Multiple sequence alignment - TraesCS2D01G103300

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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 TraesCS2D01G103300 chr2D 100.000 9487 0 0 1 9487 55761271 55751785 0.000000e+00 17520.0
1 TraesCS2D01G103300 chr2D 95.601 2728 76 14 2953 5672 39400451 39403142 0.000000e+00 4333.0
2 TraesCS2D01G103300 chr2D 93.526 587 11 7 5679 6260 39403181 39403745 0.000000e+00 848.0
3 TraesCS2D01G103300 chr2D 87.975 158 16 3 2323 2480 243656161 243656315 5.850000e-42 183.0
4 TraesCS2D01G103300 chr2B 93.666 3631 146 24 107 3722 88432242 88428681 0.000000e+00 5354.0
5 TraesCS2D01G103300 chr2B 97.217 2767 71 4 6126 8890 88426412 88423650 0.000000e+00 4678.0
6 TraesCS2D01G103300 chr2B 96.634 1842 50 9 3751 5588 88428684 88426851 0.000000e+00 3048.0
7 TraesCS2D01G103300 chr2B 87.097 558 37 14 8946 9487 88423653 88423115 4.900000e-167 599.0
8 TraesCS2D01G103300 chr2B 90.465 409 12 7 5620 6004 88426850 88426445 1.830000e-141 514.0
9 TraesCS2D01G103300 chr2B 100.000 28 0 0 8684 8711 88190987 88190960 1.700000e-02 52.8
10 TraesCS2D01G103300 chr2A 97.846 2785 53 4 6126 8905 57166872 57164090 0.000000e+00 4804.0
11 TraesCS2D01G103300 chr2A 95.408 2657 76 24 3024 5672 57170055 57167437 0.000000e+00 4189.0
12 TraesCS2D01G103300 chr2A 93.447 2472 98 26 562 3026 57172774 57170360 0.000000e+00 3609.0
13 TraesCS2D01G103300 chr2A 95.796 452 10 2 5679 6125 57167398 57166951 0.000000e+00 721.0
14 TraesCS2D01G103300 chr2A 89.279 569 39 10 8901 9449 57163977 57163411 0.000000e+00 693.0
15 TraesCS2D01G103300 chr2A 87.611 452 41 8 107 544 57173456 57173006 2.360000e-140 510.0
16 TraesCS2D01G103300 chr1D 92.414 145 10 1 2338 2481 260320839 260320983 1.250000e-48 206.0
17 TraesCS2D01G103300 chr1D 92.361 144 11 0 2338 2481 268963358 268963501 1.250000e-48 206.0
18 TraesCS2D01G103300 chr1D 91.489 47 4 0 2 48 391885600 391885646 2.210000e-06 65.8
19 TraesCS2D01G103300 chr1D 91.304 46 4 0 2 47 340515259 340515304 7.950000e-06 63.9
20 TraesCS2D01G103300 chr1D 91.304 46 4 0 2 47 442451596 442451551 7.950000e-06 63.9
21 TraesCS2D01G103300 chr4A 93.333 135 9 0 2338 2472 240371264 240371398 5.810000e-47 200.0
22 TraesCS2D01G103300 chr6D 90.972 144 12 1 2338 2481 210769663 210769521 9.720000e-45 193.0
23 TraesCS2D01G103300 chr3A 90.780 141 11 2 2339 2478 566903566 566903705 4.520000e-43 187.0
24 TraesCS2D01G103300 chr6A 90.210 143 13 1 2338 2480 381088844 381088703 1.630000e-42 185.0
25 TraesCS2D01G103300 chr1B 100.000 59 0 0 48 106 95336732 95336674 1.010000e-19 110.0
26 TraesCS2D01G103300 chr1B 100.000 59 0 0 48 106 95482678 95482736 1.010000e-19 110.0
27 TraesCS2D01G103300 chr1B 95.385 65 2 1 48 111 614281285 614281221 1.690000e-17 102.0
28 TraesCS2D01G103300 chr1B 93.617 47 1 2 5183 5228 229263445 229263490 1.710000e-07 69.4
29 TraesCS2D01G103300 chr1B 93.478 46 3 0 2 47 252628780 252628735 1.710000e-07 69.4
30 TraesCS2D01G103300 chr6B 98.361 61 0 1 48 107 48534051 48533991 1.300000e-18 106.0
31 TraesCS2D01G103300 chr6B 95.385 65 2 1 48 111 705918208 705918272 1.690000e-17 102.0
32 TraesCS2D01G103300 chr6B 93.478 46 3 0 2 47 277015649 277015604 1.710000e-07 69.4
33 TraesCS2D01G103300 chr7B 96.825 63 1 1 48 109 69751790 69751852 4.690000e-18 104.0
34 TraesCS2D01G103300 chr7B 96.774 62 1 1 48 109 28070180 28070240 1.690000e-17 102.0
35 TraesCS2D01G103300 chr3D 95.312 64 3 0 48 111 115638189 115638126 1.690000e-17 102.0
36 TraesCS2D01G103300 chr3D 89.474 76 7 1 32 107 112348660 112348586 2.820000e-15 95.3
37 TraesCS2D01G103300 chr7D 93.617 47 3 0 2 48 304405464 304405510 4.750000e-08 71.3
38 TraesCS2D01G103300 chr7D 93.478 46 3 0 2 47 470184575 470184620 1.710000e-07 69.4
39 TraesCS2D01G103300 chr3B 93.478 46 3 0 2 47 666159852 666159897 1.710000e-07 69.4
40 TraesCS2D01G103300 chr1A 91.489 47 4 0 2 48 165199289 165199243 2.210000e-06 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G103300 chr2D 55751785 55761271 9486 True 17520.0 17520 100.000000 1 9487 1 chr2D.!!$R1 9486
1 TraesCS2D01G103300 chr2D 39400451 39403745 3294 False 2590.5 4333 94.563500 2953 6260 2 chr2D.!!$F2 3307
2 TraesCS2D01G103300 chr2B 88423115 88432242 9127 True 2838.6 5354 93.015800 107 9487 5 chr2B.!!$R2 9380
3 TraesCS2D01G103300 chr2A 57163411 57173456 10045 True 2421.0 4804 93.231167 107 9449 6 chr2A.!!$R1 9342

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
30 31 0.034283 GGGCAAACGGGTAATGGGTA 60.034 55.000 0.00 0.00 0.00 3.69 F
931 1174 0.035036 ACTCACGAGTCACGAGGAGA 59.965 55.000 17.33 2.57 43.50 3.71 F
1908 2152 0.111704 CGTGAACAGTTGCGTCGAAG 60.112 55.000 0.00 0.00 0.00 3.79 F
1956 2200 1.667724 GCATATCATGGCCGCTGATAC 59.332 52.381 23.08 12.41 38.16 2.24 F
1966 2210 1.789464 GCCGCTGATACGAAGATTCAG 59.211 52.381 0.00 0.00 40.81 3.02 F
