Multiple sequence alignment - TraesCS5D01G531400

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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 TraesCS5D01G531400 chr5D 100.000 4821 0 0 1 4821 546925649 546920829 0.000000e+00 8903.0
1 TraesCS5D01G531400 chr5D 83.654 312 36 10 1061 1366 469276176 469276478 3.670000e-71 279.0
2 TraesCS5D01G531400 chr4A 95.005 1842 75 10 2992 4821 621815284 621817120 0.000000e+00 2876.0
3 TraesCS5D01G531400 chr4A 89.228 1244 58 34 521 1740 621812602 621813793 0.000000e+00 1485.0
4 TraesCS5D01G531400 chr4A 77.208 351 37 24 2120 2451 621814188 621814514 1.070000e-36 165.0
5 TraesCS5D01G531400 chr5B 94.469 1808 66 20 3028 4821 690094673 690092886 0.000000e+00 2754.0
6 TraesCS5D01G531400 chr5B 92.078 1237 31 24 523 1725 690097660 690096457 0.000000e+00 1679.0
7 TraesCS5D01G531400 chr5B 83.454 689 105 7 3028 3710 576251838 576252523 2.450000e-177 632.0
8 TraesCS5D01G531400 chr5B 81.831 699 92 22 1039 1724 576249243 576249919 5.450000e-154 555.0
9 TraesCS5D01G531400 chr5B 81.768 362 49 7 160 521 689480383 689480039 2.200000e-73 287.0
10 TraesCS5D01G531400 chr5B 91.579 95 5 1 2701 2792 690095444 690095350 1.410000e-25 128.0
11 TraesCS5D01G531400 chr5B 83.333 138 14 5 1941 2075 592625855 592625724 8.480000e-23 119.0
12 TraesCS5D01G531400 chr1D 93.159 497 30 3 28 521 22783563 22784058 0.000000e+00 726.0
13 TraesCS5D01G531400 chr1D 92.829 502 35 1 20 521 22784485 22784985 0.000000e+00 726.0
14 TraesCS5D01G531400 chr1D 81.614 669 75 27 1432 2075 197245168 197244523 1.200000e-140 510.0
15 TraesCS5D01G531400 chr5A 83.791 765 99 18 3028 3778 589383384 589384137 0.000000e+00 702.0
16 TraesCS5D01G531400 chr5A 81.965 682 80 28 1061 1725 589379526 589380181 5.490000e-149 538.0
17 TraesCS5D01G531400 chr7B 87.476 519 65 0 3 521 117792298 117791780 2.480000e-167 599.0
18 TraesCS5D01G531400 chr7B 77.184 206 41 5 4529 4732 393317605 393317404 1.100000e-21 115.0
19 TraesCS5D01G531400 chr7B 85.366 82 12 0 1258 1339 7357969 7357888 8.600000e-13 86.1
20 TraesCS5D01G531400 chr2B 87.234 517 61 5 9 521 75687335 75687850 6.950000e-163 584.0
21 TraesCS5D01G531400 chr2B 88.136 59 5 2 1580 1637 143969454 143969511 8.660000e-08 69.4
22 TraesCS5D01G531400 chr2B 88.136 59 5 2 1580 1637 144035084 144035141 8.660000e-08 69.4
23 TraesCS5D01G531400 chr1A 86.782 522 60 8 3 521 94111167 94111682 1.510000e-159 573.0
24 TraesCS5D01G531400 chr4D 84.971 519 61 6 3 521 4821855 4822356 1.200000e-140 510.0
25 TraesCS5D01G531400 chr6B 84.975 406 38 14 1535 1934 149849896 149850284 1.630000e-104 390.0
26 TraesCS5D01G531400 chr6B 79.365 378 68 8 3 374 116112400 116112027 1.720000e-64 257.0
27 TraesCS5D01G531400 chr4B 84.906 371 42 6 154 523 80961082 80961439 3.550000e-96 363.0
28 TraesCS5D01G531400 chr4B 89.362 141 15 0 1425 1565 666858656 666858796 1.380000e-40 178.0
29 TraesCS5D01G531400 chr4B 86.897 145 19 0 1425 1569 238304592 238304448 3.860000e-36 163.0
30 TraesCS5D01G531400 chr3B 84.946 372 41 4 152 522 50152733 50152376 3.550000e-96 363.0
31 TraesCS5D01G531400 chr6D 77.811 338 66 7 187 521 141537065 141537396 2.940000e-47 200.0
32 TraesCS5D01G531400 chr7D 88.966 145 16 0 1425 1569 74098330 74098474 3.830000e-41 180.0
33 TraesCS5D01G531400 chr7D 76.961 204 45 2 4529 4732 393578650 393578449 1.100000e-21 115.0
34 TraesCS5D01G531400 chr7D 84.810 79 11 1 1258 1336 65601036 65600959 1.440000e-10 78.7
35 TraesCS5D01G531400 chr3D 92.683 123 9 0 1425 1547 492051764 492051642 1.380000e-40 178.0
36 TraesCS5D01G531400 chr2D 88.276 145 17 0 1425 1569 67949682 67949538 1.780000e-39 174.0
37 TraesCS5D01G531400 chr2D 88.136 59 5 2 1580 1637 92832548 92832605 8.660000e-08 69.4
38 TraesCS5D01G531400 chrUn 87.342 79 9 1 1258 1336 84039963 84039886 6.650000e-14 89.8
39 TraesCS5D01G531400 chr7A 85.366 82 12 0 1255 1336 69974888 69974969 8.600000e-13 86.1
40 TraesCS5D01G531400 chr7A 86.076 79 10 1 1258 1336 69901609 69901686 3.090000e-12 84.2


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 TraesCS5D01G531400 chr5D 546920829 546925649 4820 True 8903.000000 8903 100.000000 1 4821 1 chr5D.!!$R1 4820
1 TraesCS5D01G531400 chr4A 621812602 621817120 4518 False 1508.666667 2876 87.147000 521 4821 3 chr4A.!!$F1 4300
2 TraesCS5D01G531400 chr5B 690092886 690097660 4774 True 1520.333333 2754 92.708667 523 4821 3 chr5B.!!$R3 4298
3 TraesCS5D01G531400 chr5B 576249243 576252523 3280 False 593.500000 632 82.642500 1039 3710 2 chr5B.!!$F1 2671
4 TraesCS5D01G531400 chr1D 22783563 22784985 1422 False 726.000000 726 92.994000 20 521 2 chr1D.!!$F1 501
5 TraesCS5D01G531400 chr1D 197244523 197245168 645 True 510.000000 510 81.614000 1432 2075 1 chr1D.!!$R1 643
6 TraesCS5D01G531400 chr5A 589379526 589384137 4611 False 620.000000 702 82.878000 1061 3778 2 chr5A.!!$F1 2717
7 TraesCS5D01G531400 chr7B 117791780 117792298 518 True 599.000000 599 87.476000 3 521 1 chr7B.!!$R2 518
8 TraesCS5D01G531400 chr2B 75687335 75687850 515 False 584.000000 584 87.234000 9 521 1 chr2B.!!$F1 512
9 TraesCS5D01G531400 chr1A 94111167 94111682 515 False 573.000000 573 86.782000 3 521 1 chr1A.!!$F1 518
10 TraesCS5D01G531400 chr4D 4821855 4822356 501 False 510.000000 510 84.971000 3 521 1 chr4D.!!$F1 518

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
670 1635 0.036875 TGAACCCACACACACACACA 59.963 50.0 0.0 0.0 0.0 3.72 F
