Multiple sequence alignment - TraesCS3D01G258100

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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 TraesCS3D01G258100 chr3D 100.000 8363 0 0 1 8363 360552086 360560448 0.000000e+00 15444.0
1 TraesCS3D01G258100 chr3D 92.609 2016 128 9 3762 5761 360332424 360334434 0.000000e+00 2878.0
2 TraesCS3D01G258100 chr3D 89.160 1393 120 16 6186 7559 360334807 360336187 0.000000e+00 1707.0
3 TraesCS3D01G258100 chr3D 83.814 1421 146 41 1968 3323 360329984 360331385 0.000000e+00 1273.0
4 TraesCS3D01G258100 chr3D 90.054 734 62 2 7641 8363 25694811 25695544 0.000000e+00 941.0
5 TraesCS3D01G258100 chr3D 85.516 504 49 12 1028 1526 360329242 360329726 9.690000e-139 505.0
6 TraesCS3D01G258100 chr3D 90.634 331 31 0 5759 6089 360334463 360334793 2.770000e-119 440.0
7 TraesCS3D01G258100 chr3D 93.000 300 20 1 8064 8363 461594823 461595121 3.580000e-118 436.0
8 TraesCS3D01G258100 chr3D 90.291 206 20 0 7637 7842 461594283 461594488 3.850000e-68 270.0
9 TraesCS3D01G258100 chr3D 88.889 108 6 5 6092 6197 112712666 112712769 2.450000e-25 128.0
10 TraesCS3D01G258100 chr3B 93.882 5901 227 68 261 6103 466605085 466610909 0.000000e+00 8774.0
11 TraesCS3D01G258100 chr3B 90.332 2503 175 30 3636 6089 466262633 466265117 0.000000e+00 3219.0
12 TraesCS3D01G258100 chr3B 97.463 1419 30 3 6165 7577 466610904 466612322 0.000000e+00 2416.0
13 TraesCS3D01G258100 chr3B 89.179 1377 119 14 6186 7546 466265131 466266493 0.000000e+00 1690.0
14 TraesCS3D01G258100 chr3B 84.015 1639 167 53 2049 3623 466260095 466261702 0.000000e+00 1487.0
15 TraesCS3D01G258100 chr3B 84.962 665 79 5 7699 8363 60746711 60747354 0.000000e+00 654.0
16 TraesCS3D01G258100 chr3B 79.706 749 127 11 7636 8361 331559652 331560398 1.240000e-142 518.0
17 TraesCS3D01G258100 chr3B 85.646 418 45 8 1028 1445 466256787 466257189 7.760000e-115 425.0
18 TraesCS3D01G258100 chr3B 84.800 125 19 0 7859 7983 254828610 254828486 8.810000e-25 126.0
19 TraesCS3D01G258100 chr3A 95.559 4413 144 15 1725 6103 480046707 480051101 0.000000e+00 7016.0
20 TraesCS3D01G258100 chr3A 90.489 2513 179 24 3620 6089 479770278 479772773 0.000000e+00 3262.0
21 TraesCS3D01G258100 chr3A 90.436 1307 101 12 6185 7475 480051100 480052398 0.000000e+00 1700.0
22 TraesCS3D01G258100 chr3A 89.091 1375 122 13 6186 7546 479772787 479774147 0.000000e+00 1683.0
23 TraesCS3D01G258100 chr3A 85.417 1152 121 31 2495 3623 479768566 479769693 0.000000e+00 1153.0
24 TraesCS3D01G258100 chr3A 95.251 716 25 3 971 1686 480046002 480046708 0.000000e+00 1125.0
25 TraesCS3D01G258100 chr3A 85.683 461 45 11 1033 1488 479767061 479767505 4.570000e-127 466.0
26 TraesCS3D01G258100 chr3A 86.819 349 39 4 1998 2340 479767971 479768318 4.740000e-102 383.0
27 TraesCS3D01G258100 chr3A 87.739 261 18 6 717 967 480045665 480045921 8.210000e-75 292.0
28 TraesCS3D01G258100 chr6D 88.287 2527 230 36 3618 6103 71140956 71143457 0.000000e+00 2966.0
29 TraesCS3D01G258100 chr6D 87.490 1295 134 13 6206 7480 71135414 71136700 0.000000e+00 1469.0
30 TraesCS3D01G258100 chr6D 83.565 1655 175 54 2036 3623 71139074 71140698 0.000000e+00 1459.0
31 TraesCS3D01G258100 chr6D 88.424 1218 116 13 6181 7381 71143452 71144661 0.000000e+00 1445.0
32 TraesCS3D01G258100 chr6D 86.256 1266 132 22 4875 6103 71134152 71135412 0.000000e+00 1336.0
33 TraesCS3D01G258100 chr6D 84.750 1141 143 22 2495 3623 71123488 71124609 0.000000e+00 1114.0
34 TraesCS3D01G258100 chr6D 83.157 944 124 25 2694 3623 71131181 71132103 0.000000e+00 830.0
35 TraesCS3D01G258100 chr6D 86.423 383 42 7 2028 2402 71122987 71123367 2.170000e-110 411.0
36 TraesCS3D01G258100 chr6D 76.936 594 94 25 1 559 242225753 242225168 1.760000e-76 298.0
37 TraesCS3D01G258100 chr6D 89.474 76 8 0 8214 8289 194203832 194203757 6.910000e-16 97.1
38 TraesCS3D01G258100 chr6A 88.189 2540 224 29 3620 6103 87928178 87930697 0.000000e+00 2959.0
39 TraesCS3D01G258100 chr6A 87.888 1321 131 13 6181 7480 87930692 87932004 0.000000e+00 1526.0
40 TraesCS3D01G258100 chr6A 82.931 1324 143 39 2352 3623 87926627 87927919 0.000000e+00 1116.0
41 TraesCS3D01G258100 chr6A 79.613 569 111 5 7792 8358 572213490 572212925 3.640000e-108 403.0
42 TraesCS3D01G258100 chr6A 81.585 429 76 3 7797 8225 77547607 77548032 1.340000e-92 351.0
43 TraesCS3D01G258100 chr6A 75.576 651 112 33 1 622 337578542 337579174 2.300000e-70 278.0
44 TraesCS3D01G258100 chr6A 91.346 104 8 1 6096 6198 594831701 594831598 3.150000e-29 141.0
45 TraesCS3D01G258100 chr6A 87.963 108 13 0 1 108 510885437 510885544 2.450000e-25 128.0
46 TraesCS3D01G258100 chr6B 88.030 2523 237 31 3620 6103 145888403 145890899 0.000000e+00 2926.0