3161 3716 1.895131 AGGTGTGGCATGGTTTTCATC 59.105 47.619 0.00 0.00 32.92 2.92 F
4221 4785 2.747446 GTGGCCTGGTTATGTTGTACTG 59.253 50.000 3.32 0.00 0.00 2.74 F
5184 5753 3.127895 TGCTACGTTGTTGAAGCTTTTGT 59.872 39.130 0.00 0.00 35.95 2.83 F
5589 6159 1.463674 ATGAAATTGGTGGCGGAGTC 58.536 50.000 0.00 0.00 0.00 3.36 F
7029 7721 1.696988 CCGTTGCATTGCAGGTTTAC 58.303 50.000 11.76 5.92 40.61 2.01 F
8090 8784 1.003718 GTTGGAAGACCCTGGACCG 60.004 63.158 0.00 0.00 35.38 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1908 2152 0.240945 CAAAGCCATGACGGTGTTCC 59.759 55.000 0.00 0.00 36.97 3.62 R
2419 2666 0.466124 GGGGTAGGCTAGAGTTGCAG 59.534 60.000 0.00 0.00 0.00 4.41 R
3588 4143 0.892755 CAGCATTGGCCACATTCACT 59.107 50.000 3.88 0.00 42.56 3.41 R
3928 4486 7.101054 ACAAAACATGATCAAATTGCTAGCAT 58.899 30.769 20.13 1.20 0.00 3.79 R
4085 4646 3.009805 GGGGAGGGTTAAAAGCTAAGACA 59.990 47.826 0.00 0.00 0.00 3.41 R
5245 5814 0.528017 TGCTCACAAGAGTAGCCTCG 59.472 55.000 0.00 0.00 44.00 4.63 R
5247 5816 1.001406 GTGTGCTCACAAGAGTAGCCT 59.999 52.381 13.83 0.00 43.77 4.58 R
6883 7575 0.181350 GCTGGAAATCCTCCCGTGAT 59.819 55.000 0.44 0.00 44.69 3.06 R
7127 7819 1.304381 GCTGGGCCATTCAGTTCCA 60.304 57.895 6.72 0.00 34.89 3.53 R
8369 9063 1.611673 CCCACGGCAATCTTCTTCAGT 60.612 52.381 0.00 0.00 0.00 3.41 R
9262 10093 0.181350 CCTCGGGAAGGCTAGCAAAT 59.819 55.000 18.24 0.85 38.67 2.32 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 2.670251 CGCAGGGCAAACGGGTAA 60.670 61.111 0.00 0.00 0.00 2.85
25 26 2.043980 CGCAGGGCAAACGGGTAAT 61.044 57.895 0.00 0.00 0.00 1.89
26 27 1.510844 GCAGGGCAAACGGGTAATG 59.489 57.895 0.00 0.00 0.00 1.90
27 28 1.944234 GCAGGGCAAACGGGTAATGG 61.944 60.000 0.00 0.00 0.00 3.16
28 29 1.000145 AGGGCAAACGGGTAATGGG 60.000 57.895 0.00 0.00 0.00 4.00
29 30 1.304630 GGGCAAACGGGTAATGGGT 60.305 57.895 0.00 0.00 0.00 4.51
30 31 0.034283 GGGCAAACGGGTAATGGGTA 60.034 55.000 0.00 0.00 0.00 3.69
31 32 1.097232 GGCAAACGGGTAATGGGTAC 58.903 55.000 0.00 0.00 0.00 3.34
47 48 3.127425 GGTACCCATTGCCATCTCTAC 57.873 52.381 0.00 0.00 0.00 2.59
48 49 2.224548 GGTACCCATTGCCATCTCTACC 60.225 54.545 0.00 0.00 0.00 3.18
49 50 0.846693 ACCCATTGCCATCTCTACCC 59.153 55.000 0.00 0.00 0.00 3.69
50 51 0.846015 CCCATTGCCATCTCTACCCA 59.154 55.000 0.00 0.00 0.00 4.51
51 52 1.477558 CCCATTGCCATCTCTACCCAC 60.478 57.143 0.00 0.00 0.00 4.61
52 53 1.586422 CATTGCCATCTCTACCCACG 58.414 55.000 0.00 0.00 0.00 4.94
53 54 1.138859 CATTGCCATCTCTACCCACGA 59.861 52.381 0.00 0.00 0.00 4.35
54 55 0.824109 TTGCCATCTCTACCCACGAG 59.176 55.000 0.00 0.00 0.00 4.18
55 56 1.043116 TGCCATCTCTACCCACGAGG 61.043 60.000 0.00 0.00 43.78 4.63
56 57 1.742768 CCATCTCTACCCACGAGGC 59.257 63.158 0.00 0.00 40.58 4.70
57 58 0.757188 CCATCTCTACCCACGAGGCT 60.757 60.000 0.00 0.00 40.58 4.58
58 59 0.671251 CATCTCTACCCACGAGGCTC 59.329 60.000 3.87 3.87 40.58 4.70
59 60 0.259065 ATCTCTACCCACGAGGCTCA 59.741 55.000 15.95 0.00 40.58 4.26
60 61 0.039180 TCTCTACCCACGAGGCTCAA 59.961 55.000 15.95 0.00 40.58 3.02
61 62 0.457851 CTCTACCCACGAGGCTCAAG 59.542 60.000 15.95 5.75 40.58 3.02
62 63 1.153549 CTACCCACGAGGCTCAAGC 60.154 63.158 15.95 0.00 40.58 4.01
63 64 1.888436 CTACCCACGAGGCTCAAGCA 61.888 60.000 15.95 0.00 44.36 3.91
64 65 1.476845 TACCCACGAGGCTCAAGCAA 61.477 55.000 15.95 0.00 44.36 3.91
65 66 1.377725 CCCACGAGGCTCAAGCAAT 60.378 57.895 15.95 0.00 44.36 3.56
66 67 0.107703 CCCACGAGGCTCAAGCAATA 60.108 55.000 15.95 0.00 44.36 1.90
67 68 1.009829 CCACGAGGCTCAAGCAATAC 58.990 55.000 15.95 0.00 44.36 1.89
68 69 1.675714 CCACGAGGCTCAAGCAATACA 60.676 52.381 15.95 0.00 44.36 2.29
69 70 2.076100 CACGAGGCTCAAGCAATACAA 58.924 47.619 15.95 0.00 44.36 2.41
70 71 2.076863 ACGAGGCTCAAGCAATACAAC 58.923 47.619 15.95 0.00 44.36 3.32
71 72 2.076100 CGAGGCTCAAGCAATACAACA 58.924 47.619 15.95 0.00 44.36 3.33
72 73 2.483877 CGAGGCTCAAGCAATACAACAA 59.516 45.455 15.95 0.00 44.36 2.83
73 74 3.667960 CGAGGCTCAAGCAATACAACAAC 60.668 47.826 15.95 0.00 44.36 3.32
74 75 3.490348 AGGCTCAAGCAATACAACAACT 58.510 40.909 4.13 0.00 44.36 3.16
75 76 4.651778 AGGCTCAAGCAATACAACAACTA 58.348 39.130 4.13 0.00 44.36 2.24
76 77 5.256474 AGGCTCAAGCAATACAACAACTAT 58.744 37.500 4.13 0.00 44.36 2.12
77 78 5.711976 AGGCTCAAGCAATACAACAACTATT 59.288 36.000 4.13 0.00 44.36 1.73
78 79 6.030228 GGCTCAAGCAATACAACAACTATTC 58.970 40.000 4.13 0.00 44.36 1.75
79 80 6.030228 GCTCAAGCAATACAACAACTATTCC 58.970 40.000 0.00 0.00 41.59 3.01
80 81 6.349280 GCTCAAGCAATACAACAACTATTCCA 60.349 38.462 0.00 0.00 41.59 3.53
81 82 7.629222 GCTCAAGCAATACAACAACTATTCCAT 60.629 37.037 0.00 0.00 41.59 3.41
82 83 7.761409 TCAAGCAATACAACAACTATTCCATC 58.239 34.615 0.00 0.00 0.00 3.51
83 84 7.392953 TCAAGCAATACAACAACTATTCCATCA 59.607 33.333 0.00 0.00 0.00 3.07
