Multiple sequence alignment - TraesCS5D01G197000

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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 TraesCS5D01G197000 chr5D 100.000 4522 0 0 1 4522 300142003 300146524 0.000000e+00 8351
1 TraesCS5D01G197000 chr5D 89.323 1049 82 14 3503 4522 300957530 300956483 0.000000e+00 1290
2 TraesCS5D01G197000 chr5D 88.443 1047 80 16 2886 3912 300313843 300314868 0.000000e+00 1225
3 TraesCS5D01G197000 chr5D 83.346 1279 168 34 2087 3343 307089311 307090566 0.000000e+00 1140
4 TraesCS5D01G197000 chr5D 92.403 724 30 7 3821 4522 299390409 299389689 0.000000e+00 1009
5 TraesCS5D01G197000 chr5D 92.652 626 31 4 2886 3510 300958241 300957630 0.000000e+00 887
6 TraesCS5D01G197000 chr5D 89.316 702 43 17 3845 4522 300321719 300322412 0.000000e+00 852
7 TraesCS5D01G197000 chr5D 83.708 178 26 2 992 1169 307086216 307086390 1.010000e-36 165
8 TraesCS5D01G197000 chr5A 91.178 4364 187 89 236 4522 397781856 397786098 0.000000e+00 5744
9 TraesCS5D01G197000 chr5A 83.304 1719 208 44 1982 3650 415629130 415627441 0.000000e+00 1511
10 TraesCS5D01G197000 chr5A 92.025 815 56 6 2828 3639 396418218 396417410 0.000000e+00 1136
11 TraesCS5D01G197000 chr5A 82.734 1280 179 29 2087 3343 390367470 390366210 0.000000e+00 1101
12 TraesCS5D01G197000 chr5A 87.104 853 47 27 3706 4522 396417402 396416577 0.000000e+00 907
13 TraesCS5D01G197000 chr5A 95.333 150 7 0 75 224 397761584 397761733 5.850000e-59 239
14 TraesCS5D01G197000 chr5A 84.884 172 23 2 998 1169 390370470 390370302 2.160000e-38 171
15 TraesCS5D01G197000 chr5B 94.354 3188 114 23 649 3800 343947768 343950925 0.000000e+00 4830
16 TraesCS5D01G197000 chr5B 95.350 2129 73 10 2411 4522 339980742 339978623 0.000000e+00 3360
17 TraesCS5D01G197000 chr5B 96.587 967 30 3 2532 3497 340137497 340136533 0.000000e+00 1600
18 TraesCS5D01G197000 chr5B 96.587 967 30 3 2532 3497 340327570 340326606 0.000000e+00 1600
19 TraesCS5D01G197000 chr5B 94.123 1055 40 8 3483 4522 340136519 340135472 0.000000e+00 1585
20 TraesCS5D01G197000 chr5B 94.123 1055 40 8 3483 4522 340326592 340325545 0.000000e+00 1585
21 TraesCS5D01G197000 chr5B 89.610 1155 86 14 3400 4522 344238941 344240093 0.000000e+00 1437
22 TraesCS5D01G197000 chr5B 82.777 1289 165 38 2087 3343 352309786 352311049 0.000000e+00 1098
23 TraesCS5D01G197000 chr5B 91.656 755 32 10 3789 4522 343951096 343951840 0.000000e+00 1016
24 TraesCS5D01G197000 chr5B 89.872 701 39 16 3846 4522 340569170 340568478 0.000000e+00 872
25 TraesCS5D01G197000 chr5B 90.820 512 35 3 2886 3397 344232333 344232832 0.000000e+00 675
26 TraesCS5D01G197000 chr5B 97.810 137 3 0 2411 2547 340154662 340154526 2.100000e-58 237
27 TraesCS5D01G197000 chr5B 97.101 138 3 1 2411 2547 340344750 340344613 9.780000e-57 231
28 TraesCS5D01G197000 chr5B 84.302 172 24 2 998 1169 352306553 352306721 1.010000e-36 165
29 TraesCS5D01G197000 chr3D 85.090 1442 172 27 2101 3510 482007265 482005835 0.000000e+00 1432
30 TraesCS5D01G197000 chr1D 84.089 1433 184 34 2099 3501 18804382 18802964 0.000000e+00 1343


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 TraesCS5D01G197000 chr5D 300142003 300146524 4521 False 8351.0 8351 100.0000 1 4522 1 chr5D.!!$F1 4521
1 TraesCS5D01G197000 chr5D 300313843 300314868 1025 False 1225.0 1225 88.4430 2886 3912 1 chr5D.!!$F2 1026
2 TraesCS5D01G197000 chr5D 300956483 300958241 1758 True 1088.5 1290 90.9875 2886 4522 2 chr5D.!!$R2 1636
3 TraesCS5D01G197000 chr5D 299389689 299390409 720 True 1009.0 1009 92.4030 3821 4522 1 chr5D.!!$R1 701
4 TraesCS5D01G197000 chr5D 300321719 300322412 693 False 852.0 852 89.3160 3845 4522 1 chr5D.!!$F3 677
5 TraesCS5D01G197000 chr5D 307086216 307090566 4350 False 652.5 1140 83.5270 992 3343 2 chr5D.!!$F4 2351
6 TraesCS5D01G197000 chr5A 397781856 397786098 4242 False 5744.0 5744 91.1780 236 4522 1 chr5A.!!$F2 4286
7 TraesCS5D01G197000 chr5A 415627441 415629130 1689 True 1511.0 1511 83.3040 1982 3650 1 chr5A.!!$R1 1668
8 TraesCS5D01G197000 chr5A 396416577 396418218 1641 True 1021.5 1136 89.5645 2828 4522 2 chr5A.!!$R3 1694
9 TraesCS5D01G197000 chr5A 390366210 390370470 4260 True 636.0 1101 83.8090 998 3343 2 chr5A.!!$R2 2345
10 TraesCS5D01G197000 chr5B 339978623 339980742 2119 True 3360.0 3360 95.3500 2411 4522 1 chr5B.!!$R1 2111
11 TraesCS5D01G197000 chr5B 343947768 343951840 4072 False 2923.0 4830 93.0050 649 4522 2 chr5B.!!$F3 3873
12 TraesCS5D01G197000 chr5B 340135472 340137497 2025 True 1592.5 1600 95.3550 2532 4522 2 chr5B.!!$R5 1990
13 TraesCS5D01G197000 chr5B 340325545 340327570 2025 True 1592.5 1600 95.3550 2532 4522 2 chr5B.!!$R6 1990
14 TraesCS5D01G197000 chr5B 344238941 344240093 1152 False 1437.0 1437 89.6100 3400 4522 1 chr5B.!!$F2 1122
15 TraesCS5D01G197000 chr5B 340568478 340569170 692 True 872.0 872 89.8720 3846 4522 1 chr5B.!!$R4 676
16 TraesCS5D01G197000 chr5B 352306553 352311049 4496 False 631.5 1098 83.5395 998 3343 2 chr5B.!!$F4 2345
17 TraesCS5D01G197000 chr3D 482005835 482007265 1430 True 1432.0 1432 85.0900 2101 3510 1 chr3D.!!$R1 1409
18 TraesCS5D01G197000 chr1D 18802964 18804382 1418 True 1343.0 1343 84.0890 2099 3501 1 chr1D.!!$R1 1402

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
188 189 0.040058 TGCAGGGCCAGTGAATGATT 59.960 50.000 6.18 0.00 0.00 2.57 F
