Multiple sequence alignment - TraesCS2D01G338700

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 TraesCS2D01G338700 chr2D 100.000 3901 0 0 1 3901 432036650 432032750 0.000000e+00 7204.0
1 TraesCS2D01G338700 chr2D 89.931 288 25 3 3569 3852 607943938 607944225 6.160000e-98 368.0
2 TraesCS2D01G338700 chr2D 95.082 183 9 0 2185 2367 604277654 604277472 4.930000e-74 289.0
3 TraesCS2D01G338700 chr2A 92.263 866 39 19 1 845 554428891 554429749 0.000000e+00 1203.0
4 TraesCS2D01G338700 chr2A 92.928 707 43 5 2562 3263 554452694 554453398 0.000000e+00 1022.0
5 TraesCS2D01G338700 chr2A 87.131 847 57 16 838 1649 554450892 554451721 0.000000e+00 913.0
6 TraesCS2D01G338700 chr2A 94.167 360 16 3 1822 2179 554451972 554452328 9.530000e-151 544.0
7 TraesCS2D01G338700 chr2A 90.645 310 23 5 2192 2497 554452372 554452679 1.300000e-109 407.0
8 TraesCS2D01G338700 chr2A 77.990 209 24 6 3332 3520 756966918 756967124 1.150000e-20 111.0
9 TraesCS2D01G338700 chr2B 93.600 625 34 4 2594 3216 510796571 510795951 0.000000e+00 928.0
10 TraesCS2D01G338700 chr2B 88.544 742 50 9 1815 2521 510797318 510796577 0.000000e+00 867.0
11 TraesCS2D01G338700 chr2B 87.950 722 52 13 735 1433 510798424 510797715 0.000000e+00 819.0
12 TraesCS2D01G338700 chr2B 87.639 720 44 21 1 714 510799226 510798546 0.000000e+00 795.0
13 TraesCS2D01G338700 chr2B 92.437 119 8 1 3162 3279 510795951 510795833 6.700000e-38 169.0
14 TraesCS2D01G338700 chr2B 85.938 64 9 0 1508 1571 510797622 510797559 6.990000e-08 69.4
15 TraesCS2D01G338700 chr7B 89.273 289 26 3 3569 3852 388852565 388852853 1.330000e-94 357.0
16 TraesCS2D01G338700 chr7B 88.889 288 28 3 3569 3852 337925308 337925021 6.200000e-93 351.0
17 TraesCS2D01G338700 chr7B 88.927 289 27 3 3569 3852 388838640 388838928 6.200000e-93 351.0
18 TraesCS2D01G338700 chr7B 88.811 286 27 3 3569 3849 388867169 388867454 2.890000e-91 346.0
19 TraesCS2D01G338700 chr7B 79.079 239 31 10 3321 3541 337926066 337925829 3.140000e-31 147.0
20 TraesCS2D01G338700 chr7B 77.119 236 36 11 3321 3538 388851834 388852069 1.900000e-23 121.0
21 TraesCS2D01G338700 chr6D 89.123 285 27 3 3569 3849 384285042 384285326 6.200000e-93 351.0
22 TraesCS2D01G338700 chr5D 88.581 289 27 5 3569 3852 497788691 497788404 2.890000e-91 346.0
23 TraesCS2D01G338700 chr5D 80.000 220 33 4 3332 3541 5122576 5122358 6.750000e-33 152.0
24 TraesCS2D01G338700 chr5B 88.542 288 29 3 3569 3852 429426166 429426453 2.890000e-91 346.0
25 TraesCS2D01G338700 chr5B 88.384 198 8 2 2185 2367 710871038 710871235 1.410000e-54 224.0
26 TraesCS2D01G338700 chr5B 91.971 137 11 0 1815 1951 710870903 710871039 3.980000e-45 193.0
27 TraesCS2D01G338700 chr5B 82.326 215 27 4 3341 3545 118590822 118590609 4.010000e-40 176.0
28 TraesCS2D01G338700 chr5B 83.929 112 15 3 3309 3420 429425153 429425261 1.920000e-18 104.0
29 TraesCS2D01G338700 chr3B 88.542 288 29 3 3569 3852 802298226 802298513 2.890000e-91 346.0
30 TraesCS2D01G338700 chr3B 93.443 183 10 1 2185 2367 572076937 572077117 1.790000e-68 270.0
31 TraesCS2D01G338700 chr3B 92.896 183 13 0 2185 2367 83313072 83313254 2.310000e-67 267.0
32 TraesCS2D01G338700 chr3B 93.431 137 9 0 1815 1951 83312937 83313073 1.840000e-48 204.0
33 TraesCS2D01G338700 chr3B 86.364 66 9 0 1511 1576 572076572 572076637 5.410000e-09 73.1
34 TraesCS2D01G338700 chr6B 83.028 218 29 1 3332 3541 33587810 33588027 1.430000e-44 191.0
35 TraesCS2D01G338700 chr1B 77.419 248 35 7 3315 3541 169668565 169668318 1.140000e-25 128.0
36 TraesCS2D01G338700 chr1B 78.322 143 23 1 3387 3521 40880929 40880787 6.940000e-13 86.1
37 TraesCS2D01G338700 chr5A 76.695 236 36 5 3321 3538 435693024 435693258 3.190000e-21 113.0


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 TraesCS2D01G338700 chr2D 432032750 432036650 3900 True 7204.0 7204 100.000000 1 3901 1 chr2D.!!$R1 3900
1 TraesCS2D01G338700 chr2A 554428891 554429749 858 False 1203.0 1203 92.263000 1 845 1 chr2A.!!$F1 844
2 TraesCS2D01G338700 chr2A 554450892 554453398 2506 False 721.5 1022 91.217750 838 3263 4 chr2A.!!$F3 2425
3 TraesCS2D01G338700 chr2B 510795833 510799226 3393 True 607.9 928 89.351333 1 3279 6 chr2B.!!$R1 3278
4 TraesCS2D01G338700 chr7B 337925021 337926066 1045 True 249.0 351 83.984000 3321 3852 2 chr7B.!!$R1 531
5 TraesCS2D01G338700 chr7B 388851834 388852853 1019 False 239.0 357 83.196000 3321 3852 2 chr7B.!!$F3 531
6 TraesCS2D01G338700 chr5B 429425153 429426453 1300 False 225.0 346 86.235500 3309 3852 2 chr5B.!!$F1 543

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
48 49 0.808125 AGTTGCGTGCACAGTTTTCA 59.192 45.0 18.64 1.41 0.0 2.69 F
1301 1460 0.463620 AAGCCGATTCAGGAGAGAGC 59.536 55.0 0.00 0.00 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1303 1462 0.232303 CGAGTCCAAACGTGCAACTC 59.768 55.0 9.41 9.41 34.81 3.01 R
3283 3783 0.108424 CTCTCAGCCTCGTCCTTTGG 60.108 60.0 0.00 0.00 0.00 3.28 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
21 22 2.224314 CCGGTTTCTCTGTCTTTCAAGC 59.776 50.000 0.00 0.00 0.00 4.01
22 23 3.134458 CGGTTTCTCTGTCTTTCAAGCT 58.866 45.455 0.00 0.00 0.00 3.74
