Multiple sequence alignment - TraesCS4D01G152700

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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 TraesCS4D01G152700 chr4D 100.000 7812 0 0 1 7812 188706734 188714545 0.000000e+00 14427.0
1 TraesCS4D01G152700 chr4D 93.657 268 17 0 1260 1527 363568572 363568839 1.220000e-107 401.0
2 TraesCS4D01G152700 chr4D 97.727 88 2 0 5092 5179 61961186 61961273 1.360000e-32 152.0
3 TraesCS4D01G152700 chr4A 95.175 4539 130 31 499 4977 288673759 288678268 0.000000e+00 7086.0
4 TraesCS4D01G152700 chr4A 96.141 1814 48 7 5175 6982 288679082 288680879 0.000000e+00 2942.0
5 TraesCS4D01G152700 chr4A 92.933 750 43 4 7068 7810 288680884 288681630 0.000000e+00 1083.0
6 TraesCS4D01G152700 chr4A 90.504 516 19 12 1 513 288657737 288658225 0.000000e+00 654.0
7 TraesCS4D01G152700 chr4A 82.957 487 48 18 1017 1502 641295559 641296011 2.620000e-109 407.0
8 TraesCS4D01G152700 chr4A 90.706 269 23 2 1262 1530 467312860 467312594 2.680000e-94 357.0
9 TraesCS4D01G152700 chr4A 96.241 133 4 1 4963 5094 288678959 288679091 4.750000e-52 217.0
10 TraesCS4D01G152700 chr4B 95.654 4372 103 31 778 5094 203203637 203207976 0.000000e+00 6940.0
11 TraesCS4D01G152700 chr4B 96.885 2151 42 6 5175 7303 203207974 203210121 0.000000e+00 3578.0
12 TraesCS4D01G152700 chr4B 91.928 446 19 9 280 711 203202580 203203022 6.700000e-170 608.0
13 TraesCS4D01G152700 chr4B 92.073 328 20 2 7298 7622 203210950 203211274 2.570000e-124 457.0
14 TraesCS4D01G152700 chr4B 93.929 280 16 1 2 281 203195825 203196103 9.370000e-114 422.0
15 TraesCS4D01G152700 chr4B 93.333 180 11 1 7634 7812 203211321 203211500 1.670000e-66 265.0
16 TraesCS4D01G152700 chr4B 97.468 79 2 0 1 79 203195704 203195782 1.370000e-27 135.0
17 TraesCS4D01G152700 chr4B 91.667 72 3 2 711 780 203203290 203203360 6.450000e-16 97.1
18 TraesCS4D01G152700 chr5A 83.441 465 44 16 1039 1502 29933 29501 1.220000e-107 401.0
19 TraesCS4D01G152700 chr5A 91.882 271 22 0 1260 1530 243810674 243810404 5.720000e-101 379.0
20 TraesCS4D01G152700 chr5A 90.037 271 25 2 1260 1530 675530888 675530620 4.490000e-92 350.0
21 TraesCS4D01G152700 chr5A 87.864 206 16 2 1545 1750 29502 29306 4.710000e-57 233.0
22 TraesCS4D01G152700 chr7B 83.226 465 45 13 1039 1502 5929163 5928731 5.680000e-106 396.0
23 TraesCS4D01G152700 chr7B 87.864 206 16 2 1545 1750 5928732 5928536 4.710000e-57 233.0
24 TraesCS4D01G152700 chr3B 82.546 487 50 18 1017 1502 647898805 647899257 5.680000e-106 396.0
25 TraesCS4D01G152700 chr3B 91.144 271 24 0 1260 1530 796471719 796471449 1.240000e-97 368.0
26 TraesCS4D01G152700 chr3B 87.864 206 16 2 1545 1750 647899256 647899452 4.710000e-57 233.0
27 TraesCS4D01G152700 chr3B 94.000 100 4 2 5091 5188 807575514 807575415 4.880000e-32 150.0
28 TraesCS4D01G152700 chr2B 83.226 465 45 16 1039 1502 587240613 587240181 5.680000e-106 396.0
29 TraesCS4D01G152700 chr2B 87.864 206 16 2 1545 1750 587240182 587239986 4.710000e-57 233.0
30 TraesCS4D01G152700 chr1B 83.011 465 46 16 1039 1502 16461905 16461473 2.640000e-104 390.0
31 TraesCS4D01G152700 chr1B 88.350 206 19 2 1545 1750 16461474 16461274 7.830000e-60 243.0
32 TraesCS4D01G152700 chr1B 95.789 95 4 0 5091 5185 555953885 555953791 3.770000e-33 154.0
33 TraesCS4D01G152700 chr6B 90.037 271 25 2 1260 1530 646638779 646638511 4.490000e-92 350.0
34 TraesCS4D01G152700 chr6B 90.909 77 7 0 1094 1170 164816951 164817027 3.860000e-18 104.0
35 TraesCS4D01G152700 chr6A 89.500 200 20 1 1303 1502 40918503 40918305 1.300000e-62 252.0
36 TraesCS4D01G152700 chr6A 86.893 206 18 1 1545 1750 40918306 40918110 1.020000e-53 222.0
37 TraesCS4D01G152700 chr1A 87.864 206 16 2 1545 1750 111984740 111984544 4.710000e-57 233.0
38 TraesCS4D01G152700 chr1D 100.000 86 0 0 5092 5177 387899503 387899588 8.110000e-35 159.0
39 TraesCS4D01G152700 chr1D 94.118 102 6 0 5086 5187 124331899 124332000 1.050000e-33 156.0
40 TraesCS4D01G152700 chr1D 97.753 89 2 0 5091 5179 225701733 225701821 3.770000e-33 154.0
41 TraesCS4D01G152700 chr3A 93.204 103 6 1 5089 5191 42130182 42130283 4.880000e-32 150.0
42 TraesCS4D01G152700 chr3A 92.233 103 7 1 5089 5191 42067365 42067466 2.270000e-30 145.0
43 TraesCS4D01G152700 chr7A 90.741 108 9 1 5086 5192 82929896 82929789 8.170000e-30 143.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G152700 chr4D 188706734 188714545 7811 False 14427.00 14427 100.0000 1 7812 1 chr4D.!!$F2 7811
