Multiple sequence alignment - TraesCS2B01G096300

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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 TraesCS2B01G096300 chr2B 100.000 4325 0 0 1 4325 56521161 56525485 0.000000e+00 7987.0
1 TraesCS2B01G096300 chr2B 90.909 99 9 0 2954 3052 56606146 56606244 2.710000e-27 134.0
2 TraesCS2B01G096300 chr2B 88.462 104 4 3 3614 3717 56623917 56624012 7.600000e-23 119.0
3 TraesCS2B01G096300 chr2A 89.052 3060 175 48 746 3717 37089052 37092039 0.000000e+00 3648.0
4 TraesCS2B01G096300 chr2A 88.725 541 26 8 5 539 37088250 37088761 2.840000e-176 628.0
5 TraesCS2B01G096300 chr2A 88.372 344 24 8 3957 4285 469785923 469786265 2.420000e-107 399.0
6 TraesCS2B01G096300 chr2A 79.792 480 51 24 1037 1485 760016393 760015929 1.510000e-79 307.0
7 TraesCS2B01G096300 chr2A 92.593 216 8 2 3732 3946 469785674 469785882 1.950000e-78 303.0
8 TraesCS2B01G096300 chr2A 97.368 38 1 0 4286 4323 469786298 469786335 1.000000e-06 65.8
9 TraesCS2B01G096300 chr2D 88.644 3135 163 62 681 3717 34231866 34234905 0.000000e+00 3639.0
10 TraesCS2B01G096300 chr2D 89.982 549 20 10 5 543 34231263 34231786 0.000000e+00 676.0
11 TraesCS2B01G096300 chr7D 78.285 548 60 32 988 1501 450003554 450003032 9.090000e-77 298.0
12 TraesCS2B01G096300 chr1A 80.601 366 32 22 1029 1368 582061056 582060704 3.340000e-61 246.0
13 TraesCS2B01G096300 chr1A 86.842 152 11 6 996 1138 364020295 364020144 1.240000e-35 161.0
14 TraesCS2B01G096300 chr1A 88.710 124 11 1 996 1116 11442088 11441965 9.690000e-32 148.0
15 TraesCS2B01G096300 chr6A 79.778 361 42 20 1029 1368 15396905 15397255 2.600000e-57 233.0
16 TraesCS2B01G096300 chr4D 86.730 211 10 6 996 1188 434801290 434801500 7.280000e-53 219.0
17 TraesCS2B01G096300 chrUn 84.906 212 19 2 2954 3165 348369257 348369059 7.330000e-48 202.0
18 TraesCS2B01G096300 chrUn 85.167 209 18 2 2954 3162 358923323 358923518 7.330000e-48 202.0
19 TraesCS2B01G096300 chrUn 84.906 212 19 2 2954 3165 404533609 404533411 7.330000e-48 202.0
20 TraesCS2B01G096300 chrUn 85.167 209 18 2 2954 3162 457757428 457757623 7.330000e-48 202.0
21 TraesCS2B01G096300 chrUn 88.462 104 4 3 3614 3717 217883430 217883525 7.600000e-23 119.0
22 TraesCS2B01G096300 chrUn 88.462 104 4 3 3614 3717 340507733 340507828 7.600000e-23 119.0
23 TraesCS2B01G096300 chrUn 87.387 111 4 4 3614 3722 340698577 340698475 7.600000e-23 119.0
24 TraesCS2B01G096300 chrUn 87.387 111 4 4 3614 3722 340701110 340701008 7.600000e-23 119.0
25 TraesCS2B01G096300 chrUn 87.387 111 4 4 3614 3722 392834572 392834470 7.600000e-23 119.0
26 TraesCS2B01G096300 chr6B 92.857 140 7 2 996 1135 442429670 442429534 2.640000e-47 200.0
27 TraesCS2B01G096300 chr4A 88.043 92 7 2 1241 1332 193109016 193108929 5.920000e-19 106.0


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 TraesCS2B01G096300 chr2B 56521161 56525485 4324 False 7987.000000 7987 100.000000 1 4325 1 chr2B.!!$F1 4324
1 TraesCS2B01G096300 chr2A 37088250 37092039 3789 False 2138.000000 3648 88.888500 5 3717 2 chr2A.!!$F1 3712
2 TraesCS2B01G096300 chr2A 469785674 469786335 661 False 255.933333 399 92.777667 3732 4323 3 chr2A.!!$F2 591
3 TraesCS2B01G096300 chr2D 34231263 34234905 3642 False 2157.500000 3639 89.313000 5 3717 2 chr2D.!!$F1 3712
4 TraesCS2B01G096300 chr7D 450003032 450003554 522 True 298.000000 298 78.285000 988 1501 1 chr7D.!!$R1 513

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
640 720 0.039437 GTCGACCGAGACTCAGCAAA 60.039 55.0 3.51 0.0 38.09 3.68 F
1386 1688 0.108520 TCGCATACCAGGTCCGTTTC 60.109 55.0 0.00 0.0 0.00 2.78 F
1782 2096 0.099791 AGGTTTTGTGCACGGTTTCG 59.900 50.0 13.13 0.0 43.02 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1648 1958 0.391597 ACGACACATGTCCCGAAACT 59.608 50.000 19.47 0.0 41.86 2.66 R
3123 3442 1.000938 GCCATTGATGCCTCGAAATCC 60.001 52.381 0.00 0.0 0.00 3.01 R
3588 3939 0.534203 GCCGACCAACACTTCTCCAA 60.534 55.000 0.00 0.0 0.00 3.53 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
28 29 1.097232 TTTTGCAGGATGAGGATGCG 58.903 50.000 0.00 0.00 42.92 4.73
175 177 5.147330 AGAGTAAATCCATGTGTGTCGAA 57.853 39.130 0.00 0.00 0.00 3.71
270 278 9.439500 AAGAAGAAGAAGATCATGAAGAAGAAG 57.561 33.333 0.00 0.00 0.00 2.85
271 279 8.814931 AGAAGAAGAAGATCATGAAGAAGAAGA 58.185 33.333 0.00 0.00 0.00 2.87
272 280 9.434420 GAAGAAGAAGATCATGAAGAAGAAGAA 57.566 33.333 0.00 0.00 0.00 2.52
288 314 6.822676 AGAAGAAGAAGAGCAATAAGGATGTG 59.177 38.462 0.00 0.00 0.00 3.21
289 315 6.059787 AGAAGAAGAGCAATAAGGATGTGT 57.940 37.500 0.00 0.00 0.00 3.72
292 318 4.946157 AGAAGAGCAATAAGGATGTGTTGG 59.054 41.667 0.00 0.00 0.00 3.77
293 319 3.019564 AGAGCAATAAGGATGTGTTGGC 58.980 45.455 0.00 0.00 0.00 4.52
294 320 2.099756 GAGCAATAAGGATGTGTTGGCC 59.900 50.000 0.00 0.00 0.00 5.36
295 321 2.102578 GCAATAAGGATGTGTTGGCCT 58.897 47.619 3.32 0.00 0.00 5.19
296 322 2.159198 GCAATAAGGATGTGTTGGCCTG 60.159 50.000 3.32 0.00 31.06 4.85
297 323 1.767759 ATAAGGATGTGTTGGCCTGC 58.232 50.000 3.32 0.00 31.06 4.85
298 324 0.698238 TAAGGATGTGTTGGCCTGCT 59.302 50.000 3.32 0.00 31.06 4.24
