Multiple sequence alignment - TraesCS3A01G439300

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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 TraesCS3A01G439300 chr3A 100.000 3586 0 0 1 3586 682331319 682334904 0.000000e+00 6623.0
1 TraesCS3A01G439300 chr3D 93.003 3530 188 35 65 3586 545919442 545922920 0.000000e+00 5096.0
2 TraesCS3A01G439300 chr3B 92.853 3330 203 22 68 3391 722364268 722367568 0.000000e+00 4798.0
3 TraesCS3A01G439300 chr3B 89.796 147 14 1 3438 3584 722444933 722445078 1.700000e-43 187.0
4 TraesCS3A01G439300 chr7A 100.000 46 0 0 1 46 18672578 18672623 6.380000e-13 86.1
5 TraesCS3A01G439300 chr7A 100.000 46 0 0 1 46 96090621 96090576 6.380000e-13 86.1
6 TraesCS3A01G439300 chr7A 100.000 46 0 0 1 46 635547897 635547852 6.380000e-13 86.1
7 TraesCS3A01G439300 chr7A 100.000 46 0 0 1 46 718223388 718223343 6.380000e-13 86.1
8 TraesCS3A01G439300 chr4A 100.000 46 0 0 1 46 5768515 5768470 6.380000e-13 86.1
9 TraesCS3A01G439300 chr4A 79.048 105 12 9 1534 1637 24905733 24905638 2.990000e-06 63.9
10 TraesCS3A01G439300 chr1A 100.000 46 0 0 1 46 3807669 3807624 6.380000e-13 86.1
11 TraesCS3A01G439300 chr1A 100.000 46 0 0 1 46 280876550 280876595 6.380000e-13 86.1
12 TraesCS3A01G439300 chr1A 100.000 46 0 0 1 46 549571754 549571709 6.380000e-13 86.1
13 TraesCS3A01G439300 chr1A 100.000 46 0 0 1 46 580443031 580442986 6.380000e-13 86.1
14 TraesCS3A01G439300 chr2A 88.235 51 5 1 1588 1638 99682976 99683025 3.870000e-05 60.2
15 TraesCS3A01G439300 chr2A 100.000 31 0 0 1606 1636 10409036 10409006 1.390000e-04 58.4
16 TraesCS3A01G439300 chr5A 100.000 29 0 0 1606 1634 708609334 708609306 2.000000e-03 54.7


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 TraesCS3A01G439300 chr3A 682331319 682334904 3585 False 6623 6623 100.000 1 3586 1 chr3A.!!$F1 3585
1 TraesCS3A01G439300 chr3D 545919442 545922920 3478 False 5096 5096 93.003 65 3586 1 chr3D.!!$F1 3521
2 TraesCS3A01G439300 chr3B 722364268 722367568 3300 False 4798 4798 92.853 68 3391 1 chr3B.!!$F1 3323

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
236 239 0.182299 GGCTTGCCTAGGCTTGATCT 59.818 55.0 33.07 0.0 45.6 2.75 F
942 964 0.333652 TGACCGGGTATCCACTCTCA 59.666 55.0 6.32 0.0 0.0 3.27 F
1209 1233 0.399949 TGGAGGTGGAGGCGGATATT 60.400 55.0 0.00 0.0 0.0 1.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1639 1663 0.251354 GCTCATGAGTTGCCTCTGGA 59.749 55.0 23.38 0.0 38.61 3.86 R
1999 2023 1.089920 GCATGTACCTCTGCAACCAG 58.910 55.0 7.15 0.0 40.54 4.00 R
3101 3131 0.458260 TGTGGCGTCGCATGTAGTAT 59.542 50.0 20.50 0.0 0.00 2.12 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
