Multiple sequence alignment - TraesCS1D01G258000

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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 TraesCS1D01G258000 chr1D 100.000 3452 0 0 1 3452 350944579 350948030 0.000000e+00 6375.0
1 TraesCS1D01G258000 chr1D 75.615 447 74 23 303 734 409018992 409018566 4.550000e-44 189.0
2 TraesCS1D01G258000 chr1B 94.019 2558 112 20 76 2597 473551796 473554348 0.000000e+00 3838.0
3 TraesCS1D01G258000 chr1B 96.501 343 10 2 2830 3171 473554346 473554687 1.800000e-157 566.0
4 TraesCS1D01G258000 chr1B 93.333 300 6 3 3167 3452 473554843 473555142 6.840000e-117 431.0
5 TraesCS1D01G258000 chr1A 96.741 1657 40 6 949 2597 451849842 451851492 0.000000e+00 2748.0
6 TraesCS1D01G258000 chr1A 94.479 634 24 4 2830 3452 451851490 451852123 0.000000e+00 966.0
7 TraesCS1D01G258000 chr5D 85.629 501 61 11 303 799 482288326 482288819 1.840000e-142 516.0
8 TraesCS1D01G258000 chr5D 92.739 303 22 0 1 303 215135015 215135317 4.090000e-119 438.0
9 TraesCS1D01G258000 chr5D 92.739 303 22 0 1 303 365586765 365587067 4.090000e-119 438.0
10 TraesCS1D01G258000 chr5D 91.401 314 24 3 1 314 215287714 215288024 8.850000e-116 427.0
11 TraesCS1D01G258000 chr3D 84.676 509 58 12 303 799 16268225 16267725 1.110000e-134 490.0
12 TraesCS1D01G258000 chr3D 88.235 85 10 0 3027 3111 247881573 247881657 6.100000e-18 102.0
13 TraesCS1D01G258000 chr4B 84.314 510 59 18 303 799 417407479 417407980 2.410000e-131 479.0
14 TraesCS1D01G258000 chr4B 92.079 303 24 0 1 303 597298602 597298904 8.850000e-116 427.0
15 TraesCS1D01G258000 chr4B 90.717 237 20 2 2596 2830 253685577 253685341 7.190000e-82 315.0
16 TraesCS1D01G258000 chr7D 93.750 304 19 0 1 304 136024296 136023993 1.130000e-124 457.0
17 TraesCS1D01G258000 chr7D 93.069 303 20 1 1 303 368702013 368701712 3.160000e-120 442.0
18 TraesCS1D01G258000 chr7D 92.105 304 24 0 1 304 462272463 462272160 2.460000e-116 429.0
19 TraesCS1D01G258000 chr7D 93.249 237 16 0 2596 2832 632401360 632401124 1.970000e-92 350.0
20 TraesCS1D01G258000 chr2D 92.763 304 22 0 1 304 169713508 169713811 1.140000e-119 440.0
21 TraesCS1D01G258000 chr2D 75.826 484 84 20 307 777 481450239 481449776 7.500000e-52 215.0
22 TraesCS1D01G258000 chr2D 85.057 87 13 0 3026 3112 376817637 376817551 4.750000e-14 89.8
23 TraesCS1D01G258000 chr2B 96.667 240 8 0 2593 2832 26513146 26513385 1.930000e-107 399.0
24 TraesCS1D01G258000 chr2B 89.412 85 9 0 3027 3111 236459194 236459110 1.310000e-19 108.0
25 TraesCS1D01G258000 chr2B 89.474 57 6 0 3031 3087 703704161 703704105 4.780000e-09 73.1
26 TraesCS1D01G258000 chr7A 81.657 507 68 16 303 799 681732024 681732515 6.940000e-107 398.0
27 TraesCS1D01G258000 chr7A 84.426 366 42 10 303 658 207031090 207030730 2.550000e-91 346.0
28 TraesCS1D01G258000 chr5A 96.567 233 8 0 2598 2830 34915174 34914942 1.500000e-103 387.0
29 TraesCS1D01G258000 chr5A 86.747 83 9 2 3031 3112 279115739 279115820 1.320000e-14 91.6
30 TraesCS1D01G258000 chr4A 91.189 227 18 2 2596 2820 300464017 300464243 1.200000e-79 307.0
31 TraesCS1D01G258000 chr4A 90.769 65 6 0 3032 3096 614099448 614099512 1.710000e-13 87.9
32 TraesCS1D01G258000 chr4D 90.608 181 16 1 2596 2775 210453571 210453391 4.450000e-59 239.0
33 TraesCS1D01G258000 chr7B 96.923 130 4 0 2698 2827 642274269 642274140 5.800000e-53 219.0
34 TraesCS1D01G258000 chr7B 96.063 127 5 0 2595 2721 642274008 642274134 1.260000e-49 207.0
35 TraesCS1D01G258000 chr3A 88.235 85 10 0 3027 3111 256236276 256236360 6.100000e-18 102.0


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 TraesCS1D01G258000 chr1D 350944579 350948030 3451 False 6375.000000 6375 100.000000 1 3452 1 chr1D.!!$F1 3451
1 TraesCS1D01G258000 chr1B 473551796 473555142 3346 False 1611.666667 3838 94.617667 76 3452 3 chr1B.!!$F1 3376
2 TraesCS1D01G258000 chr1A 451849842 451852123 2281 False 1857.000000 2748 95.610000 949 3452 2 chr1A.!!$F1 2503
3 TraesCS1D01G258000 chr3D 16267725 16268225 500 True 490.000000 490 84.676000 303 799 1 chr3D.!!$R1 496
4 TraesCS1D01G258000 chr4B 417407479 417407980 501 False 479.000000 479 84.314000 303 799 1 chr4B.!!$F1 496

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
71 72 0.032017 ATAGGAGACCGTTCCAGCCT 60.032 55.0 0.0 0.0 39.84 4.58 F
1035 1075 0.037734 CTAACCGGCCTTTCCCTGTT 59.962 55.0 0.0 0.0 32.83 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1049 1089 2.270257 ATTGGGACGACCGACGACA 61.270 57.895 0.0 2.94 45.77 4.35 R
2773 2820 0.033601 ACCCATCGGCAGCCAAAATA 60.034 50.000 13.3 0.00 0.00 1.40 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
24 25 7.818493 TGAAAGTGACTAGATGAAATTCTCG 57.182 36.000 0.00 0.00 0.00 4.04