299 325 0.896940 AAGGATGTGTTGGCCTGCTG 60.897 55.000 3.32 0.00 31.06 4.41
300 326 2.570181 GATGTGTTGGCCTGCTGC 59.430 61.111 3.32 0.00 40.16 5.25
301 327 3.332493 GATGTGTTGGCCTGCTGCG 62.332 63.158 3.32 0.00 42.61 5.18
311 337 2.827190 CTGCTGCGGCCATGTCAT 60.827 61.111 16.57 0.00 37.74 3.06
312 338 3.120979 CTGCTGCGGCCATGTCATG 62.121 63.158 16.57 5.79 37.74 3.07
313 339 3.136123 GCTGCGGCCATGTCATGT 61.136 61.111 6.12 0.00 0.00 3.21
314 340 2.795973 CTGCGGCCATGTCATGTG 59.204 61.111 11.84 4.75 0.00 3.21
315 341 2.033911 TGCGGCCATGTCATGTGT 59.966 55.556 11.84 0.00 0.00 3.72
316 342 1.588824 CTGCGGCCATGTCATGTGTT 61.589 55.000 11.84 0.00 0.00 3.32
317 343 0.322008 TGCGGCCATGTCATGTGTTA 60.322 50.000 11.84 0.00 0.00 2.41
318 344 0.808125 GCGGCCATGTCATGTGTTAA 59.192 50.000 11.84 0.00 0.00 2.01
326 352 5.801947 GCCATGTCATGTGTTAATTTGTCTC 59.198 40.000 11.84 0.00 0.00 3.36
454 483 2.890945 AGTTCCTTTCCGGTTGAATTGG 59.109 45.455 0.00 0.00 31.67 3.16
511 540 0.962356 CTCATTTGGCCGTGGAGCTT 60.962 55.000 0.00 0.00 0.00 3.74
524 553 4.381612 CCGTGGAGCTTATCTCAGTGTTTA 60.382 45.833 0.00 0.00 43.70 2.01
557 596 2.159014 TGTCGTGGCTAGTTCTGTGTTT 60.159 45.455 0.00 0.00 0.00 2.83
558 597 3.068448 TGTCGTGGCTAGTTCTGTGTTTA 59.932 43.478 0.00 0.00 0.00 2.01
559 598 4.243270 GTCGTGGCTAGTTCTGTGTTTAT 58.757 43.478 0.00 0.00 0.00 1.40
560 599 4.689345 GTCGTGGCTAGTTCTGTGTTTATT 59.311 41.667 0.00 0.00 0.00 1.40
561 600 4.927425 TCGTGGCTAGTTCTGTGTTTATTC 59.073 41.667 0.00 0.00 0.00 1.75
562 601 4.929808 CGTGGCTAGTTCTGTGTTTATTCT 59.070 41.667 0.00 0.00 0.00 2.40
563 602 5.408604 CGTGGCTAGTTCTGTGTTTATTCTT 59.591 40.000 0.00 0.00 0.00 2.52
577 657 5.471797 TGTTTATTCTTTTGATCTCCACGCA 59.528 36.000 0.00 0.00 0.00 5.24
581 661 3.942829 TCTTTTGATCTCCACGCAAGAT 58.057 40.909 0.00 0.00 43.62 2.40
598 678 7.533222 CACGCAAGATCAAAAGAATATAGCATC 59.467 37.037 0.00 0.00 43.62 3.91
599 679 6.735510 CGCAAGATCAAAAGAATATAGCATCG 59.264 38.462 0.00 0.00 43.02 3.84
601 681 8.449397 GCAAGATCAAAAGAATATAGCATCGAT 58.551 33.333 0.00 0.00 0.00 3.59
606 686 6.808704 TCAAAAGAATATAGCATCGATCGAGG 59.191 38.462 24.45 24.45 0.00 4.63
620 700 3.802139 CGATCGAGGCATAAGCAAGTTTA 59.198 43.478 10.26 0.00 44.61 2.01
621 701 4.084849 CGATCGAGGCATAAGCAAGTTTAG 60.085 45.833 10.26 0.00 44.61 1.85
622 702 4.202245 TCGAGGCATAAGCAAGTTTAGT 57.798 40.909 0.00 0.00 44.61 2.24
623 703 4.181578 TCGAGGCATAAGCAAGTTTAGTC 58.818 43.478 0.00 0.00 44.61 2.59
624 704 3.000322 CGAGGCATAAGCAAGTTTAGTCG 60.000 47.826 0.00 0.00 44.61 4.18
625 705 4.181578 GAGGCATAAGCAAGTTTAGTCGA 58.818 43.478 0.00 0.00 44.61 4.20
626 706 3.933332 AGGCATAAGCAAGTTTAGTCGAC 59.067 43.478 7.70 7.70 44.61 4.20
627 707 3.063588 GGCATAAGCAAGTTTAGTCGACC 59.936 47.826 13.01 0.00 44.61 4.79
628 708 3.241995 GCATAAGCAAGTTTAGTCGACCG 60.242 47.826 13.01 0.00 41.58 4.79
629 709 2.806608 AAGCAAGTTTAGTCGACCGA 57.193 45.000 13.01 0.00 0.00 4.69
630 710 2.349297 AGCAAGTTTAGTCGACCGAG 57.651 50.000 13.01 0.00 0.00 4.63
631 711 1.884579 AGCAAGTTTAGTCGACCGAGA 59.115 47.619 13.01 0.00 0.00 4.04
632 712 1.984297 GCAAGTTTAGTCGACCGAGAC 59.016 52.381 13.01 6.29 41.23 3.36
638 718 3.264947 GTCGACCGAGACTCAGCA 58.735 61.111 3.51 0.00 38.09 4.41
639 719 1.579932 GTCGACCGAGACTCAGCAA 59.420 57.895 3.51 0.00 38.09 3.91
640 720 0.039437 GTCGACCGAGACTCAGCAAA 60.039 55.000 3.51 0.00 38.09 3.68
641 721 0.671796 TCGACCGAGACTCAGCAAAA 59.328 50.000 2.82 0.00 0.00 2.44
642 722 0.784778 CGACCGAGACTCAGCAAAAC 59.215 55.000 2.82 0.00 0.00 2.43
643 723 1.603172 CGACCGAGACTCAGCAAAACT 60.603 52.381 2.82 0.00 0.00 2.66
671 751 2.975410 ATGTGTCATCGTTTGCTGTG 57.025 45.000 0.00 0.00 0.00 3.66
727 933 3.364441 GTGCATCGTGGCAGGCAA 61.364 61.111 0.00 0.00 45.96 4.52
733 939 3.376078 CGTGGCAGGCAAGGCAAT 61.376 61.111 0.00 0.00 46.19 3.56
734 940 2.045708 CGTGGCAGGCAAGGCAATA 61.046 57.895 0.00 0.00 46.19 1.90
735 941 1.811860 GTGGCAGGCAAGGCAATAG 59.188 57.895 0.00 0.00 46.19 1.73
736 942 2.053865 TGGCAGGCAAGGCAATAGC 61.054 57.895 0.00 0.00 41.47 2.97
762 968 1.758862 GTAGTGCATACGTACCCCCTT 59.241 52.381 0.00 0.00 0.00 3.95
816 1022 8.540492 CAAATATCTTTTGCTGATCTTGCATTC 58.460 33.333 13.14 0.00 40.34 2.67
818 1024 5.654603 TCTTTTGCTGATCTTGCATTCAT 57.345 34.783 13.14 0.00 40.34 2.57
821 1027 7.200455 TCTTTTGCTGATCTTGCATTCATATG 58.800 34.615 13.14 0.00 40.34 1.78
893 1099 1.532078 GGAAGGGCCGGAAAACCAA 60.532 57.895 5.05 0.00 0.00 3.67
912 1142 4.075793 TCCCTCCCTCCACTCCGG 62.076 72.222 0.00 0.00 0.00 5.14
1229 1515 2.355126 CATCGCGCTGCCTCGTAT 60.355 61.111 5.56 0.00 0.00 3.06
1276 1578 2.087095 CTCGCTGCGCTTCTGTATGC 62.087 60.000 18.65 0.00 0.00 3.14
1279 1581 1.220529 GCTGCGCTTCTGTATGCATA 58.779 50.000 9.73 1.16 36.64 3.14
1284 1586 4.631131 TGCGCTTCTGTATGCATATAAGT 58.369 39.130 10.16 0.00 31.31 2.24
1298 1600 7.987268 TGCATATAAGTATATAAGCGTGCTC 57.013 36.000 0.00 0.00 40.10 4.26
1386 1688 0.108520 TCGCATACCAGGTCCGTTTC 60.109 55.000 0.00 0.00 0.00 2.78
1405 1707 3.662759 TCCTCTCCTCCTCTCTTCTTC 57.337 52.381 0.00 0.00 0.00 2.87
1406 1708 3.197983 TCCTCTCCTCCTCTCTTCTTCT 58.802 50.000 0.00 0.00 0.00 2.85
