Multiple sequence alignment - TraesCS3D01G373100

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS3D01G373100 chr3D 100.000 1586 0 0 679 2264 486682262 486680677 0.000000e+00 2929.0
1 TraesCS3D01G373100 chr3D 93.086 998 51 4 679 1674 230694498 230695479 0.000000e+00 1445.0
2 TraesCS3D01G373100 chr3D 90.291 412 33 3 1666 2070 230695502 230695913 1.190000e-147 532.0
3 TraesCS3D01G373100 chr3D 90.291 412 33 3 1666 2070 230710827 230711238 1.190000e-147 532.0
4 TraesCS3D01G373100 chr3D 90.244 410 31 5 1666 2069 230593534 230593940 5.540000e-146 527.0
5 TraesCS3D01G373100 chr3D 100.000 256 0 0 1 256 486682940 486682685 7.320000e-130 473.0
6 TraesCS3D01G373100 chr3D 94.872 195 10 0 2070 2264 491823382 491823576 2.830000e-79 305.0
7 TraesCS3D01G373100 chr3D 86.364 132 16 2 36 166 486682775 486682905 2.340000e-30 143.0
8 TraesCS3D01G373100 chr3D 84.783 92 14 0 1 92 605963180 605963271 2.390000e-15 93.5
9 TraesCS3D01G373100 chr5D 94.790 998 34 4 679 1674 527486663 527487644 0.000000e+00 1539.0
10 TraesCS3D01G373100 chr5D 94.845 194 10 0 2071 2264 276033548 276033355 1.020000e-78 303.0
11 TraesCS3D01G373100 chr5D 94.359 195 11 0 2070 2264 114686761 114686955 1.310000e-77 300.0
12 TraesCS3D01G373100 chr5D 93.970 199 11 1 2066 2264 408192811 408192614 1.310000e-77 300.0
13 TraesCS3D01G373100 chr5D 82.143 168 15 5 52 205 527486534 527486368 1.820000e-26 130.0
14 TraesCS3D01G373100 chr5A 92.786 998 53 10 679 1674 588455205 588454225 0.000000e+00 1426.0
15 TraesCS3D01G373100 chr5A 88.696 115 13 0 91 205 588455417 588455303 8.430000e-30 141.0
16 TraesCS3D01G373100 chr5A 89.362 94 5 5 2 92 484630046 484629955 1.840000e-21 113.0
17 TraesCS3D01G373100 chr1A 92.663 995 55 4 682 1674 259893444 259892466 0.000000e+00 1417.0
18 TraesCS3D01G373100 chr1A 91.337 404 34 1 1667 2069 259892442 259892039 3.290000e-153 551.0
19 TraesCS3D01G373100 chr4A 91.683 998 54 5 679 1674 598516300 598517270 0.000000e+00 1356.0
20 TraesCS3D01G373100 chr4A 93.500 200 13 0 2065 2264 58107162 58106963 4.730000e-77 298.0
21 TraesCS3D01G373100 chr4A 82.412 199 26 8 11 205 598515940 598515747 5.000000e-37 165.0
22 TraesCS3D01G373100 chr4A 86.207 116 13 3 52 165 598515800 598515914 3.050000e-24 122.0
23 TraesCS3D01G373100 chr4B 90.827 992 61 4 681 1671 612515160 612514198 0.000000e+00 1301.0
24 TraesCS3D01G373100 chr4B 93.204 412 27 1 1292 1702 648203274 648202863 2.490000e-169 604.0
25 TraesCS3D01G373100 chr4B 92.718 412 29 1 1292 1702 648228533 648228122 5.380000e-166 593.0
26 TraesCS3D01G373100 chr4B 92.476 412 30 1 1292 1702 648182024 648181613 2.510000e-164 588.0
27 TraesCS3D01G373100 chr4B 92.476 412 30 1 1292 1702 648252544 648252133 2.510000e-164 588.0
28 TraesCS3D01G373100 chr4B 90.365 384 27 5 1666 2045 612514171 612513794 1.560000e-136 496.0
29 TraesCS3D01G373100 chr4B 86.555 119 16 0 90 208 612515385 612515267 5.070000e-27 132.0
30 TraesCS3D01G373100 chr4B 86.813 91 12 0 1 91 612515471 612515561 3.980000e-18 102.0
31 TraesCS3D01G373100 chr7B 90.352 995 78 8 680 1673 65835683 65836660 0.000000e+00 1290.0
32 TraesCS3D01G373100 chr7B 93.571 560 33 3 679 1237 685956154 685956711 0.000000e+00 832.0
33 TraesCS3D01G373100 chr7B 93.375 317 18 2 1666 1981 685957091 685957405 1.220000e-127 466.0
34 TraesCS3D01G373100 chr7B 95.361 194 9 0 2070 2263 246935366 246935173 2.180000e-80 309.0
35 TraesCS3D01G373100 chr7B 88.636 88 10 0 121 208 65835489 65835576 8.550000e-20 108.0
36 TraesCS3D01G373100 chr7B 83.621 116 14 5 92 206 118209970 118210081 1.110000e-18 104.0
37 TraesCS3D01G373100 chr7B 87.952 83 10 0 10 92 400947090 400947008 5.150000e-17 99.0
38 TraesCS3D01G373100 chr2B 88.790 1008 77 13 679 1674 40122543 40123526 0.000000e+00 1203.0
39 TraesCS3D01G373100 chr2B 90.489 736 46 10 990 1702 166034871 166035605 0.000000e+00 950.0
40 TraesCS3D01G373100 chr2B 90.123 405 37 2 1666 2069 730044340 730044742 7.160000e-145 523.0
41 TraesCS3D01G373100 chr2B 85.827 127 18 0 82 208 609251090 609251216 3.920000e-28 135.0
42 TraesCS3D01G373100 chr2B 94.595 37 2 0 1949 1985 609254251 609254287 8.730000e-05 58.4
43 TraesCS3D01G373100 chr5B 90.761 736 44 10 990 1702 516276204 516275470 0.000000e+00 961.0
44 TraesCS3D01G373100 chr3B 90.502 737 45 11 990 1702 499180494 499181229 0.000000e+00 950.0
45 TraesCS3D01G373100 chr1B 90.082 736 47 11 990 1702 670665146 670665878 0.000000e+00 931.0
46 TraesCS3D01G373100 chr1B 86.951 751 55 22 990 1702 551878018 551877273 0.000000e+00 804.0
47 TraesCS3D01G373100 chr1B 89.055 402 37 4 1666 2060 642719570 642719971 2.020000e-135 492.0
48 TraesCS3D01G373100 chr1D 88.835 412 39 3 1666 2070 465921361 465921772 1.210000e-137 499.0
49 TraesCS3D01G373100 chr4D 94.845 194 9 1 2070 2262 271916910 271917103 3.650000e-78 302.0
50 TraesCS3D01G373100 chr4D 85.106 94 10 3 1 92 85739419 85739328 2.390000e-15 93.5
51 TraesCS3D01G373100 chr7D 93.970 199 10 2 2064 2260 628546712 628546910 1.310000e-77 300.0
