Multiple sequence alignment - TraesCS7D01G451900

Loading Multiple Alignment...

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 TraesCS7D01G451900 chr7D 100.000 6422 0 0 1 6422 571721053 571714632 0.000000e+00 11860.0
1 TraesCS7D01G451900 chr7D 86.597 955 98 21 4331 5277 634578442 634579374 0.000000e+00 1027.0
2 TraesCS7D01G451900 chr7D 83.244 561 48 19 3862 4403 634577907 634578440 2.100000e-129 473.0
3 TraesCS7D01G451900 chr7D 91.489 47 3 1 3543 3589 17770616 17770571 5.380000e-06 63.9
4 TraesCS7D01G451900 chr7B 93.533 3572 130 46 1 3521 627988263 627984742 0.000000e+00 5223.0
5 TraesCS7D01G451900 chr7B 95.051 2061 79 9 3550 5590 627984631 627982574 0.000000e+00 3219.0
6 TraesCS7D01G451900 chr7B 81.337 643 60 26 5723 6319 32678877 32678249 9.750000e-128 468.0
7 TraesCS7D01G451900 chr7B 79.666 359 34 13 5731 6079 678132687 678132358 8.380000e-54 222.0
8 TraesCS7D01G451900 chr7B 83.333 138 5 6 5585 5722 627973850 627973731 1.890000e-20 111.0
9 TraesCS7D01G451900 chr7B 97.561 41 0 1 3550 3589 367017137 367017097 1.160000e-07 69.4
10 TraesCS7D01G451900 chr7A 93.291 3592 149 45 1 3559 660555530 660551998 0.000000e+00 5214.0
11 TraesCS7D01G451900 chr7A 96.408 1030 32 4 4449 5475 660551111 660550084 0.000000e+00 1692.0
12 TraesCS7D01G451900 chr7A 83.613 1489 164 36 3862 5324 731632107 731630673 0.000000e+00 1325.0
13 TraesCS7D01G451900 chr7A 94.786 537 26 2 3550 4085 660551911 660551376 0.000000e+00 835.0
14 TraesCS7D01G451900 chr7A 88.406 276 8 4 4125 4382 660551374 660551105 1.740000e-80 311.0
15 TraesCS7D01G451900 chr7A 80.488 164 10 11 5546 5708 660549849 660549707 8.810000e-19 106.0
16 TraesCS7D01G451900 chr6D 84.628 618 45 19 5731 6311 445781620 445781016 2.600000e-158 569.0
17 TraesCS7D01G451900 chr6D 83.702 362 34 8 5732 6078 54852750 54852399 1.040000e-82 318.0
18 TraesCS7D01G451900 chr6D 93.333 45 1 2 3550 3593 325600834 325600877 1.490000e-06 65.8
19 TraesCS7D01G451900 chr2D 83.388 614 57 19 5731 6318 44072105 44071511 1.590000e-145 527.0
20 TraesCS7D01G451900 chr2D 83.175 630 48 20 5731 6318 87656454 87655841 2.050000e-144 523.0
21 TraesCS7D01G451900 chr4D 83.094 627 48 23 5731 6316 501179613 501179004 9.540000e-143 518.0
22 TraesCS7D01G451900 chr4B 82.047 635 47 28 5725 6311 592997772 592998387 4.500000e-131 479.0
23 TraesCS7D01G451900 chr4B 80.218 642 67 24 5723 6316 345282528 345283157 1.650000e-115 427.0
24 TraesCS7D01G451900 chr3A 81.646 632 50 16 5731 6312 658307820 658308435 1.260000e-126 464.0
25 TraesCS7D01G451900 chr3D 86.079 431 55 4 2161 2590 597179295 597179721 5.870000e-125 459.0
26 TraesCS7D01G451900 chr3D 85.847 431 54 6 2161 2590 577345555 577345131 9.820000e-123 451.0
27 TraesCS7D01G451900 chr3D 85.515 359 30 14 1023 1379 577345947 577345609 7.920000e-94 355.0
28 TraesCS7D01G451900 chr3D 85.237 359 31 14 1023 1379 597178903 597179241 3.680000e-92 350.0
29 TraesCS7D01G451900 chr1B 81.026 643 52 24 5720 6311 4317612 4316989 1.270000e-121 448.0
30 TraesCS7D01G451900 chr5A 80.595 639 63 37 5721 6315 680083759 680083138 2.750000e-118 436.0
31 TraesCS7D01G451900 chr5A 87.017 362 45 2 2162 2522 480302404 480302764 2.160000e-109 407.0
32 TraesCS7D01G451900 chr5A 80.488 246 36 6 6082 6316 534832315 534832559 1.840000e-40 178.0
33 TraesCS7D01G451900 chr5A 97.500 40 1 0 3550 3589 657987048 657987087 1.160000e-07 69.4
34 TraesCS7D01G451900 chr1A 81.739 575 51 12 5716 6244 504270741 504270175 1.280000e-116 431.0
35 TraesCS7D01G451900 chr1A 95.556 45 1 1 3550 3594 30182736 30182779 3.210000e-08 71.3
36 TraesCS7D01G451900 chr6A 84.944 445 28 8 5896 6311 3004196 3004630 1.290000e-111 414.0
37 TraesCS7D01G451900 chr6A 97.561 41 1 0 3548 3588 155254042 155254002 3.210000e-08 71.3
38 TraesCS7D01G451900 chr5B 83.589 457 49 16 2122 2575 708516894 708517327 7.750000e-109 405.0
39 TraesCS7D01G451900 chr5B 85.000 360 30 19 1023 1379 708516560 708516898 1.710000e-90 344.0
40 TraesCS7D01G451900 chr6B 85.237 359 32 15 1023 1379 506712716 506713055 3.680000e-92 350.0
41 TraesCS7D01G451900 chr6B 83.444 151 23 2 2161 2310 506713109 506713258 8.680000e-29 139.0
42 TraesCS7D01G451900 chr2B 78.422 621 74 27 5725 6312 607955952 607956545 3.680000e-92 350.0
43 TraesCS7D01G451900 chr2B 78.906 384 50 12 5721 6086 464880329 464879959 1.390000e-56 231.0
44 TraesCS7D01G451900 chr2B 80.658 243 35 6 6085 6316 589029235 589028994 1.840000e-40 178.0
45 TraesCS7D01G451900 chr2B 78.302 106 10 6 5618 5713 775365574 775365472 8.990000e-04 56.5
46 TraesCS7D01G451900 chr5D 86.475 244 19 5 6085 6318 465033323 465033562 8.260000e-64 255.0
47 TraesCS7D01G451900 chr3B 81.070 243 34 6 6085 6316 744075877 744075636 3.950000e-42 183.0
48 TraesCS7D01G451900 chr3B 79.424 243 38 7 6085 6316 558563158 558562917 1.850000e-35 161.0
49 TraesCS7D01G451900 chr2A 91.489 47 2 2 3550 3595 660282948 660282903 5.380000e-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 TraesCS7D01G451900 chr7D 571714632 571721053 6421 True 11860.0 11860 100.0000 1 6422 1 chr7D.!!$R2 6421
1 TraesCS7D01G451900 chr7D 634577907 634579374 1467 False 750.0 1027 84.9205 3862 5277 2 chr7D.!!$F1 1415
2 TraesCS7D01G451900 chr7B 627982574 627988263 5689 True 4221.0 5223 94.2920 1 5590 2 chr7B.!!$R5 5589
