Multiple sequence alignment - TraesCS4D01G115900

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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 TraesCS4D01G115900 chr4D 100.000 3570 0 0 1 3570 96899051 96895482 0.000000e+00 6593.0
1 TraesCS4D01G115900 chr4D 96.616 1980 21 9 242 2183 96731116 96729145 0.000000e+00 3243.0
2 TraesCS4D01G115900 chr4D 90.000 140 12 2 3432 3570 96720557 96720419 2.830000e-41 180.0
3 TraesCS4D01G115900 chr4A 93.975 2058 72 13 142 2183 479424396 479426417 0.000000e+00 3066.0
4 TraesCS4D01G115900 chr4A 89.080 1978 128 52 234 2183 480550933 480552850 0.000000e+00 2375.0
5 TraesCS4D01G115900 chr4A 95.219 1255 28 7 2316 3551 481059897 481061138 0.000000e+00 1956.0
6 TraesCS4D01G115900 chr4A 91.056 1364 76 14 234 1581 481042806 481044139 0.000000e+00 1801.0
7 TraesCS4D01G115900 chr4A 95.867 750 20 3 1577 2318 481059099 481059845 0.000000e+00 1203.0
8 TraesCS4D01G115900 chr4A 94.364 550 26 3 1515 2064 479598425 479598969 0.000000e+00 839.0
9 TraesCS4D01G115900 chr4A 93.648 551 31 2 1514 2064 480561924 480562470 0.000000e+00 821.0
10 TraesCS4D01G115900 chr4A 92.629 502 29 4 1563 2064 479725691 479726184 0.000000e+00 715.0
11 TraesCS4D01G115900 chr4A 93.886 458 24 2 1607 2064 479930305 479930758 0.000000e+00 688.0
12 TraesCS4D01G115900 chr4A 91.549 142 4 1 2050 2183 479612036 479612177 4.710000e-44 189.0
13 TraesCS4D01G115900 chr4A 88.571 140 14 2 3432 3570 479427753 479427891 6.130000e-38 169.0
14 TraesCS4D01G115900 chr4A 87.143 140 16 2 3432 3570 479613483 479613621 1.330000e-34 158.0
15 TraesCS4D01G115900 chr4A 95.050 101 4 1 142 241 481012513 481012613 1.330000e-34 158.0
16 TraesCS4D01G115900 chr4A 97.753 89 2 0 2095 2183 479895608 479895696 1.720000e-33 154.0
17 TraesCS4D01G115900 chr4A 94.059 101 5 1 142 241 480550721 480550821 6.170000e-33 152.0
18 TraesCS4D01G115900 chr4A 81.395 129 13 3 2585 2702 479427296 479427424 1.060000e-15 95.3
19 TraesCS4D01G115900 chr4A 81.250 128 13 3 2586 2702 480553724 480553851 3.790000e-15 93.5
20 TraesCS4D01G115900 chr4A 80.469 128 14 5 2586 2702 479613053 479613180 1.770000e-13 87.9
21 TraesCS4D01G115900 chr4B 86.962 1534 81 74 234 1710 138283790 138282319 0.000000e+00 1615.0
22 TraesCS4D01G115900 chr4B 86.605 1523 88 69 234 1710 137707865 137706413 0.000000e+00 1576.0
23 TraesCS4D01G115900 chr4B 84.969 479 40 16 2399 2846 138281312 138280835 1.170000e-124 457.0
24 TraesCS4D01G115900 chr4B 88.514 296 8 8 1749 2041 137706408 137706136 5.710000e-88 335.0
25 TraesCS4D01G115900 chr4B 90.204 245 8 4 3012 3256 138280735 138280507 4.480000e-79 305.0
26 TraesCS4D01G115900 chr4B 96.988 166 2 1 3257 3419 138280362 138280197 3.510000e-70 276.0
27 TraesCS4D01G115900 chr4B 88.119 101 10 2 3471 3570 138280194 138280095 6.260000e-23 119.0
28 TraesCS4D01G115900 chrUn 90.891 999 36 30 234 1208 413236153 413235186 0.000000e+00 1290.0
29 TraesCS4D01G115900 chr3D 91.273 275 14 2 1917 2183 328974276 328974004 2.030000e-97 366.0