34 35 7.015226 GCACACATTTATGCAAGTATAGTCA 57.985 36.000 0.00 0.00 41.65 3.41
35 36 6.907212 GCACACATTTATGCAAGTATAGTCAC 59.093 38.462 0.00 0.00 41.65 3.67
36 37 7.413988 GCACACATTTATGCAAGTATAGTCACA 60.414 37.037 0.00 0.00 41.65 3.58
37 38 7.904977 CACACATTTATGCAAGTATAGTCACAC 59.095 37.037 0.00 0.00 0.00 3.82
38 39 7.606073 ACACATTTATGCAAGTATAGTCACACA 59.394 33.333 0.00 0.00 0.00 3.72
39 40 8.615211 CACATTTATGCAAGTATAGTCACACAT 58.385 33.333 0.00 0.00 0.00 3.21
40 41 8.615211 ACATTTATGCAAGTATAGTCACACATG 58.385 33.333 0.00 0.00 0.00 3.21
41 42 8.829612 CATTTATGCAAGTATAGTCACACATGA 58.170 33.333 0.00 0.00 0.00 3.07
42 43 8.785329 TTTATGCAAGTATAGTCACACATGAA 57.215 30.769 0.00 0.00 36.31 2.57
43 44 8.785329 TTATGCAAGTATAGTCACACATGAAA 57.215 30.769 0.00 0.00 36.31 2.69
44 45 7.686438 ATGCAAGTATAGTCACACATGAAAA 57.314 32.000 0.00 0.00 36.31 2.29
45 46 7.686438 TGCAAGTATAGTCACACATGAAAAT 57.314 32.000 0.00 0.00 36.31 1.82
46 47 8.109705 TGCAAGTATAGTCACACATGAAAATT 57.890 30.769 0.00 0.00 36.31 1.82
47 48 8.575589 TGCAAGTATAGTCACACATGAAAATTT 58.424 29.630 0.00 0.00 36.31 1.82
48 49 8.853345 GCAAGTATAGTCACACATGAAAATTTG 58.147 33.333 0.00 0.00 36.31 2.32
49 50 9.345517 CAAGTATAGTCACACATGAAAATTTGG 57.654 33.333 0.00 0.00 36.31 3.28
50 51 8.862325 AGTATAGTCACACATGAAAATTTGGA 57.138 30.769 0.00 0.00 36.31 3.53
51 52 9.295825 AGTATAGTCACACATGAAAATTTGGAA 57.704 29.630 0.00 0.00 36.31 3.53
52 53 9.559958 GTATAGTCACACATGAAAATTTGGAAG 57.440 33.333 0.00 0.00 36.31 3.46
53 54 6.713762 AGTCACACATGAAAATTTGGAAGA 57.286 33.333 0.00 0.00 36.31 2.87
54 55 7.294017 AGTCACACATGAAAATTTGGAAGAT 57.706 32.000 0.00 0.00 36.31 2.40
55 56 7.729116 AGTCACACATGAAAATTTGGAAGATT 58.271 30.769 0.00 0.00 36.31 2.40
56 57 7.869429 AGTCACACATGAAAATTTGGAAGATTC 59.131 33.333 0.00 0.00 36.31 2.52
57 58 7.652909 GTCACACATGAAAATTTGGAAGATTCA 59.347 33.333 0.00 0.00 36.31 2.57
58 59 8.369424 TCACACATGAAAATTTGGAAGATTCAT 58.631 29.630 0.00 0.00 40.37 2.57
59 60 8.653338 CACACATGAAAATTTGGAAGATTCATC 58.347 33.333 0.00 0.00 38.34 2.92
60 61 8.369424 ACACATGAAAATTTGGAAGATTCATCA 58.631 29.630 0.00 0.00 38.34 3.07
61 62 9.378551 CACATGAAAATTTGGAAGATTCATCAT 57.621 29.630 0.00 0.00 38.34 2.45
62 63 9.378551 ACATGAAAATTTGGAAGATTCATCATG 57.621 29.630 15.51 15.51 41.10 3.07
63 64 9.594478 CATGAAAATTTGGAAGATTCATCATGA 57.406 29.630 13.25 0.00 39.72 3.07
140 141 1.337118 TTGGAATTGAGCCAACACCC 58.663 50.000 0.00 0.00 40.32 4.61
152 153 2.483197 AACACCCGCCGAACCAAAC 61.483 57.895 0.00 0.00 0.00 2.93
153 154 3.666253 CACCCGCCGAACCAAACC 61.666 66.667 0.00 0.00 0.00 3.27
155 156 4.992511 CCCGCCGAACCAAACCGA 62.993 66.667 0.00 0.00 0.00 4.69
