Multiple sequence alignment - TraesCS6B01G072700

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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 TraesCS6B01G072700 chr6B 100.000 3473 0 0 432 3904 49281299 49277827 0.000000e+00 6414.0
1 TraesCS6B01G072700 chr6B 93.464 2968 109 32 798 3744 49409429 49406526 0.000000e+00 4327.0
2 TraesCS6B01G072700 chr6B 100.000 270 0 0 1 270 49281730 49281461 2.090000e-137 499.0
3 TraesCS6B01G072700 chr6B 74.862 907 189 30 1309 2198 47927900 47928784 3.680000e-100 375.0
4 TraesCS6B01G072700 chr6B 90.809 272 21 2 3 270 49410102 49409831 1.030000e-95 361.0
5 TraesCS6B01G072700 chr6B 84.502 271 26 9 471 738 49409695 49409438 1.800000e-63 254.0
6 TraesCS6B01G072700 chr6B 93.789 161 10 0 3741 3901 49405330 49405170 3.900000e-60 243.0
7 TraesCS6B01G072700 chr6B 77.033 418 81 14 1018 1428 60615000 60615409 3.920000e-55 226.0
8 TraesCS6B01G072700 chr6B 76.722 421 84 12 1015 1428 60657203 60657616 5.080000e-54 222.0
9 TraesCS6B01G072700 chr6B 74.181 519 109 20 1015 1524 60631690 60632192 3.980000e-45 193.0
10 TraesCS6B01G072700 chr6B 84.932 73 11 0 3794 3866 48539896 48539824 1.500000e-09 75.0
11 TraesCS6B01G072700 chr6B 71.014 345 80 15 1174 1511 57581842 57582173 9.050000e-07 65.8
12 TraesCS6B01G072700 chr6B 100.000 34 0 0 3818 3851 48489965 48489932 3.260000e-06 63.9
13 TraesCS6B01G072700 chr6A 94.048 2520 97 24 807 3294 28329004 28326506 0.000000e+00 3773.0
14 TraesCS6B01G072700 chr6A 92.960 625 26 4 3279 3901 28326486 28325878 0.000000e+00 894.0
15 TraesCS6B01G072700 chr6A 90.476 273 23 1 1 270 28350103 28349831 1.330000e-94 357.0
16 TraesCS6B01G072700 chr6A 86.989 269 27 5 469 736 28349697 28349436 2.950000e-76 296.0
17 TraesCS6B01G072700 chr6A 70.681 822 193 37 1235 2044 30440201 30440986 5.260000e-29 139.0
18 TraesCS6B01G072700 chr6A 79.508 122 18 7 134 251 9365290 9365172 3.230000e-11 80.5
19 TraesCS6B01G072700 chr6A 85.294 68 10 0 3804 3871 27746839 27746772 1.950000e-08 71.3
20 TraesCS6B01G072700 chr6A 75.573 131 28 4 1163 1292 33216380 33216253 1.170000e-05 62.1
21 TraesCS6B01G072700 chr6A 76.923 104 20 3 2689 2789 47142075 47142177 5.450000e-04 56.5
22 TraesCS6B01G072700 chrUn 78.179 1384 245 44 1020 2367 96739186 96740548 0.000000e+00 830.0
23 TraesCS6B01G072700 chrUn 87.273 55 7 0 197 251 101168612 101168558 3.260000e-06 63.9
24 TraesCS6B01G072700 chr6D 74.490 490 105 15 1032 1514 30067476 30067000 1.110000e-45 195.0
25 TraesCS6B01G072700 chr6D 81.452 124 16 7 136 255 8915742 8915622 1.150000e-15 95.3
26 TraesCS6B01G072700 chr6D 84.211 76 12 0 36 111 27300160 27300085 1.500000e-09 75.0
27 TraesCS6B01G072700 chr6D 100.000 33 0 0 219 251 8578322 8578354 1.170000e-05 62.1
28 TraesCS6B01G072700 chr1D 100.000 54 0 0 741 794 287617460 287617407 2.480000e-17 100.0
29 TraesCS6B01G072700 chr1D 98.148 54 1 0 741 794 72438109 72438056 1.150000e-15 95.3
