Multiple sequence alignment - TraesCS1A01G373800

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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 TraesCS1A01G373800 chr1A 100.000 2968 0 0 1 2968 549525212 549522245 0.000000e+00 5481.0
1 TraesCS1A01G373800 chr1B 87.542 1766 99 63 430 2130 626252121 626250412 0.000000e+00 1930.0
2 TraesCS1A01G373800 chr1B 89.141 396 34 8 12 405 626252502 626252114 4.450000e-133 484.0
3 TraesCS1A01G373800 chr1B 92.208 231 12 2 2164 2388 626250422 626250192 3.690000e-84 322.0
4 TraesCS1A01G373800 chr1B 89.627 241 16 5 2736 2968 626250161 626249922 6.220000e-77 298.0
5 TraesCS1A01G373800 chr1B 81.343 268 19 15 519 773 626305928 626305679 3.910000e-44 189.0
6 TraesCS1A01G373800 chr1B 97.059 34 0 1 365 398 636744599 636744567 4.130000e-04 56.5
7 TraesCS1A01G373800 chr1D 89.342 1201 69 31 430 1591 455805076 455803896 0.000000e+00 1454.0
8 TraesCS1A01G373800 chr1D 83.724 811 49 22 1632 2420 455803819 455803070 0.000000e+00 689.0
9 TraesCS1A01G373800 chr1D 88.386 508 34 17 2475 2968 455802936 455802440 3.300000e-164 588.0
10 TraesCS1A01G373800 chr1D 83.171 410 44 11 6 405 455805463 455805069 4.710000e-93 351.0
11 TraesCS1A01G373800 chr1D 83.756 197 16 8 521 703 455993226 455993032 3.930000e-39 172.0
12 TraesCS1A01G373800 chr3B 88.286 350 34 4 49 394 139462390 139462736 2.130000e-111 412.0
13 TraesCS1A01G373800 chr3B 89.583 48 1 4 365 412 525228871 525228828 1.150000e-04 58.4
14 TraesCS1A01G373800 chr7A 100.000 34 0 0 365 398 106812208 106812241 2.470000e-06 63.9
15 TraesCS1A01G373800 chr3A 95.000 40 1 1 365 404 714162064 714162102 8.880000e-06 62.1
16 TraesCS1A01G373800 chr3D 97.059 34 0 1 365 398 135751003 135751035 4.130000e-04 56.5
17 TraesCS1A01G373800 chr3D 100.000 29 0 0 365 393 371442838 371442810 1.000000e-03 54.7
18 TraesCS1A01G373800 chr2B 92.500 40 1 2 365 404 757861029 757861066 4.130000e-04 56.5


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 TraesCS1A01G373800 chr1A 549522245 549525212 2967 True 5481.0 5481 100.00000 1 2968 1 chr1A.!!$R1 2967
1 TraesCS1A01G373800 chr1B 626249922 626252502 2580 True 758.5 1930 89.62950 12 2968 4 chr1B.!!$R3 2956
2 TraesCS1A01G373800 chr1D 455802440 455805463 3023 True 770.5 1454 86.15575 6 2968 4 chr1D.!!$R2 2962

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
457 464 0.385473 GGACGGTGTTGCGTCATTTG 60.385 55.0 0.0 0.0 36.91 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2349 2491 0.03582 GTGGTGCCGTCTAATCCCAA 60.036 55.0 0.0 0.0 0.0 4.12 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
38 39 6.608405 TGAAAAGGTAGATACAATAGGGACGA 59.392 38.462 0.00 0.00 0.00 4.20
39 40 7.289317 TGAAAAGGTAGATACAATAGGGACGAT 59.711 37.037 0.00 0.00 0.00 3.73
40 41 6.591750 AAGGTAGATACAATAGGGACGATG 57.408 41.667 0.00 0.00 0.00 3.84
41 42 5.642165 AGGTAGATACAATAGGGACGATGT 58.358 41.667 0.00 0.00 0.00 3.06
43 44 7.411808 AGGTAGATACAATAGGGACGATGTAT 58.588 38.462 0.00 0.00 0.00 2.29
44 45 7.556996 AGGTAGATACAATAGGGACGATGTATC 59.443 40.741 13.98 13.98 36.18 2.24
45 46 7.338703 GGTAGATACAATAGGGACGATGTATCA 59.661 40.741 20.53 8.96 37.16 2.15
46 47 7.397892 AGATACAATAGGGACGATGTATCAG 57.602 40.000 20.53 0.00 37.16 2.90
47 48 6.948886 AGATACAATAGGGACGATGTATCAGT 59.051 38.462 20.53 4.80 37.16 3.41
50 51 0.753262 AGGGACGATGTATCAGTGGC 59.247 55.000 0.00 0.00 0.00 5.01
54 55 2.361119 GGACGATGTATCAGTGGCTACA 59.639 50.000 2.02 8.35 32.75 2.74
75 76 1.987807 TTGATAGGCTGGGCTGCTCC 61.988 60.000 6.93 0.00 0.00 4.70
87 88 1.001503 CTGCTCCCTCACTCCCTCT 59.998 63.158 0.00 0.00 0.00 3.69
88 89 0.617249 CTGCTCCCTCACTCCCTCTT 60.617 60.000 0.00 0.00 0.00 2.85
90 91 0.988063 GCTCCCTCACTCCCTCTTTT 59.012 55.000 0.00 0.00 0.00 2.27
170 171 6.982724 ACAGAAGGAAAAGAAGCAGAAAAATG 59.017 34.615 0.00 0.00 0.00 2.32
224 226 2.383298 ACAAAAATGCGTCACACGAG 57.617 45.000 0.00 0.00 46.05 4.18
258 260 3.130340 TGAAGTCAAAGGTGCAGAAAACC 59.870 43.478 0.00 0.00 38.03 3.27
321 323 7.156876 TCAAAGCCTAAGACCATTACATTTG 57.843 36.000 0.00 0.00 0.00 2.32
325 331 7.158099 AGCCTAAGACCATTACATTTGTTTC 57.842 36.000 0.00 0.00 0.00 2.78
405 412 6.015856 GCATTCAGCTAGTTATCAGGTAGAGA 60.016 42.308 0.00 0.00 41.15 3.10
406 413 6.945938 TTCAGCTAGTTATCAGGTAGAGAC 57.054 41.667 0.00 0.00 0.00 3.36
407 414 5.057819 TCAGCTAGTTATCAGGTAGAGACG 58.942 45.833 0.00 0.00 0.00 4.18
408 415 5.057819 CAGCTAGTTATCAGGTAGAGACGA 58.942 45.833 0.00 0.00 0.00 4.20
409 416 5.049954 CAGCTAGTTATCAGGTAGAGACGAC 60.050 48.000 0.00 0.00 0.00 4.34
410 417 4.084433 GCTAGTTATCAGGTAGAGACGACG 60.084 50.000 0.00 0.00 0.00 5.12
411 418 3.204526 AGTTATCAGGTAGAGACGACGG 58.795 50.000 0.00 0.00 0.00 4.79
412 419 2.941720 GTTATCAGGTAGAGACGACGGT 59.058 50.000 0.00 0.00 0.00 4.83
413 420 1.380524 ATCAGGTAGAGACGACGGTG 58.619 55.000 0.00 0.00 0.00 4.94
414 421 0.675837 TCAGGTAGAGACGACGGTGG 60.676 60.000 0.00 0.00 0.00 4.61
