Multiple sequence alignment - TraesCS3B01G533600

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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 TraesCS3B01G533600 chr3B 100.000 2471 0 0 1 2471 773763403 773760933 0.000000e+00 4564.0
1 TraesCS3B01G533600 chr3B 92.643 802 59 0 872 1673 773897294 773898095 0.000000e+00 1155.0
2 TraesCS3B01G533600 chr3B 85.940 1074 100 25 442 1500 773746574 773745537 0.000000e+00 1099.0
3 TraesCS3B01G533600 chr3B 88.555 699 38 13 1778 2463 773898093 773898762 0.000000e+00 809.0
4 TraesCS3B01G533600 chr3D 90.953 1879 117 19 599 2463 579583602 579585441 0.000000e+00 2479.0
5 TraesCS3B01G533600 chr3D 92.165 702 50 2 804 1500 579425743 579425042 0.000000e+00 987.0
6 TraesCS3B01G533600 chr3D 84.494 445 43 18 388 826 579398116 579397692 1.370000e-112 416.0
7 TraesCS3B01G533600 chr3D 84.352 409 33 6 2058 2466 579396412 579396035 3.000000e-99 372.0
8 TraesCS3B01G533600 chr3D 86.322 329 31 9 1 323 579426658 579426338 1.820000e-91 346.0
9 TraesCS3B01G533600 chr3D 90.179 224 22 0 2243 2466 579423948 579423725 2.400000e-75 292.0
10 TraesCS3B01G533600 chr3D 83.590 195 25 1 1667 1854 354613837 354613643 2.530000e-40 176.0
11 TraesCS3B01G533600 chr3D 82.703 185 22 2 1669 1853 463808657 463808831 3.290000e-34 156.0
12 TraesCS3B01G533600 chr3A 88.754 1156 96 14 376 1500 714624706 714625858 0.000000e+00 1384.0
13 TraesCS3B01G533600 chr3A 88.939 1103 93 15 403 1498 714604131 714603051 0.000000e+00 1334.0
14 TraesCS3B01G533600 chr3A 92.282 609 47 0 892 1500 714594291 714593683 0.000000e+00 865.0
15 TraesCS3B01G533600 chr3A 93.348 466 30 1 1999 2463 714643357 714643822 0.000000e+00 688.0
16 TraesCS3B01G533600 chr3A 82.000 550 49 13 1929 2466 714592043 714591532 2.940000e-114 422.0
17 TraesCS3B01G533600 chr3A 82.427 239 36 2 557 794 714594995 714594762 1.160000e-48 204.0
18 TraesCS3B01G533600 chr3A 94.737 57 3 0 1527 1583 714602967 714602911 3.380000e-14 89.8
19 TraesCS3B01G533600 chr3A 96.970 33 1 0 1497 1529 714625876 714625908 3.430000e-04 56.5
20 TraesCS3B01G533600 chr2B 89.385 179 17 1 1674 1850 411541460 411541282 8.890000e-55 224.0
21 TraesCS3B01G533600 chr7D 88.043 184 14 6 1678 1856 263946172 263946352 6.920000e-51 211.0
22 TraesCS3B01G533600 chr2A 88.953 172 17 1 1669 1838 457912620 457912791 6.920000e-51 211.0
23 TraesCS3B01G533600 chr2D 92.199 141 11 0 1674 1814 345853336 345853196 1.500000e-47 200.0
24 TraesCS3B01G533600 chr7B 86.207 174 19 5 1664 1834 750591679 750591508 1.510000e-42 183.0
25 TraesCS3B01G533600 chr4D 87.821 156 18 1 1675 1829 122199878 122200033 5.430000e-42 182.0