1407 1709 3.596046 TCCTCTCCTCCTCTCTTCTTCTT 59.404 47.826 0.00 0.00 0.00 2.52
1412 1714 4.349365 TCCTCCTCTCTTCTTCTTCTTCC 58.651 47.826 0.00 0.00 0.00 3.46
1431 1741 1.204312 GAGAAAACACTGACGGCGC 59.796 57.895 6.90 0.00 0.00 6.53
1474 1784 3.414700 GCAACGCCACTCTGACCG 61.415 66.667 0.00 0.00 0.00 4.79
1488 1798 1.153349 GACCGACCAATCTCAGGGC 60.153 63.158 0.00 0.00 0.00 5.19
1591 1901 1.132500 CTTCCAGGTACCATCCCTCC 58.868 60.000 15.94 0.00 0.00 4.30
1592 1902 0.689745 TTCCAGGTACCATCCCTCCG 60.690 60.000 15.94 0.00 0.00 4.63
1593 1903 2.808206 CCAGGTACCATCCCTCCGC 61.808 68.421 15.94 0.00 0.00 5.54
1594 1904 2.446036 AGGTACCATCCCTCCGCC 60.446 66.667 15.94 0.00 0.00 6.13
1595 1905 2.766651 GGTACCATCCCTCCGCCA 60.767 66.667 7.15 0.00 0.00 5.69
1596 1906 2.147387 GGTACCATCCCTCCGCCAT 61.147 63.158 7.15 0.00 0.00 4.40
1599 1909 2.613576 TACCATCCCTCCGCCATCCA 62.614 60.000 0.00 0.00 0.00 3.41
1644 1954 2.552591 CCTGATCCTCTCCAATCCATGC 60.553 54.545 0.00 0.00 0.00 4.06
1648 1958 0.256752 CCTCTCCAATCCATGCCACA 59.743 55.000 0.00 0.00 0.00 4.17
1666 1976 0.790207 CAGTTTCGGGACATGTGTCG 59.210 55.000 1.15 7.11 45.65 4.35
1669 1979 1.723003 GTTTCGGGACATGTGTCGTAC 59.277 52.381 1.15 6.42 45.65 3.67
1670 1980 1.250328 TTCGGGACATGTGTCGTACT 58.750 50.000 1.15 0.00 45.65 2.73
1671 1981 2.112380 TCGGGACATGTGTCGTACTA 57.888 50.000 1.15 0.00 45.65 1.82
1672 1982 2.011947 TCGGGACATGTGTCGTACTAG 58.988 52.381 1.15 0.00 45.65 2.57
1673 1983 1.741706 CGGGACATGTGTCGTACTAGT 59.258 52.381 1.15 0.00 45.65 2.57
1674 1984 2.938451 CGGGACATGTGTCGTACTAGTA 59.062 50.000 1.15 0.00 45.65 1.82
1675 1985 3.002042 CGGGACATGTGTCGTACTAGTAG 59.998 52.174 1.15 0.00 45.65 2.57
1676 1986 3.944015 GGGACATGTGTCGTACTAGTAGT 59.056 47.826 1.15 8.14 45.65 2.73
1677 1987 5.118990 GGGACATGTGTCGTACTAGTAGTA 58.881 45.833 1.15 5.90 45.65 1.82
1689 1999 6.484308 TCGTACTAGTAGTATATTGCAGTGCA 59.516 38.462 15.37 15.37 32.65 4.57
1713 2023 1.486310 ACCATCACAGTATGCACCGAT 59.514 47.619 0.00 0.00 42.53 4.18
1725 2035 5.928839 AGTATGCACCGATTGATATCTTGTC 59.071 40.000 3.98 0.00 0.00 3.18
1726 2036 4.406648 TGCACCGATTGATATCTTGTCT 57.593 40.909 3.98 0.00 0.00 3.41
1744 2058 8.589335 TCTTGTCTAAATTAGCACCGATTATC 57.411 34.615 0.00 0.00 0.00 1.75
1758 2072 4.040461 ACCGATTATCACCATAGGAACCAG 59.960 45.833 0.00 0.00 0.00 4.00
1782 2096 0.099791 AGGTTTTGTGCACGGTTTCG 59.900 50.000 13.13 0.00 43.02 3.46
1796 2110 0.660300 GTTTCGGCGAGCTGGTTTTG 60.660 55.000 10.46 0.00 0.00 2.44
1799 2114 1.019278 TCGGCGAGCTGGTTTTGATC 61.019 55.000 4.99 0.00 0.00 2.92
1825 2141 0.471617 CCCCTAGTTGATCTGCCAGG 59.528 60.000 0.00 0.00 0.00 4.45
1839 2155 2.202797 CAGGCATCGACCGTCAGG 60.203 66.667 0.00 0.00 45.13 3.86
1855 2171 5.465051 CCGTCAGGTAGTGATATGATCTTG 58.535 45.833 0.00 0.00 37.56 3.02
1856 2172 5.010112 CCGTCAGGTAGTGATATGATCTTGT 59.990 44.000 0.00 0.00 37.56 3.16
1947 2263 1.261619 GGCAGCATACATCGCAACTAC 59.738 52.381 0.00 0.00 0.00 2.73
1965 2281 2.586792 GACCTCCTGCTTCGCCAT 59.413 61.111 0.00 0.00 0.00 4.40
2064 2380 2.191375 CGGAGTGCCATGAGCCAT 59.809 61.111 0.00 0.00 42.71 4.40
2082 2398 1.065854 CATCCTCAGGTGAGTTGGACC 60.066 57.143 6.25 0.00 40.48 4.46
2093 2409 3.071479 TGAGTTGGACCGTTTTATCAGC 58.929 45.455 0.00 0.00 0.00 4.26
2132 2448 7.946207 TGTTTGATTCACCTGTTTAAATGCTA 58.054 30.769 0.00 0.00 0.00 3.49
2133 2449 8.081633 TGTTTGATTCACCTGTTTAAATGCTAG 58.918 33.333 0.00 0.00 0.00 3.42
2134 2450 6.194796 TGATTCACCTGTTTAAATGCTAGC 57.805 37.500 8.10 8.10 0.00 3.42
2135 2451 5.945784 TGATTCACCTGTTTAAATGCTAGCT 59.054 36.000 17.23 0.00 0.00 3.32
2136 2452 5.627499 TTCACCTGTTTAAATGCTAGCTG 57.373 39.130 17.23 0.88 0.00 4.24
2137 2453 4.651778 TCACCTGTTTAAATGCTAGCTGT 58.348 39.130 17.23 1.42 0.00 4.40
2139 2455 5.181245 TCACCTGTTTAAATGCTAGCTGTTC 59.819 40.000 17.23 1.07 0.00 3.18
2140 2456 4.459337 ACCTGTTTAAATGCTAGCTGTTCC 59.541 41.667 17.23 3.01 0.00 3.62
2141 2457 4.702131 CCTGTTTAAATGCTAGCTGTTCCT 59.298 41.667 17.23 0.13 0.00 3.36
2143 2459 6.294731 CCTGTTTAAATGCTAGCTGTTCCTTT 60.295 38.462 17.23 8.35 0.00 3.11
2144 2460 6.677913 TGTTTAAATGCTAGCTGTTCCTTTC 58.322 36.000 17.23 0.20 0.00 2.62
2145 2461 6.490040 TGTTTAAATGCTAGCTGTTCCTTTCT 59.510 34.615 17.23 0.00 0.00 2.52
2146 2462 7.014230 TGTTTAAATGCTAGCTGTTCCTTTCTT 59.986 33.333 17.23 0.00 0.00 2.52
2147 2463 8.512138 GTTTAAATGCTAGCTGTTCCTTTCTTA 58.488 33.333 17.23 0.00 0.00 2.10
2197 2513 1.369689 GCAAACACTGACGCAGCTG 60.370 57.895 10.11 10.11 34.37 4.24
2278 2594 2.721274 TGATGGCATTGTTTGGTTCG 57.279 45.000 0.00 0.00 0.00 3.95
2315 2631 5.880332 TCACTTCTTTGTCTTTGTTAGCAGT 59.120 36.000 0.00 0.00 0.00 4.40
2322 2638 7.551262 TCTTTGTCTTTGTTAGCAGTAGTTTCA 59.449 33.333 0.00 0.00 0.00 2.69
2423 2741 1.106351 TGCCGTTGCCAGTTCATTGT 61.106 50.000 0.00 0.00 36.33 2.71
2476 2794 9.778741 CTTGCAGAAAATATCCAGGTATAACTA 57.221 33.333 0.00 0.00 0.00 2.24
2611 2929 0.620556 AACCCATCATTCCTCGCACT 59.379 50.000 0.00 0.00 0.00 4.40
2991 3310 1.126846 CGCCGCTGAAGTAAGAACAAG 59.873 52.381 0.00 0.00 0.00 3.16
3026 3345 2.979813 GTTTCATTTAACAGCGCACAGG 59.020 45.455 11.47 0.00 0.00 4.00