3 TraesCS7D01G451900 chr7B 32678249 32678877 628 True 468.0 468 81.3370 5723 6319 1 chr7B.!!$R1 596
4 TraesCS7D01G451900 chr7A 660549707 660555530 5823 True 1631.6 5214 90.6758 1 5708 5 chr7A.!!$R2 5707
5 TraesCS7D01G451900 chr7A 731630673 731632107 1434 True 1325.0 1325 83.6130 3862 5324 1 chr7A.!!$R1 1462
6 TraesCS7D01G451900 chr6D 445781016 445781620 604 True 569.0 569 84.6280 5731 6311 1 chr6D.!!$R2 580
7 TraesCS7D01G451900 chr2D 44071511 44072105 594 True 527.0 527 83.3880 5731 6318 1 chr2D.!!$R1 587
8 TraesCS7D01G451900 chr2D 87655841 87656454 613 True 523.0 523 83.1750 5731 6318 1 chr2D.!!$R2 587
9 TraesCS7D01G451900 chr4D 501179004 501179613 609 True 518.0 518 83.0940 5731 6316 1 chr4D.!!$R1 585
10 TraesCS7D01G451900 chr4B 592997772 592998387 615 False 479.0 479 82.0470 5725 6311 1 chr4B.!!$F2 586
11 TraesCS7D01G451900 chr4B 345282528 345283157 629 False 427.0 427 80.2180 5723 6316 1 chr4B.!!$F1 593
12 TraesCS7D01G451900 chr3A 658307820 658308435 615 False 464.0 464 81.6460 5731 6312 1 chr3A.!!$F1 581
13 TraesCS7D01G451900 chr3D 597178903 597179721 818 False 404.5 459 85.6580 1023 2590 2 chr3D.!!$F1 1567
14 TraesCS7D01G451900 chr3D 577345131 577345947 816 True 403.0 451 85.6810 1023 2590 2 chr3D.!!$R1 1567
15 TraesCS7D01G451900 chr1B 4316989 4317612 623 True 448.0 448 81.0260 5720 6311 1 chr1B.!!$R1 591
16 TraesCS7D01G451900 chr5A 680083138 680083759 621 True 436.0 436 80.5950 5721 6315 1 chr5A.!!$R1 594
17 TraesCS7D01G451900 chr1A 504270175 504270741 566 True 431.0 431 81.7390 5716 6244 1 chr1A.!!$R1 528
18 TraesCS7D01G451900 chr5B 708516560 708517327 767 False 374.5 405 84.2945 1023 2575 2 chr5B.!!$F1 1552
19 TraesCS7D01G451900 chr6B 506712716 506713258 542 False 244.5 350 84.3405 1023 2310 2 chr6B.!!$F1 1287
20 TraesCS7D01G451900 chr2B 607955952 607956545 593 False 350.0 350 78.4220 5725 6312 1 chr2B.!!$F1 587

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
989 1049 0.038892 GATAGCGCCATTGCCCATTG 60.039 55.000 2.29 0.00 34.65 2.82 F
1036 1096 0.101040 TTGTGTTGTGCTTGCAGCTC 59.899 50.000 9.12 6.51 42.97 4.09 F
1140 1200 0.368907 CGTCGGGCAGAACAATAACG 59.631 55.000 0.00 0.00 0.00 3.18 F
2563 2652 1.002624 TTGGAAGGGGCGATGTGTC 60.003 57.895 0.00 0.00 0.00 3.67 F
4128 4316 2.119495 ACAGAGGTGACAAACTGACCT 58.881 47.619 0.00 0.00 43.06 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2101 2164 1.417890 ACTACAGCCAGTTCTGCAAGT 59.582 47.619 0.0 0.0 37.59 3.16 R
3043 3132 3.200825 ACTTTGATCCCATGAACCGATCT 59.799 43.478 0.0 0.0 34.70 2.75 R
3048 3137 8.160106 AGATAGATTACTTTGATCCCATGAACC 58.840 37.037 0.0 0.0 0.00 3.62 R
4379 4657 0.694771 AAGCAGGGCAATCTCAGTCA 59.305 50.000 0.0 0.0 0.00 3.41 R
5686 6179 0.685097 TCAACGGGAGGAAGGAACTG 59.315 55.000 0.0 0.0 40.86 3.16 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
34 35 2.123033 GGGCCCTCTCCTCTCTCC 60.123 72.222 17.04 0.00 0.00 3.71
40 41 1.152839 CTCTCCTCTCTCCCCGGTC 60.153 68.421 0.00 0.00 0.00 4.79
65 68 4.541482 CATGCAATTCGCGCCGCT 62.541 61.111 7.78 0.00 46.97 5.52
85 88 4.162690 GATCCGGGCACGCTTCCT 62.163 66.667 0.58 0.00 39.22 3.36
118 126 1.064946 CATCTCGCGGGACTCTGTC 59.935 63.158 12.89 0.00 0.00 3.51
127 135 2.608752 GCGGGACTCTGTCTTTCGTTTA 60.609 50.000 0.00 0.00 32.47 2.01
154 167 2.028125 AATCCCATCGGCGTGATCGT 62.028 55.000 6.85 0.00 39.49 3.73
243 266 4.047059 GGCATGCACGCACAAGCT 62.047 61.111 21.36 0.00 39.10 3.74
252 275 1.446099 CGCACAAGCTCCGCTCTTA 60.446 57.895 0.00 0.00 38.25 2.10
256 279 1.936547 CACAAGCTCCGCTCTTAATCC 59.063 52.381 0.00 0.00 38.25 3.01
257 280 1.834263 ACAAGCTCCGCTCTTAATCCT 59.166 47.619 0.00 0.00 38.25 3.24
258 281 2.237392 ACAAGCTCCGCTCTTAATCCTT 59.763 45.455 0.00 0.00 38.25 3.36
259 282 3.274288 CAAGCTCCGCTCTTAATCCTTT 58.726 45.455 0.00 0.00 38.25 3.11
260 283 3.636153 AGCTCCGCTCTTAATCCTTTT 57.364 42.857 0.00 0.00 30.62 2.27
261 284 3.536570 AGCTCCGCTCTTAATCCTTTTC 58.463 45.455 0.00 0.00 30.62 2.29
262 285 2.614520 GCTCCGCTCTTAATCCTTTTCC 59.385 50.000 0.00 0.00 0.00 3.13
263 286 2.866762 CTCCGCTCTTAATCCTTTTCCG 59.133 50.000 0.00 0.00 0.00 4.30
264 287 2.235402 TCCGCTCTTAATCCTTTTCCGT 59.765 45.455 0.00 0.00 0.00 4.69
265 288 3.007635 CCGCTCTTAATCCTTTTCCGTT 58.992 45.455 0.00 0.00 0.00 4.44
266 289 3.181510 CCGCTCTTAATCCTTTTCCGTTG 60.182 47.826 0.00 0.00 0.00 4.10
267 290 3.435671 CGCTCTTAATCCTTTTCCGTTGT 59.564 43.478 0.00 0.00 0.00 3.32
268 291 4.083484 CGCTCTTAATCCTTTTCCGTTGTT 60.083 41.667 0.00 0.00 0.00 2.83
269 292 5.121142 CGCTCTTAATCCTTTTCCGTTGTTA 59.879 40.000 0.00 0.00 0.00 2.41
270 293 6.347888 CGCTCTTAATCCTTTTCCGTTGTTAA 60.348 38.462 0.00 0.00 0.00 2.01
271 294 7.535997 GCTCTTAATCCTTTTCCGTTGTTAAT 58.464 34.615 0.00 0.00 0.00 1.40
272 295 7.696872 GCTCTTAATCCTTTTCCGTTGTTAATC 59.303 37.037 0.00 0.00 0.00 1.75
277 300 6.308371 TCCTTTTCCGTTGTTAATCTCAAC 57.692 37.500 0.00 0.00 40.89 3.18
279 302 5.009210 CCTTTTCCGTTGTTAATCTCAACCA 59.991 40.000 0.00 0.00 41.13 3.67
286 309 5.567534 CGTTGTTAATCTCAACCATTTTCCG 59.432 40.000 0.00 0.00 41.13 4.30
301 324 7.967178 ACCATTTTCCGTAGTTAATTCTTACG 58.033 34.615 8.52 8.52 0.00 3.18
320 348 6.765036 TCTTACGTTTCTCATCTACCTACGAT 59.235 38.462 0.00 0.00 0.00 3.73