655 668 0.175989 GAGAACCGGCCCTAACTGAG 59.824 60.000 0.00 0.00 0.00 3.35 F
669 682 0.252421 ACTGAGTGGGGCAGATCAGA 60.252 55.000 13.06 0.00 41.35 3.27 F
1670 4052 0.699981 TTACCCCACCCAAAGTAGGC 59.300 55.000 0.00 0.00 0.00 3.93 F
1671 4053 1.555477 TACCCCACCCAAAGTAGGCG 61.555 60.000 0.00 0.00 0.00 5.52 F
1705 4087 3.230134 TGTGTGAGCCCTTAAATTTGCT 58.770 40.909 0.00 0.17 36.62 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 4354 0.242017 ACAAGTACGCGGTAGGTCAC 59.758 55.000 12.47 0.00 0.00 3.67 R
1974 4359 2.342910 ACAAGACAAGTACGCGGTAG 57.657 50.000 12.47 0.00 0.00 3.18 R
2037 4543 6.710295 ACAATTTTGCTCACAGTGTATAGTCA 59.290 34.615 0.00 0.00 0.00 3.41 R
3255 5870 4.276926 CAGAATCTGTTTAATAGCAGGGGC 59.723 45.833 1.31 0.00 41.61 5.80 R
3373 5997 8.106462 TGACATTCTCATTCTTTATACAACCCA 58.894 33.333 0.00 0.00 0.00 4.51 R
3960 6932 0.393077 AGTCGTTGCTAGCAAGGTGT 59.607 50.000 36.01 25.99 41.08 4.16 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
18 19 3.965888 AGCTTCTCGGCCAGAAAAT 57.034 47.368 15.54 7.17 40.83 1.82
19 20 1.457346 AGCTTCTCGGCCAGAAAATG 58.543 50.000 15.54 8.06 40.83 2.32
20 21 1.003580 AGCTTCTCGGCCAGAAAATGA 59.996 47.619 15.54 0.00 40.83 2.57
21 22 2.019984 GCTTCTCGGCCAGAAAATGAT 58.980 47.619 15.54 0.00 40.83 2.45
22 23 2.223433 GCTTCTCGGCCAGAAAATGATG 60.223 50.000 15.54 6.99 40.83 3.07
23 24 2.042686 TCTCGGCCAGAAAATGATGG 57.957 50.000 2.24 0.00 39.73 3.51
24 25 1.559219 TCTCGGCCAGAAAATGATGGA 59.441 47.619 2.24 0.00 39.02 3.41
25 26 1.672881 CTCGGCCAGAAAATGATGGAC 59.327 52.381 2.24 0.00 41.60 4.02
26 27 1.004161 TCGGCCAGAAAATGATGGACA 59.996 47.619 2.24 0.00 45.70 4.02
27 28 2.026641 CGGCCAGAAAATGATGGACAT 58.973 47.619 2.24 0.00 45.70 3.06
28 29 3.118075 TCGGCCAGAAAATGATGGACATA 60.118 43.478 2.24 0.00 45.70 2.29
29 30 3.631686 CGGCCAGAAAATGATGGACATAA 59.368 43.478 2.24 0.00 45.70 1.90
30 31 4.498009 CGGCCAGAAAATGATGGACATAAC 60.498 45.833 2.24 0.00 45.70 1.89
31 32 4.402155 GGCCAGAAAATGATGGACATAACA 59.598 41.667 0.00 0.00 44.69 2.41
32 33 5.343249 GCCAGAAAATGATGGACATAACAC 58.657 41.667 0.00 0.00 39.02 3.32
33 34 5.679638 GCCAGAAAATGATGGACATAACACC 60.680 44.000 0.00 0.00 39.02 4.16
34 35 5.163519 CCAGAAAATGATGGACATAACACCC 60.164 44.000 0.00 0.00 39.02 4.61
35 36 4.640201 AGAAAATGATGGACATAACACCCG 59.360 41.667 0.00 0.00 38.38 5.28
36 37 3.644966 AATGATGGACATAACACCCGT 57.355 42.857 0.00 0.00 38.38 5.28
37 38 2.684001 TGATGGACATAACACCCGTC 57.316 50.000 0.00 0.00 36.71 4.79
38 39 2.184533 TGATGGACATAACACCCGTCT 58.815 47.619 0.00 0.00 37.01 4.18
39 40 2.167693 TGATGGACATAACACCCGTCTC 59.832 50.000 0.00 0.00 37.01 3.36
40 41 1.634960 TGGACATAACACCCGTCTCA 58.365 50.000 0.00 0.00 0.00 3.27
41 42 1.548719 TGGACATAACACCCGTCTCAG 59.451 52.381 0.00 0.00 0.00 3.35
42 43 1.641577 GACATAACACCCGTCTCAGC 58.358 55.000 0.00 0.00 0.00 4.26
43 44 1.204941 GACATAACACCCGTCTCAGCT 59.795 52.381 0.00 0.00 0.00 4.24
44 45 1.066858 ACATAACACCCGTCTCAGCTG 60.067 52.381 7.63 7.63 0.00 4.24
45 46 1.066858 CATAACACCCGTCTCAGCTGT 60.067 52.381 14.67 0.00 0.00 4.40
46 47 1.045407 TAACACCCGTCTCAGCTGTT 58.955 50.000 14.67 0.22 0.00 3.16
47 48 0.180406 AACACCCGTCTCAGCTGTTT 59.820 50.000 14.67 0.00 0.00 2.83
48 49 0.532862 ACACCCGTCTCAGCTGTTTG 60.533 55.000 14.67 5.73 0.00 2.93
49 50 0.249868 CACCCGTCTCAGCTGTTTGA 60.250 55.000 14.67 8.09 0.00 2.69
50 51 0.468226 ACCCGTCTCAGCTGTTTGAA 59.532 50.000 14.67 0.00 0.00 2.69
51 52 1.151668 CCCGTCTCAGCTGTTTGAAG 58.848 55.000 14.67 12.19 0.00 3.02
52 53 1.270305 CCCGTCTCAGCTGTTTGAAGA 60.270 52.381 14.67 5.74 0.00 2.87
53 54 2.064762 CCGTCTCAGCTGTTTGAAGAG 58.935 52.381 14.67 1.43 0.00 2.85
54 55 1.458827 CGTCTCAGCTGTTTGAAGAGC 59.541 52.381 14.67 4.84 44.89 4.09
55 56 2.487934 GTCTCAGCTGTTTGAAGAGCA 58.512 47.619 14.67 0.00 46.75 4.26
56 57 2.222911 GTCTCAGCTGTTTGAAGAGCAC 59.777 50.000 14.67 1.44 46.75 4.40
57 58 1.534595 CTCAGCTGTTTGAAGAGCACC 59.465 52.381 14.67 0.00 46.75 5.01
58 59 0.236711 CAGCTGTTTGAAGAGCACCG 59.763 55.000 14.25 0.36 46.75 4.94
59 60 1.081840 GCTGTTTGAAGAGCACCGC 60.082 57.895 7.87 0.00 44.05 5.68
60 61 1.785041 GCTGTTTGAAGAGCACCGCA 61.785 55.000 7.87 0.00 44.05 5.69
61 62 0.236711 CTGTTTGAAGAGCACCGCAG 59.763 55.000 0.00 0.00 0.00 5.18
62 63 1.081840 GTTTGAAGAGCACCGCAGC 60.082 57.895 0.00 0.00 0.00 5.25
63 64 1.525765 TTTGAAGAGCACCGCAGCA 60.526 52.632 0.00 0.00 36.85 4.41
64 65 1.509644 TTTGAAGAGCACCGCAGCAG 61.510 55.000 0.00 0.00 36.85 4.24
65 66 3.123620 GAAGAGCACCGCAGCAGG 61.124 66.667 0.00 0.00 36.85 4.85
66 67 3.596066 GAAGAGCACCGCAGCAGGA 62.596 63.158 9.87 0.00 36.85 3.86
67 68 2.866085 GAAGAGCACCGCAGCAGGAT 62.866 60.000 9.87 0.00 36.85 3.24
68 69 2.437359 GAGCACCGCAGCAGGATT 60.437 61.111 9.87 0.00 36.85 3.01
69 70 2.034687 AGCACCGCAGCAGGATTT 59.965 55.556 9.87 0.00 36.85 2.17
70 71 1.589716 GAGCACCGCAGCAGGATTTT 61.590 55.000 9.87 0.00 36.85 1.82
71 72 1.444895 GCACCGCAGCAGGATTTTG 60.445 57.895 9.87 0.14 34.73 2.44
72 73 1.959085 CACCGCAGCAGGATTTTGT 59.041 52.632 9.87 0.00 34.73 2.83
73 74 0.314935 CACCGCAGCAGGATTTTGTT 59.685 50.000 9.87 0.00 34.73 2.83
74 75 1.539388 CACCGCAGCAGGATTTTGTTA 59.461 47.619 9.87 0.00 34.73 2.41
75 76 2.030363 CACCGCAGCAGGATTTTGTTAA 60.030 45.455 9.87 0.00 34.73 2.01
76 77 2.228822 ACCGCAGCAGGATTTTGTTAAG 59.771 45.455 9.87 0.00 34.73 1.85
