Multiple sequence alignment - TraesCS2B01G081800

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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 TraesCS2B01G081800 chr2B 100.000 4018 0 0 1 4018 45643517 45639500 0.000000e+00 7420.0
1 TraesCS2B01G081800 chr2B 93.843 1819 95 5 1268 3074 44942892 44941079 0.000000e+00 2723.0
2 TraesCS2B01G081800 chr2B 94.203 1587 79 5 1276 2862 45608235 45609808 0.000000e+00 2409.0
3 TraesCS2B01G081800 chr2B 90.909 715 39 7 3103 3803 44941083 44940381 0.000000e+00 937.0
4 TraesCS2B01G081800 chr2B 95.000 260 13 0 300 559 45642251 45642510 3.740000e-110 409.0
5 TraesCS2B01G081800 chr2B 95.000 260 13 0 1008 1267 45642959 45643218 3.740000e-110 409.0
6 TraesCS2B01G081800 chr2B 95.833 216 9 0 3803 4018 608208834 608208619 2.300000e-92 350.0
7 TraesCS2B01G081800 chr2B 89.015 264 22 6 296 555 770607258 770607518 1.800000e-83 320.0
8 TraesCS2B01G081800 chr2B 88.760 258 27 2 3338 3594 45032156 45032412 8.380000e-82 315.0
9 TraesCS2B01G081800 chr2B 88.627 255 27 2 3341 3594 45535276 45535023 3.900000e-80 309.0
10 TraesCS2B01G081800 chr2B 87.597 258 30 2 3338 3594 45040366 45040622 8.440000e-77 298.0
11 TraesCS2B01G081800 chr2B 89.252 214 21 1 1373 1586 45607551 45607762 2.380000e-67 267.0
12 TraesCS2B01G081800 chr2B 90.909 176 8 4 125 298 44943054 44942885 3.120000e-56 230.0
13 TraesCS2B01G081800 chr2B 85.366 164 14 4 120 282 45608068 45608222 1.160000e-35 161.0
14 TraesCS2B01G081800 chr2B 92.754 69 4 1 2898 2966 45609805 45609872 9.190000e-17 99.0
15 TraesCS2B01G081800 chr2D 93.979 1694 74 6 1276 2969 28407644 28409309 0.000000e+00 2538.0
16 TraesCS2B01G081800 chr2D 90.117 597 48 6 1268 1857 28048604 28049196 0.000000e+00 765.0
17 TraesCS2B01G081800 chr2D 90.698 387 18 5 1268 1653 28099444 28099813 2.160000e-137 499.0
18 TraesCS2B01G081800 chr2D 87.879 429 26 6 2541 2969 28052157 28052559 7.810000e-132 481.0
19 TraesCS2B01G081800 chr2D 92.218 257 20 0 3338 3594 28411514 28411770 8.210000e-97 364.0
20 TraesCS2B01G081800 chr2D 85.266 319 26 7 1272 1586 28364482 28364783 3.900000e-80 309.0
21 TraesCS2B01G081800 chr2D 88.189 254 28 2 3341 3593 27957773 27957521 6.530000e-78 302.0
22 TraesCS2B01G081800 chr2D 87.597 258 30 2 3338 3594 28008255 28008511 8.440000e-77 298.0
23 TraesCS2B01G081800 chr2D 85.778 225 26 6 1406 1630 28324982 28325200 2.410000e-57 233.0
24 TraesCS2B01G081800 chr2D 78.628 379 62 12 2419 2791 613326945 613327310 2.410000e-57 233.0
25 TraesCS2B01G081800 chr2D 92.537 134 4 1 165 298 28099324 28099451 1.910000e-43 187.0
26 TraesCS2B01G081800 chr2D 85.417 144 14 3 120 262 28407466 28407603 4.190000e-30 143.0
27 TraesCS2B01G081800 chr2D 97.059 34 1 0 120 153 28099292 28099325 1.560000e-04 58.4
28 TraesCS2B01G081800 chr2A 89.468 1728 126 29 1270 2971 30222813 30224510 0.000000e+00 2132.0
29 TraesCS2B01G081800 chr2A 89.303 617 43 5 299 912 60003858 60003262 0.000000e+00 752.0
30 TraesCS2B01G081800 chr2A 88.283 367 31 3 910 1267 60002980 60002617 2.870000e-116 429.0
31 TraesCS2B01G081800 chr2A 94.815 270 13 1 3338 3607 30224966 30225234 1.730000e-113 420.0
32 TraesCS2B01G081800 chr2A 91.538 260 22 0 1008 1267 60003598 60003857 3.820000e-95 359.0
33 TraesCS2B01G081800 chr2A 87.170 265 33 1 1005 1269 62097328 62097591 2.350000e-77 300.0
34 TraesCS2B01G081800 chr2A 87.597 258 30 2 3338 3594 30187097 30187353 8.440000e-77 298.0
35 TraesCS2B01G081800 chr2A 85.305 279 18 4 3082 3337 30224660 30224938 2.380000e-67 267.0
36 TraesCS2B01G081800 chr6A 89.425 974 67 10 299 1269 517901232 517900292 0.000000e+00 1195.0
37 TraesCS2B01G081800 chr6A 91.154 260 23 0 1008 1267 517900972 517901231 1.780000e-93 353.0
38 TraesCS2B01G081800 chr6B 88.458 979 73 13 298 1269 545320445 545319500 0.000000e+00 1146.0
39 TraesCS2B01G081800 chr6B 90.769 260 24 0 1008 1267 545320184 545320443 8.260000e-92 348.0
40 TraesCS2B01G081800 chr6B 86.957 276 36 0 994 1269 469853811 469853536 1.080000e-80 311.0
41 TraesCS2B01G081800 chr6B 86.111 288 30 5 642 926 469854221 469853941 6.530000e-78 302.0
42 TraesCS2B01G081800 chr6B 87.500 56 5 1 578 631 469853856 469853911 3.350000e-06 63.9
43 TraesCS2B01G081800 chr3D 87.136 995 78 9 290 1272 505454504 505453548 0.000000e+00 1083.0
44 TraesCS2B01G081800 chr3D 85.398 678 49 23 602 1267 603526875 603526236 0.000000e+00 658.0
45 TraesCS2B01G081800 chr3D 90.038 261 26 0 1008 1268 505454234 505454494 4.970000e-89 339.0
46 TraesCS2B01G081800 chr3D 89.615 260 27 0 300 559 505453552 505453811 8.320000e-87 331.0
47 TraesCS2B01G081800 chr5D 78.341 1459 257 40 1380 2791 464324750 464326196 0.000000e+00 889.0
48 TraesCS2B01G081800 chr5D 87.925 265 32 0 1004 1268 459224596 459224332 3.010000e-81 313.0
49 TraesCS2B01G081800 chr5D 87.629 194 24 0 3804 3997 566055471 566055664 4.040000e-55 226.0
50 TraesCS2B01G081800 chr5B 77.610 1456 273 33 1380 2791 571480055 571481501 0.000000e+00 833.0
51 TraesCS2B01G081800 chr5B 87.206 680 66 13 602 1272 511018712 511018045 0.000000e+00 754.0
52 TraesCS2B01G081800 chr5A 77.289 1431 263 38 1385 2791 584716389 584717781 0.000000e+00 785.0
53 TraesCS2B01G081800 chr3B 84.588 558 48 13 300 840 752450109 752450645 1.660000e-143 520.0
54 TraesCS2B01G081800 chr3B 96.330 218 8 0 3801 4018 44850888 44851105 3.820000e-95 359.0
55 TraesCS2B01G081800 chr3B 87.629 291 36 0 978 1268 752452025 752452315 4.970000e-89 339.0
56 TraesCS2B01G081800 chr3B 87.732 269 30 3 1000 1267 563403331 563403065 1.080000e-80 311.0
