Multiple sequence alignment - TraesCS4A01G383700

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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 TraesCS4A01G383700 chr4A 100.000 2195 0 0 1 2195 661302646 661300452 0.000000e+00 4054
1 TraesCS4A01G383700 chr4A 89.030 237 12 5 175 407 661318605 661318379 4.610000e-72 281
2 TraesCS4A01G383700 chr4A 86.441 177 17 5 145 320 661313323 661313153 1.030000e-43 187
3 TraesCS4A01G383700 chr7A 87.397 1706 89 54 567 2195 49234136 49232480 0.000000e+00 1844
4 TraesCS4A01G383700 chr7A 83.463 387 33 10 145 519 49234499 49234132 4.520000e-87 331
5 TraesCS4A01G383700 chr7A 87.558 217 22 3 184 400 49354179 49353968 1.680000e-61 246
6 TraesCS4A01G383700 chr7A 87.435 191 23 1 184 374 49270754 49270565 3.670000e-53 219
7 TraesCS4A01G383700 chr7D 88.349 1502 99 43 320 1789 46965230 46963773 0.000000e+00 1735
8 TraesCS4A01G383700 chr7D 88.542 384 29 8 1812 2195 46961519 46961151 3.320000e-123 451
9 TraesCS4A01G383700 chr7D 94.928 138 4 3 145 280 47113905 47113769 1.710000e-51 213
10 TraesCS4A01G383700 chr7D 88.667 150 10 2 317 466 47113693 47113551 2.240000e-40 176
11 TraesCS4A01G383700 chr7D 90.476 126 12 0 188 313 46965404 46965279 1.350000e-37 167
12 TraesCS4A01G383700 chr7D 86.184 152 13 3 317 467 47184975 47184831 8.110000e-35 158
13 TraesCS4A01G383700 chr7D 86.429 140 15 4 184 321 47188877 47188740 1.360000e-32 150
14 TraesCS4A01G383700 chr7D 85.065 154 13 4 317 467 47056312 47056166 4.880000e-32 148
15 TraesCS4A01G383700 chr7D 91.667 72 6 0 43 114 47113972 47113901 1.390000e-17 100
16 TraesCS4A01G383700 chr1B 92.920 113 1 6 170 279 636127823 636127931 8.110000e-35 158


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 TraesCS4A01G383700 chr4A 661300452 661302646 2194 True 4054.000000 4054 100.000000 1 2195 1 chr4A.!!$R1 2194
1 TraesCS4A01G383700 chr7A 49232480 49234499 2019 True 1087.500000 1844 85.430000 145 2195 2 chr7A.!!$R3 2050
2 TraesCS4A01G383700 chr7D 46961151 46965404 4253 True 784.333333 1735 89.122333 188 2195 3 chr7D.!!$R2 2007

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 0.24912 TTGCGTGGCTGCTATGTACT 59.751 50.0 7.07 0.0 35.36 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 4326 0.724453 CACACGCGCGTTAGCAAAAT 60.724 50.0 35.9 5.04 45.49 1.82 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
21 22 2.036958 TTATTGCGTGGCTGCTATGT 57.963 45.000 7.07 0.00 32.64 2.29
22 23 2.900716 TATTGCGTGGCTGCTATGTA 57.099 45.000 7.07 0.00 32.64 2.29
23 24 1.299541 ATTGCGTGGCTGCTATGTAC 58.700 50.000 7.07 0.00 35.36 2.90
24 25 0.249120 TTGCGTGGCTGCTATGTACT 59.751 50.000 7.07 0.00 35.36 2.73
25 26 1.107945 TGCGTGGCTGCTATGTACTA 58.892 50.000 7.07 0.00 35.36 1.82
26 27 1.202371 TGCGTGGCTGCTATGTACTAC 60.202 52.381 7.07 0.00 35.36 2.73
27 28 1.067212 GCGTGGCTGCTATGTACTACT 59.933 52.381 7.07 0.00 0.00 2.57