2098 3420 0.179018 AACTCCAGACCACTTGCACC 60.179 55.0 0.0 0.0 0.0 5.01 F
2693 5109 0.037232 AGCTTCCAGTACAACGAGCC 60.037 55.0 0.0 0.0 0.0 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2134 3456 0.107643 TGCACCGATCTGTCAAACCA 59.892 50.000 0.0 0.0 0.00 3.67 R
3011 6998 0.039437 TTTCTCTCCGTCAGTCGCAC 60.039 55.000 0.0 0.0 38.35 5.34 R
3958 7977 1.005867 TCGTTGGCGGTGGTTAGAC 60.006 57.895 0.0 0.0 38.89 2.59 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
145 151 2.300437 ACTAAGTGAGCAAGAGGACCAC 59.700 50.000 0.00 0.00 0.00 4.16
174 180 2.899339 GAGCGGGCATGAGCTTCC 60.899 66.667 11.17 0.00 44.69 3.46
204 1137 6.298361 TGGCATATGTGAGTGTTATAGCAAT 58.702 36.000 4.29 0.00 0.00 3.56
222 1155 8.841444 ATAGCAATAATTTCACAGTTTTAGCG 57.159 30.769 0.00 0.00 0.00 4.26
244 1177 3.704061 GTGGAATAGGAGCTCTCAAGAGT 59.296 47.826 14.64 0.00 43.85 3.24
255 1188 3.443329 GCTCTCAAGAGTCTCAGATGACA 59.557 47.826 8.73 0.00 43.85 3.58
272 1205 2.158871 TGACAACCACTAACTGACACCC 60.159 50.000 0.00 0.00 0.00 4.61
375 1308 5.120830 GGCAATCTGACACGATATATGAACC 59.879 44.000 0.00 0.00 0.00 3.62
419 1352 9.345517 CATAATTAAATCACAAGTCAACACAGG 57.654 33.333 0.00 0.00 0.00 4.00
439 1372 8.264347 ACACAGGTAAAATCCAAAGAAAACAAT 58.736 29.630 0.00 0.00 0.00 2.71
491 1424 6.418946 AGAGTTAATCCCAGAATGAAGAACC 58.581 40.000 0.00 0.00 39.69 3.62
604 1557 2.159338 CGTGTGTGTATTACTACCGCCT 60.159 50.000 0.00 0.00 0.00 5.52
667 1632 1.014352 GACTGAACCCACACACACAC 58.986 55.000 0.00 0.00 0.00 3.82
668 1633 0.326595 ACTGAACCCACACACACACA 59.673 50.000 0.00 0.00 0.00 3.72
669 1634 0.732571 CTGAACCCACACACACACAC 59.267 55.000 0.00 0.00 0.00 3.82
670 1635 0.036875 TGAACCCACACACACACACA 59.963 50.000 0.00 0.00 0.00 3.72
688 1653 9.066892 ACACACACACTAATAATCTGTTTGATT 57.933 29.630 0.00 0.00 46.22 2.57
720 1689 0.681564 CTCCTACCTCAGACACGGCT 60.682 60.000 0.00 0.00 0.00 5.52
1237 2221 2.923035 CACTCCACCACCGGTCCT 60.923 66.667 2.59 0.00 31.02 3.85
1336 2320 1.134901 CCTCGTCGTCGACTTCCTG 59.865 63.158 22.18 7.29 41.35 3.86
1392 2376 2.907917 CTACCTCTCCCTCGCCGG 60.908 72.222 0.00 0.00 0.00 6.13
1516 2503 1.212751 CCTCAGCGTCGACATCACA 59.787 57.895 17.16 0.00 0.00 3.58
1615 2617 3.702048 GCGCTGTACTGGGTGGGA 61.702 66.667 16.36 0.00 0.00 4.37
1752 2763 7.773149 ACTAGTACCTCAATTAGTTAGCACAG 58.227 38.462 0.00 0.00 0.00 3.66
1753 2764 5.978814 AGTACCTCAATTAGTTAGCACAGG 58.021 41.667 0.00 0.00 0.00 4.00
1754 2765 3.610911 ACCTCAATTAGTTAGCACAGGC 58.389 45.455 0.00 0.00 41.61 4.85
1786 2797 7.121907 AGCTAGTGGTTACCAGTACTAACTAAC 59.878 40.741 14.42 2.23 38.30 2.34
1802 2813 8.723942 ACTAACTAACTTTCAGCCTGAATATG 57.276 34.615 8.18 4.72 36.11 1.78
1805 2816 8.723942 AACTAACTTTCAGCCTGAATATGTAG 57.276 34.615 8.18 9.89 36.11 2.74
1832 2843 2.283617 CGTGCTCTCATATGCTGTGTTC 59.716 50.000 0.00 0.00 0.00 3.18
1836 2847 3.372206 GCTCTCATATGCTGTGTTCGTTT 59.628 43.478 0.00 0.00 0.00 3.60
1877 2902 8.792831 CATTACTTCACAAATGCTTATCCATC 57.207 34.615 0.00 0.00 0.00 3.51
1888 2913 8.504815 CAAATGCTTATCCATCAATCTAGAGTG 58.495 37.037 13.98 13.98 0.00 3.51
1956 3109 2.251409 TGCTTGCCAGATCTCATAGC 57.749 50.000 0.00 0.41 0.00 2.97
2001 3267 7.817962 TGACTGTTATTTAGAACTAAGTGCTCC 59.182 37.037 0.00 0.00 0.00 4.70
2002 3268 7.676947 ACTGTTATTTAGAACTAAGTGCTCCA 58.323 34.615 0.00 0.00 0.00 3.86
2014 3280 3.268023 AGTGCTCCATAAGTAGTTGGC 57.732 47.619 0.00 0.00 32.80 4.52
2024 3290 6.093495 TCCATAAGTAGTTGGCGAAAATGAAG 59.907 38.462 0.00 0.00 32.80 3.02
2038 3304 6.684555 GCGAAAATGAAGATGCAGTTAGTTAG 59.315 38.462 0.00 0.00 0.00 2.34
2039 3305 6.684555 CGAAAATGAAGATGCAGTTAGTTAGC 59.315 38.462 0.00 0.00 0.00 3.09
2040 3306 7.452880 AAAATGAAGATGCAGTTAGTTAGCA 57.547 32.000 0.00 0.00 43.14 3.49
2041 3307 6.428385 AATGAAGATGCAGTTAGTTAGCAC 57.572 37.500 0.00 0.00 41.60 4.40
2078 3400 3.770263 CTCTCAGAGCTCAGAAGTCAG 57.230 52.381 17.77 1.09 0.00 3.51
2085 3407 2.560542 GAGCTCAGAAGTCAGAACTCCA 59.439 50.000 9.40 0.00 33.48 3.86
2086 3408 2.562298 AGCTCAGAAGTCAGAACTCCAG 59.438 50.000 0.00 0.00 33.48 3.86
2089 3411 2.894126 TCAGAAGTCAGAACTCCAGACC 59.106 50.000 0.00 0.00 33.48 3.85
2090 3412 2.630098 CAGAAGTCAGAACTCCAGACCA 59.370 50.000 0.00 0.00 33.48 4.02
2093 3415 2.683768 AGTCAGAACTCCAGACCACTT 58.316 47.619 0.00 0.00 32.82 3.16
2095 3417 1.070758 TCAGAACTCCAGACCACTTGC 59.929 52.381 0.00 0.00 0.00 4.01
2096 3418 1.131638 AGAACTCCAGACCACTTGCA 58.868 50.000 0.00 0.00 0.00 4.08
2097 3419 1.202698 AGAACTCCAGACCACTTGCAC 60.203 52.381 0.00 0.00 0.00 4.57
2098 3420 0.179018 AACTCCAGACCACTTGCACC 60.179 55.000 0.00 0.00 0.00 5.01
2100 3422 2.111043 CCAGACCACTTGCACCGT 59.889 61.111 0.00 0.00 0.00 4.83
2101 3423 1.961277 CCAGACCACTTGCACCGTC 60.961 63.158 0.00 0.00 0.00 4.79
2103 3425 0.532862 CAGACCACTTGCACCGTCTT 60.533 55.000 0.00 0.00 33.34 3.01
2104 3426 0.532862 AGACCACTTGCACCGTCTTG 60.533 55.000 0.00 0.00 31.58 3.02
2106 3428 1.095228 ACCACTTGCACCGTCTTGTG 61.095 55.000 0.00 0.00 39.29 3.33
2107 3429 0.813610 CCACTTGCACCGTCTTGTGA 60.814 55.000 0.00 0.00 38.55 3.58
2108 3430 1.229428 CACTTGCACCGTCTTGTGAT 58.771 50.000 0.00 0.00 38.55 3.06
2109 3431 1.069703 CACTTGCACCGTCTTGTGATG 60.070 52.381 0.00 0.00 38.55 3.07
2110 3432 1.229428 CTTGCACCGTCTTGTGATGT 58.771 50.000 0.00 0.00 38.55 3.06
2111 3433 0.943673 TTGCACCGTCTTGTGATGTG 59.056 50.000 0.00 0.00 38.55 3.21
