Multiple sequence alignment - TraesCS5A01G094400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5A01G094400 chr5A 100.000 7210 0 0 1 7210 130543132 130535923 0.000000e+00 13315.0
1 TraesCS5A01G094400 chr5A 88.571 105 12 0 1321 1425 706441173 706441069 2.110000e-25 128.0
2 TraesCS5A01G094400 chr5D 94.577 5182 186 34 1423 6557 120346019 120340886 0.000000e+00 7925.0
3 TraesCS5A01G094400 chr5D 91.439 1355 51 25 13 1343 120347329 120346016 0.000000e+00 1799.0
4 TraesCS5A01G094400 chr5D 96.206 659 21 1 6556 7210 120340851 120340193 0.000000e+00 1075.0
5 TraesCS5A01G094400 chr5D 91.824 159 11 1 2465 2623 528717431 528717275 3.390000e-53 220.0
6 TraesCS5A01G094400 chr5D 94.118 85 5 0 1341 1425 42242304 42242388 5.870000e-26 130.0
7 TraesCS5A01G094400 chr5D 92.135 89 7 0 1337 1425 42242392 42242304 7.590000e-25 126.0
8 TraesCS5A01G094400 chr5D 94.737 38 1 1 5926 5962 522111485 522111522 2.810000e-04 58.4
9 TraesCS5A01G094400 chr5D 90.698 43 1 3 5926 5966 547069840 547069799 4.000000e-03 54.7
10 TraesCS5A01G094400 chr5D 88.889 45 2 3 5926 5968 500118325 500118282 1.300000e-02 52.8
11 TraesCS5A01G094400 chr5B 93.924 5201 213 29 1423 6557 133599279 133594116 0.000000e+00 7758.0
12 TraesCS5A01G094400 chr5B 90.699 1301 53 20 56 1314 133600551 133599277 0.000000e+00 1670.0
13 TraesCS5A01G094400 chr5B 94.402 661 28 4 6556 7210 133594080 133593423 0.000000e+00 1007.0
14 TraesCS5A01G094400 chr5B 95.122 41 1 1 5926 5965 406172735 406172775 6.040000e-06 63.9
15 TraesCS5A01G094400 chr5B 93.023 43 0 3 5926 5966 704452661 704452702 7.810000e-05 60.2
16 TraesCS5A01G094400 chr6A 93.631 157 10 0 2465 2621 411770408 411770252 1.210000e-57 235.0
17 TraesCS5A01G094400 chr6A 83.735 166 12 4 1421 1576 608882431 608882591 7.540000e-30 143.0
18 TraesCS5A01G094400 chr7D 94.118 153 9 0 2468 2620 34756866 34757018 4.350000e-57 233.0
19 TraesCS5A01G094400 chr7D 93.506 154 9 1 2468 2620 454079230 454079077 2.020000e-55 228.0
20 TraesCS5A01G094400 chr7D 93.182 44 2 1 5926 5968 167359345 167359302 6.040000e-06 63.9
21 TraesCS5A01G094400 chr7D 97.143 35 0 1 5926 5960 479747849 479747882 2.810000e-04 58.4
22 TraesCS5A01G094400 chr7B 93.464 153 10 0 2468 2620 369872871 369872719 2.020000e-55 228.0
23 TraesCS5A01G094400 chr6D 92.453 159 10 2 2465 2621 303060010 303059852 7.280000e-55 226.0
24 TraesCS5A01G094400 chr6D 100.000 31 0 0 5926 5956 142148743 142148713 2.810000e-04 58.4
25 TraesCS5A01G094400 chr6D 100.000 30 0 0 5929 5958 52335471 52335500 1.000000e-03 56.5
26 TraesCS5A01G094400 chr6D 94.595 37 0 2 5926 5961 363038107 363038072 1.000000e-03 56.5
27 TraesCS5A01G094400 chr6D 94.595 37 1 1 5926 5961 429498267 429498303 1.000000e-03 56.5
28 TraesCS5A01G094400 chr6D 97.059 34 0 1 5926 5958 446215238 446215205 1.000000e-03 56.5
29 TraesCS5A01G094400 chr6D 100.000 29 0 0 5926 5954 3346614 3346586 4.000000e-03 54.7
30 TraesCS5A01G094400 chr6D 100.000 29 0 0 5926 5954 84071860 84071832 4.000000e-03 54.7
31 TraesCS5A01G094400 chr6D 94.444 36 0 2 5929 5963 126426600 126426566 4.000000e-03 54.7
32 TraesCS5A01G094400 chr6D 96.970 33 0 1 5926 5957 185368136 185368168 4.000000e-03 54.7
33 TraesCS5A01G094400 chr2A 92.857 154 11 0 2468 2621 141506318 141506471 2.620000e-54 224.0
34 TraesCS5A01G094400 chr2B 86.735 196 10 5 1421 1605 615943242 615943052 3.410000e-48 204.0
35 TraesCS5A01G094400 chrUn 86.224 196 11 5 1421 1605 86509207 86509397 1.590000e-46 198.0
36 TraesCS5A01G094400 chrUn 86.224 196 11 5 1421 1605 260202922 260203112 1.590000e-46 198.0
37 TraesCS5A01G094400 chrUn 86.224 196 11 5 1421 1605 270908417 270908607 1.590000e-46 198.0
38 TraesCS5A01G094400 chrUn 86.224 196 11 5 1421 1605 282363891 282364081 1.590000e-46 198.0
39 TraesCS5A01G094400 chrUn 91.579 95 8 0 4453 4547 55797773 55797679 1.630000e-26 132.0
40 TraesCS5A01G094400 chrUn 100.000 31 0 0 5928 5958 119058237 119058267 2.810000e-04 58.4
41 TraesCS5A01G094400 chr4D 86.224 196 11 5 1421 1605 123424519 123424329 1.590000e-46 198.0
42 TraesCS5A01G094400 chr4D 90.526 95 9 0 4453 4547 138280217 138280123 7.590000e-25 126.0
43 TraesCS5A01G094400 chr4D 100.000 32 0 0 5926 5957 440036026 440036057 7.810000e-05 60.2
44 TraesCS5A01G094400 chr4D 94.737 38 0 2 5926 5961 405770456 405770493 2.810000e-04 58.4
45 TraesCS5A01G094400 chr4D 100.000 31 0 0 5926 5956 491950793 491950763 2.810000e-04 58.4
46 TraesCS5A01G094400 chr4D 90.698 43 2 2 5926 5966 8783992 8784034 1.000000e-03 56.5
47 TraesCS5A01G094400 chr4D 97.059 34 0 1 5926 5958 82293389 82293356 1.000000e-03 56.5
48 TraesCS5A01G094400 chr4D 87.500 48 5 1 5908 5954 509646602 509646555 4.000000e-03 54.7
49 TraesCS5A01G094400 chr4D 100.000 28 0 0 5929 5956 190533052 190533079 1.300000e-02 52.8
50 TraesCS5A01G094400 chr3A 86.096 187 12 3 1425 1601 227656345 227656163 9.550000e-44 189.0
51 TraesCS5A01G094400 chr3A 93.407 91 6 0 1341 1431 696400904 696400994 1.260000e-27 135.0
52 TraesCS5A01G094400 chr3A 87.850 107 9 4 1330 1432 725059524 725059418 9.820000e-24 122.0