25 26 7.378966 TGAAAGTGACTAGATGAAATTCTCGT 58.621 34.615 0.00 0.00 0.00 4.18
26 27 7.329471 TGAAAGTGACTAGATGAAATTCTCGTG 59.671 37.037 0.00 0.00 0.00 4.35
27 28 6.274157 AGTGACTAGATGAAATTCTCGTGT 57.726 37.500 0.00 0.00 0.00 4.49
28 29 6.096036 AGTGACTAGATGAAATTCTCGTGTG 58.904 40.000 0.00 0.00 0.00 3.82
29 30 4.864806 TGACTAGATGAAATTCTCGTGTGC 59.135 41.667 0.00 0.00 0.00 4.57
30 31 4.184629 ACTAGATGAAATTCTCGTGTGCC 58.815 43.478 0.00 0.00 0.00 5.01
31 32 2.359900 AGATGAAATTCTCGTGTGCCC 58.640 47.619 0.00 0.00 0.00 5.36
32 33 2.026822 AGATGAAATTCTCGTGTGCCCT 60.027 45.455 0.00 0.00 0.00 5.19
33 34 1.808411 TGAAATTCTCGTGTGCCCTC 58.192 50.000 0.00 0.00 0.00 4.30
34 35 1.071542 TGAAATTCTCGTGTGCCCTCA 59.928 47.619 0.00 0.00 0.00 3.86
35 36 2.151202 GAAATTCTCGTGTGCCCTCAA 58.849 47.619 0.00 0.00 0.00 3.02
36 37 1.813513 AATTCTCGTGTGCCCTCAAG 58.186 50.000 0.00 0.00 0.00 3.02
37 38 0.976641 ATTCTCGTGTGCCCTCAAGA 59.023 50.000 0.00 0.00 0.00 3.02
38 39 0.318441 TTCTCGTGTGCCCTCAAGAG 59.682 55.000 6.86 6.86 42.30 2.85
39 40 1.739562 CTCGTGTGCCCTCAAGAGC 60.740 63.158 1.57 0.00 37.20 4.09
40 41 3.114616 CGTGTGCCCTCAAGAGCG 61.115 66.667 0.00 0.00 0.00 5.03
41 42 3.426568 GTGTGCCCTCAAGAGCGC 61.427 66.667 0.00 0.00 39.93 5.92
42 43 3.630013 TGTGCCCTCAAGAGCGCT 61.630 61.111 11.27 11.27 40.18 5.92
43 44 2.359230 GTGCCCTCAAGAGCGCTT 60.359 61.111 13.26 0.00 36.57 4.68
44 45 1.968540 GTGCCCTCAAGAGCGCTTT 60.969 57.895 13.26 1.42 36.57 3.51
45 46 1.968017 TGCCCTCAAGAGCGCTTTG 60.968 57.895 13.26 17.61 33.60 2.77
46 47 2.873288 CCCTCAAGAGCGCTTTGC 59.127 61.111 13.26 0.00 46.98 3.68
60 61 5.270812 GCGCTTTGCTTATTATAGGAGAC 57.729 43.478 0.00 0.00 41.73 3.36
61 62 4.152580 GCGCTTTGCTTATTATAGGAGACC 59.847 45.833 0.00 0.00 41.73 3.85
62 63 4.386049 CGCTTTGCTTATTATAGGAGACCG 59.614 45.833 0.00 0.00 0.00 4.79
63 64 5.298347 GCTTTGCTTATTATAGGAGACCGT 58.702 41.667 0.00 0.00 0.00 4.83
64 65 5.758784 GCTTTGCTTATTATAGGAGACCGTT 59.241 40.000 0.00 0.00 0.00 4.44
65 66 6.073711 GCTTTGCTTATTATAGGAGACCGTTC 60.074 42.308 0.00 0.00 0.00 3.95
66 67 5.464030 TGCTTATTATAGGAGACCGTTCC 57.536 43.478 0.00 0.00 37.52 3.62
67 68 4.897076 TGCTTATTATAGGAGACCGTTCCA 59.103 41.667 1.40 0.00 39.84 3.53
68 69 5.010719 TGCTTATTATAGGAGACCGTTCCAG 59.989 44.000 1.40 0.00 39.84 3.86
69 70 5.464030 TTATTATAGGAGACCGTTCCAGC 57.536 43.478 1.40 0.00 39.84 4.85
70 71 1.700955 TATAGGAGACCGTTCCAGCC 58.299 55.000 1.40 0.00 39.84 4.85
71 72 0.032017 ATAGGAGACCGTTCCAGCCT 60.032 55.000 0.00 0.00 39.84 4.58
72 73 0.970937 TAGGAGACCGTTCCAGCCTG 60.971 60.000 0.00 0.00 39.84 4.85
73 74 2.584391 GGAGACCGTTCCAGCCTGT 61.584 63.158 0.00 0.00 37.20 4.00
74 75 1.079750 GAGACCGTTCCAGCCTGTC 60.080 63.158 0.00 0.00 0.00 3.51
89 90 3.319122 AGCCTGTCCTTTGCTACAAAAAG 59.681 43.478 0.00 0.00 34.94 2.27
99 101 7.214467 CTTTGCTACAAAAAGGATTGGACTA 57.786 36.000 0.00 0.00 34.56 2.59
119 121 6.403309 GGACTACCTTGCTGCACTTTATTTAC 60.403 42.308 0.00 0.00 0.00 2.01
137 139 2.438868 ACCGTTACCGTTACTTGTCC 57.561 50.000 0.00 0.00 0.00 4.02
138 140 1.686052 ACCGTTACCGTTACTTGTCCA 59.314 47.619 0.00 0.00 0.00 4.02
139 141 2.288395 ACCGTTACCGTTACTTGTCCAG 60.288 50.000 0.00 0.00 0.00 3.86
178 180 4.325028 TCAAACTACTTGCTACCGACAA 57.675 40.909 0.00 0.00 34.76 3.18
187 189 3.120321 TGCTACCGACAATTTCAGTGT 57.880 42.857 0.00 0.00 0.00 3.55
200 202 8.715191 ACAATTTCAGTGTTTGCAGAAATTAA 57.285 26.923 16.92 0.00 44.39 1.40
214 216 5.107875 GCAGAAATTAACTTGCTGAAAACCG 60.108 40.000 8.84 0.00 0.00 4.44
215 217 4.982295 AGAAATTAACTTGCTGAAAACCGC 59.018 37.500 0.00 0.00 0.00 5.68
271 273 7.281774 TCGACACTATTACTTATCGAAAGGACT 59.718 37.037 10.65 1.73 35.80 3.85
350 352 3.760035 CGCACGCAGGACCTAGGT 61.760 66.667 16.26 16.26 0.00 3.08
375 377 1.488705 AAGTCGGTTCTGGCCATCCA 61.489 55.000 5.51 0.00 40.85 3.41
438 440 1.338020 GCAACAGGAAAACAGAGGTGG 59.662 52.381 0.00 0.00 0.00 4.61
456 458 0.730840 GGAACCAAAATAGACCGGCG 59.269 55.000 0.00 0.00 0.00 6.46
504 516 1.039856 AAAAACTGACTTGCCCGCAT 58.960 45.000 0.00 0.00 0.00 4.73
505 517 1.039856 AAAACTGACTTGCCCGCATT 58.960 45.000 0.00 0.00 0.00 3.56
538 550 3.708734 CCGGCGTTCGTGTTGGAC 61.709 66.667 6.01 0.00 37.11 4.02
609 621 2.579201 CAGGAGCCGGACGTGAAT 59.421 61.111 5.05 0.00 0.00 2.57
672 684 1.303236 CACCGCCTTCACCATCCAA 60.303 57.895 0.00 0.00 0.00 3.53
680 692 0.820074 TTCACCATCCAAACGCCGTT 60.820 50.000 0.00 0.00 0.00 4.44
681 693 0.820074 TCACCATCCAAACGCCGTTT 60.820 50.000 9.83 9.83 36.05 3.60
770 782 4.675029 CCGACGCCAAACCTCCGT 62.675 66.667 0.00 0.00 37.99 4.69
807 820 1.457643 CGACCTCCTGCCCCTGATA 60.458 63.158 0.00 0.00 0.00 2.15
