Multiple sequence alignment - TraesCS3B01G432000

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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 TraesCS3B01G432000 chr3B 100.000 5764 0 0 1 5764 671022175 671016412 0.000000e+00 10645
1 TraesCS3B01G432000 chr3A 88.832 4531 309 101 3 4410 646132422 646127966 0.000000e+00 5382
2 TraesCS3B01G432000 chr3A 92.730 729 44 5 4846 5573 646127633 646126913 0.000000e+00 1044
3 TraesCS3B01G432000 chr3A 92.899 338 20 4 4461 4798 646127966 646127633 6.710000e-134 488
4 TraesCS3B01G432000 chr3A 88.205 195 22 1 5571 5764 646126831 646126637 1.250000e-56 231
5 TraesCS3B01G432000 chr3D 90.149 2751 171 51 1 2689 508387996 508385284 0.000000e+00 3487
6 TraesCS3B01G432000 chr3D 92.263 1732 115 11 2693 4410 508385176 508383450 0.000000e+00 2438
7 TraesCS3B01G432000 chr3D 90.429 815 56 12 4461 5264 508383453 508382650 0.000000e+00 1053
8 TraesCS3B01G432000 chr3D 84.526 517 39 19 5262 5764 508382594 508382105 1.880000e-129 473
9 TraesCS3B01G432000 chr3D 80.303 396 54 11 5371 5764 508382065 508381692 1.580000e-70 278


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 TraesCS3B01G432000 chr3B 671016412 671022175 5763 True 10645.00 10645 100.0000 1 5764 1 chr3B.!!$R1 5763
1 TraesCS3B01G432000 chr3A 646126637 646132422 5785 True 1786.25 5382 90.6665 3 5764 4 chr3A.!!$R1 5761
2 TraesCS3B01G432000 chr3D 508381692 508387996 6304 True 1545.80 3487 87.5340 1 5764 5 chr3D.!!$R1 5763

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
611 630 0.035534 TGGCCGAGCTTCATTTGCTA 60.036 50.000 0.00 0.00 41.30 3.49 F
1483 1571 0.250901 CCTTGACACTGGGTGGGAAG 60.251 60.000 0.00 3.99 37.94 3.46 F
1568 1667 0.178995 TGGCCAGTGAATTGCTGACA 60.179 50.000 0.00 4.77 36.12 3.58 F
1576 1675 0.458669 GAATTGCTGACATGGCCTGG 59.541 55.000 3.32 0.00 0.00 4.45 F
1990 2093 1.001633 GAGTTCAGTAACAAGGGCCGA 59.998 52.381 0.00 0.00 38.12 5.54 F
3362 3592 1.199624 CGCAAGGTTTGTCTTGTTGC 58.800 50.000 6.48 0.00 44.26 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1546 1643 0.524862 CAGCAATTCACTGGCCACTC 59.475 55.000 0.00 0.0 0.00 3.51 R
3336 3566 0.317854 GACAAACCTTGCGCTTCCAC 60.318 55.000 9.73 0.0 0.00 4.02 R
3509 3739 3.056821 TCAAGTGTCGAGTCCAATACCAG 60.057 47.826 0.00 0.0 0.00 4.00 R
3566 3796 3.243704 TGCAACAGTTCATGGTAAAAGCC 60.244 43.478 0.00 0.0 0.00 4.35 R
3758 3989 0.038159 ACCTGCACACGAGTAAGCTC 60.038 55.000 0.00 0.0 38.35 4.09 R
5355 5664 0.108662 TGCCATACACTGCTGAGTCG 60.109 55.000 0.00 0.0 0.00 4.18 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