30 TraesCS6B01G072700 chr2D 81.667 120 17 4 134 250 582489714 582489597 1.150000e-15 95.3
31 TraesCS6B01G072700 chr2B 81.513 119 19 3 134 250 701197842 701197725 1.150000e-15 95.3
32 TraesCS6B01G072700 chr2B 80.833 120 20 3 134 251 701484762 701484644 1.490000e-14 91.6


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 TraesCS6B01G072700 chr6B 49277827 49281730 3903 True 3456.50 6414 100.0000 1 3904 2 chr6B.!!$R3 3903
1 TraesCS6B01G072700 chr6B 49405170 49410102 4932 True 1296.25 4327 90.6410 3 3901 4 chr6B.!!$R4 3898
2 TraesCS6B01G072700 chr6B 47927900 47928784 884 False 375.00 375 74.8620 1309 2198 1 chr6B.!!$F1 889
3 TraesCS6B01G072700 chr6A 28325878 28329004 3126 True 2333.50 3773 93.5040 807 3901 2 chr6A.!!$R4 3094
4 TraesCS6B01G072700 chr6A 28349436 28350103 667 True 326.50 357 88.7325 1 736 2 chr6A.!!$R5 735
5 TraesCS6B01G072700 chrUn 96739186 96740548 1362 False 830.00 830 78.1790 1020 2367 1 chrUn.!!$F1 1347

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
187 191 0.034756 CATCACCCTGACGTGTTCCA 59.965 55.0 0.00 0.0 35.18 3.53 F
972 986 0.105964 TCCACTTCACTTCACACCCG 59.894 55.0 0.00 0.0 0.00 5.28 F
1845 1883 0.111639 GTGGTGGCCTTGGTTTCCTA 59.888 55.0 3.32 0.0 0.00 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2016 2060 0.389296 CGATAACTGGTGTCCACGCA 60.389 55.0 0.00 0.0 0.0 5.24 R
2017 2061 1.082117 CCGATAACTGGTGTCCACGC 61.082 60.0 0.00 0.0 0.0 5.34 R
3524 3646 0.039798 CACTGCTGCATCGCAAGTTT 60.040 50.0 1.31 0.0 39.8 2.66 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
18 19 2.012237 GCAGTCGCATGAGTGATGG 58.988 57.895 0.00 0.00 46.58 3.51
100 104 1.071605 CTCCGCTTTCTTCTTCACCG 58.928 55.000 0.00 0.00 0.00 4.94
108 112 1.266178 TCTTCTTCACCGCCATCTCA 58.734 50.000 0.00 0.00 0.00 3.27
129 133 4.462834 TCATTCCTCGTACTTGACATCACT 59.537 41.667 0.00 0.00 0.00 3.41
130 134 5.650703 TCATTCCTCGTACTTGACATCACTA 59.349 40.000 0.00 0.00 0.00 2.74
158 162 1.360192 GCACACCAACACCTTCTGC 59.640 57.895 0.00 0.00 0.00 4.26
187 191 0.034756 CATCACCCTGACGTGTTCCA 59.965 55.000 0.00 0.00 35.18 3.53
452 457 4.931661 ACGAAGTTCTACTTTGTCTGGA 57.068 40.909 6.63 0.00 46.95 3.86
453 458 5.272283 ACGAAGTTCTACTTTGTCTGGAA 57.728 39.130 6.63 0.00 46.95 3.53
454 459 5.290386 ACGAAGTTCTACTTTGTCTGGAAG 58.710 41.667 6.63 0.00 46.95 3.46
455 460 5.068723 ACGAAGTTCTACTTTGTCTGGAAGA 59.931 40.000 6.63 0.00 46.95 2.87
456 461 5.983720 CGAAGTTCTACTTTGTCTGGAAGAA 59.016 40.000 0.56 0.00 41.56 2.52
457 462 6.647067 CGAAGTTCTACTTTGTCTGGAAGAAT 59.353 38.462 0.56 0.00 41.56 2.40
458 463 7.171678 CGAAGTTCTACTTTGTCTGGAAGAATT 59.828 37.037 0.56 0.00 41.56 2.17
459 464 8.159344 AAGTTCTACTTTGTCTGGAAGAATTG 57.841 34.615 0.00 0.00 39.37 2.32
460 465 7.229506 AAGTTCTACTTTGTCTGGAAGAATTGG 59.770 37.037 0.00 0.00 39.37 3.16
469 474 4.517285 TCTGGAAGAATTGGAAGAATCGG 58.483 43.478 0.00 0.00 42.31 4.18
