Multiple sequence alignment - TraesCS2D01G597300

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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 TraesCS2D01G597300 chr2D 100.000 2530 0 0 1 2530 649782640 649780111 0.000000e+00 4673.0
1 TraesCS2D01G597300 chr2D 100.000 33 0 0 1096 1128 649781509 649781477 7.560000e-06 62.1
2 TraesCS2D01G597300 chr2D 100.000 33 0 0 1132 1164 649781545 649781513 7.560000e-06 62.1
3 TraesCS2D01G597300 chr2A 95.934 1402 43 5 1132 2530 775065018 775066408 0.000000e+00 2261.0
4 TraesCS2D01G597300 chr2A 95.643 459 14 2 675 1128 775064593 775065050 0.000000e+00 732.0
5 TraesCS2D01G597300 chr2A 96.353 329 10 2 40 366 775037296 775037624 7.960000e-150 540.0
6 TraesCS2D01G597300 chr2A 97.368 114 3 0 527 640 775064480 775064593 7.140000e-46 195.0
7 TraesCS2D01G597300 chr2A 95.726 117 4 1 409 524 775037621 775037737 1.190000e-43 187.0
8 TraesCS2D01G597300 chr2B 93.053 1094 41 11 992 2081 785821506 785820444 0.000000e+00 1567.0
9 TraesCS2D01G597300 chr2B 89.920 1121 63 11 79 1164 785822494 785821389 0.000000e+00 1399.0
10 TraesCS2D01G597300 chr2B 96.212 264 9 1 2073 2335 785797101 785796838 5.000000e-117 431.0
11 TraesCS2D01G597300 chr2B 97.710 131 3 0 2400 2530 785796827 785796697 2.530000e-55 226.0
12 TraesCS2D01G597300 chr2B 83.784 148 18 6 330 476 766060803 766060661 4.390000e-28 135.0
13 TraesCS2D01G597300 chrUn 83.077 65 9 2 239 303 74660686 74660624 9.780000e-05 58.4
14 TraesCS2D01G597300 chrUn 83.077 65 9 2 239 303 229381583 229381645 9.780000e-05 58.4


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 TraesCS2D01G597300 chr2D 649780111 649782640 2529 True 1599.066667 4673 100.0000 1 2530 3 chr2D.!!$R1 2529
1 TraesCS2D01G597300 chr2A 775064480 775066408 1928 False 1062.666667 2261 96.3150 527 2530 3 chr2A.!!$F2 2003
2 TraesCS2D01G597300 chr2B 785820444 785822494 2050 True 1483.000000 1567 91.4865 79 2081 2 chr2B.!!$R3 2002

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
812 844 0.315869 GCCGCACGTGCATGTAATAC 60.316 55.0 37.03 14.5 42.21 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1989 2064 0.179103 GGAAAATTGCGGGATGGCAG 60.179 55.0 0.0 0.0 44.94 4.85 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
43 44 5.886960 AGTCCAGTTTATGATGAGTTTGC 57.113 39.130 0.00 0.00 0.00 3.68
44 45 5.316167 AGTCCAGTTTATGATGAGTTTGCA 58.684 37.500 0.00 0.00 0.00 4.08
45 46 5.948162 AGTCCAGTTTATGATGAGTTTGCAT 59.052 36.000 0.00 0.00 0.00 3.96
46 47 7.112122 AGTCCAGTTTATGATGAGTTTGCATA 58.888 34.615 0.00 0.00 0.00 3.14