156 157 2.973600 CCGCCGAACCAAACCGAA 60.974 61.111 0.00 0.00 0.00 4.30
157 158 2.250190 CGCCGAACCAAACCGAAC 59.750 61.111 0.00 0.00 0.00 3.95
158 159 2.640989 GCCGAACCAAACCGAACC 59.359 61.111 0.00 0.00 0.00 3.62
159 160 2.188161 GCCGAACCAAACCGAACCA 61.188 57.895 0.00 0.00 0.00 3.67
160 161 1.726533 GCCGAACCAAACCGAACCAA 61.727 55.000 0.00 0.00 0.00 3.67
161 162 0.739561 CCGAACCAAACCGAACCAAA 59.260 50.000 0.00 0.00 0.00 3.28
166 167 4.854839 CGAACCAAACCGAACCAAATAATC 59.145 41.667 0.00 0.00 0.00 1.75
176 177 3.963383 ACCAAATAATCGGCGTTGATC 57.037 42.857 6.85 0.00 0.00 2.92
236 239 0.182299 GGCTTGCCTAGGCTTGATCT 59.818 55.000 33.07 0.00 45.60 2.75
272 275 2.570415 TTTACACCAATTCCTCGGCA 57.430 45.000 0.00 0.00 0.00 5.69
278 281 1.351017 ACCAATTCCTCGGCAAGAAGA 59.649 47.619 0.00 0.00 0.00 2.87
283 286 1.821332 CCTCGGCAAGAAGATGGCC 60.821 63.158 0.00 0.00 42.49 5.36
339 358 1.691195 TTTGGCGTGACTGGTGGAGA 61.691 55.000 0.00 0.00 0.00 3.71
354 373 3.522553 GTGGAGACCGAATCTAAACAGG 58.477 50.000 0.00 0.00 38.00 4.00
377 396 7.864379 CAGGCCTTCTAACTTTGCATAATATTG 59.136 37.037 0.00 0.00 0.00 1.90
445 464 4.099633 TCTTCATGGAGACCATTCACTCT 58.900 43.478 0.00 0.00 42.23 3.24
446 465 4.533707 TCTTCATGGAGACCATTCACTCTT 59.466 41.667 0.00 0.00 42.23 2.85
465 484 5.116069 TCTTTTAAAATGACAACCTCGGC 57.884 39.130 0.09 0.00 0.00 5.54
591 610 6.384224 AGACGGATCGCAAATCGTATTAATA 58.616 36.000 0.00 0.00 39.67 0.98
711 733 2.996155 GCAAGATCTCATTGGCATTCG 58.004 47.619 0.00 0.00 0.00 3.34
750 772 2.223641 GCATCCACACCTATGCAATGTG 60.224 50.000 13.79 13.79 46.19 3.21
816 838 4.171005 CAGATGGATGAAAACATGCACAC 58.829 43.478 6.56 5.07 35.79 3.82
922 944 1.349357 TGCTACTTGTATGCACCACCA 59.651 47.619 0.00 0.00 0.00 4.17
942 964 0.333652 TGACCGGGTATCCACTCTCA 59.666 55.000 6.32 0.00 0.00 3.27
1044 1068 3.706373 GAGGAGGCGGTGGAGCAA 61.706 66.667 0.00 0.00 39.27 3.91
1209 1233 0.399949 TGGAGGTGGAGGCGGATATT 60.400 55.000 0.00 0.00 0.00 1.28
1242 1266 1.235281 GGGTGTCGGCCAAGAAGAAC 61.235 60.000 2.24 0.00 0.00 3.01
1398 1422 3.663995 TTTTATGGAACCTCGTCACGA 57.336 42.857 0.00 0.00 0.00 4.35
1440 1464 5.426689 TGCATTATGAAGAGGAGAGTTGT 57.573 39.130 0.00 0.00 0.00 3.32
1555 1579 2.910688 AAAACACTCGAGCTTGAGGA 57.089 45.000 30.37 6.72 40.39 3.71
1573 1597 6.978674 TGAGGATAGGATTAAGACGAACAT 57.021 37.500 0.00 0.00 0.00 2.71
1585 1609 5.654603 AAGACGAACATACACATACTCCA 57.345 39.130 0.00 0.00 0.00 3.86
1639 1663 2.917227 CGCCAAGGCCCAAAACCT 60.917 61.111 5.34 0.00 40.02 3.50
1665 1689 2.436417 GGCAACTCATGAGCAACCTTA 58.564 47.619 22.83 0.00 0.00 2.69
1698 1722 3.102985 CAACGGGTCGTGTTGCAA 58.897 55.556 0.00 0.00 39.99 4.08
