Multiple sequence alignment - TraesCS1A01G192700

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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 TraesCS1A01G192700 chr1A 100.000 5208 0 0 1 5208 347928115 347922908 0.000000e+00 9618.0
1 TraesCS1A01G192700 chr1A 87.705 122 14 1 2 122 248252346 248252467 1.960000e-29 141.0
2 TraesCS1A01G192700 chr1A 92.857 70 4 1 3787 3856 256814050 256813982 3.320000e-17 100.0
3 TraesCS1A01G192700 chr1D 96.127 2040 70 6 1738 3771 275626568 275624532 0.000000e+00 3321.0
4 TraesCS1A01G192700 chr1D 96.067 1195 43 3 565 1759 275627784 275626594 0.000000e+00 1943.0
5 TraesCS1A01G192700 chr1D 94.363 958 41 9 3861 4814 275624527 275623579 0.000000e+00 1458.0
6 TraesCS1A01G192700 chr1D 93.439 503 30 2 1 501 275630172 275629671 0.000000e+00 743.0
7 TraesCS1A01G192700 chr1D 93.137 408 25 2 4801 5208 275622287 275621883 3.470000e-166 595.0
8 TraesCS1A01G192700 chr1D 92.337 261 18 2 563 823 275628138 275627880 2.290000e-98 370.0
9 TraesCS1A01G192700 chr1B 93.790 1417 58 10 615 2029 374875526 374874138 0.000000e+00 2102.0
10 TraesCS1A01G192700 chr1B 96.475 1078 31 4 2026 3102 374874059 374872988 0.000000e+00 1773.0
11 TraesCS1A01G192700 chr1B 93.895 688 39 3 3098 3782 374869116 374868429 0.000000e+00 1035.0
12 TraesCS1A01G192700 chr1B 94.277 664 24 9 3861 4520 374868437 374867784 0.000000e+00 1003.0
13 TraesCS1A01G192700 chr1B 92.785 596 36 2 4613 5208 374866132 374865544 0.000000e+00 856.0
14 TraesCS1A01G192700 chr1B 90.213 470 42 3 34 499 374911911 374911442 1.240000e-170 610.0
15 TraesCS1A01G192700 chr1B 78.851 435 51 21 1286 1704 49248906 49248497 6.690000e-64 255.0
16 TraesCS1A01G192700 chr1B 76.266 316 54 10 2668 2964 34775334 34775647 1.170000e-31 148.0
17 TraesCS1A01G192700 chr1B 87.805 123 15 0 1871 1993 49248386 49248264 1.510000e-30 145.0
18 TraesCS1A01G192700 chr1B 89.744 78 8 0 1044 1121 49249100 49249023 3.320000e-17 100.0
19 TraesCS1A01G192700 chr5A 81.419 775 108 21 2264 3012 706056816 706057580 7.460000e-168 601.0
20 TraesCS1A01G192700 chr5A 80.303 528 96 8 3207 3731 706057896 706058418 4.890000e-105 392.0
21 TraesCS1A01G192700 chr5A 80.000 395 47 15 1329 1704 706056063 706056444 4.000000e-66 263.0
22 TraesCS1A01G192700 chr5A 83.871 124 18 1 2 123 535455842 535455719 3.300000e-22 117.0
23 TraesCS1A01G192700 chr5A 91.304 69 4 2 4576 4643 382336357 382336290 5.550000e-15 93.5
24 TraesCS1A01G192700 chr5A 86.905 84 5 6 4558 4637 398285898 398285979 7.180000e-14 89.8
25 TraesCS1A01G192700 chr5A 85.714 56 3 3 721 771 706055600 706055655 3.000000e-03 54.7
26 TraesCS1A01G192700 chrUn 80.224 536 91 14 3205 3731 134302331 134301802 6.320000e-104 388.0
27 TraesCS1A01G192700 chrUn 76.867 549 92 20 1166 1704 134304285 134303762 1.430000e-70 278.0
28 TraesCS1A01G192700 chrUn 92.308 78 6 0 1044 1121 134304371 134304294 1.530000e-20 111.0
29 TraesCS1A01G192700 chrUn 74.558 283 47 9 3920 4192 134301690 134301423 3.320000e-17 100.0
30 TraesCS1A01G192700 chrUn 80.734 109 16 4 4133 4240 108249582 108249686 4.320000e-11 80.5
31 TraesCS1A01G192700 chrUn 89.831 59 6 0 4128 4186 134301300 134301242 5.590000e-10 76.8
32 TraesCS1A01G192700 chrUn 92.157 51 3 1 3305 3355 108301858 108301907 2.600000e-08 71.3
33 TraesCS1A01G192700 chr4B 76.550 371 44 21 1289 1641 666591149 666590804 4.170000e-36 163.0
34 TraesCS1A01G192700 chr4B 85.417 96 11 3 3770 3865 619445595 619445687 4.290000e-16 97.1
35 TraesCS1A01G192700 chr4B 78.169 142 22 4 3205 3345 665922660 665922527 1.200000e-11 82.4
36 TraesCS1A01G192700 chr4A 81.643 207 29 6 2764 2964 594020433 594020636 4.170000e-36 163.0
37 TraesCS1A01G192700 chr2D 76.899 316 52 10 2668 2964 287839061 287838748 5.400000e-35 159.0
38 TraesCS1A01G192700 chr2D 83.871 124 16 3 2 122 289196413 289196291 1.190000e-21 115.0
39 TraesCS1A01G192700 chr5D 76.656 317 53 10 2668 2965 443808160 443807846 6.980000e-34 156.0
40 TraesCS1A01G192700 chr5D 84.426 122 18 1 2 122 530559424 530559545 9.160000e-23 119.0
41 TraesCS1A01G192700 chr5D 91.463 82 6 1 3770 3851 264494445 264494525 1.530000e-20 111.0
42 TraesCS1A01G192700 chr5D 88.636 88 9 1 3770 3857 134916579 134916493 7.130000e-19 106.0
43 TraesCS1A01G192700 chr5D 93.548 62 2 2 4565 4625 28023617 28023677 2.000000e-14 91.6
44 TraesCS1A01G192700 chr4D 76.582 316 53 11 2668 2964 216528816 216529129 2.510000e-33 154.0
