Multiple sequence alignment - TraesCS1D01G011900

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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 TraesCS1D01G011900 chr1D 100.000 2585 0 0 1 2585 6368391 6365807 0.000000e+00 4774.0
1 TraesCS1D01G011900 chr1D 86.449 428 42 8 1002 1424 6411346 6410930 3.030000e-124 455.0
2 TraesCS1D01G011900 chr1D 83.090 343 37 13 1096 1424 6399895 6399560 2.520000e-75 292.0
3 TraesCS1D01G011900 chr1D 81.201 383 30 21 1735 2085 6382836 6382464 1.180000e-68 270.0
4 TraesCS1D01G011900 chr1D 87.162 148 9 5 1422 1559 6399512 6399365 2.660000e-35 159.0
5 TraesCS1D01G011900 chr1B 88.029 1654 110 33 792 2409 8711162 8709561 0.000000e+00 1877.0
6 TraesCS1D01G011900 chr1B 88.323 471 49 4 223 687 8712158 8711688 6.250000e-156 560.0
7 TraesCS1D01G011900 chr1B 83.747 443 36 10 1002 1423 8715936 8715509 1.120000e-103 387.0
8 TraesCS1D01G011900 chr1B 82.812 192 15 11 1904 2078 8712567 8712377 3.440000e-34 156.0
9 TraesCS1D01G011900 chr1B 94.231 52 3 0 2534 2585 288367865 288367814 2.130000e-11 80.5
10 TraesCS1D01G011900 chr1A 87.027 1056 80 35 757 1786 7685940 7684916 0.000000e+00 1138.0
11 TraesCS1D01G011900 chr1A 84.900 702 62 14 100 775 7687896 7687213 0.000000e+00 669.0
12 TraesCS1D01G011900 chr1A 88.224 518 45 11 1002 1512 7697703 7697195 2.850000e-169 604.0
13 TraesCS1D01G011900 chr1A 82.734 139 23 1 2445 2583 75590496 75590359 3.490000e-24 122.0
14 TraesCS1D01G011900 chr1A 89.157 83 7 2 1932 2012 7688402 7688320 4.550000e-18 102.0
15 TraesCS1D01G011900 chr1A 80.198 101 12 4 1686 1786 508078185 508078277 4.620000e-08 69.4
16 TraesCS1D01G011900 chr7B 87.674 576 46 16 792 1366 452495647 452496198 0.000000e+00 647.0
17 TraesCS1D01G011900 chr7B 85.621 612 60 15 223 806 452494787 452495398 3.650000e-173 617.0
18 TraesCS1D01G011900 chr7B 86.882 526 41 10 1383 1883 452496569 452497091 4.830000e-157 564.0
19 TraesCS1D01G011900 chr7B 92.174 230 13 3 1199 1423 452468281 452468510 1.150000e-83 320.0
20 TraesCS1D01G011900 chr7B 80.420 143 22 4 2226 2364 222549873 222549733 1.270000e-18 104.0
21 TraesCS1D01G011900 chr4D 88.321 137 14 2 2437 2573 11082690 11082556 2.060000e-36 163.0
22 TraesCS1D01G011900 chr4D 87.500 144 14 3 2432 2573 163758252 163758393 2.060000e-36 163.0
23 TraesCS1D01G011900 chr4D 89.796 49 4 1 1707 1755 442404365 442404412 7.720000e-06 62.1
24 TraesCS1D01G011900 chr7D 89.683 126 13 0 98 223 65602122 65602247 7.400000e-36 161.0
25 TraesCS1D01G011900 chr7D 87.273 110 7 5 2220 2322 66409147 66409038 4.520000e-23 119.0
26 TraesCS1D01G011900 chr7D 79.739 153 27 4 2215 2364 575748755 575748604 9.780000e-20 108.0
27 TraesCS1D01G011900 chr2A 85.606 132 17 2 92 223 696238705 696238834 1.250000e-28 137.0
28 TraesCS1D01G011900 chr2A 81.410 156 22 5 2215 2364 86377829 86377675 1.260000e-23 121.0
29 TraesCS1D01G011900 chr2D 79.487 195 32 7 2215 2402 85919993 85919800 5.800000e-27 132.0
30 TraesCS1D01G011900 chr2B 82.000 150 19 6 2222 2364 177133608 177133460 1.260000e-23 121.0
31 TraesCS1D01G011900 chr6B 81.290 155 22 7 2215 2363 245893323 245893476 4.520000e-23 119.0
32 TraesCS1D01G011900 chr6B 80.142 141 21 5 2448 2585 45276812 45276676 5.890000e-17 99.0
33 TraesCS1D01G011900 chr3D 82.308 130 22 1 2442 2571 231988853 231988981 7.560000e-21 111.0
34 TraesCS1D01G011900 chr3D 82.243 107 16 3 2441 2546 419661462 419661566 3.540000e-14 89.8
35 TraesCS1D01G011900 chr3D 91.228 57 5 0 2441 2497 58191326 58191270 7.670000e-11 78.7
36 TraesCS1D01G011900 chr3A 86.667 90 9 3 2226 2313 336046959 336047047 2.120000e-16 97.1
37 TraesCS1D01G011900 chr7A 80.645 124 12 6 1664 1786 30088594 30088706 4.580000e-13 86.1
38 TraesCS1D01G011900 chr7A 91.304 46 4 0 2528 2573 451180936 451180981 2.150000e-06 63.9
39 TraesCS1D01G011900 chr6D 90.909 55 5 0 1706 1760 291218216 291218270 9.920000e-10 75.0
40 TraesCS1D01G011900 chr4B 91.304 46 4 0 2528 2573 399537660 399537705 2.150000e-06 63.9
41 TraesCS1D01G011900 chr5D 89.130 46 5 0 2528 2573 232237597 232237642 9.990000e-05 58.4


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 TraesCS1D01G011900 chr1D 6365807 6368391 2584 True 4774.000000 4774 100.000000 1 2585 1 chr1D.!!$R1 2584
1 TraesCS1D01G011900 chr1D 6399365 6399895 530 True 225.500000 292 85.126000 1096 1559 2 chr1D.!!$R4 463
2 TraesCS1D01G011900 chr1B 8709561 8715936 6375 True 745.000000 1877 85.727750 223 2409 4 chr1B.!!$R2 2186
3 TraesCS1D01G011900 chr1A 7684916 7688402 3486 True 636.333333 1138 87.028000 100 2012 3 chr1A.!!$R3 1912
4 TraesCS1D01G011900 chr1A 7697195 7697703 508 True 604.000000 604 88.224000 1002 1512 1 chr1A.!!$R1 510
5 TraesCS1D01G011900 chr7B 452494787 452497091 2304 False 609.333333 647 86.725667 223 1883 3 chr7B.!!$F2 1660

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
