Multiple sequence alignment - TraesCS7B01G197100

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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 TraesCS7B01G197100 chr7B 100.000 2876 0 0 1 2876 339646664 339643789 0.000000e+00 5312
1 TraesCS7B01G197100 chr7B 98.344 483 7 1 18 499 162573796 162573314 0.000000e+00 846
2 TraesCS7B01G197100 chr7B 98.732 473 6 0 18 490 49557883 49557411 0.000000e+00 841
3 TraesCS7B01G197100 chr7B 90.391 614 23 7 18 613 629568872 629568277 0.000000e+00 774
4 TraesCS7B01G197100 chr7D 92.526 1659 72 14 718 2354 296514921 296513293 0.000000e+00 2329
5 TraesCS7B01G197100 chr7D 90.274 329 17 6 2377 2691 296513312 296512985 1.590000e-112 416
6 TraesCS7B01G197100 chr7D 92.241 116 8 1 2762 2876 296512939 296512824 2.290000e-36 163
7 TraesCS7B01G197100 chrUn 91.401 1663 90 17 718 2348 116439780 116438139 0.000000e+00 2230
8 TraesCS7B01G197100 chrUn 92.430 502 25 4 2387 2876 116438136 116437636 0.000000e+00 704
9 TraesCS7B01G197100 chr3B 97.342 602 9 4 18 614 302582509 302583108 0.000000e+00 1016
10 TraesCS7B01G197100 chr3B 98.498 466 7 0 18 483 823642710 823642245 0.000000e+00 822
11 TraesCS7B01G197100 chr3B 95.946 148 0 2 461 602 558563313 558563460 4.790000e-58 235
12 TraesCS7B01G197100 chr3B 93.496 123 3 5 603 720 583374985 583374863 8.190000e-41 178
13 TraesCS7B01G197100 chr3A 98.934 563 6 0 18 580 125438149 125438711 0.000000e+00 1007
14 TraesCS7B01G197100 chr3A 99.154 473 4 0 18 490 216706044 216706516 0.000000e+00 852
15 TraesCS7B01G197100 chr2B 97.099 586 9 5 18 603 500991497 500990920 0.000000e+00 981
16 TraesCS7B01G197100 chr2B 94.828 116 3 3 603 715 505214058 505213943 8.190000e-41 178
17 TraesCS7B01G197100 chr5A 98.464 521 7 1 18 538 118352447 118351928 0.000000e+00 917
18 TraesCS7B01G197100 chr1A 98.109 476 8 1 18 492 583909369 583908894 0.000000e+00 828
19 TraesCS7B01G197100 chr2A 80.480 333 32 18 281 584 773202659 773202331 1.040000e-54 224
20 TraesCS7B01G197100 chr2A 94.958 119 3 3 603 718 82188264 82188146 1.760000e-42 183
21 TraesCS7B01G197100 chr7A 94.828 116 3 3 603 715 44657519 44657404 8.190000e-41 178
22 TraesCS7B01G197100 chr5B 95.575 113 2 3 603 712 709520857 709520969 8.190000e-41 178
23 TraesCS7B01G197100 chr1B 95.575 113 2 3 603 712 681393405 681393517 8.190000e-41 178
24 TraesCS7B01G197100 chr6A 94.690 113 3 3 603 712 598863055 598863167 3.810000e-39 172
25 TraesCS7B01G197100 chr4D 94.690 113 3 3 603 712 221295785 221295897 3.810000e-39 172
26 TraesCS7B01G197100 chr4B 92.683 123 4 5 603 720 283253314 283253192 3.810000e-39 172
27 TraesCS7B01G197100 chr4B 93.333 120 3 5 606 720 365086754 365086635 3.810000e-39 172
28 TraesCS7B01G197100 chr4B 92.683 123 4 5 603 720 607858970 607858848 3.810000e-39 172
29 TraesCS7B01G197100 chr4B 92.000 125 5 5 603 723 240981549 240981426 1.370000e-38 171
30 TraesCS7B01G197100 chr2D 94.690 113 3 3 603 712 157206778 157206890 3.810000e-39 172


