Multiple sequence alignment - TraesCS3B01G273800

Loading Multiple Alignment...

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 TraesCS3B01G273800 chr3B 100.000 2096 0 0 894 2989 440680046 440677951 0.000000e+00 3871
1 TraesCS3B01G273800 chr3B 100.000 562 0 0 1 562 440680939 440680378 0.000000e+00 1038
2 TraesCS3B01G273800 chr3A 96.731 2080 62 5 913 2989 461151055 461153131 0.000000e+00 3459
3 TraesCS3B01G273800 chr3A 97.368 380 8 2 160 539 461150396 461150773 0.000000e+00 645
4 TraesCS3B01G273800 chr3D 97.275 1725 43 4 939 2661 341888511 341886789 0.000000e+00 2922
5 TraesCS3B01G273800 chr3D 96.308 325 12 0 160 484 341889252 341888928 4.390000e-148 534
6 TraesCS3B01G273800 chr3D 96.241 266 9 1 2724 2989 341886797 341886533 4.580000e-118 435
7 TraesCS3B01G273800 chrUn 84.466 309 26 11 2600 2886 389445897 389446205 4.880000e-73 285
8 TraesCS3B01G273800 chrUn 84.142 309 27 13 2600 2886 346595633 346595325 2.270000e-71 279
9 TraesCS3B01G273800 chrUn 83.190 232 16 14 2677 2886 444245493 444245263 1.090000e-44 191
10 TraesCS3B01G273800 chr5D 84.466 309 26 13 2600 2886 446174645 446174953 4.880000e-73 285
11 TraesCS3B01G273800 chr5D 84.466 309 26 11 2600 2886 503219079 503219387 4.880000e-73 285
12 TraesCS3B01G273800 chr5D 84.091 308 28 12 2600 2886 381175353 381175046 8.160000e-71 278
13 TraesCS3B01G273800 chr4D 84.142 309 27 11 2600 2886 30387137 30386829 2.270000e-71 279
14 TraesCS3B01G273800 chr1D 84.142 309 27 13 2600 2886 254397249 254396941 2.270000e-71 279
15 TraesCS3B01G273800 chr6D 84.262 305 26 11 2600 2882 168255787 168256091 8.160000e-71 278
16 TraesCS3B01G273800 chr6D 83.495 309 29 13 2600 2886 135463582 135463274 4.910000e-68 268
17 TraesCS3B01G273800 chr5A 83.819 309 28 13 2600 2886 607275260 607275568 1.060000e-69 274


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 TraesCS3B01G273800 chr3B 440677951 440680939 2988 True 2454.5 3871 100.0000 1 2989 2 chr3B.!!$R1 2988
1 TraesCS3B01G273800 chr3A 461150396 461153131 2735 False 2052.0 3459 97.0495 160 2989 2 chr3A.!!$F1 2829
2 TraesCS3B01G273800 chr3D 341886533 341889252 2719 True 1297.0 2922 96.6080 160 2989 3 chr3D.!!$R1 2829

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
107 108 0.107081 AAACCGGACGAACATGGTGA 59.893 50.0 9.46 0.0 34.26 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1998 1999 0.249868 GACCAGCACAGTGTAGCACA 60.25 55.0 16.52 0.0 36.74 4.57 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
