Multiple sequence alignment - TraesCS5B01G261500

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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 TraesCS5B01G261500 chr5B 100.000 4685 0 0 1 4685 446011355 446006671 0.000000e+00 8652.0
1 TraesCS5B01G261500 chr5B 93.822 1214 53 11 953 2156 446411296 446412497 0.000000e+00 1807.0
2 TraesCS5B01G261500 chr5B 90.511 1233 48 21 953 2172 447207239 447206063 0.000000e+00 1565.0
3 TraesCS5B01G261500 chr5B 84.968 1244 103 55 2281 3490 447205619 447204426 0.000000e+00 1184.0
4 TraesCS5B01G261500 chr5B 86.876 1082 71 44 2159 3195 446412934 446413989 0.000000e+00 1146.0
5 TraesCS5B01G261500 chr5B 87.705 854 76 18 3847 4685 670996197 670997036 0.000000e+00 968.0
6 TraesCS5B01G261500 chr5B 83.168 707 90 17 4003 4685 656511258 656510557 1.850000e-173 619.0
7 TraesCS5B01G261500 chr5B 86.008 243 19 8 613 854 447207671 447207443 3.620000e-61 246.0
8 TraesCS5B01G261500 chr5B 90.683 161 11 1 53 213 447209318 447209162 1.320000e-50 211.0
9 TraesCS5B01G261500 chr5B 87.349 166 6 5 382 543 447208857 447208703 4.820000e-40 176.0
10 TraesCS5B01G261500 chr5B 87.037 162 12 5 11 172 446364966 446365118 1.730000e-39 174.0
11 TraesCS5B01G261500 chr5B 86.154 130 17 1 3716 3844 446829886 446830015 6.320000e-29 139.0
12 TraesCS5B01G261500 chr5B 78.899 218 23 12 3268 3482 446414033 446414230 4.920000e-25 126.0
13 TraesCS5B01G261500 chr5B 100.000 31 0 0 901 931 447207442 447207412 1.820000e-04 58.4
14 TraesCS5B01G261500 chr5D 87.621 2270 104 54 53 2209 374294317 374296522 0.000000e+00 2471.0
15 TraesCS5B01G261500 chr5D 86.717 1182 103 32 2279 3444 374296607 374297750 0.000000e+00 1264.0
16 TraesCS5B01G261500 chr5D 87.307 323 33 7 4369 4685 126517332 126517652 3.450000e-96 363.0
17 TraesCS5B01G261500 chr5D 96.875 32 1 0 2240 2271 374296523 374296554 2.000000e-03 54.7
18 TraesCS5B01G261500 chr5A 90.861 1499 69 32 723 2174 476072448 476073925 0.000000e+00 1947.0
19 TraesCS5B01G261500 chr5A 87.213 915 69 22 2281 3191 476074005 476074875 0.000000e+00 998.0
20 TraesCS5B01G261500 chr5A 84.211 380 30 12 3253 3624 476075017 476075374 4.490000e-90 342.0
21 TraesCS5B01G261500 chr5A 79.852 541 40 29 53 588 476071845 476072321 9.720000e-87 331.0
22 TraesCS5B01G261500 chr5A 93.836 146 8 1 3704 3848 476075860 476076005 7.890000e-53 219.0
23 TraesCS5B01G261500 chr5A 91.724 145 7 2 439 583 476080229 476080368 3.700000e-46 196.0
24 TraesCS5B01G261500 chr5A 80.556 180 24 5 613 781 476080467 476080646 1.370000e-25 128.0
25 TraesCS5B01G261500 chr5A 93.333 75 3 1 289 361 476080114 476080188 4.960000e-20 110.0
26 TraesCS5B01G261500 chr5A 96.491 57 2 0 613 669 476072377 476072433 1.390000e-15 95.3
27 TraesCS5B01G261500 chr5A 100.000 29 0 0 587 615 476080430 476080458 2.000000e-03 54.7
28 TraesCS5B01G261500 chr3D 90.555 847 54 14 3848 4675 584572379 584573218 0.000000e+00 1098.0
29 TraesCS5B01G261500 chr3D 84.848 1056 123 24 1110 2145 174455348 174456386 0.000000e+00 1029.0
30 TraesCS5B01G261500 chr3D 93.823 599 24 6 1626 2222 584112500 584111913 0.000000e+00 889.0
31 TraesCS5B01G261500 chr3D 81.672 873 128 27 2324 3190 174456538 174457384 0.000000e+00 697.0
32 TraesCS5B01G261500 chr3A 85.014 1061 116 26 1110 2145 213256365 213257407 0.000000e+00 1038.0
33 TraesCS5B01G261500 chr3A 92.727 55 4 0 2324 2378 213257547 213257601 3.890000e-11 80.5
34 TraesCS5B01G261500 chr3B 86.768 854 85 17 3848 4685 228823304 228824145 0.000000e+00 926.0
35 TraesCS5B01G261500 chr3B 81.787 873 125 31 2324 3190 252958103 252958947 0.000000e+00 701.0
36 TraesCS5B01G261500 chr3B 87.548 522 53 8 1646 2157 252957445 252957964 1.120000e-165 593.0
37 TraesCS5B01G261500 chr3B 84.342 479 60 10 1110 1586 252956902 252957367 5.530000e-124 455.0
38 TraesCS5B01G261500 chr4B 86.300 854 83 23 3848 4685 619359166 619360001 0.000000e+00 898.0
39 TraesCS5B01G261500 chr4B 93.103 58 4 0 3848 3905 638996647 638996590 8.350000e-13 86.1
40 TraesCS5B01G261500 chr2B 87.535 722 71 12 3850 4561 715970055 715969343 0.000000e+00 817.0
41 TraesCS5B01G261500 chr7A 81.316 942 133 36 1252 2162 221741695 221740766 0.000000e+00 725.0
42 TraesCS5B01G261500 chr7B 86.322 541 54 8 4155 4685 553430689 553431219 5.260000e-159 571.0
43 TraesCS5B01G261500 chr7B 90.566 318 28 2 4370 4685 426840475 426840158 2.020000e-113 420.0
44 TraesCS5B01G261500 chr2D 81.778 675 71 27 3848 4498 536992490 536991844 6.950000e-143 518.0
45 TraesCS5B01G261500 chr2D 87.850 321 34 4 4369 4685 536991845 536991526 5.730000e-99 372.0
46 TraesCS5B01G261500 chr2D 91.379 58 5 0 3848 3905 584850897 584850840 3.890000e-11 80.5
47 TraesCS5B01G261500 chr4A 81.157 674 75 29 3847 4498 611230619 611229976 1.170000e-135 494.0
48 TraesCS5B01G261500 chr4A 80.981 673 74 29 3848 4498 583769144 583768504 7.050000e-133 484.0
49 TraesCS5B01G261500 chr4A 88.820 322 30 6 4369 4685 611229977 611229657 1.580000e-104 390.0
50 TraesCS5B01G261500 chr7D 86.095 338 38 8 1252 1583 208656645 208656311 5.770000e-94 355.0
51 TraesCS5B01G261500 chr1A 76.812 345 44 20 3848 4183 359915311 359915628 1.350000e-35 161.0
52 TraesCS5B01G261500 chr1B 90.164 61 5 1 3848 3907 630571850 630571790 1.400000e-10 78.7