2112 3434 0.179059 TGCACCGTCTTGTGATGTGT 60.179 50.000 0.00 0.00 38.55 3.72
2113 3435 0.512952 GCACCGTCTTGTGATGTGTC 59.487 55.000 0.00 0.00 38.55 3.67
2114 3436 1.148310 CACCGTCTTGTGATGTGTCC 58.852 55.000 0.00 0.00 38.55 4.02
2115 3437 1.048601 ACCGTCTTGTGATGTGTCCT 58.951 50.000 0.00 0.00 0.00 3.85
2116 3438 1.416401 ACCGTCTTGTGATGTGTCCTT 59.584 47.619 0.00 0.00 0.00 3.36
2118 3440 1.195448 CGTCTTGTGATGTGTCCTTGC 59.805 52.381 0.00 0.00 0.00 4.01
2119 3441 2.221169 GTCTTGTGATGTGTCCTTGCA 58.779 47.619 0.00 0.00 0.00 4.08
2120 3442 2.031682 GTCTTGTGATGTGTCCTTGCAC 60.032 50.000 0.00 0.00 39.65 4.57
2123 3445 1.948834 TGTGATGTGTCCTTGCACTTG 59.051 47.619 0.00 0.00 39.89 3.16
2125 3447 2.031682 GTGATGTGTCCTTGCACTTGTC 60.032 50.000 0.00 0.00 39.89 3.18
2126 3448 2.221169 GATGTGTCCTTGCACTTGTCA 58.779 47.619 0.00 0.00 39.89 3.58
2127 3449 1.667236 TGTGTCCTTGCACTTGTCAG 58.333 50.000 0.00 0.00 39.89 3.51
2128 3450 1.209261 TGTGTCCTTGCACTTGTCAGA 59.791 47.619 0.00 0.00 39.89 3.27
2131 3453 1.876156 GTCCTTGCACTTGTCAGAAGG 59.124 52.381 0.00 0.00 35.46 3.46
2132 3454 1.202806 TCCTTGCACTTGTCAGAAGGG 60.203 52.381 0.00 0.00 34.97 3.95
2134 3456 2.301346 CTTGCACTTGTCAGAAGGGTT 58.699 47.619 0.00 0.00 0.00 4.11
2135 3457 1.679139 TGCACTTGTCAGAAGGGTTG 58.321 50.000 0.00 0.00 0.00 3.77
2136 3458 0.954452 GCACTTGTCAGAAGGGTTGG 59.046 55.000 0.00 0.00 0.00 3.77
2147 3469 3.503748 CAGAAGGGTTGGTTTGACAGATC 59.496 47.826 0.00 0.00 0.00 2.75
2190 3517 8.343168 TGATTAAATTCGGTGTGGTTAATTCT 57.657 30.769 0.00 0.00 0.00 2.40
2200 3527 5.585047 GGTGTGGTTAATTCTTAGCTACTGG 59.415 44.000 0.00 0.00 30.99 4.00
2205 3536 3.567478 AATTCTTAGCTACTGGCCTGG 57.433 47.619 14.82 4.64 43.05 4.45
2223 3554 2.266055 CCTGACCTGGCCTCGAAC 59.734 66.667 3.32 0.00 0.00 3.95
2226 4217 2.154798 CTGACCTGGCCTCGAACGAA 62.155 60.000 3.32 0.00 0.00 3.85
2246 4237 7.179076 ACGAATGAGGGTACATTAGTTACTT 57.821 36.000 0.00 0.00 40.95 2.24
2247 4238 7.039882 ACGAATGAGGGTACATTAGTTACTTG 58.960 38.462 0.00 0.00 40.95 3.16
2249 4240 7.010183 CGAATGAGGGTACATTAGTTACTTGTG 59.990 40.741 0.42 0.00 40.03 3.33
2297 4306 5.122512 TGTAAGTAGTGAGTGAGCTGTTC 57.877 43.478 0.00 0.00 0.00 3.18
2313 4322 5.858381 AGCTGTTCTTCTTCATGAACACTA 58.142 37.500 3.38 0.00 44.89 2.74
2319 4328 5.935945 TCTTCTTCATGAACACTACCCAAA 58.064 37.500 3.38 0.00 0.00 3.28
2382 4392 0.245539 TGCCGACACTTACTACTGCC 59.754 55.000 0.00 0.00 0.00 4.85
2387 4397 1.201647 GACACTTACTACTGCCGCTCA 59.798 52.381 0.00 0.00 0.00 4.26
2388 4398 1.825474 ACACTTACTACTGCCGCTCAT 59.175 47.619 0.00 0.00 0.00 2.90
2404 4424 2.795470 GCTCATCGATCCCGTCTTAAAC 59.205 50.000 0.00 0.00 37.05 2.01
2408 4428 2.449464 TCGATCCCGTCTTAAACTCCA 58.551 47.619 0.00 0.00 37.05 3.86
2413 4433 4.903045 TCCCGTCTTAAACTCCATCTTT 57.097 40.909 0.00 0.00 0.00 2.52
2414 4434 5.237236 TCCCGTCTTAAACTCCATCTTTT 57.763 39.130 0.00 0.00 0.00 2.27
2415 4435 5.627135 TCCCGTCTTAAACTCCATCTTTTT 58.373 37.500 0.00 0.00 0.00 1.94
2434 4454 5.333566 TTTTACCTTTGTCCCTGGAGAAT 57.666 39.130 0.00 0.00 0.00 2.40
2453 4473 6.201806 GGAGAATACAATGCAACTAGCTAGTG 59.798 42.308 26.70 19.87 45.94 2.74
2460 4483 6.934645 ACAATGCAACTAGCTAGTGTTTCTAA 59.065 34.615 26.70 9.21 45.94 2.10
2461 4484 6.969828 ATGCAACTAGCTAGTGTTTCTAAC 57.030 37.500 26.70 10.54 45.94 2.34
2465 4488 6.128795 GCAACTAGCTAGTGTTTCTAACTGTG 60.129 42.308 26.70 16.42 41.15 3.66
2480 4503 2.024414 ACTGTGTCCCTTGCAAGAAAC 58.976 47.619 28.05 22.54 0.00 2.78
2481 4504 2.023673 CTGTGTCCCTTGCAAGAAACA 58.976 47.619 28.05 24.64 0.00 2.83
2486 4509 2.226674 GTCCCTTGCAAGAAACAGCTAC 59.773 50.000 28.05 9.31 0.00 3.58
2487 4510 2.106511 TCCCTTGCAAGAAACAGCTACT 59.893 45.455 28.05 0.00 0.00 2.57
2488 4511 2.227388 CCCTTGCAAGAAACAGCTACTG 59.773 50.000 28.05 6.02 37.52 2.74
2489 4512 2.351157 CCTTGCAAGAAACAGCTACTGC 60.351 50.000 28.05 0.00 34.37 4.40
2490 4513 1.965935 TGCAAGAAACAGCTACTGCA 58.034 45.000 0.00 0.00 42.74 4.41
2491 4514 2.507484 TGCAAGAAACAGCTACTGCAT 58.493 42.857 0.00 0.00 42.74 3.96
2512 4539 8.635765 TGCATAAAAGAAGAGTAAATTCCACT 57.364 30.769 0.00 0.00 0.00 4.00
2524 4551 1.560505 ATTCCACTGTGAATTGCCCC 58.439 50.000 9.86 0.00 30.88 5.80
2550 4594 5.880332 TGTGTTTCTTTCTACAGCTGAAGTT 59.120 36.000 23.35 0.00 0.00 2.66
2566 4610 3.569701 TGAAGTTCTGGTCTGAATTTGGC 59.430 43.478 4.17 0.00 0.00 4.52
2572 4616 2.486982 CTGGTCTGAATTTGGCTCAGTG 59.513 50.000 1.96 0.00 41.00 3.66
2578 4622 5.008613 GTCTGAATTTGGCTCAGTGTTGTTA 59.991 40.000 1.96 0.00 41.00 2.41
2586 4630 7.429636 TTGGCTCAGTGTTGTTAAGTTATAC 57.570 36.000 0.00 0.00 0.00 1.47
2590 4634 6.183360 GCTCAGTGTTGTTAAGTTATACGGTC 60.183 42.308 0.00 0.00 0.00 4.79
2591 4635 6.747125 TCAGTGTTGTTAAGTTATACGGTCA 58.253 36.000 0.00 0.00 0.00 4.02
2594 4638 6.643770 AGTGTTGTTAAGTTATACGGTCACTG 59.356 38.462 0.00 0.00 31.56 3.66
2600 5016 8.905850 TGTTAAGTTATACGGTCACTGATGATA 58.094 33.333 0.00 0.00 37.14 2.15
2601 5017 9.740239 GTTAAGTTATACGGTCACTGATGATAA 57.260 33.333 0.00 0.00 37.14 1.75
2604 5020 6.916387 AGTTATACGGTCACTGATGATAAACG 59.084 38.462 0.00 0.00 37.14 3.60
2607 5023 4.112634 ACGGTCACTGATGATAAACGATG 58.887 43.478 0.00 0.00 37.14 3.84
2612 5028 7.042725 CGGTCACTGATGATAAACGATGTTAAT 60.043 37.037 0.00 0.00 37.14 1.40
2614 5030 9.425893 GTCACTGATGATAAACGATGTTAATTG 57.574 33.333 0.00 0.00 37.14 2.32
2627 5043 5.457799 CGATGTTAATTGGAGTAGTGTACCG 59.542 44.000 0.00 0.00 0.00 4.02
