Multiple sequence alignment - TraesCS3A01G006300

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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 TraesCS3A01G006300 chr3A 100.000 3687 0 0 1 3687 7276146 7272460 0.000000e+00 6809.0
1 TraesCS3A01G006300 chr3A 98.824 85 1 0 42 126 197111136 197111220 6.380000e-33 152.0
2 TraesCS3A01G006300 chr3B 90.062 3059 161 51 275 3272 4784955 4787931 0.000000e+00 3832.0
3 TraesCS3A01G006300 chr3B 90.036 3061 160 52 275 3272 3898029 3901007 0.000000e+00 3829.0
4 TraesCS3A01G006300 chr3B 93.243 444 22 5 3236 3671 3901014 3901457 0.000000e+00 647.0
5 TraesCS3A01G006300 chr3B 92.793 444 24 5 3236 3671 4787938 4788381 1.440000e-178 636.0
6 TraesCS3A01G006300 chr3B 83.478 115 3 4 124 238 3897794 3897892 3.920000e-15 93.5
7 TraesCS3A01G006300 chr3B 83.478 115 3 4 124 238 4784720 4784818 3.920000e-15 93.5
8 TraesCS3A01G006300 chr3B 95.556 45 1 1 1 44 3897753 3897797 1.840000e-08 71.3
9 TraesCS3A01G006300 chr3B 95.556 45 1 1 1 44 4784679 4784723 1.840000e-08 71.3
10 TraesCS3A01G006300 chr3D 87.395 2269 152 62 622 2794 1748171 1750401 0.000000e+00 2483.0
11 TraesCS3A01G006300 chr3D 82.133 347 33 15 243 569 1747836 1748173 1.690000e-68 270.0
12 TraesCS3A01G006300 chr3D 86.022 186 13 10 3474 3654 1751026 1751203 1.750000e-43 187.0
13 TraesCS3A01G006300 chr3D 92.174 115 5 1 124 238 1747608 1747718 3.810000e-35 159.0
14 TraesCS3A01G006300 chr3D 94.000 100 6 0 42 141 116159960 116160059 6.380000e-33 152.0
15 TraesCS3A01G006300 chr3D 94.030 67 4 0 3157 3223 581576644 581576710 6.510000e-18 102.0
16 TraesCS3A01G006300 chr7A 95.146 103 2 2 26 127 47050716 47050816 3.810000e-35 159.0
17 TraesCS3A01G006300 chr7A 94.000 100 6 0 28 127 736097202 736097301 6.380000e-33 152.0
18 TraesCS3A01G006300 chr6D 94.286 105 4 2 24 127 14202697 14202800 3.810000e-35 159.0
19 TraesCS3A01G006300 chr6D 94.286 70 4 0 2180 2249 362635200 362635269 1.400000e-19 108.0
20 TraesCS3A01G006300 chr6D 94.286 70 4 0 2180 2249 362888789 362888858 1.400000e-19 108.0
21 TraesCS3A01G006300 chr6D 92.857 70 5 0 2180 2249 362954662 362954731 6.510000e-18 102.0
22 TraesCS3A01G006300 chr5D 98.876 89 1 0 38 126 17391245 17391157 3.810000e-35 159.0
23 TraesCS3A01G006300 chr5A 97.802 91 2 0 41 131 481924203 481924293 1.370000e-34 158.0
24 TraesCS3A01G006300 chr4B 97.802 91 2 0 37 127 496424329 496424239 1.370000e-34 158.0
25 TraesCS3A01G006300 chr2D 93.269 104 4 2 23 126 49878626 49878726 2.290000e-32 150.0
26 TraesCS3A01G006300 chr6A 94.286 70 4 0 2180 2249 502929856 502929925 1.400000e-19 108.0
27 TraesCS3A01G006300 chr6A 94.286 70 4 0 2180 2249 503249528 503249597 1.400000e-19 108.0
28 TraesCS3A01G006300 chr6B 92.857 70 5 0 2180 2249 543826371 543826440 6.510000e-18 102.0


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 TraesCS3A01G006300 chr3A 7272460 7276146 3686 True 6809.00 6809 100.00000 1 3687 1 chr3A.!!$R1 3686
