Multiple sequence alignment - TraesCS6B01G194400

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 TraesCS6B01G194400 chr6B 100.000 4880 0 0 1 4880 229213480 229208601 0.000000e+00 9012.0
1 TraesCS6B01G194400 chr6B 92.532 616 44 2 1 615 229276352 229275738 0.000000e+00 881.0
2 TraesCS6B01G194400 chr6B 91.883 616 43 2 1 615 229274292 229273683 0.000000e+00 854.0
3 TraesCS6B01G194400 chr6B 82.143 168 11 5 614 771 229273731 229273573 5.130000e-25 126.0
4 TraesCS6B01G194400 chr6D 94.068 2950 117 23 732 3666 131694806 131691900 0.000000e+00 4425.0
5 TraesCS6B01G194400 chr6D 92.801 1153 64 8 3665 4813 131691614 131690477 0.000000e+00 1652.0
6 TraesCS6B01G194400 chr6D 86.066 610 68 6 23 616 131696333 131695725 1.480000e-179 640.0
7 TraesCS6B01G194400 chr6A 93.062 2681 116 28 785 3437 170020812 170018174 0.000000e+00 3856.0
8 TraesCS6B01G194400 chr6A 97.033 573 15 2 3665 4237 170017665 170017095 0.000000e+00 963.0
9 TraesCS6B01G194400 chr6A 89.402 585 47 10 4233 4813 170015654 170015081 0.000000e+00 723.0
10 TraesCS6B01G194400 chr6A 91.456 316 25 2 1 315 170518046 170517732 2.700000e-117 433.0
11 TraesCS6B01G194400 chr6A 90.354 311 28 2 6 315 170308425 170308116 1.640000e-109 407.0
12 TraesCS6B01G194400 chr6A 85.714 252 36 0 364 615 170021337 170021086 2.900000e-67 267.0
13 TraesCS6B01G194400 chr6A 97.600 125 3 0 3510 3634 170018171 170018047 1.060000e-51 215.0
14 TraesCS6B01G194400 chr5D 87.209 86 10 1 184 269 132885998 132886082 4.020000e-16 97.1
15 TraesCS6B01G194400 chr5B 87.209 86 10 1 184 269 144246738 144246822 4.020000e-16 97.1
16 TraesCS6B01G194400 chr3A 78.947 95 20 0 2232 2326 584956127 584956221 1.130000e-06 65.8


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 TraesCS6B01G194400 chr6B 229208601 229213480 4879 True 9012.000000 9012 100.000000 1 4880 1 chr6B.!!$R1 4879
1 TraesCS6B01G194400 chr6B 229273573 229276352 2779 True 620.333333 881 88.852667 1 771 3 chr6B.!!$R2 770
2 TraesCS6B01G194400 chr6D 131690477 131696333 5856 True 2239.000000 4425 90.978333 23 4813 3 chr6D.!!$R1 4790
3 TraesCS6B01G194400 chr6A 170015081 170021337 6256 True 1204.800000 3856 92.562200 364 4813 5 chr6A.!!$R3 4449

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
635 652 0.458669 TGAATCCTAAGCCGGTCGAC 59.541 55.000 7.13 7.13 0.0 4.20 F
636 653 0.594284 GAATCCTAAGCCGGTCGACG 60.594 60.000 9.92 4.95 43.8 5.12 F
677 694 0.696501 TGAGGTTTAGGGTTGAGGCC 59.303 55.000 0.00 0.00 0.0 5.19 F
1990 3080 0.108377 ACACGGTTGCGATGCTCATA 60.108 50.000 0.00 0.00 0.0 2.15 F
2939 5258 2.076100 CTCACGCCATAAGTTTGCAGA 58.924 47.619 0.00 0.00 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 2912 0.466372 GGAGCAAGATGTTAGCCCCC 60.466 60.000 0.00 0.00 0.00 5.40 R
1843 2933 1.153429 CATCGGAAACCCGGGTCTC 60.153 63.158 30.40 24.66 46.72 3.36 R
2665 4984 1.268899 CAGAAGGACTCGGTACACGTT 59.731 52.381 0.00 0.00 44.69 3.99 R
3445 5765 3.245264 GGGATTTTTCCAACAGAGGGAGA 60.245 47.826 0.00 0.00 35.46 3.71 R
4661 8829 0.107993 CCAGATTCCTCTCTTGCGCA 60.108 55.000 5.66 5.66 0.00 6.09 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
140 144 3.668447 CTCTGCACCTACAAACTGTCAT 58.332 45.455 0.00 0.00 0.00 3.06
251 260 1.153289 CTTCACGATGAGGGCCTGG 60.153 63.158 12.95 0.00 0.00 4.45
272 281 1.514087 CTGGGGTAAGCGCTTCGTA 59.486 57.895 28.82 6.44 0.00 3.43
279 288 2.864343 GGTAAGCGCTTCGTATGTGATT 59.136 45.455 28.82 0.00 0.00 2.57
312 321 4.288626 ACTTTGGGTCAGAATAACTGCCTA 59.711 41.667 0.00 0.00 45.38 3.93
317 326 5.885912 TGGGTCAGAATAACTGCCTATTTTC 59.114 40.000 0.00 0.00 45.38 2.29
348 357 6.124316 ACATCAATTGCCTGATCTAGCTAT 57.876 37.500 12.93 4.39 33.66 2.97
359 376 6.291377 CCTGATCTAGCTATGGTTAAAAGCA 58.709 40.000 0.00 0.00 38.75 3.91
442 459 5.721960 ACAACTAGGATGGAGACTACACAAT 59.278 40.000 0.00 0.00 0.00 2.71
517 534 3.813443 CCTTGATTCAATGGACGAGGAT 58.187 45.455 0.00 0.00 36.36 3.24
520 537 4.694760 TGATTCAATGGACGAGGATGAT 57.305 40.909 0.00 0.00 0.00 2.45
546 563 1.193874 GGATTTTGTCGTGACACGGTC 59.806 52.381 26.55 19.41 42.81 4.79
550 567 2.027024 GTCGTGACACGGTCTGCA 59.973 61.111 26.55 4.38 42.81 4.41
555 572 2.335369 GACACGGTCTGCACTCGT 59.665 61.111 0.00 0.00 37.64 4.18
557 574 0.874607 GACACGGTCTGCACTCGTTT 60.875 55.000 2.07 0.00 34.73 3.60
582 599 8.506168 TTTATTGAAGAATGAATCCTAACGCT 57.494 30.769 0.00 0.00 0.00 5.07
598 615 4.406173 CTGGTCGACGCGCTCTGT 62.406 66.667 5.73 0.00 0.00 3.41
599 616 4.400109 TGGTCGACGCGCTCTGTC 62.400 66.667 5.73 4.67 0.00 3.51
607 624 4.357947 GCGCTCTGTCCGGTCACA 62.358 66.667 0.00 0.00 0.00 3.58
608 625 2.338620 CGCTCTGTCCGGTCACAA 59.661 61.111 0.00 0.00 0.00 3.33
609 626 1.734477 CGCTCTGTCCGGTCACAAG 60.734 63.158 0.00 1.55 0.00 3.16