23 24 4.307432 CGGTTTCTCTGTCTTTCAAGCTA 58.693 43.478 0.00 0.00 0.00 3.32
24 25 4.387256 CGGTTTCTCTGTCTTTCAAGCTAG 59.613 45.833 0.00 0.00 0.00 3.42
48 49 0.808125 AGTTGCGTGCACAGTTTTCA 59.192 45.000 18.64 1.41 0.00 2.69
271 274 3.419943 TGCACCTTGTTCATGATGCTTA 58.580 40.909 15.60 0.00 34.18 3.09
286 289 8.924691 TCATGATGCTTAGTTTGTTTAATTTGC 58.075 29.630 0.00 0.00 0.00 3.68
375 378 9.864034 GTATATTGACGAAAAATATCACACCAG 57.136 33.333 0.00 0.00 33.38 4.00
424 430 5.013287 TGGTTCCACTTATGCAGTTAACCTA 59.987 40.000 14.67 0.00 43.64 3.08
483 489 1.402896 TATCGCTGAAGCAGAGGGGG 61.403 60.000 2.79 0.00 42.21 5.40
585 599 3.215151 GTCTCGGACACAGATGGATAGA 58.785 50.000 0.00 0.00 32.09 1.98
714 730 3.032459 TGTAAACTGGGGTTTTGTTCCC 58.968 45.455 0.00 0.00 42.28 3.97
747 877 3.610677 GCCAATTTCGTACAATTTTCCCG 59.389 43.478 0.00 0.00 0.00 5.14
760 890 5.167845 CAATTTTCCCGTGGATTTTACTGG 58.832 41.667 0.00 0.00 0.00 4.00
765 895 2.167662 CCGTGGATTTTACTGGCCTTT 58.832 47.619 3.32 0.00 0.00 3.11
824 961 1.227823 TGTGACTGGCCCGTGAAAG 60.228 57.895 3.79 0.00 0.00 2.62
850 987 0.837691 AGTGGTGGTCTCTGGATGCA 60.838 55.000 0.00 0.00 0.00 3.96
915 1052 1.747367 CTGTCGAGACGAGGCTCCT 60.747 63.158 9.32 0.22 36.23 3.69
956 1093 2.347490 CTCCCCACACCTGTTCGG 59.653 66.667 0.00 0.00 39.35 4.30
984 1128 1.140252 GCTTCTTATAGCGGGGTTCCA 59.860 52.381 0.00 0.00 0.00 3.53
985 1129 2.835027 CTTCTTATAGCGGGGTTCCAC 58.165 52.381 0.00 0.00 0.00 4.02
986 1130 2.170012 TCTTATAGCGGGGTTCCACT 57.830 50.000 0.00 0.00 0.00 4.00
1046 1190 2.657237 CTCGTCCCGCTTCCTGTT 59.343 61.111 0.00 0.00 0.00 3.16
1215 1372 4.328712 CCTTTTTGTTTGTTGTACTGCCAC 59.671 41.667 0.00 0.00 0.00 5.01
1220 1377 2.809696 GTTTGTTGTACTGCCACCGTAT 59.190 45.455 0.00 0.00 0.00 3.06
1267 1426 7.306749 GCGGCAAATTGGATGATTAATTAACTG 60.307 37.037 0.00 0.00 0.00 3.16
1299 1458 3.769844 AGTTTAAGCCGATTCAGGAGAGA 59.230 43.478 0.00 0.00 0.00 3.10
1300 1459 4.116238 GTTTAAGCCGATTCAGGAGAGAG 58.884 47.826 0.00 0.00 0.00 3.20
1301 1460 0.463620 AAGCCGATTCAGGAGAGAGC 59.536 55.000 0.00 0.00 0.00 4.09
1302 1461 0.396974 AGCCGATTCAGGAGAGAGCT 60.397 55.000 0.00 0.00 0.00 4.09
1303 1462 0.249405 GCCGATTCAGGAGAGAGCTG 60.249 60.000 0.00 0.00 0.00 4.24
1381 1551 5.479375 TCGGTGGATTTTAGTCTTGTAGAGT 59.521 40.000 0.00 0.00 0.00 3.24
1433 1603 1.141657 TGGAGAGCACAGGAATATGGC 59.858 52.381 0.00 0.00 0.00 4.40
1502 1712 2.034558 AGTGGTTGGTGCTGAAAATTCG 59.965 45.455 0.00 0.00 0.00 3.34
1503 1713 2.028130 TGGTTGGTGCTGAAAATTCGT 58.972 42.857 0.00 0.00 0.00 3.85
1591 1802 3.282021 ACCATGTTATGCAGGTAGCTTG 58.718 45.455 0.00 0.00 45.94 4.01
1621 1832 4.640201 GCAGAAACTAGGAATTATGTGCCA 59.360 41.667 0.00 0.00 0.00 4.92
1640 1851 6.375455 TGTGCCAACAAACATTTTATTTTGGT 59.625 30.769 0.00 0.00 37.08 3.67
1641 1852 7.552687 TGTGCCAACAAACATTTTATTTTGGTA 59.447 29.630 0.00 0.00 37.08 3.25
1642 1853 8.398665 GTGCCAACAAACATTTTATTTTGGTAA 58.601 29.630 0.00 0.00 37.08 2.85
1643 1854 8.956426 TGCCAACAAACATTTTATTTTGGTAAA 58.044 25.926 0.00 0.00 37.08 2.01
1644 1855 9.444534 GCCAACAAACATTTTATTTTGGTAAAG 57.555 29.630 0.00 0.00 37.08 1.85
1645 1856 9.943163 CCAACAAACATTTTATTTTGGTAAAGG 57.057 29.630 0.00 0.00 37.08 3.11
1646 1857 9.943163 CAACAAACATTTTATTTTGGTAAAGGG 57.057 29.630 0.00 0.00 37.08 3.95
1647 1858 8.160521 ACAAACATTTTATTTTGGTAAAGGGC 57.839 30.769 0.00 0.00 37.08 5.19
1648 1859 7.775561 ACAAACATTTTATTTTGGTAAAGGGCA 59.224 29.630 0.00 0.00 37.08 5.36
1649 1860 8.624776 CAAACATTTTATTTTGGTAAAGGGCAA 58.375 29.630 0.00 0.00 0.00 4.52
1650 1861 8.753497 AACATTTTATTTTGGTAAAGGGCAAA 57.247 26.923 0.00 0.00 0.00 3.68
1651 1862 8.753497 ACATTTTATTTTGGTAAAGGGCAAAA 57.247 26.923 0.00 0.00 0.00 2.44
1652 1863 9.190317 ACATTTTATTTTGGTAAAGGGCAAAAA 57.810 25.926 0.00 0.00 31.55 1.94
1688 1899 4.207955 GGGAAAGGGCAATTTACTCCTAG 58.792 47.826 0.00 0.00 0.00 3.02
1747 1958 7.909267 TGAAATCCGCGATCATCATATATTTC 58.091 34.615 8.23 7.41 33.52 2.17
1754 1965 5.352293 GCGATCATCATATATTTCTGGCACA 59.648 40.000 0.00 0.00 0.00 4.57
1755 1966 6.674037 GCGATCATCATATATTTCTGGCACAC 60.674 42.308 0.00 0.00 0.00 3.82
1799 2020 0.319040 TCGTTGCTGCTCAGTGACTC 60.319 55.000 0.00 0.00 0.00 3.36
1804 2025 0.034616 GCTGCTCAGTGACTCCAAGT 59.965 55.000 0.00 0.00 0.00 3.16
1807 2028 1.618837 TGCTCAGTGACTCCAAGTACC 59.381 52.381 0.00 0.00 0.00 3.34
1867 2266 4.574013 TGTTTAACTTGCAGCAATTTTGGG 59.426 37.500 15.24 2.37 0.00 4.12
1935 2334 3.135994 ACAGTATGGTGTTGTTCGAACC 58.864 45.455 24.78 11.03 43.62 3.62
1986 2385 2.199236 GACCGAGCCTTATTTGTACCG 58.801 52.381 0.00 0.00 0.00 4.02
2061 2460 2.609427 TATCTGCTCCTCACATGCAC 57.391 50.000 0.00 0.00 32.91 4.57
2089 2488 5.006386 CCTGCTTAGAACTGTTGAAGGATT 58.994 41.667 0.00 0.00 0.00 3.01
2142 2541 2.622942 TGGATCAGGTTTGTTGTTGCTC 59.377 45.455 0.00 0.00 0.00 4.26
2169 2572 4.082190 GCCTGATACACTGTCACTCTGTTA 60.082 45.833 0.00 0.00 0.00 2.41
2170 2573 5.645624 CCTGATACACTGTCACTCTGTTAG 58.354 45.833 0.00 0.00 0.00 2.34
2171 2574 5.184096 CCTGATACACTGTCACTCTGTTAGT 59.816 44.000 0.00 0.00 39.81 2.24
