Multiple sequence alignment - TraesCS7D01G365500

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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 TraesCS7D01G365500 chr7D 100.000 3003 0 0 1 3003 471933851 471930849 0.000000e+00 5546.0
1 TraesCS7D01G365500 chr7D 75.714 280 40 10 147 402 285227616 285227341 6.800000e-22 115.0
2 TraesCS7D01G365500 chr7B 94.192 2858 107 12 173 3003 495760447 495757622 0.000000e+00 4303.0
3 TraesCS7D01G365500 chr7B 90.270 185 9 4 1 185 495772973 495772798 1.800000e-57 233.0
4 TraesCS7D01G365500 chr7A 85.355 2547 179 88 575 3003 524638926 524641396 0.000000e+00 2459.0
5 TraesCS7D01G365500 chr7A 84.000 250 21 8 294 543 524638701 524638931 3.900000e-54 222.0
6 TraesCS7D01G365500 chr5D 82.927 123 17 4 284 402 446741134 446741256 1.140000e-19 108.0
7 TraesCS7D01G365500 chr4B 85.507 69 8 2 283 350 380718821 380718888 1.490000e-08 71.3


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 TraesCS7D01G365500 chr7D 471930849 471933851 3002 True 5546.0 5546 100.0000 1 3003 1 chr7D.!!$R2 3002
1 TraesCS7D01G365500 chr7B 495757622 495760447 2825 True 4303.0 4303 94.1920 173 3003 1 chr7B.!!$R1 2830
2 TraesCS7D01G365500 chr7A 524638701 524641396 2695 False 1340.5 2459 84.6775 294 3003 2 chr7A.!!$F1 2709

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
41 42 0.033601 ATTTGACCGGCCCATTAGCA 60.034 50.0 0.0 0.0 0.00 3.49 F
50 51 0.034089 GCCCATTAGCAGGAGGTGTT 60.034 55.0 0.0 0.0 0.00 3.32 F
259 260 0.180406 GACTGGGCCGACATACCATT 59.820 55.0 0.0 0.0 33.07 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1429 1468 0.398318 GCCCTGTCCTGTGAGAAGTT 59.602 55.0 0.0 0.0 0.0 2.66 R
1643 1691 0.809241 CTCCATGCTCTTGACGGCTC 60.809 60.0 0.0 0.0 0.0 4.70 R
2213 2286 0.463620 ATGGTTTGTGTGTTGTGCCC 59.536 50.0 0.0 0.0 0.0 5.36 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
19 20 2.543777 TGAGGTAGCGCTCAACTTTT 57.456 45.000 16.34 0.00 0.00 2.27
20 21 2.846193 TGAGGTAGCGCTCAACTTTTT 58.154 42.857 16.34 0.00 0.00 1.94
39 40 4.993029 TTTTATTTGACCGGCCCATTAG 57.007 40.909 0.00 0.00 0.00 1.73
40 41 1.975660 TATTTGACCGGCCCATTAGC 58.024 50.000 0.00 0.00 0.00 3.09
41 42 0.033601 ATTTGACCGGCCCATTAGCA 60.034 50.000 0.00 0.00 0.00 3.49
42 43 0.679640 TTTGACCGGCCCATTAGCAG 60.680 55.000 0.00 0.00 0.00 4.24
46 47 2.111878 CGGCCCATTAGCAGGAGG 59.888 66.667 0.00 0.00 0.00 4.30
47 48 2.746375 CGGCCCATTAGCAGGAGGT 61.746 63.158 0.00 0.00 0.00 3.85
48 49 1.152881 GGCCCATTAGCAGGAGGTG 60.153 63.158 0.00 0.00 0.00 4.00
49 50 1.609783 GCCCATTAGCAGGAGGTGT 59.390 57.895 0.00 0.00 0.00 4.16
50 51 0.034089 GCCCATTAGCAGGAGGTGTT 60.034 55.000 0.00 0.00 0.00 3.32
51 52 2.019156 GCCCATTAGCAGGAGGTGTTC 61.019 57.143 0.00 0.00 0.00 3.18
59 60 4.821935 GGAGGTGTTCCCCAACTG 57.178 61.111 0.00 0.00 42.71 3.16
60 61 1.074951 GGAGGTGTTCCCCAACTGG 59.925 63.158 0.00 0.00 42.71 4.00
61 62 1.603739 GAGGTGTTCCCCAACTGGC 60.604 63.158 0.00 0.00 42.71 4.85
62 63 2.983592 GGTGTTCCCCAACTGGCG 60.984 66.667 0.00 0.00 33.17 5.69
63 64 3.670377 GTGTTCCCCAACTGGCGC 61.670 66.667 0.00 0.00 33.17 6.53
64 65 4.196778 TGTTCCCCAACTGGCGCA 62.197 61.111 10.83 0.00 33.17 6.09