28 29 2.292569 GCGTGGCTGCTATGTACTACTA 59.707 50.000 7.07 0.00 0.00 1.82
29 30 3.609644 GCGTGGCTGCTATGTACTACTAG 60.610 52.174 7.07 0.00 0.00 2.57
30 31 3.564644 CGTGGCTGCTATGTACTACTAGT 59.435 47.826 0.00 0.00 0.00 2.57
31 32 4.753610 CGTGGCTGCTATGTACTACTAGTA 59.246 45.833 1.89 1.89 0.00 1.82
43 44 6.088719 GTACTACTAGTACGTGACAGTGAC 57.911 45.833 10.05 0.00 41.27 3.67
44 45 4.635223 ACTACTAGTACGTGACAGTGACA 58.365 43.478 0.00 0.00 0.00 3.58
45 46 5.243981 ACTACTAGTACGTGACAGTGACAT 58.756 41.667 0.00 0.00 0.00 3.06
46 47 4.421033 ACTAGTACGTGACAGTGACATG 57.579 45.455 12.40 12.40 0.00 3.21
47 48 3.819337 ACTAGTACGTGACAGTGACATGT 59.181 43.478 21.17 21.17 40.08 3.21
48 49 4.999311 ACTAGTACGTGACAGTGACATGTA 59.001 41.667 19.39 19.39 38.28 2.29
51 52 2.739292 ACGTGACAGTGACATGTACAC 58.261 47.619 17.12 16.12 36.01 2.90
52 53 1.713932 CGTGACAGTGACATGTACACG 59.286 52.381 17.18 16.96 42.41 4.49
53 54 2.603652 CGTGACAGTGACATGTACACGA 60.604 50.000 21.51 8.87 46.09 4.35
54 55 2.980476 GTGACAGTGACATGTACACGAG 59.020 50.000 17.18 16.13 42.25 4.18
55 56 2.882137 TGACAGTGACATGTACACGAGA 59.118 45.455 17.18 5.95 42.25 4.04
56 57 3.235195 GACAGTGACATGTACACGAGAC 58.765 50.000 17.18 12.58 42.25 3.36
57 58 2.242564 CAGTGACATGTACACGAGACG 58.757 52.381 17.18 0.00 42.25 4.18
58 59 1.199327 AGTGACATGTACACGAGACGG 59.801 52.381 17.18 0.00 42.25 4.79
59 60 0.524414 TGACATGTACACGAGACGGG 59.476 55.000 0.00 0.00 35.82 5.28
60 61 0.806868 GACATGTACACGAGACGGGA 59.193 55.000 0.00 0.00 32.98 5.14
61 62 1.404391 GACATGTACACGAGACGGGAT 59.596 52.381 0.00 0.00 32.98 3.85
62 63 2.615447 GACATGTACACGAGACGGGATA 59.385 50.000 0.00 0.00 32.98 2.59
63 64 2.357009 ACATGTACACGAGACGGGATAC 59.643 50.000 0.00 0.72 32.98 2.24
64 65 2.408271 TGTACACGAGACGGGATACT 57.592 50.000 0.00 0.00 32.98 2.12
65 66 2.283298 TGTACACGAGACGGGATACTC 58.717 52.381 0.00 0.00 32.98 2.59
73 74 2.791170 ACGGGATACTCGTCCAGAC 58.209 57.895 0.17 0.00 38.81 3.51
83 84 3.952811 GTCCAGACGTTCACCTGC 58.047 61.111 0.00 0.00 0.00 4.85
84 85 1.668151 GTCCAGACGTTCACCTGCC 60.668 63.158 0.00 0.00 0.00 4.85
85 86 2.738521 CCAGACGTTCACCTGCCG 60.739 66.667 0.00 0.00 0.00 5.69
86 87 2.738521 CAGACGTTCACCTGCCGG 60.739 66.667 0.00 0.00 0.00 6.13
87 88 4.681978 AGACGTTCACCTGCCGGC 62.682 66.667 22.73 22.73 0.00 6.13
91 92 4.025401 GTTCACCTGCCGGCGTTG 62.025 66.667 23.90 18.25 0.00 4.10
102 103 2.435234 GGCGTTGCCCGTGATACA 60.435 61.111 0.00 0.00 44.06 2.29
103 104 1.817941 GGCGTTGCCCGTGATACAT 60.818 57.895 0.00 0.00 44.06 2.29
104 105 1.373590 GGCGTTGCCCGTGATACATT 61.374 55.000 0.00 0.00 44.06 2.71
105 106 1.292061 GCGTTGCCCGTGATACATTA 58.708 50.000 0.00 0.00 39.32 1.90
106 107 1.260561 GCGTTGCCCGTGATACATTAG 59.739 52.381 0.00 0.00 39.32 1.73
107 108 2.816689 CGTTGCCCGTGATACATTAGA 58.183 47.619 0.00 0.00 0.00 2.10
