 2420 0 0 1 2420 354220252 354217833 0.000000e+00 4470.0
1 TraesCS5A01G165500 chr5A 91.946 2446 151 8 1 2420 354255404 354252979 0.000000e+00 3384.0
2 TraesCS5A01G165500 chr5A 93.285 417 25 3 2006 2420 104757082 104757497 1.590000e-171 612.0
3 TraesCS5A01G165500 chr5A 81.004 458 40 15 1002 1457 244307985 244307573 1.080000e-83 320.0
4 TraesCS5A01G165500 chr5A 80.306 457 43 18 1003 1457 244299939 244299528 3.910000e-78 302.0
5 TraesCS5A01G165500 chr5A 91.282 195 16 1 1614 1808 416427574 416427767 5.130000e-67 265.0
6 TraesCS5A01G165500 chr5A 84.644 267 31 7 2158 2415 258440019 258439754 8.580000e-65 257.0
7 TraesCS5A01G165500 chr5A 86.307 241 25 7 2182 2419 143154978 143154743 3.090000e-64 255.0
8 TraesCS5A01G165500 chr5A 90.206 194 19 0 1614 1807 174804658 174804465 1.110000e-63 254.0
9 TraesCS5A01G165500 chr5A 87.685 203 24 1 1615 1816 165885723 165885521 4.020000e-58 235.0
10 TraesCS5A01G165500 chr5A 93.506 154 10 0 1154 1307 366626180 366626333 1.870000e-56 230.0
11 TraesCS5A01G165500 chr5A 87.368 95 9 3 1299 1391 636362993 636363086 3.290000e-19 106.0
12 TraesCS5A01G165500 chr7A 83.073 1471 190 38 1 1457 337602837 337604262 0.000000e+00 1282.0
13 TraesCS5A01G165500 chr7A 89.178 961 80 17 1 955 225587593 225588535 0.000000e+00 1177.0
14 TraesCS5A01G165500 chr7A 85.385 650 73 10 810 1457 337594943 337595572 0.000000e+00 654.0
15 TraesCS5A01G165500 chr7A 86.640 247 30 2 1005 1248 387102173 387102419 1.100000e-68 270.0
16 TraesCS5A01G165500 chr7A 86.290 248 27 4 1004 1248 387084834 387085077 1.850000e-66 263.0
17 TraesCS5A01G165500 chr3A 87.227 963 103 15 1 956 302724126 302725075 0.000000e+00 1079.0
18 TraesCS5A01G165500 chr3A 86.943 965 101 17 1 957 302715940 302716887 0.000000e+00 1061.0
19 TraesCS5A01G165500 chr3A 87.802 910 90 18 1 900 325475383 325476281 0.000000e+00 1046.0
20 TraesCS5A01G165500 chr3A 83.592 774 112 14 2 770 226630909 226630146 0.000000e+00 712.0
21 TraesCS5A01G165500 chr3A 94.211 190 8 3 2231 2420 683303406 683303592 1.090000e-73 287.0
22 TraesCS5A01G165500 chr3A 87.398 246 30 1 1004 1248 286499471 286499226 5.090000e-72 281.0
23 TraesCS5A01G165500 chr3A 91.237 194 17 0 1614 1807 216527926 216528119 5.130000e-67 265.0
24 TraesCS5A01G165500 chr3A 85.714 245 34 1 1005 1248 286479461 286479217 8.580000e-65 257.0
25 TraesCS5A01G165500 chr3A 88.482 191 20 2 1156 1345 268380893 268381082 1.870000e-56 230.0
26 TraesCS5A01G165500 chr3A 85.246 122 7 6 1336 1457 557446003 557446113 5.470000e-22 115.0