65 66 2.676471 GTTCCCCAACTGGCGCAT 60.676 61.111 10.83 0.00 0.00 4.73
66 67 1.377987 GTTCCCCAACTGGCGCATA 60.378 57.895 10.83 0.00 0.00 3.14
67 68 0.963355 GTTCCCCAACTGGCGCATAA 60.963 55.000 10.83 0.00 0.00 1.90
68 69 0.679640 TTCCCCAACTGGCGCATAAG 60.680 55.000 10.83 6.04 0.00 1.73
69 70 2.120909 CCCCAACTGGCGCATAAGG 61.121 63.158 10.83 3.73 0.00 2.69
70 71 1.378514 CCCAACTGGCGCATAAGGT 60.379 57.895 10.83 0.00 0.00 3.50
71 72 0.965363 CCCAACTGGCGCATAAGGTT 60.965 55.000 10.83 3.26 0.00 3.50
72 73 0.887933 CCAACTGGCGCATAAGGTTT 59.112 50.000 10.83 0.00 0.00 3.27
73 74 1.135402 CCAACTGGCGCATAAGGTTTC 60.135 52.381 10.83 0.00 0.00 2.78
74 75 1.812571 CAACTGGCGCATAAGGTTTCT 59.187 47.619 10.83 0.00 0.00 2.52
75 76 1.739067 ACTGGCGCATAAGGTTTCTC 58.261 50.000 10.83 0.00 0.00 2.87
76 77 1.279271 ACTGGCGCATAAGGTTTCTCT 59.721 47.619 10.83 0.00 0.00 3.10
77 78 1.936547 CTGGCGCATAAGGTTTCTCTC 59.063 52.381 10.83 0.00 0.00 3.20
78 79 1.555075 TGGCGCATAAGGTTTCTCTCT 59.445 47.619 10.83 0.00 0.00 3.10
79 80 2.205911 GGCGCATAAGGTTTCTCTCTC 58.794 52.381 10.83 0.00 0.00 3.20
80 81 2.418746 GGCGCATAAGGTTTCTCTCTCA 60.419 50.000 10.83 0.00 0.00 3.27
81 82 3.262420 GCGCATAAGGTTTCTCTCTCAA 58.738 45.455 0.30 0.00 0.00 3.02
82 83 3.684788 GCGCATAAGGTTTCTCTCTCAAA 59.315 43.478 0.30 0.00 0.00 2.69
83 84 4.154195 GCGCATAAGGTTTCTCTCTCAAAA 59.846 41.667 0.30 0.00 0.00 2.44
84 85 5.334879 GCGCATAAGGTTTCTCTCTCAAAAA 60.335 40.000 0.30 0.00 0.00 1.94
105 106 2.723124 AAAAACTGGCGCATAAGGTG 57.277 45.000 10.83 0.00 0.00 4.00
106 107 1.616159 AAAACTGGCGCATAAGGTGT 58.384 45.000 10.83 0.00 0.00 4.16
107 108 1.165270 AAACTGGCGCATAAGGTGTC 58.835 50.000 10.83 0.00 0.00 3.67
108 109 0.324943 AACTGGCGCATAAGGTGTCT 59.675 50.000 10.83 0.00 31.33 3.41
109 110 1.191535 ACTGGCGCATAAGGTGTCTA 58.808 50.000 10.83 0.00 31.33 2.59
110 111 1.762957 ACTGGCGCATAAGGTGTCTAT 59.237 47.619 10.83 0.00 31.33 1.98
111 112 2.138320 CTGGCGCATAAGGTGTCTATG 58.862 52.381 10.83 0.00 31.33 2.23
112 113 1.484653 TGGCGCATAAGGTGTCTATGT 59.515 47.619 10.83 0.00 31.33 2.29
113 114 1.867233 GGCGCATAAGGTGTCTATGTG 59.133 52.381 10.83 0.00 35.49 3.21
114 115 2.550978 GCGCATAAGGTGTCTATGTGT 58.449 47.619 0.30 0.00 35.02 3.72
115 116 2.936498 GCGCATAAGGTGTCTATGTGTT 59.064 45.455 0.30 0.00 35.02 3.32
116 117 3.374058 GCGCATAAGGTGTCTATGTGTTT 59.626 43.478 0.30 0.00 35.02 2.83
117 118 4.727734 GCGCATAAGGTGTCTATGTGTTTG 60.728 45.833 0.30 0.00 35.02 2.93
118 119 4.391830 CGCATAAGGTGTCTATGTGTTTGT 59.608 41.667 0.00 0.00 0.00 2.83
119 120 5.445939 CGCATAAGGTGTCTATGTGTTTGTC 60.446 44.000 0.00 0.00 0.00 3.18
120 121 5.445939 GCATAAGGTGTCTATGTGTTTGTCG 60.446 44.000 0.00 0.00 0.00 4.35
121 122 2.413837 AGGTGTCTATGTGTTTGTCGC 58.586 47.619 0.00 0.00 0.00 5.19
122 123 1.463444 GGTGTCTATGTGTTTGTCGCC 59.537 52.381 0.00 0.00 0.00 5.54
123 124 1.463444 GTGTCTATGTGTTTGTCGCCC 59.537 52.381 0.00 0.00 0.00 6.13
124 125 1.084289 GTCTATGTGTTTGTCGCCCC 58.916 55.000 0.00 0.00 0.00 5.80
125 126 0.687920 TCTATGTGTTTGTCGCCCCA 59.312 50.000 0.00 0.00 0.00 4.96
126 127 1.086696 CTATGTGTTTGTCGCCCCAG 58.913 55.000 0.00 0.00 0.00 4.45
