Multiple sequence alignment - TraesCS6B01G300100

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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 TraesCS6B01G300100 chr6B 100.000 5018 0 0 1 5018 538069673 538064656 0.000000e+00 9267.0
1 TraesCS6B01G300100 chr6B 96.835 316 9 1 1629 1944 115140541 115140855 1.240000e-145 527.0
2 TraesCS6B01G300100 chr6B 94.595 222 10 1 1931 2152 687066543 687066324 4.810000e-90 342.0
3 TraesCS6B01G300100 chr6B 100.000 28 0 0 3587 3614 696028963 696028936 9.000000e-03 52.8
4 TraesCS6B01G300100 chr6A 96.355 2798 80 14 2233 5018 499208559 499205772 0.000000e+00 4582.0
5 TraesCS6B01G300100 chr6A 93.739 591 21 4 961 1537 499209316 499208728 0.000000e+00 872.0
6 TraesCS6B01G300100 chr6A 86.130 447 45 6 523 960 429379592 429379154 2.740000e-127 466.0
7 TraesCS6B01G300100 chr6A 90.057 352 32 3 94 443 1956441 1956091 2.130000e-123 453.0
8 TraesCS6B01G300100 chr6A 89.205 352 35 2 94 443 34957090 34957440 2.150000e-118 436.0
9 TraesCS6B01G300100 chr6A 92.432 185 14 0 94 278 34971027 34970843 1.070000e-66 265.0
10 TraesCS6B01G300100 chr6A 86.932 176 23 0 789 964 429384436 429384611 1.100000e-46 198.0
11 TraesCS6B01G300100 chr6A 75.104 482 75 31 514 963 34970562 34971030 3.090000e-42 183.0
12 TraesCS6B01G300100 chr6A 97.260 73 2 0 1566 1638 499208623 499208551 1.900000e-24 124.0
13 TraesCS6B01G300100 chr6D 96.949 2524 64 9 2500 5018 356733495 356730980 0.000000e+00 4222.0
14 TraesCS6B01G300100 chr6D 93.570 591 24 2 961 1537 356734464 356733874 0.000000e+00 869.0
15 TraesCS6B01G300100 chr6D 87.361 538 43 16 452 966 6238012 6238547 1.200000e-165 593.0
16 TraesCS6B01G300100 chr6D 88.657 335 23 5 452 773 50999526 50999858 1.310000e-105 394.0
17 TraesCS6B01G300100 chr6D 93.478 230 12 1 2203 2432 356733717 356733491 6.220000e-89 339.0
18 TraesCS6B01G300100 chr6D 88.372 172 20 0 789 960 6236592 6236421 1.830000e-49 207.0
19 TraesCS6B01G300100 chr6D 87.931 174 18 3 94 266 6238539 6238368 8.520000e-48 202.0
20 TraesCS6B01G300100 chr6D 90.345 145 13 1 94 238 51000236 51000093 6.630000e-44 189.0
21 TraesCS6B01G300100 chr6D 77.072 362 49 23 94 449 50997934 50998267 1.440000e-40 178.0
22 TraesCS6B01G300100 chr6D 81.022 137 23 3 827 962 6057454 6057320 6.870000e-19 106.0
23 TraesCS6B01G300100 chr6D 96.774 62 2 0 1577 1638 356733781 356733720 2.470000e-18 104.0
24 TraesCS6B01G300100 chr6D 94.872 39 1 1 923 961 6057494 6057531 5.430000e-05 60.2
25 TraesCS6B01G300100 chr6D 97.143 35 0 1 2164 2198 455883631 455883664 1.950000e-04 58.4
26 TraesCS6B01G300100 chr2B 90.323 527 44 6 1634 2153 795119900 795120426 0.000000e+00 684.0
27 TraesCS6B01G300100 chr2B 95.045 222 11 0 1931 2152 679054802 679055023 2.870000e-92 350.0
28 TraesCS6B01G300100 chr2B 94.690 226 10 2 1931 2154 682130784 682130559 2.870000e-92 350.0
29 TraesCS6B01G300100 chr2B 94.977 219 11 0 1931 2149 556701734 556701952 1.340000e-90 344.0
30 TraesCS6B01G300100 chr2B 89.831 59 3 3 2361 2416 572154802 572154744 6.970000e-09 73.1
31 TraesCS6B01G300100 chr2D 89.943 527 32 5 452 959 480134151 480133627 0.000000e+00 660.0
32 TraesCS6B01G300100 chr2D 88.418 354 33 6 96 447 46870521 46870174 2.160000e-113 420.0
33 TraesCS6B01G300100 chr2D 91.447 304 20 5 89 389 480136806 480136506 3.610000e-111 412.0
34 TraesCS6B01G300100 chr2D 97.368 38 1 0 2165 2202 34235969 34235932 1.170000e-06 65.8
35 TraesCS6B01G300100 chr2D 100.000 29 0 0 3586 3614 61299845 61299873 3.000000e-03 54.7
36 TraesCS6B01G300100 chr7D 87.337 537 38 13 452 961 171328093 171327560 5.600000e-164 588.0
37 TraesCS6B01G300100 chr7D 87.151 537 39 13 452 961 171334888 171334355 2.600000e-162 582.0
38 TraesCS6B01G300100 chr7D 86.778 537 42 12 452 961 556308910 556309444 5.640000e-159 571.0
39 TraesCS6B01G300100 chr7D 84.601 539 51 16 452 962 88606661 88606127 1.610000e-139 507.0
40 TraesCS6B01G300100 chr7D 89.017 173 19 0 789 961 556307314 556307142 1.090000e-51 215.0
41 TraesCS6B01G300100 chr7D 86.982 169 22 0 789 957 171332827 171332995 1.840000e-44 191.0
42 TraesCS6B01G300100 chr7D 86.982 169 22 0 789 957 171339622 171339790 1.840000e-44 191.0
43 TraesCS6B01G300100 chr7D 97.059 34 1 0 2164 2197 462673296 462673263 1.950000e-04 58.4
44 TraesCS6B01G300100 chr1D 86.220 537 40 15 452 960 288098992 288098462 7.340000e-153 551.0
45 TraesCS6B01G300100 chr1D 85.632 174 24 1 789 962 288100411 288100583 1.110000e-41 182.0
46 TraesCS6B01G300100 chr1D 91.489 47 4 0 1482 1528 435295824 435295870 1.170000e-06 65.8
47 TraesCS6B01G300100 chr1D 97.143 35 1 0 2163 2197 16894238 16894272 5.430000e-05 60.2
48 TraesCS6B01G300100 chr7B 97.785 316 7 0 1629 1944 29238019 29237704 3.420000e-151 545.0
49 TraesCS6B01G300100 chr7B 99.007 302 3 0 1634 1935 529283492 529283793 4.420000e-150 542.0
50 TraesCS6B01G300100 chr7B 96.865 319 8 2 1633 1951 655112187 655112503 2.660000e-147 532.0
51 TraesCS6B01G300100 chr7B 96.835 316 10 0 1629 1944 29274445 29274130 3.440000e-146 529.0
52 TraesCS6B01G300100 chr7B 96.835 316 10 0 1629 1944 111833266 111833581 3.440000e-146 529.0
53 TraesCS6B01G300100 chr7B 89.394 396 34 8 1634 2024 653904141 653904533 4.510000e-135 492.0
54 TraesCS6B01G300100 chr7B 95.000 220 10 1 1930 2149 9688149 9687931 1.340000e-90 344.0
