Multiple sequence alignment - TraesCS4A01G473400

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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 TraesCS4A01G473400 chr4A 100.000 3405 0 0 1 3405 733429875 733433279 0.000000e+00 6288
1 TraesCS4A01G473400 chr4A 100.000 1054 0 0 4023 5076 733433897 733434950 0.000000e+00 1947
2 TraesCS4A01G473400 chr4A 100.000 462 0 0 3533 3994 733433407 733433868 0.000000e+00 854
3 TraesCS4A01G473400 chr4A 91.546 414 26 2 4664 5076 733516424 733516829 3.430000e-156 562
4 TraesCS4A01G473400 chr4A 77.571 914 127 49 968 1843 698680616 698681489 9.880000e-132 481
5 TraesCS4A01G473400 chr4A 76.898 909 135 42 967 1837 423962577 423963448 3.610000e-121 446
6 TraesCS4A01G473400 chr4A 87.136 412 25 6 4072 4482 733516070 733516454 4.660000e-120 442
7 TraesCS4A01G473400 chr4A 83.955 268 33 5 4023 4289 733528534 733528792 1.090000e-61 248
8 TraesCS4A01G473400 chr4A 85.116 215 28 3 3784 3994 733528303 733528517 3.080000e-52 217
9 TraesCS4A01G473400 chr7D 92.593 1215 63 16 2201 3405 6770869 6769672 0.000000e+00 1720
10 TraesCS4A01G473400 chr7D 95.238 462 17 3 3533 3994 6769570 6769114 0.000000e+00 726
11 TraesCS4A01G473400 chr7D 92.978 413 21 5 4664 5076 6768701 6768297 3.380000e-166 595
12 TraesCS4A01G473400 chr7D 83.892 627 48 29 821 1424 6772611 6772015 2.670000e-152 549
13 TraesCS4A01G473400 chr7D 93.140 379 15 3 4104 4482 6769038 6768671 3.460000e-151 545
14 TraesCS4A01G473400 chr7D 84.978 446 53 11 1463 1904 6772011 6771576 1.680000e-119 440
15 TraesCS4A01G473400 chr7D 87.981 208 19 1 1994 2201 6771194 6770993 1.830000e-59 241
16 TraesCS4A01G473400 chr7D 85.268 224 27 5 4664 4884 6760560 6760340 5.110000e-55 226
17 TraesCS4A01G473400 chr7D 89.076 119 11 2 628 745 6772904 6772787 4.100000e-31 147
18 TraesCS4A01G473400 chr7D 83.721 86 6 3 742 819 6772725 6772640 1.960000e-09 75
19 TraesCS4A01G473400 chrUn 99.846 651 1 0 1754 2404 349640458 349641108 0.000000e+00 1197
20 TraesCS4A01G473400 chrUn 99.846 651 1 0 1754 2404 386311258 386310608 0.000000e+00 1197
21 TraesCS4A01G473400 chrUn 99.846 651 1 0 1754 2404 450094232 450094882 0.000000e+00 1197
22 TraesCS4A01G473400 chrUn 99.364 472 2 1 4023 4493 326456989 326456518 0.000000e+00 854
23 TraesCS4A01G473400 chrUn 100.000 462 0 0 3533 3994 326457445 326456984 0.000000e+00 854
24 TraesCS4A01G473400 chrUn 100.000 398 0 0 1754 2151 479019114 479018717 0.000000e+00 736
25 TraesCS4A01G473400 chrUn 88.350 412 20 13 4072 4482 377321283 377321667 2.140000e-128 470
26 TraesCS4A01G473400 chrUn 89.606 279 21 1 4798 5076 455531797 455532067 1.050000e-91 348
27 TraesCS4A01G473400 chrUn 93.407 182 12 0 4692 4873 318545449 318545268 2.330000e-68 270
28 TraesCS4A01G473400 chrUn 99.306 144 1 0 4659 4802 326456535 326456392 1.400000e-65 261
29 TraesCS4A01G473400 chrUn 93.233 133 9 0 4664 4796 377321637 377321769 4.010000e-46 196
30 TraesCS4A01G473400 chr7A 92.766 788 34 11 2386 3169 7729125 7728357 0.000000e+00 1118
31 TraesCS4A01G473400 chr7A 90.305 722 53 5 1728 2446 7729859 7729152 0.000000e+00 929
32 TraesCS4A01G473400 chr7A 86.257 895 69 29 821 1681 7730742 7729868 0.000000e+00 922
33 TraesCS4A01G473400 chr7A 96.760 463 14 1 3533 3994 7728061 7727599 0.000000e+00 771
34 TraesCS4A01G473400 chr7A 95.983 473 16 3 4023 4493 7727582 7727111 0.000000e+00 765
35 TraesCS4A01G473400 chr7A 85.402 733 69 20 18 745 7731544 7730845 0.000000e+00 726
36 TraesCS4A01G473400 chr7A 90.625 416 30 2 4661 5076 7727126 7726720 1.240000e-150 544
37 TraesCS4A01G473400 chr7A 100.000 174 0 0 4485 4658 605175535 605175708 6.340000e-84 322
38 TraesCS4A01G473400 chr7A 91.121 214 18 1 3192 3405 7728373 7728161 6.430000e-74 289
39 TraesCS4A01G473400 chr5D 81.403 941 124 35 2379 3278 432878032 432877102 0.000000e+00 721
40 TraesCS4A01G473400 chr5D 79.745 943 122 39 935 1843 483271713 483270806 2.010000e-173 619
41 TraesCS4A01G473400 chr5D 96.309 298 11 0 3533 3830 432876916 432876619 1.640000e-134 490
42 TraesCS4A01G473400 chr5D 88.148 270 18 4 4023 4289 432876468 432876210 4.940000e-80 309
43 TraesCS4A01G473400 chr5D 98.529 136 2 0 998 1133 432878655 432878520 1.830000e-59 241
44 TraesCS4A01G473400 chr5D 90.299 134 11 2 3863 3994 432876618 432876485 1.880000e-39 174
45 TraesCS4A01G473400 chr5D 92.045 88 4 3 3319 3405 432877103 432877018 2.480000e-23 121
46 TraesCS4A01G473400 chr5B 83.977 699 75 24 2612 3279 525816645 525815953 1.990000e-178 636
47 TraesCS4A01G473400 chr5B 94.966 298 15 0 3533 3830 525815769 525815472 7.700000e-128 468
48 TraesCS4A01G473400 chr5B 89.630 270 22 3 4023 4289 525815321 525815055 6.300000e-89 339
49 TraesCS4A01G473400 chr5B 98.396 187 3 0 4475 4661 418812333 418812147 3.790000e-86 329
50 TraesCS4A01G473400 chr5B 100.000 175 0 0 4485 4659 215888249 215888075 1.760000e-84 324
51 TraesCS4A01G473400 chr5B 97.810 137 3 0 998 1134 525817664 525817528 2.360000e-58 237
52 TraesCS4A01G473400 chr5B 84.513 226 18 11 4700 4921 525814760 525814548 1.850000e-49 207
53 TraesCS4A01G473400 chr5B 93.827 81 3 2 3326 3405 525815949 525815870 2.480000e-23 121
54 TraesCS4A01G473400 chr5A 83.926 703 71 25 2612 3279 547416963 547416268 7.170000e-178 634
55 TraesCS4A01G473400 chr5A 95.302 298 14 0 3533 3830 547416083 547415786 1.650000e-129 473
56 TraesCS4A01G473400 chr5A 91.481 270 20 3 4023 4289 547415634 547415365 8.030000e-98 368
57 TraesCS4A01G473400 chr5A 100.000 175 0 0 4485 4659 177619418 177619244 1.760000e-84 324
