Multiple sequence alignment - TraesCS5B01G221600

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 TraesCS5B01G221600 chr5B 100.000 6044 0 0 1 6044 395926819 395920776 0.000000e+00 11162
1 TraesCS5B01G221600 chr5B 86.391 169 21 2 1105 1272 680918703 680918870 3.720000e-42 183
2 TraesCS5B01G221600 chr5D 96.157 3383 97 14 2060 5423 337304703 337301335 0.000000e+00 5496
3 TraesCS5B01G221600 chr5D 93.317 1242 39 17 337 1557 337306292 337305074 0.000000e+00 1794
4 TraesCS5B01G221600 chr5D 95.462 639 19 4 5407 6044 337301304 337300675 0.000000e+00 1011
5 TraesCS5B01G221600 chr5D 91.371 394 23 6 1579 1965 337305086 337304697 4.150000e-146 529
6 TraesCS5B01G221600 chr5D 95.600 250 6 2 1 246 337306690 337306442 4.390000e-106 396
7 TraesCS5B01G221600 chr5A 94.372 3358 127 31 2060 5363 438474859 438471510 0.000000e+00 5097
8 TraesCS5B01G221600 chr5A 90.504 1190 47 22 390 1560 438476374 438475232 0.000000e+00 1511
9 TraesCS5B01G221600 chr5A 87.600 500 45 6 5551 6044 438471261 438470773 1.140000e-156 564
10 TraesCS5B01G221600 chr5A 90.977 399 22 7 1578 1965 438475248 438474853 5.370000e-145 525
11 TraesCS5B01G221600 chr5A 92.675 314 15 5 14 320 438476716 438476404 4.300000e-121 446
12 TraesCS5B01G221600 chr1A 85.741 533 76 0 4481 5013 256827136 256827668 1.140000e-156 564
13 TraesCS5B01G221600 chr1A 81.311 610 106 7 2067 2672 256824713 256825318 7.040000e-134 488
14 TraesCS5B01G221600 chr1A 83.569 353 53 3 3992 4343 256826666 256827014 5.840000e-85 326
15 TraesCS5B01G221600 chr1A 84.496 258 38 2 2758 3014 256825322 256825578 2.800000e-63 254
16 TraesCS5B01G221600 chr1D 85.178 533 79 0 4481 5013 202569645 202570177 1.150000e-151 547
17 TraesCS5B01G221600 chr1D 80.984 610 108 7 2067 2672 202567231 202567836 1.520000e-130 477
18 TraesCS5B01G221600 chr1D 82.927 369 58 3 3992 4359 202569173 202569537 1.620000e-85 327
19 TraesCS5B01G221600 chr1D 86.047 258 34 2 2758 3014 202567840 202568096 5.970000e-70 276
20 TraesCS5B01G221600 chr1B 85.283 530 78 0 4481 5010 296502128 296502657 1.150000e-151 547
21 TraesCS5B01G221600 chr1B 81.639 610 104 7 2067 2672 296499678 296500283 3.250000e-137 499
22 TraesCS5B01G221600 chr1B 82.927 369 58 3 3992 4359 296501656 296502020 1.620000e-85 327
23 TraesCS5B01G221600 chr1B 84.884 258 37 2 2758 3014 296500287 296500543 6.010000e-65 259
24 TraesCS5B01G221600 chr6A 81.949 554 90 5 4499 5047 47902465 47903013 1.530000e-125 460
25 TraesCS5B01G221600 chr2D 94.400 250 9 4 1 246 640258489 640258241 4.420000e-101 379
26 TraesCS5B01G221600 chr3B 79.563 504 97 4 4489 4992 525611444 525611941 7.450000e-94 355
27 TraesCS5B01G221600 chr7A 76.103 544 100 22 2364 2895 546709385 546709910 2.160000e-64 257
28 TraesCS5B01G221600 chr7A 74.201 438 98 14 4550 4978 14189969 14189538 1.040000e-37 169
29 TraesCS5B01G221600 chr7D 75.000 552 102 27 2364 2895 449060843 449060308 7.880000e-54 222
30 TraesCS5B01G221600 chr7D 74.541 436 98 12 4550 4977 14880893 14880463 1.730000e-40 178
31 TraesCS5B01G221600 chr4A 92.063 126 10 0 1147 1272 629365341 629365216 1.730000e-40 178
32 TraesCS5B01G221600 chr7B 82.877 146 21 4 2751 2894 466972133 466971990 1.770000e-25 128


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 TraesCS5B01G221600 chr5B 395920776 395926819 6043 True 11162.00 11162 100.00000 1 6044 1 chr5B.!!$R1 6043
1 TraesCS5B01G221600 chr5D 337300675 337306690 6015 True 1845.20 5496 94.38140 1 6044 5 chr5D.!!$R1 6043
2 TraesCS5B01G221600 chr5A 438470773 438476716 5943 True 1628.60 5097 91.22560 14 6044 5 chr5A.!!$R1 6030
3 TraesCS5B01G221600 chr1A 256824713 256827668 2955 False 408.00 564 83.77925 2067 5013 4 chr1A.!!$F1 2946
4 TraesCS5B01G221600 chr1D 202567231 202570177 2946 False 406.75 547 83.78400 2067 5013 4 chr1D.!!$F1 2946
5 TraesCS5B01G221600 chr1B 296499678 296502657 2979 False 408.00 547 83.68325 2067 5010 4 chr1B.!!$F1 2943
6 TraesCS5B01G221600 chr6A 47902465 47903013 548 False 460.00 460 81.94900 4499 5047 1 chr6A.!!$F1 548
7 TraesCS5B01G221600 chr7A 546709385 546709910 525 False 257.00 257 76.10300 2364 2895 1 chr7A.!!$F1 531
8 TraesCS5B01G221600 chr7D 449060308 449060843 535 True 222.00 222 75.00000 2364 2895 1 chr7D.!!$R2 531

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
404 475 0.034574 TGTATTTGGCATGCCCGACT 60.035 50.0 33.44 18.05 35.87 4.18 F
1547 1648 0.036388 TTCTCCGTGTCCATCAAGCC 60.036 55.0 0.00 0.00 0.00 4.35 F
1557 1658 0.178767 CCATCAAGCCCTCGATCACA 59.821 55.0 0.00 0.00 0.00 3.58 F
2033 2145 0.241749 AACCGTTGCTCACATGCATG 59.758 50.0 25.09 25.09 42.96 4.06 F
