Multiple sequence alignment - TraesCS5B01G539800

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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 TraesCS5B01G539800 chr5B 100.000 7118 0 0 1 7118 695479440 695486557 0.000000e+00 13145.0
1 TraesCS5B01G539800 chr5B 97.692 3510 81 0 2810 6319 695787032 695790541 0.000000e+00 6034.0
2 TraesCS5B01G539800 chr5B 96.708 2035 44 11 801 2831 695785009 695787024 0.000000e+00 3365.0
3 TraesCS5B01G539800 chr5B 86.493 2643 338 15 3086 5713 711134023 711131385 0.000000e+00 2885.0
4 TraesCS5B01G539800 chr5B 87.162 2516 314 7 3225 5735 711183846 711181335 0.000000e+00 2848.0
5 TraesCS5B01G539800 chr5B 86.920 2500 304 20 3086 5568 711241024 711238531 0.000000e+00 2784.0
6 TraesCS5B01G539800 chr5B 83.872 2815 428 22 3202 6000 710962997 710960193 0.000000e+00 2660.0
7 TraesCS5B01G539800 chr5B 86.282 1560 173 21 1506 3036 711136910 711135363 0.000000e+00 1657.0
8 TraesCS5B01G539800 chr5B 87.912 1365 148 12 1386 2746 711941158 711942509 0.000000e+00 1591.0
9 TraesCS5B01G539800 chr5B 85.591 1388 174 19 1534 2908 711915202 711913828 0.000000e+00 1432.0
10 TraesCS5B01G539800 chr5B 81.250 912 160 10 5095 6000 712378809 712379715 0.000000e+00 726.0
11 TraesCS5B01G539800 chr5B 83.306 611 100 2 5510 6119 643325345 643324736 4.820000e-156 562.0
12 TraesCS5B01G539800 chr5B 80.357 616 113 5 5540 6152 711946426 711947036 1.810000e-125 460.0
13 TraesCS5B01G539800 chr5B 82.520 492 84 2 5510 6000 643335016 643334526 1.420000e-116 431.0
14 TraesCS5B01G539800 chr5B 81.874 491 89 0 5510 6000 643334872 643334382 1.430000e-111 414.0
15 TraesCS5B01G539800 chr5B 85.934 391 46 6 927 1316 711940747 711941129 6.650000e-110 409.0
16 TraesCS5B01G539800 chr5B 96.234 239 8 1 6880 7118 695791260 695791497 2.410000e-104 390.0
17 TraesCS5B01G539800 chr5B 84.478 335 52 0 996 1330 710965355 710965021 1.480000e-86 331.0
18 TraesCS5B01G539800 chr5B 96.629 89 3 0 6318 6406 695791126 695791214 1.600000e-31 148.0
19 TraesCS5B01G539800 chr5B 91.919 99 2 2 711 804 695784876 695784973 4.480000e-27 134.0
20 TraesCS5B01G539800 chr5B 86.066 122 7 4 169 281 695784553 695784673 9.700000e-24 122.0
21 TraesCS5B01G539800 chr5D 96.856 2926 91 1 3394 6319 555429230 555426306 0.000000e+00 4892.0
22 TraesCS5B01G539800 chr5D 96.078 2601 93 6 801 3398 555434286 555431692 0.000000e+00 4229.0
23 TraesCS5B01G539800 chr5D 85.813 2904 367 27 3092 5985 560534879 560532011 0.000000e+00 3038.0
24 TraesCS5B01G539800 chr5D 85.491 1537 184 22 1495 2995 560496850 560498383 0.000000e+00 1567.0
25 TraesCS5B01G539800 chr5D 87.779 1301 143 12 1429 2725 561950473 561951761 0.000000e+00 1507.0
26 TraesCS5B01G539800 chr5D 91.273 825 40 12 6319 7118 555425509 555424692 0.000000e+00 1096.0
27 TraesCS5B01G539800 chr5D 94.393 535 23 3 272 804 555434851 555434322 0.000000e+00 815.0
28 TraesCS5B01G539800 chr5D 85.392 664 73 16 927 1589 552854685 552854045 0.000000e+00 667.0
29 TraesCS5B01G539800 chr5D 86.255 502 54 11 927 1426 561949858 561950346 1.360000e-146 531.0
30 TraesCS5B01G539800 chr5D 84.783 414 35 9 6469 6873 555446761 555446367 2.410000e-104 390.0
31 TraesCS5B01G539800 chr5D 89.362 141 14 1 6329 6469 555446930 555446791 7.340000e-40 176.0
32 TraesCS5B01G539800 chr5D 91.176 68 5 1 833 899 561647100 561647033 2.730000e-14 91.6
33 TraesCS5B01G539800 chr7A 86.569 2658 346 9 3206 5856 688997494 688994841 0.000000e+00 2920.0
34 TraesCS5B01G539800 chr7A 85.642 1574 185 31 1519 3069 689000065 688998510 0.000000e+00 1616.0
35 TraesCS5B01G539800 chr7B 87.055 2557 321 9 3162 5712 1322925 1325477 0.000000e+00 2880.0
36 TraesCS5B01G539800 chr7B 83.772 2052 242 50 1053 3069 1313278 1315273 0.000000e+00 1860.0
37 TraesCS5B01G539800 chr4A 86.050 1534 178 21 1495 2995 603675434 603676964 0.000000e+00 1615.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5B01G539800 chr5B 695479440 695486557 7117 False 13145.000000 13145 100.000000 1 7118 1 chr5B.!!$F1 7117
1 TraesCS5B01G539800 chr5B 711181335 711183846 2511 True 2848.000000 2848 87.162000 3225 5735 1 chr5B.!!$R2 2510
2 TraesCS5B01G539800 chr5B 711238531 711241024 2493 True 2784.000000 2784 86.920000 3086 5568 1 chr5B.!!$R3 2482
3 TraesCS5B01G539800 chr5B 711131385 711136910 5525 True 2271.000000 2885 86.387500 1506 5713 2 chr5B.!!$R7 4207
4 TraesCS5B01G539800 chr5B 695784553 695791497 6944 False 1698.833333 6034 94.208000 169 7118 6 chr5B.!!$F3 6949
5 TraesCS5B01G539800 chr5B 710960193 710965355 5162 True 1495.500000 2660 84.175000 996 6000 2 chr5B.!!$R6 5004
6 TraesCS5B01G539800 chr5B 711913828 711915202 1374 True 1432.000000 1432 85.591000 1534 2908 1 chr5B.!!$R4 1374
7 TraesCS5B01G539800 chr5B 711940747 711947036 6289 False 820.000000 1591 84.734333 927 6152 3 chr5B.!!$F4 5225
8 TraesCS5B01G539800 chr5B 712378809 712379715 906 False 726.000000 726 81.250000 5095 6000 1 chr5B.!!$F2 905
