Multiple sequence alignment - TraesCS6D01G269300

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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 TraesCS6D01G269300 chr6D 100.000 4789 0 0 1 4789 379519371 379524159 0.000000e+00 8844.0
1 TraesCS6D01G269300 chr6D 99.020 102 1 0 4513 4614 379523783 379523884 2.940000e-42 183.0
2 TraesCS6D01G269300 chr6D 99.020 102 1 0 4413 4514 379523883 379523984 2.940000e-42 183.0
3 TraesCS6D01G269300 chr6A 92.123 1663 95 24 1 1650 521481588 521479949 0.000000e+00 2313.0
4 TraesCS6D01G269300 chr6A 94.437 773 24 11 2576 3331 521478477 521477707 0.000000e+00 1171.0
5 TraesCS6D01G269300 chr6A 92.692 561 33 5 3331 3889 521477673 521477119 0.000000e+00 802.0
6 TraesCS6D01G269300 chr6A 94.683 489 19 3 2086 2574 521478990 521478509 0.000000e+00 752.0
7 TraesCS6D01G269300 chr6A 93.386 378 25 0 1675 2052 521479807 521479430 1.160000e-155 560.0
8 TraesCS6D01G269300 chr6A 86.505 289 23 7 3932 4214 521477119 521476841 2.170000e-78 303.0
9 TraesCS6D01G269300 chr6A 86.447 273 31 5 4519 4789 521473937 521473669 1.300000e-75 294.0
10 TraesCS6D01G269300 chr6A 93.750 80 3 2 2649 2726 521478199 521478120 8.420000e-23 119.0
11 TraesCS6D01G269300 chr6B 92.518 1390 62 20 1 1370 567474170 567472803 0.000000e+00 1953.0
12 TraesCS6D01G269300 chr6B 90.578 467 25 8 3415 3877 567470745 567470294 6.860000e-168 601.0
13 TraesCS6D01G269300 chr6B 92.308 286 19 3 1776 2060 567472423 567472140 2.080000e-108 403.0
14 TraesCS6D01G269300 chr6B 83.333 372 36 16 2143 2503 567471966 567471610 2.150000e-83 320.0
15 TraesCS6D01G269300 chr6B 86.833 281 31 5 4513 4789 567469264 567468986 4.650000e-80 309.0
16 TraesCS6D01G269300 chr6B 82.166 314 34 12 2869 3176 567471374 567471077 2.860000e-62 250.0
17 TraesCS6D01G269300 chr6B 96.117 103 3 1 3929 4031 567470174 567470073 2.960000e-37 167.0
18 TraesCS6D01G269300 chr6B 84.932 146 17 4 4513 4655 567469080 567468937 5.000000e-30 143.0
19 TraesCS6D01G269300 chr6B 81.871 171 27 2 4513 4680 169168710 169168879 1.800000e-29 141.0
20 TraesCS6D01G269300 chr6B 91.176 68 6 0 3861 3928 567470277 567470210 5.100000e-15 93.5
21 TraesCS6D01G269300 chr5D 95.902 122 5 0 2733 2854 503284335 503284456 1.050000e-46 198.0
22 TraesCS6D01G269300 chr5D 95.082 122 6 0 2733 2854 483806549 483806428 4.890000e-45 193.0
23 TraesCS6D01G269300 chr5D 83.815 173 21 5 4513 4680 405393881 405393711 1.780000e-34 158.0
24 TraesCS6D01G269300 chr5D 91.781 73 4 1 1384 1456 435886114 435886184 3.050000e-17 100.0
25 TraesCS6D01G269300 chrUn 95.082 122 6 0 2733 2854 442414397 442414276 4.890000e-45 193.0
26 TraesCS6D01G269300 chrUn 88.764 89 5 4 1377 1463 320256094 320256179 2.360000e-18 104.0
27 TraesCS6D01G269300 chrUn 88.764 89 5 4 1377 1463 357700744 357700829 2.360000e-18 104.0
28 TraesCS6D01G269300 chr5A 95.082 122 6 0 2733 2854 607203047 607202926 4.890000e-45 193.0
29 TraesCS6D01G269300 chr4A 95.082 122 6 0 2733 2854 310733557 310733436 4.890000e-45 193.0
30 TraesCS6D01G269300 chr3D 95.082 122 6 0 2733 2854 598875839 598875960 4.890000e-45 193.0
31 TraesCS6D01G269300 chr3B 95.082 122 6 0 2733 2854 101922011 101921890 4.890000e-45 193.0
32 TraesCS6D01G269300 chr3B 86.139 101 9 4 1377 1475 755174884 755174787 2.360000e-18 104.0
33 TraesCS6D01G269300 chr3B 88.764 89 5 4 1377 1463 756117488 756117573 2.360000e-18 104.0
34 TraesCS6D01G269300 chr2A 95.082 122 6 0 2733 2854 335833612 335833491 4.890000e-45 193.0
35 TraesCS6D01G269300 chr4D 80.513 195 30 6 4316 4506 451301742 451301932 5.000000e-30 143.0
36 TraesCS6D01G269300 chr7B 90.588 85 4 3 1384 1466 7562500 7562418 5.070000e-20 110.0
37 TraesCS6D01G269300 chr4B 75.263 190 38 7 4321 4505 122519469 122519284 1.100000e-11 82.4
38 TraesCS6D01G269300 chr7A 94.231 52 2 1 1384 1434 107815935 107815986 1.430000e-10 78.7
39 TraesCS6D01G269300 chr1A 93.023 43 2 1 1384 1426 33858042 33858001 1.440000e-05 62.1


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 TraesCS6D01G269300 chr6D 379519371 379524159 4788 False 3070.000000 8844 99.346667 1 4789 3 chr6D.!!$F1 4788
1 TraesCS6D01G269300 chr6A 521473669 521481588 7919 True 789.250000 2313 91.752875 1 4789 8 chr6A.!!$R1 4788
2 TraesCS6D01G269300 chr6B 567468937 567474170 5233 True 471.055556 1953 88.884556 1 4789 9 chr6B.!!$R1 4788

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
716 721 0.108615 CACGAAGAGAATCGGTGGCT 60.109 55.0 1.59 0.0 46.82 4.75 F
1600 1624 0.037697 TCTTCCGTGAACCATGTCGG 60.038 55.0 0.00 0.0 43.65 4.79 F
2097 2663 0.248012 TCGAAAGAATGCCCACGCTA 59.752 50.0 0.00 0.0 37.03 4.26 F
2862 3607 0.461961 AGGCTCTATCCGTGCACTTC 59.538 55.0 16.19 0.0 33.89 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2087 2653 0.323302 TCAACTCAATAGCGTGGGCA 59.677 50.000 0.00 0.0 43.41 5.36 R
3071 3827 0.324943 TGGTCTGCCCAACTTAGAGC 59.675 55.000 0.00 0.0 41.50 4.09 R
3728 4617 1.674651 AGCGCAGTACCAGACTCGA 60.675 57.895 11.47 0.0 35.64 4.04 R
4244 8021 0.039256 CCAGGCAACCAAACATCACG 60.039 55.000 0.00 0.0 37.17 4.35 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
74 75 7.865706 AGATATAGTTCCATTTCACGCTTTT 57.134 32.000 0.00 0.00 0.00 2.27
78 79 5.108385 AGTTCCATTTCACGCTTTTACAG 57.892 39.130 0.00 0.00 0.00 2.74
89 90 3.493503 ACGCTTTTACAGTAGTTGTCAGC 59.506 43.478 0.00 0.00 41.29 4.26