1 TraesCS4D01G152700 chr4A 288673759 288681630 7871 False 2832.00 7086 95.1225 499 7810 4 chr4A.!!$F3 7311
2 TraesCS4D01G152700 chr4B 203202580 203211500 8920 False 1990.85 6940 93.5900 280 7812 6 chr4B.!!$F2 7532
3 TraesCS4D01G152700 chr5A 29306 29933 627 True 317.00 401 85.6525 1039 1750 2 chr5A.!!$R3 711
4 TraesCS4D01G152700 chr7B 5928536 5929163 627 True 314.50 396 85.5450 1039 1750 2 chr7B.!!$R1 711
5 TraesCS4D01G152700 chr3B 647898805 647899452 647 False 314.50 396 85.2050 1017 1750 2 chr3B.!!$F1 733
6 TraesCS4D01G152700 chr2B 587239986 587240613 627 True 314.50 396 85.5450 1039 1750 2 chr2B.!!$R1 711
7 TraesCS4D01G152700 chr1B 16461274 16461905 631 True 316.50 390 85.6805 1039 1750 2 chr1B.!!$R2 711

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
486 489 0.247460 CCGACTCAGGACAGCAATGA 59.753 55.000 0.00 0.00 0.00 2.57 F
518 521 3.544356 GGAGCTTAATAATTCAGCGCC 57.456 47.619 2.29 5.99 44.76 6.53 F
1466 2046 2.158769 TCTGCTTCCTTCACTTGCTTGA 60.159 45.455 0.00 0.00 0.00 3.02 F
1859 2472 0.318784 AAGTGTTCGAGCCGAGTGAC 60.319 55.000 0.00 0.00 37.14 3.67 F
2681 3318 0.249699 TGCCTGGTACAACGTGACTG 60.250 55.000 0.00 0.00 38.70 3.51 F
3415 4057 2.092429 AGTCCAAGCTCCTGTTTGTTCA 60.092 45.455 0.00 0.00 33.39 3.18 F
4666 5310 0.523072 ATTTGCAGGTGCTTAGTGCG 59.477 50.000 3.18 0.00 46.63 5.34 F
4844 5488 2.032681 GGGCTGGTCGCTTGAGTT 59.967 61.111 0.00 0.00 39.13 3.01 F
6655 8025 1.868469 GCTACACACACGGTTGGTAA 58.132 50.000 0.00 0.00 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1466 2046 2.159198 GGCATGCACGAAATGAAGGAAT 60.159 45.455 21.36 0.00 0.00 3.01 R
1482 2062 2.652095 CCCAAACCCAGCAGGCATG 61.652 63.158 0.00 0.00 40.58 4.06 R
2681 3318 1.592400 GGCCTGTTCCCCGCTTTAAC 61.592 60.000 0.00 0.00 0.00 2.01 R
2906 3543 3.072915 TGTCCTCTTCAGCTCCAATTTCA 59.927 43.478 0.00 0.00 0.00 2.69 R
4666 5310 0.685097 TATCACAGGATAAGCGGCCC 59.315 55.000 0.00 0.00 33.11 5.80 R
4778 5422 4.892934 AGTGCAACCAAGTAAAAATCCAGA 59.107 37.500 0.00 0.00 37.80 3.86 R
6452 7802 1.127582 GAGTCAGCAGTCGCAAACATC 59.872 52.381 0.00 0.00 42.27 3.06 R
6678 8048 3.073798 TGGGGTTAGCTTCAAGAACATCA 59.926 43.478 0.00 0.00 0.00 3.07 R
7755 10000 0.608308 AAGCGGGGAAACTAGTTGGC 60.608 55.000 9.34 8.12 0.00 4.52 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 9.288576 TGTGATCTTTATTCTCTTGTTGAATGT 57.711 29.630 0.00 0.00 35.90 2.71
28 29 9.552114 GTGATCTTTATTCTCTTGTTGAATGTG 57.448 33.333 0.00 0.00 35.90 3.21
29 30 8.239314 TGATCTTTATTCTCTTGTTGAATGTGC 58.761 33.333 0.00 0.00 35.90 4.57
30 31 7.750229 TCTTTATTCTCTTGTTGAATGTGCT 57.250 32.000 0.00 0.00 35.90 4.40
31 32 7.810658 TCTTTATTCTCTTGTTGAATGTGCTC 58.189 34.615 0.00 0.00 35.90 4.26
32 33 6.500684 TTATTCTCTTGTTGAATGTGCTCC 57.499 37.500 0.00 0.00 35.90 4.70
33 34 3.777106 TCTCTTGTTGAATGTGCTCCT 57.223 42.857 0.00 0.00 0.00 3.69
34 35 4.890158 TCTCTTGTTGAATGTGCTCCTA 57.110 40.909 0.00 0.00 0.00 2.94
35 36 4.825422 TCTCTTGTTGAATGTGCTCCTAG 58.175 43.478 0.00 0.00 0.00 3.02
36 37 4.528206 TCTCTTGTTGAATGTGCTCCTAGA 59.472 41.667 0.00 0.00 0.00 2.43
37 38 5.188555 TCTCTTGTTGAATGTGCTCCTAGAT 59.811 40.000 0.00 0.00 0.00 1.98
38 39 5.181009 TCTTGTTGAATGTGCTCCTAGATG 58.819 41.667 0.00 0.00 0.00 2.90
39 40 4.558226 TGTTGAATGTGCTCCTAGATGT 57.442 40.909 0.00 0.00 0.00 3.06
40 41 5.675684 TGTTGAATGTGCTCCTAGATGTA 57.324 39.130 0.00 0.00 0.00 2.29
41 42 5.664457 TGTTGAATGTGCTCCTAGATGTAG 58.336 41.667 0.00 0.00 0.00 2.74
42 43 5.422012 TGTTGAATGTGCTCCTAGATGTAGA 59.578 40.000 0.00 0.00 0.00 2.59
43 44 6.098838 TGTTGAATGTGCTCCTAGATGTAGAT 59.901 38.462 0.00 0.00 0.00 1.98
44 45 6.737720 TGAATGTGCTCCTAGATGTAGATT 57.262 37.500 0.00 0.00 0.00 2.40
45 46 7.129457 TGAATGTGCTCCTAGATGTAGATTT 57.871 36.000 0.00 0.00 0.00 2.17
46 47 7.212976 TGAATGTGCTCCTAGATGTAGATTTC 58.787 38.462 0.00 0.00 0.00 2.17
47 48 6.737720 ATGTGCTCCTAGATGTAGATTTCA 57.262 37.500 0.00 0.00 0.00 2.69
48 49 6.737720 TGTGCTCCTAGATGTAGATTTCAT 57.262 37.500 0.00 0.00 0.00 2.57
49 50 6.753180 TGTGCTCCTAGATGTAGATTTCATC 58.247 40.000 0.00 0.00 41.11 2.92
50 51 6.324770 TGTGCTCCTAGATGTAGATTTCATCA 59.675 38.462 0.00 0.00 42.63 3.07
51 52 7.147672 TGTGCTCCTAGATGTAGATTTCATCAA 60.148 37.037 0.00 0.00 42.63 2.57
52 53 7.877097 GTGCTCCTAGATGTAGATTTCATCAAT 59.123 37.037 0.00 0.00 42.63 2.57
53 54 9.093458 TGCTCCTAGATGTAGATTTCATCAATA 57.907 33.333 0.00 0.00 42.63 1.90
65 66 8.092521 AGATTTCATCAATATAAGAGGCAACG 57.907 34.615 0.00 0.00 46.39 4.10
66 67 7.933577 AGATTTCATCAATATAAGAGGCAACGA 59.066 33.333 0.00 0.00 46.39 3.85