53 TraesCS5A01G094400 chr6B 95.556 90 3 1 1341 1430 582391481 582391393 7.540000e-30 143.0
54 TraesCS5A01G094400 chr6B 92.857 42 1 2 5926 5966 416897354 416897314 7.810000e-05 60.2
55 TraesCS5A01G094400 chr1D 95.294 85 4 0 1341 1425 471923468 471923552 1.260000e-27 135.0
56 TraesCS5A01G094400 chr1D 92.683 41 1 2 5926 5965 59875976 59875937 2.810000e-04 58.4
57 TraesCS5A01G094400 chr1D 92.683 41 1 2 5926 5965 231154444 231154483 2.810000e-04 58.4
58 TraesCS5A01G094400 chr1D 92.500 40 2 1 5926 5965 403131008 403130970 1.000000e-03 56.5
59 TraesCS5A01G094400 chr2D 92.473 93 7 0 1341 1433 639896713 639896805 4.540000e-27 134.0
60 TraesCS5A01G094400 chr2D 94.595 37 1 1 5929 5965 335449700 335449665 1.000000e-03 56.5
61 TraesCS5A01G094400 chr1A 94.118 85 5 0 1341 1425 582452014 582452098 5.870000e-26 130.0
62 TraesCS5A01G094400 chr1A 92.500 40 2 1 5926 5964 7181306 7181267 1.000000e-03 56.5
63 TraesCS5A01G094400 chr4A 88.776 98 11 0 4450 4547 418077448 418077545 3.530000e-23 121.0
64 TraesCS5A01G094400 chr1B 100.000 34 0 0 5926 5959 159061451 159061484 6.040000e-06 63.9
65 TraesCS5A01G094400 chr3D 83.099 71 8 4 5926 5994 25199375 25199307 2.170000e-05 62.1
66 TraesCS5A01G094400 chr3D 92.857 42 2 1 5927 5967 379684620 379684661 7.810000e-05 60.2
67 TraesCS5A01G094400 chr3D 94.737 38 0 2 5929 5966 26166839 26166874 2.810000e-04 58.4
68 TraesCS5A01G094400 chr4B 92.683 41 1 2 5926 5965 190259966 190260005 2.810000e-04 58.4
69 TraesCS5A01G094400 chr4B 89.362 47 2 3 5926 5971 492210826 492210782 1.000000e-03 56.5
70 TraesCS5A01G094400 chr4B 85.714 56 2 5 5929 5982 582368320 582368269 4.000000e-03 54.7
71 TraesCS5A01G094400 chr3B 92.683 41 1 2 5929 5967 520448012 520448052 2.810000e-04 58.4


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 TraesCS5A01G094400 chr5A 130535923 130543132 7209 True 13315.000000 13315 100.000000 1 7210 1 chr5A.!!$R1 7209
1 TraesCS5A01G094400 chr5D 120340193 120347329 7136 True 3599.666667 7925 94.074000 13 7210 3 chr5D.!!$R5 7197
2 TraesCS5A01G094400 chr5B 133593423 133600551 7128 True 3478.333333 7758 93.008333 56 7210 3 chr5B.!!$R1 7154

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
408 443 0.322546 TGCAGACAGAGGTAGCTCGA 60.323 55.000 15.91 0.0 0.00 4.04 F
1355 1394 0.042131 AATGTACTCCCTCCGTCCCA 59.958 55.000 0.00 0.0 0.00 4.37 F
2025 2072 0.035317 AAATGTGAGCGCCTCTGTGA 59.965 50.000 2.29 0.0 0.00 3.58 F
3011 3064 2.227865 GCGTTATTCTTGTTGGAGGCAA 59.772 45.455 0.00 0.0 0.00 4.52 F
4160 4216 1.471119 CAGTACCGCCTAGTTCCTCA 58.529 55.000 0.00 0.0 0.00 3.86 F
5068 5130 0.107263 TGTTGCAAGGCACAGTCTCA 60.107 50.000 0.00 0.0 38.71 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1410 1449 0.549413 AAAGGTACCCCCTCTGTCCC 60.549 60.000 8.74 0.00 45.47 4.46 R
2964 3017 1.355971 CCCACGAAACCTGTACATCG 58.644 55.000 13.56 13.56 40.90 3.84 R
3078 3131 1.614413 CTATCGGGCAGAGGAGGTTAC 59.386 57.143 0.00 0.00 0.00 2.50 R
4440 4496 0.469705 ACCCTGCATGAACCAAGCAA 60.470 50.000 0.00 0.00 37.62 3.91 R
5616 5685 0.107606 CCTTGAGCAGCTCAGCATCT 60.108 55.000 24.15 0.00 41.75 2.90 R
6212 6324 0.387565 GCCCCGCTTCTTGTTTTGAA 59.612 50.000 0.00 0.00 0.00 2.69 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
31 32 3.639222 CGCAAGTTGTAAGCGTGAG 57.361 52.632 4.48 0.00 45.82 3.51
52 53 0.941542 ACGGAATGACGTGTGTTTGG 59.058 50.000 0.00 0.00 46.64 3.28
53 54 1.222300 CGGAATGACGTGTGTTTGGA 58.778 50.000 0.00 0.00 0.00 3.53
54 55 1.070175 CGGAATGACGTGTGTTTGGAC 60.070 52.381 0.00 0.00 0.00 4.02
343 355 4.680237 CTTCCACCACGCCAGCGA 62.680 66.667 20.32 0.00 42.83 4.93
358 370 3.333189 CGACATCGCCATCGCCAG 61.333 66.667 0.00 0.00 35.26 4.85
408 443 0.322546 TGCAGACAGAGGTAGCTCGA 60.323 55.000 15.91 0.00 0.00 4.04
423 458 1.098869 CTCGAGCAGCACTTCTCCTA 58.901 55.000 0.00 0.00 0.00 2.94
445 480 0.533032 CTTCCTTCTCCCTCGGTGAC 59.467 60.000 0.00 0.00 0.00 3.67
463 498 1.416049 CGATTTCGTGCGTCTGGTG 59.584 57.895 0.00 0.00 34.11 4.17
465 500 0.949105 GATTTCGTGCGTCTGGTGGT 60.949 55.000 0.00 0.00 0.00 4.16
466 501 0.534203 ATTTCGTGCGTCTGGTGGTT 60.534 50.000 0.00 0.00 0.00 3.67
467 502 1.433053 TTTCGTGCGTCTGGTGGTTG 61.433 55.000 0.00 0.00 0.00 3.77
483 518 4.522789 GGTGGTTGAGCAAATTCCTTCTTA 59.477 41.667 0.00 0.00 0.00 2.10
512 547 3.989600 TGAATCCCTCTCCATCTCTCT 57.010 47.619 0.00 0.00 0.00 3.10
548 583 2.527100 GCAACAGCAATGCATCTTCTC 58.473 47.619 8.35 0.00 43.29 2.87
556 591 3.946558 GCAATGCATCTTCTCCTTCTTCT 59.053 43.478 0.00 0.00 0.00 2.85
557 592 4.398673 GCAATGCATCTTCTCCTTCTTCTT 59.601 41.667 0.00 0.00 0.00 2.52
558 593 5.448904 GCAATGCATCTTCTCCTTCTTCTTC 60.449 44.000 0.00 0.00 0.00 2.87
559 594 5.697082 ATGCATCTTCTCCTTCTTCTTCT 57.303 39.130 0.00 0.00 0.00 2.85
560 595 5.495926 TGCATCTTCTCCTTCTTCTTCTT 57.504 39.130 0.00 0.00 0.00 2.52
561 596 5.486526 TGCATCTTCTCCTTCTTCTTCTTC 58.513 41.667 0.00 0.00 0.00 2.87
562 597 5.248020 TGCATCTTCTCCTTCTTCTTCTTCT 59.752 40.000 0.00 0.00 0.00 2.85
563 598 5.812127 GCATCTTCTCCTTCTTCTTCTTCTC 59.188 44.000 0.00 0.00 0.00 2.87