110 111 6.212791 TCAGCGATAAGTAGGGCCTAATAAAT 59.787 38.462 16.44 11.46 0.00 1.40
111 112 6.313905 CAGCGATAAGTAGGGCCTAATAAATG 59.686 42.308 16.44 6.84 0.00 2.32
135 136 4.142160 ACTCAAAGAGCTGGAACCAAAAAC 60.142 41.667 0.00 0.00 32.04 2.43
178 179 4.192317 GAGACGGTCCTCATGCTATTTTT 58.808 43.478 4.14 0.00 33.50 1.94
185 186 2.539547 CCTCATGCTATTTTTCCGTGCG 60.540 50.000 0.00 0.00 0.00 5.34
205 206 2.350522 GCATGAGACACCGATGAGTTT 58.649 47.619 0.00 0.00 0.00 2.66
213 214 3.551846 ACACCGATGAGTTTGAAGGTTT 58.448 40.909 0.00 0.00 0.00 3.27
356 358 5.248477 ACTTCACTTAGGATGAGCTTAACCA 59.752 40.000 7.56 0.00 0.00 3.67
357 359 5.957771 TCACTTAGGATGAGCTTAACCAT 57.042 39.130 7.56 0.00 0.00 3.55
358 360 6.313519 TCACTTAGGATGAGCTTAACCATT 57.686 37.500 7.56 0.00 0.00 3.16
359 361 6.115446 TCACTTAGGATGAGCTTAACCATTG 58.885 40.000 7.56 0.00 0.00 2.82
456 458 0.652592 CGGCGGCATCTAAAACTCTG 59.347 55.000 10.53 0.00 0.00 3.35
471 473 6.934048 AAAACTCTGTCCTTCTTCTTCTTG 57.066 37.500 0.00 0.00 0.00 3.02
524 526 3.873801 GCCAGCTTCTTATCAACCTTGGA 60.874 47.826 0.00 0.00 0.00 3.53
525 527 4.335416 CCAGCTTCTTATCAACCTTGGAA 58.665 43.478 0.00 0.00 0.00 3.53
558 560 3.565482 CCTTCTTGTCTACAAAGCAGCAA 59.435 43.478 0.00 0.00 35.15 3.91
562 564 6.875948 TCTTGTCTACAAAGCAGCAAATTA 57.124 33.333 0.00 0.00 35.15 1.40
565 567 7.809331 TCTTGTCTACAAAGCAGCAAATTATTG 59.191 33.333 0.00 0.00 36.14 1.90
616 620 0.880278 TCGAGAAGCAACAGTGTGCC 60.880 55.000 12.26 0.60 46.14 5.01
621 625 1.731433 AAGCAACAGTGTGCCTGCAG 61.731 55.000 18.16 6.78 46.14 4.41
624 628 0.309922 CAACAGTGTGCCTGCAGAAG 59.690 55.000 17.39 0.00 45.68 2.85
678 683 1.135972 CCGAGAACAAATCAGCAACGG 60.136 52.381 0.00 0.00 0.00 4.44
716 721 0.108615 CACGAAGAGAATCGGTGGCT 60.109 55.000 1.59 0.00 46.82 4.75
722 728 4.261656 CGAAGAGAATCGGTGGCTATAAGT 60.262 45.833 0.00 0.00 42.67 2.24
885 894 1.140312 GGTGGGCCTGATTCTATCCA 58.860 55.000 4.53 0.00 0.00 3.41
894 903 0.603975 GATTCTATCCAGGCCCGCAC 60.604 60.000 0.00 0.00 0.00 5.34
907 916 3.314331 CGCACTCCAGGGACCAGT 61.314 66.667 0.00 0.00 0.00 4.00
1169 1182 3.110178 GTTCGCCGAGGTTCGTGG 61.110 66.667 0.00 0.00 38.40 4.94
1186 1199 4.349682 GGATTTTCCCCGTTCCCC 57.650 61.111 0.00 0.00 0.00 4.81
1189 1202 1.471119 GATTTTCCCCGTTCCCCTTC 58.529 55.000 0.00 0.00 0.00 3.46
1191 1204 0.111639 TTTTCCCCGTTCCCCTTCTG 59.888 55.000 0.00 0.00 0.00 3.02
1192 1205 1.785353 TTTCCCCGTTCCCCTTCTGG 61.785 60.000 0.00 0.00 0.00 3.86
1225 1241 0.391597 TTCCTGGGTTCAGTCGTGAC 59.608 55.000 0.00 0.00 39.31 3.67
1236 1254 1.011574 GTCGTGACGTGGTTGTTGC 60.012 57.895 4.40 0.00 0.00 4.17
1239 1257 1.711060 CGTGACGTGGTTGTTGCCTT 61.711 55.000 0.00 0.00 0.00 4.35
1240 1258 0.454196 GTGACGTGGTTGTTGCCTTT 59.546 50.000 0.00 0.00 0.00 3.11
1307 1325 2.109126 GGTGGTCAAGAGCATCCGC 61.109 63.158 5.17 0.00 41.20 5.54
1382 1405 5.128827 TCCTGCTTGGTAGGAGTAATTAGTG 59.871 44.000 0.00 0.00 39.41 2.74
1411 1434 7.382759 CCCTCTGTAAGAAATATAAGAGCGTTC 59.617 40.741 0.00 0.00 46.34 3.95
1514 1537 3.134804 GCTCTGGGCTTAATTCCTCTGTA 59.865 47.826 0.00 0.00 38.06 2.74
1517 1540 5.030147 TCTGGGCTTAATTCCTCTGTAAGA 58.970 41.667 0.00 0.00 43.69 2.10
1552 1576 0.321298 GTGGTGCGGGTGATACTTGT 60.321 55.000 0.00 0.00 0.00 3.16
1587 1611 2.555199 CAAGGGCAGATAACTCTTCCG 58.445 52.381 0.00 0.00 35.81 4.30
1592 1616 2.930682 GGCAGATAACTCTTCCGTGAAC 59.069 50.000 0.00 0.00 0.00 3.18
1600 1624 0.037697 TCTTCCGTGAACCATGTCGG 60.038 55.000 0.00 0.00 43.65 4.79
1632 1656 1.134946 ACTTGCTTGCAAGTTGTGTCC 59.865 47.619 28.63 9.43 42.16 4.02
1633 1657 1.406539 CTTGCTTGCAAGTTGTGTCCT 59.593 47.619 26.55 0.00 0.00 3.85
1634 1658 2.340210 TGCTTGCAAGTTGTGTCCTA 57.660 45.000 26.55 1.22 0.00 2.94
1635 1659 2.221169 TGCTTGCAAGTTGTGTCCTAG 58.779 47.619 26.55 0.00 0.00 3.02
1636 1660 2.222027 GCTTGCAAGTTGTGTCCTAGT 58.778 47.619 26.55 0.00 0.00 2.57
1637 1661 3.181459 TGCTTGCAAGTTGTGTCCTAGTA 60.181 43.478 26.55 0.00 0.00 1.82
1638 1662 3.433615 GCTTGCAAGTTGTGTCCTAGTAG 59.566 47.826 26.55 0.00 0.00 2.57
1639 1663 4.632153 CTTGCAAGTTGTGTCCTAGTAGT 58.368 43.478 18.65 0.00 0.00 2.73
1640 1664 3.990092 TGCAAGTTGTGTCCTAGTAGTG 58.010 45.455 4.48 0.00 0.00 2.74
1641 1665 3.386726 TGCAAGTTGTGTCCTAGTAGTGT 59.613 43.478 4.48 0.00 0.00 3.55
1642 1666 4.585581 TGCAAGTTGTGTCCTAGTAGTGTA 59.414 41.667 4.48 0.00 0.00 2.90
1698 1846 6.683974 ACATACTGAATGATTTAGTGTGCC 57.316 37.500 21.00 0.00 37.14 5.01
1699 1847 5.294306 ACATACTGAATGATTTAGTGTGCCG 59.706 40.000 21.00 4.58 37.14 5.69
1725 1873 3.355378 TGTTGATGATGGGATTGTCCAC 58.645 45.455 0.00 0.00 39.97 4.02
1745 1893 4.813161 CCACTTGCCACTATATGAAGTCAG 59.187 45.833 0.00 0.00 0.00 3.51
1773 1924 6.651643 ACTGCGTGTGTCCTTATTTATGTTAA 59.348 34.615 0.00 0.00 0.00 2.01
1940 2133 7.050377 ACATATATGTGACCTCAAAAGAGGTG 58.950 38.462 20.92 6.66 45.64 4.00
2005 2198 9.764363 GTAATCCATGAGTTGTATCTTATCACA 57.236 33.333 0.00 0.00 0.00 3.58
2059 2625 7.230712 ACCTTAACAACCTAAAATCTTCACCAG 59.769 37.037 0.00 0.00 0.00 4.00
2071 2637 5.633830 ATCTTCACCAGCAACTAATTGTG 57.366 39.130 0.00 0.00 38.17 3.33
2095 2661 3.573558 TCGAAAGAATGCCCACGC 58.426 55.556 0.00 0.00 37.03 5.34
2096 2662 1.003839 TCGAAAGAATGCCCACGCT 60.004 52.632 0.00 0.00 37.03 5.07
2097 2663 0.248012 TCGAAAGAATGCCCACGCTA 59.752 50.000 0.00 0.00 37.03 4.26
2098 2664 1.134521 TCGAAAGAATGCCCACGCTAT 60.135 47.619 0.00 0.00 37.03 2.97