67 68 7.857734 TTTCATCAATATAAGAGGCAACGAA 57.142 32.000 0.00 0.00 46.39 3.85
68 69 7.857734 TTCATCAATATAAGAGGCAACGAAA 57.142 32.000 0.00 0.00 46.39 3.46
69 70 7.246674 TCATCAATATAAGAGGCAACGAAAC 57.753 36.000 0.00 0.00 46.39 2.78
70 71 6.821160 TCATCAATATAAGAGGCAACGAAACA 59.179 34.615 0.00 0.00 46.39 2.83
71 72 7.335673 TCATCAATATAAGAGGCAACGAAACAA 59.664 33.333 0.00 0.00 46.39 2.83
72 73 7.624360 TCAATATAAGAGGCAACGAAACAAT 57.376 32.000 0.00 0.00 46.39 2.71
73 74 8.725405 TCAATATAAGAGGCAACGAAACAATA 57.275 30.769 0.00 0.00 46.39 1.90
74 75 9.168451 TCAATATAAGAGGCAACGAAACAATAA 57.832 29.630 0.00 0.00 46.39 1.40
75 76 9.950680 CAATATAAGAGGCAACGAAACAATAAT 57.049 29.630 0.00 0.00 46.39 1.28
76 77 9.950680 AATATAAGAGGCAACGAAACAATAATG 57.049 29.630 0.00 0.00 46.39 1.90
77 78 5.705609 AAGAGGCAACGAAACAATAATGT 57.294 34.783 0.00 0.00 42.22 2.71
78 79 6.811253 AAGAGGCAACGAAACAATAATGTA 57.189 33.333 0.00 0.00 40.02 2.29
79 80 7.391148 AAGAGGCAACGAAACAATAATGTAT 57.609 32.000 0.00 0.00 40.02 2.29
80 81 7.391148 AGAGGCAACGAAACAATAATGTATT 57.609 32.000 0.00 0.00 40.02 1.89
81 82 8.500753 AGAGGCAACGAAACAATAATGTATTA 57.499 30.769 0.00 0.00 40.02 0.98
82 83 8.952278 AGAGGCAACGAAACAATAATGTATTAA 58.048 29.630 0.00 0.00 40.02 1.40
83 84 9.562583 GAGGCAACGAAACAATAATGTATTAAA 57.437 29.630 0.00 0.00 40.02 1.52
84 85 9.915629 AGGCAACGAAACAATAATGTATTAAAA 57.084 25.926 0.00 0.00 40.02 1.52
106 107 8.791327 AAAATGGATAATCAAATTGGAACCAC 57.209 30.769 0.00 0.00 0.00 4.16
107 108 5.574891 TGGATAATCAAATTGGAACCACG 57.425 39.130 0.00 0.00 0.00 4.94
108 109 5.257262 TGGATAATCAAATTGGAACCACGA 58.743 37.500 0.00 0.00 0.00 4.35
109 110 5.124776 TGGATAATCAAATTGGAACCACGAC 59.875 40.000 0.00 0.00 0.00 4.34
110 111 5.124776 GGATAATCAAATTGGAACCACGACA 59.875 40.000 0.00 0.00 0.00 4.35
111 112 4.503741 AATCAAATTGGAACCACGACAG 57.496 40.909 0.00 0.00 0.00 3.51
112 113 3.201353 TCAAATTGGAACCACGACAGA 57.799 42.857 0.00 0.00 0.00 3.41
113 114 3.750371 TCAAATTGGAACCACGACAGAT 58.250 40.909 0.00 0.00 0.00 2.90
114 115 4.900684 TCAAATTGGAACCACGACAGATA 58.099 39.130 0.00 0.00 0.00 1.98
115 116 5.309638 TCAAATTGGAACCACGACAGATAA 58.690 37.500 0.00 0.00 0.00 1.75
116 117 5.180492 TCAAATTGGAACCACGACAGATAAC 59.820 40.000 0.00 0.00 0.00 1.89
117 118 4.553330 ATTGGAACCACGACAGATAACT 57.447 40.909 0.00 0.00 0.00 2.24
118 119 5.670792 ATTGGAACCACGACAGATAACTA 57.329 39.130 0.00 0.00 0.00 2.24
119 120 4.713824 TGGAACCACGACAGATAACTAG 57.286 45.455 0.00 0.00 0.00 2.57
120 121 4.338012 TGGAACCACGACAGATAACTAGA 58.662 43.478 0.00 0.00 0.00 2.43
121 122 4.954202 TGGAACCACGACAGATAACTAGAT 59.046 41.667 0.00 0.00 0.00 1.98
122 123 6.124340 TGGAACCACGACAGATAACTAGATA 58.876 40.000 0.00 0.00 0.00 1.98
123 124 6.604396 TGGAACCACGACAGATAACTAGATAA 59.396 38.462 0.00 0.00 0.00 1.75
124 125 7.123098 TGGAACCACGACAGATAACTAGATAAA 59.877 37.037 0.00 0.00 0.00 1.40
125 126 8.142551 GGAACCACGACAGATAACTAGATAAAT 58.857 37.037 0.00 0.00 0.00 1.40
126 127 9.530633 GAACCACGACAGATAACTAGATAAATT 57.469 33.333 0.00 0.00 0.00 1.82
127 128 9.530633 AACCACGACAGATAACTAGATAAATTC 57.469 33.333 0.00 0.00 0.00 2.17
128 129 8.915036 ACCACGACAGATAACTAGATAAATTCT 58.085 33.333 0.00 0.00 38.57 2.40
196 197 9.793259 ATTACTTGATGAGTTTTTCCTAAGTCA 57.207 29.630 0.00 0.00 40.63 3.41
197 198 9.621629 TTACTTGATGAGTTTTTCCTAAGTCAA 57.378 29.630 0.00 0.00 39.99 3.18
198 199 8.519799 ACTTGATGAGTTTTTCCTAAGTCAAA 57.480 30.769 0.00 0.00 39.99 2.69
199 200 8.406297 ACTTGATGAGTTTTTCCTAAGTCAAAC 58.594 33.333 0.00 0.00 39.99 2.93
200 201 8.519799 TTGATGAGTTTTTCCTAAGTCAAACT 57.480 30.769 0.00 0.00 39.99 2.66
201 202 8.519799 TGATGAGTTTTTCCTAAGTCAAACTT 57.480 30.769 0.00 0.00 39.99 2.66
202 203 8.966868 TGATGAGTTTTTCCTAAGTCAAACTTT 58.033 29.630 0.00 0.00 39.99 2.66
203 204 9.803315 GATGAGTTTTTCCTAAGTCAAACTTTT 57.197 29.630 0.00 0.00 39.99 2.27
222 223 2.373335 TTTTAAGGCTGGCCAACTCA 57.627 45.000 7.01 0.00 38.92 3.41
223 224 2.373335 TTTAAGGCTGGCCAACTCAA 57.627 45.000 7.01 0.00 38.92 3.02
224 225 1.616159 TTAAGGCTGGCCAACTCAAC 58.384 50.000 7.01 0.00 38.92 3.18
225 226 0.605319 TAAGGCTGGCCAACTCAACG 60.605 55.000 7.01 0.00 38.92 4.10
226 227 2.281484 GGCTGGCCAACTCAACGA 60.281 61.111 7.01 0.00 35.81 3.85
227 228 1.896660 GGCTGGCCAACTCAACGAA 60.897 57.895 7.01 0.00 35.81 3.85
228 229 1.452145 GGCTGGCCAACTCAACGAAA 61.452 55.000 7.01 0.00 35.81 3.46
229 230 0.383949 GCTGGCCAACTCAACGAAAA 59.616 50.000 7.01 0.00 0.00 2.29
