Multiple sequence alignment - TraesCS1B01G039200

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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 TraesCS1B01G039200 chr1B 100.000 4355 0 0 1 4355 18866715 18871069 0.000000e+00 8043.0
1 TraesCS1B01G039200 chr1B 90.902 2396 197 4 989 3364 17896576 17894182 0.000000e+00 3197.0
2 TraesCS1B01G039200 chr1B 91.463 2331 193 6 1037 3364 18118595 18116268 0.000000e+00 3197.0
3 TraesCS1B01G039200 chr1B 90.921 2335 201 6 1039 3364 18683410 18685742 0.000000e+00 3127.0
4 TraesCS1B01G039200 chr1B 93.061 1888 120 4 960 2840 539933661 539931778 0.000000e+00 2750.0
5 TraesCS1B01G039200 chr1B 92.542 1904 141 1 1462 3364 18093320 18091417 0.000000e+00 2728.0
6 TraesCS1B01G039200 chr1B 90.467 2014 179 7 1356 3364 539872559 539870554 0.000000e+00 2643.0
7 TraesCS1B01G039200 chr1B 89.486 2083 201 16 1291 3364 19075902 19073829 0.000000e+00 2617.0
8 TraesCS1B01G039200 chr1B 86.865 571 54 9 989 1539 17966254 17965685 1.720000e-173 619.0
9 TraesCS1B01G039200 chr1B 92.099 405 15 7 968 1355 539873282 539872878 4.920000e-154 555.0
10 TraesCS1B01G039200 chr1B 79.937 638 122 6 3 637 613243195 613243829 8.530000e-127 464.0
11 TraesCS1B01G039200 chr1B 88.791 339 26 6 4016 4354 18115274 18114948 5.240000e-109 405.0
12 TraesCS1B01G039200 chr1B 82.000 500 46 24 3785 4279 539870067 539869607 6.830000e-103 385.0
13 TraesCS1B01G039200 chr1B 89.922 258 18 8 4019 4275 17963579 17963329 4.200000e-85 326.0
14 TraesCS1B01G039200 chr1B 85.893 319 26 9 4043 4354 18112796 18112490 5.430000e-84 322.0
15 TraesCS1B01G039200 chr1B 85.141 249 34 3 3368 3615 539870316 539870070 7.230000e-63 252.0
16 TraesCS1B01G039200 chr1B 86.404 228 21 5 4028 4252 19072999 19072779 1.570000e-59 241.0
17 TraesCS1B01G039200 chr1B 76.129 465 75 27 3824 4274 18360752 18360310 1.230000e-50 211.0
18 TraesCS1B01G039200 chr1B 84.434 212 6 11 768 952 18854548 18854759 2.680000e-42 183.0
19 TraesCS1B01G039200 chr1B 88.983 118 7 1 4238 4355 19072618 19072507 1.630000e-29 141.0
20 TraesCS1B01G039200 chr1B 81.988 161 20 5 3824 3983 17963732 17963580 1.270000e-25 128.0
21 TraesCS1B01G039200 chr1B 93.750 64 1 3 639 702 369615135 369615075 4.640000e-15 93.5
22 TraesCS1B01G039200 chr1B 96.226 53 2 0 703 755 18854595 18854647 2.160000e-13 87.9
23 TraesCS1B01G039200 chr1B 92.157 51 4 0 4224 4274 18089017 18088967 6.040000e-09 73.1
24 TraesCS1B01G039200 chr1D 94.078 3411 150 14 960 4355 13252241 13255614 0.000000e+00 5132.0
25 TraesCS1B01G039200 chr1D 88.731 2396 245 11 986 3364 13262427 13264814 0.000000e+00 2905.0
26 TraesCS1B01G039200 chr1D 87.437 2396 274 13 989 3364 12551992 12549604 0.000000e+00 2732.0
27 TraesCS1B01G039200 chr1D 81.379 290 49 5 3824 4112 13265593 13265878 9.420000e-57 231.0
28 TraesCS1B01G039200 chr1D 86.341 205 7 9 764 952 13251993 13252192 2.050000e-48 204.0
29 TraesCS1B01G039200 chr1D 89.506 162 12 2 4100 4261 13255760 13255916 2.660000e-47 200.0
30 TraesCS1B01G039200 chr1D 92.000 75 5 1 703 777 13252037 13252110 2.140000e-18 104.0
31 TraesCS1B01G039200 chr1A 86.886 2341 279 22 1037 3364 14577621 14579946 0.000000e+00 2597.0
32 TraesCS1B01G039200 chr5B 90.047 633 62 1 6 637 665571094 665570462 0.000000e+00 819.0
33 TraesCS1B01G039200 chr4B 90.047 633 60 2 6 637 481582638 481582008 0.000000e+00 817.0
34 TraesCS1B01G039200 chr4B 96.610 59 1 1 645 703 377934418 377934361 3.580000e-16 97.1
35 TraesCS1B01G039200 chr3B 88.486 634 71 2 6 637 171815184 171814551 0.000000e+00 765.0
36 TraesCS1B01G039200 chr5A 88.640 625 70 1 6 629 367618128 367617504 0.000000e+00 760.0
37 TraesCS1B01G039200 chr3A 79.439 642 121 11 1 636 478699913 478700549 1.110000e-120 444.0
38 TraesCS1B01G039200 chr5D 78.227 643 128 12 1 636 16231922 16232559 6.780000e-108 401.0
39 TraesCS1B01G039200 chr5D 96.825 63 1 1 642 704 332940599 332940660 2.140000e-18 104.0
40 TraesCS1B01G039200 chr5D 96.610 59 2 0 650 708 74173489 74173547 9.970000e-17 99.0
41 TraesCS1B01G039200 chr2B 98.387 62 0 1 642 703 600775227 600775287 1.660000e-19 108.0
42 TraesCS1B01G039200 chr2B 95.385 65 1 2 639 703 447785653 447785591 7.710000e-18 102.0
43 TraesCS1B01G039200 chr2B 93.939 66 2 2 639 704 103256258 103256321 9.970000e-17 99.0