2112 2712 3.425359 CCACGCTATTGAGTTGAAAGCTG 60.425 47.826 0.00 0.00 0.00 4.24
2128 2728 6.785191 TGAAAGCTGTTTGTTTTCTCTACTG 58.215 36.000 0.00 0.00 43.39 2.74
2140 2740 8.015185 TGTTTTCTCTACTGTTAGTACCTTGT 57.985 34.615 0.00 0.00 0.00 3.16
2141 2741 9.135189 TGTTTTCTCTACTGTTAGTACCTTGTA 57.865 33.333 0.00 0.00 0.00 2.41
2183 2783 3.308053 CACATCACATTCTAAGGAGCACG 59.692 47.826 0.00 0.00 0.00 5.34
2199 2799 5.593095 AGGAGCACGATGTAGTTGTCTTATA 59.407 40.000 0.00 0.00 0.00 0.98
2239 2839 6.543465 TGTTCTATTCAATTATCTGTGCTGGG 59.457 38.462 0.00 0.00 0.00 4.45
2359 2966 2.807967 CCTTGCATTCTGTTGAGTCGAA 59.192 45.455 0.00 0.00 0.00 3.71
2405 3012 4.277174 ACCAGCTTATCTATCAGTCTGACG 59.723 45.833 4.21 0.00 0.00 4.35
2410 3017 5.681337 TTATCTATCAGTCTGACGCAGAG 57.319 43.478 4.21 0.14 41.46 3.35
2421 3028 5.361285 AGTCTGACGCAGAGGTTCTATATTT 59.639 40.000 9.38 0.00 41.46 1.40
2426 3033 6.127281 TGACGCAGAGGTTCTATATTTGGTTA 60.127 38.462 0.00 0.00 0.00 2.85
2472 3079 1.065273 CATTTGCCTCCGCATGCTC 59.935 57.895 17.13 0.17 46.67 4.26
2510 3117 4.743151 GCATGCATGTTTTCCTGATGTATG 59.257 41.667 26.79 0.00 40.88 2.39
2547 3260 1.742761 CTGTACCAAGCCCACATCAG 58.257 55.000 0.00 0.00 0.00 2.90
2570 3283 7.395772 TCAGAGGCCAACATAAATCATTTACAA 59.604 33.333 5.01 0.00 0.00 2.41
2574 3287 6.105333 GCCAACATAAATCATTTACAAGCCA 58.895 36.000 0.00 0.00 0.00 4.75
2575 3288 6.593382 GCCAACATAAATCATTTACAAGCCAA 59.407 34.615 0.00 0.00 0.00 4.52
2576 3289 7.412891 GCCAACATAAATCATTTACAAGCCAAC 60.413 37.037 0.00 0.00 0.00 3.77
2661 3404 7.659390 CCTTGGTGTATTTTCCTTGCATTTTAA 59.341 33.333 0.00 0.00 0.00 1.52
2745 3490 0.693622 TCACATAACCTTTCCCCGCA 59.306 50.000 0.00 0.00 0.00 5.69
2746 3491 1.283613 TCACATAACCTTTCCCCGCAT 59.716 47.619 0.00 0.00 0.00 4.73
2757 3502 1.046472 TCCCCGCATCCGACACTAAT 61.046 55.000 0.00 0.00 36.29 1.73
2769 3514 7.792508 GCATCCGACACTAATCTATTTTTAACG 59.207 37.037 0.00 0.00 0.00 3.18
2814 3559 5.897377 TCCAATTAGGAAGTTAAGCTTGC 57.103 39.130 9.86 1.67 45.65 4.01
2859 3604 1.227380 CCAGGCTCTATCCGTGCAC 60.227 63.158 6.82 6.82 33.89 4.57
2862 3607 0.461961 AGGCTCTATCCGTGCACTTC 59.538 55.000 16.19 0.00 33.89 3.01
2925 3672 0.855349 CGCATAGCAACTAAGGAGCG 59.145 55.000 0.00 0.00 37.91 5.03
2952 3699 5.764686 ACATAGTTGTCTTGTCAATTGCTGA 59.235 36.000 0.00 0.00 0.00 4.26
2969 3716 8.469200 CAATTGCTGATATTTTTCTTCCCAGTA 58.531 33.333 0.00 0.00 0.00 2.74
3022 3778 8.069574 CCCTTTAAAATCATTTTGCAACAACTC 58.930 33.333 5.56 0.00 34.19 3.01
3071 3827 5.013495 TCTCATTAATCTTCCCTATGGCCTG 59.987 44.000 3.32 0.00 0.00 4.85
3295 4143 6.530019 AGAAACTTGACACATTTGGAAAGT 57.470 33.333 0.00 0.00 35.25 2.66
3296 4144 7.639113 AGAAACTTGACACATTTGGAAAGTA 57.361 32.000 2.90 0.00 33.59 2.24
3556 4441 3.652869 AGGTGAAGGAGAAACTGGAATCA 59.347 43.478 0.00 0.00 0.00 2.57
3591 4476 1.961394 TGTAACTGAAGTCGCTGAGGT 59.039 47.619 0.00 0.00 0.00 3.85
3599 4484 3.258372 TGAAGTCGCTGAGGTTACATCTT 59.742 43.478 0.00 0.00 0.00 2.40
3602 4487 4.270834 AGTCGCTGAGGTTACATCTTCTA 58.729 43.478 0.00 0.00 0.00 2.10
3623 4508 9.605275 CTTCTATGTTCTGAGAACATTTCCATA 57.395 33.333 36.66 21.34 40.87 2.74
3627 4512 3.797039 TCTGAGAACATTTCCATAGCCG 58.203 45.455 0.00 0.00 0.00 5.52
3628 4513 2.288666 TGAGAACATTTCCATAGCCGC 58.711 47.619 0.00 0.00 0.00 6.53
3629 4514 1.261619 GAGAACATTTCCATAGCCGCG 59.738 52.381 0.00 0.00 0.00 6.46
3630 4515 1.014352 GAACATTTCCATAGCCGCGT 58.986 50.000 4.92 0.00 0.00 6.01
3631 4516 0.732571 AACATTTCCATAGCCGCGTG 59.267 50.000 4.92 0.00 0.00 5.34
3633 4518 0.813610 CATTTCCATAGCCGCGTGGA 60.814 55.000 21.76 11.76 42.55 4.02
3712 4601 4.976731 GCTAGTGATCGACGTGTTTATCAT 59.023 41.667 0.00 0.00 31.49 2.45
3728 4617 6.830324 TGTTTATCATGGAGCTTTAAGCATCT 59.170 34.615 19.63 0.00 45.56 2.90
3747 4636 1.515088 CGAGTCTGGTACTGCGCTG 60.515 63.158 13.23 13.23 39.07 5.18
3769 4658 4.396790 TGTTCGGTTGGCCATTAGATAAAC 59.603 41.667 6.09 6.10 34.09 2.01
3802 4691 6.545666 TGCATTGTTAACTAATATGGGTGAGG 59.454 38.462 7.22 0.00 0.00 3.86
3845 4734 3.068732 GCATAGATGTGACTACCTGAGCA 59.931 47.826 0.00 0.00 0.00 4.26
3864 4786 2.930887 GCACTCGAGCCATGTTCACTTA 60.931 50.000 13.61 0.00 0.00 2.24
3905 4827 9.268268 TCGTAAAAATATTGAAGTTGAGACTGT 57.732 29.630 0.00 0.00 35.91 3.55
3906 4828 9.530129 CGTAAAAATATTGAAGTTGAGACTGTC 57.470 33.333 0.00 0.00 35.91 3.51
3917 4839 4.841246 AGTTGAGACTGTCTATTGGTCCTT 59.159 41.667 10.86 0.00 33.99 3.36
3918 4840 5.308237 AGTTGAGACTGTCTATTGGTCCTTT 59.692 40.000 10.86 0.00 33.99 3.11
3920 4842 4.838423 TGAGACTGTCTATTGGTCCTTTCA 59.162 41.667 10.86 0.00 0.00 2.69
3949 4906 2.357593 CTTGGTTGCCTGGGACCACT 62.358 60.000 8.56 0.00 45.14 4.00
4046 5009 6.532657 CAGAAATTCTTCAGTTGTGCTTTTGT 59.467 34.615 0.00 0.00 33.64 2.83
4064 5027 8.226448 TGCTTTTGTACAAACACAGAAATTTTG 58.774 29.630 20.43 0.00 34.61 2.44
4065 5028 7.691877 GCTTTTGTACAAACACAGAAATTTTGG 59.308 33.333 20.43 0.00 34.61 3.28
4096 5059 7.638444 TGATAGAGGAGAGATATAGTGGAAGG 58.362 42.308 0.00 0.00 0.00 3.46
4181 5144 6.773976 TGGACCCTCAGCTAAATTTTTATG 57.226 37.500 0.00 0.00 0.00 1.90
4209 5172 1.534729 AGGAAGCGTTTGGTTGATCC 58.465 50.000 0.00 0.00 35.57 3.36
4219 7996 2.734755 TGGTTGATCCCATTAGGCTG 57.265 50.000 0.00 0.00 34.51 4.85
4221 7998 1.494721 GGTTGATCCCATTAGGCTGGA 59.505 52.381 0.00 0.00 38.69 3.86
4244 8021 2.951458 CCCGCGTGGAAGGAAAAC 59.049 61.111 18.79 0.00 37.49 2.43