57 TraesCS2B01G081800 chr3B 87.437 199 25 0 3803 4001 756683770 756683572 3.120000e-56 230.0
58 TraesCS2B01G081800 chr7D 86.921 367 36 4 600 961 64669515 64669156 6.250000e-108 401.0
59 TraesCS2B01G081800 chr7B 96.262 214 8 0 3805 4018 605112029 605111816 6.390000e-93 351.0
60 TraesCS2B01G081800 chr7B 89.354 263 21 6 300 558 616817479 616817220 1.390000e-84 324.0
61 TraesCS2B01G081800 chr7A 93.953 215 12 1 3804 4018 540764267 540764480 1.390000e-84 324.0
62 TraesCS2B01G081800 chr1D 87.273 275 35 0 994 1268 492585845 492585571 8.380000e-82 315.0
63 TraesCS2B01G081800 chr1D 92.308 195 14 1 3807 4001 13098145 13097952 3.960000e-70 276.0
64 TraesCS2B01G081800 chr3A 86.792 265 33 2 1004 1267 723331356 723331093 1.090000e-75 294.0
65 TraesCS2B01G081800 chr4A 87.558 217 27 0 3802 4018 703335754 703335970 6.670000e-63 252.0
66 TraesCS2B01G081800 chr1B 93.421 152 9 1 3800 3950 627106531 627106380 1.450000e-54 224.0


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 TraesCS2B01G081800 chr2B 45639500 45643517 4017 True 7420.000000 7420 100.000000 1 4018 1 chr2B.!!$R2 4017
1 TraesCS2B01G081800 chr2B 44940381 44943054 2673 True 1296.666667 2723 91.887000 125 3803 3 chr2B.!!$R4 3678
2 TraesCS2B01G081800 chr2B 45607551 45609872 2321 False 734.000000 2409 90.393750 120 2966 4 chr2B.!!$F4 2846
3 TraesCS2B01G081800 chr2B 45642251 45643218 967 False 409.000000 409 95.000000 300 1267 2 chr2B.!!$F5 967
4 TraesCS2B01G081800 chr2D 28407466 28411770 4304 False 1015.000000 2538 90.538000 120 3594 3 chr2D.!!$F7 3474
5 TraesCS2B01G081800 chr2D 28048604 28052559 3955 False 623.000000 765 88.998000 1268 2969 2 chr2D.!!$F5 1701
6 TraesCS2B01G081800 chr2D 28099292 28099813 521 False 248.133333 499 93.431333 120 1653 3 chr2D.!!$F6 1533
7 TraesCS2B01G081800 chr2A 30222813 30225234 2421 False 939.666667 2132 89.862667 1270 3607 3 chr2A.!!$F4 2337
8 TraesCS2B01G081800 chr2A 60002617 60003858 1241 True 590.500000 752 88.793000 299 1267 2 chr2A.!!$R1 968
9 TraesCS2B01G081800 chr6A 517900292 517901232 940 True 1195.000000 1195 89.425000 299 1269 1 chr6A.!!$R1 970
10 TraesCS2B01G081800 chr6B 545319500 545320445 945 True 1146.000000 1146 88.458000 298 1269 1 chr6B.!!$R1 971
11 TraesCS2B01G081800 chr6B 469853536 469854221 685 True 306.500000 311 86.534000 642 1269 2 chr6B.!!$R2 627
12 TraesCS2B01G081800 chr3D 505453548 505454504 956 True 1083.000000 1083 87.136000 290 1272 1 chr3D.!!$R1 982
13 TraesCS2B01G081800 chr3D 603526236 603526875 639 True 658.000000 658 85.398000 602 1267 1 chr3D.!!$R2 665
14 TraesCS2B01G081800 chr3D 505453552 505454494 942 False 335.000000 339 89.826500 300 1268 2 chr3D.!!$F1 968
15 TraesCS2B01G081800 chr5D 464324750 464326196 1446 False 889.000000 889 78.341000 1380 2791 1 chr5D.!!$F1 1411
16 TraesCS2B01G081800 chr5B 571480055 571481501 1446 False 833.000000 833 77.610000 1380 2791 1 chr5B.!!$F1 1411
17 TraesCS2B01G081800 chr5B 511018045 511018712 667 True 754.000000 754 87.206000 602 1272 1 chr5B.!!$R1 670
18 TraesCS2B01G081800 chr5A 584716389 584717781 1392 False 785.000000 785 77.289000 1385 2791 1 chr5A.!!$F1 1406
19 TraesCS2B01G081800 chr3B 752450109 752452315 2206 False 429.500000 520 86.108500 300 1268 2 chr3B.!!$F2 968

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
55 56 0.036875 ACTTGGTCTGGTGGCTTAGC 59.963 55.0 0.0 0.0 0.0 3.09 F
106 107 0.250295 CGAATCCCCGCACCACATAT 60.250 55.0 0.0 0.0 0.0 1.78 F
109 110 1.729586 ATCCCCGCACCACATATAGT 58.270 50.0 0.0 0.0 0.0 2.12 F
1819 3992 1.841663 GCCATGCGTCACGTTCAACT 61.842 55.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1707 3880 0.036010 CCCTGATGAGCGTTTCCTGT 60.036 55.000 0.00 0.0 0.00 4.00 R
2007 4207 1.571460 GAAGCAGTCACCTTGCACG 59.429 57.895 0.00 0.0 43.92 5.34 R
2118 4318 3.009115 GCAGTGACAGGGGGCCTA 61.009 66.667 0.84 0.0 29.64 3.93 R
3241 8134 0.250901 AACAACTCGCTTCATGGCCT 60.251 50.000 3.32 0.0 0.00 5.19 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
24 25 7.798710 AACTACATATATAGGGTGTGCATCT 57.201 36.000 0.00 0.00 0.00 2.90
25 26 7.411486 ACTACATATATAGGGTGTGCATCTC 57.589 40.000 0.00 0.00 0.00 2.75
26 27 6.954102 ACTACATATATAGGGTGTGCATCTCA 59.046 38.462 0.00 0.00 0.00 3.27
27 28 6.881067 ACATATATAGGGTGTGCATCTCAT 57.119 37.500 0.00 0.00 0.00 2.90
28 29 6.647229 ACATATATAGGGTGTGCATCTCATG 58.353 40.000 0.00 0.00 0.00 3.07
39 40 0.800631 CATCTCATGCGTGCACACTT 59.199 50.000 18.64 2.02 0.00 3.16
40 41 0.800631 ATCTCATGCGTGCACACTTG 59.199 50.000 18.64 15.49 0.00 3.16
41 42 1.208358 CTCATGCGTGCACACTTGG 59.792 57.895 18.64 6.29 0.00 3.61
43 44 1.081906 CATGCGTGCACACTTGGTC 60.082 57.895 18.64 0.00 0.00 4.02
44 45 1.227943 ATGCGTGCACACTTGGTCT 60.228 52.632 18.64 0.00 0.00 3.85
45 46 1.509644 ATGCGTGCACACTTGGTCTG 61.510 55.000 18.64 0.00 0.00 3.51
46 47 2.896801 GCGTGCACACTTGGTCTGG 61.897 63.158 18.64 0.00 0.00 3.86
49 50 1.152984 TGCACACTTGGTCTGGTGG 60.153 57.895 0.00 0.00 37.72 4.61
52 53 0.466189 CACACTTGGTCTGGTGGCTT 60.466 55.000 0.00 0.00 37.72 4.35
53 54 1.136828 ACACTTGGTCTGGTGGCTTA 58.863 50.000 0.00 0.00 37.72 3.09
54 55 1.072331 ACACTTGGTCTGGTGGCTTAG 59.928 52.381 0.00 0.00 37.72 2.18
55 56 0.036875 ACTTGGTCTGGTGGCTTAGC 59.963 55.000 0.00 0.00 0.00 3.09
56 57 1.003839 TTGGTCTGGTGGCTTAGCG 60.004 57.895 0.00 0.00 0.00 4.26
57 58 1.764571 TTGGTCTGGTGGCTTAGCGT 61.765 55.000 0.00 0.00 0.00 5.07