58 TraesCS4A01G473400 chr5A 91.852 135 8 3 3863 3994 547415785 547415651 8.680000e-43 185
59 TraesCS4A01G473400 chr5A 91.358 81 5 2 3326 3405 547416264 547416185 5.370000e-20 110
60 TraesCS4A01G473400 chr2B 78.242 910 129 38 968 1843 561291812 561292686 2.090000e-143 520
61 TraesCS4A01G473400 chr1D 85.086 409 32 10 862 1265 10223253 10223637 1.710000e-104 390
62 TraesCS4A01G473400 chr3B 82.203 472 59 21 3533 3994 25895770 25896226 2.870000e-102 383
63 TraesCS4A01G473400 chr3B 82.166 471 61 19 3533 3994 25990472 25990928 2.870000e-102 383
64 TraesCS4A01G473400 chr3B 81.953 471 62 19 3533 3994 25857271 25857727 1.330000e-100 377
65 TraesCS4A01G473400 chr3B 79.146 398 63 9 3009 3403 26287264 26287644 1.810000e-64 257
66 TraesCS4A01G473400 chr3B 84.016 244 23 6 4024 4256 26329212 26329450 2.380000e-53 220
67 TraesCS4A01G473400 chr3B 83.607 244 24 6 4024 4256 25990946 25991184 1.110000e-51 215
68 TraesCS4A01G473400 chr3B 83.197 244 25 6 4024 4256 25823393 25823631 5.150000e-50 209
69 TraesCS4A01G473400 chr3B 83.197 244 25 6 4024 4256 25857745 25857983 5.150000e-50 209
70 TraesCS4A01G473400 chr3A 98.413 189 3 0 4481 4669 290424122 290423934 2.930000e-87 333
71 TraesCS4A01G473400 chr7B 100.000 175 0 0 4484 4658 672656196 672656370 1.760000e-84 324
72 TraesCS4A01G473400 chr6A 100.000 174 0 0 4485 4658 168007205 168007032 6.340000e-84 322
73 TraesCS4A01G473400 chr1A 100.000 174 0 0 4485 4658 99155043 99154870 6.340000e-84 322
74 TraesCS4A01G473400 chr1A 100.000 174 0 0 4485 4658 259052829 259053002 6.340000e-84 322
75 TraesCS4A01G473400 chr3D 83.003 353 42 10 4664 5008 606358207 606357865 2.300000e-78 303


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 TraesCS4A01G473400 chr4A 733429875 733434950 5075 False 3029.666667 6288 100.000000 1 5076 3 chr4A.!!$F3 5075
1 TraesCS4A01G473400 chr4A 733516070 733516829 759 False 502.000000 562 89.341000 4072 5076 2 chr4A.!!$F4 1004
2 TraesCS4A01G473400 chr4A 698680616 698681489 873 False 481.000000 481 77.571000 968 1843 1 chr4A.!!$F2 875
3 TraesCS4A01G473400 chr4A 423962577 423963448 871 False 446.000000 446 76.898000 967 1837 1 chr4A.!!$F1 870
4 TraesCS4A01G473400 chr7D 6768297 6772904 4607 True 559.777778 1720 89.288556 628 5076 9 chr7D.!!$R2 4448
5 TraesCS4A01G473400 chrUn 349640458 349641108 650 False 1197.000000 1197 99.846000 1754 2404 1 chrUn.!!$F1 650
6 TraesCS4A01G473400 chrUn 386310608 386311258 650 True 1197.000000 1197 99.846000 1754 2404 1 chrUn.!!$R2 650
7 TraesCS4A01G473400 chrUn 450094232 450094882 650 False 1197.000000 1197 99.846000 1754 2404 1 chrUn.!!$F2 650
8 TraesCS4A01G473400 chrUn 326456392 326457445 1053 True 656.333333 854 99.556667 3533 4802 3 chrUn.!!$R4 1269
9 TraesCS4A01G473400 chr7A 7726720 7731544 4824 True 758.000000 1118 91.152375 18 5076 8 chr7A.!!$R1 5058
10 TraesCS4A01G473400 chr5D 483270806 483271713 907 True 619.000000 619 79.745000 935 1843 1 chr5D.!!$R1 908
11 TraesCS4A01G473400 chr5D 432876210 432878655 2445 True 342.666667 721 91.122167 998 4289 6 chr5D.!!$R2 3291
12 TraesCS4A01G473400 chr5B 525814548 525817664 3116 True 334.666667 636 90.787167 998 4921 6 chr5B.!!$R3 3923
13 TraesCS4A01G473400 chr5A 547415365 547416963 1598 True 354.000000 634 90.783800 2612 4289 5 chr5A.!!$R2 1677
14 TraesCS4A01G473400 chr2B 561291812 561292686 874 False 520.000000 520 78.242000 968 1843 1 chr2B.!!$F1 875
15 TraesCS4A01G473400 chr3B 25990472 25991184 712 False 299.000000 383 82.886500 3533 4256 2 chr3B.!!$F6 723
16 TraesCS4A01G473400 chr3B 25857271 25857983 712 False 293.000000 377 82.575000 3533 4256 2 chr3B.!!$F5 723

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
243 244 0.035820 CTTACAGGCTGGCCCGTTAA 60.036 55.0 20.34 6.16 39.21 2.01 F
1153 1274 0.107557 AATTAAACCCCGCCGTCGAT 60.108 50.0 0.00 0.00 38.10 3.59 F
1284 1488 0.108472 CGAACGGGTTCTAGGGTTCC 60.108 60.0 9.62 0.00 36.34 3.62 F
1523 1747 0.322816 ATTCTGTGCGAGGTTGCCAT 60.323 50.0 0.00 0.00 0.00 4.40 F
3184 4164 0.242825 GCATTGCATGGATGGGATCG 59.757 55.0 3.15 0.00 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1265 1469 0.108472 GGAACCCTAGAACCCGTTCG 60.108 60.000 2.06 0.00 43.97 3.95 R
2574 3511 0.962356 ATCAAAGAACTGCCAGCCCG 60.962 55.000 0.00 0.00 0.00 6.13 R
3160 4138 1.066071 CCCATCCATGCAATGCAACAA 60.066 47.619 13.45 0.04 44.97 2.83 R
3301 4293 2.159338 CCGACTGCAATGAAAAGGATGG 60.159 50.000 0.00 0.00 0.00 3.51 R
4577 5727 0.170339 GGAAAATCGACCGCTTTGGG 59.830 55.000 0.00 0.00 44.64 4.12 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
121 122 7.881232 AGATAAAAATGGACTTAAACCGAGTGA 59.119 33.333 0.00 0.00 0.00 3.41
133 134 8.074370 ACTTAAACCGAGTGAAATAAGAAAAGC 58.926 33.333 0.00 0.00 0.00 3.51
134 135 6.385649 AAACCGAGTGAAATAAGAAAAGCA 57.614 33.333 0.00 0.00 0.00 3.91
172 173 6.098266 ACATAAAATATTGGTGGGGAAGCTTC 59.902 38.462 18.54 18.54 0.00 3.86
175 176 1.075601 ATTGGTGGGGAAGCTTCTGA 58.924 50.000 25.05 7.39 0.00 3.27
196 197 3.769739 AAGTTTCCCAAAAATGGAGGC 57.230 42.857 0.00 0.00 32.37 4.70
215 216 3.319122 AGGCGCTTCTGAAAAATGAACTT 59.681 39.130 7.64 0.00 0.00 2.66
237 238 3.283259 AACTAATCTTACAGGCTGGCC 57.717 47.619 20.34 3.00 0.00 5.36
243 244 0.035820 CTTACAGGCTGGCCCGTTAA 60.036 55.000 20.34 6.16 39.21 2.01
257 258 1.743394 CCGTTAAGAACAATGGGGAGC 59.257 52.381 0.00 0.00 31.89 4.70
261 262 0.984230 AAGAACAATGGGGAGCGAGA 59.016 50.000 0.00 0.00 0.00 4.04
