Multiple sequence alignment - TraesCS7D01G046400

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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 TraesCS7D01G046400 chr7D 100.000 2731 0 0 1 2731 23999373 24002103 0.000000e+00 5044.0
1 TraesCS7D01G046400 chr7D 87.413 2145 209 33 224 2330 24114066 24116187 0.000000e+00 2409.0
2 TraesCS7D01G046400 chr7D 92.163 1697 121 6 151 1846 23541710 23540025 0.000000e+00 2386.0
3 TraesCS7D01G046400 chr7D 83.921 1729 227 35 224 1925 23509720 23511424 0.000000e+00 1605.0
4 TraesCS7D01G046400 chr7D 92.542 885 62 2 1842 2725 23529051 23528170 0.000000e+00 1266.0
5 TraesCS7D01G046400 chr7D 81.655 556 76 15 1193 1736 23507187 23507728 3.230000e-119 438.0
6 TraesCS7D01G046400 chr7D 87.003 377 42 3 698 1073 23982722 23983092 4.210000e-113 418.0
7 TraesCS7D01G046400 chr7D 81.365 381 62 5 200 571 23579999 23579619 4.420000e-78 302.0
8 TraesCS7D01G046400 chr7D 96.429 112 4 0 1 112 23541820 23541709 4.640000e-43 185.0
9 TraesCS7D01G046400 chr7D 90.476 42 0 1 105 146 195306468 195306431 5.000000e-03 52.8
10 TraesCS7D01G046400 chr4A 84.074 1733 213 40 224 1925 708300490 708298790 0.000000e+00 1613.0
11 TraesCS7D01G046400 chr7A 85.304 1429 163 31 521 1925 24627144 24628549 0.000000e+00 1432.0
12 TraesCS7D01G046400 chr7A 84.034 1428 179 30 521 1925 24539721 24538320 0.000000e+00 1328.0
13 TraesCS7D01G046400 chr7A 84.050 558 72 12 1191 1736 24624504 24625056 3.120000e-144 521.0
14 TraesCS7D01G046400 chr7A 84.644 267 36 3 224 486 24626873 24627138 7.500000e-66 261.0
15 TraesCS7D01G046400 chr6A 80.917 545 77 13 951 1494 310480527 310481045 3.270000e-109 405.0
16 TraesCS7D01G046400 chr6A 89.712 243 25 0 1489 1731 310681614 310681856 7.340000e-81 311.0
17 TraesCS7D01G046400 chr6A 84.295 312 36 11 2414 2722 310583328 310583629 2.660000e-75 292.0
18 TraesCS7D01G046400 chr6A 87.755 49 2 1 105 153 539198216 539198260 1.000000e-03 54.7
19 TraesCS7D01G046400 chr4B 84.270 89 9 2 109 192 642776549 642776461 6.270000e-12 82.4
20 TraesCS7D01G046400 chr1D 89.831 59 4 2 2613 2670 63356322 63356265 1.050000e-09 75.0
21 TraesCS7D01G046400 chr2D 88.136 59 5 2 2613 2670 299521309 299521366 4.880000e-08 69.4
22 TraesCS7D01G046400 chr2D 79.570 93 10 3 105 192 296173764 296173676 1.060000e-04 58.4
23 TraesCS7D01G046400 chr2D 78.218 101 13 3 102 197 641601009 641601105 3.800000e-04 56.5
24 TraesCS7D01G046400 chr1B 97.297 37 1 0 2613 2649 101142001 101141965 2.270000e-06 63.9
25 TraesCS7D01G046400 chr5D 94.595 37 2 0 2613 2649 435266439 435266403 1.060000e-04 58.4
26 TraesCS7D01G046400 chr3D 79.570 93 10 5 105 192 42630770 42630682 1.060000e-04 58.4
27 TraesCS7D01G046400 chr3D 100.000 29 0 0 2613 2641 5417298 5417326 1.000000e-03 54.7
28 TraesCS7D01G046400 chr3D 100.000 29 0 0 2613 2641 184438610 184438638 1.000000e-03 54.7
29 TraesCS7D01G046400 chr6D 100.000 29 0 0 2613 2641 225590337 225590365 1.000000e-03 54.7
30 TraesCS7D01G046400 chr3B 100.000 29 0 0 104 132 590683110 590683138 1.000000e-03 54.7
31 TraesCS7D01G046400 chrUn 88.889 45 1 3 106 146 259667581 259667537 5.000000e-03 52.8