1 TraesCS3A01G006300 chr3B 3897753 3901457 3704 False 1160.20 3829 90.57825 1 3671 4 chr3B.!!$F1 3670
2 TraesCS3A01G006300 chr3B 4784679 4788381 3702 False 1158.20 3832 90.47225 1 3671 4 chr3B.!!$F2 3670
3 TraesCS3A01G006300 chr3D 1747608 1751203 3595 False 774.75 2483 86.93100 124 3654 4 chr3D.!!$F3 3530

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
920 1095 0.111253 CCTCTTTGCACTTGACCCCT 59.889 55.0 0.00 0.0 0.00 4.79 F
1159 1344 0.178767 AACAGTGACACAGAGCAGCA 59.821 50.0 8.59 0.0 0.00 4.41 F
1852 2055 0.184933 AGGCCAAAGTTGTGCCTACA 59.815 50.0 18.70 0.0 46.18 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2176 2393 0.108329 GGTGACCATGTCCACCTACG 60.108 60.000 20.36 0.0 33.89 3.51 R
2353 2571 1.135831 CGCAAACACACCGAATATGCA 60.136 47.619 0.00 0.0 32.80 3.96 R
3595 4051 1.957562 GATGGCATCATCAGCAGCC 59.042 57.895 22.23 0.0 46.74 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
40 42 5.221048 CCCGGCACAAGATATTCTTTTAAGG 60.221 44.000 0.00 0.00 33.78 2.69
41 43 5.357032 CCGGCACAAGATATTCTTTTAAGGT 59.643 40.000 0.00 0.00 33.78 3.50
42 44 6.540914 CCGGCACAAGATATTCTTTTAAGGTA 59.459 38.462 0.00 0.00 33.78 3.08
43 45 7.407337 CGGCACAAGATATTCTTTTAAGGTAC 58.593 38.462 0.00 0.00 33.78 3.34
44 46 7.280205 CGGCACAAGATATTCTTTTAAGGTACT 59.720 37.037 0.00 0.00 35.09 2.73
45 47 8.957466 GGCACAAGATATTCTTTTAAGGTACTT 58.043 33.333 0.00 0.00 43.35 2.24
46 48 9.989869 GCACAAGATATTCTTTTAAGGTACTTC 57.010 33.333 0.00 0.00 41.02 3.01
64 66 9.646522 AGGTACTTCCTCCGTAAACTAATATAA 57.353 33.333 0.00 0.00 44.42 0.98
65 67 9.905171 GGTACTTCCTCCGTAAACTAATATAAG 57.095 37.037 0.00 0.00 0.00 1.73
68 70 8.358895 ACTTCCTCCGTAAACTAATATAAGAGC 58.641 37.037 0.00 0.00 0.00 4.09
69 71 6.906659 TCCTCCGTAAACTAATATAAGAGCG 58.093 40.000 0.00 0.00 0.00 5.03
70 72 6.488006 TCCTCCGTAAACTAATATAAGAGCGT 59.512 38.462 0.00 0.00 0.00 5.07
71 73 7.013655 TCCTCCGTAAACTAATATAAGAGCGTT 59.986 37.037 0.00 0.00 0.00 4.84
72 74 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
73 75 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
74 76 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
75 77 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
120 122 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
121 123 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
122 124 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
164 166 4.579869 GATTTCCCATGTGCGTAGGATAT 58.420 43.478 0.00 0.00 0.00 1.63
187 189 1.954528 GCATGGATGGATGCTTCCG 59.045 57.895 13.54 2.84 45.89 4.30
197 199 1.666189 GGATGCTTCCGCTCAGTTTAC 59.334 52.381 2.39 0.00 36.97 2.01
238 240 3.548014 CCAGTAGTTTTGAGCCACGTTTG 60.548 47.826 0.00 0.00 0.00 2.93
239 241 3.064820 CAGTAGTTTTGAGCCACGTTTGT 59.935 43.478 0.00 0.00 0.00 2.83
250 365 3.004315 AGCCACGTTTGTTAATGAAGGTG 59.996 43.478 14.54 14.54 39.84 4.00
