Multiple sequence alignment - TraesCS7B01G268400

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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 TraesCS7B01G268400 chr7B 100.000 3274 0 0 1 3274 491391165 491394438 0.000000e+00 6047.0
1 TraesCS7B01G268400 chr7B 90.123 81 4 2 1552 1632 491392595 491392671 5.780000e-18 102.0
2 TraesCS7B01G268400 chr7B 90.123 81 4 2 1431 1507 491392716 491392796 5.780000e-18 102.0
3 TraesCS7B01G268400 chr7B 84.810 79 9 3 1775 1853 46894807 46894882 3.500000e-10 76.8
4 TraesCS7B01G268400 chr7D 96.919 2824 66 10 464 3274 467990464 467993279 0.000000e+00 4713.0
5 TraesCS7B01G268400 chr7D 92.969 128 9 0 45 172 6484597 6484470 1.550000e-43 187.0
6 TraesCS7B01G268400 chr7D 85.616 146 17 1 173 318 467990322 467990463 2.040000e-32 150.0
7 TraesCS7B01G268400 chr7D 93.023 86 5 1 1547 1632 467991426 467991510 1.230000e-24 124.0
8 TraesCS7B01G268400 chr7A 93.238 843 35 2 464 1305 532685489 532684668 0.000000e+00 1221.0
9 TraesCS7B01G268400 chr7A 86.111 432 58 2 1854 2283 532679926 532679495 6.400000e-127 464.0
10 TraesCS7B01G268400 chr7A 92.593 135 9 1 161 295 532685640 532685507 3.330000e-45 193.0
11 TraesCS7B01G268400 chr7A 87.349 166 16 3 11 172 637172364 637172528 5.580000e-43 185.0
12 TraesCS7B01G268400 chr7A 76.404 178 27 5 1689 1852 536776117 536775941 7.530000e-12 82.4
13 TraesCS7B01G268400 chr7A 94.444 36 2 0 1689 1724 690204248 690204283 4.560000e-04 56.5
14 TraesCS7B01G268400 chr2D 86.986 730 78 8 575 1297 40803 40084 0.000000e+00 806.0
15 TraesCS7B01G268400 chr2D 91.241 137 8 4 46 180 565942948 565942814 2.010000e-42 183.0
16 TraesCS7B01G268400 chr2D 88.148 135 15 1 333 466 638561871 638561737 3.380000e-35 159.0
17 TraesCS7B01G268400 chr2B 86.245 727 85 10 575 1298 10992924 10992210 0.000000e+00 774.0
18 TraesCS7B01G268400 chr2B 92.366 131 9 1 42 172 715532040 715531911 5.580000e-43 185.0
19 TraesCS7B01G268400 chr2B 90.441 136 13 0 38 173 4632108 4632243 2.600000e-41 180.0
20 TraesCS7B01G268400 chr2B 87.681 138 16 1 330 466 490480977 490481114 3.380000e-35 159.0
21 TraesCS7B01G268400 chr4B 92.366 131 10 0 43 173 626638044 626638174 1.550000e-43 187.0
22 TraesCS7B01G268400 chr4B 86.747 83 9 1 1775 1857 373979773 373979693 1.250000e-14 91.6
23 TraesCS7B01G268400 chr1B 92.969 128 9 0 45 172 571434298 571434425 1.550000e-43 187.0
24 TraesCS7B01G268400 chr1B 89.116 147 14 2 27 172 110625932 110625787 7.220000e-42 182.0
25 TraesCS7B01G268400 chr1B 87.500 80 7 3 1775 1853 8563664 8563741 4.500000e-14 89.8
26 TraesCS7B01G268400 chr1B 82.828 99 12 3 1763 1857 675952196 675952293 2.090000e-12 84.2
27 TraesCS7B01G268400 chr1B 97.297 37 0 1 11 47 432613508 432613473 9.810000e-06 62.1
28 TraesCS7B01G268400 chr1B 92.500 40 3 0 1 40 135249767 135249806 1.270000e-04 58.4
29 TraesCS7B01G268400 chr5D 90.000 140 12 2 38 176 565275234 565275096 2.600000e-41 180.0
30 TraesCS7B01G268400 chr5D 88.550 131 15 0 333 463 399959008 399958878 3.380000e-35 159.0
31 TraesCS7B01G268400 chr5D 97.368 38 0 1 11 48 385784282 385784246 2.730000e-06 63.9
32 TraesCS7B01G268400 chr6B 88.571 140 15 1 330 468 439350100 439350239 5.620000e-38 169.0
33 TraesCS7B01G268400 chr6B 87.407 135 16 1 333 466 191919563 191919429 1.570000e-33 154.0
34 TraesCS7B01G268400 chr6B 95.000 40 0 2 11 49 507462377 507462339 9.810000e-06 62.1
35 TraesCS7B01G268400 chr5B 88.889 135 14 1 333 466 523203444 523203310 7.270000e-37 165.0
36 TraesCS7B01G268400 chr5B 83.951 81 11 2 1774 1853 654926937 654927016 3.500000e-10 76.8
37 TraesCS7B01G268400 chr5B 92.500 40 3 0 1 40 632061715 632061754 1.270000e-04 58.4
38 TraesCS7B01G268400 chr3B 88.550 131 15 0 333 463 635215899 635215769 3.380000e-35 159.0
39 TraesCS7B01G268400 chr3B 95.000 40 1 1 11 49 169691926 169691965 9.810000e-06 62.1
40 TraesCS7B01G268400 chr2A 87.407 135 16 1 333 466 644076031 644075897 1.570000e-33 154.0
41 TraesCS7B01G268400 chr2A 87.313 134 17 0 330 463 661576571 661576704 1.570000e-33 154.0
42 TraesCS7B01G268400 chr4D 87.654 81 6 3 1775 1853 8594010 8593932 1.250000e-14 91.6
43 TraesCS7B01G268400 chr3A 85.882 85 8 4 1775 1857 46569133 46569215 1.620000e-13 87.9
44 TraesCS7B01G268400 chr3A 97.368 38 1 0 10 47 116517790 116517753 7.580000e-07 65.8
45 TraesCS7B01G268400 chr1A 86.076 79 10 1 1776 1853 9969951 9969873 2.090000e-12 84.2
46 TraesCS7B01G268400 chr4A 94.444 36 2 0 1689 1724 696105137 696105102 4.560000e-04 56.5
47 TraesCS7B01G268400 chr5A 100.000 29 0 0 1696 1724 687153697 687153725 2.000000e-03 54.7


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 TraesCS7B01G268400 chr7B 491391165 491394438 3273 False 2083.666667 6047 93.415333 1 3274 3 chr7B.!!$F2 3273
1 TraesCS7B01G268400 chr7D 467990322 467993279 2957 False 1662.333333 4713 91.852667 173 3274 3 chr7D.!!$F1 3101
2 TraesCS7B01G268400 chr7A 532684668 532685640 972 True 707.000000 1221 92.915500 161 1305 2 chr7A.!!$R3 1144
3 TraesCS7B01G268400 chr2D 40084 40803 719 True 806.000000 806 86.986000 575 1297 1 chr2D.!!$R1 722