108 109 3.390135 CGTTGCCCGTGATACATTAGAT 58.610 45.455 0.00 0.00 0.00 1.98
109 110 4.552355 CGTTGCCCGTGATACATTAGATA 58.448 43.478 0.00 0.00 0.00 1.98
110 111 4.384846 CGTTGCCCGTGATACATTAGATAC 59.615 45.833 0.00 0.00 0.00 2.24
111 112 4.168922 TGCCCGTGATACATTAGATACG 57.831 45.455 0.00 0.00 0.00 3.06
112 113 3.570975 TGCCCGTGATACATTAGATACGT 59.429 43.478 0.00 0.00 0.00 3.57
113 114 4.761227 TGCCCGTGATACATTAGATACGTA 59.239 41.667 0.00 0.00 0.00 3.57
114 115 5.091431 GCCCGTGATACATTAGATACGTAC 58.909 45.833 0.00 0.00 0.00 3.67
115 116 5.634896 CCCGTGATACATTAGATACGTACC 58.365 45.833 0.00 0.00 0.00 3.34
116 117 5.181811 CCCGTGATACATTAGATACGTACCA 59.818 44.000 0.00 0.00 0.00 3.25
117 118 6.127814 CCCGTGATACATTAGATACGTACCAT 60.128 42.308 0.00 0.00 0.00 3.55
118 119 6.745907 CCGTGATACATTAGATACGTACCATG 59.254 42.308 0.00 0.60 0.00 3.66
119 120 6.250739 CGTGATACATTAGATACGTACCATGC 59.749 42.308 0.00 0.00 0.00 4.06
120 121 7.088272 GTGATACATTAGATACGTACCATGCA 58.912 38.462 0.00 0.00 0.00 3.96
121 122 7.597369 GTGATACATTAGATACGTACCATGCAA 59.403 37.037 0.00 0.00 0.00 4.08
122 123 8.145122 TGATACATTAGATACGTACCATGCAAA 58.855 33.333 0.00 0.00 0.00 3.68
123 124 8.896320 ATACATTAGATACGTACCATGCAAAA 57.104 30.769 0.00 0.00 0.00 2.44
124 125 7.618502 ACATTAGATACGTACCATGCAAAAA 57.381 32.000 0.00 0.00 0.00 1.94
170 171 9.590451 ACGTAGATTTTAGATATTTTTGACCGA 57.410 29.630 0.00 0.00 0.00 4.69
179 180 3.934457 ATTTTTGACCGAGGCGAAAAT 57.066 38.095 10.32 10.32 35.53 1.82
182 183 1.885560 TTGACCGAGGCGAAAATGAA 58.114 45.000 0.00 0.00 0.00 2.57
185 186 2.619177 TGACCGAGGCGAAAATGAAAAA 59.381 40.909 0.00 0.00 0.00 1.94
186 187 2.977829 GACCGAGGCGAAAATGAAAAAC 59.022 45.455 0.00 0.00 0.00 2.43
281 283 6.072112 ACTACAACGACTTTGATGCAAAAT 57.928 33.333 0.00 0.00 38.73 1.82
282 284 6.503524 ACTACAACGACTTTGATGCAAAATT 58.496 32.000 0.00 0.00 38.73 1.82
283 285 5.640218 ACAACGACTTTGATGCAAAATTG 57.360 34.783 0.00 0.00 38.73 2.32
284 286 5.108517 ACAACGACTTTGATGCAAAATTGT 58.891 33.333 0.00 0.00 38.73 2.71
350 394 3.113514 TTGAGTGGTCGGCAGCCAA 62.114 57.895 13.30 0.00 37.81 4.52
376 425 1.524621 CATCCAAGCTAGGTGGCGG 60.525 63.158 0.00 0.00 35.99 6.13
377 426 2.746375 ATCCAAGCTAGGTGGCGGG 61.746 63.158 0.00 0.00 35.99 6.13
431 480 3.468140 GGTGGAGCCTACGGGACC 61.468 72.222 0.00 0.00 33.58 4.46
448 497 3.411351 CACAGGAAACGTCGGCGG 61.411 66.667 16.39 0.00 43.45 6.13
485 547 5.045651 AGACCCAGAACATGTTACATCATGA 60.046 40.000 11.95 0.00 45.41 3.07
555 624 4.072088 CGAACCACGCCACGCTTC 62.072 66.667 0.00 0.00 34.51 3.86
556 625 3.723348 GAACCACGCCACGCTTCC 61.723 66.667 0.00 0.00 0.00 3.46
557 626 4.555709 AACCACGCCACGCTTCCA 62.556 61.111 0.00 0.00 0.00 3.53
558 627 4.988598 ACCACGCCACGCTTCCAG 62.989 66.667 0.00 0.00 0.00 3.86
560 629 4.988598 CACGCCACGCTTCCAGGT 62.989 66.667 0.00 0.00 0.00 4.00
