Multiple sequence alignment - TraesCS7A01G189700

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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 TraesCS7A01G189700 chr7A 100.000 2576 0 0 892 3467 146977673 146975098 0.000000e+00 4758.0
1 TraesCS7A01G189700 chr7A 100.000 673 0 0 1 673 146978564 146977892 0.000000e+00 1243.0
2 TraesCS7A01G189700 chr7A 88.077 671 53 7 9 673 33092682 33092033 0.000000e+00 771.0
3 TraesCS7A01G189700 chr7A 100.000 145 0 0 3656 3800 146974909 146974765 6.260000e-68 268.0
4 TraesCS7A01G189700 chr7B 97.033 2056 60 1 985 3040 108484342 108482288 0.000000e+00 3458.0
5 TraesCS7A01G189700 chr7B 88.863 431 42 3 3040 3467 108482087 108481660 3.360000e-145 525.0
6 TraesCS7A01G189700 chr7B 79.861 288 49 6 3058 3337 491918853 491919139 6.440000e-48 202.0
7 TraesCS7A01G189700 chr7D 96.791 2057 59 4 985 3040 146185406 146183356 0.000000e+00 3426.0
8 TraesCS7A01G189700 chr7D 85.947 676 76 15 6 673 566126030 566126694 0.000000e+00 704.0
9 TraesCS7A01G189700 chr7D 91.521 401 22 7 3068 3467 146183088 146182699 3.340000e-150 542.0
10 TraesCS7A01G189700 chr7D 79.514 288 50 6 3058 3337 468510098 468510384 2.990000e-46 196.0
11 TraesCS7A01G189700 chr7D 92.105 76 6 0 3725 3800 146182287 146182212 1.440000e-19 108.0
12 TraesCS7A01G189700 chr4A 90.950 663 59 1 12 673 27574044 27573382 0.000000e+00 891.0
13 TraesCS7A01G189700 chr6A 89.971 678 54 4 1 673 586671694 586671026 0.000000e+00 863.0
14 TraesCS7A01G189700 chr6A 80.592 304 48 4 3048 3341 520435407 520435709 1.370000e-54 224.0
15 TraesCS7A01G189700 chr3A 89.197 685 62 6 1 673 606846617 606847301 0.000000e+00 845.0
16 TraesCS7A01G189700 chr3A 89.318 674 64 5 1 673 80616574 80615908 0.000000e+00 839.0
17 TraesCS7A01G189700 chrUn 88.077 671 53 7 9 673 82019240 82019889 0.000000e+00 771.0
18 TraesCS7A01G189700 chr6B 87.407 675 70 11 9 673 293978757 293979426 0.000000e+00 761.0
19 TraesCS7A01G189700 chr6B 79.487 312 41 11 3048 3342 538944166 538943861 2.310000e-47 200.0
20 TraesCS7A01G189700 chr2D 85.820 677 81 11 9 673 42871513 42870840 0.000000e+00 704.0
21 TraesCS7A01G189700 chr2D 80.000 335 48 7 3030 3346 92738732 92739065 2.950000e-56 230.0
22 TraesCS7A01G189700 chr5A 77.644 331 56 6 3030 3343 605366641 605366970 6.480000e-43 185.0
23 TraesCS7A01G189700 chr1A 77.032 283 55 6 3045 3318 521884925 521885206 1.830000e-33 154.0
24 TraesCS7A01G189700 chr4B 80.296 203 24 7 3049 3236 654924470 654924671 5.120000e-29 139.0
25 TraesCS7A01G189700 chr3B 79.330 179 20 5 3079 3242 525604886 525605062 4.010000e-20 110.0