4 TraesCS7B01G268400 chr2B 10992210 10992924 714 True 774.000000 774 86.245000 575 1298 1 chr2B.!!$R1 723

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
402 403 0.044855 ACCCTCCTTGCCTGGATACT 59.955 55.0 0.0 0.0 35.3 2.12 F
434 435 0.178944 AAGCCCCCAACTAACCCAAC 60.179 55.0 0.0 0.0 0.0 3.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 2163 1.051556 ATCCCCTTCTCCTTCTCGCC 61.052 60.000 0.00 0.0 0.0 5.54 R
2390 2402 1.226491 TCGGCGAGCGCTTTACTAC 60.226 57.895 13.26 0.0 41.6 2.73 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
33 34 9.512435 TCGAAAGACTTATATTTAAGAACGGAG 57.488 33.333 9.58 0.00 38.56 4.63
34 35 8.753175 CGAAAGACTTATATTTAAGAACGGAGG 58.247 37.037 9.58 0.00 38.56 4.30
35 36 8.959705 AAAGACTTATATTTAAGAACGGAGGG 57.040 34.615 9.58 0.00 38.56 4.30
36 37 7.909485 AGACTTATATTTAAGAACGGAGGGA 57.091 36.000 9.58 0.00 38.56 4.20
37 38 7.953752 AGACTTATATTTAAGAACGGAGGGAG 58.046 38.462 9.58 0.00 38.56 4.30
38 39 7.564292 AGACTTATATTTAAGAACGGAGGGAGT 59.436 37.037 9.58 0.00 38.56 3.85
39 40 8.773033 ACTTATATTTAAGAACGGAGGGAGTA 57.227 34.615 9.58 0.00 38.56 2.59
40 41 8.637099 ACTTATATTTAAGAACGGAGGGAGTAC 58.363 37.037 9.58 0.00 38.56 2.73
41 42 8.773033 TTATATTTAAGAACGGAGGGAGTACT 57.227 34.615 0.00 0.00 0.00 2.73
42 43 7.672122 ATATTTAAGAACGGAGGGAGTACTT 57.328 36.000 0.00 0.00 0.00 2.24
43 44 8.773033 ATATTTAAGAACGGAGGGAGTACTTA 57.227 34.615 0.00 0.00 0.00 2.24
44 45 5.904362 TTAAGAACGGAGGGAGTACTTAC 57.096 43.478 0.00 0.00 0.00 2.34
45 46 3.735720 AGAACGGAGGGAGTACTTACT 57.264 47.619 0.00 0.00 39.71 2.24
46 47 4.851639 AGAACGGAGGGAGTACTTACTA 57.148 45.455 0.00 0.00 36.50 1.82
47 48 4.522114 AGAACGGAGGGAGTACTTACTAC 58.478 47.826 0.00 0.00 36.50 2.73
48 49 4.227073 AGAACGGAGGGAGTACTTACTACT 59.773 45.833 0.00 0.00 37.32 2.57
58 59 6.638096 GAGTACTTACTACTCCTTCCATCC 57.362 45.833 0.00 0.00 44.14 3.51
59 60 5.456779 AGTACTTACTACTCCTTCCATCCC 58.543 45.833 0.00 0.00 34.13 3.85
60 61 4.348020 ACTTACTACTCCTTCCATCCCA 57.652 45.455 0.00 0.00 0.00 4.37
61 62 4.695606 ACTTACTACTCCTTCCATCCCAA 58.304 43.478 0.00 0.00 0.00 4.12
62 63 5.098663 ACTTACTACTCCTTCCATCCCAAA 58.901 41.667 0.00 0.00 0.00 3.28
63 64 5.550403 ACTTACTACTCCTTCCATCCCAAAA 59.450 40.000 0.00 0.00 0.00 2.44
64 65 6.217693 ACTTACTACTCCTTCCATCCCAAAAT 59.782 38.462 0.00 0.00 0.00 1.82
65 66 5.536497 ACTACTCCTTCCATCCCAAAATT 57.464 39.130 0.00 0.00 0.00 1.82
66 67 5.510430 ACTACTCCTTCCATCCCAAAATTC 58.490 41.667 0.00 0.00 0.00 2.17
67 68 4.682021 ACTCCTTCCATCCCAAAATTCT 57.318 40.909 0.00 0.00 0.00 2.40
68 69 5.015813 ACTCCTTCCATCCCAAAATTCTT 57.984 39.130 0.00 0.00 0.00 2.52
69 70 4.774200 ACTCCTTCCATCCCAAAATTCTTG 59.226 41.667 0.00 0.00 0.00 3.02
70 71 4.750941 TCCTTCCATCCCAAAATTCTTGT 58.249 39.130 0.00 0.00 0.00 3.16
71 72 4.772100 TCCTTCCATCCCAAAATTCTTGTC 59.228 41.667 0.00 0.00 0.00 3.18
72 73 4.774200 CCTTCCATCCCAAAATTCTTGTCT 59.226 41.667 0.00 0.00 0.00 3.41
73 74 5.246883 CCTTCCATCCCAAAATTCTTGTCTT 59.753 40.000 0.00 0.00 0.00 3.01
74 75 6.437162 CCTTCCATCCCAAAATTCTTGTCTTA 59.563 38.462 0.00 0.00 0.00 2.10
75 76 7.363268 CCTTCCATCCCAAAATTCTTGTCTTAG 60.363 40.741 0.00 0.00 0.00 2.18
76 77 6.789268 TCCATCCCAAAATTCTTGTCTTAGA 58.211 36.000 0.00 0.00 0.00 2.10
77 78 7.413446 TCCATCCCAAAATTCTTGTCTTAGAT 58.587 34.615 0.00 0.00 0.00 1.98
78 79 7.895429 TCCATCCCAAAATTCTTGTCTTAGATT 59.105 33.333 0.00 0.00 0.00 2.40
79 80 9.189156 CCATCCCAAAATTCTTGTCTTAGATTA 57.811 33.333 0.00 0.00 0.00 1.75
81 82 9.981460 ATCCCAAAATTCTTGTCTTAGATTAGT 57.019 29.630 0.00 0.00 0.00 2.24
82 83 9.449719 TCCCAAAATTCTTGTCTTAGATTAGTC 57.550 33.333 0.00 0.00 0.00 2.59
83 84 9.454859 CCCAAAATTCTTGTCTTAGATTAGTCT 57.545 33.333 0.00 0.00 38.52 3.24
91 92 9.491675 TCTTGTCTTAGATTAGTCTAGATACGG 57.508 37.037 0.00 0.00 38.17 4.02
92 93 9.491675 CTTGTCTTAGATTAGTCTAGATACGGA 57.508 37.037 0.00 0.00 38.17 4.69
94 95 9.438228 TGTCTTAGATTAGTCTAGATACGGATG 57.562 37.037 0.00 0.00 38.17 3.51
95 96 9.439500 GTCTTAGATTAGTCTAGATACGGATGT 57.561 37.037 0.00 0.00 38.17 3.06
136 137 9.803315 TGTGACTTGATACATCTGTATTTAGAC 57.197 33.333 14.44 10.85 40.99 2.59
137 138 9.803315 GTGACTTGATACATCTGTATTTAGACA 57.197 33.333 14.44 12.43 40.99 3.41
167 168 7.576861 AAGACAAGAATTTTAAAACGGAGGA 57.423 32.000 1.97 0.00 0.00 3.71
220 221 1.805945 GCCTACACGTCGCTTGGAG 60.806 63.158 0.00 0.00 0.00 3.86
227 228 2.343758 GTCGCTTGGAGCCTGACA 59.656 61.111 3.97 0.00 38.18 3.58
230 231 2.758089 CGCTTGGAGCCTGACATGC 61.758 63.158 0.00 0.00 38.18 4.06
303 304 1.130054 AAGCAGGCAGGAGGTCTTCA 61.130 55.000 0.00 0.00 0.00 3.02
304 305 1.376553 GCAGGCAGGAGGTCTTCAC 60.377 63.158 0.00 0.00 0.00 3.18
318 319 1.151668 CTTCACCTTCTCCTGCGTTG 58.848 55.000 0.00 0.00 0.00 4.10
319 320 0.250295 TTCACCTTCTCCTGCGTTGG 60.250 55.000 0.00 0.00 0.00 3.77
320 321 1.672356 CACCTTCTCCTGCGTTGGG 60.672 63.158 0.00 0.00 0.00 4.12
321 322 2.147387 ACCTTCTCCTGCGTTGGGT 61.147 57.895 0.00 0.00 0.00 4.51
322 323 1.073199 CCTTCTCCTGCGTTGGGTT 59.927 57.895 0.00 0.00 0.00 4.11
323 324 0.323629 CCTTCTCCTGCGTTGGGTTA 59.676 55.000 0.00 0.00 0.00 2.85
