Multiple sequence alignment - TraesCS3A01G187200

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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 TraesCS3A01G187200 chr3A 100.000 8072 0 0 1 8072 222459240 222451169 0.000000e+00 14907.0
1 TraesCS3A01G187200 chr3A 79.772 351 42 13 7559 7896 686536574 686536240 2.270000e-55 228.0
2 TraesCS3A01G187200 chr3A 91.176 68 5 1 13 80 222459181 222459115 3.100000e-14 91.6
3 TraesCS3A01G187200 chr3A 94.000 50 2 1 6283 6331 231013840 231013791 3.120000e-09 75.0
4 TraesCS3A01G187200 chr3D 95.325 3251 85 21 2018 5238 179460379 179457166 0.000000e+00 5099.0
5 TraesCS3A01G187200 chr3D 95.175 1140 24 6 889 2004 179461496 179460364 0.000000e+00 1772.0
6 TraesCS3A01G187200 chr3D 96.234 717 23 3 5581 6293 179456647 179455931 0.000000e+00 1171.0
7 TraesCS3A01G187200 chr3D 91.322 726 59 4 62 785 179464948 179464225 0.000000e+00 989.0
8 TraesCS3A01G187200 chr3D 97.727 528 10 2 6329 6855 179455946 179455420 0.000000e+00 907.0
9 TraesCS3A01G187200 chr3D 90.028 702 67 3 62 762 305598144 305597445 0.000000e+00 905.0
10 TraesCS3A01G187200 chr3D 94.220 346 16 3 5237 5579 179457072 179456728 7.180000e-145 525.0
11 TraesCS3A01G187200 chr3D 82.500 360 37 18 7503 7853 116078961 116078619 7.920000e-75 292.0
12 TraesCS3A01G187200 chr3D 97.778 45 1 0 854 898 179463133 179463089 2.420000e-10 78.7
13 TraesCS3A01G187200 chr3B 95.746 1810 54 9 2709 4505 257523115 257521316 0.000000e+00 2894.0
14 TraesCS3A01G187200 chr3B 95.331 1328 55 6 4972 6294 257517336 257516011 0.000000e+00 2102.0
15 TraesCS3A01G187200 chr3B 93.978 1179 36 6 854 2004 257524992 257523821 0.000000e+00 1751.0
16 TraesCS3A01G187200 chr3B 98.161 707 12 1 2018 2723 257523836 257523130 0.000000e+00 1232.0
17 TraesCS3A01G187200 chr3B 96.162 495 15 4 6363 6855 257515984 257515492 0.000000e+00 806.0
18 TraesCS3A01G187200 chr3B 95.508 423 18 1 4489 4911 257517870 257517449 0.000000e+00 675.0
19 TraesCS3A01G187200 chr3B 89.848 197 17 2 7549 7745 169656839 169656646 4.840000e-62 250.0
20 TraesCS3A01G187200 chr4A 85.886 1247 120 26 6848 8072 647915812 647917024 0.000000e+00 1277.0
21 TraesCS3A01G187200 chr2D 90.537 708 62 5 62 767 484936584 484937288 0.000000e+00 931.0
22 TraesCS3A01G187200 chr2D 88.873 701 63 12 66 762 388052123 388052812 0.000000e+00 848.0
23 TraesCS3A01G187200 chr2D 95.745 47 2 0 6285 6331 421800661 421800615 8.690000e-10 76.8
24 TraesCS3A01G187200 chr7D 89.453 749 52 13 6851 7590 509579704 509578974 0.000000e+00 920.0
25 TraesCS3A01G187200 chr7D 90.424 637 55 6 62 697 618331259 618331890 0.000000e+00 833.0
26 TraesCS3A01G187200 chr7D 84.877 529 47 16 7573 8072 509577822 509577298 3.360000e-138 503.0
27 TraesCS3A01G187200 chr6D 89.037 748 55 13 6852 7590 271102167 271101438 0.000000e+00 902.0
28 TraesCS3A01G187200 chr6D 85.199 527 46 16 7574 8072 271100268 271099746 5.590000e-141 512.0
29 TraesCS3A01G187200 chr2B 89.327 684 70 3 90 772 532551707 532551026 0.000000e+00 856.0
30 TraesCS3A01G187200 chr2B 86.809 705 85 7 66 766 24826279 24825579 0.000000e+00 780.0
31 TraesCS3A01G187200 chr2B 97.826 46 1 0 6287 6332 764727068 764727113 6.720000e-11 80.5
32 TraesCS3A01G187200 chr2A 87.767 703 67 11 62 762 524723443 524724128 0.000000e+00 804.0
33 TraesCS3A01G187200 chrUn 86.648 704 90 4 62 764 101060032 101060732 0.000000e+00 776.0
34 TraesCS3A01G187200 chrUn 95.122 41 2 0 4726 4766 82493392 82493432 1.880000e-06 65.8
35 TraesCS3A01G187200 chr6B 89.065 631 55 7 6852 7471 565207086 565206459 0.000000e+00 771.0
36 TraesCS3A01G187200 chr6B 87.477 551 34 10 7549 8071 565206373 565205830 3.220000e-168 603.0
37 TraesCS3A01G187200 chr6B 86.751 551 38 10 7549 8071 403197696 403198239 1.510000e-161 580.0
38 TraesCS3A01G187200 chr6B 90.758 422 35 3 7052 7471 403197191 403197610 1.970000e-155 560.0
39 TraesCS3A01G187200 chr6B 89.952 209 19 2 6852 7059 403196951 403197158 1.340000e-67 268.0
40 TraesCS3A01G187200 chr6B 97.826 46 1 0 6286 6331 529711919 529711964 6.720000e-11 80.5
41 TraesCS3A01G187200 chr6B 86.364 66 7 2 6267 6331 321300598 321300662 4.040000e-08 71.3
42 TraesCS3A01G187200 chr5A 90.119 587 54 4 6852 7437 31964018 31963435 0.000000e+00 760.0
43 TraesCS3A01G187200 chr5A 90.977 532 46 2 6891 7421 28391382 28391912 0.000000e+00 715.0
44 TraesCS3A01G187200 chr5A 92.276 246 17 2 7722 7966 31656788 31656544 1.670000e-91 348.0
45 TraesCS3A01G187200 chr5A 92.276 246 17 2 7722 7966 31863751 31863507 1.670000e-91 348.0
46 TraesCS3A01G187200 chr5A 91.870 246 18 2 7722 7966 31622624 31622380 7.760000e-90 342.0
47 TraesCS3A01G187200 chr5A 91.870 246 18 2 7722 7966 31688262 31688018 7.760000e-90 342.0
48 TraesCS3A01G187200 chr5A 83.483 333 24 14 7413 7738 31592821 31592513 1.720000e-71 281.0
