Multiple sequence alignment - TraesCS6B01G347900

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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 TraesCS6B01G347900 chr6B 100.000 3552 0 0 1 3552 612846963 612850514 0.000000e+00 6560.0
1 TraesCS6B01G347900 chr6B 80.287 1461 244 34 1028 2479 612857372 612858797 0.000000e+00 1062.0
2 TraesCS6B01G347900 chr6B 95.050 303 15 0 2812 3114 705177029 705177331 8.920000e-131 477.0
3 TraesCS6B01G347900 chr6B 93.871 310 19 0 2807 3116 719752494 719752185 5.370000e-128 468.0
4 TraesCS6B01G347900 chr6B 90.000 180 13 4 1 176 554343228 554343050 9.920000e-56 228.0
5 TraesCS6B01G347900 chr6B 90.714 140 13 0 180 319 616328865 616329004 1.680000e-43 187.0
6 TraesCS6B01G347900 chr6D 93.674 1802 81 12 768 2553 408182991 408184775 0.000000e+00 2665.0
7 TraesCS6B01G347900 chr6D 80.316 1458 251 28 1028 2479 408213422 408214849 0.000000e+00 1070.0
8 TraesCS6B01G347900 chr6D 92.611 203 15 0 394 596 3331884 3331682 3.470000e-75 292.0
9 TraesCS6B01G347900 chr6D 92.611 203 15 0 394 596 3337764 3337562 3.470000e-75 292.0
10 TraesCS6B01G347900 chr6D 91.626 203 17 0 394 596 3326008 3325806 7.510000e-72 281.0
11 TraesCS6B01G347900 chr6D 83.696 184 18 7 1 180 452846480 452846305 2.840000e-36 163.0
12 TraesCS6B01G347900 chr6D 74.510 255 48 14 1026 1270 430401676 430401923 1.050000e-15 95.3
13 TraesCS6B01G347900 chr6D 86.585 82 10 1 1 81 28252090 28252009 4.880000e-14 89.8
14 TraesCS6B01G347900 chr6A 92.692 1820 95 14 983 2787 553925942 553927738 0.000000e+00 2590.0
15 TraesCS6B01G347900 chr6A 79.823 1472 257 32 1028 2478 554302880 554304332 0.000000e+00 1037.0
16 TraesCS6B01G347900 chr6A 89.189 185 14 4 1 180 607138507 607138690 3.570000e-55 226.0
17 TraesCS6B01G347900 chr6A 89.189 185 14 4 1 180 607277151 607277334 3.570000e-55 226.0
18 TraesCS6B01G347900 chr6A 84.188 234 16 9 178 398 607138840 607139065 1.290000e-49 207.0
19 TraesCS6B01G347900 chr6A 84.188 234 16 9 178 398 607277484 607277709 1.290000e-49 207.0
20 TraesCS6B01G347900 chr6A 77.863 131 27 2 1026 1155 576911124 576911253 2.940000e-11 80.5
21 TraesCS6B01G347900 chr6A 82.474 97 8 6 607 694 607139100 607139196 3.800000e-10 76.8
22 TraesCS6B01G347900 chr6A 82.474 97 8 6 607 694 607277744 607277840 3.800000e-10 76.8
23 TraesCS6B01G347900 chr7B 87.265 746 86 7 2812 3552 718595407 718594666 0.000000e+00 843.0
24 TraesCS6B01G347900 chr7B 96.568 437 15 0 3116 3552 548372151 548371715 0.000000e+00 725.0
25 TraesCS6B01G347900 chr7B 95.881 437 17 1 3116 3552 583157930 583157495 0.000000e+00 706.0
26 TraesCS6B01G347900 chr7B 95.881 437 17 1 3116 3552 643202891 643202456 0.000000e+00 706.0
27 TraesCS6B01G347900 chr7B 95.082 305 14 1 2812 3116 526845737 526846040 2.480000e-131 479.0
28 TraesCS6B01G347900 chr7B 93.333 210 12 2 394 601 678131976 678132185 3.440000e-80 309.0
29 TraesCS6B01G347900 chr7B 93.659 205 13 0 400 604 117500850 117500646 1.240000e-79 307.0
30 TraesCS6B01G347900 chr7B 92.488 213 14 2 394 604 30391855 30391643 1.600000e-78 303.0
31 TraesCS6B01G347900 chr5B 96.110 437 17 0 3116 3552 614364587 614364151 0.000000e+00 713.0
32 TraesCS6B01G347900 chr5B 95.410 305 13 1 2812 3116 699242908 699242605 5.330000e-133 484.0
33 TraesCS6B01G347900 chr5B 95.082 305 15 0 2812 3116 614364920 614364616 6.900000e-132 481.0
34 TraesCS6B01G347900 chr5B 86.154 195 22 2 180 369 542734922 542734728 4.650000e-49 206.0
35 TraesCS6B01G347900 chrUn 95.312 448 16 4 3102 3549 371064766 371065208 0.000000e+00 706.0
36 TraesCS6B01G347900 chrUn 94.923 453 16 6 3102 3552 2576592 2577039 0.000000e+00 702.0
37 TraesCS6B01G347900 chrUn 95.089 448 17 4 3102 3549 43163600 43164042 0.000000e+00 701.0
38 TraesCS6B01G347900 chrUn 94.463 307 15 2 2811 3116 293082283 293081978 4.150000e-129 472.0
39 TraesCS6B01G347900 chrUn 93.810 210 11 2 394 601 282758359 282758568 7.400000e-82 315.0
40 TraesCS6B01G347900 chrUn 93.427 213 12 2 394 604 291518138 291517926 7.400000e-82 315.0
41 TraesCS6B01G347900 chrUn 93.564 202 12 1 400 601 322259837 322260037 2.070000e-77 300.0
42 TraesCS6B01G347900 chrUn 92.195 205 15 1 400 604 3504368 3504571 4.490000e-74 289.0
43 TraesCS6B01G347900 chrUn 92.195 205 15 1 400 604 244454673 244454876 4.490000e-74 289.0
44 TraesCS6B01G347900 chrUn 91.878 197 16 0 400 596 103268589 103268393 3.490000e-70 276.0
45 TraesCS6B01G347900 chrUn 90.909 209 13 3 394 596 348381653 348381445 3.490000e-70 276.0
46 TraesCS6B01G347900 chrUn 90.594 202 19 0 400 601 118800278 118800479 5.840000e-68 268.0
47 TraesCS6B01G347900 chrUn 91.327 196 17 0 401 596 340274698 340274503 5.840000e-68 268.0
48 TraesCS6B01G347900 chrUn 90.244 205 18 2 394 596 338512852 338512648 2.100000e-67 267.0
49 TraesCS6B01G347900 chrUn 89.189 185 14 4 1 180 308646092 308646275 3.570000e-55 226.0
50 TraesCS6B01G347900 chrUn 84.188 234 16 9 178 398 308646425 308646650 1.290000e-49 207.0