9 TraesCS5B01G539800 chr5B 643324736 643325345 609 True 562.000000 562 83.306000 5510 6119 1 chr5B.!!$R1 609
10 TraesCS5B01G539800 chr5B 643334382 643335016 634 True 422.500000 431 82.197000 5510 6000 2 chr5B.!!$R5 490
11 TraesCS5B01G539800 chr5D 560532011 560534879 2868 True 3038.000000 3038 85.813000 3092 5985 1 chr5D.!!$R2 2893
12 TraesCS5B01G539800 chr5D 555424692 555434851 10159 True 2758.000000 4892 94.650000 272 7118 4 chr5D.!!$R4 6846
13 TraesCS5B01G539800 chr5D 560496850 560498383 1533 False 1567.000000 1567 85.491000 1495 2995 1 chr5D.!!$F1 1500
14 TraesCS5B01G539800 chr5D 561949858 561951761 1903 False 1019.000000 1507 87.017000 927 2725 2 chr5D.!!$F2 1798
15 TraesCS5B01G539800 chr5D 552854045 552854685 640 True 667.000000 667 85.392000 927 1589 1 chr5D.!!$R1 662
16 TraesCS5B01G539800 chr5D 555446367 555446930 563 True 283.000000 390 87.072500 6329 6873 2 chr5D.!!$R5 544
17 TraesCS5B01G539800 chr7A 688994841 689000065 5224 True 2268.000000 2920 86.105500 1519 5856 2 chr7A.!!$R1 4337
18 TraesCS5B01G539800 chr7B 1322925 1325477 2552 False 2880.000000 2880 87.055000 3162 5712 1 chr7B.!!$F2 2550
19 TraesCS5B01G539800 chr7B 1313278 1315273 1995 False 1860.000000 1860 83.772000 1053 3069 1 chr7B.!!$F1 2016
20 TraesCS5B01G539800 chr4A 603675434 603676964 1530 False 1615.000000 1615 86.050000 1495 2995 1 chr4A.!!$F1 1500

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
116 117 0.033920 GCTTTCAACTTTGGGGCCTG 59.966 55.000 0.84 0.00 0.00 4.85 F
122 123 0.105504 AACTTTGGGGCCTGCTTCTT 60.106 50.000 0.84 0.00 0.00 2.52 F
154 155 0.411058 AAAGGGGCCAAGCATTCTCT 59.589 50.000 4.39 0.00 0.00 3.10 F
155 156 0.411058 AAGGGGCCAAGCATTCTCTT 59.589 50.000 4.39 0.00 0.00 2.85 F
818 873 0.614812 GCAAAATGGACCAGGCCAAT 59.385 50.000 5.01 0.00 42.16 3.16 F
2185 2528 0.813821 ACCCGAAACCTACGAGTAGC 59.186 55.000 4.81 0.00 31.95 3.58 F
2640 2984 7.009260 GCAATGGAATGCTCTTGGATACATTC 61.009 42.308 6.11 6.11 45.02 2.67 F
3830 8696 8.721133 TGCTATTTGGATCTATCTGGTAGTAA 57.279 34.615 0.00 0.00 0.00 2.24 F
4825 9691 0.106819 GGACAGGCTCGTACCTCCTA 60.107 60.000 0.00 0.00 38.26 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1028 1087 0.243636 GATTTGTTTCCCCACGGCAG 59.756 55.000 0.00 0.0 0.00 4.85 R
1589 1908 2.727123 TGTGGGGCATGATTATTCGT 57.273 45.000 0.00 0.0 0.00 3.85 R
1728 2047 5.065859 CAGTTTTCGTGCCATCACCATAATA 59.934 40.000 0.00 0.0 40.04 0.98 R
1943 2271 7.334090 TCCCAATTTTGTTCAAATCAAACTGA 58.666 30.769 0.00 0.0 33.60 3.41 R
2640 2984 0.392863 TGACCATCGTGCCTGGAATG 60.393 55.000 0.00 0.0 37.22 2.67 R
3830 8696 2.630580 GCAGGTAGCTTACTGAGGCTAT 59.369 50.000 18.30 0.0 42.01 2.97 R
4080 8946 3.326747 GTTCAGATGCTCTAAACACGGT 58.673 45.455 0.00 0.0 0.00 4.83 R
5247 10113 0.886490 CTCGCTCTGGCAAAACTGGT 60.886 55.000 0.00 0.0 38.60 4.00 R
6272 11856 0.927029 TACCTCCTCTGCAGCTCCTA 59.073 55.000 9.47 0.0 0.00 2.94 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
19 20 0.988439 CTTTCTCTCTCTCAACGCGC 59.012 55.000 5.73 0.00 0.00 6.86
20 21 0.598562 TTTCTCTCTCTCAACGCGCT 59.401 50.000 5.73 0.00 0.00 5.92
21 22 0.169230 TTCTCTCTCTCAACGCGCTC 59.831 55.000 5.73 0.00 0.00 5.03
22 23 0.675208 TCTCTCTCTCAACGCGCTCT 60.675 55.000 5.73 0.00 0.00 4.09
23 24 0.248054 CTCTCTCTCAACGCGCTCTC 60.248 60.000 5.73 0.00 0.00 3.20
24 25 0.675208 TCTCTCTCAACGCGCTCTCT 60.675 55.000 5.73 0.00 0.00 3.10
25 26 0.248054 CTCTCTCAACGCGCTCTCTC 60.248 60.000 5.73 0.00 0.00 3.20
26 27 0.675208 TCTCTCAACGCGCTCTCTCT 60.675 55.000 5.73 0.00 0.00 3.10
27 28 0.170116 CTCTCAACGCGCTCTCTCTT 59.830 55.000 5.73 0.00 0.00 2.85
28 29 0.598562 TCTCAACGCGCTCTCTCTTT 59.401 50.000 5.73 0.00 0.00 2.52
29 30 0.988439 CTCAACGCGCTCTCTCTTTC 59.012 55.000 5.73 0.00 0.00 2.62
30 31 0.598562 TCAACGCGCTCTCTCTTTCT 59.401 50.000 5.73 0.00 0.00 2.52
31 32 0.988439 CAACGCGCTCTCTCTTTCTC 59.012 55.000 5.73 0.00 0.00 2.87
32 33 0.885196 AACGCGCTCTCTCTTTCTCT 59.115 50.000 5.73 0.00 0.00 3.10
33 34 0.450184 ACGCGCTCTCTCTTTCTCTC 59.550 55.000 5.73 0.00 0.00 3.20
34 35 0.732571 CGCGCTCTCTCTTTCTCTCT 59.267 55.000 5.56 0.00 0.00 3.10
35 36 1.268032 CGCGCTCTCTCTTTCTCTCTC 60.268 57.143 5.56 0.00 0.00 3.20
36 37 1.742831 GCGCTCTCTCTTTCTCTCTCA 59.257 52.381 0.00 0.00 0.00 3.27
37 38 2.358898 GCGCTCTCTCTTTCTCTCTCAT 59.641 50.000 0.00 0.00 0.00 2.90
38 39 3.793129 GCGCTCTCTCTTTCTCTCTCATG 60.793 52.174 0.00 0.00 0.00 3.07
39 40 3.378112 CGCTCTCTCTTTCTCTCTCATGT 59.622 47.826 0.00 0.00 0.00 3.21
40 41 4.675510 GCTCTCTCTTTCTCTCTCATGTG 58.324 47.826 0.00 0.00 0.00 3.21
41 42 4.440525 GCTCTCTCTTTCTCTCTCATGTGG 60.441 50.000 0.00 0.00 0.00 4.17
42 43 4.671831 TCTCTCTTTCTCTCTCATGTGGT 58.328 43.478 0.00 0.00 0.00 4.16
43 44 5.083122 TCTCTCTTTCTCTCTCATGTGGTT 58.917 41.667 0.00 0.00 0.00 3.67
44 45 5.541868 TCTCTCTTTCTCTCTCATGTGGTTT 59.458 40.000 0.00 0.00 0.00 3.27
