Multiple sequence alignment - TraesCS7D01G356900

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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 TraesCS7D01G356900 chr7D 100.000 2354 0 0 1 2354 459949980 459952333 0.000000e+00 4348
1 TraesCS7D01G356900 chr7D 98.176 2193 33 2 162 2354 199527703 199525518 0.000000e+00 3821
2 TraesCS7D01G356900 chr5D 98.314 2195 29 3 162 2354 475866408 475864220 0.000000e+00 3842
3 TraesCS7D01G356900 chr5D 97.319 2163 33 6 193 2354 320405050 320402912 0.000000e+00 3650
4 TraesCS7D01G356900 chr5D 97.481 794 14 1 162 955 475868011 475867224 0.000000e+00 1351
5 TraesCS7D01G356900 chr5D 97.358 795 14 2 162 955 475867210 475866422 0.000000e+00 1345
6 TraesCS7D01G356900 chr5D 96.977 794 16 3 162 955 475868810 475868025 0.000000e+00 1327
7 TraesCS7D01G356900 chr5D 96.725 794 19 2 162 955 475869610 475868824 0.000000e+00 1315
8 TraesCS7D01G356900 chr1D 97.356 2194 35 4 162 2354 209366691 209368862 0.000000e+00 3709
9 TraesCS7D01G356900 chr1D 85.616 876 104 15 638 1495 488789187 488790058 0.000000e+00 900
10 TraesCS7D01G356900 chr1D 94.937 158 5 3 1 157 111964581 111964736 6.500000e-61 244
11 TraesCS7D01G356900 chr2D 97.052 1798 27 4 162 1957 9572326 9570553 0.000000e+00 3003
12 TraesCS7D01G356900 chr2D 97.317 410 11 0 1945 2354 9570534 9570125 0.000000e+00 697
13 TraesCS7D01G356900 chr7A 91.210 1843 79 17 573 2354 369529208 369527388 0.000000e+00 2429
14 TraesCS7D01G356900 chr6B 96.147 1168 30 4 317 1476 9852199 9853359 0.000000e+00 1893
15 TraesCS7D01G356900 chr6B 97.480 873 21 1 1482 2354 9853411 9854282 0.000000e+00 1489
16 TraesCS7D01G356900 chr2A 95.359 905 40 2 573 1476 753533539 753532636 0.000000e+00 1437
17 TraesCS7D01G356900 chr2A 94.231 624 18 3 1482 2091 753532584 753531965 0.000000e+00 937
18 TraesCS7D01G356900 chr2A 92.531 241 8 2 331 567 753533845 753533611 1.040000e-88 337
19 TraesCS7D01G356900 chr2A 95.270 148 7 0 2207 2354 753531600 753531453 3.910000e-58 235
20 TraesCS7D01G356900 chr4A 96.334 873 30 2 1482 2354 650381906 650381036 0.000000e+00 1434
21 TraesCS7D01G356900 chr4A 95.833 432 8 2 162 589 650382532 650382107 0.000000e+00 689
22 TraesCS7D01G356900 chr4A 94.304 158 6 3 1 157 734658141 734658296 3.020000e-59 239
23 TraesCS7D01G356900 chr4A 94.304 158 6 3 1 157 734668682 734668837 3.020000e-59 239
