Multiple sequence alignment - TraesCS7D01G530500

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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 TraesCS7D01G530500 chr7D 100.000 4409 0 0 1 4409 625249531 625253939 0.000000e+00 8142.0
1 TraesCS7D01G530500 chr7D 85.779 2658 337 26 771 3404 625355626 625352986 0.000000e+00 2776.0
2 TraesCS7D01G530500 chr7D 84.612 2476 363 12 944 3405 625227765 625225294 0.000000e+00 2446.0
3 TraesCS7D01G530500 chr7D 81.839 2665 404 49 905 3526 448855308 448857935 0.000000e+00 2167.0
4 TraesCS7D01G530500 chr7D 83.643 269 36 5 40 307 563446439 563446178 3.410000e-61 246.0
5 TraesCS7D01G530500 chr7D 91.837 49 4 0 4102 4150 548565028 548565076 7.910000e-08 69.4
6 TraesCS7D01G530500 chr7A 94.882 3927 135 23 307 4214 720865032 720861153 0.000000e+00 6078.0
7 TraesCS7D01G530500 chr7A 84.464 2240 324 17 1180 3402 720885032 720887264 0.000000e+00 2187.0
8 TraesCS7D01G530500 chr7B 94.842 3645 127 23 307 3908 723903665 723900039 0.000000e+00 5633.0
9 TraesCS7D01G530500 chr7B 87.009 2471 293 17 955 3404 724955982 724953519 0.000000e+00 2760.0
10 TraesCS7D01G530500 chr7B 83.164 2661 373 50 905 3526 466668788 466671412 0.000000e+00 2362.0
11 TraesCS7D01G530500 chr7B 83.776 2410 373 16 1003 3402 723929179 723931580 0.000000e+00 2268.0
12 TraesCS7D01G530500 chr7B 83.961 1434 207 15 1620 3044 723837107 723835688 0.000000e+00 1352.0
13 TraesCS7D01G530500 chr7B 83.897 503 33 12 3907 4409 723899950 723899496 1.880000e-118 436.0
14 TraesCS7D01G530500 chr1B 80.762 2994 481 66 438 3396 623546991 623549924 0.000000e+00 2250.0
15 TraesCS7D01G530500 chr1B 87.037 54 6 1 3922 3974 599832389 599832442 4.760000e-05 60.2
16 TraesCS7D01G530500 chr1B 87.037 54 6 1 3922 3974 599978242 599978295 4.760000e-05 60.2
17 TraesCS7D01G530500 chr1D 82.261 2627 416 30 798 3396 453113137 453115741 0.000000e+00 2224.0
18 TraesCS7D01G530500 chr1D 92.157 306 11 1 1 306 297543222 297543514 1.900000e-113 420.0
19 TraesCS7D01G530500 chr1D 82.911 158 25 2 4096 4251 441735842 441735999 1.650000e-29 141.0
20 TraesCS7D01G530500 chr6A 82.923 2477 404 14 944 3405 608493856 608491384 0.000000e+00 2213.0
21 TraesCS7D01G530500 chr5D 97.727 308 7 0 1 308 549786417 549786724 8.400000e-147 531.0
22 TraesCS7D01G530500 chr5D 83.861 316 29 14 6 306 549785435 549785127 9.340000e-72 281.0
23 TraesCS7D01G530500 chr5D 80.524 267 45 6 44 307 458842105 458841843 9.670000e-47 198.0
24 TraesCS7D01G530500 chr2D 94.118 306 5 1 1 306 613437651 613437943 1.870000e-123 453.0
25 TraesCS7D01G530500 chr2D 89.831 59 2 3 4102 4156 52950033 52950091 6.120000e-09 73.1
26 TraesCS7D01G530500 chrUn 83.165 297 37 10 12 306 90818102 90817817 4.370000e-65 259.0
27 TraesCS7D01G530500 chrUn 82.828 297 38 10 12 306 45273143 45272858 2.040000e-63 254.0
28 TraesCS7D01G530500 chrUn 82.828 297 38 10 12 306 391516032 391516317 2.040000e-63 254.0
29 TraesCS7D01G530500 chrUn 78.049 205 33 9 4067 4261 15473526 15473728 7.750000e-23 119.0
30 TraesCS7D01G530500 chr4D 82.550 298 42 7 12 308 435205418 435205130 2.040000e-63 254.0
31 TraesCS7D01G530500 chr1A 85.606 132 18 1 4091 4221 465490148 465490017 2.140000e-28 137.0
32 TraesCS7D01G530500 chr2A 79.104 201 33 7 4066 4262 74763838 74764033 3.580000e-26 130.0
33 TraesCS7D01G530500 chr2A 79.200 125 18 6 4102 4219 16842692 16842815 3.660000e-11 80.5
34 TraesCS7D01G530500 chr4A 78.788 198 30 10 4066 4255 584401485 584401292 5.990000e-24 122.0
35 TraesCS7D01G530500 chr5A 77.301 163 26 10 4096 4250 596577188 596577347 7.860000e-13 86.1
36 TraesCS7D01G530500 chr3D 77.698 139 23 8 4096 4228 571097151 571097287 1.310000e-10 78.7
37 TraesCS7D01G530500 chr3D 89.130 46 4 1 3929 3973 102195159 102195114 6.160000e-04 56.5
38 TraesCS7D01G530500 chr4B 87.500 64 6 2 3922 3983 389424804 389424867 6.120000e-09 73.1
39 TraesCS7D01G530500 chr3A 86.792 53 4 2 3930 3981 646134082 646134032 6.160000e-04 56.5


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 TraesCS7D01G530500 chr7D 625249531 625253939 4408 False 8142.0 8142 100.0000 1 4409 1 chr7D.!!$F3 4408
1 TraesCS7D01G530500 chr7D 625352986 625355626 2640 True 2776.0 2776 85.7790 771 3404 1 chr7D.!!$R3 2633
2 TraesCS7D01G530500 chr7D 625225294 625227765 2471 True 2446.0 2446 84.6120 944 3405 1 chr7D.!!$R2 2461
3 TraesCS7D01G530500 chr7D 448855308 448857935 2627 False 2167.0 2167 81.8390 905 3526 1 chr7D.!!$F1 2621
4 TraesCS7D01G530500 chr7A 720861153 720865032 3879 True 6078.0 6078 94.8820 307 4214 1 chr7A.!!$R1 3907
5 TraesCS7D01G530500 chr7A 720885032 720887264 2232 False 2187.0 2187 84.4640 1180 3402 1 chr7A.!!$F1 2222
6 TraesCS7D01G530500 chr7B 723899496 723903665 4169 True 3034.5 5633 89.3695 307 4409 2 chr7B.!!$R3 4102
7 TraesCS7D01G530500 chr7B 724953519 724955982 2463 True 2760.0 2760 87.0090 955 3404 1 chr7B.!!$R2 2449
8 TraesCS7D01G530500 chr7B 466668788 466671412 2624 False 2362.0 2362 83.1640 905 3526 1 chr7B.!!$F1 2621
9 TraesCS7D01G530500 chr7B 723929179 723931580 2401 False 2268.0 2268 83.7760 1003 3402 1 chr7B.!!$F2 2399
10 TraesCS7D01G530500 chr7B 723835688 723837107 1419 True 1352.0 1352 83.9610 1620 3044 1 chr7B.!!$R1 1424
11 TraesCS7D01G530500 chr1B 623546991 623549924 2933 False 2250.0 2250 80.7620 438 3396 1 chr1B.!!$F3 2958
12 TraesCS7D01G530500 chr1D 453113137 453115741 2604 False 2224.0 2224 82.2610 798 3396 1 chr1D.!!$F3 2598