53 TraesCS5B01G261500 chr1D 88.136 59 7 0 3847 3905 334049862 334049804 2.340000e-08 71.3


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 TraesCS5B01G261500 chr5B 446006671 446011355 4684 True 8652.000000 8652 100.000000 1 4685 1 chr5B.!!$R1 4684
1 TraesCS5B01G261500 chr5B 446411296 446414230 2934 False 1026.333333 1807 86.532333 953 3482 3 chr5B.!!$F4 2529
2 TraesCS5B01G261500 chr5B 670996197 670997036 839 False 968.000000 968 87.705000 3847 4685 1 chr5B.!!$F3 838
3 TraesCS5B01G261500 chr5B 656510557 656511258 701 True 619.000000 619 83.168000 4003 4685 1 chr5B.!!$R2 682
4 TraesCS5B01G261500 chr5B 447204426 447209318 4892 True 573.400000 1565 89.919833 53 3490 6 chr5B.!!$R3 3437
5 TraesCS5B01G261500 chr5D 374294317 374297750 3433 False 1263.233333 2471 90.404333 53 3444 3 chr5D.!!$F2 3391
6 TraesCS5B01G261500 chr5A 476071845 476076005 4160 False 655.383333 1947 88.744000 53 3848 6 chr5A.!!$F1 3795
7 TraesCS5B01G261500 chr3D 584572379 584573218 839 False 1098.000000 1098 90.555000 3848 4675 1 chr3D.!!$F1 827
8 TraesCS5B01G261500 chr3D 584111913 584112500 587 True 889.000000 889 93.823000 1626 2222 1 chr3D.!!$R1 596
9 TraesCS5B01G261500 chr3D 174455348 174457384 2036 False 863.000000 1029 83.260000 1110 3190 2 chr3D.!!$F2 2080
10 TraesCS5B01G261500 chr3A 213256365 213257601 1236 False 559.250000 1038 88.870500 1110 2378 2 chr3A.!!$F1 1268
11 TraesCS5B01G261500 chr3B 228823304 228824145 841 False 926.000000 926 86.768000 3848 4685 1 chr3B.!!$F1 837
12 TraesCS5B01G261500 chr3B 252956902 252958947 2045 False 583.000000 701 84.559000 1110 3190 3 chr3B.!!$F2 2080
13 TraesCS5B01G261500 chr4B 619359166 619360001 835 False 898.000000 898 86.300000 3848 4685 1 chr4B.!!$F1 837
14 TraesCS5B01G261500 chr2B 715969343 715970055 712 True 817.000000 817 87.535000 3850 4561 1 chr2B.!!$R1 711
15 TraesCS5B01G261500 chr7A 221740766 221741695 929 True 725.000000 725 81.316000 1252 2162 1 chr7A.!!$R1 910
16 TraesCS5B01G261500 chr7B 553430689 553431219 530 False 571.000000 571 86.322000 4155 4685 1 chr7B.!!$F1 530
17 TraesCS5B01G261500 chr2D 536991526 536992490 964 True 445.000000 518 84.814000 3848 4685 2 chr2D.!!$R2 837
18 TraesCS5B01G261500 chr4A 583768504 583769144 640 True 484.000000 484 80.981000 3848 4498 1 chr4A.!!$R1 650
19 TraesCS5B01G261500 chr4A 611229657 611230619 962 True 442.000000 494 84.988500 3847 4685 2 chr4A.!!$R2 838

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
362 553 0.318360 TTGCTCGATCGTGTTGACGT 60.318 50.000 15.94 0.0 46.2 4.34 F
762 1936 0.391597 TCGATTTGGGGATAGCGGTC 59.608 55.000 0.00 0.0 0.0 4.79 F
2181 4058 1.064758 TCCCTCTCTCTCTCTGCTCAC 60.065 57.143 0.00 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1623 3008 0.713883 CCGCACAATGTCAGTACGAC 59.286 55.0 9.87 9.87 45.61 4.34 R
2462 4792 0.316204 CAGGCCCTGCAAAAGAGTTG 59.684 55.0 0.00 0.00 0.00 3.16 R
3736 6600 0.161024 GACGTTGTGCGACTTGCTAC 59.839 55.0 0.00 0.00 46.63 3.58 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
69 70 2.420568 GGATCGGCCACTCGTACCA 61.421 63.158 2.24 0.00 36.34 3.25
114 115 2.352805 CAGGGACCAACTCCAGGC 59.647 66.667 0.00 0.00 41.63 4.85
122 123 2.972505 AACTCCAGGCAACGCACG 60.973 61.111 0.00 0.00 46.39 5.34
196 197 1.227527 CGGGCGTGCATTGATAGGA 60.228 57.895 0.00 0.00 0.00 2.94
203 204 3.785505 GCGTGCATTGATAGGAAAACGAG 60.786 47.826 0.00 0.00 31.76 4.18
215 216 5.080969 AGGAAAACGAGATCGATTTACCA 57.919 39.130 14.33 0.00 43.27 3.25
300 483 1.671379 GCAGGACACGGGGAGAAAC 60.671 63.158 0.00 0.00 0.00 2.78
362 553 0.318360 TTGCTCGATCGTGTTGACGT 60.318 50.000 15.94 0.00 46.20 4.34
363 554 1.001745 TGCTCGATCGTGTTGACGTG 61.002 55.000 15.94 0.00 46.20 4.49
364 555 1.696644 CTCGATCGTGTTGACGTGC 59.303 57.895 15.94 0.00 46.20 5.34
365 556 1.987608 CTCGATCGTGTTGACGTGCG 61.988 60.000 15.94 0.00 46.20 5.34
366 557 2.093983 GATCGTGTTGACGTGCGC 59.906 61.111 0.00 0.00 46.20 6.09
367 558 2.355837 ATCGTGTTGACGTGCGCT 60.356 55.556 9.73 0.00 46.20 5.92
368 559 1.886861 GATCGTGTTGACGTGCGCTT 61.887 55.000 9.73 0.00 46.20 4.68
369 560 0.665068 ATCGTGTTGACGTGCGCTTA 60.665 50.000 9.73 0.00 46.20 3.09
370 561 1.127817 CGTGTTGACGTGCGCTTAG 59.872 57.895 9.73 1.91 40.91 2.18
371 562 1.545614 CGTGTTGACGTGCGCTTAGT 61.546 55.000 9.73 5.74 40.91 2.24
372 563 1.411394 GTGTTGACGTGCGCTTAGTA 58.589 50.000 9.73 0.00 0.00 1.82
373 564 1.990563 GTGTTGACGTGCGCTTAGTAT 59.009 47.619 9.73 0.00 0.00 2.12
374 565 2.410730 GTGTTGACGTGCGCTTAGTATT 59.589 45.455 9.73 0.00 0.00 1.89
375 566 3.061322 TGTTGACGTGCGCTTAGTATTT 58.939 40.909 9.73 0.00 0.00 1.40
376 567 3.495377 TGTTGACGTGCGCTTAGTATTTT 59.505 39.130 9.73 0.00 0.00 1.82
377 568 4.024725 TGTTGACGTGCGCTTAGTATTTTT 60.025 37.500 9.73 0.00 0.00 1.94
378 569 4.060288 TGACGTGCGCTTAGTATTTTTG 57.940 40.909 9.73 0.00 0.00 2.44
379 570 3.495377 TGACGTGCGCTTAGTATTTTTGT 59.505 39.130 9.73 0.00 0.00 2.83
380 571 4.685165 TGACGTGCGCTTAGTATTTTTGTA 59.315 37.500 9.73 0.00 0.00 2.41
381 572 5.349270 TGACGTGCGCTTAGTATTTTTGTAT 59.651 36.000 9.73 0.00 0.00 2.29
382 573 6.128499 TGACGTGCGCTTAGTATTTTTGTATT 60.128 34.615 9.73 0.00 0.00 1.89
383 574 6.019152 ACGTGCGCTTAGTATTTTTGTATTG 58.981 36.000 9.73 0.00 0.00 1.90