230 231 1.000274 GCTGGCCAACTCAACGAAAAT 60.000 47.619 7.01 0.00 0.00 1.82
231 232 2.227865 GCTGGCCAACTCAACGAAAATA 59.772 45.455 7.01 0.00 0.00 1.40
232 233 3.119495 GCTGGCCAACTCAACGAAAATAT 60.119 43.478 7.01 0.00 0.00 1.28
233 234 4.095782 GCTGGCCAACTCAACGAAAATATA 59.904 41.667 7.01 0.00 0.00 0.86
234 235 5.392595 GCTGGCCAACTCAACGAAAATATAA 60.393 40.000 7.01 0.00 0.00 0.98
235 236 6.576662 TGGCCAACTCAACGAAAATATAAA 57.423 33.333 0.61 0.00 0.00 1.40
236 237 7.164230 TGGCCAACTCAACGAAAATATAAAT 57.836 32.000 0.61 0.00 0.00 1.40
237 238 7.254852 TGGCCAACTCAACGAAAATATAAATC 58.745 34.615 0.61 0.00 0.00 2.17
238 239 7.122055 TGGCCAACTCAACGAAAATATAAATCT 59.878 33.333 0.61 0.00 0.00 2.40
239 240 8.617809 GGCCAACTCAACGAAAATATAAATCTA 58.382 33.333 0.00 0.00 0.00 1.98
486 489 0.247460 CCGACTCAGGACAGCAATGA 59.753 55.000 0.00 0.00 0.00 2.57
518 521 3.544356 GGAGCTTAATAATTCAGCGCC 57.456 47.619 2.29 5.99 44.76 6.53
543 555 8.298140 CCGAAAACCACACCTAAAATACATTTA 58.702 33.333 0.00 0.00 32.27 1.40
813 1380 6.656314 AGATAAATATTTCAACGTGTCGCA 57.344 33.333 3.39 0.00 0.00 5.10
856 1423 3.895656 CCGACCTACCCATTATTCTCTCA 59.104 47.826 0.00 0.00 0.00 3.27
879 1447 7.631933 TCACCCCGTCCTTTTCTATAAAATAA 58.368 34.615 0.00 0.00 34.18 1.40
880 1448 8.276477 TCACCCCGTCCTTTTCTATAAAATAAT 58.724 33.333 0.00 0.00 34.18 1.28
1466 2046 2.158769 TCTGCTTCCTTCACTTGCTTGA 60.159 45.455 0.00 0.00 0.00 3.02
1482 2062 3.174375 GCTTGATTCCTTCATTTCGTGC 58.826 45.455 0.00 0.00 33.34 5.34
1507 2087 3.268032 CTGGGTTTGGGGGCTCCT 61.268 66.667 4.32 0.00 36.20 3.69
1527 2107 5.727434 TCCTAAACTCTATCGGGTTGAAAC 58.273 41.667 0.00 0.00 0.00 2.78
1609 2190 4.011517 GTGGGAGGAAACGGGCGA 62.012 66.667 0.00 0.00 0.00 5.54
1654 2241 4.915158 TGATATCATTGCGCCAATTTGA 57.085 36.364 4.18 0.74 31.05 2.69
1859 2472 0.318784 AAGTGTTCGAGCCGAGTGAC 60.319 55.000 0.00 0.00 37.14 3.67
2321 2946 5.091261 GAGGTGATTTCTCCATGTACTGT 57.909 43.478 0.00 0.00 32.20 3.55
2505 3142 6.042666 GGTCCTAATCAGATTAGCCTCTTTCT 59.957 42.308 20.94 0.00 40.65 2.52
2544 3181 1.381867 TTCCCTCCATGTGGAATGGT 58.618 50.000 13.86 0.00 44.91 3.55
2554 3191 4.955450 CCATGTGGAATGGTTAGAAATCCA 59.045 41.667 0.00 0.00 37.83 3.41
2595 3232 2.505407 TCCATGAACATACAGAGGGTGG 59.495 50.000 0.00 0.00 0.00 4.61
2681 3318 0.249699 TGCCTGGTACAACGTGACTG 60.250 55.000 0.00 0.00 38.70 3.51
2906 3543 5.125578 TCTCTGTACAGACGAAATATGCACT 59.874 40.000 21.74 0.00 33.22 4.40
3098 3735 8.097038 TCCTCTGCATATTCAGGACATAAATAC 58.903 37.037 2.41 0.00 34.91 1.89
3324 3966 9.708222 GTTGAAATTATAATGCTCTGTACACAG 57.292 33.333 2.84 2.84 45.08 3.66
3382 4024 4.776349 TGTACTTAACCGATGCATGGATT 58.224 39.130 18.41 7.77 0.00 3.01
3383 4025 5.189928 TGTACTTAACCGATGCATGGATTT 58.810 37.500 18.41 10.31 0.00 2.17
3415 4057 2.092429 AGTCCAAGCTCCTGTTTGTTCA 60.092 45.455 0.00 0.00 33.39 3.18
3440 4082 4.696877 TGAATTCAGGTTATGCAGTGTGAG 59.303 41.667 3.38 0.00 0.00 3.51
3504 4146 5.919755 TGAATAGTTGTAACCACTGACACA 58.080 37.500 0.00 0.00 0.00 3.72
3505 4147 6.530120 TGAATAGTTGTAACCACTGACACAT 58.470 36.000 0.00 0.00 0.00 3.21
3506 4148 6.426633 TGAATAGTTGTAACCACTGACACATG 59.573 38.462 0.00 0.00 0.00 3.21
3507 4149 3.476552 AGTTGTAACCACTGACACATGG 58.523 45.455 0.00 0.19 42.13 3.66
4327 4969 6.795098 ACTTCTGATTAATGCGTTGTTACA 57.205 33.333 0.08 0.00 0.00 2.41
4330 4972 6.976636 TCTGATTAATGCGTTGTTACATGA 57.023 33.333 0.00 0.00 0.00 3.07
4378 5022 7.119846 AGAGTCCTGTTATTAGTGCAAATTCAC 59.880 37.037 0.00 0.00 37.24 3.18
4576 5220 7.147497 TGCCTGAAGAATATTTCTAGGTCATCA 60.147 37.037 7.54 0.00 39.61 3.07
4666 5310 0.523072 ATTTGCAGGTGCTTAGTGCG 59.477 50.000 3.18 0.00 46.63 5.34
4821 5465 6.072286 TGCACTTCAAATCTTCCTTGATTCTC 60.072 38.462 0.00 0.00 35.82 2.87
4844 5488 2.032681 GGGCTGGTCGCTTGAGTT 59.967 61.111 0.00 0.00 39.13 3.01
4940 5584 6.608405 TGCCCTCTTTGATATTGTTGATGAAT 59.392 34.615 0.00 0.00 0.00 2.57
5094 6444 8.270030 AGGAGGTATACCTTTGGTATTTTGTAC 58.730 37.037 25.30 7.33 45.54 2.90
5096 6446 9.322773 GAGGTATACCTTTGGTATTTTGTACTC 57.677 37.037 25.30 3.20 45.54 2.59
5097 6447 8.270030 AGGTATACCTTTGGTATTTTGTACTCC 58.730 37.037 19.27 5.65 45.54 3.85
5098 6448 7.500227 GGTATACCTTTGGTATTTTGTACTCCC 59.500 40.741 15.09 0.03 45.54 4.30
5100 6450 5.567430 ACCTTTGGTATTTTGTACTCCCTC 58.433 41.667 0.00 0.00 32.11 4.30
5101 6451 4.948004 CCTTTGGTATTTTGTACTCCCTCC 59.052 45.833 0.00 0.00 0.00 4.30
5102 6452 5.515886 CCTTTGGTATTTTGTACTCCCTCCA 60.516 44.000 0.00 0.00 0.00 3.86