4248 8025 2.313267 GCGTGGAAGGAAAACGTGA 58.687 52.632 0.00 0.00 39.45 4.35
4260 8037 3.957383 AACGTGATGTTTGGTTGCC 57.043 47.368 0.00 0.00 37.59 4.52
4261 8038 1.398692 AACGTGATGTTTGGTTGCCT 58.601 45.000 0.00 0.00 37.59 4.75
4262 8039 0.667993 ACGTGATGTTTGGTTGCCTG 59.332 50.000 0.00 0.00 0.00 4.85
4264 8041 0.319813 GTGATGTTTGGTTGCCTGGC 60.320 55.000 12.87 12.87 0.00 4.85
4265 8042 1.293179 GATGTTTGGTTGCCTGGCC 59.707 57.895 17.53 0.00 0.00 5.36
4266 8043 1.152269 ATGTTTGGTTGCCTGGCCT 60.152 52.632 17.53 0.00 0.00 5.19
4267 8044 0.114168 ATGTTTGGTTGCCTGGCCTA 59.886 50.000 17.53 0.67 0.00 3.93
4268 8045 0.825840 TGTTTGGTTGCCTGGCCTAC 60.826 55.000 17.53 13.94 0.00 3.18
4269 8046 0.825840 GTTTGGTTGCCTGGCCTACA 60.826 55.000 17.53 9.19 0.00 2.74
4270 8047 0.114168 TTTGGTTGCCTGGCCTACAT 59.886 50.000 17.53 0.00 0.00 2.29
4285 8062 2.487934 CTACATCAGAATCTTGGCCCG 58.512 52.381 0.00 0.00 0.00 6.13
4288 8065 0.749454 ATCAGAATCTTGGCCCGCAC 60.749 55.000 0.00 0.00 0.00 5.34
4300 8077 2.432628 CCGCACGAACCTCACTCC 60.433 66.667 0.00 0.00 0.00 3.85
4302 8079 1.444553 CGCACGAACCTCACTCCTC 60.445 63.158 0.00 0.00 0.00 3.71
4305 8082 0.389166 CACGAACCTCACTCCTCAGC 60.389 60.000 0.00 0.00 0.00 4.26
4306 8083 1.216710 CGAACCTCACTCCTCAGCC 59.783 63.158 0.00 0.00 0.00 4.85
4307 8084 1.536073 CGAACCTCACTCCTCAGCCA 61.536 60.000 0.00 0.00 0.00 4.75
4309 8086 0.617413 AACCTCACTCCTCAGCCATG 59.383 55.000 0.00 0.00 0.00 3.66
4310 8087 1.153208 CCTCACTCCTCAGCCATGC 60.153 63.158 0.00 0.00 0.00 4.06
4311 8088 1.600638 CTCACTCCTCAGCCATGCA 59.399 57.895 0.00 0.00 0.00 3.96
4312 8089 0.180642 CTCACTCCTCAGCCATGCAT 59.819 55.000 0.00 0.00 0.00 3.96
4313 8090 0.179702 TCACTCCTCAGCCATGCATC 59.820 55.000 0.00 0.00 0.00 3.91
4360 8648 4.838486 GGAGCTCGCGTGTCTCCG 62.838 72.222 24.87 0.00 37.28 4.63
4390 8680 2.746277 GGCGAATTGGTCACCGCT 60.746 61.111 0.00 0.00 46.02 5.52
4394 8684 1.741770 GAATTGGTCACCGCTCGCT 60.742 57.895 0.00 0.00 0.00 4.93
4421 8711 0.041238 TCGCCCTATATAGCCAGCCT 59.959 55.000 4.04 0.00 0.00 4.58
4422 8712 0.461961 CGCCCTATATAGCCAGCCTC 59.538 60.000 4.04 0.00 0.00 4.70
4423 8713 1.573108 GCCCTATATAGCCAGCCTCA 58.427 55.000 4.04 0.00 0.00 3.86
4424 8714 2.122768 GCCCTATATAGCCAGCCTCAT 58.877 52.381 4.04 0.00 0.00 2.90
4425 8715 2.507471 GCCCTATATAGCCAGCCTCATT 59.493 50.000 4.04 0.00 0.00 2.57
4426 8716 3.683847 GCCCTATATAGCCAGCCTCATTG 60.684 52.174 4.04 0.00 0.00 2.82
4427 8717 3.539604 CCTATATAGCCAGCCTCATTGC 58.460 50.000 4.04 0.00 0.00 3.56
4428 8718 3.054875 CCTATATAGCCAGCCTCATTGCA 60.055 47.826 4.04 0.00 0.00 4.08
4429 8719 3.513909 ATATAGCCAGCCTCATTGCAA 57.486 42.857 0.00 0.00 0.00 4.08
4430 8720 1.396653 ATAGCCAGCCTCATTGCAAC 58.603 50.000 0.00 0.00 0.00 4.17
4431 8721 1.026182 TAGCCAGCCTCATTGCAACG 61.026 55.000 0.00 0.00 0.00 4.10
4432 8722 2.334946 GCCAGCCTCATTGCAACGA 61.335 57.895 0.00 0.00 0.00 3.85
4433 8723 1.503542 CCAGCCTCATTGCAACGAC 59.496 57.895 0.00 0.00 0.00 4.34
4434 8724 1.236616 CCAGCCTCATTGCAACGACA 61.237 55.000 0.00 0.00 0.00 4.35
4435 8725 0.592637 CAGCCTCATTGCAACGACAA 59.407 50.000 0.00 0.00 0.00 3.18
4436 8726 1.001487 CAGCCTCATTGCAACGACAAA 60.001 47.619 0.00 0.00 32.27 2.83
4437 8727 1.680735 AGCCTCATTGCAACGACAAAA 59.319 42.857 0.00 0.00 32.27 2.44
4438 8728 1.786579 GCCTCATTGCAACGACAAAAC 59.213 47.619 0.00 0.00 32.27 2.43
4439 8729 2.543653 GCCTCATTGCAACGACAAAACT 60.544 45.455 0.00 0.00 32.27 2.66
4440 8730 3.300009 CCTCATTGCAACGACAAAACTC 58.700 45.455 0.00 0.00 32.27 3.01
4441 8731 3.300009 CTCATTGCAACGACAAAACTCC 58.700 45.455 0.00 0.00 32.27 3.85
4442 8732 2.948979 TCATTGCAACGACAAAACTCCT 59.051 40.909 0.00 0.00 32.27 3.69
4443 8733 2.842208 TTGCAACGACAAAACTCCTG 57.158 45.000 0.00 0.00 0.00 3.86
4444 8734 1.745232 TGCAACGACAAAACTCCTGT 58.255 45.000 0.00 0.00 0.00 4.00
4445 8735 1.668751 TGCAACGACAAAACTCCTGTC 59.331 47.619 0.00 0.00 39.89 3.51
4446 8736 1.668751 GCAACGACAAAACTCCTGTCA 59.331 47.619 4.07 0.00 42.80 3.58
4447 8737 2.538939 GCAACGACAAAACTCCTGTCAC 60.539 50.000 4.07 0.00 42.80 3.67
4448 8738 1.949465 ACGACAAAACTCCTGTCACC 58.051 50.000 4.07 0.00 42.80 4.02
4449 8739 1.208535 ACGACAAAACTCCTGTCACCA 59.791 47.619 4.07 0.00 42.80 4.17
4450 8740 2.158813 ACGACAAAACTCCTGTCACCAT 60.159 45.455 4.07 0.00 42.80 3.55
4451 8741 2.878406 CGACAAAACTCCTGTCACCATT 59.122 45.455 4.07 0.00 42.80 3.16
4452 8742 3.058914 CGACAAAACTCCTGTCACCATTC 60.059 47.826 4.07 0.00 42.80 2.67
4453 8743 3.222603 ACAAAACTCCTGTCACCATTCC 58.777 45.455 0.00 0.00 0.00 3.01
4454 8744 2.558359 CAAAACTCCTGTCACCATTCCC 59.442 50.000 0.00 0.00 0.00 3.97
4455 8745 0.698818 AACTCCTGTCACCATTCCCC 59.301 55.000 0.00 0.00 0.00 4.81
4456 8746 1.208165 ACTCCTGTCACCATTCCCCC 61.208 60.000 0.00 0.00 0.00 5.40
4457 8747 0.916358 CTCCTGTCACCATTCCCCCT 60.916 60.000 0.00 0.00 0.00 4.79
4458 8748 0.914417 TCCTGTCACCATTCCCCCTC 60.914 60.000 0.00 0.00 0.00 4.30
4459 8749 0.916358 CCTGTCACCATTCCCCCTCT 60.916 60.000 0.00 0.00 0.00 3.69
4460 8750 0.543749 CTGTCACCATTCCCCCTCTC 59.456 60.000 0.00 0.00 0.00 3.20
4461 8751 0.119155 TGTCACCATTCCCCCTCTCT 59.881 55.000 0.00 0.00 0.00 3.10
4462 8752 1.290134 GTCACCATTCCCCCTCTCTT 58.710 55.000 0.00 0.00 0.00 2.85
4463 8753 1.065126 GTCACCATTCCCCCTCTCTTG 60.065 57.143 0.00 0.00 0.00 3.02
4464 8754 1.203428 TCACCATTCCCCCTCTCTTGA 60.203 52.381 0.00 0.00 0.00 3.02