45 46 6.042552 TCTCTCTTTCTCTCTCATGTGGTTTT 59.957 38.462 0.00 0.00 0.00 2.43
46 47 7.233553 TCTCTCTTTCTCTCTCATGTGGTTTTA 59.766 37.037 0.00 0.00 0.00 1.52
47 48 7.735917 TCTCTTTCTCTCTCATGTGGTTTTAA 58.264 34.615 0.00 0.00 0.00 1.52
48 49 7.657761 TCTCTTTCTCTCTCATGTGGTTTTAAC 59.342 37.037 0.00 0.00 0.00 2.01
49 50 7.509546 TCTTTCTCTCTCATGTGGTTTTAACT 58.490 34.615 0.00 0.00 0.00 2.24
50 51 7.657761 TCTTTCTCTCTCATGTGGTTTTAACTC 59.342 37.037 0.00 0.00 0.00 3.01
51 52 6.419484 TCTCTCTCATGTGGTTTTAACTCA 57.581 37.500 0.00 0.00 0.00 3.41
52 53 6.826668 TCTCTCTCATGTGGTTTTAACTCAA 58.173 36.000 0.00 0.00 0.00 3.02
53 54 7.453393 TCTCTCTCATGTGGTTTTAACTCAAT 58.547 34.615 0.00 0.00 0.00 2.57
54 55 7.604164 TCTCTCTCATGTGGTTTTAACTCAATC 59.396 37.037 0.00 0.00 0.00 2.67
55 56 7.223584 TCTCTCATGTGGTTTTAACTCAATCA 58.776 34.615 0.00 0.00 0.00 2.57
56 57 7.388776 TCTCTCATGTGGTTTTAACTCAATCAG 59.611 37.037 0.00 0.00 0.00 2.90
57 58 7.223584 TCTCATGTGGTTTTAACTCAATCAGA 58.776 34.615 0.00 0.00 0.00 3.27
58 59 7.884877 TCTCATGTGGTTTTAACTCAATCAGAT 59.115 33.333 0.00 0.00 0.00 2.90
59 60 8.044060 TCATGTGGTTTTAACTCAATCAGATC 57.956 34.615 0.00 0.00 0.00 2.75
60 61 7.665145 TCATGTGGTTTTAACTCAATCAGATCA 59.335 33.333 0.00 0.00 0.00 2.92
61 62 7.815840 TGTGGTTTTAACTCAATCAGATCAA 57.184 32.000 0.00 0.00 0.00 2.57
62 63 8.408043 TGTGGTTTTAACTCAATCAGATCAAT 57.592 30.769 0.00 0.00 0.00 2.57
63 64 8.514594 TGTGGTTTTAACTCAATCAGATCAATC 58.485 33.333 0.00 0.00 0.00 2.67
64 65 8.514594 GTGGTTTTAACTCAATCAGATCAATCA 58.485 33.333 0.00 0.00 0.00 2.57
65 66 8.733458 TGGTTTTAACTCAATCAGATCAATCAG 58.267 33.333 0.00 0.00 0.00 2.90
66 67 8.186821 GGTTTTAACTCAATCAGATCAATCAGG 58.813 37.037 0.00 0.00 0.00 3.86
67 68 7.870509 TTTAACTCAATCAGATCAATCAGGG 57.129 36.000 0.00 0.00 0.00 4.45
68 69 5.705397 AACTCAATCAGATCAATCAGGGA 57.295 39.130 0.00 0.00 0.00 4.20
69 70 5.908562 ACTCAATCAGATCAATCAGGGAT 57.091 39.130 0.00 0.00 0.00 3.85
70 71 6.263412 ACTCAATCAGATCAATCAGGGATT 57.737 37.500 0.00 0.00 31.86 3.01
71 72 7.384524 ACTCAATCAGATCAATCAGGGATTA 57.615 36.000 0.00 0.00 30.44 1.75
72 73 7.809238 ACTCAATCAGATCAATCAGGGATTAA 58.191 34.615 0.00 0.00 30.44 1.40
73 74 8.446394 ACTCAATCAGATCAATCAGGGATTAAT 58.554 33.333 0.00 0.00 30.44 1.40
74 75 9.298250 CTCAATCAGATCAATCAGGGATTAATT 57.702 33.333 0.00 0.00 30.44 1.40
75 76 9.293404 TCAATCAGATCAATCAGGGATTAATTC 57.707 33.333 0.00 0.00 30.44 2.17
76 77 7.918536 ATCAGATCAATCAGGGATTAATTCG 57.081 36.000 0.00 0.00 30.44 3.34
77 78 6.830912 TCAGATCAATCAGGGATTAATTCGT 58.169 36.000 0.00 0.00 30.44 3.85
78 79 6.931281 TCAGATCAATCAGGGATTAATTCGTC 59.069 38.462 0.00 0.00 30.44 4.20
79 80 6.707608 CAGATCAATCAGGGATTAATTCGTCA 59.292 38.462 0.00 0.00 30.44 4.35
80 81 6.933521 AGATCAATCAGGGATTAATTCGTCAG 59.066 38.462 0.00 0.00 30.44 3.51
81 82 5.989477 TCAATCAGGGATTAATTCGTCAGT 58.011 37.500 0.00 0.00 30.44 3.41
82 83 5.817296 TCAATCAGGGATTAATTCGTCAGTG 59.183 40.000 0.00 0.00 30.44 3.66
83 84 4.137116 TCAGGGATTAATTCGTCAGTGG 57.863 45.455 0.00 0.00 0.00 4.00
84 85 3.517901 TCAGGGATTAATTCGTCAGTGGT 59.482 43.478 0.00 0.00 0.00 4.16
85 86 4.712829 TCAGGGATTAATTCGTCAGTGGTA 59.287 41.667 0.00 0.00 0.00 3.25
86 87 5.050490 CAGGGATTAATTCGTCAGTGGTAG 58.950 45.833 0.00 0.00 0.00 3.18
87 88 3.808174 GGGATTAATTCGTCAGTGGTAGC 59.192 47.826 0.00 0.00 0.00 3.58
88 89 4.439057 GGATTAATTCGTCAGTGGTAGCA 58.561 43.478 0.00 0.00 0.00 3.49
89 90 4.873827 GGATTAATTCGTCAGTGGTAGCAA 59.126 41.667 0.00 0.00 0.00 3.91
90 91 5.527582 GGATTAATTCGTCAGTGGTAGCAAT 59.472 40.000 0.00 0.00 0.00 3.56
91 92 6.038271 GGATTAATTCGTCAGTGGTAGCAATT 59.962 38.462 0.00 0.00 0.00 2.32
92 93 6.811253 TTAATTCGTCAGTGGTAGCAATTT 57.189 33.333 0.00 0.00 0.00 1.82
93 94 4.685169 ATTCGTCAGTGGTAGCAATTTG 57.315 40.909 0.00 0.00 0.00 2.32
94 95 3.394674 TCGTCAGTGGTAGCAATTTGA 57.605 42.857 0.00 0.00 0.00 2.69
95 96 3.325870 TCGTCAGTGGTAGCAATTTGAG 58.674 45.455 0.00 0.00 0.00 3.02
96 97 3.067106 CGTCAGTGGTAGCAATTTGAGT 58.933 45.455 0.00 0.00 0.00 3.41
97 98 3.120546 CGTCAGTGGTAGCAATTTGAGTG 60.121 47.826 0.00 0.00 0.00 3.51
98 99 2.813754 TCAGTGGTAGCAATTTGAGTGC 59.186 45.455 0.00 0.00 42.55 4.40
108 109 5.723492 GCAATTTGAGTGCTTTCAACTTT 57.277 34.783 0.00 0.00 36.84 2.66
109 110 5.495502 GCAATTTGAGTGCTTTCAACTTTG 58.504 37.500 0.00 14.44 36.84 2.77
110 111 5.502869 GCAATTTGAGTGCTTTCAACTTTGG 60.503 40.000 17.37 6.99 36.84 3.28
111 112 3.799281 TTGAGTGCTTTCAACTTTGGG 57.201 42.857 0.20 0.00 32.39 4.12
112 113 2.031120 TGAGTGCTTTCAACTTTGGGG 58.969 47.619 0.00 0.00 0.00 4.96
113 114 0.752658 AGTGCTTTCAACTTTGGGGC 59.247 50.000 0.00 0.00 0.00 5.80
114 115 0.249868 GTGCTTTCAACTTTGGGGCC 60.250 55.000 0.00 0.00 0.00 5.80
115 116 0.398381 TGCTTTCAACTTTGGGGCCT 60.398 50.000 0.84 0.00 0.00 5.19
116 117 0.033920 GCTTTCAACTTTGGGGCCTG 59.966 55.000 0.84 0.00 0.00 4.85