32 33 3.663464 CATACTGTGCTCATTGAACGG 57.337 47.619 0.00 0.00 36.63 4.44
33 34 3.261580 CATACTGTGCTCATTGAACGGA 58.738 45.455 4.66 0.00 34.12 4.69
34 35 1.512926 ACTGTGCTCATTGAACGGAC 58.487 50.000 4.66 0.00 34.12 4.79
35 36 1.202639 ACTGTGCTCATTGAACGGACA 60.203 47.619 4.66 2.97 34.12 4.02
36 37 1.872952 CTGTGCTCATTGAACGGACAA 59.127 47.619 2.70 0.00 32.04 3.18
37 38 1.872952 TGTGCTCATTGAACGGACAAG 59.127 47.619 0.00 0.00 33.22 3.16
38 39 2.143122 GTGCTCATTGAACGGACAAGA 58.857 47.619 3.33 1.38 33.22 3.02
39 40 2.744202 GTGCTCATTGAACGGACAAGAT 59.256 45.455 3.33 0.00 33.22 2.40
40 41 2.743664 TGCTCATTGAACGGACAAGATG 59.256 45.455 3.33 0.00 33.22 2.90
41 42 2.476854 GCTCATTGAACGGACAAGATGC 60.477 50.000 3.33 3.56 33.22 3.91
42 43 2.743664 CTCATTGAACGGACAAGATGCA 59.256 45.455 0.00 0.00 33.22 3.96
43 44 3.145286 TCATTGAACGGACAAGATGCAA 58.855 40.909 0.00 0.00 33.22 4.08
44 45 3.758023 TCATTGAACGGACAAGATGCAAT 59.242 39.130 0.00 0.00 33.22 3.56
45 46 3.829886 TTGAACGGACAAGATGCAATC 57.170 42.857 0.00 0.00 46.04 2.67
61 62 2.878991 TCGAAATGCGACCGCGAG 60.879 61.111 8.23 0.00 45.59 5.03
62 63 3.179265 CGAAATGCGACCGCGAGT 61.179 61.111 8.23 3.14 45.51 4.18
63 64 2.726691 CGAAATGCGACCGCGAGTT 61.727 57.895 8.23 4.84 45.51 3.01
64 65 1.225745 GAAATGCGACCGCGAGTTG 60.226 57.895 8.23 9.24 45.51 3.16
65 66 2.563086 GAAATGCGACCGCGAGTTGG 62.563 60.000 8.23 1.63 45.51 3.77
66 67 3.876589 AATGCGACCGCGAGTTGGT 62.877 57.895 8.23 0.00 45.51 3.67
71 72 2.279918 ACCGCGAGTTGGTCACAC 60.280 61.111 8.23 0.00 33.35 3.82
72 73 3.403057 CCGCGAGTTGGTCACACG 61.403 66.667 8.23 0.00 41.93 4.49
73 74 3.403057 CGCGAGTTGGTCACACGG 61.403 66.667 0.00 0.00 39.63 4.94
74 75 3.712881 GCGAGTTGGTCACACGGC 61.713 66.667 0.00 0.00 39.63 5.68
75 76 3.041940 CGAGTTGGTCACACGGCC 61.042 66.667 0.00 0.00 35.98 6.13
76 77 3.041940 GAGTTGGTCACACGGCCG 61.042 66.667 26.86 26.86 0.00 6.13
88 89 4.585526 CGGCCGCCGCATCTAGAA 62.586 66.667 20.79 0.00 41.17 2.10
89 90 2.203015 GGCCGCCGCATCTAGAAA 60.203 61.111 0.00 0.00 36.38 2.52
90 91 1.817941 GGCCGCCGCATCTAGAAAA 60.818 57.895 0.00 0.00 36.38 2.29
91 92 1.352056 GCCGCCGCATCTAGAAAAC 59.648 57.895 0.00 0.00 34.03 2.43
92 93 2.014594 CCGCCGCATCTAGAAAACC 58.985 57.895 0.00 0.00 0.00 3.27
93 94 1.636340 CGCCGCATCTAGAAAACCG 59.364 57.895 0.00 0.00 0.00 4.44
94 95 1.762222 CGCCGCATCTAGAAAACCGG 61.762 60.000 15.26 15.26 38.76 5.28
