Multiple sequence alignment - TraesCS5B01G248500

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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 TraesCS5B01G248500 chr5B 100.000 3749 0 0 1 3749 430732071 430735819 0.000000e+00 6924.0
1 TraesCS5B01G248500 chr5D 95.976 3181 102 16 573 3749 364736916 364740074 0.000000e+00 5142.0
2 TraesCS5B01G248500 chr5D 94.767 344 14 3 244 586 364736560 364736900 1.980000e-147 532.0
3 TraesCS5B01G248500 chr5D 100.000 80 0 0 65 144 364736449 364736528 8.390000e-32 148.0
4 TraesCS5B01G248500 chr5A 94.162 2535 98 24 722 3236 466012904 466015408 0.000000e+00 3816.0
5 TraesCS5B01G248500 chr5A 91.247 457 28 6 3298 3749 466015576 466016025 2.480000e-171 612.0
6 TraesCS5B01G248500 chr5A 94.118 68 4 0 3 70 276978561 276978494 1.840000e-18 104.0
7 TraesCS5B01G248500 chr2D 76.724 232 42 6 79 301 449525822 449526050 6.580000e-23 119.0
8 TraesCS5B01G248500 chr2D 94.915 59 3 0 12 70 36346401 36346459 3.990000e-15 93.5
9 TraesCS5B01G248500 chr4D 94.118 68 4 0 3 70 44409873 44409940 1.840000e-18 104.0


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 TraesCS5B01G248500 chr5B 430732071 430735819 3748 False 6924.000000 6924 100.000000 1 3749 1 chr5B.!!$F1 3748
1 TraesCS5B01G248500 chr5D 364736449 364740074 3625 False 1940.666667 5142 96.914333 65 3749 3 chr5D.!!$F1 3684
2 TraesCS5B01G248500 chr5A 466012904 466016025 3121 False 2214.000000 3816 92.704500 722 3749 2 chr5A.!!$F1 3027

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
930 971 0.036010 ACCCTTGCCATCGTCTTCAG 60.036 55.0 0.0 0.0 0.0 3.02 F
1598 1645 0.321653 GTGTTCCGGGAGATGCTTGT 60.322 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1967 2014 0.396811 ACCTTCCTCGACAAACCCTG 59.603 55.000 0.00 0.0 0.0 4.45 R
3200 3252 1.774856 AGTTGGTCCTGTGGCTTAAGT 59.225 47.619 4.02 0.0 0.0 2.24 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
17 18 4.979204 TTGTCGCCACGGTCTTAG 57.021 55.556 0.00 0.00 0.00 2.18
18 19 2.343506 TTGTCGCCACGGTCTTAGA 58.656 52.632 0.00 0.00 0.00 2.10
19 20 0.242825 TTGTCGCCACGGTCTTAGAG 59.757 55.000 0.00 0.00 0.00 2.43
20 21 0.607217 TGTCGCCACGGTCTTAGAGA 60.607 55.000 0.00 0.00 0.00 3.10
21 22 0.739561 GTCGCCACGGTCTTAGAGAT 59.260 55.000 0.00 0.00 0.00 2.75
22 23 0.738975 TCGCCACGGTCTTAGAGATG 59.261 55.000 0.00 0.00 0.00 2.90
23 24 0.249073 CGCCACGGTCTTAGAGATGG 60.249 60.000 2.86 2.86 0.00 3.51
24 25 1.112113 GCCACGGTCTTAGAGATGGA 58.888 55.000 9.70 0.00 0.00 3.41
25 26 1.480954 GCCACGGTCTTAGAGATGGAA 59.519 52.381 9.70 0.00 0.00 3.53
26 27 2.482142 GCCACGGTCTTAGAGATGGAAG 60.482 54.545 9.70 0.00 0.00 3.46
