Multiple sequence alignment - TraesCS5B01G259200

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 TraesCS5B01G259200 chr5B 100.000 4066 0 0 3620 7685 441640453 441636388 0.000000e+00 7509.0
1 TraesCS5B01G259200 chr5B 100.000 3261 0 0 1 3261 441644072 441640812 0.000000e+00 6023.0
2 TraesCS5B01G259200 chr5B 83.847 1232 174 16 4918 6134 448121933 448123154 0.000000e+00 1149.0
3 TraesCS5B01G259200 chr5B 81.607 473 70 11 6217 6681 448123155 448123618 7.280000e-100 375.0
4 TraesCS5B01G259200 chr5B 94.118 102 6 0 1136 1237 45261728 45261627 1.030000e-33 156.0
5 TraesCS5B01G259200 chr5A 97.266 3145 63 10 3751 6877 474819019 474815880 0.000000e+00 5310.0
6 TraesCS5B01G259200 chr5A 96.709 1185 26 4 2078 3261 474820721 474819549 0.000000e+00 1960.0
7 TraesCS5B01G259200 chr5A 91.581 1259 82 13 4887 6134 474781779 474780534 0.000000e+00 1716.0
8 TraesCS5B01G259200 chr5A 97.805 820 6 2 6877 7685 474815644 474814826 0.000000e+00 1404.0
9 TraesCS5B01G259200 chr5A 95.029 865 26 5 1226 2084 474821599 474820746 0.000000e+00 1343.0
10 TraesCS5B01G259200 chr5A 83.468 1240 165 22 4918 6134 476658121 476659343 0.000000e+00 1118.0
11 TraesCS5B01G259200 chr5A 88.905 703 35 17 459 1145 474822271 474821596 0.000000e+00 826.0
12 TraesCS5B01G259200 chr5A 82.489 474 66 10 6217 6683 476659344 476659807 4.320000e-107 399.0
13 TraesCS5B01G259200 chr5A 82.512 406 44 19 1 394 474825879 474825489 1.600000e-86 331.0
14 TraesCS5B01G259200 chr5A 94.828 58 3 0 6217 6274 474780533 474780476 2.950000e-14 91.6
15 TraesCS5B01G259200 chr5A 78.906 128 20 6 221 346 369642691 369642813 6.390000e-11 80.5
16 TraesCS5B01G259200 chr5A 97.619 42 1 0 4655 4696 476657976 476658017 1.070000e-08 73.1
17 TraesCS5B01G259200 chr5D 98.306 2539 25 7 3656 6181 371788971 371786438 0.000000e+00 4434.0
18 TraesCS5B01G259200 chr5D 98.482 1186 16 2 2078 3261 371792709 371791524 0.000000e+00 2089.0
19 TraesCS5B01G259200 chr5D 96.065 864 18 6 1226 2084 371793586 371792734 0.000000e+00 1393.0
20 TraesCS5B01G259200 chr5D 83.874 1234 170 15 4918 6134 375280533 375281754 0.000000e+00 1149.0
21 TraesCS5B01G259200 chr5D 96.661 569 18 1 6147 6714 371786437 371785869 0.000000e+00 944.0
22 TraesCS5B01G259200 chr5D 82.265 468 68 9 6217 6678 375281755 375282213 2.600000e-104 390.0
23 TraesCS5B01G259200 chr5D 78.216 583 115 8 5298 5878 375408407 375407835 5.670000e-96 363.0
24 TraesCS5B01G259200 chr5D 91.954 87 5 2 1060 1145 371793665 371793580 3.770000e-23 121.0
25 TraesCS5B01G259200 chr5D 89.412 85 9 0 6132 6216 47024606 47024522 2.930000e-19 108.0
26 TraesCS5B01G259200 chr7B 83.940 2005 254 34 4181 6134 92906642 92908629 0.000000e+00 1857.0
27 TraesCS5B01G259200 chr7B 83.402 482 70 7 6217 6692 92908630 92909107 9.160000e-119 438.0
28 TraesCS5B01G259200 chr7B 83.736 455 48 14 3746 4174 92904704 92905158 2.580000e-109 407.0
29 TraesCS5B01G259200 chr7B 82.895 380 39 13 1714 2079 92902676 92903043 1.240000e-82 318.0
30 TraesCS5B01G259200 chr7B 86.923 130 10 5 3620 3743 92904793 92904665 1.040000e-28 139.0
31 TraesCS5B01G259200 chr7B 78.626 131 26 2 2774 2903 12482884 12482755 1.370000e-12 86.1
32 TraesCS5B01G259200 chr7B 80.435 92 16 2 272 361 243574333 243574242 1.380000e-07 69.4
33 TraesCS5B01G259200 chrUn 89.737 380 23 11 536 913 474375579 474375944 9.030000e-129 472.0
34 TraesCS5B01G259200 chrUn 97.802 91 2 0 1141 1231 248121968 248121878 2.870000e-34 158.0
35 TraesCS5B01G259200 chr6A 83.511 376 41 11 7037 7398 81255358 81255726 1.600000e-86 331.0
36 TraesCS5B01G259200 chr6A 89.011 91 6 4 6126 6213 14350979 14351068 8.150000e-20 110.0
37 TraesCS5B01G259200 chr6A 88.636 88 10 0 6133 6220 209391425 209391338 2.930000e-19 108.0
38 TraesCS5B01G259200 chr6A 83.186 113 17 2 254 364 201915274 201915386 1.360000e-17 102.0
39 TraesCS5B01G259200 chr6A 77.099 131 26 4 211 339 565320726 565320598 1.070000e-08 73.1
40 TraesCS5B01G259200 chr1B 76.571 350 74 6 6348 6692 594009978 594009632 1.320000e-42 185.0
41 TraesCS5B01G259200 chr1B 95.833 96 1 3 1134 1229 516970292 516970384 1.340000e-32 152.0
42 TraesCS5B01G259200 chr1B 80.672 119 20 3 219 335 482212844 482212727 1.060000e-13 89.8
43 TraesCS5B01G259200 chr1A 76.347 334 73 5 6363 6692 535037053 535036722 2.850000e-39 174.0
44 TraesCS5B01G259200 chr4A 98.864 88 1 0 1144 1231 646312883 646312796 2.870000e-34 158.0
45 TraesCS5B01G259200 chr2B 97.802 91 2 0 1141 1231 654648533 654648443 2.870000e-34 158.0
46 TraesCS5B01G259200 chr2B 97.802 91 2 0 1141 1231 654726115 654726025 2.870000e-34 158.0
47 TraesCS5B01G259200 chr2B 93.939 99 6 0 1132 1230 249224120 249224218 4.800000e-32 150.0
48 TraesCS5B01G259200 chr6B 94.118 102 4 2 1129 1229 693119981 693120081 3.710000e-33 154.0
49 TraesCS5B01G259200 chr6B 87.121 132 12 3 7116 7242 139891596 139891727 2.240000e-30 145.0
50 TraesCS5B01G259200 chr6B 79.018 224 16 15 7413 7625 139891834 139892037 2.910000e-24 124.0
51 TraesCS5B01G259200 chr6B 88.636 88 10 0 6133 6220 278674697 278674610 2.930000e-19 108.0
52 TraesCS5B01G259200 chr6B 89.610 77 5 2 272 347 617309287 617309213 2.280000e-15 95.3
53 TraesCS5B01G259200 chr3B 95.789 95 2 1 1144 1238 193961303 193961395 1.340000e-32 152.0
