Multiple sequence alignment - TraesCS2D01G412400

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 TraesCS2D01G412400 chr2D 100.000 2822 0 0 1 2822 527295067 527292246 0.000000e+00 5212
1 TraesCS2D01G412400 chr2D 95.161 62 3 0 508 569 527294504 527294443 6.430000e-17 99
2 TraesCS2D01G412400 chr2D 95.161 62 3 0 564 625 527294560 527294499 6.430000e-17 99
3 TraesCS2D01G412400 chr2A 89.635 2354 116 51 564 2818 672293169 672290845 0.000000e+00 2878
4 TraesCS2D01G412400 chr2A 92.655 354 20 2 118 465 672293596 672293243 3.240000e-139 505
5 TraesCS2D01G412400 chr2B 92.321 1719 73 24 135 1824 624356627 624354939 0.000000e+00 2388
6 TraesCS2D01G412400 chr2B 94.541 403 16 3 2421 2822 624354297 624353900 3.990000e-173 617
7 TraesCS2D01G412400 chr2B 90.808 359 17 7 1858 2214 624354846 624354502 1.530000e-127 466
8 TraesCS2D01G412400 chr6D 89.961 259 26 0 1285 1543 326540360 326540618 4.500000e-88 335
9 TraesCS2D01G412400 chr6D 86.090 266 34 2 1285 1550 326760711 326760973 1.650000e-72 283
10 TraesCS2D01G412400 chr6B 89.961 259 26 0 1285 1543 495806711 495806453 4.500000e-88 335
11 TraesCS2D01G412400 chr6B 86.466 266 33 2 1285 1550 495543773 495543511 3.560000e-74 289
12 TraesCS2D01G412400 chr6A 89.961 259 26 0 1285 1543 465231917 465232175 4.500000e-88 335
13 TraesCS2D01G412400 chr6A 88.618 246 28 0 1285 1530 465389787 465390032 1.640000e-77 300
14 TraesCS2D01G412400 chr1A 86.364 264 31 4 1283 1542 388849402 388849664 1.650000e-72 283


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 TraesCS2D01G412400 chr2D 527292246 527295067 2821 True 1803.333333 5212 96.774000 1 2822 3 chr2D.!!$R1 2821
1 TraesCS2D01G412400 chr2A 672290845 672293596 2751 True 1691.500000 2878 91.145000 118 2818 2 chr2A.!!$R1 2700
2 TraesCS2D01G412400 chr2B 624353900 624356627 2727 True 1157.000000 2388 92.556667 135 2822 3 chr2B.!!$R1 2687

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
555 604 0.184692 TGACCAATTGACTGCACCCA 59.815 50.0 7.12 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2266 2426 0.753262 AACAGTCCACAGTTCGCTCT 59.247 50.0 0.0 0.0 0.0 4.09 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 3.763097 CACATGCGGTGTATCATTTGT 57.237 42.857 0.00 0.00 42.75 2.83
21 22 4.095410 CACATGCGGTGTATCATTTGTT 57.905 40.909 0.00 0.00 42.75 2.83
22 23 5.228579 CACATGCGGTGTATCATTTGTTA 57.771 39.130 0.00 0.00 42.75 2.41
23 24 5.027737 CACATGCGGTGTATCATTTGTTAC 58.972 41.667 0.00 0.00 42.75 2.50
24 25 4.095782 ACATGCGGTGTATCATTTGTTACC 59.904 41.667 0.00 0.00 39.91 2.85
25 26 3.676093 TGCGGTGTATCATTTGTTACCA 58.324 40.909 0.00 0.00 0.00 3.25
26 27 3.437395 TGCGGTGTATCATTTGTTACCAC 59.563 43.478 0.00 0.00 0.00 4.16
27 28 3.181504 GCGGTGTATCATTTGTTACCACC 60.182 47.826 0.00 0.00 0.00 4.61
28 29 4.004314 CGGTGTATCATTTGTTACCACCA 58.996 43.478 0.00 0.00 30.56 4.17
29 30 4.638421 CGGTGTATCATTTGTTACCACCAT 59.362 41.667 0.00 0.00 30.56 3.55
