Multiple sequence alignment - TraesCS1A01G198100

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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 TraesCS1A01G198100 chr1A 100.000 6213 0 0 1 6213 355736246 355730034 0.000000e+00 11474.0
1 TraesCS1A01G198100 chr1A 100.000 208 0 0 6407 6614 355729840 355729633 1.040000e-102 385.0
2 TraesCS1A01G198100 chr1A 94.958 119 5 1 425 542 11269145 11269027 1.130000e-42 185.0
3 TraesCS1A01G198100 chr1A 96.262 107 4 0 436 542 584070099 584070205 6.820000e-40 176.0
4 TraesCS1A01G198100 chr1D 96.914 2981 73 15 560 3534 284306060 284303093 0.000000e+00 4977.0
5 TraesCS1A01G198100 chr1D 95.833 1920 49 13 4299 6213 284301745 284299852 0.000000e+00 3073.0
6 TraesCS1A01G198100 chr1D 94.286 280 11 3 3553 3830 284302745 284302469 2.200000e-114 424.0
7 TraesCS1A01G198100 chr1D 93.416 243 10 5 4061 4299 284302317 284302077 8.160000e-94 355.0
8 TraesCS1A01G198100 chr1D 91.038 212 14 3 6407 6614 284299836 284299626 1.400000e-71 281.0
9 TraesCS1A01G198100 chr1D 93.889 180 11 0 4741 4920 7197371 7197550 8.450000e-69 272.0
10 TraesCS1A01G198100 chr1D 96.129 155 5 1 3865 4019 284302470 284302317 1.100000e-62 252.0
11 TraesCS1A01G198100 chr1D 100.000 31 0 0 3998 4028 475808460 475808430 2.580000e-04 58.4
12 TraesCS1A01G198100 chr1B 96.243 2981 87 14 560 3534 386268746 386265785 0.000000e+00 4861.0
13 TraesCS1A01G198100 chr1B 96.096 1588 41 12 4487 6060 386264075 386262495 0.000000e+00 2569.0
14 TraesCS1A01G198100 chr1B 88.298 752 29 17 3553 4299 386265287 386264590 0.000000e+00 846.0
15 TraesCS1A01G198100 chr1B 88.066 729 66 10 5120 5829 672851666 672852392 0.000000e+00 845.0
16 TraesCS1A01G198100 chr1B 81.365 381 32 16 4742 5112 672850460 672850811 2.350000e-69 274.0
17 TraesCS1A01G198100 chr1B 96.800 125 3 1 4331 4455 386264197 386264074 2.420000e-49 207.0
18 TraesCS1A01G198100 chr1B 88.571 140 9 2 6081 6213 386262519 386262380 5.310000e-36 163.0
19 TraesCS1A01G198100 chr1B 89.189 111 11 1 3 112 386269273 386269163 3.220000e-28 137.0
20 TraesCS1A01G198100 chr1B 86.842 114 12 2 5932 6043 569514289 569514177 2.500000e-24 124.0
21 TraesCS1A01G198100 chr1B 85.470 117 10 6 5931 6042 584476220 584476106 1.510000e-21 115.0
22 TraesCS1A01G198100 chr7D 88.203 729 67 5 5120 5829 568318279 568317551 0.000000e+00 852.0
23 TraesCS1A01G198100 chr7D 87.448 239 21 5 4742 4975 568319507 568319273 3.930000e-67 267.0
24 TraesCS1A01G198100 chr7D 84.615 117 13 4 5934 6046 42920557 42920442 1.950000e-20 111.0
25 TraesCS1A01G198100 chr7D 100.000 29 0 0 4033 4061 559225265 559225293 3.000000e-03 54.7
26 TraesCS1A01G198100 chr2B 88.065 310 26 4 5417 5725 745507206 745507505 2.270000e-94 357.0
27 TraesCS1A01G198100 chr2B 84.818 303 28 6 5121 5423 745494906 745495190 8.390000e-74 289.0
28 TraesCS1A01G198100 chr2B 92.562 121 7 2 423 542 33962078 33962197 8.820000e-39 172.0
29 TraesCS1A01G198100 chr2B 91.406 128 7 3 418 545 460807156 460807279 8.820000e-39 172.0
30 TraesCS1A01G198100 chr2B 84.746 118 12 4 5931 6043 4050487 4050603 5.420000e-21 113.0
31 TraesCS1A01G198100 chr7A 96.396 111 4 0 435 545 92804166 92804276 4.070000e-42 183.0
32 TraesCS1A01G198100 chr7A 94.068 118 7 0 425 542 187189477 187189594 5.270000e-41 180.0
33 TraesCS1A01G198100 chr7A 90.385 52 4 1 3934 3984 694792682 694792631 4.280000e-07 67.6
34 TraesCS1A01G198100 chr7A 90.385 52 4 1 3934 3984 694930246 694930195 4.280000e-07 67.6
35 TraesCS1A01G198100 chr7A 90.385 52 4 1 3934 3984 695056493 695056442 4.280000e-07 67.6
36 TraesCS1A01G198100 chr7A 91.489 47 3 1 3934 3979 694970798 694970752 5.540000e-06 63.9
37 TraesCS1A01G198100 chr2A 95.575 113 4 1 436 548 722814008 722814119 5.270000e-41 180.0
38 TraesCS1A01G198100 chr2A 93.277 119 8 0 435 553 183328457 183328339 6.820000e-40 176.0
39 TraesCS1A01G198100 chr6A 94.783 115 5 1 436 550 108945314 108945427 1.900000e-40 178.0
40 TraesCS1A01G198100 chr6D 90.385 104 10 0 4819 4922 37682809 37682706 3.220000e-28 137.0
41 TraesCS1A01G198100 chr2D 90.385 104 10 0 4819 4922 191027506 191027403 3.220000e-28 137.0
42 TraesCS1A01G198100 chrUn 87.395 119 10 2 5933 6046 24530582 24530464 1.500000e-26 132.0
43 TraesCS1A01G198100 chr4B 85.714 119 11 4 5930 6043 427518731 427518848 3.240000e-23 121.0
44 TraesCS1A01G198100 chr3A 87.736 106 10 2 5940 6043 76557714 76557818 3.240000e-23 121.0
45 TraesCS1A01G198100 chr4A 86.111 72 8 2 3637 3708 610481285 610481216 7.110000e-10 76.8
46 TraesCS1A01G198100 chr5B 100.000 29 0 0 4034 4062 284372843 284372871 3.000000e-03 54.7
47 TraesCS1A01G198100 chr5D 100.000 28 0 0 4034 4061 372097397 372097370 1.200000e-02 52.8


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 TraesCS1A01G198100 chr1A 355729633 355736246 6613 True 5929.500000 11474 100.000000 1 6614 2 chr1A.!!$R2 6613
1 TraesCS1A01G198100 chr1D 284299626 284306060 6434 True 1560.333333 4977 94.602667 560 6614 6 chr1D.!!$R2 6054
2 TraesCS1A01G198100 chr1B 386262380 386269273 6893 True 1463.833333 4861 92.532833 3 6213 6 chr1B.!!$R3 6210
3 TraesCS1A01G198100 chr1B 672850460 672852392 1932 False 559.500000 845 84.715500 4742 5829 2 chr1B.!!$F1 1087
4 TraesCS1A01G198100 chr7D 568317551 568319507 1956 True 559.500000 852 87.825500 4742 5829 2 chr7D.!!$R2 1087

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