384 575 6.128499 ACGTGCGCTTAGTATTTTTGTATTGA 60.128 34.615 9.73 0.00 0.00 2.57
385 576 6.192137 CGTGCGCTTAGTATTTTTGTATTGAC 59.808 38.462 9.73 0.00 0.00 3.18
386 577 6.468000 GTGCGCTTAGTATTTTTGTATTGACC 59.532 38.462 9.73 0.00 0.00 4.02
387 578 6.149640 TGCGCTTAGTATTTTTGTATTGACCA 59.850 34.615 9.73 0.00 0.00 4.02
505 702 4.778415 CAGGTCGCCACGTCCGAG 62.778 72.222 7.97 0.00 39.76 4.63
678 1851 9.840427 TCATTACTACAATCTTTTTAAAGCAGC 57.160 29.630 0.00 0.00 35.99 5.25
716 1890 8.530269 TTTTTAGGAAGATCAGTACGTCTTTC 57.470 34.615 10.95 9.57 34.97 2.62
759 1933 2.240493 ACTTCGATTTGGGGATAGCG 57.760 50.000 0.00 0.00 0.00 4.26
760 1934 1.202651 ACTTCGATTTGGGGATAGCGG 60.203 52.381 0.00 0.00 0.00 5.52
762 1936 0.391597 TCGATTTGGGGATAGCGGTC 59.608 55.000 0.00 0.00 0.00 4.79
780 1954 3.606687 GGTCAAAATGGTCACGTAGGAT 58.393 45.455 0.00 0.00 0.00 3.24
789 1963 9.457436 AAAATGGTCACGTAGGATAAGTAATTT 57.543 29.630 0.00 0.00 30.36 1.82
790 1964 8.433421 AATGGTCACGTAGGATAAGTAATTTG 57.567 34.615 0.00 0.00 30.36 2.32
791 1965 7.172868 TGGTCACGTAGGATAAGTAATTTGA 57.827 36.000 0.00 0.00 30.36 2.69
792 1966 7.788026 TGGTCACGTAGGATAAGTAATTTGAT 58.212 34.615 0.00 0.00 30.36 2.57
832 2006 2.171725 GTAATCTGACGTGGCGGCC 61.172 63.158 13.32 13.32 31.60 6.13
876 2050 1.404851 GCTTCTCTAGCTTGGTCGCTT 60.405 52.381 0.00 0.00 46.77 4.68
898 2072 2.281761 ACTTGGACCTGCCGCTTG 60.282 61.111 0.00 0.00 40.66 4.01
899 2073 3.741476 CTTGGACCTGCCGCTTGC 61.741 66.667 0.00 0.00 40.66 4.01
951 2310 6.090358 CGAACAGTAATAAATCACGAGGTGTT 59.910 38.462 0.00 0.00 34.79 3.32
1068 2433 1.452651 CGGCTGGGTGCAGATCATT 60.453 57.895 0.00 0.00 45.15 2.57
1112 2482 4.681942 CCATAACGATCTCTTGGATTCGAC 59.318 45.833 0.00 0.00 34.33 4.20
1113 2483 2.873133 ACGATCTCTTGGATTCGACC 57.127 50.000 0.00 0.00 34.33 4.79
1114 2484 1.065701 ACGATCTCTTGGATTCGACCG 59.934 52.381 0.00 0.00 34.33 4.79
1115 2485 1.600663 CGATCTCTTGGATTCGACCGG 60.601 57.143 0.00 0.00 34.33 5.28
1203 2573 2.261361 CCCTGCACGACATCACGA 59.739 61.111 0.00 0.00 37.03 4.35
1322 2692 4.212913 ATCTGCGCGCTGGTCGAT 62.213 61.111 33.04 21.63 41.67 3.59
1620 3005 1.351430 CCGCGCGACTGATTCTTTCA 61.351 55.000 34.63 0.00 0.00 2.69
1622 3007 1.136363 CGCGCGACTGATTCTTTCAAA 60.136 47.619 28.94 0.00 32.78 2.69
1623 3008 2.499896 GCGCGACTGATTCTTTCAAAG 58.500 47.619 12.10 0.00 32.78 2.77
2174 4051 2.092429 TCTTGCTCTCCCTCTCTCTCTC 60.092 54.545 0.00 0.00 0.00 3.20
2176 4053 1.212688 TGCTCTCCCTCTCTCTCTCTG 59.787 57.143 0.00 0.00 0.00 3.35
2177 4054 1.972872 CTCTCCCTCTCTCTCTCTGC 58.027 60.000 0.00 0.00 0.00 4.26
2178 4055 1.492176 CTCTCCCTCTCTCTCTCTGCT 59.508 57.143 0.00 0.00 0.00 4.24
2179 4056 1.490490 TCTCCCTCTCTCTCTCTGCTC 59.510 57.143 0.00 0.00 0.00 4.26
2180 4057 1.212688 CTCCCTCTCTCTCTCTGCTCA 59.787 57.143 0.00 0.00 0.00 4.26
2181 4058 1.064758 TCCCTCTCTCTCTCTGCTCAC 60.065 57.143 0.00 0.00 0.00 3.51
2203 4383 5.122396 CACTTAGGAAAATGACTGGTGTAGC 59.878 44.000 0.00 0.00 0.00 3.58
2209 4389 5.048083 GGAAAATGACTGGTGTAGCATTCAA 60.048 40.000 7.94 0.00 34.36 2.69
2210 4390 6.350445 GGAAAATGACTGGTGTAGCATTCAAT 60.350 38.462 7.94 0.00 34.36 2.57
2211 4391 7.148086 GGAAAATGACTGGTGTAGCATTCAATA 60.148 37.037 7.94 0.00 34.36 1.90
2212 4392 7.886629 AAATGACTGGTGTAGCATTCAATAT 57.113 32.000 7.94 0.00 34.36 1.28
2213 4393 6.872628 ATGACTGGTGTAGCATTCAATATG 57.127 37.500 7.94 0.00 0.00 1.78
2214 4394 5.744171 TGACTGGTGTAGCATTCAATATGT 58.256 37.500 2.24 0.00 0.00 2.29
2215 4395 6.179756 TGACTGGTGTAGCATTCAATATGTT 58.820 36.000 2.24 0.00 0.00 2.71
2216 4396 6.316140 TGACTGGTGTAGCATTCAATATGTTC 59.684 38.462 2.24 0.00 0.00 3.18
2217 4397 6.418101 ACTGGTGTAGCATTCAATATGTTCT 58.582 36.000 0.00 0.00 0.00 3.01
2218 4398 6.886459 ACTGGTGTAGCATTCAATATGTTCTT 59.114 34.615 0.00 0.00 0.00 2.52
2219 4399 7.087409 TGGTGTAGCATTCAATATGTTCTTG 57.913 36.000 0.00 0.00 0.00 3.02
2220 4400 6.658816 TGGTGTAGCATTCAATATGTTCTTGT 59.341 34.615 0.00 0.00 0.00 3.16
2221 4401 6.968904 GGTGTAGCATTCAATATGTTCTTGTG 59.031 38.462 0.00 0.00 0.00 3.33
2222 4402 7.148255 GGTGTAGCATTCAATATGTTCTTGTGA 60.148 37.037 0.00 0.00 0.00 3.58
2223 4403 8.400947 GTGTAGCATTCAATATGTTCTTGTGAT 58.599 33.333 0.00 0.00 0.00 3.06
2224 4404 8.615211 TGTAGCATTCAATATGTTCTTGTGATC 58.385 33.333 0.00 0.00 0.00 2.92
2225 4405 7.876936 AGCATTCAATATGTTCTTGTGATCT 57.123 32.000 0.00 0.00 0.00 2.75
2226 4406 7.704271 AGCATTCAATATGTTCTTGTGATCTG 58.296 34.615 0.00 0.00 0.00 2.90
2227 4407 6.916387 GCATTCAATATGTTCTTGTGATCTGG 59.084 38.462 0.00 0.00 0.00 3.86
2228 4408 6.441093 TTCAATATGTTCTTGTGATCTGGC 57.559 37.500 0.00 0.00 0.00 4.85
2229 4409 5.748402 TCAATATGTTCTTGTGATCTGGCT 58.252 37.500 0.00 0.00 0.00 4.75
2230 4410 6.888105 TCAATATGTTCTTGTGATCTGGCTA 58.112 36.000 0.00 0.00 0.00 3.93
2231 4411 6.988580 TCAATATGTTCTTGTGATCTGGCTAG 59.011 38.462 0.00 0.00 0.00 3.42
2272 4501 5.598005 ACTCTTGGTCAAACATTTCATGGAA 59.402 36.000 0.00 0.00 33.60 3.53
2273 4502 5.841810 TCTTGGTCAAACATTTCATGGAAC 58.158 37.500 0.00 0.00 33.60 3.62
2274 4503 4.235939 TGGTCAAACATTTCATGGAACG 57.764 40.909 0.00 0.00 33.60 3.95
2305 4607 5.511545 GCGTTTAGTTATCTGATGGGGATCT 60.512 44.000 0.00 0.00 0.00 2.75
2306 4608 6.159988 CGTTTAGTTATCTGATGGGGATCTC 58.840 44.000 0.00 0.00 0.00 2.75
