Multiple sequence alignment - TraesCS5B01G044400

Loading Multiple Alignment...

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 TraesCS5B01G044400 chr5B 100.000 2688 0 0 1 2688 49881809 49884496 0.000000e+00 4964.0
1 TraesCS5B01G044400 chr5B 83.232 656 53 37 1053 1688 688589489 688588871 1.410000e-152 549.0
2 TraesCS5B01G044400 chr5B 84.697 379 39 12 1 364 581689148 581689522 7.070000e-96 361.0
3 TraesCS5B01G044400 chr5B 78.319 226 22 18 1473 1688 664243822 664244030 1.310000e-23 121.0
4 TraesCS5B01G044400 chr5D 94.866 1383 58 10 382 1759 47081944 47083318 0.000000e+00 2148.0
5 TraesCS5B01G044400 chr5D 88.203 907 37 24 871 1761 47286614 47285762 0.000000e+00 1018.0
6 TraesCS5B01G044400 chr5D 89.683 504 24 11 999 1477 47517094 47516594 3.800000e-173 617.0
7 TraesCS5B01G044400 chr5D 87.781 401 31 11 1 390 47081525 47081918 1.130000e-123 453.0
8 TraesCS5B01G044400 chr5D 85.501 469 24 11 2236 2688 47085294 47085734 1.470000e-122 449.0
9 TraesCS5B01G044400 chr5D 87.667 300 20 4 2211 2504 47285361 47285073 1.540000e-87 333.0
10 TraesCS5B01G044400 chr5D 85.141 249 19 11 1804 2050 47084826 47085058 3.460000e-59 239.0
11 TraesCS5B01G044400 chr5D 100.000 51 0 0 1873 1923 47285680 47285630 7.920000e-16 95.3
12 TraesCS5B01G044400 chr5D 83.099 71 7 3 1804 1874 47285720 47285655 2.890000e-05 60.2
13 TraesCS5B01G044400 chr5A 87.184 1225 52 41 871 2050 37922645 37923809 0.000000e+00 1295.0
14 TraesCS5B01G044400 chr5A 85.443 474 34 15 2236 2688 37924025 37924484 6.780000e-126 460.0
15 TraesCS5B01G044400 chr5A 81.841 402 57 10 1 390 59813098 59813495 9.280000e-85 324.0
16 TraesCS5B01G044400 chr5A 81.633 98 10 6 2106 2202 37923848 37923938 1.030000e-09 75.0
17 TraesCS5B01G044400 chr7D 82.496 657 58 36 1053 1688 484694369 484693749 8.530000e-145 523.0
18 TraesCS5B01G044400 chr7D 85.603 514 48 10 1 489 199002767 199002255 1.430000e-142 516.0
19 TraesCS5B01G044400 chr2A 83.879 397 55 4 1 389 373452470 373452865 1.180000e-98 370.0
20 TraesCS5B01G044400 chr2D 83.709 399 55 4 1 390 299375339 299375736 4.230000e-98 368.0
21 TraesCS5B01G044400 chr2D 83.127 403 51 13 1 391 199842123 199841726 4.260000e-93 351.0
22 TraesCS5B01G044400 chr6B 83.709 399 49 10 3 390 522849657 522850050 1.970000e-96 363.0
23 TraesCS5B01G044400 chr2B 83.333 402 54 8 1 390 355869474 355869074 2.540000e-95 359.0
24 TraesCS5B01G044400 chr2B 79.070 258 28 15 618 851 30242752 30243007 1.290000e-33 154.0
25 TraesCS5B01G044400 chr3B 83.966 237 30 7 618 851 547346037 547345806 1.250000e-53 220.0
26 TraesCS5B01G044400 chr3B 85.629 167 22 2 618 782 666434684 666434518 9.890000e-40 174.0
27 TraesCS5B01G044400 chr3B 75.847 236 46 7 618 844 12312423 12312656 2.830000e-20 110.0