30 31 5.818336 CGGTGTATCATTTGTTACCACCATA 59.182 40.000 0.00 0.00 30.56 2.74
31 32 6.485313 CGGTGTATCATTTGTTACCACCATAT 59.515 38.462 0.00 0.00 30.56 1.78
32 33 7.012894 CGGTGTATCATTTGTTACCACCATATT 59.987 37.037 0.00 0.00 30.56 1.28
33 34 8.691797 GGTGTATCATTTGTTACCACCATATTT 58.308 33.333 0.00 0.00 30.56 1.40
34 35 9.730420 GTGTATCATTTGTTACCACCATATTTC 57.270 33.333 0.00 0.00 0.00 2.17
35 36 9.467796 TGTATCATTTGTTACCACCATATTTCA 57.532 29.630 0.00 0.00 0.00 2.69
38 39 8.586879 TCATTTGTTACCACCATATTTCATGA 57.413 30.769 0.00 0.00 0.00 3.07
39 40 8.685427 TCATTTGTTACCACCATATTTCATGAG 58.315 33.333 0.00 0.00 0.00 2.90
40 41 8.685427 CATTTGTTACCACCATATTTCATGAGA 58.315 33.333 0.00 0.00 0.00 3.27
41 42 7.864108 TTGTTACCACCATATTTCATGAGAG 57.136 36.000 0.00 0.00 0.00 3.20
42 43 6.957631 TGTTACCACCATATTTCATGAGAGT 58.042 36.000 0.00 0.00 0.00 3.24
43 44 6.823182 TGTTACCACCATATTTCATGAGAGTG 59.177 38.462 0.00 0.00 0.00 3.51
44 45 5.698741 ACCACCATATTTCATGAGAGTGA 57.301 39.130 0.00 0.00 0.00 3.41
45 46 5.431765 ACCACCATATTTCATGAGAGTGAC 58.568 41.667 0.00 0.00 0.00 3.67
46 47 4.818546 CCACCATATTTCATGAGAGTGACC 59.181 45.833 0.00 0.00 0.00 4.02
47 48 5.397221 CCACCATATTTCATGAGAGTGACCT 60.397 44.000 0.00 0.00 0.00 3.85
48 49 6.118170 CACCATATTTCATGAGAGTGACCTT 58.882 40.000 0.00 0.00 0.00 3.50
49 50 6.600822 CACCATATTTCATGAGAGTGACCTTT 59.399 38.462 0.00 0.00 0.00 3.11
50 51 6.600822 ACCATATTTCATGAGAGTGACCTTTG 59.399 38.462 0.00 0.00 0.00 2.77
51 52 6.459298 CCATATTTCATGAGAGTGACCTTTGC 60.459 42.308 0.00 0.00 0.00 3.68
52 53 3.490439 TTCATGAGAGTGACCTTTGCA 57.510 42.857 0.00 0.00 0.00 4.08
53 54 3.049708 TCATGAGAGTGACCTTTGCAG 57.950 47.619 0.00 0.00 0.00 4.41
55 56 1.423584 TGAGAGTGACCTTTGCAGGA 58.576 50.000 0.00 0.00 44.19 3.86
56 57 1.345741 TGAGAGTGACCTTTGCAGGAG 59.654 52.381 0.00 0.00 44.19 3.69
57 58 0.689623 AGAGTGACCTTTGCAGGAGG 59.310 55.000 14.70 14.70 44.19 4.30
58 59 0.322008 GAGTGACCTTTGCAGGAGGG 60.322 60.000 18.98 4.28 44.19 4.30
59 60 1.303643 GTGACCTTTGCAGGAGGGG 60.304 63.158 18.98 6.96 44.19 4.79
60 61 1.774217 TGACCTTTGCAGGAGGGGT 60.774 57.895 18.98 9.68 44.19 4.95
61 62 0.474854 TGACCTTTGCAGGAGGGGTA 60.475 55.000 18.98 5.55 44.19 3.69
62 63 0.919710 GACCTTTGCAGGAGGGGTAT 59.080 55.000 18.98 1.94 44.19 2.73
63 64 0.919710 ACCTTTGCAGGAGGGGTATC 59.080 55.000 18.98 0.00 44.19 2.24
64 65 1.216990 CCTTTGCAGGAGGGGTATCT 58.783 55.000 9.71 0.00 44.19 1.98
65 66 1.133976 CCTTTGCAGGAGGGGTATCTG 60.134 57.143 9.71 0.00 44.19 2.90
66 67 0.918983 TTTGCAGGAGGGGTATCTGG 59.081 55.000 0.00 0.00 0.00 3.86
67 68 0.253160 TTGCAGGAGGGGTATCTGGT 60.253 55.000 0.00 0.00 0.00 4.00
68 69 0.253160 TGCAGGAGGGGTATCTGGTT 60.253 55.000 0.00 0.00 0.00 3.67
69 70 0.919710 GCAGGAGGGGTATCTGGTTT 59.080 55.000 0.00 0.00 0.00 3.27
70 71 1.285078 GCAGGAGGGGTATCTGGTTTT 59.715 52.381 0.00 0.00 0.00 2.43
71 72 2.684038 GCAGGAGGGGTATCTGGTTTTC 60.684 54.545 0.00 0.00 0.00 2.29