559 566 1.208165 AAAGGGGGCGGTGAAGAGAT 61.208 55.000 0.00 0.00 0.00 2.75
571 579 0.915364 GAAGAGATGGGTGGAAGGCT 59.085 55.000 0.00 0.00 0.00 4.58
585 593 3.103742 GGAAGGCTAGGGATATGAGAGG 58.896 54.545 0.00 0.00 0.00 3.69
592 600 3.488355 AGGGATATGAGAGGAGATGGG 57.512 52.381 0.00 0.00 0.00 4.00
596 604 3.768757 GGATATGAGAGGAGATGGGTGAG 59.231 52.174 0.00 0.00 0.00 3.51
646 654 2.421739 GACAGTGTCAGCACCGGT 59.578 61.111 18.54 0.00 46.35 5.28
647 655 1.227556 GACAGTGTCAGCACCGGTT 60.228 57.895 18.54 0.00 46.35 4.44
691 700 2.144730 CGTCGGGTTTGGAATGTGTTA 58.855 47.619 0.00 0.00 0.00 2.41
692 701 2.745281 CGTCGGGTTTGGAATGTGTTAT 59.255 45.455 0.00 0.00 0.00 1.89
693 702 3.181514 CGTCGGGTTTGGAATGTGTTATC 60.182 47.826 0.00 0.00 0.00 1.75
694 703 4.007659 GTCGGGTTTGGAATGTGTTATCT 58.992 43.478 0.00 0.00 0.00 1.98
695 704 4.457949 GTCGGGTTTGGAATGTGTTATCTT 59.542 41.667 0.00 0.00 0.00 2.40
696 705 5.048294 GTCGGGTTTGGAATGTGTTATCTTT 60.048 40.000 0.00 0.00 0.00 2.52
697 706 5.536916 TCGGGTTTGGAATGTGTTATCTTTT 59.463 36.000 0.00 0.00 0.00 2.27
765 774 2.403252 TTGAGCAAAGGGTAGCTAGC 57.597 50.000 14.67 14.67 42.04 3.42
766 775 0.541863 TGAGCAAAGGGTAGCTAGCC 59.458 55.000 30.68 30.68 42.04 3.93
779 788 7.617041 GGGTAGCTAGCCTTTATTGATTATG 57.383 40.000 30.54 0.00 40.60 1.90
780 789 6.094186 GGGTAGCTAGCCTTTATTGATTATGC 59.906 42.308 30.54 2.23 40.60 3.14
781 790 6.655003 GGTAGCTAGCCTTTATTGATTATGCA 59.345 38.462 12.13 0.00 0.00 3.96
782 791 6.814506 AGCTAGCCTTTATTGATTATGCAG 57.185 37.500 12.13 0.00 0.00 4.41
783 792 5.709164 AGCTAGCCTTTATTGATTATGCAGG 59.291 40.000 12.13 0.00 0.00 4.85
784 793 5.707298 GCTAGCCTTTATTGATTATGCAGGA 59.293 40.000 2.29 0.00 0.00 3.86
785 794 6.376581 GCTAGCCTTTATTGATTATGCAGGAT 59.623 38.462 2.29 0.00 0.00 3.24
786 795 6.585695 AGCCTTTATTGATTATGCAGGATG 57.414 37.500 0.00 0.00 40.87 3.51
787 796 6.073314 AGCCTTTATTGATTATGCAGGATGT 58.927 36.000 0.00 0.00 39.31 3.06
788 797 6.552350 AGCCTTTATTGATTATGCAGGATGTT 59.448 34.615 0.00 0.00 39.31 2.71
789 798 6.865205 GCCTTTATTGATTATGCAGGATGTTC 59.135 38.462 0.00 0.00 39.31 3.18
790 799 7.080099 CCTTTATTGATTATGCAGGATGTTCG 58.920 38.462 0.00 0.00 39.31 3.95
791 800 7.255242 CCTTTATTGATTATGCAGGATGTTCGT 60.255 37.037 0.00 0.00 39.31 3.85
792 801 4.880886 TTGATTATGCAGGATGTTCGTG 57.119 40.909 0.00 0.00 39.31 4.35
793 802 3.205338 TGATTATGCAGGATGTTCGTGG 58.795 45.455 0.00 0.00 39.31 4.94
794 803 2.779755 TTATGCAGGATGTTCGTGGT 57.220 45.000 0.00 0.00 39.31 4.16
795 804 2.779755 TATGCAGGATGTTCGTGGTT 57.220 45.000 0.00 0.00 39.31 3.67
796 805 1.909700 ATGCAGGATGTTCGTGGTTT 58.090 45.000 0.00 0.00 39.31 3.27
797 806 1.686355 TGCAGGATGTTCGTGGTTTT 58.314 45.000 0.00 0.00 39.31 2.43
798 807 2.028130 TGCAGGATGTTCGTGGTTTTT 58.972 42.857 0.00 0.00 39.31 1.94
883 897 4.039245 GGGCCTAAAATCTATTTTCAGGGC 59.961 45.833 23.63 23.63 44.13 5.19
972 986 0.105964 TCCACTTCACTTCACACCCG 59.894 55.000 0.00 0.00 0.00 5.28