52 TraesCS3D01G373100 chr3A 93.500 200 12 1 2065 2264 458150625 458150427 1.700000e-76 296.0
53 TraesCS3D01G373100 chr6D 76.682 223 29 11 1 200 421592892 421593114 3.980000e-18 102.0
54 TraesCS3D01G373100 chr6D 85.106 94 10 4 1 92 421592804 421592713 2.390000e-15 93.5


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 TraesCS3D01G373100 chr3D 486680677 486682940 2263 True 1701.0 2929 100.0000 1 2264 2 chr3D.!!$R1 2263
1 TraesCS3D01G373100 chr3D 230694498 230695913 1415 False 988.5 1445 91.6885 679 2070 2 chr3D.!!$F6 1391
2 TraesCS3D01G373100 chr5D 527486663 527487644 981 False 1539.0 1539 94.7900 679 1674 1 chr5D.!!$F2 995
3 TraesCS3D01G373100 chr5A 588454225 588455417 1192 True 783.5 1426 90.7410 91 1674 2 chr5A.!!$R2 1583
4 TraesCS3D01G373100 chr1A 259892039 259893444 1405 True 984.0 1417 92.0000 682 2069 2 chr1A.!!$R1 1387
5 TraesCS3D01G373100 chr4A 598515800 598517270 1470 False 739.0 1356 88.9450 52 1674 2 chr4A.!!$F1 1622
6 TraesCS3D01G373100 chr4B 612513794 612515385 1591 True 643.0 1301 89.2490 90 2045 3 chr4B.!!$R5 1955
7 TraesCS3D01G373100 chr7B 65835489 65836660 1171 False 699.0 1290 89.4940 121 1673 2 chr7B.!!$F2 1552
8 TraesCS3D01G373100 chr7B 685956154 685957405 1251 False 649.0 832 93.4730 679 1981 2 chr7B.!!$F3 1302
9 TraesCS3D01G373100 chr2B 40122543 40123526 983 False 1203.0 1203 88.7900 679 1674 1 chr2B.!!$F1 995
10 TraesCS3D01G373100 chr2B 166034871 166035605 734 False 950.0 950 90.4890 990 1702 1 chr2B.!!$F2 712
11 TraesCS3D01G373100 chr5B 516275470 516276204 734 True 961.0 961 90.7610 990 1702 1 chr5B.!!$R1 712
12 TraesCS3D01G373100 chr3B 499180494 499181229 735 False 950.0 950 90.5020 990 1702 1 chr3B.!!$F1 712
13 TraesCS3D01G373100 chr1B 670665146 670665878 732 False 931.0 931 90.0820 990 1702 1 chr1B.!!$F2 712
14 TraesCS3D01G373100 chr1B 551877273 551878018 745 True 804.0 804 86.9510 990 1702 1 chr1B.!!$R1 712

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
254 554 0.10741 ACACACAAACCCGAAGCTCA 60.107 50.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1985 2418 0.108329 GTGTAGTGCGTGTGCCCTAT 60.108 55.0 0.0 0.0 41.78 2.57 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
23 24 6.566197 CTGCACCTTGACTTAGAGAATTTT 57.434 37.500 0.00 0.00 0.00 1.82
24 25 6.959639 TGCACCTTGACTTAGAGAATTTTT 57.040 33.333 0.00 0.00 0.00 1.94
25 26 6.738114 TGCACCTTGACTTAGAGAATTTTTG 58.262 36.000 0.00 0.00 0.00 2.44
26 27 6.152379 GCACCTTGACTTAGAGAATTTTTGG 58.848 40.000 0.00 0.00 0.00 3.28
27 28 6.152379 CACCTTGACTTAGAGAATTTTTGGC 58.848 40.000 0.00 0.00 0.00 4.52
28 29 5.833131 ACCTTGACTTAGAGAATTTTTGGCA 59.167 36.000 0.00 0.00 0.00 4.92
29 30 6.323739 ACCTTGACTTAGAGAATTTTTGGCAA 59.676 34.615 0.00 0.00 0.00 4.52
30 31 6.865205 CCTTGACTTAGAGAATTTTTGGCAAG 59.135 38.462 0.00 0.00 0.00 4.01
31 32 6.331369 TGACTTAGAGAATTTTTGGCAAGG 57.669 37.500 0.00 0.00 0.00 3.61
32 33 6.068010 TGACTTAGAGAATTTTTGGCAAGGA 58.932 36.000 0.00 0.00 0.00 3.36
33 34 6.549364 TGACTTAGAGAATTTTTGGCAAGGAA 59.451 34.615 0.00 0.06 0.00 3.36
34 35 7.069331 TGACTTAGAGAATTTTTGGCAAGGAAA 59.931 33.333 0.00 0.00 0.00 3.13
35 36 7.436933 ACTTAGAGAATTTTTGGCAAGGAAAG 58.563 34.615 0.00 0.00 0.00 2.62
36 37 4.635223 AGAGAATTTTTGGCAAGGAAAGC 58.365 39.130 0.00 0.00 0.00 3.51
37 38 4.346127 AGAGAATTTTTGGCAAGGAAAGCT 59.654 37.500 0.00 1.66 0.00 3.74
38 39 5.539955 AGAGAATTTTTGGCAAGGAAAGCTA 59.460 36.000 0.00 0.00 0.00 3.32
39 40 5.541845 AGAATTTTTGGCAAGGAAAGCTAC 58.458 37.500 0.00 0.00 0.00 3.58
40 41 5.305386 AGAATTTTTGGCAAGGAAAGCTACT 59.695 36.000 0.00 0.00 0.00 2.57
41 42 4.320608 TTTTTGGCAAGGAAAGCTACTG 57.679 40.909 0.00 0.00 0.00 2.74
42 43 1.909700 TTGGCAAGGAAAGCTACTGG 58.090 50.000 0.00 0.00 0.00 4.00
43 44 1.064003 TGGCAAGGAAAGCTACTGGA 58.936 50.000 0.00 0.00 0.00 3.86
44 45 1.423541 TGGCAAGGAAAGCTACTGGAA 59.576 47.619 0.00 0.00 0.00 3.53
45 46 2.041620 TGGCAAGGAAAGCTACTGGAAT 59.958 45.455 0.00 0.00 0.00 3.01
46 47 3.265737 TGGCAAGGAAAGCTACTGGAATA 59.734 43.478 0.00 0.00 0.00 1.75
47 48 3.879892 GGCAAGGAAAGCTACTGGAATAG 59.120 47.826 0.00 0.00 0.00 1.73
48 49 4.518249 GCAAGGAAAGCTACTGGAATAGT 58.482 43.478 0.00 0.00 43.56 2.12
49 50 4.333926 GCAAGGAAAGCTACTGGAATAGTG 59.666 45.833 0.00 0.00 40.65 2.74
50 51 5.491982 CAAGGAAAGCTACTGGAATAGTGT 58.508 41.667 0.00 0.00 40.65 3.55
153 155 2.224378 CCAGTCCAGAGAGCAACAGAAA 60.224 50.000 0.00 0.00 0.00 2.52
208 447 3.580193 GCTAGGCGCTGCACATGG 61.580 66.667 7.64 0.00 35.14 3.66
209 448 3.580193 CTAGGCGCTGCACATGGC 61.580 66.667 7.64 0.00 45.13 4.40
254 554 0.107410 ACACACAAACCCGAAGCTCA 60.107 50.000 0.00 0.00 0.00 4.26
255 555 0.588252 CACACAAACCCGAAGCTCAG 59.412 55.000 0.00 0.00 0.00 3.35
1105 1445 3.601443 AGGTGAAGGAGAAAGATGTCG 57.399 47.619 0.00 0.00 0.00 4.35
1132 1472 3.346315 CTGCCATGTTGGTGTGAAGATA 58.654 45.455 0.00 0.00 40.46 1.98
1276 1652 6.070938 ACCGGTAAGCTAGAGAAGTAAAATGT 60.071 38.462 4.49 0.00 0.00 2.71
1277 1653 6.817140 CCGGTAAGCTAGAGAAGTAAAATGTT 59.183 38.462 0.00 0.00 0.00 2.71
