Multiple sequence alignment - TraesCS1B01G399000

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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 TraesCS1B01G399000 chr1B 100.000 5925 0 0 1 5925 630067515 630061591 0.000000e+00 10942.0
1 TraesCS1B01G399000 chr1B 85.212 1109 115 30 1630 2718 630259204 630258125 0.000000e+00 1094.0
2 TraesCS1B01G399000 chr1B 86.452 465 38 13 2721 3182 630257996 630257554 2.480000e-133 486.0
3 TraesCS1B01G399000 chr1B 95.455 44 1 1 1487 1530 52302607 52302565 1.070000e-07 69.4
4 TraesCS1B01G399000 chr1D 92.752 4277 191 46 1733 5925 458681502 458677261 0.000000e+00 6071.0
5 TraesCS1B01G399000 chr1D 90.767 834 41 14 592 1410 458682660 458681848 0.000000e+00 1081.0
6 TraesCS1B01G399000 chr1D 87.212 782 64 24 2401 3172 458722538 458721783 0.000000e+00 857.0
7 TraesCS1B01G399000 chr1D 85.049 709 79 17 1679 2376 458723366 458722674 0.000000e+00 697.0
8 TraesCS1B01G399000 chr1D 84.512 297 20 10 1413 1701 458681776 458681498 2.720000e-68 270.0
9 TraesCS1B01G399000 chr1A 91.976 3776 203 58 2224 5925 551054023 551050274 0.000000e+00 5203.0
10 TraesCS1B01G399000 chr1A 89.276 774 36 21 580 1322 551055838 551055081 0.000000e+00 926.0
11 TraesCS1B01G399000 chr1A 87.919 745 66 17 1638 2374 551149803 551149075 0.000000e+00 856.0
12 TraesCS1B01G399000 chr1A 90.642 545 46 4 1630 2173 551054581 551054041 0.000000e+00 719.0
13 TraesCS1B01G399000 chr1A 84.138 725 66 19 2446 3164 551149038 551148357 0.000000e+00 656.0
14 TraesCS1B01G399000 chr1A 79.600 500 64 19 1 495 551057571 551057105 2.060000e-84 324.0
15 TraesCS1B01G399000 chr1A 85.714 84 12 0 26 109 493567279 493567196 8.180000e-14 89.8
16 TraesCS1B01G399000 chr1A 94.444 54 3 0 519 572 551057100 551057047 3.810000e-12 84.2
17 TraesCS1B01G399000 chr4D 84.954 545 67 12 2591 3126 278187321 278186783 6.760000e-149 538.0
18 TraesCS1B01G399000 chr3D 86.304 460 51 7 953 1410 52182965 52182516 1.920000e-134 490.0
19 TraesCS1B01G399000 chr3D 76.325 283 57 10 35 311 428534781 428534503 6.190000e-30 143.0
20 TraesCS1B01G399000 chr3D 95.455 44 1 1 1487 1530 52182352 52182310 1.070000e-07 69.4
21 TraesCS1B01G399000 chr2D 86.304 460 50 8 953 1410 333354375 333353927 6.900000e-134 488.0
22 TraesCS1B01G399000 chr2D 79.720 143 26 3 35 176 408343684 408343544 3.780000e-17 100.0
23 TraesCS1B01G399000 chr2D 95.455 44 1 1 1487 1530 333353763 333353721 1.070000e-07 69.4
24 TraesCS1B01G399000 chr6A 84.716 458 52 11 953 1406 152802590 152803033 5.450000e-120 442.0
25 TraesCS1B01G399000 chr6A 75.401 374 80 12 35 402 597317340 597317707 2.840000e-38 171.0
26 TraesCS1B01G399000 chr2B 81.679 524 70 11 1974 2479 281948576 281948061 4.270000e-111 412.0
27 TraesCS1B01G399000 chr2B 80.871 528 73 18 1967 2476 272481825 272482342 2.000000e-104 390.0
28 TraesCS1B01G399000 chr2A 81.250 528 70 13 1967 2476 12621689 12622205 3.330000e-107 399.0
29 TraesCS1B01G399000 chr2A 86.337 344 40 5 953 1295 191764816 191764479 9.380000e-98 368.0
30 TraesCS1B01G399000 chr2A 73.448 290 63 10 1 286 758430681 758430402 4.890000e-16 97.1
31 TraesCS1B01G399000 chr4A 81.096 529 69 22 1967 2476 728678539 728679055 1.550000e-105 394.0
32 TraesCS1B01G399000 chrUn 87.106 349 37 7 950 1295 1840059 1840402 7.200000e-104 388.0
33 TraesCS1B01G399000 chr5A 87.246 345 35 7 953 1295 595670170 595669833 9.310000e-103 385.0
34 TraesCS1B01G399000 chr7B 86.297 343 43 3 953 1295 594099209 594099547 2.610000e-98 370.0
35 TraesCS1B01G399000 chr7A 79.487 468 68 16 2032 2479 720730845 720730386 2.070000e-79 307.0
36 TraesCS1B01G399000 chr6D 75.683 366 73 13 35 395 362869788 362870142 1.020000e-37 169.0
37 TraesCS1B01G399000 chr5B 74.387 367 86 7 35 396 496150778 496150415 3.700000e-32 150.0
38 TraesCS1B01G399000 chr7D 88.571 105 12 0 2069 2173 104221522 104221418 1.730000e-25 128.0
39 TraesCS1B01G399000 chr3B 79.070 129 26 1 1 129 559322220 559322093 2.940000e-13 87.9
40 TraesCS1B01G399000 chr5D 93.182 44 2 1 1487 1530 546417652 546417694 4.960000e-06 63.9


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 TraesCS1B01G399000 chr1B 630061591 630067515 5924 True 10942.00 10942 100.000000 1 5925 1 chr1B.!!$R2 5924
1 TraesCS1B01G399000 chr1B 630257554 630259204 1650 True 790.00 1094 85.832000 1630 3182 2 chr1B.!!$R3 1552
2 TraesCS1B01G399000 chr1D 458677261 458682660 5399 True 2474.00 6071 89.343667 592 5925 3 chr1D.!!$R1 5333
3 TraesCS1B01G399000 chr1D 458721783 458723366 1583 True 777.00 857 86.130500 1679 3172 2 chr1D.!!$R2 1493
4 TraesCS1B01G399000 chr1A 551050274 551057571 7297 True 1451.24 5203 89.187600 1 5925 5 chr1A.!!$R2 5924
5 TraesCS1B01G399000 chr1A 551148357 551149803 1446 True 756.00 856 86.028500 1638 3164 2 chr1A.!!$R3 1526
6 TraesCS1B01G399000 chr4D 278186783 278187321 538 True 538.00 538 84.954000 2591 3126 1 chr4D.!!$R1 535
7 TraesCS1B01G399000 chr3D 52182310 52182965 655 True 279.70 490 90.879500 953 1530 2 chr3D.!!$R2 577
8 TraesCS1B01G399000 chr2D 333353721 333354375 654 True 278.70 488 90.879500 953 1530 2 chr2D.!!$R2 577
9 TraesCS1B01G399000 chr2B 281948061 281948576 515 True 412.00 412 81.679000 1974 2479 1 chr2B.!!$R1 505
10 TraesCS1B01G399000 chr2B 272481825 272482342 517 False 390.00 390 80.871000 1967 2476 1 chr2B.!!$F1 509