610 627 1.367840 GCTCTGTCCGGTCACAAGT 59.632 57.895 0.00 0.00 0.00 3.16
611 628 0.601558 GCTCTGTCCGGTCACAAGTA 59.398 55.000 0.00 0.00 0.00 2.24
612 629 1.204941 GCTCTGTCCGGTCACAAGTAT 59.795 52.381 0.00 0.00 0.00 2.12
613 630 2.881074 CTCTGTCCGGTCACAAGTATG 58.119 52.381 0.00 0.00 0.00 2.39
614 631 2.492088 CTCTGTCCGGTCACAAGTATGA 59.508 50.000 0.00 0.00 0.00 2.15
615 632 2.894765 TCTGTCCGGTCACAAGTATGAA 59.105 45.455 0.00 0.00 0.00 2.57
616 633 3.513912 TCTGTCCGGTCACAAGTATGAAT 59.486 43.478 0.00 0.00 0.00 2.57
617 634 3.595173 TGTCCGGTCACAAGTATGAATG 58.405 45.455 0.00 0.00 0.00 2.67
618 635 3.259625 TGTCCGGTCACAAGTATGAATGA 59.740 43.478 0.00 0.00 0.00 2.57
619 636 4.250464 GTCCGGTCACAAGTATGAATGAA 58.750 43.478 0.00 0.00 0.00 2.57
620 637 4.876107 GTCCGGTCACAAGTATGAATGAAT 59.124 41.667 0.00 0.00 0.00 2.57
621 638 5.006746 GTCCGGTCACAAGTATGAATGAATC 59.993 44.000 0.00 0.00 0.00 2.52
622 639 4.273480 CCGGTCACAAGTATGAATGAATCC 59.727 45.833 0.00 0.00 0.00 3.01
623 640 5.118990 CGGTCACAAGTATGAATGAATCCT 58.881 41.667 0.00 0.00 0.00 3.24
624 641 6.280643 CGGTCACAAGTATGAATGAATCCTA 58.719 40.000 0.00 0.00 0.00 2.94
625 642 6.761242 CGGTCACAAGTATGAATGAATCCTAA 59.239 38.462 0.00 0.00 0.00 2.69
626 643 7.042456 CGGTCACAAGTATGAATGAATCCTAAG 60.042 40.741 0.00 0.00 0.00 2.18
627 644 7.254932 GGTCACAAGTATGAATGAATCCTAAGC 60.255 40.741 0.00 0.00 0.00 3.09
628 645 6.767902 TCACAAGTATGAATGAATCCTAAGCC 59.232 38.462 0.00 0.00 0.00 4.35
629 646 5.760253 ACAAGTATGAATGAATCCTAAGCCG 59.240 40.000 0.00 0.00 0.00 5.52
630 647 4.899502 AGTATGAATGAATCCTAAGCCGG 58.100 43.478 0.00 0.00 0.00 6.13
631 648 3.864789 ATGAATGAATCCTAAGCCGGT 57.135 42.857 1.90 0.00 0.00 5.28
632 649 3.194005 TGAATGAATCCTAAGCCGGTC 57.806 47.619 1.90 0.00 0.00 4.79
633 650 2.135933 GAATGAATCCTAAGCCGGTCG 58.864 52.381 1.90 0.00 0.00 4.79
634 651 1.410004 ATGAATCCTAAGCCGGTCGA 58.590 50.000 1.90 0.00 0.00 4.20
635 652 0.458669 TGAATCCTAAGCCGGTCGAC 59.541 55.000 7.13 7.13 0.00 4.20
636 653 0.594284 GAATCCTAAGCCGGTCGACG 60.594 60.000 9.92 4.95 43.80 5.12
637 654 2.624437 AATCCTAAGCCGGTCGACGC 62.624 60.000 9.92 8.46 42.52 5.19
639 656 4.471726 CTAAGCCGGTCGACGCGT 62.472 66.667 13.85 13.85 42.52 6.01
640 657 3.958822 CTAAGCCGGTCGACGCGTT 62.959 63.158 15.53 13.37 42.52 4.84
652 669 2.126071 CGCGTTCTGTCCGGTCAT 60.126 61.111 0.00 0.00 0.00 3.06
676 693 2.808906 ATGAGGTTTAGGGTTGAGGC 57.191 50.000 0.00 0.00 0.00 4.70
677 694 0.696501 TGAGGTTTAGGGTTGAGGCC 59.303 55.000 0.00 0.00 0.00 5.19
678 695 0.992695 GAGGTTTAGGGTTGAGGCCT 59.007 55.000 3.86 3.86 0.00 5.19
679 696 1.354705 GAGGTTTAGGGTTGAGGCCTT 59.645 52.381 6.77 0.00 0.00 4.35
680 697 1.075536 AGGTTTAGGGTTGAGGCCTTG 59.924 52.381 6.77 0.00 0.00 3.61
681 698 1.074889 GGTTTAGGGTTGAGGCCTTGA 59.925 52.381 6.77 0.00 0.00 3.02
682 699 2.437413 GTTTAGGGTTGAGGCCTTGAG 58.563 52.381 6.77 0.00 0.00 3.02
683 700 0.991920 TTAGGGTTGAGGCCTTGAGG 59.008 55.000 6.77 0.00 38.53 3.86
707 1249 3.150458 TCAAACCCGACTCTCTCACTA 57.850 47.619 0.00 0.00 0.00 2.74
749 1624 1.303317 GGGCCTTGTCGACACCAAT 60.303 57.895 19.90 0.00 0.00 3.16
773 1648 4.040339 TGGATGACTAGTGAAGACTTGCAA 59.960 41.667 0.00 0.00 33.21 4.08
782 1657 3.625764 GTGAAGACTTGCAACCACTAACA 59.374 43.478 0.00 0.00 0.00 2.41
866 1877 5.841957 AGCTGGTTGCCTTGAAATAATAG 57.158 39.130 0.00 0.00 44.23 1.73
867 1878 5.509498 AGCTGGTTGCCTTGAAATAATAGA 58.491 37.500 0.00 0.00 44.23 1.98
868 1879 5.591877 AGCTGGTTGCCTTGAAATAATAGAG 59.408 40.000 0.00 0.00 44.23 2.43
872 1883 6.945435 TGGTTGCCTTGAAATAATAGAGTTGA 59.055 34.615 0.00 0.00 0.00 3.18
873 1884 7.450014 TGGTTGCCTTGAAATAATAGAGTTGAA 59.550 33.333 0.00 0.00 0.00 2.69
874 1885 7.970614 GGTTGCCTTGAAATAATAGAGTTGAAG 59.029 37.037 0.00 0.00 0.00 3.02
875 1886 7.630242 TGCCTTGAAATAATAGAGTTGAAGG 57.370 36.000 0.00 0.00 45.83 3.46
876 1887 7.175104 TGCCTTGAAATAATAGAGTTGAAGGT 58.825 34.615 5.21 0.00 45.13 3.50
878 1889 7.475840 CCTTGAAATAATAGAGTTGAAGGTGC 58.524 38.462 0.00 0.00 40.40 5.01
879 1890 7.337942 CCTTGAAATAATAGAGTTGAAGGTGCT 59.662 37.037 0.00 0.00 40.40 4.40
880 1891 7.849804 TGAAATAATAGAGTTGAAGGTGCTC 57.150 36.000 0.00 0.00 0.00 4.26
881 1892 7.624549 TGAAATAATAGAGTTGAAGGTGCTCT 58.375 34.615 0.00 0.00 41.78 4.09
882 1893 8.103305 TGAAATAATAGAGTTGAAGGTGCTCTT 58.897 33.333 0.00 0.00 39.87 2.85
919 1930 7.005709 ACAGTAGCACTAAATACCAAGAAGT 57.994 36.000 0.00 0.00 0.00 3.01
920 1931 7.450903 ACAGTAGCACTAAATACCAAGAAGTT 58.549 34.615 0.00 0.00 0.00 2.66
965 1976 6.368791 GGAATCCCTTGAACAAAATAAACTGC 59.631 38.462 0.00 0.00 0.00 4.40
1081 2099 2.750237 GGCGTTTCTTCCGGCCAT 60.750 61.111 2.24 0.00 44.91 4.40
1337 2355 2.347490 GTGAGCACGTCCACCCAT 59.653 61.111 0.00 0.00 0.00 4.00