24 TraesCS7D01G356900 chr4A 94.304 158 6 3 1 157 734676135 734676290 3.020000e-59 239
25 TraesCS7D01G356900 chr6A 94.937 158 5 3 1 157 100671142 100670987 6.500000e-61 244
26 TraesCS7D01G356900 chrUn 94.304 158 6 3 1 157 418726071 418725916 3.020000e-59 239
27 TraesCS7D01G356900 chr5B 94.304 158 6 3 1 157 566048983 566049138 3.020000e-59 239
28 TraesCS7D01G356900 chr4B 94.304 158 6 3 1 157 22262211 22262366 3.020000e-59 239
29 TraesCS7D01G356900 chr3D 94.304 158 6 3 1 157 500829270 500829115 3.020000e-59 239


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 TraesCS7D01G356900 chr7D 459949980 459952333 2353 False 4348.0 4348 100.00000 1 2354 1 chr7D.!!$F1 2353
1 TraesCS7D01G356900 chr7D 199525518 199527703 2185 True 3821.0 3821 98.17600 162 2354 1 chr7D.!!$R1 2192
2 TraesCS7D01G356900 chr5D 320402912 320405050 2138 True 3650.0 3650 97.31900 193 2354 1 chr5D.!!$R1 2161
3 TraesCS7D01G356900 chr5D 475864220 475869610 5390 True 1836.0 3842 97.37100 162 2354 5 chr5D.!!$R2 2192
4 TraesCS7D01G356900 chr1D 209366691 209368862 2171 False 3709.0 3709 97.35600 162 2354 1 chr1D.!!$F2 2192
5 TraesCS7D01G356900 chr1D 488789187 488790058 871 False 900.0 900 85.61600 638 1495 1 chr1D.!!$F3 857
6 TraesCS7D01G356900 chr2D 9570125 9572326 2201 True 1850.0 3003 97.18450 162 2354 2 chr2D.!!$R1 2192
7 TraesCS7D01G356900 chr7A 369527388 369529208 1820 True 2429.0 2429 91.21000 573 2354 1 chr7A.!!$R1 1781
8 TraesCS7D01G356900 chr6B 9852199 9854282 2083 False 1691.0 1893 96.81350 317 2354 2 chr6B.!!$F1 2037
9 TraesCS7D01G356900 chr2A 753531453 753533845 2392 True 736.5 1437 94.34775 331 2354 4 chr2A.!!$R1 2023
10 TraesCS7D01G356900 chr4A 650381036 650382532 1496 True 1061.5 1434 96.08350 162 2354 2 chr4A.!!$R1 2192

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
99 100 0.319405 ACCGCTATAATACCGCACCC 59.681 55.0 0.0 0.0 0.0 4.61 F
154 155 0.392998 CCCTGCGTTCCTGTGCTATT 60.393 55.0 0.0 0.0 0.0 1.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1132 4422 2.229784 GCATAGCTGCTGGTTCAAAACT 59.770 45.455 13.43 0.0 45.32 2.66 R
2071 5454 4.357325 AGATATAGCAGTTGATCCCGGAT 58.643 43.478 0.73 0.0 0.00 4.18 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
22 23 5.042671 CGACATCGAGATTTGTTAACGAG 57.957 43.478 0.26 0.00 43.02 4.18
23 24 4.027621 CGACATCGAGATTTGTTAACGAGG 60.028 45.833 0.26 0.00 43.02 4.63