27 28 2.101582 CCACGGTCTTAGAGATGGAAGG 59.898 54.545 1.29 0.00 0.00 3.46
28 29 1.757699 ACGGTCTTAGAGATGGAAGGC 59.242 52.381 0.00 0.00 0.00 4.35
29 30 1.069358 CGGTCTTAGAGATGGAAGGCC 59.931 57.143 0.00 0.00 33.86 5.19
30 31 1.069358 GGTCTTAGAGATGGAAGGCCG 59.931 57.143 0.00 0.00 36.79 6.13
31 32 1.069358 GTCTTAGAGATGGAAGGCCGG 59.931 57.143 0.00 0.00 36.79 6.13
32 33 0.394565 CTTAGAGATGGAAGGCCGGG 59.605 60.000 2.18 0.00 36.79 5.73
33 34 1.696097 TTAGAGATGGAAGGCCGGGC 61.696 60.000 22.67 22.67 36.79 6.13
34 35 4.918201 GAGATGGAAGGCCGGGCG 62.918 72.222 23.81 0.00 36.79 6.13
55 56 4.277239 TCGAAGACCCATGCGTTG 57.723 55.556 0.00 0.00 0.00 4.10
56 57 2.032634 TCGAAGACCCATGCGTTGC 61.033 57.895 0.00 0.00 0.00 4.17
57 58 2.480555 GAAGACCCATGCGTTGCG 59.519 61.111 0.00 0.00 0.00 4.85
58 59 2.281484 AAGACCCATGCGTTGCGT 60.281 55.556 0.00 0.00 0.00 5.24
59 60 1.852067 GAAGACCCATGCGTTGCGTT 61.852 55.000 0.00 0.00 0.00 4.84
60 61 2.126888 GACCCATGCGTTGCGTTG 60.127 61.111 0.00 0.00 0.00 4.10
61 62 4.341502 ACCCATGCGTTGCGTTGC 62.342 61.111 0.00 0.00 0.00 4.17
62 63 4.041917 CCCATGCGTTGCGTTGCT 62.042 61.111 0.00 0.00 0.00 3.91
63 64 2.050168 CCATGCGTTGCGTTGCTT 60.050 55.556 0.00 0.00 0.00 3.91
144 145 1.527034 ACTAGCCAACACATGTGCTG 58.473 50.000 25.68 22.68 36.58 4.41
145 146 0.169672 CTAGCCAACACATGTGCTGC 59.830 55.000 25.68 22.90 36.58 5.25
146 147 0.250858 TAGCCAACACATGTGCTGCT 60.251 50.000 28.87 28.87 36.58 4.24
147 148 0.250858 AGCCAACACATGTGCTGCTA 60.251 50.000 26.53 0.00 35.21 3.49
148 149 0.109597 GCCAACACATGTGCTGCTAC 60.110 55.000 25.68 11.73 0.00 3.58
149 150 0.166597 CCAACACATGTGCTGCTACG 59.833 55.000 25.68 7.24 0.00 3.51
150 151 0.453282 CAACACATGTGCTGCTACGC 60.453 55.000 25.68 0.00 0.00 4.42
151 152 0.603707 AACACATGTGCTGCTACGCT 60.604 50.000 25.68 0.00 0.00 5.07
152 153 1.016130 ACACATGTGCTGCTACGCTC 61.016 55.000 25.68 0.00 0.00 5.03
153 154 1.448540 ACATGTGCTGCTACGCTCC 60.449 57.895 0.00 0.00 0.00 4.70
154 155 1.153489 CATGTGCTGCTACGCTCCT 60.153 57.895 0.00 0.00 0.00 3.69
155 156 0.742281 CATGTGCTGCTACGCTCCTT 60.742 55.000 0.00 0.00 0.00 3.36
156 157 0.460987 ATGTGCTGCTACGCTCCTTC 60.461 55.000 0.00 0.00 0.00 3.46
157 158 1.216710 GTGCTGCTACGCTCCTTCT 59.783 57.895 0.00 0.00 0.00 2.85
158 159 0.456221 GTGCTGCTACGCTCCTTCTA 59.544 55.000 0.00 0.00 0.00 2.10
159 160 1.135083 GTGCTGCTACGCTCCTTCTAA 60.135 52.381 0.00 0.00 0.00 2.10
200 204 3.336138 GGGGACGAGAGAATTGAAGTT 57.664 47.619 0.00 0.00 0.00 2.66
201 205 4.467198 GGGGACGAGAGAATTGAAGTTA 57.533 45.455 0.00 0.00 0.00 2.24
202 206 5.024785 GGGGACGAGAGAATTGAAGTTAT 57.975 43.478 0.00 0.00 0.00 1.89
203 207 5.051153 GGGGACGAGAGAATTGAAGTTATC 58.949 45.833 0.00 0.00 0.00 1.75