117 118 0.033920 CTTTCAACTTTGGGGCCTGC 59.966 55.000 0.84 0.00 0.00 4.85
118 119 0.398381 TTTCAACTTTGGGGCCTGCT 60.398 50.000 0.84 0.00 0.00 4.24
119 120 0.398381 TTCAACTTTGGGGCCTGCTT 60.398 50.000 0.84 0.00 0.00 3.91
120 121 0.827507 TCAACTTTGGGGCCTGCTTC 60.828 55.000 0.84 0.00 0.00 3.86
121 122 0.829182 CAACTTTGGGGCCTGCTTCT 60.829 55.000 0.84 0.00 0.00 2.85
122 123 0.105504 AACTTTGGGGCCTGCTTCTT 60.106 50.000 0.84 0.00 0.00 2.52
123 124 0.829182 ACTTTGGGGCCTGCTTCTTG 60.829 55.000 0.84 0.00 0.00 3.02
124 125 2.163601 CTTTGGGGCCTGCTTCTTGC 62.164 60.000 0.84 0.00 43.25 4.01
125 126 4.684134 TGGGGCCTGCTTCTTGCC 62.684 66.667 0.84 0.00 44.59 4.52
128 129 4.684134 GGCCTGCTTCTTGCCCCA 62.684 66.667 0.00 0.00 42.00 4.96
129 130 2.601367 GCCTGCTTCTTGCCCCAA 60.601 61.111 0.00 0.00 42.00 4.12
130 131 2.643232 GCCTGCTTCTTGCCCCAAG 61.643 63.158 0.00 0.00 42.25 3.61
131 132 1.075482 CCTGCTTCTTGCCCCAAGA 59.925 57.895 3.69 3.69 46.93 3.02
140 141 3.440127 TCTTGCCCCAAGAAATAAAGGG 58.560 45.455 5.26 0.00 45.84 3.95
144 145 2.246091 CCCAAGAAATAAAGGGGCCA 57.754 50.000 4.39 0.00 37.66 5.36
145 146 2.545810 CCCAAGAAATAAAGGGGCCAA 58.454 47.619 4.39 0.00 37.66 4.52
146 147 2.501316 CCCAAGAAATAAAGGGGCCAAG 59.499 50.000 4.39 0.00 37.66 3.61
147 148 2.093500 CCAAGAAATAAAGGGGCCAAGC 60.093 50.000 4.39 0.00 0.00 4.01
148 149 2.566724 CAAGAAATAAAGGGGCCAAGCA 59.433 45.455 4.39 0.00 0.00 3.91
149 150 3.120468 AGAAATAAAGGGGCCAAGCAT 57.880 42.857 4.39 0.00 0.00 3.79
150 151 3.453868 AGAAATAAAGGGGCCAAGCATT 58.546 40.909 4.39 0.00 0.00 3.56
151 152 3.452264 AGAAATAAAGGGGCCAAGCATTC 59.548 43.478 4.39 2.44 0.00 2.67
152 153 2.854736 ATAAAGGGGCCAAGCATTCT 57.145 45.000 4.39 0.00 0.00 2.40
153 154 2.143876 TAAAGGGGCCAAGCATTCTC 57.856 50.000 4.39 0.00 0.00 2.87
154 155 0.411058 AAAGGGGCCAAGCATTCTCT 59.589 50.000 4.39 0.00 0.00 3.10
155 156 0.411058 AAGGGGCCAAGCATTCTCTT 59.589 50.000 4.39 0.00 0.00 2.85
156 157 0.411058 AGGGGCCAAGCATTCTCTTT 59.589 50.000 4.39 0.00 0.00 2.52
157 158 0.820226 GGGGCCAAGCATTCTCTTTC 59.180 55.000 4.39 0.00 0.00 2.62
158 159 1.618074 GGGGCCAAGCATTCTCTTTCT 60.618 52.381 4.39 0.00 0.00 2.52
159 160 1.475682 GGGCCAAGCATTCTCTTTCTG 59.524 52.381 4.39 0.00 0.00 3.02
160 161 2.165998 GGCCAAGCATTCTCTTTCTGT 58.834 47.619 0.00 0.00 0.00 3.41
161 162 2.560105 GGCCAAGCATTCTCTTTCTGTT 59.440 45.455 0.00 0.00 0.00 3.16
162 163 3.758554 GGCCAAGCATTCTCTTTCTGTTA 59.241 43.478 0.00 0.00 0.00 2.41
163 164 4.379918 GGCCAAGCATTCTCTTTCTGTTAC 60.380 45.833 0.00 0.00 0.00 2.50
164 165 4.457257 GCCAAGCATTCTCTTTCTGTTACT 59.543 41.667 0.00 0.00 0.00 2.24
165 166 5.618640 GCCAAGCATTCTCTTTCTGTTACTG 60.619 44.000 0.00 0.00 0.00 2.74
166 167 5.388944 CAAGCATTCTCTTTCTGTTACTGC 58.611 41.667 0.00 0.00 0.00 4.40
167 168 4.904241 AGCATTCTCTTTCTGTTACTGCT 58.096 39.130 0.00 0.00 32.92 4.24
181 182 8.677148 TCTGTTACTGCTTCTGTTAAATCTTT 57.323 30.769 0.00 0.00 0.00 2.52
183 184 8.445275 TGTTACTGCTTCTGTTAAATCTTTCA 57.555 30.769 0.00 0.00 0.00 2.69
199 200 4.096681 TCTTTCATACCTCTTGCCTCTCA 58.903 43.478 0.00 0.00 0.00 3.27
216 217 4.217118 CCTCTCATGTTTCTTTCAGTTGGG 59.783 45.833 0.00 0.00 0.00 4.12
217 218 5.047566 TCTCATGTTTCTTTCAGTTGGGA 57.952 39.130 0.00 0.00 0.00 4.37
218 219 5.065914 TCTCATGTTTCTTTCAGTTGGGAG 58.934 41.667 0.00 0.00 0.00 4.30
224 229 3.228188 TCTTTCAGTTGGGAGTTGCAT 57.772 42.857 0.00 0.00 0.00 3.96
263 272 2.093890 TGCAGCAGGACATTATTGGTG 58.906 47.619 0.00 0.00 41.78 4.17
274 283 7.331687 CAGGACATTATTGGTGCCTTTTTAAAG 59.668 37.037 0.00 0.00 35.79 1.85
286 295 4.991153 CTTTTTAAAGGATCTGGGAGCC 57.009 45.455 0.00 0.00 38.56 4.70
304 313 2.171003 GCCAGCATATTTATGGGGGAC 58.829 52.381 0.10 0.00 34.52 4.46
423 434 1.413445 CAGCTCAGGAGGGAAGAGATG 59.587 57.143 0.00 0.00 39.10 2.90
520 531 6.074409 TGTTGTGCATCGAAAATGAAATCAAC 60.074 34.615 0.00 0.00 0.00 3.18
528 539 5.237561 TCGAAAATGAAATCAACTGGTTCGA 59.762 36.000 12.06 12.06 41.20 3.71
582 593 6.683974 GCTTTAAGCATGATAGTGAAAGGA 57.316 37.500 12.54 0.00 41.89 3.36
600 611 1.541015 GGAGCACATCACACTGTCACA 60.541 52.381 0.00 0.00 0.00 3.58
643 654 5.449999 GCAAGTGGCAGTTAGTTTACACTTT 60.450 40.000 7.35 0.00 44.10 2.66
672 683 4.880120 AGCCAGTGTTATGTTGATCTGATG 59.120 41.667 0.00 0.00 0.00 3.07
674 685 5.430886 CCAGTGTTATGTTGATCTGATGGA 58.569 41.667 0.00 0.00 0.00 3.41
675 686 5.295292 CCAGTGTTATGTTGATCTGATGGAC 59.705 44.000 0.00 0.00 0.00 4.02
676 687 5.876460 CAGTGTTATGTTGATCTGATGGACA 59.124 40.000 0.00 0.00 0.00 4.02
677 688 5.877012 AGTGTTATGTTGATCTGATGGACAC 59.123 40.000 0.00 10.07 35.24 3.67
718 729 3.511146 TGGACTGAAAAAGGAATGATGCC 59.489 43.478 0.00 0.00 0.00 4.40
788 804 3.751479 ACTTTGGTTCCATTGGCTTTC 57.249 42.857 0.00 0.00 0.00 2.62
818 873 0.614812 GCAAAATGGACCAGGCCAAT 59.385 50.000 5.01 0.00 42.16 3.16