54 TraesCS5B01G259200 chr3B 80.147 136 20 6 218 347 37384223 37384089 2.280000e-15 95.3
55 TraesCS5B01G259200 chr3D 91.358 81 7 0 6133 6213 108916262 108916342 2.270000e-20 111.0
56 TraesCS5B01G259200 chr3D 87.931 58 7 0 6044 6101 471420054 471419997 1.380000e-07 69.4
57 TraesCS5B01G259200 chr2D 90.244 82 8 0 6132 6213 649145860 649145941 2.930000e-19 108.0
58 TraesCS5B01G259200 chr7A 88.158 76 8 1 272 346 585430992 585431067 1.060000e-13 89.8
59 TraesCS5B01G259200 chr4D 89.552 67 7 0 280 346 163164510 163164576 1.370000e-12 86.1
60 TraesCS5B01G259200 chr3A 88.889 54 6 0 6048 6101 614125453 614125400 4.980000e-07 67.6


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 TraesCS5B01G259200 chr5B 441636388 441644072 7684 True 6766.000000 7509 100.000000 1 7685 2 chr5B.!!$R2 7684
1 TraesCS5B01G259200 chr5B 448121933 448123618 1685 False 762.000000 1149 82.727000 4918 6681 2 chr5B.!!$F1 1763
2 TraesCS5B01G259200 chr5A 474814826 474825879 11053 True 1862.333333 5310 93.037667 1 7685 6 chr5A.!!$R2 7684
3 TraesCS5B01G259200 chr5A 474780476 474781779 1303 True 903.800000 1716 93.204500 4887 6274 2 chr5A.!!$R1 1387
4 TraesCS5B01G259200 chr5A 476657976 476659807 1831 False 530.033333 1118 87.858667 4655 6683 3 chr5A.!!$F2 2028
5 TraesCS5B01G259200 chr5D 371785869 371793665 7796 True 1796.200000 4434 96.293600 1060 6714 5 chr5D.!!$R3 5654
6 TraesCS5B01G259200 chr5D 375280533 375282213 1680 False 769.500000 1149 83.069500 4918 6678 2 chr5D.!!$F1 1760
7 TraesCS5B01G259200 chr5D 375407835 375408407 572 True 363.000000 363 78.216000 5298 5878 1 chr5D.!!$R2 580
8 TraesCS5B01G259200 chr7B 92902676 92909107 6431 False 755.000000 1857 83.493250 1714 6692 4 chr7B.!!$F1 4978

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
482 3659 0.108615 ACGCTTTCTCCATCAGGACG 60.109 55.000 0.00 0.00 39.61 4.79 F
1121 4315 0.179258 CGCGTCGCCTAAGTTGTTTC 60.179 55.000 12.44 0.00 0.00 2.78 F
1160 4354 0.258194 AGTACTCCCTCCGTTCCGAT 59.742 55.000 0.00 0.00 0.00 4.18 F
2373 5652 1.003580 TGCTCAATTCAGTCCTCACCC 59.996 52.381 0.00 0.00 0.00 4.61 F
2636 5915 1.131126 GACGTGCAATGGATCAACCTG 59.869 52.381 0.00 0.00 39.86 4.00 F
3128 6695 8.303876 GCTTGGAGTATTTGGAAAGAACAAATA 58.696 33.333 6.53 6.53 44.27 1.40 F
3640 7207 2.492088 GCATGGACCAAGTTTTACCTCC 59.508 50.000 0.00 0.00 0.00 4.30 F
3647 7214 3.053170 ACCAAGTTTTACCTCCTTGTGGT 60.053 43.478 0.00 0.00 41.28 4.16 F
5387 12669 0.610232 GTGCTTTCCATCCCACAGCT 60.610 55.000 0.00 0.00 0.00 4.24 F
6306 13658 3.838244 TGGATGCAGGTATTACAGACC 57.162 47.619 0.00 0.00 37.22 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1412 4608 0.725117 GTAATGTACGCTGGGTGTGC 59.275 55.000 7.71 0.00 0.00 4.57 R
2197 5444 2.945440 GCAGCCAATTCCATGGTAGTCA 60.945 50.000 12.58 0.00 42.75 3.41 R
3128 6695 2.639839 CGATCCCTTGGGAGATATGGTT 59.360 50.000 14.30 0.00 0.00 3.67 R
3619 7186 2.492088 GGAGGTAAAACTTGGTCCATGC 59.508 50.000 4.67 0.00 0.00 4.06 R
3625 7192 3.053170 ACCACAAGGAGGTAAAACTTGGT 60.053 43.478 8.30 0.00 44.35 3.67 R
5072 12348 1.483004 CATGCATTTCCAATCAGGCCA 59.517 47.619 5.01 0.00 37.29 5.36 R
5387 12669 2.023673 CTTGTCAAGCAACCAAGTCCA 58.976 47.619 0.00 0.00 32.76 4.02 R
5496 12779 3.076621 GGCAGATGATCTTGTCACAACA 58.923 45.455 0.00 0.00 40.28 3.33 R
6498 13850 0.833287 ATCCATCAGTGTCTTCCCGG 59.167 55.000 0.00 0.00 0.00 5.73 R
7321 14919 1.192534 CGAAACGAAGTCTGTGGCTTC 59.807 52.381 2.19 2.19 45.00 3.86 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
38 39 2.766925 AAGCAGAGTGGCCACCCAA 61.767 57.895 32.29 0.00 44.33 4.12
40 41 2.674380 CAGAGTGGCCACCCAAGC 60.674 66.667 32.29 16.09 44.33 4.01
41 42 2.856000 AGAGTGGCCACCCAAGCT 60.856 61.111 32.29 18.03 44.33 3.74
42 43 2.360475 GAGTGGCCACCCAAGCTC 60.360 66.667 32.29 18.04 44.33 4.09
43 44 3.177884 AGTGGCCACCCAAGCTCA 61.178 61.111 32.29 0.00 44.33 4.26
44 45 2.985847 GTGGCCACCCAAGCTCAC 60.986 66.667 26.31 0.00 44.33 3.51
45 46 3.497115 TGGCCACCCAAGCTCACA 61.497 61.111 0.00 0.00 38.46 3.58
46 47 2.985847 GGCCACCCAAGCTCACAC 60.986 66.667 0.00 0.00 0.00 3.82
47 48 3.357079 GCCACCCAAGCTCACACG 61.357 66.667 0.00 0.00 0.00 4.49
48 49 3.357079 CCACCCAAGCTCACACGC 61.357 66.667 0.00 0.00 0.00 5.34
49 50 3.357079 CACCCAAGCTCACACGCC 61.357 66.667 0.00 0.00 0.00 5.68
50 51 4.643387 ACCCAAGCTCACACGCCC 62.643 66.667 0.00 0.00 0.00 6.13
51 52 4.335647 CCCAAGCTCACACGCCCT 62.336 66.667 0.00 0.00 0.00 5.19
52 53 3.052082 CCAAGCTCACACGCCCTG 61.052 66.667 0.00 0.00 0.00 4.45
53 54 3.052082 CAAGCTCACACGCCCTGG 61.052 66.667 0.00 0.00 0.00 4.45
54 55 4.335647 AAGCTCACACGCCCTGGG 62.336 66.667 8.86 8.86 0.00 4.45
100 113 4.338710 TGCACCGCCCCTTGTACC 62.339 66.667 0.00 0.00 0.00 3.34
105 118 4.109675 CGCCCCTTGTACCCCTGG 62.110 72.222 0.00 0.00 0.00 4.45
111 124 2.698967 CCCCTTGTACCCCTGGATCATA 60.699 54.545 0.00 0.00 0.00 2.15
127 140 6.059484 TGGATCATAAATACCTCGAAAACCC 58.941 40.000 0.00 0.00 0.00 4.11
129 142 6.771267 GGATCATAAATACCTCGAAAACCCTT 59.229 38.462 0.00 0.00 0.00 3.95
145 158 7.433708 AAAACCCTTGTTGTTTTCTTTGAAG 57.566 32.000 0.00 0.00 40.85 3.02
147 160 4.530553 ACCCTTGTTGTTTTCTTTGAAGGT 59.469 37.500 0.00 0.00 0.00 3.50
188 201 3.436001 CGTGGCGGACAAATCTAGT 57.564 52.632 0.00 0.00 0.00 2.57