45 TraesCS1A01G192700 chr4D 87.500 112 13 1 12 122 374106557 374106668 1.520000e-25 128.0
46 TraesCS1A01G192700 chr4D 83.740 123 18 2 3 124 224158566 224158445 1.190000e-21 115.0
47 TraesCS1A01G192700 chr6D 76.101 318 53 10 2668 2964 393649506 393649821 1.510000e-30 145.0
48 TraesCS1A01G192700 chr6D 85.714 119 15 1 6 122 298615296 298615414 1.970000e-24 124.0
49 TraesCS1A01G192700 chr6D 89.888 89 7 2 3769 3857 174373699 174373785 4.260000e-21 113.0
50 TraesCS1A01G192700 chr6D 93.750 64 3 1 4561 4624 73497330 73497392 1.540000e-15 95.3
51 TraesCS1A01G192700 chr2B 89.011 91 9 1 3768 3858 394722949 394723038 1.530000e-20 111.0
52 TraesCS1A01G192700 chr6B 88.506 87 8 2 3770 3856 422359783 422359699 2.570000e-18 104.0
53 TraesCS1A01G192700 chr2A 87.778 90 7 3 3770 3856 60193322 60193410 9.230000e-18 102.0
54 TraesCS1A01G192700 chr2A 86.813 91 10 2 3770 3859 705588289 705588378 3.320000e-17 100.0
55 TraesCS1A01G192700 chr6A 89.744 78 4 3 4561 4635 89893712 89893788 4.290000e-16 97.1
56 TraesCS1A01G192700 chr6A 96.552 58 0 2 4568 4624 104056454 104056398 1.540000e-15 95.3
57 TraesCS1A01G192700 chr6A 93.846 65 1 3 4561 4624 146554559 146554497 1.540000e-15 95.3
58 TraesCS1A01G192700 chr7A 93.846 65 1 3 4561 4624 335980809 335980747 1.540000e-15 95.3


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G192700 chr1A 347922908 347928115 5207 True 9618.000 9618 100.0000 1 5208 1 chr1A.!!$R2 5207
1 TraesCS1A01G192700 chr1D 275621883 275630172 8289 True 1405.000 3321 94.2450 1 5208 6 chr1D.!!$R1 5207
2 TraesCS1A01G192700 chr1B 374865544 374875526 9982 True 1353.800 2102 94.2444 615 5208 5 chr1B.!!$R3 4593
3 TraesCS1A01G192700 chr5A 706055600 706058418 2818 False 327.675 601 81.8590 721 3731 4 chr5A.!!$F2 3010

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
595 2096 0.397254 GGAGTAGCTACCAGCCCAGA 60.397 60.000 20.31 0.0 43.77 3.86 F
598 2099 1.007238 AGTAGCTACCAGCCCAGAAGA 59.993 52.381 20.31 0.0 43.77 2.87 F
2008 3961 0.838122 AGGTCACTGTAGCCAGCCTT 60.838 55.000 3.25 0.0 42.81 4.35 F
2066 4101 0.162507 CTGAGTGCTTGAAACTCGCG 59.837 55.000 0.00 0.0 45.81 5.87 F
3858 10045 0.635009 TTGGATCGGAGGGAGTAGGT 59.365 55.000 0.00 0.0 0.00 3.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 3880 0.250234 CCATGCTTCTCTTCCCGACA 59.750 55.000 0.00 0.0 0.00 4.35 R
2049 4084 0.859232 TTCGCGAGTTTCAAGCACTC 59.141 50.000 9.59 0.0 37.84 3.51 R
3839 10026 0.635009 ACCTACTCCCTCCGATCCAA 59.365 55.000 0.00 0.0 0.00 3.53 R
4012 10203 1.076705 GATGGCTTCCCCTTGGTCC 60.077 63.158 0.00 0.0 0.00 4.46 R
4778 12547 1.112916 TGAACGTCTGCTGGACCTGA 61.113 55.000 1.91 0.0 41.64 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
34 35 1.545136 TGCCGACACAATGCAAATGAT 59.455 42.857 9.59 0.00 30.85 2.45
63 64 9.697250 GATGATGAATGCAACAAACAAATAATG 57.303 29.630 0.00 0.00 30.24 1.90
77 78 4.515191 ACAAATAATGAACGCGGCTATCAT 59.485 37.500 12.47 11.85 35.39 2.45
83 84 2.095213 TGAACGCGGCTATCATGAAAAC 59.905 45.455 12.47 0.00 0.00 2.43
86 87 2.032054 ACGCGGCTATCATGAAAACATG 59.968 45.455 12.47 0.00 0.00 3.21
112 113 0.889638 AACTGGAGCGTCAGTCTCGA 60.890 55.000 13.79 0.00 46.17 4.04
113 114 1.302383 ACTGGAGCGTCAGTCTCGAG 61.302 60.000 5.93 5.93 43.82 4.04
121 122 2.603892 GCGTCAGTCTCGAGTTGTTACA 60.604 50.000 13.13 0.00 0.00 2.41
134 135 6.805271 TCGAGTTGTTACAGCTATGTCTTTAC 59.195 38.462 0.86 0.00 41.01 2.01
138 139 4.221262 TGTTACAGCTATGTCTTTACGGGT 59.779 41.667 0.00 0.00 41.01 5.28
168 169 6.553953 TGTACCTTTATTGAGGCAGATACA 57.446 37.500 0.00 0.00 40.65 2.29
186 187 3.091633 ACAAGTCAGCATAAGGGCATT 57.908 42.857 0.00 0.00 35.83 3.56
225 226 5.929058 TGCAACTATGAGAATGAGAGACT 57.071 39.130 0.00 0.00 0.00 3.24
227 228 7.410120 TGCAACTATGAGAATGAGAGACTAA 57.590 36.000 0.00 0.00 0.00 2.24
228 229 7.840931 TGCAACTATGAGAATGAGAGACTAAA 58.159 34.615 0.00 0.00 0.00 1.85
233 234 5.923733 TGAGAATGAGAGACTAAAGGGTC 57.076 43.478 0.00 0.00 36.56 4.46
240 241 3.935828 GAGAGACTAAAGGGTCATTGTGC 59.064 47.826 0.00 0.00 38.57 4.57
286 287 3.127533 GTGGCATGACTCGGGTGC 61.128 66.667 0.00 0.00 38.12 5.01
299 300 3.728373 GGTGCCCTCCGGGTCAAT 61.728 66.667 0.00 0.00 46.51 2.57
300 301 2.438434 GTGCCCTCCGGGTCAATG 60.438 66.667 0.00 0.00 46.51 2.82
301 302 2.609299 TGCCCTCCGGGTCAATGA 60.609 61.111 0.00 0.00 46.51 2.57
302 303 2.000701 TGCCCTCCGGGTCAATGAT 61.001 57.895 0.00 0.00 46.51 2.45
303 304 0.692756 TGCCCTCCGGGTCAATGATA 60.693 55.000 0.00 0.00 46.51 2.15