30 TraesCS4D01G115900 chr3B 91.273 275 14 2 1917 2183 426309525 426309253 2.030000e-97 366.0
31 TraesCS4D01G115900 chr3A 91.273 275 14 2 1917 2183 443816110 443815838 2.030000e-97 366.0
32 TraesCS4D01G115900 chr1A 92.857 56 1 2 3 58 561277407 561277355 1.060000e-10 78.7
33 TraesCS4D01G115900 chr1B 100.000 39 0 0 92 130 72834075 72834037 4.940000e-09 73.1
34 TraesCS4D01G115900 chr2D 97.059 34 0 1 2779 2812 489007124 489007092 4.980000e-04 56.5


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 TraesCS4D01G115900 chr4D 96895482 96899051 3569 True 6593.0 6593 100.000000 1 3570 1 chr4D.!!$R3 3569
1 TraesCS4D01G115900 chr4D 96729145 96731116 1971 True 3243.0 3243 96.616000 242 2183 1 chr4D.!!$R2 1941
2 TraesCS4D01G115900 chr4A 481042806 481044139 1333 False 1801.0 1801 91.056000 234 1581 1 chr4A.!!$F7 1347
3 TraesCS4D01G115900 chr4A 481059099 481061138 2039 False 1579.5 1956 95.543000 1577 3551 2 chr4A.!!$F11 1974
4 TraesCS4D01G115900 chr4A 479424396 479427891 3495 False 1110.1 3066 87.980333 142 3570 3 chr4A.!!$F8 3428
5 TraesCS4D01G115900 chr4A 480550721 480553851 3130 False 873.5 2375 88.129667 142 2702 3 chr4A.!!$F10 2560
6 TraesCS4D01G115900 chr4A 479598425 479598969 544 False 839.0 839 94.364000 1515 2064 1 chr4A.!!$F1 549
7 TraesCS4D01G115900 chr4A 480561924 480562470 546 False 821.0 821 93.648000 1514 2064 1 chr4A.!!$F5 550
8 TraesCS4D01G115900 chr4B 137706136 137707865 1729 True 955.5 1576 87.559500 234 2041 2 chr4B.!!$R1 1807
9 TraesCS4D01G115900 chr4B 138280095 138283790 3695 True 554.4 1615 89.448400 234 3570 5 chr4B.!!$R2 3336
10 TraesCS4D01G115900 chrUn 413235186 413236153 967 True 1290.0 1290 90.891000 234 1208 1 chrUn.!!$R1 974

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
333 454 0.161024 GTTTCGTTTCGTCGAGCAGG 59.839 55.0 0.0 0.0 40.86 4.85 F
763 917 0.687354 GTGCCCAACCAGAGAGAGAA 59.313 55.0 0.0 0.0 0.00 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1633 1872 2.919859 GCATGATCGATCGTACCTCATG 59.080 50.000 27.96 27.96 43.76 3.07 R
2671 3543 3.259123 ACCAAAGGCCATTCACAAGATTC 59.741 43.478 5.01 0.00 0.00 2.52 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
28 29 9.938280 AAGTACAACTAATATGTAGAACAAGCA 57.062 29.630 0.00 0.00 34.14 3.91
32 33 9.102757 ACAACTAATATGTAGAACAAGCATCTG 57.897 33.333 0.00 0.00 0.00 2.90
33 34 7.721286 ACTAATATGTAGAACAAGCATCTGC 57.279 36.000 0.00 0.00 42.49 4.26
34 35 7.275183 ACTAATATGTAGAACAAGCATCTGCA 58.725 34.615 4.79 0.00 42.43 4.41
38 39 5.801350 TGTAGAACAAGCATCTGCATAAC 57.199 39.130 4.79 0.00 45.16 1.89
39 40 5.491070 TGTAGAACAAGCATCTGCATAACT 58.509 37.500 4.79 0.56 45.16 2.24
40 41 6.639563 TGTAGAACAAGCATCTGCATAACTA 58.360 36.000 4.79 0.00 45.16 2.24
41 42 6.758416 TGTAGAACAAGCATCTGCATAACTAG 59.242 38.462 4.79 0.00 45.16 2.57
42 43 5.738909 AGAACAAGCATCTGCATAACTAGT 58.261 37.500 4.79 0.00 45.16 2.57
43 44 5.814705 AGAACAAGCATCTGCATAACTAGTC 59.185 40.000 4.79 0.00 45.16 2.59
