Multiple sequence alignment - TraesCS6D01G327600

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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 TraesCS6D01G327600 chr6D 100.000 2869 0 0 1 2869 432851695 432854563 0.000000e+00 5299.0
1 TraesCS6D01G327600 chr6D 84.475 219 17 4 546 756 432845323 432845532 1.740000e-47 200.0
2 TraesCS6D01G327600 chr6D 88.889 144 9 3 380 522 432845077 432845214 1.370000e-38 171.0
3 TraesCS6D01G327600 chr6D 74.101 417 68 33 1172 1556 432824017 432824425 4.990000e-28 135.0
4 TraesCS6D01G327600 chr6D 100.000 67 0 0 2803 2869 432870881 432870947 1.080000e-24 124.0
5 TraesCS6D01G327600 chr6A 89.946 1492 85 28 413 1880 578954123 578955573 0.000000e+00 1864.0
6 TraesCS6D01G327600 chr6A 84.929 491 22 17 1925 2398 578955571 578956026 1.570000e-122 449.0
7 TraesCS6D01G327600 chr6A 86.350 337 21 11 2429 2760 578956024 578956340 7.610000e-91 344.0
8 TraesCS6D01G327600 chr6A 74.690 403 64 34 1172 1543 578942373 578942768 8.280000e-31 145.0
9 TraesCS6D01G327600 chr6B 90.063 1439 69 28 380 1789 652982991 652984384 0.000000e+00 1797.0
10 TraesCS6D01G327600 chr6B 89.056 466 21 10 2342 2802 652985265 652985705 4.180000e-153 551.0
11 TraesCS6D01G327600 chr6B 84.657 554 32 23 1815 2342 652984676 652985202 1.190000e-138 503.0
12 TraesCS6D01G327600 chr6B 88.119 303 33 3 34 334 652982689 652982990 9.780000e-95 357.0
13 TraesCS6D01G327600 chr6B 74.396 414 72 31 1172 1556 652945494 652945902 2.300000e-31 147.0
14 TraesCS6D01G327600 chr1D 100.000 67 0 0 2803 2869 121402783 121402717 1.080000e-24 124.0
15 TraesCS6D01G327600 chr1D 98.485 66 1 0 2803 2868 121398073 121398008 1.810000e-22 117.0
16 TraesCS6D01G327600 chr3D 98.507 67 1 0 2802 2868 464077234 464077300 5.020000e-23 119.0
17 TraesCS6D01G327600 chr3D 97.015 67 2 0 2803 2869 464108668 464108734 2.340000e-21 113.0
18 TraesCS6D01G327600 chr2D 95.588 68 3 0 2802 2869 232791097 232791030 3.020000e-20 110.0
19 TraesCS6D01G327600 chr2D 96.923 65 2 0 2803 2867 232813023 232812959 3.020000e-20 110.0
20 TraesCS6D01G327600 chr1B 95.652 69 0 3 2803 2869 582117843 582117776 1.090000e-19 108.0
21 TraesCS6D01G327600 chr1B 91.892 74 2 4 2798 2869 582140092 582140021 1.820000e-17 100.0
22 TraesCS6D01G327600 chr4A 100.000 28 0 0 202 229 573878623 573878596 5.000000e-03 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 TraesCS6D01G327600 chr6D 432851695 432854563 2868 False 5299.000000 5299 100.00000 1 2869 1 chr6D.!!$F2 2868
1 TraesCS6D01G327600 chr6A 578954123 578956340 2217 False 885.666667 1864 87.07500 413 2760 3 chr6A.!!$F2 2347
2 TraesCS6D01G327600 chr6B 652982689 652985705 3016 False 802.000000 1797 87.97375 34 2802 4 chr6B.!!$F2 2768

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
950 983 0.106469 GATTTCTTGCCCTCCCTCCC 60.106 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2828 3271 0.036294 CCCAAACCGAGTTCTCCTCC 60.036 60.0 0.0 0.0 36.82 4.3 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
18 19 3.533697 TACTGCCCTACCTGCCTAG 57.466 57.895 0.00 0.00 0.00 3.02
19 20 0.759436 TACTGCCCTACCTGCCTAGC 60.759 60.000 0.00 0.00 0.00 3.42
20 21 1.764054 CTGCCCTACCTGCCTAGCT 60.764 63.158 0.00 0.00 0.00 3.32
21 22 1.753368 CTGCCCTACCTGCCTAGCTC 61.753 65.000 0.00 0.00 0.00 4.09
22 23 1.762460 GCCCTACCTGCCTAGCTCA 60.762 63.158 0.00 0.00 0.00 4.26
23 24 1.338136 GCCCTACCTGCCTAGCTCAA 61.338 60.000 0.00 0.00 0.00 3.02
24 25 0.755686 CCCTACCTGCCTAGCTCAAG 59.244 60.000 0.00 0.00 0.00 3.02
25 26 1.689575 CCCTACCTGCCTAGCTCAAGA 60.690 57.143 0.00 0.00 0.00 3.02
26 27 2.111384 CCTACCTGCCTAGCTCAAGAA 58.889 52.381 0.00 0.00 0.00 2.52
27 28 2.501723 CCTACCTGCCTAGCTCAAGAAA 59.498 50.000 0.00 0.00 0.00 2.52
28 29 2.481289 ACCTGCCTAGCTCAAGAAAC 57.519 50.000 0.00 0.00 0.00 2.78
29 30 1.981495 ACCTGCCTAGCTCAAGAAACT 59.019 47.619 0.00 0.00 0.00 2.66
30 31 3.173965 ACCTGCCTAGCTCAAGAAACTA 58.826 45.455 0.00 0.00 0.00 2.24
31 32 3.583086 ACCTGCCTAGCTCAAGAAACTAA 59.417 43.478 0.00 0.00 0.00 2.24
32 33 4.187694 CCTGCCTAGCTCAAGAAACTAAG 58.812 47.826 0.00 0.00 0.00 2.18
38 39 6.540551 GCCTAGCTCAAGAAACTAAGCTAATT 59.459 38.462 0.00 0.00 44.35 1.40
41 42 7.986085 AGCTCAAGAAACTAAGCTAATTTCA 57.014 32.000 15.67 0.38 43.04 2.69
55 56 8.836268 AAGCTAATTTCAATGCAGAAAAATCA 57.164 26.923 5.35 0.00 40.54 2.57
61 62 5.885230 TCAATGCAGAAAAATCACGAGAT 57.115 34.783 0.00 0.00 35.53 2.75
63 64 7.008440 TCAATGCAGAAAAATCACGAGATAG 57.992 36.000 0.00 0.00 33.08 2.08
65 66 3.306973 TGCAGAAAAATCACGAGATAGCG 59.693 43.478 0.00 0.00 33.08 4.26
68 69 5.331905 GCAGAAAAATCACGAGATAGCGTAG 60.332 44.000 0.00 0.00 43.59 3.51
73 74 2.487934 TCACGAGATAGCGTAGGGTAC 58.512 52.381 0.00 0.00 43.59 3.34
83 84 3.028850 AGCGTAGGGTACAAATGCTAGA 58.971 45.455 0.00 0.00 0.00 2.43
87 88 3.550437 AGGGTACAAATGCTAGAGCTG 57.450 47.619 2.72 0.00 42.66 4.24
95 96 2.461300 ATGCTAGAGCTGTCTACCCA 57.539 50.000 2.72 0.00 42.66 4.51
97 98 0.382515 GCTAGAGCTGTCTACCCACG 59.617 60.000 0.00 0.00 38.21 4.94
104 105 4.073549 GAGCTGTCTACCCACGTCTATAT 58.926 47.826 0.00 0.00 0.00 0.86