51 TraesCS6B01G347900 chrUn 82.474 97 8 6 607 694 308646685 308646781 3.800000e-10 76.8
52 TraesCS6B01G347900 chr7A 94.678 451 20 3 3102 3552 540868749 540869195 0.000000e+00 697.0
53 TraesCS6B01G347900 chr2B 95.066 304 15 0 2813 3116 675704909 675704606 2.480000e-131 479.0
54 TraesCS6B01G347900 chr2B 94.118 221 10 1 178 398 666728706 666728923 2.040000e-87 333.0
55 TraesCS6B01G347900 chr2B 93.458 214 12 2 394 605 782101369 782101582 2.060000e-82 316.0
56 TraesCS6B01G347900 chr2B 92.925 212 13 2 392 601 681818166 681818377 1.240000e-79 307.0
57 TraesCS6B01G347900 chr2B 95.679 162 7 0 603 764 666728953 666729114 9.780000e-66 261.0
58 TraesCS6B01G347900 chr2B 74.848 493 106 15 1974 2456 18949329 18948845 1.290000e-49 207.0
59 TraesCS6B01G347900 chr2B 88.372 172 17 1 198 369 5163136 5162968 1.670000e-48 204.0
60 TraesCS6B01G347900 chr1A 94.737 304 16 0 2813 3116 585041357 585041054 1.150000e-129 473.0
61 TraesCS6B01G347900 chr1A 90.868 219 17 3 386 604 291233046 291232831 1.250000e-74 291.0
62 TraesCS6B01G347900 chr1A 83.333 120 15 5 2168 2286 130150345 130150460 4.850000e-19 106.0
63 TraesCS6B01G347900 chr2D 95.122 205 10 0 400 604 452402037 452401833 1.230000e-84 324.0
64 TraesCS6B01G347900 chr2D 84.545 110 14 2 269 375 573914118 573914227 4.850000e-19 106.0
65 TraesCS6B01G347900 chr3B 94.118 204 12 0 401 604 813188507 813188304 9.580000e-81 311.0
66 TraesCS6B01G347900 chr3B 88.360 189 20 2 180 367 805329201 805329388 3.570000e-55 226.0
67 TraesCS6B01G347900 chr1B 91.403 221 17 1 178 398 626650190 626649972 5.760000e-78 302.0
68 TraesCS6B01G347900 chr1B 92.056 214 15 2 393 604 139035572 139035785 2.070000e-77 300.0
69 TraesCS6B01G347900 chr1B 92.381 210 14 2 394 601 654508410 654508619 7.450000e-77 298.0
70 TraesCS6B01G347900 chr1B 89.730 185 13 5 1 180 626650592 626650409 7.670000e-57 231.0
71 TraesCS6B01G347900 chr4B 91.781 219 12 5 382 595 65592574 65592791 2.070000e-77 300.0
72 TraesCS6B01G347900 chr4B 93.814 194 12 0 402 595 106082777 106082584 3.470000e-75 292.0
73 TraesCS6B01G347900 chr4B 90.909 220 17 3 384 601 495325101 495325319 3.470000e-75 292.0
74 TraesCS6B01G347900 chr4B 91.905 210 15 2 394 601 673166276 673166485 3.470000e-75 292.0
75 TraesCS6B01G347900 chr4B 92.121 165 13 0 178 342 623403521 623403357 2.130000e-57 233.0
76 TraesCS6B01G347900 chr4B 86.170 188 16 4 1 186 623403847 623403668 1.010000e-45 195.0
77 TraesCS6B01G347900 chr4B 72.805 467 101 18 1922 2371 663656882 663657339 6.190000e-28 135.0
78 TraesCS6B01G347900 chr1D 90.950 221 18 1 178 398 457045206 457044988 2.680000e-76 296.0
79 TraesCS6B01G347900 chr1D 92.271 207 16 0 400 606 7431242 7431036 9.640000e-76 294.0
80 TraesCS6B01G347900 chr1D 90.950 221 15 4 178 398 228041443 228041228 3.470000e-75 292.0
81 TraesCS6B01G347900 chr1D 91.220 205 17 1 400 604 46331027 46330824 9.710000e-71 278.0
82 TraesCS6B01G347900 chr1D 92.391 184 9 5 1 180 457045524 457045342 1.270000e-64 257.0
83 TraesCS6B01G347900 chr1D 87.027 185 14 6 1 180 467125370 467125191 2.160000e-47 200.0
84 TraesCS6B01G347900 chr1D 86.339 183 19 5 1 180 467125843 467125664 1.010000e-45 195.0
85 TraesCS6B01G347900 chr1D 86.264 182 15 8 1 180 228041773 228041600 4.680000e-44 189.0
86 TraesCS6B01G347900 chr1D 87.421 159 9 7 616 764 457044943 457044786 4.710000e-39 172.0
87 TraesCS6B01G347900 chr1D 90.000 50 2 2 269 316 24773188 24773140 1.060000e-05 62.1
88 TraesCS6B01G347900 chr7D 90.498 221 18 3 389 606 385395537 385395317 4.490000e-74 289.0
89 TraesCS6B01G347900 chr7D 87.065 201 17 8 1 197 117466985 117467180 5.970000e-53 219.0
90 TraesCS6B01G347900 chr7D 93.525 139 9 0 178 316 236001857 236001719 1.290000e-49 207.0
91 TraesCS6B01G347900 chr7D 86.702 188 15 7 1 180 71581310 71581495 2.160000e-47 200.0
92 TraesCS6B01G347900 chr7D 93.333 135 7 1 264 398 236001735 236001603 7.780000e-47 198.0
93 TraesCS6B01G347900 chr3D 91.707 205 17 0 400 604 108291053 108290849 5.800000e-73 285.0
94 TraesCS6B01G347900 chr3D 77.869 244 45 7 1055 1292 54985865 54985625 3.700000e-30 143.0
95 TraesCS6B01G347900 chr4D 92.893 197 10 2 400 596 117654565 117654757 2.090000e-72 283.0
96 TraesCS6B01G347900 chr4D 90.610 213 15 2 394 604 295141451 295141242 9.710000e-71 278.0
97 TraesCS6B01G347900 chr4D 89.720 214 19 2 386 596 96715626 96715839 1.630000e-68 270.0
98 TraesCS6B01G347900 chr4D 89.720 214 18 4 387 596 462467735 462467522 1.630000e-68 270.0
99 TraesCS6B01G347900 chr4D 90.000 190 19 0 180 369 481460417 481460606 2.740000e-61 246.0
100 TraesCS6B01G347900 chr4D 80.524 267 40 8 1029 1292 477911975 477912232 1.010000e-45 195.0
101 TraesCS6B01G347900 chr4A 80.060 336 53 8 1037 1371 662110802 662110480 1.650000e-58 237.0
102 TraesCS6B01G347900 chr4A 85.443 158 22 1 180 337 668354711 668354867 2.840000e-36 163.0
103 TraesCS6B01G347900 chr5A 89.503 181 14 3 1 177 605698099 605698278 1.280000e-54 224.0
