Multiple sequence alignment - TraesCS6D01G098000

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 TraesCS6D01G098000 chr6D 100.000 2612 0 0 1 2612 61599128 61601739 0.000000e+00 4824
1 TraesCS6D01G098000 chr6D 95.181 83 4 0 2530 2612 439623363 439623281 5.870000e-27 132
2 TraesCS6D01G098000 chr6D 88.889 99 11 0 10 108 308886662 308886564 3.530000e-24 122
3 TraesCS6D01G098000 chr6B 94.163 1165 52 8 538 1689 135484504 135485665 0.000000e+00 1760
4 TraesCS6D01G098000 chr6B 90.123 324 13 5 106 426 135482126 135482433 1.130000e-108 403
5 TraesCS6D01G098000 chr6A 89.880 1334 85 26 400 1689 78984199 78985526 0.000000e+00 1670
6 TraesCS6D01G098000 chr6A 89.000 300 25 2 106 404 78981300 78981592 5.310000e-97 364
7 TraesCS6D01G098000 chr7B 95.050 606 28 2 1698 2302 735987046 735986442 0.000000e+00 952
8 TraesCS6D01G098000 chr7B 94.309 615 32 3 1698 2311 608187687 608187075 0.000000e+00 939
9 TraesCS6D01G098000 chr7B 93.641 629 35 4 1687 2312 217303295 217303921 0.000000e+00 935
10 TraesCS6D01G098000 chr4B 93.661 631 36 4 1682 2311 546575593 546576220 0.000000e+00 941
11 TraesCS6D01G098000 chr4B 93.651 630 36 4 1684 2311 119336084 119336711 0.000000e+00 939
12 TraesCS6D01G098000 chr4B 93.333 630 38 4 1683 2311 617392720 617393346 0.000000e+00 928
13 TraesCS6D01G098000 chr3B 94.032 620 35 2 1687 2305 758628856 758628238 0.000000e+00 939
14 TraesCS6D01G098000 chr3B 93.471 628 36 5 1687 2311 650613830 650614455 0.000000e+00 928
15 TraesCS6D01G098000 chr5B 93.502 631 36 4 1684 2311 276897425 276898053 0.000000e+00 933
16 TraesCS6D01G098000 chr5B 95.062 81 3 1 31 111 16642551 16642630 2.730000e-25 126
17 TraesCS6D01G098000 chr5B 95.062 81 3 1 31 111 16666756 16666835 2.730000e-25 126
18 TraesCS6D01G098000 chr5B 91.860 86 5 2 27 111 16571600 16571684 4.570000e-23 119
19 TraesCS6D01G098000 chr2B 94.231 104 6 0 3 106 773173870 773173767 2.690000e-35 159
20 TraesCS6D01G098000 chr3A 91.346 104 8 1 3 106 456717240 456717342 9.750000e-30 141
21 TraesCS6D01G098000 chr7D 94.382 89 5 0 2524 2612 538671641 538671553 1.260000e-28 137
22 TraesCS6D01G098000 chr4A 94.382 89 5 0 2524 2612 662081294 662081382 1.260000e-28 137
23 TraesCS6D01G098000 chr3D 94.382 89 5 0 2524 2612 298240645 298240733 1.260000e-28 137
24 TraesCS6D01G098000 chr5D 93.258 89 6 0 2524 2612 497141492 497141580 5.870000e-27 132
25 TraesCS6D01G098000 chr5D 93.333 90 5 1 2524 2612 497230814 497230903 5.870000e-27 132
26 TraesCS6D01G098000 chr5D 95.238 84 3 1 2530 2612 497423665 497423582 5.870000e-27 132
27 TraesCS6D01G098000 chr5D 95.181 83 4 0 2530 2612 497461337 497461255 5.870000e-27 132
28 TraesCS6D01G098000 chr5D 91.579 95 5 3 2518 2612 2689136 2689227 7.590000e-26 128
29 TraesCS6D01G098000 chr5D 89.583 96 10 0 11 106 332520312 332520217 3.530000e-24 122
30 TraesCS6D01G098000 chr1D 88.571 105 11 1 3 107 18988597 18988700 2.730000e-25 126
31 TraesCS6D01G098000 chrUn 92.771 83 4 2 30 111 419598103 419598022 4.570000e-23 119


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 TraesCS6D01G098000 chr6D 61599128 61601739 2611 False 4824.0 4824 100.000 1 2612 1 chr6D.!!$F1 2611
1 TraesCS6D01G098000 chr6B 135482126 135485665 3539 False 1081.5 1760 92.143 106 1689 2 chr6B.!!$F1 1583
2 TraesCS6D01G098000 chr6A 78981300 78985526 4226 False 1017.0 1670 89.440 106 1689 2 chr6A.!!$F1 1583
3 TraesCS6D01G098000 chr7B 735986442 735987046 604 True 952.0 952 95.050 1698 2302 1 chr7B.!!$R2 604
4 TraesCS6D01G098000 chr7B 608187075 608187687 612 True 939.0 939 94.309 1698 2311 1 chr7B.!!$R1 613
5 TraesCS6D01G098000 chr7B 217303295 217303921 626 False 935.0 935 93.641 1687 2312 1 chr7B.!!$F1 625
6 TraesCS6D01G098000 chr4B 546575593 546576220 627 False 941.0 941 93.661 1682 2311 1 chr4B.!!$F2 629
7 TraesCS6D01G098000 chr4B 119336084 119336711 627 False 939.0 939 93.651 1684 2311 1 chr4B.!!$F1 627
8 TraesCS6D01G098000 chr4B 617392720 617393346 626 False 928.0 928 93.333 1683 2311 1 chr4B.!!$F3 628
9 TraesCS6D01G098000 chr3B 758628238 758628856 618 True 939.0 939 94.032 1687 2305 1 chr3B.!!$R1 618
10 TraesCS6D01G098000 chr3B 650613830 650614455 625 False 928.0 928 93.471 1687 2311 1 chr3B.!!$F1 624
11 TraesCS6D01G098000 chr5B 276897425 276898053 628 False 933.0 933 93.502 1684 2311 1 chr5B.!!$F4 627

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
290 304 0.179094 AGTCGACGTTCCAACAGCAA 60.179 50.0 10.46 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2285 6912 0.252927 AGCTAGGGTTTCTGCCTCCT 60.253 55.0 0.0 0.0 0.0 3.69 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
22 23 4.837972 GAGATCTGTTTTGTAAGAGGGCT 58.162 43.478 0.00 0.00 0.00 5.19
23 24 4.583871 AGATCTGTTTTGTAAGAGGGCTG 58.416 43.478 0.00 0.00 0.00 4.85