1359 2383 3.851128 GGGCCGGCTACTCCAGTC 61.851 72.222 28.56 5.59 34.01 3.51
1360 2384 3.851128 GGCCGGCTACTCCAGTCC 61.851 72.222 28.56 0.41 34.01 3.85
1361 2385 3.075005 GCCGGCTACTCCAGTCCA 61.075 66.667 22.15 0.00 34.01 4.02
1365 2389 1.330655 CGGCTACTCCAGTCCACCAT 61.331 60.000 0.00 0.00 34.01 3.55
1389 2413 0.905357 GGTGTGTGGCTAGGACTCAT 59.095 55.000 0.00 0.00 0.00 2.90
1402 2426 3.037549 AGGACTCATTCTCCTCCATGTC 58.962 50.000 0.00 0.00 32.06 3.06
1445 2475 4.775058 CAGTCGTCTGGAATATAGGAGG 57.225 50.000 1.35 0.00 37.97 4.30
1471 2501 5.428253 TCTCATAAATGCACTTACCCTGTC 58.572 41.667 0.00 0.00 0.00 3.51
1520 2560 7.633193 ACAACACAATCTACTAGTCTAGGAG 57.367 40.000 12.47 12.47 38.14 3.69
1537 2577 7.069578 AGTCTAGGAGTACTTCTTTTGAACACA 59.930 37.037 9.53 0.00 34.31 3.72
1538 2578 7.169476 GTCTAGGAGTACTTCTTTTGAACACAC 59.831 40.741 9.53 0.00 34.31 3.82
1545 2585 7.770897 AGTACTTCTTTTGAACACACTTCATCT 59.229 33.333 0.00 0.00 34.31 2.90
1548 2588 7.121168 ACTTCTTTTGAACACACTTCATCTGAA 59.879 33.333 0.00 0.00 34.31 3.02
1554 2594 9.554395 TTTGAACACACTTCATCTGAATAACTA 57.446 29.630 0.00 0.00 33.01 2.24
1620 2668 5.990996 CCTGCAACATTTAGTTTGTCCAAAT 59.009 36.000 0.00 0.00 38.74 2.32
1622 2670 7.307337 CCTGCAACATTTAGTTTGTCCAAATTC 60.307 37.037 0.00 0.00 38.74 2.17
1642 2732 3.216800 TCTTGCTGGCCAATATCACATC 58.783 45.455 7.01 0.00 31.91 3.06
1660 2750 7.815840 TCACATCATCTGTTTCCAAAAGTTA 57.184 32.000 0.00 0.00 35.29 2.24
1668 2758 3.898741 TGTTTCCAAAAGTTACCATCCCC 59.101 43.478 0.00 0.00 0.00 4.81
1735 2825 2.093341 AGAGTACCTGTCTCGAGACCTC 60.093 54.545 36.01 31.27 44.15 3.85
1741 2831 2.018515 CTGTCTCGAGACCTCCCTTAC 58.981 57.143 36.01 14.51 44.15 2.34
1762 2852 5.791336 ACGAGCTTTCACCAGATGATATA 57.209 39.130 0.00 0.00 37.11 0.86
1774 2864 6.894654 CACCAGATGATATATACCTGACCTCT 59.105 42.308 9.02 0.00 0.00 3.69
1783 2873 1.153489 CCTGACCTCTGGATGCGTG 60.153 63.158 0.00 0.00 37.15 5.34
1822 2912 3.965539 CTCTGTCCTTGCCCAGCCG 62.966 68.421 0.00 0.00 0.00 5.52
1843 2933 0.815615 GGGCTAACATCTTGCTCCCG 60.816 60.000 0.00 0.00 0.00 5.14
1889 2979 1.079819 CGGACCACATTCAGCGAGT 60.080 57.895 0.00 0.00 0.00 4.18
1960 3050 2.428890 CCTCGAGTCTGTGAAGGCTATT 59.571 50.000 12.31 0.00 0.00 1.73
1990 3080 0.108377 ACACGGTTGCGATGCTCATA 60.108 50.000 0.00 0.00 0.00 2.15
2290 4240 6.043243 TCACCTTGGGAGCTATATCTAAAAGG 59.957 42.308 8.71 8.71 0.00 3.11
2317 4636 3.365265 CCTGGTTGGCGACTTGGC 61.365 66.667 4.59 0.00 45.12 4.52
2389 4708 6.429692 TGAACGTTTGATCTACAATTGGATGT 59.570 34.615 10.83 0.00 38.36 3.06
2466 4785 8.311109 TGTATATAAATTCTGCGCTTCATCCTA 58.689 33.333 9.73 0.00 0.00 2.94
2598 4917 4.863689 TGTTTCGTTCGTAACTGAGTTTCA 59.136 37.500 1.97 0.00 0.00 2.69
2637 4956 4.820894 TTTCTCTGTACCCTCCTAAAGC 57.179 45.455 0.00 0.00 0.00 3.51
2665 4984 9.973450 TTTGCTATGTTTTAGTTTTTGCTATCA 57.027 25.926 0.00 0.00 0.00 2.15
2713 5032 5.278169 GGTCATGCTGGCAGTCTTAATATTG 60.278 44.000 17.16 1.63 0.00 1.90
2719 5038 5.431765 CTGGCAGTCTTAATATTGTCACCT 58.568 41.667 6.28 0.00 0.00 4.00
2753 5072 6.402226 GGCTTGGTTACTTATCTTTGTTCTCG 60.402 42.308 0.00 0.00 0.00 4.04
2841 5160 9.890629 TTCAGGTACATATATGCCTTATCATTC 57.109 33.333 12.79 0.00 0.00 2.67
2844 5163 7.629315 AGGTACATATATGCCTTATCATTCCCT 59.371 37.037 12.79 0.00 0.00 4.20
2939 5258 2.076100 CTCACGCCATAAGTTTGCAGA 58.924 47.619 0.00 0.00 0.00 4.26
3146 5465 2.163412 GTGATGGTAAGGAAATGCGCAA 59.837 45.455 17.11 0.00 0.00 4.85
3270 5589 4.736759 GCTTGGATGGCTTTTCTGATGATG 60.737 45.833 0.00 0.00 0.00 3.07
3445 5765 3.805207 ACTTTCTAGTTTGCAAGACCGT 58.195 40.909 0.00 0.00 0.00 4.83
3467 5787 3.092301 CTCCCTCTGTTGGAAAAATCCC 58.908 50.000 0.00 0.00 0.00 3.85
3477 5797 5.602145 TGTTGGAAAAATCCCTCTGTTTCAT 59.398 36.000 0.00 0.00 32.72 2.57
3491 5811 8.043710 CCCTCTGTTTCATTATACAAGAGTCTT 58.956 37.037 0.00 0.00 0.00 3.01
3492 5812 9.092876 CCTCTGTTTCATTATACAAGAGTCTTC 57.907 37.037 1.26 0.00 0.00 2.87
3493 5813 9.645059 CTCTGTTTCATTATACAAGAGTCTTCA 57.355 33.333 1.26 0.00 0.00 3.02
3494 5814 9.424319 TCTGTTTCATTATACAAGAGTCTTCAC 57.576 33.333 1.26 0.00 0.00 3.18
3495 5815 9.208022 CTGTTTCATTATACAAGAGTCTTCACA 57.792 33.333 1.26 0.00 0.00 3.58
3496 5816 9.554395 TGTTTCATTATACAAGAGTCTTCACAA 57.446 29.630 1.26 0.00 0.00 3.33
3569 5889 2.105477 GACCAGACATGCATGACCCTAT 59.895 50.000 32.75 9.47 0.00 2.57
3608 5928 8.239998 GCATTATACATTTCTAAAGGATGGAGC 58.760 37.037 0.00 0.00 0.00 4.70
3722 6433 0.105964 TTGTGCTGCTACTCCGTTGT 59.894 50.000 0.00 0.00 0.00 3.32
3748 6459 6.599244 TCAAATCTTCCCTGATGTACATGAAC 59.401 38.462 14.43 0.00 0.00 3.18
3873 6584 3.181501 GCGAGAGGCATGCTATAGTAGAG 60.182 52.174 18.92 2.03 42.87 2.43