2628 5044 5.726980 TGTTAATTGGAGTAGTGTACCGT 57.273 39.130 0.00 0.00 0.00 4.83
2634 5050 3.076621 TGGAGTAGTGTACCGTGTACTG 58.923 50.000 13.14 0.00 0.00 2.74
2635 5051 3.077359 GGAGTAGTGTACCGTGTACTGT 58.923 50.000 13.14 0.00 0.00 3.55
2641 5057 8.511604 AGTAGTGTACCGTGTACTGTATAATT 57.488 34.615 13.14 0.00 0.00 1.40
2642 5058 8.616076 AGTAGTGTACCGTGTACTGTATAATTC 58.384 37.037 13.14 0.00 0.00 2.17
2644 5060 8.059798 AGTGTACCGTGTACTGTATAATTCTT 57.940 34.615 13.14 0.00 0.00 2.52
2645 5061 7.972277 AGTGTACCGTGTACTGTATAATTCTTG 59.028 37.037 13.14 0.00 0.00 3.02
2646 5062 7.756722 GTGTACCGTGTACTGTATAATTCTTGT 59.243 37.037 13.14 0.00 0.00 3.16
2647 5063 7.970061 TGTACCGTGTACTGTATAATTCTTGTC 59.030 37.037 13.14 0.00 0.00 3.18
2650 5066 6.019801 CCGTGTACTGTATAATTCTTGTCTGC 60.020 42.308 0.00 0.00 0.00 4.26
2686 5102 1.003355 GCCTGCAGCTTCCAGTACA 60.003 57.895 8.66 0.00 38.99 2.90
2687 5103 0.606401 GCCTGCAGCTTCCAGTACAA 60.606 55.000 8.66 0.00 38.99 2.41
2693 5109 0.037232 AGCTTCCAGTACAACGAGCC 60.037 55.000 0.00 0.00 0.00 4.70
2694 5110 0.320421 GCTTCCAGTACAACGAGCCA 60.320 55.000 0.00 0.00 0.00 4.75
2695 5111 1.714794 CTTCCAGTACAACGAGCCAG 58.285 55.000 0.00 0.00 0.00 4.85
2696 5112 1.000955 CTTCCAGTACAACGAGCCAGT 59.999 52.381 0.00 0.00 0.00 4.00
2697 5113 0.317160 TCCAGTACAACGAGCCAGTG 59.683 55.000 0.00 0.00 0.00 3.66
2699 5115 1.004918 AGTACAACGAGCCAGTGCC 60.005 57.895 0.00 0.00 38.69 5.01
2703 5119 4.643387 AACGAGCCAGTGCCACCC 62.643 66.667 0.00 0.00 38.69 4.61
2740 5639 1.446907 CCATTCACTGCACTGTCTCC 58.553 55.000 0.00 0.00 0.00 3.71
2804 5706 4.383118 GCCTCAATTTCTGCTACCTACTCA 60.383 45.833 0.00 0.00 0.00 3.41
2808 5710 5.480422 TCAATTTCTGCTACCTACTCACTCA 59.520 40.000 0.00 0.00 0.00 3.41
2809 5711 6.014584 TCAATTTCTGCTACCTACTCACTCAA 60.015 38.462 0.00 0.00 0.00 3.02
2810 5712 5.801531 TTTCTGCTACCTACTCACTCAAA 57.198 39.130 0.00 0.00 0.00 2.69
2813 5715 5.265191 TCTGCTACCTACTCACTCAAATCT 58.735 41.667 0.00 0.00 0.00 2.40
2814 5716 6.424032 TCTGCTACCTACTCACTCAAATCTA 58.576 40.000 0.00 0.00 0.00 1.98
2816 5718 7.561722 TCTGCTACCTACTCACTCAAATCTAAT 59.438 37.037 0.00 0.00 0.00 1.73
2817 5719 8.079211 TGCTACCTACTCACTCAAATCTAATT 57.921 34.615 0.00 0.00 0.00 1.40
2832 5734 9.691362 TCAAATCTAATTAAAAACAAGCTGTCC 57.309 29.630 0.00 0.00 0.00 4.02
2833 5735 9.696917 CAAATCTAATTAAAAACAAGCTGTCCT 57.303 29.630 0.00 0.00 0.00 3.85
2836 5738 9.696917 ATCTAATTAAAAACAAGCTGTCCTTTG 57.303 29.630 0.00 0.00 0.00 2.77
2837 5739 8.691797 TCTAATTAAAAACAAGCTGTCCTTTGT 58.308 29.630 0.00 0.00 0.00 2.83
2839 5741 6.959671 TTAAAAACAAGCTGTCCTTTGTTG 57.040 33.333 0.16 0.00 30.54 3.33
2840 5742 4.799564 AAAACAAGCTGTCCTTTGTTGA 57.200 36.364 0.16 0.00 30.54 3.18
2842 5744 5.343307 AAACAAGCTGTCCTTTGTTGAAT 57.657 34.783 0.16 0.00 30.54 2.57
2844 5746 6.463995 AACAAGCTGTCCTTTGTTGAATAA 57.536 33.333 0.00 0.00 0.00 1.40
2845 5747 6.463995 ACAAGCTGTCCTTTGTTGAATAAA 57.536 33.333 0.00 0.00 0.00 1.40
2846 5748 6.507023 ACAAGCTGTCCTTTGTTGAATAAAG 58.493 36.000 7.35 7.35 35.45 1.85
2847 5749 6.321181 ACAAGCTGTCCTTTGTTGAATAAAGA 59.679 34.615 14.80 0.44 37.33 2.52
2848 5750 6.959639 AGCTGTCCTTTGTTGAATAAAGAA 57.040 33.333 14.80 0.00 37.33 2.52
2850 5752 7.203218 AGCTGTCCTTTGTTGAATAAAGAAAC 58.797 34.615 14.80 12.35 37.33 2.78
2851 5753 7.068716 AGCTGTCCTTTGTTGAATAAAGAAACT 59.931 33.333 14.80 3.67 37.33 2.66
2852 5754 7.168135 GCTGTCCTTTGTTGAATAAAGAAACTG 59.832 37.037 14.80 14.97 37.33 3.16
2855 5757 8.626526 GTCCTTTGTTGAATAAAGAAACTGGTA 58.373 33.333 14.80 0.00 37.33 3.25
2856 5758 9.191479 TCCTTTGTTGAATAAAGAAACTGGTAA 57.809 29.630 14.80 0.00 37.33 2.85
2867 5769 9.860898 ATAAAGAAACTGGTAAAGATTGATTGC 57.139 29.630 0.00 0.00 0.00 3.56
2869 5771 7.288810 AGAAACTGGTAAAGATTGATTGCAA 57.711 32.000 0.00 0.00 38.60 4.08
2875 6740 9.995003 ACTGGTAAAGATTGATTGCAAAATAAA 57.005 25.926 1.71 0.00 37.59 1.40
2877 6742 9.434420 TGGTAAAGATTGATTGCAAAATAAAGG 57.566 29.630 1.71 0.00 37.59 3.11
2882 6747 9.783081 AAGATTGATTGCAAAATAAAGGAAACT 57.217 25.926 1.71 0.00 39.30 2.66
2884 6749 7.727331 TTGATTGCAAAATAAAGGAAACTGG 57.273 32.000 1.71 0.00 42.68 4.00
2886 6751 6.705381 TGATTGCAAAATAAAGGAAACTGGTG 59.295 34.615 1.71 0.00 42.68 4.17
2919 6784 5.389642 CAATCATGCTGTTGATCATTTGC 57.610 39.130 0.00 1.73 35.29 3.68
2920 6785 5.109210 CAATCATGCTGTTGATCATTTGCT 58.891 37.500 0.00 0.00 35.29 3.91
2921 6786 4.365899 TCATGCTGTTGATCATTTGCTC 57.634 40.909 0.00 0.00 0.00 4.26
2922 6787 4.014406 TCATGCTGTTGATCATTTGCTCT 58.986 39.130 0.00 0.00 0.00 4.09
2923 6788 4.461431 TCATGCTGTTGATCATTTGCTCTT 59.539 37.500 0.00 0.00 0.00 2.85
2934 6799 4.014406 TCATTTGCTCTTCATGCAGTCAT 58.986 39.130 0.00 0.00 41.71 3.06
2987 6918 8.940768 TTTTTCCTTTCTGATCAAATTTTCGT 57.059 26.923 0.00 0.00 0.00 3.85
2989 6920 7.510549 TTCCTTTCTGATCAAATTTTCGTCT 57.489 32.000 0.00 0.00 0.00 4.18
2990 6921 7.133891 TCCTTTCTGATCAAATTTTCGTCTC 57.866 36.000 0.00 0.00 0.00 3.36
3011 6998 7.249147 GTCTCATCAATTTGGAGTGATTTCTG 58.751 38.462 0.00 0.00 38.44 3.02
3027 7014 1.154131 CTGTGCGACTGACGGAGAG 60.154 63.158 3.99 3.99 45.27 3.20
3271 7267 4.919987 GCCGACTACTACGCCGCC 62.920 72.222 0.00 0.00 0.00 6.13
3451 7447 2.261671 GACGGCGTCCACATGACT 59.738 61.111 28.72 0.00 42.13 3.41
3687 7701 6.090088 GTGTGATTTGTGAGACAGATGTAGTC 59.910 42.308 0.00 0.00 36.26 2.59