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 TraesCS7B01G197100 chr7B 339643789 339646664 2875 True 5312.000000 5312 100.000000 1 2876 1 chr7B.!!$R3 2875
1 TraesCS7B01G197100 chr7B 629568277 629568872 595 True 774.000000 774 90.391000 18 613 1 chr7B.!!$R4 595
2 TraesCS7B01G197100 chr7D 296512824 296514921 2097 True 969.333333 2329 91.680333 718 2876 3 chr7D.!!$R1 2158
3 TraesCS7B01G197100 chrUn 116437636 116439780 2144 True 1467.000000 2230 91.915500 718 2876 2 chrUn.!!$R1 2158
4 TraesCS7B01G197100 chr3B 302582509 302583108 599 False 1016.000000 1016 97.342000 18 614 1 chr3B.!!$F1 596
5 TraesCS7B01G197100 chr3A 125438149 125438711 562 False 1007.000000 1007 98.934000 18 580 1 chr3A.!!$F1 562
6 TraesCS7B01G197100 chr2B 500990920 500991497 577 True 981.000000 981 97.099000 18 603 1 chr2B.!!$R1 585
7 TraesCS7B01G197100 chr5A 118351928 118352447 519 True 917.000000 917 98.464000 18 538 1 chr5A.!!$R1 520

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
604 627 0.105039 CTACCGAAGCAAGGCCCTAG 59.895 60.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2375 2434 0.539986 TCAAGATTGGCGTACCTCCC 59.46 55.0 0.0 0.0 36.63 4.3 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
259 260 1.295423 CGACGGGTGAAGTTGGGAT 59.705 57.895 0.00 0.00 0.00 3.85
604 627 0.105039 CTACCGAAGCAAGGCCCTAG 59.895 60.000 0.00 0.00 0.00 3.02
609 632 2.567615 CCGAAGCAAGGCCCTAGTATAT 59.432 50.000 0.00 0.00 0.00 0.86
614 637 6.321690 CGAAGCAAGGCCCTAGTATATATAGT 59.678 42.308 0.00 5.43 0.00 2.12
615 638 7.501559 CGAAGCAAGGCCCTAGTATATATAGTA 59.498 40.741 0.00 7.03 0.00 1.82
616 639 8.536340 AAGCAAGGCCCTAGTATATATAGTAC 57.464 38.462 0.00 0.00 0.00 2.73
617 640 7.068061 AGCAAGGCCCTAGTATATATAGTACC 58.932 42.308 0.00 4.51 0.00 3.34
618 641 6.837568 GCAAGGCCCTAGTATATATAGTACCA 59.162 42.308 0.00 0.00 0.00 3.25
619 642 7.201893 GCAAGGCCCTAGTATATATAGTACCAC 60.202 44.444 0.00 3.25 0.00 4.16
620 643 7.535390 AGGCCCTAGTATATATAGTACCACA 57.465 40.000 0.00 0.00 0.00 4.17
621 644 8.127442 AGGCCCTAGTATATATAGTACCACAT 57.873 38.462 0.00 0.00 0.00 3.21
622 645 8.005388 AGGCCCTAGTATATATAGTACCACATG 58.995 40.741 0.00 0.00 0.00 3.21
623 646 7.255871 GGCCCTAGTATATATAGTACCACATGC 60.256 44.444 3.54 1.90 0.00 4.06
624 647 7.506261 GCCCTAGTATATATAGTACCACATGCT 59.494 40.741 3.54 0.00 0.00 3.79
636 659 7.455641 AGTACCACATGCTAGTATATGAGAC 57.544 40.000 0.06 0.00 0.00 3.36
637 660 7.004691 AGTACCACATGCTAGTATATGAGACA 58.995 38.462 0.06 0.00 0.00 3.41
638 661 6.924913 ACCACATGCTAGTATATGAGACAT 57.075 37.500 0.06 0.00 0.00 3.06
639 662 6.695429 ACCACATGCTAGTATATGAGACATG 58.305 40.000 0.06 0.74 39.38 3.21
640 663 6.268617 ACCACATGCTAGTATATGAGACATGT 59.731 38.462 0.00 0.00 45.39 3.21
642 665 6.695429 ACATGCTAGTATATGAGACATGTGG 58.305 40.000 1.15 0.00 43.50 4.17
643 666 5.728637 TGCTAGTATATGAGACATGTGGG 57.271 43.478 1.15 0.00 0.00 4.61
644 667 4.528206 TGCTAGTATATGAGACATGTGGGG 59.472 45.833 1.15 0.00 0.00 4.96