44 TraesCS1B01G039200 chr7B 95.312 64 2 1 642 705 205152056 205151994 2.770000e-17 100.0
45 TraesCS1B01G039200 chr7D 93.651 63 4 0 642 704 66963006 66963068 1.290000e-15 95.3


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 TraesCS1B01G039200 chr1B 18866715 18871069 4354 False 8043.000000 8043 100.000000 1 4355 1 chr1B.!!$F2 4354
1 TraesCS1B01G039200 chr1B 17894182 17896576 2394 True 3197.000000 3197 90.902000 989 3364 1 chr1B.!!$R1 2375
2 TraesCS1B01G039200 chr1B 18683410 18685742 2332 False 3127.000000 3127 90.921000 1039 3364 1 chr1B.!!$F1 2325
3 TraesCS1B01G039200 chr1B 539931778 539933661 1883 True 2750.000000 2750 93.061000 960 2840 1 chr1B.!!$R4 1880
4 TraesCS1B01G039200 chr1B 18088967 18093320 4353 True 1400.550000 2728 92.349500 1462 4274 2 chr1B.!!$R6 2812
5 TraesCS1B01G039200 chr1B 18112490 18118595 6105 True 1308.000000 3197 88.715667 1037 4354 3 chr1B.!!$R7 3317
6 TraesCS1B01G039200 chr1B 19072507 19075902 3395 True 999.666667 2617 88.291000 1291 4355 3 chr1B.!!$R8 3064
7 TraesCS1B01G039200 chr1B 539869607 539873282 3675 True 958.750000 2643 87.426750 968 4279 4 chr1B.!!$R9 3311
8 TraesCS1B01G039200 chr1B 613243195 613243829 634 False 464.000000 464 79.937000 3 637 1 chr1B.!!$F3 634
9 TraesCS1B01G039200 chr1B 17963329 17966254 2925 True 357.666667 619 86.258333 989 4275 3 chr1B.!!$R5 3286
10 TraesCS1B01G039200 chr1D 12549604 12551992 2388 True 2732.000000 2732 87.437000 989 3364 1 chr1D.!!$R1 2375
11 TraesCS1B01G039200 chr1D 13262427 13265878 3451 False 1568.000000 2905 85.055000 986 4112 2 chr1D.!!$F2 3126
12 TraesCS1B01G039200 chr1D 13251993 13255916 3923 False 1410.000000 5132 90.481250 703 4355 4 chr1D.!!$F1 3652
13 TraesCS1B01G039200 chr1A 14577621 14579946 2325 False 2597.000000 2597 86.886000 1037 3364 1 chr1A.!!$F1 2327
14 TraesCS1B01G039200 chr5B 665570462 665571094 632 True 819.000000 819 90.047000 6 637 1 chr5B.!!$R1 631
15 TraesCS1B01G039200 chr4B 481582008 481582638 630 True 817.000000 817 90.047000 6 637 1 chr4B.!!$R2 631
16 TraesCS1B01G039200 chr3B 171814551 171815184 633 True 765.000000 765 88.486000 6 637 1 chr3B.!!$R1 631
17 TraesCS1B01G039200 chr5A 367617504 367618128 624 True 760.000000 760 88.640000 6 629 1 chr5A.!!$R1 623
18 TraesCS1B01G039200 chr3A 478699913 478700549 636 False 444.000000 444 79.439000 1 636 1 chr3A.!!$F1 635
19 TraesCS1B01G039200 chr5D 16231922 16232559 637 False 401.000000 401 78.227000 1 636 1 chr5D.!!$F1 635

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
451 453 0.103937 CCTCTTCCGTCAGATCCAGC 59.896 60.0 0.00 0.00 0.00 4.85 F
459 461 0.106819 GTCAGATCCAGCTTGCCCAT 60.107 55.0 0.00 0.00 0.00 4.00 F
460 462 0.182061 TCAGATCCAGCTTGCCCATC 59.818 55.0 0.00 0.00 0.00 3.51 F
604 606 0.240145 CCGCTTTTTCCCTCGAAACC 59.760 55.0 0.00 0.00 37.72 3.27 F
605 607 0.240145 CGCTTTTTCCCTCGAAACCC 59.760 55.0 0.00 0.00 37.72 4.11 F
3122 3535 0.176680 TCAATGGAGAAGAGCGGCTC 59.823 55.0 22.13 22.13 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2073 2486 2.423892 GCTGAAGATACGACAGTCAGGA 59.576 50.000 0.41 0.00 36.93 3.86 R
2104 2517 5.649395 GCTTCCCAGATTTAGCATATGCATA 59.351 40.000 28.62 9.27 45.16 3.14 R
2716 3129 9.701098 TCCATCCAGTATGACGTTATAATTAAC 57.299 33.333 1.05 0.00 39.69 2.01 R
3122 3535 6.801539 TTAACATCCAAGAGTTTGCAGTAG 57.198 37.500 0.00 0.00 32.79 2.57 R
3283 3696 8.388484 AGCAATTTGATGTGGTCTCTATATTC 57.612 34.615 0.00 0.00 0.00 1.75 R
3939 4971 4.684485 GCCTTAACACCAGCATGATCTAGT 60.684 45.833 0.00 0.00 39.69 2.57 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 26 2.389962 CCCATTGGGTCAAATTGCAG 57.610 50.000 14.10 0.00 38.25 4.41
63 65 2.681848 CAATTTGTTTTGCCACTGCCAA 59.318 40.909 0.00 0.00 36.33 4.52
205 207 4.126437 CGTGTTTACTGATATGCCATGGA 58.874 43.478 18.40 0.31 0.00 3.41
288 290 1.819208 CCGCCGGCATGAAGATCAA 60.819 57.895 28.98 0.00 0.00 2.57
349 351 5.286438 CAGATCGTTTGGATATGGAACGTA 58.714 41.667 12.00 3.71 44.54 3.57
376 378 1.025113 GTAGAACTTTCCCCGCCAGC 61.025 60.000 0.00 0.00 0.00 4.85
439 441 4.475135 GGCGTGGCCTCCTCTTCC 62.475 72.222 3.32 0.00 46.69 3.46
440 442 4.821589 GCGTGGCCTCCTCTTCCG 62.822 72.222 3.32 0.00 0.00 4.30
441 443 3.382832 CGTGGCCTCCTCTTCCGT 61.383 66.667 3.32 0.00 0.00 4.69
442 444 2.579738 GTGGCCTCCTCTTCCGTC 59.420 66.667 3.32 0.00 0.00 4.79
