Multiple sequence alignment - TraesCS4A01G114700

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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 TraesCS4A01G114700 chr4A 100.000 4091 0 0 255 4345 139544268 139548358 0.000000e+00 7555.0
1 TraesCS4A01G114700 chr4A 88.525 122 9 4 3655 3772 25799291 25799411 4.530000e-30 143.0
2 TraesCS4A01G114700 chr4A 86.585 82 9 2 3673 3753 39066464 39066544 5.980000e-14 89.8
3 TraesCS4A01G114700 chr4A 100.000 35 0 0 1 35 139544014 139544048 1.010000e-06 65.8
4 TraesCS4A01G114700 chr4D 96.703 1577 43 6 2048 3618 334117847 334116274 0.000000e+00 2615.0
5 TraesCS4A01G114700 chr4D 90.615 1236 48 29 877 2064 334119077 334117862 0.000000e+00 1578.0
6 TraesCS4A01G114700 chr4D 87.129 404 20 17 430 833 334119444 334119073 3.100000e-116 429.0
7 TraesCS4A01G114700 chr4B 95.906 1539 39 10 2048 3584 412107229 412105713 0.000000e+00 2471.0
8 TraesCS4A01G114700 chr4B 88.921 1363 75 31 740 2064 412108568 412107244 0.000000e+00 1611.0
9 TraesCS4A01G114700 chr4B 90.625 256 10 4 500 755 412108827 412108586 1.170000e-85 327.0
10 TraesCS4A01G114700 chr5A 87.852 922 85 16 2596 3499 19541003 19540091 0.000000e+00 1057.0
11 TraesCS4A01G114700 chr5A 86.043 652 65 20 997 1632 19542262 19541621 0.000000e+00 676.0
12 TraesCS4A01G114700 chr5A 93.168 322 22 0 2179 2500 19541345 19541024 1.410000e-129 473.0
13 TraesCS4A01G114700 chr5A 85.047 214 28 4 1381 1592 328810622 328810411 9.460000e-52 215.0
14 TraesCS4A01G114700 chr5A 92.105 152 11 1 1705 1855 19541582 19541431 3.400000e-51 213.0
15 TraesCS4A01G114700 chr5A 79.554 269 49 3 2215 2480 328808308 328808043 2.060000e-43 187.0
16 TraesCS4A01G114700 chr5A 97.297 37 1 0 3651 3687 709180563 709180599 3.630000e-06 63.9
17 TraesCS4A01G114700 chr5D 86.988 953 87 25 2582 3502 28880957 28880010 0.000000e+00 1038.0
18 TraesCS4A01G114700 chr5D 83.087 881 100 25 997 1855 28882212 28881359 0.000000e+00 756.0
19 TraesCS4A01G114700 chr5D 93.478 322 21 0 2179 2500 28881282 28880961 3.040000e-131 479.0
20 TraesCS4A01G114700 chr5D 85.514 214 27 4 1381 1592 244628172 244627961 2.030000e-53 220.0
21 TraesCS4A01G114700 chr5D 80.292 274 52 2 2215 2487 244626057 244625785 5.700000e-49 206.0
22 TraesCS4A01G114700 chr5B 89.429 350 31 4 2997 3340 21381465 21381116 1.860000e-118 436.0
23 TraesCS4A01G114700 chr5B 78.909 275 56 2 2215 2488 278013731 278013458 7.420000e-43 185.0
24 TraesCS4A01G114700 chr2A 79.811 634 96 26 3730 4345 157528155 157528774 2.400000e-117 433.0
25 TraesCS4A01G114700 chr2A 90.164 122 10 2 2722 2842 104117120 104117240 1.620000e-34 158.0
26 TraesCS4A01G114700 chr2D 79.367 664 93 18 2186 2842 107716167 107716793 1.120000e-115 427.0
27 TraesCS4A01G114700 chr2D 81.132 212 33 6 4137 4344 398417732 398417524 3.480000e-36 163.0
28 TraesCS4A01G114700 chr3A 83.905 379 57 4 1224 1600 596794306 596794682 4.130000e-95 359.0
29 TraesCS4A01G114700 chr3D 83.465 381 59 4 1224 1602 454746032 454746410 6.910000e-93 351.0
30 TraesCS4A01G114700 chr3B 83.465 381 57 6 1225 1602 597545442 597545819 2.490000e-92 350.0
31 TraesCS4A01G114700 chr3B 76.436 505 88 19 3655 4143 785729231 785729720 1.210000e-60 244.0
32 TraesCS4A01G114700 chr1D 77.654 537 88 26 3648 4164 27786322 27785798 9.140000e-77 298.0
33 TraesCS4A01G114700 chr1D 74.689 644 108 41 3662 4282 27878082 27878693 7.260000e-58 235.0
34 TraesCS4A01G114700 chr1D 76.980 404 56 26 3655 4038 491763322 491763708 3.430000e-46 196.0
35 TraesCS4A01G114700 chr1D 75.141 354 82 6 1245 1595 381019051 381019401 1.250000e-35 161.0
36 TraesCS4A01G114700 chr1D 74.661 221 50 6 2992 3209 379911257 379911040 4.630000e-15 93.5
37 TraesCS4A01G114700 chr1D 94.872 39 2 0 2450 2488 379911733 379911695 1.300000e-05 62.1
38 TraesCS4A01G114700 chrUn 74.433 661 121 37 3638 4281 146316715 146316086 1.560000e-59 241.0
39 TraesCS4A01G114700 chrUn 73.570 647 120 39 3655 4281 146405573 146404958 2.650000e-47 200.0
40 TraesCS4A01G114700 chr2B 81.570 293 41 12 4062 4344 223837624 223837335 3.380000e-56 230.0
41 TraesCS4A01G114700 chr7D 80.392 306 49 11 4041 4337 68927629 68927932 5.660000e-54 222.0
42 TraesCS4A01G114700 chr7D 84.106 151 23 1 4196 4345 557354990 557354840 1.260000e-30 145.0
43 TraesCS4A01G114700 chr7D 92.857 42 3 0 3657 3698 40262168 40262209 1.300000e-05 62.1
44 TraesCS4A01G114700 chr1B 75.989 354 77 8 1245 1594 510808834 510809183 4.470000e-40 176.0
45 TraesCS4A01G114700 chr7A 91.892 74 5 1 3655 3727 79228477 79228550 7.690000e-18 102.0
46 TraesCS4A01G114700 chr1A 94.737 38 2 0 2450 2487 480934894 480934857 4.690000e-05 60.2
47 TraesCS4A01G114700 chr6D 100.000 28 0 0 2793 2820 27460525 27460498 8.000000e-03 52.8
48 TraesCS4A01G114700 chr6A 100.000 28 0 0 2793 2820 30796775 30796748 8.000000e-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 TraesCS4A01G114700 chr4A 139544014 139548358 4344 False 3810.400000 7555 100.000000 1 4345 2 chr4A.!!$F3 4344
1 TraesCS4A01G114700 chr4D 334116274 334119444 3170 True 1540.666667 2615 91.482333 430 3618 3 chr4D.!!$R1 3188
2 TraesCS4A01G114700 chr4B 412105713 412108827 3114 True 1469.666667 2471 91.817333 500 3584 3 chr4B.!!$R1 3084
3 TraesCS4A01G114700 chr5A 19540091 19542262 2171 True 604.750000 1057 89.792000 997 3499 4 chr5A.!!$R1 2502
4 TraesCS4A01G114700 chr5A 328808043 328810622 2579 True 201.000000 215 82.300500 1381 2480 2 chr5A.!!$R2 1099
5 TraesCS4A01G114700 chr5D 28880010 28882212 2202 True 757.666667 1038 87.851000 997 3502 3 chr5D.!!$R1 2505