3045 3364 1.508632 GTTGAGCTGCACGGAAACTA 58.491 50.000 1.02 0.00 0.00 2.24
3052 3371 4.261801 AGCTGCACGGAAACTATATTGTT 58.738 39.130 1.02 0.00 0.00 2.83
3053 3372 4.094887 AGCTGCACGGAAACTATATTGTTG 59.905 41.667 1.02 0.00 0.00 3.33
3054 3373 4.094294 GCTGCACGGAAACTATATTGTTGA 59.906 41.667 3.24 0.00 0.00 3.18
3055 3374 5.727791 GCTGCACGGAAACTATATTGTTGAG 60.728 44.000 3.24 1.73 0.00 3.02
3056 3375 4.094294 TGCACGGAAACTATATTGTTGAGC 59.906 41.667 3.24 3.11 0.00 4.26
3057 3376 4.332819 GCACGGAAACTATATTGTTGAGCT 59.667 41.667 3.24 0.00 0.00 4.09
3058 3377 5.727791 GCACGGAAACTATATTGTTGAGCTG 60.728 44.000 3.24 4.72 0.00 4.24
3059 3378 4.332819 ACGGAAACTATATTGTTGAGCTGC 59.667 41.667 3.24 0.00 0.00 5.25
3060 3379 4.332543 CGGAAACTATATTGTTGAGCTGCA 59.667 41.667 1.02 0.00 0.00 4.41
3061 3380 5.573146 GGAAACTATATTGTTGAGCTGCAC 58.427 41.667 1.02 0.00 0.00 4.57
3062 3381 4.864916 AACTATATTGTTGAGCTGCACG 57.135 40.909 1.02 0.00 0.00 5.34
3063 3382 3.198068 ACTATATTGTTGAGCTGCACGG 58.802 45.455 1.02 0.00 0.00 4.94
3064 3383 2.401583 ATATTGTTGAGCTGCACGGA 57.598 45.000 1.02 0.00 0.00 4.69
3065 3384 1.725641 TATTGTTGAGCTGCACGGAG 58.274 50.000 1.02 0.00 0.00 4.63
3120 3439 4.466726 AGGCACTTCGACTACCTTTTCTAT 59.533 41.667 0.00 0.00 27.25 1.98
3123 3442 5.062308 GCACTTCGACTACCTTTTCTATGTG 59.938 44.000 0.00 0.00 0.00 3.21
3190 3509 6.764560 TCTGAGTAACTTAAAGGTGTGGTTTC 59.235 38.462 0.00 0.00 0.00 2.78
3223 3549 1.071699 GGTCTGGTGGTTAAGTGAGCA 59.928 52.381 0.00 0.00 0.00 4.26
3270 3597 5.529014 TTTTGTTTTTGCAGCAAGAGTTC 57.471 34.783 8.12 0.04 0.00 3.01
3328 3655 0.392706 TGTCACCGAAGCATGAGTGT 59.607 50.000 0.00 0.00 0.00 3.55
3542 3893 5.297547 TCGACATATGTATCTCTTTTGCCC 58.702 41.667 8.71 0.00 0.00 5.36
3561 3912 0.501854 CGAGAGCTCGCGAAATGATG 59.498 55.000 32.56 2.07 46.50 3.07
3571 3922 3.380004 TCGCGAAATGATGGGCTTTTATT 59.620 39.130 6.20 0.00 0.00 1.40
3575 3926 7.041030 TCGCGAAATGATGGGCTTTTATTATTA 60.041 33.333 6.20 0.00 0.00 0.98
3583 3934 9.739276 TGATGGGCTTTTATTATTATAGGAGTG 57.261 33.333 0.00 0.00 0.00 3.51
3588 3939 9.067986 GGCTTTTATTATTATAGGAGTGCTTGT 57.932 33.333 0.00 0.00 0.00 3.16
3596 3947 2.557920 AGGAGTGCTTGTTGGAGAAG 57.442 50.000 0.00 0.00 0.00 2.85
3597 3948 1.771255 AGGAGTGCTTGTTGGAGAAGT 59.229 47.619 0.00 0.00 0.00 3.01
3604 3957 2.033424 GCTTGTTGGAGAAGTGTTGGTC 59.967 50.000 0.00 0.00 0.00 4.02
3607 3960 0.534203 TTGGAGAAGTGTTGGTCGGC 60.534 55.000 0.00 0.00 0.00 5.54
3654 4007 7.334421 TGGTGATAGTTTAAAGTCTCAAGCATC 59.666 37.037 11.48 3.56 0.00 3.91
3680 4033 7.346751 AGTGTGATGTTTATGTTTGAGGTTT 57.653 32.000 0.00 0.00 0.00 3.27
3682 4035 7.285401 AGTGTGATGTTTATGTTTGAGGTTTCT 59.715 33.333 0.00 0.00 0.00 2.52
3683 4036 8.564574 GTGTGATGTTTATGTTTGAGGTTTCTA 58.435 33.333 0.00 0.00 0.00 2.10
3684 4037 9.295825 TGTGATGTTTATGTTTGAGGTTTCTAT 57.704 29.630 0.00 0.00 0.00 1.98
3689 4042 8.736244 TGTTTATGTTTGAGGTTTCTATAAGCC 58.264 33.333 0.00 0.00 36.27 4.35
3717 4070 4.177026 TGCGTGTGTTATTTGCAAAGTTT 58.823 34.783 18.19 3.42 31.69 2.66
3718 4071 4.627467 TGCGTGTGTTATTTGCAAAGTTTT 59.373 33.333 18.19 3.03 31.69 2.43
3719 4072 5.120830 TGCGTGTGTTATTTGCAAAGTTTTT 59.879 32.000 18.19 2.63 31.69 1.94
3779 4132 6.831769 ACATCGTTTATGACATCTGAAACAC 58.168 36.000 11.14 0.00 39.07 3.32
3785 4138 8.708742 CGTTTATGACATCTGAAACACTAAAGA 58.291 33.333 11.14 0.00 32.49 2.52
3855 4208 2.006888 TCTAGCTAAATTGTGCGCCAC 58.993 47.619 4.18 3.72 34.56 5.01
3856 4209 1.064060 CTAGCTAAATTGTGCGCCACC 59.936 52.381 4.18 0.00 32.73 4.61
3857 4210 0.893270 AGCTAAATTGTGCGCCACCA 60.893 50.000 4.18 0.00 32.73 4.17
3858 4211 0.038709 GCTAAATTGTGCGCCACCAA 60.039 50.000 4.18 5.76 32.73 3.67
3859 4212 1.696988 CTAAATTGTGCGCCACCAAC 58.303 50.000 4.18 0.00 32.73 3.77
3860 4213 0.315568 TAAATTGTGCGCCACCAACC 59.684 50.000 4.18 0.00 32.73 3.77
3861 4214 2.691674 AAATTGTGCGCCACCAACCG 62.692 55.000 4.18 0.00 32.73 4.44
3878 4231 2.625823 CGCCATGTTTGCTTCCCGT 61.626 57.895 0.00 0.00 0.00 5.28
3886 4239 3.971150 TGTTTGCTTCCCGTTTACAATG 58.029 40.909 0.00 0.00 0.00 2.82
3912 4266 7.912250 GCTCAAAGAGATTGTACCAATACATTG 59.088 37.037 0.00 0.00 41.02 2.82
3946 4300 2.219458 CATTCTGCAAGGATCGCTGAT 58.781 47.619 0.00 0.00 37.22 2.90
3948 4302 1.945387 TCTGCAAGGATCGCTGATTC 58.055 50.000 0.00 0.00 33.09 2.52
3949 4303 0.942962 CTGCAAGGATCGCTGATTCC 59.057 55.000 0.00 0.00 0.00 3.01
3950 4304 0.252761 TGCAAGGATCGCTGATTCCA 59.747 50.000 0.00 0.00 0.00 3.53
3951 4305 1.134007 TGCAAGGATCGCTGATTCCAT 60.134 47.619 0.00 0.00 0.00 3.41
3952 4306 2.104622 TGCAAGGATCGCTGATTCCATA 59.895 45.455 0.00 0.00 0.00 2.74
3953 4307 3.141398 GCAAGGATCGCTGATTCCATAA 58.859 45.455 0.00 0.00 0.00 1.90
3955 4309 4.217118 GCAAGGATCGCTGATTCCATAATT 59.783 41.667 0.00 0.00 0.00 1.40
3957 4311 6.621596 GCAAGGATCGCTGATTCCATAATTAC 60.622 42.308 0.00 0.00 0.00 1.89
3958 4312 6.365970 AGGATCGCTGATTCCATAATTACT 57.634 37.500 0.00 0.00 0.00 2.24
3988 4371 9.206690 TCAAGAGAGTCTGATTCCATAATTACT 57.793 33.333 0.00 0.00 0.00 2.24
4067 4465 7.096312 CGTTAAACAAGTGACTAAGAGGTGTAC 60.096 40.741 0.00 0.00 0.00 2.90
4072 4470 5.968528 AGTGACTAAGAGGTGTACAAGAG 57.031 43.478 0.00 0.00 0.00 2.85