3803 4028 0.392998 CCACGTTCATGGAGGAAGGG 60.393 60.0 0.00 0.00 43.02 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 2118 0.400213 TGAGCAACGGTTCTTGGGAT 59.600 50.0 0.00 0.0 0.00 3.85 R
3410 3566 0.251916 CGTCCAGCCCCTTCATGTTA 59.748 55.0 0.00 0.0 0.00 2.41 R
3431 3587 0.828022 CGTACACTGGCCCTTGGATA 59.172 55.0 0.00 0.0 0.00 2.59 R
3996 4375 0.979187 GACCCGTAGATCCACCCCAA 60.979 60.0 0.00 0.0 0.00 4.12 R
5412 5889 0.799534 GCGGCTGCTGTAATGCAAAG 60.800 55.0 11.21 0.0 42.83 2.77 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
109 115 2.797278 CGCTGGCTAGTAGGTGGGG 61.797 68.421 0.00 0.00 0.00 4.96
234 241 0.855349 CGCTCAATGCTCCATACGAC 59.145 55.000 0.00 0.00 40.11 4.34
285 315 1.225426 TCCTGAGGACATGCATGGC 59.775 57.895 29.41 27.45 34.16 4.40
314 348 4.010667 TGTTCACCGGTAGCAAGTAAAT 57.989 40.909 6.87 0.00 0.00 1.40
320 354 3.050619 CCGGTAGCAAGTAAATAGAGCG 58.949 50.000 0.00 0.00 0.00 5.03
324 358 4.686554 GGTAGCAAGTAAATAGAGCGATGG 59.313 45.833 0.00 0.00 0.00 3.51
325 359 4.408182 AGCAAGTAAATAGAGCGATGGT 57.592 40.909 0.00 0.00 0.00 3.55
330 364 7.171678 AGCAAGTAAATAGAGCGATGGTATTTC 59.828 37.037 1.87 0.00 30.74 2.17
339 373 7.624360 AGAGCGATGGTATTTCATTTTTGTA 57.376 32.000 0.00 0.00 0.00 2.41
342 376 9.301153 GAGCGATGGTATTTCATTTTTGTATTT 57.699 29.630 0.00 0.00 0.00 1.40
343 377 9.086336 AGCGATGGTATTTCATTTTTGTATTTG 57.914 29.630 0.00 0.00 0.00 2.32
344 378 8.327429 GCGATGGTATTTCATTTTTGTATTTGG 58.673 33.333 0.00 0.00 0.00 3.28
351 418 4.815269 TCATTTTTGTATTTGGCGGGAAG 58.185 39.130 0.00 0.00 0.00 3.46
365 432 1.808133 CGGGAAGCACATAAGCTCTCC 60.808 57.143 0.00 0.00 45.89 3.71
398 469 6.476706 GGATTTTTCTACTGTATTTGGCATGC 59.523 38.462 9.90 9.90 0.00 4.06
399 470 4.981806 TTTCTACTGTATTTGGCATGCC 57.018 40.909 30.54 30.54 0.00 4.40
403 474 0.381801 CTGTATTTGGCATGCCCGAC 59.618 55.000 33.44 23.59 35.87 4.79
404 475 0.034574 TGTATTTGGCATGCCCGACT 60.035 50.000 33.44 18.05 35.87 4.18
420 491 0.875059 GACTGTGGCGAGGAAAAAGG 59.125 55.000 0.00 0.00 0.00 3.11
421 492 1.172812 ACTGTGGCGAGGAAAAAGGC 61.173 55.000 0.00 0.00 0.00 4.35
422 493 1.152860 TGTGGCGAGGAAAAAGGCA 60.153 52.632 0.00 0.00 38.13 4.75
433 504 3.384789 AGGAAAAAGGCAGGACAAAGTTC 59.615 43.478 0.00 0.00 0.00 3.01
475 551 3.980775 CGCGTCCATTTCTTTTCAATTGT 59.019 39.130 5.13 0.00 0.00 2.71
505 581 4.020485 AGGTACTACTCACCAATCACCAAC 60.020 45.833 0.00 0.00 38.62 3.77
608 687 4.489795 GAGATGCACGCACGCACG 62.490 66.667 0.00 0.00 46.56 5.34
818 897 4.794439 CGGACGCACCAGATCGCA 62.794 66.667 0.43 0.00 38.90 5.10
826 905 2.653448 CCAGATCGCACTCGCTCG 60.653 66.667 0.00 0.00 36.12 5.03
1514 1603 0.944311 CGCTCCATGCCGGTATACAC 60.944 60.000 4.13 0.00 38.78 2.90
1518 1615 1.771854 TCCATGCCGGTATACACCATT 59.228 47.619 4.13 0.00 46.14 3.16
1541 1642 1.276421 CCTTCACTTCTCCGTGTCCAT 59.724 52.381 0.00 0.00 36.33 3.41
1542 1643 2.611518 CTTCACTTCTCCGTGTCCATC 58.388 52.381 0.00 0.00 36.33 3.51
1543 1644 1.627864 TCACTTCTCCGTGTCCATCA 58.372 50.000 0.00 0.00 36.33 3.07
1544 1645 1.967779 TCACTTCTCCGTGTCCATCAA 59.032 47.619 0.00 0.00 36.33 2.57
1545 1646 2.029020 TCACTTCTCCGTGTCCATCAAG 60.029 50.000 0.00 0.00 36.33 3.02
1546 1647 1.338200 ACTTCTCCGTGTCCATCAAGC 60.338 52.381 0.00 0.00 0.00 4.01
1547 1648 0.036388 TTCTCCGTGTCCATCAAGCC 60.036 55.000 0.00 0.00 0.00 4.35
1548 1649 1.450312 CTCCGTGTCCATCAAGCCC 60.450 63.158 0.00 0.00 0.00 5.19
1549 1650 1.903877 CTCCGTGTCCATCAAGCCCT 61.904 60.000 0.00 0.00 0.00 5.19
1550 1651 1.450312 CCGTGTCCATCAAGCCCTC 60.450 63.158 0.00 0.00 0.00 4.30
1551 1652 1.811266 CGTGTCCATCAAGCCCTCG 60.811 63.158 0.00 0.00 0.00 4.63
1552 1653 1.596934 GTGTCCATCAAGCCCTCGA 59.403 57.895 0.00 0.00 0.00 4.04
1553 1654 0.179000 GTGTCCATCAAGCCCTCGAT 59.821 55.000 0.00 0.00 0.00 3.59
1554 1655 0.465705 TGTCCATCAAGCCCTCGATC 59.534 55.000 0.00 0.00 0.00 3.69
1555 1656 0.465705 GTCCATCAAGCCCTCGATCA 59.534 55.000 0.00 0.00 0.00 2.92
1556 1657 0.465705 TCCATCAAGCCCTCGATCAC 59.534 55.000 0.00 0.00 0.00 3.06
1557 1658 0.178767 CCATCAAGCCCTCGATCACA 59.821 55.000 0.00 0.00 0.00 3.58
1558 1659 1.293924 CATCAAGCCCTCGATCACAC 58.706 55.000 0.00 0.00 0.00 3.82
1559 1660 1.134580 CATCAAGCCCTCGATCACACT 60.135 52.381 0.00 0.00 0.00 3.55
1560 1661 0.976641 TCAAGCCCTCGATCACACTT 59.023 50.000 0.00 0.00 0.00 3.16
1561 1662 1.081892 CAAGCCCTCGATCACACTTG 58.918 55.000 0.00 0.00 0.00 3.16
1562 1663 0.687354 AAGCCCTCGATCACACTTGT 59.313 50.000 0.00 0.00 0.00 3.16
1563 1664 0.687354 AGCCCTCGATCACACTTGTT 59.313 50.000 0.00 0.00 0.00 2.83
1564 1665 1.072331 AGCCCTCGATCACACTTGTTT 59.928 47.619 0.00 0.00 0.00 2.83