127 128 0.958382 TATGTGTTTGTCGCCCCAGC 60.958 55.000 0.00 0.00 0.00 4.85
128 129 2.594592 GTGTTTGTCGCCCCAGCT 60.595 61.111 0.00 0.00 36.60 4.24
129 130 2.193536 GTGTTTGTCGCCCCAGCTT 61.194 57.895 0.00 0.00 36.60 3.74
130 131 1.896660 TGTTTGTCGCCCCAGCTTC 60.897 57.895 0.00 0.00 36.60 3.86
131 132 1.600916 GTTTGTCGCCCCAGCTTCT 60.601 57.895 0.00 0.00 36.60 2.85
132 133 1.302511 TTTGTCGCCCCAGCTTCTC 60.303 57.895 0.00 0.00 36.60 2.87
133 134 3.589654 TTGTCGCCCCAGCTTCTCG 62.590 63.158 0.00 0.00 36.60 4.04
134 135 4.070552 GTCGCCCCAGCTTCTCGT 62.071 66.667 0.00 0.00 36.60 4.18
135 136 4.069232 TCGCCCCAGCTTCTCGTG 62.069 66.667 0.00 0.00 36.60 4.35
137 138 4.400961 GCCCCAGCTTCTCGTGCT 62.401 66.667 0.00 0.00 42.06 4.40
138 139 2.348998 CCCCAGCTTCTCGTGCTT 59.651 61.111 0.00 0.00 38.92 3.91
139 140 1.302832 CCCCAGCTTCTCGTGCTTT 60.303 57.895 0.00 0.00 38.92 3.51
140 141 0.890996 CCCCAGCTTCTCGTGCTTTT 60.891 55.000 0.00 0.00 38.92 2.27
141 142 0.954452 CCCAGCTTCTCGTGCTTTTT 59.046 50.000 0.00 0.00 38.92 1.94
142 143 2.151202 CCCAGCTTCTCGTGCTTTTTA 58.849 47.619 0.00 0.00 38.92 1.52
143 144 2.749621 CCCAGCTTCTCGTGCTTTTTAT 59.250 45.455 0.00 0.00 38.92 1.40
144 145 3.938963 CCCAGCTTCTCGTGCTTTTTATA 59.061 43.478 0.00 0.00 38.92 0.98
145 146 4.034510 CCCAGCTTCTCGTGCTTTTTATAG 59.965 45.833 0.00 0.00 38.92 1.31
146 147 4.870426 CCAGCTTCTCGTGCTTTTTATAGA 59.130 41.667 0.00 0.00 38.92 1.98
147 148 5.351465 CCAGCTTCTCGTGCTTTTTATAGAA 59.649 40.000 0.00 0.00 38.92 2.10
148 149 6.244275 CAGCTTCTCGTGCTTTTTATAGAAC 58.756 40.000 0.00 0.00 38.92 3.01
149 150 5.932303 AGCTTCTCGTGCTTTTTATAGAACA 59.068 36.000 0.00 0.00 37.52 3.18
150 151 6.016111 GCTTCTCGTGCTTTTTATAGAACAC 58.984 40.000 0.00 0.00 0.00 3.32
153 154 4.657075 CGTGCTTTTTATAGAACACGGT 57.343 40.909 9.84 0.00 45.11 4.83
154 155 5.766702 CGTGCTTTTTATAGAACACGGTA 57.233 39.130 9.84 0.00 45.11 4.02
155 156 5.544621 CGTGCTTTTTATAGAACACGGTAC 58.455 41.667 9.84 0.00 45.11 3.34
156 157 5.118971 CGTGCTTTTTATAGAACACGGTACA 59.881 40.000 9.84 0.00 45.11 2.90
157 158 6.346758 CGTGCTTTTTATAGAACACGGTACAA 60.347 38.462 9.84 0.00 45.11 2.41
158 159 7.354257 GTGCTTTTTATAGAACACGGTACAAA 58.646 34.615 0.00 0.00 0.00 2.83
159 160 7.321984 GTGCTTTTTATAGAACACGGTACAAAC 59.678 37.037 0.00 0.00 0.00 2.93
160 161 6.517374 GCTTTTTATAGAACACGGTACAAACG 59.483 38.462 0.00 0.00 37.36 3.60
161 162 5.514059 TTTATAGAACACGGTACAAACGC 57.486 39.130 0.00 0.00 34.00 4.84
162 163 2.505628 TAGAACACGGTACAAACGCA 57.494 45.000 0.00 0.00 34.00 5.24
163 164 1.214367 AGAACACGGTACAAACGCAG 58.786 50.000 0.00 0.00 34.00 5.18
164 165 0.233848 GAACACGGTACAAACGCAGG 59.766 55.000 0.00 0.00 34.00 4.85
165 166 1.778027 AACACGGTACAAACGCAGGC 61.778 55.000 0.00 0.00 34.00 4.85
166 167 3.039588 ACGGTACAAACGCAGGCG 61.040 61.111 12.71 12.71 46.03 5.52
167 168 4.439472 CGGTACAAACGCAGGCGC 62.439 66.667 14.32 0.00 44.19 6.53
168 169 3.047877 GGTACAAACGCAGGCGCT 61.048 61.111 14.32 0.00 44.19 5.92
169 170 2.474712 GTACAAACGCAGGCGCTC 59.525 61.111 14.32 0.00 44.19 5.03
170 171 2.029815 TACAAACGCAGGCGCTCA 59.970 55.556 14.32 0.00 44.19 4.26
171 172 1.375396 TACAAACGCAGGCGCTCAT 60.375 52.632 14.32 0.00 44.19 2.90