4081 4479 0.727398 GTGTACAAGAGCCCGCAATC 59.273 55.000 0.00 0.00 0.00 2.67
4101 4499 1.846782 CGCTTCTCCAAGATCGTTACG 59.153 52.381 0.00 0.00 0.00 3.18
4102 4500 2.194271 GCTTCTCCAAGATCGTTACGG 58.806 52.381 4.53 0.00 0.00 4.02
4133 4531 1.153349 GCACCTCCCGTTCCATCTC 60.153 63.158 0.00 0.00 0.00 2.75
4159 4557 6.541278 CCAAGAAAGATGCATCTACATTCAGA 59.459 38.462 28.66 0.00 35.76 3.27
4195 4593 0.532115 GGGGCTTGCACCAACTTATG 59.468 55.000 9.30 0.00 0.00 1.90
4197 4595 1.202348 GGGCTTGCACCAACTTATGTC 59.798 52.381 0.00 0.00 0.00 3.06
4218 4616 3.264193 TCATGTGGGATAGCTTTGTGACT 59.736 43.478 0.00 0.00 0.00 3.41
4232 4630 1.135141 TGTGACTTGCAGCACCAAAAC 60.135 47.619 0.00 0.00 34.19 2.43
4244 4642 5.458779 GCAGCACCAAAACTACTTGTTAAAG 59.541 40.000 0.00 0.00 38.03 1.85
4261 4659 5.477984 TGTTAAAGCCTGAATTCTGAATGCT 59.522 36.000 13.45 10.51 0.00 3.79
4265 4663 2.223203 GCCTGAATTCTGAATGCTGACG 60.223 50.000 14.82 2.99 0.00 4.35
4315 4745 5.888161 ACCAGGATCCAGTCACAATTAATTC 59.112 40.000 15.82 0.00 0.00 2.17
4323 4753 5.183713 CCAGTCACAATTAATTCCTTCAGCA 59.816 40.000 0.00 0.00 0.00 4.41
4324 4754 6.088824 CAGTCACAATTAATTCCTTCAGCAC 58.911 40.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.487762 TCATCCTGCAAAACCAATCGAC 59.512 45.455 0.00 0.00 0.00 4.20
1 2 2.749076 CTCATCCTGCAAAACCAATCGA 59.251 45.455 0.00 0.00 0.00 3.59
2 3 2.159338 CCTCATCCTGCAAAACCAATCG 60.159 50.000 0.00 0.00 0.00 3.34
3 4 3.091545 TCCTCATCCTGCAAAACCAATC 58.908 45.455 0.00 0.00 0.00 2.67
8 9 1.202222 CGCATCCTCATCCTGCAAAAC 60.202 52.381 0.00 0.00 35.64 2.43
28 29 2.404215 TCAGCGTAGTCAGCAAAGAAC 58.596 47.619 0.00 0.00 37.01 3.01
150 151 4.382040 CGACACACATGGATTTACTCTCCT 60.382 45.833 0.00 0.00 33.69 3.69
175 177 3.614870 GCCTCGCCAAATCTGAAAAACAT 60.615 43.478 0.00 0.00 0.00 2.71
235 243 8.610896 CATGATCTTCTTCTTCTTCATTACCAC 58.389 37.037 0.00 0.00 0.00 4.16
237 245 8.954950 TCATGATCTTCTTCTTCTTCATTACC 57.045 34.615 0.00 0.00 0.00 2.85
270 278 4.439289 GCCAACACATCCTTATTGCTCTTC 60.439 45.833 0.00 0.00 0.00 2.87
271 279 3.445096 GCCAACACATCCTTATTGCTCTT 59.555 43.478 0.00 0.00 0.00 2.85
272 280 3.019564 GCCAACACATCCTTATTGCTCT 58.980 45.455 0.00 0.00 0.00 4.09
294 320 2.827190 ATGACATGGCCGCAGCAG 60.827 61.111 0.00 0.00 42.56 4.24
295 321 3.135457 CATGACATGGCCGCAGCA 61.135 61.111 7.60 0.00 42.56 4.41
296 322 3.136123 ACATGACATGGCCGCAGC 61.136 61.111 19.39 0.00 38.76 5.25
297 323 1.588824 AACACATGACATGGCCGCAG 61.589 55.000 19.39 4.91 33.60 5.18
298 324 0.322008 TAACACATGACATGGCCGCA 60.322 50.000 19.39 0.00 33.60 5.69
299 325 0.808125 TTAACACATGACATGGCCGC 59.192 50.000 19.39 0.00 33.60 6.53
300 326 3.781079 AATTAACACATGACATGGCCG 57.219 42.857 19.39 9.78 33.60 6.13
301 327 4.819769 ACAAATTAACACATGACATGGCC 58.180 39.130 19.39 0.00 33.60 5.36
302 328 5.713025 AGACAAATTAACACATGACATGGC 58.287 37.500 19.39 0.00 33.60 4.40
303 329 6.023435 CGAGACAAATTAACACATGACATGG 58.977 40.000 19.39 10.68 33.60 3.66
304 330 6.738200 GTCGAGACAAATTAACACATGACATG 59.262 38.462 14.02 14.02 0.00 3.21
305 331 6.650807 AGTCGAGACAAATTAACACATGACAT 59.349 34.615 0.00 0.00 0.00 3.06
306 332 5.989168 AGTCGAGACAAATTAACACATGACA 59.011 36.000 0.00 0.00 0.00 3.58
307 333 6.467723 AGTCGAGACAAATTAACACATGAC 57.532 37.500 0.00 0.00 0.00 3.06
308 334 6.073276 CCAAGTCGAGACAAATTAACACATGA 60.073 38.462 0.00 0.00 0.00 3.07
309 335 6.073276 TCCAAGTCGAGACAAATTAACACATG 60.073 38.462 5.99 0.00 0.00 3.21
310 336 5.995282 TCCAAGTCGAGACAAATTAACACAT 59.005 36.000 5.99 0.00 0.00 3.21
311 337 5.361427 TCCAAGTCGAGACAAATTAACACA 58.639 37.500 5.99 0.00 0.00 3.72
312 338 5.917541 TCCAAGTCGAGACAAATTAACAC 57.082 39.130 5.99 0.00 0.00 3.32
313 339 8.092068 TCTAATCCAAGTCGAGACAAATTAACA 58.908 33.333 5.99 0.00 0.00 2.41
314 340 8.475331 TCTAATCCAAGTCGAGACAAATTAAC 57.525 34.615 5.99 0.00 0.00 2.01
315 341 9.098355 CATCTAATCCAAGTCGAGACAAATTAA 57.902 33.333 5.99 0.00 0.00 1.40
316 342 7.710907 CCATCTAATCCAAGTCGAGACAAATTA 59.289 37.037 5.99 3.65 0.00 1.40
317 343 6.540189 CCATCTAATCCAAGTCGAGACAAATT 59.460 38.462 5.99 2.78 0.00 1.82
318 344 6.051717 CCATCTAATCCAAGTCGAGACAAAT 58.948 40.000 5.99 0.00 0.00 2.32
326 352 2.545952 CCGACCCATCTAATCCAAGTCG 60.546 54.545 0.00 0.00 43.76 4.18
454 483 1.386533 TCGTCCTCGACAGGGAATAC 58.613 55.000 0.00 0.00 41.35 1.89
503 532 7.617041 AAATAAACACTGAGATAAGCTCCAC 57.383 36.000 0.00 0.00 43.26 4.02
505 534 8.613482 GGTAAAATAAACACTGAGATAAGCTCC 58.387 37.037 0.00 0.00 43.26 4.70
511 540 8.946085 CAAGCTGGTAAAATAAACACTGAGATA 58.054 33.333 0.00 0.00 0.00 1.98
524 553 1.539827 GCCACGACAAGCTGGTAAAAT 59.460 47.619 0.00 0.00 0.00 1.82
557 596 5.487433 TCTTGCGTGGAGATCAAAAGAATA 58.513 37.500 0.00 0.00 0.00 1.75
558 597 4.326826 TCTTGCGTGGAGATCAAAAGAAT 58.673 39.130 0.00 0.00 0.00 2.40
559 598 3.738982 TCTTGCGTGGAGATCAAAAGAA 58.261 40.909 0.00 0.00 0.00 2.52
560 599 3.401033 TCTTGCGTGGAGATCAAAAGA 57.599 42.857 0.00 0.00 0.00 2.52
561 600 4.270178 GATCTTGCGTGGAGATCAAAAG 57.730 45.455 15.34 0.00 45.63 2.27
571 651 6.138761 GCTATATTCTTTTGATCTTGCGTGG 58.861 40.000 0.00 0.00 0.00 4.94