49 TraesCS3A01G187200 chr5A 83.483 333 24 14 7413 7738 31657969 31657661 1.720000e-71 281.0
50 TraesCS3A01G187200 chr5A 83.483 333 24 14 7413 7738 31741789 31741481 1.720000e-71 281.0
51 TraesCS3A01G187200 chr5A 83.183 333 25 14 7413 7738 31623805 31623497 7.980000e-70 276.0
52 TraesCS3A01G187200 chr5A 83.183 333 25 14 7413 7738 31689442 31689134 7.980000e-70 276.0
53 TraesCS3A01G187200 chr6A 90.000 570 54 2 6854 7421 454692530 454693098 0.000000e+00 734.0
54 TraesCS3A01G187200 chr6A 91.009 456 41 0 6851 7306 39091066 39090611 4.140000e-172 616.0
55 TraesCS3A01G187200 chr5D 84.597 409 43 8 7503 7896 445393668 445394071 9.820000e-104 388.0
56 TraesCS3A01G187200 chr1B 82.240 366 47 12 7504 7854 626597503 626597141 4.740000e-77 300.0
57 TraesCS3A01G187200 chr1B 80.163 368 42 14 7503 7853 165762323 165761970 6.260000e-61 246.0
58 TraesCS3A01G187200 chr1B 89.655 58 4 2 6274 6331 141293765 141293820 1.120000e-08 73.1
59 TraesCS3A01G187200 chr4B 80.196 409 55 16 7509 7900 546130739 546130340 4.770000e-72 283.0
60 TraesCS3A01G187200 chr4D 100.000 44 0 0 6287 6330 92862601 92862558 1.870000e-11 82.4
61 TraesCS3A01G187200 chr4D 100.000 43 0 0 6289 6331 179880353 179880311 6.720000e-11 80.5
62 TraesCS3A01G187200 chr1D 100.000 43 0 0 6289 6331 379151997 379151955 6.720000e-11 80.5
63 TraesCS3A01G187200 chr7B 97.059 34 1 0 6851 6884 708504459 708504426 3.150000e-04 58.4


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 TraesCS3A01G187200 chr3A 222451169 222459240 8071 True 7499.300000 14907 95.588000 1 8072 2 chr3A.!!$R3 8071
1 TraesCS3A01G187200 chr3D 179455420 179464948 9528 True 1505.957143 5099 95.397286 62 6855 7 chr3D.!!$R3 6793
2 TraesCS3A01G187200 chr3D 305597445 305598144 699 True 905.000000 905 90.028000 62 762 1 chr3D.!!$R2 700
3 TraesCS3A01G187200 chr3B 257515492 257524992 9500 True 1576.666667 2894 95.814333 854 6855 6 chr3B.!!$R2 6001
4 TraesCS3A01G187200 chr4A 647915812 647917024 1212 False 1277.000000 1277 85.886000 6848 8072 1 chr4A.!!$F1 1224
5 TraesCS3A01G187200 chr2D 484936584 484937288 704 False 931.000000 931 90.537000 62 767 1 chr2D.!!$F2 705
6 TraesCS3A01G187200 chr2D 388052123 388052812 689 False 848.000000 848 88.873000 66 762 1 chr2D.!!$F1 696
7 TraesCS3A01G187200 chr7D 618331259 618331890 631 False 833.000000 833 90.424000 62 697 1 chr7D.!!$F1 635
8 TraesCS3A01G187200 chr7D 509577298 509579704 2406 True 711.500000 920 87.165000 6851 8072 2 chr7D.!!$R1 1221
9 TraesCS3A01G187200 chr6D 271099746 271102167 2421 True 707.000000 902 87.118000 6852 8072 2 chr6D.!!$R1 1220
10 TraesCS3A01G187200 chr2B 532551026 532551707 681 True 856.000000 856 89.327000 90 772 1 chr2B.!!$R2 682
11 TraesCS3A01G187200 chr2B 24825579 24826279 700 True 780.000000 780 86.809000 66 766 1 chr2B.!!$R1 700
12 TraesCS3A01G187200 chr2A 524723443 524724128 685 False 804.000000 804 87.767000 62 762 1 chr2A.!!$F1 700
13 TraesCS3A01G187200 chrUn 101060032 101060732 700 False 776.000000 776 86.648000 62 764 1 chrUn.!!$F2 702
14 TraesCS3A01G187200 chr6B 565205830 565207086 1256 True 687.000000 771 88.271000 6852 8071 2 chr6B.!!$R1 1219
15 TraesCS3A01G187200 chr6B 403196951 403198239 1288 False 469.333333 580 89.153667 6852 8071 3 chr6B.!!$F3 1219
16 TraesCS3A01G187200 chr5A 31963435 31964018 583 True 760.000000 760 90.119000 6852 7437 1 chr5A.!!$R4 585
17 TraesCS3A01G187200 chr5A 28391382 28391912 530 False 715.000000 715 90.977000 6891 7421 1 chr5A.!!$F1 530
18 TraesCS3A01G187200 chr5A 31656544 31657969 1425 True 314.500000 348 87.879500 7413 7966 2 chr5A.!!$R6 553
19 TraesCS3A01G187200 chr5A 31622380 31623805 1425 True 309.000000 342 87.526500 7413 7966 2 chr5A.!!$R5 553
20 TraesCS3A01G187200 chr5A 31688018 31689442 1424 True 309.000000 342 87.526500 7413 7966 2 chr5A.!!$R7 553
21 TraesCS3A01G187200 chr6A 454692530 454693098 568 False 734.000000 734 90.000000 6854 7421 1 chr6A.!!$F1 567

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
684 690 0.251386 TGCGGGCCAGGTTTTTGATA 60.251 50.000 4.39 0.00 0.00 2.15 F
846 1861 1.681538 TTAGCTCACCTAGGCTCGAG 58.318 55.000 9.30 13.45 39.65 4.04 F
2218 4918 1.382522 CACTGCACAGGACAACAACT 58.617 50.000 2.21 0.00 0.00 3.16 F
2657 5357 1.686355 TCTTTGGTCGGCAATGTGTT 58.314 45.000 0.00 0.00 0.00 3.32 F
2983 5717 2.236146 ACTGATGCCGGTATGTCTTTGA 59.764 45.455 10.77 0.00 0.00 2.69 F
3823 6564 1.270465 TGTGAGTGAGTGTGGATGCAG 60.270 52.381 0.00 0.00 0.00 4.41 F
4698 10922 1.471684 CTTGGAATCAGGAAGCACAGC 59.528 52.381 0.00 0.00 0.00 4.40 F
5325 11736 0.241749 TATTCACGTCTGTTCGCGGT 59.758 50.000 6.13 0.00 0.00 5.68 F
6320 12820 1.018910 GCTTTCGCCCCGCTTTATAA 58.981 50.000 0.00 0.00 0.00 0.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2218 4918 2.356665 TGAGTAAGGCTTGGTTTGCA 57.643 45.000 10.69 0.00 0.00 4.08 R