81 84 6.162079 GCATGAGCTAGTGCAGATATTAGAA 58.838 40.000 15.73 0.00 42.74 2.10
82 85 6.090628 GCATGAGCTAGTGCAGATATTAGAAC 59.909 42.308 15.73 0.00 42.74 3.01
103 108 7.591165 AGAACATTCATCATCACTGAAAACAG 58.409 34.615 0.00 0.00 36.30 3.16
111 116 5.316167 TCATCACTGAAAACAGGCTGTTAT 58.684 37.500 31.34 17.08 40.14 1.89
112 117 6.472016 TCATCACTGAAAACAGGCTGTTATA 58.528 36.000 31.34 19.12 40.14 0.98
113 118 6.939730 TCATCACTGAAAACAGGCTGTTATAA 59.060 34.615 31.34 18.36 40.14 0.98
114 119 6.801539 TCACTGAAAACAGGCTGTTATAAG 57.198 37.500 31.34 26.70 40.14 1.73
116 121 6.426937 TCACTGAAAACAGGCTGTTATAAGTC 59.573 38.462 31.34 21.69 40.14 3.01
121 126 8.946085 TGAAAACAGGCTGTTATAAGTCATAAG 58.054 33.333 31.34 0.00 40.14 1.73
227 237 2.821991 AAAACTGTACTCGAGCTGCT 57.178 45.000 13.61 0.00 0.00 4.24
228 238 2.821991 AAACTGTACTCGAGCTGCTT 57.178 45.000 13.61 0.00 0.00 3.91
229 239 2.071688 AACTGTACTCGAGCTGCTTG 57.928 50.000 13.61 10.76 0.00 4.01
230 240 0.389166 ACTGTACTCGAGCTGCTTGC 60.389 55.000 13.61 0.00 43.29 4.01
276 286 5.514204 GTCACTAGAAAATTGCATGCACATC 59.486 40.000 22.58 15.56 0.00 3.06
289 300 1.272212 TGCACATCGTAGCAGACTGAA 59.728 47.619 6.65 0.00 35.51 3.02
420 435 0.322322 AACCGCGGTGGAATTCTACA 59.678 50.000 34.95 2.39 42.00 2.74
426 441 2.460918 CGGTGGAATTCTACAGCTACG 58.539 52.381 21.72 12.44 33.22 3.51
428 443 2.418197 GGTGGAATTCTACAGCTACGCA 60.418 50.000 21.72 0.00 32.68 5.24
429 444 3.458189 GTGGAATTCTACAGCTACGCAT 58.542 45.455 16.33 0.00 0.00 4.73
431 446 2.221981 GGAATTCTACAGCTACGCATGC 59.778 50.000 7.91 7.91 0.00 4.06
433 448 0.824109 TTCTACAGCTACGCATGCCT 59.176 50.000 13.15 2.75 0.00 4.75
435 450 1.609072 TCTACAGCTACGCATGCCTAG 59.391 52.381 13.15 15.26 0.00 3.02
437 452 0.103208 ACAGCTACGCATGCCTAGTC 59.897 55.000 20.36 14.24 0.00 2.59
438 453 0.598680 CAGCTACGCATGCCTAGTCC 60.599 60.000 20.36 8.68 0.00 3.85
439 454 1.043116 AGCTACGCATGCCTAGTCCA 61.043 55.000 20.36 0.00 0.00 4.02
440 455 0.598680 GCTACGCATGCCTAGTCCAG 60.599 60.000 20.36 7.37 0.00 3.86
441 456 0.747255 CTACGCATGCCTAGTCCAGT 59.253 55.000 13.15 3.88 0.00 4.00
453 472 1.446272 GTCCAGTAGCACCACGAGC 60.446 63.158 0.00 0.00 0.00 5.03
587 606 3.925630 CTCCATTGGCTGGCACCGT 62.926 63.158 2.29 0.00 45.52 4.83
611 630 0.035534 TGGCCGAGCTTCATTTGCTA 60.036 50.000 0.00 0.00 41.30 3.49
612 631 1.094785 GGCCGAGCTTCATTTGCTAA 58.905 50.000 0.00 0.00 41.30 3.09
797 828 1.375013 CCCCGGTCGTCACGAATTT 60.375 57.895 0.00 0.00 37.72 1.82
