Multiple sequence alignment - TraesCS4A01G205700

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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 TraesCS4A01G205700 chr4A 100.000 3677 0 0 1 3677 498214790 498211114 0.000000e+00 6791.0
1 TraesCS4A01G205700 chr4A 97.504 1763 38 4 1910 3668 498146904 498145144 0.000000e+00 3007.0
2 TraesCS4A01G205700 chr4A 81.592 1369 140 53 157 1450 498164929 498163598 0.000000e+00 1029.0
3 TraesCS4A01G205700 chr4A 82.069 435 56 3 1488 1916 498163593 498163175 5.840000e-93 351.0
4 TraesCS4A01G205700 chr4A 100.000 32 0 0 52 83 498165277 498165246 3.970000e-05 60.2
5 TraesCS4A01G205700 chr4D 92.266 2922 156 30 655 3539 84803445 84800557 0.000000e+00 4080.0
6 TraesCS4A01G205700 chr4D 81.331 541 51 18 157 652 84804013 84803478 9.570000e-106 394.0
7 TraesCS4A01G205700 chr4D 92.562 121 8 1 3548 3668 84799449 84799330 4.880000e-39 172.0


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 TraesCS4A01G205700 chr4A 498211114 498214790 3676 True 6791.000000 6791 100.000000 1 3677 1 chr4A.!!$R2 3676
1 TraesCS4A01G205700 chr4A 498145144 498146904 1760 True 3007.000000 3007 97.504000 1910 3668 1 chr4A.!!$R1 1758
2 TraesCS4A01G205700 chr4A 498163175 498165277 2102 True 480.066667 1029 87.887000 52 1916 3 chr4A.!!$R3 1864
3 TraesCS4A01G205700 chr4D 84799330 84804013 4683 True 1548.666667 4080 88.719667 157 3668 3 chr4D.!!$R1 3511

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
751 1075 0.969409 AGCTCTGGAAATTGGCAGGC 60.969 55.0 0.0 0.0 0.00 4.85 F
1812 2154 0.899717 TTGCAGGGGACAGGCAAATC 60.900 55.0 0.0 0.0 45.73 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2454 2796 0.392060 CAGCACAGGTCATAGCAGCA 60.392 55.0 0.0 0.0 0.00 4.41 R
2998 3362 2.768527 TGAGCCTCCCTCATTAGACAAG 59.231 50.0 0.0 0.0 45.44 3.16 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 41 5.828299 TTTTTAGGGACAACTGAACAGTG 57.172 39.130 8.25 5.73 41.58 3.66
41 42 4.497291 TTTAGGGACAACTGAACAGTGT 57.503 40.909 8.25 8.56 41.58 3.55
42 43 4.497291 TTAGGGACAACTGAACAGTGTT 57.503 40.909 8.61 8.61 41.58 3.32
43 44 3.366052 AGGGACAACTGAACAGTGTTT 57.634 42.857 10.45 0.00 41.58 2.83
44 45 3.697166 AGGGACAACTGAACAGTGTTTT 58.303 40.909 10.45 0.00 41.58 2.43
45 46 4.086457 AGGGACAACTGAACAGTGTTTTT 58.914 39.130 10.45 1.49 41.58 1.94
46 47 4.157840 AGGGACAACTGAACAGTGTTTTTC 59.842 41.667 10.45 0.00 41.58 2.29
47 48 4.157840 GGGACAACTGAACAGTGTTTTTCT 59.842 41.667 10.45 0.00 41.58 2.52
48 49 5.336451 GGGACAACTGAACAGTGTTTTTCTT 60.336 40.000 10.45 0.00 41.58 2.52
49 50 6.127842 GGGACAACTGAACAGTGTTTTTCTTA 60.128 38.462 10.45 0.00 41.58 2.10
50 51 6.967199 GGACAACTGAACAGTGTTTTTCTTAG 59.033 38.462 10.45 5.16 41.58 2.18
101 231 2.294479 CGTGCACCGTGTTTTCTTAG 57.706 50.000 12.15 0.00 0.00 2.18
103 233 2.096909 CGTGCACCGTGTTTTCTTAGAG 60.097 50.000 12.15 0.00 0.00 2.43