1565 1666 1.464997 GCCCTCGATCACACTTGTTTC 59.535 52.381 0.00 0.00 0.00 2.78
1566 1667 2.766313 CCCTCGATCACACTTGTTTCA 58.234 47.619 0.00 0.00 0.00 2.69
1567 1668 3.138304 CCCTCGATCACACTTGTTTCAA 58.862 45.455 0.00 0.00 0.00 2.69
1568 1669 3.563808 CCCTCGATCACACTTGTTTCAAA 59.436 43.478 0.00 0.00 0.00 2.69
1569 1670 4.036262 CCCTCGATCACACTTGTTTCAAAA 59.964 41.667 0.00 0.00 0.00 2.44
1570 1671 5.449862 CCCTCGATCACACTTGTTTCAAAAA 60.450 40.000 0.00 0.00 0.00 1.94
1610 1711 9.851043 CGATTACTCTAGCAGCTTAAATTAAAC 57.149 33.333 0.00 0.00 0.00 2.01
1619 1720 6.040391 AGCAGCTTAAATTAAACTGTTCACCA 59.960 34.615 15.06 0.00 0.00 4.17
1620 1721 6.868339 GCAGCTTAAATTAAACTGTTCACCAT 59.132 34.615 15.06 0.00 0.00 3.55
1700 1805 0.473694 TCTCCTCCTCCCTGCACAAA 60.474 55.000 0.00 0.00 0.00 2.83
1739 1844 1.248785 TGTCCGAGCCAGGTGACTAC 61.249 60.000 0.00 0.00 40.21 2.73
1740 1845 0.966370 GTCCGAGCCAGGTGACTACT 60.966 60.000 0.00 0.00 40.21 2.57
1745 1850 2.230508 CGAGCCAGGTGACTACTTTACA 59.769 50.000 0.00 0.00 40.21 2.41
1749 1854 4.161754 AGCCAGGTGACTACTTTACATACC 59.838 45.833 0.00 0.00 40.21 2.73
1798 1907 2.491693 AGTTCCTTGTGTTGTGTTGGTG 59.508 45.455 0.00 0.00 0.00 4.17
1821 1930 5.122869 TGAGCTCAAGTTAGCAACATGAATC 59.877 40.000 15.67 8.81 45.30 2.52
1829 1938 7.493743 AGTTAGCAACATGAATCTGATGATC 57.506 36.000 0.00 0.00 31.51 2.92
1836 1948 4.659368 ACATGAATCTGATGATCAGGGAGT 59.341 41.667 21.27 3.52 44.39 3.85
1959 2071 4.382320 GCCGACGTGCCCCTGTAA 62.382 66.667 0.00 0.00 0.00 2.41
1960 2072 2.125673 CCGACGTGCCCCTGTAAG 60.126 66.667 0.00 0.00 0.00 2.34
1961 2073 2.813908 CGACGTGCCCCTGTAAGC 60.814 66.667 0.00 0.00 0.00 3.09
1962 2074 2.813908 GACGTGCCCCTGTAAGCG 60.814 66.667 0.00 0.00 0.00 4.68
1963 2075 3.291101 GACGTGCCCCTGTAAGCGA 62.291 63.158 0.00 0.00 0.00 4.93
1964 2076 2.813908 CGTGCCCCTGTAAGCGAC 60.814 66.667 0.00 0.00 0.00 5.19
1965 2077 2.436115 GTGCCCCTGTAAGCGACC 60.436 66.667 0.00 0.00 0.00 4.79
1966 2078 3.712907 TGCCCCTGTAAGCGACCC 61.713 66.667 0.00 0.00 0.00 4.46
1967 2079 3.400054 GCCCCTGTAAGCGACCCT 61.400 66.667 0.00 0.00 0.00 4.34
1968 2080 2.901042 CCCCTGTAAGCGACCCTC 59.099 66.667 0.00 0.00 0.00 4.30
1969 2081 1.987855 CCCCTGTAAGCGACCCTCA 60.988 63.158 0.00 0.00 0.00 3.86
1970 2082 1.218316 CCCTGTAAGCGACCCTCAC 59.782 63.158 0.00 0.00 0.00 3.51
1971 2083 1.541310 CCCTGTAAGCGACCCTCACA 61.541 60.000 0.00 0.00 0.00 3.58
1972 2084 0.320374 CCTGTAAGCGACCCTCACAA 59.680 55.000 0.00 0.00 0.00 3.33
1973 2085 1.270625 CCTGTAAGCGACCCTCACAAA 60.271 52.381 0.00 0.00 0.00 2.83
1974 2086 2.489971 CTGTAAGCGACCCTCACAAAA 58.510 47.619 0.00 0.00 0.00 2.44
1975 2087 2.875933 CTGTAAGCGACCCTCACAAAAA 59.124 45.455 0.00 0.00 0.00 1.94
1976 2088 2.614983 TGTAAGCGACCCTCACAAAAAC 59.385 45.455 0.00 0.00 0.00 2.43
1977 2089 1.757682 AAGCGACCCTCACAAAAACA 58.242 45.000 0.00 0.00 0.00 2.83
1978 2090 1.757682 AGCGACCCTCACAAAAACAA 58.242 45.000 0.00 0.00 0.00 2.83
1979 2091 1.404035 AGCGACCCTCACAAAAACAAC 59.596 47.619 0.00 0.00 0.00 3.32
1980 2092 1.535226 GCGACCCTCACAAAAACAACC 60.535 52.381 0.00 0.00 0.00 3.77
1981 2093 1.066454 CGACCCTCACAAAAACAACCC 59.934 52.381 0.00 0.00 0.00 4.11
1982 2094 2.104170 GACCCTCACAAAAACAACCCA 58.896 47.619 0.00 0.00 0.00 4.51
1983 2095 1.828595 ACCCTCACAAAAACAACCCAC 59.171 47.619 0.00 0.00 0.00 4.61
1984 2096 1.202359 CCCTCACAAAAACAACCCACG 60.202 52.381 0.00 0.00 0.00 4.94
1985 2097 1.555477 CTCACAAAAACAACCCACGC 58.445 50.000 0.00 0.00 0.00 5.34
1986 2098 0.888619 TCACAAAAACAACCCACGCA 59.111 45.000 0.00 0.00 0.00 5.24
1987 2099 1.478510 TCACAAAAACAACCCACGCAT 59.521 42.857 0.00 0.00 0.00 4.73
1988 2100 1.592081 CACAAAAACAACCCACGCATG 59.408 47.619 0.00 0.00 0.00 4.06
1989 2101 0.581053 CAAAAACAACCCACGCATGC 59.419 50.000 7.91 7.91 0.00 4.06
1990 2102 0.873743 AAAAACAACCCACGCATGCG 60.874 50.000 36.79 36.79 46.03 4.73
1991 2103 3.839642 AAACAACCCACGCATGCGC 62.840 57.895 38.15 0.00 44.19 6.09
1993 2105 4.764336 CAACCCACGCATGCGCTG 62.764 66.667 38.15 30.81 44.19 5.18
2001 2113 4.137872 GCATGCGCTGTGCCCAAT 62.138 61.111 22.30 0.00 45.60 3.16
2002 2114 2.574929 CATGCGCTGTGCCCAATT 59.425 55.556 9.73 0.00 45.60 2.32
2003 2115 1.517694 CATGCGCTGTGCCCAATTC 60.518 57.895 9.73 0.00 45.60 2.17
2004 2116 1.978080 ATGCGCTGTGCCCAATTCA 60.978 52.632 9.73 0.00 45.60 2.57
2005 2117 1.324740 ATGCGCTGTGCCCAATTCAT 61.325 50.000 9.73 0.00 45.60 2.57
2006 2118 0.679321 TGCGCTGTGCCCAATTCATA 60.679 50.000 9.73 0.00 45.60 2.15
2007 2119 0.670162 GCGCTGTGCCCAATTCATAT 59.330 50.000 0.00 0.00 37.76 1.78
2008 2120 1.335324 GCGCTGTGCCCAATTCATATC 60.335 52.381 0.00 0.00 37.76 1.63