77 78 2.487762 CCGCAGCAGGATTTTGTTAAGA 59.512 45.455 0.00 0.00 0.00 2.10
78 79 3.129287 CCGCAGCAGGATTTTGTTAAGAT 59.871 43.478 0.00 0.00 0.00 2.40
79 80 4.380867 CCGCAGCAGGATTTTGTTAAGATT 60.381 41.667 0.00 0.00 0.00 2.40
80 81 5.163663 CCGCAGCAGGATTTTGTTAAGATTA 60.164 40.000 0.00 0.00 0.00 1.75
81 82 6.321717 CGCAGCAGGATTTTGTTAAGATTAA 58.678 36.000 0.00 0.00 0.00 1.40
82 83 6.974622 CGCAGCAGGATTTTGTTAAGATTAAT 59.025 34.615 0.00 0.00 0.00 1.40
83 84 7.043854 CGCAGCAGGATTTTGTTAAGATTAATG 60.044 37.037 0.00 0.00 0.00 1.90
84 85 7.761249 GCAGCAGGATTTTGTTAAGATTAATGT 59.239 33.333 0.00 0.00 0.00 2.71
85 86 9.079833 CAGCAGGATTTTGTTAAGATTAATGTG 57.920 33.333 0.00 0.00 0.00 3.21
86 87 8.253113 AGCAGGATTTTGTTAAGATTAATGTGG 58.747 33.333 0.00 0.00 0.00 4.17
87 88 8.250332 GCAGGATTTTGTTAAGATTAATGTGGA 58.750 33.333 0.00 0.00 0.00 4.02
94 95 8.800370 TTGTTAAGATTAATGTGGATAGTGCA 57.200 30.769 0.00 0.00 0.00 4.57
95 96 8.978874 TGTTAAGATTAATGTGGATAGTGCAT 57.021 30.769 0.00 0.00 0.00 3.96
96 97 9.407380 TGTTAAGATTAATGTGGATAGTGCATT 57.593 29.630 0.00 0.00 36.83 3.56
99 100 8.523915 AAGATTAATGTGGATAGTGCATTTCA 57.476 30.769 0.00 0.00 34.97 2.69
100 101 8.701908 AGATTAATGTGGATAGTGCATTTCAT 57.298 30.769 0.00 0.00 34.97 2.57
101 102 8.573885 AGATTAATGTGGATAGTGCATTTCATG 58.426 33.333 0.00 0.00 34.97 3.07
102 103 7.878547 TTAATGTGGATAGTGCATTTCATGA 57.121 32.000 0.00 0.00 34.97 3.07
103 104 6.971726 AATGTGGATAGTGCATTTCATGAT 57.028 33.333 0.00 0.00 29.59 2.45
104 105 5.761165 TGTGGATAGTGCATTTCATGATG 57.239 39.130 0.00 0.00 0.00 3.07
105 106 5.438833 TGTGGATAGTGCATTTCATGATGA 58.561 37.500 0.00 0.00 0.00 2.92
106 107 5.887035 TGTGGATAGTGCATTTCATGATGAA 59.113 36.000 3.29 3.29 34.03 2.57
107 108 6.548251 TGTGGATAGTGCATTTCATGATGAAT 59.452 34.615 8.90 0.00 36.11 2.57
108 109 7.082602 GTGGATAGTGCATTTCATGATGAATC 58.917 38.462 8.90 0.94 36.11 2.52
109 110 7.002276 TGGATAGTGCATTTCATGATGAATCT 58.998 34.615 8.90 5.83 36.11 2.40
110 111 8.158789 TGGATAGTGCATTTCATGATGAATCTA 58.841 33.333 8.90 7.57 36.11 1.98
111 112 8.666573 GGATAGTGCATTTCATGATGAATCTAG 58.333 37.037 8.90 1.13 36.11 2.43
112 113 9.433153 GATAGTGCATTTCATGATGAATCTAGA 57.567 33.333 8.90 0.00 36.11 2.43
113 114 7.493743 AGTGCATTTCATGATGAATCTAGAC 57.506 36.000 8.90 3.27 36.11 2.59
114 115 7.052248 AGTGCATTTCATGATGAATCTAGACA 58.948 34.615 8.90 0.01 36.11 3.41
115 116 7.720074 AGTGCATTTCATGATGAATCTAGACAT 59.280 33.333 8.90 0.00 36.11 3.06
116 117 7.803659 GTGCATTTCATGATGAATCTAGACATG 59.196 37.037 8.90 8.72 36.11 3.21
117 118 7.040686 TGCATTTCATGATGAATCTAGACATGG 60.041 37.037 8.90 5.62 36.11 3.66
118 119 7.040617 GCATTTCATGATGAATCTAGACATGGT 60.041 37.037 8.90 4.98 36.11 3.55
119 120 7.797038 TTTCATGATGAATCTAGACATGGTG 57.203 36.000 8.90 8.42 36.11 4.17
120 121 5.861727 TCATGATGAATCTAGACATGGTGG 58.138 41.667 16.17 0.00 38.82 4.61
121 122 4.077300 TGATGAATCTAGACATGGTGGC 57.923 45.455 0.00 0.00 0.00 5.01
122 123 3.713248 TGATGAATCTAGACATGGTGGCT 59.287 43.478 0.00 0.00 40.22 4.75
123 124 3.548745 TGAATCTAGACATGGTGGCTG 57.451 47.619 0.00 0.00 35.73 4.85
124 125 2.171237 TGAATCTAGACATGGTGGCTGG 59.829 50.000 0.00 0.00 35.73 4.85
125 126 1.135094 ATCTAGACATGGTGGCTGGG 58.865 55.000 0.00 0.00 35.73 4.45
126 127 0.982852 TCTAGACATGGTGGCTGGGG 60.983 60.000 0.00 0.00 35.73 4.96
127 128 1.229820 TAGACATGGTGGCTGGGGT 60.230 57.895 0.00 0.00 35.73 4.95
128 129 1.561769 TAGACATGGTGGCTGGGGTG 61.562 60.000 0.00 0.00 35.73 4.61
129 130 3.185203 ACATGGTGGCTGGGGTGT 61.185 61.111 0.00 0.00 0.00 4.16
130 131 2.677524 CATGGTGGCTGGGGTGTG 60.678 66.667 0.00 0.00 0.00 3.82
131 132 2.858476 ATGGTGGCTGGGGTGTGA 60.858 61.111 0.00 0.00 0.00 3.58
132 133 2.240918 ATGGTGGCTGGGGTGTGAT 61.241 57.895 0.00 0.00 0.00 3.06
133 134 0.918799 ATGGTGGCTGGGGTGTGATA 60.919 55.000 0.00 0.00 0.00 2.15
134 135 0.918799 TGGTGGCTGGGGTGTGATAT 60.919 55.000 0.00 0.00 0.00 1.63
135 136 0.466189 GGTGGCTGGGGTGTGATATG 60.466 60.000 0.00 0.00 0.00 1.78
136 137 1.103398 GTGGCTGGGGTGTGATATGC 61.103 60.000 0.00 0.00 0.00 3.14
137 138 1.529244 GGCTGGGGTGTGATATGCC 60.529 63.158 0.00 0.00 0.00 4.40
138 139 1.227102 GCTGGGGTGTGATATGCCA 59.773 57.895 0.00 0.00 0.00 4.92
139 140 0.178981 GCTGGGGTGTGATATGCCAT 60.179 55.000 0.00 0.00 0.00 4.40
140 141 1.612676 CTGGGGTGTGATATGCCATG 58.387 55.000 0.00 0.00 0.00 3.66
141 142 1.143481 CTGGGGTGTGATATGCCATGA 59.857 52.381 0.00 0.00 0.00 3.07
142 143 1.133823 TGGGGTGTGATATGCCATGAC 60.134 52.381 0.00 0.00 0.00 3.06
143 144 1.143684 GGGGTGTGATATGCCATGACT 59.856 52.381 0.00 0.00 0.00 3.41
144 145 2.498167 GGGTGTGATATGCCATGACTC 58.502 52.381 0.00 0.00 0.00 3.36
145 146 2.158769 GGGTGTGATATGCCATGACTCA 60.159 50.000 0.00 0.00 0.00 3.41
146 147 3.136763 GGTGTGATATGCCATGACTCAG 58.863 50.000 0.00 0.00 0.00 3.35
147 148 3.181462 GGTGTGATATGCCATGACTCAGA 60.181 47.826 0.00 0.00 0.00 3.27
148 149 4.504514 GGTGTGATATGCCATGACTCAGAT 60.505 45.833 0.00 0.00 0.00 2.90
149 150 5.061853 GTGTGATATGCCATGACTCAGATT 58.938 41.667 0.00 0.00 0.00 2.40
150 151 5.178996 GTGTGATATGCCATGACTCAGATTC 59.821 44.000 0.00 0.00 0.00 2.52
151 152 4.388165 GTGATATGCCATGACTCAGATTCG 59.612 45.833 0.00 0.00 0.00 3.34
152 153 2.251409 ATGCCATGACTCAGATTCGG 57.749 50.000 0.00 0.00 0.00 4.30
153 154 1.194218 TGCCATGACTCAGATTCGGA 58.806 50.000 0.00 0.00 0.00 4.55