11 TraesCS1B01G399000 chr2A 12621689 12622205 516 False 399.00 399 81.250000 1967 2476 1 chr2A.!!$F1 509
12 TraesCS1B01G399000 chr4A 728678539 728679055 516 False 394.00 394 81.096000 1967 2476 1 chr4A.!!$F1 509

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
585 605 0.023354 CGAAATCGCGACGTTCCTTC 59.977 55.000 22.06 13.00 0.00 3.46 F
587 607 0.320073 AAATCGCGACGTTCCTTCCA 60.320 50.000 12.93 0.00 0.00 3.53 F
1996 3523 0.167689 GAAAAGCCGCTCTTGCTGAG 59.832 55.000 0.00 3.46 45.33 3.35 F
3264 5056 1.400888 GCAGACACTCGTGACTCTCTG 60.401 57.143 3.74 7.41 33.60 3.35 F
3941 5734 0.538516 AGGTGACGTCTGCTCTCTGT 60.539 55.000 17.92 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 3409 0.177141 GCACAAGCATGATGGGCATT 59.823 50.000 18.13 0.00 46.48 3.56 R
2399 4051 0.681564 ACCACTGCTCGAGGGACTAG 60.682 60.000 15.58 1.26 41.55 2.57 R
3742 5535 1.402968 CAAGGAAGGAATCACATGCCG 59.597 52.381 0.00 0.00 0.00 5.69 R
4462 6288 0.533755 ACGATAGCAAGATGGGCAGC 60.534 55.000 0.00 0.00 42.67 5.25 R
5270 7109 0.389817 GCACTACCATGCTGTCGTCA 60.390 55.000 0.00 0.00 42.62 4.35 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 3.784573 CTCCCCATCTAGCCTCCG 58.215 66.667 0.00 0.00 0.00 4.63
21 22 0.546598 CCCCATCTAGCCTCCGTTTT 59.453 55.000 0.00 0.00 0.00 2.43
22 23 1.475213 CCCCATCTAGCCTCCGTTTTC 60.475 57.143 0.00 0.00 0.00 2.29
33 34 4.415490 CGTTTTCGGTGATGCGTG 57.585 55.556 0.00 0.00 39.94 5.34
50 51 1.090052 GTGTAGCATTGTCGGAGGGC 61.090 60.000 0.00 0.00 0.00 5.19
112 113 1.067776 AGTGTTCGTCTTCGGTGGATC 60.068 52.381 0.00 0.00 37.69 3.36
122 123 3.009033 TCTTCGGTGGATCTGTTTGGATT 59.991 43.478 0.00 0.00 0.00 3.01
133 134 6.348868 GGATCTGTTTGGATTCAGTCTTTGTC 60.349 42.308 0.00 0.00 33.89 3.18
153 154 9.208022 CTTTGTCTGTCTTCATTTATGTGTCTA 57.792 33.333 0.00 0.00 0.00 2.59
154 155 9.725019 TTTGTCTGTCTTCATTTATGTGTCTAT 57.275 29.630 0.00 0.00 0.00 1.98
172 173 7.491372 TGTGTCTATAAGTTGGATCATTTCGAC 59.509 37.037 0.00 0.00 0.00 4.20
173 174 6.984474 TGTCTATAAGTTGGATCATTTCGACC 59.016 38.462 0.00 0.00 0.00 4.79
175 176 8.358148 GTCTATAAGTTGGATCATTTCGACCTA 58.642 37.037 0.00 0.00 0.00 3.08
176 177 8.358148 TCTATAAGTTGGATCATTTCGACCTAC 58.642 37.037 0.00 0.00 0.00 3.18
179 180 5.118990 AGTTGGATCATTTCGACCTACATG 58.881 41.667 0.00 0.00 32.43 3.21
181 182 5.097742 TGGATCATTTCGACCTACATGTT 57.902 39.130 2.30 0.00 0.00 2.71
182 183 4.875536 TGGATCATTTCGACCTACATGTTG 59.124 41.667 2.30 0.84 0.00 3.33
183 184 4.273480 GGATCATTTCGACCTACATGTTGG 59.727 45.833 22.67 22.67 0.00 3.77
184 185 4.545208 TCATTTCGACCTACATGTTGGA 57.455 40.909 29.56 9.91 0.00 3.53
190 193 3.513912 TCGACCTACATGTTGGATTCAGT 59.486 43.478 29.56 8.79 0.00 3.41
193 196 4.579869 ACCTACATGTTGGATTCAGTGAC 58.420 43.478 29.56 0.00 0.00 3.67
195 198 4.633126 CCTACATGTTGGATTCAGTGACAG 59.367 45.833 20.22 0.00 0.00 3.51
218 221 5.470098 AGTTGTTATTCTAGTGTGCTGGTTG 59.530 40.000 0.00 0.00 0.00 3.77
222 225 6.593770 TGTTATTCTAGTGTGCTGGTTGTATG 59.406 38.462 0.00 0.00 0.00 2.39
224 227 2.236146 TCTAGTGTGCTGGTTGTATGGG 59.764 50.000 0.00 0.00 0.00 4.00
227 230 0.037590 TGTGCTGGTTGTATGGGGTC 59.962 55.000 0.00 0.00 0.00 4.46
243 246 5.255397 TGGGGTCTTAACATGATGACTTT 57.745 39.130 0.00 0.00 0.00 2.66
246 249 5.253330 GGGTCTTAACATGATGACTTTCCA 58.747 41.667 0.00 0.00 0.00 3.53
248 251 6.349363 GGGTCTTAACATGATGACTTTCCAAC 60.349 42.308 0.00 0.00 0.00 3.77
250 253 7.301054 GTCTTAACATGATGACTTTCCAACTG 58.699 38.462 0.00 0.00 0.00 3.16
256 259 4.894784 TGATGACTTTCCAACTGTCTACC 58.105 43.478 0.00 0.00 0.00 3.18
257 260 4.346709 TGATGACTTTCCAACTGTCTACCA 59.653 41.667 0.00 0.00 0.00 3.25
272 275 7.001674 ACTGTCTACCACAATAAATTTGACCA 58.998 34.615 0.00 0.00 33.31 4.02
277 280 6.575162 ACCACAATAAATTTGACCAGACTC 57.425 37.500 0.00 0.00 0.00 3.36
288 291 2.023598 TGACCAGACTCTGATGAGGGAT 60.024 50.000 7.69 0.00 44.29 3.85
289 292 2.364970 GACCAGACTCTGATGAGGGATG 59.635 54.545 7.69 0.00 44.29 3.51
290 293 1.070445 CCAGACTCTGATGAGGGATGC 59.930 57.143 7.69 0.00 44.29 3.91
291 294 1.039068 AGACTCTGATGAGGGATGCG 58.961 55.000 0.00 0.00 44.29 4.73
292 295 0.599728 GACTCTGATGAGGGATGCGC 60.600 60.000 0.00 0.00 44.29 6.09
293 296 1.664017 CTCTGATGAGGGATGCGCG 60.664 63.158 0.00 0.00 36.70 6.86
294 297 2.080222 CTCTGATGAGGGATGCGCGA 62.080 60.000 12.10 0.00 36.70 5.87
295 298 1.005275 CTGATGAGGGATGCGCGAT 60.005 57.895 12.10 0.00 0.00 4.58
296 299 1.289800 CTGATGAGGGATGCGCGATG 61.290 60.000 12.10 0.00 0.00 3.84
297 300 1.005748 GATGAGGGATGCGCGATGA 60.006 57.895 12.10 0.00 0.00 2.92
298 301 1.287730 GATGAGGGATGCGCGATGAC 61.288 60.000 12.10 0.00 0.00 3.06
299 302 3.032609 GAGGGATGCGCGATGACG 61.033 66.667 12.10 0.00 42.93 4.35
300 303 4.592192 AGGGATGCGCGATGACGG 62.592 66.667 12.10 0.00 40.15 4.79
301 304 4.891727 GGGATGCGCGATGACGGT 62.892 66.667 12.10 0.00 40.15 4.83
334 337 0.882927 TTCACACCGGTGCTTGTAGC 60.883 55.000 34.26 0.00 44.87 3.58
404 424 8.314021 TCTGTGTTCTTTATACTGTCATGACAT 58.686 33.333 28.00 19.34 41.01 3.06
405 425 8.255394 TGTGTTCTTTATACTGTCATGACATG 57.745 34.615 28.00 22.20 41.01 3.21
406 426 7.877612 TGTGTTCTTTATACTGTCATGACATGT 59.122 33.333 28.00 25.87 41.01 3.21
407 427 8.383619 GTGTTCTTTATACTGTCATGACATGTC 58.616 37.037 28.00 19.27 41.01 3.06