288 289 2.412937 GCAATCGGGCCGGATTTG 59.587 61.111 30.14 25.21 34.50 2.32
318 319 1.552799 CCTTTCCCAAACCCATGCCC 61.553 60.000 0.00 0.00 0.00 5.36
338 339 2.159085 CCGACACCTTATCTGGTCCTTC 60.159 54.545 0.00 0.00 38.45 3.46
340 341 3.108376 GACACCTTATCTGGTCCTTCCT 58.892 50.000 0.00 0.00 38.45 3.36
352 353 3.245122 TGGTCCTTCCTAAACCCATGAAC 60.245 47.826 0.00 0.00 37.07 3.18
355 356 3.010138 TCCTTCCTAAACCCATGAACCTG 59.990 47.826 0.00 0.00 0.00 4.00
362 363 5.245977 CCTAAACCCATGAACCTGAACAAAT 59.754 40.000 0.00 0.00 0.00 2.32
405 406 6.194967 TGGGAGTGACATATAGAAGTGAGAA 58.805 40.000 0.00 0.00 0.00 2.87
415 416 3.704800 AGAAGTGAGAAAAGGCCTACC 57.295 47.619 5.16 0.00 0.00 3.18
433 434 1.992557 ACCAATGGGCTGACCTCTTAA 59.007 47.619 3.55 0.00 41.11 1.85
434 435 2.582636 ACCAATGGGCTGACCTCTTAAT 59.417 45.455 3.55 0.00 41.11 1.40
435 436 3.785887 ACCAATGGGCTGACCTCTTAATA 59.214 43.478 3.55 0.00 41.11 0.98
438 439 5.242393 CCAATGGGCTGACCTCTTAATAATG 59.758 44.000 0.00 0.00 41.11 1.90
439 440 3.820557 TGGGCTGACCTCTTAATAATGC 58.179 45.455 0.00 0.00 41.11 3.56
440 441 3.149981 GGGCTGACCTCTTAATAATGCC 58.850 50.000 0.00 0.00 37.34 4.40
441 442 3.181439 GGGCTGACCTCTTAATAATGCCT 60.181 47.826 0.00 0.00 38.07 4.75
442 443 4.464947 GGCTGACCTCTTAATAATGCCTT 58.535 43.478 0.00 0.00 35.44 4.35
443 444 5.456186 GGGCTGACCTCTTAATAATGCCTTA 60.456 44.000 0.00 0.00 38.07 2.69
444 445 6.241645 GGCTGACCTCTTAATAATGCCTTAT 58.758 40.000 0.00 0.00 35.44 1.73
445 446 6.717084 GGCTGACCTCTTAATAATGCCTTATT 59.283 38.462 11.12 11.12 40.04 1.40
446 447 7.231519 GGCTGACCTCTTAATAATGCCTTATTT 59.768 37.037 11.53 0.00 38.30 1.40
447 448 8.633561 GCTGACCTCTTAATAATGCCTTATTTT 58.366 33.333 11.53 0.00 38.30 1.82
449 450 9.920946 TGACCTCTTAATAATGCCTTATTTTCT 57.079 29.630 11.53 0.00 38.30 2.52
451 452 8.633561 ACCTCTTAATAATGCCTTATTTTCTGC 58.366 33.333 11.53 0.00 38.30 4.26
452 453 7.805071 CCTCTTAATAATGCCTTATTTTCTGCG 59.195 37.037 11.53 0.00 38.30 5.18
453 454 8.220755 TCTTAATAATGCCTTATTTTCTGCGT 57.779 30.769 11.53 0.00 38.30 5.24
454 455 8.128582 TCTTAATAATGCCTTATTTTCTGCGTG 58.871 33.333 11.53 0.00 38.30 5.34
455 456 6.449635 AATAATGCCTTATTTTCTGCGTGA 57.550 33.333 1.53 0.00 34.57 4.35
456 457 3.764885 ATGCCTTATTTTCTGCGTGAC 57.235 42.857 0.00 0.00 0.00 3.67
457 458 2.778299 TGCCTTATTTTCTGCGTGACT 58.222 42.857 0.00 0.00 0.00 3.41
458 459 3.932822 TGCCTTATTTTCTGCGTGACTA 58.067 40.909 0.00 0.00 0.00 2.59
459 460 3.682858 TGCCTTATTTTCTGCGTGACTAC 59.317 43.478 0.00 0.00 0.00 2.73
482 483 9.817365 CTACGCTACTTACATACGTTATATGTT 57.183 33.333 7.69 0.00 38.84 2.71
615 616 6.098695 TGAACTTATACACATACCCTACCCAC 59.901 42.308 0.00 0.00 0.00 4.61
619 620 2.627933 ACACATACCCTACCCACAACT 58.372 47.619 0.00 0.00 0.00 3.16
621 622 4.169666 ACACATACCCTACCCACAACTAA 58.830 43.478 0.00 0.00 0.00 2.24
623 624 5.104652 ACACATACCCTACCCACAACTAATC 60.105 44.000 0.00 0.00 0.00 1.75
625 626 5.130477 ACATACCCTACCCACAACTAATCAG 59.870 44.000 0.00 0.00 0.00 2.90
626 627 3.798515 ACCCTACCCACAACTAATCAGA 58.201 45.455 0.00 0.00 0.00 3.27
632 636 5.112129 ACCCACAACTAATCAGATTACCC 57.888 43.478 0.00 0.00 0.00 3.69
635 639 5.104527 CCCACAACTAATCAGATTACCCAGA 60.105 44.000 0.00 0.00 0.00 3.86
676 681 0.466963 GACAACCCATACCCTACCCG 59.533 60.000 0.00 0.00 0.00 5.28
698 703 4.101448 GGTCGGGTGCTCATGGCT 62.101 66.667 7.54 0.00 42.39 4.75
711 716 1.203038 TCATGGCTGTGTGAACCCATT 60.203 47.619 0.00 0.00 35.97 3.16
723 728 2.562298 TGAACCCATTTGTCAGATTGCC 59.438 45.455 0.00 0.00 0.00 4.52
776 847 3.554342 CGGAGGAGGCCCATCCAG 61.554 72.222 20.32 11.75 42.26 3.86
777 848 2.040464 GGAGGAGGCCCATCCAGA 60.040 66.667 17.00 0.00 42.26 3.86
779 850 2.367512 AGGAGGCCCATCCAGACC 60.368 66.667 13.29 0.00 42.26 3.85
852 958 1.779157 GGAAACAAAAACGCGCTTCTC 59.221 47.619 5.73 0.00 0.00 2.87
856 962 0.307760 CAAAAACGCGCTTCTCCAGT 59.692 50.000 5.73 0.00 0.00 4.00
857 963 0.586802 AAAAACGCGCTTCTCCAGTC 59.413 50.000 5.73 0.00 0.00 3.51
858 964 1.228657 AAAACGCGCTTCTCCAGTCC 61.229 55.000 5.73 0.00 0.00 3.85
859 965 2.377628 AAACGCGCTTCTCCAGTCCA 62.378 55.000 5.73 0.00 0.00 4.02
860 966 2.507992 CGCGCTTCTCCAGTCCAG 60.508 66.667 5.56 0.00 0.00 3.86
878 985 0.698818 AGGGTCCTCTCCGCAAAATT 59.301 50.000 0.00 0.00 0.00 1.82
901 1008 0.541296 TTCCTCTTTCCCCGTCGTCT 60.541 55.000 0.00 0.00 0.00 4.18
902 1009 0.964358 TCCTCTTTCCCCGTCGTCTC 60.964 60.000 0.00 0.00 0.00 3.36
903 1010 0.966370 CCTCTTTCCCCGTCGTCTCT 60.966 60.000 0.00 0.00 0.00 3.10
904 1011 0.452585 CTCTTTCCCCGTCGTCTCTC 59.547 60.000 0.00 0.00 0.00 3.20
951 1064 1.819905 CGAAGGAGGAAGAGAGGCC 59.180 63.158 0.00 0.00 0.00 5.19
955 1068 2.498726 GAGGAAGAGAGGCCAGCG 59.501 66.667 5.01 0.00 0.00 5.18
956 1069 3.731653 GAGGAAGAGAGGCCAGCGC 62.732 68.421 5.01 0.00 0.00 5.92
1153 1274 0.107557 AATTAAACCCCGCCGTCGAT 60.108 50.000 0.00 0.00 38.10 3.59
1186 1312 1.876714 CGCTGTGGTACCGAATCCG 60.877 63.158 7.57 2.48 0.00 4.18
1265 1469 0.981183 GAATTTGGGGTTGGGGGAAC 59.019 55.000 0.00 0.00 0.00 3.62
1266 1470 0.834261 AATTTGGGGTTGGGGGAACG 60.834 55.000 0.00 0.00 35.12 3.95
1267 1471 1.731324 ATTTGGGGTTGGGGGAACGA 61.731 55.000 0.00 0.00 35.12 3.85
1268 1472 1.946063 TTTGGGGTTGGGGGAACGAA 61.946 55.000 0.00 0.00 35.12 3.85
1269 1473 2.282674 GGGGTTGGGGGAACGAAC 60.283 66.667 0.00 0.00 37.10 3.95
1284 1488 0.108472 CGAACGGGTTCTAGGGTTCC 60.108 60.000 9.62 0.00 36.34 3.62
1339 1562 1.429148 CTCCGCGTGGTAGAATTGCC 61.429 60.000 16.01 0.00 36.30 4.52
1347 1570 1.022451 GGTAGAATTGCCGGCGACAA 61.022 55.000 21.40 11.79 0.00 3.18