154 155 1.134699 TGCCATGACTCAGATTCGGAC 60.135 52.381 0.00 0.00 0.00 4.79
155 156 1.134699 GCCATGACTCAGATTCGGACA 60.135 52.381 0.00 0.00 0.00 4.02
156 157 2.484417 GCCATGACTCAGATTCGGACAT 60.484 50.000 0.00 0.00 0.00 3.06
157 158 3.388308 CCATGACTCAGATTCGGACATC 58.612 50.000 0.00 0.00 0.00 3.06
158 159 3.388308 CATGACTCAGATTCGGACATCC 58.612 50.000 0.00 0.00 0.00 3.51
159 160 2.456577 TGACTCAGATTCGGACATCCA 58.543 47.619 0.00 0.00 35.14 3.41
160 161 2.831526 TGACTCAGATTCGGACATCCAA 59.168 45.455 0.00 0.00 35.14 3.53
161 162 3.452264 TGACTCAGATTCGGACATCCAAT 59.548 43.478 0.00 0.00 35.14 3.16
162 163 4.080919 TGACTCAGATTCGGACATCCAATT 60.081 41.667 0.00 0.00 35.14 2.32
163 164 4.848357 ACTCAGATTCGGACATCCAATTT 58.152 39.130 0.00 0.00 35.14 1.82
164 165 5.989477 ACTCAGATTCGGACATCCAATTTA 58.011 37.500 0.00 0.00 35.14 1.40
165 166 6.595682 ACTCAGATTCGGACATCCAATTTAT 58.404 36.000 0.00 0.00 35.14 1.40
166 167 6.484643 ACTCAGATTCGGACATCCAATTTATG 59.515 38.462 0.00 0.00 35.14 1.90
176 177 0.105408 CCAATTTATGGCTGCAGGGC 59.895 55.000 17.12 9.25 43.80 5.19
184 185 2.362120 GCTGCAGGGCCAGTGAAT 60.362 61.111 17.12 0.00 35.28 2.57
185 186 2.707849 GCTGCAGGGCCAGTGAATG 61.708 63.158 17.12 0.00 35.28 2.67
186 187 1.001764 CTGCAGGGCCAGTGAATGA 60.002 57.895 6.18 0.00 0.00 2.57
187 188 0.395311 CTGCAGGGCCAGTGAATGAT 60.395 55.000 6.18 0.00 0.00 2.45
188 189 0.040058 TGCAGGGCCAGTGAATGATT 59.960 50.000 6.18 0.00 0.00 2.57
189 190 1.188863 GCAGGGCCAGTGAATGATTT 58.811 50.000 6.18 0.00 0.00 2.17
190 191 1.134907 GCAGGGCCAGTGAATGATTTG 60.135 52.381 6.18 0.00 0.00 2.32
191 192 1.479323 CAGGGCCAGTGAATGATTTGG 59.521 52.381 6.18 0.00 0.00 3.28
197 198 4.041740 CCAGTGAATGATTTGGCTCATG 57.958 45.455 0.00 0.00 36.03 3.07
198 199 3.444916 CAGTGAATGATTTGGCTCATGC 58.555 45.455 0.00 0.00 36.03 4.06
208 209 4.487412 GCTCATGCCTTGCACGCC 62.487 66.667 2.63 0.00 43.04 5.68
209 210 4.170062 CTCATGCCTTGCACGCCG 62.170 66.667 2.63 0.00 43.04 6.46
210 211 4.695993 TCATGCCTTGCACGCCGA 62.696 61.111 0.00 0.00 43.04 5.54
211 212 4.170062 CATGCCTTGCACGCCGAG 62.170 66.667 0.00 0.00 43.04 4.63
229 230 4.012138 GCCATGGCCCTTTTACGT 57.988 55.556 27.24 0.00 34.56 3.57
230 231 1.510844 GCCATGGCCCTTTTACGTG 59.489 57.895 27.24 0.00 34.56 4.49
231 232 1.944234 GCCATGGCCCTTTTACGTGG 61.944 60.000 27.24 0.00 42.75 4.94
232 233 0.610785 CCATGGCCCTTTTACGTGGT 60.611 55.000 0.00 0.00 36.70 4.16
233 234 1.253100 CATGGCCCTTTTACGTGGTT 58.747 50.000 0.00 0.00 0.00 3.67
234 235 1.067915 CATGGCCCTTTTACGTGGTTG 60.068 52.381 0.00 0.00 0.00 3.77
313 321 5.431179 AGATTTACGCCCTTTTTCTAGGA 57.569 39.130 0.00 0.00 37.50 2.94
345 353 8.476447 GTTGAGCCCTTAATTAGTAAGAGTAGT 58.524 37.037 0.66 0.00 41.70 2.73
405 413 4.692228 TGTTCGCTGCATAGTATGATTCA 58.308 39.130 14.52 1.87 0.00 2.57
447 455 6.223120 GCAGGGCAATTTCTTTAAAGAAGAA 58.777 36.000 25.38 15.58 45.01 2.52
448 456 6.367149 GCAGGGCAATTTCTTTAAAGAAGAAG 59.633 38.462 25.38 19.87 45.01 2.85
546 558 0.250295 TCCCCTTTCAGCTGACGTTG 60.250 55.000 18.03 5.71 0.00 4.10
547 559 1.576421 CCCTTTCAGCTGACGTTGC 59.424 57.895 18.03 6.40 0.00 4.17
562 574 4.388773 TGACGTTGCTCACTTATCATTGTC 59.611 41.667 0.00 0.00 0.00 3.18
594 607 5.484173 TCGATTGGTATGTCAAATCAAGC 57.516 39.130 0.00 0.00 0.00 4.01
599 612 2.754552 GGTATGTCAAATCAAGCTGGCA 59.245 45.455 0.00 0.00 0.00 4.92
600 613 3.181493 GGTATGTCAAATCAAGCTGGCAG 60.181 47.826 10.94 10.94 29.16 4.85
601 614 1.250328 TGTCAAATCAAGCTGGCAGG 58.750 50.000 17.64 0.00 0.00 4.85
602 615 1.202915 TGTCAAATCAAGCTGGCAGGA 60.203 47.619 17.64 5.46 0.00 3.86
603 616 1.888512 GTCAAATCAAGCTGGCAGGAA 59.111 47.619 17.64 0.00 0.00 3.36
604 617 1.888512 TCAAATCAAGCTGGCAGGAAC 59.111 47.619 17.64 0.00 0.00 3.62
605 618 1.614903 CAAATCAAGCTGGCAGGAACA 59.385 47.619 17.64 0.00 0.00 3.18
606 619 1.999648 AATCAAGCTGGCAGGAACAA 58.000 45.000 17.64 0.00 0.00 2.83
607 620 1.251251 ATCAAGCTGGCAGGAACAAC 58.749 50.000 17.64 0.00 0.00 3.32
608 621 0.183492 TCAAGCTGGCAGGAACAACT 59.817 50.000 17.64 0.00 0.00 3.16
609 622 1.035139 CAAGCTGGCAGGAACAACTT 58.965 50.000 17.64 6.80 0.00 2.66
610 623 2.158682 TCAAGCTGGCAGGAACAACTTA 60.159 45.455 17.64 0.00 0.00 2.24
611 624 2.821969 CAAGCTGGCAGGAACAACTTAT 59.178 45.455 17.64 0.00 0.00 1.73
655 668 0.175989 GAGAACCGGCCCTAACTGAG 59.824 60.000 0.00 0.00 0.00 3.35
669 682 0.252421 ACTGAGTGGGGCAGATCAGA 60.252 55.000 13.06 0.00 41.35 3.27
670 683 1.129917 CTGAGTGGGGCAGATCAGAT 58.870 55.000 0.00 0.00 41.35 2.90
671 684 1.070445 CTGAGTGGGGCAGATCAGATC 59.930 57.143 1.64 1.64 41.35 2.75
672 685 1.126488 GAGTGGGGCAGATCAGATCA 58.874 55.000 13.14 0.00 0.00 2.92
673 686 1.070445 GAGTGGGGCAGATCAGATCAG 59.930 57.143 13.14 5.81 0.00 2.90
678 691 1.070445 GGGCAGATCAGATCAGTCCAG 59.930 57.143 19.14 1.29 39.99 3.86
679 692 1.540797 GGCAGATCAGATCAGTCCAGC 60.541 57.143 13.14 6.36 0.00 4.85
703 716 4.021016 TCCAGTAGCTGTTCTTCTTCCTTC 60.021 45.833 0.00 0.00 0.00 3.46
754 767 2.552155 CGTCATCTTTCCTTCCACCCAA 60.552 50.000 0.00 0.00 0.00 4.12
836 867 2.950433 TCGCGTTCCGAGAATAAACTT 58.050 42.857 5.77 0.00 41.89 2.66
837 868 2.919229 TCGCGTTCCGAGAATAAACTTC 59.081 45.455 5.77 0.00 41.89 3.01
838 869 2.284288 CGCGTTCCGAGAATAAACTTCG 60.284 50.000 0.00 0.00 40.02 3.79
927 971 2.502947 AGTATTGACTGCTGGCTCATCA 59.497 45.455 0.00 0.00 33.41 3.07