95 96 0.461339 GCCGCATCTAGAAAACCGGA 60.461 55.000 20.74 0.00 38.04 5.14
96 97 1.287425 CCGCATCTAGAAAACCGGAC 58.713 55.000 9.46 0.00 38.04 4.79
97 98 0.921347 CGCATCTAGAAAACCGGACG 59.079 55.000 9.46 0.00 0.00 4.79
98 99 1.468565 CGCATCTAGAAAACCGGACGA 60.469 52.381 9.46 0.00 0.00 4.20
99 100 2.613691 GCATCTAGAAAACCGGACGAA 58.386 47.619 9.46 0.00 0.00 3.85
100 101 2.347755 GCATCTAGAAAACCGGACGAAC 59.652 50.000 9.46 0.00 0.00 3.95
101 102 3.581755 CATCTAGAAAACCGGACGAACA 58.418 45.455 9.46 0.00 0.00 3.18
102 103 3.947910 TCTAGAAAACCGGACGAACAT 57.052 42.857 9.46 0.00 0.00 2.71
103 104 3.581755 TCTAGAAAACCGGACGAACATG 58.418 45.455 9.46 0.00 0.00 3.21
104 105 1.519408 AGAAAACCGGACGAACATGG 58.481 50.000 9.46 0.00 0.00 3.66
105 106 1.202722 AGAAAACCGGACGAACATGGT 60.203 47.619 9.46 0.00 35.90 3.55
106 107 0.948678 AAAACCGGACGAACATGGTG 59.051 50.000 9.46 0.00 34.26 4.17
107 108 0.107081 AAACCGGACGAACATGGTGA 59.893 50.000 9.46 0.00 34.26 4.02
108 109 0.601841 AACCGGACGAACATGGTGAC 60.602 55.000 9.46 0.00 34.26 3.67
109 110 1.740296 CCGGACGAACATGGTGACC 60.740 63.158 0.00 0.00 0.00 4.02
110 111 1.740296 CGGACGAACATGGTGACCC 60.740 63.158 0.00 0.00 0.00 4.46
112 113 0.250553 GGACGAACATGGTGACCCAA 60.251 55.000 0.00 0.00 46.04 4.12
113 114 1.600023 GACGAACATGGTGACCCAAA 58.400 50.000 0.00 0.00 46.04 3.28
114 115 1.265905 GACGAACATGGTGACCCAAAC 59.734 52.381 0.00 0.00 46.04 2.93
115 116 0.237235 CGAACATGGTGACCCAAACG 59.763 55.000 0.00 0.00 46.04 3.60
116 117 0.596082 GAACATGGTGACCCAAACGG 59.404 55.000 0.00 0.00 46.04 4.44
117 118 0.183971 AACATGGTGACCCAAACGGA 59.816 50.000 0.00 0.00 46.04 4.69
118 119 0.536460 ACATGGTGACCCAAACGGAC 60.536 55.000 0.00 0.00 46.04 4.79
119 120 1.074248 ATGGTGACCCAAACGGACC 59.926 57.895 0.00 0.00 46.04 4.46
120 121 1.710996 ATGGTGACCCAAACGGACCA 61.711 55.000 0.00 0.00 46.04 4.02
121 122 1.152922 GGTGACCCAAACGGACCAA 60.153 57.895 0.00 0.00 30.21 3.67
122 123 0.752376 GGTGACCCAAACGGACCAAA 60.752 55.000 0.00 0.00 30.21 3.28
123 124 1.104630 GTGACCCAAACGGACCAAAA 58.895 50.000 0.00 0.00 34.64 2.44
124 125 1.477295 GTGACCCAAACGGACCAAAAA 59.523 47.619 0.00 0.00 34.64 1.94
125 126 1.477295 TGACCCAAACGGACCAAAAAC 59.523 47.619 0.00 0.00 34.64 2.43
126 127 1.477295 GACCCAAACGGACCAAAAACA 59.523 47.619 0.00 0.00 34.64 2.83
127 128 1.900486 ACCCAAACGGACCAAAAACAA 59.100 42.857 0.00 0.00 34.64 2.83
128 129 2.302157 ACCCAAACGGACCAAAAACAAA 59.698 40.909 0.00 0.00 34.64 2.83