28 TraesCS5B01G044400 chr7B 80.303 264 29 13 618 858 14776313 14776050 7.650000e-41 178.0
29 TraesCS5B01G044400 chr1B 80.469 256 27 14 618 851 604148803 604148549 9.890000e-40 174.0
30 TraesCS5B01G044400 chr6A 79.767 257 29 13 618 851 534739902 534739646 5.950000e-37 165.0


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 TraesCS5B01G044400 chr5B 49881809 49884496 2687 False 4964.000 4964 100.000000 1 2688 1 chr5B.!!$F1 2687
1 TraesCS5B01G044400 chr5B 688588871 688589489 618 True 549.000 549 83.232000 1053 1688 1 chr5B.!!$R1 635
2 TraesCS5B01G044400 chr5D 47081525 47085734 4209 False 822.250 2148 88.322250 1 2688 4 chr5D.!!$F1 2687
3 TraesCS5B01G044400 chr5D 47516594 47517094 500 True 617.000 617 89.683000 999 1477 1 chr5D.!!$R1 478
4 TraesCS5B01G044400 chr5D 47285073 47286614 1541 True 376.625 1018 89.742250 871 2504 4 chr5D.!!$R2 1633
5 TraesCS5B01G044400 chr5A 37922645 37924484 1839 False 610.000 1295 84.753333 871 2688 3 chr5A.!!$F2 1817
6 TraesCS5B01G044400 chr7D 484693749 484694369 620 True 523.000 523 82.496000 1053 1688 1 chr7D.!!$R2 635
7 TraesCS5B01G044400 chr7D 199002255 199002767 512 True 516.000 516 85.603000 1 489 1 chr7D.!!$R1 488

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
992 1047 0.46187 AACAGAGCGCAACACAGACA 60.462 50.0 11.47 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2143 3768 0.036732 TCCACCAACAGTCCAGCATC 59.963 55.0 0.0 0.0 0.0 3.91 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
103 105 8.228035 TCAATTGTGCTAATCATCATGATTGA 57.772 30.769 21.30 6.76 45.77 2.57
105 107 8.349983 CAATTGTGCTAATCATCATGATTGAGA 58.650 33.333 21.30 0.64 45.77 3.27
120 122 9.569122 TCATGATTGAGATGATAATTGTGATGT 57.431 29.630 0.00 0.00 0.00 3.06
124 126 9.378597 GATTGAGATGATAATTGTGATGTTTCG 57.621 33.333 0.00 0.00 0.00 3.46
126 128 7.687445 TGAGATGATAATTGTGATGTTTCGTG 58.313 34.615 0.00 0.00 0.00 4.35
170 172 9.585369 TTAACCTTCATGATGAATATGCCATTA 57.415 29.630 8.50 0.00 35.59 1.90
225 227 4.330944 TTGGAAGAGCGTCAACTTTAGA 57.669 40.909 0.00 0.00 0.00 2.10
254 256 5.359194 TGATCCCACTACTTTGGAGAATC 57.641 43.478 0.00 0.00 39.24 2.52
261 263 6.604795 CCCACTACTTTGGAGAATCATCAATT 59.395 38.462 0.00 0.00 39.24 2.32
336 339 9.699410 TGATGATAATCCCACTATTTTGAAAGT 57.301 29.630 0.00 0.00 0.00 2.66
547 594 1.955080 GGGTATCGACTGATCTCCGTT 59.045 52.381 0.00 0.00 35.99 4.44
550 597 4.217983 GGGTATCGACTGATCTCCGTTATT 59.782 45.833 0.00 0.00 35.99 1.40
562 609 9.566530 CTGATCTCCGTTATTGATGTATCTAAG 57.433 37.037 0.00 0.00 0.00 2.18
563 610 8.029522 TGATCTCCGTTATTGATGTATCTAAGC 58.970 37.037 0.00 0.00 0.00 3.09
573 620 5.872963 TGATGTATCTAAGCGGGTCTACTA 58.127 41.667 0.00 0.00 0.00 1.82
603 650 6.425721 AGAAGTGTTATTACTAAAACTGCGCA 59.574 34.615 10.98 10.98 36.25 6.09
634 681 1.202710 TGAGCCGGACTTGTAAAAGCA 60.203 47.619 5.05 0.00 0.00 3.91