13 TraesCS7D01G530500 chr6A 608491384 608493856 2472 True 2213.0 2213 82.9230 944 3405 1 chr6A.!!$R1 2461

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
108 109 0.034337 ATGCCACGTCAGTTAACGGT 59.966 50.0 5.64 0.0 46.72 4.83 F
147 148 0.101399 ATCAGAGCTCTTACACGCGG 59.899 55.0 15.27 0.0 0.00 6.46 F
1681 1777 0.106669 GGTCCTTGATAGTTGGGGGC 60.107 60.0 0.00 0.0 0.00 5.80 F
1911 2009 1.530013 GGCCTTCTTGTGCATGTGCT 61.530 55.0 6.55 0.0 42.66 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1135 1221 0.106519 AAGCCACAGGTGAAAGTGCT 60.107 50.000 0.0 0.0 34.48 4.40 R
1911 2009 2.625314 GTCGATGATCTCATGTCCAGGA 59.375 50.000 0.0 0.0 36.57 3.86 R
2667 2780 3.876914 TCACACTCAGTTCATGTTGGAAC 59.123 43.478 0.0 0.0 45.87 3.62 R
3855 4001 1.296056 GCGCAGTGGTCAAATACGGT 61.296 55.000 0.3 0.0 0.00 4.83 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
21 22 4.812476 TGCGCGAGGACCCGATTG 62.812 66.667 12.10 0.00 0.00 2.67
23 24 4.514577 CGCGAGGACCCGATTGCT 62.515 66.667 0.00 0.00 0.00 3.91
24 25 2.125106 GCGAGGACCCGATTGCTT 60.125 61.111 6.56 0.00 0.00 3.91
25 26 1.745489 GCGAGGACCCGATTGCTTT 60.745 57.895 6.56 0.00 0.00 3.51
26 27 1.305930 GCGAGGACCCGATTGCTTTT 61.306 55.000 6.56 0.00 0.00 2.27
27 28 1.165270 CGAGGACCCGATTGCTTTTT 58.835 50.000 0.00 0.00 0.00 1.94
28 29 1.130561 CGAGGACCCGATTGCTTTTTC 59.869 52.381 0.00 0.00 0.00 2.29
29 30 2.437413 GAGGACCCGATTGCTTTTTCT 58.563 47.619 0.00 0.00 0.00 2.52
30 31 3.606687 GAGGACCCGATTGCTTTTTCTA 58.393 45.455 0.00 0.00 0.00 2.10
31 32 3.610911 AGGACCCGATTGCTTTTTCTAG 58.389 45.455 0.00 0.00 0.00 2.43
32 33 3.263425 AGGACCCGATTGCTTTTTCTAGA 59.737 43.478 0.00 0.00 0.00 2.43
33 34 4.007659 GGACCCGATTGCTTTTTCTAGAA 58.992 43.478 0.00 0.00 0.00 2.10
34 35 4.457949 GGACCCGATTGCTTTTTCTAGAAA 59.542 41.667 13.99 13.99 0.00 2.52
35 36 5.125578 GGACCCGATTGCTTTTTCTAGAAAT 59.874 40.000 18.37 2.61 0.00 2.17
36 37 6.317893 GGACCCGATTGCTTTTTCTAGAAATA 59.682 38.462 18.37 12.76 0.00 1.40
37 38 7.013369 GGACCCGATTGCTTTTTCTAGAAATAT 59.987 37.037 18.37 7.62 0.00 1.28
38 39 8.293699 ACCCGATTGCTTTTTCTAGAAATATT 57.706 30.769 18.37 1.75 0.00 1.28
39 40 8.749354 ACCCGATTGCTTTTTCTAGAAATATTT 58.251 29.630 18.37 0.00 0.00 1.40
49 50 8.726870 TTTTCTAGAAATATTTACAGGACCCG 57.273 34.615 18.37 0.00 0.00 5.28
50 51 7.664552 TTCTAGAAATATTTACAGGACCCGA 57.335 36.000 1.68 0.00 0.00 5.14
51 52 7.850935 TCTAGAAATATTTACAGGACCCGAT 57.149 36.000 0.00 0.00 0.00 4.18
52 53 8.258850 TCTAGAAATATTTACAGGACCCGATT 57.741 34.615 0.00 0.00 0.00 3.34
53 54 8.148351 TCTAGAAATATTTACAGGACCCGATTG 58.852 37.037 0.00 0.00 0.00 2.67
54 55 5.531287 AGAAATATTTACAGGACCCGATTGC 59.469 40.000 0.00 0.00 0.00 3.56
55 56 4.706842 ATATTTACAGGACCCGATTGCT 57.293 40.909 0.00 0.00 0.00 3.91
56 57 2.871096 TTTACAGGACCCGATTGCTT 57.129 45.000 0.00 0.00 0.00 3.91
57 58 2.871096 TTACAGGACCCGATTGCTTT 57.129 45.000 0.00 0.00 0.00 3.51
58 59 2.871096 TACAGGACCCGATTGCTTTT 57.129 45.000 0.00 0.00 0.00 2.27
59 60 1.995376 ACAGGACCCGATTGCTTTTT 58.005 45.000 0.00 0.00 0.00 1.94
60 61 3.149005 ACAGGACCCGATTGCTTTTTA 57.851 42.857 0.00 0.00 0.00 1.52
61 62 3.697166 ACAGGACCCGATTGCTTTTTAT 58.303 40.909 0.00 0.00 0.00 1.40
62 63 4.086457 ACAGGACCCGATTGCTTTTTATT 58.914 39.130 0.00 0.00 0.00 1.40
63 64 4.526650 ACAGGACCCGATTGCTTTTTATTT 59.473 37.500 0.00 0.00 0.00 1.40
64 65 5.011635 ACAGGACCCGATTGCTTTTTATTTT 59.988 36.000 0.00 0.00 0.00 1.82
65 66 5.931724 CAGGACCCGATTGCTTTTTATTTTT 59.068 36.000 0.00 0.00 0.00 1.94
82 83 2.397044 TTTTTGGCAGGGACCTGATT 57.603 45.000 22.03 0.00 46.30 2.57
83 84 1.631405 TTTTGGCAGGGACCTGATTG 58.369 50.000 22.03 0.00 46.30 2.67
84 85 0.776810 TTTGGCAGGGACCTGATTGA 59.223 50.000 22.03 2.07 46.30 2.57
85 86 1.002069 TTGGCAGGGACCTGATTGAT 58.998 50.000 22.03 0.00 46.30 2.57
86 87 1.002069 TGGCAGGGACCTGATTGATT 58.998 50.000 22.03 0.00 46.30 2.57
87 88 1.358787 TGGCAGGGACCTGATTGATTT 59.641 47.619 22.03 0.00 46.30 2.17
88 89 2.225343 TGGCAGGGACCTGATTGATTTT 60.225 45.455 22.03 0.00 46.30 1.82
89 90 3.011144 TGGCAGGGACCTGATTGATTTTA 59.989 43.478 22.03 0.00 46.30 1.52
90 91 4.218312 GGCAGGGACCTGATTGATTTTAT 58.782 43.478 22.03 0.00 46.30 1.40
91 92 4.038402 GGCAGGGACCTGATTGATTTTATG 59.962 45.833 22.03 0.00 46.30 1.90
92 93 4.500375 GCAGGGACCTGATTGATTTTATGC 60.500 45.833 22.03 0.00 46.30 3.14
93 94 4.038402 CAGGGACCTGATTGATTTTATGCC 59.962 45.833 13.06 0.00 46.30 4.40
94 95 3.960102 GGGACCTGATTGATTTTATGCCA 59.040 43.478 0.00 0.00 0.00 4.92
95 96 4.202151 GGGACCTGATTGATTTTATGCCAC 60.202 45.833 0.00 0.00 0.00 5.01
96 97 4.498009 GGACCTGATTGATTTTATGCCACG 60.498 45.833 0.00 0.00 0.00 4.94
97 98 4.016444 ACCTGATTGATTTTATGCCACGT 58.984 39.130 0.00 0.00 0.00 4.49
98 99 4.096382 ACCTGATTGATTTTATGCCACGTC 59.904 41.667 0.00 0.00 0.00 4.34
99 100 4.096231 CCTGATTGATTTTATGCCACGTCA 59.904 41.667 0.00 0.00 0.00 4.35
100 101 5.233957 TGATTGATTTTATGCCACGTCAG 57.766 39.130 0.00 0.00 0.00 3.51
101 102 4.699735 TGATTGATTTTATGCCACGTCAGT 59.300 37.500 0.00 0.00 0.00 3.41
102 103 5.182950 TGATTGATTTTATGCCACGTCAGTT 59.817 36.000 0.00 0.00 0.00 3.16
103 104 6.372937 TGATTGATTTTATGCCACGTCAGTTA 59.627 34.615 0.00 0.00 0.00 2.24
104 105 6.561737 TTGATTTTATGCCACGTCAGTTAA 57.438 33.333 0.00 0.00 0.00 2.01
105 106 5.933790 TGATTTTATGCCACGTCAGTTAAC 58.066 37.500 0.00 0.00 0.00 2.01
107 108 1.999048 TATGCCACGTCAGTTAACGG 58.001 50.000 0.00 0.00 46.72 4.44
108 109 0.034337 ATGCCACGTCAGTTAACGGT 59.966 50.000 5.64 0.00 46.72 4.83