47 TraesCS3D01G258100 chr6B 89.653 1962 168 16 3620 5563 145896571 145898515 0.000000e+00 2466.0
48 TraesCS3D01G258100 chr6B 83.767 1651 184 44 2036 3623 145894678 145896307 0.000000e+00 1487.0
49 TraesCS3D01G258100 chr6B 88.433 1219 112 14 6183 7381 145898508 145899717 0.000000e+00 1443.0
50 TraesCS3D01G258100 chr6B 85.000 1140 142 19 2495 3623 145886993 145888114 0.000000e+00 1131.0
51 TraesCS3D01G258100 chr6B 86.637 898 95 9 6601 7480 145891418 145892308 0.000000e+00 970.0
52 TraesCS3D01G258100 chr6B 86.544 379 42 6 2031 2402 145886485 145886861 7.810000e-110 409.0
53 TraesCS3D01G258100 chr2D 92.469 478 36 0 7886 8363 179666574 179667051 0.000000e+00 684.0
54 TraesCS3D01G258100 chr2D 98.551 69 1 0 7637 7705 179666011 179666079 1.140000e-23 122.0
55 TraesCS3D01G258100 chr5A 82.555 728 86 25 7637 8363 64882944 64882257 3.340000e-168 603.0
56 TraesCS3D01G258100 chr4D 94.295 298 17 0 7785 8082 373884536 373884239 2.750000e-124 457.0
57 TraesCS3D01G258100 chr4D 89.759 166 10 2 7629 7787 373897001 373896836 1.100000e-48 206.0
58 TraesCS3D01G258100 chr4D 75.000 380 75 17 98 468 113414177 113414545 3.120000e-34 158.0
59 TraesCS3D01G258100 chr4D 84.722 72 9 2 1 71 320754220 320754150 4.190000e-08 71.3
60 TraesCS3D01G258100 chr4A 79.070 473 86 12 99 567 499087051 499087514 6.300000e-81 313.0
61 TraesCS3D01G258100 chr4A 74.699 415 84 18 101 506 463891590 463891188 1.870000e-36 165.0
62 TraesCS3D01G258100 chr4A 86.111 108 15 0 1 108 133952587 133952694 5.300000e-22 117.0
63 TraesCS3D01G258100 chr4B 78.986 414 58 19 1 388 417231936 417231526 1.080000e-63 255.0
64 TraesCS3D01G258100 chr4B 87.310 197 25 0 8167 8363 483702577 483702381 8.450000e-55 226.0
65 TraesCS3D01G258100 chr4B 74.939 411 83 16 98 500 173975157 173975555 4.010000e-38 171.0
66 TraesCS3D01G258100 chr4B 74.242 396 86 11 98 487 96196223 96196608 1.450000e-32 152.0
67 TraesCS3D01G258100 chr1D 76.437 522 91 22 1 493 343261621 343261103 3.870000e-63 254.0
68 TraesCS3D01G258100 chr2B 75.634 513 77 31 1 486 486774854 486775345 2.360000e-50 211.0
69 TraesCS3D01G258100 chr5D 76.823 384 80 7 114 493 368074619 368074997 3.060000e-49 207.0
70 TraesCS3D01G258100 chr5D 95.652 92 4 0 6102 6193 411995116 411995025 1.880000e-31 148.0
71 TraesCS3D01G258100 chr5D 94.505 91 4 1 6102 6192 382868411 382868500 1.130000e-28 139.0
72 TraesCS3D01G258100 chr5D 92.784 97 6 1 6099 6195 384413492 384413587 1.130000e-28 139.0
73 TraesCS3D01G258100 chr7D 77.358 318 62 9 182 493 170035225 170034912 6.670000e-41 180.0
74 TraesCS3D01G258100 chr7D 90.566 106 9 1 6089 6194 141292184 141292080 1.130000e-28 139.0
75 TraesCS3D01G258100 chr7D 92.632 95 6 1 6102 6196 219834458 219834551 1.460000e-27 135.0
76 TraesCS3D01G258100 chr7D 91.753 97 8 0 6098 6194 519264634 519264538 1.460000e-27 135.0
77 TraesCS3D01G258100 chr2A 90.909 99 9 0 6095 6193 102692165 102692067 5.270000e-27 134.0


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 TraesCS3D01G258100 chr3D 360552086 360560448 8362 False 15444.000000 15444 100.000000 1 8363 1 chr3D.!!$F3 8362
1 TraesCS3D01G258100 chr3D 360329242 360336187 6945 False 1360.600000 2878 88.346600 1028 7559 5 chr3D.!!$F4 6531
2 TraesCS3D01G258100 chr3D 25694811 25695544 733 False 941.000000 941 90.054000 7641 8363 1 chr3D.!!$F1 722
3 TraesCS3D01G258100 chr3D 461594283 461595121 838 False 353.000000 436 91.645500 7637 8363 2 chr3D.!!$F5 726
4 TraesCS3D01G258100 chr3B 466605085 466612322 7237 False 5595.000000 8774 95.672500 261 7577 2 chr3B.!!$F4 7316
5 TraesCS3D01G258100 chr3B 466256787 466266493 9706 False 1705.250000 3219 87.293000 1028 7546 4 chr3B.!!$F3 6518
6 TraesCS3D01G258100 chr3B 60746711 60747354 643 False 654.000000 654 84.962000 7699 8363 1 chr3B.!!$F1 664
7 TraesCS3D01G258100 chr3B 331559652 331560398 746 False 518.000000 518 79.706000 7636 8361 1 chr3B.!!$F2 725
8 TraesCS3D01G258100 chr3A 480045665 480052398 6733 False 2533.250000 7016 92.246250 717 7475 4 chr3A.!!$F2 6758
9 TraesCS3D01G258100 chr3A 479767061 479774147 7086 False 1389.400000 3262 87.499800 1033 7546 5 chr3A.!!$F1 6513
10 TraesCS3D01G258100 chr6D 71131181 71144661 13480 False 1584.166667 2966 86.196500 2036 7480 6 chr6D.!!$F2 5444
11 TraesCS3D01G258100 chr6D 71122987 71124609 1622 False 762.500000 1114 85.586500 2028 3623 2 chr6D.!!$F1 1595
12 TraesCS3D01G258100 chr6D 242225168 242225753 585 True 298.000000 298 76.936000 1 559 1 chr6D.!!$R2 558
13 TraesCS3D01G258100 chr6A 87926627 87932004 5377 False 1867.000000 2959 86.336000 2352 7480 3 chr6A.!!$F4 5128
14 TraesCS3D01G258100 chr6A 572212925 572213490 565 True 403.000000 403 79.613000 7792 8358 1 chr6A.!!$R1 566