32 TraesCS7D01G046400 chr4D 100.000 28 0 0 105 132 41710233 41710260 5.000000e-03 52.8


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 TraesCS7D01G046400 chr7D 23999373 24002103 2730 False 5044.0 5044 100.000 1 2731 1 chr7D.!!$F2 2730
1 TraesCS7D01G046400 chr7D 24114066 24116187 2121 False 2409.0 2409 87.413 224 2330 1 chr7D.!!$F3 2106
2 TraesCS7D01G046400 chr7D 23540025 23541820 1795 True 1285.5 2386 94.296 1 1846 2 chr7D.!!$R4 1845
3 TraesCS7D01G046400 chr7D 23528170 23529051 881 True 1266.0 1266 92.542 1842 2725 1 chr7D.!!$R1 883
4 TraesCS7D01G046400 chr7D 23507187 23511424 4237 False 1021.5 1605 82.788 224 1925 2 chr7D.!!$F4 1701
5 TraesCS7D01G046400 chr4A 708298790 708300490 1700 True 1613.0 1613 84.074 224 1925 1 chr4A.!!$R1 1701
6 TraesCS7D01G046400 chr7A 24538320 24539721 1401 True 1328.0 1328 84.034 521 1925 1 chr7A.!!$R1 1404
7 TraesCS7D01G046400 chr7A 24624504 24628549 4045 False 738.0 1432 84.666 224 1925 3 chr7A.!!$F1 1701
8 TraesCS7D01G046400 chr6A 310480527 310481045 518 False 405.0 405 80.917 951 1494 1 chr6A.!!$F1 543

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
189 190 0.034477 GTATTATGGGGCGGATGGGG 60.034 60.0 0.0 0.0 0.0 4.96 F
190 191 0.476808 TATTATGGGGCGGATGGGGT 60.477 55.0 0.0 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1041 3500 1.204113 CCTTCTCCCCAAGCTGGTCT 61.204 60.000 0.00 0.00 35.17 3.85 R
2012 4524 1.615392 GGAAGCATGCTCAAACAACCT 59.385 47.619 22.93 0.59 0.00 3.50 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
102 103 7.730364 TTTGAGATTCTTCTGTTTGGTACTC 57.270 36.000 0.00 0.00 30.30 2.59
104 105 5.167303 AGATTCTTCTGTTTGGTACTCCC 57.833 43.478 0.00 0.00 0.00 4.30
106 107 5.310857 AGATTCTTCTGTTTGGTACTCCCTT 59.689 40.000 0.00 0.00 0.00 3.95
107 108 5.382664 TTCTTCTGTTTGGTACTCCCTTT 57.617 39.130 0.00 0.00 0.00 3.11
109 110 6.503560 TCTTCTGTTTGGTACTCCCTTTTA 57.496 37.500 0.00 0.00 0.00 1.52
110 111 6.293698 TCTTCTGTTTGGTACTCCCTTTTAC 58.706 40.000 0.00 0.00 0.00 2.01
111 112 5.899631 TCTGTTTGGTACTCCCTTTTACT 57.100 39.130 0.00 0.00 0.00 2.24
112 113 5.861727 TCTGTTTGGTACTCCCTTTTACTC 58.138 41.667 0.00 0.00 0.00 2.59
113 114 4.976864 TGTTTGGTACTCCCTTTTACTCC 58.023 43.478 0.00 0.00 0.00 3.85
115 116 3.572661 TGGTACTCCCTTTTACTCCCT 57.427 47.619 0.00 0.00 0.00 4.20
116 117 3.447950 TGGTACTCCCTTTTACTCCCTC 58.552 50.000 0.00 0.00 0.00 4.30
117 118 2.770802 GGTACTCCCTTTTACTCCCTCC 59.229 54.545 0.00 0.00 0.00 4.30
118 119 1.569653 ACTCCCTTTTACTCCCTCCG 58.430 55.000 0.00 0.00 0.00 4.63
120 121 1.481363 CTCCCTTTTACTCCCTCCGTC 59.519 57.143 0.00 0.00 0.00 4.79
121 122 0.540454 CCCTTTTACTCCCTCCGTCC 59.460 60.000 0.00 0.00 0.00 4.79
122 123 0.540454 CCTTTTACTCCCTCCGTCCC 59.460 60.000 0.00 0.00 0.00 4.46
124 125 1.838077 CTTTTACTCCCTCCGTCCCAT 59.162 52.381 0.00 0.00 0.00 4.00
125 126 2.852714 TTTACTCCCTCCGTCCCATA 57.147 50.000 0.00 0.00 0.00 2.74
126 127 2.852714 TTACTCCCTCCGTCCCATAA 57.147 50.000 0.00 0.00 0.00 1.90
129 130 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
130 131 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