443 445 2.119611 TGGCCTCCTCTTCCGTCA 59.880 61.111 3.32 0.00 0.00 4.35
444 446 1.984570 TGGCCTCCTCTTCCGTCAG 60.985 63.158 3.32 0.00 0.00 3.51
445 447 1.682684 GGCCTCCTCTTCCGTCAGA 60.683 63.158 0.00 0.00 0.00 3.27
446 448 1.045911 GGCCTCCTCTTCCGTCAGAT 61.046 60.000 0.00 0.00 0.00 2.90
447 449 0.387565 GCCTCCTCTTCCGTCAGATC 59.612 60.000 0.00 0.00 0.00 2.75
448 450 1.036707 CCTCCTCTTCCGTCAGATCC 58.963 60.000 0.00 0.00 0.00 3.36
449 451 1.686428 CCTCCTCTTCCGTCAGATCCA 60.686 57.143 0.00 0.00 0.00 3.41
450 452 1.680735 CTCCTCTTCCGTCAGATCCAG 59.319 57.143 0.00 0.00 0.00 3.86
451 453 0.103937 CCTCTTCCGTCAGATCCAGC 59.896 60.000 0.00 0.00 0.00 4.85
452 454 1.110442 CTCTTCCGTCAGATCCAGCT 58.890 55.000 0.00 0.00 0.00 4.24
453 455 1.480137 CTCTTCCGTCAGATCCAGCTT 59.520 52.381 0.00 0.00 0.00 3.74
454 456 1.205655 TCTTCCGTCAGATCCAGCTTG 59.794 52.381 0.00 0.00 0.00 4.01
455 457 0.391661 TTCCGTCAGATCCAGCTTGC 60.392 55.000 0.00 0.00 0.00 4.01
456 458 1.817099 CCGTCAGATCCAGCTTGCC 60.817 63.158 0.00 0.00 0.00 4.52
457 459 1.817099 CGTCAGATCCAGCTTGCCC 60.817 63.158 0.00 0.00 0.00 5.36
458 460 1.300963 GTCAGATCCAGCTTGCCCA 59.699 57.895 0.00 0.00 0.00 5.36
459 461 0.106819 GTCAGATCCAGCTTGCCCAT 60.107 55.000 0.00 0.00 0.00 4.00
460 462 0.182061 TCAGATCCAGCTTGCCCATC 59.818 55.000 0.00 0.00 0.00 3.51
461 463 1.147824 AGATCCAGCTTGCCCATCG 59.852 57.895 0.00 0.00 0.00 3.84
462 464 2.517875 ATCCAGCTTGCCCATCGC 60.518 61.111 0.00 0.00 38.31 4.58
463 465 4.802051 TCCAGCTTGCCCATCGCC 62.802 66.667 0.00 0.00 36.24 5.54
464 466 4.809496 CCAGCTTGCCCATCGCCT 62.809 66.667 0.00 0.00 36.24 5.52
465 467 3.207669 CAGCTTGCCCATCGCCTC 61.208 66.667 0.00 0.00 36.24 4.70
466 468 4.496336 AGCTTGCCCATCGCCTCC 62.496 66.667 0.00 0.00 36.24 4.30
467 469 4.496336 GCTTGCCCATCGCCTCCT 62.496 66.667 0.00 0.00 36.24 3.69
468 470 2.203126 CTTGCCCATCGCCTCCTC 60.203 66.667 0.00 0.00 36.24 3.71
469 471 3.764160 CTTGCCCATCGCCTCCTCC 62.764 68.421 0.00 0.00 36.24 4.30
471 473 4.247380 GCCCATCGCCTCCTCCAG 62.247 72.222 0.00 0.00 0.00 3.86
472 474 4.247380 CCCATCGCCTCCTCCAGC 62.247 72.222 0.00 0.00 0.00 4.85
473 475 4.247380 CCATCGCCTCCTCCAGCC 62.247 72.222 0.00 0.00 0.00 4.85
474 476 4.598894 CATCGCCTCCTCCAGCCG 62.599 72.222 0.00 0.00 0.00 5.52
491 493 3.365265 GTGCCCTTGCCGTCCTTG 61.365 66.667 0.00 0.00 36.33 3.61
492 494 4.659172 TGCCCTTGCCGTCCTTGG 62.659 66.667 0.00 0.00 36.33 3.61
493 495 4.660938 GCCCTTGCCGTCCTTGGT 62.661 66.667 0.00 0.00 0.00 3.67
494 496 2.672996 CCCTTGCCGTCCTTGGTG 60.673 66.667 0.00 0.00 0.00 4.17
495 497 2.429930 CCTTGCCGTCCTTGGTGA 59.570 61.111 0.00 0.00 0.00 4.02
496 498 1.672356 CCTTGCCGTCCTTGGTGAG 60.672 63.158 0.00 0.00 0.00 3.51
497 499 1.371183 CTTGCCGTCCTTGGTGAGA 59.629 57.895 0.00 0.00 0.00 3.27
498 500 0.671781 CTTGCCGTCCTTGGTGAGAG 60.672 60.000 0.00 0.00 0.00 3.20
499 501 2.111999 TTGCCGTCCTTGGTGAGAGG 62.112 60.000 0.00 0.00 35.53 3.69
500 502 2.982130 CCGTCCTTGGTGAGAGGG 59.018 66.667 0.00 0.00 34.93 4.30
501 503 1.913762 CCGTCCTTGGTGAGAGGGT 60.914 63.158 0.00 0.00 34.14 4.34
502 504 1.293498 CGTCCTTGGTGAGAGGGTG 59.707 63.158 0.00 0.00 34.93 4.61
503 505 1.003233 GTCCTTGGTGAGAGGGTGC 60.003 63.158 0.00 0.00 34.93 5.01
504 506 2.224159 TCCTTGGTGAGAGGGTGCC 61.224 63.158 0.00 0.00 34.93 5.01
505 507 2.227036 CCTTGGTGAGAGGGTGCCT 61.227 63.158 0.00 0.00 36.03 4.75
506 508 1.002868 CTTGGTGAGAGGGTGCCTG 60.003 63.158 0.00 0.00 31.76 4.85
507 509 3.196207 TTGGTGAGAGGGTGCCTGC 62.196 63.158 0.00 0.00 31.76 4.85
508 510 4.416738 GGTGAGAGGGTGCCTGCC 62.417 72.222 0.00 0.00 31.76 4.85
509 511 3.325753 GTGAGAGGGTGCCTGCCT 61.326 66.667 0.00 0.00 31.76 4.75
510 512 2.530151 TGAGAGGGTGCCTGCCTT 60.530 61.111 0.00 0.00 31.76 4.35
511 513 2.270527 GAGAGGGTGCCTGCCTTC 59.729 66.667 0.00 0.00 31.76 3.46
512 514 2.204059 AGAGGGTGCCTGCCTTCT 60.204 61.111 0.00 0.00 39.72 2.85
513 515 2.270527 GAGGGTGCCTGCCTTCTC 59.729 66.667 0.00 0.00 31.76 2.87
514 516 3.334054 AGGGTGCCTGCCTTCTCC 61.334 66.667 0.00 0.00 29.57 3.71
515 517 3.334054 GGGTGCCTGCCTTCTCCT 61.334 66.667 0.00 0.00 0.00 3.69
516 518 2.759795 GGTGCCTGCCTTCTCCTT 59.240 61.111 0.00 0.00 0.00 3.36
517 519 1.676967 GGTGCCTGCCTTCTCCTTG 60.677 63.158 0.00 0.00 0.00 3.61