564 599 5.993748 TCTTCTCCTTCTTCTTCTTCTCC 57.006 43.478 0.00 0.00 0.00 3.71
565 600 5.650283 TCTTCTCCTTCTTCTTCTTCTCCT 58.350 41.667 0.00 0.00 0.00 3.69
566 601 5.714806 TCTTCTCCTTCTTCTTCTTCTCCTC 59.285 44.000 0.00 0.00 0.00 3.71
567 602 5.269554 TCTCCTTCTTCTTCTTCTCCTCT 57.730 43.478 0.00 0.00 0.00 3.69
568 603 5.650283 TCTCCTTCTTCTTCTTCTCCTCTT 58.350 41.667 0.00 0.00 0.00 2.85
569 604 6.081356 TCTCCTTCTTCTTCTTCTCCTCTTT 58.919 40.000 0.00 0.00 0.00 2.52
600 635 2.222227 AAAGGGAAGGAATGTGGCTC 57.778 50.000 0.00 0.00 0.00 4.70
614 649 3.584947 GGCTCTTCTTGGCCATTCT 57.415 52.632 6.09 0.00 46.84 2.40
615 650 1.844687 GGCTCTTCTTGGCCATTCTT 58.155 50.000 6.09 0.00 46.84 2.52
619 654 1.005924 TCTTCTTGGCCATTCTTCCCC 59.994 52.381 6.09 0.00 0.00 4.81
620 655 0.783206 TTCTTGGCCATTCTTCCCCA 59.217 50.000 6.09 0.00 0.00 4.96
751 789 0.322546 AATCCCAGGACGAGGCAAAC 60.323 55.000 0.00 0.00 0.00 2.93
810 848 6.796705 TTATTTTTCCTTCTTGGTCTCGTC 57.203 37.500 0.00 0.00 37.07 4.20
838 876 2.112815 GTTCCCCTGATTTCCGCCG 61.113 63.158 0.00 0.00 0.00 6.46
839 877 2.598787 TTCCCCTGATTTCCGCCGT 61.599 57.895 0.00 0.00 0.00 5.68
890 929 3.246314 ACCAAATCCCCATTTACCACCAT 60.246 43.478 0.00 0.00 30.51 3.55
973 1012 1.142097 GCGGTCTGCTTCTAGGACC 59.858 63.158 5.32 5.32 44.16 4.46
1020 1059 3.722295 TTTGCTTTCTCGCGCCGG 61.722 61.111 0.00 0.00 0.00 6.13
1168 1207 2.485814 GTGATGGTTTCTGGTGAGAAGC 59.514 50.000 0.00 0.00 39.44 3.86
1169 1208 2.373169 TGATGGTTTCTGGTGAGAAGCT 59.627 45.455 0.00 0.00 39.44 3.74
1170 1209 3.181440 TGATGGTTTCTGGTGAGAAGCTT 60.181 43.478 0.00 0.00 39.44 3.74
1275 1314 5.940192 ACTTTATTGTGCAAACGATGAGA 57.060 34.783 0.00 0.00 0.00 3.27
1345 1384 8.106247 TGACTAAATTTGGTGAAATGTACTCC 57.894 34.615 12.36 0.00 31.83 3.85
1346 1385 7.175990 TGACTAAATTTGGTGAAATGTACTCCC 59.824 37.037 12.36 0.00 31.83 4.30
1347 1386 7.238710 ACTAAATTTGGTGAAATGTACTCCCT 58.761 34.615 6.37 0.00 31.83 4.20
1348 1387 6.590234 AAATTTGGTGAAATGTACTCCCTC 57.410 37.500 0.00 0.00 31.83 4.30
1349 1388 3.713826 TTGGTGAAATGTACTCCCTCC 57.286 47.619 0.00 0.00 0.00 4.30
1350 1389 1.553248 TGGTGAAATGTACTCCCTCCG 59.447 52.381 0.00 0.00 0.00 4.63
1351 1390 1.553704 GGTGAAATGTACTCCCTCCGT 59.446 52.381 0.00 0.00 0.00 4.69
1352 1391 2.418334 GGTGAAATGTACTCCCTCCGTC 60.418 54.545 0.00 0.00 0.00 4.79
1353 1392 1.829222 TGAAATGTACTCCCTCCGTCC 59.171 52.381 0.00 0.00 0.00 4.79
1354 1393 1.138464 GAAATGTACTCCCTCCGTCCC 59.862 57.143 0.00 0.00 0.00 4.46
1355 1394 0.042131 AATGTACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
1356 1395 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
1357 1396 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
1358 1397 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
1359 1398 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
1360 1399 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
1361 1400 2.488836 ACTCCCTCCGTCCCAAAATAT 58.511 47.619 0.00 0.00 0.00 1.28
1362 1401 3.660959 ACTCCCTCCGTCCCAAAATATA 58.339 45.455 0.00 0.00 0.00 0.86
1363 1402 4.042174 ACTCCCTCCGTCCCAAAATATAA 58.958 43.478 0.00 0.00 0.00 0.98
1364 1403 4.102681 ACTCCCTCCGTCCCAAAATATAAG 59.897 45.833 0.00 0.00 0.00 1.73
1365 1404 4.300345 TCCCTCCGTCCCAAAATATAAGA 58.700 43.478 0.00 0.00 0.00 2.10
1366 1405 4.347000 TCCCTCCGTCCCAAAATATAAGAG 59.653 45.833 0.00 0.00 0.00 2.85
1367 1406 4.102681 CCCTCCGTCCCAAAATATAAGAGT 59.897 45.833 0.00 0.00 0.00 3.24
1368 1407 5.057149 CCTCCGTCCCAAAATATAAGAGTG 58.943 45.833 0.00 0.00 0.00 3.51
1369 1408 5.396436 CCTCCGTCCCAAAATATAAGAGTGT 60.396 44.000 0.00 0.00 0.00 3.55
1370 1409 6.057321 TCCGTCCCAAAATATAAGAGTGTT 57.943 37.500 0.00 0.00 0.00 3.32
1371 1410 6.478129 TCCGTCCCAAAATATAAGAGTGTTT 58.522 36.000 0.00 0.00 0.00 2.83
1372 1411 6.943718 TCCGTCCCAAAATATAAGAGTGTTTT 59.056 34.615 0.00 0.00 0.00 2.43
1373 1412 7.449086 TCCGTCCCAAAATATAAGAGTGTTTTT 59.551 33.333 0.00 0.00 0.00 1.94
1374 1413 7.753580 CCGTCCCAAAATATAAGAGTGTTTTTC 59.246 37.037 0.00 0.00 0.00 2.29
1375 1414 8.293867 CGTCCCAAAATATAAGAGTGTTTTTCA 58.706 33.333 0.00 0.00 0.00 2.69
1414 1453 9.634163 ATGAAAAACGTTCTTATATTTTGGGAC 57.366 29.630 0.00 0.00 0.00 4.46
1415 1454 8.630917 TGAAAAACGTTCTTATATTTTGGGACA 58.369 29.630 0.00 0.00 0.00 4.02
1416 1455 9.124807 GAAAAACGTTCTTATATTTTGGGACAG 57.875 33.333 0.00 0.00 42.39 3.51
1417 1456 7.989416 AAACGTTCTTATATTTTGGGACAGA 57.011 32.000 0.00 0.00 42.39 3.41
1418 1457 7.611213 AACGTTCTTATATTTTGGGACAGAG 57.389 36.000 0.00 0.00 42.39 3.35
1419 1458 6.113411 ACGTTCTTATATTTTGGGACAGAGG 58.887 40.000 0.00 0.00 42.39 3.69
1420 1459 5.527582 CGTTCTTATATTTTGGGACAGAGGG 59.472 44.000 0.00 0.00 42.39 4.30
1421 1460 5.646692 TCTTATATTTTGGGACAGAGGGG 57.353 43.478 0.00 0.00 42.39 4.79
1510 1556 6.552445 ATCCTCACTTGACTAAGCATAAGT 57.448 37.500 0.00 0.00 37.43 2.24
1521 1567 5.061179 ACTAAGCATAAGTGAAAACGTGGT 58.939 37.500 0.00 0.00 0.00 4.16
1742 1789 4.532490 GCGGTTAGCCTATGCACA 57.468 55.556 0.00 0.00 41.13 4.57
2015 2062 1.198637 GTCAGCCTGTCAAATGTGAGC 59.801 52.381 0.00 0.00 33.27 4.26