104 234 3.128349 GTGCACCGTGTTTTCTTAGAGA 58.872 45.455 5.22 0.00 0.00 3.10
105 235 3.558418 GTGCACCGTGTTTTCTTAGAGAA 59.442 43.478 5.22 0.00 31.28 2.87
106 236 3.558418 TGCACCGTGTTTTCTTAGAGAAC 59.442 43.478 8.47 8.47 33.26 3.01
108 238 4.213482 GCACCGTGTTTTCTTAGAGAACAT 59.787 41.667 18.89 3.53 38.54 2.71
109 239 5.614887 GCACCGTGTTTTCTTAGAGAACATC 60.615 44.000 18.89 12.46 38.54 3.06
110 240 5.696724 CACCGTGTTTTCTTAGAGAACATCT 59.303 40.000 18.89 4.76 38.54 2.90
111 241 5.696724 ACCGTGTTTTCTTAGAGAACATCTG 59.303 40.000 18.89 13.26 38.54 2.90
112 242 5.389935 CCGTGTTTTCTTAGAGAACATCTGC 60.390 44.000 18.89 7.51 38.54 4.26
113 243 5.177511 CGTGTTTTCTTAGAGAACATCTGCA 59.822 40.000 18.89 0.00 38.54 4.41
114 244 6.366630 GTGTTTTCTTAGAGAACATCTGCAC 58.633 40.000 18.89 4.30 38.54 4.57
115 245 5.177511 TGTTTTCTTAGAGAACATCTGCACG 59.822 40.000 13.29 0.00 39.20 5.34
116 246 4.521130 TTCTTAGAGAACATCTGCACGT 57.479 40.909 0.00 0.00 39.20 4.49
117 247 4.521130 TCTTAGAGAACATCTGCACGTT 57.479 40.909 0.00 0.00 39.20 3.99
122 252 4.820897 AGAGAACATCTGCACGTTATTGA 58.179 39.130 0.00 0.00 36.69 2.57
123 253 5.423015 AGAGAACATCTGCACGTTATTGAT 58.577 37.500 0.00 0.00 36.69 2.57
124 254 5.877012 AGAGAACATCTGCACGTTATTGATT 59.123 36.000 0.00 0.00 36.69 2.57
126 256 7.549134 AGAGAACATCTGCACGTTATTGATTAA 59.451 33.333 0.00 0.00 36.69 1.40
128 258 5.810525 ACATCTGCACGTTATTGATTAAGC 58.189 37.500 0.00 0.00 0.00 3.09
130 260 5.871465 TCTGCACGTTATTGATTAAGCAA 57.129 34.783 8.84 8.84 0.00 3.91
131 261 5.627172 TCTGCACGTTATTGATTAAGCAAC 58.373 37.500 8.56 0.00 0.00 4.17
132 262 5.180304 TCTGCACGTTATTGATTAAGCAACA 59.820 36.000 8.56 0.00 0.00 3.33
133 263 5.763088 TGCACGTTATTGATTAAGCAACAA 58.237 33.333 8.56 0.00 0.00 2.83
134 264 6.385843 TGCACGTTATTGATTAAGCAACAAT 58.614 32.000 8.56 6.73 37.82 2.71
135 265 6.307558 TGCACGTTATTGATTAAGCAACAATG 59.692 34.615 13.61 13.61 36.06 2.82
136 266 6.237542 GCACGTTATTGATTAAGCAACAATGG 60.238 38.462 18.06 9.91 36.06 3.16
137 267 5.804979 ACGTTATTGATTAAGCAACAATGGC 59.195 36.000 18.06 0.00 36.06 4.40
138 268 5.804473 CGTTATTGATTAAGCAACAATGGCA 59.196 36.000 8.56 0.00 36.06 4.92
139 269 6.020440 CGTTATTGATTAAGCAACAATGGCAG 60.020 38.462 8.56 0.00 36.06 4.85
141 271 5.465532 TTGATTAAGCAACAATGGCAGAA 57.534 34.783 1.13 0.00 0.00 3.02
142 272 5.465532 TGATTAAGCAACAATGGCAGAAA 57.534 34.783 0.00 0.00 0.00 2.52
144 274 5.243507 TGATTAAGCAACAATGGCAGAAAGA 59.756 36.000 0.00 0.00 0.00 2.52
146 276 4.612264 AAGCAACAATGGCAGAAAGAAT 57.388 36.364 0.00 0.00 0.00 2.40
148 278 4.563061 AGCAACAATGGCAGAAAGAATTC 58.437 39.130 0.00 0.00 35.70 2.17
150 280 4.248058 CAACAATGGCAGAAAGAATTCCC 58.752 43.478 0.65 0.00 36.12 3.97
151 281 2.833943 ACAATGGCAGAAAGAATTCCCC 59.166 45.455 0.65 0.00 36.12 4.81
152 282 2.833338 CAATGGCAGAAAGAATTCCCCA 59.167 45.455 0.65 0.38 39.99 4.96