451 527 0.256752 TCATACTCCCTCCGTTCGGA 59.743 55.000 13.34 13.34 0.00 4.55 F
829 909 0.403453 ATCCGATCCCCCAATCCCTT 60.403 55.000 0.00 0.00 0.00 3.95 F
830 910 0.626277 TCCGATCCCCCAATCCCTTT 60.626 55.000 0.00 0.00 0.00 3.11 F
2150 2231 1.468520 CATTCCGCCAAGTTACCACTG 59.531 52.381 0.00 0.00 31.60 3.66 F
3815 4388 0.258774 ATGCTACCCTTCCGCCAAAT 59.741 50.000 0.00 0.00 0.00 2.32 F
4021 4596 0.039527 GGTTTGCTACCAGTTTGCCG 60.040 55.000 4.00 0.00 46.92 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2271 2352 0.804989 GACTCCAATCAACGGCCAAG 59.195 55.000 2.24 0.0 0.00 3.61 R
2296 2377 2.524394 TGGATCCTCCTAGGCCGC 60.524 66.667 14.23 0.0 37.46 6.53 R
2585 2667 4.000928 AGGATCTGCTTTTCTCTCCCTA 57.999 45.455 0.00 0.0 0.00 3.53 R
3877 4450 0.536460 GTTTGGCGGAAGGTGAAGGA 60.536 55.000 0.00 0.0 0.00 3.36 R
5241 7076 1.900545 CTCCTGGAGGTCCGTTTCCC 61.901 65.000 16.19 0.0 39.43 3.97 R
5691 7534 2.124570 ATGGCCACCAGACGATGC 60.125 61.111 8.16 0.0 36.75 3.91 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 6.215121 ACAACCATGTACAACATCAAATGTG 58.785 36.000 0.00 0.00 39.48 3.21
33 34 4.276678 ACAACATCAAATGTGACACCTCAG 59.723 41.667 2.45 0.00 44.07 3.35
37 38 3.743521 TCAAATGTGACACCTCAGGAAG 58.256 45.455 0.00 0.00 0.00 3.46
38 39 3.136443 TCAAATGTGACACCTCAGGAAGT 59.864 43.478 0.00 0.00 0.00 3.01
49 50 3.397955 ACCTCAGGAAGTTACAACCCAAT 59.602 43.478 0.00 0.00 0.00 3.16
50 51 4.141018 ACCTCAGGAAGTTACAACCCAATT 60.141 41.667 0.00 0.00 0.00 2.32
69 70 6.902341 CCAATTATGAGGGATATCAAACGTG 58.098 40.000 4.83 0.00 31.76 4.49
105 106 5.818678 TTTTGCTCTCAGGGTCTTAACTA 57.181 39.130 0.00 0.00 0.00 2.24
106 107 4.803098 TTGCTCTCAGGGTCTTAACTAC 57.197 45.455 0.00 0.00 0.00 2.73
108 109 3.097614 GCTCTCAGGGTCTTAACTACCA 58.902 50.000 4.95 0.00 38.87 3.25
116 191 4.842380 AGGGTCTTAACTACCACTGCTTAA 59.158 41.667 4.95 0.00 38.87 1.85
123 198 7.988599 TCTTAACTACCACTGCTTAACTTTCAA 59.011 33.333 0.00 0.00 0.00 2.69
129 204 6.273071 ACCACTGCTTAACTTTCAATTTGAC 58.727 36.000 0.00 0.00 0.00 3.18
138 213 3.636764 ACTTTCAATTTGACAGGGTGGTC 59.363 43.478 15.14 0.00 38.29 4.02
148 223 1.133915 ACAGGGTGGTCGAATTTGTGT 60.134 47.619 0.00 0.00 0.00 3.72
150 225 0.879090 GGGTGGTCGAATTTGTGTCC 59.121 55.000 0.00 0.00 0.00 4.02
159 234 3.033185 CGAATTTGTGTCCACGTCAAAC 58.967 45.455 1.92 0.00 34.63 2.93
178 253 3.253371 ACGCTCGTTTCACTCAAATTG 57.747 42.857 0.00 0.00 0.00 2.32
186 261 5.291371 TCGTTTCACTCAAATTGACGTGTAA 59.709 36.000 18.10 14.41 31.83 2.41
204 279 7.879070 ACGTGTAATTAAGAGAAGAGTACACA 58.121 34.615 11.97 0.00 39.71 3.72
237 312 2.162608 AGAGTAGTGTGAGTGATGCGTC 59.837 50.000 0.00 0.00 0.00 5.19
244 319 1.728971 GTGAGTGATGCGTCAGGAAAG 59.271 52.381 9.39 0.00 34.36 2.62
250 325 4.645136 AGTGATGCGTCAGGAAAGTCTATA 59.355 41.667 9.39 0.00 34.36 1.31
262 337 6.253727 CAGGAAAGTCTATACACGTTGATGTC 59.746 42.308 0.00 0.00 33.85 3.06
276 351 4.342772 GTTGATGTCGTATCCATGCAAAC 58.657 43.478 0.00 0.00 0.00 2.93
277 352 3.604582 TGATGTCGTATCCATGCAAACA 58.395 40.909 0.00 0.00 0.00 2.83
284 359 4.269123 TCGTATCCATGCAAACAACGTATC 59.731 41.667 0.00 0.00 0.00 2.24
287 362 2.091541 CCATGCAAACAACGTATCCCT 58.908 47.619 0.00 0.00 0.00 4.20
288 363 2.491693 CCATGCAAACAACGTATCCCTT 59.508 45.455 0.00 0.00 0.00 3.95
316 392 3.066380 CAAATTTGCCAAGCTACCCAAC 58.934 45.455 5.01 0.00 0.00 3.77
329 405 0.546988 ACCCAACTACCCTCCTCCAC 60.547 60.000 0.00 0.00 0.00 4.02
331 407 1.358152 CCAACTACCCTCCTCCACAA 58.642 55.000 0.00 0.00 0.00 3.33
356 432 0.981183 TGGTTACTTGGGATGCGAGT 59.019 50.000 0.00 0.00 0.00 4.18
357 433 1.066430 TGGTTACTTGGGATGCGAGTC 60.066 52.381 0.00 0.00 0.00 3.36
364 440 0.608035 TGGGATGCGAGTCCAAAACC 60.608 55.000 8.52 0.00 40.17 3.27
365 441 0.608035 GGGATGCGAGTCCAAAACCA 60.608 55.000 8.52 0.00 40.17 3.67
374 450 4.601019 CGAGTCCAAAACCATATGCAATC 58.399 43.478 0.00 0.00 0.00 2.67
378 454 5.248020 AGTCCAAAACCATATGCAATCCAAA 59.752 36.000 0.00 0.00 0.00 3.28
381 457 6.598457 TCCAAAACCATATGCAATCCAAAATG 59.402 34.615 0.00 0.00 0.00 2.32
382 458 6.598457 CCAAAACCATATGCAATCCAAAATGA 59.402 34.615 0.00 0.00 0.00 2.57
389 465 9.767228 CCATATGCAATCCAAAATGAGATAAAA 57.233 29.630 0.00 0.00 0.00 1.52
441 517 6.472686 AAGTACTCACTTCATCATACTCCC 57.527 41.667 0.00 0.00 41.25 4.30
443 519 5.830991 AGTACTCACTTCATCATACTCCCTC 59.169 44.000 0.00 0.00 0.00 4.30
444 520 3.964031 ACTCACTTCATCATACTCCCTCC 59.036 47.826 0.00 0.00 0.00 4.30
446 522 2.695666 CACTTCATCATACTCCCTCCGT 59.304 50.000 0.00 0.00 0.00 4.69
448 524 3.385111 ACTTCATCATACTCCCTCCGTTC 59.615 47.826 0.00 0.00 0.00 3.95
449 525 1.954382 TCATCATACTCCCTCCGTTCG 59.046 52.381 0.00 0.00 0.00 3.95
451 527 0.256752 TCATACTCCCTCCGTTCGGA 59.743 55.000 13.34 13.34 0.00 4.55
452 528 1.108776 CATACTCCCTCCGTTCGGAA 58.891 55.000 14.79 0.00 33.41 4.30
453 529 1.687123 CATACTCCCTCCGTTCGGAAT 59.313 52.381 14.79 2.14 33.41 3.01
454 530 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
455 531 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
456 532 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
457 533 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
458 534 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
459 535 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
460 536 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
461 537 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
462 538 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