343 344 3.070018 CAAGCAGATGTCCGAGTCTTTT 58.930 45.455 0.00 0.00 0.00 2.27
359 360 3.004839 GTCTTTTCAGGGTTTGAGGCTTC 59.995 47.826 0.00 0.00 37.07 3.86
480 483 8.981659 TCTGATTAGAACCATTCAGTCAGATTA 58.018 33.333 12.53 0.00 38.04 1.75
539 542 7.502561 AGCTTGTCAGTTTAATAAAGACAACCT 59.497 33.333 13.23 10.80 42.35 3.50
553 556 7.770801 AAAGACAACCTTAAATCAAAACTGC 57.229 32.000 0.00 0.00 34.00 4.40
554 557 5.842907 AGACAACCTTAAATCAAAACTGCC 58.157 37.500 0.00 0.00 0.00 4.85
557 560 5.105146 ACAACCTTAAATCAAAACTGCCACA 60.105 36.000 0.00 0.00 0.00 4.17
558 561 5.806654 ACCTTAAATCAAAACTGCCACAT 57.193 34.783 0.00 0.00 0.00 3.21
568 571 8.776376 ATCAAAACTGCCACATTTATTTTAGG 57.224 30.769 0.00 0.00 0.00 2.69
584 2085 8.619683 TTATTTTAGGTAAAGAGGGAGTAGCT 57.380 34.615 0.00 0.00 0.00 3.32
592 2093 1.075151 AGGGAGTAGCTACCAGCCC 60.075 63.158 27.52 27.52 43.77 5.19
593 2094 1.382695 GGGAGTAGCTACCAGCCCA 60.383 63.158 28.82 0.00 43.77 5.36
594 2095 1.403687 GGGAGTAGCTACCAGCCCAG 61.404 65.000 28.82 0.00 43.77 4.45
595 2096 0.397254 GGAGTAGCTACCAGCCCAGA 60.397 60.000 20.31 0.00 43.77 3.86
596 2097 1.486211 GAGTAGCTACCAGCCCAGAA 58.514 55.000 20.31 0.00 43.77 3.02
597 2098 1.410882 GAGTAGCTACCAGCCCAGAAG 59.589 57.143 20.31 0.00 43.77 2.85
598 2099 1.007238 AGTAGCTACCAGCCCAGAAGA 59.993 52.381 20.31 0.00 43.77 2.87
599 2100 2.043227 GTAGCTACCAGCCCAGAAGAT 58.957 52.381 13.20 0.00 43.77 2.40
601 2102 2.983296 AGCTACCAGCCCAGAAGATAT 58.017 47.619 0.00 0.00 43.77 1.63
621 2122 1.756172 CTGCCACCACACCCAAACA 60.756 57.895 0.00 0.00 0.00 2.83
671 2172 2.177778 GCGCCAGAAAAGAGCTGC 59.822 61.111 0.00 0.00 32.06 5.25
675 2176 1.461559 GCCAGAAAAGAGCTGCTCAT 58.538 50.000 29.49 17.00 32.06 2.90
686 2187 4.506758 AGAGCTGCTCATTTTTCTCTCTC 58.493 43.478 29.49 0.06 32.06 3.20
692 2193 4.449068 TGCTCATTTTTCTCTCTCGTTGTC 59.551 41.667 0.00 0.00 0.00 3.18
881 2734 4.129148 ATTCCCCCGCCAGCTTCC 62.129 66.667 0.00 0.00 0.00 3.46
997 2851 3.391382 CTGTCCCCGTCAGACCCC 61.391 72.222 0.00 0.00 35.20 4.95
1168 3022 4.880537 AGCCGCGCTCCAATCTCG 62.881 66.667 5.56 0.00 30.62 4.04
1665 3552 1.837439 AGTGTGCTCGGGGAATTCATA 59.163 47.619 7.93 0.00 0.00 2.15
1745 3632 9.537848 CACTTTAATCTTACACGAAATTACCAC 57.462 33.333 0.00 0.00 0.00 4.16
1761 3695 5.705609 TTACCACTGCTTTGAATTCCTTC 57.294 39.130 2.27 0.00 0.00 3.46
1781 3732 4.579454 TCGTCACTGTAAAACTGTAGCT 57.421 40.909 0.00 0.00 0.00 3.32
1789 3740 6.866770 CACTGTAAAACTGTAGCTAAGCACTA 59.133 38.462 0.00 0.00 0.00 2.74
2008 3961 0.838122 AGGTCACTGTAGCCAGCCTT 60.838 55.000 3.25 0.00 42.81 4.35
2023 3976 5.716703 AGCCAGCCTTTGAACAAATTACTAT 59.283 36.000 0.44 0.00 0.00 2.12
2061 4096 3.883489 AGGTAAACCTGAGTGCTTGAAAC 59.117 43.478 0.00 0.00 46.55 2.78
2064 4099 1.871080 ACCTGAGTGCTTGAAACTCG 58.129 50.000 0.00 0.00 45.81 4.18
2065 4100 0.514691 CCTGAGTGCTTGAAACTCGC 59.485 55.000 0.00 0.00 45.81 5.03
2066 4101 0.162507 CTGAGTGCTTGAAACTCGCG 59.837 55.000 0.00 0.00 45.81 5.87
2168 4215 3.598019 ATGGCGCATTTTCTGTTTCAT 57.402 38.095 10.83 0.00 0.00 2.57
2695 4748 2.238521 ACCTTGATGCCGTTGAACATT 58.761 42.857 0.00 0.00 0.00 2.71
2765 4818 9.770097 ACATACTAGGTCTGTATGAATGATTTG 57.230 33.333 17.32 0.00 45.91 2.32
3042 5246 1.689984 TGAAACTGCAATGTGCCAGA 58.310 45.000 0.00 0.00 44.23 3.86
3113 9193 6.000840 TGTTGTTTCTGTTGTAGCCATCATA 58.999 36.000 0.00 0.00 0.00 2.15
3175 9255 6.165659 ACTGTCTGTTCGCATTGTTATAAC 57.834 37.500 8.75 8.75 0.00 1.89
3377 9562 6.968904 CACTATGATGGTTTGCAATTCAGTAC 59.031 38.462 0.00 0.00 0.00 2.73
3514 9701 7.379529 GTGTCACCTTATTTCATTTTCTGTGTG 59.620 37.037 0.00 0.00 0.00 3.82
3521 9708 8.846943 TTATTTCATTTTCTGTGTGAGCTCTA 57.153 30.769 16.19 0.75 0.00 2.43
3524 9711 5.858381 TCATTTTCTGTGTGAGCTCTACTT 58.142 37.500 16.19 0.00 0.00 2.24
3531 9718 4.883083 TGTGTGAGCTCTACTTTACCTTG 58.117 43.478 16.19 0.00 0.00 3.61
3622 9809 5.096443 TGTGATTTTCCCTTTTGCTTTGT 57.904 34.783 0.00 0.00 0.00 2.83
3718 9905 1.239347 GAGTTGAACCAAGTGAGCCC 58.761 55.000 0.00 0.00 0.00 5.19
3720 9907 0.818040 GTTGAACCAAGTGAGCCCGT 60.818 55.000 0.00 0.00 0.00 5.28
3732 9919 1.291132 GAGCCCGTCTACAAGCATTC 58.709 55.000 0.00 0.00 0.00 2.67
3737 9924 3.081804 CCCGTCTACAAGCATTCCTTTT 58.918 45.455 0.00 0.00 0.00 2.27
3739 9926 4.379499 CCCGTCTACAAGCATTCCTTTTTC 60.379 45.833 0.00 0.00 0.00 2.29
3754 9941 3.365364 CCTTTTTCTTAAGCTGGACTGCG 60.365 47.826 0.00 0.00 38.13 5.18
3765 9952 1.193203 CTGGACTGCGCGCATATTAAG 59.807 52.381 36.48 23.86 0.00 1.85