47 48 7.776969 AGTCCAGTTTATGATGAGTTTGCATAT 59.223 33.333 0.00 0.00 0.00 1.78
48 49 8.408601 GTCCAGTTTATGATGAGTTTGCATATT 58.591 33.333 0.00 0.00 0.00 1.28
49 50 8.970020 TCCAGTTTATGATGAGTTTGCATATTT 58.030 29.630 0.00 0.00 0.00 1.40
50 51 9.027129 CCAGTTTATGATGAGTTTGCATATTTG 57.973 33.333 0.00 0.00 0.00 2.32
51 52 9.577110 CAGTTTATGATGAGTTTGCATATTTGT 57.423 29.630 0.00 0.00 0.00 2.83
56 57 7.887996 TGATGAGTTTGCATATTTGTTTTCC 57.112 32.000 0.00 0.00 0.00 3.13
57 58 7.669427 TGATGAGTTTGCATATTTGTTTTCCT 58.331 30.769 0.00 0.00 0.00 3.36
58 59 8.149647 TGATGAGTTTGCATATTTGTTTTCCTT 58.850 29.630 0.00 0.00 0.00 3.36
59 60 7.712264 TGAGTTTGCATATTTGTTTTCCTTG 57.288 32.000 0.00 0.00 0.00 3.61
60 61 7.271511 TGAGTTTGCATATTTGTTTTCCTTGT 58.728 30.769 0.00 0.00 0.00 3.16
61 62 7.224362 TGAGTTTGCATATTTGTTTTCCTTGTG 59.776 33.333 0.00 0.00 0.00 3.33
62 63 7.271511 AGTTTGCATATTTGTTTTCCTTGTGA 58.728 30.769 0.00 0.00 0.00 3.58
63 64 7.933033 AGTTTGCATATTTGTTTTCCTTGTGAT 59.067 29.630 0.00 0.00 0.00 3.06
64 65 7.655236 TTGCATATTTGTTTTCCTTGTGATG 57.345 32.000 0.00 0.00 0.00 3.07
65 66 6.990798 TGCATATTTGTTTTCCTTGTGATGA 58.009 32.000 0.00 0.00 0.00 2.92
66 67 7.092079 TGCATATTTGTTTTCCTTGTGATGAG 58.908 34.615 0.00 0.00 0.00 2.90
67 68 6.532657 GCATATTTGTTTTCCTTGTGATGAGG 59.467 38.462 0.00 0.00 35.53 3.86
68 69 7.605449 CATATTTGTTTTCCTTGTGATGAGGT 58.395 34.615 0.00 0.00 35.71 3.85
69 70 5.514274 TTTGTTTTCCTTGTGATGAGGTC 57.486 39.130 0.00 0.00 35.71 3.85
70 71 4.437682 TGTTTTCCTTGTGATGAGGTCT 57.562 40.909 0.00 0.00 35.71 3.85
71 72 4.792068 TGTTTTCCTTGTGATGAGGTCTT 58.208 39.130 0.00 0.00 35.71 3.01
72 73 5.200483 TGTTTTCCTTGTGATGAGGTCTTT 58.800 37.500 0.00 0.00 35.71 2.52
73 74 5.299279 TGTTTTCCTTGTGATGAGGTCTTTC 59.701 40.000 0.00 0.00 35.71 2.62
74 75 4.705110 TTCCTTGTGATGAGGTCTTTCA 57.295 40.909 0.00 0.00 35.71 2.69
75 76 4.705110 TCCTTGTGATGAGGTCTTTCAA 57.295 40.909 0.00 0.00 35.71 2.69
76 77 5.047566 TCCTTGTGATGAGGTCTTTCAAA 57.952 39.130 0.00 0.00 35.71 2.69
77 78 5.634118 TCCTTGTGATGAGGTCTTTCAAAT 58.366 37.500 0.00 0.00 35.71 2.32
78 79 6.778821 TCCTTGTGATGAGGTCTTTCAAATA 58.221 36.000 0.00 0.00 35.71 1.40
79 80 7.405292 TCCTTGTGATGAGGTCTTTCAAATAT 58.595 34.615 0.00 0.00 35.71 1.28
80 81 7.337689 TCCTTGTGATGAGGTCTTTCAAATATG 59.662 37.037 0.00 0.00 35.71 1.78
81 82 7.395190 TTGTGATGAGGTCTTTCAAATATGG 57.605 36.000 0.00 0.00 0.00 2.74
82 83 5.357878 TGTGATGAGGTCTTTCAAATATGGC 59.642 40.000 0.00 0.00 0.00 4.40