37 38 0.324738 CCAGTGTCAGGGGCTAGAGA 60.325 60.0 0.0 0.0 0.0 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1789 7555 0.172803 GGTTAGCGTCGGTGTCTCAT 59.827 55.0 7.3 0.0 0.0 2.9 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
22 23 5.382618 GATGTTTCTTGAGAAATGCCAGT 57.617 39.130 9.20 0.00 44.69 4.00
23 24 4.572985 TGTTTCTTGAGAAATGCCAGTG 57.427 40.909 9.20 0.00 44.69 3.66
25 26 4.036734 TGTTTCTTGAGAAATGCCAGTGTC 59.963 41.667 9.20 0.00 44.69 3.67
26 27 3.490439 TCTTGAGAAATGCCAGTGTCA 57.510 42.857 0.00 0.00 0.00 3.58
27 28 3.405831 TCTTGAGAAATGCCAGTGTCAG 58.594 45.455 0.00 0.00 0.00 3.51
28 29 2.189594 TGAGAAATGCCAGTGTCAGG 57.810 50.000 0.00 0.00 0.00 3.86
34 35 2.586792 GCCAGTGTCAGGGGCTAG 59.413 66.667 7.32 0.00 44.32 3.42
37 38 0.324738 CCAGTGTCAGGGGCTAGAGA 60.325 60.000 0.00 0.00 0.00 3.10
39 40 2.114616 CAGTGTCAGGGGCTAGAGAAT 58.885 52.381 0.00 0.00 0.00 2.40
40 41 2.114616 AGTGTCAGGGGCTAGAGAATG 58.885 52.381 0.00 0.00 0.00 2.67
41 42 0.833287 TGTCAGGGGCTAGAGAATGC 59.167 55.000 0.00 0.00 0.00 3.56
43 44 1.210478 GTCAGGGGCTAGAGAATGCAA 59.790 52.381 0.00 0.00 0.00 4.08
45 46 2.511218 TCAGGGGCTAGAGAATGCAATT 59.489 45.455 0.00 0.00 40.93 2.32
46 47 3.053395 TCAGGGGCTAGAGAATGCAATTT 60.053 43.478 0.00 0.00 36.07 1.82
47 48 4.165950 TCAGGGGCTAGAGAATGCAATTTA 59.834 41.667 0.00 0.00 36.07 1.40
48 49 5.075493 CAGGGGCTAGAGAATGCAATTTAT 58.925 41.667 0.00 0.00 36.07 1.40
50 51 5.772169 AGGGGCTAGAGAATGCAATTTATTC 59.228 40.000 0.00 4.68 36.07 1.75
51 52 5.536161 GGGGCTAGAGAATGCAATTTATTCA 59.464 40.000 12.36 0.00 36.07 2.57
52 53 6.294397 GGGGCTAGAGAATGCAATTTATTCAG 60.294 42.308 12.36 5.08 36.07 3.02
55 56 5.526506 AGAGAATGCAATTTATTCAGGCC 57.473 39.130 0.00 0.00 36.07 5.19
57 58 3.701040 AGAATGCAATTTATTCAGGCCGT 59.299 39.130 0.00 0.00 36.07 5.68
58 59 3.715628 ATGCAATTTATTCAGGCCGTC 57.284 42.857 0.00 0.00 0.00 4.79
62 63 4.887071 TGCAATTTATTCAGGCCGTCTATT 59.113 37.500 0.00 0.00 0.00 1.73
63 64 5.008613 TGCAATTTATTCAGGCCGTCTATTC 59.991 40.000 0.00 0.00 0.00 1.75
64 65 5.239525 GCAATTTATTCAGGCCGTCTATTCT 59.760 40.000 0.00 0.00 0.00 2.40
65 66 6.566753 GCAATTTATTCAGGCCGTCTATTCTC 60.567 42.308 0.00 0.00 0.00 2.87
66 67 4.602340 TTATTCAGGCCGTCTATTCTCC 57.398 45.455 0.00 0.00 0.00 3.71
68 69 2.160721 TCAGGCCGTCTATTCTCCTT 57.839 50.000 0.00 0.00 0.00 3.36
69 70 2.467880 TCAGGCCGTCTATTCTCCTTT 58.532 47.619 0.00 0.00 0.00 3.11
71 72 2.939103 CAGGCCGTCTATTCTCCTTTTG 59.061 50.000 0.00 0.00 0.00 2.44
72 73 2.572104 AGGCCGTCTATTCTCCTTTTGT 59.428 45.455 0.00 0.00 0.00 2.83
73 74 3.009143 AGGCCGTCTATTCTCCTTTTGTT 59.991 43.478 0.00 0.00 0.00 2.83
74 75 4.224370 AGGCCGTCTATTCTCCTTTTGTTA 59.776 41.667 0.00 0.00 0.00 2.41
76 77 5.589050 GGCCGTCTATTCTCCTTTTGTTATT 59.411 40.000 0.00 0.00 0.00 1.40
77 78 6.095021 GGCCGTCTATTCTCCTTTTGTTATTT 59.905 38.462 0.00 0.00 0.00 1.40
80 81 9.379791 CCGTCTATTCTCCTTTTGTTATTTACT 57.620 33.333 0.00 0.00 0.00 2.24
135 543 4.615513 AGTCTTATAGTCAAGAGGCCACT 58.384 43.478 5.01 0.00 35.25 4.00
139 547 7.345914 AGTCTTATAGTCAAGAGGCCACTAATT 59.654 37.037 5.01 0.00 35.25 1.40
142 550 4.479786 AGTCAAGAGGCCACTAATTCTC 57.520 45.455 5.01 0.00 0.00 2.87
150 558 6.352516 AGAGGCCACTAATTCTCAATACAAG 58.647 40.000 5.01 0.00 0.00 3.16
151 559 5.440610 AGGCCACTAATTCTCAATACAAGG 58.559 41.667 5.01 0.00 0.00 3.61
182 590 3.011119 GACCAACCACACAACAGTTGTA 58.989 45.455 18.74 0.00 43.23 2.41
187 595 3.793559 ACCACACAACAGTTGTACTCTC 58.206 45.455 18.74 0.00 43.23 3.20
189 597 2.794910 CACACAACAGTTGTACTCTCGG 59.205 50.000 18.74 7.31 43.23 4.63
191 599 3.633525 ACACAACAGTTGTACTCTCGGTA 59.366 43.478 18.74 0.00 43.23 4.02
209 617 3.858247 GGTACGGCTATAATTGGCTAGG 58.142 50.000 0.00 0.00 0.00 3.02
216 624 3.868077 GCTATAATTGGCTAGGCGATCTG 59.132 47.826 18.81 10.46 0.00 2.90
243 3747 8.386606 CAACTCGAAGAATTTTCTGAGGATAAG 58.613 37.037 10.61 0.18 37.65 1.73
271 3777 8.791327 TCTAATGCACATTAACTCTTTGATCA 57.209 30.769 4.74 0.00 33.34 2.92
285 3791 7.072030 ACTCTTTGATCAACGAAGAATTTTCG 58.928 34.615 14.77 16.15 45.14 3.46
299 3858 7.064728 CGAAGAATTTTCGGAGGATAAAACTCT 59.935 37.037 12.18 0.00 33.84 3.24
345 3904 1.680860 CCCGAACCAAAGGACCATACC 60.681 57.143 0.00 0.00 0.00 2.73
352 3911 2.041081 CCAAAGGACCATACCCAGAACA 59.959 50.000 0.00 0.00 0.00 3.18
374 3933 1.483004 TCCAGTCCACTGTTCGACAAA 59.517 47.619 5.99 0.00 42.27 2.83
378 3937 2.676342 AGTCCACTGTTCGACAAACAAC 59.324 45.455 7.35 0.00 46.95 3.32
390 3949 3.249799 CGACAAACAACATAGTGCTTCCA 59.750 43.478 0.00 0.00 0.00 3.53
393 3952 4.400884 ACAAACAACATAGTGCTTCCAACA 59.599 37.500 0.00 0.00 0.00 3.33
401 3960 1.072331 AGTGCTTCCAACAAGTCCGAT 59.928 47.619 0.00 0.00 0.00 4.18
522 4083 7.657352 TGTTTCCTTAGGGGGCTATTAATAT 57.343 36.000 0.00 0.00 35.33 1.28
749 4470 5.948742 AGGGGAAAAGTGAAACATGAAAA 57.051 34.783 0.00 0.00 41.43 2.29
876 6182 6.411376 AGATAGAGACTATGGACTATGGACG 58.589 44.000 0.00 0.00 0.00 4.79
897 6203 4.102054 ACGTTTTCCCTTCTAGTCAAGGAA 59.898 41.667 11.03 6.91 45.41 3.36