26 TraesCS7A01G189700 chr3D 90.164 61 4 1 3184 3242 394918870 394918930 1.130000e-10 78.7
27 TraesCS7A01G189700 chr6D 89.831 59 3 2 3199 3255 384226608 384226665 5.270000e-09 73.1
28 TraesCS7A01G189700 chr4D 92.308 52 1 2 3193 3242 363923493 363923543 1.890000e-08 71.3


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G189700 chr7A 146974765 146978564 3799 True 2089.666667 4758 100.000000 1 3800 3 chr7A.!!$R2 3799
1 TraesCS7A01G189700 chr7A 33092033 33092682 649 True 771.000000 771 88.077000 9 673 1 chr7A.!!$R1 664
2 TraesCS7A01G189700 chr7B 108481660 108484342 2682 True 1991.500000 3458 92.948000 985 3467 2 chr7B.!!$R1 2482
3 TraesCS7A01G189700 chr7D 146182212 146185406 3194 True 1358.666667 3426 93.472333 985 3800 3 chr7D.!!$R1 2815
4 TraesCS7A01G189700 chr7D 566126030 566126694 664 False 704.000000 704 85.947000 6 673 1 chr7D.!!$F2 667
5 TraesCS7A01G189700 chr4A 27573382 27574044 662 True 891.000000 891 90.950000 12 673 1 chr4A.!!$R1 661
6 TraesCS7A01G189700 chr6A 586671026 586671694 668 True 863.000000 863 89.971000 1 673 1 chr6A.!!$R1 672
7 TraesCS7A01G189700 chr3A 606846617 606847301 684 False 845.000000 845 89.197000 1 673 1 chr3A.!!$F1 672
8 TraesCS7A01G189700 chr3A 80615908 80616574 666 True 839.000000 839 89.318000 1 673 1 chr3A.!!$R1 672
9 TraesCS7A01G189700 chrUn 82019240 82019889 649 False 771.000000 771 88.077000 9 673 1 chrUn.!!$F1 664
10 TraesCS7A01G189700 chr6B 293978757 293979426 669 False 761.000000 761 87.407000 9 673 1 chr6B.!!$F1 664
11 TraesCS7A01G189700 chr2D 42870840 42871513 673 True 704.000000 704 85.820000 9 673 1 chr2D.!!$R1 664

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
956 1001 0.036858 GCCGGAGATGCTCTTATCCC 60.037 60.0 5.05 0.0 0.0 3.85 F
975 1020 0.107456 CATCATAGGCGGGAGTTGCT 59.893 55.0 0.00 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2712 2757 0.108615 CGATCTCCCGCTCAAACACT 60.109 55.0 0.00 0.0 0.0 3.55 R
2810 2855 5.163723 ACCAAGACGATTTTCTGCATATGTG 60.164 40.0 4.29 0.0 0.0 3.21 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
460 467 3.552384 AGGGACGGCCGTGTCAAA 61.552 61.111 39.65 0.00 40.72 2.69
479 495 2.282958 AGGAGAAGCCCGACGACA 60.283 61.111 0.00 0.00 37.37 4.35
491 507 4.578898 ACGACAACGGCAGCGACA 62.579 61.111 0.00 0.00 44.46 4.35
493 509 2.248431 GACAACGGCAGCGACAAC 59.752 61.111 0.00 0.00 0.00 3.32
494 510 2.512745 ACAACGGCAGCGACAACA 60.513 55.556 0.00 0.00 0.00 3.33
589 616 8.816640 ATATATGCCAAATTTGACCGAAATTC 57.183 30.769 19.86 0.00 42.41 2.17
662 707 4.779733 AGTCCTGGGACCGGCGAT 62.780 66.667 9.30 0.00 45.59 4.58
916 961 3.334463 GCCCGATGAGGCGATTTC 58.666 61.111 0.00 0.00 44.57 2.17
