Multiple sequence alignment - TraesCS4D01G358100

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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 TraesCS4D01G358100 chr4D 100.000 3910 0 0 1 3910 506049808 506053717 0.000000e+00 7221.0
1 TraesCS4D01G358100 chr4D 84.984 939 89 22 524 1435 506287959 506287046 0.000000e+00 905.0
2 TraesCS4D01G358100 chr4D 78.035 906 140 40 2220 3083 506286133 506285245 2.080000e-142 516.0
3 TraesCS4D01G358100 chr4D 91.389 360 30 1 1556 1914 506286980 506286621 3.510000e-135 492.0
4 TraesCS4D01G358100 chr4D 89.333 75 8 0 2020 2094 506286300 506286226 1.160000e-15 95.3
5 TraesCS4D01G358100 chr5A 91.362 1285 61 26 224 1479 702225322 702226585 0.000000e+00 1712.0
6 TraesCS4D01G358100 chr5A 92.547 1060 47 12 2190 3217 702227540 702228599 0.000000e+00 1491.0
7 TraesCS4D01G358100 chr5A 87.382 1268 92 34 669 1911 702523221 702521997 0.000000e+00 1393.0
8 TraesCS4D01G358100 chr5A 90.545 624 26 14 1560 2151 702226623 702227245 0.000000e+00 795.0
9 TraesCS4D01G358100 chr5A 80.198 909 107 53 2220 3083 702521493 702520613 7.180000e-172 614.0
10 TraesCS4D01G358100 chr5A 84.821 224 17 8 1 222 300117490 300117698 3.960000e-50 209.0
11 TraesCS4D01G358100 chr4B 90.809 1273 74 20 1981 3215 661304954 661306221 0.000000e+00 1663.0
12 TraesCS4D01G358100 chr4B 87.766 1267 95 28 224 1463 661303218 661304451 0.000000e+00 1426.0
13 TraesCS4D01G358100 chr4B 89.975 808 57 12 661 1466 662421851 662421066 0.000000e+00 1022.0
14 TraesCS4D01G358100 chr4B 91.163 645 33 13 2592 3215 661310037 661310678 0.000000e+00 854.0
15 TraesCS4D01G358100 chr4B 93.692 428 23 3 1510 1935 661304463 661304888 4.260000e-179 638.0
16 TraesCS4D01G358100 chr4B 78.595 911 122 40 2226 3083 662420175 662419285 5.750000e-148 534.0
17 TraesCS4D01G358100 chr4B 89.706 408 37 4 1510 1914 662421057 662420652 2.080000e-142 516.0
18 TraesCS4D01G358100 chr4B 87.640 89 10 1 58 146 66818412 66818325 6.910000e-18 102.0
19 TraesCS4D01G358100 chr4B 90.541 74 7 0 2023 2096 662420344 662420271 8.940000e-17 99.0
20 TraesCS4D01G358100 chr3D 96.403 695 19 3 3218 3910 565116646 565115956 0.000000e+00 1140.0
21 TraesCS4D01G358100 chr3D 97.099 655 15 4 3256 3910 500471561 500470911 0.000000e+00 1101.0
22 TraesCS4D01G358100 chr3D 96.468 538 12 3 3374 3910 593771348 593771879 0.000000e+00 881.0
23 TraesCS4D01G358100 chr3D 90.286 350 30 4 1562 1909 544360834 544360487 4.610000e-124 455.0
24 TraesCS4D01G358100 chr3D 82.057 418 61 7 2261 2666 544360405 544359990 1.040000e-90 344.0
25 TraesCS4D01G358100 chr3D 91.327 196 17 0 1243 1438 544361104 544360909 6.440000e-68 268.0
26 TraesCS4D01G358100 chr3D 79.828 233 35 9 1 222 4981210 4981441 4.040000e-35 159.0
27 TraesCS4D01G358100 chr3D 79.487 234 33 10 1 222 574719472 574719702 6.770000e-33 152.0
28 TraesCS4D01G358100 chr3D 78.414 227 39 9 1 222 129693072 129692851 5.270000e-29 139.0
29 TraesCS4D01G358100 chr2B 93.516 694 42 2 3217 3910 63222077 63222767 0.000000e+00 1029.0
30 TraesCS4D01G358100 chr7D 92.907 719 24 10 3218 3910 583038706 583039423 0.000000e+00 1020.0
31 TraesCS4D01G358100 chr7D 81.532 222 25 8 1 220 424709966 424709759 6.720000e-38 169.0
32 TraesCS4D01G358100 chr2D 92.816 696 29 11 3215 3910 631266110 631266784 0.000000e+00 989.0
33 TraesCS4D01G358100 chr2D 82.160 213 31 5 1 211 335684126 335683919 4.020000e-40 176.0
34 TraesCS4D01G358100 chr1B 91.155 701 50 6 3218 3910 483882919 483883615 0.000000e+00 941.0
35 TraesCS4D01G358100 chr1B 90.199 704 57 5 3218 3910 35973641 35972939 0.000000e+00 907.0
36 TraesCS4D01G358100 chr3B 84.559 952 89 19 524 1441 799813268 799812341 0.000000e+00 891.0
37 TraesCS4D01G358100 chr3B 79.777 895 126 39 2226 3085 799811472 799810598 2.010000e-167 599.0
38 TraesCS4D01G358100 chr3B 92.500 360 26 1 1556 1914 799812280 799811921 7.490000e-142 514.0
39 TraesCS4D01G358100 chr3B 90.805 348 28 4 1559 1904 720218990 720218645 2.750000e-126 462.0
40 TraesCS4D01G358100 chr3B 77.494 822 120 43 2261 3027 720218542 720217731 2.160000e-117 433.0
41 TraesCS4D01G358100 chr3B 91.166 283 25 0 3218 3500 697081338 697081620 6.130000e-103 385.0
42 TraesCS4D01G358100 chr3B 75.629 755 80 62 764 1438 720219780 720219050 2.970000e-71 279.0
43 TraesCS4D01G358100 chr3B 92.208 77 6 0 2020 2096 799811623 799811547 4.130000e-20 110.0
44 TraesCS4D01G358100 chr7B 89.162 692 59 9 3234 3910 732938508 732939198 0.000000e+00 848.0
45 TraesCS4D01G358100 chr7B 84.889 225 19 7 1 223 9815408 9815619 3.060000e-51 213.0
46 TraesCS4D01G358100 chr6B 89.568 671 53 6 3256 3910 3820712 3820043 0.000000e+00 835.0