104 TraesCS6B01G347900 chr5A 78.244 262 46 10 2167 2424 468871330 468871584 1.320000e-34 158.0
105 TraesCS6B01G347900 chr5A 78.995 219 40 6 2167 2382 533082967 533082752 1.030000e-30 145.0
106 TraesCS6B01G347900 chr2A 88.172 186 19 2 185 369 16020471 16020654 5.970000e-53 219.0
107 TraesCS6B01G347900 chr5D 88.462 182 15 3 1 176 378954560 378954741 7.720000e-52 215.0
108 TraesCS6B01G347900 chr5D 91.346 104 8 1 282 385 539865810 539865912 1.330000e-29 141.0
109 TraesCS6B01G347900 chr3A 76.642 274 55 6 1025 1292 65466659 65466929 3.700000e-30 143.0


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 TraesCS6B01G347900 chr6B 612846963 612850514 3551 False 6560.000000 6560 100.0000 1 3552 1 chr6B.!!$F1 3551
1 TraesCS6B01G347900 chr6B 612857372 612858797 1425 False 1062.000000 1062 80.2870 1028 2479 1 chr6B.!!$F2 1451
2 TraesCS6B01G347900 chr6D 408182991 408184775 1784 False 2665.000000 2665 93.6740 768 2553 1 chr6D.!!$F1 1785
3 TraesCS6B01G347900 chr6D 408213422 408214849 1427 False 1070.000000 1070 80.3160 1028 2479 1 chr6D.!!$F2 1451
4 TraesCS6B01G347900 chr6A 553925942 553927738 1796 False 2590.000000 2590 92.6920 983 2787 1 chr6A.!!$F1 1804
5 TraesCS6B01G347900 chr6A 554302880 554304332 1452 False 1037.000000 1037 79.8230 1028 2478 1 chr6A.!!$F2 1450
6 TraesCS6B01G347900 chr7B 718594666 718595407 741 True 843.000000 843 87.2650 2812 3552 1 chr7B.!!$R6 740
7 TraesCS6B01G347900 chr5B 614364151 614364920 769 True 597.000000 713 95.5960 2812 3552 2 chr5B.!!$R3 740
8 TraesCS6B01G347900 chr1B 626649972 626650592 620 True 266.500000 302 90.5665 1 398 2 chr1B.!!$R1 397
9 TraesCS6B01G347900 chr1D 457044786 457045524 738 True 241.666667 296 90.2540 1 764 3 chr1D.!!$R5 763
10 TraesCS6B01G347900 chr1D 228041228 228041773 545 True 240.500000 292 88.6070 1 398 2 chr1D.!!$R4 397

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
941 1192 0.095935 CACTGCCGAAATCGAGCTTG 59.904 55.0 4.04 0.0 43.02 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2553 2844 0.042188 GCATATACACGCGCACTTGG 60.042 55.0 5.73 0.0 0.0 3.61 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
40 41 4.661125 TGCATATTTCGACAAGTGCAATC 58.339 39.130 10.59 0.00 39.36 2.67
42 43 4.731961 GCATATTTCGACAAGTGCAATCTG 59.268 41.667 6.65 0.00 33.09 2.90
44 45 6.545508 CATATTTCGACAAGTGCAATCTGAA 58.454 36.000 0.00 0.00 0.00 3.02
45 46 4.891627 TTTCGACAAGTGCAATCTGAAA 57.108 36.364 0.00 0.00 0.00 2.69
183 424 3.838244 ATACCAGTGCCACGAATATGT 57.162 42.857 0.00 0.00 0.00 2.29
197 438 7.195646 CCACGAATATGTTCAGTTTTGCATAT 58.804 34.615 2.95 0.00 36.45 1.78
262 503 8.913487 AATATGTGTGAGAATGCTATTCATCA 57.087 30.769 10.26 8.30 33.40 3.07
272 513 7.281098 AGAATGCTATTCATCAGTGAGATTGT 58.719 34.615 0.00 0.00 35.39 2.71
278 519 6.615264 ATTCATCAGTGAGATTGTACATGC 57.385 37.500 0.00 0.00 35.39 4.06
320 561 4.976864 TGTGAGATTGCACATATAGCCAT 58.023 39.130 0.00 0.00 43.35 4.40
330 571 6.067350 TGCACATATAGCCATTAACCATTGA 58.933 36.000 0.00 0.00 0.00 2.57
343 584 9.111613 CCATTAACCATTGAATGCAATTATGTT 57.888 29.630 0.00 3.88 41.87 2.71
376 617 8.874156 TGCTATTCATAGGTCATCTACAAAGAT 58.126 33.333 0.00 0.00 43.54 2.40
388 629 8.416329 GTCATCTACAAAGATTTGGCCAATTAT 58.584 33.333 21.26 11.15 40.65 1.28
389 630 9.639563 TCATCTACAAAGATTTGGCCAATTATA 57.360 29.630 21.26 4.13 40.65 0.98
402 643 8.967779 TTGGCCAATTATACTATACTACCTCT 57.032 34.615 16.05 0.00 0.00 3.69
403 644 8.591114 TGGCCAATTATACTATACTACCTCTC 57.409 38.462 0.61 0.00 0.00 3.20
404 645 8.399529 TGGCCAATTATACTATACTACCTCTCT 58.600 37.037 0.61 0.00 0.00 3.10
405 646 8.905850 GGCCAATTATACTATACTACCTCTCTC 58.094 40.741 0.00 0.00 0.00 3.20
415 656 9.398538 ACTATACTACCTCTCTCAGTTTACAAG 57.601 37.037 0.00 0.00 0.00 3.16
417 658 3.686916 ACCTCTCTCAGTTTACAAGGC 57.313 47.619 0.00 0.00 0.00 4.35
418 659 2.028930 ACCTCTCTCAGTTTACAAGGCG 60.029 50.000 0.00 0.00 0.00 5.52
419 660 2.028930 CCTCTCTCAGTTTACAAGGCGT 60.029 50.000 0.00 0.00 0.00 5.68
420 661 2.989840 CTCTCTCAGTTTACAAGGCGTG 59.010 50.000 0.00 0.00 0.00 5.34
421 662 1.461127 CTCTCAGTTTACAAGGCGTGC 59.539 52.381 0.00 0.00 0.00 5.34
422 663 0.163788 CTCAGTTTACAAGGCGTGCG 59.836 55.000 0.00 0.00 0.00 5.34
423 664 1.440353 CAGTTTACAAGGCGTGCGC 60.440 57.895 8.17 8.17 41.06 6.09
424 665 2.498887 GTTTACAAGGCGTGCGCG 60.499 61.111 16.86 16.86 43.06 6.86
425 666 2.968156 TTTACAAGGCGTGCGCGT 60.968 55.556 22.18 8.25 43.06 6.01
426 667 1.664017 TTTACAAGGCGTGCGCGTA 60.664 52.632 22.18 0.00 43.06 4.42
427 668 1.888958 TTTACAAGGCGTGCGCGTAC 61.889 55.000 22.18 17.94 43.06 3.67
434 675 4.564116 CGTGCGCGTACCCCTAGG 62.564 72.222 21.71 0.06 40.04 3.02
436 677 3.142838 TGCGCGTACCCCTAGGTC 61.143 66.667 8.43 0.00 46.45 3.85
437 678 4.261781 GCGCGTACCCCTAGGTCG 62.262 72.222 8.43 8.12 46.45 4.79
438 679 2.825836 CGCGTACCCCTAGGTCGT 60.826 66.667 8.29 6.00 46.45 4.34
439 680 2.828128 CGCGTACCCCTAGGTCGTC 61.828 68.421 8.29 3.46 46.45 4.20
440 681 1.750399 GCGTACCCCTAGGTCGTCA 60.750 63.158 8.29 0.00 46.45 4.35