257 372 5.619607 CGTTTGTTAATGAAGGTGAAGTTCG 59.380 40.000 0.00 0.00 0.00 3.95
262 377 2.234300 TGAAGGTGAAGTTCGTGTCC 57.766 50.000 0.00 0.00 0.00 4.02
265 380 3.322541 TGAAGGTGAAGTTCGTGTCCATA 59.677 43.478 0.00 0.00 0.00 2.74
314 429 8.299570 ACACAAGAAACTATAATTTGCTTCCAG 58.700 33.333 0.00 0.00 0.00 3.86
345 465 9.930693 AGTAGTAGGAGATAGTTTCTTGTTTTG 57.069 33.333 0.00 0.00 33.74 2.44
388 515 1.479323 TGCTAGCAGGTACCTAAACCG 59.521 52.381 15.80 2.55 44.77 4.44
478 615 9.077885 TCAATATACCAGGGAAATAATTGAAGC 57.922 33.333 0.00 0.00 0.00 3.86
484 621 5.449553 CAGGGAAATAATTGAAGCTACCCT 58.550 41.667 0.00 0.00 44.83 4.34
486 623 6.712547 CAGGGAAATAATTGAAGCTACCCTAG 59.287 42.308 0.00 0.00 42.52 3.02
530 671 0.546598 GGCTACCTTACACATGGGCT 59.453 55.000 0.00 0.00 0.00 5.19
531 672 1.766496 GGCTACCTTACACATGGGCTA 59.234 52.381 0.00 0.00 0.00 3.93
657 802 3.841643 AGCTTGTTTCATGCATGCTAAC 58.158 40.909 25.31 25.31 42.81 2.34
659 804 3.367703 GCTTGTTTCATGCATGCTAACCT 60.368 43.478 27.24 0.00 35.13 3.50
661 806 4.439305 TGTTTCATGCATGCTAACCTTC 57.561 40.909 27.24 13.33 0.00 3.46
830 998 3.100671 AGGGTTAGCTCCACTTCTACTG 58.899 50.000 0.00 0.00 0.00 2.74
907 1082 1.622811 CTGCTGTCTGTCTCCCTCTTT 59.377 52.381 0.00 0.00 0.00 2.52
920 1095 0.111253 CCTCTTTGCACTTGACCCCT 59.889 55.000 0.00 0.00 0.00 4.79
993 1170 2.787680 CGCCTACTCGATTAAGAAACCG 59.212 50.000 0.00 0.00 0.00 4.44
1123 1304 1.303074 ACCGTCACCAGTAGCTCGA 60.303 57.895 0.00 0.00 0.00 4.04
1159 1344 0.178767 AACAGTGACACAGAGCAGCA 59.821 50.000 8.59 0.00 0.00 4.41
1224 1410 3.039988 CTCCGGGCGATGTACGAT 58.960 61.111 0.00 0.00 45.77 3.73
1287 1473 2.564975 GTGGTCGTCGACGGTGAT 59.435 61.111 35.05 0.00 40.29 3.06
1296 1482 1.025041 TCGACGGTGATGATGAGGAG 58.975 55.000 0.00 0.00 0.00 3.69
1298 1484 0.390860 GACGGTGATGATGAGGAGGG 59.609 60.000 0.00 0.00 0.00 4.30
1434 1623 2.686835 GCCTCCTCCAGCTCCACT 60.687 66.667 0.00 0.00 0.00 4.00
1495 1684 5.065914 GTCATCAGCTGGCTTATAATTCCA 58.934 41.667 15.13 6.47 0.00 3.53
1503 1692 3.053693 TGGCTTATAATTCCAGCACAGGT 60.054 43.478 5.95 0.00 35.05 4.00
1515 1704 0.319900 GCACAGGTGACGATGACTGT 60.320 55.000 3.10 0.00 44.36 3.55
1532 1721 2.103042 GTGCGCTCTGGATGGACAC 61.103 63.158 9.73 0.00 0.00 3.67
1664 1859 2.950194 GCGCTCGAGCTCGGTAAC 60.950 66.667 33.98 19.67 40.29 2.50
1680 1875 6.206243 GCTCGGTAACTACCTACATCAGATTA 59.794 42.308 4.45 0.00 44.25 1.75
1681 1876 7.255381 GCTCGGTAACTACCTACATCAGATTAA 60.255 40.741 4.45 0.00 44.25 1.40
1683 1878 9.139734 TCGGTAACTACCTACATCAGATTAATT 57.860 33.333 4.45 0.00 44.25 1.40
1684 1879 9.760077 CGGTAACTACCTACATCAGATTAATTT 57.240 33.333 4.45 0.00 44.25 1.82
1852 2055 0.184933 AGGCCAAAGTTGTGCCTACA 59.815 50.000 18.70 0.00 46.18 2.74
1869 2072 1.122019 ACAAAGGACCCTCAGAGCGT 61.122 55.000 0.00 0.00 0.00 5.07
1887 2090 2.350498 GCGTCGTTGCAAAGGTACATAT 59.650 45.455 12.54 0.00 32.62 1.78