2307 4609 6.468543 GTTTAGTTATCTGATGGGGATCTCC 58.531 44.000 3.99 3.99 0.00 3.71
2308 4610 4.219392 AGTTATCTGATGGGGATCTCCA 57.781 45.455 18.95 18.95 41.60 3.86
2320 4634 4.470664 TGGGGATCTCCATTTTTGATTTGG 59.529 41.667 11.36 0.00 37.91 3.28
2379 4693 2.691984 CGTTTTCGGGGTAAGTTTGG 57.308 50.000 0.00 0.00 39.94 3.28
2380 4694 1.948834 CGTTTTCGGGGTAAGTTTGGT 59.051 47.619 0.00 0.00 39.94 3.67
2381 4695 2.358582 CGTTTTCGGGGTAAGTTTGGTT 59.641 45.455 0.00 0.00 39.94 3.67
2382 4696 3.708890 GTTTTCGGGGTAAGTTTGGTTG 58.291 45.455 0.00 0.00 0.00 3.77
2393 4707 7.438564 GGGTAAGTTTGGTTGTACATTTTCAT 58.561 34.615 0.00 0.00 0.00 2.57
2462 4792 3.067742 CAGAACTGAATGGATCAATGGCC 59.932 47.826 0.00 0.00 37.67 5.36
2465 4795 2.762327 ACTGAATGGATCAATGGCCAAC 59.238 45.455 10.96 0.00 37.67 3.77
2466 4796 3.028850 CTGAATGGATCAATGGCCAACT 58.971 45.455 10.96 0.00 37.67 3.16
2467 4797 3.025978 TGAATGGATCAATGGCCAACTC 58.974 45.455 10.96 3.93 37.78 3.01
2487 4819 1.345415 CTTTTGCAGGGCCTGATTGTT 59.655 47.619 37.07 0.00 32.44 2.83
2490 4822 0.112995 TGCAGGGCCTGATTGTTCTT 59.887 50.000 37.07 0.00 32.44 2.52
2610 4942 7.720515 AGAATCATCTCCTCTGATCATTTTTCC 59.279 37.037 0.00 0.00 32.22 3.13
2628 4960 1.833630 TCCGAGACAATCAATCTGCCT 59.166 47.619 0.00 0.00 0.00 4.75
2645 4977 2.200067 GCCTCATGAACTCACTCGATG 58.800 52.381 0.00 0.00 0.00 3.84
2646 4978 2.159184 GCCTCATGAACTCACTCGATGA 60.159 50.000 0.00 0.00 35.45 2.92
2647 4979 3.492309 GCCTCATGAACTCACTCGATGAT 60.492 47.826 0.00 0.00 36.48 2.45
2780 5113 2.393768 GCAGTGGCACATCGTCCTG 61.394 63.158 21.41 8.41 44.52 3.86
2843 5176 2.990479 GGCCTGACGGACATCCTT 59.010 61.111 0.00 0.00 38.64 3.36
3174 5507 3.374402 CGGCTCTCACGGTCCTGT 61.374 66.667 0.00 0.00 0.00 4.00
3185 5518 2.193536 GGTCCTGTTGCCAACGCTT 61.194 57.895 2.68 0.00 35.36 4.68
3198 5531 3.139077 CCAACGCTTGGTAAGTTCTCTT 58.861 45.455 8.17 0.00 45.93 2.85
3200 5533 3.746045 ACGCTTGGTAAGTTCTCTTCA 57.254 42.857 0.00 0.00 35.36 3.02
3203 5536 3.997021 CGCTTGGTAAGTTCTCTTCATGT 59.003 43.478 0.00 0.00 35.36 3.21
3204 5537 4.143030 CGCTTGGTAAGTTCTCTTCATGTG 60.143 45.833 0.00 0.00 35.36 3.21
3205 5538 4.997395 GCTTGGTAAGTTCTCTTCATGTGA 59.003 41.667 0.00 0.00 35.36 3.58
3206 5539 5.645497 GCTTGGTAAGTTCTCTTCATGTGAT 59.355 40.000 0.00 0.00 35.36 3.06
3207 5540 6.402983 GCTTGGTAAGTTCTCTTCATGTGATG 60.403 42.308 0.00 0.00 35.36 3.07
3208 5541 6.358974 TGGTAAGTTCTCTTCATGTGATGA 57.641 37.500 0.00 0.00 37.55 2.92
3209 5542 6.401394 TGGTAAGTTCTCTTCATGTGATGAG 58.599 40.000 15.86 15.86 43.61 2.90
3230 5599 9.650539 GATGAGAAAATAATCTGCAGAGCTATA 57.349 33.333 22.96 12.36 0.00 1.31
3232 5601 8.646004 TGAGAAAATAATCTGCAGAGCTATACT 58.354 33.333 22.96 17.67 0.00 2.12
3234 5603 9.921637 AGAAAATAATCTGCAGAGCTATACTAC 57.078 33.333 22.96 12.30 0.00 2.73
3235 5604 9.921637 GAAAATAATCTGCAGAGCTATACTACT 57.078 33.333 22.96 0.00 0.00 2.57
3237 5606 8.877864 AATAATCTGCAGAGCTATACTACTCT 57.122 34.615 22.96 0.00 44.06 3.24
3239 5608 7.595819 AATCTGCAGAGCTATACTACTCTTT 57.404 36.000 22.96 3.06 41.31 2.52
3240 5609 8.698973 AATCTGCAGAGCTATACTACTCTTTA 57.301 34.615 22.96 0.00 41.31 1.85
3241 5610 8.877864 ATCTGCAGAGCTATACTACTCTTTAT 57.122 34.615 22.96 0.00 41.31 1.40
3260 5673 8.250143 TCTTTATATACTCTGGCACTGAATCA 57.750 34.615 0.00 0.00 35.46 2.57
3265 5678 2.840038 ACTCTGGCACTGAATCATGGTA 59.160 45.455 0.00 0.00 35.46 3.25
3266 5679 3.118482 ACTCTGGCACTGAATCATGGTAG 60.118 47.826 0.00 0.00 35.46 3.18
3277 5690 7.011202 CACTGAATCATGGTAGTTCTCTTGATG 59.989 40.741 0.00 0.00 31.18 3.07
3308 5721 1.523154 TTGCGGTCTTTGGCATGGAC 61.523 55.000 10.58 10.58 39.21 4.02
3345 5764 2.293122 CGTGCTGGAAATTCAGTTGGAA 59.707 45.455 0.00 0.00 40.46 3.53
3364 5793 7.596248 AGTTGGAATTTTTGAACATCTCAATCG 59.404 33.333 0.00 0.00 43.64 3.34
3365 5794 5.863397 TGGAATTTTTGAACATCTCAATCGC 59.137 36.000 0.00 0.00 43.64 4.58
3373 5802 3.090952 ACATCTCAATCGCTAGACTGC 57.909 47.619 0.00 0.00 0.00 4.40
3378 5807 2.359214 CTCAATCGCTAGACTGCAGGTA 59.641 50.000 19.93 8.26 0.00 3.08
3379 5808 2.359214 TCAATCGCTAGACTGCAGGTAG 59.641 50.000 19.93 18.24 0.00 3.18
3380 5809 1.323412 ATCGCTAGACTGCAGGTAGG 58.677 55.000 19.93 11.73 0.00 3.18
3381 5810 0.034380 TCGCTAGACTGCAGGTAGGT 60.034 55.000 19.93 0.00 0.00 3.08
3382 5811 0.818296 CGCTAGACTGCAGGTAGGTT 59.182 55.000 19.93 0.00 0.00 3.50
3383 5812 2.022195 CGCTAGACTGCAGGTAGGTTA 58.978 52.381 19.93 0.27 0.00 2.85
3384 5813 2.426024 CGCTAGACTGCAGGTAGGTTAA 59.574 50.000 19.93 0.00 0.00 2.01
3385 5814 3.068307 CGCTAGACTGCAGGTAGGTTAAT 59.932 47.826 19.93 0.00 0.00 1.40
3386 5815 4.277672 CGCTAGACTGCAGGTAGGTTAATA 59.722 45.833 19.93 0.00 0.00 0.98
3387 5816 5.530712 GCTAGACTGCAGGTAGGTTAATAC 58.469 45.833 19.93 0.68 0.00 1.89
3388 5817 4.650754 AGACTGCAGGTAGGTTAATACG 57.349 45.455 19.93 0.00 0.00 3.06
3391 5820 3.181493 ACTGCAGGTAGGTTAATACGACG 60.181 47.826 19.93 0.00 0.00 5.12
3411 5843 4.916183 ACGAGTAGTGTTTAGTAGGAGGT 58.084 43.478 0.00 0.00 0.00 3.85
3461 5893 1.131126 GTGTCATTGCCTCATGAACGG 59.869 52.381 0.00 0.00 0.00 4.44
3482 5917 5.104277 ACGGTATGGGGTCATATTCTTTTCA 60.104 40.000 0.00 0.00 38.06 2.69
3490 5925 8.429641 TGGGGTCATATTCTTTTCAGTATCTAC 58.570 37.037 0.00 0.00 0.00 2.59
3491 5926 8.652290 GGGGTCATATTCTTTTCAGTATCTACT 58.348 37.037 0.00 0.00 36.90 2.57