441 682 1.315257 GCGTACCCCTAGGTCGTCAA 61.315 60.000 8.29 0.00 46.45 3.18
442 683 1.396653 CGTACCCCTAGGTCGTCAAT 58.603 55.000 8.29 0.00 46.45 2.57
443 684 1.753073 CGTACCCCTAGGTCGTCAATT 59.247 52.381 8.29 0.00 46.45 2.32
444 685 2.167075 CGTACCCCTAGGTCGTCAATTT 59.833 50.000 8.29 0.00 46.45 1.82
445 686 2.781681 ACCCCTAGGTCGTCAATTTG 57.218 50.000 8.29 0.00 46.45 2.32
446 687 2.262637 ACCCCTAGGTCGTCAATTTGA 58.737 47.619 8.29 0.00 46.45 2.69
447 688 2.027469 ACCCCTAGGTCGTCAATTTGAC 60.027 50.000 17.76 17.76 46.45 3.18
448 689 5.201262 ACCCCTAGGTCGTCAATTTGACC 62.201 52.174 20.87 10.15 46.45 4.02
456 697 5.622770 GTCGTCAATTTGACCAACCTAAT 57.377 39.130 20.87 0.00 44.20 1.73
457 698 6.730960 GTCGTCAATTTGACCAACCTAATA 57.269 37.500 20.87 0.00 44.20 0.98
458 699 7.316544 GTCGTCAATTTGACCAACCTAATAT 57.683 36.000 20.87 0.00 44.20 1.28
459 700 8.428186 GTCGTCAATTTGACCAACCTAATATA 57.572 34.615 20.87 0.00 44.20 0.86
460 701 8.885722 GTCGTCAATTTGACCAACCTAATATAA 58.114 33.333 20.87 0.00 44.20 0.98
461 702 9.104965 TCGTCAATTTGACCAACCTAATATAAG 57.895 33.333 20.87 4.88 44.20 1.73
462 703 8.889717 CGTCAATTTGACCAACCTAATATAAGT 58.110 33.333 20.87 0.00 44.20 2.24
517 758 9.784531 AACTTCAGATGTTCTATTCTCAAAAGA 57.215 29.630 0.00 0.00 0.00 2.52
518 759 9.956640 ACTTCAGATGTTCTATTCTCAAAAGAT 57.043 29.630 0.00 0.00 0.00 2.40
568 809 7.919385 ATTAGGGTGATTAAATTGGCAATCT 57.081 32.000 14.04 1.39 33.26 2.40
570 811 6.966534 AGGGTGATTAAATTGGCAATCTAG 57.033 37.500 14.04 0.00 33.26 2.43
571 812 6.672593 AGGGTGATTAAATTGGCAATCTAGA 58.327 36.000 14.04 0.00 33.26 2.43
572 813 7.300658 AGGGTGATTAAATTGGCAATCTAGAT 58.699 34.615 14.04 0.00 33.26 1.98
573 814 8.448008 AGGGTGATTAAATTGGCAATCTAGATA 58.552 33.333 14.04 0.00 33.26 1.98
574 815 9.247861 GGGTGATTAAATTGGCAATCTAGATAT 57.752 33.333 14.04 2.01 33.26 1.63
580 821 9.772973 TTAAATTGGCAATCTAGATATACGTGT 57.227 29.630 14.04 0.00 0.00 4.49
582 823 8.988064 AATTGGCAATCTAGATATACGTGTAG 57.012 34.615 14.04 0.00 0.00 2.74
583 824 6.510879 TGGCAATCTAGATATACGTGTAGG 57.489 41.667 5.46 0.00 0.00 3.18
584 825 6.243148 TGGCAATCTAGATATACGTGTAGGA 58.757 40.000 5.46 0.00 0.00 2.94
585 826 6.150641 TGGCAATCTAGATATACGTGTAGGAC 59.849 42.308 5.46 0.00 0.00 3.85
586 827 6.374894 GGCAATCTAGATATACGTGTAGGACT 59.625 42.308 5.46 0.19 0.00 3.85
587 828 7.094291 GGCAATCTAGATATACGTGTAGGACTT 60.094 40.741 5.46 0.00 0.00 3.01
588 829 7.751348 GCAATCTAGATATACGTGTAGGACTTG 59.249 40.741 5.46 0.00 0.00 3.16
589 830 8.784994 CAATCTAGATATACGTGTAGGACTTGT 58.215 37.037 5.46 0.00 0.00 3.16
592 833 9.836864 TCTAGATATACGTGTAGGACTTGTAAA 57.163 33.333 0.00 0.00 0.00 2.01
593 834 9.875675 CTAGATATACGTGTAGGACTTGTAAAC 57.124 37.037 0.00 0.00 0.00 2.01
594 835 8.517062 AGATATACGTGTAGGACTTGTAAACT 57.483 34.615 0.00 0.00 0.00 2.66
595 836 8.404000 AGATATACGTGTAGGACTTGTAAACTG 58.596 37.037 0.00 0.00 0.00 3.16
596 837 4.660789 ACGTGTAGGACTTGTAAACTGT 57.339 40.909 0.00 0.00 0.00 3.55
597 838 4.365723 ACGTGTAGGACTTGTAAACTGTG 58.634 43.478 0.00 0.00 0.00 3.66
598 839 4.098349 ACGTGTAGGACTTGTAAACTGTGA 59.902 41.667 0.00 0.00 0.00 3.58
599 840 4.443394 CGTGTAGGACTTGTAAACTGTGAC 59.557 45.833 0.00 0.00 0.00 3.67
600 841 4.443394 GTGTAGGACTTGTAAACTGTGACG 59.557 45.833 0.00 0.00 0.00 4.35
601 842 4.338964 TGTAGGACTTGTAAACTGTGACGA 59.661 41.667 0.00 0.00 0.00 4.20
602 843 4.395959 AGGACTTGTAAACTGTGACGAA 57.604 40.909 0.00 0.00 0.00 3.85
603 844 4.369182 AGGACTTGTAAACTGTGACGAAG 58.631 43.478 0.00 0.00 0.00 3.79
604 845 4.098960 AGGACTTGTAAACTGTGACGAAGA 59.901 41.667 0.00 0.00 0.00 2.87
605 846 4.989168 GGACTTGTAAACTGTGACGAAGAT 59.011 41.667 0.00 0.00 0.00 2.40
606 847 5.465724 GGACTTGTAAACTGTGACGAAGATT 59.534 40.000 0.00 0.00 0.00 2.40
607 848 6.287107 ACTTGTAAACTGTGACGAAGATTG 57.713 37.500 0.00 0.00 0.00 2.67
608 849 5.236478 ACTTGTAAACTGTGACGAAGATTGG 59.764 40.000 0.00 0.00 0.00 3.16
609 850 3.496884 TGTAAACTGTGACGAAGATTGGC 59.503 43.478 0.00 0.00 0.00 4.52
610 851 2.550830 AACTGTGACGAAGATTGGCT 57.449 45.000 0.00 0.00 0.00 4.75
611 852 2.086054 ACTGTGACGAAGATTGGCTC 57.914 50.000 0.00 0.00 0.00 4.70
612 853 0.994995 CTGTGACGAAGATTGGCTCG 59.005 55.000 0.00 0.00 0.00 5.03
613 854 0.389817 TGTGACGAAGATTGGCTCGG 60.390 55.000 0.00 0.00 0.00 4.63
614 855 1.447838 TGACGAAGATTGGCTCGGC 60.448 57.895 0.00 0.00 0.00 5.54
697 947 5.887598 TGCCTAATTAATCATGCTTGACTGT 59.112 36.000 4.14 0.00 33.85 3.55
711 961 4.703897 CTTGACTGTAACAGAGTTTGGGA 58.296 43.478 0.00 0.00 35.18 4.37
717 967 6.306987 ACTGTAACAGAGTTTGGGATCAATT 58.693 36.000 0.00 0.00 35.18 2.32
726 976 2.806945 TGGGATCAATTGACTGACCC 57.193 50.000 23.45 23.45 37.27 4.46
730 980 3.445096 GGGATCAATTGACTGACCCAAAG 59.555 47.826 24.44 0.00 36.98 2.77
733 983 5.335976 GGATCAATTGACTGACCCAAAGTTC 60.336 44.000 11.07 0.00 0.00 3.01
747 997 6.001460 ACCCAAAGTTCATTTCAGTCGATTA 58.999 36.000 0.00 0.00 0.00 1.75