27 TraesCS5A01G165500 chr3A 96.154 52 2 0 1572 1623 100337959 100337908 4.290000e-13 86.1
28 TraesCS5A01G165500 chr3A 94.340 53 2 1 973 1024 226637729 226637677 1.990000e-11 80.5
29 TraesCS5A01G165500 chr4A 87.217 884 98 11 3 879 221237271 221236396 0.000000e+00 992.0
30 TraesCS5A01G165500 chr4A 85.417 960 117 21 1 953 238460004 238459061 0.000000e+00 976.0
31 TraesCS5A01G165500 chr4A 81.395 430 67 12 615 1038 196408070 196407648 2.980000e-89 339.0
32 TraesCS5A01G165500 chr4A 79.650 457 46 12 1003 1457 303354022 303354433 3.940000e-73 285.0
33 TraesCS5A01G165500 chr4A 90.196 204 18 2 1614 1816 318073386 318073184 5.130000e-67 265.0
34 TraesCS5A01G165500 chr4A 89.583 96 8 2 1298 1391 245997349 245997254 1.180000e-23 121.0
35 TraesCS5A01G165500 chr4A 84.426 122 8 5 1336 1457 198180127 198180237 2.540000e-20 110.0
36 TraesCS5A01G165500 chr6A 85.931 924 106 17 1 919 406436966 406436062 0.000000e+00 965.0
37 TraesCS5A01G165500 chr6A 83.333 312 44 8 2087 2396 244968830 244968525 5.090000e-72 281.0
38 TraesCS5A01G165500 chr6A 86.290 124 16 1 1492 1614 209667449 209667572 1.510000e-27 134.0
39 TraesCS5A01G165500 chr1A 83.680 1011 139 23 1 997 44436483 44437481 0.000000e+00 929.0
40 TraesCS5A01G165500 chr1A 89.109 202 21 1 1614 1815 380697412 380697612 1.440000e-62 250.0
41 TraesCS5A01G165500 chr1A 89.109 202 21 1 1614 1815 380713484 380713684 1.440000e-62 250.0
42 TraesCS5A01G165500 chr1A 83.750 160 18 5 1332 1490 99980117 99979965 6.970000e-31 145.0
43 TraesCS5A01G165500 chr1A 89.655 87 9 0 952 1038 177533759 177533673 7.070000e-21 111.0
44 TraesCS5A01G165500 chr2A 86.024 415 48 9 1989 2396 448415410 448414999 1.030000e-118 436.0
45 TraesCS5A01G165500 chr2A 85.542 415 50 9 1989 2396 448424191 448423780 2.220000e-115 425.0
46 TraesCS5A01G165500 chr2A 84.641 306 36 11 2120 2420 263575383 263575682 6.540000e-76 294.0
47 TraesCS5A01G165500 chr2A 91.282 195 16 1 1614 1808 552182667 552182474 5.130000e-67 265.0
48 TraesCS5A01G165500 chr2A 76.012 321 52 16 2087 2396 286860569 286860263 2.510000e-30 143.0
49 TraesCS5A01G165500 chr2A 89.412 85 6 3 933 1016 476405675 476405757 1.180000e-18 104.0
50 TraesCS5A01G165500 chr2A 89.412 85 6 3 933 1016 476413850 476413932 1.180000e-18 104.0
51 TraesCS5A01G165500 chr2A 95.000 60 2 1 2120 2179 533140199 533140257 2.560000e-15 93.5
52 TraesCS5A01G165500 chr2A 87.692 65 8 0 2115 2179 449365980 449366044 2.580000e-10 76.8
53 TraesCS5A01G165500 chr4B 90.000 150 14 1 1333 1482 286705784 286705636 2.460000e-45 193.0