83 84 4.889409 TGATGAGGTCTTTCAAATATGGCC 59.111 41.667 0.00 0.00 0.00 5.36
84 85 4.314522 TGAGGTCTTTCAAATATGGCCA 57.685 40.909 8.56 8.56 0.00 5.36
85 86 4.016444 TGAGGTCTTTCAAATATGGCCAC 58.984 43.478 8.16 0.00 0.00 5.01
99 100 8.658609 CAAATATGGCCACTTTAAACTCATTTG 58.341 33.333 8.16 7.53 0.00 2.32
100 101 7.716799 ATATGGCCACTTTAAACTCATTTGA 57.283 32.000 8.16 0.00 0.00 2.69
186 187 7.666804 TCAAATACTAAAACCCTAAACCTGGAC 59.333 37.037 0.00 0.00 0.00 4.02
215 229 9.833917 CTAAAACTCTAAACCCTAATCCTAAGG 57.166 37.037 0.00 0.00 0.00 2.69
226 240 5.160386 CCTAATCCTAAGGCCTAAACCCTA 58.840 45.833 5.16 0.00 30.93 3.53
241 255 1.840635 ACCCTAAGAGCAGATGGAACC 59.159 52.381 0.00 0.00 0.00 3.62
325 340 7.862512 TGCATCTGTCAAATGTATTCATGTA 57.137 32.000 0.00 0.00 34.19 2.29
347 362 3.831323 TGATCTTGTTTCAAAGCCCTCA 58.169 40.909 0.00 0.00 0.00 3.86
349 364 4.460382 TGATCTTGTTTCAAAGCCCTCATC 59.540 41.667 0.00 0.00 0.00 2.92
371 386 4.946772 TCGCCAGGAACATGAATATGAAAA 59.053 37.500 0.00 0.00 37.73 2.29
483 498 3.618351 ACCATGCAATCTCTGAAGAAGG 58.382 45.455 0.00 0.00 34.49 3.46
543 558 1.567504 CTAAGCCATGCATGCAAAGC 58.432 50.000 28.57 28.57 0.00 3.51
660 675 4.709397 TGTGTTCATTTGTTTTCCCTCTGT 59.291 37.500 0.00 0.00 0.00 3.41
812 844 0.315869 GCCGCACGTGCATGTAATAC 60.316 55.000 37.03 14.50 42.21 1.89
848 880 1.550327 TCTGCCTGAGACGAGTCATT 58.450 50.000 5.99 0.00 0.00 2.57
859 891 2.024176 CGAGTCATTCGTCCCCATTT 57.976 50.000 0.00 0.00 44.27 2.32
943 975 1.292061 CAACCACAAGAAACGTCGGA 58.708 50.000 0.00 0.00 0.00 4.55
997 1029 1.080093 GATTGGTCTGGACGCGACA 60.080 57.895 15.93 10.91 33.11 4.35
1421 1496 1.903890 GGGCTCCTGATCGGATCGA 60.904 63.158 12.99 4.73 42.12 3.59
1537 1612 5.348986 GGTGATCGTAAAGTAGAGATTGCA 58.651 41.667 0.00 0.00 0.00 4.08
1554 1629 1.072489 TGCACCCATGAACGTTAGGAA 59.928 47.619 13.71 0.00 0.00 3.36
1588 1663 2.969628 TCTTCTCTTCGAATCCCAGC 57.030 50.000 0.00 0.00 0.00 4.85
1593 1668 2.365617 TCTCTTCGAATCCCAGCCATAC 59.634 50.000 0.00 0.00 0.00 2.39
1594 1669 2.366916 CTCTTCGAATCCCAGCCATACT 59.633 50.000 0.00 0.00 0.00 2.12
1639 1714 4.263025 GGCAAGAACAATTTGGGAAATCCT 60.263 41.667 0.78 0.00 36.20 3.24
1655 1730 1.905839 TCCTAGGGGGAAATGATGCA 58.094 50.000 9.46 0.00 41.91 3.96
1795 1870 6.939730 ACAGGTTGTGTTGTCATTGACATATA 59.060 34.615 19.63 8.29 42.40 0.86
1796 1871 7.611467 ACAGGTTGTGTTGTCATTGACATATAT 59.389 33.333 19.63 0.00 42.40 0.86
1877 1952 4.406456 GGGGGCATGATATGTTCATTACA 58.594 43.478 0.00 0.00 42.62 2.41
1918 1993 5.163343 ACACTAACATATCAAGGTATGGCGT 60.163 40.000 5.42 0.00 36.58 5.68