26 TraesCS3B01G533600 chr5D 85.465 172 19 5 1664 1831 508111944 508112113 9.080000e-40 174.0


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 TraesCS3B01G533600 chr3B 773760933 773763403 2470 True 4564.000000 4564 100.000000 1 2471 1 chr3B.!!$R2 2470
1 TraesCS3B01G533600 chr3B 773745537 773746574 1037 True 1099.000000 1099 85.940000 442 1500 1 chr3B.!!$R1 1058
2 TraesCS3B01G533600 chr3B 773897294 773898762 1468 False 982.000000 1155 90.599000 872 2463 2 chr3B.!!$F1 1591
3 TraesCS3B01G533600 chr3D 579583602 579585441 1839 False 2479.000000 2479 90.953000 599 2463 1 chr3D.!!$F2 1864
4 TraesCS3B01G533600 chr3D 579423725 579426658 2933 True 541.666667 987 89.555333 1 2466 3 chr3D.!!$R3 2465
5 TraesCS3B01G533600 chr3D 579396035 579398116 2081 True 394.000000 416 84.423000 388 2466 2 chr3D.!!$R2 2078
6 TraesCS3B01G533600 chr3A 714624706 714625908 1202 False 720.250000 1384 92.862000 376 1529 2 chr3A.!!$F2 1153
7 TraesCS3B01G533600 chr3A 714602911 714604131 1220 True 711.900000 1334 91.838000 403 1583 2 chr3A.!!$R2 1180
8 TraesCS3B01G533600 chr3A 714591532 714594995 3463 True 497.000000 865 85.569667 557 2466 3 chr3A.!!$R1 1909

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
133 134 0.119155 TGATCACTCCCCAACTCCCT 59.881 55.0 0.0 0.0 0.0 4.20 F
882 1119 0.405198 TTGCTTGAATCCTGCCTCCA 59.595 50.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1016 1661 0.041839 CAGAAGCTTGACGTGCACAC 60.042 55.0 18.64 10.76 0.00 3.82 R
2255 4428 0.390472 GACCAAGTGGAGAGAAGGCG 60.390 60.0 3.83 0.00 38.94 5.52 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
50 51 4.503314 GGCCGGACCGTAACCTCG 62.503 72.222 13.94 0.00 0.00 4.63
52 53 4.503314 CCGGACCGTAACCTCGCC 62.503 72.222 13.94 0.00 0.00 5.54
53 54 3.751246 CGGACCGTAACCTCGCCA 61.751 66.667 5.48 0.00 0.00 5.69
54 55 2.183555 GGACCGTAACCTCGCCAG 59.816 66.667 0.00 0.00 0.00 4.85
55 56 2.508663 GACCGTAACCTCGCCAGC 60.509 66.667 0.00 0.00 0.00 4.85
56 57 4.430765 ACCGTAACCTCGCCAGCG 62.431 66.667 5.50 5.50 41.35 5.18
126 127 1.257750 CGTCCAGTGATCACTCCCCA 61.258 60.000 25.58 6.91 40.20 4.96
127 128 0.984230 GTCCAGTGATCACTCCCCAA 59.016 55.000 25.58 6.72 40.20 4.12
128 129 0.984230 TCCAGTGATCACTCCCCAAC 59.016 55.000 25.58 0.00 40.20 3.77
129 130 0.987294 CCAGTGATCACTCCCCAACT 59.013 55.000 25.58 0.00 40.20 3.16
133 134 0.119155 TGATCACTCCCCAACTCCCT 59.881 55.000 0.00 0.00 0.00 4.20
135 136 0.119155 ATCACTCCCCAACTCCCTGA 59.881 55.000 0.00 0.00 0.00 3.86
136 137 0.836400 TCACTCCCCAACTCCCTGAC 60.836 60.000 0.00 0.00 0.00 3.51