55 TraesCS6B01G300100 chr7B 97.436 39 1 0 2164 2202 39554316 39554354 3.240000e-07 67.6
56 TraesCS6B01G300100 chr3B 96.835 316 10 0 1629 1944 787100628 787100313 3.440000e-146 529.0
57 TraesCS6B01G300100 chr3B 85.098 510 60 10 452 957 275917420 275916923 1.610000e-139 507.0
58 TraesCS6B01G300100 chr3B 95.516 223 10 0 1930 2152 812801601 812801379 1.720000e-94 357.0
59 TraesCS6B01G300100 chr1A 84.023 532 53 13 452 956 30359975 30359449 2.720000e-132 483.0
60 TraesCS6B01G300100 chr1A 86.969 353 40 5 94 443 589038757 589038408 4.710000e-105 392.0
61 TraesCS6B01G300100 chr1A 92.432 185 14 0 94 278 524400408 524400592 1.070000e-66 265.0
62 TraesCS6B01G300100 chr1A 90.860 186 15 2 94 278 589034127 589034311 1.080000e-61 248.0
63 TraesCS6B01G300100 chr1A 88.235 170 17 3 98 266 30359449 30359616 3.060000e-47 200.0
64 TraesCS6B01G300100 chr1A 74.895 478 76 28 514 962 524400868 524400406 1.440000e-40 178.0
65 TraesCS6B01G300100 chr1A 85.816 141 18 2 821 960 524401449 524401588 1.130000e-31 148.0
66 TraesCS6B01G300100 chr1A 74.215 446 69 31 545 960 589034556 589034127 1.460000e-30 145.0
67 TraesCS6B01G300100 chr1A 83.688 141 21 2 821 960 589038618 589038757 1.130000e-26 132.0
68 TraesCS6B01G300100 chr1A 91.489 47 4 0 2165 2211 341013574 341013528 1.170000e-06 65.8
69 TraesCS6B01G300100 chr7A 90.857 350 29 2 96 443 218243802 218243454 2.740000e-127 466.0
70 TraesCS6B01G300100 chr7A 88.485 165 19 0 796 960 78183984 78183820 3.060000e-47 200.0
71 TraesCS6B01G300100 chr7A 97.143 35 1 0 2163 2197 630330383 630330417 5.430000e-05 60.2
72 TraesCS6B01G300100 chr4B 89.773 352 33 2 94 443 42231421 42231071 9.910000e-122 448.0
73 TraesCS6B01G300100 chr4B 95.023 221 11 0 1931 2151 30754333 30754113 1.030000e-91 348.0
74 TraesCS6B01G300100 chr3A 88.564 376 30 7 452 827 262527045 262526683 1.280000e-120 444.0
75 TraesCS6B01G300100 chr5B 89.235 353 34 3 94 443 319313951 319314302 5.960000e-119 438.0
76 TraesCS6B01G300100 chr5B 88.352 352 38 2 94 443 643304295 643304645 2.160000e-113 420.0
77 TraesCS6B01G300100 chr5B 85.372 376 47 7 73 443 275700729 275700357 2.830000e-102 383.0
78 TraesCS6B01G300100 chr5B 95.982 224 9 0 1929 2152 711617038 711616815 1.030000e-96 364.0
79 TraesCS6B01G300100 chr5B 84.615 325 36 5 637 961 352128346 352128656 1.360000e-80 311.0
80 TraesCS6B01G300100 chr1B 89.235 353 34 3 94 443 466927416 466927767 5.960000e-119 438.0
81 TraesCS6B01G300100 chr1B 100.000 36 0 0 2165 2200 353270379 353270344 3.240000e-07 67.6
82 TraesCS6B01G300100 chr1B 96.970 33 1 0 3586 3618 6540858 6540890 7.020000e-04 56.5
83 TraesCS6B01G300100 chr1B 100.000 30 0 0 3589 3618 325271733 325271762 7.020000e-04 56.5
84 TraesCS6B01G300100 chr1B 90.244 41 2 2 3575 3613 664698999 664699039 9.000000e-03 52.8
85 TraesCS6B01G300100 chr2A 88.952 353 35 3 94 443 84142027 84142378 2.770000e-117 433.0
86 TraesCS6B01G300100 chr2A 88.125 160 19 0 803 962 544154315 544154474 1.840000e-44 191.0
87 TraesCS6B01G300100 chr2A 100.000 29 0 0 3586 3614 61773252 61773280 3.000000e-03 54.7
88 TraesCS6B01G300100 chr3D 82.420 529 59 15 452 956 192054706 192055224 9.980000e-117 431.0
89 TraesCS6B01G300100 chr3D 90.000 140 14 0 94 233 35357032 35356893 1.110000e-41 182.0
90 TraesCS6B01G300100 chr3D 88.489 139 14 1 84 222 35355926 35356062 3.110000e-37 167.0
91 TraesCS6B01G300100 chr4A 88.102 353 38 3 94 443 34863276 34862925 2.790000e-112 416.0
92 TraesCS6B01G300100 chr4A 97.059 34 1 0 2164 2197 3350370 3350403 1.950000e-04 58.4
93 TraesCS6B01G300100 chr5D 89.297 327 31 3 119 443 87168938 87168614 1.680000e-109 407.0
94 TraesCS6B01G300100 chr5D 89.189 185 20 0 94 278 87163542 87163726 1.090000e-56 231.0
95 TraesCS6B01G300100 chr5D 73.278 479 83 30 514 960 87164007 87163542 3.150000e-27 134.0
96 TraesCS6B01G300100 chr4D 87.535 353 26 12 95 443 373808512 373808174 4.710000e-105 392.0
97 TraesCS6B01G300100 chr4D 89.730 185 18 1 94 278 373781670 373781853 8.400000e-58 235.0
98 TraesCS6B01G300100 chr4D 73.767 446 77 26 545 963 373782098 373781666 6.770000e-29 139.0


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 TraesCS6B01G300100 chr6B 538064656 538069673 5017 True 9267.000000 9267 100.000000 1 5018 1 chr6B.!!$R1 5017
1 TraesCS6B01G300100 chr6A 499205772 499209316 3544 True 1859.333333 4582 95.784667 961 5018 3 chr6A.!!$R4 4057
2 TraesCS6B01G300100 chr6D 356730980 356734464 3484 True 1383.500000 4222 95.192750 961 5018 4 chr6D.!!$R4 4057
3 TraesCS6B01G300100 chr6D 6238012 6238547 535 False 593.000000 593 87.361000 452 966 1 chr6D.!!$F2 514
4 TraesCS6B01G300100 chr6D 50997934 50999858 1924 False 286.000000 394 82.864500 94 773 2 chr6D.!!$F4 679
5 TraesCS6B01G300100 chr6D 6236421 6238539 2118 True 204.500000 207 88.151500 94 960 2 chr6D.!!$R3 866
6 TraesCS6B01G300100 chr2B 795119900 795120426 526 False 684.000000 684 90.323000 1634 2153 1 chr2B.!!$F3 519
7 TraesCS6B01G300100 chr2D 480133627 480136806 3179 True 536.000000 660 90.695000 89 959 2 chr2D.!!$R3 870
8 TraesCS6B01G300100 chr7D 171327560 171328093 533 True 588.000000 588 87.337000 452 961 1 chr7D.!!$R2 509
9 TraesCS6B01G300100 chr7D 171334355 171334888 533 True 582.000000 582 87.151000 452 961 1 chr7D.!!$R3 509