153 283 2.220653 TGGCAGAAAGAATTCCCCAG 57.779 50.000 0.65 0.00 34.40 4.45
155 285 2.312741 TGGCAGAAAGAATTCCCCAGAT 59.687 45.455 0.65 0.00 34.40 2.90
164 408 3.641906 AGAATTCCCCAGATACTGTACGG 59.358 47.826 0.65 0.00 0.00 4.02
176 420 2.778299 ACTGTACGGTTTGCATCATGT 58.222 42.857 0.04 0.00 0.00 3.21
187 431 5.697633 GGTTTGCATCATGTTGACATTTTCT 59.302 36.000 7.98 0.00 33.61 2.52
213 459 3.465871 ACACAAAATGACACATTTGGGC 58.534 40.909 14.59 0.00 42.35 5.36
214 460 2.475864 CACAAAATGACACATTTGGGCG 59.524 45.455 15.95 3.83 40.09 6.13
241 487 9.831737 CATGTTCGAGAAATAAAAGTTTGAGAT 57.168 29.630 0.00 0.00 0.00 2.75
276 533 1.762957 AGGTACAGACTTGCACACTGT 59.237 47.619 18.79 18.79 45.06 3.55
278 535 2.135933 GTACAGACTTGCACACTGTCC 58.864 52.381 18.48 7.97 42.65 4.02
319 577 4.252570 TGGGGTCAGTTTCCTTGTTTAA 57.747 40.909 0.00 0.00 0.00 1.52
320 578 4.611367 TGGGGTCAGTTTCCTTGTTTAAA 58.389 39.130 0.00 0.00 0.00 1.52
378 636 9.035607 CACCGGATTAATGAATAGTCTATATGC 57.964 37.037 9.46 0.00 0.00 3.14
434 714 5.517770 GTGCTTGAATAATTGCTGGAATGTC 59.482 40.000 0.00 0.00 0.00 3.06
440 720 7.709947 TGAATAATTGCTGGAATGTCTGATTC 58.290 34.615 0.00 2.12 0.00 2.52
516 809 7.580600 ACAAAATTTGTTGTTTGTGGAACTTC 58.419 30.769 5.41 0.00 44.24 3.01
518 811 4.768130 TTTGTTGTTTGTGGAACTTCGA 57.232 36.364 0.00 0.00 39.08 3.71
533 826 2.930040 ACTTCGATGCAAGTACCATTCG 59.070 45.455 0.00 0.00 34.70 3.34
534 827 1.934589 TCGATGCAAGTACCATTCGG 58.065 50.000 0.00 0.00 38.77 4.30
636 929 4.158786 TGGAAGCCAAAAATCCTCAATCA 58.841 39.130 0.00 0.00 34.24 2.57
637 930 4.592351 TGGAAGCCAAAAATCCTCAATCAA 59.408 37.500 0.00 0.00 34.24 2.57
640 933 4.162651 AGCCAAAAATCCTCAATCAACCT 58.837 39.130 0.00 0.00 0.00 3.50
663 986 9.264653 ACCTAATATAGTATACTGGTAAAGGGC 57.735 37.037 15.90 0.00 0.00 5.19
670 993 6.534634 AGTATACTGGTAAAGGGCAATGATC 58.465 40.000 4.10 0.00 0.00 2.92
702 1025 4.756642 TCACTAGCATTTCTCACCAAACAG 59.243 41.667 0.00 0.00 0.00 3.16
710 1033 4.981806 TTCTCACCAAACAGAAAACCAG 57.018 40.909 0.00 0.00 0.00 4.00
716 1039 7.013274 TCTCACCAAACAGAAAACCAGATAAAG 59.987 37.037 0.00 0.00 0.00 1.85
717 1040 6.605594 TCACCAAACAGAAAACCAGATAAAGT 59.394 34.615 0.00 0.00 0.00 2.66
718 1041 7.776030 TCACCAAACAGAAAACCAGATAAAGTA 59.224 33.333 0.00 0.00 0.00 2.24
724 1048 9.574516 AACAGAAAACCAGATAAAGTAATGAGT 57.425 29.630 0.00 0.00 0.00 3.41
751 1075 0.969409 AGCTCTGGAAATTGGCAGGC 60.969 55.000 0.00 0.00 0.00 4.85
765 1093 1.617740 GCAGGCGCAAAGTTTGTATC 58.382 50.000 16.70 6.76 38.36 2.24
766 1094 1.200020 GCAGGCGCAAAGTTTGTATCT 59.800 47.619 16.70 8.72 38.36 1.98
860 1191 7.855375 TCAATTAATTTTGGCCCATGAATACA 58.145 30.769 0.00 0.00 0.00 2.29
861 1192 8.492782 TCAATTAATTTTGGCCCATGAATACAT 58.507 29.630 0.00 0.00 37.19 2.29
885 1216 1.052124 TGGTGGTCGACTTTGGTCCT 61.052 55.000 16.46 0.00 39.15 3.85