1981 2056 9.743057 TTGAGGTGTAAAGACAAAATTAATGTG 57.257 29.630 1.82 0.00 37.31 3.21
1982 2057 8.908903 TGAGGTGTAAAGACAAAATTAATGTGT 58.091 29.630 5.03 5.03 37.31 3.72
1983 2058 9.744468 GAGGTGTAAAGACAAAATTAATGTGTT 57.256 29.630 6.51 1.96 37.31 3.32
1987 2062 9.968870 TGTAAAGACAAAATTAATGTGTTACCC 57.031 29.630 15.86 7.29 33.66 3.69
1988 2063 9.968870 GTAAAGACAAAATTAATGTGTTACCCA 57.031 29.630 6.99 0.00 33.66 4.51
1989 2064 8.880878 AAAGACAAAATTAATGTGTTACCCAC 57.119 30.769 6.99 0.00 44.78 4.61
1990 2065 7.833285 AGACAAAATTAATGTGTTACCCACT 57.167 32.000 6.51 0.00 44.81 4.00
2064 2149 7.849804 ACTACAACACATTTTATAGAGCCAG 57.150 36.000 0.00 0.00 0.00 4.85
2104 2190 7.986085 AATATTATTGAGGTGAGGTGCATAC 57.014 36.000 0.00 0.00 0.00 2.39
2302 2390 8.601845 AACCATAAGCAAACAAGGAAATAAAC 57.398 30.769 0.00 0.00 0.00 2.01
2359 2447 0.914417 CCATACCACACCCTCCCACT 60.914 60.000 0.00 0.00 0.00 4.00
2361 2449 0.417841 ATACCACACCCTCCCACTCT 59.582 55.000 0.00 0.00 0.00 3.24
2369 2457 2.136026 ACCCTCCCACTCTTTTTCACT 58.864 47.619 0.00 0.00 0.00 3.41
2398 2486 0.603065 CACTCTCCGTGTCACCATGA 59.397 55.000 0.00 0.00 38.84 3.07
2453 2541 0.522915 GAATGCAGCTCGCTTTGCTC 60.523 55.000 11.90 0.00 43.06 4.26
2497 2585 2.668457 GTCTGAATCCTAACACGCACAG 59.332 50.000 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 8.296713 GCAAACTCATCATAAACTGGACTTTTA 58.703 33.333 0.00 0.00 0.00 1.52
18 19 7.147976 GCAAACTCATCATAAACTGGACTTTT 58.852 34.615 0.00 0.00 0.00 2.27
19 20 6.265196 TGCAAACTCATCATAAACTGGACTTT 59.735 34.615 0.00 0.00 0.00 2.66
20 21 5.769662 TGCAAACTCATCATAAACTGGACTT 59.230 36.000 0.00 0.00 0.00 3.01
21 22 5.316167 TGCAAACTCATCATAAACTGGACT 58.684 37.500 0.00 0.00 0.00 3.85
22 23 5.627499 TGCAAACTCATCATAAACTGGAC 57.373 39.130 0.00 0.00 0.00 4.02
23 24 8.523915 AATATGCAAACTCATCATAAACTGGA 57.476 30.769 0.00 0.00 0.00 3.86
24 25 9.027129 CAAATATGCAAACTCATCATAAACTGG 57.973 33.333 0.00 0.00 0.00 4.00
25 26 9.577110 ACAAATATGCAAACTCATCATAAACTG 57.423 29.630 0.00 0.00 0.00 3.16
30 31 9.585099 GGAAAACAAATATGCAAACTCATCATA 57.415 29.630 0.00 0.00 0.00 2.15
31 32 8.316214 AGGAAAACAAATATGCAAACTCATCAT 58.684 29.630 0.00 0.00 0.00 2.45
32 33 7.669427 AGGAAAACAAATATGCAAACTCATCA 58.331 30.769 0.00 0.00 0.00 3.07
33 34 8.437742 CAAGGAAAACAAATATGCAAACTCATC 58.562 33.333 0.00 0.00 0.00 2.92
34 35 7.933033 ACAAGGAAAACAAATATGCAAACTCAT 59.067 29.630 0.00 0.00 0.00 2.90
35 36 7.224362 CACAAGGAAAACAAATATGCAAACTCA 59.776 33.333 0.00 0.00 0.00 3.41