518 520 2.034687 TGCCTGCCTTCTCCTTGC 59.965 61.111 0.00 0.00 0.00 4.01
519 521 2.753446 GCCTGCCTTCTCCTTGCC 60.753 66.667 0.00 0.00 0.00 4.52
520 522 2.759114 CCTGCCTTCTCCTTGCCA 59.241 61.111 0.00 0.00 0.00 4.92
521 523 1.378250 CCTGCCTTCTCCTTGCCAG 60.378 63.158 0.00 0.00 0.00 4.85
522 524 2.034687 TGCCTTCTCCTTGCCAGC 59.965 61.111 0.00 0.00 0.00 4.85
523 525 3.130160 GCCTTCTCCTTGCCAGCG 61.130 66.667 0.00 0.00 0.00 5.18
524 526 3.130160 CCTTCTCCTTGCCAGCGC 61.130 66.667 0.00 0.00 0.00 5.92
525 527 3.130160 CTTCTCCTTGCCAGCGCC 61.130 66.667 2.29 0.00 0.00 6.53
541 543 3.147595 CCGGACGAGGCCATCTCA 61.148 66.667 5.01 0.00 42.55 3.27
542 544 2.415010 CGGACGAGGCCATCTCAG 59.585 66.667 5.01 0.00 42.55 3.35
543 545 2.107953 GGACGAGGCCATCTCAGC 59.892 66.667 5.01 0.00 42.55 4.26
544 546 2.279120 GACGAGGCCATCTCAGCG 60.279 66.667 5.01 0.00 42.55 5.18
545 547 4.521062 ACGAGGCCATCTCAGCGC 62.521 66.667 5.01 0.00 42.55 5.92
546 548 4.218578 CGAGGCCATCTCAGCGCT 62.219 66.667 2.64 2.64 42.55 5.92
547 549 2.588314 GAGGCCATCTCAGCGCTG 60.588 66.667 31.53 31.53 42.02 5.18
548 550 3.382803 GAGGCCATCTCAGCGCTGT 62.383 63.158 34.70 15.44 42.02 4.40
549 551 2.894387 GGCCATCTCAGCGCTGTC 60.894 66.667 34.70 17.66 0.00 3.51
550 552 2.894387 GCCATCTCAGCGCTGTCC 60.894 66.667 34.70 14.89 0.00 4.02
551 553 2.584418 CCATCTCAGCGCTGTCCG 60.584 66.667 34.70 23.60 40.75 4.79
574 576 3.661131 CGCCCCGTCGATCGAGAT 61.661 66.667 20.09 0.00 42.86 2.75
575 577 2.255856 GCCCCGTCGATCGAGATC 59.744 66.667 20.09 6.06 42.86 2.75
583 585 4.213700 GATCGAGATCGGACGTGC 57.786 61.111 0.00 0.00 40.29 5.34
584 586 1.355563 GATCGAGATCGGACGTGCA 59.644 57.895 8.11 0.00 40.29 4.57
585 587 0.930742 GATCGAGATCGGACGTGCAC 60.931 60.000 6.82 6.82 40.29 4.57
586 588 2.337749 ATCGAGATCGGACGTGCACC 62.338 60.000 12.15 0.00 40.29 5.01
592 594 3.645975 CGGACGTGCACCGCTTTT 61.646 61.111 12.15 0.00 43.74 2.27
593 595 2.719354 GGACGTGCACCGCTTTTT 59.281 55.556 12.15 0.00 41.42 1.94
594 596 1.370051 GGACGTGCACCGCTTTTTC 60.370 57.895 12.15 0.09 41.42 2.29
595 597 1.370051 GACGTGCACCGCTTTTTCC 60.370 57.895 12.15 0.00 41.42 3.13
596 598 2.050442 CGTGCACCGCTTTTTCCC 60.050 61.111 12.15 0.00 0.00 3.97
597 599 2.551912 CGTGCACCGCTTTTTCCCT 61.552 57.895 12.15 0.00 0.00 4.20
598 600 1.285950 GTGCACCGCTTTTTCCCTC 59.714 57.895 5.22 0.00 0.00 4.30
599 601 2.258013 TGCACCGCTTTTTCCCTCG 61.258 57.895 0.00 0.00 0.00 4.63
600 602 1.964373 GCACCGCTTTTTCCCTCGA 60.964 57.895 0.00 0.00 0.00 4.04
601 603 1.512156 GCACCGCTTTTTCCCTCGAA 61.512 55.000 0.00 0.00 0.00 3.71
602 604 0.948678 CACCGCTTTTTCCCTCGAAA 59.051 50.000 0.00 0.00 36.18 3.46
603 605 0.949397 ACCGCTTTTTCCCTCGAAAC 59.051 50.000 0.00 0.00 37.72 2.78
604 606 0.240145 CCGCTTTTTCCCTCGAAACC 59.760 55.000 0.00 0.00 37.72 3.27
605 607 0.240145 CGCTTTTTCCCTCGAAACCC 59.760 55.000 0.00 0.00 37.72 4.11
606 608 1.617322 GCTTTTTCCCTCGAAACCCT 58.383 50.000 0.00 0.00 37.72 4.34
607 609 2.786777 GCTTTTTCCCTCGAAACCCTA 58.213 47.619 0.00 0.00 37.72 3.53
608 610 3.151554 GCTTTTTCCCTCGAAACCCTAA 58.848 45.455 0.00 0.00 37.72 2.69
609 611 3.762288 GCTTTTTCCCTCGAAACCCTAAT 59.238 43.478 0.00 0.00 37.72 1.73
610 612 4.142447 GCTTTTTCCCTCGAAACCCTAATC 60.142 45.833 0.00 0.00 37.72 1.75
611 613 2.973694 TTCCCTCGAAACCCTAATCG 57.026 50.000 0.00 0.00 40.31 3.34
612 614 0.462789 TCCCTCGAAACCCTAATCGC 59.537 55.000 0.00 0.00 38.87 4.58
613 615 0.532196 CCCTCGAAACCCTAATCGCC 60.532 60.000 0.00 0.00 38.87 5.54
614 616 0.464452 CCTCGAAACCCTAATCGCCT 59.536 55.000 0.00 0.00 38.87 5.52
615 617 1.571919 CTCGAAACCCTAATCGCCTG 58.428 55.000 0.00 0.00 38.87 4.85
616 618 0.899720 TCGAAACCCTAATCGCCTGT 59.100 50.000 0.00 0.00 38.87 4.00
617 619 1.134907 TCGAAACCCTAATCGCCTGTC 60.135 52.381 0.00 0.00 38.87 3.51
618 620 1.404986 CGAAACCCTAATCGCCTGTCA 60.405 52.381 0.00 0.00 31.71 3.58
619 621 2.280628 GAAACCCTAATCGCCTGTCAG 58.719 52.381 0.00 0.00 0.00 3.51
620 622 0.541863 AACCCTAATCGCCTGTCAGG 59.458 55.000 15.15 15.15 38.80 3.86
621 623 0.325296 ACCCTAATCGCCTGTCAGGA 60.325 55.000 23.77 2.48 37.67 3.86
622 624 0.390860 CCCTAATCGCCTGTCAGGAG 59.609 60.000 23.77 19.78 37.67 3.69
623 625 0.390860 CCTAATCGCCTGTCAGGAGG 59.609 60.000 23.77 15.41 37.67 4.30
624 626 1.115467 CTAATCGCCTGTCAGGAGGT 58.885 55.000 23.77 13.42 37.67 3.85