72 73 2.846827 CAGGAGGGGTATCTGGTTTTCT 59.153 50.000 0.00 0.00 0.00 2.52
73 74 4.037927 CAGGAGGGGTATCTGGTTTTCTA 58.962 47.826 0.00 0.00 0.00 2.10
74 75 4.101741 CAGGAGGGGTATCTGGTTTTCTAG 59.898 50.000 0.00 0.00 0.00 2.43
75 76 4.038633 GGAGGGGTATCTGGTTTTCTAGT 58.961 47.826 0.00 0.00 0.00 2.57
76 77 4.141688 GGAGGGGTATCTGGTTTTCTAGTG 60.142 50.000 0.00 0.00 0.00 2.74
77 78 4.695606 AGGGGTATCTGGTTTTCTAGTGA 58.304 43.478 0.00 0.00 0.00 3.41
78 79 5.289510 AGGGGTATCTGGTTTTCTAGTGAT 58.710 41.667 0.00 0.00 0.00 3.06
79 80 5.731678 AGGGGTATCTGGTTTTCTAGTGATT 59.268 40.000 0.00 0.00 0.00 2.57
80 81 6.217693 AGGGGTATCTGGTTTTCTAGTGATTT 59.782 38.462 0.00 0.00 0.00 2.17
81 82 6.890268 GGGGTATCTGGTTTTCTAGTGATTTT 59.110 38.462 0.00 0.00 0.00 1.82
82 83 7.067129 GGGGTATCTGGTTTTCTAGTGATTTTC 59.933 40.741 0.00 0.00 0.00 2.29
83 84 7.201617 GGGTATCTGGTTTTCTAGTGATTTTCG 60.202 40.741 0.00 0.00 0.00 3.46
84 85 6.743575 ATCTGGTTTTCTAGTGATTTTCGG 57.256 37.500 0.00 0.00 0.00 4.30
85 86 5.001232 TCTGGTTTTCTAGTGATTTTCGGG 58.999 41.667 0.00 0.00 0.00 5.14
86 87 4.721132 TGGTTTTCTAGTGATTTTCGGGT 58.279 39.130 0.00 0.00 0.00 5.28
87 88 5.134661 TGGTTTTCTAGTGATTTTCGGGTT 58.865 37.500 0.00 0.00 0.00 4.11
88 89 5.595133 TGGTTTTCTAGTGATTTTCGGGTTT 59.405 36.000 0.00 0.00 0.00 3.27
89 90 6.147581 GGTTTTCTAGTGATTTTCGGGTTTC 58.852 40.000 0.00 0.00 0.00 2.78
90 91 6.016527 GGTTTTCTAGTGATTTTCGGGTTTCT 60.017 38.462 0.00 0.00 0.00 2.52
91 92 6.796705 TTTCTAGTGATTTTCGGGTTTCTC 57.203 37.500 0.00 0.00 0.00 2.87
92 93 4.491676 TCTAGTGATTTTCGGGTTTCTCG 58.508 43.478 0.00 0.00 0.00 4.04
93 94 3.396260 AGTGATTTTCGGGTTTCTCGA 57.604 42.857 0.00 0.00 34.62 4.04
94 95 3.939066 AGTGATTTTCGGGTTTCTCGAT 58.061 40.909 0.00 0.00 36.49 3.59
95 96 5.080969 AGTGATTTTCGGGTTTCTCGATA 57.919 39.130 0.00 0.00 36.49 2.92
96 97 5.671493 AGTGATTTTCGGGTTTCTCGATAT 58.329 37.500 0.00 0.00 36.49 1.63
97 98 5.523916 AGTGATTTTCGGGTTTCTCGATATG 59.476 40.000 0.00 0.00 36.49 1.78
98 99 5.522460 GTGATTTTCGGGTTTCTCGATATGA 59.478 40.000 0.00 0.00 36.49 2.15
99 100 6.202954 GTGATTTTCGGGTTTCTCGATATGAT 59.797 38.462 0.00 0.00 36.49 2.45
100 101 5.984233 TTTTCGGGTTTCTCGATATGATG 57.016 39.130 0.00 0.00 36.49 3.07
101 102 4.929819 TTCGGGTTTCTCGATATGATGA 57.070 40.909 0.00 0.00 36.49 2.92
102 103 5.468540 TTCGGGTTTCTCGATATGATGAT 57.531 39.130 0.00 0.00 36.49 2.45
103 104 5.060662 TCGGGTTTCTCGATATGATGATC 57.939 43.478 0.00 0.00 0.00 2.92
104 105 4.767409 TCGGGTTTCTCGATATGATGATCT 59.233 41.667 0.00 0.00 0.00 2.75
105 106 4.861462 CGGGTTTCTCGATATGATGATCTG 59.139 45.833 0.00 0.00 0.00 2.90
106 107 5.174395 GGGTTTCTCGATATGATGATCTGG 58.826 45.833 0.00 0.00 0.00 3.86
107 108 5.174395 GGTTTCTCGATATGATGATCTGGG 58.826 45.833 0.00 0.00 0.00 4.45
108 109 5.279708 GGTTTCTCGATATGATGATCTGGGT 60.280 44.000 0.00 0.00 0.00 4.51
109 110 5.397142 TTCTCGATATGATGATCTGGGTG 57.603 43.478 0.00 0.00 0.00 4.61
110 111 3.766051 TCTCGATATGATGATCTGGGTGG 59.234 47.826 0.00 0.00 0.00 4.61