109 110 0.598158 TGCCACGTCAGTTAACGGTC 60.598 55.000 5.64 0.00 46.72 4.79
110 111 0.598158 GCCACGTCAGTTAACGGTCA 60.598 55.000 5.64 0.00 46.72 4.02
111 112 1.855513 CCACGTCAGTTAACGGTCAA 58.144 50.000 5.64 0.00 46.72 3.18
112 113 2.203401 CCACGTCAGTTAACGGTCAAA 58.797 47.619 5.64 0.00 46.72 2.69
113 114 2.033492 CCACGTCAGTTAACGGTCAAAC 60.033 50.000 5.64 0.00 46.72 2.93
114 115 2.604011 CACGTCAGTTAACGGTCAAACA 59.396 45.455 5.64 0.00 46.72 2.83
115 116 3.062369 CACGTCAGTTAACGGTCAAACAA 59.938 43.478 5.64 0.00 46.72 2.83
116 117 3.683822 ACGTCAGTTAACGGTCAAACAAA 59.316 39.130 5.64 0.00 46.72 2.83
117 118 4.153835 ACGTCAGTTAACGGTCAAACAAAA 59.846 37.500 5.64 0.00 46.72 2.44
118 119 4.492998 CGTCAGTTAACGGTCAAACAAAAC 59.507 41.667 5.64 0.00 38.96 2.43
119 120 4.492998 GTCAGTTAACGGTCAAACAAAACG 59.507 41.667 5.64 0.00 0.00 3.60
120 121 3.787105 CAGTTAACGGTCAAACAAAACGG 59.213 43.478 0.00 0.00 0.00 4.44
121 122 3.439825 AGTTAACGGTCAAACAAAACGGT 59.560 39.130 0.00 0.00 0.00 4.83
122 123 2.547913 AACGGTCAAACAAAACGGTC 57.452 45.000 0.00 0.00 0.00 4.79
123 124 1.451067 ACGGTCAAACAAAACGGTCA 58.549 45.000 0.00 0.00 0.00 4.02
124 125 1.811359 ACGGTCAAACAAAACGGTCAA 59.189 42.857 0.00 0.00 0.00 3.18
125 126 2.228343 ACGGTCAAACAAAACGGTCAAA 59.772 40.909 0.00 0.00 0.00 2.69
126 127 2.595095 CGGTCAAACAAAACGGTCAAAC 59.405 45.455 0.00 0.00 0.00 2.93
127 128 3.576648 GGTCAAACAAAACGGTCAAACA 58.423 40.909 0.00 0.00 0.00 2.83
128 129 3.988517 GGTCAAACAAAACGGTCAAACAA 59.011 39.130 0.00 0.00 0.00 2.83
129 130 4.627900 GGTCAAACAAAACGGTCAAACAAT 59.372 37.500 0.00 0.00 0.00 2.71
130 131 5.220322 GGTCAAACAAAACGGTCAAACAATC 60.220 40.000 0.00 0.00 0.00 2.67
131 132 5.346281 GTCAAACAAAACGGTCAAACAATCA 59.654 36.000 0.00 0.00 0.00 2.57
132 133 5.574830 TCAAACAAAACGGTCAAACAATCAG 59.425 36.000 0.00 0.00 0.00 2.90
133 134 4.974368 ACAAAACGGTCAAACAATCAGA 57.026 36.364 0.00 0.00 0.00 3.27
134 135 4.920376 ACAAAACGGTCAAACAATCAGAG 58.080 39.130 0.00 0.00 0.00 3.35
135 136 3.626028 AAACGGTCAAACAATCAGAGC 57.374 42.857 0.00 0.00 0.00 4.09
136 137 2.550830 ACGGTCAAACAATCAGAGCT 57.449 45.000 0.00 0.00 0.00 4.09
137 138 2.417719 ACGGTCAAACAATCAGAGCTC 58.582 47.619 5.27 5.27 0.00 4.09
138 139 2.037772 ACGGTCAAACAATCAGAGCTCT 59.962 45.455 11.45 11.45 0.00 4.09
139 140 3.070018 CGGTCAAACAATCAGAGCTCTT 58.930 45.455 15.27 0.00 0.00 2.85
140 141 4.245660 CGGTCAAACAATCAGAGCTCTTA 58.754 43.478 15.27 6.83 0.00 2.10
141 142 4.092091 CGGTCAAACAATCAGAGCTCTTAC 59.908 45.833 15.27 1.46 0.00 2.34
142 143 4.997395 GGTCAAACAATCAGAGCTCTTACA 59.003 41.667 15.27 0.76 0.00 2.41
143 144 5.106908 GGTCAAACAATCAGAGCTCTTACAC 60.107 44.000 15.27 0.00 0.00 2.90
144 145 4.686091 TCAAACAATCAGAGCTCTTACACG 59.314 41.667 15.27 2.07 0.00 4.49
145 146 2.611518 ACAATCAGAGCTCTTACACGC 58.388 47.619 15.27 0.00 0.00 5.34
146 147 1.585668 CAATCAGAGCTCTTACACGCG 59.414 52.381 15.27 3.53 0.00 6.01
147 148 0.101399 ATCAGAGCTCTTACACGCGG 59.899 55.000 15.27 0.00 0.00 6.46
148 149 1.517257 CAGAGCTCTTACACGCGGG 60.517 63.158 15.27 6.92 0.00 6.13
149 150 2.886124 GAGCTCTTACACGCGGGC 60.886 66.667 9.12 1.19 0.00 6.13
150 151 4.452733 AGCTCTTACACGCGGGCC 62.453 66.667 9.12 0.00 0.00 5.80
152 153 4.077184 CTCTTACACGCGGGCCCA 62.077 66.667 24.92 0.00 0.00 5.36
153 154 3.599285 CTCTTACACGCGGGCCCAA 62.599 63.158 24.92 6.15 0.00 4.12
154 155 3.428282 CTTACACGCGGGCCCAAC 61.428 66.667 24.92 12.72 0.00 3.77
162 163 2.035626 CGGGCCCAACCTGTCATT 59.964 61.111 24.92 0.00 40.35 2.57
163 164 1.301623 CGGGCCCAACCTGTCATTA 59.698 57.895 24.92 0.00 40.35 1.90
164 165 0.106719 CGGGCCCAACCTGTCATTAT 60.107 55.000 24.92 0.00 40.35 1.28
165 166 1.692411 GGGCCCAACCTGTCATTATC 58.308 55.000 19.95 0.00 39.10 1.75
166 167 1.308998 GGCCCAACCTGTCATTATCG 58.691 55.000 0.00 0.00 34.51 2.92
167 168 0.663153 GCCCAACCTGTCATTATCGC 59.337 55.000 0.00 0.00 0.00 4.58
168 169 0.937304 CCCAACCTGTCATTATCGCG 59.063 55.000 0.00 0.00 0.00 5.87
169 170 1.472552 CCCAACCTGTCATTATCGCGA 60.473 52.381 13.09 13.09 0.00 5.87
170 171 2.483876 CCAACCTGTCATTATCGCGAT 58.516 47.619 26.78 26.78 0.00 4.58
171 172 2.476619 CCAACCTGTCATTATCGCGATC 59.523 50.000 27.45 11.52 0.00 3.69
172 173 2.051879 ACCTGTCATTATCGCGATCG 57.948 50.000 27.45 15.44 0.00 3.69
173 174 1.335964 ACCTGTCATTATCGCGATCGG 60.336 52.381 27.45 15.36 36.13 4.18
174 175 1.335964 CCTGTCATTATCGCGATCGGT 60.336 52.381 27.45 9.99 36.13 4.69
175 176 2.394708 CTGTCATTATCGCGATCGGTT 58.605 47.619 27.45 4.26 36.13 4.44
176 177 2.124122 TGTCATTATCGCGATCGGTTG 58.876 47.619 27.45 17.79 36.13 3.77
177 178 2.124903 GTCATTATCGCGATCGGTTGT 58.875 47.619 27.45 2.48 36.13 3.32
178 179 3.243134 TGTCATTATCGCGATCGGTTGTA 60.243 43.478 27.45 2.51 36.13 2.41
179 180 3.732219 GTCATTATCGCGATCGGTTGTAA 59.268 43.478 27.45 12.91 36.13 2.41
180 181 4.207635 GTCATTATCGCGATCGGTTGTAAA 59.792 41.667 27.45 12.10 36.13 2.01
181 182 4.804665 TCATTATCGCGATCGGTTGTAAAA 59.195 37.500 27.45 11.32 36.13 1.52
182 183 4.503767 TTATCGCGATCGGTTGTAAAAC 57.496 40.909 27.45 0.00 36.13 2.43
183 184 1.780806 TCGCGATCGGTTGTAAAACA 58.219 45.000 18.30 0.00 27.66 2.83
184 185 1.456544 TCGCGATCGGTTGTAAAACAC 59.543 47.619 18.30 0.00 27.66 3.32
185 186 1.192757 CGCGATCGGTTGTAAAACACA 59.807 47.619 18.30 0.00 27.66 3.72
186 187 2.348685 CGCGATCGGTTGTAAAACACAA 60.349 45.455 18.30 0.00 44.97 3.33
196 197 3.971150 TGTAAAACACAAGGCGATTTGG 58.029 40.909 4.67 0.00 32.95 3.28
197 198 2.524569 AAAACACAAGGCGATTTGGG 57.475 45.000 0.64 0.64 37.49 4.12