6 TraesCS4A01G114700 chr5D 244625785 244628172 2387 True 213.000000 220 82.903000 1381 2487 2 chr5D.!!$R2 1106
7 TraesCS4A01G114700 chr2A 157528155 157528774 619 False 433.000000 433 79.811000 3730 4345 1 chr2A.!!$F2 615
8 TraesCS4A01G114700 chr2D 107716167 107716793 626 False 427.000000 427 79.367000 2186 2842 1 chr2D.!!$F1 656
9 TraesCS4A01G114700 chr1D 27785798 27786322 524 True 298.000000 298 77.654000 3648 4164 1 chr1D.!!$R1 516
10 TraesCS4A01G114700 chr1D 27878082 27878693 611 False 235.000000 235 74.689000 3662 4282 1 chr1D.!!$F1 620
11 TraesCS4A01G114700 chrUn 146316086 146316715 629 True 241.000000 241 74.433000 3638 4281 1 chrUn.!!$R1 643

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
826 860 0.029300 CAAACAACCGCACTGACCTG 59.971 55.0 0.00 0.00 0.00 4.00 F
1648 1752 0.043907 CGTAGCACGCATGTCGATTG 60.044 55.0 14.88 6.26 41.67 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2173 4164 1.000274 TCGTCTCTGTGTGGTGATGTG 60.000 52.381 0.0 0.0 0.00 3.21 R
3491 5517 0.397564 AGGAGGCCCGTAACGAAAAA 59.602 50.000 0.0 0.0 37.58 1.94 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
17 18 2.979676 TCAAGGTTGCAGCAGCGG 60.980 61.111 2.05 0.00 46.23 5.52
18 19 2.979676 CAAGGTTGCAGCAGCGGA 60.980 61.111 2.05 0.00 46.23 5.54
19 20 2.670934 AAGGTTGCAGCAGCGGAG 60.671 61.111 2.05 0.00 46.23 4.63
20 21 3.182590 AAGGTTGCAGCAGCGGAGA 62.183 57.895 2.05 0.00 46.23 3.71
21 22 2.437359 GGTTGCAGCAGCGGAGAT 60.437 61.111 2.05 0.00 46.23 2.75
22 23 1.153369 GGTTGCAGCAGCGGAGATA 60.153 57.895 2.05 0.00 46.23 1.98
23 24 0.533755 GGTTGCAGCAGCGGAGATAT 60.534 55.000 2.05 0.00 46.23 1.63
24 25 0.585357 GTTGCAGCAGCGGAGATATG 59.415 55.000 0.00 0.00 46.23 1.78
25 26 0.178767 TTGCAGCAGCGGAGATATGT 59.821 50.000 0.00 0.00 46.23 2.29
26 27 0.531311 TGCAGCAGCGGAGATATGTG 60.531 55.000 0.00 0.00 46.23 3.21
27 28 0.531532 GCAGCAGCGGAGATATGTGT 60.532 55.000 0.00 0.00 0.00 3.72
28 29 1.495878 CAGCAGCGGAGATATGTGTC 58.504 55.000 0.00 0.00 0.00 3.67
29 30 1.114627 AGCAGCGGAGATATGTGTCA 58.885 50.000 0.00 0.00 0.00 3.58
30 31 1.482182 AGCAGCGGAGATATGTGTCAA 59.518 47.619 0.00 0.00 0.00 3.18
31 32 2.103771 AGCAGCGGAGATATGTGTCAAT 59.896 45.455 0.00 0.00 0.00 2.57
32 33 2.874701 GCAGCGGAGATATGTGTCAATT 59.125 45.455 0.00 0.00 0.00 2.32
33 34 3.313526 GCAGCGGAGATATGTGTCAATTT 59.686 43.478 0.00 0.00 0.00 1.82
34 35 4.553547 GCAGCGGAGATATGTGTCAATTTC 60.554 45.833 0.00 0.00 0.00 2.17
293 294 3.890674 GGAGGCAACACCGATGTC 58.109 61.111 0.00 0.00 46.52 3.06
294 295 2.100631 GGAGGCAACACCGATGTCG 61.101 63.158 0.00 0.00 46.52 4.35
295 296 1.080093 GAGGCAACACCGATGTCGA 60.080 57.895 3.62 0.00 46.52 4.20
296 297 0.460284 GAGGCAACACCGATGTCGAT 60.460 55.000 3.62 0.00 46.52 3.59
297 298 0.740868 AGGCAACACCGATGTCGATG 60.741 55.000 3.62 0.00 46.52 3.84
298 299 1.060937 GCAACACCGATGTCGATGC 59.939 57.895 3.62 5.53 36.00 3.91
299 300 1.634757 GCAACACCGATGTCGATGCA 61.635 55.000 0.02 0.00 36.00 3.96
300 301 0.371301 CAACACCGATGTCGATGCAG 59.629 55.000 3.62 0.00 36.00 4.41
301 302 0.037326 AACACCGATGTCGATGCAGT 60.037 50.000 3.62 0.00 36.00 4.40
302 303 0.737367 ACACCGATGTCGATGCAGTG 60.737 55.000 3.62 5.71 36.00 3.66
303 304 0.737367 CACCGATGTCGATGCAGTGT 60.737 55.000 3.62 0.00 43.02 3.55
304 305 0.737367 ACCGATGTCGATGCAGTGTG 60.737 55.000 3.62 0.00 43.02 3.82
305 306 0.458370 CCGATGTCGATGCAGTGTGA 60.458 55.000 3.62 0.00 43.02 3.58
306 307 0.919300 CGATGTCGATGCAGTGTGAG 59.081 55.000 0.00 0.00 43.02 3.51
307 308 0.649475 GATGTCGATGCAGTGTGAGC 59.351 55.000 0.00 0.00 0.00 4.26
308 309 1.080435 ATGTCGATGCAGTGTGAGCG 61.080 55.000 0.00 0.00 33.85 5.03
309 310 2.125952 TCGATGCAGTGTGAGCGG 60.126 61.111 0.00 0.00 33.85 5.52
310 311 2.125952 CGATGCAGTGTGAGCGGA 60.126 61.111 0.00 0.00 33.85 5.54
311 312 1.520120 CGATGCAGTGTGAGCGGAT 60.520 57.895 0.00 0.00 33.85 4.18
312 313 1.485838 CGATGCAGTGTGAGCGGATC 61.486 60.000 0.00 0.00 33.85 3.36
313 314 0.460811 GATGCAGTGTGAGCGGATCA 60.461 55.000 0.00 0.00 34.79 2.92
314 315 0.461516 ATGCAGTGTGAGCGGATCAG 60.462 55.000 0.00 0.00 39.07 2.90
315 316 1.216444 GCAGTGTGAGCGGATCAGA 59.784 57.895 0.00 0.00 39.07 3.27
316 317 0.805322 GCAGTGTGAGCGGATCAGAG 60.805 60.000 0.00 0.00 39.07 3.35
317 318 0.179116 CAGTGTGAGCGGATCAGAGG 60.179 60.000 0.00 0.00 39.07 3.69
318 319 1.142748 GTGTGAGCGGATCAGAGGG 59.857 63.158 0.00 0.00 39.07 4.30
319 320 2.107953 GTGAGCGGATCAGAGGGC 59.892 66.667 0.00 0.00 39.07 5.19
320 321 3.157252 TGAGCGGATCAGAGGGCC 61.157 66.667 0.00 0.00 32.77 5.80
326 327 3.808984 GGATCAGAGGGCCGAAATT 57.191 52.632 0.00 0.00 0.00 1.82
327 328 2.930826 GGATCAGAGGGCCGAAATTA 57.069 50.000 0.00 0.00 0.00 1.40
328 329 3.425162 GGATCAGAGGGCCGAAATTAT 57.575 47.619 0.00 0.00 0.00 1.28
329 330 3.756117 GGATCAGAGGGCCGAAATTATT 58.244 45.455 0.00 0.00 0.00 1.40
330 331 3.753797 GGATCAGAGGGCCGAAATTATTC 59.246 47.826 0.00 0.00 0.00 1.75
331 332 3.208747 TCAGAGGGCCGAAATTATTCC 57.791 47.619 0.00 0.00 31.52 3.01
332 333 1.873591 CAGAGGGCCGAAATTATTCCG 59.126 52.381 0.00 0.00 31.52 4.30
333 334 1.766496 AGAGGGCCGAAATTATTCCGA 59.234 47.619 0.00 0.00 31.52 4.55
334 335 2.143925 GAGGGCCGAAATTATTCCGAG 58.856 52.381 0.00 0.00 31.52 4.63
335 336 1.766496 AGGGCCGAAATTATTCCGAGA 59.234 47.619 0.00 0.00 31.52 4.04
336 337 2.171870 AGGGCCGAAATTATTCCGAGAA 59.828 45.455 0.00 0.00 31.52 2.87
337 338 3.146847 GGGCCGAAATTATTCCGAGAAT 58.853 45.455 0.00 4.82 31.52 2.40
338 339 3.568430 GGGCCGAAATTATTCCGAGAATT 59.432 43.478 0.00 0.00 31.52 2.17