1278 1654 7.333672 CCGGTAAGCTAGAGAAGTAAAATGTTT 59.666 37.037 0.00 0.00 0.00 2.83
1279 1655 8.169268 CGGTAAGCTAGAGAAGTAAAATGTTTG 58.831 37.037 0.00 0.00 0.00 2.93
1280 1656 9.000486 GGTAAGCTAGAGAAGTAAAATGTTTGT 58.000 33.333 0.00 0.00 0.00 2.83
1282 1658 8.677148 AAGCTAGAGAAGTAAAATGTTTGTCA 57.323 30.769 0.00 0.00 0.00 3.58
1283 1659 8.677148 AGCTAGAGAAGTAAAATGTTTGTCAA 57.323 30.769 0.00 0.00 0.00 3.18
1284 1660 8.560374 AGCTAGAGAAGTAAAATGTTTGTCAAC 58.440 33.333 0.00 0.00 0.00 3.18
1286 1662 9.651718 CTAGAGAAGTAAAATGTTTGTCAACAC 57.348 33.333 0.00 0.00 45.88 3.32
1287 1663 8.281212 AGAGAAGTAAAATGTTTGTCAACACT 57.719 30.769 0.00 0.00 45.88 3.55
1288 1664 8.739972 AGAGAAGTAAAATGTTTGTCAACACTT 58.260 29.630 0.00 0.00 45.88 3.16
1289 1665 9.997482 GAGAAGTAAAATGTTTGTCAACACTTA 57.003 29.630 0.00 0.00 45.88 2.24
1290 1666 9.783256 AGAAGTAAAATGTTTGTCAACACTTAC 57.217 29.630 10.92 10.92 45.88 2.34
1557 1950 2.781158 GCTCGTGAGGAGGAGAGGC 61.781 68.421 4.18 0.00 43.36 4.70
1577 1970 1.505425 CAAGAAAGCTTGCAAAGGCC 58.495 50.000 7.33 0.00 46.35 5.19
1583 1976 3.443045 CTTGCAAAGGCCCGCGAT 61.443 61.111 8.23 0.00 41.27 4.58
1731 2156 7.789026 ACTATGTCGTAGTAGGCCTAAATTTT 58.211 34.615 15.83 0.68 41.84 1.82
1785 2210 6.767902 GTGAGGTTATGTGATATGTTGGTGAT 59.232 38.462 0.00 0.00 0.00 3.06
1920 2347 8.556194 TCAAGTTATTGTAAGTGTTGTGATGTC 58.444 33.333 0.00 0.00 37.68 3.06
1985 2418 2.542178 CAGTTAACAGTACTGCAACGCA 59.458 45.455 22.90 0.00 36.88 5.24
1995 2428 2.257286 CTGCAACGCATAGGGCACAC 62.257 60.000 0.00 0.00 45.17 3.82
2037 2470 1.003355 CCCAACAGTCAGGCGTCAT 60.003 57.895 0.00 0.00 0.00 3.06
2074 2507 3.382048 CCTTACCCTTAGGCGTGATAC 57.618 52.381 0.00 0.00 36.11 2.24
2075 2508 2.288030 CCTTACCCTTAGGCGTGATACG 60.288 54.545 0.00 0.00 45.88 3.06
2076 2509 2.057137 TACCCTTAGGCGTGATACGT 57.943 50.000 0.00 0.00 44.73 3.57
2083 2516 2.662150 GGCGTGATACGTCTCCAAC 58.338 57.895 0.00 0.00 43.82 3.77
2096 2529 5.928601 CGTCTCCAACGTATCTACTTTTC 57.071 43.478 0.00 0.00 46.42 2.29
2097 2530 4.797349 CGTCTCCAACGTATCTACTTTTCC 59.203 45.833 0.00 0.00 46.42 3.13
2098 2531 5.392811 CGTCTCCAACGTATCTACTTTTCCT 60.393 44.000 0.00 0.00 46.42 3.36
2099 2532 6.183360 CGTCTCCAACGTATCTACTTTTCCTA 60.183 42.308 0.00 0.00 46.42 2.94
2100 2533 7.542025 GTCTCCAACGTATCTACTTTTCCTAA 58.458 38.462 0.00 0.00 0.00 2.69
2101 2534 7.487509 GTCTCCAACGTATCTACTTTTCCTAAC 59.512 40.741 0.00 0.00 0.00 2.34
2102 2535 7.177216 TCTCCAACGTATCTACTTTTCCTAACA 59.823 37.037 0.00 0.00 0.00 2.41
2103 2536 7.092716 TCCAACGTATCTACTTTTCCTAACAC 58.907 38.462 0.00 0.00 0.00 3.32
2104 2537 7.039504 TCCAACGTATCTACTTTTCCTAACACT 60.040 37.037 0.00 0.00 0.00 3.55
2105 2538 7.275123 CCAACGTATCTACTTTTCCTAACACTC 59.725 40.741 0.00 0.00 0.00 3.51
2106 2539 7.700022 ACGTATCTACTTTTCCTAACACTCT 57.300 36.000 0.00 0.00 0.00 3.24
2107 2540 8.120140 ACGTATCTACTTTTCCTAACACTCTT 57.880 34.615 0.00 0.00 0.00 2.85
2108 2541 8.242739 ACGTATCTACTTTTCCTAACACTCTTC 58.757 37.037 0.00 0.00 0.00 2.87
2109 2542 7.701501 CGTATCTACTTTTCCTAACACTCTTCC 59.298 40.741 0.00 0.00 0.00 3.46
2110 2543 7.800300 ATCTACTTTTCCTAACACTCTTCCT 57.200 36.000 0.00 0.00 0.00 3.36
2111 2544 7.229581 TCTACTTTTCCTAACACTCTTCCTC 57.770 40.000 0.00 0.00 0.00 3.71
2112 2545 7.011382 TCTACTTTTCCTAACACTCTTCCTCT 58.989 38.462 0.00 0.00 0.00 3.69
2113 2546 6.502074 ACTTTTCCTAACACTCTTCCTCTT 57.498 37.500 0.00 0.00 0.00 2.85
2114 2547 6.292150 ACTTTTCCTAACACTCTTCCTCTTG 58.708 40.000 0.00 0.00 0.00 3.02
2115 2548 5.888982 TTTCCTAACACTCTTCCTCTTGT 57.111 39.130 0.00 0.00 0.00 3.16
2116 2549 5.888982 TTCCTAACACTCTTCCTCTTGTT 57.111 39.130 0.00 0.00 36.23 2.83
2117 2550 5.888982 TCCTAACACTCTTCCTCTTGTTT 57.111 39.130 0.00 0.00 34.15 2.83
2118 2551 6.248569 TCCTAACACTCTTCCTCTTGTTTT 57.751 37.500 0.00 0.00 34.15 2.43
2119 2552 6.055588 TCCTAACACTCTTCCTCTTGTTTTG 58.944 40.000 0.00 0.00 34.15 2.44
2120 2553 5.239525 CCTAACACTCTTCCTCTTGTTTTGG 59.760 44.000 0.00 0.00 34.15 3.28
2121 2554 4.503714 ACACTCTTCCTCTTGTTTTGGA 57.496 40.909 0.00 0.00 0.00 3.53
2122 2555 4.200092 ACACTCTTCCTCTTGTTTTGGAC 58.800 43.478 0.00 0.00 0.00 4.02
2123 2556 4.080299 ACACTCTTCCTCTTGTTTTGGACT 60.080 41.667 0.00 0.00 0.00 3.85
2124 2557 4.513318 CACTCTTCCTCTTGTTTTGGACTC 59.487 45.833 0.00 0.00 0.00 3.36
2125 2558 4.410555 ACTCTTCCTCTTGTTTTGGACTCT 59.589 41.667 0.00 0.00 0.00 3.24
2126 2559 5.602978 ACTCTTCCTCTTGTTTTGGACTCTA 59.397 40.000 0.00 0.00 0.00 2.43
2127 2560 6.099845 ACTCTTCCTCTTGTTTTGGACTCTAA 59.900 38.462 0.00 0.00 0.00 2.10
2128 2561 7.079451 TCTTCCTCTTGTTTTGGACTCTAAT 57.921 36.000 0.00 0.00 0.00 1.73
2129 2562 7.518188 TCTTCCTCTTGTTTTGGACTCTAATT 58.482 34.615 0.00 0.00 0.00 1.40
2130 2563 7.998964 TCTTCCTCTTGTTTTGGACTCTAATTT 59.001 33.333 0.00 0.00 0.00 1.82
2131 2564 7.510549 TCCTCTTGTTTTGGACTCTAATTTG 57.489 36.000 0.00 0.00 0.00 2.32
2132 2565 6.016276 TCCTCTTGTTTTGGACTCTAATTTGC 60.016 38.462 0.00 0.00 0.00 3.68