129 130 2.673862 CCCAAACGGACCAAAAACAAAC 59.326 45.455 0.00 0.00 0.00 2.93
130 131 2.345942 CCAAACGGACCAAAAACAAACG 59.654 45.455 0.00 0.00 0.00 3.60
131 132 2.987821 CAAACGGACCAAAAACAAACGT 59.012 40.909 0.00 0.00 34.25 3.99
132 133 2.547913 ACGGACCAAAAACAAACGTC 57.452 45.000 0.00 0.00 0.00 4.34
133 134 1.132834 ACGGACCAAAAACAAACGTCC 59.867 47.619 0.00 0.00 39.73 4.79
134 135 1.830086 GGACCAAAAACAAACGTCCG 58.170 50.000 0.00 0.00 34.15 4.79
135 136 1.132834 GGACCAAAAACAAACGTCCGT 59.867 47.619 0.00 0.00 34.15 4.69
136 137 2.415759 GGACCAAAAACAAACGTCCGTT 60.416 45.455 0.00 0.00 40.45 4.44
143 144 3.281395 AAACGTCCGTTTGGGCCG 61.281 61.111 16.18 0.00 45.34 6.13
144 145 4.550697 AACGTCCGTTTGGGCCGT 62.551 61.111 0.00 0.00 42.45 5.68
156 157 3.365265 GGCCGTGCCTTGGAGTTG 61.365 66.667 7.58 0.00 46.69 3.16
157 158 3.365265 GCCGTGCCTTGGAGTTGG 61.365 66.667 0.00 0.00 0.00 3.77
178 179 0.110644 CTGAGCGCGTTGAAAGGTTC 60.111 55.000 8.43 0.00 0.00 3.62
236 237 1.479709 CCTCCCTGTGTAGAGACCTG 58.520 60.000 0.00 0.00 31.43 4.00
539 540 2.041405 CCACCTCCCTCCTCTCCC 60.041 72.222 0.00 0.00 0.00 4.30
540 541 2.443016 CACCTCCCTCCTCTCCCG 60.443 72.222 0.00 0.00 0.00 5.14
541 542 4.467107 ACCTCCCTCCTCTCCCGC 62.467 72.222 0.00 0.00 0.00 6.13
542 543 4.150454 CCTCCCTCCTCTCCCGCT 62.150 72.222 0.00 0.00 0.00 5.52
543 544 2.520741 CTCCCTCCTCTCCCGCTC 60.521 72.222 0.00 0.00 0.00 5.03
544 545 4.507916 TCCCTCCTCTCCCGCTCG 62.508 72.222 0.00 0.00 0.00 5.03
911 912 4.150454 CCCCTCCGCCCTCTCTCT 62.150 72.222 0.00 0.00 0.00 3.10
1087 1088 2.638154 CCGACGCTCCTATCGACC 59.362 66.667 0.00 0.00 40.86 4.79
1144 1145 1.741770 GCCTGCTCCTACAACACCG 60.742 63.158 0.00 0.00 0.00 4.94
1284 1285 4.785453 CGGGAGGGCTGCTTGGAC 62.785 72.222 0.00 0.00 0.00 4.02
1314 1315 3.244735 TGGAGATGTTTGACGAAATGGGA 60.245 43.478 0.00 0.00 0.00 4.37
1344 1345 6.458232 GGTATTGCACCCAATGTTATTACA 57.542 37.500 0.00 0.00 41.58 2.41
1405 1406 2.708051 CATCATCAGCACTGGACTTGT 58.292 47.619 0.00 0.00 0.00 3.16
1417 1418 2.104792 CTGGACTTGTTGGAGAGGTTGA 59.895 50.000 0.00 0.00 0.00 3.18
1615 1616 2.440409 CTGTGGAGGCTGCAAATTACT 58.560 47.619 11.29 0.00 0.00 2.24
1784 1785 2.292267 CATTTCTACCGAGCCAAGCAT 58.708 47.619 0.00 0.00 0.00 3.79
1840 1841 2.601905 ACCATTTGGAGAAAGCAGCTT 58.398 42.857 0.21 0.21 38.94 3.74
2040 2041 2.370445 CCTTCCCCGGACTCTGCAT 61.370 63.158 0.73 0.00 0.00 3.96
2144 2146 0.580104 GAACCGACACACTTGTTCCG 59.420 55.000 0.00 0.00 35.47 4.30