111 112 2.833943 TCGATATGATGATCTGGGTGGG 59.166 50.000 0.00 0.00 0.00 4.61
112 113 2.568956 CGATATGATGATCTGGGTGGGT 59.431 50.000 0.00 0.00 0.00 4.51
113 114 3.618263 CGATATGATGATCTGGGTGGGTG 60.618 52.174 0.00 0.00 0.00 4.61
114 115 1.600058 ATGATGATCTGGGTGGGTGT 58.400 50.000 0.00 0.00 0.00 4.16
115 116 1.371467 TGATGATCTGGGTGGGTGTT 58.629 50.000 0.00 0.00 0.00 3.32
116 117 1.710244 TGATGATCTGGGTGGGTGTTT 59.290 47.619 0.00 0.00 0.00 2.83
195 201 3.826729 AGGAAACCATGGTAGAGTTTTGC 59.173 43.478 20.12 12.86 34.00 3.68
199 205 4.098914 ACCATGGTAGAGTTTTGCTCAA 57.901 40.909 18.10 0.00 46.47 3.02
208 214 7.669722 TGGTAGAGTTTTGCTCAATAGGATTTT 59.330 33.333 0.00 0.00 46.47 1.82
296 312 7.658982 TCATGCTATCACTATCCAATCAAGTTC 59.341 37.037 0.00 0.00 0.00 3.01
345 362 1.233019 CCAATCTGACGATGATGCCC 58.767 55.000 0.00 0.00 0.00 5.36
395 412 6.176183 AGCAGATTCTACAAGCAAATAGTGT 58.824 36.000 0.00 0.00 0.00 3.55
398 415 7.201679 GCAGATTCTACAAGCAAATAGTGTCAT 60.202 37.037 0.00 0.00 0.00 3.06
462 507 5.069318 TCACATGCTGTTTCAATGGTTAGA 58.931 37.500 0.00 0.00 0.00 2.10
467 512 7.933033 ACATGCTGTTTCAATGGTTAGAAATTT 59.067 29.630 0.00 0.00 36.29 1.82
475 520 8.761575 TTCAATGGTTAGAAATTTCATTCTGC 57.238 30.769 19.99 4.28 39.87 4.26
477 522 8.587608 TCAATGGTTAGAAATTTCATTCTGCTT 58.412 29.630 19.99 0.00 39.87 3.91
502 551 6.237901 AGTAAACCAGTTGATTGTAGCATGA 58.762 36.000 0.00 0.00 0.00 3.07
527 576 7.962964 TTTAAATACAGTTCAGTGACCTCTG 57.037 36.000 13.98 13.98 36.85 3.35
552 601 7.384660 TGATTTTAATTGACCAATTGACTGCAC 59.615 33.333 15.90 4.89 40.83 4.57
555 604 0.184692 TGACCAATTGACTGCACCCA 59.815 50.000 7.12 0.00 0.00 4.51
590 639 4.985538 AGTTCAGTGGCCTCTGATTTTAA 58.014 39.130 32.19 17.91 42.84 1.52
769 838 4.580167 TCAATCCTCACTTCACCTTGTTTG 59.420 41.667 0.00 0.00 0.00 2.93
776 845 7.776030 TCCTCACTTCACCTTGTTTGTTTAATA 59.224 33.333 0.00 0.00 0.00 0.98
862 931 3.060978 AGGAAAACAAACGAAACGCTC 57.939 42.857 0.00 0.00 0.00 5.03
956 1025 0.955919 CCAAGTCCCCACGCTTCTTC 60.956 60.000 0.00 0.00 0.00 2.87
992 1061 1.153005 GGCCTTCAGATCCCTGCTG 60.153 63.158 0.00 0.00 40.20 4.41
1240 1309 3.112709 GCAGCACCGACGAAGACC 61.113 66.667 0.00 0.00 0.00 3.85
1632 1719 4.459089 GAGTCACCGGAGCCTGCC 62.459 72.222 9.46 0.00 0.00 4.85
1824 1911 0.970937 TCTTGTGGGCCGAGTAGGAG 60.971 60.000 0.00 0.00 45.00 3.69
1826 1913 1.541310 TTGTGGGCCGAGTAGGAGTG 61.541 60.000 0.00 0.00 45.00 3.51
1828 1915 1.229082 TGGGCCGAGTAGGAGTGTT 60.229 57.895 0.00 0.00 45.00 3.32
1831 1918 1.271217 GGGCCGAGTAGGAGTGTTTTT 60.271 52.381 0.00 0.00 45.00 1.94
1856 1954 8.856153 TTTTACTGTACCTCATGAATTGCTTA 57.144 30.769 0.00 0.00 0.00 3.09
1859 1957 4.842574 TGTACCTCATGAATTGCTTAGCA 58.157 39.130 1.39 1.39 36.47 3.49
1884 2029 7.787725 AGGATAAAAAGATTTAGTGGTAGCG 57.212 36.000 0.00 0.00 34.62 4.26
2196 2346 4.763793 GGTGATATTCATATGCTGTTGCCT 59.236 41.667 0.00 0.00 38.71 4.75