645 668 4.528596 GCTAGTATATGAGACATGTGGGGT 59.471 45.833 1.15 0.00 0.00 4.95
646 669 5.715279 GCTAGTATATGAGACATGTGGGGTA 59.285 44.000 1.15 0.00 0.00 3.69
647 670 6.210784 GCTAGTATATGAGACATGTGGGGTAA 59.789 42.308 1.15 0.00 0.00 2.85
648 671 6.420913 AGTATATGAGACATGTGGGGTAAC 57.579 41.667 1.15 0.00 0.00 2.50
649 672 6.143915 AGTATATGAGACATGTGGGGTAACT 58.856 40.000 1.15 0.00 0.00 2.24
650 673 7.302948 AGTATATGAGACATGTGGGGTAACTA 58.697 38.462 1.15 0.00 0.00 2.24
651 674 4.755266 ATGAGACATGTGGGGTAACTAC 57.245 45.455 1.15 0.00 0.00 2.73
652 675 2.835764 TGAGACATGTGGGGTAACTACC 59.164 50.000 1.15 0.00 45.71 3.18
669 692 1.754745 CCACCGGGTGATAGGATGG 59.245 63.158 28.36 5.14 35.23 3.51
670 693 0.762842 CCACCGGGTGATAGGATGGA 60.763 60.000 28.36 0.00 35.23 3.41
671 694 1.352083 CACCGGGTGATAGGATGGAT 58.648 55.000 22.77 0.00 35.23 3.41
672 695 1.699634 CACCGGGTGATAGGATGGATT 59.300 52.381 22.77 0.00 35.23 3.01
673 696 2.106511 CACCGGGTGATAGGATGGATTT 59.893 50.000 22.77 0.00 35.23 2.17
674 697 2.372172 ACCGGGTGATAGGATGGATTTC 59.628 50.000 6.32 0.00 0.00 2.17
675 698 2.290323 CCGGGTGATAGGATGGATTTCC 60.290 54.545 0.00 0.00 35.90 3.13
676 699 2.290323 CGGGTGATAGGATGGATTTCCC 60.290 54.545 0.00 0.00 36.35 3.97
677 700 2.989571 GGGTGATAGGATGGATTTCCCT 59.010 50.000 0.00 0.00 36.35 4.20
678 701 4.175962 GGGTGATAGGATGGATTTCCCTA 58.824 47.826 0.00 0.00 36.35 3.53
679 702 4.790790 GGGTGATAGGATGGATTTCCCTAT 59.209 45.833 0.00 0.00 43.77 2.57
680 703 5.970640 GGGTGATAGGATGGATTTCCCTATA 59.029 44.000 0.00 0.00 41.82 1.31
681 704 6.621514 GGGTGATAGGATGGATTTCCCTATAT 59.378 42.308 0.00 0.00 41.82 0.86
682 705 7.794683 GGGTGATAGGATGGATTTCCCTATATA 59.205 40.741 0.00 0.00 41.82 0.86
683 706 9.398921 GGTGATAGGATGGATTTCCCTATATAT 57.601 37.037 0.00 0.00 41.82 0.86
773 796 2.774234 AGCTGCCAGTACCTCATATTGT 59.226 45.455 0.00 0.00 0.00 2.71
774 797 3.134458 GCTGCCAGTACCTCATATTGTC 58.866 50.000 0.00 0.00 0.00 3.18
775 798 3.733337 CTGCCAGTACCTCATATTGTCC 58.267 50.000 0.00 0.00 0.00 4.02
776 799 3.384168 TGCCAGTACCTCATATTGTCCT 58.616 45.455 0.00 0.00 0.00 3.85
777 800 3.780294 TGCCAGTACCTCATATTGTCCTT 59.220 43.478 0.00 0.00 0.00 3.36
778 801 4.130118 GCCAGTACCTCATATTGTCCTTG 58.870 47.826 0.00 0.00 0.00 3.61
779 802 4.384208 GCCAGTACCTCATATTGTCCTTGT 60.384 45.833 0.00 0.00 0.00 3.16
780 803 5.745227 CCAGTACCTCATATTGTCCTTGTT 58.255 41.667 0.00 0.00 0.00 2.83
781 804 5.586243 CCAGTACCTCATATTGTCCTTGTTG 59.414 44.000 0.00 0.00 0.00 3.33
825 848 1.363744 GTCATCCTCAAACTGCTCCG 58.636 55.000 0.00 0.00 0.00 4.63
909 937 9.828852 ACTTGTCATCGCGTATTTTAATAAAAA 57.171 25.926 5.77 0.00 38.87 1.94
1007 1038 3.254166 AGTTGTTGTCCATTCATGTCTGC 59.746 43.478 0.00 0.00 0.00 4.26
1010 1041 2.408271 TGTCCATTCATGTCTGCTCC 57.592 50.000 0.00 0.00 0.00 4.70
1032 1063 4.838486 GCGCCTCTCGTCGTCCTG 62.838 72.222 0.00 0.00 41.07 3.86
1101 1132 1.010125 CAAACACGGCAGGTTCACG 60.010 57.895 0.00 0.00 0.00 4.35