1717 1741 7.220491 TGTTGCAATCACATGCTTATATTTTCG 59.780 33.333 0.59 0.00 46.54 3.46
1909 1933 8.010105 TGGACAATAGGCCAAGGATATATTTTT 58.990 33.333 5.01 0.00 0.00 1.94
1934 1958 5.691754 CCAGTTTACTTCTTGGCATTGAAAC 59.308 40.000 0.00 0.00 0.00 2.78
1961 1985 7.010160 TCATGAATCTTTTGTTCTAAAGGGGT 58.990 34.615 0.00 0.00 36.12 4.95
1999 2023 8.737648 GCTATTTCTCTCATTCGTAAAAATTGC 58.262 33.333 0.00 0.00 0.00 3.56
2073 2098 3.322828 GGGATGGGTACGAATGCTTACTA 59.677 47.826 0.00 0.00 0.00 1.82
2079 2104 5.421693 TGGGTACGAATGCTTACTAACCTTA 59.578 40.000 0.00 0.00 0.00 2.69
2102 2127 6.715347 ACCTTTTACTGCTTGATGTTTTCT 57.285 33.333 0.00 0.00 0.00 2.52
2199 2226 4.469945 TCGGAGATCCTAAAGAACAATGGT 59.530 41.667 0.00 0.00 0.00 3.55
2239 2266 9.326413 AGAGTAAGCCACATAATTGTTGTATAC 57.674 33.333 0.00 0.00 32.34 1.47
2241 2268 7.982919 AGTAAGCCACATAATTGTTGTATACGA 59.017 33.333 0.00 0.00 32.34 3.43
2318 2345 5.012893 GTCAATGATTTTGTTCCTCTCCCT 58.987 41.667 0.00 0.00 0.00 4.20
2362 2389 1.522668 TTGGCACCAAAGATGAGTCG 58.477 50.000 0.00 0.00 32.44 4.18
2507 2534 5.682234 TGTTTCAGATTGAGATCCTGCTA 57.318 39.130 0.00 0.00 32.44 3.49
2732 2759 5.942236 AGTGCATTCAAGTGATATGTGTCTT 59.058 36.000 0.00 0.00 0.00 3.01
2780 2807 4.141981 TGTTCCAGCTCAAATCTGCAAAAA 60.142 37.500 0.00 0.00 0.00 1.94
2841 2869 8.908786 TGATGATGAAATGTACTTAGAATCCC 57.091 34.615 0.00 0.00 0.00 3.85
2845 2873 4.080807 TGAAATGTACTTAGAATCCCGCCA 60.081 41.667 0.00 0.00 0.00 5.69
2911 2940 5.212194 GTGTTGTACCTTTTGTGCATGTAG 58.788 41.667 0.00 0.00 39.44 2.74
2950 2979 7.877612 ACATGCAAATCGGTACTATGATCAATA 59.122 33.333 0.00 0.00 0.00 1.90
2984 3013 4.241590 TCAAAGCTGTACTTGCAAATGG 57.758 40.909 0.00 0.00 39.09 3.16
3020 3049 9.163899 GGTTTTTCCTTACTTATCTGAACTAGG 57.836 37.037 0.00 0.00 0.00 3.02
3025 3054 8.307582 TCCTTACTTATCTGAACTAGGAAAGG 57.692 38.462 0.00 0.00 0.00 3.11
3137 3168 3.486383 CCACACCATGGTCTTACTTTGT 58.514 45.455 16.53 4.26 44.46 2.83
3144 3175 7.103641 CACCATGGTCTTACTTTGTAGTACAT 58.896 38.462 16.53 0.00 36.61 2.29
3203 3234 6.538945 AAGGTAAAAGGCAGTTGAGAAAAA 57.461 33.333 0.00 0.00 0.00 1.94
3205 3236 7.124573 AGGTAAAAGGCAGTTGAGAAAAATT 57.875 32.000 0.00 0.00 0.00 1.82
3401 3433 7.059788 TCAATATGCCTCTTTGCCTTGTAATA 58.940 34.615 0.00 0.00 0.00 0.98
3405 3437 5.964758 TGCCTCTTTGCCTTGTAATATTTG 58.035 37.500 0.00 0.00 0.00 2.32
3416 3448 6.986231 GCCTTGTAATATTTGGAAAATGGGAG 59.014 38.462 0.00 0.00 0.00 4.30
3439 3471 2.042464 CTAGGTTGGCTCTCCTATGCA 58.958 52.381 0.00 0.00 36.00 3.96
3488 3520 9.191995 GTTACTGCATTTAACAAAGCAATTACT 57.808 29.630 11.64 0.00 36.44 2.24
3514 3546 5.769662 AGTTATCTGATGAAGTTGGCAAACA 59.230 36.000 6.76 3.40 38.88 2.83