198 199 1.408969 AAACACAAGGCGATTTGGGT 58.591 45.000 1.85 1.85 46.21 4.51
199 200 1.408969 AACACAAGGCGATTTGGGTT 58.591 45.000 12.46 12.46 46.80 4.11
200 201 1.408969 ACACAAGGCGATTTGGGTTT 58.591 45.000 1.85 0.00 41.77 3.27
201 202 1.760029 ACACAAGGCGATTTGGGTTTT 59.240 42.857 1.85 0.00 41.77 2.43
202 203 2.169561 ACACAAGGCGATTTGGGTTTTT 59.830 40.909 1.85 0.00 41.77 1.94
220 221 4.681835 TTTTTGAGACAACCGACGAAAA 57.318 36.364 0.00 0.00 0.00 2.29
221 222 4.681835 TTTTGAGACAACCGACGAAAAA 57.318 36.364 0.00 0.00 0.00 1.94
241 242 5.818678 AAAAGTGGTAGGTATCAGTCACA 57.181 39.130 0.00 0.00 0.00 3.58
242 243 5.818678 AAAGTGGTAGGTATCAGTCACAA 57.181 39.130 0.00 0.00 0.00 3.33
243 244 5.818678 AAGTGGTAGGTATCAGTCACAAA 57.181 39.130 0.00 0.00 0.00 2.83
244 245 5.148651 AGTGGTAGGTATCAGTCACAAAC 57.851 43.478 0.00 0.00 0.00 2.93
245 246 4.591498 AGTGGTAGGTATCAGTCACAAACA 59.409 41.667 0.00 0.00 0.00 2.83
246 247 5.071250 AGTGGTAGGTATCAGTCACAAACAA 59.929 40.000 0.00 0.00 0.00 2.83
247 248 5.761234 GTGGTAGGTATCAGTCACAAACAAA 59.239 40.000 0.00 0.00 0.00 2.83
248 249 6.261381 GTGGTAGGTATCAGTCACAAACAAAA 59.739 38.462 0.00 0.00 0.00 2.44
249 250 6.829298 TGGTAGGTATCAGTCACAAACAAAAA 59.171 34.615 0.00 0.00 0.00 1.94
282 283 5.699097 TTTTGGAACCATAGGACGAAAAG 57.301 39.130 0.00 0.00 0.00 2.27
283 284 4.360951 TTGGAACCATAGGACGAAAAGT 57.639 40.909 0.00 0.00 0.00 2.66
284 285 3.670625 TGGAACCATAGGACGAAAAGTG 58.329 45.455 0.00 0.00 0.00 3.16
285 286 3.007635 GGAACCATAGGACGAAAAGTGG 58.992 50.000 0.00 0.00 0.00 4.00
286 287 3.558533 GGAACCATAGGACGAAAAGTGGT 60.559 47.826 0.00 0.00 41.42 4.16
287 288 4.322953 GGAACCATAGGACGAAAAGTGGTA 60.323 45.833 6.90 0.00 38.91 3.25
288 289 4.467198 ACCATAGGACGAAAAGTGGTAG 57.533 45.455 0.00 0.00 38.13 3.18
289 290 3.836562 ACCATAGGACGAAAAGTGGTAGT 59.163 43.478 0.00 0.00 38.13 2.73
290 291 4.285260 ACCATAGGACGAAAAGTGGTAGTT 59.715 41.667 0.00 0.00 38.13 2.24
291 292 5.221783 ACCATAGGACGAAAAGTGGTAGTTT 60.222 40.000 0.00 0.00 38.13 2.66
292 293 5.704053 CCATAGGACGAAAAGTGGTAGTTTT 59.296 40.000 0.00 0.00 33.74 2.43
293 294 6.875195 CCATAGGACGAAAAGTGGTAGTTTTA 59.125 38.462 0.00 0.00 31.40 1.52
294 295 7.551617 CCATAGGACGAAAAGTGGTAGTTTTAT 59.448 37.037 0.00 0.00 31.40 1.40
295 296 6.796705 AGGACGAAAAGTGGTAGTTTTATG 57.203 37.500 0.00 0.00 31.40 1.90
296 297 5.180680 AGGACGAAAAGTGGTAGTTTTATGC 59.819 40.000 0.00 0.00 31.40 3.14
297 298 5.180680 GGACGAAAAGTGGTAGTTTTATGCT 59.819 40.000 0.00 0.00 31.40 3.79
298 299 6.369615 GGACGAAAAGTGGTAGTTTTATGCTA 59.630 38.462 0.00 0.00 31.40 3.49
299 300 7.065443 GGACGAAAAGTGGTAGTTTTATGCTAT 59.935 37.037 0.00 0.00 31.40 2.97
300 301 7.748847 ACGAAAAGTGGTAGTTTTATGCTATG 58.251 34.615 0.00 0.00 31.40 2.23
301 302 7.389607 ACGAAAAGTGGTAGTTTTATGCTATGT 59.610 33.333 0.00 0.00 31.40 2.29
302 303 8.875803 CGAAAAGTGGTAGTTTTATGCTATGTA 58.124 33.333 0.00 0.00 31.40 2.29
303 304 9.983804 GAAAAGTGGTAGTTTTATGCTATGTAC 57.016 33.333 0.00 0.00 31.40 2.90
304 305 9.734984 AAAAGTGGTAGTTTTATGCTATGTACT 57.265 29.630 0.00 0.00 29.59 2.73
305 306 8.943909 AAGTGGTAGTTTTATGCTATGTACTC 57.056 34.615 0.00 0.00 0.00 2.59
369 371 2.025981 CCTGAAACATGGATGGACCTGA 60.026 50.000 0.00 0.00 39.86 3.86
381 383 4.156739 GGATGGACCTGATTGAAAGACAAC 59.843 45.833 0.00 0.00 37.20 3.32
428 430 4.759693 TGACCGAATAGAACAAGTTGCAAT 59.240 37.500 0.59 0.00 0.00 3.56
429 431 5.240623 TGACCGAATAGAACAAGTTGCAATT 59.759 36.000 0.59 0.00 0.00 2.32
430 432 5.699839 ACCGAATAGAACAAGTTGCAATTC 58.300 37.500 0.59 1.99 0.00 2.17
431 433 5.095490 CCGAATAGAACAAGTTGCAATTCC 58.905 41.667 0.59 0.00 0.00 3.01
432 434 5.335583 CCGAATAGAACAAGTTGCAATTCCA 60.336 40.000 0.59 0.00 0.00 3.53
433 435 6.148948 CGAATAGAACAAGTTGCAATTCCAA 58.851 36.000 0.59 0.00 0.00 3.53
434 436 6.808212 CGAATAGAACAAGTTGCAATTCCAAT 59.192 34.615 0.59 0.00 0.00 3.16
482 484 5.060662 TGAGAGAAGGATACGTGAAACAG 57.939 43.478 0.00 0.00 46.39 3.16
516 518 6.753180 TGCTGCAAAGTTGACCATTTATTTA 58.247 32.000 0.00 0.00 0.00 1.40
518 520 6.868339 GCTGCAAAGTTGACCATTTATTTACT 59.132 34.615 0.00 0.00 0.00 2.24
537 540 8.868522 ATTTACTGAGAAACAATTGATCCTGA 57.131 30.769 13.59 0.00 0.00 3.86
616 644 6.261381 TCACCACACAACTGAAATAAGTAACC 59.739 38.462 0.00 0.00 0.00 2.85
669 698 0.250901 AATTTGAGCACGAGTGGCCT 60.251 50.000 3.32 0.00 0.00 5.19
1135 1221 4.019051 CCCATATGCTCCATTCACCAGATA 60.019 45.833 0.00 0.00 0.00 1.98
1681 1777 0.106669 GGTCCTTGATAGTTGGGGGC 60.107 60.000 0.00 0.00 0.00 5.80
1911 2009 1.530013 GGCCTTCTTGTGCATGTGCT 61.530 55.000 6.55 0.00 42.66 4.40
2052 2159 8.265764 GGTAATGACCAAAGTAAGAATACCTCT 58.734 37.037 0.00 0.00 46.12 3.69
2477 2590 2.119495 CTTACCAGGAGTATGGCCAGT 58.881 52.381 13.05 3.03 44.80 4.00
2667 2780 0.326927 TAAACCAAGGCGGGGAAGAG 59.673 55.000 4.45 0.00 40.22 2.85
2821 2943 7.868906 ACTTTGTTTAGTAGCACAAGGTTAA 57.131 32.000 6.35 0.00 39.45 2.01
3252 3383 2.092103 GGGTGGCCAACAGTTATGGATA 60.092 50.000 25.24 0.00 40.56 2.59
3428 3566 1.240641 TGCAACAACATGCTACCCCG 61.241 55.000 0.00 0.00 46.54 5.73
3539 3678 2.902705 TCCTGTTTGAGTAAGCACGT 57.097 45.000 0.00 0.00 0.00 4.49
3541 3680 2.101750 TCCTGTTTGAGTAAGCACGTCA 59.898 45.455 0.00 0.00 0.00 4.35
3551 3695 7.739498 TGAGTAAGCACGTCATGTATCTATA 57.261 36.000 0.00 0.00 0.00 1.31
3552 3696 8.336801 TGAGTAAGCACGTCATGTATCTATAT 57.663 34.615 0.00 0.00 0.00 0.86
3553 3697 8.793592 TGAGTAAGCACGTCATGTATCTATATT 58.206 33.333 0.00 0.00 0.00 1.28