2133 2566 6.239008 CCTCTTGTTTTGGACTCTAATTTGCA 60.239 38.462 0.00 0.00 0.00 4.08
2134 2567 7.288810 TCTTGTTTTGGACTCTAATTTGCAT 57.711 32.000 0.00 0.00 0.00 3.96
2135 2568 7.147312 TCTTGTTTTGGACTCTAATTTGCATG 58.853 34.615 0.00 0.00 0.00 4.06
2136 2569 6.647334 TGTTTTGGACTCTAATTTGCATGA 57.353 33.333 0.00 0.00 0.00 3.07
2137 2570 7.230849 TGTTTTGGACTCTAATTTGCATGAT 57.769 32.000 0.00 0.00 0.00 2.45
2138 2571 7.669427 TGTTTTGGACTCTAATTTGCATGATT 58.331 30.769 0.00 0.00 0.00 2.57
2139 2572 8.149647 TGTTTTGGACTCTAATTTGCATGATTT 58.850 29.630 0.00 0.00 0.00 2.17
2140 2573 9.638239 GTTTTGGACTCTAATTTGCATGATTTA 57.362 29.630 0.00 0.00 0.00 1.40
2144 2577 9.806203 TGGACTCTAATTTGCATGATTTAAATG 57.194 29.630 5.17 0.00 0.00 2.32
2154 2587 8.770438 TTGCATGATTTAAATGAAACTAACCC 57.230 30.769 5.17 0.00 0.00 4.11
2155 2588 7.327214 TGCATGATTTAAATGAAACTAACCCC 58.673 34.615 5.17 0.00 0.00 4.95
2156 2589 6.475402 GCATGATTTAAATGAAACTAACCCCG 59.525 38.462 5.17 0.00 0.00 5.73
2157 2590 6.518208 TGATTTAAATGAAACTAACCCCGG 57.482 37.500 5.17 0.00 0.00 5.73
2158 2591 6.246919 TGATTTAAATGAAACTAACCCCGGA 58.753 36.000 0.73 0.00 0.00 5.14
2159 2592 5.963176 TTTAAATGAAACTAACCCCGGAC 57.037 39.130 0.73 0.00 0.00 4.79
2160 2593 3.801307 AAATGAAACTAACCCCGGACT 57.199 42.857 0.73 0.00 0.00 3.85
2161 2594 4.914177 AAATGAAACTAACCCCGGACTA 57.086 40.909 0.73 0.00 0.00 2.59
2162 2595 4.914177 AATGAAACTAACCCCGGACTAA 57.086 40.909 0.73 0.00 0.00 2.24
2163 2596 3.683365 TGAAACTAACCCCGGACTAAC 57.317 47.619 0.73 0.00 0.00 2.34
2164 2597 2.971330 TGAAACTAACCCCGGACTAACA 59.029 45.455 0.73 0.00 0.00 2.41
2165 2598 3.244181 TGAAACTAACCCCGGACTAACAC 60.244 47.826 0.73 0.00 0.00 3.32
2166 2599 2.315720 ACTAACCCCGGACTAACACT 57.684 50.000 0.73 0.00 0.00 3.55
2167 2600 1.897802 ACTAACCCCGGACTAACACTG 59.102 52.381 0.73 0.00 0.00 3.66
2168 2601 1.206371 CTAACCCCGGACTAACACTGG 59.794 57.143 0.73 0.00 0.00 4.00
2169 2602 0.765519 AACCCCGGACTAACACTGGT 60.766 55.000 0.73 0.00 32.38 4.00
2170 2603 0.765519 ACCCCGGACTAACACTGGTT 60.766 55.000 0.73 0.00 41.06 3.67
2171 2604 0.399075 CCCCGGACTAACACTGGTTT 59.601 55.000 0.73 0.00 38.45 3.27
2172 2605 1.609841 CCCCGGACTAACACTGGTTTC 60.610 57.143 0.73 0.00 38.45 2.78
2173 2606 1.071071 CCCGGACTAACACTGGTTTCA 59.929 52.381 0.73 0.00 38.45 2.69
2174 2607 2.413837 CCGGACTAACACTGGTTTCAG 58.586 52.381 0.00 0.00 46.10 3.02
2175 2608 1.798813 CGGACTAACACTGGTTTCAGC 59.201 52.381 0.00 0.00 44.59 4.26
2176 2609 2.805295 CGGACTAACACTGGTTTCAGCA 60.805 50.000 0.00 0.00 44.59 4.41
2178 2611 3.494398 GGACTAACACTGGTTTCAGCAGA 60.494 47.826 9.86 0.00 45.98 4.26
2179 2612 4.127171 GACTAACACTGGTTTCAGCAGAA 58.873 43.478 9.86 0.00 45.98 3.02
2180 2613 3.877508 ACTAACACTGGTTTCAGCAGAAC 59.122 43.478 9.86 0.00 45.98 3.01
2181 2614 2.717639 ACACTGGTTTCAGCAGAACT 57.282 45.000 9.86 0.00 45.98 3.01
2182 2615 3.838244 ACACTGGTTTCAGCAGAACTA 57.162 42.857 9.86 0.00 45.98 2.24
2183 2616 3.467803 ACACTGGTTTCAGCAGAACTAC 58.532 45.455 9.86 0.00 45.98 2.73
2184 2617 2.808543 CACTGGTTTCAGCAGAACTACC 59.191 50.000 9.86 5.90 45.98 3.18
2185 2618 2.438021 ACTGGTTTCAGCAGAACTACCA 59.562 45.455 13.07 13.07 45.98 3.25
2186 2619 3.073062 ACTGGTTTCAGCAGAACTACCAT 59.927 43.478 13.85 4.63 45.98 3.55
2187 2620 3.411446 TGGTTTCAGCAGAACTACCATG 58.589 45.455 10.44 0.00 38.89 3.66
2188 2621 2.749621 GGTTTCAGCAGAACTACCATGG 59.250 50.000 11.19 11.19 35.58 3.66
2189 2622 3.412386 GTTTCAGCAGAACTACCATGGT 58.588 45.455 23.55 23.55 32.39 3.55
2190 2623 2.768253 TCAGCAGAACTACCATGGTG 57.232 50.000 28.17 18.63 42.34 4.17
2191 2624 1.977854 TCAGCAGAACTACCATGGTGT 59.022 47.619 28.17 19.28 41.82 4.16
2192 2625 2.371841 TCAGCAGAACTACCATGGTGTT 59.628 45.455 28.17 25.64 41.82 3.32
2193 2626 2.485426 CAGCAGAACTACCATGGTGTTG 59.515 50.000 28.17 18.42 37.59 3.33
2194 2627 2.106511 AGCAGAACTACCATGGTGTTGT 59.893 45.455 28.17 21.97 0.00 3.32
2195 2628 2.884639 GCAGAACTACCATGGTGTTGTT 59.115 45.455 28.17 25.31 37.00 2.83
2196 2629 3.317993 GCAGAACTACCATGGTGTTGTTT 59.682 43.478 28.17 12.20 34.98 2.83
2197 2630 4.202111 GCAGAACTACCATGGTGTTGTTTT 60.202 41.667 28.17 19.18 34.98 2.43
2198 2631 5.681179 GCAGAACTACCATGGTGTTGTTTTT 60.681 40.000 28.17 16.35 34.98 1.94
2199 2632 5.748152 CAGAACTACCATGGTGTTGTTTTTG 59.252 40.000 28.17 21.81 34.98 2.44
2200 2633 5.420739 AGAACTACCATGGTGTTGTTTTTGT 59.579 36.000 28.17 7.82 34.98 2.83
2201 2634 5.004922 ACTACCATGGTGTTGTTTTTGTG 57.995 39.130 28.17 5.23 0.00 3.33
2202 2635 2.626840 ACCATGGTGTTGTTTTTGTGC 58.373 42.857 18.99 0.00 0.00 4.57
2203 2636 2.027745 ACCATGGTGTTGTTTTTGTGCA 60.028 40.909 18.99 0.00 0.00 4.57
2204 2637 2.608546 CCATGGTGTTGTTTTTGTGCAG 59.391 45.455 2.57 0.00 0.00 4.41
2205 2638 3.519579 CATGGTGTTGTTTTTGTGCAGA 58.480 40.909 0.00 0.00 0.00 4.26
2206 2639 3.667497 TGGTGTTGTTTTTGTGCAGAA 57.333 38.095 0.00 0.00 0.00 3.02
2207 2640 3.995199 TGGTGTTGTTTTTGTGCAGAAA 58.005 36.364 4.66 4.66 0.00 2.52
2208 2641 4.573900 TGGTGTTGTTTTTGTGCAGAAAT 58.426 34.783 10.13 0.00 0.00 2.17