2172 2575 6.374613 CCTGATACACTGTCACTCTGTTAGTA 59.625 42.308 0.00 0.00 35.76 1.82
2173 2576 7.142306 TGATACACTGTCACTCTGTTAGTAC 57.858 40.000 0.00 0.00 35.76 2.73
2175 2578 4.471548 ACACTGTCACTCTGTTAGTACCT 58.528 43.478 0.00 0.00 35.76 3.08
2177 2580 5.009811 ACACTGTCACTCTGTTAGTACCTTC 59.990 44.000 0.00 0.00 35.76 3.46
2178 2581 5.009710 CACTGTCACTCTGTTAGTACCTTCA 59.990 44.000 0.00 0.00 35.76 3.02
2180 2583 6.097839 ACTGTCACTCTGTTAGTACCTTCAAA 59.902 38.462 0.00 0.00 35.76 2.69
2181 2584 7.062749 TGTCACTCTGTTAGTACCTTCAAAT 57.937 36.000 0.00 0.00 35.76 2.32
2200 2635 7.026631 TCAAATACAACTTTGTCCAACTGAG 57.973 36.000 0.00 0.00 42.35 3.35
2210 2647 4.437682 TGTCCAACTGAGATTTTGTCCT 57.562 40.909 0.00 0.00 0.00 3.85
2215 2652 5.997746 TCCAACTGAGATTTTGTCCTAACTG 59.002 40.000 0.00 0.00 0.00 3.16
2227 2664 1.134699 TCCTAACTGCTGCCATCTTCG 60.135 52.381 0.00 0.00 0.00 3.79
2229 2666 1.662629 CTAACTGCTGCCATCTTCGTG 59.337 52.381 0.00 0.00 0.00 4.35
2230 2667 0.250467 AACTGCTGCCATCTTCGTGT 60.250 50.000 0.00 0.00 0.00 4.49
2241 2679 5.012046 TGCCATCTTCGTGTATTCCTATCAT 59.988 40.000 0.00 0.00 0.00 2.45
2251 2689 5.012148 GTGTATTCCTATCATAGGCAGTGGT 59.988 44.000 5.74 0.00 45.82 4.16
2260 2698 3.838317 TCATAGGCAGTGGTTACTTGACT 59.162 43.478 0.00 0.00 34.07 3.41
2266 2704 2.031682 CAGTGGTTACTTGACTGCTTGC 60.032 50.000 0.00 0.00 34.07 4.01
2326 2764 4.156739 GGGATTGAACACATTCCTGAACTC 59.843 45.833 0.00 0.00 35.59 3.01
2331 2769 3.194005 ACACATTCCTGAACTCGTTGT 57.806 42.857 0.00 0.00 0.00 3.32
2338 2776 2.158957 TCCTGAACTCGTTGTTGCTTCT 60.159 45.455 1.75 0.00 39.30 2.85
2416 2854 6.899393 TCTTTTCATGTTTCAGGTATGCTT 57.101 33.333 0.00 0.00 0.00 3.91
2421 2859 5.069318 TCATGTTTCAGGTATGCTTGTTGA 58.931 37.500 0.00 0.00 0.00 3.18
2433 2871 6.202954 GGTATGCTTGTTGATGTACTATGGTC 59.797 42.308 0.00 0.00 0.00 4.02
2483 2922 2.604969 TAATTTGCGCTGGTCGTTTC 57.395 45.000 9.73 0.00 41.07 2.78
2492 2931 1.941325 CTGGTCGTTTCATAGCCTCC 58.059 55.000 0.00 0.00 0.00 4.30
2497 2936 3.335579 GTCGTTTCATAGCCTCCAAACT 58.664 45.455 0.00 0.00 0.00 2.66
2503 2942 6.072673 CGTTTCATAGCCTCCAAACTTTAGTT 60.073 38.462 0.00 0.00 40.50 2.24
2504 2943 6.817765 TTCATAGCCTCCAAACTTTAGTTG 57.182 37.500 0.00 0.00 38.44 3.16
2506 2945 3.595190 AGCCTCCAAACTTTAGTTGGT 57.405 42.857 3.28 0.00 38.44 3.67
2508 2947 3.636764 AGCCTCCAAACTTTAGTTGGTTG 59.363 43.478 3.28 0.00 38.44 3.77
2509 2948 3.243737 GCCTCCAAACTTTAGTTGGTTGG 60.244 47.826 4.33 4.33 38.44 3.77
2510 2949 3.958147 CCTCCAAACTTTAGTTGGTTGGT 59.042 43.478 9.90 0.00 38.44 3.67
2511 2950 4.037565 CCTCCAAACTTTAGTTGGTTGGTC 59.962 45.833 9.90 0.00 38.44 4.02
2513 2952 6.003859 TCCAAACTTTAGTTGGTTGGTCTA 57.996 37.500 9.90 0.00 38.44 2.59
2514 2953 6.059484 TCCAAACTTTAGTTGGTTGGTCTAG 58.941 40.000 9.90 0.00 38.44 2.43
2515 2954 5.278315 CCAAACTTTAGTTGGTTGGTCTAGC 60.278 44.000 2.67 0.00 38.44 3.42
2516 2955 4.017177 ACTTTAGTTGGTTGGTCTAGCC 57.983 45.455 0.00 0.00 37.90 3.93
2518 2957 1.636148 TAGTTGGTTGGTCTAGCCGT 58.364 50.000 0.00 0.00 41.21 5.68
2520 2959 0.320697 GTTGGTTGGTCTAGCCGTCT 59.679 55.000 0.00 0.00 41.21 4.18
2521 2960 1.547372 GTTGGTTGGTCTAGCCGTCTA 59.453 52.381 0.00 0.00 41.21 2.59
2522 2961 1.471119 TGGTTGGTCTAGCCGTCTAG 58.529 55.000 0.00 0.00 42.87 2.43
2524 2963 1.404748 GGTTGGTCTAGCCGTCTAGTC 59.595 57.143 0.00 0.00 42.28 2.59
2525 2964 2.089980 GTTGGTCTAGCCGTCTAGTCA 58.910 52.381 0.00 0.00 42.28 3.41
2527 2966 3.851458 TGGTCTAGCCGTCTAGTCATA 57.149 47.619 0.00 0.00 42.28 2.15
2528 2967 4.368565 TGGTCTAGCCGTCTAGTCATAT 57.631 45.455 0.00 0.00 42.28 1.78
2529 2968 4.726583 TGGTCTAGCCGTCTAGTCATATT 58.273 43.478 0.00 0.00 42.28 1.28
2530 2969 5.138276 TGGTCTAGCCGTCTAGTCATATTT 58.862 41.667 0.00 0.00 42.28 1.40
2531 2970 5.597182 TGGTCTAGCCGTCTAGTCATATTTT 59.403 40.000 0.00 0.00 42.28 1.82
2532 2971 6.097839 TGGTCTAGCCGTCTAGTCATATTTTT 59.902 38.462 0.00 0.00 42.28 1.94
2558 2997 8.932945 TTCTCGATAGTCATATTTGGATATGC 57.067 34.615 0.00 0.00 43.13 3.14
2559 2998 8.298729 TCTCGATAGTCATATTTGGATATGCT 57.701 34.615 0.00 5.53 43.13 3.79
2560 2999 8.409371 TCTCGATAGTCATATTTGGATATGCTC 58.591 37.037 0.00 0.00 43.13 4.26
2628 3068 6.889198 AGCATATGGAGCTTAAGTTGTCTTA 58.111 36.000 4.56 0.00 39.87 2.10
2645 3085 8.196771 AGTTGTCTTATTGCAATTCTCAAAACA 58.803 29.630 18.75 6.00 0.00 2.83
2729 3169 2.444706 CCTGAGATCCCTCGGCCA 60.445 66.667 2.24 0.00 43.03 5.36
2774 3214 1.145377 GCGGATGGTCATACCCGTT 59.855 57.895 11.12 0.00 43.51 4.44
2814 3254 0.445436 GCAGGTGATTGACAAGAGCG 59.555 55.000 0.00 0.00 0.00 5.03
2921 3361 1.047002 ATCCTTCGCTCTGGATCTGG 58.953 55.000 0.00 0.00 38.60 3.86
2949 3389 4.444388 GTGTGTGTATATATGTGAGTGCCG 59.556 45.833 0.00 0.00 0.00 5.69
2985 3425 2.030007 CCAATGTGGCGTCTGATGTTTT 60.030 45.455 0.00 0.00 0.00 2.43
3002 3442 7.560368 TGATGTTTTAGATGGTTTGGTTTTGT 58.440 30.769 0.00 0.00 0.00 2.83
3003 3443 8.696374 TGATGTTTTAGATGGTTTGGTTTTGTA 58.304 29.630 0.00 0.00 0.00 2.41
3099 3545 1.765230 TTGTGTGGCCTTTTTACGGT 58.235 45.000 3.32 0.00 0.00 4.83
3109 3555 5.244178 TGGCCTTTTTACGGTATGATTTGTT 59.756 36.000 3.32 0.00 0.00 2.83