463 539 1.060122 CCGTTCGGAATTACTTGTCGC 59.940 52.381 5.19 0.00 0.00 5.19
464 540 1.722464 CGTTCGGAATTACTTGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
465 541 2.471749 CGTTCGGAATTACTTGTCGCAC 60.472 50.000 0.00 0.00 0.00 5.34
466 542 2.442212 TCGGAATTACTTGTCGCACA 57.558 45.000 0.00 0.00 0.00 4.57
467 543 2.063266 TCGGAATTACTTGTCGCACAC 58.937 47.619 0.00 0.00 0.00 3.82
468 544 1.795872 CGGAATTACTTGTCGCACACA 59.204 47.619 0.00 0.00 0.00 3.72
469 545 2.415168 CGGAATTACTTGTCGCACACAT 59.585 45.455 0.00 0.00 33.90 3.21
470 546 3.724716 CGGAATTACTTGTCGCACACATG 60.725 47.826 0.00 0.00 33.90 3.21
471 547 3.426159 GGAATTACTTGTCGCACACATGG 60.426 47.826 0.00 0.00 34.98 3.66
472 548 2.535012 TTACTTGTCGCACACATGGA 57.465 45.000 0.00 0.00 34.98 3.41
473 549 2.760634 TACTTGTCGCACACATGGAT 57.239 45.000 0.00 0.00 34.98 3.41
474 550 1.159285 ACTTGTCGCACACATGGATG 58.841 50.000 0.00 0.00 34.98 3.51
475 551 1.159285 CTTGTCGCACACATGGATGT 58.841 50.000 0.00 0.00 42.84 3.06
476 552 2.289382 ACTTGTCGCACACATGGATGTA 60.289 45.455 0.00 0.00 39.39 2.29
477 553 2.689553 TGTCGCACACATGGATGTAT 57.310 45.000 0.00 0.00 39.39 2.29
478 554 2.278854 TGTCGCACACATGGATGTATG 58.721 47.619 0.00 0.00 39.39 2.39
479 555 2.279741 GTCGCACACATGGATGTATGT 58.720 47.619 0.00 0.00 37.51 2.29
480 556 3.118956 TGTCGCACACATGGATGTATGTA 60.119 43.478 0.00 0.00 37.51 2.29
481 557 3.490896 GTCGCACACATGGATGTATGTAG 59.509 47.826 0.00 0.00 37.51 2.74
482 558 3.383185 TCGCACACATGGATGTATGTAGA 59.617 43.478 0.00 0.00 37.51 2.59
483 559 4.039124 TCGCACACATGGATGTATGTAGAT 59.961 41.667 0.00 0.00 37.51 1.98
484 560 4.151157 CGCACACATGGATGTATGTAGATG 59.849 45.833 0.00 0.00 37.51 2.90
485 561 5.059161 GCACACATGGATGTATGTAGATGT 58.941 41.667 0.00 0.00 37.51 3.06
486 562 6.223120 GCACACATGGATGTATGTAGATGTA 58.777 40.000 0.00 0.00 37.51 2.29
487 563 6.875726 GCACACATGGATGTATGTAGATGTAT 59.124 38.462 0.00 0.00 37.51 2.29
488 564 7.388776 GCACACATGGATGTATGTAGATGTATT 59.611 37.037 0.00 0.00 37.51 1.89
489 565 9.276590 CACACATGGATGTATGTAGATGTATTT 57.723 33.333 0.00 0.00 39.17 1.40
490 566 9.851686 ACACATGGATGTATGTAGATGTATTTT 57.148 29.630 0.00 0.00 39.17 1.82
516 592 8.651589 AGTTTTAGATACATCCATATCCGAGA 57.348 34.615 0.00 0.00 32.76 4.04
517 593 8.524487 AGTTTTAGATACATCCATATCCGAGAC 58.476 37.037 0.00 0.00 32.76 3.36
518 594 8.304596 GTTTTAGATACATCCATATCCGAGACA 58.695 37.037 0.00 0.00 32.76 3.41
519 595 8.417273 TTTAGATACATCCATATCCGAGACAA 57.583 34.615 0.00 0.00 32.76 3.18
520 596 6.522625 AGATACATCCATATCCGAGACAAG 57.477 41.667 0.00 0.00 32.76 3.16
521 597 6.013379 AGATACATCCATATCCGAGACAAGT 58.987 40.000 0.00 0.00 32.76 3.16
522 598 7.175797 AGATACATCCATATCCGAGACAAGTA 58.824 38.462 0.00 0.00 32.76 2.24
523 599 7.670140 AGATACATCCATATCCGAGACAAGTAA 59.330 37.037 0.00 0.00 32.76 2.24
524 600 6.672266 ACATCCATATCCGAGACAAGTAAT 57.328 37.500 0.00 0.00 0.00 1.89
525 601 7.067496 ACATCCATATCCGAGACAAGTAATT 57.933 36.000 0.00 0.00 0.00 1.40
526 602 7.155328 ACATCCATATCCGAGACAAGTAATTC 58.845 38.462 0.00 0.00 0.00 2.17
527 603 6.097915 TCCATATCCGAGACAAGTAATTCC 57.902 41.667 0.00 0.00 0.00 3.01
528 604 4.923871 CCATATCCGAGACAAGTAATTCCG 59.076 45.833 0.00 0.00 0.00 4.30
529 605 5.278808 CCATATCCGAGACAAGTAATTCCGA 60.279 44.000 0.00 0.00 0.00 4.55
530 606 4.730949 ATCCGAGACAAGTAATTCCGAA 57.269 40.909 0.00 0.00 0.00 4.30
531 607 3.841643 TCCGAGACAAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
532 608 2.597305 CCGAGACAAGTAATTCCGAACG 59.403 50.000 0.00 0.00 0.00 3.95
533 609 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
534 610 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
535 611 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
536 612 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
537 613 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
538 614 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
539 615 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
540 616 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
541 617 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
542 618 2.083628 ATTCCGAACGGAGGGAGTAT 57.916 50.000 15.34 3.38 46.06 2.12
543 619 2.734755 TTCCGAACGGAGGGAGTATA 57.265 50.000 15.34 0.00 46.06 1.47
544 620 2.734755 TCCGAACGGAGGGAGTATAA 57.265 50.000 12.04 0.00 39.76 0.98
545 621 3.234234 TCCGAACGGAGGGAGTATAAT 57.766 47.619 12.04 0.00 39.76 1.28
546 622 4.371624 TCCGAACGGAGGGAGTATAATA 57.628 45.455 12.04 0.00 39.76 0.98
547 623 4.927049 TCCGAACGGAGGGAGTATAATAT 58.073 43.478 12.04 0.00 39.76 1.28
548 624 6.065976 TCCGAACGGAGGGAGTATAATATA 57.934 41.667 12.04 0.00 39.76 0.86
549 625 6.484288 TCCGAACGGAGGGAGTATAATATAA 58.516 40.000 12.04 0.00 39.76 0.98
550 626 6.600822 TCCGAACGGAGGGAGTATAATATAAG 59.399 42.308 12.04 0.00 39.76 1.73
551 627 6.600822 CCGAACGGAGGGAGTATAATATAAGA 59.399 42.308 7.53 0.00 37.50 2.10
552 628 7.414984 CCGAACGGAGGGAGTATAATATAAGAC 60.415 44.444 7.53 0.00 37.50 3.01
553 629 7.336427 CGAACGGAGGGAGTATAATATAAGACT 59.664 40.741 0.00 0.00 0.00 3.24
554 630 8.953223 AACGGAGGGAGTATAATATAAGACTT 57.047 34.615 0.00 0.00 0.00 3.01
555 631 8.953223 ACGGAGGGAGTATAATATAAGACTTT 57.047 34.615 0.00 0.00 0.00 2.66
556 632 9.377238 ACGGAGGGAGTATAATATAAGACTTTT 57.623 33.333 0.00 0.00 0.00 2.27
557 633 9.857957 CGGAGGGAGTATAATATAAGACTTTTC 57.142 37.037 0.00 0.00 0.00 2.29