2183 2187 4.816925 AGTGAGAGAGTTTTGCTACCAAAC 59.183 41.667 0.00 0.00 40.45 2.93
2399 2403 6.202188 TGTGTCTTCTGTTTCCTTATTTCGTC 59.798 38.462 0.00 0.00 0.00 4.20
2429 2433 5.743636 ATGTTTGTTCAGGGTTATTGCAT 57.256 34.783 0.00 0.00 0.00 3.96
2466 2470 5.079689 TGCGTGGTATGACTTCAAGAATA 57.920 39.130 0.00 0.00 0.00 1.75
2651 2655 3.613877 TTTCCATGCCTGCCGCGTA 62.614 57.895 4.92 0.00 42.08 4.42
2941 2945 5.743636 AAATTGTGGTATGTGCCAAAGAT 57.256 34.783 0.00 0.00 40.68 2.40
2966 2970 8.392631 TGTATCCAATATATTATCCTGCCAGT 57.607 34.615 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.062639 GTCCGTTCAATGAGCACAGTATG 59.937 47.826 0.00 0.00 46.00 2.39
13 14 3.262420 GTCCGTTCAATGAGCACAGTAT 58.738 45.455 0.00 0.00 0.00 2.12
14 15 2.036604 TGTCCGTTCAATGAGCACAGTA 59.963 45.455 0.00 0.00 0.00 2.74
15 16 1.202639 TGTCCGTTCAATGAGCACAGT 60.203 47.619 0.00 0.00 0.00 3.55
16 17 1.511850 TGTCCGTTCAATGAGCACAG 58.488 50.000 0.00 0.00 0.00 3.66
17 18 1.872952 CTTGTCCGTTCAATGAGCACA 59.127 47.619 0.00 0.00 0.00 4.57
18 19 2.143122 TCTTGTCCGTTCAATGAGCAC 58.857 47.619 0.00 0.00 0.00 4.40
19 20 2.542020 TCTTGTCCGTTCAATGAGCA 57.458 45.000 0.00 0.00 0.00 4.26
20 21 2.476854 GCATCTTGTCCGTTCAATGAGC 60.477 50.000 0.00 0.00 0.00 4.26
21 22 2.743664 TGCATCTTGTCCGTTCAATGAG 59.256 45.455 0.00 0.00 0.00 2.90
22 23 2.777094 TGCATCTTGTCCGTTCAATGA 58.223 42.857 0.00 0.00 0.00 2.57
23 24 3.557577 TTGCATCTTGTCCGTTCAATG 57.442 42.857 0.00 0.00 0.00 2.82
24 25 3.181507 CGATTGCATCTTGTCCGTTCAAT 60.182 43.478 0.00 0.00 0.00 2.57
25 26 2.159430 CGATTGCATCTTGTCCGTTCAA 59.841 45.455 0.00 0.00 0.00 2.69
26 27 1.731709 CGATTGCATCTTGTCCGTTCA 59.268 47.619 0.00 0.00 0.00 3.18
27 28 1.999735 TCGATTGCATCTTGTCCGTTC 59.000 47.619 0.00 0.00 0.00 3.95
28 29 2.093306 TCGATTGCATCTTGTCCGTT 57.907 45.000 0.00 0.00 0.00 4.44
29 30 2.093306 TTCGATTGCATCTTGTCCGT 57.907 45.000 0.00 0.00 0.00 4.69
30 31 3.357021 CATTTCGATTGCATCTTGTCCG 58.643 45.455 0.00 0.00 0.00 4.79
31 32 3.111098 GCATTTCGATTGCATCTTGTCC 58.889 45.455 14.11 0.00 39.90 4.02
32 33 2.780014 CGCATTTCGATTGCATCTTGTC 59.220 45.455 17.75 0.00 40.14 3.18
33 34 2.419673 TCGCATTTCGATTGCATCTTGT 59.580 40.909 17.75 0.00 43.16 3.16
34 35 3.055613 TCGCATTTCGATTGCATCTTG 57.944 42.857 17.75 4.65 43.16 3.02
44 45 2.878991 CTCGCGGTCGCATTTCGA 60.879 61.111 15.68 3.28 46.29 3.71
45 46 2.726691 AACTCGCGGTCGCATTTCG 61.727 57.895 15.68 0.00 42.06 3.46