147 152 2.232298 CTCCCTGACCTCAAGACCGC 62.232 65.000 0.00 0.00 0.00 5.68
172 177 1.941734 CGCTCGGAGCTCGTGAATC 60.942 63.158 25.96 2.64 39.60 2.52
246 251 2.357881 CAGGCGTCAGCTGCTTCA 60.358 61.111 9.47 0.00 44.37 3.02
247 252 2.358003 AGGCGTCAGCTGCTTCAC 60.358 61.111 9.47 0.32 44.37 3.18
249 254 3.426568 GCGTCAGCTGCTTCACCC 61.427 66.667 9.47 0.00 41.01 4.61
251 256 2.343758 GTCAGCTGCTTCACCCGA 59.656 61.111 9.47 0.00 0.00 5.14
252 257 2.029844 GTCAGCTGCTTCACCCGAC 61.030 63.158 9.47 0.00 0.00 4.79
278 285 1.203287 GAGCAAGGGCAAGGTGAATTC 59.797 52.381 0.00 0.00 44.61 2.17
281 288 2.825532 GCAAGGGCAAGGTGAATTCTAA 59.174 45.455 7.05 0.00 40.72 2.10
285 292 4.273318 AGGGCAAGGTGAATTCTAATCAC 58.727 43.478 7.05 0.00 45.08 3.06
313 320 7.714377 TGAATTCCTGTATTGCAAACATTTTGT 59.286 29.630 1.71 0.00 0.00 2.83
315 322 6.841443 TCCTGTATTGCAAACATTTTGTTG 57.159 33.333 1.71 0.00 40.14 3.33
318 325 7.981789 TCCTGTATTGCAAACATTTTGTTGTTA 59.018 29.630 1.71 0.00 40.14 2.41
323 330 6.426980 TGCAAACATTTTGTTGTTATTGCA 57.573 29.167 10.84 10.84 44.69 4.08
324 331 6.845302 TGCAAACATTTTGTTGTTATTGCAA 58.155 28.000 0.00 0.00 44.28 4.08
325 332 7.307694 TGCAAACATTTTGTTGTTATTGCAAA 58.692 26.923 1.71 0.00 44.28 3.68
328 335 9.286946 CAAACATTTTGTTGTTATTGCAAACAT 57.713 25.926 1.71 0.00 40.14 2.71
329 336 9.500864 AAACATTTTGTTGTTATTGCAAACATC 57.499 25.926 1.71 4.32 40.14 3.06
332 339 6.503616 TTTGTTGTTATTGCAAACATCGAC 57.496 33.333 1.71 5.58 39.04 4.20
333 340 5.431420 TGTTGTTATTGCAAACATCGACT 57.569 34.783 1.71 0.00 39.04 4.18
334 341 5.826586 TGTTGTTATTGCAAACATCGACTT 58.173 33.333 1.71 0.00 39.04 3.01
337 368 7.041712 TGTTGTTATTGCAAACATCGACTTAGA 60.042 33.333 1.71 0.00 39.04 2.10
339 370 6.649141 TGTTATTGCAAACATCGACTTAGAGT 59.351 34.615 1.71 0.00 34.50 3.24
348 379 6.328641 ACATCGACTTAGAGTTGTACTGTT 57.671 37.500 0.00 0.00 31.48 3.16
349 380 6.380190 ACATCGACTTAGAGTTGTACTGTTC 58.620 40.000 0.00 0.00 31.48 3.18
353 384 5.800941 CGACTTAGAGTTGTACTGTTCCATC 59.199 44.000 0.00 0.00 0.00 3.51
354 385 6.038997 ACTTAGAGTTGTACTGTTCCATCC 57.961 41.667 0.00 0.00 0.00 3.51
363 394 1.003580 ACTGTTCCATCCGCTTGTCAT 59.996 47.619 0.00 0.00 0.00 3.06
371 402 2.839486 TCCGCTTGTCATCTTCAGTT 57.161 45.000 0.00 0.00 0.00 3.16
373 404 3.849911 TCCGCTTGTCATCTTCAGTTAG 58.150 45.455 0.00 0.00 0.00 2.34
415 465 3.430790 CGATGCAGGAGGATTCAGTACAA 60.431 47.826 0.00 0.00 0.00 2.41
416 466 4.712476 GATGCAGGAGGATTCAGTACAAT 58.288 43.478 0.00 0.00 0.00 2.71
424 474 5.355350 GGAGGATTCAGTACAATTCTGGTTG 59.645 44.000 0.00 0.00 34.15 3.77