10 TraesCS6B01G300100 chr7D 556308910 556309444 534 False 571.000000 571 86.778000 452 961 1 chr7D.!!$F3 509
11 TraesCS6B01G300100 chr7D 88606127 88606661 534 True 507.000000 507 84.601000 452 962 1 chr7D.!!$R1 510
12 TraesCS6B01G300100 chr1D 288098462 288098992 530 True 551.000000 551 86.220000 452 960 1 chr1D.!!$R1 508
13 TraesCS6B01G300100 chr1A 30359449 30359975 526 True 483.000000 483 84.023000 452 956 1 chr1A.!!$R1 504
14 TraesCS6B01G300100 chr1A 589034127 589038757 4630 True 268.500000 392 80.592000 94 960 2 chr1A.!!$R4 866
15 TraesCS6B01G300100 chr1A 524400408 524401588 1180 False 206.500000 265 89.124000 94 960 2 chr1A.!!$F4 866
16 TraesCS6B01G300100 chr3D 192054706 192055224 518 False 431.000000 431 82.420000 452 956 1 chr3D.!!$F2 504


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
73 74 0.770499 TCTGTTGATTCCAGGGCACA 59.230 50.0 0.0 0.0 0.00 4.57 F
1656 7115 0.323542 ACTCCCTCCGTCTAGGTGTG 60.324 60.0 0.0 0.0 41.99 3.82 F
2401 7904 0.320050 TCATCCTGTAGCAACGCACA 59.680 50.0 0.0 0.0 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 7145 0.385473 CACCGCGCCTAAGTGTTTTG 60.385 55.0 0.00 0.0 0.0 2.44 R
2616 8122 0.304705 GCGTCTCTTTGTGTGGTGTG 59.695 55.0 0.00 0.0 0.0 3.82 R
4234 9746 1.963172 AACAGACCGGACAGGAAAAC 58.037 50.0 9.46 0.0 45.0 2.43 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
17 18 4.481112 GCCAATCAACGGCGCCTG 62.481 66.667 26.68 20.24 40.35 4.85
18 19 3.055719 CCAATCAACGGCGCCTGT 61.056 61.111 26.68 20.95 0.00 4.00
19 20 2.625823 CCAATCAACGGCGCCTGTT 61.626 57.895 26.68 25.34 0.00 3.16
20 21 1.154225 CAATCAACGGCGCCTGTTC 60.154 57.895 26.39 2.27 0.00 3.18
21 22 2.332654 AATCAACGGCGCCTGTTCC 61.333 57.895 26.39 1.55 0.00 3.62
30 31 2.915137 GCCTGTTCCCCGCCAAAA 60.915 61.111 0.00 0.00 0.00 2.44
31 32 2.503382 GCCTGTTCCCCGCCAAAAA 61.503 57.895 0.00 0.00 0.00 1.94
68 69 2.977914 ACGACATCTGTTGATTCCAGG 58.022 47.619 4.58 0.00 33.65 4.45
69 70 2.283298 CGACATCTGTTGATTCCAGGG 58.717 52.381 0.00 0.00 0.00 4.45
70 71 2.019984 GACATCTGTTGATTCCAGGGC 58.980 52.381 0.00 0.00 0.00 5.19
71 72 1.355381 ACATCTGTTGATTCCAGGGCA 59.645 47.619 0.00 0.00 0.00 5.36
72 73 1.747355 CATCTGTTGATTCCAGGGCAC 59.253 52.381 0.00 0.00 0.00 5.01
73 74 0.770499 TCTGTTGATTCCAGGGCACA 59.230 50.000 0.00 0.00 0.00 4.57
74 75 1.355381 TCTGTTGATTCCAGGGCACAT 59.645 47.619 0.00 0.00 0.00 3.21
75 76 2.173519 CTGTTGATTCCAGGGCACATT 58.826 47.619 0.00 0.00 0.00 2.71
76 77 2.564062 CTGTTGATTCCAGGGCACATTT 59.436 45.455 0.00 0.00 0.00 2.32
77 78 2.971330 TGTTGATTCCAGGGCACATTTT 59.029 40.909 0.00 0.00 0.00 1.82
78 79 3.006752 TGTTGATTCCAGGGCACATTTTC 59.993 43.478 0.00 0.00 0.00 2.29
79 80 2.178580 TGATTCCAGGGCACATTTTCC 58.821 47.619 0.00 0.00 0.00 3.13
80 81 2.225343 TGATTCCAGGGCACATTTTCCT 60.225 45.455 0.00 0.00 0.00 3.36
81 82 2.397044 TTCCAGGGCACATTTTCCTT 57.603 45.000 0.00 0.00 0.00 3.36
82 83 1.631405 TCCAGGGCACATTTTCCTTG 58.369 50.000 0.00 0.00 0.00 3.61
83 84 1.133199 TCCAGGGCACATTTTCCTTGT 60.133 47.619 0.00 0.00 0.00 3.16
84 85 1.693606 CCAGGGCACATTTTCCTTGTT 59.306 47.619 0.00 0.00 0.00 2.83
85 86 2.104622 CCAGGGCACATTTTCCTTGTTT 59.895 45.455 0.00 0.00 0.00 2.83
86 87 3.392882 CAGGGCACATTTTCCTTGTTTC 58.607 45.455 0.00 0.00 0.00 2.78
87 88 3.070015 CAGGGCACATTTTCCTTGTTTCT 59.930 43.478 0.00 0.00 0.00 2.52
88 89 3.711190 AGGGCACATTTTCCTTGTTTCTT 59.289 39.130 0.00 0.00 0.00 2.52
89 90 4.164030 AGGGCACATTTTCCTTGTTTCTTT 59.836 37.500 0.00 0.00 0.00 2.52
90 91 4.881273 GGGCACATTTTCCTTGTTTCTTTT 59.119 37.500 0.00 0.00 0.00 2.27
91 92 5.007626 GGGCACATTTTCCTTGTTTCTTTTC 59.992 40.000 0.00 0.00 0.00 2.29
92 93 5.007626 GGCACATTTTCCTTGTTTCTTTTCC 59.992 40.000 0.00 0.00 0.00 3.13
109 110 1.803334 TCCGAGTAAAATGCAAGCGT 58.197 45.000 0.00 0.00 0.00 5.07
155 156 5.535030 GTGTCACTTGGGTCCTAATTCTTTT 59.465 40.000 0.00 0.00 0.00 2.27
197 198 9.052759 GTCCTAAATCTTTCTAAGTTGTTCACA 57.947 33.333 0.00 0.00 0.00 3.58
207 208 1.485066 AGTTGTTCACACGAGGTCCTT 59.515 47.619 0.00 0.00 0.00 3.36
208 209 2.093128 AGTTGTTCACACGAGGTCCTTT 60.093 45.455 0.00 0.00 0.00 3.11
225 226 3.646650 TTTTTCGTCTGACCGTCGT 57.353 47.368 1.55 0.00 0.00 4.34
273 277 3.054503 CCACGTCGACTCGAGGGT 61.055 66.667 21.64 11.51 44.42 4.34
278 282 1.970114 GTCGACTCGAGGGTCCACA 60.970 63.158 18.41 0.00 36.23 4.17
282 286 0.970937 GACTCGAGGGTCCACATGGA 60.971 60.000 18.41 0.00 43.08 3.41
336 340 1.080638 AATGTGGCCCCTGGAGTTTA 58.919 50.000 0.00 0.00 0.00 2.01
353 359 4.934356 AGTTTATGCTTTCCTCATTCCCA 58.066 39.130 0.00 0.00 0.00 4.37
389 410 1.447317 GCTCGCTCTCTCCCTCTCTG 61.447 65.000 0.00 0.00 0.00 3.35
390 411 0.819259 CTCGCTCTCTCCCTCTCTGG 60.819 65.000 0.00 0.00 0.00 3.86
391 412 2.489275 CGCTCTCTCCCTCTCTGGC 61.489 68.421 0.00 0.00 0.00 4.85
394 415 3.535962 CTCTCCCTCTCTGGCGCC 61.536 72.222 22.73 22.73 0.00 6.53
424 450 3.807538 GCCATGTCTGCTGCCACG 61.808 66.667 0.00 0.00 0.00 4.94
443 668 1.465387 CGAGCTCGTCTACTGTGAAGT 59.535 52.381 27.79 0.00 34.11 3.01
450 5701 2.228103 CGTCTACTGTGAAGTGCCACTA 59.772 50.000 0.00 0.00 37.89 2.74
475 5726 2.682856 TCCTACATTGCAAAGGATTCGC 59.317 45.455 13.31 0.00 34.46 4.70
500 5763 7.563888 TCATTGATTCTGCCTAAATGAGAAG 57.436 36.000 0.00 0.00 33.50 2.85
501 5764 5.824904 TTGATTCTGCCTAAATGAGAAGC 57.175 39.130 0.00 0.00 33.64 3.86