58 59 1.741770 GGTCTGGTGGCTTAGCGTG 60.742 63.158 0.00 0.00 0.00 5.34
60 61 3.490759 CTGGTGGCTTAGCGTGCG 61.491 66.667 0.00 0.00 0.00 5.34
87 88 3.656045 CCCACGTGTTGCGGGTTC 61.656 66.667 15.65 0.00 43.72 3.62
89 90 2.962786 CACGTGTTGCGGGTTCGA 60.963 61.111 7.58 0.00 46.52 3.71
90 91 2.202905 ACGTGTTGCGGGTTCGAA 60.203 55.556 0.00 0.00 46.52 3.71
92 93 1.131826 CGTGTTGCGGGTTCGAATC 59.868 57.895 0.00 0.00 39.00 2.52
93 94 1.500396 GTGTTGCGGGTTCGAATCC 59.500 57.895 18.00 18.00 39.00 3.01
95 96 2.045731 TTGCGGGTTCGAATCCCC 60.046 61.111 21.74 16.96 41.78 4.81
99 100 2.822701 GGGTTCGAATCCCCGCAC 60.823 66.667 17.16 0.00 39.08 5.34
100 101 2.822701 GGTTCGAATCCCCGCACC 60.823 66.667 0.00 0.00 38.51 5.01
101 102 2.046700 GTTCGAATCCCCGCACCA 60.047 61.111 0.00 0.00 0.00 4.17
102 103 2.046700 TTCGAATCCCCGCACCAC 60.047 61.111 0.00 0.00 0.00 4.16
103 104 2.884980 TTCGAATCCCCGCACCACA 61.885 57.895 0.00 0.00 0.00 4.17
104 105 2.124736 CGAATCCCCGCACCACAT 60.125 61.111 0.00 0.00 0.00 3.21
105 106 1.145156 CGAATCCCCGCACCACATA 59.855 57.895 0.00 0.00 0.00 2.29
106 107 0.250295 CGAATCCCCGCACCACATAT 60.250 55.000 0.00 0.00 0.00 1.78
108 109 2.699954 GAATCCCCGCACCACATATAG 58.300 52.381 0.00 0.00 0.00 1.31
109 110 1.729586 ATCCCCGCACCACATATAGT 58.270 50.000 0.00 0.00 0.00 2.12
110 111 2.385135 TCCCCGCACCACATATAGTA 57.615 50.000 0.00 0.00 0.00 1.82
111 112 2.680251 TCCCCGCACCACATATAGTAA 58.320 47.619 0.00 0.00 0.00 2.24
112 113 3.244582 TCCCCGCACCACATATAGTAAT 58.755 45.455 0.00 0.00 0.00 1.89
114 115 4.839550 TCCCCGCACCACATATAGTAATTA 59.160 41.667 0.00 0.00 0.00 1.40
117 118 6.351881 CCCCGCACCACATATAGTAATTATCT 60.352 42.308 0.00 0.00 0.00 1.98
118 119 6.757010 CCCGCACCACATATAGTAATTATCTC 59.243 42.308 0.00 0.00 0.00 2.75
123 124 9.692749 CACCACATATAGTAATTATCTCGTGTT 57.307 33.333 0.00 0.00 0.00 3.32
153 552 4.787135 TGGATTTCCAGCACCACATATA 57.213 40.909 0.00 0.00 42.01 0.86
156 555 5.368230 TGGATTTCCAGCACCACATATAGTA 59.632 40.000 0.00 0.00 42.01 1.82
157 556 6.126623 TGGATTTCCAGCACCACATATAGTAA 60.127 38.462 0.00 0.00 42.01 2.24
184 585 9.944376 TTTAAGATGTCAAGATTTGCTACTACT 57.056 29.630 0.00 0.00 0.00 2.57
185 586 9.587772 TTAAGATGTCAAGATTTGCTACTACTC 57.412 33.333 0.00 0.00 0.00 2.59
290 699 8.023050 AGTTTATTCTTTCAATCGACACTGAG 57.977 34.615 0.00 0.00 0.00 3.35
291 700 4.935885 ATTCTTTCAATCGACACTGAGC 57.064 40.909 0.00 0.00 0.00 4.26
292 701 3.385193 TCTTTCAATCGACACTGAGCA 57.615 42.857 0.00 0.00 0.00 4.26
294 703 4.318332 TCTTTCAATCGACACTGAGCAAT 58.682 39.130 0.00 0.00 0.00 3.56
295 704 5.478407 TCTTTCAATCGACACTGAGCAATA 58.522 37.500 0.00 0.00 0.00 1.90
296 705 5.578336 TCTTTCAATCGACACTGAGCAATAG 59.422 40.000 0.00 0.00 0.00 1.73
297 706 3.785486 TCAATCGACACTGAGCAATAGG 58.215 45.455 0.00 0.00 0.00 2.57
414 823 2.159142 ACAGTCCGTGACGTTTCTTCTT 60.159 45.455 3.64 0.00 37.67 2.52
457 866 2.734606 CTCGCGTTTCAACTCCACATTA 59.265 45.455 5.77 0.00 0.00 1.90
579 1081 3.447586 TGGTAGCTAGCTGAGTTTAGTGG 59.552 47.826 27.68 0.00 0.00 4.00
582 1084 4.993029 AGCTAGCTGAGTTTAGTGGTAG 57.007 45.455 18.57 0.00 34.71 3.18
584 1086 3.131400 GCTAGCTGAGTTTAGTGGTAGCT 59.869 47.826 7.70 0.00 46.53 3.32
586 1088 4.993029 AGCTGAGTTTAGTGGTAGCTAG 57.007 45.455 0.00 0.00 39.50 3.42
588 1090 3.131400 GCTGAGTTTAGTGGTAGCTAGCT 59.869 47.826 23.12 23.12 0.00 3.32
589 1091 4.677584 CTGAGTTTAGTGGTAGCTAGCTG 58.322 47.826 27.68 0.77 0.00 4.24
590 1092 4.341487 TGAGTTTAGTGGTAGCTAGCTGA 58.659 43.478 27.68 8.15 0.00 4.26
591 1093 4.399618 TGAGTTTAGTGGTAGCTAGCTGAG 59.600 45.833 27.68 0.00 0.00 3.35
592 1094 4.345854 AGTTTAGTGGTAGCTAGCTGAGT 58.654 43.478 27.68 15.15 0.00 3.41
593 1095 4.773149 AGTTTAGTGGTAGCTAGCTGAGTT 59.227 41.667 27.68 11.07 0.00 3.01
594 1096 5.246429 AGTTTAGTGGTAGCTAGCTGAGTTT 59.754 40.000 27.68 12.11 0.00 2.66
595 1097 6.436532 AGTTTAGTGGTAGCTAGCTGAGTTTA 59.563 38.462 27.68 11.13 0.00 2.01
597 1099 4.345854 AGTGGTAGCTAGCTGAGTTTAGT 58.654 43.478 27.68 7.50 0.00 2.24
598 1100 4.158764 AGTGGTAGCTAGCTGAGTTTAGTG 59.841 45.833 27.68 0.00 0.00 2.74
601 1103 4.082136 GGTAGCTAGCTGAGTTTAGTGTGT 60.082 45.833 27.68 0.00 0.00 3.72
602 1104 4.181309 AGCTAGCTGAGTTTAGTGTGTC 57.819 45.455 18.57 0.00 0.00 3.67
603 1105 3.056465 AGCTAGCTGAGTTTAGTGTGTCC 60.056 47.826 18.57 0.00 0.00 4.02
604 1106 3.056465 GCTAGCTGAGTTTAGTGTGTCCT 60.056 47.826 7.70 0.00 0.00 3.85
605 1107 4.158025 GCTAGCTGAGTTTAGTGTGTCCTA 59.842 45.833 7.70 0.00 0.00 2.94
644 1152 9.621629 TTTCTATCCCAAATAAATGACACGTAT 57.378 29.630 0.00 0.00 0.00 3.06
655 1174 5.537300 AATGACACGTATCTGCTCCTATT 57.463 39.130 0.00 0.00 0.00 1.73
725 1289 5.931146 CCTCATGCAAGAATATCTACTGTCC 59.069 44.000 0.00 0.00 0.00 4.02
847 1992 4.798907 CGCAATGAGTAGACAAGACGTATT 59.201 41.667 0.00 0.00 0.00 1.89
887 2273 3.879295 CTCGATTCATGCATGTAAGGGTT 59.121 43.478 25.43 1.17 0.00 4.11
908 2296 7.039993 AGGGTTCGTGAGCACTTAAAATAAATT 60.040 33.333 0.00 0.00 0.00 1.82
957 2630 6.122277 AGCATGCAAAGAAAGCCTACTAATA 58.878 36.000 21.98 0.00 0.00 0.98
1153 3291 4.866508 ATCTCGGCGTTTCTATATGGAA 57.133 40.909 6.85 0.00 0.00 3.53
1208 3346 5.805728 AGGGTCAGATCGTGAAATACTTTT 58.194 37.500 0.00 0.00 36.74 2.27
1819 3992 1.841663 GCCATGCGTCACGTTCAACT 61.842 55.000 0.00 0.00 0.00 3.16
1824 3997 1.937223 TGCGTCACGTTCAACTTCATT 59.063 42.857 0.00 0.00 0.00 2.57
2118 4318 4.402192 CGTGCGTACATGCTAGCT 57.598 55.556 17.23 0.00 35.36 3.32
2119 4319 3.544615 CGTGCGTACATGCTAGCTA 57.455 52.632 17.23 2.58 35.36 3.32