625 627 1.482593 CTAATCGCCTGTCAGGAGGTT 59.517 52.381 22.72 22.72 41.50 3.50
626 628 0.250513 AATCGCCTGTCAGGAGGTTC 59.749 55.000 23.77 3.16 32.86 3.62
627 629 1.617947 ATCGCCTGTCAGGAGGTTCC 61.618 60.000 23.77 2.39 37.67 3.62
638 640 2.398252 GGAGGTTCCTAGGTTTTCCG 57.602 55.000 9.08 0.00 38.16 4.30
639 641 1.627329 GGAGGTTCCTAGGTTTTCCGT 59.373 52.381 9.08 0.00 38.16 4.69
640 642 2.833943 GGAGGTTCCTAGGTTTTCCGTA 59.166 50.000 9.08 0.00 38.16 4.02
641 643 3.453717 GGAGGTTCCTAGGTTTTCCGTAT 59.546 47.826 9.08 0.00 38.16 3.06
642 644 4.651045 GGAGGTTCCTAGGTTTTCCGTATA 59.349 45.833 9.08 0.00 38.16 1.47
643 645 5.306419 GGAGGTTCCTAGGTTTTCCGTATAT 59.694 44.000 9.08 0.00 38.16 0.86
644 646 6.183361 GGAGGTTCCTAGGTTTTCCGTATATT 60.183 42.308 9.08 0.00 38.16 1.28
645 647 7.204243 AGGTTCCTAGGTTTTCCGTATATTT 57.796 36.000 9.08 0.00 46.35 1.40
646 648 7.052248 AGGTTCCTAGGTTTTCCGTATATTTG 58.948 38.462 9.08 0.00 46.35 2.32
647 649 7.049754 GGTTCCTAGGTTTTCCGTATATTTGA 58.950 38.462 9.08 0.00 46.35 2.69
648 650 7.718314 GGTTCCTAGGTTTTCCGTATATTTGAT 59.282 37.037 9.08 0.00 46.35 2.57
649 651 9.768662 GTTCCTAGGTTTTCCGTATATTTGATA 57.231 33.333 9.08 0.00 46.35 2.15
677 679 8.784994 TCTCTTCTTCTATAAAGCTATGGTACG 58.215 37.037 0.00 0.00 0.00 3.67
678 680 7.368833 TCTTCTTCTATAAAGCTATGGTACGC 58.631 38.462 0.00 0.00 0.00 4.42
679 681 6.644248 TCTTCTATAAAGCTATGGTACGCA 57.356 37.500 0.00 0.00 0.00 5.24
680 682 7.046292 TCTTCTATAAAGCTATGGTACGCAA 57.954 36.000 0.00 0.00 0.00 4.85
681 683 7.667557 TCTTCTATAAAGCTATGGTACGCAAT 58.332 34.615 0.00 0.00 0.00 3.56
682 684 8.148351 TCTTCTATAAAGCTATGGTACGCAATT 58.852 33.333 0.00 0.00 0.00 2.32
683 685 8.671384 TTCTATAAAGCTATGGTACGCAATTT 57.329 30.769 0.00 0.00 0.00 1.82
684 686 8.083462 TCTATAAAGCTATGGTACGCAATTTG 57.917 34.615 0.00 0.00 0.00 2.32
685 687 3.420839 AAGCTATGGTACGCAATTTGC 57.579 42.857 11.42 11.42 40.69 3.68
695 697 3.877801 GCAATTTGCGTACTCTCGG 57.122 52.632 5.49 0.00 31.71 4.63
696 698 1.355971 GCAATTTGCGTACTCTCGGA 58.644 50.000 5.49 0.00 31.71 4.55
697 699 1.730064 GCAATTTGCGTACTCTCGGAA 59.270 47.619 5.49 0.00 39.14 4.30
748 750 9.594936 TTCCCCTAGAAAAAGAACATAATTTGA 57.405 29.630 0.00 0.00 0.00 2.69
749 751 9.768215 TCCCCTAGAAAAAGAACATAATTTGAT 57.232 29.630 0.00 0.00 0.00 2.57
911 928 3.193691 ACAGTAATCTCCCACTCGTCTTG 59.806 47.826 0.00 0.00 0.00 3.02
915 932 0.904865 TCTCCCACTCGTCTTGCCAT 60.905 55.000 0.00 0.00 0.00 4.40
933 950 3.734293 GCCATAGTTCACGACCTACTCAC 60.734 52.174 0.00 0.00 0.00 3.51
939 956 4.581824 AGTTCACGACCTACTCACTGTAAA 59.418 41.667 0.00 0.00 0.00 2.01
1759 2172 3.904800 TGGTTGATGATGGTGTCGTAT 57.095 42.857 0.00 0.00 0.00 3.06
1870 2283 1.553704 GTCGGAGGGTTACACCAGATT 59.446 52.381 0.00 0.00 41.02 2.40
2073 2486 5.319453 TCAATGGAAAGAGACTGCATTCTT 58.681 37.500 8.12 5.35 33.13 2.52
3087 3500 2.155279 GAAGGTTCAGTGGAAGAAGCC 58.845 52.381 0.00 0.00 42.73 4.35
3122 3535 0.176680 TCAATGGAGAAGAGCGGCTC 59.823 55.000 22.13 22.13 0.00 4.70
3283 3696 2.108250 TCTCTGTTTTCAAGGGAAGGGG 59.892 50.000 0.00 0.00 33.82 4.79
3334 3747 9.053472 TCCCTATAAAGTATCAGTTTCTGGAAA 57.947 33.333 0.00 0.00 31.51 3.13
3385 4048 0.891373 CATGGGAGAGTGTCAGTCGT 59.109 55.000 1.94 0.00 0.00 4.34
3535 4319 4.182433 TGCGTGCCCCTTGTGTCA 62.182 61.111 0.00 0.00 0.00 3.58
3536 4320 2.904866 GCGTGCCCCTTGTGTCAA 60.905 61.111 0.00 0.00 0.00 3.18
3681 4465 4.511527 ACTGTTGTGATAGCTCTTGATGG 58.488 43.478 0.00 0.00 0.00 3.51
3782 4805 5.048507 AGTCTTCTTTCCACGTACAAGTTC 58.951 41.667 0.00 0.00 0.00 3.01
3870 4897 6.892485 AGGTGTACAGGTTTAGTTTAGTGTT 58.108 36.000 0.00 0.00 0.00 3.32
3883 4910 4.653801 AGTTTAGTGTTGGGCTCCAATTTT 59.346 37.500 9.49 2.50 45.80 1.82
3884 4911 4.864704 TTAGTGTTGGGCTCCAATTTTC 57.135 40.909 9.49 0.00 45.80 2.29
3939 4971 7.122948 TGAGTTTAACCCTGCAACTTTTCTTAA 59.877 33.333 0.00 0.00 30.71 1.85
4148 5233 5.752892 ATATCACGGCGGTATGACTATAG 57.247 43.478 13.24 0.00 0.00 1.31
4267 6853 4.459337 ACAGAAAGCAGGCAGTAATAAACC 59.541 41.667 0.00 0.00 0.00 3.27
4279 6865 7.656137 AGGCAGTAATAAACCGATATGTTGTAG 59.344 37.037 0.00 0.00 0.00 2.74
4280 6866 7.095355 GGCAGTAATAAACCGATATGTTGTAGG 60.095 40.741 0.00 0.00 0.00 3.18
4281 6867 7.654520 GCAGTAATAAACCGATATGTTGTAGGA 59.345 37.037 0.00 0.00 0.00 2.94