415 444 2.885135 TTGATGACCTCATGCCACTT 57.115 45.000 0.00 0.00 36.57 3.16
434 463 2.203070 CGGCCGCCATTAAGCTCT 60.203 61.111 14.67 0.00 0.00 4.09
436 465 0.320771 CGGCCGCCATTAAGCTCTAT 60.321 55.000 14.67 0.00 0.00 1.98
443 472 4.084013 CCGCCATTAAGCTCTATTAAACCG 60.084 45.833 0.00 0.00 0.00 4.44
461 497 8.745464 TTAAACCGCTTTCCATTATTTTACAC 57.255 30.769 0.00 0.00 0.00 2.90
542 597 2.021355 AGCTAGCACTACTACGTCGT 57.979 50.000 18.83 2.21 0.00 4.34
565 620 3.545078 CGCTGAAGCTTGCAATTCAATAC 59.455 43.478 14.61 7.94 39.32 1.89
604 660 7.568199 AGATACATTGGGTACTGTTTATTGC 57.432 36.000 0.00 0.00 34.07 3.56
616 672 9.780186 GGTACTGTTTATTGCTTCTATATTCCT 57.220 33.333 0.00 0.00 0.00 3.36
637 693 1.064060 GATGCTGCGTTGGTAATCACC 59.936 52.381 0.00 0.00 46.00 4.02
765 823 4.022068 TGCCAGATCAAGATTGGTTGAAAC 60.022 41.667 0.00 0.00 39.84 2.78
798 856 3.127589 TGTACACACACACACACTATGC 58.872 45.455 0.00 0.00 0.00 3.14
799 857 2.323968 ACACACACACACACTATGCA 57.676 45.000 0.00 0.00 0.00 3.96
800 858 2.212652 ACACACACACACACTATGCAG 58.787 47.619 0.00 0.00 0.00 4.41
806 864 5.047306 ACACACACACACTATGCAGTACTAT 60.047 40.000 0.00 0.00 32.21 2.12
984 1044 3.248029 CGAGATAGCGCCATTGCC 58.752 61.111 2.29 0.00 34.65 4.52
985 1045 2.320587 CGAGATAGCGCCATTGCCC 61.321 63.158 2.29 0.00 34.65 5.36
986 1046 1.227943 GAGATAGCGCCATTGCCCA 60.228 57.895 2.29 0.00 34.65 5.36
987 1047 0.607489 GAGATAGCGCCATTGCCCAT 60.607 55.000 2.29 0.00 34.65 4.00
988 1048 0.178981 AGATAGCGCCATTGCCCATT 60.179 50.000 2.29 0.00 34.65 3.16
989 1049 0.038892 GATAGCGCCATTGCCCATTG 60.039 55.000 2.29 0.00 34.65 2.82
990 1050 2.091102 ATAGCGCCATTGCCCATTGC 62.091 55.000 2.29 0.00 41.77 3.56
1035 1095 0.101759 CTTGTGTTGTGCTTGCAGCT 59.898 50.000 9.12 0.00 42.97 4.24
1036 1096 0.101040 TTGTGTTGTGCTTGCAGCTC 59.899 50.000 9.12 6.51 42.97 4.09
1037 1097 1.031029 TGTGTTGTGCTTGCAGCTCA 61.031 50.000 9.12 8.67 42.97 4.26
1140 1200 0.368907 CGTCGGGCAGAACAATAACG 59.631 55.000 0.00 0.00 0.00 3.18
1246 1308 9.918630 CTTGATAGTTCTTGATTGGTTTTGAAT 57.081 29.630 0.00 0.00 0.00 2.57
1361 1423 1.929169 CATGTGCGTCTGATGTACTGG 59.071 52.381 17.08 7.24 0.00 4.00
1436 1498 6.258230 TGCTGAATTTATTTCTGGACAGTG 57.742 37.500 0.00 0.00 35.23 3.66
1467 1529 7.596248 CAGATGAGGAAAACTAACCAACAATTG 59.404 37.037 3.24 3.24 0.00 2.32
1653 1715 8.195436 AGCTCATGAAAATAAATTCTGTCCATG 58.805 33.333 0.00 0.00 0.00 3.66
1975 2038 1.129998 GACATGCAGCACTAGCACTTG 59.870 52.381 0.00 0.00 45.95 3.16
1992 2055 4.527564 CACTTGATCCTTGTTTCGTTGAC 58.472 43.478 0.00 0.00 0.00 3.18
1994 2057 3.201353 TGATCCTTGTTTCGTTGACCA 57.799 42.857 0.00 0.00 0.00 4.02
1996 2059 3.501828 TGATCCTTGTTTCGTTGACCATG 59.498 43.478 0.00 0.00 0.00 3.66
1999 2062 4.062293 TCCTTGTTTCGTTGACCATGTAG 58.938 43.478 0.00 0.00 0.00 2.74
2004 2067 2.831685 TCGTTGACCATGTAGTGCTT 57.168 45.000 0.00 0.00 0.00 3.91
2101 2164 9.699410 AAGGTCACAAATTTCATCTTATGGATA 57.301 29.630 0.00 0.00 32.64 2.59
2467 2554 5.994416 ATATGGGGTAAGAACATGTCCTT 57.006 39.130 1.92 1.92 0.00 3.36
2563 2652 1.002624 TTGGAAGGGGCGATGTGTC 60.003 57.895 0.00 0.00 0.00 3.67
2927 3016 3.431626 CCGTAAGCTTCACATCCACCATA 60.432 47.826 0.00 0.00 0.00 2.74
3048 3137 9.021863 GTACTATCAAGAAAAGTACCAAGATCG 57.978 37.037 11.89 0.00 39.66 3.69
3194 3285 8.902806 CACCTAATTTGTTTATCCTTGCTGATA 58.097 33.333 0.00 0.00 0.00 2.15
3239 3330 9.191995 CTAAACAATTTATGTGTTCCAACTTCC 57.808 33.333 0.00 0.00 42.99 3.46
3306 3397 8.641541 AGATGACATACATTTGTTTCCACTTTT 58.358 29.630 0.00 0.00 39.56 2.27
3600 3787 2.483188 GGAGTACTATGGTTTCGGCAGG 60.483 54.545 0.00 0.00 0.00 4.85
3665 3852 5.758924 CTGTATACGTCATGTGCTAAGCTA 58.241 41.667 0.00 0.00 0.00 3.32
3767 3954 7.684529 AGTTATCTCTGACTTTGAGGATTTGT 58.315 34.615 0.00 0.00 32.78 2.83
4003 4191 7.443272 TCATGCAGGTATTGATCACTTCTATTG 59.557 37.037 0.00 0.00 0.00 1.90
4128 4316 2.119495 ACAGAGGTGACAAACTGACCT 58.881 47.619 0.00 0.00 43.06 3.85
4145 4333 3.002862 TGACCTTGTTGTGCGATTGTTAC 59.997 43.478 0.00 0.00 0.00 2.50
4146 4334 2.946329 ACCTTGTTGTGCGATTGTTACA 59.054 40.909 0.00 0.00 0.00 2.41
4243 4449 8.597662 ATTGATGTTCCATCTTTTCTTGTTTG 57.402 30.769 5.87 0.00 0.00 2.93
4379 4657 6.653740 GGTAGTAAGCTTCGGGCAAAATATAT 59.346 38.462 0.00 0.00 44.79 0.86
4690 4971 0.729116 CGATCTTTGCTTCGGTGCAT 59.271 50.000 4.28 0.00 42.96 3.96
4802 5083 4.499183 CTTTTGCTCTAGTACCACTCCTG 58.501 47.826 0.00 0.00 0.00 3.86
4871 5152 1.609932 TCGTAAGTCGTTCATCGCAC 58.390 50.000 0.00 0.00 40.80 5.34
4879 5160 1.198867 TCGTTCATCGCACAATTTGGG 59.801 47.619 0.78 0.00 39.67 4.12
4942 5225 0.808125 CGCGTCCAATTTCCATTCCA 59.192 50.000 0.00 0.00 0.00 3.53
4952 5235 5.295787 CCAATTTCCATTCCAATGCAGATTG 59.704 40.000 0.00 0.00 39.04 2.67
5080 5363 2.224305 CCAGGTGTTCTCCGGGATATTC 60.224 54.545 0.00 0.00 43.79 1.75
5270 5553 2.202851 AGCTTCCTCATCAGCGCG 60.203 61.111 0.00 0.00 41.24 6.86
5323 5607 4.202161 CCGCAGTGAGGAAACTAGATATGT 60.202 45.833 7.18 0.00 44.43 2.29
5379 5664 4.955811 ACTGAACAGTTAGGTGTCATCA 57.044 40.909 1.32 0.00 38.83 3.07
5475 5760 7.033530 TGGTATAGTTGCCAATAATTTTCGG 57.966 36.000 0.00 0.00 34.32 4.30
5476 5761 5.918576 GGTATAGTTGCCAATAATTTTCGGC 59.081 40.000 5.08 5.08 45.11 5.54
5484 5769 3.359654 CAATAATTTTCGGCGGTACTGC 58.640 45.455 18.83 18.83 0.00 4.40