47 TraesCS4D01G358100 chr6B 81.081 222 26 10 15 222 514663120 514662901 3.130000e-36 163.0
48 TraesCS4D01G358100 chr3A 90.028 351 31 4 1560 1908 681343403 681343055 5.960000e-123 451.0
49 TraesCS4D01G358100 chr3A 82.641 409 66 4 2261 2665 681342978 681342571 1.340000e-94 357.0
50 TraesCS4D01G358100 chr3A 90.306 196 19 0 1243 1438 681343663 681343468 1.390000e-64 257.0
51 TraesCS4D01G358100 chr5D 84.293 191 22 6 36 224 471567301 471567117 3.100000e-41 180.0
52 TraesCS4D01G358100 chr5D 81.356 236 27 12 1 222 28271634 28271866 4.020000e-40 176.0
53 TraesCS4D01G358100 chr5D 83.158 190 25 4 36 224 471778081 471777898 2.420000e-37 167.0
54 TraesCS4D01G358100 chr5D 78.995 219 34 8 1 208 552794748 552794965 5.270000e-29 139.0
55 TraesCS4D01G358100 chr5D 93.023 43 3 0 60 102 224869238 224869280 3.260000e-06 63.9
56 TraesCS4D01G358100 chr2A 81.140 228 36 7 1 226 40082822 40083044 4.020000e-40 176.0
57 TraesCS4D01G358100 chr1A 80.426 235 34 9 3 226 7192124 7192357 6.720000e-38 169.0
58 TraesCS4D01G358100 chr1A 76.724 232 37 13 1 222 497411425 497411201 3.190000e-21 113.0
59 TraesCS4D01G358100 chr6D 80.342 234 34 10 1 222 467879832 467879599 2.420000e-37 167.0
60 TraesCS4D01G358100 chr6D 78.355 231 38 10 1 222 54386753 54386526 5.270000e-29 139.0
61 TraesCS4D01G358100 chr5B 80.645 217 34 7 8 221 235449238 235449027 1.120000e-35 161.0
62 TraesCS4D01G358100 chr1D 79.184 245 41 7 1 237 482108537 482108295 1.120000e-35 161.0
63 TraesCS4D01G358100 chr1D 79.574 235 30 13 1 222 471764558 471764329 6.770000e-33 152.0
64 TraesCS4D01G358100 chr1D 80.214 187 20 6 36 222 252597883 252598052 1.480000e-24 124.0
65 TraesCS4D01G358100 chr1D 77.143 210 36 8 24 225 471832094 471832299 1.150000e-20 111.0


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 TraesCS4D01G358100 chr4D 506049808 506053717 3909 False 7221.000000 7221 100.000000 1 3910 1 chr4D.!!$F1 3909
1 TraesCS4D01G358100 chr4D 506285245 506287959 2714 True 502.075000 905 85.935250 524 3083 4 chr4D.!!$R1 2559
2 TraesCS4D01G358100 chr5A 702225322 702228599 3277 False 1332.666667 1712 91.484667 224 3217 3 chr5A.!!$F2 2993
3 TraesCS4D01G358100 chr5A 702520613 702523221 2608 True 1003.500000 1393 83.790000 669 3083 2 chr5A.!!$R1 2414
4 TraesCS4D01G358100 chr4B 661303218 661310678 7460 False 1145.250000 1663 90.857500 224 3215 4 chr4B.!!$F1 2991
5 TraesCS4D01G358100 chr4B 662419285 662421851 2566 True 542.750000 1022 87.204250 661 3083 4 chr4B.!!$R2 2422
6 TraesCS4D01G358100 chr3D 565115956 565116646 690 True 1140.000000 1140 96.403000 3218 3910 1 chr3D.!!$R3 692
7 TraesCS4D01G358100 chr3D 500470911 500471561 650 True 1101.000000 1101 97.099000 3256 3910 1 chr3D.!!$R2 654
8 TraesCS4D01G358100 chr3D 593771348 593771879 531 False 881.000000 881 96.468000 3374 3910 1 chr3D.!!$F3 536
9 TraesCS4D01G358100 chr3D 544359990 544361104 1114 True 355.666667 455 87.890000 1243 2666 3 chr3D.!!$R4 1423
10 TraesCS4D01G358100 chr2B 63222077 63222767 690 False 1029.000000 1029 93.516000 3217 3910 1 chr2B.!!$F1 693
11 TraesCS4D01G358100 chr7D 583038706 583039423 717 False 1020.000000 1020 92.907000 3218 3910 1 chr7D.!!$F1 692
12 TraesCS4D01G358100 chr2D 631266110 631266784 674 False 989.000000 989 92.816000 3215 3910 1 chr2D.!!$F1 695
13 TraesCS4D01G358100 chr1B 483882919 483883615 696 False 941.000000 941 91.155000 3218 3910 1 chr1B.!!$F1 692
14 TraesCS4D01G358100 chr1B 35972939 35973641 702 True 907.000000 907 90.199000 3218 3910 1 chr1B.!!$R1 692
15 TraesCS4D01G358100 chr3B 799810598 799813268 2670 True 528.500000 891 87.261000 524 3085 4 chr3B.!!$R2 2561
16 TraesCS4D01G358100 chr3B 720217731 720219780 2049 True 391.333333 462 81.309333 764 3027 3 chr3B.!!$R1 2263
17 TraesCS4D01G358100 chr7B 732938508 732939198 690 False 848.000000 848 89.162000 3234 3910 1 chr7B.!!$F2 676
18 TraesCS4D01G358100 chr6B 3820043 3820712 669 True 835.000000 835 89.568000 3256 3910 1 chr6B.!!$R1 654
19 TraesCS4D01G358100 chr3A 681342571 681343663 1092 True 355.000000 451 87.658333 1243 2665 3 chr3A.!!$R1 1422

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
599 618 0.244994 ACACAAAACTTGGTTGCGCA 59.755 45.000 5.66 5.66 34.12 6.09 F
600 619 1.134848 ACACAAAACTTGGTTGCGCAT 60.135 42.857 12.75 0.00 34.12 4.73 F
1508 1665 1.003116 GTCGTGGCATGATCAGCATTC 60.003 52.381 13.34 0.00 34.15 2.67 F
1509 1666 1.018910 CGTGGCATGATCAGCATTCA 58.981 50.000 15.83 5.44 34.15 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1414 1571 0.396695 TACCGGTGAGGATGAGGACC 60.397 60.000 19.93 0.0 45.00 4.46 R
1595 1758 1.067635 GCCATGCGGATGTTGTTCTTT 60.068 47.619 16.17 0.0 0.00 2.52 R