2818 5548 2.425668 GCAGCCCAACATACCGTTTTAT 59.574 45.455 0.00 0.00 34.86 1.40 R
3594 6328 0.038892 GGGCACAAGCACAGTTCATG 60.039 55.000 0.00 0.00 45.91 3.07 R
3804 6538 1.436600 CTGCATCCACACTCACTCAC 58.563 55.000 0.00 0.00 0.00 3.51 R
4801 11025 0.039798 AAGCTTCAAGTGCACATGCG 60.040 50.000 21.04 12.55 45.83 4.73 R
4828 11052 0.466007 TTTTGCTGCAGCCAGAGACA 60.466 50.000 34.64 12.62 41.77 3.41 R
6487 12997 1.815421 GGCACACAGGCTCCGTATG 60.815 63.158 0.00 0.00 40.24 2.39 R
7001 13516 0.326238 ATGTAGGTCCGGGGTGATGT 60.326 55.000 0.00 0.00 0.00 3.06 R
8037 17925 1.000955 AGTGTTCTGGTACAAGAGCCG 59.999 52.381 11.25 0.00 38.70 5.52 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
17 18 2.398429 CGTGCATCTCAGCTTGCG 59.602 61.111 3.79 0.00 41.80 4.85
18 19 2.099831 GTGCATCTCAGCTTGCGC 59.900 61.111 0.00 0.00 41.80 6.09
19 20 3.129502 TGCATCTCAGCTTGCGCC 61.130 61.111 4.18 0.00 41.80 6.53
20 21 4.233635 GCATCTCAGCTTGCGCCG 62.234 66.667 4.18 0.00 36.60 6.46
21 22 3.570638 CATCTCAGCTTGCGCCGG 61.571 66.667 4.18 0.00 36.60 6.13
33 34 4.933064 CGCCGGCTCGAGGATGAC 62.933 72.222 26.68 0.00 0.00 3.06
34 35 4.933064 GCCGGCTCGAGGATGACG 62.933 72.222 22.15 2.01 0.00 4.35
35 36 4.933064 CCGGCTCGAGGATGACGC 62.933 72.222 15.58 0.00 0.00 5.19
36 37 4.933064 CGGCTCGAGGATGACGCC 62.933 72.222 15.58 7.06 37.40 5.68
37 38 4.933064 GGCTCGAGGATGACGCCG 62.933 72.222 15.58 0.00 0.00 6.46
38 39 4.933064 GCTCGAGGATGACGCCGG 62.933 72.222 15.58 0.00 0.00 6.13
39 40 4.933064 CTCGAGGATGACGCCGGC 62.933 72.222 19.07 19.07 0.00 6.13
51 52 4.632458 GCCGGCGTCCTCGAGATC 62.632 72.222 12.58 5.37 39.71 2.75
52 53 3.967335 CCGGCGTCCTCGAGATCC 61.967 72.222 15.71 7.99 39.71 3.36
53 54 3.967335 CGGCGTCCTCGAGATCCC 61.967 72.222 15.71 7.60 39.71 3.85
54 55 3.607661 GGCGTCCTCGAGATCCCC 61.608 72.222 15.71 5.20 39.71 4.81
55 56 2.519780 GCGTCCTCGAGATCCCCT 60.520 66.667 15.71 0.00 39.71 4.79
56 57 2.557372 GCGTCCTCGAGATCCCCTC 61.557 68.421 15.71 0.00 39.71 4.30
57 58 1.899534 CGTCCTCGAGATCCCCTCC 60.900 68.421 15.71 0.00 38.71 4.30
58 59 1.532078 GTCCTCGAGATCCCCTCCC 60.532 68.421 15.71 0.00 38.71 4.30
59 60 2.203714 CCTCGAGATCCCCTCCCC 60.204 72.222 15.71 0.00 38.71 4.81
60 61 2.784654 CCTCGAGATCCCCTCCCCT 61.785 68.421 15.71 0.00 38.71 4.79
123 124 2.434884 CTTGCACCGGACGCAGAT 60.435 61.111 19.75 0.00 41.18 2.90
490 495 1.128188 AGAGGGAGTGGGTGTGAACC 61.128 60.000 0.00 0.00 0.00 3.62
521 526 4.361971 ACGAGAGAGGGCGTGGGA 62.362 66.667 0.00 0.00 39.56 4.37
684 690 0.251386 TGCGGGCCAGGTTTTTGATA 60.251 50.000 4.39 0.00 0.00 2.15
693 699 3.420893 CAGGTTTTTGATACAGCCCAGA 58.579 45.455 0.00 0.00 0.00 3.86
706 712 4.666512 ACAGCCCAGACAATCAAATAAGT 58.333 39.130 0.00 0.00 0.00 2.24
769 775 5.183228 CCAACCAAACACGTCCTAATAGAT 58.817 41.667 0.00 0.00 0.00 1.98
772 778 4.188462 CCAAACACGTCCTAATAGATGCA 58.812 43.478 0.00 0.00 0.00 3.96
773 779 4.271049 CCAAACACGTCCTAATAGATGCAG 59.729 45.833 0.00 0.00 0.00 4.41
774 780 5.109210 CAAACACGTCCTAATAGATGCAGA 58.891 41.667 0.00 0.00 0.00 4.26
775 781 5.537300 AACACGTCCTAATAGATGCAGAT 57.463 39.130 0.00 0.00 0.00 2.90
776 782 4.876125 ACACGTCCTAATAGATGCAGATG 58.124 43.478 0.00 0.00 0.00 2.90
777 783 4.342378 ACACGTCCTAATAGATGCAGATGT 59.658 41.667 0.00 0.00 0.00 3.06
778 784 5.163405 ACACGTCCTAATAGATGCAGATGTT 60.163 40.000 0.00 0.00 0.00 2.71
779 785 5.176406 CACGTCCTAATAGATGCAGATGTTG 59.824 44.000 0.00 0.00 0.00 3.33
780 786 4.687948 CGTCCTAATAGATGCAGATGTTGG 59.312 45.833 0.00 0.00 0.00 3.77
781 787 5.615289 GTCCTAATAGATGCAGATGTTGGT 58.385 41.667 0.00 0.00 0.00 3.67
782 788 6.516693 CGTCCTAATAGATGCAGATGTTGGTA 60.517 42.308 0.00 0.00 0.00 3.25
783 789 7.390027 GTCCTAATAGATGCAGATGTTGGTAT 58.610 38.462 0.00 0.00 0.00 2.73
784 790 7.880195 GTCCTAATAGATGCAGATGTTGGTATT 59.120 37.037 0.00 0.00 0.00 1.89
785 791 7.879677 TCCTAATAGATGCAGATGTTGGTATTG 59.120 37.037 0.00 0.00 0.00 1.90
786 792 7.663081 CCTAATAGATGCAGATGTTGGTATTGT 59.337 37.037 0.00 0.00 0.00 2.71
787 793 7.502120 AATAGATGCAGATGTTGGTATTGTC 57.498 36.000 0.00 0.00 0.00 3.18
788 794 5.108187 AGATGCAGATGTTGGTATTGTCT 57.892 39.130 0.00 0.00 0.00 3.41
789 795 6.239217 AGATGCAGATGTTGGTATTGTCTA 57.761 37.500 0.00 0.00 0.00 2.59
790 796 6.653020 AGATGCAGATGTTGGTATTGTCTAA 58.347 36.000 0.00 0.00 0.00 2.10
791 797 7.112122 AGATGCAGATGTTGGTATTGTCTAAA 58.888 34.615 0.00 0.00 0.00 1.85
792 798 7.611467 AGATGCAGATGTTGGTATTGTCTAAAA 59.389 33.333 0.00 0.00 0.00 1.52
793 799 7.517614 TGCAGATGTTGGTATTGTCTAAAAA 57.482 32.000 0.00 0.00 0.00 1.94
819 825 5.796424 AAAGATGCAGATGTTGGTTTTCT 57.204 34.783 0.00 0.00 0.00 2.52
820 826 5.382618 AAGATGCAGATGTTGGTTTTCTC 57.617 39.130 0.00 0.00 0.00 2.87
821 827 4.401022 AGATGCAGATGTTGGTTTTCTCA 58.599 39.130 0.00 0.00 0.00 3.27
822 828 3.988379 TGCAGATGTTGGTTTTCTCAC 57.012 42.857 0.00 0.00 0.00 3.51