2209 2642 5.724328 TGGTGTTGTTTTTGTGCAGAAATA 58.276 33.333 10.13 2.40 0.00 1.40
2210 2643 6.166279 TGGTGTTGTTTTTGTGCAGAAATAA 58.834 32.000 10.13 5.07 0.00 1.40
2211 2644 6.820656 TGGTGTTGTTTTTGTGCAGAAATAAT 59.179 30.769 10.13 0.00 0.00 1.28
2212 2645 7.981789 TGGTGTTGTTTTTGTGCAGAAATAATA 59.018 29.630 10.13 3.76 0.00 0.98
2213 2646 8.487176 GGTGTTGTTTTTGTGCAGAAATAATAG 58.513 33.333 10.13 0.00 0.00 1.73
2214 2647 9.030301 GTGTTGTTTTTGTGCAGAAATAATAGT 57.970 29.630 10.13 0.00 0.00 2.12
2215 2648 9.593134 TGTTGTTTTTGTGCAGAAATAATAGTT 57.407 25.926 10.13 0.00 0.00 2.24
2219 2652 9.777843 GTTTTTGTGCAGAAATAATAGTTTTCG 57.222 29.630 10.13 0.00 37.98 3.46
2220 2653 7.561237 TTTGTGCAGAAATAATAGTTTTCGC 57.439 32.000 4.66 0.00 37.98 4.70
2221 2654 6.247727 TGTGCAGAAATAATAGTTTTCGCA 57.752 33.333 0.00 9.74 38.73 5.10
2222 2655 6.673106 TGTGCAGAAATAATAGTTTTCGCAA 58.327 32.000 13.16 5.98 40.56 4.85
2223 2656 7.312154 TGTGCAGAAATAATAGTTTTCGCAAT 58.688 30.769 13.16 0.00 40.56 3.56
2224 2657 7.273164 TGTGCAGAAATAATAGTTTTCGCAATG 59.727 33.333 13.16 0.60 40.56 2.82
2225 2658 6.751425 TGCAGAAATAATAGTTTTCGCAATGG 59.249 34.615 10.74 0.00 38.43 3.16
2226 2659 6.972328 GCAGAAATAATAGTTTTCGCAATGGA 59.028 34.615 0.00 0.00 37.98 3.41
2227 2660 7.487829 GCAGAAATAATAGTTTTCGCAATGGAA 59.512 33.333 0.00 0.00 37.98 3.53
2228 2661 8.798153 CAGAAATAATAGTTTTCGCAATGGAAC 58.202 33.333 0.00 0.00 37.98 3.62
2229 2662 7.696453 AGAAATAATAGTTTTCGCAATGGAACG 59.304 33.333 0.00 0.00 37.98 3.95
2230 2663 6.671614 ATAATAGTTTTCGCAATGGAACGA 57.328 33.333 0.00 0.00 36.32 3.85
2231 2664 5.365403 AATAGTTTTCGCAATGGAACGAA 57.635 34.783 0.00 0.00 45.74 3.85
2236 2669 3.701532 TTCGCAATGGAACGAAACTTT 57.298 38.095 0.00 0.00 44.57 2.66
2237 2670 2.993545 TCGCAATGGAACGAAACTTTG 58.006 42.857 0.00 0.00 34.93 2.77
2238 2671 1.451651 CGCAATGGAACGAAACTTTGC 59.548 47.619 13.86 13.86 41.53 3.68
2239 2672 2.468831 GCAATGGAACGAAACTTTGCA 58.531 42.857 16.77 0.00 43.26 4.08
2240 2673 2.863137 GCAATGGAACGAAACTTTGCAA 59.137 40.909 16.77 0.00 43.26 4.08
2241 2674 3.060339 GCAATGGAACGAAACTTTGCAAG 60.060 43.478 16.77 0.00 43.26 4.01
2242 2675 2.861462 TGGAACGAAACTTTGCAAGG 57.139 45.000 7.07 7.07 0.00 3.61
2243 2676 2.370349 TGGAACGAAACTTTGCAAGGA 58.630 42.857 16.36 0.00 0.00 3.36
2244 2677 2.955660 TGGAACGAAACTTTGCAAGGAT 59.044 40.909 16.36 0.00 0.00 3.24
2245 2678 3.383185 TGGAACGAAACTTTGCAAGGATT 59.617 39.130 16.36 9.86 0.00 3.01
2246 2679 4.142049 TGGAACGAAACTTTGCAAGGATTT 60.142 37.500 16.36 11.45 0.00 2.17
2247 2680 4.808895 GGAACGAAACTTTGCAAGGATTTT 59.191 37.500 16.36 6.22 0.00 1.82
2248 2681 5.293324 GGAACGAAACTTTGCAAGGATTTTT 59.707 36.000 16.36 5.47 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.566197 AAAATTCTCTAAGTCAAGGTGCAG 57.434 37.500 0.00 0.00 0.00 4.41
1 2 6.239008 CCAAAAATTCTCTAAGTCAAGGTGCA 60.239 38.462 0.00 0.00 0.00 4.57
2 3 6.152379 CCAAAAATTCTCTAAGTCAAGGTGC 58.848 40.000 0.00 0.00 0.00 5.01
3 4 6.152379 GCCAAAAATTCTCTAAGTCAAGGTG 58.848 40.000 0.00 0.00 0.00 4.00
4 5 5.833131 TGCCAAAAATTCTCTAAGTCAAGGT 59.167 36.000 0.00 0.00 0.00 3.50
5 6 6.331369 TGCCAAAAATTCTCTAAGTCAAGG 57.669 37.500 0.00 0.00 0.00 3.61
6 7 6.865205 CCTTGCCAAAAATTCTCTAAGTCAAG 59.135 38.462 0.00 0.00 0.00 3.02
7 8 6.549364 TCCTTGCCAAAAATTCTCTAAGTCAA 59.451 34.615 0.00 0.00 0.00 3.18
8 9 6.068010 TCCTTGCCAAAAATTCTCTAAGTCA 58.932 36.000 0.00 0.00 0.00 3.41
9 10 6.575162 TCCTTGCCAAAAATTCTCTAAGTC 57.425 37.500 0.00 0.00 0.00 3.01
10 11 6.976934 TTCCTTGCCAAAAATTCTCTAAGT 57.023 33.333 0.00 0.00 0.00 2.24
11 12 6.367149 GCTTTCCTTGCCAAAAATTCTCTAAG 59.633 38.462 0.00 0.00 0.00 2.18
12 13 6.041979 AGCTTTCCTTGCCAAAAATTCTCTAA 59.958 34.615 0.00 0.00 0.00 2.10
13 14 5.539955 AGCTTTCCTTGCCAAAAATTCTCTA 59.460 36.000 0.00 0.00 0.00 2.43
14 15 4.346127 AGCTTTCCTTGCCAAAAATTCTCT 59.654 37.500 0.00 0.00 0.00 3.10
15 16 4.635223 AGCTTTCCTTGCCAAAAATTCTC 58.365 39.130 0.00 0.00 0.00 2.87
16 17 4.694760 AGCTTTCCTTGCCAAAAATTCT 57.305 36.364 0.00 0.00 0.00 2.40
17 18 5.406477 CAGTAGCTTTCCTTGCCAAAAATTC 59.594 40.000 0.00 0.00 0.00 2.17
18 19 5.299949 CAGTAGCTTTCCTTGCCAAAAATT 58.700 37.500 0.00 0.00 0.00 1.82
19 20 4.262592 CCAGTAGCTTTCCTTGCCAAAAAT 60.263 41.667 0.00 0.00 0.00 1.82
20 21 3.069443 CCAGTAGCTTTCCTTGCCAAAAA 59.931 43.478 0.00 0.00 0.00 1.94
21 22 2.627699 CCAGTAGCTTTCCTTGCCAAAA 59.372 45.455 0.00 0.00 0.00 2.44
22 23 2.158534 TCCAGTAGCTTTCCTTGCCAAA 60.159 45.455 0.00 0.00 0.00 3.28
23 24 1.423541 TCCAGTAGCTTTCCTTGCCAA 59.576 47.619 0.00 0.00 0.00 4.52
24 25 1.064003 TCCAGTAGCTTTCCTTGCCA 58.936 50.000 0.00 0.00 0.00 4.92
25 26 2.200373 TTCCAGTAGCTTTCCTTGCC 57.800 50.000 0.00 0.00 0.00 4.52
26 27 4.333926 CACTATTCCAGTAGCTTTCCTTGC 59.666 45.833 0.00 0.00 34.98 4.01
27 28 5.491982 ACACTATTCCAGTAGCTTTCCTTG 58.508 41.667 0.00 0.00 34.98 3.61
28 29 5.763876 ACACTATTCCAGTAGCTTTCCTT 57.236 39.130 0.00 0.00 34.98 3.36
29 30 5.013183 ACAACACTATTCCAGTAGCTTTCCT 59.987 40.000 0.00 0.00 34.98 3.36