15 TraesCS3D01G258100 chr6A 337578542 337579174 632 False 278.000000 278 75.576000 1 622 1 chr6A.!!$F2 621
16 TraesCS3D01G258100 chr6B 145886485 145899717 13232 False 1547.428571 2926 86.866286 2031 7480 7 chr6B.!!$F1 5449
17 TraesCS3D01G258100 chr2D 179666011 179667051 1040 False 403.000000 684 95.510000 7637 8363 2 chr2D.!!$F1 726
18 TraesCS3D01G258100 chr5A 64882257 64882944 687 True 603.000000 603 82.555000 7637 8363 1 chr5A.!!$R1 726
19 TraesCS3D01G258100 chr1D 343261103 343261621 518 True 254.000000 254 76.437000 1 493 1 chr1D.!!$R1 492

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
375 411 0.036858 GAGTGACTCACTTGAGCCCC 60.037 60.000 13.06 0.0 45.44 5.80 F
1910 2368 1.004292 GTCGGGTGAGTTTTGTTGTCG 60.004 52.381 0.00 0.0 0.00 4.35 F
2668 19127 0.472044 TCTGCACAACTGCTAACCCA 59.528 50.000 0.00 0.0 44.57 4.51 F
2670 19129 0.472044 TGCACAACTGCTAACCCAGA 59.528 50.000 0.00 0.0 44.57 3.86 F
3989 21566 1.980052 CTACCCTGCAAGACCCGAA 59.020 57.895 0.00 0.0 34.07 4.30 F
4610 22188 2.431771 TCGTCGTTGCCCATCGTG 60.432 61.111 0.00 0.0 0.00 4.35 F
5672 23280 1.470098 GGTGCACAAGGTTATGCTCAG 59.530 52.381 20.43 0.0 42.55 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2173 10318 0.322816 GTGCCTTTCTCCTGCCATCA 60.323 55.000 0.00 0.00 0.00 3.07 R
3215 19696 1.164411 TTCACAAGGCATGCGTAAGG 58.836 50.000 14.17 8.99 38.28 2.69 R
4163 21740 1.274728 CCGATCTGCCCTCTTATCCAG 59.725 57.143 0.00 0.00 0.00 3.86 R
4292 21869 1.399440 TCGATGAAGCTTGCTGCATTC 59.601 47.619 16.36 5.29 45.94 2.67 R
4998 22594 3.001330 CGTCTTTGTTCTGTTCACCTGTC 59.999 47.826 0.00 0.00 0.00 3.51 R
6165 23832 1.946984 ACTTCCTCCGTCCCATAACA 58.053 50.000 0.00 0.00 0.00 2.41 R
7612 25317 0.247460 GCCCCAGTCAATTCAAAGGC 59.753 55.000 0.00 0.00 0.00 4.35 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 86 1.689273 GGCAACAAACCCAACACCATA 59.311 47.619 0.00 0.00 0.00 2.74
92 101 3.204158 ACACCATATGCCCTATTGTCCAA 59.796 43.478 0.00 0.00 0.00 3.53
133 168 1.084370 GCTCCATGACGGCACTGTAC 61.084 60.000 0.00 0.00 33.14 2.90
134 169 0.802222 CTCCATGACGGCACTGTACG 60.802 60.000 0.00 3.02 33.14 3.67
138 173 2.126189 GACGGCACTGTACGGGTC 60.126 66.667 6.65 0.00 0.00 4.46
147 182 0.902531 CTGTACGGGTCAAGGTGGAT 59.097 55.000 0.00 0.00 0.00 3.41
149 184 0.743345 GTACGGGTCAAGGTGGATGC 60.743 60.000 0.00 0.00 0.00 3.91
151 186 2.043953 GGGTCAAGGTGGATGCCC 60.044 66.667 0.00 0.00 0.00 5.36
167 202 2.435586 CCTGACCGGCTTGCTCTG 60.436 66.667 0.00 0.00 0.00 3.35
218 253 2.295885 GCCAGTCATGCTGCTAAAGAT 58.704 47.619 10.54 0.00 43.71 2.40
294 330 3.027412 ACGTGATCAGTAGCCTTCTCAT 58.973 45.455 0.00 0.00 0.00 2.90
310 346 4.322080 TCTCATGACCAATACGGATGAC 57.678 45.455 0.00 0.00 38.63 3.06
342 378 5.392767 TTCCTGAGTGTCTGAATAGTCAC 57.607 43.478 0.00 0.00 41.39 3.67
375 411 0.036858 GAGTGACTCACTTGAGCCCC 60.037 60.000 13.06 0.00 45.44 5.80
450 489 1.444933 TTGGGTGGGAGTGTTGAGAT 58.555 50.000 0.00 0.00 0.00 2.75
522 561 6.815089 AGTTGTGATTGGCATGTTAGAAAAA 58.185 32.000 0.00 0.00 0.00 1.94
569 608 3.090504 TGGTGTGGCCATGGTACTA 57.909 52.632 9.72 1.17 43.61 1.82
570 609 1.590591 TGGTGTGGCCATGGTACTAT 58.409 50.000 9.72 0.00 43.61 2.12
571 610 1.211703 TGGTGTGGCCATGGTACTATG 59.788 52.381 9.72 12.04 43.61 2.23
606 645 9.513906 TTGATTTCAATAAGATTGTGTAGGTGA 57.486 29.630 0.00 0.00 0.00 4.02
635 676 6.817765 TTCCATTGTGATGTTAAGACCTTC 57.182 37.500 0.00 0.00 0.00 3.46
652 693 2.484770 CCTTCGAGTTTGGACACTTGGA 60.485 50.000 0.00 0.00 0.00 3.53
657 698 6.479972 TCGAGTTTGGACACTTGGATATAT 57.520 37.500 0.00 0.00 0.00 0.86
658 699 6.513180 TCGAGTTTGGACACTTGGATATATC 58.487 40.000 3.96 3.96 0.00 1.63
678 719 7.716799 ATATCGGCTCTTCTCTTTCTGATAT 57.283 36.000 0.00 0.00 33.34 1.63
679 720 5.193663 TCGGCTCTTCTCTTTCTGATATG 57.806 43.478 0.00 0.00 0.00 1.78
680 721 4.646945 TCGGCTCTTCTCTTTCTGATATGT 59.353 41.667 0.00 0.00 0.00 2.29
681 722 4.744137 CGGCTCTTCTCTTTCTGATATGTG 59.256 45.833 0.00 0.00 0.00 3.21
682 723 5.055812 GGCTCTTCTCTTTCTGATATGTGG 58.944 45.833 0.00 0.00 0.00 4.17
683 724 5.396213 GGCTCTTCTCTTTCTGATATGTGGT 60.396 44.000 0.00 0.00 0.00 4.16
684 725 6.112058 GCTCTTCTCTTTCTGATATGTGGTT 58.888 40.000 0.00 0.00 0.00 3.67
685 726 6.036953 GCTCTTCTCTTTCTGATATGTGGTTG 59.963 42.308 0.00 0.00 0.00 3.77
686 727 7.244886 TCTTCTCTTTCTGATATGTGGTTGA 57.755 36.000 0.00 0.00 0.00 3.18
687 728 7.099764 TCTTCTCTTTCTGATATGTGGTTGAC 58.900 38.462 0.00 0.00 0.00 3.18
1285 1419 3.974642 ACTCCCTTAACTTGAAGAGTGGT 59.025 43.478 0.00 0.00 39.00 4.16
1654 2075 6.358974 TGGTCAGTGAAATGAACAGAGATA 57.641 37.500 0.00 0.00 41.92 1.98
1810 2255 2.549754 CCTTGGCCGTAGCTTGATATTG 59.450 50.000 0.00 0.00 39.73 1.90