815 828 4.326530 CCTCCTGCCCCTGATACTAGATAT 60.327 50.000 0.00 0.00 0.00 1.63
820 833 6.402981 TGCCCCTGATACTAGATATCTACA 57.597 41.667 8.44 4.72 40.52 2.74
824 837 9.594936 GCCCCTGATACTAGATATCTACAATAT 57.405 37.037 8.44 7.13 40.52 1.28
876 889 4.678509 TTCACAAGACAATTGCGGTATC 57.321 40.909 5.05 0.00 0.00 2.24
883 896 6.258727 ACAAGACAATTGCGGTATCTAAGATG 59.741 38.462 5.05 0.00 0.00 2.90
885 898 5.070446 AGACAATTGCGGTATCTAAGATGGA 59.930 40.000 5.05 0.00 0.00 3.41
898 911 9.232473 GTATCTAAGATGGACTTTTCTTTTGGT 57.768 33.333 0.00 0.00 39.72 3.67
907 920 6.586844 TGGACTTTTCTTTTGGTTGTAAAACG 59.413 34.615 0.00 0.00 35.09 3.60
909 922 5.349270 ACTTTTCTTTTGGTTGTAAAACGGC 59.651 36.000 0.00 0.00 35.09 5.68
917 930 2.483491 GGTTGTAAAACGGCGGTTATGA 59.517 45.455 12.04 0.00 34.62 2.15
938 951 5.632118 TGAGGGATGTGGTAGAGTATAGAC 58.368 45.833 0.00 0.00 0.00 2.59
942 955 2.579873 TGTGGTAGAGTATAGACGGCC 58.420 52.381 0.00 0.00 0.00 6.13
943 956 1.534595 GTGGTAGAGTATAGACGGCCG 59.465 57.143 26.86 26.86 0.00 6.13
985 998 4.166919 TCCCAAAAACCACCATCCAAAAAT 59.833 37.500 0.00 0.00 0.00 1.82
1028 1068 1.965643 GAAAAACCCTAACCGGCCTTT 59.034 47.619 0.00 0.00 0.00 3.11
1035 1075 0.037734 CTAACCGGCCTTTCCCTGTT 59.962 55.000 0.00 0.00 32.83 3.16
1049 1089 2.121963 TGTTGCCAGTCCCCTCCT 60.122 61.111 0.00 0.00 0.00 3.69
1145 1191 3.292159 GGCCGTTTCCACCACCAC 61.292 66.667 0.00 0.00 0.00 4.16
1146 1192 3.292159 GCCGTTTCCACCACCACC 61.292 66.667 0.00 0.00 0.00 4.61
1147 1193 2.193517 CCGTTTCCACCACCACCA 59.806 61.111 0.00 0.00 0.00 4.17
1497 1543 2.046023 CGCAGCATCCAGGACCAA 60.046 61.111 0.00 0.00 0.00 3.67
1786 1832 3.798548 GCCCATGTTCGTCAACACATTTT 60.799 43.478 0.00 0.00 45.47 1.82
1889 1935 1.370587 GCCTTAATGTTGCGGCGGTA 61.371 55.000 9.78 0.00 32.22 4.02
2061 2107 0.689623 CACTGCTGAGGAAGGAAGGT 59.310 55.000 0.00 0.00 0.00 3.50
2120 2166 4.473199 GTGGCTAAAATGAAACGGTTCTC 58.527 43.478 15.41 0.00 34.60 2.87
2247 2293 1.005215 CCCAGGAAGATGAGCCTTTGT 59.995 52.381 0.00 0.00 30.41 2.83
2594 2641 1.165270 GCAGTGAGGCCATAACGTTT 58.835 50.000 5.91 0.00 0.00 3.60
2595 2642 1.539827 GCAGTGAGGCCATAACGTTTT 59.460 47.619 5.91 0.00 0.00 2.43
2596 2643 2.745281 GCAGTGAGGCCATAACGTTTTA 59.255 45.455 5.91 0.00 0.00 1.52
2597 2644 3.181510 GCAGTGAGGCCATAACGTTTTAG 60.182 47.826 5.91 0.00 0.00 1.85
2598 2645 3.374058 CAGTGAGGCCATAACGTTTTAGG 59.626 47.826 5.91 7.56 0.00 2.69
2599 2646 2.681344 GTGAGGCCATAACGTTTTAGGG 59.319 50.000 5.91 0.89 41.36 3.53
2600 2647 2.294979 GAGGCCATAACGTTTTAGGGG 58.705 52.381 5.91 2.56 39.21 4.79
2602 2649 1.758936 GCCATAACGTTTTAGGGGCT 58.241 50.000 5.91 0.00 39.21 5.19
2603 2650 1.404035 GCCATAACGTTTTAGGGGCTG 59.596 52.381 5.91 0.00 39.21 4.85
2604 2651 2.718563 CCATAACGTTTTAGGGGCTGT 58.281 47.619 5.91 0.00 35.78 4.40
2605 2652 3.086282 CCATAACGTTTTAGGGGCTGTT 58.914 45.455 5.91 0.00 35.78 3.16
2606 2653 3.508402 CCATAACGTTTTAGGGGCTGTTT 59.492 43.478 5.91 0.00 35.78 2.83
2607 2654 4.481463 CATAACGTTTTAGGGGCTGTTTG 58.519 43.478 5.91 0.00 0.00 2.93
2608 2655 1.324383 ACGTTTTAGGGGCTGTTTGG 58.676 50.000 0.00 0.00 0.00 3.28
2609 2656 1.133730 ACGTTTTAGGGGCTGTTTGGA 60.134 47.619 0.00 0.00 0.00 3.53
2610 2657 2.167662 CGTTTTAGGGGCTGTTTGGAT 58.832 47.619 0.00 0.00 0.00 3.41
2611 2658 2.163613 CGTTTTAGGGGCTGTTTGGATC 59.836 50.000 0.00 0.00 0.00 3.36
2612 2659 2.122783 TTTAGGGGCTGTTTGGATCG 57.877 50.000 0.00 0.00 0.00 3.69
2613 2660 0.393808 TTAGGGGCTGTTTGGATCGC 60.394 55.000 0.00 0.00 0.00 4.58
2614 2661 1.271840 TAGGGGCTGTTTGGATCGCT 61.272 55.000 0.00 0.00 0.00 4.93
2615 2662 1.223487 GGGGCTGTTTGGATCGCTA 59.777 57.895 0.00 0.00 0.00 4.26
2616 2663 1.095807 GGGGCTGTTTGGATCGCTAC 61.096 60.000 0.00 0.00 0.00 3.58
2617 2664 1.095807 GGGCTGTTTGGATCGCTACC 61.096 60.000 0.00 0.00 0.00 3.18
2618 2665 0.107654 GGCTGTTTGGATCGCTACCT 60.108 55.000 0.00 0.00 0.00 3.08
2619 2666 1.679032 GGCTGTTTGGATCGCTACCTT 60.679 52.381 0.00 0.00 0.00 3.50
2620 2667 1.398390 GCTGTTTGGATCGCTACCTTG 59.602 52.381 0.00 0.00 0.00 3.61
2621 2668 2.935238 GCTGTTTGGATCGCTACCTTGA 60.935 50.000 0.00 0.00 0.00 3.02
2622 2669 2.932614 CTGTTTGGATCGCTACCTTGAG 59.067 50.000 0.00 0.00 0.00 3.02
2623 2670 1.666189 GTTTGGATCGCTACCTTGAGC 59.334 52.381 0.00 0.00 39.20 4.26
2624 2671 1.195115 TTGGATCGCTACCTTGAGCT 58.805 50.000 0.00 0.00 40.51 4.09
2625 2672 0.461548 TGGATCGCTACCTTGAGCTG 59.538 55.000 0.00 0.00 40.51 4.24
2626 2673 0.878086 GGATCGCTACCTTGAGCTGC 60.878 60.000 0.00 0.00 40.51 5.25
2627 2674 0.878086 GATCGCTACCTTGAGCTGCC 60.878 60.000 0.00 0.00 40.51 4.85
2628 2675 2.317149 ATCGCTACCTTGAGCTGCCC 62.317 60.000 0.00 0.00 40.51 5.36