240 253 0.546122 TCCAATGTCGGAGGGGATTG 59.454 55.000 0.00 0.00 0.00 2.67
242 255 1.340991 CCAATGTCGGAGGGGATTGTT 60.341 52.381 0.00 0.00 0.00 2.83
243 256 1.745087 CAATGTCGGAGGGGATTGTTG 59.255 52.381 0.00 0.00 0.00 3.33
259 272 1.271543 TGTTGTCCTTCAGAGCCATGG 60.272 52.381 7.63 7.63 0.00 3.66
262 275 2.515523 CCTTCAGAGCCATGGCCG 60.516 66.667 33.14 21.38 43.17 6.13
264 277 3.694058 CTTCAGAGCCATGGCCGCT 62.694 63.158 33.14 26.32 43.17 5.52
272 285 0.819259 GCCATGGCCGCTAAGAATCA 60.819 55.000 27.24 0.00 34.56 2.57
275 288 2.551721 CCATGGCCGCTAAGAATCAGAT 60.552 50.000 0.00 0.00 0.00 2.90
276 289 2.245159 TGGCCGCTAAGAATCAGATG 57.755 50.000 0.00 0.00 0.00 2.90
279 292 1.070758 GCCGCTAAGAATCAGATGGGA 59.929 52.381 0.00 0.00 0.00 4.37
280 293 2.485479 GCCGCTAAGAATCAGATGGGAA 60.485 50.000 0.00 0.00 0.00 3.97
281 294 3.808728 CCGCTAAGAATCAGATGGGAAA 58.191 45.455 0.00 0.00 0.00 3.13
282 295 3.561725 CCGCTAAGAATCAGATGGGAAAC 59.438 47.826 0.00 0.00 0.00 2.78
318 339 2.414806 GGGAACGTCAAGGAAGAAGAC 58.585 52.381 0.00 0.00 0.00 3.01
324 345 3.662247 GTCAAGGAAGAAGACGAAGGA 57.338 47.619 0.00 0.00 0.00 3.36
335 358 2.042435 CGAAGGAGGGGGCTCTCT 60.042 66.667 0.00 0.00 34.39 3.10
336 359 1.687493 CGAAGGAGGGGGCTCTCTT 60.687 63.158 0.00 0.00 34.39 2.85
337 360 1.681486 CGAAGGAGGGGGCTCTCTTC 61.681 65.000 0.00 0.00 34.39 2.87
345 368 1.578897 GGGGCTCTCTTCCTCTTTCT 58.421 55.000 0.00 0.00 0.00 2.52
346 369 1.912731 GGGGCTCTCTTCCTCTTTCTT 59.087 52.381 0.00 0.00 0.00 2.52
347 370 2.307392 GGGGCTCTCTTCCTCTTTCTTT 59.693 50.000 0.00 0.00 0.00 2.52
348 371 3.245087 GGGGCTCTCTTCCTCTTTCTTTT 60.245 47.826 0.00 0.00 0.00 2.27
409 520 4.703093 TGTCATTCATCTGTGACATGCAAT 59.297 37.500 4.25 0.00 46.97 3.56
478 3655 1.734465 GTTGGACGCTTTCTCCATCAG 59.266 52.381 0.00 0.00 37.65 2.90
482 3659 0.108615 ACGCTTTCTCCATCAGGACG 60.109 55.000 0.00 0.00 39.61 4.79
516 3694 5.725362 TGGATTCTTTGTTGTTTCGGTTTT 58.275 33.333 0.00 0.00 0.00 2.43
519 3697 4.112716 TCTTTGTTGTTTCGGTTTTCCC 57.887 40.909 0.00 0.00 36.42 3.97
522 3700 3.786516 TGTTGTTTCGGTTTTCCCTTC 57.213 42.857 0.00 0.00 36.42 3.46
525 3703 4.221041 TGTTGTTTCGGTTTTCCCTTCTTT 59.779 37.500 0.00 0.00 36.42 2.52
528 3706 4.142116 TGTTTCGGTTTTCCCTTCTTTTCC 60.142 41.667 0.00 0.00 36.42 3.13
535 3725 5.518546 GGTTTTCCCTTCTTTTCCCCTATCT 60.519 44.000 0.00 0.00 0.00 1.98
539 3729 6.980795 TCCCTTCTTTTCCCCTATCTTTTA 57.019 37.500 0.00 0.00 0.00 1.52
564 3754 8.487313 AGGTTTTCTTGGTTTTTATTGACAAC 57.513 30.769 0.00 0.00 0.00 3.32
593 3784 1.042229 ACATGCATTGTGCCACTTGT 58.958 45.000 0.00 0.00 44.23 3.16
639 3831 9.521503 GATAACCTTTGCAAAGATTATTTCCTC 57.478 33.333 30.69 19.32 35.38 3.71
640 3832 6.916360 ACCTTTGCAAAGATTATTTCCTCA 57.084 33.333 35.25 0.00 38.28 3.86
641 3833 7.301868 ACCTTTGCAAAGATTATTTCCTCAA 57.698 32.000 35.25 0.00 38.28 3.02
642 3834 7.154656 ACCTTTGCAAAGATTATTTCCTCAAC 58.845 34.615 35.25 0.00 38.28 3.18
643 3835 7.015584 ACCTTTGCAAAGATTATTTCCTCAACT 59.984 33.333 35.25 1.14 38.28 3.16
644 3836 8.522830 CCTTTGCAAAGATTATTTCCTCAACTA 58.477 33.333 35.25 0.00 38.28 2.24
645 3837 9.912634 CTTTGCAAAGATTATTTCCTCAACTAA 57.087 29.630 31.24 0.00 38.28 2.24
697 3889 4.070009 GAGAAACAAAATACCGGTCCAGT 58.930 43.478 12.40 0.56 0.00 4.00
707 3899 0.880278 CCGGTCCAGTCATATTGCCG 60.880 60.000 0.00 0.00 37.72 5.69
734 3926 3.181439 GCCTCTTAGATGGGCTGGTAAAT 60.181 47.826 5.39 0.00 42.31 1.40
736 3928 3.817647 CTCTTAGATGGGCTGGTAAATGC 59.182 47.826 0.00 0.00 0.00 3.56
737 3929 2.254546 TAGATGGGCTGGTAAATGCG 57.745 50.000 0.00 0.00 0.00 4.73
738 3930 0.466189 AGATGGGCTGGTAAATGCGG 60.466 55.000 0.00 0.00 0.00 5.69
740 3932 3.527427 GGGCTGGTAAATGCGGGC 61.527 66.667 0.00 0.00 0.00 6.13
741 3933 2.440247 GGCTGGTAAATGCGGGCT 60.440 61.111 0.00 0.00 0.00 5.19
816 4009 3.112709 GGTTCACGCCGCTGAGTC 61.113 66.667 0.00 0.00 0.00 3.36
817 4010 3.112709 GTTCACGCCGCTGAGTCC 61.113 66.667 0.00 0.00 0.00 3.85
818 4011 3.303135 TTCACGCCGCTGAGTCCT 61.303 61.111 0.00 0.00 0.00 3.85
819 4012 3.573772 TTCACGCCGCTGAGTCCTG 62.574 63.158 0.00 0.00 0.00 3.86
823 4016 4.479993 GCCGCTGAGTCCTGCCAT 62.480 66.667 0.51 0.00 34.24 4.40
824 4017 3.094062 GCCGCTGAGTCCTGCCATA 62.094 63.158 0.51 0.00 34.24 2.74
825 4018 1.068753 CCGCTGAGTCCTGCCATAG 59.931 63.158 0.51 0.00 34.24 2.23
826 4019 1.680522 CCGCTGAGTCCTGCCATAGT 61.681 60.000 0.51 0.00 34.24 2.12
896 4089 7.252865 CGTCCGATTCAAAATCGAAATTGTAAC 60.253 37.037 20.33 7.00 43.59 2.50
981 4174 2.435938 TGCCCCGATTTCTCGTGC 60.436 61.111 0.00 0.00 43.49 5.34
983 4176 2.513897 CCCCGATTTCTCGTGCCC 60.514 66.667 0.00 0.00 43.49 5.36
1005 4198 1.426251 TTCAGCAGGGTGTCATGGGT 61.426 55.000 0.00 0.00 0.00 4.51
1040 4233 1.438562 CGATTGATGTCCATGCGGCA 61.439 55.000 4.58 4.58 0.00 5.69
1121 4315 0.179258 CGCGTCGCCTAAGTTGTTTC 60.179 55.000 12.44 0.00 0.00 2.78
1145 4339 5.475273 TGTGCAGACATACTACGTAGTAC 57.525 43.478 32.09 21.51 45.11 2.73
1147 4341 5.292834 TGTGCAGACATACTACGTAGTACTC 59.707 44.000 32.09 26.97 45.11 2.59
1148 4342 4.813161 TGCAGACATACTACGTAGTACTCC 59.187 45.833 32.09 23.06 45.11 3.85
1149 4343 4.213059 GCAGACATACTACGTAGTACTCCC 59.787 50.000 32.09 21.63 45.11 4.30
1150 4344 5.609423 CAGACATACTACGTAGTACTCCCT 58.391 45.833 32.09 23.09 45.11 4.20