5103 6453 5.789574 TTGGTATTTTGTACTCCCTCCAT 57.210 39.130 0.00 0.00 0.00 3.41
5104 6454 6.894735 TTGGTATTTTGTACTCCCTCCATA 57.105 37.500 0.00 0.00 0.00 2.74
5105 6455 6.894735 TGGTATTTTGTACTCCCTCCATAA 57.105 37.500 0.00 0.00 0.00 1.90
5106 6456 7.273457 TGGTATTTTGTACTCCCTCCATAAA 57.727 36.000 0.00 0.00 0.00 1.40
5107 6457 7.114095 TGGTATTTTGTACTCCCTCCATAAAC 58.886 38.462 0.00 0.00 0.00 2.01
5108 6458 7.037153 TGGTATTTTGTACTCCCTCCATAAACT 60.037 37.037 0.00 0.00 0.00 2.66
5109 6459 8.488668 GGTATTTTGTACTCCCTCCATAAACTA 58.511 37.037 0.00 0.00 0.00 2.24
5110 6460 9.895138 GTATTTTGTACTCCCTCCATAAACTAA 57.105 33.333 0.00 0.00 0.00 2.24
5119 6469 8.817876 ACTCCCTCCATAAACTAATATAAGAGC 58.182 37.037 0.00 0.00 0.00 4.09
5120 6470 7.837863 TCCCTCCATAAACTAATATAAGAGCG 58.162 38.462 0.00 0.00 0.00 5.03
5121 6471 7.453752 TCCCTCCATAAACTAATATAAGAGCGT 59.546 37.037 0.00 0.00 0.00 5.07
5122 6472 8.095169 CCCTCCATAAACTAATATAAGAGCGTT 58.905 37.037 0.00 0.00 0.00 4.84
5123 6473 9.490379 CCTCCATAAACTAATATAAGAGCGTTT 57.510 33.333 0.00 0.00 0.00 3.60
5138 6488 7.870588 AAGAGCGTTTAGAACACTACTTTAG 57.129 36.000 0.00 0.00 0.00 1.85
5139 6489 6.979465 AGAGCGTTTAGAACACTACTTTAGT 58.021 36.000 0.00 0.00 40.28 2.24
5140 6490 8.103948 AGAGCGTTTAGAACACTACTTTAGTA 57.896 34.615 0.00 0.00 37.23 1.82
5141 6491 8.571336 AGAGCGTTTAGAACACTACTTTAGTAA 58.429 33.333 0.00 0.00 37.23 2.24
5142 6492 9.351570 GAGCGTTTAGAACACTACTTTAGTAAT 57.648 33.333 0.00 0.00 37.23 1.89
5143 6493 9.351570 AGCGTTTAGAACACTACTTTAGTAATC 57.648 33.333 0.00 0.00 37.23 1.75
5144 6494 9.351570 GCGTTTAGAACACTACTTTAGTAATCT 57.648 33.333 5.76 5.76 37.23 2.40
5173 6523 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
5175 6525 9.939424 ACTCTTATATTAGTTTACAGAGGGAGT 57.061 33.333 0.00 0.00 32.21 3.85
5601 6951 3.576550 TCAAGCCTCATATGCGGTATGTA 59.423 43.478 13.19 1.81 40.87 2.29
5737 7087 6.430308 CAGAATCTTCTTGATGGATATGTGGG 59.570 42.308 0.00 0.00 34.74 4.61
5921 7271 7.361971 CCACATGCATGAATGTAGTTTTGTAGA 60.362 37.037 32.75 0.00 38.75 2.59
6188 7538 4.918810 ACCATCTTTTGTGGTCAACTTC 57.081 40.909 0.00 0.00 46.79 3.01
6263 7613 8.294954 TGAACTTAATTTACCCAAACAGTGAA 57.705 30.769 0.00 0.00 0.00 3.18
6438 7788 7.758528 CACGACCACTTTTAGTAGCTATTTAGT 59.241 37.037 0.00 0.00 0.00 2.24
6493 7843 2.372172 CGGTTGGGAGCCTTATCCTTAT 59.628 50.000 0.00 0.00 39.50 1.73
6655 8025 1.868469 GCTACACACACGGTTGGTAA 58.132 50.000 0.00 0.00 0.00 2.85
6921 8292 2.510238 GCCATGAGCGCGAAGTCT 60.510 61.111 12.10 0.00 0.00 3.24
7043 8414 4.497473 TGTAAGTTTGTAAGCATGCCAC 57.503 40.909 15.66 13.53 0.00 5.01
7053 8424 0.111061 AGCATGCCACTTGGAGAACA 59.889 50.000 15.66 0.00 37.39 3.18
7071 8442 5.555017 AGAACATGAGTTTGTGAGTATGCT 58.445 37.500 0.00 0.00 38.30 3.79
7329 9535 1.340017 GCTCCCTCAACTTGGTATGCA 60.340 52.381 0.00 0.00 0.00 3.96
7330 9536 2.684927 GCTCCCTCAACTTGGTATGCAT 60.685 50.000 3.79 3.79 0.00 3.96
7343 9549 9.573166 AACTTGGTATGCATCAGCTAAATTATA 57.427 29.630 0.19 0.00 42.74 0.98
7344 9550 9.003658 ACTTGGTATGCATCAGCTAAATTATAC 57.996 33.333 0.19 0.00 42.74 1.47
7345 9551 9.224267 CTTGGTATGCATCAGCTAAATTATACT 57.776 33.333 0.19 0.00 42.74 2.12
7357 9563 5.235616 GCTAAATTATACTACACGCTGGCAA 59.764 40.000 0.00 0.00 0.00 4.52
7499 9708 1.475280 CGAGAAAGACATCCCGTACCA 59.525 52.381 0.00 0.00 0.00 3.25
7505 9714 1.136305 AGACATCCCGTACCATTGTCG 59.864 52.381 0.00 0.00 41.15 4.35
7573 9782 2.968574 TGGCAAGGCTTTTGAAATGGTA 59.031 40.909 0.00 0.00 0.00 3.25
7671 9916 0.038343 TAACGACGGGTACTTGTGCC 60.038 55.000 0.00 0.00 0.00 5.01
7803 10048 4.036498 GCACTACATAGTCGAGCCTTCTTA 59.964 45.833 0.00 0.00 33.46 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.288576 ACATTCAACAAGAGAATAAAGATCACA 57.711 29.630 0.00 0.00 34.14 3.58
3 4 8.239314 GCACATTCAACAAGAGAATAAAGATCA 58.761 33.333 0.00 0.00 34.14 2.92
5 6 8.345724 AGCACATTCAACAAGAGAATAAAGAT 57.654 30.769 0.00 0.00 34.14 2.40
6 7 7.094634 GGAGCACATTCAACAAGAGAATAAAGA 60.095 37.037 0.00 0.00 34.14 2.52
7 8 7.025963 GGAGCACATTCAACAAGAGAATAAAG 58.974 38.462 0.00 0.00 34.14 1.85
8 9 6.716628 AGGAGCACATTCAACAAGAGAATAAA 59.283 34.615 0.00 0.00 34.14 1.40
9 10 6.240894 AGGAGCACATTCAACAAGAGAATAA 58.759 36.000 0.00 0.00 34.14 1.40
10 11 5.809001 AGGAGCACATTCAACAAGAGAATA 58.191 37.500 0.00 0.00 34.14 1.75
11 12 4.660168 AGGAGCACATTCAACAAGAGAAT 58.340 39.130 0.00 0.00 36.19 2.40
12 13 4.090761 AGGAGCACATTCAACAAGAGAA 57.909 40.909 0.00 0.00 0.00 2.87