339 340 4.537015 GGCCGAAATTATTCCGAGAATTG 58.463 43.478 4.76 0.00 31.52 2.32
340 341 4.274950 GGCCGAAATTATTCCGAGAATTGA 59.725 41.667 4.76 0.00 31.52 2.57
341 342 5.205565 GCCGAAATTATTCCGAGAATTGAC 58.794 41.667 4.76 0.00 31.52 3.18
342 343 5.220777 GCCGAAATTATTCCGAGAATTGACA 60.221 40.000 4.76 0.00 31.52 3.58
343 344 6.513393 GCCGAAATTATTCCGAGAATTGACAT 60.513 38.462 4.76 0.00 31.52 3.06
344 345 7.072030 CCGAAATTATTCCGAGAATTGACATC 58.928 38.462 4.76 0.00 31.52 3.06
345 346 6.787515 CGAAATTATTCCGAGAATTGACATCG 59.212 38.462 4.76 6.07 36.24 3.84
352 353 4.864916 CGAGAATTGACATCGGACAAAT 57.135 40.909 0.00 0.00 32.71 2.32
353 354 5.966636 CGAGAATTGACATCGGACAAATA 57.033 39.130 0.00 0.00 32.71 1.40
354 355 6.530913 CGAGAATTGACATCGGACAAATAT 57.469 37.500 0.00 0.00 32.71 1.28
355 356 7.637709 CGAGAATTGACATCGGACAAATATA 57.362 36.000 0.00 0.00 32.71 0.86
356 357 8.244494 CGAGAATTGACATCGGACAAATATAT 57.756 34.615 0.00 0.00 32.71 0.86
357 358 8.712363 CGAGAATTGACATCGGACAAATATATT 58.288 33.333 0.00 0.00 32.71 1.28
363 364 8.615878 TGACATCGGACAAATATATTTAAGGG 57.384 34.615 10.34 1.57 0.00 3.95
364 365 7.174253 TGACATCGGACAAATATATTTAAGGGC 59.826 37.037 10.34 1.22 0.00 5.19
365 366 7.001674 ACATCGGACAAATATATTTAAGGGCA 58.998 34.615 10.34 0.00 0.00 5.36
366 367 7.504238 ACATCGGACAAATATATTTAAGGGCAA 59.496 33.333 10.34 0.00 0.00 4.52
367 368 7.504924 TCGGACAAATATATTTAAGGGCAAG 57.495 36.000 10.34 0.00 0.00 4.01
368 369 6.016610 TCGGACAAATATATTTAAGGGCAAGC 60.017 38.462 10.34 0.00 0.00 4.01
369 370 6.455647 GGACAAATATATTTAAGGGCAAGCC 58.544 40.000 10.34 1.52 0.00 4.35
370 371 6.084326 ACAAATATATTTAAGGGCAAGCCG 57.916 37.500 10.34 0.00 36.85 5.52
371 372 5.830991 ACAAATATATTTAAGGGCAAGCCGA 59.169 36.000 10.34 0.00 36.85 5.54
372 373 6.016276 ACAAATATATTTAAGGGCAAGCCGAG 60.016 38.462 10.34 0.00 36.85 4.63
373 374 1.675552 TATTTAAGGGCAAGCCGAGC 58.324 50.000 4.80 0.00 36.85 5.03
388 389 4.074647 AGCCGGCGCTTAAAACTT 57.925 50.000 23.20 0.00 45.55 2.66
389 390 2.337361 AGCCGGCGCTTAAAACTTT 58.663 47.368 23.20 0.00 45.55 2.66
390 391 0.039527 AGCCGGCGCTTAAAACTTTG 60.040 50.000 23.20 0.00 45.55 2.77
391 392 0.039888 GCCGGCGCTTAAAACTTTGA 60.040 50.000 12.58 0.00 0.00 2.69
392 393 1.600912 GCCGGCGCTTAAAACTTTGAA 60.601 47.619 12.58 0.00 0.00 2.69
393 394 2.315901 CCGGCGCTTAAAACTTTGAAG 58.684 47.619 7.64 0.00 0.00 3.02
394 395 2.315901 CGGCGCTTAAAACTTTGAAGG 58.684 47.619 7.64 0.00 0.00 3.46
395 396 2.031508 CGGCGCTTAAAACTTTGAAGGA 60.032 45.455 7.64 0.00 0.00 3.36
396 397 3.565516 GGCGCTTAAAACTTTGAAGGAG 58.434 45.455 7.64 0.00 0.00 3.69
397 398 3.004419 GGCGCTTAAAACTTTGAAGGAGT 59.996 43.478 7.64 0.00 0.00 3.85
398 399 4.499188 GGCGCTTAAAACTTTGAAGGAGTT 60.499 41.667 7.64 0.00 38.92 3.01
399 400 5.278120 GGCGCTTAAAACTTTGAAGGAGTTA 60.278 40.000 7.64 0.00 36.38 2.24
400 401 6.379386 GCGCTTAAAACTTTGAAGGAGTTAT 58.621 36.000 0.00 0.00 36.38 1.89
401 402 7.361457 GGCGCTTAAAACTTTGAAGGAGTTATA 60.361 37.037 7.64 0.00 36.38 0.98
402 403 8.019094 GCGCTTAAAACTTTGAAGGAGTTATAA 58.981 33.333 0.00 0.00 36.38 0.98
403 404 9.543018 CGCTTAAAACTTTGAAGGAGTTATAAG 57.457 33.333 1.44 0.00 36.38 1.73
404 405 9.343103 GCTTAAAACTTTGAAGGAGTTATAAGC 57.657 33.333 1.44 0.00 36.38 3.09
408 409 8.691661 AAACTTTGAAGGAGTTATAAGCAAGA 57.308 30.769 0.00 0.00 36.38 3.02
409 410 8.870075 AACTTTGAAGGAGTTATAAGCAAGAT 57.130 30.769 0.00 0.00 35.68 2.40
410 411 9.959721 AACTTTGAAGGAGTTATAAGCAAGATA 57.040 29.630 0.00 0.00 35.68 1.98
411 412 9.959721 ACTTTGAAGGAGTTATAAGCAAGATAA 57.040 29.630 0.00 0.00 0.00 1.75
413 414 9.959721 TTTGAAGGAGTTATAAGCAAGATAAGT 57.040 29.630 0.00 0.00 0.00 2.24
414 415 8.948631 TGAAGGAGTTATAAGCAAGATAAGTG 57.051 34.615 0.00 0.00 0.00 3.16
415 416 8.540388 TGAAGGAGTTATAAGCAAGATAAGTGT 58.460 33.333 0.00 0.00 0.00 3.55
416 417 9.384764 GAAGGAGTTATAAGCAAGATAAGTGTT 57.615 33.333 0.00 0.00 0.00 3.32
417 418 8.723942 AGGAGTTATAAGCAAGATAAGTGTTG 57.276 34.615 0.00 0.00 0.00 3.33
418 419 7.770897 AGGAGTTATAAGCAAGATAAGTGTTGG 59.229 37.037 0.00 0.00 0.00 3.77
419 420 7.769044 GGAGTTATAAGCAAGATAAGTGTTGGA 59.231 37.037 0.00 0.00 0.00 3.53
420 421 8.494016 AGTTATAAGCAAGATAAGTGTTGGAC 57.506 34.615 0.00 0.00 0.00 4.02
421 422 7.553044 AGTTATAAGCAAGATAAGTGTTGGACC 59.447 37.037 0.00 0.00 0.00 4.46
422 423 3.788227 AGCAAGATAAGTGTTGGACCA 57.212 42.857 0.00 0.00 0.00 4.02
423 424 3.679389 AGCAAGATAAGTGTTGGACCAG 58.321 45.455 0.00 0.00 0.00 4.00
424 425 2.749621 GCAAGATAAGTGTTGGACCAGG 59.250 50.000 0.00 0.00 0.00 4.45
425 426 3.810743 GCAAGATAAGTGTTGGACCAGGT 60.811 47.826 0.00 0.00 0.00 4.00
426 427 3.983044 AGATAAGTGTTGGACCAGGTC 57.017 47.619 11.70 11.70 0.00 3.85
444 445 4.631813 CAGGTCCGATTTAACTCCTCAAAG 59.368 45.833 0.00 0.00 0.00 2.77
446 447 3.062234 GTCCGATTTAACTCCTCAAAGCG 59.938 47.826 0.00 0.00 41.70 4.68
518 519 8.700973 AGAGAAACTCTTAGTCAGAAAAGAAGT 58.299 33.333 0.00 0.00 37.60 3.01
548 549 2.679355 TTTCAACGTTTGCTCGATGG 57.321 45.000 0.00 0.00 35.07 3.51
578 579 3.021695 TCTACCTTGTCGATTGACCGAT 58.978 45.455 10.69 0.00 44.86 4.18
621 622 1.271054 GGCCGATCTACCATTCTGCAT 60.271 52.381 0.00 0.00 0.00 3.96
624 625 3.257393 CCGATCTACCATTCTGCATAGC 58.743 50.000 0.00 0.00 0.00 2.97
625 626 3.306294 CCGATCTACCATTCTGCATAGCA 60.306 47.826 0.00 0.00 36.92 3.49
626 627 4.502016 CGATCTACCATTCTGCATAGCAT 58.498 43.478 0.00 0.00 38.13 3.79
665 666 1.470494 TGAGCAAAGTGAAACGCAACA 59.530 42.857 0.00 0.00 45.86 3.33