178 179 1.191944 CGCAGGCGCTCATATATACG 58.808 55.000 7.64 0.00 35.30 3.06
202 203 5.530915 GCACATGCACTTATCCCTATAAACA 59.469 40.000 0.00 0.00 41.59 2.83
205 206 8.632679 CACATGCACTTATCCCTATAAACAAAT 58.367 33.333 0.00 0.00 0.00 2.32
214 215 9.515226 TTATCCCTATAAACAAATACATGGAGC 57.485 33.333 0.00 0.00 0.00 4.70
225 226 0.573279 ACATGGAGCCCTACCCCTAT 59.427 55.000 0.00 0.00 0.00 2.57
236 237 2.158755 CCTACCCCTATGAGCACTTTGG 60.159 54.545 0.00 0.00 0.00 3.28
245 246 2.575532 TGAGCACTTTGGAAAGACTGG 58.424 47.619 6.13 0.00 39.31 4.00
251 252 0.536460 TTTGGAAAGACTGGGCCGAC 60.536 55.000 0.00 0.00 0.00 4.79
259 260 0.180406 GACTGGGCCGACATACCATT 59.820 55.000 0.00 0.00 33.07 3.16
371 372 7.744649 GAGCATCATGACTTAATCCTTATGGGA 60.745 40.741 0.00 0.00 41.65 4.37
398 399 1.372501 ACCACTGCCTCCTAACCATT 58.627 50.000 0.00 0.00 0.00 3.16
426 427 6.917533 ACTTTCCATTTCTTAGCAGTTGATG 58.082 36.000 0.00 0.00 0.00 3.07
496 497 5.290386 AGAAGACTTTCCGAACTTGTACAG 58.710 41.667 0.00 0.00 33.64 2.74
516 517 1.064505 GTGCCGATCACATCCACAATG 59.935 52.381 0.00 0.00 44.98 2.82
935 959 1.072173 CGTTATCCATCCAGCCCATCA 59.928 52.381 0.00 0.00 0.00 3.07
1036 1069 0.958091 ACTGCGCATTTTGTTGCCTA 59.042 45.000 12.24 0.00 39.52 3.93
1215 1248 2.954611 TGTCGAGCCTGACAGACG 59.045 61.111 3.32 7.13 43.62 4.18
1216 1249 1.599797 TGTCGAGCCTGACAGACGA 60.600 57.895 3.32 9.34 43.62 4.20
1217 1250 1.154188 GTCGAGCCTGACAGACGAC 60.154 63.158 22.77 22.77 44.19 4.34
1218 1251 2.202362 CGAGCCTGACAGACGACG 60.202 66.667 3.32 0.54 0.00 5.12
1219 1252 2.677979 CGAGCCTGACAGACGACGA 61.678 63.158 3.32 0.00 0.00 4.20
1240 1273 2.752238 CGACGCAGAGTCCTCCCT 60.752 66.667 0.00 0.00 46.92 4.20
1400 1437 2.029380 GCATACTTGTTCCCAACCCAAC 60.029 50.000 0.00 0.00 0.00 3.77
1573 1612 1.624323 GAGCCGTTCGTCGATTTCG 59.376 57.895 0.00 2.02 42.86 3.46
1584 1626 1.065358 TCGATTTCGCTTCACGTTCC 58.935 50.000 0.00 0.00 44.19 3.62
1607 1649 0.806102 GCCTCGCAGCAAGACGATAA 60.806 55.000 0.00 0.00 37.72 1.75
1608 1650 0.924090 CCTCGCAGCAAGACGATAAC 59.076 55.000 0.00 0.00 37.72 1.89
1618 1666 3.001954 GCAAGACGATAACGAAGAAGACG 60.002 47.826 0.00 0.00 42.66 4.18
1619 1667 3.402058 AGACGATAACGAAGAAGACGG 57.598 47.619 0.00 0.00 42.66 4.79
1750 1802 7.840342 CAGAGATTTCTGCTAGCTAAAGAAA 57.160 36.000 23.34 23.34 43.98 2.52
1875 1928 5.931146 CAGTAGAGATTTCTGCAACTGAAGT 59.069 40.000 8.35 0.00 38.78 3.01
1949 2010 2.103771 ACTGCATATGCTCGGTGATTCT 59.896 45.455 27.13 0.00 42.66 2.40
1958 2019 2.611518 CTCGGTGATTCTGAGGACAAC 58.388 52.381 0.00 0.00 43.70 3.32
1972 2033 2.139118 GGACAACTTGCTGAGACTGTC 58.861 52.381 0.00 0.00 39.19 3.51
2056 2127 6.801539 TTCAGACATTTGGTTAGTTAGCAG 57.198 37.500 0.00 0.00 35.32 4.24
2067 2138 7.182817 TGGTTAGTTAGCAGTGTCTGAATAT 57.817 36.000 0.66 0.00 32.44 1.28
2193 2266 5.106752 ACAACTTGTGGTGCAATTTTTGAAC 60.107 36.000 0.00 0.00 38.55 3.18
2213 2286 4.392921 ACTTGTATCACCAATCCTCTCG 57.607 45.455 0.00 0.00 0.00 4.04
2225 2298 1.961277 CCTCTCGGGCACAACACAC 60.961 63.158 0.00 0.00 0.00 3.82
2353 2456 3.120041 CCGCCAACTTAAACAACTTTGG 58.880 45.455 0.00 0.00 39.86 3.28