3688 7702 5.578727 GTGATTTGTGAGACAGATGTAGTCC 59.421 44.000 0.00 0.00 36.68 3.85
3755 7772 4.956085 AGTTTCAGGTTAAAATGGCCAAC 58.044 39.130 10.96 1.76 0.00 3.77
3759 7776 4.415596 TCAGGTTAAAATGGCCAACTCAT 58.584 39.130 10.96 0.00 0.00 2.90
3770 7787 4.272489 TGGCCAACTCATATTTCTTCCAG 58.728 43.478 0.61 0.00 0.00 3.86
3785 7802 2.671177 CCAGCAAGACAGAACGCCG 61.671 63.158 0.00 0.00 0.00 6.46
3799 7817 8.922676 AGACAGAACGCCGTAATAATAATAATG 58.077 33.333 0.00 0.00 0.00 1.90
3800 7818 8.025243 ACAGAACGCCGTAATAATAATAATGG 57.975 34.615 0.00 0.00 0.00 3.16
3934 7953 3.249080 TCGTTTTGAAATGAAGACCGACC 59.751 43.478 0.00 0.00 31.38 4.79
3970 7989 1.472188 ACTAGAGGTCTAACCACCGC 58.528 55.000 0.00 0.00 41.95 5.68
4036 8061 4.039973 AGGAACAGACTGTAACCGAATTCA 59.960 41.667 8.91 0.00 34.01 2.57
4115 8140 0.608640 GAGGCTCAGGACCGAGAAAA 59.391 55.000 10.25 0.00 34.79 2.29
4116 8141 1.208293 GAGGCTCAGGACCGAGAAAAT 59.792 52.381 10.25 0.73 34.79 1.82
4117 8142 1.630878 AGGCTCAGGACCGAGAAAATT 59.369 47.619 14.93 0.00 34.79 1.82
4118 8143 2.838202 AGGCTCAGGACCGAGAAAATTA 59.162 45.455 14.93 0.00 34.79 1.40
4119 8144 3.456277 AGGCTCAGGACCGAGAAAATTAT 59.544 43.478 14.93 0.00 34.79 1.28
4120 8145 3.561725 GGCTCAGGACCGAGAAAATTATG 59.438 47.826 14.93 0.00 34.79 1.90
4121 8146 4.442706 GCTCAGGACCGAGAAAATTATGA 58.557 43.478 14.93 0.00 34.79 2.15
4122 8147 4.271291 GCTCAGGACCGAGAAAATTATGAC 59.729 45.833 14.93 0.00 34.79 3.06
4181 8206 1.622607 ATCTCCCGTCGATTTGCCCA 61.623 55.000 0.00 0.00 0.00 5.36
4262 8288 4.884164 GGACCCCTACTGATTCAAGAAATG 59.116 45.833 0.00 0.00 0.00 2.32
4278 8304 8.032952 TCAAGAAATGCTTACATTAGACACAG 57.967 34.615 0.00 0.00 45.90 3.66
4285 8311 4.213270 GCTTACATTAGACACAGTTGCACA 59.787 41.667 0.00 0.00 0.00 4.57
4286 8312 5.615544 GCTTACATTAGACACAGTTGCACAG 60.616 44.000 0.00 0.00 0.00 3.66
4329 8355 9.435688 CAGAAAAAGAAAAGAAAAGAAAAGGGA 57.564 29.630 0.00 0.00 0.00 4.20
4342 8368 5.959618 AGAAAAGGGAAACATCTTTACCG 57.040 39.130 0.00 0.00 44.53 4.02
4431 8457 1.291184 TGGTTGCTCTTGATGACGCG 61.291 55.000 3.53 3.53 0.00 6.01
4446 8472 1.727723 CGCGATCTCTTCTAGGCGC 60.728 63.158 0.00 0.00 42.27 6.53
4533 8559 3.120796 ACACTCGGTGTACAGTCCA 57.879 52.632 7.76 0.00 45.56 4.02
4718 8744 5.426689 AACAATGATCTCTCAGCAACCTA 57.573 39.130 0.00 0.00 34.12 3.08
4719 8745 4.764172 ACAATGATCTCTCAGCAACCTAC 58.236 43.478 0.00 0.00 34.12 3.18
4742 8768 4.696479 AGTAGCATAAGCACCATTAGCT 57.304 40.909 0.00 0.00 45.97 3.32
4743 8769 5.808366 AGTAGCATAAGCACCATTAGCTA 57.192 39.130 0.00 0.00 42.53 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 151 2.818714 CCGCTCAGCTTGGCTCTG 60.819 66.667 0.00 0.00 36.40 3.35
174 180 1.674441 CACTCACATATGCCAGCCAAG 59.326 52.381 1.58 0.00 0.00 3.61
204 1137 6.621316 TTCCACGCTAAAACTGTGAAATTA 57.379 33.333 0.00 0.00 35.66 1.40
222 1155 3.704061 ACTCTTGAGAGCTCCTATTCCAC 59.296 47.826 10.93 0.00 45.79 4.02
244 1177 4.832823 TCAGTTAGTGGTTGTCATCTGAGA 59.167 41.667 0.00 0.00 0.00 3.27
255 1188 1.420138 CCTGGGTGTCAGTTAGTGGTT 59.580 52.381 0.00 0.00 41.83 3.67
272 1205 4.438200 GGTGTATTTACATGTTTCGGCCTG 60.438 45.833 2.30 0.00 38.63 4.85
384 1317 8.911662 ACTTGTGATTTAATTATGTTTTGACGC 58.088 29.630 0.00 0.00 0.00 5.19
482 1415 1.169661 TTTGCCACGCGGTTCTTCAT 61.170 50.000 12.47 0.00 33.28 2.57
583 1536 2.159338 AGGCGGTAGTAATACACACACG 60.159 50.000 2.37 0.00 0.00 4.49
586 1539 4.907879 ACTAGGCGGTAGTAATACACAC 57.092 45.455 2.37 0.00 40.47 3.82
604 1557 6.215841 TGGGATTTGTTAGGTGGTCATTACTA 59.784 38.462 0.00 0.00 0.00 1.82
667 1632 9.941664 GGATGAATCAAACAGATTATTAGTGTG 57.058 33.333 0.00 0.00 46.76 3.82
668 1633 9.685276 TGGATGAATCAAACAGATTATTAGTGT 57.315 29.630 0.00 0.00 46.76 3.55
669 1634 9.941664 GTGGATGAATCAAACAGATTATTAGTG 57.058 33.333 0.00 0.00 46.76 2.74
670 1635 9.685276 TGTGGATGAATCAAACAGATTATTAGT 57.315 29.630 0.00 0.00 46.76 2.24
688 1653 2.520120 AGGTAGGAGGAGATGTGGATGA 59.480 50.000 0.00 0.00 0.00 2.92
720 1689 3.295973 GTTAAGGGGCCAAGCATAATGA 58.704 45.455 4.39 0.00 0.00 2.57
1516 2503 1.153568 CGTCATGATGGACTGCGGT 60.154 57.895 7.06 0.00 35.63 5.68
1615 2617 3.449227 TCGTTGGCGCCGATCTCT 61.449 61.111 21.90 0.00 38.14 3.10
1754 2765 1.001974 TGGTAACCACTAGCTGTGCAG 59.998 52.381 0.00 0.00 44.92 4.41
1755 2766 1.001974 CTGGTAACCACTAGCTGTGCA 59.998 52.381 0.00 0.00 44.92 4.57
1756 2767 1.002087 ACTGGTAACCACTAGCTGTGC 59.998 52.381 0.00 0.00 44.92 4.57
1760 2771 5.578073 AGTTAGTACTGGTAACCACTAGCT 58.422 41.667 5.39 0.00 36.76 3.32
1761 2772 5.911378 AGTTAGTACTGGTAACCACTAGC 57.089 43.478 5.39 0.00 36.76 3.42
1762 2773 8.572855 AGTTAGTTAGTACTGGTAACCACTAG 57.427 38.462 5.39 0.00 39.10 2.57
1767 2778 7.330454 GCTGAAAGTTAGTTAGTACTGGTAACC 59.670 40.741 5.39 0.11 33.91 2.85
1773 2784 6.688578 TCAGGCTGAAAGTTAGTTAGTACTG 58.311 40.000 16.28 0.00 33.91 2.74
1775 2786 9.819267 ATATTCAGGCTGAAAGTTAGTTAGTAC 57.181 33.333 31.57 0.00 40.12 2.73
1786 2797 7.168302 CGACTAACTACATATTCAGGCTGAAAG 59.832 40.741 31.57 24.75 40.12 2.62
1802 2813 4.912766 GCATATGAGAGCACGACTAACTAC 59.087 45.833 6.97 0.00 0.00 2.73
1805 2816 3.733224 CAGCATATGAGAGCACGACTAAC 59.267 47.826 6.97 0.00 0.00 2.34
1832 2843 1.707632 CCAGAGAGTGAGAGCAAACG 58.292 55.000 0.00 0.00 0.00 3.60
1836 2847 1.273759 AATGCCAGAGAGTGAGAGCA 58.726 50.000 0.00 0.00 34.28 4.26
1888 2913 1.062047 CGACATGCATGCTCACTGC 59.938 57.895 26.53 6.51 43.25 4.40
1929 2958 0.110104 ATCTGGCAAGCATCCCTAGC 59.890 55.000 0.00 0.00 0.00 3.42