4465 8755 1.211457 CACCATTCCCCCTCTCTTGAG 59.789 57.143 0.00 0.00 39.92 3.02
4466 8756 0.182299 CCATTCCCCCTCTCTTGAGC 59.818 60.000 0.00 0.00 38.93 4.26
4467 8757 1.211456 CATTCCCCCTCTCTTGAGCT 58.789 55.000 0.00 0.00 38.93 4.09
4468 8758 1.563410 CATTCCCCCTCTCTTGAGCTT 59.437 52.381 0.00 0.00 38.93 3.74
4469 8759 1.747444 TTCCCCCTCTCTTGAGCTTT 58.253 50.000 0.00 0.00 38.93 3.51
4470 8760 1.280457 TCCCCCTCTCTTGAGCTTTC 58.720 55.000 0.00 0.00 38.93 2.62
4471 8761 0.254462 CCCCCTCTCTTGAGCTTTCC 59.746 60.000 0.00 0.00 38.93 3.13
4472 8762 0.254462 CCCCTCTCTTGAGCTTTCCC 59.746 60.000 0.00 0.00 38.93 3.97
4473 8763 1.284313 CCCTCTCTTGAGCTTTCCCT 58.716 55.000 0.00 0.00 38.93 4.20
4474 8764 1.209261 CCCTCTCTTGAGCTTTCCCTC 59.791 57.143 0.00 0.00 38.93 4.30
4475 8765 1.209261 CCTCTCTTGAGCTTTCCCTCC 59.791 57.143 0.00 0.00 38.93 4.30
4476 8766 2.187100 CTCTCTTGAGCTTTCCCTCCT 58.813 52.381 0.00 0.00 33.12 3.69
4477 8767 1.905215 TCTCTTGAGCTTTCCCTCCTG 59.095 52.381 0.00 0.00 0.00 3.86
4478 8768 0.326264 TCTTGAGCTTTCCCTCCTGC 59.674 55.000 0.00 0.00 0.00 4.85
4479 8769 1.003355 TTGAGCTTTCCCTCCTGCG 60.003 57.895 0.00 0.00 0.00 5.18
4480 8770 2.821810 GAGCTTTCCCTCCTGCGC 60.822 66.667 0.00 0.00 0.00 6.09
4481 8771 3.612247 GAGCTTTCCCTCCTGCGCA 62.612 63.158 10.98 10.98 0.00 6.09
4482 8772 3.130160 GCTTTCCCTCCTGCGCAG 61.130 66.667 30.52 30.52 0.00 5.18
4483 8773 2.665000 CTTTCCCTCCTGCGCAGA 59.335 61.111 38.06 22.07 0.00 4.26
4484 8774 1.449246 CTTTCCCTCCTGCGCAGAG 60.449 63.158 38.06 28.76 0.00 3.35
4509 8799 2.886124 GGCGACGAGGTAAGCAGC 60.886 66.667 0.00 0.00 0.00 5.25
4510 8800 3.248171 GCGACGAGGTAAGCAGCG 61.248 66.667 0.00 0.00 0.00 5.18
4511 8801 3.248171 CGACGAGGTAAGCAGCGC 61.248 66.667 0.00 0.00 0.00 5.92
4512 8802 2.182030 GACGAGGTAAGCAGCGCT 59.818 61.111 2.64 2.64 42.56 5.92
4513 8803 1.432251 GACGAGGTAAGCAGCGCTA 59.568 57.895 10.99 0.00 38.25 4.26
4514 8804 0.592754 GACGAGGTAAGCAGCGCTAG 60.593 60.000 10.99 5.98 38.25 3.42
4515 8805 1.946650 CGAGGTAAGCAGCGCTAGC 60.947 63.158 10.99 16.77 38.25 3.42
4516 8806 1.592939 GAGGTAAGCAGCGCTAGCC 60.593 63.158 22.52 14.82 46.67 3.93
4517 8807 2.186903 GGTAAGCAGCGCTAGCCA 59.813 61.111 22.52 12.01 46.67 4.75
4518 8808 1.884926 GGTAAGCAGCGCTAGCCAG 60.885 63.158 22.52 7.66 46.67 4.85
4519 8809 2.202932 TAAGCAGCGCTAGCCAGC 60.203 61.111 22.52 16.49 46.67 4.85
4520 8810 3.740128 TAAGCAGCGCTAGCCAGCC 62.740 63.158 22.52 0.00 45.64 4.85
4524 8814 3.160047 AGCGCTAGCCAGCCTCAT 61.160 61.111 8.99 0.00 45.64 2.90
4529 8819 1.033746 GCTAGCCAGCCTCATTGCAA 61.034 55.000 2.29 0.00 42.37 4.08
4541 8831 3.300009 CTCATTGCAACGACAAAACTCC 58.700 45.455 0.00 0.00 32.27 3.85
4552 8842 2.225727 GACAAAACTCCCGTCACCATTC 59.774 50.000 0.00 0.00 0.00 2.67
4658 8950 1.009449 CGGCGATTCGACTCCTCTC 60.009 63.158 10.88 0.00 29.68 3.20
4715 9008 4.007644 CAGCCTCACCGCAGTGGA 62.008 66.667 7.13 0.00 44.64 4.02
4723 9016 1.134220 TCACCGCAGTGGAAAAACTCT 60.134 47.619 7.13 0.00 44.64 3.24
4733 9026 3.186613 GTGGAAAAACTCTCGTCACCATC 59.813 47.826 0.00 0.00 0.00 3.51
4734 9027 2.742589 GGAAAAACTCTCGTCACCATCC 59.257 50.000 0.00 0.00 0.00 3.51
4735 9028 2.474410 AAAACTCTCGTCACCATCCC 57.526 50.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 5.892160 ACTTATCGCTGACAACTACTGTA 57.108 39.130 0.00 0.00 38.84 2.74
78 79 4.608951 CCCTACTTATCGCTGACAACTAC 58.391 47.826 0.00 0.00 0.00 2.73
89 90 7.612677 AGTCATTTATTAGGCCCTACTTATCG 58.387 38.462 0.00 0.00 0.00 2.92
110 111 1.768275 TGGTTCCAGCTCTTTGAGTCA 59.232 47.619 0.00 0.00 31.39 3.41
111 112 2.550830 TGGTTCCAGCTCTTTGAGTC 57.449 50.000 0.00 0.00 31.39 3.36
135 136 3.436704 TCATTTCCTGAGCGCTTGTTAAG 59.563 43.478 13.26 4.69 0.00 1.85
178 179 2.432456 GTGTCTCATGCGCACGGA 60.432 61.111 14.90 13.35 0.00 4.69
185 186 2.015736 AACTCATCGGTGTCTCATGC 57.984 50.000 0.00 0.00 0.00 4.06
223 224 7.972832 AACGTAGAATGGTATGACAGAAAAA 57.027 32.000 0.00 0.00 0.00 1.94
314 315 8.298030 AGTGAAGTTTGTATGCTTAAAAATGC 57.702 30.769 0.00 0.00 0.00 3.56
357 359 9.342308 TGCCATTTTGTTTTGGATAATTAACAA 57.658 25.926 0.00 0.00 38.35 2.83
358 360 8.908786 TGCCATTTTGTTTTGGATAATTAACA 57.091 26.923 0.00 0.00 34.81 2.41
359 361 8.450180 CCTGCCATTTTGTTTTGGATAATTAAC 58.550 33.333 0.00 0.00 34.81 2.01
435 437 0.373716 GAGTTTTAGATGCCGCCGTG 59.626 55.000 0.00 0.00 0.00 4.94
441 443 4.837972 AGAAGGACAGAGTTTTAGATGCC 58.162 43.478 0.00 0.00 0.00 4.40
456 458 2.741517 GCAGCTCAAGAAGAAGAAGGAC 59.258 50.000 0.00 0.00 0.00 3.85
471 473 1.405391 GGAGTGAAGAGGAAGCAGCTC 60.405 57.143 0.00 0.00 0.00 4.09
524 526 1.026718 CAAGAAGGCTTCGCGGGATT 61.027 55.000 20.78 6.48 30.14 3.01
525 527 1.450312 CAAGAAGGCTTCGCGGGAT 60.450 57.895 20.78 0.00 30.14 3.85
558 560 3.963129 TGGGAGGCGAAAGTCAATAATT 58.037 40.909 0.00 0.00 38.99 1.40
562 564 2.286365 TTTGGGAGGCGAAAGTCAAT 57.714 45.000 0.00 0.00 38.99 2.57
565 567 1.130561 CGAATTTGGGAGGCGAAAGTC 59.869 52.381 0.00 0.00 0.00 3.01
616 620 1.827344 GGAAATTTCCCCCTTCTGCAG 59.173 52.381 24.44 7.63 41.62 4.41
621 625 0.530744 GTGCGGAAATTTCCCCCTTC 59.469 55.000 27.72 14.01 44.67 3.46
624 628 0.902984 AAGGTGCGGAAATTTCCCCC 60.903 55.000 27.72 23.50 44.67 5.40
678 683 0.733223 GTTCTTCCTCGTGGACGCTC 60.733 60.000 5.53 0.00 43.06 5.03
716 721 0.940126 GACGCCGACGAGGACTTATA 59.060 55.000 0.00 0.00 45.00 0.98