3141 3587 5.376625 AGTTCAGTTCAGGTGCAATTTCTA 58.623 37.500 0.00 0.00 0.00 2.10
3147 3593 6.638468 CAGTTCAGGTGCAATTTCTAAACTTC 59.362 38.462 0.00 0.00 0.00 3.01
3148 3594 5.705609 TCAGGTGCAATTTCTAAACTTCC 57.294 39.130 0.00 0.00 0.00 3.46
3154 3600 6.024049 GTGCAATTTCTAAACTTCCGAGATG 58.976 40.000 0.00 0.00 0.00 2.90
3185 3631 5.821470 CAGCATTATCCTCTCAACTTCATGT 59.179 40.000 0.00 0.00 0.00 3.21
3231 3731 2.672098 TGTCCCCTTTTGCTTGCTAAA 58.328 42.857 2.73 2.73 0.00 1.85
3233 3733 2.029020 GTCCCCTTTTGCTTGCTAAAGG 60.029 50.000 28.62 28.62 46.44 3.11
3244 3744 1.214305 TGCTAAAGGTGATGGGCCCT 61.214 55.000 25.70 8.64 0.00 5.19
3252 3752 1.457643 TGATGGGCCCTAGAGACCG 60.458 63.158 25.70 0.00 0.00 4.79
3267 3767 0.320508 GACCGAAGTCCTTCCGCTTT 60.321 55.000 1.61 0.00 37.00 3.51
3268 3768 0.602905 ACCGAAGTCCTTCCGCTTTG 60.603 55.000 1.61 0.00 36.27 2.77
3273 3773 3.058224 CGAAGTCCTTCCGCTTTGAAAAT 60.058 43.478 1.61 0.00 36.27 1.82
3274 3774 3.923017 AGTCCTTCCGCTTTGAAAATG 57.077 42.857 0.00 0.00 0.00 2.32
3275 3775 2.029918 AGTCCTTCCGCTTTGAAAATGC 60.030 45.455 0.00 0.00 42.89 3.56
3277 3777 1.339711 CTTCCGCTTTGAAAATGCCG 58.660 50.000 0.00 0.00 43.35 5.69
3280 3780 2.094066 CGCTTTGAAAATGCCGGGC 61.094 57.895 13.32 13.32 43.35 6.13
3281 3781 1.293179 GCTTTGAAAATGCCGGGCT 59.707 52.632 21.46 0.00 40.73 5.19
3282 3782 0.320683 GCTTTGAAAATGCCGGGCTT 60.321 50.000 21.46 11.55 40.73 4.35
3283 3783 1.713597 CTTTGAAAATGCCGGGCTTC 58.286 50.000 21.46 15.76 0.00 3.86
3284 3784 0.320050 TTTGAAAATGCCGGGCTTCC 59.680 50.000 21.46 7.62 0.00 3.46
3285 3785 0.829602 TTGAAAATGCCGGGCTTCCA 60.830 50.000 21.46 10.02 0.00 3.53
3286 3786 0.829602 TGAAAATGCCGGGCTTCCAA 60.830 50.000 21.46 0.00 0.00 3.53
3287 3787 0.320050 GAAAATGCCGGGCTTCCAAA 59.680 50.000 21.46 0.00 0.00 3.28
3288 3788 0.321346 AAAATGCCGGGCTTCCAAAG 59.679 50.000 21.46 0.00 0.00 2.77
3289 3789 1.543944 AAATGCCGGGCTTCCAAAGG 61.544 55.000 21.46 0.00 0.00 3.11
3290 3790 2.439553 AATGCCGGGCTTCCAAAGGA 62.440 55.000 21.46 0.00 0.00 3.36
3291 3791 3.062466 GCCGGGCTTCCAAAGGAC 61.062 66.667 12.87 0.00 0.00 3.85
3292 3792 2.746277 CCGGGCTTCCAAAGGACG 60.746 66.667 0.00 0.00 0.00 4.79
3293 3793 2.345991 CGGGCTTCCAAAGGACGA 59.654 61.111 0.00 0.00 0.00 4.20
3294 3794 1.741770 CGGGCTTCCAAAGGACGAG 60.742 63.158 0.00 0.00 0.00 4.18
3295 3795 1.377333 GGGCTTCCAAAGGACGAGG 60.377 63.158 0.00 0.00 0.00 4.63
3296 3796 2.041115 GGCTTCCAAAGGACGAGGC 61.041 63.158 0.00 0.00 30.13 4.70
3297 3797 1.003233 GCTTCCAAAGGACGAGGCT 60.003 57.895 0.00 0.00 0.00 4.58
3298 3798 1.301677 GCTTCCAAAGGACGAGGCTG 61.302 60.000 0.00 0.00 0.00 4.85
3299 3799 0.321671 CTTCCAAAGGACGAGGCTGA 59.678 55.000 0.00 0.00 0.00 4.26
3300 3800 0.321671 TTCCAAAGGACGAGGCTGAG 59.678 55.000 0.00 0.00 0.00 3.35
3301 3801 0.541998 TCCAAAGGACGAGGCTGAGA 60.542 55.000 0.00 0.00 0.00 3.27
3302 3802 0.108424 CCAAAGGACGAGGCTGAGAG 60.108 60.000 0.00 0.00 0.00 3.20
3303 3803 0.108424 CAAAGGACGAGGCTGAGAGG 60.108 60.000 0.00 0.00 0.00 3.69
3304 3804 0.251832 AAAGGACGAGGCTGAGAGGA 60.252 55.000 0.00 0.00 0.00 3.71
3305 3805 0.251832 AAGGACGAGGCTGAGAGGAA 60.252 55.000 0.00 0.00 0.00 3.36
3306 3806 0.968393 AGGACGAGGCTGAGAGGAAC 60.968 60.000 0.00 0.00 0.00 3.62
3318 3818 3.192380 AGGAACTCCTCTCCCCGT 58.808 61.111 0.00 0.00 44.77 5.28
3319 3819 2.406687 AGGAACTCCTCTCCCCGTA 58.593 57.895 0.00 0.00 44.77 4.02
3380 3880 3.083997 CCGCCTAGCCCCTGTCTT 61.084 66.667 0.00 0.00 0.00 3.01
3385 3885 0.618968 CCTAGCCCCTGTCTTCCACT 60.619 60.000 0.00 0.00 0.00 4.00
3394 3894 0.787084 TGTCTTCCACTCCTCCTCCT 59.213 55.000 0.00 0.00 0.00 3.69
3458 4230 4.048470 GCGGCCCCCTTCTTCCTT 62.048 66.667 0.00 0.00 0.00 3.36
3465 4237 0.910088 CCCCTTCTTCCTTCCCTCGT 60.910 60.000 0.00 0.00 0.00 4.18
3472 4244 0.473117 TTCCTTCCCTCGTGGTTCCT 60.473 55.000 2.33 0.00 34.77 3.36
3474 4246 1.192146 CCTTCCCTCGTGGTTCCTCA 61.192 60.000 2.33 0.00 34.77 3.86
3475 4247 0.685097 CTTCCCTCGTGGTTCCTCAA 59.315 55.000 2.33 0.00 34.77 3.02
3480 4252 0.596577 CTCGTGGTTCCTCAACTCGA 59.403 55.000 0.00 0.00 36.91 4.04
3485 4257 1.289380 GTTCCTCAACTCGAGCGGT 59.711 57.895 13.61 0.00 40.78 5.68
3489 4261 1.444553 CTCAACTCGAGCGGTGGTC 60.445 63.158 13.61 0.00 34.18 4.02
3516 4288 3.640407 GGTGCTCCTCAGTGGGCA 61.640 66.667 0.00 1.73 38.87 5.36
3541 4313 2.421739 GGTGTCTATCGGGCGCAT 59.578 61.111 10.83 0.00 0.00 4.73
3572 4417 0.109342 CCCAGATATGGGTCACCTGC 59.891 60.000 17.89 0.00 44.08 4.85
3573 4418 1.135094 CCAGATATGGGTCACCTGCT 58.865 55.000 0.00 0.00 37.76 4.24
3595 4872 2.359900 GCGTCACCATCCTTCTTGAAT 58.640 47.619 0.00 0.00 0.00 2.57
3623 4900 1.476477 GAGTACCTCTCCTCCGCTTT 58.524 55.000 0.00 0.00 37.22 3.51
3635 4912 0.896940 TCCGCTTTCCTCCGTGTACT 60.897 55.000 0.00 0.00 0.00 2.73
3693 4971 0.318784 GTCGTCGCAGTCCTTCTTGT 60.319 55.000 0.00 0.00 0.00 3.16
3708 4986 4.385825 CTTCTTGTAGGTGTTGCTTGGTA 58.614 43.478 0.00 0.00 0.00 3.25
3711 4989 1.413445 TGTAGGTGTTGCTTGGTACGT 59.587 47.619 0.00 0.00 0.00 3.57
3782 5064 0.717784 GCGGGTACTACAACTTTCGC 59.282 55.000 0.00 0.00 35.34 4.70