831 886 4.186159 CCAGGCCAATCAAAGCAAAATAG 58.814 43.478 5.01 0.00 0.00 1.73
884 940 2.739379 CGAAGCTTCCTTCCTCTTCAAC 59.261 50.000 20.62 0.00 43.66 3.18
893 949 3.615155 CTTCCTCTTCAACCCAATCCTC 58.385 50.000 0.00 0.00 0.00 3.71
894 950 2.631384 TCCTCTTCAACCCAATCCTCA 58.369 47.619 0.00 0.00 0.00 3.86
899 955 4.144297 TCTTCAACCCAATCCTCAAACAG 58.856 43.478 0.00 0.00 0.00 3.16
909 965 3.795688 TCCTCAAACAGCAATCCTCTT 57.204 42.857 0.00 0.00 0.00 2.85
922 979 5.762218 AGCAATCCTCTTTATATGTGTCTGC 59.238 40.000 0.00 0.00 0.00 4.26
1589 1908 3.318839 CCAGAAACAATCAACTCCTGCAA 59.681 43.478 0.00 0.00 0.00 4.08
1728 2047 3.825143 ACAATGAAACTTTTGCAGCCT 57.175 38.095 0.00 0.00 0.00 4.58
1827 2155 4.965200 AGTGAAGCTAACCAGGATATCC 57.035 45.455 14.41 14.41 0.00 2.59
1943 2271 6.947733 TCTCAATCTGGTTTAATGTGTCCAAT 59.052 34.615 0.00 0.00 0.00 3.16
2185 2528 0.813821 ACCCGAAACCTACGAGTAGC 59.186 55.000 4.81 0.00 31.95 3.58
2640 2984 7.009260 GCAATGGAATGCTCTTGGATACATTC 61.009 42.308 6.11 6.11 45.02 2.67
3830 8696 8.721133 TGCTATTTGGATCTATCTGGTAGTAA 57.279 34.615 0.00 0.00 0.00 2.24
4080 8946 6.653320 CCAAACTACCTGACAATGTAAGCTTA 59.347 38.462 0.86 0.86 0.00 3.09
4180 9046 5.808366 ACTTGAGTTCATGAACCTGTCTA 57.192 39.130 30.34 18.60 42.06 2.59
4440 9306 0.745845 CCTCCTCATTTGGCGACCTG 60.746 60.000 0.00 0.00 0.00 4.00
4825 9691 0.106819 GGACAGGCTCGTACCTCCTA 60.107 60.000 0.00 0.00 38.26 2.94
4865 9731 2.233922 GGCTATGTGGGTATACGAGCAT 59.766 50.000 0.00 3.78 35.19 3.79
4983 9849 4.141959 CCATTAGGGGCACTACCAAATTTG 60.142 45.833 11.40 11.40 42.05 2.32
5060 9926 1.183549 GGAGAGAGCGGACCTTGTAA 58.816 55.000 0.00 0.00 0.00 2.41
5247 10113 1.474478 TGGTTTTTGAGCAACAGCGAA 59.526 42.857 0.00 0.00 31.67 4.70
5475 10342 7.624360 AAATTTGGTATCGTTGAATGAGCTA 57.376 32.000 0.00 0.00 0.00 3.32
5559 10426 0.523072 CCAACCTGACATCTTTGCCG 59.477 55.000 0.00 0.00 0.00 5.69
5621 10488 2.513738 TGATAGGGTGCAAAGGCCTAAT 59.486 45.455 5.16 0.00 40.13 1.73
5827 10838 3.005684 AGAAATTTCAATTGGCGACTGCA 59.994 39.130 19.99 0.00 45.35 4.41
5838 10990 2.661566 CGACTGCAGCAACCTGACG 61.662 63.158 15.27 3.45 41.77 4.35
6057 11641 2.306805 TGAATGTCCAGGTCTGATTGCT 59.693 45.455 0.00 0.00 0.00 3.91
6078 11662 2.614969 TGCCAAGGGGAGGATGCT 60.615 61.111 0.00 0.00 35.59 3.79
6160 11744 0.108472 TCATGCAGAGCTCAAGGTCG 60.108 55.000 17.77 0.00 46.33 4.79
6162 11746 0.322975 ATGCAGAGCTCAAGGTCGTT 59.677 50.000 17.77 0.00 46.33 3.85
6272 11856 0.765510 GAGGTTGTCCTGTTGGTCCT 59.234 55.000 0.00 0.00 45.24 3.85
6325 12707 9.327628 TGGATGGATTATAACATGCAAAAATTG 57.672 29.630 7.52 0.00 41.46 2.32
6442 12824 4.164843 ACTGAAAAAGGTCTGGTGCTAA 57.835 40.909 0.00 0.00 0.00 3.09
6491 12903 0.853530 AAAGAGGGTGGCCTCAGTTT 59.146 50.000 3.32 0.00 39.13 2.66
6498 12910 2.570302 GGGTGGCCTCAGTTTCTACTTA 59.430 50.000 3.32 0.00 30.26 2.24
6521 12933 3.141002 ACATTCATTGCGTCTGATTGC 57.859 42.857 0.00 0.00 30.72 3.56
6525 12937 0.379669 CATTGCGTCTGATTGCCTCC 59.620 55.000 2.96 0.00 0.00 4.30
6702 13128 1.527034 TGCTGATTCTCGCTTGCTTT 58.473 45.000 0.00 0.00 0.00 3.51
6722 13148 5.564651 GCTTTCTTATTTGCTGCTTGGTACA 60.565 40.000 0.00 0.00 0.00 2.90
6762 13190 5.295431 TGAATTGCTGTCGTTTATTCTGG 57.705 39.130 0.00 0.00 0.00 3.86
6813 13241 4.220693 TGATCAGGTTTACATGTCCTGG 57.779 45.455 24.46 11.53 45.97 4.45
6844 13272 4.621068 TGCTGCTGCATCATAAAGTAAC 57.379 40.909 14.93 0.00 45.31 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.988439 GCGCGTTGAGAGAGAGAAAG 59.012 55.000 8.43 0.00 0.00 2.62
2 3 0.169230 GAGCGCGTTGAGAGAGAGAA 59.831 55.000 8.43 0.00 0.00 2.87
5 6 0.675208 AGAGAGCGCGTTGAGAGAGA 60.675 55.000 8.43 0.00 0.00 3.10
6 7 0.248054 GAGAGAGCGCGTTGAGAGAG 60.248 60.000 8.43 0.00 0.00 3.20
7 8 0.675208 AGAGAGAGCGCGTTGAGAGA 60.675 55.000 8.43 0.00 0.00 3.10
8 9 0.170116 AAGAGAGAGCGCGTTGAGAG 59.830 55.000 8.43 0.00 0.00 3.20
9 10 0.598562 AAAGAGAGAGCGCGTTGAGA 59.401 50.000 8.43 0.00 0.00 3.27
10 11 0.988439 GAAAGAGAGAGCGCGTTGAG 59.012 55.000 8.43 0.00 0.00 3.02
11 12 0.598562 AGAAAGAGAGAGCGCGTTGA 59.401 50.000 8.43 0.00 0.00 3.18
12 13 0.988439 GAGAAAGAGAGAGCGCGTTG 59.012 55.000 8.43 0.00 0.00 4.10
13 14 0.885196 AGAGAAAGAGAGAGCGCGTT 59.115 50.000 8.43 0.00 0.00 4.84
14 15 0.450184 GAGAGAAAGAGAGAGCGCGT 59.550 55.000 8.43 0.00 0.00 6.01
15 16 0.732571 AGAGAGAAAGAGAGAGCGCG 59.267 55.000 0.00 0.00 0.00 6.86
16 17 1.742831 TGAGAGAGAAAGAGAGAGCGC 59.257 52.381 0.00 0.00 0.00 5.92
17 18 3.378112 ACATGAGAGAGAAAGAGAGAGCG 59.622 47.826 0.00 0.00 0.00 5.03
18 19 4.440525 CCACATGAGAGAGAAAGAGAGAGC 60.441 50.000 0.00 0.00 0.00 4.09
19 20 4.706476 ACCACATGAGAGAGAAAGAGAGAG 59.294 45.833 0.00 0.00 0.00 3.20
20 21 4.671831 ACCACATGAGAGAGAAAGAGAGA 58.328 43.478 0.00 0.00 0.00 3.10
21 22 5.404466 AACCACATGAGAGAGAAAGAGAG 57.596 43.478 0.00 0.00 0.00 3.20
22 23 5.815233 AAACCACATGAGAGAGAAAGAGA 57.185 39.130 0.00 0.00 0.00 3.10