1889 2092 4.549489 GCGTCGTTGCAAAGGTACATATAC 60.549 45.833 12.54 0.05 32.62 1.47
1890 2093 4.563580 CGTCGTTGCAAAGGTACATATACA 59.436 41.667 12.54 0.00 32.40 2.29
1891 2094 5.276207 CGTCGTTGCAAAGGTACATATACAG 60.276 44.000 12.54 0.00 32.40 2.74
1892 2095 5.006358 GTCGTTGCAAAGGTACATATACAGG 59.994 44.000 12.54 0.00 32.40 4.00
1900 2103 3.008375 AGGTACATATACAGGCAGCATGG 59.992 47.826 12.54 0.00 31.87 3.66
1901 2104 3.007940 GGTACATATACAGGCAGCATGGA 59.992 47.826 12.54 2.26 31.87 3.41
1927 2130 3.433306 TTCTCCCTATTGTTGTGGTGG 57.567 47.619 0.00 0.00 0.00 4.61
2058 2262 2.746362 CAAAGTTCTGCAGGATCTGGTC 59.254 50.000 15.13 0.00 31.21 4.02
2100 2317 4.024556 CGTACCATGATTTCTTCTCATGCC 60.025 45.833 7.59 0.00 45.59 4.40
2176 2393 3.896648 TTCTGAATGAAACCAACTCGC 57.103 42.857 0.00 0.00 0.00 5.03
2254 2471 0.729116 CTGCAAGTCAAGGTATGCGG 59.271 55.000 0.00 0.00 41.61 5.69
2256 2474 1.305219 GCAAGTCAAGGTATGCGGCA 61.305 55.000 4.58 4.58 0.00 5.69
2263 2481 0.393808 AAGGTATGCGGCAATCGGTT 60.394 50.000 6.82 0.00 39.69 4.44
2267 2485 2.139917 GTATGCGGCAATCGGTTATCA 58.860 47.619 6.82 0.00 39.69 2.15
2299 2517 3.771577 ACTCTTTCGACCCAATTCACT 57.228 42.857 0.00 0.00 0.00 3.41
2314 2532 7.554118 ACCCAATTCACTTCTATGAACTACATG 59.446 37.037 0.00 0.00 41.29 3.21
2353 2571 5.916318 TGTATGAATTATAACCCGGTTCGT 58.084 37.500 5.94 0.00 0.00 3.85
2369 2587 2.087501 TCGTGCATATTCGGTGTGTT 57.912 45.000 0.00 0.00 0.00 3.32
2380 2600 2.655044 GTGTGTTTGCGCAGGTGC 60.655 61.111 11.31 3.57 35.58 5.01
2412 2632 4.659172 TTCTGGCCGGTGCAAGGG 62.659 66.667 12.43 5.82 39.20 3.95
2667 2919 3.343617 TGTGATCGGGATTTGAAGTTCC 58.656 45.455 0.00 0.00 0.00 3.62
2694 2946 9.654663 GATCACTGTAACTAGTCCAATAAAACT 57.345 33.333 0.00 0.00 0.00 2.66
2825 3087 3.387962 TGCAGGGAACATAAGATCCTCT 58.612 45.455 0.00 0.00 36.94 3.69
2861 3125 0.930310 CAACGCACGATCGGATTCAT 59.070 50.000 20.98 0.00 0.00 2.57
2871 3135 5.453266 CACGATCGGATTCATTGAAATGTTG 59.547 40.000 20.98 0.00 37.65 3.33
2872 3136 5.123820 ACGATCGGATTCATTGAAATGTTGT 59.876 36.000 20.98 0.00 37.65 3.32
2891 3186 7.173863 TGTTGTTATCTTGAGTTCTTCGAAC 57.826 36.000 0.00 0.00 0.00 3.95
2943 3238 4.380843 AAGGGTATTTGACACCACATGA 57.619 40.909 0.00 0.00 37.84 3.07
2956 3287 6.312426 TGACACCACATGAAAAACAAATGAAC 59.688 34.615 0.00 0.00 0.00 3.18
2966 3297 9.651913 ATGAAAAACAAATGAACTGTACAAAGT 57.348 25.926 0.00 0.00 0.00 2.66
2969 3300 6.524101 AACAAATGAACTGTACAAAGTGGT 57.476 33.333 0.00 0.00 0.00 4.16
2974 3308 6.767524 ATGAACTGTACAAAGTGGTTTGAA 57.232 33.333 4.91 0.00 45.22 2.69
3001 3335 6.581712 CAAACCAATCCTCAGGAAAGAAAAA 58.418 36.000 0.00 0.00 34.34 1.94
3004 3338 6.136155 ACCAATCCTCAGGAAAGAAAAAGAA 58.864 36.000 0.00 0.00 34.34 2.52
3089 3423 0.704076 CCTCAGGGGTTTGGATCCAA 59.296 55.000 23.63 23.63 0.00 3.53
3090 3424 1.341383 CCTCAGGGGTTTGGATCCAAG 60.341 57.143 25.69 14.13 37.24 3.61
3091 3425 1.355720 CTCAGGGGTTTGGATCCAAGT 59.644 52.381 25.69 8.18 37.24 3.16