666 667 2.095008 TGAGCAAAGTGAAACGCAACAA 60.095 40.909 0.00 0.00 45.86 2.83
667 668 2.258755 AGCAAAGTGAAACGCAACAAC 58.741 42.857 0.00 0.00 45.86 3.32
668 669 1.007524 GCAAAGTGAAACGCAACAACG 60.008 47.619 0.00 0.00 45.86 4.10
669 670 1.007524 CAAAGTGAAACGCAACAACGC 60.008 47.619 0.00 0.00 45.86 4.84
670 671 0.169230 AAGTGAAACGCAACAACGCA 59.831 45.000 0.00 0.00 45.86 5.24
671 672 0.380378 AGTGAAACGCAACAACGCAT 59.620 45.000 0.00 0.00 45.86 4.73
672 673 0.498095 GTGAAACGCAACAACGCATG 59.502 50.000 0.00 0.00 36.19 4.06
673 674 0.593518 TGAAACGCAACAACGCATGG 60.594 50.000 0.00 0.00 36.19 3.66
674 675 1.875419 GAAACGCAACAACGCATGGC 61.875 55.000 0.00 0.00 36.19 4.40
747 748 0.613777 AGACCGTCCTTAAAGGGCAG 59.386 55.000 0.00 0.00 40.96 4.85
826 860 0.029300 CAAACAACCGCACTGACCTG 59.971 55.000 0.00 0.00 0.00 4.00
827 861 0.107410 AAACAACCGCACTGACCTGA 60.107 50.000 0.00 0.00 0.00 3.86
829 863 1.961277 CAACCGCACTGACCTGACC 60.961 63.158 0.00 0.00 0.00 4.02
830 864 2.140792 AACCGCACTGACCTGACCT 61.141 57.895 0.00 0.00 0.00 3.85
836 870 2.122729 CTGACCTGACCTCCCCCA 59.877 66.667 0.00 0.00 0.00 4.96
838 872 2.450243 GACCTGACCTCCCCCAGA 59.550 66.667 0.00 0.00 32.37 3.86
878 912 2.902846 CGATCGGCGAGAGGACCT 60.903 66.667 17.22 0.00 44.57 3.85
888 922 4.751098 CGGCGAGAGGACCTCTATATATAC 59.249 50.000 24.36 8.88 41.35 1.47
889 923 5.453621 CGGCGAGAGGACCTCTATATATACT 60.454 48.000 24.36 0.00 41.35 2.12
901 935 7.045416 CCTCTATATATACTCAGTCTCGCACT 58.955 42.308 0.00 0.00 34.67 4.40
930 964 3.384146 TGTCATCAAGGCAACAACAACAT 59.616 39.130 0.00 0.00 41.41 2.71
932 966 3.890756 TCATCAAGGCAACAACAACATCT 59.109 39.130 0.00 0.00 41.41 2.90
959 993 2.290514 TGGCAGAATTAAGTGAGCAGCT 60.291 45.455 0.00 0.00 0.00 4.24
960 994 3.055167 TGGCAGAATTAAGTGAGCAGCTA 60.055 43.478 0.00 0.00 0.00 3.32
961 995 3.559242 GGCAGAATTAAGTGAGCAGCTAG 59.441 47.826 0.00 0.00 0.00 3.42
962 996 3.002144 GCAGAATTAAGTGAGCAGCTAGC 59.998 47.826 6.62 6.62 46.19 3.42
994 1028 1.561542 CCCATTGGAAGGAGCTAGTGT 59.438 52.381 3.62 0.00 0.00 3.55
995 1029 2.025887 CCCATTGGAAGGAGCTAGTGTT 60.026 50.000 3.62 0.00 0.00 3.32
1060 1107 0.610174 CTGCTGCCTCTCTGGTGTTA 59.390 55.000 0.00 0.00 38.35 2.41
1062 1109 1.208052 TGCTGCCTCTCTGGTGTTATC 59.792 52.381 0.00 0.00 38.35 1.75
1130 1185 3.712162 CGAGTTCGTTGTACGTCTCTA 57.288 47.619 17.09 0.00 43.14 2.43
1634 1716 1.028868 AGTCGTCCTGGGTACGTAGC 61.029 60.000 16.33 16.33 41.08 3.58
1648 1752 0.043907 CGTAGCACGCATGTCGATTG 60.044 55.000 14.88 6.26 41.67 2.67
1659 1763 4.363138 GCATGTCGATTGATACTGTCTGA 58.637 43.478 0.00 0.00 0.00 3.27
1660 1764 4.443725 GCATGTCGATTGATACTGTCTGAG 59.556 45.833 0.00 0.00 0.00 3.35
1661 1765 5.734503 GCATGTCGATTGATACTGTCTGAGA 60.735 44.000 0.00 0.00 0.00 3.27
1662 1766 5.491635 TGTCGATTGATACTGTCTGAGAG 57.508 43.478 0.00 0.00 0.00 3.20
1665 1769 5.525745 GTCGATTGATACTGTCTGAGAGAGA 59.474 44.000 14.03 0.00 0.00 3.10
1693 3226 5.048643 TCACTTGGTTTGTTTCGTTTCTGAA 60.049 36.000 0.00 0.00 0.00 3.02
1694 3227 5.804979 CACTTGGTTTGTTTCGTTTCTGAAT 59.195 36.000 0.00 0.00 0.00 2.57
1695 3228 6.310224 CACTTGGTTTGTTTCGTTTCTGAATT 59.690 34.615 0.00 0.00 0.00 2.17
1696 3229 6.530181 ACTTGGTTTGTTTCGTTTCTGAATTC 59.470 34.615 0.00 0.00 0.00 2.17
1701 3234 7.113544 GGTTTGTTTCGTTTCTGAATTCTGATC 59.886 37.037 14.89 10.58 0.00 2.92
1872 3816 2.717809 GAGCGTCGCTTCGGTTGTC 61.718 63.158 22.67 1.79 39.88 3.18
1910 3854 5.570973 CGATTCATTATTGCGGTTGTTGAAA 59.429 36.000 0.00 0.00 0.00 2.69
1940 3900 6.261826 CAGTGTTCTTTTGAGTTCTCCATTCT 59.738 38.462 0.00 0.00 0.00 2.40
1949 3909 3.672808 AGTTCTCCATTCTCTTGCAGTG 58.327 45.455 0.00 0.00 0.00 3.66
1977 3937 4.411256 TCCAGATATGGTTAAACCGACC 57.589 45.455 6.21 0.00 42.58 4.79
1988 3948 5.185442 TGGTTAAACCGACCAAAAGAACTTT 59.815 36.000 0.00 0.00 43.87 2.66
2029 3989 2.146342 CCATCTCAGCACGTGAAAGTT 58.854 47.619 22.23 4.96 33.60 2.66
2080 4071 3.505293 GGTCTTGTCTAACACTACGACCT 59.495 47.826 0.00 0.00 37.34 3.85
2081 4072 4.697352 GGTCTTGTCTAACACTACGACCTA 59.303 45.833 0.00 0.00 37.34 3.08
2082 4073 5.391416 GGTCTTGTCTAACACTACGACCTAC 60.391 48.000 0.00 0.00 37.34 3.18
2807 4805 0.163788 CGAGCATGAACAACGTGTCC 59.836 55.000 0.00 0.00 37.77 4.02
3335 5333 4.803426 CTCGACCTGCCCGTCTGC 62.803 72.222 0.00 0.00 0.00 4.26
3491 5517 8.785329 TTTGAAATTGTAAAGAAAAGGCAAGT 57.215 26.923 0.00 0.00 0.00 3.16
3521 5547 6.512253 CGTTACGGGCCTCCTTTTTATTTATC 60.512 42.308 0.84 0.00 0.00 1.75
3589 5619 0.618458 TGAAGCGGCCTCCTTACAAT 59.382 50.000 0.00 0.00 0.00 2.71
3595 5625 3.453353 AGCGGCCTCCTTACAATTAACTA 59.547 43.478 0.00 0.00 0.00 2.24
3600 5630 6.504398 GGCCTCCTTACAATTAACTAAATGC 58.496 40.000 0.00 0.00 0.00 3.56
3603 5633 7.649306 GCCTCCTTACAATTAACTAAATGCATG 59.351 37.037 0.00 0.00 0.00 4.06
3604 5634 8.902806 CCTCCTTACAATTAACTAAATGCATGA 58.097 33.333 0.00 0.00 0.00 3.07
3605 5635 9.722056 CTCCTTACAATTAACTAAATGCATGAC 57.278 33.333 0.00 0.00 0.00 3.06
3642 5673 7.680730 ACCCTAAATACATGTCCTAAGCTATG 58.319 38.462 0.00 0.00 0.00 2.23
3645 5676 2.938956 ACATGTCCTAAGCTATGGCC 57.061 50.000 0.00 0.00 39.73 5.36
3652 5683 1.366319 CTAAGCTATGGCCAGGGGAT 58.634 55.000 13.05 0.00 39.73 3.85
3653 5684 2.551270 CTAAGCTATGGCCAGGGGATA 58.449 52.381 13.05 0.00 39.73 2.59
3759 5790 3.074412 AGTACAGAACCGAAAATGCAGG 58.926 45.455 0.00 0.00 0.00 4.85
3802 5836 0.462759 GAAGGGATGGAACCAGCGAG 60.463 60.000 3.04 0.00 32.44 5.03
3820 5854 2.326897 CGCATGCGCATCCTTCTG 59.673 61.111 29.09 11.36 38.40 3.02