84 85 7.701539 AGCAATACAACAACTATTCCATCAA 57.298 32.000 0.00 0.00 0.00 2.57
85 86 8.121305 AGCAATACAACAACTATTCCATCAAA 57.879 30.769 0.00 0.00 0.00 2.69
86 87 8.752187 AGCAATACAACAACTATTCCATCAAAT 58.248 29.630 0.00 0.00 0.00 2.32
87 88 9.023967 GCAATACAACAACTATTCCATCAAATC 57.976 33.333 0.00 0.00 0.00 2.17
88 89 9.520204 CAATACAACAACTATTCCATCAAATCC 57.480 33.333 0.00 0.00 0.00 3.01
89 90 6.530019 ACAACAACTATTCCATCAAATCCC 57.470 37.500 0.00 0.00 0.00 3.85
90 91 6.256053 ACAACAACTATTCCATCAAATCCCT 58.744 36.000 0.00 0.00 0.00 4.20
91 92 6.378280 ACAACAACTATTCCATCAAATCCCTC 59.622 38.462 0.00 0.00 0.00 4.30
92 93 6.332976 ACAACTATTCCATCAAATCCCTCT 57.667 37.500 0.00 0.00 0.00 3.69
93 94 6.360618 ACAACTATTCCATCAAATCCCTCTC 58.639 40.000 0.00 0.00 0.00 3.20
94 95 6.159398 ACAACTATTCCATCAAATCCCTCTCT 59.841 38.462 0.00 0.00 0.00 3.10
95 96 6.432403 ACTATTCCATCAAATCCCTCTCTC 57.568 41.667 0.00 0.00 0.00 3.20
96 97 4.720775 ATTCCATCAAATCCCTCTCTCC 57.279 45.455 0.00 0.00 0.00 3.71
97 98 2.412591 TCCATCAAATCCCTCTCTCCC 58.587 52.381 0.00 0.00 0.00 4.30
98 99 2.021639 TCCATCAAATCCCTCTCTCCCT 60.022 50.000 0.00 0.00 0.00 4.20
99 100 2.782341 CCATCAAATCCCTCTCTCCCTT 59.218 50.000 0.00 0.00 0.00 3.95
100 101 3.181446 CCATCAAATCCCTCTCTCCCTTC 60.181 52.174 0.00 0.00 0.00 3.46
101 102 2.482494 TCAAATCCCTCTCTCCCTTCC 58.518 52.381 0.00 0.00 0.00 3.46
102 103 2.200081 CAAATCCCTCTCTCCCTTCCA 58.800 52.381 0.00 0.00 0.00 3.53
103 104 2.578021 CAAATCCCTCTCTCCCTTCCAA 59.422 50.000 0.00 0.00 0.00 3.53
104 105 1.886422 ATCCCTCTCTCCCTTCCAAC 58.114 55.000 0.00 0.00 0.00 3.77
105 106 0.491823 TCCCTCTCTCCCTTCCAACA 59.508 55.000 0.00 0.00 0.00 3.33
200 203 3.572682 CCAACATAATGCATGGATGAGCT 59.427 43.478 22.44 0.00 39.13 4.09
251 262 5.164138 GCGTCGCTCAAATGATTCTATCTAC 60.164 44.000 10.68 0.00 0.00 2.59
257 268 7.517417 CGCTCAAATGATTCTATCTACGCTTTT 60.517 37.037 0.00 0.00 0.00 2.27
262 273 6.222038 TGATTCTATCTACGCTTTTGTCCT 57.778 37.500 0.00 0.00 0.00 3.85
303 317 4.651994 CTTGCATCTACATTCCGTGTTTC 58.348 43.478 0.00 0.00 42.29 2.78
344 358 7.576236 TCTTCAACAGAAAAATCGATGAAGTC 58.424 34.615 15.43 5.40 41.68 3.01
377 391 1.414181 ACCCACATGATAGCTCCTTCG 59.586 52.381 0.00 0.00 0.00 3.79
494 516 0.110010 GACGCAAGGAAGAAGCAAGC 60.110 55.000 0.00 0.00 46.39 4.01
544 566 4.433615 CATACACCTGATACAGTCACCAC 58.566 47.826 0.00 0.00 32.22 4.16
545 567 1.623811 ACACCTGATACAGTCACCACC 59.376 52.381 0.00 0.00 32.22 4.61
546 568 1.066143 CACCTGATACAGTCACCACCC 60.066 57.143 0.00 0.00 32.22 4.61
559 581 1.223487 CCACCCCATAACGGTCAGG 59.777 63.158 0.00 0.00 0.00 3.86
560 582 1.451387 CACCCCATAACGGTCAGGC 60.451 63.158 0.00 0.00 0.00 4.85
603 839 3.110139 CCATGCGCGTTTATGCCT 58.890 55.556 8.43 0.00 0.00 4.75
605 841 0.660488 CCATGCGCGTTTATGCCTAA 59.340 50.000 8.43 0.00 0.00 2.69
606 842 1.064803 CCATGCGCGTTTATGCCTAAA 59.935 47.619 8.43 0.00 0.00 1.85
608 844 3.371168 CATGCGCGTTTATGCCTAAATT 58.629 40.909 8.43 0.00 0.00 1.82
610 846 3.839293 TGCGCGTTTATGCCTAAATTTT 58.161 36.364 8.43 0.00 0.00 1.82
611 847 3.854809 TGCGCGTTTATGCCTAAATTTTC 59.145 39.130 8.43 0.00 0.00 2.29
613 849 4.561213 GCGCGTTTATGCCTAAATTTTCTT 59.439 37.500 8.43 0.00 0.00 2.52
617 853 6.472486 GCGTTTATGCCTAAATTTTCTTCTCC 59.528 38.462 0.00 0.00 0.00 3.71
618 854 7.628580 GCGTTTATGCCTAAATTTTCTTCTCCT 60.629 37.037 0.00 0.00 0.00 3.69
684 920 0.887933 ACACAATGGGCAATTCGTCC 59.112 50.000 0.00 0.00 41.21 4.79
717 953 4.183686 CGATTGGCCAGGCGCTTG 62.184 66.667 13.36 13.36 37.74 4.01
718 954 4.503314 GATTGGCCAGGCGCTTGC 62.503 66.667 15.01 10.81 37.74 4.01
739 975 2.769617 CGCACACGTCATTCCGTC 59.230 61.111 0.00 0.00 39.45 4.79
824 1060 1.362355 CCCACGCCAAAACAGAACC 59.638 57.895 0.00 0.00 0.00 3.62
835 1071 1.827399 AACAGAACCATCCGACGGCT 61.827 55.000 9.66 0.00 0.00 5.52
921 1159 2.248248 TCCATCCAAAGACTCACGAGT 58.752 47.619 0.00 0.00 45.84 4.18
931 1174 0.035036 ACTCACGAGTCACGAGGAGA 59.965 55.000 17.33 2.57 43.50 3.71
1368 1612 1.093496 CCCGCCGTTTGGAAGGATAC 61.093 60.000 0.00 0.00 36.90 2.24
1502 1746 4.316823 TGTCTCTCCTGGCCGGGT 62.317 66.667 30.31 0.00 0.00 5.28
1678 1922 2.675056 CGCTGCTCTGCAACTGTCC 61.675 63.158 0.00 0.00 38.41 4.02
1798 2042 3.059597 GCGGTATTTCATCTGGAATGACG 60.060 47.826 0.00 0.71 34.91 4.35
1804 2048 1.134699 TCATCTGGAATGACGCAGGAC 60.135 52.381 0.00 0.00 0.00 3.85
1824 2068 4.421131 GACCAGGAGAGTGTATATCCCAT 58.579 47.826 0.00 0.00 40.46 4.00
1908 2152 0.111704 CGTGAACAGTTGCGTCGAAG 60.112 55.000 0.00 0.00 0.00 3.79
1956 2200 1.667724 GCATATCATGGCCGCTGATAC 59.332 52.381 23.08 12.41 38.16 2.24
1966 2210 1.789464 GCCGCTGATACGAAGATTCAG 59.211 52.381 0.00 0.00 40.81 3.02
2129 2373 3.714798 GGTTACCATGTGAGGATAAGGGA 59.285 47.826 0.00 0.00 0.00 4.20
2238 2485 3.503748 GCTGCATTTCTGTAGGTTGTTCT 59.496 43.478 0.00 0.00 35.80 3.01