428 478 6.016276 GGATTCAGTACAATTCTGGTTGTGTT 60.016 38.462 0.00 0.00 42.02 3.32
436 486 5.238650 ACAATTCTGGTTGTGTTACTGCTAC 59.761 40.000 0.00 0.00 40.60 3.58
438 488 4.409718 TCTGGTTGTGTTACTGCTACAA 57.590 40.909 0.00 0.00 32.39 2.41
519 577 4.201685 CGTTCATCCCGTGTGTTAGATTTC 60.202 45.833 0.00 0.00 0.00 2.17
569 630 4.660938 GGTGGTTTGCTCCCCGCT 62.661 66.667 0.00 0.00 40.11 5.52
576 637 1.552799 TTTGCTCCCCGCTCTGATCA 61.553 55.000 0.00 0.00 40.11 2.92
630 714 2.259204 CCACCATGGTTTGCTGCG 59.741 61.111 16.84 1.30 31.35 5.18
669 755 8.918202 ACCAATTAACTACAGAATCTGAAACA 57.082 30.769 18.20 0.00 35.18 2.83
748 837 8.970020 TGCTCATGTTATCTATTTTGTTGGATT 58.030 29.630 0.00 0.00 0.00 3.01
809 899 5.984233 TTGAGCTATAGTTGTTTATGCCG 57.016 39.130 0.84 0.00 0.00 5.69
829 919 4.691216 GCCGTGATATGGGATACTTTTCTC 59.309 45.833 0.00 0.00 0.00 2.87
847 944 7.378995 ACTTTTCTCGTTAGTTATATGCGCTAG 59.621 37.037 9.73 0.00 0.00 3.42
877 1114 1.252904 TGGGCTTGCTTGAATCCTGC 61.253 55.000 0.00 0.00 0.00 4.85
882 1119 0.405198 TTGCTTGAATCCTGCCTCCA 59.595 50.000 0.00 0.00 0.00 3.86
895 1132 6.065976 TCCTGCCTCCACCAATTATATATG 57.934 41.667 0.00 0.00 0.00 1.78
941 1572 8.716646 TCGTCATGTATGATAAAACTGTGAAT 57.283 30.769 0.00 0.00 39.30 2.57
965 1596 7.815840 TCTCTAATTACATCTCCACTCTGAG 57.184 40.000 2.45 2.45 0.00 3.35
969 1600 6.798427 AATTACATCTCCACTCTGAGCTTA 57.202 37.500 4.19 0.00 32.22 3.09
977 1608 2.681848 CCACTCTGAGCTTAATTGCCTG 59.318 50.000 4.19 0.00 0.00 4.85
995 1640 1.935873 CTGATGGGTTGTATGCAGACG 59.064 52.381 7.03 0.00 0.00 4.18
1016 1661 0.467384 AGCATGGACTCCCTTCATCG 59.533 55.000 0.00 0.00 0.00 3.84
1062 1707 1.987855 CCTCCTCACGCTAACCCCA 60.988 63.158 0.00 0.00 0.00 4.96
1110 1755 2.281208 TGTGGCCGTACAGTTGCC 60.281 61.111 0.00 5.92 45.56 4.52
1174 1819 1.070758 AGAAGTTTCTGCGCTTCCTGA 59.929 47.619 9.73 0.00 41.29 3.86
1494 2139 4.273318 GTTTGCCTTGGAGGATCTTATGT 58.727 43.478 0.00 0.00 37.67 2.29
1587 2287 9.089601 TGCATTTGATTTACTTCATTTATGCAG 57.910 29.630 0.00 0.00 38.69 4.41
1642 2343 1.759562 GCAGAGGCCCCTAGTGATAGT 60.760 57.143 0.00 0.00 0.00 2.12
1673 2374 4.827284 ACTTGGGTGAAGTAATCAAGGTTG 59.173 41.667 0.00 0.00 43.54 3.77
1675 2376 4.394729 TGGGTGAAGTAATCAAGGTTGAC 58.605 43.478 0.00 0.00 40.50 3.18
1684 2385 1.315690 TCAAGGTTGACGAGTCGACT 58.684 50.000 20.18 20.18 42.32 4.18
1688 2389 2.502295 AGGTTGACGAGTCGACTAGTT 58.498 47.619 28.42 14.82 42.32 2.24
1689 2390 3.668447 AGGTTGACGAGTCGACTAGTTA 58.332 45.455 28.42 22.88 42.32 2.24
1693 2394 4.871993 TGACGAGTCGACTAGTTATTCC 57.128 45.455 28.42 17.31 31.94 3.01
