Multiple sequence alignment - TraesCS3D01G525300

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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 TraesCS3D01G525300 chr3D 100.000 6296 0 0 1 6296 604683098 604689393 0.000000e+00 11627.0
1 TraesCS3D01G525300 chr3D 94.291 508 25 2 5579 6083 604708451 604708957 0.000000e+00 774.0
2 TraesCS3D01G525300 chr3D 94.805 385 16 2 5579 5960 604743664 604743281 1.170000e-166 597.0
3 TraesCS3D01G525300 chr3D 85.333 300 41 3 1 299 446115324 446115027 2.200000e-79 307.0
4 TraesCS3D01G525300 chr3D 94.928 138 7 0 6157 6294 604709237 604709374 3.820000e-52 217.0
5 TraesCS3D01G525300 chr3D 90.566 106 8 2 393 497 412593296 412593400 8.510000e-29 139.0
6 TraesCS3D01G525300 chr3D 88.889 63 6 1 5380 5442 52093304 52093365 6.770000e-10 76.8
7 TraesCS3D01G525300 chr3A 92.410 3913 182 61 484 4321 734837992 734841864 0.000000e+00 5474.0
8 TraesCS3D01G525300 chr3A 93.778 2652 128 18 1689 4321 734884615 734887248 0.000000e+00 3949.0
9 TraesCS3D01G525300 chr3A 96.078 561 22 0 5736 6296 735359355 735359915 0.000000e+00 915.0
10 TraesCS3D01G525300 chr3A 91.713 543 41 3 4554 5095 734842603 734843142 0.000000e+00 750.0
11 TraesCS3D01G525300 chr3A 91.360 544 43 3 4553 5095 734887986 734888526 0.000000e+00 741.0
12 TraesCS3D01G525300 chr3A 88.908 595 44 5 5371 5944 734858789 734859382 0.000000e+00 713.0
13 TraesCS3D01G525300 chr3A 87.731 595 51 5 5371 5944 734904216 734904809 0.000000e+00 675.0
14 TraesCS3D01G525300 chr3A 94.417 412 21 2 1 410 734837565 734837976 3.200000e-177 632.0
15 TraesCS3D01G525300 chr3A 93.932 412 23 2 1 410 734817694 734818105 6.930000e-174 621.0
16 TraesCS3D01G525300 chr3A 97.348 264 3 3 5132 5394 734851023 734851283 4.480000e-121 446.0
17 TraesCS3D01G525300 chr3A 96.970 264 4 3 5132 5394 734818463 734818723 2.080000e-119 440.0
18 TraesCS3D01G525300 chr3A 96.241 266 2 4 5132 5394 734896435 734896695 4.510000e-116 429.0
19 TraesCS3D01G525300 chr3A 85.016 307 46 0 5 311 643213552 643213246 4.740000e-81 313.0
20 TraesCS3D01G525300 chr3A 83.851 322 51 1 1 322 17602929 17603249 7.930000e-79 305.0
21 TraesCS3D01G525300 chr3A 98.765 81 1 0 484 564 734818121 734818201 1.830000e-30 145.0
22 TraesCS3D01G525300 chr3B 91.475 2170 128 30 2261 4416 812459143 812461269 0.000000e+00 2929.0
23 TraesCS3D01G525300 chr3B 94.254 818 37 7 4594 5408 812461741 812462551 0.000000e+00 1242.0
24 TraesCS3D01G525300 chr3B 91.443 783 46 11 1444 2209 812458366 812459144 0.000000e+00 1055.0
25 TraesCS3D01G525300 chr3B 89.655 638 40 10 5377 5997 812462585 812463213 0.000000e+00 789.0
26 TraesCS3D01G525300 chr3B 87.671 511 22 22 848 1337 812457872 812458362 1.980000e-154 556.0
27 TraesCS3D01G525300 chr3B 92.857 98 5 2 401 497 821931585 821931489 2.370000e-29 141.0
28 TraesCS3D01G525300 chr5A 84.914 1339 151 38 2952 4258 623024452 623023133 0.000000e+00 1306.0
29 TraesCS3D01G525300 chr5A 85.565 478 63 5 4605 5079 623022742 623022268 4.380000e-136 496.0
30 TraesCS3D01G525300 chr5A 87.629 388 47 1 1777 2164 623025701 623025315 3.460000e-122 449.0
31 TraesCS3D01G525300 chr5A 89.456 294 21 8 1048 1337 623026433 623026146 4.640000e-96 363.0
32 TraesCS3D01G525300 chr5D 84.778 1327 150 38 2952 4244 498732208 498730900 0.000000e+00 1284.0
33 TraesCS3D01G525300 chr5D 82.282 666 96 16 4431 5079 498730640 498729980 1.980000e-154 556.0
34 TraesCS3D01G525300 chr5D 87.277 393 45 1 1772 2164 498733460 498733073 1.610000e-120 444.0
35 TraesCS3D01G525300 chr5D 88.514 296 25 6 1048 1337 498734183 498733891 3.610000e-92 350.0
36 TraesCS3D01G525300 chr5D 91.509 106 7 2 393 497 420827963 420828067 1.830000e-30 145.0
37 TraesCS3D01G525300 chr5D 94.681 94 4 1 393 485 440533069 440532976 1.830000e-30 145.0
38 TraesCS3D01G525300 chr5D 93.684 95 5 1 392 485 37951363 37951269 2.370000e-29 141.0
39 TraesCS3D01G525300 chr5B 84.187 1347 156 38 2952 4258 618284722 618283393 0.000000e+00 1254.0
40 TraesCS3D01G525300 chr5B 83.107 663 90 16 4433 5079 618283148 618282492 9.100000e-163 584.0
41 TraesCS3D01G525300 chr5B 87.629 388 47 1 1777 2164 618285968 618285582 3.460000e-122 449.0
42 TraesCS3D01G525300 chr5B 96.040 202 8 0 1048 1249 618286909 618286708 4.710000e-86 329.0
43 TraesCS3D01G525300 chr5B 91.262 103 7 2 393 494 212481095 212481196 8.510000e-29 139.0
44 TraesCS3D01G525300 chr5B 90.541 74 5 1 5377 5448 4178664 4178591 5.200000e-16 97.1
45 TraesCS3D01G525300 chr7D 91.742 884 31 8 2716 3598 499627412 499626570 0.000000e+00 1190.0
46 TraesCS3D01G525300 chr7D 90.476 756 53 11 3632 4382 499626571 499625830 0.000000e+00 979.0
47 TraesCS3D01G525300 chr7D 83.333 420 54 8 5880 6296 321047890 321047484 2.140000e-99 374.0
48 TraesCS3D01G525300 chr7D 92.784 97 5 2 411 506 252284022 252284117 8.510000e-29 139.0
49 TraesCS3D01G525300 chr7D 89.855 69 7 0 5383 5451 592882323 592882255 8.690000e-14 89.8