1348 1571 1.014352 GTAGAATTGCCGGCGACAAT 58.986 50.000 21.40 15.80 39.38 2.71
1358 1581 3.602103 GCGACAATTGGCCATGGA 58.398 55.556 18.40 0.00 0.00 3.41
1400 1623 1.597027 GTCTGGGGTTGGTCGTGTG 60.597 63.158 0.00 0.00 0.00 3.82
1439 1662 2.171003 GGTTTTGCATCTGCTTAGGGT 58.829 47.619 3.53 0.00 42.66 4.34
1470 1694 0.840722 CAGTACAACCCACCCTCCCT 60.841 60.000 0.00 0.00 0.00 4.20
1493 1717 1.821216 AATCGCTTGGAAATGGACGT 58.179 45.000 0.00 0.00 0.00 4.34
1494 1718 1.086696 ATCGCTTGGAAATGGACGTG 58.913 50.000 0.00 0.00 0.00 4.49
1523 1747 0.322816 ATTCTGTGCGAGGTTGCCAT 60.323 50.000 0.00 0.00 0.00 4.40
1526 1750 3.443045 GTGCGAGGTTGCCATGGG 61.443 66.667 15.13 0.00 0.00 4.00
1527 1751 3.965258 TGCGAGGTTGCCATGGGT 61.965 61.111 15.13 0.00 0.00 4.51
1551 1779 7.977853 GGTTTAGGTCGATTTCTGTACAATCTA 59.022 37.037 0.00 0.00 0.00 1.98
1558 1786 8.488764 GTCGATTTCTGTACAATCTAATAAGCC 58.511 37.037 0.00 0.00 0.00 4.35
1559 1787 8.421784 TCGATTTCTGTACAATCTAATAAGCCT 58.578 33.333 0.00 0.00 0.00 4.58
1576 1807 1.933853 GCCTATGCACTACTTGTTCGG 59.066 52.381 0.00 0.00 37.47 4.30
1593 1824 4.219033 GTTCGGTGCAACAACAGAATTAG 58.781 43.478 0.98 0.00 39.98 1.73
1607 1840 8.789762 ACAACAGAATTAGTTAACCAACATACC 58.210 33.333 0.88 0.00 37.10 2.73
1620 1853 4.134563 CCAACATACCTACATACTTGGCC 58.865 47.826 0.00 0.00 0.00 5.36
1668 1902 5.796424 ACCTGCAAAGATCAGACAAAATT 57.204 34.783 0.00 0.00 33.54 1.82
1670 1904 6.218746 ACCTGCAAAGATCAGACAAAATTTC 58.781 36.000 0.00 0.00 33.54 2.17
1682 1916 3.047093 ACAAAATTTCGCCGTTTGCTAC 58.953 40.909 0.00 0.00 36.01 3.58
1683 1917 3.243267 ACAAAATTTCGCCGTTTGCTACT 60.243 39.130 0.00 0.00 36.01 2.57
1684 1918 3.636282 AAATTTCGCCGTTTGCTACTT 57.364 38.095 0.00 0.00 38.05 2.24
1685 1919 2.894307 ATTTCGCCGTTTGCTACTTC 57.106 45.000 0.00 0.00 38.05 3.01
1689 1923 1.062258 CGCCGTTTGCTACTTCGTTA 58.938 50.000 0.00 0.00 38.05 3.18
1691 1925 1.392510 GCCGTTTGCTACTTCGTTAGG 59.607 52.381 0.00 0.00 36.87 2.69
1692 1926 2.680577 CCGTTTGCTACTTCGTTAGGT 58.319 47.619 0.00 0.00 0.00 3.08
1696 1930 3.308438 TTGCTACTTCGTTAGGTGGTC 57.692 47.619 0.00 0.00 0.00 4.02
1704 1938 1.952990 TCGTTAGGTGGTCGTACACAA 59.047 47.619 12.73 0.00 43.08 3.33
1709 1943 2.557317 AGGTGGTCGTACACAAAACAG 58.443 47.619 12.73 0.00 43.08 3.16
1712 1946 3.450578 GTGGTCGTACACAAAACAGAGA 58.549 45.455 7.24 0.00 40.99 3.10
1722 1956 6.966435 ACACAAAACAGAGAACCATTTTTG 57.034 33.333 0.00 0.00 41.08 2.44
1725 1959 6.035975 CACAAAACAGAGAACCATTTTTGGAC 59.964 38.462 9.26 0.00 40.10 4.02
1726 1960 5.930837 AAACAGAGAACCATTTTTGGACA 57.069 34.783 0.00 0.00 0.00 4.02
1735 1969 3.390639 ACCATTTTTGGACATTTGGAGCA 59.609 39.130 0.00 0.00 0.00 4.26
1736 1970 3.747529 CCATTTTTGGACATTTGGAGCAC 59.252 43.478 0.00 0.00 0.00 4.40
1737 1971 3.467374 TTTTTGGACATTTGGAGCACC 57.533 42.857 0.00 0.00 0.00 5.01
2151 2683 3.561313 GGTTCAAGGTTGCCAGGATTAGA 60.561 47.826 0.00 0.00 0.00 2.10
2426 3173 9.322773 CTGCATCAAGAGAGTAAATCTATGAAA 57.677 33.333 0.00 0.00 38.84 2.69
2459 3206 8.759481 TTAGCATGGTTCATATATTTGGTTCA 57.241 30.769 1.12 0.00 0.00 3.18
2482 3232 8.096621 TCATCATCTGGGTTTATTACCTGTTA 57.903 34.615 0.00 0.00 46.86 2.41
2483 3233 7.990886 TCATCATCTGGGTTTATTACCTGTTAC 59.009 37.037 0.00 0.00 46.86 2.50
2484 3234 7.260387 TCATCTGGGTTTATTACCTGTTACA 57.740 36.000 0.00 0.00 46.86 2.41
2559 3490 6.545666 ACATGATTGTTTAGTTCTTGACACCA 59.454 34.615 0.00 0.00 29.55 4.17
2574 3511 9.974980 TTCTTGACACCAAATCCTTAATAAAAC 57.025 29.630 0.00 0.00 0.00 2.43
2602 3539 4.696877 TGGCAGTTCTTTGATGTCTACATG 59.303 41.667 0.00 0.00 36.57 3.21
2744 3699 6.980416 AGTCCTATGTTGGTAATACCTCTC 57.020 41.667 11.16 2.13 39.58 3.20
2762 3717 2.363680 TCTCGATCCATCTGCTCTTTCC 59.636 50.000 0.00 0.00 0.00 3.13
2801 3758 3.285484 AGTGCTTGCCATATCCTTTCTG 58.715 45.455 0.00 0.00 0.00 3.02
2936 3901 2.557490 AGAAGGTCGGTGACACTACTTC 59.443 50.000 16.78 16.78 33.68 3.01
2959 3924 6.508777 TCACCAAAATTTGTTTAGTGCCTAC 58.491 36.000 4.92 0.00 0.00 3.18
2967 3935 2.803956 TGTTTAGTGCCTACGTTCAAGC 59.196 45.455 0.00 0.00 0.00 4.01
2986 3954 8.405531 GTTCAAGCCAGCATAATGATTTACTTA 58.594 33.333 0.00 0.00 0.00 2.24
2987 3955 7.930217 TCAAGCCAGCATAATGATTTACTTAC 58.070 34.615 0.00 0.00 0.00 2.34
2989 3957 7.736447 AGCCAGCATAATGATTTACTTACTC 57.264 36.000 0.00 0.00 0.00 2.59
2990 3958 7.512992 AGCCAGCATAATGATTTACTTACTCT 58.487 34.615 0.00 0.00 0.00 3.24
2991 3959 7.443575 AGCCAGCATAATGATTTACTTACTCTG 59.556 37.037 0.00 0.00 0.00 3.35
3094 4068 7.174946 GGAACTCAAAAGTGATGATGAAAGGTA 59.825 37.037 0.00 0.00 35.36 3.08
3160 4138 7.230108 TCAAAATGCTGATGAGACTCTTCTTTT 59.770 33.333 16.77 12.38 29.47 2.27
3184 4164 0.242825 GCATTGCATGGATGGGATCG 59.757 55.000 3.15 0.00 0.00 3.69
3232 4220 2.470057 TTTATCCTGAATTGGGGCCC 57.530 50.000 18.17 18.17 0.00 5.80
3247 4235 2.525368 GGGCCCAAAATGTTCACTAGT 58.475 47.619 19.95 0.00 0.00 2.57
3301 4293 5.991606 TGATACACATTCTTATGCTGGCTAC 59.008 40.000 0.00 0.00 35.03 3.58
3305 4297 4.214971 CACATTCTTATGCTGGCTACCATC 59.785 45.833 0.00 0.00 35.03 3.51
4300 5427 8.141298 TGTTTCTATTAGTACATTGACCTGGA 57.859 34.615 0.00 0.00 0.00 3.86
4476 5626 7.769272 TTTGATTGTTTTCTGGTTTTGCTAG 57.231 32.000 0.00 0.00 0.00 3.42
4477 5627 5.841810 TGATTGTTTTCTGGTTTTGCTAGG 58.158 37.500 0.00 0.00 0.00 3.02
4478 5628 5.362430 TGATTGTTTTCTGGTTTTGCTAGGT 59.638 36.000 0.00 0.00 0.00 3.08
4479 5629 4.647424 TGTTTTCTGGTTTTGCTAGGTG 57.353 40.909 0.00 0.00 0.00 4.00