3771 9958 3.428870 ACTGCGCGCATATTAAGTGATAC 59.571 43.478 36.48 0.00 0.00 2.24
3773 9960 4.800784 TGCGCGCATATTAAGTGATACTA 58.199 39.130 33.09 0.00 0.00 1.82
3774 9961 4.619760 TGCGCGCATATTAAGTGATACTAC 59.380 41.667 33.09 0.00 0.00 2.73
3775 9962 4.857588 GCGCGCATATTAAGTGATACTACT 59.142 41.667 29.10 0.00 0.00 2.57
3776 9963 5.345202 GCGCGCATATTAAGTGATACTACTT 59.655 40.000 29.10 0.00 43.03 2.24
3777 9964 6.452611 GCGCGCATATTAAGTGATACTACTTC 60.453 42.308 29.10 0.00 41.01 3.01
3778 9965 6.033619 CGCGCATATTAAGTGATACTACTTCC 59.966 42.308 8.75 0.00 41.01 3.46
3779 9966 6.310711 GCGCATATTAAGTGATACTACTTCCC 59.689 42.308 0.30 0.00 41.01 3.97
3780 9967 7.375834 CGCATATTAAGTGATACTACTTCCCA 58.624 38.462 0.00 0.00 41.01 4.37
3781 9968 8.035394 CGCATATTAAGTGATACTACTTCCCAT 58.965 37.037 0.00 0.00 41.01 4.00
3782 9969 9.372369 GCATATTAAGTGATACTACTTCCCATC 57.628 37.037 0.00 0.00 41.01 3.51
3783 9970 9.877178 CATATTAAGTGATACTACTTCCCATCC 57.123 37.037 0.00 0.00 41.01 3.51
3784 9971 4.939052 AAGTGATACTACTTCCCATCCG 57.061 45.455 0.00 0.00 36.16 4.18
3785 9972 3.912248 AGTGATACTACTTCCCATCCGT 58.088 45.455 0.00 0.00 0.00 4.69
3786 9973 5.057843 AGTGATACTACTTCCCATCCGTA 57.942 43.478 0.00 0.00 0.00 4.02
3787 9974 5.452255 AGTGATACTACTTCCCATCCGTAA 58.548 41.667 0.00 0.00 0.00 3.18
3788 9975 6.075984 AGTGATACTACTTCCCATCCGTAAT 58.924 40.000 0.00 0.00 0.00 1.89
3789 9976 7.236529 AGTGATACTACTTCCCATCCGTAATA 58.763 38.462 0.00 0.00 0.00 0.98
3790 9977 7.727186 AGTGATACTACTTCCCATCCGTAATAA 59.273 37.037 0.00 0.00 0.00 1.40
3791 9978 8.362639 GTGATACTACTTCCCATCCGTAATAAA 58.637 37.037 0.00 0.00 0.00 1.40
3792 9979 8.582437 TGATACTACTTCCCATCCGTAATAAAG 58.418 37.037 0.00 0.00 0.00 1.85
3793 9980 6.803366 ACTACTTCCCATCCGTAATAAAGT 57.197 37.500 0.00 0.00 0.00 2.66
3794 9981 6.579865 ACTACTTCCCATCCGTAATAAAGTG 58.420 40.000 0.00 0.00 0.00 3.16
3795 9982 5.687166 ACTTCCCATCCGTAATAAAGTGA 57.313 39.130 0.00 0.00 0.00 3.41
3796 9983 5.425630 ACTTCCCATCCGTAATAAAGTGAC 58.574 41.667 0.00 0.00 0.00 3.67
3797 9984 4.049546 TCCCATCCGTAATAAAGTGACG 57.950 45.455 0.00 0.00 36.36 4.35
3798 9985 2.542595 CCCATCCGTAATAAAGTGACGC 59.457 50.000 0.00 0.00 35.28 5.19
3799 9986 2.217847 CCATCCGTAATAAAGTGACGCG 59.782 50.000 3.53 3.53 35.28 6.01
3800 9987 1.912001 TCCGTAATAAAGTGACGCGG 58.088 50.000 12.47 0.00 39.13 6.46
3801 9988 1.202114 TCCGTAATAAAGTGACGCGGT 59.798 47.619 12.47 0.00 38.89 5.68
3802 9989 1.994779 CCGTAATAAAGTGACGCGGTT 59.005 47.619 12.47 0.00 35.28 4.44
3803 9990 2.412770 CCGTAATAAAGTGACGCGGTTT 59.587 45.455 12.47 7.14 35.28 3.27
3804 9991 3.120580 CCGTAATAAAGTGACGCGGTTTT 60.121 43.478 12.47 7.79 35.28 2.43
3805 9992 3.836348 CGTAATAAAGTGACGCGGTTTTG 59.164 43.478 12.47 0.00 0.00 2.44
3806 9993 4.376210 CGTAATAAAGTGACGCGGTTTTGA 60.376 41.667 12.47 0.00 0.00 2.69
3807 9994 4.555348 AATAAAGTGACGCGGTTTTGAA 57.445 36.364 12.47 0.00 0.00 2.69
3808 9995 2.182904 AAAGTGACGCGGTTTTGAAC 57.817 45.000 12.47 0.00 0.00 3.18
3809 9996 1.375551 AAGTGACGCGGTTTTGAACT 58.624 45.000 12.47 0.00 0.00 3.01
3810 9997 2.228138 AGTGACGCGGTTTTGAACTA 57.772 45.000 12.47 0.00 0.00 2.24
3811 9998 2.553086 AGTGACGCGGTTTTGAACTAA 58.447 42.857 12.47 0.00 0.00 2.24
3812 9999 2.286025 AGTGACGCGGTTTTGAACTAAC 59.714 45.455 12.47 0.00 0.00 2.34
3813 10000 1.598601 TGACGCGGTTTTGAACTAACC 59.401 47.619 12.47 0.00 41.31 2.85
3814 10001 1.869132 GACGCGGTTTTGAACTAACCT 59.131 47.619 12.47 0.00 42.31 3.50
3815 10002 1.869132 ACGCGGTTTTGAACTAACCTC 59.131 47.619 12.47 0.00 42.31 3.85
3816 10003 1.868498 CGCGGTTTTGAACTAACCTCA 59.132 47.619 0.00 0.00 42.31 3.86
3817 10004 2.096417 CGCGGTTTTGAACTAACCTCAG 60.096 50.000 0.00 0.00 42.31 3.35
3818 10005 2.876550 GCGGTTTTGAACTAACCTCAGT 59.123 45.455 0.00 0.00 42.31 3.41
3819 10006 3.314357 GCGGTTTTGAACTAACCTCAGTT 59.686 43.478 0.00 0.00 42.31 3.16
3841 10028 8.687824 AGTTCAAAACTGTGACACTTATTTTG 57.312 30.769 22.79 22.79 41.01 2.44
3842 10029 7.759433 AGTTCAAAACTGTGACACTTATTTTGG 59.241 33.333 25.38 15.70 41.01 3.28
3843 10030 7.397892 TCAAAACTGTGACACTTATTTTGGA 57.602 32.000 25.38 16.87 37.53 3.53
3844 10031 8.006298 TCAAAACTGTGACACTTATTTTGGAT 57.994 30.769 25.38 5.14 37.53 3.41
3845 10032 8.134895 TCAAAACTGTGACACTTATTTTGGATC 58.865 33.333 25.38 0.00 37.53 3.36
3846 10033 5.862924 ACTGTGACACTTATTTTGGATCG 57.137 39.130 7.20 0.00 0.00 3.69
3847 10034 4.695455 ACTGTGACACTTATTTTGGATCGG 59.305 41.667 7.20 0.00 0.00 4.18