2018 2065 1.503542 CCTGTCAAATGTGAGCGCC 59.496 57.895 2.29 0.00 33.27 6.53
2025 2072 0.035317 AAATGTGAGCGCCTCTGTGA 59.965 50.000 2.29 0.00 0.00 3.58
2156 2205 2.283298 CGTGCAGATGACCTTGCTTAT 58.717 47.619 0.00 0.00 0.00 1.73
2334 2383 4.928020 CCCTCATCAGAATGTCGATATGTG 59.072 45.833 0.00 0.00 37.40 3.21
2431 2480 7.825681 TGTTGGATGATACAAAGGTAATTGTG 58.174 34.615 0.00 0.00 43.13 3.33
2634 2684 3.646162 AGGGAGTATCATGTTATTCGGCA 59.354 43.478 0.00 0.00 36.25 5.69
2649 2699 8.075574 TGTTATTCGGCAATTGACATTATGATC 58.924 33.333 12.81 0.00 0.00 2.92
2890 2940 5.941555 ATAATTATTTTTCCGTTGGGCCA 57.058 34.783 0.00 0.00 0.00 5.36
2923 2976 4.385825 TGGACCTGACAACTGAAATACAC 58.614 43.478 0.00 0.00 0.00 2.90
2964 3017 7.714813 AGAGAAATAGCTAAGCTTGATCCTTTC 59.285 37.037 9.86 12.22 40.44 2.62
3011 3064 2.227865 GCGTTATTCTTGTTGGAGGCAA 59.772 45.455 0.00 0.00 0.00 4.52
3056 3109 2.910688 TCAGGTTCTCACACTTCCAC 57.089 50.000 0.00 0.00 0.00 4.02
3078 3131 5.184479 CACAGCCCTTGGATTTATATGATGG 59.816 44.000 0.00 0.00 0.00 3.51
3140 3193 3.230134 TGCAGTTTGGGCTTTCAATACT 58.770 40.909 0.00 0.00 0.00 2.12
3146 3199 5.362430 AGTTTGGGCTTTCAATACTGAAACA 59.638 36.000 0.00 0.00 44.76 2.83
3227 3283 4.452455 AGTGCTATGCTGCGGTTAAATATC 59.548 41.667 0.00 0.00 35.36 1.63
3443 3499 3.009723 TGAATTCCGAAGAATCCTGTGC 58.990 45.455 2.27 0.00 42.03 4.57
3447 3503 2.176045 TCCGAAGAATCCTGTGCAGTA 58.824 47.619 0.00 0.00 0.00 2.74
3484 3540 8.674263 TCAAATTTGCTTCATGGTTACATTTT 57.326 26.923 13.54 0.00 34.35 1.82
3665 3721 5.231702 TGCTGCATTGTATGATGATAGGA 57.768 39.130 0.00 0.00 0.00 2.94
3691 3747 5.221048 CCTTTTAATATTTGGAGGCCACTCG 60.221 44.000 5.01 0.00 44.93 4.18
3805 3861 5.238432 TCGGTATGATGCATGTTAATGGTTC 59.762 40.000 2.46 0.00 34.09 3.62
3806 3862 5.239306 CGGTATGATGCATGTTAATGGTTCT 59.761 40.000 2.46 0.00 34.09 3.01
4017 4073 3.873361 AGATTCTGGTTCATATGTGCACG 59.127 43.478 13.13 0.00 0.00 5.34
4048 4104 3.627395 TTAGAAGAATGCCGTGTCCAT 57.373 42.857 0.00 0.00 0.00 3.41
4160 4216 1.471119 CAGTACCGCCTAGTTCCTCA 58.529 55.000 0.00 0.00 0.00 3.86
4295 4351 4.898829 TCATGTTTGTGTTCTGGACTTG 57.101 40.909 0.00 0.00 0.00 3.16
4436 4492 8.956533 TTATCTCATTTTATCACATGAACCGA 57.043 30.769 0.00 0.00 0.00 4.69
4437 4493 9.559732 TTATCTCATTTTATCACATGAACCGAT 57.440 29.630 0.00 0.00 0.00 4.18
4438 4494 7.864108 TCTCATTTTATCACATGAACCGATT 57.136 32.000 0.00 0.00 0.00 3.34
4439 4495 8.279970 TCTCATTTTATCACATGAACCGATTT 57.720 30.769 0.00 0.00 0.00 2.17
4440 4496 8.739039 TCTCATTTTATCACATGAACCGATTTT 58.261 29.630 0.00 0.00 0.00 1.82
4441 4497 9.357652 CTCATTTTATCACATGAACCGATTTTT 57.642 29.630 0.00 0.00 0.00 1.94
4442 4498 9.138062 TCATTTTATCACATGAACCGATTTTTG 57.862 29.630 0.00 0.00 0.00 2.44
4443 4499 6.942886 TTTATCACATGAACCGATTTTTGC 57.057 33.333 0.00 0.00 0.00 3.68
4444 4500 4.789012 ATCACATGAACCGATTTTTGCT 57.211 36.364 0.00 0.00 0.00 3.91
4445 4501 4.582701 TCACATGAACCGATTTTTGCTT 57.417 36.364 0.00 0.00 0.00 3.91
4447 4503 3.429543 CACATGAACCGATTTTTGCTTGG 59.570 43.478 0.00 0.00 0.00 3.61
4611 4670 9.749490 GTTGCATTCTCATTTTGAACAAATATG 57.251 29.630 0.82 7.94 0.00 1.78
4645 4704 4.522722 ACTTCTCCTCGTGTTCTAAAGG 57.477 45.455 0.00 0.00 0.00 3.11
4657 4716 3.250040 TGTTCTAAAGGCTTTCAACGAGC 59.750 43.478 17.13 11.07 39.41 5.03
4658 4717 3.120321 TCTAAAGGCTTTCAACGAGCA 57.880 42.857 17.13 0.00 41.89 4.26
4659 4718 3.472652 TCTAAAGGCTTTCAACGAGCAA 58.527 40.909 17.13 0.00 41.89 3.91
4660 4719 2.492019 AAAGGCTTTCAACGAGCAAC 57.508 45.000 6.68 0.00 41.89 4.17
4661 4720 1.680338 AAGGCTTTCAACGAGCAACT 58.320 45.000 0.00 0.00 41.89 3.16
4662 4721 1.680338 AGGCTTTCAACGAGCAACTT 58.320 45.000 0.00 0.00 41.89 2.66
4663 4722 2.024414 AGGCTTTCAACGAGCAACTTT 58.976 42.857 0.00 0.00 41.89 2.66
4664 4723 2.427095 AGGCTTTCAACGAGCAACTTTT 59.573 40.909 0.00 0.00 41.89 2.27
4665 4724 3.119137 AGGCTTTCAACGAGCAACTTTTT 60.119 39.130 0.00 0.00 41.89 1.94
4700 4759 3.927142 ACTTTATCAGCGTTGTAGTGCTC 59.073 43.478 0.00 0.00 40.03 4.26
4760 4821 5.192927 TCCCTTGAGTATATTTGGCACTTG 58.807 41.667 0.00 0.00 0.00 3.16
4771 4833 9.237846 GTATATTTGGCACTTGCTTTCTAATTC 57.762 33.333 0.38 0.00 41.70 2.17
4777 4839 5.860716 GGCACTTGCTTTCTAATTCTTGAAG 59.139 40.000 0.38 0.00 41.70 3.02
4779 4841 6.920210 GCACTTGCTTTCTAATTCTTGAAGTT 59.080 34.615 0.00 0.00 38.21 2.66
4794 4856 7.857734 TCTTGAAGTTTGTGTAATTGTCTCA 57.142 32.000 0.00 0.00 0.00 3.27
4799 4861 8.128582 TGAAGTTTGTGTAATTGTCTCATCAAC 58.871 33.333 0.00 0.00 0.00 3.18
4802 4864 8.077991 AGTTTGTGTAATTGTCTCATCAACATG 58.922 33.333 0.00 0.00 0.00 3.21
4837 4899 7.537715 TGCACCTGAATATACTGAAACATTTG 58.462 34.615 0.00 0.00 0.00 2.32
4882 4944 5.752892 ATTGAGATGCATCACTGAACATC 57.247 39.130 27.81 14.28 39.35 3.06
4885 4947 4.757019 AGATGCATCACTGAACATCTCT 57.243 40.909 27.81 0.29 44.50 3.10
4886 4948 4.443621 AGATGCATCACTGAACATCTCTG 58.556 43.478 27.81 0.00 44.50 3.35
4909 4971 6.694447 TGTGGTTATCTGTAGGTTGAAGTAC 58.306 40.000 0.00 0.00 0.00 2.73
4911 4973 6.812160 GTGGTTATCTGTAGGTTGAAGTACTG 59.188 42.308 0.00 0.00 0.00 2.74
4917 4979 4.482030 TGTAGGTTGAAGTACTGGTGGTA 58.518 43.478 0.00 0.00 0.00 3.25