324 325 1.676014 CCTTCTCCTGCGTTGGGTTAG 60.676 57.143 0.00 0.00 0.00 2.34
325 326 1.275291 CTTCTCCTGCGTTGGGTTAGA 59.725 52.381 0.00 0.00 0.00 2.10
326 327 1.568504 TCTCCTGCGTTGGGTTAGAT 58.431 50.000 0.00 0.00 0.00 1.98
327 328 1.207089 TCTCCTGCGTTGGGTTAGATG 59.793 52.381 0.00 0.00 0.00 2.90
328 329 0.251916 TCCTGCGTTGGGTTAGATGG 59.748 55.000 0.00 0.00 0.00 3.51
329 330 0.251916 CCTGCGTTGGGTTAGATGGA 59.748 55.000 0.00 0.00 0.00 3.41
330 331 1.339631 CCTGCGTTGGGTTAGATGGAA 60.340 52.381 0.00 0.00 0.00 3.53
331 332 1.737793 CTGCGTTGGGTTAGATGGAAC 59.262 52.381 0.00 0.00 0.00 3.62
332 333 1.349688 TGCGTTGGGTTAGATGGAACT 59.650 47.619 0.00 0.00 0.00 3.01
333 334 2.568062 TGCGTTGGGTTAGATGGAACTA 59.432 45.455 0.00 0.00 0.00 2.24
334 335 3.008157 TGCGTTGGGTTAGATGGAACTAA 59.992 43.478 0.00 0.00 0.00 2.24
335 336 3.621715 GCGTTGGGTTAGATGGAACTAAG 59.378 47.826 0.00 0.00 33.79 2.18
336 337 3.621715 CGTTGGGTTAGATGGAACTAAGC 59.378 47.826 0.00 0.00 44.77 3.09
337 338 4.585879 GTTGGGTTAGATGGAACTAAGCA 58.414 43.478 15.79 4.04 46.23 3.91
338 339 5.193679 GTTGGGTTAGATGGAACTAAGCAT 58.806 41.667 15.79 0.00 46.23 3.79
339 340 5.036117 TGGGTTAGATGGAACTAAGCATC 57.964 43.478 15.79 0.00 46.23 3.91
340 341 4.721776 TGGGTTAGATGGAACTAAGCATCT 59.278 41.667 15.79 0.00 46.23 2.90
341 342 5.163301 TGGGTTAGATGGAACTAAGCATCTC 60.163 44.000 15.79 3.66 46.23 2.75
342 343 5.071115 GGGTTAGATGGAACTAAGCATCTCT 59.929 44.000 15.79 0.00 46.23 3.10
343 344 6.220201 GGTTAGATGGAACTAAGCATCTCTC 58.780 44.000 0.00 0.00 44.82 3.20
344 345 4.953940 AGATGGAACTAAGCATCTCTCC 57.046 45.455 0.00 0.00 29.28 3.71
345 346 4.293494 AGATGGAACTAAGCATCTCTCCA 58.707 43.478 0.00 0.09 37.37 3.86
346 347 3.895232 TGGAACTAAGCATCTCTCCAC 57.105 47.619 0.00 0.00 0.00 4.02
347 348 2.501723 TGGAACTAAGCATCTCTCCACC 59.498 50.000 0.00 0.00 0.00 4.61
348 349 2.482142 GGAACTAAGCATCTCTCCACCG 60.482 54.545 0.00 0.00 0.00 4.94
349 350 1.115467 ACTAAGCATCTCTCCACCGG 58.885 55.000 0.00 0.00 0.00 5.28
350 351 1.115467 CTAAGCATCTCTCCACCGGT 58.885 55.000 0.00 0.00 0.00 5.28
351 352 2.307768 CTAAGCATCTCTCCACCGGTA 58.692 52.381 6.87 0.00 0.00 4.02
352 353 1.794714 AAGCATCTCTCCACCGGTAT 58.205 50.000 6.87 0.00 0.00 2.73
353 354 2.677542 AGCATCTCTCCACCGGTATA 57.322 50.000 6.87 0.00 0.00 1.47
354 355 2.520069 AGCATCTCTCCACCGGTATAG 58.480 52.381 6.87 8.04 0.00 1.31
355 356 2.158445 AGCATCTCTCCACCGGTATAGT 60.158 50.000 6.87 0.00 0.00 2.12
356 357 2.628657 GCATCTCTCCACCGGTATAGTT 59.371 50.000 6.87 0.00 0.00 2.24
357 358 3.553096 GCATCTCTCCACCGGTATAGTTG 60.553 52.174 6.87 8.81 0.00 3.16
358 359 2.662866 TCTCTCCACCGGTATAGTTGG 58.337 52.381 6.87 2.78 0.00 3.77
359 360 2.242965 TCTCTCCACCGGTATAGTTGGA 59.757 50.000 6.87 8.07 0.00 3.53
360 361 3.117246 TCTCTCCACCGGTATAGTTGGAT 60.117 47.826 6.87 0.00 0.00 3.41
361 362 3.641906 CTCTCCACCGGTATAGTTGGATT 59.358 47.826 6.87 0.00 0.00 3.01
362 363 4.806892 TCTCCACCGGTATAGTTGGATTA 58.193 43.478 6.87 0.00 0.00 1.75
363 364 4.831155 TCTCCACCGGTATAGTTGGATTAG 59.169 45.833 6.87 0.00 0.00 1.73
364 365 4.806892 TCCACCGGTATAGTTGGATTAGA 58.193 43.478 6.87 0.00 0.00 2.10
365 366 5.399991 TCCACCGGTATAGTTGGATTAGAT 58.600 41.667 6.87 0.00 0.00 1.98
366 367 5.245301 TCCACCGGTATAGTTGGATTAGATG 59.755 44.000 6.87 0.00 0.00 2.90
367 368 5.245301 CCACCGGTATAGTTGGATTAGATGA 59.755 44.000 6.87 0.00 0.00 2.92
368 369 6.239487 CCACCGGTATAGTTGGATTAGATGAA 60.239 42.308 6.87 0.00 0.00 2.57
369 370 7.214381 CACCGGTATAGTTGGATTAGATGAAA 58.786 38.462 6.87 0.00 0.00 2.69
370 371 7.170998 CACCGGTATAGTTGGATTAGATGAAAC 59.829 40.741 6.87 0.00 0.00 2.78
371 372 7.070821 ACCGGTATAGTTGGATTAGATGAAACT 59.929 37.037 4.49 0.00 35.39 2.66
372 373 8.582437 CCGGTATAGTTGGATTAGATGAAACTA 58.418 37.037 0.00 0.00 37.64 2.24
373 374 9.976511 CGGTATAGTTGGATTAGATGAAACTAA 57.023 33.333 0.00 0.00 37.02 2.24
386 387 7.939784 AGATGAAACTAATCCACTTTAACCC 57.060 36.000 0.00 0.00 0.00 4.11
387 388 7.699878 AGATGAAACTAATCCACTTTAACCCT 58.300 34.615 0.00 0.00 0.00 4.34
388 389 7.829706 AGATGAAACTAATCCACTTTAACCCTC 59.170 37.037 0.00 0.00 0.00 4.30
389 390 6.243148 TGAAACTAATCCACTTTAACCCTCC 58.757 40.000 0.00 0.00 0.00 4.30
390 391 6.045106 TGAAACTAATCCACTTTAACCCTCCT 59.955 38.462 0.00 0.00 0.00 3.69
391 392 6.464530 AACTAATCCACTTTAACCCTCCTT 57.535 37.500 0.00 0.00 0.00 3.36
392 393 5.816682 ACTAATCCACTTTAACCCTCCTTG 58.183 41.667 0.00 0.00 0.00 3.61
393 394 2.579410 TCCACTTTAACCCTCCTTGC 57.421 50.000 0.00 0.00 0.00 4.01
394 395 1.074889 TCCACTTTAACCCTCCTTGCC 59.925 52.381 0.00 0.00 0.00 4.52
395 396 1.075536 CCACTTTAACCCTCCTTGCCT 59.924 52.381 0.00 0.00 0.00 4.75
396 397 2.162681 CACTTTAACCCTCCTTGCCTG 58.837 52.381 0.00 0.00 0.00 4.85
397 398 1.075536 ACTTTAACCCTCCTTGCCTGG 59.924 52.381 0.00 0.00 0.00 4.45
398 399 1.354368 CTTTAACCCTCCTTGCCTGGA 59.646 52.381 0.00 0.00 34.52 3.86
399 400 1.681229 TTAACCCTCCTTGCCTGGAT 58.319 50.000 0.00 0.00 35.30 3.41
400 401 2.579624 TAACCCTCCTTGCCTGGATA 57.420 50.000 0.00 0.00 35.30 2.59
401 402 0.919710 AACCCTCCTTGCCTGGATAC 59.080 55.000 0.00 0.00 35.30 2.24
402 403 0.044855 ACCCTCCTTGCCTGGATACT 59.955 55.000 0.00 0.00 35.30 2.12