975 989 0.532862 ACTTCACTTCACACCCGCAG 60.533 55.000 0.00 0.00 0.00 5.18
1011 1025 1.821936 CGAGAAGATGAGCAGCCCT 59.178 57.895 0.00 0.00 0.00 5.19
1845 1883 0.111639 GTGGTGGCCTTGGTTTCCTA 59.888 55.000 3.32 0.00 0.00 2.94
1958 2002 2.912956 ACAAGCTACTTCCCCTGAATCA 59.087 45.455 0.00 0.00 0.00 2.57
2016 2060 4.702131 GCTGAGGAGAATAATGTGGTGTTT 59.298 41.667 0.00 0.00 0.00 2.83
2017 2061 5.392380 GCTGAGGAGAATAATGTGGTGTTTG 60.392 44.000 0.00 0.00 0.00 2.93
2018 2062 4.458989 TGAGGAGAATAATGTGGTGTTTGC 59.541 41.667 0.00 0.00 0.00 3.68
2026 2070 1.063488 GTGGTGTTTGCGTGGACAC 59.937 57.895 8.25 8.25 44.09 3.67
2118 2172 9.399403 GTTATCTTCCATTTGAAAGTGTCTTTC 57.601 33.333 13.28 13.28 31.06 2.62
2259 2325 6.985188 TCACATCCTTTCATGTTAAGCTAC 57.015 37.500 0.00 0.00 34.60 3.58
2262 2328 5.648092 ACATCCTTTCATGTTAAGCTACCAC 59.352 40.000 0.00 0.00 32.81 4.16
2637 2719 3.034030 GCTGTTGCTGGTGGACAC 58.966 61.111 0.00 0.00 36.03 3.67
2734 2816 5.073311 TGAGGTATCTGAACAGCTGTTAC 57.927 43.478 31.20 23.48 38.56 2.50
2747 2829 9.646427 TGAACAGCTGTTACAAAAACTATTTTT 57.354 25.926 31.20 3.57 39.71 1.94
2801 2883 8.370182 ACCAAATTGCAAGAAAGATTGTAAGAT 58.630 29.630 4.94 0.00 38.02 2.40
2944 3026 4.853924 ATGACAGTCATTTTGGACCAAC 57.146 40.909 10.53 0.00 38.59 3.77
2972 3054 9.661187 GAAGTGTGAATTAATAAGATGATGCAG 57.339 33.333 0.00 0.00 0.00 4.41
2995 3077 5.074239 AGAATCCCTTGCTTGAGGCTTATAT 59.926 40.000 0.00 0.00 42.39 0.86
3000 3082 4.498682 CCTTGCTTGAGGCTTATATTGCAC 60.499 45.833 0.00 0.00 42.39 4.57
3006 3088 6.535150 GCTTGAGGCTTATATTGCACGATATA 59.465 38.462 0.00 0.00 38.06 0.86
3008 3090 9.750125 CTTGAGGCTTATATTGCACGATATATA 57.250 33.333 0.00 0.00 0.00 0.86
3096 3178 9.334693 CTTTATCAAAGCTGATTGTTTAGTGAC 57.665 33.333 0.00 0.00 39.36 3.67
3097 3179 8.621532 TTATCAAAGCTGATTGTTTAGTGACT 57.378 30.769 0.00 0.00 39.36 3.41
3098 3180 9.719355 TTATCAAAGCTGATTGTTTAGTGACTA 57.281 29.630 0.00 0.00 39.36 2.59
3099 3181 7.658179 TCAAAGCTGATTGTTTAGTGACTAG 57.342 36.000 0.00 0.00 0.00 2.57
3123 3205 7.419204 AGCTAGCTAACTCGTACATTTCTAAG 58.581 38.462 17.69 0.00 0.00 2.18
3168 3250 1.985614 TGAGCCCCTCATGTGTCAG 59.014 57.895 0.00 0.00 35.39 3.51
3376 3497 5.042593 TGCAGCTTTTGACACAATTTACAG 58.957 37.500 0.00 0.00 0.00 2.74
3413 3534 9.210426 GCTAATGTTTATTGTTTGAGACATACG 57.790 33.333 0.00 0.00 38.26 3.06
3519 3641 6.662663 GGTATCTAGAGTTATATTCCGGTGGT 59.337 42.308 0.00 0.00 0.00 4.16
3520 3642 7.178097 GGTATCTAGAGTTATATTCCGGTGGTT 59.822 40.741 0.00 0.00 0.00 3.67
3521 3643 6.401047 TCTAGAGTTATATTCCGGTGGTTG 57.599 41.667 0.00 0.00 0.00 3.77
3522 3644 5.895534 TCTAGAGTTATATTCCGGTGGTTGT 59.104 40.000 0.00 0.00 0.00 3.32
3523 3645 4.766375 AGAGTTATATTCCGGTGGTTGTG 58.234 43.478 0.00 0.00 0.00 3.33
3524 3646 4.468510 AGAGTTATATTCCGGTGGTTGTGA 59.531 41.667 0.00 0.00 0.00 3.58
3525 3647 5.046159 AGAGTTATATTCCGGTGGTTGTGAA 60.046 40.000 0.00 0.00 0.00 3.18