1867 2314 8.766000 TTTTCCCTTCTTCTTTGTTGTTTAAC 57.234 30.769 0.00 0.00 37.32 2.01
1910 2368 1.004292 GTCGGGTGAGTTTTGTTGTCG 60.004 52.381 0.00 0.00 0.00 4.35
1943 2401 9.362539 TCTTCGTCTTAATACAAAAGGATACAC 57.637 33.333 4.37 0.00 41.41 2.90
2173 10318 0.900182 TCAGAGGTGTCGTGCTGGAT 60.900 55.000 0.00 0.00 0.00 3.41
2668 19127 0.472044 TCTGCACAACTGCTAACCCA 59.528 50.000 0.00 0.00 44.57 4.51
2670 19129 0.472044 TGCACAACTGCTAACCCAGA 59.528 50.000 0.00 0.00 44.57 3.86
2815 19276 6.308766 CAGTTAATTCAAATTGTAGCAGCCAC 59.691 38.462 0.00 0.00 0.00 5.01
2864 19327 2.160417 GTGTCCTTCAATGGCGAGAAAG 59.840 50.000 0.00 0.00 0.00 2.62
3100 19581 4.935808 ACGTGAGTTCCTGAAATCATTACC 59.064 41.667 12.47 0.64 45.34 2.85
3637 20980 9.927668 CAGGTGTAAATTATTCTGTTTCCATTT 57.072 29.630 0.00 0.00 0.00 2.32
3891 21468 3.408634 GAAACGATTGAGAGGAAACCCA 58.591 45.455 0.00 0.00 0.00 4.51
3989 21566 1.980052 CTACCCTGCAAGACCCGAA 59.020 57.895 0.00 0.00 34.07 4.30
4176 21753 4.141620 TGAATCTTGACTGGATAAGAGGGC 60.142 45.833 0.00 0.00 36.47 5.19
4610 22188 2.431771 TCGTCGTTGCCCATCGTG 60.432 61.111 0.00 0.00 0.00 4.35
4654 22232 4.079665 CTGCATCACAGTTGTTCATCAG 57.920 45.455 0.00 0.00 41.86 2.90
4692 22270 8.884726 GGAACAAGGTTAGAATCTCTTGAATAC 58.115 37.037 14.57 3.47 38.96 1.89
4756 22337 5.801531 ATGATGATTCATTCACCCCATTG 57.198 39.130 0.00 0.00 39.64 2.82
4906 22487 6.424812 GCACAATTCCTTATCAAAAAGCACTT 59.575 34.615 0.00 0.00 0.00 3.16
4986 22582 3.817084 CCTTCAGATCTGTTGAGTTGCAA 59.183 43.478 21.92 0.00 0.00 4.08
4998 22594 5.159209 GTTGAGTTGCAAGAGGATGAAATG 58.841 41.667 0.00 0.00 37.12 2.32
5406 23006 7.094634 CCCTCAAATTCCAGGTATCATATTTCG 60.095 40.741 2.71 0.00 0.00 3.46
5672 23280 1.470098 GGTGCACAAGGTTATGCTCAG 59.530 52.381 20.43 0.00 42.55 3.35
5970 23637 4.159693 GGTTTTGGTTTCTCACTCTTGGTT 59.840 41.667 0.00 0.00 0.00 3.67
6112 23779 9.986157 TTTGTATATAGATATTACTCCCTCCGT 57.014 33.333 0.00 0.00 0.00 4.69
6113 23780 9.624373 TTGTATATAGATATTACTCCCTCCGTC 57.376 37.037 0.00 0.00 0.00 4.79
6114 23781 8.216423 TGTATATAGATATTACTCCCTCCGTCC 58.784 40.741 0.00 0.00 0.00 4.79
6115 23782 3.172471 AGATATTACTCCCTCCGTCCC 57.828 52.381 0.00 0.00 0.00 4.46
6116 23783 2.449730 AGATATTACTCCCTCCGTCCCA 59.550 50.000 0.00 0.00 0.00 4.37
6117 23784 3.077695 AGATATTACTCCCTCCGTCCCAT 59.922 47.826 0.00 0.00 0.00 4.00
6118 23785 4.294168 AGATATTACTCCCTCCGTCCCATA 59.706 45.833 0.00 0.00 0.00 2.74
6119 23786 2.852714 TTACTCCCTCCGTCCCATAA 57.147 50.000 0.00 0.00 0.00 1.90
6120 23787 3.339713 TTACTCCCTCCGTCCCATAAT 57.660 47.619 0.00 0.00 0.00 1.28
6121 23788 4.474303 TTACTCCCTCCGTCCCATAATA 57.526 45.455 0.00 0.00 0.00 0.98
6122 23789 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
6123 23790 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
6124 23791 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
6125 23792 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
6126 23793 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
6127 23794 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
6128 23795 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
6129 23796 4.466370 CCTCCGTCCCATAATATAAGAGCA 59.534 45.833 0.00 0.00 0.00 4.26
6130 23797 5.046591 CCTCCGTCCCATAATATAAGAGCAA 60.047 44.000 0.00 0.00 0.00 3.91
6131 23798 6.352222 CCTCCGTCCCATAATATAAGAGCAAT 60.352 42.308 0.00 0.00 0.00 3.56
6132 23799 7.016153 TCCGTCCCATAATATAAGAGCAATT 57.984 36.000 0.00 0.00 0.00 2.32
6133 23800 7.458397 TCCGTCCCATAATATAAGAGCAATTT 58.542 34.615 0.00 0.00 0.00 1.82
6134 23801 7.942341 TCCGTCCCATAATATAAGAGCAATTTT 59.058 33.333 0.00 0.00 0.00 1.82
6135 23802 8.023128 CCGTCCCATAATATAAGAGCAATTTTG 58.977 37.037 0.00 0.00 0.00 2.44
6136 23803 8.783093 CGTCCCATAATATAAGAGCAATTTTGA 58.217 33.333 0.00 0.00 0.00 2.69
6137 23804 9.899226 GTCCCATAATATAAGAGCAATTTTGAC 57.101 33.333 0.00 0.00 0.00 3.18
6138 23805 9.639563 TCCCATAATATAAGAGCAATTTTGACA 57.360 29.630 0.00 0.00 0.00 3.58
6139 23806 9.683069 CCCATAATATAAGAGCAATTTTGACAC 57.317 33.333 0.00 0.00 0.00 3.67
6144 23811 6.759497 ATAAGAGCAATTTTGACACTACCC 57.241 37.500 0.00 0.00 0.00 3.69
6145 23812 4.373156 AGAGCAATTTTGACACTACCCT 57.627 40.909 0.00 0.00 0.00 4.34
6146 23813 5.499004 AGAGCAATTTTGACACTACCCTA 57.501 39.130 0.00 0.00 0.00 3.53
6147 23814 5.491982 AGAGCAATTTTGACACTACCCTAG 58.508 41.667 0.00 0.00 0.00 3.02
6148 23815 5.013183 AGAGCAATTTTGACACTACCCTAGT 59.987 40.000 0.00 0.00 40.28 2.57
6159 23826 3.396560 ACTACCCTAGTGTCAAAAACGC 58.603 45.455 0.00 0.00 37.69 4.84
6161 23828 2.490991 ACCCTAGTGTCAAAAACGCTC 58.509 47.619 0.00 0.00 45.69 5.03
6162 23829 2.104281 ACCCTAGTGTCAAAAACGCTCT 59.896 45.455 0.00 0.00 45.69 4.09
6163 23830 3.139077 CCCTAGTGTCAAAAACGCTCTT 58.861 45.455 0.00 0.00 45.69 2.85