1694 2395 4.256110 TGACGAGTCGACTAGTTATTCCA 58.744 43.478 28.42 19.39 31.94 3.53
1710 2411 8.954950 AGTTATTCCAATGTTGAGACTCATAG 57.045 34.615 5.87 0.00 0.00 2.23
1711 2412 8.762645 AGTTATTCCAATGTTGAGACTCATAGA 58.237 33.333 5.87 0.00 0.00 1.98
1712 2413 8.821894 GTTATTCCAATGTTGAGACTCATAGAC 58.178 37.037 5.87 2.32 0.00 2.59
1713 2414 6.611613 TTCCAATGTTGAGACTCATAGACT 57.388 37.500 5.87 0.00 0.00 3.24
1714 2415 7.718334 TTCCAATGTTGAGACTCATAGACTA 57.282 36.000 5.87 0.00 0.00 2.59
1715 2416 7.340122 TCCAATGTTGAGACTCATAGACTAG 57.660 40.000 5.87 0.00 0.00 2.57
1716 2417 6.892456 TCCAATGTTGAGACTCATAGACTAGT 59.108 38.462 5.87 0.00 0.00 2.57
1717 2418 7.067615 TCCAATGTTGAGACTCATAGACTAGTC 59.932 40.741 15.41 15.41 42.02 2.59
1718 2419 6.612247 ATGTTGAGACTCATAGACTAGTCG 57.388 41.667 17.07 5.27 45.47 4.18
1719 2420 5.489249 TGTTGAGACTCATAGACTAGTCGT 58.511 41.667 17.07 8.55 45.47 4.34
1738 2439 3.251487 TCGTGACTAATCGTGACAAGTCA 59.749 43.478 10.48 10.48 44.47 3.41
1744 2445 6.080648 ACTAATCGTGACAAGTCAACACTA 57.919 37.500 4.20 0.00 41.85 2.74
1751 2452 5.028375 GTGACAAGTCAACACTAAAGTTGC 58.972 41.667 4.20 0.00 46.44 4.17
1754 2455 4.574828 ACAAGTCAACACTAAAGTTGCGAT 59.425 37.500 2.14 0.00 46.44 4.58
1927 4051 4.222145 TGGGACAGAGAAAGTATGGTGTAC 59.778 45.833 0.00 0.00 0.00 2.90
2022 4156 7.173907 GTGATGTATTAGAATCCATTCCACCAG 59.826 40.741 0.00 0.00 37.51 4.00
2024 4158 6.591935 TGTATTAGAATCCATTCCACCAGTC 58.408 40.000 0.00 0.00 37.51 3.51
2031 4165 1.156736 CATTCCACCAGTCGAACCAC 58.843 55.000 0.00 0.00 0.00 4.16
2032 4166 0.762418 ATTCCACCAGTCGAACCACA 59.238 50.000 0.00 0.00 0.00 4.17
2033 4167 0.762418 TTCCACCAGTCGAACCACAT 59.238 50.000 0.00 0.00 0.00 3.21
2034 4168 0.034756 TCCACCAGTCGAACCACATG 59.965 55.000 0.00 0.00 0.00 3.21
2076 4227 0.602905 CCCTCCGTTCACACTTCACC 60.603 60.000 0.00 0.00 0.00 4.02
2083 4242 2.661675 CGTTCACACTTCACCGTCTATG 59.338 50.000 0.00 0.00 0.00 2.23
2137 4307 5.039480 CAGTTCACCTATTTCAACTGCAG 57.961 43.478 13.48 13.48 39.37 4.41
2212 4384 0.117140 TCCCCTTCTCTGCTCCTGAA 59.883 55.000 0.00 0.00 0.00 3.02
2255 4428 0.106015 AAGGGGGTAAGCATGCATCC 60.106 55.000 21.98 17.56 0.00 3.51
2312 4485 1.246737 CCTTGGCCCTTCAGTTCAGC 61.247 60.000 0.00 0.00 0.00 4.26
2331 4504 1.871772 GCTTCTGTGCGCATCTGTT 59.128 52.632 15.91 0.00 0.00 3.16
2344 4517 2.807967 GCATCTGTTAGTGTGCTTGTCA 59.192 45.455 0.00 0.00 34.85 3.58
2422 4595 1.290134 AGGCTTCTTTACCCCCTCAG 58.710 55.000 0.00 0.00 0.00 3.35
2424 4597 1.210722 GGCTTCTTTACCCCCTCAGAG 59.789 57.143 0.00 0.00 0.00 3.35
2463 4636 2.486203 TGTTGGCATATGGTTCAACGAC 59.514 45.455 4.56 0.00 41.45 4.34