2244 2395 0.885196 TTTATGGCCGGTGAAACAGC 59.115 50.000 1.90 0.00 39.98 4.40
2266 2426 5.068987 AGCTACAAGCAAGAAAATCAAACCA 59.931 36.000 1.22 0.00 45.56 3.67
2291 2451 2.287915 CGAACTGTGGACTGTTTCCTTG 59.712 50.000 3.87 0.00 46.10 3.61
2295 2455 0.954452 GTGGACTGTTTCCTTGCTGG 59.046 55.000 0.00 0.00 46.10 4.85
2328 2488 1.815003 GTTTGGCAGTGAGGAATGGAG 59.185 52.381 0.00 0.00 0.00 3.86
2392 2555 4.082679 AGGTGCACTTTTAACGAACAAACA 60.083 37.500 17.98 0.00 0.00 2.83
2393 2556 4.621886 GGTGCACTTTTAACGAACAAACAA 59.378 37.500 17.98 0.00 0.00 2.83
2419 2582 3.393089 TTTCCACAGAGCTCTGACTTC 57.607 47.619 42.76 4.57 46.59 3.01
2475 2678 3.240310 TCTCTAGAATTACGGAGGGGG 57.760 52.381 0.00 0.00 0.00 5.40
2566 2780 4.035612 AGGTGAAGTACTGAGCTGTAGA 57.964 45.455 0.00 0.00 0.00 2.59
2567 2781 4.408276 AGGTGAAGTACTGAGCTGTAGAA 58.592 43.478 0.00 0.00 0.00 2.10
2568 2782 4.461081 AGGTGAAGTACTGAGCTGTAGAAG 59.539 45.833 0.00 0.00 0.00 2.85
2569 2783 4.381079 GGTGAAGTACTGAGCTGTAGAAGG 60.381 50.000 0.00 0.00 0.00 3.46
2760 3001 2.593346 AAAACGCAAAGCCAATGACA 57.407 40.000 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.095782 GGTAACAAATGATACACCGCATGT 59.904 41.667 0.00 0.00 46.06 3.21
2 3 4.597079 GGTAACAAATGATACACCGCATG 58.403 43.478 3.70 0.00 0.00 4.06
3 4 4.893424 GGTAACAAATGATACACCGCAT 57.107 40.909 3.70 0.00 0.00 4.73
19 20 7.011482 GTCACTCTCATGAAATATGGTGGTAAC 59.989 40.741 0.00 0.00 0.00 2.50
20 21 7.047891 GTCACTCTCATGAAATATGGTGGTAA 58.952 38.462 0.00 0.00 0.00 2.85
21 22 6.408092 GGTCACTCTCATGAAATATGGTGGTA 60.408 42.308 0.00 0.00 0.00 3.25
22 23 5.431765 GTCACTCTCATGAAATATGGTGGT 58.568 41.667 0.00 0.00 0.00 4.16
23 24 4.818546 GGTCACTCTCATGAAATATGGTGG 59.181 45.833 0.00 0.00 0.00 4.61
24 25 5.678583 AGGTCACTCTCATGAAATATGGTG 58.321 41.667 0.00 0.62 0.00 4.17
25 26 5.965033 AGGTCACTCTCATGAAATATGGT 57.035 39.130 0.00 0.00 0.00 3.55
26 27 6.459298 GCAAAGGTCACTCTCATGAAATATGG 60.459 42.308 0.00 0.00 0.00 2.74
27 28 6.094464 TGCAAAGGTCACTCTCATGAAATATG 59.906 38.462 0.00 0.00 0.00 1.78
28 29 6.182627 TGCAAAGGTCACTCTCATGAAATAT 58.817 36.000 0.00 0.00 0.00 1.28
29 30 5.559770 TGCAAAGGTCACTCTCATGAAATA 58.440 37.500 0.00 0.00 0.00 1.40
30 31 4.401022 TGCAAAGGTCACTCTCATGAAAT 58.599 39.130 0.00 0.00 0.00 2.17
31 32 3.817084 CTGCAAAGGTCACTCTCATGAAA 59.183 43.478 0.00 0.00 0.00 2.69
32 33 3.405831 CTGCAAAGGTCACTCTCATGAA 58.594 45.455 0.00 0.00 0.00 2.57
33 34 2.289882 CCTGCAAAGGTCACTCTCATGA 60.290 50.000 0.00 0.00 0.00 3.07
34 35 2.082231 CCTGCAAAGGTCACTCTCATG 58.918 52.381 0.00 0.00 0.00 3.07
35 36 1.980765 TCCTGCAAAGGTCACTCTCAT 59.019 47.619 0.00 0.00 0.00 2.90
36 37 1.345741 CTCCTGCAAAGGTCACTCTCA 59.654 52.381 0.00 0.00 0.00 3.27
37 38 1.338579 CCTCCTGCAAAGGTCACTCTC 60.339 57.143 6.63 0.00 0.00 3.20
38 39 0.689623 CCTCCTGCAAAGGTCACTCT 59.310 55.000 6.63 0.00 0.00 3.24
39 40 0.322008 CCCTCCTGCAAAGGTCACTC 60.322 60.000 12.56 0.00 31.51 3.51
40 41 1.763770 CCCTCCTGCAAAGGTCACT 59.236 57.895 12.56 0.00 31.51 3.41