1151 4345 5.695816 CAGACATACTACGTAGTACTCCCTC 59.304 48.000 32.09 21.37 45.11 4.30
1152 4346 4.967036 ACATACTACGTAGTACTCCCTCC 58.033 47.826 32.09 0.00 45.11 4.30
1153 4347 2.611225 ACTACGTAGTACTCCCTCCG 57.389 55.000 26.36 0.00 45.11 4.63
1154 4348 1.834263 ACTACGTAGTACTCCCTCCGT 59.166 52.381 26.36 4.30 45.11 4.69
1155 4349 2.237392 ACTACGTAGTACTCCCTCCGTT 59.763 50.000 26.36 0.00 45.11 4.44
1156 4350 1.743996 ACGTAGTACTCCCTCCGTTC 58.256 55.000 0.00 0.00 41.94 3.95
1157 4351 1.020437 CGTAGTACTCCCTCCGTTCC 58.980 60.000 0.00 0.00 0.00 3.62
1158 4352 1.020437 GTAGTACTCCCTCCGTTCCG 58.980 60.000 0.00 0.00 0.00 4.30
1159 4353 0.911769 TAGTACTCCCTCCGTTCCGA 59.088 55.000 0.00 0.00 0.00 4.55
1160 4354 0.258194 AGTACTCCCTCCGTTCCGAT 59.742 55.000 0.00 0.00 0.00 4.18
1161 4355 1.109609 GTACTCCCTCCGTTCCGATT 58.890 55.000 0.00 0.00 0.00 3.34
1162 4356 1.479730 GTACTCCCTCCGTTCCGATTT 59.520 52.381 0.00 0.00 0.00 2.17
1163 4357 1.856629 ACTCCCTCCGTTCCGATTTA 58.143 50.000 0.00 0.00 0.00 1.40
1164 4358 1.479730 ACTCCCTCCGTTCCGATTTAC 59.520 52.381 0.00 0.00 0.00 2.01
1165 4359 1.755380 CTCCCTCCGTTCCGATTTACT 59.245 52.381 0.00 0.00 0.00 2.24
1166 4360 1.753073 TCCCTCCGTTCCGATTTACTC 59.247 52.381 0.00 0.00 0.00 2.59
1168 4362 1.133790 CCTCCGTTCCGATTTACTCGT 59.866 52.381 0.00 0.00 46.18 4.18
1169 4363 2.448219 CTCCGTTCCGATTTACTCGTC 58.552 52.381 0.00 0.00 46.18 4.20
1170 4364 1.811965 TCCGTTCCGATTTACTCGTCA 59.188 47.619 0.00 0.00 46.18 4.35
1171 4365 2.424601 TCCGTTCCGATTTACTCGTCAT 59.575 45.455 0.00 0.00 46.18 3.06
1172 4366 2.534349 CCGTTCCGATTTACTCGTCATG 59.466 50.000 0.00 0.00 46.18 3.07
1173 4367 2.534349 CGTTCCGATTTACTCGTCATGG 59.466 50.000 0.00 0.00 46.18 3.66
1174 4368 3.518590 GTTCCGATTTACTCGTCATGGT 58.481 45.455 0.00 0.00 46.18 3.55
1175 4369 3.880047 TCCGATTTACTCGTCATGGTT 57.120 42.857 0.00 0.00 46.18 3.67
1176 4370 4.196626 TCCGATTTACTCGTCATGGTTT 57.803 40.909 0.00 0.00 46.18 3.27
1177 4371 4.571919 TCCGATTTACTCGTCATGGTTTT 58.428 39.130 0.00 0.00 46.18 2.43
1178 4372 5.722263 TCCGATTTACTCGTCATGGTTTTA 58.278 37.500 0.00 0.00 46.18 1.52
1179 4373 5.808540 TCCGATTTACTCGTCATGGTTTTAG 59.191 40.000 0.00 0.00 46.18 1.85
1180 4374 5.579511 CCGATTTACTCGTCATGGTTTTAGT 59.420 40.000 0.00 0.00 46.18 2.24
1181 4375 6.091713 CCGATTTACTCGTCATGGTTTTAGTT 59.908 38.462 0.00 0.00 46.18 2.24
1182 4376 7.171434 CGATTTACTCGTCATGGTTTTAGTTC 58.829 38.462 0.00 0.00 42.56 3.01
1183 4377 7.148705 CGATTTACTCGTCATGGTTTTAGTTCA 60.149 37.037 0.00 0.00 42.56 3.18
1184 4378 7.789273 TTTACTCGTCATGGTTTTAGTTCAA 57.211 32.000 0.00 0.00 0.00 2.69
1185 4379 7.972832 TTACTCGTCATGGTTTTAGTTCAAT 57.027 32.000 0.00 0.00 0.00 2.57
1186 4380 6.877611 ACTCGTCATGGTTTTAGTTCAATT 57.122 33.333 0.00 0.00 0.00 2.32
1187 4381 7.272037 ACTCGTCATGGTTTTAGTTCAATTT 57.728 32.000 0.00 0.00 0.00 1.82
1188 4382 7.712797 ACTCGTCATGGTTTTAGTTCAATTTT 58.287 30.769 0.00 0.00 0.00 1.82
1189 4383 7.647715 ACTCGTCATGGTTTTAGTTCAATTTTG 59.352 33.333 0.00 0.00 0.00 2.44
1190 4384 7.708051 TCGTCATGGTTTTAGTTCAATTTTGA 58.292 30.769 0.00 0.00 34.92 2.69
1191 4385 8.191446 TCGTCATGGTTTTAGTTCAATTTTGAA 58.809 29.630 1.66 1.66 44.31 2.69
1204 4398 7.743520 TTCAATTTTGAACTAAAACCACGAC 57.256 32.000 1.66 0.00 41.88 4.34
1205 4399 5.966503 TCAATTTTGAACTAAAACCACGACG 59.033 36.000 0.00 0.00 40.80 5.12
1206 4400 5.738118 ATTTTGAACTAAAACCACGACGA 57.262 34.783 0.00 0.00 40.80 4.20
1207 4401 4.782252 TTTGAACTAAAACCACGACGAG 57.218 40.909 0.00 0.00 0.00 4.18
1208 4402 3.441496 TGAACTAAAACCACGACGAGT 57.559 42.857 0.00 0.00 0.00 4.18
1209 4403 4.566545 TGAACTAAAACCACGACGAGTA 57.433 40.909 0.00 0.00 0.00 2.59
1210 4404 4.930963 TGAACTAAAACCACGACGAGTAA 58.069 39.130 0.00 0.00 0.00 2.24
1211 4405 5.347342 TGAACTAAAACCACGACGAGTAAA 58.653 37.500 0.00 0.00 0.00 2.01
1212 4406 5.984926 TGAACTAAAACCACGACGAGTAAAT 59.015 36.000 0.00 0.00 0.00 1.40
1213 4407 6.144402 TGAACTAAAACCACGACGAGTAAATC 59.856 38.462 0.00 0.00 0.00 2.17
1234 4428 3.041508 GGAACGGAGGGAGTATTATGC 57.958 52.381 0.00 0.00 0.00 3.14
1235 4429 2.367567 GGAACGGAGGGAGTATTATGCA 59.632 50.000 0.00 0.00 0.00 3.96
1236 4430 3.008049 GGAACGGAGGGAGTATTATGCAT 59.992 47.826 3.79 3.79 0.00 3.96
1412 4608 3.484649 CACAATATTACGGTTCGAGACGG 59.515 47.826 14.01 9.00 34.94 4.79
1435 4631 4.377021 CACACCCAGCGTACATTACATAT 58.623 43.478 0.00 0.00 0.00 1.78
1487 4686 9.665719 TCTTTATGTTAATGTCTGCACTATTCA 57.334 29.630 0.00 0.00 0.00 2.57
1490 4689 9.612066 TTATGTTAATGTCTGCACTATTCATGA 57.388 29.630 0.00 0.00 0.00 3.07
1491 4690 7.920160 TGTTAATGTCTGCACTATTCATGAA 57.080 32.000 11.26 11.26 0.00 2.57
1492 4691 8.334263 TGTTAATGTCTGCACTATTCATGAAA 57.666 30.769 13.09 1.39 0.00 2.69
1515 4714 3.457012 TCATGACCATGGATGATGTGTCT 59.543 43.478 21.47 0.00 39.24 3.41
1564 4763 1.693083 CTAAACGAAAGGGCTCGCCG 61.693 60.000 1.24 0.00 42.69 6.46
1741 4940 4.256920 AGGCTAAATGTAAGCTGTGACAG 58.743 43.478 8.52 8.52 39.97 3.51
1804 5003 8.958043 GTTGTTAAAAGTGTGAAGAGCAAATAG 58.042 33.333 0.00 0.00 0.00 1.73
1832 5031 1.228398 TCGGAATGCTGGGCACAAA 60.228 52.632 0.00 0.00 43.04 2.83
2012 5224 6.379133 AGTTCTCGGTATTACTCAATGGTGTA 59.621 38.462 0.00 0.00 0.00 2.90
2087 5333 2.032549 CCACTCGTATTTGCTAGCATGC 60.033 50.000 20.13 10.51 0.00 4.06