204 208 5.163395 GGGGACGAGAGAATTGAAGTTATCT 60.163 44.000 0.00 0.00 32.71 1.98
205 209 5.980715 GGGACGAGAGAATTGAAGTTATCTC 59.019 44.000 0.00 1.34 41.00 2.75
223 227 9.482175 AGTTATCTCTCTGAATATATGGTACCC 57.518 37.037 10.07 0.00 0.00 3.69
224 228 8.697292 GTTATCTCTCTGAATATATGGTACCCC 58.303 40.741 10.07 0.00 0.00 4.95
236 240 3.536075 TGGTACCCCATCGATCTATCA 57.464 47.619 10.07 0.00 35.17 2.15
237 241 4.061131 TGGTACCCCATCGATCTATCAT 57.939 45.455 10.07 0.00 35.17 2.45
238 242 4.023980 TGGTACCCCATCGATCTATCATC 58.976 47.826 10.07 0.00 35.17 2.92
239 243 3.385111 GGTACCCCATCGATCTATCATCC 59.615 52.174 0.00 0.00 0.00 3.51
240 244 2.472029 ACCCCATCGATCTATCATCCC 58.528 52.381 0.00 0.00 0.00 3.85
241 245 1.765314 CCCCATCGATCTATCATCCCC 59.235 57.143 0.00 0.00 0.00 4.81
242 246 1.410517 CCCATCGATCTATCATCCCCG 59.589 57.143 0.00 0.00 0.00 5.73
243 247 1.410517 CCATCGATCTATCATCCCCGG 59.589 57.143 0.00 0.00 0.00 5.73
244 248 2.379005 CATCGATCTATCATCCCCGGA 58.621 52.381 0.73 0.00 0.00 5.14
245 249 1.835494 TCGATCTATCATCCCCGGAC 58.165 55.000 0.73 0.00 0.00 4.79
246 250 1.354705 TCGATCTATCATCCCCGGACT 59.645 52.381 0.73 0.00 0.00 3.85
295 299 6.371825 CACTCCATATCAATCATCACATCCAG 59.628 42.308 0.00 0.00 0.00 3.86
305 309 3.074390 TCATCACATCCAGGAACCAGTTT 59.926 43.478 0.00 0.00 0.00 2.66
326 330 8.846211 CAGTTTTGAAGGTTATTTGAGGACTTA 58.154 33.333 0.00 0.00 0.00 2.24
374 379 4.493547 CTTCCAAGCTCTTAGAGAGTGTG 58.506 47.826 14.14 4.43 44.12 3.82
378 383 5.059833 CCAAGCTCTTAGAGAGTGTGTTTT 58.940 41.667 14.14 0.00 44.12 2.43
456 461 5.178797 AGATAGAAAACTTGGGACACATCG 58.821 41.667 0.00 0.00 39.29 3.84
465 470 0.804989 GGGACACATCGAAAGCCAAG 59.195 55.000 0.00 0.00 0.00 3.61
479 484 0.445436 GCCAAGCTCTCGTGTGATTG 59.555 55.000 9.77 9.77 34.20 2.67
607 641 8.495260 TCTTTTTAATTAGGGGAAGATCTCCTC 58.505 37.037 1.11 4.11 46.81 3.71
629 664 9.010029 TCCTCGTTTCTTTAGCAAAAATCTATT 57.990 29.630 0.00 0.00 0.00 1.73
688 723 0.952280 CATGCTCCTGTGATGGATGC 59.048 55.000 0.00 0.00 35.30 3.91
695 730 1.422781 CCTGTGATGGATGCCCTATGT 59.577 52.381 0.00 0.00 0.00 2.29
818 859 4.316025 GGCCCAATAGAATTATAGCCCA 57.684 45.455 0.00 0.00 32.93 5.36
820 861 4.263949 GGCCCAATAGAATTATAGCCCAGT 60.264 45.833 0.00 0.00 32.93 4.00
821 862 5.045140 GGCCCAATAGAATTATAGCCCAGTA 60.045 44.000 0.00 0.00 32.93 2.74
822 863 6.353951 GGCCCAATAGAATTATAGCCCAGTAT 60.354 42.308 0.00 0.00 32.93 2.12
825 866 9.614792 CCCAATAGAATTATAGCCCAGTATAAC 57.385 37.037 0.00 0.00 29.60 1.89
830 871 7.545489 AGAATTATAGCCCAGTATAACTACGC 58.455 38.462 0.00 0.00 32.82 4.42
837 878 3.005050 CCCAGTATAACTACGCGGATTGA 59.995 47.826 12.47 0.00 32.82 2.57