3526 3648 5.562635 AGTTATATTCCGGTGGTTGTGAAA 58.437 37.500 0.00 0.00 0.00 2.69
3527 3649 5.413523 AGTTATATTCCGGTGGTTGTGAAAC 59.586 40.000 0.00 0.00 37.35 2.78
3541 3663 4.510452 TGTGAAACTTGCGATGCAGCAG 62.510 50.000 1.53 0.00 41.29 4.24
3744 3866 4.275810 ACTGCATAGCCAGTGATTCAATT 58.724 39.130 0.00 0.00 44.00 2.32
3757 5078 3.694072 TGATTCAATTAGGGCAGGTTTCG 59.306 43.478 0.00 0.00 0.00 3.46
3898 5219 6.771749 TCATTCATTCCTGGCAAAAACAAAAT 59.228 30.769 0.00 0.00 0.00 1.82
3901 5222 8.688747 TTCATTCCTGGCAAAAACAAAATATT 57.311 26.923 0.00 0.00 0.00 1.28
3902 5223 8.688747 TCATTCCTGGCAAAAACAAAATATTT 57.311 26.923 0.00 0.00 0.00 1.40
3903 5224 9.784531 TCATTCCTGGCAAAAACAAAATATTTA 57.215 25.926 0.01 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.277273 CAGCAGTTCTCCCATCACTCA 59.723 52.381 0.00 0.00 0.00 3.41
16 17 1.361204 TTCCATCAGCAGTTCTCCCA 58.639 50.000 0.00 0.00 0.00 4.37
17 18 2.295885 CATTCCATCAGCAGTTCTCCC 58.704 52.381 0.00 0.00 0.00 4.30
18 19 2.295885 CCATTCCATCAGCAGTTCTCC 58.704 52.381 0.00 0.00 0.00 3.71
82 86 0.949105 GCGGTGAAGAAGAAAGCGGA 60.949 55.000 0.00 0.00 35.48 5.54
100 104 3.126831 CAAGTACGAGGAATGAGATGGC 58.873 50.000 0.00 0.00 0.00 4.40
108 112 6.525578 TTAGTGATGTCAAGTACGAGGAAT 57.474 37.500 0.00 0.00 0.00 3.01
129 133 2.113562 GGTGTGCCCCGTGGTTTA 59.886 61.111 0.00 0.00 0.00 2.01
130 134 3.663815 TTGGTGTGCCCCGTGGTTT 62.664 57.895 0.00 0.00 0.00 3.27
158 162 3.576356 GGGTGATGGTCGCATGCG 61.576 66.667 33.61 33.61 41.35 4.73
431 436 4.931661 TCCAGACAAAGTAGAACTTCGT 57.068 40.909 0.00 0.00 37.47 3.85
432 437 5.529791 TCTTCCAGACAAAGTAGAACTTCG 58.470 41.667 0.00 0.00 37.47 3.79
433 438 7.971183 ATTCTTCCAGACAAAGTAGAACTTC 57.029 36.000 0.00 0.00 37.47 3.01
434 439 7.229506 CCAATTCTTCCAGACAAAGTAGAACTT 59.770 37.037 0.00 0.00 40.80 2.66
435 440 6.712547 CCAATTCTTCCAGACAAAGTAGAACT 59.287 38.462 0.00 0.00 0.00 3.01
436 441 6.710744 TCCAATTCTTCCAGACAAAGTAGAAC 59.289 38.462 0.00 0.00 0.00 3.01
437 442 6.837312 TCCAATTCTTCCAGACAAAGTAGAA 58.163 36.000 0.00 0.00 0.00 2.10
438 443 6.433847 TCCAATTCTTCCAGACAAAGTAGA 57.566 37.500 0.00 0.00 0.00 2.59
439 444 6.936900 TCTTCCAATTCTTCCAGACAAAGTAG 59.063 38.462 0.00 0.00 0.00 2.57
440 445 6.837312 TCTTCCAATTCTTCCAGACAAAGTA 58.163 36.000 0.00 0.00 0.00 2.24
441 446 5.694995 TCTTCCAATTCTTCCAGACAAAGT 58.305 37.500 0.00 0.00 0.00 2.66
442 447 6.639632 TTCTTCCAATTCTTCCAGACAAAG 57.360 37.500 0.00 0.00 0.00 2.77
443 448 6.072508 CGATTCTTCCAATTCTTCCAGACAAA 60.073 38.462 0.00 0.00 0.00 2.83
444 449 5.412594 CGATTCTTCCAATTCTTCCAGACAA 59.587 40.000 0.00 0.00 0.00 3.18
445 450 4.937620 CGATTCTTCCAATTCTTCCAGACA 59.062 41.667 0.00 0.00 0.00 3.41
446 451 4.333926 CCGATTCTTCCAATTCTTCCAGAC 59.666 45.833 0.00 0.00 0.00 3.51
447 452 4.517285 CCGATTCTTCCAATTCTTCCAGA 58.483 43.478 0.00 0.00 0.00 3.86
448 453 3.065925 GCCGATTCTTCCAATTCTTCCAG 59.934 47.826 0.00 0.00 0.00 3.86