50 TraesCS3D01G525300 chr7D 86.667 75 10 0 5377 5451 634114105 634114031 4.040000e-12 84.2
51 TraesCS3D01G525300 chr4B 90.011 881 42 9 2716 3595 642737038 642737873 0.000000e+00 1098.0
52 TraesCS3D01G525300 chr4B 89.460 759 60 12 3631 4383 642737873 642738617 0.000000e+00 941.0
53 TraesCS3D01G525300 chr4B 94.681 94 4 1 393 485 252326028 252326121 1.830000e-30 145.0
54 TraesCS3D01G525300 chr7A 90.850 765 32 7 2833 3595 109230796 109230068 0.000000e+00 990.0
55 TraesCS3D01G525300 chr7A 90.707 764 33 7 2833 3595 61493737 61493011 0.000000e+00 983.0
56 TraesCS3D01G525300 chr7A 88.918 758 62 13 3631 4383 61493011 61492271 0.000000e+00 915.0
57 TraesCS3D01G525300 chr7A 88.859 754 65 11 3634 4383 109230066 109229328 0.000000e+00 909.0
58 TraesCS3D01G525300 chr2B 92.730 619 17 2 2978 3595 30335319 30334728 0.000000e+00 869.0
59 TraesCS3D01G525300 chr2B 94.898 490 25 0 3631 4120 30334728 30334239 0.000000e+00 767.0
60 TraesCS3D01G525300 chr2B 93.443 61 4 0 5388 5448 50797335 50797275 2.420000e-14 91.6
61 TraesCS3D01G525300 chr2B 93.220 59 4 0 5390 5448 53364444 53364502 3.130000e-13 87.9
62 TraesCS3D01G525300 chr2A 88.976 508 49 4 2453 2958 17648294 17647792 6.930000e-174 621.0
63 TraesCS3D01G525300 chr2A 88.065 310 37 0 1 310 564613782 564614091 9.970000e-98 368.0
64 TraesCS3D01G525300 chr2A 85.015 327 48 1 1 327 761285702 761286027 1.310000e-86 331.0
65 TraesCS3D01G525300 chr6D 88.802 509 48 6 2453 2958 7261898 7262400 3.230000e-172 616.0
66 TraesCS3D01G525300 chr6D 85.294 510 45 17 2562 3060 7276571 7276081 3.390000e-137 499.0
67 TraesCS3D01G525300 chr6D 91.549 71 6 0 5377 5447 145006560 145006630 1.440000e-16 99.0
68 TraesCS3D01G525300 chr2D 85.055 542 45 19 2564 3091 402014701 402015220 2.600000e-143 520.0
69 TraesCS3D01G525300 chrUn 90.127 395 25 9 2360 2750 480790319 480790703 9.420000e-138 501.0
70 TraesCS3D01G525300 chr1B 84.416 539 53 16 2564 3091 635793024 635793542 9.420000e-138 501.0
71 TraesCS3D01G525300 chr1B 87.013 77 8 1 5377 5451 12310969 12310893 1.120000e-12 86.1
72 TraesCS3D01G525300 chr6A 84.277 318 50 0 1 318 11128363 11128680 1.700000e-80 311.0
73 TraesCS3D01G525300 chr4D 83.025 324 52 2 1 323 505724671 505724350 2.220000e-74 291.0
74 TraesCS3D01G525300 chr4A 92.857 98 6 1 389 485 700163021 700163118 2.370000e-29 141.0
75 TraesCS3D01G525300 chr4A 86.000 100 10 4 5352 5448 645673376 645673474 3.100000e-18 104.0
76 TraesCS3D01G525300 chr4A 89.333 75 8 0 5377 5451 711968291 711968217 1.870000e-15 95.3
77 TraesCS3D01G525300 chr4A 92.857 56 4 0 5396 5451 689340814 689340759 1.450000e-11 82.4
78 TraesCS3D01G525300 chr7B 91.262 103 7 2 393 494 121719491 121719592 8.510000e-29 139.0
79 TraesCS3D01G525300 chr1D 90.000 70 7 0 5382 5451 24835905 24835836 2.420000e-14 91.6
80 TraesCS3D01G525300 chr1D 88.406 69 7 1 5373 5440 465778853 465778921 1.450000e-11 82.4


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 TraesCS3D01G525300 chr3D 604683098 604689393 6295 False 11627.000000 11627 100.000000 1 6296 1 chr3D.!!$F3 6295
1 TraesCS3D01G525300 chr3D 604708451 604709374 923 False 495.500000 774 94.609500 5579 6294 2 chr3D.!!$F4 715
2 TraesCS3D01G525300 chr3A 734884615 734888526 3911 False 2345.000000 3949 92.569000 1689 5095 2 chr3A.!!$F9 3406
3 TraesCS3D01G525300 chr3A 734837565 734843142 5577 False 2285.333333 5474 92.846667 1 5095 3 chr3A.!!$F8 5094
4 TraesCS3D01G525300 chr3A 735359355 735359915 560 False 915.000000 915 96.078000 5736 6296 1 chr3A.!!$F6 560
5 TraesCS3D01G525300 chr3A 734858789 734859382 593 False 713.000000 713 88.908000 5371 5944 1 chr3A.!!$F3 573
6 TraesCS3D01G525300 chr3A 734904216 734904809 593 False 675.000000 675 87.731000 5371 5944 1 chr3A.!!$F5 573
7 TraesCS3D01G525300 chr3A 734817694 734818723 1029 False 402.000000 621 96.555667 1 5394 3 chr3A.!!$F7 5393
8 TraesCS3D01G525300 chr3B 812457872 812463213 5341 False 1314.200000 2929 90.899600 848 5997 5 chr3B.!!$F1 5149
9 TraesCS3D01G525300 chr5A 623022268 623026433 4165 True 653.500000 1306 86.891000 1048 5079 4 chr5A.!!$R1 4031
10 TraesCS3D01G525300 chr5D 498729980 498734183 4203 True 658.500000 1284 85.712750 1048 5079 4 chr5D.!!$R3 4031
11 TraesCS3D01G525300 chr5B 618282492 618286909 4417 True 654.000000 1254 87.740750 1048 5079 4 chr5B.!!$R2 4031
12 TraesCS3D01G525300 chr7D 499625830 499627412 1582 True 1084.500000 1190 91.109000 2716 4382 2 chr7D.!!$R4 1666
13 TraesCS3D01G525300 chr4B 642737038 642738617 1579 False 1019.500000 1098 89.735500 2716 4383 2 chr4B.!!$F2 1667
14 TraesCS3D01G525300 chr7A 109229328 109230796 1468 True 949.500000 990 89.854500 2833 4383 2 chr7A.!!$R2 1550
15 TraesCS3D01G525300 chr7A 61492271 61493737 1466 True 949.000000 983 89.812500 2833 4383 2 chr7A.!!$R1 1550
16 TraesCS3D01G525300 chr2B 30334239 30335319 1080 True 818.000000 869 93.814000 2978 4120 2 chr2B.!!$R2 1142
17 TraesCS3D01G525300 chr2A 17647792 17648294 502 True 621.000000 621 88.976000 2453 2958 1 chr2A.!!$R1 505
