Multiple sequence alignment - TraesCS3A01G166600

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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 TraesCS3A01G166600 chr3A 100.000 6781 0 0 1 6781 171180640 171173860 0.000000e+00 12523.0
1 TraesCS3A01G166600 chr3A 86.712 444 43 13 6339 6781 171138423 171137995 4.760000e-131 479.0
2 TraesCS3A01G166600 chr3A 89.855 69 6 1 1416 1484 690715344 690715277 3.370000e-13 87.9
3 TraesCS3A01G166600 chr3D 97.746 2041 34 5 3760 5794 157099392 157101426 0.000000e+00 3504.0
4 TraesCS3A01G166600 chr3D 96.197 2156 50 14 1536 3682 157097275 157099407 0.000000e+00 3498.0
5 TraesCS3A01G166600 chr3D 90.900 1000 44 12 5817 6781 157101620 157102607 0.000000e+00 1299.0
6 TraesCS3A01G166600 chr3D 86.008 729 42 19 735 1418 157096563 157097276 0.000000e+00 726.0
7 TraesCS3A01G166600 chr3D 86.353 447 42 11 6275 6719 157179448 157179877 2.860000e-128 470.0
8 TraesCS3A01G166600 chr3D 81.020 353 39 13 391 720 567194171 567193824 8.730000e-64 255.0
9 TraesCS3A01G166600 chr3D 95.714 70 2 1 1415 1484 55092869 55092801 2.000000e-20 111.0
10 TraesCS3A01G166600 chr3D 98.000 50 1 0 3632 3681 36979760 36979711 3.370000e-13 87.9
11 TraesCS3A01G166600 chr3D 100.000 40 0 0 1504 1543 435704551 435704512 2.620000e-09 75.0
12 TraesCS3A01G166600 chr3B 95.803 2168 64 11 1536 3682 228204075 228206236 0.000000e+00 3474.0
13 TraesCS3A01G166600 chr3B 97.986 1440 25 3 3760 5199 228206221 228207656 0.000000e+00 2495.0
14 TraesCS3A01G166600 chr3B 93.908 1625 60 15 5187 6781 228207673 228209288 0.000000e+00 2416.0
15 TraesCS3A01G166600 chr3B 88.839 663 37 18 727 1368 228203388 228204034 0.000000e+00 780.0
16 TraesCS3A01G166600 chr3B 83.172 517 69 14 6268 6781 228300178 228300679 2.230000e-124 457.0
17 TraesCS3A01G166600 chr3B 87.059 255 31 2 6528 6781 18542631 18542378 3.090000e-73 287.0
18 TraesCS3A01G166600 chr3B 86.047 258 33 3 6525 6781 644434008 644434263 2.410000e-69 274.0
19 TraesCS3A01G166600 chr3B 91.176 102 8 1 3674 3774 558519758 558519859 3.300000e-28 137.0
20 TraesCS3A01G166600 chr3B 91.429 70 6 0 991 1060 425681420 425681351 5.600000e-16 97.1
21 TraesCS3A01G166600 chr3B 97.959 49 1 0 3761 3809 696979219 696979171 1.210000e-12 86.1
22 TraesCS3A01G166600 chr3B 96.078 51 2 0 3761 3811 252558353 252558303 4.360000e-12 84.2
23 TraesCS3A01G166600 chr4D 93.612 407 25 1 313 719 49738013 49737608 2.090000e-169 606.0
24 TraesCS3A01G166600 chr4D 90.069 433 15 8 313 718 105147548 105147117 2.780000e-148 536.0
25 TraesCS3A01G166600 chr4D 94.422 251 14 0 69 319 105147906 105147656 2.970000e-103 387.0
26 TraesCS3A01G166600 chr4D 91.262 206 10 3 115 320 49738320 49738123 2.410000e-69 274.0
27 TraesCS3A01G166600 chr5B 93.646 362 18 4 365 722 233807263 233807623 2.780000e-148 536.0
28 TraesCS3A01G166600 chr5B 92.697 356 23 2 371 723 542199161 542199516 1.690000e-140 510.0
29 TraesCS3A01G166600 chr5B 94.715 246 13 0 74 319 542198823 542199068 3.840000e-102 383.0
30 TraesCS3A01G166600 chr5B 92.800 250 17 1 70 319 233806927 233807175 1.800000e-95 361.0
31 TraesCS3A01G166600 chr5B 83.523 352 38 8 390 722 415786971 415787321 1.840000e-80 311.0
32 TraesCS3A01G166600 chr5B 81.323 257 26 14 6525 6779 468307030 468307266 8.980000e-44 189.0
33 TraesCS3A01G166600 chr5B 81.287 171 28 4 553 720 81187819 81187650 1.190000e-27 135.0
34 TraesCS3A01G166600 chr5B 92.593 54 4 0 3629 3682 222371370 222371317 2.030000e-10 78.7
35 TraesCS3A01G166600 chr7B 86.591 440 27 4 313 721 392823942 392823504 2.230000e-124 457.0
36 TraesCS3A01G166600 chr7B 95.192 208 10 0 70 277 392824264 392824057 5.070000e-86 329.0
37 TraesCS3A01G166600 chr7B 84.699 183 24 4 3632 3812 173865923 173865743 5.400000e-41 180.0
38 TraesCS3A01G166600 chr7B 95.604 91 4 0 3679 3769 446149572 446149482 5.480000e-31 147.0
39 TraesCS3A01G166600 chr7B 94.118 68 3 1 1417 1484 718351011 718351077 1.200000e-17 102.0
40 TraesCS3A01G166600 chr7B 82.456 114 20 0 69 182 3922400 3922513 4.330000e-17 100.0
41 TraesCS3A01G166600 chr5A 84.665 463 16 6 313 722 46412662 46412202 1.760000e-110 411.0
42 TraesCS3A01G166600 chr5A 94.800 250 13 0 71 320 46413021 46412772 2.290000e-104 390.0
43 TraesCS3A01G166600 chr1B 81.214 527 54 26 6274 6781 676747225 676746725 3.840000e-102 383.0
44 TraesCS3A01G166600 chr1B 95.652 92 4 0 3676 3767 604705775 604705684 1.520000e-31 148.0
45 TraesCS3A01G166600 chr1B 92.647 68 4 1 1417 1484 49636633 49636699 5.600000e-16 97.1
46 TraesCS3A01G166600 chr1B 91.379 58 5 0 3761 3818 109734428 109734371 5.640000e-11 80.5
47 TraesCS3A01G166600 chr1B 94.231 52 3 0 3631 3682 336350857 336350806 5.640000e-11 80.5
48 TraesCS3A01G166600 chr1B 92.593 54 4 0 3629 3682 681844681 681844734 2.030000e-10 78.7
49 TraesCS3A01G166600 chr5D 92.126 254 20 0 6528 6781 62528482 62528229 6.470000e-95 359.0
50 TraesCS3A01G166600 chr5D 78.037 214 41 4 70 280 79165316 79165526 5.520000e-26 130.0
51 TraesCS3A01G166600 chr5D 100.000 39 0 0 1502 1540 459866630 459866592 9.430000e-09 73.1
52 TraesCS3A01G166600 chr1A 88.636 264 24 2 6524 6781 583605183 583604920 3.950000e-82 316.0
53 TraesCS3A01G166600 chr1A 89.831 59 4 1 3760 3816 535075310 535075368 2.620000e-09 75.0
54 TraesCS3A01G166600 chr1A 88.679 53 5 1 1504 1556 48711114 48711063 5.680000e-06 63.9