917 962 2.598632 GCCCGATGAGGCGATTTCG 61.599 63.158 0.00 0.00 44.57 3.46
918 963 3.630204 CCGATGAGGCGATTTCGG 58.370 61.111 1.75 6.78 44.37 4.30
919 964 1.956170 CCGATGAGGCGATTTCGGG 60.956 63.158 11.62 0.00 45.65 5.14
920 965 2.598632 CGATGAGGCGATTTCGGGC 61.599 63.158 1.75 0.00 40.23 6.13
921 966 2.588877 ATGAGGCGATTTCGGGCG 60.589 61.111 1.75 0.00 40.23 6.13
927 972 4.230002 CGATTTCGGGCGCCCCTA 62.230 66.667 39.24 25.34 42.67 3.53
928 973 2.280865 GATTTCGGGCGCCCCTAG 60.281 66.667 39.24 25.64 42.67 3.02
929 974 3.826926 GATTTCGGGCGCCCCTAGG 62.827 68.421 39.24 25.25 42.67 3.02
947 992 3.512516 GGCAACAGCCGGAGATGC 61.513 66.667 17.43 17.43 38.93 3.91
948 993 2.437359 GCAACAGCCGGAGATGCT 60.437 61.111 18.11 0.12 40.41 3.79
949 994 2.467826 GCAACAGCCGGAGATGCTC 61.468 63.158 18.11 0.00 36.81 4.26
950 995 1.220206 CAACAGCCGGAGATGCTCT 59.780 57.895 5.05 0.00 36.81 4.09
951 996 0.392193 CAACAGCCGGAGATGCTCTT 60.392 55.000 5.05 0.00 36.81 2.85
952 997 1.134699 CAACAGCCGGAGATGCTCTTA 60.135 52.381 5.05 0.00 36.81 2.10
953 998 1.418334 ACAGCCGGAGATGCTCTTAT 58.582 50.000 5.05 0.00 36.81 1.73
954 999 1.342819 ACAGCCGGAGATGCTCTTATC 59.657 52.381 5.05 0.00 36.81 1.75
955 1000 0.972883 AGCCGGAGATGCTCTTATCC 59.027 55.000 5.05 0.00 32.41 2.59
956 1001 0.036858 GCCGGAGATGCTCTTATCCC 60.037 60.000 5.05 0.00 0.00 3.85
957 1002 1.342074 CCGGAGATGCTCTTATCCCA 58.658 55.000 0.00 0.00 0.00 4.37
958 1003 1.905215 CCGGAGATGCTCTTATCCCAT 59.095 52.381 0.00 0.00 0.00 4.00
959 1004 2.093764 CCGGAGATGCTCTTATCCCATC 60.094 54.545 0.00 0.00 36.49 3.51
960 1005 2.564504 CGGAGATGCTCTTATCCCATCA 59.435 50.000 0.00 0.00 38.21 3.07
961 1006 3.197333 CGGAGATGCTCTTATCCCATCAT 59.803 47.826 0.00 0.00 38.21 2.45
962 1007 4.403752 CGGAGATGCTCTTATCCCATCATA 59.596 45.833 0.00 0.00 38.21 2.15
963 1008 5.451659 CGGAGATGCTCTTATCCCATCATAG 60.452 48.000 0.00 0.00 38.21 2.23
964 1009 5.163322 GGAGATGCTCTTATCCCATCATAGG 60.163 48.000 0.00 0.00 38.21 2.57
965 1010 3.988976 TGCTCTTATCCCATCATAGGC 57.011 47.619 0.00 0.00 0.00 3.93
966 1011 2.234661 TGCTCTTATCCCATCATAGGCG 59.765 50.000 0.00 0.00 0.00 5.52
967 1012 2.419297 GCTCTTATCCCATCATAGGCGG 60.419 54.545 0.00 0.00 0.00 6.13
968 1013 2.169352 CTCTTATCCCATCATAGGCGGG 59.831 54.545 0.00 0.00 41.76 6.13
970 1015 4.215370 TCCCATCATAGGCGGGAG 57.785 61.111 0.69 0.00 44.28 4.30
971 1016 1.235989 TCCCATCATAGGCGGGAGT 59.764 57.895 0.69 0.00 44.28 3.85
972 1017 0.399949 TCCCATCATAGGCGGGAGTT 60.400 55.000 0.69 0.00 44.28 3.01
973 1018 0.250467 CCCATCATAGGCGGGAGTTG 60.250 60.000 0.00 0.00 43.21 3.16