13 14 3.777106 AGGAGCACATTCAACAAGAGA 57.223 42.857 0.00 0.00 0.00 3.10
14 15 4.825422 TCTAGGAGCACATTCAACAAGAG 58.175 43.478 0.00 0.00 0.00 2.85
15 16 4.890158 TCTAGGAGCACATTCAACAAGA 57.110 40.909 0.00 0.00 0.00 3.02
16 17 4.940046 ACATCTAGGAGCACATTCAACAAG 59.060 41.667 0.00 0.00 0.00 3.16
17 18 4.910195 ACATCTAGGAGCACATTCAACAA 58.090 39.130 0.00 0.00 0.00 2.83
18 19 4.558226 ACATCTAGGAGCACATTCAACA 57.442 40.909 0.00 0.00 0.00 3.33
19 20 5.907207 TCTACATCTAGGAGCACATTCAAC 58.093 41.667 0.00 0.00 0.00 3.18
20 21 6.737720 ATCTACATCTAGGAGCACATTCAA 57.262 37.500 0.00 0.00 0.00 2.69
21 22 6.737720 AATCTACATCTAGGAGCACATTCA 57.262 37.500 0.00 0.00 0.00 2.57
22 23 7.212976 TGAAATCTACATCTAGGAGCACATTC 58.787 38.462 0.00 0.00 0.00 2.67
23 24 7.129457 TGAAATCTACATCTAGGAGCACATT 57.871 36.000 0.00 0.00 0.00 2.71
24 25 6.737720 TGAAATCTACATCTAGGAGCACAT 57.262 37.500 0.00 0.00 0.00 3.21
25 26 6.324770 TGATGAAATCTACATCTAGGAGCACA 59.675 38.462 0.00 0.00 45.81 4.57
26 27 6.753180 TGATGAAATCTACATCTAGGAGCAC 58.247 40.000 0.00 0.00 45.81 4.40
27 28 6.983906 TGATGAAATCTACATCTAGGAGCA 57.016 37.500 0.00 0.00 45.81 4.26
39 40 9.208022 CGTTGCCTCTTATATTGATGAAATCTA 57.792 33.333 0.00 0.00 45.81 1.98
40 41 7.933577 TCGTTGCCTCTTATATTGATGAAATCT 59.066 33.333 0.00 0.00 45.81 2.40
41 42 8.087982 TCGTTGCCTCTTATATTGATGAAATC 57.912 34.615 0.00 0.00 45.83 2.17
42 43 8.450578 TTCGTTGCCTCTTATATTGATGAAAT 57.549 30.769 0.00 0.00 0.00 2.17
43 44 7.857734 TTCGTTGCCTCTTATATTGATGAAA 57.142 32.000 0.00 0.00 0.00 2.69
44 45 7.335673 TGTTTCGTTGCCTCTTATATTGATGAA 59.664 33.333 0.00 0.00 0.00 2.57
45 46 6.821160 TGTTTCGTTGCCTCTTATATTGATGA 59.179 34.615 0.00 0.00 0.00 2.92
46 47 7.015226 TGTTTCGTTGCCTCTTATATTGATG 57.985 36.000 0.00 0.00 0.00 3.07
47 48 7.624360 TTGTTTCGTTGCCTCTTATATTGAT 57.376 32.000 0.00 0.00 0.00 2.57
48 49 7.624360 ATTGTTTCGTTGCCTCTTATATTGA 57.376 32.000 0.00 0.00 0.00 2.57
49 50 9.950680 ATTATTGTTTCGTTGCCTCTTATATTG 57.049 29.630 0.00 0.00 0.00 1.90
50 51 9.950680 CATTATTGTTTCGTTGCCTCTTATATT 57.049 29.630 0.00 0.00 0.00 1.28
51 52 9.120538 ACATTATTGTTTCGTTGCCTCTTATAT 57.879 29.630 0.00 0.00 29.55 0.86
52 53 8.500753 ACATTATTGTTTCGTTGCCTCTTATA 57.499 30.769 0.00 0.00 29.55 0.98
53 54 7.391148 ACATTATTGTTTCGTTGCCTCTTAT 57.609 32.000 0.00 0.00 29.55 1.73
54 55 6.811253 ACATTATTGTTTCGTTGCCTCTTA 57.189 33.333 0.00 0.00 29.55 2.10
55 56 5.705609 ACATTATTGTTTCGTTGCCTCTT 57.294 34.783 0.00 0.00 29.55 2.85
56 57 7.391148 AATACATTATTGTTTCGTTGCCTCT 57.609 32.000 0.00 0.00 37.28 3.69
57 58 9.562583 TTTAATACATTATTGTTTCGTTGCCTC 57.437 29.630 0.00 0.00 37.28 4.70
58 59 9.915629 TTTTAATACATTATTGTTTCGTTGCCT 57.084 25.926 0.00 0.00 37.28 4.75
80 81 9.883142 GTGGTTCCAATTTGATTATCCATTTTA 57.117 29.630 0.00 0.00 0.00 1.52
81 82 7.548780 CGTGGTTCCAATTTGATTATCCATTTT 59.451 33.333 0.00 0.00 0.00 1.82
82 83 7.041107 CGTGGTTCCAATTTGATTATCCATTT 58.959 34.615 0.00 0.00 0.00 2.32
83 84 6.379703 TCGTGGTTCCAATTTGATTATCCATT 59.620 34.615 0.00 0.00 0.00 3.16
84 85 5.890985 TCGTGGTTCCAATTTGATTATCCAT 59.109 36.000 0.00 0.00 0.00 3.41
85 86 5.124776 GTCGTGGTTCCAATTTGATTATCCA 59.875 40.000 0.00 0.00 0.00 3.41
86 87 5.124776 TGTCGTGGTTCCAATTTGATTATCC 59.875 40.000 0.00 0.00 0.00 2.59
87 88 6.093495 TCTGTCGTGGTTCCAATTTGATTATC 59.907 38.462 0.00 0.00 0.00 1.75
88 89 5.943416 TCTGTCGTGGTTCCAATTTGATTAT 59.057 36.000 0.00 0.00 0.00 1.28
89 90 5.309638 TCTGTCGTGGTTCCAATTTGATTA 58.690 37.500 0.00 0.00 0.00 1.75
90 91 4.141287 TCTGTCGTGGTTCCAATTTGATT 58.859 39.130 0.00 0.00 0.00 2.57
91 92 3.750371 TCTGTCGTGGTTCCAATTTGAT 58.250 40.909 0.00 0.00 0.00 2.57
92 93 3.201353 TCTGTCGTGGTTCCAATTTGA 57.799 42.857 0.00 0.00 0.00 2.69
93 94 5.181245 AGTTATCTGTCGTGGTTCCAATTTG 59.819 40.000 0.00 0.00 0.00 2.32
94 95 5.313712 AGTTATCTGTCGTGGTTCCAATTT 58.686 37.500 0.00 0.00 0.00 1.82
95 96 4.906618 AGTTATCTGTCGTGGTTCCAATT 58.093 39.130 0.00 0.00 0.00 2.32
96 97 4.553330 AGTTATCTGTCGTGGTTCCAAT 57.447 40.909 0.00 0.00 0.00 3.16
97 98 4.768448 TCTAGTTATCTGTCGTGGTTCCAA 59.232 41.667 0.00 0.00 0.00 3.53
98 99 4.338012 TCTAGTTATCTGTCGTGGTTCCA 58.662 43.478 0.00 0.00 0.00 3.53
99 100 4.978083 TCTAGTTATCTGTCGTGGTTCC 57.022 45.455 0.00 0.00 0.00 3.62
100 101 9.530633 AATTTATCTAGTTATCTGTCGTGGTTC 57.469 33.333 0.00 0.00 0.00 3.62
101 102 9.530633 GAATTTATCTAGTTATCTGTCGTGGTT 57.469 33.333 0.00 0.00 0.00 3.67
102 103 8.915036 AGAATTTATCTAGTTATCTGTCGTGGT 58.085 33.333 0.00 0.00 36.32 4.16