638 715 2.225522 TGATGGTGTACAGGGAGAAGGA 60.226 50.000 0.00 0.00 0.00 3.36
683 762 8.712103 AGGATGAGAATGAGAAAGTATGAATCA 58.288 33.333 0.00 0.00 0.00 2.57
706 785 4.097892 ACAAACCAAAGTTGTGGACTCATC 59.902 41.667 10.03 0.00 41.65 2.92
720 799 4.021104 TGGACTCATCAATCGAAACTGACT 60.021 41.667 0.00 0.00 0.00 3.41
755 834 1.490490 AGCATCCAAAGGCGAGGATAA 59.510 47.619 7.84 0.00 42.61 1.75
829 909 0.403453 ATCCGATCCCCCAATCCCTT 60.403 55.000 0.00 0.00 0.00 3.95
830 910 0.626277 TCCGATCCCCCAATCCCTTT 60.626 55.000 0.00 0.00 0.00 3.11
843 923 4.141711 CCAATCCCTTTTCTCACTCCGATA 60.142 45.833 0.00 0.00 0.00 2.92
1065 1145 2.943978 GCAGTACGAGCTGGTGGGT 61.944 63.158 12.14 0.00 37.00 4.51
1322 1402 2.345760 CCTGCGCTTGCCCTTTGAT 61.346 57.895 9.73 0.00 38.03 2.57
1522 1602 9.171877 GTATGAAATTCAAATCCAACTCTCTCT 57.828 33.333 0.00 0.00 0.00 3.10
1531 1611 6.642707 AATCCAACTCTCTCTACGGAATAG 57.357 41.667 0.00 0.00 0.00 1.73
1801 1881 3.990933 TGATCTATCCTACCTGTCTCCCT 59.009 47.826 0.00 0.00 0.00 4.20
1858 1938 7.386851 TCAAGCCTTCTAATATACTGGTATGC 58.613 38.462 3.76 0.00 0.00 3.14
2118 2199 5.891551 GGATGGTACTTTGGTAATGGAATGT 59.108 40.000 0.00 0.00 0.00 2.71
2150 2231 1.468520 CATTCCGCCAAGTTACCACTG 59.531 52.381 0.00 0.00 31.60 3.66
2180 2261 7.363031 TCTCAGGTTCCCACTATTCTTATAGT 58.637 38.462 0.00 0.00 46.18 2.12
2271 2352 7.312657 TGAGTTCAAGTATCTGAATGCAATC 57.687 36.000 0.00 0.00 37.63 2.67
2296 2377 1.745087 CCGTTGATTGGAGTCCATTGG 59.255 52.381 14.00 3.31 31.53 3.16
2585 2667 3.149196 CAAGTGCTGTTGGTATCCTTGT 58.851 45.455 0.00 0.00 0.00 3.16
2783 2865 4.084328 GCAGTTGCACTCAGTTAGTTAGTG 60.084 45.833 0.00 0.00 42.80 2.74
2806 2888 8.082242 AGTGTTGCCATCTTGTTTTTAGATTAC 58.918 33.333 0.00 0.00 30.05 1.89
2874 2957 5.064198 TCAAGTAATTTTCCTCCGTTATGCG 59.936 40.000 0.00 0.00 40.95 4.73
2923 3006 2.848887 CGTCTTGTAGCTCGATCAACTG 59.151 50.000 0.00 0.00 0.00 3.16
3009 3092 6.865205 TCATGCTCATCAGAAATATACTCACG 59.135 38.462 0.00 0.00 0.00 4.35
3152 3235 2.006169 GTTGAGCTGCTCTAAGAAGGC 58.994 52.381 28.04 6.33 0.00 4.35
3275 3358 2.005451 CCTGCATTTGACCTTCTCTCG 58.995 52.381 0.00 0.00 0.00 4.04
3284 3367 2.828520 TGACCTTCTCTCGAGAATGCTT 59.171 45.455 17.36 0.72 45.40 3.91
3528 3613 6.939163 GGATGCTTCTGTTTCCATATCTGTAT 59.061 38.462 0.00 0.00 0.00 2.29
3529 3614 8.097038 GGATGCTTCTGTTTCCATATCTGTATA 58.903 37.037 0.00 0.00 0.00 1.47
3530 3615 9.494271 GATGCTTCTGTTTCCATATCTGTATAA 57.506 33.333 0.00 0.00 0.00 0.98
3531 3616 8.662781 TGCTTCTGTTTCCATATCTGTATAAC 57.337 34.615 0.00 0.00 0.00 1.89
3532 3617 8.486210 TGCTTCTGTTTCCATATCTGTATAACT 58.514 33.333 0.00 0.00 0.00 2.24
3533 3618 9.982651 GCTTCTGTTTCCATATCTGTATAACTA 57.017 33.333 0.00 0.00 0.00 2.24
3611 4183 2.791501 TAGCCTTCCGACAAACGCCC 62.792 60.000 0.00 0.00 41.07 6.13
3709 4281 1.392589 CCATTTAGTGGCTTCCGCAT 58.607 50.000 0.00 0.00 42.12 4.73
3815 4388 0.258774 ATGCTACCCTTCCGCCAAAT 59.741 50.000 0.00 0.00 0.00 2.32
3817 4390 1.493022 TGCTACCCTTCCGCCAAATAT 59.507 47.619 0.00 0.00 0.00 1.28
3823 4396 4.542697 ACCCTTCCGCCAAATATGTTAAT 58.457 39.130 0.00 0.00 0.00 1.40
3824 4397 4.959839 ACCCTTCCGCCAAATATGTTAATT 59.040 37.500 0.00 0.00 0.00 1.40
3825 4398 6.130569 ACCCTTCCGCCAAATATGTTAATTA 58.869 36.000 0.00 0.00 0.00 1.40
3826 4399 6.264518 ACCCTTCCGCCAAATATGTTAATTAG 59.735 38.462 0.00 0.00 0.00 1.73
3827 4400 6.264518 CCCTTCCGCCAAATATGTTAATTAGT 59.735 38.462 0.00 0.00 0.00 2.24
3828 4401 7.138736 CCTTCCGCCAAATATGTTAATTAGTG 58.861 38.462 0.00 0.00 0.00 2.74
3829 4402 6.067263 TCCGCCAAATATGTTAATTAGTGC 57.933 37.500 0.00 0.00 0.00 4.40
3830 4403 5.009210 TCCGCCAAATATGTTAATTAGTGCC 59.991 40.000 0.00 0.00 0.00 5.01
3831 4404 5.221145 CCGCCAAATATGTTAATTAGTGCCA 60.221 40.000 0.00 0.00 0.00 4.92
3832 4405 5.685511 CGCCAAATATGTTAATTAGTGCCAC 59.314 40.000 0.00 0.00 0.00 5.01
3833 4406 6.459573 CGCCAAATATGTTAATTAGTGCCACT 60.460 38.462 1.54 1.54 0.00 4.00
3834 4407 7.264947 GCCAAATATGTTAATTAGTGCCACTT 58.735 34.615 1.02 0.00 0.00 3.16
3835 4408 8.410141 GCCAAATATGTTAATTAGTGCCACTTA 58.590 33.333 1.02 0.00 0.00 2.24
3877 4450 0.674895 CTAGCAGCTTCCGCCAAACT 60.675 55.000 0.00 0.00 36.60 2.66
3900 4473 1.228124 CACCTTCCGCCAAACAGGA 60.228 57.895 0.00 0.00 41.22 3.86
4020 4595 3.886044 GGTTTGCTACCAGTTTGCC 57.114 52.632 4.00 0.00 46.92 4.52
4021 4596 0.039527 GGTTTGCTACCAGTTTGCCG 60.040 55.000 4.00 0.00 46.92 5.69
4022 4597 0.039527 GTTTGCTACCAGTTTGCCGG 60.040 55.000 0.00 0.00 0.00 6.13
4023 4598 0.179015 TTTGCTACCAGTTTGCCGGA 60.179 50.000 5.05 0.00 0.00 5.14
4078 4653 1.602311 GGATAGCACTGGATGGCAAG 58.398 55.000 0.00 0.00 0.00 4.01
4079 4654 1.133976 GGATAGCACTGGATGGCAAGT 60.134 52.381 0.00 0.00 0.00 3.16
4115 4692 5.163953 CGCAAAGGACATATACGGATGATTC 60.164 44.000 0.00 0.00 0.00 2.52
4124 4701 0.686441 ACGGATGATTCGAGGGTCCA 60.686 55.000 0.00 0.00 0.00 4.02
4173 4750 8.057623 AGTCTGGAATTATTCTTGGAATCATGT 58.942 33.333 4.87 0.00 0.00 3.21
4189 4766 7.279981 TGGAATCATGTCTATGTTTTAACCTCG 59.720 37.037 0.00 0.00 35.73 4.63
4192 4769 7.827819 TCATGTCTATGTTTTAACCTCGAAG 57.172 36.000 0.00 0.00 35.73 3.79
4233 4810 7.753309 ATAAAATGGTTTTAAAACAAGGGGC 57.247 32.000 27.56 12.90 40.63 5.80
4261 4839 7.574217 GCCTTCTGATTTCCGTTATTACAAACA 60.574 37.037 0.00 0.00 0.00 2.83
4283 4861 3.587797 TTAGGAGTTCGTTACAGCAGG 57.412 47.619 0.00 0.00 0.00 4.85