894 903 3.719121 CTCCACTGGTCCCTGGAG 58.281 66.667 15.28 15.28 45.97 3.86
1169 1182 0.040646 AAGGGGAACGGGGAAAATCC 59.959 55.000 0.00 0.00 35.23 3.01
1186 1199 4.751600 GGAAAACTTGATTTTGGCCAGAAG 59.248 41.667 14.78 10.96 40.73 2.85
1189 1202 4.060205 CAGGAAAACTTGATTTTGGCCAG 58.940 43.478 5.11 0.00 40.73 4.85
1191 1204 3.402110 CCAGGAAAACTTGATTTTGGCC 58.598 45.455 0.00 0.00 40.73 5.36
1192 1205 3.181455 ACCCAGGAAAACTTGATTTTGGC 60.181 43.478 0.00 0.00 40.73 4.52
1225 1241 0.172352 ACACAAAGGCAACAACCACG 59.828 50.000 0.00 0.00 41.41 4.94
1236 1254 1.856802 GAGGCTGCAAAACACAAAGG 58.143 50.000 0.50 0.00 0.00 3.11
1239 1257 0.749818 TCCGAGGCTGCAAAACACAA 60.750 50.000 0.50 0.00 0.00 3.33
1240 1258 1.153066 TCCGAGGCTGCAAAACACA 60.153 52.632 0.50 0.00 0.00 3.72
1307 1325 2.115266 AACCCTTTGCTCCCACGG 59.885 61.111 0.00 0.00 0.00 4.94
1382 1405 6.871492 GCTCTTATATTTCTTACAGAGGGAGC 59.129 42.308 0.00 0.00 34.36 4.70
1387 1410 8.858003 TGAACGCTCTTATATTTCTTACAGAG 57.142 34.615 0.00 0.00 0.00 3.35
1388 1411 7.921214 CCTGAACGCTCTTATATTTCTTACAGA 59.079 37.037 0.00 0.00 0.00 3.41
1389 1412 7.707035 ACCTGAACGCTCTTATATTTCTTACAG 59.293 37.037 0.00 0.00 0.00 2.74
1390 1413 7.553334 ACCTGAACGCTCTTATATTTCTTACA 58.447 34.615 0.00 0.00 0.00 2.41
1391 1414 7.705325 TGACCTGAACGCTCTTATATTTCTTAC 59.295 37.037 0.00 0.00 0.00 2.34
1392 1415 7.705325 GTGACCTGAACGCTCTTATATTTCTTA 59.295 37.037 0.00 0.00 0.00 2.10
1458 1481 8.647256 ACAATACCATACTATAGTGTACTCCC 57.353 38.462 15.90 0.00 28.41 4.30
1460 1483 9.517868 AGGACAATACCATACTATAGTGTACTC 57.482 37.037 15.90 5.45 36.10 2.59
1469 1492 7.242359 AGCTCTGTAGGACAATACCATACTAT 58.758 38.462 0.00 0.00 0.00 2.12
1514 1537 4.705023 ACCACACTTAGCAACAAGTTTCTT 59.295 37.500 0.00 0.00 36.61 2.52
1517 1540 3.428862 GCACCACACTTAGCAACAAGTTT 60.429 43.478 0.00 0.00 36.61 2.66
1552 1576 4.348486 TGCCCTTGGTTGATTGCTATTAA 58.652 39.130 0.00 0.00 0.00 1.40
1587 1611 0.887933 AAATGCCCGACATGGTTCAC 59.112 50.000 0.00 0.00 39.60 3.18
1592 1616 3.381272 AGTCAAATAAATGCCCGACATGG 59.619 43.478 0.00 0.00 39.60 3.66
1600 1624 3.995705 TGCAAGCAAGTCAAATAAATGCC 59.004 39.130 0.00 0.00 37.73 4.40
1671 1819 8.830580 GCACACTAAATCATTCAGTATGTATGT 58.169 33.333 0.00 0.00 43.37 2.29
1698 1846 2.028420 TCCCATCATCAACAAGAGCG 57.972 50.000 0.00 0.00 0.00 5.03
1699 1847 3.698040 ACAATCCCATCATCAACAAGAGC 59.302 43.478 0.00 0.00 0.00 4.09
1725 1873 4.101585 TCCCTGACTTCATATAGTGGCAAG 59.898 45.833 0.00 0.00 0.00 4.01
1752 1900 7.067532 TGCTTAACATAAATAAGGACACACG 57.932 36.000 0.00 0.00 32.24 4.49
1773 1924 1.884579 CAAGTCAAGCCACTGAATGCT 59.115 47.619 0.00 0.00 40.17 3.79
1811 2004 3.067180 ACCTGCATGAAACAGAACAACAG 59.933 43.478 0.00 0.00 37.32 3.16
1940 2133 2.798976 TTGGAGTGAAAATGCAGCAC 57.201 45.000 0.00 0.00 30.98 4.40
1985 2178 9.712359 CAAATGTGTGATAAGATACAACTCATG 57.288 33.333 0.00 0.00 0.00 3.07
2005 2198 3.254166 GGAGACACAGTCATTGCAAATGT 59.746 43.478 1.71 3.62 34.60 2.71
2059 2625 5.029650 TCGATGTTCACACAATTAGTTGC 57.970 39.130 0.00 0.00 38.96 4.17
2071 2637 2.487762 TGGGCATTCTTTCGATGTTCAC 59.512 45.455 0.00 0.00 0.00 3.18
2087 2653 0.323302 TCAACTCAATAGCGTGGGCA 59.677 50.000 0.00 0.00 43.41 5.36
2090 2656 2.744202 AGCTTTCAACTCAATAGCGTGG 59.256 45.455 0.00 0.00 36.96 4.94
2092 2658 3.403038 ACAGCTTTCAACTCAATAGCGT 58.597 40.909 0.00 0.00 36.96 5.07
2094 2660 5.523369 ACAAACAGCTTTCAACTCAATAGC 58.477 37.500 0.00 0.00 0.00 2.97
2095 2661 7.992180 AAACAAACAGCTTTCAACTCAATAG 57.008 32.000 0.00 0.00 0.00 1.73
2096 2662 8.250332 AGAAAACAAACAGCTTTCAACTCAATA 58.750 29.630 0.00 0.00 35.30 1.90
2097 2663 7.099120 AGAAAACAAACAGCTTTCAACTCAAT 58.901 30.769 0.00 0.00 35.30 2.57
2098 2664 6.454795 AGAAAACAAACAGCTTTCAACTCAA 58.545 32.000 0.00 0.00 35.30 3.02
2112 2712 8.883954 AGGTACTAACAGTAGAGAAAACAAAC 57.116 34.615 0.00 0.00 36.02 2.93
2128 2728 5.645067 GGGGAACATTGTACAAGGTACTAAC 59.355 44.000 24.66 13.59 38.49 2.34
2239 2839 7.622893 AGAGATGTTTCTTTTCTCATTAGCC 57.377 36.000 0.00 0.00 38.67 3.93
2379 2986 7.367285 GTCAGACTGATAGATAAGCTGGTAAG 58.633 42.308 8.73 0.00 0.00 2.34
2472 3079 7.379098 ACATGCATGCTATCTCAAATGATAG 57.621 36.000 26.53 7.05 45.17 2.08
2510 3117 8.259049 TGGTACAGCAATACAGTTACAAATAC 57.741 34.615 0.00 0.00 0.00 1.89
2547 3260 6.476706 GCTTGTAAATGATTTATGTTGGCCTC 59.523 38.462 3.32 0.00 0.00 4.70
2570 3283 5.395768 GGACAAGAGAGTACATATGTTGGCT 60.396 44.000 14.77 10.02 0.00 4.75
2574 3287 5.187772 TGCTGGACAAGAGAGTACATATGTT 59.812 40.000 14.77 0.00 30.54 2.71
2575 3288 4.711846 TGCTGGACAAGAGAGTACATATGT 59.288 41.667 13.93 13.93 30.54 2.29
2576 3289 5.268118 TGCTGGACAAGAGAGTACATATG 57.732 43.478 0.00 0.00 30.54 1.78
2581 3324 8.768955 CATATATTTTGCTGGACAAGAGAGTAC 58.231 37.037 0.00 0.00 40.06 2.73
2745 3490 8.937634 ACGTTAAAAATAGATTAGTGTCGGAT 57.062 30.769 0.00 0.00 0.00 4.18
2746 3491 8.246180 AGACGTTAAAAATAGATTAGTGTCGGA 58.754 33.333 0.00 0.00 0.00 4.55
2769 3514 6.652900 GGAATGATTCCCTGCTCTAATTAGAC 59.347 42.308 13.26 9.09 44.30 2.59
2810 3555 5.531634 TCTGGTGAAATAAAAAGCAGCAAG 58.468 37.500 0.00 0.00 38.88 4.01
2814 3559 7.153985 TCCAATTCTGGTGAAATAAAAAGCAG 58.846 34.615 0.00 0.00 43.97 4.24
2854 3599 6.021596 CACTCCGTTATTTATTGAAGTGCAC 58.978 40.000 9.40 9.40 0.00 4.57
2859 3604 8.504005 ACTTGTTCACTCCGTTATTTATTGAAG 58.496 33.333 0.00 0.00 0.00 3.02
2925 3672 5.853282 GCAATTGACAAGACAACTATGTGAC 59.147 40.000 10.34 0.00 40.74 3.67