170 171 9.793259 TGACTTAGGAAAAACTCATCAAGTAAT 57.207 29.630 0.00 0.00 37.17 1.89
171 172 9.621629 TTGACTTAGGAAAAACTCATCAAGTAA 57.378 29.630 0.00 0.00 37.17 2.24
172 173 9.621629 TTTGACTTAGGAAAAACTCATCAAGTA 57.378 29.630 0.00 0.00 37.17 2.24
173 174 8.406297 GTTTGACTTAGGAAAAACTCATCAAGT 58.594 33.333 0.00 0.00 41.10 3.16
174 175 8.624776 AGTTTGACTTAGGAAAAACTCATCAAG 58.375 33.333 4.22 0.00 38.19 3.02
175 176 8.519799 AGTTTGACTTAGGAAAAACTCATCAA 57.480 30.769 4.22 0.00 38.19 2.57
176 177 8.519799 AAGTTTGACTTAGGAAAAACTCATCA 57.480 30.769 8.77 0.00 40.91 3.07
177 178 9.803315 AAAAGTTTGACTTAGGAAAAACTCATC 57.197 29.630 8.77 0.00 40.91 2.92
202 203 2.672098 TGAGTTGGCCAGCCTTAAAAA 58.328 42.857 16.95 0.00 36.94 1.94
203 204 2.364002 GTTGAGTTGGCCAGCCTTAAAA 59.636 45.455 16.95 5.29 36.94 1.52
204 205 1.960689 GTTGAGTTGGCCAGCCTTAAA 59.039 47.619 16.95 7.55 36.94 1.52
205 206 1.616159 GTTGAGTTGGCCAGCCTTAA 58.384 50.000 16.95 11.35 36.94 1.85
206 207 0.605319 CGTTGAGTTGGCCAGCCTTA 60.605 55.000 16.95 5.42 36.94 2.69
207 208 1.898574 CGTTGAGTTGGCCAGCCTT 60.899 57.895 16.95 0.00 36.94 4.35
208 209 2.281761 CGTTGAGTTGGCCAGCCT 60.282 61.111 16.95 11.49 36.94 4.58
209 210 1.452145 TTTCGTTGAGTTGGCCAGCC 61.452 55.000 16.95 8.49 0.00 4.85
210 211 0.383949 TTTTCGTTGAGTTGGCCAGC 59.616 50.000 12.39 12.39 0.00 4.85
211 212 4.701956 ATATTTTCGTTGAGTTGGCCAG 57.298 40.909 5.11 0.00 0.00 4.85
212 213 6.576662 TTTATATTTTCGTTGAGTTGGCCA 57.423 33.333 0.00 0.00 0.00 5.36
213 214 7.480810 AGATTTATATTTTCGTTGAGTTGGCC 58.519 34.615 0.00 0.00 0.00 5.36
372 375 9.857656 AGAGCATATTTCATCTCTTCCAAATTA 57.142 29.630 0.00 0.00 32.44 1.40
373 376 8.763984 AGAGCATATTTCATCTCTTCCAAATT 57.236 30.769 0.00 0.00 32.44 1.82
418 421 6.553100 GGATGATCCTACTATCTTATGGAGGG 59.447 46.154 3.71 0.00 32.53 4.30
451 454 4.141597 TGAGTCGGCCATACATTTGGAATA 60.142 41.667 2.24 0.00 39.25 1.75
486 489 2.584835 TAAGCTCCCACTTGTGCAAT 57.415 45.000 0.00 0.00 0.00 3.56
518 521 9.120422 GTAAATGTATTTTAGGTGTGGTTTTCG 57.880 33.333 0.00 0.00 30.46 3.46
543 555 5.482878 TGGGAACTATCCTCGTAGAAAAAGT 59.517 40.000 0.00 0.00 45.77 2.66
726 1010 6.885918 TGTGAGACACATGGTGAAATGATTAT 59.114 34.615 2.98 0.00 39.62 1.28
803 1370 1.896660 AATGGGCTTGCGACACGTT 60.897 52.632 0.00 0.00 0.00 3.99
813 1380 1.777272 GACCTCCTATCCAATGGGCTT 59.223 52.381 0.00 0.00 0.00 4.35
930 1498 0.106669 GCTCCGGGCTCCCTTTATTT 60.107 55.000 0.00 0.00 38.06 1.40
931 1499 1.532238 GCTCCGGGCTCCCTTTATT 59.468 57.895 0.00 0.00 38.06 1.40
933 1501 3.467226 CGCTCCGGGCTCCCTTTA 61.467 66.667 0.00 0.00 39.13 1.85
1061 1641 2.047179 AGAAAGGCGCGGAGGAAC 60.047 61.111 8.83 0.00 0.00 3.62
1154 1734 3.522731 CTCCCTCTCCGCGTCCTG 61.523 72.222 4.92 0.00 0.00 3.86
1466 2046 2.159198 GGCATGCACGAAATGAAGGAAT 60.159 45.455 21.36 0.00 0.00 3.01
1482 2062 2.652095 CCCAAACCCAGCAGGCATG 61.652 63.158 0.00 0.00 40.58 4.06
1507 2087 9.729281 ATAAAAGTTTCAACCCGATAGAGTTTA 57.271 29.630 0.00 0.00 39.76 2.01
1859 2472 5.336690 CCAACCATGATTTAGTTCCAAGTGG 60.337 44.000 0.00 0.00 0.00 4.00
2064 2678 8.579850 AGCAATATCTTCACTATTTCAACCAA 57.420 30.769 0.00 0.00 0.00 3.67
2065 2679 7.828717 TGAGCAATATCTTCACTATTTCAACCA 59.171 33.333 0.00 0.00 0.00 3.67
2321 2946 3.536956 AATAGGATCTCCGACGCAAAA 57.463 42.857 0.00 0.00 42.08 2.44
2357 2993 4.202111 CCTCCAAATAATACCCCGCAAAAG 60.202 45.833 0.00 0.00 0.00 2.27
2428 3064 6.795144 TTGAATGCAATCATGGTCCTATTT 57.205 33.333 5.05 0.00 32.23 1.40
2505 3142 7.520798 AGGGAAAATATAAGTCTGATGCATCA 58.479 34.615 27.10 27.10 35.16 3.07
2544 3181 7.450014 TGTGAACAATTAGGCTTGGATTTCTAA 59.550 33.333 0.00 0.00 0.00 2.10
2554 3191 5.263599 TGGATCATGTGAACAATTAGGCTT 58.736 37.500 0.00 0.00 0.00 4.35
2595 3232 5.751028 GTGCAGTAACACCTCTAGAATCATC 59.249 44.000 0.00 0.00 34.35 2.92
2681 3318 1.592400 GGCCTGTTCCCCGCTTTAAC 61.592 60.000 0.00 0.00 0.00 2.01
2906 3543 3.072915 TGTCCTCTTCAGCTCCAATTTCA 59.927 43.478 0.00 0.00 0.00 2.69
3100 3737 8.052748 TGAACTGGATATTGTAGCCTAAACAAT 58.947 33.333 6.67 6.67 46.49 2.71
3102 3739 6.821665 GTGAACTGGATATTGTAGCCTAAACA 59.178 38.462 0.00 0.00 34.68 2.83
3103 3740 6.260271 GGTGAACTGGATATTGTAGCCTAAAC 59.740 42.308 0.00 0.00 34.68 2.01
3104 3741 6.157994 AGGTGAACTGGATATTGTAGCCTAAA 59.842 38.462 0.00 0.00 34.68 1.85
3367 4009 6.299141 ACTCTTATAAATCCATGCATCGGTT 58.701 36.000 12.89 0.00 0.00 4.44
3382 4024 5.721960 AGGAGCTTGGACTGAACTCTTATAA 59.278 40.000 0.00 0.00 0.00 0.98
3383 4025 5.127845 CAGGAGCTTGGACTGAACTCTTATA 59.872 44.000 0.00 0.00 34.21 0.98