2423 2532 2.923426 TTCTCCAGCGCCGCCAATAG 62.923 60.000 4.98 0.00 0.00 1.73
2695 2829 4.577283 TGCCTGTACTTTCCTTTTGTGTAC 59.423 41.667 0.00 0.00 35.43 2.90
2786 2920 5.123805 AGACTGTACGACCTCTCTTTTTC 57.876 43.478 0.00 0.00 0.00 2.29
2828 2968 4.527038 ACTCAAAGTCGGAGAAAGATGGTA 59.473 41.667 0.00 0.00 39.69 3.25
2829 2969 5.187967 ACTCAAAGTCGGAGAAAGATGGTAT 59.812 40.000 0.00 0.00 39.69 2.73
2859 2999 7.094377 GCCTAACTTCAAAATGATCCACTAACA 60.094 37.037 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.543777 AAAAGTTGAGCGCTACCTCA 57.456 45.000 11.50 0.00 39.94 3.86
17 18 4.382147 GCTAATGGGCCGGTCAAATAAAAA 60.382 41.667 9.07 0.00 0.00 1.94
18 19 3.131400 GCTAATGGGCCGGTCAAATAAAA 59.869 43.478 9.07 0.00 0.00 1.52
19 20 2.691011 GCTAATGGGCCGGTCAAATAAA 59.309 45.455 9.07 0.00 0.00 1.40
20 21 2.303175 GCTAATGGGCCGGTCAAATAA 58.697 47.619 9.07 0.00 0.00 1.40
21 22 1.213182 TGCTAATGGGCCGGTCAAATA 59.787 47.619 9.07 0.00 0.00 1.40
22 23 0.033601 TGCTAATGGGCCGGTCAAAT 60.034 50.000 9.07 0.00 0.00 2.32
23 24 0.679640 CTGCTAATGGGCCGGTCAAA 60.680 55.000 9.07 0.00 0.00 2.69
24 25 1.077787 CTGCTAATGGGCCGGTCAA 60.078 57.895 9.07 0.00 0.00 3.18
25 26 2.589540 CTGCTAATGGGCCGGTCA 59.410 61.111 9.07 5.06 0.00 4.02
26 27 2.203209 CCTGCTAATGGGCCGGTC 60.203 66.667 1.90 0.00 32.99 4.79
27 28 2.690881 TCCTGCTAATGGGCCGGT 60.691 61.111 1.90 0.00 37.73 5.28
28 29 2.111878 CTCCTGCTAATGGGCCGG 59.888 66.667 0.00 0.00 37.83 6.13
29 30 2.111878 CCTCCTGCTAATGGGCCG 59.888 66.667 0.00 0.00 0.00 6.13
30 31 1.152881 CACCTCCTGCTAATGGGCC 60.153 63.158 0.00 0.00 0.00 5.80
31 32 0.034089 AACACCTCCTGCTAATGGGC 60.034 55.000 0.00 0.00 0.00 5.36
32 33 1.408822 GGAACACCTCCTGCTAATGGG 60.409 57.143 0.00 0.00 41.61 4.00
33 34 1.408822 GGGAACACCTCCTGCTAATGG 60.409 57.143 0.00 0.00 44.68 3.16
34 35 1.408822 GGGGAACACCTCCTGCTAATG 60.409 57.143 0.00 0.00 44.68 1.90
35 36 0.919710 GGGGAACACCTCCTGCTAAT 59.080 55.000 0.00 0.00 44.68 1.73
36 37 0.474854 TGGGGAACACCTCCTGCTAA 60.475 55.000 0.00 0.00 44.68 3.09
37 38 0.474854 TTGGGGAACACCTCCTGCTA 60.475 55.000 0.00 0.00 44.68 3.49
38 39 1.774217 TTGGGGAACACCTCCTGCT 60.774 57.895 0.00 0.00 44.68 4.24
39 40 1.603739 GTTGGGGAACACCTCCTGC 60.604 63.158 0.00 0.00 44.68 4.85
40 41 0.250901 CAGTTGGGGAACACCTCCTG 60.251 60.000 0.00 0.00 44.68 3.86
41 42 1.427072 CCAGTTGGGGAACACCTCCT 61.427 60.000 0.00 0.00 44.68 3.69
42 43 1.074951 CCAGTTGGGGAACACCTCC 59.925 63.158 0.00 0.00 44.54 4.30
43 44 1.603739 GCCAGTTGGGGAACACCTC 60.604 63.158 0.00 0.00 40.03 3.85
44 45 2.520968 GCCAGTTGGGGAACACCT 59.479 61.111 0.00 0.00 40.03 4.00
52 53 0.965363 AACCTTATGCGCCAGTTGGG 60.965 55.000 4.18 2.08 40.85 4.12
53 54 0.887933 AAACCTTATGCGCCAGTTGG 59.112 50.000 4.18 3.26 38.53 3.77
54 55 1.812571 AGAAACCTTATGCGCCAGTTG 59.187 47.619 4.18 0.00 0.00 3.16
55 56 2.084546 GAGAAACCTTATGCGCCAGTT 58.915 47.619 4.18 0.00 0.00 3.16
56 57 1.279271 AGAGAAACCTTATGCGCCAGT 59.721 47.619 4.18 0.00 0.00 4.00
57 58 1.936547 GAGAGAAACCTTATGCGCCAG 59.063 52.381 4.18 0.00 0.00 4.85
58 59 1.555075 AGAGAGAAACCTTATGCGCCA 59.445 47.619 4.18 0.00 0.00 5.69
59 60 2.205911 GAGAGAGAAACCTTATGCGCC 58.794 52.381 4.18 0.00 0.00 6.53