2969 3716 7.147976 GTGCCTTTTTCTCAATTAGACAACAT 58.852 34.615 0.00 0.00 32.51 2.71
3008 3755 5.243060 GGTACTAAGGGAGTTGTTGCAAAAT 59.757 40.000 0.00 0.00 39.81 1.82
3022 3778 4.296056 AGACCCATGTAAGGTACTAAGGG 58.704 47.826 0.00 0.00 38.49 3.95
3071 3827 0.324943 TGGTCTGCCCAACTTAGAGC 59.675 55.000 0.00 0.00 41.50 4.09
3295 4143 9.875691 CTGGTAGCTGATACTATGCATTTTATA 57.124 33.333 3.54 0.00 34.56 0.98
3296 4144 8.378565 ACTGGTAGCTGATACTATGCATTTTAT 58.621 33.333 3.54 1.63 34.56 1.40
3469 4354 2.846532 CAGGTGGGCCTCTTGGTT 59.153 61.111 9.64 0.00 44.97 3.67
3556 4441 5.865085 TCAGTTACAACCTGCTTGTATTCT 58.135 37.500 0.00 0.00 43.51 2.40
3599 4484 7.712639 GCTATGGAAATGTTCTCAGAACATAGA 59.287 37.037 29.38 15.66 39.73 1.98
3602 4487 5.591877 GGCTATGGAAATGTTCTCAGAACAT 59.408 40.000 24.91 24.91 42.19 2.71
3629 4514 9.166234 GACAGAAAGATGTTCATGGTTCTCCAC 62.166 44.444 0.00 0.00 39.03 4.02
3630 4515 7.242800 GACAGAAAGATGTTCATGGTTCTCCA 61.243 42.308 0.00 0.00 39.91 3.86
3631 4516 5.006386 ACAGAAAGATGTTCATGGTTCTCC 58.994 41.667 0.00 0.00 0.00 3.71
3633 4518 5.874093 AGACAGAAAGATGTTCATGGTTCT 58.126 37.500 0.00 0.00 32.25 3.01
3712 4601 2.497675 ACTCGAGATGCTTAAAGCTCCA 59.502 45.455 21.68 0.00 42.97 3.86
3728 4617 1.674651 AGCGCAGTACCAGACTCGA 60.675 57.895 11.47 0.00 35.64 4.04
3747 4636 4.396790 TGTTTATCTAATGGCCAACCGAAC 59.603 41.667 10.96 9.41 39.70 3.95
3802 4691 7.919313 ATGCAACATCAACGATAATGATTTC 57.081 32.000 0.00 0.00 35.38 2.17
3845 4734 3.055819 ACATAAGTGAACATGGCTCGAGT 60.056 43.478 15.13 0.00 0.00 4.18
3864 4786 9.998106 ATATTTTTACGATTAGCTACTCCACAT 57.002 29.630 5.58 0.00 0.00 3.21
3905 4827 6.659242 GTCTGGATTTTGAAAGGACCAATAGA 59.341 38.462 0.00 0.00 0.00 1.98
3906 4828 6.660949 AGTCTGGATTTTGAAAGGACCAATAG 59.339 38.462 0.00 0.00 0.00 1.73
3917 4839 3.069443 GGCAACCAAGTCTGGATTTTGAA 59.931 43.478 0.00 0.00 46.92 2.69
3918 4840 2.627699 GGCAACCAAGTCTGGATTTTGA 59.372 45.455 0.00 0.00 46.92 2.69
3920 4842 2.629617 CAGGCAACCAAGTCTGGATTTT 59.370 45.455 0.00 0.00 46.92 1.82
3949 4906 3.256879 CCCTAAGATATTGCTCGCTCTCA 59.743 47.826 0.00 0.00 0.00 3.27
3984 4941 1.736696 GCACTGCATTTTCCCCATTCG 60.737 52.381 0.00 0.00 0.00 3.34
4031 4994 5.157781 GTGTTTGTACAAAAGCACAACTGA 58.842 37.500 25.60 1.69 35.69 3.41
4046 5009 7.920151 CAGTCATCCAAAATTTCTGTGTTTGTA 59.080 33.333 0.00 0.00 31.66 2.41
4064 5027 8.494433 ACTATATCTCTCCTCTATCAGTCATCC 58.506 40.741 0.00 0.00 0.00 3.51
4065 5028 9.330063 CACTATATCTCTCCTCTATCAGTCATC 57.670 40.741 0.00 0.00 0.00 2.92
4148 5111 3.525199 AGCTGAGGGTCCAACTATGAAAT 59.475 43.478 0.00 0.00 0.00 2.17
4181 5144 3.181484 ACCAAACGCTTCCTAAACAAACC 60.181 43.478 0.00 0.00 0.00 3.27
4209 5172 0.753111 GGCCTGTTCCAGCCTAATGG 60.753 60.000 0.00 0.00 42.11 3.16
4233 8010 3.067461 CCAAACATCACGTTTTCCTTCCA 59.933 43.478 0.00 0.00 45.79 3.53
4244 8021 0.039256 CCAGGCAACCAAACATCACG 60.039 55.000 0.00 0.00 37.17 4.35
4248 8025 0.114168 TAGGCCAGGCAACCAAACAT 59.886 50.000 15.19 0.00 37.17 2.71
4256 8033 0.991146 TTCTGATGTAGGCCAGGCAA 59.009 50.000 15.19 0.00 0.00 4.52
4257 8034 1.141657 GATTCTGATGTAGGCCAGGCA 59.858 52.381 15.19 0.00 0.00 4.75
4258 8035 1.419387 AGATTCTGATGTAGGCCAGGC 59.581 52.381 5.01 1.26 0.00 4.85
4259 8036 3.474600 CAAGATTCTGATGTAGGCCAGG 58.525 50.000 5.01 0.00 0.00 4.45
4260 8037 3.474600 CCAAGATTCTGATGTAGGCCAG 58.525 50.000 5.01 0.00 0.00 4.85
4261 8038 2.421952 GCCAAGATTCTGATGTAGGCCA 60.422 50.000 5.01 0.00 34.94 5.36
4262 8039 2.225467 GCCAAGATTCTGATGTAGGCC 58.775 52.381 0.00 0.00 34.94 5.19
4264 8041 2.808202 CGGGCCAAGATTCTGATGTAGG 60.808 54.545 4.39 0.00 0.00 3.18
4265 8042 2.487934 CGGGCCAAGATTCTGATGTAG 58.512 52.381 4.39 0.00 0.00 2.74
4266 8043 1.475034 GCGGGCCAAGATTCTGATGTA 60.475 52.381 4.39 0.00 0.00 2.29
4267 8044 0.749454 GCGGGCCAAGATTCTGATGT 60.749 55.000 4.39 0.00 0.00 3.06
4268 8045 0.749091 TGCGGGCCAAGATTCTGATG 60.749 55.000 4.39 0.00 0.00 3.07
4269 8046 0.749454 GTGCGGGCCAAGATTCTGAT 60.749 55.000 4.39 0.00 0.00 2.90
4270 8047 1.377202 GTGCGGGCCAAGATTCTGA 60.377 57.895 4.39 0.00 0.00 3.27
4285 8062 0.389166 CTGAGGAGTGAGGTTCGTGC 60.389 60.000 0.00 0.00 0.00 5.34
4288 8065 1.216710 GGCTGAGGAGTGAGGTTCG 59.783 63.158 0.00 0.00 0.00 3.95
4300 8077 1.015109 GTGAGTGATGCATGGCTGAG 58.985 55.000 2.46 0.00 0.00 3.35
4302 8079 0.393944 AGGTGAGTGATGCATGGCTG 60.394 55.000 2.46 0.00 0.00 4.85
4305 8082 0.545171 AGGAGGTGAGTGATGCATGG 59.455 55.000 2.46 0.00 0.00 3.66
4306 8083 1.664873 CAGGAGGTGAGTGATGCATG 58.335 55.000 2.46 0.00 0.00 4.06
4307 8084 0.107312 GCAGGAGGTGAGTGATGCAT 60.107 55.000 0.00 0.00 33.92 3.96
4309 8086 1.812922 CGCAGGAGGTGAGTGATGC 60.813 63.158 0.00 0.00 0.00 3.91
4310 8087 1.812922 GCGCAGGAGGTGAGTGATG 60.813 63.158 0.30 0.00 0.00 3.07
4311 8088 2.581354 GCGCAGGAGGTGAGTGAT 59.419 61.111 0.30 0.00 0.00 3.06
4312 8089 3.695606 GGCGCAGGAGGTGAGTGA 61.696 66.667 10.83 0.00 0.00 3.41
4313 8090 4.767255 GGGCGCAGGAGGTGAGTG 62.767 72.222 10.83 0.00 0.00 3.51
4333 8619 4.292178 CGAGCTCCCGGCATCTCC 62.292 72.222 8.47 0.00 44.79 3.71
4344 8630 4.838486 CCGGAGACACGCGAGCTC 62.838 72.222 15.93 15.67 0.00 4.09
4390 8680 4.508128 GGGCGACCGAATCAGCGA 62.508 66.667 0.00 0.00 43.64 4.93
4421 8711 2.948979 AGGAGTTTTGTCGTTGCAATGA 59.051 40.909 17.41 17.41 0.00 2.57
4422 8712 3.044986 CAGGAGTTTTGTCGTTGCAATG 58.955 45.455 12.66 12.66 0.00 2.82