24 25 4.817517 ACATCGAGATTTGTTAACGAGGT 58.182 39.130 0.00 0.00 41.62 3.85
25 26 5.235516 ACATCGAGATTTGTTAACGAGGTT 58.764 37.500 0.00 0.00 43.27 3.50
26 27 5.347907 ACATCGAGATTTGTTAACGAGGTTC 59.652 40.000 0.00 0.00 43.27 3.62
27 28 4.873817 TCGAGATTTGTTAACGAGGTTCA 58.126 39.130 0.26 0.00 0.00 3.18
28 29 4.682860 TCGAGATTTGTTAACGAGGTTCAC 59.317 41.667 0.26 0.00 0.00 3.18
29 30 4.684703 CGAGATTTGTTAACGAGGTTCACT 59.315 41.667 0.26 0.00 0.00 3.41
30 31 5.388475 CGAGATTTGTTAACGAGGTTCACTG 60.388 44.000 0.26 0.00 0.00 3.66
31 32 5.607477 AGATTTGTTAACGAGGTTCACTGA 58.393 37.500 0.26 0.00 0.00 3.41
32 33 6.231211 AGATTTGTTAACGAGGTTCACTGAT 58.769 36.000 0.26 0.00 0.00 2.90
33 34 7.383687 AGATTTGTTAACGAGGTTCACTGATA 58.616 34.615 0.26 0.00 0.00 2.15
34 35 8.041323 AGATTTGTTAACGAGGTTCACTGATAT 58.959 33.333 0.26 0.00 0.00 1.63
35 36 6.961359 TTGTTAACGAGGTTCACTGATATG 57.039 37.500 0.26 0.00 0.00 1.78
36 37 5.416083 TGTTAACGAGGTTCACTGATATGG 58.584 41.667 0.26 0.00 0.00 2.74
37 38 2.604046 ACGAGGTTCACTGATATGGC 57.396 50.000 0.00 0.00 0.00 4.40
38 39 2.111384 ACGAGGTTCACTGATATGGCT 58.889 47.619 0.00 0.00 0.00 4.75
39 40 3.296854 ACGAGGTTCACTGATATGGCTA 58.703 45.455 0.00 0.00 0.00 3.93
40 41 3.068307 ACGAGGTTCACTGATATGGCTAC 59.932 47.826 0.00 0.00 0.00 3.58
41 42 3.068165 CGAGGTTCACTGATATGGCTACA 59.932 47.826 0.00 0.00 0.00 2.74
42 43 4.262207 CGAGGTTCACTGATATGGCTACAT 60.262 45.833 0.00 0.00 41.13 2.29
43 44 5.220710 AGGTTCACTGATATGGCTACATC 57.779 43.478 0.00 0.00 38.53 3.06
44 45 4.040952 AGGTTCACTGATATGGCTACATCC 59.959 45.833 0.00 0.00 38.53 3.51
45 46 4.319177 GTTCACTGATATGGCTACATCCC 58.681 47.826 0.00 0.00 38.53 3.85
46 47 2.906389 TCACTGATATGGCTACATCCCC 59.094 50.000 0.00 0.00 38.53 4.81
47 48 1.902508 ACTGATATGGCTACATCCCCG 59.097 52.381 0.00 0.00 38.53 5.73
48 49 1.208052 CTGATATGGCTACATCCCCGG 59.792 57.143 0.00 0.00 38.53 5.73
49 50 0.541863 GATATGGCTACATCCCCGGG 59.458 60.000 15.80 15.80 38.53 5.73
50 51 0.914417 ATATGGCTACATCCCCGGGG 60.914 60.000 35.80 35.80 38.53 5.73
54 55 3.560251 CTACATCCCCGGGGCCTG 61.560 72.222 36.68 32.77 34.68 4.85
55 56 4.096816 TACATCCCCGGGGCCTGA 62.097 66.667 35.53 22.46 34.68 3.86
58 59 4.843331 ATCCCCGGGGCCTGACAT 62.843 66.667 36.68 19.54 34.68 3.06
68 69 3.790437 CCTGACATGGGCGCTCCT 61.790 66.667 3.94 0.00 36.20 3.69