3511 5948 4.296690 ACTACCTAATTTGTATCGAGCGC 58.703 43.478 0.00 0.00 0.00 5.92
3533 5970 6.349611 GCGCTTCCATTTCCATGTGAATATAT 60.350 38.462 0.00 0.00 31.67 0.86
3534 5971 7.148255 GCGCTTCCATTTCCATGTGAATATATA 60.148 37.037 0.00 0.00 31.67 0.86
3535 5972 8.896744 CGCTTCCATTTCCATGTGAATATATAT 58.103 33.333 0.00 0.00 31.67 0.86
3558 5995 2.032550 CCGAAATCATCTGGTGCACATC 59.967 50.000 20.43 2.20 0.00 3.06
3560 5997 4.122046 CGAAATCATCTGGTGCACATCTA 58.878 43.478 20.43 0.63 0.00 1.98
3561 5998 4.571984 CGAAATCATCTGGTGCACATCTAA 59.428 41.667 20.43 0.00 0.00 2.10
3582 6019 2.733956 TGAAACCACAAGGCAGAGTTT 58.266 42.857 0.00 0.00 39.06 2.66
3587 6024 1.542915 CCACAAGGCAGAGTTTGGATG 59.457 52.381 0.00 0.00 0.00 3.51
3588 6025 2.233271 CACAAGGCAGAGTTTGGATGT 58.767 47.619 0.00 0.00 0.00 3.06
3589 6026 3.411446 CACAAGGCAGAGTTTGGATGTA 58.589 45.455 0.00 0.00 0.00 2.29
3590 6027 3.438087 CACAAGGCAGAGTTTGGATGTAG 59.562 47.826 0.00 0.00 0.00 2.74
3591 6028 3.012518 CAAGGCAGAGTTTGGATGTAGG 58.987 50.000 0.00 0.00 0.00 3.18
3592 6029 2.551270 AGGCAGAGTTTGGATGTAGGA 58.449 47.619 0.00 0.00 0.00 2.94
3607 6044 1.067212 GTAGGAGTACATCACCGGCAG 59.933 57.143 0.00 0.00 32.04 4.85
3613 6050 0.246360 TACATCACCGGCAGACTGTG 59.754 55.000 0.00 0.00 0.00 3.66
3614 6051 1.004560 CATCACCGGCAGACTGTGT 60.005 57.895 0.00 0.00 0.00 3.72
3644 6508 8.835734 TGGGTTATATATAAACAGCTCCATGAT 58.164 33.333 19.70 0.00 31.62 2.45
3645 6509 9.113838 GGGTTATATATAAACAGCTCCATGATG 57.886 37.037 19.70 0.00 38.19 3.07
3650 6514 9.833917 ATATATAAACAGCTCCATGATGATGAG 57.166 33.333 9.48 0.00 35.75 2.90
3651 6515 2.257691 ACAGCTCCATGATGATGAGC 57.742 50.000 13.59 13.59 35.75 4.26
3654 6518 3.326880 ACAGCTCCATGATGATGAGCATA 59.673 43.478 20.53 0.00 37.34 3.14
3655 6519 4.019231 ACAGCTCCATGATGATGAGCATAT 60.019 41.667 20.53 7.24 37.34 1.78
3656 6520 4.572795 CAGCTCCATGATGATGAGCATATC 59.427 45.833 20.53 0.00 37.34 1.63
3660 6524 6.368779 TCCATGATGATGAGCATATCAAGA 57.631 37.500 6.94 0.00 42.53 3.02
3661 6525 6.958767 TCCATGATGATGAGCATATCAAGAT 58.041 36.000 6.94 0.95 42.53 2.40
3662 6526 7.048512 TCCATGATGATGAGCATATCAAGATC 58.951 38.462 6.94 2.38 42.53 2.75
3663 6527 7.051000 CCATGATGATGAGCATATCAAGATCT 58.949 38.462 6.94 0.00 42.53 2.75
3664 6528 7.011857 CCATGATGATGAGCATATCAAGATCTG 59.988 40.741 0.00 0.00 42.53 2.90
3665 6529 7.005709 TGATGATGAGCATATCAAGATCTGT 57.994 36.000 0.00 0.00 42.53 3.41
3666 6530 8.130671 TGATGATGAGCATATCAAGATCTGTA 57.869 34.615 0.00 0.00 42.53 2.74
3667 6531 8.759782 TGATGATGAGCATATCAAGATCTGTAT 58.240 33.333 0.00 0.00 42.53 2.29
3691 6555 4.785346 ACAATTCCACTATGAGGAGCAT 57.215 40.909 0.00 0.00 41.08 3.79
3695 6559 4.613925 TTCCACTATGAGGAGCATGATC 57.386 45.455 1.26 1.26 37.87 2.92
3699 6563 4.159321 CCACTATGAGGAGCATGATCGTAT 59.841 45.833 6.09 2.63 37.87 3.06
3700 6564 5.339177 CACTATGAGGAGCATGATCGTATC 58.661 45.833 6.09 4.48 37.87 2.24
3701 6565 2.997485 TGAGGAGCATGATCGTATCG 57.003 50.000 6.09 0.00 0.00 2.92
3702 6566 1.068264 TGAGGAGCATGATCGTATCGC 60.068 52.381 6.09 0.00 0.00 4.58
3703 6567 0.961753 AGGAGCATGATCGTATCGCA 59.038 50.000 4.00 0.00 0.00 5.10
3736 6600 5.301045 ACTCCATAACCAATTGCATGATGAG 59.699 40.000 0.00 8.24 0.00 2.90
3749 6613 1.996292 TGATGAGTAGCAAGTCGCAC 58.004 50.000 0.00 0.00 46.13 5.34
3781 6646 3.679502 GCATTGCCTTTATTGTTGACACC 59.320 43.478 0.00 0.00 0.00 4.16
3804 6669 5.359194 TTTCCCTGTCATCTTATCACTCC 57.641 43.478 0.00 0.00 0.00 3.85
3821 6686 0.988063 TCCCGGTGATGATGGACAAA 59.012 50.000 0.00 0.00 0.00 2.83
3832 6697 4.140518 TGATGGACAAAAACATTCGACG 57.859 40.909 0.00 0.00 0.00 5.12
3887 6752 3.705934 TTGCCGCGCCCATCCATTA 62.706 57.895 0.00 0.00 0.00 1.90
3895 6760 3.057596 CGCGCCCATCCATTATTACAATT 60.058 43.478 0.00 0.00 0.00 2.32
3961 6827 3.194005 ACAAGAACTCGAAGCTTTGGA 57.806 42.857 13.87 7.36 0.00 3.53
3963 6829 4.137543 ACAAGAACTCGAAGCTTTGGAAT 58.862 39.130 13.87 0.09 0.00 3.01
4000 6868 8.754080 AGAGTTGCAGAAATAAGATAGTACACT 58.246 33.333 0.00 0.00 0.00 3.55
4055 6925 4.644103 ATCAAAATTCGAGGGCAAGATG 57.356 40.909 0.00 0.00 0.00 2.90
4066 6936 3.152341 AGGGCAAGATGTTCAAGTGAAG 58.848 45.455 0.00 0.00 34.27 3.02
4169 7046 5.972935 TCATAAATACAAAGCTCACTCCGA 58.027 37.500 0.00 0.00 0.00 4.55
4246 7129 7.703298 AAAGACATCAAACATTTCACATGTG 57.297 32.000 20.18 20.18 31.80 3.21
4281 7165 1.174712 ACTGCCAAATCAAGCACGCT 61.175 50.000 0.00 0.00 34.68 5.07
4399 7554 2.551644 TGCTGCTGCATCTGTTCTG 58.448 52.632 14.93 0.00 45.31 3.02
4455 7621 6.145338 AGTTATATCGTCTACCACCACAAG 57.855 41.667 0.00 0.00 0.00 3.16
4527 7696 4.422073 TTTCAGCCTGTTCAAAGAGAGA 57.578 40.909 0.00 0.00 0.00 3.10
4608 7779 7.581011 GTTGTATAATTTGCAACCTTTCAGG 57.419 36.000 0.00 0.00 42.97 3.86
4640 7811 3.119352 GCTCCCCTTCATAAGCAACAAAG 60.119 47.826 0.00 0.00 34.86 2.77
4642 7813 2.415893 CCCCTTCATAAGCAACAAAGCG 60.416 50.000 0.00 0.00 40.15 4.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 2.025727 GTACGAGTGGCCGATCCG 59.974 66.667 0.00 1.23 37.80 4.18
51 52 2.351336 CTGGTACGAGTGGCCGATCC 62.351 65.000 0.00 0.00 0.00 3.36
69 70 3.198409 TGCGATTACTCATCATTGGCT 57.802 42.857 0.00 0.00 0.00 4.75
129 130 3.704231 CTCCCCGGGATGCAACCAG 62.704 68.421 26.32 10.89 0.00 4.00