54 TraesCS5A01G165500 chr4B 84.211 152 17 4 1333 1483 570216954 570216809 9.020000e-30 141.0
55 TraesCS5A01G165500 chr1B 97.778 90 2 0 1727 1816 366702961 366703050 3.220000e-34 156.0
56 TraesCS5A01G165500 chr1B 97.778 90 2 0 1727 1816 378902461 378902372 3.220000e-34 156.0
57 TraesCS5A01G165500 chr1B 96.667 90 3 0 1727 1816 378909128 378909039 1.500000e-32 150.0
58 TraesCS5A01G165500 chr7B 88.618 123 8 6 1696 1816 471105694 471105812 6.970000e-31 145.0


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 TraesCS5A01G165500 chr5A 354217833 354220252 2419 True 4470 4470 100.000 1 2420 1 chr5A.!!$R7 2419
1 TraesCS5A01G165500 chr5A 354252979 354255404 2425 True 3384 3384 91.946 1 2420 1 chr5A.!!$R8 2419
2 TraesCS5A01G165500 chr7A 337602837 337604262 1425 False 1282 1282 83.073 1 1457 1 chr7A.!!$F3 1456
3 TraesCS5A01G165500 chr7A 225587593 225588535 942 False 1177 1177 89.178 1 955 1 chr7A.!!$F1 954
4 TraesCS5A01G165500 chr7A 337594943 337595572 629 False 654 654 85.385 810 1457 1 chr7A.!!$F2 647
5 TraesCS5A01G165500 chr3A 302724126 302725075 949 False 1079 1079 87.227 1 956 1 chr3A.!!$F4 955
6 TraesCS5A01G165500 chr3A 302715940 302716887 947 False 1061 1061 86.943 1 957 1 chr3A.!!$F3 956
7 TraesCS5A01G165500 chr3A 325475383 325476281 898 False 1046 1046 87.802 1 900 1 chr3A.!!$F5 899
8 TraesCS5A01G165500 chr3A 226630146 226630909 763 True 712 712 83.592 2 770 1 chr3A.!!$R2 768
9 TraesCS5A01G165500 chr4A 221236396 221237271 875 True 992 992 87.217 3 879 1 chr4A.!!$R2 876
10 TraesCS5A01G165500 chr4A 238459061 238460004 943 True 976 976 85.417 1 953 1 chr4A.!!$R3 952
11 TraesCS5A01G165500 chr6A 406436062 406436966 904 True 965 965 85.931 1 919 1 chr6A.!!$R2 918
12 TraesCS5A01G165500 chr1A 44436483 44437481 998 False 929 929 83.680 1 997 1 chr1A.!!$F1 996

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
719 756 0.034186 GTCATGCAAGGATGGTGGGA 60.034 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2246 2318 1.008571 ACTTCTTCCCCTACCCTCCTC 59.991 57.143 0.0 0.0 0.0 3.71 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
120 123 4.142138 ACGAAACCGAAGCTAATGAGAGAT 60.142 41.667 0.00 0.00 0.00 2.75
159 164 3.708563 AGCAACATGGTAAACACACAC 57.291 42.857 0.00 0.00 0.00 3.82
203 209 2.936202 ACCAAGTATGATGCATGTCCC 58.064 47.619 2.46 0.00 0.00 4.46
213 220 5.493133 TGATGCATGTCCCGTTTAAATAC 57.507 39.130 2.46 0.00 0.00 1.89
252 261 5.633182 AGTGCACAAACAAAACTACAAGTTG 59.367 36.000 21.04 0.00 38.66 3.16