44 45 5.350504 ACAAGCATCTGCATAACTAGTCT 57.649 39.130 4.79 0.00 45.16 3.24
45 46 5.114780 ACAAGCATCTGCATAACTAGTCTG 58.885 41.667 4.79 0.00 45.16 3.51
46 47 3.726607 AGCATCTGCATAACTAGTCTGC 58.273 45.455 18.71 18.71 45.16 4.26
47 48 2.805099 GCATCTGCATAACTAGTCTGCC 59.195 50.000 21.28 7.51 41.59 4.85
48 49 3.742327 GCATCTGCATAACTAGTCTGCCA 60.742 47.826 21.28 12.21 41.59 4.92
49 50 4.445453 CATCTGCATAACTAGTCTGCCAA 58.555 43.478 21.28 13.01 35.02 4.52
50 51 3.861840 TCTGCATAACTAGTCTGCCAAC 58.138 45.455 21.28 2.39 35.02 3.77
51 52 3.260632 TCTGCATAACTAGTCTGCCAACA 59.739 43.478 21.28 7.56 35.02 3.33
52 53 4.002982 CTGCATAACTAGTCTGCCAACAA 58.997 43.478 21.28 7.28 35.02 2.83
53 54 4.002982 TGCATAACTAGTCTGCCAACAAG 58.997 43.478 21.28 0.00 35.02 3.16
54 55 3.181506 GCATAACTAGTCTGCCAACAAGC 60.182 47.826 15.97 0.00 0.00 4.01
55 56 2.638480 AACTAGTCTGCCAACAAGCA 57.362 45.000 0.00 0.00 41.46 3.91
56 57 2.867109 ACTAGTCTGCCAACAAGCAT 57.133 45.000 0.00 0.00 43.09 3.79
57 58 2.704572 ACTAGTCTGCCAACAAGCATC 58.295 47.619 0.00 0.00 43.09 3.91
58 59 2.012673 CTAGTCTGCCAACAAGCATCC 58.987 52.381 0.00 0.00 43.09 3.51
59 60 0.957395 AGTCTGCCAACAAGCATCCG 60.957 55.000 0.00 0.00 43.09 4.18
60 61 2.180017 CTGCCAACAAGCATCCGC 59.820 61.111 0.00 0.00 43.09 5.54
61 62 2.596923 TGCCAACAAGCATCCGCA 60.597 55.556 0.00 0.00 42.27 5.69
62 63 2.144833 CTGCCAACAAGCATCCGCAA 62.145 55.000 0.00 0.00 43.09 4.85
63 64 1.006337 GCCAACAAGCATCCGCAAA 60.006 52.632 0.00 0.00 42.27 3.68
64 65 0.599728 GCCAACAAGCATCCGCAAAA 60.600 50.000 0.00 0.00 42.27 2.44
65 66 1.421382 CCAACAAGCATCCGCAAAAG 58.579 50.000 0.00 0.00 42.27 2.27
66 67 1.000385 CCAACAAGCATCCGCAAAAGA 60.000 47.619 0.00 0.00 42.27 2.52
67 68 2.545532 CCAACAAGCATCCGCAAAAGAA 60.546 45.455 0.00 0.00 42.27 2.52
68 69 2.712057 ACAAGCATCCGCAAAAGAAG 57.288 45.000 0.00 0.00 42.27 2.85
69 70 1.956477 ACAAGCATCCGCAAAAGAAGT 59.044 42.857 0.00 0.00 42.27 3.01
70 71 3.146066 ACAAGCATCCGCAAAAGAAGTA 58.854 40.909 0.00 0.00 42.27 2.24
71 72 3.058224 ACAAGCATCCGCAAAAGAAGTAC 60.058 43.478 0.00 0.00 42.27 2.73
72 73 2.778299 AGCATCCGCAAAAGAAGTACA 58.222 42.857 0.00 0.00 42.27 2.90
73 74 3.146066 AGCATCCGCAAAAGAAGTACAA 58.854 40.909 0.00 0.00 42.27 2.41
74 75 3.058224 AGCATCCGCAAAAGAAGTACAAC 60.058 43.478 0.00 0.00 42.27 3.32
75 76 3.058224 GCATCCGCAAAAGAAGTACAACT 60.058 43.478 0.00 0.00 38.36 3.16
76 77 4.153475 GCATCCGCAAAAGAAGTACAACTA 59.847 41.667 0.00 0.00 38.36 2.24
77 78 5.334569 GCATCCGCAAAAGAAGTACAACTAA 60.335 40.000 0.00 0.00 38.36 2.24
78 79 6.664515 CATCCGCAAAAGAAGTACAACTAAA 58.335 36.000 0.00 0.00 0.00 1.85
79 80 6.870971 TCCGCAAAAGAAGTACAACTAAAT 57.129 33.333 0.00 0.00 0.00 1.40
80 81 7.266922 TCCGCAAAAGAAGTACAACTAAATT 57.733 32.000 0.00 0.00 0.00 1.82
81 82 7.136119 TCCGCAAAAGAAGTACAACTAAATTG 58.864 34.615 0.00 2.76 44.60 2.32
96 97 6.183309 ACTAAATTGTAACAAGCAGCTAGC 57.817 37.500 6.62 6.62 46.19 3.42
97 98 7.784910 CAACTAAATTGTAACAAGCAGCTAGCA 60.785 37.037 18.83 0.00 38.54 3.49