46 47 1.225745 CAACTCGCGGTCGCATTTC 60.226 57.895 15.68 0.00 42.06 2.17
47 48 2.677003 CCAACTCGCGGTCGCATTT 61.677 57.895 15.68 2.13 42.06 2.32
48 49 3.118454 CCAACTCGCGGTCGCATT 61.118 61.111 15.68 3.71 42.06 3.56
49 50 4.373116 ACCAACTCGCGGTCGCAT 62.373 61.111 15.68 0.00 42.06 4.73
54 55 2.279918 GTGTGACCAACTCGCGGT 60.280 61.111 6.13 0.00 40.30 5.68
55 56 3.403057 CGTGTGACCAACTCGCGG 61.403 66.667 6.13 0.00 40.64 6.46
56 57 3.403057 CCGTGTGACCAACTCGCG 61.403 66.667 0.00 0.00 42.88 5.87
57 58 3.712881 GCCGTGTGACCAACTCGC 61.713 66.667 0.00 0.00 42.88 5.03
58 59 3.041940 GGCCGTGTGACCAACTCG 61.042 66.667 0.00 0.00 43.64 4.18
59 60 3.041940 CGGCCGTGTGACCAACTC 61.042 66.667 19.50 0.00 0.00 3.01
72 73 1.817941 TTTTCTAGATGCGGCGGCC 60.818 57.895 14.25 9.54 38.85 6.13
73 74 1.352056 GTTTTCTAGATGCGGCGGC 59.648 57.895 9.78 9.68 40.52 6.53
74 75 1.762222 CGGTTTTCTAGATGCGGCGG 61.762 60.000 9.78 0.00 0.00 6.13
75 76 1.636340 CGGTTTTCTAGATGCGGCG 59.364 57.895 0.51 0.51 0.00 6.46
76 77 0.461339 TCCGGTTTTCTAGATGCGGC 60.461 55.000 0.00 0.00 0.00 6.53
77 78 1.287425 GTCCGGTTTTCTAGATGCGG 58.713 55.000 0.00 0.00 0.00 5.69
78 79 0.921347 CGTCCGGTTTTCTAGATGCG 59.079 55.000 0.00 0.00 0.00 4.73
79 80 2.288961 TCGTCCGGTTTTCTAGATGC 57.711 50.000 0.00 0.00 0.00 3.91
80 81 3.581755 TGTTCGTCCGGTTTTCTAGATG 58.418 45.455 0.00 0.00 0.00 2.90
81 82 3.947910 TGTTCGTCCGGTTTTCTAGAT 57.052 42.857 0.00 0.00 0.00 1.98
82 83 3.581755 CATGTTCGTCCGGTTTTCTAGA 58.418 45.455 0.00 0.00 0.00 2.43
83 84 2.671396 CCATGTTCGTCCGGTTTTCTAG 59.329 50.000 0.00 0.00 0.00 2.43
84 85 2.037511 ACCATGTTCGTCCGGTTTTCTA 59.962 45.455 0.00 0.00 0.00 2.10
85 86 1.202722 ACCATGTTCGTCCGGTTTTCT 60.203 47.619 0.00 0.00 0.00 2.52
86 87 1.069500 CACCATGTTCGTCCGGTTTTC 60.069 52.381 0.00 0.00 0.00 2.29
87 88 0.948678 CACCATGTTCGTCCGGTTTT 59.051 50.000 0.00 0.00 0.00 2.43
88 89 0.107081 TCACCATGTTCGTCCGGTTT 59.893 50.000 0.00 0.00 0.00 3.27
89 90 0.601841 GTCACCATGTTCGTCCGGTT 60.602 55.000 0.00 0.00 0.00 4.44
90 91 1.005394 GTCACCATGTTCGTCCGGT 60.005 57.895 0.00 0.00 0.00 5.28
91 92 1.740296 GGTCACCATGTTCGTCCGG 60.740 63.158 0.00 0.00 0.00 5.14
92 93 1.740296 GGGTCACCATGTTCGTCCG 60.740 63.158 0.00 0.00 36.50 4.79
93 94 1.373435 TGGGTCACCATGTTCGTCC 59.627 57.895 0.00 0.00 43.37 4.79
103 104 0.752376 TTTGGTCCGTTTGGGTCACC 60.752 55.000 0.00 0.00 37.00 4.02
104 105 1.104630 TTTTGGTCCGTTTGGGTCAC 58.895 50.000 0.00 0.00 37.00 3.67