2629 2676 2.671070 GCTACCTTGAGCTGCCCA 59.329 61.111 0.00 0.00 39.50 5.36
2630 2677 1.451028 GCTACCTTGAGCTGCCCAG 60.451 63.158 0.00 0.00 39.50 4.45
2660 2707 4.368808 CGTTGACCGCAGCGTTGG 62.369 66.667 15.05 0.34 42.71 3.77
2661 2708 3.276846 GTTGACCGCAGCGTTGGT 61.277 61.111 15.05 4.22 42.42 3.67
2662 2709 1.957186 GTTGACCGCAGCGTTGGTA 60.957 57.895 15.05 0.00 38.99 3.25
2663 2710 1.004320 TTGACCGCAGCGTTGGTAT 60.004 52.632 15.05 0.00 38.99 2.73
2664 2711 1.017177 TTGACCGCAGCGTTGGTATC 61.017 55.000 15.05 2.05 38.99 2.24
2665 2712 2.125269 ACCGCAGCGTTGGTATCC 60.125 61.111 15.05 0.00 36.50 2.59
2666 2713 3.261951 CCGCAGCGTTGGTATCCG 61.262 66.667 15.05 0.00 0.00 4.18
2667 2714 2.508439 CGCAGCGTTGGTATCCGT 60.508 61.111 6.65 0.00 0.00 4.69
2668 2715 2.098233 CGCAGCGTTGGTATCCGTT 61.098 57.895 6.65 0.00 0.00 4.44
2669 2716 1.632046 CGCAGCGTTGGTATCCGTTT 61.632 55.000 6.65 0.00 0.00 3.60
2670 2717 0.179200 GCAGCGTTGGTATCCGTTTG 60.179 55.000 0.16 0.00 0.00 2.93
2671 2718 0.446222 CAGCGTTGGTATCCGTTTGG 59.554 55.000 0.00 0.00 0.00 3.28
2672 2719 1.135939 GCGTTGGTATCCGTTTGGC 59.864 57.895 0.00 0.00 34.14 4.52
2673 2720 1.303091 GCGTTGGTATCCGTTTGGCT 61.303 55.000 0.00 0.00 34.14 4.75
2674 2721 0.446222 CGTTGGTATCCGTTTGGCTG 59.554 55.000 0.00 0.00 34.14 4.85
2675 2722 0.808755 GTTGGTATCCGTTTGGCTGG 59.191 55.000 0.00 0.00 34.14 4.85
2676 2723 0.322997 TTGGTATCCGTTTGGCTGGG 60.323 55.000 0.00 0.00 34.14 4.45
2677 2724 2.119029 GGTATCCGTTTGGCTGGGC 61.119 63.158 0.00 0.00 34.14 5.36
2678 2725 1.077716 GTATCCGTTTGGCTGGGCT 60.078 57.895 0.00 0.00 34.14 5.19
2679 2726 1.095807 GTATCCGTTTGGCTGGGCTC 61.096 60.000 0.00 0.00 34.14 4.70
2680 2727 2.265467 TATCCGTTTGGCTGGGCTCC 62.265 60.000 0.00 0.00 34.14 4.70
2681 2728 4.659172 CCGTTTGGCTGGGCTCCA 62.659 66.667 0.00 0.00 0.00 3.86
2682 2729 2.597217 CGTTTGGCTGGGCTCCAA 60.597 61.111 3.08 3.08 41.47 3.53
2684 2731 4.716025 TTTGGCTGGGCTCCAAAA 57.284 50.000 13.71 0.11 46.95 2.44
2685 2732 3.162394 TTTGGCTGGGCTCCAAAAT 57.838 47.368 13.71 0.00 46.95 1.82
2686 2733 1.433121 TTTGGCTGGGCTCCAAAATT 58.567 45.000 13.71 0.00 46.95 1.82
2687 2734 1.433121 TTGGCTGGGCTCCAAAATTT 58.567 45.000 4.43 0.00 40.35 1.82
2688 2735 1.433121 TGGCTGGGCTCCAAAATTTT 58.567 45.000 0.00 0.00 30.80 1.82
2689 2736 1.072015 TGGCTGGGCTCCAAAATTTTG 59.928 47.619 21.65 21.65 37.90 2.44
2700 2747 3.524763 CAAAATTTTGGCTTGCGAAGG 57.475 42.857 21.00 0.00 34.59 3.46
2707 2754 2.182537 GCTTGCGAAGGCCCATTG 59.817 61.111 0.00 0.00 38.85 2.82
2708 2755 2.887360 CTTGCGAAGGCCCATTGG 59.113 61.111 0.00 0.00 38.85 3.16
2719 2766 3.677963 CCCATTGGCTCTTTCCAGT 57.322 52.632 0.00 0.00 37.44 4.00
2720 2767 1.180029 CCCATTGGCTCTTTCCAGTG 58.820 55.000 0.00 0.00 41.75 3.66
2721 2768 0.529378 CCATTGGCTCTTTCCAGTGC 59.471 55.000 0.00 0.00 41.04 4.40
2722 2769 1.250328 CATTGGCTCTTTCCAGTGCA 58.750 50.000 0.00 0.00 40.69 4.57
2723 2770 1.822990 CATTGGCTCTTTCCAGTGCAT 59.177 47.619 0.00 0.00 40.69 3.96
2724 2771 1.999648 TTGGCTCTTTCCAGTGCATT 58.000 45.000 0.00 0.00 40.69 3.56
2725 2772 1.538047 TGGCTCTTTCCAGTGCATTC 58.462 50.000 0.00 0.00 40.69 2.67
2726 2773 0.449388 GGCTCTTTCCAGTGCATTCG 59.551 55.000 0.00 0.00 40.69 3.34
2727 2774 1.442769 GCTCTTTCCAGTGCATTCGA 58.557 50.000 0.00 0.00 39.05 3.71
2728 2775 2.012673 GCTCTTTCCAGTGCATTCGAT 58.987 47.619 0.00 0.00 39.05 3.59
2729 2776 3.198068 GCTCTTTCCAGTGCATTCGATA 58.802 45.455 0.00 0.00 39.05 2.92
2730 2777 3.247173 GCTCTTTCCAGTGCATTCGATAG 59.753 47.826 0.00 0.00 39.05 2.08
2731 2778 3.198068 TCTTTCCAGTGCATTCGATAGC 58.802 45.455 0.00 2.91 0.00 2.97
2732 2779 1.953559 TTCCAGTGCATTCGATAGCC 58.046 50.000 7.08 0.04 0.00 3.93
2733 2780 0.829990 TCCAGTGCATTCGATAGCCA 59.170 50.000 7.08 0.00 0.00 4.75
2734 2781 1.209261 TCCAGTGCATTCGATAGCCAA 59.791 47.619 7.08 0.00 0.00 4.52
2735 2782 2.158769 TCCAGTGCATTCGATAGCCAAT 60.159 45.455 7.08 0.00 0.00 3.16
2736 2783 2.620115 CCAGTGCATTCGATAGCCAATT 59.380 45.455 7.08 0.00 0.00 2.32
2737 2784 3.304257 CCAGTGCATTCGATAGCCAATTC 60.304 47.826 7.08 0.00 0.00 2.17
2738 2785 2.880890 AGTGCATTCGATAGCCAATTCC 59.119 45.455 7.08 0.00 0.00 3.01
2739 2786 2.880890 GTGCATTCGATAGCCAATTCCT 59.119 45.455 7.08 0.00 0.00 3.36
2740 2787 2.880268 TGCATTCGATAGCCAATTCCTG 59.120 45.455 7.08 0.00 0.00 3.86
2742 2789 2.638480 TTCGATAGCCAATTCCTGGG 57.362 50.000 0.00 0.00 46.54 4.45
2747 2794 2.272146 GCCAATTCCTGGGCGAGA 59.728 61.111 0.00 0.00 46.54 4.04
2748 2795 2.115291 GCCAATTCCTGGGCGAGAC 61.115 63.158 0.00 0.00 46.54 3.36
2749 2796 1.299648 CCAATTCCTGGGCGAGACA 59.700 57.895 0.00 0.00 42.17 3.41
2750 2797 1.026718 CCAATTCCTGGGCGAGACAC 61.027 60.000 0.00 0.00 42.17 3.67