131 132 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
132 133 5.600749 ACTCCCTCCGTCCCATAATATAAT 58.399 41.667 0.00 0.00 0.00 1.28
134 135 7.194050 ACTCCCTCCGTCCCATAATATAATTA 58.806 38.462 0.00 0.00 0.00 1.40
135 136 7.681168 ACTCCCTCCGTCCCATAATATAATTAA 59.319 37.037 0.00 0.00 0.00 1.40
136 137 8.086143 TCCCTCCGTCCCATAATATAATTAAG 57.914 38.462 0.00 0.00 0.00 1.85
137 138 7.902401 TCCCTCCGTCCCATAATATAATTAAGA 59.098 37.037 0.00 0.00 0.00 2.10
138 139 8.545472 CCCTCCGTCCCATAATATAATTAAGAA 58.455 37.037 0.00 0.00 0.00 2.52
139 140 9.379791 CCTCCGTCCCATAATATAATTAAGAAC 57.620 37.037 0.00 0.00 0.00 3.01
140 141 8.991243 TCCGTCCCATAATATAATTAAGAACG 57.009 34.615 0.00 0.00 0.00 3.95
168 169 8.940768 TTTTAAGCTAGCTTCAAAAACATTGT 57.059 26.923 32.51 7.60 37.47 2.71
169 170 8.940768 TTTAAGCTAGCTTCAAAAACATTGTT 57.059 26.923 32.51 7.14 37.47 2.83
170 171 6.833342 AAGCTAGCTTCAAAAACATTGTTG 57.167 33.333 24.42 0.00 0.00 3.33
171 172 5.906073 AGCTAGCTTCAAAAACATTGTTGT 58.094 33.333 12.68 0.00 37.82 3.32
179 180 8.442384 GCTTCAAAAACATTGTTGTATTATGGG 58.558 33.333 2.13 0.00 34.06 4.00
180 181 8.839310 TTCAAAAACATTGTTGTATTATGGGG 57.161 30.769 2.13 0.00 34.06 4.96
181 182 6.876257 TCAAAAACATTGTTGTATTATGGGGC 59.124 34.615 2.13 0.00 34.06 5.80
182 183 4.647424 AACATTGTTGTATTATGGGGCG 57.353 40.909 0.15 0.00 34.06 6.13
183 184 2.955660 ACATTGTTGTATTATGGGGCGG 59.044 45.455 0.00 0.00 33.16 6.13
184 185 3.218453 CATTGTTGTATTATGGGGCGGA 58.782 45.455 0.00 0.00 0.00 5.54
185 186 3.586470 TTGTTGTATTATGGGGCGGAT 57.414 42.857 0.00 0.00 0.00 4.18
186 187 2.857483 TGTTGTATTATGGGGCGGATG 58.143 47.619 0.00 0.00 0.00 3.51
187 188 2.159382 GTTGTATTATGGGGCGGATGG 58.841 52.381 0.00 0.00 0.00 3.51
189 190 0.034477 GTATTATGGGGCGGATGGGG 60.034 60.000 0.00 0.00 0.00 4.96
190 191 0.476808 TATTATGGGGCGGATGGGGT 60.477 55.000 0.00 0.00 0.00 4.95
191 192 0.476808 ATTATGGGGCGGATGGGGTA 60.477 55.000 0.00 0.00 0.00 3.69
194 195 0.476808 ATGGGGCGGATGGGGTAATA 60.477 55.000 0.00 0.00 0.00 0.98
195 196 0.698198 TGGGGCGGATGGGGTAATAA 60.698 55.000 0.00 0.00 0.00 1.40
201 202 5.340194 GGGGCGGATGGGGTAATAAATATAA 60.340 44.000 0.00 0.00 0.00 0.98
202 203 5.826208 GGGCGGATGGGGTAATAAATATAAG 59.174 44.000 0.00 0.00 0.00 1.73
203 204 5.826208 GGCGGATGGGGTAATAAATATAAGG 59.174 44.000 0.00 0.00 0.00 2.69
205 206 5.826208 CGGATGGGGTAATAAATATAAGGCC 59.174 44.000 0.00 0.00 0.00 5.19
208 209 6.744802 TGGGGTAATAAATATAAGGCCCAT 57.255 37.500 0.00 0.00 36.68 4.00
209 210 7.848821 TGGGGTAATAAATATAAGGCCCATA 57.151 36.000 0.00 0.00 36.68 2.74
212 213 9.197306 GGGGTAATAAATATAAGGCCCATAAAG 57.803 37.037 0.00 0.00 36.68 1.85
213 214 9.763837 GGGTAATAAATATAAGGCCCATAAAGT 57.236 33.333 0.00 0.00 35.15 2.66
222 223 9.832445 ATATAAGGCCCATAAAGTATTCATACG 57.168 33.333 0.00 0.00 38.28 3.06
271 2726 2.187100 GGGAAGCATGGGAAAATCCAA 58.813 47.619 0.00 0.00 40.62 3.53
359 2817 2.281070 CACCACGACCAGCAGCTT 60.281 61.111 0.00 0.00 0.00 3.74
366 2824 4.254709 ACCAGCAGCTTGCCACGA 62.255 61.111 0.00 0.00 46.52 4.35
368 2826 4.081030 CAGCAGCTTGCCACGACG 62.081 66.667 0.00 0.00 46.52 5.12