5506 5791 3.512680 CGATTGTAGACAAGTGGGTCTC 58.487 50.000 0.00 0.00 44.63 3.36
5548 6040 8.758633 AGAAAAAGAATGAATTTCATCTGCTG 57.241 30.769 12.15 0.00 35.76 4.41
5577 6069 5.048991 CACGCTTTACCCAAGTTAACAGAAT 60.049 40.000 8.61 0.00 34.56 2.40
5583 6076 3.139397 ACCCAAGTTAACAGAATGGTCCA 59.861 43.478 8.61 0.00 43.62 4.02
5599 6092 5.339008 TGGTCCAACTATGTCACATCTAC 57.661 43.478 0.00 0.00 0.00 2.59
5601 6094 5.105351 TGGTCCAACTATGTCACATCTACAG 60.105 44.000 0.00 0.00 0.00 2.74
5602 6095 5.105310 GGTCCAACTATGTCACATCTACAGT 60.105 44.000 0.00 0.00 0.00 3.55
5603 6096 6.096423 GGTCCAACTATGTCACATCTACAGTA 59.904 42.308 0.00 0.00 0.00 2.74
5604 6097 7.197017 GTCCAACTATGTCACATCTACAGTAG 58.803 42.308 0.00 0.47 0.00 2.57
5606 6099 7.067129 TCCAACTATGTCACATCTACAGTAGAC 59.933 40.741 12.75 1.43 37.69 2.59
5607 6100 6.606234 ACTATGTCACATCTACAGTAGACG 57.394 41.667 12.75 7.30 37.69 4.18
5608 6101 6.114089 ACTATGTCACATCTACAGTAGACGT 58.886 40.000 12.75 8.02 37.69 4.34
5609 6102 4.680171 TGTCACATCTACAGTAGACGTG 57.320 45.455 24.80 24.80 46.95 4.49
5616 6109 7.485418 ACATCTACAGTAGACGTGAGATAAG 57.515 40.000 12.75 0.00 37.69 1.73
5617 6110 7.273712 ACATCTACAGTAGACGTGAGATAAGA 58.726 38.462 12.75 0.00 37.69 2.10
5618 6111 7.769507 ACATCTACAGTAGACGTGAGATAAGAA 59.230 37.037 12.75 0.00 37.69 2.52
5619 6112 8.613482 CATCTACAGTAGACGTGAGATAAGAAA 58.387 37.037 12.75 0.00 37.69 2.52
5620 6113 8.199176 TCTACAGTAGACGTGAGATAAGAAAG 57.801 38.462 6.15 0.00 0.00 2.62
5666 6159 1.559682 TCATCTACTTTGTGGCCCCTC 59.440 52.381 0.00 0.00 0.00 4.30
5671 6164 1.607467 CTTTGTGGCCCCTCCCTTG 60.607 63.158 0.00 0.00 0.00 3.61
5672 6165 3.826265 TTTGTGGCCCCTCCCTTGC 62.826 63.158 0.00 0.00 0.00 4.01
5676 6169 4.079961 GGCCCCTCCCTTGCCATT 62.080 66.667 0.00 0.00 44.70 3.16
5677 6170 2.761213 GCCCCTCCCTTGCCATTG 60.761 66.667 0.00 0.00 0.00 2.82
5686 6179 1.133025 CCCTTGCCATTGACAACGATC 59.867 52.381 0.00 0.00 0.00 3.69
5687 6180 1.811965 CCTTGCCATTGACAACGATCA 59.188 47.619 0.00 0.00 0.00 2.92
5700 6193 1.196012 ACGATCAGTTCCTTCCTCCC 58.804 55.000 0.00 0.00 0.00 4.30
5708 6201 1.133363 TTCCTTCCTCCCGTTGACAA 58.867 50.000 0.00 0.00 0.00 3.18
5709 6202 0.395312 TCCTTCCTCCCGTTGACAAC 59.605 55.000 8.34 8.34 0.00 3.32
5710 6203 0.396811 CCTTCCTCCCGTTGACAACT 59.603 55.000 16.02 0.00 0.00 3.16
5711 6204 1.202770 CCTTCCTCCCGTTGACAACTT 60.203 52.381 16.02 0.00 0.00 2.66
5712 6205 2.143925 CTTCCTCCCGTTGACAACTTC 58.856 52.381 16.02 0.00 0.00 3.01
5713 6206 1.124780 TCCTCCCGTTGACAACTTCA 58.875 50.000 16.02 0.00 0.00 3.02
5714 6207 1.697432 TCCTCCCGTTGACAACTTCAT 59.303 47.619 16.02 0.00 32.84 2.57
5718 6211 2.081462 CCCGTTGACAACTTCATACCC 58.919 52.381 16.02 0.00 32.84 3.69
5726 6219 2.178106 ACAACTTCATACCCCCAACCAA 59.822 45.455 0.00 0.00 0.00 3.67
5781 6275 6.455780 GGCTAAAGTCAATAGCGAGAAAACTC 60.456 42.308 0.00 0.00 45.32 3.01
5782 6276 5.864628 AAAGTCAATAGCGAGAAAACTCC 57.135 39.130 0.00 0.00 0.00 3.85
5783 6277 3.863041 AGTCAATAGCGAGAAAACTCCC 58.137 45.455 0.00 0.00 0.00 4.30
5784 6278 3.260884 AGTCAATAGCGAGAAAACTCCCA 59.739 43.478 0.00 0.00 0.00 4.37
5785 6279 4.000988 GTCAATAGCGAGAAAACTCCCAA 58.999 43.478 0.00 0.00 0.00 4.12
5786 6280 4.454504 GTCAATAGCGAGAAAACTCCCAAA 59.545 41.667 0.00 0.00 0.00 3.28
5787 6281 5.048991 GTCAATAGCGAGAAAACTCCCAAAA 60.049 40.000 0.00 0.00 0.00 2.44
5789 6283 2.650322 AGCGAGAAAACTCCCAAAACA 58.350 42.857 0.00 0.00 0.00 2.83
5790 6284 2.357952 AGCGAGAAAACTCCCAAAACAC 59.642 45.455 0.00 0.00 0.00 3.32
5792 6286 3.562557 GCGAGAAAACTCCCAAAACACTA 59.437 43.478 0.00 0.00 0.00 2.74
5793 6287 4.554134 GCGAGAAAACTCCCAAAACACTAC 60.554 45.833 0.00 0.00 0.00 2.73
5799 6303 9.027202 AGAAAACTCCCAAAACACTACTTAAAA 57.973 29.630 0.00 0.00 0.00 1.52
5833 6342 6.749923 AACCTTGTTGATAAGCTCAGAATC 57.250 37.500 0.00 0.00 34.68 2.52
5842 6351 6.294473 TGATAAGCTCAGAATCTCCCAAATC 58.706 40.000 0.00 0.00 0.00 2.17
5992 6514 4.779993 AGTTGGAGGAGGGATTACAATC 57.220 45.455 0.00 0.00 34.66 2.67
5993 6515 4.111577 AGTTGGAGGAGGGATTACAATCA 58.888 43.478 4.45 0.00 37.15 2.57
5994 6516 4.164988 AGTTGGAGGAGGGATTACAATCAG 59.835 45.833 4.45 0.00 37.15 2.90
5995 6517 3.736094 TGGAGGAGGGATTACAATCAGT 58.264 45.455 4.45 0.00 37.15 3.41
5996 6518 3.711704 TGGAGGAGGGATTACAATCAGTC 59.288 47.826 4.45 0.52 37.15 3.51
5997 6519 3.711704 GGAGGAGGGATTACAATCAGTCA 59.288 47.826 4.45 0.00 37.15 3.41
5998 6520 4.164221 GGAGGAGGGATTACAATCAGTCAA 59.836 45.833 4.45 0.00 37.15 3.18
5999 6521 5.163152 GGAGGAGGGATTACAATCAGTCAAT 60.163 44.000 4.45 0.00 37.15 2.57
6062 6584 2.027192 TGATAGGTTCAGGTTCAGTGCC 60.027 50.000 0.00 0.00 0.00 5.01
6070 6595 3.169908 TCAGGTTCAGTGCCAGTACATA 58.830 45.455 0.00 0.00 0.00 2.29
6079 6604 4.815846 CAGTGCCAGTACATACATGCATAA 59.184 41.667 0.00 0.00 37.33 1.90
6180 6739 1.066716 GTATGGTGCCTGTTCGGTGTA 60.067 52.381 0.00 0.00 34.25 2.90
6254 6843 9.726438 AGCTGTGATGAAAGTACTAGTAAAAAT 57.274 29.630 3.61 0.00 0.00 1.82
6312 6901 0.179051 CCTCCTAGTAGACTCGCCGT 60.179 60.000 0.00 0.00 0.00 5.68
6318 6907 0.677842 AGTAGACTCGCCGTTGGTTT 59.322 50.000 0.00 0.00 0.00 3.27
6319 6908 1.069668 AGTAGACTCGCCGTTGGTTTT 59.930 47.619 0.00 0.00 0.00 2.43
6320 6909 1.458445 GTAGACTCGCCGTTGGTTTTC 59.542 52.381 0.00 0.00 0.00 2.29