3821 5855 2.175621 CGCATGCGCATCCTTCTGA 61.176 57.895 29.09 0.00 38.40 3.27
3822 5856 1.647629 GCATGCGCATCCTTCTGAG 59.352 57.895 22.51 7.89 38.36 3.35
3823 5857 0.812811 GCATGCGCATCCTTCTGAGA 60.813 55.000 22.51 0.00 38.36 3.27
3824 5858 1.660167 CATGCGCATCCTTCTGAGAA 58.340 50.000 22.51 0.00 0.00 2.87
3825 5859 2.011947 CATGCGCATCCTTCTGAGAAA 58.988 47.619 22.51 0.00 0.00 2.52
3826 5860 2.183478 TGCGCATCCTTCTGAGAAAA 57.817 45.000 5.66 0.00 0.00 2.29
3827 5861 2.715046 TGCGCATCCTTCTGAGAAAAT 58.285 42.857 5.66 0.00 0.00 1.82
3828 5862 2.421073 TGCGCATCCTTCTGAGAAAATG 59.579 45.455 5.66 11.04 0.00 2.32
3840 5874 0.731417 AGAAAATGCTGCTGCTAGCG 59.269 50.000 17.00 6.22 46.26 4.26
3843 5877 1.712977 AAATGCTGCTGCTAGCGAGC 61.713 55.000 23.83 23.83 46.26 5.03
3852 5886 3.354131 GCTAGCGAGCTTAGCTTGT 57.646 52.632 21.13 11.39 45.98 3.16
3854 5888 1.737363 GCTAGCGAGCTTAGCTTGTGT 60.737 52.381 21.13 12.27 45.98 3.72
3855 5889 2.479730 GCTAGCGAGCTTAGCTTGTGTA 60.480 50.000 21.13 12.69 45.98 2.90
3857 5891 0.640768 GCGAGCTTAGCTTGTGTACG 59.359 55.000 21.13 13.71 41.74 3.67
3886 5935 4.584394 CGCATATTAAGAACCAAACCGAC 58.416 43.478 0.00 0.00 0.00 4.79
3890 5940 1.504359 TAAGAACCAAACCGACTGCG 58.496 50.000 0.00 0.00 37.24 5.18
3909 5959 3.058777 TGCGGATCCGAACACTTTTAAAC 60.059 43.478 37.64 14.90 42.83 2.01
3931 5982 6.720012 ACTTTGAACGCAAAACAATTTTCT 57.280 29.167 0.00 0.00 42.96 2.52
3968 6020 4.491234 TGTTTTATGAAACCGCGAACAT 57.509 36.364 8.23 9.91 43.57 2.71
4073 6136 9.480861 TTTTAAAACTCCCCCAAAAATTGAAAT 57.519 25.926 0.00 0.00 0.00 2.17
4078 6141 1.999024 CCCCAAAAATTGAAATCGCGG 59.001 47.619 6.13 0.00 0.00 6.46
4081 6144 3.312828 CCAAAAATTGAAATCGCGGACA 58.687 40.909 6.13 0.00 0.00 4.02
4087 6150 5.761818 AATTGAAATCGCGGACATTTTTC 57.238 34.783 6.13 7.34 0.00 2.29
4094 6157 3.623863 TCGCGGACATTTTTCTGAAAAC 58.376 40.909 14.70 4.18 37.56 2.43
4149 6214 7.769719 TTAGATACGCAAACATTTTCGAAAC 57.230 32.000 10.79 0.00 31.46 2.78
4154 6220 3.733224 CGCAAACATTTTCGAAACATGGA 59.267 39.130 24.09 9.04 0.00 3.41
4307 6377 9.295825 ACTACCAGACAACAATTGAAAATATGA 57.704 29.630 13.59 0.00 0.00 2.15
4310 6380 9.829507 ACCAGACAACAATTGAAAATATGAAAA 57.170 25.926 13.59 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.979676 CCGCTGCTGCAACCTTGA 60.980 61.111 16.29 0.00 39.64 3.02
1 2 2.974489 CTCCGCTGCTGCAACCTTG 61.974 63.158 16.29 0.00 39.64 3.61
2 3 2.475371 ATCTCCGCTGCTGCAACCTT 62.475 55.000 16.29 0.00 39.64 3.50
3 4 1.617018 TATCTCCGCTGCTGCAACCT 61.617 55.000 16.29 0.00 39.64 3.50
4 5 0.533755 ATATCTCCGCTGCTGCAACC 60.534 55.000 16.29 0.00 39.64 3.77
5 6 0.585357 CATATCTCCGCTGCTGCAAC 59.415 55.000 16.29 0.00 39.64 4.17
6 7 0.178767 ACATATCTCCGCTGCTGCAA 59.821 50.000 16.29 2.03 39.64 4.08
7 8 0.531311 CACATATCTCCGCTGCTGCA 60.531 55.000 16.29 0.88 39.64 4.41
8 9 0.531532 ACACATATCTCCGCTGCTGC 60.532 55.000 5.34 5.34 0.00 5.25
9 10 1.202452 TGACACATATCTCCGCTGCTG 60.202 52.381 0.00 0.00 0.00 4.41
10 11 1.114627 TGACACATATCTCCGCTGCT 58.885 50.000 0.00 0.00 0.00 4.24
11 12 1.939974 TTGACACATATCTCCGCTGC 58.060 50.000 0.00 0.00 0.00 5.25
12 13 5.088141 GAAATTGACACATATCTCCGCTG 57.912 43.478 0.00 0.00 0.00 5.18
274 275 2.819595 CATCGGTGTTGCCTCCGG 60.820 66.667 0.00 0.00 45.48 5.14
275 276 2.047274 ACATCGGTGTTGCCTCCG 60.047 61.111 0.00 0.00 46.50 4.63
276 277 2.100631 CGACATCGGTGTTGCCTCC 61.101 63.158 1.13 0.00 39.09 4.30
277 278 0.460284 ATCGACATCGGTGTTGCCTC 60.460 55.000 11.47 0.00 39.09 4.70
278 279 0.740868 CATCGACATCGGTGTTGCCT 60.741 55.000 11.47 0.00 44.76 4.75
279 280 1.715585 CATCGACATCGGTGTTGCC 59.284 57.895 11.47 0.00 44.76 4.52
285 286 0.737367 CACACTGCATCGACATCGGT 60.737 55.000 0.73 0.00 40.29 4.69
286 287 0.458370 TCACACTGCATCGACATCGG 60.458 55.000 0.73 0.00 40.29 4.18
287 288 0.919300 CTCACACTGCATCGACATCG 59.081 55.000 0.00 0.00 41.45 3.84
288 289 0.649475 GCTCACACTGCATCGACATC 59.351 55.000 0.00 0.00 0.00 3.06
289 290 1.080435 CGCTCACACTGCATCGACAT 61.080 55.000 0.00 0.00 0.00 3.06
290 291 1.734117 CGCTCACACTGCATCGACA 60.734 57.895 0.00 0.00 0.00 4.35
291 292 2.447887 CCGCTCACACTGCATCGAC 61.448 63.158 0.00 0.00 0.00 4.20
292 293 1.948721 ATCCGCTCACACTGCATCGA 61.949 55.000 0.00 0.00 0.00 3.59
293 294 1.485838 GATCCGCTCACACTGCATCG 61.486 60.000 0.00 0.00 0.00 3.84
294 295 0.460811 TGATCCGCTCACACTGCATC 60.461 55.000 0.00 0.00 0.00 3.91
295 296 0.461516 CTGATCCGCTCACACTGCAT 60.462 55.000 0.00 0.00 0.00 3.96
296 297 1.079612 CTGATCCGCTCACACTGCA 60.080 57.895 0.00 0.00 0.00 4.41
297 298 0.805322 CTCTGATCCGCTCACACTGC 60.805 60.000 0.00 0.00 0.00 4.40
298 299 0.179116 CCTCTGATCCGCTCACACTG 60.179 60.000 0.00 0.00 0.00 3.66
299 300 1.326213 CCCTCTGATCCGCTCACACT 61.326 60.000 0.00 0.00 0.00 3.55
300 301 1.142748 CCCTCTGATCCGCTCACAC 59.857 63.158 0.00 0.00 0.00 3.82
301 302 2.725312 GCCCTCTGATCCGCTCACA 61.725 63.158 0.00 0.00 0.00 3.58
302 303 2.107953 GCCCTCTGATCCGCTCAC 59.892 66.667 0.00 0.00 0.00 3.51
303 304 3.157252 GGCCCTCTGATCCGCTCA 61.157 66.667 0.00 0.00 0.00 4.26
304 305 4.292178 CGGCCCTCTGATCCGCTC 62.292 72.222 0.00 0.00 36.53 5.03
305 306 4.841617 TCGGCCCTCTGATCCGCT 62.842 66.667 0.00 0.00 42.65 5.52
306 307 2.666596 ATTTCGGCCCTCTGATCCGC 62.667 60.000 0.00 0.00 42.65 5.54
307 308 0.179045 AATTTCGGCCCTCTGATCCG 60.179 55.000 0.00 6.76 44.16 4.18
308 309 2.930826 TAATTTCGGCCCTCTGATCC 57.069 50.000 0.00 0.00 0.00 3.36
309 310 3.753797 GGAATAATTTCGGCCCTCTGATC 59.246 47.826 0.00 0.00 32.28 2.92
310 311 3.756117 GGAATAATTTCGGCCCTCTGAT 58.244 45.455 0.00 0.00 32.28 2.90