449 454 3.016736 GCCGATTCTTCCAATTCTTCCA 58.983 45.455 0.00 0.00 0.00 3.53
450 455 2.359214 GGCCGATTCTTCCAATTCTTCC 59.641 50.000 0.00 0.00 0.00 3.46
451 456 2.032178 CGGCCGATTCTTCCAATTCTTC 59.968 50.000 24.07 0.00 0.00 2.87
452 457 2.017049 CGGCCGATTCTTCCAATTCTT 58.983 47.619 24.07 0.00 0.00 2.52
453 458 1.668419 CGGCCGATTCTTCCAATTCT 58.332 50.000 24.07 0.00 0.00 2.40
454 459 0.029433 GCGGCCGATTCTTCCAATTC 59.971 55.000 33.48 1.16 0.00 2.17
455 460 0.679640 TGCGGCCGATTCTTCCAATT 60.680 50.000 33.48 0.00 0.00 2.32
456 461 1.077787 TGCGGCCGATTCTTCCAAT 60.078 52.632 33.48 0.00 0.00 3.16
457 462 1.745115 CTGCGGCCGATTCTTCCAA 60.745 57.895 33.48 0.35 0.00 3.53
458 463 2.125147 CTGCGGCCGATTCTTCCA 60.125 61.111 33.48 14.68 0.00 3.53
459 464 2.897350 CCTGCGGCCGATTCTTCC 60.897 66.667 33.48 9.92 0.00 3.46
460 465 1.305930 AAACCTGCGGCCGATTCTTC 61.306 55.000 33.48 10.79 0.00 2.87
461 466 1.303317 AAACCTGCGGCCGATTCTT 60.303 52.632 33.48 11.85 0.00 2.52
462 467 1.745489 GAAACCTGCGGCCGATTCT 60.745 57.895 33.48 7.01 0.00 2.40
463 468 2.791927 GAAACCTGCGGCCGATTC 59.208 61.111 33.48 19.26 0.00 2.52
464 469 3.124921 CGAAACCTGCGGCCGATT 61.125 61.111 33.48 14.17 0.00 3.34
465 470 4.077184 TCGAAACCTGCGGCCGAT 62.077 61.111 33.48 7.72 0.00 4.18
469 474 3.479269 CTCGTCGAAACCTGCGGC 61.479 66.667 0.00 0.00 0.00 6.53
502 507 2.014033 TTTCCCCGAACCCTGGCTTT 62.014 55.000 0.00 0.00 0.00 3.51
511 516 2.739671 CCCGTCGTTTCCCCGAAC 60.740 66.667 0.00 0.00 38.80 3.95
514 519 4.303993 ACACCCGTCGTTTCCCCG 62.304 66.667 0.00 0.00 0.00 5.73
546 553 1.450312 CACCCATCTCTTCACCGCC 60.450 63.158 0.00 0.00 0.00 6.13
559 566 0.645496 TATCCCTAGCCTTCCACCCA 59.355 55.000 0.00 0.00 0.00 4.51
571 579 3.932562 ACCCATCTCCTCTCATATCCCTA 59.067 47.826 0.00 0.00 0.00 3.53
585 593 2.035632 AGATTCGTCCTCACCCATCTC 58.964 52.381 0.00 0.00 0.00 2.75
646 654 3.236604 GGTAACCTTACCGCTGCAA 57.763 52.632 0.00 0.00 43.30 4.08
665 673 0.178533 TTCCAAACCCGACGTTCACT 59.821 50.000 0.00 0.00 31.78 3.41
697 706 6.800072 AACCACACTCCATTTCCTTAAAAA 57.200 33.333 0.00 0.00 0.00 1.94
743 752 3.506067 GCTAGCTACCCTTTGCTCAAAAA 59.494 43.478 7.70 0.00 40.35 1.94
745 754 2.618045 GGCTAGCTACCCTTTGCTCAAA 60.618 50.000 15.72 0.00 40.35 2.69
748 757 0.833949 AGGCTAGCTACCCTTTGCTC 59.166 55.000 15.72 0.00 40.35 4.26
749 758 1.290134 AAGGCTAGCTACCCTTTGCT 58.710 50.000 15.72 0.00 38.24 3.91
750 759 2.130272 AAAGGCTAGCTACCCTTTGC 57.870 50.000 25.79 11.28 46.67 3.68
753 762 5.913946 ATCAATAAAGGCTAGCTACCCTT 57.086 39.130 15.72 13.71 43.07 3.95
754 763 5.913946 AATCAATAAAGGCTAGCTACCCT 57.086 39.130 15.72 1.36 0.00 4.34
755 764 6.094186 GCATAATCAATAAAGGCTAGCTACCC 59.906 42.308 15.72 0.00 0.00 3.69
756 765 6.655003 TGCATAATCAATAAAGGCTAGCTACC 59.345 38.462 15.72 0.00 0.00 3.18
757 766 7.148340 CCTGCATAATCAATAAAGGCTAGCTAC 60.148 40.741 15.72 0.00 0.00 3.58