639 686 2.161609 CCGGACTTGTAAAAGCATGACC 59.838 50.000 0.00 0.00 0.00 4.02
697 744 2.577449 ACACTTTGTTTTCAAGCCCG 57.423 45.000 0.00 0.00 41.09 6.13
702 749 1.460273 TTGTTTTCAAGCCCGAGCCC 61.460 55.000 0.00 0.00 41.25 5.19
716 763 1.474330 GAGCCCGTCCCAAAATCAAT 58.526 50.000 0.00 0.00 0.00 2.57
743 790 2.279810 CCGAAAACCCGGCCCAAAT 61.280 57.895 0.00 0.00 43.25 2.32
807 854 0.609406 AAAAAGAGAAGCCCGAGCCC 60.609 55.000 0.00 0.00 41.25 5.19
922 977 5.243283 GTCTCGGTGCTCCTCCTATAAATAA 59.757 44.000 2.85 0.00 0.00 1.40
974 1029 6.270463 TCTGTACACCTACCAATACCAAGAAA 59.730 38.462 0.00 0.00 0.00 2.52
992 1047 0.461870 AACAGAGCGCAACACAGACA 60.462 50.000 11.47 0.00 0.00 3.41
1138 1204 2.755103 TCTTGAGCAGCTCGTGAATCTA 59.245 45.455 17.81 0.00 32.35 1.98
1286 1379 3.485431 CGCACGAGCAAGAGCAGG 61.485 66.667 5.50 0.00 45.49 4.85
1398 1500 0.534203 ATGGTGGACAACGTGGTGAC 60.534 55.000 0.00 0.00 0.00 3.67
1633 1750 1.257539 CGTCGACCGCTTTCTTCTAC 58.742 55.000 10.58 0.00 0.00 2.59
1727 1852 4.494091 AGAAATTCCATGTCGATCCACT 57.506 40.909 0.00 0.00 0.00 4.00
1728 1853 4.194640 AGAAATTCCATGTCGATCCACTG 58.805 43.478 0.00 0.00 0.00 3.66
1777 3337 8.967664 AAATAAGTTGTTGGTGAACTAGTGTA 57.032 30.769 0.00 0.00 33.20 2.90
1815 3411 6.913673 GGTTTAGCTGTAGAATCTACTCTTCG 59.086 42.308 19.76 6.09 0.00 3.79
1816 3412 7.201714 GGTTTAGCTGTAGAATCTACTCTTCGA 60.202 40.741 19.76 0.00 0.00 3.71
1818 3414 6.952773 AGCTGTAGAATCTACTCTTCGATT 57.047 37.500 19.76 0.00 32.86 3.34
1819 3415 6.966021 AGCTGTAGAATCTACTCTTCGATTC 58.034 40.000 19.76 0.00 43.56 2.52
1855 3451 2.315176 CCTCTCAAGGATCGGATCTGT 58.685 52.381 16.96 3.10 46.67 3.41
1923 3519 3.583806 TGTGCTTTTGTTGAGTTTGTGG 58.416 40.909 0.00 0.00 0.00 4.17
1924 3520 2.929398 GTGCTTTTGTTGAGTTTGTGGG 59.071 45.455 0.00 0.00 0.00 4.61
1928 3524 1.384525 TTGTTGAGTTTGTGGGGACG 58.615 50.000 0.00 0.00 0.00 4.79
1948 3545 2.223595 CGGGTATGCTAGTGTGAGTGAG 60.224 54.545 0.00 0.00 0.00 3.51
1952 3549 5.302059 GGGTATGCTAGTGTGAGTGAGATTA 59.698 44.000 0.00 0.00 0.00 1.75
1953 3550 6.183360 GGGTATGCTAGTGTGAGTGAGATTAA 60.183 42.308 0.00 0.00 0.00 1.40
1954 3551 7.437748 GGTATGCTAGTGTGAGTGAGATTAAT 58.562 38.462 0.00 0.00 0.00 1.40
1955 3552 7.928706 GGTATGCTAGTGTGAGTGAGATTAATT 59.071 37.037 0.00 0.00 0.00 1.40
1956 3553 7.783090 ATGCTAGTGTGAGTGAGATTAATTG 57.217 36.000 0.00 0.00 0.00 2.32
1957 3554 6.935167 TGCTAGTGTGAGTGAGATTAATTGA 58.065 36.000 0.00 0.00 0.00 2.57
1958 3555 7.559486 TGCTAGTGTGAGTGAGATTAATTGAT 58.441 34.615 0.00 0.00 0.00 2.57
1967 3564 7.223387 TGAGTGAGATTAATTGATGATGACACG 59.777 37.037 0.00 0.00 0.00 4.49
1969 3566 5.050837 TGAGATTAATTGATGATGACACGCG 60.051 40.000 3.53 3.53 0.00 6.01
1974 3571 0.100503 TGATGATGACACGCGTCGAT 59.899 50.000 9.86 0.30 45.80 3.59