55 TraesCS3A01G166600 chr1D 87.879 264 25 3 6524 6781 486014916 486014654 3.070000e-78 303.0
56 TraesCS3A01G166600 chr1D 89.157 166 11 5 6274 6435 486015133 486014971 4.150000e-47 200.0
57 TraesCS3A01G166600 chr1D 95.745 47 2 0 3767 3813 49932247 49932201 7.290000e-10 76.8
58 TraesCS3A01G166600 chr6B 87.209 258 31 2 6525 6781 527622309 527622565 6.650000e-75 292.0
59 TraesCS3A01G166600 chr6B 88.439 173 10 2 6264 6432 6194174 6194340 4.150000e-47 200.0
60 TraesCS3A01G166600 chr6B 92.000 100 6 2 3675 3772 23039932 23040031 9.170000e-29 139.0
61 TraesCS3A01G166600 chr6A 79.198 399 33 18 6072 6422 1961926 1961530 1.470000e-56 231.0
62 TraesCS3A01G166600 chr6D 89.595 173 8 2 6264 6432 3024976 3025142 1.920000e-50 211.0
63 TraesCS3A01G166600 chr6D 91.176 68 4 1 1417 1484 347355602 347355537 2.600000e-14 91.6
64 TraesCS3A01G166600 chr7D 94.565 92 5 0 3674 3765 204732460 204732369 7.090000e-30 143.0
65 TraesCS3A01G166600 chr7D 90.566 106 9 1 3661 3766 10560713 10560609 9.170000e-29 139.0
66 TraesCS3A01G166600 chr7D 92.593 54 3 1 3760 3813 497023291 497023239 7.290000e-10 76.8
67 TraesCS3A01G166600 chr7D 95.349 43 2 0 1504 1546 532599515 532599557 1.220000e-07 69.4
68 TraesCS3A01G166600 chr2B 90.741 108 8 2 3660 3766 43275153 43275259 7.090000e-30 143.0
69 TraesCS3A01G166600 chr7A 90.909 99 9 0 3673 3771 57610065 57610163 4.270000e-27 134.0
70 TraesCS3A01G166600 chr7A 89.552 67 6 1 1418 1484 533577719 533577654 4.360000e-12 84.2
71 TraesCS3A01G166600 chr7A 86.667 75 8 2 1411 1484 47010972 47011045 1.570000e-11 82.4
72 TraesCS3A01G166600 chr7A 93.617 47 2 1 1503 1549 636899740 636899695 1.220000e-07 69.4
73 TraesCS3A01G166600 chr4A 82.734 139 23 1 69 207 667700100 667699963 9.240000e-24 122.0
74 TraesCS3A01G166600 chr4A 91.379 58 4 1 3761 3818 631960096 631960152 2.030000e-10 78.7
75 TraesCS3A01G166600 chr4A 95.455 44 1 1 1503 1546 626960534 626960492 1.220000e-07 69.4
76 TraesCS3A01G166600 chr4A 92.000 50 3 1 1504 1552 714743764 714743715 1.220000e-07 69.4
77 TraesCS3A01G166600 chr2A 92.857 70 4 1 1415 1484 712971471 712971403 4.330000e-17 100.0
78 TraesCS3A01G166600 chr2A 92.647 68 4 1 1417 1484 776162408 776162474 5.600000e-16 97.1
79 TraesCS3A01G166600 chr2A 96.000 50 2 0 3632 3681 606237573 606237622 1.570000e-11 82.4
80 TraesCS3A01G166600 chr2A 92.727 55 4 0 3760 3814 78845811 78845865 5.640000e-11 80.5
81 TraesCS3A01G166600 chr2D 92.727 55 4 0 3760 3814 78563865 78563919 5.640000e-11 80.5
82 TraesCS3A01G166600 chr2D 92.453 53 4 0 3630 3682 52051478 52051426 7.290000e-10 76.8
83 TraesCS3A01G166600 chrUn 92.000 50 3 1 1504 1552 461112335 461112384 1.220000e-07 69.4
84 TraesCS3A01G166600 chr4B 93.478 46 3 0 1503 1548 642169713 642169758 1.220000e-07 69.4


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 TraesCS3A01G166600 chr3A 171173860 171180640 6780 True 12523.00 12523 100.00000 1 6781 1 chr3A.!!$R2 6780
1 TraesCS3A01G166600 chr3D 157096563 157102607 6044 False 2256.75 3504 92.71275 735 6781 4 chr3D.!!$F2 6046
2 TraesCS3A01G166600 chr3B 228203388 228209288 5900 False 2291.25 3474 94.13400 727 6781 4 chr3B.!!$F4 6054
3 TraesCS3A01G166600 chr3B 228300178 228300679 501 False 457.00 457 83.17200 6268 6781 1 chr3B.!!$F1 513
4 TraesCS3A01G166600 chr4D 105147117 105147906 789 True 461.50 536 92.24550 69 718 2 chr4D.!!$R2 649
5 TraesCS3A01G166600 chr4D 49737608 49738320 712 True 440.00 606 92.43700 115 719 2 chr4D.!!$R1 604
6 TraesCS3A01G166600 chr5B 233806927 233807623 696 False 448.50 536 93.22300 70 722 2 chr5B.!!$F3 652
7 TraesCS3A01G166600 chr5B 542198823 542199516 693 False 446.50 510 93.70600 74 723 2 chr5B.!!$F4 649
8 TraesCS3A01G166600 chr7B 392823504 392824264 760 True 393.00 457 90.89150 70 721 2 chr7B.!!$R3 651
9 TraesCS3A01G166600 chr5A 46412202 46413021 819 True 400.50 411 89.73250 71 722 2 chr5A.!!$R1 651
10 TraesCS3A01G166600 chr1B 676746725 676747225 500 True 383.00 383 81.21400 6274 6781 1 chr1B.!!$R4 507

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
722 956 0.035739 GGAACCAAACACGCCCTAGA 59.964 55.000 0.00 0.0 0.00 2.43 F
1502 1785 0.107081 TCCACCCGCGAAAGAAAAGA 59.893 50.000 8.23 0.0 0.00 2.52 F
1503 1786 0.948678 CCACCCGCGAAAGAAAAGAA 59.051 50.000 8.23 0.0 0.00 2.52 F
3279 3582 0.549902 TCATCAGAGGGCCAGGGAAA 60.550 55.000 6.18 0.0 0.00 3.13 F
4217 4525 1.401905 GCTTACCAGAAAAGATGGCCG 59.598 52.381 0.00 0.0 41.87 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 2101 0.388659 ACAAGGCGCAATCAAGCAAA 59.611 45.000 10.83 0.00 34.54 3.68 R
3264 3567 1.301293 GAGTTTCCCTGGCCCTCTG 59.699 63.158 0.00 0.00 0.00 3.35 R
3431 3735 5.335661 GCAAAGATGTCCGTAAAAACAGGAT 60.336 40.000 0.00 0.00 36.34 3.24 R
4612 4920 0.938637 GATCGCTCTGCACATCTCCG 60.939 60.000 0.00 0.00 0.00 4.63 R
5877 6392 0.038159 CAAGTCCCTCCTGTGTCGAC 60.038 60.000 9.11 9.11 0.00 4.20 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
22 23 4.072839 CCCAAACTCTAGTTTCTTCACCC 58.927 47.826 5.13 0.00 45.54 4.61
23 24 4.445735 CCCAAACTCTAGTTTCTTCACCCA 60.446 45.833 5.13 0.00 45.54 4.51
24 25 5.130350 CCAAACTCTAGTTTCTTCACCCAA 58.870 41.667 5.13 0.00 45.54 4.12
25 26 5.592688 CCAAACTCTAGTTTCTTCACCCAAA 59.407 40.000 5.13 0.00 45.54 3.28