904 1235 8.243961 TGGTCCTTTCTTCAATGAACAAATAA 57.756 30.769 0.00 0.00 0.00 1.40
908 1239 7.867403 TCCTTTCTTCAATGAACAAATAACAGC 59.133 33.333 0.00 0.00 0.00 4.40
910 1241 9.252962 CTTTCTTCAATGAACAAATAACAGCTT 57.747 29.630 0.00 0.00 0.00 3.74
958 1291 2.018355 TGAGTGTTACCTGGCTACCA 57.982 50.000 0.00 0.00 0.00 3.25
967 1301 8.110908 AGTGTTACCTGGCTACCATTTTAATAA 58.889 33.333 0.00 0.00 30.82 1.40
969 1303 9.127277 TGTTACCTGGCTACCATTTTAATAATC 57.873 33.333 0.00 0.00 30.82 1.75
1032 1368 7.340232 AGCATTATTGTTCCTGTGTACATCAAT 59.660 33.333 0.00 6.69 0.00 2.57
1047 1383 1.301244 CAATGCGCCCGAGCTATCT 60.301 57.895 4.18 0.00 38.13 1.98
1103 1439 9.880064 GTATCTTACCAAGACAAGAAAAGTTTC 57.120 33.333 0.00 0.00 41.01 2.78
1106 1442 4.998788 ACCAAGACAAGAAAAGTTTCTGC 58.001 39.130 7.05 1.32 46.22 4.26
1242 1578 3.491581 GGCTGATCCGTATGTACCG 57.508 57.895 0.00 0.00 0.00 4.02
1334 1670 6.210078 AGAAACGTAAAGACTTGACAGAGAG 58.790 40.000 3.54 0.00 0.00 3.20
1356 1692 5.308825 AGTCCTACTCACCAAAATCAAGTG 58.691 41.667 0.00 0.00 0.00 3.16
1457 1793 1.746517 GTCACCCTGAAGTGGACGT 59.253 57.895 0.00 0.00 38.34 4.34
1462 1798 1.202651 ACCCTGAAGTGGACGTGAAAG 60.203 52.381 0.00 0.00 0.00 2.62
1653 1995 6.322456 TCGGTTCATTGAAGAGATCAGAGTAT 59.678 38.462 0.00 0.00 39.77 2.12
1736 2078 3.258872 CCTGCATTTTGGAAACCTGATCA 59.741 43.478 0.00 0.00 0.00 2.92
1737 2079 4.262549 CCTGCATTTTGGAAACCTGATCAA 60.263 41.667 0.00 0.00 0.00 2.57
1746 2088 5.003804 TGGAAACCTGATCAAAAGCTAGTC 58.996 41.667 0.00 0.00 0.00 2.59
1767 2109 4.778143 CAGGTGTACGCCCTGGCC 62.778 72.222 21.89 0.00 44.77 5.36
1812 2154 0.899717 TTGCAGGGGACAGGCAAATC 60.900 55.000 0.00 0.00 45.73 2.17
1894 2236 3.431725 GGCTTTGTTCGCCTCCGG 61.432 66.667 0.00 0.00 44.17 5.14
2034 2376 2.381911 AGCACATGGTCATGGAATTCC 58.618 47.619 18.17 18.17 42.91 3.01
2044 2386 3.087781 TCATGGAATTCCGACAATGCAA 58.912 40.909 19.57 0.00 39.43 4.08
2060 2402 6.567050 ACAATGCAACTAAATATGAAGGCAG 58.433 36.000 0.00 0.00 33.09 4.85
2088 2430 5.319453 AGGAAGTTTGCTGATTCTTCATCA 58.681 37.500 0.00 0.00 39.82 3.07
2283 2625 4.997395 ACTACCACTCATGCTGTTGTAAAG 59.003 41.667 0.00 0.00 0.00 1.85
2454 2796 2.103263 AGAAGAACAACTTGAGGTCGCT 59.897 45.455 0.00 0.00 39.13 4.93
2706 3049 1.521616 GAGGAGCCTGCTTCCTGAG 59.478 63.158 12.78 0.00 33.37 3.35
2713 3056 1.544314 GCCTGCTTCCTGAGACTTTGT 60.544 52.381 0.00 0.00 0.00 2.83
3164 3528 2.366640 TTAGTGGGAGCGCTATCTCT 57.633 50.000 11.50 14.04 33.70 3.10
3219 3583 3.288092 GGTAATCTGACCCATGGGAAAC 58.712 50.000 38.07 25.18 38.96 2.78
3220 3584 3.308832 GGTAATCTGACCCATGGGAAACA 60.309 47.826 38.07 27.92 38.96 2.83
3222 3586 3.763557 ATCTGACCCATGGGAAACAAT 57.236 42.857 38.07 19.17 38.96 2.71
3319 3687 0.537143 ACGGCTGCAAATGAAGTGGA 60.537 50.000 0.50 0.00 0.00 4.02
3668 5139 7.122650 TGGCATTTTACTTCTTGAGGGATTTAG 59.877 37.037 0.00 0.00 0.00 1.85