18 TraesCS3D01G525300 chr6D 7261898 7262400 502 False 616.000000 616 88.802000 2453 2958 1 chr6D.!!$F1 505
19 TraesCS3D01G525300 chr2D 402014701 402015220 519 False 520.000000 520 85.055000 2564 3091 1 chr2D.!!$F1 527
20 TraesCS3D01G525300 chr1B 635793024 635793542 518 False 501.000000 501 84.416000 2564 3091 1 chr1B.!!$F1 527

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
244 246 0.108756 GCCCTAAGACCACACGAGAC 60.109 60.000 0.00 0.0 0.00 3.36 F
1023 1044 0.319555 CCGCGGAACTCAAGACTCAA 60.320 55.000 24.07 0.0 0.00 3.02 F
2198 2520 0.101219 GCCGATGCAATCTGGAAACC 59.899 55.000 0.00 0.0 42.58 3.27 F
2289 2612 3.449737 CCTACCTTTCGAATACACCTCCA 59.550 47.826 0.00 0.0 0.00 3.86 F
4114 4850 3.542712 TTCAATTCTTCTGAACTGCGC 57.457 42.857 0.00 0.0 34.71 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1266 1295 0.248843 AAGGGAAGAAGAGCAGAGCG 59.751 55.000 0.0 0.0 0.00 5.03 R
2577 2908 1.279271 GCAGTGGTAGTCAATCAGGGT 59.721 52.381 0.0 0.0 0.00 4.34 R
4120 4856 0.108207 ATCCCTATGCAGCACTGAGC 59.892 55.000 0.0 0.0 46.19 4.26 R
4121 4857 1.693062 AGATCCCTATGCAGCACTGAG 59.307 52.381 0.0 0.0 0.00 3.35 R
5705 7083 1.343465 GACCGTGAAGGACAGGAGAAA 59.657 52.381 0.0 0.0 45.00 2.52 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.170256 GAGATCCGCCGAAGATAAATCTC 58.830 47.826 0.00 0.00 35.76 2.75
69 70 3.472652 ACGATGCTAGAAACACCAACAA 58.527 40.909 0.00 0.00 0.00 2.83
103 104 3.073209 GGAGGGGAGAACCTTATTCCATC 59.927 52.174 0.00 0.00 42.10 3.51
109 110 5.131142 GGGAGAACCTTATTCCATCTTCAGA 59.869 44.000 0.00 0.00 35.85 3.27
133 134 3.073735 CTGCCGCCTCACCTCTCT 61.074 66.667 0.00 0.00 0.00 3.10
137 138 2.493973 CGCCTCACCTCTCTGAGC 59.506 66.667 0.00 0.00 37.01 4.26
139 140 1.516892 GCCTCACCTCTCTGAGCAG 59.483 63.158 0.00 0.00 37.01 4.24
140 141 1.516892 CCTCACCTCTCTGAGCAGC 59.483 63.158 0.00 0.00 37.01 5.25
170 171 4.038042 AGCCTAACAAAACTCAAAAGAGCC 59.962 41.667 0.00 0.00 0.00 4.70
239 241 0.328258 ACATGGCCCTAAGACCACAC 59.672 55.000 0.00 0.00 39.19 3.82
244 246 0.108756 GCCCTAAGACCACACGAGAC 60.109 60.000 0.00 0.00 0.00 3.36
310 312 2.163509 GCCAAAGGGTCCTCTTTCTTC 58.836 52.381 3.17 0.00 35.04 2.87
314 316 2.011122 AGGGTCCTCTTTCTTCGACA 57.989 50.000 0.00 0.00 0.00 4.35
340 343 1.790818 AAGGAACGATCTCCCCCTAC 58.209 55.000 0.00 0.00 35.95 3.18
367 370 7.222611 ACAATGTCTTCTTTGTGTAAATGTTGC 59.777 33.333 0.00 0.00 39.39 4.17
415 418 9.693739 ATCAAATATTTGTAGTACATTGTCCCA 57.306 29.630 23.95 3.38 39.18 4.37
416 419 9.693739 TCAAATATTTGTAGTACATTGTCCCAT 57.306 29.630 23.95 0.00 39.18 4.00
428 431 9.706691 AGTACATTGTCCCATAATATAAGAACG 57.293 33.333 0.00 0.00 0.00 3.95
429 432 9.485206 GTACATTGTCCCATAATATAAGAACGT 57.515 33.333 0.00 0.00 0.00 3.99
430 433 8.974060 ACATTGTCCCATAATATAAGAACGTT 57.026 30.769 0.00 0.00 0.00 3.99
431 434 9.403583 ACATTGTCCCATAATATAAGAACGTTT 57.596 29.630 0.46 0.00 0.00 3.60
435 438 9.451002 TGTCCCATAATATAAGAACGTTTTTGA 57.549 29.630 13.87 2.81 0.00 2.69
436 439 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
437 440 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
438 441 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
444 447 7.781548 ATAAGAACGTTTTTGACACTACACT 57.218 32.000 13.87 0.00 0.00 3.55
445 448 8.876275 ATAAGAACGTTTTTGACACTACACTA 57.124 30.769 13.87 0.00 0.00 2.74
446 449 6.823678 AGAACGTTTTTGACACTACACTAG 57.176 37.500 0.46 0.00 0.00 2.57
447 450 6.335777 AGAACGTTTTTGACACTACACTAGT 58.664 36.000 0.46 0.00 40.28 2.57
460 463 6.579491 ACTACACTAGTGTCAAAAACGTTC 57.421 37.500 31.11 0.00 43.74 3.95
461 464 6.335777 ACTACACTAGTGTCAAAAACGTTCT 58.664 36.000 31.11 5.44 43.74 3.01
462 465 6.815142 ACTACACTAGTGTCAAAAACGTTCTT 59.185 34.615 31.11 4.99 43.74 2.52
463 466 7.975616 ACTACACTAGTGTCAAAAACGTTCTTA 59.024 33.333 31.11 8.36 43.74 2.10
464 467 7.781548 ACACTAGTGTCAAAAACGTTCTTAT 57.218 32.000 22.95 0.00 40.24 1.73
465 468 8.876275 ACACTAGTGTCAAAAACGTTCTTATA 57.124 30.769 22.95 0.00 40.24 0.98
466 469 9.485206 ACACTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 22.95 0.00 40.24 0.86
472 475 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
473 476 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
474 477 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
475 478 8.605746 TCAAAAACGTTCTTATATTATGGGACG 58.394 33.333 0.00 9.33 0.00 4.79
476 479 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
477 480 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
478 481 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
479 482 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
480 483 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
481 484 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
482 485 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
554 557 1.139095 GGCAAGACTACCTCCGACG 59.861 63.158 0.00 0.00 0.00 5.12
564 567 1.371022 CCTCCGACGAGATGCGATG 60.371 63.158 0.00 0.00 44.57 3.84