846 1861 1.681538 TTAGCTCACCTAGGCTCGAG 58.318 55.000 9.30 13.45 39.65 4.04
1002 3667 4.592936 CTCGGCGCCTCGACTACG 62.593 72.222 26.68 8.62 41.26 3.51
1052 3725 4.570874 GGCGAGATGGCTTCCCCC 62.571 72.222 0.00 0.00 40.72 5.40
1053 3726 4.918201 GCGAGATGGCTTCCCCCG 62.918 72.222 0.00 0.71 0.00 5.73
1054 3727 3.154473 CGAGATGGCTTCCCCCGA 61.154 66.667 0.00 0.00 0.00 5.14
1159 3835 3.470888 CTTCGATCCCAGCCCCGT 61.471 66.667 0.00 0.00 0.00 5.28
1426 4105 2.027653 CCAGTTCCTCTTCAGGTCCTTC 60.028 54.545 0.00 0.00 41.28 3.46
1629 4309 3.128415 GGACGTTCTACTGTTAGGTCCTC 59.872 52.174 15.66 0.00 39.42 3.71
1723 4403 8.570068 TTCAGGTTAACATATACTTTTGTCCC 57.430 34.615 8.10 0.00 0.00 4.46
1919 4619 6.042143 CCATAAAATTTGGTCAGCATGGTAC 58.958 40.000 0.00 0.00 36.16 3.34
1994 4694 9.148879 AGATAGATACTGTATGTTTTGCTACCT 57.851 33.333 4.79 0.00 0.00 3.08
1995 4695 9.197694 GATAGATACTGTATGTTTTGCTACCTG 57.802 37.037 4.79 0.00 0.00 4.00
1996 4696 6.947464 AGATACTGTATGTTTTGCTACCTGT 58.053 36.000 4.79 0.00 0.00 4.00
1997 4697 7.394816 AGATACTGTATGTTTTGCTACCTGTT 58.605 34.615 4.79 0.00 0.00 3.16
1998 4698 5.941948 ACTGTATGTTTTGCTACCTGTTC 57.058 39.130 0.00 0.00 0.00 3.18
1999 4699 5.621193 ACTGTATGTTTTGCTACCTGTTCT 58.379 37.500 0.00 0.00 0.00 3.01
2000 4700 6.062095 ACTGTATGTTTTGCTACCTGTTCTT 58.938 36.000 0.00 0.00 0.00 2.52
2001 4701 7.221450 ACTGTATGTTTTGCTACCTGTTCTTA 58.779 34.615 0.00 0.00 0.00 2.10
2002 4702 7.717875 ACTGTATGTTTTGCTACCTGTTCTTAA 59.282 33.333 0.00 0.00 0.00 1.85
2003 4703 8.630054 TGTATGTTTTGCTACCTGTTCTTAAT 57.370 30.769 0.00 0.00 0.00 1.40
2004 4704 9.073475 TGTATGTTTTGCTACCTGTTCTTAATT 57.927 29.630 0.00 0.00 0.00 1.40
2005 4705 9.908152 GTATGTTTTGCTACCTGTTCTTAATTT 57.092 29.630 0.00 0.00 0.00 1.82
2007 4707 9.830975 ATGTTTTGCTACCTGTTCTTAATTTTT 57.169 25.926 0.00 0.00 0.00 1.94
2218 4918 1.382522 CACTGCACAGGACAACAACT 58.617 50.000 2.21 0.00 0.00 3.16
2320 5020 8.766000 TTGCATGTTCTATTTACGTTTCTCTA 57.234 30.769 0.00 0.00 0.00 2.43
2647 5347 8.328864 GCTTCAACTAGTAAATATCTTTGGTCG 58.671 37.037 0.00 0.00 0.00 4.79
2657 5357 1.686355 TCTTTGGTCGGCAATGTGTT 58.314 45.000 0.00 0.00 0.00 3.32
2818 5548 8.527810 GTTCTGTGTTAATATTTCCATCCCAAA 58.472 33.333 0.00 0.00 0.00 3.28
2983 5717 2.236146 ACTGATGCCGGTATGTCTTTGA 59.764 45.455 10.77 0.00 0.00 2.69
3000 5734 6.017933 GTCTTTGAAATTGCAGAGTATGACG 58.982 40.000 3.97 0.00 0.00 4.35
3475 6209 7.001073 AGAGAGCAGAACTTTTTGGTATTTCT 58.999 34.615 0.00 0.00 0.00 2.52
3715 6449 8.007405 ACCTTTATATATCAAAGCAAACCCAC 57.993 34.615 0.00 0.00 32.69 4.61
3747 6481 5.106442 CGTTAAATTCATGTTAAAGGGGGC 58.894 41.667 0.00 0.00 0.00 5.80
3804 6538 1.336755 CTGGGTTGGTCGGAAGTTTTG 59.663 52.381 0.00 0.00 0.00 2.44
3823 6564 1.270465 TGTGAGTGAGTGTGGATGCAG 60.270 52.381 0.00 0.00 0.00 4.41
4049 6799 9.739276 TGGACAGATTGATATTTAAGAAGTTGT 57.261 29.630 0.00 0.00 0.00 3.32
4129 6879 9.108284 ACGTTTAAAGTTAACTAGCCTTGTAAA 57.892 29.630 8.92 3.35 0.00 2.01
4418 7176 5.128171 TCTGTTACATCCGCCTACTTAATGT 59.872 40.000 0.00 0.00 35.00 2.71
4525 10749 6.867662 TCAGAGAGAACCTTTTCACATTTC 57.132 37.500 0.00 0.00 33.72 2.17
4697 10921 3.063510 TCTTGGAATCAGGAAGCACAG 57.936 47.619 0.00 0.00 0.00 3.66
4698 10922 1.471684 CTTGGAATCAGGAAGCACAGC 59.528 52.381 0.00 0.00 0.00 4.40
4717 10941 5.856455 CACAGCGTTGTTAATTTTAAGAGGG 59.144 40.000 0.63 0.00 34.62 4.30
4724 10948 7.596995 CGTTGTTAATTTTAAGAGGGCATTGAA 59.403 33.333 0.00 0.00 0.00 2.69
4801 11025 6.724694 TCAACAAATGCAATTATTTCTGCC 57.275 33.333 0.00 0.00 33.67 4.85
4804 11028 3.523606 AATGCAATTATTTCTGCCGCA 57.476 38.095 0.00 0.00 37.79 5.69
4923 11238 5.045432 ACTCAAATAGTCGGTATCCCCAAAA 60.045 40.000 0.00 0.00 30.33 2.44
5200 11516 2.412870 CGCACATGTCTGACAACCTAA 58.587 47.619 15.31 0.00 0.00 2.69
5272 11683 6.097554 TGAACCATACACACCAACTTTCAATT 59.902 34.615 0.00 0.00 0.00 2.32
5323 11734 3.789756 ACTATTATTCACGTCTGTTCGCG 59.210 43.478 0.00 0.00 0.00 5.87
5324 11735 1.342555 TTATTCACGTCTGTTCGCGG 58.657 50.000 6.13 0.00 0.00 6.46
5325 11736 0.241749 TATTCACGTCTGTTCGCGGT 59.758 50.000 6.13 0.00 0.00 5.68
5381 11795 5.796424 AAGGAACATGCAAACTTTCTGAT 57.204 34.783 0.00 0.00 0.00 2.90
5383 11797 6.165700 AGGAACATGCAAACTTTCTGATTT 57.834 33.333 0.00 0.00 0.00 2.17
5417 11831 5.884771 ACAGCTTGTTGAAAGAAACTCTTC 58.115 37.500 0.00 0.00 35.27 2.87
5486 11900 6.804677 TGTGGCGCATTATGAATCTAATTTT 58.195 32.000 10.83 0.00 0.00 1.82
5715 12209 6.016360 TGTCGCCATATTCCCTCAAAATATTG 60.016 38.462 0.00 0.00 37.92 1.90
6015 12512 3.625649 TGCATACCTTGTGCACATCTA 57.374 42.857 22.39 10.50 46.76 1.98
6057 12554 1.301677 CGACTTGAAAGGGGCTGAGC 61.302 60.000 0.00 0.00 0.00 4.26
6078 12575 6.426025 TGAGCTGAATCATGAACTACATATGC 59.574 38.462 0.00 0.00 37.46 3.14
6093 12590 8.696043 ACTACATATGCACACAAAATATGGAT 57.304 30.769 1.58 0.00 38.19 3.41