1976 3573 0.179137 ATGATGACACGCGTCGATGT 60.179 50.000 9.86 3.65 45.80 3.06
1977 3574 0.388006 TGATGACACGCGTCGATGTT 60.388 50.000 9.86 0.00 45.80 2.71
1987 3584 2.034842 CGCGTCGATGTTTCAGTTATCC 60.035 50.000 6.48 0.00 0.00 2.59
1994 3591 6.020837 GTCGATGTTTCAGTTATCCGTTCTAC 60.021 42.308 0.00 0.00 0.00 2.59
1995 3592 5.803461 CGATGTTTCAGTTATCCGTTCTACA 59.197 40.000 0.00 0.00 0.00 2.74
1998 3595 6.154445 TGTTTCAGTTATCCGTTCTACAGAC 58.846 40.000 0.00 0.00 0.00 3.51
2053 3651 5.971895 GAACAAACAAATGCATGTTCAGT 57.028 34.783 18.96 12.27 46.75 3.41
2055 3653 6.826893 AACAAACAAATGCATGTTCAGTAC 57.173 33.333 0.00 0.00 42.49 2.73
2056 3654 6.147864 ACAAACAAATGCATGTTCAGTACT 57.852 33.333 0.00 0.00 42.49 2.73
2057 3655 5.978919 ACAAACAAATGCATGTTCAGTACTG 59.021 36.000 17.17 17.17 42.49 2.74
2058 3656 4.164822 ACAAATGCATGTTCAGTACTGC 57.835 40.909 18.45 6.79 33.93 4.40
2059 3657 3.057315 ACAAATGCATGTTCAGTACTGCC 60.057 43.478 18.45 11.23 33.00 4.85
2060 3658 2.795231 ATGCATGTTCAGTACTGCCT 57.205 45.000 18.45 0.00 33.00 4.75
2061 3659 2.566833 TGCATGTTCAGTACTGCCTT 57.433 45.000 18.45 6.49 33.00 4.35
2062 3660 2.426522 TGCATGTTCAGTACTGCCTTC 58.573 47.619 18.45 8.41 33.00 3.46
2063 3661 2.224499 TGCATGTTCAGTACTGCCTTCA 60.224 45.455 18.45 13.29 33.00 3.02
2064 3662 2.813754 GCATGTTCAGTACTGCCTTCAA 59.186 45.455 18.45 3.90 0.00 2.69
2065 3663 3.253188 GCATGTTCAGTACTGCCTTCAAA 59.747 43.478 18.45 3.14 0.00 2.69
2066 3664 4.261572 GCATGTTCAGTACTGCCTTCAAAA 60.262 41.667 18.45 2.31 0.00 2.44
2067 3665 5.735922 GCATGTTCAGTACTGCCTTCAAAAA 60.736 40.000 18.45 1.57 0.00 1.94
2090 3688 4.155063 TGCATGTTCAGTACTGGCATAT 57.845 40.909 22.48 10.55 33.60 1.78
2092 3714 5.868454 TGCATGTTCAGTACTGGCATATAT 58.132 37.500 22.48 7.20 33.60 0.86
2093 3715 6.298361 TGCATGTTCAGTACTGGCATATATT 58.702 36.000 22.48 4.67 33.60 1.28
2096 3718 7.255242 GCATGTTCAGTACTGGCATATATTTGT 60.255 37.037 22.48 2.77 0.00 2.83
2097 3719 7.552458 TGTTCAGTACTGGCATATATTTGTG 57.448 36.000 22.48 0.00 0.00 3.33
2098 3720 6.542005 TGTTCAGTACTGGCATATATTTGTGG 59.458 38.462 22.48 0.00 0.00 4.17
2099 3721 6.247229 TCAGTACTGGCATATATTTGTGGT 57.753 37.500 22.48 0.00 0.00 4.16
2101 3723 4.821805 AGTACTGGCATATATTTGTGGTGC 59.178 41.667 0.00 0.00 35.17 5.01
2122 3747 5.182001 GTGCCAGTTCTGAATGATTTACAGT 59.818 40.000 1.00 0.00 33.93 3.55
2130 3755 9.793252 GTTCTGAATGATTTACAGTGCATATTT 57.207 29.630 0.00 0.00 33.93 1.40
2135 3760 9.669353 GAATGATTTACAGTGCATATTTACTGG 57.331 33.333 16.45 3.85 46.52 4.00
2137 3762 7.984391 TGATTTACAGTGCATATTTACTGGTG 58.016 34.615 16.45 0.00 46.52 4.17
2138 3763 5.811399 TTACAGTGCATATTTACTGGTGC 57.189 39.130 16.45 0.00 46.52 5.01
2139 3764 3.955471 ACAGTGCATATTTACTGGTGCT 58.045 40.909 16.45 0.00 46.52 4.40