3515 3547 4.778534 ATCTGATGAAGTTGGCAAACAG 57.221 40.909 6.76 5.61 38.88 3.16
3517 3549 3.565482 TCTGATGAAGTTGGCAAACAGTC 59.435 43.478 6.76 3.78 38.88 3.51
3527 3559 1.610522 GGCAAACAGTCTTGATGCAGT 59.389 47.619 0.00 0.00 40.18 4.40
3552 3584 6.397272 TGTCGGGTTTTACGAATGTAGTTAT 58.603 36.000 0.00 0.00 42.55 1.89
3556 3588 5.812127 GGGTTTTACGAATGTAGTTATCGGT 59.188 40.000 0.00 0.00 40.71 4.69
3557 3589 6.313658 GGGTTTTACGAATGTAGTTATCGGTT 59.686 38.462 0.00 0.00 40.71 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.907212 GTGACTATACTTGCATAAATGTGTGC 59.093 38.462 0.00 0.00 41.94 4.57
11 12 7.904977 GTGTGACTATACTTGCATAAATGTGTG 59.095 37.037 0.00 0.00 0.00 3.82
12 13 7.606073 TGTGTGACTATACTTGCATAAATGTGT 59.394 33.333 0.00 0.00 0.00 3.72
13 14 7.973601 TGTGTGACTATACTTGCATAAATGTG 58.026 34.615 0.00 0.00 0.00 3.21
14 15 8.615211 CATGTGTGACTATACTTGCATAAATGT 58.385 33.333 0.00 0.00 0.00 2.71
15 16 8.829612 TCATGTGTGACTATACTTGCATAAATG 58.170 33.333 0.00 0.00 0.00 2.32
16 17 8.962884 TCATGTGTGACTATACTTGCATAAAT 57.037 30.769 0.00 0.00 0.00 1.40
17 18 8.785329 TTCATGTGTGACTATACTTGCATAAA 57.215 30.769 0.00 0.00 33.11 1.40
18 19 8.785329 TTTCATGTGTGACTATACTTGCATAA 57.215 30.769 0.00 0.00 33.11 1.90
19 20 8.785329 TTTTCATGTGTGACTATACTTGCATA 57.215 30.769 0.00 0.00 33.11 3.14
20 21 7.686438 TTTTCATGTGTGACTATACTTGCAT 57.314 32.000 0.00 0.00 33.11 3.96
21 22 7.686438 ATTTTCATGTGTGACTATACTTGCA 57.314 32.000 0.00 0.00 33.11 4.08
22 23 8.853345 CAAATTTTCATGTGTGACTATACTTGC 58.147 33.333 0.00 0.00 33.11 4.01
23 24 9.345517 CCAAATTTTCATGTGTGACTATACTTG 57.654 33.333 0.00 0.00 33.11 3.16
24 25 9.295825 TCCAAATTTTCATGTGTGACTATACTT 57.704 29.630 0.00 0.00 33.11 2.24
25 26 8.862325 TCCAAATTTTCATGTGTGACTATACT 57.138 30.769 0.00 0.00 33.11 2.12
26 27 9.559958 CTTCCAAATTTTCATGTGTGACTATAC 57.440 33.333 0.00 0.00 33.11 1.47
27 28 9.513906 TCTTCCAAATTTTCATGTGTGACTATA 57.486 29.630 0.00 0.00 33.11 1.31
28 29 8.408043 TCTTCCAAATTTTCATGTGTGACTAT 57.592 30.769 0.00 0.00 33.11 2.12
29 30 7.815840 TCTTCCAAATTTTCATGTGTGACTA 57.184 32.000 0.00 0.00 33.11 2.59
30 31 6.713762 TCTTCCAAATTTTCATGTGTGACT 57.286 33.333 0.00 0.00 33.11 3.41
31 32 7.652909 TGAATCTTCCAAATTTTCATGTGTGAC 59.347 33.333 0.00 0.00 33.11 3.67
32 33 7.724287 TGAATCTTCCAAATTTTCATGTGTGA 58.276 30.769 0.00 0.00 0.00 3.58
33 34 7.949903 TGAATCTTCCAAATTTTCATGTGTG 57.050 32.000 0.00 0.00 0.00 3.82
34 35 8.369424 TGATGAATCTTCCAAATTTTCATGTGT 58.631 29.630 4.44 0.00 37.20 3.72
35 36 8.766000 TGATGAATCTTCCAAATTTTCATGTG 57.234 30.769 4.44 0.00 37.20 3.21
36 37 9.378551 CATGATGAATCTTCCAAATTTTCATGT 57.621 29.630 11.41 0.00 37.20 3.21