69 70 2.202987 CTGACATGGGCGCTCCTC 60.203 66.667 3.94 0.00 36.20 3.71
70 71 2.685017 TGACATGGGCGCTCCTCT 60.685 61.111 3.94 0.00 36.20 3.69
71 72 2.107953 GACATGGGCGCTCCTCTC 59.892 66.667 3.94 0.00 36.20 3.20
72 73 3.453070 GACATGGGCGCTCCTCTCC 62.453 68.421 3.94 0.00 36.20 3.71
73 74 4.247380 CATGGGCGCTCCTCTCCC 62.247 72.222 3.94 0.00 40.47 4.30
77 78 4.292178 GGCGCTCCTCTCCCGATG 62.292 72.222 7.64 0.00 0.00 3.84
78 79 3.219928 GCGCTCCTCTCCCGATGA 61.220 66.667 0.00 0.00 0.00 2.92
79 80 2.725008 CGCTCCTCTCCCGATGAC 59.275 66.667 0.00 0.00 0.00 3.06
80 81 2.121538 CGCTCCTCTCCCGATGACA 61.122 63.158 0.00 0.00 0.00 3.58
81 82 1.439644 GCTCCTCTCCCGATGACAC 59.560 63.158 0.00 0.00 0.00 3.67
82 83 2.022240 GCTCCTCTCCCGATGACACC 62.022 65.000 0.00 0.00 0.00 4.16
83 84 1.729470 CTCCTCTCCCGATGACACCG 61.729 65.000 0.00 0.00 0.00 4.94
84 85 2.105128 CTCTCCCGATGACACCGC 59.895 66.667 0.00 0.00 0.00 5.68
85 86 2.362503 TCTCCCGATGACACCGCT 60.363 61.111 0.00 0.00 0.00 5.52
86 87 1.077285 TCTCCCGATGACACCGCTA 60.077 57.895 0.00 0.00 0.00 4.26
87 88 0.467474 TCTCCCGATGACACCGCTAT 60.467 55.000 0.00 0.00 0.00 2.97
88 89 1.202842 TCTCCCGATGACACCGCTATA 60.203 52.381 0.00 0.00 0.00 1.31
89 90 1.611977 CTCCCGATGACACCGCTATAA 59.388 52.381 0.00 0.00 0.00 0.98
90 91 2.231478 CTCCCGATGACACCGCTATAAT 59.769 50.000 0.00 0.00 0.00 1.28
91 92 3.423749 TCCCGATGACACCGCTATAATA 58.576 45.455 0.00 0.00 0.00 0.98
92 93 3.192001 TCCCGATGACACCGCTATAATAC 59.808 47.826 0.00 0.00 0.00 1.89
93 94 3.508762 CCGATGACACCGCTATAATACC 58.491 50.000 0.00 0.00 0.00 2.73
94 95 3.168963 CGATGACACCGCTATAATACCG 58.831 50.000 0.00 0.00 0.00 4.02
95 96 2.427232 TGACACCGCTATAATACCGC 57.573 50.000 0.00 0.00 0.00 5.68
96 97 1.682323 TGACACCGCTATAATACCGCA 59.318 47.619 0.00 0.00 0.00 5.69
97 98 2.056577 GACACCGCTATAATACCGCAC 58.943 52.381 0.00 0.00 0.00 5.34
98 99 1.269936 ACACCGCTATAATACCGCACC 60.270 52.381 0.00 0.00 0.00 5.01
99 100 0.319405 ACCGCTATAATACCGCACCC 59.681 55.000 0.00 0.00 0.00 4.61
100 101 0.734942 CCGCTATAATACCGCACCCG 60.735 60.000 0.00 0.00 0.00 5.28
146 147 4.035102 GGCTTCCCCTGCGTTCCT 62.035 66.667 0.00 0.00 0.00 3.36
147 148 2.747855 GCTTCCCCTGCGTTCCTG 60.748 66.667 0.00 0.00 0.00 3.86
148 149 2.750350 CTTCCCCTGCGTTCCTGT 59.250 61.111 0.00 0.00 0.00 4.00
149 150 1.672356 CTTCCCCTGCGTTCCTGTG 60.672 63.158 0.00 0.00 0.00 3.66