2466 4639 2.682352 TGGCATATGGTTCAACGACATG 59.318 45.455 4.56 0.00 0.00 3.21
2467 4640 2.682856 GGCATATGGTTCAACGACATGT 59.317 45.455 0.00 0.00 0.00 3.21
2468 4641 3.242739 GGCATATGGTTCAACGACATGTC 60.243 47.826 16.21 16.21 0.00 3.06
2469 4642 3.623060 GCATATGGTTCAACGACATGTCT 59.377 43.478 22.95 8.01 0.00 3.41
2470 4643 4.494690 GCATATGGTTCAACGACATGTCTG 60.495 45.833 22.95 17.83 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 4.778143 GGGATTGCGGCGGACAGT 62.778 66.667 9.78 0.00 0.00 3.55
108 109 0.984230 TTGGGGAGTGATCACTGGAC 59.016 55.000 32.50 20.45 42.66 4.02
116 117 0.119155 TCAGGGAGTTGGGGAGTGAT 59.881 55.000 0.00 0.00 0.00 3.06
126 127 1.353091 GGTCTTGAGGTCAGGGAGTT 58.647 55.000 0.00 0.00 0.00 3.01
127 128 0.900647 CGGTCTTGAGGTCAGGGAGT 60.901 60.000 0.00 0.00 0.00 3.85
128 129 1.893786 CGGTCTTGAGGTCAGGGAG 59.106 63.158 0.00 0.00 0.00 4.30
129 130 2.283529 GCGGTCTTGAGGTCAGGGA 61.284 63.158 0.00 0.00 0.00 4.20
133 134 2.649034 GACGCGGTCTTGAGGTCA 59.351 61.111 12.47 0.00 0.00 4.02
135 136 4.052229 CCGACGCGGTCTTGAGGT 62.052 66.667 12.47 0.00 42.73 3.85
164 169 4.508128 GGGCGAGGCGATTCACGA 62.508 66.667 0.00 0.00 45.77 4.35
237 242 1.004440 GAAGTCGGGTGAAGCAGCT 60.004 57.895 0.00 0.00 31.98 4.24
242 247 0.390472 GCTCTGGAAGTCGGGTGAAG 60.390 60.000 0.00 0.00 33.76 3.02
243 248 1.118965 TGCTCTGGAAGTCGGGTGAA 61.119 55.000 0.00 0.00 33.76 3.18
246 251 1.674057 CTTGCTCTGGAAGTCGGGT 59.326 57.895 0.00 0.00 33.76 5.28
247 252 1.078848 CCTTGCTCTGGAAGTCGGG 60.079 63.158 0.00 0.00 33.76 5.14
249 254 1.743252 GCCCTTGCTCTGGAAGTCG 60.743 63.158 0.00 0.00 33.76 4.18
251 256 0.251077 CTTGCCCTTGCTCTGGAAGT 60.251 55.000 0.00 0.00 38.71 3.01
252 257 0.964358 CCTTGCCCTTGCTCTGGAAG 60.964 60.000 0.00 0.00 38.71 3.46
278 285 7.988737 TGCAATACAGGAATTCAAGTGATTAG 58.011 34.615 7.93 0.00 0.00 1.73
281 288 6.839124 TTGCAATACAGGAATTCAAGTGAT 57.161 33.333 7.93 0.00 0.00 3.06
285 292 7.894376 AATGTTTGCAATACAGGAATTCAAG 57.106 32.000 7.93 1.20 0.00 3.02
313 320 7.172532 ACTCTAAGTCGATGTTTGCAATAACAA 59.827 33.333 7.98 0.00 41.02 2.83
315 322 7.061752 ACTCTAAGTCGATGTTTGCAATAAC 57.938 36.000 0.00 0.00 0.00 1.89
318 325 5.470098 ACAACTCTAAGTCGATGTTTGCAAT 59.530 36.000 0.00 0.00 0.00 3.56
323 330 6.746120 ACAGTACAACTCTAAGTCGATGTTT 58.254 36.000 0.00 0.00 0.00 2.83
324 331 6.328641 ACAGTACAACTCTAAGTCGATGTT 57.671 37.500 0.00 0.00 0.00 2.71
325 332 5.961396 ACAGTACAACTCTAAGTCGATGT 57.039 39.130 0.00 0.00 0.00 3.06
328 335 4.823442 TGGAACAGTACAACTCTAAGTCGA 59.177 41.667 0.00 0.00 0.00 4.20