3669 5140 7.339466 GGCATTTTACTTCTTGAGGGATTTAGA 59.661 37.037 0.00 0.00 0.00 2.10
3670 5141 8.401709 GCATTTTACTTCTTGAGGGATTTAGAG 58.598 37.037 0.00 0.00 0.00 2.43
3671 5142 7.923414 TTTTACTTCTTGAGGGATTTAGAGC 57.077 36.000 0.00 0.00 0.00 4.09
3672 5143 6.620877 TTACTTCTTGAGGGATTTAGAGCA 57.379 37.500 0.00 0.00 0.00 4.26
3673 5144 5.707066 ACTTCTTGAGGGATTTAGAGCAT 57.293 39.130 0.00 0.00 0.00 3.79
3674 5145 5.435291 ACTTCTTGAGGGATTTAGAGCATG 58.565 41.667 0.00 0.00 0.00 4.06
3675 5146 3.813443 TCTTGAGGGATTTAGAGCATGC 58.187 45.455 10.51 10.51 0.00 4.06
3676 5147 3.457380 TCTTGAGGGATTTAGAGCATGCT 59.543 43.478 22.92 22.92 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 5.258051 ACACTGTTCAGTTGTCCCTAAAAA 58.742 37.500 2.47 0.00 0.00 1.94
19 20 4.850680 ACACTGTTCAGTTGTCCCTAAAA 58.149 39.130 2.47 0.00 0.00 1.52
20 21 4.497291 ACACTGTTCAGTTGTCCCTAAA 57.503 40.909 2.47 0.00 0.00 1.85
21 22 4.497291 AACACTGTTCAGTTGTCCCTAA 57.503 40.909 2.47 0.00 0.00 2.69
22 23 4.497291 AAACACTGTTCAGTTGTCCCTA 57.503 40.909 2.47 0.00 0.00 3.53
23 24 3.366052 AAACACTGTTCAGTTGTCCCT 57.634 42.857 2.47 0.00 0.00 4.20
24 25 4.157840 AGAAAAACACTGTTCAGTTGTCCC 59.842 41.667 2.47 0.00 0.00 4.46
25 26 5.310720 AGAAAAACACTGTTCAGTTGTCC 57.689 39.130 2.47 0.00 0.00 4.02
26 27 7.748847 TCTAAGAAAAACACTGTTCAGTTGTC 58.251 34.615 2.47 0.00 0.00 3.18
27 28 7.681939 TCTAAGAAAAACACTGTTCAGTTGT 57.318 32.000 2.47 3.11 0.00 3.32
28 29 8.964420 TTTCTAAGAAAAACACTGTTCAGTTG 57.036 30.769 2.47 2.55 0.00 3.16
49 50 8.680903 CCAAGTTTGCAGATCTATGTTATTTCT 58.319 33.333 0.00 0.00 0.00 2.52
50 51 8.462016 ACCAAGTTTGCAGATCTATGTTATTTC 58.538 33.333 0.00 0.00 0.00 2.17
94 224 4.883083 ACGTGCAGATGTTCTCTAAGAAA 58.117 39.130 0.00 0.00 35.75 2.52
95 225 4.521130 ACGTGCAGATGTTCTCTAAGAA 57.479 40.909 0.00 0.00 31.13 2.52
97 227 6.531594 TCAATAACGTGCAGATGTTCTCTAAG 59.468 38.462 2.47 0.00 33.22 2.18
98 228 6.394809 TCAATAACGTGCAGATGTTCTCTAA 58.605 36.000 2.47 0.00 33.22 2.10
99 229 5.961272 TCAATAACGTGCAGATGTTCTCTA 58.039 37.500 2.47 0.00 33.22 2.43
100 230 4.820897 TCAATAACGTGCAGATGTTCTCT 58.179 39.130 2.47 0.00 33.22 3.10
101 231 5.725110 ATCAATAACGTGCAGATGTTCTC 57.275 39.130 2.47 0.00 33.22 2.87
103 233 6.412072 GCTTAATCAATAACGTGCAGATGTTC 59.588 38.462 2.47 0.00 33.22 3.18
104 234 6.128035 TGCTTAATCAATAACGTGCAGATGTT 60.128 34.615 0.00 0.00 35.41 2.71
105 235 5.353956 TGCTTAATCAATAACGTGCAGATGT 59.646 36.000 0.00 0.00 0.00 3.06
106 236 5.809464 TGCTTAATCAATAACGTGCAGATG 58.191 37.500 0.00 0.00 0.00 2.90
108 238 5.180304 TGTTGCTTAATCAATAACGTGCAGA 59.820 36.000 0.00 0.00 0.00 4.26
109 239 5.389778 TGTTGCTTAATCAATAACGTGCAG 58.610 37.500 0.00 0.00 0.00 4.41
110 240 5.363979 TGTTGCTTAATCAATAACGTGCA 57.636 34.783 0.00 0.00 0.00 4.57