561 630 4.681978 ACGCCACGCTTCCAGGTC 62.682 66.667 0.00 0.00 0.00 3.85
564 633 4.003788 CCACGCTTCCAGGTCGGT 62.004 66.667 0.00 0.00 35.57 4.69
565 634 2.432628 CACGCTTCCAGGTCGGTC 60.433 66.667 0.00 0.00 35.57 4.79
577 646 1.808390 GTCGGTCGGCCATGTGTAC 60.808 63.158 6.96 0.00 34.09 2.90
657 747 4.323843 CTACCGGGCCGATCGACG 62.324 72.222 30.79 17.16 42.18 5.12
722 812 3.311110 TGGGACGTGGAGACCTGC 61.311 66.667 0.00 0.00 35.00 4.85
753 843 3.709348 TAGCAGCCATGGCCAGCAG 62.709 63.158 37.92 23.63 42.54 4.24
814 904 6.150140 ACGGAGTTGGTTAACACTACTAGTAG 59.850 42.308 25.30 25.30 37.78 2.57
857 948 4.210304 GCGCGACGAGCCATCAAC 62.210 66.667 12.10 0.00 44.76 3.18
860 951 1.815421 GCGACGAGCCATCAACCAT 60.815 57.895 0.00 0.00 40.81 3.55
861 952 1.766143 GCGACGAGCCATCAACCATC 61.766 60.000 0.00 0.00 40.81 3.51
862 953 1.154205 CGACGAGCCATCAACCATCC 61.154 60.000 0.00 0.00 0.00 3.51
863 954 1.153369 ACGAGCCATCAACCATCCG 60.153 57.895 0.00 0.00 0.00 4.18
864 955 1.153369 CGAGCCATCAACCATCCGT 60.153 57.895 0.00 0.00 0.00 4.69
865 956 1.154205 CGAGCCATCAACCATCCGTC 61.154 60.000 0.00 0.00 0.00 4.79
866 957 0.815615 GAGCCATCAACCATCCGTCC 60.816 60.000 0.00 0.00 0.00 4.79
867 958 1.077787 GCCATCAACCATCCGTCCA 60.078 57.895 0.00 0.00 0.00 4.02
868 959 0.466189 GCCATCAACCATCCGTCCAT 60.466 55.000 0.00 0.00 0.00 3.41
869 960 1.597742 CCATCAACCATCCGTCCATC 58.402 55.000 0.00 0.00 0.00 3.51
903 994 5.888691 TCAAAGCGAATTATTGGCTGTTA 57.111 34.783 14.76 0.00 44.26 2.41
961 1052 1.375396 CCCGTTGATCGTGCCAAGA 60.375 57.895 0.00 0.00 37.94 3.02
975 1066 1.277557 GCCAAGAAGAAGCAGAGGAGA 59.722 52.381 0.00 0.00 0.00 3.71
978 1069 3.007831 CCAAGAAGAAGCAGAGGAGAAGT 59.992 47.826 0.00 0.00 0.00 3.01
979 1070 3.959535 AGAAGAAGCAGAGGAGAAGTG 57.040 47.619 0.00 0.00 0.00 3.16
1080 1186 4.803426 CGGCTCGTGCACCTCCTC 62.803 72.222 12.15 0.00 41.91 3.71
1202 1308 1.756561 TCATCGCCTGATCGGTCCA 60.757 57.895 0.00 0.00 30.49 4.02
1281 1387 5.105310 TCCTGCTGTTCTTCCTCTTGTATAC 60.105 44.000 0.00 0.00 0.00 1.47
1284 1390 5.480422 TGCTGTTCTTCCTCTTGTATACTCA 59.520 40.000 4.17 0.00 0.00 3.41
1289 1395 1.681793 TCCTCTTGTATACTCAGCGCC 59.318 52.381 2.29 0.00 0.00 6.53
1323 1429 2.048503 GGCGCGTCCTAGTTGTGT 60.049 61.111 8.43 0.00 0.00 3.72
1334 1440 3.006537 TCCTAGTTGTGTGTAGCTGTTCC 59.993 47.826 0.00 0.00 0.00 3.62
1358 1464 1.095600 GAAAGGATCAAAGGACCGGC 58.904 55.000 0.00 0.00 0.00 6.13
1404 1514 4.170723 CGAACCCGCTCTCTGTTC 57.829 61.111 0.00 0.00 36.02 3.18
1405 1515 1.446272 CGAACCCGCTCTCTGTTCC 60.446 63.158 0.00 0.00 35.99 3.62
1422 1532 3.389656 TGTTCCCCCTTTTGATTTTGACC 59.610 43.478 0.00 0.00 0.00 4.02
1425 1535 3.116939 TCCCCCTTTTGATTTTGACCTCA 60.117 43.478 0.00 0.00 0.00 3.86
1528 1640 3.875727 CTGAGCGATGATCCTGTTTTCAT 59.124 43.478 0.00 0.00 35.33 2.57
1622 1741 1.525718 TTCGGGGTCACGATTGTCGA 61.526 55.000 6.34 0.00 43.74 4.20