2009 2121 1.267806 CGCTGTGCCCAATTCATATCC 59.732 52.381 0.00 0.00 0.00 2.59
2010 2122 1.615392 GCTGTGCCCAATTCATATCCC 59.385 52.381 0.00 0.00 0.00 3.85
2011 2123 2.948115 CTGTGCCCAATTCATATCCCA 58.052 47.619 0.00 0.00 0.00 4.37
2012 2124 3.298619 CTGTGCCCAATTCATATCCCAA 58.701 45.455 0.00 0.00 0.00 4.12
2013 2125 3.298619 TGTGCCCAATTCATATCCCAAG 58.701 45.455 0.00 0.00 0.00 3.61
2014 2126 3.053019 TGTGCCCAATTCATATCCCAAGA 60.053 43.478 0.00 0.00 0.00 3.02
2015 2127 3.960102 GTGCCCAATTCATATCCCAAGAA 59.040 43.478 0.00 0.00 0.00 2.52
2016 2128 3.960102 TGCCCAATTCATATCCCAAGAAC 59.040 43.478 0.00 0.00 0.00 3.01
2017 2129 3.321968 GCCCAATTCATATCCCAAGAACC 59.678 47.826 0.00 0.00 0.00 3.62
2018 2130 3.569701 CCCAATTCATATCCCAAGAACCG 59.430 47.826 0.00 0.00 0.00 4.44
2019 2131 4.207165 CCAATTCATATCCCAAGAACCGT 58.793 43.478 0.00 0.00 0.00 4.83
2020 2132 4.644685 CCAATTCATATCCCAAGAACCGTT 59.355 41.667 0.00 0.00 0.00 4.44
2021 2133 5.450412 CCAATTCATATCCCAAGAACCGTTG 60.450 44.000 0.00 0.00 0.00 4.10
2022 2134 2.639065 TCATATCCCAAGAACCGTTGC 58.361 47.619 0.00 0.00 0.00 4.17
2023 2135 2.238646 TCATATCCCAAGAACCGTTGCT 59.761 45.455 0.00 0.00 0.00 3.91
2024 2136 2.396590 TATCCCAAGAACCGTTGCTC 57.603 50.000 0.00 0.00 0.00 4.26
2025 2137 0.400213 ATCCCAAGAACCGTTGCTCA 59.600 50.000 0.00 0.00 0.00 4.26
2026 2138 0.534203 TCCCAAGAACCGTTGCTCAC 60.534 55.000 0.00 0.00 0.00 3.51
2027 2139 0.817634 CCCAAGAACCGTTGCTCACA 60.818 55.000 0.00 0.00 0.00 3.58
2028 2140 1.238439 CCAAGAACCGTTGCTCACAT 58.762 50.000 0.00 0.00 0.00 3.21
2029 2141 1.069022 CCAAGAACCGTTGCTCACATG 60.069 52.381 0.00 0.00 0.00 3.21
2030 2142 0.593128 AAGAACCGTTGCTCACATGC 59.407 50.000 0.00 0.00 0.00 4.06
2031 2143 0.534877 AGAACCGTTGCTCACATGCA 60.535 50.000 0.00 0.00 41.65 3.96
2032 2144 0.523072 GAACCGTTGCTCACATGCAT 59.477 50.000 0.00 0.00 42.96 3.96
2033 2145 0.241749 AACCGTTGCTCACATGCATG 59.758 50.000 25.09 25.09 42.96 4.06
2034 2146 0.606130 ACCGTTGCTCACATGCATGA 60.606 50.000 32.75 11.95 42.96 3.07
2035 2147 0.736636 CCGTTGCTCACATGCATGAT 59.263 50.000 32.75 14.29 42.96 2.45
2036 2148 1.268386 CCGTTGCTCACATGCATGATC 60.268 52.381 32.75 17.09 42.96 2.92
2037 2149 1.399089 CGTTGCTCACATGCATGATCA 59.601 47.619 32.75 19.23 42.96 2.92
2038 2150 2.032924 CGTTGCTCACATGCATGATCAT 59.967 45.455 32.75 7.78 42.96 2.45
2039 2151 3.488553 CGTTGCTCACATGCATGATCATT 60.489 43.478 32.75 7.36 42.96 2.57
2040 2152 3.708563 TGCTCACATGCATGATCATTG 57.291 42.857 32.75 19.38 38.12 2.82
2041 2153 3.020984 TGCTCACATGCATGATCATTGT 58.979 40.909 32.75 7.43 38.12 2.71
2042 2154 3.181491 TGCTCACATGCATGATCATTGTG 60.181 43.478 32.75 24.05 38.12 3.33
2043 2155 3.372060 CTCACATGCATGATCATTGTGC 58.628 45.455 32.75 19.22 39.26 4.57
2044 2156 2.116366 CACATGCATGATCATTGTGCG 58.884 47.619 32.75 8.84 41.61 5.34
2045 2157 1.746787 ACATGCATGATCATTGTGCGT 59.253 42.857 32.75 7.08 41.61 5.24
2046 2158 2.944349 ACATGCATGATCATTGTGCGTA 59.056 40.909 32.75 0.00 41.61 4.42
2047 2159 3.377798 ACATGCATGATCATTGTGCGTAA 59.622 39.130 32.75 0.00 41.61 3.18
2048 2160 3.403613 TGCATGATCATTGTGCGTAAC 57.596 42.857 5.16 0.00 41.61 2.50
2049 2161 2.222999 TGCATGATCATTGTGCGTAACG 60.223 45.455 5.16 0.00 41.61 3.18
2155 2267 1.066587 CATCCTCCGCCTCTTCGTC 59.933 63.158 0.00 0.00 0.00 4.20
2179 2291 2.042831 CGTCTTCCTCCGGTACCGT 61.043 63.158 31.24 0.00 37.81 4.83
2191 2303 0.755079 GGTACCGTATCCTCAACCCC 59.245 60.000 0.00 0.00 0.00 4.95
2733 2858 4.641541 TCGCCATGAACATTTCTGATCATT 59.358 37.500 0.00 0.00 40.77 2.57
2735 2860 5.231357 CGCCATGAACATTTCTGATCATTTG 59.769 40.000 0.00 0.00 40.77 2.32
2736 2861 5.522460 GCCATGAACATTTCTGATCATTTGG 59.478 40.000 0.00 0.00 40.77 3.28
2739 2864 6.669125 TGAACATTTCTGATCATTTGGGTT 57.331 33.333 0.00 0.00 30.08 4.11
2740 2865 6.457355 TGAACATTTCTGATCATTTGGGTTG 58.543 36.000 0.00 0.00 30.08 3.77
2741 2866 4.824289 ACATTTCTGATCATTTGGGTTGC 58.176 39.130 0.00 0.00 0.00 4.17
2742 2867 3.959535 TTTCTGATCATTTGGGTTGCC 57.040 42.857 0.00 0.00 0.00 4.52
2743 2868 2.601240 TCTGATCATTTGGGTTGCCA 57.399 45.000 0.00 0.00 0.00 4.92
3061 3190 3.190744 AGAGCTTCGTCGTAAATGTCAGA 59.809 43.478 0.00 0.00 0.00 3.27
3358 3508 5.815740 GGTTCGATCACACCTACATTATGTT 59.184 40.000 2.23 0.00 0.00 2.71
3359 3509 6.315393 GGTTCGATCACACCTACATTATGTTT 59.685 38.462 2.23 0.00 0.00 2.83
3378 3528 5.023452 TGTTTTAGTCTAGGAGAGCCATGA 58.977 41.667 0.00 0.00 36.29 3.07
3389 3539 5.153675 AGGAGAGCCATGAATCTGAGATTA 58.846 41.667 7.82 0.00 36.29 1.75
3390 3540 5.011943 AGGAGAGCCATGAATCTGAGATTAC 59.988 44.000 7.82 3.03 36.29 1.89
3410 3566 8.986991 AGATTACTAGTTCTTGGTGATCAGATT 58.013 33.333 0.00 0.00 36.23 2.40