6207 12707 8.538409 AAAATACATCATTTGGCTCAAAAGAC 57.462 30.769 7.45 0.00 34.67 3.01
6272 12772 5.105554 TGCCGTATTTTCAGCAAAATGGTAT 60.106 36.000 5.28 0.00 41.47 2.73
6276 12776 7.543868 CCGTATTTTCAGCAAAATGGTATTTCA 59.456 33.333 5.28 0.00 41.47 2.69
6277 12777 8.920665 CGTATTTTCAGCAAAATGGTATTTCAA 58.079 29.630 5.28 0.00 41.47 2.69
6283 12783 9.995003 TTCAGCAAAATGGTATTTCAAAATAGT 57.005 25.926 0.00 0.00 31.94 2.12
6284 12784 9.421806 TCAGCAAAATGGTATTTCAAAATAGTG 57.578 29.630 0.00 0.00 31.94 2.74
6285 12785 8.658609 CAGCAAAATGGTATTTCAAAATAGTGG 58.341 33.333 0.00 0.00 31.94 4.00
6286 12786 7.823799 AGCAAAATGGTATTTCAAAATAGTGGG 59.176 33.333 0.00 0.00 31.94 4.61
6287 12787 7.606073 GCAAAATGGTATTTCAAAATAGTGGGT 59.394 33.333 0.00 0.00 31.94 4.51
6288 12788 9.500785 CAAAATGGTATTTCAAAATAGTGGGTT 57.499 29.630 0.00 0.00 31.94 4.11
6293 12793 8.586744 TGGTATTTCAAAATAGTGGGTTTTACC 58.413 33.333 0.00 0.00 32.81 2.85
6294 12794 8.036575 GGTATTTCAAAATAGTGGGTTTTACCC 58.963 37.037 7.98 7.98 43.63 3.69
6307 12807 3.805422 GGTTTTACCCAAAAAGGCTTTCG 59.195 43.478 13.76 7.62 37.74 3.46
6308 12808 2.804697 TTACCCAAAAAGGCTTTCGC 57.195 45.000 13.76 0.00 35.39 4.70
6318 12818 3.509659 GCTTTCGCCCCGCTTTAT 58.490 55.556 0.00 0.00 0.00 1.40
6319 12819 2.697819 GCTTTCGCCCCGCTTTATA 58.302 52.632 0.00 0.00 0.00 0.98
6320 12820 1.018910 GCTTTCGCCCCGCTTTATAA 58.981 50.000 0.00 0.00 0.00 0.98
6321 12821 1.402613 GCTTTCGCCCCGCTTTATAAA 59.597 47.619 0.00 0.00 0.00 1.40
6322 12822 2.034179 GCTTTCGCCCCGCTTTATAAAT 59.966 45.455 0.00 0.00 0.00 1.40
6323 12823 3.251487 GCTTTCGCCCCGCTTTATAAATA 59.749 43.478 0.00 0.00 0.00 1.40
6324 12824 4.261280 GCTTTCGCCCCGCTTTATAAATAA 60.261 41.667 0.00 0.00 0.00 1.40
6325 12825 5.733937 GCTTTCGCCCCGCTTTATAAATAAA 60.734 40.000 0.00 0.00 0.00 1.40
6487 12997 6.591834 ACTGAATAGAGAATGTACTGTTGTGC 59.408 38.462 0.00 0.00 0.00 4.57
6523 13033 3.879892 GTGCCTGTAGATTTCTGAATCCC 59.120 47.826 0.00 0.00 42.16 3.85
6524 13034 3.117888 TGCCTGTAGATTTCTGAATCCCC 60.118 47.826 0.00 0.00 42.16 4.81
6575 13085 3.677963 CTTGAGGAGCACCCCAAAT 57.322 52.632 0.00 0.00 36.73 2.32
6778 13288 4.182132 CTGAGGAAGCTGCGAGTG 57.818 61.111 0.00 0.00 0.00 3.51
6897 13409 4.572223 CCACGGGTCTATAGGGGATCTATT 60.572 50.000 0.00 0.00 39.30 1.73
6904 13417 5.485708 GTCTATAGGGGATCTATTGCAAGGT 59.514 44.000 4.94 0.00 39.30 3.50
6957 13472 6.037830 AGTCATTTGTTACCGCGCTATAAATT 59.962 34.615 5.56 0.00 0.00 1.82
6966 13481 3.307242 CCGCGCTATAAATTCTCCTATGC 59.693 47.826 5.56 0.00 0.00 3.14
7001 13516 8.832521 AGTTTGTAAAATTGTCGTAGTCATTCA 58.167 29.630 0.00 0.00 0.00 2.57
7007 13522 6.408858 AATTGTCGTAGTCATTCACATCAC 57.591 37.500 0.00 0.00 0.00 3.06
7011 13526 2.550978 GTAGTCATTCACATCACCCCG 58.449 52.381 0.00 0.00 0.00 5.73
7050 13565 5.329191 TCTATCATCCCTAACCTACGGAA 57.671 43.478 0.00 0.00 0.00 4.30
7098 13653 6.918569 TCGCTCTACTTCAGCTATTACATTTC 59.081 38.462 0.00 0.00 34.45 2.17
7118 13673 0.523072 CACCTTGCTCCAAATCCACG 59.477 55.000 0.00 0.00 0.00 4.94
7149 13704 2.682856 TCTAAGTCGCCAAATTGCCATC 59.317 45.455 0.00 0.00 0.00 3.51
7181 13736 2.433239 TCGTCCCTAACTTCTAATGGCC 59.567 50.000 0.00 0.00 0.00 5.36
7191 13746 2.148446 TCTAATGGCCTGCAGCATTT 57.852 45.000 20.21 9.04 46.50 2.32
7274 13829 7.279758 TGTCATACATCATAAATCGCAAAGTCA 59.720 33.333 0.00 0.00 0.00 3.41
7282 13839 4.691860 AAATCGCAAAGTCATCTCCTTG 57.308 40.909 0.00 0.00 0.00 3.61
7317 13874 5.452496 GCATTAGAGCTCATAGTTCCACTCA 60.452 44.000 17.77 0.00 0.00 3.41
7475 14079 3.721625 CGAGAGAATCGTTGCCTCA 57.278 52.632 0.00 0.00 46.62 3.86
7477 14081 2.544685 CGAGAGAATCGTTGCCTCAAT 58.455 47.619 0.00 0.00 46.62 2.57
7478 14082 3.706698 CGAGAGAATCGTTGCCTCAATA 58.293 45.455 0.00 0.00 46.62 1.90
7482 14086 6.238211 CGAGAGAATCGTTGCCTCAATAAATT 60.238 38.462 0.00 0.00 46.62 1.82
7483 14087 7.042725 CGAGAGAATCGTTGCCTCAATAAATTA 60.043 37.037 0.00 0.00 46.62 1.40
7542 14147 6.260271 GCTCTCAGGTATAATTACACCCAAAC 59.740 42.308 9.36 0.00 35.25 2.93
7547 14152 7.608761 TCAGGTATAATTACACCCAAACTTGTC 59.391 37.037 9.36 0.00 35.25 3.18
7787 17649 1.976045 GCAGAACATTTTTGTACGCCG 59.024 47.619 0.00 0.00 0.00 6.46
7808 17670 4.979815 CCGGAAAGTTTATTGCGAAAAAGT 59.020 37.500 0.00 0.00 45.49 2.66
7827 17689 8.590719 AAAAAGTTTTTGGAACGTTTTGACTA 57.409 26.923 12.74 0.00 39.24 2.59
7909 17771 3.092301 GGTATTTTCCCTTGAAGCTGCT 58.908 45.455 0.00 0.00 0.00 4.24
7937 17799 2.625639 ACCTCACAGTCCAAGGAAGAT 58.374 47.619 0.00 0.00 34.16 2.40
7953 17815 0.038166 AGATTCCACCAACCATGCGT 59.962 50.000 0.00 0.00 0.00 5.24
7966 17828 3.273434 ACCATGCGTATATGATGATGGC 58.727 45.455 13.89 0.00 34.82 4.40
7967 17829 3.054875 ACCATGCGTATATGATGATGGCT 60.055 43.478 13.89 4.16 34.82 4.75
7988 17876 1.153208 CTCCTCTGGCAGCCATCAC 60.153 63.158 16.64 0.00 30.82 3.06