6321 6910 0.106149 AGACTCGCCGTTGGTTTTCT 59.894 50.000 0.00 0.00 0.00 2.52
6322 6911 0.942252 GACTCGCCGTTGGTTTTCTT 59.058 50.000 0.00 0.00 0.00 2.52
6323 6912 0.942252 ACTCGCCGTTGGTTTTCTTC 59.058 50.000 0.00 0.00 0.00 2.87
6324 6913 0.237498 CTCGCCGTTGGTTTTCTTCC 59.763 55.000 0.00 0.00 0.00 3.46
6325 6914 1.082366 CGCCGTTGGTTTTCTTCCG 60.082 57.895 0.00 0.00 0.00 4.30
6326 6915 1.284715 GCCGTTGGTTTTCTTCCGG 59.715 57.895 0.00 0.00 38.45 5.14
6327 6916 1.449726 GCCGTTGGTTTTCTTCCGGT 61.450 55.000 0.00 0.00 37.76 5.28
6328 6917 1.026584 CCGTTGGTTTTCTTCCGGTT 58.973 50.000 0.00 0.00 0.00 4.44
6329 6918 1.268845 CCGTTGGTTTTCTTCCGGTTG 60.269 52.381 0.00 0.00 0.00 3.77
6330 6919 1.402613 CGTTGGTTTTCTTCCGGTTGT 59.597 47.619 0.00 0.00 0.00 3.32
6331 6920 2.159352 CGTTGGTTTTCTTCCGGTTGTT 60.159 45.455 0.00 0.00 0.00 2.83
6332 6921 3.673866 CGTTGGTTTTCTTCCGGTTGTTT 60.674 43.478 0.00 0.00 0.00 2.83
6333 6922 3.512033 TGGTTTTCTTCCGGTTGTTTG 57.488 42.857 0.00 0.00 0.00 2.93
6334 6923 2.826725 TGGTTTTCTTCCGGTTGTTTGT 59.173 40.909 0.00 0.00 0.00 2.83
6335 6924 3.258622 TGGTTTTCTTCCGGTTGTTTGTT 59.741 39.130 0.00 0.00 0.00 2.83
6336 6925 4.247258 GGTTTTCTTCCGGTTGTTTGTTT 58.753 39.130 0.00 0.00 0.00 2.83
6337 6926 4.092237 GGTTTTCTTCCGGTTGTTTGTTTG 59.908 41.667 0.00 0.00 0.00 2.93
6338 6927 4.522722 TTTCTTCCGGTTGTTTGTTTGT 57.477 36.364 0.00 0.00 0.00 2.83
6339 6928 4.522722 TTCTTCCGGTTGTTTGTTTGTT 57.477 36.364 0.00 0.00 0.00 2.83
6340 6929 4.522722 TCTTCCGGTTGTTTGTTTGTTT 57.477 36.364 0.00 0.00 0.00 2.83
6341 6930 4.238514 TCTTCCGGTTGTTTGTTTGTTTG 58.761 39.130 0.00 0.00 0.00 2.93
6342 6931 3.662247 TCCGGTTGTTTGTTTGTTTGT 57.338 38.095 0.00 0.00 0.00 2.83
6343 6932 3.576648 TCCGGTTGTTTGTTTGTTTGTC 58.423 40.909 0.00 0.00 0.00 3.18
6344 6933 2.342948 CCGGTTGTTTGTTTGTTTGTCG 59.657 45.455 0.00 0.00 0.00 4.35
6345 6934 2.222398 CGGTTGTTTGTTTGTTTGTCGC 60.222 45.455 0.00 0.00 0.00 5.19
6346 6935 2.222398 GGTTGTTTGTTTGTTTGTCGCG 60.222 45.455 0.00 0.00 0.00 5.87
6347 6936 1.618861 TGTTTGTTTGTTTGTCGCGG 58.381 45.000 6.13 0.00 0.00 6.46
6348 6937 0.296349 GTTTGTTTGTTTGTCGCGGC 59.704 50.000 2.29 2.29 0.00 6.53
6349 6938 0.802607 TTTGTTTGTTTGTCGCGGCC 60.803 50.000 8.89 0.00 0.00 6.13
6350 6939 2.354188 GTTTGTTTGTCGCGGCCC 60.354 61.111 8.89 0.00 0.00 5.80
6351 6940 2.829003 TTTGTTTGTCGCGGCCCA 60.829 55.556 8.89 0.00 0.00 5.36
6352 6941 2.840066 TTTGTTTGTCGCGGCCCAG 61.840 57.895 8.89 0.00 0.00 4.45
6366 6955 4.232061 CCAGCCCAAACCACCCCA 62.232 66.667 0.00 0.00 0.00 4.96
6367 6956 2.120274 CAGCCCAAACCACCCCAT 59.880 61.111 0.00 0.00 0.00 4.00
6368 6957 2.120274 AGCCCAAACCACCCCATG 59.880 61.111 0.00 0.00 0.00 3.66
6369 6958 3.705289 GCCCAAACCACCCCATGC 61.705 66.667 0.00 0.00 0.00 4.06
6370 6959 3.002583 CCCAAACCACCCCATGCC 61.003 66.667 0.00 0.00 0.00 4.40
6371 6960 3.002583 CCAAACCACCCCATGCCC 61.003 66.667 0.00 0.00 0.00 5.36
6372 6961 3.002583 CAAACCACCCCATGCCCC 61.003 66.667 0.00 0.00 0.00 5.80
6373 6962 4.330960 AAACCACCCCATGCCCCC 62.331 66.667 0.00 0.00 0.00 5.40
6382 6971 4.047125 CATGCCCCCAACGGACCT 62.047 66.667 0.00 0.00 0.00 3.85
6383 6972 3.264845 ATGCCCCCAACGGACCTT 61.265 61.111 0.00 0.00 0.00 3.50
6384 6973 3.583882 ATGCCCCCAACGGACCTTG 62.584 63.158 0.00 0.00 0.00 3.61
6385 6974 4.280019 GCCCCCAACGGACCTTGT 62.280 66.667 0.00 0.00 0.00 3.16
6386 6975 2.282180 CCCCCAACGGACCTTGTG 60.282 66.667 0.00 0.00 0.00 3.33
6387 6976 2.282180 CCCCAACGGACCTTGTGG 60.282 66.667 0.00 0.00 39.83 4.17
6388 6977 2.824880 CCCCAACGGACCTTGTGGA 61.825 63.158 6.54 0.00 37.04 4.02
6389 6978 1.378762 CCCAACGGACCTTGTGGAT 59.621 57.895 6.54 0.00 37.04 3.41
6390 6979 0.616371 CCCAACGGACCTTGTGGATA 59.384 55.000 6.54 0.00 37.04 2.59
6391 6980 1.003812 CCCAACGGACCTTGTGGATAA 59.996 52.381 6.54 0.00 37.04 1.75
6392 6981 2.553466 CCCAACGGACCTTGTGGATAAA 60.553 50.000 6.54 0.00 37.04 1.40
6393 6982 2.747446 CCAACGGACCTTGTGGATAAAG 59.253 50.000 0.00 0.00 37.04 1.85
6395 6984 1.339727 ACGGACCTTGTGGATAAAGGC 60.340 52.381 2.12 0.00 46.94 4.35
6396 6985 1.763968 GGACCTTGTGGATAAAGGCC 58.236 55.000 0.00 0.00 46.94 5.19
6397 6986 1.685180 GGACCTTGTGGATAAAGGCCC 60.685 57.143 0.00 0.00 46.94 5.80
6398 6987 1.285078 GACCTTGTGGATAAAGGCCCT 59.715 52.381 0.00 0.00 46.94 5.19
6399 6988 2.508300 GACCTTGTGGATAAAGGCCCTA 59.492 50.000 0.00 0.00 46.94 3.53
6400 6989 2.923629 ACCTTGTGGATAAAGGCCCTAA 59.076 45.455 0.00 0.00 46.94 2.69
6401 6990 3.335484 ACCTTGTGGATAAAGGCCCTAAA 59.665 43.478 0.00 0.00 46.94 1.85
6402 6991 3.954258 CCTTGTGGATAAAGGCCCTAAAG 59.046 47.826 0.00 0.00 37.96 1.85
6403 6992 4.569865 CCTTGTGGATAAAGGCCCTAAAGT 60.570 45.833 0.00 0.00 37.96 2.66
6404 6993 4.668138 TGTGGATAAAGGCCCTAAAGTT 57.332 40.909 0.00 0.00 0.00 2.66
6405 6994 5.005628 TGTGGATAAAGGCCCTAAAGTTT 57.994 39.130 0.00 0.00 0.00 2.66
6406 6995 6.142259 TGTGGATAAAGGCCCTAAAGTTTA 57.858 37.500 0.00 0.00 0.00 2.01
6407 6996 6.553857 TGTGGATAAAGGCCCTAAAGTTTAA 58.446 36.000 0.00 0.00 0.00 1.52
6408 6997 7.186268 TGTGGATAAAGGCCCTAAAGTTTAAT 58.814 34.615 0.00 0.00 0.00 1.40
6409 6998 7.123547 TGTGGATAAAGGCCCTAAAGTTTAATG 59.876 37.037 0.00 0.00 0.00 1.90
6410 6999 7.123697 GTGGATAAAGGCCCTAAAGTTTAATGT 59.876 37.037 0.00 0.00 0.00 2.71