2140 3765 5.097742 ACAGTGCATATTTACTGGTGCTA 57.902 39.130 16.45 0.00 46.52 3.49
2142 3767 6.826668 ACAGTGCATATTTACTGGTGCTATA 58.173 36.000 16.45 0.00 46.52 1.31
2143 3768 6.931281 ACAGTGCATATTTACTGGTGCTATAG 59.069 38.462 16.45 0.00 46.52 1.31
2144 3769 7.154656 CAGTGCATATTTACTGGTGCTATAGA 58.845 38.462 3.21 0.00 40.38 1.98
2147 3772 6.595326 TGCATATTTACTGGTGCTATAGATGC 59.405 38.462 3.21 5.88 38.37 3.91
2148 3773 6.820656 GCATATTTACTGGTGCTATAGATGCT 59.179 38.462 3.21 0.00 34.85 3.79
2149 3774 7.201591 GCATATTTACTGGTGCTATAGATGCTG 60.202 40.741 3.21 0.00 34.85 4.41
2150 3775 4.607293 TTACTGGTGCTATAGATGCTGG 57.393 45.455 3.21 0.00 0.00 4.85
2151 3776 2.682594 ACTGGTGCTATAGATGCTGGA 58.317 47.619 3.21 0.00 0.00 3.86
2152 3777 2.366916 ACTGGTGCTATAGATGCTGGAC 59.633 50.000 3.21 0.00 0.00 4.02
2185 3810 5.596836 ACATGCAAGAAAGAACCAAAAGA 57.403 34.783 0.00 0.00 0.00 2.52
2187 3812 7.288810 ACATGCAAGAAAGAACCAAAAGATA 57.711 32.000 0.00 0.00 0.00 1.98
2192 3817 9.612066 TGCAAGAAAGAACCAAAAGATAAAAAT 57.388 25.926 0.00 0.00 0.00 1.82
2193 3818 9.868389 GCAAGAAAGAACCAAAAGATAAAAATG 57.132 29.630 0.00 0.00 0.00 2.32
2244 3922 1.335810 TCCATATACACGTCGAGGCAC 59.664 52.381 4.75 0.00 0.00 5.01
2254 3932 0.654683 GTCGAGGCACAATCTGATGC 59.345 55.000 0.00 0.00 41.29 3.91
2262 3940 4.579340 AGGCACAATCTGATGCTTATCTTG 59.421 41.667 2.18 0.00 41.74 3.02
2278 3956 7.147976 GCTTATCTTGTTCCACATTTGAAAGT 58.852 34.615 0.00 0.00 0.00 2.66
2300 3978 6.206498 AGTATGAAAACTGAAAAACGCTTCC 58.794 36.000 0.00 0.00 0.00 3.46
2303 3981 4.082463 TGAAAACTGAAAAACGCTTCCACT 60.082 37.500 0.00 0.00 0.00 4.00
2306 3984 1.946768 CTGAAAAACGCTTCCACTGGA 59.053 47.619 0.00 0.00 0.00 3.86
2309 3987 2.863401 AAAACGCTTCCACTGGAAAC 57.137 45.000 11.77 6.56 41.54 2.78
2425 4111 6.149633 AGTTGTTTCCGATGATAAAAACTGC 58.850 36.000 0.00 0.00 33.75 4.40
2451 4137 3.689161 CACCTATCGTGATTGGCAAGAAA 59.311 43.478 5.96 0.00 46.20 2.52
2452 4138 4.155826 CACCTATCGTGATTGGCAAGAAAA 59.844 41.667 5.96 0.00 46.20 2.29
2453 4139 4.764823 ACCTATCGTGATTGGCAAGAAAAA 59.235 37.500 5.96 0.00 38.48 1.94
2505 4215 1.074405 ACAGATGAGCACCACCAATGT 59.926 47.619 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 105 7.334171 TCACACGAAACATCACAATTATCATCT 59.666 33.333 0.00 0.00 0.00 2.90
105 107 7.376435 TCACACGAAACATCACAATTATCAT 57.624 32.000 0.00 0.00 0.00 2.45
114 116 4.990543 TCAAGATCACACGAAACATCAC 57.009 40.909 0.00 0.00 0.00 3.06
177 179 7.602265 ACCCACTTTCAATATTATTGCAAACAC 59.398 33.333 1.71 0.00 0.00 3.32
225 227 9.170890 TCTCCAAAGTAGTGGGATCATTATTAT 57.829 33.333 0.00 0.00 39.34 1.28
278 280 3.976015 TGACCTCTTCAACCCACTTTTT 58.024 40.909 0.00 0.00 0.00 1.94
290 292 7.099764 TCATCAACTAAAGTCATGACCTCTTC 58.900 38.462 22.21 0.00 0.00 2.87