2751 2798 1.026718 CAATTCCTGGGCGAGACACC 61.027 60.000 0.00 0.00 0.00 4.16
2752 2799 2.521958 AATTCCTGGGCGAGACACCG 62.522 60.000 0.00 0.00 0.00 4.94
2778 2825 3.602390 CGAATCGGTCGCCAATATTTT 57.398 42.857 0.00 0.00 44.14 1.82
2779 2826 3.288242 CGAATCGGTCGCCAATATTTTG 58.712 45.455 0.00 0.00 44.14 2.44
2789 2836 2.746269 CCAATATTTTGGCTGCCGATG 58.254 47.619 14.98 6.83 45.71 3.84
2790 2837 2.546373 CCAATATTTTGGCTGCCGATGG 60.546 50.000 14.98 12.34 45.71 3.51
2791 2838 1.331214 ATATTTTGGCTGCCGATGGG 58.669 50.000 14.98 0.00 0.00 4.00
2792 2839 0.033601 TATTTTGGCTGCCGATGGGT 60.034 50.000 14.98 1.51 34.97 4.51
2793 2840 0.904394 ATTTTGGCTGCCGATGGGTT 60.904 50.000 14.98 0.00 34.97 4.11
2794 2841 1.814772 TTTTGGCTGCCGATGGGTTG 61.815 55.000 14.98 0.00 34.97 3.77
2795 2842 4.738998 TGGCTGCCGATGGGTTGG 62.739 66.667 14.98 0.00 34.97 3.77
2802 2849 4.431131 CGATGGGTTGGCAGGGCT 62.431 66.667 0.00 0.00 0.00 5.19
2803 2850 2.757099 GATGGGTTGGCAGGGCTG 60.757 66.667 0.00 0.00 0.00 4.85
2820 2867 4.492604 GCTGTGGGCAGTAACCAA 57.507 55.556 0.00 0.00 44.32 3.67
2821 2868 2.727103 GCTGTGGGCAGTAACCAAA 58.273 52.632 0.00 0.00 44.32 3.28
2822 2869 0.313987 GCTGTGGGCAGTAACCAAAC 59.686 55.000 0.00 0.00 44.32 2.93
2823 2870 1.686355 CTGTGGGCAGTAACCAAACA 58.314 50.000 0.00 0.00 40.24 2.83
2824 2871 1.608590 CTGTGGGCAGTAACCAAACAG 59.391 52.381 0.00 0.00 40.24 3.16
2825 2872 0.313987 GTGGGCAGTAACCAAACAGC 59.686 55.000 0.00 0.00 40.24 4.40
2827 2874 1.964448 GGCAGTAACCAAACAGCCC 59.036 57.895 0.00 0.00 44.04 5.19
2828 2875 1.532604 GGCAGTAACCAAACAGCCCC 61.533 60.000 0.00 0.00 44.04 5.80
3010 3057 9.689976 CATGGTAAATTTTGTGTAATTCTGTCA 57.310 29.630 0.00 0.00 0.00 3.58
3233 3443 1.961793 TGTTTCTTGACCGGGAACAG 58.038 50.000 6.32 0.00 0.00 3.16
3383 3602 3.989817 GCACTAAACTGGAATTTGCCTTG 59.010 43.478 0.00 0.00 0.00 3.61
3420 3650 2.548493 GCCATCTCTCCTGAATGAGCTC 60.548 54.545 6.82 6.82 32.22 4.09
3430 3660 3.008330 CTGAATGAGCTCCCAGAACTTG 58.992 50.000 12.15 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.329471 CACGAGAATTTCATCTAGTCACTTTCA 59.671 37.037 0.00 0.00 33.69 2.69
1 2 7.329717 ACACGAGAATTTCATCTAGTCACTTTC 59.670 37.037 0.00 0.00 33.69 2.62
2 3 7.116948 CACACGAGAATTTCATCTAGTCACTTT 59.883 37.037 0.00 0.00 33.69 2.66
3 4 6.587990 CACACGAGAATTTCATCTAGTCACTT 59.412 38.462 0.00 0.00 33.69 3.16
4 5 6.096036 CACACGAGAATTTCATCTAGTCACT 58.904 40.000 0.00 0.00 33.69 3.41
5 6 5.220303 GCACACGAGAATTTCATCTAGTCAC 60.220 44.000 0.00 0.00 33.69 3.67
6 7 4.864806 GCACACGAGAATTTCATCTAGTCA 59.135 41.667 0.00 0.00 33.69 3.41
7 8 4.268884 GGCACACGAGAATTTCATCTAGTC 59.731 45.833 0.00 0.00 33.69 2.59
8 9 4.184629 GGCACACGAGAATTTCATCTAGT 58.815 43.478 0.00 0.00 35.95 2.57
9 10 3.557595 GGGCACACGAGAATTTCATCTAG 59.442 47.826 0.00 0.00 0.00 2.43
10 11 3.197766 AGGGCACACGAGAATTTCATCTA 59.802 43.478 0.00 0.00 0.00 1.98
11 12 2.026822 AGGGCACACGAGAATTTCATCT 60.027 45.455 0.00 0.00 0.00 2.90
12 13 2.352960 GAGGGCACACGAGAATTTCATC 59.647 50.000 0.00 0.00 0.00 2.92
13 14 2.290260 TGAGGGCACACGAGAATTTCAT 60.290 45.455 0.00 0.00 0.00 2.57
14 15 1.071542 TGAGGGCACACGAGAATTTCA 59.928 47.619 0.00 0.00 0.00 2.69
15 16 1.808411 TGAGGGCACACGAGAATTTC 58.192 50.000 0.00 0.00 0.00 2.17
16 17 2.154462 CTTGAGGGCACACGAGAATTT 58.846 47.619 0.00 0.00 0.00 1.82
17 18 1.347707 TCTTGAGGGCACACGAGAATT 59.652 47.619 0.12 0.00 0.00 2.17
18 19 0.976641 TCTTGAGGGCACACGAGAAT 59.023 50.000 0.12 0.00 0.00 2.40
19 20 0.318441 CTCTTGAGGGCACACGAGAA 59.682 55.000 4.79 0.00 38.05 2.87
20 21 1.967535 CTCTTGAGGGCACACGAGA 59.032 57.895 3.12 3.12 38.05 4.04
21 22 1.739562 GCTCTTGAGGGCACACGAG 60.740 63.158 11.10 11.10 38.57 4.18
22 23 2.343758 GCTCTTGAGGGCACACGA 59.656 61.111 0.00 0.00 0.00 4.35
23 24 3.114616 CGCTCTTGAGGGCACACG 61.115 66.667 3.47 0.00 0.00 4.49
24 25 3.426568 GCGCTCTTGAGGGCACAC 61.427 66.667 27.17 4.95 45.45 3.82
28 29 2.873288 CAAAGCGCTCTTGAGGGC 59.127 61.111 25.58 25.58 46.33 5.19
29 30 2.873288 GCAAAGCGCTCTTGAGGG 59.127 61.111 26.05 9.88 37.77 4.30
38 39 4.152580 GGTCTCCTATAATAAGCAAAGCGC 59.847 45.833 0.00 0.00 42.91 5.92
39 40 4.386049 CGGTCTCCTATAATAAGCAAAGCG 59.614 45.833 0.00 0.00 0.00 4.68
40 41 5.298347 ACGGTCTCCTATAATAAGCAAAGC 58.702 41.667 0.00 0.00 0.00 3.51
41 42 6.424207 GGAACGGTCTCCTATAATAAGCAAAG 59.576 42.308 0.00 0.00 32.21 2.77
42 43 6.126997 TGGAACGGTCTCCTATAATAAGCAAA 60.127 38.462 0.00 0.00 36.35 3.68
43 44 5.364446 TGGAACGGTCTCCTATAATAAGCAA 59.636 40.000 0.00 0.00 36.35 3.91
44 45 4.897076 TGGAACGGTCTCCTATAATAAGCA 59.103 41.667 0.00 0.00 36.35 3.91
45 46 5.464030 TGGAACGGTCTCCTATAATAAGC 57.536 43.478 0.00 0.00 36.35 3.09