415 422 2.045131 AGGTAGAGACGACGGTGGC 61.045 63.158 0.00 0.00 0.00 5.01
416 423 2.338015 GGTAGAGACGACGGTGGCA 61.338 63.158 0.00 0.00 0.00 4.92
417 424 1.136984 GTAGAGACGACGGTGGCAG 59.863 63.158 0.00 0.00 0.00 4.85
418 425 1.303074 TAGAGACGACGGTGGCAGT 60.303 57.895 0.00 0.00 0.00 4.40
419 426 1.303799 TAGAGACGACGGTGGCAGTC 61.304 60.000 0.00 0.00 35.41 3.51
420 427 2.910479 AGACGACGGTGGCAGTCA 60.910 61.111 7.54 0.00 38.46 3.41
421 428 2.028484 GACGACGGTGGCAGTCAA 59.972 61.111 7.54 0.00 38.46 3.18
422 429 1.593209 GACGACGGTGGCAGTCAAA 60.593 57.895 7.54 0.00 38.46 2.69
423 430 1.153329 ACGACGGTGGCAGTCAAAA 60.153 52.632 7.54 0.00 38.46 2.44
424 431 0.745128 ACGACGGTGGCAGTCAAAAA 60.745 50.000 7.54 0.00 38.46 1.94
450 457 0.456312 GTAGAGAGGACGGTGTTGCG 60.456 60.000 0.00 0.00 0.00 4.85
457 464 0.385473 GGACGGTGTTGCGTCATTTG 60.385 55.000 0.00 0.00 36.91 2.32
480 487 2.014335 GCCTGGTGAATTTGGCAATC 57.986 50.000 0.00 0.00 44.34 2.67
517 529 6.295745 GGATAAGCCTCCTAGTGGTTATAACC 60.296 46.154 25.22 25.22 39.68 2.85
537 549 4.594136 ACCGAAGAACAAAGCTTTTTACG 58.406 39.130 9.53 9.45 0.00 3.18
680 695 2.413239 CGTAGCAACCAACAAGATGCAG 60.413 50.000 0.00 0.00 41.18 4.41
760 775 2.726351 CCCGAGTCTTGGAGGCTCC 61.726 68.421 26.95 26.95 43.81 4.70
795 810 3.647771 GGTCCCCGGCAAACCTCT 61.648 66.667 10.06 0.00 0.00 3.69
834 849 4.506255 CCGGCATCCCTCCAACCC 62.506 72.222 0.00 0.00 0.00 4.11
835 850 4.506255 CGGCATCCCTCCAACCCC 62.506 72.222 0.00 0.00 0.00 4.95
836 851 4.143301 GGCATCCCTCCAACCCCC 62.143 72.222 0.00 0.00 0.00 5.40
837 852 4.506255 GCATCCCTCCAACCCCCG 62.506 72.222 0.00 0.00 0.00 5.73
838 853 3.015145 CATCCCTCCAACCCCCGT 61.015 66.667 0.00 0.00 0.00 5.28
839 854 3.015145 ATCCCTCCAACCCCCGTG 61.015 66.667 0.00 0.00 0.00 4.94
840 855 3.883822 ATCCCTCCAACCCCCGTGT 62.884 63.158 0.00 0.00 0.00 4.49
841 856 4.344865 CCCTCCAACCCCCGTGTG 62.345 72.222 0.00 0.00 0.00 3.82
907 922 2.123428 ATGCTCTTTCCGGCATGGC 61.123 57.895 9.69 9.69 45.81 4.40
908 923 2.751436 GCTCTTTCCGGCATGGCA 60.751 61.111 20.37 0.00 37.80 4.92
910 925 1.377725 CTCTTTCCGGCATGGCAGT 60.378 57.895 20.37 0.00 37.80 4.40
1013 1032 3.440415 AGCGATGGCGACGACTCA 61.440 61.111 0.65 0.00 46.35 3.41
1020 1039 2.276994 GCGACGACTCAGAGAGCG 60.277 66.667 3.79 9.95 36.12 5.03
1038 1057 4.353437 ACGGTTCCTCACGTCCGC 62.353 66.667 10.66 0.00 45.76 5.54
1056 1075 2.124653 AGCGACTCCGAGTCCGAT 60.125 61.111 20.57 12.64 42.12 4.18
1188 1212 3.576078 TTTTCCCTCTGAGCTGTTCAA 57.424 42.857 0.00 0.00 34.81 2.69
1189 1213 3.795688 TTTCCCTCTGAGCTGTTCAAT 57.204 42.857 0.00 0.00 34.81 2.57
1190 1214 3.795688 TTCCCTCTGAGCTGTTCAATT 57.204 42.857 0.00 0.00 34.81 2.32
1191 1215 3.795688 TCCCTCTGAGCTGTTCAATTT 57.204 42.857 0.00 0.00 34.81 1.82
1192 1216 3.679389 TCCCTCTGAGCTGTTCAATTTC 58.321 45.455 0.00 0.00 34.81 2.17
1193 1217 3.328931 TCCCTCTGAGCTGTTCAATTTCT 59.671 43.478 0.00 0.00 34.81 2.52
1195 1219 4.321718 CCTCTGAGCTGTTCAATTTCTGA 58.678 43.478 0.00 0.00 34.81 3.27
1204 1228 1.872388 TCAATTTCTGAACGTCGGCA 58.128 45.000 0.00 0.00 0.00 5.69
1205 1229 2.214347 TCAATTTCTGAACGTCGGCAA 58.786 42.857 0.00 0.00 0.00 4.52
1206 1230 2.811431 TCAATTTCTGAACGTCGGCAAT 59.189 40.909 0.00 0.00 0.00 3.56
1207 1231 3.997681 TCAATTTCTGAACGTCGGCAATA 59.002 39.130 0.00 0.00 0.00 1.90
1209 1233 5.813157 TCAATTTCTGAACGTCGGCAATATA 59.187 36.000 0.00 0.00 0.00 0.86
1210 1234 6.481976 TCAATTTCTGAACGTCGGCAATATAT 59.518 34.615 0.00 0.00 0.00 0.86
1211 1235 5.651172 TTTCTGAACGTCGGCAATATATG 57.349 39.130 0.00 0.00 0.00 1.78
1451 1501 2.604686 AGCACGCCTTCAGGGAGA 60.605 61.111 0.00 0.00 38.31 3.71
1548 1598 2.761208 AGAAGTTCCTCTCGGTACCATG 59.239 50.000 13.54 3.62 31.44 3.66
1591 1645 2.642425 GCCCCATGCATCATCTGAG 58.358 57.895 0.00 0.00 40.77 3.35
1592 1646 1.524863 GCCCCATGCATCATCTGAGC 61.525 60.000 0.00 0.00 40.77 4.26
1593 1647 0.110678 CCCCATGCATCATCTGAGCT 59.889 55.000 0.00 0.00 0.00 4.09
1594 1648 1.524848 CCCATGCATCATCTGAGCTC 58.475 55.000 6.82 6.82 0.00 4.09
1595 1649 1.202770 CCCATGCATCATCTGAGCTCA 60.203 52.381 17.19 17.19 0.00 4.26
1596 1650 2.147150 CCATGCATCATCTGAGCTCAG 58.853 52.381 33.73 33.73 45.08 3.35
1597 1651 2.485657 CCATGCATCATCTGAGCTCAGT 60.486 50.000 36.32 23.73 44.12 3.41
1598 1652 2.311124 TGCATCATCTGAGCTCAGTG 57.689 50.000 36.32 31.02 44.12 3.66
1599 1653 1.829222 TGCATCATCTGAGCTCAGTGA 59.171 47.619 36.32 33.98 44.12 3.41
1600 1654 2.235402 TGCATCATCTGAGCTCAGTGAA 59.765 45.455 36.32 22.78 44.12 3.18
1604 1658 5.658468 CATCATCTGAGCTCAGTGAACTAA 58.342 41.667 36.32 20.22 44.12 2.24
1609 1663 5.164233 TCTGAGCTCAGTGAACTAATTTCG 58.836 41.667 36.32 12.73 44.12 3.46
1612 1666 4.246458 AGCTCAGTGAACTAATTTCGTCC 58.754 43.478 0.00 0.00 36.97 4.79
1613 1667 3.994392 GCTCAGTGAACTAATTTCGTCCA 59.006 43.478 0.00 0.00 36.97 4.02
1614 1668 4.631813 GCTCAGTGAACTAATTTCGTCCAT 59.368 41.667 0.00 0.00 36.97 3.41