23 24 7.659390 AGTTAAAACCACATGAGAGAGAAAGAG 59.341 37.037 0.00 0.00 0.00 2.85
24 25 7.509546 AGTTAAAACCACATGAGAGAGAAAGA 58.490 34.615 0.00 0.00 0.00 2.52
25 26 7.442364 TGAGTTAAAACCACATGAGAGAGAAAG 59.558 37.037 0.00 0.00 0.00 2.62
26 27 7.279615 TGAGTTAAAACCACATGAGAGAGAAA 58.720 34.615 0.00 0.00 0.00 2.52
27 28 6.826668 TGAGTTAAAACCACATGAGAGAGAA 58.173 36.000 0.00 0.00 0.00 2.87
28 29 6.419484 TGAGTTAAAACCACATGAGAGAGA 57.581 37.500 0.00 0.00 0.00 3.10
29 30 7.388776 TGATTGAGTTAAAACCACATGAGAGAG 59.611 37.037 0.00 0.00 0.00 3.20
30 31 7.223584 TGATTGAGTTAAAACCACATGAGAGA 58.776 34.615 0.00 0.00 0.00 3.10
31 32 7.388776 TCTGATTGAGTTAAAACCACATGAGAG 59.611 37.037 0.00 0.00 0.00 3.20
32 33 7.223584 TCTGATTGAGTTAAAACCACATGAGA 58.776 34.615 0.00 0.00 0.00 3.27
33 34 7.439157 TCTGATTGAGTTAAAACCACATGAG 57.561 36.000 0.00 0.00 0.00 2.90
34 35 7.665145 TGATCTGATTGAGTTAAAACCACATGA 59.335 33.333 0.00 0.00 0.00 3.07
35 36 7.819644 TGATCTGATTGAGTTAAAACCACATG 58.180 34.615 0.00 0.00 0.00 3.21
36 37 8.408043 TTGATCTGATTGAGTTAAAACCACAT 57.592 30.769 0.00 0.00 0.00 3.21
37 38 7.815840 TTGATCTGATTGAGTTAAAACCACA 57.184 32.000 0.00 0.00 0.00 4.17
38 39 8.514594 TGATTGATCTGATTGAGTTAAAACCAC 58.485 33.333 0.00 0.00 0.00 4.16
39 40 8.634335 TGATTGATCTGATTGAGTTAAAACCA 57.366 30.769 0.00 0.00 0.00 3.67
40 41 8.186821 CCTGATTGATCTGATTGAGTTAAAACC 58.813 37.037 0.00 0.00 0.00 3.27
41 42 8.186821 CCCTGATTGATCTGATTGAGTTAAAAC 58.813 37.037 0.00 0.00 0.00 2.43
42 43 8.108999 TCCCTGATTGATCTGATTGAGTTAAAA 58.891 33.333 0.00 0.00 0.00 1.52
43 44 7.632861 TCCCTGATTGATCTGATTGAGTTAAA 58.367 34.615 0.00 0.00 0.00 1.52
44 45 7.199167 TCCCTGATTGATCTGATTGAGTTAA 57.801 36.000 0.00 0.00 0.00 2.01
45 46 6.813293 TCCCTGATTGATCTGATTGAGTTA 57.187 37.500 0.00 0.00 0.00 2.24
46 47 5.705397 TCCCTGATTGATCTGATTGAGTT 57.295 39.130 0.00 0.00 0.00 3.01
47 48 5.908562 ATCCCTGATTGATCTGATTGAGT 57.091 39.130 0.00 0.00 0.00 3.41
48 49 8.865420 ATTAATCCCTGATTGATCTGATTGAG 57.135 34.615 0.00 0.00 33.95 3.02
49 50 9.293404 GAATTAATCCCTGATTGATCTGATTGA 57.707 33.333 0.00 6.43 33.95 2.57
50 51 8.235226 CGAATTAATCCCTGATTGATCTGATTG 58.765 37.037 0.00 0.00 33.95 2.67
51 52 7.941238 ACGAATTAATCCCTGATTGATCTGATT 59.059 33.333 0.00 0.00 33.95 2.57
52 53 7.456725 ACGAATTAATCCCTGATTGATCTGAT 58.543 34.615 0.00 0.00 33.95 2.90
53 54 6.830912 ACGAATTAATCCCTGATTGATCTGA 58.169 36.000 0.00 0.00 33.95 3.27
54 55 6.707608 TGACGAATTAATCCCTGATTGATCTG 59.292 38.462 0.00 0.00 33.95 2.90
55 56 6.830912 TGACGAATTAATCCCTGATTGATCT 58.169 36.000 0.00 0.00 33.95 2.75
56 57 6.708054 ACTGACGAATTAATCCCTGATTGATC 59.292 38.462 0.00 0.00 33.95 2.92
57 58 6.484643 CACTGACGAATTAATCCCTGATTGAT 59.515 38.462 0.00 0.00 33.95 2.57
58 59 5.817296 CACTGACGAATTAATCCCTGATTGA 59.183 40.000 0.00 0.00 33.95 2.57
59 60 5.008019 CCACTGACGAATTAATCCCTGATTG 59.992 44.000 0.00 0.00 33.95 2.67
60 61 5.126067 CCACTGACGAATTAATCCCTGATT 58.874 41.667 0.00 0.00 36.20 2.57
61 62 4.164221 ACCACTGACGAATTAATCCCTGAT 59.836 41.667 0.00 0.00 0.00 2.90
62 63 3.517901 ACCACTGACGAATTAATCCCTGA 59.482 43.478 0.00 0.00 0.00 3.86
63 64 3.873910 ACCACTGACGAATTAATCCCTG 58.126 45.455 0.00 0.00 0.00 4.45
64 65 4.443034 GCTACCACTGACGAATTAATCCCT 60.443 45.833 0.00 0.00 0.00 4.20
65 66 3.808174 GCTACCACTGACGAATTAATCCC 59.192 47.826 0.00 0.00 0.00 3.85
66 67 4.439057 TGCTACCACTGACGAATTAATCC 58.561 43.478 0.00 0.00 0.00 3.01
67 68 6.604735 ATTGCTACCACTGACGAATTAATC 57.395 37.500 0.00 0.00 0.00 1.75
68 69 7.120579 TCAAATTGCTACCACTGACGAATTAAT 59.879 33.333 0.00 0.00 0.00 1.40
69 70 6.428465 TCAAATTGCTACCACTGACGAATTAA 59.572 34.615 0.00 0.00 0.00 1.40
70 71 5.935206 TCAAATTGCTACCACTGACGAATTA 59.065 36.000 0.00 0.00 0.00 1.40
71 72 4.759693 TCAAATTGCTACCACTGACGAATT 59.240 37.500 0.00 0.00 0.00 2.17
72 73 4.323417 TCAAATTGCTACCACTGACGAAT 58.677 39.130 0.00 0.00 0.00 3.34
73 74 3.734463 TCAAATTGCTACCACTGACGAA 58.266 40.909 0.00 0.00 0.00 3.85
74 75 3.244078 ACTCAAATTGCTACCACTGACGA 60.244 43.478 0.00 0.00 0.00 4.20
75 76 3.067106 ACTCAAATTGCTACCACTGACG 58.933 45.455 0.00 0.00 0.00 4.35
76 77 3.365364 GCACTCAAATTGCTACCACTGAC 60.365 47.826 0.00 0.00 37.00 3.51
77 78 2.813754 GCACTCAAATTGCTACCACTGA 59.186 45.455 0.00 0.00 37.00 3.41
78 79 3.207474 GCACTCAAATTGCTACCACTG 57.793 47.619 0.00 0.00 37.00 3.66
86 87 5.495502 CAAAGTTGAAAGCACTCAAATTGC 58.504 37.500 12.37 0.00 41.38 3.56
87 88 5.006941 CCCAAAGTTGAAAGCACTCAAATTG 59.993 40.000 12.37 13.53 41.38 2.32
88 89 5.118286 CCCAAAGTTGAAAGCACTCAAATT 58.882 37.500 7.43 7.43 43.39 1.82
89 90 4.443315 CCCCAAAGTTGAAAGCACTCAAAT 60.443 41.667 2.38 0.00 37.08 2.32
90 91 3.118811 CCCCAAAGTTGAAAGCACTCAAA 60.119 43.478 2.38 0.00 37.08 2.69
91 92 2.430332 CCCCAAAGTTGAAAGCACTCAA 59.570 45.455 0.00 0.00 32.89 3.02
92 93 2.031120 CCCCAAAGTTGAAAGCACTCA 58.969 47.619 0.00 0.00 0.00 3.41