46 47 5.471257 GCTGGAACGGTCTCCTATAATAAG 58.529 45.833 0.00 0.00 36.35 1.73
47 48 4.282703 GGCTGGAACGGTCTCCTATAATAA 59.717 45.833 0.00 0.00 35.72 1.40
48 49 3.830755 GGCTGGAACGGTCTCCTATAATA 59.169 47.826 0.00 0.00 35.72 0.98
49 50 2.633481 GGCTGGAACGGTCTCCTATAAT 59.367 50.000 0.00 0.00 35.72 1.28
50 51 2.037144 GGCTGGAACGGTCTCCTATAA 58.963 52.381 0.00 0.00 35.72 0.98
51 52 1.700955 GGCTGGAACGGTCTCCTATA 58.299 55.000 0.00 0.00 35.72 1.31
52 53 2.517609 GGCTGGAACGGTCTCCTAT 58.482 57.895 0.00 0.00 35.72 2.57
53 54 4.029472 GGCTGGAACGGTCTCCTA 57.971 61.111 0.00 0.00 35.72 2.94
58 59 2.047179 GGACAGGCTGGAACGGTC 60.047 66.667 20.34 5.71 41.46 4.79
59 60 1.705997 AAAGGACAGGCTGGAACGGT 61.706 55.000 20.34 0.00 36.83 4.83
60 61 1.073199 AAAGGACAGGCTGGAACGG 59.927 57.895 20.34 0.00 38.10 4.44
61 62 1.856265 GCAAAGGACAGGCTGGAACG 61.856 60.000 20.34 3.09 0.00 3.95
62 63 0.538287 AGCAAAGGACAGGCTGGAAC 60.538 55.000 20.34 8.32 36.34 3.62
63 64 1.064003 TAGCAAAGGACAGGCTGGAA 58.936 50.000 20.34 0.00 38.55 3.53
64 65 0.324943 GTAGCAAAGGACAGGCTGGA 59.675 55.000 20.34 0.00 38.55 3.86
65 66 0.036732 TGTAGCAAAGGACAGGCTGG 59.963 55.000 20.34 0.16 38.55 4.85
66 67 1.896220 TTGTAGCAAAGGACAGGCTG 58.104 50.000 14.16 14.16 38.55 4.85
67 68 2.656947 TTTGTAGCAAAGGACAGGCT 57.343 45.000 0.00 0.00 41.51 4.58
68 69 3.642705 CTTTTTGTAGCAAAGGACAGGC 58.357 45.455 0.00 0.00 0.00 4.85
89 90 1.340017 TGCAGCAAGGTAGTCCAATCC 60.340 52.381 0.00 0.00 35.89 3.01
91 92 1.352352 AGTGCAGCAAGGTAGTCCAAT 59.648 47.619 0.00 0.00 35.89 3.16
92 93 0.764890 AGTGCAGCAAGGTAGTCCAA 59.235 50.000 0.00 0.00 35.89 3.53
94 95 1.897560 AAAGTGCAGCAAGGTAGTCC 58.102 50.000 0.00 0.00 0.00 3.85
96 97 5.414765 GGTAAATAAAGTGCAGCAAGGTAGT 59.585 40.000 0.00 0.00 0.00 2.73
99 101 3.190535 CGGTAAATAAAGTGCAGCAAGGT 59.809 43.478 0.00 0.00 0.00 3.50
158 160 5.607119 AATTGTCGGTAGCAAGTAGTTTG 57.393 39.130 0.00 0.00 39.88 2.93
169 171 4.219033 GCAAACACTGAAATTGTCGGTAG 58.781 43.478 0.00 0.00 44.55 3.18
178 180 8.819974 CAAGTTAATTTCTGCAAACACTGAAAT 58.180 29.630 4.09 4.09 44.91 2.17
187 189 7.201600 GGTTTTCAGCAAGTTAATTTCTGCAAA 60.202 33.333 0.00 2.39 0.00 3.68
200 202 1.065551 GACAAGCGGTTTTCAGCAAGT 59.934 47.619 8.55 0.00 43.16 3.16
214 216 2.163211 GGAGCAGAAGGAAATGACAAGC 59.837 50.000 0.00 0.00 0.00 4.01
215 217 3.683802 AGGAGCAGAAGGAAATGACAAG 58.316 45.455 0.00 0.00 0.00 3.16
271 273 5.245301 CCACAAGTATAGGGGATCAATCGTA 59.755 44.000 0.00 0.00 0.00 3.43
438 440 0.098200 GCGCCGGTCTATTTTGGTTC 59.902 55.000 1.90 0.00 0.00 3.62
489 501 2.629656 GCAATGCGGGCAAGTCAGT 61.630 57.895 0.00 0.00 0.00 3.41
520 532 4.224274 TCCAACACGAACGCCGGT 62.224 61.111 1.90 0.00 43.93 5.28
528 540 1.098712 GCAAACCAGGTCCAACACGA 61.099 55.000 0.00 0.00 0.00 4.35
538 550 0.671781 CGAGACTCAGGCAAACCAGG 60.672 60.000 2.82 0.00 39.06 4.45
609 621 1.318158 GGTTCCTCCCTTCGAGCGTA 61.318 60.000 0.00 0.00 37.27 4.42
680 692 0.599204 GGCCAGTTTCTCGTCGTCAA 60.599 55.000 0.00 0.00 0.00 3.18
681 693 1.006571 GGCCAGTTTCTCGTCGTCA 60.007 57.895 0.00 0.00 0.00 4.35
683 695 2.049433 CGGCCAGTTTCTCGTCGT 60.049 61.111 2.24 0.00 0.00 4.34
686 698 2.357517 CTGCGGCCAGTTTCTCGT 60.358 61.111 2.24 0.00 34.31 4.18
845 858 8.910666 CGCAATTGTCTTGTGAAAATTATACAA 58.089 29.630 7.40 0.00 37.87 2.41
849 862 6.454795 ACCGCAATTGTCTTGTGAAAATTAT 58.545 32.000 7.40 0.00 37.87 1.28
861 874 5.070446 TCCATCTTAGATACCGCAATTGTCT 59.930 40.000 7.40 4.12 0.00 3.41
876 889 7.716612 ACAACCAAAAGAAAAGTCCATCTTAG 58.283 34.615 0.00 0.00 34.90 2.18
883 896 6.035220 CCGTTTTACAACCAAAAGAAAAGTCC 59.965 38.462 0.00 0.00 0.00 3.85
885 898 5.349270 GCCGTTTTACAACCAAAAGAAAAGT 59.651 36.000 0.00 0.00 0.00 2.66
898 911 2.743126 CCTCATAACCGCCGTTTTACAA 59.257 45.455 0.00 0.00 33.17 2.41
907 920 0.535102 CCACATCCCTCATAACCGCC 60.535 60.000 0.00 0.00 0.00 6.13
909 922 2.963101 TCTACCACATCCCTCATAACCG 59.037 50.000 0.00 0.00 0.00 4.44
917 930 4.506979 CCGTCTATACTCTACCACATCCCT 60.507 50.000 0.00 0.00 0.00 4.20
938 951 1.461559 TTGGGGTTTATAAACGGCCG 58.538 50.000 26.86 26.86 39.77 6.13
942 955 4.082081 GGGAGGTTTTGGGGTTTATAAACG 60.082 45.833 19.48 0.00 39.77 3.60
943 956 4.839550 TGGGAGGTTTTGGGGTTTATAAAC 59.160 41.667 18.30 18.30 38.17 2.01
1035 1075 2.607750 GACAGGAGGGGACTGGCA 60.608 66.667 0.00 0.00 43.56 4.92
1049 1089 2.270257 ATTGGGACGACCGACGACA 61.270 57.895 0.00 2.94 45.77 4.35
1145 1191 4.329545 CGGAGGTGGTGGTGGTGG 62.330 72.222 0.00 0.00 0.00 4.61
1146 1192 3.238497 TCGGAGGTGGTGGTGGTG 61.238 66.667 0.00 0.00 0.00 4.17
1147 1193 3.239253 GTCGGAGGTGGTGGTGGT 61.239 66.667 0.00 0.00 0.00 4.16