930 971 0.036010 ACCCTTGCCATCGTCTTCAG 60.036 55.000 0.00 0.00 0.00 3.02
1014 1055 3.474570 GCGATGCCTCCTCCCACT 61.475 66.667 0.00 0.00 0.00 4.00
1383 1430 3.804153 CTGCGGGATGCTCTGCGAT 62.804 63.158 0.00 0.00 46.63 4.58
1419 1466 1.843376 CTATGGGCCCGAGGTGGAT 60.843 63.158 19.37 5.41 42.00 3.41
1598 1645 0.321653 GTGTTCCGGGAGATGCTTGT 60.322 55.000 0.00 0.00 0.00 3.16
1599 1646 1.066430 GTGTTCCGGGAGATGCTTGTA 60.066 52.381 0.00 0.00 0.00 2.41
1647 1694 2.535984 GACATTGGTGAGCGTAATCTCG 59.464 50.000 0.00 0.00 35.90 4.04
1824 1871 1.289066 GTGTGCACTGAGGAGCGTA 59.711 57.895 19.41 0.00 31.76 4.42
1830 1877 1.950909 GCACTGAGGAGCGTAGATACT 59.049 52.381 0.00 0.00 0.00 2.12
1839 1886 3.492656 GGAGCGTAGATACTTGGAATGCA 60.493 47.826 0.00 0.00 0.00 3.96
1967 2014 2.505557 GAATGCTTGCAGCCACGC 60.506 61.111 0.87 0.00 41.51 5.34
1987 2034 0.396811 AGGGTTTGTCGAGGAAGGTG 59.603 55.000 0.00 0.00 0.00 4.00
2016 2063 9.358872 GGTTATTTTGAGAGAATGACAAATTCC 57.641 33.333 0.00 0.00 34.33 3.01
2043 2090 2.755469 GTGCCCGACATTGCCCAT 60.755 61.111 0.00 0.00 0.00 4.00
2046 2093 1.034838 TGCCCGACATTGCCCATTAC 61.035 55.000 0.00 0.00 0.00 1.89
2064 2111 5.221561 CCATTACGGTTGTATGGTGGATCTA 60.222 44.000 0.00 0.00 33.32 1.98
2067 2114 4.957296 ACGGTTGTATGGTGGATCTATTC 58.043 43.478 0.00 0.00 0.00 1.75
2073 2120 1.496060 TGGTGGATCTATTCTGCCGT 58.504 50.000 0.00 0.00 0.00 5.68
2148 2195 2.595463 GCTGCTGTGTGGAAGGCA 60.595 61.111 0.00 0.00 0.00 4.75
2151 2198 1.512996 CTGCTGTGTGGAAGGCACTG 61.513 60.000 0.00 0.00 40.86 3.66
2202 2249 1.073923 GAGTTGGGAAAGAAGGCAGGA 59.926 52.381 0.00 0.00 0.00 3.86
2235 2282 0.745845 AGGCTGCACCGAATGATCAC 60.746 55.000 0.00 0.00 46.52 3.06
2238 2285 2.321060 GCACCGAATGATCACGCG 59.679 61.111 3.53 3.53 0.00 6.01
2251 2298 0.825410 TCACGCGGGGTATGTGTTAT 59.175 50.000 9.32 0.00 35.20 1.89
2334 2381 2.622942 GTTGGATTGTGGAGTGCAGAAA 59.377 45.455 0.00 0.00 0.00 2.52
2425 2472 6.495181 TCACTCAAGGAAGAGGGATGTATATC 59.505 42.308 0.00 0.00 42.88 1.63
2436 2483 7.188381 AGAGGGATGTATATCAGATGCTAAGT 58.812 38.462 1.63 0.00 34.90 2.24
2642 2689 4.081420 GGTCTGTGGAGACTGTCATAATGT 60.081 45.833 10.88 0.00 46.96 2.71
2961 3013 1.071385 ACCCTCTTGTGTCTCAGCAAG 59.929 52.381 0.00 0.00 42.32 4.01
3131 3183 7.915508 TGATACATACTTAATGCTGTTTTCCG 58.084 34.615 0.00 0.00 39.39 4.30
3256 3333 2.024414 AGTTTTGGCCTGTGAACTGAC 58.976 47.619 3.32 0.00 31.59 3.51
3385 3543 9.929180 TGTAGGTACATCTATATTTGCAGATTC 57.071 33.333 0.00 0.00 28.88 2.52
3389 3547 7.276658 GGTACATCTATATTTGCAGATTCTCCG 59.723 40.741 0.00 0.00 28.88 4.63
3418 3576 3.747854 TTGATTGCACATTCTTTGGCA 57.252 38.095 0.00 0.00 32.07 4.92