565 568 2.013483 CTCCGACGAGATGCGATGC 61.013 63.158 0.00 0.00 44.57 3.91
566 569 3.390017 CCGACGAGATGCGATGCG 61.390 66.667 0.00 0.00 44.57 4.73
567 570 2.352343 CGACGAGATGCGATGCGA 60.352 61.111 0.00 0.00 44.57 5.10
568 571 2.353074 CGACGAGATGCGATGCGAG 61.353 63.158 0.00 0.00 44.57 5.03
577 580 1.770957 TGCGATGCGAGATATCACAC 58.229 50.000 5.32 0.00 0.00 3.82
587 590 4.441792 CGAGATATCACACATTTGGTCCA 58.558 43.478 5.32 0.00 0.00 4.02
588 591 4.509230 CGAGATATCACACATTTGGTCCAG 59.491 45.833 5.32 0.00 0.00 3.86
589 592 4.202441 AGATATCACACATTTGGTCCAGC 58.798 43.478 5.32 0.00 0.00 4.85
590 593 2.592102 ATCACACATTTGGTCCAGCT 57.408 45.000 0.00 0.00 0.00 4.24
608 611 2.774809 AGCTAGGAAGAAAGATGGTCCC 59.225 50.000 0.00 0.00 0.00 4.46
609 612 2.483889 GCTAGGAAGAAAGATGGTCCCG 60.484 54.545 0.00 0.00 0.00 5.14
716 719 2.536803 CGTCAAACTTTCGAAACTCCGA 59.463 45.455 6.47 0.00 36.70 4.55
719 722 4.741676 GTCAAACTTTCGAAACTCCGACTA 59.258 41.667 6.47 0.00 38.39 2.59
737 740 9.146984 CTCCGACTACTAATGTGTTTTCAAATA 57.853 33.333 0.00 0.00 0.00 1.40
814 819 9.990868 AAATCATTTTTGTAAGTACTCCCCTAT 57.009 29.630 0.00 0.00 0.00 2.57
1020 1041 2.048127 GCCGCGGAACTCAAGACT 60.048 61.111 33.48 0.00 0.00 3.24
1022 1043 1.289066 CCGCGGAACTCAAGACTCA 59.711 57.895 24.07 0.00 0.00 3.41
1023 1044 0.319555 CCGCGGAACTCAAGACTCAA 60.320 55.000 24.07 0.00 0.00 3.02
1111 1132 0.462047 CCGTGATCAAGTACTGGGGC 60.462 60.000 7.88 0.00 0.00 5.80
1250 1271 3.056328 GGCTCAACGGCAAGGTCC 61.056 66.667 0.00 0.00 38.25 4.46
1261 1290 2.531942 AAGGTCCGCCCCCTTCTT 60.532 61.111 0.00 0.00 37.82 2.52
1271 1300 3.775654 CCCTTCTTCCCGCGCTCT 61.776 66.667 5.56 0.00 0.00 4.09
1272 1301 2.510238 CCTTCTTCCCGCGCTCTG 60.510 66.667 5.56 0.00 0.00 3.35
1298 1336 6.918033 TCTTCTTCCCTTTTCCTTTTCCTTA 58.082 36.000 0.00 0.00 0.00 2.69
1299 1337 7.535738 TCTTCTTCCCTTTTCCTTTTCCTTAT 58.464 34.615 0.00 0.00 0.00 1.73
1306 1344 5.705905 CCTTTTCCTTTTCCTTATCTCACGT 59.294 40.000 0.00 0.00 0.00 4.49
1425 1705 1.741401 CAGGAGCACGCCGATTTGA 60.741 57.895 0.00 0.00 0.00 2.69
1432 1712 1.080093 ACGCCGATTTGAGCTTCGA 60.080 52.632 7.10 0.00 37.55 3.71
1440 1720 0.106708 TTTGAGCTTCGAGCCTGTGT 59.893 50.000 0.00 0.00 43.77 3.72
1552 1834 1.364171 GGATAGACAGTCGGCGCAT 59.636 57.895 10.83 0.00 0.00 4.73
1684 1999 6.406370 TGATGGACCAATACAAGTAGTTCTG 58.594 40.000 0.00 0.00 0.00 3.02
1687 2002 6.694447 TGGACCAATACAAGTAGTTCTGTAC 58.306 40.000 0.00 0.00 0.00 2.90
1713 2028 4.935808 GGTCTTTAACTGGGTGTGATGTAG 59.064 45.833 0.00 0.00 0.00 2.74
1735 2050 4.866486 AGCACAACTGCAAGAAAAAGAAAG 59.134 37.500 0.00 0.00 46.97 2.62
1747 2062 9.868389 GCAAGAAAAAGAAAGACAAATTATTGG 57.132 29.630 0.00 0.00 41.01 3.16
2053 2375 4.129380 TGTCAGGAAAACAGATGTGTGAG 58.871 43.478 0.00 0.00 36.84 3.51
2075 2397 7.066525 GTGAGTAAAATTGTGGATATTTCGGGA 59.933 37.037 0.00 0.00 0.00 5.14
2090 2412 2.408565 TCGGGATAGGCTTGGATTTCT 58.591 47.619 0.00 0.00 0.00 2.52
2095 2417 5.450550 CGGGATAGGCTTGGATTTCTTTTTC 60.451 44.000 0.00 0.00 0.00 2.29
2114 2436 3.198409 TCTTTTCTGCTCTTCTGCACA 57.802 42.857 0.00 0.00 38.12 4.57
2163 2485 6.663734 AGGGGGTGTATTTCTTATTCTCTTG 58.336 40.000 0.00 0.00 0.00 3.02
2181 2503 5.934625 TCTCTTGTAGAATTGTTCTCTTGCC 59.065 40.000 0.00 0.00 41.14 4.52
2198 2520 0.101219 GCCGATGCAATCTGGAAACC 59.899 55.000 0.00 0.00 42.58 3.27
2253 2576 5.127356 GCTACAAGTGGACTGTTATCCTAGT 59.873 44.000 0.00 0.00 39.75 2.57
2289 2612 3.449737 CCTACCTTTCGAATACACCTCCA 59.550 47.826 0.00 0.00 0.00 3.86
2577 2908 5.825593 ATCTGGTCCTGAGTCTTGTTTTA 57.174 39.130 4.63 0.00 0.00 1.52
2858 3200 7.396339 TCTTCAATAGCAAGGTCTGTACTCTAA 59.604 37.037 0.00 0.00 0.00 2.10
3760 4495 4.037690 GCACTGCACTACTTTTTCTTGTG 58.962 43.478 0.00 0.00 0.00 3.33
3775 4510 5.353394 TTCTTGTGTTCCAGACTGTAGTT 57.647 39.130 0.93 0.00 0.00 2.24
3938 4674 5.047519 ACGTCACACAGGTAGTTTTATAGCT 60.048 40.000 0.00 0.00 33.86 3.32
3953 4689 8.103305 AGTTTTATAGCTGTCCTGATTTTGAGA 58.897 33.333 0.00 0.00 0.00 3.27
4086 4822 4.630894 TGTTCCTGTTTAACACTTGCTG 57.369 40.909 0.00 0.00 32.07 4.41
4091 4827 3.550842 CCTGTTTAACACTTGCTGCCTTC 60.551 47.826 0.00 0.00 0.00 3.46
4114 4850 3.542712 TTCAATTCTTCTGAACTGCGC 57.457 42.857 0.00 0.00 34.71 6.09
4120 4856 1.572085 CTTCTGAACTGCGCCAGTGG 61.572 60.000 4.18 4.20 44.62 4.00
4121 4857 3.730761 CTGAACTGCGCCAGTGGC 61.731 66.667 25.07 25.07 44.62 5.01
4144 4881 3.906218 TCAGTGCTGCATAGGGATCTAAT 59.094 43.478 5.27 0.00 0.00 1.73
4175 4930 5.795972 TGGTTAACCTTCGTTATGACATGA 58.204 37.500 24.78 0.00 34.44 3.07
4210 4965 4.846779 TTTCACTGCACTGGATAAAACC 57.153 40.909 0.00 0.00 0.00 3.27
4231 4986 7.807977 AACCTATTTAACTAGCATCACATGG 57.192 36.000 0.00 0.00 0.00 3.66
4245 5000 8.297470 AGCATCACATGGTGAAGTAATTTAAT 57.703 30.769 2.87 0.00 45.96 1.40
4292 5056 5.860941 TGCCACCTTGTTGAAAGAAATTA 57.139 34.783 0.00 0.00 0.00 1.40