3431 3587 2.610859 ATGAAGGGGCTGGACGGT 60.611 61.111 0.00 0.00 0.00 4.83
3443 3599 3.316029 GACGGTATCCAAGGGCCA 58.684 61.111 6.18 0.00 0.00 5.36
3746 3971 5.191426 CAGATGATGTCCCAGATGAACTTT 58.809 41.667 0.00 0.00 0.00 2.66
3803 4028 0.392998 CCACGTTCATGGAGGAAGGG 60.393 60.000 0.00 0.00 43.02 3.95
3934 4170 2.225019 GCACAATCACCACTTCAGACAG 59.775 50.000 0.00 0.00 0.00 3.51
3937 4173 3.144506 CAATCACCACTTCAGACAGCTT 58.855 45.455 0.00 0.00 0.00 3.74
3944 4180 4.202357 ACCACTTCAGACAGCTTCACATAA 60.202 41.667 0.00 0.00 0.00 1.90
3958 4194 7.010923 CAGCTTCACATAAATAGTTCCAGACTC 59.989 40.741 0.00 0.00 39.86 3.36
4127 4506 2.125512 GCGCCGATCAACCTGTCT 60.126 61.111 0.00 0.00 0.00 3.41
4146 4525 1.046472 TGACCGTCTCAACCAGGTGT 61.046 55.000 0.00 0.00 37.07 4.16
4301 4680 4.135153 CCGCTGCTCGCCTACTGT 62.135 66.667 0.00 0.00 36.73 3.55
4361 4817 3.760035 CCGCCGGTCAGTGCTAGT 61.760 66.667 1.90 0.00 0.00 2.57
4362 4818 2.412323 CCGCCGGTCAGTGCTAGTA 61.412 63.158 1.90 0.00 0.00 1.82
4364 4820 0.108992 CGCCGGTCAGTGCTAGTAAA 60.109 55.000 1.90 0.00 0.00 2.01
4366 4822 1.337447 GCCGGTCAGTGCTAGTAAACA 60.337 52.381 1.90 0.00 0.00 2.83
4367 4823 2.607187 CCGGTCAGTGCTAGTAAACAG 58.393 52.381 0.00 0.00 0.00 3.16
4368 4824 1.993370 CGGTCAGTGCTAGTAAACAGC 59.007 52.381 0.00 0.00 39.56 4.40
4369 4825 2.352814 CGGTCAGTGCTAGTAAACAGCT 60.353 50.000 0.00 0.00 39.83 4.24
4370 4826 3.119602 CGGTCAGTGCTAGTAAACAGCTA 60.120 47.826 0.00 0.00 39.83 3.32
4371 4827 4.425520 GGTCAGTGCTAGTAAACAGCTAG 58.574 47.826 0.00 0.00 39.83 3.42
5028 5491 1.595382 GCCTGACGTGAAGCAGTGT 60.595 57.895 0.00 0.00 0.00 3.55
5246 5715 4.136796 TGTGTTTTAGCTGTGATTGCTCT 58.863 39.130 0.00 0.00 41.46 4.09
5299 5768 7.793927 ATCAAAGCCTAATGTAGCTAAGAAC 57.206 36.000 0.00 0.00 38.74 3.01
5303 5772 5.109903 AGCCTAATGTAGCTAAGAACAACG 58.890 41.667 0.00 0.00 37.64 4.10
5318 5787 2.577700 ACAACGGGTGCATTTACTTGA 58.422 42.857 0.00 0.00 0.00 3.02
5334 5803 9.777843 CATTTACTTGATTTTTGAACGTAAAGC 57.222 29.630 0.00 0.00 31.48 3.51
5345 5814 8.652810 TTTTGAACGTAAAGCTTAAGAGTAGT 57.347 30.769 6.67 0.00 0.00 2.73
5363 5833 9.702253 AAGAGTAGTATTCAGACTGAGGATAAA 57.298 33.333 5.10 0.00 0.00 1.40
5367 5837 7.118496 AGTATTCAGACTGAGGATAAACAGG 57.882 40.000 5.10 0.00 0.00 4.00
5412 5889 9.520204 CCATCATAAATGTACAATTCAAAGGAC 57.480 33.333 0.00 0.00 0.00 3.85
5429 5953 1.135286 GGACTTTGCATTACAGCAGCC 60.135 52.381 0.00 0.00 46.54 4.85
5500 6063 7.095695 TCAAAGACTTTAAACTTGGAACTGG 57.904 36.000 0.00 0.00 0.00 4.00
5539 6167 7.069085 CAGAATTCTGATATCCACCAAACCATT 59.931 37.037 28.13 0.00 46.59 3.16
5659 6293 1.958579 GGGGTTGGTTAAGGTGACAAC 59.041 52.381 0.00 0.00 41.71 3.32
5738 6372 9.061435 CCATATCTTTCAGTATCTTTTTCCCTC 57.939 37.037 0.00 0.00 0.00 4.30
5806 6440 2.291605 GGAAAAGAATGGGGCACTACCT 60.292 50.000 0.00 0.00 39.10 3.08
5943 6578 2.674852 AGTTGTTATCTGCACAGCATCG 59.325 45.455 0.00 0.00 38.13 3.84
5976 6611 3.139077 GCAGGGGGATGTTTAATACTCG 58.861 50.000 0.00 0.00 0.00 4.18
6003 6638 6.366877 TCGTTTTGTTATTTCTTCTCTACGGG 59.633 38.462 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 67 5.412526 TGATCGTGTAACAAACAAGGAAC 57.587 39.130 0.00 0.00 40.63 3.62
67 69 4.454161 CCATGATCGTGTAACAAACAAGGA 59.546 41.667 13.81 0.00 40.63 3.36
68 70 4.722194 CCATGATCGTGTAACAAACAAGG 58.278 43.478 13.81 0.00 40.63 3.61
109 115 3.258123 ACCTTAATTTGGTGGCACATGTC 59.742 43.478 20.82 1.98 44.52 3.06
226 233 0.711670 CGTTGGTTCGTGTCGTATGG 59.288 55.000 0.00 0.00 0.00 2.74
234 241 2.671619 ATGGGCCGTTGGTTCGTG 60.672 61.111 0.00 0.00 0.00 4.35
255 262 1.078567 CTCAGGACCCAGCTTCAGC 60.079 63.158 0.00 0.00 42.49 4.26
284 314 0.031994 ACCGGTGAACAAATGCAAGC 59.968 50.000 6.12 0.00 0.00 4.01
285 315 2.668279 GCTACCGGTGAACAAATGCAAG 60.668 50.000 19.93 2.33 0.00 4.01
314 348 7.624360 ACAAAAATGAAATACCATCGCTCTA 57.376 32.000 0.00 0.00 0.00 2.43
320 354 8.327429 CGCCAAATACAAAAATGAAATACCATC 58.673 33.333 0.00 0.00 0.00 3.51
324 358 6.814146 TCCCGCCAAATACAAAAATGAAATAC 59.186 34.615 0.00 0.00 0.00 1.89
325 359 6.936279 TCCCGCCAAATACAAAAATGAAATA 58.064 32.000 0.00 0.00 0.00 1.40
330 364 3.370672 GCTTCCCGCCAAATACAAAAATG 59.629 43.478 0.00 0.00 0.00 2.32
339 373 1.750778 CTTATGTGCTTCCCGCCAAAT 59.249 47.619 0.00 0.00 38.05 2.32
342 376 1.748879 GCTTATGTGCTTCCCGCCA 60.749 57.895 0.00 0.00 38.05 5.69
343 377 1.440145 GAGCTTATGTGCTTCCCGCC 61.440 60.000 0.00 0.00 44.17 6.13
344 378 0.462759 AGAGCTTATGTGCTTCCCGC 60.463 55.000 0.00 0.00 44.17 6.13
351 418 2.019249 TGCAATGGAGAGCTTATGTGC 58.981 47.619 0.00 0.00 0.00 4.57