4031 6742 6.659242 ACATATTTTGTACTCTTCCTGGTTGG 59.341 38.462 0.00 0.00 36.57 3.77
4035 6746 1.623811 GTACTCTTCCTGGTTGGCTCA 59.376 52.381 0.00 0.00 35.26 4.26
4042 6753 1.602237 CTGGTTGGCTCATACCGGT 59.398 57.895 13.98 13.98 37.23 5.28
4124 6835 8.336235 AGATGATTTAAGGGTCAGTATTTTCCA 58.664 33.333 0.00 0.00 0.00 3.53
4168 6879 7.652909 CAGGCAATTGAAGTTGAAAATAACTCA 59.347 33.333 10.34 0.00 39.86 3.41
4215 6926 0.251653 AGTCCAGACTGGCTTACCGA 60.252 55.000 17.33 0.00 40.75 4.69
4238 8394 3.434940 TTCTCAAGCCCCTTTCTTACC 57.565 47.619 0.00 0.00 0.00 2.85
4280 8436 5.047235 GTGTGTAATTATCCCGGAGATAGCT 60.047 44.000 0.73 0.00 38.69 3.32
4286 8442 0.551396 TCCCGGAGATAGCTCAGTCA 59.449 55.000 10.68 0.00 43.14 3.41
4330 8486 3.431626 CCTCTTCTCTCTCTCGCTACTCA 60.432 52.174 0.00 0.00 0.00 3.41
4351 8507 0.394938 TAGGGTTCACTGCTTTCGCA 59.605 50.000 0.00 0.00 45.60 5.10
4373 8532 2.520968 GTTTGCCCACCTCCCACT 59.479 61.111 0.00 0.00 0.00 4.00
4375 8534 2.391130 TTTGCCCACCTCCCACTGT 61.391 57.895 0.00 0.00 0.00 3.55
4406 8565 2.037620 ATCCATGGCCTCGTGCTCTC 62.038 60.000 6.96 0.00 40.92 3.20
4498 8658 6.628919 TCGAGGTCGTCATTTCATATTCTA 57.371 37.500 0.00 0.00 40.80 2.10
4500 8660 6.485648 TCGAGGTCGTCATTTCATATTCTAGA 59.514 38.462 0.00 0.00 40.80 2.43
4505 8665 8.552034 GGTCGTCATTTCATATTCTAGAAAAGG 58.448 37.037 9.71 0.74 37.30 3.11
4524 8684 1.143969 GGGTACGCCTTGTCGATTCG 61.144 60.000 0.00 0.00 34.45 3.34
4525 8685 0.179156 GGTACGCCTTGTCGATTCGA 60.179 55.000 4.29 4.29 0.00 3.71
4565 8725 5.180680 GGGGACATTAAGTAAGTGAACACAC 59.819 44.000 7.68 0.00 35.07 3.82
4567 8727 6.293244 GGGACATTAAGTAAGTGAACACACAC 60.293 42.308 7.68 4.65 40.60 3.82
4568 8728 6.259167 GGACATTAAGTAAGTGAACACACACA 59.741 38.462 7.68 0.00 42.45 3.72
4569 8729 7.011828 ACATTAAGTAAGTGAACACACACAC 57.988 36.000 7.68 0.00 42.45 3.82
4570 8730 6.596106 ACATTAAGTAAGTGAACACACACACA 59.404 34.615 7.68 0.00 42.45 3.72
4571 8731 4.939509 AAGTAAGTGAACACACACACAC 57.060 40.909 7.68 0.00 42.45 3.82
4572 8732 3.932822 AGTAAGTGAACACACACACACA 58.067 40.909 7.68 0.00 42.45 3.72
4573 8733 3.682858 AGTAAGTGAACACACACACACAC 59.317 43.478 7.68 0.00 42.45 3.82
4574 8734 2.177394 AGTGAACACACACACACACA 57.823 45.000 7.68 0.00 42.45 3.72
4575 8735 1.804151 AGTGAACACACACACACACAC 59.196 47.619 7.68 0.00 42.45 3.82
4576 8736 1.533299 GTGAACACACACACACACACA 59.467 47.619 0.00 0.00 40.11 3.72
4577 8737 1.533299 TGAACACACACACACACACAC 59.467 47.619 0.00 0.00 0.00 3.82
4578 8738 1.533299 GAACACACACACACACACACA 59.467 47.619 0.00 0.00 0.00 3.72
4579 8739 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4580 8740 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
4581 8741 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
4643 8810 1.283029 CAGCTTGGAGGAAGGGATTCA 59.717 52.381 0.00 0.00 31.56 2.57
4647 8814 3.625716 GCTTGGAGGAAGGGATTCAATCA 60.626 47.826 0.00 0.00 31.56 2.57
4648 8815 3.652057 TGGAGGAAGGGATTCAATCAC 57.348 47.619 0.00 0.00 0.00 3.06
4659 8827 2.869101 TTCAATCACGATCCAACCCA 57.131 45.000 0.00 0.00 0.00 4.51
4661 8829 1.628340 TCAATCACGATCCAACCCAGT 59.372 47.619 0.00 0.00 0.00 4.00
4663 8831 0.392998 ATCACGATCCAACCCAGTGC 60.393 55.000 0.00 0.00 33.28 4.40
4676 8844 0.392193 CCAGTGCGCAAGAGAGGAAT 60.392 55.000 14.00 0.00 43.02 3.01
4680 8848 0.107993 TGCGCAAGAGAGGAATCTGG 60.108 55.000 8.16 0.00 43.02 3.86
4691 8859 5.013495 AGAGAGGAATCTGGATGTGTTGAAA 59.987 40.000 0.00 0.00 0.00 2.69
4722 8890 3.382546 ACATTTGCATACTTGGGAGATGC 59.617 43.478 0.00 0.00 45.02 3.91
4745 8913 1.265236 TGGGTTGGAATGTTGGATGC 58.735 50.000 0.00 0.00 0.00 3.91
4752 8920 1.202486 GGAATGTTGGATGCCATGCTG 60.202 52.381 0.00 0.00 31.53 4.41
4781 8949 1.024579 CCTTGCCGTGTACCCATGTC 61.025 60.000 0.00 0.00 0.00 3.06
4795 8963 6.481976 TGTACCCATGTCGATAATCATCAAAC 59.518 38.462 0.00 0.00 0.00 2.93
4813 8981 6.762077 TCAAACATGATCATCCTATACCCA 57.238 37.500 4.86 0.00 0.00 4.51
4814 8982 6.772605 TCAAACATGATCATCCTATACCCAG 58.227 40.000 4.86 0.00 0.00 4.45
4815 8983 6.329986 TCAAACATGATCATCCTATACCCAGT 59.670 38.462 4.86 0.00 0.00 4.00
4816 8984 5.752036 ACATGATCATCCTATACCCAGTG 57.248 43.478 4.86 0.00 0.00 3.66
4817 8985 4.533707 ACATGATCATCCTATACCCAGTGG 59.466 45.833 4.86 0.63 37.80 4.00
4818 8986 2.906389 TGATCATCCTATACCCAGTGGC 59.094 50.000 2.61 0.00 33.59 5.01
4819 8987 1.338107 TCATCCTATACCCAGTGGCG 58.662 55.000 2.61 0.00 33.59 5.69
4820 8988 0.321671 CATCCTATACCCAGTGGCGG 59.678 60.000 2.61 0.00 33.59 6.13
4821 8989 0.190069 ATCCTATACCCAGTGGCGGA 59.810 55.000 2.61 4.34 33.59 5.54
4824 8992 0.674534 CTATACCCAGTGGCGGAGAC 59.325 60.000 2.61 0.00 33.59 3.36
4833 9001 4.394712 GGCGGAGACAGGTGGGTG 62.395 72.222 0.00 0.00 31.66 4.61