26 27 6.265422 CCAAACTCTAGTTTCTTCACCCAAAT 59.735 38.462 5.13 0.00 45.54 2.32
27 28 7.201911 CCAAACTCTAGTTTCTTCACCCAAATT 60.202 37.037 5.13 0.00 45.54 1.82
28 29 7.511959 AACTCTAGTTTCTTCACCCAAATTC 57.488 36.000 0.00 0.00 33.93 2.17
29 30 5.701290 ACTCTAGTTTCTTCACCCAAATTCG 59.299 40.000 0.00 0.00 0.00 3.34
30 31 5.860611 TCTAGTTTCTTCACCCAAATTCGA 58.139 37.500 0.00 0.00 0.00 3.71
31 32 6.472887 TCTAGTTTCTTCACCCAAATTCGAT 58.527 36.000 0.00 0.00 0.00 3.59
32 33 5.629079 AGTTTCTTCACCCAAATTCGATC 57.371 39.130 0.00 0.00 0.00 3.69
33 34 5.316987 AGTTTCTTCACCCAAATTCGATCT 58.683 37.500 0.00 0.00 0.00 2.75
34 35 5.412904 AGTTTCTTCACCCAAATTCGATCTC 59.587 40.000 0.00 0.00 0.00 2.75
35 36 3.521560 TCTTCACCCAAATTCGATCTCG 58.478 45.455 0.00 0.00 41.45 4.04
46 47 2.081725 TCGATCTCGATCTCCCTACG 57.918 55.000 0.00 0.00 44.22 3.51
47 48 1.080298 CGATCTCGATCTCCCTACGG 58.920 60.000 5.47 0.00 43.02 4.02
48 49 1.455248 GATCTCGATCTCCCTACGGG 58.545 60.000 0.00 0.00 46.11 5.28
58 59 4.483243 CCTACGGGGCGTGCCATT 62.483 66.667 13.76 0.00 41.39 3.16
59 60 2.437716 CTACGGGGCGTGCCATTT 60.438 61.111 13.76 0.00 41.39 2.32
60 61 2.437002 TACGGGGCGTGCCATTTC 60.437 61.111 13.76 0.00 41.39 2.17
61 62 2.869503 CTACGGGGCGTGCCATTTCT 62.870 60.000 13.76 0.00 41.39 2.52
62 63 2.862674 TACGGGGCGTGCCATTTCTC 62.863 60.000 13.76 0.00 41.39 2.87
63 64 3.140814 GGGGCGTGCCATTTCTCC 61.141 66.667 13.76 0.00 37.98 3.71
64 65 3.508840 GGGCGTGCCATTTCTCCG 61.509 66.667 13.76 0.00 37.98 4.63
65 66 3.508840 GGCGTGCCATTTCTCCGG 61.509 66.667 5.89 0.00 35.81 5.14
66 67 2.746277 GCGTGCCATTTCTCCGGT 60.746 61.111 0.00 0.00 0.00 5.28
67 68 2.750888 GCGTGCCATTTCTCCGGTC 61.751 63.158 0.00 0.00 0.00 4.79
68 69 2.452813 CGTGCCATTTCTCCGGTCG 61.453 63.158 0.00 0.00 0.00 4.79
90 91 3.223589 GGGCGTGTTTGGTTGCCT 61.224 61.111 1.77 0.00 46.72 4.75
97 98 1.760480 GTTTGGTTGCCTGGGTGGT 60.760 57.895 0.00 0.00 38.35 4.16
203 204 3.887621 ACTTGTACGTCATGGCTGTAT 57.112 42.857 0.00 0.00 0.00 2.29
311 320 1.905894 TGATTCCAGACGGTTGGATCA 59.094 47.619 10.48 12.24 46.22 2.92
676 910 4.075682 TCAAACGACCCAGATTTTGCATA 58.924 39.130 0.00 0.00 0.00 3.14
722 956 0.035739 GGAACCAAACACGCCCTAGA 59.964 55.000 0.00 0.00 0.00 2.43
723 957 1.339727 GGAACCAAACACGCCCTAGAT 60.340 52.381 0.00 0.00 0.00 1.98
724 958 2.433436 GAACCAAACACGCCCTAGATT 58.567 47.619 0.00 0.00 0.00 2.40
725 959 3.602483 GAACCAAACACGCCCTAGATTA 58.398 45.455 0.00 0.00 0.00 1.75
732 966 6.202954 CCAAACACGCCCTAGATTAATTAGAG 59.797 42.308 0.00 0.00 0.00 2.43
845 1087 3.495193 GTGTCGCTTAGTTCGTCATACA 58.505 45.455 0.00 0.00 0.00 2.29
925 1168 2.567169 TGGAAGAGCTCGAATTTCCTCA 59.433 45.455 24.87 9.99 39.80 3.86
926 1169 2.933260 GGAAGAGCTCGAATTTCCTCAC 59.067 50.000 20.05 0.23 36.88 3.51
927 1170 3.368948 GGAAGAGCTCGAATTTCCTCACT 60.369 47.826 20.05 0.00 36.88 3.41
928 1171 3.518634 AGAGCTCGAATTTCCTCACTC 57.481 47.619 8.37 0.00 0.00 3.51
1108 1352 3.066621 TGCTTGATTTGTCTCGTGCTTTT 59.933 39.130 0.00 0.00 0.00 2.27
1115 1359 2.221169 TGTCTCGTGCTTTTCTGCAAT 58.779 42.857 0.00 0.00 45.12 3.56
1123 1367 2.559668 TGCTTTTCTGCAATCCAAGAGG 59.440 45.455 0.00 0.00 40.29 3.69
1131 1375 2.291475 TGCAATCCAAGAGGGCATGTTA 60.291 45.455 0.00 0.00 36.21 2.41
1132 1376 2.760092 GCAATCCAAGAGGGCATGTTAA 59.240 45.455 0.00 0.00 36.21 2.01
1138 1382 6.266131 TCCAAGAGGGCATGTTAAGATTAT 57.734 37.500 0.00 0.00 36.21 1.28
1155 1399 2.435533 TATGTACCGCGTGTGTTTGA 57.564 45.000 4.92 0.00 0.00 2.69
1157 1401 0.179105 TGTACCGCGTGTGTTTGACT 60.179 50.000 4.92 0.00 0.00 3.41
1175 1419 3.070878 TGACTGATTGTGTGGCTGAGTTA 59.929 43.478 0.00 0.00 0.00 2.24
1176 1420 3.668447 ACTGATTGTGTGGCTGAGTTAG 58.332 45.455 0.00 0.00 0.00 2.34
1177 1421 3.071602 ACTGATTGTGTGGCTGAGTTAGT 59.928 43.478 0.00 0.00 0.00 2.24
1179 1423 2.543777 TTGTGTGGCTGAGTTAGTCC 57.456 50.000 0.00 0.00 0.00 3.85
1180 1424 0.317160 TGTGTGGCTGAGTTAGTCCG 59.683 55.000 0.00 0.00 0.00 4.79
1181 1425 1.014564 GTGTGGCTGAGTTAGTCCGC 61.015 60.000 0.00 0.00 34.74 5.54
1235 1499 3.433343 TGGATTTGGATCATGTGCAGTT 58.567 40.909 0.00 0.00 33.77 3.16
1238 1502 4.439700 GGATTTGGATCATGTGCAGTTGAG 60.440 45.833 4.94 0.00 33.77 3.02
1252 1516 1.272769 AGTTGAGCTGGAACGTAGTCC 59.727 52.381 0.00 0.00 45.00 3.85
1256 1520 0.537188 AGCTGGAACGTAGTCCATGG 59.463 55.000 9.38 4.97 45.00 3.66
1267 1531 3.057456 CGTAGTCCATGGGCTACAGTATC 60.057 52.174 41.20 23.07 37.90 2.24
1283 1547 4.570772 ACAGTATCACGGGATCAAATTTCG 59.429 41.667 1.73 0.00 34.89 3.46
1293 1557 4.217767 GGGATCAAATTTCGGCCTTATACC 59.782 45.833 0.00 0.00 0.00 2.73
1297 1561 4.642885 TCAAATTTCGGCCTTATACCTTGG 59.357 41.667 0.00 0.00 0.00 3.61
1335 1607 1.174712 CCCACTTCACTTGTGCAGGG 61.175 60.000 5.52 0.95 34.38 4.45
1384 1667 2.413112 CGGTGATATCGTTCCATGATGC 59.587 50.000 0.00 0.00 0.00 3.91
1390 1673 0.904649 TCGTTCCATGATGCTCTGGT 59.095 50.000 0.00 0.00 34.03 4.00
1422 1705 7.989826 TGTTCGTCTAATTACTTACTACTCCC 58.010 38.462 0.00 0.00 0.00 4.30
1423 1706 7.831193 TGTTCGTCTAATTACTTACTACTCCCT 59.169 37.037 0.00 0.00 0.00 4.20
1424 1707 8.341903 GTTCGTCTAATTACTTACTACTCCCTC 58.658 40.741 0.00 0.00 0.00 4.30
1425 1708 6.995091 TCGTCTAATTACTTACTACTCCCTCC 59.005 42.308 0.00 0.00 0.00 4.30
1426 1709 6.073331 CGTCTAATTACTTACTACTCCCTCCG 60.073 46.154 0.00 0.00 0.00 4.63