111 241 6.237542 CCATTGTTGCTTAATCAATAACGTGC 60.238 38.462 3.73 0.00 31.55 5.34
112 242 6.237542 GCCATTGTTGCTTAATCAATAACGTG 60.238 38.462 3.73 0.85 31.55 4.49
113 243 5.804979 GCCATTGTTGCTTAATCAATAACGT 59.195 36.000 3.73 0.00 31.55 3.99
114 244 5.804473 TGCCATTGTTGCTTAATCAATAACG 59.196 36.000 3.73 0.00 31.55 3.18
115 245 7.035004 TCTGCCATTGTTGCTTAATCAATAAC 58.965 34.615 3.73 0.00 31.55 1.89
116 246 7.167924 TCTGCCATTGTTGCTTAATCAATAA 57.832 32.000 4.08 4.08 32.91 1.40
117 247 6.772360 TCTGCCATTGTTGCTTAATCAATA 57.228 33.333 0.00 0.00 31.76 1.90
122 252 5.726980 TCTTTCTGCCATTGTTGCTTAAT 57.273 34.783 0.00 0.00 0.00 1.40
123 253 5.528043 TTCTTTCTGCCATTGTTGCTTAA 57.472 34.783 0.00 0.00 0.00 1.85
124 254 5.726980 ATTCTTTCTGCCATTGTTGCTTA 57.273 34.783 0.00 0.00 0.00 3.09
126 256 4.562143 GGAATTCTTTCTGCCATTGTTGCT 60.562 41.667 5.23 0.00 32.16 3.91
128 258 4.248058 GGGAATTCTTTCTGCCATTGTTG 58.752 43.478 5.23 0.00 32.16 3.33
130 260 2.833943 GGGGAATTCTTTCTGCCATTGT 59.166 45.455 5.23 0.00 32.16 2.71
131 261 2.833338 TGGGGAATTCTTTCTGCCATTG 59.167 45.455 5.23 0.00 32.16 2.82
132 262 3.102204 CTGGGGAATTCTTTCTGCCATT 58.898 45.455 5.23 0.00 32.16 3.16
133 263 2.312741 TCTGGGGAATTCTTTCTGCCAT 59.687 45.455 5.23 0.00 32.16 4.40
134 264 1.710244 TCTGGGGAATTCTTTCTGCCA 59.290 47.619 5.23 0.00 32.16 4.92
135 265 2.514458 TCTGGGGAATTCTTTCTGCC 57.486 50.000 5.23 0.00 32.16 4.85
136 266 4.578105 CAGTATCTGGGGAATTCTTTCTGC 59.422 45.833 5.23 0.00 32.16 4.26
137 267 5.749462 ACAGTATCTGGGGAATTCTTTCTG 58.251 41.667 5.23 6.05 35.51 3.02
138 268 6.407074 CGTACAGTATCTGGGGAATTCTTTCT 60.407 42.308 5.23 0.00 35.51 2.52
139 269 5.753921 CGTACAGTATCTGGGGAATTCTTTC 59.246 44.000 5.23 0.00 35.51 2.62
141 271 4.101119 CCGTACAGTATCTGGGGAATTCTT 59.899 45.833 5.23 0.00 35.51 2.52
142 272 3.641906 CCGTACAGTATCTGGGGAATTCT 59.358 47.826 5.23 0.00 35.51 2.40
144 274 3.381335 ACCGTACAGTATCTGGGGAATT 58.619 45.455 0.00 0.00 35.51 2.17
146 276 2.537633 ACCGTACAGTATCTGGGGAA 57.462 50.000 0.00 0.00 35.51 3.97
148 278 2.901249 CAAACCGTACAGTATCTGGGG 58.099 52.381 0.00 2.83 35.51 4.96
150 280 2.967362 TGCAAACCGTACAGTATCTGG 58.033 47.619 0.00 0.00 35.51 3.86
151 281 4.180817 TGATGCAAACCGTACAGTATCTG 58.819 43.478 0.00 0.00 37.52 2.90
152 282 4.465632 TGATGCAAACCGTACAGTATCT 57.534 40.909 0.00 0.00 0.00 1.98
153 283 4.570772 ACATGATGCAAACCGTACAGTATC 59.429 41.667 0.00 0.00 0.00 2.24
155 285 3.932822 ACATGATGCAAACCGTACAGTA 58.067 40.909 0.00 0.00 0.00 2.74
164 408 6.586751 CAGAAAATGTCAACATGATGCAAAC 58.413 36.000 0.00 0.00 36.56 2.93
187 431 5.752472 CCAAATGTGTCATTTTGTGTTAGCA 59.248 36.000 5.17 0.00 32.23 3.49
213 459 6.577055 TCAAACTTTTATTTCTCGAACATGCG 59.423 34.615 0.00 0.00 0.00 4.73
214 460 7.803189 TCTCAAACTTTTATTTCTCGAACATGC 59.197 33.333 0.00 0.00 0.00 4.06
260 506 0.541392 TGGACAGTGTGCAAGTCTGT 59.459 50.000 15.81 16.05 43.72 3.41