291 293 7.009179 TCATCAACTAAAGTCATGACCTCTT 57.991 36.000 22.21 14.93 0.00 2.85
411 458 9.551734 AGAGGTAATTGAGTAACGTAAAAGTTT 57.448 29.630 0.00 0.00 35.70 2.66
420 467 7.025963 ACGTTAAGAGAGGTAATTGAGTAACG 58.974 38.462 9.76 9.76 44.02 3.18
441 488 7.325097 GGACGAATCATTAACAATTTGAACGTT 59.675 33.333 0.00 0.00 36.96 3.99
460 507 2.859165 TGCAAGGAAGAAGGACGAAT 57.141 45.000 0.00 0.00 0.00 3.34
500 547 6.425735 TCATAATGAAGGACATGGTTGACAT 58.574 36.000 0.00 0.00 41.57 3.06
501 548 5.814481 TCATAATGAAGGACATGGTTGACA 58.186 37.500 0.00 0.00 39.39 3.58
502 549 6.757897 TTCATAATGAAGGACATGGTTGAC 57.242 37.500 0.00 0.00 39.39 3.18
527 574 1.606903 ACGGAGATCAGTCGATACCC 58.393 55.000 8.87 0.00 29.66 3.69
547 594 6.946583 AGTAGACCCGCTTAGATACATCAATA 59.053 38.462 0.00 0.00 0.00 1.90
550 597 4.726583 AGTAGACCCGCTTAGATACATCA 58.273 43.478 0.00 0.00 0.00 3.07
634 681 2.291217 GGGCTTGAGAAAGGAAGGTCAT 60.291 50.000 0.00 0.00 0.00 3.06
639 686 1.731720 CTCGGGCTTGAGAAAGGAAG 58.268 55.000 1.75 0.00 38.28 3.46
666 713 4.929819 AACAAAGTGTATTTCGGGCTTT 57.070 36.364 0.00 0.00 0.00 3.51
672 719 5.174943 GGGCTTGAAAACAAAGTGTATTTCG 59.825 40.000 0.00 0.00 33.86 3.46
697 744 1.405463 GATTGATTTTGGGACGGGCTC 59.595 52.381 0.00 0.00 0.00 4.70
702 749 1.745232 TCGGGATTGATTTTGGGACG 58.255 50.000 0.00 0.00 0.00 4.79
716 763 2.032987 GGTTTTCGGGCTTCGGGA 59.967 61.111 0.75 0.00 39.77 5.14
761 808 1.078497 CGGGCTGGTCTTGCACATA 60.078 57.895 0.00 0.00 32.55 2.29
807 854 3.340727 CGTAAGGTAGTTCAGGCCG 57.659 57.895 0.00 0.00 0.00 6.13
922 977 3.043998 AGAGCTTGTGGTCTCGACT 57.956 52.632 0.00 0.00 46.84 4.18
974 1029 1.143838 TGTCTGTGTTGCGCTCTGT 59.856 52.632 9.73 0.00 0.00 3.41
992 1047 1.133668 GCCCCATAGCCATTCTTCTGT 60.134 52.381 0.00 0.00 0.00 3.41
1138 1204 4.472833 AGCTGAATGAGTTAGGGACTGAAT 59.527 41.667 0.00 0.00 41.52 2.57
1286 1379 2.456119 CGCCGGAGTTCATGTGCTC 61.456 63.158 5.05 9.66 0.00 4.26
1699 1816 6.238211 GGATCGACATGGAATTTCTTGTACAG 60.238 42.308 5.29 1.75 0.00 2.74
1700 1817 5.584649 GGATCGACATGGAATTTCTTGTACA 59.415 40.000 5.29 0.00 0.00 2.90
1701 1818 5.584649 TGGATCGACATGGAATTTCTTGTAC 59.415 40.000 5.29 0.22 0.00 2.90
1727 1852 1.487300 TCATACGGACGGAAATCCCA 58.513 50.000 0.00 0.00 35.03 4.37
1728 1853 2.036733 TCATCATACGGACGGAAATCCC 59.963 50.000 0.00 0.00 35.03 3.85
1763 3323 2.555325 CACGGAGTACACTAGTTCACCA 59.445 50.000 0.00 0.00 41.61 4.17
1815 3411 4.950050 AGGATTACACATCCGTGAGAATC 58.050 43.478 0.00 7.71 46.80 2.52
1816 3412 4.651503 AGAGGATTACACATCCGTGAGAAT 59.348 41.667 0.00 0.00 46.80 2.40
1818 3414 3.632333 AGAGGATTACACATCCGTGAGA 58.368 45.455 0.00 0.00 46.80 3.27
1819 3415 3.381590 TGAGAGGATTACACATCCGTGAG 59.618 47.826 0.00 0.00 46.80 3.51
1848 3444 6.942532 TTATTCTGCAACCATAACAGATCC 57.057 37.500 0.00 0.00 39.99 3.36