1616 1670 6.312918 GCTCAGTGAACTAATTTCGTCCATTA 59.687 38.462 0.00 0.00 36.97 1.90
1617 1671 7.011482 GCTCAGTGAACTAATTTCGTCCATTAT 59.989 37.037 0.00 0.00 36.97 1.28
1618 1672 8.786826 TCAGTGAACTAATTTCGTCCATTATT 57.213 30.769 0.00 0.00 36.97 1.40
1620 1674 8.883731 CAGTGAACTAATTTCGTCCATTATTCT 58.116 33.333 0.00 0.00 36.97 2.40
1621 1675 9.449719 AGTGAACTAATTTCGTCCATTATTCTT 57.550 29.630 0.00 0.00 36.97 2.52
1622 1676 9.490663 GTGAACTAATTTCGTCCATTATTCTTG 57.509 33.333 0.00 0.00 36.97 3.02
1623 1677 9.226606 TGAACTAATTTCGTCCATTATTCTTGT 57.773 29.630 0.00 0.00 36.97 3.16
1626 1680 9.449719 ACTAATTTCGTCCATTATTCTTGTTCT 57.550 29.630 0.00 0.00 0.00 3.01
1627 1681 9.708222 CTAATTTCGTCCATTATTCTTGTTCTG 57.292 33.333 0.00 0.00 0.00 3.02
1628 1682 7.921786 ATTTCGTCCATTATTCTTGTTCTGA 57.078 32.000 0.00 0.00 0.00 3.27
1630 1684 6.721571 TCGTCCATTATTCTTGTTCTGAAC 57.278 37.500 13.49 13.49 0.00 3.18
1711 1804 2.230750 ACTCTGGTCTACGTTGGTAAGC 59.769 50.000 0.00 0.00 0.00 3.09
1714 1807 3.119245 TCTGGTCTACGTTGGTAAGCATC 60.119 47.826 0.00 0.00 0.00 3.91
1716 1809 2.547826 GTCTACGTTGGTAAGCATCCC 58.452 52.381 0.00 0.00 0.00 3.85
1717 1810 1.483415 TCTACGTTGGTAAGCATCCCC 59.517 52.381 0.00 0.00 0.00 4.81
1718 1811 0.176219 TACGTTGGTAAGCATCCCCG 59.824 55.000 0.00 0.00 0.00 5.73
1719 1812 1.219664 CGTTGGTAAGCATCCCCGA 59.780 57.895 0.00 0.00 0.00 5.14
1721 1814 1.745827 CGTTGGTAAGCATCCCCGAAT 60.746 52.381 0.00 0.00 0.00 3.34
1722 1815 2.375146 GTTGGTAAGCATCCCCGAATT 58.625 47.619 0.00 0.00 0.00 2.17
1724 1817 3.094484 TGGTAAGCATCCCCGAATTTT 57.906 42.857 0.00 0.00 0.00 1.82
1725 1818 2.757868 TGGTAAGCATCCCCGAATTTTG 59.242 45.455 0.00 0.00 0.00 2.44
1727 1820 3.636764 GGTAAGCATCCCCGAATTTTGAT 59.363 43.478 0.00 0.00 0.00 2.57
1728 1821 4.261614 GGTAAGCATCCCCGAATTTTGATC 60.262 45.833 0.00 0.00 0.00 2.92
1729 1822 3.017048 AGCATCCCCGAATTTTGATCA 57.983 42.857 0.00 0.00 0.00 2.92
1730 1823 3.364549 AGCATCCCCGAATTTTGATCAA 58.635 40.909 3.38 3.38 0.00 2.57
1731 1824 3.131046 AGCATCCCCGAATTTTGATCAAC 59.869 43.478 7.89 0.00 0.00 3.18
1733 1826 4.620332 GCATCCCCGAATTTTGATCAACAA 60.620 41.667 7.89 6.58 36.65 2.83
1737 1834 4.447389 CCCCGAATTTTGATCAACAACAAC 59.553 41.667 7.89 0.00 38.29 3.32
1764 1869 6.558771 AAAAAGACATGATGATCGACAACA 57.441 33.333 0.00 0.00 35.86 3.33
1765 1870 6.558771 AAAAGACATGATGATCGACAACAA 57.441 33.333 0.00 0.00 35.10 2.83
1768 1873 6.558771 AGACATGATGATCGACAACAAAAA 57.441 33.333 0.00 0.00 35.10 1.94
1982 2098 2.034812 CCACTAGCTAGGGTTCATCGAC 59.965 54.545 24.35 0.00 0.00 4.20
1993 2109 1.665679 GTTCATCGACCAATGCATCGT 59.334 47.619 0.00 0.00 39.38 3.73
1994 2110 2.863740 GTTCATCGACCAATGCATCGTA 59.136 45.455 0.00 0.00 39.38 3.43
1995 2111 2.469826 TCATCGACCAATGCATCGTAC 58.530 47.619 0.00 0.00 39.38 3.67
1996 2112 2.159170 TCATCGACCAATGCATCGTACA 60.159 45.455 0.00 0.00 39.38 2.90
2007 2123 4.354071 TGCATCGTACATGGTTGATTTG 57.646 40.909 0.00 0.00 0.00 2.32
2014 2130 2.450476 ACATGGTTGATTTGAGGAGGC 58.550 47.619 0.00 0.00 0.00 4.70
2031 2147 1.377202 GCCGTGATGGTGATGGTGT 60.377 57.895 0.00 0.00 41.21 4.16
2087 2205 4.322953 GGAAATGGCAATGGACTCACAAAT 60.323 41.667 0.00 0.00 0.00 2.32
2088 2206 4.895668 AATGGCAATGGACTCACAAATT 57.104 36.364 0.00 0.00 0.00 1.82
2089 2207 5.999205 AATGGCAATGGACTCACAAATTA 57.001 34.783 0.00 0.00 0.00 1.40
2127 2245 0.248054 GTCGTGGCAAAGTGTGTGTG 60.248 55.000 0.00 0.00 0.00 3.82
2131 2249 0.525311 TGGCAAAGTGTGTGTGTGTG 59.475 50.000 0.00 0.00 0.00 3.82
2132 2250 0.525761 GGCAAAGTGTGTGTGTGTGT 59.474 50.000 0.00 0.00 0.00 3.72
2133 2251 1.616620 GCAAAGTGTGTGTGTGTGTG 58.383 50.000 0.00 0.00 0.00 3.82
2134 2252 1.068610 GCAAAGTGTGTGTGTGTGTGT 60.069 47.619 0.00 0.00 0.00 3.72
2135 2253 2.583739 CAAAGTGTGTGTGTGTGTGTG 58.416 47.619 0.00 0.00 0.00 3.82
2136 2254 1.890876 AAGTGTGTGTGTGTGTGTGT 58.109 45.000 0.00 0.00 0.00 3.72
2137 2255 1.155889 AGTGTGTGTGTGTGTGTGTG 58.844 50.000 0.00 0.00 0.00 3.82
2138 2256 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2139 2257 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2140 2258 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2141 2259 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2142 2260 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2143 2261 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2144 2262 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2145 2263 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2146 2264 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2147 2265 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2148 2266 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2149 2267 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2150 2268 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2255 2373 6.358974 TGAGTGATGTTCCTGTGAGAATTA 57.641 37.500 0.00 0.00 0.00 1.40