37 38 9.594478 TCATGATGAATCTTCCAAATTTTCATG 57.406 29.630 12.67 12.67 37.20 3.07
109 110 8.495160 TGGCTCAATTCCAAATATATCCAAAT 57.505 30.769 0.00 0.00 0.00 2.32
126 127 2.676471 GGCGGGTGTTGGCTCAAT 60.676 61.111 0.00 0.00 0.00 2.57
140 141 2.250190 GTTCGGTTTGGTTCGGCG 59.750 61.111 0.00 0.00 0.00 6.46
144 145 4.854839 CGATTATTTGGTTCGGTTTGGTTC 59.145 41.667 0.00 0.00 0.00 3.62
153 154 2.094575 TCAACGCCGATTATTTGGTTCG 59.905 45.455 0.00 0.00 0.00 3.95
154 155 3.750639 TCAACGCCGATTATTTGGTTC 57.249 42.857 0.00 0.00 0.00 3.62
155 156 3.242608 CGATCAACGCCGATTATTTGGTT 60.243 43.478 0.00 0.00 34.51 3.67
156 157 2.286833 CGATCAACGCCGATTATTTGGT 59.713 45.455 0.00 0.00 34.51 3.67
157 158 2.286833 ACGATCAACGCCGATTATTTGG 59.713 45.455 0.00 0.00 46.94 3.28
158 159 3.242284 ACACGATCAACGCCGATTATTTG 60.242 43.478 0.00 0.00 46.94 2.32
159 160 2.933906 ACACGATCAACGCCGATTATTT 59.066 40.909 0.00 0.00 46.94 1.40
160 161 2.284150 CACACGATCAACGCCGATTATT 59.716 45.455 0.00 0.00 46.94 1.40
161 162 1.858458 CACACGATCAACGCCGATTAT 59.142 47.619 0.00 0.00 46.94 1.28
166 167 2.736995 ACCACACGATCAACGCCG 60.737 61.111 0.00 0.00 46.94 6.46
176 177 1.021202 AAATGGACACACACCACACG 58.979 50.000 0.00 0.00 40.36 4.49
236 239 0.749649 AAAATTGAACTGCCACCGCA 59.250 45.000 0.00 0.00 44.78 5.69
245 248 6.294508 CCGAGGAATTGGTGTAAAATTGAACT 60.295 38.462 0.00 0.00 0.00 3.01
272 275 1.613437 CGTTTTGGTGGCCATCTTCTT 59.387 47.619 18.94 0.00 31.53 2.52
278 281 1.805428 GCTGACGTTTTGGTGGCCAT 61.805 55.000 9.72 0.00 31.53 4.40
283 286 2.507339 AATTGGCTGACGTTTTGGTG 57.493 45.000 0.00 0.00 0.00 4.17
314 333 1.608590 ACCAGTCACGCCAAATCTTTG 59.391 47.619 0.00 0.00 37.90 2.77
315 334 1.608590 CACCAGTCACGCCAAATCTTT 59.391 47.619 0.00 0.00 0.00 2.52
316 335 1.238439 CACCAGTCACGCCAAATCTT 58.762 50.000 0.00 0.00 0.00 2.40
317 336 0.606401 CCACCAGTCACGCCAAATCT 60.606 55.000 0.00 0.00 0.00 2.40
318 337 0.605319 TCCACCAGTCACGCCAAATC 60.605 55.000 0.00 0.00 0.00 2.17
319 338 0.606401 CTCCACCAGTCACGCCAAAT 60.606 55.000 0.00 0.00 0.00 2.32
320 339 1.227823 CTCCACCAGTCACGCCAAA 60.228 57.895 0.00 0.00 0.00 3.28
321 340 2.137528 TCTCCACCAGTCACGCCAA 61.138 57.895 0.00 0.00 0.00 4.52
322 341 2.523168 TCTCCACCAGTCACGCCA 60.523 61.111 0.00 0.00 0.00 5.69
323 342 2.048127 GTCTCCACCAGTCACGCC 60.048 66.667 0.00 0.00 0.00 5.68
324 343 2.048127 GGTCTCCACCAGTCACGC 60.048 66.667 0.00 0.00 43.17 5.34
325 344 1.802337 TTCGGTCTCCACCAGTCACG 61.802 60.000 0.00 0.00 44.02 4.35
326 345 0.608640 ATTCGGTCTCCACCAGTCAC 59.391 55.000 0.00 0.00 44.02 3.67
327 346 0.895530 GATTCGGTCTCCACCAGTCA 59.104 55.000 0.00 0.00 44.02 3.41