8008 17896 0.038166 CAGTGTACCATGCCCACCTT 59.962 55.000 0.00 0.00 0.00 3.50
8022 17910 0.252479 CACCTTGCAGCTCTCCTCAT 59.748 55.000 0.00 0.00 0.00 2.90
8033 17921 2.029470 GCTCTCCTCATTCTCATACCGG 60.029 54.545 0.00 0.00 0.00 5.28
8037 17925 3.223435 TCCTCATTCTCATACCGGACTC 58.777 50.000 9.46 0.00 0.00 3.36
8065 17953 1.116536 TACCAGAACACTGCCGTGGA 61.117 55.000 13.14 0.00 45.50 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.398429 CGCAAGCTGAGATGCACG 59.602 61.111 8.72 0.00 42.68 5.34
16 17 4.933064 GTCATCCTCGAGCCGGCG 62.933 72.222 23.20 8.11 0.00 6.46
17 18 4.933064 CGTCATCCTCGAGCCGGC 62.933 72.222 21.89 21.89 0.00 6.13
18 19 4.933064 GCGTCATCCTCGAGCCGG 62.933 72.222 6.99 0.00 0.00 6.13
19 20 4.933064 GGCGTCATCCTCGAGCCG 62.933 72.222 6.99 4.73 38.28 5.52
20 21 4.933064 CGGCGTCATCCTCGAGCC 62.933 72.222 6.99 2.85 44.00 4.70
21 22 4.933064 CCGGCGTCATCCTCGAGC 62.933 72.222 6.99 0.00 0.00 5.03
22 23 4.933064 GCCGGCGTCATCCTCGAG 62.933 72.222 12.58 5.13 0.00 4.04
34 35 4.632458 GATCTCGAGGACGCCGGC 62.632 72.222 19.07 19.07 39.58 6.13
35 36 3.967335 GGATCTCGAGGACGCCGG 61.967 72.222 13.56 0.00 39.58 6.13
36 37 3.967335 GGGATCTCGAGGACGCCG 61.967 72.222 13.56 0.00 39.58 6.46
37 38 3.607661 GGGGATCTCGAGGACGCC 61.608 72.222 21.82 21.82 39.58 5.68
38 39 2.519780 AGGGGATCTCGAGGACGC 60.520 66.667 13.56 14.21 39.58 5.19
39 40 1.899534 GGAGGGGATCTCGAGGACG 60.900 68.421 13.56 0.00 43.34 4.79
40 41 1.532078 GGGAGGGGATCTCGAGGAC 60.532 68.421 13.56 6.90 43.34 3.85
41 42 2.780185 GGGGAGGGGATCTCGAGGA 61.780 68.421 13.56 0.00 43.34 3.71
42 43 2.203714 GGGGAGGGGATCTCGAGG 60.204 72.222 13.56 0.00 43.34 4.63
43 44 1.118356 CAAGGGGAGGGGATCTCGAG 61.118 65.000 5.93 5.93 43.34 4.04
44 45 1.075226 CAAGGGGAGGGGATCTCGA 60.075 63.158 0.00 0.00 43.34 4.04
45 46 2.812619 GCAAGGGGAGGGGATCTCG 61.813 68.421 0.00 0.00 43.34 4.04
46 47 1.694169 TGCAAGGGGAGGGGATCTC 60.694 63.158 0.00 0.00 41.71 2.75
47 48 2.003548 GTGCAAGGGGAGGGGATCT 61.004 63.158 0.00 0.00 0.00 2.75
48 49 2.597903 GTGCAAGGGGAGGGGATC 59.402 66.667 0.00 0.00 0.00 3.36
49 50 3.023735 GGTGCAAGGGGAGGGGAT 61.024 66.667 0.00 0.00 0.00 3.85
54 55 4.785453 GAGCCGGTGCAAGGGGAG 62.785 72.222 1.90 0.00 41.13 4.30
57 58 4.697756 TTCGAGCCGGTGCAAGGG 62.698 66.667 1.90 5.82 41.13 3.95
58 59 2.859273 ATCTTCGAGCCGGTGCAAGG 62.859 60.000 1.90 5.17 41.13 3.61
59 60 1.448540 ATCTTCGAGCCGGTGCAAG 60.449 57.895 1.90 0.55 41.13 4.01
60 61 1.741401 CATCTTCGAGCCGGTGCAA 60.741 57.895 1.90 0.00 41.13 4.08
354 357 3.948719 GAGGTGGGTTGACGGCCA 61.949 66.667 2.24 0.00 0.00 5.36
360 363 1.630369 CATCCAAGAGAGGTGGGTTGA 59.370 52.381 0.00 0.00 36.73 3.18
507 512 0.252103 TAACTTCCCACGCCCTCTCT 60.252 55.000 0.00 0.00 0.00 3.10
521 526 1.588404 CGACGCGATTGCTCATAACTT 59.412 47.619 15.93 0.00 39.65 2.66
614 619 1.218316 GAGGAACGGCTGAATCGGT 59.782 57.895 0.00 0.00 0.00 4.69
684 690 4.666512 ACTTATTTGATTGTCTGGGCTGT 58.333 39.130 0.00 0.00 0.00 4.40
693 699 8.454106 CGGAAAGAATCTGACTTATTTGATTGT 58.546 33.333 0.00 0.00 36.44 2.71
706 712 0.740868 CCTGCGCGGAAAGAATCTGA 60.741 55.000 20.25 0.00 36.44 3.27
769 775 7.517614 TTTTTAGACAATACCAACATCTGCA 57.482 32.000 0.00 0.00 0.00 4.41
795 801 6.585416 AGAAAACCAACATCTGCATCTTTTT 58.415 32.000 0.00 0.00 0.00 1.94
796 802 6.165700 AGAAAACCAACATCTGCATCTTTT 57.834 33.333 0.00 0.00 0.00 2.27
797 803 5.302568 TGAGAAAACCAACATCTGCATCTTT 59.697 36.000 0.00 0.00 0.00 2.52
798 804 4.828939 TGAGAAAACCAACATCTGCATCTT 59.171 37.500 0.00 0.00 0.00 2.40
799 805 4.217118 GTGAGAAAACCAACATCTGCATCT 59.783 41.667 0.00 0.00 0.00 2.90
800 806 4.217118 AGTGAGAAAACCAACATCTGCATC 59.783 41.667 0.00 0.00 0.00 3.91
801 807 4.022589 CAGTGAGAAAACCAACATCTGCAT 60.023 41.667 0.00 0.00 0.00 3.96
802 808 3.316029 CAGTGAGAAAACCAACATCTGCA 59.684 43.478 0.00 0.00 0.00 4.41
803 809 3.316308 ACAGTGAGAAAACCAACATCTGC 59.684 43.478 0.00 0.00 0.00 4.26
804 810 5.505173 AACAGTGAGAAAACCAACATCTG 57.495 39.130 0.00 0.00 0.00 2.90
819 825 3.306780 GCCTAGGTGAGCTAAAACAGTGA 60.307 47.826 11.31 0.00 0.00 3.41
820 826 3.003480 GCCTAGGTGAGCTAAAACAGTG 58.997 50.000 11.31 0.00 0.00 3.66
821 827 2.907042 AGCCTAGGTGAGCTAAAACAGT 59.093 45.455 11.31 0.00 37.64 3.55
822 828 3.526534 GAGCCTAGGTGAGCTAAAACAG 58.473 50.000 11.31 0.00 40.11 3.16
898 1960 2.279741 GCTAGGATGCGTGATTTGTCA 58.720 47.619 0.00 0.00 0.00 3.58
1002 3667 3.195825 CGGGGGAATCTGTAGGATGTATC 59.804 52.174 0.00 0.00 34.45 2.24
1124 3800 0.680061 AGGTGGAGTGAACGAGGTTC 59.320 55.000 1.65 1.65 42.26 3.62
1133 3809 0.252057 TGGGATCGAAGGTGGAGTGA 60.252 55.000 0.00 0.00 0.00 3.41
1209 3888 3.127589 TTCAGTGTGAAATCGCGAGAAA 58.872 40.909 16.66 0.00 35.88 2.52
1426 4105 0.244994 CAGAAGGACTGGGTGTCGAG 59.755 60.000 0.00 0.00 46.24 4.04
1723 4403 9.821662 GATATATTGTTGACATCACATCACATG 57.178 33.333 0.00 0.00 0.00 3.21