311 312 2.484770 CGGAATAATTTCGGCCCTCTGA 60.485 50.000 0.00 0.00 32.28 3.27
312 313 1.873591 CGGAATAATTTCGGCCCTCTG 59.126 52.381 0.00 0.00 32.28 3.35
313 314 1.766496 TCGGAATAATTTCGGCCCTCT 59.234 47.619 0.00 0.00 33.47 3.69
314 315 2.143925 CTCGGAATAATTTCGGCCCTC 58.856 52.381 0.00 0.00 33.47 4.30
315 316 1.766496 TCTCGGAATAATTTCGGCCCT 59.234 47.619 0.00 0.00 33.47 5.19
316 317 2.249844 TCTCGGAATAATTTCGGCCC 57.750 50.000 0.00 0.00 33.47 5.80
317 318 4.274950 TCAATTCTCGGAATAATTTCGGCC 59.725 41.667 0.00 0.00 33.47 6.13
318 319 5.205565 GTCAATTCTCGGAATAATTTCGGC 58.794 41.667 0.42 0.00 33.47 5.54
319 320 6.358118 TGTCAATTCTCGGAATAATTTCGG 57.642 37.500 0.42 0.00 34.44 4.30
320 321 6.787515 CGATGTCAATTCTCGGAATAATTTCG 59.212 38.462 0.42 0.00 32.28 3.46
331 332 4.864916 ATTTGTCCGATGTCAATTCTCG 57.135 40.909 0.00 0.00 0.00 4.04
337 338 9.062524 CCCTTAAATATATTTGTCCGATGTCAA 57.937 33.333 18.98 2.61 0.00 3.18
338 339 7.174253 GCCCTTAAATATATTTGTCCGATGTCA 59.826 37.037 18.98 0.00 0.00 3.58
339 340 7.174253 TGCCCTTAAATATATTTGTCCGATGTC 59.826 37.037 18.98 2.65 0.00 3.06
340 341 7.001674 TGCCCTTAAATATATTTGTCCGATGT 58.998 34.615 18.98 0.00 0.00 3.06
341 342 7.447374 TGCCCTTAAATATATTTGTCCGATG 57.553 36.000 18.98 3.23 0.00 3.84
342 343 7.309194 GCTTGCCCTTAAATATATTTGTCCGAT 60.309 37.037 18.98 0.00 0.00 4.18
343 344 6.016610 GCTTGCCCTTAAATATATTTGTCCGA 60.017 38.462 18.98 0.00 0.00 4.55
344 345 6.149633 GCTTGCCCTTAAATATATTTGTCCG 58.850 40.000 18.98 6.82 0.00 4.79
345 346 6.455647 GGCTTGCCCTTAAATATATTTGTCC 58.544 40.000 18.98 5.45 0.00 4.02
346 347 6.016610 TCGGCTTGCCCTTAAATATATTTGTC 60.017 38.462 18.98 2.43 0.00 3.18
347 348 5.830991 TCGGCTTGCCCTTAAATATATTTGT 59.169 36.000 18.98 0.00 0.00 2.83
348 349 6.325919 TCGGCTTGCCCTTAAATATATTTG 57.674 37.500 18.98 5.01 0.00 2.32
349 350 5.048013 GCTCGGCTTGCCCTTAAATATATTT 60.048 40.000 14.86 14.86 0.00 1.40
350 351 4.459337 GCTCGGCTTGCCCTTAAATATATT 59.541 41.667 6.02 0.00 0.00 1.28
351 352 4.010349 GCTCGGCTTGCCCTTAAATATAT 58.990 43.478 6.02 0.00 0.00 0.86
352 353 3.408634 GCTCGGCTTGCCCTTAAATATA 58.591 45.455 6.02 0.00 0.00 0.86
353 354 2.230660 GCTCGGCTTGCCCTTAAATAT 58.769 47.619 6.02 0.00 0.00 1.28
354 355 1.675552 GCTCGGCTTGCCCTTAAATA 58.324 50.000 6.02 0.00 0.00 1.40
355 356 1.037579 GGCTCGGCTTGCCCTTAAAT 61.038 55.000 6.02 0.00 44.32 1.40
356 357 1.677633 GGCTCGGCTTGCCCTTAAA 60.678 57.895 6.02 0.00 44.32 1.52
357 358 2.045340 GGCTCGGCTTGCCCTTAA 60.045 61.111 6.02 0.00 44.32 1.85
372 373 0.039888 TCAAAGTTTTAAGCGCCGGC 60.040 50.000 19.07 19.07 40.37 6.13
373 374 2.315901 CTTCAAAGTTTTAAGCGCCGG 58.684 47.619 2.29 0.00 0.00 6.13
374 375 2.031508 TCCTTCAAAGTTTTAAGCGCCG 60.032 45.455 2.29 0.00 0.00 6.46
375 376 3.004419 ACTCCTTCAAAGTTTTAAGCGCC 59.996 43.478 2.29 0.00 0.00 6.53
376 377 4.224715 ACTCCTTCAAAGTTTTAAGCGC 57.775 40.909 0.00 0.00 0.00 5.92
377 378 9.543018 CTTATAACTCCTTCAAAGTTTTAAGCG 57.457 33.333 4.31 1.29 39.31 4.68
382 383 9.131791 TCTTGCTTATAACTCCTTCAAAGTTTT 57.868 29.630 0.00 0.00 38.00 2.43
383 384 8.691661 TCTTGCTTATAACTCCTTCAAAGTTT 57.308 30.769 0.00 0.00 38.00 2.66
384 385 8.870075 ATCTTGCTTATAACTCCTTCAAAGTT 57.130 30.769 0.00 0.00 40.06 2.66
385 386 9.959721 TTATCTTGCTTATAACTCCTTCAAAGT 57.040 29.630 0.00 0.00 0.00 2.66
387 388 9.959721 ACTTATCTTGCTTATAACTCCTTCAAA 57.040 29.630 0.00 0.00 0.00 2.69
388 389 9.383519 CACTTATCTTGCTTATAACTCCTTCAA 57.616 33.333 0.00 0.00 0.00 2.69
389 390 8.540388 ACACTTATCTTGCTTATAACTCCTTCA 58.460 33.333 0.00 0.00 0.00 3.02
390 391 8.950208 ACACTTATCTTGCTTATAACTCCTTC 57.050 34.615 0.00 0.00 0.00 3.46
391 392 9.167311 CAACACTTATCTTGCTTATAACTCCTT 57.833 33.333 0.00 0.00 0.00 3.36
392 393 7.770897 CCAACACTTATCTTGCTTATAACTCCT 59.229 37.037 0.00 0.00 0.00 3.69
393 394 7.769044 TCCAACACTTATCTTGCTTATAACTCC 59.231 37.037 0.00 0.00 0.00 3.85
394 395 8.604890 GTCCAACACTTATCTTGCTTATAACTC 58.395 37.037 0.00 0.00 0.00 3.01
395 396 7.553044 GGTCCAACACTTATCTTGCTTATAACT 59.447 37.037 0.00 0.00 0.00 2.24
396 397 7.335924 TGGTCCAACACTTATCTTGCTTATAAC 59.664 37.037 0.00 0.00 0.00 1.89
397 398 7.398829 TGGTCCAACACTTATCTTGCTTATAA 58.601 34.615 0.00 0.00 0.00 0.98
398 399 6.953101 TGGTCCAACACTTATCTTGCTTATA 58.047 36.000 0.00 0.00 0.00 0.98
399 400 5.815581 TGGTCCAACACTTATCTTGCTTAT 58.184 37.500 0.00 0.00 0.00 1.73
400 401 5.235850 TGGTCCAACACTTATCTTGCTTA 57.764 39.130 0.00 0.00 0.00 3.09
401 402 4.074970 CTGGTCCAACACTTATCTTGCTT 58.925 43.478 0.00 0.00 0.00 3.91
402 403 3.560025 CCTGGTCCAACACTTATCTTGCT 60.560 47.826 0.00 0.00 0.00 3.91
403 404 2.749621 CCTGGTCCAACACTTATCTTGC 59.250 50.000 0.00 0.00 0.00 4.01
404 405 4.003648 GACCTGGTCCAACACTTATCTTG 58.996 47.826 16.14 0.00 0.00 3.02
405 406 4.287766 GACCTGGTCCAACACTTATCTT 57.712 45.455 16.14 0.00 0.00 2.40
406 407 3.983044 GACCTGGTCCAACACTTATCT 57.017 47.619 16.14 0.00 0.00 1.98
418 419 2.500504 AGGAGTTAAATCGGACCTGGTC 59.499 50.000 18.65 18.65 0.00 4.02
419 420 2.500504 GAGGAGTTAAATCGGACCTGGT 59.499 50.000 0.00 0.00 0.00 4.00
420 421 2.500098 TGAGGAGTTAAATCGGACCTGG 59.500 50.000 0.00 0.00 0.00 4.45
421 422 3.887621 TGAGGAGTTAAATCGGACCTG 57.112 47.619 0.00 0.00 0.00 4.00
422 423 4.833390 CTTTGAGGAGTTAAATCGGACCT 58.167 43.478 0.00 0.00 0.00 3.85
423 424 3.374367 GCTTTGAGGAGTTAAATCGGACC 59.626 47.826 0.00 0.00 0.00 4.46
424 425 3.062234 CGCTTTGAGGAGTTAAATCGGAC 59.938 47.826 0.00 0.00 0.00 4.79
425 426 3.056393 TCGCTTTGAGGAGTTAAATCGGA 60.056 43.478 0.00 0.00 0.00 4.55