329 336 5.117355 TGGAACAGTACAACTCTAAGTCG 57.883 43.478 0.00 0.00 0.00 4.18
348 379 1.554617 TGAAGATGACAAGCGGATGGA 59.445 47.619 0.00 0.00 0.00 3.41
349 380 1.938577 CTGAAGATGACAAGCGGATGG 59.061 52.381 0.00 0.00 0.00 3.51
353 384 3.849911 TCTAACTGAAGATGACAAGCGG 58.150 45.455 0.00 0.00 0.00 5.52
354 385 6.292061 GCTAATCTAACTGAAGATGACAAGCG 60.292 42.308 0.00 0.00 36.34 4.68
363 394 6.150396 GCTACAGGCTAATCTAACTGAAGA 57.850 41.667 0.00 0.00 38.06 2.87
415 465 4.968259 TGTAGCAGTAACACAACCAGAAT 58.032 39.130 0.00 0.00 0.00 2.40
416 466 4.409718 TGTAGCAGTAACACAACCAGAA 57.590 40.909 0.00 0.00 0.00 3.02
424 474 3.921677 TGTAGGCTTGTAGCAGTAACAC 58.078 45.455 0.00 0.00 44.75 3.32
428 478 2.565391 TGCTTGTAGGCTTGTAGCAGTA 59.435 45.455 11.51 0.00 44.75 2.74
436 486 1.527034 TTGCTCTGCTTGTAGGCTTG 58.473 50.000 0.00 0.00 0.00 4.01
438 488 3.118112 ACATATTGCTCTGCTTGTAGGCT 60.118 43.478 0.00 0.00 0.00 4.58
519 577 3.213506 TCAAGGAAACCACACACTGATG 58.786 45.455 0.00 0.00 0.00 3.07
630 714 6.993079 AGTTAATTGGTTGGTTTCAGATTCC 58.007 36.000 0.00 0.00 0.00 3.01
669 755 3.313012 TCGGACTGAATTGAACACGAT 57.687 42.857 0.00 0.00 0.00 3.73
758 848 9.109393 GCACAACTATGGTAGAATTAGAAATCA 57.891 33.333 0.00 0.00 0.00 2.57
779 869 6.573664 AACAACTATAGCTCAATTGCACAA 57.426 33.333 0.00 0.00 34.99 3.33
809 899 8.142551 ACTAACGAGAAAAGTATCCCATATCAC 58.857 37.037 0.00 0.00 0.00 3.06
829 919 6.988109 AAAGTCTAGCGCATATAACTAACG 57.012 37.500 11.47 0.00 0.00 3.18
941 1572 6.264292 GCTCAGAGTGGAGATGTAATTAGAGA 59.736 42.308 0.00 0.00 37.05 3.10
947 1578 6.798427 TTAAGCTCAGAGTGGAGATGTAAT 57.202 37.500 0.00 0.00 37.05 1.89
965 1596 2.497273 ACAACCCATCAGGCAATTAAGC 59.503 45.455 0.00 0.00 40.58 3.09
969 1600 2.431782 GCATACAACCCATCAGGCAATT 59.568 45.455 0.00 0.00 40.58 2.32
977 1608 0.657840 GCGTCTGCATACAACCCATC 59.342 55.000 2.93 0.00 42.15 3.51
995 1640 0.106819 ATGAAGGGAGTCCATGCTGC 60.107 55.000 12.30 0.00 34.83 5.25
1016 1661 0.041839 CAGAAGCTTGACGTGCACAC 60.042 55.000 18.64 10.76 0.00 3.82
1062 1707 2.279252 GGCGGCGATGTATGTCGT 60.279 61.111 12.98 0.00 43.27 4.34
1174 1819 1.341679 ACAGCCAGTGCCATCATCAAT 60.342 47.619 0.00 0.00 38.69 2.57
1366 2011 1.666700 CTCCTCTAGAACCACGTCTCG 59.333 57.143 0.00 0.00 0.00 4.04
1494 2139 6.093495 CAGTAACCACAGAAAGAAACACAGAA 59.907 38.462 0.00 0.00 0.00 3.02
1642 2343 1.077140 TTCACCCAAGTGCAGTGCA 60.077 52.632 15.37 15.37 44.16 4.57
1673 2374 4.871993 TGGAATAACTAGTCGACTCGTC 57.128 45.455 23.89 9.58 0.00 4.20
1675 2376 5.579718 ACATTGGAATAACTAGTCGACTCG 58.420 41.667 23.89 18.96 0.00 4.18