927 6233 2.162681 GCTTTCTTGCTAGGGCTTGAA 58.837 47.619 0.00 0.00 39.59 2.69
1000 6309 2.158035 AGATGGTAGCTCCCCTCATCAT 60.158 50.000 3.52 0.00 37.33 2.45
1051 6360 2.289694 GGGTGAAGCAAGAGAGCAAGTA 60.290 50.000 0.00 0.00 36.85 2.24
1067 6376 3.368843 GCAAGTACAGAAGAGAGATGGCA 60.369 47.826 0.00 0.00 0.00 4.92
1147 6461 3.524606 CCTCGTCGCCACGGGTAT 61.525 66.667 2.33 0.00 45.92 2.73
1184 6498 2.755876 TCCCAGCGATCGAGCAGT 60.756 61.111 21.57 0.00 40.15 4.40
1191 6505 2.604914 CAGCGATCGAGCAGTTGTAAAT 59.395 45.455 21.57 0.00 40.15 1.40
1308 6632 1.966762 CCACAATTTCAAGGGCGCT 59.033 52.632 7.64 0.00 0.00 5.92
1508 7251 6.392354 CATGCATGTTGTTTAGGTGAAGATT 58.608 36.000 18.91 0.00 0.00 2.40
1545 7288 3.234386 GTGTTTGCGGCTTCAATTAGTC 58.766 45.455 0.00 0.00 0.00 2.59
1613 7358 1.198637 GGCTTCTCTGTGTTGTGATGC 59.801 52.381 0.00 0.00 33.09 3.91
1633 7396 2.349817 GCGTTGTGTTGGATTCAGTCAG 60.350 50.000 0.00 0.00 0.00 3.51
1635 7398 3.312421 CGTTGTGTTGGATTCAGTCAGTT 59.688 43.478 0.00 0.00 0.00 3.16
1660 7424 4.740205 GCAGTTAGTTGGCTTGTCTTTTTC 59.260 41.667 0.00 0.00 0.00 2.29
1668 7432 6.934083 AGTTGGCTTGTCTTTTTCTTCAAAAA 59.066 30.769 0.00 0.00 38.84 1.94
1704 7468 7.698506 TTACGATATAGATTCACCGGATTCT 57.301 36.000 9.46 6.95 37.48 2.40
1768 7534 3.260475 TGGACCATCAAATCGAACGAT 57.740 42.857 3.80 3.80 36.23 3.73
1788 7554 1.063166 GTTGCTGCCGCTAGAATGC 59.937 57.895 0.70 0.00 36.97 3.56
1789 7555 1.377072 TTGCTGCCGCTAGAATGCA 60.377 52.632 0.70 0.00 36.97 3.96
1790 7556 0.749091 TTGCTGCCGCTAGAATGCAT 60.749 50.000 0.70 0.00 36.97 3.96
1791 7557 1.281960 GCTGCCGCTAGAATGCATG 59.718 57.895 0.00 0.00 33.97 4.06
1793 7559 0.866427 CTGCCGCTAGAATGCATGAG 59.134 55.000 0.00 0.00 33.97 2.90
1794 7560 0.465287 TGCCGCTAGAATGCATGAGA 59.535 50.000 0.00 0.00 0.00 3.27
1795 7561 0.864455 GCCGCTAGAATGCATGAGAC 59.136 55.000 0.00 0.00 0.00 3.36
1798 7564 1.863454 CGCTAGAATGCATGAGACACC 59.137 52.381 0.00 0.00 0.00 4.16
1799 7565 1.863454 GCTAGAATGCATGAGACACCG 59.137 52.381 0.00 0.00 0.00 4.94
1800 7566 2.481969 GCTAGAATGCATGAGACACCGA 60.482 50.000 0.00 0.00 0.00 4.69
1801 7567 2.015736 AGAATGCATGAGACACCGAC 57.984 50.000 0.00 0.00 0.00 4.79
1802 7568 0.647410 GAATGCATGAGACACCGACG 59.353 55.000 0.00 0.00 0.00 5.12
1803 7569 1.361668 AATGCATGAGACACCGACGC 61.362 55.000 0.00 0.00 0.00 5.19
1810 7582 1.915614 GAGACACCGACGCTAACCGA 61.916 60.000 0.00 0.00 41.02 4.69
1849 7621 6.931840 GGAAGTCTTCAGTGACAAATCTACTT 59.068 38.462 14.49 0.00 39.27 2.24
1850 7622 8.088981 GGAAGTCTTCAGTGACAAATCTACTTA 58.911 37.037 14.49 0.00 39.27 2.24
1993 7765 7.408132 TCATCTTCACGTTCTTAGTTTTGAG 57.592 36.000 0.00 0.00 0.00 3.02
2008 7780 8.491045 TTAGTTTTGAGAATGGAAAGGGAAAT 57.509 30.769 0.00 0.00 0.00 2.17
2020 7792 4.466015 GGAAAGGGAAATAAATGCTGGTGA 59.534 41.667 0.00 0.00 0.00 4.02
2022 7794 3.016736 AGGGAAATAAATGCTGGTGACG 58.983 45.455 0.00 0.00 0.00 4.35
2032 7804 2.363795 TGGTGACGGGGGCTAGAG 60.364 66.667 0.00 0.00 0.00 2.43
2036 7808 0.105039 GTGACGGGGGCTAGAGAATG 59.895 60.000 0.00 0.00 0.00 2.67
2050 7822 5.470098 GCTAGAGAATGCAATTTATTCGGGA 59.530 40.000 0.00 0.00 36.07 5.14
2054 7826 2.223711 AATGCAATTTATTCGGGACGGC 60.224 45.455 0.00 0.00 45.11 5.68
2072 7844 5.589050 GGACGGCTATTCTCCTTTTGTTATT 59.411 40.000 0.00 0.00 0.00 1.40
2093 7865 2.057137 ACTATTGCAATGCCCGTGAT 57.943 45.000 22.27 0.00 0.00 3.06
2222 7994 6.350445 CCTGCCCATATTAAGACAATTATGCC 60.350 42.308 0.00 0.00 0.00 4.40
2331 8103 6.184789 TCATATGGGAAGGTTAGACCAAAAC 58.815 40.000 2.13 0.00 41.95 2.43
2332 8104 3.955524 TGGGAAGGTTAGACCAAAACA 57.044 42.857 0.00 0.00 41.95 2.83
2333 8105 4.252570 TGGGAAGGTTAGACCAAAACAA 57.747 40.909 0.00 0.00 41.95 2.83
2361 8133 7.039714 AGGAAAAGATAAGTGAAACATGGAACC 60.040 37.037 0.00 0.00 41.43 3.62
2434 8206 9.073475 AGATAGATAGCACTAGTAGAAAACAGG 57.927 37.037 3.59 0.00 0.00 4.00
2435 8207 6.472686 AGATAGCACTAGTAGAAAACAGGG 57.527 41.667 3.59 0.00 0.00 4.45
2436 8208 5.958987 AGATAGCACTAGTAGAAAACAGGGT 59.041 40.000 3.59 0.00 0.00 4.34
2437 8209 7.124052 AGATAGCACTAGTAGAAAACAGGGTA 58.876 38.462 3.59 0.00 0.00 3.69
2438 8210 5.402997 AGCACTAGTAGAAAACAGGGTAC 57.597 43.478 3.59 0.00 0.00 3.34
2439 8211 5.085219 AGCACTAGTAGAAAACAGGGTACT 58.915 41.667 3.59 0.00 0.00 2.73
2440 8212 5.543020 AGCACTAGTAGAAAACAGGGTACTT 59.457 40.000 3.59 0.00 0.00 2.24
2441 8213 5.638234 GCACTAGTAGAAAACAGGGTACTTG 59.362 44.000 3.59 0.00 0.00 3.16
2442 8214 6.740681 GCACTAGTAGAAAACAGGGTACTTGT 60.741 42.308 3.59 0.00 33.55 3.16
2443 8215 6.867293 CACTAGTAGAAAACAGGGTACTTGTC 59.133 42.308 3.59 0.00 31.76 3.18
2444 8216 4.879598 AGTAGAAAACAGGGTACTTGTCG 58.120 43.478 4.44 0.00 0.00 4.35
2445 8217 3.121738 AGAAAACAGGGTACTTGTCGG 57.878 47.619 4.44 0.00 0.00 4.79
2446 8218 2.148768 GAAAACAGGGTACTTGTCGGG 58.851 52.381 4.44 0.00 0.00 5.14
2447 8219 0.399075 AAACAGGGTACTTGTCGGGG 59.601 55.000 4.44 0.00 0.00 5.73