2424 3173 1.129251 GTGACATGTCAGCACGGAATG 59.871 52.381 28.54 0.0 40.75 2.67 R
2954 8222 1.913951 TTCTGGATGTCATGGCGGCT 61.914 55.000 11.43 0.0 0.00 5.52 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
47 48 7.667043 TTATTGTTCATGTACTGTTCTGACC 57.333 36.000 4.01 0.00 0.00 4.02
48 49 4.955811 TGTTCATGTACTGTTCTGACCT 57.044 40.909 4.01 0.00 0.00 3.85
49 50 4.631131 TGTTCATGTACTGTTCTGACCTG 58.369 43.478 4.01 0.00 0.00 4.00
50 51 4.343814 TGTTCATGTACTGTTCTGACCTGA 59.656 41.667 4.01 0.00 0.00 3.86
51 52 5.012046 TGTTCATGTACTGTTCTGACCTGAT 59.988 40.000 4.01 0.00 0.00 2.90
52 53 5.745312 TCATGTACTGTTCTGACCTGATT 57.255 39.130 0.00 0.00 0.00 2.57
53 54 6.114187 TCATGTACTGTTCTGACCTGATTT 57.886 37.500 0.00 0.00 0.00 2.17
54 55 7.239763 TCATGTACTGTTCTGACCTGATTTA 57.760 36.000 0.00 0.00 0.00 1.40
55 56 7.851228 TCATGTACTGTTCTGACCTGATTTAT 58.149 34.615 0.00 0.00 0.00 1.40
56 57 7.765819 TCATGTACTGTTCTGACCTGATTTATG 59.234 37.037 0.00 0.00 0.00 1.90
57 58 7.004555 TGTACTGTTCTGACCTGATTTATGT 57.995 36.000 0.00 0.00 0.00 2.29
58 59 7.450074 TGTACTGTTCTGACCTGATTTATGTT 58.550 34.615 0.00 0.00 0.00 2.71
59 60 7.936847 TGTACTGTTCTGACCTGATTTATGTTT 59.063 33.333 0.00 0.00 0.00 2.83
60 61 7.823745 ACTGTTCTGACCTGATTTATGTTTT 57.176 32.000 0.00 0.00 0.00 2.43
61 62 8.237811 ACTGTTCTGACCTGATTTATGTTTTT 57.762 30.769 0.00 0.00 0.00 1.94
62 63 8.137437 ACTGTTCTGACCTGATTTATGTTTTTG 58.863 33.333 0.00 0.00 0.00 2.44
63 64 6.922957 TGTTCTGACCTGATTTATGTTTTTGC 59.077 34.615 0.00 0.00 0.00 3.68
64 65 6.899393 TCTGACCTGATTTATGTTTTTGCT 57.101 33.333 0.00 0.00 0.00 3.91
65 66 6.680810 TCTGACCTGATTTATGTTTTTGCTG 58.319 36.000 0.00 0.00 0.00 4.41
66 67 6.489700 TCTGACCTGATTTATGTTTTTGCTGA 59.510 34.615 0.00 0.00 0.00 4.26
67 68 6.680810 TGACCTGATTTATGTTTTTGCTGAG 58.319 36.000 0.00 0.00 0.00 3.35
68 69 6.489700 TGACCTGATTTATGTTTTTGCTGAGA 59.510 34.615 0.00 0.00 0.00 3.27
69 70 6.917533 ACCTGATTTATGTTTTTGCTGAGAG 58.082 36.000 0.00 0.00 0.00 3.20
70 71 5.803967 CCTGATTTATGTTTTTGCTGAGAGC 59.196 40.000 0.00 0.00 42.82 4.09
71 72 6.349944 CCTGATTTATGTTTTTGCTGAGAGCT 60.350 38.462 0.00 0.00 42.97 4.09
72 73 7.148188 CCTGATTTATGTTTTTGCTGAGAGCTA 60.148 37.037 0.00 0.00 42.97 3.32
73 74 7.530010 TGATTTATGTTTTTGCTGAGAGCTAC 58.470 34.615 0.00 0.00 42.97 3.58
74 75 7.391554 TGATTTATGTTTTTGCTGAGAGCTACT 59.608 33.333 0.00 0.00 42.97 2.57
75 76 7.510549 TTTATGTTTTTGCTGAGAGCTACTT 57.489 32.000 0.00 0.00 42.97 2.24
76 77 8.615878 TTTATGTTTTTGCTGAGAGCTACTTA 57.384 30.769 0.00 0.00 42.97 2.24
77 78 6.734104 ATGTTTTTGCTGAGAGCTACTTAG 57.266 37.500 0.00 0.00 42.97 2.18
78 79 5.853936 TGTTTTTGCTGAGAGCTACTTAGA 58.146 37.500 8.48 0.00 42.97 2.10
79 80 6.467677 TGTTTTTGCTGAGAGCTACTTAGAT 58.532 36.000 8.48 0.00 42.97 1.98
80 81 6.369890 TGTTTTTGCTGAGAGCTACTTAGATG 59.630 38.462 8.48 0.00 42.97 2.90
81 82 5.667539 TTTGCTGAGAGCTACTTAGATGT 57.332 39.130 8.48 0.00 42.97 3.06
82 83 4.909696 TGCTGAGAGCTACTTAGATGTC 57.090 45.455 8.48 0.00 42.97 3.06
83 84 3.634448 TGCTGAGAGCTACTTAGATGTCC 59.366 47.826 8.48 0.00 42.97 4.02
84 85 3.634448 GCTGAGAGCTACTTAGATGTCCA 59.366 47.826 8.48 0.00 38.45 4.02
85 86 4.098654 GCTGAGAGCTACTTAGATGTCCAA 59.901 45.833 8.48 0.00 38.45 3.53
86 87 5.394663 GCTGAGAGCTACTTAGATGTCCAAA 60.395 44.000 8.48 0.00 38.45 3.28
87 88 6.685116 GCTGAGAGCTACTTAGATGTCCAAAT 60.685 42.308 8.48 0.00 38.45 2.32
88 89 6.577103 TGAGAGCTACTTAGATGTCCAAATG 58.423 40.000 0.00 0.00 31.79 2.32
89 90 6.381133 TGAGAGCTACTTAGATGTCCAAATGA 59.619 38.462 0.00 0.00 31.79 2.57
90 91 7.070447 TGAGAGCTACTTAGATGTCCAAATGAT 59.930 37.037 0.00 0.00 31.79 2.45
91 92 7.441017 AGAGCTACTTAGATGTCCAAATGATC 58.559 38.462 0.00 0.00 0.00 2.92
92 93 7.289782 AGAGCTACTTAGATGTCCAAATGATCT 59.710 37.037 0.00 0.00 0.00 2.75
93 94 7.215789 AGCTACTTAGATGTCCAAATGATCTG 58.784 38.462 0.00 0.00 0.00 2.90
94 95 7.070447 AGCTACTTAGATGTCCAAATGATCTGA 59.930 37.037 0.00 0.00 0.00 3.27
95 96 7.712639 GCTACTTAGATGTCCAAATGATCTGAA 59.287 37.037 0.00 0.00 0.00 3.02
96 97 9.605275 CTACTTAGATGTCCAAATGATCTGAAA 57.395 33.333 0.00 0.00 0.00 2.69
97 98 8.868522 ACTTAGATGTCCAAATGATCTGAAAA 57.131 30.769 0.00 0.00 0.00 2.29
98 99 9.471702 ACTTAGATGTCCAAATGATCTGAAAAT 57.528 29.630 0.00 0.00 0.00 1.82
101 102 7.553334 AGATGTCCAAATGATCTGAAAATTGG 58.447 34.615 0.00 7.95 38.88 3.16
102 103 6.914654 TGTCCAAATGATCTGAAAATTGGA 57.085 33.333 11.25 11.25 42.84 3.53
103 104 6.927416 TGTCCAAATGATCTGAAAATTGGAG 58.073 36.000 14.09 0.00 44.92 3.86
104 105 6.720748 TGTCCAAATGATCTGAAAATTGGAGA 59.279 34.615 14.09 11.63 44.92 3.71