1746 1792 3.253061 TCACCGGGTTCCATGCCA 61.253 61.111 6.32 0.00 0.00 4.92
1786 1832 5.195940 GGTCTTCATCTTGGAAATGATGGA 58.804 41.667 0.00 0.00 40.13 3.41
2061 2107 2.707791 CTGATGATTCCCCTCTGGCTTA 59.292 50.000 0.00 0.00 0.00 3.09
2120 2166 2.753966 GGCTGCACATACACCTGCG 61.754 63.158 0.50 0.00 36.08 5.18
2247 2293 0.541392 ACTGCATAGGCCGATGACAA 59.459 50.000 27.95 12.10 40.13 3.18
2505 2552 2.508526 ACACATTCTGAGGCCTGAAAC 58.491 47.619 12.00 0.00 34.61 2.78
2594 2641 0.393808 GCGATCCAAACAGCCCCTAA 60.394 55.000 0.00 0.00 0.00 2.69
2595 2642 1.223487 GCGATCCAAACAGCCCCTA 59.777 57.895 0.00 0.00 0.00 3.53
2596 2643 1.271840 TAGCGATCCAAACAGCCCCT 61.272 55.000 0.00 0.00 0.00 4.79
2597 2644 1.095807 GTAGCGATCCAAACAGCCCC 61.096 60.000 0.00 0.00 0.00 5.80
2598 2645 1.095807 GGTAGCGATCCAAACAGCCC 61.096 60.000 0.00 0.00 0.00 5.19
2599 2646 0.107654 AGGTAGCGATCCAAACAGCC 60.108 55.000 0.00 0.00 0.00 4.85
2600 2647 1.398390 CAAGGTAGCGATCCAAACAGC 59.602 52.381 0.00 0.00 0.00 4.40
2601 2648 2.932614 CTCAAGGTAGCGATCCAAACAG 59.067 50.000 0.00 0.00 0.00 3.16
2602 2649 2.935238 GCTCAAGGTAGCGATCCAAACA 60.935 50.000 0.00 0.00 31.76 2.83
2603 2650 1.666189 GCTCAAGGTAGCGATCCAAAC 59.334 52.381 0.00 0.00 31.76 2.93
2604 2651 2.024176 GCTCAAGGTAGCGATCCAAA 57.976 50.000 0.00 0.00 31.76 3.28
2605 2652 3.760693 GCTCAAGGTAGCGATCCAA 57.239 52.632 0.00 0.00 31.76 3.53
2612 2659 1.451028 CTGGGCAGCTCAAGGTAGC 60.451 63.158 0.00 0.00 43.11 3.58
2613 2660 4.950479 CTGGGCAGCTCAAGGTAG 57.050 61.111 0.00 0.00 0.00 3.18
2644 2691 1.296056 ATACCAACGCTGCGGTCAAC 61.296 55.000 26.95 0.00 36.69 3.18
2645 2692 1.004320 ATACCAACGCTGCGGTCAA 60.004 52.632 26.95 7.52 36.69 3.18
2646 2693 1.447140 GATACCAACGCTGCGGTCA 60.447 57.895 26.95 7.53 36.69 4.02
2647 2694 2.171725 GGATACCAACGCTGCGGTC 61.172 63.158 26.95 7.11 36.69 4.79
2648 2695 2.125269 GGATACCAACGCTGCGGT 60.125 61.111 26.95 18.66 39.41 5.68
2649 2696 3.261951 CGGATACCAACGCTGCGG 61.262 66.667 26.95 11.12 0.00 5.69
2650 2697 1.632046 AAACGGATACCAACGCTGCG 61.632 55.000 21.91 21.91 0.00 5.18
2651 2698 0.179200 CAAACGGATACCAACGCTGC 60.179 55.000 0.00 0.00 0.00 5.25
2652 2699 0.446222 CCAAACGGATACCAACGCTG 59.554 55.000 0.00 0.00 0.00 5.18
2653 2700 1.303091 GCCAAACGGATACCAACGCT 61.303 55.000 0.00 0.00 0.00 5.07
2654 2701 1.135939 GCCAAACGGATACCAACGC 59.864 57.895 0.00 0.00 0.00 4.84
2655 2702 0.446222 CAGCCAAACGGATACCAACG 59.554 55.000 0.00 0.00 0.00 4.10
2656 2703 0.808755 CCAGCCAAACGGATACCAAC 59.191 55.000 0.00 0.00 0.00 3.77
2657 2704 0.322997 CCCAGCCAAACGGATACCAA 60.323 55.000 0.00 0.00 0.00 3.67
2658 2705 1.301623 CCCAGCCAAACGGATACCA 59.698 57.895 0.00 0.00 0.00 3.25
2659 2706 2.119029 GCCCAGCCAAACGGATACC 61.119 63.158 0.00 0.00 0.00 2.73
2660 2707 1.077716 AGCCCAGCCAAACGGATAC 60.078 57.895 0.00 0.00 0.00 2.24
2661 2708 1.223487 GAGCCCAGCCAAACGGATA 59.777 57.895 0.00 0.00 0.00 2.59
2662 2709 2.044946 GAGCCCAGCCAAACGGAT 60.045 61.111 0.00 0.00 0.00 4.18
2663 2710 4.344865 GGAGCCCAGCCAAACGGA 62.345 66.667 0.00 0.00 0.00 4.69
2664 2711 4.659172 TGGAGCCCAGCCAAACGG 62.659 66.667 0.00 0.00 31.13 4.44
2665 2712 2.597217 TTGGAGCCCAGCCAAACG 60.597 61.111 0.00 0.00 42.13 3.60
2668 2715 1.433121 AAATTTTGGAGCCCAGCCAA 58.567 45.000 0.00 0.00 43.31 4.52
2669 2716 1.072015 CAAAATTTTGGAGCCCAGCCA 59.928 47.619 21.00 0.00 33.81 4.75
2670 2717 1.812235 CAAAATTTTGGAGCCCAGCC 58.188 50.000 21.00 0.00 33.81 4.85
2679 2726 5.437053 GCCTTCGCAAGCCAAAATTTTGG 62.437 47.826 35.73 35.73 46.68 3.28
2680 2727 2.349722 GCCTTCGCAAGCCAAAATTTTG 60.350 45.455 21.65 21.65 34.85 2.44
2681 2728 1.872952 GCCTTCGCAAGCCAAAATTTT 59.127 42.857 0.00 0.00 34.03 1.82
2682 2729 1.511850 GCCTTCGCAAGCCAAAATTT 58.488 45.000 0.00 0.00 34.03 1.82
2683 2730 3.215642 GCCTTCGCAAGCCAAAATT 57.784 47.368 0.00 0.00 34.03 1.82
2684 2731 4.994744 GCCTTCGCAAGCCAAAAT 57.005 50.000 0.00 0.00 34.03 1.82
2690 2737 2.182537 CAATGGGCCTTCGCAAGC 59.817 61.111 4.53 0.00 38.69 4.01
2691 2738 2.887360 CCAATGGGCCTTCGCAAG 59.113 61.111 4.53 0.00 38.69 4.01
2701 2748 1.180029 CACTGGAAAGAGCCAATGGG 58.820 55.000 0.00 0.00 37.52 4.00
2702 2749 0.529378 GCACTGGAAAGAGCCAATGG 59.471 55.000 0.00 0.00 35.77 3.16
2703 2750 1.250328 TGCACTGGAAAGAGCCAATG 58.750 50.000 0.00 0.00 38.16 2.82
2704 2751 2.226962 ATGCACTGGAAAGAGCCAAT 57.773 45.000 0.00 0.00 37.52 3.16
2705 2752 1.888512 GAATGCACTGGAAAGAGCCAA 59.111 47.619 0.00 0.00 37.52 4.52
2706 2753 1.538047 GAATGCACTGGAAAGAGCCA 58.462 50.000 0.00 0.00 36.30 4.75
2707 2754 0.449388 CGAATGCACTGGAAAGAGCC 59.551 55.000 0.00 0.00 0.00 4.70
2708 2755 1.442769 TCGAATGCACTGGAAAGAGC 58.557 50.000 0.00 0.00 0.00 4.09