41 42 1.303643 CCCCTCCTGCAAAGGTCAC 60.304 63.158 12.56 0.00 31.51 3.67
42 43 0.474854 TACCCCTCCTGCAAAGGTCA 60.475 55.000 12.56 0.00 31.51 4.02
43 44 0.919710 ATACCCCTCCTGCAAAGGTC 59.080 55.000 12.56 0.00 31.51 3.85
44 45 0.919710 GATACCCCTCCTGCAAAGGT 59.080 55.000 12.56 6.14 31.51 3.50
45 46 1.133976 CAGATACCCCTCCTGCAAAGG 60.134 57.143 7.67 7.67 0.00 3.11
46 47 1.133976 CCAGATACCCCTCCTGCAAAG 60.134 57.143 0.00 0.00 0.00 2.77
47 48 0.918983 CCAGATACCCCTCCTGCAAA 59.081 55.000 0.00 0.00 0.00 3.68
48 49 0.253160 ACCAGATACCCCTCCTGCAA 60.253 55.000 0.00 0.00 0.00 4.08
49 50 0.253160 AACCAGATACCCCTCCTGCA 60.253 55.000 0.00 0.00 0.00 4.41
50 51 0.919710 AAACCAGATACCCCTCCTGC 59.080 55.000 0.00 0.00 0.00 4.85
51 52 2.846827 AGAAAACCAGATACCCCTCCTG 59.153 50.000 0.00 0.00 0.00 3.86
52 53 3.222394 AGAAAACCAGATACCCCTCCT 57.778 47.619 0.00 0.00 0.00 3.69
53 54 4.038633 ACTAGAAAACCAGATACCCCTCC 58.961 47.826 0.00 0.00 0.00 4.30
54 55 4.715297 TCACTAGAAAACCAGATACCCCTC 59.285 45.833 0.00 0.00 0.00 4.30
55 56 4.695606 TCACTAGAAAACCAGATACCCCT 58.304 43.478 0.00 0.00 0.00 4.79
56 57 5.632034 ATCACTAGAAAACCAGATACCCC 57.368 43.478 0.00 0.00 0.00 4.95
57 58 7.201617 CGAAAATCACTAGAAAACCAGATACCC 60.202 40.741 0.00 0.00 0.00 3.69
58 59 7.201617 CCGAAAATCACTAGAAAACCAGATACC 60.202 40.741 0.00 0.00 0.00 2.73
59 60 7.201617 CCCGAAAATCACTAGAAAACCAGATAC 60.202 40.741 0.00 0.00 0.00 2.24
60 61 6.821665 CCCGAAAATCACTAGAAAACCAGATA 59.178 38.462 0.00 0.00 0.00 1.98
61 62 5.648092 CCCGAAAATCACTAGAAAACCAGAT 59.352 40.000 0.00 0.00 0.00 2.90
62 63 5.001232 CCCGAAAATCACTAGAAAACCAGA 58.999 41.667 0.00 0.00 0.00 3.86
63 64 4.760204 ACCCGAAAATCACTAGAAAACCAG 59.240 41.667 0.00 0.00 0.00 4.00
64 65 4.721132 ACCCGAAAATCACTAGAAAACCA 58.279 39.130 0.00 0.00 0.00 3.67
65 66 5.700722 AACCCGAAAATCACTAGAAAACC 57.299 39.130 0.00 0.00 0.00 3.27
66 67 6.967135 AGAAACCCGAAAATCACTAGAAAAC 58.033 36.000 0.00 0.00 0.00 2.43
67 68 6.073440 CGAGAAACCCGAAAATCACTAGAAAA 60.073 38.462 0.00 0.00 0.00 2.29
68 69 5.407387 CGAGAAACCCGAAAATCACTAGAAA 59.593 40.000 0.00 0.00 0.00 2.52
69 70 4.927425 CGAGAAACCCGAAAATCACTAGAA 59.073 41.667 0.00 0.00 0.00 2.10
70 71 4.219070 TCGAGAAACCCGAAAATCACTAGA 59.781 41.667 0.00 0.00 32.64 2.43
71 72 4.491676 TCGAGAAACCCGAAAATCACTAG 58.508 43.478 0.00 0.00 32.64 2.57
72 73 4.524316 TCGAGAAACCCGAAAATCACTA 57.476 40.909 0.00 0.00 32.64 2.74
73 74 3.396260 TCGAGAAACCCGAAAATCACT 57.604 42.857 0.00 0.00 32.64 3.41
74 75 5.522460 TCATATCGAGAAACCCGAAAATCAC 59.478 40.000 0.00 0.00 39.62 3.06
75 76 5.666462 TCATATCGAGAAACCCGAAAATCA 58.334 37.500 0.00 0.00 39.62 2.57
76 77 6.423905 TCATCATATCGAGAAACCCGAAAATC 59.576 38.462 0.00 0.00 39.62 2.17
77 78 6.288294 TCATCATATCGAGAAACCCGAAAAT 58.712 36.000 0.00 0.00 39.62 1.82
78 79 5.666462 TCATCATATCGAGAAACCCGAAAA 58.334 37.500 0.00 0.00 39.62 2.29
79 80 5.270893 TCATCATATCGAGAAACCCGAAA 57.729 39.130 0.00 0.00 39.62 3.46