1427 1710 6.770303 GTCTAATTACTTACTACTCCCTCCGT 59.230 42.308 0.00 0.00 0.00 4.69
1428 1711 6.995091 TCTAATTACTTACTACTCCCTCCGTC 59.005 42.308 0.00 0.00 0.00 4.79
1429 1712 2.433662 ACTTACTACTCCCTCCGTCC 57.566 55.000 0.00 0.00 0.00 4.79
1430 1713 1.637553 ACTTACTACTCCCTCCGTCCA 59.362 52.381 0.00 0.00 0.00 4.02
1431 1714 2.042162 ACTTACTACTCCCTCCGTCCAA 59.958 50.000 0.00 0.00 0.00 3.53
1432 1715 3.297736 CTTACTACTCCCTCCGTCCAAT 58.702 50.000 0.00 0.00 0.00 3.16
1433 1716 4.079558 ACTTACTACTCCCTCCGTCCAATA 60.080 45.833 0.00 0.00 0.00 1.90
1434 1717 3.393426 ACTACTCCCTCCGTCCAATAA 57.607 47.619 0.00 0.00 0.00 1.40
1435 1718 3.924922 ACTACTCCCTCCGTCCAATAAT 58.075 45.455 0.00 0.00 0.00 1.28
1436 1719 5.070823 ACTACTCCCTCCGTCCAATAATA 57.929 43.478 0.00 0.00 0.00 0.98
1437 1720 5.652324 ACTACTCCCTCCGTCCAATAATAT 58.348 41.667 0.00 0.00 0.00 1.28
1438 1721 6.797707 ACTACTCCCTCCGTCCAATAATATA 58.202 40.000 0.00 0.00 0.00 0.86
1439 1722 7.243824 ACTACTCCCTCCGTCCAATAATATAA 58.756 38.462 0.00 0.00 0.00 0.98
1440 1723 6.607004 ACTCCCTCCGTCCAATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
1441 1724 6.320518 ACTCCCTCCGTCCAATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
1442 1725 6.437793 ACTCCCTCCGTCCAATAATATAAGAG 59.562 42.308 0.00 0.00 0.00 2.85
1443 1726 6.320518 TCCCTCCGTCCAATAATATAAGAGT 58.679 40.000 0.00 0.00 0.00 3.24
1444 1727 6.210784 TCCCTCCGTCCAATAATATAAGAGTG 59.789 42.308 0.00 0.00 0.00 3.51
1445 1728 6.014499 CCCTCCGTCCAATAATATAAGAGTGT 60.014 42.308 0.00 0.00 0.00 3.55
1446 1729 7.442656 CCTCCGTCCAATAATATAAGAGTGTT 58.557 38.462 0.00 0.00 0.00 3.32
1447 1730 7.931948 CCTCCGTCCAATAATATAAGAGTGTTT 59.068 37.037 0.00 0.00 0.00 2.83
1448 1731 9.326413 CTCCGTCCAATAATATAAGAGTGTTTT 57.674 33.333 0.00 0.00 0.00 2.43
1449 1732 9.675464 TCCGTCCAATAATATAAGAGTGTTTTT 57.325 29.630 0.00 0.00 0.00 1.94
1490 1773 2.814280 AACGCTCTTATATCCACCCG 57.186 50.000 0.00 0.00 0.00 5.28
1491 1774 0.317479 ACGCTCTTATATCCACCCGC 59.683 55.000 0.00 0.00 0.00 6.13
1492 1775 0.732880 CGCTCTTATATCCACCCGCG 60.733 60.000 0.00 0.00 0.00 6.46
1493 1776 0.601558 GCTCTTATATCCACCCGCGA 59.398 55.000 8.23 0.00 0.00 5.87
1494 1777 1.000506 GCTCTTATATCCACCCGCGAA 59.999 52.381 8.23 0.00 0.00 4.70
1495 1778 2.547218 GCTCTTATATCCACCCGCGAAA 60.547 50.000 8.23 0.00 0.00 3.46
1496 1779 3.318017 CTCTTATATCCACCCGCGAAAG 58.682 50.000 8.23 0.00 0.00 2.62
1497 1780 2.960384 TCTTATATCCACCCGCGAAAGA 59.040 45.455 8.23 0.00 0.00 2.52
1498 1781 3.385433 TCTTATATCCACCCGCGAAAGAA 59.615 43.478 8.23 0.00 0.00 2.52
1499 1782 2.702592 ATATCCACCCGCGAAAGAAA 57.297 45.000 8.23 0.00 0.00 2.52
1500 1783 2.476126 TATCCACCCGCGAAAGAAAA 57.524 45.000 8.23 0.00 0.00 2.29
1501 1784 1.165270 ATCCACCCGCGAAAGAAAAG 58.835 50.000 8.23 0.00 0.00 2.27
1502 1785 0.107081 TCCACCCGCGAAAGAAAAGA 59.893 50.000 8.23 0.00 0.00 2.52
1503 1786 0.948678 CCACCCGCGAAAGAAAAGAA 59.051 50.000 8.23 0.00 0.00 2.52
1504 1787 1.335496 CCACCCGCGAAAGAAAAGAAA 59.665 47.619 8.23 0.00 0.00 2.52
1505 1788 2.223618 CCACCCGCGAAAGAAAAGAAAA 60.224 45.455 8.23 0.00 0.00 2.29
1506 1789 3.440228 CACCCGCGAAAGAAAAGAAAAA 58.560 40.909 8.23 0.00 0.00 1.94
1528 1811 6.780706 AAACGCTCTTATATTATGGAACGG 57.219 37.500 0.00 0.00 0.00 4.44
1529 1812 5.717078 ACGCTCTTATATTATGGAACGGA 57.283 39.130 0.00 0.00 0.00 4.69
1530 1813 5.710984 ACGCTCTTATATTATGGAACGGAG 58.289 41.667 0.00 0.00 0.00 4.63
1531 1814 5.103000 CGCTCTTATATTATGGAACGGAGG 58.897 45.833 0.00 0.00 0.00 4.30
1532 1815 5.420409 GCTCTTATATTATGGAACGGAGGG 58.580 45.833 0.00 0.00 0.00 4.30
1533 1816 5.187186 GCTCTTATATTATGGAACGGAGGGA 59.813 44.000 0.00 0.00 0.00 4.20
1534 1817 6.628398 GCTCTTATATTATGGAACGGAGGGAG 60.628 46.154 0.00 0.00 0.00 4.30
1539 1822 2.249309 ATGGAACGGAGGGAGTAGTT 57.751 50.000 0.00 0.00 0.00 2.24
1675 1958 5.097742 TGGGTGACATGAAAGTAGTATGG 57.902 43.478 0.00 0.00 0.00 2.74
1733 2016 2.841215 ACGTTCCAAATCGTCTTCCAA 58.159 42.857 0.00 0.00 35.30 3.53
1842 2126 3.836949 CTTGATTGCGCCTTGTTGTATT 58.163 40.909 4.18 0.00 0.00 1.89
1872 2157 2.171237 CAGCCCAATATGTCCTCACTCA 59.829 50.000 0.00 0.00 0.00 3.41
1946 2231 9.688091 TTTGTGTAGCATTTACCAGGAAATATA 57.312 29.630 0.00 0.00 0.00 0.86
1969 2255 3.359695 TTTAGCCCATAAGTGTCACCC 57.640 47.619 0.00 0.00 0.00 4.61
2236 2522 7.124750 CCCCCATCTTCATTAAGAGACATTTTT 59.875 37.037 0.00 0.00 44.79 1.94
2390 2676 6.710744 CCTAAAGTAAGCCTCAGTTTTTCAGA 59.289 38.462 0.00 0.00 0.00 3.27
2407 2693 4.656100 TCAGATTCCTGATTTTGGACCA 57.344 40.909 0.00 0.00 44.01 4.02
2408 2694 4.335416 TCAGATTCCTGATTTTGGACCAC 58.665 43.478 0.00 0.00 44.01 4.16
2409 2695 4.043310 TCAGATTCCTGATTTTGGACCACT 59.957 41.667 0.00 0.00 44.01 4.00
2428 2714 6.389906 ACCACTCTCTGTTTTCTTGTTTTTG 58.610 36.000 0.00 0.00 0.00 2.44
2429 2715 6.015434 ACCACTCTCTGTTTTCTTGTTTTTGT 60.015 34.615 0.00 0.00 0.00 2.83
2453 2739 9.403583 TGTTTCACTATTTAGTTGTTCCTTTCT 57.596 29.630 0.00 0.00 33.46 2.52
2485 2771 7.658982 GGATCTGATATTGTCTACTGCAAATCA 59.341 37.037 0.00 0.00 0.00 2.57
2761 3062 8.469200 CAGAATTTGGGCTCATTAACTTATGAA 58.531 33.333 0.00 0.00 34.32 2.57
2944 3245 6.183360 CCACTCACTCGTGATTCATTTACTTC 60.183 42.308 0.00 0.00 39.13 3.01
3264 3567 4.122776 ACCGAGCAACAGATACAATCATC 58.877 43.478 0.00 0.00 0.00 2.92