2243 2490 5.932303 GCATTTCTGTAGGTTGTTCTGACTA 59.068 40.000 0.00 0.00 0.00 2.59
2419 2666 3.477210 AGGTTTCGAGATCTTATGGGC 57.523 47.619 0.00 0.00 0.00 5.36
2562 2810 6.823689 ACATCACCTTGCCTAACAACTATTAG 59.176 38.462 0.00 0.00 33.68 1.73
2596 2844 7.287696 ACTTGTCAGTCCATTTATTCTTTGGTT 59.712 33.333 0.00 0.00 0.00 3.67
2597 2845 6.980593 TGTCAGTCCATTTATTCTTTGGTTG 58.019 36.000 0.00 0.00 0.00 3.77
2599 2847 7.084486 GTCAGTCCATTTATTCTTTGGTTGAC 58.916 38.462 0.00 0.00 38.13 3.18
2626 2874 7.656707 AAGAATCAACATTACAAATGGCAAC 57.343 32.000 0.00 0.00 0.00 4.17
2742 2990 5.182380 ACTCGAGAGATTATTGCCTACTAGC 59.818 44.000 21.68 0.00 40.84 3.42
3070 3625 8.940952 GTCTGAAGAGCTTTTTACATATCTGTT 58.059 33.333 0.00 0.00 36.79 3.16
3161 3716 1.895131 AGGTGTGGCATGGTTTTCATC 59.105 47.619 0.00 0.00 32.92 2.92
3260 3815 8.662781 AAACTTTTAAAGCTCTTTGGATTTCC 57.337 30.769 4.42 0.00 34.23 3.13
3588 4143 7.016153 ACTTCTTGTACCACCTTCATCATTA 57.984 36.000 0.00 0.00 0.00 1.90
3826 4382 4.907582 GCATTTCTGAAAAATGTTGCTTGC 59.092 37.500 14.97 9.92 39.25 4.01
3893 4449 8.695456 ACTTCTTTTAACAATGTCATGTCCTTT 58.305 29.630 0.00 0.00 31.81 3.11
4002 4561 5.364157 AGTGGATCCTGGTAGTATTCTGTTC 59.636 44.000 14.23 0.00 0.00 3.18
4221 4785 2.747446 GTGGCCTGGTTATGTTGTACTG 59.253 50.000 3.32 0.00 0.00 2.74
4481 5047 7.073265 GCTGTAAAGCGAAGTTAAAACACATA 58.927 34.615 0.00 0.00 0.00 2.29
4642 5208 6.882610 TTTGTCTATTCAGTGTTGCAGAAT 57.117 33.333 3.90 3.90 37.19 2.40
4755 5321 8.846211 CGTGGTTGGAATATTCAGGTAATTTAT 58.154 33.333 17.07 0.00 0.00 1.40
5183 5752 3.690422 TGCTACGTTGTTGAAGCTTTTG 58.310 40.909 0.00 0.00 35.95 2.44
5184 5753 3.127895 TGCTACGTTGTTGAAGCTTTTGT 59.872 39.130 0.00 0.00 35.95 2.83
5285 5854 3.067461 CACACGGAAATGGGTCTGAAAAA 59.933 43.478 0.00 0.00 0.00 1.94
5320 5889 9.320352 GGCAACTTTTCCTTTAAAACATCTTAA 57.680 29.630 0.00 0.00 33.49 1.85
5588 6158 2.799126 TATGAAATTGGTGGCGGAGT 57.201 45.000 0.00 0.00 0.00 3.85
5589 6159 1.463674 ATGAAATTGGTGGCGGAGTC 58.536 50.000 0.00 0.00 0.00 3.36
5672 6256 7.497925 AAGTAGAAAAAGAAGCGAGTTCATT 57.502 32.000 0.00 0.00 37.67 2.57
5676 6260 4.510038 AAAAGAAGCGAGTTCATTGCAT 57.490 36.364 0.00 0.00 41.26 3.96
5677 6261 3.482722 AAGAAGCGAGTTCATTGCATG 57.517 42.857 0.00 0.00 41.26 4.06
5817 6425 7.503230 AGTGCATGTGGATATAAATTGATGTCA 59.497 33.333 2.27 0.00 0.00 3.58
6026 6634 4.393371 GTGCCTCTGGATTAGTTTCTTGAC 59.607 45.833 0.00 0.00 0.00 3.18
6081 6689 9.038803 GTACTAAAGCTTTAATATTGGTACGCT 57.961 33.333 19.10 0.00 32.60 5.07
6083 6691 9.038803 ACTAAAGCTTTAATATTGGTACGCTAC 57.961 33.333 19.10 0.00 0.00 3.58
6084 6692 9.257651 CTAAAGCTTTAATATTGGTACGCTACT 57.742 33.333 19.10 0.00 0.00 2.57
6088 6696 7.380602 AGCTTTAATATTGGTACGCTACTTACG 59.619 37.037 0.00 0.00 0.00 3.18
6401 7093 5.009210 TCTCCGGTTGTGGAAATTTTACAAG 59.991 40.000 17.19 9.98 37.64 3.16
6524 7216 5.992217 CCCAAATTCATCTGCTACTAGTACC 59.008 44.000 0.00 0.00 0.00 3.34
6710 7402 7.151308 ACAAAATTTTGAGTATGATTTGCCGA 58.849 30.769 32.20 0.00 40.55 5.54
6716 7408 7.579589 TTTGAGTATGATTTGCCGAAAAATG 57.420 32.000 0.69 0.00 29.89 2.32
6797 7489 6.322712 GTGGTTCCTCTCTAAGTACATCTGAT 59.677 42.308 0.00 0.00 0.00 2.90
6948 7640 5.665916 ACCTCCTTGCTTCCATTTTAATG 57.334 39.130 0.00 0.00 36.17 1.90
7029 7721 1.696988 CCGTTGCATTGCAGGTTTAC 58.303 50.000 11.76 5.92 40.61 2.01
7127 7819 4.803329 ATGGAAAGCTGTCCCTATGAAT 57.197 40.909 20.80 2.80 36.80 2.57
7217 7909 3.708403 TCTGCTGGTGTTCAGATTCAT 57.292 42.857 0.00 0.00 46.18 2.57
7236 7928 3.253432 TCATAGCTGCTATCCACGTACAG 59.747 47.826 18.87 5.50 0.00 2.74
7317 8009 3.181503 CCTTCAGGTTTTCAGCATCATCG 60.182 47.826 0.00 0.00 0.00 3.84
7907 8601 1.452108 GTCTTCCAATGGGCCTCCG 60.452 63.158 4.53 0.00 35.24 4.63
8090 8784 1.003718 GTTGGAAGACCCTGGACCG 60.004 63.158 0.00 0.00 35.38 4.79
8369 9063 2.105134 ACGGGACATAAAACTGGACACA 59.895 45.455 0.00 0.00 0.00 3.72
8386 9080 2.146342 CACACTGAAGAAGATTGCCGT 58.854 47.619 0.00 0.00 0.00 5.68
8411 9105 0.602638 TTCGAAGTTGGCACGAGCAT 60.603 50.000 7.26 0.00 44.61 3.79
8451 9145 1.595993 CGAGCGAGGAGGACCAAAGA 61.596 60.000 0.00 0.00 38.94 2.52
8615 9310 2.958818 TCTGTGGAGTAGTGTCAGGTT 58.041 47.619 0.00 0.00 0.00 3.50
8620 9315 5.084519 TGTGGAGTAGTGTCAGGTTATCTT 58.915 41.667 0.00 0.00 0.00 2.40
8748 9443 0.391927 TAACATGGGGCACTGTACGC 60.392 55.000 0.00 0.00 0.00 4.42
8848 9543 0.469518 GGTAGGTCGGCTATGGAGGT 60.470 60.000 0.00 0.00 0.00 3.85
8870 9565 8.280258 AGGTTCTGAATCTTTGGGATATCATA 57.720 34.615 4.83 0.00 33.71 2.15
8872 9567 7.120432 GGTTCTGAATCTTTGGGATATCATAGC 59.880 40.741 4.83 0.00 33.71 2.97
8890 9585 3.252974 AGCGGTAAGGAATCTCTGTTG 57.747 47.619 0.00 0.00 0.00 3.33
8923 9735 7.266922 TGTACTGTTTTAGGTTTTGACATCC 57.733 36.000 0.00 0.00 0.00 3.51
9002 9815 8.975439 GTTAACGTAGTGTTATCATGGGAATAG 58.025 37.037 0.00 0.00 45.00 1.73