426 427 3.259064 TCGCTTTGAGGAGTTAAATCGG 58.741 45.455 0.00 0.00 0.00 4.18
427 428 4.921470 TTCGCTTTGAGGAGTTAAATCG 57.079 40.909 0.00 0.00 0.00 3.34
491 492 9.191995 CTTCTTTTCTGACTAAGAGTTTCTCTC 57.808 37.037 0.00 0.00 40.28 3.20
492 493 8.700973 ACTTCTTTTCTGACTAAGAGTTTCTCT 58.299 33.333 0.00 0.00 43.37 3.10
493 494 8.760569 CACTTCTTTTCTGACTAAGAGTTTCTC 58.239 37.037 0.00 0.00 35.91 2.87
494 495 8.478877 TCACTTCTTTTCTGACTAAGAGTTTCT 58.521 33.333 0.00 0.00 35.91 2.52
495 496 8.649973 TCACTTCTTTTCTGACTAAGAGTTTC 57.350 34.615 0.00 0.00 35.91 2.78
496 497 9.267084 GATCACTTCTTTTCTGACTAAGAGTTT 57.733 33.333 0.00 0.00 35.91 2.66
506 507 4.965814 AGCAGTGATCACTTCTTTTCTGA 58.034 39.130 25.84 0.00 40.20 3.27
518 519 4.350346 CAAACGTTGAAAAGCAGTGATCA 58.650 39.130 0.00 0.00 0.00 2.92
548 549 8.231837 GTCAATCGACAAGGTAGATAGATAGAC 58.768 40.741 0.00 0.00 42.13 2.59
578 579 3.305064 GGTGCTTTTCTGACCGCATTAAA 60.305 43.478 0.00 0.00 34.60 1.52
592 593 0.743345 GTAGATCGGCCGGTGCTTTT 60.743 55.000 27.83 6.87 37.74 2.27
601 602 0.106708 TGCAGAATGGTAGATCGGCC 59.893 55.000 0.00 0.00 36.16 6.13
621 622 3.434167 GGAATTCTTCCTGCTCCATGCTA 60.434 47.826 5.23 0.00 46.57 3.49
677 678 4.584518 TGCACCCACTGGCCACTG 62.585 66.667 0.00 2.66 33.59 3.66
678 679 3.819652 TTGCACCCACTGGCCACT 61.820 61.111 0.00 0.00 33.59 4.00
679 680 3.605664 GTTGCACCCACTGGCCAC 61.606 66.667 0.00 0.00 33.59 5.01
680 681 3.668922 TTGTTGCACCCACTGGCCA 62.669 57.895 4.71 4.71 33.59 5.36
681 682 2.837291 TTGTTGCACCCACTGGCC 60.837 61.111 0.00 0.00 33.59 5.36
747 748 1.472480 TGCGCCTGCTCTTTTAATTCC 59.528 47.619 4.18 0.00 43.34 3.01
873 907 6.480981 GCGAGACTGAGTATATATAGAGGTCC 59.519 46.154 0.00 0.00 0.00 4.46
878 912 7.334671 CCAAGTGCGAGACTGAGTATATATAGA 59.665 40.741 0.00 0.00 34.02 1.98
888 922 1.871080 AAACCAAGTGCGAGACTGAG 58.129 50.000 0.00 0.00 34.02 3.35
889 923 1.939934 CAAAACCAAGTGCGAGACTGA 59.060 47.619 0.00 0.00 34.02 3.41
901 935 3.196469 TGTTGCCTTGATGACAAAACCAA 59.804 39.130 0.00 0.00 35.49 3.67
930 964 4.041567 TCACTTAATTCTGCCAGGTGAAGA 59.958 41.667 0.00 0.00 30.81 2.87
932 966 4.326826 CTCACTTAATTCTGCCAGGTGAA 58.673 43.478 0.00 0.00 32.96 3.18
962 996 4.195334 AATGGGCGGGCTAGCTGG 62.195 66.667 15.72 7.93 37.29 4.85
972 1006 0.533755 CTAGCTCCTTCCAATGGGCG 60.534 60.000 0.00 0.00 0.00 6.13
994 1028 1.153449 CGGTCGCCTCCATTGCTAA 60.153 57.895 0.00 0.00 0.00 3.09
995 1029 2.499205 CGGTCGCCTCCATTGCTA 59.501 61.111 0.00 0.00 0.00 3.49
1060 1107 0.326427 AGCAGGAAGGAGAGCAGGAT 60.326 55.000 0.00 0.00 0.00 3.24
1062 1109 1.521616 GAGCAGGAAGGAGAGCAGG 59.478 63.158 0.00 0.00 0.00 4.85
1095 1142 2.335316 ACTCGTAGAATCGCTCCTCT 57.665 50.000 0.00 0.00 34.09 3.69
1154 1209 9.140286 GCATTGCTATCACGAACTAAGAATATA 57.860 33.333 0.16 0.00 0.00 0.86
1155 1210 7.875041 AGCATTGCTATCACGAACTAAGAATAT 59.125 33.333 10.00 0.00 36.99 1.28
1175 1241 5.165911 ACAAGCAGATCGATTAAGCATTG 57.834 39.130 16.48 17.04 0.00 2.82
1268 1339 1.145759 CCGTTCACCGTGATGATCCG 61.146 60.000 1.09 0.86 33.66 4.18
1450 1521 3.782443 GTGTAGCTGGACCCCGGG 61.782 72.222 15.80 15.80 0.00 5.73
1634 1716 2.860136 ACAGTATCAATCGACATGCGTG 59.140 45.455 3.82 3.82 41.80 5.34
1659 1763 3.322254 ACAAACCAAGTGATCGTCTCTCT 59.678 43.478 0.00 0.00 0.00 3.10
1660 1764 3.654414 ACAAACCAAGTGATCGTCTCTC 58.346 45.455 0.00 0.00 0.00 3.20
1661 1765 3.753294 ACAAACCAAGTGATCGTCTCT 57.247 42.857 0.00 0.00 0.00 3.10
1662 1766 4.608445 CGAAACAAACCAAGTGATCGTCTC 60.608 45.833 0.00 0.00 0.00 3.36
1665 1769 2.940410 ACGAAACAAACCAAGTGATCGT 59.060 40.909 0.00 0.00 37.31 3.73
1693 3226 3.766051 TCCATCGATGATCCGATCAGAAT 59.234 43.478 26.86 7.06 46.26 2.40
1694 3227 3.157087 TCCATCGATGATCCGATCAGAA 58.843 45.455 26.86 5.17 46.26 3.02
1695 3228 2.795329 TCCATCGATGATCCGATCAGA 58.205 47.619 26.86 8.90 46.26 3.27
1696 3229 3.797451 ATCCATCGATGATCCGATCAG 57.203 47.619 26.86 6.58 46.26 2.90
1872 3816 1.212616 GAATCGATCTCCCGCACAAG 58.787 55.000 0.00 0.00 0.00 3.16
1910 3854 7.090808 GGAGAACTCAAAAGAACACTGTTTTT 58.909 34.615 4.23 0.00 0.00 1.94
1932 3891 1.817357 TGCACTGCAAGAGAATGGAG 58.183 50.000 0.00 0.00 43.62 3.86
1940 3900 9.450870 CCATATCTGGAAATTTGCACTGCAAGA 62.451 40.741 15.84 8.86 46.55 3.02
1949 3909 6.475402 CGGTTTAACCATATCTGGAAATTTGC 59.525 38.462 14.97 2.22 46.37 3.68
2008 3968 1.070758 ACTTTCACGTGCTGAGATGGT 59.929 47.619 11.67 0.00 0.00 3.55
2009 3969 1.800805 ACTTTCACGTGCTGAGATGG 58.199 50.000 11.67 0.00 0.00 3.51
2044 4004 4.061596 GACAAGACCTATGCCAAGCTATC 58.938 47.826 0.00 0.00 0.00 2.08
2081 4072 8.912988 CCCCATTTCAATATTGTATTGTACTGT 58.087 33.333 14.97 0.00 0.00 3.55
2082 4073 9.130661 TCCCCATTTCAATATTGTATTGTACTG 57.869 33.333 14.97 5.21 0.00 2.74
2143 4134 4.026062 CAGCGCGCAAATGATTAGTTACTA 60.026 41.667 35.10 0.00 0.00 1.82
2144 4135 2.936498 AGCGCGCAAATGATTAGTTACT 59.064 40.909 35.10 2.61 0.00 2.24
2145 4136 3.029074 CAGCGCGCAAATGATTAGTTAC 58.971 45.455 35.10 0.00 0.00 2.50
2173 4164 1.000274 TCGTCTCTGTGTGGTGATGTG 60.000 52.381 0.00 0.00 0.00 3.21
2475 4470 1.719780 CGCGTTCTTGTACTGGAAGAC 59.280 52.381 0.00 0.00 37.43 3.01
2807 4805 1.303643 GGTGTTGGGGAGCTGGAAG 60.304 63.158 0.00 0.00 0.00 3.46
3218 5216 2.738139 TCGATGTGGCAGTGCACG 60.738 61.111 18.61 13.37 0.00 5.34
3330 5328 4.208686 CCTCTACGGGCCGCAGAC 62.209 72.222 28.71 0.00 0.00 3.51
3335 5333 2.186125 GGAAACCTCTACGGGCCG 59.814 66.667 27.06 27.06 36.97 6.13
3340 5338 1.893801 AGTCACCAGGAAACCTCTACG 59.106 52.381 0.00 0.00 0.00 3.51