117 118 6.533012 CCCACGTCTATATGCAAGATTATCAG 59.467 42.308 0.00 0.00 0.00 2.90
119 120 7.274468 CCACGTCTATATGCAAGATTATCAGTC 59.726 40.741 0.00 0.00 0.00 3.51
133 134 6.674419 AGATTATCAGTCCAAACTACTCCCTT 59.326 38.462 0.00 0.00 33.25 3.95
134 135 4.559862 ATCAGTCCAAACTACTCCCTTG 57.440 45.455 0.00 0.00 33.25 3.61
139 140 4.079385 AGTCCAAACTACTCCCTTGGTTTT 60.079 41.667 0.35 0.00 40.47 2.43
189 190 9.646336 GTACACTCTTATATTATGGCGTTTTTG 57.354 33.333 0.00 0.00 0.00 2.44
199 201 2.357075 TGGCGTTTTTGACAGTACACA 58.643 42.857 0.00 0.00 0.00 3.72
200 202 2.353269 TGGCGTTTTTGACAGTACACAG 59.647 45.455 0.00 0.00 0.00 3.66
214 216 8.418662 TGACAGTACACAGTTATATTATGGGAC 58.581 37.037 0.00 0.00 0.00 4.46
229 231 0.616964 GGGACGGAGGGAGTAACCTT 60.617 60.000 0.00 0.00 42.10 3.50
240 242 5.311265 AGGGAGTAACCTTTTTAGTTTCGG 58.689 41.667 0.00 0.00 37.69 4.30
252 254 1.959226 GTTTCGGACAGCGCTTCCA 60.959 57.895 27.09 16.84 31.94 3.53
287 289 2.441717 TGTGTTGGCAAGGCAGCA 60.442 55.556 8.99 8.99 35.83 4.41
307 309 3.670627 GCAAATCTGAGTTGTAAAGGGCG 60.671 47.826 17.77 0.00 0.00 6.13
334 337 1.270305 GGTGAGCTTGACAGTGTGCTA 60.270 52.381 0.00 0.00 35.76 3.49
335 338 1.795286 GTGAGCTTGACAGTGTGCTAC 59.205 52.381 0.00 0.00 35.76 3.58
336 339 1.688735 TGAGCTTGACAGTGTGCTACT 59.311 47.619 0.00 0.00 41.36 2.57
337 340 2.288457 TGAGCTTGACAGTGTGCTACTC 60.288 50.000 0.00 3.27 37.60 2.59
338 341 1.001406 AGCTTGACAGTGTGCTACTCC 59.999 52.381 0.00 0.00 37.60 3.85
339 342 1.941668 GCTTGACAGTGTGCTACTCCC 60.942 57.143 0.00 0.00 37.60 4.30
340 343 1.620819 CTTGACAGTGTGCTACTCCCT 59.379 52.381 0.00 0.00 37.60 4.20
341 344 1.257743 TGACAGTGTGCTACTCCCTC 58.742 55.000 0.00 0.00 37.60 4.30
342 345 0.533032 GACAGTGTGCTACTCCCTCC 59.467 60.000 0.00 0.00 37.60 4.30
343 346 1.251527 ACAGTGTGCTACTCCCTCCG 61.252 60.000 0.00 0.00 37.60 4.63
344 347 1.076906 AGTGTGCTACTCCCTCCGT 59.923 57.895 0.00 0.00 33.17 4.69
345 348 0.542232 AGTGTGCTACTCCCTCCGTT 60.542 55.000 0.00 0.00 33.17 4.44
346 349 0.320697 GTGTGCTACTCCCTCCGTTT 59.679 55.000 0.00 0.00 0.00 3.60
347 350 0.320374 TGTGCTACTCCCTCCGTTTG 59.680 55.000 0.00 0.00 0.00 2.93
348 351 0.606604 GTGCTACTCCCTCCGTTTGA 59.393 55.000 0.00 0.00 0.00 2.69
349 352 1.001633 GTGCTACTCCCTCCGTTTGAA 59.998 52.381 0.00 0.00 0.00 2.69
350 353 1.695242 TGCTACTCCCTCCGTTTGAAA 59.305 47.619 0.00 0.00 0.00 2.69
351 354 2.304761 TGCTACTCCCTCCGTTTGAAAT 59.695 45.455 0.00 0.00 0.00 2.17
352 355 3.244770 TGCTACTCCCTCCGTTTGAAATT 60.245 43.478 0.00 0.00 0.00 1.82
353 356 3.374367 GCTACTCCCTCCGTTTGAAATTC 59.626 47.826 0.00 0.00 0.00 2.17
354 357 3.790089 ACTCCCTCCGTTTGAAATTCT 57.210 42.857 0.00 0.00 0.00 2.40
355 358 4.100279 ACTCCCTCCGTTTGAAATTCTT 57.900 40.909 0.00 0.00 0.00 2.52
356 359 4.470602 ACTCCCTCCGTTTGAAATTCTTT 58.529 39.130 0.00 0.00 0.00 2.52
357 360 4.278419 ACTCCCTCCGTTTGAAATTCTTTG 59.722 41.667 0.00 0.00 0.00 2.77
358 361 4.211920 TCCCTCCGTTTGAAATTCTTTGT 58.788 39.130 0.00 0.00 0.00 2.83
359 362 4.277423 TCCCTCCGTTTGAAATTCTTTGTC 59.723 41.667 0.00 0.00 0.00 3.18
360 363 4.219033 CCTCCGTTTGAAATTCTTTGTCG 58.781 43.478 0.00 0.00 0.00 4.35
361 364 3.623863 TCCGTTTGAAATTCTTTGTCGC 58.376 40.909 0.00 0.00 0.00 5.19
362 365 2.400408 CCGTTTGAAATTCTTTGTCGCG 59.600 45.455 0.00 0.00 0.00 5.87
363 366 2.400408 CGTTTGAAATTCTTTGTCGCGG 59.600 45.455 6.13 0.00 0.00 6.46
364 367 3.623863 GTTTGAAATTCTTTGTCGCGGA 58.376 40.909 6.13 0.00 0.00 5.54
365 368 3.972950 TTGAAATTCTTTGTCGCGGAA 57.027 38.095 6.13 0.93 0.00 4.30
366 369 3.972950 TGAAATTCTTTGTCGCGGAAA 57.027 38.095 6.13 5.10 0.00 3.13
367 370 4.497473 TGAAATTCTTTGTCGCGGAAAT 57.503 36.364 6.13 0.00 0.00 2.17
368 371 4.225984 TGAAATTCTTTGTCGCGGAAATG 58.774 39.130 6.13 3.80 0.00 2.32
369 372 2.919666 ATTCTTTGTCGCGGAAATGG 57.080 45.000 6.13 0.00 0.00 3.16
370 373 1.885560 TTCTTTGTCGCGGAAATGGA 58.114 45.000 6.13 0.00 0.00 3.41
371 374 2.107950 TCTTTGTCGCGGAAATGGAT 57.892 45.000 6.13 0.00 0.00 3.41
372 375 1.737236 TCTTTGTCGCGGAAATGGATG 59.263 47.619 6.13 0.00 0.00 3.51
373 376 1.468520 CTTTGTCGCGGAAATGGATGT 59.531 47.619 6.13 0.00 0.00 3.06
374 377 2.388310 TTGTCGCGGAAATGGATGTA 57.612 45.000 6.13 0.00 0.00 2.29
375 378 2.613026 TGTCGCGGAAATGGATGTAT 57.387 45.000 6.13 0.00 0.00 2.29
376 379 2.479837 TGTCGCGGAAATGGATGTATC 58.520 47.619 6.13 0.00 0.00 2.24
377 380 2.102420 TGTCGCGGAAATGGATGTATCT 59.898 45.455 6.13 0.00 0.00 1.98
378 381 3.319689 TGTCGCGGAAATGGATGTATCTA 59.680 43.478 6.13 0.00 0.00 1.98
404 407 2.762327 GCCATTCCCTGTTGATTCATGT 59.238 45.455 0.00 0.00 0.00 3.21
454 457 1.710013 CGCGTCTTTCTGCCTCTTTA 58.290 50.000 0.00 0.00 0.00 1.85
462 465 5.934625 GTCTTTCTGCCTCTTTATGTCTGAA 59.065 40.000 0.00 0.00 0.00 3.02
486 489 1.559368 CACCCTGGCCAATTGAATGA 58.441 50.000 7.01 0.00 0.00 2.57
522 525 0.738975 CAGCTGTTCCATCATGCCAG 59.261 55.000 5.25 0.00 0.00 4.85
524 527 0.454600 GCTGTTCCATCATGCCAGTG 59.545 55.000 0.00 0.00 0.00 3.66
525 528 1.830279 CTGTTCCATCATGCCAGTGT 58.170 50.000 0.00 0.00 0.00 3.55
536 555 1.374758 GCCAGTGTCCCAGAGTTCG 60.375 63.158 0.00 0.00 0.00 3.95