2258 2376 6.402222 AGTGATGTTCCTGTGAGAATTACTC 58.598 40.000 0.00 0.00 45.11 2.59
2270 2388 5.179555 GTGAGAATTACTCCTTGTTGGTGTC 59.820 44.000 0.00 0.00 44.34 3.67
2271 2389 4.652822 AGAATTACTCCTTGTTGGTGTCC 58.347 43.478 0.00 0.00 42.05 4.02
2272 2390 4.351111 AGAATTACTCCTTGTTGGTGTCCT 59.649 41.667 0.00 0.00 42.05 3.85
2273 2391 3.485463 TTACTCCTTGTTGGTGTCCTG 57.515 47.619 0.00 0.00 42.05 3.86
2274 2392 1.507140 ACTCCTTGTTGGTGTCCTGA 58.493 50.000 0.00 0.00 38.02 3.86
2275 2393 2.057922 ACTCCTTGTTGGTGTCCTGAT 58.942 47.619 0.00 0.00 38.02 2.90
2276 2394 2.224621 ACTCCTTGTTGGTGTCCTGATG 60.225 50.000 0.00 0.00 38.02 3.07
2277 2395 0.883833 CCTTGTTGGTGTCCTGATGC 59.116 55.000 0.00 0.00 0.00 3.91
2278 2396 1.608055 CTTGTTGGTGTCCTGATGCA 58.392 50.000 0.00 0.00 0.00 3.96
2279 2397 2.165167 CTTGTTGGTGTCCTGATGCAT 58.835 47.619 0.00 0.00 0.00 3.96
2280 2398 1.536940 TGTTGGTGTCCTGATGCATG 58.463 50.000 2.46 0.00 0.00 4.06
2281 2399 0.813184 GTTGGTGTCCTGATGCATGG 59.187 55.000 2.46 0.00 0.00 3.66
2282 2400 0.966875 TTGGTGTCCTGATGCATGGC 60.967 55.000 2.46 0.00 0.00 4.40
2283 2401 1.077212 GGTGTCCTGATGCATGGCT 60.077 57.895 2.46 0.00 0.00 4.75
2284 2402 0.682209 GGTGTCCTGATGCATGGCTT 60.682 55.000 2.46 0.00 0.00 4.35
2285 2403 0.737219 GTGTCCTGATGCATGGCTTC 59.263 55.000 2.46 0.00 34.04 3.86
2286 2404 0.745486 TGTCCTGATGCATGGCTTCG 60.745 55.000 2.46 0.00 35.83 3.79
2287 2405 0.745845 GTCCTGATGCATGGCTTCGT 60.746 55.000 2.46 0.00 35.83 3.85
2288 2406 0.462581 TCCTGATGCATGGCTTCGTC 60.463 55.000 2.46 0.00 35.83 4.20
2289 2407 0.463295 CCTGATGCATGGCTTCGTCT 60.463 55.000 2.46 0.00 35.83 4.18
2290 2408 0.935898 CTGATGCATGGCTTCGTCTC 59.064 55.000 2.46 0.00 35.83 3.36
2291 2409 0.538584 TGATGCATGGCTTCGTCTCT 59.461 50.000 2.46 0.00 35.83 3.10
2343 2485 6.317140 CAGTGCCAAGCAAAATAGAGAAGATA 59.683 38.462 0.00 0.00 41.47 1.98
2366 2508 2.052782 AATTGGGATTAGACGGCACC 57.947 50.000 0.00 0.00 0.00 5.01
2388 2534 2.516930 CCCGTCATGTCATGGGCC 60.517 66.667 12.90 0.00 35.71 5.80
2404 2550 3.196613 GCCTAGGGCTCGATTAACG 57.803 57.895 11.72 0.00 46.69 3.18
2407 2553 1.884579 CCTAGGGCTCGATTAACGCTA 59.115 52.381 0.00 0.00 42.26 4.26
2422 2568 3.234730 CTATCTTCCCGCCGCCCT 61.235 66.667 0.00 0.00 0.00 5.19
2438 2684 2.735772 CCTACTGATGCCGGGCACT 61.736 63.158 26.48 13.74 43.04 4.40
2454 2700 2.739292 GCACTATTGCGACCGATCTTA 58.261 47.619 0.00 0.00 39.50 2.10
2455 2701 3.120792 GCACTATTGCGACCGATCTTAA 58.879 45.455 0.00 0.00 39.50 1.85
2456 2702 3.741344 GCACTATTGCGACCGATCTTAAT 59.259 43.478 0.00 0.00 39.50 1.40
2457 2703 4.211374 GCACTATTGCGACCGATCTTAATT 59.789 41.667 0.00 0.00 39.50 1.40
2458 2704 5.277345 GCACTATTGCGACCGATCTTAATTT 60.277 40.000 0.00 0.00 39.50 1.82
2459 2705 6.355638 CACTATTGCGACCGATCTTAATTTC 58.644 40.000 0.00 0.00 0.00 2.17
2460 2706 6.019075 CACTATTGCGACCGATCTTAATTTCA 60.019 38.462 0.00 0.00 0.00 2.69
2461 2707 5.811399 ATTGCGACCGATCTTAATTTCAA 57.189 34.783 0.00 0.00 0.00 2.69
2462 2708 4.857871 TGCGACCGATCTTAATTTCAAG 57.142 40.909 0.00 0.00 0.00 3.02
2463 2709 3.621268 TGCGACCGATCTTAATTTCAAGG 59.379 43.478 0.00 0.00 0.00 3.61
2464 2710 3.546218 GCGACCGATCTTAATTTCAAGGC 60.546 47.826 0.00 0.00 0.00 4.35
2465 2711 3.621268 CGACCGATCTTAATTTCAAGGCA 59.379 43.478 0.00 0.00 0.00 4.75
2466 2712 4.273480 CGACCGATCTTAATTTCAAGGCAT 59.727 41.667 0.00 0.00 0.00 4.40
2467 2713 5.505173 ACCGATCTTAATTTCAAGGCATG 57.495 39.130 0.00 0.00 0.00 4.06
2468 2714 5.192927 ACCGATCTTAATTTCAAGGCATGA 58.807 37.500 0.00 0.00 35.85 3.07
2469 2715 5.297776 ACCGATCTTAATTTCAAGGCATGAG 59.702 40.000 0.00 0.00 39.77 2.90
2470 2716 5.528690 CCGATCTTAATTTCAAGGCATGAGA 59.471 40.000 0.00 0.00 39.77 3.27
2471 2717 6.425504 CGATCTTAATTTCAAGGCATGAGAC 58.574 40.000 0.00 0.00 39.77 3.36
2472 2718 6.037500 CGATCTTAATTTCAAGGCATGAGACA 59.962 38.462 0.00 0.00 39.77 3.41
2473 2719 7.414429 CGATCTTAATTTCAAGGCATGAGACAA 60.414 37.037 0.00 0.00 39.77 3.18
2474 2720 7.707624 TCTTAATTTCAAGGCATGAGACAAT 57.292 32.000 0.00 0.00 39.77 2.71
2475 2721 8.125978 TCTTAATTTCAAGGCATGAGACAATT 57.874 30.769 0.00 6.24 39.77 2.32
2476 2722 8.246180 TCTTAATTTCAAGGCATGAGACAATTC 58.754 33.333 0.00 0.00 39.77 2.17
2477 2723 5.988310 ATTTCAAGGCATGAGACAATTCA 57.012 34.783 0.00 0.00 39.77 2.57
2478 2724 5.988310 TTTCAAGGCATGAGACAATTCAT 57.012 34.783 0.00 0.00 39.77 2.57
2513 2759 7.171678 ACAACTAATTTCTCTCAAGTAGCACAC 59.828 37.037 0.00 0.00 29.15 3.82
2515 2761 7.217200 ACTAATTTCTCTCAAGTAGCACACAA 58.783 34.615 0.00 0.00 29.15 3.33
2521 2767 2.212652 TCAAGTAGCACACAACAGCAG 58.787 47.619 0.00 0.00 0.00 4.24
2612 2858 4.526262 CCCATGGTACTTGTGGAATTTTGA 59.474 41.667 11.73 0.00 34.94 2.69
2666 2912 5.251700 CCTATATGGATTAAGGACAAGCCCT 59.748 44.000 0.00 0.00 38.35 5.19
2668 2914 3.366052 TGGATTAAGGACAAGCCCTTC 57.634 47.619 0.00 0.00 44.88 3.46
2669 2915 2.289565 GGATTAAGGACAAGCCCTTCG 58.710 52.381 0.00 0.00 44.88 3.79