9009 9822 8.554490 AGTGTTATCATGGGAATAGTACTCTT 57.446 34.615 0.00 0.00 0.00 2.85
9010 9823 8.424918 AGTGTTATCATGGGAATAGTACTCTTG 58.575 37.037 0.00 0.00 0.00 3.02
9011 9824 8.421784 GTGTTATCATGGGAATAGTACTCTTGA 58.578 37.037 0.00 0.00 0.00 3.02
9012 9825 8.421784 TGTTATCATGGGAATAGTACTCTTGAC 58.578 37.037 0.00 0.00 0.00 3.18
9014 9827 7.682787 ATCATGGGAATAGTACTCTTGACTT 57.317 36.000 0.00 0.00 0.00 3.01
9025 9840 5.705441 AGTACTCTTGACTTCTCACTCAGAG 59.295 44.000 0.00 0.00 46.14 3.35
9196 10011 3.515071 ATTACTTTGCGTCGTCAACAC 57.485 42.857 0.00 0.00 0.00 3.32
9228 10058 3.253921 TCGACGAGGATTGTGACTTTGTA 59.746 43.478 0.00 0.00 28.27 2.41
9231 10061 4.957296 ACGAGGATTGTGACTTTGTAAGT 58.043 39.130 0.00 0.00 46.38 2.24
9232 10062 5.365619 ACGAGGATTGTGACTTTGTAAGTT 58.634 37.500 0.00 0.00 43.03 2.66
9233 10063 5.820947 ACGAGGATTGTGACTTTGTAAGTTT 59.179 36.000 0.00 0.00 43.03 2.66
9234 10064 6.317893 ACGAGGATTGTGACTTTGTAAGTTTT 59.682 34.615 0.00 0.00 43.03 2.43
9235 10065 7.496591 ACGAGGATTGTGACTTTGTAAGTTTTA 59.503 33.333 0.00 0.00 43.03 1.52
9247 10078 7.728532 ACTTTGTAAGTTTTATTCAGACCCCAT 59.271 33.333 0.00 0.00 39.04 4.00
9261 10092 0.033504 CCCCATGGAACGGATAGTCG 59.966 60.000 15.22 0.00 0.00 4.18
9262 10093 1.037493 CCCATGGAACGGATAGTCGA 58.963 55.000 15.22 0.00 0.00 4.20
9277 10108 1.134371 AGTCGATTTGCTAGCCTTCCC 60.134 52.381 13.29 0.00 0.00 3.97
9351 10183 1.255882 ATGCGCCACTTCCATGAAAA 58.744 45.000 4.18 0.00 0.00 2.29
9355 10187 2.664916 CGCCACTTCCATGAAAACAAG 58.335 47.619 0.00 0.00 0.00 3.16
9362 10194 6.593382 CCACTTCCATGAAAACAAGTTTGAAA 59.407 34.615 0.00 0.00 32.36 2.69
9398 10230 2.638855 TGGCATCAAGGAAGGCAATTTT 59.361 40.909 0.00 0.00 33.24 1.82
9418 10250 6.771934 TTTTATTGGTGGAAAGGGGAAAAT 57.228 33.333 0.00 0.00 0.00 1.82
9465 10298 3.623510 GCAGAAGGTAGCATTAGTCCAAC 59.376 47.826 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.670251 CGTTTGCCCTGCGGGTAA 60.670 61.111 11.58 11.72 45.39 2.85
3 4 4.708386 CCGTTTGCCCTGCGGGTA 62.708 66.667 11.58 5.51 46.51 3.69
6 7 4.708386 TACCCGTTTGCCCTGCGG 62.708 66.667 0.00 0.00 44.55 5.69
7 8 2.043980 ATTACCCGTTTGCCCTGCG 61.044 57.895 0.00 0.00 0.00 5.18
8 9 1.510844 CATTACCCGTTTGCCCTGC 59.489 57.895 0.00 0.00 0.00 4.85
9 10 1.319614 CCCATTACCCGTTTGCCCTG 61.320 60.000 0.00 0.00 0.00 4.45
10 11 1.000145 CCCATTACCCGTTTGCCCT 60.000 57.895 0.00 0.00 0.00 5.19
11 12 0.034283 TACCCATTACCCGTTTGCCC 60.034 55.000 0.00 0.00 0.00 5.36
12 13 1.097232 GTACCCATTACCCGTTTGCC 58.903 55.000 0.00 0.00 0.00 4.52
13 14 1.097232 GGTACCCATTACCCGTTTGC 58.903 55.000 0.00 0.00 44.41 3.68
28 29 2.224548 GGGTAGAGATGGCAATGGGTAC 60.225 54.545 0.00 0.00 0.00 3.34
29 30 2.054799 GGGTAGAGATGGCAATGGGTA 58.945 52.381 0.00 0.00 0.00 3.69
30 31 0.846693 GGGTAGAGATGGCAATGGGT 59.153 55.000 0.00 0.00 0.00 4.51
31 32 0.846015 TGGGTAGAGATGGCAATGGG 59.154 55.000 0.00 0.00 0.00 4.00
32 33 1.811558 CGTGGGTAGAGATGGCAATGG 60.812 57.143 0.00 0.00 0.00 3.16
33 34 1.138859 TCGTGGGTAGAGATGGCAATG 59.861 52.381 0.00 0.00 0.00 2.82
34 35 1.414181 CTCGTGGGTAGAGATGGCAAT 59.586 52.381 0.00 0.00 37.93 3.56
35 36 0.824109 CTCGTGGGTAGAGATGGCAA 59.176 55.000 0.00 0.00 37.93 4.52
36 37 1.043116 CCTCGTGGGTAGAGATGGCA 61.043 60.000 0.00 0.00 37.93 4.92
37 38 1.742768 CCTCGTGGGTAGAGATGGC 59.257 63.158 0.00 0.00 37.93 4.40
38 39 0.757188 AGCCTCGTGGGTAGAGATGG 60.757 60.000 6.40 0.00 43.12 3.51
39 40 0.671251 GAGCCTCGTGGGTAGAGATG 59.329 60.000 8.42 0.00 45.24 2.90
40 41 0.259065 TGAGCCTCGTGGGTAGAGAT 59.741 55.000 8.42 0.00 45.24 2.75
41 42 0.039180 TTGAGCCTCGTGGGTAGAGA 59.961 55.000 8.42 0.00 45.24 3.10
42 43 0.457851 CTTGAGCCTCGTGGGTAGAG 59.542 60.000 8.42 5.88 45.24 2.43
43 44 1.605058 GCTTGAGCCTCGTGGGTAGA 61.605 60.000 8.42 0.00 45.24 2.59
44 45 1.153549 GCTTGAGCCTCGTGGGTAG 60.154 63.158 8.42 4.72 45.24 3.18
45 46 1.476845 TTGCTTGAGCCTCGTGGGTA 61.477 55.000 8.42 0.00 45.24 3.69
47 48 0.107703 TATTGCTTGAGCCTCGTGGG 60.108 55.000 5.54 0.00 41.18 4.61
48 49 1.009829 GTATTGCTTGAGCCTCGTGG 58.990 55.000 0.00 0.00 41.18 4.94
49 50 1.725641 TGTATTGCTTGAGCCTCGTG 58.274 50.000 0.00 0.00 41.18 4.35
50 51 2.076863 GTTGTATTGCTTGAGCCTCGT 58.923 47.619 0.00 0.00 41.18 4.18
51 52 2.076100 TGTTGTATTGCTTGAGCCTCG 58.924 47.619 0.00 0.00 41.18 4.63
52 53 3.503748 AGTTGTTGTATTGCTTGAGCCTC 59.496 43.478 0.00 0.00 41.18 4.70
53 54 3.490348 AGTTGTTGTATTGCTTGAGCCT 58.510 40.909 0.00 0.00 41.18 4.58
54 55 3.923017 AGTTGTTGTATTGCTTGAGCC 57.077 42.857 0.00 0.00 41.18 4.70
55 56 6.030228 GGAATAGTTGTTGTATTGCTTGAGC 58.970 40.000 0.00 0.00 42.50 4.26
56 57 7.144722 TGGAATAGTTGTTGTATTGCTTGAG 57.855 36.000 0.00 0.00 31.43 3.02
57 58 7.392953 TGATGGAATAGTTGTTGTATTGCTTGA 59.607 33.333 0.00 0.00 31.43 3.02
58 59 7.537715 TGATGGAATAGTTGTTGTATTGCTTG 58.462 34.615 0.00 0.00 31.43 4.01