4282 6868 9.193133 CAGTAATAAACCGATATGTTGTAGGAG 57.807 37.037 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 26 8.922058 ACAAATTGATAAGAATGCTCAATCAC 57.078 30.769 0.00 0.00 38.36 3.06
63 65 1.606889 AGGAACGAGAAGCGAGGGT 60.607 57.895 0.00 0.00 44.57 4.34
117 119 6.426633 TGAACTTCAATTCGATAAACTGCAGA 59.573 34.615 23.35 0.00 0.00 4.26
181 183 1.930503 TGGCATATCAGTAAACACGCG 59.069 47.619 3.53 3.53 0.00 6.01
259 261 1.830847 GCCGGCGGGGGAAAATATT 60.831 57.895 29.48 0.00 35.78 1.28
349 351 2.421529 GGGGAAAGTTCTACATCGCCAT 60.422 50.000 11.30 0.00 42.61 4.40
438 440 1.817099 GGCAAGCTGGATCTGACGG 60.817 63.158 0.00 0.00 0.00 4.79
439 441 1.817099 GGGCAAGCTGGATCTGACG 60.817 63.158 0.00 0.00 0.00 4.35
440 442 0.106819 ATGGGCAAGCTGGATCTGAC 60.107 55.000 0.00 0.00 0.00 3.51
441 443 0.182061 GATGGGCAAGCTGGATCTGA 59.818 55.000 0.00 0.00 0.00 3.27
442 444 1.164662 CGATGGGCAAGCTGGATCTG 61.165 60.000 0.00 0.00 0.00 2.90
443 445 1.147824 CGATGGGCAAGCTGGATCT 59.852 57.895 0.00 0.00 0.00 2.75
444 446 2.550101 GCGATGGGCAAGCTGGATC 61.550 63.158 0.00 0.00 42.87 3.36
445 447 2.517875 GCGATGGGCAAGCTGGAT 60.518 61.111 0.00 0.00 42.87 3.41
446 448 4.802051 GGCGATGGGCAAGCTGGA 62.802 66.667 0.00 0.00 46.16 3.86
447 449 4.809496 AGGCGATGGGCAAGCTGG 62.809 66.667 3.67 0.00 46.16 4.85
448 450 3.207669 GAGGCGATGGGCAAGCTG 61.208 66.667 3.67 0.00 46.16 4.24
449 451 4.496336 GGAGGCGATGGGCAAGCT 62.496 66.667 3.67 0.00 46.16 3.74
450 452 4.496336 AGGAGGCGATGGGCAAGC 62.496 66.667 3.67 0.00 46.16 4.01
451 453 2.203126 GAGGAGGCGATGGGCAAG 60.203 66.667 3.67 0.00 46.16 4.01
452 454 3.797353 GGAGGAGGCGATGGGCAA 61.797 66.667 3.67 0.00 46.16 4.52
454 456 4.247380 CTGGAGGAGGCGATGGGC 62.247 72.222 0.00 0.00 42.51 5.36
455 457 4.247380 GCTGGAGGAGGCGATGGG 62.247 72.222 0.00 0.00 0.00 4.00
456 458 4.247380 GGCTGGAGGAGGCGATGG 62.247 72.222 0.00 0.00 37.53 3.51
474 476 3.365265 CAAGGACGGCAAGGGCAC 61.365 66.667 0.00 0.00 43.71 5.01
475 477 4.659172 CCAAGGACGGCAAGGGCA 62.659 66.667 0.00 0.00 43.71 5.36
476 478 4.660938 ACCAAGGACGGCAAGGGC 62.661 66.667 0.00 0.00 40.13 5.19
477 479 2.672996 CACCAAGGACGGCAAGGG 60.673 66.667 0.00 0.00 0.00 3.95
478 480 1.672356 CTCACCAAGGACGGCAAGG 60.672 63.158 0.00 0.00 0.00 3.61
479 481 0.671781 CTCTCACCAAGGACGGCAAG 60.672 60.000 0.00 0.00 0.00 4.01
480 482 1.371183 CTCTCACCAAGGACGGCAA 59.629 57.895 0.00 0.00 0.00 4.52
481 483 2.583441 CCTCTCACCAAGGACGGCA 61.583 63.158 0.00 0.00 35.83 5.69
482 484 2.266055 CCTCTCACCAAGGACGGC 59.734 66.667 0.00 0.00 35.83 5.68
483 485 1.913762 ACCCTCTCACCAAGGACGG 60.914 63.158 0.00 0.00 35.83 4.79
484 486 1.293498 CACCCTCTCACCAAGGACG 59.707 63.158 0.00 0.00 35.83 4.79
485 487 1.003233 GCACCCTCTCACCAAGGAC 60.003 63.158 0.00 0.00 35.83 3.85
486 488 2.224159 GGCACCCTCTCACCAAGGA 61.224 63.158 0.00 0.00 35.83 3.36
487 489 2.227036 AGGCACCCTCTCACCAAGG 61.227 63.158 0.00 0.00 0.00 3.61
488 490 1.002868 CAGGCACCCTCTCACCAAG 60.003 63.158 0.00 0.00 0.00 3.61
489 491 3.160585 CAGGCACCCTCTCACCAA 58.839 61.111 0.00 0.00 0.00 3.67
490 492 3.640407 GCAGGCACCCTCTCACCA 61.640 66.667 0.00 0.00 0.00 4.17
491 493 4.416738 GGCAGGCACCCTCTCACC 62.417 72.222 0.00 0.00 0.00 4.02
492 494 2.811542 GAAGGCAGGCACCCTCTCAC 62.812 65.000 0.00 0.00 0.00 3.51
493 495 2.530151 AAGGCAGGCACCCTCTCA 60.530 61.111 0.00 0.00 0.00 3.27
494 496 2.250741 GAGAAGGCAGGCACCCTCTC 62.251 65.000 8.82 8.82 0.00 3.20
495 497 2.204059 AGAAGGCAGGCACCCTCT 60.204 61.111 0.00 0.00 0.00 3.69
496 498 2.270527 GAGAAGGCAGGCACCCTC 59.729 66.667 0.00 0.00 0.00 4.30
497 499 3.334054 GGAGAAGGCAGGCACCCT 61.334 66.667 0.00 0.00 0.00 4.34
498 500 2.911926 AAGGAGAAGGCAGGCACCC 61.912 63.158 0.00 0.00 0.00 4.61
499 501 1.676967 CAAGGAGAAGGCAGGCACC 60.677 63.158 0.00 0.00 0.00 5.01
500 502 2.338785 GCAAGGAGAAGGCAGGCAC 61.339 63.158 0.00 0.00 0.00 5.01
501 503 2.034687 GCAAGGAGAAGGCAGGCA 59.965 61.111 0.00 0.00 0.00 4.75
502 504 2.753446 GGCAAGGAGAAGGCAGGC 60.753 66.667 0.00 0.00 0.00 4.85
503 505 2.759114 TGGCAAGGAGAAGGCAGG 59.241 61.111 0.00 0.00 35.21 4.85
505 507 2.034687 GCTGGCAAGGAGAAGGCA 59.965 61.111 0.00 0.00 38.67 4.75
506 508 3.130160 CGCTGGCAAGGAGAAGGC 61.130 66.667 0.00 0.00 0.00 4.35