2169 5416 5.319453 TCAAGGTCAGCTTTCAGAAATCAT 58.681 37.500 0.00 0.00 0.00 2.45
2197 5444 6.498538 TGGTACCCATAAACATTTTGGATCT 58.501 36.000 10.07 0.00 31.94 2.75
2373 5652 1.003580 TGCTCAATTCAGTCCTCACCC 59.996 52.381 0.00 0.00 0.00 4.61
2448 5727 5.329035 ACAATTTGATAAAATCAGGCGCT 57.671 34.783 7.64 0.00 40.94 5.92
2471 5750 4.400251 TGATGTCATTGGAGCAAGAAATCC 59.600 41.667 0.00 0.00 36.05 3.01
2636 5915 1.131126 GACGTGCAATGGATCAACCTG 59.869 52.381 0.00 0.00 39.86 4.00
3128 6695 8.303876 GCTTGGAGTATTTGGAAAGAACAAATA 58.696 33.333 6.53 6.53 44.27 1.40
3639 7206 3.850122 GCATGGACCAAGTTTTACCTC 57.150 47.619 0.00 0.00 0.00 3.85
3640 7207 2.492088 GCATGGACCAAGTTTTACCTCC 59.508 50.000 0.00 0.00 0.00 4.30
3641 7208 3.814316 GCATGGACCAAGTTTTACCTCCT 60.814 47.826 0.00 0.00 0.00 3.69
3642 7209 4.407365 CATGGACCAAGTTTTACCTCCTT 58.593 43.478 0.00 0.00 0.00 3.36
3644 7211 3.203487 TGGACCAAGTTTTACCTCCTTGT 59.797 43.478 0.00 0.00 35.02 3.16
3645 7212 3.568430 GGACCAAGTTTTACCTCCTTGTG 59.432 47.826 0.00 0.00 35.02 3.33
3647 7214 3.053170 ACCAAGTTTTACCTCCTTGTGGT 60.053 43.478 0.00 0.00 41.28 4.16
3648 7215 4.166531 ACCAAGTTTTACCTCCTTGTGGTA 59.833 41.667 0.00 0.00 38.88 3.25
3649 7216 5.163023 ACCAAGTTTTACCTCCTTGTGGTAT 60.163 40.000 0.00 0.00 39.49 2.73
3652 7219 7.449086 CCAAGTTTTACCTCCTTGTGGTATAAA 59.551 37.037 0.00 0.00 39.49 1.40
3653 7220 9.020731 CAAGTTTTACCTCCTTGTGGTATAAAT 57.979 33.333 0.00 0.00 39.49 1.40
3654 7221 9.596308 AAGTTTTACCTCCTTGTGGTATAAATT 57.404 29.630 0.00 0.00 39.49 1.82
3695 9420 9.591792 TTCTGACATCTCTTATGACTGTTAATG 57.408 33.333 0.00 0.00 0.00 1.90
4110 9861 7.865707 ACAAGCGATATTTCTTCCATGATTAC 58.134 34.615 0.00 0.00 0.00 1.89
4111 9862 7.041098 ACAAGCGATATTTCTTCCATGATTACC 60.041 37.037 0.00 0.00 0.00 2.85
4374 11615 6.745907 GCAATTTCGGTTAAATCTTAGTCACC 59.254 38.462 0.00 0.00 36.76 4.02
4473 11714 7.875041 TCTTAATGAGCCTAGAAGCATACAATC 59.125 37.037 0.00 0.00 34.23 2.67
4490 11731 4.377021 ACAATCACGCACTTTCAGAGTTA 58.623 39.130 0.00 0.00 36.10 2.24
4905 12181 5.201243 GGTTAAAGGATCCACTTGCCTATT 58.799 41.667 15.82 0.00 0.00 1.73
5072 12348 6.183361 ACCTCACCCTAAATAGTGAAACACTT 60.183 38.462 9.63 0.00 42.59 3.16
5387 12669 0.610232 GTGCTTTCCATCCCACAGCT 60.610 55.000 0.00 0.00 0.00 4.24
5481 12764 4.908601 TCCAACTCTCTTGCTATGGAAA 57.091 40.909 0.00 0.00 34.21 3.13
5496 12779 6.379133 TGCTATGGAAAAGCTGAATCTGAATT 59.621 34.615 0.00 0.00 40.73 2.17
5728 13011 4.201851 CCTTGTTCATTATGCTCGTTCCAG 60.202 45.833 0.00 0.00 0.00 3.86
6145 13459 9.393512 GTCACTTCTCCTCTACTACTTATGTTA 57.606 37.037 0.00 0.00 0.00 2.41
6213 13563 5.927115 CGTCTTATATTTAGGAACAGAGGGC 59.073 44.000 0.00 0.00 0.00 5.19
6306 13658 3.838244 TGGATGCAGGTATTACAGACC 57.162 47.619 0.00 0.00 37.22 3.85
6498 13850 8.861033 TTATGTTGGACACTGTATACGATAAC 57.139 34.615 0.00 0.00 0.00 1.89
6572 13930 4.103365 CGATAGGCAGGAGTATGATCAC 57.897 50.000 0.00 0.00 0.00 3.06
6812 14170 0.394565 GAGCTGTGTTCTGTCCAGGT 59.605 55.000 0.00 0.00 39.45 4.00
6827 14185 4.134563 GTCCAGGTTGTTCTGTGTAATGT 58.865 43.478 0.00 0.00 33.14 2.71
6828 14186 4.213482 GTCCAGGTTGTTCTGTGTAATGTC 59.787 45.833 0.00 0.00 33.14 3.06
6829 14187 4.133820 CCAGGTTGTTCTGTGTAATGTCA 58.866 43.478 0.00 0.00 33.14 3.58
6830 14188 4.761739 CCAGGTTGTTCTGTGTAATGTCAT 59.238 41.667 0.00 0.00 33.14 3.06
6832 14190 6.239008 CCAGGTTGTTCTGTGTAATGTCATTT 60.239 38.462 2.79 0.00 33.14 2.32
6833 14191 6.638063 CAGGTTGTTCTGTGTAATGTCATTTG 59.362 38.462 2.79 0.00 0.00 2.32
6877 14239 1.152860 TTTCGTGCCCTTGCCAGAA 60.153 52.632 0.00 0.00 36.33 3.02
6879 14241 0.753479 TTCGTGCCCTTGCCAGAAAA 60.753 50.000 0.00 0.00 36.33 2.29
6880 14242 0.539438 TCGTGCCCTTGCCAGAAAAT 60.539 50.000 0.00 0.00 36.33 1.82
6881 14243 1.173043 CGTGCCCTTGCCAGAAAATA 58.827 50.000 0.00 0.00 36.33 1.40
6883 14245 2.171003 GTGCCCTTGCCAGAAAATACT 58.829 47.619 0.00 0.00 36.33 2.12
6884 14246 2.562738 GTGCCCTTGCCAGAAAATACTT 59.437 45.455 0.00 0.00 36.33 2.24
6885 14247 3.006859 GTGCCCTTGCCAGAAAATACTTT 59.993 43.478 0.00 0.00 36.33 2.66
7087 14685 0.179032 ACACAGACGGGTTGATGCAA 60.179 50.000 0.00 0.00 0.00 4.08
7153 14751 8.659925 TTGAACACATAATCAACAAAGCAAAT 57.340 26.923 0.00 0.00 30.94 2.32
7233 14831 5.909621 ATCTACGGTAGACAAAGCAACTA 57.090 39.130 19.47 0.00 37.69 2.24
7290 14888 1.072159 GGATCGGCTCATCAAGGGG 59.928 63.158 0.00 0.00 0.00 4.79
7321 14919 4.285807 TGATTTGAGTCACACCAAAACG 57.714 40.909 0.00 0.00 36.10 3.60
7512 15121 3.687698 ACCAATTCGTATGAAAGAACCCG 59.312 43.478 0.55 0.00 37.71 5.28
7657 15266 0.787787 CAAAAACTGCGACGATCGGA 59.212 50.000 20.98 5.68 40.84 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.135460 GCCACTCTGCTTGATCTTTGC 60.135 52.381 0.00 0.00 0.00 3.68
56 57 0.683504 ACACGTCCTAGCCACCCTAG 60.684 60.000 0.00 0.00 42.68 3.02
57 58 0.968901 CACACGTCCTAGCCACCCTA 60.969 60.000 0.00 0.00 0.00 3.53
58 59 2.119832 ACACGTCCTAGCCACCCT 59.880 61.111 0.00 0.00 0.00 4.34
59 60 2.264794 CACACGTCCTAGCCACCC 59.735 66.667 0.00 0.00 0.00 4.61
60 61 2.264794 CCACACGTCCTAGCCACC 59.735 66.667 0.00 0.00 0.00 4.61
61 62 2.264794 CCCACACGTCCTAGCCAC 59.735 66.667 0.00 0.00 0.00 5.01
62 63 3.702048 GCCCACACGTCCTAGCCA 61.702 66.667 0.00 0.00 0.00 4.75