690 5998 2.966309 GCCCTGTTTTCGCCAGACG 61.966 63.158 0.00 0.00 45.62 4.18
792 6128 2.067605 ATGGCCGGTCGTTATCCCA 61.068 57.895 0.00 0.00 0.00 4.37
808 6144 3.901087 CCACATGGGCATTCTGGTA 57.099 52.632 0.00 0.00 0.00 3.25
810 6146 2.669781 CCACATGGGCATTCTGGTATT 58.330 47.619 0.00 0.00 0.00 1.89
854 6211 3.294214 GTCAGACGGGATTAGGACCTTA 58.706 50.000 0.00 0.00 0.00 2.69
858 6215 4.831155 CAGACGGGATTAGGACCTTACATA 59.169 45.833 0.00 0.00 0.00 2.29
867 6224 9.239551 GGATTAGGACCTTACATAAACAACTTT 57.760 33.333 0.00 0.00 0.00 2.66
970 6327 5.371115 TGCATTTTACTCTTCTTTTCCCG 57.629 39.130 0.00 0.00 0.00 5.14
989 6346 3.515286 CCTTCGGCTCGGCTCGTA 61.515 66.667 0.00 0.00 0.00 3.43
1113 6471 2.892425 CCCACCTTCGCGCTCATC 60.892 66.667 5.56 0.00 0.00 2.92
1195 6553 3.306780 CGTCACCATCCTCAAGGTAAACT 60.307 47.826 0.00 0.00 36.07 2.66
1219 6577 2.415491 CGTGATTCCGAGTGCTTACTGA 60.415 50.000 0.00 0.00 0.00 3.41
1480 6851 7.241376 CGGTTTAATTAAAGAGTAGTTGGCAG 58.759 38.462 10.92 0.00 0.00 4.85
1494 6865 1.299850 GGCAGGTTGTTGTTTCGCC 60.300 57.895 0.00 0.00 0.00 5.54
1540 6995 0.672711 GGAAACCTACCGCTGTGTCC 60.673 60.000 0.00 0.00 31.93 4.02
1550 7005 2.997986 ACCGCTGTGTCCGTTTAAATAG 59.002 45.455 0.00 0.00 0.00 1.73
1551 7006 2.350498 CCGCTGTGTCCGTTTAAATAGG 59.650 50.000 6.39 6.39 0.00 2.57
1552 7007 2.997986 CGCTGTGTCCGTTTAAATAGGT 59.002 45.455 11.03 0.00 0.00 3.08
1555 7010 5.292589 CGCTGTGTCCGTTTAAATAGGTTAT 59.707 40.000 11.03 0.00 0.00 1.89
1557 7012 6.964934 GCTGTGTCCGTTTAAATAGGTTATTG 59.035 38.462 11.03 4.24 0.00 1.90
1558 7013 7.361457 GCTGTGTCCGTTTAAATAGGTTATTGT 60.361 37.037 11.03 0.00 0.00 2.71
1559 7014 8.393671 TGTGTCCGTTTAAATAGGTTATTGTT 57.606 30.769 11.03 0.00 0.00 2.83
1560 7015 8.848182 TGTGTCCGTTTAAATAGGTTATTGTTT 58.152 29.630 11.03 0.00 0.00 2.83
1561 7016 9.681692 GTGTCCGTTTAAATAGGTTATTGTTTT 57.318 29.630 11.03 0.00 0.00 2.43
1642 7101 4.563786 GGCCTGCAGATAATTAGTACTCCC 60.564 50.000 17.39 0.00 0.00 4.30
1645 7104 5.046950 CCTGCAGATAATTAGTACTCCCTCC 60.047 48.000 17.39 0.00 0.00 4.30
1656 7115 0.323542 ACTCCCTCCGTCTAGGTGTG 60.324 60.000 0.00 0.00 41.99 3.82
1670 7129 9.720809 CCGTCTAGGTGTGTAAGTCATCTTACG 62.721 48.148 11.67 0.00 44.84 3.18
1685 7144 8.674607 AGTCATCTTACGAAAACCAAATAATCC 58.325 33.333 0.00 0.00 0.00 3.01
1686 7145 7.913821 GTCATCTTACGAAAACCAAATAATCCC 59.086 37.037 0.00 0.00 0.00 3.85
1700 7159 5.576447 AATAATCCCAAAACACTTAGGCG 57.424 39.130 0.00 0.00 0.00 5.52
1729 7188 7.481798 GTGCATTAAATTCTACCTCGTTTCTTG 59.518 37.037 0.00 0.00 0.00 3.02
1772 7231 0.731417 GAGATGTGAGGTGTGCATGC 59.269 55.000 11.82 11.82 0.00 4.06
1799 7258 7.724305 TTAATGACTTGAGACTACCAAACAC 57.276 36.000 0.00 0.00 0.00 3.32
1817 7276 2.143122 CACGACATGCAGTGGTTAGTT 58.857 47.619 11.93 0.00 37.03 2.24
1818 7277 2.157668 CACGACATGCAGTGGTTAGTTC 59.842 50.000 11.93 0.00 37.03 3.01
1823 7282 3.057315 ACATGCAGTGGTTAGTTCATTGC 60.057 43.478 0.00 4.92 44.56 3.56
1913 7372 5.348997 GTGCACAACCTAAGATGACTTACTC 59.651 44.000 13.17 0.00 37.53 2.59
1978 7444 2.828128 CGCGTACCCCTAGGTCGTC 61.828 68.421 8.29 3.46 46.45 4.20
1979 7445 1.452833 GCGTACCCCTAGGTCGTCT 60.453 63.158 8.29 0.00 46.45 4.18
2000 7466 7.762615 TCGTCTATTTGACCAACCTAATACAAG 59.237 37.037 0.00 0.00 42.49 3.16
2105 7571 1.047801 AGGGTGGTCAAATTGGCAAC 58.952 50.000 0.00 0.00 0.00 4.17
2132 7598 5.300286 AGGTATACGCGTAGGACTTGTAAAT 59.700 40.000 24.78 6.54 0.00 1.40
2136 7602 3.924686 ACGCGTAGGACTTGTAAATTGAG 59.075 43.478 11.67 0.00 0.00 3.02
2140 7606 4.561606 CGTAGGACTTGTAAATTGAGACGG 59.438 45.833 0.00 0.00 0.00 4.79
2144 7610 3.933332 GACTTGTAAATTGAGACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
2149 7615 4.401519 TGTAAATTGAGACGGAGGGAGTAG 59.598 45.833 0.00 0.00 0.00 2.57
2153 7619 1.489649 TGAGACGGAGGGAGTAGTAGG 59.510 57.143 0.00 0.00 0.00 3.18
2154 7620 0.845337 AGACGGAGGGAGTAGTAGGG 59.155 60.000 0.00 0.00 0.00 3.53
2155 7621 0.842635 GACGGAGGGAGTAGTAGGGA 59.157 60.000 0.00 0.00 0.00 4.20
2156 7622 0.845337 ACGGAGGGAGTAGTAGGGAG 59.155 60.000 0.00 0.00 0.00 4.30
2157 7623 0.845337 CGGAGGGAGTAGTAGGGAGT 59.155 60.000 0.00 0.00 0.00 3.85
2158 7624 1.214923 CGGAGGGAGTAGTAGGGAGTT 59.785 57.143 0.00 0.00 0.00 3.01
2159 7625 2.357986 CGGAGGGAGTAGTAGGGAGTTT 60.358 54.545 0.00 0.00 0.00 2.66
2160 7626 3.722172 GGAGGGAGTAGTAGGGAGTTTT 58.278 50.000 0.00 0.00 0.00 2.43
2161 7627 4.102598 GGAGGGAGTAGTAGGGAGTTTTT 58.897 47.826 0.00 0.00 0.00 1.94
2162 7628 4.161942 GGAGGGAGTAGTAGGGAGTTTTTC 59.838 50.000 0.00 0.00 0.00 2.29
2163 7629 5.024785 GAGGGAGTAGTAGGGAGTTTTTCT 58.975 45.833 0.00 0.00 0.00 2.52
2164 7630 6.163110 AGGGAGTAGTAGGGAGTTTTTCTA 57.837 41.667 0.00 0.00 0.00 2.10
2165 7631 5.957168 AGGGAGTAGTAGGGAGTTTTTCTAC 59.043 44.000 0.00 0.00 35.03 2.59
2172 7638 1.743394 GGGAGTTTTTCTACCGCATGG 59.257 52.381 0.00 0.00 37.42 3.66
2173 7639 1.743394 GGAGTTTTTCTACCGCATGGG 59.257 52.381 2.06 2.06 40.75 4.00
2174 7640 2.617021 GGAGTTTTTCTACCGCATGGGA 60.617 50.000 12.02 0.00 40.75 4.37
2175 7641 2.418976 GAGTTTTTCTACCGCATGGGAC 59.581 50.000 12.02 0.00 40.75 4.46
2189 7655 2.666272 TGGGACATGTGGTTAGCAAA 57.334 45.000 1.15 0.00 0.00 3.68
2190 7656 2.950781 TGGGACATGTGGTTAGCAAAA 58.049 42.857 1.15 0.00 0.00 2.44
2191 7657 3.505386 TGGGACATGTGGTTAGCAAAAT 58.495 40.909 1.15 0.00 0.00 1.82