1956 3109 9.829507 AACAGTCATGAAATTAGGAGAATCTAG 57.170 33.333 0.00 0.00 33.73 2.43
2001 3267 7.072177 TCTTCATTTTCGCCAACTACTTATG 57.928 36.000 0.00 0.00 0.00 1.90
2002 3268 7.679638 GCATCTTCATTTTCGCCAACTACTTAT 60.680 37.037 0.00 0.00 0.00 1.73
2014 3280 6.684555 GCTAACTAACTGCATCTTCATTTTCG 59.315 38.462 0.00 0.00 0.00 3.46
2024 3290 4.268884 GTGCTAGTGCTAACTAACTGCATC 59.731 45.833 0.00 0.00 38.84 3.91
2076 3398 1.202687 TGCAAGTGGTCTGGAGTTCTG 60.203 52.381 0.00 0.00 0.00 3.02
2077 3399 1.131638 TGCAAGTGGTCTGGAGTTCT 58.868 50.000 0.00 0.00 0.00 3.01
2078 3400 1.230324 GTGCAAGTGGTCTGGAGTTC 58.770 55.000 0.00 0.00 0.00 3.01
2085 3407 0.532862 CAAGACGGTGCAAGTGGTCT 60.533 55.000 0.39 2.94 41.25 3.85
2086 3408 0.814010 ACAAGACGGTGCAAGTGGTC 60.814 55.000 0.39 0.64 0.00 4.02
2089 3411 1.069703 CATCACAAGACGGTGCAAGTG 60.070 52.381 0.39 0.00 38.66 3.16
2090 3412 1.229428 CATCACAAGACGGTGCAAGT 58.771 50.000 0.00 0.00 38.66 3.16
2093 3415 0.179059 ACACATCACAAGACGGTGCA 60.179 50.000 0.00 0.00 38.66 4.57
2095 3417 1.148310 GGACACATCACAAGACGGTG 58.852 55.000 0.00 0.00 40.16 4.94
2096 3418 1.048601 AGGACACATCACAAGACGGT 58.951 50.000 0.00 0.00 0.00 4.83
2097 3419 1.800586 CAAGGACACATCACAAGACGG 59.199 52.381 0.00 0.00 0.00 4.79
2098 3420 1.195448 GCAAGGACACATCACAAGACG 59.805 52.381 0.00 0.00 0.00 4.18
2100 3422 2.158769 AGTGCAAGGACACATCACAAGA 60.159 45.455 0.00 0.00 43.23 3.02
2101 3423 2.224606 AGTGCAAGGACACATCACAAG 58.775 47.619 0.00 0.00 43.23 3.16
2103 3425 1.948834 CAAGTGCAAGGACACATCACA 59.051 47.619 0.00 0.00 43.23 3.58
2104 3426 1.949525 ACAAGTGCAAGGACACATCAC 59.050 47.619 0.00 0.00 43.23 3.06
2106 3428 2.221169 TGACAAGTGCAAGGACACATC 58.779 47.619 0.00 0.00 43.23 3.06
2107 3429 2.158769 TCTGACAAGTGCAAGGACACAT 60.159 45.455 0.00 0.00 43.23 3.21
2108 3430 1.209261 TCTGACAAGTGCAAGGACACA 59.791 47.619 0.00 0.00 43.23 3.72
2109 3431 1.953559 TCTGACAAGTGCAAGGACAC 58.046 50.000 0.00 0.00 41.02 3.67
2110 3432 2.564771 CTTCTGACAAGTGCAAGGACA 58.435 47.619 0.00 0.00 0.00 4.02
2111 3433 1.876156 CCTTCTGACAAGTGCAAGGAC 59.124 52.381 0.00 0.00 36.48 3.85
2112 3434 1.202806 CCCTTCTGACAAGTGCAAGGA 60.203 52.381 0.00 0.00 36.48 3.36
2113 3435 1.242076 CCCTTCTGACAAGTGCAAGG 58.758 55.000 0.00 0.00 34.47 3.61
2114 3436 1.972872 ACCCTTCTGACAAGTGCAAG 58.027 50.000 0.00 0.00 0.00 4.01
2115 3437 2.023673 CAACCCTTCTGACAAGTGCAA 58.976 47.619 0.00 0.00 0.00 4.08
2116 3438 1.679139 CAACCCTTCTGACAAGTGCA 58.321 50.000 0.00 0.00 0.00 4.57
2118 3440 2.348411 ACCAACCCTTCTGACAAGTG 57.652 50.000 0.00 0.00 0.00 3.16
2119 3441 3.023832 CAAACCAACCCTTCTGACAAGT 58.976 45.455 0.00 0.00 0.00 3.16
2120 3442 3.066760 GTCAAACCAACCCTTCTGACAAG 59.933 47.826 0.00 0.00 34.64 3.16
2123 3445 2.618709 CTGTCAAACCAACCCTTCTGAC 59.381 50.000 0.00 0.00 34.99 3.51
2125 3447 2.930950 TCTGTCAAACCAACCCTTCTG 58.069 47.619 0.00 0.00 0.00 3.02
2126 3448 3.756117 GATCTGTCAAACCAACCCTTCT 58.244 45.455 0.00 0.00 0.00 2.85
2127 3449 2.484264 CGATCTGTCAAACCAACCCTTC 59.516 50.000 0.00 0.00 0.00 3.46
2128 3450 2.504367 CGATCTGTCAAACCAACCCTT 58.496 47.619 0.00 0.00 0.00 3.95
2131 3453 1.535462 CACCGATCTGTCAAACCAACC 59.465 52.381 0.00 0.00 0.00 3.77
2132 3454 1.069227 GCACCGATCTGTCAAACCAAC 60.069 52.381 0.00 0.00 0.00 3.77
2134 3456 0.107643 TGCACCGATCTGTCAAACCA 59.892 50.000 0.00 0.00 0.00 3.67
2135 3457 1.453155 ATGCACCGATCTGTCAAACC 58.547 50.000 0.00 0.00 0.00 3.27
2136 3458 3.559238 AAATGCACCGATCTGTCAAAC 57.441 42.857 0.00 0.00 0.00 2.93
2147 3469 8.958175 TTTAATCAAAGTAAGTAAATGCACCG 57.042 30.769 0.00 0.00 0.00 4.94
2210 3541 1.079127 CATTCGTTCGAGGCCAGGT 60.079 57.895 5.01 0.00 0.00 4.00
2211 3542 0.807667 CTCATTCGTTCGAGGCCAGG 60.808 60.000 5.01 0.00 0.00 4.45
2214 3545 1.521681 CCCTCATTCGTTCGAGGCC 60.522 63.158 0.00 0.00 46.37 5.19
2215 3546 0.458669 TACCCTCATTCGTTCGAGGC 59.541 55.000 10.15 0.00 46.37 4.70
2217 3548 2.933495 TGTACCCTCATTCGTTCGAG 57.067 50.000 0.00 0.00 0.00 4.04
2220 3551 7.263496 AGTAACTAATGTACCCTCATTCGTTC 58.737 38.462 10.80 5.85 40.36 3.95
2223 3554 7.010183 CACAAGTAACTAATGTACCCTCATTCG 59.990 40.741 0.00 0.00 38.68 3.34
2226 4217 6.214819 ACCACAAGTAACTAATGTACCCTCAT 59.785 38.462 0.00 0.00 0.00 2.90
2242 4233 5.367352 TGGAAAGGTAGAGAAACCACAAGTA 59.633 40.000 0.00 0.00 42.40 2.24
2243 4234 4.165372 TGGAAAGGTAGAGAAACCACAAGT 59.835 41.667 0.00 0.00 42.40 3.16
2244 4235 4.714632 TGGAAAGGTAGAGAAACCACAAG 58.285 43.478 0.00 0.00 42.40 3.16
2246 4237 4.651778 CATGGAAAGGTAGAGAAACCACA 58.348 43.478 0.00 0.00 42.40 4.17
2247 4238 3.440522 GCATGGAAAGGTAGAGAAACCAC 59.559 47.826 0.00 0.00 42.40 4.16
2249 4240 3.686016 TGCATGGAAAGGTAGAGAAACC 58.314 45.455 0.00 0.00 40.06 3.27
2276 4274 5.379732 AGAACAGCTCACTCACTACTTAC 57.620 43.478 0.00 0.00 0.00 2.34
2277 4275 5.770663 AGAAGAACAGCTCACTCACTACTTA 59.229 40.000 0.00 0.00 0.00 2.24
2281 4279 4.584743 TGAAGAAGAACAGCTCACTCACTA 59.415 41.667 0.00 0.00 0.00 2.74
2282 4280 3.386078 TGAAGAAGAACAGCTCACTCACT 59.614 43.478 0.00 0.00 0.00 3.41
2297 4306 6.294176 CCTTTTGGGTAGTGTTCATGAAGAAG 60.294 42.308 8.80 0.00 34.46 2.85
2313 4322 2.062636 TCTACTCTTGGCCTTTTGGGT 58.937 47.619 3.32 0.00 40.82 4.51
2382 4392 0.591659 TAAGACGGGATCGATGAGCG 59.408 55.000 0.54 0.00 40.11 5.03
2387 4397 3.028850 TGGAGTTTAAGACGGGATCGAT 58.971 45.455 0.00 0.00 40.11 3.59