425 2883 2.286833 TCTTTTCAAGAAAGACGGTGCG 59.713 45.455 0.00 0.00 33.83 5.34
455 2913 1.078143 GGCATCCAAGCTTCGGTCT 60.078 57.895 12.71 2.47 34.17 3.85
537 2995 5.397109 CCCGGTATAGTACTCCACCAATTTT 60.397 44.000 20.25 0.00 0.00 1.82
577 3035 5.989249 TCGTATTCATGTTGCTTCATATGC 58.011 37.500 0.00 0.00 0.00 3.14
596 3054 1.020861 CACGTTCCTGCATGCAGCTA 61.021 55.000 37.11 25.62 45.94 3.32
602 3060 2.910199 TCCTGCATGCAGCTAAGTAAG 58.090 47.619 37.11 22.64 45.94 2.34
683 3141 0.674895 GGCCACTCGAAGACAAGCAT 60.675 55.000 0.00 0.00 0.00 3.79
749 3207 2.993264 GGGAACGACCGGGTGAGA 60.993 66.667 3.30 0.00 40.11 3.27
772 3230 2.487445 CGCCAGACCAGATCCTAGACTA 60.487 54.545 0.00 0.00 0.00 2.59
781 3239 4.141367 CCAGATCCTAGACTAGTCTGACCA 60.141 50.000 31.47 13.51 40.71 4.02
860 3318 1.732259 CCCGAAAACTTCAGGTCATCG 59.268 52.381 0.00 0.00 36.41 3.84
873 3331 2.036992 AGGTCATCGATTGATCTGAGCC 59.963 50.000 10.74 5.21 44.40 4.70
893 3351 4.023291 GCCATGTCTTCCCAAATTTCCTA 58.977 43.478 0.00 0.00 0.00 2.94
898 3356 3.948473 GTCTTCCCAAATTTCCTAGCTCC 59.052 47.826 0.00 0.00 0.00 4.70
915 3373 2.678336 GCTCCGGGTTTAAGAATCAGTG 59.322 50.000 0.00 0.00 0.00 3.66
939 3398 5.221880 GCTCATATTTTGTGTGTTTGCAGA 58.778 37.500 0.00 0.00 0.00 4.26
990 3449 2.241430 TGGGAGAGTGAAGGACGATCTA 59.759 50.000 0.00 0.00 0.00 1.98
993 3452 3.949113 GGAGAGTGAAGGACGATCTACTT 59.051 47.826 0.00 0.00 0.00 2.24
1012 3471 2.266689 GGGCAATGGCAAAGCTGG 59.733 61.111 9.51 0.00 43.71 4.85
1041 3500 3.988379 AACCACGACGACTACTTTGTA 57.012 42.857 0.00 0.00 0.00 2.41
1146 3605 1.078848 GCCTCACTGCGATGGAACT 60.079 57.895 0.00 0.00 0.00 3.01
1458 3955 9.803315 ATTTTGTTGAAAGTTTCTAAGGTCTTC 57.197 29.630 16.33 0.00 0.00 2.87
1474 3972 4.000988 GGTCTTCGGCTGATTGAGTTAAA 58.999 43.478 0.00 0.00 0.00 1.52
1643 4142 5.627182 ATGAGAAGAGACCAGCATTGTAT 57.373 39.130 0.00 0.00 0.00 2.29
1673 4173 7.439108 AGTTAAGGTCAAGGACTATATTGCT 57.561 36.000 0.00 0.00 32.47 3.91
1694 4194 4.133078 CTGGGCTCTATGAACATTTCTCC 58.867 47.826 0.00 0.00 0.00 3.71
1719 4219 6.550854 CCAAGGGACAATGGTTATTGATACAT 59.449 38.462 6.98 0.00 45.21 2.29
1823 4332 5.933790 TCGTGTATTGTTAAATGGCAAGTC 58.066 37.500 0.00 0.00 0.00 3.01
1838 4347 5.278061 TGGCAAGTCTATTAAGTACTCCCT 58.722 41.667 0.00 0.00 0.00 4.20
1850 4359 8.706322 ATTAAGTACTCCCTTTTGTTCAACAT 57.294 30.769 0.00 0.00 0.00 2.71
1857 4366 3.742369 CCCTTTTGTTCAACATCACATGC 59.258 43.478 0.00 0.00 0.00 4.06
1998 4510 8.761575 ATAGTACCAATGAAAAATGCAAGTTG 57.238 30.769 0.00 0.00 0.00 3.16
2002 4514 5.163322 ACCAATGAAAAATGCAAGTTGGAGA 60.163 36.000 4.75 0.00 38.33 3.71
2012 4524 4.905429 TGCAAGTTGGAGAACTATTGCTA 58.095 39.130 4.75 0.00 41.87 3.49
2044 4556 0.909610 ATGCTTCCCGAGGGACAAGA 60.910 55.000 10.98 0.00 45.11 3.02
2145 4658 9.195411 CACAATAAGAATATGGCGCAAAAATAT 57.805 29.630 10.83 4.02 0.00 1.28
2223 4736 1.227943 GAACACACCTGCCTGCTGA 60.228 57.895 0.00 0.00 0.00 4.26
2246 4759 2.043248 GTCCCTCGCTCCCACCTA 60.043 66.667 0.00 0.00 0.00 3.08
2251 4764 0.830648 CCTCGCTCCCACCTAATGAA 59.169 55.000 0.00 0.00 0.00 2.57
2263 4776 2.092592 ACCTAATGAATCCCCGTGGTTC 60.093 50.000 0.00 0.00 0.00 3.62