24 25 2.504367 TCTGTTTTGTAAGAGGGCTGC 58.496 47.619 0.00 0.00 0.00 5.25
25 26 1.541588 CTGTTTTGTAAGAGGGCTGCC 59.458 52.381 11.05 11.05 0.00 4.85
26 27 1.144913 TGTTTTGTAAGAGGGCTGCCT 59.855 47.619 19.68 4.34 0.00 4.75
27 28 1.813178 GTTTTGTAAGAGGGCTGCCTC 59.187 52.381 19.68 13.66 37.11 4.70
29 30 0.905357 TTGTAAGAGGGCTGCCTCTC 59.095 55.000 19.68 21.18 45.28 3.20
30 31 0.978146 TGTAAGAGGGCTGCCTCTCC 60.978 60.000 24.47 16.28 45.28 3.71
31 32 0.978146 GTAAGAGGGCTGCCTCTCCA 60.978 60.000 24.47 15.01 45.28 3.86
32 33 0.978146 TAAGAGGGCTGCCTCTCCAC 60.978 60.000 24.47 7.69 45.28 4.02
33 34 3.791586 GAGGGCTGCCTCTCCACC 61.792 72.222 19.68 0.00 34.30 4.61
34 35 4.345286 AGGGCTGCCTCTCCACCT 62.345 66.667 19.68 1.73 0.00 4.00
35 36 3.334054 GGGCTGCCTCTCCACCTT 61.334 66.667 19.68 0.00 0.00 3.50
36 37 2.045536 GGCTGCCTCTCCACCTTG 60.046 66.667 12.43 0.00 0.00 3.61
37 38 2.753029 GCTGCCTCTCCACCTTGT 59.247 61.111 0.00 0.00 0.00 3.16
38 39 1.553690 GGCTGCCTCTCCACCTTGTA 61.554 60.000 12.43 0.00 0.00 2.41
39 40 0.543749 GCTGCCTCTCCACCTTGTAT 59.456 55.000 0.00 0.00 0.00 2.29
40 41 1.474143 GCTGCCTCTCCACCTTGTATC 60.474 57.143 0.00 0.00 0.00 2.24
41 42 0.824109 TGCCTCTCCACCTTGTATCG 59.176 55.000 0.00 0.00 0.00 2.92
42 43 0.824759 GCCTCTCCACCTTGTATCGT 59.175 55.000 0.00 0.00 0.00 3.73
43 44 1.207329 GCCTCTCCACCTTGTATCGTT 59.793 52.381 0.00 0.00 0.00 3.85
44 45 2.738964 GCCTCTCCACCTTGTATCGTTC 60.739 54.545 0.00 0.00 0.00 3.95
45 46 2.479730 CCTCTCCACCTTGTATCGTTCG 60.480 54.545 0.00 0.00 0.00 3.95
46 47 2.422479 CTCTCCACCTTGTATCGTTCGA 59.578 50.000 0.00 0.00 0.00 3.71
47 48 2.163010 TCTCCACCTTGTATCGTTCGAC 59.837 50.000 0.00 0.00 0.00 4.20
48 49 1.203052 TCCACCTTGTATCGTTCGACC 59.797 52.381 0.00 0.00 0.00 4.79
49 50 1.265568 CACCTTGTATCGTTCGACCG 58.734 55.000 0.00 0.00 0.00 4.79
50 51 0.883833 ACCTTGTATCGTTCGACCGT 59.116 50.000 1.29 0.00 0.00 4.83
51 52 1.265568 CCTTGTATCGTTCGACCGTG 58.734 55.000 1.29 0.00 0.00 4.94
52 53 1.401931 CCTTGTATCGTTCGACCGTGT 60.402 52.381 1.29 0.00 0.00 4.49
53 54 2.159531 CCTTGTATCGTTCGACCGTGTA 60.160 50.000 1.29 0.00 0.00 2.90
54 55 2.525750 TGTATCGTTCGACCGTGTAC 57.474 50.000 1.29 7.82 0.00 2.90
55 56 2.076100 TGTATCGTTCGACCGTGTACT 58.924 47.619 16.37 0.00 0.00 2.73
56 57 2.483877 TGTATCGTTCGACCGTGTACTT 59.516 45.455 16.37 0.00 0.00 2.24
57 58 2.712057 ATCGTTCGACCGTGTACTTT 57.288 45.000 1.29 0.00 0.00 2.66
58 59 1.757574 TCGTTCGACCGTGTACTTTG 58.242 50.000 1.29 0.00 0.00 2.77
59 60 1.065401 TCGTTCGACCGTGTACTTTGT 59.935 47.619 1.29 0.00 0.00 2.83
60 61 1.854126 CGTTCGACCGTGTACTTTGTT 59.146 47.619 0.00 0.00 0.00 2.83
61 62 2.097733 CGTTCGACCGTGTACTTTGTTC 60.098 50.000 0.00 0.00 0.00 3.18
62 63 1.757574 TCGACCGTGTACTTTGTTCG 58.242 50.000 0.00 0.00 0.00 3.95
63 64 0.780002 CGACCGTGTACTTTGTTCGG 59.220 55.000 0.00 0.00 45.53 4.30
66 67 2.656192 CCGTGTACTTTGTTCGGTTG 57.344 50.000 0.00 0.00 36.99 3.77
67 68 1.262151 CCGTGTACTTTGTTCGGTTGG 59.738 52.381 0.00 0.00 36.99 3.77
68 69 1.935199 CGTGTACTTTGTTCGGTTGGT 59.065 47.619 0.00 0.00 0.00 3.67
69 70 2.285950 CGTGTACTTTGTTCGGTTGGTG 60.286 50.000 0.00 0.00 0.00 4.17
70 71 1.671845 TGTACTTTGTTCGGTTGGTGC 59.328 47.619 0.00 0.00 0.00 5.01
71 72 1.944709 GTACTTTGTTCGGTTGGTGCT 59.055 47.619 0.00 0.00 0.00 4.40
72 73 1.470051 ACTTTGTTCGGTTGGTGCTT 58.530 45.000 0.00 0.00 0.00 3.91
73 74 1.822371 ACTTTGTTCGGTTGGTGCTTT 59.178 42.857 0.00 0.00 0.00 3.51
74 75 3.018149 ACTTTGTTCGGTTGGTGCTTTA 58.982 40.909 0.00 0.00 0.00 1.85
75 76 3.634910 ACTTTGTTCGGTTGGTGCTTTAT 59.365 39.130 0.00 0.00 0.00 1.40
76 77 3.907894 TTGTTCGGTTGGTGCTTTATC 57.092 42.857 0.00 0.00 0.00 1.75
77 78 3.134574 TGTTCGGTTGGTGCTTTATCT 57.865 42.857 0.00 0.00 0.00 1.98
78 79 4.274602 TGTTCGGTTGGTGCTTTATCTA 57.725 40.909 0.00 0.00 0.00 1.98
79 80 4.839121 TGTTCGGTTGGTGCTTTATCTAT 58.161 39.130 0.00 0.00 0.00 1.98
80 81 5.979993 TGTTCGGTTGGTGCTTTATCTATA 58.020 37.500 0.00 0.00 0.00 1.31
81 82 6.408035 TGTTCGGTTGGTGCTTTATCTATAA 58.592 36.000 0.00 0.00 0.00 0.98
82 83 6.879993 TGTTCGGTTGGTGCTTTATCTATAAA 59.120 34.615 0.00 0.00 0.00 1.40
278 282 4.978186 TCTTAGAACCAACATAGTCGACG 58.022 43.478 10.46 0.00 0.00 5.12
286 300 3.054166 CAACATAGTCGACGTTCCAACA 58.946 45.455 10.46 0.00 0.00 3.33
287 301 2.942710 ACATAGTCGACGTTCCAACAG 58.057 47.619 10.46 0.00 0.00 3.16
288 302 1.654105 CATAGTCGACGTTCCAACAGC 59.346 52.381 10.46 0.00 0.00 4.40
289 303 0.669619 TAGTCGACGTTCCAACAGCA 59.330 50.000 10.46 0.00 0.00 4.41
290 304 0.179094 AGTCGACGTTCCAACAGCAA 60.179 50.000 10.46 0.00 0.00 3.91
291 305 0.865769 GTCGACGTTCCAACAGCAAT 59.134 50.000 0.00 0.00 0.00 3.56
292 306 1.136336 GTCGACGTTCCAACAGCAATC 60.136 52.381 0.00 0.00 0.00 2.67
293 307 0.179250 CGACGTTCCAACAGCAATCG 60.179 55.000 0.00 0.00 0.00 3.34
294 308 0.452784 GACGTTCCAACAGCAATCGC 60.453 55.000 0.00 0.00 38.99 4.58