408 428 8.093927 TGTTCTTTATACTGTCATGACATGTCA 58.906 33.333 29.67 29.67 44.59 3.58
421 441 4.388485 TGACATGTCATGATAAATCCCCG 58.612 43.478 24.56 0.00 34.14 5.73
422 442 3.149196 ACATGTCATGATAAATCCCCGC 58.851 45.455 19.77 0.00 0.00 6.13
423 443 3.148412 CATGTCATGATAAATCCCCGCA 58.852 45.455 7.04 0.00 0.00 5.69
424 444 3.289407 TGTCATGATAAATCCCCGCAA 57.711 42.857 0.00 0.00 0.00 4.85
425 445 3.625853 TGTCATGATAAATCCCCGCAAA 58.374 40.909 0.00 0.00 0.00 3.68
426 446 4.019858 TGTCATGATAAATCCCCGCAAAA 58.980 39.130 0.00 0.00 0.00 2.44
427 447 4.464244 TGTCATGATAAATCCCCGCAAAAA 59.536 37.500 0.00 0.00 0.00 1.94
472 492 8.970859 AATAGATCGAAAGTCATCTTGGAAAT 57.029 30.769 0.00 0.00 33.79 2.17
499 519 9.744468 AAAAACAAAATGTCAAGGTCATACTAC 57.256 29.630 0.00 0.00 0.00 2.73
500 520 8.458573 AAACAAAATGTCAAGGTCATACTACA 57.541 30.769 0.00 0.00 0.00 2.74
501 521 8.458573 AACAAAATGTCAAGGTCATACTACAA 57.541 30.769 0.00 0.00 0.00 2.41
502 522 7.871853 ACAAAATGTCAAGGTCATACTACAAC 58.128 34.615 0.00 0.00 0.00 3.32
504 524 7.435068 AAATGTCAAGGTCATACTACAACAC 57.565 36.000 0.00 0.00 0.00 3.32
505 525 5.538849 TGTCAAGGTCATACTACAACACA 57.461 39.130 0.00 0.00 0.00 3.72
506 526 5.919755 TGTCAAGGTCATACTACAACACAA 58.080 37.500 0.00 0.00 0.00 3.33
507 527 5.989168 TGTCAAGGTCATACTACAACACAAG 59.011 40.000 0.00 0.00 0.00 3.16
509 529 3.939066 AGGTCATACTACAACACAAGGC 58.061 45.455 0.00 0.00 0.00 4.35
510 530 3.007635 GGTCATACTACAACACAAGGCC 58.992 50.000 0.00 0.00 0.00 5.19
511 531 3.007635 GTCATACTACAACACAAGGCCC 58.992 50.000 0.00 0.00 0.00 5.80
512 532 2.026636 TCATACTACAACACAAGGCCCC 60.027 50.000 0.00 0.00 0.00 5.80
513 533 0.322322 TACTACAACACAAGGCCCCG 59.678 55.000 0.00 0.00 0.00 5.73
514 534 1.072505 CTACAACACAAGGCCCCGT 59.927 57.895 0.00 0.00 0.00 5.28
515 535 0.536460 CTACAACACAAGGCCCCGTT 60.536 55.000 0.00 0.00 0.00 4.44
516 536 0.106619 TACAACACAAGGCCCCGTTT 60.107 50.000 0.00 0.00 0.00 3.60
517 537 0.106619 ACAACACAAGGCCCCGTTTA 60.107 50.000 0.00 0.00 0.00 2.01
518 538 1.033574 CAACACAAGGCCCCGTTTAA 58.966 50.000 0.00 0.00 0.00 1.52
519 539 1.616374 CAACACAAGGCCCCGTTTAAT 59.384 47.619 0.00 0.00 0.00 1.40
520 540 1.541379 ACACAAGGCCCCGTTTAATC 58.459 50.000 0.00 0.00 0.00 1.75
521 541 1.202952 ACACAAGGCCCCGTTTAATCA 60.203 47.619 0.00 0.00 0.00 2.57
522 542 1.889829 CACAAGGCCCCGTTTAATCAA 59.110 47.619 0.00 0.00 0.00 2.57
523 543 2.297597 CACAAGGCCCCGTTTAATCAAA 59.702 45.455 0.00 0.00 0.00 2.69
524 544 2.297880 ACAAGGCCCCGTTTAATCAAAC 59.702 45.455 0.00 0.00 40.60 2.93
525 545 2.560981 CAAGGCCCCGTTTAATCAAACT 59.439 45.455 0.00 0.00 41.62 2.66
526 546 2.884320 AGGCCCCGTTTAATCAAACTT 58.116 42.857 0.00 0.00 41.62 2.66
527 547 2.560981 AGGCCCCGTTTAATCAAACTTG 59.439 45.455 0.00 0.00 41.62 3.16
528 548 2.333926 GCCCCGTTTAATCAAACTTGC 58.666 47.619 0.00 0.00 41.62 4.01
572 592 1.136774 GGCGAACTTGGGCGAAATC 59.863 57.895 0.00 0.00 0.00 2.17
573 593 1.226018 GCGAACTTGGGCGAAATCG 60.226 57.895 11.11 11.11 43.27 3.34
583 603 3.763319 CGAAATCGCGACGTTCCT 58.237 55.556 22.06 0.53 0.00 3.36
584 604 2.067616 CGAAATCGCGACGTTCCTT 58.932 52.632 22.06 6.67 0.00 3.36
585 605 0.023354 CGAAATCGCGACGTTCCTTC 59.977 55.000 22.06 13.00 0.00 3.46
586 606 0.369248 GAAATCGCGACGTTCCTTCC 59.631 55.000 12.93 0.00 0.00 3.46
587 607 0.320073 AAATCGCGACGTTCCTTCCA 60.320 50.000 12.93 0.00 0.00 3.53
588 608 0.320073 AATCGCGACGTTCCTTCCAA 60.320 50.000 12.93 0.00 0.00 3.53
589 609 0.320073 ATCGCGACGTTCCTTCCAAA 60.320 50.000 12.93 0.00 0.00 3.28
590 610 1.203313 CGCGACGTTCCTTCCAAAC 59.797 57.895 0.00 0.00 0.00 2.93
638 1857 1.144969 TGACCTGCGAAAAAGCGTAG 58.855 50.000 0.00 0.00 42.47 3.51
676 1896 2.201210 AACCCCACCCAGCAAAGG 59.799 61.111 0.00 0.00 0.00 3.11
779 1999 0.541863 AACAGATAACTGCTCCCCGG 59.458 55.000 0.00 0.00 46.95 5.73
781 2001 2.111251 GATAACTGCTCCCCGGCC 59.889 66.667 0.00 0.00 0.00 6.13
782 2002 2.366972 ATAACTGCTCCCCGGCCT 60.367 61.111 0.00 0.00 0.00 5.19
783 2003 1.984288 GATAACTGCTCCCCGGCCTT 61.984 60.000 0.00 0.00 0.00 4.35
785 2005 1.785353 TAACTGCTCCCCGGCCTTTT 61.785 55.000 0.00 0.00 0.00 2.27
786 2006 1.785353 AACTGCTCCCCGGCCTTTTA 61.785 55.000 0.00 0.00 0.00 1.52
788 2008 2.198304 CTGCTCCCCGGCCTTTTACT 62.198 60.000 0.00 0.00 0.00 2.24
790 2010 1.223763 CTCCCCGGCCTTTTACTCC 59.776 63.158 0.00 0.00 0.00 3.85
791 2011 1.539372 TCCCCGGCCTTTTACTCCA 60.539 57.895 0.00 0.00 0.00 3.86
792 2012 1.378119 CCCCGGCCTTTTACTCCAC 60.378 63.158 0.00 0.00 0.00 4.02
793 2013 1.683441 CCCGGCCTTTTACTCCACT 59.317 57.895 0.00 0.00 0.00 4.00
794 2014 0.676782 CCCGGCCTTTTACTCCACTG 60.677 60.000 0.00 0.00 0.00 3.66
888 2124 3.130227 GCGGAGGCTACTAGTGGG 58.870 66.667 5.39 0.00 35.83 4.61
889 2125 1.455217 GCGGAGGCTACTAGTGGGA 60.455 63.158 5.39 0.00 35.83 4.37
1176 2422 1.446272 CTTCGACGCCTTCCTCACC 60.446 63.158 0.00 0.00 0.00 4.02
1302 2549 2.957576 CGATTTGATCTGGAATCGCC 57.042 50.000 18.97 0.00 45.20 5.54
1320 2567 2.600731 GCCAGATGGATACGAATCGAG 58.399 52.381 10.55 0.00 42.51 4.04
1321 2568 2.672478 GCCAGATGGATACGAATCGAGG 60.672 54.545 10.55 0.00 42.51 4.63
1322 2569 2.820197 CCAGATGGATACGAATCGAGGA 59.180 50.000 10.55 0.00 42.51 3.71
1323 2570 3.445450 CCAGATGGATACGAATCGAGGAT 59.555 47.826 10.55 0.00 42.51 3.24