2293 4807 4.260784 CGACAAGCTTTTGAGCTAGTTGTT 60.261 41.667 0.00 0.00 45.54 2.83
2303 4817 3.187700 GAGCTAGTTGTTGTACCCATCG 58.812 50.000 0.00 0.00 0.00 3.84
2369 4887 7.759489 AGTGTATCTCTCTATGCTAAAGAGG 57.241 40.000 9.64 3.21 40.77 3.69
2371 4889 8.170061 AGTGTATCTCTCTATGCTAAAGAGGAT 58.830 37.037 9.64 11.86 40.77 3.24
2377 4895 5.079998 TCTATGCTAAAGAGGATGGGAGA 57.920 43.478 0.00 0.00 35.08 3.71
2394 4912 8.684520 GGATGGGAGATCATTTGATTATTGATC 58.315 37.037 0.00 4.39 43.87 2.92
2396 4914 7.452562 TGGGAGATCATTTGATTATTGATCGA 58.547 34.615 0.00 0.00 46.60 3.59
2397 4915 7.388776 TGGGAGATCATTTGATTATTGATCGAC 59.611 37.037 0.00 5.59 46.60 4.20
2422 4940 3.433306 ACAAGTGCTATGTTTGGGCTA 57.567 42.857 0.00 0.00 0.00 3.93
2433 4951 1.080638 TTTGGGCTATGGTTCAGGGT 58.919 50.000 0.00 0.00 0.00 4.34
2492 5010 8.398665 GGTAAGATGTAAAATAGACTGCAAAGG 58.601 37.037 0.00 0.00 0.00 3.11
2512 5030 4.259356 AGGCGTAAATAGACCAAAGGAAC 58.741 43.478 0.00 0.00 0.00 3.62
2515 5033 3.943381 CGTAAATAGACCAAAGGAACCCC 59.057 47.826 0.00 0.00 0.00 4.95
2542 5060 7.934120 GTCTGCTATTTCCTAATCATTGGTACT 59.066 37.037 0.00 0.00 0.00 2.73
2589 5107 7.554959 TTAAGTCAGGATCTTTGGTCTTACT 57.445 36.000 0.00 0.00 0.00 2.24
2593 5111 4.467795 TCAGGATCTTTGGTCTTACTCTGG 59.532 45.833 0.00 0.00 0.00 3.86
2606 5124 6.264518 GGTCTTACTCTGGAACCATTGAAAAA 59.735 38.462 0.00 0.00 0.00 1.94
2650 5168 4.437772 AGACTCTAAAGTGCCGTAGAAC 57.562 45.455 0.00 0.00 35.28 3.01
2653 5171 4.304939 ACTCTAAAGTGCCGTAGAACAAC 58.695 43.478 0.00 0.00 33.32 3.32
2661 5179 5.357257 AGTGCCGTAGAACAACCTATATTG 58.643 41.667 0.00 0.00 35.59 1.90
2706 5224 3.838565 TCTGTGGCAATTTTCCCTAACA 58.161 40.909 0.00 0.00 0.00 2.41
2712 5230 6.212388 TGTGGCAATTTTCCCTAACATTATGT 59.788 34.615 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.106317 GGACACCGCAAATCATTTCTCTAAA 60.106 40.000 0.00 0.00 0.00 1.85
25 26 2.749621 GGACACCGCAAATCATTTCTCT 59.250 45.455 0.00 0.00 0.00 3.10
30 31 2.159393 CGATTGGACACCGCAAATCATT 60.159 45.455 0.00 0.00 0.00 2.57
73 74 8.641498 ACCAAACAGAAGAATCTCAAATGTAT 57.359 30.769 0.00 0.00 32.03 2.29
74 75 8.999431 GTACCAAACAGAAGAATCTCAAATGTA 58.001 33.333 0.00 0.00 32.03 2.29
75 76 6.966534 ACCAAACAGAAGAATCTCAAATGT 57.033 33.333 0.00 0.00 32.03 2.71
76 77 8.103948 AGTACCAAACAGAAGAATCTCAAATG 57.896 34.615 0.00 0.00 32.03 2.32
78 79 6.710744 GGAGTACCAAACAGAAGAATCTCAAA 59.289 38.462 0.00 0.00 32.64 2.69
79 80 6.231211 GGAGTACCAAACAGAAGAATCTCAA 58.769 40.000 0.00 0.00 32.64 3.02
80 81 5.280011 GGGAGTACCAAACAGAAGAATCTCA 60.280 44.000 0.00 0.00 39.85 3.27
81 82 5.046231 AGGGAGTACCAAACAGAAGAATCTC 60.046 44.000 0.00 0.00 43.89 2.75
82 83 4.846940 AGGGAGTACCAAACAGAAGAATCT 59.153 41.667 0.00 0.00 43.89 2.40
83 84 5.167303 AGGGAGTACCAAACAGAAGAATC 57.833 43.478 0.00 0.00 43.89 2.52
87 88 6.296803 AGTAAAAGGGAGTACCAAACAGAAG 58.703 40.000 0.00 0.00 43.89 2.85
90 91 5.001874 GGAGTAAAAGGGAGTACCAAACAG 58.998 45.833 0.00 0.00 43.89 3.16
92 93 4.042560 AGGGAGTAAAAGGGAGTACCAAAC 59.957 45.833 0.00 0.00 43.89 2.93
94 95 3.842436 GAGGGAGTAAAAGGGAGTACCAA 59.158 47.826 0.00 0.00 43.89 3.67