130 131 3.727258 CTCCCCGGGATGCAACCA 61.727 66.667 26.32 0.00 0.00 3.67
196 197 4.035208 GCCATGGTAAATCGATCTCGTTTT 59.965 41.667 14.67 11.88 41.98 2.43
203 204 1.537202 GGCTGCCATGGTAAATCGATC 59.463 52.381 15.17 0.00 0.00 3.69
331 514 6.128282 ACACGATCGAGCAATTTTGTATTTCT 60.128 34.615 24.34 0.00 0.00 2.52
361 552 6.468000 GGTCAATACAAAAATACTAAGCGCAC 59.532 38.462 11.47 0.00 0.00 5.34
362 553 6.149640 TGGTCAATACAAAAATACTAAGCGCA 59.850 34.615 11.47 0.00 0.00 6.09
363 554 6.548171 TGGTCAATACAAAAATACTAAGCGC 58.452 36.000 0.00 0.00 0.00 5.92
364 555 9.009327 CAATGGTCAATACAAAAATACTAAGCG 57.991 33.333 0.00 0.00 0.00 4.68
373 564 8.233868 CGACATACTCAATGGTCAATACAAAAA 58.766 33.333 0.00 0.00 40.16 1.94
374 565 7.604545 TCGACATACTCAATGGTCAATACAAAA 59.395 33.333 0.00 0.00 40.16 2.44
375 566 7.064134 GTCGACATACTCAATGGTCAATACAAA 59.936 37.037 11.55 0.00 40.16 2.83
376 567 6.533723 GTCGACATACTCAATGGTCAATACAA 59.466 38.462 11.55 0.00 40.16 2.41
377 568 6.040247 GTCGACATACTCAATGGTCAATACA 58.960 40.000 11.55 0.00 40.16 2.29
378 569 6.040247 TGTCGACATACTCAATGGTCAATAC 58.960 40.000 15.76 0.00 40.16 1.89
379 570 6.215495 TGTCGACATACTCAATGGTCAATA 57.785 37.500 15.76 0.00 40.16 1.90
380 571 5.084818 TGTCGACATACTCAATGGTCAAT 57.915 39.130 15.76 0.00 40.16 2.57
381 572 4.529109 TGTCGACATACTCAATGGTCAA 57.471 40.909 15.76 0.00 40.16 3.18
382 573 4.081697 ACATGTCGACATACTCAATGGTCA 60.082 41.667 29.52 0.00 40.16 4.02
383 574 4.433615 ACATGTCGACATACTCAATGGTC 58.566 43.478 29.52 0.00 40.16 4.02
384 575 4.160439 AGACATGTCGACATACTCAATGGT 59.840 41.667 29.52 20.03 35.80 3.55
385 576 4.505556 CAGACATGTCGACATACTCAATGG 59.494 45.833 29.52 17.08 35.80 3.16
386 577 4.505556 CCAGACATGTCGACATACTCAATG 59.494 45.833 29.52 19.41 36.80 2.82
387 578 4.686972 CCAGACATGTCGACATACTCAAT 58.313 43.478 29.52 11.69 34.26 2.57
532 729 0.742281 CGTGGAACCAGCTCATGAGG 60.742 60.000 23.89 11.24 0.00 3.86
678 1851 8.608844 ATCTTCCTAAAAATATAGAAGCACCG 57.391 34.615 0.00 0.00 0.00 4.94
729 1903 0.953960 AATCGAAGTTCCACGCCACC 60.954 55.000 0.00 0.00 0.00 4.61
759 1933 3.048337 TCCTACGTGACCATTTTGACC 57.952 47.619 0.00 0.00 0.00 4.02
760 1934 5.873164 ACTTATCCTACGTGACCATTTTGAC 59.127 40.000 0.00 0.00 0.00 3.18
762 1936 7.837202 TTACTTATCCTACGTGACCATTTTG 57.163 36.000 0.00 0.00 0.00 2.44
789 1963 8.683615 ACATACAGAAATACGAACTACTCATCA 58.316 33.333 0.00 0.00 0.00 3.07
800 1974 7.642586 CACGTCAGATTACATACAGAAATACGA 59.357 37.037 0.00 0.00 0.00 3.43
801 1975 7.096599 CCACGTCAGATTACATACAGAAATACG 60.097 40.741 0.00 0.00 0.00 3.06
816 1990 3.706373 AGGCCGCCACGTCAGATT 61.706 61.111 13.15 0.00 0.00 2.40
832 2006 3.127721 TCAGCTCTGACAAGTCGTATCAG 59.872 47.826 0.00 0.00 41.06 2.90
868 2042 1.227823 CCAAGTGTCCAAGCGACCA 60.228 57.895 0.00 0.00 41.18 4.02
876 2050 2.836154 GGCAGGTCCAAGTGTCCA 59.164 61.111 0.00 0.00 34.01 4.02
931 2105 6.045072 TGGAACACCTCGTGATTTATTACT 57.955 37.500 0.00 0.00 36.96 2.24
932 2106 6.370718 ACTTGGAACACCTCGTGATTTATTAC 59.629 38.462 0.00 0.00 39.29 1.89
933 2107 6.469410 ACTTGGAACACCTCGTGATTTATTA 58.531 36.000 0.00 0.00 39.29 0.98
934 2108 5.313712 ACTTGGAACACCTCGTGATTTATT 58.686 37.500 0.00 0.00 39.29 1.40
935 2109 4.906618 ACTTGGAACACCTCGTGATTTAT 58.093 39.130 0.00 0.00 39.29 1.40
951 2310 3.815809 ACTGTTCGATTGGAAACTTGGA 58.184 40.909 0.00 0.00 36.14 3.53
1088 2458 3.430218 CGAATCCAAGAGATCGTTATGGC 59.570 47.826 5.35 0.00 32.47 4.40
1620 3005 2.475111 CGCACAATGTCAGTACGACTTT 59.525 45.455 15.47 13.04 45.60 2.66
1622 3007 1.668919 CCGCACAATGTCAGTACGACT 60.669 52.381 15.47 0.00 45.60 4.18
1623 3008 0.713883 CCGCACAATGTCAGTACGAC 59.286 55.000 9.87 9.87 45.61 4.34
1896 3332 4.408821 GTGAGCGTGGCCATCCCA 62.409 66.667 9.72 1.90 42.79 4.37
2174 4051 4.394300 CCAGTCATTTTCCTAAGTGAGCAG 59.606 45.833 0.00 0.00 31.57 4.24
2176 4053 4.154918 CACCAGTCATTTTCCTAAGTGAGC 59.845 45.833 0.00 0.00 31.57 4.26
2177 4054 5.308825 ACACCAGTCATTTTCCTAAGTGAG 58.691 41.667 0.00 0.00 31.57 3.51
2178 4055 5.304686 ACACCAGTCATTTTCCTAAGTGA 57.695 39.130 0.00 0.00 0.00 3.41
2179 4056 5.122396 GCTACACCAGTCATTTTCCTAAGTG 59.878 44.000 0.00 0.00 0.00 3.16
2180 4057 5.221843 TGCTACACCAGTCATTTTCCTAAGT 60.222 40.000 0.00 0.00 0.00 2.24
2181 4058 5.245531 TGCTACACCAGTCATTTTCCTAAG 58.754 41.667 0.00 0.00 0.00 2.18
2203 4383 6.916387 GCCAGATCACAAGAACATATTGAATG 59.084 38.462 0.00 0.00 0.00 2.67
2209 4389 6.491714 ACTAGCCAGATCACAAGAACATAT 57.508 37.500 0.00 0.00 0.00 1.78
2210 4390 5.939764 ACTAGCCAGATCACAAGAACATA 57.060 39.130 0.00 0.00 0.00 2.29
2211 4391 4.833478 ACTAGCCAGATCACAAGAACAT 57.167 40.909 0.00 0.00 0.00 2.71
2212 4392 4.623932 AACTAGCCAGATCACAAGAACA 57.376 40.909 0.00 0.00 0.00 3.18
2213 4393 4.997395 TCAAACTAGCCAGATCACAAGAAC 59.003 41.667 0.00 0.00 0.00 3.01
2214 4394 5.227569 TCAAACTAGCCAGATCACAAGAA 57.772 39.130 0.00 0.00 0.00 2.52
2215 4395 4.890158 TCAAACTAGCCAGATCACAAGA 57.110 40.909 0.00 0.00 0.00 3.02
2216 4396 6.506500 AATTCAAACTAGCCAGATCACAAG 57.493 37.500 0.00 0.00 0.00 3.16
2217 4397 6.899393 AAATTCAAACTAGCCAGATCACAA 57.101 33.333 0.00 0.00 0.00 3.33
2218 4398 6.899393 AAAATTCAAACTAGCCAGATCACA 57.101 33.333 0.00 0.00 0.00 3.58
2219 4399 9.129209 GTTTAAAATTCAAACTAGCCAGATCAC 57.871 33.333 0.00 0.00 33.91 3.06