4321 5085 9.503427 AAAATACGAGTTTATGCTTATGCTTTC 57.497 29.630 1.96 0.00 40.48 2.62
4335 5106 1.412343 TGCTTTCAGCCCTTTGGTTTC 59.588 47.619 0.00 0.00 41.51 2.78
4337 5108 2.546584 GCTTTCAGCCCTTTGGTTTCTG 60.547 50.000 0.00 0.00 34.48 3.02
4347 5325 3.509967 CCTTTGGTTTCTGGGGAACATAC 59.490 47.826 0.00 0.00 0.00 2.39
4348 5326 2.483014 TGGTTTCTGGGGAACATACG 57.517 50.000 0.00 0.00 0.00 3.06
4352 5330 3.307621 GGTTTCTGGGGAACATACGGTTA 60.308 47.826 0.00 0.00 40.63 2.85
4354 5332 4.847990 TTCTGGGGAACATACGGTTAAT 57.152 40.909 0.00 0.00 40.63 1.40
4364 5342 7.248437 GGAACATACGGTTAATTTTGAAGAGG 58.752 38.462 0.00 0.00 40.63 3.69
4406 5388 1.066143 ACTGGTATTGGTTCTGGAGCG 60.066 52.381 0.00 0.00 0.00 5.03
4426 5474 3.213506 CGGTCAATTGCTAATGGGATGA 58.786 45.455 0.00 0.00 0.00 2.92
4428 5476 4.498009 CGGTCAATTGCTAATGGGATGAAC 60.498 45.833 0.00 0.00 0.00 3.18
4431 5479 6.407299 GGTCAATTGCTAATGGGATGAACAAT 60.407 38.462 0.00 0.00 0.00 2.71
4432 5480 7.201902 GGTCAATTGCTAATGGGATGAACAATA 60.202 37.037 0.00 0.00 0.00 1.90
4434 5482 8.756927 TCAATTGCTAATGGGATGAACAATAAA 58.243 29.630 0.00 0.00 0.00 1.40
4435 5483 9.550406 CAATTGCTAATGGGATGAACAATAAAT 57.450 29.630 0.00 0.00 0.00 1.40
4439 5487 9.812347 TGCTAATGGGATGAACAATAAATATCT 57.188 29.630 0.00 0.00 0.00 1.98
4462 5518 4.052159 AGTATGCCGTCATCAAAGAGAG 57.948 45.455 0.00 0.00 34.22 3.20
4467 5523 3.498397 TGCCGTCATCAAAGAGAGAAAAC 59.502 43.478 0.00 0.00 0.00 2.43
4468 5524 3.120165 GCCGTCATCAAAGAGAGAAAACC 60.120 47.826 0.00 0.00 0.00 3.27
4473 5529 5.760253 GTCATCAAAGAGAGAAAACCAGTGA 59.240 40.000 0.00 0.00 0.00 3.41
4477 5533 8.786898 CATCAAAGAGAGAAAACCAGTGAAATA 58.213 33.333 0.00 0.00 0.00 1.40
4483 5539 7.231317 AGAGAGAAAACCAGTGAAATATTGCAA 59.769 33.333 0.00 0.00 0.00 4.08
4515 5571 4.330944 TCGTCTATTTGTGTTGTCTGGT 57.669 40.909 0.00 0.00 0.00 4.00
4518 5574 6.097356 TCGTCTATTTGTGTTGTCTGGTATC 58.903 40.000 0.00 0.00 0.00 2.24
4563 5626 2.103094 TCCATCGGGTGATTGATCTGAC 59.897 50.000 0.00 0.00 34.93 3.51
4570 5860 4.384056 GGGTGATTGATCTGACATACTGG 58.616 47.826 0.00 0.00 0.00 4.00
4598 5891 7.339466 ACCAACTTTTGTGTGAAGACTTCTAAT 59.661 33.333 16.02 0.00 0.00 1.73
4601 5894 9.573133 AACTTTTGTGTGAAGACTTCTAATTTG 57.427 29.630 16.02 3.29 0.00 2.32
4603 5896 5.689383 TGTGTGAAGACTTCTAATTTGGC 57.311 39.130 16.02 0.06 0.00 4.52
4605 5898 5.769662 TGTGTGAAGACTTCTAATTTGGCAT 59.230 36.000 16.02 0.00 0.00 4.40
4608 5901 7.115378 GTGTGAAGACTTCTAATTTGGCATTTG 59.885 37.037 16.02 0.00 0.00 2.32
4610 5903 6.267471 TGAAGACTTCTAATTTGGCATTTGGT 59.733 34.615 16.02 0.00 0.00 3.67
4611 5904 6.272822 AGACTTCTAATTTGGCATTTGGTC 57.727 37.500 0.00 0.00 0.00 4.02
4614 5907 7.015584 AGACTTCTAATTTGGCATTTGGTCTTT 59.984 33.333 0.00 0.00 0.00 2.52
4620 5913 9.218440 CTAATTTGGCATTTGGTCTTTTTGTAT 57.782 29.630 0.00 0.00 0.00 2.29
4624 5917 6.586344 TGGCATTTGGTCTTTTTGTATTTGA 58.414 32.000 0.00 0.00 0.00 2.69
4683 5976 2.030457 CCTAATAGCACGAAACCGCAAG 59.970 50.000 0.00 0.00 0.00 4.01
4873 6167 6.154445 GTCGGCGATAAATCAATCCTAAGTA 58.846 40.000 14.79 0.00 0.00 2.24
4902 6196 3.944015 GAGTGCAATCCTTAGCTGACATT 59.056 43.478 1.86 0.00 0.00 2.71
4940 6234 1.275291 TCCGGAGATGAAGACACCAAC 59.725 52.381 0.00 0.00 0.00 3.77
4950 6244 5.428184 TGAAGACACCAACCCAAAAATTT 57.572 34.783 0.00 0.00 0.00 1.82
4974 6268 3.134804 AGGGCGATGTTAGCTACTTCATT 59.865 43.478 0.00 0.00 32.01 2.57
5019 6313 1.551452 AAGTTCTCACCGAGGAGAGG 58.449 55.000 14.89 0.00 44.23 3.69
5433 6793 4.418973 GGGACTCCCTAGAAATTACCAC 57.581 50.000 6.90 0.00 41.34 4.16
5489 6864 1.884235 CGCAGATTAACCCATCCCTC 58.116 55.000 0.00 0.00 0.00 4.30
5494 6869 4.042187 GCAGATTAACCCATCCCTCTGTAT 59.958 45.833 0.00 0.00 34.13 2.29
5505 6880 7.615757 ACCCATCCCTCTGTATTAAAAGAAAAG 59.384 37.037 0.00 0.00 0.00 2.27
5634 7009 6.294342 CCAACATATAAGCACAATCCTCATGG 60.294 42.308 0.00 0.00 0.00 3.66
5669 7044 6.487828 TCATGTCTTCCTTCATTGATCCTTT 58.512 36.000 0.00 0.00 0.00 3.11
5769 7149 4.096682 GTCTCTTAGTACAGCCGTCATCTT 59.903 45.833 0.00 0.00 0.00 2.40
5780 7160 1.405933 CCGTCATCTTCATGTGCCTCA 60.406 52.381 0.00 0.00 0.00 3.86
5786 7166 3.777106 TCTTCATGTGCCTCAGTCTTT 57.223 42.857 0.00 0.00 0.00 2.52
5787 7167 4.090761 TCTTCATGTGCCTCAGTCTTTT 57.909 40.909 0.00 0.00 0.00 2.27
5917 7297 9.031360 GGATGTGAAGGAAAAAGAAGTTAAAAC 57.969 33.333 0.00 0.00 0.00 2.43
6123 7503 8.696410 TTTTAAGTTTTTGTGATTGTCCTGTC 57.304 30.769 0.00 0.00 0.00 3.51
6131 7511 2.816087 GTGATTGTCCTGTCTGTGCATT 59.184 45.455 0.00 0.00 0.00 3.56
6187 7773 5.339008 AGTGACCTCGATTTGCTAATACA 57.661 39.130 0.00 0.00 0.00 2.29
6196 7782 4.034048 CGATTTGCTAATACAGTGTCCCAC 59.966 45.833 0.00 0.00 34.10 4.61
6278 7864 6.677431 GCTGCCTTTTCAGAATAATCAGTGAG 60.677 42.308 0.00 0.00 36.19 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 2.702302 CCCCTCCTAGTCCCCGTCT 61.702 68.421 0.00 0.00 0.00 4.18
103 104 1.810441 CGGCAGCAGCTCTCTGAAG 60.810 63.158 14.83 5.37 42.95 3.02