105 106 7.094075 TGTCCAAATGATCTGAAAATTGGAGAG 60.094 37.037 14.09 0.00 44.92 3.20
106 107 6.379133 TCCAAATGATCTGAAAATTGGAGAGG 59.621 38.462 11.25 0.00 40.87 3.69
107 108 6.379133 CCAAATGATCTGAAAATTGGAGAGGA 59.621 38.462 8.37 0.00 39.69 3.71
108 109 7.069578 CCAAATGATCTGAAAATTGGAGAGGAT 59.930 37.037 8.37 0.00 39.69 3.24
109 110 7.820578 AATGATCTGAAAATTGGAGAGGATC 57.179 36.000 0.00 0.00 0.00 3.36
129 130 9.562583 GAGGATCTCACACGATAAATTATCTAC 57.437 37.037 10.82 0.00 33.01 2.59
130 131 8.524487 AGGATCTCACACGATAAATTATCTACC 58.476 37.037 10.82 0.00 33.01 3.18
131 132 8.304596 GGATCTCACACGATAAATTATCTACCA 58.695 37.037 10.82 0.00 33.01 3.25
132 133 9.862371 GATCTCACACGATAAATTATCTACCAT 57.138 33.333 10.82 0.00 33.01 3.55
133 134 9.645059 ATCTCACACGATAAATTATCTACCATG 57.355 33.333 10.82 4.65 33.01 3.66
134 135 7.598869 TCTCACACGATAAATTATCTACCATGC 59.401 37.037 10.82 0.00 33.01 4.06
135 136 7.213678 TCACACGATAAATTATCTACCATGCA 58.786 34.615 10.82 0.00 33.01 3.96
136 137 7.713073 TCACACGATAAATTATCTACCATGCAA 59.287 33.333 10.82 0.00 33.01 4.08
137 138 8.341903 CACACGATAAATTATCTACCATGCAAA 58.658 33.333 10.82 0.00 33.01 3.68
138 139 8.898761 ACACGATAAATTATCTACCATGCAAAA 58.101 29.630 10.82 0.00 33.01 2.44
139 140 9.729023 CACGATAAATTATCTACCATGCAAAAA 57.271 29.630 10.82 0.00 33.01 1.94
187 188 8.755696 TTTTTGTGAATTATTTTCTGATCGGG 57.244 30.769 0.62 0.00 0.00 5.14
188 189 7.461182 TTTGTGAATTATTTTCTGATCGGGT 57.539 32.000 0.62 0.00 0.00 5.28
189 190 8.568676 TTTGTGAATTATTTTCTGATCGGGTA 57.431 30.769 0.62 0.00 0.00 3.69
190 191 7.548196 TGTGAATTATTTTCTGATCGGGTAC 57.452 36.000 0.62 0.00 0.00 3.34
191 192 7.106890 TGTGAATTATTTTCTGATCGGGTACA 58.893 34.615 0.62 0.00 0.00 2.90
192 193 7.608376 TGTGAATTATTTTCTGATCGGGTACAA 59.392 33.333 0.62 0.00 0.00 2.41
193 194 8.455682 GTGAATTATTTTCTGATCGGGTACAAA 58.544 33.333 0.62 0.00 0.00 2.83
194 195 9.184523 TGAATTATTTTCTGATCGGGTACAAAT 57.815 29.630 0.62 4.80 0.00 2.32
195 196 9.450807 GAATTATTTTCTGATCGGGTACAAATG 57.549 33.333 0.62 0.00 0.00 2.32
196 197 8.746052 ATTATTTTCTGATCGGGTACAAATGA 57.254 30.769 0.62 0.22 0.00 2.57
197 198 6.683974 ATTTTCTGATCGGGTACAAATGAG 57.316 37.500 0.62 0.00 0.00 2.90
198 199 3.179443 TCTGATCGGGTACAAATGAGC 57.821 47.619 0.62 0.00 0.00 4.26
199 200 2.158957 TCTGATCGGGTACAAATGAGCC 60.159 50.000 0.62 0.00 0.00 4.70
200 201 1.837439 TGATCGGGTACAAATGAGCCT 59.163 47.619 0.00 0.00 32.01 4.58
201 202 2.213499 GATCGGGTACAAATGAGCCTG 58.787 52.381 0.00 0.00 32.01 4.85
202 203 0.251916 TCGGGTACAAATGAGCCTGG 59.748 55.000 0.00 0.00 32.01 4.45
203 204 0.748005 CGGGTACAAATGAGCCTGGG 60.748 60.000 0.00 0.00 32.01 4.45
204 205 1.037579 GGGTACAAATGAGCCTGGGC 61.038 60.000 3.00 3.00 42.33 5.36
205 206 0.323360 GGTACAAATGAGCCTGGGCA 60.323 55.000 14.39 0.00 44.88 5.36
206 207 0.811281 GTACAAATGAGCCTGGGCAC 59.189 55.000 14.39 8.23 44.88 5.01
219 220 4.166011 GGCACCGAATCGCTGCAC 62.166 66.667 22.09 9.74 39.78 4.57
220 221 3.121030 GCACCGAATCGCTGCACT 61.121 61.111 16.90 0.00 38.19 4.40
221 222 3.084579 CACCGAATCGCTGCACTC 58.915 61.111 0.00 0.00 0.00 3.51
222 223 2.125512 ACCGAATCGCTGCACTCC 60.126 61.111 0.00 0.00 0.00 3.85
223 224 2.125552 CCGAATCGCTGCACTCCA 60.126 61.111 0.00 0.00 0.00 3.86
224 225 1.741401 CCGAATCGCTGCACTCCAA 60.741 57.895 0.00 0.00 0.00 3.53
225 226 1.298157 CCGAATCGCTGCACTCCAAA 61.298 55.000 0.00 0.00 0.00 3.28
226 227 0.516877 CGAATCGCTGCACTCCAAAA 59.483 50.000 0.00 0.00 0.00 2.44
227 228 1.464687 CGAATCGCTGCACTCCAAAAG 60.465 52.381 0.00 0.00 0.00 2.27
228 229 1.806542 GAATCGCTGCACTCCAAAAGA 59.193 47.619 0.00 0.00 0.00 2.52
229 230 2.119801 ATCGCTGCACTCCAAAAGAT 57.880 45.000 0.00 0.00 0.00 2.40
230 231 1.159285 TCGCTGCACTCCAAAAGATG 58.841 50.000 0.00 0.00 0.00 2.90
231 232 0.877071 CGCTGCACTCCAAAAGATGT 59.123 50.000 0.00 0.00 0.00 3.06
232 233 2.076100 CGCTGCACTCCAAAAGATGTA 58.924 47.619 0.00 0.00 0.00 2.29
233 234 2.483877 CGCTGCACTCCAAAAGATGTAA 59.516 45.455 0.00 0.00 0.00 2.41
234 235 3.667960 CGCTGCACTCCAAAAGATGTAAC 60.668 47.826 0.00 0.00 0.00 2.50
235 236 3.503748 GCTGCACTCCAAAAGATGTAACT 59.496 43.478 0.00 0.00 0.00 2.24
236 237 4.695455 GCTGCACTCCAAAAGATGTAACTA 59.305 41.667 0.00 0.00 0.00 2.24
291 293 9.995003 TTTTGATATTTCTAGCACACCAAAATT 57.005 25.926 0.00 0.00 0.00 1.82
319 322 9.550406 AATCCAGCAATATTCCAAATATGTTTG 57.450 29.630 7.89 7.89 43.43 2.93
350 353 1.032014 GGCAAAGAAGTTGTGCTCCA 58.968 50.000 0.00 0.00 39.63 3.86
353 356 2.294233 GCAAAGAAGTTGTGCTCCATCA 59.706 45.455 0.00 0.00 39.63 3.07
362 365 2.076100 TGTGCTCCATCATTTCGTGAC 58.924 47.619 0.00 0.00 40.28 3.67
376 379 2.122167 GTGACCGGCACAAAACCCA 61.122 57.895 19.85 0.00 46.91 4.51