328 347 1.187087 AGATTCGGTCTCCACCAGTC 58.813 55.000 0.00 0.00 44.02 3.51
339 358 2.572104 AGAAGGCCTGTTTAGATTCGGT 59.428 45.455 5.69 0.00 0.00 4.69
354 373 7.629027 GCAATATTATGCAAAGTTAGAAGGC 57.371 36.000 0.00 0.00 45.70 4.35
445 464 3.564644 TCGCCGAGGTTGTCATTTTAAAA 59.435 39.130 2.51 2.51 0.00 1.52
446 465 3.058777 GTCGCCGAGGTTGTCATTTTAAA 60.059 43.478 0.00 0.00 0.00 1.52
465 484 5.007626 CCCCATTAGTTGTCACATTATGTCG 59.992 44.000 0.00 0.00 0.00 4.35
526 545 1.947456 ACGAGGGCTTCAAAACAAGAC 59.053 47.619 0.00 0.00 0.00 3.01
632 654 5.532032 TCACACAACATTCTGATGTCAACAT 59.468 36.000 0.00 0.00 45.58 2.71
645 667 2.174639 TGGAGGAACCTCACACAACATT 59.825 45.455 20.39 0.00 44.40 2.71
649 671 1.545428 GCATGGAGGAACCTCACACAA 60.545 52.381 20.39 3.32 44.40 3.33
711 733 0.097674 GCATGCACTCCGATGTTGTC 59.902 55.000 14.21 0.00 0.00 3.18
774 796 3.386063 TGGACCGGGGAATAGATTAACA 58.614 45.455 6.32 0.00 0.00 2.41
816 838 4.464008 AGTGGTTATTCCTGGTGCATATG 58.536 43.478 0.00 0.00 37.07 1.78
922 944 1.063190 TGAGAGTGGATACCCGGTCAT 60.063 52.381 0.00 0.00 34.29 3.06
942 964 2.907892 TGGGACAATGAGAGAGAGGTT 58.092 47.619 0.00 0.00 31.92 3.50
1209 1233 4.664267 ACCCCAGCCTCAGCCTCA 62.664 66.667 0.00 0.00 41.25 3.86
1242 1266 2.584608 GTGGACACCTGGATCCGG 59.415 66.667 14.26 14.26 37.87 5.14
1398 1422 1.963985 ATTGTGGGAGCTCTCTTCCT 58.036 50.000 16.21 0.00 38.89 3.36
1401 1425 1.074405 TGCAATTGTGGGAGCTCTCTT 59.926 47.619 16.21 0.00 0.00 2.85
1503 1527 4.501198 CGTGTTTGTATTTGGTTTTCGCTT 59.499 37.500 0.00 0.00 0.00 4.68
1552 1576 7.287005 TGTGTATGTTCGTCTTAATCCTATCCT 59.713 37.037 0.00 0.00 0.00 3.24
1555 1579 9.909644 GTATGTGTATGTTCGTCTTAATCCTAT 57.090 33.333 0.00 0.00 0.00 2.57
1573 1597 4.221041 TCCGTGATGTTTGGAGTATGTGTA 59.779 41.667 0.00 0.00 0.00 2.90
1585 1609 4.071423 TCACATGATGTTCCGTGATGTTT 58.929 39.130 0.00 0.00 33.61 2.83
1639 1663 0.251354 GCTCATGAGTTGCCTCTGGA 59.749 55.000 23.38 0.00 38.61 3.86
1665 1689 6.339587 ACCCGTTGTTAATGTGAATCAAAT 57.660 33.333 0.00 0.00 0.00 2.32
1717 1741 8.250332 TCATTGATTGGCCATTTTCTAAACTAC 58.750 33.333 6.09 0.00 0.00 2.73
1909 1933 4.724399 TCAATGCCAAGAAGTAAACTGGA 58.276 39.130 0.00 0.00 0.00 3.86
1934 1958 8.031277 CCCCTTTAGAACAAAAGATTCATGAAG 58.969 37.037 14.54 1.46 38.50 3.02
1961 1985 6.515832 TGAGAGAAATAGCATGCTAATTCGA 58.484 36.000 33.93 22.75 41.07 3.71
1999 2023 1.089920 GCATGTACCTCTGCAACCAG 58.910 55.000 7.15 0.00 40.54 4.00
2073 2098 6.068670 ACATCAAGCAGTAAAAGGTAAGGTT 58.931 36.000 0.00 0.00 0.00 3.50
2079 2104 6.715347 AGAAAACATCAAGCAGTAAAAGGT 57.285 33.333 0.00 0.00 0.00 3.50
2102 2127 8.121305 ACATAGCCAACAATGAAGTGATTAAA 57.879 30.769 0.00 0.00 0.00 1.52