1849 3445 8.623903 TGATTTATTCTGCAACCATAACAGATC 58.376 33.333 0.00 0.00 39.99 2.75
1850 3446 8.523915 TGATTTATTCTGCAACCATAACAGAT 57.476 30.769 0.00 0.00 39.99 2.90
1851 3447 7.936496 TGATTTATTCTGCAACCATAACAGA 57.064 32.000 0.00 0.00 38.62 3.41
1852 3448 9.241317 GATTGATTTATTCTGCAACCATAACAG 57.759 33.333 0.00 0.00 0.00 3.16
1855 3451 9.806203 CTTGATTGATTTATTCTGCAACCATAA 57.194 29.630 0.00 0.00 0.00 1.90
1923 3519 0.104304 CACACTAGCATACCCGTCCC 59.896 60.000 0.00 0.00 0.00 4.46
1924 3520 1.067212 CTCACACTAGCATACCCGTCC 59.933 57.143 0.00 0.00 0.00 4.79
1928 3524 3.024547 TCTCACTCACACTAGCATACCC 58.975 50.000 0.00 0.00 0.00 3.69
1948 3545 5.083136 ACGCGTGTCATCATCAATTAATC 57.917 39.130 12.93 0.00 0.00 1.75
1952 3549 1.324435 CGACGCGTGTCATCATCAATT 59.676 47.619 27.16 0.00 45.80 2.32
1953 3550 0.923403 CGACGCGTGTCATCATCAAT 59.077 50.000 27.16 0.00 45.80 2.57
1954 3551 0.109504 TCGACGCGTGTCATCATCAA 60.110 50.000 27.16 2.24 45.80 2.57
1955 3552 0.100503 ATCGACGCGTGTCATCATCA 59.899 50.000 27.16 5.30 45.80 3.07
1956 3553 0.500178 CATCGACGCGTGTCATCATC 59.500 55.000 27.16 0.00 45.80 2.92
1957 3554 0.179137 ACATCGACGCGTGTCATCAT 60.179 50.000 27.16 13.51 45.80 2.45
1958 3555 0.388006 AACATCGACGCGTGTCATCA 60.388 50.000 27.16 11.83 45.80 3.07
1967 3564 2.034842 CGGATAACTGAAACATCGACGC 60.035 50.000 0.00 0.00 0.00 5.19
1969 3566 4.863131 AGAACGGATAACTGAAACATCGAC 59.137 41.667 0.00 0.00 0.00 4.20
1974 3571 6.015688 AGTCTGTAGAACGGATAACTGAAACA 60.016 38.462 0.00 0.00 35.69 2.83
1976 3573 6.585695 AGTCTGTAGAACGGATAACTGAAA 57.414 37.500 0.00 0.00 35.69 2.69
1977 3574 6.585695 AAGTCTGTAGAACGGATAACTGAA 57.414 37.500 0.00 0.00 35.69 3.02
1987 3584 7.639162 AACTGAAACATAAGTCTGTAGAACG 57.361 36.000 0.00 0.00 0.00 3.95
2064 3662 4.039004 TGCCAGTACTGAACATGCATTTTT 59.961 37.500 24.68 0.00 33.51 1.94
2065 3663 3.573538 TGCCAGTACTGAACATGCATTTT 59.426 39.130 24.68 0.00 33.51 1.82
2066 3664 3.156293 TGCCAGTACTGAACATGCATTT 58.844 40.909 24.68 0.00 33.51 2.32
2067 3665 2.794103 TGCCAGTACTGAACATGCATT 58.206 42.857 24.68 0.00 33.51 3.56
2068 3666 2.495155 TGCCAGTACTGAACATGCAT 57.505 45.000 24.68 0.00 33.51 3.96
2069 3667 2.495155 ATGCCAGTACTGAACATGCA 57.505 45.000 24.68 22.56 39.99 3.96
2070 3668 6.808008 AATATATGCCAGTACTGAACATGC 57.192 37.500 27.90 21.18 32.26 4.06
2077 3675 5.277974 GCACCACAAATATATGCCAGTACTG 60.278 44.000 16.34 16.34 0.00 2.74
2078 3676 4.821805 GCACCACAAATATATGCCAGTACT 59.178 41.667 0.00 0.00 0.00 2.73
2085 3683 4.339247 AGAACTGGCACCACAAATATATGC 59.661 41.667 0.00 0.00 35.51 3.14
2090 3688 3.500448 TCAGAACTGGCACCACAAATA 57.500 42.857 1.93 0.00 0.00 1.40
2092 3714 2.136298 TTCAGAACTGGCACCACAAA 57.864 45.000 1.93 0.00 0.00 2.83