386 389 3.530535 GCACAAAACCCACACAAATCTT 58.469 40.909 0.00 0.00 0.00 2.40
441 459 8.093927 GTCTCTAATTGAAATCCTATCTCAGGG 58.906 40.741 0.00 0.00 45.58 4.45
450 468 2.053244 CCTATCTCAGGGTCAATGGCT 58.947 52.381 0.00 0.00 41.26 4.75
470 488 2.945008 CTGTTTCAGCTTCCACAACTGA 59.055 45.455 0.00 0.00 38.62 3.41
471 489 3.351740 TGTTTCAGCTTCCACAACTGAA 58.648 40.909 0.75 0.75 45.95 3.02
511 529 7.907214 ACTCTACAAAATCCAGAACATGTAC 57.093 36.000 0.00 0.00 0.00 2.90
569 588 1.002888 CCACATCACTCTGTCAGGCTT 59.997 52.381 0.00 0.00 0.00 4.35
578 597 3.580458 ACTCTGTCAGGCTTGTCTAACAT 59.420 43.478 0.00 0.00 0.00 2.71
599 618 0.244994 ACACAAAACTTGGTTGCGCA 59.755 45.000 5.66 5.66 34.12 6.09
600 619 1.134848 ACACAAAACTTGGTTGCGCAT 60.135 42.857 12.75 0.00 34.12 4.73
610 632 1.418264 TGGTTGCGCATATAAGGGCTA 59.582 47.619 12.75 7.67 46.41 3.93
722 746 9.799106 TCAATTGCCCCAAAATAAATAGAAAAA 57.201 25.926 0.00 0.00 0.00 1.94
939 1014 9.924650 GAATATATAAATCGTAGTGGACCAGTT 57.075 33.333 7.25 0.00 0.00 3.16
1078 1196 2.435410 CAGGTCATGCAGCGCTCA 60.435 61.111 7.13 9.72 0.00 4.26
1480 1637 9.617523 AATTTTTCAATCCAACATCTTGTCTTT 57.382 25.926 0.00 0.00 0.00 2.52
1481 1638 8.422973 TTTTTCAATCCAACATCTTGTCTTTG 57.577 30.769 0.00 0.00 0.00 2.77
1500 1657 2.503331 TGTTTTGAGTCGTGGCATGAT 58.497 42.857 13.34 2.07 0.00 2.45
1508 1665 1.003116 GTCGTGGCATGATCAGCATTC 60.003 52.381 13.34 0.00 34.15 2.67
1509 1666 1.018910 CGTGGCATGATCAGCATTCA 58.981 50.000 15.83 5.44 34.15 2.57
1511 1668 1.029681 TGGCATGATCAGCATTCAGC 58.970 50.000 15.83 5.47 46.19 4.26
1552 1715 2.639065 ACGTGTGTTGGTGAATGAACT 58.361 42.857 0.00 0.00 0.00 3.01
1553 1716 2.612212 ACGTGTGTTGGTGAATGAACTC 59.388 45.455 0.00 0.00 0.00 3.01
1554 1717 2.611751 CGTGTGTTGGTGAATGAACTCA 59.388 45.455 0.00 0.00 0.00 3.41
1649 1812 4.020617 CAGGGTTGCAGCTCCGGA 62.021 66.667 2.93 2.93 0.00 5.14
1712 1875 1.664649 CGACTGCAGTGGCGAAGAA 60.665 57.895 27.27 0.00 45.35 2.52
1935 2333 9.037305 ACAACCTCTATCCCTCCCATATATATA 57.963 37.037 0.00 0.00 0.00 0.86
1966 2406 5.535029 ACCAAGTAATAGTAGGGACCATCA 58.465 41.667 0.00 0.00 0.00 3.07
2424 3173 2.027192 TCCATGTCAAAGCTAGGTGTCC 60.027 50.000 0.00 0.00 0.00 4.02
2435 3184 0.249120 TAGGTGTCCATTCCGTGCTG 59.751 55.000 0.00 0.00 0.00 4.41
2669 3418 0.976073 CGGGGTGGAGGTGAGTACAT 60.976 60.000 0.00 0.00 0.00 2.29
2902 8167 1.271102 GAGATAGCCGATCAGTGGGAC 59.729 57.143 0.00 0.00 36.98 4.46
2954 8222 1.040646 GATAGCCGATCACCTCACCA 58.959 55.000 0.00 0.00 34.35 4.17
2964 8234 4.100084 CCTCACCAGCCGCCATGA 62.100 66.667 0.00 0.00 0.00 3.07
3035 8319 5.236047 CCCTACTGTACTGTACGTCTGTATC 59.764 48.000 12.87 0.00 34.10 2.24
3194 8498 2.780094 CCAAAGTGCGTTGGGTGCA 61.780 57.895 8.66 0.00 43.79 4.57
3262 8566 2.426023 GGCCGAACCTATGCCGAT 59.574 61.111 0.00 0.00 35.08 4.18
3292 8596 3.511934 GTCGGCATAGATTGTCCTATCCT 59.488 47.826 0.00 0.00 0.00 3.24
3343 8647 1.731969 GCCGTCGGCGTATATCCAC 60.732 63.158 22.50 0.00 39.62 4.02
3446 8750 1.138036 CGTCGGCATAGAACGTGGA 59.862 57.895 0.00 0.00 0.00 4.02
3649 8953 1.983481 GCCCATGGATGTTGCCACA 60.983 57.895 15.22 0.00 41.56 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 8.730680 GGTCAGAACAGTACATGAACAATAATT 58.269 33.333 0.00 0.00 29.64 1.40
22 23 8.103305 AGGTCAGAACAGTACATGAACAATAAT 58.897 33.333 0.00 0.00 31.65 1.28
23 24 7.387673 CAGGTCAGAACAGTACATGAACAATAA 59.612 37.037 0.00 0.00 31.65 1.40
24 25 6.873605 CAGGTCAGAACAGTACATGAACAATA 59.126 38.462 0.00 0.00 31.65 1.90
25 26 5.702670 CAGGTCAGAACAGTACATGAACAAT 59.297 40.000 0.00 0.00 31.65 2.71
26 27 5.056480 CAGGTCAGAACAGTACATGAACAA 58.944 41.667 0.00 0.00 31.65 2.83
27 28 4.343814 TCAGGTCAGAACAGTACATGAACA 59.656 41.667 0.00 0.00 31.66 3.18
28 29 4.883083 TCAGGTCAGAACAGTACATGAAC 58.117 43.478 0.00 0.00 31.66 3.18
29 30 5.745312 ATCAGGTCAGAACAGTACATGAA 57.255 39.130 0.00 0.00 37.46 2.57
30 31 5.745312 AATCAGGTCAGAACAGTACATGA 57.255 39.130 0.00 0.00 38.18 3.07
31 32 7.550551 ACATAAATCAGGTCAGAACAGTACATG 59.449 37.037 0.00 0.00 0.00 3.21
32 33 7.624549 ACATAAATCAGGTCAGAACAGTACAT 58.375 34.615 0.00 0.00 0.00 2.29
33 34 7.004555 ACATAAATCAGGTCAGAACAGTACA 57.995 36.000 0.00 0.00 0.00 2.90
34 35 7.907214 AACATAAATCAGGTCAGAACAGTAC 57.093 36.000 0.00 0.00 0.00 2.73
35 36 8.918202 AAAACATAAATCAGGTCAGAACAGTA 57.082 30.769 0.00 0.00 0.00 2.74
36 37 7.823745 AAAACATAAATCAGGTCAGAACAGT 57.176 32.000 0.00 0.00 0.00 3.55
37 38 7.115378 GCAAAAACATAAATCAGGTCAGAACAG 59.885 37.037 0.00 0.00 0.00 3.16
38 39 6.922957 GCAAAAACATAAATCAGGTCAGAACA 59.077 34.615 0.00 0.00 0.00 3.18
39 40 7.115378 CAGCAAAAACATAAATCAGGTCAGAAC 59.885 37.037 0.00 0.00 0.00 3.01