4835 9003 4.394712 CGGAGACAGGTGGGTGCC 62.395 72.222 0.00 0.00 0.00 5.01
4837 9005 2.348998 GAGACAGGTGGGTGCCAG 59.651 66.667 0.00 0.00 32.34 4.85
4851 9019 3.766691 CCAGCCAGGCCAACATGC 61.767 66.667 8.22 0.00 0.00 4.06
4852 9020 2.992689 CAGCCAGGCCAACATGCA 60.993 61.111 8.22 0.00 0.00 3.96
4853 9021 2.203669 AGCCAGGCCAACATGCAA 60.204 55.556 8.22 0.00 0.00 4.08
4854 9022 1.837947 AGCCAGGCCAACATGCAAA 60.838 52.632 8.22 0.00 0.00 3.68
4855 9023 1.196104 AGCCAGGCCAACATGCAAAT 61.196 50.000 8.22 0.00 0.00 2.32
4856 9024 0.536260 GCCAGGCCAACATGCAAATA 59.464 50.000 5.01 0.00 0.00 1.40
4857 9025 1.472026 GCCAGGCCAACATGCAAATAG 60.472 52.381 5.01 0.00 0.00 1.73
4858 9026 1.826720 CCAGGCCAACATGCAAATAGT 59.173 47.619 5.01 0.00 0.00 2.12
4859 9027 2.234414 CCAGGCCAACATGCAAATAGTT 59.766 45.455 5.01 0.00 0.00 2.24
4860 9028 3.514645 CAGGCCAACATGCAAATAGTTC 58.485 45.455 5.01 0.00 0.00 3.01
4861 9029 2.497273 AGGCCAACATGCAAATAGTTCC 59.503 45.455 5.01 0.00 0.00 3.62
4862 9030 2.233431 GGCCAACATGCAAATAGTTCCA 59.767 45.455 0.00 0.00 0.00 3.53
4863 9031 3.253230 GCCAACATGCAAATAGTTCCAC 58.747 45.455 0.00 0.00 0.00 4.02
4864 9032 3.056607 GCCAACATGCAAATAGTTCCACT 60.057 43.478 0.00 0.00 0.00 4.00
4865 9033 4.157656 GCCAACATGCAAATAGTTCCACTA 59.842 41.667 0.00 0.00 34.82 2.74
4866 9034 5.640732 CCAACATGCAAATAGTTCCACTAC 58.359 41.667 0.00 0.00 32.84 2.73
4867 9035 5.323900 CAACATGCAAATAGTTCCACTACG 58.676 41.667 0.00 0.00 32.84 3.51
4868 9036 4.827692 ACATGCAAATAGTTCCACTACGA 58.172 39.130 0.00 0.00 32.84 3.43
4869 9037 4.630069 ACATGCAAATAGTTCCACTACGAC 59.370 41.667 0.00 0.00 32.84 4.34
4870 9038 4.260139 TGCAAATAGTTCCACTACGACA 57.740 40.909 0.00 0.00 32.84 4.35
4871 9039 3.991773 TGCAAATAGTTCCACTACGACAC 59.008 43.478 0.00 0.00 32.84 3.67
4872 9040 4.243270 GCAAATAGTTCCACTACGACACT 58.757 43.478 0.00 0.00 32.84 3.55
4873 9041 4.091509 GCAAATAGTTCCACTACGACACTG 59.908 45.833 0.00 0.00 32.84 3.66
4874 9042 5.466819 CAAATAGTTCCACTACGACACTGA 58.533 41.667 0.00 0.00 32.84 3.41
4875 9043 4.966965 ATAGTTCCACTACGACACTGAG 57.033 45.455 0.00 0.00 32.84 3.35
4876 9044 2.584236 AGTTCCACTACGACACTGAGT 58.416 47.619 0.00 0.00 0.00 3.41
4877 9045 3.748083 AGTTCCACTACGACACTGAGTA 58.252 45.455 0.00 0.00 0.00 2.59
4878 9046 4.333690 AGTTCCACTACGACACTGAGTAT 58.666 43.478 0.00 0.00 0.00 2.12
4879 9047 4.765856 AGTTCCACTACGACACTGAGTATT 59.234 41.667 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.770164 ACAAGAGTTGGCTAAGCGAT 57.230 45.000 0.00 0.00 34.12 4.58
8 9 1.464997 GGAACAAGAGTTGGCTAAGCG 59.535 52.381 0.00 0.00 38.30 4.68
16 17 1.226746 GGTGACCGGAACAAGAGTTG 58.773 55.000 9.46 0.00 38.30 3.16
18 19 1.366366 CGGTGACCGGAACAAGAGT 59.634 57.895 17.80 0.00 44.15 3.24
122 125 3.138304 GTGATGACAGTTTGTAGGTGCA 58.862 45.455 0.00 0.00 0.00 4.57
140 144 1.406341 GGCGTGGTTAGGCATAAGTGA 60.406 52.381 0.00 0.00 39.38 3.41
251 260 1.449778 GAAGCGCTTACCCCAGGTC 60.450 63.158 25.11 2.97 37.09 3.85
272 281 7.643123 ACCCAAAGTATTAGAAGGAATCACAT 58.357 34.615 0.00 0.00 0.00 3.21
279 288 6.945636 TTCTGACCCAAAGTATTAGAAGGA 57.054 37.500 0.00 0.00 0.00 3.36
348 357 7.821652 TCACGAATAAATCATGCTTTTAACCA 58.178 30.769 0.00 0.00 0.00 3.67
359 376 7.403312 TGGATTGGTTTCACGAATAAATCAT 57.597 32.000 0.00 0.00 27.64 2.45
420 437 7.015682 CCATATTGTGTAGTCTCCATCCTAGTT 59.984 40.741 0.00 0.00 0.00 2.24
442 459 4.141135 TCCTCCCAGAAAACAAACACCATA 60.141 41.667 0.00 0.00 0.00 2.74
517 534 3.081061 CACGACAAAATCCCCTTCATCA 58.919 45.455 0.00 0.00 0.00 3.07
520 537 2.158740 TGTCACGACAAAATCCCCTTCA 60.159 45.455 0.00 0.00 38.56 3.02
546 563 7.077605 TCATTCTTCAATAAAAACGAGTGCAG 58.922 34.615 0.00 0.00 0.00 4.41
550 567 9.014297 AGGATTCATTCTTCAATAAAAACGAGT 57.986 29.630 0.00 0.00 0.00 4.18
555 572 9.567848 GCGTTAGGATTCATTCTTCAATAAAAA 57.432 29.630 0.00 0.00 0.00 1.94
557 574 8.397906 CAGCGTTAGGATTCATTCTTCAATAAA 58.602 33.333 0.00 0.00 0.00 1.40
582 599 4.400109 GACAGAGCGCGTCGACCA 62.400 66.667 10.58 0.00 0.00 4.02
595 612 3.313012 TTCATACTTGTGACCGGACAG 57.687 47.619 9.46 0.00 0.00 3.51
596 613 3.259625 TCATTCATACTTGTGACCGGACA 59.740 43.478 9.46 5.04 0.00 4.02
597 614 3.857052 TCATTCATACTTGTGACCGGAC 58.143 45.455 9.46 1.07 0.00 4.79
598 615 4.545208 TTCATTCATACTTGTGACCGGA 57.455 40.909 9.46 0.00 0.00 5.14
599 616 4.273480 GGATTCATTCATACTTGTGACCGG 59.727 45.833 0.00 0.00 0.00 5.28
600 617 5.118990 AGGATTCATTCATACTTGTGACCG 58.881 41.667 0.00 0.00 0.00 4.79
601 618 7.254932 GCTTAGGATTCATTCATACTTGTGACC 60.255 40.741 0.00 0.00 0.00 4.02
602 619 7.254932 GGCTTAGGATTCATTCATACTTGTGAC 60.255 40.741 0.00 0.00 0.00 3.67
603 620 6.767902 GGCTTAGGATTCATTCATACTTGTGA 59.232 38.462 0.00 0.00 0.00 3.58