537 556 1.816863 GCCAGTGTCCCAGAGTTCGA 61.817 60.000 0.00 0.00 0.00 3.71
538 557 0.898320 CCAGTGTCCCAGAGTTCGAT 59.102 55.000 0.00 0.00 0.00 3.59
539 558 1.134965 CCAGTGTCCCAGAGTTCGATC 60.135 57.143 0.00 0.00 0.00 3.69
540 559 1.546029 CAGTGTCCCAGAGTTCGATCA 59.454 52.381 0.00 0.00 0.00 2.92
542 561 2.028930 AGTGTCCCAGAGTTCGATCAAC 60.029 50.000 0.00 0.00 34.86 3.18
544 563 2.367241 TGTCCCAGAGTTCGATCAACAA 59.633 45.455 9.64 0.00 37.48 2.83
546 565 3.813166 GTCCCAGAGTTCGATCAACAAAA 59.187 43.478 9.64 0.00 37.48 2.44
556 575 8.733857 AGTTCGATCAACAAAATTTCTGAATC 57.266 30.769 9.64 0.00 37.48 2.52
567 586 9.485206 ACAAAATTTCTGAATCATCTCCAAAAG 57.515 29.630 0.00 0.00 0.00 2.27
575 594 6.392354 TGAATCATCTCCAAAAGCATTTGTC 58.608 36.000 12.94 2.77 43.59 3.18
577 596 5.381174 TCATCTCCAAAAGCATTTGTCTG 57.619 39.130 12.94 5.38 43.59 3.51
613 640 3.181516 GCAACTTAACTGAAGCGGATGAG 60.182 47.826 0.00 0.00 38.92 2.90
616 643 2.760634 TAACTGAAGCGGATGAGCAA 57.239 45.000 0.00 0.00 40.15 3.91
619 646 2.440409 ACTGAAGCGGATGAGCAATTT 58.560 42.857 0.00 0.00 40.15 1.82
623 650 3.181511 TGAAGCGGATGAGCAATTTAACG 60.182 43.478 0.00 0.00 40.15 3.18
624 651 1.670811 AGCGGATGAGCAATTTAACGG 59.329 47.619 0.00 0.00 40.15 4.44
626 653 2.791158 GCGGATGAGCAATTTAACGGTG 60.791 50.000 0.00 0.00 37.05 4.94
639 666 6.727824 ATTTAACGGTGAATTCAGAGACAG 57.272 37.500 8.80 0.32 0.00 3.51
674 707 1.866853 GAAAAGACGGGCCAAGGCAG 61.867 60.000 13.87 8.73 44.11 4.85
677 710 4.660938 GACGGGCCAAGGCAGGTT 62.661 66.667 13.87 0.00 44.11 3.50
755 788 3.587797 AGCAGCAATTTGATTCCAGTG 57.412 42.857 0.00 0.00 0.00 3.66
756 789 2.232941 AGCAGCAATTTGATTCCAGTGG 59.767 45.455 1.40 1.40 0.00 4.00
757 790 2.231964 GCAGCAATTTGATTCCAGTGGA 59.768 45.455 8.12 8.12 0.00 4.02
758 791 3.675228 GCAGCAATTTGATTCCAGTGGAG 60.675 47.826 12.67 0.00 31.21 3.86
759 792 3.508793 CAGCAATTTGATTCCAGTGGAGT 59.491 43.478 12.67 9.86 31.21 3.85
794 827 1.001887 AATAAGCACCGCCCGGAAA 60.002 52.632 14.44 0.00 38.96 3.13
949 982 0.922626 AGATTTCTTGCCCTCCCTCC 59.077 55.000 0.00 0.00 0.00 4.30
950 983 0.106469 GATTTCTTGCCCTCCCTCCC 60.106 60.000 0.00 0.00 0.00 4.30
951 984 0.553612 ATTTCTTGCCCTCCCTCCCT 60.554 55.000 0.00 0.00 0.00 4.20
952 985 1.208165 TTTCTTGCCCTCCCTCCCTC 61.208 60.000 0.00 0.00 0.00 4.30
953 986 3.093172 CTTGCCCTCCCTCCCTCC 61.093 72.222 0.00 0.00 0.00 4.30
954 987 4.760220 TTGCCCTCCCTCCCTCCC 62.760 72.222 0.00 0.00 0.00 4.30
956 989 4.890306 GCCCTCCCTCCCTCCCTC 62.890 77.778 0.00 0.00 0.00 4.30
1029 1065 2.362889 CACCCACCTCCAATGGCC 60.363 66.667 0.00 0.00 35.74 5.36
1030 1066 3.672503 ACCCACCTCCAATGGCCC 61.673 66.667 0.00 0.00 35.74 5.80
1031 1067 4.463788 CCCACCTCCAATGGCCCC 62.464 72.222 0.00 0.00 35.74 5.80
1032 1068 4.463788 CCACCTCCAATGGCCCCC 62.464 72.222 0.00 0.00 0.00 5.40
1033 1069 3.350163 CACCTCCAATGGCCCCCT 61.350 66.667 0.00 0.00 0.00 4.79
1034 1070 3.023735 ACCTCCAATGGCCCCCTC 61.024 66.667 0.00 0.00 0.00 4.30
1035 1071 3.825623 CCTCCAATGGCCCCCTCC 61.826 72.222 0.00 0.00 0.00 4.30
1036 1072 2.697644 CTCCAATGGCCCCCTCCT 60.698 66.667 0.00 0.00 0.00 3.69
1037 1073 2.696125 TCCAATGGCCCCCTCCTC 60.696 66.667 0.00 0.00 0.00 3.71
1620 1672 4.436998 CGCCTCGCCGGTCTTCTT 62.437 66.667 1.90 0.00 34.25 2.52
1621 1673 2.509561 GCCTCGCCGGTCTTCTTC 60.510 66.667 1.90 0.00 34.25 2.87
1622 1674 2.970639 CCTCGCCGGTCTTCTTCA 59.029 61.111 1.90 0.00 0.00 3.02
1623 1675 1.446272 CCTCGCCGGTCTTCTTCAC 60.446 63.158 1.90 0.00 0.00 3.18
1624 1676 1.289066 CTCGCCGGTCTTCTTCACA 59.711 57.895 1.90 0.00 0.00 3.58
1625 1677 0.108615 CTCGCCGGTCTTCTTCACAT 60.109 55.000 1.90 0.00 0.00 3.21
1628 1680 1.808411 GCCGGTCTTCTTCACATTCA 58.192 50.000 1.90 0.00 0.00 2.57
1790 1847 6.085555 TGCTATACTACTGGTACTGCATTC 57.914 41.667 0.00 0.00 37.19 2.67
1791 1848 5.833667 TGCTATACTACTGGTACTGCATTCT 59.166 40.000 0.00 0.00 37.19 2.40
1792 1849 7.002276 TGCTATACTACTGGTACTGCATTCTA 58.998 38.462 0.00 0.00 37.19 2.10
1793 1850 7.504574 TGCTATACTACTGGTACTGCATTCTAA 59.495 37.037 0.00 0.00 37.19 2.10
1794 1851 8.024285 GCTATACTACTGGTACTGCATTCTAAG 58.976 40.741 0.00 0.00 34.43 2.18
1810 1867 7.559533 TGCATTCTAAGTATTTATCCTTGCCAA 59.440 33.333 0.00 0.00 0.00 4.52
1823 2150 9.528489 TTTATCCTTGCCAAAATATATACTCCC 57.472 33.333 0.00 0.00 0.00 4.30
1882 2209 3.193691 AGCTACGTATTTGACTGCTCTGT 59.806 43.478 0.00 0.00 0.00 3.41
1883 2210 3.548268 GCTACGTATTTGACTGCTCTGTC 59.452 47.826 0.00 0.69 37.47 3.51
1893 2220 7.566760 TTTGACTGCTCTGTCTCAAATAAAA 57.433 32.000 8.09 0.00 37.79 1.52
1914 2241 1.269958 AAAGGCATTCCTCCCTTTGC 58.730 50.000 4.03 0.00 46.67 3.68
1915 2242 0.411058 AAGGCATTCCTCCCTTTGCT 59.589 50.000 0.00 0.00 43.40 3.91
1916 2243 0.033699 AGGCATTCCTCCCTTTGCTC 60.034 55.000 0.00 0.00 38.72 4.26
1957 2288 7.197071 ACTCGTATGCTTGTAAAAATGACAA 57.803 32.000 0.00 0.00 35.55 3.18
1962 2293 8.155294 CGTATGCTTGTAAAAATGACAACATTG 58.845 33.333 0.00 0.00 44.67 2.82
1971 2302 9.900264 GTAAAAATGACAACATTGTTCTCAAAC 57.100 29.630 10.86 3.11 44.67 2.93