40 41 7.014134 TCAGCAAAAACATAAATCAGGTCAGAA 59.986 33.333 0.00 0.00 0.00 3.02
41 42 6.489700 TCAGCAAAAACATAAATCAGGTCAGA 59.510 34.615 0.00 0.00 0.00 3.27
42 43 6.680810 TCAGCAAAAACATAAATCAGGTCAG 58.319 36.000 0.00 0.00 0.00 3.51
43 44 6.489700 TCTCAGCAAAAACATAAATCAGGTCA 59.510 34.615 0.00 0.00 0.00 4.02
44 45 6.913170 TCTCAGCAAAAACATAAATCAGGTC 58.087 36.000 0.00 0.00 0.00 3.85
45 46 6.571150 GCTCTCAGCAAAAACATAAATCAGGT 60.571 38.462 0.00 0.00 41.89 4.00
46 47 5.803967 GCTCTCAGCAAAAACATAAATCAGG 59.196 40.000 0.00 0.00 41.89 3.86
47 48 6.618811 AGCTCTCAGCAAAAACATAAATCAG 58.381 36.000 0.00 0.00 45.56 2.90
48 49 6.579666 AGCTCTCAGCAAAAACATAAATCA 57.420 33.333 0.00 0.00 45.56 2.57
49 50 7.756558 AGTAGCTCTCAGCAAAAACATAAATC 58.243 34.615 0.00 0.00 45.56 2.17
50 51 7.693969 AGTAGCTCTCAGCAAAAACATAAAT 57.306 32.000 0.00 0.00 45.56 1.40
51 52 7.510549 AAGTAGCTCTCAGCAAAAACATAAA 57.489 32.000 0.00 0.00 45.56 1.40
52 53 8.094548 TCTAAGTAGCTCTCAGCAAAAACATAA 58.905 33.333 0.00 0.00 45.56 1.90
53 54 7.611770 TCTAAGTAGCTCTCAGCAAAAACATA 58.388 34.615 0.00 0.00 45.56 2.29
54 55 6.467677 TCTAAGTAGCTCTCAGCAAAAACAT 58.532 36.000 0.00 0.00 45.56 2.71
55 56 5.853936 TCTAAGTAGCTCTCAGCAAAAACA 58.146 37.500 0.00 0.00 45.56 2.83
56 57 6.370166 ACATCTAAGTAGCTCTCAGCAAAAAC 59.630 38.462 0.00 0.00 45.56 2.43
57 58 6.467677 ACATCTAAGTAGCTCTCAGCAAAAA 58.532 36.000 0.00 0.00 45.56 1.94
58 59 6.042638 ACATCTAAGTAGCTCTCAGCAAAA 57.957 37.500 0.00 0.00 45.56 2.44
59 60 5.394663 GGACATCTAAGTAGCTCTCAGCAAA 60.395 44.000 0.00 0.00 45.56 3.68
60 61 4.098654 GGACATCTAAGTAGCTCTCAGCAA 59.901 45.833 0.00 0.00 45.56 3.91
61 62 3.634448 GGACATCTAAGTAGCTCTCAGCA 59.366 47.826 0.00 0.00 45.56 4.41
62 63 3.634448 TGGACATCTAAGTAGCTCTCAGC 59.366 47.826 0.00 0.00 42.84 4.26
63 64 5.843673 TTGGACATCTAAGTAGCTCTCAG 57.156 43.478 0.00 0.00 0.00 3.35
64 65 6.381133 TCATTTGGACATCTAAGTAGCTCTCA 59.619 38.462 0.00 0.00 0.00 3.27
65 66 6.810911 TCATTTGGACATCTAAGTAGCTCTC 58.189 40.000 0.00 0.00 0.00 3.20
66 67 6.798427 TCATTTGGACATCTAAGTAGCTCT 57.202 37.500 0.00 0.00 0.00 4.09
67 68 7.384660 CAGATCATTTGGACATCTAAGTAGCTC 59.615 40.741 0.00 0.00 0.00 4.09
68 69 7.070447 TCAGATCATTTGGACATCTAAGTAGCT 59.930 37.037 0.00 0.00 0.00 3.32
69 70 7.212976 TCAGATCATTTGGACATCTAAGTAGC 58.787 38.462 0.00 0.00 0.00 3.58
70 71 9.605275 TTTCAGATCATTTGGACATCTAAGTAG 57.395 33.333 0.00 0.00 0.00 2.57
71 72 9.958180 TTTTCAGATCATTTGGACATCTAAGTA 57.042 29.630 0.00 0.00 0.00 2.24
72 73 8.868522 TTTTCAGATCATTTGGACATCTAAGT 57.131 30.769 0.00 0.00 0.00 2.24
75 76 8.689061 CCAATTTTCAGATCATTTGGACATCTA 58.311 33.333 0.00 0.00 36.55 1.98
76 77 7.398047 TCCAATTTTCAGATCATTTGGACATCT 59.602 33.333 0.00 0.00 38.10 2.90
77 78 7.549839 TCCAATTTTCAGATCATTTGGACATC 58.450 34.615 0.00 0.00 38.10 3.06
78 79 7.398047 TCTCCAATTTTCAGATCATTTGGACAT 59.602 33.333 0.00 0.00 38.10 3.06
79 80 6.720748 TCTCCAATTTTCAGATCATTTGGACA 59.279 34.615 0.00 0.00 38.10 4.02
80 81 7.161773 TCTCCAATTTTCAGATCATTTGGAC 57.838 36.000 0.00 0.00 38.10 4.02
81 82 6.379133 CCTCTCCAATTTTCAGATCATTTGGA 59.621 38.462 0.00 1.67 40.08 3.53
82 83 6.379133 TCCTCTCCAATTTTCAGATCATTTGG 59.621 38.462 0.00 0.00 35.93 3.28
83 84 7.400599 TCCTCTCCAATTTTCAGATCATTTG 57.599 36.000 0.00 0.00 0.00 2.32
84 85 8.060075 AGATCCTCTCCAATTTTCAGATCATTT 58.940 33.333 0.00 0.00 33.04 2.32
85 86 7.584532 AGATCCTCTCCAATTTTCAGATCATT 58.415 34.615 0.00 0.00 33.04 2.57
86 87 7.147355 TGAGATCCTCTCCAATTTTCAGATCAT 60.147 37.037 0.00 0.00 42.73 2.45
87 88 6.157471 TGAGATCCTCTCCAATTTTCAGATCA 59.843 38.462 0.00 0.00 42.73 2.92
88 89 6.482973 GTGAGATCCTCTCCAATTTTCAGATC 59.517 42.308 1.90 0.00 42.73 2.75
89 90 6.069789 TGTGAGATCCTCTCCAATTTTCAGAT 60.070 38.462 1.90 0.00 42.73 2.90
90 91 5.249163 TGTGAGATCCTCTCCAATTTTCAGA 59.751 40.000 1.90 0.00 42.73 3.27
91 92 5.353678 GTGTGAGATCCTCTCCAATTTTCAG 59.646 44.000 1.90 0.00 42.73 3.02
92 93 5.248640 GTGTGAGATCCTCTCCAATTTTCA 58.751 41.667 1.90 0.00 42.73 2.69
93 94 4.331168 CGTGTGAGATCCTCTCCAATTTTC 59.669 45.833 1.90 0.00 42.73 2.29
94 95 4.020218 TCGTGTGAGATCCTCTCCAATTTT 60.020 41.667 1.90 0.00 42.73 1.82
95 96 3.515502 TCGTGTGAGATCCTCTCCAATTT 59.484 43.478 1.90 0.00 42.73 1.82
96 97 3.099905 TCGTGTGAGATCCTCTCCAATT 58.900 45.455 1.90 0.00 42.73 2.32
97 98 2.739943 TCGTGTGAGATCCTCTCCAAT 58.260 47.619 1.90 0.00 42.73 3.16
98 99 2.215942 TCGTGTGAGATCCTCTCCAA 57.784 50.000 1.90 0.00 42.73 3.53
99 100 2.443958 ATCGTGTGAGATCCTCTCCA 57.556 50.000 1.90 0.00 42.73 3.86
100 101 4.920640 TTTATCGTGTGAGATCCTCTCC 57.079 45.455 1.90 0.00 42.73 3.71