150 151 3.842925 TTCCCCTGCGTTCCTGTGC 62.843 63.158 0.00 0.00 0.00 4.57
151 152 4.335647 CCCCTGCGTTCCTGTGCT 62.336 66.667 0.00 0.00 0.00 4.40
152 153 2.662596 CCCTGCGTTCCTGTGCTA 59.337 61.111 0.00 0.00 0.00 3.49
153 154 1.221840 CCCTGCGTTCCTGTGCTAT 59.778 57.895 0.00 0.00 0.00 2.97
154 155 0.392998 CCCTGCGTTCCTGTGCTATT 60.393 55.000 0.00 0.00 0.00 1.73
155 156 1.134521 CCCTGCGTTCCTGTGCTATTA 60.135 52.381 0.00 0.00 0.00 0.98
156 157 2.485479 CCCTGCGTTCCTGTGCTATTAT 60.485 50.000 0.00 0.00 0.00 1.28
157 158 2.802816 CCTGCGTTCCTGTGCTATTATC 59.197 50.000 0.00 0.00 0.00 1.75
158 159 3.493350 CCTGCGTTCCTGTGCTATTATCT 60.493 47.826 0.00 0.00 0.00 1.98
159 160 3.717707 TGCGTTCCTGTGCTATTATCTC 58.282 45.455 0.00 0.00 0.00 2.75
160 161 3.384789 TGCGTTCCTGTGCTATTATCTCT 59.615 43.478 0.00 0.00 0.00 3.10
486 2091 7.065563 CGTTGATCAATCTCCTTCTTTCAATCT 59.934 37.037 12.12 0.00 0.00 2.40
526 2131 0.600557 TGGTTTACTTGGCGCCAATG 59.399 50.000 40.03 32.26 35.20 2.82
527 2132 0.885196 GGTTTACTTGGCGCCAATGA 59.115 50.000 40.03 27.72 35.20 2.57
528 2133 1.271102 GGTTTACTTGGCGCCAATGAA 59.729 47.619 40.03 31.21 35.20 2.57
529 2134 2.288518 GGTTTACTTGGCGCCAATGAAA 60.289 45.455 40.03 34.20 35.20 2.69
530 2135 3.385577 GTTTACTTGGCGCCAATGAAAA 58.614 40.909 40.03 32.05 35.20 2.29
531 2136 3.951775 TTACTTGGCGCCAATGAAAAT 57.048 38.095 40.03 22.75 35.20 1.82
571 3044 6.321435 TCAGATCAGTCAATATACGTCCTTGT 59.679 38.462 0.00 0.00 0.00 3.16
714 3989 4.974438 TCCCGTTGGCCCTCCACT 62.974 66.667 0.00 0.00 43.33 4.00
726 4001 3.451556 CTCCACTGCCGATCGCCAT 62.452 63.158 10.32 0.00 36.24 4.40
829 4111 6.092122 CAGACATGTAAGGTTCAGCGAAATAA 59.908 38.462 0.00 0.00 0.00 1.40
2253 5885 0.244721 GTGGCATTGGTTTCCTGCTC 59.755 55.000 0.00 0.00 36.18 4.26
2263 5895 1.280421 GTTTCCTGCTCATCTGTCCCT 59.720 52.381 0.00 0.00 0.00 4.20
2283 5916 2.758979 CTGCCTCCAATTCAATCAGCTT 59.241 45.455 0.00 0.00 0.00 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.027621 CCTCGTTAACAAATCTCGATGTCG 60.028 45.833 6.39 0.00 41.45 4.35
1 2 4.863131 ACCTCGTTAACAAATCTCGATGTC 59.137 41.667 6.39 0.00 0.00 3.06
2 3 4.817517 ACCTCGTTAACAAATCTCGATGT 58.182 39.130 6.39 0.00 0.00 3.06
3 4 5.347635 TGAACCTCGTTAACAAATCTCGATG 59.652 40.000 6.39 0.00 0.00 3.84
4 5 5.347907 GTGAACCTCGTTAACAAATCTCGAT 59.652 40.000 6.39 0.00 27.94 3.59