4480 5630 3.383185 TGTTTTCTGGTTTTGCTAGGTGG 59.617 43.478 0.00 0.00 0.00 4.61
4481 5631 3.586470 TTTCTGGTTTTGCTAGGTGGA 57.414 42.857 0.00 0.00 0.00 4.02
4482 5632 3.806949 TTCTGGTTTTGCTAGGTGGAT 57.193 42.857 0.00 0.00 0.00 3.41
4483 5633 3.806949 TCTGGTTTTGCTAGGTGGATT 57.193 42.857 0.00 0.00 0.00 3.01
4484 5634 3.686016 TCTGGTTTTGCTAGGTGGATTC 58.314 45.455 0.00 0.00 0.00 2.52
4485 5635 3.330701 TCTGGTTTTGCTAGGTGGATTCT 59.669 43.478 0.00 0.00 0.00 2.40
4486 5636 4.534500 TCTGGTTTTGCTAGGTGGATTCTA 59.466 41.667 0.00 0.00 0.00 2.10
4487 5637 5.191722 TCTGGTTTTGCTAGGTGGATTCTAT 59.808 40.000 0.00 0.00 0.00 1.98
4488 5638 5.192927 TGGTTTTGCTAGGTGGATTCTATG 58.807 41.667 0.00 0.00 0.00 2.23
4489 5639 5.193679 GGTTTTGCTAGGTGGATTCTATGT 58.806 41.667 0.00 0.00 0.00 2.29
4490 5640 5.652452 GGTTTTGCTAGGTGGATTCTATGTT 59.348 40.000 0.00 0.00 0.00 2.71
4491 5641 6.152831 GGTTTTGCTAGGTGGATTCTATGTTT 59.847 38.462 0.00 0.00 0.00 2.83
4492 5642 7.309805 GGTTTTGCTAGGTGGATTCTATGTTTT 60.310 37.037 0.00 0.00 0.00 2.43
4493 5643 7.775053 TTTGCTAGGTGGATTCTATGTTTTT 57.225 32.000 0.00 0.00 0.00 1.94
4494 5644 8.871629 TTTGCTAGGTGGATTCTATGTTTTTA 57.128 30.769 0.00 0.00 0.00 1.52
4495 5645 8.871629 TTGCTAGGTGGATTCTATGTTTTTAA 57.128 30.769 0.00 0.00 0.00 1.52
4496 5646 8.506168 TGCTAGGTGGATTCTATGTTTTTAAG 57.494 34.615 0.00 0.00 0.00 1.85
4497 5647 7.556275 TGCTAGGTGGATTCTATGTTTTTAAGG 59.444 37.037 0.00 0.00 0.00 2.69
4498 5648 6.775594 AGGTGGATTCTATGTTTTTAAGGC 57.224 37.500 0.00 0.00 0.00 4.35
4499 5649 5.357032 AGGTGGATTCTATGTTTTTAAGGCG 59.643 40.000 0.00 0.00 0.00 5.52
4500 5650 5.355910 GGTGGATTCTATGTTTTTAAGGCGA 59.644 40.000 0.00 0.00 0.00 5.54
4501 5651 6.255950 GTGGATTCTATGTTTTTAAGGCGAC 58.744 40.000 0.00 0.00 0.00 5.19
4502 5652 5.064198 TGGATTCTATGTTTTTAAGGCGACG 59.936 40.000 0.00 0.00 0.00 5.12
4503 5653 4.330740 TTCTATGTTTTTAAGGCGACGC 57.669 40.909 12.43 12.43 0.00 5.19
4515 5665 2.491152 CGACGCCTTACCGCCTTA 59.509 61.111 0.00 0.00 0.00 2.69
4516 5666 1.588139 CGACGCCTTACCGCCTTAG 60.588 63.158 0.00 0.00 0.00 2.18
4517 5667 1.227176 GACGCCTTACCGCCTTAGG 60.227 63.158 0.00 0.00 37.30 2.69
4518 5668 2.108362 CGCCTTACCGCCTTAGGG 59.892 66.667 0.00 0.00 35.02 3.53
4519 5669 2.428925 CGCCTTACCGCCTTAGGGA 61.429 63.158 0.00 0.00 35.02 4.20
4520 5670 1.446366 GCCTTACCGCCTTAGGGAG 59.554 63.158 0.00 0.00 35.02 4.30
4566 5716 4.467084 CTAGGCGGGCGCTTTGGA 62.467 66.667 7.64 0.00 41.60 3.53
4567 5717 4.770874 TAGGCGGGCGCTTTGGAC 62.771 66.667 7.64 0.00 41.60 4.02
4575 5725 3.195698 CGCTTTGGACGCCTAGGC 61.196 66.667 24.75 24.75 37.85 3.93
4593 5743 3.274067 GCCCAAAGCGGTCGATTT 58.726 55.556 0.55 0.55 33.72 2.17
4594 5744 1.584495 GCCCAAAGCGGTCGATTTT 59.416 52.632 3.79 0.00 30.80 1.82
4595 5745 0.456142 GCCCAAAGCGGTCGATTTTC 60.456 55.000 3.79 0.00 30.80 2.29
4596 5746 0.170339 CCCAAAGCGGTCGATTTTCC 59.830 55.000 3.79 0.00 30.80 3.13
4597 5747 0.878416 CCAAAGCGGTCGATTTTCCA 59.122 50.000 3.79 0.00 30.80 3.53
4598 5748 1.268352 CCAAAGCGGTCGATTTTCCAA 59.732 47.619 3.79 0.00 30.80 3.53
4599 5749 2.287909 CCAAAGCGGTCGATTTTCCAAA 60.288 45.455 3.79 0.00 30.80 3.28
4600 5750 2.979813 CAAAGCGGTCGATTTTCCAAAG 59.020 45.455 3.79 0.00 30.80 2.77
4601 5751 0.521735 AGCGGTCGATTTTCCAAAGC 59.478 50.000 0.00 0.00 0.00 3.51
4602 5752 0.793104 GCGGTCGATTTTCCAAAGCG 60.793 55.000 0.54 0.54 0.00 4.68
4603 5753 0.179200 CGGTCGATTTTCCAAAGCGG 60.179 55.000 7.00 0.00 0.00 5.52
4604 5754 1.161843 GGTCGATTTTCCAAAGCGGA 58.838 50.000 7.00 0.00 44.40 5.54
4611 5761 3.009115 TCCAAAGCGGAGGGGGAG 61.009 66.667 0.00 0.00 39.64 4.30
4612 5762 4.803908 CCAAAGCGGAGGGGGAGC 62.804 72.222 0.00 0.00 36.56 4.70
4620 5770 4.516195 GAGGGGGAGCGCTTCGAC 62.516 72.222 13.26 5.82 0.00 4.20
4646 5796 2.577593 GTCGCCTTAGGGACGCTT 59.422 61.111 0.00 0.00 44.82 4.68
4647 5797 1.079336 GTCGCCTTAGGGACGCTTT 60.079 57.895 0.00 0.00 44.82 3.51
4648 5798 0.174162 GTCGCCTTAGGGACGCTTTA 59.826 55.000 0.00 0.00 44.82 1.85
4649 5799 0.896923 TCGCCTTAGGGACGCTTTAA 59.103 50.000 0.00 0.00 34.09 1.52
4650 5800 1.275856 TCGCCTTAGGGACGCTTTAAA 59.724 47.619 0.00 0.00 34.09 1.52
4651 5801 2.078392 CGCCTTAGGGACGCTTTAAAA 58.922 47.619 0.00 0.00 33.58 1.52
4652 5802 2.485038 CGCCTTAGGGACGCTTTAAAAA 59.515 45.455 0.00 0.00 33.58 1.94
4653 5803 3.668757 CGCCTTAGGGACGCTTTAAAAAC 60.669 47.826 0.00 0.00 33.58 2.43
4654 5804 3.253921 GCCTTAGGGACGCTTTAAAAACA 59.746 43.478 0.00 0.00 33.58 2.83
4655 5805 4.082408 GCCTTAGGGACGCTTTAAAAACAT 60.082 41.667 0.00 0.00 33.58 2.71
4656 5806 5.124297 GCCTTAGGGACGCTTTAAAAACATA 59.876 40.000 0.00 0.00 33.58 2.29
4657 5807 6.677187 GCCTTAGGGACGCTTTAAAAACATAG 60.677 42.308 0.00 0.00 33.58 2.23
4717 5867 5.475909 ACAGTTAGTGACAGTTTATCCGAGA 59.524 40.000 0.00 0.00 0.00 4.04
4882 6034 5.997746 TCTCCTTGTTTATTTGGTCAGTCAG 59.002 40.000 0.00 0.00 0.00 3.51
4883 6035 5.690865 TCCTTGTTTATTTGGTCAGTCAGT 58.309 37.500 0.00 0.00 0.00 3.41
4884 6036 5.530915 TCCTTGTTTATTTGGTCAGTCAGTG 59.469 40.000 0.00 0.00 0.00 3.66
4885 6037 5.530915 CCTTGTTTATTTGGTCAGTCAGTGA 59.469 40.000 0.00 0.00 0.00 3.41
4923 6075 3.338249 TGGTTGCTTCTGCTGTATTCTC 58.662 45.455 0.00 0.00 40.48 2.87
4964 6116 8.226448 GCATAGAAGATATCTTGATTTTGTCGG 58.774 37.037 22.61 3.97 39.71 4.79
4965 6117 6.610741 AGAAGATATCTTGATTTTGTCGGC 57.389 37.500 22.61 3.74 33.39 5.54
4976 6128 1.522668 TTTGTCGGCTGATGTTGAGG 58.477 50.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 8.512138 CACTCGGTTTAAGTCCATTTTTATCTT 58.488 33.333 0.00 0.00 0.00 2.40