1880 4580 8.921205 CAAATTTTATGGAGAATGAGGATTCCT 58.079 33.333 4.44 4.44 39.14 3.36
1919 4619 6.483307 ACACAAGATTATCATAATCCACCGTG 59.517 38.462 13.01 15.35 0.00 4.94
1973 4673 7.549488 AGAACAGGTAGCAAAACATACAGTATC 59.451 37.037 0.00 0.00 0.00 2.24
1974 4674 7.394816 AGAACAGGTAGCAAAACATACAGTAT 58.605 34.615 0.00 0.00 0.00 2.12
1975 4675 6.765403 AGAACAGGTAGCAAAACATACAGTA 58.235 36.000 0.00 0.00 0.00 2.74
1976 4676 5.621193 AGAACAGGTAGCAAAACATACAGT 58.379 37.500 0.00 0.00 0.00 3.55
2007 4707 5.570234 AAGAACAGGTAGCGTTTCAAAAA 57.430 34.783 10.10 0.00 0.00 1.94
2008 4708 6.680874 TTAAGAACAGGTAGCGTTTCAAAA 57.319 33.333 10.10 2.98 0.00 2.44
2009 4709 6.483974 TGATTAAGAACAGGTAGCGTTTCAAA 59.516 34.615 10.10 5.56 0.00 2.69
2010 4710 5.992829 TGATTAAGAACAGGTAGCGTTTCAA 59.007 36.000 10.10 4.00 0.00 2.69
2011 4711 5.543714 TGATTAAGAACAGGTAGCGTTTCA 58.456 37.500 10.10 4.87 0.00 2.69
2012 4712 6.147328 ACTTGATTAAGAACAGGTAGCGTTTC 59.853 38.462 3.94 2.88 37.36 2.78
2013 4713 5.995897 ACTTGATTAAGAACAGGTAGCGTTT 59.004 36.000 3.94 0.00 37.36 3.60
2014 4714 5.548406 ACTTGATTAAGAACAGGTAGCGTT 58.452 37.500 3.94 2.58 37.36 4.84
2015 4715 5.148651 ACTTGATTAAGAACAGGTAGCGT 57.851 39.130 3.94 0.00 37.36 5.07
2016 4716 5.671329 GCAACTTGATTAAGAACAGGTAGCG 60.671 44.000 3.94 0.00 37.36 4.26
2017 4717 5.181245 TGCAACTTGATTAAGAACAGGTAGC 59.819 40.000 3.94 0.00 37.36 3.58
2171 4871 4.337836 TGTTTACAGCTGCTGTCAATTCAA 59.662 37.500 35.98 21.61 41.21 2.69
2218 4918 2.356665 TGAGTAAGGCTTGGTTTGCA 57.643 45.000 10.69 0.00 0.00 4.08
2647 5347 4.989279 AAGGACATATGAACACATTGCC 57.011 40.909 10.38 0.00 0.00 4.52
2775 5505 8.169977 ACACAGAACAGTATTGATTCACATTT 57.830 30.769 0.00 0.00 0.00 2.32
2818 5548 2.425668 GCAGCCCAACATACCGTTTTAT 59.574 45.455 0.00 0.00 34.86 1.40
2983 5717 3.372206 GTCTGCGTCATACTCTGCAATTT 59.628 43.478 0.00 0.00 36.82 1.82
3000 5734 0.531974 TGGACTGGTTTGTCGTCTGC 60.532 55.000 0.00 0.00 37.81 4.26
3278 6012 9.959721 ACTGTGAACCTACAAGACAAAATATAT 57.040 29.630 0.00 0.00 0.00 0.86
3475 6209 6.335471 TGAGTCAAAGAATACGTAACTCCA 57.665 37.500 15.25 4.89 32.61 3.86
3582 6316 5.837979 AGCACAGTTCATGATAGAGGAGTAT 59.162 40.000 0.00 0.00 0.00 2.12
3594 6328 0.038892 GGGCACAAGCACAGTTCATG 60.039 55.000 0.00 0.00 45.91 3.07
3595 6329 2.344535 GGGCACAAGCACAGTTCAT 58.655 52.632 0.00 0.00 45.91 2.57
3706 6440 2.439409 ACGTAATAAGGGTGGGTTTGC 58.561 47.619 0.00 0.00 0.00 3.68
3747 6481 3.255725 CTTGCCAGCACAATATTGTTGG 58.744 45.455 25.56 25.56 40.42 3.77
3804 6538 1.436600 CTGCATCCACACTCACTCAC 58.563 55.000 0.00 0.00 0.00 3.51
3823 6564 8.954350 AGTATATGGCAGATATTGAATTTGAGC 58.046 33.333 4.97 0.00 0.00 4.26
3948 6690 4.323417 CACACAGCCTAATCCAACTACAA 58.677 43.478 0.00 0.00 0.00 2.41
4102 6852 7.558161 ACAAGGCTAGTTAACTTTAAACGTT 57.442 32.000 14.49 0.00 0.00 3.99
4104 6854 9.373750 GTTTACAAGGCTAGTTAACTTTAAACG 57.626 33.333 14.49 2.10 0.00 3.60
4239 6990 3.209410 GCTGCATAGGTGACAGCTAAAT 58.791 45.455 17.73 1.33 44.63 1.40
4371 7129 3.635373 CCAAAGAAGCATCAGTGGCATAT 59.365 43.478 0.00 0.00 0.00 1.78
4480 7242 5.425217 TGAAATGCCTACTATCTGAAGGACA 59.575 40.000 0.00 0.00 31.64 4.02
4525 10749 4.730613 GCAAAAATGCCTCCACATACTACG 60.731 45.833 0.00 0.00 0.00 3.51
4675 10899 3.349927 TGTGCTTCCTGATTCCAAGATG 58.650 45.455 0.00 0.00 0.00 2.90
4697 10921 4.800784 TGCCCTCTTAAAATTAACAACGC 58.199 39.130 0.00 0.00 0.00 4.84
4698 10922 7.087639 TCAATGCCCTCTTAAAATTAACAACG 58.912 34.615 0.00 0.00 0.00 4.10
4717 10941 9.585099 TGTAATCAGGAATACAAATTTCAATGC 57.415 29.630 0.00 0.00 0.00 3.56
4801 11025 0.039798 AAGCTTCAAGTGCACATGCG 60.040 50.000 21.04 12.55 45.83 4.73
4804 11028 3.973657 CTTCAAAGCTTCAAGTGCACAT 58.026 40.909 21.04 3.48 0.00 3.21
4828 11052 0.466007 TTTTGCTGCAGCCAGAGACA 60.466 50.000 34.64 12.62 41.77 3.41
5200 11516 3.825328 AGTCTGTTTGGAATCTGTTGCT 58.175 40.909 0.00 0.00 0.00 3.91
5241 11652 8.871629 AAGTTGGTGTGTATGGTTCATTTATA 57.128 30.769 0.00 0.00 0.00 0.98
5316 11727 1.411246 AGATATTGCCTACCGCGAACA 59.589 47.619 8.23 0.00 42.08 3.18
5323 11734 1.734465 GCATGCGAGATATTGCCTACC 59.266 52.381 0.00 0.00 0.00 3.18
5324 11735 2.416747 TGCATGCGAGATATTGCCTAC 58.583 47.619 14.09 0.00 34.20 3.18
5325 11736 2.837532 TGCATGCGAGATATTGCCTA 57.162 45.000 14.09 0.00 34.20 3.93
5355 11766 6.534793 TCAGAAAGTTTGCATGTTCCTTTTTC 59.465 34.615 0.00 0.00 0.00 2.29
5356 11767 6.405538 TCAGAAAGTTTGCATGTTCCTTTTT 58.594 32.000 0.00 0.00 0.00 1.94
5357 11768 5.976458 TCAGAAAGTTTGCATGTTCCTTTT 58.024 33.333 0.00 0.00 0.00 2.27
5361 11772 5.117592 CGAAATCAGAAAGTTTGCATGTTCC 59.882 40.000 0.00 0.00 0.00 3.62
5362 11773 5.914635 TCGAAATCAGAAAGTTTGCATGTTC 59.085 36.000 0.00 0.00 0.00 3.18
5381 11795 5.525745 TCAACAAGCTGTATTTGTCTCGAAA 59.474 36.000 0.00 0.00 37.77 3.46
5383 11797 4.627058 TCAACAAGCTGTATTTGTCTCGA 58.373 39.130 0.00 0.00 37.77 4.04