1137 1168 2.511600 GCGCACGCCACCTTCTAT 60.512 61.111 0.30 0.00 34.56 1.98
1247 1278 2.663478 GCACCGCGATGTTCAACGA 61.663 57.895 8.23 0.00 0.00 3.85
1482 1513 1.537814 TTGTGCCCATCTCGTACCGT 61.538 55.000 0.00 0.00 0.00 4.83
1519 1550 6.619801 AGCACACGTAAGATTTCTCTTTTT 57.380 33.333 0.00 0.00 41.91 1.94
1557 1588 5.173131 CAGCTGGTTGAAAATTTTGTACGTC 59.827 40.000 8.47 0.00 0.00 4.34
1577 1618 3.958822 GATGCAGTGTGCCTTGCGC 62.959 63.158 0.00 0.00 44.23 6.09
1653 1694 4.651008 GTGACGAACGTGGGCGGA 62.651 66.667 4.19 0.00 43.45 5.54
1797 1838 2.186903 GTCATGACCGGCGACCAT 59.813 61.111 15.31 8.41 0.00 3.55
1845 1886 2.113139 CGGGACTGGCAGTTTGGT 59.887 61.111 22.98 0.00 0.00 3.67
1887 1928 5.485209 AGAACTTCTAACCACCCTGTAAG 57.515 43.478 0.00 0.00 0.00 2.34
1889 1930 5.785940 AGAACTTCTAACCACCCTGTAAGAT 59.214 40.000 0.00 0.00 34.07 2.40
1910 1951 2.437359 GCTAGCCAGCCAGGTGTG 60.437 66.667 2.29 0.00 42.37 3.82
1916 1957 1.926511 GCCAGCCAGGTGTGAATTCG 61.927 60.000 0.04 0.00 40.61 3.34
1946 1987 0.534203 TGTTTTGTGTCCCTCGGAGC 60.534 55.000 0.00 0.00 29.39 4.70
1975 2016 1.069513 CCAACTCCAACAGGACGTACA 59.930 52.381 0.00 0.00 0.00 2.90
1978 2019 1.968493 ACTCCAACAGGACGTACATGT 59.032 47.619 2.69 2.69 45.64 3.21
2006 2047 5.885465 AGAAACAAGATTCCCTCTGACAAT 58.115 37.500 0.00 0.00 33.29 2.71
2014 2055 3.423539 TCCCTCTGACAATTGACAAGG 57.576 47.619 13.59 18.54 0.00 3.61
2032 2086 7.954835 TGACAAGGAACAAAGAATGAATGAAT 58.045 30.769 0.00 0.00 0.00 2.57
2060 2114 1.867233 GACTTGTGTCTGACGTTGCAT 59.133 47.619 2.98 0.00 39.94 3.96
2096 2151 0.538287 GCTGCACCCAGGAAAGAACT 60.538 55.000 0.00 0.00 39.54 3.01
2144 2199 4.980805 GCGGCACAGAACGGGACA 62.981 66.667 0.00 0.00 0.00 4.02
2148 2203 1.296715 GCACAGAACGGGACATCCT 59.703 57.895 0.00 0.00 35.95 3.24
2187 2242 5.221028 GGACACACACAACTTCATCATCAAA 60.221 40.000 0.00 0.00 0.00 2.69
2192 2247 3.910170 CACAACTTCATCATCAAACAGCG 59.090 43.478 0.00 0.00 0.00 5.18
2259 2314 4.430007 CTTTCCTCCACGATTCGATGTTA 58.570 43.478 13.95 0.00 0.00 2.41
2318 2377 3.108289 CGCGCAGTCTGTGGACAG 61.108 66.667 15.06 0.00 44.36 3.51
2345 2404 1.876714 CGGCGTCAATGGAGGTACG 60.877 63.158 0.00 0.00 38.34 3.67
2378 2437 3.608912 TTTTTGAGGGAGGGAGGGA 57.391 52.632 0.00 0.00 0.00 4.20
2379 2438 1.372501 TTTTTGAGGGAGGGAGGGAG 58.627 55.000 0.00 0.00 0.00 4.30
2380 2439 0.550147 TTTTGAGGGAGGGAGGGAGG 60.550 60.000 0.00 0.00 0.00 4.30
2381 2440 1.761780 TTTGAGGGAGGGAGGGAGGT 61.762 60.000 0.00 0.00 0.00 3.85
2382 2441 0.858598 TTGAGGGAGGGAGGGAGGTA 60.859 60.000 0.00 0.00 0.00 3.08
2383 2442 1.233659 GAGGGAGGGAGGGAGGTAC 59.766 68.421 0.00 0.00 0.00 3.34
2419 2478 1.069049 GCCTTTGCTCCACACAAACAT 59.931 47.619 0.00 0.00 33.62 2.71
2473 2532 6.139679 AGAAAATTATGGTTGGGACTCTCA 57.860 37.500 0.00 0.00 0.00 3.27
2487 2546 1.646447 ACTCTCATCCCTCCACTACCA 59.354 52.381 0.00 0.00 0.00 3.25
2510 2569 3.321396 TGTTGCAATGCTGATTTGGAAGA 59.679 39.130 6.82 0.00 35.48 2.87