2448 8220 1.486145 AACAGGGTACTTGTCGGGGG 61.486 60.000 4.44 0.00 0.00 5.40
2469 8241 4.791069 GGACCCCGGGTAGCCTCA 62.791 72.222 21.85 0.00 35.25 3.86
2470 8242 2.446036 GACCCCGGGTAGCCTCAT 60.446 66.667 21.85 0.00 35.25 2.90
2471 8243 2.446036 ACCCCGGGTAGCCTCATC 60.446 66.667 21.85 0.00 32.11 2.92
2472 8244 3.242291 CCCCGGGTAGCCTCATCC 61.242 72.222 21.85 0.00 0.00 3.51
2473 8245 3.616721 CCCGGGTAGCCTCATCCG 61.617 72.222 14.18 0.00 41.90 4.18
2474 8246 4.301027 CCGGGTAGCCTCATCCGC 62.301 72.222 9.73 0.00 41.02 5.54
2475 8247 3.536917 CGGGTAGCCTCATCCGCA 61.537 66.667 9.73 0.00 35.95 5.69
2476 8248 2.109181 GGGTAGCCTCATCCGCAC 59.891 66.667 2.95 0.00 0.00 5.34
2477 8249 2.109181 GGTAGCCTCATCCGCACC 59.891 66.667 0.00 0.00 0.00 5.01
2478 8250 2.109181 GTAGCCTCATCCGCACCC 59.891 66.667 0.00 0.00 0.00 4.61
2479 8251 2.041922 TAGCCTCATCCGCACCCT 60.042 61.111 0.00 0.00 0.00 4.34
2480 8252 1.113517 GTAGCCTCATCCGCACCCTA 61.114 60.000 0.00 0.00 0.00 3.53
2481 8253 0.178932 TAGCCTCATCCGCACCCTAT 60.179 55.000 0.00 0.00 0.00 2.57
2482 8254 0.178932 AGCCTCATCCGCACCCTATA 60.179 55.000 0.00 0.00 0.00 1.31
2483 8255 0.685097 GCCTCATCCGCACCCTATAA 59.315 55.000 0.00 0.00 0.00 0.98
2484 8256 1.608283 GCCTCATCCGCACCCTATAAC 60.608 57.143 0.00 0.00 0.00 1.89
2485 8257 1.691976 CCTCATCCGCACCCTATAACA 59.308 52.381 0.00 0.00 0.00 2.41
2486 8258 2.303022 CCTCATCCGCACCCTATAACAT 59.697 50.000 0.00 0.00 0.00 2.71
2487 8259 3.244561 CCTCATCCGCACCCTATAACATT 60.245 47.826 0.00 0.00 0.00 2.71
2488 8260 4.389374 CTCATCCGCACCCTATAACATTT 58.611 43.478 0.00 0.00 0.00 2.32
2489 8261 4.385825 TCATCCGCACCCTATAACATTTC 58.614 43.478 0.00 0.00 0.00 2.17
2490 8262 3.916359 TCCGCACCCTATAACATTTCA 57.084 42.857 0.00 0.00 0.00 2.69
2491 8263 4.223556 TCCGCACCCTATAACATTTCAA 57.776 40.909 0.00 0.00 0.00 2.69
2492 8264 4.196193 TCCGCACCCTATAACATTTCAAG 58.804 43.478 0.00 0.00 0.00 3.02
2493 8265 4.080807 TCCGCACCCTATAACATTTCAAGA 60.081 41.667 0.00 0.00 0.00 3.02
2494 8266 4.638421 CCGCACCCTATAACATTTCAAGAA 59.362 41.667 0.00 0.00 0.00 2.52
2495 8267 5.124776 CCGCACCCTATAACATTTCAAGAAA 59.875 40.000 0.00 0.00 34.46 2.52
2496 8268 6.183360 CCGCACCCTATAACATTTCAAGAAAT 60.183 38.462 2.31 2.31 41.33 2.17
2497 8269 7.257722 CGCACCCTATAACATTTCAAGAAATT 58.742 34.615 5.34 0.00 38.84 1.82
2498 8270 7.220683 CGCACCCTATAACATTTCAAGAAATTG 59.779 37.037 5.34 4.86 38.84 2.32
2499 8271 7.492344 GCACCCTATAACATTTCAAGAAATTGG 59.508 37.037 5.34 0.00 38.84 3.16
2500 8272 7.981225 CACCCTATAACATTTCAAGAAATTGGG 59.019 37.037 5.34 7.84 38.84 4.12
2501 8273 6.986231 CCCTATAACATTTCAAGAAATTGGGC 59.014 38.462 5.34 0.00 38.84 5.36
2502 8274 6.986231 CCTATAACATTTCAAGAAATTGGGCC 59.014 38.462 5.34 0.00 38.84 5.80
2503 8275 4.980339 AACATTTCAAGAAATTGGGCCT 57.020 36.364 4.53 0.00 38.84 5.19
2504 8276 7.732222 ATAACATTTCAAGAAATTGGGCCTA 57.268 32.000 4.53 0.00 38.84 3.93
2505 8277 5.665916 ACATTTCAAGAAATTGGGCCTAG 57.334 39.130 4.53 0.00 38.84 3.02
2506 8278 5.086621 ACATTTCAAGAAATTGGGCCTAGT 58.913 37.500 4.53 0.00 38.84 2.57
2507 8279 5.047092 ACATTTCAAGAAATTGGGCCTAGTG 60.047 40.000 4.53 0.00 38.84 2.74
2508 8280 2.446435 TCAAGAAATTGGGCCTAGTGC 58.554 47.619 4.53 0.00 40.16 4.40
2509 8281 2.170166 CAAGAAATTGGGCCTAGTGCA 58.830 47.619 4.53 0.00 43.89 4.57
2510 8282 2.134789 AGAAATTGGGCCTAGTGCAG 57.865 50.000 4.53 0.00 43.89 4.41
2511 8283 0.457443 GAAATTGGGCCTAGTGCAGC 59.543 55.000 4.53 0.00 43.89 5.25
2516 8288 4.182433 GGCCTAGTGCAGCCCCTC 62.182 72.222 3.32 0.00 43.76 4.30
2517 8289 3.402681 GCCTAGTGCAGCCCCTCA 61.403 66.667 0.00 0.00 40.77 3.86
2518 8290 2.971598 GCCTAGTGCAGCCCCTCAA 61.972 63.158 0.00 0.00 40.77 3.02
2519 8291 1.685224 CCTAGTGCAGCCCCTCAAA 59.315 57.895 0.00 0.00 0.00 2.69
2520 8292 0.393537 CCTAGTGCAGCCCCTCAAAG 60.394 60.000 0.00 0.00 0.00 2.77
2521 8293 1.002134 TAGTGCAGCCCCTCAAAGC 60.002 57.895 0.00 0.00 0.00 3.51
2522 8294 2.484287 TAGTGCAGCCCCTCAAAGCC 62.484 60.000 0.00 0.00 0.00 4.35
2523 8295 3.900862 TGCAGCCCCTCAAAGCCA 61.901 61.111 0.00 0.00 0.00 4.75
2524 8296 2.601367 GCAGCCCCTCAAAGCCAA 60.601 61.111 0.00 0.00 0.00 4.52
2525 8297 2.935740 GCAGCCCCTCAAAGCCAAC 61.936 63.158 0.00 0.00 0.00 3.77
2526 8298 1.531365 CAGCCCCTCAAAGCCAACA 60.531 57.895 0.00 0.00 0.00 3.33
2527 8299 1.228675 AGCCCCTCAAAGCCAACAG 60.229 57.895 0.00 0.00 0.00 3.16
2528 8300 1.228552 GCCCCTCAAAGCCAACAGA 60.229 57.895 0.00 0.00 0.00 3.41
2529 8301 1.527433 GCCCCTCAAAGCCAACAGAC 61.527 60.000 0.00 0.00 0.00 3.51
2530 8302 0.895559 CCCCTCAAAGCCAACAGACC 60.896 60.000 0.00 0.00 0.00 3.85
2531 8303 0.178992 CCCTCAAAGCCAACAGACCA 60.179 55.000 0.00 0.00 0.00 4.02
2532 8304 1.548582 CCCTCAAAGCCAACAGACCAT 60.549 52.381 0.00 0.00 0.00 3.55
2533 8305 1.542915 CCTCAAAGCCAACAGACCATG 59.457 52.381 0.00 0.00 0.00 3.66
2534 8306 0.961019 TCAAAGCCAACAGACCATGC 59.039 50.000 0.00 0.00 0.00 4.06