105 106 1.477295 GTTTTTGGTCCGTTTGGGTCA 59.523 47.619 0.00 0.00 37.00 4.02
106 107 1.477295 TGTTTTTGGTCCGTTTGGGTC 59.523 47.619 0.00 0.00 37.00 4.46
107 108 1.558233 TGTTTTTGGTCCGTTTGGGT 58.442 45.000 0.00 0.00 37.00 4.51
108 109 2.673862 GTTTGTTTTTGGTCCGTTTGGG 59.326 45.455 0.00 0.00 35.24 4.12
109 110 2.345942 CGTTTGTTTTTGGTCCGTTTGG 59.654 45.455 0.00 0.00 0.00 3.28
110 111 2.987821 ACGTTTGTTTTTGGTCCGTTTG 59.012 40.909 0.00 0.00 0.00 2.93
111 112 3.244156 GACGTTTGTTTTTGGTCCGTTT 58.756 40.909 0.00 0.00 0.00 3.60
112 113 2.415759 GGACGTTTGTTTTTGGTCCGTT 60.416 45.455 0.00 0.00 37.96 4.44
113 114 1.132834 GGACGTTTGTTTTTGGTCCGT 59.867 47.619 0.00 0.00 37.96 4.69
114 115 1.830086 GGACGTTTGTTTTTGGTCCG 58.170 50.000 0.00 0.00 37.96 4.79
115 116 1.132834 ACGGACGTTTGTTTTTGGTCC 59.867 47.619 0.00 0.00 42.88 4.46
116 117 2.547913 ACGGACGTTTGTTTTTGGTC 57.452 45.000 0.00 0.00 0.00 4.02
117 118 3.300852 AAACGGACGTTTGTTTTTGGT 57.699 38.095 20.42 0.00 45.34 3.67
140 141 3.365265 CCAACTCCAAGGCACGGC 61.365 66.667 0.00 0.00 0.00 5.68
146 147 1.676967 GCTCAGGCCAACTCCAAGG 60.677 63.158 5.01 0.00 0.00 3.61
147 148 2.037136 CGCTCAGGCCAACTCCAAG 61.037 63.158 5.01 0.00 34.44 3.61
148 149 2.032528 CGCTCAGGCCAACTCCAA 59.967 61.111 5.01 0.00 34.44 3.53
149 150 4.704833 GCGCTCAGGCCAACTCCA 62.705 66.667 5.01 0.00 34.44 3.86
152 153 4.626081 AACGCGCTCAGGCCAACT 62.626 61.111 5.73 0.00 34.44 3.16
153 154 4.389576 CAACGCGCTCAGGCCAAC 62.390 66.667 5.73 0.00 34.44 3.77
154 155 4.617520 TCAACGCGCTCAGGCCAA 62.618 61.111 5.73 0.00 34.44 4.52
155 156 4.617520 TTCAACGCGCTCAGGCCA 62.618 61.111 5.73 0.00 34.44 5.36
156 157 3.314388 CTTTCAACGCGCTCAGGCC 62.314 63.158 5.73 0.00 34.44 5.19
157 158 2.174349 CTTTCAACGCGCTCAGGC 59.826 61.111 5.73 0.00 0.00 4.85
158 159 1.507141 AACCTTTCAACGCGCTCAGG 61.507 55.000 5.73 7.48 0.00 3.86
178 179 2.128035 CTTCAGCTATTTCCGCCTACG 58.872 52.381 0.00 0.00 39.67 3.51
224 225 1.446272 GCGGCACAGGTCTCTACAC 60.446 63.158 0.00 0.00 0.00 2.90
894 895 4.150454 AGAGAGAGGGCGGAGGGG 62.150 72.222 0.00 0.00 0.00 4.79
895 896 2.520741 GAGAGAGAGGGCGGAGGG 60.521 72.222 0.00 0.00 0.00 4.30
896 897 2.520741 GGAGAGAGAGGGCGGAGG 60.521 72.222 0.00 0.00 0.00 4.30
897 898 2.520741 GGGAGAGAGAGGGCGGAG 60.521 72.222 0.00 0.00 0.00 4.63
898 899 4.144727 GGGGAGAGAGAGGGCGGA 62.145 72.222 0.00 0.00 0.00 5.54
900 901 4.465446 TGGGGGAGAGAGAGGGCG 62.465 72.222 0.00 0.00 0.00 6.13
901 902 2.766229 GTGGGGGAGAGAGAGGGC 60.766 72.222 0.00 0.00 0.00 5.19