133 134 0.108396 TAGGCTTTGTGTGCTGCTCA 59.892 50.000 0.00 0.00 0.00 4.26
137 138 3.435105 TTTGTTAGGCTTTGTGTGCTG 57.565 42.857 0.00 0.00 0.00 4.41
139 140 3.780902 AGTTTTGTTAGGCTTTGTGTGC 58.219 40.909 0.00 0.00 0.00 4.57
140 141 4.992688 TGAGTTTTGTTAGGCTTTGTGTG 58.007 39.130 0.00 0.00 0.00 3.82
239 241 0.582482 CATCGGTCTACCTCGTCTCG 59.418 60.000 0.00 0.00 0.00 4.04
244 246 2.331805 CGCCATCGGTCTACCTCG 59.668 66.667 0.00 0.00 0.00 4.63
269 271 3.993535 GGCTTCTTGTGCCTCCTG 58.006 61.111 0.00 0.00 46.38 3.86
310 312 2.433868 TCGTTCCTTTCTTCCTGTCG 57.566 50.000 0.00 0.00 0.00 4.35
314 316 2.502130 GGGAGATCGTTCCTTTCTTCCT 59.498 50.000 1.35 0.00 37.40 3.36
324 326 1.481871 TGTGTAGGGGGAGATCGTTC 58.518 55.000 0.00 0.00 0.00 3.95
367 370 5.299582 TGTTGTGTGTCTATGAATGCATG 57.700 39.130 0.00 0.00 35.94 4.06
410 413 9.712359 GTCAAAAACGTTCTTATATTATGGGAC 57.288 33.333 0.00 0.00 0.00 4.46
411 414 9.451002 TGTCAAAAACGTTCTTATATTATGGGA 57.549 29.630 0.00 0.00 0.00 4.37
412 415 9.498307 GTGTCAAAAACGTTCTTATATTATGGG 57.502 33.333 0.00 0.00 0.00 4.00
418 421 9.485206 AGTGTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 0.00 0.00 0.00 0.86
419 422 8.876275 AGTGTAGTGTCAAAAACGTTCTTATA 57.124 30.769 0.00 0.00 0.00 0.98
421 424 7.975616 ACTAGTGTAGTGTCAAAAACGTTCTTA 59.024 33.333 0.00 0.00 37.69 2.10
423 426 6.335777 ACTAGTGTAGTGTCAAAAACGTTCT 58.664 36.000 0.00 0.00 37.69 3.01
424 427 6.579491 ACTAGTGTAGTGTCAAAAACGTTC 57.421 37.500 0.00 0.00 37.69 3.95
437 440 6.335777 AGAACGTTTTTGACACTAGTGTAGT 58.664 36.000 27.98 15.35 45.05 2.73
438 441 6.823678 AGAACGTTTTTGACACTAGTGTAG 57.176 37.500 27.98 14.79 45.05 2.74
439 442 8.876275 ATAAGAACGTTTTTGACACTAGTGTA 57.124 30.769 27.98 11.50 45.05 2.90
446 449 9.498307 CCCATAATATAAGAACGTTTTTGACAC 57.502 33.333 13.87 0.00 0.00 3.67
447 450 9.451002 TCCCATAATATAAGAACGTTTTTGACA 57.549 29.630 13.87 0.01 0.00 3.58
448 451 9.712359 GTCCCATAATATAAGAACGTTTTTGAC 57.288 33.333 13.87 5.89 0.00 3.18
449 452 8.605746 CGTCCCATAATATAAGAACGTTTTTGA 58.394 33.333 13.87 2.81 0.00 2.69
450 453 7.853929 CCGTCCCATAATATAAGAACGTTTTTG 59.146 37.037 13.87 0.00 0.00 2.44
451 454 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
452 455 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
453 456 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
454 457 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
455 458 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
456 459 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
457 460 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
458 461 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
459 462 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
460 463 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
461 464 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
462 465 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
463 466 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
464 467 4.474303 TTACTCCCTCCGTCCCATAATA 57.526 45.455 0.00 0.00 0.00 0.98
465 468 3.339713 TTACTCCCTCCGTCCCATAAT 57.660 47.619 0.00 0.00 0.00 1.28
466 469 2.852714 TTACTCCCTCCGTCCCATAA 57.147 50.000 0.00 0.00 0.00 1.90
467 470 4.474303 TTATTACTCCCTCCGTCCCATA 57.526 45.455 0.00 0.00 0.00 2.74
468 471 3.339713 TTATTACTCCCTCCGTCCCAT 57.660 47.619 0.00 0.00 0.00 4.00
469 472 2.852714 TTATTACTCCCTCCGTCCCA 57.147 50.000 0.00 0.00 0.00 4.37
470 473 3.236896 TCATTATTACTCCCTCCGTCCC 58.763 50.000 0.00 0.00 0.00 4.46
471 474 4.950205 TTCATTATTACTCCCTCCGTCC 57.050 45.455 0.00 0.00 0.00 4.79
472 475 6.260271 CCTTTTTCATTATTACTCCCTCCGTC 59.740 42.308 0.00 0.00 0.00 4.79
473 476 6.069847 TCCTTTTTCATTATTACTCCCTCCGT 60.070 38.462 0.00 0.00 0.00 4.69
474 477 6.354130 TCCTTTTTCATTATTACTCCCTCCG 58.646 40.000 0.00 0.00 0.00 4.63
475 478 8.467598 GTTTCCTTTTTCATTATTACTCCCTCC 58.532 37.037 0.00 0.00 0.00 4.30
476 479 9.020731 TGTTTCCTTTTTCATTATTACTCCCTC 57.979 33.333 0.00 0.00 0.00 4.30
477 480 8.950007 TGTTTCCTTTTTCATTATTACTCCCT 57.050 30.769 0.00 0.00 0.00 4.20
478 481 9.586435 CATGTTTCCTTTTTCATTATTACTCCC 57.414 33.333 0.00 0.00 0.00 4.30
479 482 9.087424 GCATGTTTCCTTTTTCATTATTACTCC 57.913 33.333 0.00 0.00 0.00 3.85
480 483 9.860898 AGCATGTTTCCTTTTTCATTATTACTC 57.139 29.630 0.00 0.00 0.00 2.59
554 557 2.851235 GTGATATCTCGCATCGCATCTC 59.149 50.000 3.98 0.00 33.92 2.75
564 567 3.248602 GGACCAAATGTGTGATATCTCGC 59.751 47.826 10.66 10.66 0.00 5.03
565 568 4.441792 TGGACCAAATGTGTGATATCTCG 58.558 43.478 3.98 0.00 0.00 4.04
566 569 4.274459 GCTGGACCAAATGTGTGATATCTC 59.726 45.833 3.98 0.63 0.00 2.75
567 570 4.080129 AGCTGGACCAAATGTGTGATATCT 60.080 41.667 3.98 0.00 0.00 1.98
568 571 4.202441 AGCTGGACCAAATGTGTGATATC 58.798 43.478 0.00 0.00 0.00 1.63
577 580 3.634397 TCTTCCTAGCTGGACCAAATG 57.366 47.619 0.00 0.00 46.14 2.32
587 590 2.774809 GGGACCATCTTTCTTCCTAGCT 59.225 50.000 0.00 0.00 0.00 3.32
588 591 2.483889 CGGGACCATCTTTCTTCCTAGC 60.484 54.545 0.00 0.00 0.00 3.42