1324 2571 4.081972 CCAGATGGATACGAATCGAGGATT 60.082 45.833 10.55 0.00 42.51 3.01
1325 2572 5.098893 CAGATGGATACGAATCGAGGATTC 58.901 45.833 10.55 8.02 43.31 2.52
1357 2604 3.276091 TGTGGCGCGTGGTTTCAG 61.276 61.111 8.43 0.00 0.00 3.02
1402 2649 4.437820 GCAAATCGGAAATGATTAGTTCGC 59.562 41.667 0.00 0.00 37.59 4.70
1410 2657 5.049818 GGAAATGATTAGTTCGCCTCTGATG 60.050 44.000 0.00 0.00 31.92 3.07
1411 2658 4.944619 ATGATTAGTTCGCCTCTGATGA 57.055 40.909 0.00 0.00 0.00 2.92
1443 2760 1.742761 ATGTCTGAAATCGCCACTGG 58.257 50.000 0.00 0.00 0.00 4.00
1457 2784 1.100510 CACTGGCTGGAACATGATGG 58.899 55.000 0.00 0.00 38.20 3.51
1472 2799 7.329226 GGAACATGATGGTTTTGTTAACTCATG 59.671 37.037 21.16 21.16 42.48 3.07
1477 2804 5.957842 TGGTTTTGTTAACTCATGCTAGG 57.042 39.130 7.22 0.00 0.00 3.02
1479 2806 6.065374 TGGTTTTGTTAACTCATGCTAGGAA 58.935 36.000 7.22 0.00 0.00 3.36
1480 2807 6.016610 TGGTTTTGTTAACTCATGCTAGGAAC 60.017 38.462 7.22 0.00 0.00 3.62
1481 2808 6.379386 GTTTTGTTAACTCATGCTAGGAACC 58.621 40.000 7.22 0.00 0.00 3.62
1483 2810 3.585289 TGTTAACTCATGCTAGGAACCCA 59.415 43.478 7.22 0.00 0.00 4.51
1522 2867 6.592994 TGTTTCATTCTAGAATCTGTGCTCTG 59.407 38.462 15.24 2.99 0.00 3.35
1530 2875 3.132646 AGAATCTGTGCTCTGGAGATGTC 59.867 47.826 1.35 0.00 0.00 3.06
1535 2880 0.689080 TGCTCTGGAGATGTCCCCTC 60.689 60.000 6.41 0.00 43.15 4.30
1539 2884 2.706071 GGAGATGTCCCCTCCCCT 59.294 66.667 0.00 0.00 43.37 4.79
1540 2885 1.004891 GGAGATGTCCCCTCCCCTT 59.995 63.158 0.00 0.00 43.37 3.95
1556 2901 2.093500 CCCCTTCCAAGCTTATTTTGGC 60.093 50.000 0.00 0.00 43.81 4.52
1581 2946 7.467403 GCTTGACTTGTTAGGCTATTGGTATTC 60.467 40.741 0.00 0.00 0.00 1.75
1643 3150 1.610673 ACGGGTGATCTCACTGCCT 60.611 57.895 9.98 0.00 45.73 4.75
1677 3186 7.772757 AGGGAATTTTCACTGATAGAACATCTC 59.227 37.037 0.00 0.00 40.03 2.75
1721 3231 5.672819 GCTGCTTGCCAAATTTGAATTCATC 60.673 40.000 19.86 3.34 35.15 2.92
1726 3236 7.118101 GCTTGCCAAATTTGAATTCATCTTACA 59.882 33.333 19.86 0.00 0.00 2.41
1767 3277 6.799926 ATTTTACCATTGACCATGCAAAAC 57.200 33.333 0.00 0.00 32.42 2.43
1772 3282 3.991773 CCATTGACCATGCAAAACTTGAG 59.008 43.478 0.00 0.00 0.00 3.02
1787 3297 2.089980 CTTGAGGGATTGACTGGCTTG 58.910 52.381 0.00 0.00 0.00 4.01
1791 3301 1.034292 GGGATTGACTGGCTTGCCTC 61.034 60.000 13.18 3.72 0.00 4.70
1796 3306 2.282040 ACTGGCTTGCCTCTGTGC 60.282 61.111 13.18 0.00 0.00 4.57
1878 3402 3.572255 TCCGGCTTGTTTTATTTCTGCTT 59.428 39.130 0.00 0.00 0.00 3.91
1884 3409 7.806014 CGGCTTGTTTTATTTCTGCTTACTAAA 59.194 33.333 0.00 0.00 0.00 1.85
1996 3523 0.167689 GAAAAGCCGCTCTTGCTGAG 59.832 55.000 0.00 3.46 45.33 3.35
2134 3661 1.797025 ACAGTACTTCTCGCAAAGGC 58.203 50.000 0.00 0.00 0.00 4.35
2176 3703 9.626045 GTTTGCTCAAGCTAAACAACTAATAAT 57.374 29.630 17.44 0.00 42.66 1.28
2222 3752 2.153645 CAGTTCTGTTACTGCATGGCA 58.846 47.619 0.00 0.00 39.12 4.92
2230 3760 4.480541 TGTTACTGCATGGCAAAATAACG 58.519 39.130 0.00 0.00 38.41 3.18
2267 3800 8.201554 TGATGTGCATCTTCAGTTTATAGTTC 57.798 34.615 12.64 0.00 38.60 3.01
2318 3852 6.324254 GGCTAGAAATACAGGAGGTTCTTCTA 59.676 42.308 0.00 0.00 33.63 2.10
2327 3861 6.784031 ACAGGAGGTTCTTCTAATGTGAAAT 58.216 36.000 0.00 0.00 0.00 2.17
2328 3862 7.234355 ACAGGAGGTTCTTCTAATGTGAAATT 58.766 34.615 0.00 0.00 0.00 1.82
2409 4061 3.946558 ACTGCTAACTTACTAGTCCCTCG 59.053 47.826 0.00 0.00 31.99 4.63
2683 4336 8.934023 TTTTCTCCCAACTATTTCACTATTGT 57.066 30.769 0.00 0.00 0.00 2.71
2746 4528 8.956533 AATTTTGTGCACCTATTTTTGTTACT 57.043 26.923 15.69 0.00 0.00 2.24
2821 4606 7.727331 ATTCTGTTGCTTAGATGCTTCTATC 57.273 36.000 9.91 6.37 34.44 2.08
2826 4611 7.978982 TGTTGCTTAGATGCTTCTATCTTTTC 58.021 34.615 9.91 2.18 38.35 2.29
2829 4614 6.477033 TGCTTAGATGCTTCTATCTTTTCGTC 59.523 38.462 9.91 0.00 38.35 4.20
2830 4615 6.477033 GCTTAGATGCTTCTATCTTTTCGTCA 59.523 38.462 9.91 0.00 38.35 4.35
2865 4651 9.630098 CATTACAGGCATGATGGATTTATTAAC 57.370 33.333 4.84 0.00 0.00 2.01
2957 4746 5.649395 TCCAAACAATGCTTCAGATCCTAAG 59.351 40.000 0.00 0.00 0.00 2.18
3020 4810 9.955208 TGCATAAAATCTTATTTCATGCACTAG 57.045 29.630 15.82 0.00 41.53 2.57
3063 4854 4.806330 TCAGAACCTTCGTTGATGTACTC 58.194 43.478 0.00 0.00 30.30 2.59
3157 4949 3.857157 TGGAGCACAAGGTTCTAGTTT 57.143 42.857 0.00 0.00 0.00 2.66
3161 4953 6.303839 TGGAGCACAAGGTTCTAGTTTAATT 58.696 36.000 0.00 0.00 0.00 1.40
3164 4956 8.957466 GGAGCACAAGGTTCTAGTTTAATTATT 58.043 33.333 0.00 0.00 0.00 1.40
3187 4979 7.739022 TTAAAATTCGCAAATGACATGCTAG 57.261 32.000 0.00 0.00 41.64 3.42
3201 4993 3.571401 ACATGCTAGTTGCTGCTCTTTTT 59.429 39.130 0.00 0.00 43.37 1.94
3264 5056 1.400888 GCAGACACTCGTGACTCTCTG 60.401 57.143 3.74 7.41 33.60 3.35
3333 5125 4.589216 TGAGGGTGCTCTTTTGAATTTG 57.411 40.909 0.00 0.00 0.00 2.32
3358 5150 9.967346 TGTAGTGATGAAGTATAGTTATTCTGC 57.033 33.333 0.00 0.00 0.00 4.26
3580 5373 3.131709 TCTTATGCTTAGCCTGATGCC 57.868 47.619 0.29 0.00 42.71 4.40
3581 5374 2.439135 TCTTATGCTTAGCCTGATGCCA 59.561 45.455 0.29 0.00 42.71 4.92
3614 5407 9.753674 TTTCTATGTGTTCTCTTAAATTGGGAT 57.246 29.630 0.00 0.00 0.00 3.85
3639 5432 1.952193 TGATATCCCACGCACACATG 58.048 50.000 0.00 0.00 0.00 3.21
3649 5442 3.253230 CACGCACACATGATCTGAACTA 58.747 45.455 0.00 0.00 0.00 2.24