3153 3491 1.134250 GGGAGCCTTCCTGAGATGAAC 60.134 57.143 0.00 0.00 43.49 3.18
3268 3652 8.234546 AGTAGTTAAAATCAATTTCGCGTCAAT 58.765 29.630 5.77 2.95 32.27 2.57
3330 3736 5.623335 TCGTGCAAACCTTATTATTTCACG 58.377 37.500 0.00 0.00 38.81 4.35
3408 3815 3.976169 TCGCAAACAAAAAGGGATCTTG 58.024 40.909 0.00 0.00 32.75 3.02
3575 4031 0.747255 GCGTGATTAGAGGAGGCTCA 59.253 55.000 17.69 0.00 0.00 4.26
3595 4051 2.932614 CAAGACAACTCCTTAGGATGCG 59.067 50.000 0.00 0.00 0.00 4.73
3600 4056 1.596477 CTCCTTAGGATGCGGCTGC 60.596 63.158 11.65 11.65 43.20 5.25
3644 4103 5.047021 CACTAGAGTGGAGACAATTCCTCAA 60.047 44.000 0.00 0.00 46.06 3.02
3649 4108 4.137543 GTGGAGACAATTCCTCAACAACT 58.862 43.478 6.91 0.00 46.06 3.16
3654 4113 7.013274 TGGAGACAATTCCTCAACAACTAAAAG 59.987 37.037 6.69 0.00 38.12 2.27
3671 4130 7.801716 ACTAAAAGACATTGTTGCTGAGTAA 57.198 32.000 0.00 0.00 0.00 2.24
3672 4131 8.220755 ACTAAAAGACATTGTTGCTGAGTAAA 57.779 30.769 0.00 0.00 0.00 2.01
3673 4132 8.682710 ACTAAAAGACATTGTTGCTGAGTAAAA 58.317 29.630 0.00 0.00 0.00 1.52
3674 4133 9.515020 CTAAAAGACATTGTTGCTGAGTAAAAA 57.485 29.630 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 44 8.358895 GCTCTTATATTAGTTTACGGAGGAAGT 58.641 37.037 0.00 0.00 0.00 3.01
43 45 7.537991 CGCTCTTATATTAGTTTACGGAGGAAG 59.462 40.741 0.00 0.00 0.00 3.46
44 46 7.013655 ACGCTCTTATATTAGTTTACGGAGGAA 59.986 37.037 0.00 0.00 0.00 3.36
45 47 6.488006 ACGCTCTTATATTAGTTTACGGAGGA 59.512 38.462 0.00 0.00 0.00 3.71
46 48 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
47 49 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
48 50 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
49 51 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
94 96 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
95 97 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
96 98 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
97 99 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
98 100 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
102 104 9.632638 ACGTACTCCCTCTGTAAACTAATATAA 57.367 33.333 0.00 0.00 0.00 0.98
103 105 9.060347 CACGTACTCCCTCTGTAAACTAATATA 57.940 37.037 0.00 0.00 0.00 0.86
104 106 7.559170 ACACGTACTCCCTCTGTAAACTAATAT 59.441 37.037 0.00 0.00 0.00 1.28
105 107 6.886459 ACACGTACTCCCTCTGTAAACTAATA 59.114 38.462 0.00 0.00 0.00 0.98
106 108 5.713861 ACACGTACTCCCTCTGTAAACTAAT 59.286 40.000 0.00 0.00 0.00 1.73
107 109 5.048504 CACACGTACTCCCTCTGTAAACTAA 60.049 44.000 0.00 0.00 0.00 2.24
108 110 4.456911 CACACGTACTCCCTCTGTAAACTA 59.543 45.833 0.00 0.00 0.00 2.24
109 111 3.255149 CACACGTACTCCCTCTGTAAACT 59.745 47.826 0.00 0.00 0.00 2.66
110 112 3.254166 TCACACGTACTCCCTCTGTAAAC 59.746 47.826 0.00 0.00 0.00 2.01
111 113 3.489355 TCACACGTACTCCCTCTGTAAA 58.511 45.455 0.00 0.00 0.00 2.01
112 114 3.144657 TCACACGTACTCCCTCTGTAA 57.855 47.619 0.00 0.00 0.00 2.41