764 1014 1.196104 TTAACCAGTAGCCACGCCCT 61.196 55.000 0.00 0.00 0.00 5.19
765 1015 0.324552 TAACCAGTAGCCACGCCCTA 60.325 55.000 0.00 0.00 0.00 3.53
766 1016 1.614241 AACCAGTAGCCACGCCCTAG 61.614 60.000 0.00 0.00 0.00 3.02
767 1017 2.107141 CAGTAGCCACGCCCTAGC 59.893 66.667 0.00 0.00 0.00 3.42
779 1029 1.689582 CCCTAGCGAGAAACCCCCT 60.690 63.158 0.00 0.00 0.00 4.79
781 1031 0.751452 CCTAGCGAGAAACCCCCTAC 59.249 60.000 0.00 0.00 0.00 3.18
810 1060 4.699522 GGTGGGCAGGTGTCCGTC 62.700 72.222 0.00 0.00 44.44 4.79
818 1069 0.666577 CAGGTGTCCGTCGTCTTTCC 60.667 60.000 0.00 0.00 0.00 3.13
822 1073 1.373873 GTCCGTCGTCTTTCCCCAC 60.374 63.158 0.00 0.00 0.00 4.61
825 1076 3.110178 GTCGTCTTTCCCCACGCG 61.110 66.667 3.53 3.53 35.93 6.01
826 1077 3.296836 TCGTCTTTCCCCACGCGA 61.297 61.111 15.93 0.00 35.93 5.87
831 1082 1.078426 CTTTCCCCACGCGAGGATT 60.078 57.895 24.92 0.00 30.55 3.01
832 1083 0.177141 CTTTCCCCACGCGAGGATTA 59.823 55.000 24.92 5.77 30.55 1.75
833 1084 0.614294 TTTCCCCACGCGAGGATTAA 59.386 50.000 24.92 11.62 30.55 1.40
868 1119 4.354212 CAACGTCACGCGCCACTG 62.354 66.667 5.73 0.00 46.11 3.66
923 1174 0.106419 GTTTCACCCCTCACCCAACA 60.106 55.000 0.00 0.00 0.00 3.33
937 1188 0.443869 CCAACACTGCCGAAATCGAG 59.556 55.000 4.04 0.00 43.02 4.04
941 1192 0.095935 CACTGCCGAAATCGAGCTTG 59.904 55.000 4.04 0.00 43.02 4.01
955 1217 2.334946 GCTTGCAAGCGGATCACCA 61.335 57.895 33.75 0.00 42.88 4.17
956 1218 1.798735 CTTGCAAGCGGATCACCAG 59.201 57.895 14.65 0.00 35.59 4.00
959 1221 1.375908 GCAAGCGGATCACCAGTCA 60.376 57.895 0.00 0.00 35.59 3.41
962 1224 0.687354 AAGCGGATCACCAGTCAACT 59.313 50.000 0.00 0.00 35.59 3.16
963 1225 0.247736 AGCGGATCACCAGTCAACTC 59.752 55.000 0.00 0.00 35.59 3.01
968 1230 1.546476 GATCACCAGTCAACTCCGAGT 59.454 52.381 0.00 0.00 0.00 4.18
977 1239 1.162698 CAACTCCGAGTACTCCGTCA 58.837 55.000 17.23 0.00 0.00 4.35
980 1242 2.037913 CTCCGAGTACTCCGTCAGCG 62.038 65.000 17.23 4.16 37.95 5.18
1326 1591 2.348998 CCGTTCAGGGAGCTGCTT 59.651 61.111 2.53 0.00 35.97 3.91
1336 1604 0.036010 GGAGCTGCTTGTCAGGCTTA 60.036 55.000 2.53 0.00 43.06 3.09
1392 1663 2.510238 GGCGTCATGAGCTTCGCT 60.510 61.111 22.61 0.00 46.37 4.93
1556 1830 4.772624 TGGCTAGTACAGATTGACAGTTCT 59.227 41.667 0.00 0.00 0.00 3.01
1702 1993 1.004044 CCCAGCTTCATCAGAACCACT 59.996 52.381 0.00 0.00 0.00 4.00
1801 2092 4.045771 TACGACGCGCTGGAGCAA 62.046 61.111 5.73 0.00 42.21 3.91
2296 2587 3.618780 CTGCTGGCCCTTCTTCGCT 62.619 63.158 0.00 0.00 0.00 4.93
2547 2838 1.526887 CCGGGTGTGATGGTGCTAT 59.473 57.895 0.00 0.00 0.00 2.97
2553 2844 2.939103 GGTGTGATGGTGCTATCTGAAC 59.061 50.000 0.00 0.00 0.00 3.18
2554 2845 2.939103 GTGTGATGGTGCTATCTGAACC 59.061 50.000 0.00 0.00 45.03 3.62
2560 2851 1.740025 GGTGCTATCTGAACCAAGTGC 59.260 52.381 0.00 0.00 44.17 4.40
2561 2852 1.394917 GTGCTATCTGAACCAAGTGCG 59.605 52.381 0.00 0.00 0.00 5.34
2562 2853 0.375106 GCTATCTGAACCAAGTGCGC 59.625 55.000 0.00 0.00 0.00 6.09
2563 2854 0.647410 CTATCTGAACCAAGTGCGCG 59.353 55.000 0.00 0.00 0.00 6.86
2564 2855 0.037697 TATCTGAACCAAGTGCGCGT 60.038 50.000 8.43 0.00 0.00 6.01
2565 2856 1.568612 ATCTGAACCAAGTGCGCGTG 61.569 55.000 8.43 6.19 0.00 5.34
2566 2857 2.512745 TGAACCAAGTGCGCGTGT 60.513 55.556 8.43 0.00 0.00 4.49
2567 2858 1.218875 CTGAACCAAGTGCGCGTGTA 61.219 55.000 8.43 0.00 0.00 2.90
2568 2859 0.601576 TGAACCAAGTGCGCGTGTAT 60.602 50.000 8.43 0.26 0.00 2.29
2569 2860 1.336980 TGAACCAAGTGCGCGTGTATA 60.337 47.619 8.43 0.00 0.00 1.47
2575 2869 0.875908 AGTGCGCGTGTATATGCTGG 60.876 55.000 8.43 0.00 36.66 4.85
2586 2880 1.410850 ATATGCTGGTCTCCCCGGTG 61.411 60.000 0.00 0.00 42.20 4.94
2589 2883 3.775654 CTGGTCTCCCCGGTGCTC 61.776 72.222 0.00 0.00 34.56 4.26
2606 2900 2.037121 TGCTCGGATGTTTTCTGTCTCA 59.963 45.455 0.00 0.00 32.10 3.27
2614 2910 5.335191 GGATGTTTTCTGTCTCATTTCGCTT 60.335 40.000 0.00 0.00 0.00 4.68
2620 2916 1.952990 TGTCTCATTTCGCTTTGCCAA 59.047 42.857 0.00 0.00 0.00 4.52
2636 2932 2.951642 TGCCAAGTTTCCTTCACTGAAG 59.048 45.455 11.37 11.37 39.17 3.02
2637 2933 3.214328 GCCAAGTTTCCTTCACTGAAGA 58.786 45.455 18.82 4.05 41.71 2.87
2671 2971 7.771927 ATCACAAAGATGGAAGAAACAAGAT 57.228 32.000 0.00 0.00 35.06 2.40
2680 2980 8.547173 AGATGGAAGAAACAAGATAGAATGAGT 58.453 33.333 0.00 0.00 0.00 3.41
2707 3007 4.746115 TGAAATTCTGCAGTGTGATTTTGC 59.254 37.500 14.67 6.51 38.30 3.68
2708 3008 2.798976 TTCTGCAGTGTGATTTTGCC 57.201 45.000 14.67 0.00 37.03 4.52
2723 3023 2.398803 TGCCGCGCTGCAAATAATA 58.601 47.368 24.67 0.00 38.56 0.98
2725 3025 1.120437 GCCGCGCTGCAAATAATAAC 58.880 50.000 19.50 0.00 0.00 1.89
2727 3027 0.764226 CGCGCTGCAAATAATAACGC 59.236 50.000 5.56 0.00 41.32 4.84
2728 3028 0.764226 GCGCTGCAAATAATAACGCG 59.236 50.000 3.53 3.53 41.74 6.01
2729 3029 1.854434 GCGCTGCAAATAATAACGCGT 60.854 47.619 5.58 5.58 41.00 6.01
2730 3030 1.767405 CGCTGCAAATAATAACGCGTG 59.233 47.619 14.98 0.00 35.02 5.34
2731 3031 2.780993 GCTGCAAATAATAACGCGTGT 58.219 42.857 14.98 5.77 0.00 4.49