5068 5130 0.107263 TGTTGCAAGGCACAGTCTCA 60.107 50.000 0.00 0.00 38.71 3.27
5079 5141 2.094957 GCACAGTCTCACCTCTACAGTC 60.095 54.545 0.00 0.00 0.00 3.51
5142 5204 2.419297 GCTCCACAGGAAGTATGGTCAG 60.419 54.545 0.00 0.00 34.89 3.51
5153 5215 5.163499 GGAAGTATGGTCAGGTAGAAGACTG 60.163 48.000 0.00 0.00 35.18 3.51
5154 5216 3.702045 AGTATGGTCAGGTAGAAGACTGC 59.298 47.826 0.00 0.00 35.18 4.40
5155 5217 2.009681 TGGTCAGGTAGAAGACTGCA 57.990 50.000 0.00 0.00 35.18 4.41
5398 5467 5.155278 TGTAGCCGTCAAGGAAGAAAATA 57.845 39.130 0.00 0.00 45.00 1.40
5468 5537 4.002982 GACATCAGCCATCTGTACAACAA 58.997 43.478 0.00 0.00 41.10 2.83
5607 5676 2.297129 GGAGAAGAGGCTGGCCAGT 61.297 63.158 32.81 15.59 38.92 4.00
5616 5685 2.612493 GCTGGCCAGTAGGGGGAAA 61.612 63.158 32.81 0.00 37.04 3.13
5619 5688 0.253630 TGGCCAGTAGGGGGAAAGAT 60.254 55.000 0.00 0.00 37.04 2.40
5688 5757 4.615513 AGGAGTCTAACAGCCTGTCTAAT 58.384 43.478 0.00 0.00 0.00 1.73
5780 5849 0.326238 AAGGCAAGGACGATCCCCTA 60.326 55.000 2.08 0.00 37.19 3.53
5920 5991 4.777896 AGCTACAGGTATTTGAGACCTTGA 59.222 41.667 0.00 0.00 45.40 3.02
5921 5992 5.248477 AGCTACAGGTATTTGAGACCTTGAA 59.752 40.000 0.00 0.00 45.40 2.69
5922 5993 5.351740 GCTACAGGTATTTGAGACCTTGAAC 59.648 44.000 0.00 0.00 45.40 3.18
5923 5994 4.315803 ACAGGTATTTGAGACCTTGAACG 58.684 43.478 0.00 0.00 45.40 3.95
5924 5995 3.684788 CAGGTATTTGAGACCTTGAACGG 59.315 47.826 0.00 0.00 45.40 4.44
5967 6058 6.490721 ACGGAGGGAGTACTTAGAATAGAATG 59.509 42.308 0.00 0.00 0.00 2.67
6001 6092 1.340991 GGCCAGCATAGGTTTTCAGGA 60.341 52.381 0.00 0.00 0.00 3.86
6029 6120 9.071221 GCATCAGACTCTTATTCGTCATAATAG 57.929 37.037 0.00 0.00 32.68 1.73
6054 6145 4.995487 GTGTAAAGTCTCCCAAAATCGTCT 59.005 41.667 0.00 0.00 0.00 4.18
6110 6222 6.211384 TCTGTTCCTGAACACTCATGATCTTA 59.789 38.462 8.58 0.00 45.42 2.10
6117 6229 7.148507 CCTGAACACTCATGATCTTACTGTTTC 60.149 40.741 0.00 0.00 0.00 2.78
6118 6230 7.445121 TGAACACTCATGATCTTACTGTTTCT 58.555 34.615 0.00 0.00 0.00 2.52
6119 6231 7.386025 TGAACACTCATGATCTTACTGTTTCTG 59.614 37.037 0.00 0.00 0.00 3.02
6120 6232 6.997655 ACACTCATGATCTTACTGTTTCTGA 58.002 36.000 0.00 0.00 0.00 3.27
6153 6265 1.004044 AGGTGTTCCATCTGAAGCAGG 59.996 52.381 0.00 0.00 32.37 4.85
6179 6291 1.227292 GACGGCGGAAGGAAGATCC 60.227 63.158 13.24 0.00 36.58 3.36
6213 6325 7.880265 AGGAAGCCTCATAATCCTTAGTATT 57.120 36.000 0.00 0.00 39.23 1.89
6219 6331 9.343539 AGCCTCATAATCCTTAGTATTCAAAAC 57.656 33.333 0.00 0.00 0.00 2.43
6354 6466 3.228749 GTGTGTGAATCATTGTGCTTCG 58.771 45.455 0.00 0.00 0.00 3.79
6364 6476 3.127376 TCATTGTGCTTCGTGGATTGATG 59.873 43.478 0.00 0.00 0.00 3.07
6404 6516 4.013728 AGATAGTCGACTGAGAGCAACTT 58.986 43.478 28.12 0.00 0.00 2.66
6405 6517 2.715737 AGTCGACTGAGAGCAACTTC 57.284 50.000 19.30 0.00 0.00 3.01
6497 6609 5.009410 AGCTGATTTTCTTTCCTTGTCTGTG 59.991 40.000 0.00 0.00 0.00 3.66
6538 6650 9.793259 TTAATTTGATTAACTCAAGTCAGGTCT 57.207 29.630 0.00 0.00 44.48 3.85
6615 6770 6.649557 ACCAAATTAAACTAGAAGGTGAGTCG 59.350 38.462 0.00 0.00 0.00 4.18
6629 6784 3.057033 GGTGAGTCGGCAGTTTAGTCTTA 60.057 47.826 0.00 0.00 0.00 2.10
6729 6888 2.062971 AGCCCACATCACCATGATTC 57.937 50.000 0.00 0.00 34.28 2.52
6797 6956 5.227908 ACACATTACTTTTCATCGTCGTCT 58.772 37.500 0.00 0.00 0.00 4.18
6800 6959 5.924254 ACATTACTTTTCATCGTCGTCTTCA 59.076 36.000 0.00 0.00 0.00 3.02
6818 6977 3.988379 TCATCGTCGTCATCATCATCA 57.012 42.857 0.00 0.00 0.00 3.07
6914 7073 2.492012 CTTGCACTCAGCTTCTCAACT 58.508 47.619 0.00 0.00 45.94 3.16
7012 7171 4.354587 GCTTGCGCTTTTATTGCTTCTAT 58.645 39.130 9.73 0.00 0.00 1.98
7019 7178 4.574828 GCTTTTATTGCTTCTATGTCCGGA 59.425 41.667 0.00 0.00 0.00 5.14
7188 7347 5.597813 TTCGATCTGAGCTTTTTCAGTTC 57.402 39.130 3.26 4.06 43.96 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.162181 ACTTGCGCGATGGATGGATG 61.162 55.000 12.10 0.00 0.00 3.51
1 2 0.464373 AACTTGCGCGATGGATGGAT 60.464 50.000 12.10 0.00 0.00 3.41
2 3 1.078497 AACTTGCGCGATGGATGGA 60.078 52.632 12.10 0.00 0.00 3.41
3 4 1.063006 CAACTTGCGCGATGGATGG 59.937 57.895 12.10 0.00 0.00 3.51
4 5 1.006086 TACAACTTGCGCGATGGATG 58.994 50.000 12.10 5.06 0.00 3.51
5 6 1.665679 CTTACAACTTGCGCGATGGAT 59.334 47.619 12.10 0.00 0.00 3.41
6 7 1.075542 CTTACAACTTGCGCGATGGA 58.924 50.000 12.10 0.00 0.00 3.41
7 8 0.521242 GCTTACAACTTGCGCGATGG 60.521 55.000 12.10 0.00 0.00 3.51
8 9 0.853224 CGCTTACAACTTGCGCGATG 60.853 55.000 12.10 0.00 45.99 3.84
9 10 1.419922 CGCTTACAACTTGCGCGAT 59.580 52.632 12.10 0.00 45.99 4.58
10 11 2.850404 CGCTTACAACTTGCGCGA 59.150 55.556 12.10 0.00 45.99 5.87
31 32 2.601266 CCAAACACACGTCATTCCGTTC 60.601 50.000 0.00 0.00 39.45 3.95
52 53 0.320421 TGGCTACACGCTCCAAAGTC 60.320 55.000 0.00 0.00 39.13 3.01
53 54 0.320771 CTGGCTACACGCTCCAAAGT 60.321 55.000 0.00 0.00 39.13 2.66
54 55 1.639298 GCTGGCTACACGCTCCAAAG 61.639 60.000 0.00 0.00 39.13 2.77
69 70 1.386525 AATACCATTGCGCTGGCTGG 61.387 55.000 15.15 14.45 40.15 4.85
361 373 1.451028 GAGGATCCACTGGCACTGC 60.451 63.158 15.82 0.00 0.00 4.40