3784 5066 1.990563 CGGGTACTACAACTTTCGCTG 59.009 52.381 0.00 0.00 0.00 5.18
3797 5079 4.827087 CGCTGATCCGGTGCTGCT 62.827 66.667 19.42 0.00 0.00 4.24
3814 5096 3.441572 GCTGCTGGCATTTCTTTCTCTTA 59.558 43.478 0.00 0.00 41.35 2.10
3815 5097 4.097589 GCTGCTGGCATTTCTTTCTCTTAT 59.902 41.667 0.00 0.00 41.35 1.73
3817 5099 5.957798 TGCTGGCATTTCTTTCTCTTATTG 58.042 37.500 0.00 0.00 0.00 1.90
3840 5122 5.344665 TGTTCTCTTGTTTTTCTTTTGTGCG 59.655 36.000 0.00 0.00 0.00 5.34
3852 5134 2.200792 TTTGTGCGTGATTGTGTTGG 57.799 45.000 0.00 0.00 0.00 3.77
3853 5135 0.383590 TTGTGCGTGATTGTGTTGGG 59.616 50.000 0.00 0.00 0.00 4.12
3854 5136 1.285641 GTGCGTGATTGTGTTGGGG 59.714 57.895 0.00 0.00 0.00 4.96
3855 5137 2.258286 GCGTGATTGTGTTGGGGC 59.742 61.111 0.00 0.00 0.00 5.80
3856 5138 2.268076 GCGTGATTGTGTTGGGGCT 61.268 57.895 0.00 0.00 0.00 5.19
3857 5139 1.875963 CGTGATTGTGTTGGGGCTC 59.124 57.895 0.00 0.00 0.00 4.70
3858 5140 0.606401 CGTGATTGTGTTGGGGCTCT 60.606 55.000 0.00 0.00 0.00 4.09
3859 5141 1.620822 GTGATTGTGTTGGGGCTCTT 58.379 50.000 0.00 0.00 0.00 2.85
3860 5142 1.963515 GTGATTGTGTTGGGGCTCTTT 59.036 47.619 0.00 0.00 0.00 2.52
3861 5143 2.029918 GTGATTGTGTTGGGGCTCTTTC 60.030 50.000 0.00 0.00 0.00 2.62
3862 5144 2.158475 TGATTGTGTTGGGGCTCTTTCT 60.158 45.455 0.00 0.00 0.00 2.52
3863 5145 1.981256 TTGTGTTGGGGCTCTTTCTC 58.019 50.000 0.00 0.00 0.00 2.87
3864 5146 1.140312 TGTGTTGGGGCTCTTTCTCT 58.860 50.000 0.00 0.00 0.00 3.10
3865 5147 1.494721 TGTGTTGGGGCTCTTTCTCTT 59.505 47.619 0.00 0.00 0.00 2.85
3866 5148 2.708861 TGTGTTGGGGCTCTTTCTCTTA 59.291 45.455 0.00 0.00 0.00 2.10
3867 5149 3.330701 TGTGTTGGGGCTCTTTCTCTTAT 59.669 43.478 0.00 0.00 0.00 1.73
3868 5150 4.202567 TGTGTTGGGGCTCTTTCTCTTATT 60.203 41.667 0.00 0.00 0.00 1.40
3869 5151 4.767409 GTGTTGGGGCTCTTTCTCTTATTT 59.233 41.667 0.00 0.00 0.00 1.40
3870 5152 5.243954 GTGTTGGGGCTCTTTCTCTTATTTT 59.756 40.000 0.00 0.00 0.00 1.82
3871 5153 5.838521 TGTTGGGGCTCTTTCTCTTATTTTT 59.161 36.000 0.00 0.00 0.00 1.94
3872 5154 6.015434 TGTTGGGGCTCTTTCTCTTATTTTTC 60.015 38.462 0.00 0.00 0.00 2.29
3873 5155 5.892348 TGGGGCTCTTTCTCTTATTTTTCT 58.108 37.500 0.00 0.00 0.00 2.52
3874 5156 6.314917 TGGGGCTCTTTCTCTTATTTTTCTT 58.685 36.000 0.00 0.00 0.00 2.52
3875 5157 6.782494 TGGGGCTCTTTCTCTTATTTTTCTTT 59.218 34.615 0.00 0.00 0.00 2.52
3876 5158 7.290014 TGGGGCTCTTTCTCTTATTTTTCTTTT 59.710 33.333 0.00 0.00 0.00 2.27
3877 5159 7.600375 GGGGCTCTTTCTCTTATTTTTCTTTTG 59.400 37.037 0.00 0.00 0.00 2.44
3878 5160 8.144478 GGGCTCTTTCTCTTATTTTTCTTTTGT 58.856 33.333 0.00 0.00 0.00 2.83
3879 5161 9.534565 GGCTCTTTCTCTTATTTTTCTTTTGTT 57.465 29.630 0.00 0.00 0.00 2.83
3892 5174 7.828685 TTTTCTTTTGTTTTTCTTTTGTGCG 57.171 28.000 0.00 0.00 0.00 5.34
3893 5175 6.532365 TTCTTTTGTTTTTCTTTTGTGCGT 57.468 29.167 0.00 0.00 0.00 5.24
3894 5176 7.639162 TTCTTTTGTTTTTCTTTTGTGCGTA 57.361 28.000 0.00 0.00 0.00 4.42
3895 5177 7.639162 TCTTTTGTTTTTCTTTTGTGCGTAA 57.361 28.000 0.00 0.00 0.00 3.18
3896 5178 8.245701 TCTTTTGTTTTTCTTTTGTGCGTAAT 57.754 26.923 0.00 0.00 0.00 1.89
3897 5179 8.713271 TCTTTTGTTTTTCTTTTGTGCGTAATT 58.287 25.926 0.00 0.00 0.00 1.40
3898 5180 8.647035 TTTTGTTTTTCTTTTGTGCGTAATTG 57.353 26.923 0.00 0.00 0.00 2.32
3899 5181 6.952935 TGTTTTTCTTTTGTGCGTAATTGT 57.047 29.167 0.00 0.00 0.00 2.71
3900 5182 6.756176 TGTTTTTCTTTTGTGCGTAATTGTG 58.244 32.000 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.230508 TGCACGCAACTACTACTAGCTT 59.769 45.455 0.00 0.00 0.00 3.74
20 21 1.918609 GTGCACGCAACTACTACTAGC 59.081 52.381 0.00 0.00 0.00 3.42
21 22 3.172050 CTGTGCACGCAACTACTACTAG 58.828 50.000 13.13 0.00 0.00 2.57
22 23 2.555325 ACTGTGCACGCAACTACTACTA 59.445 45.455 13.13 0.00 0.00 1.82
23 24 1.340248 ACTGTGCACGCAACTACTACT 59.660 47.619 13.13 0.00 0.00 2.57
24 25 1.779569 ACTGTGCACGCAACTACTAC 58.220 50.000 13.13 0.00 0.00 2.73
239 242 2.944129 ACAAGGTGCAGGAAAGCTTTA 58.056 42.857 12.68 0.00 33.24 1.85
240 243 1.780503 ACAAGGTGCAGGAAAGCTTT 58.219 45.000 12.53 12.53 33.24 3.51
245 248 2.942804 TCATGAACAAGGTGCAGGAAA 58.057 42.857 0.00 0.00 28.30 3.13
271 274 3.716601 AGCTGCGCAAATTAAACAAACT 58.283 36.364 13.05 0.00 0.00 2.66
375 378 9.013490 CAAATGTTACTTGTTATTAGCATGAGC 57.987 33.333 0.00 0.00 42.56 4.26
424 430 5.064558 CAGCCTCTGCAAGATAGAATTCAT 58.935 41.667 8.44 0.00 45.62 2.57
433 439 0.252479 CTGGACAGCCTCTGCAAGAT 59.748 55.000 0.00 0.00 45.62 2.40
483 489 1.971167 TGGGCTCAATTGTGGTCGC 60.971 57.895 5.13 0.87 0.00 5.19
585 599 1.589716 GATTGCTTCAGGCGCCTTGT 61.590 55.000 30.60 2.44 45.43 3.16
622 636 3.548014 GGGTGACACAAACAACATTCTCG 60.548 47.826 8.08 0.00 0.00 4.04
714 730 1.401931 CGAAATTGGCTGCAGACTTGG 60.402 52.381 22.80 4.24 0.00 3.61
747 877 8.251750 GATTTTAAAAGGCCAGTAAAATCCAC 57.748 34.615 27.90 16.08 42.78 4.02
760 890 1.797713 GCGCGGAGGATTTTAAAAGGC 60.798 52.381 8.83 1.33 0.00 4.35
765 895 0.746563 CCCAGCGCGGAGGATTTTAA 60.747 55.000 17.96 0.00 36.56 1.52
802 933 4.295119 ACGGGCCAGTCACACGTC 62.295 66.667 4.39 0.00 31.39 4.34