3603 3747 5.220970 GGTTTGAAATTCTTCACCAAGTCGA 60.221 40.000 0.00 0.00 41.34 4.20
3644 3788 7.995289 TGTATATTGTAATGAAAAGCCACCAG 58.005 34.615 0.00 0.00 0.00 4.00
3672 3817 0.234106 CAGATAGCAGCGCCAAATCG 59.766 55.000 2.29 0.00 0.00 3.34
3717 3862 4.112341 GCTTTGCTGCAGAGGCCG 62.112 66.667 20.43 1.83 40.13 6.13
3756 3901 7.350744 TGCAAAATCAATAGGCTTCATGTAT 57.649 32.000 0.00 0.00 0.00 2.29
3764 3909 3.170791 AGGCTTCATGTATGTGAGTCG 57.829 47.619 0.00 0.00 0.00 4.18
3846 3992 3.255888 TCCACGAGCCACTAATATGCTAG 59.744 47.826 0.00 0.00 34.99 3.42
3856 4002 9.877178 AGCCACTAATATGCTAGTATTGAATAC 57.123 33.333 7.23 7.23 32.56 1.89
3876 4022 1.019278 CGTATTTGACCACTGCGCCT 61.019 55.000 4.18 0.00 0.00 5.52
3877 4023 1.737696 CGTATTTGACCACTGCGCCTA 60.738 52.381 4.18 0.00 0.00 3.93
3966 4210 0.396435 ATGTGAGCTCGGGTGAACAA 59.604 50.000 9.64 0.00 0.00 2.83
3974 4218 4.589908 AGCTCGGGTGAACAATAAAATCT 58.410 39.130 0.00 0.00 0.00 2.40
4045 4289 3.476552 AGCTTCCAAAGTTTCGTCATGA 58.523 40.909 0.00 0.00 0.00 3.07
4046 4290 3.882888 AGCTTCCAAAGTTTCGTCATGAA 59.117 39.130 0.00 0.00 33.85 2.57
4047 4291 3.975035 GCTTCCAAAGTTTCGTCATGAAC 59.025 43.478 0.00 0.00 35.97 3.18
4048 4292 4.497340 GCTTCCAAAGTTTCGTCATGAACA 60.497 41.667 0.00 0.00 35.97 3.18
4049 4293 5.762045 CTTCCAAAGTTTCGTCATGAACAT 58.238 37.500 0.00 0.00 35.97 2.71
4050 4294 5.107109 TCCAAAGTTTCGTCATGAACATG 57.893 39.130 0.00 8.31 35.97 3.21
4051 4295 4.578516 TCCAAAGTTTCGTCATGAACATGT 59.421 37.500 13.35 0.00 39.72 3.21
4052 4296 4.676471 CCAAAGTTTCGTCATGAACATGTG 59.324 41.667 13.35 8.47 39.72 3.21
4053 4297 4.488126 AAGTTTCGTCATGAACATGTGG 57.512 40.909 13.35 7.73 39.72 4.17
4054 4298 3.476552 AGTTTCGTCATGAACATGTGGT 58.523 40.909 13.35 0.00 39.72 4.16
4055 4299 4.637276 AGTTTCGTCATGAACATGTGGTA 58.363 39.130 13.35 0.00 39.72 3.25
4056 4300 5.060506 AGTTTCGTCATGAACATGTGGTAA 58.939 37.500 13.35 5.63 39.72 2.85
4057 4301 5.705441 AGTTTCGTCATGAACATGTGGTAAT 59.295 36.000 13.35 0.00 39.72 1.89
4058 4302 6.876789 AGTTTCGTCATGAACATGTGGTAATA 59.123 34.615 13.35 0.00 39.72 0.98
4059 4303 7.552687 AGTTTCGTCATGAACATGTGGTAATAT 59.447 33.333 13.35 0.00 39.72 1.28
4060 4304 7.857734 TTCGTCATGAACATGTGGTAATATT 57.142 32.000 13.35 0.00 39.72 1.28
4061 4305 8.950208 TTCGTCATGAACATGTGGTAATATTA 57.050 30.769 13.35 0.00 39.72 0.98
4062 4306 8.950208 TCGTCATGAACATGTGGTAATATTAA 57.050 30.769 13.35 0.00 39.72 1.40
4063 4307 9.384764 TCGTCATGAACATGTGGTAATATTAAA 57.615 29.630 13.35 0.00 39.72 1.52
4064 4308 9.995957 CGTCATGAACATGTGGTAATATTAAAA 57.004 29.630 13.35 0.00 39.72 1.52
4192 4436 1.879380 TCCGGTGATGAAACTTTGCAG 59.121 47.619 0.00 0.00 0.00 4.41
4200 4444 6.072508 GGTGATGAAACTTTGCAGTCTATCAA 60.073 38.462 0.00 0.00 32.63 2.57
4284 4528 5.887598 TCTTAGCACTTGTGATGGCAATATT 59.112 36.000 4.79 0.00 0.00 1.28
4288 4532 7.822161 AGCACTTGTGATGGCAATATTTATA 57.178 32.000 4.79 0.00 0.00 0.98
4334 4578 2.031683 CGTTGTTCTTGTTCCGCTCTTT 59.968 45.455 0.00 0.00 0.00 2.52
4338 4582 5.204409 TGTTCTTGTTCCGCTCTTTACTA 57.796 39.130 0.00 0.00 0.00 1.82
4344 4588 1.772836 TCCGCTCTTTACTAGGTCCC 58.227 55.000 0.00 0.00 0.00 4.46
4374 4618 2.383527 CCGAAGCTCCGAGTTGTGC 61.384 63.158 0.00 0.00 0.00 4.57
4379 4623 2.959357 GCTCCGAGTTGTGCTGTGC 61.959 63.158 0.00 0.00 0.00 4.57
4381 4625 1.287730 CTCCGAGTTGTGCTGTGCTC 61.288 60.000 0.00 0.00 0.00 4.26
4384 4628 1.605457 CCGAGTTGTGCTGTGCTCTAA 60.605 52.381 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.812476 CAATCGGGTCCTCGCGCA 62.812 66.667 8.75 0.00 46.89 6.09
7 8 1.305930 AAAAGCAATCGGGTCCTCGC 61.306 55.000 0.00 0.00 0.00 5.03
8 9 1.130561 GAAAAAGCAATCGGGTCCTCG 59.869 52.381 0.00 0.00 0.00 4.63
9 10 2.437413 AGAAAAAGCAATCGGGTCCTC 58.563 47.619 0.00 0.00 0.00 3.71
10 11 2.586648 AGAAAAAGCAATCGGGTCCT 57.413 45.000 0.00 0.00 0.00 3.85
11 12 3.606687 TCTAGAAAAAGCAATCGGGTCC 58.393 45.455 0.00 0.00 0.00 4.46
12 13 5.622770 TTTCTAGAAAAAGCAATCGGGTC 57.377 39.130 15.57 0.00 0.00 4.46
13 14 7.881775 ATATTTCTAGAAAAAGCAATCGGGT 57.118 32.000 21.26 3.69 33.56 5.28
23 24 9.169592 CGGGTCCTGTAAATATTTCTAGAAAAA 57.830 33.333 21.26 0.23 33.56 1.94
24 25 8.542080 TCGGGTCCTGTAAATATTTCTAGAAAA 58.458 33.333 21.26 11.34 33.56 2.29
25 26 8.081517 TCGGGTCCTGTAAATATTTCTAGAAA 57.918 34.615 19.83 19.83 34.46 2.52
26 27 7.664552 TCGGGTCCTGTAAATATTTCTAGAA 57.335 36.000 3.39 0.00 0.00 2.10
27 28 7.850935 ATCGGGTCCTGTAAATATTTCTAGA 57.149 36.000 3.39 0.00 0.00 2.43
28 29 7.095187 GCAATCGGGTCCTGTAAATATTTCTAG 60.095 40.741 3.39 4.51 0.00 2.43
29 30 6.708949 GCAATCGGGTCCTGTAAATATTTCTA 59.291 38.462 3.39 0.00 0.00 2.10
30 31 5.531287 GCAATCGGGTCCTGTAAATATTTCT 59.469 40.000 3.39 0.00 0.00 2.52
31 32 5.531287 AGCAATCGGGTCCTGTAAATATTTC 59.469 40.000 3.39 0.00 0.00 2.17
32 33 5.445964 AGCAATCGGGTCCTGTAAATATTT 58.554 37.500 5.89 5.89 0.00 1.40
33 34 5.048846 AGCAATCGGGTCCTGTAAATATT 57.951 39.130 0.00 0.00 0.00 1.28
34 35 4.706842 AGCAATCGGGTCCTGTAAATAT 57.293 40.909 0.00 0.00 0.00 1.28
35 36 4.497291 AAGCAATCGGGTCCTGTAAATA 57.503 40.909 0.00 0.00 0.00 1.40
36 37 3.366052 AAGCAATCGGGTCCTGTAAAT 57.634 42.857 0.00 0.00 0.00 1.40
37 38 2.871096 AAGCAATCGGGTCCTGTAAA 57.129 45.000 0.00 0.00 0.00 2.01
38 39 2.871096 AAAGCAATCGGGTCCTGTAA 57.129 45.000 0.00 0.00 0.00 2.41
39 40 2.871096 AAAAGCAATCGGGTCCTGTA 57.129 45.000 0.00 0.00 0.00 2.74
40 41 1.995376 AAAAAGCAATCGGGTCCTGT 58.005 45.000 0.00 0.00 0.00 4.00