6164 23831 4.202284 ACCCTAGTGTCAAAAACGCTCTTA 60.202 41.667 0.00 0.00 45.69 2.10
6165 23832 4.935808 CCCTAGTGTCAAAAACGCTCTTAT 59.064 41.667 0.00 0.00 45.69 1.73
6166 23833 5.163854 CCCTAGTGTCAAAAACGCTCTTATG 60.164 44.000 0.00 0.00 45.69 1.90
6167 23834 5.408604 CCTAGTGTCAAAAACGCTCTTATGT 59.591 40.000 0.00 0.00 45.69 2.29
6195 23862 5.353400 GGGACGGAGGAAGTAAGTTTTAATG 59.647 44.000 0.00 0.00 0.00 1.90
6197 23864 6.091849 GGACGGAGGAAGTAAGTTTTAATGAC 59.908 42.308 0.00 0.00 0.00 3.06
6868 24553 3.713764 CTGGTTAAGAGATCAGATGGGGT 59.286 47.826 0.00 0.00 0.00 4.95
6969 24654 4.368808 CAAGTCACGGTTGCGGCG 62.369 66.667 0.51 0.51 0.00 6.46
7044 24729 0.245539 CGGTTGGCGAGAAAGGAGTA 59.754 55.000 0.00 0.00 0.00 2.59
7158 24843 2.279517 GATGCGGAATCGGAGCGT 60.280 61.111 0.00 0.00 40.70 5.07
7385 25071 7.401060 AGAATATGTGTATATTTGACCCCCA 57.599 36.000 0.00 0.00 39.10 4.96
7515 25217 1.835483 CGCGGAAGGCATATGAGCAC 61.835 60.000 6.97 0.00 43.84 4.40
7520 25222 2.408050 GAAGGCATATGAGCACGGTAG 58.592 52.381 6.97 0.00 35.83 3.18
7521 25223 0.681733 AGGCATATGAGCACGGTAGG 59.318 55.000 6.97 0.00 35.83 3.18
7560 25265 7.277760 TCAACTCTGTGTACCAATTGATTATCG 59.722 37.037 7.12 0.00 0.00 2.92
7577 25282 2.012937 TCGGTAATGTTAACTGGCCG 57.987 50.000 18.32 18.32 39.13 6.13
7578 25283 1.549620 TCGGTAATGTTAACTGGCCGA 59.450 47.619 21.05 21.05 43.47 5.54
7579 25284 1.662122 CGGTAATGTTAACTGGCCGAC 59.338 52.381 19.10 5.72 40.04 4.79
7580 25285 1.662122 GGTAATGTTAACTGGCCGACG 59.338 52.381 7.22 0.00 0.00 5.12
7581 25286 2.340337 GTAATGTTAACTGGCCGACGT 58.660 47.619 7.22 0.00 0.00 4.34
7582 25287 1.886886 AATGTTAACTGGCCGACGTT 58.113 45.000 7.22 4.07 0.00 3.99
7583 25288 1.886886 ATGTTAACTGGCCGACGTTT 58.113 45.000 7.22 0.00 0.00 3.60
7584 25289 0.938713 TGTTAACTGGCCGACGTTTG 59.061 50.000 7.22 0.00 0.00 2.93
7585 25290 0.939419 GTTAACTGGCCGACGTTTGT 59.061 50.000 9.71 0.00 0.00 2.83
7586 25291 1.331447 GTTAACTGGCCGACGTTTGTT 59.669 47.619 9.71 3.62 0.00 2.83
7587 25292 0.938713 TAACTGGCCGACGTTTGTTG 59.061 50.000 9.71 0.00 0.00 3.33
7588 25293 1.027792 AACTGGCCGACGTTTGTTGT 61.028 50.000 0.00 0.00 0.00 3.32
7589 25294 1.010125 CTGGCCGACGTTTGTTGTG 60.010 57.895 0.00 0.00 0.00 3.33
7590 25295 2.353030 GGCCGACGTTTGTTGTGC 60.353 61.111 0.00 0.00 0.00 4.57
7591 25296 2.713154 GCCGACGTTTGTTGTGCT 59.287 55.556 0.00 0.00 0.00 4.40
7592 25297 1.654137 GCCGACGTTTGTTGTGCTG 60.654 57.895 0.00 0.00 0.00 4.41
7593 25298 1.010125 CCGACGTTTGTTGTGCTGG 60.010 57.895 0.00 0.00 0.00 4.85
7594 25299 1.433053 CCGACGTTTGTTGTGCTGGA 61.433 55.000 0.00 0.00 0.00 3.86
7595 25300 0.586319 CGACGTTTGTTGTGCTGGAT 59.414 50.000 0.00 0.00 0.00 3.41
7596 25301 1.002900 CGACGTTTGTTGTGCTGGATT 60.003 47.619 0.00 0.00 0.00 3.01
7597 25302 2.222213 CGACGTTTGTTGTGCTGGATTA 59.778 45.455 0.00 0.00 0.00 1.75
7598 25303 3.120338 CGACGTTTGTTGTGCTGGATTAT 60.120 43.478 0.00 0.00 0.00 1.28
7599 25304 4.092237 CGACGTTTGTTGTGCTGGATTATA 59.908 41.667 0.00 0.00 0.00 0.98
7600 25305 5.545658 ACGTTTGTTGTGCTGGATTATAG 57.454 39.130 0.00 0.00 0.00 1.31
7601 25306 5.242434 ACGTTTGTTGTGCTGGATTATAGA 58.758 37.500 0.00 0.00 0.00 1.98
7602 25307 5.880332 ACGTTTGTTGTGCTGGATTATAGAT 59.120 36.000 0.00 0.00 0.00 1.98
7603 25308 6.183360 ACGTTTGTTGTGCTGGATTATAGATG 60.183 38.462 0.00 0.00 0.00 2.90
7604 25309 6.498304 GTTTGTTGTGCTGGATTATAGATGG 58.502 40.000 0.00 0.00 0.00 3.51
7605 25310 4.717877 TGTTGTGCTGGATTATAGATGGG 58.282 43.478 0.00 0.00 0.00 4.00
7606 25311 3.423539 TGTGCTGGATTATAGATGGGC 57.576 47.619 0.00 0.00 0.00 5.36
7607 25312 2.981784 TGTGCTGGATTATAGATGGGCT 59.018 45.455 0.00 0.00 0.00 5.19
7608 25313 4.167319 TGTGCTGGATTATAGATGGGCTA 58.833 43.478 0.00 0.00 0.00 3.93
7609 25314 4.597075 TGTGCTGGATTATAGATGGGCTAA 59.403 41.667 0.00 0.00 31.66 3.09
7610 25315 5.251468 TGTGCTGGATTATAGATGGGCTAAT 59.749 40.000 0.00 0.00 31.66 1.73
7611 25316 6.183347 GTGCTGGATTATAGATGGGCTAATT 58.817 40.000 0.00 0.00 31.66 1.40
7612 25317 6.094603 GTGCTGGATTATAGATGGGCTAATTG 59.905 42.308 0.00 0.00 31.66 2.32
7613 25318 5.067023 GCTGGATTATAGATGGGCTAATTGC 59.933 44.000 0.00 0.00 41.94 3.56
7628 25333 4.866486 GCTAATTGCCTTTGAATTGACTGG 59.134 41.667 0.00 0.00 35.15 4.00
7629 25334 3.967332 ATTGCCTTTGAATTGACTGGG 57.033 42.857 0.00 0.00 0.00 4.45
7630 25335 1.631405 TGCCTTTGAATTGACTGGGG 58.369 50.000 0.00 0.00 0.00 4.96
7631 25336 0.247460 GCCTTTGAATTGACTGGGGC 59.753 55.000 0.00 0.00 0.00 5.80
7632 25337 1.631405 CCTTTGAATTGACTGGGGCA 58.369 50.000 0.00 0.00 0.00 5.36
7633 25338 1.547372 CCTTTGAATTGACTGGGGCAG 59.453 52.381 0.00 0.00 37.52 4.85
7634 25339 1.547372 CTTTGAATTGACTGGGGCAGG 59.453 52.381 0.00 0.00 35.51 4.85