817 954 3.377172 ACCACCACTCTTTTTCTTTCACG 59.623 43.478 0.00 0.00 0.00 4.35
824 961 3.142174 CCAGAGACCACCACTCTTTTTC 58.858 50.000 0.00 0.00 41.94 2.29
868 1005 0.245539 CCGCCGTTCTTTCTAGTCCA 59.754 55.000 0.00 0.00 0.00 4.02
891 1028 1.210413 CTCGTCTCGACAGGTGGTG 59.790 63.158 0.00 0.00 0.00 4.17
956 1093 0.320858 GCTATAAGAAGCGGGAGGGC 60.321 60.000 0.00 0.00 31.76 5.19
964 1108 1.140252 TGGAACCCCGCTATAAGAAGC 59.860 52.381 0.00 0.00 39.21 3.86
966 1110 2.994186 GTGGAACCCCGCTATAAGAA 57.006 50.000 0.00 0.00 39.82 2.52
978 1122 2.813908 CTGGCGCGTAGTGGAACC 60.814 66.667 8.43 0.00 37.80 3.62
979 1123 3.488090 GCTGGCGCGTAGTGGAAC 61.488 66.667 8.43 0.00 39.19 3.62
1034 1178 4.351054 AGGGCAACAGGAAGCGGG 62.351 66.667 0.00 0.00 39.74 6.13
1193 1350 4.328712 GGTGGCAGTACAACAAACAAAAAG 59.671 41.667 0.00 0.00 0.00 2.27
1215 1372 5.556382 GCAATCGTCAAACAGTCATATACGG 60.556 44.000 0.00 0.00 0.00 4.02
1220 1377 3.125146 GCAGCAATCGTCAAACAGTCATA 59.875 43.478 0.00 0.00 0.00 2.15
1267 1426 1.025113 GGCTTAAACTCGAGGGTGCC 61.025 60.000 18.41 17.44 0.00 5.01
1299 1458 0.463654 TCCAAACGTGCAACTCAGCT 60.464 50.000 0.00 0.00 34.99 4.24
1300 1459 0.317020 GTCCAAACGTGCAACTCAGC 60.317 55.000 0.00 0.00 31.75 4.26
1301 1460 1.261619 GAGTCCAAACGTGCAACTCAG 59.738 52.381 12.92 0.00 36.64 3.35
1302 1461 1.295792 GAGTCCAAACGTGCAACTCA 58.704 50.000 12.92 0.00 36.64 3.41
1303 1462 0.232303 CGAGTCCAAACGTGCAACTC 59.768 55.000 9.41 9.41 34.81 3.01
1381 1551 4.937201 TCATAATCGCTCTCCTTTAGCA 57.063 40.909 0.00 0.00 40.08 3.49
1433 1603 0.320374 TAGCTGGACCAAGTTCACCG 59.680 55.000 0.00 0.00 0.00 4.94
1482 1692 2.223711 ACGAATTTTCAGCACCAACCAC 60.224 45.455 0.00 0.00 0.00 4.16
1483 1693 2.028130 ACGAATTTTCAGCACCAACCA 58.972 42.857 0.00 0.00 0.00 3.67
1502 1712 6.237969 GCTTGCAGAAGATAGCTAACACTAAC 60.238 42.308 0.00 0.00 0.00 2.34
1503 1713 5.812642 GCTTGCAGAAGATAGCTAACACTAA 59.187 40.000 0.00 0.00 0.00 2.24
1561 1772 4.889409 CCTGCATAACATGGTTAGGTTCAT 59.111 41.667 0.00 0.00 32.39 2.57
1572 1783 4.034858 CAGACAAGCTACCTGCATAACATG 59.965 45.833 0.00 0.00 45.94 3.21
1576 1787 3.981071 ACAGACAAGCTACCTGCATAA 57.019 42.857 9.12 0.00 45.94 1.90
1578 1789 2.430465 CAACAGACAAGCTACCTGCAT 58.570 47.619 9.12 0.00 45.94 3.96
1581 1792 1.802960 CTGCAACAGACAAGCTACCTG 59.197 52.381 7.99 7.99 32.44 4.00
1591 1802 5.948992 AATTCCTAGTTTCTGCAACAGAC 57.051 39.130 0.00 0.00 40.46 3.51
1621 1832 8.625651 GCCCTTTACCAAAATAAAATGTTTGTT 58.374 29.630 0.00 0.00 33.71 2.83
1664 1875 2.108168 GAGTAAATTGCCCTTTCCCCC 58.892 52.381 0.00 0.00 0.00 5.40
1665 1876 2.108168 GGAGTAAATTGCCCTTTCCCC 58.892 52.381 0.00 0.00 0.00 4.81
1666 1877 3.101643 AGGAGTAAATTGCCCTTTCCC 57.898 47.619 0.00 0.00 0.00 3.97
1667 1878 3.632604 GCTAGGAGTAAATTGCCCTTTCC 59.367 47.826 0.00 0.00 0.00 3.13
1668 1879 4.270008 TGCTAGGAGTAAATTGCCCTTTC 58.730 43.478 0.00 0.00 0.00 2.62
1677 1888 3.555956 CGTCGCATTTGCTAGGAGTAAAT 59.444 43.478 0.51 0.00 40.38 1.40
1688 1899 1.534028 CATAACACCGTCGCATTTGC 58.466 50.000 0.00 0.00 37.78 3.68
1699 1910 9.964303 TTCATTACATTGATATTGCATAACACC 57.036 29.630 0.00 0.00 0.00 4.16
1729 1940 4.567959 TGCCAGAAATATATGATGATCGCG 59.432 41.667 0.00 0.00 0.00 5.87
1747 1958 4.275689 TCACTAAAACATTCAGTGTGCCAG 59.724 41.667 0.00 0.00 41.14 4.85
1754 1965 6.639632 ATGTGCTTCACTAAAACATTCAGT 57.360 33.333 0.00 0.00 35.11 3.41
1755 1966 9.282247 GAATATGTGCTTCACTAAAACATTCAG 57.718 33.333 0.00 0.00 35.11 3.02
1799 2020 4.403432 TCATAGGTAAACTCCGGTACTTGG 59.597 45.833 0.00 0.00 0.00 3.61
1804 2025 3.205056 TCCCTCATAGGTAAACTCCGGTA 59.795 47.826 0.00 0.00 31.93 4.02
1807 2028 4.831155 TGTATCCCTCATAGGTAAACTCCG 59.169 45.833 0.00 0.00 31.93 4.63
1867 2266 2.499289 TCTTCTCCAGTGATCCTTCAGC 59.501 50.000 0.00 0.00 30.85 4.26
1935 2334 5.116180 TCCATAACTTCTGCCACTTTATCG 58.884 41.667 0.00 0.00 0.00 2.92
2006 2405 2.289072 CCAATAGGCATAGGACTGTCGG 60.289 54.545 0.00 0.00 31.78 4.79
2007 2406 2.365617 ACCAATAGGCATAGGACTGTCG 59.634 50.000 0.00 0.00 39.06 4.35
2089 2488 2.433662 TGCATGCCTGGCTGTAAATA 57.566 45.000 21.03 0.00 0.00 1.40
2142 2541 2.028658 AGTGACAGTGTATCAGGCTGTG 60.029 50.000 15.27 6.69 42.71 3.66
2169 2572 7.057894 TGGACAAAGTTGTATTTGAAGGTACT 58.942 34.615 6.22 0.00 42.43 2.73
2170 2573 7.266922 TGGACAAAGTTGTATTTGAAGGTAC 57.733 36.000 6.22 0.00 42.43 3.34
2171 2574 7.558444 AGTTGGACAAAGTTGTATTTGAAGGTA 59.442 33.333 6.22 0.00 42.43 3.08
2172 2575 6.379988 AGTTGGACAAAGTTGTATTTGAAGGT 59.620 34.615 6.22 0.00 42.43 3.50
2173 2576 6.697019 CAGTTGGACAAAGTTGTATTTGAAGG 59.303 38.462 6.22 0.00 42.43 3.46
2175 2578 7.338196 TCTCAGTTGGACAAAGTTGTATTTGAA 59.662 33.333 6.22 0.00 42.43 2.69
2177 2580 7.026631 TCTCAGTTGGACAAAGTTGTATTTG 57.973 36.000 0.00 0.00 42.43 2.32
2178 2581 7.823745 ATCTCAGTTGGACAAAGTTGTATTT 57.176 32.000 0.00 0.00 42.43 1.40
2180 2583 7.823745 AAATCTCAGTTGGACAAAGTTGTAT 57.176 32.000 0.00 0.00 42.43 2.29
2181 2584 7.122055 ACAAAATCTCAGTTGGACAAAGTTGTA 59.878 33.333 0.00 0.00 42.43 2.41
2200 2635 2.819608 TGGCAGCAGTTAGGACAAAATC 59.180 45.455 0.00 0.00 0.00 2.17