3491 5517 0.397564 AGGAGGCCCGTAACGAAAAA 59.602 50.000 0.00 0.00 37.58 1.94
3521 5547 5.006358 GCCCACTGTGTAAACACTTATATCG 59.994 44.000 13.95 0.00 46.55 2.92
3530 5560 0.840617 TGAGGCCCACTGTGTAAACA 59.159 50.000 0.00 0.00 0.00 2.83
3589 5619 8.423906 TTTTTAGGGGTCATGCATTTAGTTAA 57.576 30.769 0.00 0.00 0.00 2.01
3618 5649 7.106239 CCATAGCTTAGGACATGTATTTAGGG 58.894 42.308 0.00 0.00 0.00 3.53
3619 5650 6.595716 GCCATAGCTTAGGACATGTATTTAGG 59.404 42.308 0.00 0.00 35.50 2.69
3620 5651 6.595716 GGCCATAGCTTAGGACATGTATTTAG 59.404 42.308 0.00 0.00 39.73 1.85
3621 5652 6.043822 TGGCCATAGCTTAGGACATGTATTTA 59.956 38.462 0.00 0.00 38.22 1.40
3622 5653 5.163099 TGGCCATAGCTTAGGACATGTATTT 60.163 40.000 0.00 0.00 38.22 1.40
3623 5654 4.350816 TGGCCATAGCTTAGGACATGTATT 59.649 41.667 0.00 0.00 38.22 1.89
3624 5655 3.909995 TGGCCATAGCTTAGGACATGTAT 59.090 43.478 0.00 0.00 38.22 2.29
3625 5656 3.313791 TGGCCATAGCTTAGGACATGTA 58.686 45.455 0.00 0.00 38.22 2.29
3626 5657 2.105477 CTGGCCATAGCTTAGGACATGT 59.895 50.000 5.51 0.00 43.32 3.21
3627 5658 2.551721 CCTGGCCATAGCTTAGGACATG 60.552 54.545 5.51 6.95 43.32 3.21
3628 5659 1.701847 CCTGGCCATAGCTTAGGACAT 59.298 52.381 5.51 0.00 43.32 3.06
3629 5660 1.131638 CCTGGCCATAGCTTAGGACA 58.868 55.000 5.51 11.74 42.39 4.02
3630 5661 0.398318 CCCTGGCCATAGCTTAGGAC 59.602 60.000 5.51 5.71 42.39 3.85
3631 5662 0.768221 CCCCTGGCCATAGCTTAGGA 60.768 60.000 5.51 0.00 42.39 2.94
3632 5663 0.768221 TCCCCTGGCCATAGCTTAGG 60.768 60.000 5.51 0.88 40.68 2.69
3633 5664 1.366319 ATCCCCTGGCCATAGCTTAG 58.634 55.000 5.51 0.00 39.73 2.18
3634 5665 2.733298 TATCCCCTGGCCATAGCTTA 57.267 50.000 5.51 0.00 39.73 3.09
3635 5666 1.918957 GATATCCCCTGGCCATAGCTT 59.081 52.381 5.51 0.00 39.73 3.74
3636 5667 1.589414 GATATCCCCTGGCCATAGCT 58.411 55.000 5.51 0.00 39.73 3.32
3642 5673 2.122768 CAGATAGGATATCCCCTGGCC 58.877 57.143 18.56 0.00 37.10 5.36
3645 5676 1.759445 CGGCAGATAGGATATCCCCTG 59.241 57.143 18.56 20.99 37.10 4.45
3652 5683 2.441410 CAGAGAGCGGCAGATAGGATA 58.559 52.381 1.45 0.00 0.00 2.59
3653 5684 1.255882 CAGAGAGCGGCAGATAGGAT 58.744 55.000 1.45 0.00 0.00 3.24
3773 5807 2.609747 TCCATCCCTTCTTATAGCGCT 58.390 47.619 17.26 17.26 0.00 5.92
3774 5808 3.067833 GTTCCATCCCTTCTTATAGCGC 58.932 50.000 0.00 0.00 0.00 5.92
3775 5809 3.071023 TGGTTCCATCCCTTCTTATAGCG 59.929 47.826 0.00 0.00 0.00 4.26
3778 5812 3.071023 CGCTGGTTCCATCCCTTCTTATA 59.929 47.826 0.00 0.00 0.00 0.98
3779 5813 2.158755 CGCTGGTTCCATCCCTTCTTAT 60.159 50.000 0.00 0.00 0.00 1.73
3784 5818 1.604378 CTCGCTGGTTCCATCCCTT 59.396 57.895 0.00 0.00 0.00 3.95
3810 5844 3.734293 GCAGCATTTTCTCAGAAGGATGC 60.734 47.826 21.58 21.58 41.76 3.91
3811 5845 3.695060 AGCAGCATTTTCTCAGAAGGATG 59.305 43.478 7.98 7.98 0.00 3.51
3812 5846 3.695060 CAGCAGCATTTTCTCAGAAGGAT 59.305 43.478 0.00 0.00 0.00 3.24
3813 5847 3.079578 CAGCAGCATTTTCTCAGAAGGA 58.920 45.455 0.00 0.00 0.00 3.36
3814 5848 2.415625 GCAGCAGCATTTTCTCAGAAGG 60.416 50.000 0.00 0.00 41.58 3.46
3815 5849 2.488545 AGCAGCAGCATTTTCTCAGAAG 59.511 45.455 3.17 0.00 45.49 2.85
3816 5850 2.511659 AGCAGCAGCATTTTCTCAGAA 58.488 42.857 3.17 0.00 45.49 3.02
3817 5851 2.195741 AGCAGCAGCATTTTCTCAGA 57.804 45.000 3.17 0.00 45.49 3.27
3818 5852 2.223294 GCTAGCAGCAGCATTTTCTCAG 60.223 50.000 10.63 0.00 45.49 3.35
3819 5853 1.741706 GCTAGCAGCAGCATTTTCTCA 59.258 47.619 10.63 0.00 45.49 3.27
3820 5854 1.267932 CGCTAGCAGCAGCATTTTCTC 60.268 52.381 16.45 0.00 42.58 2.87
3821 5855 0.731417 CGCTAGCAGCAGCATTTTCT 59.269 50.000 16.45 0.00 42.58 2.52
3822 5856 0.729116 TCGCTAGCAGCAGCATTTTC 59.271 50.000 16.45 0.00 42.58 2.29
3823 5857 0.731417 CTCGCTAGCAGCAGCATTTT 59.269 50.000 16.45 0.00 42.58 1.82
3824 5858 2.391469 CTCGCTAGCAGCAGCATTT 58.609 52.632 16.45 0.00 42.58 2.32
3825 5859 4.121691 CTCGCTAGCAGCAGCATT 57.878 55.556 16.45 0.00 42.58 3.56
3840 5874 2.282820 GCATCGTACACAAGCTAAGCTC 59.717 50.000 0.00 0.00 38.25 4.09
3843 5877 2.029728 GCTGCATCGTACACAAGCTAAG 59.970 50.000 0.00 0.00 0.00 2.18
3845 5879 1.640428 GCTGCATCGTACACAAGCTA 58.360 50.000 0.00 0.00 0.00 3.32
3850 5884 2.048690 TGCGCTGCATCGTACACA 60.049 55.556 12.03 0.00 31.71 3.72
3886 5935 1.156736 AAAAGTGTTCGGATCCGCAG 58.843 50.000 29.62 3.75 39.59 5.18
3890 5940 6.731164 TCAAAGTTTAAAAGTGTTCGGATCC 58.269 36.000 0.00 0.00 0.00 3.36
3909 5959 7.232994 TCAAGAAAATTGTTTTGCGTTCAAAG 58.767 30.769 0.00 0.00 42.50 2.77
3941 5993 3.606346 CGCGGTTTCATAAAACATTCACC 59.394 43.478 0.00 0.00 45.44 4.02
4073 6136 3.314080 AGTTTTCAGAAAAATGTCCGCGA 59.686 39.130 8.23 0.00 36.77 5.87
4078 6141 8.424274 AATGTTCCAGTTTTCAGAAAAATGTC 57.576 30.769 26.40 18.70 42.93 3.06
4094 6157 9.837525 TGTTTTTGAATTTGAAAAATGTTCCAG 57.162 25.926 9.24 0.00 35.37 3.86
4127 6192 5.753744 TGTTTCGAAAATGTTTGCGTATCT 58.246 33.333 13.10 0.00 40.12 1.98
4144 6209 8.977505 AGTTCATAAAAATGTTTCCATGTTTCG 58.022 29.630 0.00 0.00 37.77 3.46
4265 6335 8.307483 TGTCTGGTAGTTTCAAAAATTGTTCAA 58.693 29.630 0.00 0.00 0.00 2.69
4266 6336 7.831753 TGTCTGGTAGTTTCAAAAATTGTTCA 58.168 30.769 0.00 0.00 0.00 3.18
4307 6377 9.617975 TTTTGTTCGCAAATTTCAAGAATTTTT 57.382 22.222 0.00 0.00 45.34 1.94
4310 6380 9.786105 AAATTTTGTTCGCAAATTTCAAGAATT 57.214 22.222 0.00 0.00 45.34 2.17
4311 6381 9.224058 CAAATTTTGTTCGCAAATTTCAAGAAT 57.776 25.926 0.78 0.00 45.34 2.40
4323 6393 3.397482 CCCATTCCAAATTTTGTTCGCA 58.603 40.909 8.26 0.00 0.00 5.10


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

AutoCloner maintained by Alex Coulton.