335 349 3.131396 GACGGCCGATTACATTCTGAAT 58.869 45.455 35.90 2.70 0.00 2.57
363 377 5.822278 TGTCGAGCTAGATTATGTGACTTC 58.178 41.667 0.00 0.00 0.00 3.01
367 381 6.943146 TCGAGCTAGATTATGTGACTTCCTAT 59.057 38.462 0.00 0.00 0.00 2.57
368 382 7.448777 TCGAGCTAGATTATGTGACTTCCTATT 59.551 37.037 0.00 0.00 0.00 1.73
369 383 7.753132 CGAGCTAGATTATGTGACTTCCTATTC 59.247 40.741 0.00 0.00 0.00 1.75
370 384 7.598278 AGCTAGATTATGTGACTTCCTATTCG 58.402 38.462 0.00 0.00 0.00 3.34
371 385 7.448777 AGCTAGATTATGTGACTTCCTATTCGA 59.551 37.037 0.00 0.00 0.00 3.71
387 401 4.561735 ATTCGATTCGACTCTCTTCTCC 57.438 45.455 8.55 0.00 34.89 3.71
426 3051 2.676342 GGAGACAACGTGTTGAGTTTGT 59.324 45.455 18.87 0.00 42.93 2.83
572 5160 5.123979 GGGAGCTTACTGTTTTAGGTGATTG 59.876 44.000 0.00 0.00 0.00 2.67
628 5220 4.765273 ACATCTTTTTGCCGAAAACCTTT 58.235 34.783 0.00 0.00 33.78 3.11
633 5225 6.270064 TCTTTTTGCCGAAAACCTTTTCTAG 58.730 36.000 8.50 2.30 43.27 2.43
683 5277 2.091665 AGGAATTCGCCTGGGATGAAAT 60.092 45.455 0.00 0.00 36.76 2.17
755 5358 5.359576 TCACAAACTTGGTTGCTAGATTGTT 59.640 36.000 0.00 0.00 35.88 2.83
1072 5686 0.512952 CTTCCTCGTTGCTTTGACCG 59.487 55.000 0.00 0.00 0.00 4.79
1320 5934 4.830765 TCGTACATGCTGGCGGGC 62.831 66.667 0.00 0.00 0.00 6.13
1353 5967 0.691904 TGCTGATGGTGTCCATGACA 59.308 50.000 5.98 0.00 45.26 3.58
1377 5991 4.508128 CTCACGGGCGGCGTGTAT 62.508 66.667 24.64 0.00 38.38 2.29
1617 6234 5.227184 CGGCGTTTTGAATATTTAGTGAAGC 59.773 40.000 0.00 0.00 0.00 3.86
1618 6235 6.322491 GGCGTTTTGAATATTTAGTGAAGCT 58.678 36.000 0.00 0.00 0.00 3.74
1619 6236 6.469275 GGCGTTTTGAATATTTAGTGAAGCTC 59.531 38.462 0.00 0.00 0.00 4.09
1620 6237 6.469275 GCGTTTTGAATATTTAGTGAAGCTCC 59.531 38.462 0.00 0.00 0.00 4.70
1654 6278 5.927030 TCGAATAAGTGCAATGTTTGAGTC 58.073 37.500 0.00 0.00 0.00 3.36
1659 6283 4.825546 AGTGCAATGTTTGAGTCTTCTG 57.174 40.909 0.00 0.00 0.00 3.02
1663 6287 4.035558 TGCAATGTTTGAGTCTTCTGTGTC 59.964 41.667 0.00 0.00 0.00 3.67
1674 6298 3.675698 GTCTTCTGTGTCTTCGTGATTCC 59.324 47.826 0.00 0.00 0.00 3.01
1730 6356 6.872628 TCTATTCATCTTCAATCATGGCAC 57.127 37.500 0.00 0.00 0.00 5.01
1742 6368 5.877564 TCAATCATGGCACTACAACGAATAA 59.122 36.000 0.00 0.00 0.00 1.40
1811 6437 0.033366 TACAAGCACTGAAGCGAGCA 59.967 50.000 0.00 0.00 40.15 4.26
1936 6562 2.972505 CAGAACAGCAACCGCCGT 60.973 61.111 0.00 0.00 39.83 5.68
1948 6574 2.225068 ACCGCCGTAGATGAAGAATG 57.775 50.000 0.00 0.00 0.00 2.67
1962 6588 7.424803 AGATGAAGAATGACGTAGATCAGAAG 58.575 38.462 0.00 0.00 30.46 2.85
1981 6607 2.248248 AGGATCCAACTCGAAGACACA 58.752 47.619 15.82 0.00 0.00 3.72
2101 6727 2.757099 GGAACGGGGTCTAGGCGA 60.757 66.667 0.00 0.00 0.00 5.54
2175 6801 4.202212 GCAGGACACAAACCCTAACAAAAT 60.202 41.667 0.00 0.00 0.00 1.82
2181 6807 7.334671 GGACACAAACCCTAACAAAATTGAAAA 59.665 33.333 0.00 0.00 0.00 2.29
2268 6895 2.835431 CACCGGAGAGGAGCGGAT 60.835 66.667 9.46 0.00 45.00 4.18
2302 6929 0.107459 GCAGGAGGCAGAAACCCTAG 60.107 60.000 0.00 0.00 43.97 3.02
2305 6932 0.179234 GGAGGCAGAAACCCTAGCTC 59.821 60.000 0.00 0.00 31.41 4.09
2328 6955 3.896648 TTTTCCACGATGCTCAAGTTC 57.103 42.857 0.00 0.00 0.00 3.01
2329 6956 2.542020 TTCCACGATGCTCAAGTTCA 57.458 45.000 0.00 0.00 0.00 3.18
2330 6957 2.768253 TCCACGATGCTCAAGTTCAT 57.232 45.000 0.00 0.00 0.00 2.57
2331 6958 3.057969 TCCACGATGCTCAAGTTCATT 57.942 42.857 0.00 0.00 0.00 2.57
2332 6959 3.411446 TCCACGATGCTCAAGTTCATTT 58.589 40.909 0.00 0.00 0.00 2.32
2333 6960 3.189080 TCCACGATGCTCAAGTTCATTTG 59.811 43.478 0.00 0.00 0.00 2.32
2334 6961 3.058016 CCACGATGCTCAAGTTCATTTGT 60.058 43.478 0.00 0.00 0.00 2.83
2335 6962 4.539870 CACGATGCTCAAGTTCATTTGTT 58.460 39.130 0.00 0.00 0.00 2.83
2336 6963 4.977963 CACGATGCTCAAGTTCATTTGTTT 59.022 37.500 0.00 0.00 0.00 2.83
2337 6964 5.116074 CACGATGCTCAAGTTCATTTGTTTC 59.884 40.000 0.00 0.00 0.00 2.78
2338 6965 4.319115 CGATGCTCAAGTTCATTTGTTTCG 59.681 41.667 0.00 0.00 0.00 3.46
2339 6966 4.891627 TGCTCAAGTTCATTTGTTTCGA 57.108 36.364 0.00 0.00 0.00 3.71
2340 6967 5.242069 TGCTCAAGTTCATTTGTTTCGAA 57.758 34.783 0.00 0.00 0.00 3.71
2341 6968 5.830912 TGCTCAAGTTCATTTGTTTCGAAT 58.169 33.333 0.00 0.00 0.00 3.34
2342 6969 6.272318 TGCTCAAGTTCATTTGTTTCGAATT 58.728 32.000 0.00 0.00 0.00 2.17
2343 6970 6.198778 TGCTCAAGTTCATTTGTTTCGAATTG 59.801 34.615 0.00 0.00 0.00 2.32
2344 6971 6.509317 TCAAGTTCATTTGTTTCGAATTGC 57.491 33.333 0.00 0.00 0.00 3.56
2345 6972 5.461737 TCAAGTTCATTTGTTTCGAATTGCC 59.538 36.000 0.00 0.00 0.00 4.52
2346 6973 5.200368 AGTTCATTTGTTTCGAATTGCCT 57.800 34.783 0.00 0.00 0.00 4.75
2347 6974 5.600696 AGTTCATTTGTTTCGAATTGCCTT 58.399 33.333 0.00 0.00 0.00 4.35
2348 6975 6.048509 AGTTCATTTGTTTCGAATTGCCTTT 58.951 32.000 0.00 0.00 0.00 3.11