3459 3617 6.756542 GGATTTAACTTGCTGTTGTGTTCTTT 59.243 34.615 6.04 0.00 39.55 2.52
3493 3655 1.674962 GAGGGCATCAGAAACTCATGC 59.325 52.381 0.00 0.00 41.93 4.06
3583 3745 4.466828 CTTGCTACCTGTTGTTGATTTCG 58.533 43.478 0.00 0.00 0.00 3.46
3599 3761 3.401033 TTTCGGAAGAGACATGAAGCA 57.599 42.857 0.00 0.00 43.69 3.91
3681 3843 4.557205 ACAAGGACAAAGATCGACACTAC 58.443 43.478 0.00 0.00 0.00 2.73
3688 3850 5.892568 ACAAAGATCGACACTACTGGATAC 58.107 41.667 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.242825 CTCTAAGACCGTGGCGACAA 59.757 55.000 0.00 0.00 46.06 3.18
1 2 0.607217 TCTCTAAGACCGTGGCGACA 60.607 55.000 0.00 0.00 38.70 4.35
2 3 0.739561 ATCTCTAAGACCGTGGCGAC 59.260 55.000 0.00 0.00 0.00 5.19
3 4 0.738975 CATCTCTAAGACCGTGGCGA 59.261 55.000 0.00 0.00 0.00 5.54
4 5 0.249073 CCATCTCTAAGACCGTGGCG 60.249 60.000 0.00 0.00 0.00 5.69
5 6 1.112113 TCCATCTCTAAGACCGTGGC 58.888 55.000 0.00 0.00 0.00 5.01
6 7 2.101582 CCTTCCATCTCTAAGACCGTGG 59.898 54.545 0.00 0.00 0.00 4.94
7 8 2.482142 GCCTTCCATCTCTAAGACCGTG 60.482 54.545 0.00 0.00 0.00 4.94
8 9 1.757699 GCCTTCCATCTCTAAGACCGT 59.242 52.381 0.00 0.00 0.00 4.83
9 10 1.069358 GGCCTTCCATCTCTAAGACCG 59.931 57.143 0.00 0.00 0.00 4.79
10 11 1.069358 CGGCCTTCCATCTCTAAGACC 59.931 57.143 0.00 0.00 0.00 3.85
11 12 1.069358 CCGGCCTTCCATCTCTAAGAC 59.931 57.143 0.00 0.00 0.00 3.01
12 13 1.414158 CCGGCCTTCCATCTCTAAGA 58.586 55.000 0.00 0.00 0.00 2.10
13 14 0.394565 CCCGGCCTTCCATCTCTAAG 59.605 60.000 0.00 0.00 0.00 2.18
14 15 1.696097 GCCCGGCCTTCCATCTCTAA 61.696 60.000 0.00 0.00 0.00 2.10
15 16 2.140792 GCCCGGCCTTCCATCTCTA 61.141 63.158 0.00 0.00 0.00 2.43
16 17 3.483869 GCCCGGCCTTCCATCTCT 61.484 66.667 0.00 0.00 0.00 3.10
17 18 4.918201 CGCCCGGCCTTCCATCTC 62.918 72.222 3.10 0.00 0.00 2.75
32 33 4.814294 ATGGGTCTTCGACGCCGC 62.814 66.667 8.31 0.00 43.42 6.53
33 34 2.885644 CATGGGTCTTCGACGCCG 60.886 66.667 8.31 0.00 43.42 6.46
34 35 3.195698 GCATGGGTCTTCGACGCC 61.196 66.667 8.31 2.53 43.42 5.68
35 36 3.554692 CGCATGGGTCTTCGACGC 61.555 66.667 0.68 4.35 44.15 5.19
36 37 1.736645 AACGCATGGGTCTTCGACG 60.737 57.895 16.57 0.00 32.65 5.12
37 38 1.787847 CAACGCATGGGTCTTCGAC 59.212 57.895 16.57 0.00 0.00 4.20
38 39 2.032634 GCAACGCATGGGTCTTCGA 61.033 57.895 16.57 0.00 0.00 3.71
39 40 2.480555 GCAACGCATGGGTCTTCG 59.519 61.111 16.57 6.55 0.00 3.79
40 41 2.480555 CGCAACGCATGGGTCTTC 59.519 61.111 16.57 7.31 37.22 2.87
45 46 3.556543 AAGCAACGCAACGCATGGG 62.557 57.895 8.44 8.44 46.83 4.00
46 47 2.050168 AAGCAACGCAACGCATGG 60.050 55.556 0.00 0.00 0.00 3.66
47 48 2.082366 GGAAGCAACGCAACGCATG 61.082 57.895 0.00 0.00 0.00 4.06