331 341 2.221055 AGTTCGCTCTTGTTTAAGCACG 59.779 45.455 0.00 0.00 38.45 5.34
370 382 4.922206 TCTTAACATGGCAAGAGGTGAAT 58.078 39.130 7.06 0.00 0.00 2.57
441 455 8.137437 ACAACAAACAACAATAATTCTGGAGAG 58.863 33.333 0.00 0.00 0.00 3.20
652 684 0.112412 AAGGCAACATTCCGGGTTCT 59.888 50.000 0.00 0.00 41.41 3.01
719 756 0.034186 GTCATGCAAGGATGGTGGGA 60.034 55.000 0.00 0.00 0.00 4.37
836 875 3.212685 TCATTCAACACACATGCACTCA 58.787 40.909 0.00 0.00 0.00 3.41
866 909 0.747644 TCGTCTCGGCGGTTATACCA 60.748 55.000 7.21 0.00 38.47 3.25
969 1014 1.047034 GTGGTACTACCGGCCCTCAT 61.047 60.000 0.00 0.00 42.58 2.90
1039 1084 2.396590 ATTGGCGATGGTAGTCGTTT 57.603 45.000 0.00 0.00 43.27 3.60
1045 1090 2.331194 CGATGGTAGTCGTTTCCGTTT 58.669 47.619 0.00 0.00 36.88 3.60
1062 1107 4.164822 CGTTTGTTCGGAGAGGTACTTA 57.835 45.455 0.00 0.00 41.55 2.24
1070 1115 5.113446 TCGGAGAGGTACTTAATGACTCT 57.887 43.478 0.00 0.00 41.55 3.24
1082 1127 1.195115 ATGACTCTAAGCCCTTCGCA 58.805 50.000 0.00 0.00 41.38 5.10
1090 1135 2.501223 AAGCCCTTCGCAATCGACGA 62.501 55.000 0.00 0.00 45.43 4.20
1111 1156 4.083855 CGATAGTTGAACTTGAAGCTTGCA 60.084 41.667 2.10 0.00 0.00 4.08
1116 1161 0.386838 AACTTGAAGCTTGCAGTGCC 59.613 50.000 13.72 0.00 0.00 5.01
1126 1171 0.178995 TTGCAGTGCCCATGTCTTCA 60.179 50.000 13.72 0.00 0.00 3.02
1139 1184 2.429478 TGTCTTCATCGACGGTAGTGA 58.571 47.619 0.00 0.00 36.71 3.41
1174 1219 2.955609 GGACTTGGCGAAAATCCCA 58.044 52.632 1.14 0.00 0.00 4.37
1307 1353 1.070786 CGGTGCAGTGGTACTTGGT 59.929 57.895 0.00 0.00 0.00 3.67
1342 1388 4.003788 ACCAGACGGTCTTGGCGG 62.004 66.667 19.81 15.36 44.71 6.13
1435 1481 2.249125 TGAGGAGGAGGGGCTCTGA 61.249 63.158 0.00 0.00 0.00 3.27
1439 1485 1.610673 GAGGAGGGGCTCTGACACA 60.611 63.158 0.00 0.00 0.00 3.72
1458 1504 4.687215 GACCAGCAGCGAGGCACA 62.687 66.667 6.83 0.00 35.83 4.57
1473 1519 1.582968 CACACACATGCAGGAAGGC 59.417 57.895 4.84 0.00 0.00 4.35
1483 1529 2.203788 AGGAAGGCGGTGAGGTCA 60.204 61.111 0.00 0.00 0.00 4.02
1509 1555 0.393402 TAGCAGCATGGGAAGTGCAG 60.393 55.000 0.00 0.00 44.87 4.41
1510 1556 1.975407 GCAGCATGGGAAGTGCAGT 60.975 57.895 0.00 0.00 44.87 4.40
1532 1578 1.750399 GGTGGCGATCATGTGGCTT 60.750 57.895 9.45 0.00 0.00 4.35
1573 1619 0.676736 CATAGGGAGACGAAGGCCTC 59.323 60.000 5.23 0.00 0.00 4.70
1672 1718 2.107953 GCCAGAGCTGATCCGACC 59.892 66.667 0.00 0.00 35.50 4.79
1675 1721 0.467384 CCAGAGCTGATCCGACCATT 59.533 55.000 0.00 0.00 0.00 3.16
1822 1878 3.519930 GAGGTCGAGGTCCGGAGC 61.520 72.222 26.17 26.17 39.14 4.70
1826 1882 4.043100 TCGAGGTCCGGAGCAGGA 62.043 66.667 33.52 25.66 39.14 3.86