2047 2407 1.106285 GGCTTTTAGGTGGCTGGATG 58.894 55.000 0.00 0.00 0.00 3.51
2048 2408 1.106285 GCTTTTAGGTGGCTGGATGG 58.894 55.000 0.00 0.00 0.00 3.51
2049 2409 1.340991 GCTTTTAGGTGGCTGGATGGA 60.341 52.381 0.00 0.00 0.00 3.41
2050 2410 2.687914 GCTTTTAGGTGGCTGGATGGAT 60.688 50.000 0.00 0.00 0.00 3.41
2062 2422 1.213678 TGGATGGATTCCTTCCTGCTG 59.786 52.381 28.58 0.00 44.99 4.41
2095 2455 0.318699 GTGAGCTGTGTACGTGAGCA 60.319 55.000 0.00 0.00 35.03 4.26
2096 2456 0.603065 TGAGCTGTGTACGTGAGCAT 59.397 50.000 0.00 0.00 35.03 3.79
2097 2457 0.994995 GAGCTGTGTACGTGAGCATG 59.005 55.000 0.00 0.00 35.03 4.06
2098 2458 1.016130 AGCTGTGTACGTGAGCATGC 61.016 55.000 10.51 10.51 35.03 4.06
2099 2459 1.291184 GCTGTGTACGTGAGCATGCA 61.291 55.000 21.98 0.00 32.70 3.96
2396 2825 3.827898 CCACGGAGTCTCTCGGCC 61.828 72.222 13.15 0.00 41.61 6.13
2481 2914 4.632153 AGTATCATATGCGGGTCAAAGAC 58.368 43.478 0.00 0.00 0.00 3.01
2483 2916 0.937304 CATATGCGGGTCAAAGACGG 59.063 55.000 0.00 0.00 32.65 4.79
2492 2925 0.178301 GTCAAAGACGGAGGGATCCC 59.822 60.000 24.59 24.59 0.00 3.85
2532 2968 2.266055 GGTCAAGGTCTCGGCTGG 59.734 66.667 0.00 0.00 0.00 4.85
2534 2970 3.003173 TCAAGGTCTCGGCTGGGG 61.003 66.667 0.00 0.00 0.00 4.96
2535 2971 4.785453 CAAGGTCTCGGCTGGGGC 62.785 72.222 0.00 0.00 37.82 5.80
2563 3000 0.952497 CGAGGATGTTGCAGTGCAGT 60.952 55.000 18.81 8.65 40.61 4.40
2564 3001 0.520404 GAGGATGTTGCAGTGCAGTG 59.480 55.000 18.81 17.56 40.61 3.66
2565 3002 1.080974 GGATGTTGCAGTGCAGTGC 60.081 57.895 34.65 34.65 40.61 4.40
2620 3057 2.047274 GTTGGGTAGAGCGCTGCA 60.047 61.111 18.48 0.00 0.00 4.41
2629 3066 1.665916 GAGCGCTGCAGACTTGACA 60.666 57.895 18.48 0.00 0.00 3.58
2636 3073 2.843701 CTGCAGACTTGACAAAGGAGT 58.156 47.619 8.42 0.00 37.76 3.85
2663 3106 3.235437 CTCGCGCGCTTGCAATTG 61.235 61.111 30.48 11.00 39.07 2.32
2802 3245 1.589716 GCTTGCAGCCCGAAAGATGT 61.590 55.000 0.00 0.00 34.48 3.06
2803 3246 0.169672 CTTGCAGCCCGAAAGATGTG 59.830 55.000 0.00 0.00 0.00 3.21
2804 3247 0.250684 TTGCAGCCCGAAAGATGTGA 60.251 50.000 0.00 0.00 0.00 3.58
2805 3248 0.250684 TGCAGCCCGAAAGATGTGAA 60.251 50.000 0.00 0.00 0.00 3.18
2806 3249 0.449388 GCAGCCCGAAAGATGTGAAG 59.551 55.000 0.00 0.00 0.00 3.02
2807 3250 1.089920 CAGCCCGAAAGATGTGAAGG 58.910 55.000 0.00 0.00 0.00 3.46
2808 3251 0.984230 AGCCCGAAAGATGTGAAGGA 59.016 50.000 0.00 0.00 0.00 3.36
2809 3252 1.065854 AGCCCGAAAGATGTGAAGGAG 60.066 52.381 0.00 0.00 0.00 3.69
2810 3253 1.373570 CCCGAAAGATGTGAAGGAGC 58.626 55.000 0.00 0.00 0.00 4.70
2811 3254 1.373570 CCGAAAGATGTGAAGGAGCC 58.626 55.000 0.00 0.00 0.00 4.70
2812 3255 1.065854 CCGAAAGATGTGAAGGAGCCT 60.066 52.381 0.00 0.00 0.00 4.58
2813 3256 2.168521 CCGAAAGATGTGAAGGAGCCTA 59.831 50.000 0.00 0.00 0.00 3.93
2814 3257 3.369471 CCGAAAGATGTGAAGGAGCCTAA 60.369 47.826 0.00 0.00 0.00 2.69
2815 3258 4.253685 CGAAAGATGTGAAGGAGCCTAAA 58.746 43.478 0.00 0.00 0.00 1.85
2816 3259 4.093556 CGAAAGATGTGAAGGAGCCTAAAC 59.906 45.833 0.00 0.00 0.00 2.01
2817 3260 4.917906 AAGATGTGAAGGAGCCTAAACT 57.082 40.909 0.00 0.00 0.00 2.66
2818 3261 6.374417 AAAGATGTGAAGGAGCCTAAACTA 57.626 37.500 0.00 0.00 0.00 2.24
2819 3262 5.346181 AGATGTGAAGGAGCCTAAACTAC 57.654 43.478 0.00 0.00 0.00 2.73
2820 3263 3.587797 TGTGAAGGAGCCTAAACTACG 57.412 47.619 0.00 0.00 0.00 3.51
2821 3264 3.159472 TGTGAAGGAGCCTAAACTACGA 58.841 45.455 0.00 0.00 0.00 3.43
2822 3265 3.575256 TGTGAAGGAGCCTAAACTACGAA 59.425 43.478 0.00 0.00 0.00 3.85
2823 3266 3.925299 GTGAAGGAGCCTAAACTACGAAC 59.075 47.826 0.00 0.00 0.00 3.95
2824 3267 2.935481 AGGAGCCTAAACTACGAACG 57.065 50.000 0.00 0.00 0.00 3.95
2825 3268 1.475682 AGGAGCCTAAACTACGAACGG 59.524 52.381 0.00 0.00 0.00 4.44
2826 3269 1.275505 GAGCCTAAACTACGAACGGC 58.724 55.000 0.00 0.00 37.80 5.68
2827 3270 0.604578 AGCCTAAACTACGAACGGCA 59.395 50.000 0.00 0.00 39.91 5.69
2828 3271 0.997196 GCCTAAACTACGAACGGCAG 59.003 55.000 0.00 0.00 37.48 4.85
2829 3272 1.636988 CCTAAACTACGAACGGCAGG 58.363 55.000 0.00 0.00 0.00 4.85
2830 3273 1.203052 CCTAAACTACGAACGGCAGGA 59.797 52.381 0.00 0.00 0.00 3.86
2831 3274 2.527100 CTAAACTACGAACGGCAGGAG 58.473 52.381 0.00 0.00 0.00 3.69
2832 3275 0.037605 AAACTACGAACGGCAGGAGG 60.038 55.000 0.00 0.00 0.00 4.30
2833 3276 0.896940 AACTACGAACGGCAGGAGGA 60.897 55.000 0.00 0.00 0.00 3.71
2834 3277 1.313812 ACTACGAACGGCAGGAGGAG 61.314 60.000 0.00 0.00 0.00 3.69
2835 3278 1.001764 TACGAACGGCAGGAGGAGA 60.002 57.895 0.00 0.00 0.00 3.71
2836 3279 0.609957 TACGAACGGCAGGAGGAGAA 60.610 55.000 0.00 0.00 0.00 2.87
2837 3280 1.446272 CGAACGGCAGGAGGAGAAC 60.446 63.158 0.00 0.00 0.00 3.01
2838 3281 1.878656 CGAACGGCAGGAGGAGAACT 61.879 60.000 0.00 0.00 0.00 3.01
2839 3282 0.108567 GAACGGCAGGAGGAGAACTC 60.109 60.000 0.00 0.00 45.84 3.01
2847 3290 3.534721 GAGGAGAACTCGGTTTGGG 57.465 57.895 0.00 0.00 36.29 4.12
2848 3291 0.036294 GAGGAGAACTCGGTTTGGGG 60.036 60.000 0.00 0.00 36.29 4.96
2849 3292 1.674651 GGAGAACTCGGTTTGGGGC 60.675 63.158 0.00 0.00 0.00 5.80
2850 3293 1.072505 GAGAACTCGGTTTGGGGCA 59.927 57.895 0.00 0.00 0.00 5.36