2670 2916 2.093128 GGATTAAGGACAAGCCCTTCGA 60.093 50.000 0.00 0.00 44.88 3.71
2671 2917 3.433740 GGATTAAGGACAAGCCCTTCGAT 60.434 47.826 0.00 0.00 44.88 3.59
2672 2918 2.981859 TAAGGACAAGCCCTTCGATC 57.018 50.000 0.00 0.00 44.88 3.69
2674 2920 0.909610 AGGACAAGCCCTTCGATCCA 60.910 55.000 0.66 0.00 37.37 3.41
2675 2921 0.744771 GGACAAGCCCTTCGATCCAC 60.745 60.000 0.00 0.00 0.00 4.02
2676 2922 1.079127 ACAAGCCCTTCGATCCACG 60.079 57.895 0.00 0.00 44.09 4.94
2704 2950 2.357009 GGCTAACACTCGACGGAATCTA 59.643 50.000 0.00 0.00 0.00 1.98
2724 2970 3.598715 GCTTGCAGCACAGCACCA 61.599 61.111 18.96 0.00 45.61 4.17
2726 2972 1.299620 CTTGCAGCACAGCACCAAC 60.300 57.895 0.00 0.00 45.61 3.77
2728 2974 1.602327 TTGCAGCACAGCACCAACAA 61.602 50.000 0.00 0.00 45.61 2.83
2806 3069 9.847706 CATGTGGTGATACTTATACTAGATGTC 57.152 37.037 0.00 0.00 0.00 3.06
2830 3093 6.385759 TCCATATTAGTTAGGCTTGAGGACAA 59.614 38.462 0.00 0.00 34.65 3.18
2840 3105 4.953579 AGGCTTGAGGACAACTAAAAACAA 59.046 37.500 0.00 0.00 32.27 2.83
2898 3163 1.208614 CTTGCGGAGTCTTTGCAGC 59.791 57.895 5.62 0.00 40.15 5.25
2901 3166 0.890542 TGCGGAGTCTTTGCAGCAAT 60.891 50.000 9.12 0.00 34.03 3.56
2912 3177 4.699735 TCTTTGCAGCAATTAATTCTCGGA 59.300 37.500 9.12 0.00 0.00 4.55
2922 3187 2.005971 AATTCTCGGACCGCTTGTAC 57.994 50.000 9.66 0.00 0.00 2.90
2959 3224 6.892691 AGTTTTGACTCAAGAGCTTAAATCG 58.107 36.000 0.00 0.00 0.00 3.34
2964 3229 4.065088 ACTCAAGAGCTTAAATCGTGCAA 58.935 39.130 0.00 0.00 0.00 4.08
2965 3230 4.083802 ACTCAAGAGCTTAAATCGTGCAAC 60.084 41.667 0.00 0.00 0.00 4.17
2966 3231 3.812609 TCAAGAGCTTAAATCGTGCAACA 59.187 39.130 0.00 0.00 35.74 3.33
2967 3232 4.455533 TCAAGAGCTTAAATCGTGCAACAT 59.544 37.500 0.00 0.00 35.74 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.628500 GTCCCTATTGTATCTACCTTTTCAAAT 57.372 33.333 0.00 0.00 0.00 2.32
11 12 7.767198 CGTCCCTATTGTATCTACCTTTTCAAA 59.233 37.037 0.00 0.00 0.00 2.69
12 13 7.124599 TCGTCCCTATTGTATCTACCTTTTCAA 59.875 37.037 0.00 0.00 0.00 2.69
13 14 6.608405 TCGTCCCTATTGTATCTACCTTTTCA 59.392 38.462 0.00 0.00 0.00 2.69
14 15 7.047460 TCGTCCCTATTGTATCTACCTTTTC 57.953 40.000 0.00 0.00 0.00 2.29
15 16 7.070821 ACATCGTCCCTATTGTATCTACCTTTT 59.929 37.037 0.00 0.00 0.00 2.27
16 17 6.553852 ACATCGTCCCTATTGTATCTACCTTT 59.446 38.462 0.00 0.00 0.00 3.11
19 20 5.979288 ACATCGTCCCTATTGTATCTACC 57.021 43.478 0.00 0.00 0.00 3.18
31 32 0.753262 GCCACTGATACATCGTCCCT 59.247 55.000 0.00 0.00 0.00 4.20
33 34 2.361119 TGTAGCCACTGATACATCGTCC 59.639 50.000 0.00 0.00 38.38 4.79
46 47 2.555199 CAGCCTATCAAGTGTAGCCAC 58.445 52.381 0.00 0.00 42.17 5.01
47 48 1.486310 CCAGCCTATCAAGTGTAGCCA 59.514 52.381 0.00 0.00 0.00 4.75
50 51 1.765314 AGCCCAGCCTATCAAGTGTAG 59.235 52.381 0.00 0.00 0.00 2.74
54 55 1.225704 GCAGCCCAGCCTATCAAGT 59.774 57.895 0.00 0.00 0.00 3.16
56 57 1.528824 GAGCAGCCCAGCCTATCAA 59.471 57.895 0.00 0.00 34.23 2.57
148 149 6.644181 CCTCATTTTTCTGCTTCTTTTCCTTC 59.356 38.462 0.00 0.00 0.00 3.46
170 171 8.246871 CCTCTTTCATCTCAAATTAAAACCCTC 58.753 37.037 0.00 0.00 0.00 4.30
224 226 5.416952 ACCTTTGACTTCATCATGTTCCATC 59.583 40.000 0.00 0.00 37.11 3.51
241 243 3.096092 ACTTGGTTTTCTGCACCTTTGA 58.904 40.909 0.00 0.00 35.07 2.69
243 245 6.322712 TGTTATACTTGGTTTTCTGCACCTTT 59.677 34.615 0.00 0.00 35.07 3.11
286 288 7.232534 TGGTCTTAGGCTTTGAAATATGTTTGT 59.767 33.333 0.00 0.00 0.00 2.83
287 289 7.601856 TGGTCTTAGGCTTTGAAATATGTTTG 58.398 34.615 0.00 0.00 0.00 2.93
346 352 6.370994 TGCCACGGTTACGAAAGAATTAATTA 59.629 34.615 0.00 0.00 44.60 1.40
405 412 0.745128 TTTTTGACTGCCACCGTCGT 60.745 50.000 0.00 0.00 34.17 4.34
406 413 2.018544 TTTTTGACTGCCACCGTCG 58.981 52.632 0.00 0.00 34.17 5.12
425 432 2.970640 ACACCGTCCTCTCTACCTTTTT 59.029 45.455 0.00 0.00 0.00 1.94
426 433 2.606378 ACACCGTCCTCTCTACCTTTT 58.394 47.619 0.00 0.00 0.00 2.27
427 434 2.299297 CAACACCGTCCTCTCTACCTTT 59.701 50.000 0.00 0.00 0.00 3.11
428 435 1.893801 CAACACCGTCCTCTCTACCTT 59.106 52.381 0.00 0.00 0.00 3.50
429 436 1.546961 CAACACCGTCCTCTCTACCT 58.453 55.000 0.00 0.00 0.00 3.08
430 437 0.108756 GCAACACCGTCCTCTCTACC 60.109 60.000 0.00 0.00 0.00 3.18
431 438 0.456312 CGCAACACCGTCCTCTCTAC 60.456 60.000 0.00 0.00 0.00 2.59
432 439 0.892358 ACGCAACACCGTCCTCTCTA 60.892 55.000 0.00 0.00 36.61 2.43
433 440 2.201022 ACGCAACACCGTCCTCTCT 61.201 57.895 0.00 0.00 36.61 3.10
434 441 2.338984 ACGCAACACCGTCCTCTC 59.661 61.111 0.00 0.00 36.61 3.20
440 447 1.018148 TTCAAATGACGCAACACCGT 58.982 45.000 0.00 0.00 45.30 4.83
450 457 3.940209 TTCACCAGGCATTCAAATGAC 57.060 42.857 6.91 3.60 44.99 3.06
457 464 2.014335 GCCAAATTCACCAGGCATTC 57.986 50.000 0.00 0.00 46.26 2.67
478 485 2.566057 TTATCCACGGCGTGCACGAT 62.566 55.000 41.19 28.72 43.02 3.73
479 486 3.284133 TTATCCACGGCGTGCACGA 62.284 57.895 41.19 24.65 43.02 4.35
480 487 2.798501 CTTATCCACGGCGTGCACG 61.799 63.158 34.01 34.01 43.27 5.34