5 6 4.682860 GTGAACCTCGTTAACAAATCTCGA 59.317 41.667 6.39 0.00 27.94 4.04
6 7 4.684703 AGTGAACCTCGTTAACAAATCTCG 59.315 41.667 6.39 0.00 29.69 4.04
7 8 5.694910 TCAGTGAACCTCGTTAACAAATCTC 59.305 40.000 6.39 0.00 29.69 2.75
8 9 5.607477 TCAGTGAACCTCGTTAACAAATCT 58.393 37.500 6.39 0.00 29.69 2.40
9 10 5.917541 TCAGTGAACCTCGTTAACAAATC 57.082 39.130 6.39 0.00 29.69 2.17
10 11 7.065803 CCATATCAGTGAACCTCGTTAACAAAT 59.934 37.037 6.39 0.00 29.69 2.32
11 12 6.370442 CCATATCAGTGAACCTCGTTAACAAA 59.630 38.462 6.39 0.00 29.69 2.83
12 13 5.872617 CCATATCAGTGAACCTCGTTAACAA 59.127 40.000 6.39 0.00 29.69 2.83
13 14 5.416083 CCATATCAGTGAACCTCGTTAACA 58.584 41.667 6.39 0.00 29.69 2.41
14 15 4.270325 GCCATATCAGTGAACCTCGTTAAC 59.730 45.833 0.00 0.00 0.00 2.01
15 16 4.161565 AGCCATATCAGTGAACCTCGTTAA 59.838 41.667 0.00 0.00 0.00 2.01
16 17 3.704566 AGCCATATCAGTGAACCTCGTTA 59.295 43.478 0.00 0.00 0.00 3.18
17 18 2.501723 AGCCATATCAGTGAACCTCGTT 59.498 45.455 0.00 0.00 0.00 3.85
18 19 2.111384 AGCCATATCAGTGAACCTCGT 58.889 47.619 0.00 0.00 0.00 4.18
19 20 2.898729 AGCCATATCAGTGAACCTCG 57.101 50.000 0.00 0.00 0.00 4.63
20 21 4.672587 TGTAGCCATATCAGTGAACCTC 57.327 45.455 0.00 0.00 0.00 3.85
21 22 4.040952 GGATGTAGCCATATCAGTGAACCT 59.959 45.833 0.00 0.00 0.00 3.50
22 23 4.319177 GGATGTAGCCATATCAGTGAACC 58.681 47.826 0.00 0.00 0.00 3.62
23 24 4.319177 GGGATGTAGCCATATCAGTGAAC 58.681 47.826 0.00 0.00 0.00 3.18
24 25 3.327757 GGGGATGTAGCCATATCAGTGAA 59.672 47.826 0.00 0.00 0.00 3.18
25 26 2.906389 GGGGATGTAGCCATATCAGTGA 59.094 50.000 0.00 0.00 0.00 3.41
26 27 2.354103 CGGGGATGTAGCCATATCAGTG 60.354 54.545 0.00 0.00 0.00 3.66
27 28 1.902508 CGGGGATGTAGCCATATCAGT 59.097 52.381 0.00 0.00 0.00 3.41
28 29 1.208052 CCGGGGATGTAGCCATATCAG 59.792 57.143 0.00 0.00 0.00 2.90
29 30 1.275666 CCGGGGATGTAGCCATATCA 58.724 55.000 0.00 0.00 0.00 2.15
30 31 0.541863 CCCGGGGATGTAGCCATATC 59.458 60.000 14.71 0.00 0.00 1.63
31 32 0.914417 CCCCGGGGATGTAGCCATAT 60.914 60.000 38.41 0.00 37.50 1.78
32 33 1.537889 CCCCGGGGATGTAGCCATA 60.538 63.158 38.41 0.00 37.50 2.74
33 34 2.854032 CCCCGGGGATGTAGCCAT 60.854 66.667 38.41 0.00 37.50 4.40
37 38 3.560251 CAGGCCCCGGGGATGTAG 61.560 72.222 44.86 22.59 37.50 2.74
38 39 4.096816 TCAGGCCCCGGGGATGTA 62.097 66.667 44.86 24.26 37.50 2.29