2851 3294 0.536460 GAGAACTCGGTTTGGGGCAA 60.536 55.000 0.00 0.00 0.00 4.52
2852 3295 0.822121 AGAACTCGGTTTGGGGCAAC 60.822 55.000 0.00 0.00 0.00 4.17
2853 3296 0.822121 GAACTCGGTTTGGGGCAACT 60.822 55.000 0.00 0.00 0.00 3.16
2854 3297 1.106944 AACTCGGTTTGGGGCAACTG 61.107 55.000 0.00 0.00 0.00 3.16
2855 3298 1.228124 CTCGGTTTGGGGCAACTGA 60.228 57.895 0.00 0.00 0.00 3.41
2856 3299 0.609131 CTCGGTTTGGGGCAACTGAT 60.609 55.000 0.00 0.00 0.00 2.90
2857 3300 0.178975 TCGGTTTGGGGCAACTGATT 60.179 50.000 0.00 0.00 0.00 2.57
2858 3301 0.678950 CGGTTTGGGGCAACTGATTT 59.321 50.000 0.00 0.00 0.00 2.17
2859 3302 1.336795 CGGTTTGGGGCAACTGATTTC 60.337 52.381 0.00 0.00 0.00 2.17
2860 3303 1.691434 GGTTTGGGGCAACTGATTTCA 59.309 47.619 0.00 0.00 0.00 2.69
2861 3304 2.302733 GGTTTGGGGCAACTGATTTCAT 59.697 45.455 0.00 0.00 0.00 2.57
2862 3305 3.244526 GGTTTGGGGCAACTGATTTCATT 60.245 43.478 0.00 0.00 0.00 2.57
2863 3306 3.681593 TTGGGGCAACTGATTTCATTG 57.318 42.857 0.00 0.00 0.00 2.82
2864 3307 2.886913 TGGGGCAACTGATTTCATTGA 58.113 42.857 0.00 0.00 0.00 2.57
2865 3308 3.443052 TGGGGCAACTGATTTCATTGAT 58.557 40.909 0.00 0.00 0.00 2.57
2866 3309 3.839490 TGGGGCAACTGATTTCATTGATT 59.161 39.130 0.00 0.00 0.00 2.57
2867 3310 4.186159 GGGGCAACTGATTTCATTGATTG 58.814 43.478 0.00 0.00 0.00 2.67
2868 3311 4.186159 GGGCAACTGATTTCATTGATTGG 58.814 43.478 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.759436 GCTAGGCAGGTAGGGCAGTA 60.759 60.000 0.00 0.00 35.46 2.74
1 2 2.066999 GCTAGGCAGGTAGGGCAGT 61.067 63.158 0.00 0.00 35.46 4.40
2 3 1.753368 GAGCTAGGCAGGTAGGGCAG 61.753 65.000 0.00 0.00 35.46 4.85
3 4 1.762460 GAGCTAGGCAGGTAGGGCA 60.762 63.158 0.00 0.00 35.46 5.36
4 5 1.338136 TTGAGCTAGGCAGGTAGGGC 61.338 60.000 0.00 0.00 30.99 5.19
5 6 0.755686 CTTGAGCTAGGCAGGTAGGG 59.244 60.000 0.00 0.00 30.99 3.53
6 7 1.781786 TCTTGAGCTAGGCAGGTAGG 58.218 55.000 0.00 0.00 30.99 3.18
7 8 3.196685 AGTTTCTTGAGCTAGGCAGGTAG 59.803 47.826 0.00 0.00 30.99 3.18
8 9 3.173965 AGTTTCTTGAGCTAGGCAGGTA 58.826 45.455 0.00 0.00 30.99 3.08
9 10 1.981495 AGTTTCTTGAGCTAGGCAGGT 59.019 47.619 0.00 0.00 34.43 4.00
10 11 2.777832 AGTTTCTTGAGCTAGGCAGG 57.222 50.000 0.00 0.00 0.00 4.85
11 12 3.620821 GCTTAGTTTCTTGAGCTAGGCAG 59.379 47.826 0.00 0.00 41.67 4.85
12 13 3.261897 AGCTTAGTTTCTTGAGCTAGGCA 59.738 43.478 14.94 0.00 43.56 4.75
13 14 3.867857 AGCTTAGTTTCTTGAGCTAGGC 58.132 45.455 0.00 0.00 43.21 3.93
14 15 8.499403 AAATTAGCTTAGTTTCTTGAGCTAGG 57.501 34.615 0.00 0.00 45.36 3.02
15 16 9.155975 TGAAATTAGCTTAGTTTCTTGAGCTAG 57.844 33.333 14.95 0.00 45.36 3.42
16 17 9.502091 TTGAAATTAGCTTAGTTTCTTGAGCTA 57.498 29.630 14.95 0.16 43.21 3.32
17 18 7.986085 TGAAATTAGCTTAGTTTCTTGAGCT 57.014 32.000 14.95 2.10 46.40 4.09
18 19 9.070149 CATTGAAATTAGCTTAGTTTCTTGAGC 57.930 33.333 14.95 0.00 35.96 4.26
19 20 9.070149 GCATTGAAATTAGCTTAGTTTCTTGAG 57.930 33.333 14.95 7.38 35.96 3.02
20 21 8.575589 TGCATTGAAATTAGCTTAGTTTCTTGA 58.424 29.630 14.95 6.12 35.96 3.02
21 22 8.746922 TGCATTGAAATTAGCTTAGTTTCTTG 57.253 30.769 14.95 13.39 35.96 3.02
22 23 8.796475 TCTGCATTGAAATTAGCTTAGTTTCTT 58.204 29.630 14.95 4.97 35.96 2.52
23 24 8.340618 TCTGCATTGAAATTAGCTTAGTTTCT 57.659 30.769 14.95 0.00 35.96 2.52
24 25 8.970691 TTCTGCATTGAAATTAGCTTAGTTTC 57.029 30.769 0.00 1.20 35.65 2.78
25 26 9.762933 TTTTCTGCATTGAAATTAGCTTAGTTT 57.237 25.926 0.00 0.00 36.07 2.66
26 27 9.762933 TTTTTCTGCATTGAAATTAGCTTAGTT 57.237 25.926 0.00 0.00 36.07 2.24
27 28 9.933723 ATTTTTCTGCATTGAAATTAGCTTAGT 57.066 25.926 0.00 0.00 36.07 2.24
29 30 9.926158 TGATTTTTCTGCATTGAAATTAGCTTA 57.074 25.926 0.00 0.00 36.07 3.09
30 31 8.715088 GTGATTTTTCTGCATTGAAATTAGCTT 58.285 29.630 0.00 0.00 36.07 3.74
31 32 7.062605 CGTGATTTTTCTGCATTGAAATTAGCT 59.937 33.333 2.33 0.00 36.07 3.32
32 33 7.062138 TCGTGATTTTTCTGCATTGAAATTAGC 59.938 33.333 2.33 0.00 36.07 3.09
38 39 5.687770 TCTCGTGATTTTTCTGCATTGAA 57.312 34.783 0.00 0.00 0.00 2.69
41 42 5.503031 CGCTATCTCGTGATTTTTCTGCATT 60.503 40.000 5.15 0.00 34.32 3.56
55 56 2.627515 TGTACCCTACGCTATCTCGT 57.372 50.000 0.00 0.00 45.49 4.18
61 62 4.209538 TCTAGCATTTGTACCCTACGCTA 58.790 43.478 0.00 0.00 0.00 4.26
63 64 3.381949 CTCTAGCATTTGTACCCTACGC 58.618 50.000 0.00 0.00 0.00 4.42
65 66 4.141914 ACAGCTCTAGCATTTGTACCCTAC 60.142 45.833 4.54 0.00 45.16 3.18
68 69 3.118592 AGACAGCTCTAGCATTTGTACCC 60.119 47.826 4.54 0.00 45.16 3.69
73 74 3.118629 TGGGTAGACAGCTCTAGCATTTG 60.119 47.826 12.58 0.00 45.71 2.32
83 84 2.438800 ATAGACGTGGGTAGACAGCT 57.561 50.000 0.00 0.00 0.00 4.24
87 88 4.277672 TCTTGCATATAGACGTGGGTAGAC 59.722 45.833 0.00 0.00 0.00 2.59
95 96 7.039714 TGGACTGATAATCTTGCATATAGACGT 60.040 37.037 0.00 0.00 0.00 4.34
97 98 9.494271 TTTGGACTGATAATCTTGCATATAGAC 57.506 33.333 0.00 0.00 0.00 2.59
104 105 6.711277 AGTAGTTTGGACTGATAATCTTGCA 58.289 36.000 0.00 0.00 36.60 4.08
117 118 3.503800 AACCAAGGGAGTAGTTTGGAC 57.496 47.619 9.28 0.00 43.15 4.02
119 120 8.589701 ATTATAAAACCAAGGGAGTAGTTTGG 57.410 34.615 1.18 1.18 45.37 3.28
149 150 8.754230 ATAAGAGTGTACCGTTAAAAACTCTC 57.246 34.615 8.25 0.00 42.59 3.20