365 432 9.590451 AAATACAGTAGAAAAATCCATGCAATG 57.410 29.630 0.00 0.00 46.21 2.82
376 443 5.337169 GGGCATGCCAAATACAGTAGAAAAA 60.337 40.000 36.56 0.00 37.98 1.94
384 451 0.381801 GTCGGGCATGCCAAATACAG 59.618 55.000 36.56 17.84 37.98 2.74
386 453 0.381801 CAGTCGGGCATGCCAAATAC 59.618 55.000 36.56 25.76 37.98 1.89
388 459 1.304381 ACAGTCGGGCATGCCAAAT 60.304 52.632 36.56 21.09 37.98 2.32
398 469 2.725203 TTTTCCTCGCCACAGTCGGG 62.725 60.000 0.00 0.00 0.00 5.14
399 470 0.882927 TTTTTCCTCGCCACAGTCGG 60.883 55.000 0.00 0.00 0.00 4.79
403 474 1.172180 TGCCTTTTTCCTCGCCACAG 61.172 55.000 0.00 0.00 0.00 3.66
404 475 1.152860 TGCCTTTTTCCTCGCCACA 60.153 52.632 0.00 0.00 0.00 4.17
413 484 3.066203 TCGAACTTTGTCCTGCCTTTTTC 59.934 43.478 0.00 0.00 0.00 2.29
420 491 2.484889 AGAACTCGAACTTTGTCCTGC 58.515 47.619 0.00 0.00 0.00 4.85
421 492 3.669122 CGTAGAACTCGAACTTTGTCCTG 59.331 47.826 0.00 0.00 0.00 3.86
422 493 3.305199 CCGTAGAACTCGAACTTTGTCCT 60.305 47.826 0.00 0.00 0.00 3.85
433 504 1.100510 TCCATGTCCCGTAGAACTCG 58.899 55.000 0.00 0.00 0.00 4.18
475 551 8.092687 GTGATTGGTGAGTAGTACCTTAAAGAA 58.907 37.037 0.00 0.00 39.01 2.52
527 603 9.726438 CATCTCCTTTTTCTTCTCCTAAAACTA 57.274 33.333 0.00 0.00 0.00 2.24
783 862 4.498520 ATGGAGTCCACGAGCGCG 62.499 66.667 15.86 8.75 44.79 6.86
784 863 2.583593 GATGGAGTCCACGAGCGC 60.584 66.667 15.86 0.00 35.80 5.92
785 864 2.278206 CGATGGAGTCCACGAGCG 60.278 66.667 15.86 12.23 35.80 5.03
826 905 2.034221 GGTGAGGGGTGGCTGTTC 59.966 66.667 0.00 0.00 0.00 3.18
926 1005 3.966543 GGGTGTGGAGGTGGTGGG 61.967 72.222 0.00 0.00 0.00 4.61
989 1075 4.899239 CCTCCATGGTCGCTCGCC 62.899 72.222 12.58 0.00 0.00 5.54
992 1078 4.899239 CCGCCTCCATGGTCGCTC 62.899 72.222 12.58 0.00 38.35 5.03
1409 1498 1.834822 GCCCTCCCGTAGCTCATCT 60.835 63.158 0.00 0.00 0.00 2.90
1467 1556 3.260100 ATGATGGGCGGGATCCCC 61.260 66.667 25.73 17.13 45.97 4.81
1514 1603 2.290323 ACGGAGAAGTGAAGGGAAATGG 60.290 50.000 0.00 0.00 0.00 3.16
1518 1615 1.343465 GACACGGAGAAGTGAAGGGAA 59.657 52.381 4.00 0.00 44.43 3.97
1541 1642 0.976641 AAGTGTGATCGAGGGCTTGA 59.023 50.000 0.00 0.00 0.00 3.02
1542 1643 1.081892 CAAGTGTGATCGAGGGCTTG 58.918 55.000 0.00 0.00 0.00 4.01
1543 1644 0.687354 ACAAGTGTGATCGAGGGCTT 59.313 50.000 0.00 0.00 0.00 4.35
1544 1645 0.687354 AACAAGTGTGATCGAGGGCT 59.313 50.000 0.00 0.00 0.00 5.19
1545 1646 1.464997 GAAACAAGTGTGATCGAGGGC 59.535 52.381 0.00 0.00 0.00 5.19
1546 1647 2.766313 TGAAACAAGTGTGATCGAGGG 58.234 47.619 0.00 0.00 0.00 4.30
1547 1648 4.811555 TTTGAAACAAGTGTGATCGAGG 57.188 40.909 0.00 0.00 0.00 4.63
1574 1675 4.081087 TGCTAGAGTAATCGAGGGCTTTTT 60.081 41.667 2.51 0.00 0.00 1.94
1575 1676 3.451178 TGCTAGAGTAATCGAGGGCTTTT 59.549 43.478 2.51 0.00 0.00 2.27
1576 1677 3.031736 TGCTAGAGTAATCGAGGGCTTT 58.968 45.455 2.51 0.00 0.00 3.51
1577 1678 2.625790 CTGCTAGAGTAATCGAGGGCTT 59.374 50.000 2.51 0.00 0.00 4.35
1578 1679 2.235016 CTGCTAGAGTAATCGAGGGCT 58.765 52.381 2.51 0.00 0.00 5.19
1588 1689 9.720769 AACAGTTTAATTTAAGCTGCTAGAGTA 57.279 29.630 24.45 0.00 46.77 2.59
1610 1711 6.642131 CCTAAATTGTTGTGAATGGTGAACAG 59.358 38.462 0.00 0.00 30.37 3.16
1619 1720 4.082787 CCGCTCACCTAAATTGTTGTGAAT 60.083 41.667 5.90 0.00 37.29 2.57
1620 1721 3.252215 CCGCTCACCTAAATTGTTGTGAA 59.748 43.478 5.90 0.00 37.29 3.18
1700 1805 2.507854 CGGGTAGGGATGGATGCGT 61.508 63.158 0.00 0.00 0.00 5.24
1749 1854 4.446371 CTTCCTTAGCATCAACCAGTAGG 58.554 47.826 0.00 0.00 42.21 3.18
1784 1893 1.339535 TGAGCTCACCAACACAACACA 60.340 47.619 13.74 0.00 0.00 3.72
1798 1907 5.353678 AGATTCATGTTGCTAACTTGAGCTC 59.646 40.000 6.82 6.82 43.58 4.09
1821 1930 2.704464 TTGCACTCCCTGATCATCAG 57.296 50.000 7.79 7.79 43.91 2.90
1829 1938 1.604593 CCCCACTTTGCACTCCCTG 60.605 63.158 0.00 0.00 0.00 4.45
1957 2069 2.920524 TGTTTTTGTGAGGGTCGCTTA 58.079 42.857 0.00 0.00 0.00 3.09
1958 2070 1.757682 TGTTTTTGTGAGGGTCGCTT 58.242 45.000 0.00 0.00 0.00 4.68
1959 2071 1.404035 GTTGTTTTTGTGAGGGTCGCT 59.596 47.619 0.00 0.00 0.00 4.93
1960 2072 1.535226 GGTTGTTTTTGTGAGGGTCGC 60.535 52.381 0.00 0.00 0.00 5.19
1961 2073 1.066454 GGGTTGTTTTTGTGAGGGTCG 59.934 52.381 0.00 0.00 0.00 4.79
1962 2074 2.104170 TGGGTTGTTTTTGTGAGGGTC 58.896 47.619 0.00 0.00 0.00 4.46
1963 2075 1.828595 GTGGGTTGTTTTTGTGAGGGT 59.171 47.619 0.00 0.00 0.00 4.34
1964 2076 1.202359 CGTGGGTTGTTTTTGTGAGGG 60.202 52.381 0.00 0.00 0.00 4.30
1965 2077 1.801025 GCGTGGGTTGTTTTTGTGAGG 60.801 52.381 0.00 0.00 0.00 3.86
1966 2078 1.135257 TGCGTGGGTTGTTTTTGTGAG 60.135 47.619 0.00 0.00 0.00 3.51
1967 2079 0.888619 TGCGTGGGTTGTTTTTGTGA 59.111 45.000 0.00 0.00 0.00 3.58