41 42 4.843331 ATGTCAGGCCCCGGGGAT 62.843 66.667 44.86 28.05 37.50 3.85
51 52 3.746949 GAGGAGCGCCCATGTCAGG 62.747 68.421 15.92 0.00 37.41 3.86
52 53 2.202987 GAGGAGCGCCCATGTCAG 60.203 66.667 15.92 0.00 37.41 3.51
53 54 2.685017 AGAGGAGCGCCCATGTCA 60.685 61.111 15.92 0.00 37.41 3.58
54 55 2.107953 GAGAGGAGCGCCCATGTC 59.892 66.667 15.92 1.00 37.41 3.06
55 56 3.474570 GGAGAGGAGCGCCCATGT 61.475 66.667 15.92 0.00 37.41 3.21
60 61 4.292178 CATCGGGAGAGGAGCGCC 62.292 72.222 2.29 0.00 44.82 6.53
61 62 3.219928 TCATCGGGAGAGGAGCGC 61.220 66.667 0.00 0.00 45.71 5.92
66 67 2.808315 CGGTGTCATCGGGAGAGG 59.192 66.667 0.00 0.00 45.48 3.69
67 68 1.101635 TAGCGGTGTCATCGGGAGAG 61.102 60.000 7.76 0.00 45.48 3.20
68 69 0.467474 ATAGCGGTGTCATCGGGAGA 60.467 55.000 7.76 0.00 46.90 3.71
69 70 1.244816 TATAGCGGTGTCATCGGGAG 58.755 55.000 7.76 0.00 0.00 4.30
70 71 1.694844 TTATAGCGGTGTCATCGGGA 58.305 50.000 7.76 0.00 0.00 5.14
71 72 2.743636 ATTATAGCGGTGTCATCGGG 57.256 50.000 7.76 0.00 0.00 5.14
72 73 3.508762 GGTATTATAGCGGTGTCATCGG 58.491 50.000 7.76 0.00 0.00 4.18
73 74 3.168963 CGGTATTATAGCGGTGTCATCG 58.831 50.000 15.02 0.00 45.08 3.84
83 84 0.319405 ACCGGGTGCGGTATTATAGC 59.681 55.000 6.32 0.00 40.96 2.97
84 85 1.401931 CGACCGGGTGCGGTATTATAG 60.402 57.143 3.30 0.00 43.07 1.31
85 86 0.597568 CGACCGGGTGCGGTATTATA 59.402 55.000 3.30 0.00 43.07 0.98
86 87 1.364901 CGACCGGGTGCGGTATTAT 59.635 57.895 3.30 0.00 43.07 1.28
87 88 2.806929 CGACCGGGTGCGGTATTA 59.193 61.111 3.30 0.00 43.07 0.98
88 89 4.825252 GCGACCGGGTGCGGTATT 62.825 66.667 3.30 0.00 43.07 1.89
129 130 4.035102 AGGAACGCAGGGGAAGCC 62.035 66.667 0.00 0.00 0.00 4.35
130 131 2.747855 CAGGAACGCAGGGGAAGC 60.748 66.667 0.00 0.00 0.00 3.86
131 132 1.672356 CACAGGAACGCAGGGGAAG 60.672 63.158 0.00 0.00 0.00 3.46
132 133 2.429930 CACAGGAACGCAGGGGAA 59.570 61.111 0.00 0.00 0.00 3.97
133 134 4.329545 GCACAGGAACGCAGGGGA 62.330 66.667 0.00 0.00 0.00 4.81
134 135 2.257409 ATAGCACAGGAACGCAGGGG 62.257 60.000 0.00 0.00 0.00 4.79
135 136 0.392998 AATAGCACAGGAACGCAGGG 60.393 55.000 0.00 0.00 0.00 4.45
136 137 2.309528 TAATAGCACAGGAACGCAGG 57.690 50.000 0.00 0.00 0.00 4.85
137 138 3.722147 AGATAATAGCACAGGAACGCAG 58.278 45.455 0.00 0.00 0.00 5.18
138 139 3.384789 AGAGATAATAGCACAGGAACGCA 59.615 43.478 0.00 0.00 0.00 5.24
139 140 3.983741 AGAGATAATAGCACAGGAACGC 58.016 45.455 0.00 0.00 0.00 4.84