159 160 6.154445 CGCCATAATATAAGAGTGTACCGTT 58.846 40.000 0.00 0.00 0.00 4.44
162 163 7.958053 AAACGCCATAATATAAGAGTGTACC 57.042 36.000 0.00 0.00 0.00 3.34
189 190 7.594015 CGTCCCATAATATAACTGTGTACTGTC 59.406 40.741 0.00 0.00 0.00 3.51
199 201 5.019657 TCCCTCCGTCCCATAATATAACT 57.980 43.478 0.00 0.00 0.00 2.24
200 202 4.776308 ACTCCCTCCGTCCCATAATATAAC 59.224 45.833 0.00 0.00 0.00 1.89
214 216 4.548451 ACTAAAAAGGTTACTCCCTCCG 57.452 45.455 0.00 0.00 36.75 4.63
229 231 1.873698 AGCGCTGTCCGAAACTAAAA 58.126 45.000 10.39 0.00 40.02 1.52
240 242 1.357991 GCTCTTCTGGAAGCGCTGTC 61.358 60.000 12.58 10.95 43.59 3.51
252 254 2.425312 CACAGTGATAGTCGGCTCTTCT 59.575 50.000 0.00 0.00 0.00 2.85
287 289 2.488153 GCGCCCTTTACAACTCAGATTT 59.512 45.455 0.00 0.00 0.00 2.17
307 309 1.000938 CTGTCAAGCTCACCAAAAGGC 60.001 52.381 0.00 0.00 0.00 4.35
316 318 1.688735 AGTAGCACACTGTCAAGCTCA 59.311 47.619 1.96 0.00 38.47 4.26
322 325 1.257743 GAGGGAGTAGCACACTGTCA 58.742 55.000 0.00 0.00 37.72 3.58
334 337 3.790089 AGAATTTCAAACGGAGGGAGT 57.210 42.857 0.00 0.00 0.00 3.85
335 338 4.278419 ACAAAGAATTTCAAACGGAGGGAG 59.722 41.667 0.00 0.00 35.03 4.30
336 339 4.211920 ACAAAGAATTTCAAACGGAGGGA 58.788 39.130 0.00 0.00 35.03 4.20
337 340 4.546570 GACAAAGAATTTCAAACGGAGGG 58.453 43.478 0.00 0.00 35.03 4.30
338 341 4.219033 CGACAAAGAATTTCAAACGGAGG 58.781 43.478 0.00 0.00 35.03 4.30
339 342 3.664025 GCGACAAAGAATTTCAAACGGAG 59.336 43.478 0.00 0.00 35.03 4.63
340 343 3.623863 GCGACAAAGAATTTCAAACGGA 58.376 40.909 0.00 0.00 35.03 4.69
341 344 2.400408 CGCGACAAAGAATTTCAAACGG 59.600 45.455 0.00 0.00 35.03 4.44
342 345 2.400408 CCGCGACAAAGAATTTCAAACG 59.600 45.455 8.23 0.00 35.03 3.60
343 346 3.623863 TCCGCGACAAAGAATTTCAAAC 58.376 40.909 8.23 0.00 35.03 2.93
344 347 3.972950 TCCGCGACAAAGAATTTCAAA 57.027 38.095 8.23 0.00 35.03 2.69
345 348 3.972950 TTCCGCGACAAAGAATTTCAA 57.027 38.095 8.23 0.00 35.03 2.69
346 349 3.972950 TTTCCGCGACAAAGAATTTCA 57.027 38.095 8.23 0.00 35.03 2.69
347 350 3.608073 CCATTTCCGCGACAAAGAATTTC 59.392 43.478 8.23 0.00 35.03 2.17
348 351 3.254657 TCCATTTCCGCGACAAAGAATTT 59.745 39.130 8.23 0.00 40.26 1.82
349 352 2.817258 TCCATTTCCGCGACAAAGAATT 59.183 40.909 8.23 0.00 0.00 2.17
350 353 2.432444 TCCATTTCCGCGACAAAGAAT 58.568 42.857 8.23 0.00 0.00 2.40
351 354 1.885560 TCCATTTCCGCGACAAAGAA 58.114 45.000 8.23 0.00 0.00 2.52
352 355 1.737236 CATCCATTTCCGCGACAAAGA 59.263 47.619 8.23 1.35 0.00 2.52
353 356 1.468520 ACATCCATTTCCGCGACAAAG 59.531 47.619 8.23 0.00 0.00 2.77
354 357 1.529226 ACATCCATTTCCGCGACAAA 58.471 45.000 8.23 6.67 0.00 2.83
355 358 2.388310 TACATCCATTTCCGCGACAA 57.612 45.000 8.23 0.00 0.00 3.18
356 359 2.102420 AGATACATCCATTTCCGCGACA 59.898 45.455 8.23 0.00 0.00 4.35
357 360 2.755650 AGATACATCCATTTCCGCGAC 58.244 47.619 8.23 0.00 0.00 5.19
358 361 3.614150 GCTAGATACATCCATTTCCGCGA 60.614 47.826 8.23 0.00 0.00 5.87
359 362 2.668457 GCTAGATACATCCATTTCCGCG 59.332 50.000 0.00 0.00 0.00 6.46
360 363 3.664107 TGCTAGATACATCCATTTCCGC 58.336 45.455 0.00 0.00 0.00 5.54
361 364 4.093998 GCATGCTAGATACATCCATTTCCG 59.906 45.833 11.37 0.00 0.00 4.30
362 365 4.397417 GGCATGCTAGATACATCCATTTCC 59.603 45.833 18.92 0.00 0.00 3.13
363 366 5.005740 TGGCATGCTAGATACATCCATTTC 58.994 41.667 18.92 0.00 0.00 2.17
364 367 4.989277 TGGCATGCTAGATACATCCATTT 58.011 39.130 18.92 0.00 0.00 2.32
365 368 4.645863 TGGCATGCTAGATACATCCATT 57.354 40.909 18.92 0.00 0.00 3.16
366 369 4.857130 ATGGCATGCTAGATACATCCAT 57.143 40.909 18.92 5.30 33.94 3.41
367 370 4.566278 GGAATGGCATGCTAGATACATCCA 60.566 45.833 18.92 2.84 32.80 3.41
368 371 3.944015 GGAATGGCATGCTAGATACATCC 59.056 47.826 18.92 9.83 0.00 3.51
369 372 3.944015 GGGAATGGCATGCTAGATACATC 59.056 47.826 18.92 4.66 0.00 3.06
370 373 3.590630 AGGGAATGGCATGCTAGATACAT 59.409 43.478 18.92 8.35 0.00 2.29
371 374 2.981784 AGGGAATGGCATGCTAGATACA 59.018 45.455 18.92 6.05 0.00 2.29
372 375 3.244700 ACAGGGAATGGCATGCTAGATAC 60.245 47.826 18.92 5.45 0.00 2.24
373 376 2.981784 ACAGGGAATGGCATGCTAGATA 59.018 45.455 18.92 0.00 0.00 1.98
374 377 1.779092 ACAGGGAATGGCATGCTAGAT 59.221 47.619 18.92 4.58 0.00 1.98
375 378 1.216064 ACAGGGAATGGCATGCTAGA 58.784 50.000 18.92 2.09 0.00 2.43
376 379 1.679680 CAACAGGGAATGGCATGCTAG 59.320 52.381 18.92 0.45 0.00 3.42
377 380 1.284491 TCAACAGGGAATGGCATGCTA 59.716 47.619 18.92 12.99 0.00 3.49
378 381 0.040058 TCAACAGGGAATGGCATGCT 59.960 50.000 18.92 0.00 0.00 3.79
439 442 5.745312 TCAGACATAAAGAGGCAGAAAGA 57.255 39.130 0.00 0.00 0.00 2.52
522 525 2.288825 TGTTGATCGAACTCTGGGACAC 60.289 50.000 0.00 0.00 35.37 3.67
524 527 2.743636 TGTTGATCGAACTCTGGGAC 57.256 50.000 0.00 0.00 35.37 4.46
525 528 3.762407 TTTGTTGATCGAACTCTGGGA 57.238 42.857 0.00 0.00 35.37 4.37
536 555 9.298774 GGAGATGATTCAGAAATTTTGTTGATC 57.701 33.333 0.00 0.00 0.00 2.92
537 556 8.809066 TGGAGATGATTCAGAAATTTTGTTGAT 58.191 29.630 0.00 0.00 0.00 2.57
538 557 8.180706 TGGAGATGATTCAGAAATTTTGTTGA 57.819 30.769 0.00 0.00 0.00 3.18
539 558 8.821147 TTGGAGATGATTCAGAAATTTTGTTG 57.179 30.769 0.00 0.00 0.00 3.33