517 529 5.735427 TGTTCGTAAAAAGCTTTGTTCTTCG 59.265 36.000 13.54 11.72 0.00 3.79
537 549 3.181465 TGGGTTCAGAGTTCAGACTGTTC 60.181 47.826 1.59 0.00 35.88 3.18
652 667 1.957186 TTGGTTGCTACGTGCGTCC 60.957 57.895 0.00 7.22 46.63 4.79
680 695 5.275741 GCTTTTTAAAACAGTGTCTTGCGTC 60.276 40.000 0.00 0.00 0.00 5.19
850 865 2.509964 GGGAAGGAAGGGATAGCTTTGA 59.490 50.000 0.00 0.00 0.00 2.69
920 938 3.378112 TGCAGGTCACAAAAGTTTCTCAG 59.622 43.478 0.00 0.00 0.00 3.35
921 939 3.351740 TGCAGGTCACAAAAGTTTCTCA 58.648 40.909 0.00 0.00 0.00 3.27
953 971 1.023513 GCAGGTGTGATCTGGTGAGC 61.024 60.000 0.00 0.00 33.16 4.26
955 973 0.035317 GTGCAGGTGTGATCTGGTGA 59.965 55.000 0.00 0.00 33.16 4.02
957 975 0.473755 TTGTGCAGGTGTGATCTGGT 59.526 50.000 0.00 0.00 33.16 4.00
958 976 0.877071 GTTGTGCAGGTGTGATCTGG 59.123 55.000 0.00 0.00 33.16 3.86
959 977 1.265095 GTGTTGTGCAGGTGTGATCTG 59.735 52.381 0.00 0.00 35.49 2.90
961 979 0.235665 CGTGTTGTGCAGGTGTGATC 59.764 55.000 0.00 0.00 0.00 2.92
1013 1032 1.303398 TGAGGAACCGTCGCTCTCT 60.303 57.895 0.00 0.00 0.00 3.10
1038 1057 2.473760 ATCGGACTCGGAGTCGCTG 61.474 63.158 26.86 20.00 45.96 5.18
1184 1208 2.214347 TGCCGACGTTCAGAAATTGAA 58.786 42.857 0.00 0.00 43.40 2.69
1185 1209 1.872388 TGCCGACGTTCAGAAATTGA 58.128 45.000 0.00 0.00 0.00 2.57
1188 1212 5.758296 ACATATATTGCCGACGTTCAGAAAT 59.242 36.000 0.00 0.00 0.00 2.17
1189 1213 5.006261 CACATATATTGCCGACGTTCAGAAA 59.994 40.000 0.00 0.00 0.00 2.52
1190 1214 4.506288 CACATATATTGCCGACGTTCAGAA 59.494 41.667 0.00 0.00 0.00 3.02
1191 1215 4.048504 CACATATATTGCCGACGTTCAGA 58.951 43.478 0.00 0.00 0.00 3.27
1192 1216 3.184379 CCACATATATTGCCGACGTTCAG 59.816 47.826 0.00 0.00 0.00 3.02
1193 1217 3.127589 CCACATATATTGCCGACGTTCA 58.872 45.455 0.00 0.00 0.00 3.18
1195 1219 1.871039 GCCACATATATTGCCGACGTT 59.129 47.619 0.00 0.00 0.00 3.99
1198 1222 2.224079 CACTGCCACATATATTGCCGAC 59.776 50.000 0.00 0.00 0.00 4.79
1199 1223 2.493035 CACTGCCACATATATTGCCGA 58.507 47.619 0.00 0.00 0.00 5.54
1200 1224 1.536766 CCACTGCCACATATATTGCCG 59.463 52.381 0.00 0.00 0.00 5.69
1201 1225 1.270550 GCCACTGCCACATATATTGCC 59.729 52.381 0.00 0.00 0.00 4.52
1202 1226 1.069022 CGCCACTGCCACATATATTGC 60.069 52.381 0.00 0.00 0.00 3.56
1204 1228 1.419762 TCCGCCACTGCCACATATATT 59.580 47.619 0.00 0.00 0.00 1.28
1205 1229 1.055849 TCCGCCACTGCCACATATAT 58.944 50.000 0.00 0.00 0.00 0.86
1206 1230 0.105964 GTCCGCCACTGCCACATATA 59.894 55.000 0.00 0.00 0.00 0.86
1207 1231 1.153168 GTCCGCCACTGCCACATAT 60.153 57.895 0.00 0.00 0.00 1.78
1414 1464 2.404186 CGACACGATCACCTCCGGA 61.404 63.158 2.93 2.93 0.00 5.14
1548 1598 2.362077 TGCAAACAAGGGAGAAGAAAGC 59.638 45.455 0.00 0.00 0.00 3.51
1591 1645 3.994392 TGGACGAAATTAGTTCACTGAGC 59.006 43.478 0.00 0.00 35.83 4.26
1592 1646 6.727824 AATGGACGAAATTAGTTCACTGAG 57.272 37.500 0.00 0.00 35.83 3.35
1593 1647 8.786826 AATAATGGACGAAATTAGTTCACTGA 57.213 30.769 0.00 0.00 35.83 3.41
1594 1648 8.883731 AGAATAATGGACGAAATTAGTTCACTG 58.116 33.333 0.00 0.00 35.83 3.66
1595 1649 9.449719 AAGAATAATGGACGAAATTAGTTCACT 57.550 29.630 0.00 0.00 35.83 3.41
1596 1650 9.490663 CAAGAATAATGGACGAAATTAGTTCAC 57.509 33.333 0.00 0.00 35.83 3.18
1597 1651 9.226606 ACAAGAATAATGGACGAAATTAGTTCA 57.773 29.630 0.00 0.00 35.83 3.18
1600 1654 9.449719 AGAACAAGAATAATGGACGAAATTAGT 57.550 29.630 0.00 0.00 0.00 2.24
1604 1658 7.921786 TCAGAACAAGAATAATGGACGAAAT 57.078 32.000 0.00 0.00 0.00 2.17
1609 1663 5.106712 TGCGTTCAGAACAAGAATAATGGAC 60.107 40.000 13.82 0.00 0.00 4.02
1612 1666 5.796935 CCTTGCGTTCAGAACAAGAATAATG 59.203 40.000 13.82 0.00 42.71 1.90
1613 1667 5.473504 ACCTTGCGTTCAGAACAAGAATAAT 59.526 36.000 13.82 0.00 42.71 1.28
1614 1668 4.819630 ACCTTGCGTTCAGAACAAGAATAA 59.180 37.500 13.82 0.00 42.71 1.40
1616 1670 3.003689 CACCTTGCGTTCAGAACAAGAAT 59.996 43.478 13.82 0.58 42.71 2.40
1617 1671 2.354510 CACCTTGCGTTCAGAACAAGAA 59.645 45.455 13.82 1.93 42.71 2.52
1618 1672 1.939934 CACCTTGCGTTCAGAACAAGA 59.060 47.619 13.82 0.00 42.71 3.02
1620 1674 2.031258 TCACCTTGCGTTCAGAACAA 57.969 45.000 13.82 0.41 0.00 2.83
1621 1675 2.254546 ATCACCTTGCGTTCAGAACA 57.745 45.000 13.82 0.00 0.00 3.18
1622 1676 2.350772 CCAATCACCTTGCGTTCAGAAC 60.351 50.000 2.85 2.85 33.20 3.01
1623 1677 1.879380 CCAATCACCTTGCGTTCAGAA 59.121 47.619 0.00 0.00 33.20 3.02
1625 1679 1.522668 TCCAATCACCTTGCGTTCAG 58.477 50.000 0.00 0.00 33.20 3.02
1626 1680 2.083774 GATCCAATCACCTTGCGTTCA 58.916 47.619 0.00 0.00 33.20 3.18
1627 1681 2.352960 GAGATCCAATCACCTTGCGTTC 59.647 50.000 0.00 0.00 33.20 3.95
1628 1682 2.026822 AGAGATCCAATCACCTTGCGTT 60.027 45.455 0.00 0.00 33.20 4.84
1630 1684 1.938577 CAGAGATCCAATCACCTTGCG 59.061 52.381 0.00 0.00 33.20 4.85
1711 1804 4.717233 TGTTGATCAAAATTCGGGGATG 57.283 40.909 10.35 0.00 0.00 3.51
1714 1807 4.250116 TGTTGTTGATCAAAATTCGGGG 57.750 40.909 10.35 0.00 37.81 5.73
1716 1809 6.580963 TTGTTGTTGTTGATCAAAATTCGG 57.419 33.333 10.35 0.00 37.81 4.30