4374 5313 1.227527 GCAAAAGCGGCCAAAACCT 60.228 52.632 2.24 0.00 0.00 3.50
4545 5484 5.339990 ACAAAATCATAGTTGTAATGCGGC 58.660 37.500 0.00 0.00 36.22 6.53
4567 5506 5.049954 GGCGATATTGGCGATTACAGTTTAA 60.050 40.000 0.00 0.00 0.00 1.52
4571 5510 9.689075 CGATATTGGCGATTACAGTTTAATATG 57.311 33.333 0.00 0.00 0.00 1.78
4739 5678 5.821204 AGAAAGTGATGGTTTTTCTTGTCG 58.179 37.500 0.00 0.00 37.78 4.35
4971 5915 7.667575 TGATAGAGAAGAGCTTAGTGGAAAT 57.332 36.000 0.00 0.00 0.00 2.17
5068 6022 4.133013 AGCAAAATCATCTTCCAATGGC 57.867 40.909 0.00 0.00 0.00 4.40
5074 6028 0.379669 CATCTTCCAATGGCGCAGAC 59.620 55.000 10.83 0.00 0.00 3.51
5241 7076 2.159352 TGCATTCATGTTTCAGCCATCG 60.159 45.455 0.00 0.00 0.00 3.84
5244 7079 0.617935 TCATGTTTCAGCCATCGGGA 59.382 50.000 0.00 0.00 35.59 5.14
5507 7350 3.223157 GTTTGAATAACGCTTGTGACGG 58.777 45.455 0.00 0.00 34.00 4.79
5627 7470 2.691241 GCTTCTGACATCCTCCCTCCTA 60.691 54.545 0.00 0.00 0.00 2.94
5919 7775 4.564782 TCTTCTGCTCATGTTGGAAGAT 57.435 40.909 14.17 0.00 37.88 2.40
5941 7798 3.119173 TGAGTGGTTTGGCAAAAAGTCAG 60.119 43.478 21.56 0.00 30.49 3.51
6080 7940 8.810990 AATTATGATGCATTGTTTTGGGAATT 57.189 26.923 0.00 0.00 0.00 2.17
6081 7941 9.902684 AATTATGATGCATTGTTTTGGGAATTA 57.097 25.926 0.00 0.00 0.00 1.40
6083 7943 7.795482 ATGATGCATTGTTTTGGGAATTATG 57.205 32.000 0.00 0.00 0.00 1.90
6084 7944 6.944096 TGATGCATTGTTTTGGGAATTATGA 58.056 32.000 0.00 0.00 0.00 2.15
6085 7945 7.566569 TGATGCATTGTTTTGGGAATTATGAT 58.433 30.769 0.00 0.00 0.00 2.45
6086 7946 7.496263 TGATGCATTGTTTTGGGAATTATGATG 59.504 33.333 0.00 0.00 0.00 3.07
6087 7947 5.585445 TGCATTGTTTTGGGAATTATGATGC 59.415 36.000 0.00 0.00 37.32 3.91
6088 7948 5.585445 GCATTGTTTTGGGAATTATGATGCA 59.415 36.000 0.00 0.00 36.92 3.96
6089 7949 6.261381 GCATTGTTTTGGGAATTATGATGCAT 59.739 34.615 0.00 0.00 36.92 3.96
6090 7950 7.201750 GCATTGTTTTGGGAATTATGATGCATT 60.202 33.333 0.00 0.00 36.92 3.56
6091 7951 7.846644 TTGTTTTGGGAATTATGATGCATTC 57.153 32.000 0.00 0.00 0.00 2.67
6092 7952 7.185318 TGTTTTGGGAATTATGATGCATTCT 57.815 32.000 0.00 0.00 31.16 2.40
6093 7953 7.622713 TGTTTTGGGAATTATGATGCATTCTT 58.377 30.769 0.00 0.00 31.16 2.52
6094 7954 8.102047 TGTTTTGGGAATTATGATGCATTCTTT 58.898 29.630 0.00 0.00 31.16 2.52
6095 7955 8.949177 GTTTTGGGAATTATGATGCATTCTTTT 58.051 29.630 0.00 0.00 31.16 2.27
6096 7956 8.495361 TTTGGGAATTATGATGCATTCTTTTG 57.505 30.769 0.00 0.00 31.16 2.44
6097 7957 6.584488 TGGGAATTATGATGCATTCTTTTGG 58.416 36.000 0.00 0.00 31.16 3.28
6098 7958 5.993441 GGGAATTATGATGCATTCTTTTGGG 59.007 40.000 0.00 0.00 31.16 4.12
6099 7959 6.183360 GGGAATTATGATGCATTCTTTTGGGA 60.183 38.462 0.00 0.00 31.16 4.37
6100 7960 7.274447 GGAATTATGATGCATTCTTTTGGGAA 58.726 34.615 0.00 0.00 31.16 3.97
6101 7961 7.935210 GGAATTATGATGCATTCTTTTGGGAAT 59.065 33.333 0.00 0.00 36.49 3.01
6118 7978 7.946381 TTGGGAATTATGTATGTAAAGCACA 57.054 32.000 0.00 0.00 42.69 4.57
6121 7981 8.465999 TGGGAATTATGTATGTAAAGCACAAAG 58.534 33.333 0.00 0.00 41.55 2.77
6171 8031 5.824421 AGAATTGAGGGTCAAGATGTGATT 58.176 37.500 0.00 0.00 40.05 2.57
6188 8048 8.066668 GATGTGATTACTTAAACATCTCCTCG 57.933 38.462 7.98 0.00 43.54 4.63
6475 8339 3.323403 CCAAAATGGGCCTCACAAAAGTA 59.677 43.478 4.53 0.00 32.67 2.24
6482 8346 3.317150 GGCCTCACAAAAGTATGCAAAC 58.683 45.455 0.00 0.00 0.00 2.93
6499 8363 3.678806 GCAAACATCTCCACGGACAGATA 60.679 47.826 0.00 0.00 0.00 1.98
6520 8384 8.095792 CAGATATAGCAGAAGAGTCCATTCAAT 58.904 37.037 0.00 0.00 0.00 2.57
6530 8394 1.002033 GTCCATTCAATCGCAGGCATC 60.002 52.381 0.00 0.00 0.00 3.91
6560 8424 5.317808 TGGTCCCATTTCAAACGAATCTTA 58.682 37.500 0.00 0.00 0.00 2.10
6561 8425 5.770663 TGGTCCCATTTCAAACGAATCTTAA 59.229 36.000 0.00 0.00 0.00 1.85
6596 8460 7.088905 ACGAAATTCACACTAAACTAGACGAT 58.911 34.615 0.00 0.00 0.00 3.73
6603 8467 8.906636 TCACACTAAACTAGACGATATTTGTC 57.093 34.615 0.00 1.82 36.60 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.040278 TCACATTTGATGTTGTACATGGTTGT 59.960 34.615 0.00 0.00 42.70 3.32
1 2 6.363088 GTCACATTTGATGTTGTACATGGTTG 59.637 38.462 0.00 0.00 42.70 3.77
9 10 5.372373 TGAGGTGTCACATTTGATGTTGTA 58.628 37.500 5.12 0.00 42.70 2.41
22 23 3.746045 TGTAACTTCCTGAGGTGTCAC 57.254 47.619 0.00 0.00 0.00 3.67
24 25 3.400255 GGTTGTAACTTCCTGAGGTGTC 58.600 50.000 0.00 0.00 0.00 3.67
33 34 5.359860 CCCTCATAATTGGGTTGTAACTTCC 59.640 44.000 0.00 0.00 38.65 3.46
37 38 7.942341 TGATATCCCTCATAATTGGGTTGTAAC 59.058 37.037 0.00 0.00 43.74 2.50
38 39 8.051468 TGATATCCCTCATAATTGGGTTGTAA 57.949 34.615 0.00 0.00 43.74 2.41
69 70 9.606631 CCTGAGAGCAAAATAGGGATATATTAC 57.393 37.037 0.00 0.00 0.00 1.89
105 106 6.127479 TGTCAAATTGAAAGTTAAGCAGTGGT 60.127 34.615 0.00 0.00 0.00 4.16
106 107 6.272318 TGTCAAATTGAAAGTTAAGCAGTGG 58.728 36.000 0.00 0.00 0.00 4.00
108 109 6.461509 CCCTGTCAAATTGAAAGTTAAGCAGT 60.462 38.462 11.82 0.00 29.59 4.40
116 191 3.636764 GACCACCCTGTCAAATTGAAAGT 59.363 43.478 11.82 0.00 29.59 2.66
123 198 2.879103 ATTCGACCACCCTGTCAAAT 57.121 45.000 0.00 0.00 34.88 2.32
129 204 1.535462 GACACAAATTCGACCACCCTG 59.465 52.381 0.00 0.00 0.00 4.45
138 213 3.033185 GTTTGACGTGGACACAAATTCG 58.967 45.455 0.00 0.00 36.25 3.34
148 223 0.806884 AAACGAGCGTTTGACGTGGA 60.807 50.000 18.81 0.00 45.34 4.02
150 225 0.299300 TGAAACGAGCGTTTGACGTG 59.701 50.000 23.56 0.00 46.80 4.49
159 234 3.218398 GTCAATTTGAGTGAAACGAGCG 58.782 45.455 0.00 0.00 45.86 5.03