604 621 6.293081 CGGCTTAGGATTCATTCATACTTGTG 60.293 42.308 0.00 0.00 0.00 3.33
605 622 5.760253 CGGCTTAGGATTCATTCATACTTGT 59.240 40.000 0.00 0.00 0.00 3.16
606 623 5.180117 CCGGCTTAGGATTCATTCATACTTG 59.820 44.000 0.00 0.00 0.00 3.16
607 624 5.163195 ACCGGCTTAGGATTCATTCATACTT 60.163 40.000 0.00 0.00 34.73 2.24
608 625 4.348168 ACCGGCTTAGGATTCATTCATACT 59.652 41.667 0.00 0.00 34.73 2.12
609 626 4.642429 ACCGGCTTAGGATTCATTCATAC 58.358 43.478 0.00 0.00 34.73 2.39
610 627 4.560716 CGACCGGCTTAGGATTCATTCATA 60.561 45.833 0.00 0.00 34.73 2.15
611 628 3.744660 GACCGGCTTAGGATTCATTCAT 58.255 45.455 0.00 0.00 34.73 2.57
612 629 2.483013 CGACCGGCTTAGGATTCATTCA 60.483 50.000 0.00 0.00 34.73 2.57
613 630 2.135933 CGACCGGCTTAGGATTCATTC 58.864 52.381 0.00 0.00 34.73 2.67
614 631 1.760613 TCGACCGGCTTAGGATTCATT 59.239 47.619 0.00 0.00 34.73 2.57
615 632 1.068741 GTCGACCGGCTTAGGATTCAT 59.931 52.381 3.51 0.00 34.73 2.57
616 633 0.458669 GTCGACCGGCTTAGGATTCA 59.541 55.000 3.51 0.00 34.73 2.57
617 634 0.594284 CGTCGACCGGCTTAGGATTC 60.594 60.000 10.58 0.00 34.73 2.52
618 635 1.436336 CGTCGACCGGCTTAGGATT 59.564 57.895 10.58 0.00 34.73 3.01
619 636 3.117372 CGTCGACCGGCTTAGGAT 58.883 61.111 10.58 0.00 34.73 3.24
620 637 3.818787 GCGTCGACCGGCTTAGGA 61.819 66.667 10.58 0.00 36.94 2.94
622 639 3.958822 AACGCGTCGACCGGCTTAG 62.959 63.158 23.77 8.65 36.94 2.18
623 640 3.951655 GAACGCGTCGACCGGCTTA 62.952 63.158 23.77 0.00 36.94 3.09
627 644 4.695231 ACAGAACGCGTCGACCGG 62.695 66.667 23.77 13.46 36.94 5.28
628 645 3.164011 GACAGAACGCGTCGACCG 61.164 66.667 14.44 20.16 40.40 4.79
629 646 2.804090 GGACAGAACGCGTCGACC 60.804 66.667 14.44 10.61 34.04 4.79
630 647 3.164011 CGGACAGAACGCGTCGAC 61.164 66.667 14.44 5.18 34.04 4.20
631 648 4.394078 CCGGACAGAACGCGTCGA 62.394 66.667 14.44 0.00 34.04 4.20
632 649 4.695231 ACCGGACAGAACGCGTCG 62.695 66.667 14.44 10.90 34.04 5.12
633 650 2.804090 GACCGGACAGAACGCGTC 60.804 66.667 14.44 6.38 0.00 5.19
634 651 1.588824 TATGACCGGACAGAACGCGT 61.589 55.000 9.46 5.58 0.00 6.01
635 652 0.457166 TTATGACCGGACAGAACGCG 60.457 55.000 9.46 3.53 0.00 6.01
636 653 1.278238 CTTATGACCGGACAGAACGC 58.722 55.000 9.46 0.00 0.00 4.84
637 654 2.649331 ACTTATGACCGGACAGAACG 57.351 50.000 9.46 8.68 0.00 3.95
638 655 5.258456 TCATACTTATGACCGGACAGAAC 57.742 43.478 9.46 0.00 37.76 3.01
639 656 4.341235 CCTCATACTTATGACCGGACAGAA 59.659 45.833 9.46 11.77 37.76 3.02
640 657 3.889538 CCTCATACTTATGACCGGACAGA 59.110 47.826 9.46 1.35 37.76 3.41
652 669 5.104652 GCCTCAACCCTAAACCTCATACTTA 60.105 44.000 0.00 0.00 0.00 2.24
683 700 2.758979 TGAGAGAGTCGGGTTTGATACC 59.241 50.000 0.00 0.00 46.99 2.73
749 1624 4.040339 TGCAAGTCTTCACTAGTCATCCAA 59.960 41.667 0.00 0.00 30.14 3.53
773 1648 6.878923 TCATTTGATTCTCGATTGTTAGTGGT 59.121 34.615 0.00 0.00 0.00 4.16
782 1657 6.207417 ACCAACTTGTCATTTGATTCTCGATT 59.793 34.615 0.00 0.00 0.00 3.34
828 1839 2.093973 CCAGCTTCGTAATGGACAGAGT 60.094 50.000 0.00 0.00 36.09 3.24
866 1877 6.038271 TGTTTCTTTAAGAGCACCTTCAACTC 59.962 38.462 0.00 0.00 36.34 3.01
867 1878 5.885912 TGTTTCTTTAAGAGCACCTTCAACT 59.114 36.000 0.00 0.00 36.34 3.16
868 1879 5.971792 GTGTTTCTTTAAGAGCACCTTCAAC 59.028 40.000 15.67 7.40 36.34 3.18
872 1883 5.297029 GTCAGTGTTTCTTTAAGAGCACCTT 59.703 40.000 19.93 7.46 34.63 3.50
873 1884 4.816925 GTCAGTGTTTCTTTAAGAGCACCT 59.183 41.667 19.93 10.47 34.63 4.00
874 1885 4.574828 TGTCAGTGTTTCTTTAAGAGCACC 59.425 41.667 19.93 11.00 34.63 5.01
875 1886 5.294552 ACTGTCAGTGTTTCTTTAAGAGCAC 59.705 40.000 17.57 17.57 34.44 4.40
876 1887 5.428253 ACTGTCAGTGTTTCTTTAAGAGCA 58.572 37.500 4.21 0.00 0.00 4.26
878 1889 6.701841 TGCTACTGTCAGTGTTTCTTTAAGAG 59.298 38.462 16.03 1.47 0.00 2.85
879 1890 6.479001 GTGCTACTGTCAGTGTTTCTTTAAGA 59.521 38.462 16.03 0.00 0.00 2.10
880 1891 6.480320 AGTGCTACTGTCAGTGTTTCTTTAAG 59.520 38.462 16.03 2.70 0.00 1.85
881 1892 6.346096 AGTGCTACTGTCAGTGTTTCTTTAA 58.654 36.000 16.03 0.00 0.00 1.52
882 1893 5.914033 AGTGCTACTGTCAGTGTTTCTTTA 58.086 37.500 16.03 0.00 0.00 1.85
919 1930 6.855763 TCCTATTTCCTCGTTAGGTTACAA 57.144 37.500 0.00 0.00 44.09 2.41
920 1931 6.855763 TTCCTATTTCCTCGTTAGGTTACA 57.144 37.500 0.00 0.00 44.09 2.41
960 1971 1.678101 GTCTCTTGTTGCTTGGCAGTT 59.322 47.619 0.00 0.00 40.61 3.16
965 1976 1.299541 ACGTGTCTCTTGTTGCTTGG 58.700 50.000 0.00 0.00 0.00 3.61
1361 2385 1.377202 GCCACACACCGATGATGGT 60.377 57.895 6.68 0.00 45.21 3.55
1365 2389 0.613572 TCCTAGCCACACACCGATGA 60.614 55.000 0.00 0.00 0.00 2.92
1402 2426 4.164221 TGGATAGTTTCCTTTCCTAGCCAG 59.836 45.833 1.08 0.00 45.68 4.85
1445 2475 5.066505 CAGGGTAAGTGCATTTATGAGAACC 59.933 44.000 4.86 3.11 0.00 3.62
1471 2501 7.520119 TTTGTACTACTGCGAAATACATCAG 57.480 36.000 0.00 0.00 0.00 2.90