2192 7658 4.667573 TGGGACATGTGGTTAGCAAAATA 58.332 39.130 1.15 0.00 0.00 1.40
2193 7659 5.080337 TGGGACATGTGGTTAGCAAAATAA 58.920 37.500 1.15 0.00 0.00 1.40
2194 7660 5.540337 TGGGACATGTGGTTAGCAAAATAAA 59.460 36.000 1.15 0.00 0.00 1.40
2195 7661 6.042093 TGGGACATGTGGTTAGCAAAATAAAA 59.958 34.615 1.15 0.00 0.00 1.52
2196 7662 6.931840 GGGACATGTGGTTAGCAAAATAAAAA 59.068 34.615 1.15 0.00 0.00 1.94
2222 7688 7.725818 AAAGAGTAAGGAGTTTTTCTAACCG 57.274 36.000 0.00 0.00 0.00 4.44
2223 7689 6.416631 AGAGTAAGGAGTTTTTCTAACCGT 57.583 37.500 0.00 0.00 0.00 4.83
2224 7690 7.530426 AGAGTAAGGAGTTTTTCTAACCGTA 57.470 36.000 0.00 0.00 0.00 4.02
2225 7691 8.131847 AGAGTAAGGAGTTTTTCTAACCGTAT 57.868 34.615 0.00 0.00 0.00 3.06
2226 7692 8.591940 AGAGTAAGGAGTTTTTCTAACCGTATT 58.408 33.333 0.00 0.00 0.00 1.89
2227 7693 9.212641 GAGTAAGGAGTTTTTCTAACCGTATTT 57.787 33.333 0.00 0.00 0.00 1.40
2228 7694 9.565090 AGTAAGGAGTTTTTCTAACCGTATTTT 57.435 29.630 0.00 0.00 0.00 1.82
2229 7695 9.817365 GTAAGGAGTTTTTCTAACCGTATTTTC 57.183 33.333 0.00 0.00 0.00 2.29
2230 7696 7.444629 AGGAGTTTTTCTAACCGTATTTTCC 57.555 36.000 0.00 0.00 0.00 3.13
2231 7697 6.432162 AGGAGTTTTTCTAACCGTATTTTCCC 59.568 38.462 0.00 0.00 0.00 3.97
2232 7698 6.432162 GGAGTTTTTCTAACCGTATTTTCCCT 59.568 38.462 0.00 0.00 0.00 4.20
2233 7699 7.607607 GGAGTTTTTCTAACCGTATTTTCCCTA 59.392 37.037 0.00 0.00 0.00 3.53
2234 7700 8.922931 AGTTTTTCTAACCGTATTTTCCCTAA 57.077 30.769 0.00 0.00 0.00 2.69
2235 7701 9.524496 AGTTTTTCTAACCGTATTTTCCCTAAT 57.476 29.630 0.00 0.00 0.00 1.73
2241 7707 8.579863 TCTAACCGTATTTTCCCTAATACTAGC 58.420 37.037 0.00 0.00 38.34 3.42
2268 7771 7.286316 AGAGATTATTTCCAAAACAGCCCATAG 59.714 37.037 0.00 0.00 0.00 2.23
2311 7814 5.869888 CCTAGAATAATTAGCCACCGACATC 59.130 44.000 0.00 0.00 0.00 3.06
2339 7842 4.329545 AGTCAATGCCACCGCGGT 62.330 61.111 28.70 28.70 38.08 5.68
2396 7899 8.243426 TCAAATATTGTTTCATCCTGTAGCAAC 58.757 33.333 0.00 0.00 0.00 4.17
2401 7904 0.320050 TCATCCTGTAGCAACGCACA 59.680 50.000 0.00 0.00 0.00 4.57
2444 7947 8.803397 ATTAGTGGGGTAGTGTTTTTCTTATC 57.197 34.615 0.00 0.00 0.00 1.75
2448 7951 6.371825 GTGGGGTAGTGTTTTTCTTATCTGAG 59.628 42.308 0.00 0.00 0.00 3.35
2455 7958 8.147642 AGTGTTTTTCTTATCTGAGTTGACAG 57.852 34.615 0.00 0.00 39.02 3.51
2460 7963 3.506067 TCTTATCTGAGTTGACAGTCGCA 59.494 43.478 0.00 0.00 38.79 5.10
2462 7965 2.070262 TCTGAGTTGACAGTCGCATG 57.930 50.000 0.00 0.00 38.79 4.06
2504 8007 4.710324 TCAAATTGTTCGGAGTTGGTAGT 58.290 39.130 0.00 0.00 0.00 2.73
2564 8068 4.482025 TGGAGGGGAATGAAATAGGACAAT 59.518 41.667 0.00 0.00 0.00 2.71
2616 8122 6.935167 TGGAAAAATCTGGAATAAAAGCTCC 58.065 36.000 0.00 0.00 0.00 4.70
2637 8143 0.583438 CACCACACAAAGAGACGCAG 59.417 55.000 0.00 0.00 0.00 5.18
2675 8181 6.425114 CAGATATCTCCGTCCTAAACAAATGG 59.575 42.308 1.03 0.00 0.00 3.16
2684 8190 6.586082 CCGTCCTAAACAAATGGAATTTTCAG 59.414 38.462 0.00 0.00 46.10 3.02
2753 8262 7.553881 TTATTAAGAAGGAATTGCGGAGAAG 57.446 36.000 0.00 0.00 0.00 2.85
3007 8516 3.519510 CCCCTCCAAGAGATGAAGTTACA 59.480 47.826 0.00 0.00 0.00 2.41
3042 8551 5.590818 AGGAGATACTAAAGGTCTGGTGAA 58.409 41.667 0.00 0.00 0.00 3.18
3043 8552 6.023603 AGGAGATACTAAAGGTCTGGTGAAA 58.976 40.000 0.00 0.00 0.00 2.69
3044 8553 6.500751 AGGAGATACTAAAGGTCTGGTGAAAA 59.499 38.462 0.00 0.00 0.00 2.29
3328 8838 8.079203 AGATACATATAACTGAAGAGCAACTCG 58.921 37.037 0.00 0.00 35.36 4.18
3729 9240 5.716228 TCTGAACCTTGGCATGAATAATTGT 59.284 36.000 0.00 0.00 0.00 2.71
3752 9263 4.929211 TGAATACAGACTCACCACGAATTG 59.071 41.667 0.00 0.00 0.00 2.32
3873 9384 1.363744 CAGATGCACCGTTTCCTCTC 58.636 55.000 0.00 0.00 0.00 3.20
3918 9429 4.911514 TTCAGCTTTTGTTAAGGGTGAC 57.088 40.909 2.07 0.00 44.31 3.67
3999 9510 6.956202 AAGTATACCACAGTTAGCGAGTAT 57.044 37.500 0.00 0.00 0.00 2.12
4083 9594 9.985318 TTTGTTTCAATTGACATTTTGAATGAC 57.015 25.926 7.89 10.05 40.46 3.06
4115 9626 6.998074 AGTGATGAATGTGTTCCAAGTTCTTA 59.002 34.615 0.00 0.00 33.26 2.10
4121 9632 3.745975 TGTGTTCCAAGTTCTTATGCTCG 59.254 43.478 0.00 0.00 0.00 5.03
4234 9746 4.631377 TGAAGCCGTCAGATGTTCTTATTG 59.369 41.667 0.00 0.00 0.00 1.90
4303 9815 6.560003 TCCTGTTCATTCCAGCTAATCTTA 57.440 37.500 0.00 0.00 0.00 2.10
4314 9826 4.514441 CCAGCTAATCTTATGAAGCACCAG 59.486 45.833 5.41 0.00 37.44 4.00
4591 10103 3.885901 GTGCTTTGGTTTCTTCTCTCCTT 59.114 43.478 0.00 0.00 0.00 3.36
4687 10201 4.991153 TCTGTCTATAACTCCTGCTGTG 57.009 45.455 0.00 0.00 0.00 3.66
4745 10259 2.565841 AGAAAGTCATATCGCCCTTGC 58.434 47.619 0.00 0.00 0.00 4.01
4747 10261 2.717639 AAGTCATATCGCCCTTGCTT 57.282 45.000 0.00 0.00 34.43 3.91
4900 10415 7.607250 ACCAGATATTTCATTCGAGATACCTC 58.393 38.462 0.00 0.00 36.08 3.85
4932 10447 3.376234 ACTTCAATCAGATGGCATGAACG 59.624 43.478 3.81 0.08 0.00 3.95
4940 10455 0.466189 ATGGCATGAACGGATGGACC 60.466 55.000 0.00 0.00 0.00 4.46
4944 10459 2.639065 GCATGAACGGATGGACCTAAA 58.361 47.619 0.00 0.00 36.31 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.527547 GAACAGGCGCCGTTGATTGG 62.528 60.000 31.41 14.58 0.00 3.16
3 4 2.332654 GGAACAGGCGCCGTTGATT 61.333 57.895 31.41 18.98 0.00 2.57
4 5 2.746277 GGAACAGGCGCCGTTGAT 60.746 61.111 31.41 17.87 0.00 2.57
14 15 3.863606 TTTTTGGCGGGGAACAGG 58.136 55.556 0.00 0.00 0.00 4.00