161 236 4.203828 CACGTCAATTTGAGTGAAACGAG 58.796 43.478 17.10 6.26 45.86 4.18
163 238 3.935450 ACACGTCAATTTGAGTGAAACG 58.065 40.909 23.68 15.69 45.86 3.60
167 242 8.596271 TCTTAATTACACGTCAATTTGAGTGA 57.404 30.769 23.68 9.03 37.95 3.41
178 253 8.019669 TGTGTACTCTTCTCTTAATTACACGTC 58.980 37.037 0.00 0.00 40.34 4.34
209 284 6.868864 GCATCACTCACACTACTCTTTTCTAA 59.131 38.462 0.00 0.00 0.00 2.10
213 288 3.990469 CGCATCACTCACACTACTCTTTT 59.010 43.478 0.00 0.00 0.00 2.27
225 300 1.344438 ACTTTCCTGACGCATCACTCA 59.656 47.619 0.00 0.00 0.00 3.41
232 307 3.427098 CGTGTATAGACTTTCCTGACGCA 60.427 47.826 0.00 0.00 0.00 5.24
237 312 6.100004 ACATCAACGTGTATAGACTTTCCTG 58.900 40.000 0.00 0.00 0.00 3.86
244 319 5.850128 GGATACGACATCAACGTGTATAGAC 59.150 44.000 0.00 0.00 43.73 2.59
250 325 3.186909 CATGGATACGACATCAACGTGT 58.813 45.455 0.00 0.00 43.73 4.49
262 337 2.892373 ACGTTGTTTGCATGGATACG 57.108 45.000 3.57 6.70 42.51 3.06
305 381 1.080666 AGGAGGGTAGTTGGGTAGCTT 59.919 52.381 0.00 0.00 0.00 3.74
316 392 0.818296 CTCGTTGTGGAGGAGGGTAG 59.182 60.000 0.00 0.00 36.78 3.18
329 405 1.071071 TCCCAAGTAACCACCTCGTTG 59.929 52.381 0.00 0.00 0.00 4.10
331 407 1.278127 CATCCCAAGTAACCACCTCGT 59.722 52.381 0.00 0.00 0.00 4.18
342 418 0.400213 TTTGGACTCGCATCCCAAGT 59.600 50.000 2.69 0.00 40.59 3.16
356 432 5.752036 TTTGGATTGCATATGGTTTTGGA 57.248 34.783 4.56 0.00 0.00 3.53
357 433 6.598457 TCATTTTGGATTGCATATGGTTTTGG 59.402 34.615 4.56 0.00 0.00 3.28
420 496 5.010213 GGAGGGAGTATGATGAAGTGAGTAC 59.990 48.000 0.00 0.00 0.00 2.73
425 501 2.695666 ACGGAGGGAGTATGATGAAGTG 59.304 50.000 0.00 0.00 0.00 3.16
426 502 3.033659 ACGGAGGGAGTATGATGAAGT 57.966 47.619 0.00 0.00 0.00 3.01
429 505 1.954382 CGAACGGAGGGAGTATGATGA 59.046 52.381 0.00 0.00 0.00 2.92
431 507 1.133575 TCCGAACGGAGGGAGTATGAT 60.134 52.381 12.04 0.00 39.76 2.45
434 510 2.083628 ATTCCGAACGGAGGGAGTAT 57.916 50.000 15.34 3.38 46.06 2.12
435 511 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
437 513 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
438 514 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
439 515 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
440 516 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
441 517 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
443 519 1.060122 GCGACAAGTAATTCCGAACGG 59.940 52.381 6.94 6.94 0.00 4.44
444 520 1.722464 TGCGACAAGTAATTCCGAACG 59.278 47.619 0.00 0.00 0.00 3.95
446 522 2.477375 GTGTGCGACAAGTAATTCCGAA 59.523 45.455 0.00 0.00 0.00 4.30
448 524 1.795872 TGTGTGCGACAAGTAATTCCG 59.204 47.619 0.00 0.00 0.00 4.30
449 525 3.426159 CCATGTGTGCGACAAGTAATTCC 60.426 47.826 0.00 0.00 38.36 3.01
451 527 3.407698 TCCATGTGTGCGACAAGTAATT 58.592 40.909 0.00 0.00 38.36 1.40
452 528 3.052455 TCCATGTGTGCGACAAGTAAT 57.948 42.857 0.00 0.00 38.36 1.89
453 529 2.535012 TCCATGTGTGCGACAAGTAA 57.465 45.000 0.00 0.00 38.36 2.24
454 530 2.289382 ACATCCATGTGTGCGACAAGTA 60.289 45.455 0.00 0.00 40.03 2.24
455 531 1.159285 CATCCATGTGTGCGACAAGT 58.841 50.000 0.00 0.00 38.36 3.16
456 532 1.159285 ACATCCATGTGTGCGACAAG 58.841 50.000 0.00 0.00 40.03 3.16
457 533 2.464157 TACATCCATGTGTGCGACAA 57.536 45.000 2.26 0.00 41.89 3.18
458 534 2.278854 CATACATCCATGTGTGCGACA 58.721 47.619 3.79 0.00 41.71 4.35
464 540 9.851686 AAAATACATCTACATACATCCATGTGT 57.148 29.630 2.26 0.00 41.89 3.72
490 566 9.749340 TCTCGGATATGGATGTATCTAAAACTA 57.251 33.333 0.00 0.00 32.78 2.24
491 567 8.524487 GTCTCGGATATGGATGTATCTAAAACT 58.476 37.037 0.00 0.00 32.78 2.66
492 568 8.304596 TGTCTCGGATATGGATGTATCTAAAAC 58.695 37.037 0.00 0.00 32.78 2.43
493 569 8.417273 TGTCTCGGATATGGATGTATCTAAAA 57.583 34.615 0.00 0.00 32.78 1.52
494 570 8.417273 TTGTCTCGGATATGGATGTATCTAAA 57.583 34.615 0.00 0.00 32.78 1.85
495 571 7.670140 ACTTGTCTCGGATATGGATGTATCTAA 59.330 37.037 0.00 0.00 32.78 2.10
496 572 7.175797 ACTTGTCTCGGATATGGATGTATCTA 58.824 38.462 0.00 0.00 32.78 1.98
497 573 6.013379 ACTTGTCTCGGATATGGATGTATCT 58.987 40.000 0.00 0.00 32.78 1.98
498 574 6.274157 ACTTGTCTCGGATATGGATGTATC 57.726 41.667 0.00 0.00 0.00 2.24
499 575 7.776618 TTACTTGTCTCGGATATGGATGTAT 57.223 36.000 0.00 0.00 0.00 2.29
500 576 7.776618 ATTACTTGTCTCGGATATGGATGTA 57.223 36.000 0.00 0.00 0.00 2.29
501 577 6.672266 ATTACTTGTCTCGGATATGGATGT 57.328 37.500 0.00 0.00 0.00 3.06
502 578 6.591834 GGAATTACTTGTCTCGGATATGGATG 59.408 42.308 0.00 0.00 0.00 3.51
503 579 6.572509 CGGAATTACTTGTCTCGGATATGGAT 60.573 42.308 0.00 0.00 0.00 3.41
504 580 5.278808 CGGAATTACTTGTCTCGGATATGGA 60.279 44.000 0.00 0.00 0.00 3.41
505 581 4.923871 CGGAATTACTTGTCTCGGATATGG 59.076 45.833 0.00 0.00 0.00 2.74
506 582 5.769367 TCGGAATTACTTGTCTCGGATATG 58.231 41.667 0.00 0.00 0.00 1.78
507 583 6.214399 GTTCGGAATTACTTGTCTCGGATAT 58.786 40.000 0.00 0.00 0.00 1.63
508 584 5.585390 GTTCGGAATTACTTGTCTCGGATA 58.415 41.667 0.00 0.00 0.00 2.59
509 585 4.430908 GTTCGGAATTACTTGTCTCGGAT 58.569 43.478 0.00 0.00 0.00 4.18
510 586 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
511 587 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
512 588 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
513 589 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
514 590 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
515 591 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