2210 2647 1.001974 ACACGAAGATGGCAGCAGTTA 59.998 47.619 5.19 0.00 0.00 2.24
2215 2652 1.599542 GGAATACACGAAGATGGCAGC 59.400 52.381 0.00 0.00 0.00 5.25
2230 2667 7.512746 AAGTAACCACTGCCTATGATAGGAATA 59.487 37.037 22.31 6.54 40.93 1.75
2241 2679 3.678056 CAGTCAAGTAACCACTGCCTA 57.322 47.619 0.00 0.00 34.36 3.93
2251 2689 2.687425 TGCAAAGCAAGCAGTCAAGTAA 59.313 40.909 0.00 0.00 37.02 2.24
2266 2704 1.133025 GGTCCGACCATCATTGCAAAG 59.867 52.381 13.05 0.00 38.42 2.77
2326 2764 5.510671 ACATTTTCAGTAGAAGCAACAACG 58.489 37.500 0.00 0.00 34.71 4.10
2331 2769 5.333035 CGTTCGACATTTTCAGTAGAAGCAA 60.333 40.000 0.00 0.00 32.56 3.91
2338 2776 3.985279 CACTCCGTTCGACATTTTCAGTA 59.015 43.478 0.00 0.00 0.00 2.74
2375 2813 6.550854 TGAAAAGAAAGTGAACCATCCTTCAT 59.449 34.615 0.00 0.00 32.78 2.57
2416 2854 6.353404 TCAACAGACCATAGTACATCAACA 57.647 37.500 0.00 0.00 0.00 3.33
2421 2859 3.774766 TGGCTCAACAGACCATAGTACAT 59.225 43.478 0.00 0.00 0.00 2.29
2433 2871 5.823209 TGATGTATTGAATGGCTCAACAG 57.177 39.130 0.00 0.00 46.80 3.16
2483 2922 5.010282 ACCAACTAAAGTTTGGAGGCTATG 58.990 41.667 5.91 0.00 35.83 2.23
2492 2931 5.278315 GGCTAGACCAACCAACTAAAGTTTG 60.278 44.000 0.00 0.00 38.86 2.93
2497 2936 2.369532 ACGGCTAGACCAACCAACTAAA 59.630 45.455 0.00 0.00 39.03 1.85
2503 2942 1.272313 ACTAGACGGCTAGACCAACCA 60.272 52.381 31.97 0.00 45.71 3.67
2504 2943 1.404748 GACTAGACGGCTAGACCAACC 59.595 57.143 31.97 9.15 45.71 3.77
2506 2945 2.502142 TGACTAGACGGCTAGACCAA 57.498 50.000 31.97 8.02 45.71 3.67
2508 2947 5.708877 AAATATGACTAGACGGCTAGACC 57.291 43.478 31.97 21.18 45.71 3.85
2532 2971 9.371136 GCATATCCAAATATGACTATCGAGAAA 57.629 33.333 9.11 0.00 45.16 2.52
2533 2972 8.753133 AGCATATCCAAATATGACTATCGAGAA 58.247 33.333 9.11 0.00 45.16 2.87
2534 2973 8.298729 AGCATATCCAAATATGACTATCGAGA 57.701 34.615 9.11 0.00 45.16 4.04
2535 2974 8.193438 TGAGCATATCCAAATATGACTATCGAG 58.807 37.037 9.11 0.00 45.16 4.04
2536 2975 8.066612 TGAGCATATCCAAATATGACTATCGA 57.933 34.615 9.11 0.00 45.16 3.59
2537 2976 8.883954 ATGAGCATATCCAAATATGACTATCG 57.116 34.615 9.11 0.00 45.16 2.92
2540 2979 9.551734 GCATATGAGCATATCCAAATATGACTA 57.448 33.333 6.97 0.00 45.16 2.59
2541 2980 8.050930 TGCATATGAGCATATCCAAATATGACT 58.949 33.333 6.97 6.03 45.16 3.41
2542 2981 8.217131 TGCATATGAGCATATCCAAATATGAC 57.783 34.615 6.97 3.87 45.16 3.06
2557 2996 8.429493 TGCTTTATGATAGTATGCATATGAGC 57.571 34.615 10.16 8.47 37.22 4.26
2605 3044 7.736447 ATAAGACAACTTAAGCTCCATATGC 57.264 36.000 1.29 0.00 41.15 3.14
2609 3048 5.945784 TGCAATAAGACAACTTAAGCTCCAT 59.054 36.000 1.29 0.00 41.15 3.41
2628 3068 6.425721 CCATCTGTTGTTTTGAGAATTGCAAT 59.574 34.615 5.99 5.99 0.00 3.56
2645 3085 0.407139 AGCCAAGCCTTCCATCTGTT 59.593 50.000 0.00 0.00 0.00 3.16
2774 3214 1.195115 GGTCCTGAGAGTATGTGCCA 58.805 55.000 0.00 0.00 0.00 4.92
2804 3244 4.717629 CCGTCGGCGCTCTTGTCA 62.718 66.667 2.51 0.00 36.67 3.58
2920 3360 8.551205 CACTCACATATATACACACACATTTCC 58.449 37.037 0.00 0.00 0.00 3.13
2921 3361 8.064222 GCACTCACATATATACACACACATTTC 58.936 37.037 0.00 0.00 0.00 2.17
2949 3389 5.220931 GCCACATTGGTAGACAAAGATCATC 60.221 44.000 0.00 0.00 43.46 2.92
2985 3425 8.588290 AGCATTATACAAAACCAAACCATCTA 57.412 30.769 0.00 0.00 0.00 1.98
3099 3545 6.971602 TGAACTTAAACCGCAACAAATCATA 58.028 32.000 0.00 0.00 0.00 2.15
3109 3555 2.875933 CCTGAACTGAACTTAAACCGCA 59.124 45.455 0.00 0.00 0.00 5.69
3141 3587 3.937706 CTGCATCTTCATCTCGGAAGTTT 59.062 43.478 0.00 0.00 43.72 2.66
3147 3593 1.880271 ATGCTGCATCTTCATCTCGG 58.120 50.000 9.81 0.00 0.00 4.63
3148 3594 4.093115 GGATAATGCTGCATCTTCATCTCG 59.907 45.833 16.55 0.00 0.00 4.04
3154 3600 4.639334 TGAGAGGATAATGCTGCATCTTC 58.361 43.478 16.55 14.66 0.00 2.87
3185 3631 6.138967 TGGTCAGATAAAGATGATGAGAGGA 58.861 40.000 0.00 0.00 0.00 3.71
3231 3731 0.399233 GTCTCTAGGGCCCATCACCT 60.399 60.000 27.56 3.89 40.89 4.00
3233 3733 1.749334 CGGTCTCTAGGGCCCATCAC 61.749 65.000 27.56 12.59 0.00 3.06
3244 3744 1.747709 CGGAAGGACTTCGGTCTCTA 58.252 55.000 10.42 0.00 43.94 2.43
3252 3752 3.982576 TTTTCAAAGCGGAAGGACTTC 57.017 42.857 3.48 3.48 38.80 3.01
3267 3767 0.829602 TTGGAAGCCCGGCATTTTCA 60.830 50.000 13.15 0.00 34.29 2.69
3268 3768 0.320050 TTTGGAAGCCCGGCATTTTC 59.680 50.000 13.15 6.76 34.29 2.29
3273 3773 3.575247 TCCTTTGGAAGCCCGGCA 61.575 61.111 13.15 0.00 34.29 5.69
3274 3774 3.062466 GTCCTTTGGAAGCCCGGC 61.062 66.667 0.00 0.00 31.38 6.13
3275 3775 2.746277 CGTCCTTTGGAAGCCCGG 60.746 66.667 0.00 0.00 31.38 5.73
3277 3777 1.377333 CCTCGTCCTTTGGAAGCCC 60.377 63.158 0.00 0.00 31.38 5.19
3280 3780 0.321671 TCAGCCTCGTCCTTTGGAAG 59.678 55.000 0.00 0.00 31.38 3.46
3281 3781 0.321671 CTCAGCCTCGTCCTTTGGAA 59.678 55.000 0.00 0.00 31.38 3.53
3282 3782 0.541998 TCTCAGCCTCGTCCTTTGGA 60.542 55.000 0.00 0.00 0.00 3.53
3283 3783 0.108424 CTCTCAGCCTCGTCCTTTGG 60.108 60.000 0.00 0.00 0.00 3.28
3284 3784 0.108424 CCTCTCAGCCTCGTCCTTTG 60.108 60.000 0.00 0.00 0.00 2.77
3285 3785 0.251832 TCCTCTCAGCCTCGTCCTTT 60.252 55.000 0.00 0.00 0.00 3.11
3286 3786 0.251832 TTCCTCTCAGCCTCGTCCTT 60.252 55.000 0.00 0.00 0.00 3.36