2535 8307 0.387622 CAAAGCCAACAGACCATGCG 60.388 55.000 0.00 0.00 0.00 4.73
2536 8308 1.526575 AAAGCCAACAGACCATGCGG 61.527 55.000 0.00 0.00 38.77 5.69
2537 8309 4.120331 GCCAACAGACCATGCGGC 62.120 66.667 0.00 0.00 41.93 6.53
2538 8310 3.443045 CCAACAGACCATGCGGCC 61.443 66.667 0.00 0.00 34.57 6.13
2539 8311 3.803082 CAACAGACCATGCGGCCG 61.803 66.667 24.05 24.05 34.57 6.13
2551 8323 4.082523 CGGCCGGCTTCCAGAAGA 62.083 66.667 28.56 0.00 40.79 2.87
2552 8324 2.436824 GGCCGGCTTCCAGAAGAC 60.437 66.667 28.56 7.41 42.98 3.01
2556 8328 2.815647 GGCTTCCAGAAGACGGCG 60.816 66.667 11.57 4.80 40.79 6.46
2557 8329 2.048127 GCTTCCAGAAGACGGCGT 60.048 61.111 14.65 14.65 40.79 5.68
2558 8330 2.383527 GCTTCCAGAAGACGGCGTG 61.384 63.158 21.19 1.39 40.79 5.34
2559 8331 2.357034 TTCCAGAAGACGGCGTGC 60.357 61.111 21.19 9.52 0.00 5.34
2560 8332 3.876589 TTCCAGAAGACGGCGTGCC 62.877 63.158 21.19 3.26 0.00 5.01
2562 8334 4.379243 CAGAAGACGGCGTGCCCT 62.379 66.667 21.19 5.36 0.00 5.19
2563 8335 3.626924 AGAAGACGGCGTGCCCTT 61.627 61.111 21.19 15.42 0.00 3.95
2564 8336 2.263540 GAAGACGGCGTGCCCTTA 59.736 61.111 21.19 0.00 0.00 2.69
2565 8337 1.375013 GAAGACGGCGTGCCCTTAA 60.375 57.895 21.19 0.00 0.00 1.85
2566 8338 0.952010 GAAGACGGCGTGCCCTTAAA 60.952 55.000 21.19 0.00 0.00 1.52
2567 8339 0.535553 AAGACGGCGTGCCCTTAAAA 60.536 50.000 21.19 0.00 0.00 1.52
2568 8340 0.953960 AGACGGCGTGCCCTTAAAAG 60.954 55.000 21.19 0.00 0.00 2.27
2569 8341 1.918868 GACGGCGTGCCCTTAAAAGG 61.919 60.000 21.19 1.47 46.06 3.11
2575 8347 3.599584 GCCCTTAAAAGGCGGACC 58.400 61.111 3.03 0.00 45.10 4.46
2576 8348 2.404186 GCCCTTAAAAGGCGGACCG 61.404 63.158 10.29 10.29 45.10 4.79
2577 8349 1.747745 CCCTTAAAAGGCGGACCGG 60.748 63.158 17.22 0.00 45.10 5.28
2578 8350 1.297364 CCTTAAAAGGCGGACCGGA 59.703 57.895 17.22 0.00 42.76 5.14
2579 8351 1.022982 CCTTAAAAGGCGGACCGGAC 61.023 60.000 17.22 0.00 42.76 4.79
2580 8352 1.003476 TTAAAAGGCGGACCGGACC 60.003 57.895 17.22 11.81 42.76 4.46
2581 8353 1.766625 TTAAAAGGCGGACCGGACCA 61.767 55.000 22.85 0.00 42.76 4.02
2582 8354 2.453379 TAAAAGGCGGACCGGACCAC 62.453 60.000 22.85 13.19 42.76 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.159209 CACTGGCATTTCTCAAGAAACATC 58.841 41.667 7.32 1.77 45.55 3.06
3 4 4.036734 TGACACTGGCATTTCTCAAGAAAC 59.963 41.667 7.32 0.00 45.55 2.78
5 6 3.817084 CTGACACTGGCATTTCTCAAGAA 59.183 43.478 0.00 0.00 0.00 2.52
6 7 3.405831 CTGACACTGGCATTTCTCAAGA 58.594 45.455 0.00 0.00 0.00 3.02
7 8 2.486982 CCTGACACTGGCATTTCTCAAG 59.513 50.000 0.00 0.00 0.00 3.02
8 9 2.507484 CCTGACACTGGCATTTCTCAA 58.493 47.619 0.00 0.00 0.00 3.02
9 10 1.271543 CCCTGACACTGGCATTTCTCA 60.272 52.381 0.00 0.00 0.00 3.27
14 15 2.036256 GCCCCTGACACTGGCATT 59.964 61.111 5.75 0.00 44.70 3.56
18 19 0.324738 TCTCTAGCCCCTGACACTGG 60.325 60.000 0.00 0.00 0.00 4.00
19 20 1.561643 TTCTCTAGCCCCTGACACTG 58.438 55.000 0.00 0.00 0.00 3.66
21 22 1.474143 GCATTCTCTAGCCCCTGACAC 60.474 57.143 0.00 0.00 0.00 3.67
22 23 0.833287 GCATTCTCTAGCCCCTGACA 59.167 55.000 0.00 0.00 0.00 3.58
23 24 0.833287 TGCATTCTCTAGCCCCTGAC 59.167 55.000 0.00 0.00 0.00 3.51
25 26 2.653234 ATTGCATTCTCTAGCCCCTG 57.347 50.000 0.00 0.00 0.00 4.45
26 27 3.677156 AAATTGCATTCTCTAGCCCCT 57.323 42.857 0.00 0.00 0.00 4.79
27 28 5.536161 TGAATAAATTGCATTCTCTAGCCCC 59.464 40.000 12.04 0.00 34.21 5.80
28 29 6.294397 CCTGAATAAATTGCATTCTCTAGCCC 60.294 42.308 12.04 0.00 34.21 5.19
31 32 6.567321 CGGCCTGAATAAATTGCATTCTCTAG 60.567 42.308 0.00 0.00 34.21 2.43
33 34 4.037208 CGGCCTGAATAAATTGCATTCTCT 59.963 41.667 0.00 0.00 34.21 3.10
34 35 4.202050 ACGGCCTGAATAAATTGCATTCTC 60.202 41.667 0.00 4.51 34.21 2.87
37 38 3.701040 AGACGGCCTGAATAAATTGCATT 59.299 39.130 0.00 0.00 0.00 3.56
39 40 2.722094 AGACGGCCTGAATAAATTGCA 58.278 42.857 0.00 0.00 0.00 4.08
40 41 5.239525 AGAATAGACGGCCTGAATAAATTGC 59.760 40.000 0.00 0.00 0.00 3.56
41 42 6.073003 GGAGAATAGACGGCCTGAATAAATTG 60.073 42.308 0.00 0.00 0.00 2.32
43 44 5.308237 AGGAGAATAGACGGCCTGAATAAAT 59.692 40.000 0.00 0.00 0.00 1.40
45 46 4.223953 AGGAGAATAGACGGCCTGAATAA 58.776 43.478 0.00 0.00 0.00 1.40
46 47 3.845860 AGGAGAATAGACGGCCTGAATA 58.154 45.455 0.00 0.00 0.00 1.75
47 48 2.683768 AGGAGAATAGACGGCCTGAAT 58.316 47.619 0.00 0.00 0.00 2.57
48 49 2.160721 AGGAGAATAGACGGCCTGAA 57.839 50.000 0.00 0.00 0.00 3.02
50 51 2.939103 CAAAAGGAGAATAGACGGCCTG 59.061 50.000 0.00 0.00 0.00 4.85
51 52 2.572104 ACAAAAGGAGAATAGACGGCCT 59.428 45.455 0.00 0.00 0.00 5.19
52 53 2.987232 ACAAAAGGAGAATAGACGGCC 58.013 47.619 0.00 0.00 0.00 6.13
116 524 7.731054 AGAATTAGTGGCCTCTTGACTATAAG 58.269 38.462 13.50 0.00 0.00 1.73
130 538 5.066505 CCACCTTGTATTGAGAATTAGTGGC 59.933 44.000 0.00 0.00 35.13 5.01
135 543 5.045213 TGGCTCCACCTTGTATTGAGAATTA 60.045 40.000 0.00 0.00 40.22 1.40
139 547 2.265367 TGGCTCCACCTTGTATTGAGA 58.735 47.619 0.00 0.00 40.22 3.27