2514 2573 4.751098 TGCAATGCTGATTTGGAAGAAAAC 59.249 37.500 6.82 0.00 0.00 2.43
2522 2581 6.346040 GCTGATTTGGAAGAAAACAATCAACG 60.346 38.462 0.00 0.00 0.00 4.10
2593 2663 5.167845 TCAAAACTGTTTTCTGTTGGAAGC 58.832 37.500 15.17 0.00 40.78 3.86
2618 2688 1.272807 GGTAACCCTAGCTCACCACA 58.727 55.000 0.00 0.00 0.00 4.17
2627 2697 4.141620 CCCTAGCTCACCACATATCAAACT 60.142 45.833 0.00 0.00 0.00 2.66
2739 2818 3.383505 CCATCGATTATGACGCCCCTATA 59.616 47.826 0.00 0.00 37.86 1.31
2825 2905 9.294030 CAAATTTAAGAGGTACTTGAATGCATC 57.706 33.333 0.00 0.00 41.67 3.91
2827 2907 8.757982 ATTTAAGAGGTACTTGAATGCATCAT 57.242 30.769 0.00 0.00 41.21 2.45
2830 2910 3.470709 AGGTACTTGAATGCATCATCCG 58.529 45.455 0.00 0.00 38.03 4.18
2851 2931 5.008217 TCCGTAAAAACTCATCAAACAGTGG 59.992 40.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.174783 CGACGGGGGATAGATACAGG 58.825 60.000 0.00 0.00 0.00 4.00
1 2 1.811359 GTCGACGGGGGATAGATACAG 59.189 57.143 0.00 0.00 0.00 2.74
3 4 0.801251 CGTCGACGGGGGATAGATAC 59.199 60.000 29.70 0.00 35.37 2.24
5 6 0.888285 GTCGTCGACGGGGGATAGAT 60.888 60.000 35.05 0.00 40.29 1.98
6 7 1.524621 GTCGTCGACGGGGGATAGA 60.525 63.158 35.05 12.79 40.29 1.98
7 8 1.783031 CTGTCGTCGACGGGGGATAG 61.783 65.000 35.05 20.15 40.29 2.08
8 9 1.820906 CTGTCGTCGACGGGGGATA 60.821 63.158 35.05 14.35 40.29 2.59
9 10 3.138798 CTGTCGTCGACGGGGGAT 61.139 66.667 35.05 0.00 40.29 3.85
10 11 4.648626 ACTGTCGTCGACGGGGGA 62.649 66.667 35.05 15.53 42.66 4.81
11 12 4.415332 CACTGTCGTCGACGGGGG 62.415 72.222 35.05 25.25 42.66 5.40
13 14 4.039357 AGCACTGTCGTCGACGGG 62.039 66.667 35.05 25.88 42.66 5.28
14 15 2.801162 CAGCACTGTCGTCGACGG 60.801 66.667 35.05 28.43 43.83 4.79
15 16 3.461982 GCAGCACTGTCGTCGACG 61.462 66.667 31.30 31.30 41.45 5.12
16 17 3.461982 CGCAGCACTGTCGTCGAC 61.462 66.667 18.51 18.51 0.00 4.20
124 125 3.618750 GAACCCCGTCCGACACCA 61.619 66.667 0.00 0.00 0.00 4.17
259 260 4.794439 CGTCGCCGCATCTCACCA 62.794 66.667 0.00 0.00 0.00 4.17
614 637 7.451566 ACATGTCTCATATACTAGCATGTGGTA 59.548 37.037 16.56 0.00 42.26 3.25
615 638 6.268617 ACATGTCTCATATACTAGCATGTGGT 59.731 38.462 16.56 0.00 42.26 4.16
616 639 6.695429 ACATGTCTCATATACTAGCATGTGG 58.305 40.000 16.56 0.00 42.26 4.17
618 641 6.295518 CCCACATGTCTCATATACTAGCATGT 60.296 42.308 0.00 14.02 43.91 3.21
619 642 6.104665 CCCACATGTCTCATATACTAGCATG 58.895 44.000 0.00 0.00 38.41 4.06
620 643 5.188555 CCCCACATGTCTCATATACTAGCAT 59.811 44.000 0.00 0.00 0.00 3.79
621 644 4.528206 CCCCACATGTCTCATATACTAGCA 59.472 45.833 0.00 0.00 0.00 3.49
622 645 4.528596 ACCCCACATGTCTCATATACTAGC 59.471 45.833 0.00 0.00 0.00 3.42
623 646 7.451877 AGTTACCCCACATGTCTCATATACTAG 59.548 40.741 0.00 0.00 0.00 2.57
624 647 7.302948 AGTTACCCCACATGTCTCATATACTA 58.697 38.462 0.00 0.00 0.00 1.82
625 648 6.143915 AGTTACCCCACATGTCTCATATACT 58.856 40.000 0.00 0.00 0.00 2.12
626 649 6.420913 AGTTACCCCACATGTCTCATATAC 57.579 41.667 0.00 0.00 0.00 1.47