1669 1788 4.529219 TGATGTGCTAGCCCGCCG 62.529 66.667 13.29 0.00 0.00 6.46
1710 1829 1.001974 ACTCAATCAAGCACGCCACTA 59.998 47.619 0.00 0.00 0.00 2.74
1711 1830 1.394917 CTCAATCAAGCACGCCACTAC 59.605 52.381 0.00 0.00 0.00 2.73
1712 1831 1.001974 TCAATCAAGCACGCCACTACT 59.998 47.619 0.00 0.00 0.00 2.57
1785 1904 9.065798 TCTTGTTTCATGATAAGATCAAACACA 57.934 29.630 11.40 0.00 43.50 3.72
1795 1914 7.451255 TGATAAGATCAAACACAAACTTCCCAT 59.549 33.333 0.00 0.00 36.11 4.00
1808 1957 8.252417 CACAAACTTCCCATGATTTATCATTCA 58.748 33.333 2.51 0.00 44.70 2.57
1809 1958 8.984855 ACAAACTTCCCATGATTTATCATTCAT 58.015 29.630 2.51 0.00 44.70 2.57
1850 4199 2.473816 TCGTTGCACACTGAAGAAGAG 58.526 47.619 0.00 0.00 0.00 2.85
1851 4200 2.100749 TCGTTGCACACTGAAGAAGAGA 59.899 45.455 0.00 0.00 0.00 3.10
1883 4232 3.683365 ATCATCGTACATATGCTGGCA 57.317 42.857 1.58 0.00 0.00 4.92
1885 4234 1.462283 CATCGTACATATGCTGGCAGC 59.538 52.381 31.91 31.91 42.82 5.25
1897 4249 3.515330 GCTGGCAGCAATTTAGAATGT 57.485 42.857 33.33 0.00 41.89 2.71
1898 4250 4.637483 GCTGGCAGCAATTTAGAATGTA 57.363 40.909 33.33 0.00 41.89 2.29
1899 4251 4.354587 GCTGGCAGCAATTTAGAATGTAC 58.645 43.478 33.33 0.00 41.89 2.90
1941 4293 7.130099 TGAAAGGACTGGATACTGGATAAGTA 58.870 38.462 0.00 0.00 45.47 2.24
1942 4294 7.622081 TGAAAGGACTGGATACTGGATAAGTAA 59.378 37.037 0.00 0.00 44.57 2.24
1943 4295 7.989947 AAGGACTGGATACTGGATAAGTAAA 57.010 36.000 0.00 0.00 44.57 2.01
1944 4296 7.989947 AGGACTGGATACTGGATAAGTAAAA 57.010 36.000 0.00 0.00 44.57 1.52
1974 4326 1.347707 GGCCATGGATAAGATGGACGA 59.652 52.381 18.40 0.00 42.81 4.20
2057 4409 8.429493 CATGAGAACAACATGTATATGTGACT 57.571 34.615 5.81 4.01 46.54 3.41
2062 4414 8.314021 AGAACAACATGTATATGTGACTTCTCA 58.686 33.333 5.81 0.00 46.54 3.27
2106 4458 8.766000 ACATGAGTACAAAATGTATACGTGAA 57.234 30.769 0.00 0.00 35.05 3.18
2165 4520 1.664333 GTGTTTGGTTGCCCGCATG 60.664 57.895 0.00 0.00 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.738982 ACATAGCAGCCACGCAATAATA 58.261 40.909 0.00 0.00 0.00 0.98
2 3 2.036958 ACATAGCAGCCACGCAATAA 57.963 45.000 0.00 0.00 0.00 1.40
3 4 2.102420 AGTACATAGCAGCCACGCAATA 59.898 45.455 0.00 0.00 0.00 1.90
5 6 0.249120 AGTACATAGCAGCCACGCAA 59.751 50.000 0.00 0.00 0.00 4.85
6 7 1.107945 TAGTACATAGCAGCCACGCA 58.892 50.000 0.00 0.00 0.00 5.24
7 8 1.067212 AGTAGTACATAGCAGCCACGC 59.933 52.381 2.52 0.00 0.00 5.34
20 21 5.635280 TGTCACTGTCACGTACTAGTAGTAC 59.365 44.000 24.79 24.79 45.71 2.73
21 22 5.783111 TGTCACTGTCACGTACTAGTAGTA 58.217 41.667 5.90 5.90 0.00 1.82
22 23 4.635223 TGTCACTGTCACGTACTAGTAGT 58.365 43.478 8.14 8.14 0.00 2.73
23 24 5.121925 ACATGTCACTGTCACGTACTAGTAG 59.878 44.000 1.87 0.00 0.00 2.57
24 25 4.999311 ACATGTCACTGTCACGTACTAGTA 59.001 41.667 0.00 0.00 0.00 1.82
25 26 3.819337 ACATGTCACTGTCACGTACTAGT 59.181 43.478 0.00 0.00 0.00 2.57