2388 4398 2.449464 TGGAGTTTAAGACGGGATCGA 58.551 47.619 0.00 0.00 40.11 3.59
2404 4424 5.183904 CAGGGACAAAGGTAAAAAGATGGAG 59.816 44.000 0.00 0.00 0.00 3.86
2408 4428 5.074515 TCTCCAGGGACAAAGGTAAAAAGAT 59.925 40.000 0.00 0.00 0.00 2.40
2413 4433 5.311121 TGTATTCTCCAGGGACAAAGGTAAA 59.689 40.000 0.00 0.00 0.00 2.01
2414 4434 4.847512 TGTATTCTCCAGGGACAAAGGTAA 59.152 41.667 0.00 0.00 0.00 2.85
2415 4435 4.431378 TGTATTCTCCAGGGACAAAGGTA 58.569 43.478 0.00 0.00 0.00 3.08
2434 4454 6.464222 AGAAACACTAGCTAGTTGCATTGTA 58.536 36.000 23.94 0.00 45.94 2.41
2453 4473 3.211045 TGCAAGGGACACAGTTAGAAAC 58.789 45.455 0.00 0.00 0.00 2.78
2460 4483 2.024414 GTTTCTTGCAAGGGACACAGT 58.976 47.619 25.73 0.00 0.00 3.55
2461 4484 2.023673 TGTTTCTTGCAAGGGACACAG 58.976 47.619 25.73 0.00 0.00 3.66
2465 4488 1.322442 AGCTGTTTCTTGCAAGGGAC 58.678 50.000 25.73 22.19 0.00 4.46
2480 4503 7.834068 TTACTCTTCTTTTATGCAGTAGCTG 57.166 36.000 0.00 0.00 42.74 4.24
2481 4504 9.454859 AATTTACTCTTCTTTTATGCAGTAGCT 57.545 29.630 0.00 0.00 42.74 3.32
2486 4509 8.734386 AGTGGAATTTACTCTTCTTTTATGCAG 58.266 33.333 0.00 0.00 0.00 4.41
2487 4510 8.514594 CAGTGGAATTTACTCTTCTTTTATGCA 58.485 33.333 0.00 0.00 0.00 3.96
2488 4511 8.515414 ACAGTGGAATTTACTCTTCTTTTATGC 58.485 33.333 0.00 0.00 0.00 3.14
2489 4512 9.831737 CACAGTGGAATTTACTCTTCTTTTATG 57.168 33.333 0.00 0.00 0.00 1.90
2490 4513 9.793259 TCACAGTGGAATTTACTCTTCTTTTAT 57.207 29.630 0.00 0.00 0.00 1.40
2491 4514 9.621629 TTCACAGTGGAATTTACTCTTCTTTTA 57.378 29.630 0.00 0.00 0.00 1.52
2512 4539 1.714541 AACACATGGGGCAATTCACA 58.285 45.000 0.00 0.00 0.00 3.58
2524 4551 5.929697 TCAGCTGTAGAAAGAAACACATG 57.070 39.130 14.67 0.00 0.00 3.21
2550 4594 2.373169 ACTGAGCCAAATTCAGACCAGA 59.627 45.455 9.06 0.00 43.75 3.86
2566 4610 6.864685 TGACCGTATAACTTAACAACACTGAG 59.135 38.462 0.00 0.00 0.00 3.35
2572 4616 7.543172 TCATCAGTGACCGTATAACTTAACAAC 59.457 37.037 0.00 0.00 0.00 3.32
2578 4622 7.434307 CGTTTATCATCAGTGACCGTATAACTT 59.566 37.037 0.00 0.00 37.14 2.66
2586 4630 4.112634 ACATCGTTTATCATCAGTGACCG 58.887 43.478 0.00 0.00 37.14 4.79
2590 4634 8.611757 TCCAATTAACATCGTTTATCATCAGTG 58.388 33.333 0.00 0.00 0.00 3.66
2591 4635 8.731275 TCCAATTAACATCGTTTATCATCAGT 57.269 30.769 0.00 0.00 0.00 3.41
2600 5016 7.332678 GGTACACTACTCCAATTAACATCGTTT 59.667 37.037 0.00 0.00 0.00 3.60
2601 5017 6.815142 GGTACACTACTCCAATTAACATCGTT 59.185 38.462 0.00 0.00 0.00 3.85
2604 5020 6.255020 CACGGTACACTACTCCAATTAACATC 59.745 42.308 0.00 0.00 0.00 3.06
2607 5023 5.473039 ACACGGTACACTACTCCAATTAAC 58.527 41.667 0.00 0.00 0.00 2.01
2612 5028 3.503363 CAGTACACGGTACACTACTCCAA 59.497 47.826 14.11 0.00 0.00 3.53
2614 5030 3.077359 ACAGTACACGGTACACTACTCC 58.923 50.000 14.11 0.00 0.00 3.85
2620 5036 7.756722 ACAAGAATTATACAGTACACGGTACAC 59.243 37.037 14.11 0.00 29.86 2.90
2627 5043 6.019801 CGGCAGACAAGAATTATACAGTACAC 60.020 42.308 0.00 0.00 0.00 2.90
2628 5044 6.040247 CGGCAGACAAGAATTATACAGTACA 58.960 40.000 0.00 0.00 0.00 2.90
2634 5050 5.064707 TCAAAGCGGCAGACAAGAATTATAC 59.935 40.000 1.45 0.00 0.00 1.47
2635 5051 5.182487 TCAAAGCGGCAGACAAGAATTATA 58.818 37.500 1.45 0.00 0.00 0.98
2641 5057 1.159285 CATCAAAGCGGCAGACAAGA 58.841 50.000 1.45 0.00 0.00 3.02
2642 5058 1.129998 CTCATCAAAGCGGCAGACAAG 59.870 52.381 1.45 0.00 0.00 3.16
2644 5060 0.674581 CCTCATCAAAGCGGCAGACA 60.675 55.000 1.45 0.00 0.00 3.41
2645 5061 1.986575 GCCTCATCAAAGCGGCAGAC 61.987 60.000 1.45 0.00 42.06 3.51
2646 5062 1.746615 GCCTCATCAAAGCGGCAGA 60.747 57.895 1.45 0.00 42.06 4.26
2647 5063 2.796651 GCCTCATCAAAGCGGCAG 59.203 61.111 1.45 0.00 42.06 4.85
2670 5086 0.792640 CGTTGTACTGGAAGCTGCAG 59.207 55.000 10.11 10.11 41.93 4.41
2671 5087 0.391228 TCGTTGTACTGGAAGCTGCA 59.609 50.000 1.02 0.00 37.60 4.41
2672 5088 1.071605 CTCGTTGTACTGGAAGCTGC 58.928 55.000 0.00 0.00 37.60 5.25
2673 5089 1.071605 GCTCGTTGTACTGGAAGCTG 58.928 55.000 0.00 0.00 37.60 4.24
2674 5090 0.037232 GGCTCGTTGTACTGGAAGCT 60.037 55.000 9.59 0.00 37.60 3.74
2675 5091 0.320421 TGGCTCGTTGTACTGGAAGC 60.320 55.000 0.00 0.00 37.60 3.86
2677 5093 1.045407 ACTGGCTCGTTGTACTGGAA 58.955 50.000 0.00 0.00 0.00 3.53
2686 5102 4.643387 GGGTGGCACTGGCTCGTT 62.643 66.667 18.45 0.00 40.87 3.85
2693 5109 1.910580 ATTAGGTCGGGGTGGCACTG 61.911 60.000 18.45 8.10 0.00 3.66
2694 5110 1.205460 AATTAGGTCGGGGTGGCACT 61.205 55.000 18.45 0.00 0.00 4.40
2695 5111 0.323087 AAATTAGGTCGGGGTGGCAC 60.323 55.000 9.70 9.70 0.00 5.01
2696 5112 0.406361 AAAATTAGGTCGGGGTGGCA 59.594 50.000 0.00 0.00 0.00 4.92
2697 5113 0.815095 CAAAATTAGGTCGGGGTGGC 59.185 55.000 0.00 0.00 0.00 5.01
2699 5115 2.687935 CCATCAAAATTAGGTCGGGGTG 59.312 50.000 0.00 0.00 0.00 4.61
2703 5119 2.374184 TGGCCATCAAAATTAGGTCGG 58.626 47.619 0.00 0.00 0.00 4.79
2810 5712 9.696917 CAAAGGACAGCTTGTTTTTAATTAGAT 57.303 29.630 0.00 0.00 0.00 1.98
2813 5715 9.092876 CAACAAAGGACAGCTTGTTTTTAATTA 57.907 29.630 0.00 0.00 41.77 1.40
2814 5716 7.821846 TCAACAAAGGACAGCTTGTTTTTAATT 59.178 29.630 0.00 0.00 41.77 1.40
2816 5718 6.692486 TCAACAAAGGACAGCTTGTTTTTAA 58.308 32.000 0.00 0.00 41.77 1.52
2817 5719 6.274157 TCAACAAAGGACAGCTTGTTTTTA 57.726 33.333 0.00 0.00 41.77 1.52
2819 5721 4.799564 TCAACAAAGGACAGCTTGTTTT 57.200 36.364 0.00 0.00 41.77 2.43
2821 5723 6.463995 TTATTCAACAAAGGACAGCTTGTT 57.536 33.333 0.00 0.00 44.53 2.83
2822 5724 6.321181 TCTTTATTCAACAAAGGACAGCTTGT 59.679 34.615 0.00 0.00 37.36 3.16