142 550 2.749621 GTCTTGGCTCCACCTTGTATTG 59.250 50.000 0.00 0.00 40.22 1.90
150 558 1.603739 GGTTGGTCTTGGCTCCACC 60.604 63.158 0.00 0.00 39.84 4.61
151 559 1.150536 TGGTTGGTCTTGGCTCCAC 59.849 57.895 0.00 0.00 33.12 4.02
182 590 3.255149 CCAATTATAGCCGTACCGAGAGT 59.745 47.826 0.00 0.00 0.00 3.24
187 595 2.450609 AGCCAATTATAGCCGTACCG 57.549 50.000 0.00 0.00 0.00 4.02
189 597 3.259902 GCCTAGCCAATTATAGCCGTAC 58.740 50.000 0.00 0.00 0.00 3.67
191 599 1.337823 CGCCTAGCCAATTATAGCCGT 60.338 52.381 0.00 0.00 0.00 5.68
206 614 0.815095 TTCGAGTTGCAGATCGCCTA 59.185 50.000 15.51 3.73 41.33 3.93
209 617 1.350193 TTCTTCGAGTTGCAGATCGC 58.650 50.000 15.51 3.07 38.79 4.58
216 624 4.452455 TCCTCAGAAAATTCTTCGAGTTGC 59.548 41.667 8.73 0.00 34.74 4.17
243 3747 8.256611 TCAAAGAGTTAATGTGCATTAGAGTC 57.743 34.615 0.00 8.36 35.02 3.36
271 3777 7.174426 AGTTTTATCCTCCGAAAATTCTTCGTT 59.826 33.333 16.21 0.00 40.04 3.85
285 3791 6.349300 TGTGCATTAGAGAGTTTTATCCTCC 58.651 40.000 0.00 0.00 0.00 4.30
299 3858 9.102757 GAGATCAAAGAGTTAATGTGCATTAGA 57.897 33.333 0.00 0.00 35.02 2.10
345 3904 1.051812 AGTGGACTGGAGTGTTCTGG 58.948 55.000 0.00 0.00 0.00 3.86
374 3933 4.207165 ACTTGTTGGAAGCACTATGTTGT 58.793 39.130 0.00 0.00 0.00 3.32
378 3937 2.416547 CGGACTTGTTGGAAGCACTATG 59.583 50.000 0.00 0.00 0.00 2.23
390 3949 5.062558 CGGTTATCGTTTAATCGGACTTGTT 59.937 40.000 6.12 0.00 0.00 2.83
503 4062 9.408648 CACAATTATATTAATAGCCCCCTAAGG 57.591 37.037 1.02 0.00 0.00 2.69
688 4392 8.306761 CCCCTATGATAATCACTTTAATTTGCC 58.693 37.037 0.00 0.00 0.00 4.52
699 4404 7.387643 GTCTAACCTTCCCCTATGATAATCAC 58.612 42.308 0.00 0.00 0.00 3.06
711 4420 0.540454 CCCTTCGTCTAACCTTCCCC 59.460 60.000 0.00 0.00 0.00 4.81
876 6182 7.526142 AAATTCCTTGACTAGAAGGGAAAAC 57.474 36.000 14.44 0.00 42.63 2.43
927 6233 1.445582 CGCGTCCCTTCGTAGCTTT 60.446 57.895 0.00 0.00 0.00 3.51
935 6241 1.177256 TATAGCTCCCGCGTCCCTTC 61.177 60.000 4.92 0.00 42.32 3.46
972 6278 3.075582 AGGGGAGCTACCATCTCGTTATA 59.924 47.826 19.26 0.00 41.20 0.98
973 6279 2.158295 AGGGGAGCTACCATCTCGTTAT 60.158 50.000 19.26 0.00 41.20 1.89
974 6280 1.217183 AGGGGAGCTACCATCTCGTTA 59.783 52.381 19.26 0.00 41.20 3.18
975 6281 0.032017 AGGGGAGCTACCATCTCGTT 60.032 55.000 19.26 0.00 41.20 3.85
1024 6333 0.390472 CTCTTGCTTCACCCGAGTCC 60.390 60.000 0.00 0.00 0.00 3.85
1025 6334 0.603569 TCTCTTGCTTCACCCGAGTC 59.396 55.000 0.00 0.00 0.00 3.36
1051 6360 1.767681 GGGATGCCATCTCTCTTCTGT 59.232 52.381 4.41 0.00 0.00 3.41
1110 6419 1.383803 GGAGCAGGATGAGGAGGGT 60.384 63.158 0.00 0.00 39.69 4.34
1147 6461 3.760035 GAGGAAGCTCGCCGGACA 61.760 66.667 5.05 0.00 0.00 4.02
1184 6498 6.967767 CGCCGGTGATTAATTACAATTTACAA 59.032 34.615 10.20 0.00 0.00 2.41
1191 6505 2.634600 AGCGCCGGTGATTAATTACAA 58.365 42.857 21.76 0.00 0.00 2.41
1308 6632 0.463654 AGTTGGTGTCGCTGAAGCAA 60.464 50.000 2.79 0.00 42.21 3.91
1613 7358 2.872245 ACTGACTGAATCCAACACAACG 59.128 45.455 0.00 0.00 0.00 4.10
1633 7396 3.066760 AGACAAGCCAACTAACTGCAAAC 59.933 43.478 0.00 0.00 0.00 2.93
1635 7398 2.930950 AGACAAGCCAACTAACTGCAA 58.069 42.857 0.00 0.00 0.00 4.08
1675 7439 8.797350 TCCGGTGAATCTATATCGTAATAGAA 57.203 34.615 0.00 0.00 40.82 2.10
1733 7499 4.649267 TGGTCCATGGACTTTGATGTAA 57.351 40.909 37.26 13.95 44.04 2.41
1788 7554 1.269166 GTTAGCGTCGGTGTCTCATG 58.731 55.000 7.30 0.00 0.00 3.07
1789 7555 0.172803 GGTTAGCGTCGGTGTCTCAT 59.827 55.000 7.30 0.00 0.00 2.90
1790 7556 1.582968 GGTTAGCGTCGGTGTCTCA 59.417 57.895 7.30 0.00 0.00 3.27
1791 7557 1.513586 CGGTTAGCGTCGGTGTCTC 60.514 63.158 7.30 0.00 0.00 3.36
1793 7559 1.799121 GTCGGTTAGCGTCGGTGTC 60.799 63.158 7.30 0.00 0.00 3.67
1794 7560 2.256461 GTCGGTTAGCGTCGGTGT 59.744 61.111 7.30 0.00 0.00 4.16
1795 7561 2.505557 GGTCGGTTAGCGTCGGTG 60.506 66.667 7.30 0.00 0.00 4.94
1798 7564 1.513586 GTCAGGTCGGTTAGCGTCG 60.514 63.158 3.21 0.00 0.00 5.12
1799 7565 1.153881 GGTCAGGTCGGTTAGCGTC 60.154 63.158 3.21 0.00 0.00 5.19
1800 7566 1.183676 AAGGTCAGGTCGGTTAGCGT 61.184 55.000 3.21 0.00 0.00 5.07
1801 7567 0.736325 CAAGGTCAGGTCGGTTAGCG 60.736 60.000 0.00 0.00 0.00 4.26
1802 7568 0.320697 ACAAGGTCAGGTCGGTTAGC 59.679 55.000 0.00 0.00 0.00 3.09
1803 7569 2.365408 GACAAGGTCAGGTCGGTTAG 57.635 55.000 0.00 0.00 32.09 2.34
1810 7582 0.763223 ACTTCCCGACAAGGTCAGGT 60.763 55.000 0.00 0.00 38.74 4.00
1849 7621 3.383505 TGCTCCGCTTAATAGACAAGCTA 59.616 43.478 5.62 0.00 45.00 3.32
1850 7622 2.168521 TGCTCCGCTTAATAGACAAGCT 59.831 45.455 5.62 0.00 45.00 3.74
1978 7750 7.078228 CCTTTCCATTCTCAAAACTAAGAACG 58.922 38.462 0.00 0.00 34.52 3.95
1993 7765 6.051074 CCAGCATTTATTTCCCTTTCCATTC 58.949 40.000 0.00 0.00 0.00 2.67
2008 7780 1.301623 CCCCCGTCACCAGCATTTA 59.698 57.895 0.00 0.00 0.00 1.40
2020 7792 1.271840 TTGCATTCTCTAGCCCCCGT 61.272 55.000 0.00 0.00 0.00 5.28
2022 7794 2.371658 AATTGCATTCTCTAGCCCCC 57.628 50.000 0.00 0.00 0.00 5.40