36 37 7.437862 TCACAAGGAAAACAAATATGCAAACTC 59.562 33.333 0.00 0.00 0.00 3.01
37 38 7.271511 TCACAAGGAAAACAAATATGCAAACT 58.728 30.769 0.00 0.00 0.00 2.66
38 39 7.475771 TCACAAGGAAAACAAATATGCAAAC 57.524 32.000 0.00 0.00 0.00 2.93
39 40 7.930325 TCATCACAAGGAAAACAAATATGCAAA 59.070 29.630 0.00 0.00 0.00 3.68
40 41 7.440198 TCATCACAAGGAAAACAAATATGCAA 58.560 30.769 0.00 0.00 0.00 4.08
41 42 6.990798 TCATCACAAGGAAAACAAATATGCA 58.009 32.000 0.00 0.00 0.00 3.96
42 43 6.532657 CCTCATCACAAGGAAAACAAATATGC 59.467 38.462 0.00 0.00 35.83 3.14
43 44 7.605449 ACCTCATCACAAGGAAAACAAATATG 58.395 34.615 0.00 0.00 37.35 1.78
44 45 7.671398 AGACCTCATCACAAGGAAAACAAATAT 59.329 33.333 0.00 0.00 37.35 1.28
45 46 7.004086 AGACCTCATCACAAGGAAAACAAATA 58.996 34.615 0.00 0.00 37.35 1.40
46 47 5.835280 AGACCTCATCACAAGGAAAACAAAT 59.165 36.000 0.00 0.00 37.35 2.32
47 48 5.200483 AGACCTCATCACAAGGAAAACAAA 58.800 37.500 0.00 0.00 37.35 2.83
48 49 4.792068 AGACCTCATCACAAGGAAAACAA 58.208 39.130 0.00 0.00 37.35 2.83
49 50 4.437682 AGACCTCATCACAAGGAAAACA 57.562 40.909 0.00 0.00 37.35 2.83
50 51 5.299279 TGAAAGACCTCATCACAAGGAAAAC 59.701 40.000 0.00 0.00 37.35 2.43
51 52 5.445069 TGAAAGACCTCATCACAAGGAAAA 58.555 37.500 0.00 0.00 37.35 2.29
52 53 5.047566 TGAAAGACCTCATCACAAGGAAA 57.952 39.130 0.00 0.00 37.35 3.13
53 54 4.705110 TGAAAGACCTCATCACAAGGAA 57.295 40.909 0.00 0.00 37.35 3.36
54 55 4.705110 TTGAAAGACCTCATCACAAGGA 57.295 40.909 0.00 0.00 37.35 3.36
55 56 5.972107 ATTTGAAAGACCTCATCACAAGG 57.028 39.130 0.00 0.00 39.96 3.61
56 57 7.478322 CCATATTTGAAAGACCTCATCACAAG 58.522 38.462 0.00 0.00 0.00 3.16
57 58 6.127647 GCCATATTTGAAAGACCTCATCACAA 60.128 38.462 0.00 0.00 0.00 3.33
58 59 5.357878 GCCATATTTGAAAGACCTCATCACA 59.642 40.000 0.00 0.00 0.00 3.58
59 60 5.221126 GGCCATATTTGAAAGACCTCATCAC 60.221 44.000 0.00 0.00 0.00 3.06
60 61 4.889409 GGCCATATTTGAAAGACCTCATCA 59.111 41.667 0.00 0.00 0.00 3.07
61 62 4.889409 TGGCCATATTTGAAAGACCTCATC 59.111 41.667 0.00 0.00 0.00 2.92
62 63 4.646492 GTGGCCATATTTGAAAGACCTCAT 59.354 41.667 9.72 0.00 0.00 2.90
63 64 4.016444 GTGGCCATATTTGAAAGACCTCA 58.984 43.478 9.72 0.00 0.00 3.86
64 65 4.273318 AGTGGCCATATTTGAAAGACCTC 58.727 43.478 9.72 0.00 0.00 3.85
65 66 4.322057 AGTGGCCATATTTGAAAGACCT 57.678 40.909 9.72 0.00 0.00 3.85
66 67 5.405935 AAAGTGGCCATATTTGAAAGACC 57.594 39.130 9.72 0.00 0.00 3.85
67 68 8.088365 AGTTTAAAGTGGCCATATTTGAAAGAC 58.912 33.333 22.54 13.03 0.00 3.01
68 69 8.189119 AGTTTAAAGTGGCCATATTTGAAAGA 57.811 30.769 22.54 5.71 0.00 2.52