95 96 3.447950 GAGGGAGTAAAAGGGAGTACCA 58.552 50.000 0.00 0.00 43.89 3.25
96 97 2.770802 GGAGGGAGTAAAAGGGAGTACC 59.229 54.545 0.00 0.00 40.67 3.34
102 103 0.540454 GGACGGAGGGAGTAAAAGGG 59.460 60.000 0.00 0.00 0.00 3.95
104 105 1.272807 TGGGACGGAGGGAGTAAAAG 58.727 55.000 0.00 0.00 0.00 2.27
106 107 2.852714 TATGGGACGGAGGGAGTAAA 57.147 50.000 0.00 0.00 0.00 2.01
107 108 2.852714 TTATGGGACGGAGGGAGTAA 57.147 50.000 0.00 0.00 0.00 2.24
109 110 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
110 111 6.561519 AATTATATTATGGGACGGAGGGAG 57.438 41.667 0.00 0.00 0.00 4.30
111 112 7.902401 TCTTAATTATATTATGGGACGGAGGGA 59.098 37.037 0.00 0.00 0.00 4.20
112 113 8.086143 TCTTAATTATATTATGGGACGGAGGG 57.914 38.462 0.00 0.00 0.00 4.30
113 114 9.379791 GTTCTTAATTATATTATGGGACGGAGG 57.620 37.037 0.00 0.00 0.00 4.30
115 116 8.587608 ACGTTCTTAATTATATTATGGGACGGA 58.412 33.333 16.39 0.00 0.00 4.69
116 117 8.767478 ACGTTCTTAATTATATTATGGGACGG 57.233 34.615 16.39 0.00 0.00 4.79
143 144 8.940768 ACAATGTTTTTGAAGCTAGCTTAAAA 57.059 26.923 28.97 28.97 35.29 1.52
144 145 8.816144 CAACAATGTTTTTGAAGCTAGCTTAAA 58.184 29.630 29.39 25.25 36.26 1.52
146 147 7.488322 ACAACAATGTTTTTGAAGCTAGCTTA 58.512 30.769 29.39 12.97 35.91 3.09
149 150 7.873739 ATACAACAATGTTTTTGAAGCTAGC 57.126 32.000 6.62 6.62 41.05 3.42
152 153 9.206870 CCATAATACAACAATGTTTTTGAAGCT 57.793 29.630 0.00 0.00 41.05 3.74
153 154 8.442384 CCCATAATACAACAATGTTTTTGAAGC 58.558 33.333 0.00 0.00 41.05 3.86
155 156 7.389053 GCCCCATAATACAACAATGTTTTTGAA 59.611 33.333 0.00 0.00 41.05 2.69
157 158 6.183360 CGCCCCATAATACAACAATGTTTTTG 60.183 38.462 0.00 0.00 41.05 2.44
158 159 5.872070 CGCCCCATAATACAACAATGTTTTT 59.128 36.000 0.00 0.00 41.05 1.94
160 161 4.142049 CCGCCCCATAATACAACAATGTTT 60.142 41.667 0.00 0.00 41.05 2.83
162 163 2.955660 CCGCCCCATAATACAACAATGT 59.044 45.455 0.00 0.00 43.74 2.71
163 164 3.218453 TCCGCCCCATAATACAACAATG 58.782 45.455 0.00 0.00 0.00 2.82
166 167 2.488167 CCATCCGCCCCATAATACAACA 60.488 50.000 0.00 0.00 0.00 3.33
167 168 2.159382 CCATCCGCCCCATAATACAAC 58.841 52.381 0.00 0.00 0.00 3.32
168 169 1.074727 CCCATCCGCCCCATAATACAA 59.925 52.381 0.00 0.00 0.00 2.41
169 170 0.695924 CCCATCCGCCCCATAATACA 59.304 55.000 0.00 0.00 0.00 2.29
170 171 0.034477 CCCCATCCGCCCCATAATAC 60.034 60.000 0.00 0.00 0.00 1.89
171 172 0.476808 ACCCCATCCGCCCCATAATA 60.477 55.000 0.00 0.00 0.00 0.98
177 178 0.479378 TTTATTACCCCATCCGCCCC 59.521 55.000 0.00 0.00 0.00 5.80
179 180 5.826208 CCTTATATTTATTACCCCATCCGCC 59.174 44.000 0.00 0.00 0.00 6.13
180 181 5.298527 GCCTTATATTTATTACCCCATCCGC 59.701 44.000 0.00 0.00 0.00 5.54
181 182 5.826208 GGCCTTATATTTATTACCCCATCCG 59.174 44.000 0.00 0.00 0.00 4.18
182 183 6.134055 GGGCCTTATATTTATTACCCCATCC 58.866 44.000 0.84 0.00 0.00 3.51
183 184 6.737608 TGGGCCTTATATTTATTACCCCATC 58.262 40.000 4.53 0.00 35.21 3.51
184 185 6.744802 TGGGCCTTATATTTATTACCCCAT 57.255 37.500 4.53 0.00 35.21 4.00
185 186 6.744802 ATGGGCCTTATATTTATTACCCCA 57.255 37.500 4.53 0.00 43.49 4.96
186 187 9.197306 CTTTATGGGCCTTATATTTATTACCCC 57.803 37.037 4.53 0.00 35.09 4.95