59 60 7.701539 TGATGGAATAGTTGTTGTATTGCTT 57.298 32.000 0.00 0.00 31.43 3.91
60 61 7.701539 TTGATGGAATAGTTGTTGTATTGCT 57.298 32.000 0.00 0.00 31.43 3.91
61 62 8.931385 ATTTGATGGAATAGTTGTTGTATTGC 57.069 30.769 0.00 0.00 0.00 3.56
62 63 9.520204 GGATTTGATGGAATAGTTGTTGTATTG 57.480 33.333 0.00 0.00 0.00 1.90
63 64 8.695456 GGGATTTGATGGAATAGTTGTTGTATT 58.305 33.333 0.00 0.00 0.00 1.89
64 65 8.061304 AGGGATTTGATGGAATAGTTGTTGTAT 58.939 33.333 0.00 0.00 0.00 2.29
65 66 7.410174 AGGGATTTGATGGAATAGTTGTTGTA 58.590 34.615 0.00 0.00 0.00 2.41
66 67 6.256053 AGGGATTTGATGGAATAGTTGTTGT 58.744 36.000 0.00 0.00 0.00 3.32
67 68 6.604795 AGAGGGATTTGATGGAATAGTTGTTG 59.395 38.462 0.00 0.00 0.00 3.33
68 69 6.735556 AGAGGGATTTGATGGAATAGTTGTT 58.264 36.000 0.00 0.00 0.00 2.83
69 70 6.159398 AGAGAGGGATTTGATGGAATAGTTGT 59.841 38.462 0.00 0.00 0.00 3.32
70 71 6.599445 AGAGAGGGATTTGATGGAATAGTTG 58.401 40.000 0.00 0.00 0.00 3.16
71 72 6.183361 GGAGAGAGGGATTTGATGGAATAGTT 60.183 42.308 0.00 0.00 0.00 2.24
72 73 5.309282 GGAGAGAGGGATTTGATGGAATAGT 59.691 44.000 0.00 0.00 0.00 2.12
73 74 5.280419 GGGAGAGAGGGATTTGATGGAATAG 60.280 48.000 0.00 0.00 0.00 1.73
74 75 4.599241 GGGAGAGAGGGATTTGATGGAATA 59.401 45.833 0.00 0.00 0.00 1.75
75 76 3.397282 GGGAGAGAGGGATTTGATGGAAT 59.603 47.826 0.00 0.00 0.00 3.01
76 77 2.780010 GGGAGAGAGGGATTTGATGGAA 59.220 50.000 0.00 0.00 0.00 3.53
77 78 2.021639 AGGGAGAGAGGGATTTGATGGA 60.022 50.000 0.00 0.00 0.00 3.41
78 79 2.416638 AGGGAGAGAGGGATTTGATGG 58.583 52.381 0.00 0.00 0.00 3.51
79 80 3.181446 GGAAGGGAGAGAGGGATTTGATG 60.181 52.174 0.00 0.00 0.00 3.07
80 81 3.052329 GGAAGGGAGAGAGGGATTTGAT 58.948 50.000 0.00 0.00 0.00 2.57
81 82 2.225882 TGGAAGGGAGAGAGGGATTTGA 60.226 50.000 0.00 0.00 0.00 2.69
82 83 2.200081 TGGAAGGGAGAGAGGGATTTG 58.800 52.381 0.00 0.00 0.00 2.32
83 84 2.578480 GTTGGAAGGGAGAGAGGGATTT 59.422 50.000 0.00 0.00 0.00 2.17
84 85 2.200955 GTTGGAAGGGAGAGAGGGATT 58.799 52.381 0.00 0.00 0.00 3.01
85 86 1.081174 TGTTGGAAGGGAGAGAGGGAT 59.919 52.381 0.00 0.00 0.00 3.85
86 87 0.491823 TGTTGGAAGGGAGAGAGGGA 59.508 55.000 0.00 0.00 0.00 4.20
87 88 1.589414 ATGTTGGAAGGGAGAGAGGG 58.411 55.000 0.00 0.00 0.00 4.30
88 89 4.518249 GTTAATGTTGGAAGGGAGAGAGG 58.482 47.826 0.00 0.00 0.00 3.69
89 90 4.081642 TCGTTAATGTTGGAAGGGAGAGAG 60.082 45.833 0.00 0.00 0.00 3.20
90 91 3.835978 TCGTTAATGTTGGAAGGGAGAGA 59.164 43.478 0.00 0.00 0.00 3.10
91 92 4.202245 TCGTTAATGTTGGAAGGGAGAG 57.798 45.455 0.00 0.00 0.00 3.20
92 93 4.837093 ATCGTTAATGTTGGAAGGGAGA 57.163 40.909 0.00 0.00 0.00 3.71
93 94 4.700213 ACAATCGTTAATGTTGGAAGGGAG 59.300 41.667 11.90 0.00 0.00 4.30
94 95 4.658063 ACAATCGTTAATGTTGGAAGGGA 58.342 39.130 11.90 0.00 0.00 4.20
95 96 5.385509 AACAATCGTTAATGTTGGAAGGG 57.614 39.130 11.90 0.00 38.29 3.95
102 103 9.689976 TGAAAATCATCAACAATCGTTAATGTT 57.310 25.926 0.00 0.00 40.24 2.71
103 104 9.345517 CTGAAAATCATCAACAATCGTTAATGT 57.654 29.630 0.00 0.00 33.15 2.71
104 105 9.345517 ACTGAAAATCATCAACAATCGTTAATG 57.654 29.630 0.00 0.00 32.69 1.90
120 121 6.642131 GCAATGCACTTTTCTACTGAAAATCA 59.358 34.615 0.00 4.70 46.90 2.57
129 130 2.094545 CCCTGGCAATGCACTTTTCTAC 60.095 50.000 7.79 0.00 0.00 2.59
130 131 2.170166 CCCTGGCAATGCACTTTTCTA 58.830 47.619 7.79 0.00 0.00 2.10
165 166 5.594317 GCATTATGTTGGGGGACATATATCC 59.406 44.000 0.00 0.00 40.94 2.59
169 170 4.467861 TGCATTATGTTGGGGGACATAT 57.532 40.909 0.00 0.00 40.94 1.78
200 203 1.301423 CCGTCCTTCGAACCACAAAA 58.699 50.000 0.00 0.00 42.86 2.44
235 246 7.852945 GGACAAAAGCGTAGATAGAATCATTTG 59.147 37.037 0.00 0.00 0.00 2.32
251 262 0.040067 GTCTGGCAAGGACAAAAGCG 60.040 55.000 2.30 0.00 34.23 4.68
257 268 1.461268 TCCCTGTCTGGCAAGGACA 60.461 57.895 5.26 7.29 40.78 4.02
262 273 2.935481 CCCCTCCCTGTCTGGCAA 60.935 66.667 0.00 0.00 0.00 4.52
303 317 7.390440 TCTGTTGAAGAAACTACAATACATGGG 59.610 37.037 0.00 0.00 39.70 4.00
344 358 5.621197 TCATGTGGGTTTTTGATAAGACG 57.379 39.130 0.00 0.00 0.00 4.18
350 364 4.646492 GGAGCTATCATGTGGGTTTTTGAT 59.354 41.667 0.00 0.00 33.59 2.57
377 391 4.609336 CGTGCTAGTCAAAGTCTTTCTTGC 60.609 45.833 11.17 11.17 36.40 4.01
472 494 0.884704 TGCTTCTTCCTTGCGTCCAC 60.885 55.000 0.00 0.00 0.00 4.02
473 495 0.179032 TTGCTTCTTCCTTGCGTCCA 60.179 50.000 0.00 0.00 0.00 4.02
474 496 0.519077 CTTGCTTCTTCCTTGCGTCC 59.481 55.000 0.00 0.00 0.00 4.79
475 497 0.110010 GCTTGCTTCTTCCTTGCGTC 60.110 55.000 0.00 0.00 0.00 5.19
476 498 1.845809 CGCTTGCTTCTTCCTTGCGT 61.846 55.000 0.00 0.00 37.62 5.24
477 499 1.154338 CGCTTGCTTCTTCCTTGCG 60.154 57.895 0.00 0.00 36.19 4.85
494 516 0.460109 TCGATTGTCATGGTGCTCCG 60.460 55.000 0.00 0.00 36.30 4.63
544 566 2.192175 GGCCTGACCGTTATGGGG 59.808 66.667 0.00 0.00 44.64 4.96
598 834 9.706529 ATTCTTAGGAGAAGAAAATTTAGGCAT 57.293 29.630 4.01 0.00 44.65 4.40
603 839 9.255029 CCCCAATTCTTAGGAGAAGAAAATTTA 57.745 33.333 4.01 0.00 44.65 1.40