627 650 6.495872 GGTAGTTACCCCACATGTCTCATATA 59.504 42.308 0.00 0.00 40.53 0.86
628 651 5.307196 GGTAGTTACCCCACATGTCTCATAT 59.693 44.000 0.00 0.00 40.53 1.78
629 652 4.652421 GGTAGTTACCCCACATGTCTCATA 59.348 45.833 0.00 0.00 40.53 2.15
630 653 3.454812 GGTAGTTACCCCACATGTCTCAT 59.545 47.826 0.00 0.00 40.53 2.90
631 654 2.835764 GGTAGTTACCCCACATGTCTCA 59.164 50.000 0.00 0.00 40.53 3.27
632 655 2.835764 TGGTAGTTACCCCACATGTCTC 59.164 50.000 0.00 0.00 45.87 3.36
633 656 2.910544 TGGTAGTTACCCCACATGTCT 58.089 47.619 0.00 0.00 45.87 3.41
640 663 1.613035 CCCGGTGGTAGTTACCCCA 60.613 63.158 0.00 0.00 45.87 4.96
641 664 1.613332 ACCCGGTGGTAGTTACCCC 60.613 63.158 0.00 5.97 45.45 4.95
642 665 0.904394 TCACCCGGTGGTAGTTACCC 60.904 60.000 17.76 0.00 45.57 3.69
643 666 1.197812 ATCACCCGGTGGTAGTTACC 58.802 55.000 17.76 1.25 45.57 2.85
644 667 2.363359 CCTATCACCCGGTGGTAGTTAC 59.637 54.545 28.64 0.00 45.57 2.50
645 668 2.244510 TCCTATCACCCGGTGGTAGTTA 59.755 50.000 28.64 17.64 45.57 2.24
646 669 1.007479 TCCTATCACCCGGTGGTAGTT 59.993 52.381 28.64 9.25 45.57 2.24
647 670 0.632835 TCCTATCACCCGGTGGTAGT 59.367 55.000 28.64 12.18 45.57 2.73
648 671 1.618837 CATCCTATCACCCGGTGGTAG 59.381 57.143 25.67 25.67 45.57 3.18
649 672 1.712056 CATCCTATCACCCGGTGGTA 58.288 55.000 17.76 13.93 45.57 3.25
651 674 0.762842 TCCATCCTATCACCCGGTGG 60.763 60.000 17.76 1.28 33.87 4.61
652 675 1.352083 ATCCATCCTATCACCCGGTG 58.648 55.000 11.73 11.73 34.45 4.94
653 676 2.118403 AATCCATCCTATCACCCGGT 57.882 50.000 0.00 0.00 0.00 5.28
654 677 2.290323 GGAAATCCATCCTATCACCCGG 60.290 54.545 0.00 0.00 36.50 5.73
655 678 2.290323 GGGAAATCCATCCTATCACCCG 60.290 54.545 1.22 0.00 39.57 5.28
656 679 2.989571 AGGGAAATCCATCCTATCACCC 59.010 50.000 1.22 0.00 39.57 4.61
657 680 7.698163 ATATAGGGAAATCCATCCTATCACC 57.302 40.000 1.22 0.00 41.46 4.02
706 729 9.965824 CGCTGACCTGGAAATAATTAAATAAAT 57.034 29.630 0.00 0.00 0.00 1.40
707 730 8.962679 ACGCTGACCTGGAAATAATTAAATAAA 58.037 29.630 0.00 0.00 0.00 1.40
708 731 8.514330 ACGCTGACCTGGAAATAATTAAATAA 57.486 30.769 0.00 0.00 0.00 1.40
709 732 8.514330 AACGCTGACCTGGAAATAATTAAATA 57.486 30.769 0.00 0.00 0.00 1.40
710 733 7.404671 AACGCTGACCTGGAAATAATTAAAT 57.595 32.000 0.00 0.00 0.00 1.40
711 734 6.827586 AACGCTGACCTGGAAATAATTAAA 57.172 33.333 0.00 0.00 0.00 1.52
712 735 6.616947 CAAACGCTGACCTGGAAATAATTAA 58.383 36.000 0.00 0.00 0.00 1.40
713 736 5.392595 GCAAACGCTGACCTGGAAATAATTA 60.393 40.000 0.00 0.00 0.00 1.40
714 737 4.618227 GCAAACGCTGACCTGGAAATAATT 60.618 41.667 0.00 0.00 0.00 1.40
715 738 3.119495 GCAAACGCTGACCTGGAAATAAT 60.119 43.478 0.00 0.00 0.00 1.28
716 739 2.227865 GCAAACGCTGACCTGGAAATAA 59.772 45.455 0.00 0.00 0.00 1.40
720 743 0.884704 GAGCAAACGCTGACCTGGAA 60.885 55.000 0.00 0.00 40.78 3.53
773 796 1.311859 CAGACTGCAAGCAACAAGGA 58.688 50.000 0.00 0.00 37.60 3.36
774 797 1.027357 ACAGACTGCAAGCAACAAGG 58.973 50.000 1.25 0.00 37.60 3.61
775 798 2.855963 CAAACAGACTGCAAGCAACAAG 59.144 45.455 1.25 0.00 37.60 3.16