109 110 3.330267 GCAGCTAGCAAGTTCAACTAGT 58.670 45.455 18.83 0.00 44.79 2.57
110 111 3.369451 GCAGCTAGCAAGTTCAACTAGTC 59.631 47.826 18.83 0.00 44.79 2.59
111 112 3.929610 CAGCTAGCAAGTTCAACTAGTCC 59.070 47.826 18.83 0.00 36.57 3.85
112 113 3.578716 AGCTAGCAAGTTCAACTAGTCCA 59.421 43.478 18.83 0.00 36.57 4.02
113 114 4.040461 AGCTAGCAAGTTCAACTAGTCCAA 59.960 41.667 18.83 0.00 36.57 3.53
114 115 4.938226 GCTAGCAAGTTCAACTAGTCCAAT 59.062 41.667 10.63 0.00 36.57 3.16
115 116 5.412904 GCTAGCAAGTTCAACTAGTCCAATT 59.587 40.000 10.63 0.00 36.57 2.32
116 117 5.948992 AGCAAGTTCAACTAGTCCAATTC 57.051 39.130 0.00 0.00 0.00 2.17
117 118 5.376625 AGCAAGTTCAACTAGTCCAATTCA 58.623 37.500 0.00 0.00 0.00 2.57
118 119 5.827797 AGCAAGTTCAACTAGTCCAATTCAA 59.172 36.000 0.00 0.00 0.00 2.69
119 120 6.491403 AGCAAGTTCAACTAGTCCAATTCAAT 59.509 34.615 0.00 0.00 0.00 2.57
120 121 7.014615 AGCAAGTTCAACTAGTCCAATTCAATT 59.985 33.333 0.00 0.00 0.00 2.32
121 122 7.115378 GCAAGTTCAACTAGTCCAATTCAATTG 59.885 37.037 2.80 2.80 39.94 2.32
122 123 7.823745 AGTTCAACTAGTCCAATTCAATTGT 57.176 32.000 9.31 0.00 38.59 2.71
123 124 8.237811 AGTTCAACTAGTCCAATTCAATTGTT 57.762 30.769 9.31 0.00 38.59 2.83
124 125 8.137437 AGTTCAACTAGTCCAATTCAATTGTTG 58.863 33.333 9.31 6.06 38.59 3.33
125 126 7.815840 TCAACTAGTCCAATTCAATTGTTGA 57.184 32.000 9.31 8.13 38.59 3.18
126 127 8.408043 TCAACTAGTCCAATTCAATTGTTGAT 57.592 30.769 9.31 0.00 39.84 2.57
127 128 8.514594 TCAACTAGTCCAATTCAATTGTTGATC 58.485 33.333 9.31 1.32 39.84 2.92
128 129 7.076842 ACTAGTCCAATTCAATTGTTGATCG 57.923 36.000 9.31 0.00 39.84 3.69
129 130 6.878923 ACTAGTCCAATTCAATTGTTGATCGA 59.121 34.615 9.31 0.00 39.84 3.59
130 131 5.942872 AGTCCAATTCAATTGTTGATCGAC 58.057 37.500 9.31 6.11 39.84 4.20
131 132 5.473162 AGTCCAATTCAATTGTTGATCGACA 59.527 36.000 11.98 11.98 39.84 4.35
132 133 5.796935 GTCCAATTCAATTGTTGATCGACAG 59.203 40.000 15.36 5.31 39.84 3.51
133 134 4.560035 CCAATTCAATTGTTGATCGACAGC 59.440 41.667 15.36 0.00 39.84 4.40
134 135 5.396484 CAATTCAATTGTTGATCGACAGCT 58.604 37.500 15.36 5.31 39.84 4.24
135 136 6.403527 CCAATTCAATTGTTGATCGACAGCTA 60.404 38.462 15.36 2.24 39.84 3.32
136 137 5.784750 TTCAATTGTTGATCGACAGCTAG 57.215 39.130 15.36 7.92 39.84 3.42
137 138 4.183865 TCAATTGTTGATCGACAGCTAGG 58.816 43.478 15.36 6.06 34.08 3.02
138 139 2.672961 TTGTTGATCGACAGCTAGGG 57.327 50.000 15.36 0.00 0.00 3.53
139 140 1.847328 TGTTGATCGACAGCTAGGGA 58.153 50.000 11.98 0.00 0.00 4.20
140 141 1.751351 TGTTGATCGACAGCTAGGGAG 59.249 52.381 11.98 0.00 0.00 4.30
333 454 0.161024 GTTTCGTTTCGTCGAGCAGG 59.839 55.000 0.00 0.00 40.86 4.85
763 917 0.687354 GTGCCCAACCAGAGAGAGAA 59.313 55.000 0.00 0.00 0.00 2.87
1633 1872 1.743996 GGACAGGAACAAGGATGAGC 58.256 55.000 0.00 0.00 0.00 4.26
2020 2270 2.752903 TCGATCTTGATGAAGTGACCGA 59.247 45.455 0.00 0.00 0.00 4.69
2184 2504 7.907389 AGAATGTGTATCTTTCCTTAGTGTCA 58.093 34.615 0.00 0.00 32.70 3.58
2454 3242 6.374053 TCTTTTCAGATTGATCGCCATAACAA 59.626 34.615 0.00 0.00 0.00 2.83