953 1004 4.087892 ACTCTCAGCGCGCCCATT 62.088 61.111 30.33 5.98 0.00 3.16
1248 1325 1.250840 GGTTCATGTCCACTTGGCCC 61.251 60.000 0.00 0.00 34.44 5.80
1378 3554 7.598189 TTTTCAAACCGTGTTGATATCGATA 57.402 32.000 7.75 7.75 37.36 2.92
1380 3556 6.139048 TCAAACCGTGTTGATATCGATAGA 57.861 37.500 11.41 0.00 40.33 1.98
1529 3911 7.770897 AGTTGGCTTAATAATCAAGGTCAGTAG 59.229 37.037 0.00 0.00 0.00 2.57
1531 3913 8.034313 TGGCTTAATAATCAAGGTCAGTAGAT 57.966 34.615 0.00 0.00 0.00 1.98
1533 3915 8.778358 GGCTTAATAATCAAGGTCAGTAGATTG 58.222 37.037 0.00 0.00 33.22 2.67
1547 3929 6.769822 GTCAGTAGATTGGATTGGATCAATGT 59.230 38.462 0.00 0.00 33.90 2.71
1557 3939 7.312154 TGGATTGGATCAATGTTTAAGTTTCG 58.688 34.615 0.00 0.00 33.90 3.46
1586 3968 2.079158 CGTGCTCCTCATGTTGTCATT 58.921 47.619 0.00 0.00 31.15 2.57
1601 3983 2.028203 TGTCATTGTCGCTCCTCATTGA 60.028 45.455 0.00 0.00 0.00 2.57
1604 3986 4.811024 GTCATTGTCGCTCCTCATTGATAA 59.189 41.667 0.00 0.00 0.00 1.75
1647 4029 3.057876 TCGCGGATTTGCTAAACAACATT 60.058 39.130 6.13 0.00 38.23 2.71
1664 4046 1.974236 CATTTGCTTACCCCACCCAAA 59.026 47.619 0.00 0.00 0.00 3.28
1670 4052 0.699981 TTACCCCACCCAAAGTAGGC 59.300 55.000 0.00 0.00 0.00 3.93
1671 4053 1.555477 TACCCCACCCAAAGTAGGCG 61.555 60.000 0.00 0.00 0.00 5.52
1687 4069 4.870426 AGTAGGCGTTTAGATCATGTTGTG 59.130 41.667 0.00 0.00 0.00 3.33
1704 4086 3.658757 TGTGTGAGCCCTTAAATTTGC 57.341 42.857 0.00 0.00 0.00 3.68
1705 4087 3.230134 TGTGTGAGCCCTTAAATTTGCT 58.770 40.909 0.00 0.17 36.62 3.91
1769 4151 8.470040 ACAATTAATCAAAGCATTCACACATC 57.530 30.769 0.00 0.00 0.00 3.06
1770 4152 8.308931 ACAATTAATCAAAGCATTCACACATCT 58.691 29.630 0.00 0.00 0.00 2.90
1771 4153 9.146984 CAATTAATCAAAGCATTCACACATCTT 57.853 29.630 0.00 0.00 0.00 2.40
1772 4154 9.715121 AATTAATCAAAGCATTCACACATCTTT 57.285 25.926 0.00 0.00 0.00 2.52
1773 4155 8.746922 TTAATCAAAGCATTCACACATCTTTC 57.253 30.769 0.00 0.00 0.00 2.62
1774 4156 5.125100 TCAAAGCATTCACACATCTTTCC 57.875 39.130 0.00 0.00 0.00 3.13
1775 4157 4.022068 TCAAAGCATTCACACATCTTTCCC 60.022 41.667 0.00 0.00 0.00 3.97
1776 4158 3.446442 AGCATTCACACATCTTTCCCT 57.554 42.857 0.00 0.00 0.00 4.20
1777 4159 4.574674 AGCATTCACACATCTTTCCCTA 57.425 40.909 0.00 0.00 0.00 3.53
1778 4160 4.922206 AGCATTCACACATCTTTCCCTAA 58.078 39.130 0.00 0.00 0.00 2.69
1779 4161 5.513233 AGCATTCACACATCTTTCCCTAAT 58.487 37.500 0.00 0.00 0.00 1.73
1780 4162 6.662755 AGCATTCACACATCTTTCCCTAATA 58.337 36.000 0.00 0.00 0.00 0.98
1781 4163 7.118723 AGCATTCACACATCTTTCCCTAATAA 58.881 34.615 0.00 0.00 0.00 1.40
1782 4164 7.781693 AGCATTCACACATCTTTCCCTAATAAT 59.218 33.333 0.00 0.00 0.00 1.28
1962 4347 5.683681 TCTAATCTAACATCATTGCAGCCA 58.316 37.500 0.00 0.00 0.00 4.75
1969 4354 3.748083 ACATCATTGCAGCCATAGGTAG 58.252 45.455 0.00 0.00 0.00 3.18
2013 4398 5.258456 TGTTACATAAGTCATCGGGAGTC 57.742 43.478 0.00 0.00 0.00 3.36
2176 4725 4.263905 TGGAAAGGGATATGACAAGCTTGT 60.264 41.667 31.57 31.57 45.65 3.16
2440 5024 4.787551 TGTTTGTTTTTCTCTCCAGGCTA 58.212 39.130 0.00 0.00 0.00 3.93
2860 5453 3.914426 TTCTGGATCCTAAGAAGCACC 57.086 47.619 14.23 0.00 0.00 5.01
2924 5531 7.792374 TTACCTGATTAGAAAGCAGCATTAG 57.208 36.000 0.00 0.00 43.32 1.73
3050 5660 7.432869 TCTACAGAACCTCGTACTACTATCTC 58.567 42.308 0.00 0.00 0.00 2.75
3373 5997 2.225091 TGGGAATGAGAATGGTGCAAGT 60.225 45.455 0.00 0.00 0.00 3.16
3551 6322 4.234550 AGGTGATGCTATCATTCAGGGTA 58.765 43.478 2.80 0.00 42.04 3.69
4038 7033 1.671054 GGCGTTGCTGCTTCCAGTA 60.671 57.895 0.00 0.00 41.26 2.74
4041 7036 1.671850 GCGTTGCTGCTTCCAGTAGTA 60.672 52.381 0.00 0.00 41.26 1.82
4127 7128 0.179034 ATCAATGCCGAGCCTCTTCC 60.179 55.000 0.00 0.00 0.00 3.46
4270 7271 0.607489 GCTGCTCACATGTTGGAGGT 60.607 55.000 13.43 0.00 0.00 3.85
4293 7294 4.643387 GGCCGGTGCTGGACTGTT 62.643 66.667 1.90 0.00 37.74 3.16
4348 7364 2.948720 GCCGGAGTGCTCTGAACCT 61.949 63.158 5.05 0.00 38.21 3.50
4355 7371 0.389166 GTGCTCTGAACCTGAGTCGG 60.389 60.000 0.00 0.00 33.06 4.79
4491 7531 1.681793 CACGATCAGTAACGGGGAGAT 59.318 52.381 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.003580 TCATTTTCTGGCCGAGAAGCT 59.996 47.619 14.59 6.62 41.86 3.74
1 2 1.453155 TCATTTTCTGGCCGAGAAGC 58.547 50.000 14.59 0.00 41.86 3.86
2 3 2.357009 CCATCATTTTCTGGCCGAGAAG 59.643 50.000 14.59 0.13 41.86 2.85
3 4 2.026356 TCCATCATTTTCTGGCCGAGAA 60.026 45.455 12.03 12.03 39.05 2.87
4 5 1.559219 TCCATCATTTTCTGGCCGAGA 59.441 47.619 0.00 0.00 32.30 4.04
5 6 1.672881 GTCCATCATTTTCTGGCCGAG 59.327 52.381 0.00 0.00 32.30 4.63
6 7 1.004161 TGTCCATCATTTTCTGGCCGA 59.996 47.619 0.00 0.00 32.30 5.54
7 8 1.462616 TGTCCATCATTTTCTGGCCG 58.537 50.000 0.00 0.00 32.30 6.13
8 9 4.402155 TGTTATGTCCATCATTTTCTGGCC 59.598 41.667 0.00 0.00 37.91 5.36
9 10 5.343249 GTGTTATGTCCATCATTTTCTGGC 58.657 41.667 0.00 0.00 37.91 4.85
10 11 5.163519 GGGTGTTATGTCCATCATTTTCTGG 60.164 44.000 0.00 0.00 37.91 3.86
11 12 5.449041 CGGGTGTTATGTCCATCATTTTCTG 60.449 44.000 0.00 0.00 37.91 3.02
12 13 4.640201 CGGGTGTTATGTCCATCATTTTCT 59.360 41.667 0.00 0.00 37.91 2.52
13 14 4.398044 ACGGGTGTTATGTCCATCATTTTC 59.602 41.667 0.00 0.00 37.91 2.29
14 15 4.340617 ACGGGTGTTATGTCCATCATTTT 58.659 39.130 0.00 0.00 37.91 1.82
15 16 3.945285 GACGGGTGTTATGTCCATCATTT 59.055 43.478 0.00 0.00 37.91 2.32