48 49 2.255252 GGAAGCAACGCAACGCAT 59.745 55.556 0.00 0.00 0.00 4.73
49 50 3.179869 CTGGAAGCAACGCAACGCA 62.180 57.895 0.00 0.00 0.00 5.24
50 51 2.187599 ATCTGGAAGCAACGCAACGC 62.188 55.000 0.00 0.00 0.00 4.84
51 52 0.238289 AATCTGGAAGCAACGCAACG 59.762 50.000 0.00 0.00 0.00 4.10
52 53 3.234386 GTTAATCTGGAAGCAACGCAAC 58.766 45.455 0.00 0.00 0.00 4.17
53 54 2.881513 TGTTAATCTGGAAGCAACGCAA 59.118 40.909 0.00 0.00 0.00 4.85
54 55 2.483877 CTGTTAATCTGGAAGCAACGCA 59.516 45.455 0.00 0.00 0.00 5.24
55 56 2.159517 CCTGTTAATCTGGAAGCAACGC 60.160 50.000 0.00 0.00 37.33 4.84
56 57 2.420022 CCCTGTTAATCTGGAAGCAACG 59.580 50.000 0.00 0.00 37.33 4.10
57 58 3.686016 TCCCTGTTAATCTGGAAGCAAC 58.314 45.455 0.00 0.00 37.33 4.17
58 59 4.591321 ATCCCTGTTAATCTGGAAGCAA 57.409 40.909 0.00 0.00 37.33 3.91
59 60 4.591321 AATCCCTGTTAATCTGGAAGCA 57.409 40.909 0.00 0.00 37.33 3.91
60 61 5.437060 TGTAATCCCTGTTAATCTGGAAGC 58.563 41.667 0.00 0.00 37.33 3.86
61 62 7.282585 TGATGTAATCCCTGTTAATCTGGAAG 58.717 38.462 0.00 0.00 44.73 3.46
62 63 7.206789 TGATGTAATCCCTGTTAATCTGGAA 57.793 36.000 0.00 0.00 44.73 3.53
63 64 6.823286 TGATGTAATCCCTGTTAATCTGGA 57.177 37.500 0.00 0.00 44.73 3.86
159 160 4.440940 CCCGTGGTTTAAGCTTCAGTTTTT 60.441 41.667 0.00 0.00 0.00 1.94
178 179 1.204941 CTTCAATTCTCTCGTCCCCGT 59.795 52.381 0.00 0.00 35.01 5.28
218 222 3.385111 GGGATGATAGATCGATGGGGTAC 59.615 52.174 0.54 0.00 0.00 3.34
219 223 3.630054 GGGGATGATAGATCGATGGGGTA 60.630 52.174 0.54 0.00 0.00 3.69
220 224 2.472029 GGGATGATAGATCGATGGGGT 58.528 52.381 0.54 0.00 0.00 4.95
221 225 1.765314 GGGGATGATAGATCGATGGGG 59.235 57.143 0.54 0.00 0.00 4.96
222 226 1.410517 CGGGGATGATAGATCGATGGG 59.589 57.143 0.54 0.00 0.00 4.00
223 227 1.410517 CCGGGGATGATAGATCGATGG 59.589 57.143 0.54 0.00 0.00 3.51
224 228 2.099921 GTCCGGGGATGATAGATCGATG 59.900 54.545 0.54 0.00 0.00 3.84
225 229 2.024846 AGTCCGGGGATGATAGATCGAT 60.025 50.000 0.00 0.00 0.00 3.59
226 230 1.354705 AGTCCGGGGATGATAGATCGA 59.645 52.381 0.00 0.00 0.00 3.59
227 231 1.474478 CAGTCCGGGGATGATAGATCG 59.526 57.143 0.00 0.00 0.00 3.69
228 232 1.205893 GCAGTCCGGGGATGATAGATC 59.794 57.143 0.00 0.00 0.00 2.75
229 233 1.270907 GCAGTCCGGGGATGATAGAT 58.729 55.000 0.00 0.00 0.00 1.98
230 234 0.832135 GGCAGTCCGGGGATGATAGA 60.832 60.000 0.00 0.00 0.00 1.98
231 235 1.121407 TGGCAGTCCGGGGATGATAG 61.121 60.000 0.00 0.00 34.14 2.08
232 236 1.074850 TGGCAGTCCGGGGATGATA 60.075 57.895 0.00 0.00 34.14 2.15
233 237 2.366837 TGGCAGTCCGGGGATGAT 60.367 61.111 0.00 0.00 34.14 2.45
234 238 3.399181 GTGGCAGTCCGGGGATGA 61.399 66.667 0.00 0.00 34.14 2.92
235 239 3.716195 TGTGGCAGTCCGGGGATG 61.716 66.667 0.00 0.00 34.14 3.51