3712 5505 9.588096 TGATTTACTCTAGCCTAATATCTGACA 57.412 33.333 0.00 0.00 0.00 3.58
3742 5535 3.753272 TCAGCAGACCATACTTTGCTTTC 59.247 43.478 0.00 0.00 43.91 2.62
3776 5569 5.393866 TCCTTCCTTGTAGAGCCAATTTTT 58.606 37.500 0.00 0.00 0.00 1.94
3779 5572 7.673926 TCCTTCCTTGTAGAGCCAATTTTTATT 59.326 33.333 0.00 0.00 0.00 1.40
3780 5573 8.314021 CCTTCCTTGTAGAGCCAATTTTTATTT 58.686 33.333 0.00 0.00 0.00 1.40
3885 5678 6.424509 TCTTATTTTGGTTTTTGCTGCAGATG 59.575 34.615 20.43 0.00 0.00 2.90
3891 5684 3.491447 GGTTTTTGCTGCAGATGTTCTGT 60.491 43.478 20.43 0.00 45.94 3.41
3941 5734 0.538516 AGGTGACGTCTGCTCTCTGT 60.539 55.000 17.92 0.00 0.00 3.41
3954 5757 8.607459 CGTCTGCTCTCTGTATAATTTTCATTT 58.393 33.333 0.00 0.00 0.00 2.32
3993 5797 6.827586 TTTTGGTATTATGCGGACTCTTTT 57.172 33.333 0.00 0.00 0.00 2.27
4045 5852 2.489329 CGGACAGGCAGATGAAAAATGT 59.511 45.455 0.00 0.00 0.00 2.71
4415 6241 6.835488 TGATGAAAGAAGAAAAGGATATGGGG 59.165 38.462 0.00 0.00 0.00 4.96
4443 6269 3.750130 CGATCCATCATTTCCTAAGGCTG 59.250 47.826 0.00 0.00 0.00 4.85
4502 6328 1.000163 TCTTCAAGCAGGACGAGTGAC 60.000 52.381 0.00 0.00 0.00 3.67
4538 6364 4.212143 TGACTGGAATGAGGATGAAGTG 57.788 45.455 0.00 0.00 0.00 3.16
4542 6368 6.126863 ACTGGAATGAGGATGAAGTGTTTA 57.873 37.500 0.00 0.00 0.00 2.01
4575 6401 3.014304 ACTACTATGGGAAGACGCTCA 57.986 47.619 0.00 0.00 0.00 4.26
4621 6447 2.045047 TGGAGTCTCTTCAAGGGAGGAT 59.955 50.000 0.00 0.00 0.00 3.24
4641 6467 1.745489 CAAGTAGGGGCGGCACTTC 60.745 63.158 22.71 15.79 30.20 3.01
4679 6505 1.376424 ACATGCTGCAAGAGTCCCG 60.376 57.895 12.28 0.00 34.07 5.14
4705 6531 3.797507 CTGCCCTGGGTGTTGCAGT 62.798 63.158 15.56 0.00 44.69 4.40
4835 6661 9.573166 CATTTTAGGTTGGTAGGATATCATTCA 57.427 33.333 4.83 0.00 27.62 2.57
4840 6666 6.006449 GGTTGGTAGGATATCATTCATTGCT 58.994 40.000 4.83 0.00 27.62 3.91
5026 6852 6.552445 AATCTTGGTAAGTAGCTCACAGAT 57.448 37.500 0.00 0.00 0.00 2.90
5027 6853 5.330455 TCTTGGTAAGTAGCTCACAGATG 57.670 43.478 0.00 0.00 0.00 2.90
5036 6868 5.426504 AGTAGCTCACAGATGAAAATCCAG 58.573 41.667 0.00 0.00 33.30 3.86
5041 6873 5.412594 GCTCACAGATGAAAATCCAGTGTTA 59.587 40.000 0.00 0.00 33.30 2.41
5111 6945 3.712016 TGCACCTTGTTATAGGCTCAA 57.288 42.857 0.00 0.00 38.99 3.02
5157 6991 4.232188 AGTTGTGATCTGATTGCTGGAT 57.768 40.909 0.00 0.00 0.00 3.41
5173 7007 4.080413 TGCTGGATATGGATGAACTGTTGA 60.080 41.667 0.00 0.00 0.00 3.18
5184 7019 4.933505 TGAACTGTTGATGCCATTTGAA 57.066 36.364 0.00 0.00 0.00 2.69
5199 7037 5.563867 GCCATTTGAACCGTGAATTGAACTA 60.564 40.000 0.00 0.00 0.00 2.24
5270 7109 5.643379 ATGGTATCGAAATTTGTGCTGTT 57.357 34.783 0.00 0.00 0.00 3.16
5320 7159 5.104527 AGGCTGATATACCTTACACAAGCAA 60.105 40.000 0.00 0.00 29.74 3.91
5369 7208 6.593382 AGCAACAATAACAACAACAACAATGT 59.407 30.769 0.00 0.00 43.14 2.71
5386 7225 3.895232 ATGTAGGCGACAGAGTGATTT 57.105 42.857 6.59 0.00 42.79 2.17
5401 7240 6.002704 AGAGTGATTTCTGCATTTTCTCTGT 58.997 36.000 0.00 0.00 0.00 3.41
5421 7260 3.956233 GTGCATCGAATGTACATTGCAT 58.044 40.909 27.05 16.10 44.02 3.96
5461 7300 3.687125 TCATCGTGTACTCCTGTCTCTT 58.313 45.455 0.00 0.00 0.00 2.85
5465 7304 2.552743 CGTGTACTCCTGTCTCTTGTCA 59.447 50.000 0.00 0.00 0.00 3.58
5473 7312 3.854666 CCTGTCTCTTGTCATGTACAGG 58.145 50.000 19.08 19.08 45.64 4.00
5483 7322 2.496070 GTCATGTACAGGAGGCACACTA 59.504 50.000 11.08 0.00 0.00 2.74
5493 7332 4.100035 CAGGAGGCACACTACATCTTCATA 59.900 45.833 0.00 0.00 29.75 2.15
5498 7337 4.272018 GGCACACTACATCTTCATAGCTTG 59.728 45.833 0.00 0.00 0.00 4.01
5516 7355 0.392706 TGTGAAGCGAGTGTCCATGT 59.607 50.000 0.00 0.00 0.00 3.21
5522 7361 4.099419 TGAAGCGAGTGTCCATGTATGTAT 59.901 41.667 0.00 0.00 0.00 2.29
5557 7396 8.882415 TTTCTTTCGATATACACAGGTATTCC 57.118 34.615 0.00 0.00 40.61 3.01
5564 7403 6.967767 CGATATACACAGGTATTCCGAAGATC 59.032 42.308 0.00 0.00 40.61 2.75
5673 7545 3.745480 CGCATCCAGGTCCATATCTGTTT 60.745 47.826 0.00 0.00 31.30 2.83
5763 7635 2.747855 CCTGCGGCTTCTGGTTCC 60.748 66.667 0.00 0.00 0.00 3.62
5805 7677 1.336702 TGCATTGCGTTCCATTTCCAC 60.337 47.619 3.84 0.00 0.00 4.02
5812 7690 1.200020 CGTTCCATTTCCACTTCAGCC 59.800 52.381 0.00 0.00 0.00 4.85
5833 7711 7.014134 TCAGCCAGAAACTTCATAAACATTTCA 59.986 33.333 0.00 0.00 32.78 2.69
5835 7713 7.014615 AGCCAGAAACTTCATAAACATTTCAGT 59.985 33.333 0.00 0.00 32.78 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.301087 ACGCATCACCGAAAACGGA 60.301 52.632 15.45 0.00 0.00 4.69
15 16 1.154488 CACGCATCACCGAAAACGG 60.154 57.895 7.12 7.12 0.00 4.44
17 18 1.463528 GCTACACGCATCACCGAAAAC 60.464 52.381 0.00 0.00 38.92 2.43
21 22 2.966590 TGCTACACGCATCACCGA 59.033 55.556 0.00 0.00 45.47 4.69
33 34 1.883084 CGCCCTCCGACAATGCTAC 60.883 63.158 0.00 0.00 40.02 3.58
44 45 4.394712 CACCTCCACACGCCCTCC 62.395 72.222 0.00 0.00 0.00 4.30
71 72 1.598130 CCGAATCCCGCAAGATCCC 60.598 63.158 0.00 0.00 43.02 3.85
72 73 0.463833 AACCGAATCCCGCAAGATCC 60.464 55.000 0.00 0.00 43.02 3.36
78 79 0.322322 AACACTAACCGAATCCCGCA 59.678 50.000 0.00 0.00 36.84 5.69
81 82 2.094338 AGACGAACACTAACCGAATCCC 60.094 50.000 0.00 0.00 0.00 3.85
112 113 5.297776 ACAGACAAAGACTGAATCCAAACAG 59.702 40.000 0.00 0.00 38.55 3.16
122 123 7.933577 ACATAAATGAAGACAGACAAAGACTGA 59.066 33.333 0.00 0.00 38.55 3.41