16 17 3.199946 AGACGGGTGTTATGTCCATCATT 59.800 43.478 0.00 0.00 37.91 2.57
17 18 2.771943 AGACGGGTGTTATGTCCATCAT 59.228 45.455 0.00 0.00 40.25 2.45
18 19 2.167693 GAGACGGGTGTTATGTCCATCA 59.832 50.000 0.00 0.00 33.09 3.07
19 20 2.167693 TGAGACGGGTGTTATGTCCATC 59.832 50.000 0.00 0.00 33.09 3.51
20 21 2.168521 CTGAGACGGGTGTTATGTCCAT 59.831 50.000 0.00 0.00 33.09 3.41
21 22 1.548719 CTGAGACGGGTGTTATGTCCA 59.451 52.381 0.00 0.00 33.09 4.02
22 23 1.739371 GCTGAGACGGGTGTTATGTCC 60.739 57.143 0.00 0.00 33.09 4.02
23 24 1.204941 AGCTGAGACGGGTGTTATGTC 59.795 52.381 0.00 0.00 0.00 3.06
24 25 1.066858 CAGCTGAGACGGGTGTTATGT 60.067 52.381 8.42 0.00 34.05 2.29
25 26 1.645034 CAGCTGAGACGGGTGTTATG 58.355 55.000 8.42 0.00 34.05 1.90
30 31 0.249868 TCAAACAGCTGAGACGGGTG 60.250 55.000 23.35 7.14 43.04 4.61
31 32 0.468226 TTCAAACAGCTGAGACGGGT 59.532 50.000 23.35 0.00 0.00 5.28
32 33 1.151668 CTTCAAACAGCTGAGACGGG 58.848 55.000 23.35 3.53 0.00 5.28
33 34 2.064762 CTCTTCAAACAGCTGAGACGG 58.935 52.381 23.35 10.21 0.00 4.79
34 35 1.458827 GCTCTTCAAACAGCTGAGACG 59.541 52.381 23.35 12.49 32.48 4.18
35 36 2.222911 GTGCTCTTCAAACAGCTGAGAC 59.777 50.000 23.35 7.68 36.53 3.36
36 37 2.487934 GTGCTCTTCAAACAGCTGAGA 58.512 47.619 23.35 11.37 36.53 3.27
37 38 1.534595 GGTGCTCTTCAAACAGCTGAG 59.465 52.381 23.35 6.90 36.53 3.35
38 39 1.597742 GGTGCTCTTCAAACAGCTGA 58.402 50.000 23.35 0.00 36.53 4.26
39 40 0.236711 CGGTGCTCTTCAAACAGCTG 59.763 55.000 13.48 13.48 36.53 4.24
40 41 1.510480 GCGGTGCTCTTCAAACAGCT 61.510 55.000 0.00 0.00 36.53 4.24
41 42 1.081840 GCGGTGCTCTTCAAACAGC 60.082 57.895 0.00 0.00 36.08 4.40
42 43 0.236711 CTGCGGTGCTCTTCAAACAG 59.763 55.000 0.00 0.00 0.00 3.16
43 44 1.785041 GCTGCGGTGCTCTTCAAACA 61.785 55.000 0.00 0.00 0.00 2.83
44 45 1.081840 GCTGCGGTGCTCTTCAAAC 60.082 57.895 0.00 0.00 0.00 2.93
45 46 1.509644 CTGCTGCGGTGCTCTTCAAA 61.510 55.000 0.00 0.00 0.00 2.69
46 47 1.962822 CTGCTGCGGTGCTCTTCAA 60.963 57.895 0.00 0.00 0.00 2.69
47 48 2.357881 CTGCTGCGGTGCTCTTCA 60.358 61.111 0.00 0.00 0.00 3.02
48 49 2.866085 ATCCTGCTGCGGTGCTCTTC 62.866 60.000 7.82 0.00 0.00 2.87
49 50 2.475371 AATCCTGCTGCGGTGCTCTT 62.475 55.000 7.82 0.00 0.00 2.85
50 51 2.475371 AAATCCTGCTGCGGTGCTCT 62.475 55.000 7.82 0.00 0.00 4.09
51 52 1.589716 AAAATCCTGCTGCGGTGCTC 61.590 55.000 7.82 0.00 0.00 4.26
52 53 1.604593 AAAATCCTGCTGCGGTGCT 60.605 52.632 7.82 0.00 0.00 4.40
53 54 1.444895 CAAAATCCTGCTGCGGTGC 60.445 57.895 7.82 0.00 0.00 5.01
54 55 0.314935 AACAAAATCCTGCTGCGGTG 59.685 50.000 7.82 1.09 0.00 4.94
55 56 1.904287 TAACAAAATCCTGCTGCGGT 58.096 45.000 7.82 0.00 0.00 5.68
56 57 2.487762 TCTTAACAAAATCCTGCTGCGG 59.512 45.455 0.26 0.26 0.00 5.69
57 58 3.829886 TCTTAACAAAATCCTGCTGCG 57.170 42.857 0.00 0.00 0.00 5.18
58 59 7.761249 ACATTAATCTTAACAAAATCCTGCTGC 59.239 33.333 0.00 0.00 0.00 5.25
59 60 9.079833 CACATTAATCTTAACAAAATCCTGCTG 57.920 33.333 0.00 0.00 0.00 4.41
60 61 8.253113 CCACATTAATCTTAACAAAATCCTGCT 58.747 33.333 0.00 0.00 0.00 4.24
61 62 8.250332 TCCACATTAATCTTAACAAAATCCTGC 58.750 33.333 0.00 0.00 0.00 4.85
68 69 9.237187 TGCACTATCCACATTAATCTTAACAAA 57.763 29.630 0.00 0.00 0.00 2.83
69 70 8.800370 TGCACTATCCACATTAATCTTAACAA 57.200 30.769 0.00 0.00 0.00 2.83
70 71 8.978874 ATGCACTATCCACATTAATCTTAACA 57.021 30.769 0.00 0.00 0.00 2.41
73 74 9.625747 TGAAATGCACTATCCACATTAATCTTA 57.374 29.630 0.00 0.00 33.01 2.10
74 75 8.523915 TGAAATGCACTATCCACATTAATCTT 57.476 30.769 0.00 0.00 33.01 2.40
75 76 8.573885 CATGAAATGCACTATCCACATTAATCT 58.426 33.333 0.00 0.00 37.62 2.40
76 77 8.570488 TCATGAAATGCACTATCCACATTAATC 58.430 33.333 0.00 0.00 46.21 1.75
77 78 8.467963 TCATGAAATGCACTATCCACATTAAT 57.532 30.769 0.00 0.00 46.21 1.40
78 79 7.878547 TCATGAAATGCACTATCCACATTAA 57.121 32.000 0.00 0.00 46.21 1.40
79 80 7.720515 TCATCATGAAATGCACTATCCACATTA 59.279 33.333 0.00 0.00 46.21 1.90
80 81 6.548251 TCATCATGAAATGCACTATCCACATT 59.452 34.615 0.00 0.00 46.21 2.71
81 82 6.066032 TCATCATGAAATGCACTATCCACAT 58.934 36.000 0.00 0.00 46.21 3.21
82 83 5.438833 TCATCATGAAATGCACTATCCACA 58.561 37.500 0.00 0.00 46.21 4.17
83 84 6.381481 TTCATCATGAAATGCACTATCCAC 57.619 37.500 0.00 0.00 46.21 4.02
84 85 7.002276 AGATTCATCATGAAATGCACTATCCA 58.998 34.615 3.63 0.00 46.21 3.41
85 86 7.450124 AGATTCATCATGAAATGCACTATCC 57.550 36.000 3.63 0.00 46.21 2.59
86 87 9.433153 TCTAGATTCATCATGAAATGCACTATC 57.567 33.333 3.63 0.00 46.21 2.08
87 88 9.217278 GTCTAGATTCATCATGAAATGCACTAT 57.783 33.333 3.63 0.00 46.21 2.12
88 89 8.206189 TGTCTAGATTCATCATGAAATGCACTA 58.794 33.333 3.63 3.52 46.21 2.74
89 90 7.052248 TGTCTAGATTCATCATGAAATGCACT 58.948 34.615 3.63 2.58 46.21 4.40
90 91 7.255491 TGTCTAGATTCATCATGAAATGCAC 57.745 36.000 3.63 0.00 46.21 4.57
91 92 7.040686 CCATGTCTAGATTCATCATGAAATGCA 60.041 37.037 17.50 0.00 46.21 3.96
92 93 7.040617 ACCATGTCTAGATTCATCATGAAATGC 60.041 37.037 17.50 0.00 46.21 3.56
94 95 7.447545 CCACCATGTCTAGATTCATCATGAAAT 59.552 37.037 17.50 0.00 40.12 2.17
95 96 6.769341 CCACCATGTCTAGATTCATCATGAAA 59.231 38.462 17.50 0.00 40.12 2.69
96 97 6.293698 CCACCATGTCTAGATTCATCATGAA 58.706 40.000 17.50 1.59 41.09 2.57
97 98 5.744007 GCCACCATGTCTAGATTCATCATGA 60.744 44.000 17.50 0.00 38.35 3.07
98 99 4.454847 GCCACCATGTCTAGATTCATCATG 59.545 45.833 11.50 11.50 36.60 3.07