974 1019 0.886490 CCATCATAGGCGGGAGTTGC 60.886 60.000 0.00 0.00 0.00 4.17
975 1020 0.107456 CATCATAGGCGGGAGTTGCT 59.893 55.000 0.00 0.00 0.00 3.91
976 1021 0.394565 ATCATAGGCGGGAGTTGCTC 59.605 55.000 0.00 0.00 0.00 4.26
977 1022 0.687757 TCATAGGCGGGAGTTGCTCT 60.688 55.000 0.00 0.00 0.00 4.09
978 1023 0.249657 CATAGGCGGGAGTTGCTCTC 60.250 60.000 1.79 1.79 42.07 3.20
1005 1050 2.185350 CGAGCTCCGGCAATGTCT 59.815 61.111 8.47 0.00 41.70 3.41
1213 1258 2.815647 CGCTCTTCAACCCGCTCC 60.816 66.667 0.00 0.00 0.00 4.70
1644 1689 2.665185 GACGCGCTGGAGGTGTTT 60.665 61.111 5.73 0.00 0.00 2.83
1784 1829 0.322975 AGCGGGATACAGATGGATGC 59.677 55.000 0.00 0.00 39.74 3.91
1858 1903 2.633657 CATGGCGCGTATTCCAGC 59.366 61.111 8.43 0.00 35.57 4.85
1942 1987 1.073025 TGCAAGGACGCCATTGAGT 59.927 52.632 0.00 0.00 0.00 3.41
2166 2211 1.471676 GCCAAGAAGGTGATCGACGAT 60.472 52.381 10.78 10.78 40.61 3.73
2172 2217 0.241213 AGGTGATCGACGATATGCCG 59.759 55.000 10.97 0.00 0.00 5.69
2292 2337 2.367202 GGATCCCCAGAACAGCGGA 61.367 63.158 0.00 0.00 0.00 5.54
2299 2344 1.287815 CAGAACAGCGGACGGTACA 59.712 57.895 0.00 0.00 0.00 2.90
2412 2457 4.570663 GGGCGGTCCGTGATCGAG 62.571 72.222 13.94 0.00 38.59 4.04
2589 2634 2.881352 GAGGCGTCGCTGCTGTAC 60.881 66.667 18.11 0.00 34.52 2.90
2712 2757 4.215908 AGGCTACCAAGTTGATATCTCGA 58.784 43.478 3.87 0.00 0.00 4.04
2774 2819 2.761786 CATCATTTCAGGGATGGGGT 57.238 50.000 0.00 0.00 37.77 4.95
2875 2920 4.765813 TTCGGGAAAATAACCCCTAGAG 57.234 45.455 0.00 0.00 44.09 2.43
2945 2990 9.872757 GAAAAATCTTGACGTGAATAGTGTAAA 57.127 29.630 0.00 0.00 0.00 2.01
3046 3350 6.314896 CAGATGTCTTGGGAACATTAAGAGAC 59.685 42.308 0.00 0.00 41.46 3.36
3072 3376 2.260247 GCTTGATGCTCTGTTGGCA 58.740 52.632 0.00 0.00 44.05 4.92
3171 3479 8.898761 TGTTTACTGTTTGACACTATTCAATGT 58.101 29.630 0.00 0.00 35.42 2.71
3282 3590 8.556213 GGATTTCCCCAAAACTTTAAAATACC 57.444 34.615 0.00 0.00 0.00 2.73
3328 3637 6.424683 GTTTTCACCGAAACTTCGTTTCTAT 58.575 36.000 15.07 3.24 46.55 1.98
3365 3674 6.820152 TCATTGGAAGTTATGATCACTGACAG 59.180 38.462 0.00 0.00 0.00 3.51
3391 3700 1.392853 GTCAAAGAGCGCATGTCAGAG 59.607 52.381 11.47 0.00 0.00 3.35
3457 3766 7.133891 ACTATGTTGCACTGAAGAAACATAC 57.866 36.000 11.62 0.00 41.94 2.39
3674 4157 3.353836 CCGTTGTTGGCCACTCCG 61.354 66.667 3.88 5.53 37.80 4.63
3685 4168 1.448540 CCACTCCGACCATGTCAGC 60.449 63.158 0.00 0.00 32.09 4.26
3694 4177 2.498167 GACCATGTCAGCCACCATATC 58.502 52.381 0.00 0.00 32.09 1.63
3697 4180 2.224606 CATGTCAGCCACCATATCACC 58.775 52.381 0.00 0.00 0.00 4.02
3701 4184 0.465705 CAGCCACCATATCACCGTCT 59.534 55.000 0.00 0.00 0.00 4.18