3279 3582 0.549902 TCATCAGAGGGCCAGGGAAA 60.550 55.000 6.18 0.00 0.00 3.13
3645 3953 1.480869 GGCTTATACTCCCTCCGTCCT 60.481 57.143 0.00 0.00 0.00 3.85
3661 3969 4.398988 TCCGTCCTAAAATAAGTGTCGCTA 59.601 41.667 0.00 0.00 0.00 4.26
3674 3982 9.649167 AATAAGTGTCGCTAATTTAGTACAACT 57.351 29.630 12.43 10.22 0.00 3.16
3675 3983 7.958053 AAGTGTCGCTAATTTAGTACAACTT 57.042 32.000 12.43 13.52 0.00 2.66
3676 3984 7.958053 AGTGTCGCTAATTTAGTACAACTTT 57.042 32.000 12.43 0.00 0.00 2.66
3677 3985 7.793902 AGTGTCGCTAATTTAGTACAACTTTG 58.206 34.615 12.43 0.00 0.00 2.77
3678 3986 7.440255 AGTGTCGCTAATTTAGTACAACTTTGT 59.560 33.333 12.43 0.00 44.86 2.83
3679 3987 8.702438 GTGTCGCTAATTTAGTACAACTTTGTA 58.298 33.333 12.43 0.00 42.35 2.41
3689 3997 3.832615 ACAACTTTGTACTTCCTCCGT 57.167 42.857 0.00 0.00 40.16 4.69
3690 3998 4.942761 ACAACTTTGTACTTCCTCCGTA 57.057 40.909 0.00 0.00 40.16 4.02
3691 3999 5.280654 ACAACTTTGTACTTCCTCCGTAA 57.719 39.130 0.00 0.00 40.16 3.18
3692 4000 5.673514 ACAACTTTGTACTTCCTCCGTAAA 58.326 37.500 0.00 0.00 40.16 2.01
3693 4001 5.525012 ACAACTTTGTACTTCCTCCGTAAAC 59.475 40.000 0.00 0.00 40.16 2.01
3694 4002 5.541953 ACTTTGTACTTCCTCCGTAAACT 57.458 39.130 0.00 0.00 0.00 2.66
3695 4003 6.655078 ACTTTGTACTTCCTCCGTAAACTA 57.345 37.500 0.00 0.00 0.00 2.24
3696 4004 7.054491 ACTTTGTACTTCCTCCGTAAACTAA 57.946 36.000 0.00 0.00 0.00 2.24
3697 4005 7.674120 ACTTTGTACTTCCTCCGTAAACTAAT 58.326 34.615 0.00 0.00 0.00 1.73
3698 4006 8.806146 ACTTTGTACTTCCTCCGTAAACTAATA 58.194 33.333 0.00 0.00 0.00 0.98
3699 4007 9.813446 CTTTGTACTTCCTCCGTAAACTAATAT 57.187 33.333 0.00 0.00 0.00 1.28
3706 4014 9.178427 CTTCCTCCGTAAACTAATATAAGAACG 57.822 37.037 0.00 0.00 0.00 3.95
3707 4015 8.225603 TCCTCCGTAAACTAATATAAGAACGT 57.774 34.615 0.00 0.00 0.00 3.99
3708 4016 8.686334 TCCTCCGTAAACTAATATAAGAACGTT 58.314 33.333 0.00 0.00 0.00 3.99
3709 4017 9.305925 CCTCCGTAAACTAATATAAGAACGTTT 57.694 33.333 0.46 0.00 0.00 3.60
3757 4065 9.530633 AAACGCTCTTATATTAGTTTACTGAGG 57.469 33.333 0.00 0.00 31.14 3.86
3758 4066 7.659186 ACGCTCTTATATTAGTTTACTGAGGG 58.341 38.462 0.00 0.00 37.76 4.30
3759 4067 7.504911 ACGCTCTTATATTAGTTTACTGAGGGA 59.495 37.037 0.00 0.00 36.36 4.20
3760 4068 8.024285 CGCTCTTATATTAGTTTACTGAGGGAG 58.976 40.741 0.00 0.00 35.10 4.30
3761 4069 8.862085 GCTCTTATATTAGTTTACTGAGGGAGT 58.138 37.037 0.00 0.00 38.88 3.85
4114 4422 2.867287 TGCTGTGTGTGTTCAAATGG 57.133 45.000 0.00 0.00 0.00 3.16
4115 4423 2.098614 TGCTGTGTGTGTTCAAATGGT 58.901 42.857 0.00 0.00 0.00 3.55
4217 4525 1.401905 GCTTACCAGAAAAGATGGCCG 59.598 52.381 0.00 0.00 41.87 6.13
4612 4920 4.454728 TTGGGCTTGCAAGAATTATGAC 57.545 40.909 30.39 9.17 0.00 3.06
4890 5198 7.524717 AGTGTTTTACTATTGGAAATGCACT 57.475 32.000 13.00 13.00 38.04 4.40
5327 5664 6.096423 GTCTTCTAAACTTTGGTGGGAGTTTT 59.904 38.462 6.77 0.00 41.86 2.43
5347 5684 8.405418 AGTTTTCACTTTAGGAAGGTTATTCC 57.595 34.615 0.00 0.00 37.19 3.01
5535 5874 0.698238 TGGGAACAGTGGAATCTGGG 59.302 55.000 0.00 0.00 39.48 4.45
5586 5925 1.127951 CACGGACCAACGTAATTCTGC 59.872 52.381 0.00 0.00 46.75 4.26
5601 5940 6.813152 CGTAATTCTGCCATTTCTTTCCATTT 59.187 34.615 0.00 0.00 0.00 2.32
5629 5972 3.679824 ACAGTACACAGGGCTTAGTTC 57.320 47.619 0.00 0.00 0.00 3.01
5634 5977 6.043411 CAGTACACAGGGCTTAGTTCTAATC 58.957 44.000 0.00 0.00 0.00 1.75
5644 5987 7.282450 AGGGCTTAGTTCTAATCGGTTATTTTG 59.718 37.037 0.00 0.00 0.00 2.44
5645 5988 7.281549 GGGCTTAGTTCTAATCGGTTATTTTGA 59.718 37.037 0.00 0.00 0.00 2.69
5646 5989 8.671028 GGCTTAGTTCTAATCGGTTATTTTGAA 58.329 33.333 0.00 0.00 0.00 2.69
5681 6024 2.191128 AATTGCTTCTCTTGGCGTCT 57.809 45.000 0.00 0.00 0.00 4.18
5929 6457 6.745450 CCTATAATACAAGGTTTGCGTTTGTG 59.255 38.462 0.00 0.00 0.00 3.33
6096 6634 3.682696 AGTCATTTCATGCAGCTCTTCA 58.317 40.909 0.00 0.00 0.00 3.02
6102 6640 3.109044 TCATGCAGCTCTTCAGATAGC 57.891 47.619 0.00 0.00 39.08 2.97
6115 6653 3.995199 TCAGATAGCGATGTCCAAATCC 58.005 45.455 0.00 0.00 0.00 3.01
6201 6743 7.602265 ACTTTATTCAAACATTGTAATGCCACC 59.398 33.333 4.58 0.00 40.04 4.61
6247 6789 2.479566 TCTGAAGCTGGTCATCCAAC 57.520 50.000 0.00 0.00 43.81 3.77
6297 6850 3.510459 TCAGTTTCCTCTCATCACAGGA 58.490 45.455 0.00 0.00 37.00 3.86
6314 6867 1.648467 GGACAACCTGAAGCCGATGC 61.648 60.000 0.00 0.00 37.95 3.91
6315 6868 0.955428 GACAACCTGAAGCCGATGCA 60.955 55.000 0.00 0.00 41.13 3.96
6432 7017 1.270274 TGTCATCACATTGTTGCAGCC 59.730 47.619 0.00 0.00 0.00 4.85
6500 7085 5.347635 GTGAAGTCCCAACTTTGAACAAAAC 59.652 40.000 1.76 0.00 45.80 2.43
6526 7111 4.256920 ACTGTACTATCAAAGCTGCCAAG 58.743 43.478 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.204882 CGAATTTGGGTGAAGAAACTAGAGTT 59.795 38.462 0.00 0.00 40.50 3.01
5 6 5.701290 CGAATTTGGGTGAAGAAACTAGAGT 59.299 40.000 0.00 0.00 0.00 3.24
6 7 5.932303 TCGAATTTGGGTGAAGAAACTAGAG 59.068 40.000 0.00 0.00 0.00 2.43
7 8 5.860611 TCGAATTTGGGTGAAGAAACTAGA 58.139 37.500 0.00 0.00 0.00 2.43
8 9 6.595716 AGATCGAATTTGGGTGAAGAAACTAG 59.404 38.462 0.00 0.00 0.00 2.57
9 10 6.472887 AGATCGAATTTGGGTGAAGAAACTA 58.527 36.000 0.00 0.00 0.00 2.24
10 11 5.316987 AGATCGAATTTGGGTGAAGAAACT 58.683 37.500 0.00 0.00 0.00 2.66
11 12 5.629079 AGATCGAATTTGGGTGAAGAAAC 57.371 39.130 0.00 0.00 0.00 2.78
13 14 3.932710 CGAGATCGAATTTGGGTGAAGAA 59.067 43.478 0.00 0.00 43.02 2.52