99 100 4.350225 AGCCACCATGTCTAGATTCATCAT 59.650 41.667 0.00 0.00 0.00 2.45
100 101 3.713248 AGCCACCATGTCTAGATTCATCA 59.287 43.478 0.00 0.00 0.00 3.07
101 102 4.063689 CAGCCACCATGTCTAGATTCATC 58.936 47.826 0.00 0.00 0.00 2.92
102 103 3.181447 CCAGCCACCATGTCTAGATTCAT 60.181 47.826 0.00 0.00 0.00 2.57
103 104 2.171237 CCAGCCACCATGTCTAGATTCA 59.829 50.000 0.00 0.00 0.00 2.57
104 105 2.486191 CCCAGCCACCATGTCTAGATTC 60.486 54.545 0.00 0.00 0.00 2.52
105 106 1.492176 CCCAGCCACCATGTCTAGATT 59.508 52.381 0.00 0.00 0.00 2.40
106 107 1.135094 CCCAGCCACCATGTCTAGAT 58.865 55.000 0.00 0.00 0.00 1.98
107 108 0.982852 CCCCAGCCACCATGTCTAGA 60.983 60.000 0.00 0.00 0.00 2.43
108 109 1.274703 ACCCCAGCCACCATGTCTAG 61.275 60.000 0.00 0.00 0.00 2.43
109 110 1.229820 ACCCCAGCCACCATGTCTA 60.230 57.895 0.00 0.00 0.00 2.59
110 111 2.532715 ACCCCAGCCACCATGTCT 60.533 61.111 0.00 0.00 0.00 3.41
111 112 2.361610 CACCCCAGCCACCATGTC 60.362 66.667 0.00 0.00 0.00 3.06
112 113 3.185203 ACACCCCAGCCACCATGT 61.185 61.111 0.00 0.00 0.00 3.21
113 114 2.503846 ATCACACCCCAGCCACCATG 62.504 60.000 0.00 0.00 0.00 3.66
114 115 0.918799 TATCACACCCCAGCCACCAT 60.919 55.000 0.00 0.00 0.00 3.55
115 116 0.918799 ATATCACACCCCAGCCACCA 60.919 55.000 0.00 0.00 0.00 4.17
116 117 0.466189 CATATCACACCCCAGCCACC 60.466 60.000 0.00 0.00 0.00 4.61
117 118 1.103398 GCATATCACACCCCAGCCAC 61.103 60.000 0.00 0.00 0.00 5.01
118 119 1.227102 GCATATCACACCCCAGCCA 59.773 57.895 0.00 0.00 0.00 4.75
119 120 1.529244 GGCATATCACACCCCAGCC 60.529 63.158 0.00 0.00 0.00 4.85
120 121 0.178981 ATGGCATATCACACCCCAGC 60.179 55.000 0.00 0.00 0.00 4.85
121 122 1.143481 TCATGGCATATCACACCCCAG 59.857 52.381 0.00 0.00 0.00 4.45
122 123 1.133823 GTCATGGCATATCACACCCCA 60.134 52.381 0.00 0.00 0.00 4.96
123 124 1.143684 AGTCATGGCATATCACACCCC 59.856 52.381 0.00 0.00 0.00 4.95
124 125 2.158769 TGAGTCATGGCATATCACACCC 60.159 50.000 0.00 0.00 0.00 4.61
125 126 3.136763 CTGAGTCATGGCATATCACACC 58.863 50.000 0.00 0.00 0.00 4.16
126 127 4.063998 TCTGAGTCATGGCATATCACAC 57.936 45.455 0.00 0.00 0.00 3.82
127 128 4.968971 ATCTGAGTCATGGCATATCACA 57.031 40.909 0.00 0.59 0.00 3.58
128 129 4.388165 CGAATCTGAGTCATGGCATATCAC 59.612 45.833 0.00 0.00 0.00 3.06
129 130 4.562143 CCGAATCTGAGTCATGGCATATCA 60.562 45.833 0.00 4.39 0.00 2.15
130 131 3.931468 CCGAATCTGAGTCATGGCATATC 59.069 47.826 0.00 0.00 0.00 1.63
131 132 3.580022 TCCGAATCTGAGTCATGGCATAT 59.420 43.478 0.00 0.00 0.00 1.78
132 133 2.965147 TCCGAATCTGAGTCATGGCATA 59.035 45.455 0.00 0.00 0.00 3.14
133 134 1.764723 TCCGAATCTGAGTCATGGCAT 59.235 47.619 0.00 0.00 0.00 4.40
134 135 1.134699 GTCCGAATCTGAGTCATGGCA 60.135 52.381 0.00 0.00 0.00 4.92
135 136 1.134699 TGTCCGAATCTGAGTCATGGC 60.135 52.381 5.91 0.00 0.00 4.40
136 137 2.967599 TGTCCGAATCTGAGTCATGG 57.032 50.000 5.91 0.00 0.00 3.66
137 138 3.181472 TGGATGTCCGAATCTGAGTCATG 60.181 47.826 5.91 0.00 39.43 3.07
138 139 3.033909 TGGATGTCCGAATCTGAGTCAT 58.966 45.455 5.91 0.00 39.43 3.06
139 140 2.456577 TGGATGTCCGAATCTGAGTCA 58.543 47.619 5.91 0.00 39.43 3.41
140 141 3.526931 TTGGATGTCCGAATCTGAGTC 57.473 47.619 0.00 0.00 39.43 3.36
141 142 4.494091 AATTGGATGTCCGAATCTGAGT 57.506 40.909 0.00 0.00 39.43 3.41
142 143 6.895898 CATAAATTGGATGTCCGAATCTGAG 58.104 40.000 0.00 0.00 39.43 3.35
143 144 6.866010 CATAAATTGGATGTCCGAATCTGA 57.134 37.500 0.00 0.00 39.43 3.27
158 159 3.673173 GCCCTGCAGCCATAAATTG 57.327 52.632 8.66 0.00 0.00 2.32
167 168 2.362120 ATTCACTGGCCCTGCAGC 60.362 61.111 8.66 0.00 0.00 5.25
168 169 0.395311 ATCATTCACTGGCCCTGCAG 60.395 55.000 6.78 6.78 0.00 4.41
169 170 0.040058 AATCATTCACTGGCCCTGCA 59.960 50.000 0.00 0.00 0.00 4.41
170 171 1.134907 CAAATCATTCACTGGCCCTGC 60.135 52.381 0.00 0.00 0.00 4.85
171 172 1.479323 CCAAATCATTCACTGGCCCTG 59.521 52.381 0.00 0.00 0.00 4.45
172 173 1.856629 CCAAATCATTCACTGGCCCT 58.143 50.000 0.00 0.00 0.00 5.19
176 177 3.737047 GCATGAGCCAAATCATTCACTGG 60.737 47.826 0.00 0.00 37.84 4.00
177 178 3.444916 GCATGAGCCAAATCATTCACTG 58.555 45.455 0.00 0.00 37.84 3.66
178 179 3.795623 GCATGAGCCAAATCATTCACT 57.204 42.857 0.00 0.00 37.84 3.41
212 213 1.510844 CACGTAAAAGGGCCATGGC 59.489 57.895 29.47 29.47 41.06 4.40
213 214 0.610785 ACCACGTAAAAGGGCCATGG 60.611 55.000 7.63 7.63 0.00 3.66
214 215 1.067915 CAACCACGTAAAAGGGCCATG 60.068 52.381 6.18 0.00 0.00 3.66
215 216 1.253100 CAACCACGTAAAAGGGCCAT 58.747 50.000 6.18 0.00 0.00 4.40
216 217 0.106619 ACAACCACGTAAAAGGGCCA 60.107 50.000 6.18 0.00 0.00 5.36
217 218 1.894881 TACAACCACGTAAAAGGGCC 58.105 50.000 0.00 0.00 0.00 5.80
218 219 3.272439 GTTACAACCACGTAAAAGGGC 57.728 47.619 0.00 0.00 33.31 5.19
230 231 1.003718 AGAGCTGCCGGTTACAACC 60.004 57.895 1.90 0.73 45.76 3.77
231 232 2.162716 CAGAGCTGCCGGTTACAAC 58.837 57.895 1.90 0.00 0.00 3.32
232 233 4.693532 CAGAGCTGCCGGTTACAA 57.306 55.556 1.90 0.00 0.00 2.41
245 246 3.459232 TTCCATTAGATCACGGCAGAG 57.541 47.619 0.00 0.00 0.00 3.35
300 302 5.570320 TCAACATTCCTCCTAGAAAAAGGG 58.430 41.667 0.00 0.00 37.24 3.95
313 321 6.079712 ACTAATTAAGGGCTCAACATTCCT 57.920 37.500 0.00 0.00 0.00 3.36
345 353 6.431543 TGCGGTCCAAATTTTATTGTAGAAGA 59.568 34.615 0.00 0.00 0.00 2.87
365 373 1.202486 ACATTCGTCGGATATTGCGGT 60.202 47.619 0.00 0.00 0.00 5.68
405 413 5.163652 GCCCTGCGTTTATGAAGAAACTATT 60.164 40.000 0.00 0.00 37.20 1.73