41 42 4.718940 AATAAAAAGCAATCGGGTCCTG 57.281 40.909 0.00 0.00 0.00 3.86
42 43 5.738619 AAAATAAAAAGCAATCGGGTCCT 57.261 34.783 0.00 0.00 0.00 3.85
63 64 1.969923 CAATCAGGTCCCTGCCAAAAA 59.030 47.619 8.53 0.00 43.31 1.94
64 65 1.146774 TCAATCAGGTCCCTGCCAAAA 59.853 47.619 8.53 0.00 43.31 2.44
65 66 0.776810 TCAATCAGGTCCCTGCCAAA 59.223 50.000 8.53 0.00 43.31 3.28
66 67 1.002069 ATCAATCAGGTCCCTGCCAA 58.998 50.000 8.53 0.00 43.31 4.52
67 68 1.002069 AATCAATCAGGTCCCTGCCA 58.998 50.000 8.53 0.00 43.31 4.92
68 69 2.149973 AAATCAATCAGGTCCCTGCC 57.850 50.000 8.53 0.00 43.31 4.85
69 70 4.500375 GCATAAAATCAATCAGGTCCCTGC 60.500 45.833 8.53 0.00 43.31 4.85
70 71 4.038402 GGCATAAAATCAATCAGGTCCCTG 59.962 45.833 7.02 7.02 44.86 4.45
71 72 4.218312 GGCATAAAATCAATCAGGTCCCT 58.782 43.478 0.00 0.00 0.00 4.20
72 73 3.960102 TGGCATAAAATCAATCAGGTCCC 59.040 43.478 0.00 0.00 0.00 4.46
73 74 4.498009 CGTGGCATAAAATCAATCAGGTCC 60.498 45.833 0.00 0.00 0.00 4.46
74 75 4.096382 ACGTGGCATAAAATCAATCAGGTC 59.904 41.667 0.00 0.00 0.00 3.85
75 76 4.016444 ACGTGGCATAAAATCAATCAGGT 58.984 39.130 0.00 0.00 0.00 4.00
76 77 4.096231 TGACGTGGCATAAAATCAATCAGG 59.904 41.667 0.00 0.00 0.00 3.86
77 78 5.163723 ACTGACGTGGCATAAAATCAATCAG 60.164 40.000 0.00 0.00 34.61 2.90
78 79 4.699735 ACTGACGTGGCATAAAATCAATCA 59.300 37.500 0.00 0.00 0.00 2.57
79 80 5.235305 ACTGACGTGGCATAAAATCAATC 57.765 39.130 0.00 0.00 0.00 2.67
80 81 5.643379 AACTGACGTGGCATAAAATCAAT 57.357 34.783 0.00 0.00 0.00 2.57
81 82 6.375377 GTTAACTGACGTGGCATAAAATCAA 58.625 36.000 0.00 0.00 0.00 2.57
82 83 5.390040 CGTTAACTGACGTGGCATAAAATCA 60.390 40.000 3.71 0.00 38.19 2.57
83 84 5.019498 CGTTAACTGACGTGGCATAAAATC 58.981 41.667 3.71 0.00 38.19 2.17
84 85 4.142773 CCGTTAACTGACGTGGCATAAAAT 60.143 41.667 3.71 0.00 41.26 1.82
85 86 3.186817 CCGTTAACTGACGTGGCATAAAA 59.813 43.478 3.71 0.00 41.26 1.52
86 87 2.737783 CCGTTAACTGACGTGGCATAAA 59.262 45.455 3.71 0.00 41.26 1.40
87 88 2.288948 ACCGTTAACTGACGTGGCATAA 60.289 45.455 3.84 0.00 41.26 1.90
88 89 1.273048 ACCGTTAACTGACGTGGCATA 59.727 47.619 3.84 0.00 41.26 3.14
89 90 0.034337 ACCGTTAACTGACGTGGCAT 59.966 50.000 3.84 0.00 41.26 4.40
90 91 0.598158 GACCGTTAACTGACGTGGCA 60.598 55.000 3.84 0.00 41.26 4.92
91 92 0.598158 TGACCGTTAACTGACGTGGC 60.598 55.000 3.84 0.00 41.26 5.01
92 93 1.855513 TTGACCGTTAACTGACGTGG 58.144 50.000 3.84 0.00 41.26 4.94
93 94 2.604011 TGTTTGACCGTTAACTGACGTG 59.396 45.455 3.84 0.00 41.26 4.49
94 95 2.891112 TGTTTGACCGTTAACTGACGT 58.109 42.857 3.84 0.00 41.26 4.34
95 96 3.929417 TTGTTTGACCGTTAACTGACG 57.071 42.857 3.84 0.00 42.43 4.35
96 97 4.492998 CGTTTTGTTTGACCGTTAACTGAC 59.507 41.667 3.84 0.00 0.00 3.51
97 98 4.437121 CCGTTTTGTTTGACCGTTAACTGA 60.437 41.667 3.84 0.00 0.00 3.41
98 99 3.787105 CCGTTTTGTTTGACCGTTAACTG 59.213 43.478 3.71 0.00 0.00 3.16
99 100 3.439825 ACCGTTTTGTTTGACCGTTAACT 59.560 39.130 3.71 0.00 0.00 2.24
100 101 3.757184 ACCGTTTTGTTTGACCGTTAAC 58.243 40.909 0.00 0.00 0.00 2.01
101 102 3.438087 TGACCGTTTTGTTTGACCGTTAA 59.562 39.130 0.00 0.00 0.00 2.01
102 103 3.005554 TGACCGTTTTGTTTGACCGTTA 58.994 40.909 0.00 0.00 0.00 3.18
103 104 1.811359 TGACCGTTTTGTTTGACCGTT 59.189 42.857 0.00 0.00 0.00 4.44
104 105 1.451067 TGACCGTTTTGTTTGACCGT 58.549 45.000 0.00 0.00 0.00 4.83
105 106 2.546195 TTGACCGTTTTGTTTGACCG 57.454 45.000 0.00 0.00 0.00 4.79
106 107 3.576648 TGTTTGACCGTTTTGTTTGACC 58.423 40.909 0.00 0.00 0.00 4.02
107 108 5.346281 TGATTGTTTGACCGTTTTGTTTGAC 59.654 36.000 0.00 0.00 0.00 3.18
108 109 5.470368 TGATTGTTTGACCGTTTTGTTTGA 58.530 33.333 0.00 0.00 0.00 2.69
109 110 5.574830 TCTGATTGTTTGACCGTTTTGTTTG 59.425 36.000 0.00 0.00 0.00 2.93
110 111 5.715070 TCTGATTGTTTGACCGTTTTGTTT 58.285 33.333 0.00 0.00 0.00 2.83
111 112 5.317733 TCTGATTGTTTGACCGTTTTGTT 57.682 34.783 0.00 0.00 0.00 2.83
112 113 4.733523 GCTCTGATTGTTTGACCGTTTTGT 60.734 41.667 0.00 0.00 0.00 2.83
113 114 3.730715 GCTCTGATTGTTTGACCGTTTTG 59.269 43.478 0.00 0.00 0.00 2.44
114 115 3.632145 AGCTCTGATTGTTTGACCGTTTT 59.368 39.130 0.00 0.00 0.00 2.43
115 116 3.214328 AGCTCTGATTGTTTGACCGTTT 58.786 40.909 0.00 0.00 0.00 3.60
116 117 2.808543 GAGCTCTGATTGTTTGACCGTT 59.191 45.455 6.43 0.00 0.00 4.44
117 118 2.037772 AGAGCTCTGATTGTTTGACCGT 59.962 45.455 17.42 0.00 0.00 4.83
118 119 2.693069 AGAGCTCTGATTGTTTGACCG 58.307 47.619 17.42 0.00 0.00 4.79
119 120 4.997395 TGTAAGAGCTCTGATTGTTTGACC 59.003 41.667 19.06 0.00 0.00 4.02
120 121 5.388890 CGTGTAAGAGCTCTGATTGTTTGAC 60.389 44.000 19.06 5.22 0.00 3.18
121 122 4.686091 CGTGTAAGAGCTCTGATTGTTTGA 59.314 41.667 19.06 0.00 0.00 2.69
122 123 4.667668 GCGTGTAAGAGCTCTGATTGTTTG 60.668 45.833 19.06 4.16 0.00 2.93
123 124 3.433615 GCGTGTAAGAGCTCTGATTGTTT 59.566 43.478 19.06 1.47 0.00 2.83
124 125 2.996621 GCGTGTAAGAGCTCTGATTGTT 59.003 45.455 19.06 2.31 0.00 2.83
125 126 2.611518 GCGTGTAAGAGCTCTGATTGT 58.388 47.619 19.06 3.15 0.00 2.71
126 127 1.585668 CGCGTGTAAGAGCTCTGATTG 59.414 52.381 19.06 7.90 0.00 2.67
127 128 1.469940 CCGCGTGTAAGAGCTCTGATT 60.470 52.381 19.06 4.02 0.00 2.57
128 129 0.101399 CCGCGTGTAAGAGCTCTGAT 59.899 55.000 19.06 4.87 0.00 2.90
129 130 1.506718 CCGCGTGTAAGAGCTCTGA 59.493 57.895 19.06 6.91 0.00 3.27
130 131 1.517257 CCCGCGTGTAAGAGCTCTG 60.517 63.158 19.06 5.21 0.00 3.35
131 132 2.885861 CCCGCGTGTAAGAGCTCT 59.114 61.111 11.45 11.45 0.00 4.09
132 133 2.886124 GCCCGCGTGTAAGAGCTC 60.886 66.667 5.27 5.27 0.00 4.09