2320 5103 2.121832 TGGGTGGTGAGGACGGAT 59.878 61.111 0.00 0.00 0.00 4.18
2437 5402 3.948719 GTGGGGGCCTTCGTGACA 61.949 66.667 0.84 0.00 0.00 3.58
2617 7268 3.067461 CGAGGTATGAAGAGAAGGAGGTG 59.933 52.174 0.00 0.00 0.00 4.00
2653 7304 3.047280 GCACGGGCATTGACGACA 61.047 61.111 3.77 0.00 40.72 4.35
2793 7444 2.194859 AGATGACCTCATGGAAGCTGT 58.805 47.619 0.00 0.00 36.57 4.40
2828 7479 3.372954 GGAAGGACGACGATATGAAGTG 58.627 50.000 0.00 0.00 0.00 3.16
2864 7515 7.662604 AAATCCTTTCTTTTGCTGCTTTATG 57.337 32.000 0.00 0.00 0.00 1.90
3007 7833 4.815308 TCCTTGTAACAAATCCGAACGAAA 59.185 37.500 0.00 0.00 0.00 3.46
3042 7869 2.083774 GTGTCTGCCGGAATGAATTGA 58.916 47.619 5.05 0.00 0.00 2.57
3043 7870 2.684881 GTGTCTGCCGGAATGAATTGAT 59.315 45.455 5.05 0.00 0.00 2.57
3060 7887 1.414550 TGATCGTGAACCAACCTGTGA 59.585 47.619 0.00 0.00 0.00 3.58
3063 7890 2.925724 TCGTGAACCAACCTGTGATTT 58.074 42.857 0.00 0.00 0.00 2.17
3088 7958 5.968676 TGGTTATAAGGATAGTGGTGCTT 57.031 39.130 0.00 0.00 34.05 3.91
3126 7997 3.806949 AGGTAAGTTGCCATCCAAAGA 57.193 42.857 12.91 0.00 34.68 2.52
3274 8167 3.250762 CGAGTTGTTTGGAAGATCAAGCA 59.749 43.478 0.00 0.00 36.37 3.91
3321 9874 0.918310 AAGCAAGGATCAGGCCCTCT 60.918 55.000 0.00 0.00 32.57 3.69
3425 10007 7.581213 AATGACATGTTGTAAAGAGGAAACA 57.419 32.000 0.00 0.00 36.98 2.83
3483 10065 3.005791 AGGTCAAGCAGTTTTGTAATGCC 59.994 43.478 0.00 0.00 40.89 4.40
3506 10088 7.154656 GCCACTCAAACTTTCCAGAATTAATT 58.845 34.615 0.00 0.00 0.00 1.40
3665 10247 1.002502 GGCCGCCACCTAAAGAACT 60.003 57.895 3.91 0.00 0.00 3.01
3674 10256 1.270678 ACCTAAAGAACTGTCGGCCAC 60.271 52.381 2.24 0.25 0.00 5.01
3675 10257 1.439679 CTAAAGAACTGTCGGCCACC 58.560 55.000 2.24 0.00 0.00 4.61
3677 10259 0.535102 AAAGAACTGTCGGCCACCAG 60.535 55.000 15.33 15.33 34.82 4.00
3678 10260 3.050275 GAACTGTCGGCCACCAGC 61.050 66.667 16.53 0.59 42.60 4.85
3688 10270 1.817099 GCCACCAGCAGAATCCTCG 60.817 63.158 0.00 0.00 42.97 4.63
3789 10372 2.575532 CTTGGCTTCTGGTCTTGTTCA 58.424 47.619 0.00 0.00 0.00 3.18
3796 10379 3.708403 TCTGGTCTTGTTCATCAGCAT 57.292 42.857 0.00 0.00 0.00 3.79
3803 10386 1.746470 TGTTCATCAGCATGCTCAGG 58.254 50.000 19.68 7.21 34.76 3.86
3804 10387 1.279846 TGTTCATCAGCATGCTCAGGA 59.720 47.619 19.68 10.32 34.76 3.86
3805 10388 2.092592 TGTTCATCAGCATGCTCAGGAT 60.093 45.455 19.68 15.13 34.76 3.24
3806 10389 2.950309 GTTCATCAGCATGCTCAGGATT 59.050 45.455 19.68 0.34 34.76 3.01
3807 10390 3.292492 TCATCAGCATGCTCAGGATTT 57.708 42.857 19.68 0.00 34.76 2.17
3808 10391 3.628008 TCATCAGCATGCTCAGGATTTT 58.372 40.909 19.68 0.00 34.76 1.82
3809 10392 4.021229 TCATCAGCATGCTCAGGATTTTT 58.979 39.130 19.68 0.00 34.76 1.94
3828 10411 4.364415 TTTTGTCGAAAGAAACCACCTG 57.636 40.909 0.00 0.00 45.01 4.00
3829 10412 2.702592 TGTCGAAAGAAACCACCTGT 57.297 45.000 0.00 0.00 45.01 4.00
3830 10413 2.285083 TGTCGAAAGAAACCACCTGTG 58.715 47.619 0.00 0.00 45.01 3.66
3831 10414 1.002792 GTCGAAAGAAACCACCTGTGC 60.003 52.381 0.00 0.00 45.01 4.57
3832 10415 1.021202 CGAAAGAAACCACCTGTGCA 58.979 50.000 0.00 0.00 0.00 4.57
3833 10416 1.002468 CGAAAGAAACCACCTGTGCAG 60.002 52.381 0.00 0.00 0.00 4.41
3834 10417 0.746659 AAAGAAACCACCTGTGCAGC 59.253 50.000 0.00 0.00 0.00 5.25
3835 10418 1.109323 AAGAAACCACCTGTGCAGCC 61.109 55.000 0.00 0.00 0.00 4.85
3836 10419 2.906897 AAACCACCTGTGCAGCCG 60.907 61.111 0.00 0.00 0.00 5.52
3837 10420 3.414136 AAACCACCTGTGCAGCCGA 62.414 57.895 0.00 0.00 0.00 5.54
3838 10421 2.902423 AAACCACCTGTGCAGCCGAA 62.902 55.000 0.00 0.00 0.00 4.30
3839 10422 2.360350 CCACCTGTGCAGCCGAAT 60.360 61.111 0.00 0.00 0.00 3.34
3840 10423 1.973281 CCACCTGTGCAGCCGAATT 60.973 57.895 0.00 0.00 0.00 2.17
3841 10424 1.210931 CACCTGTGCAGCCGAATTG 59.789 57.895 0.00 0.00 0.00 2.32
3842 10425 2.180017 CCTGTGCAGCCGAATTGC 59.820 61.111 0.00 0.00 41.86 3.56
3843 10426 2.180017 CTGTGCAGCCGAATTGCC 59.820 61.111 0.00 0.00 40.81 4.52
3844 10427 2.596923 TGTGCAGCCGAATTGCCA 60.597 55.556 0.00 0.14 40.81 4.92
3845 10428 2.180017 GTGCAGCCGAATTGCCAG 59.820 61.111 0.00 0.00 40.81 4.85
3846 10429 2.033911 TGCAGCCGAATTGCCAGA 59.966 55.556 0.00 0.00 40.81 3.86
3847 10430 1.603171 TGCAGCCGAATTGCCAGAA 60.603 52.632 0.00 0.00 40.81 3.02
3848 10431 1.177895 TGCAGCCGAATTGCCAGAAA 61.178 50.000 0.00 0.00 40.81 2.52
3849 10432 0.038343 GCAGCCGAATTGCCAGAAAA 60.038 50.000 0.00 0.00 35.54 2.29
3850 10433 1.986698 CAGCCGAATTGCCAGAAAAG 58.013 50.000 0.00 0.00 0.00 2.27
3851 10434 1.541147 CAGCCGAATTGCCAGAAAAGA 59.459 47.619 0.00 0.00 0.00 2.52
3852 10435 1.541588 AGCCGAATTGCCAGAAAAGAC 59.458 47.619 0.00 0.00 0.00 3.01
3853 10436 1.402852 GCCGAATTGCCAGAAAAGACC 60.403 52.381 0.00 0.00 0.00 3.85
3854 10437 1.202348 CCGAATTGCCAGAAAAGACCC 59.798 52.381 0.00 0.00 0.00 4.46
3855 10438 1.202348 CGAATTGCCAGAAAAGACCCC 59.798 52.381 0.00 0.00 0.00 4.95
3856 10439 1.550524 GAATTGCCAGAAAAGACCCCC 59.449 52.381 0.00 0.00 0.00 5.40
3857 10440 0.786435 ATTGCCAGAAAAGACCCCCT 59.214 50.000 0.00 0.00 0.00 4.79
3858 10441 0.560688 TTGCCAGAAAAGACCCCCTT 59.439 50.000 0.00 0.00 36.47 3.95
3859 10442 0.560688 TGCCAGAAAAGACCCCCTTT 59.439 50.000 0.00 0.00 46.47 3.11
3860 10443 1.783979 TGCCAGAAAAGACCCCCTTTA 59.216 47.619 0.00 0.00 43.90 1.85
3861 10444 2.178106 TGCCAGAAAAGACCCCCTTTAA 59.822 45.455 0.00 0.00 43.90 1.52
3862 10445 2.826128 GCCAGAAAAGACCCCCTTTAAG 59.174 50.000 0.00 0.00 43.90 1.85
3863 10446 3.499745 GCCAGAAAAGACCCCCTTTAAGA 60.500 47.826 0.00 0.00 43.90 2.10