2770 3070 3.307550 GGGAGTTGGGAGGAGTAGTTTTC 60.308 52.174 0.00 0.00 0.00 2.29
2796 3096 9.544314 CCTCGAGATGTAAATTATTAGTACTCG 57.456 37.037 15.71 0.00 38.16 4.18
2797 3097 9.544314 CTCGAGATGTAAATTATTAGTACTCGG 57.456 37.037 6.58 0.00 37.83 4.63
2798 3098 8.509690 TCGAGATGTAAATTATTAGTACTCGGG 58.490 37.037 0.00 0.00 37.83 5.14
2799 3099 8.509690 CGAGATGTAAATTATTAGTACTCGGGA 58.490 37.037 0.00 0.00 36.02 5.14
2892 3192 5.007332 ACGTAAAGACTGACATGACAAAACC 59.993 40.000 0.00 0.00 0.00 3.27
2902 3202 7.012894 ACTGACATGACAAAACCGAAAAGATAA 59.987 33.333 0.00 0.00 0.00 1.75
2924 3224 3.229276 AGAACATCTCTGAGCTTGACG 57.771 47.619 12.47 0.00 31.12 4.35
2967 3267 3.550431 ACCACGACTGCAGCCACT 61.550 61.111 15.27 0.00 0.00 4.00
2971 3271 1.146041 ACGACTGCAGCCACTGAAA 59.854 52.632 15.27 0.00 32.44 2.69
3009 3309 3.062466 CCTCACCCGAGCTCGACA 61.062 66.667 36.59 15.73 43.02 4.35
3011 3311 2.282251 TCACCCGAGCTCGACACT 60.282 61.111 36.59 12.90 43.02 3.55
3029 3329 1.690893 ACTGCTCCATCGCTGATATGT 59.309 47.619 0.00 0.00 33.66 2.29
3093 3393 2.814280 ACCGTTGAACGAATCAGACT 57.186 45.000 20.47 0.00 46.05 3.24
3176 3505 0.398696 AACCACGAACCCAGCACATA 59.601 50.000 0.00 0.00 0.00 2.29
3225 3554 0.463295 CCACAATCTGCATCCGCTCT 60.463 55.000 0.00 0.00 39.64 4.09
3316 3645 4.082523 CCACCACGAGGATGCCGT 62.083 66.667 5.68 0.00 41.36 5.68
3439 3768 4.794439 CTGTCATCGTCGCCGCCA 62.794 66.667 0.00 0.00 0.00 5.69
3459 3788 4.497340 GCCAAAACAAAGACGATGAACAGA 60.497 41.667 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.631145 TGCTTTCAGATTGCACTTGTC 57.369 42.857 0.00 0.00 0.00 3.18
30 31 5.235616 ACAATTTGCTTTCAGATTGCACTTG 59.764 36.000 8.01 12.89 44.23 3.16
40 41 7.524294 AAACTTACACACAATTTGCTTTCAG 57.476 32.000 0.00 0.00 0.00 3.02
42 43 7.958674 TCAAAACTTACACACAATTTGCTTTC 58.041 30.769 0.00 0.00 0.00 2.62
44 45 7.897575 TTCAAAACTTACACACAATTTGCTT 57.102 28.000 0.00 0.00 0.00 3.91
45 46 7.602265 ACTTTCAAAACTTACACACAATTTGCT 59.398 29.630 0.00 0.00 0.00 3.91
143 224 7.523415 TGGTATTACCCTTTCAGAAAAGAACT 58.477 34.615 10.37 0.00 41.50 3.01
144 225 7.447545 ACTGGTATTACCCTTTCAGAAAAGAAC 59.552 37.037 10.37 0.00 41.50 3.01
145 226 7.447238 CACTGGTATTACCCTTTCAGAAAAGAA 59.553 37.037 10.37 0.00 41.50 2.52
146 227 6.940298 CACTGGTATTACCCTTTCAGAAAAGA 59.060 38.462 10.37 0.00 41.50 2.52
147 228 6.349363 GCACTGGTATTACCCTTTCAGAAAAG 60.349 42.308 10.37 0.00 41.36 2.27
320 561 9.716531 TCAAACATAATTGCATTCAATGGTTAA 57.283 25.926 0.00 0.00 41.77 2.01
330 571 6.276832 AGCACTCTCAAACATAATTGCATT 57.723 33.333 0.00 0.00 0.00 3.56
343 584 6.552725 AGATGACCTATGAATAGCACTCTCAA 59.447 38.462 0.00 0.00 0.00 3.02
376 617 9.388672 AGAGGTAGTATAGTATAATTGGCCAAA 57.611 33.333 24.71 7.42 0.00 3.28
389 630 9.398538 CTTGTAAACTGAGAGAGGTAGTATAGT 57.601 37.037 0.00 0.00 0.00 2.12
398 639 2.028930 ACGCCTTGTAAACTGAGAGAGG 60.029 50.000 0.00 0.00 0.00 3.69
399 640 2.989840 CACGCCTTGTAAACTGAGAGAG 59.010 50.000 0.00 0.00 0.00 3.20
400 641 2.866460 GCACGCCTTGTAAACTGAGAGA 60.866 50.000 0.00 0.00 0.00 3.10
402 643 1.508632 GCACGCCTTGTAAACTGAGA 58.491 50.000 0.00 0.00 0.00 3.27
403 644 0.163788 CGCACGCCTTGTAAACTGAG 59.836 55.000 0.00 0.00 0.00 3.35
404 645 1.837538 GCGCACGCCTTGTAAACTGA 61.838 55.000 0.30 0.00 34.56 3.41
405 646 1.440353 GCGCACGCCTTGTAAACTG 60.440 57.895 0.30 0.00 34.56 3.16
409 650 2.049341 TACGCGCACGCCTTGTAA 60.049 55.556 5.73 0.00 45.53 2.41
410 651 2.806198 GTACGCGCACGCCTTGTA 60.806 61.111 5.73 3.39 45.53 2.41
424 665 4.916984 GTCAAATTGACGACCTAGGGGTAC 60.917 50.000 14.81 2.61 40.90 3.34
425 666 3.196254 GTCAAATTGACGACCTAGGGGTA 59.804 47.826 14.81 0.00 40.90 3.69
426 667 2.027469 GTCAAATTGACGACCTAGGGGT 60.027 50.000 14.81 10.74 42.37 4.95
427 668 2.629051 GTCAAATTGACGACCTAGGGG 58.371 52.381 14.81 7.16 37.67 4.79
491 732 9.784531 TCTTTTGAGAATAGAACATCTGAAGTT 57.215 29.630 0.00 0.00 0.00 2.66
492 733 9.956640 ATCTTTTGAGAATAGAACATCTGAAGT 57.043 29.630 0.00 0.00 0.00 3.01
542 783 9.605951 AGATTGCCAATTTAATCACCCTAATAT 57.394 29.630 0.00 0.00 36.11 1.28
544 785 7.919385 AGATTGCCAATTTAATCACCCTAAT 57.081 32.000 0.00 0.00 36.11 1.73
545 786 8.278639 TCTAGATTGCCAATTTAATCACCCTAA 58.721 33.333 0.00 0.00 36.11 2.69
546 787 7.811282 TCTAGATTGCCAATTTAATCACCCTA 58.189 34.615 0.00 0.00 36.11 3.53
547 788 6.672593 TCTAGATTGCCAATTTAATCACCCT 58.327 36.000 0.00 0.00 36.11 4.34
548 789 6.959639 TCTAGATTGCCAATTTAATCACCC 57.040 37.500 0.00 0.00 36.11 4.61
554 795 9.772973 ACACGTATATCTAGATTGCCAATTTAA 57.227 29.630 11.25 0.00 0.00 1.52
556 797 9.424319 CTACACGTATATCTAGATTGCCAATTT 57.576 33.333 11.25 0.00 0.00 1.82
557 798 8.035394 CCTACACGTATATCTAGATTGCCAATT 58.965 37.037 11.25 0.00 0.00 2.32
558 799 7.396339 TCCTACACGTATATCTAGATTGCCAAT 59.604 37.037 11.25 0.18 0.00 3.16
559 800 6.717997 TCCTACACGTATATCTAGATTGCCAA 59.282 38.462 11.25 0.00 0.00 4.52
560 801 6.150641 GTCCTACACGTATATCTAGATTGCCA 59.849 42.308 11.25 0.00 0.00 4.92