133 134 4.452733 GGCCCGCGTGTAAGAGCT 62.453 66.667 4.92 0.00 0.00 4.09
135 136 3.599285 TTGGGCCCGCGTGTAAGAG 62.599 63.158 19.37 0.00 0.00 2.85
136 137 3.627952 TTGGGCCCGCGTGTAAGA 61.628 61.111 19.37 0.00 0.00 2.10
137 138 3.428282 GTTGGGCCCGCGTGTAAG 61.428 66.667 19.37 0.00 0.00 2.34
144 145 2.830186 TAATGACAGGTTGGGCCCGC 62.830 60.000 19.37 12.84 38.26 6.13
145 146 0.106719 ATAATGACAGGTTGGGCCCG 60.107 55.000 19.37 4.36 38.26 6.13
146 147 1.692411 GATAATGACAGGTTGGGCCC 58.308 55.000 17.59 17.59 38.26 5.80
147 148 1.308998 CGATAATGACAGGTTGGGCC 58.691 55.000 0.00 0.00 37.58 5.80
148 149 0.663153 GCGATAATGACAGGTTGGGC 59.337 55.000 0.00 0.00 0.00 5.36
149 150 0.937304 CGCGATAATGACAGGTTGGG 59.063 55.000 0.00 0.00 0.00 4.12
150 151 1.934589 TCGCGATAATGACAGGTTGG 58.065 50.000 3.71 0.00 0.00 3.77
151 152 2.153817 CGATCGCGATAATGACAGGTTG 59.846 50.000 23.76 0.00 40.82 3.77
152 153 2.394708 CGATCGCGATAATGACAGGTT 58.605 47.619 23.76 0.00 40.82 3.50
153 154 1.335964 CCGATCGCGATAATGACAGGT 60.336 52.381 23.76 0.00 40.82 4.00
154 155 1.335964 ACCGATCGCGATAATGACAGG 60.336 52.381 23.76 17.35 40.82 4.00
155 156 2.051879 ACCGATCGCGATAATGACAG 57.948 50.000 23.76 3.90 40.82 3.51
156 157 2.124122 CAACCGATCGCGATAATGACA 58.876 47.619 23.76 0.00 40.82 3.58
157 158 2.124903 ACAACCGATCGCGATAATGAC 58.875 47.619 23.76 8.20 40.82 3.06
158 159 2.502213 ACAACCGATCGCGATAATGA 57.498 45.000 23.76 0.00 40.82 2.57
159 160 4.702247 TTTACAACCGATCGCGATAATG 57.298 40.909 23.76 19.22 40.82 1.90
160 161 4.567558 TGTTTTACAACCGATCGCGATAAT 59.432 37.500 23.76 7.54 40.82 1.28
161 162 3.925299 TGTTTTACAACCGATCGCGATAA 59.075 39.130 23.76 7.92 40.82 1.75
162 163 3.304026 GTGTTTTACAACCGATCGCGATA 59.696 43.478 23.76 0.57 40.82 2.92
163 164 2.093152 GTGTTTTACAACCGATCGCGAT 59.907 45.455 23.97 23.97 40.82 4.58
164 165 1.456544 GTGTTTTACAACCGATCGCGA 59.543 47.619 13.09 13.09 40.82 5.87
165 166 1.192757 TGTGTTTTACAACCGATCGCG 59.807 47.619 10.32 0.00 36.06 5.87
166 167 2.953640 TGTGTTTTACAACCGATCGC 57.046 45.000 10.32 0.00 36.06 4.58
167 168 3.805823 CCTTGTGTTTTACAACCGATCG 58.194 45.455 8.51 8.51 44.07 3.69
168 169 3.561503 GCCTTGTGTTTTACAACCGATC 58.438 45.455 0.00 0.00 44.07 3.69
169 170 2.031508 CGCCTTGTGTTTTACAACCGAT 60.032 45.455 0.00 0.00 44.07 4.18
170 171 1.331138 CGCCTTGTGTTTTACAACCGA 59.669 47.619 0.00 0.00 44.07 4.69
171 172 1.331138 TCGCCTTGTGTTTTACAACCG 59.669 47.619 0.00 0.00 44.07 4.44
172 173 3.636282 ATCGCCTTGTGTTTTACAACC 57.364 42.857 0.00 0.00 44.07 3.77
173 174 4.208253 CCAAATCGCCTTGTGTTTTACAAC 59.792 41.667 0.00 0.00 44.07 3.32
174 175 4.363999 CCAAATCGCCTTGTGTTTTACAA 58.636 39.130 0.00 0.00 46.62 2.41
175 176 3.243569 CCCAAATCGCCTTGTGTTTTACA 60.244 43.478 0.00 0.00 37.56 2.41
176 177 3.243602 ACCCAAATCGCCTTGTGTTTTAC 60.244 43.478 0.00 0.00 0.00 2.01
177 178 2.959707 ACCCAAATCGCCTTGTGTTTTA 59.040 40.909 0.00 0.00 0.00 1.52
178 179 1.760029 ACCCAAATCGCCTTGTGTTTT 59.240 42.857 0.00 0.00 0.00 2.43
179 180 1.408969 ACCCAAATCGCCTTGTGTTT 58.591 45.000 0.00 0.00 0.00 2.83
180 181 1.408969 AACCCAAATCGCCTTGTGTT 58.591 45.000 0.00 0.00 0.00 3.32
181 182 1.408969 AAACCCAAATCGCCTTGTGT 58.591 45.000 0.00 0.00 0.00 3.72
182 183 2.524569 AAAACCCAAATCGCCTTGTG 57.475 45.000 0.00 0.00 0.00 3.33
199 200 4.681835 TTTTCGTCGGTTGTCTCAAAAA 57.318 36.364 0.00 0.00 0.00 1.94
200 201 4.681835 TTTTTCGTCGGTTGTCTCAAAA 57.318 36.364 0.00 0.00 0.00 2.44
218 219 6.182507 TGTGACTGATACCTACCACTTTTT 57.817 37.500 0.00 0.00 0.00 1.94
219 220 5.818678 TGTGACTGATACCTACCACTTTT 57.181 39.130 0.00 0.00 0.00 2.27
220 221 5.818678 TTGTGACTGATACCTACCACTTT 57.181 39.130 0.00 0.00 0.00 2.66
221 222 5.071250 TGTTTGTGACTGATACCTACCACTT 59.929 40.000 0.00 0.00 0.00 3.16
222 223 4.591498 TGTTTGTGACTGATACCTACCACT 59.409 41.667 0.00 0.00 0.00 4.00
223 224 4.890088 TGTTTGTGACTGATACCTACCAC 58.110 43.478 0.00 0.00 0.00 4.16
224 225 5.554437 TTGTTTGTGACTGATACCTACCA 57.446 39.130 0.00 0.00 0.00 3.25
225 226 6.870971 TTTTGTTTGTGACTGATACCTACC 57.129 37.500 0.00 0.00 0.00 3.18
259 260 5.595133 ACTTTTCGTCCTATGGTTCCAAAAA 59.405 36.000 0.00 0.00 0.00 1.94
260 261 5.009210 CACTTTTCGTCCTATGGTTCCAAAA 59.991 40.000 0.00 0.00 0.00 2.44
261 262 4.517453 CACTTTTCGTCCTATGGTTCCAAA 59.483 41.667 0.00 0.00 0.00 3.28
262 263 4.069304 CACTTTTCGTCCTATGGTTCCAA 58.931 43.478 0.00 0.00 0.00 3.53
263 264 3.558321 CCACTTTTCGTCCTATGGTTCCA 60.558 47.826 0.00 0.00 0.00 3.53
264 265 3.007635 CCACTTTTCGTCCTATGGTTCC 58.992 50.000 0.00 0.00 0.00 3.62
265 266 3.671716 ACCACTTTTCGTCCTATGGTTC 58.328 45.455 0.00 0.00 37.12 3.62
266 267 3.782656 ACCACTTTTCGTCCTATGGTT 57.217 42.857 0.00 0.00 37.12 3.67
267 268 3.836562 ACTACCACTTTTCGTCCTATGGT 59.163 43.478 8.15 8.15 42.90 3.55
268 269 4.467198 ACTACCACTTTTCGTCCTATGG 57.533 45.455 0.00 0.00 0.00 2.74
269 270 6.796705 AAAACTACCACTTTTCGTCCTATG 57.203 37.500 0.00 0.00 0.00 2.23
270 271 7.065443 GCATAAAACTACCACTTTTCGTCCTAT 59.935 37.037 0.00 0.00 0.00 2.57
271 272 6.369615 GCATAAAACTACCACTTTTCGTCCTA 59.630 38.462 0.00 0.00 0.00 2.94
272 273 5.180680 GCATAAAACTACCACTTTTCGTCCT 59.819 40.000 0.00 0.00 0.00 3.85
273 274 5.180680 AGCATAAAACTACCACTTTTCGTCC 59.819 40.000 0.00 0.00 0.00 4.79
274 275 6.237313 AGCATAAAACTACCACTTTTCGTC 57.763 37.500 0.00 0.00 0.00 4.20
275 276 7.389607 ACATAGCATAAAACTACCACTTTTCGT 59.610 33.333 0.00 0.00 0.00 3.85
276 277 7.748847 ACATAGCATAAAACTACCACTTTTCG 58.251 34.615 0.00 0.00 0.00 3.46