3848 10035 4.900684 TGTGACACTTATTTTGGATCGGA 58.099 39.130 7.20 0.00 0.00 4.55
3849 10036 4.935205 TGTGACACTTATTTTGGATCGGAG 59.065 41.667 7.20 0.00 0.00 4.63
3850 10037 4.332819 GTGACACTTATTTTGGATCGGAGG 59.667 45.833 0.00 0.00 0.00 4.30
3851 10038 3.877508 GACACTTATTTTGGATCGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
3852 10039 3.521937 ACACTTATTTTGGATCGGAGGGA 59.478 43.478 0.00 0.00 0.00 4.20
3853 10040 4.130118 CACTTATTTTGGATCGGAGGGAG 58.870 47.826 0.00 0.00 0.00 4.30
3854 10041 3.780850 ACTTATTTTGGATCGGAGGGAGT 59.219 43.478 0.00 0.00 0.00 3.85
3855 10042 4.966805 ACTTATTTTGGATCGGAGGGAGTA 59.033 41.667 0.00 0.00 0.00 2.59
3856 10043 5.070580 ACTTATTTTGGATCGGAGGGAGTAG 59.929 44.000 0.00 0.00 0.00 2.57
3857 10044 1.789523 TTTGGATCGGAGGGAGTAGG 58.210 55.000 0.00 0.00 0.00 3.18
3858 10045 0.635009 TTGGATCGGAGGGAGTAGGT 59.365 55.000 0.00 0.00 0.00 3.08
3859 10046 0.635009 TGGATCGGAGGGAGTAGGTT 59.365 55.000 0.00 0.00 0.00 3.50
3866 10053 4.617593 TCGGAGGGAGTAGGTTATTTTCT 58.382 43.478 0.00 0.00 0.00 2.52
3897 10084 5.373981 ACTAGTCTACTGTGTAAGTGTGC 57.626 43.478 0.00 0.00 40.26 4.57
3929 10120 2.473530 TGCTTGCTTGTTTCAGAACG 57.526 45.000 0.00 0.00 38.65 3.95
4012 10203 2.258013 TTTCGCTGTTGAAGGCCCG 61.258 57.895 0.00 0.00 0.00 6.13
4061 10252 7.391148 TTCATAAAGATTGAAGGTACAAGCC 57.609 36.000 0.00 0.00 36.94 4.35
4066 10257 6.478512 AAGATTGAAGGTACAAGCCAAAAA 57.521 33.333 0.00 0.00 36.94 1.94
4108 10299 6.951062 TCAATCATGAACTGTGGTGTAAAA 57.049 33.333 0.00 0.00 30.99 1.52
4245 10436 5.888724 ACTCTCTCGATCAACAAATCCTCTA 59.111 40.000 0.00 0.00 0.00 2.43
4339 10530 1.720852 GGCGTTGCTTTGCATGTTAAG 59.279 47.619 0.00 0.00 38.76 1.85
4404 10595 4.722194 ACGTGTGAATTGTGATTATGCAC 58.278 39.130 0.00 0.00 39.22 4.57
4436 10627 9.030301 TCTGTATACGTGTGAATTGTGATATTG 57.970 33.333 0.00 0.00 0.00 1.90
4498 10689 6.972901 TGTGTGATCTGAGAATAATGTCGTAC 59.027 38.462 0.00 0.00 0.00 3.67
4656 12425 2.131854 TCAGGAACCCAAGTTTCTCCA 58.868 47.619 0.00 0.00 40.05 3.86
4745 12514 6.206395 TGATAGTGTAAAATTGCCCATGTG 57.794 37.500 0.00 0.00 0.00 3.21
4748 12517 4.085733 AGTGTAAAATTGCCCATGTGCTA 58.914 39.130 0.86 0.00 0.00 3.49
4778 12547 6.583562 AGAACAGACTTGCTTAGTGTTTACT 58.416 36.000 0.00 0.00 37.17 2.24
4791 12560 2.037251 GTGTTTACTCAGGTCCAGCAGA 59.963 50.000 0.00 0.00 0.00 4.26
4919 13993 0.168788 CACACGTCCCATGCATGAAC 59.831 55.000 28.31 21.90 0.00 3.18
4921 13995 1.003839 ACGTCCCATGCATGAACGT 60.004 52.632 34.66 34.66 0.00 3.99
4951 14028 6.200114 AGCTACCAATTCCTACCAACTACTA 58.800 40.000 0.00 0.00 0.00 1.82
4952 14029 6.844917 AGCTACCAATTCCTACCAACTACTAT 59.155 38.462 0.00 0.00 0.00 2.12
4953 14030 8.008922 AGCTACCAATTCCTACCAACTACTATA 58.991 37.037 0.00 0.00 0.00 1.31
4954 14031 8.305317 GCTACCAATTCCTACCAACTACTATAG 58.695 40.741 0.00 0.00 0.00 1.31
4955 14032 9.364653 CTACCAATTCCTACCAACTACTATAGT 57.635 37.037 10.87 10.87 41.73 2.12
5045 14122 2.426887 CCGTTGGTTACCGGTGGT 59.573 61.111 19.93 0.00 39.38 4.16
5048 14125 0.947180 CGTTGGTTACCGGTGGTCAG 60.947 60.000 19.93 0.00 37.09 3.51
5131 14208 0.852777 CACTGTGTCCGTGTTCTTCG 59.147 55.000 0.00 0.00 0.00 3.79
5136 14213 1.662446 GTCCGTGTTCTTCGGCGAA 60.662 57.895 22.33 22.33 46.49 4.70
5158 14235 4.162690 ATCTCCTCGTTGGGCGGC 62.163 66.667 0.00 0.00 41.72 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.107897 TTGTGTCGGCACTCTGTTGT 60.108 50.000 22.43 0.00 45.44 3.32
29 30 4.202070 TGTTGCATTCATCATCGCATCATT 60.202 37.500 0.00 0.00 33.71 2.57
34 35 3.244156 GTTTGTTGCATTCATCATCGCA 58.756 40.909 0.00 0.00 0.00 5.10
63 64 2.095213 TGTTTTCATGATAGCCGCGTTC 59.905 45.455 4.92 0.00 0.00 3.95
77 78 3.703556 TCCAGTTGCCTTTCATGTTTTCA 59.296 39.130 0.00 0.00 0.00 2.69
83 84 0.169672 CGCTCCAGTTGCCTTTCATG 59.830 55.000 0.00 0.00 0.00 3.07
86 87 0.884704 TGACGCTCCAGTTGCCTTTC 60.885 55.000 0.00 0.00 0.00 2.62
105 106 4.459685 ACATAGCTGTAACAACTCGAGACT 59.540 41.667 21.68 2.24 32.49 3.24
112 113 5.867716 CCGTAAAGACATAGCTGTAACAACT 59.132 40.000 0.00 0.00 35.14 3.16
113 114 5.063060 CCCGTAAAGACATAGCTGTAACAAC 59.937 44.000 0.00 0.00 35.14 3.32
121 122 2.167900 GGTGACCCGTAAAGACATAGCT 59.832 50.000 0.00 0.00 0.00 3.32
138 139 4.571919 CCTCAATAAAGGTACAACGGTGA 58.428 43.478 7.88 0.00 0.00 4.02
168 169 3.370840 TCAATGCCCTTATGCTGACTT 57.629 42.857 0.00 0.00 0.00 3.01
186 187 8.720562 CATAGTTGCATCAATAACGGAATATCA 58.279 33.333 0.00 0.00 32.24 2.15