263 509 1.668419 AGTTGGACAGTGTGCAAGTC 58.332 50.000 28.01 18.06 42.26 3.01
276 533 6.183361 CCCAATGATCTGATTCTCTAGTTGGA 60.183 42.308 0.00 0.00 35.57 3.53
278 535 5.996513 CCCCAATGATCTGATTCTCTAGTTG 59.003 44.000 0.00 0.00 0.00 3.16
319 577 9.638176 ATTGCTCATTCCTGAAAGATTATACTT 57.362 29.630 0.00 0.00 34.07 2.24
348 606 9.847224 ATAGACTATTCATTAATCCGGTGTTTT 57.153 29.630 0.00 0.00 0.00 2.43
352 610 9.035607 GCATATAGACTATTCATTAATCCGGTG 57.964 37.037 0.00 0.00 0.00 4.94
375 633 4.519213 CCAATGAACCAAATGGAATGCAT 58.481 39.130 6.42 0.00 38.94 3.96
376 634 3.869140 GCCAATGAACCAAATGGAATGCA 60.869 43.478 6.42 0.00 38.94 3.96
377 635 2.679336 GCCAATGAACCAAATGGAATGC 59.321 45.455 6.42 0.00 38.94 3.56
378 636 3.685756 GTGCCAATGAACCAAATGGAATG 59.314 43.478 6.42 0.00 38.94 2.67
387 645 1.408340 CTGTTGTGTGCCAATGAACCA 59.592 47.619 0.00 0.00 35.02 3.67
422 702 4.564782 AGAGAATCAGACATTCCAGCAA 57.435 40.909 0.00 0.00 37.82 3.91
469 750 4.034975 GTGCCAAAATGTTTGCTGCTTTAA 59.965 37.500 0.00 0.00 0.00 1.52
474 755 1.297664 TGTGCCAAAATGTTTGCTGC 58.702 45.000 0.00 0.00 0.00 5.25
497 778 4.768130 TCGAAGTTCCACAAACAACAAA 57.232 36.364 0.00 0.00 40.56 2.83
507 793 2.415512 GGTACTTGCATCGAAGTTCCAC 59.584 50.000 6.97 0.00 41.03 4.02
510 796 4.492570 CGAATGGTACTTGCATCGAAGTTC 60.493 45.833 0.00 0.00 37.38 3.01
516 809 0.937304 CCCGAATGGTACTTGCATCG 59.063 55.000 0.00 0.00 0.00 3.84
586 879 7.264947 CACAACTAAGTCCAGAACCAATTTTT 58.735 34.615 0.00 0.00 0.00 1.94
592 885 2.486548 GGCACAACTAAGTCCAGAACCA 60.487 50.000 0.00 0.00 0.00 3.67
598 891 1.429930 TCCAGGCACAACTAAGTCCA 58.570 50.000 0.00 0.00 0.00 4.02
601 894 1.545651 GGCTTCCAGGCACAACTAAGT 60.546 52.381 0.00 0.00 40.97 2.24
637 930 9.264653 GCCCTTTACCAGTATACTATATTAGGT 57.735 37.037 4.74 10.01 0.00 3.08
652 945 4.530875 AGAAGATCATTGCCCTTTACCAG 58.469 43.478 0.00 0.00 0.00 4.00
653 946 4.591321 AGAAGATCATTGCCCTTTACCA 57.409 40.909 0.00 0.00 0.00 3.25
663 986 9.491675 AATGCTAGTGAAGATAGAAGATCATTG 57.508 33.333 0.00 0.00 0.00 2.82
670 993 7.437862 GGTGAGAAATGCTAGTGAAGATAGAAG 59.562 40.741 0.00 0.00 0.00 2.85
722 1046 7.039082 TGCCAATTTCCAGAGCTAAATAAAACT 60.039 33.333 0.00 0.00 0.00 2.66
724 1048 7.238486 TGCCAATTTCCAGAGCTAAATAAAA 57.762 32.000 0.00 0.00 0.00 1.52
751 1075 6.176975 TGGAATGTAGATACAAACTTTGCG 57.823 37.500 1.14 0.00 39.99 4.85
765 1093 5.124457 CCCAATCTCACTTGTTGGAATGTAG 59.876 44.000 5.01 0.00 43.98 2.74
766 1094 5.009631 CCCAATCTCACTTGTTGGAATGTA 58.990 41.667 5.01 0.00 43.98 2.29
834 1165 7.986320 TGTATTCATGGGCCAAAATTAATTGAG 59.014 33.333 11.89 0.00 31.84 3.02
835 1166 7.855375 TGTATTCATGGGCCAAAATTAATTGA 58.145 30.769 11.89 3.81 31.84 2.57
837 1168 9.697990 AAATGTATTCATGGGCCAAAATTAATT 57.302 25.926 11.89 12.98 34.19 1.40
874 1205 6.183360 TGTTCATTGAAGAAAGGACCAAAGTC 60.183 38.462 0.00 0.00 42.73 3.01