403 404 1.216990 CCCTCCTTGCCTGGATACTT 58.783 55.000 0.00 0.00 35.30 2.24
404 405 1.566231 CCCTCCTTGCCTGGATACTTT 59.434 52.381 0.00 0.00 35.30 2.66
405 406 2.024941 CCCTCCTTGCCTGGATACTTTT 60.025 50.000 0.00 0.00 35.30 2.27
406 407 3.202151 CCCTCCTTGCCTGGATACTTTTA 59.798 47.826 0.00 0.00 35.30 1.52
407 408 4.325030 CCCTCCTTGCCTGGATACTTTTAA 60.325 45.833 0.00 0.00 35.30 1.52
408 409 5.261216 CCTCCTTGCCTGGATACTTTTAAA 58.739 41.667 0.00 0.00 35.30 1.52
409 410 5.893824 CCTCCTTGCCTGGATACTTTTAAAT 59.106 40.000 0.00 0.00 35.30 1.40
410 411 6.381133 CCTCCTTGCCTGGATACTTTTAAATT 59.619 38.462 0.00 0.00 35.30 1.82
411 412 7.559897 CCTCCTTGCCTGGATACTTTTAAATTA 59.440 37.037 0.00 0.00 35.30 1.40
412 413 9.136323 CTCCTTGCCTGGATACTTTTAAATTAT 57.864 33.333 0.00 0.00 35.30 1.28
413 414 9.487442 TCCTTGCCTGGATACTTTTAAATTATT 57.513 29.630 0.00 0.00 37.61 1.40
422 423 9.991906 GGATACTTTTAAATTATTTAAGCCCCC 57.008 33.333 9.64 5.53 36.56 5.40
426 427 8.886369 ACTTTTAAATTATTTAAGCCCCCAACT 58.114 29.630 9.64 0.00 36.56 3.16
430 431 6.801718 AATTATTTAAGCCCCCAACTAACC 57.198 37.500 0.00 0.00 0.00 2.85
431 432 2.608593 TTTAAGCCCCCAACTAACCC 57.391 50.000 0.00 0.00 0.00 4.11
432 433 1.458017 TTAAGCCCCCAACTAACCCA 58.542 50.000 0.00 0.00 0.00 4.51
433 434 1.458017 TAAGCCCCCAACTAACCCAA 58.542 50.000 0.00 0.00 0.00 4.12
434 435 0.178944 AAGCCCCCAACTAACCCAAC 60.179 55.000 0.00 0.00 0.00 3.77
435 436 1.608336 GCCCCCAACTAACCCAACC 60.608 63.158 0.00 0.00 0.00 3.77
436 437 2.089116 GCCCCCAACTAACCCAACCT 62.089 60.000 0.00 0.00 0.00 3.50
437 438 1.374572 CCCCCAACTAACCCAACCTA 58.625 55.000 0.00 0.00 0.00 3.08
438 439 1.283905 CCCCCAACTAACCCAACCTAG 59.716 57.143 0.00 0.00 0.00 3.02
439 440 1.340697 CCCCAACTAACCCAACCTAGC 60.341 57.143 0.00 0.00 0.00 3.42
440 441 1.633945 CCCAACTAACCCAACCTAGCT 59.366 52.381 0.00 0.00 0.00 3.32
441 442 2.355818 CCCAACTAACCCAACCTAGCTC 60.356 54.545 0.00 0.00 0.00 4.09
442 443 2.572104 CCAACTAACCCAACCTAGCTCT 59.428 50.000 0.00 0.00 0.00 4.09
443 444 3.773119 CCAACTAACCCAACCTAGCTCTA 59.227 47.826 0.00 0.00 0.00 2.43
444 445 4.224370 CCAACTAACCCAACCTAGCTCTAA 59.776 45.833 0.00 0.00 0.00 2.10
445 446 5.176592 CAACTAACCCAACCTAGCTCTAAC 58.823 45.833 0.00 0.00 0.00 2.34
446 447 4.685807 ACTAACCCAACCTAGCTCTAACT 58.314 43.478 0.00 0.00 0.00 2.24
447 448 4.710865 ACTAACCCAACCTAGCTCTAACTC 59.289 45.833 0.00 0.00 0.00 3.01
448 449 2.468915 ACCCAACCTAGCTCTAACTCC 58.531 52.381 0.00 0.00 0.00 3.85
449 450 2.225547 ACCCAACCTAGCTCTAACTCCA 60.226 50.000 0.00 0.00 0.00 3.86
450 451 3.041946 CCCAACCTAGCTCTAACTCCAT 58.958 50.000 0.00 0.00 0.00 3.41
451 452 3.181461 CCCAACCTAGCTCTAACTCCATG 60.181 52.174 0.00 0.00 0.00 3.66
452 453 3.706594 CCAACCTAGCTCTAACTCCATGA 59.293 47.826 0.00 0.00 0.00 3.07
453 454 4.346418 CCAACCTAGCTCTAACTCCATGAT 59.654 45.833 0.00 0.00 0.00 2.45
454 455 5.510520 CCAACCTAGCTCTAACTCCATGATC 60.511 48.000 0.00 0.00 0.00 2.92
455 456 4.156477 ACCTAGCTCTAACTCCATGATCC 58.844 47.826 0.00 0.00 0.00 3.36
456 457 4.155709 CCTAGCTCTAACTCCATGATCCA 58.844 47.826 0.00 0.00 0.00 3.41
457 458 4.590647 CCTAGCTCTAACTCCATGATCCAA 59.409 45.833 0.00 0.00 0.00 3.53
458 459 5.070981 CCTAGCTCTAACTCCATGATCCAAA 59.929 44.000 0.00 0.00 0.00 3.28
459 460 4.775236 AGCTCTAACTCCATGATCCAAAC 58.225 43.478 0.00 0.00 0.00 2.93
460 461 4.225942 AGCTCTAACTCCATGATCCAAACA 59.774 41.667 0.00 0.00 0.00 2.83
461 462 4.574013 GCTCTAACTCCATGATCCAAACAG 59.426 45.833 0.00 0.00 0.00 3.16
462 463 5.102953 TCTAACTCCATGATCCAAACAGG 57.897 43.478 0.00 0.00 39.47 4.00
467 468 2.513317 TCCATGATCCAAACAGGCCATA 59.487 45.455 5.01 0.00 37.29 2.74
478 479 1.303309 CAGGCCATAGTGCTACAAGC 58.697 55.000 5.01 0.00 42.82 4.01
529 531 4.639078 TCACAAAGAACTCCATCCATGA 57.361 40.909 0.00 0.00 0.00 3.07
530 532 5.183530 TCACAAAGAACTCCATCCATGAT 57.816 39.130 0.00 0.00 0.00 2.45
976 984 2.031163 GCACGCTGGTGGAGTTCT 59.969 61.111 0.00 0.00 44.54 3.01
992 1000 1.479323 GTTCTACATGGAGGGCGTGTA 59.521 52.381 4.74 0.00 0.00 2.90
1460 1472 2.773993 TAGGCAAAGACGGGGTAAAG 57.226 50.000 0.00 0.00 0.00 1.85
1471 1483 2.959707 ACGGGGTAAAGCACAAATTTCA 59.040 40.909 0.00 0.00 0.00 2.69
1704 1716 7.495934 AGTTTATGTTGGATCGGTAAATCTCAG 59.504 37.037 0.00 0.00 0.00 3.35
1745 1757 6.980978 CCAATGTTACACTCGTGAGATCTTAT 59.019 38.462 3.44 0.00 40.84 1.73
1756 1768 5.473846 TCGTGAGATCTTATGTGTAGATCCC 59.526 44.000 6.61 0.00 45.92 3.85
1760 1772 2.673258 TCTTATGTGTAGATCCCCGCA 58.327 47.619 0.00 0.00 0.00 5.69
1761 1773 3.035363 TCTTATGTGTAGATCCCCGCAA 58.965 45.455 0.22 0.00 0.00 4.85
1797 1809 8.876790 CCATTTTCTTTCTCTTTTGAATATGCC 58.123 33.333 0.00 0.00 31.40 4.40
1873 1885 7.226325 CACACCTTTTGCAAATTTGAATCCTAA 59.774 33.333 22.31 0.00 0.00 2.69
1908 1920 6.754209 AGAAGCGGAATAATAGATTCTATGCG 59.246 38.462 6.96 4.55 38.62 4.73
1915 1927 7.067494 GGAATAATAGATTCTATGCGCCCAAAT 59.933 37.037 4.18 0.00 0.00 2.32
2151 2163 1.827969 AGATCTTCGACTGGGAGTTGG 59.172 52.381 0.00 0.00 30.44 3.77
2157 2169 2.203788 ACTGGGAGTTGGGCGAGA 60.204 61.111 0.00 0.00 0.00 4.04