605 841 6.669591 CCCCCAATTCTTAGGAGAAGAAAATT 59.330 38.462 4.01 0.00 44.65 1.82
606 842 6.197903 CCCCCAATTCTTAGGAGAAGAAAAT 58.802 40.000 4.01 0.00 44.65 1.82
608 844 4.606255 ACCCCCAATTCTTAGGAGAAGAAA 59.394 41.667 4.01 0.00 44.65 2.52
610 846 3.780850 GACCCCCAATTCTTAGGAGAAGA 59.219 47.826 0.00 0.00 44.65 2.87
611 847 3.783082 AGACCCCCAATTCTTAGGAGAAG 59.217 47.826 0.00 0.00 44.65 2.85
613 849 3.508952 AGACCCCCAATTCTTAGGAGA 57.491 47.619 0.00 0.00 0.00 3.71
617 853 6.857437 AAAATGAAGACCCCCAATTCTTAG 57.143 37.500 0.00 0.00 32.04 2.18
648 884 9.546428 CCCATTGTGTCTTCTTTTTCTTTTTAT 57.454 29.630 0.00 0.00 0.00 1.40
649 885 7.494298 GCCCATTGTGTCTTCTTTTTCTTTTTA 59.506 33.333 0.00 0.00 0.00 1.52
651 887 5.817296 GCCCATTGTGTCTTCTTTTTCTTTT 59.183 36.000 0.00 0.00 0.00 2.27
652 888 5.104982 TGCCCATTGTGTCTTCTTTTTCTTT 60.105 36.000 0.00 0.00 0.00 2.52
655 891 4.320608 TGCCCATTGTGTCTTCTTTTTC 57.679 40.909 0.00 0.00 0.00 2.29
658 894 4.559300 CGAATTGCCCATTGTGTCTTCTTT 60.559 41.667 0.00 0.00 0.00 2.52
700 936 4.183686 CAAGCGCCTGGCCAATCG 62.184 66.667 18.74 18.74 45.17 3.34
718 954 1.154413 GGAATGACGTGTGCGCAAG 60.154 57.895 14.00 11.79 42.83 4.01
719 955 2.942879 GGAATGACGTGTGCGCAA 59.057 55.556 14.00 0.00 42.83 4.85
921 1159 0.992695 TTCCCTCTCTCTCCTCGTGA 59.007 55.000 0.00 0.00 0.00 4.35
922 1160 1.388547 CTTCCCTCTCTCTCCTCGTG 58.611 60.000 0.00 0.00 0.00 4.35
923 1161 0.257616 CCTTCCCTCTCTCTCCTCGT 59.742 60.000 0.00 0.00 0.00 4.18
924 1162 1.106944 GCCTTCCCTCTCTCTCCTCG 61.107 65.000 0.00 0.00 0.00 4.63
931 1174 0.461961 CGATTTCGCCTTCCCTCTCT 59.538 55.000 0.00 0.00 0.00 3.10
1344 1587 0.318360 CTTCCAAACGGCGGGAAAAC 60.318 55.000 13.24 0.00 42.31 2.43
1359 1602 1.022735 TCACTCTCGCGTATCCTTCC 58.977 55.000 5.77 0.00 0.00 3.46
1502 1746 5.244402 TGAACCCTTACTTGTCACGATTAGA 59.756 40.000 0.00 0.00 0.00 2.10
1678 1922 1.539827 CCAGAAACCCCGTAGCTTTTG 59.460 52.381 0.00 0.00 0.00 2.44
1798 2042 1.490574 ATACACTCTCCTGGTCCTGC 58.509 55.000 0.00 0.00 0.00 4.85
1804 2048 4.840680 TCAATGGGATATACACTCTCCTGG 59.159 45.833 0.00 0.00 0.00 4.45
1908 2152 0.240945 CAAAGCCATGACGGTGTTCC 59.759 55.000 0.00 0.00 36.97 3.62
1956 2200 2.538333 CGCAGAAATGCCTGAATCTTCG 60.538 50.000 0.00 0.00 36.29 3.79
1966 2210 2.658285 CATATCAAGCGCAGAAATGCC 58.342 47.619 11.47 0.00 0.00 4.40
2197 2444 5.709631 TGCAGCTTTACCTTGACATCATTAA 59.290 36.000 0.00 0.00 0.00 1.40
2238 2485 4.265893 TGTGCAAAGTGGAAAAGTAGTCA 58.734 39.130 0.00 0.00 0.00 3.41
2243 2490 5.009010 CACTATCTGTGCAAAGTGGAAAAGT 59.991 40.000 3.21 0.00 40.06 2.66
2363 2610 2.029623 ACGTGGATAGCTAACGTCCAT 58.970 47.619 15.86 0.90 46.86 3.41
2419 2666 0.466124 GGGGTAGGCTAGAGTTGCAG 59.534 60.000 0.00 0.00 0.00 4.41
2562 2810 8.871686 ATAAATGGACTGACAAGTTGTTTTTC 57.128 30.769 10.45 6.56 36.52 2.29
2596 2844 8.739039 CCATTTGTAATGTTGATTCTTAGGTCA 58.261 33.333 0.00 0.00 0.00 4.02
2597 2845 7.702348 GCCATTTGTAATGTTGATTCTTAGGTC 59.298 37.037 0.00 0.00 0.00 3.85
2599 2847 7.546358 TGCCATTTGTAATGTTGATTCTTAGG 58.454 34.615 0.00 0.00 0.00 2.69
2742 2990 7.948357 ACATCACCAGATCATCAATTTTATGG 58.052 34.615 0.00 0.00 30.20 2.74
3070 3625 6.018425 GTCGGTTACTATATCAAGACGACAGA 60.018 42.308 0.00 0.00 45.08 3.41
3161 3716 7.672983 ATCAAGGCAAATATGGTATTAGTCG 57.327 36.000 0.00 0.00 0.00 4.18
3327 3882 3.502595 GGAGGCCACAAAAGAAGTAAGTC 59.497 47.826 5.01 0.00 0.00 3.01
3588 4143 0.892755 CAGCATTGGCCACATTCACT 59.107 50.000 3.88 0.00 42.56 3.41
3826 4382 7.962918 CCTAACAGGAAAAATCACAAATACTCG 59.037 37.037 0.00 0.00 37.67 4.18
3928 4486 7.101054 ACAAAACATGATCAAATTGCTAGCAT 58.899 30.769 20.13 1.20 0.00 3.79
4083 4644 4.458295 GGGAGGGTTAAAAGCTAAGACAAC 59.542 45.833 0.00 0.00 0.00 3.32
4084 4645 4.507869 GGGGAGGGTTAAAAGCTAAGACAA 60.508 45.833 0.00 0.00 0.00 3.18
4085 4646 3.009805 GGGGAGGGTTAAAAGCTAAGACA 59.990 47.826 0.00 0.00 0.00 3.41
4221 4785 2.391724 TATCCTTCGAATGCCCCGGC 62.392 60.000 0.00 0.00 42.35 6.13
4410 4974 2.674357 TGCTTTAAAATACTCGGCGGAC 59.326 45.455 7.21 0.00 0.00 4.79
4642 5208 3.936453 GCGATGTGGTACAGTTTATCCAA 59.064 43.478 0.00 0.00 41.80 3.53
4710 5276 1.653667 CACAAGTGATGCACCGCAA 59.346 52.632 0.00 0.00 43.62 4.85
4826 5393 9.232473 AGACCTAAGGAATTTTGATTAGTTGTC 57.768 33.333 0.00 0.00 0.00 3.18
4828 5395 9.846248 CAAGACCTAAGGAATTTTGATTAGTTG 57.154 33.333 0.00 0.00 0.00 3.16
4864 5432 5.352569 AGATCAACTCGCCAAAAATCACTAG 59.647 40.000 0.00 0.00 0.00 2.57
4999 5567 4.932799 TGAACTATTTGCTTAACGCTAGCA 59.067 37.500 16.45 2.93 46.26 3.49
5183 5752 9.793252 TCAAACGGATGTATCTAGTAAGTAAAC 57.207 33.333 0.00 0.00 0.00 2.01
5245 5814 0.528017 TGCTCACAAGAGTAGCCTCG 59.472 55.000 0.00 0.00 44.00 4.63
5247 5816 1.001406 GTGTGCTCACAAGAGTAGCCT 59.999 52.381 13.83 0.00 43.77 4.58
5285 5854 8.650143 TTAAAGGAAAAGTTGCCAGATAGAAT 57.350 30.769 0.00 0.00 0.00 2.40