902 903 1.075600 GAGTGGGGGAGAGAGAGGG 60.076 68.421 0.00 0.00 0.00 4.30
903 904 1.075600 GGAGTGGGGGAGAGAGAGG 60.076 68.421 0.00 0.00 0.00 3.69
904 905 1.454847 CGGAGTGGGGGAGAGAGAG 60.455 68.421 0.00 0.00 0.00 3.20
905 906 2.684104 CGGAGTGGGGGAGAGAGA 59.316 66.667 0.00 0.00 0.00 3.10
906 907 3.151022 GCGGAGTGGGGGAGAGAG 61.151 72.222 0.00 0.00 0.00 3.20
907 908 4.779733 GGCGGAGTGGGGGAGAGA 62.780 72.222 0.00 0.00 0.00 3.10
1144 1145 2.583593 GCAGAGCCCGTCGATGAC 60.584 66.667 6.11 0.00 0.00 3.06
1227 1228 3.973657 AGTCGTGTAAGTAACCACTGTG 58.026 45.455 0.00 0.00 34.36 3.66
1284 1285 2.094894 GTCAAACATCTCCAGTGCATCG 59.905 50.000 0.00 0.00 0.00 3.84
1344 1345 9.334947 CACAAACCATCAATCAGAGAACTATAT 57.665 33.333 0.00 0.00 0.00 0.86
1387 1388 2.497138 CAACAAGTCCAGTGCTGATGA 58.503 47.619 0.02 0.00 0.00 2.92
1405 1406 1.699634 CTCCTTGGTCAACCTCTCCAA 59.300 52.381 0.10 0.00 38.65 3.53
1580 1581 1.030488 CACAGCCCTTCCTGCATCAG 61.030 60.000 0.00 0.00 36.29 2.90
1615 1616 3.349927 CAGCAAGAACCATCTCATCCAA 58.650 45.455 0.00 0.00 33.77 3.53
1840 1841 2.491298 ACAACATGTCAAGCACAACACA 59.509 40.909 0.00 0.00 38.97 3.72
1908 1909 5.731591 ACTTTCTTCTTACTCCAATACCCG 58.268 41.667 0.00 0.00 0.00 5.28
1998 1999 0.249868 GACCAGCACAGTGTAGCACA 60.250 55.000 16.52 0.00 36.74 4.57
2040 2041 1.376683 GTGCATGTGGTCCCGCTTA 60.377 57.895 0.00 0.00 0.00 3.09
2049 2050 2.282674 ACAGCCTGGTGCATGTGG 60.283 61.111 0.00 0.00 44.83 4.17
2144 2146 0.314935 CACTTGTGCAACCCCATGAC 59.685 55.000 0.00 0.00 34.36 3.06
2183 2187 2.437413 GAAGCACTGGAGTTTAAGGGG 58.563 52.381 0.00 0.00 0.00 4.79
2399 2403 3.181480 ACCCTGAACAAACATTTTGGTCG 60.181 43.478 11.13 6.81 38.90 4.79
2429 2433 1.525197 CACGCAGCTTTTAAGTCGTCA 59.475 47.619 0.00 0.00 30.72 4.35
2494 2498 8.348285 TCCAAAATTAACATGTCTAGGAAAGG 57.652 34.615 0.00 0.00 0.00 3.11
2499 2503 9.981114 AGTTTTTCCAAAATTAACATGTCTAGG 57.019 29.630 0.00 0.00 0.00 3.02
2638 2642 0.819259 ATCAAATACGCGGCAGGCAT 60.819 50.000 12.47 0.00 43.84 4.40
2714 2718 9.261180 CATAACATAGGAACAATATGAACTCGT 57.739 33.333 0.24 0.00 35.15 4.18
2745 2749 6.881065 CGGAACCTCATCCATCATGTATATTT 59.119 38.462 0.00 0.00 39.61 1.40
2765 2769 1.112113 TGGCTCTCTATCCACGGAAC 58.888 55.000 0.00 0.00 0.00 3.62
2966 2970 2.034939 CAGAAATGAACAGTGCTGGCAA 59.965 45.455 2.70 0.00 34.19 4.52


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

AutoCloner maintained by Alex Coulton.