2291 2303 9.622004 GATATATGAATATATGTACCCGGTTCG 57.378 37.037 0.00 0.00 36.38 3.95
2390 2402 3.770040 TCGGTCGGCCTGGACATG 61.770 66.667 3.66 4.90 38.70 3.21
2391 2403 4.082523 CGGTCGGCCTGGACATGT 62.083 66.667 3.66 0.00 38.70 3.21
2392 2404 2.717044 CGGTCGGCCTGGACATGTA 61.717 63.158 3.66 0.00 38.70 2.29
2603 2620 4.680237 CTTCAGCACGACGCCCCA 62.680 66.667 0.00 0.00 44.04 4.96
2628 2646 2.654289 AAAAACGGCGCCCCATTC 59.346 55.556 23.46 0.00 0.00 2.67
2653 2671 3.275143 TCCTTCTTTGAGACAAAACGCA 58.725 40.909 0.00 0.00 0.00 5.24
2703 2722 6.262944 TGCAACACTATGACTTGAACAAGAAT 59.737 34.615 19.35 14.14 40.79 2.40
2746 2765 1.053424 AGAGCAGAAACGTAACCCCA 58.947 50.000 0.00 0.00 0.00 4.96
2765 2784 4.160626 CCCCAAAACACAGTAAAGGACAAA 59.839 41.667 0.00 0.00 0.00 2.83
2886 2905 3.008049 GTCCTAAACTCACCACCAGACAT 59.992 47.826 0.00 0.00 0.00 3.06
2887 2906 3.260884 TCCTAAACTCACCACCAGACATC 59.739 47.826 0.00 0.00 0.00 3.06
2916 2935 4.744570 CAGGAACGCAAGAGTATCAGTTA 58.255 43.478 0.00 0.00 43.62 2.24
2934 2953 1.858739 TACGGGGAAATTGCCTGCCT 61.859 55.000 12.50 0.00 37.83 4.75
2967 2986 3.862845 TCTTTGCTTCGCCAAAAGAAAAC 59.137 39.130 0.00 0.00 34.59 2.43
2968 2987 2.217429 TGCTTCGCCAAAAGAAAACC 57.783 45.000 0.00 0.00 0.00 3.27
2973 2992 2.379972 TCGCCAAAAGAAAACCAAGGA 58.620 42.857 0.00 0.00 0.00 3.36
2974 2993 2.761208 TCGCCAAAAGAAAACCAAGGAA 59.239 40.909 0.00 0.00 0.00 3.36
3045 3064 1.410153 ACCACCAAAGCAAGAAAGCAG 59.590 47.619 0.00 0.00 36.85 4.24
3048 3067 2.360165 CACCAAAGCAAGAAAGCAGAGT 59.640 45.455 0.00 0.00 36.85 3.24
3067 3087 4.657039 AGAGTAACAAGTCACAGGGGTTTA 59.343 41.667 0.00 0.00 0.00 2.01
3068 3088 5.131475 AGAGTAACAAGTCACAGGGGTTTAA 59.869 40.000 0.00 0.00 0.00 1.52
3200 3220 0.729116 AGCATGCACACAAGATACGC 59.271 50.000 21.98 0.00 0.00 4.42
3217 3237 1.066858 ACGCTGATGTGAGAACGGAAT 60.067 47.619 0.00 0.00 0.00 3.01
3238 3258 6.348540 GGAATATACGACAGGGAAAATGCATC 60.349 42.308 0.00 0.00 0.00 3.91
3246 3266 6.038161 CGACAGGGAAAATGCATCATTAACTA 59.962 38.462 0.00 0.00 32.43 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.512435 CTCCGTTCTTAAATATAAGTCTTTCGA 57.488 33.333 0.00 0.00 39.65 3.71
8 9 8.753175 CCTCCGTTCTTAAATATAAGTCTTTCG 58.247 37.037 0.00 0.00 39.65 3.46
9 10 9.043079 CCCTCCGTTCTTAAATATAAGTCTTTC 57.957 37.037 0.00 0.00 39.65 2.62
10 11 8.765517 TCCCTCCGTTCTTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 39.65 2.52
11 12 8.315220 TCCCTCCGTTCTTAAATATAAGTCTT 57.685 34.615 0.00 0.00 39.65 3.01
12 13 7.564292 ACTCCCTCCGTTCTTAAATATAAGTCT 59.436 37.037 0.00 0.00 39.65 3.24
13 14 7.724287 ACTCCCTCCGTTCTTAAATATAAGTC 58.276 38.462 0.00 0.00 39.65 3.01
14 15 7.672122 ACTCCCTCCGTTCTTAAATATAAGT 57.328 36.000 0.00 0.00 39.65 2.24
15 16 8.858094 AGTACTCCCTCCGTTCTTAAATATAAG 58.142 37.037 0.00 0.00 39.97 1.73
16 17 8.773033 AGTACTCCCTCCGTTCTTAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
17 18 8.773033 AAGTACTCCCTCCGTTCTTAAATATA 57.227 34.615 0.00 0.00 0.00 0.86
18 19 7.672122 AAGTACTCCCTCCGTTCTTAAATAT 57.328 36.000 0.00 0.00 0.00 1.28
19 20 7.836183 AGTAAGTACTCCCTCCGTTCTTAAATA 59.164 37.037 0.00 0.00 29.88 1.40
20 21 6.666980 AGTAAGTACTCCCTCCGTTCTTAAAT 59.333 38.462 0.00 0.00 29.88 1.40
21 22 6.012745 AGTAAGTACTCCCTCCGTTCTTAAA 58.987 40.000 0.00 0.00 29.88 1.52
22 23 5.574188 AGTAAGTACTCCCTCCGTTCTTAA 58.426 41.667 0.00 0.00 29.88 1.85
23 24 5.184892 AGTAAGTACTCCCTCCGTTCTTA 57.815 43.478 0.00 0.00 0.00 2.10
24 25 4.044946 AGTAAGTACTCCCTCCGTTCTT 57.955 45.455 0.00 0.00 0.00 2.52
25 26 3.735720 AGTAAGTACTCCCTCCGTTCT 57.264 47.619 0.00 0.00 0.00 3.01
26 27 4.522114 AGTAGTAAGTACTCCCTCCGTTC 58.478 47.826 0.00 0.00 37.41 3.95
27 28 4.582973 AGTAGTAAGTACTCCCTCCGTT 57.417 45.455 0.00 0.00 37.41 4.44
36 37 5.043582 TGGGATGGAAGGAGTAGTAAGTACT 60.044 44.000 0.00 0.00 45.34 2.73
37 38 5.206587 TGGGATGGAAGGAGTAGTAAGTAC 58.793 45.833 0.00 0.00 0.00 2.73
38 39 5.476950 TGGGATGGAAGGAGTAGTAAGTA 57.523 43.478 0.00 0.00 0.00 2.24
39 40 4.348020 TGGGATGGAAGGAGTAGTAAGT 57.652 45.455 0.00 0.00 0.00 2.24
40 41 5.693769 TTTGGGATGGAAGGAGTAGTAAG 57.306 43.478 0.00 0.00 0.00 2.34
41 42 6.652205 ATTTTGGGATGGAAGGAGTAGTAA 57.348 37.500 0.00 0.00 0.00 2.24
42 43 6.447084 AGAATTTTGGGATGGAAGGAGTAGTA 59.553 38.462 0.00 0.00 0.00 1.82
43 44 5.254032 AGAATTTTGGGATGGAAGGAGTAGT 59.746 40.000 0.00 0.00 0.00 2.73
44 45 5.760131 AGAATTTTGGGATGGAAGGAGTAG 58.240 41.667 0.00 0.00 0.00 2.57
45 46 5.796502 AGAATTTTGGGATGGAAGGAGTA 57.203 39.130 0.00 0.00 0.00 2.59
46 47 4.682021 AGAATTTTGGGATGGAAGGAGT 57.318 40.909 0.00 0.00 0.00 3.85
47 48 4.774200 ACAAGAATTTTGGGATGGAAGGAG 59.226 41.667 5.68 0.00 0.00 3.69
48 49 4.750941 ACAAGAATTTTGGGATGGAAGGA 58.249 39.130 5.68 0.00 0.00 3.36
49 50 4.774200 AGACAAGAATTTTGGGATGGAAGG 59.226 41.667 5.68 0.00 0.00 3.46
50 51 5.990120 AGACAAGAATTTTGGGATGGAAG 57.010 39.130 5.68 0.00 0.00 3.46
51 52 7.237982 TCTAAGACAAGAATTTTGGGATGGAA 58.762 34.615 5.68 0.00 0.00 3.53
52 53 6.789268 TCTAAGACAAGAATTTTGGGATGGA 58.211 36.000 5.68 0.00 0.00 3.41
53 54 7.651027 ATCTAAGACAAGAATTTTGGGATGG 57.349 36.000 5.68 0.00 0.00 3.51