98 99 7.804843 TTCACTCGGTTTAAGTCCATTTTTA 57.195 32.000 0.00 0.00 0.00 1.52
109 110 7.932335 TGCTTTTCTTATTTCACTCGGTTTAA 58.068 30.769 0.00 0.00 0.00 1.52
110 111 7.308348 CCTGCTTTTCTTATTTCACTCGGTTTA 60.308 37.037 0.00 0.00 0.00 2.01
114 115 4.695455 TCCTGCTTTTCTTATTTCACTCGG 59.305 41.667 0.00 0.00 0.00 4.63
121 122 7.826744 TGTTTTTGGTTCCTGCTTTTCTTATTT 59.173 29.630 0.00 0.00 0.00 1.40
134 135 9.500785 CCAATATTTTATGTGTTTTTGGTTCCT 57.499 29.630 0.00 0.00 0.00 3.36
172 173 5.299949 CCTCCATTTTTGGGAAACTTTCAG 58.700 41.667 3.93 0.00 33.11 3.02
175 176 3.494223 CGCCTCCATTTTTGGGAAACTTT 60.494 43.478 0.00 0.00 33.11 2.66
185 186 1.909700 TCAGAAGCGCCTCCATTTTT 58.090 45.000 2.29 0.00 0.00 1.94
196 197 7.914537 AGTTTAAGTTCATTTTTCAGAAGCG 57.085 32.000 0.00 0.00 0.00 4.68
215 216 4.384868 GGGCCAGCCTGTAAGATTAGTTTA 60.385 45.833 4.39 0.00 34.07 2.01
229 230 1.002502 GTTCTTAACGGGCCAGCCT 60.003 57.895 4.39 0.00 36.10 4.58
237 238 1.743394 GCTCCCCATTGTTCTTAACGG 59.257 52.381 0.00 0.00 0.00 4.44
243 244 0.539051 CTCTCGCTCCCCATTGTTCT 59.461 55.000 0.00 0.00 0.00 3.01
275 276 4.460683 CGACCAAATCCGGCCCGA 62.461 66.667 3.71 0.00 0.00 5.14
294 295 1.783071 TGGGTTTGGGAAAGGTCAAC 58.217 50.000 0.00 0.00 0.00 3.18
301 302 1.910772 CGGGCATGGGTTTGGGAAA 60.911 57.895 0.00 0.00 0.00 3.13
304 305 3.068064 GTCGGGCATGGGTTTGGG 61.068 66.667 0.00 0.00 0.00 4.12
318 319 2.159085 GGAAGGACCAGATAAGGTGTCG 60.159 54.545 0.00 0.00 43.38 4.35
338 339 3.761897 TGTTCAGGTTCATGGGTTTAGG 58.238 45.455 0.00 0.00 0.00 2.69
340 341 8.310382 CAATATTTGTTCAGGTTCATGGGTTTA 58.690 33.333 0.00 0.00 0.00 2.01
352 353 3.705579 TCATGGCCCAATATTTGTTCAGG 59.294 43.478 0.00 0.00 0.00 3.86
355 356 6.429385 TGTTTTTCATGGCCCAATATTTGTTC 59.571 34.615 0.00 0.00 0.00 3.18
405 406 4.785575 GCCCATTGGTAGGCCTTT 57.214 55.556 12.58 0.00 43.76 3.11
415 416 5.278660 GCATTATTAAGAGGTCAGCCCATTG 60.279 44.000 0.00 0.00 34.66 2.82
433 434 5.590259 AGTCACGCAGAAAATAAGGCATTAT 59.410 36.000 0.00 0.00 32.81 1.28
434 435 4.941263 AGTCACGCAGAAAATAAGGCATTA 59.059 37.500 0.00 0.00 0.00 1.90
435 436 3.758554 AGTCACGCAGAAAATAAGGCATT 59.241 39.130 0.00 0.00 0.00 3.56
438 439 3.241995 CGTAGTCACGCAGAAAATAAGGC 60.242 47.826 0.00 0.00 42.05 4.35
439 440 4.500703 CGTAGTCACGCAGAAAATAAGG 57.499 45.455 0.00 0.00 42.05 2.69
452 453 5.149054 ACGTATGTAAGTAGCGTAGTCAC 57.851 43.478 0.00 0.00 33.85 3.67
453 454 5.801350 AACGTATGTAAGTAGCGTAGTCA 57.199 39.130 0.00 0.00 35.22 3.41
454 455 9.470490 CATATAACGTATGTAAGTAGCGTAGTC 57.530 37.037 0.00 0.00 35.22 2.59
455 456 8.993121 ACATATAACGTATGTAAGTAGCGTAGT 58.007 33.333 0.56 0.00 36.49 2.73
456 457 9.817365 AACATATAACGTATGTAAGTAGCGTAG 57.183 33.333 2.98 0.00 37.18 3.51
543 544 8.460428 GGTCACCCGATTAACATTAACAATTTA 58.540 33.333 0.00 0.00 0.00 1.40
544 545 7.177744 AGGTCACCCGATTAACATTAACAATTT 59.822 33.333 0.00 0.00 35.12 1.82
549 550 6.145048 CGATAGGTCACCCGATTAACATTAAC 59.855 42.308 0.00 0.00 35.12 2.01
582 583 7.599245 GGGTATGTGTATAAGTTCATGCTAGTC 59.401 40.741 0.00 0.00 0.00 2.59
585 586 7.612065 AGGGTATGTGTATAAGTTCATGCTA 57.388 36.000 0.00 0.00 0.00 3.49
615 616 8.696374 TCTTACTCTGGGTAATCTGATTAGTTG 58.304 37.037 10.26 2.76 39.36 3.16
619 620 6.553852 GGGTCTTACTCTGGGTAATCTGATTA 59.446 42.308 6.01 6.01 39.36 1.75
621 622 4.902448 GGGTCTTACTCTGGGTAATCTGAT 59.098 45.833 0.00 0.00 39.36 2.90
623 624 4.030913 TGGGTCTTACTCTGGGTAATCTG 58.969 47.826 0.00 0.00 39.36 2.90
625 626 4.202367 CCATGGGTCTTACTCTGGGTAATC 60.202 50.000 2.85 0.00 39.36 1.75
626 627 3.716872 CCATGGGTCTTACTCTGGGTAAT 59.283 47.826 2.85 0.00 39.36 1.89
632 636 4.163078 ACTTCATCCATGGGTCTTACTCTG 59.837 45.833 13.02 0.00 0.00 3.35
635 639 4.536090 TCAACTTCATCCATGGGTCTTACT 59.464 41.667 13.02 0.00 0.00 2.24
676 681 3.310860 ATGAGCACCCGACCCGAAC 62.311 63.158 0.00 0.00 0.00 3.95
697 702 3.213506 TCTGACAAATGGGTTCACACAG 58.786 45.455 0.00 0.00 29.81 3.66
698 703 3.289407 TCTGACAAATGGGTTCACACA 57.711 42.857 0.00 0.00 0.00 3.72
723 728 2.125512 CCCCCTCGCTTCAAGTCG 60.126 66.667 0.00 0.00 0.00 4.18
816 895 1.488705 TTCCTTCGTGGTGGGCTGAT 61.489 55.000 0.00 0.00 37.07 2.90
819 898 1.228154 GTTTCCTTCGTGGTGGGCT 60.228 57.895 0.00 0.00 37.07 5.19
824 930 2.732912 GCGTTTTTGTTTCCTTCGTGGT 60.733 45.455 0.00 0.00 37.07 4.16
852 958 1.687493 GGAGAGGACCCTGGACTGG 60.687 68.421 0.00 0.00 0.00 4.00
856 962 3.539593 TTGCGGAGAGGACCCTGGA 62.540 63.158 0.00 0.00 0.00 3.86
857 963 2.124507 TTTTGCGGAGAGGACCCTGG 62.125 60.000 0.00 0.00 0.00 4.45
858 964 0.035056 ATTTTGCGGAGAGGACCCTG 60.035 55.000 0.00 0.00 0.00 4.45
859 965 0.698818 AATTTTGCGGAGAGGACCCT 59.301 50.000 0.00 0.00 0.00 4.34
860 966 0.811281 CAATTTTGCGGAGAGGACCC 59.189 55.000 0.00 0.00 0.00 4.46
878 985 1.838073 GACGGGGAAAGAGGAAGGCA 61.838 60.000 0.00 0.00 0.00 4.75
901 1008 1.816863 GACTGGCGTTGGTGGAGAGA 61.817 60.000 0.00 0.00 0.00 3.10
902 1009 1.374758 GACTGGCGTTGGTGGAGAG 60.375 63.158 0.00 0.00 0.00 3.20
903 1010 2.741092 GACTGGCGTTGGTGGAGA 59.259 61.111 0.00 0.00 0.00 3.71
904 1011 2.358737 GGACTGGCGTTGGTGGAG 60.359 66.667 0.00 0.00 0.00 3.86
951 1064 2.512515 GGAACCCTAGCTGCGCTG 60.513 66.667 9.73 10.04 40.10 5.18
955 1068 3.741830 GAGGCGGAACCCTAGCTGC 62.742 68.421 0.00 0.00 40.58 5.25
956 1069 2.501610 GAGGCGGAACCCTAGCTG 59.498 66.667 0.00 0.00 40.58 4.24
1172 1298 3.259751 GCGCGGATTCGGTACCAC 61.260 66.667 13.54 0.00 36.79 4.16
1173 1299 4.517815 GGCGCGGATTCGGTACCA 62.518 66.667 13.54 0.00 36.79 3.25