14 15 3.194755 TCGAGATCGAATTTGGGTGAAGA 59.805 43.478 1.76 0.00 46.30 2.87
15 16 3.521560 TCGAGATCGAATTTGGGTGAAG 58.478 45.455 1.76 0.00 46.30 3.02
16 17 3.603158 TCGAGATCGAATTTGGGTGAA 57.397 42.857 1.76 0.00 46.30 3.18
42 43 2.437716 AAATGGCACGCCCCGTAG 60.438 61.111 5.42 0.00 38.32 3.51
43 44 2.437002 GAAATGGCACGCCCCGTA 60.437 61.111 5.42 0.00 38.32 4.02
44 45 4.344865 AGAAATGGCACGCCCCGT 62.345 61.111 5.42 0.00 42.36 5.28
45 46 3.508840 GAGAAATGGCACGCCCCG 61.509 66.667 5.42 0.00 34.56 5.73
46 47 3.140814 GGAGAAATGGCACGCCCC 61.141 66.667 5.42 0.00 34.56 5.80
47 48 3.508840 CGGAGAAATGGCACGCCC 61.509 66.667 5.42 0.00 34.56 6.13
48 49 3.508840 CCGGAGAAATGGCACGCC 61.509 66.667 0.00 0.00 0.00 5.68
49 50 2.746277 ACCGGAGAAATGGCACGC 60.746 61.111 9.46 0.00 0.00 5.34
50 51 2.452813 CGACCGGAGAAATGGCACG 61.453 63.158 9.46 0.00 0.00 5.34
51 52 2.750888 GCGACCGGAGAAATGGCAC 61.751 63.158 9.46 0.00 0.00 5.01
52 53 1.609635 TAGCGACCGGAGAAATGGCA 61.610 55.000 9.46 0.00 0.00 4.92
53 54 0.876342 CTAGCGACCGGAGAAATGGC 60.876 60.000 9.46 0.00 0.00 4.40
54 55 0.249489 CCTAGCGACCGGAGAAATGG 60.249 60.000 9.46 0.00 0.00 3.16
55 56 0.249489 CCCTAGCGACCGGAGAAATG 60.249 60.000 9.46 0.00 0.00 2.32
56 57 1.400530 CCCCTAGCGACCGGAGAAAT 61.401 60.000 9.46 0.00 0.00 2.17
57 58 2.056223 CCCCTAGCGACCGGAGAAA 61.056 63.158 9.46 0.00 0.00 2.52
58 59 2.441532 CCCCTAGCGACCGGAGAA 60.442 66.667 9.46 0.00 0.00 2.87
68 69 1.602605 AACCAAACACGCCCCTAGC 60.603 57.895 0.00 0.00 38.52 3.42
90 91 2.830923 CAATGCATCCTAAAACCACCCA 59.169 45.455 0.00 0.00 0.00 4.51
203 204 3.777106 ATTCAGAAGAACTGCACCTCA 57.223 42.857 0.00 0.00 45.38 3.86
283 292 1.901085 GTCTGGAATCACCGAGCCT 59.099 57.895 0.00 0.00 42.61 4.58
350 475 2.281484 GTTCGCCTCCACCAAGCA 60.281 61.111 0.00 0.00 0.00 3.91
432 603 1.341187 CCACCTCCGTTCTCCTCTACT 60.341 57.143 0.00 0.00 0.00 2.57
676 910 3.092511 ATCTGGCCCGCATCCACT 61.093 61.111 0.00 0.00 0.00 4.00
722 956 4.593206 TGAGTGATCGGCCCTCTAATTAAT 59.407 41.667 0.00 0.00 0.00 1.40
723 957 3.964688 TGAGTGATCGGCCCTCTAATTAA 59.035 43.478 0.00 0.00 0.00 1.40
724 958 3.572642 TGAGTGATCGGCCCTCTAATTA 58.427 45.455 0.00 0.00 0.00 1.40
725 959 2.398588 TGAGTGATCGGCCCTCTAATT 58.601 47.619 0.00 0.00 0.00 1.40
732 966 1.375523 ACGTTTGAGTGATCGGCCC 60.376 57.895 0.00 0.00 0.00 5.80
947 1190 3.898509 CTCCGGAGCGAGCAGAGG 61.899 72.222 20.67 0.00 0.00 3.69
948 1191 2.335052 CTTCTCCGGAGCGAGCAGAG 62.335 65.000 27.39 10.80 0.00 3.35
949 1192 2.361230 TTCTCCGGAGCGAGCAGA 60.361 61.111 27.39 4.72 0.00 4.26
950 1193 2.103934 CTTCTCCGGAGCGAGCAG 59.896 66.667 27.39 12.51 0.00 4.24
951 1194 3.452786 CCTTCTCCGGAGCGAGCA 61.453 66.667 27.39 6.09 0.00 4.26
952 1195 4.882396 GCCTTCTCCGGAGCGAGC 62.882 72.222 27.39 22.64 0.00 5.03
957 1200 1.739049 CAGCTAGCCTTCTCCGGAG 59.261 63.158 26.32 26.32 0.00 4.63
958 1201 2.427245 GCAGCTAGCCTTCTCCGGA 61.427 63.158 12.13 2.93 37.23 5.14
1108 1352 0.627451 ATGCCCTCTTGGATTGCAGA 59.373 50.000 0.00 0.00 32.94 4.26
1115 1359 4.591321 AATCTTAACATGCCCTCTTGGA 57.409 40.909 0.00 0.00 35.39 3.53
1123 1367 4.377022 CGCGGTACATAATCTTAACATGCC 60.377 45.833 0.00 0.00 0.00 4.40
1131 1375 3.241067 ACACACGCGGTACATAATCTT 57.759 42.857 12.47 0.00 0.00 2.40
1132 1376 2.953466 ACACACGCGGTACATAATCT 57.047 45.000 12.47 0.00 0.00 2.40
1138 1382 0.179105 AGTCAAACACACGCGGTACA 60.179 50.000 12.47 0.00 0.00 2.90
1155 1399 2.645838 AACTCAGCCACACAATCAGT 57.354 45.000 0.00 0.00 0.00 3.41
1157 1401 3.557054 GGACTAACTCAGCCACACAATCA 60.557 47.826 0.00 0.00 0.00 2.57
1175 1419 4.033776 CACCACCATGGGCGGACT 62.034 66.667 25.06 4.85 43.37 3.85
1179 1423 2.829914 CATCCACCACCATGGGCG 60.830 66.667 18.09 7.79 43.37 6.13
1180 1424 0.397535 ATTCATCCACCACCATGGGC 60.398 55.000 18.09 0.00 43.37 5.36
1181 1425 2.163810 AATTCATCCACCACCATGGG 57.836 50.000 18.09 4.89 43.37 4.00
1190 1451 7.414540 CCAAGTAAAGCAGACTAATTCATCCAC 60.415 40.741 0.00 0.00 0.00 4.02
1194 1455 8.814038 AATCCAAGTAAAGCAGACTAATTCAT 57.186 30.769 0.00 0.00 0.00 2.57
1235 1499 3.045518 TGGACTACGTTCCAGCTCA 57.954 52.632 4.82 0.00 41.00 4.26
1252 1516 1.270305 CCCGTGATACTGTAGCCCATG 60.270 57.143 0.02 1.25 0.00 3.66
1256 1520 1.961394 TGATCCCGTGATACTGTAGCC 59.039 52.381 0.02 0.00 0.00 3.93
1267 1531 0.100503 GGCCGAAATTTGATCCCGTG 59.899 55.000 0.00 0.00 0.00 4.94
1283 1547 3.646736 AGAACACCAAGGTATAAGGCC 57.353 47.619 0.00 0.00 0.00 5.19
1293 1557 0.326264 AGGCTGCCTAGAACACCAAG 59.674 55.000 21.98 0.00 28.47 3.61
1297 1561 1.308783 GCCAAGGCTGCCTAGAACAC 61.309 60.000 23.69 5.00 38.26 3.32
1318 1590 1.679139 TTCCCTGCACAAGTGAAGTG 58.321 50.000 7.39 0.00 34.33 3.16
1335 1607 7.872483 ACAACTTCACCCAAATAATCACATTTC 59.128 33.333 0.00 0.00 0.00 2.17
1384 1667 8.425577 AATTAGACGAACATTAATCACCAGAG 57.574 34.615 0.00 0.00 0.00 3.35
1417 1700 6.320518 TCTTATATTATTGGACGGAGGGAGT 58.679 40.000 0.00 0.00 0.00 3.85
1418 1701 6.437793 ACTCTTATATTATTGGACGGAGGGAG 59.562 42.308 0.00 0.00 0.00 4.30
1419 1702 6.210784 CACTCTTATATTATTGGACGGAGGGA 59.789 42.308 0.00 0.00 0.00 4.20
1421 1704 6.994221 ACACTCTTATATTATTGGACGGAGG 58.006 40.000 0.00 0.00 0.00 4.30
1422 1705 8.888579 AAACACTCTTATATTATTGGACGGAG 57.111 34.615 0.00 0.00 0.00 4.63