2220 4400 8.020819 CGTTTAAAATTCAAACTAGCCAGATCA 58.979 33.333 11.63 0.00 34.43 2.92
2221 4401 8.234546 TCGTTTAAAATTCAAACTAGCCAGATC 58.765 33.333 11.63 0.00 34.43 2.75
2222 4402 8.106247 TCGTTTAAAATTCAAACTAGCCAGAT 57.894 30.769 11.63 0.00 34.43 2.90
2223 4403 7.499321 TCGTTTAAAATTCAAACTAGCCAGA 57.501 32.000 11.63 1.69 34.43 3.86
2224 4404 7.860872 AGTTCGTTTAAAATTCAAACTAGCCAG 59.139 33.333 11.63 0.00 34.43 4.85
2225 4405 7.708998 AGTTCGTTTAAAATTCAAACTAGCCA 58.291 30.769 11.63 0.00 34.43 4.75
2226 4406 8.074370 AGAGTTCGTTTAAAATTCAAACTAGCC 58.926 33.333 11.63 2.07 34.43 3.93
2227 4407 9.447040 AAGAGTTCGTTTAAAATTCAAACTAGC 57.553 29.630 11.63 5.51 34.43 3.42
2229 4409 9.724839 CCAAGAGTTCGTTTAAAATTCAAACTA 57.275 29.630 11.63 1.69 34.43 2.24
2230 4410 8.248253 ACCAAGAGTTCGTTTAAAATTCAAACT 58.752 29.630 11.63 0.00 34.43 2.66
2231 4411 8.402326 ACCAAGAGTTCGTTTAAAATTCAAAC 57.598 30.769 0.00 5.83 33.47 2.93
2272 4501 6.615088 TCAGATAACTAAACGCTAGTTTCGT 58.385 36.000 13.86 0.00 46.73 3.85
2273 4502 7.306051 CCATCAGATAACTAAACGCTAGTTTCG 60.306 40.741 13.86 0.00 46.73 3.46
2274 4503 7.042658 CCCATCAGATAACTAAACGCTAGTTTC 60.043 40.741 13.86 11.35 46.73 2.78
2305 4607 2.305343 CCTGGCCCAAATCAAAAATGGA 59.695 45.455 0.00 0.00 36.27 3.41
2306 4608 2.040145 ACCTGGCCCAAATCAAAAATGG 59.960 45.455 0.00 0.00 0.00 3.16
2307 4609 3.337358 GACCTGGCCCAAATCAAAAATG 58.663 45.455 0.00 0.00 0.00 2.32
2308 4610 2.305635 GGACCTGGCCCAAATCAAAAAT 59.694 45.455 0.00 0.00 0.00 1.82
2393 4707 7.253905 AGGCTAAGTAGAACATTTTACTGGA 57.746 36.000 0.00 0.00 30.85 3.86
2410 4724 3.721087 TCAGGGGAGAAAAAGGCTAAG 57.279 47.619 0.00 0.00 0.00 2.18
2411 4725 3.499745 GGTTCAGGGGAGAAAAAGGCTAA 60.500 47.826 0.00 0.00 0.00 3.09
2462 4792 0.316204 CAGGCCCTGCAAAAGAGTTG 59.684 55.000 0.00 0.00 0.00 3.16
2465 4795 1.203994 CAATCAGGCCCTGCAAAAGAG 59.796 52.381 5.66 0.00 0.00 2.85
2466 4796 1.259609 CAATCAGGCCCTGCAAAAGA 58.740 50.000 5.66 0.00 0.00 2.52
2467 4797 0.971386 ACAATCAGGCCCTGCAAAAG 59.029 50.000 5.66 0.00 0.00 2.27
2487 4819 0.537188 GGCTCCTCGTCATCCAAAGA 59.463 55.000 0.00 0.00 0.00 2.52
2490 4822 0.614697 TCAGGCTCCTCGTCATCCAA 60.615 55.000 0.00 0.00 0.00 3.53
2568 4900 4.460263 TGATTCTTGGTGCACTTACAGTT 58.540 39.130 17.98 0.00 0.00 3.16
2628 4960 3.181472 CCCATCATCGAGTGAGTTCATGA 60.181 47.826 0.00 0.00 40.92 3.07
3185 5518 6.211384 TCTCATCACATGAAGAGAACTTACCA 59.789 38.462 13.05 0.00 43.35 3.25
3195 5528 8.618677 GCAGATTATTTTCTCATCACATGAAGA 58.381 33.333 0.00 0.00 39.11 2.87
3198 5531 7.771826 TCTGCAGATTATTTTCTCATCACATGA 59.228 33.333 13.74 0.00 37.76 3.07
3200 5533 7.255173 GCTCTGCAGATTATTTTCTCATCACAT 60.255 37.037 18.63 0.00 0.00 3.21
3203 5536 6.354938 AGCTCTGCAGATTATTTTCTCATCA 58.645 36.000 18.63 0.00 0.00 3.07
3204 5537 6.864360 AGCTCTGCAGATTATTTTCTCATC 57.136 37.500 18.63 0.00 0.00 2.92
3205 5538 9.434420 GTATAGCTCTGCAGATTATTTTCTCAT 57.566 33.333 18.63 2.23 0.00 2.90
3206 5539 8.646004 AGTATAGCTCTGCAGATTATTTTCTCA 58.354 33.333 18.63 0.26 0.00 3.27
3208 5541 9.921637 GTAGTATAGCTCTGCAGATTATTTTCT 57.078 33.333 18.63 16.46 0.00 2.52
3209 5542 9.921637 AGTAGTATAGCTCTGCAGATTATTTTC 57.078 33.333 18.63 11.47 0.00 2.29
3230 5599 7.999545 TCAGTGCCAGAGTATATAAAGAGTAGT 59.000 37.037 0.00 0.00 0.00 2.73
3232 5601 8.762481 TTCAGTGCCAGAGTATATAAAGAGTA 57.238 34.615 0.00 0.00 0.00 2.59
3233 5602 7.661536 TTCAGTGCCAGAGTATATAAAGAGT 57.338 36.000 0.00 0.00 0.00 3.24
3234 5603 8.363390 TGATTCAGTGCCAGAGTATATAAAGAG 58.637 37.037 0.00 0.00 0.00 2.85
3235 5604 8.250143 TGATTCAGTGCCAGAGTATATAAAGA 57.750 34.615 0.00 0.00 0.00 2.52
3237 5606 7.879677 CCATGATTCAGTGCCAGAGTATATAAA 59.120 37.037 0.00 0.00 0.00 1.40
3239 5608 6.498303 ACCATGATTCAGTGCCAGAGTATATA 59.502 38.462 0.00 0.00 0.00 0.86
3240 5609 5.309020 ACCATGATTCAGTGCCAGAGTATAT 59.691 40.000 0.00 0.00 0.00 0.86
3241 5610 4.655649 ACCATGATTCAGTGCCAGAGTATA 59.344 41.667 0.00 0.00 0.00 1.47
3251 5664 6.401394 TCAAGAGAACTACCATGATTCAGTG 58.599 40.000 0.00 0.00 0.00 3.66
3260 5673 5.121811 GCATCACATCAAGAGAACTACCAT 58.878 41.667 0.00 0.00 0.00 3.55
3265 5678 3.008813 ACCTGCATCACATCAAGAGAACT 59.991 43.478 0.00 0.00 0.00 3.01
3266 5679 3.126514 CACCTGCATCACATCAAGAGAAC 59.873 47.826 0.00 0.00 0.00 3.01
3296 5709 1.180029 CCTTCTGGTCCATGCCAAAG 58.820 55.000 0.00 0.00 38.18 2.77
3308 5721 2.431057 AGCACGTTCCTATACCTTCTGG 59.569 50.000 0.00 0.00 39.83 3.86
3357 5776 1.135915 ACCTGCAGTCTAGCGATTGAG 59.864 52.381 13.81 0.00 37.31 3.02
3364 5793 4.674281 ATTAACCTACCTGCAGTCTAGC 57.326 45.455 13.81 0.00 0.00 3.42
3365 5794 5.530171 TCGTATTAACCTACCTGCAGTCTAG 59.470 44.000 13.81 10.45 0.00 2.43
3373 5802 4.889832 ACTCGTCGTATTAACCTACCTG 57.110 45.455 0.00 0.00 0.00 4.00
3378 5807 5.886960 AACACTACTCGTCGTATTAACCT 57.113 39.130 0.00 0.00 0.00 3.50
3379 5808 7.244192 ACTAAACACTACTCGTCGTATTAACC 58.756 38.462 0.00 0.00 0.00 2.85
3380 5809 9.414834 CTACTAAACACTACTCGTCGTATTAAC 57.585 37.037 0.00 0.00 0.00 2.01
3381 5810 8.604035 CCTACTAAACACTACTCGTCGTATTAA 58.396 37.037 0.00 0.00 0.00 1.40
3382 5811 7.979537 TCCTACTAAACACTACTCGTCGTATTA 59.020 37.037 0.00 0.00 0.00 0.98
3383 5812 6.818644 TCCTACTAAACACTACTCGTCGTATT 59.181 38.462 0.00 0.00 0.00 1.89