1908 1964 4.702081 GCGCTCGACGTCAGTGGT 62.702 66.667 17.16 0.00 46.11 4.16
1909 1965 2.502080 CGCTCGACGTCAGTGGTC 60.502 66.667 17.16 0.00 36.87 4.02
1936 1992 1.349026 CTCTTTGGAGTGAGGAAGGCA 59.651 52.381 0.00 0.00 35.03 4.75
1960 2016 1.293498 GCTGGTCGAAGGAGCTCAA 59.707 57.895 17.19 0.00 41.26 3.02
1971 2027 1.066587 GAGCTCAAGACGGGGATCG 59.933 63.158 9.40 0.00 45.88 3.69
2020 2092 0.469144 AGGAAGGGAGCGAGAGGATC 60.469 60.000 0.00 0.00 0.00 3.36
2056 2128 4.856607 GCGCGAGGGAACGAGGAG 62.857 72.222 12.10 0.00 34.05 3.69
2059 2131 2.128507 GCGAGGGAACGAGGAGGAT 61.129 63.158 0.00 0.00 35.09 3.24
2074 2146 2.111878 GATGGGTGCAGGGGATCG 59.888 66.667 0.00 0.00 0.00 3.69
2085 2157 1.766496 CAGGGGATCGGGCTAGTTTAA 59.234 52.381 0.00 0.00 0.00 1.52
2106 2178 4.176752 GGGTTAGAGCGGGGGCTG 62.177 72.222 0.00 0.00 0.00 4.85
2142 2214 3.451894 CCTCGGTGCAAATGGGCC 61.452 66.667 0.00 0.00 0.00 5.80
2196 2268 1.076044 GCAGGCTCTCTCTCCCTCT 60.076 63.158 0.00 0.00 0.00 3.69
2218 2290 8.878769 CCTCTCTTCTCTTATTTTCTTTAGCAC 58.121 37.037 0.00 0.00 0.00 4.40
2233 2305 6.503524 TCTTTAGCACAAAACAATTCCAGAC 58.496 36.000 0.00 0.00 0.00 3.51
2246 2318 8.707938 AACAATTCCAGACAAGAAAAAGAAAG 57.292 30.769 0.00 0.00 0.00 2.62
2247 2319 8.066612 ACAATTCCAGACAAGAAAAAGAAAGA 57.933 30.769 0.00 0.00 0.00 2.52
2259 2331 2.272074 AAGAAAGAGGAGGGTAGGGG 57.728 55.000 0.00 0.00 0.00 4.79
2275 2347 2.065799 AGGGGAAGAAGTTGGACACAT 58.934 47.619 0.00 0.00 0.00 3.21
2287 2359 7.671398 AGAAGTTGGACACATGGATAAATTTCT 59.329 33.333 0.00 0.70 0.00 2.52
2288 2360 7.396540 AGTTGGACACATGGATAAATTTCTC 57.603 36.000 0.00 0.00 0.00 2.87
2289 2361 6.947733 AGTTGGACACATGGATAAATTTCTCA 59.052 34.615 5.99 0.00 0.00 3.27
2308 2380 4.883585 TCTCAGACTCACAAAAATGTGCTT 59.116 37.500 4.13 0.00 39.49 3.91
2310 2382 4.398988 TCAGACTCACAAAAATGTGCTTGT 59.601 37.500 4.13 3.61 39.49 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 77 2.413837 CGGAGTTGTGAGGATTCGTTT 58.586 47.619 0.00 0.00 0.00 3.60
120 123 1.066908 CTTGCTTCTTTCCGGTTTGCA 59.933 47.619 0.00 2.24 0.00 4.08
159 164 1.977188 CATCATGCCATGCTTATGCG 58.023 50.000 0.00 0.00 43.34 4.73
203 209 3.042189 CCATGCCATGCGTATTTAAACG 58.958 45.455 0.00 0.00 45.58 3.60
213 220 1.807981 CACTTTGCCATGCCATGCG 60.808 57.895 0.00 0.00 0.00 4.73
252 261 2.286294 CGTTGCATATTGAGCTCCACTC 59.714 50.000 12.15 0.00 46.45 3.51
719 756 2.900546 GACACCTAGAATCCGGGATCAT 59.099 50.000 10.56 4.62 0.00 2.45
754 793 2.699954 CACGTTCCTCATTAGCCTTGT 58.300 47.619 0.00 0.00 0.00 3.16