63 64 4.814294 CGCCCACACGTCCTAGCC 62.814 72.222 0.00 0.00 0.00 3.93
65 66 4.814294 GGCGCCCACACGTCCTAG 62.814 72.222 18.11 0.00 34.88 3.02
81 82 4.028490 TACAAGGGGCGGTGCAGG 62.028 66.667 0.00 0.00 0.00 4.85
83 84 4.338710 GGTACAAGGGGCGGTGCA 62.339 66.667 0.00 0.00 0.00 4.57
85 86 4.419921 GGGGTACAAGGGGCGGTG 62.420 72.222 0.00 0.00 0.00 4.94
86 87 4.669773 AGGGGTACAAGGGGCGGT 62.670 66.667 0.00 0.00 0.00 5.68
87 88 4.109675 CAGGGGTACAAGGGGCGG 62.110 72.222 0.00 0.00 0.00 6.13
88 89 4.109675 CCAGGGGTACAAGGGGCG 62.110 72.222 0.00 0.00 0.00 6.13
92 105 4.788925 TTTATGATCCAGGGGTACAAGG 57.211 45.455 0.00 0.00 0.00 3.61
97 110 4.775780 CGAGGTATTTATGATCCAGGGGTA 59.224 45.833 0.00 0.00 0.00 3.69
100 113 5.483685 TTCGAGGTATTTATGATCCAGGG 57.516 43.478 0.00 0.00 0.00 4.45
105 118 7.282450 ACAAGGGTTTTCGAGGTATTTATGATC 59.718 37.037 0.00 0.00 0.00 2.92
111 124 4.891168 ACAACAAGGGTTTTCGAGGTATTT 59.109 37.500 0.00 0.00 34.21 1.40
206 219 4.030913 ACATTGGATCTAACCTTCTCCGA 58.969 43.478 0.00 0.00 0.00 4.55
240 253 1.457346 CCATGGCTCTGAAGGACAAC 58.543 55.000 0.00 0.00 0.00 3.32
242 255 1.300963 GCCATGGCTCTGAAGGACA 59.699 57.895 29.98 0.00 38.26 4.02
243 256 1.452833 GGCCATGGCTCTGAAGGAC 60.453 63.158 34.70 12.27 41.60 3.85
259 272 1.070758 TCCCATCTGATTCTTAGCGGC 59.929 52.381 0.00 0.00 0.00 6.53
262 275 3.885901 GGGTTTCCCATCTGATTCTTAGC 59.114 47.826 0.00 0.00 44.65 3.09
275 288 4.636413 CCTAGATAGGAGAAGGGTTTCCCA 60.636 50.000 7.60 0.00 45.93 4.37
276 289 3.904965 CCTAGATAGGAGAAGGGTTTCCC 59.095 52.174 0.00 0.00 46.63 3.97
279 292 3.540687 TCCCCTAGATAGGAGAAGGGTTT 59.459 47.826 7.51 0.00 46.28 3.27
280 293 3.148331 TCCCCTAGATAGGAGAAGGGTT 58.852 50.000 7.51 0.00 46.28 4.11
281 294 2.816113 TCCCCTAGATAGGAGAAGGGT 58.184 52.381 7.51 0.00 46.28 4.34
282 295 3.512496 GTTCCCCTAGATAGGAGAAGGG 58.488 54.545 7.51 0.00 46.63 3.95
283 296 3.158676 CGTTCCCCTAGATAGGAGAAGG 58.841 54.545 7.51 7.80 46.63 3.46
291 312 3.675348 TCCTTGACGTTCCCCTAGATA 57.325 47.619 0.00 0.00 0.00 1.98
318 339 1.681486 GAAGAGAGCCCCCTCCTTCG 61.681 65.000 0.00 0.00 38.96 3.79
324 345 0.120172 AAAGAGGAAGAGAGCCCCCT 59.880 55.000 0.00 0.00 0.00 4.79
335 358 3.253188 CGATGCCACAAAAGAAAGAGGAA 59.747 43.478 0.00 0.00 0.00 3.36
336 359 2.813754 CGATGCCACAAAAGAAAGAGGA 59.186 45.455 0.00 0.00 0.00 3.71
337 360 2.095059 CCGATGCCACAAAAGAAAGAGG 60.095 50.000 0.00 0.00 0.00 3.69
394 418 5.654603 AATGTTCATTGCATGTCACAGAT 57.345 34.783 0.00 0.00 31.45 2.90
405 516 4.209703 CCACACAGTGAAAATGTTCATTGC 59.790 41.667 18.37 0.00 46.63 3.56
409 520 3.625853 TCCCACACAGTGAAAATGTTCA 58.374 40.909 7.81 0.00 46.63 3.18
411 522 2.362077 GCTCCCACACAGTGAAAATGTT 59.638 45.455 7.81 0.00 46.63 2.71
419 530 1.302033 GGAGTGCTCCCACACAGTG 60.302 63.158 6.98 0.00 44.53 3.66
420 531 3.151906 GGAGTGCTCCCACACAGT 58.848 61.111 6.98 0.00 44.53 3.55
453 3616 1.197721 GGAGAAAGCGTCCAACATGTG 59.802 52.381 0.00 0.00 33.84 3.21
454 3617 1.202758 TGGAGAAAGCGTCCAACATGT 60.203 47.619 0.00 0.00 41.32 3.21
455 3618 1.522668 TGGAGAAAGCGTCCAACATG 58.477 50.000 0.00 0.00 41.32 3.21
462 3639 1.646189 GTCCTGATGGAGAAAGCGTC 58.354 55.000 0.00 0.00 44.16 5.19
499 3676 4.118093 AGGGAAAACCGAAACAACAAAG 57.882 40.909 0.00 0.00 46.96 2.77
503 3681 4.380841 AAGAAGGGAAAACCGAAACAAC 57.619 40.909 0.00 0.00 46.96 3.32
516 3694 5.878484 AAAAGATAGGGGAAAAGAAGGGA 57.122 39.130 0.00 0.00 0.00 4.20
519 3697 8.651589 AAACCTAAAAGATAGGGGAAAAGAAG 57.348 34.615 6.48 0.00 39.00 2.85
522 3700 8.651589 AGAAAACCTAAAAGATAGGGGAAAAG 57.348 34.615 6.48 0.00 39.00 2.27
525 3703 6.951778 CCAAGAAAACCTAAAAGATAGGGGAA 59.048 38.462 6.48 0.00 39.00 3.97
528 3706 7.776618 AACCAAGAAAACCTAAAAGATAGGG 57.223 36.000 6.48 0.00 39.00 3.53
539 3729 8.097662 TGTTGTCAATAAAAACCAAGAAAACCT 58.902 29.630 0.00 0.00 0.00 3.50
555 3745 7.824672 TGCATGTATGTCATTTGTTGTCAATA 58.175 30.769 0.00 0.00 34.09 1.90
556 3746 6.689554 TGCATGTATGTCATTTGTTGTCAAT 58.310 32.000 0.00 0.00 34.09 2.57
557 3747 6.081872 TGCATGTATGTCATTTGTTGTCAA 57.918 33.333 0.00 0.00 34.09 3.18
559 3749 6.587226 ACAATGCATGTATGTCATTTGTTGTC 59.413 34.615 0.00 0.00 41.63 3.18
560 3750 6.366604 CACAATGCATGTATGTCATTTGTTGT 59.633 34.615 0.00 0.00 41.46 3.32
561 3751 6.671164 GCACAATGCATGTATGTCATTTGTTG 60.671 38.462 0.00 0.00 44.26 3.33
562 3752 5.349270 GCACAATGCATGTATGTCATTTGTT 59.651 36.000 0.00 0.00 44.26 2.83
564 3754 5.383984 GCACAATGCATGTATGTCATTTG 57.616 39.130 0.00 0.00 44.26 2.32
593 3784 3.396565 TCATCAAATCCTCTGATGGGGA 58.603 45.455 11.72 0.00 46.75 4.81
619 3811 9.912634 TTAGTTGAGGAAATAATCTTTGCAAAG 57.087 29.630 29.53 29.53 37.36 2.77
672 3864 3.816523 GGACCGGTATTTTGTTTCTCACA 59.183 43.478 7.34 0.00 0.00 3.58
673 3865 3.816523 TGGACCGGTATTTTGTTTCTCAC 59.183 43.478 7.34 0.00 0.00 3.51
674 3866 4.069304 CTGGACCGGTATTTTGTTTCTCA 58.931 43.478 7.34 0.00 0.00 3.27
676 3868 4.070009 GACTGGACCGGTATTTTGTTTCT 58.930 43.478 7.34 0.00 0.00 2.52
677 3869 3.816523 TGACTGGACCGGTATTTTGTTTC 59.183 43.478 7.34 0.00 0.00 2.78
678 3870 3.822940 TGACTGGACCGGTATTTTGTTT 58.177 40.909 7.34 0.00 0.00 2.83
681 3873 5.505654 GCAATATGACTGGACCGGTATTTTG 60.506 44.000 7.34 9.21 0.00 2.44
707 3899 1.453669 CCCATCTAAGAGGCCCAGC 59.546 63.158 0.00 0.00 0.00 4.85