1968 2080 1.592081 CATGCGTGGGTTGTTTTTGTG 59.408 47.619 0.00 0.00 0.00 3.33
1969 2081 1.933247 CATGCGTGGGTTGTTTTTGT 58.067 45.000 0.00 0.00 0.00 2.83
1970 2082 0.581053 GCATGCGTGGGTTGTTTTTG 59.419 50.000 8.27 0.00 0.00 2.44
1971 2083 0.873743 CGCATGCGTGGGTTGTTTTT 60.874 50.000 31.33 0.00 33.90 1.94
1972 2084 1.299773 CGCATGCGTGGGTTGTTTT 60.300 52.632 31.33 0.00 33.90 2.43
1973 2085 2.334653 CGCATGCGTGGGTTGTTT 59.665 55.556 31.33 0.00 33.90 2.83
1974 2086 4.341502 GCGCATGCGTGGGTTGTT 62.342 61.111 37.54 0.00 42.09 2.83
1988 2100 0.670162 ATATGAATTGGGCACAGCGC 59.330 50.000 0.00 0.00 41.94 5.92
1989 2101 1.267806 GGATATGAATTGGGCACAGCG 59.732 52.381 0.00 0.00 0.00 5.18
1990 2102 1.615392 GGGATATGAATTGGGCACAGC 59.385 52.381 0.00 0.00 0.00 4.40
1991 2103 2.948115 TGGGATATGAATTGGGCACAG 58.052 47.619 0.00 0.00 0.00 3.66
1992 2104 3.053019 TCTTGGGATATGAATTGGGCACA 60.053 43.478 0.00 0.00 0.00 4.57
1993 2105 3.565307 TCTTGGGATATGAATTGGGCAC 58.435 45.455 0.00 0.00 0.00 5.01
1994 2106 3.960102 GTTCTTGGGATATGAATTGGGCA 59.040 43.478 0.00 0.00 0.00 5.36
1995 2107 3.321968 GGTTCTTGGGATATGAATTGGGC 59.678 47.826 0.00 0.00 0.00 5.36
1996 2108 3.569701 CGGTTCTTGGGATATGAATTGGG 59.430 47.826 0.00 0.00 0.00 4.12
1997 2109 4.207165 ACGGTTCTTGGGATATGAATTGG 58.793 43.478 0.00 0.00 0.00 3.16
1998 2110 5.581605 CAACGGTTCTTGGGATATGAATTG 58.418 41.667 0.00 0.00 0.00 2.32
1999 2111 4.097892 GCAACGGTTCTTGGGATATGAATT 59.902 41.667 0.00 0.00 0.00 2.17
2000 2112 3.632145 GCAACGGTTCTTGGGATATGAAT 59.368 43.478 0.00 0.00 0.00 2.57
2001 2113 3.013921 GCAACGGTTCTTGGGATATGAA 58.986 45.455 0.00 0.00 0.00 2.57
2002 2114 2.238646 AGCAACGGTTCTTGGGATATGA 59.761 45.455 0.00 0.00 0.00 2.15
2003 2115 2.614057 GAGCAACGGTTCTTGGGATATG 59.386 50.000 0.00 0.00 0.00 1.78
2004 2116 2.238646 TGAGCAACGGTTCTTGGGATAT 59.761 45.455 0.00 0.00 0.00 1.63
2005 2117 1.626321 TGAGCAACGGTTCTTGGGATA 59.374 47.619 0.00 0.00 0.00 2.59
2006 2118 0.400213 TGAGCAACGGTTCTTGGGAT 59.600 50.000 0.00 0.00 0.00 3.85
2007 2119 0.534203 GTGAGCAACGGTTCTTGGGA 60.534 55.000 0.00 0.00 0.00 4.37
2008 2120 0.817634 TGTGAGCAACGGTTCTTGGG 60.818 55.000 0.00 0.00 0.00 4.12
2009 2121 1.069022 CATGTGAGCAACGGTTCTTGG 60.069 52.381 0.00 0.00 0.00 3.61
2010 2122 1.664016 GCATGTGAGCAACGGTTCTTG 60.664 52.381 0.00 0.00 0.00 3.02
2011 2123 0.593128 GCATGTGAGCAACGGTTCTT 59.407 50.000 0.00 0.00 0.00 2.52
2012 2124 0.534877 TGCATGTGAGCAACGGTTCT 60.535 50.000 0.00 0.00 42.46 3.01
2013 2125 1.948508 TGCATGTGAGCAACGGTTC 59.051 52.632 0.00 0.00 42.46 3.62
2014 2126 4.155950 TGCATGTGAGCAACGGTT 57.844 50.000 0.00 0.00 42.46 4.44
2016 2128 5.093296 ATGATCATGCATGTGAGCAACGG 62.093 47.826 25.43 0.00 46.22 4.44
2017 2129 2.032924 ATGATCATGCATGTGAGCAACG 59.967 45.455 25.43 0.00 46.22 4.10
2018 2130 3.710326 ATGATCATGCATGTGAGCAAC 57.290 42.857 25.43 6.15 46.22 4.17
2019 2131 3.445805 ACAATGATCATGCATGTGAGCAA 59.554 39.130 25.43 6.27 46.22 3.91
2021 2133 3.372060 CACAATGATCATGCATGTGAGC 58.628 45.455 25.11 12.44 35.18 4.26
2022 2134 3.372060 GCACAATGATCATGCATGTGAG 58.628 45.455 30.16 16.35 39.23 3.51
2023 2135 2.223386 CGCACAATGATCATGCATGTGA 60.223 45.455 30.16 9.66 39.39 3.58
2024 2136 2.116366 CGCACAATGATCATGCATGTG 58.884 47.619 25.04 25.04 39.39 3.21
2025 2137 1.746787 ACGCACAATGATCATGCATGT 59.253 42.857 25.43 13.42 39.39 3.21
2026 2138 2.485266 ACGCACAATGATCATGCATG 57.515 45.000 21.07 21.07 39.39 4.06
2027 2139 3.546616 CGTTACGCACAATGATCATGCAT 60.547 43.478 17.51 7.03 39.39 3.96
2028 2140 2.222999 CGTTACGCACAATGATCATGCA 60.223 45.455 17.51 0.00 39.39 3.96
2029 2141 2.365948 CGTTACGCACAATGATCATGC 58.634 47.619 9.46 9.38 35.96 4.06
2044 2156 1.226018 GTTCCTGCATGCGCGTTAC 60.226 57.895 14.09 3.69 42.97 2.50
2045 2157 2.735677 CGTTCCTGCATGCGCGTTA 61.736 57.895 14.09 0.00 42.97 3.18
2046 2158 4.088762 CGTTCCTGCATGCGCGTT 62.089 61.111 14.09 0.00 42.97 4.84
2048 2160 4.505217 GTCGTTCCTGCATGCGCG 62.505 66.667 14.09 0.00 42.97 6.86
2049 2161 4.505217 CGTCGTTCCTGCATGCGC 62.505 66.667 14.09 0.00 39.24 6.09
2050 2162 2.792290 CTCGTCGTTCCTGCATGCG 61.792 63.158 14.09 7.87 0.00 4.73
2051 2163 2.456119 CCTCGTCGTTCCTGCATGC 61.456 63.158 11.82 11.82 0.00 4.06
2052 2164 2.456119 GCCTCGTCGTTCCTGCATG 61.456 63.158 0.00 0.00 0.00 4.06
2053 2165 2.125512 GCCTCGTCGTTCCTGCAT 60.126 61.111 0.00 0.00 0.00 3.96
2054 2166 4.717629 CGCCTCGTCGTTCCTGCA 62.718 66.667 0.00 0.00 0.00 4.41
2055 2167 4.415332 TCGCCTCGTCGTTCCTGC 62.415 66.667 0.00 0.00 0.00 4.85
2056 2168 2.202492 CTCGCCTCGTCGTTCCTG 60.202 66.667 0.00 0.00 0.00 3.86