55 56 9.981460 ACTAATCTAAGACAAGAATTTTGGGAT 57.019 29.630 5.68 0.00 0.00 3.85
56 57 9.449719 GACTAATCTAAGACAAGAATTTTGGGA 57.550 33.333 5.68 0.00 0.00 4.37
57 58 9.454859 AGACTAATCTAAGACAAGAATTTTGGG 57.545 33.333 5.68 0.00 31.46 4.12
65 66 9.491675 CCGTATCTAGACTAATCTAAGACAAGA 57.508 37.037 0.00 0.00 36.98 3.02
66 67 9.491675 TCCGTATCTAGACTAATCTAAGACAAG 57.508 37.037 0.00 0.00 36.98 3.16
68 69 9.438228 CATCCGTATCTAGACTAATCTAAGACA 57.562 37.037 0.00 0.00 36.98 3.41
69 70 9.439500 ACATCCGTATCTAGACTAATCTAAGAC 57.561 37.037 0.00 0.00 36.98 3.01
110 111 9.803315 GTCTAAATACAGATGTATCAAGTCACA 57.197 33.333 5.97 0.00 40.10 3.58
111 112 9.803315 TGTCTAAATACAGATGTATCAAGTCAC 57.197 33.333 5.97 3.82 40.10 3.67
139 140 9.893305 CTCCGTTTTAAAATTCTTGTCTTACAT 57.107 29.630 3.52 0.00 0.00 2.29
140 141 8.347035 CCTCCGTTTTAAAATTCTTGTCTTACA 58.653 33.333 3.52 0.00 0.00 2.41
141 142 8.562052 TCCTCCGTTTTAAAATTCTTGTCTTAC 58.438 33.333 3.52 0.00 0.00 2.34
142 143 8.680039 TCCTCCGTTTTAAAATTCTTGTCTTA 57.320 30.769 3.52 0.00 0.00 2.10
143 144 7.576861 TCCTCCGTTTTAAAATTCTTGTCTT 57.423 32.000 3.52 0.00 0.00 3.01
144 145 7.284716 ACTTCCTCCGTTTTAAAATTCTTGTCT 59.715 33.333 3.52 0.00 0.00 3.41
145 146 7.423199 ACTTCCTCCGTTTTAAAATTCTTGTC 58.577 34.615 3.52 0.00 0.00 3.18
146 147 7.342769 ACTTCCTCCGTTTTAAAATTCTTGT 57.657 32.000 3.52 0.00 0.00 3.16
147 148 7.537649 GCTACTTCCTCCGTTTTAAAATTCTTG 59.462 37.037 3.52 0.00 0.00 3.02
148 149 7.447545 AGCTACTTCCTCCGTTTTAAAATTCTT 59.552 33.333 3.52 0.00 0.00 2.52
149 150 6.940867 AGCTACTTCCTCCGTTTTAAAATTCT 59.059 34.615 3.52 0.00 0.00 2.40
150 151 7.142306 AGCTACTTCCTCCGTTTTAAAATTC 57.858 36.000 3.52 0.00 0.00 2.17
151 152 8.625786 TTAGCTACTTCCTCCGTTTTAAAATT 57.374 30.769 3.52 0.00 0.00 1.82
152 153 8.803397 ATTAGCTACTTCCTCCGTTTTAAAAT 57.197 30.769 3.52 0.00 0.00 1.82
153 154 8.508875 CAATTAGCTACTTCCTCCGTTTTAAAA 58.491 33.333 0.00 0.00 0.00 1.52
154 155 7.662669 ACAATTAGCTACTTCCTCCGTTTTAAA 59.337 33.333 0.00 0.00 0.00 1.52
155 156 7.118680 CACAATTAGCTACTTCCTCCGTTTTAA 59.881 37.037 0.00 0.00 0.00 1.52
156 157 6.592607 CACAATTAGCTACTTCCTCCGTTTTA 59.407 38.462 0.00 0.00 0.00 1.52
157 158 5.411669 CACAATTAGCTACTTCCTCCGTTTT 59.588 40.000 0.00 0.00 0.00 2.43
158 159 4.935808 CACAATTAGCTACTTCCTCCGTTT 59.064 41.667 0.00 0.00 0.00 3.60
159 160 4.222145 TCACAATTAGCTACTTCCTCCGTT 59.778 41.667 0.00 0.00 0.00 4.44
197 198 2.488087 AAGCGACGTGTAGGCCAGAC 62.488 60.000 5.01 2.55 0.00 3.51
201 202 2.813908 CCAAGCGACGTGTAGGCC 60.814 66.667 0.00 0.00 0.00 5.19
227 228 1.478510 CTGAGTAGGAACTGACGGCAT 59.521 52.381 0.00 0.00 41.52 4.40
230 231 1.178276 AGCTGAGTAGGAACTGACGG 58.822 55.000 0.00 0.00 41.52 4.79
298 299 1.048601 AACGCAGGAGAAGGTGAAGA 58.951 50.000 0.00 0.00 0.00 2.87
303 304 1.705997 AACCCAACGCAGGAGAAGGT 61.706 55.000 0.00 0.00 0.00 3.50
304 305 0.323629 TAACCCAACGCAGGAGAAGG 59.676 55.000 0.00 0.00 0.00 3.46
306 307 1.344065 TCTAACCCAACGCAGGAGAA 58.656 50.000 0.00 0.00 0.00 2.87
308 309 1.656652 CATCTAACCCAACGCAGGAG 58.343 55.000 0.00 0.00 0.00 3.69
318 319 5.071115 AGAGATGCTTAGTTCCATCTAACCC 59.929 44.000 3.38 0.00 45.93 4.11
319 320 6.168270 AGAGATGCTTAGTTCCATCTAACC 57.832 41.667 3.38 0.00 45.93 2.85
320 321 6.183360 TGGAGAGATGCTTAGTTCCATCTAAC 60.183 42.308 3.38 1.97 45.93 2.34
321 322 5.899547 TGGAGAGATGCTTAGTTCCATCTAA 59.100 40.000 3.38 0.00 45.93 2.10
322 323 5.303078 GTGGAGAGATGCTTAGTTCCATCTA 59.697 44.000 3.38 0.00 45.93 1.98
324 325 4.376146 GTGGAGAGATGCTTAGTTCCATC 58.624 47.826 3.75 0.00 37.10 3.51
325 326 3.135530 GGTGGAGAGATGCTTAGTTCCAT 59.864 47.826 3.75 0.00 37.10 3.41
326 327 2.501723 GGTGGAGAGATGCTTAGTTCCA 59.498 50.000 0.00 0.00 32.62 3.53
327 328 2.482142 CGGTGGAGAGATGCTTAGTTCC 60.482 54.545 0.00 0.00 0.00 3.62
328 329 2.482142 CCGGTGGAGAGATGCTTAGTTC 60.482 54.545 0.00 0.00 0.00 3.01
329 330 1.482593 CCGGTGGAGAGATGCTTAGTT 59.517 52.381 0.00 0.00 0.00 2.24
330 331 1.115467 CCGGTGGAGAGATGCTTAGT 58.885 55.000 0.00 0.00 0.00 2.24
331 332 1.115467 ACCGGTGGAGAGATGCTTAG 58.885 55.000 6.12 0.00 0.00 2.18
332 333 2.447408 TACCGGTGGAGAGATGCTTA 57.553 50.000 19.93 0.00 0.00 3.09
333 334 1.794714 ATACCGGTGGAGAGATGCTT 58.205 50.000 19.93 0.00 0.00 3.91
334 335 2.158445 ACTATACCGGTGGAGAGATGCT 60.158 50.000 19.93 0.00 0.00 3.79
335 336 2.240279 ACTATACCGGTGGAGAGATGC 58.760 52.381 19.93 0.00 0.00 3.91
336 337 3.005897 CCAACTATACCGGTGGAGAGATG 59.994 52.174 19.93 9.79 0.00 2.90
337 338 3.117246 TCCAACTATACCGGTGGAGAGAT 60.117 47.826 19.93 3.55 0.00 2.75
338 339 2.242965 TCCAACTATACCGGTGGAGAGA 59.757 50.000 19.93 10.70 0.00 3.10
339 340 2.662866 TCCAACTATACCGGTGGAGAG 58.337 52.381 19.93 7.50 0.00 3.20
340 341 2.832643 TCCAACTATACCGGTGGAGA 57.167 50.000 19.93 0.00 0.00 3.71
341 342 4.831155 TCTAATCCAACTATACCGGTGGAG 59.169 45.833 19.93 16.53 0.00 3.86
342 343 4.806892 TCTAATCCAACTATACCGGTGGA 58.193 43.478 19.93 14.97 0.00 4.02
343 344 5.245301 TCATCTAATCCAACTATACCGGTGG 59.755 44.000 19.93 9.03 0.00 4.61
344 345 6.340962 TCATCTAATCCAACTATACCGGTG 57.659 41.667 19.93 2.36 0.00 4.94