417 425 4.535526 AAAGAAATTGCCCTGCGTTTAT 57.464 36.364 0.00 0.00 0.00 1.40
483 491 8.950007 TTTTTCAACTTTACCCCATAGAAGAT 57.050 30.769 0.00 0.00 0.00 2.40
513 521 0.706433 AGGGGATGGCAAGTGAATGT 59.294 50.000 0.00 0.00 0.00 2.71
519 527 0.613012 GCTGAAAGGGGATGGCAAGT 60.613 55.000 0.00 0.00 0.00 3.16
571 584 5.647658 AGCTTGATTTGACATACCAATCGAA 59.352 36.000 0.00 0.00 0.00 3.71
573 586 5.268544 CAGCTTGATTTGACATACCAATCG 58.731 41.667 0.00 0.00 0.00 3.34
594 607 4.559153 CCAAAATAAGTTGTTCCTGCCAG 58.441 43.478 0.00 0.00 0.00 4.85
599 612 3.006859 GGCTGCCAAAATAAGTTGTTCCT 59.993 43.478 15.17 0.00 0.00 3.36
600 613 3.244044 TGGCTGCCAAAATAAGTTGTTCC 60.244 43.478 21.08 0.00 0.00 3.62
601 614 3.988819 TGGCTGCCAAAATAAGTTGTTC 58.011 40.909 21.08 0.00 0.00 3.18
602 615 4.568956 GATGGCTGCCAAAATAAGTTGTT 58.431 39.130 27.24 3.77 36.95 2.83
603 616 3.367292 CGATGGCTGCCAAAATAAGTTGT 60.367 43.478 27.24 4.38 36.95 3.32
604 617 3.119531 TCGATGGCTGCCAAAATAAGTTG 60.120 43.478 27.24 11.18 36.95 3.16
605 618 3.088532 TCGATGGCTGCCAAAATAAGTT 58.911 40.909 27.24 6.10 36.95 2.66
606 619 2.722094 TCGATGGCTGCCAAAATAAGT 58.278 42.857 27.24 6.97 36.95 2.24
607 620 3.996150 ATCGATGGCTGCCAAAATAAG 57.004 42.857 27.24 12.91 36.95 1.73
608 621 4.261572 GCTTATCGATGGCTGCCAAAATAA 60.262 41.667 27.24 23.77 36.95 1.40
609 622 3.253188 GCTTATCGATGGCTGCCAAAATA 59.747 43.478 27.24 18.93 36.95 1.40
610 623 2.035066 GCTTATCGATGGCTGCCAAAAT 59.965 45.455 27.24 19.92 36.95 1.82
611 624 1.405105 GCTTATCGATGGCTGCCAAAA 59.595 47.619 27.24 14.21 36.95 2.44
655 668 0.835941 ACTGATCTGATCTGCCCCAC 59.164 55.000 20.34 0.00 0.00 4.61
679 692 3.513515 AGGAAGAAGAACAGCTACTGGAG 59.486 47.826 0.00 0.00 35.51 3.86
689 702 2.299297 GGACGGAGAAGGAAGAAGAACA 59.701 50.000 0.00 0.00 0.00 3.18
754 767 1.944177 AGCCCACTGTCTGTCTGTAT 58.056 50.000 0.00 0.00 0.00 2.29
824 855 6.539324 TGTTTATTGGCGAAGTTTATTCTCG 58.461 36.000 0.00 0.00 0.00 4.04
836 867 5.310451 AGAACTAACCTTGTTTATTGGCGA 58.690 37.500 0.00 0.00 0.00 5.54
837 868 5.622770 AGAACTAACCTTGTTTATTGGCG 57.377 39.130 0.00 0.00 0.00 5.69
838 869 5.633601 GCAAGAACTAACCTTGTTTATTGGC 59.366 40.000 0.00 0.00 42.11 4.52
927 971 0.107945 GCGCTGAGAGTGGGAAGAAT 60.108 55.000 0.00 0.00 0.00 2.40
1248 1325 4.141711 TGGGAAAACAAGAGAGATATCCCG 60.142 45.833 0.00 0.00 46.69 5.14
1318 3313 1.410004 TCCAGGTCAACGTTGAGACT 58.590 50.000 30.38 26.03 37.98 3.24
1407 3583 3.985279 TGAAACGAAGAGTACCAACGATG 59.015 43.478 0.00 0.00 0.00 3.84
1529 3911 9.657419 AAACTTAAACATTGATCCAATCCAATC 57.343 29.630 0.00 0.00 31.05 2.67
1531 3913 7.812191 CGAAACTTAAACATTGATCCAATCCAA 59.188 33.333 0.00 0.00 31.05 3.53
1533 3915 7.273381 CACGAAACTTAAACATTGATCCAATCC 59.727 37.037 0.00 0.00 31.05 3.01
1547 3929 1.874872 CGGGAAGCCACGAAACTTAAA 59.125 47.619 0.00 0.00 0.00 1.52
1557 3939 3.959991 GAGGAGCACGGGAAGCCAC 62.960 68.421 0.00 0.00 0.00 5.01
1586 3968 7.047891 AGTATTTTTATCAATGAGGAGCGACA 58.952 34.615 0.00 0.00 0.00 4.35
1601 3983 8.830580 CGATCTCCACATGACAAGTATTTTTAT 58.169 33.333 0.00 0.00 0.00 1.40
1604 3986 5.065218 GCGATCTCCACATGACAAGTATTTT 59.935 40.000 0.00 0.00 0.00 1.82
1647 4029 0.558712 ACTTTGGGTGGGGTAAGCAA 59.441 50.000 0.00 0.00 0.00 3.91
1664 4046 4.870426 CACAACATGATCTAAACGCCTACT 59.130 41.667 0.00 0.00 0.00 2.57
1670 4052 4.436050 GGCTCACACAACATGATCTAAACG 60.436 45.833 0.00 0.00 0.00 3.60
1671 4053 4.142600 GGGCTCACACAACATGATCTAAAC 60.143 45.833 0.00 0.00 0.00 2.01
1687 4069 5.385509 TGTTAGCAAATTTAAGGGCTCAC 57.614 39.130 4.18 5.15 37.79 3.51
1704 4086 9.793259 ATCCAAATTGTACCCTATGTATGTTAG 57.207 33.333 0.00 0.00 0.00 2.34
1739 4121 9.926158 TGTGAATGCTTTGATTAATTGTTACAT 57.074 25.926 0.00 0.00 0.00 2.29
1804 4186 7.615365 AGAGGCAATTCATAAACTTCCATGTTA 59.385 33.333 0.00 0.00 0.00 2.41
1805 4187 6.438425 AGAGGCAATTCATAAACTTCCATGTT 59.562 34.615 0.00 0.00 0.00 2.71
1969 4354 0.242017 ACAAGTACGCGGTAGGTCAC 59.758 55.000 12.47 0.00 0.00 3.67
1974 4359 2.342910 ACAAGACAAGTACGCGGTAG 57.657 50.000 12.47 0.00 0.00 3.18
2037 4543 6.710295 ACAATTTTGCTCACAGTGTATAGTCA 59.290 34.615 0.00 0.00 0.00 3.41
2176 4725 7.880160 TTCTTTCTCCTTTCATCTGTTTCAA 57.120 32.000 0.00 0.00 0.00 2.69
2860 5453 4.881850 AGAACAACCAAGAGTGTTTACCTG 59.118 41.667 0.00 0.00 0.00 4.00
2924 5531 9.382244 CAAAATGCACTACAAAACTTAGTAGAC 57.618 33.333 6.60 0.06 40.02 2.59
3050 5660 6.428385 AGTGAAAACAAGAGAGTGTTGAAG 57.572 37.500 0.00 0.00 40.86 3.02
3255 5870 4.276926 CAGAATCTGTTTAATAGCAGGGGC 59.723 45.833 1.31 0.00 41.61 5.80
3373 5997 8.106462 TGACATTCTCATTCTTTATACAACCCA 58.894 33.333 0.00 0.00 0.00 4.51
3955 6927 4.267928 GTCGTTGCTAGCAAGGTGTTATAG 59.732 45.833 36.01 18.12 41.08 1.31
3960 6932 0.393077 AGTCGTTGCTAGCAAGGTGT 59.607 50.000 36.01 25.99 41.08 4.16
4038 7033 2.240279 ACCTCAAGCTTGACGACTACT 58.760 47.619 25.16 2.63 32.90 2.57
4041 7036 2.490115 CTCTACCTCAAGCTTGACGACT 59.510 50.000 25.16 9.07 32.90 4.18
4270 7271 4.720902 CCAGCACCGGCCATCACA 62.721 66.667 0.00 0.00 42.56 3.58
4355 7371 1.639298 GACACTGATTCCGGCAGCAC 61.639 60.000 7.41 0.00 36.86 4.40
4433 7467 1.153353 GTCGAAGATGAAACCGCCAA 58.847 50.000 0.00 0.00 40.67 4.52
4469 7509 0.968901 TCCCCGTTACTGATCGTGCT 60.969 55.000 1.23 0.00 0.00 4.40
4478 7518 1.623542 GGTGGCATCTCCCCGTTACT 61.624 60.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.