423 458 1.834263 CACCGAGGGAGAAGGAAGAAT 59.166 52.381 0.00 0.00 0.00 2.40
445 480 1.416049 CACCAGACGCACGAAATCG 59.584 57.895 0.48 0.48 46.33 3.34
446 481 0.949105 ACCACCAGACGCACGAAATC 60.949 55.000 0.00 0.00 0.00 2.17
447 482 0.534203 AACCACCAGACGCACGAAAT 60.534 50.000 0.00 0.00 0.00 2.17
448 483 1.153329 AACCACCAGACGCACGAAA 60.153 52.632 0.00 0.00 0.00 3.46
449 484 1.885388 CAACCACCAGACGCACGAA 60.885 57.895 0.00 0.00 0.00 3.85
450 485 2.279851 CAACCACCAGACGCACGA 60.280 61.111 0.00 0.00 0.00 4.35
458 493 2.242043 AGGAATTTGCTCAACCACCAG 58.758 47.619 0.00 0.00 0.00 4.00
459 494 2.380064 AGGAATTTGCTCAACCACCA 57.620 45.000 0.00 0.00 0.00 4.17
463 498 8.090831 AGAAAATAAGAAGGAATTTGCTCAACC 58.909 33.333 0.00 0.00 26.52 3.77
465 500 8.859090 TCAGAAAATAAGAAGGAATTTGCTCAA 58.141 29.630 0.00 0.00 30.02 3.02
466 501 8.408043 TCAGAAAATAAGAAGGAATTTGCTCA 57.592 30.769 0.00 0.00 30.02 4.26
467 502 9.298774 CATCAGAAAATAAGAAGGAATTTGCTC 57.701 33.333 0.00 0.00 30.02 4.26
483 518 5.722172 TGGAGAGGGATTCATCAGAAAAT 57.278 39.130 0.00 0.00 37.29 1.82
512 547 5.651576 TGCTGTTGCATATACCAGATCAAAA 59.348 36.000 0.00 0.00 45.31 2.44
548 583 5.012561 TCCAAAGAGGAGAAGAAGAAGAAGG 59.987 44.000 0.00 0.00 43.07 3.46
600 635 1.272648 TGGGGAAGAATGGCCAAGAAG 60.273 52.381 10.96 0.00 0.00 2.85
810 848 3.382832 AGGGGAACGAGGCGACAG 61.383 66.667 0.00 0.00 0.00 3.51
838 876 0.732538 GGCTTGCGCACACCAAATAC 60.733 55.000 20.29 0.00 38.10 1.89
839 877 1.583986 GGCTTGCGCACACCAAATA 59.416 52.632 20.29 0.00 38.10 1.40
897 936 6.576185 ACAAGTCAATGCAAGAAATCAGTTT 58.424 32.000 0.00 0.00 0.00 2.66
973 1012 4.711355 TGGCTTCCTATTTCTCCCAAATTG 59.289 41.667 0.00 0.00 0.00 2.32
1020 1059 1.168714 ACCTTCCAAGCTTCATTCGC 58.831 50.000 0.00 0.00 0.00 4.70
1047 1086 6.480981 CAGGAGCTTAATAATTGCCAAAATGG 59.519 38.462 0.00 0.00 41.55 3.16
1170 1209 9.408648 ACAGTCCATTAAAAGAAAGAAAGAAGA 57.591 29.630 0.00 0.00 0.00 2.87
1321 1360 7.393515 AGGGAGTACATTTCACCAAATTTAGTC 59.606 37.037 0.00 0.00 35.54 2.59
1339 1378 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
1340 1379 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
1341 1380 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
1342 1381 4.347000 TCTTATATTTTGGGACGGAGGGAG 59.653 45.833 0.00 0.00 0.00 4.30
1343 1382 4.300345 TCTTATATTTTGGGACGGAGGGA 58.700 43.478 0.00 0.00 0.00 4.20
1344 1383 4.102681 ACTCTTATATTTTGGGACGGAGGG 59.897 45.833 0.00 0.00 0.00 4.30
1345 1384 5.057149 CACTCTTATATTTTGGGACGGAGG 58.943 45.833 0.00 0.00 0.00 4.30
1346 1385 5.671493 ACACTCTTATATTTTGGGACGGAG 58.329 41.667 0.00 0.00 0.00 4.63
1347 1386 5.687166 ACACTCTTATATTTTGGGACGGA 57.313 39.130 0.00 0.00 0.00 4.69
1348 1387 6.753107 AAACACTCTTATATTTTGGGACGG 57.247 37.500 0.00 0.00 0.00 4.79
1349 1388 8.293867 TGAAAAACACTCTTATATTTTGGGACG 58.706 33.333 0.00 0.00 0.00 4.79
1388 1427 9.634163 GTCCCAAAATATAAGAACGTTTTTCAT 57.366 29.630 7.42 0.51 0.00 2.57
1389 1428 8.630917 TGTCCCAAAATATAAGAACGTTTTTCA 58.369 29.630 7.42 0.00 0.00 2.69
1390 1429 9.124807 CTGTCCCAAAATATAAGAACGTTTTTC 57.875 33.333 7.42 0.00 0.00 2.29
1391 1430 8.852135 TCTGTCCCAAAATATAAGAACGTTTTT 58.148 29.630 9.22 9.22 0.00 1.94
1392 1431 8.398878 TCTGTCCCAAAATATAAGAACGTTTT 57.601 30.769 0.46 0.00 0.00 2.43
1393 1432 7.120726 CCTCTGTCCCAAAATATAAGAACGTTT 59.879 37.037 0.46 0.00 0.00 3.60
1394 1433 6.598064 CCTCTGTCCCAAAATATAAGAACGTT 59.402 38.462 0.00 0.00 0.00 3.99
1395 1434 6.113411 CCTCTGTCCCAAAATATAAGAACGT 58.887 40.000 0.00 0.00 0.00 3.99
1396 1435 5.527582 CCCTCTGTCCCAAAATATAAGAACG 59.472 44.000 0.00 0.00 0.00 3.95
1397 1436 5.828328 CCCCTCTGTCCCAAAATATAAGAAC 59.172 44.000 0.00 0.00 0.00 3.01
1398 1437 5.103686 CCCCCTCTGTCCCAAAATATAAGAA 60.104 44.000 0.00 0.00 0.00 2.52
1399 1438 4.415512 CCCCCTCTGTCCCAAAATATAAGA 59.584 45.833 0.00 0.00 0.00 2.10
1400 1439 4.168088 ACCCCCTCTGTCCCAAAATATAAG 59.832 45.833 0.00 0.00 0.00 1.73
1401 1440 4.123745 ACCCCCTCTGTCCCAAAATATAA 58.876 43.478 0.00 0.00 0.00 0.98
1402 1441 3.754976 ACCCCCTCTGTCCCAAAATATA 58.245 45.455 0.00 0.00 0.00 0.86
1403 1442 2.584773 ACCCCCTCTGTCCCAAAATAT 58.415 47.619 0.00 0.00 0.00 1.28
1404 1443 2.068831 ACCCCCTCTGTCCCAAAATA 57.931 50.000 0.00 0.00 0.00 1.40
1405 1444 1.639108 GTACCCCCTCTGTCCCAAAAT 59.361 52.381 0.00 0.00 0.00 1.82
1406 1445 1.069775 GTACCCCCTCTGTCCCAAAA 58.930 55.000 0.00 0.00 0.00 2.44
1407 1446 0.843343 GGTACCCCCTCTGTCCCAAA 60.843 60.000 0.00 0.00 0.00 3.28
1408 1447 1.229723 GGTACCCCCTCTGTCCCAA 60.230 63.158 0.00 0.00 0.00 4.12
1409 1448 1.757508 AAGGTACCCCCTCTGTCCCA 61.758 60.000 8.74 0.00 45.47 4.37
1410 1449 0.549413 AAAGGTACCCCCTCTGTCCC 60.549 60.000 8.74 0.00 45.47 4.46
1411 1450 1.369403 AAAAGGTACCCCCTCTGTCC 58.631 55.000 8.74 0.00 45.47 4.02
1412 1451 4.384978 GGATTAAAAGGTACCCCCTCTGTC 60.385 50.000 8.74 0.00 45.47 3.51
1413 1452 3.526430 GGATTAAAAGGTACCCCCTCTGT 59.474 47.826 8.74 0.00 45.47 3.41
1414 1453 3.526019 TGGATTAAAAGGTACCCCCTCTG 59.474 47.826 8.74 0.00 45.47 3.35
1415 1454 3.822880 TGGATTAAAAGGTACCCCCTCT 58.177 45.455 8.74 0.00 45.47 3.69