46 47 3.125829 CCTGGAATCAACAGATGTCGTTG 59.874 47.826 0.00 0.00 44.11 4.10
47 48 3.338249 CCTGGAATCAACAGATGTCGTT 58.662 45.455 0.00 0.00 38.20 3.85
48 49 2.355108 CCCTGGAATCAACAGATGTCGT 60.355 50.000 0.00 0.00 38.20 4.34
49 50 2.283298 CCCTGGAATCAACAGATGTCG 58.717 52.381 0.00 0.00 38.20 4.35
50 51 2.019984 GCCCTGGAATCAACAGATGTC 58.980 52.381 0.00 0.00 38.20 3.06
51 52 1.355381 TGCCCTGGAATCAACAGATGT 59.645 47.619 0.00 0.00 38.20 3.06
52 53 1.747355 GTGCCCTGGAATCAACAGATG 59.253 52.381 0.00 0.00 38.20 2.90
53 54 1.355381 TGTGCCCTGGAATCAACAGAT 59.645 47.619 0.00 0.00 38.20 2.90
54 55 0.770499 TGTGCCCTGGAATCAACAGA 59.230 50.000 0.00 0.00 38.20 3.41
55 56 1.843368 ATGTGCCCTGGAATCAACAG 58.157 50.000 0.00 0.00 35.74 3.16
56 57 2.307496 AATGTGCCCTGGAATCAACA 57.693 45.000 0.00 0.00 0.00 3.33
57 58 3.588955 GAAAATGTGCCCTGGAATCAAC 58.411 45.455 0.00 0.00 0.00 3.18
58 59 2.566724 GGAAAATGTGCCCTGGAATCAA 59.433 45.455 0.00 0.00 0.00 2.57
59 60 2.178580 GGAAAATGTGCCCTGGAATCA 58.821 47.619 0.00 0.00 0.00 2.57
60 61 2.460669 AGGAAAATGTGCCCTGGAATC 58.539 47.619 0.00 0.00 0.00 2.52
61 62 2.568509 CAAGGAAAATGTGCCCTGGAAT 59.431 45.455 0.00 0.00 0.00 3.01
62 63 1.969923 CAAGGAAAATGTGCCCTGGAA 59.030 47.619 0.00 0.00 0.00 3.53
63 64 1.133199 ACAAGGAAAATGTGCCCTGGA 60.133 47.619 0.00 0.00 0.00 3.86
64 65 1.341080 ACAAGGAAAATGTGCCCTGG 58.659 50.000 0.00 0.00 0.00 4.45
65 66 3.070015 AGAAACAAGGAAAATGTGCCCTG 59.930 43.478 0.00 0.00 0.00 4.45
66 67 3.308401 AGAAACAAGGAAAATGTGCCCT 58.692 40.909 0.00 0.00 0.00 5.19
67 68 3.751479 AGAAACAAGGAAAATGTGCCC 57.249 42.857 0.00 0.00 0.00 5.36
68 69 5.007626 GGAAAAGAAACAAGGAAAATGTGCC 59.992 40.000 0.00 0.00 0.00 5.01
69 70 5.276820 CGGAAAAGAAACAAGGAAAATGTGC 60.277 40.000 0.00 0.00 0.00 4.57
70 71 6.039616 TCGGAAAAGAAACAAGGAAAATGTG 58.960 36.000 0.00 0.00 0.00 3.21
71 72 6.127451 ACTCGGAAAAGAAACAAGGAAAATGT 60.127 34.615 0.00 0.00 0.00 2.71
72 73 6.273071 ACTCGGAAAAGAAACAAGGAAAATG 58.727 36.000 0.00 0.00 0.00 2.32
73 74 6.465439 ACTCGGAAAAGAAACAAGGAAAAT 57.535 33.333 0.00 0.00 0.00 1.82
74 75 5.907866 ACTCGGAAAAGAAACAAGGAAAA 57.092 34.783 0.00 0.00 0.00 2.29
75 76 7.393841 TTTACTCGGAAAAGAAACAAGGAAA 57.606 32.000 0.00 0.00 0.00 3.13
76 77 7.393841 TTTTACTCGGAAAAGAAACAAGGAA 57.606 32.000 0.00 0.00 0.00 3.36
77 78 7.422399 CATTTTACTCGGAAAAGAAACAAGGA 58.578 34.615 0.00 0.00 32.06 3.36
78 79 6.143919 GCATTTTACTCGGAAAAGAAACAAGG 59.856 38.462 0.00 0.00 32.06 3.61
79 80 6.695278 TGCATTTTACTCGGAAAAGAAACAAG 59.305 34.615 0.00 0.00 32.06 3.16
80 81 6.565234 TGCATTTTACTCGGAAAAGAAACAA 58.435 32.000 0.00 0.00 32.06 2.83
81 82 6.137794 TGCATTTTACTCGGAAAAGAAACA 57.862 33.333 0.00 0.00 32.06 2.83
82 83 6.345803 GCTTGCATTTTACTCGGAAAAGAAAC 60.346 38.462 0.00 0.00 32.06 2.78
83 84 5.689961 GCTTGCATTTTACTCGGAAAAGAAA 59.310 36.000 0.00 0.00 32.06 2.52
84 85 5.219633 GCTTGCATTTTACTCGGAAAAGAA 58.780 37.500 0.00 0.00 32.06 2.52
85 86 4.612712 CGCTTGCATTTTACTCGGAAAAGA 60.613 41.667 0.00 0.00 32.06 2.52
86 87 3.603770 CGCTTGCATTTTACTCGGAAAAG 59.396 43.478 0.00 0.00 32.06 2.27
87 88 3.003897 ACGCTTGCATTTTACTCGGAAAA 59.996 39.130 0.00 0.00 33.04 2.29
88 89 2.550606 ACGCTTGCATTTTACTCGGAAA 59.449 40.909 0.00 0.00 0.00 3.13
89 90 2.095969 CACGCTTGCATTTTACTCGGAA 60.096 45.455 0.00 0.00 0.00 4.30
90 91 1.463056 CACGCTTGCATTTTACTCGGA 59.537 47.619 0.00 0.00 0.00 4.55
91 92 1.465689 CCACGCTTGCATTTTACTCGG 60.466 52.381 0.00 0.00 0.00 4.63
92 93 1.196808 ACCACGCTTGCATTTTACTCG 59.803 47.619 0.00 0.00 0.00 4.18
109 110 7.060421 ACACTTTCAGAAAAGAATTAGGACCA 58.940 34.615 4.99 0.00 43.90 4.02
155 156 8.448008 AGATTTAGGACCCAGATATGCATTTTA 58.552 33.333 3.54 0.00 0.00 1.52
207 208 1.589320 CAACGACGGTCAGACGAAAAA 59.411 47.619 9.10 0.00 40.26 1.94
208 209 1.202203 CAACGACGGTCAGACGAAAA 58.798 50.000 9.10 0.00 40.26 2.29
222 223 3.973516 ACGCGAGCTGGTCAACGA 61.974 61.111 15.93 0.00 0.00 3.85
282 286 2.438434 CCAGCCGCGGGAAATCTT 60.438 61.111 29.38 0.00 0.00 2.40
336 340 3.359950 GACTTGGGAATGAGGAAAGCAT 58.640 45.455 0.00 0.00 0.00 3.79
353 359 2.462723 GAGCAGAAGACCTAGGGACTT 58.537 52.381 18.90 18.90 40.05 3.01
424 450 2.857618 CACTTCACAGTAGACGAGCTC 58.142 52.381 2.73 2.73 0.00 4.09
434 659 1.699634 ACCATAGTGGCACTTCACAGT 59.300 47.619 27.24 13.32 42.67 3.55
443 668 2.421388 GCAATGTAGGACCATAGTGGCA 60.421 50.000 0.00 0.00 42.67 4.92
450 5701 3.737559 TCCTTTGCAATGTAGGACCAT 57.262 42.857 13.31 0.00 33.23 3.55
475 5726 7.563888 TTCTCATTTAGGCAGAATCAATGAG 57.436 36.000 12.14 12.14 46.58 2.90
500 5763 2.180432 ACTGTTTAGTTCCCCTTCGC 57.820 50.000 0.00 0.00 31.66 4.70
501 5764 3.512724 TCCTACTGTTTAGTTCCCCTTCG 59.487 47.826 0.00 0.00 38.36 3.79
667 5975 0.321741 TGGCGAAAACAGGGCGATTA 60.322 50.000 0.00 0.00 0.00 1.75
690 5998 1.690985 CACCCCTCTCCTTCTCCCC 60.691 68.421 0.00 0.00 0.00 4.81
697 6005 2.184631 TCTTCCCCACCCCTCTCCT 61.185 63.158 0.00 0.00 0.00 3.69
792 6128 3.290710 GTCAATACCAGAATGCCCATGT 58.709 45.455 0.00 0.00 31.97 3.21
800 6136 2.027192 AGTGCCACGTCAATACCAGAAT 60.027 45.455 0.00 0.00 0.00 2.40
801 6137 1.346395 AGTGCCACGTCAATACCAGAA 59.654 47.619 0.00 0.00 0.00 3.02
808 6144 0.603707 CTGACCAGTGCCACGTCAAT 60.604 55.000 6.94 0.00 36.16 2.57
810 6146 2.421314 CTGACCAGTGCCACGTCA 59.579 61.111 5.61 5.61 35.34 4.35