1423 1706 9.675464 AAAAACACTCTTATATTATTGGACGGA 57.325 29.630 0.00 0.00 0.00 4.69
1468 1751 3.875134 CGGGTGGATATAAGAGCGTTTTT 59.125 43.478 0.00 0.00 0.00 1.94
1469 1752 3.463944 CGGGTGGATATAAGAGCGTTTT 58.536 45.455 0.00 0.00 0.00 2.43
1470 1753 2.805657 GCGGGTGGATATAAGAGCGTTT 60.806 50.000 0.00 0.00 0.00 3.60
1471 1754 1.270147 GCGGGTGGATATAAGAGCGTT 60.270 52.381 0.00 0.00 0.00 4.84
1472 1755 0.317479 GCGGGTGGATATAAGAGCGT 59.683 55.000 0.00 0.00 0.00 5.07
1473 1756 0.732880 CGCGGGTGGATATAAGAGCG 60.733 60.000 0.00 0.00 40.37 5.03
1474 1757 0.601558 TCGCGGGTGGATATAAGAGC 59.398 55.000 6.13 0.00 0.00 4.09
1475 1758 3.005472 TCTTTCGCGGGTGGATATAAGAG 59.995 47.826 6.13 0.00 0.00 2.85
1476 1759 2.960384 TCTTTCGCGGGTGGATATAAGA 59.040 45.455 6.13 0.00 0.00 2.10
1477 1760 3.380479 TCTTTCGCGGGTGGATATAAG 57.620 47.619 6.13 0.00 0.00 1.73
1478 1761 3.823281 TTCTTTCGCGGGTGGATATAA 57.177 42.857 6.13 0.00 0.00 0.98
1479 1762 3.823281 TTTCTTTCGCGGGTGGATATA 57.177 42.857 6.13 0.00 0.00 0.86
1480 1763 2.702592 TTTCTTTCGCGGGTGGATAT 57.297 45.000 6.13 0.00 0.00 1.63
1481 1764 2.027929 TCTTTTCTTTCGCGGGTGGATA 60.028 45.455 6.13 0.00 0.00 2.59
1482 1765 1.165270 CTTTTCTTTCGCGGGTGGAT 58.835 50.000 6.13 0.00 0.00 3.41
1483 1766 0.107081 TCTTTTCTTTCGCGGGTGGA 59.893 50.000 6.13 0.00 0.00 4.02
1484 1767 0.948678 TTCTTTTCTTTCGCGGGTGG 59.051 50.000 6.13 0.00 0.00 4.61
1485 1768 2.766970 TTTCTTTTCTTTCGCGGGTG 57.233 45.000 6.13 0.00 0.00 4.61
1486 1769 3.786516 TTTTTCTTTTCTTTCGCGGGT 57.213 38.095 6.13 0.00 0.00 5.28
1503 1786 7.496591 TCCGTTCCATAATATAAGAGCGTTTTT 59.503 33.333 7.53 0.00 32.01 1.94
1504 1787 6.987992 TCCGTTCCATAATATAAGAGCGTTTT 59.012 34.615 7.53 0.00 32.01 2.43
1505 1788 6.518493 TCCGTTCCATAATATAAGAGCGTTT 58.482 36.000 7.53 0.00 32.01 3.60
1506 1789 6.092955 TCCGTTCCATAATATAAGAGCGTT 57.907 37.500 7.53 0.00 32.01 4.84
1507 1790 5.336531 CCTCCGTTCCATAATATAAGAGCGT 60.337 44.000 7.53 0.00 32.01 5.07
1508 1791 5.103000 CCTCCGTTCCATAATATAAGAGCG 58.897 45.833 3.06 3.06 33.46 5.03
1509 1792 5.187186 TCCCTCCGTTCCATAATATAAGAGC 59.813 44.000 0.00 0.00 0.00 4.09
1510 1793 6.437793 ACTCCCTCCGTTCCATAATATAAGAG 59.562 42.308 0.00 0.00 0.00 2.85
1511 1794 6.320518 ACTCCCTCCGTTCCATAATATAAGA 58.679 40.000 0.00 0.00 0.00 2.10
1512 1795 6.607004 ACTCCCTCCGTTCCATAATATAAG 57.393 41.667 0.00 0.00 0.00 1.73
1513 1796 7.243824 ACTACTCCCTCCGTTCCATAATATAA 58.756 38.462 0.00 0.00 0.00 0.98
1514 1797 6.797707 ACTACTCCCTCCGTTCCATAATATA 58.202 40.000 0.00 0.00 0.00 0.86
1515 1798 5.652324 ACTACTCCCTCCGTTCCATAATAT 58.348 41.667 0.00 0.00 0.00 1.28
1516 1799 5.070823 ACTACTCCCTCCGTTCCATAATA 57.929 43.478 0.00 0.00 0.00 0.98
1517 1800 3.924922 ACTACTCCCTCCGTTCCATAAT 58.075 45.455 0.00 0.00 0.00 1.28
1518 1801 3.393426 ACTACTCCCTCCGTTCCATAA 57.607 47.619 0.00 0.00 0.00 1.90
1519 1802 3.393426 AACTACTCCCTCCGTTCCATA 57.607 47.619 0.00 0.00 0.00 2.74
1520 1803 2.249309 AACTACTCCCTCCGTTCCAT 57.751 50.000 0.00 0.00 0.00 3.41
1521 1804 2.019807 AAACTACTCCCTCCGTTCCA 57.980 50.000 0.00 0.00 0.00 3.53
1522 1805 3.095332 AGTAAACTACTCCCTCCGTTCC 58.905 50.000 0.00 0.00 32.47 3.62
1523 1806 4.337836 CCTAGTAAACTACTCCCTCCGTTC 59.662 50.000 0.00 0.00 40.14 3.95
1524 1807 4.264128 ACCTAGTAAACTACTCCCTCCGTT 60.264 45.833 0.00 0.00 40.14 4.44
1525 1808 3.268072 ACCTAGTAAACTACTCCCTCCGT 59.732 47.826 0.00 0.00 40.14 4.69
1526 1809 3.631227 CACCTAGTAAACTACTCCCTCCG 59.369 52.174 0.00 0.00 40.14 4.63
1527 1810 3.384146 GCACCTAGTAAACTACTCCCTCC 59.616 52.174 0.00 0.00 40.14 4.30
1528 1811 4.279982 AGCACCTAGTAAACTACTCCCTC 58.720 47.826 0.00 0.00 40.14 4.30
1529 1812 4.334208 AGCACCTAGTAAACTACTCCCT 57.666 45.455 0.00 0.00 40.14 4.20
1530 1813 4.465305 TGAAGCACCTAGTAAACTACTCCC 59.535 45.833 0.00 0.00 40.14 4.30
1531 1814 5.185442 AGTGAAGCACCTAGTAAACTACTCC 59.815 44.000 0.00 0.00 36.27 3.85
1532 1815 6.094061 CAGTGAAGCACCTAGTAAACTACTC 58.906 44.000 0.00 0.00 36.27 2.59
1533 1816 5.539193 ACAGTGAAGCACCTAGTAAACTACT 59.461 40.000 0.00 0.00 37.68 2.57
1534 1817 5.634020 CACAGTGAAGCACCTAGTAAACTAC 59.366 44.000 0.00 0.00 34.49 2.73
1539 1822 5.995565 ATACACAGTGAAGCACCTAGTAA 57.004 39.130 7.81 0.00 34.49 2.24
1675 1958 4.387862 CAGTGTATCTTCCACGTGGTTAAC 59.612 45.833 32.74 22.83 37.88 2.01
1689 1972 7.065085 CGTTTTTCATCTTCCATCAGTGTATCT 59.935 37.037 0.00 0.00 0.00 1.98
1817 2101 0.388659 ACAAGGCGCAATCAAGCAAA 59.611 45.000 10.83 0.00 34.54 3.68
1821 2105 2.987413 TACAACAAGGCGCAATCAAG 57.013 45.000 10.83 0.00 0.00 3.02
1842 2126 2.779430 ACATATTGGGCTGACATCTGGA 59.221 45.455 0.00 0.00 0.00 3.86
1872 2157 6.483640 CACTTTTTCAGCCACTACTAACTTCT 59.516 38.462 0.00 0.00 0.00 2.85
1946 2231 4.709886 GGGTGACACTTATGGGCTAAAAAT 59.290 41.667 5.39 0.00 0.00 1.82
1979 2265 2.154462 CAAAAGCATCGTCTCCCAACT 58.846 47.619 0.00 0.00 0.00 3.16
2236 2522 8.252417 AGCTGCATGATCAACAAACATATTTAA 58.748 29.630 0.00 0.00 0.00 1.52
2237 2523 7.774134 AGCTGCATGATCAACAAACATATTTA 58.226 30.769 0.00 0.00 0.00 1.40
2390 2676 4.290722 AGAGAGTGGTCCAAAATCAGGAAT 59.709 41.667 0.00 0.00 36.80 3.01
2400 2686 4.199310 CAAGAAAACAGAGAGTGGTCCAA 58.801 43.478 0.00 0.00 0.00 3.53
2404 2690 6.015434 ACAAAAACAAGAAAACAGAGAGTGGT 60.015 34.615 0.00 0.00 0.00 4.16
2407 2693 8.141268 TGAAACAAAAACAAGAAAACAGAGAGT 58.859 29.630 0.00 0.00 0.00 3.24