1240 1404 0.320050 CCAACCCCAAATTCCAACGG 59.680 55.000 0.00 0.00 0.00 4.44
1265 1469 0.108472 GGAACCCTAGAACCCGTTCG 60.108 60.000 2.06 0.00 43.97 3.95
1266 1470 1.206610 GAGGAACCCTAGAACCCGTTC 59.793 57.143 0.00 0.00 35.25 3.95
1267 1471 1.273759 GAGGAACCCTAGAACCCGTT 58.726 55.000 0.00 0.00 31.76 4.44
1268 1472 0.969409 CGAGGAACCCTAGAACCCGT 60.969 60.000 0.00 0.00 31.76 5.28
1269 1473 1.814527 CGAGGAACCCTAGAACCCG 59.185 63.158 0.00 0.00 31.76 5.28
1327 1549 1.448893 GTCGCCGGCAATTCTACCA 60.449 57.895 28.98 0.00 0.00 3.25
1358 1581 2.801631 GCGACCAGGCAGGAGCTAT 61.802 63.158 1.67 0.00 41.22 2.97
1381 1604 1.764854 ACACGACCAACCCCAGACT 60.765 57.895 0.00 0.00 0.00 3.24
1382 1605 1.597027 CACACGACCAACCCCAGAC 60.597 63.158 0.00 0.00 0.00 3.51
1383 1606 2.035237 GACACACGACCAACCCCAGA 62.035 60.000 0.00 0.00 0.00 3.86
1400 1623 2.165845 ACCACTATACAGAGTTGGCGAC 59.834 50.000 0.00 0.00 0.00 5.19
1493 1717 0.740868 GCACAGAATAGCAGGCGACA 60.741 55.000 0.00 0.00 0.00 4.35
1494 1718 1.756375 CGCACAGAATAGCAGGCGAC 61.756 60.000 0.00 0.00 46.65 5.19
1523 1747 4.283978 TGTACAGAAATCGACCTAAACCCA 59.716 41.667 0.00 0.00 0.00 4.51
1526 1750 7.829378 AGATTGTACAGAAATCGACCTAAAC 57.171 36.000 0.00 0.00 38.74 2.01
1551 1779 5.523916 CGAACAAGTAGTGCATAGGCTTATT 59.476 40.000 0.00 0.00 41.91 1.40
1553 1781 4.430007 CGAACAAGTAGTGCATAGGCTTA 58.570 43.478 0.00 0.00 41.91 3.09
1576 1807 6.500041 TGGTTAACTAATTCTGTTGTTGCAC 58.500 36.000 5.42 0.00 0.00 4.57
1593 1824 7.201670 GCCAAGTATGTAGGTATGTTGGTTAAC 60.202 40.741 0.00 0.00 36.22 2.01
1607 1840 6.663944 GACTTTTGTAGGCCAAGTATGTAG 57.336 41.667 5.01 0.00 33.75 2.74
1620 1853 2.159653 GCACGCATCTGGACTTTTGTAG 60.160 50.000 0.00 0.00 0.00 2.74
1656 1889 3.915437 AACGGCGAAATTTTGTCTGAT 57.085 38.095 16.62 0.00 0.00 2.90
1660 1893 2.553536 GCAAACGGCGAAATTTTGTC 57.446 45.000 16.62 3.56 33.57 3.18
1668 1902 2.135231 AACGAAGTAGCAAACGGCGAA 61.135 47.619 16.62 0.00 46.65 4.70
1670 1904 1.058695 CTAACGAAGTAGCAAACGGCG 59.941 52.381 4.80 4.80 46.65 6.46
1682 1916 2.030893 TGTGTACGACCACCTAACGAAG 60.031 50.000 0.00 0.00 34.35 3.79
1683 1917 1.952990 TGTGTACGACCACCTAACGAA 59.047 47.619 0.00 0.00 34.35 3.85
1684 1918 1.603456 TGTGTACGACCACCTAACGA 58.397 50.000 0.00 0.00 34.35 3.85
1685 1919 2.420628 TTGTGTACGACCACCTAACG 57.579 50.000 0.00 0.00 34.35 3.18
1689 1923 2.168936 TCTGTTTTGTGTACGACCACCT 59.831 45.455 0.00 0.00 34.35 4.00
1691 1925 3.450578 TCTCTGTTTTGTGTACGACCAC 58.549 45.455 0.00 0.00 35.86 4.16
1692 1926 3.804786 TCTCTGTTTTGTGTACGACCA 57.195 42.857 0.00 0.00 0.00 4.02
1696 1930 5.418310 AATGGTTCTCTGTTTTGTGTACG 57.582 39.130 0.00 0.00 0.00 3.67
1704 1938 5.930837 TGTCCAAAAATGGTTCTCTGTTT 57.069 34.783 0.00 0.00 0.00 2.83
1709 1943 5.852827 TCCAAATGTCCAAAAATGGTTCTC 58.147 37.500 0.00 0.00 0.00 2.87
1712 1946 4.141528 TGCTCCAAATGTCCAAAAATGGTT 60.142 37.500 0.00 0.00 0.00 3.67
1722 1956 2.046285 CCCGGTGCTCCAAATGTCC 61.046 63.158 0.00 0.00 0.00 4.02
1725 1959 0.748005 CTACCCCGGTGCTCCAAATG 60.748 60.000 0.00 0.00 0.00 2.32
1726 1960 1.607612 CTACCCCGGTGCTCCAAAT 59.392 57.895 0.00 0.00 0.00 2.32
2151 2683 6.016276 GTGTCTGGGTTTGTACAGAAATCAAT 60.016 38.462 0.00 0.00 44.53 2.57
2432 3179 7.765695 ACCAAATATATGAACCATGCTAAGG 57.234 36.000 0.00 0.00 0.00 2.69
2437 3184 7.660112 TGATGAACCAAATATATGAACCATGC 58.340 34.615 0.00 0.00 0.00 4.06
2482 3232 6.182507 TGGTGTTCTAGGTTCTGTTTATGT 57.817 37.500 0.00 0.00 0.00 2.29
2483 3233 8.964476 ATATGGTGTTCTAGGTTCTGTTTATG 57.036 34.615 0.00 0.00 0.00 1.90
2559 3490 4.142026 GCCAGCCCGTTTTATTAAGGATTT 60.142 41.667 0.00 0.00 0.00 2.17
2574 3511 0.962356 ATCAAAGAACTGCCAGCCCG 60.962 55.000 0.00 0.00 0.00 6.13
2602 3539 2.301346 CACATAAGGGGGAATGTCAGC 58.699 52.381 0.00 0.00 34.12 4.26
2744 3699 1.542108 GGGGAAAGAGCAGATGGATCG 60.542 57.143 0.00 0.00 36.90 3.69
2801 3758 6.119144 ACAACAATAGATAAACATCACGGC 57.881 37.500 0.00 0.00 0.00 5.68
2936 3901 5.401079 CGTAGGCACTAAACAAATTTTGGTG 59.599 40.000 13.42 11.59 45.48 4.17
2943 3908 5.562113 GCTTGAACGTAGGCACTAAACAAAT 60.562 40.000 0.00 0.00 45.48 2.32
2959 3924 3.976793 ATCATTATGCTGGCTTGAACG 57.023 42.857 0.00 0.00 0.00 3.95
2967 3935 8.668510 ACAGAGTAAGTAAATCATTATGCTGG 57.331 34.615 0.00 0.00 0.00 4.85
2986 3954 3.904339 ACCTGTGATTACCAGAACAGAGT 59.096 43.478 3.32 0.00 42.09 3.24
2987 3955 4.543590 ACCTGTGATTACCAGAACAGAG 57.456 45.455 3.32 0.00 42.09 3.35
2989 3957 4.641396 TGAACCTGTGATTACCAGAACAG 58.359 43.478 0.00 0.00 39.78 3.16
2990 3958 4.698201 TGAACCTGTGATTACCAGAACA 57.302 40.909 0.00 0.00 31.38 3.18
2991 3959 6.206498 GTTTTGAACCTGTGATTACCAGAAC 58.794 40.000 0.00 0.00 31.38 3.01
3094 4068 9.726438 ATAAACTACTGAGCAAGAACTAAACAT 57.274 29.630 0.00 0.00 0.00 2.71
3160 4138 1.066071 CCCATCCATGCAATGCAACAA 60.066 47.619 13.45 0.04 44.97 2.83
3184 4164 7.976135 ATTCATGCAGTTAGAAGATGTATCC 57.024 36.000 0.00 0.00 0.00 2.59
3247 4235 9.747898 AATTCCAAAGTGTATGGTAGATAACAA 57.252 29.630 0.00 0.00 39.09 2.83
3262 4254 4.522405 TGTGTATCACCCAATTCCAAAGTG 59.478 41.667 0.00 0.00 32.73 3.16
3301 4293 2.159338 CCGACTGCAATGAAAAGGATGG 60.159 50.000 0.00 0.00 0.00 3.51
3305 4297 3.855689 AATCCGACTGCAATGAAAAGG 57.144 42.857 0.00 0.00 0.00 3.11
4300 5427 8.198109 AGAGTACTCGACAAGCATACATATTTT 58.802 33.333 17.07 0.00 34.09 1.82
4476 5626 5.355910 TCGCCTTAAAAACATAGAATCCACC 59.644 40.000 0.00 0.00 0.00 4.61
4477 5627 6.255950 GTCGCCTTAAAAACATAGAATCCAC 58.744 40.000 0.00 0.00 0.00 4.02