60 61 2.893637 TGAGAGAGAAACCTTATGCGC 58.106 47.619 0.00 0.00 0.00 6.09
61 62 5.862924 TTTTGAGAGAGAAACCTTATGCG 57.137 39.130 0.00 0.00 0.00 4.73
86 87 1.960689 ACACCTTATGCGCCAGTTTTT 59.039 42.857 4.18 0.00 0.00 1.94
87 88 1.539827 GACACCTTATGCGCCAGTTTT 59.460 47.619 4.18 0.00 0.00 2.43
88 89 1.165270 GACACCTTATGCGCCAGTTT 58.835 50.000 4.18 0.00 0.00 2.66
89 90 0.324943 AGACACCTTATGCGCCAGTT 59.675 50.000 4.18 0.00 0.00 3.16
90 91 1.191535 TAGACACCTTATGCGCCAGT 58.808 50.000 4.18 0.00 0.00 4.00
91 92 2.138320 CATAGACACCTTATGCGCCAG 58.862 52.381 4.18 0.00 0.00 4.85
92 93 1.484653 ACATAGACACCTTATGCGCCA 59.515 47.619 4.18 0.00 0.00 5.69
93 94 1.867233 CACATAGACACCTTATGCGCC 59.133 52.381 4.18 0.00 0.00 6.53
94 95 2.550978 ACACATAGACACCTTATGCGC 58.449 47.619 0.00 0.00 0.00 6.09
95 96 4.391830 ACAAACACATAGACACCTTATGCG 59.608 41.667 0.00 0.00 0.00 4.73
96 97 5.445939 CGACAAACACATAGACACCTTATGC 60.446 44.000 0.00 0.00 0.00 3.14
97 98 5.445939 GCGACAAACACATAGACACCTTATG 60.446 44.000 0.00 0.00 0.00 1.90
98 99 4.630069 GCGACAAACACATAGACACCTTAT 59.370 41.667 0.00 0.00 0.00 1.73
99 100 3.991773 GCGACAAACACATAGACACCTTA 59.008 43.478 0.00 0.00 0.00 2.69
100 101 2.806244 GCGACAAACACATAGACACCTT 59.194 45.455 0.00 0.00 0.00 3.50
101 102 2.413837 GCGACAAACACATAGACACCT 58.586 47.619 0.00 0.00 0.00 4.00
102 103 1.463444 GGCGACAAACACATAGACACC 59.537 52.381 0.00 0.00 0.00 4.16
103 104 1.463444 GGGCGACAAACACATAGACAC 59.537 52.381 0.00 0.00 0.00 3.67
104 105 1.609580 GGGGCGACAAACACATAGACA 60.610 52.381 0.00 0.00 0.00 3.41
105 106 1.084289 GGGGCGACAAACACATAGAC 58.916 55.000 0.00 0.00 0.00 2.59
106 107 0.687920 TGGGGCGACAAACACATAGA 59.312 50.000 0.00 0.00 0.00 1.98
107 108 1.086696 CTGGGGCGACAAACACATAG 58.913 55.000 0.00 0.00 0.00 2.23
108 109 0.958382 GCTGGGGCGACAAACACATA 60.958 55.000 0.00 0.00 0.00 2.29
109 110 2.268076 GCTGGGGCGACAAACACAT 61.268 57.895 0.00 0.00 0.00 3.21
110 111 2.902423 AAGCTGGGGCGACAAACACA 62.902 55.000 0.00 0.00 44.37 3.72
111 112 2.130073 GAAGCTGGGGCGACAAACAC 62.130 60.000 0.00 0.00 44.37 3.32
112 113 1.896660 GAAGCTGGGGCGACAAACA 60.897 57.895 0.00 0.00 44.37 2.83
113 114 1.578206 GAGAAGCTGGGGCGACAAAC 61.578 60.000 0.00 0.00 44.37 2.93
114 115 1.302511 GAGAAGCTGGGGCGACAAA 60.303 57.895 0.00 0.00 44.37 2.83
115 116 2.347490 GAGAAGCTGGGGCGACAA 59.653 61.111 0.00 0.00 44.37 3.18
116 117 4.069232 CGAGAAGCTGGGGCGACA 62.069 66.667 0.00 0.00 44.37 4.35
117 118 4.070552 ACGAGAAGCTGGGGCGAC 62.071 66.667 5.68 0.00 44.37 5.19
118 119 4.069232 CACGAGAAGCTGGGGCGA 62.069 66.667 5.68 0.00 44.37 5.54
120 121 3.909086 AAGCACGAGAAGCTGGGGC 62.909 63.158 0.00 0.00 42.53 5.80
121 122 0.890996 AAAAGCACGAGAAGCTGGGG 60.891 55.000 0.00 0.00 42.53 4.96
122 123 0.954452 AAAAAGCACGAGAAGCTGGG 59.046 50.000 0.00 0.00 42.53 4.45
123 124 4.870426 TCTATAAAAAGCACGAGAAGCTGG 59.130 41.667 0.00 0.00 42.53 4.85
124 125 6.128553 TGTTCTATAAAAAGCACGAGAAGCTG 60.129 38.462 0.00 0.00 42.53 4.24
125 126 5.932303 TGTTCTATAAAAAGCACGAGAAGCT 59.068 36.000 0.00 0.00 45.97 3.74
126 127 6.016111 GTGTTCTATAAAAAGCACGAGAAGC 58.984 40.000 0.00 0.00 0.00 3.86
132 133 4.657075 ACCGTGTTCTATAAAAAGCACG 57.343 40.909 7.75 7.75 45.97 5.34