3384 5813 6.341316 TCCTACTAAACACTACTCGTCGTAT 58.659 40.000 0.00 0.00 0.00 3.06
3385 5814 5.720202 TCCTACTAAACACTACTCGTCGTA 58.280 41.667 0.00 0.00 0.00 3.43
3386 5815 4.569943 TCCTACTAAACACTACTCGTCGT 58.430 43.478 0.00 0.00 0.00 4.34
3387 5816 4.033817 CCTCCTACTAAACACTACTCGTCG 59.966 50.000 0.00 0.00 0.00 5.12
3388 5817 4.940654 ACCTCCTACTAAACACTACTCGTC 59.059 45.833 0.00 0.00 0.00 4.20
3391 5820 8.964772 TCAATAACCTCCTACTAAACACTACTC 58.035 37.037 0.00 0.00 0.00 2.59
3411 5843 9.647797 CTATACACTGTACAACAACCTCAATAA 57.352 33.333 0.00 0.00 0.00 1.40
3461 5893 9.220767 GATACTGAAAAGAATATGACCCCATAC 57.779 37.037 0.00 0.00 38.02 2.39
3490 5925 4.547532 AGCGCTCGATACAAATTAGGTAG 58.452 43.478 2.64 0.00 0.00 3.18
3491 5926 4.579454 AGCGCTCGATACAAATTAGGTA 57.421 40.909 2.64 0.00 0.00 3.08
3492 5927 3.454371 AGCGCTCGATACAAATTAGGT 57.546 42.857 2.64 0.00 0.00 3.08
3493 5928 3.184581 GGAAGCGCTCGATACAAATTAGG 59.815 47.826 12.06 0.00 0.00 2.69
3533 5970 4.141824 TGTGCACCAGATGATTTCGGTATA 60.142 41.667 15.69 0.00 32.38 1.47
3534 5971 3.206150 GTGCACCAGATGATTTCGGTAT 58.794 45.455 5.22 0.00 32.38 2.73
3535 5972 2.027653 TGTGCACCAGATGATTTCGGTA 60.028 45.455 15.69 0.00 32.38 4.02
3536 5973 1.271325 TGTGCACCAGATGATTTCGGT 60.271 47.619 15.69 0.00 33.39 4.69
3537 5974 1.452110 TGTGCACCAGATGATTTCGG 58.548 50.000 15.69 0.00 0.00 4.30
3538 5975 2.941064 AGATGTGCACCAGATGATTTCG 59.059 45.455 15.69 0.00 0.00 3.46
3558 5995 4.074970 ACTCTGCCTTGTGGTTTCATTAG 58.925 43.478 0.00 0.00 35.27 1.73
3560 5997 2.949447 ACTCTGCCTTGTGGTTTCATT 58.051 42.857 0.00 0.00 35.27 2.57
3561 5998 2.664402 ACTCTGCCTTGTGGTTTCAT 57.336 45.000 0.00 0.00 35.27 2.57
3587 6024 1.067212 CTGCCGGTGATGTACTCCTAC 59.933 57.143 1.90 0.00 0.00 3.18
3588 6025 1.064240 TCTGCCGGTGATGTACTCCTA 60.064 52.381 1.90 0.00 0.00 2.94
3589 6026 0.324368 TCTGCCGGTGATGTACTCCT 60.324 55.000 1.90 0.00 0.00 3.69
3590 6027 0.179108 GTCTGCCGGTGATGTACTCC 60.179 60.000 1.90 0.00 0.00 3.85
3591 6028 0.818296 AGTCTGCCGGTGATGTACTC 59.182 55.000 1.90 0.00 0.00 2.59
3592 6029 0.532573 CAGTCTGCCGGTGATGTACT 59.467 55.000 1.90 0.00 0.00 2.73
3632 6496 1.489230 TGCTCATCATCATGGAGCTGT 59.511 47.619 17.98 0.00 35.68 4.40
3654 6518 9.911788 AGTGGAATTGTTTATACAGATCTTGAT 57.088 29.630 0.00 0.00 35.28 2.57
3660 6524 9.784531 CCTCATAGTGGAATTGTTTATACAGAT 57.215 33.333 0.00 0.00 35.28 2.90
3661 6525 8.988060 TCCTCATAGTGGAATTGTTTATACAGA 58.012 33.333 0.00 0.00 35.28 3.41
3662 6526 9.265901 CTCCTCATAGTGGAATTGTTTATACAG 57.734 37.037 0.00 0.00 32.46 2.74
3663 6527 7.715249 GCTCCTCATAGTGGAATTGTTTATACA 59.285 37.037 0.00 0.00 32.61 2.29
3664 6528 7.715249 TGCTCCTCATAGTGGAATTGTTTATAC 59.285 37.037 0.00 0.00 32.61 1.47
3665 6529 7.801104 TGCTCCTCATAGTGGAATTGTTTATA 58.199 34.615 0.00 0.00 32.61 0.98
3666 6530 6.662755 TGCTCCTCATAGTGGAATTGTTTAT 58.337 36.000 0.00 0.00 32.61 1.40
3667 6531 6.061022 TGCTCCTCATAGTGGAATTGTTTA 57.939 37.500 0.00 0.00 32.61 2.01
3668 6532 4.922206 TGCTCCTCATAGTGGAATTGTTT 58.078 39.130 0.00 0.00 32.61 2.83
3669 6533 4.574674 TGCTCCTCATAGTGGAATTGTT 57.425 40.909 0.00 0.00 32.61 2.83
3670 6534 4.164796 TCATGCTCCTCATAGTGGAATTGT 59.835 41.667 0.00 0.00 33.19 2.71
3671 6535 4.711399 TCATGCTCCTCATAGTGGAATTG 58.289 43.478 0.00 0.00 33.19 2.32
3672 6536 5.558818 GATCATGCTCCTCATAGTGGAATT 58.441 41.667 0.00 0.00 33.19 2.17
3673 6537 4.322574 CGATCATGCTCCTCATAGTGGAAT 60.323 45.833 0.00 0.00 33.19 3.01
3674 6538 3.006217 CGATCATGCTCCTCATAGTGGAA 59.994 47.826 0.00 0.00 33.19 3.53
3675 6539 2.560105 CGATCATGCTCCTCATAGTGGA 59.440 50.000 0.00 0.00 33.19 4.02
3676 6540 2.298446 ACGATCATGCTCCTCATAGTGG 59.702 50.000 0.00 0.00 33.19 4.00
3677 6541 3.657015 ACGATCATGCTCCTCATAGTG 57.343 47.619 0.00 0.00 33.19 2.74
3678 6542 4.095632 CGATACGATCATGCTCCTCATAGT 59.904 45.833 0.00 0.00 33.19 2.12
3679 6543 4.596097 CGATACGATCATGCTCCTCATAG 58.404 47.826 0.00 0.00 33.19 2.23
3702 6566 3.289836 TGGTTATGGAGTGGCAATCATG 58.710 45.455 17.47 0.00 0.00 3.07
3703 6567 3.668141 TGGTTATGGAGTGGCAATCAT 57.332 42.857 17.47 10.55 0.00 2.45
3736 6600 0.161024 GACGTTGTGCGACTTGCTAC 59.839 55.000 0.00 0.00 46.63 3.58
3744 6608 1.163420 AATGCTTGGACGTTGTGCGA 61.163 50.000 0.00 0.00 44.77 5.10
3749 6613 0.314935 AAGGCAATGCTTGGACGTTG 59.685 50.000 4.82 0.00 39.16 4.10
3781 6646 5.363939 GGAGTGATAAGATGACAGGGAAAG 58.636 45.833 0.00 0.00 0.00 2.62
3804 6669 2.556189 TGTTTTTGTCCATCATCACCGG 59.444 45.455 0.00 0.00 0.00 5.28
3821 6686 0.719465 GGATGTCGCGTCGAATGTTT 59.281 50.000 5.77 0.00 37.72 2.83
3832 6697 1.150567 CTAGTGCAGCAGGATGTCGC 61.151 60.000 0.00 0.00 39.31 5.19
4000 6868 9.575868 TCTTGGTAATTGTAACCTCAATGTTAA 57.424 29.630 0.00 0.00 37.96 2.01
4169 7046 7.839907 TGCAGATCTTTATTTTGCATAAAGGT 58.160 30.769 15.08 10.14 39.61 3.50
4319 7213 2.924421 CAGGGGGCTAGATCAAAGTTC 58.076 52.381 0.00 0.00 0.00 3.01
4399 7554 6.149142 AGACTGAACTTCAAATGATCTGCTTC 59.851 38.462 0.00 0.00 0.00 3.86
4455 7621 4.693095 TGGTGTTTTTGGCTTGAGAAAAAC 59.307 37.500 13.07 13.07 45.80 2.43
4562 7733 7.668052 ACAACTACCTTTATGCACCTTTAATCA 59.332 33.333 0.00 0.00 0.00 2.57
4608 7779 0.106967 GAAGGGGAGCTTCATGGGTC 60.107 60.000 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.