2108 2133 7.765307 AGAAATACATAGCCAACAATGAAGTG 58.235 34.615 0.00 0.00 0.00 3.16
2109 2134 7.944729 AGAAATACATAGCCAACAATGAAGT 57.055 32.000 0.00 0.00 0.00 3.01
2166 2193 2.588620 AGGATCTCCGATACAGTCACC 58.411 52.381 0.00 0.00 42.08 4.02
2199 2226 3.317993 GCTTACTCTTTTCTGTGGCCAAA 59.682 43.478 7.24 0.00 0.00 3.28
2302 2329 3.260205 TGGAGAGGGAGAGGAACAAAAT 58.740 45.455 0.00 0.00 0.00 1.82
2318 2345 3.677156 TGATGTCAGGATCTCTGGAGA 57.323 47.619 2.63 2.63 43.53 3.71
2362 2389 4.493747 CGGACGAGTCGCCCCTTC 62.494 72.222 12.62 1.83 0.00 3.46
2507 2534 9.624373 ATGCTATTGAAGTTCTCTGATTTACAT 57.376 29.630 4.17 0.00 0.00 2.29
2567 2594 7.799081 ACAATTATCAGACCTTCATCTCATCA 58.201 34.615 0.00 0.00 0.00 3.07
2621 2648 1.601171 GTGCTGCCTCTCACCATCT 59.399 57.895 0.00 0.00 0.00 2.90
2723 2750 7.907389 ACAATTAAGAGGAGACAAGACACATA 58.093 34.615 0.00 0.00 0.00 2.29
2732 2759 5.489792 AGAGCAACAATTAAGAGGAGACA 57.510 39.130 0.00 0.00 0.00 3.41
2845 2873 7.945278 TCTTAGGAATACTATCTCCAGCCTAT 58.055 38.462 0.00 0.00 33.83 2.57
2950 2979 7.996385 AGTACAGCTTTGAAAACATTACAACT 58.004 30.769 0.00 0.00 0.00 3.16
2969 2998 4.050553 CAAACCACCATTTGCAAGTACAG 58.949 43.478 0.00 0.00 33.07 2.74
2984 3013 6.156748 AGTAAGGAAAAACCATCAAACCAC 57.843 37.500 0.00 0.00 42.04 4.16
3024 3053 2.879103 TTTGGACTGGAGGAACATCC 57.121 50.000 0.00 0.00 40.03 3.51
3025 3054 2.489722 GCTTTTGGACTGGAGGAACATC 59.510 50.000 0.00 0.00 0.00 3.06
3101 3131 0.458260 TGTGGCGTCGCATGTAGTAT 59.542 50.000 20.50 0.00 0.00 2.12
3108 3138 3.126879 CATGGTGTGGCGTCGCAT 61.127 61.111 20.50 0.00 35.69 4.73
3304 3335 6.301486 TGCACTCATGGAGATGCTAATAATT 58.699 36.000 16.11 0.00 37.48 1.40
3306 3337 5.294734 TGCACTCATGGAGATGCTAATAA 57.705 39.130 16.11 0.98 37.48 1.40
3401 3433 6.402981 ACCTAGTACTCCCATTTTCCAAAT 57.597 37.500 0.00 0.00 0.00 2.32
3405 3437 4.524053 CCAACCTAGTACTCCCATTTTCC 58.476 47.826 0.00 0.00 0.00 3.13
3416 3448 3.006003 GCATAGGAGAGCCAACCTAGTAC 59.994 52.174 0.00 0.00 41.24 2.73
3488 3520 7.446931 TGTTTGCCAACTTCATCAGATAACTTA 59.553 33.333 2.01 0.00 33.58 2.24
3489 3521 6.265196 TGTTTGCCAACTTCATCAGATAACTT 59.735 34.615 2.01 0.00 33.58 2.66
3507 3539 1.610522 ACTGCATCAAGACTGTTTGCC 59.389 47.619 0.00 0.00 34.15 4.52
3514 3546 1.609061 CCCGACAACTGCATCAAGACT 60.609 52.381 0.00 0.00 0.00 3.24
3515 3547 0.798776 CCCGACAACTGCATCAAGAC 59.201 55.000 0.00 0.00 0.00 3.01
3517 3549 1.238439 AACCCGACAACTGCATCAAG 58.762 50.000 0.00 0.00 0.00 3.02
3527 3559 4.630111 ACTACATTCGTAAAACCCGACAA 58.370 39.130 0.00 0.00 33.41 3.18


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

AutoCloner maintained by Alex Coulton.