577 657 8.867935 CGATCGATGCTATATTCTTTTGATCTT 58.132 33.333 10.26 0.00 0.00 2.40
581 661 6.808704 CCTCGATCGATGCTATATTCTTTTGA 59.191 38.462 19.78 0.00 0.00 2.69
586 666 3.696548 TGCCTCGATCGATGCTATATTCT 59.303 43.478 34.56 0.00 36.84 2.40
598 678 1.858091 ACTTGCTTATGCCTCGATCG 58.142 50.000 9.36 9.36 38.71 3.69
599 679 4.811557 ACTAAACTTGCTTATGCCTCGATC 59.188 41.667 0.00 0.00 38.71 3.69
601 681 4.181578 GACTAAACTTGCTTATGCCTCGA 58.818 43.478 0.00 0.00 38.71 4.04
606 686 3.241995 CGGTCGACTAAACTTGCTTATGC 60.242 47.826 16.46 0.00 40.20 3.14
620 700 0.889638 TTGCTGAGTCTCGGTCGACT 60.890 55.000 16.46 0.00 46.39 4.18
621 701 0.039437 TTTGCTGAGTCTCGGTCGAC 60.039 55.000 7.13 7.13 0.00 4.20
622 702 0.671796 TTTTGCTGAGTCTCGGTCGA 59.328 50.000 10.43 0.49 0.00 4.20
623 703 0.784778 GTTTTGCTGAGTCTCGGTCG 59.215 55.000 10.43 0.00 0.00 4.79
624 704 2.156343 AGTTTTGCTGAGTCTCGGTC 57.844 50.000 10.43 3.74 0.00 4.79
634 714 5.165676 ACACATAATGCATCAGTTTTGCTG 58.834 37.500 0.00 0.00 46.34 4.41
635 715 5.047872 TGACACATAATGCATCAGTTTTGCT 60.048 36.000 0.00 0.00 40.77 3.91
636 716 5.162794 TGACACATAATGCATCAGTTTTGC 58.837 37.500 0.00 0.00 40.55 3.68
637 717 6.195798 CGATGACACATAATGCATCAGTTTTG 59.804 38.462 0.00 0.00 39.69 2.44
638 718 6.127925 ACGATGACACATAATGCATCAGTTTT 60.128 34.615 0.00 0.00 39.69 2.43
639 719 5.355071 ACGATGACACATAATGCATCAGTTT 59.645 36.000 0.00 0.00 39.69 2.66
640 720 4.877823 ACGATGACACATAATGCATCAGTT 59.122 37.500 0.00 0.00 39.69 3.16
641 721 4.445453 ACGATGACACATAATGCATCAGT 58.555 39.130 0.00 0.00 39.69 3.41
642 722 5.413969 AACGATGACACATAATGCATCAG 57.586 39.130 0.00 0.00 39.69 2.90
643 723 5.571277 CAAACGATGACACATAATGCATCA 58.429 37.500 0.00 0.00 39.69 3.07
644 724 4.438797 GCAAACGATGACACATAATGCATC 59.561 41.667 0.00 0.00 37.95 3.91
645 725 4.096833 AGCAAACGATGACACATAATGCAT 59.903 37.500 0.00 0.00 33.89 3.96
646 726 3.439825 AGCAAACGATGACACATAATGCA 59.560 39.130 0.00 0.00 33.89 3.96
647 727 3.787634 CAGCAAACGATGACACATAATGC 59.212 43.478 0.00 0.00 0.00 3.56
648 728 4.789629 CACAGCAAACGATGACACATAATG 59.210 41.667 0.00 0.00 0.00 1.90
649 729 4.142622 CCACAGCAAACGATGACACATAAT 60.143 41.667 0.00 0.00 0.00 1.28
650 730 3.188254 CCACAGCAAACGATGACACATAA 59.812 43.478 0.00 0.00 0.00 1.90
651 731 2.741517 CCACAGCAAACGATGACACATA 59.258 45.455 0.00 0.00 0.00 2.29
652 732 1.536766 CCACAGCAAACGATGACACAT 59.463 47.619 0.00 0.00 0.00 3.21
656 736 1.210155 GCCCACAGCAAACGATGAC 59.790 57.895 0.00 0.00 42.97 3.06
733 939 1.875514 CGTATGCACTACTACCGGCTA 59.124 52.381 0.00 0.00 0.00 3.93
734 940 0.666913 CGTATGCACTACTACCGGCT 59.333 55.000 0.00 0.00 0.00 5.52
735 941 0.383231 ACGTATGCACTACTACCGGC 59.617 55.000 0.00 0.00 0.00 6.13
736 942 2.031682 GGTACGTATGCACTACTACCGG 60.032 54.545 0.00 0.00 30.94 5.28
737 943 2.031682 GGGTACGTATGCACTACTACCG 60.032 54.545 0.00 0.00 36.25 4.02
738 944 2.294512 GGGGTACGTATGCACTACTACC 59.705 54.545 0.00 16.07 35.51 3.18
739 945 2.294512 GGGGGTACGTATGCACTACTAC 59.705 54.545 0.00 0.00 0.00 2.73
740 946 2.175499 AGGGGGTACGTATGCACTACTA 59.825 50.000 0.00 0.00 0.00 1.82
745 951 1.758862 AGTAAGGGGGTACGTATGCAC 59.241 52.381 0.00 0.00 0.00 4.57
747 953 1.342496 GGAGTAAGGGGGTACGTATGC 59.658 57.143 0.00 0.00 0.00 3.14
803 1009 5.004448 AGCTCCATATGAATGCAAGATCAG 58.996 41.667 3.65 0.00 0.00 2.90
834 1040 6.653526 TGATTCGGCAATCATTAATTCCAT 57.346 33.333 7.85 0.00 42.99 3.41
849 1055 0.671251 TTGGTGTTTGGTGATTCGGC 59.329 50.000 0.00 0.00 0.00 5.54
893 1099 2.781406 GGAGTGGAGGGAGGGAGT 59.219 66.667 0.00 0.00 0.00 3.85
912 1142 4.943093 TGTTAAACTTATAAACGAGGGGGC 59.057 41.667 0.00 0.00 0.00 5.80
1229 1515 1.905843 CAAACAACCATCCCGGCCA 60.906 57.895 2.24 0.00 39.03 5.36
1276 1578 8.616377 AACGAGCACGCTTATATACTTATATG 57.384 34.615 2.62 0.00 43.96 1.78
1279 1581 7.326305 CAGAAACGAGCACGCTTATATACTTAT 59.674 37.037 2.62 0.00 43.96 1.73
1284 1586 5.177725 TCAGAAACGAGCACGCTTATATA 57.822 39.130 2.62 0.00 43.96 0.86
1298 1600 1.508088 GGCCCTGCATTCAGAAACG 59.492 57.895 0.00 0.00 42.95 3.60
1371 1673 2.108970 GAGAGGAAACGGACCTGGTAT 58.891 52.381 0.00 0.00 37.93 2.73
1386 1688 3.669939 AGAAGAAGAGAGGAGGAGAGG 57.330 52.381 0.00 0.00 0.00 3.69
1405 1707 3.182572 CGTCAGTGTTTTCTCGGAAGAAG 59.817 47.826 0.00 0.00 42.36 2.85
1406 1708 3.120792 CGTCAGTGTTTTCTCGGAAGAA 58.879 45.455 0.00 0.00 41.32 2.52
1407 1709 2.545113 CCGTCAGTGTTTTCTCGGAAGA 60.545 50.000 0.00 0.00 40.29 2.87
1412 1714 1.487231 CGCCGTCAGTGTTTTCTCG 59.513 57.895 0.00 0.00 0.00 4.04
1431 1741 3.060674 GCATCGTCGTCAGAATCATTCAG 60.061 47.826 0.00 0.00 0.00 3.02
1474 1784 1.452833 GGCAGCCCTGAGATTGGTC 60.453 63.158 0.00 0.00 0.00 4.02
1520 1830 2.764547 AGCTCGGGTAGGCCTTCC 60.765 66.667 19.90 19.90 34.45 3.46
1591 1901 1.171308 GGATTGATGGATGGATGGCG 58.829 55.000 0.00 0.00 0.00 5.69
1592 1902 1.891150 GTGGATTGATGGATGGATGGC 59.109 52.381 0.00 0.00 0.00 4.40
1593 1903 3.418995 GAGTGGATTGATGGATGGATGG 58.581 50.000 0.00 0.00 0.00 3.51
1594 1904 3.181437 TGGAGTGGATTGATGGATGGATG 60.181 47.826 0.00 0.00 0.00 3.51
1595 1905 3.058341 TGGAGTGGATTGATGGATGGAT 58.942 45.455 0.00 0.00 0.00 3.41