589 592 3.031736 TCGGGACCATCTTTCTTCCTAG 58.968 50.000 0.00 0.00 0.00 3.02
590 593 3.110293 TCGGGACCATCTTTCTTCCTA 57.890 47.619 0.00 0.00 0.00 2.94
627 630 8.718102 ATGTGGACACTAACACTTATATTGAC 57.282 34.615 3.91 0.00 38.39 3.18
644 647 2.727123 ACCTTTGTGTGATGTGGACA 57.273 45.000 0.00 0.00 0.00 4.02
680 683 4.192453 ACGGGTTTTGCCGGGTCA 62.192 61.111 2.18 0.00 41.39 4.02
821 826 8.208718 TCATGTCGGAGTTTCCTAAATATTTG 57.791 34.615 11.05 1.40 33.30 2.32
872 883 8.588472 ACTACGTTTTAGTCCTACCAAAATACT 58.412 33.333 0.00 0.00 0.00 2.12
873 884 8.763049 ACTACGTTTTAGTCCTACCAAAATAC 57.237 34.615 0.00 0.00 0.00 1.89
892 903 3.614390 GCTGCTAAGGACTTTGACTACGT 60.614 47.826 0.00 0.00 0.00 3.57
1016 1037 1.670087 CGTCGCCATTGAGTTGAGTCT 60.670 52.381 0.00 0.00 0.00 3.24
1017 1038 0.716108 CGTCGCCATTGAGTTGAGTC 59.284 55.000 0.00 0.00 0.00 3.36
1018 1039 0.670546 CCGTCGCCATTGAGTTGAGT 60.671 55.000 0.00 0.00 0.00 3.41
1020 1041 0.389817 CTCCGTCGCCATTGAGTTGA 60.390 55.000 0.00 0.00 0.00 3.18
1022 1043 1.079127 CCTCCGTCGCCATTGAGTT 60.079 57.895 0.00 0.00 0.00 3.01
1023 1044 2.579201 CCTCCGTCGCCATTGAGT 59.421 61.111 0.00 0.00 0.00 3.41
1265 1294 1.813337 GGGAAGAAGAGCAGAGCGC 60.813 63.158 0.00 0.00 42.91 5.92
1266 1295 0.248843 AAGGGAAGAAGAGCAGAGCG 59.751 55.000 0.00 0.00 0.00 5.03
1267 1296 2.488204 AAAGGGAAGAAGAGCAGAGC 57.512 50.000 0.00 0.00 0.00 4.09
1271 1300 3.884037 AAGGAAAAGGGAAGAAGAGCA 57.116 42.857 0.00 0.00 0.00 4.26
1272 1301 4.021894 GGAAAAGGAAAAGGGAAGAAGAGC 60.022 45.833 0.00 0.00 0.00 4.09
1298 1336 2.722201 GGGGGAGCGAACGTGAGAT 61.722 63.158 0.00 0.00 0.00 2.75
1299 1337 3.379445 GGGGGAGCGAACGTGAGA 61.379 66.667 0.00 0.00 0.00 3.27
1341 1403 0.250234 CGGATCACTGCAGGAAGGAA 59.750 55.000 19.93 0.00 0.00 3.36
1425 1705 1.291588 CTGACACAGGCTCGAAGCT 59.708 57.895 6.78 0.00 41.99 3.74
1581 1863 4.526650 ACAAACAGAAAGGTGTCTTTTGGT 59.473 37.500 0.00 0.00 42.72 3.67
1684 1999 3.072038 ACACCCAGTTAAAGACCTGGTAC 59.928 47.826 0.00 0.00 35.34 3.34
1687 2002 2.105821 TCACACCCAGTTAAAGACCTGG 59.894 50.000 3.39 3.39 36.77 4.45
1735 2050 4.454728 TCCAAGCAGCCAATAATTTGTC 57.545 40.909 0.00 0.00 0.00 3.18
2053 2375 8.512138 CCTATCCCGAAATATCCACAATTTTAC 58.488 37.037 0.00 0.00 0.00 2.01
2075 2397 8.874156 AGAAAAGAAAAAGAAATCCAAGCCTAT 58.126 29.630 0.00 0.00 0.00 2.57
2090 2412 5.105797 TGTGCAGAAGAGCAGAAAAGAAAAA 60.106 36.000 0.00 0.00 46.69 1.94
2095 2417 2.615447 TGTGTGCAGAAGAGCAGAAAAG 59.385 45.455 0.00 0.00 46.69 2.27
2128 2450 1.867363 ACACCCCCTCTGCTACTAAG 58.133 55.000 0.00 0.00 0.00 2.18
2163 2485 4.494855 GCATCGGCAAGAGAACAATTCTAC 60.495 45.833 0.00 0.00 39.15 2.59
2181 2503 2.223112 CGAAGGTTTCCAGATTGCATCG 60.223 50.000 0.00 0.00 0.00 3.84
2193 2515 2.032924 CACCCTCAACAACGAAGGTTTC 59.967 50.000 0.00 0.00 32.98 2.78
2198 2520 4.188247 TCTATCACCCTCAACAACGAAG 57.812 45.455 0.00 0.00 0.00 3.79
2268 2591 4.730949 TGGAGGTGTATTCGAAAGGTAG 57.269 45.455 0.00 0.00 0.00 3.18
2289 2612 9.970553 ATTGTCCTATTATCATGAATAGCACAT 57.029 29.630 10.59 1.99 38.98 3.21
2550 2881 7.496346 AACAAGACTCAGGACCAGATATTAA 57.504 36.000 0.00 0.00 0.00 1.40
2577 2908 1.279271 GCAGTGGTAGTCAATCAGGGT 59.721 52.381 0.00 0.00 0.00 4.34
2858 3200 8.260818 AGAGTGTTGCTACATAATGTATCAGTT 58.739 33.333 3.85 0.00 36.50 3.16
3412 4112 3.689161 TGACCTAATTCCACAAAGCATCG 59.311 43.478 0.00 0.00 0.00 3.84
3760 4495 2.633481 ACCTGGAACTACAGTCTGGAAC 59.367 50.000 0.00 0.00 36.75 3.62
3775 4510 3.631686 CCATTTTCAATATGCGACCTGGA 59.368 43.478 0.00 0.00 0.00 3.86
3938 4674 7.453393 AGTAACAGAATCTCAAAATCAGGACA 58.547 34.615 0.00 0.00 0.00 4.02
3953 4689 7.181125 ACTCTGGGATTTCAGTAGTAACAGAAT 59.819 37.037 0.00 0.00 31.98 2.40
4064 4800 4.676723 GCAGCAAGTGTTAAACAGGAACAA 60.677 41.667 0.00 0.00 38.48 2.83
4086 4822 6.640092 CAGTTCAGAAGAATTGAAAAGAAGGC 59.360 38.462 0.00 0.00 42.25 4.35
4091 4827 4.380974 GCGCAGTTCAGAAGAATTGAAAAG 59.619 41.667 0.30 0.00 42.25 2.27
4120 4856 0.108207 ATCCCTATGCAGCACTGAGC 59.892 55.000 0.00 0.00 46.19 4.26
4121 4857 1.693062 AGATCCCTATGCAGCACTGAG 59.307 52.381 0.00 0.00 0.00 3.35
4122 4858 1.798626 AGATCCCTATGCAGCACTGA 58.201 50.000 0.00 0.00 0.00 3.41
4125 4861 6.989169 CCTTATATTAGATCCCTATGCAGCAC 59.011 42.308 0.00 0.00 0.00 4.40
4159 4914 5.407502 TGTACTGTCATGTCATAACGAAGG 58.592 41.667 0.00 0.00 0.00 3.46
4163 4918 8.407457 ACTTATTGTACTGTCATGTCATAACG 57.593 34.615 0.00 0.00 0.00 3.18
4175 4930 6.542370 AGTGCAGTGAAAACTTATTGTACTGT 59.458 34.615 0.00 0.00 37.11 3.55
4210 4965 8.437360 TTCACCATGTGATGCTAGTTAAATAG 57.563 34.615 5.58 5.58 42.40 1.73
4292 5056 8.458843 AGCATAAGCATAAACTCGTATTTTTGT 58.541 29.630 0.00 0.00 45.49 2.83
4321 5085 1.187567 CCCCAGAAACCAAAGGGCTG 61.188 60.000 0.00 0.00 40.07 4.85
4335 5106 5.416326 TCAAAATTAACCGTATGTTCCCCAG 59.584 40.000 0.00 0.00 38.42 4.45
4337 5108 5.900865 TCAAAATTAACCGTATGTTCCCC 57.099 39.130 0.00 0.00 38.42 4.81