345 346 6.989155 TTCATCTAATCCAACTATACCGGT 57.011 37.500 13.98 13.98 0.00 5.28
346 347 7.442656 AGTTTCATCTAATCCAACTATACCGG 58.557 38.462 0.00 0.00 0.00 5.28
347 348 9.976511 TTAGTTTCATCTAATCCAACTATACCG 57.023 33.333 0.00 0.00 31.62 4.02
360 361 9.457436 GGGTTAAAGTGGATTAGTTTCATCTAA 57.543 33.333 0.00 0.00 33.96 2.10
361 362 8.832735 AGGGTTAAAGTGGATTAGTTTCATCTA 58.167 33.333 0.00 0.00 33.96 1.98
362 363 7.699878 AGGGTTAAAGTGGATTAGTTTCATCT 58.300 34.615 0.00 0.00 33.96 2.90
363 364 7.067129 GGAGGGTTAAAGTGGATTAGTTTCATC 59.933 40.741 0.00 0.00 33.96 2.92
364 365 6.890268 GGAGGGTTAAAGTGGATTAGTTTCAT 59.110 38.462 0.00 0.00 33.96 2.57
365 366 6.045106 AGGAGGGTTAAAGTGGATTAGTTTCA 59.955 38.462 0.00 0.00 33.96 2.69
366 367 6.482524 AGGAGGGTTAAAGTGGATTAGTTTC 58.517 40.000 0.00 0.00 33.96 2.78
367 368 6.464530 AGGAGGGTTAAAGTGGATTAGTTT 57.535 37.500 0.00 0.00 36.03 2.66
368 369 6.246163 CAAGGAGGGTTAAAGTGGATTAGTT 58.754 40.000 0.00 0.00 0.00 2.24
369 370 5.806734 GCAAGGAGGGTTAAAGTGGATTAGT 60.807 44.000 0.00 0.00 0.00 2.24
370 371 4.640647 GCAAGGAGGGTTAAAGTGGATTAG 59.359 45.833 0.00 0.00 0.00 1.73
371 372 4.569015 GGCAAGGAGGGTTAAAGTGGATTA 60.569 45.833 0.00 0.00 0.00 1.75
372 373 3.431415 GCAAGGAGGGTTAAAGTGGATT 58.569 45.455 0.00 0.00 0.00 3.01
373 374 2.291605 GGCAAGGAGGGTTAAAGTGGAT 60.292 50.000 0.00 0.00 0.00 3.41
374 375 1.074889 GGCAAGGAGGGTTAAAGTGGA 59.925 52.381 0.00 0.00 0.00 4.02
375 376 1.075536 AGGCAAGGAGGGTTAAAGTGG 59.924 52.381 0.00 0.00 0.00 4.00
376 377 2.162681 CAGGCAAGGAGGGTTAAAGTG 58.837 52.381 0.00 0.00 0.00 3.16
377 378 1.075536 CCAGGCAAGGAGGGTTAAAGT 59.924 52.381 0.00 0.00 0.00 2.66
378 379 1.354368 TCCAGGCAAGGAGGGTTAAAG 59.646 52.381 0.00 0.00 32.77 1.85
379 380 1.451449 TCCAGGCAAGGAGGGTTAAA 58.549 50.000 0.00 0.00 32.77 1.52
380 381 1.681229 ATCCAGGCAAGGAGGGTTAA 58.319 50.000 4.98 0.00 41.90 2.01
381 382 2.124411 GTATCCAGGCAAGGAGGGTTA 58.876 52.381 4.98 0.00 41.90 2.85
382 383 0.919710 GTATCCAGGCAAGGAGGGTT 59.080 55.000 4.98 0.00 41.90 4.11
383 384 0.044855 AGTATCCAGGCAAGGAGGGT 59.955 55.000 4.98 0.00 41.90 4.34
384 385 1.216990 AAGTATCCAGGCAAGGAGGG 58.783 55.000 4.98 0.00 41.90 4.30
385 386 3.372440 AAAAGTATCCAGGCAAGGAGG 57.628 47.619 4.98 0.00 41.90 4.30
386 387 7.410120 AATTTAAAAGTATCCAGGCAAGGAG 57.590 36.000 4.98 0.00 41.90 3.69
387 388 9.487442 AATAATTTAAAAGTATCCAGGCAAGGA 57.513 29.630 0.99 0.99 43.01 3.36
396 397 9.991906 GGGGGCTTAAATAATTTAAAAGTATCC 57.008 33.333 0.00 0.00 34.93 2.59
400 401 8.886369 AGTTGGGGGCTTAAATAATTTAAAAGT 58.114 29.630 0.00 0.00 34.93 2.66
404 405 8.760735 GGTTAGTTGGGGGCTTAAATAATTTAA 58.239 33.333 0.00 0.00 34.24 1.52
405 406 7.345132 GGGTTAGTTGGGGGCTTAAATAATTTA 59.655 37.037 0.00 0.00 0.00 1.40
406 407 6.157297 GGGTTAGTTGGGGGCTTAAATAATTT 59.843 38.462 0.00 0.00 0.00 1.82
407 408 5.664006 GGGTTAGTTGGGGGCTTAAATAATT 59.336 40.000 0.00 0.00 0.00 1.40
408 409 5.213519 GGGTTAGTTGGGGGCTTAAATAAT 58.786 41.667 0.00 0.00 0.00 1.28
409 410 4.045590 TGGGTTAGTTGGGGGCTTAAATAA 59.954 41.667 0.00 0.00 0.00 1.40
410 411 3.596956 TGGGTTAGTTGGGGGCTTAAATA 59.403 43.478 0.00 0.00 0.00 1.40
411 412 2.384029 TGGGTTAGTTGGGGGCTTAAAT 59.616 45.455 0.00 0.00 0.00 1.40
412 413 1.787676 TGGGTTAGTTGGGGGCTTAAA 59.212 47.619 0.00 0.00 0.00 1.52
413 414 1.458017 TGGGTTAGTTGGGGGCTTAA 58.542 50.000 0.00 0.00 0.00 1.85
414 415 1.075861 GTTGGGTTAGTTGGGGGCTTA 59.924 52.381 0.00 0.00 0.00 3.09
415 416 0.178944 GTTGGGTTAGTTGGGGGCTT 60.179 55.000 0.00 0.00 0.00 4.35
416 417 1.463375 GTTGGGTTAGTTGGGGGCT 59.537 57.895 0.00 0.00 0.00 5.19
417 418 1.608336 GGTTGGGTTAGTTGGGGGC 60.608 63.158 0.00 0.00 0.00 5.80
418 419 1.283905 CTAGGTTGGGTTAGTTGGGGG 59.716 57.143 0.00 0.00 0.00 5.40
419 420 1.340697 GCTAGGTTGGGTTAGTTGGGG 60.341 57.143 0.00 0.00 0.00 4.96
420 421 1.633945 AGCTAGGTTGGGTTAGTTGGG 59.366 52.381 0.00 0.00 0.00 4.12
421 422 2.572104 AGAGCTAGGTTGGGTTAGTTGG 59.428 50.000 0.00 0.00 0.00 3.77
422 423 3.983044 AGAGCTAGGTTGGGTTAGTTG 57.017 47.619 0.00 0.00 0.00 3.16
423 424 5.092259 AGTTAGAGCTAGGTTGGGTTAGTT 58.908 41.667 0.00 0.00 0.00 2.24
424 425 4.685807 AGTTAGAGCTAGGTTGGGTTAGT 58.314 43.478 0.00 0.00 0.00 2.24
425 426 4.099727 GGAGTTAGAGCTAGGTTGGGTTAG 59.900 50.000 0.00 0.00 0.00 2.34
426 427 4.028825 GGAGTTAGAGCTAGGTTGGGTTA 58.971 47.826 0.00 0.00 0.00 2.85
427 428 2.838813 GGAGTTAGAGCTAGGTTGGGTT 59.161 50.000 0.00 0.00 0.00 4.11
428 429 2.225547 TGGAGTTAGAGCTAGGTTGGGT 60.226 50.000 0.00 0.00 0.00 4.51
429 430 2.467880 TGGAGTTAGAGCTAGGTTGGG 58.532 52.381 0.00 0.00 0.00 4.12
430 431 3.706594 TCATGGAGTTAGAGCTAGGTTGG 59.293 47.826 0.00 0.00 0.00 3.77
431 432 5.510520 GGATCATGGAGTTAGAGCTAGGTTG 60.511 48.000 0.00 0.00 0.00 3.77
432 433 4.591072 GGATCATGGAGTTAGAGCTAGGTT 59.409 45.833 0.00 0.00 0.00 3.50
433 434 4.156477 GGATCATGGAGTTAGAGCTAGGT 58.844 47.826 0.00 0.00 0.00 3.08
434 435 4.155709 TGGATCATGGAGTTAGAGCTAGG 58.844 47.826 0.00 0.00 0.00 3.02
435 436 5.798125 TTGGATCATGGAGTTAGAGCTAG 57.202 43.478 0.00 0.00 0.00 3.42
436 437 5.425217 TGTTTGGATCATGGAGTTAGAGCTA 59.575 40.000 0.00 0.00 0.00 3.32