561 802 6.374894 AGTCCTACACGTATATCTAGATTGCC 59.625 42.308 11.25 0.00 0.00 4.52
562 803 7.380431 AGTCCTACACGTATATCTAGATTGC 57.620 40.000 11.25 2.19 0.00 3.56
563 804 8.784994 ACAAGTCCTACACGTATATCTAGATTG 58.215 37.037 11.25 5.18 0.00 2.67
564 805 8.921353 ACAAGTCCTACACGTATATCTAGATT 57.079 34.615 11.25 1.81 0.00 2.40
566 807 9.836864 TTTACAAGTCCTACACGTATATCTAGA 57.163 33.333 0.00 0.00 0.00 2.43
567 808 9.875675 GTTTACAAGTCCTACACGTATATCTAG 57.124 37.037 0.00 0.00 0.00 2.43
568 809 9.618890 AGTTTACAAGTCCTACACGTATATCTA 57.381 33.333 0.00 0.00 0.00 1.98
569 810 8.404000 CAGTTTACAAGTCCTACACGTATATCT 58.596 37.037 0.00 0.00 0.00 1.98
570 811 8.186821 ACAGTTTACAAGTCCTACACGTATATC 58.813 37.037 0.00 0.00 0.00 1.63
571 812 7.972277 CACAGTTTACAAGTCCTACACGTATAT 59.028 37.037 0.00 0.00 0.00 0.86
572 813 7.174772 TCACAGTTTACAAGTCCTACACGTATA 59.825 37.037 0.00 0.00 0.00 1.47
573 814 6.016024 TCACAGTTTACAAGTCCTACACGTAT 60.016 38.462 0.00 0.00 0.00 3.06
574 815 5.299028 TCACAGTTTACAAGTCCTACACGTA 59.701 40.000 0.00 0.00 0.00 3.57
575 816 4.098349 TCACAGTTTACAAGTCCTACACGT 59.902 41.667 0.00 0.00 0.00 4.49
576 817 4.443394 GTCACAGTTTACAAGTCCTACACG 59.557 45.833 0.00 0.00 0.00 4.49
577 818 4.443394 CGTCACAGTTTACAAGTCCTACAC 59.557 45.833 0.00 0.00 0.00 2.90
578 819 4.338964 TCGTCACAGTTTACAAGTCCTACA 59.661 41.667 0.00 0.00 0.00 2.74
579 820 4.863491 TCGTCACAGTTTACAAGTCCTAC 58.137 43.478 0.00 0.00 0.00 3.18
580 821 5.300034 TCTTCGTCACAGTTTACAAGTCCTA 59.700 40.000 0.00 0.00 0.00 2.94
581 822 4.098960 TCTTCGTCACAGTTTACAAGTCCT 59.901 41.667 0.00 0.00 0.00 3.85
582 823 4.365723 TCTTCGTCACAGTTTACAAGTCC 58.634 43.478 0.00 0.00 0.00 3.85
583 824 6.355638 CAATCTTCGTCACAGTTTACAAGTC 58.644 40.000 0.00 0.00 0.00 3.01
584 825 5.236478 CCAATCTTCGTCACAGTTTACAAGT 59.764 40.000 0.00 0.00 0.00 3.16
585 826 5.679906 CCAATCTTCGTCACAGTTTACAAG 58.320 41.667 0.00 0.00 0.00 3.16
586 827 4.024387 GCCAATCTTCGTCACAGTTTACAA 60.024 41.667 0.00 0.00 0.00 2.41
587 828 3.496884 GCCAATCTTCGTCACAGTTTACA 59.503 43.478 0.00 0.00 0.00 2.41
588 829 3.746492 AGCCAATCTTCGTCACAGTTTAC 59.254 43.478 0.00 0.00 0.00 2.01
589 830 3.994392 GAGCCAATCTTCGTCACAGTTTA 59.006 43.478 0.00 0.00 0.00 2.01
590 831 2.808543 GAGCCAATCTTCGTCACAGTTT 59.191 45.455 0.00 0.00 0.00 2.66
591 832 2.417719 GAGCCAATCTTCGTCACAGTT 58.582 47.619 0.00 0.00 0.00 3.16
592 833 1.670087 CGAGCCAATCTTCGTCACAGT 60.670 52.381 0.00 0.00 0.00 3.55
593 834 0.994995 CGAGCCAATCTTCGTCACAG 59.005 55.000 0.00 0.00 0.00 3.66
594 835 0.389817 CCGAGCCAATCTTCGTCACA 60.390 55.000 0.00 0.00 0.00 3.58
595 836 1.696832 GCCGAGCCAATCTTCGTCAC 61.697 60.000 0.00 0.00 0.00 3.67
596 837 1.447838 GCCGAGCCAATCTTCGTCA 60.448 57.895 0.00 0.00 0.00 4.35
597 838 1.424493 CTGCCGAGCCAATCTTCGTC 61.424 60.000 0.00 0.00 0.00 4.20
598 839 1.448540 CTGCCGAGCCAATCTTCGT 60.449 57.895 0.00 0.00 0.00 3.85
599 840 0.179111 TACTGCCGAGCCAATCTTCG 60.179 55.000 0.00 0.00 0.00 3.79
600 841 2.246719 ATACTGCCGAGCCAATCTTC 57.753 50.000 0.00 0.00 0.00 2.87
601 842 2.292267 CAATACTGCCGAGCCAATCTT 58.708 47.619 0.00 0.00 0.00 2.40
602 843 1.475751 CCAATACTGCCGAGCCAATCT 60.476 52.381 0.00 0.00 0.00 2.40
603 844 0.947244 CCAATACTGCCGAGCCAATC 59.053 55.000 0.00 0.00 0.00 2.67
604 845 0.546122 TCCAATACTGCCGAGCCAAT 59.454 50.000 0.00 0.00 0.00 3.16
605 846 0.392461 GTCCAATACTGCCGAGCCAA 60.392 55.000 0.00 0.00 0.00 4.52
606 847 1.220749 GTCCAATACTGCCGAGCCA 59.779 57.895 0.00 0.00 0.00 4.75
607 848 1.522569 AGTCCAATACTGCCGAGCC 59.477 57.895 0.00 0.00 36.93 4.70
697 947 6.430925 CAGTCAATTGATCCCAAACTCTGTTA 59.569 38.462 12.12 0.00 35.67 2.41
711 961 5.139727 TGAACTTTGGGTCAGTCAATTGAT 58.860 37.500 12.12 0.00 0.00 2.57
717 967 4.531854 TGAAATGAACTTTGGGTCAGTCA 58.468 39.130 0.00 0.00 0.00 3.41
726 976 7.359595 TGGTTAATCGACTGAAATGAACTTTG 58.640 34.615 0.00 0.00 0.00 2.77
730 980 6.481954 ACTGGTTAATCGACTGAAATGAAC 57.518 37.500 0.00 0.00 0.00 3.18
733 983 5.006746 GGCTACTGGTTAATCGACTGAAATG 59.993 44.000 0.00 0.00 0.00 2.32
747 997 1.611261 TAGGGCGTGGCTACTGGTT 60.611 57.895 0.00 0.00 0.00 3.67
764 1014 0.337428 AGGTAGGGGGTTTCTCGCTA 59.663 55.000 0.00 0.00 0.00 4.26
765 1015 0.976590 GAGGTAGGGGGTTTCTCGCT 60.977 60.000 0.00 0.00 0.00 4.93
766 1016 0.976590 AGAGGTAGGGGGTTTCTCGC 60.977 60.000 0.00 0.00 0.00 5.03
767 1017 2.030371 GTAGAGGTAGGGGGTTTCTCG 58.970 57.143 0.00 0.00 0.00 4.04
768 1018 2.765135 GTGTAGAGGTAGGGGGTTTCTC 59.235 54.545 0.00 0.00 0.00 2.87
769 1019 2.830293 GTGTAGAGGTAGGGGGTTTCT 58.170 52.381 0.00 0.00 0.00 2.52
770 1020 1.479730 CGTGTAGAGGTAGGGGGTTTC 59.520 57.143 0.00 0.00 0.00 2.78
771 1021 1.565067 CGTGTAGAGGTAGGGGGTTT 58.435 55.000 0.00 0.00 0.00 3.27
772 1022 0.974525 GCGTGTAGAGGTAGGGGGTT 60.975 60.000 0.00 0.00 0.00 4.11
773 1023 1.380920 GCGTGTAGAGGTAGGGGGT 60.381 63.158 0.00 0.00 0.00 4.95
774 1024 1.380785 TGCGTGTAGAGGTAGGGGG 60.381 63.158 0.00 0.00 0.00 5.40