69 70 8.087750 TGAGTTTAAAGTGGCCATATTTGAAAG 58.912 33.333 22.54 0.00 0.00 2.62
70 71 7.957002 TGAGTTTAAAGTGGCCATATTTGAAA 58.043 30.769 22.54 14.44 0.00 2.69
71 72 7.531857 TGAGTTTAAAGTGGCCATATTTGAA 57.468 32.000 22.54 18.87 0.00 2.69
72 73 7.716799 ATGAGTTTAAAGTGGCCATATTTGA 57.283 32.000 22.54 15.03 0.00 2.69
73 74 8.658609 CAAATGAGTTTAAAGTGGCCATATTTG 58.341 33.333 22.54 15.15 0.00 2.32
74 75 8.592809 TCAAATGAGTTTAAAGTGGCCATATTT 58.407 29.630 9.72 16.13 0.00 1.40
75 76 8.133024 TCAAATGAGTTTAAAGTGGCCATATT 57.867 30.769 9.72 10.16 0.00 1.28
76 77 7.716799 TCAAATGAGTTTAAAGTGGCCATAT 57.283 32.000 9.72 0.00 0.00 1.78
77 78 7.531857 TTCAAATGAGTTTAAAGTGGCCATA 57.468 32.000 9.72 0.00 0.00 2.74
78 79 6.418057 TTCAAATGAGTTTAAAGTGGCCAT 57.582 33.333 9.72 0.00 0.00 4.40
79 80 5.860941 TTCAAATGAGTTTAAAGTGGCCA 57.139 34.783 0.00 0.00 0.00 5.36
80 81 7.546778 TTTTTCAAATGAGTTTAAAGTGGCC 57.453 32.000 0.00 0.00 0.00 5.36
179 180 6.013898 GGGTTTAGAGTTTTAGTAGTCCAGGT 60.014 42.308 0.00 0.00 0.00 4.00
215 229 3.471680 CATCTGCTCTTAGGGTTTAGGC 58.528 50.000 0.00 0.00 0.00 3.93
226 240 1.004044 CACCAGGTTCCATCTGCTCTT 59.996 52.381 0.00 0.00 0.00 2.85
241 255 3.860641 AGTTTTTGCCAAGTTTCACCAG 58.139 40.909 0.00 0.00 0.00 4.00
299 313 7.604549 ACATGAATACATTTGACAGATGCAAA 58.395 30.769 0.00 0.00 39.31 3.68
300 314 7.160547 ACATGAATACATTTGACAGATGCAA 57.839 32.000 0.00 0.00 34.15 4.08
302 316 8.562052 TCATACATGAATACATTTGACAGATGC 58.438 33.333 0.00 0.00 34.15 3.91
322 337 5.324409 AGGGCTTTGAAACAAGATCATACA 58.676 37.500 0.00 0.00 0.00 2.29
325 340 4.410099 TGAGGGCTTTGAAACAAGATCAT 58.590 39.130 0.00 0.00 0.00 2.45
347 362 4.356405 TCATATTCATGTTCCTGGCGAT 57.644 40.909 0.00 0.00 33.57 4.58
349 364 4.898829 TTTCATATTCATGTTCCTGGCG 57.101 40.909 0.00 0.00 33.57 5.69
427 442 6.482973 TCATTTCCCATGCTTTTTCTTTTGAC 59.517 34.615 0.00 0.00 0.00 3.18
503 518 7.363443 GCTTAGCTTTTGATTATGTTTGGGGTA 60.363 37.037 0.00 0.00 0.00 3.69
543 558 7.544915 AGATTCTCGTGCATACATGATTATCTG 59.455 37.037 0.00 0.00 40.98 2.90
812 844 2.671070 GCAGAACCAAAATAAGGGTGCG 60.671 50.000 0.00 0.00 37.82 5.34
848 880 3.794481 TCACCGAAATGGGGACGA 58.206 55.556 0.00 0.00 45.51 4.20
859 891 4.388499 GCTTCCCCGCTTCACCGA 62.388 66.667 0.00 0.00 0.00 4.69
943 975 1.787057 GATCGATCACCGGCGAGTCT 61.787 60.000 20.52 0.00 40.14 3.24
997 1029 0.316204 GCTGTGCTTTCTGCCATTGT 59.684 50.000 0.00 0.00 42.00 2.71
1012 1044 0.609131 GGTGGTGGTGCTATTGCTGT 60.609 55.000 0.00 0.00 40.48 4.40
1017 1049 1.616159 GTTGTGGTGGTGGTGCTATT 58.384 50.000 0.00 0.00 0.00 1.73