101 102 8.519526 AGATAATTTATCGTGTGAGATCCTCTC 58.480 37.037 10.08 0.00 40.66 3.20
102 103 8.415950 AGATAATTTATCGTGTGAGATCCTCT 57.584 34.615 10.08 0.00 40.12 3.69
103 104 9.562583 GTAGATAATTTATCGTGTGAGATCCTC 57.437 37.037 10.08 0.00 40.12 3.71
104 105 8.524487 GGTAGATAATTTATCGTGTGAGATCCT 58.476 37.037 10.08 0.00 40.12 3.24
105 106 8.304596 TGGTAGATAATTTATCGTGTGAGATCC 58.695 37.037 10.08 5.43 40.12 3.36
106 107 9.862371 ATGGTAGATAATTTATCGTGTGAGATC 57.138 33.333 10.08 0.00 40.12 2.75
107 108 9.645059 CATGGTAGATAATTTATCGTGTGAGAT 57.355 33.333 10.08 0.00 40.12 2.75
108 109 7.598869 GCATGGTAGATAATTTATCGTGTGAGA 59.401 37.037 10.08 0.00 40.12 3.27
109 110 7.384932 TGCATGGTAGATAATTTATCGTGTGAG 59.615 37.037 10.08 3.69 40.12 3.51
110 111 7.213678 TGCATGGTAGATAATTTATCGTGTGA 58.786 34.615 10.08 0.00 40.12 3.58
111 112 7.420184 TGCATGGTAGATAATTTATCGTGTG 57.580 36.000 10.08 7.82 40.12 3.82
112 113 8.445275 TTTGCATGGTAGATAATTTATCGTGT 57.555 30.769 10.08 0.00 40.12 4.49
113 114 9.729023 TTTTTGCATGGTAGATAATTTATCGTG 57.271 29.630 10.08 7.29 40.12 4.35
162 163 8.364142 ACCCGATCAGAAAATAATTCACAAAAA 58.636 29.630 0.00 0.00 0.00 1.94
163 164 7.891561 ACCCGATCAGAAAATAATTCACAAAA 58.108 30.769 0.00 0.00 0.00 2.44
164 165 7.461182 ACCCGATCAGAAAATAATTCACAAA 57.539 32.000 0.00 0.00 0.00 2.83
165 166 7.608376 TGTACCCGATCAGAAAATAATTCACAA 59.392 33.333 0.00 0.00 0.00 3.33
166 167 7.106890 TGTACCCGATCAGAAAATAATTCACA 58.893 34.615 0.00 0.00 0.00 3.58
167 168 7.548196 TGTACCCGATCAGAAAATAATTCAC 57.452 36.000 0.00 0.00 0.00 3.18
168 169 8.568676 TTTGTACCCGATCAGAAAATAATTCA 57.431 30.769 0.00 0.00 0.00 2.57
169 170 9.450807 CATTTGTACCCGATCAGAAAATAATTC 57.549 33.333 0.00 0.00 0.00 2.17
170 171 9.184523 TCATTTGTACCCGATCAGAAAATAATT 57.815 29.630 0.00 0.00 0.00 1.40
171 172 8.746052 TCATTTGTACCCGATCAGAAAATAAT 57.254 30.769 0.00 0.00 0.00 1.28
172 173 7.201696 GCTCATTTGTACCCGATCAGAAAATAA 60.202 37.037 0.00 0.00 0.00 1.40
173 174 6.260050 GCTCATTTGTACCCGATCAGAAAATA 59.740 38.462 0.00 0.00 0.00 1.40
174 175 5.066505 GCTCATTTGTACCCGATCAGAAAAT 59.933 40.000 0.00 0.00 0.00 1.82
175 176 4.394920 GCTCATTTGTACCCGATCAGAAAA 59.605 41.667 0.00 0.00 0.00 2.29
176 177 3.938963 GCTCATTTGTACCCGATCAGAAA 59.061 43.478 0.00 0.00 0.00 2.52
177 178 3.531538 GCTCATTTGTACCCGATCAGAA 58.468 45.455 0.00 0.00 0.00 3.02
178 179 2.158957 GGCTCATTTGTACCCGATCAGA 60.159 50.000 0.00 0.00 0.00 3.27
179 180 2.158900 AGGCTCATTTGTACCCGATCAG 60.159 50.000 0.00 0.00 0.00 2.90
180 181 1.837439 AGGCTCATTTGTACCCGATCA 59.163 47.619 0.00 0.00 0.00 2.92
181 182 2.213499 CAGGCTCATTTGTACCCGATC 58.787 52.381 0.00 0.00 0.00 3.69
182 183 1.134098 CCAGGCTCATTTGTACCCGAT 60.134 52.381 0.00 0.00 0.00 4.18
183 184 0.251916 CCAGGCTCATTTGTACCCGA 59.748 55.000 0.00 0.00 0.00 5.14
184 185 0.748005 CCCAGGCTCATTTGTACCCG 60.748 60.000 0.00 0.00 0.00 5.28
185 186 1.037579 GCCCAGGCTCATTTGTACCC 61.038 60.000 0.08 0.00 38.26 3.69
186 187 0.323360 TGCCCAGGCTCATTTGTACC 60.323 55.000 10.58 0.00 42.51 3.34
187 188 0.811281 GTGCCCAGGCTCATTTGTAC 59.189 55.000 10.58 0.00 42.51 2.90
188 189 0.323360 GGTGCCCAGGCTCATTTGTA 60.323 55.000 10.58 0.00 42.51 2.41
189 190 1.607467 GGTGCCCAGGCTCATTTGT 60.607 57.895 10.58 0.00 42.51 2.83
190 191 2.703798 CGGTGCCCAGGCTCATTTG 61.704 63.158 10.58 0.00 42.51 2.32
191 192 2.361610 CGGTGCCCAGGCTCATTT 60.362 61.111 10.58 0.00 42.51 2.32
192 193 2.215451 ATTCGGTGCCCAGGCTCATT 62.215 55.000 10.58 0.00 42.51 2.57
193 194 2.615227 GATTCGGTGCCCAGGCTCAT 62.615 60.000 10.58 0.00 42.51 2.90
194 195 3.329542 GATTCGGTGCCCAGGCTCA 62.330 63.158 10.58 0.00 42.51 4.26
195 196 2.514824 GATTCGGTGCCCAGGCTC 60.515 66.667 10.58 6.18 42.51 4.70
196 197 4.473520 CGATTCGGTGCCCAGGCT 62.474 66.667 10.58 0.00 42.51 4.58
198 199 4.473520 AGCGATTCGGTGCCCAGG 62.474 66.667 10.37 0.00 35.85 4.45
205 206 2.125512 GGAGTGCAGCGATTCGGT 60.126 61.111 4.68 4.68 38.40 4.69
206 207 1.298157 TTTGGAGTGCAGCGATTCGG 61.298 55.000 8.34 0.00 0.00 4.30
207 208 0.516877 TTTTGGAGTGCAGCGATTCG 59.483 50.000 0.62 0.62 0.00 3.34
208 209 1.806542 TCTTTTGGAGTGCAGCGATTC 59.193 47.619 0.00 0.00 0.00 2.52
209 210 1.896220 TCTTTTGGAGTGCAGCGATT 58.104 45.000 0.00 0.00 0.00 3.34
210 211 1.741706 CATCTTTTGGAGTGCAGCGAT 59.258 47.619 0.00 0.00 0.00 4.58
211 212 1.159285 CATCTTTTGGAGTGCAGCGA 58.841 50.000 0.00 0.00 0.00 4.93
212 213 0.877071 ACATCTTTTGGAGTGCAGCG 59.123 50.000 0.00 0.00 0.00 5.18
213 214 3.503748 AGTTACATCTTTTGGAGTGCAGC 59.496 43.478 0.00 0.00 0.00 5.25
214 215 6.037610 GGATAGTTACATCTTTTGGAGTGCAG 59.962 42.308 0.00 0.00 0.00 4.41
215 216 5.880332 GGATAGTTACATCTTTTGGAGTGCA 59.120 40.000 0.00 0.00 0.00 4.57