113 115 2.865119 TCACACGTACTCCCTCTGTA 57.135 50.000 0.00 0.00 0.00 2.74
114 116 1.991121 TTCACACGTACTCCCTCTGT 58.009 50.000 0.00 0.00 0.00 3.41
115 117 4.082408 TGTTATTCACACGTACTCCCTCTG 60.082 45.833 0.00 0.00 0.00 3.35
116 118 4.084287 TGTTATTCACACGTACTCCCTCT 58.916 43.478 0.00 0.00 0.00 3.69
117 119 4.445452 TGTTATTCACACGTACTCCCTC 57.555 45.455 0.00 0.00 0.00 4.30
118 120 4.877378 TTGTTATTCACACGTACTCCCT 57.123 40.909 0.00 0.00 33.98 4.20
119 121 4.143263 CGTTTGTTATTCACACGTACTCCC 60.143 45.833 0.00 0.00 42.81 4.30
120 122 4.681025 TCGTTTGTTATTCACACGTACTCC 59.319 41.667 6.46 0.00 46.28 3.85
121 123 5.811018 TCGTTTGTTATTCACACGTACTC 57.189 39.130 6.46 0.00 46.28 2.59
122 124 6.774354 AATCGTTTGTTATTCACACGTACT 57.226 33.333 6.46 0.00 46.28 2.73
187 189 3.736530 CAGACATGCAGTAAACTGAGC 57.263 47.619 14.21 0.00 46.59 4.26
238 240 5.333875 GGACACGAACTTCACCTTCATTAAC 60.334 44.000 0.00 0.00 0.00 2.01
239 241 4.753107 GGACACGAACTTCACCTTCATTAA 59.247 41.667 0.00 0.00 0.00 1.40
314 429 7.885009 AGAAACTATCTCCTACTACTTCCAC 57.115 40.000 0.00 0.00 30.46 4.02
367 487 2.481449 CGGTTTAGGTACCTGCTAGCAG 60.481 54.545 33.58 33.58 43.26 4.24
478 615 8.480133 AATATGTGTAGGTTCTTCTAGGGTAG 57.520 38.462 0.00 0.00 0.00 3.18
484 621 9.515226 AAGCAAAAATATGTGTAGGTTCTTCTA 57.485 29.630 0.00 0.00 0.00 2.10
486 623 7.542130 CCAAGCAAAAATATGTGTAGGTTCTTC 59.458 37.037 0.00 0.00 0.00 2.87
657 802 6.583806 GTGACAAGCTTGTATTCAATTGAAGG 59.416 38.462 31.20 13.04 42.43 3.46
659 804 7.036996 TGTGACAAGCTTGTATTCAATTGAA 57.963 32.000 31.20 22.52 42.43 2.69
661 806 6.129378 CGTTGTGACAAGCTTGTATTCAATTG 60.129 38.462 31.20 23.01 42.43 2.32
807 975 4.339814 CAGTAGAAGTGGAGCTAACCCTAG 59.660 50.000 0.00 0.00 0.00 3.02
808 976 4.264262 ACAGTAGAAGTGGAGCTAACCCTA 60.264 45.833 0.00 0.00 0.00 3.53
809 977 3.100671 CAGTAGAAGTGGAGCTAACCCT 58.899 50.000 0.00 0.00 0.00 4.34
810 978 2.832733 ACAGTAGAAGTGGAGCTAACCC 59.167 50.000 0.00 0.00 0.00 4.11
811 979 4.705991 AGTACAGTAGAAGTGGAGCTAACC 59.294 45.833 0.00 0.00 0.00 2.85
907 1082 3.118038 GTGGAATATAGGGGTCAAGTGCA 60.118 47.826 0.00 0.00 0.00 4.57
920 1095 5.163405 GGTCTTGAGCTGTCAGTGGAATATA 60.163 44.000 0.93 0.00 32.98 0.86
993 1170 4.156190 TGCGGCTACTTATATAGAGTGAGC 59.844 45.833 0.00 10.15 0.00 4.26
1123 1304 3.272551 ACTGTTCCCTACCTAGGTGAGAT 59.727 47.826 25.33 0.00 42.03 2.75
1224 1410 2.060383 CATGGAGGAGGGCTCGTCA 61.060 63.158 0.00 0.00 43.92 4.35
1287 1473 2.359169 GGTGTCGCCCTCCTCATCA 61.359 63.158 0.00 0.00 0.00 3.07
1362 1548 2.439701 TAGTAGTCCGCCGCTGCT 60.440 61.111 0.00 0.00 34.43 4.24
1363 1549 2.278661 GTAGTAGTCCGCCGCTGC 60.279 66.667 0.00 0.00 0.00 5.25
1364 1550 1.064296 CTGTAGTAGTCCGCCGCTG 59.936 63.158 0.00 0.00 0.00 5.18
1365 1551 2.772691 GCTGTAGTAGTCCGCCGCT 61.773 63.158 0.00 0.00 0.00 5.52
1434 1623 1.202639 TCAAAGCTGAGCACCGAAGAA 60.203 47.619 7.39 0.00 0.00 2.52