776 799 2.230992 ACAAACAGACTGCAAGCAACAA 59.769 40.909 1.25 0.00 37.60 2.83
777 800 1.818060 ACAAACAGACTGCAAGCAACA 59.182 42.857 1.25 0.00 37.60 3.33
778 801 2.098117 AGACAAACAGACTGCAAGCAAC 59.902 45.455 1.25 0.00 37.60 4.17
779 802 2.368439 AGACAAACAGACTGCAAGCAA 58.632 42.857 1.25 0.00 37.60 3.91
780 803 2.042686 AGACAAACAGACTGCAAGCA 57.957 45.000 1.25 0.00 37.60 3.91
781 804 2.724349 CAAGACAAACAGACTGCAAGC 58.276 47.619 1.25 0.00 37.60 4.01
825 848 3.043635 CATGCAATGCAGTTAGACGTC 57.956 47.619 14.98 7.70 43.65 4.34
909 937 5.796424 AGTTTTCTGATGCATTGTCCTTT 57.204 34.783 0.00 0.00 0.00 3.11
911 939 8.757982 ATAATAGTTTTCTGATGCATTGTCCT 57.242 30.769 0.00 0.00 0.00 3.85
1247 1278 4.003788 CCCCGCAAGTCTCACCGT 62.004 66.667 0.00 0.00 0.00 4.83
1287 1318 3.314331 CACCACTCCGGGCTGTCT 61.314 66.667 0.00 0.00 40.22 3.41
1335 1366 2.737376 GGACACAGGTTCGTCGCC 60.737 66.667 0.00 0.00 32.74 5.54
1350 1381 2.606519 AGCTGGTAGTTGGGCGGA 60.607 61.111 0.00 0.00 0.00 5.54
1482 1513 3.055110 TGCTACCGTACGCACCGA 61.055 61.111 10.49 0.00 0.00 4.69
1577 1618 4.918201 GGATCCCGCCCAGCTTCG 62.918 72.222 0.00 0.00 0.00 3.79
1797 1838 2.661537 CAGGACGTGTGCTTGCGA 60.662 61.111 0.00 0.00 0.00 5.10
1842 1883 1.460497 TGCCTGGTAGGTGACACCA 60.460 57.895 26.30 9.81 43.82 4.17
1845 1886 2.221299 GGGTGCCTGGTAGGTGACA 61.221 63.158 0.00 0.00 37.80 3.58
1910 1951 5.107065 ACAAAACAGGAGATTCGACGAATTC 60.107 40.000 23.06 19.56 31.89 2.17
1916 1957 3.186613 GGACACAAAACAGGAGATTCGAC 59.813 47.826 0.00 0.00 0.00 4.20
1946 1987 3.691118 CCTGTTGGAGTTGGACATACATG 59.309 47.826 0.00 0.00 34.57 3.21
1975 2016 5.388654 AGGGAATCTTGTTTCTTGACACAT 58.611 37.500 0.00 0.00 0.00 3.21
1978 2019 5.065914 CAGAGGGAATCTTGTTTCTTGACA 58.934 41.667 0.00 0.00 35.47 3.58
2006 2047 7.345422 TCATTCATTCTTTGTTCCTTGTCAA 57.655 32.000 0.00 0.00 0.00 3.18
2050 2104 2.672651 CCCAGCCATGCAACGTCA 60.673 61.111 0.00 0.00 0.00 4.35
2054 2108 2.103339 AAAGTGCCCAGCCATGCAAC 62.103 55.000 0.00 0.00 39.57 4.17
2060 2114 2.277591 GCATGAAAGTGCCCAGCCA 61.278 57.895 0.00 0.00 39.18 4.75
2096 2151 5.607477 CCCGGCTATGTCTAATTGTTTCTA 58.393 41.667 0.00 0.00 0.00 2.10
2128 2183 2.047274 ATGTCCCGTTCTGTGCCG 60.047 61.111 0.00 0.00 0.00 5.69
2144 2199 2.635915 TCCAACTCCAACGTTACAGGAT 59.364 45.455 0.00 0.00 0.00 3.24
2148 2203 2.093606 TGTGTCCAACTCCAACGTTACA 60.094 45.455 0.00 0.00 0.00 2.41
2187 2242 2.842462 TGGTGGTGTCCTCGCTGT 60.842 61.111 0.00 0.00 0.00 4.40
2192 2247 2.430367 GGTGGTGGTGGTGTCCTC 59.570 66.667 0.00 0.00 0.00 3.71
2286 2345 2.721167 CGCGGGAAGGAGGATCACA 61.721 63.158 0.00 0.00 36.25 3.58
2360 2419 1.372501 CTCCCTCCCTCCCTCAAAAA 58.627 55.000 0.00 0.00 0.00 1.94
2361 2420 0.550147 CCTCCCTCCCTCCCTCAAAA 60.550 60.000 0.00 0.00 0.00 2.44
2362 2421 1.082954 CCTCCCTCCCTCCCTCAAA 59.917 63.158 0.00 0.00 0.00 2.69
2363 2422 0.858598 TACCTCCCTCCCTCCCTCAA 60.859 60.000 0.00 0.00 0.00 3.02