516 592 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
517 593 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
518 594 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
519 595 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
520 596 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
521 597 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
522 598 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
523 599 2.083628 ATACTCCCTCCGTTCGGAAT 57.916 50.000 14.79 2.14 33.41 3.01
524 600 2.734755 TATACTCCCTCCGTTCGGAA 57.265 50.000 14.79 0.00 33.41 4.30
525 601 2.734755 TTATACTCCCTCCGTTCGGA 57.265 50.000 13.34 13.34 0.00 4.55
526 602 6.600822 TCTTATATTATACTCCCTCCGTTCGG 59.399 42.308 4.74 4.74 0.00 4.30
527 603 7.336427 AGTCTTATATTATACTCCCTCCGTTCG 59.664 40.741 0.00 0.00 0.00 3.95
528 604 8.578448 AGTCTTATATTATACTCCCTCCGTTC 57.422 38.462 0.00 0.00 0.00 3.95
529 605 8.953223 AAGTCTTATATTATACTCCCTCCGTT 57.047 34.615 0.00 0.00 0.00 4.44
530 606 8.953223 AAAGTCTTATATTATACTCCCTCCGT 57.047 34.615 0.00 0.00 0.00 4.69
531 607 9.857957 GAAAAGTCTTATATTATACTCCCTCCG 57.142 37.037 0.00 0.00 0.00 4.63
603 679 8.330466 TGTACACCATCAATATTTTCGTTCTT 57.670 30.769 0.00 0.00 0.00 2.52
619 696 2.642171 TCCTTCTCCCTGTACACCAT 57.358 50.000 0.00 0.00 0.00 3.55
626 703 5.527026 AAGATTTCATTCCTTCTCCCTGT 57.473 39.130 0.00 0.00 0.00 4.00
657 736 8.712103 TGATTCATACTTTCTCATTCTCATCCT 58.288 33.333 0.00 0.00 0.00 3.24
683 762 3.426615 TGAGTCCACAACTTTGGTTTGT 58.573 40.909 0.00 0.00 38.74 2.83
706 785 1.135859 GGCTGCAGTCAGTTTCGATTG 60.136 52.381 14.88 0.00 42.29 2.67
720 799 2.203112 GCTGATCGGATGGCTGCA 60.203 61.111 5.48 0.00 0.00 4.41
755 834 0.684153 AAAATATGCAGCGTGGCCCT 60.684 50.000 0.00 0.00 0.00 5.19
817 897 1.359130 AGTGAGAAAAGGGATTGGGGG 59.641 52.381 0.00 0.00 0.00 5.40
954 1034 6.155049 CAGATCCCTCTCTTTCTTCTTCTTCT 59.845 42.308 0.00 0.00 0.00 2.85
1065 1145 2.792947 GGTGCCCTCGCCGATCTTA 61.793 63.158 0.00 0.00 32.51 2.10
1095 1175 4.673298 TTGAGGCGCGCGAGGAAA 62.673 61.111 37.18 18.82 0.00 3.13
1281 1361 8.553153 CAGGGAGAGAGATTACAGTCCTATATA 58.447 40.741 0.00 0.00 0.00 0.86
1522 1602 7.975616 AGTGCTTCGTTAATTAACTATTCCGTA 59.024 33.333 22.57 5.16 34.12 4.02
1531 1611 5.532025 AGAGCAGTGCTTCGTTAATTAAC 57.468 39.130 20.80 16.87 39.88 2.01
1700 1780 2.753452 AGCTTGTGGAGAATCATGCTTG 59.247 45.455 0.00 0.00 40.43 4.01
1701 1781 2.753452 CAGCTTGTGGAGAATCATGCTT 59.247 45.455 0.00 0.00 41.03 3.91
1801 1881 4.473196 TGGATAATCCAGTTACTGCAGGAA 59.527 41.667 19.93 14.19 42.67 3.36
2073 2153 7.202186 CCATCCTTTGGTTCCCTCATATTACTA 60.202 40.741 0.00 0.00 40.99 1.82
2118 2199 2.499693 TGGCGGAATGAGTGAATGACTA 59.500 45.455 0.00 0.00 33.83 2.59
2180 2261 6.757947 GCAATTGCCAATTATAAGCTTTGAGA 59.242 34.615 20.06 0.00 34.31 3.27
2197 2278 8.385111 GTGATAATATATTTGCATGCAATTGCC 58.615 33.333 32.27 17.93 42.06 4.52
2271 2352 0.804989 GACTCCAATCAACGGCCAAG 59.195 55.000 2.24 0.00 0.00 3.61
2296 2377 2.524394 TGGATCCTCCTAGGCCGC 60.524 66.667 14.23 0.00 37.46 6.53
2363 2445 6.098679 ACTACGTGCCGTAATTAATGTACAA 58.901 36.000 0.00 0.00 41.82 2.41
2385 2467 7.174946 AGCAGTGTTGTGCAAAATAATACTACT 59.825 33.333 0.00 0.00 46.60 2.57
2400 2482 4.155462 AGCTATTCATGAAGCAGTGTTGTG 59.845 41.667 19.08 0.00 41.32 3.33
2585 2667 4.000928 AGGATCTGCTTTTCTCTCCCTA 57.999 45.455 0.00 0.00 0.00 3.53
2783 2865 8.986477 ATGTAATCTAAAAACAAGATGGCAAC 57.014 30.769 0.00 0.00 33.95 4.17
2840 2922 7.554118 GGAGGAAAATTACTTGAGACATGATCA 59.446 37.037 0.00 0.00 0.00 2.92
2858 2940 2.680841 CCAATCGCATAACGGAGGAAAA 59.319 45.455 0.00 0.00 43.89 2.29
2923 3006 7.997773 ACCTAAGACCTTAAAAATCTTGTCC 57.002 36.000 6.01 0.00 34.55 4.02
3009 3092 7.339482 ACCTTCAGAAGAGTTGGGTTATTATC 58.661 38.462 12.14 0.00 0.00 1.75
3529 3614 9.535878 GCATCAGCTAAGAACTAGTTAATAGTT 57.464 33.333 20.17 4.70 46.17 2.24
3530 3615 8.696374 TGCATCAGCTAAGAACTAGTTAATAGT 58.304 33.333 20.17 10.29 43.56 2.12
3531 3616 9.703892 ATGCATCAGCTAAGAACTAGTTAATAG 57.296 33.333 8.42 14.08 42.74 1.73
3533 3618 9.482627 GTATGCATCAGCTAAGAACTAGTTAAT 57.517 33.333 8.42 2.96 42.74 1.40
3534 3619 7.926555 GGTATGCATCAGCTAAGAACTAGTTAA 59.073 37.037 8.42 0.00 42.74 2.01
3602 4174 6.038936 GTGTTATCTTAATATGGGGCGTTTGT 59.961 38.462 0.00 0.00 0.00 2.83
3611 4183 7.066284 GGGCTAGCATGTGTTATCTTAATATGG 59.934 40.741 18.24 0.00 0.00 2.74
3709 4281 0.756903 GGCGGAAGGGTAGCATCTTA 59.243 55.000 0.00 0.00 0.00 2.10
3831 4404 5.761234 TGTTTGACGGAAGCACTAATTAAGT 59.239 36.000 0.00 0.00 39.81 2.24
3832 4405 6.236017 TGTTTGACGGAAGCACTAATTAAG 57.764 37.500 0.00 0.00 0.00 1.85
3833 4406 6.607689 CATGTTTGACGGAAGCACTAATTAA 58.392 36.000 0.00 0.00 0.00 1.40
3834 4407 5.391523 GCATGTTTGACGGAAGCACTAATTA 60.392 40.000 0.00 0.00 0.00 1.40
3835 4408 4.615912 GCATGTTTGACGGAAGCACTAATT 60.616 41.667 0.00 0.00 0.00 1.40
3836 4409 3.119849 GCATGTTTGACGGAAGCACTAAT 60.120 43.478 0.00 0.00 0.00 1.73
3849 4422 2.086869 GGAAGCTGCTAGCATGTTTGA 58.913 47.619 19.72 0.00 45.56 2.69
3877 4450 0.536460 GTTTGGCGGAAGGTGAAGGA 60.536 55.000 0.00 0.00 0.00 3.36
3995 4570 3.503099 GGTAGCAAACCTGGGGGA 58.497 61.111 0.00 0.00 45.75 4.81
4018 4593 2.311294 CGGATGTCTGAATTCCGGC 58.689 57.895 17.32 0.00 46.67 6.13
4021 4596 1.571919 CGTCCGGATGTCTGAATTCC 58.428 55.000 15.98 0.00 0.00 3.01
4022 4597 0.931005 GCGTCCGGATGTCTGAATTC 59.069 55.000 24.33 0.00 0.00 2.17