3864 10447 4.079970 CCAGAAAAGACCCCCTTTAAGAC 58.920 47.826 0.00 0.00 43.90 3.01
3865 10448 4.447180 CCAGAAAAGACCCCCTTTAAGACA 60.447 45.833 0.00 0.00 43.90 3.41
3866 10449 5.137551 CAGAAAAGACCCCCTTTAAGACAA 58.862 41.667 0.00 0.00 43.90 3.18
3867 10450 5.775195 CAGAAAAGACCCCCTTTAAGACAAT 59.225 40.000 0.00 0.00 43.90 2.71
3868 10451 6.267699 CAGAAAAGACCCCCTTTAAGACAATT 59.732 38.462 0.00 0.00 43.90 2.32
3869 10452 6.844388 AGAAAAGACCCCCTTTAAGACAATTT 59.156 34.615 0.00 0.00 43.90 1.82
3870 10453 6.419484 AAAGACCCCCTTTAAGACAATTTG 57.581 37.500 0.00 0.00 42.93 2.32
3871 10454 5.333566 AGACCCCCTTTAAGACAATTTGA 57.666 39.130 2.79 0.00 0.00 2.69
3872 10455 5.077564 AGACCCCCTTTAAGACAATTTGAC 58.922 41.667 2.79 0.00 0.00 3.18
3873 10456 4.810345 ACCCCCTTTAAGACAATTTGACA 58.190 39.130 2.79 0.00 0.00 3.58
3874 10457 5.212745 ACCCCCTTTAAGACAATTTGACAA 58.787 37.500 2.79 0.00 0.00 3.18
3875 10458 5.663556 ACCCCCTTTAAGACAATTTGACAAA 59.336 36.000 2.48 2.48 0.00 2.83
3876 10459 6.157123 ACCCCCTTTAAGACAATTTGACAAAA 59.843 34.615 4.41 2.13 0.00 2.44
3877 10460 7.051000 CCCCCTTTAAGACAATTTGACAAAAA 58.949 34.615 4.41 1.81 0.00 1.94
3878 10461 7.226523 CCCCCTTTAAGACAATTTGACAAAAAG 59.773 37.037 4.41 10.13 0.00 2.27
3879 10462 7.226523 CCCCTTTAAGACAATTTGACAAAAAGG 59.773 37.037 22.84 22.84 36.71 3.11
3880 10463 7.984617 CCCTTTAAGACAATTTGACAAAAAGGA 59.015 33.333 26.91 0.00 37.84 3.36
3881 10464 8.817100 CCTTTAAGACAATTTGACAAAAAGGAC 58.183 33.333 24.09 5.15 37.84 3.85
3882 10465 8.710835 TTTAAGACAATTTGACAAAAAGGACC 57.289 30.769 4.41 0.00 0.00 4.46
3883 10466 5.276461 AGACAATTTGACAAAAAGGACCC 57.724 39.130 4.41 0.00 0.00 4.46
3884 10467 4.100963 AGACAATTTGACAAAAAGGACCCC 59.899 41.667 4.41 0.00 0.00 4.95
3885 10468 3.135712 ACAATTTGACAAAAAGGACCCCC 59.864 43.478 4.41 0.00 0.00 5.40
3921 10504 3.327754 GCGTCAAGCGACACGTGT 61.328 61.111 23.64 23.64 42.74 4.49
3922 10505 2.837280 CGTCAAGCGACACGTGTC 59.163 61.111 33.76 33.76 42.74 3.67
3923 10506 1.942223 CGTCAAGCGACACGTGTCA 60.942 57.895 39.14 22.54 44.99 3.58
3924 10507 1.558383 GTCAAGCGACACGTGTCAC 59.442 57.895 39.14 32.69 44.99 3.67
3925 10508 1.590525 TCAAGCGACACGTGTCACC 60.591 57.895 39.14 30.31 44.99 4.02
3926 10509 1.591594 CAAGCGACACGTGTCACCT 60.592 57.895 39.14 31.70 44.99 4.00
3927 10510 1.591594 AAGCGACACGTGTCACCTG 60.592 57.895 39.14 27.02 44.99 4.00
3928 10511 3.702555 GCGACACGTGTCACCTGC 61.703 66.667 39.14 31.34 44.99 4.85
3929 10512 2.027605 CGACACGTGTCACCTGCT 59.972 61.111 39.14 10.09 44.99 4.24
3930 10513 2.302952 CGACACGTGTCACCTGCTG 61.303 63.158 39.14 22.34 44.99 4.41
3931 10514 2.588877 ACACGTGTCACCTGCTGC 60.589 61.111 17.22 0.00 0.00 5.25
3932 10515 3.349006 CACGTGTCACCTGCTGCC 61.349 66.667 7.58 0.00 0.00 4.85
3933 10516 3.860605 ACGTGTCACCTGCTGCCA 61.861 61.111 0.00 0.00 0.00 4.92
3934 10517 3.349006 CGTGTCACCTGCTGCCAC 61.349 66.667 0.00 0.00 0.00 5.01
3935 10518 2.111878 GTGTCACCTGCTGCCACT 59.888 61.111 0.00 0.00 0.00 4.00
3936 10519 2.111669 TGTCACCTGCTGCCACTG 59.888 61.111 0.00 0.00 0.00 3.66
3937 10520 2.111878 GTCACCTGCTGCCACTGT 59.888 61.111 0.00 0.00 0.00 3.55
3938 10521 2.111669 TCACCTGCTGCCACTGTG 59.888 61.111 0.00 0.00 0.00 3.66
3939 10522 3.667282 CACCTGCTGCCACTGTGC 61.667 66.667 1.29 0.00 0.00 4.57
3941 10524 4.994471 CCTGCTGCCACTGTGCGA 62.994 66.667 1.29 0.00 0.00 5.10
3942 10525 3.420606 CTGCTGCCACTGTGCGAG 61.421 66.667 1.29 1.21 0.00 5.03
3943 10526 4.994471 TGCTGCCACTGTGCGAGG 62.994 66.667 1.29 0.00 0.00 4.63
4002 10585 1.941325 CTGGAACGGGAATCAGCTAC 58.059 55.000 0.00 0.00 0.00 3.58
4003 10586 1.482593 CTGGAACGGGAATCAGCTACT 59.517 52.381 0.00 0.00 0.00 2.57
4004 10587 1.207089 TGGAACGGGAATCAGCTACTG 59.793 52.381 0.00 0.00 0.00 2.74
4005 10588 1.291132 GAACGGGAATCAGCTACTGC 58.709 55.000 0.00 0.00 40.05 4.40
4006 10589 0.460284 AACGGGAATCAGCTACTGCG 60.460 55.000 0.00 0.00 45.42 5.18
4007 10590 1.320344 ACGGGAATCAGCTACTGCGA 61.320 55.000 0.00 0.00 45.42 5.10
4008 10591 0.032678 CGGGAATCAGCTACTGCGAT 59.967 55.000 0.00 0.00 45.42 4.58
4009 10592 1.506493 GGGAATCAGCTACTGCGATG 58.494 55.000 0.00 0.00 45.42 3.84
4010 10593 1.069204 GGGAATCAGCTACTGCGATGA 59.931 52.381 0.00 0.00 45.42 2.92
4011 10594 2.483714 GGGAATCAGCTACTGCGATGAA 60.484 50.000 0.00 0.00 45.42 2.57
4012 10595 3.198068 GGAATCAGCTACTGCGATGAAA 58.802 45.455 0.00 0.00 45.42 2.69
4013 10596 3.001736 GGAATCAGCTACTGCGATGAAAC 59.998 47.826 0.00 0.00 45.42 2.78
4014 10597 1.629013 TCAGCTACTGCGATGAAACG 58.371 50.000 0.00 0.00 45.42 3.60
4015 10598 0.647410 CAGCTACTGCGATGAAACGG 59.353 55.000 0.00 0.00 45.42 4.44
4016 10599 0.460284 AGCTACTGCGATGAAACGGG 60.460 55.000 0.00 0.00 45.42 5.28
4017 10600 2.006772 CTACTGCGATGAAACGGGC 58.993 57.895 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.954102 TGAGATGCACACCCTATATATGTAGT 59.046 38.462 5.85 0.00 0.00 2.73
3 4 7.785033 CATGAGATGCACACCCTATATATGTA 58.215 38.462 0.00 0.00 0.00 2.29
20 21 0.800631 AAGTGTGCACGCATGAGATG 59.199 50.000 30.53 0.00 36.20 2.90
21 22 0.800631 CAAGTGTGCACGCATGAGAT 59.199 50.000 30.53 7.47 36.20 2.75
23 24 1.208358 CCAAGTGTGCACGCATGAG 59.792 57.895 31.07 19.35 36.20 2.90
24 25 1.506309 GACCAAGTGTGCACGCATGA 61.506 55.000 31.07 3.30 36.20 3.07
25 26 1.081906 GACCAAGTGTGCACGCATG 60.082 57.895 30.53 27.48 36.20 4.06
26 27 1.227943 AGACCAAGTGTGCACGCAT 60.228 52.632 30.53 17.94 36.20 4.73
27 28 2.179547 CAGACCAAGTGTGCACGCA 61.180 57.895 30.53 2.55 36.20 5.24