819 858 3.003585 GTGAATGAGTGCATGTGTGTTGA 59.996 43.478 0.00 0.00 34.26 3.18
866 909 1.164411 TCCGAAATGCACGCTTCAAT 58.836 45.000 0.00 0.00 0.00 2.57
932 976 1.034292 ACTACTTCCCCTACGACCGC 61.034 60.000 0.00 0.00 0.00 5.68
959 1004 2.644555 CTACCGTCAATGAGGGCCGG 62.645 65.000 20.59 14.26 40.79 6.13
963 1008 1.191535 TCCACTACCGTCAATGAGGG 58.808 55.000 19.26 19.26 42.55 4.30
969 1014 2.559668 CCACTACTTCCACTACCGTCAA 59.440 50.000 0.00 0.00 0.00 3.18
1001 1046 4.825634 CCAATATCACGAGTACCTCTACCA 59.174 45.833 0.00 0.00 0.00 3.25
1045 1090 5.014858 AGTCATTAAGTACCTCTCCGAACA 58.985 41.667 0.00 0.00 0.00 3.18
1062 1107 1.555075 TGCGAAGGGCTTAGAGTCATT 59.445 47.619 0.00 0.00 44.05 2.57
1082 1127 5.062308 GCTTCAAGTTCAACTATCGTCGATT 59.938 40.000 13.91 0.00 0.00 3.34
1090 1135 4.823989 ACTGCAAGCTTCAAGTTCAACTAT 59.176 37.500 0.00 0.00 37.60 2.12
1104 1149 1.975407 GACATGGGCACTGCAAGCT 60.975 57.895 10.25 0.00 37.60 3.74
1111 1156 0.904649 TCGATGAAGACATGGGCACT 59.095 50.000 0.00 0.00 36.82 4.40
1116 1161 2.099263 ACTACCGTCGATGAAGACATGG 59.901 50.000 6.11 0.00 40.98 3.66
1126 1171 4.701765 ACTAGTGTATCACTACCGTCGAT 58.298 43.478 0.00 0.00 43.46 3.59
1139 1184 2.778850 AGTCCCTCTCCGACTAGTGTAT 59.221 50.000 0.00 0.00 38.82 2.29
1174 1219 3.143211 ACGACTACAGAACCTGAGACT 57.857 47.619 0.45 0.00 35.18 3.24
1307 1353 0.310543 GTGCTGCATGTTTCGGTTCA 59.689 50.000 5.27 0.00 0.00 3.18
1435 1481 1.301244 CTCGCTGCTGGTCTTGTGT 60.301 57.895 0.00 0.00 0.00 3.72
1439 1485 3.630013 TGCCTCGCTGCTGGTCTT 61.630 61.111 9.62 0.00 0.00 3.01
1458 1504 2.360350 CCGCCTTCCTGCATGTGT 60.360 61.111 0.00 0.00 0.00 3.72
1473 1519 0.732880 CTACGCTGTTGACCTCACCG 60.733 60.000 0.00 0.00 0.00 4.94
1483 1529 1.746615 CCCATGCTGCTACGCTGTT 60.747 57.895 0.00 0.00 0.00 3.16
1489 1535 0.677731 TGCACTTCCCATGCTGCTAC 60.678 55.000 0.00 0.00 43.77 3.58
1498 1544 0.976641 CACCTCTACTGCACTTCCCA 59.023 55.000 0.00 0.00 0.00 4.37
1500 1546 0.391793 GCCACCTCTACTGCACTTCC 60.392 60.000 0.00 0.00 0.00 3.46
1509 1555 1.539065 CCACATGATCGCCACCTCTAC 60.539 57.143 0.00 0.00 0.00 2.59
1510 1556 0.752658 CCACATGATCGCCACCTCTA 59.247 55.000 0.00 0.00 0.00 2.43
1532 1578 2.899838 GCTGTGTGCACCCGTGAA 60.900 61.111 15.69 0.00 42.31 3.18
1684 1730 3.276091 CAAGACCGTGTGCCGCAA 61.276 61.111 0.00 0.00 34.38 4.85
1690 1736 3.403057 CGTCGCCAAGACCGTGTG 61.403 66.667 0.00 0.00 46.92 3.82
1691 1737 4.657824 CCGTCGCCAAGACCGTGT 62.658 66.667 0.00 0.00 46.92 4.49
1713 1759 4.869440 CCTCGCCGCTCTCTGCTG 62.869 72.222 0.00 0.00 40.11 4.41