736 3928 4.148825 CCTCGTCCTGGAAGCCCG 62.149 72.222 4.63 1.37 34.29 6.13
737 3929 1.677637 CTACCTCGTCCTGGAAGCCC 61.678 65.000 4.63 0.00 0.00 5.19
738 3930 0.683504 TCTACCTCGTCCTGGAAGCC 60.684 60.000 4.63 0.00 0.00 4.35
740 3932 1.394618 CCTCTACCTCGTCCTGGAAG 58.605 60.000 0.00 0.00 0.00 3.46
741 3933 0.683504 GCCTCTACCTCGTCCTGGAA 60.684 60.000 0.00 0.00 0.00 3.53
785 3978 2.093128 CGTGAACCAAACCCTATAGGCT 60.093 50.000 13.85 0.00 40.58 4.58
786 3979 2.285977 CGTGAACCAAACCCTATAGGC 58.714 52.381 13.85 0.00 40.58 3.93
787 3980 2.285977 GCGTGAACCAAACCCTATAGG 58.714 52.381 12.27 12.27 43.78 2.57
788 3981 2.285977 GGCGTGAACCAAACCCTATAG 58.714 52.381 0.00 0.00 0.00 1.31
789 3982 1.405797 CGGCGTGAACCAAACCCTATA 60.406 52.381 0.00 0.00 0.00 1.31
790 3983 0.675522 CGGCGTGAACCAAACCCTAT 60.676 55.000 0.00 0.00 0.00 2.57
851 4044 1.432270 GAAGGCAATTCGCGGGAGAG 61.432 60.000 6.13 0.00 43.84 3.20
963 4156 2.464459 GCACGAGAAATCGGGGCAG 61.464 63.158 1.72 0.00 36.95 4.85
964 4157 2.435938 GCACGAGAAATCGGGGCA 60.436 61.111 1.72 0.00 36.95 5.36
983 4176 1.376424 ATGACACCCTGCTGAAGCG 60.376 57.895 0.00 0.00 45.83 4.68
997 4190 2.182842 GCGCCATCAGACCCATGAC 61.183 63.158 0.00 0.00 30.46 3.06
1023 4216 1.105167 CCTGCCGCATGGACATCAAT 61.105 55.000 0.00 0.00 37.49 2.57
1084 4277 4.760220 ACGGGAGGGAGGGGCAAT 62.760 66.667 0.00 0.00 0.00 3.56
1121 4315 4.982999 ACTACGTAGTATGTCTGCACAAG 58.017 43.478 26.36 0.00 44.56 3.16
1158 4352 8.025243 TGAACTAAAACCATGACGAGTAAATC 57.975 34.615 0.00 0.00 0.00 2.17
1159 4353 7.972832 TGAACTAAAACCATGACGAGTAAAT 57.027 32.000 0.00 0.00 0.00 1.40
1160 4354 7.789273 TTGAACTAAAACCATGACGAGTAAA 57.211 32.000 0.00 0.00 0.00 2.01
1161 4355 7.972832 ATTGAACTAAAACCATGACGAGTAA 57.027 32.000 0.00 0.00 0.00 2.24
1162 4356 7.972832 AATTGAACTAAAACCATGACGAGTA 57.027 32.000 0.00 0.00 0.00 2.59
1163 4357 6.877611 AATTGAACTAAAACCATGACGAGT 57.122 33.333 0.00 0.00 0.00 4.18
1164 4358 7.860373 TCAAAATTGAACTAAAACCATGACGAG 59.140 33.333 0.00 0.00 33.55 4.18
1165 4359 7.708051 TCAAAATTGAACTAAAACCATGACGA 58.292 30.769 0.00 0.00 33.55 4.20
1166 4360 7.922505 TCAAAATTGAACTAAAACCATGACG 57.077 32.000 0.00 0.00 33.55 4.35
1180 4374 6.469595 CGTCGTGGTTTTAGTTCAAAATTGAA 59.530 34.615 4.52 4.52 44.31 2.69
1181 4375 5.966503 CGTCGTGGTTTTAGTTCAAAATTGA 59.033 36.000 0.00 0.00 38.36 2.57
1182 4376 5.966503 TCGTCGTGGTTTTAGTTCAAAATTG 59.033 36.000 0.00 0.00 38.36 2.32
1183 4377 6.121613 TCGTCGTGGTTTTAGTTCAAAATT 57.878 33.333 0.00 0.00 38.36 1.82
1184 4378 5.295045 ACTCGTCGTGGTTTTAGTTCAAAAT 59.705 36.000 0.00 0.00 38.36 1.82
1185 4379 4.630940 ACTCGTCGTGGTTTTAGTTCAAAA 59.369 37.500 0.00 0.00 33.66 2.44
1186 4380 4.183101 ACTCGTCGTGGTTTTAGTTCAAA 58.817 39.130 0.00 0.00 0.00 2.69
1187 4381 3.784338 ACTCGTCGTGGTTTTAGTTCAA 58.216 40.909 0.00 0.00 0.00 2.69
1188 4382 3.441496 ACTCGTCGTGGTTTTAGTTCA 57.559 42.857 0.00 0.00 0.00 3.18
1189 4383 5.888412 TTTACTCGTCGTGGTTTTAGTTC 57.112 39.130 0.00 0.00 0.00 3.01
1190 4384 5.117592 CGATTTACTCGTCGTGGTTTTAGTT 59.882 40.000 0.00 0.00 42.56 2.24
1191 4385 4.618489 CGATTTACTCGTCGTGGTTTTAGT 59.382 41.667 0.00 0.00 42.56 2.24
1192 4386 4.030977 CCGATTTACTCGTCGTGGTTTTAG 59.969 45.833 0.00 0.00 46.18 1.85
1193 4387 3.919804 CCGATTTACTCGTCGTGGTTTTA 59.080 43.478 0.00 0.00 46.18 1.52
1194 4388 2.733026 CCGATTTACTCGTCGTGGTTTT 59.267 45.455 0.00 0.00 46.18 2.43
1195 4389 2.030007 TCCGATTTACTCGTCGTGGTTT 60.030 45.455 0.00 0.00 46.18 3.27
1196 4390 1.541147 TCCGATTTACTCGTCGTGGTT 59.459 47.619 0.00 0.00 46.18 3.67
1197 4391 1.167851 TCCGATTTACTCGTCGTGGT 58.832 50.000 0.00 0.00 46.18 4.16
1198 4392 1.916000 GTTCCGATTTACTCGTCGTGG 59.084 52.381 0.00 0.00 46.18 4.94
1199 4393 1.576246 CGTTCCGATTTACTCGTCGTG 59.424 52.381 0.00 0.00 46.18 4.35
1200 4394 1.466360 CCGTTCCGATTTACTCGTCGT 60.466 52.381 0.00 0.00 46.18 4.34
1201 4395 1.186030 CCGTTCCGATTTACTCGTCG 58.814 55.000 0.00 0.00 46.18 5.12
1202 4396 2.448219 CTCCGTTCCGATTTACTCGTC 58.552 52.381 0.00 0.00 46.18 4.20
1203 4397 1.133790 CCTCCGTTCCGATTTACTCGT 59.866 52.381 0.00 0.00 46.18 4.18
1205 4399 1.753073 TCCCTCCGTTCCGATTTACTC 59.247 52.381 0.00 0.00 0.00 2.59
1206 4400 1.755380 CTCCCTCCGTTCCGATTTACT 59.245 52.381 0.00 0.00 0.00 2.24
1207 4401 1.479730 ACTCCCTCCGTTCCGATTTAC 59.520 52.381 0.00 0.00 0.00 2.01
1208 4402 1.856629 ACTCCCTCCGTTCCGATTTA 58.143 50.000 0.00 0.00 0.00 1.40
1209 4403 1.856629 TACTCCCTCCGTTCCGATTT 58.143 50.000 0.00 0.00 0.00 2.17
1210 4404 2.083628 ATACTCCCTCCGTTCCGATT 57.916 50.000 0.00 0.00 0.00 3.34
1211 4405 2.083628 AATACTCCCTCCGTTCCGAT 57.916 50.000 0.00 0.00 0.00 4.18
1212 4406 2.734755 TAATACTCCCTCCGTTCCGA 57.265 50.000 0.00 0.00 0.00 4.55
1213 4407 2.609737 GCATAATACTCCCTCCGTTCCG 60.610 54.545 0.00 0.00 0.00 4.30
1214 4408 2.367567 TGCATAATACTCCCTCCGTTCC 59.632 50.000 0.00 0.00 0.00 3.62
1215 4409 3.746045 TGCATAATACTCCCTCCGTTC 57.254 47.619 0.00 0.00 0.00 3.95
1216 4410 5.818678 TTATGCATAATACTCCCTCCGTT 57.181 39.130 15.21 0.00 0.00 4.44
1217 4411 5.818678 TTTATGCATAATACTCCCTCCGT 57.181 39.130 19.51 0.00 0.00 4.69
1218 4412 6.369065 GTCTTTTATGCATAATACTCCCTCCG 59.631 42.308 19.51 1.87 0.00 4.63
1219 4413 7.454225 AGTCTTTTATGCATAATACTCCCTCC 58.546 38.462 19.51 2.53 0.00 4.30