1495 1684 0.037882 CAGTCATCGTCACCTGTGCT 60.038 55.000 0.00 0.00 0.00 4.40
1503 1692 1.444383 GAGCGCACAGTCATCGTCA 60.444 57.895 11.47 0.00 0.00 4.35
1515 1704 2.265739 GTGTCCATCCAGAGCGCA 59.734 61.111 11.47 0.00 0.00 6.09
1532 1721 2.265904 CCATGCTGATCGGCCATGG 61.266 63.158 28.32 28.32 35.93 3.66
1686 1881 9.346005 ACAACATATTCTCATGAATGCATAGAA 57.654 29.630 10.48 10.48 42.34 2.10
1692 1887 7.934457 AGGTAACAACATATTCTCATGAATGC 58.066 34.615 5.23 0.00 40.52 3.56
1696 1891 8.536175 TGTGTAGGTAACAACATATTCTCATGA 58.464 33.333 0.00 0.00 40.63 3.07
1800 2003 1.345741 CTCCTCCACACTGCTTCTTCA 59.654 52.381 0.00 0.00 0.00 3.02
1852 2055 4.217112 ACGCTCTGAGGGTCCTTT 57.783 55.556 20.23 0.00 36.62 3.11
1869 2072 5.113383 CCTGTATATGTACCTTTGCAACGA 58.887 41.667 4.19 0.00 0.00 3.85
1887 2090 3.301794 AATTGATCCATGCTGCCTGTA 57.698 42.857 4.26 0.00 0.00 2.74
1889 2092 2.693591 AGAAATTGATCCATGCTGCCTG 59.306 45.455 0.00 0.00 0.00 4.85
1890 2093 2.957006 GAGAAATTGATCCATGCTGCCT 59.043 45.455 0.00 0.00 0.00 4.75
1891 2094 2.035576 GGAGAAATTGATCCATGCTGCC 59.964 50.000 0.00 0.00 35.54 4.85
1892 2095 2.035576 GGGAGAAATTGATCCATGCTGC 59.964 50.000 10.50 0.00 37.33 5.25
1900 2103 6.378280 ACCACAACAATAGGGAGAAATTGATC 59.622 38.462 2.30 0.00 36.73 2.92
1901 2104 6.153340 CACCACAACAATAGGGAGAAATTGAT 59.847 38.462 2.30 0.00 36.73 2.57
1927 2130 2.746269 TTGCAGTGCAAAGAATCTTGC 58.254 42.857 27.79 3.53 45.96 4.01
2058 2262 1.672898 CACCTTTGTGCCATTGGGG 59.327 57.895 4.53 0.00 35.31 4.96
2070 2274 3.686016 AGAAATCATGGTACGCACCTTT 58.314 40.909 6.34 0.00 45.98 3.11
2131 2348 3.719268 AGCAACTAATGACCATGACCA 57.281 42.857 0.00 0.00 0.00 4.02
2132 2349 6.699575 AATTAGCAACTAATGACCATGACC 57.300 37.500 0.00 0.00 36.85 4.02
2133 2350 8.462016 AGAAAATTAGCAACTAATGACCATGAC 58.538 33.333 0.00 0.00 36.85 3.06
2134 2351 8.461222 CAGAAAATTAGCAACTAATGACCATGA 58.539 33.333 0.00 0.00 36.85 3.07
2135 2352 8.461222 TCAGAAAATTAGCAACTAATGACCATG 58.539 33.333 0.81 0.00 36.85 3.66
2136 2353 8.579850 TCAGAAAATTAGCAACTAATGACCAT 57.420 30.769 0.81 0.00 36.85 3.55
2176 2393 0.108329 GGTGACCATGTCCACCTACG 60.108 60.000 20.36 0.00 33.89 3.51
2254 2471 2.639751 GACGCATTGATAACCGATTGC 58.360 47.619 0.00 0.00 0.00 3.56
2256 2474 2.538449 GTCGACGCATTGATAACCGATT 59.462 45.455 0.00 0.00 0.00 3.34
2263 2481 4.895224 AAGAGTAGTCGACGCATTGATA 57.105 40.909 10.46 0.00 0.00 2.15
2267 2485 2.161012 TCGAAAGAGTAGTCGACGCATT 59.839 45.455 10.46 0.00 41.13 3.56
2299 2517 6.530019 TGAGACTGCATGTAGTTCATAGAA 57.470 37.500 17.99 0.00 34.67 2.10
2314 2532 4.941657 TCATACATCAGACATGAGACTGC 58.058 43.478 0.00 0.00 39.29 4.40
2331 2549 5.333568 GCACGAACCGGGTTATAATTCATAC 60.334 44.000 13.38 0.00 30.42 2.39
2353 2571 1.135831 CGCAAACACACCGAATATGCA 60.136 47.619 0.00 0.00 32.80 3.96
2380 2600 2.504244 GAACTCGTCGGTCGCCAG 60.504 66.667 0.00 0.00 39.67 4.85
2517 2737 4.116961 CGCGATCATCTAAAACTTGGGTA 58.883 43.478 0.00 0.00 0.00 3.69