758 767 6.881065 CCTGCATAATCAATAAAGGCTAGCTA 59.119 38.462 15.72 0.00 0.00 3.32
759 768 5.709164 CCTGCATAATCAATAAAGGCTAGCT 59.291 40.000 15.72 0.00 0.00 3.32
760 769 5.707298 TCCTGCATAATCAATAAAGGCTAGC 59.293 40.000 6.04 6.04 0.00 3.42
761 770 7.392673 ACATCCTGCATAATCAATAAAGGCTAG 59.607 37.037 0.00 0.00 0.00 3.42
762 771 7.233632 ACATCCTGCATAATCAATAAAGGCTA 58.766 34.615 0.00 0.00 0.00 3.93
763 772 6.073314 ACATCCTGCATAATCAATAAAGGCT 58.927 36.000 0.00 0.00 0.00 4.58
764 773 6.336842 ACATCCTGCATAATCAATAAAGGC 57.663 37.500 0.00 0.00 0.00 4.35
765 774 7.080099 CGAACATCCTGCATAATCAATAAAGG 58.920 38.462 0.00 0.00 0.00 3.11
766 775 7.588854 CACGAACATCCTGCATAATCAATAAAG 59.411 37.037 0.00 0.00 0.00 1.85
767 776 7.416817 CACGAACATCCTGCATAATCAATAAA 58.583 34.615 0.00 0.00 0.00 1.40
768 777 6.017192 CCACGAACATCCTGCATAATCAATAA 60.017 38.462 0.00 0.00 0.00 1.40
769 778 5.469760 CCACGAACATCCTGCATAATCAATA 59.530 40.000 0.00 0.00 0.00 1.90
770 779 4.276678 CCACGAACATCCTGCATAATCAAT 59.723 41.667 0.00 0.00 0.00 2.57
771 780 3.627123 CCACGAACATCCTGCATAATCAA 59.373 43.478 0.00 0.00 0.00 2.57
772 781 3.205338 CCACGAACATCCTGCATAATCA 58.795 45.455 0.00 0.00 0.00 2.57
773 782 3.206150 ACCACGAACATCCTGCATAATC 58.794 45.455 0.00 0.00 0.00 1.75
774 783 3.281727 ACCACGAACATCCTGCATAAT 57.718 42.857 0.00 0.00 0.00 1.28
775 784 2.779755 ACCACGAACATCCTGCATAA 57.220 45.000 0.00 0.00 0.00 1.90
776 785 2.779755 AACCACGAACATCCTGCATA 57.220 45.000 0.00 0.00 0.00 3.14
777 786 1.909700 AAACCACGAACATCCTGCAT 58.090 45.000 0.00 0.00 0.00 3.96
778 787 1.686355 AAAACCACGAACATCCTGCA 58.314 45.000 0.00 0.00 0.00 4.41
779 788 2.793278 AAAAACCACGAACATCCTGC 57.207 45.000 0.00 0.00 0.00 4.85
883 897 2.289002 GCAGAGATTTAAGCCCACGATG 59.711 50.000 0.00 0.00 0.00 3.84
922 936 7.030165 CCACGATATCTAATACCTAGCAAGTG 58.970 42.308 0.34 0.00 0.00 3.16
923 937 6.153000 CCCACGATATCTAATACCTAGCAAGT 59.847 42.308 0.34 0.00 0.00 3.16
924 938 6.565234 CCCACGATATCTAATACCTAGCAAG 58.435 44.000 0.34 0.00 0.00 4.01
925 939 5.105473 GCCCACGATATCTAATACCTAGCAA 60.105 44.000 0.34 0.00 0.00 3.91
926 940 4.401519 GCCCACGATATCTAATACCTAGCA 59.598 45.833 0.34 0.00 0.00 3.49
927 941 4.202131 GGCCCACGATATCTAATACCTAGC 60.202 50.000 0.34 0.00 0.00 3.42
928 942 5.517322 GGCCCACGATATCTAATACCTAG 57.483 47.826 0.34 0.00 0.00 3.02
972 986 1.443802 CCTCGTTTTTCCTCTCCTGC 58.556 55.000 0.00 0.00 0.00 4.85
975 989 1.019805 CGCCCTCGTTTTTCCTCTCC 61.020 60.000 0.00 0.00 0.00 3.71
982 996 2.076863 CATCTTCTCGCCCTCGTTTTT 58.923 47.619 0.00 0.00 36.96 1.94
983 997 1.275291 TCATCTTCTCGCCCTCGTTTT 59.725 47.619 0.00 0.00 36.96 2.43
984 998 0.895530 TCATCTTCTCGCCCTCGTTT 59.104 50.000 0.00 0.00 36.96 3.60
1845 1883 2.464865 GCGCAGAAGTCTATCACGATT 58.535 47.619 0.30 0.00 0.00 3.34
1958 2002 6.782082 TGTATAAGTGTGCTCTCATCTCTT 57.218 37.500 0.00 0.00 0.00 2.85
2016 2060 0.389296 CGATAACTGGTGTCCACGCA 60.389 55.000 0.00 0.00 0.00 5.24