28 29 2.633657 CAGACCAAGTGTGCACGC 59.366 61.111 22.76 22.76 36.20 5.34
29 30 1.523711 ACCAGACCAAGTGTGCACG 60.524 57.895 13.13 0.00 36.20 5.34
30 31 1.447317 CCACCAGACCAAGTGTGCAC 61.447 60.000 10.75 10.75 31.88 4.57
32 33 2.555547 GCCACCAGACCAAGTGTGC 61.556 63.158 0.00 0.00 31.88 4.57
34 35 1.072331 CTAAGCCACCAGACCAAGTGT 59.928 52.381 0.00 0.00 31.88 3.55
37 38 1.021390 CGCTAAGCCACCAGACCAAG 61.021 60.000 0.00 0.00 0.00 3.61
39 40 2.214216 ACGCTAAGCCACCAGACCA 61.214 57.895 0.00 0.00 0.00 4.02
40 41 1.741770 CACGCTAAGCCACCAGACC 60.742 63.158 0.00 0.00 0.00 3.85
41 42 2.391389 GCACGCTAAGCCACCAGAC 61.391 63.158 0.00 0.00 0.00 3.51
43 44 3.490759 CGCACGCTAAGCCACCAG 61.491 66.667 0.00 0.00 0.00 4.00
72 73 1.837538 ATTCGAACCCGCAACACGTG 61.838 55.000 15.48 15.48 41.42 4.49
73 74 1.562575 GATTCGAACCCGCAACACGT 61.563 55.000 0.00 0.00 41.42 4.49
76 77 1.673009 GGGATTCGAACCCGCAACA 60.673 57.895 16.67 0.00 37.85 3.33
82 83 2.822701 GTGCGGGGATTCGAACCC 60.823 66.667 21.07 21.07 46.05 4.11
87 88 0.250295 ATATGTGGTGCGGGGATTCG 60.250 55.000 0.00 0.00 0.00 3.34
89 90 2.054799 ACTATATGTGGTGCGGGGATT 58.945 47.619 0.00 0.00 0.00 3.01
90 91 1.729586 ACTATATGTGGTGCGGGGAT 58.270 50.000 0.00 0.00 0.00 3.85
92 93 3.695830 ATTACTATATGTGGTGCGGGG 57.304 47.619 0.00 0.00 0.00 5.73
93 94 6.640518 AGATAATTACTATATGTGGTGCGGG 58.359 40.000 0.00 0.00 0.00 6.13
95 96 7.008357 CACGAGATAATTACTATATGTGGTGCG 59.992 40.741 0.00 0.00 30.31 5.34
96 97 7.813148 ACACGAGATAATTACTATATGTGGTGC 59.187 37.037 0.00 0.00 36.71 5.01
97 98 9.692749 AACACGAGATAATTACTATATGTGGTG 57.307 33.333 0.00 4.93 38.14 4.17
108 109 8.116753 CCAATCAGTGAAACACGAGATAATTAC 58.883 37.037 0.00 0.00 41.43 1.89
109 110 8.038351 TCCAATCAGTGAAACACGAGATAATTA 58.962 33.333 0.00 0.00 41.43 1.40
110 111 6.878923 TCCAATCAGTGAAACACGAGATAATT 59.121 34.615 0.00 0.00 41.43 1.40
111 112 6.406370 TCCAATCAGTGAAACACGAGATAAT 58.594 36.000 0.00 0.00 41.43 1.28
112 113 5.789521 TCCAATCAGTGAAACACGAGATAA 58.210 37.500 0.00 2.25 41.43 1.75
114 115 4.271696 TCCAATCAGTGAAACACGAGAT 57.728 40.909 0.00 0.00 41.43 2.75
117 118 4.215399 GGAAATCCAATCAGTGAAACACGA 59.785 41.667 0.00 0.00 36.27 4.35
118 119 4.023279 TGGAAATCCAATCAGTGAAACACG 60.023 41.667 0.00 0.00 44.35 4.49
123 124 3.507233 GTGCTGGAAATCCAATCAGTGAA 59.493 43.478 3.35 0.00 46.97 3.18
234 635 3.124270 CAATGCACGCCTACCGCA 61.124 61.111 0.00 0.00 41.76 5.69
290 699 1.604278 GTGATTTCGGCCTCCTATTGC 59.396 52.381 0.00 0.00 0.00 3.56
291 700 2.874701 CAGTGATTTCGGCCTCCTATTG 59.125 50.000 0.00 0.00 0.00 1.90
292 701 2.505819 ACAGTGATTTCGGCCTCCTATT 59.494 45.455 0.00 0.00 0.00 1.73
294 703 1.568504 ACAGTGATTTCGGCCTCCTA 58.431 50.000 0.00 0.00 0.00 2.94
295 704 0.693049 AACAGTGATTTCGGCCTCCT 59.307 50.000 0.00 0.00 0.00 3.69
296 705 1.087501 GAACAGTGATTTCGGCCTCC 58.912 55.000 0.00 0.00 0.00 4.30
297 706 1.734465 CAGAACAGTGATTTCGGCCTC 59.266 52.381 0.00 0.00 0.00 4.70
414 823 4.700692 AGCTATCTCGGCGTTTCTATATGA 59.299 41.667 6.85 0.00 34.52 2.15
447 856 2.073816 CTCGGCGTTTTAATGTGGAGT 58.926 47.619 6.85 0.00 0.00 3.85
457 866 0.806492 GCTAGCTAGCTCGGCGTTTT 60.806 55.000 33.71 0.00 45.62 2.43
579 1081 5.061920 ACACACTAAACTCAGCTAGCTAC 57.938 43.478 18.86 0.00 0.00 3.58
582 1084 3.056465 AGGACACACTAAACTCAGCTAGC 60.056 47.826 6.62 6.62 0.00 3.42
584 1086 5.394224 GCATAGGACACACTAAACTCAGCTA 60.394 44.000 0.00 0.00 0.00 3.32
586 1088 3.619038 GCATAGGACACACTAAACTCAGC 59.381 47.826 0.00 0.00 0.00 4.26
588 1090 4.882842 TGCATAGGACACACTAAACTCA 57.117 40.909 0.00 0.00 0.00 3.41
589 1091 4.034510 GCATGCATAGGACACACTAAACTC 59.965 45.833 14.21 0.00 0.00 3.01
590 1092 3.941483 GCATGCATAGGACACACTAAACT 59.059 43.478 14.21 0.00 0.00 2.66
591 1093 3.689161 TGCATGCATAGGACACACTAAAC 59.311 43.478 18.46 0.00 0.00 2.01
592 1094 3.949132 TGCATGCATAGGACACACTAAA 58.051 40.909 18.46 0.00 0.00 1.85
593 1095 3.625649 TGCATGCATAGGACACACTAA 57.374 42.857 18.46 0.00 0.00 2.24
594 1096 3.843893 ATGCATGCATAGGACACACTA 57.156 42.857 31.35 0.00 34.49 2.74
595 1097 2.723322 ATGCATGCATAGGACACACT 57.277 45.000 31.35 4.12 34.49 3.55
597 1099 2.158971 ACGTATGCATGCATAGGACACA 60.159 45.455 43.83 24.61 43.45 3.72
598 1100 2.483876 ACGTATGCATGCATAGGACAC 58.516 47.619 43.83 31.81 43.45 3.67
601 1103 4.071961 AGAAACGTATGCATGCATAGGA 57.928 40.909 43.83 26.49 43.45 2.94
602 1104 5.063944 GGATAGAAACGTATGCATGCATAGG 59.936 44.000 39.25 39.25 45.12 2.57
603 1105 5.063944 GGGATAGAAACGTATGCATGCATAG 59.936 44.000 34.99 28.52 39.29 2.23
604 1106 4.935205 GGGATAGAAACGTATGCATGCATA 59.065 41.667 31.75 31.75 37.82 3.14
605 1107 3.753272 GGGATAGAAACGTATGCATGCAT 59.247 43.478 33.92 33.92 40.19 3.96
644 1152 5.519808 TCCTAGTTCTTGAATAGGAGCAGA 58.480 41.667 12.90 0.00 40.09 4.26
655 1174 2.957006 GGGCTACGATCCTAGTTCTTGA 59.043 50.000 0.00 0.00 0.00 3.02
865 2010 3.470709 ACCCTTACATGCATGAATCGAG 58.529 45.455 32.75 19.25 0.00 4.04
871 2016 2.027653 TCACGAACCCTTACATGCATGA 60.028 45.455 32.75 13.72 0.00 3.07
908 2296 4.820716 GCTTAGGAGATCGTGGAGTACTAA 59.179 45.833 0.00 0.00 0.00 2.24
973 2646 6.176183 AGTGCATGCAAATAGTACTCTCTTT 58.824 36.000 24.58 0.00 0.00 2.52
974 2647 5.738909 AGTGCATGCAAATAGTACTCTCTT 58.261 37.500 24.58 0.00 0.00 2.85
975 2648 5.350504 AGTGCATGCAAATAGTACTCTCT 57.649 39.130 24.58 7.62 0.00 3.10
976 2649 4.208047 CGAGTGCATGCAAATAGTACTCTC 59.792 45.833 24.58 18.89 41.09 3.20
1153 3291 2.304751 ACAGTCCGTGACGTTTCTTT 57.695 45.000 3.64 0.00 37.67 2.52