93 94 1.269778 GCCCCAAAGTTGAAAGCACTC 60.270 52.381 0.00 0.00 0.00 3.51
94 95 0.752658 GCCCCAAAGTTGAAAGCACT 59.247 50.000 0.00 0.00 0.00 4.40
95 96 0.249868 GGCCCCAAAGTTGAAAGCAC 60.250 55.000 0.00 0.00 0.00 4.40
96 97 0.398381 AGGCCCCAAAGTTGAAAGCA 60.398 50.000 0.00 0.00 0.00 3.91
97 98 0.033920 CAGGCCCCAAAGTTGAAAGC 59.966 55.000 0.00 0.00 0.00 3.51
98 99 0.033920 GCAGGCCCCAAAGTTGAAAG 59.966 55.000 0.00 0.00 0.00 2.62
99 100 0.398381 AGCAGGCCCCAAAGTTGAAA 60.398 50.000 0.00 0.00 0.00 2.69
100 101 0.398381 AAGCAGGCCCCAAAGTTGAA 60.398 50.000 0.00 0.00 0.00 2.69
101 102 0.827507 GAAGCAGGCCCCAAAGTTGA 60.828 55.000 0.00 0.00 0.00 3.18
102 103 0.829182 AGAAGCAGGCCCCAAAGTTG 60.829 55.000 0.00 0.00 0.00 3.16
103 104 0.105504 AAGAAGCAGGCCCCAAAGTT 60.106 50.000 0.00 0.00 0.00 2.66
104 105 0.829182 CAAGAAGCAGGCCCCAAAGT 60.829 55.000 0.00 0.00 0.00 2.66
105 106 1.969862 CAAGAAGCAGGCCCCAAAG 59.030 57.895 0.00 0.00 0.00 2.77
106 107 2.209315 GCAAGAAGCAGGCCCCAAA 61.209 57.895 0.00 0.00 44.79 3.28
107 108 2.601367 GCAAGAAGCAGGCCCCAA 60.601 61.111 0.00 0.00 44.79 4.12
113 114 1.075482 TCTTGGGGCAAGAAGCAGG 59.925 57.895 0.00 0.00 45.84 4.85
114 115 4.828409 TCTTGGGGCAAGAAGCAG 57.172 55.556 0.00 0.00 45.84 4.24
119 120 3.440127 CCCTTTATTTCTTGGGGCAAGA 58.560 45.455 0.00 0.00 46.93 3.02
120 121 3.893326 CCCTTTATTTCTTGGGGCAAG 57.107 47.619 0.00 0.00 42.25 4.01
125 126 2.246091 TGGCCCCTTTATTTCTTGGG 57.754 50.000 0.00 0.00 39.37 4.12
126 127 2.093500 GCTTGGCCCCTTTATTTCTTGG 60.093 50.000 0.00 0.00 0.00 3.61
127 128 2.566724 TGCTTGGCCCCTTTATTTCTTG 59.433 45.455 0.00 0.00 0.00 3.02
128 129 2.901291 TGCTTGGCCCCTTTATTTCTT 58.099 42.857 0.00 0.00 0.00 2.52
129 130 2.621556 TGCTTGGCCCCTTTATTTCT 57.378 45.000 0.00 0.00 0.00 2.52
130 131 3.452264 AGAATGCTTGGCCCCTTTATTTC 59.548 43.478 0.00 0.00 0.00 2.17
131 132 3.452264 GAGAATGCTTGGCCCCTTTATTT 59.548 43.478 0.00 0.00 0.00 1.40
132 133 3.033909 GAGAATGCTTGGCCCCTTTATT 58.966 45.455 0.00 0.00 0.00 1.40
133 134 2.245806 AGAGAATGCTTGGCCCCTTTAT 59.754 45.455 0.00 0.00 0.00 1.40
134 135 1.640670 AGAGAATGCTTGGCCCCTTTA 59.359 47.619 0.00 0.00 0.00 1.85
135 136 0.411058 AGAGAATGCTTGGCCCCTTT 59.589 50.000 0.00 0.00 0.00 3.11
136 137 0.411058 AAGAGAATGCTTGGCCCCTT 59.589 50.000 0.00 0.00 0.00 3.95
137 138 0.411058 AAAGAGAATGCTTGGCCCCT 59.589 50.000 0.00 0.00 0.00 4.79
138 139 0.820226 GAAAGAGAATGCTTGGCCCC 59.180 55.000 0.00 0.00 0.00 5.80
139 140 1.475682 CAGAAAGAGAATGCTTGGCCC 59.524 52.381 0.00 0.00 0.00 5.80
140 141 2.165998 ACAGAAAGAGAATGCTTGGCC 58.834 47.619 0.00 0.00 0.00 5.36
141 142 3.930634 AACAGAAAGAGAATGCTTGGC 57.069 42.857 0.00 0.00 0.00 4.52
142 143 5.618640 GCAGTAACAGAAAGAGAATGCTTGG 60.619 44.000 0.00 0.00 0.00 3.61
143 144 5.180868 AGCAGTAACAGAAAGAGAATGCTTG 59.819 40.000 0.00 0.00 38.24 4.01
144 145 5.312079 AGCAGTAACAGAAAGAGAATGCTT 58.688 37.500 0.00 0.00 38.24 3.91
145 146 4.904241 AGCAGTAACAGAAAGAGAATGCT 58.096 39.130 0.00 0.00 36.70 3.79
146 147 5.411053 AGAAGCAGTAACAGAAAGAGAATGC 59.589 40.000 0.00 0.00 0.00 3.56
147 148 6.426328 ACAGAAGCAGTAACAGAAAGAGAATG 59.574 38.462 0.00 0.00 0.00 2.67
148 149 6.529220 ACAGAAGCAGTAACAGAAAGAGAAT 58.471 36.000 0.00 0.00 0.00 2.40
149 150 5.918608 ACAGAAGCAGTAACAGAAAGAGAA 58.081 37.500 0.00 0.00 0.00 2.87
150 151 5.537300 ACAGAAGCAGTAACAGAAAGAGA 57.463 39.130 0.00 0.00 0.00 3.10
151 152 7.715265 TTAACAGAAGCAGTAACAGAAAGAG 57.285 36.000 0.00 0.00 0.00 2.85
152 153 8.677148 ATTTAACAGAAGCAGTAACAGAAAGA 57.323 30.769 0.00 0.00 0.00 2.52
153 154 8.778358 AGATTTAACAGAAGCAGTAACAGAAAG 58.222 33.333 0.00 0.00 0.00 2.62
154 155 8.677148 AGATTTAACAGAAGCAGTAACAGAAA 57.323 30.769 0.00 0.00 0.00 2.52
155 156 8.677148 AAGATTTAACAGAAGCAGTAACAGAA 57.323 30.769 0.00 0.00 0.00 3.02
156 157 8.677148 AAAGATTTAACAGAAGCAGTAACAGA 57.323 30.769 0.00 0.00 0.00 3.41
157 158 8.559536 TGAAAGATTTAACAGAAGCAGTAACAG 58.440 33.333 0.00 0.00 0.00 3.16
158 159 8.445275 TGAAAGATTTAACAGAAGCAGTAACA 57.555 30.769 0.00 0.00 0.00 2.41
161 162 9.162764 GGTATGAAAGATTTAACAGAAGCAGTA 57.837 33.333 0.00 0.00 0.00 2.74
162 163 7.885399 AGGTATGAAAGATTTAACAGAAGCAGT 59.115 33.333 0.00 0.00 0.00 4.40
163 164 8.273780 AGGTATGAAAGATTTAACAGAAGCAG 57.726 34.615 0.00 0.00 0.00 4.24
164 165 8.103305 AGAGGTATGAAAGATTTAACAGAAGCA 58.897 33.333 0.00 0.00 0.00 3.91
165 166 8.499403 AGAGGTATGAAAGATTTAACAGAAGC 57.501 34.615 0.00 0.00 0.00 3.86
167 168 8.730680 GCAAGAGGTATGAAAGATTTAACAGAA 58.269 33.333 0.00 0.00 0.00 3.02
181 182 3.378512 ACATGAGAGGCAAGAGGTATGA 58.621 45.455 0.00 0.00 0.00 2.15
183 184 4.472833 AGAAACATGAGAGGCAAGAGGTAT 59.527 41.667 0.00 0.00 0.00 2.73
186 187 3.347077 AGAAACATGAGAGGCAAGAGG 57.653 47.619 0.00 0.00 0.00 3.69
199 200 4.202151 GCAACTCCCAACTGAAAGAAACAT 60.202 41.667 0.00 0.00 37.43 2.71
216 217 6.034256 GTGATGAATTTTGTAGCATGCAACTC 59.966 38.462 21.98 4.80 41.45 3.01