1596 1906 2.173356 GTGGAGTGGATTGATGGATGGA 59.827 50.000 0.00 0.00 0.00 3.41
1599 1909 2.422519 GCAGTGGAGTGGATTGATGGAT 60.423 50.000 0.00 0.00 0.00 3.41
1644 1954 0.874390 CACATGTCCCGAAACTGTGG 59.126 55.000 0.00 0.00 34.88 4.17
1648 1958 0.391597 ACGACACATGTCCCGAAACT 59.608 50.000 19.47 0.00 41.86 2.66
1666 1976 7.872881 TCTGCACTGCAATATACTACTAGTAC 58.127 38.462 4.99 0.00 38.41 2.73
1669 1979 7.169982 GGTTTCTGCACTGCAATATACTACTAG 59.830 40.741 4.99 0.00 38.41 2.57
1670 1980 6.984474 GGTTTCTGCACTGCAATATACTACTA 59.016 38.462 4.99 0.00 38.41 1.82
1671 1981 5.817816 GGTTTCTGCACTGCAATATACTACT 59.182 40.000 4.99 0.00 38.41 2.57
1672 1982 5.584649 TGGTTTCTGCACTGCAATATACTAC 59.415 40.000 4.99 0.00 38.41 2.73
1673 1983 5.739959 TGGTTTCTGCACTGCAATATACTA 58.260 37.500 4.99 0.00 38.41 1.82
1674 1984 4.588899 TGGTTTCTGCACTGCAATATACT 58.411 39.130 4.99 0.00 38.41 2.12
1675 1985 4.963276 TGGTTTCTGCACTGCAATATAC 57.037 40.909 4.99 2.27 38.41 1.47
1676 1986 5.066375 GTGATGGTTTCTGCACTGCAATATA 59.934 40.000 4.99 0.00 38.41 0.86
1677 1987 4.018490 TGATGGTTTCTGCACTGCAATAT 58.982 39.130 4.99 0.00 38.41 1.28
1689 1999 3.347216 GGTGCATACTGTGATGGTTTCT 58.653 45.455 0.00 0.00 0.00 2.52
1713 2023 8.201464 TCGGTGCTAATTTAGACAAGATATCAA 58.799 33.333 7.63 0.00 0.00 2.57
1725 2035 7.672983 ATGGTGATAATCGGTGCTAATTTAG 57.327 36.000 0.00 0.00 0.00 1.85
1726 2036 7.822334 CCTATGGTGATAATCGGTGCTAATTTA 59.178 37.037 0.00 0.00 0.00 1.40
1744 2058 2.086869 CTGTTGCTGGTTCCTATGGTG 58.913 52.381 0.00 0.00 0.00 4.17
1758 2072 1.145162 CCGTGCACAAAACCTGTTGC 61.145 55.000 18.64 0.00 35.47 4.17
1782 2096 0.449388 CAGATCAAAACCAGCTCGCC 59.551 55.000 0.00 0.00 0.00 5.54
1789 2103 2.176798 AGGGGTGTTCAGATCAAAACCA 59.823 45.455 7.30 0.00 0.00 3.67
1791 2105 4.652822 ACTAGGGGTGTTCAGATCAAAAC 58.347 43.478 0.00 0.00 0.00 2.43
1796 2110 4.407296 AGATCAACTAGGGGTGTTCAGATC 59.593 45.833 0.00 0.00 32.08 2.75
1799 2114 3.866651 CAGATCAACTAGGGGTGTTCAG 58.133 50.000 0.00 0.00 0.00 3.02
1825 2141 0.525668 CACTACCTGACGGTCGATGC 60.526 60.000 3.34 0.00 44.21 3.91
1839 2155 5.833082 ACGGACACAAGATCATATCACTAC 58.167 41.667 0.00 0.00 0.00 2.73
1855 2171 1.445582 CGGCCTGTTAGACGGACAC 60.446 63.158 0.00 0.00 0.00 3.67
1856 2172 1.466025 AACGGCCTGTTAGACGGACA 61.466 55.000 10.62 0.00 39.61 4.02
1965 2281 2.672651 CCCACAATGTGCAGCCGA 60.673 61.111 8.05 0.00 31.34 5.54
2064 2380 1.185618 CGGTCCAACTCACCTGAGGA 61.186 60.000 4.99 0.00 46.13 3.71
2082 2398 2.917933 TGGGGATGAGCTGATAAAACG 58.082 47.619 0.00 0.00 0.00 3.60
2093 2409 1.075374 TCAAACAGGGTTGGGGATGAG 59.925 52.381 0.00 0.00 0.00 2.90
2137 2453 9.705290 GCCTGAAAAACAATTATAAGAAAGGAA 57.295 29.630 0.00 0.00 0.00 3.36
2139 2455 9.358872 GAGCCTGAAAAACAATTATAAGAAAGG 57.641 33.333 0.00 0.00 0.00 3.11
2143 2459 8.028938 GCAAGAGCCTGAAAAACAATTATAAGA 58.971 33.333 0.00 0.00 33.58 2.10
2144 2460 7.008628 CGCAAGAGCCTGAAAAACAATTATAAG 59.991 37.037 0.00 0.00 43.02 1.73
2145 2461 6.806249 CGCAAGAGCCTGAAAAACAATTATAA 59.194 34.615 0.00 0.00 43.02 0.98
2146 2462 6.321717 CGCAAGAGCCTGAAAAACAATTATA 58.678 36.000 0.00 0.00 43.02 0.98
2147 2463 5.163513 CGCAAGAGCCTGAAAAACAATTAT 58.836 37.500 0.00 0.00 43.02 1.28
2197 2513 5.189180 ACAGCTTCTCTATGTTCAATTCCC 58.811 41.667 0.00 0.00 0.00 3.97
2233 2549 2.257409 ATCCTACCTTGGCTGCACCG 62.257 60.000 0.50 0.00 43.94 4.94
2278 2594 3.820777 AGAAGTGAAGAGCAATTTCGC 57.179 42.857 0.00 0.00 34.49 4.70
2322 2638 8.686334 AGTGACAACAGAATTAACTTGATGTTT 58.314 29.630 0.00 0.00 39.89 2.83
2423 2741 3.582647 TCCAGTCCATAAAGTTGAGCAGA 59.417 43.478 0.00 0.00 0.00 4.26
2476 2794 8.816894 TGATCTCTTACAGGTTTAGAATGAACT 58.183 33.333 0.00 0.00 0.00 3.01
2507 2825 7.232534 AGCTACTGTTCCCATGAATAAAAACAA 59.767 33.333 0.00 0.00 31.98 2.83
2527 2845 8.394822 TCATCCTATATAAAGAGGTGAGCTACT 58.605 37.037 0.00 0.00 35.46 2.57
2599 2917 1.869767 GGCTTATCAGTGCGAGGAATG 59.130 52.381 0.00 0.00 0.00 2.67
2602 2920 1.123077 ATGGCTTATCAGTGCGAGGA 58.877 50.000 0.00 0.00 0.00 3.71
2611 2929 5.754782 ACACATACCTTGAATGGCTTATCA 58.245 37.500 0.00 0.00 0.00 2.15
2845 3164 1.136252 CCGCATGAGTGTTGACGAAAG 60.136 52.381 0.00 0.00 0.00 2.62
3008 3327 1.890876 ACCTGTGCGCTGTTAAATGA 58.109 45.000 9.73 0.00 0.00 2.57
3019 3338 2.974148 TGCAGCTCAACCTGTGCG 60.974 61.111 0.00 0.00 41.31 5.34
3026 3345 1.508632 TAGTTTCCGTGCAGCTCAAC 58.491 50.000 0.00 0.00 0.00 3.18
3045 3364 2.283298 CTCCGTGCAGCTCAACAATAT 58.717 47.619 0.00 0.00 0.00 1.28
3052 3371 2.306847 TCATATACTCCGTGCAGCTCA 58.693 47.619 0.00 0.00 0.00 4.26
3053 3372 3.584406 ATCATATACTCCGTGCAGCTC 57.416 47.619 0.00 0.00 0.00 4.09
3054 3373 4.280929 TGTTATCATATACTCCGTGCAGCT 59.719 41.667 0.00 0.00 0.00 4.24
3055 3374 4.556233 TGTTATCATATACTCCGTGCAGC 58.444 43.478 0.00 0.00 0.00 5.25
3056 3375 7.600375 AGAAATGTTATCATATACTCCGTGCAG 59.400 37.037 0.00 0.00 33.49 4.41
3057 3376 7.441836 AGAAATGTTATCATATACTCCGTGCA 58.558 34.615 0.00 0.00 33.49 4.57
3058 3377 7.598869 TGAGAAATGTTATCATATACTCCGTGC 59.401 37.037 0.00 0.00 33.49 5.34
3059 3378 9.476202 TTGAGAAATGTTATCATATACTCCGTG 57.524 33.333 0.00 0.00 33.49 4.94
3120 3439 2.488204 TTGATGCCTCGAAATCCACA 57.512 45.000 0.00 0.00 0.00 4.17