2057 2169 3.441290 CCTCGCCTCGTCGTTCCT 61.441 66.667 0.00 0.00 0.00 3.36
2059 2171 4.415332 TGCCTCGCCTCGTCGTTC 62.415 66.667 0.00 0.00 0.00 3.95
2155 2267 2.492090 CGGAGGAAGACGCAGAGG 59.508 66.667 0.00 0.00 0.00 3.69
2179 2291 4.386591 GGGACGGGGTTGAGGATA 57.613 61.111 0.00 0.00 0.00 2.59
2733 2858 2.594303 CTCAGCGTGGCAACCCAA 60.594 61.111 0.00 0.00 44.33 4.12
2736 2861 3.730761 CTGCTCAGCGTGGCAACC 61.731 66.667 0.00 0.00 38.02 3.77
2739 2864 4.383861 CCTCTGCTCAGCGTGGCA 62.384 66.667 0.00 0.00 36.94 4.92
2741 2866 3.368190 CTCCCTCTGCTCAGCGTGG 62.368 68.421 0.00 0.00 0.00 4.94
2742 2867 1.315981 TACTCCCTCTGCTCAGCGTG 61.316 60.000 0.00 0.00 0.00 5.34
2743 2868 1.000771 TACTCCCTCTGCTCAGCGT 60.001 57.895 0.00 0.00 0.00 5.07
3061 3190 3.938963 TGAGCAAGAAACGTTCTGAGTTT 59.061 39.130 0.00 0.00 43.60 2.66
3334 3477 5.357257 ACATAATGTAGGTGTGATCGAACC 58.643 41.667 8.28 8.28 36.66 3.62
3339 3482 9.601217 AGACTAAAACATAATGTAGGTGTGATC 57.399 33.333 0.00 0.00 0.00 2.92
3358 3508 6.041409 CAGATTCATGGCTCTCCTAGACTAAA 59.959 42.308 0.00 0.00 32.57 1.85
3359 3509 5.538053 CAGATTCATGGCTCTCCTAGACTAA 59.462 44.000 0.00 0.00 32.57 2.24
3378 3528 8.367660 TCACCAAGAACTAGTAATCTCAGATT 57.632 34.615 4.98 4.98 0.00 2.40
3389 3539 7.907389 TGTTAATCTGATCACCAAGAACTAGT 58.093 34.615 0.00 0.00 0.00 2.57
3390 3540 8.824781 CATGTTAATCTGATCACCAAGAACTAG 58.175 37.037 0.00 0.00 0.00 2.57
3410 3566 0.251916 CGTCCAGCCCCTTCATGTTA 59.748 55.000 0.00 0.00 0.00 2.41
3431 3587 0.828022 CGTACACTGGCCCTTGGATA 59.172 55.000 0.00 0.00 0.00 2.59
3443 3599 1.201647 CATCCTGTTCCGACGTACACT 59.798 52.381 0.00 0.00 0.00 3.55
3746 3971 3.589654 CTGCCCGAACCGCTTCTCA 62.590 63.158 0.00 0.00 0.00 3.27
3934 4170 6.258947 GGAGTCTGGAACTATTTATGTGAAGC 59.741 42.308 0.00 0.00 38.74 3.86
3937 4173 5.724370 TGGGAGTCTGGAACTATTTATGTGA 59.276 40.000 0.00 0.00 38.74 3.58
3944 4180 5.964477 TCATTACTGGGAGTCTGGAACTATT 59.036 40.000 0.00 0.00 38.74 1.73
3958 4194 4.494091 AGGAACACAGATCATTACTGGG 57.506 45.455 0.00 0.00 43.49 4.45
3996 4375 0.979187 GACCCGTAGATCCACCCCAA 60.979 60.000 0.00 0.00 0.00 4.12
4127 4506 1.046472 ACACCTGGTTGAGACGGTCA 61.046 55.000 11.27 0.00 0.00 4.02
4364 4820 3.421844 GACAAATGGGGAAACTAGCTGT 58.578 45.455 0.00 0.00 0.00 4.40
4366 4822 2.649816 AGGACAAATGGGGAAACTAGCT 59.350 45.455 0.00 0.00 0.00 3.32
4367 4823 3.017442 GAGGACAAATGGGGAAACTAGC 58.983 50.000 0.00 0.00 0.00 3.42
4368 4824 3.267031 AGGAGGACAAATGGGGAAACTAG 59.733 47.826 0.00 0.00 0.00 2.57
4369 4825 3.265489 AGGAGGACAAATGGGGAAACTA 58.735 45.455 0.00 0.00 0.00 2.24
4370 4826 2.073776 AGGAGGACAAATGGGGAAACT 58.926 47.619 0.00 0.00 0.00 2.66
4371 4827 2.604912 AGGAGGACAAATGGGGAAAC 57.395 50.000 0.00 0.00 0.00 2.78
4464 4924 2.732412 TGAAGAAGAGACTGGCGAAG 57.268 50.000 0.00 0.00 0.00 3.79
5048 5511 6.545504 TGCACAATCTTCAGAACTCTTAAC 57.454 37.500 0.00 0.00 0.00 2.01
5110 5573 7.710044 ACAAAACATAGCATGAACAAAACATCA 59.290 29.630 0.00 0.00 0.00 3.07
5246 5715 3.868619 AACTTACCAGCTACCCACAAA 57.131 42.857 0.00 0.00 0.00 2.83
5299 5768 3.848272 ATCAAGTAAATGCACCCGTTG 57.152 42.857 0.00 0.00 0.00 4.10
5303 5772 6.346518 CGTTCAAAAATCAAGTAAATGCACCC 60.347 38.462 0.00 0.00 0.00 4.61
5334 5803 8.740123 TCCTCAGTCTGAATACTACTCTTAAG 57.260 38.462 3.67 0.00 0.00 1.85
5345 5814 7.921041 ATCCTGTTTATCCTCAGTCTGAATA 57.079 36.000 3.67 0.00 0.00 1.75
5363 5833 5.497474 GTTTGGTGAATACTGGTATCCTGT 58.503 41.667 4.00 4.00 39.06 4.00
5367 5837 6.119536 TGATGGTTTGGTGAATACTGGTATC 58.880 40.000 0.00 0.00 0.00 2.24
5412 5889 0.799534 GCGGCTGCTGTAATGCAAAG 60.800 55.000 11.21 0.00 42.83 2.77
5659 6293 3.061831 CAGATTTTGTAGCTGTGCTCTCG 59.938 47.826 0.00 0.00 40.44 4.04
5806 6440 7.119709 CCCCCTCTTTTAGTTTCTTTTCAAA 57.880 36.000 0.00 0.00 0.00 2.69
5834 6468 1.051556 CACTTCTAGCCCCTCTCCCC 61.052 65.000 0.00 0.00 0.00 4.81
5835 6469 1.691195 GCACTTCTAGCCCCTCTCCC 61.691 65.000 0.00 0.00 0.00 4.30
5836 6470 0.978146 TGCACTTCTAGCCCCTCTCC 60.978 60.000 0.00 0.00 0.00 3.71
5837 6471 0.176910 GTGCACTTCTAGCCCCTCTC 59.823 60.000 10.32 0.00 0.00 3.20
5838 6472 0.252467 AGTGCACTTCTAGCCCCTCT 60.252 55.000 15.25 0.00 0.00 3.69
5839 6473 1.486211 TAGTGCACTTCTAGCCCCTC 58.514 55.000 27.06 0.00 0.00 4.30
5943 6578 2.825836 CCCTGCCGATCAAGGTGC 60.826 66.667 5.60 0.00 0.00 5.01
5961 6596 7.293018 ACAAAACGAACGAGTATTAAACATCC 58.707 34.615 0.14 0.00 0.00 3.51
5976 6611 7.739043 CCGTAGAGAAGAAATAACAAAACGAAC 59.261 37.037 0.00 0.00 0.00 3.95
6003 6638 2.423538 ACTGTGCAAACAGACAAGGAAC 59.576 45.455 12.57 0.00 39.99 3.62


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

AutoCloner maintained by Alex Coulton.