8020 26047 2.612115 AGCTTGAGGGGTGGGGAG 60.612 66.667 0.00 0.00 0.00 4.30
8223 26250 0.391263 GCTTCGTTCGGGTCATCCTT 60.391 55.000 0.00 0.00 0.00 3.36
8227 26254 0.249398 CGTTCGGGTCATCCTTCCTT 59.751 55.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.905843 TTTGTTGCCATGGGGGACG 60.906 57.895 15.13 0.00 40.01 4.79
133 168 2.438434 GGCATCCACCTTGACCCG 60.438 66.667 0.00 0.00 0.00 5.28
134 169 2.043953 GGGCATCCACCTTGACCC 60.044 66.667 0.00 0.00 36.14 4.46
138 173 1.379044 GGTCAGGGCATCCACCTTG 60.379 63.158 0.00 0.00 38.12 3.61
149 184 3.710722 AGAGCAAGCCGGTCAGGG 61.711 66.667 1.90 0.00 44.97 4.45
151 186 3.123620 GCAGAGCAAGCCGGTCAG 61.124 66.667 1.90 0.00 44.97 3.51
178 213 1.002134 CCGTCAAGGAGGTGGCAAT 60.002 57.895 0.00 0.00 45.00 3.56
218 253 2.456577 TGATGGACGAGGAGTTGATCA 58.543 47.619 0.00 0.00 32.00 2.92
294 330 1.135527 GACCGTCATCCGTATTGGTCA 59.864 52.381 4.42 0.00 44.10 4.02
310 346 1.821753 ACACTCAGGAATCAGAGACCG 59.178 52.381 8.58 1.05 35.83 4.79
320 356 4.082733 CGTGACTATTCAGACACTCAGGAA 60.083 45.833 5.88 0.00 42.84 3.36
375 411 1.709147 GCTACCGTCAAGCATGCCAG 61.709 60.000 15.66 7.42 39.83 4.85
387 423 0.689745 TTCTATGGGCTGGCTACCGT 60.690 55.000 0.00 0.00 0.00 4.83
450 489 3.769189 TCACCCCAAGGACATAGAGTA 57.231 47.619 0.00 0.00 36.73 2.59
522 561 6.769134 AGCTTACAAACCACTTGTTTAAGT 57.231 33.333 0.00 0.00 46.49 2.24
566 605 7.944729 ATTGAAATCAAAGCACTACCATAGT 57.055 32.000 0.00 0.00 39.55 2.12
567 606 9.941664 CTTATTGAAATCAAAGCACTACCATAG 57.058 33.333 0.00 0.00 39.55 2.23
569 608 8.579850 TCTTATTGAAATCAAAGCACTACCAT 57.420 30.769 0.00 0.00 39.55 3.55
570 609 7.994425 TCTTATTGAAATCAAAGCACTACCA 57.006 32.000 0.00 0.00 39.55 3.25
571 610 9.294030 CAATCTTATTGAAATCAAAGCACTACC 57.706 33.333 0.00 0.00 39.55 3.18
606 645 6.375455 GTCTTAACATCACAATGGAATCAGGT 59.625 38.462 0.00 0.00 37.19 4.00
635 676 5.402568 CGATATATCCAAGTGTCCAAACTCG 59.597 44.000 7.15 0.00 0.00 4.18
652 693 7.716799 ATCAGAAAGAGAAGAGCCGATATAT 57.283 36.000 0.00 0.00 0.00 0.86
657 698 4.646945 ACATATCAGAAAGAGAAGAGCCGA 59.353 41.667 0.00 0.00 0.00 5.54
658 699 4.744137 CACATATCAGAAAGAGAAGAGCCG 59.256 45.833 0.00 0.00 0.00 5.52
678 719 3.011119 GTTGTACAACCAGTCAACCACA 58.989 45.455 25.31 0.00 34.77 4.17
679 720 3.064820 CAGTTGTACAACCAGTCAACCAC 59.935 47.826 30.36 6.47 42.06 4.16
680 721 3.275143 CAGTTGTACAACCAGTCAACCA 58.725 45.455 30.36 0.00 42.06 3.67
681 722 2.616842 CCAGTTGTACAACCAGTCAACC 59.383 50.000 30.36 7.00 42.06 3.77
682 723 2.616842 CCCAGTTGTACAACCAGTCAAC 59.383 50.000 30.36 8.41 42.06 3.18
683 724 2.240160 ACCCAGTTGTACAACCAGTCAA 59.760 45.455 30.36 0.00 42.06 3.18
684 725 1.841277 ACCCAGTTGTACAACCAGTCA 59.159 47.619 30.36 0.00 42.06 3.41
685 726 2.490991 GACCCAGTTGTACAACCAGTC 58.509 52.381 30.36 27.38 42.06 3.51
686 727 1.202604 CGACCCAGTTGTACAACCAGT 60.203 52.381 30.36 24.68 42.06 4.00
687 728 1.069513 TCGACCCAGTTGTACAACCAG 59.930 52.381 30.36 23.40 42.06 4.00
888 939 3.118482 AGCTGATAGGACTGTGGAATGTG 60.118 47.826 0.00 0.00 0.00 3.21
897 948 6.071447 ACAGATATAGCAAGCTGATAGGACTG 60.071 42.308 4.53 7.58 32.86 3.51
1404 1547 5.359009 CAGGAAACATGCACTCCAAGAATAT 59.641 40.000 10.13 0.00 0.00 1.28
1405 1548 4.701651 CAGGAAACATGCACTCCAAGAATA 59.298 41.667 10.13 0.00 0.00 1.75
1406 1549 3.508793 CAGGAAACATGCACTCCAAGAAT 59.491 43.478 10.13 0.00 0.00 2.40
1407 1550 2.886523 CAGGAAACATGCACTCCAAGAA 59.113 45.455 10.13 0.00 0.00 2.52
1585 1957 4.394920 GGAGATGCGGTTGAGTTTGAAATA 59.605 41.667 0.00 0.00 0.00 1.40
1588 1962 2.151202 GGAGATGCGGTTGAGTTTGAA 58.849 47.619 0.00 0.00 0.00 2.69
1654 2075 6.150307 TGTGAATATGTATCCTTTTGTTGCGT 59.850 34.615 0.00 0.00 0.00 5.24
1707 2152 5.952033 AGTAGTACGTGAGACTTTGGAATC 58.048 41.667 0.00 0.00 0.00 2.52
1718 2163 6.922980 TTTCAATTCGAAGTAGTACGTGAG 57.077 37.500 3.35 0.00 34.32 3.51
1810 2255 3.751698 CCTACACTAGCCAACAGAAAACC 59.248 47.826 0.00 0.00 0.00 3.27
1867 2314 6.551736 ACAGCTAAGTACACAAAAACACAAG 58.448 36.000 0.00 0.00 0.00 3.16
1910 2368 9.155053 CTTTTGTATTAAGACGAAGACAACAAC 57.845 33.333 9.36 0.00 39.53 3.32
1943 2401 2.766313 TCTCGGTCACACTCCAAAATG 58.234 47.619 0.00 0.00 0.00 2.32
1951 2409 2.093106 GTGTCCTATCTCGGTCACACT 58.907 52.381 0.00 0.00 41.03 3.55
2173 10318 0.322816 GTGCCTTTCTCCTGCCATCA 60.323 55.000 0.00 0.00 0.00 3.07
2668 19127 5.073311 TGTTAGTCGCTTGCTAGAAATCT 57.927 39.130 0.00 0.00 0.00 2.40
2670 19129 4.504461 CGATGTTAGTCGCTTGCTAGAAAT 59.496 41.667 0.00 0.00 34.56 2.17
2787 19246 6.749118 GCTGCTACAATTTGAATTAACTGAGG 59.251 38.462 2.79 0.00 0.00 3.86
2815 19276 7.766278 ACCTGTTAACATGAGTTGCTAGATTAG 59.234 37.037 16.57 0.00 38.69 1.73