133 134 6.470557 TGTACCGTGTTCTATAAAAAGCAC 57.529 37.500 0.00 0.00 0.00 4.40
134 135 7.354257 GTTTGTACCGTGTTCTATAAAAAGCA 58.646 34.615 0.00 0.00 0.00 3.91
135 136 6.517374 CGTTTGTACCGTGTTCTATAAAAAGC 59.483 38.462 0.00 0.00 0.00 3.51
136 137 6.517374 GCGTTTGTACCGTGTTCTATAAAAAG 59.483 38.462 0.00 0.00 0.00 2.27
137 138 6.018425 TGCGTTTGTACCGTGTTCTATAAAAA 60.018 34.615 0.00 0.00 0.00 1.94
138 139 5.464722 TGCGTTTGTACCGTGTTCTATAAAA 59.535 36.000 0.00 0.00 0.00 1.52
139 140 4.987285 TGCGTTTGTACCGTGTTCTATAAA 59.013 37.500 0.00 0.00 0.00 1.40
140 141 4.554292 TGCGTTTGTACCGTGTTCTATAA 58.446 39.130 0.00 0.00 0.00 0.98
141 142 4.168014 CTGCGTTTGTACCGTGTTCTATA 58.832 43.478 0.00 0.00 0.00 1.31
142 143 2.991190 CTGCGTTTGTACCGTGTTCTAT 59.009 45.455 0.00 0.00 0.00 1.98
143 144 2.396601 CTGCGTTTGTACCGTGTTCTA 58.603 47.619 0.00 0.00 0.00 2.10
144 145 1.214367 CTGCGTTTGTACCGTGTTCT 58.786 50.000 0.00 0.00 0.00 3.01
145 146 0.233848 CCTGCGTTTGTACCGTGTTC 59.766 55.000 0.00 0.00 0.00 3.18
146 147 1.778027 GCCTGCGTTTGTACCGTGTT 61.778 55.000 0.00 0.00 0.00 3.32
147 148 2.248835 GCCTGCGTTTGTACCGTGT 61.249 57.895 0.00 0.00 0.00 4.49
148 149 2.554272 GCCTGCGTTTGTACCGTG 59.446 61.111 0.00 0.00 0.00 4.94
149 150 3.039588 CGCCTGCGTTTGTACCGT 61.040 61.111 2.83 0.00 34.35 4.83
150 151 4.439472 GCGCCTGCGTTTGTACCG 62.439 66.667 13.57 0.00 42.09 4.02
160 161 0.924090 GCGTATATATGAGCGCCTGC 59.076 55.000 2.29 0.00 43.52 4.85
165 166 2.923020 TGCATGTGCGTATATATGAGCG 59.077 45.455 6.12 0.00 45.83 5.03
166 167 3.928992 AGTGCATGTGCGTATATATGAGC 59.071 43.478 6.12 1.54 45.83 4.26
167 168 7.043125 GGATAAGTGCATGTGCGTATATATGAG 60.043 40.741 6.12 0.00 45.83 2.90
168 169 6.756542 GGATAAGTGCATGTGCGTATATATGA 59.243 38.462 6.12 0.00 45.83 2.15
169 170 6.018751 GGGATAAGTGCATGTGCGTATATATG 60.019 42.308 0.00 0.00 45.83 1.78
170 171 6.049149 GGGATAAGTGCATGTGCGTATATAT 58.951 40.000 0.00 0.00 45.83 0.86
171 172 5.186992 AGGGATAAGTGCATGTGCGTATATA 59.813 40.000 0.00 0.00 45.83 0.86
178 179 5.530915 TGTTTATAGGGATAAGTGCATGTGC 59.469 40.000 0.00 0.00 42.50 4.57
182 183 9.860650 TGTATTTGTTTATAGGGATAAGTGCAT 57.139 29.630 0.00 0.00 0.00 3.96
202 203 1.780919 GGGGTAGGGCTCCATGTATTT 59.219 52.381 0.00 0.00 37.78 1.40
205 206 1.247260 TAGGGGTAGGGCTCCATGTA 58.753 55.000 0.00 0.00 41.40 2.29
211 212 0.471971 TGCTCATAGGGGTAGGGCTC 60.472 60.000 0.00 0.00 0.00 4.70
213 214 0.764752 AGTGCTCATAGGGGTAGGGC 60.765 60.000 0.00 0.00 0.00 5.19
214 215 1.807814 AAGTGCTCATAGGGGTAGGG 58.192 55.000 0.00 0.00 0.00 3.53
225 226 2.575532 CCAGTCTTTCCAAAGTGCTCA 58.424 47.619 0.00 0.00 37.31 4.26
236 237 1.653151 GTATGTCGGCCCAGTCTTTC 58.347 55.000 0.00 0.00 0.00 2.62
245 246 5.298276 TCAATCTAAAAATGGTATGTCGGCC 59.702 40.000 0.00 0.00 0.00 6.13
251 252 8.664798 TGACTTCGTCAATCTAAAAATGGTATG 58.335 33.333 0.00 0.00 39.78 2.39
259 260 4.624015 ACGGTGACTTCGTCAATCTAAAA 58.376 39.130 0.00 0.00 44.49 1.52
284 285 2.666069 CGTTCAGTGAGAGGAGACGTTC 60.666 54.545 4.92 0.00 0.00 3.95
339 340 7.512130 AGGATTAAGTCATGATGCTCACATTA 58.488 34.615 0.00 0.00 36.35 1.90
365 366 2.375174 GCAGTGGTATCCCAATCCCATA 59.625 50.000 0.00 0.00 44.15 2.74