800 831 1.669502 CCCGGTCGTCACGAATTTACA 60.670 52.381 0.00 0.00 37.72 2.41
802 833 2.091588 CCGGTCGTCACGAATTTACAAG 59.908 50.000 0.00 0.00 37.72 3.16
803 834 2.091588 CGGTCGTCACGAATTTACAAGG 59.908 50.000 0.00 0.00 37.72 3.61
812 843 2.223249 CGAATTTACAAGGATGCCACCG 60.223 50.000 0.00 0.00 34.73 4.94
926 971 3.243068 CGCTACAAATATTCCCTTGGCAC 60.243 47.826 0.00 0.00 0.00 5.01
953 998 3.488978 CAGCAGACGCAGCAGCTC 61.489 66.667 0.00 0.00 42.27 4.09
979 1032 3.581265 GTAGCCACTACCTACTCCTCT 57.419 52.381 0.00 0.00 33.93 3.69
987 1040 1.001282 ACCTACTCCTCTTCTCCGGT 58.999 55.000 0.00 0.00 0.00 5.28
1118 1183 2.617774 AGGAGCGATTCGAAGGTAGTAC 59.382 50.000 10.88 0.00 0.00 2.73
1140 1213 2.045536 CCCACTTCCCAGCTCAGC 60.046 66.667 0.00 0.00 0.00 4.26
1141 1214 2.045536 CCACTTCCCAGCTCAGCC 60.046 66.667 0.00 0.00 0.00 4.85
1156 1229 3.547567 AGCCTAGACTTGCTGCTTG 57.452 52.632 0.00 0.00 36.23 4.01
1167 1240 1.452651 GCTGCTTGCATGCTCCCTA 60.453 57.895 23.31 3.99 42.31 3.53
1168 1241 0.822532 GCTGCTTGCATGCTCCCTAT 60.823 55.000 23.31 0.00 42.31 2.57
1169 1242 1.236628 CTGCTTGCATGCTCCCTATC 58.763 55.000 23.31 1.82 0.00 2.08
1171 1244 1.849976 GCTTGCATGCTCCCTATCGC 61.850 60.000 20.33 5.88 0.00 4.58
1172 1245 0.533531 CTTGCATGCTCCCTATCGCA 60.534 55.000 20.33 0.00 40.87 5.10
1173 1246 0.815213 TTGCATGCTCCCTATCGCAC 60.815 55.000 20.33 0.00 39.21 5.34
1174 1247 1.963338 GCATGCTCCCTATCGCACC 60.963 63.158 11.37 0.00 39.21 5.01
1175 1248 1.750930 CATGCTCCCTATCGCACCT 59.249 57.895 0.00 0.00 39.21 4.00
1176 1249 0.602106 CATGCTCCCTATCGCACCTG 60.602 60.000 0.00 0.00 39.21 4.00
1177 1250 1.050988 ATGCTCCCTATCGCACCTGT 61.051 55.000 0.00 0.00 39.21 4.00
1178 1251 0.396556 TGCTCCCTATCGCACCTGTA 60.397 55.000 0.00 0.00 0.00 2.74
1218 1304 1.243342 TGCTGGTCCTTGCGAATTGG 61.243 55.000 0.00 0.00 0.00 3.16
1220 1306 1.755179 CTGGTCCTTGCGAATTGGAT 58.245 50.000 0.00 0.00 32.03 3.41
1277 1365 0.819582 ATTGATGGGCGCCTGAAAAG 59.180 50.000 28.56 0.00 0.00 2.27
1483 1571 0.250901 CCTTGACACTGGGTGGGAAG 60.251 60.000 0.00 3.99 37.94 3.46
1484 1572 0.474184 CTTGACACTGGGTGGGAAGT 59.526 55.000 0.00 0.00 37.94 3.01
1567 1666 0.242017 GTGGCCAGTGAATTGCTGAC 59.758 55.000 5.11 0.00 36.12 3.51
1568 1667 0.178995 TGGCCAGTGAATTGCTGACA 60.179 50.000 0.00 4.77 36.12 3.58
1569 1668 1.180029 GGCCAGTGAATTGCTGACAT 58.820 50.000 0.00 0.00 36.12 3.06
1571 1670 1.135199 GCCAGTGAATTGCTGACATGG 60.135 52.381 0.00 0.00 36.12 3.66
1572 1671 1.135199 CCAGTGAATTGCTGACATGGC 60.135 52.381 0.00 0.00 36.12 4.40
1573 1672 1.135199 CAGTGAATTGCTGACATGGCC 60.135 52.381 0.00 0.00 36.12 5.36