1512 2552 7.169476 GTGTGTTCAAAAGAAGTACTCCTAGAC 59.831 40.741 0.00 0.00 0.00 2.59
1520 2560 7.852945 CAGATGAAGTGTGTTCAAAAGAAGTAC 59.147 37.037 0.00 0.00 31.55 2.73
1554 2594 7.232534 TGAACACTACCTGAAGCCAATAAATTT 59.767 33.333 0.00 0.00 0.00 1.82
1620 2668 3.084536 TGTGATATTGGCCAGCAAGAA 57.915 42.857 5.11 0.00 0.00 2.52
1622 2670 2.953648 TGATGTGATATTGGCCAGCAAG 59.046 45.455 5.11 0.00 0.00 4.01
1642 2732 6.389906 GGATGGTAACTTTTGGAAACAGATG 58.610 40.000 0.00 0.00 39.03 2.90
1660 2750 3.083997 GCTCTGTCCGGGGATGGT 61.084 66.667 0.00 0.00 0.00 3.55
1668 2758 1.537776 GGATGTGAGATGCTCTGTCCG 60.538 57.143 0.00 0.00 0.00 4.79
1684 2774 2.126467 CTGTGTTTTGGCAAACGGATG 58.874 47.619 13.10 0.00 44.76 3.51
1688 2778 0.644843 GCACTGTGTTTTGGCAAACG 59.355 50.000 13.10 1.89 44.76 3.60
1735 2825 1.275291 TCTGGTGAAAGCTCGTAAGGG 59.725 52.381 0.00 0.00 44.72 3.95
1741 2831 6.754209 GGTATATATCATCTGGTGAAAGCTCG 59.246 42.308 0.00 0.00 40.97 5.03
1762 2852 1.043816 CGCATCCAGAGGTCAGGTAT 58.956 55.000 0.00 0.00 0.00 2.73
1774 2864 2.361483 ATGGCTTGCACGCATCCA 60.361 55.556 17.72 13.61 34.89 3.41
1783 2873 1.875009 TCATGATCTCGATGGCTTGC 58.125 50.000 0.00 0.00 0.00 4.01
1822 2912 0.466372 GGAGCAAGATGTTAGCCCCC 60.466 60.000 0.00 0.00 0.00 5.40
1843 2933 1.153429 CATCGGAAACCCGGGTCTC 60.153 63.158 30.40 24.66 46.72 3.36
1960 3050 1.511850 CAACCGTGTTCTCATCAGCA 58.488 50.000 0.00 0.00 0.00 4.41
1990 3080 4.344104 CACAAGGGTTACTGGGATTGATT 58.656 43.478 0.00 0.00 0.00 2.57
2073 3245 3.735237 AGTGAACACACTGTAGACTGG 57.265 47.619 7.68 0.00 42.34 4.00
2317 4636 1.626654 GGTCACACGTTGCGATCCAG 61.627 60.000 0.00 0.00 0.00 3.86
2452 4771 4.811024 TGTTTTAGATAGGATGAAGCGCAG 59.189 41.667 11.47 0.00 0.00 5.18
2527 4846 3.059665 GCTTTGAACTCGCCCAAATTTTG 60.060 43.478 1.99 1.99 32.60 2.44
2598 4917 5.940470 AGAGAAATTTCCGCAATTGTACTCT 59.060 36.000 14.61 3.78 36.69 3.24
2665 4984 1.268899 CAGAAGGACTCGGTACACGTT 59.731 52.381 0.00 0.00 44.69 3.99
2696 5015 5.295292 CAGGTGACAATATTAAGACTGCCAG 59.705 44.000 0.00 0.00 0.00 4.85
2713 5032 0.751643 AAGCCACACAACCAGGTGAC 60.752 55.000 0.00 0.00 41.32 3.67
2719 5038 1.064314 AGTAACCAAGCCACACAACCA 60.064 47.619 0.00 0.00 0.00 3.67
2858 5177 8.106247 ACAACACGTGTGGAAATTAATAGATT 57.894 30.769 29.51 0.95 39.72 2.40
2866 5185 6.197364 TCTTAAACAACACGTGTGGAAATT 57.803 33.333 29.51 20.56 40.60 1.82
2902 5221 4.260661 GCGTGAGAGATAGACGTACATCAA 60.261 45.833 10.53 0.00 35.52 2.57
2903 5222 3.247886 GCGTGAGAGATAGACGTACATCA 59.752 47.826 10.53 0.00 35.52 3.07
3146 5465 5.453057 CCAGCTGATCTAGAGCATGTTAACT 60.453 44.000 17.39 0.09 39.05 2.24
3425 5745 4.058817 AGACGGTCTTGCAAACTAGAAAG 58.941 43.478 4.45 0.00 29.23 2.62
3445 5765 3.245264 GGGATTTTTCCAACAGAGGGAGA 60.245 47.826 0.00 0.00 35.46 3.71
3467 5787 9.645059 TGAAGACTCTTGTATAATGAAACAGAG 57.355 33.333 0.00 0.00 32.19 3.35
3491 5811 7.181305 TCCTTCCTTGGTAAGTACATATTGTGA 59.819 37.037 0.00 0.00 0.00 3.58
3492 5812 7.280205 GTCCTTCCTTGGTAAGTACATATTGTG 59.720 40.741 0.00 0.00 0.00 3.33
3493 5813 7.336396 GTCCTTCCTTGGTAAGTACATATTGT 58.664 38.462 0.00 0.00 0.00 2.71
3494 5814 6.766467 GGTCCTTCCTTGGTAAGTACATATTG 59.234 42.308 0.00 0.00 0.00 1.90
3495 5815 6.445786 TGGTCCTTCCTTGGTAAGTACATATT 59.554 38.462 0.00 0.00 37.07 1.28
3496 5816 5.968167 TGGTCCTTCCTTGGTAAGTACATAT 59.032 40.000 0.00 0.00 37.07 1.78
3499 5819 3.589641 TGGTCCTTCCTTGGTAAGTACA 58.410 45.455 0.00 0.00 37.07 2.90
3662 5982 6.020995 GTGTTGTTGCTGTGTACATTTGTTAC 60.021 38.462 0.00 0.00 0.00 2.50
3663 5983 6.030849 GTGTTGTTGCTGTGTACATTTGTTA 58.969 36.000 0.00 0.00 0.00 2.41
3722 6433 6.720309 TCATGTACATCAGGGAAGATTTGAA 58.280 36.000 5.07 0.00 0.00 2.69
3866 6577 4.868268 TCTTTGAGCTTAGGCCTCTACTA 58.132 43.478 9.68 0.00 39.73 1.82
3873 6584 4.202441 TCAATCATCTTTGAGCTTAGGCC 58.798 43.478 0.00 0.00 39.73 5.19
4031 6742 3.126343 CCACTTACAAAACCGGTATGAGC 59.874 47.826 23.01 0.00 0.00 4.26
4035 6746 3.143211 TGCCACTTACAAAACCGGTAT 57.857 42.857 8.00 0.00 0.00 2.73
4042 6753 7.324935 TCTTCGATAGTATGCCACTTACAAAA 58.675 34.615 0.00 0.00 38.80 2.44
4124 6835 0.472471 TGAGTCCGACCCAAAAAGCT 59.528 50.000 0.00 0.00 0.00 3.74
4168 6879 7.365741 CCTTTTTCTCATAGCGCATCATATTT 58.634 34.615 11.47 0.00 0.00 1.40
4215 6926 4.772624 GGTAAGAAAGGGGCTTGAGAAATT 59.227 41.667 0.00 0.00 0.00 1.82
4238 8394 2.086869 CACCAATCTTAGGGCACACAG 58.913 52.381 0.00 0.00 0.00 3.66
4280 8436 2.961741 AGAAGTGTGCTCTCTTGACTGA 59.038 45.455 7.74 0.00 0.00 3.41
4286 8442 0.965439 AGCGAGAAGTGTGCTCTCTT 59.035 50.000 2.93 2.93 32.44 2.85
4330 8486 2.457366 CGAAAGCAGTGAACCCTAGT 57.543 50.000 0.00 0.00 0.00 2.57
4351 8507 2.032681 GAGGTGGGCAAACGCTCT 59.967 61.111 0.00 0.00 0.00 4.09