3100 19581 9.935241 ATACAGCAAATATTAGTACTGATCAGG 57.065 33.333 26.08 8.94 0.00 3.86
3201 19682 5.873179 TGCGTAAGGAAAAAGGTTATCTG 57.127 39.130 0.00 0.00 38.28 2.90
3215 19696 1.164411 TTCACAAGGCATGCGTAAGG 58.836 50.000 14.17 8.99 38.28 2.69
3559 20152 3.196469 TGGTTGATCTGTCTAGCAAGAGG 59.804 47.826 0.00 0.00 35.30 3.69
3735 21284 6.100004 ACATACGAGTACCATATGCAATAGC 58.900 40.000 0.00 0.00 42.57 2.97
3891 21468 6.350864 CCGCTGGTATCATCTGAATCTATCTT 60.351 42.308 0.00 0.00 0.00 2.40
3989 21566 7.956328 TGACAGTCCATCTAATACTAACTGT 57.044 36.000 5.04 5.04 46.09 3.55
4163 21740 1.274728 CCGATCTGCCCTCTTATCCAG 59.725 57.143 0.00 0.00 0.00 3.86
4176 21753 2.695314 GGCTAACAAGGCCGATCTG 58.305 57.895 0.00 0.00 40.19 2.90
4292 21869 1.399440 TCGATGAAGCTTGCTGCATTC 59.601 47.619 16.36 5.29 45.94 2.67
4610 22188 4.065088 TCAACATTCCTTACAGTGCTCAC 58.935 43.478 0.00 0.00 0.00 3.51
4654 22232 3.774734 ACCTTGTTCCACTATTTTCCCC 58.225 45.455 0.00 0.00 0.00 4.81
4725 22305 6.293081 GGTGAATGAATCATCATAGGTTGACG 60.293 42.308 0.00 0.00 45.60 4.35
4756 22337 4.948621 AGGACCTGTACATATAGGATACGC 59.051 45.833 8.56 0.00 46.39 4.42
4883 22464 7.955918 AGAAGTGCTTTTTGATAAGGAATTGT 58.044 30.769 0.00 0.00 34.64 2.71
4930 22511 6.866480 TGCTATTGCCAAAAGAATCTTTAGG 58.134 36.000 8.83 4.70 38.71 2.69
4986 22582 4.042062 TGTTCACCTGTCATTTCATCCTCT 59.958 41.667 0.00 0.00 0.00 3.69
4998 22594 3.001330 CGTCTTTGTTCTGTTCACCTGTC 59.999 47.826 0.00 0.00 0.00 3.51
5970 23637 9.836864 AAACATAGAGCATATGTCAGATACAAA 57.163 29.630 13.19 0.00 42.70 2.83
6101 23768 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
6102 23769 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
6103 23770 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
6104 23771 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
6105 23772 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
6106 23773 4.466370 TGCTCTTATATTATGGGACGGAGG 59.534 45.833 0.00 0.00 0.00 4.30
6107 23774 5.661056 TGCTCTTATATTATGGGACGGAG 57.339 43.478 0.00 0.00 0.00 4.63
6108 23775 6.620877 ATTGCTCTTATATTATGGGACGGA 57.379 37.500 0.00 0.00 0.00 4.69
6109 23776 7.687941 AAATTGCTCTTATATTATGGGACGG 57.312 36.000 0.00 0.00 0.00 4.79
6110 23777 8.783093 TCAAAATTGCTCTTATATTATGGGACG 58.217 33.333 0.00 0.00 0.00 4.79
6111 23778 9.899226 GTCAAAATTGCTCTTATATTATGGGAC 57.101 33.333 0.00 0.00 0.00 4.46
6112 23779 9.639563 TGTCAAAATTGCTCTTATATTATGGGA 57.360 29.630 0.00 0.00 0.00 4.37
6113 23780 9.683069 GTGTCAAAATTGCTCTTATATTATGGG 57.317 33.333 0.00 0.00 0.00 4.00
6118 23785 8.903820 GGGTAGTGTCAAAATTGCTCTTATATT 58.096 33.333 0.00 0.00 0.00 1.28
6119 23786 8.275040 AGGGTAGTGTCAAAATTGCTCTTATAT 58.725 33.333 0.00 0.00 0.00 0.86
6120 23787 7.630082 AGGGTAGTGTCAAAATTGCTCTTATA 58.370 34.615 0.00 0.00 0.00 0.98
6121 23788 6.485171 AGGGTAGTGTCAAAATTGCTCTTAT 58.515 36.000 0.00 0.00 0.00 1.73
6122 23789 5.876357 AGGGTAGTGTCAAAATTGCTCTTA 58.124 37.500 0.00 0.00 0.00 2.10
6123 23790 4.729868 AGGGTAGTGTCAAAATTGCTCTT 58.270 39.130 0.00 0.00 0.00 2.85
6124 23791 4.373156 AGGGTAGTGTCAAAATTGCTCT 57.627 40.909 0.00 0.00 0.00 4.09
6125 23792 5.246307 ACTAGGGTAGTGTCAAAATTGCTC 58.754 41.667 0.00 0.00 37.69 4.26
6126 23793 5.242795 ACTAGGGTAGTGTCAAAATTGCT 57.757 39.130 0.00 0.00 37.69 3.91
6138 23805 3.070590 AGCGTTTTTGACACTAGGGTAGT 59.929 43.478 0.00 0.00 40.28 2.73
6139 23806 3.660865 AGCGTTTTTGACACTAGGGTAG 58.339 45.455 0.00 0.00 0.00 3.18
6140 23807 3.322828 AGAGCGTTTTTGACACTAGGGTA 59.677 43.478 0.00 0.00 0.00 3.69
6141 23808 2.104281 AGAGCGTTTTTGACACTAGGGT 59.896 45.455 0.00 0.00 0.00 4.34
6142 23809 2.767505 AGAGCGTTTTTGACACTAGGG 58.232 47.619 0.00 0.00 0.00 3.53
6143 23810 5.408604 ACATAAGAGCGTTTTTGACACTAGG 59.591 40.000 0.00 0.00 0.00 3.02
6144 23811 6.467723 ACATAAGAGCGTTTTTGACACTAG 57.532 37.500 0.00 0.00 0.00 2.57
6145 23812 6.854496 AACATAAGAGCGTTTTTGACACTA 57.146 33.333 1.95 0.00 0.00 2.74
6146 23813 5.751243 AACATAAGAGCGTTTTTGACACT 57.249 34.783 1.95 0.00 0.00 3.55
6147 23814 6.523201 CCATAACATAAGAGCGTTTTTGACAC 59.477 38.462 0.00 0.00 0.00 3.67
6148 23815 6.348950 CCCATAACATAAGAGCGTTTTTGACA 60.349 38.462 0.00 0.00 0.00 3.58
6149 23816 6.027749 CCCATAACATAAGAGCGTTTTTGAC 58.972 40.000 0.00 0.00 0.00 3.18
6150 23817 5.941058 TCCCATAACATAAGAGCGTTTTTGA 59.059 36.000 0.00 0.00 0.00 2.69
6151 23818 6.027749 GTCCCATAACATAAGAGCGTTTTTG 58.972 40.000 0.00 0.00 0.00 2.44
6152 23819 5.163794 CGTCCCATAACATAAGAGCGTTTTT 60.164 40.000 0.00 0.00 0.00 1.94
6153 23820 4.331717 CGTCCCATAACATAAGAGCGTTTT 59.668 41.667 0.00 0.00 0.00 2.43
6154 23821 3.869246 CGTCCCATAACATAAGAGCGTTT 59.131 43.478 0.00 0.00 0.00 3.60
6155 23822 3.454375 CGTCCCATAACATAAGAGCGTT 58.546 45.455 0.00 0.00 0.00 4.84