4347 5325 8.673711 TCATGATTACCTCTTCAAAATTAACCG 58.326 33.333 0.00 0.00 0.00 4.44
4406 5388 4.402155 TGTTCATCCCATTAGCAATTGACC 59.598 41.667 10.34 0.00 0.00 4.02
4426 5474 9.772973 TGACGGCATACTAAGATATTTATTGTT 57.227 29.630 0.00 0.00 0.00 2.83
4431 5479 9.990360 TTTGATGACGGCATACTAAGATATTTA 57.010 29.630 2.12 0.00 34.11 1.40
4432 5480 8.902540 TTTGATGACGGCATACTAAGATATTT 57.097 30.769 2.12 0.00 34.11 1.40
4434 5482 7.896811 TCTTTGATGACGGCATACTAAGATAT 58.103 34.615 2.12 0.00 34.11 1.63
4435 5483 7.230712 TCTCTTTGATGACGGCATACTAAGATA 59.769 37.037 19.37 13.66 34.11 1.98
4436 5484 6.040955 TCTCTTTGATGACGGCATACTAAGAT 59.959 38.462 19.37 0.00 34.11 2.40
4438 5486 5.592054 TCTCTTTGATGACGGCATACTAAG 58.408 41.667 2.12 10.69 34.11 2.18
4439 5487 5.359860 TCTCTCTTTGATGACGGCATACTAA 59.640 40.000 2.12 0.00 34.11 2.24
4442 5490 4.046938 TCTCTCTTTGATGACGGCATAC 57.953 45.455 2.12 0.00 34.11 2.39
4443 5491 4.736126 TTCTCTCTTTGATGACGGCATA 57.264 40.909 2.12 0.00 34.11 3.14
4444 5492 3.616956 TTCTCTCTTTGATGACGGCAT 57.383 42.857 1.48 1.48 37.47 4.40
4448 5496 4.752101 ACTGGTTTTCTCTCTTTGATGACG 59.248 41.667 0.00 0.00 0.00 4.35
4492 5548 4.510340 ACCAGACAACACAAATAGACGAAC 59.490 41.667 0.00 0.00 0.00 3.95
4535 5591 1.275666 ATCACCCGATGGACTGTTCA 58.724 50.000 0.00 0.00 34.81 3.18
4536 5592 2.009774 CAATCACCCGATGGACTGTTC 58.990 52.381 0.00 0.00 34.81 3.18
4539 5595 2.103771 AGATCAATCACCCGATGGACTG 59.896 50.000 0.00 0.00 34.27 3.51
4541 5597 2.103094 TCAGATCAATCACCCGATGGAC 59.897 50.000 0.00 0.00 34.27 4.02
4542 5598 2.103094 GTCAGATCAATCACCCGATGGA 59.897 50.000 0.00 0.00 35.98 3.41
4543 5599 2.158914 TGTCAGATCAATCACCCGATGG 60.159 50.000 0.00 0.00 37.80 3.51
4544 5600 3.183793 TGTCAGATCAATCACCCGATG 57.816 47.619 0.00 0.00 30.13 3.84
4549 5612 5.282055 TCCAGTATGTCAGATCAATCACC 57.718 43.478 0.00 0.00 0.00 4.02
4563 5626 5.067153 TCACACAAAAGTTGGTTCCAGTATG 59.933 40.000 0.00 0.00 34.12 2.39
4570 5860 5.310720 AGTCTTCACACAAAAGTTGGTTC 57.689 39.130 0.00 0.00 34.12 3.62
4598 5891 7.554118 TCAAATACAAAAAGACCAAATGCCAAA 59.446 29.630 0.00 0.00 0.00 3.28
4601 5894 7.307930 CCTTCAAATACAAAAAGACCAAATGCC 60.308 37.037 0.00 0.00 0.00 4.40
4603 5896 8.661352 ACCTTCAAATACAAAAAGACCAAATG 57.339 30.769 0.00 0.00 0.00 2.32
4605 5898 7.065204 GCAACCTTCAAATACAAAAAGACCAAA 59.935 33.333 0.00 0.00 0.00 3.28
4608 5901 5.465390 GGCAACCTTCAAATACAAAAAGACC 59.535 40.000 0.00 0.00 0.00 3.85
4610 5903 6.478512 AGGCAACCTTCAAATACAAAAAGA 57.521 33.333 0.00 0.00 37.17 2.52
4611 5904 7.169140 GTGTAGGCAACCTTCAAATACAAAAAG 59.831 37.037 0.00 0.00 32.94 2.27
4614 5907 5.594725 TGTGTAGGCAACCTTCAAATACAAA 59.405 36.000 0.00 0.00 32.94 2.83
4620 5913 4.646945 TCAAATGTGTAGGCAACCTTCAAA 59.353 37.500 0.00 0.00 32.94 2.69
4624 5917 3.056607 GCATCAAATGTGTAGGCAACCTT 60.057 43.478 0.00 0.00 34.61 3.50
4683 5976 1.274728 TGAAGGAGAAGAGCAGCAGTC 59.725 52.381 0.00 0.00 0.00 3.51
4689 5982 0.901124 GCCTCTGAAGGAGAAGAGCA 59.099 55.000 0.00 0.00 46.67 4.26
4690 5983 1.136891 GAGCCTCTGAAGGAGAAGAGC 59.863 57.143 0.00 0.00 46.67 4.09
4692 5985 2.917713 AGAGCCTCTGAAGGAGAAGA 57.082 50.000 0.00 0.00 46.67 2.87
4732 6025 7.493971 TCAAACACACCTGTCCAAATTATTTTG 59.506 33.333 3.57 3.57 41.59 2.44
4738 6031 6.916360 ATATCAAACACACCTGTCCAAATT 57.084 33.333 0.00 0.00 0.00 1.82
4772 6065 6.202937 CCAGAAACAAACAAATGCTACGTTA 58.797 36.000 0.00 0.00 0.00 3.18
4776 6070 4.944048 ACCCAGAAACAAACAAATGCTAC 58.056 39.130 0.00 0.00 0.00 3.58
4829 6123 4.190001 GACCATATAGCTGCCATGATCAG 58.810 47.826 0.09 9.66 34.79 2.90
4891 6185 1.289160 AGGGCCTCAATGTCAGCTAA 58.711 50.000 0.00 0.00 0.00 3.09
4940 6234 4.200838 ACATCGCCCTTAAATTTTTGGG 57.799 40.909 18.53 18.53 42.41 4.12
4950 6244 3.702548 TGAAGTAGCTAACATCGCCCTTA 59.297 43.478 0.00 0.00 0.00 2.69
5019 6313 2.245096 GCTGAATCAATCAACGTGTGC 58.755 47.619 0.00 0.00 37.67 4.57
5394 6689 9.639563 GGGAGTCCCTAATTAGTATAGGTATAC 57.360 40.741 22.04 0.00 41.34 1.47
5433 6793 6.710295 TGATCCCACCAAATTACTGATTATCG 59.290 38.462 0.00 0.00 0.00 2.92
5447 6821 4.339814 GCCGTAATAATTTGATCCCACCAA 59.660 41.667 0.00 0.00 0.00 3.67
5505 6880 9.462606 TTCTCCAAAGAGGGATATAAAAGTTTC 57.537 33.333 0.00 0.00 40.83 2.78
5634 7009 3.589881 GACATGAGGCGGCCATGC 61.590 66.667 28.06 20.53 43.76 4.06
5669 7044 3.645212 CCTTCATTGAGATAGGAGAGGCA 59.355 47.826 0.00 0.00 30.59 4.75
5705 7083 1.343465 GACCGTGAAGGACAGGAGAAA 59.657 52.381 0.00 0.00 45.00 2.52
5769 7149 5.809001 AGATAAAAAGACTGAGGCACATGA 58.191 37.500 0.00 0.00 0.00 3.07
5787 7167 8.526978 CGATCAGAGGAGGATTTAATGAGATAA 58.473 37.037 0.00 0.00 0.00 1.75
5917 7297 4.261781 GACGCCCGCGGTAGTAGG 62.262 72.222 26.12 8.60 44.69 3.18
6123 7503 3.504863 CTTTTTCCGGATCAATGCACAG 58.495 45.455 4.15 0.00 0.00 3.66
6131 7511 0.695924 TCTGCCCTTTTTCCGGATCA 59.304 50.000 4.15 0.00 0.00 2.92
6196 7782 2.997138 AGGAAAGGGATCATAGGAGGG 58.003 52.381 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.