277 278 9.983804 GTACATAGCATAAAACTACCACTTTTC 57.016 33.333 0.00 0.00 0.00 2.29
278 279 9.734984 AGTACATAGCATAAAACTACCACTTTT 57.265 29.630 0.00 0.00 0.00 2.27
279 280 9.379791 GAGTACATAGCATAAAACTACCACTTT 57.620 33.333 0.00 0.00 0.00 2.66
280 281 7.985752 GGAGTACATAGCATAAAACTACCACTT 59.014 37.037 0.00 0.00 0.00 3.16
281 282 7.418712 GGGAGTACATAGCATAAAACTACCACT 60.419 40.741 0.00 0.00 37.79 4.00
282 283 6.704937 GGGAGTACATAGCATAAAACTACCAC 59.295 42.308 0.00 0.00 37.79 4.16
283 284 6.183361 GGGGAGTACATAGCATAAAACTACCA 60.183 42.308 10.77 0.00 39.34 3.25
284 285 6.042897 AGGGGAGTACATAGCATAAAACTACC 59.957 42.308 0.00 2.08 37.25 3.18
285 286 6.929606 CAGGGGAGTACATAGCATAAAACTAC 59.070 42.308 0.00 0.00 0.00 2.73
286 287 6.042781 CCAGGGGAGTACATAGCATAAAACTA 59.957 42.308 0.00 0.00 0.00 2.24
287 288 5.163195 CCAGGGGAGTACATAGCATAAAACT 60.163 44.000 0.00 0.00 0.00 2.66
288 289 5.063880 CCAGGGGAGTACATAGCATAAAAC 58.936 45.833 0.00 0.00 0.00 2.43
289 290 4.972568 TCCAGGGGAGTACATAGCATAAAA 59.027 41.667 0.00 0.00 0.00 1.52
290 291 4.562767 TCCAGGGGAGTACATAGCATAAA 58.437 43.478 0.00 0.00 0.00 1.40
291 292 4.160329 CTCCAGGGGAGTACATAGCATAA 58.840 47.826 4.08 0.00 44.25 1.90
292 293 3.779444 CTCCAGGGGAGTACATAGCATA 58.221 50.000 4.08 0.00 44.25 3.14
293 294 2.614259 CTCCAGGGGAGTACATAGCAT 58.386 52.381 4.08 0.00 44.25 3.79
294 295 2.088104 CTCCAGGGGAGTACATAGCA 57.912 55.000 4.08 0.00 44.25 3.49
304 305 1.125093 TGAAACGAAGCTCCAGGGGA 61.125 55.000 0.00 0.00 0.00 4.81
305 306 0.674895 CTGAAACGAAGCTCCAGGGG 60.675 60.000 0.00 0.00 0.00 4.79
428 430 7.846066 TCTTGTCTTTTTCTTGGAAATTGGAA 58.154 30.769 0.00 0.00 0.00 3.53
429 431 7.416964 TCTTGTCTTTTTCTTGGAAATTGGA 57.583 32.000 0.00 0.00 0.00 3.53
430 432 7.765819 ACTTCTTGTCTTTTTCTTGGAAATTGG 59.234 33.333 0.00 0.00 0.00 3.16
431 433 8.707938 ACTTCTTGTCTTTTTCTTGGAAATTG 57.292 30.769 0.00 0.00 0.00 2.32
482 484 1.615392 ACTTTGCAGCAGGGATTTCAC 59.385 47.619 0.00 0.00 0.00 3.18
516 518 5.013495 TCCTCAGGATCAATTGTTTCTCAGT 59.987 40.000 5.13 0.00 0.00 3.41
518 520 5.248640 GTCCTCAGGATCAATTGTTTCTCA 58.751 41.667 0.00 0.00 32.73 3.27
537 540 6.229936 TGCTATATTTCGTACAAAGGTCCT 57.770 37.500 0.00 0.00 0.00 3.85
616 644 4.690748 TCACGCTGGAGATAAGTGAAAAAG 59.309 41.667 0.00 0.00 38.66 2.27
633 661 4.641541 TCAAATTTCATCATCCATCACGCT 59.358 37.500 0.00 0.00 0.00 5.07
903 942 4.036852 CACACTCCAGAGAAGCGATATACA 59.963 45.833 0.70 0.00 0.00 2.29
942 986 7.666623 TGATCACAAATGGACGCTATTATAGA 58.333 34.615 3.04 0.00 0.00 1.98
1135 1221 0.106519 AAGCCACAGGTGAAAGTGCT 60.107 50.000 0.00 0.00 34.48 4.40
1681 1777 8.885494 TTTAAATTGTCACTTCCAAGGAAATG 57.115 30.769 4.00 4.00 33.27 2.32
1726 1822 3.912528 AGCCTCCTCATAATCCTAATGCA 59.087 43.478 0.00 0.00 0.00 3.96
1911 2009 2.625314 GTCGATGATCTCATGTCCAGGA 59.375 50.000 0.00 0.00 36.57 3.86
2052 2159 7.939782 TCTTCTTGCAAGTATGAAATGAAACA 58.060 30.769 25.19 0.00 0.00 2.83
2110 2217 3.201290 CTCCACTTGCTTGCCAGTATAG 58.799 50.000 0.00 0.00 0.00 1.31
2184 2294 7.164230 AGGAAGCTTGATATAGATAGAACGG 57.836 40.000 2.10 0.00 0.00 4.44
2351 2461 5.699001 CCATACAACAAGTACAAGTACTGCA 59.301 40.000 13.18 0.00 44.96 4.41
2477 2590 6.260050 GGTTATCATTTCGTAGCCAATCTCAA 59.740 38.462 0.00 0.00 0.00 3.02
2490 2603 5.004345 GCGAAAATGGTTGGTTATCATTTCG 59.996 40.000 11.60 11.60 39.34 3.46
2667 2780 3.876914 TCACACTCAGTTCATGTTGGAAC 59.123 43.478 0.00 0.00 45.87 3.62
3252 3383 4.703645 TCTCGAATCAACGAAGTCAGAT 57.296 40.909 0.00 0.00 45.00 2.90
3445 3583 8.560355 TGACATGTTGCATAGTATACAAAACT 57.440 30.769 5.50 0.00 0.00 2.66
3672 3817 7.360438 GGCTAACAATGTAAGAATCGATGGATC 60.360 40.741 0.00 0.00 30.81 3.36
3717 3862 3.848272 TTTGCAGCAGCTAAACCATAC 57.152 42.857 1.76 0.00 42.74 2.39
3756 3901 2.261361 CCCATGCGACGACTCACA 59.739 61.111 0.00 0.00 0.00 3.58
3764 3909 1.450134 TCACATCAGCCCATGCGAC 60.450 57.895 0.00 0.00 44.33 5.19
3846 3992 7.627340 CAGTGGTCAAATACGGTATTCAATAC 58.373 38.462 13.41 0.00 35.00 1.89
3855 4001 1.296056 GCGCAGTGGTCAAATACGGT 61.296 55.000 0.30 0.00 0.00 4.83
3856 4002 1.423845 GCGCAGTGGTCAAATACGG 59.576 57.895 0.30 0.00 0.00 4.02
3876 4022 5.175859 AGAGCTAGCATAACTTTTGCGTTA 58.824 37.500 18.83 0.00 44.82 3.18
3877 4023 4.003648 AGAGCTAGCATAACTTTTGCGTT 58.996 39.130 18.83 0.00 44.82 4.84
3934 4178 3.859443 AGCTCACATGAGTCAAGATCAC 58.141 45.455 10.50 0.00 43.85 3.06
3940 4184 0.247460 CCCGAGCTCACATGAGTCAA 59.753 55.000 15.40 0.00 43.85 3.18
4063 4307 9.005777 CCAACATTTTCCATGAATCTCATTTTT 57.994 29.630 0.00 0.00 34.28 1.94
4064 4308 8.377034 TCCAACATTTTCCATGAATCTCATTTT 58.623 29.630 0.00 0.00 34.28 1.82
4071 4315 7.727331 TGTTTTCCAACATTTTCCATGAATC 57.273 32.000 0.00 0.00 38.03 2.52
4087 4331 6.624861 GCATTTTGGAGTATCGATGTTTTCCA 60.625 38.462 8.54 12.23 34.37 3.53
4250 4494 9.683069 CATCACAAGTGCTAAGAAAAGTAAAAT 57.317 29.630 0.00 0.00 0.00 1.82
4310 4554 0.653636 GCGGAACAAGAACAACGACA 59.346 50.000 0.00 0.00 0.00 4.35
4311 4555 0.935196 AGCGGAACAAGAACAACGAC 59.065 50.000 0.00 0.00 0.00 4.34
4312 4556 1.202486 AGAGCGGAACAAGAACAACGA 60.202 47.619 0.00 0.00 0.00 3.85
4334 4578 2.372504 CTCAGATCCGAGGGACCTAGTA 59.627 54.545 0.00 0.00 32.98 1.82
4338 4582 1.456705 GCTCAGATCCGAGGGACCT 60.457 63.158 8.04 0.00 32.98 3.85
4361 4605 2.959357 GCACAGCACAACTCGGAGC 61.959 63.158 4.58 0.00 0.00 4.70
4374 4618 0.901124 AGGCACTCCTTAGAGCACAG 59.099 55.000 0.00 0.00 44.65 3.66


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

AutoCloner maintained by Alex Coulton.