2349 6976 6.538381 AGTTCATTTGTTTCGAATTGCCTTTT 59.462 30.769 0.00 0.00 0.00 2.27
2350 6977 6.917217 TCATTTGTTTCGAATTGCCTTTTT 57.083 29.167 0.00 0.00 0.00 1.94
2351 6978 8.331742 GTTCATTTGTTTCGAATTGCCTTTTTA 58.668 29.630 0.00 0.00 0.00 1.52
2352 6979 8.600449 TCATTTGTTTCGAATTGCCTTTTTAT 57.400 26.923 0.00 0.00 0.00 1.40
2353 6980 9.050601 TCATTTGTTTCGAATTGCCTTTTTATT 57.949 25.926 0.00 0.00 0.00 1.40
2354 6981 9.316859 CATTTGTTTCGAATTGCCTTTTTATTC 57.683 29.630 0.00 0.00 0.00 1.75
2435 7062 7.857734 TTAATGCTCTCATTAAATCGACCAA 57.142 32.000 7.71 0.00 46.43 3.67
2436 7063 5.998454 ATGCTCTCATTAAATCGACCAAG 57.002 39.130 0.00 0.00 0.00 3.61
2437 7064 5.084818 TGCTCTCATTAAATCGACCAAGA 57.915 39.130 0.00 0.00 0.00 3.02
2438 7065 5.487433 TGCTCTCATTAAATCGACCAAGAA 58.513 37.500 0.00 0.00 0.00 2.52
2439 7066 5.582269 TGCTCTCATTAAATCGACCAAGAAG 59.418 40.000 0.00 0.00 0.00 2.85
2440 7067 5.503194 GCTCTCATTAAATCGACCAAGAAGC 60.503 44.000 0.00 0.00 0.00 3.86
2441 7068 5.487433 TCTCATTAAATCGACCAAGAAGCA 58.513 37.500 0.00 0.00 0.00 3.91
2442 7069 5.582269 TCTCATTAAATCGACCAAGAAGCAG 59.418 40.000 0.00 0.00 0.00 4.24
2443 7070 4.094887 TCATTAAATCGACCAAGAAGCAGC 59.905 41.667 0.00 0.00 0.00 5.25
2444 7071 2.191128 AAATCGACCAAGAAGCAGCT 57.809 45.000 0.00 0.00 0.00 4.24
2445 7072 3.334583 AAATCGACCAAGAAGCAGCTA 57.665 42.857 0.00 0.00 0.00 3.32
2446 7073 3.334583 AATCGACCAAGAAGCAGCTAA 57.665 42.857 0.00 0.00 0.00 3.09
2447 7074 3.550437 ATCGACCAAGAAGCAGCTAAT 57.450 42.857 0.00 0.00 0.00 1.73
2448 7075 3.334583 TCGACCAAGAAGCAGCTAATT 57.665 42.857 0.00 0.00 0.00 1.40
2449 7076 3.262420 TCGACCAAGAAGCAGCTAATTC 58.738 45.455 0.00 2.56 0.00 2.17
2450 7077 3.055819 TCGACCAAGAAGCAGCTAATTCT 60.056 43.478 0.00 6.75 37.36 2.40
2451 7078 3.063180 CGACCAAGAAGCAGCTAATTCTG 59.937 47.826 12.09 5.11 35.95 3.02
2452 7079 4.256920 GACCAAGAAGCAGCTAATTCTGA 58.743 43.478 12.09 0.00 35.95 3.27
2453 7080 4.260170 ACCAAGAAGCAGCTAATTCTGAG 58.740 43.478 12.09 9.52 35.95 3.35
2454 7081 3.065095 CCAAGAAGCAGCTAATTCTGAGC 59.935 47.826 12.09 0.00 35.95 4.26
2455 7082 2.916640 AGAAGCAGCTAATTCTGAGCC 58.083 47.619 10.89 0.00 41.06 4.70
2456 7083 1.596727 GAAGCAGCTAATTCTGAGCCG 59.403 52.381 0.00 0.00 41.06 5.52
2457 7084 0.826715 AGCAGCTAATTCTGAGCCGA 59.173 50.000 0.00 0.00 41.06 5.54
2458 7085 0.933796 GCAGCTAATTCTGAGCCGAC 59.066 55.000 0.00 0.00 41.06 4.79
2459 7086 1.576356 CAGCTAATTCTGAGCCGACC 58.424 55.000 0.00 0.00 41.06 4.79
2460 7087 1.134699 CAGCTAATTCTGAGCCGACCA 60.135 52.381 0.00 0.00 41.06 4.02
2461 7088 1.555075 AGCTAATTCTGAGCCGACCAA 59.445 47.619 0.00 0.00 41.06 3.67
2462 7089 2.027192 AGCTAATTCTGAGCCGACCAAA 60.027 45.455 0.00 0.00 41.06 3.28
2463 7090 2.747446 GCTAATTCTGAGCCGACCAAAA 59.253 45.455 0.00 0.00 33.60 2.44
2464 7091 3.190535 GCTAATTCTGAGCCGACCAAAAA 59.809 43.478 0.00 0.00 33.60 1.94
2536 7163 8.760103 TTTTTAATACAGTACAGACGCATACA 57.240 30.769 0.00 0.00 0.00 2.29
2537 7164 7.745022 TTTAATACAGTACAGACGCATACAC 57.255 36.000 0.00 0.00 0.00 2.90
2538 7165 5.578005 AATACAGTACAGACGCATACACT 57.422 39.130 0.00 0.00 0.00 3.55
2539 7166 3.489180 ACAGTACAGACGCATACACTC 57.511 47.619 0.00 0.00 0.00 3.51
2540 7167 2.163815 ACAGTACAGACGCATACACTCC 59.836 50.000 0.00 0.00 0.00 3.85
2541 7168 1.749634 AGTACAGACGCATACACTCCC 59.250 52.381 0.00 0.00 0.00 4.30
2542 7169 1.108776 TACAGACGCATACACTCCCC 58.891 55.000 0.00 0.00 0.00 4.81
2543 7170 1.144057 CAGACGCATACACTCCCCC 59.856 63.158 0.00 0.00 0.00 5.40
2557 7184 4.779475 CCCCCTATGATCGCACAC 57.221 61.111 0.00 0.00 0.00 3.82
2558 7185 1.829456 CCCCCTATGATCGCACACA 59.171 57.895 0.00 0.00 0.00 3.72
2559 7186 0.532862 CCCCCTATGATCGCACACAC 60.533 60.000 0.00 0.00 0.00 3.82
2560 7187 0.875908 CCCCTATGATCGCACACACG 60.876 60.000 0.00 0.00 0.00 4.49
2561 7188 1.490693 CCCTATGATCGCACACACGC 61.491 60.000 0.00 0.00 0.00 5.34
2562 7189 0.805711 CCTATGATCGCACACACGCA 60.806 55.000 0.00 0.00 0.00 5.24
2563 7190 0.298707 CTATGATCGCACACACGCAC 59.701 55.000 0.00 0.00 0.00 5.34
2564 7191 0.389166 TATGATCGCACACACGCACA 60.389 50.000 0.00 0.00 0.00 4.57
2565 7192 1.900585 ATGATCGCACACACGCACAC 61.901 55.000 0.00 0.00 0.00 3.82
2566 7193 3.295228 GATCGCACACACGCACACC 62.295 63.158 0.00 0.00 0.00 4.16
2569 7196 2.280524 GCACACACGCACACCCTA 60.281 61.111 0.00 0.00 0.00 3.53
2570 7197 2.604174 GCACACACGCACACCCTAC 61.604 63.158 0.00 0.00 0.00 3.18
2571 7198 1.959226 CACACACGCACACCCTACC 60.959 63.158 0.00 0.00 0.00 3.18
2572 7199 2.358247 CACACGCACACCCTACCC 60.358 66.667 0.00 0.00 0.00 3.69
2573 7200 3.633116 ACACGCACACCCTACCCC 61.633 66.667 0.00 0.00 0.00 4.95
2574 7201 3.319198 CACGCACACCCTACCCCT 61.319 66.667 0.00 0.00 0.00 4.79
2575 7202 1.985662 CACGCACACCCTACCCCTA 60.986 63.158 0.00 0.00 0.00 3.53
2576 7203 1.002533 ACGCACACCCTACCCCTAT 59.997 57.895 0.00 0.00 0.00 2.57