26 27 4.421033 ACATGTCACTGTCACGTACTAG 57.579 45.455 0.00 0.00 0.00 2.57
27 28 4.756135 TGTACATGTCACTGTCACGTACTA 59.244 41.667 0.00 0.22 36.09 1.82
28 29 3.566742 TGTACATGTCACTGTCACGTACT 59.433 43.478 0.00 0.00 36.09 2.73
29 30 3.667261 GTGTACATGTCACTGTCACGTAC 59.333 47.826 0.00 5.91 35.80 3.67
30 31 3.607542 CGTGTACATGTCACTGTCACGTA 60.608 47.826 19.39 0.00 40.98 3.57
31 32 2.739292 GTGTACATGTCACTGTCACGT 58.261 47.619 0.00 0.00 33.59 4.49
32 33 1.713932 CGTGTACATGTCACTGTCACG 59.286 52.381 19.39 17.54 40.55 4.35
33 34 2.980476 CTCGTGTACATGTCACTGTCAC 59.020 50.000 14.63 12.26 34.14 3.67
34 35 2.882137 TCTCGTGTACATGTCACTGTCA 59.118 45.455 14.63 4.21 34.14 3.58
35 36 3.235195 GTCTCGTGTACATGTCACTGTC 58.765 50.000 14.63 10.53 34.14 3.51
36 37 2.350484 CGTCTCGTGTACATGTCACTGT 60.350 50.000 14.63 0.00 34.14 3.55
37 38 2.242564 CGTCTCGTGTACATGTCACTG 58.757 52.381 14.63 14.77 34.14 3.66
38 39 1.199327 CCGTCTCGTGTACATGTCACT 59.801 52.381 14.63 0.00 34.14 3.41
39 40 1.614385 CCGTCTCGTGTACATGTCAC 58.386 55.000 14.63 9.83 0.00 3.67
40 41 0.524414 CCCGTCTCGTGTACATGTCA 59.476 55.000 14.63 0.00 0.00 3.58
41 42 0.806868 TCCCGTCTCGTGTACATGTC 59.193 55.000 14.63 6.35 0.00 3.06
42 43 1.471119 ATCCCGTCTCGTGTACATGT 58.529 50.000 14.63 2.69 0.00 3.21
43 44 2.617308 AGTATCCCGTCTCGTGTACATG 59.383 50.000 8.90 8.90 0.00 3.21
44 45 2.877168 GAGTATCCCGTCTCGTGTACAT 59.123 50.000 0.00 0.00 0.00 2.29
45 46 2.283298 GAGTATCCCGTCTCGTGTACA 58.717 52.381 0.00 0.00 0.00 2.90
46 47 1.260033 CGAGTATCCCGTCTCGTGTAC 59.740 57.143 6.44 0.00 45.37 2.90
47 48 1.575244 CGAGTATCCCGTCTCGTGTA 58.425 55.000 6.44 0.00 45.37 2.90
48 49 2.391469 CGAGTATCCCGTCTCGTGT 58.609 57.895 6.44 0.00 45.37 4.49
55 56 2.791170 GTCTGGACGAGTATCCCGT 58.209 57.895 0.00 0.00 43.56 5.28
66 67 1.668151 GGCAGGTGAACGTCTGGAC 60.668 63.158 4.38 0.00 0.00 4.02
67 68 2.741092 GGCAGGTGAACGTCTGGA 59.259 61.111 4.38 0.00 0.00 3.86
68 69 2.738521 CGGCAGGTGAACGTCTGG 60.739 66.667 4.38 0.00 0.00 3.86
69 70 2.738521 CCGGCAGGTGAACGTCTG 60.739 66.667 0.00 0.00 0.00 3.51
70 71 4.681978 GCCGGCAGGTGAACGTCT 62.682 66.667 24.80 0.00 40.50 4.18
88 89 4.384846 CGTATCTAATGTATCACGGGCAAC 59.615 45.833 0.00 0.00 0.00 4.17
89 90 4.038282 ACGTATCTAATGTATCACGGGCAA 59.962 41.667 0.00 0.00 33.90 4.52
90 91 3.570975 ACGTATCTAATGTATCACGGGCA 59.429 43.478 0.00 0.00 33.90 5.36
91 92 4.170292 ACGTATCTAATGTATCACGGGC 57.830 45.455 0.00 0.00 33.90 6.13
92 93 5.181811 TGGTACGTATCTAATGTATCACGGG 59.818 44.000 7.47 0.00 36.06 5.28
93 94 6.245115 TGGTACGTATCTAATGTATCACGG 57.755 41.667 7.47 0.00 36.06 4.94
94 95 6.250739 GCATGGTACGTATCTAATGTATCACG 59.749 42.308 7.47 0.00 42.22 4.35
95 96 7.088272 TGCATGGTACGTATCTAATGTATCAC 58.912 38.462 7.47 0.00 42.22 3.06
96 97 7.222000 TGCATGGTACGTATCTAATGTATCA 57.778 36.000 7.47 0.00 43.29 2.15