4353 8509 4.660938 GGGAGGTGGGCAAACGCT 62.661 66.667 0.00 0.00 0.00 5.07
4354 8510 4.966787 TGGGAGGTGGGCAAACGC 62.967 66.667 0.00 0.00 0.00 4.84
4355 8511 2.983592 GTGGGAGGTGGGCAAACG 60.984 66.667 0.00 0.00 0.00 3.60
4356 8512 1.903404 CAGTGGGAGGTGGGCAAAC 60.903 63.158 0.00 0.00 0.00 2.93
4357 8513 2.351924 GACAGTGGGAGGTGGGCAAA 62.352 60.000 0.00 0.00 0.00 3.68
4358 8514 2.776526 ACAGTGGGAGGTGGGCAA 60.777 61.111 0.00 0.00 0.00 4.52
4373 8532 0.644380 ATGGATGGAGGAGGGAGACA 59.356 55.000 0.00 0.00 0.00 3.41
4375 8534 3.565979 CATGGATGGAGGAGGGAGA 57.434 57.895 0.00 0.00 0.00 3.71
4399 8558 1.673400 TGCTACGAGATGAGAGAGCAC 59.327 52.381 0.00 0.00 35.12 4.40
4406 8565 5.050499 GGATTTGTGATTGCTACGAGATGAG 60.050 44.000 0.00 0.00 0.00 2.90
4479 8639 8.552034 CCTTTTCTAGAATATGAAATGACGACC 58.448 37.037 5.89 0.00 33.04 4.79
4498 8658 0.769247 ACAAGGCGTACCCCTTTTCT 59.231 50.000 9.18 0.00 42.48 2.52
4500 8660 0.604511 CGACAAGGCGTACCCCTTTT 60.605 55.000 9.18 3.24 42.48 2.27
4505 8665 1.143969 CGAATCGACAAGGCGTACCC 61.144 60.000 0.00 0.00 36.11 3.69
4546 8706 6.905076 GTGTGTGTGTGTTCACTTACTTAATG 59.095 38.462 4.59 0.00 44.14 1.90
4565 8725 2.695613 TTTGTGTGTGTGTGTGTGTG 57.304 45.000 0.00 0.00 0.00 3.82
4567 8727 3.637432 AGTTTTTGTGTGTGTGTGTGTG 58.363 40.909 0.00 0.00 0.00 3.82
4568 8728 3.316588 TGAGTTTTTGTGTGTGTGTGTGT 59.683 39.130 0.00 0.00 0.00 3.72
4569 8729 3.894920 TGAGTTTTTGTGTGTGTGTGTG 58.105 40.909 0.00 0.00 0.00 3.82
4570 8730 4.576216 TTGAGTTTTTGTGTGTGTGTGT 57.424 36.364 0.00 0.00 0.00 3.72
4571 8731 5.233050 TGTTTTGAGTTTTTGTGTGTGTGTG 59.767 36.000 0.00 0.00 0.00 3.82
4572 8732 5.233263 GTGTTTTGAGTTTTTGTGTGTGTGT 59.767 36.000 0.00 0.00 0.00 3.72
4573 8733 5.233050 TGTGTTTTGAGTTTTTGTGTGTGTG 59.767 36.000 0.00 0.00 0.00 3.82
4574 8734 5.352284 TGTGTTTTGAGTTTTTGTGTGTGT 58.648 33.333 0.00 0.00 0.00 3.72
4575 8735 5.896922 TGTGTTTTGAGTTTTTGTGTGTG 57.103 34.783 0.00 0.00 0.00 3.82
4576 8736 6.910536 TTTGTGTTTTGAGTTTTTGTGTGT 57.089 29.167 0.00 0.00 0.00 3.72
4577 8737 7.163357 GTGTTTTGTGTTTTGAGTTTTTGTGTG 59.837 33.333 0.00 0.00 0.00 3.82
4578 8738 7.148407 TGTGTTTTGTGTTTTGAGTTTTTGTGT 60.148 29.630 0.00 0.00 0.00 3.72
4579 8739 7.182761 TGTGTTTTGTGTTTTGAGTTTTTGTG 58.817 30.769 0.00 0.00 0.00 3.33
4580 8740 7.308782 TGTGTTTTGTGTTTTGAGTTTTTGT 57.691 28.000 0.00 0.00 0.00 2.83
4581 8741 8.606727 TTTGTGTTTTGTGTTTTGAGTTTTTG 57.393 26.923 0.00 0.00 0.00 2.44
4643 8810 1.950484 GCACTGGGTTGGATCGTGATT 60.950 52.381 0.00 0.00 0.00 2.57
4647 8814 2.047274 CGCACTGGGTTGGATCGT 60.047 61.111 0.00 0.00 0.00 3.73
4648 8815 3.499737 GCGCACTGGGTTGGATCG 61.500 66.667 0.30 0.00 0.00 3.69
4659 8827 0.901124 AGATTCCTCTCTTGCGCACT 59.099 50.000 11.12 0.00 0.00 4.40
4661 8829 0.107993 CCAGATTCCTCTCTTGCGCA 60.108 55.000 5.66 5.66 0.00 6.09
4663 8831 2.158986 ACATCCAGATTCCTCTCTTGCG 60.159 50.000 0.00 0.00 0.00 4.85
4676 8844 4.715534 TTACCCTTTCAACACATCCAGA 57.284 40.909 0.00 0.00 0.00 3.86
4680 8848 5.957842 TGTCATTACCCTTTCAACACATC 57.042 39.130 0.00 0.00 0.00 3.06
4691 8859 5.360714 CCAAGTATGCAAATGTCATTACCCT 59.639 40.000 0.00 0.00 0.00 4.34
4781 8949 8.265165 AGGATGATCATGTTTGATGATTATCG 57.735 34.615 14.30 0.00 45.11 2.92
4795 8963 4.624843 GCCACTGGGTATAGGATGATCATG 60.625 50.000 14.30 0.00 36.17 3.07
4813 8981 3.314331 CCACCTGTCTCCGCCACT 61.314 66.667 0.00 0.00 0.00 4.00
4814 8982 4.394712 CCCACCTGTCTCCGCCAC 62.395 72.222 0.00 0.00 0.00 5.01
4815 8983 4.954118 ACCCACCTGTCTCCGCCA 62.954 66.667 0.00 0.00 0.00 5.69
4816 8984 4.394712 CACCCACCTGTCTCCGCC 62.395 72.222 0.00 0.00 0.00 6.13
4818 8986 4.394712 GGCACCCACCTGTCTCCG 62.395 72.222 0.00 0.00 0.00 4.63
4819 8987 3.249189 TGGCACCCACCTGTCTCC 61.249 66.667 0.00 0.00 0.00 3.71
4820 8988 2.348998 CTGGCACCCACCTGTCTC 59.651 66.667 0.00 0.00 0.00 3.36
4821 8989 3.958860 GCTGGCACCCACCTGTCT 61.959 66.667 0.00 0.00 0.00 3.41
4834 9002 3.766691 GCATGTTGGCCTGGCTGG 61.767 66.667 19.68 5.98 39.35 4.85
4835 9003 2.102109 TTTGCATGTTGGCCTGGCTG 62.102 55.000 19.68 9.61 0.00 4.85
4837 9005 0.536260 TATTTGCATGTTGGCCTGGC 59.464 50.000 11.05 11.05 0.00 4.85
4838 9006 1.826720 ACTATTTGCATGTTGGCCTGG 59.173 47.619 3.32 0.00 0.00 4.45
4839 9007 3.514645 GAACTATTTGCATGTTGGCCTG 58.485 45.455 3.32 0.00 0.00 4.85
4840 9008 2.497273 GGAACTATTTGCATGTTGGCCT 59.503 45.455 3.32 0.00 0.00 5.19
4841 9009 2.233431 TGGAACTATTTGCATGTTGGCC 59.767 45.455 0.00 0.00 0.00 5.36
4842 9010 3.253230 GTGGAACTATTTGCATGTTGGC 58.747 45.455 0.00 0.00 35.26 4.52
4857 9025 4.698583 ATACTCAGTGTCGTAGTGGAAC 57.301 45.455 0.00 0.00 0.00 3.62


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

AutoCloner maintained by Alex Coulton.