2364 2423 1.230853 TACCTCCCTCCCTCCCTCA 60.231 63.158 0.00 0.00 0.00 3.86
2365 2424 1.233659 GTACCTCCCTCCCTCCCTC 59.766 68.421 0.00 0.00 0.00 4.30
2366 2425 2.702302 CGTACCTCCCTCCCTCCCT 61.702 68.421 0.00 0.00 0.00 4.20
2367 2426 2.123382 CGTACCTCCCTCCCTCCC 60.123 72.222 0.00 0.00 0.00 4.30
2368 2427 2.838693 GCGTACCTCCCTCCCTCC 60.839 72.222 0.00 0.00 0.00 4.30
2369 2428 2.838693 GGCGTACCTCCCTCCCTC 60.839 72.222 0.00 0.00 0.00 4.30
2370 2429 2.547123 ATTGGCGTACCTCCCTCCCT 62.547 60.000 0.00 0.00 36.63 4.20
2371 2430 2.041206 GATTGGCGTACCTCCCTCCC 62.041 65.000 0.00 0.00 36.63 4.30
2372 2431 1.049289 AGATTGGCGTACCTCCCTCC 61.049 60.000 0.00 0.00 36.63 4.30
2373 2432 0.831307 AAGATTGGCGTACCTCCCTC 59.169 55.000 0.00 0.00 36.63 4.30
2374 2433 0.541863 CAAGATTGGCGTACCTCCCT 59.458 55.000 0.00 0.00 36.63 4.20
2375 2434 0.539986 TCAAGATTGGCGTACCTCCC 59.460 55.000 0.00 0.00 36.63 4.30
2376 2435 2.622064 ATCAAGATTGGCGTACCTCC 57.378 50.000 0.00 0.00 36.63 4.30
2377 2436 4.083802 GCATTATCAAGATTGGCGTACCTC 60.084 45.833 0.00 0.00 36.63 3.85
2378 2437 3.815401 GCATTATCAAGATTGGCGTACCT 59.185 43.478 0.00 0.00 36.63 3.08
2379 2438 3.058224 GGCATTATCAAGATTGGCGTACC 60.058 47.826 0.00 0.00 0.00 3.34
2380 2439 3.815401 AGGCATTATCAAGATTGGCGTAC 59.185 43.478 3.58 0.00 39.41 3.67
2381 2440 4.085357 AGGCATTATCAAGATTGGCGTA 57.915 40.909 3.58 0.00 39.41 4.42
2382 2441 2.936202 AGGCATTATCAAGATTGGCGT 58.064 42.857 3.58 0.00 39.41 5.68
2383 2442 3.996150 AAGGCATTATCAAGATTGGCG 57.004 42.857 3.58 0.00 39.41 5.69
2419 2478 5.784177 AGAGAAGACAAAAGAATAGCGACA 58.216 37.500 0.00 0.00 0.00 4.35
2473 2532 1.212935 GCAACATGGTAGTGGAGGGAT 59.787 52.381 0.00 0.00 0.00 3.85
2487 2546 3.965379 TCCAAATCAGCATTGCAACAT 57.035 38.095 11.91 0.00 0.00 2.71
2510 2569 6.687081 TTAAGTCTGGACGTTGATTGTTTT 57.313 33.333 0.00 0.00 36.20 2.43
2514 2573 4.032900 CGGATTAAGTCTGGACGTTGATTG 59.967 45.833 0.00 0.00 36.20 2.67
2522 2581 3.889520 AAGGTCGGATTAAGTCTGGAC 57.110 47.619 0.00 0.00 33.78 4.02
2581 2640 3.857157 ACCACTAAGCTTCCAACAGAA 57.143 42.857 0.00 0.00 0.00 3.02
2582 2641 4.504340 GGTTACCACTAAGCTTCCAACAGA 60.504 45.833 0.00 0.00 0.00 3.41
2583 2642 3.751698 GGTTACCACTAAGCTTCCAACAG 59.248 47.826 0.00 0.00 0.00 3.16
2584 2643 3.497227 GGGTTACCACTAAGCTTCCAACA 60.497 47.826 0.00 0.00 36.50 3.33
2593 2663 3.132467 GGTGAGCTAGGGTTACCACTAAG 59.868 52.174 2.98 0.00 39.10 2.18
2618 2688 2.173569 GTGGGCTGGAGGAGTTTGATAT 59.826 50.000 0.00 0.00 0.00 1.63
2663 2733 7.451501 TGTTTTTATCATGAGACATCAAGCA 57.548 32.000 0.09 0.00 39.39 3.91
2825 2905 6.578545 CACTGTTTGATGAGTTTTTACGGATG 59.421 38.462 0.00 0.00 0.00 3.51
2827 2907 5.008217 CCACTGTTTGATGAGTTTTTACGGA 59.992 40.000 0.00 0.00 0.00 4.69
2830 2910 4.982295 GCCCACTGTTTGATGAGTTTTTAC 59.018 41.667 0.00 0.00 0.00 2.01
2851 2931 0.895100 TGAGCACTCCCAAACATGCC 60.895 55.000 0.00 0.00 38.92 4.40


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

AutoCloner maintained by Alex Coulton.