3123 3442 1.000938 GCCATTGATGCCTCGAAATCC 60.001 52.381 0.00 0.00 0.00 3.01
3190 3509 1.209504 ACCAGACCATACCGACCAATG 59.790 52.381 0.00 0.00 0.00 2.82
3223 3549 2.735134 GACACGAAATAAGACACCGCTT 59.265 45.455 0.00 0.00 0.00 4.68
3270 3597 1.550976 AGAACTCTTAGGAAGGTGGCG 59.449 52.381 0.00 0.00 0.00 5.69
3328 3655 2.281484 GTTTGCTCAGGTGCCCGA 60.281 61.111 0.00 0.00 0.00 5.14
3521 3872 5.297547 TCGGGCAAAAGAGATACATATGTC 58.702 41.667 12.68 0.00 0.00 3.06
3528 3879 2.159028 AGCTCTCGGGCAAAAGAGATAC 60.159 50.000 12.50 4.69 41.96 2.24
3532 3883 2.761071 GAGCTCTCGGGCAAAAGAG 58.239 57.895 6.43 5.86 41.62 2.85
3558 3909 8.678199 GCACTCCTATAATAATAAAAGCCCATC 58.322 37.037 0.00 0.00 0.00 3.51
3561 3912 8.515414 CAAGCACTCCTATAATAATAAAAGCCC 58.485 37.037 0.00 0.00 0.00 5.19
3571 3922 7.125811 ACTTCTCCAACAAGCACTCCTATAATA 59.874 37.037 0.00 0.00 0.00 0.98
3575 3926 3.584848 ACTTCTCCAACAAGCACTCCTAT 59.415 43.478 0.00 0.00 0.00 2.57
3583 3934 2.024414 ACCAACACTTCTCCAACAAGC 58.976 47.619 0.00 0.00 0.00 4.01
3588 3939 0.534203 GCCGACCAACACTTCTCCAA 60.534 55.000 0.00 0.00 0.00 3.53
3596 3947 1.355210 CACACAAGCCGACCAACAC 59.645 57.895 0.00 0.00 0.00 3.32
3597 3948 1.078072 ACACACAAGCCGACCAACA 60.078 52.632 0.00 0.00 0.00 3.33
3604 3957 3.067106 ACTATTCAAGACACACAAGCCG 58.933 45.455 0.00 0.00 0.00 5.52
3607 3960 5.702670 ACCATCACTATTCAAGACACACAAG 59.297 40.000 0.00 0.00 0.00 3.16
3654 4007 6.738114 ACCTCAAACATAAACATCACACTTG 58.262 36.000 0.00 0.00 0.00 3.16
3680 4033 6.340962 ACACACGCATTATAGGCTTATAGA 57.659 37.500 0.00 0.00 0.00 1.98
3682 4035 9.496873 AAATAACACACGCATTATAGGCTTATA 57.503 29.630 0.00 0.00 0.00 0.98
3683 4036 7.979444 AATAACACACGCATTATAGGCTTAT 57.021 32.000 0.00 0.00 0.00 1.73
3684 4037 7.635423 CAAATAACACACGCATTATAGGCTTA 58.365 34.615 0.00 0.00 0.00 3.09
3685 4038 6.494842 CAAATAACACACGCATTATAGGCTT 58.505 36.000 0.00 0.00 0.00 4.35
3686 4039 5.505654 GCAAATAACACACGCATTATAGGCT 60.506 40.000 0.00 0.00 0.00 4.58
3687 4040 4.675114 GCAAATAACACACGCATTATAGGC 59.325 41.667 0.00 0.00 0.00 3.93
3688 4041 5.815850 TGCAAATAACACACGCATTATAGG 58.184 37.500 0.00 0.00 0.00 2.57
3689 4042 7.484641 ACTTTGCAAATAACACACGCATTATAG 59.515 33.333 13.23 0.00 31.67 1.31
3690 4043 7.309177 ACTTTGCAAATAACACACGCATTATA 58.691 30.769 13.23 0.00 31.67 0.98
3691 4044 6.155827 ACTTTGCAAATAACACACGCATTAT 58.844 32.000 13.23 0.00 31.67 1.28
3759 4112 8.708742 TCTTTAGTGTTTCAGATGTCATAAACG 58.291 33.333 5.60 0.00 35.16 3.60
3766 4119 7.708752 CCTCCTATCTTTAGTGTTTCAGATGTC 59.291 40.741 0.00 0.00 0.00 3.06
3779 4132 8.657387 TGGACTGATAATCCTCCTATCTTTAG 57.343 38.462 0.00 0.00 37.13 1.85
3812 4165 3.908382 CACGCAGTTAGCACAAATTCTTC 59.092 43.478 0.00 0.00 41.61 2.87
3855 4208 0.667184 GAAGCAAACATGGCGGTTGG 60.667 55.000 0.00 0.00 36.08 3.77
3856 4209 0.667184 GGAAGCAAACATGGCGGTTG 60.667 55.000 0.00 0.00 36.08 3.77
3857 4210 1.665442 GGAAGCAAACATGGCGGTT 59.335 52.632 0.00 0.00 36.08 4.44
3858 4211 2.275380 GGGAAGCAAACATGGCGGT 61.275 57.895 0.00 0.00 36.08 5.68
3859 4212 2.573340 GGGAAGCAAACATGGCGG 59.427 61.111 0.00 0.00 36.08 6.13
3860 4213 2.141122 AACGGGAAGCAAACATGGCG 62.141 55.000 0.00 0.00 36.08 5.69
3861 4214 0.033366 AAACGGGAAGCAAACATGGC 59.967 50.000 0.00 0.00 0.00 4.40
3878 4231 7.446931 TGGTACAATCTCTTTGAGCATTGTAAA 59.553 33.333 20.43 14.68 40.16 2.01
3912 4266 4.300803 TGCAGAATGTTTTCAGATTGCAC 58.699 39.130 0.00 0.00 37.79 4.57
3970 4353 8.421784 TGTACTCCAGTAATTATGGAATCAGAC 58.578 37.037 13.96 9.74 46.04 3.51
4004 4387 0.471591 AATGCCAAGCTTGTGGGGAA 60.472 50.000 24.35 4.60 39.26 3.97
4006 4389 0.320946 CAAATGCCAAGCTTGTGGGG 60.321 55.000 24.35 10.81 39.26 4.96
4007 4390 0.952010 GCAAATGCCAAGCTTGTGGG 60.952 55.000 24.35 11.18 39.26 4.61
4009 4392 1.873698 AAGCAAATGCCAAGCTTGTG 58.126 45.000 24.35 16.27 45.99 3.33
4034 4432 5.902051 AGTCACTTGTTTAACGCTTCTAC 57.098 39.130 0.00 0.00 0.00 2.59
4042 4440 7.707893 TGTACACCTCTTAGTCACTTGTTTAAC 59.292 37.037 0.00 0.00 0.00 2.01
4081 4479 1.846782 CGTAACGATCTTGGAGAAGCG 59.153 52.381 0.00 0.00 33.97 4.68
4101 4499 0.543749 AGGTGCAGGAGCTGTAATCC 59.456 55.000 0.00 0.00 42.74 3.01
4102 4500 1.474143 GGAGGTGCAGGAGCTGTAATC 60.474 57.143 0.00 0.00 42.74 1.75
4133 4531 5.591472 TGAATGTAGATGCATCTTTCTTGGG 59.409 40.000 32.94 0.00 38.32 4.12
4159 4557 3.394606 AGCCCCCGAAGAACATGTATAAT 59.605 43.478 0.00 0.00 0.00 1.28
4173 4571 4.966787 GTTGGTGCAAGCCCCCGA 62.967 66.667 0.00 0.00 0.00 5.14
4195 4593 3.375299 GTCACAAAGCTATCCCACATGAC 59.625 47.826 0.00 0.00 0.00 3.06
4197 4595 3.614092 AGTCACAAAGCTATCCCACATG 58.386 45.455 0.00 0.00 0.00 3.21
4218 4616 2.757868 ACAAGTAGTTTTGGTGCTGCAA 59.242 40.909 2.77 0.00 32.32 4.08
4232 4630 7.672983 TCAGAATTCAGGCTTTAACAAGTAG 57.327 36.000 8.44 0.00 31.86 2.57
4244 4642 2.223203 CGTCAGCATTCAGAATTCAGGC 60.223 50.000 8.44 0.21 0.00 4.85
4261 4659 1.067142 GTAGCATCACCAACTCCGTCA 60.067 52.381 0.00 0.00 0.00 4.35
4271 4669 8.924303 TCCTGGTATATATTATGTAGCATCACC 58.076 37.037 11.27 0.00 34.61 4.02


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

AutoCloner maintained by Alex Coulton.