2577 7204 1.335132 ACGCACACCCTACCCCTATG 61.335 60.000 0.00 0.00 0.00 2.23
2578 7205 1.046472 CGCACACCCTACCCCTATGA 61.046 60.000 0.00 0.00 0.00 2.15
2579 7206 0.759346 GCACACCCTACCCCTATGAG 59.241 60.000 0.00 0.00 0.00 2.90
2580 7207 0.759346 CACACCCTACCCCTATGAGC 59.241 60.000 0.00 0.00 0.00 4.26
2581 7208 0.341961 ACACCCTACCCCTATGAGCA 59.658 55.000 0.00 0.00 0.00 4.26
2582 7209 0.759346 CACCCTACCCCTATGAGCAC 59.241 60.000 0.00 0.00 0.00 4.40
2583 7210 0.400093 ACCCTACCCCTATGAGCACC 60.400 60.000 0.00 0.00 0.00 5.01
2584 7211 0.104934 CCCTACCCCTATGAGCACCT 60.105 60.000 0.00 0.00 0.00 4.00
2585 7212 1.695989 CCCTACCCCTATGAGCACCTT 60.696 57.143 0.00 0.00 0.00 3.50
2586 7213 2.127708 CCTACCCCTATGAGCACCTTT 58.872 52.381 0.00 0.00 0.00 3.11
2587 7214 2.158755 CCTACCCCTATGAGCACCTTTG 60.159 54.545 0.00 0.00 0.00 2.77
2588 7215 1.668826 ACCCCTATGAGCACCTTTGA 58.331 50.000 0.00 0.00 0.00 2.69
2589 7216 1.992557 ACCCCTATGAGCACCTTTGAA 59.007 47.619 0.00 0.00 0.00 2.69
2590 7217 2.378547 ACCCCTATGAGCACCTTTGAAA 59.621 45.455 0.00 0.00 0.00 2.69
2591 7218 3.019564 CCCCTATGAGCACCTTTGAAAG 58.980 50.000 0.00 0.00 0.00 2.62
2592 7219 3.308402 CCCCTATGAGCACCTTTGAAAGA 60.308 47.826 6.49 0.00 0.00 2.52
2593 7220 3.691609 CCCTATGAGCACCTTTGAAAGAC 59.308 47.826 6.49 0.00 0.00 3.01
2594 7221 3.691609 CCTATGAGCACCTTTGAAAGACC 59.308 47.826 6.49 0.00 0.00 3.85
2595 7222 1.593196 TGAGCACCTTTGAAAGACCG 58.407 50.000 6.49 0.00 0.00 4.79
2596 7223 1.140052 TGAGCACCTTTGAAAGACCGA 59.860 47.619 6.49 0.00 0.00 4.69
2597 7224 1.801178 GAGCACCTTTGAAAGACCGAG 59.199 52.381 6.49 0.00 0.00 4.63
2598 7225 0.238553 GCACCTTTGAAAGACCGAGC 59.761 55.000 6.49 0.00 0.00 5.03
2599 7226 0.875059 CACCTTTGAAAGACCGAGCC 59.125 55.000 6.49 0.00 0.00 4.70
2600 7227 0.602905 ACCTTTGAAAGACCGAGCCG 60.603 55.000 6.49 0.00 0.00 5.52
2610 7237 4.192000 CCGAGCCGGCATATCATC 57.808 61.111 31.54 15.45 41.17 2.92
2611 7238 1.593787 CCGAGCCGGCATATCATCT 59.406 57.895 31.54 4.27 41.17 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.084786 GCAGCCCTCTTACAAAACAGAT 58.915 45.455 0.00 0.00 0.00 2.90
5 6 1.541588 GGCAGCCCTCTTACAAAACAG 59.458 52.381 0.00 0.00 0.00 3.16
6 7 1.144913 AGGCAGCCCTCTTACAAAACA 59.855 47.619 8.22 0.00 36.46 2.83
7 8 1.911057 AGGCAGCCCTCTTACAAAAC 58.089 50.000 8.22 0.00 36.46 2.43
17 18 3.880033 AAGGTGGAGAGGCAGCCCT 62.880 63.158 8.22 4.77 46.74 5.19
18 19 3.334054 AAGGTGGAGAGGCAGCCC 61.334 66.667 8.22 0.00 0.00 5.19
19 20 1.553690 TACAAGGTGGAGAGGCAGCC 61.554 60.000 1.84 1.84 0.00 4.85
20 21 0.543749 ATACAAGGTGGAGAGGCAGC 59.456 55.000 0.00 0.00 0.00 5.25
21 22 1.202463 CGATACAAGGTGGAGAGGCAG 60.202 57.143 0.00 0.00 0.00 4.85
22 23 0.824109 CGATACAAGGTGGAGAGGCA 59.176 55.000 0.00 0.00 0.00 4.75
23 24 0.824759 ACGATACAAGGTGGAGAGGC 59.175 55.000 0.00 0.00 0.00 4.70
24 25 2.479730 CGAACGATACAAGGTGGAGAGG 60.480 54.545 0.00 0.00 0.00 3.69
25 26 2.422479 TCGAACGATACAAGGTGGAGAG 59.578 50.000 0.00 0.00 0.00 3.20
26 27 2.163010 GTCGAACGATACAAGGTGGAGA 59.837 50.000 0.00 0.00 0.00 3.71
27 28 2.527100 GTCGAACGATACAAGGTGGAG 58.473 52.381 0.00 0.00 0.00 3.86
28 29 1.203052 GGTCGAACGATACAAGGTGGA 59.797 52.381 0.00 0.00 0.00 4.02
29 30 1.636988 GGTCGAACGATACAAGGTGG 58.363 55.000 0.00 0.00 0.00 4.61
30 31 1.265568 CGGTCGAACGATACAAGGTG 58.734 55.000 20.37 0.00 35.47 4.00
31 32 0.883833 ACGGTCGAACGATACAAGGT 59.116 50.000 32.41 0.00 37.61 3.50
32 33 1.265568 CACGGTCGAACGATACAAGG 58.734 55.000 32.41 5.58 37.61 3.61
33 34 1.973138 ACACGGTCGAACGATACAAG 58.027 50.000 32.41 13.49 37.61 3.16
34 35 2.483877 AGTACACGGTCGAACGATACAA 59.516 45.455 32.41 6.96 37.61 2.41
35 36 2.076100 AGTACACGGTCGAACGATACA 58.924 47.619 32.41 8.54 37.61 2.29
36 37 2.813779 AGTACACGGTCGAACGATAC 57.186 50.000 32.41 27.56 37.61 2.24
37 38 3.058293 ACAAAGTACACGGTCGAACGATA 60.058 43.478 32.41 18.24 37.61 2.92
38 39 2.287788 ACAAAGTACACGGTCGAACGAT 60.288 45.455 32.41 19.36 37.61 3.73
39 40 1.065401 ACAAAGTACACGGTCGAACGA 59.935 47.619 32.41 3.66 37.61 3.85
40 41 1.480205 ACAAAGTACACGGTCGAACG 58.520 50.000 23.55 23.55 40.31 3.95
41 42 2.097733 CGAACAAAGTACACGGTCGAAC 60.098 50.000 10.13 0.00 0.00 3.95
42 43 2.118683 CGAACAAAGTACACGGTCGAA 58.881 47.619 10.13 0.00 0.00 3.71
43 44 1.600164 CCGAACAAAGTACACGGTCGA 60.600 52.381 15.55 0.00 38.97 4.20
44 45 0.780002 CCGAACAAAGTACACGGTCG 59.220 55.000 9.02 9.02 38.97 4.79
48 49 1.935199 ACCAACCGAACAAAGTACACG 59.065 47.619 0.00 0.00 0.00 4.49
49 50 2.540157 GCACCAACCGAACAAAGTACAC 60.540 50.000 0.00 0.00 0.00 2.90
50 51 1.671845 GCACCAACCGAACAAAGTACA 59.328 47.619 0.00 0.00 0.00 2.90
51 52 1.944709 AGCACCAACCGAACAAAGTAC 59.055 47.619 0.00 0.00 0.00 2.73
52 53 2.335316 AGCACCAACCGAACAAAGTA 57.665 45.000 0.00 0.00 0.00 2.24