1826 1882 4.954970 CGCCAAGCCACCAGGTGT 62.955 66.667 18.82 0.00 37.19 4.16
1904 1960 4.699522 AAAGAGGCCGCCGACCAC 62.700 66.667 1.49 0.00 0.00 4.16
1905 1961 4.697756 CAAAGAGGCCGCCGACCA 62.698 66.667 1.49 0.00 0.00 4.02
1907 1963 4.388499 TCCAAAGAGGCCGCCGAC 62.388 66.667 1.49 2.52 37.29 4.79
1908 1964 4.082523 CTCCAAAGAGGCCGCCGA 62.083 66.667 1.49 0.00 36.39 5.54
1909 1965 4.394712 ACTCCAAAGAGGCCGCCG 62.395 66.667 1.49 0.00 45.11 6.46
1910 1966 2.747855 CACTCCAAAGAGGCCGCC 60.748 66.667 1.49 0.00 45.11 6.13
1911 1967 1.743252 CTCACTCCAAAGAGGCCGC 60.743 63.158 0.00 0.00 45.11 6.53
1912 1968 1.078848 CCTCACTCCAAAGAGGCCG 60.079 63.158 0.00 0.00 44.37 6.13
1949 2005 1.219393 CCCCGTCTTGAGCTCCTTC 59.781 63.158 12.15 0.00 0.00 3.46
1960 2016 2.762875 GGTTCCCGATCCCCGTCT 60.763 66.667 0.00 0.00 36.31 4.18
1971 2027 2.273179 GCGACCAAAAGGGGTTCCC 61.273 63.158 0.00 0.00 42.53 3.97
1981 2037 2.048222 CCTCTCAGCGCGACCAAA 60.048 61.111 12.10 0.00 0.00 3.28
1982 2038 2.989253 TCCTCTCAGCGCGACCAA 60.989 61.111 12.10 0.00 0.00 3.67
2056 2128 2.517919 GATCCCCTGCACCCATCC 59.482 66.667 0.00 0.00 0.00 3.51
2074 2146 5.453057 GCTCTAACCCTAGTTAAACTAGCCC 60.453 48.000 0.00 0.00 45.21 5.19
2085 2157 1.075450 CCCCCGCTCTAACCCTAGT 60.075 63.158 0.00 0.00 0.00 2.57
2106 2178 2.908940 CATCCATTCCCGCAGCCC 60.909 66.667 0.00 0.00 0.00 5.19
2188 2260 8.442660 AAAGAAAATAAGAGAAGAGAGGGAGA 57.557 34.615 0.00 0.00 0.00 3.71
2218 2290 8.477984 TCTTTTTCTTGTCTGGAATTGTTTTG 57.522 30.769 0.00 0.00 0.00 2.44
2229 2301 5.240403 CCCTCCTCTTTCTTTTTCTTGTCTG 59.760 44.000 0.00 0.00 0.00 3.51
2233 2305 5.707764 CCTACCCTCCTCTTTCTTTTTCTTG 59.292 44.000 0.00 0.00 0.00 3.02
2246 2318 1.008571 ACTTCTTCCCCTACCCTCCTC 59.991 57.143 0.00 0.00 0.00 3.71
2247 2319 1.102938 ACTTCTTCCCCTACCCTCCT 58.897 55.000 0.00 0.00 0.00 3.69
2259 2331 6.817765 TTTATCCATGTGTCCAACTTCTTC 57.182 37.500 0.00 0.00 0.00 2.87
2275 2347 8.690203 TTTTGTGAGTCTGAGAAATTTATCCA 57.310 30.769 10.19 0.00 0.00 3.41
2287 2359 4.398988 ACAAGCACATTTTTGTGAGTCTGA 59.601 37.500 10.14 0.00 42.02 3.27
2288 2360 4.675510 ACAAGCACATTTTTGTGAGTCTG 58.324 39.130 10.14 3.74 42.02 3.51
2289 2361 4.989279 ACAAGCACATTTTTGTGAGTCT 57.011 36.364 10.14 0.00 42.02 3.24
2308 2380 3.640967 CCCACTCCAATTTTCTTGGAACA 59.359 43.478 7.98 0.00 46.85 3.18
2310 2382 2.632512 GCCCACTCCAATTTTCTTGGAA 59.367 45.455 7.98 0.00 46.85 3.53
2376 2448 3.865571 ACCCTAGTCCTAGTTCAAACCA 58.134 45.455 0.96 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.