236 240 3.717294 GTGTGGCAGTCCGGGGAT 61.717 66.667 0.00 0.00 34.14 3.85
241 245 4.293648 TGTCGGTGTGGCAGTCCG 62.294 66.667 19.78 19.78 44.76 4.79
242 246 2.665185 GTGTCGGTGTGGCAGTCC 60.665 66.667 0.00 0.00 0.00 3.85
243 247 2.665185 GGTGTCGGTGTGGCAGTC 60.665 66.667 0.00 0.00 0.00 3.51
244 248 3.475494 TGGTGTCGGTGTGGCAGT 61.475 61.111 0.00 0.00 0.00 4.40
245 249 2.972505 GTGGTGTCGGTGTGGCAG 60.973 66.667 0.00 0.00 0.00 4.85
246 250 4.555709 GGTGGTGTCGGTGTGGCA 62.556 66.667 0.00 0.00 0.00 4.92
278 282 4.079615 TGGTTCCTGGATGTGATGATTGAT 60.080 41.667 0.00 0.00 0.00 2.57
295 299 6.811954 TCAAATAACCTTCAAAACTGGTTCC 58.188 36.000 0.00 0.00 42.38 3.62
305 309 8.990163 ACTTTAAGTCCTCAAATAACCTTCAA 57.010 30.769 0.00 0.00 0.00 2.69
326 330 3.517500 CTCTAGCCCTTCTCCTGAACTTT 59.482 47.826 0.00 0.00 0.00 2.66
383 388 0.309302 TCACATGTTTTCCCGCAACG 59.691 50.000 0.00 0.00 0.00 4.10
443 448 0.804989 GGCTTTCGATGTGTCCCAAG 59.195 55.000 0.00 0.00 0.00 3.61
456 461 0.514691 CACACGAGAGCTTGGCTTTC 59.485 55.000 0.00 0.77 39.88 2.62
465 470 6.209361 TGAGATATTACAATCACACGAGAGC 58.791 40.000 0.00 0.00 0.00 4.09
629 664 7.601705 AAACATGGGAATCTCTTCTCAAAAA 57.398 32.000 0.00 0.00 44.87 1.94
688 723 3.112263 TGGGTCTTACTGGAACATAGGG 58.888 50.000 0.00 0.00 38.20 3.53
695 730 3.050089 TCCAAACTGGGTCTTACTGGAA 58.950 45.455 0.00 0.00 38.32 3.53
771 807 7.823310 CCTACAGTACTGAGAGACAAGTAGTTA 59.177 40.741 29.30 5.03 30.60 2.24
818 859 4.285292 CGTTCAATCCGCGTAGTTATACT 58.715 43.478 4.92 0.00 0.00 2.12
820 861 3.550639 CCCGTTCAATCCGCGTAGTTATA 60.551 47.826 4.92 0.00 0.00 0.98
821 862 2.466846 CCGTTCAATCCGCGTAGTTAT 58.533 47.619 4.92 0.00 0.00 1.89
822 863 1.469595 CCCGTTCAATCCGCGTAGTTA 60.470 52.381 4.92 0.00 0.00 2.24
825 866 2.522638 GCCCGTTCAATCCGCGTAG 61.523 63.158 4.92 0.00 0.00 3.51
826 867 2.509786 GCCCGTTCAATCCGCGTA 60.510 61.111 4.92 0.00 0.00 4.42
830 871 3.961838 TTCCGGCCCGTTCAATCCG 62.962 63.158 0.85 0.00 41.41 4.18
911 952 0.036010 CTGAAGACGATGGCAAGGGT 60.036 55.000 0.00 0.00 0.00 4.34
1014 1055 0.193574 AGGTGAGGAAGAAGGGGACA 59.806 55.000 0.00 0.00 0.00 4.02
1111 1158 2.434774 GGAGTCGGCTGGGGTTTT 59.565 61.111 0.00 0.00 0.00 2.43
1419 1466 0.106708 GGCAGTTCCAGGCGATCATA 59.893 55.000 0.00 0.00 34.01 2.15
1598 1645 1.003355 GGCTGGCACTCACTGCTTA 60.003 57.895 0.00 0.00 46.25 3.09
1599 1646 2.282040 GGCTGGCACTCACTGCTT 60.282 61.111 0.00 0.00 46.25 3.91
1604 1651 0.179062 CCTATCAGGCTGGCACTCAC 60.179 60.000 15.73 0.00 0.00 3.51
1647 1694 0.451783 CTCCCAAGTACGCAATTGCC 59.548 55.000 24.24 10.79 37.91 4.52
1677 1724 4.437587 GCATGTGCCCAGAGCCCT 62.438 66.667 0.00 0.00 42.71 5.19