3704 4187 1.940613 GCCACCATATCACCGTCTTTC 59.059 52.381 0.00 0.00 0.00 2.62
3705 4188 2.561569 CCACCATATCACCGTCTTTCC 58.438 52.381 0.00 0.00 0.00 3.13
3706 4189 2.170607 CCACCATATCACCGTCTTTCCT 59.829 50.000 0.00 0.00 0.00 3.36
3707 4190 3.370527 CCACCATATCACCGTCTTTCCTT 60.371 47.826 0.00 0.00 0.00 3.36
3708 4191 3.871594 CACCATATCACCGTCTTTCCTTC 59.128 47.826 0.00 0.00 0.00 3.46
3709 4192 3.775316 ACCATATCACCGTCTTTCCTTCT 59.225 43.478 0.00 0.00 0.00 2.85
3710 4193 4.122776 CCATATCACCGTCTTTCCTTCTG 58.877 47.826 0.00 0.00 0.00 3.02
3711 4194 4.141937 CCATATCACCGTCTTTCCTTCTGA 60.142 45.833 0.00 0.00 0.00 3.27
3712 4195 5.419542 CATATCACCGTCTTTCCTTCTGAA 58.580 41.667 0.00 0.00 0.00 3.02
3713 4196 3.386768 TCACCGTCTTTCCTTCTGAAG 57.613 47.619 10.46 10.46 33.63 3.02
3714 4197 2.963101 TCACCGTCTTTCCTTCTGAAGA 59.037 45.455 18.68 2.53 33.63 2.87
3715 4198 3.060602 CACCGTCTTTCCTTCTGAAGAC 58.939 50.000 18.68 7.59 33.63 3.01
3716 4199 2.288273 ACCGTCTTTCCTTCTGAAGACG 60.288 50.000 23.90 23.90 44.73 4.18
3717 4200 2.288273 CCGTCTTTCCTTCTGAAGACGT 60.288 50.000 26.66 0.00 44.26 4.34
3718 4201 2.981140 CGTCTTTCCTTCTGAAGACGTC 59.019 50.000 23.03 7.70 42.74 4.34
3719 4202 2.981140 GTCTTTCCTTCTGAAGACGTCG 59.019 50.000 18.68 1.86 33.63 5.12
3720 4203 2.882761 TCTTTCCTTCTGAAGACGTCGA 59.117 45.455 18.68 4.26 33.63 4.20
3721 4204 2.701073 TTCCTTCTGAAGACGTCGAC 57.299 50.000 18.68 5.18 0.00 4.20
3722 4205 0.879765 TCCTTCTGAAGACGTCGACC 59.120 55.000 18.68 3.96 0.00 4.79
3723 4206 0.596577 CCTTCTGAAGACGTCGACCA 59.403 55.000 18.68 8.50 0.00 4.02
3737 4220 2.446994 ACCACCTTCCCGTCACCA 60.447 61.111 0.00 0.00 0.00 4.17
3749 4232 3.472263 GTCACCACATGGCGTTTTC 57.528 52.632 0.00 0.00 39.32 2.29
3751 4234 0.466372 TCACCACATGGCGTTTTCCA 60.466 50.000 0.00 0.00 40.97 3.53
3752 4235 0.039256 CACCACATGGCGTTTTCCAG 60.039 55.000 0.00 0.00 39.89 3.86
3763 4246 2.412847 GCGTTTTCCAGTCTCCAATTCG 60.413 50.000 0.00 0.00 0.00 3.34
3769 4252 2.028112 TCCAGTCTCCAATTCGACCAAG 60.028 50.000 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 1.813092 GCCCTCGTTGATGATGATGCT 60.813 52.381 0.00 0.00 0.00 3.79
284 285 1.424493 CGCTTCCTCGCCATCTTCAC 61.424 60.000 0.00 0.00 0.00 3.18
325 326 2.963854 CGGCGATGCTGCTCGAAT 60.964 61.111 20.23 0.00 41.12 3.34
356 357 0.965866 TCGATGGCAACGACTCCTCT 60.966 55.000 16.16 0.00 42.51 3.69
369 373 2.278206 CGTCGCTGTCCTCGATGG 60.278 66.667 0.00 0.00 38.79 3.51
426 433 1.685765 CTGGTGGATCCCTGACCGA 60.686 63.158 9.90 1.08 34.77 4.69
454 461 0.321671 CGGGCTTCTCCTCTTTGACA 59.678 55.000 0.00 0.00 34.39 3.58
460 467 2.047443 GTCGTCGGGCTTCTCCTCT 61.047 63.158 0.00 0.00 34.39 3.69