2032 7804 3.628017 CCGTCCCGAATAAATTGCATTC 58.372 45.455 0.00 3.87 0.00 2.67
2036 7808 1.021968 AGCCGTCCCGAATAAATTGC 58.978 50.000 0.00 0.00 0.00 3.56
2050 7822 7.827729 AGTAAATAACAAAAGGAGAATAGCCGT 59.172 33.333 0.00 0.00 0.00 5.68
2072 7844 2.992593 TCACGGGCATTGCAATAGTAA 58.007 42.857 12.53 0.00 0.00 2.24
2312 8084 3.955524 TGTTTTGGTCTAACCTTCCCA 57.044 42.857 0.00 0.00 39.58 4.37
2318 8090 6.320418 TCTTTTCCTCTTGTTTTGGTCTAACC 59.680 38.462 0.00 0.00 39.22 2.85
2325 8097 7.940850 TCACTTATCTTTTCCTCTTGTTTTGG 58.059 34.615 0.00 0.00 0.00 3.28
2326 8098 9.801873 TTTCACTTATCTTTTCCTCTTGTTTTG 57.198 29.630 0.00 0.00 0.00 2.44
2331 8103 8.025445 CCATGTTTCACTTATCTTTTCCTCTTG 58.975 37.037 0.00 0.00 0.00 3.02
2332 8104 7.944554 TCCATGTTTCACTTATCTTTTCCTCTT 59.055 33.333 0.00 0.00 0.00 2.85
2333 8105 7.461749 TCCATGTTTCACTTATCTTTTCCTCT 58.538 34.615 0.00 0.00 0.00 3.69
2408 8180 9.073475 CCTGTTTTCTACTAGTGCTATCTATCT 57.927 37.037 5.39 0.00 0.00 1.98
2409 8181 8.301002 CCCTGTTTTCTACTAGTGCTATCTATC 58.699 40.741 5.39 0.00 0.00 2.08
2410 8182 7.785506 ACCCTGTTTTCTACTAGTGCTATCTAT 59.214 37.037 5.39 0.00 0.00 1.98
2411 8183 7.124052 ACCCTGTTTTCTACTAGTGCTATCTA 58.876 38.462 5.39 0.00 0.00 1.98
2412 8184 5.958987 ACCCTGTTTTCTACTAGTGCTATCT 59.041 40.000 5.39 0.00 0.00 1.98
2413 8185 6.223351 ACCCTGTTTTCTACTAGTGCTATC 57.777 41.667 5.39 0.00 0.00 2.08
2414 8186 6.896307 AGTACCCTGTTTTCTACTAGTGCTAT 59.104 38.462 5.39 0.00 0.00 2.97
2415 8187 6.251471 AGTACCCTGTTTTCTACTAGTGCTA 58.749 40.000 5.39 0.00 0.00 3.49
2416 8188 5.085219 AGTACCCTGTTTTCTACTAGTGCT 58.915 41.667 5.39 0.00 0.00 4.40
2417 8189 5.402997 AGTACCCTGTTTTCTACTAGTGC 57.597 43.478 5.39 0.00 0.00 4.40
2418 8190 6.756221 ACAAGTACCCTGTTTTCTACTAGTG 58.244 40.000 5.39 0.00 0.00 2.74
2419 8191 6.294397 CGACAAGTACCCTGTTTTCTACTAGT 60.294 42.308 0.00 0.00 0.00 2.57
2420 8192 6.091437 CGACAAGTACCCTGTTTTCTACTAG 58.909 44.000 0.11 0.00 0.00 2.57
2421 8193 5.047802 CCGACAAGTACCCTGTTTTCTACTA 60.048 44.000 0.11 0.00 0.00 1.82
2422 8194 4.262335 CCGACAAGTACCCTGTTTTCTACT 60.262 45.833 0.11 0.00 0.00 2.57
2423 8195 3.992427 CCGACAAGTACCCTGTTTTCTAC 59.008 47.826 0.11 0.00 0.00 2.59
2424 8196 3.007182 CCCGACAAGTACCCTGTTTTCTA 59.993 47.826 0.11 0.00 0.00 2.10
2425 8197 2.224450 CCCGACAAGTACCCTGTTTTCT 60.224 50.000 0.11 0.00 0.00 2.52
2426 8198 2.148768 CCCGACAAGTACCCTGTTTTC 58.851 52.381 0.11 0.00 0.00 2.29
2427 8199 1.202842 CCCCGACAAGTACCCTGTTTT 60.203 52.381 0.11 0.00 0.00 2.43
2428 8200 0.399075 CCCCGACAAGTACCCTGTTT 59.601 55.000 0.11 0.00 0.00 2.83
2429 8201 1.486145 CCCCCGACAAGTACCCTGTT 61.486 60.000 0.11 0.00 0.00 3.16
2430 8202 1.916777 CCCCCGACAAGTACCCTGT 60.917 63.158 0.00 0.00 0.00 4.00
2431 8203 2.987125 CCCCCGACAAGTACCCTG 59.013 66.667 0.00 0.00 0.00 4.45
2452 8224 4.791069 TGAGGCTACCCGGGGTCC 62.791 72.222 27.92 19.05 37.09 4.46
2453 8225 2.446036 ATGAGGCTACCCGGGGTC 60.446 66.667 27.92 9.79 37.09 4.46
2454 8226 2.446036 GATGAGGCTACCCGGGGT 60.446 66.667 27.92 24.58 40.16 4.95
2455 8227 3.242291 GGATGAGGCTACCCGGGG 61.242 72.222 27.92 12.73 35.76 5.73
2456 8228 3.616721 CGGATGAGGCTACCCGGG 61.617 72.222 22.25 22.25 38.42 5.73
2457 8229 4.301027 GCGGATGAGGCTACCCGG 62.301 72.222 18.90 0.00 42.02 5.73
2458 8230 3.536917 TGCGGATGAGGCTACCCG 61.537 66.667 14.82 14.82 44.34 5.28
2459 8231 2.109181 GTGCGGATGAGGCTACCC 59.891 66.667 0.00 0.00 0.00 3.69
2460 8232 2.109181 GGTGCGGATGAGGCTACC 59.891 66.667 0.00 0.00 0.00 3.18
2461 8233 1.113517 TAGGGTGCGGATGAGGCTAC 61.114 60.000 0.00 0.00 0.00 3.58
2462 8234 0.178932 ATAGGGTGCGGATGAGGCTA 60.179 55.000 0.00 0.00 0.00 3.93
2463 8235 0.178932 TATAGGGTGCGGATGAGGCT 60.179 55.000 0.00 0.00 0.00 4.58
2464 8236 0.685097 TTATAGGGTGCGGATGAGGC 59.315 55.000 0.00 0.00 0.00 4.70
2465 8237 1.691976 TGTTATAGGGTGCGGATGAGG 59.308 52.381 0.00 0.00 0.00 3.86
2466 8238 3.685139 ATGTTATAGGGTGCGGATGAG 57.315 47.619 0.00 0.00 0.00 2.90
2467 8239 4.141597 TGAAATGTTATAGGGTGCGGATGA 60.142 41.667 0.00 0.00 0.00 2.92
2468 8240 4.133820 TGAAATGTTATAGGGTGCGGATG 58.866 43.478 0.00 0.00 0.00 3.51
2469 8241 4.431416 TGAAATGTTATAGGGTGCGGAT 57.569 40.909 0.00 0.00 0.00 4.18
2470 8242 3.916359 TGAAATGTTATAGGGTGCGGA 57.084 42.857 0.00 0.00 0.00 5.54
2471 8243 4.196193 TCTTGAAATGTTATAGGGTGCGG 58.804 43.478 0.00 0.00 0.00 5.69
2472 8244 5.811399 TTCTTGAAATGTTATAGGGTGCG 57.189 39.130 0.00 0.00 0.00 5.34
2473 8245 7.492344 CCAATTTCTTGAAATGTTATAGGGTGC 59.508 37.037 9.06 0.00 34.04 5.01
2474 8246 7.981225 CCCAATTTCTTGAAATGTTATAGGGTG 59.019 37.037 9.06 1.84 34.04 4.61
2475 8247 7.364673 GCCCAATTTCTTGAAATGTTATAGGGT 60.365 37.037 9.06 0.00 34.04 4.34
2476 8248 6.986231 GCCCAATTTCTTGAAATGTTATAGGG 59.014 38.462 9.06 12.79 34.04 3.53
2477 8249 6.986231 GGCCCAATTTCTTGAAATGTTATAGG 59.014 38.462 9.06 5.93 34.04 2.57
2478 8250 7.785033 AGGCCCAATTTCTTGAAATGTTATAG 58.215 34.615 0.00 0.00 34.04 1.31