858 6215 8.966868 TGAGTCCTAAATCTTTCAAAGTTGTTT 58.033 29.630 0.00 0.96 0.00 2.83
867 6224 7.795047 TGCATATCTGAGTCCTAAATCTTTCA 58.205 34.615 0.00 0.00 0.00 2.69
908 6265 8.055279 TCTTTTCTGAAATTGTCACTTGAGTT 57.945 30.769 3.31 0.00 31.13 3.01
921 6278 5.163754 CGCGGTCCTAATTCTTTTCTGAAAT 60.164 40.000 3.31 0.00 0.00 2.17
1175 6533 3.263425 GGAGTTTACCTTGAGGATGGTGA 59.737 47.826 3.59 0.00 37.74 4.02
1195 6553 1.541310 AAGCACTCGGAATCACGGGA 61.541 55.000 0.00 0.00 37.86 5.14
1219 6577 1.298859 GATTTCGGCACAGGAAGCGT 61.299 55.000 0.00 0.00 0.00 5.07
1455 6826 7.136289 TGCCAACTACTCTTTAATTAAACCG 57.864 36.000 6.54 3.85 0.00 4.44
1480 6851 2.354188 GCGGGCGAAACAACAACC 60.354 61.111 0.00 0.00 0.00 3.77
1494 6865 3.986572 TGTTTTTGCATTAATGACTGCGG 59.013 39.130 19.73 0.00 41.32 5.69
1550 7005 9.131416 CGGTTTCCAAATACTAAAACAATAACC 57.869 33.333 0.00 0.00 34.15 2.85
1551 7006 9.896263 TCGGTTTCCAAATACTAAAACAATAAC 57.104 29.630 0.00 0.00 34.15 1.89
1555 7010 7.282675 TGTCTCGGTTTCCAAATACTAAAACAA 59.717 33.333 0.00 0.00 34.15 2.83
1557 7012 7.193377 TGTCTCGGTTTCCAAATACTAAAAC 57.807 36.000 0.00 0.00 0.00 2.43
1558 7013 7.989416 ATGTCTCGGTTTCCAAATACTAAAA 57.011 32.000 0.00 0.00 0.00 1.52
1559 7014 7.989416 AATGTCTCGGTTTCCAAATACTAAA 57.011 32.000 0.00 0.00 0.00 1.85
1560 7015 9.675464 ATTAATGTCTCGGTTTCCAAATACTAA 57.325 29.630 0.00 0.00 0.00 2.24
1561 7016 9.104965 CATTAATGTCTCGGTTTCCAAATACTA 57.895 33.333 7.32 0.00 0.00 1.82
1562 7017 7.415206 GCATTAATGTCTCGGTTTCCAAATACT 60.415 37.037 16.61 0.00 0.00 2.12
1563 7018 6.691388 GCATTAATGTCTCGGTTTCCAAATAC 59.309 38.462 16.61 0.00 0.00 1.89
1564 7019 6.375736 TGCATTAATGTCTCGGTTTCCAAATA 59.624 34.615 16.61 0.00 0.00 1.40
1617 7076 5.220710 AGTACTAATTATCTGCAGGCCTG 57.779 43.478 29.34 29.34 0.00 4.85
1642 7101 3.079578 TGACTTACACACCTAGACGGAG 58.920 50.000 0.00 0.00 36.31 4.63
1645 7104 4.966965 AGATGACTTACACACCTAGACG 57.033 45.455 0.00 0.00 0.00 4.18
1670 7129 8.445275 AAGTGTTTTGGGATTATTTGGTTTTC 57.555 30.769 0.00 0.00 0.00 2.29
1685 7144 1.209127 CCGCGCCTAAGTGTTTTGG 59.791 57.895 0.00 0.00 33.04 3.28
1686 7145 0.385473 CACCGCGCCTAAGTGTTTTG 60.385 55.000 0.00 0.00 0.00 2.44
1700 7159 3.303132 CGAGGTAGAATTTAATGCACCGC 60.303 47.826 0.00 0.00 0.00 5.68
1715 7174 5.522460 TGTCAAGAAACAAGAAACGAGGTAG 59.478 40.000 0.00 0.00 0.00 3.18
1729 7188 9.994432 CTCTTATTGGTTGATATGTCAAGAAAC 57.006 33.333 4.98 0.00 44.58 2.78
1772 7231 8.836413 TGTTTGGTAGTCTCAAGTCATTAAAAG 58.164 33.333 0.00 0.00 0.00 2.27
1799 7258 2.412870 TGAACTAACCACTGCATGTCG 58.587 47.619 0.00 0.00 0.00 4.35
1851 7310 6.311690 GGAGGAGAAAACGAGAGAACTTAATG 59.688 42.308 0.00 0.00 0.00 1.90
1871 7330 1.609501 CCGTGACCAAGGAGGAGGA 60.610 63.158 0.00 0.00 41.22 3.71
1913 7372 1.212441 AGTACTCCCTCCGTCTAGGTG 59.788 57.143 0.00 0.00 41.99 4.00
1940 7406 2.737359 CGCACGCCCTATAAACTGAGAA 60.737 50.000 0.00 0.00 0.00 2.87
1978 7444 8.786826 TGACTTGTATTAGGTTGGTCAAATAG 57.213 34.615 0.00 0.00 30.81 1.73
2077 7543 7.566879 TGCCAATTTGACCACCCTAATATAAAT 59.433 33.333 0.00 0.00 0.00 1.40
2087 7553 0.034756 GGTTGCCAATTTGACCACCC 59.965 55.000 0.00 0.00 32.41 4.61
2092 7558 5.007332 CGTATACCTAGGTTGCCAATTTGAC 59.993 44.000 22.11 1.58 0.00 3.18
2100 7566 0.386838 ACGCGTATACCTAGGTTGCC 59.613 55.000 22.11 7.02 0.00 4.52
2105 7571 3.051081 AGTCCTACGCGTATACCTAGG 57.949 52.381 20.91 18.03 0.00 3.02
2132 7598 2.092538 CCTACTACTCCCTCCGTCTCAA 60.093 54.545 0.00 0.00 0.00 3.02
2136 7602 0.842635 TCCCTACTACTCCCTCCGTC 59.157 60.000 0.00 0.00 0.00 4.79
2140 7606 5.024785 AGAAAAACTCCCTACTACTCCCTC 58.975 45.833 0.00 0.00 0.00 4.30
2144 7610 5.678361 GCGGTAGAAAAACTCCCTACTACTC 60.678 48.000 0.00 0.00 34.69 2.59
2149 7615 3.323751 TGCGGTAGAAAAACTCCCTAC 57.676 47.619 0.00 0.00 33.79 3.18
2153 7619 1.743394 CCCATGCGGTAGAAAAACTCC 59.257 52.381 0.00 0.00 0.00 3.85
2154 7620 2.418976 GTCCCATGCGGTAGAAAAACTC 59.581 50.000 0.00 0.00 0.00 3.01
2155 7621 2.224670 TGTCCCATGCGGTAGAAAAACT 60.225 45.455 0.00 0.00 0.00 2.66
2156 7622 2.156098 TGTCCCATGCGGTAGAAAAAC 58.844 47.619 0.00 0.00 0.00 2.43
2157 7623 2.570415 TGTCCCATGCGGTAGAAAAA 57.430 45.000 0.00 0.00 0.00 1.94
2158 7624 2.290641 ACATGTCCCATGCGGTAGAAAA 60.291 45.455 4.19 0.00 0.00 2.29
2159 7625 1.280710 ACATGTCCCATGCGGTAGAAA 59.719 47.619 4.19 0.00 0.00 2.52
2160 7626 0.908910 ACATGTCCCATGCGGTAGAA 59.091 50.000 4.19 0.00 0.00 2.10
2161 7627 0.177836 CACATGTCCCATGCGGTAGA 59.822 55.000 0.00 0.00 0.00 2.59
2162 7628 0.815213 CCACATGTCCCATGCGGTAG 60.815 60.000 0.00 0.00 0.00 3.18
2163 7629 1.223211 CCACATGTCCCATGCGGTA 59.777 57.895 0.00 0.00 0.00 4.02
2164 7630 2.045045 CCACATGTCCCATGCGGT 60.045 61.111 0.00 0.00 0.00 5.68
2165 7631 0.393673 TAACCACATGTCCCATGCGG 60.394 55.000 9.19 9.19 0.00 5.69
2166 7632 1.016627 CTAACCACATGTCCCATGCG 58.983 55.000 0.00 0.00 0.00 4.73
2167 7633 0.740737 GCTAACCACATGTCCCATGC 59.259 55.000 0.00 0.00 0.00 4.06
2168 7634 2.127271 TGCTAACCACATGTCCCATG 57.873 50.000 0.00 2.77 0.00 3.66
2169 7635 2.897271 TTGCTAACCACATGTCCCAT 57.103 45.000 0.00 0.00 0.00 4.00
2170 7636 2.666272 TTTGCTAACCACATGTCCCA 57.334 45.000 0.00 0.00 0.00 4.37
2171 7637 5.652994 TTATTTTGCTAACCACATGTCCC 57.347 39.130 0.00 0.00 0.00 4.46
2172 7638 7.954788 TTTTTATTTTGCTAACCACATGTCC 57.045 32.000 0.00 0.00 0.00 4.02