80 81 4.929819 TCATCATATCGAGAAACCCGAA 57.070 40.909 0.00 0.00 39.62 4.30
81 82 4.767409 AGATCATCATATCGAGAAACCCGA 59.233 41.667 0.00 0.00 40.53 5.14
82 83 4.861462 CAGATCATCATATCGAGAAACCCG 59.139 45.833 0.00 0.00 0.00 5.28
83 84 5.174395 CCAGATCATCATATCGAGAAACCC 58.826 45.833 0.00 0.00 0.00 4.11
84 85 5.174395 CCCAGATCATCATATCGAGAAACC 58.826 45.833 0.00 0.00 0.00 3.27
85 86 5.636965 CACCCAGATCATCATATCGAGAAAC 59.363 44.000 0.00 0.00 0.00 2.78
86 87 5.279657 CCACCCAGATCATCATATCGAGAAA 60.280 44.000 0.00 0.00 0.00 2.52
87 88 4.221482 CCACCCAGATCATCATATCGAGAA 59.779 45.833 0.00 0.00 0.00 2.87
88 89 3.766051 CCACCCAGATCATCATATCGAGA 59.234 47.826 0.00 0.00 0.00 4.04
89 90 3.118847 CCCACCCAGATCATCATATCGAG 60.119 52.174 0.00 0.00 0.00 4.04
90 91 2.833943 CCCACCCAGATCATCATATCGA 59.166 50.000 0.00 0.00 0.00 3.59
91 92 2.568956 ACCCACCCAGATCATCATATCG 59.431 50.000 0.00 0.00 0.00 2.92
92 93 3.328931 ACACCCACCCAGATCATCATATC 59.671 47.826 0.00 0.00 0.00 1.63
93 94 3.330198 ACACCCACCCAGATCATCATAT 58.670 45.455 0.00 0.00 0.00 1.78
94 95 2.775418 ACACCCACCCAGATCATCATA 58.225 47.619 0.00 0.00 0.00 2.15
95 96 1.600058 ACACCCACCCAGATCATCAT 58.400 50.000 0.00 0.00 0.00 2.45
96 97 1.371467 AACACCCACCCAGATCATCA 58.629 50.000 0.00 0.00 0.00 3.07
97 98 2.514458 AAACACCCACCCAGATCATC 57.486 50.000 0.00 0.00 0.00 2.92
98 99 2.999185 AAAACACCCACCCAGATCAT 57.001 45.000 0.00 0.00 0.00 2.45
99 100 2.765689 AAAAACACCCACCCAGATCA 57.234 45.000 0.00 0.00 0.00 2.92
167 168 9.462606 AAAACTCTACCATGGTTTCCTATAAAG 57.537 33.333 25.38 11.01 32.89 1.85
175 176 4.518970 TGAGCAAAACTCTACCATGGTTTC 59.481 41.667 25.38 0.00 46.41 2.78
179 185 5.297776 CCTATTGAGCAAAACTCTACCATGG 59.702 44.000 11.19 11.19 46.41 3.66
208 214 9.884636 TCGGAAACTAATTGAGATCTTTTATGA 57.115 29.630 0.00 0.00 0.00 2.15
296 312 1.452108 GTTCATCGGAGCCCCCTTG 60.452 63.158 0.00 0.00 0.00 3.61
345 362 1.219393 GCTTGTTCTCCTCCTCCCG 59.781 63.158 0.00 0.00 0.00 5.14
395 412 7.207383 ACACGTCTGATTCGGATTTATTATGA 58.793 34.615 0.00 0.00 0.00 2.15
398 415 7.436080 GGTAACACGTCTGATTCGGATTTATTA 59.564 37.037 0.00 0.00 0.00 0.98
475 520 7.667043 TGCTACAATCAACTGGTTTACTAAG 57.333 36.000 0.00 0.00 0.00 2.18
477 522 7.390823 TCATGCTACAATCAACTGGTTTACTA 58.609 34.615 0.00 0.00 0.00 1.82
479 524 6.494893 TCATGCTACAATCAACTGGTTTAC 57.505 37.500 0.00 0.00 0.00 2.01
502 551 8.375506 TCAGAGGTCACTGAACTGTATTTAAAT 58.624 33.333 0.00 5.89 42.79 1.40
527 576 7.148590 GGTGCAGTCAATTGGTCAATTAAAATC 60.149 37.037 5.42 1.22 38.84 2.17
552 601 4.460382 ACTGAACTTTATTCATGTGCTGGG 59.540 41.667 0.00 0.00 0.00 4.45
555 604 4.082571 GCCACTGAACTTTATTCATGTGCT 60.083 41.667 0.00 0.00 31.96 4.40
590 639 3.433343 TGGATGCAGTCAATTGGTCAAT 58.567 40.909 5.42 0.00 0.00 2.57
826 895 5.119434 TGTTTTCCTTTCTTTTTCAACGTGC 59.881 36.000 0.00 0.00 0.00 5.34
862 931 4.567318 GCTGGGGCCATTGAGTAG 57.433 61.111 4.39 0.00 0.00 2.57