1416 1455 4.596354 TTGGATTAAAAGGTACCCCCTC 57.404 45.455 8.74 0.00 45.47 4.30
1418 1457 5.544948 AGTTTTTGGATTAAAAGGTACCCCC 59.455 40.000 8.74 0.00 39.29 5.40
1419 1458 6.295462 GGAGTTTTTGGATTAAAAGGTACCCC 60.295 42.308 8.74 0.71 39.29 4.95
1420 1459 6.570957 CGGAGTTTTTGGATTAAAAGGTACCC 60.571 42.308 8.74 0.00 39.29 3.69
1421 1460 6.384224 CGGAGTTTTTGGATTAAAAGGTACC 58.616 40.000 2.73 2.73 39.29 3.34
1510 1556 0.547075 TCCCCTCAACCACGTTTTCA 59.453 50.000 0.00 0.00 0.00 2.69
1521 1567 1.004745 GGAATTGCTCACTCCCCTCAA 59.995 52.381 0.00 0.00 0.00 3.02
1622 1669 7.926674 ATTTGTCATTAGATCACATGTCACA 57.073 32.000 0.00 0.00 0.00 3.58
1703 1750 6.437928 CGCACATTACAAATATATGTGGCTT 58.562 36.000 14.46 0.00 45.73 4.35
2015 2062 3.851976 AGTACTTTAGTCACAGAGGCG 57.148 47.619 0.00 0.00 0.00 5.52
2156 2205 2.975732 ATGAATCAGAAGAGCAGCGA 57.024 45.000 0.00 0.00 0.00 4.93
2360 2409 4.510167 AAACTACCATCTTGCTGCCTAT 57.490 40.909 0.00 0.00 0.00 2.57
2431 2480 6.349860 GGGAGTCCATAACAACACATAAAACC 60.350 42.308 12.30 0.00 0.00 3.27
2660 2710 8.899427 TTCTCCAGATTCAATATCTGATGAAC 57.101 34.615 14.61 0.00 46.25 3.18
2882 2932 1.603326 CATTGCAAAAAGTGGCCCAAC 59.397 47.619 1.71 0.00 0.00 3.77
2890 2940 3.030291 TGTCAGGTCCATTGCAAAAAGT 58.970 40.909 1.71 0.00 0.00 2.66
2923 2976 5.998454 ATTTCTCTATCAAGCCACATTCG 57.002 39.130 0.00 0.00 0.00 3.34
2964 3017 1.355971 CCCACGAAACCTGTACATCG 58.644 55.000 13.56 13.56 40.90 3.84
3011 3064 2.417924 CGATCAGTAGCAGGCTCACTTT 60.418 50.000 0.00 0.00 0.00 2.66
3056 3109 5.327732 ACCATCATATAAATCCAAGGGCTG 58.672 41.667 0.00 0.00 0.00 4.85
3078 3131 1.614413 CTATCGGGCAGAGGAGGTTAC 59.386 57.143 0.00 0.00 0.00 2.50
3140 3193 5.034852 TCAGTGACCAAATCTCTGTTTCA 57.965 39.130 6.03 0.00 45.38 2.69
3146 3199 4.841422 CTTCCATCAGTGACCAAATCTCT 58.159 43.478 0.00 0.00 0.00 3.10
3227 3283 3.885297 ACAAACTCTGTCAGGTCAAATGG 59.115 43.478 0.00 0.00 29.87 3.16
3509 3565 9.547753 GAGTATTAGGCAGTGAAAGATTATCAA 57.452 33.333 0.00 0.00 0.00 2.57
3665 3721 6.443832 AGTGGCCTCCAAATATTAAAAGGAT 58.556 36.000 3.32 0.00 34.18 3.24
3691 3747 8.688747 ATAGATCATTCAAGGTCTTGGATTTC 57.311 34.615 10.39 7.08 36.68 2.17
3959 4015 8.855110 TCTTTCAAATGTTAGGCATAAAGTGAA 58.145 29.630 0.00 0.00 36.67 3.18
4041 4097 1.812571 GTTCCCACATGACATGGACAC 59.187 52.381 19.39 5.31 39.87 3.67
4048 4104 4.698201 TGTTAGAAGTTCCCACATGACA 57.302 40.909 0.00 0.00 0.00 3.58
4160 4216 7.722285 TGGTGGCTTACTTTCTTTGTAGTAATT 59.278 33.333 0.00 0.00 36.55 1.40
4426 4482 3.069443 ACCAAGCAAAAATCGGTTCATGT 59.931 39.130 0.00 0.00 0.00 3.21
4427 4483 3.652274 ACCAAGCAAAAATCGGTTCATG 58.348 40.909 0.00 0.00 0.00 3.07
4428 4484 4.335400 AACCAAGCAAAAATCGGTTCAT 57.665 36.364 0.00 0.00 34.95 2.57
4432 4488 3.652274 CATGAACCAAGCAAAAATCGGT 58.348 40.909 0.00 0.00 0.00 4.69
4433 4489 2.412770 GCATGAACCAAGCAAAAATCGG 59.587 45.455 0.00 0.00 0.00 4.18
4434 4490 3.058450 TGCATGAACCAAGCAAAAATCG 58.942 40.909 0.00 0.00 35.14 3.34
4435 4491 3.434299 CCTGCATGAACCAAGCAAAAATC 59.566 43.478 0.00 0.00 37.62 2.17
4436 4492 3.404899 CCTGCATGAACCAAGCAAAAAT 58.595 40.909 0.00 0.00 37.62 1.82
4437 4493 2.485124 CCCTGCATGAACCAAGCAAAAA 60.485 45.455 0.00 0.00 37.62 1.94
4438 4494 1.070445 CCCTGCATGAACCAAGCAAAA 59.930 47.619 0.00 0.00 37.62 2.44
4439 4495 0.680618 CCCTGCATGAACCAAGCAAA 59.319 50.000 0.00 0.00 37.62 3.68
4440 4496 0.469705 ACCCTGCATGAACCAAGCAA 60.470 50.000 0.00 0.00 37.62 3.91
4441 4497 0.469705 AACCCTGCATGAACCAAGCA 60.470 50.000 0.00 0.00 35.71 3.91
4442 4498 0.681175 AAACCCTGCATGAACCAAGC 59.319 50.000 0.00 0.00 0.00 4.01
4443 4499 1.962807 TGAAACCCTGCATGAACCAAG 59.037 47.619 0.00 0.00 0.00 3.61
4444 4500 1.962807 CTGAAACCCTGCATGAACCAA 59.037 47.619 0.00 0.00 0.00 3.67
4445 4501 1.619654 CTGAAACCCTGCATGAACCA 58.380 50.000 0.00 0.00 0.00 3.67
4447 4503 0.961019 TGCTGAAACCCTGCATGAAC 59.039 50.000 0.00 0.00 43.43 3.18
4611 4670 2.234908 AGGAGAAGTACACACTGCCATC 59.765 50.000 0.00 0.00 34.36 3.51
4664 4723 5.685511 GCTGATAAAGTTGCTCGTTGAAAAA 59.314 36.000 0.00 0.00 0.00 1.94
4665 4724 5.212194 GCTGATAAAGTTGCTCGTTGAAAA 58.788 37.500 0.00 0.00 0.00 2.29
4666 4725 4.610456 CGCTGATAAAGTTGCTCGTTGAAA 60.610 41.667 0.00 0.00 0.00 2.69
4667 4726 3.120683 CGCTGATAAAGTTGCTCGTTGAA 60.121 43.478 0.00 0.00 0.00 2.69
4668 4727 2.411748 CGCTGATAAAGTTGCTCGTTGA 59.588 45.455 0.00 0.00 0.00 3.18
4669 4728 2.157668 ACGCTGATAAAGTTGCTCGTTG 59.842 45.455 0.00 0.00 0.00 4.10
4670 4729 2.413837 ACGCTGATAAAGTTGCTCGTT 58.586 42.857 0.00 0.00 0.00 3.85
4671 4730 2.080286 ACGCTGATAAAGTTGCTCGT 57.920 45.000 0.00 0.00 0.00 4.18
4672 4731 2.157668 ACAACGCTGATAAAGTTGCTCG 59.842 45.455 7.37 0.00 46.41 5.03
4673 4732 3.813529 ACAACGCTGATAAAGTTGCTC 57.186 42.857 7.37 0.00 46.41 4.26
4674 4733 4.152402 CACTACAACGCTGATAAAGTTGCT 59.848 41.667 7.37 0.00 46.41 3.91
4675 4734 4.394795 CACTACAACGCTGATAAAGTTGC 58.605 43.478 7.37 0.00 46.41 4.17
4760 4821 9.730420 TTACACAAACTTCAAGAATTAGAAAGC 57.270 29.630 0.00 0.00 0.00 3.51
4771 4833 8.344831 TGATGAGACAATTACACAAACTTCAAG 58.655 33.333 0.00 0.00 0.00 3.02