97 98 8.528917 TTTGCATGGTACGTATCTAATGTATC 57.471 34.615 7.47 0.00 32.24 2.24
98 99 8.896320 TTTTGCATGGTACGTATCTAATGTAT 57.104 30.769 7.47 0.00 32.24 2.29
99 100 8.719560 TTTTTGCATGGTACGTATCTAATGTA 57.280 30.769 7.47 0.25 0.00 2.29
100 101 7.618502 TTTTTGCATGGTACGTATCTAATGT 57.381 32.000 7.47 0.00 0.00 2.71
281 283 5.827797 GGATATGGATAGCCTGTCAAAACAA 59.172 40.000 0.00 0.00 35.96 2.83
282 284 5.132648 AGGATATGGATAGCCTGTCAAAACA 59.867 40.000 2.58 0.00 46.65 2.83
283 285 5.625150 AGGATATGGATAGCCTGTCAAAAC 58.375 41.667 2.58 0.00 46.65 2.43
284 286 5.912149 AGGATATGGATAGCCTGTCAAAA 57.088 39.130 2.58 0.00 46.65 2.44
293 295 4.093998 CGCATGAACAAGGATATGGATAGC 59.906 45.833 0.00 0.00 0.00 2.97
295 297 5.482163 TCGCATGAACAAGGATATGGATA 57.518 39.130 0.00 0.00 0.00 2.59
350 394 1.492176 CCTAGCTTGGATGTGACCCAT 59.508 52.381 8.73 0.00 36.13 4.00
431 480 3.411351 CCGCCGACGTTTCCTGTG 61.411 66.667 0.00 0.00 37.70 3.66
448 497 2.698797 TCTGGGTCTCCGATTTATGTCC 59.301 50.000 0.00 0.00 35.24 4.02
548 617 2.432628 GACCGACCTGGAAGCGTG 60.433 66.667 0.00 0.00 42.00 5.34
550 619 4.796231 CCGACCGACCTGGAAGCG 62.796 72.222 0.00 0.76 42.00 4.68
552 621 4.452733 GGCCGACCGACCTGGAAG 62.453 72.222 0.00 0.00 42.00 3.46
555 624 4.838152 CATGGCCGACCGACCTGG 62.838 72.222 0.00 0.00 46.41 4.45
556 625 4.082523 ACATGGCCGACCGACCTG 62.083 66.667 0.00 0.00 39.70 4.00
557 626 4.082523 CACATGGCCGACCGACCT 62.083 66.667 0.00 0.00 39.70 3.85
558 627 3.009192 TACACATGGCCGACCGACC 62.009 63.158 0.00 0.00 39.70 4.79
559 628 1.808390 GTACACATGGCCGACCGAC 60.808 63.158 0.00 0.00 39.70 4.79
560 629 2.574929 GTACACATGGCCGACCGA 59.425 61.111 0.00 0.00 39.70 4.69
561 630 2.268988 TACGTACACATGGCCGACCG 62.269 60.000 0.00 0.00 39.70 4.79
562 631 0.803380 GTACGTACACATGGCCGACC 60.803 60.000 20.67 0.00 0.00 4.79
563 632 0.803380 GGTACGTACACATGGCCGAC 60.803 60.000 26.02 2.02 0.00 4.79
564 633 1.512230 GGTACGTACACATGGCCGA 59.488 57.895 26.02 0.00 0.00 5.54
565 634 1.519898 GGGTACGTACACATGGCCG 60.520 63.158 26.02 0.00 0.00 6.13
577 646 3.024547 TCTCTCAAATCTGGAGGGTACG 58.975 50.000 0.00 0.00 34.41 3.67
657 747 0.179045 ATATGCAACCACCGCTCTCC 60.179 55.000 0.00 0.00 0.00 3.71
722 812 2.031919 TGCTAGTTGGCCACACGG 59.968 61.111 3.88 7.24 0.00 4.94
753 843 0.309922 CGATGGACTGATTGGCATGC 59.690 55.000 9.90 9.90 0.00 4.06
814 904 6.456718 CGGAGCGGTAGTAGCTTATAAGATAC 60.457 46.154 26.29 26.29 46.13 2.24
844 935 1.154205 CGGATGGTTGATGGCTCGTC 61.154 60.000 0.00 0.00 0.00 4.20
855 946 0.532862 GCGATGATGGACGGATGGTT 60.533 55.000 0.00 0.00 0.00 3.67
857 948 2.023771 CGCGATGATGGACGGATGG 61.024 63.158 0.00 0.00 0.00 3.51
862 953 4.923710 TCGCCGCGATGATGGACG 62.924 66.667 12.39 0.00 0.00 4.79
863 954 1.891060 GATTCGCCGCGATGATGGAC 61.891 60.000 17.62 0.06 35.23 4.02
864 955 1.664649 GATTCGCCGCGATGATGGA 60.665 57.895 17.62 0.00 35.23 3.41