2479 8251 7.732222 AGGCCCAATTTCTTGAAATGTTATA 57.268 32.000 0.00 0.00 34.04 0.98
2480 8252 6.625532 AGGCCCAATTTCTTGAAATGTTAT 57.374 33.333 0.00 0.00 34.04 1.89
2481 8253 6.723977 ACTAGGCCCAATTTCTTGAAATGTTA 59.276 34.615 0.00 0.00 34.04 2.41
2482 8254 4.980339 AGGCCCAATTTCTTGAAATGTT 57.020 36.364 0.00 0.00 34.04 2.71
2483 8255 5.047092 CACTAGGCCCAATTTCTTGAAATGT 60.047 40.000 0.00 0.00 34.04 2.71
2484 8256 5.413499 CACTAGGCCCAATTTCTTGAAATG 58.587 41.667 0.00 4.62 34.04 2.32
2485 8257 4.081476 GCACTAGGCCCAATTTCTTGAAAT 60.081 41.667 0.00 3.04 33.25 2.17
2486 8258 3.258123 GCACTAGGCCCAATTTCTTGAAA 59.742 43.478 0.00 0.00 33.25 2.69
2487 8259 2.825532 GCACTAGGCCCAATTTCTTGAA 59.174 45.455 0.00 0.00 33.25 2.69
2488 8260 2.224992 TGCACTAGGCCCAATTTCTTGA 60.225 45.455 0.00 0.00 43.89 3.02
2489 8261 2.165030 CTGCACTAGGCCCAATTTCTTG 59.835 50.000 0.00 0.00 43.89 3.02
2490 8262 2.450476 CTGCACTAGGCCCAATTTCTT 58.550 47.619 0.00 0.00 43.89 2.52
2491 8263 1.957113 GCTGCACTAGGCCCAATTTCT 60.957 52.381 0.00 0.00 43.89 2.52
2492 8264 0.457443 GCTGCACTAGGCCCAATTTC 59.543 55.000 0.00 0.00 43.89 2.17
2493 8265 0.972471 GGCTGCACTAGGCCCAATTT 60.972 55.000 0.00 0.00 45.75 1.82
2494 8266 1.380380 GGCTGCACTAGGCCCAATT 60.380 57.895 0.00 0.00 45.75 2.32
2495 8267 2.276740 GGCTGCACTAGGCCCAAT 59.723 61.111 0.00 0.00 45.75 3.16
2501 8273 0.393537 CTTTGAGGGGCTGCACTAGG 60.394 60.000 0.21 0.00 0.00 3.02
2502 8274 1.028868 GCTTTGAGGGGCTGCACTAG 61.029 60.000 0.21 0.00 0.00 2.57
2503 8275 1.002134 GCTTTGAGGGGCTGCACTA 60.002 57.895 0.21 0.00 0.00 2.74
2504 8276 2.282745 GCTTTGAGGGGCTGCACT 60.283 61.111 0.21 0.00 0.00 4.40
2505 8277 3.376918 GGCTTTGAGGGGCTGCAC 61.377 66.667 0.50 0.00 0.00 4.57
2506 8278 3.449494 TTGGCTTTGAGGGGCTGCA 62.449 57.895 0.50 0.00 0.00 4.41
2507 8279 2.601367 TTGGCTTTGAGGGGCTGC 60.601 61.111 0.00 0.00 0.00 5.25
2508 8280 1.530013 CTGTTGGCTTTGAGGGGCTG 61.530 60.000 0.00 0.00 0.00 4.85
2509 8281 1.228675 CTGTTGGCTTTGAGGGGCT 60.229 57.895 0.00 0.00 0.00 5.19
2510 8282 1.228552 TCTGTTGGCTTTGAGGGGC 60.229 57.895 0.00 0.00 0.00 5.80
2511 8283 0.895559 GGTCTGTTGGCTTTGAGGGG 60.896 60.000 0.00 0.00 0.00 4.79
2512 8284 0.178992 TGGTCTGTTGGCTTTGAGGG 60.179 55.000 0.00 0.00 0.00 4.30
2513 8285 1.542915 CATGGTCTGTTGGCTTTGAGG 59.457 52.381 0.00 0.00 0.00 3.86
2514 8286 1.068055 GCATGGTCTGTTGGCTTTGAG 60.068 52.381 0.00 0.00 0.00 3.02
2515 8287 0.961019 GCATGGTCTGTTGGCTTTGA 59.039 50.000 0.00 0.00 0.00 2.69
2516 8288 0.387622 CGCATGGTCTGTTGGCTTTG 60.388 55.000 0.00 0.00 0.00 2.77
2517 8289 1.526575 CCGCATGGTCTGTTGGCTTT 61.527 55.000 0.00 0.00 0.00 3.51
2518 8290 1.973281 CCGCATGGTCTGTTGGCTT 60.973 57.895 0.00 0.00 0.00 4.35
2519 8291 2.360350 CCGCATGGTCTGTTGGCT 60.360 61.111 0.00 0.00 0.00 4.75
2520 8292 4.120331 GCCGCATGGTCTGTTGGC 62.120 66.667 0.00 0.00 39.98 4.52
2521 8293 3.443045 GGCCGCATGGTCTGTTGG 61.443 66.667 0.00 0.00 36.72 3.77
2522 8294 3.803082 CGGCCGCATGGTCTGTTG 61.803 66.667 14.67 0.00 37.90 3.33
2534 8306 4.082523 TCTTCTGGAAGCCGGCCG 62.083 66.667 26.15 21.04 38.28 6.13
2535 8307 2.436824 GTCTTCTGGAAGCCGGCC 60.437 66.667 26.15 8.83 38.28 6.13
2536 8308 2.815647 CGTCTTCTGGAAGCCGGC 60.816 66.667 21.89 21.89 36.31 6.13
2538 8310 2.815647 GCCGTCTTCTGGAAGCCG 60.816 66.667 6.78 6.78 39.23 5.52
2539 8311 2.815647 CGCCGTCTTCTGGAAGCC 60.816 66.667 5.55 0.00 38.28 4.35
2540 8312 2.048127 ACGCCGTCTTCTGGAAGC 60.048 61.111 5.55 1.29 38.28 3.86
2541 8313 2.383527 GCACGCCGTCTTCTGGAAG 61.384 63.158 4.13 4.13 39.71 3.46
2542 8314 2.357034 GCACGCCGTCTTCTGGAA 60.357 61.111 0.00 0.00 0.00 3.53
2543 8315 4.373116 GGCACGCCGTCTTCTGGA 62.373 66.667 0.00 0.00 0.00 3.86
2545 8317 2.501223 TAAGGGCACGCCGTCTTCTG 62.501 60.000 3.35 0.00 36.85 3.02
2546 8318 1.823169 TTAAGGGCACGCCGTCTTCT 61.823 55.000 3.35 0.00 36.85 2.85
2547 8319 0.952010 TTTAAGGGCACGCCGTCTTC 60.952 55.000 3.35 0.00 36.85 2.87
2548 8320 0.535553 TTTTAAGGGCACGCCGTCTT 60.536 50.000 3.35 4.40 36.85 3.01
2549 8321 0.953960 CTTTTAAGGGCACGCCGTCT 60.954 55.000 3.35 0.00 36.85 4.18
2550 8322 1.500396 CTTTTAAGGGCACGCCGTC 59.500 57.895 3.35 0.00 36.85 4.79
2551 8323 1.969589 CCTTTTAAGGGCACGCCGT 60.970 57.895 1.14 0.00 42.66 5.68
2552 8324 2.874751 CCTTTTAAGGGCACGCCG 59.125 61.111 1.14 0.00 42.66 6.46
2558 8330 2.404186 CGGTCCGCCTTTTAAGGGC 61.404 63.158 8.12 8.12 46.56 5.19
2559 8331 1.747745 CCGGTCCGCCTTTTAAGGG 60.748 63.158 5.50 0.00 46.56 3.95
2561 8333 1.022982 GGTCCGGTCCGCCTTTTAAG 61.023 60.000 5.50 0.00 0.00 1.85
2562 8334 1.003476 GGTCCGGTCCGCCTTTTAA 60.003 57.895 5.50 0.00 0.00 1.52
2563 8335 2.215625 TGGTCCGGTCCGCCTTTTA 61.216 57.895 13.27 0.00 0.00 1.52
2564 8336 3.562232 TGGTCCGGTCCGCCTTTT 61.562 61.111 13.27 0.00 0.00 2.27
2565 8337 4.324991 GTGGTCCGGTCCGCCTTT 62.325 66.667 19.22 0.00 32.43 3.11


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

AutoCloner maintained by Alex Coulton.