1220 4414 7.329717 CGAGTCTTTTATGCATAATACTCCCTC 59.670 40.741 29.02 22.30 30.85 4.30
1221 4415 7.015292 TCGAGTCTTTTATGCATAATACTCCCT 59.985 37.037 29.02 18.72 30.85 4.20
1222 4416 7.152645 TCGAGTCTTTTATGCATAATACTCCC 58.847 38.462 29.02 18.27 30.85 4.30
1223 4417 8.764524 ATCGAGTCTTTTATGCATAATACTCC 57.235 34.615 29.02 20.12 30.85 3.85
1231 4425 9.167311 AGAGTAAAAATCGAGTCTTTTATGCAT 57.833 29.630 3.79 3.79 31.57 3.96
1232 4426 8.547967 AGAGTAAAAATCGAGTCTTTTATGCA 57.452 30.769 11.02 0.00 31.57 3.96
1233 4427 9.827411 AAAGAGTAAAAATCGAGTCTTTTATGC 57.173 29.630 11.02 7.84 40.73 3.14
1324 4520 7.989947 TGGGGTTAGAAAAGAGATGTATAGT 57.010 36.000 0.00 0.00 0.00 2.12
1330 4526 5.449177 GCGAATTGGGGTTAGAAAAGAGATG 60.449 44.000 0.00 0.00 0.00 2.90
1412 4608 0.725117 GTAATGTACGCTGGGTGTGC 59.275 55.000 7.71 0.00 0.00 4.57
1435 4631 9.968870 AAAACAACAAACTAGTAGTGTTTTCAA 57.031 25.926 21.31 0.00 35.71 2.69
1485 4684 8.128816 ACATCATCCATGGTCATGATTTCATGA 61.129 37.037 20.94 17.17 46.56 3.07
1486 4685 6.015434 ACATCATCCATGGTCATGATTTCATG 60.015 38.462 20.94 20.38 44.37 3.07
1487 4686 6.015434 CACATCATCCATGGTCATGATTTCAT 60.015 38.462 20.94 8.81 41.20 2.57
1488 4687 5.300792 CACATCATCCATGGTCATGATTTCA 59.699 40.000 20.94 0.00 41.20 2.69
1489 4688 5.301045 ACACATCATCCATGGTCATGATTTC 59.699 40.000 20.94 0.00 41.20 2.17
1490 4689 5.205821 ACACATCATCCATGGTCATGATTT 58.794 37.500 20.94 14.78 41.20 2.17
1491 4690 4.800023 ACACATCATCCATGGTCATGATT 58.200 39.130 20.94 12.64 41.20 2.57
1492 4691 4.104261 AGACACATCATCCATGGTCATGAT 59.896 41.667 18.77 18.77 41.20 2.45
1515 4714 3.704566 AGCAATCGACATACCTAGGACAA 59.295 43.478 17.98 0.10 0.00 3.18
1543 4742 1.019805 GCGAGCCCTTTCGTTTAGCT 61.020 55.000 0.00 0.00 42.38 3.32
1564 4763 2.353323 GGGTTATCAACTTGTCGACCC 58.647 52.381 14.12 2.22 38.55 4.46
1804 5003 2.476320 GCATTCCGAGGAAGCTGGC 61.476 63.158 10.56 7.57 37.56 4.85
1832 5031 8.907685 GCATGTGTGTTGTAACGTTTTAAATAT 58.092 29.630 5.91 0.00 0.00 1.28
2012 5224 3.370231 GCAAATTGACGGCCGGGT 61.370 61.111 31.76 9.62 0.00 5.28
2087 5333 3.128764 TCATGAGTGTAGCCTGTCTAACG 59.871 47.826 0.00 0.00 0.00 3.18
2197 5444 2.945440 GCAGCCAATTCCATGGTAGTCA 60.945 50.000 12.58 0.00 42.75 3.41
2373 5652 4.099881 GCATATGGGGTATAATGCAATGGG 59.900 45.833 4.56 0.00 35.35 4.00
2448 5727 4.400251 GGATTTCTTGCTCCAATGACATCA 59.600 41.667 0.00 0.00 0.00 3.07
2636 5915 8.367911 TCATTACCATAGTATGTTGACCAGATC 58.632 37.037 9.28 0.00 0.00 2.75
3128 6695 2.639839 CGATCCCTTGGGAGATATGGTT 59.360 50.000 14.30 0.00 0.00 3.67
3230 6797 2.967599 GGCAGAAATAAAAGGGCCTG 57.032 50.000 6.92 0.00 38.37 4.85
3619 7186 2.492088 GGAGGTAAAACTTGGTCCATGC 59.508 50.000 4.67 0.00 0.00 4.06
3620 7187 4.034285 AGGAGGTAAAACTTGGTCCATG 57.966 45.455 3.21 3.21 0.00 3.66
3622 7189 3.203487 ACAAGGAGGTAAAACTTGGTCCA 59.797 43.478 8.30 0.00 44.35 4.02
3623 7190 3.568430 CACAAGGAGGTAAAACTTGGTCC 59.432 47.826 8.30 0.00 44.35 4.46
3625 7192 3.053170 ACCACAAGGAGGTAAAACTTGGT 60.053 43.478 8.30 0.00 44.35 3.67
3626 7193 3.562182 ACCACAAGGAGGTAAAACTTGG 58.438 45.455 8.30 0.00 44.35 3.61
3628 7195 9.596308 AATTTATACCACAAGGAGGTAAAACTT 57.404 29.630 0.00 0.00 44.25 2.66
3695 9420 9.834628 TTATGCTGCTACAACTTGTTTTATTAC 57.165 29.630 0.00 0.00 0.00 1.89
4388 11629 7.686434 AGGTAGGCTTCTTAACTTGTATTTGA 58.314 34.615 0.00 0.00 0.00 2.69
4389 11630 7.923414 AGGTAGGCTTCTTAACTTGTATTTG 57.077 36.000 0.00 0.00 0.00 2.32
4390 11631 9.043548 TCTAGGTAGGCTTCTTAACTTGTATTT 57.956 33.333 0.00 0.00 0.00 1.40
4473 11714 5.006746 AGTTCTTTAACTCTGAAAGTGCGTG 59.993 40.000 0.00 0.00 42.42 5.34
4490 11731 6.715347 AACAGATAACTTTGCCAGTTCTTT 57.285 33.333 1.76 0.00 42.62 2.52
4905 12181 7.060421 AGGAGAAAAGTTAACACTGGAATTGA 58.940 34.615 8.61 0.00 31.60 2.57
5072 12348 1.483004 CATGCATTTCCAATCAGGCCA 59.517 47.619 5.01 0.00 37.29 5.36
5387 12669 2.023673 CTTGTCAAGCAACCAAGTCCA 58.976 47.619 0.00 0.00 32.76 4.02
5481 12764 5.300034 TGTCACAACAATTCAGATTCAGCTT 59.700 36.000 0.00 0.00 30.70 3.74
5496 12779 3.076621 GGCAGATGATCTTGTCACAACA 58.923 45.455 0.00 0.00 40.28 3.33
5728 13011 4.405116 TTTGGCATAATGAATGGAAGCC 57.595 40.909 0.00 0.00 40.93 4.35
6145 13459 3.570550 TGCCAAAACGCCTTACATTTAGT 59.429 39.130 0.00 0.00 0.00 2.24
6213 13563 8.079203 AGACTAGATATCATAGTTGAAAGCACG 58.921 37.037 5.32 0.00 34.96 5.34
6306 13658 6.690098 CAGAAATCAATTCATGCTTTACTCGG 59.310 38.462 0.00 0.00 40.72 4.63
6498 13850 0.833287 ATCCATCAGTGTCTTCCCGG 59.167 55.000 0.00 0.00 0.00 5.73
6812 14170 6.977502 CCAACAAATGACATTACACAGAACAA 59.022 34.615 0.00 0.00 0.00 2.83
6877 14239 7.602517 CGTCTCAATGAGAAGGAAAGTATTT 57.397 36.000 15.28 0.00 40.59 1.40
7087 14685 7.118496 AGTACTATAGCTGATTGAAGTGCTT 57.882 36.000 0.00 0.00 37.02 3.91
7153 14751 5.660460 TCGTTCTGAAGCTGAAATGCTATA 58.340 37.500 0.00 0.00 43.24 1.31
7290 14888 4.023792 TGTGACTCAAATCATGTGACTTGC 60.024 41.667 0.00 0.00 31.96 4.01
7321 14919 1.192534 CGAAACGAAGTCTGTGGCTTC 59.807 52.381 2.19 2.19 45.00 3.86
7512 15121 1.971167 TCGGCACTTGCACAATCCC 60.971 57.895 3.15 0.00 44.36 3.85
7657 15266 3.638160 TCTGAAGCCAAATTGAACAGCTT 59.362 39.130 6.86 6.86 45.97 3.74


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

AutoCloner maintained by Alex Coulton.