2093 3715 1.955778 CATTCAGAACTGGCACCACAA 59.044 47.619 1.93 0.00 0.00 3.33
2096 3718 2.885135 ATCATTCAGAACTGGCACCA 57.115 45.000 1.93 0.00 0.00 4.17
2097 3719 4.458989 TGTAAATCATTCAGAACTGGCACC 59.541 41.667 1.93 0.00 0.00 5.01
2098 3720 5.182001 ACTGTAAATCATTCAGAACTGGCAC 59.818 40.000 1.93 0.00 33.93 5.01
2099 3721 5.181811 CACTGTAAATCATTCAGAACTGGCA 59.818 40.000 1.93 0.00 33.93 4.92
2101 3723 5.181811 TGCACTGTAAATCATTCAGAACTGG 59.818 40.000 1.93 0.00 33.93 4.00
2122 3747 6.595326 GCATCTATAGCACCAGTAAATATGCA 59.405 38.462 8.80 0.00 40.63 3.96
2130 3755 3.574396 GTCCAGCATCTATAGCACCAGTA 59.426 47.826 0.00 0.00 0.00 2.74
2132 3757 2.632028 AGTCCAGCATCTATAGCACCAG 59.368 50.000 0.00 0.00 0.00 4.00
2133 3758 2.366590 CAGTCCAGCATCTATAGCACCA 59.633 50.000 0.00 0.00 0.00 4.17
2134 3759 2.366916 ACAGTCCAGCATCTATAGCACC 59.633 50.000 0.00 0.00 0.00 5.01
2135 3760 3.742433 ACAGTCCAGCATCTATAGCAC 57.258 47.619 0.00 0.00 0.00 4.40
2137 3762 3.181461 ACCAACAGTCCAGCATCTATAGC 60.181 47.826 0.00 0.00 0.00 2.97
2138 3763 4.375272 CACCAACAGTCCAGCATCTATAG 58.625 47.826 0.00 0.00 0.00 1.31
2139 3764 3.134623 CCACCAACAGTCCAGCATCTATA 59.865 47.826 0.00 0.00 0.00 1.31
2140 3765 2.092753 CCACCAACAGTCCAGCATCTAT 60.093 50.000 0.00 0.00 0.00 1.98
2142 3767 0.037303 CCACCAACAGTCCAGCATCT 59.963 55.000 0.00 0.00 0.00 2.90
2143 3768 0.036732 TCCACCAACAGTCCAGCATC 59.963 55.000 0.00 0.00 0.00 3.91
2144 3769 0.478072 TTCCACCAACAGTCCAGCAT 59.522 50.000 0.00 0.00 0.00 3.79
2147 3772 3.798794 TGTTCCACCAACAGTCCAG 57.201 52.632 0.00 0.00 40.29 3.86
2213 3880 8.232513 TCGACGTGTATATGGAATAGTAATGAC 58.767 37.037 0.00 0.00 28.50 3.06
2216 3883 7.627939 GCCTCGACGTGTATATGGAATAGTAAT 60.628 40.741 0.00 0.00 28.50 1.89
2244 3922 6.493116 GTGGAACAAGATAAGCATCAGATTG 58.507 40.000 0.00 0.00 44.16 2.67
2262 3940 8.755018 CAGTTTTCATACTTTCAAATGTGGAAC 58.245 33.333 0.00 0.00 37.35 3.62
2278 3956 5.974751 GTGGAAGCGTTTTTCAGTTTTCATA 59.025 36.000 0.00 0.00 0.00 2.15
2300 3978 1.670674 GCACATGCATGGTTTCCAGTG 60.671 52.381 29.41 16.81 41.59 3.66
2425 4111 1.953559 CCAATCACGATAGGTGGTGG 58.046 55.000 0.00 4.03 46.96 4.61
2454 4140 5.070847 ACACCTCTGAATTGGCATTCTTTTT 59.929 36.000 9.83 0.00 39.81 1.94
2455 4141 4.590222 ACACCTCTGAATTGGCATTCTTTT 59.410 37.500 9.83 0.00 39.81 2.27
2456 4142 4.154942 ACACCTCTGAATTGGCATTCTTT 58.845 39.130 9.83 0.00 39.81 2.52
2457 4143 3.760684 GACACCTCTGAATTGGCATTCTT 59.239 43.478 9.83 0.00 39.81 2.52
2458 4144 3.350833 GACACCTCTGAATTGGCATTCT 58.649 45.455 9.83 0.00 39.81 2.40
2459 4145 2.424956 GGACACCTCTGAATTGGCATTC 59.575 50.000 0.00 0.00 39.58 2.67
2460 4146 2.450476 GGACACCTCTGAATTGGCATT 58.550 47.619 0.00 0.00 0.00 3.56
2461 4147 1.341383 GGGACACCTCTGAATTGGCAT 60.341 52.381 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.