479 495 2.713154 GTTGTTGTCGCTGCCGTT 59.287 55.556 0.00 0.00 35.54 4.44
485 501 2.410638 TAGTCGCCGTTGTTGTCGCT 62.411 55.000 0.00 0.00 0.00 4.93
489 505 0.662374 CGAGTAGTCGCCGTTGTTGT 60.662 55.000 7.09 0.00 39.88 3.32
491 507 1.080974 CCGAGTAGTCGCCGTTGTT 60.081 57.895 14.65 0.00 45.41 2.83
493 509 2.879462 GCCGAGTAGTCGCCGTTG 60.879 66.667 14.65 1.76 45.41 4.10
494 510 4.471726 CGCCGAGTAGTCGCCGTT 62.472 66.667 14.62 0.00 41.83 4.44
550 576 6.641169 TGGCATATATTAAAATGTTCGGCA 57.359 33.333 0.00 0.00 0.00 5.69
589 616 2.900046 CGAATTCGTTTAAACACGGCTG 59.100 45.455 19.67 0.00 40.74 4.85
891 936 2.892425 CTCATCGGGCAAGCCGAC 60.892 66.667 4.64 0.00 42.49 4.79
892 937 4.161295 CCTCATCGGGCAAGCCGA 62.161 66.667 5.02 5.02 43.81 5.54
900 945 3.630204 CGAAATCGCCTCATCGGG 58.370 61.111 0.00 0.00 0.00 5.14
902 947 2.598632 GCCCGAAATCGCCTCATCG 61.599 63.158 0.00 0.00 38.18 3.84
903 948 2.598632 CGCCCGAAATCGCCTCATC 61.599 63.158 0.00 0.00 38.18 2.92
904 949 2.588877 CGCCCGAAATCGCCTCAT 60.589 61.111 0.00 0.00 38.18 2.90
931 976 2.437359 AGCATCTCCGGCTGTTGC 60.437 61.111 17.08 17.08 40.80 4.17
932 977 3.805267 GAGCATCTCCGGCTGTTG 58.195 61.111 0.00 0.00 42.78 3.33
943 988 4.450053 GCCTATGATGGGATAAGAGCATC 58.550 47.826 0.00 0.00 0.00 3.91
944 989 3.118482 CGCCTATGATGGGATAAGAGCAT 60.118 47.826 0.00 0.00 0.00 3.79
945 990 2.234661 CGCCTATGATGGGATAAGAGCA 59.765 50.000 0.00 0.00 0.00 4.26
946 991 2.419297 CCGCCTATGATGGGATAAGAGC 60.419 54.545 0.00 0.00 0.00 4.09
947 992 2.169352 CCCGCCTATGATGGGATAAGAG 59.831 54.545 0.00 0.00 46.41 2.85
948 993 2.187958 CCCGCCTATGATGGGATAAGA 58.812 52.381 0.00 0.00 46.41 2.10
949 994 2.187958 TCCCGCCTATGATGGGATAAG 58.812 52.381 0.00 0.00 46.96 1.73
950 995 2.335681 TCCCGCCTATGATGGGATAA 57.664 50.000 0.00 0.00 46.96 1.75
952 997 4.998839 TCCCGCCTATGATGGGAT 57.001 55.556 0.00 0.00 46.96 3.85
954 999 0.250467 CAACTCCCGCCTATGATGGG 60.250 60.000 0.00 0.00 44.75 4.00
955 1000 0.886490 GCAACTCCCGCCTATGATGG 60.886 60.000 0.00 0.00 0.00 3.51
956 1001 0.107456 AGCAACTCCCGCCTATGATG 59.893 55.000 0.00 0.00 0.00 3.07
957 1002 0.394565 GAGCAACTCCCGCCTATGAT 59.605 55.000 0.00 0.00 0.00 2.45
958 1003 0.687757 AGAGCAACTCCCGCCTATGA 60.688 55.000 0.00 0.00 0.00 2.15
959 1004 0.249657 GAGAGCAACTCCCGCCTATG 60.250 60.000 0.33 0.00 39.53 2.23
960 1005 2.128729 GAGAGCAACTCCCGCCTAT 58.871 57.895 0.33 0.00 39.53 2.57
961 1006 3.617368 GAGAGCAACTCCCGCCTA 58.383 61.111 0.33 0.00 39.53 3.93
974 1019 2.851071 GCTCGGATGGTCGGGAGAG 61.851 68.421 0.00 0.00 41.26 3.20
975 1020 2.833582 GCTCGGATGGTCGGGAGA 60.834 66.667 0.00 0.00 31.16 3.71