225 226 3.010027 TCCATCTGCACAATGACCCTTTA 59.990 43.478 6.00 0.00 0.00 1.85
227 228 1.355381 TCCATCTGCACAATGACCCTT 59.645 47.619 6.00 0.00 0.00 3.95
228 229 0.994247 TCCATCTGCACAATGACCCT 59.006 50.000 6.00 0.00 0.00 4.34
233 234 2.688446 AGAGCAATCCATCTGCACAATG 59.312 45.455 0.00 0.00 42.48 2.82
240 241 6.040278 TCAACTAGAGTAGAGCAATCCATCTG 59.960 42.308 0.00 0.00 0.00 2.90
303 304 9.399797 TCTGCTTGATTTTCTTATCATATGTGT 57.600 29.630 1.90 0.00 34.67 3.72
343 344 2.586425 CAAAGAAGCCTCAAACCCTGA 58.414 47.619 0.00 0.00 0.00 3.86
359 360 3.624326 TGCTTCACAACGAATCCAAAG 57.376 42.857 0.00 0.00 31.69 2.77
503 506 8.770438 ATTAAACTGACAAGCTTGTTCAAAAA 57.230 26.923 31.58 20.73 42.43 1.94
504 507 9.862371 TTATTAAACTGACAAGCTTGTTCAAAA 57.138 25.926 31.58 20.26 42.43 2.44
505 508 9.862371 TTTATTAAACTGACAAGCTTGTTCAAA 57.138 25.926 31.58 19.66 42.43 2.69
506 509 9.515020 CTTTATTAAACTGACAAGCTTGTTCAA 57.485 29.630 31.58 19.22 42.43 2.69
507 510 8.898761 TCTTTATTAAACTGACAAGCTTGTTCA 58.101 29.630 31.58 25.93 42.43 3.18
508 511 9.170584 GTCTTTATTAAACTGACAAGCTTGTTC 57.829 33.333 31.58 23.22 42.43 3.18
509 512 8.682710 TGTCTTTATTAAACTGACAAGCTTGTT 58.317 29.630 31.58 18.44 42.43 2.83
510 513 8.220755 TGTCTTTATTAAACTGACAAGCTTGT 57.779 30.769 31.57 31.57 45.65 3.16
511 514 8.958043 GTTGTCTTTATTAAACTGACAAGCTTG 58.042 33.333 24.84 24.84 44.70 4.01
527 530 9.476202 GCAGTTTTGATTTAAGGTTGTCTTTAT 57.524 29.630 0.00 0.00 36.93 1.40
552 555 7.340999 TCCCTCTTTACCTAAAATAAATGTGGC 59.659 37.037 0.00 0.00 0.00 5.01
553 556 8.817092 TCCCTCTTTACCTAAAATAAATGTGG 57.183 34.615 0.00 0.00 0.00 4.17
554 557 9.462606 ACTCCCTCTTTACCTAAAATAAATGTG 57.537 33.333 0.00 0.00 0.00 3.21
557 560 9.848710 GCTACTCCCTCTTTACCTAAAATAAAT 57.151 33.333 0.00 0.00 0.00 1.40
558 561 9.054580 AGCTACTCCCTCTTTACCTAAAATAAA 57.945 33.333 0.00 0.00 0.00 1.40
568 571 3.068448 GCTGGTAGCTACTCCCTCTTTAC 59.932 52.174 22.74 3.42 38.45 2.01
584 2085 3.578716 GCAGTATATCTTCTGGGCTGGTA 59.421 47.826 0.00 0.00 32.94 3.25
592 2093 4.122776 GTGTGGTGGCAGTATATCTTCTG 58.877 47.826 0.00 0.00 35.12 3.02
593 2094 3.134804 GGTGTGGTGGCAGTATATCTTCT 59.865 47.826 0.00 0.00 0.00 2.85
594 2095 3.467803 GGTGTGGTGGCAGTATATCTTC 58.532 50.000 0.00 0.00 0.00 2.87
595 2096 2.172717 GGGTGTGGTGGCAGTATATCTT 59.827 50.000 0.00 0.00 0.00 2.40
596 2097 1.768870 GGGTGTGGTGGCAGTATATCT 59.231 52.381 0.00 0.00 0.00 1.98
597 2098 1.488812 TGGGTGTGGTGGCAGTATATC 59.511 52.381 0.00 0.00 0.00 1.63
598 2099 1.590591 TGGGTGTGGTGGCAGTATAT 58.409 50.000 0.00 0.00 0.00 0.86
599 2100 1.363246 TTGGGTGTGGTGGCAGTATA 58.637 50.000 0.00 0.00 0.00 1.47
601 2102 0.466555 GTTTGGGTGTGGTGGCAGTA 60.467 55.000 0.00 0.00 0.00 2.74
621 2122 1.153524 TGGGCTGAATGGTGTTGCT 59.846 52.632 0.00 0.00 0.00 3.91
671 2172 4.991056 TGGACAACGAGAGAGAAAAATGAG 59.009 41.667 0.00 0.00 0.00 2.90
675 2176 4.099573 AGACTGGACAACGAGAGAGAAAAA 59.900 41.667 0.00 0.00 0.00 1.94
686 2187 0.793478 CGACGCTAGACTGGACAACG 60.793 60.000 0.00 0.00 0.00 4.10
997 2851 2.029666 GGTCTCGATCGCCATGGG 59.970 66.667 15.13 3.69 0.00 4.00
1168 3022 3.712881 GTGGAGCACGCGGTTGAC 61.713 66.667 12.47 0.00 0.00 3.18
1665 3552 3.737172 GCGACGGCCTTGTTGCAT 61.737 61.111 15.90 0.00 46.47 3.96
1745 3632 3.499918 AGTGACGAAGGAATTCAAAGCAG 59.500 43.478 7.93 0.00 0.00 4.24
1761 3695 5.164080 GCTTAGCTACAGTTTTACAGTGACG 60.164 44.000 0.00 0.00 0.00 4.35
1781 3732 6.155221 AGTTCATCACTCCATTCTAGTGCTTA 59.845 38.462 0.00 0.00 43.30 3.09
1789 3740 5.688814 TCATCAGTTCATCACTCCATTCT 57.311 39.130 0.00 0.00 30.92 2.40
1927 3880 0.250234 CCATGCTTCTCTTCCCGACA 59.750 55.000 0.00 0.00 0.00 4.35
2023 3976 9.292195 CAGGTTTACCTCAGGATAAAAAGTAAA 57.708 33.333 0.00 0.00 46.65 2.01
2041 4076 4.318831 CGAGTTTCAAGCACTCAGGTTTAC 60.319 45.833 2.50 0.00 40.78 2.01
2049 4084 0.859232 TTCGCGAGTTTCAAGCACTC 59.141 50.000 9.59 0.00 37.84 3.51
2061 4096 6.071463 GCAATACAAATAAGGTATTCGCGAG 58.929 40.000 9.59 0.00 38.91 5.03
2064 4099 6.067263 TGGCAATACAAATAAGGTATTCGC 57.933 37.500 0.00 0.00 38.91 4.70
2065 4100 9.180678 GAAATGGCAATACAAATAAGGTATTCG 57.819 33.333 0.00 0.00 38.91 3.34
2168 4215 6.127535 CCTCTTCACGGTAATAAGGTTACTGA 60.128 42.308 12.33 1.18 35.71 3.41
2221 4268 8.846211 CCAGAAAGAAGGTACAGAACAAATTAA 58.154 33.333 0.00 0.00 0.00 1.40
2228 4275 4.957296 TCACCAGAAAGAAGGTACAGAAC 58.043 43.478 0.00 0.00 36.07 3.01
2695 4748 2.851263 AGTCGGACAACCTTGCATAA 57.149 45.000 11.27 0.00 0.00 1.90