30 31 5.246307 ACAACACTATTCCAGTAGCTTTCC 58.754 41.667 0.00 0.00 34.98 3.13
31 32 6.603095 CAACAACACTATTCCAGTAGCTTTC 58.397 40.000 0.00 0.00 34.98 2.62
32 33 5.048713 GCAACAACACTATTCCAGTAGCTTT 60.049 40.000 0.00 0.00 34.98 3.51
33 34 4.455877 GCAACAACACTATTCCAGTAGCTT 59.544 41.667 0.00 0.00 34.98 3.74
34 35 4.003648 GCAACAACACTATTCCAGTAGCT 58.996 43.478 0.00 0.00 34.98 3.32
35 36 4.003648 AGCAACAACACTATTCCAGTAGC 58.996 43.478 0.00 0.00 34.98 3.58
36 37 5.482908 AGAGCAACAACACTATTCCAGTAG 58.517 41.667 0.00 0.00 34.98 2.57
37 38 5.246203 AGAGAGCAACAACACTATTCCAGTA 59.754 40.000 0.00 0.00 34.98 2.74
38 39 4.040952 AGAGAGCAACAACACTATTCCAGT 59.959 41.667 0.00 0.00 38.32 4.00
39 40 4.391216 CAGAGAGCAACAACACTATTCCAG 59.609 45.833 0.00 0.00 0.00 3.86
40 41 4.318332 CAGAGAGCAACAACACTATTCCA 58.682 43.478 0.00 0.00 0.00 3.53
41 42 3.686726 CCAGAGAGCAACAACACTATTCC 59.313 47.826 0.00 0.00 0.00 3.01
42 43 4.390297 GTCCAGAGAGCAACAACACTATTC 59.610 45.833 0.00 0.00 0.00 1.75
43 44 4.040952 AGTCCAGAGAGCAACAACACTATT 59.959 41.667 0.00 0.00 0.00 1.73
44 45 3.580458 AGTCCAGAGAGCAACAACACTAT 59.420 43.478 0.00 0.00 0.00 2.12
45 46 2.965831 AGTCCAGAGAGCAACAACACTA 59.034 45.455 0.00 0.00 0.00 2.74
46 47 1.765314 AGTCCAGAGAGCAACAACACT 59.235 47.619 0.00 0.00 0.00 3.55
47 48 1.869767 CAGTCCAGAGAGCAACAACAC 59.130 52.381 0.00 0.00 0.00 3.32
48 49 1.202687 CCAGTCCAGAGAGCAACAACA 60.203 52.381 0.00 0.00 0.00 3.33
49 50 1.517242 CCAGTCCAGAGAGCAACAAC 58.483 55.000 0.00 0.00 0.00 3.32
50 51 0.250467 GCCAGTCCAGAGAGCAACAA 60.250 55.000 0.00 0.00 0.00 2.83
102 103 2.434185 TGCAGCGCCTAAAGGACG 60.434 61.111 2.29 4.46 37.39 4.79
107 109 1.026182 CCAGATGTGCAGCGCCTAAA 61.026 55.000 2.29 0.00 0.00 1.85
153 155 2.224161 GCTCGAATGGCTACTGGAATCT 60.224 50.000 0.00 0.00 0.00 2.40
208 447 4.678743 GTGGGTGGGAGGGGTTGC 62.679 72.222 0.00 0.00 0.00 4.17
209 448 3.979497 GGTGGGTGGGAGGGGTTG 61.979 72.222 0.00 0.00 0.00 3.77
740 1049 1.254975 TGGCTTCGAGATCCACGGAA 61.255 55.000 9.43 0.00 0.00 4.30
860 1170 5.996513 TCCACACAAATTTCCAAATCCAATG 59.003 36.000 0.00 0.00 0.00 2.82
986 1296 3.756434 TGAAGCCATGCCTACAAAACTAC 59.244 43.478 0.00 0.00 0.00 2.73
1105 1445 0.813184 CACCAACATGGCAGGATGTC 59.187 55.000 5.99 0.00 42.67 3.06
1132 1472 1.963515 GGACACCTTCACCTTGCAAAT 59.036 47.619 0.00 0.00 0.00 2.32
1276 1652 8.780846 TTTGAGAGTAAGTAAGTGTTGACAAA 57.219 30.769 0.00 0.00 0.00 2.83
1277 1653 8.826710 CATTTGAGAGTAAGTAAGTGTTGACAA 58.173 33.333 0.00 0.00 0.00 3.18
1278 1654 7.985184 ACATTTGAGAGTAAGTAAGTGTTGACA 59.015 33.333 0.00 0.00 0.00 3.58
1279 1655 8.276325 CACATTTGAGAGTAAGTAAGTGTTGAC 58.724 37.037 0.00 0.00 0.00 3.18
1280 1656 7.985184 ACACATTTGAGAGTAAGTAAGTGTTGA 59.015 33.333 0.00 0.00 33.19 3.18
1281 1657 8.064222 CACACATTTGAGAGTAAGTAAGTGTTG 58.936 37.037 0.00 0.00 34.62 3.33
1282 1658 7.769044 ACACACATTTGAGAGTAAGTAAGTGTT 59.231 33.333 0.00 0.00 34.62 3.32
1283 1659 7.272978 ACACACATTTGAGAGTAAGTAAGTGT 58.727 34.615 0.00 0.00 36.99 3.55
1284 1660 7.438160 TGACACACATTTGAGAGTAAGTAAGTG 59.562 37.037 0.00 0.00 0.00 3.16
1285 1661 7.497595 TGACACACATTTGAGAGTAAGTAAGT 58.502 34.615 0.00 0.00 0.00 2.24
1286 1662 7.946655 TGACACACATTTGAGAGTAAGTAAG 57.053 36.000 0.00 0.00 0.00 2.34
1287 1663 7.766738 TGTTGACACACATTTGAGAGTAAGTAA 59.233 33.333 0.00 0.00 0.00 2.24
1288 1664 7.269316 TGTTGACACACATTTGAGAGTAAGTA 58.731 34.615 0.00 0.00 0.00 2.24
1289 1665 6.112734 TGTTGACACACATTTGAGAGTAAGT 58.887 36.000 0.00 0.00 0.00 2.24
1290 1666 6.603237 TGTTGACACACATTTGAGAGTAAG 57.397 37.500 0.00 0.00 0.00 2.34
1336 1715 0.179000 CTTGCATAGAGGAGGCGGTT 59.821 55.000 0.00 0.00 37.80 4.44
1450 1830 3.283751 TCTTCCTCTAAGCCTCTTCGAG 58.716 50.000 2.28 2.28 34.97 4.04
1577 1970 2.125552 TCCTCTTGCACATCGCGG 60.126 61.111 6.13 0.00 46.97 6.46
1583 1976 0.250234 CCGAATCCTCCTCTTGCACA 59.750 55.000 0.00 0.00 0.00 4.57
1731 2156 7.665561 TCACGACACATTCATTAGAAATGAA 57.334 32.000 15.29 15.29 41.59 2.57
1866 2293 5.698089 TCACAGCAATTTGAACAAACACAAA 59.302 32.000 0.00 0.00 39.67 2.83
1920 2347 5.291178 TGACAGCAATTTCAATTCACTTGG 58.709 37.500 0.00 0.00 35.43 3.61
1981 2414 4.386951 TGCGTGTGCCCTATGCGT 62.387 61.111 0.00 0.00 45.60 5.24
1985 2418 0.108329 GTGTAGTGCGTGTGCCCTAT 60.108 55.000 0.00 0.00 41.78 2.57
2014 2447 2.743928 CCTGACTGTTGGGCGCTC 60.744 66.667 7.64 2.47 0.00 5.03
2037 2470 1.399714 AGGCGCTGCACTATACAGTA 58.600 50.000 7.64 0.00 37.47 2.74
2075 2508 5.963594 AGGAAAAGTAGATACGTTGGAGAC 58.036 41.667 0.00 0.00 0.00 3.36
2076 2509 7.177216 TGTTAGGAAAAGTAGATACGTTGGAGA 59.823 37.037 0.00 0.00 0.00 3.71
2077 2510 7.275123 GTGTTAGGAAAAGTAGATACGTTGGAG 59.725 40.741 0.00 0.00 0.00 3.86
2078 2511 7.039504 AGTGTTAGGAAAAGTAGATACGTTGGA 60.040 37.037 0.00 0.00 0.00 3.53
2079 2512 7.095270 AGTGTTAGGAAAAGTAGATACGTTGG 58.905 38.462 0.00 0.00 0.00 3.77
2080 2513 8.027771 AGAGTGTTAGGAAAAGTAGATACGTTG 58.972 37.037 0.00 0.00 0.00 4.10
2081 2514 8.120140 AGAGTGTTAGGAAAAGTAGATACGTT 57.880 34.615 0.00 0.00 0.00 3.99