507 509 3.130160 GCGCTGGCAAGGAGAAGG 61.130 66.667 0.00 0.00 39.62 3.46
508 510 3.130160 GGCGCTGGCAAGGAGAAG 61.130 66.667 7.64 0.00 42.47 2.85
524 526 3.144120 CTGAGATGGCCTCGTCCGG 62.144 68.421 3.32 0.00 44.92 5.14
525 527 2.415010 CTGAGATGGCCTCGTCCG 59.585 66.667 3.32 0.00 44.92 4.79
526 528 2.107953 GCTGAGATGGCCTCGTCC 59.892 66.667 3.32 0.00 44.92 4.79
527 529 2.279120 CGCTGAGATGGCCTCGTC 60.279 66.667 3.32 0.00 44.92 4.20
528 530 4.521062 GCGCTGAGATGGCCTCGT 62.521 66.667 3.32 0.00 44.92 4.18
529 531 4.218578 AGCGCTGAGATGGCCTCG 62.219 66.667 10.39 0.00 44.92 4.63
530 532 2.588314 CAGCGCTGAGATGGCCTC 60.588 66.667 33.66 0.00 42.30 4.70
531 533 3.382803 GACAGCGCTGAGATGGCCT 62.383 63.158 42.03 18.71 38.63 5.19
532 534 2.894387 GACAGCGCTGAGATGGCC 60.894 66.667 42.03 17.35 38.63 5.36
533 535 2.894387 GGACAGCGCTGAGATGGC 60.894 66.667 42.03 18.29 45.32 4.40
534 536 2.584418 CGGACAGCGCTGAGATGG 60.584 66.667 42.03 21.52 41.32 3.51
535 537 3.260483 GCGGACAGCGCTGAGATG 61.260 66.667 42.03 26.97 42.99 2.90
557 559 3.596667 GATCTCGATCGACGGGGCG 62.597 68.421 15.15 3.35 43.46 6.13
558 560 2.255856 GATCTCGATCGACGGGGC 59.744 66.667 15.15 0.00 43.46 5.80
566 568 0.930742 GTGCACGTCCGATCTCGATC 60.931 60.000 0.00 0.00 43.02 3.69
567 569 1.064296 GTGCACGTCCGATCTCGAT 59.936 57.895 0.00 0.00 43.02 3.59
568 570 2.483745 GTGCACGTCCGATCTCGA 59.516 61.111 0.00 0.00 43.02 4.04
569 571 2.579787 GGTGCACGTCCGATCTCG 60.580 66.667 11.45 0.00 39.44 4.04
576 578 1.370051 GAAAAAGCGGTGCACGTCC 60.370 57.895 11.45 1.09 46.52 4.79
577 579 1.370051 GGAAAAAGCGGTGCACGTC 60.370 57.895 11.45 4.73 46.52 4.34
578 580 2.719354 GGAAAAAGCGGTGCACGT 59.281 55.556 11.45 0.00 46.52 4.49
580 582 1.285950 GAGGGAAAAAGCGGTGCAC 59.714 57.895 8.80 8.80 0.00 4.57
581 583 2.258013 CGAGGGAAAAAGCGGTGCA 61.258 57.895 0.00 0.00 0.00 4.57
582 584 1.512156 TTCGAGGGAAAAAGCGGTGC 61.512 55.000 0.00 0.00 0.00 5.01
583 585 0.948678 TTTCGAGGGAAAAAGCGGTG 59.051 50.000 0.00 0.00 39.14 4.94
584 586 0.949397 GTTTCGAGGGAAAAAGCGGT 59.051 50.000 0.00 0.00 43.39 5.68
585 587 0.240145 GGTTTCGAGGGAAAAAGCGG 59.760 55.000 0.00 0.00 43.39 5.52
586 588 0.240145 GGGTTTCGAGGGAAAAAGCG 59.760 55.000 0.00 0.00 43.39 4.68
587 589 1.617322 AGGGTTTCGAGGGAAAAAGC 58.383 50.000 0.00 0.00 43.39 3.51
588 590 4.094442 CGATTAGGGTTTCGAGGGAAAAAG 59.906 45.833 0.00 0.00 43.39 2.27
589 591 4.004982 CGATTAGGGTTTCGAGGGAAAAA 58.995 43.478 0.00 0.00 43.39 1.94
590 592 3.602483 CGATTAGGGTTTCGAGGGAAAA 58.398 45.455 0.00 0.00 43.39 2.29
591 593 2.678769 GCGATTAGGGTTTCGAGGGAAA 60.679 50.000 0.00 0.00 39.77 3.13
592 594 1.134610 GCGATTAGGGTTTCGAGGGAA 60.135 52.381 0.00 0.00 37.55 3.97
593 595 0.462789 GCGATTAGGGTTTCGAGGGA 59.537 55.000 0.00 0.00 37.55 4.20
594 596 0.532196 GGCGATTAGGGTTTCGAGGG 60.532 60.000 0.00 0.00 37.55 4.30
595 597 0.464452 AGGCGATTAGGGTTTCGAGG 59.536 55.000 0.00 0.00 37.55 4.63
596 598 1.134788 ACAGGCGATTAGGGTTTCGAG 60.135 52.381 0.00 0.00 37.55 4.04
597 599 0.899720 ACAGGCGATTAGGGTTTCGA 59.100 50.000 0.00 0.00 37.55 3.71
598 600 1.287425 GACAGGCGATTAGGGTTTCG 58.713 55.000 0.00 0.00 38.37 3.46
599 601 2.280628 CTGACAGGCGATTAGGGTTTC 58.719 52.381 0.00 0.00 0.00 2.78
600 602 1.065418 CCTGACAGGCGATTAGGGTTT 60.065 52.381 8.99 0.00 0.00 3.27
601 603 0.541863 CCTGACAGGCGATTAGGGTT 59.458 55.000 8.99 0.00 0.00 4.11
602 604 0.325296 TCCTGACAGGCGATTAGGGT 60.325 55.000 17.33 0.00 34.61 4.34
603 605 0.390860 CTCCTGACAGGCGATTAGGG 59.609 60.000 17.33 0.00 34.61 3.53
604 606 0.390860 CCTCCTGACAGGCGATTAGG 59.609 60.000 17.33 13.68 34.61 2.69
605 607 1.115467 ACCTCCTGACAGGCGATTAG 58.885 55.000 17.33 8.32 36.98 1.73
606 608 1.480954 GAACCTCCTGACAGGCGATTA 59.519 52.381 17.33 0.00 36.98 1.75
607 609 0.250513 GAACCTCCTGACAGGCGATT 59.749 55.000 17.33 3.14 36.98 3.34
608 610 1.617947 GGAACCTCCTGACAGGCGAT 61.618 60.000 17.33 3.81 36.98 4.58
609 611 2.283529 GGAACCTCCTGACAGGCGA 61.284 63.158 17.33 0.00 36.98 5.54
610 612 2.266055 GGAACCTCCTGACAGGCG 59.734 66.667 17.33 10.83 36.98 5.52
619 621 1.627329 ACGGAAAACCTAGGAACCTCC 59.373 52.381 17.98 13.86 36.58 4.30
620 622 4.750021 ATACGGAAAACCTAGGAACCTC 57.250 45.455 17.98 6.10 0.00 3.85
621 623 6.819947 AATATACGGAAAACCTAGGAACCT 57.180 37.500 17.98 0.00 0.00 3.50