5338 5908 1.606668 GCGGACAACATGTTCCTGAAA 59.393 47.619 8.48 0.00 0.00 2.69
5672 6256 2.678470 TGGAGATGCCAGCATGCA 59.322 55.556 21.98 0.00 43.33 3.96
5817 6425 3.635373 CAGGAACCAAGATATTGCATGCT 59.365 43.478 20.33 1.26 0.00 3.79
5915 6523 4.164843 TGCCAGAAAAGTGGTAAGAACT 57.835 40.909 0.00 0.00 40.09 3.01
6026 6634 4.879545 GGGGTATGGCCATAACAATATACG 59.120 45.833 35.81 0.00 39.65 3.06
6081 6689 2.232399 TCACAGTGCTGACCGTAAGTA 58.768 47.619 6.17 0.00 0.00 2.24
6082 6690 1.037493 TCACAGTGCTGACCGTAAGT 58.963 50.000 6.17 0.00 0.00 2.24
6083 6691 2.370281 ATCACAGTGCTGACCGTAAG 57.630 50.000 6.17 0.00 0.00 2.34
6084 6692 3.581755 GTTATCACAGTGCTGACCGTAA 58.418 45.455 6.17 0.00 0.00 3.18
6088 6696 1.003118 TGGGTTATCACAGTGCTGACC 59.997 52.381 9.39 9.39 0.00 4.02
6401 7093 1.840635 AGACAATACTCTTGAGGGGGC 59.159 52.381 2.55 0.00 0.00 5.80
6440 7132 5.011840 GTCCAGAGTAAGTTCCAACCTTACT 59.988 44.000 11.48 11.48 43.85 2.24
6524 7216 1.016130 CCGTACTGCTGCCAGAGTTG 61.016 60.000 0.00 0.00 41.77 3.16
6710 7402 5.074804 ACTACCCCGCTTTTAGTCATTTTT 58.925 37.500 0.00 0.00 0.00 1.94
6716 7408 4.501058 CCAGATACTACCCCGCTTTTAGTC 60.501 50.000 0.00 0.00 0.00 2.59
6797 7489 2.039216 TGTCGGCCTTTGGTAAGAATCA 59.961 45.455 0.00 0.00 32.92 2.57
6883 7575 0.181350 GCTGGAAATCCTCCCGTGAT 59.819 55.000 0.44 0.00 44.69 3.06
7029 7721 3.318557 GGTAAGAAGTCCACTAGATCCCG 59.681 52.174 0.00 0.00 0.00 5.14
7127 7819 1.304381 GCTGGGCCATTCAGTTCCA 60.304 57.895 6.72 0.00 34.89 3.53
7217 7909 1.337071 GCTGTACGTGGATAGCAGCTA 59.663 52.381 4.10 4.10 46.20 3.32
7236 7928 3.480470 TGCATAAGAATAGGAAGCAGGC 58.520 45.455 0.00 0.00 0.00 4.85
7907 8601 3.680789 CGGTCGACCTGATTTTAAATGC 58.319 45.455 30.92 0.83 0.00 3.56
8090 8784 1.799258 CTTGAAGTGTGCTGGCCACC 61.799 60.000 0.00 0.00 44.01 4.61
8300 8994 4.328983 ACAAGGAATACAAAGCACGATACG 59.671 41.667 0.00 0.00 0.00 3.06
8369 9063 1.611673 CCCACGGCAATCTTCTTCAGT 60.612 52.381 0.00 0.00 0.00 3.41
8386 9080 2.282180 GCCAACTTCGAAGCCCCA 60.282 61.111 24.86 0.00 0.00 4.96
8411 9105 3.570125 CGAGTAGTGATAGGGCAAGATCA 59.430 47.826 0.00 0.00 0.00 2.92
8451 9145 4.757149 GGTTTCAACTACAGCAGAGATTGT 59.243 41.667 0.00 0.00 0.00 2.71
8615 9310 5.425217 TCCAGCAAAGAGACCATACAAGATA 59.575 40.000 0.00 0.00 0.00 1.98
8620 9315 3.264193 ACATCCAGCAAAGAGACCATACA 59.736 43.478 0.00 0.00 0.00 2.29
8748 9443 5.584551 AGGAGGGGCTAATTAATTGTAGG 57.415 43.478 11.05 0.43 0.00 3.18
8797 9492 2.159379 GGCAAACTGGAAATCTAAGCCG 60.159 50.000 0.00 0.00 0.00 5.52
8848 9543 6.875726 CGCTATGATATCCCAAAGATTCAGAA 59.124 38.462 0.00 0.00 36.33 3.02
8870 9565 2.832129 TCAACAGAGATTCCTTACCGCT 59.168 45.455 0.00 0.00 0.00 5.52
8872 9567 4.566004 TGTTCAACAGAGATTCCTTACCG 58.434 43.478 0.00 0.00 0.00 4.02
8890 9585 8.920509 AAACCTAAAACAGTACAATGTTGTTC 57.079 30.769 3.45 0.00 42.49 3.18
8923 9735 7.553881 ACATATAAGAATGGGAAAACAGTCG 57.446 36.000 0.00 0.00 40.15 4.18
8982 9794 9.080097 AGAGTACTATTCCCATGATAACACTAC 57.920 37.037 0.00 0.00 0.00 2.73
8996 9809 7.121463 TGAGTGAGAAGTCAAGAGTACTATTCC 59.879 40.741 0.00 0.00 33.27 3.01
9002 9815 5.938322 CTCTGAGTGAGAAGTCAAGAGTAC 58.062 45.833 0.00 0.00 45.39 2.73
9025 9840 7.114529 CAGTGCTCAAAATTCATCAACTCTTTC 59.885 37.037 0.00 0.00 0.00 2.62
9228 10058 5.269554 TCCATGGGGTCTGAATAAAACTT 57.730 39.130 13.02 0.00 34.93 2.66
9231 10061 4.013728 CGTTCCATGGGGTCTGAATAAAA 58.986 43.478 13.02 0.00 34.93 1.52
9232 10062 3.616219 CGTTCCATGGGGTCTGAATAAA 58.384 45.455 13.02 0.00 34.93 1.40
9233 10063 2.092646 CCGTTCCATGGGGTCTGAATAA 60.093 50.000 13.02 0.00 34.93 1.40
9234 10064 1.488812 CCGTTCCATGGGGTCTGAATA 59.511 52.381 13.02 0.00 34.93 1.75
9235 10065 0.255890 CCGTTCCATGGGGTCTGAAT 59.744 55.000 13.02 0.00 34.93 2.57
9238 10069 1.070758 CTATCCGTTCCATGGGGTCTG 59.929 57.143 13.02 0.00 34.93 3.51
9247 10078 2.167693 AGCAAATCGACTATCCGTTCCA 59.832 45.455 0.00 0.00 0.00 3.53
9261 10092 1.587547 CTCGGGAAGGCTAGCAAATC 58.412 55.000 18.24 10.82 0.00 2.17
9262 10093 0.181350 CCTCGGGAAGGCTAGCAAAT 59.819 55.000 18.24 0.85 38.67 2.32
9277 10108 2.815647 GGCGGTTCTTGCTCCTCG 60.816 66.667 0.00 0.00 0.00 4.63
9319 10150 3.683055 CGCATTCGCATTTGGCAG 58.317 55.556 0.00 0.00 45.17 4.85
9329 10160 1.063006 CATGGAAGTGGCGCATTCG 59.937 57.895 10.83 0.00 39.07 3.34
9336 10167 3.733443 ACTTGTTTTCATGGAAGTGGC 57.267 42.857 0.00 0.00 0.00 5.01
9351 10183 8.846943 AAATCCTTTGTTCTTTTCAAACTTGT 57.153 26.923 0.00 0.00 32.48 3.16
9355 10187 6.966632 GCCAAAATCCTTTGTTCTTTTCAAAC 59.033 34.615 0.00 0.00 40.38 2.93
9362 10194 5.549742 TGATGCCAAAATCCTTTGTTCTT 57.450 34.783 0.00 0.00 40.38 2.52
9398 10230 7.873699 TTTAATTTTCCCCTTTCCACCAATA 57.126 32.000 0.00 0.00 0.00 1.90
9465 10298 2.938956 ACTTGAGTTGGTTCCTGGAG 57.061 50.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.