4777 4839 7.862372 ACATGTTGATGAGACAATTACACAAAC 59.138 33.333 0.00 0.00 33.36 2.93
4779 4841 7.228308 TGACATGTTGATGAGACAATTACACAA 59.772 33.333 0.00 0.00 33.36 3.33
4794 4856 2.563620 TGCAGGCAATTGACATGTTGAT 59.436 40.909 15.18 0.00 0.00 2.57
4799 4861 0.892755 AGGTGCAGGCAATTGACATG 59.107 50.000 15.18 11.59 0.00 3.21
4802 4864 0.961019 TTCAGGTGCAGGCAATTGAC 59.039 50.000 10.34 6.35 0.00 3.18
4882 4944 5.661056 TCAACCTACAGATAACCACAGAG 57.339 43.478 0.00 0.00 0.00 3.35
4885 4947 5.818678 ACTTCAACCTACAGATAACCACA 57.181 39.130 0.00 0.00 0.00 4.17
4886 4948 6.812160 CAGTACTTCAACCTACAGATAACCAC 59.188 42.308 0.00 0.00 0.00 4.16
4909 4971 1.263217 GTCGTTTTGCAGTACCACCAG 59.737 52.381 0.00 0.00 0.00 4.00
4911 4973 0.589708 GGTCGTTTTGCAGTACCACC 59.410 55.000 2.29 2.29 0.00 4.61
4917 4979 5.163754 GCTATAAGAATGGTCGTTTTGCAGT 60.164 40.000 0.00 0.00 0.00 4.40
5068 5130 1.924320 GCACGCTCGACTGTAGAGGT 61.924 60.000 17.71 11.58 36.31 3.85
5079 5141 1.011684 CTCTCTAGACGCACGCTCG 60.012 63.158 0.00 0.00 0.00 5.03
5142 5204 0.248843 AGCTGCTGCAGTCTTCTACC 59.751 55.000 28.50 10.99 42.74 3.18
5153 5215 0.108945 CTTTTGGGCTAAGCTGCTGC 60.109 55.000 1.35 7.62 40.05 5.25
5154 5216 0.108945 GCTTTTGGGCTAAGCTGCTG 60.109 55.000 1.35 0.00 43.56 4.41
5155 5217 2.270959 GCTTTTGGGCTAAGCTGCT 58.729 52.632 0.00 0.00 43.56 4.24
5217 5279 2.095364 GCTTGCTGGACATGAAGAACAG 60.095 50.000 0.00 1.24 0.00 3.16
5398 5467 1.564348 ACTTGGTCCTTGGTTGTCAGT 59.436 47.619 0.00 0.00 0.00 3.41
5468 5537 9.300681 TCCTTCTGATCAAATCTGTTATTTTGT 57.699 29.630 0.00 0.00 35.01 2.83
5481 5550 1.438651 CCGCGTTCCTTCTGATCAAA 58.561 50.000 4.92 0.00 0.00 2.69
5607 5676 0.839946 GCTCAGCATCTTTCCCCCTA 59.160 55.000 0.00 0.00 0.00 3.53
5613 5682 1.735386 TGAGCAGCTCAGCATCTTTC 58.265 50.000 21.85 0.00 35.39 2.62
5616 5685 0.107606 CCTTGAGCAGCTCAGCATCT 60.108 55.000 24.15 0.00 41.75 2.90
5619 5688 1.190178 TCTCCTTGAGCAGCTCAGCA 61.190 55.000 24.15 10.74 41.75 4.41
5743 5812 1.672854 TTTCGGGTCTCATCCGCGAT 61.673 55.000 8.23 0.00 46.43 4.58
5780 5849 1.108776 AGCCAAAATCATCATGCGCT 58.891 45.000 9.73 0.00 0.00 5.92
5920 5991 5.563475 CGTCCCATAATATAAGACGTCCGTT 60.563 44.000 13.01 3.36 43.89 4.44
5921 5992 4.083110 CGTCCCATAATATAAGACGTCCGT 60.083 45.833 13.01 2.93 43.89 4.69
5922 5993 4.409570 CGTCCCATAATATAAGACGTCCG 58.590 47.826 13.01 0.00 43.89 4.79
5923 5994 4.460382 TCCGTCCCATAATATAAGACGTCC 59.540 45.833 13.01 0.00 46.62 4.79
5924 5995 5.392811 CCTCCGTCCCATAATATAAGACGTC 60.393 48.000 7.70 7.70 46.62 4.34
5947 6038 5.471257 CGGCATTCTATTCTAAGTACTCCC 58.529 45.833 0.00 0.00 0.00 4.30
5967 6058 2.824489 GGCCTAAGAAGCACCGGC 60.824 66.667 0.00 0.00 39.98 6.13
6001 6092 5.268118 TGACGAATAAGAGTCTGATGCAT 57.732 39.130 0.00 0.00 38.16 3.96
6029 6120 4.514066 ACGATTTTGGGAGACTTTACACAC 59.486 41.667 0.00 0.00 0.00 3.82
6054 6145 8.669946 TTTATGTCAAAGTGTATGAAGTGTCA 57.330 30.769 0.00 0.00 38.41 3.58
6118 6230 2.179427 ACACCTCGACCTGATCAATCA 58.821 47.619 0.00 0.00 35.16 2.57
6119 6231 2.969628 ACACCTCGACCTGATCAATC 57.030 50.000 0.00 0.00 0.00 2.67
6120 6232 2.093447 GGAACACCTCGACCTGATCAAT 60.093 50.000 0.00 0.00 0.00 2.57
6179 6291 1.359459 GAGGCTTCCTTGGCGTTACG 61.359 60.000 0.00 0.00 31.76 3.18
6181 6293 0.618458 ATGAGGCTTCCTTGGCGTTA 59.382 50.000 0.00 0.00 31.76 3.18
6212 6324 0.387565 GCCCCGCTTCTTGTTTTGAA 59.612 50.000 0.00 0.00 0.00 2.69
6213 6325 1.791103 CGCCCCGCTTCTTGTTTTGA 61.791 55.000 0.00 0.00 0.00 2.69
6219 6331 2.358737 AACTCGCCCCGCTTCTTG 60.359 61.111 0.00 0.00 0.00 3.02
6325 6437 4.276678 ACAATGATTCACACACAGAACCTG 59.723 41.667 0.00 0.00 37.52 4.00
6354 6466 9.132521 CAGTAAATCTTTCAAACATCAATCCAC 57.867 33.333 0.00 0.00 0.00 4.02
6486 6598 7.482169 AATAAGTCATCTACACAGACAAGGA 57.518 36.000 0.00 0.00 34.80 3.36
6525 6637 6.624352 TTTCAAATGAAGACCTGACTTGAG 57.376 37.500 0.00 0.00 35.21 3.02
6533 6645 5.385198 TGTAGCCTTTTCAAATGAAGACCT 58.615 37.500 0.00 0.00 35.21 3.85
6535 6647 6.739112 ACTTGTAGCCTTTTCAAATGAAGAC 58.261 36.000 0.00 0.00 35.21 3.01
6536 6648 6.959639 ACTTGTAGCCTTTTCAAATGAAGA 57.040 33.333 0.00 0.00 35.21 2.87
6538 6650 8.232913 AGTAACTTGTAGCCTTTTCAAATGAA 57.767 30.769 0.00 0.00 0.00 2.57
6611 6766 2.561419 TGCTAAGACTAAACTGCCGACT 59.439 45.455 0.00 0.00 0.00 4.18
6615 6770 3.873910 TGGATGCTAAGACTAAACTGCC 58.126 45.455 0.00 0.00 0.00 4.85
6797 6956 4.305989 TGATGATGATGACGACGATGAA 57.694 40.909 0.00 0.00 0.00 2.57
6800 6959 3.057946 ACGATGATGATGATGACGACGAT 60.058 43.478 0.00 0.00 0.00 3.73
6818 6977 0.463295 CTGCCTTGCCAGATGACGAT 60.463 55.000 0.00 0.00 34.77 3.73
6895 7054 2.627515 AGTTGAGAAGCTGAGTGCAA 57.372 45.000 0.00 0.00 45.94 4.08
7012 7171 1.043116 CAGTGCTCCCTATCCGGACA 61.043 60.000 6.12 0.00 33.16 4.02
7019 7178 3.978164 GGAGGCAGTGCTCCCTAT 58.022 61.111 16.11 0.00 33.81 2.57
7058 7217 0.392998 CCAACTACCGCCTTGATGCT 60.393 55.000 0.00 0.00 0.00 3.79
7188 7347 0.596083 CGGCGAATAGAGGTGCTCAG 60.596 60.000 0.00 0.00 32.06 3.35


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

AutoCloner maintained by Alex Coulton.