2196 7662 8.618677 CGGTTAGAAAAACTCCTTACTCTTTTT 58.381 33.333 0.00 0.00 0.00 1.94
2197 7663 7.772292 ACGGTTAGAAAAACTCCTTACTCTTTT 59.228 33.333 0.00 0.00 0.00 2.27
2198 7664 7.278135 ACGGTTAGAAAAACTCCTTACTCTTT 58.722 34.615 0.00 0.00 0.00 2.52
2199 7665 6.824553 ACGGTTAGAAAAACTCCTTACTCTT 58.175 36.000 0.00 0.00 0.00 2.85
2200 7666 6.416631 ACGGTTAGAAAAACTCCTTACTCT 57.583 37.500 0.00 0.00 0.00 3.24
2201 7667 8.768957 AATACGGTTAGAAAAACTCCTTACTC 57.231 34.615 0.00 0.00 0.00 2.59
2202 7668 9.565090 AAAATACGGTTAGAAAAACTCCTTACT 57.435 29.630 0.00 0.00 0.00 2.24
2203 7669 9.817365 GAAAATACGGTTAGAAAAACTCCTTAC 57.183 33.333 0.00 0.00 0.00 2.34
2204 7670 9.002600 GGAAAATACGGTTAGAAAAACTCCTTA 57.997 33.333 0.00 0.00 0.00 2.69
2205 7671 7.040201 GGGAAAATACGGTTAGAAAAACTCCTT 60.040 37.037 0.00 0.00 0.00 3.36
2206 7672 6.432162 GGGAAAATACGGTTAGAAAAACTCCT 59.568 38.462 0.00 0.00 0.00 3.69
2207 7673 6.432162 AGGGAAAATACGGTTAGAAAAACTCC 59.568 38.462 0.00 0.00 0.00 3.85
2208 7674 7.444629 AGGGAAAATACGGTTAGAAAAACTC 57.555 36.000 0.00 0.00 0.00 3.01
2209 7675 8.922931 TTAGGGAAAATACGGTTAGAAAAACT 57.077 30.769 0.00 0.00 0.00 2.66
2215 7681 8.579863 GCTAGTATTAGGGAAAATACGGTTAGA 58.420 37.037 0.00 0.00 43.87 2.10
2216 7682 8.362639 TGCTAGTATTAGGGAAAATACGGTTAG 58.637 37.037 0.00 0.00 43.87 2.34
2217 7683 8.248904 TGCTAGTATTAGGGAAAATACGGTTA 57.751 34.615 0.00 0.00 43.87 2.85
2218 7684 7.070322 TCTGCTAGTATTAGGGAAAATACGGTT 59.930 37.037 0.00 0.00 43.87 4.44
2219 7685 6.552350 TCTGCTAGTATTAGGGAAAATACGGT 59.448 38.462 0.00 0.00 43.87 4.83
2220 7686 6.989659 TCTGCTAGTATTAGGGAAAATACGG 58.010 40.000 0.00 0.00 43.87 4.02
2221 7687 7.883217 TCTCTGCTAGTATTAGGGAAAATACG 58.117 38.462 0.00 0.00 43.87 3.06
2228 7694 9.036980 GGAAATAATCTCTGCTAGTATTAGGGA 57.963 37.037 0.00 0.00 0.00 4.20
2229 7695 8.816894 TGGAAATAATCTCTGCTAGTATTAGGG 58.183 37.037 0.00 0.00 0.00 3.53
2234 7700 9.905713 TGTTTTGGAAATAATCTCTGCTAGTAT 57.094 29.630 0.00 0.00 0.00 2.12
2235 7701 9.383519 CTGTTTTGGAAATAATCTCTGCTAGTA 57.616 33.333 0.00 0.00 0.00 1.82
2236 7702 7.148171 GCTGTTTTGGAAATAATCTCTGCTAGT 60.148 37.037 0.00 0.00 0.00 2.57
2237 7703 7.192232 GCTGTTTTGGAAATAATCTCTGCTAG 58.808 38.462 0.00 0.00 0.00 3.42
2238 7704 6.095440 GGCTGTTTTGGAAATAATCTCTGCTA 59.905 38.462 0.00 0.00 0.00 3.49
2239 7705 5.105595 GGCTGTTTTGGAAATAATCTCTGCT 60.106 40.000 0.00 0.00 0.00 4.24
2240 7706 5.105063 GGCTGTTTTGGAAATAATCTCTGC 58.895 41.667 0.00 0.00 0.00 4.26
2241 7707 5.185635 TGGGCTGTTTTGGAAATAATCTCTG 59.814 40.000 0.00 0.00 0.00 3.35
2268 7771 0.721718 GTGCATGTGAAGCGGTAGAC 59.278 55.000 0.00 0.00 33.85 2.59
2311 7814 0.238289 GCATTGACTGGGTTGTGACG 59.762 55.000 0.00 0.00 0.00 4.35
2339 7842 0.605319 GTGTGACCGATTGCCCTCAA 60.605 55.000 0.00 0.00 36.51 3.02
2345 7848 3.047280 TGGCGTGTGACCGATTGC 61.047 61.111 0.00 0.00 0.00 3.56
2396 7899 4.308899 AGACTAGCTAAATACCTGTGCG 57.691 45.455 0.00 0.00 0.00 5.34
2401 7904 9.091220 CCCACTAATTAGACTAGCTAAATACCT 57.909 37.037 19.38 0.00 42.10 3.08
2444 7947 1.073964 CCATGCGACTGTCAACTCAG 58.926 55.000 8.73 0.00 40.80 3.35
2460 7963 8.450578 TTGATTCTAAATAGAACATTCGCCAT 57.549 30.769 5.07 0.00 44.30 4.40
2462 7965 9.736023 AATTTGATTCTAAATAGAACATTCGCC 57.264 29.630 5.07 0.00 44.30 5.54
2492 7995 0.892755 TGCAGGTACTACCAACTCCG 59.107 55.000 8.01 0.00 41.95 4.63
2564 8068 2.584835 AGTTTAGCCCAATGAGCACA 57.415 45.000 0.00 0.00 0.00 4.57
2616 8122 0.304705 GCGTCTCTTTGTGTGGTGTG 59.695 55.000 0.00 0.00 0.00 3.82
2675 8181 6.986904 AAAGGACGGAGATACTGAAAATTC 57.013 37.500 0.00 0.00 0.00 2.17
2684 8190 5.203060 AGATTGCTAAAGGACGGAGATAC 57.797 43.478 0.00 0.00 0.00 2.24
2761 8270 2.230508 ACTGCAACATCAGAAGCAATGG 59.769 45.455 0.00 0.00 36.44 3.16
3007 8516 8.440771 CCTTTAGTATCTCCTCCACCAAATATT 58.559 37.037 0.00 0.00 0.00 1.28
3044 8553 9.979578 CAGACAGCAATTAGAGAGAAGTAATAT 57.020 33.333 0.00 0.00 0.00 1.28
3729 9240 4.801330 ATTCGTGGTGAGTCTGTATTCA 57.199 40.909 0.00 0.00 0.00 2.57
3918 9429 6.434596 TGAGTCAATTTCAAAATACGTGTGG 58.565 36.000 0.00 0.00 0.00 4.17
3999 9510 7.040062 CCAACATTCTAAACCAGTGTATCCAAA 60.040 37.037 0.00 0.00 0.00 3.28
4011 9522 7.336931 ACATACAGATCACCAACATTCTAAACC 59.663 37.037 0.00 0.00 0.00 3.27
4083 9594 4.269603 GGAACACATTCATCACTCTCATCG 59.730 45.833 0.00 0.00 36.46 3.84
4115 9626 4.423732 GGAACACATTAAAATGCGAGCAT 58.576 39.130 4.52 4.52 40.04 3.79
4121 9632 3.507786 GGACCGGAACACATTAAAATGC 58.492 45.455 9.46 0.00 40.04 3.56
4234 9746 1.963172 AACAGACCGGACAGGAAAAC 58.037 50.000 9.46 0.00 45.00 2.43
4303 9815 5.232463 CAAAAACTAATGCTGGTGCTTCAT 58.768 37.500 0.00 0.00 40.48 2.57
4314 9826 2.416202 GCCACATGCCAAAAACTAATGC 59.584 45.455 0.00 0.00 0.00 3.56
4591 10103 2.131854 TCCTTTTCTTCCACTCCACCA 58.868 47.619 0.00 0.00 0.00 4.17
4745 10259 4.974399 AGGGAAGTTGTTACCTGAAGAAG 58.026 43.478 0.00 0.00 46.55 2.85
4932 10447 5.241728 GGATTAGCACATTTTAGGTCCATCC 59.758 44.000 0.00 0.00 0.00 3.51
4940 10455 7.944061 TGATGGATTGGATTAGCACATTTTAG 58.056 34.615 0.00 0.00 0.00 1.85
4944 10459 6.551975 TCATTGATGGATTGGATTAGCACATT 59.448 34.615 0.00 0.00 0.00 2.71
4994 10509 6.106648 TCACCAAAAATTCATGCCATACAA 57.893 33.333 0.00 0.00 0.00 2.41



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

AutoCloner maintained by Alex Coulton.