2534 3322 2.487986 GCCAATAAGAGGGACATCCAGG 60.488 54.545 0.00 0.00 38.24 4.45
2671 3543 4.378459 GCTGTTTGGAGAATTTGGTACGAG 60.378 45.833 0.00 0.00 0.00 4.18
2726 3598 6.901887 GCATGTACGAAAATCACTATGACAAG 59.098 38.462 0.00 0.00 0.00 3.16
2766 3638 5.049818 GCAGTATACATGTCAAAGCTGGATC 60.050 44.000 0.00 0.00 0.00 3.36
2957 3834 4.591038 CATGAGGGGATGCATGCA 57.409 55.556 25.04 25.04 35.93 3.96
2958 3835 3.051617 CATGAGGGGATGCATGCAT 57.948 52.632 32.66 32.66 39.69 3.96
2959 3836 0.603065 CATGAGGGGATGCATGCATG 59.397 55.000 36.73 22.70 36.70 4.06
2960 3837 0.481128 ATGAGGGGATGCATGCATGA 59.519 50.000 36.73 15.31 36.70 3.07
3027 3913 8.596380 GTTAGTAATCTGTCTCATGTTAACTGC 58.404 37.037 7.22 0.00 0.00 4.40
3139 4025 5.334646 CGATTTGGTAATCATCTGCCTCATG 60.335 44.000 0.00 0.00 40.17 3.07
3148 4034 3.943381 TCATCTGCCTCATGTCATTTGAC 59.057 43.478 3.72 3.72 44.97 3.18
3162 4048 6.851222 GTCATTTGACACGATCCTATCATT 57.149 37.500 5.84 0.00 44.18 2.57
3414 4451 5.478407 ACACTTCTTTTCCCACAACAAAAG 58.522 37.500 0.00 0.00 39.84 2.27
3427 4473 4.317291 CACAACAAAAGTAAATACGCGCTC 59.683 41.667 5.73 0.00 0.00 5.03
3430 4476 3.091417 CAAAAGTAAATACGCGCTCTGC 58.909 45.455 5.73 0.00 41.47 4.26
3526 4572 8.643324 GGACCTTACATAATGTCTCTGAACTAT 58.357 37.037 6.91 0.00 33.26 2.12
3559 4605 9.866655 ACTTATCATAGGGATTAAAAGCATCAA 57.133 29.630 0.00 0.00 37.44 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.102757 CAGATGCTTGTTCTACATATTAGTTGT 57.897 33.333 0.00 0.00 0.00 3.32
7 8 8.066595 GCAGATGCTTGTTCTACATATTAGTTG 58.933 37.037 0.00 0.00 38.21 3.16
8 9 7.770433 TGCAGATGCTTGTTCTACATATTAGTT 59.230 33.333 6.35 0.00 42.66 2.24
9 10 7.275183 TGCAGATGCTTGTTCTACATATTAGT 58.725 34.615 6.35 0.00 42.66 2.24
10 11 7.719778 TGCAGATGCTTGTTCTACATATTAG 57.280 36.000 6.35 0.00 42.66 1.73
11 12 9.777297 TTATGCAGATGCTTGTTCTACATATTA 57.223 29.630 6.35 0.00 42.66 0.98
12 13 8.562892 GTTATGCAGATGCTTGTTCTACATATT 58.437 33.333 6.35 0.00 42.66 1.28
13 14 7.935755 AGTTATGCAGATGCTTGTTCTACATAT 59.064 33.333 6.35 0.00 42.66 1.78
14 15 7.275183 AGTTATGCAGATGCTTGTTCTACATA 58.725 34.615 6.35 0.00 42.66 2.29
15 16 6.118170 AGTTATGCAGATGCTTGTTCTACAT 58.882 36.000 6.35 0.00 42.66 2.29
16 17 5.491070 AGTTATGCAGATGCTTGTTCTACA 58.509 37.500 6.35 0.00 42.66 2.74
17 18 6.758886 ACTAGTTATGCAGATGCTTGTTCTAC 59.241 38.462 6.35 0.00 42.66 2.59
18 19 6.878317 ACTAGTTATGCAGATGCTTGTTCTA 58.122 36.000 6.35 4.48 42.66 2.10
19 20 5.738909 ACTAGTTATGCAGATGCTTGTTCT 58.261 37.500 6.35 3.66 42.66 3.01
20 21 5.814705 AGACTAGTTATGCAGATGCTTGTTC 59.185 40.000 6.35 0.00 42.66 3.18
21 22 5.583854 CAGACTAGTTATGCAGATGCTTGTT 59.416 40.000 6.35 0.00 42.66 2.83
22 23 5.114780 CAGACTAGTTATGCAGATGCTTGT 58.885 41.667 6.35 0.00 42.66 3.16
23 24 4.025061 GCAGACTAGTTATGCAGATGCTTG 60.025 45.833 22.32 0.00 42.66 4.01
24 25 4.125703 GCAGACTAGTTATGCAGATGCTT 58.874 43.478 22.32 2.33 42.66 3.91
25 26 3.494048 GGCAGACTAGTTATGCAGATGCT 60.494 47.826 26.10 2.68 41.78 3.79