3415 4057 5.711506 TCACACTGCATAACCTGAATTCAAT 59.288 36.000 9.88 0.00 0.00 2.57
3504 4146 5.129155 CCAAATGATTAACCACCATCACCAT 59.871 40.000 0.00 0.00 32.19 3.55
3505 4147 4.465660 CCAAATGATTAACCACCATCACCA 59.534 41.667 0.00 0.00 32.19 4.17
3506 4148 4.680440 GCCAAATGATTAACCACCATCACC 60.680 45.833 0.00 0.00 32.19 4.02
3507 4149 4.432712 GCCAAATGATTAACCACCATCAC 58.567 43.478 0.00 0.00 32.19 3.06
3508 4150 3.450457 GGCCAAATGATTAACCACCATCA 59.550 43.478 0.00 0.00 33.92 3.07
3509 4151 3.706086 AGGCCAAATGATTAACCACCATC 59.294 43.478 5.01 0.00 0.00 3.51
4327 4969 6.357367 ACAGAACCTCAGTTAACAACTTCAT 58.643 36.000 8.61 0.00 40.46 2.57
4330 4972 7.120923 TCTACAGAACCTCAGTTAACAACTT 57.879 36.000 8.61 0.00 40.46 2.66
4378 5022 8.634475 TCAAGAATCAGTGTATTGTCTTATCG 57.366 34.615 0.00 0.00 0.00 2.92
4435 5079 4.682563 ACAAATATTGGGTCAATGGGTCA 58.317 39.130 3.65 0.00 35.54 4.02
4576 5220 7.175104 TGTAAAGAAGCATGATCCTTACCTTT 58.825 34.615 13.52 9.12 0.00 3.11
4666 5310 0.685097 TATCACAGGATAAGCGGCCC 59.315 55.000 0.00 0.00 33.11 5.80
4775 5419 7.232534 AGTGCAACCAAGTAAAAATCCAGATTA 59.767 33.333 0.00 0.00 37.80 1.75
4778 5422 4.892934 AGTGCAACCAAGTAAAAATCCAGA 59.107 37.500 0.00 0.00 37.80 3.86
4844 5488 8.187913 TCAATCATCTTTGATAAAACCCACAA 57.812 30.769 0.00 0.00 41.83 3.33
4940 5584 9.462174 CTTTGATGAGTGCAAATACAGTAAAAA 57.538 29.630 0.00 0.00 35.00 1.94
5094 6444 7.976734 CGCTCTTATATTAGTTTATGGAGGGAG 59.023 40.741 0.00 0.00 33.23 4.30
5096 6446 7.612677 ACGCTCTTATATTAGTTTATGGAGGG 58.387 38.462 0.00 0.00 35.06 4.30
5097 6447 9.490379 AAACGCTCTTATATTAGTTTATGGAGG 57.510 33.333 0.00 0.00 31.14 4.30
5118 6468 9.351570 AGATTACTAAAGTAGTGTTCTAAACGC 57.648 33.333 0.00 0.00 39.81 4.84
5147 6497 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
5149 6499 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
5168 6518 9.952188 GCATTACAAATTAGAAATTACTCCCTC 57.048 33.333 0.00 0.00 0.00 4.30
5169 6519 8.914011 GGCATTACAAATTAGAAATTACTCCCT 58.086 33.333 0.00 0.00 0.00 4.20
5170 6520 8.141909 GGGCATTACAAATTAGAAATTACTCCC 58.858 37.037 0.00 0.00 0.00 4.30
5171 6521 8.914011 AGGGCATTACAAATTAGAAATTACTCC 58.086 33.333 0.00 0.00 0.00 3.85
5174 6524 9.529325 GGAAGGGCATTACAAATTAGAAATTAC 57.471 33.333 0.00 0.00 0.00 1.89
5175 6525 9.487442 AGGAAGGGCATTACAAATTAGAAATTA 57.513 29.630 0.00 0.00 0.00 1.40
5260 6610 8.946085 CCTTTTCAGTCACAACATAGCTAATTA 58.054 33.333 0.00 0.00 0.00 1.40
5601 6951 6.409005 GCCAAGTATCATATCTGGGCATCTAT 60.409 42.308 5.79 0.00 46.72 1.98
5944 7294 7.263100 TGCGATACAAGATTATGCAATTCTT 57.737 32.000 0.00 0.00 0.00 2.52
6036 7386 9.605275 AGAAACTGAAAGATCGATAATTCATCA 57.395 29.630 19.77 9.91 37.43 3.07
6188 7538 2.715046 TGTTTATCCTTGCTCTGCAGG 58.285 47.619 15.13 5.82 40.61 4.85
6438 7788 5.009110 TCGCAAACATCAATGGAACTAACAA 59.991 36.000 0.00 0.00 0.00 2.83
6452 7802 1.127582 GAGTCAGCAGTCGCAAACATC 59.872 52.381 0.00 0.00 42.27 3.06
6493 7843 7.201830 GCATCCTAGTAGTAGACAACAATGAGA 60.202 40.741 6.14 0.00 0.00 3.27
6678 8048 3.073798 TGGGGTTAGCTTCAAGAACATCA 59.926 43.478 0.00 0.00 0.00 3.07
6903 8274 3.567797 GACTTCGCGCTCATGGCC 61.568 66.667 5.56 0.00 37.74 5.36
6921 8292 5.338632 TCAATACAGGGAGAGACCAGTAAA 58.661 41.667 0.00 0.00 41.20 2.01
7043 8414 4.818546 ACTCACAAACTCATGTTCTCCAAG 59.181 41.667 0.00 0.00 34.96 3.61
7053 8424 5.683876 AGGTAGCATACTCACAAACTCAT 57.316 39.130 0.00 0.00 42.51 2.90
7071 8442 1.276421 GCAGCTCAGGTTCTCAAGGTA 59.724 52.381 0.00 0.00 0.00 3.08
7120 8491 4.202716 ACAAAATGGGATTCTCTGGACCTT 60.203 41.667 0.00 0.00 0.00 3.50
7343 9549 1.663702 GTCGTTGCCAGCGTGTAGT 60.664 57.895 0.00 0.00 0.00 2.73
7344 9550 2.716828 CGTCGTTGCCAGCGTGTAG 61.717 63.158 0.00 0.00 0.00 2.74
7345 9551 2.127634 TACGTCGTTGCCAGCGTGTA 62.128 55.000 1.78 3.07 38.10 2.90
7357 9563 2.094182 ACAAGATTGGATGCTACGTCGT 60.094 45.455 2.21 2.21 0.00 4.34
7499 9708 7.560368 AGATCAAGAGGATAAGAAACGACAAT 58.440 34.615 0.00 0.00 36.00 2.71
7505 9714 8.785329 AAGTCAAGATCAAGAGGATAAGAAAC 57.215 34.615 0.00 0.00 36.00 2.78
7573 9782 5.938125 ACTGATGACTAAGGTAAAACGCAAT 59.062 36.000 0.00 0.00 0.00 3.56
7671 9916 3.557264 GGACTTCTTTGGTCCCACTACTG 60.557 52.174 1.80 0.00 45.31 2.74
7730 9975 5.235186 GGACTACATCCTGTCAAAATCATCG 59.765 44.000 0.00 0.00 45.22 3.84
7755 10000 0.608308 AAGCGGGGAAACTAGTTGGC 60.608 55.000 9.34 8.12 0.00 4.52
7762 10007 1.244019 GCATGTCAAGCGGGGAAACT 61.244 55.000 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.