924 993 1.007359 GGACTTGGGGGAGTAGAGAGT 59.993 57.143 0.00 0.00 0.00 3.24
1803 1890 1.258445 CCTACTCGGCCCACAAGAGT 61.258 60.000 13.77 13.77 45.85 3.24
1831 1918 7.759489 AAGCAATTCATGAGGTACAGTAAAA 57.241 32.000 0.00 0.00 0.00 1.52
1834 1921 6.049149 GCTAAGCAATTCATGAGGTACAGTA 58.951 40.000 0.00 0.00 0.00 2.74
1836 1923 4.877823 TGCTAAGCAATTCATGAGGTACAG 59.122 41.667 0.00 0.00 34.76 2.74
1838 1925 5.818136 TTGCTAAGCAATTCATGAGGTAC 57.182 39.130 0.00 0.00 43.99 3.34
1856 1954 9.178758 CTACCACTAAATCTTTTTATCCTTGCT 57.821 33.333 0.00 0.00 0.00 3.91
1859 1957 7.282450 CCGCTACCACTAAATCTTTTTATCCTT 59.718 37.037 0.00 0.00 0.00 3.36
1862 1960 7.549615 ACCGCTACCACTAAATCTTTTTATC 57.450 36.000 0.00 0.00 0.00 1.75
1863 1961 7.226128 GCTACCGCTACCACTAAATCTTTTTAT 59.774 37.037 0.00 0.00 0.00 1.40
2217 2368 1.129811 CACCGGCCATAAAACGACTTC 59.870 52.381 0.00 0.00 0.00 3.01
2244 2395 6.738114 TCTGGTTTGATTTTCTTGCTTGTAG 58.262 36.000 0.00 0.00 0.00 2.74
2266 2426 0.753262 AACAGTCCACAGTTCGCTCT 59.247 50.000 0.00 0.00 0.00 4.09
2291 2451 2.844122 AACTCGTTTGTGAAACCAGC 57.156 45.000 0.00 0.00 38.14 4.85
2295 2455 2.851824 CTGCCAAACTCGTTTGTGAAAC 59.148 45.455 18.12 6.02 46.19 2.78
2328 2488 5.444218 GCAGTATAACACGCTAACACAAGAC 60.444 44.000 0.00 0.00 0.00 3.01
2392 2555 4.287067 TCAGAGCTCTGTGGAAATTAGGTT 59.713 41.667 36.32 0.00 44.12 3.50
2393 2556 3.840666 TCAGAGCTCTGTGGAAATTAGGT 59.159 43.478 36.32 0.00 44.12 3.08
2419 2582 1.989165 GACGTAAGAGCAGCAAGAGTG 59.011 52.381 0.00 0.00 43.62 3.51
2475 2678 6.183360 GCATTGGAGTAGTGTGTAAGATTTCC 60.183 42.308 0.00 0.00 0.00 3.13
2476 2679 6.183360 GGCATTGGAGTAGTGTGTAAGATTTC 60.183 42.308 0.00 0.00 0.00 2.17
2479 2682 4.225042 TGGCATTGGAGTAGTGTGTAAGAT 59.775 41.667 0.00 0.00 0.00 2.40
2480 2683 3.580895 TGGCATTGGAGTAGTGTGTAAGA 59.419 43.478 0.00 0.00 0.00 2.10
2481 2684 3.937814 TGGCATTGGAGTAGTGTGTAAG 58.062 45.455 0.00 0.00 0.00 2.34
2484 2687 2.158682 TGTTGGCATTGGAGTAGTGTGT 60.159 45.455 0.00 0.00 0.00 3.72
2485 2688 2.503331 TGTTGGCATTGGAGTAGTGTG 58.497 47.619 0.00 0.00 0.00 3.82
2486 2689 2.949177 TGTTGGCATTGGAGTAGTGT 57.051 45.000 0.00 0.00 0.00 3.55
2487 2690 2.424601 CCATGTTGGCATTGGAGTAGTG 59.575 50.000 5.90 0.00 31.99 2.74
2488 2691 2.726821 CCATGTTGGCATTGGAGTAGT 58.273 47.619 5.90 0.00 31.99 2.73
2566 2780 4.322057 AACCCAGCAAAGATATGACCTT 57.678 40.909 0.00 0.00 0.00 3.50
2567 2781 4.019174 CAAACCCAGCAAAGATATGACCT 58.981 43.478 0.00 0.00 0.00 3.85
2568 2782 3.131046 CCAAACCCAGCAAAGATATGACC 59.869 47.826 0.00 0.00 0.00 4.02
2569 2783 3.763897 ACCAAACCCAGCAAAGATATGAC 59.236 43.478 0.00 0.00 0.00 3.06
2664 2893 5.504853 ACTTTCTTTGATCCTTCCATCTCC 58.495 41.667 0.00 0.00 0.00 3.71
2665 2894 6.094742 GGAACTTTCTTTGATCCTTCCATCTC 59.905 42.308 0.00 0.00 0.00 2.75
2760 3001 4.529769 GTGTACCTAACTCCTAACCTGGTT 59.470 45.833 17.44 17.44 0.00 3.67


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

AutoCloner maintained by Alex Coulton.