437 438 4.225942 TGTTTGGATCATGGAGTTAGAGCT 59.774 41.667 0.00 0.00 0.00 4.09
438 439 4.517285 TGTTTGGATCATGGAGTTAGAGC 58.483 43.478 0.00 0.00 0.00 4.09
439 440 5.121811 CCTGTTTGGATCATGGAGTTAGAG 58.878 45.833 0.00 0.00 38.35 2.43
440 441 4.626287 GCCTGTTTGGATCATGGAGTTAGA 60.626 45.833 0.00 0.00 38.35 2.10
441 442 3.629398 GCCTGTTTGGATCATGGAGTTAG 59.371 47.826 0.00 0.00 38.35 2.34
442 443 3.620488 GCCTGTTTGGATCATGGAGTTA 58.380 45.455 0.00 0.00 38.35 2.24
443 444 2.450476 GCCTGTTTGGATCATGGAGTT 58.550 47.619 0.00 0.00 38.35 3.01
444 445 1.341383 GGCCTGTTTGGATCATGGAGT 60.341 52.381 0.00 0.00 38.35 3.85
445 446 1.341285 TGGCCTGTTTGGATCATGGAG 60.341 52.381 3.32 0.00 38.35 3.86
446 447 0.703488 TGGCCTGTTTGGATCATGGA 59.297 50.000 3.32 0.00 38.35 3.41
447 448 1.784358 ATGGCCTGTTTGGATCATGG 58.216 50.000 3.32 0.00 38.35 3.66
448 449 3.317149 CACTATGGCCTGTTTGGATCATG 59.683 47.826 3.32 0.00 38.35 3.07
449 450 3.559069 CACTATGGCCTGTTTGGATCAT 58.441 45.455 3.32 0.00 38.35 2.45
450 451 2.945440 GCACTATGGCCTGTTTGGATCA 60.945 50.000 3.32 0.00 38.35 2.92
451 452 1.678101 GCACTATGGCCTGTTTGGATC 59.322 52.381 3.32 0.00 38.35 3.36
452 453 1.285962 AGCACTATGGCCTGTTTGGAT 59.714 47.619 3.32 0.00 38.35 3.41
453 454 0.698238 AGCACTATGGCCTGTTTGGA 59.302 50.000 3.32 0.00 38.35 3.53
454 455 2.017049 GTAGCACTATGGCCTGTTTGG 58.983 52.381 3.32 0.00 39.35 3.28
455 456 2.710377 TGTAGCACTATGGCCTGTTTG 58.290 47.619 3.32 0.00 0.00 2.93
456 457 3.347216 CTTGTAGCACTATGGCCTGTTT 58.653 45.455 3.32 0.00 0.00 2.83
457 458 2.941415 GCTTGTAGCACTATGGCCTGTT 60.941 50.000 3.32 0.00 41.89 3.16
458 459 1.407437 GCTTGTAGCACTATGGCCTGT 60.407 52.381 3.32 0.00 41.89 4.00
459 460 1.303309 GCTTGTAGCACTATGGCCTG 58.697 55.000 3.32 0.00 41.89 4.85
460 461 0.181350 GGCTTGTAGCACTATGGCCT 59.819 55.000 3.32 0.00 44.75 5.19
461 462 0.107214 TGGCTTGTAGCACTATGGCC 60.107 55.000 0.00 0.00 44.75 5.36
462 463 1.750193 TTGGCTTGTAGCACTATGGC 58.250 50.000 0.67 0.00 44.75 4.40
467 468 2.358898 CAGTGTTTTGGCTTGTAGCACT 59.641 45.455 0.67 0.00 44.75 4.40
478 479 1.408702 CAGTTGGGTCCAGTGTTTTGG 59.591 52.381 0.00 0.00 39.70 3.28
529 531 4.148825 GTCGCCGGCTCCAGTGAT 62.149 66.667 26.68 0.00 0.00 3.06
579 581 0.686441 TCAGGATCACGGACGGGATT 60.686 55.000 11.11 0.00 38.55 3.01
976 984 1.820581 GCTACACGCCCTCCATGTA 59.179 57.895 0.00 0.00 0.00 2.29
1435 1443 4.245251 ACCCCGTCTTTGCCTAATTTAT 57.755 40.909 0.00 0.00 0.00 1.40
1436 1444 3.724732 ACCCCGTCTTTGCCTAATTTA 57.275 42.857 0.00 0.00 0.00 1.40
1460 1472 8.746922 TGTTGATTCTCTTATGAAATTTGTGC 57.253 30.769 0.00 0.00 0.00 4.57
1636 1648 4.081972 ACGAGATTCAGTGTGCTAATGTCT 60.082 41.667 0.00 0.00 0.00 3.41
1704 1716 7.596248 TGTAACATTGGTTAAGTCTTAGTCGAC 59.404 37.037 7.70 7.70 40.95 4.20
1745 1757 2.570415 TTTTTGCGGGGATCTACACA 57.430 45.000 0.00 0.00 0.00 3.72
1829 1841 5.305644 AGGTGTGGCTAGATCTTAATCGATT 59.694 40.000 16.15 16.15 36.97 3.34
1873 1885 8.358148 TCTATTATTCCGCTTCTAAACGATCTT 58.642 33.333 0.00 0.00 0.00 2.40
1908 1920 2.027837 AGTGATTTTGCAGGATTTGGGC 60.028 45.455 0.00 0.00 0.00 5.36
1915 1927 8.635765 AATAGTTTCTTAGTGATTTTGCAGGA 57.364 30.769 0.00 0.00 0.00 3.86
2151 2163 1.051556 ATCCCCTTCTCCTTCTCGCC 61.052 60.000 0.00 0.00 0.00 5.54
2157 2169 3.054065 GTGTCAATCATCCCCTTCTCCTT 60.054 47.826 0.00 0.00 0.00 3.36
2291 2303 8.508875 TGAACTAAAACCTCGTCAAATATTTCC 58.491 33.333 0.00 0.00 0.00 3.13
2305 2317 5.953571 ACCCTCAAATCTGAACTAAAACCT 58.046 37.500 0.00 0.00 0.00 3.50
2386 2398 1.278238 GCGAGCGCTTTACTACATGT 58.722 50.000 13.26 2.69 38.26 3.21
2390 2402 1.226491 TCGGCGAGCGCTTTACTAC 60.226 57.895 13.26 0.00 41.60 2.73
2391 2403 1.226491 GTCGGCGAGCGCTTTACTA 60.226 57.895 13.26 0.00 41.60 1.82
2392 2404 2.506438 GTCGGCGAGCGCTTTACT 60.506 61.111 13.26 0.00 41.60 2.24
2462 2479 2.436646 AATGCTTCCAGTCCGGCG 60.437 61.111 0.00 0.00 33.14 6.46
2561 2578 2.335011 GTTGGCGCTTGGTTGGAC 59.665 61.111 7.64 0.00 0.00 4.02
2616 2634 2.489751 GAAAAGAATGGGGCGCCG 59.510 61.111 22.54 0.00 0.00 6.46
2628 2646 5.230097 GCGTTTTGTCTCAAAGAAGGAAAAG 59.770 40.000 0.00 0.00 0.00 2.27
2653 2671 1.355971 CGCTGTAATACTTGCGTGGT 58.644 50.000 17.72 0.00 42.93 4.16
2746 2765 8.962679 TGAACTATTTGTCCTTTACTGTGTTTT 58.037 29.630 0.00 0.00 0.00 2.43
2765 2784 7.629222 GCAAGTGGTAGCAAATTGATGAACTAT 60.629 37.037 19.78 0.00 0.00 2.12
2916 2935 2.679996 GGCAGGCAATTTCCCCGT 60.680 61.111 0.00 0.00 0.00 5.28
2934 2953 3.966215 GCAAAGAGCACCGTAGCA 58.034 55.556 0.00 0.00 44.79 3.49
2983 3002 4.503741 GCTTAACAAACATGAAGCCTGA 57.496 40.909 0.00 0.00 38.68 3.86
3045 3064 3.487120 AACCCCTGTGACTTGTTACTC 57.513 47.619 0.00 0.00 0.00 2.59
3048 3067 4.463070 GGTTAAACCCCTGTGACTTGTTA 58.537 43.478 0.00 0.00 30.04 2.41
3071 3091 1.274712 ACCTCCTGAAGCCTGAAGAG 58.725 55.000 0.00 0.00 0.00 2.85
3200 3220 5.625721 GTCGTATATTCCGTTCTCACATCAG 59.374 44.000 0.00 0.00 0.00 2.90
3217 3237 5.029807 TGATGCATTTTCCCTGTCGTATA 57.970 39.130 0.00 0.00 0.00 1.47
3246 3266 7.544804 AAGATGCCTTTGACTTTCCTATTTT 57.455 32.000 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.