1208 3346 9.554395 TCTTTGCCATAAAATGAACTCGATATA 57.446 29.630 0.00 0.00 0.00 0.86
1246 3384 2.359900 GGCCGAAATCACTGTTCTGAT 58.640 47.619 0.00 0.00 31.84 2.90
1331 3482 7.591006 TTCTTTGCGAATTACTACTGTTAGG 57.409 36.000 0.00 0.00 0.00 2.69
1335 3486 7.305474 CCATTTTCTTTGCGAATTACTACTGT 58.695 34.615 0.00 0.00 0.00 3.55
1558 3731 1.836999 TTCACCGGTATGCCACTGCT 61.837 55.000 6.87 0.00 38.71 4.24
1696 3869 3.887335 TTTCCTGTACGGGGCGCAC 62.887 63.158 20.89 4.83 0.00 5.34
1707 3880 0.036010 CCCTGATGAGCGTTTCCTGT 60.036 55.000 0.00 0.00 0.00 4.00
1819 3992 1.808411 GTCGAGAAGGCACCAATGAA 58.192 50.000 0.00 0.00 0.00 2.57
1824 3997 3.282745 GAGCGTCGAGAAGGCACCA 62.283 63.158 0.00 0.00 41.29 4.17
2007 4207 1.571460 GAAGCAGTCACCTTGCACG 59.429 57.895 0.00 0.00 43.92 5.34
2117 4317 3.036429 GCAGTGACAGGGGGCCTAG 62.036 68.421 0.84 0.00 29.64 3.02
2118 4318 3.009115 GCAGTGACAGGGGGCCTA 61.009 66.667 0.84 0.00 29.64 3.93
2437 5402 2.426023 GACTTCCACCCGCAGTGT 59.574 61.111 3.43 0.00 45.74 3.55
2584 7235 0.172578 CATACCTCGTGCTCCGAACA 59.827 55.000 0.99 0.00 46.75 3.18
2617 7268 1.526917 CACATCTTGGGCGGGGATC 60.527 63.158 0.00 0.00 0.00 3.36
2653 7304 1.229359 CCCTCCAGGCTGCATGAAT 59.771 57.895 16.80 0.00 0.00 2.57
2828 7479 5.956068 AGAAAGGATTTTGAGCAAGTCTC 57.044 39.130 0.00 0.00 39.27 3.36
2864 7515 4.129380 TGACCGACCATCATTCATCAATC 58.871 43.478 0.00 0.00 0.00 2.67
3007 7833 5.296780 CGGCAGACACATCATTTATTAAGGT 59.703 40.000 0.00 0.00 0.00 3.50
3042 7869 2.859165 ATCACAGGTTGGTTCACGAT 57.141 45.000 0.00 0.00 0.00 3.73
3043 7870 2.616376 CAAATCACAGGTTGGTTCACGA 59.384 45.455 0.00 0.00 0.00 4.35
3060 7887 7.448469 GCACCACTATCCTTATAACCATCAAAT 59.552 37.037 0.00 0.00 0.00 2.32
3063 7890 5.606749 AGCACCACTATCCTTATAACCATCA 59.393 40.000 0.00 0.00 0.00 3.07
3126 7997 3.903530 AGTTGTCCTTGGAAGGGAATT 57.096 42.857 5.58 0.00 46.47 2.17
3241 8134 0.250901 AACAACTCGCTTCATGGCCT 60.251 50.000 3.32 0.00 0.00 5.19
3274 8167 5.245751 TGGCCAATATGTCAAATGTTCAAGT 59.754 36.000 0.61 0.00 0.00 3.16
3307 9860 1.133199 CAGACTAGAGGGCCTGATCCT 60.133 57.143 12.95 3.76 37.33 3.24
3315 9868 1.406205 GGAAGCAACAGACTAGAGGGC 60.406 57.143 0.00 0.00 0.00 5.19
3321 9874 2.028748 GGTTACGGGAAGCAACAGACTA 60.029 50.000 0.00 0.00 35.51 2.59
3425 10007 8.918202 TTCAACAGTTTATCAGGTAATGTTCT 57.082 30.769 0.00 0.00 28.05 3.01
3506 10088 4.563580 GCTCGGCCAAAATAGGATATCAGA 60.564 45.833 2.24 0.00 0.00 3.27
3629 10211 3.075005 GGGTGCGCCTCCAGAGTA 61.075 66.667 17.49 0.00 34.45 2.59
3647 10229 1.002502 AGTTCTTTAGGTGGCGGCC 60.003 57.895 13.32 13.32 0.00 6.13
3657 10239 0.759959 TGGTGGCCGACAGTTCTTTA 59.240 50.000 0.00 0.00 0.00 1.85
3665 10247 2.803155 GATTCTGCTGGTGGCCGACA 62.803 60.000 0.00 0.00 40.92 4.35
3674 10256 2.587194 CGGCGAGGATTCTGCTGG 60.587 66.667 0.00 0.00 0.00 4.85
3675 10257 3.267860 GCGGCGAGGATTCTGCTG 61.268 66.667 12.98 1.12 38.04 4.41
3678 10260 4.918201 GGGGCGGCGAGGATTCTG 62.918 72.222 12.98 0.00 0.00 3.02
3753 10336 1.857348 AAGGAAGGTTGGGAGGGGG 60.857 63.158 0.00 0.00 0.00 5.40
3754 10337 1.384191 CAAGGAAGGTTGGGAGGGG 59.616 63.158 0.00 0.00 0.00 4.79
3806 10389 4.218852 ACAGGTGGTTTCTTTCGACAAAAA 59.781 37.500 0.00 0.00 0.00 1.94
3807 10390 3.759618 ACAGGTGGTTTCTTTCGACAAAA 59.240 39.130 0.00 0.00 0.00 2.44
3808 10391 3.127895 CACAGGTGGTTTCTTTCGACAAA 59.872 43.478 0.00 0.00 0.00 2.83
3809 10392 2.680841 CACAGGTGGTTTCTTTCGACAA 59.319 45.455 0.00 0.00 0.00 3.18
3810 10393 2.285083 CACAGGTGGTTTCTTTCGACA 58.715 47.619 0.00 0.00 0.00 4.35
3811 10394 1.002792 GCACAGGTGGTTTCTTTCGAC 60.003 52.381 1.10 0.00 0.00 4.20
3812 10395 1.305201 GCACAGGTGGTTTCTTTCGA 58.695 50.000 1.10 0.00 0.00 3.71
3813 10396 1.002468 CTGCACAGGTGGTTTCTTTCG 60.002 52.381 1.10 0.00 0.00 3.46
3814 10397 1.269257 GCTGCACAGGTGGTTTCTTTC 60.269 52.381 1.10 0.00 0.00 2.62
3815 10398 0.746659 GCTGCACAGGTGGTTTCTTT 59.253 50.000 1.10 0.00 0.00 2.52
3816 10399 1.109323 GGCTGCACAGGTGGTTTCTT 61.109 55.000 0.50 0.00 0.00 2.52
3817 10400 1.529244 GGCTGCACAGGTGGTTTCT 60.529 57.895 0.50 0.00 0.00 2.52
3818 10401 2.908073 CGGCTGCACAGGTGGTTTC 61.908 63.158 0.50 0.00 0.00 2.78
3819 10402 2.902423 TTCGGCTGCACAGGTGGTTT 62.902 55.000 0.50 0.00 0.00 3.27
3820 10403 2.697147 ATTCGGCTGCACAGGTGGTT 62.697 55.000 0.50 0.00 0.00 3.67
3821 10404 2.697147 AATTCGGCTGCACAGGTGGT 62.697 55.000 0.50 0.00 0.00 4.16
3822 10405 1.973281 AATTCGGCTGCACAGGTGG 60.973 57.895 0.50 0.00 0.00 4.61
3823 10406 1.210931 CAATTCGGCTGCACAGGTG 59.789 57.895 0.50 0.00 0.00 4.00
3824 10407 2.629656 GCAATTCGGCTGCACAGGT 61.630 57.895 0.50 0.00 39.69 4.00
3825 10408 2.180017 GCAATTCGGCTGCACAGG 59.820 61.111 0.50 0.00 39.69 4.00
3826 10409 2.180017 GGCAATTCGGCTGCACAG 59.820 61.111 0.50 0.00 41.78 3.66
3827 10410 2.596923 TGGCAATTCGGCTGCACA 60.597 55.556 0.50 0.86 41.78 4.57
3828 10411 1.865788 TTCTGGCAATTCGGCTGCAC 61.866 55.000 0.50 0.00 41.78 4.57
3829 10412 1.177895 TTTCTGGCAATTCGGCTGCA 61.178 50.000 0.50 0.00 41.78 4.41
3830 10413 0.038343 TTTTCTGGCAATTCGGCTGC 60.038 50.000 0.00 0.00 41.89 5.25
3831 10414 1.541147 TCTTTTCTGGCAATTCGGCTG 59.459 47.619 0.00 0.00 41.89 4.85
3832 10415 1.541588 GTCTTTTCTGGCAATTCGGCT 59.458 47.619 0.00 0.00 41.89 5.52
3833 10416 1.402852 GGTCTTTTCTGGCAATTCGGC 60.403 52.381 0.00 0.00 41.67 5.54
3834 10417 1.202348 GGGTCTTTTCTGGCAATTCGG 59.798 52.381 0.00 0.00 0.00 4.30
3835 10418 1.202348 GGGGTCTTTTCTGGCAATTCG 59.798 52.381 0.00 0.00 0.00 3.34