26 27 2.805099 GGCAGACTAGTTATGCAGATGC 59.195 50.000 26.10 13.87 41.78 3.91
27 28 4.063998 TGGCAGACTAGTTATGCAGATG 57.936 45.455 26.10 6.98 41.78 2.90
28 29 4.080919 TGTTGGCAGACTAGTTATGCAGAT 60.081 41.667 26.10 0.00 41.78 2.90
29 30 3.260632 TGTTGGCAGACTAGTTATGCAGA 59.739 43.478 26.10 15.72 41.78 4.26
30 31 3.599343 TGTTGGCAGACTAGTTATGCAG 58.401 45.455 26.10 2.65 41.78 4.41
31 32 3.694043 TGTTGGCAGACTAGTTATGCA 57.306 42.857 26.10 14.82 41.78 3.96
32 33 3.181506 GCTTGTTGGCAGACTAGTTATGC 60.182 47.826 20.21 20.21 39.25 3.14
33 34 4.002982 TGCTTGTTGGCAGACTAGTTATG 58.997 43.478 0.00 0.36 37.29 1.90
34 35 4.286297 TGCTTGTTGGCAGACTAGTTAT 57.714 40.909 0.00 0.00 37.29 1.89
35 36 3.762407 TGCTTGTTGGCAGACTAGTTA 57.238 42.857 0.00 2.28 37.29 2.24
36 37 2.638480 TGCTTGTTGGCAGACTAGTT 57.362 45.000 0.00 0.00 37.29 2.24
37 38 2.616510 GGATGCTTGTTGGCAGACTAGT 60.617 50.000 0.00 0.00 45.75 2.57
38 39 2.012673 GGATGCTTGTTGGCAGACTAG 58.987 52.381 0.00 0.00 45.75 2.57
39 40 1.675714 CGGATGCTTGTTGGCAGACTA 60.676 52.381 0.00 0.00 45.75 2.59
40 41 0.957395 CGGATGCTTGTTGGCAGACT 60.957 55.000 0.00 0.00 45.75 3.24
41 42 1.503542 CGGATGCTTGTTGGCAGAC 59.496 57.895 0.00 0.00 45.75 3.51
42 43 2.334946 GCGGATGCTTGTTGGCAGA 61.335 57.895 0.00 0.00 45.75 4.26
43 44 2.144833 TTGCGGATGCTTGTTGGCAG 62.145 55.000 0.00 0.00 45.75 4.85
44 45 1.742324 TTTGCGGATGCTTGTTGGCA 61.742 50.000 0.00 0.00 46.63 4.92
45 46 0.599728 TTTTGCGGATGCTTGTTGGC 60.600 50.000 0.00 0.00 43.34 4.52
46 47 1.000385 TCTTTTGCGGATGCTTGTTGG 60.000 47.619 0.00 0.00 43.34 3.77
47 48 2.420628 TCTTTTGCGGATGCTTGTTG 57.579 45.000 0.00 0.00 43.34 3.33
48 49 2.362077 ACTTCTTTTGCGGATGCTTGTT 59.638 40.909 0.00 0.00 43.34 2.83
49 50 1.956477 ACTTCTTTTGCGGATGCTTGT 59.044 42.857 0.00 0.00 43.34 3.16
50 51 2.712057 ACTTCTTTTGCGGATGCTTG 57.288 45.000 0.00 0.00 43.34 4.01
51 52 3.146066 TGTACTTCTTTTGCGGATGCTT 58.854 40.909 0.00 0.00 43.34 3.91
52 53 2.778299 TGTACTTCTTTTGCGGATGCT 58.222 42.857 0.00 0.00 43.34 3.79
53 54 3.058224 AGTTGTACTTCTTTTGCGGATGC 60.058 43.478 0.00 0.00 43.20 3.91
54 55 4.749245 AGTTGTACTTCTTTTGCGGATG 57.251 40.909 0.00 0.00 0.00 3.51
55 56 6.870971 TTTAGTTGTACTTCTTTTGCGGAT 57.129 33.333 0.00 0.00 0.00 4.18
56 57 6.870971 ATTTAGTTGTACTTCTTTTGCGGA 57.129 33.333 0.00 0.00 0.00 5.54
57 58 7.320499 CAATTTAGTTGTACTTCTTTTGCGG 57.680 36.000 0.00 0.00 33.01 5.69
70 71 7.785197 GCTAGCTGCTTGTTACAATTTAGTTGT 60.785 37.037 7.79 0.00 45.01 3.32
71 72 6.524586 GCTAGCTGCTTGTTACAATTTAGTTG 59.475 38.462 7.79 0.00 40.14 3.16
72 73 6.206634 TGCTAGCTGCTTGTTACAATTTAGTT 59.793 34.615 17.23 0.00 43.37 2.24
73 74 5.705441 TGCTAGCTGCTTGTTACAATTTAGT 59.295 36.000 17.23 0.00 43.37 2.24
74 75 6.182039 TGCTAGCTGCTTGTTACAATTTAG 57.818 37.500 17.23 0.00 43.37 1.85
75 76 6.206634 ACTTGCTAGCTGCTTGTTACAATTTA 59.793 34.615 17.23 0.00 43.37 1.40
76 77 5.010012 ACTTGCTAGCTGCTTGTTACAATTT 59.990 36.000 17.23 0.00 43.37 1.82
77 78 4.520492 ACTTGCTAGCTGCTTGTTACAATT 59.480 37.500 17.23 0.00 43.37 2.32