2784 4853 8.457261 AGAGAAATTCTGTATTCATCAAACTGC 58.543 33.333 0.00 0.00 33.93 4.40
3071 5275 3.795688 ACACACCTTGATGGATCAGTT 57.204 42.857 0.00 0.00 38.19 3.16
3113 9193 5.139727 TGATGAGGATGAAACTTTTGTGGT 58.860 37.500 0.00 0.00 0.00 4.16
3175 9255 3.454447 TGATTCAGTACCCATGGTGGTAG 59.546 47.826 11.73 0.00 41.47 3.18
3514 9701 7.603024 ACATAAACACAAGGTAAAGTAGAGCTC 59.397 37.037 5.27 5.27 0.00 4.09
3521 9708 7.875327 AGAACACATAAACACAAGGTAAAGT 57.125 32.000 0.00 0.00 0.00 2.66
3524 9711 7.971168 CACAAAGAACACATAAACACAAGGTAA 59.029 33.333 0.00 0.00 0.00 2.85
3531 9718 7.199766 TGGAATCACAAAGAACACATAAACAC 58.800 34.615 0.00 0.00 0.00 3.32
3622 9809 3.419943 TCATTAACCAAGTGCTGCATCA 58.580 40.909 5.27 0.00 0.00 3.07
3718 9905 5.613358 AGAAAAAGGAATGCTTGTAGACG 57.387 39.130 0.00 0.00 0.00 4.18
3720 9907 7.448469 AGCTTAAGAAAAAGGAATGCTTGTAGA 59.552 33.333 6.67 0.00 0.00 2.59
3732 9919 3.365364 CGCAGTCCAGCTTAAGAAAAAGG 60.365 47.826 6.67 0.00 0.00 3.11
3737 9924 1.014044 CGCGCAGTCCAGCTTAAGAA 61.014 55.000 8.75 0.00 0.00 2.52
3739 9926 3.084579 CGCGCAGTCCAGCTTAAG 58.915 61.111 8.75 0.00 0.00 1.85
3754 9941 6.310711 GGGAAGTAGTATCACTTAATATGCGC 59.689 42.308 0.00 0.00 38.86 6.09
3765 9952 5.779529 TTACGGATGGGAAGTAGTATCAC 57.220 43.478 0.00 0.00 0.00 3.06
3771 9958 6.700520 GTCACTTTATTACGGATGGGAAGTAG 59.299 42.308 0.00 0.00 0.00 2.57
3773 9960 5.425630 GTCACTTTATTACGGATGGGAAGT 58.574 41.667 0.00 0.00 0.00 3.01
3774 9961 4.506654 CGTCACTTTATTACGGATGGGAAG 59.493 45.833 0.00 0.00 33.13 3.46
3775 9962 4.435425 CGTCACTTTATTACGGATGGGAA 58.565 43.478 0.00 0.00 33.13 3.97
3776 9963 3.738899 GCGTCACTTTATTACGGATGGGA 60.739 47.826 0.00 0.00 37.12 4.37
3777 9964 2.542595 GCGTCACTTTATTACGGATGGG 59.457 50.000 0.00 0.00 37.12 4.00
3778 9965 2.217847 CGCGTCACTTTATTACGGATGG 59.782 50.000 0.00 0.00 37.12 3.51
3779 9966 2.217847 CCGCGTCACTTTATTACGGATG 59.782 50.000 4.92 0.00 41.61 3.51
3780 9967 2.159198 ACCGCGTCACTTTATTACGGAT 60.159 45.455 4.92 0.00 41.61 4.18
3781 9968 1.202114 ACCGCGTCACTTTATTACGGA 59.798 47.619 4.92 0.00 41.61 4.69
3782 9969 1.632422 ACCGCGTCACTTTATTACGG 58.368 50.000 4.92 0.00 44.49 4.02
3783 9970 3.710437 AAACCGCGTCACTTTATTACG 57.290 42.857 4.92 0.00 39.55 3.18
3784 9971 5.021120 TCAAAACCGCGTCACTTTATTAC 57.979 39.130 4.92 0.00 0.00 1.89
3785 9972 5.236911 AGTTCAAAACCGCGTCACTTTATTA 59.763 36.000 4.92 0.00 0.00 0.98
3786 9973 4.035909 AGTTCAAAACCGCGTCACTTTATT 59.964 37.500 4.92 0.00 0.00 1.40
3787 9974 3.562557 AGTTCAAAACCGCGTCACTTTAT 59.437 39.130 4.92 0.00 0.00 1.40
3788 9975 2.937799 AGTTCAAAACCGCGTCACTTTA 59.062 40.909 4.92 0.00 0.00 1.85
3789 9976 1.741145 AGTTCAAAACCGCGTCACTTT 59.259 42.857 4.92 0.00 0.00 2.66
3790 9977 1.375551 AGTTCAAAACCGCGTCACTT 58.624 45.000 4.92 0.00 0.00 3.16
3791 9978 2.228138 TAGTTCAAAACCGCGTCACT 57.772 45.000 4.92 0.00 0.00 3.41
3792 9979 2.600556 GGTTAGTTCAAAACCGCGTCAC 60.601 50.000 4.92 0.00 37.26 3.67
3793 9980 1.598601 GGTTAGTTCAAAACCGCGTCA 59.401 47.619 4.92 0.00 37.26 4.35
3794 9981 2.305252 GGTTAGTTCAAAACCGCGTC 57.695 50.000 4.92 0.00 37.26 5.19
3816 10003 7.759433 CCAAAATAAGTGTCACAGTTTTGAACT 59.241 33.333 25.69 0.00 44.06 3.01
3817 10004 7.757624 TCCAAAATAAGTGTCACAGTTTTGAAC 59.242 33.333 25.69 0.00 38.26 3.18
3818 10005 7.831753 TCCAAAATAAGTGTCACAGTTTTGAA 58.168 30.769 25.69 14.08 38.26 2.69
3819 10006 7.397892 TCCAAAATAAGTGTCACAGTTTTGA 57.602 32.000 25.69 16.39 38.26 2.69
3820 10007 7.113404 CGATCCAAAATAAGTGTCACAGTTTTG 59.887 37.037 21.35 21.35 36.70 2.44
3821 10008 7.138736 CGATCCAAAATAAGTGTCACAGTTTT 58.861 34.615 2.42 6.48 0.00 2.43
3822 10009 6.293955 CCGATCCAAAATAAGTGTCACAGTTT 60.294 38.462 2.42 0.50 0.00 2.66
3823 10010 5.181245 CCGATCCAAAATAAGTGTCACAGTT 59.819 40.000 5.62 2.74 0.00 3.16
3824 10011 4.695455 CCGATCCAAAATAAGTGTCACAGT 59.305 41.667 5.62 0.00 0.00 3.55
3825 10012 4.935205 TCCGATCCAAAATAAGTGTCACAG 59.065 41.667 5.62 0.00 0.00 3.66
3826 10013 4.900684 TCCGATCCAAAATAAGTGTCACA 58.099 39.130 5.62 0.00 0.00 3.58
3827 10014 4.332819 CCTCCGATCCAAAATAAGTGTCAC 59.667 45.833 0.00 0.00 0.00 3.67
3828 10015 4.513442 CCTCCGATCCAAAATAAGTGTCA 58.487 43.478 0.00 0.00 0.00 3.58
3829 10016 3.877508 CCCTCCGATCCAAAATAAGTGTC 59.122 47.826 0.00 0.00 0.00 3.67
3830 10017 3.521937 TCCCTCCGATCCAAAATAAGTGT 59.478 43.478 0.00 0.00 0.00 3.55
3831 10018 4.130118 CTCCCTCCGATCCAAAATAAGTG 58.870 47.826 0.00 0.00 0.00 3.16