2518 2738 2.936498 CGCGATCATCTAAAACTTGGGT 59.064 45.455 0.00 0.00 0.00 4.51
2519 2739 2.287915 CCGCGATCATCTAAAACTTGGG 59.712 50.000 8.23 0.00 0.00 4.12
2608 2851 8.924511 AGAATTGATCTAAAAGGAGTGAAACA 57.075 30.769 0.00 0.00 36.21 2.83
2667 2919 8.592998 GTTTTATTGGACTAGTTACAGTGATCG 58.407 37.037 0.00 0.00 0.00 3.69
2861 3125 9.950680 GAAGAACTCAAGATAACAACATTTCAA 57.049 29.630 0.00 0.00 0.00 2.69
2871 3135 8.967552 TTCTAGTTCGAAGAACTCAAGATAAC 57.032 34.615 17.38 0.00 45.90 1.89
2872 3136 9.976511 TTTTCTAGTTCGAAGAACTCAAGATAA 57.023 29.630 17.38 13.62 45.90 1.75
2891 3186 5.559148 ATCCCCATAGCTCAGTTTTCTAG 57.441 43.478 0.00 0.00 0.00 2.43
2943 3238 7.875554 ACCACTTTGTACAGTTCATTTGTTTTT 59.124 29.630 0.00 0.00 0.00 1.94
2956 3287 4.930963 TGCATTCAAACCACTTTGTACAG 58.069 39.130 0.00 0.00 38.38 2.74
2969 3300 4.262549 CCTGAGGATTGGTTTGCATTCAAA 60.263 41.667 0.00 0.00 39.67 2.69
2974 3308 2.905415 TCCTGAGGATTGGTTTGCAT 57.095 45.000 0.00 0.00 0.00 3.96
3040 3374 4.095946 TGGATCCTTGGAATTTCAAAGGG 58.904 43.478 25.81 11.51 0.00 3.95
3167 3505 4.479156 AAAGTGTGGGGATCCCTAAAAA 57.521 40.909 30.08 10.89 45.70 1.94
3168 3506 5.806955 ATAAAGTGTGGGGATCCCTAAAA 57.193 39.130 30.08 13.53 45.70 1.52
3169 3507 5.806955 AATAAAGTGTGGGGATCCCTAAA 57.193 39.130 30.08 17.79 45.70 1.85
3170 3508 6.911993 TTAATAAAGTGTGGGGATCCCTAA 57.088 37.500 30.08 16.26 45.70 2.69
3171 3509 7.474474 AATTAATAAAGTGTGGGGATCCCTA 57.526 36.000 30.08 22.83 45.70 3.53
3172 3510 6.355588 AATTAATAAAGTGTGGGGATCCCT 57.644 37.500 30.08 11.22 45.70 4.20
3173 3511 6.609616 TCAAATTAATAAAGTGTGGGGATCCC 59.390 38.462 23.95 23.95 45.71 3.85
3174 3512 7.654022 TCAAATTAATAAAGTGTGGGGATCC 57.346 36.000 1.92 1.92 0.00 3.36
3175 3513 7.979537 GGTTCAAATTAATAAAGTGTGGGGATC 59.020 37.037 0.00 0.00 0.00 3.36
3176 3514 7.456269 TGGTTCAAATTAATAAAGTGTGGGGAT 59.544 33.333 0.00 0.00 0.00 3.85
3177 3515 6.782988 TGGTTCAAATTAATAAAGTGTGGGGA 59.217 34.615 0.00 0.00 0.00 4.81
3178 3516 6.998802 TGGTTCAAATTAATAAAGTGTGGGG 58.001 36.000 0.00 0.00 0.00 4.96
3179 3517 8.894768 TTTGGTTCAAATTAATAAAGTGTGGG 57.105 30.769 0.00 0.00 0.00 4.61
3180 3518 9.757227 TCTTTGGTTCAAATTAATAAAGTGTGG 57.243 29.630 0.00 0.00 32.70 4.17
3244 3628 8.845648 CAATTGACGCGAAATTGATTTTAACTA 58.154 29.630 30.48 0.00 44.30 2.24
3330 3736 4.219115 TGTCAATCTCAGATCTAGACCCC 58.781 47.826 10.64 0.00 0.00 4.95
3408 3815 5.049267 TCTGTGGCGATTTACTTTGTTAACC 60.049 40.000 2.48 0.00 0.00 2.85
3575 4031 2.093447 CCGCATCCTAAGGAGTTGTCTT 60.093 50.000 0.00 0.00 34.05 3.01
3595 4051 1.957562 GATGGCATCATCAGCAGCC 59.042 57.895 22.23 0.00 46.74 4.85
3622 4078 5.047021 TGTTGAGGAATTGTCTCCACTCTAG 60.047 44.000 9.51 0.00 38.02 2.43
3644 4103 6.095440 ACTCAGCAACAATGTCTTTTAGTTGT 59.905 34.615 0.00 0.00 41.07 3.32


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

AutoCloner maintained by Alex Coulton.