153 154 6.884832 TGTAGGTCGAAATGATCCAACTTAT 58.115 36.000 0.00 0.00 0.00 1.73
154 155 6.288941 TGTAGGTCGAAATGATCCAACTTA 57.711 37.500 0.00 0.00 0.00 2.24
156 157 4.819105 TGTAGGTCGAAATGATCCAACT 57.181 40.909 0.00 0.00 0.00 3.16
164 165 5.353956 TGAATCCAACATGTAGGTCGAAATG 59.646 40.000 0.00 0.00 0.00 2.32
172 173 4.578871 TGTCACTGAATCCAACATGTAGG 58.421 43.478 0.00 0.00 0.00 3.18
173 174 5.240891 ACTGTCACTGAATCCAACATGTAG 58.759 41.667 0.00 0.00 0.00 2.74
175 176 4.090761 ACTGTCACTGAATCCAACATGT 57.909 40.909 0.00 0.00 0.00 3.21
176 177 4.276678 ACAACTGTCACTGAATCCAACATG 59.723 41.667 0.00 0.00 0.00 3.21
179 180 4.900635 AACAACTGTCACTGAATCCAAC 57.099 40.909 0.00 0.00 0.00 3.77
181 182 6.533730 AGAATAACAACTGTCACTGAATCCA 58.466 36.000 0.00 0.00 0.00 3.41
182 183 7.819900 ACTAGAATAACAACTGTCACTGAATCC 59.180 37.037 0.00 0.00 0.00 3.01
183 184 8.651588 CACTAGAATAACAACTGTCACTGAATC 58.348 37.037 0.00 0.00 0.00 2.52
184 185 8.150945 ACACTAGAATAACAACTGTCACTGAAT 58.849 33.333 0.00 0.00 0.00 2.57
190 193 5.696270 CAGCACACTAGAATAACAACTGTCA 59.304 40.000 0.00 0.00 0.00 3.58
193 196 4.997395 ACCAGCACACTAGAATAACAACTG 59.003 41.667 0.00 0.00 0.00 3.16
195 198 5.238650 ACAACCAGCACACTAGAATAACAAC 59.761 40.000 0.00 0.00 0.00 3.32
218 221 5.930135 AGTCATCATGTTAAGACCCCATAC 58.070 41.667 0.00 0.00 0.00 2.39
222 225 4.640647 GGAAAGTCATCATGTTAAGACCCC 59.359 45.833 0.00 0.00 0.00 4.95
224 227 6.431234 AGTTGGAAAGTCATCATGTTAAGACC 59.569 38.462 0.00 0.00 0.00 3.85
227 230 7.173907 AGACAGTTGGAAAGTCATCATGTTAAG 59.826 37.037 0.00 0.00 34.80 1.85
243 246 7.721842 TCAAATTTATTGTGGTAGACAGTTGGA 59.278 33.333 0.00 0.00 35.44 3.53
246 249 7.504238 TGGTCAAATTTATTGTGGTAGACAGTT 59.496 33.333 0.00 0.00 35.44 3.16
248 251 7.390440 TCTGGTCAAATTTATTGTGGTAGACAG 59.610 37.037 0.00 0.00 35.44 3.51
250 253 7.390718 AGTCTGGTCAAATTTATTGTGGTAGAC 59.609 37.037 0.00 0.00 0.00 2.59
256 259 7.439157 TCAGAGTCTGGTCAAATTTATTGTG 57.561 36.000 19.99 0.00 31.51 3.33
257 260 7.884877 TCATCAGAGTCTGGTCAAATTTATTGT 59.115 33.333 19.99 0.00 31.51 2.71
272 275 1.039068 CGCATCCCTCATCAGAGTCT 58.961 55.000 0.00 0.00 40.40 3.24
277 280 1.005275 ATCGCGCATCCCTCATCAG 60.005 57.895 8.75 0.00 0.00 2.90
315 318 0.882927 GCTACAAGCACCGGTGTGAA 60.883 55.000 33.92 15.25 45.76 3.18
320 323 0.884704 CAACAGCTACAAGCACCGGT 60.885 55.000 0.00 0.00 45.56 5.28
334 337 2.002586 CCGTAGACCATCAAGCAACAG 58.997 52.381 0.00 0.00 0.00 3.16
381 401 8.256611 ACATGTCATGACAGTATAAAGAACAC 57.743 34.615 30.63 0.00 45.48 3.32
404 424 3.289407 TTGCGGGGATTTATCATGACA 57.711 42.857 0.00 0.00 0.00 3.58
405 425 4.647424 TTTTGCGGGGATTTATCATGAC 57.353 40.909 0.00 0.00 0.00 3.06
495 515 1.072505 CGGGGCCTTGTGTTGTAGT 59.927 57.895 0.84 0.00 0.00 2.73
496 516 0.536460 AACGGGGCCTTGTGTTGTAG 60.536 55.000 0.84 0.00 0.00 2.74
498 518 0.106619 TAAACGGGGCCTTGTGTTGT 60.107 50.000 0.84 0.00 0.00 3.32
499 519 1.033574 TTAAACGGGGCCTTGTGTTG 58.966 50.000 0.84 0.00 0.00 3.33
500 520 1.890489 GATTAAACGGGGCCTTGTGTT 59.110 47.619 0.84 0.53 0.00 3.32
501 521 1.202952 TGATTAAACGGGGCCTTGTGT 60.203 47.619 0.84 0.00 0.00 3.72
502 522 1.540267 TGATTAAACGGGGCCTTGTG 58.460 50.000 0.84 0.00 0.00 3.33
504 524 2.954316 GTTTGATTAAACGGGGCCTTG 58.046 47.619 0.84 0.00 37.08 3.61
513 533 9.739786 CCGAAATTTATGCAAGTTTGATTAAAC 57.260 29.630 4.99 4.99 45.13 2.01
514 534 8.439286 GCCGAAATTTATGCAAGTTTGATTAAA 58.561 29.630 0.00 0.00 0.00 1.52
515 535 7.064016 GGCCGAAATTTATGCAAGTTTGATTAA 59.936 33.333 12.05 0.00 0.00 1.40
516 536 6.533367 GGCCGAAATTTATGCAAGTTTGATTA 59.467 34.615 12.05 0.00 0.00 1.75
517 537 5.351189 GGCCGAAATTTATGCAAGTTTGATT 59.649 36.000 12.05 0.00 0.00 2.57
518 538 4.869861 GGCCGAAATTTATGCAAGTTTGAT 59.130 37.500 12.05 0.00 0.00 2.57
519 539 4.241681 GGCCGAAATTTATGCAAGTTTGA 58.758 39.130 12.05 0.00 0.00 2.69
520 540 3.993081 TGGCCGAAATTTATGCAAGTTTG 59.007 39.130 12.05 0.00 0.00 2.93
521 541 4.264460 TGGCCGAAATTTATGCAAGTTT 57.736 36.364 12.05 0.00 0.00 2.66
522 542 3.951775 TGGCCGAAATTTATGCAAGTT 57.048 38.095 12.05 0.00 0.00 2.66
523 543 4.202111 GGTATGGCCGAAATTTATGCAAGT 60.202 41.667 12.05 2.36 0.00 3.16
524 544 4.037923 AGGTATGGCCGAAATTTATGCAAG 59.962 41.667 12.05 0.00 43.70 4.01
525 545 3.957497 AGGTATGGCCGAAATTTATGCAA 59.043 39.130 12.05 2.99 43.70 4.08
526 546 3.561143 AGGTATGGCCGAAATTTATGCA 58.439 40.909 12.05 0.00 43.70 3.96
527 547 5.001232 TCTAGGTATGGCCGAAATTTATGC 58.999 41.667 0.00 0.00 43.70 3.14
528 548 6.464222 TCTCTAGGTATGGCCGAAATTTATG 58.536 40.000 0.00 0.00 43.70 1.90
572 592 1.203313 GTTTGGAAGGAACGTCGCG 59.797 57.895 0.00 0.00 37.83 5.87
573 593 0.658897 TTGTTTGGAAGGAACGTCGC 59.341 50.000 0.00 0.00 37.83 5.19
575 595 3.103007 CGTTTTGTTTGGAAGGAACGTC 58.897 45.455 0.00 0.00 36.20 4.34
577 597 2.159352 ACCGTTTTGTTTGGAAGGAACG 60.159 45.455 0.00 0.00 39.43 3.95
578 598 3.183754 CACCGTTTTGTTTGGAAGGAAC 58.816 45.455 0.00 0.00 0.00 3.62
579 599 2.417515 GCACCGTTTTGTTTGGAAGGAA 60.418 45.455 0.00 0.00 0.00 3.36
580 600 1.135333 GCACCGTTTTGTTTGGAAGGA 59.865 47.619 0.00 0.00 0.00 3.36
581 601 1.136110 AGCACCGTTTTGTTTGGAAGG 59.864 47.619 0.00 0.00 0.00 3.46
582 602 2.192624 CAGCACCGTTTTGTTTGGAAG 58.807 47.619 0.00 0.00 0.00 3.46
583 603 1.737363 GCAGCACCGTTTTGTTTGGAA 60.737 47.619 0.00 0.00 0.00 3.53