1688 2389 8.311395 AGTCTATGAGTCTCAACATTGGAATA 57.689 34.615 6.64 0.00 0.00 1.75
1689 2390 7.192852 AGTCTATGAGTCTCAACATTGGAAT 57.807 36.000 6.64 0.00 0.00 3.01
1693 2394 6.909895 CGACTAGTCTATGAGTCTCAACATTG 59.090 42.308 20.34 0.00 40.01 2.82
1694 2395 6.600032 ACGACTAGTCTATGAGTCTCAACATT 59.400 38.462 20.34 0.00 40.01 2.71
1710 2411 4.092529 TGTCACGATTAGTCACGACTAGTC 59.907 45.833 13.18 13.18 43.92 2.59
1711 2412 3.999001 TGTCACGATTAGTCACGACTAGT 59.001 43.478 6.98 0.00 43.92 2.57
1712 2413 4.595198 TGTCACGATTAGTCACGACTAG 57.405 45.455 6.98 0.00 43.92 2.57
1713 2414 4.453478 ACTTGTCACGATTAGTCACGACTA 59.547 41.667 2.74 2.74 42.54 2.59
1714 2415 3.252701 ACTTGTCACGATTAGTCACGACT 59.747 43.478 4.87 4.87 45.02 4.18
1715 2416 3.562505 ACTTGTCACGATTAGTCACGAC 58.437 45.455 0.00 0.00 0.00 4.34
1716 2417 3.251487 TGACTTGTCACGATTAGTCACGA 59.749 43.478 0.00 0.00 41.34 4.35
1717 2418 3.561503 TGACTTGTCACGATTAGTCACG 58.438 45.455 0.00 0.00 41.34 4.35
1718 2419 4.743151 TGTTGACTTGTCACGATTAGTCAC 59.257 41.667 2.62 8.86 44.68 3.67
1719 2420 4.743151 GTGTTGACTTGTCACGATTAGTCA 59.257 41.667 2.62 0.00 43.69 3.41
1738 2439 6.874134 AGTCTATGAATCGCAACTTTAGTGTT 59.126 34.615 0.00 0.00 0.00 3.32
1744 2445 5.744345 CGACTAGTCTATGAATCGCAACTTT 59.256 40.000 20.34 0.00 0.00 2.66
1751 2452 5.234543 TCAGTGTCGACTAGTCTATGAATCG 59.765 44.000 20.34 5.71 0.00 3.34
1754 2455 5.938710 ACTTCAGTGTCGACTAGTCTATGAA 59.061 40.000 20.34 18.20 0.00 2.57
1839 2543 5.421056 TCATTACTTCCATGGACTACGAGTT 59.579 40.000 15.91 0.00 0.00 3.01
1927 4051 5.300752 TGGTAAGACAAAGAAAGCAGAGAG 58.699 41.667 0.00 0.00 0.00 3.20
2031 4165 9.241317 GCAGTATTTCAAATTCTCAATACCATG 57.759 33.333 0.00 0.00 34.08 3.66
2032 4166 8.416329 GGCAGTATTTCAAATTCTCAATACCAT 58.584 33.333 0.00 0.00 34.08 3.55
2033 4167 7.147915 GGGCAGTATTTCAAATTCTCAATACCA 60.148 37.037 0.00 0.00 34.08 3.25
2034 4168 7.068716 AGGGCAGTATTTCAAATTCTCAATACC 59.931 37.037 0.00 0.00 34.08 2.73
2042 4176 3.694566 ACGGAGGGCAGTATTTCAAATTC 59.305 43.478 0.00 0.00 0.00 2.17
2137 4307 5.536260 AGAGTGAACTACGAAAACTAACCC 58.464 41.667 0.00 0.00 0.00 4.11
2212 4384 7.009179 TCTTTGAGTTACAAGTGATGAGGAT 57.991 36.000 0.00 0.00 39.77 3.24
2255 4428 0.390472 GACCAAGTGGAGAGAAGGCG 60.390 60.000 3.83 0.00 38.94 5.52
2344 4517 0.901124 GGAGTGAGTCTCATGCCAGT 59.099 55.000 5.68 0.00 44.40 4.00
2422 4595 9.503427 GCCAACATACATATTTTTAGTTGACTC 57.497 33.333 0.00 0.00 37.62 3.36
2424 4597 9.801873 ATGCCAACATACATATTTTTAGTTGAC 57.198 29.630 0.00 0.00 37.62 3.18


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

AutoCloner maintained by Alex Coulton.