53 54 1.470051 AAGCACCAACCGAACAAAGT 58.530 45.000 0.00 0.00 0.00 2.66
54 55 2.577449 AAAGCACCAACCGAACAAAG 57.423 45.000 0.00 0.00 0.00 2.77
55 56 3.886505 AGATAAAGCACCAACCGAACAAA 59.113 39.130 0.00 0.00 0.00 2.83
56 57 3.482436 AGATAAAGCACCAACCGAACAA 58.518 40.909 0.00 0.00 0.00 2.83
57 58 3.134574 AGATAAAGCACCAACCGAACA 57.865 42.857 0.00 0.00 0.00 3.18
58 59 6.913873 TTATAGATAAAGCACCAACCGAAC 57.086 37.500 0.00 0.00 0.00 3.95
59 60 7.548196 CTTTATAGATAAAGCACCAACCGAA 57.452 36.000 8.66 0.00 41.69 4.30
70 71 9.402736 GGCTTTCGCTCCGCTTTATAGATAAAG 62.403 44.444 14.96 14.96 42.50 1.85
71 72 5.176958 GCTTTCGCTCCGCTTTATAGATAAA 59.823 40.000 0.00 0.00 0.00 1.40
72 73 4.684703 GCTTTCGCTCCGCTTTATAGATAA 59.315 41.667 0.00 0.00 0.00 1.75
73 74 4.235360 GCTTTCGCTCCGCTTTATAGATA 58.765 43.478 0.00 0.00 0.00 1.98
74 75 3.060602 GCTTTCGCTCCGCTTTATAGAT 58.939 45.455 0.00 0.00 0.00 1.98
75 76 2.470821 GCTTTCGCTCCGCTTTATAGA 58.529 47.619 0.00 0.00 0.00 1.98
76 77 1.527311 GGCTTTCGCTCCGCTTTATAG 59.473 52.381 0.00 0.00 36.09 1.31
77 78 1.138266 AGGCTTTCGCTCCGCTTTATA 59.862 47.619 0.00 0.00 36.09 0.98
78 79 0.107654 AGGCTTTCGCTCCGCTTTAT 60.108 50.000 0.00 0.00 36.09 1.40
79 80 1.019278 CAGGCTTTCGCTCCGCTTTA 61.019 55.000 0.00 0.00 36.09 1.85
80 81 2.032681 AGGCTTTCGCTCCGCTTT 59.967 55.556 0.00 0.00 36.09 3.51
81 82 2.743928 CAGGCTTTCGCTCCGCTT 60.744 61.111 0.00 0.00 36.09 4.68
82 83 3.537206 AACAGGCTTTCGCTCCGCT 62.537 57.895 0.00 0.00 36.09 5.52
83 84 2.514505 GAAACAGGCTTTCGCTCCGC 62.515 60.000 0.00 0.00 36.09 5.54
84 85 1.497722 GAAACAGGCTTTCGCTCCG 59.502 57.895 0.00 0.00 36.09 4.63
85 86 1.497722 CGAAACAGGCTTTCGCTCC 59.502 57.895 8.25 0.00 43.52 4.70
103 104 5.864474 TGCGATCTACTTTCTGAGTTTTCTC 59.136 40.000 0.00 0.00 46.33 2.87
104 105 5.784177 TGCGATCTACTTTCTGAGTTTTCT 58.216 37.500 0.00 0.00 39.86 2.52
105 106 6.091441 ACATGCGATCTACTTTCTGAGTTTTC 59.909 38.462 0.00 0.00 39.86 2.29
106 107 5.934625 ACATGCGATCTACTTTCTGAGTTTT 59.065 36.000 0.00 0.00 39.86 2.43
107 108 5.482908 ACATGCGATCTACTTTCTGAGTTT 58.517 37.500 0.00 0.00 39.86 2.66
278 282 0.730494 GCTGCGATTGCTGTTGGAAC 60.730 55.000 12.86 0.00 43.34 3.62
286 300 0.454600 CTCCAATTGCTGCGATTGCT 59.545 50.000 29.12 2.18 43.34 3.91
287 301 0.526954 CCTCCAATTGCTGCGATTGC 60.527 55.000 29.12 0.00 43.20 3.56
288 302 0.526954 GCCTCCAATTGCTGCGATTG 60.527 55.000 28.05 28.05 35.60 2.67
289 303 1.811860 GCCTCCAATTGCTGCGATT 59.188 52.632 9.32 9.32 0.00 3.34
290 304 3.518003 GCCTCCAATTGCTGCGAT 58.482 55.556 0.00 0.00 0.00 4.58
293 307 4.842091 CGCGCCTCCAATTGCTGC 62.842 66.667 0.00 1.01 0.00 5.25
294 308 4.842091 GCGCGCCTCCAATTGCTG 62.842 66.667 23.24 0.00 0.00 4.41
335 349 3.321968 ACATAATCTAGCTCGACATGCCA 59.678 43.478 10.11 0.00 0.00 4.92
363 377 5.334569 GGAGAAGAGAGTCGAATCGAATAGG 60.335 48.000 7.01 0.00 37.72 2.57
367 381 2.683867 GGGAGAAGAGAGTCGAATCGAA 59.316 50.000 7.01 0.00 37.72 3.71
368 382 2.092861 AGGGAGAAGAGAGTCGAATCGA 60.093 50.000 7.29 0.00 0.00 3.59
369 383 2.289547 GAGGGAGAAGAGAGTCGAATCG 59.710 54.545 7.29 0.00 0.00 3.34
370 384 2.289547 CGAGGGAGAAGAGAGTCGAATC 59.710 54.545 4.34 4.34 0.00 2.52
371 385 2.092861 TCGAGGGAGAAGAGAGTCGAAT 60.093 50.000 0.00 0.00 33.77 3.34
387 401 1.000506 TCCCGTTGACTTTTCTCGAGG 59.999 52.381 13.56 0.00 0.00 4.63
426 3051 5.621272 CTGCAAGAAAAACCAACGCGGTA 62.621 47.826 12.47 0.00 43.09 4.02
460 4102 1.610363 TGTTTCGCTGTATTTGGGCA 58.390 45.000 0.00 0.00 0.00 5.36
505 4147 0.318441 TCGAGAGTTTGGACAGCAGG 59.682 55.000 0.00 0.00 0.00 4.85
506 4148 1.423395 GTCGAGAGTTTGGACAGCAG 58.577 55.000 0.00 0.00 0.00 4.24
507 4149 0.318699 CGTCGAGAGTTTGGACAGCA 60.319 55.000 0.00 0.00 0.00 4.41
557 5145 3.667960 GCTCGTGCAATCACCTAAAACAG 60.668 47.826 4.26 0.00 40.04 3.16
572 5160 7.925703 TTAACTTATGTAATCTAGCTCGTGC 57.074 36.000 0.07 0.07 40.05 5.34
661 5255 1.801242 TCATCCCAGGCGAATTCCTA 58.199 50.000 0.00 0.00 33.95 2.94
683 5277 2.595124 TCTGTCTGTTGCTTTCACGA 57.405 45.000 0.00 0.00 0.00 4.35
755 5358 2.936993 GCTGCTAAGCTACTCAAAGCCA 60.937 50.000 0.00 0.00 46.60 4.75
915 5525 3.741476 GCAGCTCGGCCAACCAAG 61.741 66.667 2.24 0.00 34.57 3.61
982 5592 6.767423 TGTATCATGTGGAACGATGAATGAAT 59.233 34.615 0.00 0.00 42.39 2.57
1372 5986 1.597663 GATGGTGCTGCCGTTATACAC 59.402 52.381 0.00 0.00 41.21 2.90
1373 5987 1.804746 CGATGGTGCTGCCGTTATACA 60.805 52.381 0.00 0.00 41.21 2.29
1377 5991 2.817834 GCGATGGTGCTGCCGTTA 60.818 61.111 0.00 0.00 41.21 3.18
1588 6205 3.757745 AATATTCAAAACGCCGGACTG 57.242 42.857 5.05 0.00 0.00 3.51
1591 6208 4.936411 TCACTAAATATTCAAAACGCCGGA 59.064 37.500 5.05 0.00 0.00 5.14
1617 6234 1.826385 ATTCGAACCCAGCTTTGGAG 58.174 50.000 0.00 0.00 0.00 3.86
1618 6235 3.244770 ACTTATTCGAACCCAGCTTTGGA 60.245 43.478 0.00 0.00 0.00 3.53