584 604 0.179124 GCAGCACCGTTTTGTTTGGA 60.179 50.000 0.00 0.00 0.00 3.53
585 605 1.151172 GGCAGCACCGTTTTGTTTGG 61.151 55.000 0.00 0.00 0.00 3.28
586 606 0.179113 AGGCAGCACCGTTTTGTTTG 60.179 50.000 0.00 0.00 46.52 2.93
587 607 1.394618 TAGGCAGCACCGTTTTGTTT 58.605 45.000 0.00 0.00 46.52 2.83
588 608 1.394618 TTAGGCAGCACCGTTTTGTT 58.605 45.000 0.00 0.00 46.52 2.83
589 609 1.616159 ATTAGGCAGCACCGTTTTGT 58.384 45.000 0.00 0.00 46.52 2.83
590 610 2.595386 GAATTAGGCAGCACCGTTTTG 58.405 47.619 0.00 0.00 46.52 2.44
676 1896 1.867233 AGATGAGTGTGTTTCGTGTGC 59.133 47.619 0.00 0.00 0.00 4.57
779 1999 2.742589 GTGCTACAGTGGAGTAAAAGGC 59.257 50.000 3.79 0.00 0.00 4.35
781 2001 2.993899 CCGTGCTACAGTGGAGTAAAAG 59.006 50.000 3.79 0.00 0.00 2.27
782 2002 2.868839 GCCGTGCTACAGTGGAGTAAAA 60.869 50.000 3.79 0.00 0.00 1.52
783 2003 1.337447 GCCGTGCTACAGTGGAGTAAA 60.337 52.381 3.79 0.00 0.00 2.01
785 2005 0.896479 TGCCGTGCTACAGTGGAGTA 60.896 55.000 3.79 0.00 0.00 2.59
786 2006 1.544825 ATGCCGTGCTACAGTGGAGT 61.545 55.000 3.79 0.00 0.00 3.85
788 2008 1.079197 CATGCCGTGCTACAGTGGA 60.079 57.895 0.00 0.00 0.00 4.02
790 2010 1.372582 AATCATGCCGTGCTACAGTG 58.627 50.000 0.00 0.00 0.00 3.66
791 2011 2.483714 CCTAATCATGCCGTGCTACAGT 60.484 50.000 0.00 0.00 0.00 3.55
792 2012 2.138320 CCTAATCATGCCGTGCTACAG 58.862 52.381 0.00 0.00 0.00 2.74
793 2013 1.760029 TCCTAATCATGCCGTGCTACA 59.240 47.619 0.00 0.00 0.00 2.74
794 2014 2.526304 TCCTAATCATGCCGTGCTAC 57.474 50.000 0.00 0.00 0.00 3.58
835 2071 2.597578 TGGTTAGGGGAAAGCCTTTC 57.402 50.000 8.72 8.72 38.94 2.62
888 2124 3.447586 TGGTCAGACCAGCAGTAGTATTC 59.552 47.826 19.21 0.00 44.79 1.75
889 2125 3.441101 TGGTCAGACCAGCAGTAGTATT 58.559 45.455 19.21 0.00 44.79 1.89
1270 2517 6.036517 CCAGATCAAATCGAATCGAAGAAACT 59.963 38.462 10.12 9.19 43.58 2.66
1302 2549 4.710423 ATCCTCGATTCGTATCCATCTG 57.290 45.455 5.89 0.00 0.00 2.90
1327 2574 2.822399 CCACACCTCGGGCTATCC 59.178 66.667 0.00 0.00 0.00 2.59
1328 2575 2.109181 GCCACACCTCGGGCTATC 59.891 66.667 0.00 0.00 46.74 2.08
1357 2604 3.195698 GGCAGATCGACAACGGCC 61.196 66.667 12.43 12.43 40.21 6.13
1402 2649 2.881074 ACACGACGAAATCATCAGAGG 58.119 47.619 0.00 0.00 0.00 3.69
1410 2657 5.756950 TTCAGACATAACACGACGAAATC 57.243 39.130 0.00 0.00 0.00 2.17
1411 2658 6.453791 CGATTTCAGACATAACACGACGAAAT 60.454 38.462 0.00 0.00 35.23 2.17
1443 2760 3.665745 ACAAAACCATCATGTTCCAGC 57.334 42.857 0.00 0.00 0.00 4.85
1457 2784 6.379386 GGTTCCTAGCATGAGTTAACAAAAC 58.621 40.000 8.61 0.00 0.00 2.43
1472 2799 3.270877 CATAGTGTTGTGGGTTCCTAGC 58.729 50.000 0.00 0.00 0.00 3.42
1530 2875 0.919289 TAAGCTTGGAAGGGGAGGGG 60.919 60.000 9.86 0.00 0.00 4.79
1535 2880 2.093500 GCCAAAATAAGCTTGGAAGGGG 60.093 50.000 9.86 4.93 45.31 4.79
1536 2881 2.833943 AGCCAAAATAAGCTTGGAAGGG 59.166 45.455 9.86 6.57 45.31 3.95
1556 2901 7.552687 TGAATACCAATAGCCTAACAAGTCAAG 59.447 37.037 0.00 0.00 0.00 3.02
1643 3150 6.433847 TCAGTGAAAATTCCCTAACTGAGA 57.566 37.500 8.95 0.00 39.17 3.27
1653 3160 8.729805 AGAGATGTTCTATCAGTGAAAATTCC 57.270 34.615 0.00 0.00 33.23 3.01
1677 3186 5.863935 GCAGCAATTTACTAGGGACAAAAAG 59.136 40.000 0.00 0.00 0.00 2.27
1726 3236 9.220906 TGGTAAAATTAGTGGAGAGTATGGTAT 57.779 33.333 0.00 0.00 0.00 2.73
1767 3277 2.089980 CAAGCCAGTCAATCCCTCAAG 58.910 52.381 0.00 0.00 0.00 3.02
1772 3282 1.000396 AGGCAAGCCAGTCAATCCC 60.000 57.895 14.40 0.00 38.92 3.85
1787 3297 2.704572 AGAGTATGTTTGCACAGAGGC 58.295 47.619 0.00 0.00 35.94 4.70
1791 3301 5.334879 GGGTGTTAAGAGTATGTTTGCACAG 60.335 44.000 0.00 0.00 35.94 3.66
1796 3306 6.293955 CCAACAGGGTGTTAAGAGTATGTTTG 60.294 42.308 0.00 0.00 38.77 2.93
1801 3311 3.329520 TGCCAACAGGGTGTTAAGAGTAT 59.670 43.478 0.00 0.00 38.77 2.12
1802 3312 2.706723 TGCCAACAGGGTGTTAAGAGTA 59.293 45.455 0.00 0.00 38.77 2.59
1878 3402 4.955450 ACAAGCATGATGGGCATTTTAGTA 59.045 37.500 0.00 0.00 34.15 1.82
1884 3409 0.177141 GCACAAGCATGATGGGCATT 59.823 50.000 18.13 0.00 46.48 3.56
1996 3523 3.758554 TGCAGGTAAGGAAGAAATCAAGC 59.241 43.478 0.00 0.00 0.00 4.01
2176 3703 8.126700 GCATAATAACGCCTTTTAAGCTTCTTA 58.873 33.333 0.00 0.00 0.00 2.10
2180 3707 6.127730 ACTGCATAATAACGCCTTTTAAGCTT 60.128 34.615 3.48 3.48 0.00 3.74
2181 3708 5.357032 ACTGCATAATAACGCCTTTTAAGCT 59.643 36.000 0.00 0.00 0.00 3.74
2216 3746 6.422776 ACTTCTCTACGTTATTTTGCCATG 57.577 37.500 0.00 0.00 0.00 3.66
2230 3760 7.708322 TGAAGATGCACATCAATACTTCTCTAC 59.292 37.037 12.87 0.00 40.22 2.59
2267 3800 3.573967 AGGTTGGCAATAACAAACAGGAG 59.426 43.478 1.92 0.00 37.98 3.69
2399 4051 0.681564 ACCACTGCTCGAGGGACTAG 60.682 60.000 15.58 1.26 41.55 2.57
2409 4061 1.582968 CCAATGCACACCACTGCTC 59.417 57.895 0.00 0.00 38.07 4.26
2683 4336 8.786826 AGATGACATATCAACCGAACTTTTAA 57.213 30.769 0.00 0.00 38.69 1.52
2693 4346 5.844004 AGTTCGGTAGATGACATATCAACC 58.156 41.667 0.00 0.00 38.69 3.77
2770 4554 4.207955 TGTTAAGCCCAAATACACACACA 58.792 39.130 0.00 0.00 0.00 3.72
2821 4606 7.962918 CCTGTAATGGTAGAAATTGACGAAAAG 59.037 37.037 0.00 0.00 0.00 2.27
2826 4611 4.634004 TGCCTGTAATGGTAGAAATTGACG 59.366 41.667 0.00 0.00 0.00 4.35
2829 4614 6.698008 TCATGCCTGTAATGGTAGAAATTG 57.302 37.500 0.00 0.00 0.00 2.32
2830 4615 6.266103 CCATCATGCCTGTAATGGTAGAAATT 59.734 38.462 1.54 0.00 35.08 1.82