3836 10419 1.550524 GGGGGTCTTTTCTGGCAATTC 59.449 52.381 0.00 0.00 0.00 2.17
3837 10420 1.149923 AGGGGGTCTTTTCTGGCAATT 59.850 47.619 0.00 0.00 0.00 2.32
3838 10421 0.786435 AGGGGGTCTTTTCTGGCAAT 59.214 50.000 0.00 0.00 0.00 3.56
3839 10422 0.560688 AAGGGGGTCTTTTCTGGCAA 59.439 50.000 0.00 0.00 29.99 4.52
3840 10423 0.560688 AAAGGGGGTCTTTTCTGGCA 59.439 50.000 0.00 0.00 42.62 4.92
3841 10424 2.597578 TAAAGGGGGTCTTTTCTGGC 57.402 50.000 0.00 0.00 42.62 4.85
3842 10425 4.079970 GTCTTAAAGGGGGTCTTTTCTGG 58.920 47.826 0.00 0.00 42.62 3.86
3843 10426 4.725490 TGTCTTAAAGGGGGTCTTTTCTG 58.275 43.478 0.00 0.00 42.62 3.02
3844 10427 5.397553 TTGTCTTAAAGGGGGTCTTTTCT 57.602 39.130 0.00 0.00 42.62 2.52
3845 10428 6.665992 AATTGTCTTAAAGGGGGTCTTTTC 57.334 37.500 0.00 0.00 42.62 2.29
3846 10429 6.613679 TCAAATTGTCTTAAAGGGGGTCTTTT 59.386 34.615 0.00 0.00 42.62 2.27
3847 10430 6.041637 GTCAAATTGTCTTAAAGGGGGTCTTT 59.958 38.462 0.00 0.00 46.49 2.52
3848 10431 5.538813 GTCAAATTGTCTTAAAGGGGGTCTT 59.461 40.000 0.00 0.00 37.28 3.01
3849 10432 5.077564 GTCAAATTGTCTTAAAGGGGGTCT 58.922 41.667 0.00 0.00 0.00 3.85
3850 10433 4.830600 TGTCAAATTGTCTTAAAGGGGGTC 59.169 41.667 0.00 0.00 0.00 4.46
3851 10434 4.810345 TGTCAAATTGTCTTAAAGGGGGT 58.190 39.130 0.00 0.00 0.00 4.95
3852 10435 5.799827 TTGTCAAATTGTCTTAAAGGGGG 57.200 39.130 0.00 0.00 0.00 5.40
3853 10436 7.226523 CCTTTTTGTCAAATTGTCTTAAAGGGG 59.773 37.037 18.47 10.21 36.87 4.79
3854 10437 7.984617 TCCTTTTTGTCAAATTGTCTTAAAGGG 59.015 33.333 22.02 16.55 39.51 3.95
3855 10438 8.817100 GTCCTTTTTGTCAAATTGTCTTAAAGG 58.183 33.333 19.33 19.33 40.09 3.11
3856 10439 8.817100 GGTCCTTTTTGTCAAATTGTCTTAAAG 58.183 33.333 0.00 0.00 0.00 1.85
3857 10440 7.766738 GGGTCCTTTTTGTCAAATTGTCTTAAA 59.233 33.333 0.00 0.00 0.00 1.52
3858 10441 7.269316 GGGTCCTTTTTGTCAAATTGTCTTAA 58.731 34.615 0.00 0.00 0.00 1.85
3859 10442 6.183360 GGGGTCCTTTTTGTCAAATTGTCTTA 60.183 38.462 0.00 0.00 0.00 2.10
3860 10443 5.396324 GGGGTCCTTTTTGTCAAATTGTCTT 60.396 40.000 0.00 0.00 0.00 3.01
3861 10444 4.100963 GGGGTCCTTTTTGTCAAATTGTCT 59.899 41.667 0.00 0.00 0.00 3.41
3862 10445 4.377021 GGGGTCCTTTTTGTCAAATTGTC 58.623 43.478 0.00 0.00 0.00 3.18
3863 10446 3.135712 GGGGGTCCTTTTTGTCAAATTGT 59.864 43.478 0.00 0.00 0.00 2.71
3864 10447 3.390967 AGGGGGTCCTTTTTGTCAAATTG 59.609 43.478 0.00 0.00 41.56 2.32
3865 10448 3.664320 AGGGGGTCCTTTTTGTCAAATT 58.336 40.909 0.00 0.00 41.56 1.82
3866 10449 3.344535 AGGGGGTCCTTTTTGTCAAAT 57.655 42.857 0.00 0.00 41.56 2.32
3867 10450 2.858787 AGGGGGTCCTTTTTGTCAAA 57.141 45.000 0.00 0.00 41.56 2.69
3904 10487 3.264487 GACACGTGTCGCTTGACGC 62.264 63.158 31.03 7.70 45.95 5.19
3905 10488 2.837280 GACACGTGTCGCTTGACG 59.163 61.111 31.03 0.00 45.95 4.35
3913 10496 2.598632 GCAGCAGGTGACACGTGTC 61.599 63.158 36.01 36.01 44.97 3.67
3914 10497 2.588877 GCAGCAGGTGACACGTGT 60.589 61.111 23.64 23.64 36.45 4.49
3915 10498 3.349006 GGCAGCAGGTGACACGTG 61.349 66.667 21.16 21.16 37.08 4.49
3916 10499 3.860605 TGGCAGCAGGTGACACGT 61.861 61.111 3.25 0.00 40.35 4.49
3919 10502 2.111669 CAGTGGCAGCAGGTGACA 59.888 61.111 3.25 3.25 44.49 3.58
3920 10503 2.111878 ACAGTGGCAGCAGGTGAC 59.888 61.111 3.02 0.00 32.89 3.67
3921 10504 2.111669 CACAGTGGCAGCAGGTGA 59.888 61.111 3.02 0.00 0.00 4.02
3922 10505 3.667282 GCACAGTGGCAGCAGGTG 61.667 66.667 1.84 0.00 0.00 4.00
3924 10507 4.994471 TCGCACAGTGGCAGCAGG 62.994 66.667 1.84 0.00 0.00 4.85
3925 10508 3.420606 CTCGCACAGTGGCAGCAG 61.421 66.667 1.84 0.00 0.00 4.24
3926 10509 4.994471 CCTCGCACAGTGGCAGCA 62.994 66.667 1.84 0.00 0.00 4.41
3977 10560 3.645268 ATTCCCGTTCCAGGCAGCC 62.645 63.158 1.84 1.84 0.00 4.85
3978 10561 2.044946 ATTCCCGTTCCAGGCAGC 60.045 61.111 0.00 0.00 0.00 5.25
3979 10562 0.745845 CTGATTCCCGTTCCAGGCAG 60.746 60.000 0.00 0.00 0.00 4.85
3980 10563 1.299648 CTGATTCCCGTTCCAGGCA 59.700 57.895 0.00 0.00 0.00 4.75
3981 10564 2.115291 GCTGATTCCCGTTCCAGGC 61.115 63.158 0.00 0.00 0.00 4.85
3982 10565 0.830648 TAGCTGATTCCCGTTCCAGG 59.169 55.000 0.00 0.00 0.00 4.45
3983 10566 1.482593 AGTAGCTGATTCCCGTTCCAG 59.517 52.381 0.00 0.00 0.00 3.86
3984 10567 1.207089 CAGTAGCTGATTCCCGTTCCA 59.793 52.381 0.00 0.00 32.44 3.53
3985 10568 1.941325 CAGTAGCTGATTCCCGTTCC 58.059 55.000 0.00 0.00 32.44 3.62
3986 10569 1.291132 GCAGTAGCTGATTCCCGTTC 58.709 55.000 0.00 0.00 37.91 3.95
3987 10570 0.460284 CGCAGTAGCTGATTCCCGTT 60.460 55.000 0.00 0.00 39.10 4.44
3988 10571 1.141881 CGCAGTAGCTGATTCCCGT 59.858 57.895 0.00 0.00 39.10 5.28
3989 10572 0.032678 ATCGCAGTAGCTGATTCCCG 59.967 55.000 0.00 0.00 39.10 5.14
3990 10573 1.069204 TCATCGCAGTAGCTGATTCCC 59.931 52.381 0.00 0.00 39.10 3.97
3991 10574 2.515926 TCATCGCAGTAGCTGATTCC 57.484 50.000 0.00 0.00 39.10 3.01
3992 10575 3.302092 CGTTTCATCGCAGTAGCTGATTC 60.302 47.826 0.00 0.00 39.10 2.52
3993 10576 2.604914 CGTTTCATCGCAGTAGCTGATT 59.395 45.455 0.00 0.00 39.10 2.57
3994 10577 2.196749 CGTTTCATCGCAGTAGCTGAT 58.803 47.619 0.00 0.00 39.10 2.90
3995 10578 1.629013 CGTTTCATCGCAGTAGCTGA 58.371 50.000 0.00 0.00 39.10 4.26
3996 10579 0.647410 CCGTTTCATCGCAGTAGCTG 59.353 55.000 0.00 0.00 39.10 4.24
3997 10580 0.460284 CCCGTTTCATCGCAGTAGCT 60.460 55.000 0.00 0.00 39.10 3.32
3998 10581 2.006772 CCCGTTTCATCGCAGTAGC 58.993 57.895 0.00 0.00 37.42 3.58
3999 10582 2.006772 GCCCGTTTCATCGCAGTAG 58.993 57.895 0.00 0.00 0.00 2.57
4000 10583 4.195308 GCCCGTTTCATCGCAGTA 57.805 55.556 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.