5417 11831 0.515127 TGTGTGCGCTCAAATAACCG 59.485 50.000 14.56 0.00 0.00 4.44
5486 11900 6.097270 CCCAAATCAATAGGAGCAATTCAAGA 59.903 38.462 0.00 0.00 0.00 3.02
5503 11917 1.892474 GCTAGCCAAACACCCAAATCA 59.108 47.619 2.29 0.00 0.00 2.57
5579 11993 8.986929 AAGAACCTCAAGCAAATAATAGCTAT 57.013 30.769 0.00 0.00 40.90 2.97
5620 12113 7.753630 ACCAATCAAGGATAGAATAGAATGCT 58.246 34.615 0.00 0.00 0.00 3.79
6057 12554 7.011669 TGTGTGCATATGTAGTTCATGATTCAG 59.988 37.037 4.29 0.00 37.91 3.02
6078 12575 4.724074 AGCACCATCCATATTTTGTGTG 57.276 40.909 0.00 0.00 0.00 3.82
6093 12590 7.575414 TTTGAAAGTTAACATCTTAGCACCA 57.425 32.000 8.61 0.00 0.00 4.17
6207 12707 5.233476 CAGGCAATGCAGCAAAATATACTTG 59.767 40.000 7.79 0.00 35.83 3.16
6302 12802 3.982576 ATTTATAAAGCGGGGCGAAAG 57.017 42.857 3.94 0.00 0.00 2.62
6303 12803 5.823353 CTTTATTTATAAAGCGGGGCGAAA 58.177 37.500 8.78 0.00 41.69 3.46
6304 12804 5.427036 CTTTATTTATAAAGCGGGGCGAA 57.573 39.130 8.78 0.00 41.69 4.70
6348 12848 6.489127 TTTCAACTTTCTCGTTGTTCAGAA 57.511 33.333 3.92 0.00 43.55 3.02
6366 12875 6.432783 TCAGTGAGGAAGTGTTTTCTTTTCAA 59.567 34.615 0.00 0.00 0.00 2.69
6487 12997 1.815421 GGCACACAGGCTCCGTATG 60.815 63.158 0.00 0.00 40.24 2.39
6575 13085 2.160219 CGCTAGCTTTTGACATCAGCAA 59.840 45.455 13.93 0.00 35.88 3.91
6745 13255 2.414481 CCTCAGCGATGACACTTTCTTG 59.586 50.000 0.00 0.00 0.00 3.02
6881 13392 5.665701 ACCTTGCAATAGATCCCCTATAGA 58.334 41.667 0.00 0.00 37.09 1.98
6883 13394 5.411493 TGACCTTGCAATAGATCCCCTATA 58.589 41.667 0.00 0.00 37.09 1.31
6897 13409 2.275134 TGAAGCTGAATGACCTTGCA 57.725 45.000 0.00 0.00 0.00 4.08
6904 13417 4.454678 ACTGAAGTGTTGAAGCTGAATGA 58.545 39.130 0.00 0.00 0.00 2.57
6957 13472 6.299141 ACAAACTTGAAGAAAGCATAGGAGA 58.701 36.000 0.00 0.00 39.76 3.71
6966 13481 9.072294 ACGACAATTTTACAAACTTGAAGAAAG 57.928 29.630 0.00 0.00 42.07 2.62
7001 13516 0.326238 ATGTAGGTCCGGGGTGATGT 60.326 55.000 0.00 0.00 0.00 3.06
7007 13522 4.591924 AGAAATTAGTATGTAGGTCCGGGG 59.408 45.833 0.00 0.00 0.00 5.73
7050 13565 9.669353 GCGACTCATGATATATTCATTTGTTTT 57.331 29.630 0.00 0.00 42.62 2.43
7080 13635 6.067217 AGGTGGAAATGTAATAGCTGAAGT 57.933 37.500 0.00 0.00 0.00 3.01
7098 13653 0.890683 GTGGATTTGGAGCAAGGTGG 59.109 55.000 0.00 0.00 0.00 4.61
7118 13673 1.351153 GCGACTTAGACAGAAGGCAC 58.649 55.000 0.00 0.00 33.68 5.01
7149 13704 1.754380 TAGGGACGATGGGAATGGCG 61.754 60.000 0.00 0.00 0.00 5.69
7181 13736 2.159282 GGAGTGGATGAAAATGCTGCAG 60.159 50.000 10.11 10.11 0.00 4.41
7191 13746 6.098409 GTCATAACTTAGAGGGAGTGGATGAA 59.902 42.308 0.00 0.00 34.62 2.57
7260 13815 5.245531 ACAAGGAGATGACTTTGCGATTTA 58.754 37.500 0.00 0.00 31.55 1.40
7274 13829 5.927281 ATGCAATGCTAAAACAAGGAGAT 57.073 34.783 6.82 0.00 0.00 2.75
7282 13839 5.883661 TGAGCTCTAATGCAATGCTAAAAC 58.116 37.500 16.19 0.00 33.83 2.43
7317 13874 5.151454 CCTTGAGGTAGGAGGATTCATACT 58.849 45.833 0.00 0.00 39.79 2.12
7411 13969 8.579863 GCCTTATTTTAGTGAATAGGCAATCAT 58.420 33.333 0.00 0.00 36.66 2.45
7421 13979 8.133024 TCATTTGGTGCCTTATTTTAGTGAAT 57.867 30.769 0.00 0.00 0.00 2.57
7473 14077 8.934825 GCTTCAAGCCATGTTTTAATTTATTGA 58.065 29.630 0.00 0.00 34.48 2.57
7474 14078 8.938906 AGCTTCAAGCCATGTTTTAATTTATTG 58.061 29.630 5.53 0.00 43.77 1.90
7475 14079 8.938906 CAGCTTCAAGCCATGTTTTAATTTATT 58.061 29.630 5.53 0.00 43.77 1.40
7477 14081 6.873076 CCAGCTTCAAGCCATGTTTTAATTTA 59.127 34.615 5.53 0.00 43.77 1.40
7478 14082 5.702209 CCAGCTTCAAGCCATGTTTTAATTT 59.298 36.000 5.53 0.00 43.77 1.82
7482 14086 2.562298 CCCAGCTTCAAGCCATGTTTTA 59.438 45.455 5.53 0.00 43.77 1.52
7483 14087 1.345415 CCCAGCTTCAAGCCATGTTTT 59.655 47.619 5.53 0.00 43.77 2.43
7632 16600 6.038161 ACATGAAAGTCATTTCTTCGTGAACA 59.962 34.615 0.00 0.00 44.35 3.18
7633 16601 6.430451 ACATGAAAGTCATTTCTTCGTGAAC 58.570 36.000 0.00 0.00 44.35 3.18
7787 17649 8.994881 CAAAAACTTTTTCGCAATAAACTTTCC 58.005 29.630 0.00 0.00 0.00 3.13
7808 17670 8.244802 TCAGAAATAGTCAAAACGTTCCAAAAA 58.755 29.630 0.00 0.00 0.00 1.94
7909 17771 4.504864 CCTTGGACTGTGAGGTTTGTATCA 60.505 45.833 0.00 0.00 0.00 2.15
7937 17799 3.118223 TCATATACGCATGGTTGGTGGAA 60.118 43.478 0.00 0.00 0.00 3.53
7953 17815 5.896106 CAGAGGAGGTAGCCATCATCATATA 59.104 44.000 0.00 0.00 0.00 0.86
7966 17828 1.053264 ATGGCTGCCAGAGGAGGTAG 61.053 60.000 27.20 0.00 43.41 3.18
7967 17829 1.003442 ATGGCTGCCAGAGGAGGTA 59.997 57.895 27.20 0.00 36.75 3.08
8008 17896 1.565067 TGAGAATGAGGAGAGCTGCA 58.435 50.000 1.02 0.00 0.00 4.41
8033 17921 1.174783 TCTGGTACAAGAGCCGAGTC 58.825 55.000 0.00 0.00 38.70 3.36
8037 17925 1.000955 AGTGTTCTGGTACAAGAGCCG 59.999 52.381 11.25 0.00 38.70 5.52
8046 17934 1.116536 TCCACGGCAGTGTTCTGGTA 61.117 55.000 15.94 0.00 46.56 3.25


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

AutoCloner maintained by Alex Coulton.