3020 4810 4.216257 TGAAGGACTCAATAAACTGCTTGC 59.784 41.667 0.00 0.00 0.00 4.01
3031 4821 3.325135 ACGAAGGTTCTGAAGGACTCAAT 59.675 43.478 0.00 0.00 32.17 2.57
3063 4854 7.538678 GCTTGAACAACCTAATACAACAGATTG 59.461 37.037 0.00 0.00 41.98 2.67
3161 4953 9.449550 CTAGCATGTCATTTGCGAATTTTAATA 57.550 29.630 0.00 0.00 44.82 0.98
3164 4956 6.851609 ACTAGCATGTCATTTGCGAATTTTA 58.148 32.000 0.00 0.00 44.82 1.52
3187 4979 3.978718 AGTCAGAAAAAGAGCAGCAAC 57.021 42.857 0.00 0.00 0.00 4.17
3201 4993 5.335740 GCAAGTAACAGTAGCAGTAGTCAGA 60.336 44.000 0.00 0.00 0.00 3.27
3264 5056 8.286800 GCCACCAAAATTTGTAAAAACCTTATC 58.713 33.333 4.92 0.00 0.00 1.75
3333 5125 9.967346 TGCAGAATAACTATACTTCATCACTAC 57.033 33.333 0.00 0.00 0.00 2.73
3376 5168 5.760743 TCGACACCTATGATCAACAAAAACA 59.239 36.000 0.00 0.00 0.00 2.83
3418 5211 6.914757 GCCAGTGATCATCAAAGTTAATAAGC 59.085 38.462 0.00 0.00 0.00 3.09
3614 5407 2.027653 TGTGCGTGGGATATCAACAAGA 60.028 45.455 13.82 1.17 0.00 3.02
3712 5505 4.655963 AGTATGGTCTGCTGACAAAATGT 58.344 39.130 23.12 2.03 44.61 2.71
3721 5514 3.425359 CGAAAGCAAAGTATGGTCTGCTG 60.425 47.826 0.00 0.00 44.18 4.41
3742 5535 1.402968 CAAGGAAGGAATCACATGCCG 59.597 52.381 0.00 0.00 0.00 5.69
3779 5572 9.816787 ATCCTTTTAGTTAAACAACTATGGGAA 57.183 29.630 12.88 0.00 35.42 3.97
3869 5662 3.054878 CAGAACATCTGCAGCAAAAACC 58.945 45.455 9.47 0.00 37.72 3.27
3885 5678 4.807304 TCACTTTTACTTCCACGACAGAAC 59.193 41.667 0.00 0.00 0.00 3.01
3891 5684 5.875910 TCTTGTTTCACTTTTACTTCCACGA 59.124 36.000 0.00 0.00 0.00 4.35
4011 5815 1.822990 CCTGTCCGACAGCCTACTTTA 59.177 52.381 21.26 0.00 44.63 1.85
4024 5828 2.489329 ACATTTTTCATCTGCCTGTCCG 59.511 45.455 0.00 0.00 0.00 4.79
4067 5874 4.910195 ACCACAGCTGATTAAGTTCATGA 58.090 39.130 23.35 0.00 0.00 3.07
4131 5952 1.826385 AGGTTGATTGGCTTTCTCCG 58.174 50.000 0.00 0.00 0.00 4.63
4462 6288 0.533755 ACGATAGCAAGATGGGCAGC 60.534 55.000 0.00 0.00 42.67 5.25
4542 6368 7.504926 TCCCATAGTAGTTAACCAAGAATGT 57.495 36.000 0.88 0.00 0.00 2.71
4621 6447 4.715523 GTGCCGCCCCTACTTGCA 62.716 66.667 0.00 0.00 0.00 4.08
4641 6467 1.743321 GAGGAGGAGGCATCGTCAGG 61.743 65.000 21.04 0.00 41.21 3.86
4679 6505 2.123982 CCCAGGGCAGCTCCAATC 60.124 66.667 0.00 0.00 36.21 2.67
4705 6531 1.255882 CCCAAATGTACAGCTGGCAA 58.744 50.000 19.93 2.49 0.00 4.52
4809 6635 9.573166 TGAATGATATCCTACCAACCTAAAATG 57.427 33.333 0.00 0.00 0.00 2.32
4835 6661 1.134936 TCCGTATACGCACACAGCAAT 60.135 47.619 19.86 0.00 46.13 3.56
4840 6666 3.233684 TGAATTCCGTATACGCACACA 57.766 42.857 19.86 11.86 38.18 3.72
5026 6852 4.973168 ACAGCTCTAACACTGGATTTTCA 58.027 39.130 0.00 0.00 38.25 2.69
5027 6853 4.997395 TGACAGCTCTAACACTGGATTTTC 59.003 41.667 0.00 0.00 38.25 2.29
5064 6896 5.690464 AGGTCATCATGCTTCTCTAAGTT 57.310 39.130 0.00 0.00 34.99 2.66
5070 6902 4.034975 GCAAGTTAGGTCATCATGCTTCTC 59.965 45.833 0.00 0.00 0.00 2.87
5157 6991 4.233632 TGGCATCAACAGTTCATCCATA 57.766 40.909 0.00 0.00 0.00 2.74
5173 7007 3.257873 TCAATTCACGGTTCAAATGGCAT 59.742 39.130 0.00 0.00 0.00 4.40
5184 7019 7.094933 GGATTAACACTTAGTTCAATTCACGGT 60.095 37.037 0.00 0.00 41.64 4.83
5199 7037 6.228258 TCGCAAGACTTAAGGATTAACACTT 58.772 36.000 7.53 0.00 45.01 3.16
5228 7067 6.486056 ACCATAGACAGAGTACATCCGATAT 58.514 40.000 0.00 0.00 0.00 1.63
5270 7109 0.389817 GCACTACCATGCTGTCGTCA 60.390 55.000 0.00 0.00 42.62 4.35
5320 7159 2.627699 ACAATTCGCCAGTTCCAAATGT 59.372 40.909 0.00 0.00 0.00 2.71
5353 7192 3.378742 TCGCCTACATTGTTGTTGTTGTT 59.621 39.130 0.00 0.00 37.28 2.83
5354 7193 2.946329 TCGCCTACATTGTTGTTGTTGT 59.054 40.909 0.00 0.00 37.28 3.32
5355 7194 3.242903 TGTCGCCTACATTGTTGTTGTTG 60.243 43.478 0.00 0.00 37.28 3.33
5369 7208 2.417379 GCAGAAATCACTCTGTCGCCTA 60.417 50.000 2.81 0.00 44.04 3.93
5401 7240 5.296531 ACTTATGCAATGTACATTCGATGCA 59.703 36.000 26.70 26.70 32.86 3.96
5421 7260 9.529325 CACGATGATGTAGGAATTTTAGACTTA 57.471 33.333 0.00 0.00 0.00 2.24
5445 7284 4.021894 ACATGACAAGAGACAGGAGTACAC 60.022 45.833 0.00 0.00 0.00 2.90
5461 7300 1.001974 GTGTGCCTCCTGTACATGACA 59.998 52.381 0.00 0.00 41.79 3.58
5465 7304 2.536066 TGTAGTGTGCCTCCTGTACAT 58.464 47.619 0.00 0.00 41.79 2.29
5473 7312 4.054671 GCTATGAAGATGTAGTGTGCCTC 58.945 47.826 0.00 0.00 0.00 4.70
5477 7316 6.101997 TCACAAGCTATGAAGATGTAGTGTG 58.898 40.000 0.00 0.00 0.00 3.82
5498 7337 2.363788 TACATGGACACTCGCTTCAC 57.636 50.000 0.00 0.00 0.00 3.18
5557 7396 4.852104 GTGGCTGTACGTATATGATCTTCG 59.148 45.833 0.00 0.00 0.00 3.79
5564 7403 4.503007 GTGAGTTGTGGCTGTACGTATATG 59.497 45.833 0.00 0.00 0.00 1.78
5673 7545 0.472925 TCCAGTAGTGCACCAAGGGA 60.473 55.000 14.63 13.25 0.00 4.20
5763 7635 1.331756 GCTATGCATGGTCAGGTTTCG 59.668 52.381 10.16 0.00 0.00 3.46
5805 7677 6.317789 TGTTTATGAAGTTTCTGGCTGAAG 57.682 37.500 6.91 0.00 35.89 3.02
5845 7723 5.941647 GGCAGGTTTGTAAAACCATCTAGTA 59.058 40.000 20.82 0.00 42.69 1.82
5846 7724 4.765339 GGCAGGTTTGTAAAACCATCTAGT 59.235 41.667 20.82 0.00 42.69 2.57
5847 7725 4.764823 TGGCAGGTTTGTAAAACCATCTAG 59.235 41.667 20.82 8.55 42.69 2.43
5848 7726 4.521256 GTGGCAGGTTTGTAAAACCATCTA 59.479 41.667 20.82 9.18 42.69 1.98


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

AutoCloner maintained by Alex Coulton.