78 79 4.074970 ACTTGCTAGCTGCTTGTTACAAT 58.925 39.130 17.23 0.00 43.37 2.71
79 80 3.476552 ACTTGCTAGCTGCTTGTTACAA 58.523 40.909 17.23 5.07 43.37 2.41
80 81 3.126001 ACTTGCTAGCTGCTTGTTACA 57.874 42.857 17.23 0.00 43.37 2.41
81 82 3.498397 TGAACTTGCTAGCTGCTTGTTAC 59.502 43.478 17.23 8.18 43.37 2.50
82 83 3.738982 TGAACTTGCTAGCTGCTTGTTA 58.261 40.909 17.23 0.00 43.37 2.41
83 84 2.575532 TGAACTTGCTAGCTGCTTGTT 58.424 42.857 17.23 12.60 43.37 2.83
84 85 2.260844 TGAACTTGCTAGCTGCTTGT 57.739 45.000 17.23 4.70 43.37 3.16
85 86 2.551459 AGTTGAACTTGCTAGCTGCTTG 59.449 45.455 17.23 7.19 43.37 4.01
86 87 2.856222 AGTTGAACTTGCTAGCTGCTT 58.144 42.857 17.23 3.66 43.37 3.91
87 88 2.557920 AGTTGAACTTGCTAGCTGCT 57.442 45.000 17.23 7.57 43.37 4.24
88 89 3.330267 ACTAGTTGAACTTGCTAGCTGC 58.670 45.455 17.23 0.00 43.25 5.25
89 90 3.929610 GGACTAGTTGAACTTGCTAGCTG 59.070 47.826 17.23 11.26 36.57 4.24
90 91 3.578716 TGGACTAGTTGAACTTGCTAGCT 59.421 43.478 17.23 0.00 36.57 3.32
91 92 3.926616 TGGACTAGTTGAACTTGCTAGC 58.073 45.455 8.10 8.10 36.57 3.42
92 93 6.650807 TGAATTGGACTAGTTGAACTTGCTAG 59.349 38.462 1.97 0.00 38.43 3.42
93 94 6.530120 TGAATTGGACTAGTTGAACTTGCTA 58.470 36.000 1.97 0.00 0.00 3.49
94 95 5.376625 TGAATTGGACTAGTTGAACTTGCT 58.623 37.500 1.97 0.00 0.00 3.91
95 96 5.689383 TGAATTGGACTAGTTGAACTTGC 57.311 39.130 1.97 0.00 0.00 4.01
96 97 8.137437 ACAATTGAATTGGACTAGTTGAACTTG 58.863 33.333 20.69 3.87 44.42 3.16
97 98 8.237811 ACAATTGAATTGGACTAGTTGAACTT 57.762 30.769 20.69 0.00 44.42 2.66
98 99 7.823745 ACAATTGAATTGGACTAGTTGAACT 57.176 32.000 20.69 2.37 44.42 3.01
99 100 8.134895 TCAACAATTGAATTGGACTAGTTGAAC 58.865 33.333 20.69 0.00 44.42 3.18
100 101 8.231692 TCAACAATTGAATTGGACTAGTTGAA 57.768 30.769 20.69 4.55 44.42 2.69
101 102 7.815840 TCAACAATTGAATTGGACTAGTTGA 57.184 32.000 20.69 16.06 44.42 3.18
102 103 7.482743 CGATCAACAATTGAATTGGACTAGTTG 59.517 37.037 20.69 14.31 43.95 3.16
103 104 7.390440 TCGATCAACAATTGAATTGGACTAGTT 59.610 33.333 20.69 3.49 43.95 2.24
104 105 6.878923 TCGATCAACAATTGAATTGGACTAGT 59.121 34.615 20.69 0.00 43.95 2.57
105 106 7.148423 TGTCGATCAACAATTGAATTGGACTAG 60.148 37.037 20.69 8.52 43.95 2.57
106 107 6.652900 TGTCGATCAACAATTGAATTGGACTA 59.347 34.615 20.69 5.17 43.95 2.59
107 108 5.473162 TGTCGATCAACAATTGAATTGGACT 59.527 36.000 20.69 3.61 43.95 3.85
108 109 5.698832 TGTCGATCAACAATTGAATTGGAC 58.301 37.500 20.69 16.11 43.95 4.02
109 110 5.619757 GCTGTCGATCAACAATTGAATTGGA 60.620 40.000 20.69 10.42 43.95 3.53
110 111 4.560035 GCTGTCGATCAACAATTGAATTGG 59.440 41.667 20.69 5.48 43.95 3.16
111 112 5.396484 AGCTGTCGATCAACAATTGAATTG 58.604 37.500 15.82 15.82 43.95 2.32
112 113 5.633830 AGCTGTCGATCAACAATTGAATT 57.366 34.783 13.59 0.00 43.95 2.17
113 114 5.295292 CCTAGCTGTCGATCAACAATTGAAT 59.705 40.000 13.59 2.44 43.95 2.57
114 115 4.631377 CCTAGCTGTCGATCAACAATTGAA 59.369 41.667 13.59 0.00 43.95 2.69
115 116 4.183865 CCTAGCTGTCGATCAACAATTGA 58.816 43.478 13.59 0.00 45.01 2.57