622 624 7.049754 TCAAATATACGGAAAACCTAGGAACC 58.950 38.462 17.98 11.44 0.00 3.62
623 625 8.672823 ATCAAATATACGGAAAACCTAGGAAC 57.327 34.615 17.98 3.33 0.00 3.62
651 653 8.784994 CGTACCATAGCTTTATAGAAGAAGAGA 58.215 37.037 0.00 0.00 0.00 3.10
652 654 7.539366 GCGTACCATAGCTTTATAGAAGAAGAG 59.461 40.741 0.00 0.00 0.00 2.85
653 655 7.013942 TGCGTACCATAGCTTTATAGAAGAAGA 59.986 37.037 0.00 0.00 0.00 2.87
654 656 7.145985 TGCGTACCATAGCTTTATAGAAGAAG 58.854 38.462 0.00 0.00 0.00 2.85
655 657 7.046292 TGCGTACCATAGCTTTATAGAAGAA 57.954 36.000 0.00 0.00 0.00 2.52
656 658 6.644248 TGCGTACCATAGCTTTATAGAAGA 57.356 37.500 0.00 0.00 0.00 2.87
657 659 7.891183 ATTGCGTACCATAGCTTTATAGAAG 57.109 36.000 0.00 0.00 0.00 2.85
658 660 8.556194 CAAATTGCGTACCATAGCTTTATAGAA 58.444 33.333 0.00 0.00 0.00 2.10
659 661 7.307751 GCAAATTGCGTACCATAGCTTTATAGA 60.308 37.037 0.90 0.00 31.71 1.98
660 662 6.797033 GCAAATTGCGTACCATAGCTTTATAG 59.203 38.462 0.90 0.00 31.71 1.31
661 663 6.664515 GCAAATTGCGTACCATAGCTTTATA 58.335 36.000 0.90 0.00 31.71 0.98
662 664 5.519722 GCAAATTGCGTACCATAGCTTTAT 58.480 37.500 0.90 0.00 31.71 1.40
663 665 4.915704 GCAAATTGCGTACCATAGCTTTA 58.084 39.130 0.90 0.00 31.71 1.85
664 666 3.769536 GCAAATTGCGTACCATAGCTTT 58.230 40.909 0.90 0.00 31.71 3.51
665 667 3.420839 GCAAATTGCGTACCATAGCTT 57.579 42.857 0.90 0.00 31.71 3.74
677 679 1.355971 TCCGAGAGTACGCAAATTGC 58.644 50.000 8.09 8.09 40.69 3.56
678 680 4.398549 TTTTCCGAGAGTACGCAAATTG 57.601 40.909 0.00 0.00 0.00 2.32
722 724 9.594936 TCAAATTATGTTCTTTTTCTAGGGGAA 57.405 29.630 0.00 0.00 0.00 3.97
723 725 9.768215 ATCAAATTATGTTCTTTTTCTAGGGGA 57.232 29.630 0.00 0.00 0.00 4.81
782 784 9.946165 TCACATACTGAATAGTACGAGTAATTG 57.054 33.333 0.00 0.00 41.92 2.32
896 902 0.904865 ATGGCAAGACGAGTGGGAGA 60.905 55.000 0.00 0.00 0.00 3.71
898 904 0.824109 CTATGGCAAGACGAGTGGGA 59.176 55.000 0.00 0.00 0.00 4.37
911 928 2.426024 TGAGTAGGTCGTGAACTATGGC 59.574 50.000 0.00 0.00 32.54 4.40
915 932 3.748083 ACAGTGAGTAGGTCGTGAACTA 58.252 45.455 0.00 0.00 0.00 2.24
952 969 3.770040 TGGGAGACGACATGGGCG 61.770 66.667 8.44 8.44 0.00 6.13
953 970 2.125106 GTGGGAGACGACATGGGC 60.125 66.667 0.00 0.00 39.14 5.36
954 971 1.517832 GAGTGGGAGACGACATGGG 59.482 63.158 0.00 0.00 42.21 4.00
957 974 0.322636 AGACGAGTGGGAGACGACAT 60.323 55.000 0.00 0.00 42.21 3.06
958 975 0.536687 AAGACGAGTGGGAGACGACA 60.537 55.000 0.00 0.00 42.21 4.35
1870 2283 8.240682 GGTCATAAACATGTTGTAAGTATGCAA 58.759 33.333 12.82 0.00 0.00 4.08
2073 2486 2.423892 GCTGAAGATACGACAGTCAGGA 59.576 50.000 0.41 0.00 36.93 3.86
2104 2517 5.649395 GCTTCCCAGATTTAGCATATGCATA 59.351 40.000 28.62 9.27 45.16 3.14
2716 3129 9.701098 TCCATCCAGTATGACGTTATAATTAAC 57.299 33.333 1.05 0.00 39.69 2.01
3122 3535 6.801539 TTAACATCCAAGAGTTTGCAGTAG 57.198 37.500 0.00 0.00 32.79 2.57
3283 3696 8.388484 AGCAATTTGATGTGGTCTCTATATTC 57.612 34.615 0.00 0.00 0.00 1.75
3334 3747 3.832527 ACTATTCAACTGTGGCTGGTTT 58.167 40.909 0.00 0.00 0.00 3.27
3385 4048 2.282958 AGGAGTGAACGGCTCGGA 60.283 61.111 0.00 0.00 34.00 4.55
3535 4319 7.941790 AGCTTCTTCAAATTCCTTCTTAGACTT 59.058 33.333 0.00 0.00 0.00 3.01
3536 4320 7.390162 CAGCTTCTTCAAATTCCTTCTTAGACT 59.610 37.037 0.00 0.00 0.00 3.24
3681 4465 4.015872 TCACAAATCACCCTAACCAGAC 57.984 45.455 0.00 0.00 0.00 3.51
3746 4619 2.225467 AGAAGACTGGAAGCTGCAAAC 58.775 47.619 1.02 0.00 37.60 2.93
3782 4805 5.777802 CTGCTACTACAACTGGATCCATAG 58.222 45.833 16.63 16.02 0.00 2.23
3883 4910 3.366273 GCTGCATCGATCAAAACCAAAGA 60.366 43.478 0.00 0.00 0.00 2.52
3884 4911 2.919229 GCTGCATCGATCAAAACCAAAG 59.081 45.455 0.00 0.00 0.00 2.77
3939 4971 4.684485 GCCTTAACACCAGCATGATCTAGT 60.684 45.833 0.00 0.00 39.69 2.57
4148 5233 7.636150 AAATGCATCAGCCATATATCCTTAC 57.364 36.000 0.00 0.00 41.13 2.34
4267 6853 9.745880 ACAAAATAGTACTCCTACAACATATCG 57.254 33.333 0.00 0.00 0.00 2.92
4279 6865 8.179615 CCCGTTTCATTAACAAAATAGTACTCC 58.820 37.037 0.00 0.00 36.50 3.85
4280 6866 8.179615 CCCCGTTTCATTAACAAAATAGTACTC 58.820 37.037 0.00 0.00 36.50 2.59
4281 6867 7.666804 ACCCCGTTTCATTAACAAAATAGTACT 59.333 33.333 0.00 0.00 36.50 2.73
4282 6868 7.819644 ACCCCGTTTCATTAACAAAATAGTAC 58.180 34.615 0.00 0.00 36.50 2.73


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

AutoCloner maintained by Alex Coulton.