217 218 5.865552 GTGATGAATTTTGTAGCATGCAACT 59.134 36.000 21.98 1.04 41.45 3.16
218 219 5.062558 GGTGATGAATTTTGTAGCATGCAAC 59.937 40.000 21.98 0.00 41.45 4.17
224 229 3.825585 TGCAGGTGATGAATTTTGTAGCA 59.174 39.130 0.00 0.00 0.00 3.49
281 290 2.450476 CCCCATAAATATGCTGGCTCC 58.550 52.381 0.00 0.00 32.40 4.70
286 295 5.867903 TTTTGTCCCCCATAAATATGCTG 57.132 39.130 0.00 0.00 32.40 4.41
298 307 3.441500 AGACTCTGAATTTTGTCCCCC 57.558 47.619 0.00 0.00 0.00 5.40
304 313 7.642669 TCACTGCTTAAAGACTCTGAATTTTG 58.357 34.615 0.00 0.00 0.00 2.44
423 434 5.795441 GCAGAATGTGACGAAAAATAGTTCC 59.205 40.000 0.00 0.00 39.31 3.62
520 531 3.526931 TCTGGCTAATTCTCGAACCAG 57.473 47.619 0.00 0.00 44.87 4.00
528 539 9.193806 ACATAATTGTGAATTCTGGCTAATTCT 57.806 29.630 19.50 7.90 43.34 2.40
579 590 1.051008 TGACAGTGTGATGTGCTCCT 58.949 50.000 0.00 0.00 32.25 3.69
581 592 1.869774 TGTGACAGTGTGATGTGCTC 58.130 50.000 0.00 0.00 32.25 4.26
582 593 2.330440 TTGTGACAGTGTGATGTGCT 57.670 45.000 0.00 0.00 32.25 4.40
672 683 0.308684 CACTGCATGTGTGTGTGTCC 59.691 55.000 11.21 0.00 41.53 4.02
718 729 3.219176 AGCATAACATCATGGACTGGG 57.781 47.619 0.00 0.00 0.00 4.45
788 804 1.339644 CCATTTTGCCCCCATGGAGG 61.340 60.000 15.22 11.62 40.10 4.30
818 873 4.138290 TCGTTGTCCCTATTTTGCTTTGA 58.862 39.130 0.00 0.00 0.00 2.69
831 886 2.033448 TGCCCACATCGTTGTCCC 59.967 61.111 0.00 0.00 32.34 4.46
884 940 2.167075 GGATTGCTGTTTGAGGATTGGG 59.833 50.000 0.00 0.00 0.00 4.12
893 949 7.765307 ACACATATAAAGAGGATTGCTGTTTG 58.235 34.615 10.05 0.00 0.00 2.93
894 950 7.831193 AGACACATATAAAGAGGATTGCTGTTT 59.169 33.333 5.65 5.65 0.00 2.83
899 955 5.762218 AGCAGACACATATAAAGAGGATTGC 59.238 40.000 0.00 0.00 0.00 3.56
909 965 4.403752 AGAGTGCTGAGCAGACACATATAA 59.596 41.667 7.71 0.00 40.08 0.98
988 1047 2.588314 GCTCATGGCTGCTCTCCG 60.588 66.667 0.00 0.00 38.06 4.63
991 1050 1.221293 GACTGCTCATGGCTGCTCT 59.779 57.895 0.00 0.00 42.51 4.09
1028 1087 0.243636 GATTTGTTTCCCCACGGCAG 59.756 55.000 0.00 0.00 0.00 4.85
1589 1908 2.727123 TGTGGGGCATGATTATTCGT 57.273 45.000 0.00 0.00 0.00 3.85
1728 2047 5.065859 CAGTTTTCGTGCCATCACCATAATA 59.934 40.000 0.00 0.00 40.04 0.98
1943 2271 7.334090 TCCCAATTTTGTTCAAATCAAACTGA 58.666 30.769 0.00 0.00 33.60 3.41
2417 2761 2.742372 CCCACGGTCCTTTGCTCG 60.742 66.667 0.00 0.00 0.00 5.03
2640 2984 0.392863 TGACCATCGTGCCTGGAATG 60.393 55.000 0.00 0.00 37.22 2.67
3325 5725 3.507233 ACCAAATCATGCATGACGAGTTT 59.493 39.130 30.92 22.77 40.03 2.66
3830 8696 2.630580 GCAGGTAGCTTACTGAGGCTAT 59.369 50.000 18.30 0.00 42.01 2.97
4080 8946 3.326747 GTTCAGATGCTCTAAACACGGT 58.673 45.455 0.00 0.00 0.00 4.83
4180 9046 3.891366 AGCATTGAAACCTTGTAGCAACT 59.109 39.130 0.00 0.00 0.00 3.16
4440 9306 7.487189 CCATTCATGTGAAGTATTTGAAGCTTC 59.513 37.037 19.89 19.89 37.48 3.86
4825 9691 5.248380 AGCCAAAAGTTATCAAGAGTCCT 57.752 39.130 0.00 0.00 0.00 3.85
4865 9731 2.852449 AGCATCCAGTTAGGGAATTCCA 59.148 45.455 25.67 3.39 41.12 3.53
4983 9849 5.560966 TGTTCAACAGAAACAACCTTCTC 57.439 39.130 0.00 0.00 33.25 2.87
5060 9926 5.105675 GCCAGTAGCAGTACTCTTAGTTTCT 60.106 44.000 0.00 0.00 42.97 2.52
5247 10113 0.886490 CTCGCTCTGGCAAAACTGGT 60.886 55.000 0.00 0.00 38.60 4.00
5475 10342 2.834549 CAACCATACTGGGAGTGTCTCT 59.165 50.000 0.00 0.00 43.37 3.10
5559 10426 2.489722 GGTGAGGTTCTTCATGCTTTCC 59.510 50.000 0.00 0.00 0.00 3.13
5621 10488 4.039973 GTCCCAACGATCCTGGTAATATCA 59.960 45.833 7.53 0.00 31.45 2.15
5827 10838 1.165270 GGCAAATACGTCAGGTTGCT 58.835 50.000 18.73 0.00 44.54 3.91
5838 10990 5.314923 TCTTCATGCTTTCAGGCAAATAC 57.685 39.130 0.00 0.00 45.68 1.89
6057 11641 1.004758 ATCCTCCCCTTGGCAGCTA 59.995 57.895 0.00 0.00 0.00 3.32
6078 11662 2.170166 GGGATGTGACAAATCTTGCCA 58.830 47.619 5.59 0.00 0.00 4.92
6272 11856 0.927029 TACCTCCTCTGCAGCTCCTA 59.073 55.000 9.47 0.00 0.00 2.94
6325 12707 6.774354 ACATGTGAATTTGACAAGCATTTC 57.226 33.333 0.00 0.00 0.00 2.17
6491 12903 6.972901 CAGACGCAATGAATGTAGTAAGTAGA 59.027 38.462 0.00 0.00 0.00 2.59
6498 12910 4.201851 GCAATCAGACGCAATGAATGTAGT 60.202 41.667 3.15 0.00 31.53 2.73
6521 12933 2.292292 CACCAAAGGTAAACAACGGAGG 59.708 50.000 0.00 0.00 32.11 4.30
6525 12937 6.961576 TCTTAATCACCAAAGGTAAACAACG 58.038 36.000 0.00 0.00 32.11 4.10
6702 13128 5.009631 ACATGTACCAAGCAGCAAATAAGA 58.990 37.500 0.00 0.00 0.00 2.10
6722 13148 6.441274 CAATTCAACTTGCTAAGACACACAT 58.559 36.000 3.37 0.00 0.00 3.21
6870 13298 5.279006 CCAGTTACTCGCCATCATATACTGT 60.279 44.000 0.00 0.00 31.08 3.55
6873 13301 4.923871 CACCAGTTACTCGCCATCATATAC 59.076 45.833 0.00 0.00 0.00 1.47
6875 13303 3.244215 CCACCAGTTACTCGCCATCATAT 60.244 47.826 0.00 0.00 0.00 1.78
6876 13304 2.102420 CCACCAGTTACTCGCCATCATA 59.898 50.000 0.00 0.00 0.00 2.15
6877 13305 1.134401 CCACCAGTTACTCGCCATCAT 60.134 52.381 0.00 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.