371 372 0.846693 GGAGGCAGTGGTATCCCAAT 59.153 55.000 0.00 0.00 44.15 3.16
398 399 6.959639 ACTGCTAAGAAATGGAAAGTTTGA 57.040 33.333 0.00 0.00 0.00 2.69
426 427 4.207891 TGGAAAGTCTTATCTCAGCACC 57.792 45.455 0.00 0.00 0.00 5.01
453 454 2.511373 CGCCACGATTAGCTGCCA 60.511 61.111 0.00 0.00 0.00 4.92
496 497 4.144940 CCATTGTGGATGTGATCGGCAC 62.145 54.545 2.89 2.89 43.58 5.01
701 707 0.730834 CGGATCGATGGATGCTCGTC 60.731 60.000 0.54 0.00 38.72 4.20
1028 1061 2.884012 CACATGAACCAAGTAGGCAACA 59.116 45.455 0.00 0.00 43.14 3.33
1036 1069 3.317993 GCCTAACAACACATGAACCAAGT 59.682 43.478 0.00 0.00 0.00 3.16
1147 1180 2.045045 CGGAATCCAAGCTGGCCA 60.045 61.111 4.71 4.71 37.47 5.36
1214 1247 4.419957 TCTGCGTCGTCGTCGTCG 62.420 66.667 15.68 15.68 46.99 5.12
1215 1248 2.571096 CTCTGCGTCGTCGTCGTC 60.571 66.667 13.09 6.56 39.49 4.20
1216 1249 3.292518 GACTCTGCGTCGTCGTCGT 62.293 63.158 13.09 0.00 39.49 4.34
1217 1250 2.571096 GACTCTGCGTCGTCGTCG 60.571 66.667 7.53 7.53 39.49 5.12
1218 1251 2.202324 GGACTCTGCGTCGTCGTC 60.202 66.667 3.66 0.00 43.79 4.20
1219 1252 2.668889 AGGACTCTGCGTCGTCGT 60.669 61.111 3.66 0.00 43.79 4.34
1240 1273 2.039787 TAGGATCACCCGCCACCA 59.960 61.111 0.00 0.00 40.87 4.17
1361 1397 1.959226 CTGTGGGTTTGGACGTCGG 60.959 63.158 9.92 0.00 0.00 4.79
1429 1468 0.398318 GCCCTGTCCTGTGAGAAGTT 59.602 55.000 0.00 0.00 0.00 2.66
1573 1612 3.056328 GGCCCTGGAACGTGAAGC 61.056 66.667 0.00 0.00 0.00 3.86
1584 1626 4.399395 TCTTGCTGCGAGGCCCTG 62.399 66.667 16.59 0.00 0.00 4.45
1608 1650 4.771356 TCGGCGCCGTCTTCTTCG 62.771 66.667 44.16 19.18 40.74 3.79
1643 1691 0.809241 CTCCATGCTCTTGACGGCTC 60.809 60.000 0.00 0.00 0.00 4.70
1644 1692 1.220206 CTCCATGCTCTTGACGGCT 59.780 57.895 0.00 0.00 0.00 5.52
1747 1799 3.205338 ACAAAACCTTGCATTGCCTTTC 58.795 40.909 6.12 0.00 35.84 2.62
1748 1800 3.280197 ACAAAACCTTGCATTGCCTTT 57.720 38.095 6.12 0.00 35.84 3.11
1749 1801 4.126437 GTTACAAAACCTTGCATTGCCTT 58.874 39.130 6.12 0.00 35.84 4.35
1750 1802 3.133721 TGTTACAAAACCTTGCATTGCCT 59.866 39.130 6.12 0.00 35.84 4.75
1949 2010 2.042464 AGTCTCAGCAAGTTGTCCTCA 58.958 47.619 4.48 0.00 0.00 3.86
1958 2019 1.342496 TGTCAGGACAGTCTCAGCAAG 59.658 52.381 0.00 0.00 36.21 4.01
1972 2033 5.221422 ACAATAATGGGTTTGTGTTGTCAGG 60.221 40.000 0.00 0.00 34.87 3.86
2056 2127 5.106869 TGCCAAACGTTGTATATTCAGACAC 60.107 40.000 0.00 0.00 0.00 3.67
2067 2138 3.684103 CTGAAAGTGCCAAACGTTGTA 57.316 42.857 0.00 0.00 29.98 2.41
2213 2286 0.463620 ATGGTTTGTGTGTTGTGCCC 59.536 50.000 0.00 0.00 0.00 5.36
2225 2298 1.610038 TGCTCAGAAGTGCATGGTTTG 59.390 47.619 0.00 0.00 39.15 2.93
2353 2456 1.762370 CCATTTTTATGGCCCCACTCC 59.238 52.381 0.00 0.00 34.56 3.85
2423 2532 7.615582 TCCAATGTACTTCATCAGTTGATTC 57.384 36.000 0.00 0.00 36.88 2.52
2664 2796 8.764287 CAAAAGGAAAGTACAGGCATTAAAAAG 58.236 33.333 0.00 0.00 0.00 2.27
2695 2829 1.263484 CTTGTGCTTGTGCTCTCACTG 59.737 52.381 0.00 0.00 43.49 3.66
2828 2968 7.067494 GTGGATCATTTTGAAGTTAGGCTGTAT 59.933 37.037 0.00 0.00 0.00 2.29
2829 2969 6.374333 GTGGATCATTTTGAAGTTAGGCTGTA 59.626 38.462 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.