187 188 9.763837 ACTTTATGGGCCTTATATTTATTACCC 57.236 33.333 4.53 0.00 36.60 3.69
201 202 5.562298 ACGTATGAATACTTTATGGGCCT 57.438 39.130 4.53 0.00 0.00 5.19
202 203 5.346822 CGTACGTATGAATACTTTATGGGCC 59.653 44.000 9.25 0.00 0.00 5.80
203 204 5.922544 ACGTACGTATGAATACTTTATGGGC 59.077 40.000 21.41 0.00 0.00 5.36
205 206 8.564648 TTCACGTACGTATGAATACTTTATGG 57.435 34.615 22.34 2.66 29.89 2.74
208 209 7.761409 ACCTTCACGTACGTATGAATACTTTA 58.239 34.615 22.34 0.00 34.43 1.85
209 210 6.624423 ACCTTCACGTACGTATGAATACTTT 58.376 36.000 22.34 2.02 34.43 2.66
212 213 5.801947 ACAACCTTCACGTACGTATGAATAC 59.198 40.000 22.34 0.00 34.43 1.89
213 214 5.801444 CACAACCTTCACGTACGTATGAATA 59.199 40.000 22.34 0.43 34.43 1.75
215 216 3.982701 CACAACCTTCACGTACGTATGAA 59.017 43.478 22.34 19.26 33.82 2.57
216 217 3.567530 CACAACCTTCACGTACGTATGA 58.432 45.455 22.34 12.68 0.00 2.15
217 218 2.091588 GCACAACCTTCACGTACGTATG 59.908 50.000 22.34 13.27 0.00 2.39
218 219 2.288334 TGCACAACCTTCACGTACGTAT 60.288 45.455 22.34 0.00 0.00 3.06
222 223 1.937899 ACTTGCACAACCTTCACGTAC 59.062 47.619 0.00 0.00 0.00 3.67
271 2726 0.957395 CTCCTGCACGGTCATTGCTT 60.957 55.000 2.68 0.00 40.86 3.91
368 2826 3.195698 GGAATCGGTGCTGCGACC 61.196 66.667 10.12 10.12 0.00 4.79
383 2841 1.277273 CAGCAGAGGTCAATGACAGGA 59.723 52.381 15.86 0.00 33.68 3.86
433 2891 1.372087 CCGAAGCTTGGATGCCTCAC 61.372 60.000 10.40 0.00 0.00 3.51
467 2925 0.696501 TTACAAGGAAGAGGCCCCAC 59.303 55.000 0.00 0.00 0.00 4.61
537 2995 6.538381 TGAATACGAATGCTTGATCTTGCTAA 59.462 34.615 10.78 0.00 0.00 3.09
577 3035 1.020861 TAGCTGCATGCAGGAACGTG 61.021 55.000 40.59 20.91 45.94 4.49
683 3141 2.756760 GTCGATCAGGTTGGTGTACCTA 59.243 50.000 2.32 0.00 46.80 3.08
749 3207 1.145945 TCTAGGATCTGGTCTGGCGAT 59.854 52.381 0.00 0.00 0.00 4.58
772 3230 1.711375 TGAGGTAGAGGTGGTCAGACT 59.289 52.381 0.00 0.00 0.00 3.24
781 3239 1.903183 GCTCCACTTTGAGGTAGAGGT 59.097 52.381 0.00 0.00 32.81 3.85
860 3318 3.814283 GGAAGACATGGCTCAGATCAATC 59.186 47.826 0.00 0.00 0.00 2.67
873 3331 4.952335 AGCTAGGAAATTTGGGAAGACATG 59.048 41.667 0.00 0.00 0.00 3.21
893 3351 2.572104 ACTGATTCTTAAACCCGGAGCT 59.428 45.455 0.73 0.00 0.00 4.09
898 3356 2.678336 GAGCCACTGATTCTTAAACCCG 59.322 50.000 0.00 0.00 0.00 5.28
915 3373 4.305769 TGCAAACACACAAAATATGAGCC 58.694 39.130 0.00 0.00 0.00 4.70
939 3398 4.011966 TGTGAACTCATGCAGAACATCT 57.988 40.909 0.00 0.00 36.64 2.90
990 3449 1.966762 CTTTGCCATTGCCCGAAGT 59.033 52.632 0.00 0.00 36.33 3.01
993 3452 2.283101 AGCTTTGCCATTGCCCGA 60.283 55.556 0.00 0.00 36.33 5.14
1041 3500 1.204113 CCTTCTCCCCAAGCTGGTCT 61.204 60.000 0.00 0.00 35.17 3.85
1146 3605 5.789521 TCGACCATGAGAATTGTAAGAACA 58.210 37.500 0.00 0.00 0.00 3.18
1297 3763 6.496911 AGGCTAACATTTTAACCTGACCAAAT 59.503 34.615 0.00 0.00 33.24 2.32
1458 3955 5.108385 ACAAACTTTAACTCAATCAGCCG 57.892 39.130 0.00 0.00 0.00 5.52
1474 3972 7.395190 TTGCTCATTATCTATGCAACAAACT 57.605 32.000 0.00 0.00 38.49 2.66
1643 4142 9.725206 ATATAGTCCTTGACCTTAACTTTCCTA 57.275 33.333 0.00 0.00 32.18 2.94