1717 1810 8.871742 TTTTTGTTGTTGTTGATCAAAATTCG 57.128 26.923 10.35 0.00 37.66 3.34
1765 1870 6.028987 GCAGCACAATGAACAAAATGTTTTT 58.971 32.000 0.00 0.00 41.28 1.94
1768 1873 4.190001 TGCAGCACAATGAACAAAATGTT 58.810 34.783 0.00 0.00 44.37 2.71
1769 1874 3.794717 TGCAGCACAATGAACAAAATGT 58.205 36.364 0.00 0.00 0.00 2.71
1770 1875 3.185594 CCTGCAGCACAATGAACAAAATG 59.814 43.478 8.66 0.00 0.00 2.32
1771 1876 3.069872 TCCTGCAGCACAATGAACAAAAT 59.930 39.130 8.66 0.00 0.00 1.82
1780 1896 2.230508 CACAAGAATCCTGCAGCACAAT 59.769 45.455 8.66 0.00 0.00 2.71
1784 1900 1.579964 CGCACAAGAATCCTGCAGCA 61.580 55.000 8.66 0.00 0.00 4.41
1786 1902 1.136147 GCGCACAAGAATCCTGCAG 59.864 57.895 6.78 6.78 0.00 4.41
1819 1935 1.028330 CCCGTACCTCTCGTACAGCA 61.028 60.000 0.00 0.00 46.67 4.41
1982 2098 2.682352 TCAACCATGTACGATGCATTGG 59.318 45.455 18.31 14.28 0.00 3.16
1993 2109 3.620488 GCCTCCTCAAATCAACCATGTA 58.380 45.455 0.00 0.00 0.00 2.29
1994 2110 2.450476 GCCTCCTCAAATCAACCATGT 58.550 47.619 0.00 0.00 0.00 3.21
1995 2111 1.753073 GGCCTCCTCAAATCAACCATG 59.247 52.381 0.00 0.00 0.00 3.66
1996 2112 1.683011 CGGCCTCCTCAAATCAACCAT 60.683 52.381 0.00 0.00 0.00 3.55
2007 2123 1.690219 ATCACCATCACGGCCTCCTC 61.690 60.000 0.00 0.00 39.03 3.71
2014 2130 0.744414 GGACACCATCACCATCACGG 60.744 60.000 0.00 0.00 42.50 4.94
2031 2147 4.805231 CGTATGCACGCACCGGGA 62.805 66.667 6.32 0.00 42.05 5.14
2050 2167 2.608623 CATTTCCCCTGAAACCCAACT 58.391 47.619 0.00 0.00 42.97 3.16
2054 2171 0.544120 TGCCATTTCCCCTGAAACCC 60.544 55.000 0.00 0.00 42.97 4.11
2087 2205 4.439057 ACTCGCAACTGAACAAGACTTAA 58.561 39.130 0.00 0.00 0.00 1.85
2088 2206 4.049186 GACTCGCAACTGAACAAGACTTA 58.951 43.478 0.00 0.00 0.00 2.24
2089 2207 2.866762 GACTCGCAACTGAACAAGACTT 59.133 45.455 0.00 0.00 0.00 3.01
2127 2245 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2131 2249 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2132 2250 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2133 2251 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2134 2252 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2135 2253 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2136 2254 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2137 2255 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2138 2256 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2139 2257 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2140 2258 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2141 2259 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2142 2260 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2143 2261 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2144 2262 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2145 2263 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2146 2264 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2147 2265 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2148 2266 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2149 2267 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
2150 2268 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
2255 2373 1.507140 TCAGGACACCAACAAGGAGT 58.493 50.000 0.00 0.00 44.48 3.85
2258 2376 0.883833 GCATCAGGACACCAACAAGG 59.116 55.000 0.00 0.00 45.67 3.61
2270 2388 0.463295 AGACGAAGCCATGCATCAGG 60.463 55.000 0.00 0.00 0.00 3.86
2271 2389 0.935898 GAGACGAAGCCATGCATCAG 59.064 55.000 0.00 0.00 0.00 2.90
2272 2390 0.538584 AGAGACGAAGCCATGCATCA 59.461 50.000 0.00 0.00 0.00 3.07
2273 2391 1.216122 GAGAGACGAAGCCATGCATC 58.784 55.000 0.00 0.00 0.00 3.91
2274 2392 0.179062 GGAGAGACGAAGCCATGCAT 60.179 55.000 0.00 0.00 0.00 3.96
2275 2393 1.219124 GGAGAGACGAAGCCATGCA 59.781 57.895 0.00 0.00 0.00 3.96
2276 2394 1.522580 GGGAGAGACGAAGCCATGC 60.523 63.158 0.00 0.00 0.00 4.06
2277 2395 1.144936 GGGGAGAGACGAAGCCATG 59.855 63.158 0.00 0.00 0.00 3.66
2278 2396 2.066999 GGGGGAGAGACGAAGCCAT 61.067 63.158 0.00 0.00 0.00 4.40
2279 2397 2.683933 GGGGGAGAGACGAAGCCA 60.684 66.667 0.00 0.00 0.00 4.75
2280 2398 1.962321 GAAGGGGGAGAGACGAAGCC 61.962 65.000 0.00 0.00 0.00 4.35
2281 2399 0.973496 AGAAGGGGGAGAGACGAAGC 60.973 60.000 0.00 0.00 0.00 3.86
2282 2400 1.107945 GAGAAGGGGGAGAGACGAAG 58.892 60.000 0.00 0.00 0.00 3.79
2283 2401 0.408309 TGAGAAGGGGGAGAGACGAA 59.592 55.000 0.00 0.00 0.00 3.85
2284 2402 0.408309 TTGAGAAGGGGGAGAGACGA 59.592 55.000 0.00 0.00 0.00 4.20
2285 2403 1.205893 CTTTGAGAAGGGGGAGAGACG 59.794 57.143 0.00 0.00 0.00 4.18
2286 2404 2.027653 CACTTTGAGAAGGGGGAGAGAC 60.028 54.545 0.00 0.00 37.19 3.36
2287 2405 2.158158 TCACTTTGAGAAGGGGGAGAGA 60.158 50.000 0.00 0.00 36.90 3.10
2288 2406 2.260822 TCACTTTGAGAAGGGGGAGAG 58.739 52.381 0.00 0.00 36.90 3.20
2289 2407 2.415983 TCACTTTGAGAAGGGGGAGA 57.584 50.000 0.00 0.00 36.90 3.71
2290 2408 3.073062 TCTTTCACTTTGAGAAGGGGGAG 59.927 47.826 0.00 0.00 36.90 4.30