877 1208 6.537453 TTGTTCATTGAAGAAAGGACCAAA 57.463 33.333 6.51 0.00 29.48 3.28
885 1216 9.598517 AAAGCTGTTATTTGTTCATTGAAGAAA 57.401 25.926 20.06 20.06 38.71 2.52
928 1259 6.542370 GCCAGGTAACACTCATGTACAATATT 59.458 38.462 0.00 0.00 38.45 1.28
929 1260 6.055588 GCCAGGTAACACTCATGTACAATAT 58.944 40.000 0.00 0.00 38.45 1.28
932 1263 3.326588 AGCCAGGTAACACTCATGTACAA 59.673 43.478 0.00 0.00 38.45 2.41
940 1271 3.629142 AATGGTAGCCAGGTAACACTC 57.371 47.619 0.00 0.00 36.75 3.51
941 1272 4.382386 AAAATGGTAGCCAGGTAACACT 57.618 40.909 0.00 0.00 36.75 3.55
949 1282 8.345565 GTCACTGATTATTAAAATGGTAGCCAG 58.654 37.037 0.00 0.00 36.75 4.85
1032 1368 1.388837 TTGTAGATAGCTCGGGCGCA 61.389 55.000 10.83 0.00 44.37 6.09
1106 1442 2.475666 GCACTAAGCAGCCTTCTGG 58.524 57.895 0.00 0.00 44.79 3.86
1265 1601 3.812053 AGAAGTATGGCTTTGATCATCGC 59.188 43.478 0.00 1.90 37.59 4.58
1334 1670 5.049405 CACACTTGATTTTGGTGAGTAGGAC 60.049 44.000 0.00 0.00 35.28 3.85
1348 1684 5.036117 ACACCAGAAGTACACACTTGATT 57.964 39.130 0.00 0.00 45.18 2.57
1356 1692 3.489785 CACTCGAAACACCAGAAGTACAC 59.510 47.826 0.00 0.00 0.00 2.90
1474 1810 0.387202 CCTGGATGAGTAGCAGACGG 59.613 60.000 0.00 0.00 0.00 4.79
1517 1853 1.303155 GCTGAAACTCCTGCCAGCT 60.303 57.895 0.00 0.00 46.04 4.24
1653 1995 6.101150 ACTGTATGGTATCTGGCATTAGGAAA 59.899 38.462 0.00 0.00 0.00 3.13
1736 2078 4.082679 CGTACACCTGAGAGACTAGCTTTT 60.083 45.833 0.00 0.00 0.00 2.27
1737 2079 3.440872 CGTACACCTGAGAGACTAGCTTT 59.559 47.826 0.00 0.00 0.00 3.51
1746 2088 4.019983 AGGGCGTACACCTGAGAG 57.980 61.111 5.36 0.00 36.85 3.20
1812 2154 0.736325 CTCGTAGAACCGCCCACTTG 60.736 60.000 0.00 0.00 34.09 3.16
1894 2236 4.511082 GGCATAAATCTCAGCTGAGTTCTC 59.489 45.833 36.32 21.35 42.60 2.87
2034 2376 5.682862 GCCTTCATATTTAGTTGCATTGTCG 59.317 40.000 0.00 0.00 0.00 4.35
2044 2386 5.104360 TCCTTGCTCTGCCTTCATATTTAGT 60.104 40.000 0.00 0.00 0.00 2.24
2088 2430 3.386402 GGTAAGATAGAGCAGGAGCAACT 59.614 47.826 0.00 0.00 45.49 3.16
2093 2435 4.211125 TGTCAGGTAAGATAGAGCAGGAG 58.789 47.826 0.00 0.00 0.00 3.69
2127 2469 2.646930 CATTGCAGAGCAGGACCATAA 58.353 47.619 0.00 0.00 40.61 1.90
2283 2625 2.421619 CAGTCCAAAGTCTTCAGCTCC 58.578 52.381 0.00 0.00 0.00 4.70
2334 2676 7.805071 GCCATTGCACTAACTATTGTATCATTC 59.195 37.037 0.00 0.00 37.47 2.67
2454 2796 0.392060 CAGCACAGGTCATAGCAGCA 60.392 55.000 0.00 0.00 0.00 4.41
2534 2876 4.781087 ACTTCTTTAGTGCCATGTACCCTA 59.219 41.667 0.00 0.00 35.19 3.53
2706 3049 7.600375 TGTCAAGATCAAGTAGATGACAAAGTC 59.400 37.037 4.11 0.00 39.54 3.01
2998 3362 2.768527 TGAGCCTCCCTCATTAGACAAG 59.231 50.000 0.00 0.00 45.44 3.16
3401 3773 8.117813 ACGGAACAAAATGTCTATAAAATGGT 57.882 30.769 0.00 0.00 0.00 3.55
3409 3781 4.321675 GGGCAAACGGAACAAAATGTCTAT 60.322 41.667 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.