6411 7000 7.123547 TGGATAAAGGCCCTAAAGTTTAATGTG 59.876 37.037 0.00 0.00 0.00 3.21
6412 7001 5.738619 AAAGGCCCTAAAGTTTAATGTGG 57.261 39.130 0.00 0.00 0.00 4.17
6413 7002 3.708451 AGGCCCTAAAGTTTAATGTGGG 58.292 45.455 11.63 11.63 36.41 4.61
6416 7005 3.708451 CCCTAAAGTTTAATGTGGGCCT 58.292 45.455 4.53 0.00 0.00 5.19
6417 7006 4.093743 CCCTAAAGTTTAATGTGGGCCTT 58.906 43.478 4.53 0.00 0.00 4.35
6418 7007 4.159693 CCCTAAAGTTTAATGTGGGCCTTC 59.840 45.833 4.53 0.00 0.00 3.46
6419 7008 5.016831 CCTAAAGTTTAATGTGGGCCTTCT 58.983 41.667 4.53 0.00 0.00 2.85
6420 7009 6.184789 CCTAAAGTTTAATGTGGGCCTTCTA 58.815 40.000 4.53 0.00 0.00 2.10
6421 7010 5.977489 AAAGTTTAATGTGGGCCTTCTAC 57.023 39.130 4.53 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 2.788640 CGAATTGCATGGCCTGGGG 61.789 63.158 3.32 0.00 0.00 4.96
65 68 3.371097 GAAGCGTGCCCGGATCTGA 62.371 63.158 0.73 0.00 33.68 3.27
118 126 5.974108 TGGGATTAGAGAGGTAAACGAAAG 58.026 41.667 0.00 0.00 0.00 2.62
127 135 1.343069 GCCGATGGGATTAGAGAGGT 58.657 55.000 0.00 0.00 34.06 3.85
158 171 1.303643 AAAAGCTCCCCTCTTGCGG 60.304 57.895 0.00 0.00 0.00 5.69
159 172 1.308783 GGAAAAGCTCCCCTCTTGCG 61.309 60.000 0.00 0.00 38.44 4.85
160 173 2.572733 GGAAAAGCTCCCCTCTTGC 58.427 57.895 0.00 0.00 38.44 4.01
172 185 1.375523 CCGTCTCCGTGGGGAAAAG 60.376 63.158 0.00 0.00 43.27 2.27
243 266 2.235402 ACGGAAAAGGATTAAGAGCGGA 59.765 45.455 0.00 0.00 0.00 5.54
252 275 7.368059 GTTGAGATTAACAACGGAAAAGGATT 58.632 34.615 0.00 0.00 38.23 3.01
256 279 6.067263 TGGTTGAGATTAACAACGGAAAAG 57.933 37.500 0.00 0.00 45.56 2.27
257 280 6.642707 ATGGTTGAGATTAACAACGGAAAA 57.357 33.333 0.00 0.00 45.56 2.29
258 281 6.642707 AATGGTTGAGATTAACAACGGAAA 57.357 33.333 0.00 0.00 45.56 3.13
259 282 6.642707 AAATGGTTGAGATTAACAACGGAA 57.357 33.333 0.00 0.00 45.56 4.30
260 283 6.294286 GGAAAATGGTTGAGATTAACAACGGA 60.294 38.462 0.00 0.00 45.56 4.69
261 284 5.861787 GGAAAATGGTTGAGATTAACAACGG 59.138 40.000 0.00 0.00 45.56 4.44
262 285 5.567534 CGGAAAATGGTTGAGATTAACAACG 59.432 40.000 0.00 0.00 45.56 4.10
263 286 6.443792 ACGGAAAATGGTTGAGATTAACAAC 58.556 36.000 0.00 0.00 44.40 3.32
264 287 6.642707 ACGGAAAATGGTTGAGATTAACAA 57.357 33.333 0.00 0.00 32.22 2.83
265 288 6.938030 ACTACGGAAAATGGTTGAGATTAACA 59.062 34.615 0.00 0.00 32.22 2.41
266 289 7.373778 ACTACGGAAAATGGTTGAGATTAAC 57.626 36.000 0.00 0.00 0.00 2.01
267 290 7.989416 AACTACGGAAAATGGTTGAGATTAA 57.011 32.000 0.00 0.00 0.00 1.40
268 291 9.675464 ATTAACTACGGAAAATGGTTGAGATTA 57.325 29.630 0.00 0.00 0.00 1.75
269 292 7.989416 TTAACTACGGAAAATGGTTGAGATT 57.011 32.000 0.00 0.00 0.00 2.40
270 293 8.575649 AATTAACTACGGAAAATGGTTGAGAT 57.424 30.769 0.00 0.00 0.00 2.75
271 294 7.881232 AGAATTAACTACGGAAAATGGTTGAGA 59.119 33.333 0.00 0.00 0.00 3.27
272 295 8.040716 AGAATTAACTACGGAAAATGGTTGAG 57.959 34.615 0.00 0.00 0.00 3.02
277 300 7.967178 ACGTAAGAATTAACTACGGAAAATGG 58.033 34.615 14.40 0.00 43.62 3.16
415 444 3.750373 GAGCTTAATGGCGGCCGGA 62.750 63.158 29.38 0.00 37.29 5.14
436 465 7.813627 GGTGTAAAATAATGGAAAGCGGTTTAA 59.186 33.333 13.36 4.98 0.00 1.52
443 472 5.656859 AGAGGGGTGTAAAATAATGGAAAGC 59.343 40.000 0.00 0.00 0.00 3.51
460 496 1.075482 CATGTGGTGCAAGAGGGGT 59.925 57.895 0.00 0.00 0.00 4.95
461 497 4.007457 CATGTGGTGCAAGAGGGG 57.993 61.111 0.00 0.00 0.00 4.79
589 645 9.000486 GGAATATAGAAGCAATAAACAGTACCC 58.000 37.037 0.00 0.00 0.00 3.69
604 660 4.564041 ACGCAGCATCAGGAATATAGAAG 58.436 43.478 0.00 0.00 0.00 2.85
616 672 1.737236 GTGATTACCAACGCAGCATCA 59.263 47.619 0.00 0.00 0.00 3.07
637 693 2.623239 GGAGGTAAAGGGGGTTGAATGG 60.623 54.545 0.00 0.00 0.00 3.16
720 778 4.057428 GGACGACGCTGTGAGGCT 62.057 66.667 0.00 0.00 0.00 4.58
727 785 2.480555 GCAATTGGGACGACGCTG 59.519 61.111 7.72 0.00 0.00 5.18
765 823 3.065019 GTGTGTACACAAAAGTGGCAG 57.935 47.619 29.44 0.00 45.75 4.85
984 1044 5.493133 TTTATAGGTACGCTTTGCAATGG 57.507 39.130 13.62 5.18 0.00 3.16
985 1045 7.589954 GGTTATTTATAGGTACGCTTTGCAATG 59.410 37.037 0.00 3.50 0.00 2.82
986 1046 7.519328 CGGTTATTTATAGGTACGCTTTGCAAT 60.519 37.037 0.00 0.00 0.00 3.56
987 1047 6.238157 CGGTTATTTATAGGTACGCTTTGCAA 60.238 38.462 0.00 0.00 0.00 4.08
988 1048 5.234757 CGGTTATTTATAGGTACGCTTTGCA 59.765 40.000 0.00 0.00 0.00 4.08
989 1049 5.673029 CGGTTATTTATAGGTACGCTTTGC 58.327 41.667 0.00 0.00 0.00 3.68
990 1050 5.333568 GGCGGTTATTTATAGGTACGCTTTG 60.334 44.000 0.00 0.00 44.53 2.77
1035 1095 0.178767 CACCCTCAAGCCGATGATGA 59.821 55.000 0.00 0.00 0.00 2.92
1036 1096 0.107508 ACACCCTCAAGCCGATGATG 60.108 55.000 0.00 0.00 0.00 3.07
1037 1097 0.179000 GACACCCTCAAGCCGATGAT 59.821 55.000 0.00 0.00 0.00 2.45
1140 1200 2.056223 TCCCCGGTCCATTCGAGAC 61.056 63.158 0.00 0.00 0.00 3.36
1361 1423 6.927933 AAAAACTGCAAATTCTATACACGC 57.072 33.333 0.00 0.00 0.00 5.34
1436 1498 6.650120 TGGTTAGTTTTCCTCATCTGTATCC 58.350 40.000 0.00 0.00 0.00 2.59
1598 1660 5.096169 CGATAGCGAATGAATAGACGGAAT 58.904 41.667 0.00 0.00 40.82 3.01
1645 1707 2.225019 GTCTCAACTGCAACATGGACAG 59.775 50.000 9.55 9.55 37.45 3.51
1653 1715 0.249911 AGGTCCGTCTCAACTGCAAC 60.250 55.000 0.00 0.00 0.00 4.17
1711 1773 8.689972 CAAAAATATGCTAGAGACAAGGGAAAT 58.310 33.333 0.00 0.00 0.00 2.17