140 141 7.426410 TCTTTAGAGATAATAGCACAGGAACG 58.574 38.462 0.00 0.00 0.00 3.95
141 142 9.601217 TTTCTTTAGAGATAATAGCACAGGAAC 57.399 33.333 0.00 0.00 0.00 3.62
142 143 9.601217 GTTTCTTTAGAGATAATAGCACAGGAA 57.399 33.333 0.00 0.00 0.00 3.36
143 144 7.921214 CGTTTCTTTAGAGATAATAGCACAGGA 59.079 37.037 0.00 0.00 0.00 3.86
144 145 7.707035 ACGTTTCTTTAGAGATAATAGCACAGG 59.293 37.037 0.00 0.00 0.00 4.00
145 146 8.635877 ACGTTTCTTTAGAGATAATAGCACAG 57.364 34.615 0.00 0.00 0.00 3.66
148 149 9.745880 CCTTACGTTTCTTTAGAGATAATAGCA 57.254 33.333 0.00 0.00 0.00 3.49
149 150 9.747293 ACCTTACGTTTCTTTAGAGATAATAGC 57.253 33.333 0.00 0.00 0.00 2.97
152 153 9.597170 GGAACCTTACGTTTCTTTAGAGATAAT 57.403 33.333 0.00 0.00 33.74 1.28
153 154 7.756722 CGGAACCTTACGTTTCTTTAGAGATAA 59.243 37.037 0.00 0.00 33.74 1.75
154 155 7.253422 CGGAACCTTACGTTTCTTTAGAGATA 58.747 38.462 0.00 0.00 33.74 1.98
155 156 6.098017 CGGAACCTTACGTTTCTTTAGAGAT 58.902 40.000 0.00 0.00 33.74 2.75
156 157 5.464168 CGGAACCTTACGTTTCTTTAGAGA 58.536 41.667 0.00 0.00 33.74 3.10
157 158 5.758570 CGGAACCTTACGTTTCTTTAGAG 57.241 43.478 0.00 0.00 33.74 2.43
256 1857 1.368579 GGGAGAAAACCGGTGTCGA 59.631 57.895 8.52 0.00 39.00 4.20
486 2091 5.015178 ACCATGGTGATAGGAAAAAGGAAGA 59.985 40.000 18.99 0.00 0.00 2.87
531 2136 9.506018 TGACTGATCTGACTATTTTCATTTTCA 57.494 29.630 6.60 0.00 0.00 2.69
571 3044 2.102420 ACACGACTCATGGTTCAGAACA 59.898 45.455 15.36 2.08 0.00 3.18
726 4001 4.467082 AGCAGGAATGGATAAAATGTTGCA 59.533 37.500 0.00 0.00 0.00 4.08
778 4054 2.100584 TGGTTGACAAAGAGCGCAATTT 59.899 40.909 11.47 7.15 0.00 1.82
784 4060 2.053627 GCAATTGGTTGACAAAGAGCG 58.946 47.619 7.72 0.00 43.46 5.03
845 4131 3.513398 GTTGCGTCCCAACCTCTATTGG 61.513 54.545 0.00 0.00 46.44 3.16
848 4134 3.855159 GTTGCGTCCCAACCTCTAT 57.145 52.632 0.00 0.00 46.44 1.98
1132 4422 2.229784 GCATAGCTGCTGGTTCAAAACT 59.770 45.455 13.43 0.00 45.32 2.66
2071 5454 4.357325 AGATATAGCAGTTGATCCCGGAT 58.643 43.478 0.73 0.00 0.00 4.18
2168 5775 3.395607 CCATGGATAGGAAAGTGATCCCA 59.604 47.826 5.56 0.00 40.59 4.37
2253 5885 0.549950 ATTGGAGGCAGGGACAGATG 59.450 55.000 0.00 0.00 0.00 2.90
2263 5895 2.494471 CAAGCTGATTGAATTGGAGGCA 59.506 45.455 0.00 0.00 41.83 4.75
2283 5916 1.600107 GCACCCGGGTTGATAGTCA 59.400 57.895 27.83 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.