779 1029 0.968901 CCCACCTGCGTGTAGAGGTA 60.969 60.000 0.00 0.00 40.85 3.08
781 1031 2.579201 CCCACCTGCGTGTAGAGG 59.421 66.667 0.00 0.00 38.41 3.69
797 1047 2.710724 AAAGACGACGGACACCTGCC 62.711 60.000 0.00 0.00 0.00 4.85
810 1060 2.809601 CTCGCGTGGGGAAAGACG 60.810 66.667 5.77 0.00 38.63 4.18
811 1061 2.240162 ATCCTCGCGTGGGGAAAGAC 62.240 60.000 23.86 0.00 35.08 3.01
812 1062 1.550130 AATCCTCGCGTGGGGAAAGA 61.550 55.000 23.86 0.00 35.08 2.52
818 1069 3.199677 TGTTTATTAATCCTCGCGTGGG 58.800 45.455 25.62 18.99 0.00 4.61
832 1083 9.119418 TGACGTTGATGGATTGATATGTTTATT 57.881 29.630 0.00 0.00 0.00 1.40
833 1084 8.559536 GTGACGTTGATGGATTGATATGTTTAT 58.440 33.333 0.00 0.00 0.00 1.40
911 1162 2.282462 GGCAGTGTTGGGTGAGGG 60.282 66.667 0.00 0.00 0.00 4.30
923 1174 1.639298 GCAAGCTCGATTTCGGCAGT 61.639 55.000 13.30 1.92 40.29 4.40
941 1192 0.955428 TTGACTGGTGATCCGCTTGC 60.955 55.000 0.00 0.00 36.30 4.01
955 1217 1.271271 ACGGAGTACTCGGAGTTGACT 60.271 52.381 30.59 14.28 41.94 3.41
956 1218 1.163554 ACGGAGTACTCGGAGTTGAC 58.836 55.000 30.59 9.41 41.94 3.18
1272 1537 2.183046 GTCGACAGGCAGAGCTCC 59.817 66.667 11.55 0.00 0.00 4.70
1274 1539 1.954362 GATGGTCGACAGGCAGAGCT 61.954 60.000 18.91 0.00 36.03 4.09
1287 1552 2.482374 GCGCTGTGCTTGATGGTC 59.518 61.111 5.84 0.00 41.73 4.02
1308 1573 2.520536 AAGCAGCTCCCTGAACGGT 61.521 57.895 0.00 0.00 41.77 4.83
1326 1591 2.221169 CTGCTGTTGTTAAGCCTGACA 58.779 47.619 0.00 0.00 40.06 3.58
1336 1604 3.952675 CGGCGTGCTGCTGTTGTT 61.953 61.111 0.00 0.00 45.38 2.83
1392 1663 3.997400 CTCCTCGGCGACCCTCTGA 62.997 68.421 4.99 0.00 0.00 3.27
1419 1690 2.429930 CAGAACACCAAGGCCGGA 59.570 61.111 5.05 0.00 0.00 5.14
1594 1885 4.308526 AGTCAGGTCACTCTCATCTACA 57.691 45.455 0.00 0.00 0.00 2.74
1702 1993 2.674033 ATCACGTCGTCCGGGTCA 60.674 61.111 0.00 0.00 41.99 4.02
2131 2422 1.295423 CTTGGTGTCCCGGACGAAT 59.705 57.895 13.02 0.00 34.95 3.34
2143 2434 1.679898 GACTCCCCTGTCCTTGGTG 59.320 63.158 0.00 0.00 0.00 4.17
2296 2587 2.031012 CAGTTGGTCGGCTGCTCA 59.969 61.111 0.00 0.00 0.00 4.26
2401 2692 2.520982 CCCCTCTCGCCGTCCATA 60.521 66.667 0.00 0.00 0.00 2.74
2495 2786 0.107508 ACCAGCCGATCCATGTTCTG 60.108 55.000 0.00 0.00 0.00 3.02
2547 2838 2.108157 ACGCGCACTTGGTTCAGA 59.892 55.556 5.73 0.00 0.00 3.27
2553 2844 0.042188 GCATATACACGCGCACTTGG 60.042 55.000 5.73 0.00 0.00 3.61
2554 2845 0.930310 AGCATATACACGCGCACTTG 59.070 50.000 5.73 3.30 0.00 3.16
2556 2847 0.875908 CCAGCATATACACGCGCACT 60.876 55.000 5.73 0.00 0.00 4.40
2557 2848 1.151777 ACCAGCATATACACGCGCAC 61.152 55.000 5.73 0.00 0.00 5.34
2560 2851 1.409412 GAGACCAGCATATACACGCG 58.591 55.000 3.53 3.53 0.00 6.01
2561 2852 1.784525 GGAGACCAGCATATACACGC 58.215 55.000 0.00 0.00 0.00 5.34
2586 2880 2.688507 TGAGACAGAAAACATCCGAGC 58.311 47.619 0.00 0.00 0.00 5.03
2589 2883 4.641954 CGAAATGAGACAGAAAACATCCG 58.358 43.478 0.00 0.00 0.00 4.18
2606 2900 2.365293 AGGAAACTTGGCAAAGCGAAAT 59.635 40.909 0.00 0.00 37.44 2.17
2620 2916 7.874358 ACGCAGTTCTTCAGTGAAGGAAACT 62.874 44.000 28.33 25.97 37.78 2.66
2671 2971 8.481314 ACTGCAGAATTTCATCTACTCATTCTA 58.519 33.333 23.35 0.00 33.37 2.10
2680 2980 7.692460 AAATCACACTGCAGAATTTCATCTA 57.308 32.000 23.35 0.00 0.00 1.98
2691 2991 1.005294 GCGGCAAAATCACACTGCAG 61.005 55.000 13.48 13.48 37.83 4.41
2707 3007 1.385038 CGTTATTATTTGCAGCGCGG 58.615 50.000 8.83 2.11 0.00 6.46
2708 3008 0.764226 GCGTTATTATTTGCAGCGCG 59.236 50.000 0.00 0.00 34.34 6.86
2727 3027 3.027170 GCATCTTGGGCACGACACG 62.027 63.158 0.00 0.00 0.00 4.49
2728 3028 1.237285 AAGCATCTTGGGCACGACAC 61.237 55.000 0.00 0.00 0.00 3.67
2729 3029 1.073025 AAGCATCTTGGGCACGACA 59.927 52.632 0.00 0.00 0.00 4.35
2730 3030 1.503542 CAAGCATCTTGGGCACGAC 59.496 57.895 0.00 0.00 0.00 4.34
2731 3031 1.675310 CCAAGCATCTTGGGCACGA 60.675 57.895 15.86 0.00 35.96 4.35
2740 3040 0.622665 CTCCCAACTCCCAAGCATCT 59.377 55.000 0.00 0.00 0.00 2.90
2741 3041 0.394899 CCTCCCAACTCCCAAGCATC 60.395 60.000 0.00 0.00 0.00 3.91
2770 3070 9.544314 CGAGTACTAATAATTTACATCTCGAGG 57.456 37.037 13.56 0.00 41.92 4.63
2796 3096 2.502142 AAAAACCCACGGACTATCCC 57.498 50.000 0.00 0.00 31.13 3.85
2862 3162 6.321848 TCATGTCAGTCTTTACGTGACTTA 57.678 37.500 4.40 0.00 42.21 2.24
2874 3174 3.469008 TCGGTTTTGTCATGTCAGTCT 57.531 42.857 0.00 0.00 0.00 3.24
2878 3178 5.766150 ATCTTTTCGGTTTTGTCATGTCA 57.234 34.783 0.00 0.00 0.00 3.58
2924 3224 3.443045 CAGGTGATGGGCGTTGGC 61.443 66.667 0.00 0.00 38.90 4.52
3009 3309 1.690893 ACATATCAGCGATGGAGCAGT 59.309 47.619 0.00 0.00 40.15 4.40
3011 3311 3.582714 CTACATATCAGCGATGGAGCA 57.417 47.619 0.00 0.00 40.15 4.26
3029 3329 0.036388 CTTGGAGGTCCGCAAAGCTA 60.036 55.000 0.00 0.00 39.43 3.32
3296 3625 2.662596 GCATCCTCGTGGTGGACA 59.337 61.111 2.99 0.00 36.30 4.02
3439 3768 7.548196 TTAGTCTGTTCATCGTCTTTGTTTT 57.452 32.000 0.00 0.00 0.00 2.43
3476 3805 4.753107 GTGTGGATCGTTTTTACTTCCTCA 59.247 41.667 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.