976 1021 2.835431 AGCTCGGATGGTCGGGAG 60.835 66.667 0.00 0.00 31.16 4.30
977 1022 2.833582 GAGCTCGGATGGTCGGGA 60.834 66.667 0.00 0.00 31.16 5.14
978 1023 3.917760 GGAGCTCGGATGGTCGGG 61.918 72.222 7.83 0.00 35.52 5.14
979 1024 4.271816 CGGAGCTCGGATGGTCGG 62.272 72.222 15.82 0.00 35.52 4.79
1644 1689 1.375396 CGTCGCCCTCATTTGGTCA 60.375 57.895 0.00 0.00 0.00 4.02
1784 1829 2.887568 CCGCTGTGGCTAGCTTCG 60.888 66.667 15.72 10.53 41.51 3.79
2166 2211 1.048160 TGTCAGGCTCCATCGGCATA 61.048 55.000 0.00 0.00 0.00 3.14
2172 2217 1.340405 ACACCAATGTCAGGCTCCATC 60.340 52.381 0.00 0.00 31.55 3.51
2292 2337 2.436646 GCCAGCAGCATGTACCGT 60.437 61.111 0.00 0.00 42.97 4.83
2299 2344 2.362120 GAGGTTGGCCAGCAGCAT 60.362 61.111 22.07 3.70 46.50 3.79
2412 2457 0.524392 CACAGACCTCGCTGTCGATC 60.524 60.000 0.00 0.00 45.54 3.69
2694 2739 6.525578 AACACTCGAGATATCAACTTGGTA 57.474 37.500 21.68 0.00 0.00 3.25
2712 2757 0.108615 CGATCTCCCGCTCAAACACT 60.109 55.000 0.00 0.00 0.00 3.55
2774 2819 6.651225 TCACCAATAATCATTACACGAACACA 59.349 34.615 0.00 0.00 0.00 3.72
2810 2855 5.163723 ACCAAGACGATTTTCTGCATATGTG 60.164 40.000 4.29 0.00 0.00 3.21
2918 2963 7.730364 ACACTATTCACGTCAAGATTTTTCT 57.270 32.000 0.00 0.00 0.00 2.52
3063 3367 3.229293 TGGAATTTCACATGCCAACAGA 58.771 40.909 0.00 0.00 0.00 3.41
3064 3368 3.663995 TGGAATTTCACATGCCAACAG 57.336 42.857 0.00 0.00 0.00 3.16
3065 3369 3.387374 ACTTGGAATTTCACATGCCAACA 59.613 39.130 0.00 0.00 35.05 3.33
3066 3370 3.993920 ACTTGGAATTTCACATGCCAAC 58.006 40.909 0.00 0.00 35.05 3.77
3067 3371 4.100653 TGAACTTGGAATTTCACATGCCAA 59.899 37.500 0.00 0.00 37.13 4.52
3069 3373 4.255833 TGAACTTGGAATTTCACATGCC 57.744 40.909 0.00 0.00 0.00 4.40
3071 3375 6.534436 TGTGTTTGAACTTGGAATTTCACATG 59.466 34.615 0.00 0.00 31.42 3.21
3072 3376 6.638610 TGTGTTTGAACTTGGAATTTCACAT 58.361 32.000 0.00 0.00 31.42 3.21
3073 3377 6.030548 TGTGTTTGAACTTGGAATTTCACA 57.969 33.333 0.00 0.00 31.42 3.58
3074 3378 7.538303 AATGTGTTTGAACTTGGAATTTCAC 57.462 32.000 0.00 0.00 31.42 3.18
3075 3379 7.708752 GGTAATGTGTTTGAACTTGGAATTTCA 59.291 33.333 0.00 0.00 0.00 2.69
3131 3438 9.897744 CAAACAGTAAACATCACTTATCATTGT 57.102 29.630 0.00 0.00 0.00 2.71
3171 3479 9.892130 AACCTTACCATTTACAAACAAAATCAA 57.108 25.926 0.00 0.00 0.00 2.57
3194 3502 5.877564 TGTGAAATTCCCAAGTTCAAAAACC 59.122 36.000 1.01 0.00 45.59 3.27
3282 3590 5.685841 ACCGATGAAAACTACATGAAAACG 58.314 37.500 0.00 0.00 0.00 3.60
3339 3648 7.341030 TGTCAGTGATCATAACTTCCAATGAT 58.659 34.615 0.00 0.00 43.75 2.45
3365 3674 2.353889 ACATGCGCTCTTTGACATGATC 59.646 45.455 9.73 0.00 41.93 2.92