1619 6236 3.081804 ACTTATTCGAACCCAGCTTTGG 58.918 45.455 0.00 0.00 0.00 3.28
1620 6237 3.670627 GCACTTATTCGAACCCAGCTTTG 60.671 47.826 0.00 0.00 0.00 2.77
1654 6278 2.996621 GGGAATCACGAAGACACAGAAG 59.003 50.000 0.00 0.00 0.00 2.85
1772 6398 0.376502 GTCGTCGCTAGGTGGTCTAC 59.623 60.000 0.00 0.00 0.00 2.59
1915 6541 2.186826 GCGGTTGCTGTTCTGGTGT 61.187 57.895 0.00 0.00 38.39 4.16
1936 6562 8.451908 TTCTGATCTACGTCATTCTTCATCTA 57.548 34.615 0.00 0.00 0.00 1.98
1962 6588 2.338500 GTGTGTCTTCGAGTTGGATCC 58.662 52.381 4.20 4.20 0.00 3.36
1971 6597 1.866601 TCTACGTTCGTGTGTCTTCGA 59.133 47.619 8.14 0.00 0.00 3.71
1981 6607 1.003972 TCGTTGTTCGTCTACGTTCGT 60.004 47.619 0.00 2.91 43.41 3.85
2093 6719 3.596940 ATAAAGGTCTCCTCGCCTAGA 57.403 47.619 0.00 0.00 34.15 2.43
2101 6727 5.131809 CCTGAAGATGGAATAAAGGTCTCCT 59.868 44.000 0.00 0.00 33.87 3.69
2181 6807 3.702548 AGGGCTCCGTTTTTAGTTGTTTT 59.297 39.130 0.00 0.00 0.00 2.43
2280 6907 2.747855 GTTTCTGCCTCCTGCCGG 60.748 66.667 0.00 0.00 40.16 6.13
2285 6912 0.252927 AGCTAGGGTTTCTGCCTCCT 60.253 55.000 0.00 0.00 0.00 3.69
2311 6938 2.768253 ATGAACTTGAGCATCGTGGA 57.232 45.000 0.00 0.00 38.61 4.02
2312 6939 3.058016 ACAAATGAACTTGAGCATCGTGG 60.058 43.478 0.00 0.00 38.61 4.94
2313 6940 4.151258 ACAAATGAACTTGAGCATCGTG 57.849 40.909 0.00 0.00 38.61 4.35
2314 6941 4.836125 AACAAATGAACTTGAGCATCGT 57.164 36.364 0.00 0.00 38.61 3.73
2315 6942 4.319115 CGAAACAAATGAACTTGAGCATCG 59.681 41.667 0.00 0.00 38.61 3.84
2316 6943 5.451908 TCGAAACAAATGAACTTGAGCATC 58.548 37.500 0.00 0.00 0.00 3.91
2317 6944 5.437289 TCGAAACAAATGAACTTGAGCAT 57.563 34.783 0.00 0.00 0.00 3.79
2318 6945 4.891627 TCGAAACAAATGAACTTGAGCA 57.108 36.364 0.00 0.00 0.00 4.26
2319 6946 6.575132 CAATTCGAAACAAATGAACTTGAGC 58.425 36.000 0.00 0.00 0.00 4.26
2320 6947 6.346040 GGCAATTCGAAACAAATGAACTTGAG 60.346 38.462 0.00 0.00 0.00 3.02
2321 6948 5.461737 GGCAATTCGAAACAAATGAACTTGA 59.538 36.000 0.00 0.00 0.00 3.02
2322 6949 5.463061 AGGCAATTCGAAACAAATGAACTTG 59.537 36.000 0.00 0.00 0.00 3.16
2323 6950 5.600696 AGGCAATTCGAAACAAATGAACTT 58.399 33.333 0.00 0.00 0.00 2.66
2324 6951 5.200368 AGGCAATTCGAAACAAATGAACT 57.800 34.783 0.00 0.00 0.00 3.01
2325 6952 5.905480 AAGGCAATTCGAAACAAATGAAC 57.095 34.783 0.00 0.00 0.00 3.18
2326 6953 6.917217 AAAAGGCAATTCGAAACAAATGAA 57.083 29.167 0.00 0.00 0.00 2.57
2327 6954 6.917217 AAAAAGGCAATTCGAAACAAATGA 57.083 29.167 0.00 0.00 0.00 2.57
2328 6955 9.316859 GAATAAAAAGGCAATTCGAAACAAATG 57.683 29.630 0.00 0.00 0.00 2.32
2412 7039 7.272244 TCTTGGTCGATTTAATGAGAGCATTA 58.728 34.615 10.90 0.00 42.73 1.90
2413 7040 6.115446 TCTTGGTCGATTTAATGAGAGCATT 58.885 36.000 10.90 0.00 46.11 3.56
2414 7041 5.674525 TCTTGGTCGATTTAATGAGAGCAT 58.325 37.500 10.90 0.00 40.19 3.79
2415 7042 5.084818 TCTTGGTCGATTTAATGAGAGCA 57.915 39.130 7.48 7.48 39.02 4.26
2416 7043 5.503194 GCTTCTTGGTCGATTTAATGAGAGC 60.503 44.000 0.00 3.39 0.00 4.09
2417 7044 5.582269 TGCTTCTTGGTCGATTTAATGAGAG 59.418 40.000 0.00 0.00 0.00 3.20
2418 7045 5.487433 TGCTTCTTGGTCGATTTAATGAGA 58.513 37.500 0.00 0.00 0.00 3.27
2419 7046 5.728898 GCTGCTTCTTGGTCGATTTAATGAG 60.729 44.000 0.00 0.00 0.00 2.90
2420 7047 4.094887 GCTGCTTCTTGGTCGATTTAATGA 59.905 41.667 0.00 0.00 0.00 2.57
2421 7048 4.095483 AGCTGCTTCTTGGTCGATTTAATG 59.905 41.667 0.00 0.00 0.00 1.90
2422 7049 4.265073 AGCTGCTTCTTGGTCGATTTAAT 58.735 39.130 0.00 0.00 0.00 1.40
2423 7050 3.674997 AGCTGCTTCTTGGTCGATTTAA 58.325 40.909 0.00 0.00 0.00 1.52
2424 7051 3.334583 AGCTGCTTCTTGGTCGATTTA 57.665 42.857 0.00 0.00 0.00 1.40
2425 7052 2.191128 AGCTGCTTCTTGGTCGATTT 57.809 45.000 0.00 0.00 0.00 2.17
2426 7053 3.334583 TTAGCTGCTTCTTGGTCGATT 57.665 42.857 7.79 0.00 0.00 3.34
2427 7054 3.550437 ATTAGCTGCTTCTTGGTCGAT 57.450 42.857 7.79 0.00 0.00 3.59
2428 7055 3.055819 AGAATTAGCTGCTTCTTGGTCGA 60.056 43.478 7.79 0.00 0.00 4.20
2429 7056 3.063180 CAGAATTAGCTGCTTCTTGGTCG 59.937 47.826 7.79 0.00 29.34 4.79
2430 7057 4.256920 TCAGAATTAGCTGCTTCTTGGTC 58.743 43.478 7.79 0.00 35.86 4.02
2431 7058 4.260170 CTCAGAATTAGCTGCTTCTTGGT 58.740 43.478 7.79 0.00 35.86 3.67
2432 7059 3.065095 GCTCAGAATTAGCTGCTTCTTGG 59.935 47.826 7.79 1.44 37.01 3.61
2433 7060 3.065095 GGCTCAGAATTAGCTGCTTCTTG 59.935 47.826 7.79 1.76 39.97 3.02
2434 7061 3.277715 GGCTCAGAATTAGCTGCTTCTT 58.722 45.455 7.79 1.32 39.97 2.52
2435 7062 2.741228 CGGCTCAGAATTAGCTGCTTCT 60.741 50.000 7.79 1.29 39.36 2.85
2436 7063 1.596727 CGGCTCAGAATTAGCTGCTTC 59.403 52.381 7.79 0.00 39.36 3.86
2437 7064 1.208052 TCGGCTCAGAATTAGCTGCTT 59.792 47.619 7.79 0.00 44.46 3.91
2438 7065 0.826715 TCGGCTCAGAATTAGCTGCT 59.173 50.000 7.57 7.57 44.46 4.24
2439 7066 0.933796 GTCGGCTCAGAATTAGCTGC 59.066 55.000 0.00 0.00 44.46 5.25
2440 7067 1.134699 TGGTCGGCTCAGAATTAGCTG 60.135 52.381 0.00 1.66 45.87 4.24