4423 8713 2.687935 ACAGGAGTTTTGTCGTTGCAAT 59.312 40.909 0.59 0.00 0.00 3.56
4424 8714 2.088423 ACAGGAGTTTTGTCGTTGCAA 58.912 42.857 0.00 0.00 0.00 4.08
4425 8715 1.668751 GACAGGAGTTTTGTCGTTGCA 59.331 47.619 0.00 0.00 36.01 4.08
4426 8716 1.668751 TGACAGGAGTTTTGTCGTTGC 59.331 47.619 1.50 0.00 46.14 4.17
4427 8717 2.031683 GGTGACAGGAGTTTTGTCGTTG 59.968 50.000 1.50 0.00 46.14 4.10
4428 8718 2.285977 GGTGACAGGAGTTTTGTCGTT 58.714 47.619 1.50 0.00 46.14 3.85
4429 8719 1.208535 TGGTGACAGGAGTTTTGTCGT 59.791 47.619 1.50 0.00 46.14 4.34
4430 8720 1.948104 TGGTGACAGGAGTTTTGTCG 58.052 50.000 1.50 0.00 46.14 4.35
4443 8733 1.065126 CAAGAGAGGGGGAATGGTGAC 60.065 57.143 0.00 0.00 0.00 3.67
4444 8734 1.203428 TCAAGAGAGGGGGAATGGTGA 60.203 52.381 0.00 0.00 0.00 4.02
4445 8735 1.211457 CTCAAGAGAGGGGGAATGGTG 59.789 57.143 0.00 0.00 38.26 4.17
4446 8736 1.589414 CTCAAGAGAGGGGGAATGGT 58.411 55.000 0.00 0.00 38.26 3.55
4447 8737 0.182299 GCTCAAGAGAGGGGGAATGG 59.818 60.000 0.32 0.00 42.33 3.16
4448 8738 1.211456 AGCTCAAGAGAGGGGGAATG 58.789 55.000 0.32 0.00 42.33 2.67
4449 8739 1.978361 AAGCTCAAGAGAGGGGGAAT 58.022 50.000 0.32 0.00 42.33 3.01
4450 8740 1.630878 GAAAGCTCAAGAGAGGGGGAA 59.369 52.381 0.32 0.00 42.33 3.97
4451 8741 1.280457 GAAAGCTCAAGAGAGGGGGA 58.720 55.000 0.32 0.00 42.33 4.81
4452 8742 0.254462 GGAAAGCTCAAGAGAGGGGG 59.746 60.000 0.32 0.00 42.33 5.40
4453 8743 0.254462 GGGAAAGCTCAAGAGAGGGG 59.746 60.000 0.32 0.00 42.33 4.79
4454 8744 1.209261 GAGGGAAAGCTCAAGAGAGGG 59.791 57.143 0.32 0.00 42.33 4.30
4455 8745 1.209261 GGAGGGAAAGCTCAAGAGAGG 59.791 57.143 0.32 0.00 42.33 3.69
4456 8746 2.093553 CAGGAGGGAAAGCTCAAGAGAG 60.094 54.545 0.32 0.00 44.96 3.20
4457 8747 1.905215 CAGGAGGGAAAGCTCAAGAGA 59.095 52.381 0.32 0.00 0.00 3.10
4458 8748 1.678425 GCAGGAGGGAAAGCTCAAGAG 60.678 57.143 0.00 0.00 0.00 2.85
4459 8749 0.326264 GCAGGAGGGAAAGCTCAAGA 59.674 55.000 0.00 0.00 0.00 3.02
4460 8750 1.023513 CGCAGGAGGGAAAGCTCAAG 61.024 60.000 0.00 0.00 0.00 3.02
4461 8751 1.003355 CGCAGGAGGGAAAGCTCAA 60.003 57.895 0.00 0.00 0.00 3.02
4462 8752 2.665000 CGCAGGAGGGAAAGCTCA 59.335 61.111 0.00 0.00 0.00 4.26
4463 8753 2.821810 GCGCAGGAGGGAAAGCTC 60.822 66.667 0.30 0.00 0.00 4.09
4464 8754 3.618780 CTGCGCAGGAGGGAAAGCT 62.619 63.158 29.88 0.00 44.33 3.74
4465 8755 3.130160 CTGCGCAGGAGGGAAAGC 61.130 66.667 29.88 0.00 44.33 3.51
4473 8763 3.670637 GATGTGGCTCTGCGCAGGA 62.671 63.158 35.36 21.14 41.67 3.86
4474 8764 3.200593 GATGTGGCTCTGCGCAGG 61.201 66.667 35.36 25.98 41.67 4.85
4475 8765 3.561213 CGATGTGGCTCTGCGCAG 61.561 66.667 31.53 31.53 41.67 5.18
4485 8775 2.274232 TTACCTCGTCGCCGATGTGG 62.274 60.000 22.15 22.15 43.27 4.17
4486 8776 0.866061 CTTACCTCGTCGCCGATGTG 60.866 60.000 7.04 3.72 43.27 3.21
4487 8777 1.432251 CTTACCTCGTCGCCGATGT 59.568 57.895 6.17 1.89 43.27 3.06
4488 8778 1.944676 GCTTACCTCGTCGCCGATG 60.945 63.158 0.00 0.00 43.27 3.84
4489 8779 2.337749 CTGCTTACCTCGTCGCCGAT 62.338 60.000 0.00 0.00 43.27 4.18
4490 8780 3.047718 CTGCTTACCTCGTCGCCGA 62.048 63.158 0.00 0.00 41.73 5.54
4491 8781 2.579787 CTGCTTACCTCGTCGCCG 60.580 66.667 0.00 0.00 0.00 6.46
4492 8782 2.886124 GCTGCTTACCTCGTCGCC 60.886 66.667 0.00 0.00 0.00 5.54
4493 8783 3.248171 CGCTGCTTACCTCGTCGC 61.248 66.667 0.00 0.00 0.00 5.19
4494 8784 2.319011 TAGCGCTGCTTACCTCGTCG 62.319 60.000 22.90 0.00 40.44 5.12
4495 8785 0.592754 CTAGCGCTGCTTACCTCGTC 60.593 60.000 22.90 0.00 40.44 4.20
4496 8786 1.433879 CTAGCGCTGCTTACCTCGT 59.566 57.895 22.90 0.00 40.44 4.18
4497 8787 1.946650 GCTAGCGCTGCTTACCTCG 60.947 63.158 22.90 0.00 40.44 4.63
4498 8788 1.592939 GGCTAGCGCTGCTTACCTC 60.593 63.158 22.90 4.15 40.44 3.85
4499 8789 2.303549 CTGGCTAGCGCTGCTTACCT 62.304 60.000 22.90 0.00 40.44 3.08
4500 8790 1.884926 CTGGCTAGCGCTGCTTACC 60.885 63.158 22.90 14.16 40.44 2.85
4501 8791 2.529619 GCTGGCTAGCGCTGCTTAC 61.530 63.158 22.90 9.53 40.67 2.34
4502 8792 2.202932 GCTGGCTAGCGCTGCTTA 60.203 61.111 22.90 13.20 40.67 3.09
4511 8801 0.737219 GTTGCAATGAGGCTGGCTAG 59.263 55.000 0.59 0.00 34.04 3.42
4512 8802 1.026182 CGTTGCAATGAGGCTGGCTA 61.026 55.000 13.63 0.00 34.04 3.93
4513 8803 2.338015 CGTTGCAATGAGGCTGGCT 61.338 57.895 13.63 2.24 34.04 4.75
4514 8804 2.180017 CGTTGCAATGAGGCTGGC 59.820 61.111 13.63 0.00 34.04 4.85
4515 8805 1.236616 TGTCGTTGCAATGAGGCTGG 61.237 55.000 21.55 0.00 34.04 4.85
4516 8806 0.592637 TTGTCGTTGCAATGAGGCTG 59.407 50.000 21.55 0.00 34.04 4.85
4517 8807 1.317613 TTTGTCGTTGCAATGAGGCT 58.682 45.000 21.55 0.00 34.04 4.58
4518 8808 1.786579 GTTTTGTCGTTGCAATGAGGC 59.213 47.619 21.55 11.49 0.00 4.70
4519 8809 3.300009 GAGTTTTGTCGTTGCAATGAGG 58.700 45.455 21.55 2.65 0.00 3.86
4520 8810 3.300009 GGAGTTTTGTCGTTGCAATGAG 58.700 45.455 21.55 7.36 0.00 2.90
4521 8811 2.034053 GGGAGTTTTGTCGTTGCAATGA 59.966 45.455 17.41 17.41 0.00 2.57
4524 8814 0.378962 CGGGAGTTTTGTCGTTGCAA 59.621 50.000 0.00 0.00 0.00 4.08
4541 8831 1.972660 GAGAGGGGGAATGGTGACGG 61.973 65.000 0.00 0.00 0.00 4.79
4552 8842 0.254462 GGAAAGCTCAAGAGAGGGGG 59.746 60.000 0.32 0.00 42.33 5.40
4658 8950 3.000080 GCGCTGAACACGTCGAAGG 62.000 63.158 0.00 0.00 0.00 3.46
4742 9035 1.574702 GCCGGTTGGAAAACTCGAGG 61.575 60.000 18.41 0.00 37.49 4.63


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

AutoCloner maintained by Alex Coulton.