2082 2515 7.700022 AGAGTGTTAGGAAAAGTAGATACGT 57.300 36.000 0.00 0.00 0.00 3.57
2083 2516 7.701501 GGAAGAGTGTTAGGAAAAGTAGATACG 59.298 40.741 0.00 0.00 0.00 3.06
2084 2517 8.751242 AGGAAGAGTGTTAGGAAAAGTAGATAC 58.249 37.037 0.00 0.00 0.00 2.24
2085 2518 8.896722 AGGAAGAGTGTTAGGAAAAGTAGATA 57.103 34.615 0.00 0.00 0.00 1.98
2086 2519 7.676468 AGAGGAAGAGTGTTAGGAAAAGTAGAT 59.324 37.037 0.00 0.00 0.00 1.98
2087 2520 7.011382 AGAGGAAGAGTGTTAGGAAAAGTAGA 58.989 38.462 0.00 0.00 0.00 2.59
2088 2521 7.234661 AGAGGAAGAGTGTTAGGAAAAGTAG 57.765 40.000 0.00 0.00 0.00 2.57
2089 2522 7.070821 ACAAGAGGAAGAGTGTTAGGAAAAGTA 59.929 37.037 0.00 0.00 0.00 2.24
2090 2523 6.126739 ACAAGAGGAAGAGTGTTAGGAAAAGT 60.127 38.462 0.00 0.00 0.00 2.66
2091 2524 6.292150 ACAAGAGGAAGAGTGTTAGGAAAAG 58.708 40.000 0.00 0.00 0.00 2.27
2092 2525 6.248569 ACAAGAGGAAGAGTGTTAGGAAAA 57.751 37.500 0.00 0.00 0.00 2.29
2093 2526 5.888982 ACAAGAGGAAGAGTGTTAGGAAA 57.111 39.130 0.00 0.00 0.00 3.13
2094 2527 5.888982 AACAAGAGGAAGAGTGTTAGGAA 57.111 39.130 0.00 0.00 32.58 3.36
2095 2528 5.888982 AAACAAGAGGAAGAGTGTTAGGA 57.111 39.130 0.00 0.00 33.18 2.94
2096 2529 5.239525 CCAAAACAAGAGGAAGAGTGTTAGG 59.760 44.000 0.00 0.00 33.18 2.69
2097 2530 6.017852 GTCCAAAACAAGAGGAAGAGTGTTAG 60.018 42.308 0.00 0.00 33.18 2.34
2098 2531 5.820947 GTCCAAAACAAGAGGAAGAGTGTTA 59.179 40.000 0.00 0.00 33.18 2.41
2099 2532 4.640647 GTCCAAAACAAGAGGAAGAGTGTT 59.359 41.667 0.00 0.00 35.77 3.32
2100 2533 4.080299 AGTCCAAAACAAGAGGAAGAGTGT 60.080 41.667 0.00 0.00 32.30 3.55
2101 2534 4.455606 AGTCCAAAACAAGAGGAAGAGTG 58.544 43.478 0.00 0.00 32.30 3.51
2102 2535 4.410555 AGAGTCCAAAACAAGAGGAAGAGT 59.589 41.667 0.00 0.00 32.30 3.24
2103 2536 4.967036 AGAGTCCAAAACAAGAGGAAGAG 58.033 43.478 0.00 0.00 32.30 2.85
2104 2537 6.494666 TTAGAGTCCAAAACAAGAGGAAGA 57.505 37.500 0.00 0.00 32.30 2.87
2105 2538 7.751768 AATTAGAGTCCAAAACAAGAGGAAG 57.248 36.000 0.00 0.00 32.30 3.46
2106 2539 7.470009 GCAAATTAGAGTCCAAAACAAGAGGAA 60.470 37.037 0.00 0.00 32.30 3.36
2107 2540 6.016276 GCAAATTAGAGTCCAAAACAAGAGGA 60.016 38.462 0.00 0.00 0.00 3.71
2108 2541 6.152379 GCAAATTAGAGTCCAAAACAAGAGG 58.848 40.000 0.00 0.00 0.00 3.69
2109 2542 6.738114 TGCAAATTAGAGTCCAAAACAAGAG 58.262 36.000 0.00 0.00 0.00 2.85
2110 2543 6.707440 TGCAAATTAGAGTCCAAAACAAGA 57.293 33.333 0.00 0.00 0.00 3.02
2111 2544 7.147312 TCATGCAAATTAGAGTCCAAAACAAG 58.853 34.615 0.00 0.00 0.00 3.16
2112 2545 7.048629 TCATGCAAATTAGAGTCCAAAACAA 57.951 32.000 0.00 0.00 0.00 2.83
2113 2546 6.647334 TCATGCAAATTAGAGTCCAAAACA 57.353 33.333 0.00 0.00 0.00 2.83
2114 2547 8.538409 AAATCATGCAAATTAGAGTCCAAAAC 57.462 30.769 0.00 0.00 0.00 2.43
2118 2551 9.806203 CATTTAAATCATGCAAATTAGAGTCCA 57.194 29.630 0.00 0.00 0.00 4.02
2128 2561 9.213799 GGGTTAGTTTCATTTAAATCATGCAAA 57.786 29.630 0.00 0.00 0.00 3.68
2129 2562 7.821846 GGGGTTAGTTTCATTTAAATCATGCAA 59.178 33.333 0.00 0.00 0.00 4.08
2130 2563 7.327214 GGGGTTAGTTTCATTTAAATCATGCA 58.673 34.615 0.00 0.00 0.00 3.96
2131 2564 6.475402 CGGGGTTAGTTTCATTTAAATCATGC 59.525 38.462 0.00 0.00 0.00 4.06
2132 2565 6.978080 CCGGGGTTAGTTTCATTTAAATCATG 59.022 38.462 0.00 0.00 0.00 3.07
2133 2566 6.893005 TCCGGGGTTAGTTTCATTTAAATCAT 59.107 34.615 0.00 0.00 0.00 2.45
2134 2567 6.151480 GTCCGGGGTTAGTTTCATTTAAATCA 59.849 38.462 0.00 0.00 0.00 2.57
2135 2568 6.376299 AGTCCGGGGTTAGTTTCATTTAAATC 59.624 38.462 0.00 0.00 0.00 2.17
2136 2569 6.250711 AGTCCGGGGTTAGTTTCATTTAAAT 58.749 36.000 0.00 0.00 0.00 1.40
2137 2570 5.633117 AGTCCGGGGTTAGTTTCATTTAAA 58.367 37.500 0.00 0.00 0.00 1.52
2138 2571 5.245584 AGTCCGGGGTTAGTTTCATTTAA 57.754 39.130 0.00 0.00 0.00 1.52
2139 2572 4.914177 AGTCCGGGGTTAGTTTCATTTA 57.086 40.909 0.00 0.00 0.00 1.40
2140 2573 3.801307 AGTCCGGGGTTAGTTTCATTT 57.199 42.857 0.00 0.00 0.00 2.32
2141 2574 4.041938 TGTTAGTCCGGGGTTAGTTTCATT 59.958 41.667 0.00 0.00 0.00 2.57
2142 2575 3.583966 TGTTAGTCCGGGGTTAGTTTCAT 59.416 43.478 0.00 0.00 0.00 2.57
2143 2576 2.971330 TGTTAGTCCGGGGTTAGTTTCA 59.029 45.455 0.00 0.00 0.00 2.69
2144 2577 3.007290 AGTGTTAGTCCGGGGTTAGTTTC 59.993 47.826 0.00 0.00 0.00 2.78
2145 2578 2.974794 AGTGTTAGTCCGGGGTTAGTTT 59.025 45.455 0.00 0.00 0.00 2.66
2146 2579 2.301009 CAGTGTTAGTCCGGGGTTAGTT 59.699 50.000 0.00 0.00 0.00 2.24
2147 2580 1.897802 CAGTGTTAGTCCGGGGTTAGT 59.102 52.381 0.00 0.00 0.00 2.24
2148 2581 1.206371 CCAGTGTTAGTCCGGGGTTAG 59.794 57.143 0.00 0.00 0.00 2.34
2149 2582 1.269012 CCAGTGTTAGTCCGGGGTTA 58.731 55.000 0.00 0.00 0.00 2.85
2150 2583 0.765519 ACCAGTGTTAGTCCGGGGTT 60.766 55.000 0.00 0.00 0.00 4.11
2151 2584 0.765519 AACCAGTGTTAGTCCGGGGT 60.766 55.000 0.00 0.00 31.36 4.95
2152 2585 0.399075 AAACCAGTGTTAGTCCGGGG 59.601 55.000 0.00 0.00 33.30 5.73
2153 2586 1.071071 TGAAACCAGTGTTAGTCCGGG 59.929 52.381 0.00 0.00 33.30 5.73
2154 2587 2.413837 CTGAAACCAGTGTTAGTCCGG 58.586 52.381 0.00 0.00 33.30 5.14
2155 2588 1.798813 GCTGAAACCAGTGTTAGTCCG 59.201 52.381 0.00 0.00 33.30 4.79