3287 3787 0.968393 GTTCCTCTCAGCCTCGTCCT 60.968 60.000 0.00 0.00 0.00 3.85
3288 3788 0.968393 AGTTCCTCTCAGCCTCGTCC 60.968 60.000 0.00 0.00 0.00 4.79
3289 3789 0.454196 GAGTTCCTCTCAGCCTCGTC 59.546 60.000 0.00 0.00 42.34 4.20
3290 3790 0.968393 GGAGTTCCTCTCAGCCTCGT 60.968 60.000 0.00 0.00 44.40 4.18
3291 3791 0.682855 AGGAGTTCCTCTCAGCCTCG 60.683 60.000 0.00 0.00 44.77 4.63
3292 3792 3.298320 AGGAGTTCCTCTCAGCCTC 57.702 57.895 0.00 0.00 44.77 4.70
3302 3802 1.042003 GGTACGGGGAGAGGAGTTCC 61.042 65.000 0.00 0.00 0.00 3.62
3303 3803 1.042003 GGGTACGGGGAGAGGAGTTC 61.042 65.000 0.00 0.00 0.00 3.01
3304 3804 1.001376 GGGTACGGGGAGAGGAGTT 59.999 63.158 0.00 0.00 0.00 3.01
3305 3805 2.688538 GGGTACGGGGAGAGGAGT 59.311 66.667 0.00 0.00 0.00 3.85
3306 3806 2.123382 GGGGTACGGGGAGAGGAG 60.123 72.222 0.00 0.00 0.00 3.69
3307 3807 3.759101 GGGGGTACGGGGAGAGGA 61.759 72.222 0.00 0.00 0.00 3.71
3368 3868 0.617820 GGAGTGGAAGACAGGGGCTA 60.618 60.000 0.00 0.00 0.00 3.93
3375 3875 0.787084 AGGAGGAGGAGTGGAAGACA 59.213 55.000 0.00 0.00 0.00 3.41
3376 3876 1.190643 CAGGAGGAGGAGTGGAAGAC 58.809 60.000 0.00 0.00 0.00 3.01
3377 3877 0.616111 GCAGGAGGAGGAGTGGAAGA 60.616 60.000 0.00 0.00 0.00 2.87
3380 3880 2.039624 GGCAGGAGGAGGAGTGGA 59.960 66.667 0.00 0.00 0.00 4.02
3385 3885 4.704103 ACAGCGGCAGGAGGAGGA 62.704 66.667 1.45 0.00 0.00 3.71
3448 4220 0.250513 CCACGAGGGAAGGAAGAAGG 59.749 60.000 0.00 0.00 40.01 3.46
3453 4225 0.473117 AGGAACCACGAGGGAAGGAA 60.473 55.000 3.29 0.00 41.15 3.36
3456 4228 0.685097 TTGAGGAACCACGAGGGAAG 59.315 55.000 3.29 0.00 41.15 3.46
3457 4229 0.395312 GTTGAGGAACCACGAGGGAA 59.605 55.000 3.29 0.00 41.15 3.97
3458 4230 0.471211 AGTTGAGGAACCACGAGGGA 60.471 55.000 3.29 0.00 41.15 4.20
3465 4237 1.289066 CGCTCGAGTTGAGGAACCA 59.711 57.895 15.13 0.00 45.38 3.67
3472 4244 1.863662 GAGACCACCGCTCGAGTTGA 61.864 60.000 15.13 0.00 0.00 3.18
3474 4246 2.637383 GGAGACCACCGCTCGAGTT 61.637 63.158 15.13 0.00 33.19 3.01
3475 4247 3.063084 GGAGACCACCGCTCGAGT 61.063 66.667 15.13 0.00 33.19 4.18
3504 4276 3.640407 GGCACTGCCCACTGAGGA 61.640 66.667 9.13 0.00 44.06 3.71
3516 4288 2.423898 CGATAGACACCGGGGCACT 61.424 63.158 1.73 6.40 39.76 4.40
3578 4855 2.726821 GCCATTCAAGAAGGATGGTGA 58.273 47.619 4.45 0.00 34.99 4.02
3584 4861 0.391130 CCGACGCCATTCAAGAAGGA 60.391 55.000 0.00 0.00 0.00 3.36
3615 4892 0.458025 GTACACGGAGGAAAGCGGAG 60.458 60.000 0.00 0.00 0.00 4.63
3616 4893 0.896940 AGTACACGGAGGAAAGCGGA 60.897 55.000 0.00 0.00 0.00 5.54
3623 4900 0.406750 TTCTCCCAGTACACGGAGGA 59.593 55.000 21.72 14.43 44.99 3.71
3635 4912 5.279306 CCGACGAATCCTATAATTTCTCCCA 60.279 44.000 0.00 0.00 0.00 4.37
3645 4922 0.601558 GCTGCCCGACGAATCCTATA 59.398 55.000 0.00 0.00 0.00 1.31
3646 4923 1.367840 GCTGCCCGACGAATCCTAT 59.632 57.895 0.00 0.00 0.00 2.57
3693 4971 1.270412 CCACGTACCAAGCAACACCTA 60.270 52.381 0.00 0.00 0.00 3.08
3708 4986 4.796231 GCCATCGAGTCGCCACGT 62.796 66.667 7.92 0.00 0.00 4.49
3711 4989 1.815003 CAATGCCATCGAGTCGCCA 60.815 57.895 7.92 2.65 0.00 5.69
3768 5049 3.428452 CCGGATCAGCGAAAGTTGTAGTA 60.428 47.826 0.00 0.00 43.35 1.82
3769 5050 2.607187 CGGATCAGCGAAAGTTGTAGT 58.393 47.619 0.00 0.00 43.35 2.73
3770 5051 1.927174 CCGGATCAGCGAAAGTTGTAG 59.073 52.381 0.00 0.00 43.35 2.74
3771 5052 1.274167 ACCGGATCAGCGAAAGTTGTA 59.726 47.619 9.46 0.00 43.35 2.41
3772 5053 0.034896 ACCGGATCAGCGAAAGTTGT 59.965 50.000 9.46 0.00 43.35 3.32
3782 5064 2.513204 CCAGCAGCACCGGATCAG 60.513 66.667 9.46 0.00 0.00 2.90
3797 5079 7.667219 AGAGAACAATAAGAGAAAGAAATGCCA 59.333 33.333 0.00 0.00 0.00 4.92
3814 5096 7.411804 CGCACAAAAGAAAAACAAGAGAACAAT 60.412 33.333 0.00 0.00 0.00 2.71
3815 5097 6.128956 CGCACAAAAGAAAAACAAGAGAACAA 60.129 34.615 0.00 0.00 0.00 2.83
3817 5099 5.344933 ACGCACAAAAGAAAAACAAGAGAAC 59.655 36.000 0.00 0.00 0.00 3.01
3837 5119 2.560119 GCCCCAACACAATCACGCA 61.560 57.895 0.00 0.00 0.00 5.24
3840 5122 1.620822 AAGAGCCCCAACACAATCAC 58.379 50.000 0.00 0.00 0.00 3.06
3852 5134 8.144478 ACAAAAGAAAAATAAGAGAAAGAGCCC 58.856 33.333 0.00 0.00 0.00 5.19
3853 5135 9.534565 AACAAAAGAAAAATAAGAGAAAGAGCC 57.465 29.630 0.00 0.00 0.00 4.70
3866 5148 8.900762 CGCACAAAAGAAAAACAAAAGAAAAAT 58.099 25.926 0.00 0.00 0.00 1.82
3867 5149 7.910683 ACGCACAAAAGAAAAACAAAAGAAAAA 59.089 25.926 0.00 0.00 0.00 1.94
3868 5150 7.410485 ACGCACAAAAGAAAAACAAAAGAAAA 58.590 26.923 0.00 0.00 0.00 2.29
3869 5151 6.949449 ACGCACAAAAGAAAAACAAAAGAAA 58.051 28.000 0.00 0.00 0.00 2.52
3870 5152 6.532365 ACGCACAAAAGAAAAACAAAAGAA 57.468 29.167 0.00 0.00 0.00 2.52
3871 5153 7.639162 TTACGCACAAAAGAAAAACAAAAGA 57.361 28.000 0.00 0.00 0.00 2.52
3872 5154 8.774967 CAATTACGCACAAAAGAAAAACAAAAG 58.225 29.630 0.00 0.00 0.00 2.27
3873 5155 8.283291 ACAATTACGCACAAAAGAAAAACAAAA 58.717 25.926 0.00 0.00 0.00 2.44
3874 5156 7.742089 CACAATTACGCACAAAAGAAAAACAAA 59.258 29.630 0.00 0.00 0.00 2.83
3875 5157 7.230222 CACAATTACGCACAAAAGAAAAACAA 58.770 30.769 0.00 0.00 0.00 2.83
3876 5158 6.756176 CACAATTACGCACAAAAGAAAAACA 58.244 32.000 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.