1824 1871 6.039047 CAGCTAACATTGCATTCCAAGTATCT 59.961 38.462 0.00 0.00 36.76 1.98
1830 1877 3.164268 ACCAGCTAACATTGCATTCCAA 58.836 40.909 0.00 0.00 37.94 3.53
1967 2014 0.396811 ACCTTCCTCGACAAACCCTG 59.603 55.000 0.00 0.00 0.00 4.45
1977 2024 4.517453 TCAAAATAACCAACACCTTCCTCG 59.483 41.667 0.00 0.00 0.00 4.63
1987 2034 9.696917 ATTTGTCATTCTCTCAAAATAACCAAC 57.303 29.630 0.00 0.00 35.28 3.77
2016 2063 4.152402 GCAATGTCGGGCACAATACTATAG 59.848 45.833 0.00 0.00 38.97 1.31
2027 2074 1.034838 GTAATGGGCAATGTCGGGCA 61.035 55.000 0.00 0.00 0.00 5.36
2043 2090 6.325545 AGAATAGATCCACCATACAACCGTAA 59.674 38.462 0.00 0.00 0.00 3.18
2046 2093 4.991056 CAGAATAGATCCACCATACAACCG 59.009 45.833 0.00 0.00 0.00 4.44
2073 2120 1.600636 CTTCTCAAACAGCCCCGCA 60.601 57.895 0.00 0.00 0.00 5.69
2148 2195 2.172717 AGTTCTACAAGCACCAACCAGT 59.827 45.455 0.00 0.00 0.00 4.00
2151 2198 4.131596 TGTAAGTTCTACAAGCACCAACC 58.868 43.478 0.00 0.00 0.00 3.77
2175 2222 4.499865 GCCTTCTTTCCCAACTCAAAGTTC 60.500 45.833 0.00 0.00 36.03 3.01
2181 2228 1.202927 CCTGCCTTCTTTCCCAACTCA 60.203 52.381 0.00 0.00 0.00 3.41
2202 2249 1.952367 GCAGCCTCAATAAGCCTGTGT 60.952 52.381 0.00 0.00 0.00 3.72
2235 2282 2.997986 GGATAATAACACATACCCCGCG 59.002 50.000 0.00 0.00 0.00 6.46
2238 2285 7.833285 AATGTTGGATAATAACACATACCCC 57.167 36.000 0.00 0.00 40.47 4.95
2251 2298 4.203226 TCCAGCGCATAAATGTTGGATAA 58.797 39.130 11.47 0.00 33.35 1.75
2425 2472 4.891260 TGGCATATCTCACTTAGCATCTG 58.109 43.478 0.00 0.00 0.00 2.90
2436 2483 3.632643 TTCAACTGCTGGCATATCTCA 57.367 42.857 0.00 0.00 0.00 3.27
2821 2873 7.062322 TGGACAAGTATAATCATTGCCAGAAT 58.938 34.615 0.00 0.00 31.27 2.40
2961 3013 9.974980 TGAAAAGGACAATAATTAGGTTTCAAC 57.025 29.630 0.00 0.00 31.51 3.18
3074 3126 8.561536 TGATGATTTCTAGTCCCTACCATTTA 57.438 34.615 0.00 0.00 0.00 1.40
3200 3252 1.774856 AGTTGGTCCTGTGGCTTAAGT 59.225 47.619 4.02 0.00 0.00 2.24
3320 3478 7.043656 CGTAGACGTATCTATGATGTGCAAAAA 60.044 37.037 0.00 0.00 44.35 1.94
3385 3543 2.423185 TGCAATCAAATGGCTTACGGAG 59.577 45.455 0.00 0.00 0.00 4.63
3389 3547 5.413499 AGAATGTGCAATCAAATGGCTTAC 58.587 37.500 0.00 0.00 0.00 2.34
3418 3576 3.463048 AATCCATCAACCTCAGCCTTT 57.537 42.857 0.00 0.00 0.00 3.11
3583 3745 4.879104 CAGAATGCTTCATGTCTCTTCC 57.121 45.455 0.00 0.00 0.00 3.46
3647 3809 6.361433 TCTTTGTCCTTGTTACCAATCTCAA 58.639 36.000 0.00 0.00 0.00 3.02
3681 3843 5.360591 GGTGGAAGTGATTACTGTATCCAG 58.639 45.833 9.23 0.00 40.34 3.86
3688 3850 1.732259 GCACGGTGGAAGTGATTACTG 59.268 52.381 10.60 0.00 41.83 2.74


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

AutoCloner maintained by Alex Coulton.