2441 7068 1.195115 TGGTCGGCTCAGAATTAGCT 58.805 50.000 0.00 0.00 39.97 3.32
2442 7069 2.024176 TTGGTCGGCTCAGAATTAGC 57.976 50.000 0.00 0.00 39.33 3.09
2511 7138 8.649841 GTGTATGCGTCTGTACTGTATTAAAAA 58.350 33.333 0.00 0.00 0.00 1.94
2512 7139 8.030692 AGTGTATGCGTCTGTACTGTATTAAAA 58.969 33.333 0.00 0.00 0.00 1.52
2513 7140 7.541162 AGTGTATGCGTCTGTACTGTATTAAA 58.459 34.615 0.00 0.00 0.00 1.52
2514 7141 7.092137 AGTGTATGCGTCTGTACTGTATTAA 57.908 36.000 0.00 0.00 0.00 1.40
2515 7142 6.238566 GGAGTGTATGCGTCTGTACTGTATTA 60.239 42.308 0.00 0.00 0.00 0.98
2516 7143 5.450137 GGAGTGTATGCGTCTGTACTGTATT 60.450 44.000 0.00 0.00 0.00 1.89
2517 7144 4.036498 GGAGTGTATGCGTCTGTACTGTAT 59.964 45.833 0.00 0.00 0.00 2.29
2518 7145 3.376234 GGAGTGTATGCGTCTGTACTGTA 59.624 47.826 0.00 0.00 0.00 2.74
2519 7146 2.163815 GGAGTGTATGCGTCTGTACTGT 59.836 50.000 0.00 0.00 0.00 3.55
2520 7147 2.479730 GGGAGTGTATGCGTCTGTACTG 60.480 54.545 0.00 0.00 0.00 2.74
2521 7148 1.749634 GGGAGTGTATGCGTCTGTACT 59.250 52.381 0.00 0.00 0.00 2.73
2522 7149 1.202382 GGGGAGTGTATGCGTCTGTAC 60.202 57.143 0.00 0.00 0.00 2.90
2523 7150 1.108776 GGGGAGTGTATGCGTCTGTA 58.891 55.000 0.00 0.00 0.00 2.74
2524 7151 1.614241 GGGGGAGTGTATGCGTCTGT 61.614 60.000 0.00 0.00 0.00 3.41
2525 7152 1.144057 GGGGGAGTGTATGCGTCTG 59.856 63.158 0.00 0.00 0.00 3.51
2526 7153 3.630289 GGGGGAGTGTATGCGTCT 58.370 61.111 0.00 0.00 0.00 4.18
2540 7167 0.532862 GTGTGTGCGATCATAGGGGG 60.533 60.000 0.00 0.00 0.00 5.40
2541 7168 0.875908 CGTGTGTGCGATCATAGGGG 60.876 60.000 0.00 0.00 0.00 4.79
2542 7169 1.490693 GCGTGTGTGCGATCATAGGG 61.491 60.000 0.00 0.00 0.00 3.53
2543 7170 0.805711 TGCGTGTGTGCGATCATAGG 60.806 55.000 0.00 0.00 37.81 2.57
2544 7171 0.298707 GTGCGTGTGTGCGATCATAG 59.701 55.000 0.00 0.00 37.81 2.23
2545 7172 0.389166 TGTGCGTGTGTGCGATCATA 60.389 50.000 0.00 0.00 37.81 2.15
2546 7173 1.667510 TGTGCGTGTGTGCGATCAT 60.668 52.632 0.00 0.00 37.81 2.45
2547 7174 2.279784 TGTGCGTGTGTGCGATCA 60.280 55.556 0.00 0.00 37.81 2.92
2548 7175 2.170985 GTGTGCGTGTGTGCGATC 59.829 61.111 0.00 0.00 37.81 3.69
2549 7176 3.345808 GGTGTGCGTGTGTGCGAT 61.346 61.111 0.00 0.00 37.81 4.58
2552 7179 2.280524 TAGGGTGTGCGTGTGTGC 60.281 61.111 0.00 0.00 0.00 4.57
2553 7180 1.959226 GGTAGGGTGTGCGTGTGTG 60.959 63.158 0.00 0.00 0.00 3.82
2554 7181 2.424302 GGTAGGGTGTGCGTGTGT 59.576 61.111 0.00 0.00 0.00 3.72
2555 7182 2.358247 GGGTAGGGTGTGCGTGTG 60.358 66.667 0.00 0.00 0.00 3.82
2556 7183 2.735151 TAGGGGTAGGGTGTGCGTGT 62.735 60.000 0.00 0.00 0.00 4.49
2557 7184 1.335132 ATAGGGGTAGGGTGTGCGTG 61.335 60.000 0.00 0.00 0.00 5.34
2558 7185 1.002533 ATAGGGGTAGGGTGTGCGT 59.997 57.895 0.00 0.00 0.00 5.24
2559 7186 1.046472 TCATAGGGGTAGGGTGTGCG 61.046 60.000 0.00 0.00 0.00 5.34
2560 7187 0.759346 CTCATAGGGGTAGGGTGTGC 59.241 60.000 0.00 0.00 0.00 4.57
2561 7188 0.759346 GCTCATAGGGGTAGGGTGTG 59.241 60.000 0.00 0.00 0.00 3.82
2562 7189 0.341961 TGCTCATAGGGGTAGGGTGT 59.658 55.000 0.00 0.00 0.00 4.16
2563 7190 0.759346 GTGCTCATAGGGGTAGGGTG 59.241 60.000 0.00 0.00 0.00 4.61
2564 7191 0.400093 GGTGCTCATAGGGGTAGGGT 60.400 60.000 0.00 0.00 0.00 4.34
2565 7192 0.104934 AGGTGCTCATAGGGGTAGGG 60.105 60.000 0.00 0.00 0.00 3.53
2566 7193 1.807814 AAGGTGCTCATAGGGGTAGG 58.192 55.000 0.00 0.00 0.00 3.18
2567 7194 2.771943 TCAAAGGTGCTCATAGGGGTAG 59.228 50.000 0.00 0.00 0.00 3.18
2568 7195 2.840511 TCAAAGGTGCTCATAGGGGTA 58.159 47.619 0.00 0.00 0.00 3.69
2569 7196 1.668826 TCAAAGGTGCTCATAGGGGT 58.331 50.000 0.00 0.00 0.00 4.95
2570 7197 2.806945 TTCAAAGGTGCTCATAGGGG 57.193 50.000 0.00 0.00 0.00 4.79
2571 7198 3.691609 GTCTTTCAAAGGTGCTCATAGGG 59.308 47.826 0.00 0.00 0.00 3.53
2572 7199 3.691609 GGTCTTTCAAAGGTGCTCATAGG 59.308 47.826 0.00 0.00 0.00 2.57
2573 7200 3.372206 CGGTCTTTCAAAGGTGCTCATAG 59.628 47.826 0.00 0.00 0.00 2.23
2574 7201 3.007506 TCGGTCTTTCAAAGGTGCTCATA 59.992 43.478 0.00 0.00 0.00 2.15
2575 7202 2.154462 CGGTCTTTCAAAGGTGCTCAT 58.846 47.619 0.00 0.00 0.00 2.90
2576 7203 1.140052 TCGGTCTTTCAAAGGTGCTCA 59.860 47.619 0.00 0.00 0.00 4.26
2577 7204 1.801178 CTCGGTCTTTCAAAGGTGCTC 59.199 52.381 0.00 0.00 0.00 4.26
2578 7205 1.884235 CTCGGTCTTTCAAAGGTGCT 58.116 50.000 0.00 0.00 0.00 4.40
2579 7206 0.238553 GCTCGGTCTTTCAAAGGTGC 59.761 55.000 0.00 0.00 0.00 5.01
2580 7207 0.875059 GGCTCGGTCTTTCAAAGGTG 59.125 55.000 0.00 0.00 0.00 4.00
2581 7208 0.602905 CGGCTCGGTCTTTCAAAGGT 60.603 55.000 0.00 0.00 0.00 3.50
2582 7209 1.298859 CCGGCTCGGTCTTTCAAAGG 61.299 60.000 0.00 0.00 42.73 3.11
2583 7210 2.162716 CCGGCTCGGTCTTTCAAAG 58.837 57.895 5.56 0.00 42.73 2.77
2584 7211 4.371975 CCGGCTCGGTCTTTCAAA 57.628 55.556 5.56 0.00 42.73 2.69


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

AutoCloner maintained by Alex Coulton.