2408 2694 8.427774 GTGAAACAAAAACAAGAAAACAGAGAG 58.572 33.333 0.00 0.00 36.32 3.20
2409 2695 8.141268 AGTGAAACAAAAACAAGAAAACAGAGA 58.859 29.630 0.00 0.00 41.43 3.10
2453 2739 9.494271 GCAGTAGACAATATCAGATCCATTAAA 57.506 33.333 0.00 0.00 0.00 1.52
2461 2747 8.969260 TTGATTTGCAGTAGACAATATCAGAT 57.031 30.769 0.00 0.00 31.99 2.90
2510 2796 1.733360 GCTAGGCGATACTAGGACGAG 59.267 57.143 9.05 0.00 40.60 4.18
3264 3567 1.301293 GAGTTTCCCTGGCCCTCTG 59.699 63.158 0.00 0.00 0.00 3.35
3279 3582 7.499232 GGCTACATACCAAATATCAACTTGAGT 59.501 37.037 0.00 0.00 0.00 3.41
3431 3735 5.335661 GCAAAGATGTCCGTAAAAACAGGAT 60.336 40.000 0.00 0.00 36.34 3.24
3680 3988 9.178427 CGTTCTTATATTAGTTTACGGAGGAAG 57.822 37.037 0.00 0.00 0.00 3.46
3681 3989 8.686334 ACGTTCTTATATTAGTTTACGGAGGAA 58.314 33.333 13.71 0.00 32.54 3.36
3682 3990 8.225603 ACGTTCTTATATTAGTTTACGGAGGA 57.774 34.615 13.71 0.00 32.54 3.71
3683 3991 8.862550 AACGTTCTTATATTAGTTTACGGAGG 57.137 34.615 0.00 0.00 32.54 4.30
3731 4039 9.530633 CCTCAGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
3732 4040 8.142551 CCCTCAGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
3733 4041 7.504911 TCCCTCAGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
3734 4042 7.883217 TCCCTCAGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
3735 4043 8.862085 ACTCCCTCAGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 31.37 4.09
3746 4054 8.657712 ACAAATTTAGTACTCCCTCAGTAAACT 58.342 33.333 0.00 0.00 39.44 2.66
3747 4055 8.843885 ACAAATTTAGTACTCCCTCAGTAAAC 57.156 34.615 0.00 0.00 39.44 2.01
3748 4056 9.933723 GTACAAATTTAGTACTCCCTCAGTAAA 57.066 33.333 16.86 0.00 39.44 2.01
3749 4057 9.317827 AGTACAAATTTAGTACTCCCTCAGTAA 57.682 33.333 19.24 0.00 46.80 2.24
3750 4058 8.890410 AGTACAAATTTAGTACTCCCTCAGTA 57.110 34.615 19.24 0.00 46.80 2.74
3751 4059 7.793948 AGTACAAATTTAGTACTCCCTCAGT 57.206 36.000 19.24 0.00 46.80 3.41
3753 4061 9.933723 GTTTAGTACAAATTTAGTACTCCCTCA 57.066 33.333 24.25 12.50 46.80 3.86
3754 4062 9.376075 GGTTTAGTACAAATTTAGTACTCCCTC 57.624 37.037 24.25 16.95 46.80 4.30
3755 4063 8.883302 TGGTTTAGTACAAATTTAGTACTCCCT 58.117 33.333 24.25 12.25 46.80 4.20
3756 4064 9.159364 CTGGTTTAGTACAAATTTAGTACTCCC 57.841 37.037 24.25 21.95 46.80 4.30
3757 4065 8.663025 GCTGGTTTAGTACAAATTTAGTACTCC 58.337 37.037 24.25 20.92 46.80 3.85
3758 4066 9.211485 TGCTGGTTTAGTACAAATTTAGTACTC 57.789 33.333 24.25 16.08 46.80 2.59
3760 4068 9.603298 GTTGCTGGTTTAGTACAAATTTAGTAC 57.397 33.333 16.59 16.59 41.59 2.73
3761 4069 9.339850 TGTTGCTGGTTTAGTACAAATTTAGTA 57.660 29.630 0.00 0.00 0.00 1.82
3762 4070 8.132995 GTGTTGCTGGTTTAGTACAAATTTAGT 58.867 33.333 0.00 0.00 0.00 2.24
3763 4071 8.349983 AGTGTTGCTGGTTTAGTACAAATTTAG 58.650 33.333 0.00 0.00 0.00 1.85
3764 4072 8.228035 AGTGTTGCTGGTTTAGTACAAATTTA 57.772 30.769 0.00 0.00 0.00 1.40
3765 4073 7.107639 AGTGTTGCTGGTTTAGTACAAATTT 57.892 32.000 0.00 0.00 0.00 1.82
3766 4074 6.709018 AGTGTTGCTGGTTTAGTACAAATT 57.291 33.333 0.00 0.00 0.00 1.82
3767 4075 6.709018 AAGTGTTGCTGGTTTAGTACAAAT 57.291 33.333 0.00 0.00 0.00 2.32
4217 4525 7.900782 TGTGTTCTTGGTACTAAGATAAAGC 57.099 36.000 20.78 11.00 36.63 3.51
4612 4920 0.938637 GATCGCTCTGCACATCTCCG 60.939 60.000 0.00 0.00 0.00 4.63
4890 5198 3.260632 TCCAGCAGTAGAGCACAATGTAA 59.739 43.478 0.00 0.00 36.85 2.41
5327 5664 6.697641 ACTGGAATAACCTTCCTAAAGTGA 57.302 37.500 5.66 0.00 39.31 3.41
5379 5718 9.613428 ATCAAATAAAGTTACTGCAGCATACTA 57.387 29.630 15.27 1.24 0.00 1.82
5535 5874 6.160576 AGAGCTAGATCCTTTGTCATCTTC 57.839 41.667 3.92 0.00 31.57 2.87
5586 5925 7.601856 TGTAGCTACAAAATGGAAAGAAATGG 58.398 34.615 24.15 0.00 32.40 3.16
5601 5940 2.232941 GCCCTGTGTACTGTAGCTACAA 59.767 50.000 25.95 10.96 35.50 2.41
5676 6019 0.989890 CGGCTAACACTGTAAGACGC 59.010 55.000 0.20 0.00 34.56 5.19
5681 6024 5.395682 ACTTATCACGGCTAACACTGTAA 57.604 39.130 0.00 0.00 0.00 2.41
5816 6167 0.804933 GCATTGCAAGGCAGCTAAGC 60.805 55.000 29.55 6.55 40.61 3.09
5877 6392 0.038159 CAAGTCCCTCCTGTGTCGAC 60.038 60.000 9.11 9.11 0.00 4.20
5921 6449 1.326548 CCCTATTCGTAGCACAAACGC 59.673 52.381 0.00 0.00 40.12 4.84
5929 6457 0.928229 CACGTTGCCCTATTCGTAGC 59.072 55.000 0.00 0.00 35.13 3.58
6087 6625 3.307674 GACATCGCTATCTGAAGAGCTG 58.692 50.000 11.65 7.59 37.60 4.24
6096 6634 4.141620 ACTTGGATTTGGACATCGCTATCT 60.142 41.667 0.00 0.00 0.00 1.98
6102 6640 2.164219 CCCAACTTGGATTTGGACATCG 59.836 50.000 9.61 0.00 45.69 3.84
6115 6653 2.863809 AGGTGTAAGAAGCCCAACTTG 58.136 47.619 0.00 0.00 39.29 3.16
6201 6743 7.192148 TCAAATTGGCTTTTGATTTCATGTG 57.808 32.000 10.71 0.00 39.91 3.21
6247 6789 5.193216 CAAAGAAACATGTCGCTCATATCG 58.807 41.667 0.00 0.00 34.67 2.92
6297 6850 0.957395 CTGCATCGGCTTCAGGTTGT 60.957 55.000 0.00 0.00 41.91 3.32
6314 6867 2.107292 CCTGCTACTGCTGCTGCTG 61.107 63.158 18.66 18.66 42.70 4.41
6315 6868 2.268280 CCTGCTACTGCTGCTGCT 59.732 61.111 17.00 0.00 40.48 4.24
6432 7017 2.828520 AGAGTAGACACTGACATGGGTG 59.171 50.000 12.11 12.11 34.21 4.61
6500 7085 4.331168 GGCAGCTTTGATAGTACAGTCAAG 59.669 45.833 11.26 8.26 35.91 3.02
6526 7111 1.661112 GTCTGCGTCTTCCATGTAAGC 59.339 52.381 0.00 0.00 0.00 3.09


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

AutoCloner maintained by Alex Coulton.