4478 5628 5.064198 CGTCGCCTTAAAAACATAGAATCCA 59.936 40.000 0.00 0.00 0.00 3.41
4479 5629 5.499047 CGTCGCCTTAAAAACATAGAATCC 58.501 41.667 0.00 0.00 0.00 3.01
4480 5630 4.962151 GCGTCGCCTTAAAAACATAGAATC 59.038 41.667 5.75 0.00 0.00 2.52
4481 5631 4.201881 GGCGTCGCCTTAAAAACATAGAAT 60.202 41.667 28.98 0.00 46.69 2.40
4482 5632 3.125658 GGCGTCGCCTTAAAAACATAGAA 59.874 43.478 28.98 0.00 46.69 2.10
4483 5633 2.674357 GGCGTCGCCTTAAAAACATAGA 59.326 45.455 28.98 0.00 46.69 1.98
4484 5634 3.047613 GGCGTCGCCTTAAAAACATAG 57.952 47.619 28.98 0.00 46.69 2.23
4503 5653 1.408453 CCCTCCCTAAGGCGGTAAGG 61.408 65.000 0.00 0.00 44.71 2.69
4504 5654 1.408453 CCCCTCCCTAAGGCGGTAAG 61.408 65.000 0.00 0.00 44.71 2.34
4505 5655 1.383525 CCCCTCCCTAAGGCGGTAA 60.384 63.158 0.00 0.00 44.71 2.85
4506 5656 2.284493 CCCCTCCCTAAGGCGGTA 59.716 66.667 0.00 0.00 44.71 4.02
4507 5657 4.817909 CCCCCTCCCTAAGGCGGT 62.818 72.222 0.00 0.00 44.71 5.68
4549 5699 4.467084 TCCAAAGCGCCCGCCTAG 62.467 66.667 2.29 0.00 43.17 3.02
4550 5700 4.770874 GTCCAAAGCGCCCGCCTA 62.771 66.667 2.29 0.00 43.17 3.93
4558 5708 3.195698 GCCTAGGCGTCCAAAGCG 61.196 66.667 20.16 0.00 35.00 4.68
4576 5726 0.456142 GAAAATCGACCGCTTTGGGC 60.456 55.000 0.00 0.00 45.45 5.36
4577 5727 0.170339 GGAAAATCGACCGCTTTGGG 59.830 55.000 0.00 0.00 44.64 4.12
4578 5728 0.878416 TGGAAAATCGACCGCTTTGG 59.122 50.000 0.00 0.00 46.41 3.28
4579 5729 2.697431 TTGGAAAATCGACCGCTTTG 57.303 45.000 0.00 0.00 0.00 2.77
4580 5730 2.607038 GCTTTGGAAAATCGACCGCTTT 60.607 45.455 0.00 0.00 0.00 3.51
4581 5731 1.068541 GCTTTGGAAAATCGACCGCTT 60.069 47.619 0.00 0.00 0.00 4.68
4582 5732 0.521735 GCTTTGGAAAATCGACCGCT 59.478 50.000 0.00 0.00 0.00 5.52
4583 5733 0.793104 CGCTTTGGAAAATCGACCGC 60.793 55.000 0.00 0.00 0.00 5.68
4584 5734 0.179200 CCGCTTTGGAAAATCGACCG 60.179 55.000 0.00 0.00 42.00 4.79
4585 5735 1.161843 TCCGCTTTGGAAAATCGACC 58.838 50.000 0.00 0.00 46.38 4.79
4595 5745 4.803908 GCTCCCCCTCCGCTTTGG 62.804 72.222 0.00 0.00 40.09 3.28
4603 5753 4.516195 GTCGAAGCGCTCCCCCTC 62.516 72.222 12.06 2.47 0.00 4.30
4629 5779 0.174162 TAAAGCGTCCCTAAGGCGAC 59.826 55.000 0.00 0.00 43.57 5.19
4630 5780 0.896923 TTAAAGCGTCCCTAAGGCGA 59.103 50.000 0.00 0.00 43.57 5.54
4631 5781 1.729284 TTTAAAGCGTCCCTAAGGCG 58.271 50.000 0.00 0.00 43.57 5.52
4632 5782 3.253921 TGTTTTTAAAGCGTCCCTAAGGC 59.746 43.478 0.00 0.00 39.09 4.35
4633 5783 5.638596 ATGTTTTTAAAGCGTCCCTAAGG 57.361 39.130 0.00 0.00 0.00 2.69
4634 5784 6.183360 CCCTATGTTTTTAAAGCGTCCCTAAG 60.183 42.308 0.00 0.00 0.00 2.18
4635 5785 5.648960 CCCTATGTTTTTAAAGCGTCCCTAA 59.351 40.000 0.00 0.00 0.00 2.69
4636 5786 5.187687 CCCTATGTTTTTAAAGCGTCCCTA 58.812 41.667 0.00 0.00 0.00 3.53
4637 5787 4.014406 CCCTATGTTTTTAAAGCGTCCCT 58.986 43.478 0.00 0.00 0.00 4.20
4638 5788 3.760151 ACCCTATGTTTTTAAAGCGTCCC 59.240 43.478 0.00 0.00 0.00 4.46
4639 5789 4.380128 CCACCCTATGTTTTTAAAGCGTCC 60.380 45.833 0.00 0.00 0.00 4.79
4640 5790 4.456566 TCCACCCTATGTTTTTAAAGCGTC 59.543 41.667 0.00 0.00 0.00 5.19
4641 5791 4.400120 TCCACCCTATGTTTTTAAAGCGT 58.600 39.130 0.00 0.00 0.00 5.07
4642 5792 5.576447 ATCCACCCTATGTTTTTAAAGCG 57.424 39.130 0.00 0.00 0.00 4.68
4643 5793 7.382898 TCAAATCCACCCTATGTTTTTAAAGC 58.617 34.615 0.00 0.00 0.00 3.51
4644 5794 9.942850 AATCAAATCCACCCTATGTTTTTAAAG 57.057 29.630 0.00 0.00 0.00 1.85
4645 5795 9.717942 CAATCAAATCCACCCTATGTTTTTAAA 57.282 29.630 0.00 0.00 0.00 1.52
4646 5796 8.875168 ACAATCAAATCCACCCTATGTTTTTAA 58.125 29.630 0.00 0.00 0.00 1.52
4647 5797 8.429237 ACAATCAAATCCACCCTATGTTTTTA 57.571 30.769 0.00 0.00 0.00 1.52
4648 5798 7.315066 ACAATCAAATCCACCCTATGTTTTT 57.685 32.000 0.00 0.00 0.00 1.94
4649 5799 6.933514 ACAATCAAATCCACCCTATGTTTT 57.066 33.333 0.00 0.00 0.00 2.43
4650 5800 6.933514 AACAATCAAATCCACCCTATGTTT 57.066 33.333 0.00 0.00 0.00 2.83
4651 5801 6.933514 AAACAATCAAATCCACCCTATGTT 57.066 33.333 0.00 0.00 0.00 2.71
4652 5802 6.725834 AGAAAACAATCAAATCCACCCTATGT 59.274 34.615 0.00 0.00 0.00 2.29
4653 5803 7.037438 CAGAAAACAATCAAATCCACCCTATG 58.963 38.462 0.00 0.00 0.00 2.23
4654 5804 6.155049 CCAGAAAACAATCAAATCCACCCTAT 59.845 38.462 0.00 0.00 0.00 2.57
4655 5805 5.480073 CCAGAAAACAATCAAATCCACCCTA 59.520 40.000 0.00 0.00 0.00 3.53
4656 5806 4.284234 CCAGAAAACAATCAAATCCACCCT 59.716 41.667 0.00 0.00 0.00 4.34
4657 5807 4.040339 ACCAGAAAACAATCAAATCCACCC 59.960 41.667 0.00 0.00 0.00 4.61
4882 6034 3.304257 CCATGCAAACAGAACTGAGTCAC 60.304 47.826 8.87 0.00 0.00 3.67
4883 6035 2.880268 CCATGCAAACAGAACTGAGTCA 59.120 45.455 8.87 0.00 0.00 3.41
4884 6036 2.880890 ACCATGCAAACAGAACTGAGTC 59.119 45.455 8.87 0.00 0.00 3.36
4885 6037 2.936202 ACCATGCAAACAGAACTGAGT 58.064 42.857 8.87 0.00 0.00 3.41
4886 6038 3.635331 CAACCATGCAAACAGAACTGAG 58.365 45.455 8.87 0.06 0.00 3.35
4887 6039 3.713858 CAACCATGCAAACAGAACTGA 57.286 42.857 8.87 0.00 0.00 3.41
4909 6061 5.011023 TCTGAACAGTGAGAATACAGCAGAA 59.989 40.000 0.00 0.00 0.00 3.02
4923 6075 6.104665 TCTTCTATGCAGATTCTGAACAGTG 58.895 40.000 17.87 4.02 32.44 3.66
4964 6116 3.441572 AGCAACATTACCTCAACATCAGC 59.558 43.478 0.00 0.00 0.00 4.26
4965 6117 5.048504 ACAAGCAACATTACCTCAACATCAG 60.049 40.000 0.00 0.00 0.00 2.90
4976 6128 5.449113 CGAATTCGATGACAAGCAACATTAC 59.551 40.000 23.29 0.00 43.02 1.89
5008 6160 9.973450 AGAAGAAAAAGAAAGGAAAATAAGCTC 57.027 29.630 0.00 0.00 0.00 4.09
5026 6178 9.853177 AAATCCAAAGTAGAAGAGAGAAGAAAA 57.147 29.630 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.