865 956 1.498043 TTGATTCGCCGCGATGATGG 61.498 55.000 17.62 0.00 35.23 3.51
866 957 0.304401 TTTGATTCGCCGCGATGATG 59.696 50.000 17.62 0.00 35.23 3.07
867 958 0.583438 CTTTGATTCGCCGCGATGAT 59.417 50.000 17.62 8.08 35.23 2.45
868 959 2.005995 CTTTGATTCGCCGCGATGA 58.994 52.632 17.62 2.41 35.23 2.92
869 960 1.652329 GCTTTGATTCGCCGCGATG 60.652 57.895 17.62 0.00 35.23 3.84
903 994 2.526046 CCTCCGGTGGTTCCCAACT 61.526 63.158 14.67 0.00 39.46 3.16
961 1052 1.627834 CCCACTTCTCCTCTGCTTCTT 59.372 52.381 0.00 0.00 0.00 2.52
975 1066 1.022903 ATCTCCTCCTCCTCCCACTT 58.977 55.000 0.00 0.00 0.00 3.16
978 1069 0.994050 TCGATCTCCTCCTCCTCCCA 60.994 60.000 0.00 0.00 0.00 4.37
979 1070 0.538746 GTCGATCTCCTCCTCCTCCC 60.539 65.000 0.00 0.00 0.00 4.30
1281 1387 2.100605 AAAAACTAGGAGGCGCTGAG 57.899 50.000 7.64 0.00 0.00 3.35
1323 1429 3.646162 TCCTTTCTTGAGGAACAGCTACA 59.354 43.478 0.00 0.00 42.75 2.74
1334 1440 3.686726 CGGTCCTTTGATCCTTTCTTGAG 59.313 47.826 0.00 0.00 0.00 3.02
1358 1464 3.748568 AGCTCAAAAGAAAAGAGGTAGCG 59.251 43.478 0.00 0.00 38.24 4.26
1404 1514 3.238597 TGAGGTCAAAATCAAAAGGGGG 58.761 45.455 0.00 0.00 0.00 5.40
1405 1515 4.774200 AGATGAGGTCAAAATCAAAAGGGG 59.226 41.667 0.00 0.00 0.00 4.79
1422 1532 5.792741 ACTCAGAGGAAAACAGAAGATGAG 58.207 41.667 1.53 0.00 38.06 2.90
1425 1535 6.112058 GCATACTCAGAGGAAAACAGAAGAT 58.888 40.000 1.53 0.00 0.00 2.40
1577 1696 7.834803 TCTCGCATGATTCATCATAATACTCT 58.165 34.615 0.00 0.00 45.23 3.24
1669 1788 1.788886 GTACGACAACGACAGGAAACC 59.211 52.381 0.00 0.00 42.66 3.27
1710 1829 9.384764 GGTGAATAGCAGAAGAAATTTAGTAGT 57.615 33.333 0.00 0.00 0.00 2.73
1711 1830 8.543774 CGGTGAATAGCAGAAGAAATTTAGTAG 58.456 37.037 0.00 0.00 0.00 2.57
1712 1831 7.494625 CCGGTGAATAGCAGAAGAAATTTAGTA 59.505 37.037 0.00 0.00 0.00 1.82
1813 1962 7.116233 TGTGCAACGATGATGATATGTACATAC 59.884 37.037 17.69 11.91 42.39 2.39
1814 1963 7.116233 GTGTGCAACGATGATGATATGTACATA 59.884 37.037 17.65 17.65 42.39 2.29
1815 1964 5.990996 TGTGCAACGATGATGATATGTACAT 59.009 36.000 13.93 13.93 42.39 2.29
1820 4169 4.508861 TCAGTGTGCAACGATGATGATATG 59.491 41.667 0.00 0.00 42.39 1.78
1851 4200 9.897744 CATATGTACGATGATTTATGCCTTTTT 57.102 29.630 2.14 0.00 0.00 1.94
1897 4249 7.236019 TCCTTTCAGTGTGGATAACCTTTAGTA 59.764 37.037 0.00 0.00 37.04 1.82
1898 4250 6.043938 TCCTTTCAGTGTGGATAACCTTTAGT 59.956 38.462 0.00 0.00 37.04 2.24
1899 4251 6.371825 GTCCTTTCAGTGTGGATAACCTTTAG 59.628 42.308 5.79 0.00 37.04 1.85
1954 4306 1.347707 TCGTCCATCTTATCCATGGCC 59.652 52.381 6.96 0.00 40.77 5.36
1956 4308 5.563475 GCAAAATCGTCCATCTTATCCATGG 60.563 44.000 4.97 4.97 42.16 3.66
1970 4322 1.179717 CGCGCGTTAGCAAAATCGTC 61.180 55.000 24.19 0.00 45.49 4.20
1974 4326 0.724453 CACACGCGCGTTAGCAAAAT 60.724 50.000 35.90 5.04 45.49 1.82


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

AutoCloner maintained by Alex Coulton.