2017 2061 1.082117 CCGATAACTGGTGTCCACGC 61.082 60.000 0.00 0.00 0.00 5.34
2018 2062 1.082117 GCCGATAACTGGTGTCCACG 61.082 60.000 0.00 0.00 0.00 4.94
2026 2070 1.123928 AGGAAGAGGCCGATAACTGG 58.876 55.000 0.00 0.00 0.00 4.00
2118 2172 2.579873 AGGCATGCTATTACCTGCAAG 58.420 47.619 18.92 0.00 42.74 4.01
2259 2325 2.405892 GCAACACTGCTTACAAGTGG 57.594 50.000 8.31 0.00 45.74 4.00
2322 2388 4.005650 AGAACATTGCAGAATGACATCGT 58.994 39.130 5.39 0.00 41.49 3.73
2496 2571 4.523083 TGTCCTACACCATATTGGAAAGC 58.477 43.478 0.00 0.00 40.96 3.51
2498 2573 4.947388 GCTTGTCCTACACCATATTGGAAA 59.053 41.667 0.00 0.00 40.96 3.13
2637 2719 1.901650 GCAAAAGCTCACCTCGGTCG 61.902 60.000 0.00 0.00 0.00 4.79
2747 2829 7.889873 TGAGAAATGGTAGTGAAAAGGAAAA 57.110 32.000 0.00 0.00 0.00 2.29
2751 2833 6.884280 ACTTGAGAAATGGTAGTGAAAAGG 57.116 37.500 0.00 0.00 0.00 3.11
2944 3026 7.800380 GCATCATCTTATTAATTCACACTTCCG 59.200 37.037 0.00 0.00 0.00 4.30
3082 3164 6.531503 AGCTAGCTAGTCACTAAACAATCA 57.468 37.500 17.69 0.00 0.00 2.57
3096 3178 6.961576 AGAAATGTACGAGTTAGCTAGCTAG 58.038 40.000 23.03 16.84 0.00 3.42
3097 3179 6.939132 AGAAATGTACGAGTTAGCTAGCTA 57.061 37.500 20.67 20.67 0.00 3.32
3098 3180 5.838531 AGAAATGTACGAGTTAGCTAGCT 57.161 39.130 23.12 23.12 0.00 3.32
3099 3181 6.142639 GCTTAGAAATGTACGAGTTAGCTAGC 59.857 42.308 6.62 6.62 0.00 3.42
3123 3205 4.213270 GGTAGGAAAGCAAAAACATTTGGC 59.787 41.667 3.75 0.00 32.78 4.52
3168 3250 9.216117 TGAGTAGAGGTTAATTAAAAGAACAGC 57.784 33.333 0.00 0.00 0.00 4.40
3376 3497 8.986477 ACAATAAACATTAGCTTCACCATTTC 57.014 30.769 0.00 0.00 0.00 2.17
3413 3534 9.038803 CCGTTGGGAGTAATTCTTATAACTTAC 57.961 37.037 0.00 0.00 34.06 2.34
3519 3641 1.600164 GCTGCATCGCAAGTTTCACAA 60.600 47.619 0.00 0.00 38.41 3.33
3520 3642 0.040157 GCTGCATCGCAAGTTTCACA 60.040 50.000 0.00 0.00 38.41 3.58
3521 3643 0.040157 TGCTGCATCGCAAGTTTCAC 60.040 50.000 0.00 0.00 38.41 3.18
3522 3644 0.239082 CTGCTGCATCGCAAGTTTCA 59.761 50.000 1.31 0.00 39.80 2.69
3523 3645 0.239347 ACTGCTGCATCGCAAGTTTC 59.761 50.000 1.31 0.00 39.80 2.78
3524 3646 0.039798 CACTGCTGCATCGCAAGTTT 60.040 50.000 1.31 0.00 39.80 2.66
3525 3647 0.886043 TCACTGCTGCATCGCAAGTT 60.886 50.000 1.31 0.00 39.80 2.66
3526 3648 1.296755 CTCACTGCTGCATCGCAAGT 61.297 55.000 1.31 0.00 39.80 3.16
3527 3649 1.296755 ACTCACTGCTGCATCGCAAG 61.297 55.000 1.31 0.00 39.80 4.01
3541 3663 5.203060 AGAACCTAGACTGAACAACTCAC 57.797 43.478 0.00 0.00 0.00 3.51
3744 3866 0.905809 TAGCACCGAAACCTGCCCTA 60.906 55.000 0.00 0.00 33.57 3.53
3757 5078 2.094026 CCCAAAGAAGCCAAATAGCACC 60.094 50.000 0.00 0.00 34.23 5.01
3797 5118 4.291249 AGAACCCCAAATTTAGGCTACTCA 59.709 41.667 0.00 0.00 0.00 3.41
3853 5174 3.066481 TGAGATCTTCAGATGCTGACTCG 59.934 47.826 0.00 0.00 40.46 4.18


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

AutoCloner maintained by Alex Coulton.