2156 2589 2.808543 CTGCTGAAACCAGTGTTAGTCC 59.191 50.000 0.00 0.00 33.30 3.85
2157 2590 3.728845 TCTGCTGAAACCAGTGTTAGTC 58.271 45.455 0.00 0.00 33.30 2.59
2158 2591 3.838244 TCTGCTGAAACCAGTGTTAGT 57.162 42.857 0.00 0.00 33.30 2.24
2159 2592 4.130118 AGTTCTGCTGAAACCAGTGTTAG 58.870 43.478 7.68 0.00 33.30 2.34
2160 2593 4.150897 AGTTCTGCTGAAACCAGTGTTA 57.849 40.909 7.68 0.00 33.30 2.41
2161 2594 3.004752 AGTTCTGCTGAAACCAGTGTT 57.995 42.857 7.68 0.00 35.82 3.32
2162 2595 2.717639 AGTTCTGCTGAAACCAGTGT 57.282 45.000 7.68 0.00 33.52 3.55
2163 2596 2.808543 GGTAGTTCTGCTGAAACCAGTG 59.191 50.000 17.66 0.00 34.70 3.66
2164 2597 2.438021 TGGTAGTTCTGCTGAAACCAGT 59.562 45.455 20.10 1.73 37.85 4.00
2165 2598 3.126001 TGGTAGTTCTGCTGAAACCAG 57.874 47.619 20.10 0.00 37.85 4.00
2166 2599 3.411446 CATGGTAGTTCTGCTGAAACCA 58.589 45.455 23.93 23.93 43.27 3.67
2167 2600 2.749621 CCATGGTAGTTCTGCTGAAACC 59.250 50.000 16.36 16.36 34.98 3.27
2168 2601 3.189287 CACCATGGTAGTTCTGCTGAAAC 59.811 47.826 19.28 3.78 33.52 2.78
2169 2602 3.181445 ACACCATGGTAGTTCTGCTGAAA 60.181 43.478 19.28 0.00 33.52 2.69
2170 2603 2.371841 ACACCATGGTAGTTCTGCTGAA 59.628 45.455 19.28 1.33 0.00 3.02
2171 2604 1.977854 ACACCATGGTAGTTCTGCTGA 59.022 47.619 19.28 0.00 0.00 4.26
2172 2605 2.479566 ACACCATGGTAGTTCTGCTG 57.520 50.000 19.28 4.20 0.00 4.41
2173 2606 2.106511 ACAACACCATGGTAGTTCTGCT 59.893 45.455 19.28 0.19 0.00 4.24
2174 2607 2.504367 ACAACACCATGGTAGTTCTGC 58.496 47.619 19.28 0.00 0.00 4.26
2175 2608 5.514274 AAAACAACACCATGGTAGTTCTG 57.486 39.130 19.28 15.28 0.00 3.02
2176 2609 5.420739 ACAAAAACAACACCATGGTAGTTCT 59.579 36.000 19.28 9.33 0.00 3.01
2177 2610 5.518487 CACAAAAACAACACCATGGTAGTTC 59.482 40.000 19.28 0.00 0.00 3.01
2178 2611 5.415221 CACAAAAACAACACCATGGTAGTT 58.585 37.500 19.28 19.98 0.00 2.24
2179 2612 4.679372 GCACAAAAACAACACCATGGTAGT 60.679 41.667 19.28 15.16 0.00 2.73
2180 2613 3.801594 GCACAAAAACAACACCATGGTAG 59.198 43.478 19.28 14.48 0.00 3.18
2181 2614 3.195610 TGCACAAAAACAACACCATGGTA 59.804 39.130 19.28 0.00 0.00 3.25
2182 2615 2.027745 TGCACAAAAACAACACCATGGT 60.028 40.909 13.00 13.00 0.00 3.55
2183 2616 2.608546 CTGCACAAAAACAACACCATGG 59.391 45.455 11.19 11.19 0.00 3.66
2184 2617 3.519579 TCTGCACAAAAACAACACCATG 58.480 40.909 0.00 0.00 0.00 3.66
2185 2618 3.883830 TCTGCACAAAAACAACACCAT 57.116 38.095 0.00 0.00 0.00 3.55
2186 2619 3.667497 TTCTGCACAAAAACAACACCA 57.333 38.095 0.00 0.00 0.00 4.17
2187 2620 6.654793 TTATTTCTGCACAAAAACAACACC 57.345 33.333 0.00 0.00 0.00 4.16
2188 2621 9.030301 ACTATTATTTCTGCACAAAAACAACAC 57.970 29.630 0.00 0.00 0.00 3.32
2189 2622 9.593134 AACTATTATTTCTGCACAAAAACAACA 57.407 25.926 0.00 0.00 0.00 3.33
2193 2626 9.777843 CGAAAACTATTATTTCTGCACAAAAAC 57.222 29.630 0.00 0.00 35.19 2.43
2194 2627 8.484008 GCGAAAACTATTATTTCTGCACAAAAA 58.516 29.630 0.00 0.00 36.85 1.94
2195 2628 7.649705 TGCGAAAACTATTATTTCTGCACAAAA 59.350 29.630 11.50 0.00 39.23 2.44
2196 2629 7.142021 TGCGAAAACTATTATTTCTGCACAAA 58.858 30.769 11.50 0.00 39.23 2.83
2197 2630 6.673106 TGCGAAAACTATTATTTCTGCACAA 58.327 32.000 11.50 0.00 39.23 3.33
2198 2631 6.247727 TGCGAAAACTATTATTTCTGCACA 57.752 33.333 11.50 0.00 39.23 4.57
2199 2632 7.253750 CCATTGCGAAAACTATTATTTCTGCAC 60.254 37.037 13.69 0.00 41.36 4.57
2200 2633 6.751425 CCATTGCGAAAACTATTATTTCTGCA 59.249 34.615 11.50 11.50 40.70 4.41
2201 2634 6.972328 TCCATTGCGAAAACTATTATTTCTGC 59.028 34.615 0.00 0.00 37.11 4.26
2202 2635 8.798153 GTTCCATTGCGAAAACTATTATTTCTG 58.202 33.333 0.00 0.00 35.19 3.02
2203 2636 7.696453 CGTTCCATTGCGAAAACTATTATTTCT 59.304 33.333 0.00 0.00 35.19 2.52
2204 2637 7.694784 TCGTTCCATTGCGAAAACTATTATTTC 59.305 33.333 0.00 0.00 33.96 2.17
2205 2638 7.531716 TCGTTCCATTGCGAAAACTATTATTT 58.468 30.769 0.00 0.00 33.96 1.40
2206 2639 7.079182 TCGTTCCATTGCGAAAACTATTATT 57.921 32.000 0.00 0.00 33.96 1.40
2207 2640 6.671614 TCGTTCCATTGCGAAAACTATTAT 57.328 33.333 0.00 0.00 33.96 1.28
2208 2641 6.483385 TTCGTTCCATTGCGAAAACTATTA 57.517 33.333 0.00 0.00 42.94 0.98
2209 2642 5.365403 TTCGTTCCATTGCGAAAACTATT 57.635 34.783 0.00 0.00 42.94 1.73
2216 2649 3.367607 CAAAGTTTCGTTCCATTGCGAA 58.632 40.909 0.00 0.00 43.98 4.70
2217 2650 2.856720 GCAAAGTTTCGTTCCATTGCGA 60.857 45.455 0.00 0.00 34.57 5.10
2218 2651 1.451651 GCAAAGTTTCGTTCCATTGCG 59.548 47.619 0.00 0.00 34.57 4.85
2219 2652 2.468831 TGCAAAGTTTCGTTCCATTGC 58.531 42.857 9.77 9.77 42.49 3.56
2220 2653 3.490526 CCTTGCAAAGTTTCGTTCCATTG 59.509 43.478 0.00 0.00 44.25 2.82
2221 2654 3.383185 TCCTTGCAAAGTTTCGTTCCATT 59.617 39.130 0.00 0.00 44.25 3.16
2222 2655 2.955660 TCCTTGCAAAGTTTCGTTCCAT 59.044 40.909 0.00 0.00 44.25 3.41
2223 2656 2.370349 TCCTTGCAAAGTTTCGTTCCA 58.630 42.857 0.00 0.00 44.25 3.53
2224 2657 3.643159 ATCCTTGCAAAGTTTCGTTCC 57.357 42.857 0.00 0.00 44.25 3.62
2225 2658 5.966636 AAAATCCTTGCAAAGTTTCGTTC 57.033 34.783 0.00 0.00 44.25 3.95


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

AutoCloner maintained by Alex Coulton.