4023 4598 0.806102 CGCGTCCGGATGTCTGAATT 60.806 55.000 24.33 0.00 0.00 2.17
4115 4692 1.605058 ATCTCCAACGTGGACCCTCG 61.605 60.000 8.73 8.73 42.67 4.63
4124 4701 3.132467 GCTTCTAAGGGTATCTCCAACGT 59.868 47.826 0.00 0.00 38.11 3.99
4173 4750 7.447594 AGGAAACTTCGAGGTTAAAACATAGA 58.552 34.615 13.78 0.00 37.44 1.98
4233 4810 5.584649 TGTAATAACGGAAATCAGAAGGCAG 59.415 40.000 0.00 0.00 0.00 4.85
4261 4839 4.222145 TCCTGCTGTAACGAACTCCTAATT 59.778 41.667 0.00 0.00 0.00 1.40
4289 4868 5.949735 ACACGAATTCTGTTCTGTTTTGTT 58.050 33.333 3.52 0.00 0.00 2.83
4290 4869 5.560966 ACACGAATTCTGTTCTGTTTTGT 57.439 34.783 3.52 0.00 0.00 2.83
4291 4870 8.560576 AATAACACGAATTCTGTTCTGTTTTG 57.439 30.769 19.74 3.88 33.79 2.44
4292 4871 9.233232 GAAATAACACGAATTCTGTTCTGTTTT 57.767 29.630 19.74 15.93 33.79 2.43
4295 4874 6.710744 AGGAAATAACACGAATTCTGTTCTGT 59.289 34.615 19.74 10.54 33.79 3.41
4296 4875 7.133891 AGGAAATAACACGAATTCTGTTCTG 57.866 36.000 19.74 1.47 33.79 3.02
4297 4876 9.449719 AATAGGAAATAACACGAATTCTGTTCT 57.550 29.630 19.74 14.73 33.79 3.01
4308 5218 8.283291 GGCATTCTTCTAATAGGAAATAACACG 58.717 37.037 0.00 0.00 0.00 4.49
4521 5460 5.455525 GCCGCATTACAACTATGATTTTGTC 59.544 40.000 0.00 0.00 37.19 3.18
4545 5484 9.689075 CATATTAAACTGTAATCGCCAATATCG 57.311 33.333 0.00 0.00 0.00 2.92
4567 5506 7.293299 TCCCCAATATCAGAAGAGTTGACATAT 59.707 37.037 0.00 0.00 0.00 1.78
4571 5510 5.359194 TCCCCAATATCAGAAGAGTTGAC 57.641 43.478 0.00 0.00 0.00 3.18
4739 5678 3.373439 CAGAGAGACATTTTAGGCACAGC 59.627 47.826 0.00 0.00 0.00 4.40
5068 6022 5.755375 ACTGACTGATTAAATATGGTCTGCG 59.245 40.000 0.00 0.00 0.00 5.18
5085 6039 5.105752 GCCTACATCTAACTTGACTGACTG 58.894 45.833 0.00 0.00 0.00 3.51
5112 6074 6.603237 AATTAAACAAGAAACAAGCCTTGC 57.397 33.333 3.88 0.00 42.46 4.01
5241 7076 1.900545 CTCCTGGAGGTCCGTTTCCC 61.901 65.000 16.19 0.00 39.43 3.97
5244 7079 3.807368 CCTCCTGGAGGTCCGTTT 58.193 61.111 30.91 0.00 44.25 3.60
5465 7308 7.386848 TCAAACAACAGTAGCTAGGAACATAAC 59.613 37.037 0.00 0.00 0.00 1.89
5469 7312 5.284861 TCAAACAACAGTAGCTAGGAACA 57.715 39.130 0.00 0.00 0.00 3.18
5507 7350 5.358298 AGAAAATCAAACGGCTTACTGAC 57.642 39.130 0.00 0.00 0.00 3.51
5627 7470 4.689612 ACATTTATATCAGTCGGTGCCT 57.310 40.909 0.00 0.00 0.00 4.75
5691 7534 2.124570 ATGGCCACCAGACGATGC 60.125 61.111 8.16 0.00 36.75 3.91
5919 7775 2.828520 TGACTTTTTGCCAAACCACTCA 59.171 40.909 0.00 0.00 0.00 3.41
6080 7940 8.926374 ACATAATTCCCAAAAGAATGCATCATA 58.074 29.630 0.00 0.00 36.59 2.15
6081 7941 7.798071 ACATAATTCCCAAAAGAATGCATCAT 58.202 30.769 0.00 0.00 36.59 2.45
6082 7942 7.185318 ACATAATTCCCAAAAGAATGCATCA 57.815 32.000 0.00 0.00 36.59 3.07
6083 7943 9.199982 CATACATAATTCCCAAAAGAATGCATC 57.800 33.333 0.00 0.00 36.59 3.91
6084 7944 8.707449 ACATACATAATTCCCAAAAGAATGCAT 58.293 29.630 0.00 0.00 36.59 3.96
6085 7945 8.076910 ACATACATAATTCCCAAAAGAATGCA 57.923 30.769 0.00 0.00 36.59 3.96
6090 7950 9.249053 TGCTTTACATACATAATTCCCAAAAGA 57.751 29.630 0.00 0.00 0.00 2.52
6091 7951 9.301153 GTGCTTTACATACATAATTCCCAAAAG 57.699 33.333 0.00 0.00 0.00 2.27
6092 7952 8.807118 TGTGCTTTACATACATAATTCCCAAAA 58.193 29.630 0.00 0.00 33.42 2.44
6093 7953 8.354711 TGTGCTTTACATACATAATTCCCAAA 57.645 30.769 0.00 0.00 33.42 3.28
6094 7954 7.946381 TGTGCTTTACATACATAATTCCCAA 57.054 32.000 0.00 0.00 33.42 4.12
6095 7955 7.946381 TTGTGCTTTACATACATAATTCCCA 57.054 32.000 0.00 0.00 39.48 4.37
6096 7956 8.682710 TCTTTGTGCTTTACATACATAATTCCC 58.317 33.333 0.00 0.00 39.48 3.97
6171 8031 5.126707 GGGAGTTCGAGGAGATGTTTAAGTA 59.873 44.000 0.00 0.00 0.00 2.24
6185 8045 4.452733 GGCGGGTGGGAGTTCGAG 62.453 72.222 0.00 0.00 0.00 4.04
6188 8048 3.647771 AAGGGCGGGTGGGAGTTC 61.648 66.667 0.00 0.00 0.00 3.01
6406 8266 9.574458 CTTCGTGAAGAGATAACTATTCTCAAA 57.426 33.333 8.58 0.00 42.62 2.69
6407 8267 8.191446 CCTTCGTGAAGAGATAACTATTCTCAA 58.809 37.037 11.11 3.08 42.62 3.02
6408 8268 7.201830 CCCTTCGTGAAGAGATAACTATTCTCA 60.202 40.741 11.11 0.00 42.62 3.27
6409 8269 7.142680 CCCTTCGTGAAGAGATAACTATTCTC 58.857 42.308 11.11 4.58 42.62 2.87
6410 8270 6.461788 GCCCTTCGTGAAGAGATAACTATTCT 60.462 42.308 11.11 0.00 42.62 2.40
6411 8271 5.692654 GCCCTTCGTGAAGAGATAACTATTC 59.307 44.000 11.11 0.73 42.52 1.75
6412 8272 5.128827 TGCCCTTCGTGAAGAGATAACTATT 59.871 40.000 11.11 0.00 40.79 1.73
6413 8273 4.649674 TGCCCTTCGTGAAGAGATAACTAT 59.350 41.667 11.11 0.00 40.79 2.12
6414 8274 4.021229 TGCCCTTCGTGAAGAGATAACTA 58.979 43.478 11.11 0.00 40.79 2.24
6415 8275 2.832129 TGCCCTTCGTGAAGAGATAACT 59.168 45.455 11.11 0.00 40.79 2.24
6416 8276 3.247006 TGCCCTTCGTGAAGAGATAAC 57.753 47.619 11.11 0.00 40.79 1.89
6417 8277 3.260884 AGTTGCCCTTCGTGAAGAGATAA 59.739 43.478 11.11 0.00 40.79 1.75
6429 8289 0.955919 CCTCGTTGGAGTTGCCCTTC 60.956 60.000 0.00 0.00 38.70 3.46
6475 8339 1.271325 TGTCCGTGGAGATGTTTGCAT 60.271 47.619 0.00 0.00 38.18 3.96
6482 8346 3.507622 TGCTATATCTGTCCGTGGAGATG 59.492 47.826 0.00 0.00 31.29 2.90
6499 8363 5.295950 CGATTGAATGGACTCTTCTGCTAT 58.704 41.667 0.00 0.00 0.00 2.97
6530 8394 3.681593 TTGAAATGGGACCAGCATTTG 57.318 42.857 11.98 0.00 0.00 2.32
6538 8402 4.783764 AAGATTCGTTTGAAATGGGACC 57.216 40.909 0.00 0.00 37.71 4.46
6561 8425 6.927294 AGTGTGAATTTCGTCTCTCTTTTT 57.073 33.333 0.00 0.00 0.00 1.94
6566 8430 8.021973 TCTAGTTTAGTGTGAATTTCGTCTCTC 58.978 37.037 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.