540 559 9.835389 TTTTGGAGATGATTCAGAAATTTTGTT 57.165 25.926 0.00 0.00 0.00 2.83
542 561 8.440833 GCTTTTGGAGATGATTCAGAAATTTTG 58.559 33.333 0.00 0.00 0.00 2.44
544 563 7.673180 TGCTTTTGGAGATGATTCAGAAATTT 58.327 30.769 0.00 0.00 0.00 1.82
546 565 6.845758 TGCTTTTGGAGATGATTCAGAAAT 57.154 33.333 0.00 0.00 0.00 2.17
556 575 3.924686 GCAGACAAATGCTTTTGGAGATG 59.075 43.478 24.08 17.61 45.34 2.90
601 628 3.181511 CGTTAAATTGCTCATCCGCTTCA 60.182 43.478 0.00 0.00 0.00 3.02
613 640 5.795441 GTCTCTGAATTCACCGTTAAATTGC 59.205 40.000 3.38 0.00 0.00 3.56
616 643 5.643777 CCTGTCTCTGAATTCACCGTTAAAT 59.356 40.000 3.38 0.00 0.00 1.40
619 646 3.830178 TCCTGTCTCTGAATTCACCGTTA 59.170 43.478 3.38 0.00 0.00 3.18
623 650 4.187694 GACATCCTGTCTCTGAATTCACC 58.812 47.826 3.38 0.00 43.73 4.02
639 666 6.314784 CGTCTTTTCCAAGTAATTGACATCC 58.685 40.000 4.10 0.00 0.00 3.51
647 674 2.224917 TGGCCCGTCTTTTCCAAGTAAT 60.225 45.455 0.00 0.00 0.00 1.89
755 788 8.677148 TTATTGAATTATTAGTGCTCCACTCC 57.323 34.615 0.48 0.00 41.21 3.85
756 789 8.286097 GCTTATTGAATTATTAGTGCTCCACTC 58.714 37.037 0.48 0.00 41.21 3.51
758 791 7.857885 GTGCTTATTGAATTATTAGTGCTCCAC 59.142 37.037 0.00 0.00 34.10 4.02
759 792 7.013274 GGTGCTTATTGAATTATTAGTGCTCCA 59.987 37.037 0.00 0.00 32.69 3.86
801 834 2.865343 ATCAAATTAGCAGCAGCAGC 57.135 45.000 3.17 0.46 45.49 5.25
802 835 3.129813 TGGAATCAAATTAGCAGCAGCAG 59.870 43.478 3.17 0.00 45.49 4.24
803 836 3.090790 TGGAATCAAATTAGCAGCAGCA 58.909 40.909 3.17 0.00 45.49 4.41
937 970 4.760220 GGGAGGGAGGGAGGGCAA 62.760 72.222 0.00 0.00 0.00 4.52
949 982 0.400525 TATGGAGGCTTGGAGGGAGG 60.401 60.000 0.00 0.00 0.00 4.30
950 983 1.739750 ATATGGAGGCTTGGAGGGAG 58.260 55.000 0.00 0.00 0.00 4.30
951 984 3.585077 ATATATGGAGGCTTGGAGGGA 57.415 47.619 0.00 0.00 0.00 4.20
952 985 4.971282 TGATATATATGGAGGCTTGGAGGG 59.029 45.833 0.00 0.00 0.00 4.30
953 986 6.352516 GTTGATATATATGGAGGCTTGGAGG 58.647 44.000 0.00 0.00 0.00 4.30
954 987 6.070021 TGGTTGATATATATGGAGGCTTGGAG 60.070 42.308 0.00 0.00 0.00 3.86
955 988 5.790096 TGGTTGATATATATGGAGGCTTGGA 59.210 40.000 0.00 0.00 0.00 3.53
956 989 6.065976 TGGTTGATATATATGGAGGCTTGG 57.934 41.667 0.00 0.00 0.00 3.61
1029 1065 2.041405 GTGGAGGAGGAGGAGGGG 60.041 72.222 0.00 0.00 0.00 4.79
1030 1066 0.980231 CAAGTGGAGGAGGAGGAGGG 60.980 65.000 0.00 0.00 0.00 4.30
1031 1067 0.252467 ACAAGTGGAGGAGGAGGAGG 60.252 60.000 0.00 0.00 0.00 4.30
1032 1068 2.104170 GTACAAGTGGAGGAGGAGGAG 58.896 57.143 0.00 0.00 0.00 3.69
1033 1069 1.273098 GGTACAAGTGGAGGAGGAGGA 60.273 57.143 0.00 0.00 0.00 3.71
1034 1070 1.196012 GGTACAAGTGGAGGAGGAGG 58.804 60.000 0.00 0.00 0.00 4.30
1035 1071 1.196012 GGGTACAAGTGGAGGAGGAG 58.804 60.000 0.00 0.00 0.00 3.69
1036 1072 0.613853 CGGGTACAAGTGGAGGAGGA 60.614 60.000 0.00 0.00 0.00 3.71
1037 1073 0.613853 TCGGGTACAAGTGGAGGAGG 60.614 60.000 0.00 0.00 0.00 4.30
1551 1596 2.743636 CGGCCATCGGTATTCAGTAT 57.256 50.000 2.24 0.00 34.75 2.12
1620 1672 0.888736 CAACGGGGCTGTGAATGTGA 60.889 55.000 0.00 0.00 0.00 3.58
1621 1673 1.580942 CAACGGGGCTGTGAATGTG 59.419 57.895 0.00 0.00 0.00 3.21
1622 1674 2.268076 GCAACGGGGCTGTGAATGT 61.268 57.895 0.00 0.00 0.00 2.71
1623 1675 2.568090 GCAACGGGGCTGTGAATG 59.432 61.111 0.00 0.00 0.00 2.67
1624 1676 2.676471 GGCAACGGGGCTGTGAAT 60.676 61.111 0.58 0.00 39.42 2.57
1782 1839 7.229506 GGCAAGGATAAATACTTAGAATGCAGT 59.770 37.037 0.00 0.00 27.57 4.40
1810 1867 6.925165 CGTAACCACAACGGGAGTATATATTT 59.075 38.462 0.00 0.00 46.69 1.40
1823 2150 6.013085 CAGATTATGTTTCGTAACCACAACG 58.987 40.000 2.26 0.00 41.64 4.10
1913 2240 0.737715 ACAATCGAGACGCCAAGAGC 60.738 55.000 0.00 0.00 38.52 4.09
1914 2241 2.159366 AGTACAATCGAGACGCCAAGAG 60.159 50.000 0.00 0.00 0.00 2.85
1915 2242 1.816835 AGTACAATCGAGACGCCAAGA 59.183 47.619 0.00 0.00 0.00 3.02
1916 2243 2.186076 GAGTACAATCGAGACGCCAAG 58.814 52.381 0.00 0.00 0.00 3.61
1957 2288 7.554118 TCTTCTTCTTCTGTTTGAGAACAATGT 59.446 33.333 0.00 0.00 44.65 2.71
1962 2293 7.278868 TGTCTTCTTCTTCTTCTGTTTGAGAAC 59.721 37.037 0.00 0.00 35.64 3.01
1971 2302 5.236282 TCATGCTGTCTTCTTCTTCTTCTG 58.764 41.667 0.00 0.00 0.00 3.02
2022 2382 1.462928 CCACCTAAAAGCCACCCCA 59.537 57.895 0.00 0.00 0.00 4.96
2025 2385 1.250840 CCAGCCACCTAAAAGCCACC 61.251 60.000 0.00 0.00 0.00 4.61
2047 2407 1.207791 TCCTCAGCAGGAAGGAATCC 58.792 55.000 0.00 0.00 46.84 3.01
2062 2422 2.099405 AGCTCACTTCTACAGCTCCTC 58.901 52.381 0.00 0.00 39.37 3.71
2096 2456 0.178767 AGCCTCGACTATGCATTGCA 59.821 50.000 14.72 14.72 44.86 4.08
2097 2457 0.585357 CAGCCTCGACTATGCATTGC 59.415 55.000 3.54 0.46 0.00 3.56
2098 2458 1.224075 CCAGCCTCGACTATGCATTG 58.776 55.000 3.54 5.32 0.00 2.82
2099 2459 0.533755 GCCAGCCTCGACTATGCATT 60.534 55.000 3.54 0.00 0.00 3.56
2123 2483 2.039974 CAAGGTGGCACATGCGCTA 61.040 57.895 20.82 0.00 44.52 4.26
2124 2484 3.367743 CAAGGTGGCACATGCGCT 61.368 61.111 20.82 3.54 44.52 5.92
2273 2638 0.464554 GAGGGGAATTGAAGGAGGCG 60.465 60.000 0.00 0.00 0.00 5.52
2274 2639 0.106469 GGAGGGGAATTGAAGGAGGC 60.106 60.000 0.00 0.00 0.00 4.70