1086 1118 2.343387 GGTGGTGCCATTGGTTGC 59.657 61.111 4.26 0.00 37.17 4.17
1421 1496 2.295349 CAGCAGAAACACCAGCAAGAAT 59.705 45.455 0.00 0.00 0.00 2.40
1537 1612 3.818773 CTGTTTTCCTAACGTTCATGGGT 59.181 43.478 2.82 0.00 0.00 4.51
1554 1629 6.150140 CGAAGAGAAGAATCAAATCCCTGTTT 59.850 38.462 0.00 0.00 0.00 2.83
1588 1663 8.833231 TGTGAAGTCTTTCTTTTCTAGTATGG 57.167 34.615 0.00 0.00 36.40 2.74
1593 1668 6.147000 GCCTCTGTGAAGTCTTTCTTTTCTAG 59.853 42.308 0.00 0.00 36.40 2.43
1594 1669 5.992217 GCCTCTGTGAAGTCTTTCTTTTCTA 59.008 40.000 0.00 0.00 36.40 2.10
1639 1714 2.358090 CCAACTGCATCATTTCCCCCTA 60.358 50.000 0.00 0.00 0.00 3.53
1655 1730 0.988832 TTAGTCGCCCCATTCCAACT 59.011 50.000 0.00 0.00 0.00 3.16
1795 1870 1.203052 CTGGAATTTTGCAGCCACGAT 59.797 47.619 0.00 0.00 39.74 3.73
1796 1871 0.597568 CTGGAATTTTGCAGCCACGA 59.402 50.000 0.00 0.00 39.74 4.35
1877 1952 1.352622 TGTCCCAGGCCACTTGAGTT 61.353 55.000 5.01 0.00 0.00 3.01
1981 2056 1.451387 CGGGATGGCAGTGGGTAAC 60.451 63.158 0.00 0.00 0.00 2.50
1982 2057 2.994699 CGGGATGGCAGTGGGTAA 59.005 61.111 0.00 0.00 0.00 2.85
1983 2058 3.792736 GCGGGATGGCAGTGGGTA 61.793 66.667 0.00 0.00 0.00 3.69
1985 2060 4.738998 TTGCGGGATGGCAGTGGG 62.739 66.667 0.00 0.00 44.94 4.61
1986 2061 1.606885 AAATTGCGGGATGGCAGTGG 61.607 55.000 0.00 0.00 44.94 4.00
1987 2062 0.247185 AAAATTGCGGGATGGCAGTG 59.753 50.000 0.00 0.00 44.94 3.66
1988 2063 0.532115 GAAAATTGCGGGATGGCAGT 59.468 50.000 0.00 0.00 44.94 4.40
1989 2064 0.179103 GGAAAATTGCGGGATGGCAG 60.179 55.000 0.00 0.00 44.94 4.85
1990 2065 1.896694 GGAAAATTGCGGGATGGCA 59.103 52.632 0.00 0.00 42.12 4.92
2104 2190 7.117523 TGTGGTTTGAATTTCTTTGTTGAACTG 59.882 33.333 0.00 0.00 0.00 3.16
2183 2269 9.655769 GTGCTTGTGATTGAACTATATATGTTG 57.344 33.333 0.00 0.00 0.00 3.33
2343 2431 0.192566 AAGAGTGGGAGGGTGTGGTA 59.807 55.000 0.00 0.00 0.00 3.25
2359 2447 3.068024 GTGTCATGGCCAAGTGAAAAAGA 59.932 43.478 10.96 0.00 0.00 2.52
2361 2449 3.030291 AGTGTCATGGCCAAGTGAAAAA 58.970 40.909 10.96 0.00 0.00 1.94
2369 2457 1.296392 CGGAGAGTGTCATGGCCAA 59.704 57.895 10.96 0.00 0.00 4.52
2402 2490 4.738998 TGAGGTTGGCCGGCCATG 62.739 66.667 46.94 0.00 46.64 3.66
2403 2491 4.740822 GTGAGGTTGGCCGGCCAT 62.741 66.667 46.94 33.92 46.64 4.40
2453 2541 1.204704 TGATCACTCGGCCAGTTAGTG 59.795 52.381 15.07 15.07 41.58 2.74
2497 2585 4.518217 CATGTTTCGTCTTGAACACTGTC 58.482 43.478 0.00 0.00 35.97 3.51


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

AutoCloner maintained by Alex Coulton.