116 117 3.310774 CCCTAGCTGTCGATCAACAATTG 59.689 47.826 3.24 3.24 0.00 2.32
117 118 3.197766 TCCCTAGCTGTCGATCAACAATT 59.802 43.478 0.00 0.00 0.00 2.32
118 119 2.766263 TCCCTAGCTGTCGATCAACAAT 59.234 45.455 0.00 0.00 0.00 2.71
119 120 2.166459 CTCCCTAGCTGTCGATCAACAA 59.834 50.000 0.00 0.00 0.00 2.83
120 121 1.751351 CTCCCTAGCTGTCGATCAACA 59.249 52.381 0.00 0.00 0.00 3.33
121 122 1.751924 ACTCCCTAGCTGTCGATCAAC 59.248 52.381 0.00 0.00 0.00 3.18
122 123 2.025155 GACTCCCTAGCTGTCGATCAA 58.975 52.381 0.00 0.00 0.00 2.57
123 124 1.681538 GACTCCCTAGCTGTCGATCA 58.318 55.000 0.00 0.00 0.00 2.92
124 125 0.955905 GGACTCCCTAGCTGTCGATC 59.044 60.000 0.00 0.00 0.00 3.69
125 126 0.468400 GGGACTCCCTAGCTGTCGAT 60.468 60.000 6.90 0.00 41.34 3.59
126 127 1.076923 GGGACTCCCTAGCTGTCGA 60.077 63.158 6.90 0.00 41.34 4.20
127 128 3.527641 GGGACTCCCTAGCTGTCG 58.472 66.667 6.90 0.00 41.34 4.35
149 150 3.556999 TCTGCCTATGAGAGTACTGGTC 58.443 50.000 0.00 0.00 0.00 4.02
203 204 2.978978 TCCAAGACTCATTCAAGGTCCA 59.021 45.455 0.00 0.00 0.00 4.02
374 495 0.764752 CTCCTCCCCCTCATACCCAC 60.765 65.000 0.00 0.00 0.00 4.61
375 496 1.632164 CTCCTCCCCCTCATACCCA 59.368 63.158 0.00 0.00 0.00 4.51
376 497 1.152008 CCTCCTCCCCCTCATACCC 60.152 68.421 0.00 0.00 0.00 3.69
377 498 0.472161 GACCTCCTCCCCCTCATACC 60.472 65.000 0.00 0.00 0.00 2.73
675 819 9.631452 CCAACCATTTTCTTCTCTTTTATCTTC 57.369 33.333 0.00 0.00 0.00 2.87
1633 1872 2.919859 GCATGATCGATCGTACCTCATG 59.080 50.000 27.96 27.96 43.76 3.07
2020 2270 4.041691 CGGGGTGGTGATTTATCCTTAGAT 59.958 45.833 0.00 0.00 36.44 1.98
2184 2504 5.048991 CGGTAGAAACTAAAACATGGCAAGT 60.049 40.000 0.00 0.00 0.00 3.16
2320 2820 3.319405 ACATAGCTACCTCGTCTGGAATG 59.681 47.826 0.00 0.00 0.00 2.67
2379 2879 9.612066 AATTTATTTCACCACACAATTTGAAGT 57.388 25.926 2.79 0.00 29.96 3.01
2454 3242 3.947834 CTCAACTCCCTTGTGAAACTTGT 59.052 43.478 0.00 0.00 38.04 3.16
2671 3543 3.259123 ACCAAAGGCCATTCACAAGATTC 59.741 43.478 5.01 0.00 0.00 2.52
2766 3638 6.171921 TGATTAAAAACATGCCCAGAATTGG 58.828 36.000 0.00 0.00 44.60 3.16
2957 3834 2.885554 GCTGGGTGAAAAGGGACATCAT 60.886 50.000 0.00 0.00 0.00 2.45
2958 3835 1.547675 GCTGGGTGAAAAGGGACATCA 60.548 52.381 0.00 0.00 0.00 3.07
2959 3836 1.177401 GCTGGGTGAAAAGGGACATC 58.823 55.000 0.00 0.00 0.00 3.06
2960 3837 0.482446 TGCTGGGTGAAAAGGGACAT 59.518 50.000 0.00 0.00 0.00 3.06
3027 3913 9.071276 AGTAGGGACAAGATTGCATATAAAATG 57.929 33.333 0.00 0.00 0.00 2.32
3139 4025 6.479990 TGAATGATAGGATCGTGTCAAATGAC 59.520 38.462 17.12 6.60 44.97 3.06
3148 4034 7.374272 AGACTGTTATGAATGATAGGATCGTG 58.626 38.462 0.00 0.00 0.00 4.35
3414 4451 0.577269 CAGGCAGAGCGCGTATTTAC 59.423 55.000 8.43 0.00 43.84 2.01
3427 4473 8.871686 ATTTAGTTTGTCTTAAAAACAGGCAG 57.128 30.769 4.53 0.00 39.49 4.85
3540 4586 9.425248 TTGAAGATTGATGCTTTTAATCCCTAT 57.575 29.630 0.00 0.00 32.59 2.57


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

AutoCloner maintained by Alex Coulton.