1843 1906 2.694628 AGCTGCCAACAAAACAAGATGA 59.305 40.909 0.00 0.00 0.00 2.92
1975 2038 3.502211 ACATGGTCAACGAAACAAGGATC 59.498 43.478 0.00 0.00 0.00 3.36
2101 2164 1.417890 ACTACAGCCAGTTCTGCAAGT 59.582 47.619 0.00 0.00 37.59 3.16
3043 3132 3.200825 ACTTTGATCCCATGAACCGATCT 59.799 43.478 0.00 0.00 34.70 2.75
3048 3137 8.160106 AGATAGATTACTTTGATCCCATGAACC 58.840 37.037 0.00 0.00 0.00 3.62
3194 3285 9.944376 TTGTTTAGTCTCAATTTAGTAGAGCAT 57.056 29.630 0.00 0.00 0.00 3.79
3239 3330 8.282124 TGAAATTAGTAACGAAGATATGCTCG 57.718 34.615 0.00 2.29 0.00 5.03
3600 3787 7.849804 TGTCCATCTAATTAGCAGAAAACTC 57.150 36.000 7.67 0.00 0.00 3.01
3665 3852 3.368739 GCATAAGACCTTTGCAAATGCCT 60.369 43.478 13.23 4.78 41.18 4.75
3778 3965 6.714810 TGCATGAGTACTACTTCCACAAAAAT 59.285 34.615 0.00 0.00 0.00 1.82
3987 4174 9.842775 TGAAGAATAGCAATAGAAGTGATCAAT 57.157 29.630 0.00 0.00 0.00 2.57
4003 4191 8.103948 ACATATGGCTAACAATGAAGAATAGC 57.896 34.615 7.80 0.00 38.55 2.97
4107 4295 2.505819 AGGTCAGTTTGTCACCTCTGTT 59.494 45.455 0.00 0.00 35.47 3.16
4379 4657 0.694771 AAGCAGGGCAATCTCAGTCA 59.305 50.000 0.00 0.00 0.00 3.41
4802 5083 3.456280 TGTTTTGCTGCTGGTGAATTTC 58.544 40.909 0.00 0.00 0.00 2.17
4871 5152 6.698329 CAGCATCATTGTGTATACCCAAATTG 59.302 38.462 4.84 0.73 0.00 2.32
4879 5160 3.881795 GCTGCAGCATCATTGTGTATAC 58.118 45.455 33.36 0.00 41.59 1.47
5080 5363 4.473520 AGCATGCCGAGGAACCCG 62.474 66.667 15.66 0.00 0.00 5.28
5270 5553 1.929836 CTAGTCCAAATCAGACGCAGC 59.070 52.381 0.00 0.00 39.31 5.25
5323 5607 4.951094 TGCATCATCACCATGATCAGAAAA 59.049 37.500 0.09 0.00 45.26 2.29
5364 5648 5.977635 TCAATACCTGATGACACCTAACTG 58.022 41.667 0.00 0.00 0.00 3.16
5379 5664 4.955811 TCGGTTATCTGCATCAATACCT 57.044 40.909 0.00 0.00 0.00 3.08
5390 5675 8.765219 CCACTATAAAATCACTTCGGTTATCTG 58.235 37.037 0.00 0.00 0.00 2.90
5484 5769 2.233922 AGACCCACTTGTCTACAATCGG 59.766 50.000 0.00 0.53 43.65 4.18
5562 6054 3.761897 TGGACCATTCTGTTAACTTGGG 58.238 45.455 7.22 4.29 0.00 4.12
5577 6069 4.775253 TGTAGATGTGACATAGTTGGACCA 59.225 41.667 0.00 0.00 0.00 4.02
5583 6076 7.017498 CGTCTACTGTAGATGTGACATAGTT 57.983 40.000 23.00 0.00 37.12 2.24
5603 6096 9.357161 AGGTATTATCTTTCTTATCTCACGTCT 57.643 33.333 0.00 0.00 0.00 4.18
5604 6097 9.615295 GAGGTATTATCTTTCTTATCTCACGTC 57.385 37.037 0.00 0.00 0.00 4.34
5606 6099 9.400638 GTGAGGTATTATCTTTCTTATCTCACG 57.599 37.037 6.48 0.00 38.28 4.35
5618 6111 9.988815 GTCATGTTAGATGTGAGGTATTATCTT 57.011 33.333 0.00 0.00 32.54 2.40
5619 6112 8.300286 CGTCATGTTAGATGTGAGGTATTATCT 58.700 37.037 0.00 0.00 34.51 1.98
5620 6113 8.082852 ACGTCATGTTAGATGTGAGGTATTATC 58.917 37.037 0.00 0.00 38.68 1.75
5666 6159 1.133025 GATCGTTGTCAATGGCAAGGG 59.867 52.381 18.32 6.36 33.92 3.95
5671 6164 2.159517 GGAACTGATCGTTGTCAATGGC 60.160 50.000 4.95 0.00 35.56 4.40
5672 6165 3.338249 AGGAACTGATCGTTGTCAATGG 58.662 45.455 4.95 0.00 37.18 3.16
5673 6166 4.142816 GGAAGGAACTGATCGTTGTCAATG 60.143 45.833 7.51 0.00 40.86 2.82
5674 6167 4.003648 GGAAGGAACTGATCGTTGTCAAT 58.996 43.478 7.51 0.00 40.86 2.57
5675 6168 3.071023 AGGAAGGAACTGATCGTTGTCAA 59.929 43.478 7.51 0.00 40.86 3.18
5676 6169 2.632996 AGGAAGGAACTGATCGTTGTCA 59.367 45.455 7.51 0.00 40.86 3.58
5677 6170 3.254892 GAGGAAGGAACTGATCGTTGTC 58.745 50.000 7.51 3.54 40.86 3.18
5686 6179 0.685097 TCAACGGGAGGAAGGAACTG 59.315 55.000 0.00 0.00 40.86 3.16
5700 6193 2.081462 GGGGGTATGAAGTTGTCAACG 58.919 52.381 10.02 0.00 40.50 4.10
5708 6201 2.652348 TCATTGGTTGGGGGTATGAAGT 59.348 45.455 0.00 0.00 0.00 3.01
5709 6202 3.023832 GTCATTGGTTGGGGGTATGAAG 58.976 50.000 0.00 0.00 0.00 3.02
5710 6203 2.619332 CGTCATTGGTTGGGGGTATGAA 60.619 50.000 0.00 0.00 0.00 2.57
5711 6204 1.065053 CGTCATTGGTTGGGGGTATGA 60.065 52.381 0.00 0.00 0.00 2.15
5712 6205 1.065053 TCGTCATTGGTTGGGGGTATG 60.065 52.381 0.00 0.00 0.00 2.39
5713 6206 1.291109 TCGTCATTGGTTGGGGGTAT 58.709 50.000 0.00 0.00 0.00 2.73
5714 6207 1.065647 TTCGTCATTGGTTGGGGGTA 58.934 50.000 0.00 0.00 0.00 3.69
5718 6211 3.118408 TCCTAGATTCGTCATTGGTTGGG 60.118 47.826 0.00 0.00 0.00 4.12
5726 6219 7.497249 CCTTCATTTTCTTCCTAGATTCGTCAT 59.503 37.037 0.00 0.00 0.00 3.06
5781 6275 9.191995 GACATCATTTTTAAGTAGTGTTTTGGG 57.808 33.333 0.00 0.00 0.00 4.12
5782 6276 9.191995 GGACATCATTTTTAAGTAGTGTTTTGG 57.808 33.333 0.00 0.00 0.00 3.28
5783 6277 9.965824 AGGACATCATTTTTAAGTAGTGTTTTG 57.034 29.630 0.00 0.00 0.00 2.44
5787 6281 9.227777 GGTTAGGACATCATTTTTAAGTAGTGT 57.772 33.333 0.00 0.00 0.00 3.55
5792 6286 8.706322 ACAAGGTTAGGACATCATTTTTAAGT 57.294 30.769 0.00 0.00 0.00 2.24
5793 6287 9.410556 CAACAAGGTTAGGACATCATTTTTAAG 57.589 33.333 0.00 0.00 0.00 1.85
5799 6303 7.067494 GCTTATCAACAAGGTTAGGACATCATT 59.933 37.037 0.00 0.00 0.00 2.57
5833 6342 8.110860 ACATGTTTTAAGTAGTGATTTGGGAG 57.889 34.615 0.00 0.00 0.00 4.30
5992 6514 7.066284 CCTTCCCTTAACTATTGTGATTGACTG 59.934 40.741 0.00 0.00 0.00 3.51
5993 6515 7.112779 CCTTCCCTTAACTATTGTGATTGACT 58.887 38.462 0.00 0.00 0.00 3.41
5994 6516 6.318900 CCCTTCCCTTAACTATTGTGATTGAC 59.681 42.308 0.00 0.00 0.00 3.18
5995 6517 6.011981 ACCCTTCCCTTAACTATTGTGATTGA 60.012 38.462 0.00 0.00 0.00 2.57
5996 6518 6.187682 ACCCTTCCCTTAACTATTGTGATTG 58.812 40.000 0.00 0.00 0.00 2.67