3832 10019 3.780850 ACTCCCTCCGATCCAAAATAAGT 59.219 43.478 0.00 0.00 0.00 2.24
3833 10020 4.423625 ACTCCCTCCGATCCAAAATAAG 57.576 45.455 0.00 0.00 0.00 1.73
3834 10021 4.347000 CCTACTCCCTCCGATCCAAAATAA 59.653 45.833 0.00 0.00 0.00 1.40
3835 10022 3.901844 CCTACTCCCTCCGATCCAAAATA 59.098 47.826 0.00 0.00 0.00 1.40
3836 10023 2.706190 CCTACTCCCTCCGATCCAAAAT 59.294 50.000 0.00 0.00 0.00 1.82
3837 10024 2.116238 CCTACTCCCTCCGATCCAAAA 58.884 52.381 0.00 0.00 0.00 2.44
3838 10025 1.007963 ACCTACTCCCTCCGATCCAAA 59.992 52.381 0.00 0.00 0.00 3.28
3839 10026 0.635009 ACCTACTCCCTCCGATCCAA 59.365 55.000 0.00 0.00 0.00 3.53
3840 10027 0.635009 AACCTACTCCCTCCGATCCA 59.365 55.000 0.00 0.00 0.00 3.41
3841 10028 2.671896 TAACCTACTCCCTCCGATCC 57.328 55.000 0.00 0.00 0.00 3.36
3842 10029 5.304871 AGAAAATAACCTACTCCCTCCGATC 59.695 44.000 0.00 0.00 0.00 3.69
3843 10030 5.217400 AGAAAATAACCTACTCCCTCCGAT 58.783 41.667 0.00 0.00 0.00 4.18
3844 10031 4.617593 AGAAAATAACCTACTCCCTCCGA 58.382 43.478 0.00 0.00 0.00 4.55
3845 10032 6.667558 ATAGAAAATAACCTACTCCCTCCG 57.332 41.667 0.00 0.00 0.00 4.63
3846 10033 8.272889 ACAAATAGAAAATAACCTACTCCCTCC 58.727 37.037 0.00 0.00 0.00 4.30
3847 10034 9.110502 CACAAATAGAAAATAACCTACTCCCTC 57.889 37.037 0.00 0.00 0.00 4.30
3848 10035 8.832735 TCACAAATAGAAAATAACCTACTCCCT 58.167 33.333 0.00 0.00 0.00 4.20
3849 10036 9.457436 TTCACAAATAGAAAATAACCTACTCCC 57.543 33.333 0.00 0.00 0.00 4.30
3879 10066 1.719780 GCGCACACTTACACAGTAGAC 59.280 52.381 0.30 0.00 32.76 2.59
3891 10078 6.402550 GCAAGCAATATATATTAGCGCACACT 60.403 38.462 11.47 0.00 0.00 3.55
3897 10084 8.955061 AAACAAGCAAGCAATATATATTAGCG 57.045 30.769 7.65 0.00 0.00 4.26
3929 10120 5.947443 AGATTTGTATTCTTTGCACTGCTC 58.053 37.500 1.98 0.00 0.00 4.26
4012 10203 1.076705 GATGGCTTCCCCTTGGTCC 60.077 63.158 0.00 0.00 0.00 4.46
4072 10263 7.751047 GTTCATGATTGATTGAATGAACCAG 57.249 36.000 13.74 0.00 46.83 4.00
4076 10267 7.039574 ACCACAGTTCATGATTGATTGAATGAA 60.040 33.333 13.04 0.00 36.85 2.57
4077 10268 6.434965 ACCACAGTTCATGATTGATTGAATGA 59.565 34.615 13.04 0.00 34.60 2.57
4078 10269 6.530181 CACCACAGTTCATGATTGATTGAATG 59.470 38.462 13.04 1.70 34.60 2.67
4079 10270 6.209986 ACACCACAGTTCATGATTGATTGAAT 59.790 34.615 13.04 0.00 34.60 2.57
4084 10275 7.523293 TTTTACACCACAGTTCATGATTGAT 57.477 32.000 13.04 0.00 0.00 2.57
4089 10280 6.061441 AGTCATTTTACACCACAGTTCATGA 58.939 36.000 0.00 0.00 0.00 3.07
4090 10281 6.317789 AGTCATTTTACACCACAGTTCATG 57.682 37.500 0.00 0.00 0.00 3.07
4091 10282 9.162764 GTATAGTCATTTTACACCACAGTTCAT 57.837 33.333 0.00 0.00 0.00 2.57
4245 10436 3.263503 TACAACACTCGCTCGCGCT 62.264 57.895 5.56 0.00 39.59 5.92
4404 10595 6.145534 ACAATTCACACGTATACAGAGTTGTG 59.854 38.462 16.95 13.78 37.63 3.33
4436 10627 7.820044 TGAAGTTGATTTTTGTACAAACCAC 57.180 32.000 20.43 13.87 0.00 4.16
4492 10683 8.552469 ACATTGTTAATATACAGTCGTACGAC 57.448 34.615 35.26 35.26 44.86 4.34
4498 10689 8.126700 GGGGAAAACATTGTTAATATACAGTCG 58.873 37.037 1.76 0.00 0.00 4.18
4623 12392 6.433847 TGGGTTCCTGATATTATCAACGAT 57.566 37.500 7.73 0.00 39.11 3.73
4624 12393 5.880164 TGGGTTCCTGATATTATCAACGA 57.120 39.130 7.73 3.99 39.11 3.85
4697 12466 6.744175 AGATGCTAATGAGATTCCTTCAGA 57.256 37.500 0.00 0.00 0.00 3.27
4745 12514 4.570930 AGCAAGTCTGTTCTAAACCTAGC 58.429 43.478 0.00 0.00 0.00 3.42
4748 12517 5.992217 CACTAAGCAAGTCTGTTCTAAACCT 59.008 40.000 0.00 0.00 35.76 3.50
4778 12547 1.112916 TGAACGTCTGCTGGACCTGA 61.113 55.000 1.91 0.00 41.64 3.86
4919 13993 4.667519 AGGAATTGGTAGCTTAGGTACG 57.332 45.455 14.29 0.00 37.39 3.67
4921 13995 5.531198 TGGTAGGAATTGGTAGCTTAGGTA 58.469 41.667 0.00 0.00 0.00 3.08
4956 14033 9.898152 TCCAAATTTTGTTGAATCCTTTTTAGT 57.102 25.926 8.26 0.00 0.00 2.24
5041 14118 2.358737 CCTCCGGCAACTGACCAC 60.359 66.667 0.00 0.00 0.00 4.16
5045 14122 1.191489 TCATCACCTCCGGCAACTGA 61.191 55.000 0.00 0.00 0.00 3.41
5048 14125 2.100631 CGTCATCACCTCCGGCAAC 61.101 63.158 0.00 0.00 0.00 4.17
5062 14139 2.358193 CTGGACACCGGACAACGTCA 62.358 60.000 9.46 0.00 42.24 4.35
5106 14183 2.842462 ACGGACACAGTGGCCTCA 60.842 61.111 23.90 0.00 45.79 3.86
5107 14184 2.357517 CACGGACACAGTGGCCTC 60.358 66.667 23.90 0.00 45.79 4.70
5108 14185 2.660258 GAACACGGACACAGTGGCCT 62.660 60.000 23.90 3.92 45.79 5.19
5131 14208 2.028337 GAGGAGATCGCCTTCGCC 59.972 66.667 19.87 2.71 38.73 5.54


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

AutoCloner maintained by Alex Coulton.