1673 4173 3.117888 GGGAGAAATGTTCATAGAGCCCA 60.118 47.826 0.00 0.00 0.00 5.36
1694 4194 5.890985 TGTATCAATAACCATTGTCCCTTGG 59.109 40.000 0.00 0.00 41.96 3.61
1780 4289 4.454504 ACGATACAAACATTGGTCCTTGAC 59.545 41.667 0.00 0.00 34.12 3.18
1781 4290 4.454161 CACGATACAAACATTGGTCCTTGA 59.546 41.667 0.00 0.00 34.12 3.02
1782 4291 4.215399 ACACGATACAAACATTGGTCCTTG 59.785 41.667 0.00 0.00 34.12 3.61
1783 4292 4.394729 ACACGATACAAACATTGGTCCTT 58.605 39.130 0.00 0.00 34.12 3.36
1823 4332 9.280174 TGTTGAACAAAAGGGAGTACTTAATAG 57.720 33.333 0.00 0.00 0.00 1.73
1838 4347 4.397481 TGGCATGTGATGTTGAACAAAA 57.603 36.364 0.62 0.00 0.00 2.44
1850 4359 2.296752 CACAACCTGAAATGGCATGTGA 59.703 45.455 0.00 0.00 44.29 3.58
1857 4366 1.619827 ACCATGCACAACCTGAAATGG 59.380 47.619 0.00 0.00 39.74 3.16
1971 4483 8.353423 ACTTGCATTTTTCATTGGTACTATCT 57.647 30.769 0.00 0.00 0.00 1.98
1972 4484 8.863049 CAACTTGCATTTTTCATTGGTACTATC 58.137 33.333 0.00 0.00 0.00 2.08
1998 4510 5.938125 TCAAACAACCTAGCAATAGTTCTCC 59.062 40.000 0.00 0.00 0.00 3.71
2002 4514 5.070001 TGCTCAAACAACCTAGCAATAGTT 58.930 37.500 0.00 0.00 41.74 2.24
2012 4524 1.615392 GGAAGCATGCTCAAACAACCT 59.385 47.619 22.93 0.59 0.00 3.50
2171 4684 2.356382 CGTTTGTTTGCACTCCCTTGTA 59.644 45.455 0.00 0.00 0.00 2.41
2223 4736 2.660064 GGGAGCGAGGGACACATGT 61.660 63.158 0.00 0.00 0.00 3.21
2246 4759 1.633432 TCTGAACCACGGGGATTCATT 59.367 47.619 12.96 0.00 38.05 2.57
2251 4764 1.224592 GCATCTGAACCACGGGGAT 59.775 57.895 12.96 0.00 38.05 3.85
2263 4776 1.536766 TCAAAAGCTTGTCGGCATCTG 59.463 47.619 0.00 0.00 33.94 2.90
2303 4817 2.011222 CTCTCACTAGTCTCGGACACC 58.989 57.143 0.00 0.00 34.60 4.16
2305 4819 1.629353 ACCTCTCACTAGTCTCGGACA 59.371 52.381 0.00 0.00 34.60 4.02
2369 4887 8.396390 CGATCAATAATCAAATGATCTCCCATC 58.604 37.037 11.78 0.00 44.57 3.51
2371 4889 7.388776 GTCGATCAATAATCAAATGATCTCCCA 59.611 37.037 11.78 0.00 44.57 4.37
2394 4912 5.794945 CCAAACATAGCACTTGTAATTGTCG 59.205 40.000 0.00 0.00 0.00 4.35
2396 4914 5.566627 GCCCAAACATAGCACTTGTAATTGT 60.567 40.000 0.00 0.00 0.00 2.71
2397 4915 4.864247 GCCCAAACATAGCACTTGTAATTG 59.136 41.667 0.00 0.00 0.00 2.32
2405 4923 2.242196 ACCATAGCCCAAACATAGCACT 59.758 45.455 0.00 0.00 0.00 4.40
2422 4940 0.038744 CAAGGCTCACCCTGAACCAT 59.961 55.000 0.00 0.00 45.62 3.55
2433 4951 3.517296 TGTCCAAAATACCAAGGCTCA 57.483 42.857 0.00 0.00 0.00 4.26
2492 5010 3.376234 GGGTTCCTTTGGTCTATTTACGC 59.624 47.826 0.00 0.00 0.00 4.42
2512 5030 3.071023 TGATTAGGAAATAGCAGACGGGG 59.929 47.826 0.00 0.00 0.00 5.73
2515 5033 5.760253 ACCAATGATTAGGAAATAGCAGACG 59.240 40.000 1.57 0.00 0.00 4.18
2562 5080 9.232473 GTAAGACCAAAGATCCTGACTTAAATT 57.768 33.333 0.00 0.00 0.00 1.82
2566 5084 6.954684 AGAGTAAGACCAAAGATCCTGACTTA 59.045 38.462 0.00 0.00 0.00 2.24
2573 5091 5.179533 GTTCCAGAGTAAGACCAAAGATCC 58.820 45.833 0.00 0.00 0.00 3.36
2634 5152 3.660865 AGGTTGTTCTACGGCACTTTAG 58.339 45.455 0.00 0.00 0.00 1.85
2635 5153 3.756933 AGGTTGTTCTACGGCACTTTA 57.243 42.857 0.00 0.00 0.00 1.85
2636 5154 2.632987 AGGTTGTTCTACGGCACTTT 57.367 45.000 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.