5997 6519 6.402981 ACCCTTCCCTTAACTATTGTGATT 57.597 37.500 0.00 0.00 0.00 2.57
5998 6520 7.572861 AGATACCCTTCCCTTAACTATTGTGAT 59.427 37.037 0.00 0.00 0.00 3.06
5999 6521 6.906901 AGATACCCTTCCCTTAACTATTGTGA 59.093 38.462 0.00 0.00 0.00 3.58
6041 6563 2.027192 GGCACTGAACCTGAACCTATCA 60.027 50.000 0.00 0.00 36.38 2.15
6070 6595 6.957920 TGCAACTTATATGGTTATGCATGT 57.042 33.333 10.16 0.00 0.00 3.21
6079 6604 5.509498 AGTGTCCAATGCAACTTATATGGT 58.491 37.500 0.00 0.00 0.00 3.55
6126 6683 6.266558 CCAGCCTCTATCTACTGTAATCACTT 59.733 42.308 0.00 0.00 0.00 3.16
6254 6843 6.335781 AGCCTACCCTCCAAATAACAATAA 57.664 37.500 0.00 0.00 0.00 1.40
6312 6901 3.258622 ACAAACAACCGGAAGAAAACCAA 59.741 39.130 9.46 0.00 0.00 3.67
6318 6907 4.522722 AACAAACAAACAACCGGAAGAA 57.477 36.364 9.46 0.00 0.00 2.52
6319 6908 4.238514 CAAACAAACAAACAACCGGAAGA 58.761 39.130 9.46 0.00 0.00 2.87
6320 6909 3.991121 ACAAACAAACAAACAACCGGAAG 59.009 39.130 9.46 1.51 0.00 3.46
6321 6910 3.988517 GACAAACAAACAAACAACCGGAA 59.011 39.130 9.46 0.00 0.00 4.30
6322 6911 3.576648 GACAAACAAACAAACAACCGGA 58.423 40.909 9.46 0.00 0.00 5.14
6323 6912 2.342948 CGACAAACAAACAAACAACCGG 59.657 45.455 0.00 0.00 0.00 5.28
6324 6913 2.222398 GCGACAAACAAACAAACAACCG 60.222 45.455 0.00 0.00 0.00 4.44
6325 6914 2.222398 CGCGACAAACAAACAAACAACC 60.222 45.455 0.00 0.00 0.00 3.77
6326 6915 2.222398 CCGCGACAAACAAACAAACAAC 60.222 45.455 8.23 0.00 0.00 3.32
6327 6916 1.986378 CCGCGACAAACAAACAAACAA 59.014 42.857 8.23 0.00 0.00 2.83
6328 6917 1.618861 CCGCGACAAACAAACAAACA 58.381 45.000 8.23 0.00 0.00 2.83
6329 6918 0.296349 GCCGCGACAAACAAACAAAC 59.704 50.000 8.23 0.00 0.00 2.93
6330 6919 0.802607 GGCCGCGACAAACAAACAAA 60.803 50.000 8.23 0.00 0.00 2.83
6331 6920 1.226717 GGCCGCGACAAACAAACAA 60.227 52.632 8.23 0.00 0.00 2.83
6332 6921 2.409651 GGCCGCGACAAACAAACA 59.590 55.556 8.23 0.00 0.00 2.83
6333 6922 2.354188 GGGCCGCGACAAACAAAC 60.354 61.111 8.23 0.00 0.00 2.93
6334 6923 2.829003 TGGGCCGCGACAAACAAA 60.829 55.556 8.23 0.00 0.00 2.83
6335 6924 3.283684 CTGGGCCGCGACAAACAA 61.284 61.111 8.23 0.00 0.00 2.83
6349 6938 3.544503 ATGGGGTGGTTTGGGCTGG 62.545 63.158 0.00 0.00 0.00 4.85
6350 6939 2.120274 ATGGGGTGGTTTGGGCTG 59.880 61.111 0.00 0.00 0.00 4.85
6351 6940 2.120274 CATGGGGTGGTTTGGGCT 59.880 61.111 0.00 0.00 0.00 5.19
6352 6941 3.705289 GCATGGGGTGGTTTGGGC 61.705 66.667 0.00 0.00 0.00 5.36
6353 6942 3.002583 GGCATGGGGTGGTTTGGG 61.003 66.667 0.00 0.00 0.00 4.12
6354 6943 3.002583 GGGCATGGGGTGGTTTGG 61.003 66.667 0.00 0.00 0.00 3.28
6355 6944 3.002583 GGGGCATGGGGTGGTTTG 61.003 66.667 0.00 0.00 0.00 2.93
6356 6945 4.330960 GGGGGCATGGGGTGGTTT 62.331 66.667 0.00 0.00 0.00 3.27
6365 6954 3.583882 AAGGTCCGTTGGGGGCATG 62.584 63.158 0.00 0.00 44.60 4.06
6366 6955 3.264845 AAGGTCCGTTGGGGGCAT 61.265 61.111 0.00 0.00 44.60 4.40
6367 6956 4.278513 CAAGGTCCGTTGGGGGCA 62.279 66.667 0.00 0.00 44.60 5.36
6368 6957 4.280019 ACAAGGTCCGTTGGGGGC 62.280 66.667 4.91 0.00 40.84 5.80
6369 6958 2.282180 CACAAGGTCCGTTGGGGG 60.282 66.667 4.91 0.00 36.01 5.40
6370 6959 2.282180 CCACAAGGTCCGTTGGGG 60.282 66.667 6.62 6.62 44.58 4.96
6371 6960 0.616371 TATCCACAAGGTCCGTTGGG 59.384 55.000 6.61 0.31 35.89 4.12
6372 6961 2.483014 TTATCCACAAGGTCCGTTGG 57.517 50.000 4.91 3.78 35.89 3.77
6373 6962 2.747446 CCTTTATCCACAAGGTCCGTTG 59.253 50.000 0.00 0.00 36.74 4.10
6374 6963 2.878526 GCCTTTATCCACAAGGTCCGTT 60.879 50.000 0.83 0.00 42.68 4.44
6375 6964 1.339727 GCCTTTATCCACAAGGTCCGT 60.340 52.381 0.83 0.00 42.68 4.69
6376 6965 1.379527 GCCTTTATCCACAAGGTCCG 58.620 55.000 0.83 0.00 42.68 4.79
6377 6966 1.763968 GGCCTTTATCCACAAGGTCC 58.236 55.000 0.00 0.00 42.68 4.46
6378 6967 1.285078 AGGGCCTTTATCCACAAGGTC 59.715 52.381 0.00 0.00 44.22 3.85
6379 6968 1.382914 AGGGCCTTTATCCACAAGGT 58.617 50.000 0.00 0.00 42.68 3.50
6380 6969 3.662759 TTAGGGCCTTTATCCACAAGG 57.337 47.619 13.45 0.00 43.47 3.61
6381 6970 4.600062 ACTTTAGGGCCTTTATCCACAAG 58.400 43.478 13.45 4.32 0.00 3.16
6382 6971 4.668138 ACTTTAGGGCCTTTATCCACAA 57.332 40.909 13.45 0.00 0.00 3.33
6383 6972 4.668138 AACTTTAGGGCCTTTATCCACA 57.332 40.909 13.45 0.00 0.00 4.17
6384 6973 7.123697 ACATTAAACTTTAGGGCCTTTATCCAC 59.876 37.037 13.45 0.00 0.00 4.02
6385 6974 7.123547 CACATTAAACTTTAGGGCCTTTATCCA 59.876 37.037 13.45 0.00 0.00 3.41
6386 6975 7.417456 CCACATTAAACTTTAGGGCCTTTATCC 60.417 40.741 13.45 0.00 0.00 2.59
6387 6976 7.417456 CCCACATTAAACTTTAGGGCCTTTATC 60.417 40.741 13.45 0.00 0.00 1.75
6388 6977 6.382859 CCCACATTAAACTTTAGGGCCTTTAT 59.617 38.462 13.45 0.00 0.00 1.40
6389 6978 5.717654 CCCACATTAAACTTTAGGGCCTTTA 59.282 40.000 13.45 0.00 0.00 1.85
6390 6979 4.530553 CCCACATTAAACTTTAGGGCCTTT 59.469 41.667 13.45 1.03 0.00 3.11
6391 6980 4.093743 CCCACATTAAACTTTAGGGCCTT 58.906 43.478 13.45 0.00 0.00 4.35
6392 6981 3.708451 CCCACATTAAACTTTAGGGCCT 58.292 45.455 12.58 12.58 0.00 5.19
6395 6984 3.708451 AGGCCCACATTAAACTTTAGGG 58.292 45.455 0.00 0.00 37.87 3.53
6396 6985 5.016831 AGAAGGCCCACATTAAACTTTAGG 58.983 41.667 0.00 0.00 0.00 2.69
6397 6986 7.085052 GTAGAAGGCCCACATTAAACTTTAG 57.915 40.000 0.00 0.00 0.00 1.85
6399 6988 5.977489 GTAGAAGGCCCACATTAAACTTT 57.023 39.130 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.