216 217 5.880332 TGGATAGTTACATCTTTTGGAGTGC 59.120 40.000 0.00 0.00 0.00 4.40
217 218 8.511604 AATGGATAGTTACATCTTTTGGAGTG 57.488 34.615 0.00 0.00 0.00 3.51
218 219 9.533831 AAAATGGATAGTTACATCTTTTGGAGT 57.466 29.630 0.00 0.00 0.00 3.85
221 222 9.369904 CCAAAAATGGATAGTTACATCTTTTGG 57.630 33.333 18.23 18.23 41.61 3.28
225 226 9.308000 TGTTCCAAAAATGGATAGTTACATCTT 57.692 29.630 0.00 0.00 37.87 2.40
226 227 8.877864 TGTTCCAAAAATGGATAGTTACATCT 57.122 30.769 0.00 0.00 37.87 2.90
274 276 7.531857 TGGATTTAATTTTGGTGTGCTAGAA 57.468 32.000 0.00 0.00 0.00 2.10
315 318 4.404691 CCTGTCCTCTGGCCAAAC 57.595 61.111 7.01 3.46 0.00 2.93
328 331 1.678101 GAGCACAACTTCTTTGCCTGT 59.322 47.619 0.00 0.00 39.01 4.00
350 353 2.466867 GTGCCGGTCACGAAATGAT 58.533 52.632 12.22 0.00 44.60 2.45
362 365 1.949847 TTGTGTGGGTTTTGTGCCGG 61.950 55.000 0.00 0.00 0.00 6.13
376 379 6.065976 TGATGGTATGGAGAAGATTTGTGT 57.934 37.500 0.00 0.00 0.00 3.72
386 389 9.473007 TTTGTTGAAAATATGATGGTATGGAGA 57.527 29.630 0.00 0.00 0.00 3.71
406 409 9.918630 AGGATTTCAATTAGAGACAATTTGTTG 57.081 29.630 3.08 0.00 0.00 3.33
450 468 2.997980 TCAGTTGTGGAAGCTGAAACA 58.002 42.857 0.00 0.00 36.46 2.83
569 588 5.650266 ACCAAGTTTTGTGTCATGTTAGACA 59.350 36.000 0.00 0.00 45.64 3.41
578 597 1.734047 GCGCAACCAAGTTTTGTGTCA 60.734 47.619 0.30 0.00 36.91 3.58
638 662 7.016268 ACTCTGACAAACCTTTAGTAGATTCCA 59.984 37.037 0.00 0.00 0.00 3.53
722 746 7.595819 TGTATGTTCTTCTTTTGTGGGATTT 57.404 32.000 0.00 0.00 0.00 2.17
939 1014 4.271661 TGATGGAAGCTATGCATGTTGAA 58.728 39.130 10.16 0.00 40.61 2.69
1004 1098 1.066918 GCTTGCTTGCTTGCACTGT 59.933 52.632 3.81 0.00 43.20 3.55
1414 1571 0.396695 TACCGGTGAGGATGAGGACC 60.397 60.000 19.93 0.00 45.00 4.46
1480 1637 1.960417 TCATGCCACGACTCAAAACA 58.040 45.000 0.00 0.00 0.00 2.83
1481 1638 2.483877 TGATCATGCCACGACTCAAAAC 59.516 45.455 0.00 0.00 0.00 2.43
1500 1657 2.773993 TCATCTGTGCTGAATGCTGA 57.226 45.000 0.00 0.00 43.37 4.26
1508 1665 3.192844 AGCCAAAGAAATCATCTGTGCTG 59.807 43.478 0.00 0.00 41.44 4.41
1509 1666 3.428532 AGCCAAAGAAATCATCTGTGCT 58.571 40.909 0.00 0.00 41.44 4.40
1511 1668 5.106555 ACGTAAGCCAAAGAAATCATCTGTG 60.107 40.000 0.00 0.00 41.20 3.66
1552 1715 2.169978 CTCTCCTCATCTGCACCAATGA 59.830 50.000 0.00 0.00 0.00 2.57
1553 1716 2.562635 CTCTCCTCATCTGCACCAATG 58.437 52.381 0.00 0.00 0.00 2.82
1554 1717 1.489649 CCTCTCCTCATCTGCACCAAT 59.510 52.381 0.00 0.00 0.00 3.16
1595 1758 1.067635 GCCATGCGGATGTTGTTCTTT 60.068 47.619 16.17 0.00 0.00 2.52
1649 1812 2.765352 CTGGAACACCAGGGAGTCT 58.235 57.895 8.23 0.00 45.18 3.24
1712 1875 3.626680 CTCGTCCATGCCGTCACGT 62.627 63.158 0.00 0.00 33.89 4.49
1937 2335 7.792736 TGGTCCCTACTATTACTTGGTCAATAT 59.207 37.037 0.00 0.00 0.00 1.28
1941 2339 4.950361 TGGTCCCTACTATTACTTGGTCA 58.050 43.478 0.00 0.00 0.00 4.02
1942 2340 5.601313 TGATGGTCCCTACTATTACTTGGTC 59.399 44.000 0.00 0.00 0.00 4.02
1944 2342 5.511545 GCTGATGGTCCCTACTATTACTTGG 60.512 48.000 0.00 0.00 0.00 3.61
1946 2344 5.305644 CAGCTGATGGTCCCTACTATTACTT 59.694 44.000 8.42 0.00 0.00 2.24
1947 2345 4.835615 CAGCTGATGGTCCCTACTATTACT 59.164 45.833 8.42 0.00 0.00 2.24
1949 2347 4.160329 CCAGCTGATGGTCCCTACTATTA 58.840 47.826 17.39 0.00 44.91 0.98
1950 2348 2.975489 CCAGCTGATGGTCCCTACTATT 59.025 50.000 17.39 0.00 44.91 1.73
1951 2349 2.614259 CCAGCTGATGGTCCCTACTAT 58.386 52.381 17.39 0.00 44.91 2.12
1952 2350 2.088104 CCAGCTGATGGTCCCTACTA 57.912 55.000 17.39 0.00 44.91 1.82
1953 2351 2.922162 CCAGCTGATGGTCCCTACT 58.078 57.895 17.39 0.00 44.91 2.57
2217 2946 9.274065 GTTTCAAAAATATTTCAGCTACTACCG 57.726 33.333 0.10 0.00 0.00 4.02
2247 2976 7.201750 GCACCCGTACCTGAATTATTTTGAATA 60.202 37.037 0.00 0.00 0.00 1.75
2424 3173 1.129251 GTGACATGTCAGCACGGAATG 59.871 52.381 28.54 0.00 40.75 2.67
2627 3376 3.670377 GTTGGCCACCTTGCGGAC 61.670 66.667 3.88 0.00 0.00 4.79
2669 3418 3.507162 TTGGCTGGAGAGAAAATGTGA 57.493 42.857 0.00 0.00 0.00 3.58
2680 3429 2.426024 CTCCACATTTCATTGGCTGGAG 59.574 50.000 0.00 0.00 39.06 3.86
2727 7939 2.030007 TGCAGAGTTAACCAAATGCAGC 60.030 45.455 16.19 5.79 38.64 5.25
2954 8222 1.913951 TTCTGGATGTCATGGCGGCT 61.914 55.000 11.43 0.00 0.00 5.52
3035 8319 5.298777 AGCCTTATTACAGTGAGGTACGTAG 59.701 44.000 0.00 0.00 0.00 3.51
3189 8493 6.073819 GGTTTCAGTTTCATAAAACATGCACC 60.074 38.462 0.00 0.00 45.94 5.01
3194 8498 6.983890 GTGTGGGTTTCAGTTTCATAAAACAT 59.016 34.615 0.00 0.00 45.94 2.71
3649 8953 1.418908 AAAGGGCGGGGATCGATGAT 61.419 55.000 0.54 0.00 42.43 2.45


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

AutoCloner maintained by Alex Coulton.