2275 2640 1.298953 TGGAGGGGAATTGAAGGAGG 58.701 55.000 0.00 0.00 0.00 4.30
2492 2925 2.081425 CTCTCGCTCCTCCGGGAATG 62.081 65.000 0.00 0.00 41.69 2.67
2501 2937 2.438795 GACCGTCCTCTCGCTCCT 60.439 66.667 0.00 0.00 0.00 3.69
2532 2968 2.150051 ATCCTCGATCCCCAAGCCC 61.150 63.158 0.00 0.00 0.00 5.19
2534 2970 0.181350 AACATCCTCGATCCCCAAGC 59.819 55.000 0.00 0.00 0.00 4.01
2535 2971 1.959042 CAACATCCTCGATCCCCAAG 58.041 55.000 0.00 0.00 0.00 3.61
2537 2974 1.271127 TGCAACATCCTCGATCCCCA 61.271 55.000 0.00 0.00 0.00 4.96
2563 3000 1.528076 ATTTGCCACACGACCTGCA 60.528 52.632 0.00 0.00 0.00 4.41
2564 3001 1.081242 CATTTGCCACACGACCTGC 60.081 57.895 0.00 0.00 0.00 4.85
2565 3002 0.238289 GACATTTGCCACACGACCTG 59.762 55.000 0.00 0.00 0.00 4.00
2566 3003 0.179032 TGACATTTGCCACACGACCT 60.179 50.000 0.00 0.00 0.00 3.85
2567 3004 0.665835 TTGACATTTGCCACACGACC 59.334 50.000 0.00 0.00 0.00 4.79
2610 3047 1.373999 GTCAAGTCTGCAGCGCTCT 60.374 57.895 7.13 0.00 0.00 4.09
2620 3057 2.092968 TGCACACTCCTTTGTCAAGTCT 60.093 45.455 0.00 0.00 0.00 3.24
2629 3066 1.242076 GAGCACATGCACACTCCTTT 58.758 50.000 6.64 0.00 45.16 3.11
2663 3106 3.050275 GACGACCCTGCCACTTGC 61.050 66.667 0.00 0.00 41.77 4.01
2664 3107 2.358737 GGACGACCCTGCCACTTG 60.359 66.667 0.00 0.00 0.00 3.16
2665 3108 4.003788 CGGACGACCCTGCCACTT 62.004 66.667 0.00 0.00 0.00 3.16
2731 3174 3.157087 CCCATAGCCCATGTCCAATTAC 58.843 50.000 0.00 0.00 32.21 1.89
2733 3176 1.758841 GCCCATAGCCCATGTCCAATT 60.759 52.381 0.00 0.00 34.35 2.32
2784 3227 0.169672 CACATCTTTCGGGCTGCAAG 59.830 55.000 0.50 0.00 0.00 4.01
2802 3245 3.366679 CGTTCGTAGTTTAGGCTCCTTCA 60.367 47.826 0.00 0.00 0.00 3.02
2803 3246 3.177487 CGTTCGTAGTTTAGGCTCCTTC 58.823 50.000 0.00 0.00 0.00 3.46
2804 3247 2.094338 CCGTTCGTAGTTTAGGCTCCTT 60.094 50.000 0.00 0.00 0.00 3.36
2805 3248 1.475682 CCGTTCGTAGTTTAGGCTCCT 59.524 52.381 0.00 0.00 0.00 3.69
2806 3249 1.918595 CCGTTCGTAGTTTAGGCTCC 58.081 55.000 0.00 0.00 0.00 4.70
2807 3250 1.275505 GCCGTTCGTAGTTTAGGCTC 58.724 55.000 0.00 0.00 41.21 4.70
2808 3251 0.604578 TGCCGTTCGTAGTTTAGGCT 59.395 50.000 5.85 0.00 44.42 4.58
2809 3252 0.997196 CTGCCGTTCGTAGTTTAGGC 59.003 55.000 0.00 0.00 44.38 3.93
2810 3253 1.203052 TCCTGCCGTTCGTAGTTTAGG 59.797 52.381 0.00 0.00 0.00 2.69
2811 3254 2.527100 CTCCTGCCGTTCGTAGTTTAG 58.473 52.381 0.00 0.00 0.00 1.85
2812 3255 1.203052 CCTCCTGCCGTTCGTAGTTTA 59.797 52.381 0.00 0.00 0.00 2.01
2813 3256 0.037605 CCTCCTGCCGTTCGTAGTTT 60.038 55.000 0.00 0.00 0.00 2.66
2814 3257 0.896940 TCCTCCTGCCGTTCGTAGTT 60.897 55.000 0.00 0.00 0.00 2.24
2815 3258 1.303888 TCCTCCTGCCGTTCGTAGT 60.304 57.895 0.00 0.00 0.00 2.73
2816 3259 1.030488 TCTCCTCCTGCCGTTCGTAG 61.030 60.000 0.00 0.00 0.00 3.51
2817 3260 0.609957 TTCTCCTCCTGCCGTTCGTA 60.610 55.000 0.00 0.00 0.00 3.43
2818 3261 1.906824 TTCTCCTCCTGCCGTTCGT 60.907 57.895 0.00 0.00 0.00 3.85
2819 3262 1.446272 GTTCTCCTCCTGCCGTTCG 60.446 63.158 0.00 0.00 0.00 3.95
2820 3263 0.108567 GAGTTCTCCTCCTGCCGTTC 60.109 60.000 0.00 0.00 33.79 3.95
2821 3264 1.878656 CGAGTTCTCCTCCTGCCGTT 61.879 60.000 0.00 0.00 36.82 4.44
2822 3265 2.344203 CGAGTTCTCCTCCTGCCGT 61.344 63.158 0.00 0.00 36.82 5.68
2823 3266 2.492090 CGAGTTCTCCTCCTGCCG 59.508 66.667 0.00 0.00 36.82 5.69
2824 3267 1.545706 AACCGAGTTCTCCTCCTGCC 61.546 60.000 0.00 0.00 36.82 4.85
2825 3268 0.321996 AAACCGAGTTCTCCTCCTGC 59.678 55.000 0.00 0.00 36.82 4.85
2826 3269 1.338200 CCAAACCGAGTTCTCCTCCTG 60.338 57.143 0.00 0.00 36.82 3.86
2827 3270 0.977395 CCAAACCGAGTTCTCCTCCT 59.023 55.000 0.00 0.00 36.82 3.69
2828 3271 0.036294 CCCAAACCGAGTTCTCCTCC 60.036 60.000 0.00 0.00 36.82 4.30
2829 3272 0.036294 CCCCAAACCGAGTTCTCCTC 60.036 60.000 0.00 0.00 36.80 3.71
2830 3273 2.067197 CCCCAAACCGAGTTCTCCT 58.933 57.895 0.00 0.00 0.00 3.69
2831 3274 1.674651 GCCCCAAACCGAGTTCTCC 60.675 63.158 0.00 0.00 0.00 3.71
2832 3275 0.536460 TTGCCCCAAACCGAGTTCTC 60.536 55.000 0.00 0.00 0.00 2.87
2833 3276 0.822121 GTTGCCCCAAACCGAGTTCT 60.822 55.000 0.00 0.00 0.00 3.01
2834 3277 0.822121 AGTTGCCCCAAACCGAGTTC 60.822 55.000 0.00 0.00 0.00 3.01
2835 3278 1.106944 CAGTTGCCCCAAACCGAGTT 61.107 55.000 0.00 0.00 0.00 3.01
2836 3279 1.528309 CAGTTGCCCCAAACCGAGT 60.528 57.895 0.00 0.00 0.00 4.18
2837 3280 0.609131 ATCAGTTGCCCCAAACCGAG 60.609 55.000 0.00 0.00 0.00 4.63
2838 3281 0.178975 AATCAGTTGCCCCAAACCGA 60.179 50.000 0.00 0.00 0.00 4.69
2839 3282 0.678950 AAATCAGTTGCCCCAAACCG 59.321 50.000 0.00 0.00 0.00 4.44
2840 3283 1.691434 TGAAATCAGTTGCCCCAAACC 59.309 47.619 0.00 0.00 0.00 3.27
2841 3284 3.683365 ATGAAATCAGTTGCCCCAAAC 57.317 42.857 0.00 0.00 0.00 2.93
2842 3285 3.645212 TCAATGAAATCAGTTGCCCCAAA 59.355 39.130 0.00 0.00 0.00 3.28
2843 3286 3.237746 TCAATGAAATCAGTTGCCCCAA 58.762 40.909 0.00 0.00 0.00 4.12
2844 3287 2.886913 TCAATGAAATCAGTTGCCCCA 58.113 42.857 0.00 0.00 0.00 4.96
2845 3288 4.186159 CAATCAATGAAATCAGTTGCCCC 58.814 43.478 0.00 0.00 0.00 5.80
2846 3289 4.186159 CCAATCAATGAAATCAGTTGCCC 58.814 43.478 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.