2291 2409 3.053077 TCTTTCACTTTGAGAAGGGGGA 58.947 45.455 0.00 0.00 36.90 4.81
2349 2491 0.035820 GTGGTGCCGTCTAATCCCAA 60.036 55.000 0.00 0.00 0.00 4.12
2355 2497 2.745037 GGGTGTGGTGCCGTCTAA 59.255 61.111 0.00 0.00 0.00 2.10
2362 2504 3.055719 CATGACGGGGTGTGGTGC 61.056 66.667 0.00 0.00 0.00 5.01
2366 2508 1.026182 CCATGACATGACGGGGTGTG 61.026 60.000 17.24 0.00 0.00 3.82
2388 2534 3.440872 AGATAGCGTTAATCGAGCCCTAG 59.559 47.826 0.00 0.00 42.86 3.02
2395 2541 2.606308 GCGGGAAGATAGCGTTAATCGA 60.606 50.000 0.00 0.00 42.86 3.59
2400 2546 1.361271 CGGCGGGAAGATAGCGTTA 59.639 57.895 0.00 0.00 0.00 3.18
2402 2548 4.587189 GCGGCGGGAAGATAGCGT 62.587 66.667 9.78 0.00 0.00 5.07
2404 2550 4.990553 GGGCGGCGGGAAGATAGC 62.991 72.222 9.78 0.00 0.00 2.97
2407 2553 3.547513 GTAGGGCGGCGGGAAGAT 61.548 66.667 9.78 0.00 0.00 2.40
2420 2566 1.399744 TAGTGCCCGGCATCAGTAGG 61.400 60.000 16.96 0.00 41.91 3.18
2422 2568 1.128200 AATAGTGCCCGGCATCAGTA 58.872 50.000 16.96 5.83 41.91 2.74
2438 2684 6.018262 CCTTGAAATTAAGATCGGTCGCAATA 60.018 38.462 0.00 0.00 0.00 1.90
2450 2696 7.707624 ATTGTCTCATGCCTTGAAATTAAGA 57.292 32.000 0.00 0.00 32.78 2.10
2454 2700 6.349243 TGAATTGTCTCATGCCTTGAAATT 57.651 33.333 0.00 0.00 32.78 1.82
2455 2701 5.988310 TGAATTGTCTCATGCCTTGAAAT 57.012 34.783 0.00 0.00 32.78 2.17
2456 2702 5.716094 CATGAATTGTCTCATGCCTTGAAA 58.284 37.500 0.95 0.00 44.54 2.69
2457 2703 5.319140 CATGAATTGTCTCATGCCTTGAA 57.681 39.130 0.95 0.00 44.54 2.69
2458 2704 4.976224 CATGAATTGTCTCATGCCTTGA 57.024 40.909 0.95 0.00 44.54 3.02
2465 2711 3.617284 TGCTGCTCATGAATTGTCTCAT 58.383 40.909 0.00 0.00 36.45 2.90
2466 2712 3.062122 TGCTGCTCATGAATTGTCTCA 57.938 42.857 0.00 0.00 0.00 3.27
2467 2713 3.189910 TGTTGCTGCTCATGAATTGTCTC 59.810 43.478 0.00 0.00 0.00 3.36
2468 2714 3.151554 TGTTGCTGCTCATGAATTGTCT 58.848 40.909 0.00 0.00 0.00 3.41
2469 2715 3.564235 TGTTGCTGCTCATGAATTGTC 57.436 42.857 0.00 0.00 0.00 3.18
2470 2716 3.319972 AGTTGTTGCTGCTCATGAATTGT 59.680 39.130 0.00 0.00 0.00 2.71
2471 2717 3.909430 AGTTGTTGCTGCTCATGAATTG 58.091 40.909 0.00 0.00 0.00 2.32
2472 2718 5.710513 TTAGTTGTTGCTGCTCATGAATT 57.289 34.783 0.00 0.00 0.00 2.17
2473 2719 5.909621 ATTAGTTGTTGCTGCTCATGAAT 57.090 34.783 0.00 0.00 0.00 2.57
2474 2720 5.710513 AATTAGTTGTTGCTGCTCATGAA 57.289 34.783 0.00 0.00 0.00 2.57
2475 2721 5.474532 AGAAATTAGTTGTTGCTGCTCATGA 59.525 36.000 0.00 0.00 0.00 3.07
2476 2722 5.706916 AGAAATTAGTTGTTGCTGCTCATG 58.293 37.500 0.00 0.00 0.00 3.07
2477 2723 5.709164 AGAGAAATTAGTTGTTGCTGCTCAT 59.291 36.000 0.00 0.00 0.00 2.90
2478 2724 5.065914 AGAGAAATTAGTTGTTGCTGCTCA 58.934 37.500 0.00 0.00 0.00 4.26
2479 2725 5.180117 TGAGAGAAATTAGTTGTTGCTGCTC 59.820 40.000 0.00 0.00 0.00 4.26
2480 2726 5.065914 TGAGAGAAATTAGTTGTTGCTGCT 58.934 37.500 0.00 0.00 0.00 4.24
2513 2759 1.202687 TGAGAGTGGTTCCTGCTGTTG 60.203 52.381 0.00 0.00 0.00 3.33
2515 2761 0.683973 CTGAGAGTGGTTCCTGCTGT 59.316 55.000 0.00 0.00 0.00 4.40
2521 2767 3.935828 GCAGTAAATCTGAGAGTGGTTCC 59.064 47.826 0.00 0.00 46.27 3.62
2585 2831 1.777878 TCCACAAGTACCATGGGTTGT 59.222 47.619 18.09 18.47 37.09 3.32
2653 2899 1.485066 GGATCGAAGGGCTTGTCCTTA 59.515 52.381 6.49 0.00 46.31 2.69
2666 2912 2.024868 CCGTTGTGCGTGGATCGAA 61.025 57.895 0.00 0.00 42.86 3.71
2668 2914 4.147322 GCCGTTGTGCGTGGATCG 62.147 66.667 0.00 0.00 43.12 3.69
2669 2915 1.017177 TTAGCCGTTGTGCGTGGATC 61.017 55.000 0.00 0.00 39.32 3.36
2670 2916 1.004320 TTAGCCGTTGTGCGTGGAT 60.004 52.632 0.00 0.00 39.32 3.41
2671 2917 1.957186 GTTAGCCGTTGTGCGTGGA 60.957 57.895 0.00 0.00 39.32 4.02
2672 2918 2.248135 TGTTAGCCGTTGTGCGTGG 61.248 57.895 0.00 0.00 39.32 4.94
2674 2920 1.219522 GAGTGTTAGCCGTTGTGCGT 61.220 55.000 0.00 0.00 39.32 5.24
2675 2921 1.491563 GAGTGTTAGCCGTTGTGCG 59.508 57.895 0.00 0.00 40.95 5.34
2676 2922 0.942410 TCGAGTGTTAGCCGTTGTGC 60.942 55.000 0.00 0.00 0.00 4.57
2717 2963 1.280066 GCTTGTGTTTGTTGGTGCTG 58.720 50.000 0.00 0.00 0.00 4.41
2724 2970 4.461081 TGAGTTTGTAGGCTTGTGTTTGTT 59.539 37.500 0.00 0.00 0.00 2.83
2726 2972 4.630894 TGAGTTTGTAGGCTTGTGTTTG 57.369 40.909 0.00 0.00 0.00 2.93
2728 2974 5.852282 ATTTGAGTTTGTAGGCTTGTGTT 57.148 34.783 0.00 0.00 0.00 3.32
2806 3069 6.174720 TGTCCTCAAGCCTAACTAATATGG 57.825 41.667 0.00 0.00 0.00 2.74
2830 3093 9.554395 CCCACAAATTAATCCTTTGTTTTTAGT 57.446 29.630 3.47 0.00 42.58 2.24
2855 3120 0.036732 TCCATCCACTGCTTGTGTCC 59.963 55.000 9.00 0.00 44.81 4.02
2893 3158 2.682856 GGTCCGAGAATTAATTGCTGCA 59.317 45.455 5.17 0.00 0.00 4.41
2898 3163 3.374058 ACAAGCGGTCCGAGAATTAATTG 59.626 43.478 17.49 8.14 0.00 2.32
2901 3166 2.754946 ACAAGCGGTCCGAGAATTAA 57.245 45.000 17.49 0.00 0.00 1.40
2922 3187 6.148948 TGAGTCAAAACTTATGCAATTTCCG 58.851 36.000 0.00 0.00 35.28 4.30


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

AutoCloner maintained by Alex Coulton.