3391 3700 0.447801 CACACGCCATTAGAAGGTGC 59.552 55.000 0.00 0.00 40.28 5.01
3655 3964 1.826487 GGAGTGGCCAACAACGGTT 60.826 57.895 7.24 0.00 37.87 4.44
3660 4143 2.063015 ATGGTCGGAGTGGCCAACAA 62.063 55.000 7.24 0.00 35.74 2.83
3674 4157 2.158769 TGATATGGTGGCTGACATGGTC 60.159 50.000 0.00 0.00 0.00 4.02
3685 4168 2.170607 AGGAAAGACGGTGATATGGTGG 59.829 50.000 0.00 0.00 0.00 4.61
3694 4177 3.060602 GTCTTCAGAAGGAAAGACGGTG 58.939 50.000 10.42 0.00 34.44 4.94
3701 4184 2.288030 GGTCGACGTCTTCAGAAGGAAA 60.288 50.000 14.70 0.00 34.44 3.13
3704 4187 0.596577 TGGTCGACGTCTTCAGAAGG 59.403 55.000 14.70 0.00 0.00 3.46
3705 4188 1.666311 GGTGGTCGACGTCTTCAGAAG 60.666 57.143 14.70 3.45 0.00 2.85
3706 4189 0.313043 GGTGGTCGACGTCTTCAGAA 59.687 55.000 14.70 0.00 0.00 3.02
3707 4190 0.536687 AGGTGGTCGACGTCTTCAGA 60.537 55.000 14.70 0.00 0.00 3.27
3708 4191 0.314302 AAGGTGGTCGACGTCTTCAG 59.686 55.000 14.70 0.00 0.00 3.02
3709 4192 0.313043 GAAGGTGGTCGACGTCTTCA 59.687 55.000 25.46 11.67 35.31 3.02
3710 4193 0.388263 GGAAGGTGGTCGACGTCTTC 60.388 60.000 23.81 23.81 34.69 2.87
3711 4194 1.664306 GGAAGGTGGTCGACGTCTT 59.336 57.895 14.70 12.30 0.00 3.01
3712 4195 2.273912 GGGAAGGTGGTCGACGTCT 61.274 63.158 14.70 3.81 0.00 4.18
3713 4196 2.260743 GGGAAGGTGGTCGACGTC 59.739 66.667 9.92 5.18 0.00 4.34
3714 4197 3.677648 CGGGAAGGTGGTCGACGT 61.678 66.667 9.92 0.00 0.00 4.34
3715 4198 3.621892 GACGGGAAGGTGGTCGACG 62.622 68.421 9.92 0.00 0.00 5.12
3716 4199 2.260743 GACGGGAAGGTGGTCGAC 59.739 66.667 7.13 7.13 0.00 4.20
3717 4200 2.203523 TGACGGGAAGGTGGTCGA 60.204 61.111 0.00 0.00 33.45 4.20
3718 4201 2.048503 GTGACGGGAAGGTGGTCG 60.049 66.667 0.00 0.00 33.45 4.79
3719 4202 2.346365 GGTGACGGGAAGGTGGTC 59.654 66.667 0.00 0.00 0.00 4.02
3720 4203 2.446994 TGGTGACGGGAAGGTGGT 60.447 61.111 0.00 0.00 0.00 4.16
3721 4204 2.032071 GTGGTGACGGGAAGGTGG 59.968 66.667 0.00 0.00 0.00 4.61
3722 4205 0.955428 CATGTGGTGACGGGAAGGTG 60.955 60.000 0.00 0.00 0.00 4.00
3723 4206 1.374947 CATGTGGTGACGGGAAGGT 59.625 57.895 0.00 0.00 0.00 3.50
3737 4220 1.523758 GAGACTGGAAAACGCCATGT 58.476 50.000 0.00 0.00 37.30 3.21
3749 4232 2.350522 CTTGGTCGAATTGGAGACTGG 58.649 52.381 0.00 0.00 37.52 4.00
3751 4234 1.339151 GCCTTGGTCGAATTGGAGACT 60.339 52.381 0.00 0.00 37.52 3.24
3752 4235 1.087501 GCCTTGGTCGAATTGGAGAC 58.912 55.000 0.00 0.00 36.70 3.36
3763 4246 3.181506 CGCTTCAAAATCTAGCCTTGGTC 60.182 47.826 0.00 0.00 0.00 4.02
3769 4252 5.429957 AATCATCGCTTCAAAATCTAGCC 57.570 39.130 0.00 0.00 0.00 3.93


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

AutoCloner maintained by Alex Coulton.