6156 23823 2.223971 CCGTCCCATAACATAAGAGCGT 60.224 50.000 0.00 0.00 0.00 5.07
6157 23824 2.035449 TCCGTCCCATAACATAAGAGCG 59.965 50.000 0.00 0.00 0.00 5.03
6158 23825 3.555168 CCTCCGTCCCATAACATAAGAGC 60.555 52.174 0.00 0.00 0.00 4.09
6159 23826 3.895656 TCCTCCGTCCCATAACATAAGAG 59.104 47.826 0.00 0.00 0.00 2.85
6160 23827 3.918566 TCCTCCGTCCCATAACATAAGA 58.081 45.455 0.00 0.00 0.00 2.10
6161 23828 4.101119 ACTTCCTCCGTCCCATAACATAAG 59.899 45.833 0.00 0.00 0.00 1.73
6162 23829 4.035112 ACTTCCTCCGTCCCATAACATAA 58.965 43.478 0.00 0.00 0.00 1.90
6163 23830 3.649843 ACTTCCTCCGTCCCATAACATA 58.350 45.455 0.00 0.00 0.00 2.29
6164 23831 2.478292 ACTTCCTCCGTCCCATAACAT 58.522 47.619 0.00 0.00 0.00 2.71
6165 23832 1.946984 ACTTCCTCCGTCCCATAACA 58.053 50.000 0.00 0.00 0.00 2.41
6166 23833 3.450096 ACTTACTTCCTCCGTCCCATAAC 59.550 47.826 0.00 0.00 0.00 1.89
6167 23834 3.716431 ACTTACTTCCTCCGTCCCATAA 58.284 45.455 0.00 0.00 0.00 1.90
6809 24494 7.565398 AGCTCTTAATTTGGACTCCATCTACTA 59.435 37.037 0.00 0.00 31.53 1.82
7044 24729 1.656587 TCTGCCCACCAGATAGTTGT 58.343 50.000 0.00 0.00 45.44 3.32
7158 24843 2.777094 TCCAATGCATCTTGAACGACA 58.223 42.857 0.00 0.00 0.00 4.35
7391 25077 7.389053 ACAAACAAATGTTGTAAGCAAAAAGGA 59.611 29.630 0.00 0.00 44.59 3.36
7392 25078 7.525759 ACAAACAAATGTTGTAAGCAAAAAGG 58.474 30.769 0.00 0.00 44.59 3.11
7393 25079 8.947304 AACAAACAAATGTTGTAAGCAAAAAG 57.053 26.923 0.00 0.00 44.59 2.27
7498 25200 1.224069 CCGTGCTCATATGCCTTCCG 61.224 60.000 0.00 0.00 0.00 4.30
7515 25217 5.125739 AGTTGACTTACTCTCATTCCTACCG 59.874 44.000 0.00 0.00 0.00 4.02
7560 25265 1.662122 CGTCGGCCAGTTAACATTACC 59.338 52.381 8.61 2.84 0.00 2.85
7577 25282 2.774439 AATCCAGCACAACAAACGTC 57.226 45.000 0.00 0.00 0.00 4.34
7578 25283 5.242434 TCTATAATCCAGCACAACAAACGT 58.758 37.500 0.00 0.00 0.00 3.99
7579 25284 5.794687 TCTATAATCCAGCACAACAAACG 57.205 39.130 0.00 0.00 0.00 3.60
7580 25285 6.460123 CCCATCTATAATCCAGCACAACAAAC 60.460 42.308 0.00 0.00 0.00 2.93
7581 25286 5.593909 CCCATCTATAATCCAGCACAACAAA 59.406 40.000 0.00 0.00 0.00 2.83
7582 25287 5.132502 CCCATCTATAATCCAGCACAACAA 58.867 41.667 0.00 0.00 0.00 2.83
7583 25288 4.717877 CCCATCTATAATCCAGCACAACA 58.282 43.478 0.00 0.00 0.00 3.33
7584 25289 3.503748 GCCCATCTATAATCCAGCACAAC 59.496 47.826 0.00 0.00 0.00 3.32
7585 25290 3.395607 AGCCCATCTATAATCCAGCACAA 59.604 43.478 0.00 0.00 0.00 3.33
7586 25291 2.981784 AGCCCATCTATAATCCAGCACA 59.018 45.455 0.00 0.00 0.00 4.57
7587 25292 3.710209 AGCCCATCTATAATCCAGCAC 57.290 47.619 0.00 0.00 0.00 4.40
7588 25293 6.182627 CAATTAGCCCATCTATAATCCAGCA 58.817 40.000 0.00 0.00 0.00 4.41
7589 25294 5.067023 GCAATTAGCCCATCTATAATCCAGC 59.933 44.000 0.00 0.00 37.23 4.85
7590 25295 6.690194 GCAATTAGCCCATCTATAATCCAG 57.310 41.667 0.00 0.00 37.23 3.86
7605 25310 4.866486 CCAGTCAATTCAAAGGCAATTAGC 59.134 41.667 0.00 0.00 44.65 3.09
7606 25311 5.413499 CCCAGTCAATTCAAAGGCAATTAG 58.587 41.667 0.00 0.00 0.00 1.73
7607 25312 4.222588 CCCCAGTCAATTCAAAGGCAATTA 59.777 41.667 0.00 0.00 0.00 1.40
7608 25313 3.008266 CCCCAGTCAATTCAAAGGCAATT 59.992 43.478 0.00 0.00 0.00 2.32
7609 25314 2.568509 CCCCAGTCAATTCAAAGGCAAT 59.431 45.455 0.00 0.00 0.00 3.56
7610 25315 1.969923 CCCCAGTCAATTCAAAGGCAA 59.030 47.619 0.00 0.00 0.00 4.52
7611 25316 1.631405 CCCCAGTCAATTCAAAGGCA 58.369 50.000 0.00 0.00 0.00 4.75
7612 25317 0.247460 GCCCCAGTCAATTCAAAGGC 59.753 55.000 0.00 0.00 0.00 4.35
7613 25318 1.547372 CTGCCCCAGTCAATTCAAAGG 59.453 52.381 0.00 0.00 0.00 3.11
7614 25319 1.547372 CCTGCCCCAGTCAATTCAAAG 59.453 52.381 0.00 0.00 0.00 2.77
7615 25320 1.631405 CCTGCCCCAGTCAATTCAAA 58.369 50.000 0.00 0.00 0.00 2.69
7616 25321 0.251742 CCCTGCCCCAGTCAATTCAA 60.252 55.000 0.00 0.00 0.00 2.69
7617 25322 1.383799 CCCTGCCCCAGTCAATTCA 59.616 57.895 0.00 0.00 0.00 2.57
7618 25323 1.380380 CCCCTGCCCCAGTCAATTC 60.380 63.158 0.00 0.00 0.00 2.17
7619 25324 1.224003 ATCCCCTGCCCCAGTCAATT 61.224 55.000 0.00 0.00 0.00 2.32
7620 25325 1.623686 ATCCCCTGCCCCAGTCAAT 60.624 57.895 0.00 0.00 0.00 2.57
7621 25326 2.204291 ATCCCCTGCCCCAGTCAA 60.204 61.111 0.00 0.00 0.00 3.18
7622 25327 3.016971 CATCCCCTGCCCCAGTCA 61.017 66.667 0.00 0.00 0.00 3.41
7623 25328 3.813724 CCATCCCCTGCCCCAGTC 61.814 72.222 0.00 0.00 0.00 3.51
7624 25329 4.369591 TCCATCCCCTGCCCCAGT 62.370 66.667 0.00 0.00 0.00 4.00
7625 25330 3.496160 CTCCATCCCCTGCCCCAG 61.496 72.222 0.00 0.00 0.00 4.45
7630 25335 4.925861 GAGCGCTCCATCCCCTGC 62.926 72.222 27.22 0.00 0.00 4.85
8056 26083 4.899239 CCACGATCAGAGCGGCCC 62.899 72.222 13.59 0.00 0.00 5.80
8197 26224 3.139850 TGACCCGAACGAAGCAATAAAA 58.860 40.909 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.