2709 2756 3.247173 GCTATCGAATGCACTGGAAAGAG 59.753 47.826 7.93 0.00 0.00 2.85
2710 2757 3.198068 GCTATCGAATGCACTGGAAAGA 58.802 45.455 7.93 0.00 0.00 2.52
2711 2758 2.289002 GGCTATCGAATGCACTGGAAAG 59.711 50.000 13.61 0.00 0.00 2.62
2712 2759 2.288666 GGCTATCGAATGCACTGGAAA 58.711 47.619 13.61 0.00 0.00 3.13
2713 2760 1.209261 TGGCTATCGAATGCACTGGAA 59.791 47.619 13.61 0.00 0.00 3.53
2714 2761 0.829990 TGGCTATCGAATGCACTGGA 59.170 50.000 13.61 0.00 0.00 3.86
2715 2762 1.667236 TTGGCTATCGAATGCACTGG 58.333 50.000 13.61 0.00 0.00 4.00
2716 2763 3.304257 GGAATTGGCTATCGAATGCACTG 60.304 47.826 13.61 0.00 0.00 3.66
2717 2764 2.880890 GGAATTGGCTATCGAATGCACT 59.119 45.455 13.61 0.00 0.00 4.40
2718 2765 2.880890 AGGAATTGGCTATCGAATGCAC 59.119 45.455 13.61 5.36 0.00 4.57
2719 2766 2.880268 CAGGAATTGGCTATCGAATGCA 59.120 45.455 13.61 0.00 0.00 3.96
2720 2767 2.227388 CCAGGAATTGGCTATCGAATGC 59.773 50.000 4.67 4.67 40.87 3.56
2721 2768 2.816087 CCCAGGAATTGGCTATCGAATG 59.184 50.000 0.00 0.00 46.32 2.67
2722 2769 2.815589 GCCCAGGAATTGGCTATCGAAT 60.816 50.000 0.00 0.00 46.32 3.34
2723 2770 1.476833 GCCCAGGAATTGGCTATCGAA 60.477 52.381 0.00 0.00 46.32 3.71
2724 2771 0.108585 GCCCAGGAATTGGCTATCGA 59.891 55.000 0.00 0.00 46.32 3.59
2725 2772 1.230635 CGCCCAGGAATTGGCTATCG 61.231 60.000 3.32 0.00 46.32 2.92
2726 2773 0.108585 TCGCCCAGGAATTGGCTATC 59.891 55.000 3.32 0.00 46.32 2.08
2727 2774 0.109342 CTCGCCCAGGAATTGGCTAT 59.891 55.000 3.32 0.00 46.32 2.97
2728 2775 0.980754 TCTCGCCCAGGAATTGGCTA 60.981 55.000 3.32 0.00 46.32 3.93
2729 2776 2.273449 CTCGCCCAGGAATTGGCT 59.727 61.111 3.32 0.00 46.32 4.75
2730 2777 2.115291 GTCTCGCCCAGGAATTGGC 61.115 63.158 0.00 0.00 46.32 4.52
2732 2779 1.026718 GGTGTCTCGCCCAGGAATTG 61.027 60.000 0.00 0.00 0.00 2.32
2733 2780 1.299976 GGTGTCTCGCCCAGGAATT 59.700 57.895 0.00 0.00 0.00 2.17
2734 2781 2.990479 GGTGTCTCGCCCAGGAAT 59.010 61.111 0.00 0.00 0.00 3.01
2735 2782 3.691342 CGGTGTCTCGCCCAGGAA 61.691 66.667 0.00 0.00 0.00 3.36
2770 2817 2.546373 CCCATCGGCAGCCAAAATATTG 60.546 50.000 13.30 0.00 36.25 1.90
2771 2818 1.688197 CCCATCGGCAGCCAAAATATT 59.312 47.619 13.30 0.00 0.00 1.28
2772 2819 1.331214 CCCATCGGCAGCCAAAATAT 58.669 50.000 13.30 0.00 0.00 1.28
2773 2820 0.033601 ACCCATCGGCAGCCAAAATA 60.034 50.000 13.30 0.00 0.00 1.40
2774 2821 0.904394 AACCCATCGGCAGCCAAAAT 60.904 50.000 13.30 0.00 0.00 1.82
2775 2822 1.532794 AACCCATCGGCAGCCAAAA 60.533 52.632 13.30 0.00 0.00 2.44
2776 2823 2.117206 AACCCATCGGCAGCCAAA 59.883 55.556 13.30 0.00 0.00 3.28
2777 2824 2.676121 CAACCCATCGGCAGCCAA 60.676 61.111 13.30 0.00 0.00 4.52
2778 2825 4.738998 CCAACCCATCGGCAGCCA 62.739 66.667 13.30 0.00 0.00 4.75
2785 2832 4.431131 AGCCCTGCCAACCCATCG 62.431 66.667 0.00 0.00 0.00 3.84
2786 2833 2.757099 CAGCCCTGCCAACCCATC 60.757 66.667 0.00 0.00 0.00 3.51
2805 2852 1.686355 CTGTTTGGTTACTGCCCACA 58.314 50.000 0.00 0.00 0.00 4.17
2806 2853 0.313987 GCTGTTTGGTTACTGCCCAC 59.686 55.000 0.00 0.00 37.11 4.61
2807 2854 2.727103 GCTGTTTGGTTACTGCCCA 58.273 52.632 0.00 0.00 37.11 5.36
2810 2857 0.539669 AGGGGCTGTTTGGTTACTGC 60.540 55.000 0.00 0.00 40.85 4.40
2811 2858 1.995376 AAGGGGCTGTTTGGTTACTG 58.005 50.000 0.00 0.00 0.00 2.74
2812 2859 2.714793 AGTAAGGGGCTGTTTGGTTACT 59.285 45.455 0.00 0.00 0.00 2.24
2813 2860 3.079578 GAGTAAGGGGCTGTTTGGTTAC 58.920 50.000 0.00 0.00 0.00 2.50
2814 2861 2.983898 AGAGTAAGGGGCTGTTTGGTTA 59.016 45.455 0.00 0.00 0.00 2.85
2815 2862 1.780919 AGAGTAAGGGGCTGTTTGGTT 59.219 47.619 0.00 0.00 0.00 3.67
2816 2863 1.446016 AGAGTAAGGGGCTGTTTGGT 58.554 50.000 0.00 0.00 0.00 3.67
2817 2864 2.586648 AAGAGTAAGGGGCTGTTTGG 57.413 50.000 0.00 0.00 0.00 3.28
2818 2865 4.145052 AGAAAAGAGTAAGGGGCTGTTTG 58.855 43.478 0.00 0.00 31.23 2.93
2819 2866 4.455070 AGAAAAGAGTAAGGGGCTGTTT 57.545 40.909 0.00 0.00 31.96 2.83
2820 2867 4.455070 AAGAAAAGAGTAAGGGGCTGTT 57.545 40.909 0.00 0.00 0.00 3.16
2821 2868 4.455070 AAAGAAAAGAGTAAGGGGCTGT 57.545 40.909 0.00 0.00 0.00 4.40
2822 2869 5.791336 AAAAAGAAAAGAGTAAGGGGCTG 57.209 39.130 0.00 0.00 0.00 4.85
2940 2987 1.068055 GCAGGCTGAAAATGTGGACTG 60.068 52.381 20.86 0.00 0.00 3.51
3010 3057 9.793259 CAGAGGGTGTACCATATACAAAATATT 57.207 33.333 3.11 0.00 43.89 1.28
3011 3058 8.945193 ACAGAGGGTGTACCATATACAAAATAT 58.055 33.333 3.11 0.00 43.89 1.28
3233 3443 5.800941 CACACACTAGGATCTTTTCGTACTC 59.199 44.000 0.00 0.00 0.00 2.59
3296 3515 2.642311 TGGCTGAACCAGGTCAATCTTA 59.358 45.455 0.00 0.00 46.36 2.10
3383 3602 4.972591 GCACAACTGGGCATTGAC 57.027 55.556 0.00 0.00 45.57 3.18
3420 3650 2.517959 TGATTCAAGGCAAGTTCTGGG 58.482 47.619 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.