2825 5727 6.959639 TTCTTTATTCAACAAAGGACAGCT 57.040 33.333 0.00 0.00 34.43 4.24
2826 5728 7.168135 CAGTTTCTTTATTCAACAAAGGACAGC 59.832 37.037 0.00 0.00 34.43 4.40
2828 5730 7.123547 ACCAGTTTCTTTATTCAACAAAGGACA 59.876 33.333 0.00 0.00 34.43 4.02
2829 5731 7.489160 ACCAGTTTCTTTATTCAACAAAGGAC 58.511 34.615 0.00 0.00 34.43 3.85
2831 5733 9.810545 TTTACCAGTTTCTTTATTCAACAAAGG 57.189 29.630 0.00 0.00 34.43 3.11
2842 5744 8.855110 TGCAATCAATCTTTACCAGTTTCTTTA 58.145 29.630 0.00 0.00 0.00 1.85
2844 5746 7.288810 TGCAATCAATCTTTACCAGTTTCTT 57.711 32.000 0.00 0.00 0.00 2.52
2845 5747 6.899393 TGCAATCAATCTTTACCAGTTTCT 57.101 33.333 0.00 0.00 0.00 2.52
2846 5748 7.945033 TTTGCAATCAATCTTTACCAGTTTC 57.055 32.000 0.00 0.00 31.33 2.78
2847 5749 8.907222 ATTTTGCAATCAATCTTTACCAGTTT 57.093 26.923 0.00 0.00 31.33 2.66
2848 5750 9.995003 TTATTTTGCAATCAATCTTTACCAGTT 57.005 25.926 0.00 0.00 31.33 3.16
2851 5753 9.434420 CCTTTATTTTGCAATCAATCTTTACCA 57.566 29.630 0.00 0.00 31.33 3.25
2852 5754 9.651913 TCCTTTATTTTGCAATCAATCTTTACC 57.348 29.630 0.00 0.00 31.33 2.85
2856 5758 9.783081 AGTTTCCTTTATTTTGCAATCAATCTT 57.217 25.926 0.00 0.00 31.33 2.40
2858 5760 8.445493 CCAGTTTCCTTTATTTTGCAATCAATC 58.555 33.333 0.00 0.00 31.33 2.67
2860 5762 7.226325 CACCAGTTTCCTTTATTTTGCAATCAA 59.774 33.333 0.00 0.00 0.00 2.57
2861 5763 6.705381 CACCAGTTTCCTTTATTTTGCAATCA 59.295 34.615 0.00 0.00 0.00 2.57
2862 5764 6.928492 TCACCAGTTTCCTTTATTTTGCAATC 59.072 34.615 0.00 0.00 0.00 2.67
2863 5765 6.825610 TCACCAGTTTCCTTTATTTTGCAAT 58.174 32.000 0.00 0.00 0.00 3.56
2864 5766 6.227298 TCACCAGTTTCCTTTATTTTGCAA 57.773 33.333 0.00 0.00 0.00 4.08
2865 5767 5.860941 TCACCAGTTTCCTTTATTTTGCA 57.139 34.783 0.00 0.00 0.00 4.08
2866 5768 6.512297 TCTTCACCAGTTTCCTTTATTTTGC 58.488 36.000 0.00 0.00 0.00 3.68
2867 5769 8.981647 CAATCTTCACCAGTTTCCTTTATTTTG 58.018 33.333 0.00 0.00 0.00 2.44
2869 5771 7.154656 GCAATCTTCACCAGTTTCCTTTATTT 58.845 34.615 0.00 0.00 0.00 1.40
2875 6740 3.152341 CTGCAATCTTCACCAGTTTCCT 58.848 45.455 0.00 0.00 0.00 3.36
2877 6742 2.294233 TGCTGCAATCTTCACCAGTTTC 59.706 45.455 0.00 0.00 0.00 2.78
2905 6770 4.798907 GCATGAAGAGCAAATGATCAACAG 59.201 41.667 0.00 0.00 31.88 3.16
2910 6775 4.095932 TGACTGCATGAAGAGCAAATGATC 59.904 41.667 8.02 0.00 42.17 2.92
2917 6782 2.745821 GTTGATGACTGCATGAAGAGCA 59.254 45.455 8.02 5.57 40.19 4.26
2918 6783 3.008330 AGTTGATGACTGCATGAAGAGC 58.992 45.455 8.02 0.00 37.17 4.09
2934 6799 9.578576 TCTTTTTAGTACTACTACTCCAGTTGA 57.421 33.333 0.91 0.00 38.80 3.18
2963 6834 8.413229 AGACGAAAATTTGATCAGAAAGGAAAA 58.587 29.630 0.00 0.00 0.00 2.29
2964 6835 7.940850 AGACGAAAATTTGATCAGAAAGGAAA 58.059 30.769 0.00 0.00 0.00 3.13
2967 6838 6.902341 TGAGACGAAAATTTGATCAGAAAGG 58.098 36.000 0.00 0.00 0.00 3.11
2968 6839 8.232513 TGATGAGACGAAAATTTGATCAGAAAG 58.767 33.333 0.00 0.00 0.00 2.62
2972 6898 8.906636 AATTGATGAGACGAAAATTTGATCAG 57.093 30.769 0.00 0.00 0.00 2.90
2983 6914 4.893608 TCACTCCAAATTGATGAGACGAA 58.106 39.130 6.31 0.00 0.00 3.85
2984 6915 4.535526 TCACTCCAAATTGATGAGACGA 57.464 40.909 6.31 1.07 0.00 4.20
2985 6916 5.808042 AATCACTCCAAATTGATGAGACG 57.192 39.130 6.31 0.00 32.63 4.18
2987 6918 6.944290 ACAGAAATCACTCCAAATTGATGAGA 59.056 34.615 6.31 0.00 32.63 3.27
2989 6920 6.570957 GCACAGAAATCACTCCAAATTGATGA 60.571 38.462 0.00 0.00 32.63 2.92
2990 6921 5.575606 GCACAGAAATCACTCCAAATTGATG 59.424 40.000 0.00 0.00 32.63 3.07
3011 6998 0.039437 TTTCTCTCCGTCAGTCGCAC 60.039 55.000 0.00 0.00 38.35 5.34
3451 7447 0.249120 CGACCTTGTACATGGCCTCA 59.751 55.000 23.97 0.00 0.00 3.86
3574 7570 5.182190 GCTGAATGCTGAAGATGATGATGAT 59.818 40.000 0.00 0.00 38.95 2.45
3688 7702 1.695893 CTGTTCGTGGCCATAGCGTG 61.696 60.000 9.72 0.00 41.24 5.34
3755 7772 6.111382 TCTGTCTTGCTGGAAGAAATATGAG 58.889 40.000 13.37 3.76 42.56 2.90
3759 7776 4.690748 CGTTCTGTCTTGCTGGAAGAAATA 59.309 41.667 13.37 0.00 42.56 1.40
3770 7787 1.076332 ATTACGGCGTTCTGTCTTGC 58.924 50.000 21.24 0.00 33.08 4.01
3799 7817 2.226437 ACGTGTGAGTTGCATTCATTCC 59.774 45.455 4.91 0.00 0.00 3.01
3800 7818 3.542712 ACGTGTGAGTTGCATTCATTC 57.457 42.857 4.91 1.98 0.00 2.67
3853 7872 4.552166 TGGAAGCAGAGTTTTCTTTTCG 57.448 40.909 0.00 0.00 30.55 3.46
3958 7977 1.005867 TCGTTGGCGGTGGTTAGAC 60.006 57.895 0.00 0.00 38.89 2.59
3970 7989 1.209127 GCAAATGGTCGGTCGTTGG 59.791 57.895 0.00 0.00 0.00 3.77
4036 8061 8.884323 TCATTGCTATATCCTTTATCCTTGTCT 58.116 33.333 0.00 0.00 0.00 3.41
4109 8134 3.861569 CGGGAGCGTCATAATTTTCTC 57.138 47.619 0.00 0.00 0.00 2.87
4262 8288 4.213270 TGTGCAACTGTGTCTAATGTAAGC 59.787 41.667 0.00 0.00 38.04 3.09
4278 8304 2.225727 GGTAGTTTGTAGCCTGTGCAAC 59.774 50.000 0.00 0.00 41.13 4.17
4285 8311 1.279271 CTGCTGGGTAGTTTGTAGCCT 59.721 52.381 2.22 0.00 36.16 4.58
4286 8312 1.278127 TCTGCTGGGTAGTTTGTAGCC 59.722 52.381 0.00 0.00 33.60 3.93
4431 8457 1.683917 TGGAAGCGCCTAGAAGAGATC 59.316 52.381 2.29 0.00 37.63 2.75
4533 8559 3.599730 TTGTTCTCTGATCATGACGCT 57.400 42.857 0.00 0.00 0.00 5.07
4670 8696 3.809832 GTGGAACAATGACCATATCGAGG 59.190 47.826 7.09 0.00 44.16 4.63
4718 8744 4.576463 GCTAATGGTGCTTATGCTACTTGT 59.424 41.667 1.96 0.00 40.48 3.16
4719 8745 4.818546 AGCTAATGGTGCTTATGCTACTTG 59.181 41.667 1.96 0.00 37.52 3.16


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

AutoCloner maintained by Alex Coulton.