1574 1673 1.180029 GTGAATTGCTGACATGGCCT 58.820 50.000 3.32 0.00 0.00 5.19
1575 1674 1.135199 GTGAATTGCTGACATGGCCTG 60.135 52.381 3.32 2.01 0.00 4.85
1576 1675 0.458669 GAATTGCTGACATGGCCTGG 59.541 55.000 3.32 0.00 0.00 4.45
1631 1730 8.946085 TGTCCAATACATGAGTTTGATTAAGTC 58.054 33.333 0.00 0.00 33.53 3.01
1647 1746 5.546621 TTAAGTCACTGCTGGTTTCTAGT 57.453 39.130 0.00 0.00 0.00 2.57
1695 1794 2.214216 TTGGGAGACTCGGTGGGTG 61.214 63.158 0.00 0.00 0.00 4.61
1733 1832 2.104859 GCGAAGGGAAAGCCGGTAC 61.105 63.158 1.90 0.00 33.83 3.34
1734 1833 1.294138 CGAAGGGAAAGCCGGTACA 59.706 57.895 1.90 0.00 33.83 2.90
1791 1890 4.301628 CTGATGACAAAGGTTTGCTTTCC 58.698 43.478 2.27 0.00 41.79 3.13
1819 1922 8.792830 TCCCTCATACTTCTTGTTTAATTGAG 57.207 34.615 0.00 0.00 0.00 3.02
1830 1933 8.812513 TCTTGTTTAATTGAGGATGATGATGT 57.187 30.769 0.00 0.00 0.00 3.06
1841 1944 3.119531 GGATGATGATGTTTTGGTCGCAA 60.120 43.478 0.00 0.00 0.00 4.85
1848 1951 2.869897 TGTTTTGGTCGCAAGTCAAAC 58.130 42.857 0.00 0.00 39.62 2.93
1855 1958 2.354821 GGTCGCAAGTCAAACAAACTCT 59.645 45.455 0.00 0.00 39.48 3.24
1864 1967 5.437060 AGTCAAACAAACTCTTGCTTAGGA 58.563 37.500 0.00 0.00 35.84 2.94
1865 1968 5.297029 AGTCAAACAAACTCTTGCTTAGGAC 59.703 40.000 0.00 0.00 35.84 3.85
1881 1984 5.238214 GCTTAGGACAGCTTAATTCTGGATG 59.762 44.000 8.98 0.00 36.79 3.51
1895 1998 2.842496 TCTGGATGCTGTCTGATCCTTT 59.158 45.455 0.00 0.00 39.23 3.11
1900 2003 4.219288 GGATGCTGTCTGATCCTTTTGTTT 59.781 41.667 0.00 0.00 36.04 2.83
1905 2008 7.370383 TGCTGTCTGATCCTTTTGTTTTATTC 58.630 34.615 0.00 0.00 0.00 1.75
1906 2009 7.014134 TGCTGTCTGATCCTTTTGTTTTATTCA 59.986 33.333 0.00 0.00 0.00 2.57
1907 2010 7.327032 GCTGTCTGATCCTTTTGTTTTATTCAC 59.673 37.037 0.00 0.00 0.00 3.18
1911 2014 7.012894 TCTGATCCTTTTGTTTTATTCACGTGT 59.987 33.333 16.51 0.00 0.00 4.49
1969 2072 2.953020 GCTATCTCAGCCAAGATACCG 58.047 52.381 2.33 0.00 45.23 4.02
1990 2093 1.001633 GAGTTCAGTAACAAGGGCCGA 59.998 52.381 0.00 0.00 38.12 5.54
2008 2111 2.355716 CCGAACATTGGTGGTCCAGTAT 60.356 50.000 0.00 0.00 45.22 2.12
2068 2171 6.398918 CGGCTATATTAAGCTAATGTCTGGT 58.601 40.000 0.00 0.00 42.37 4.00
2130 2233 6.958767 ACAGGTATGTTATTGCCTACTTCTT 58.041 36.000 0.00 0.00 35.63 2.52
2131 2234 6.823689 ACAGGTATGTTATTGCCTACTTCTTG 59.176 38.462 0.00 0.00 35.63 3.02
2143 2246 3.506067 CCTACTTCTTGCCCGTTGAATTT 59.494 43.478 0.00 0.00 0.00 1.82
2145 2248 2.296190 ACTTCTTGCCCGTTGAATTTCC 59.704 45.455 0.00 0.00 0.00 3.13
2157 2260 6.294508 CCCGTTGAATTTCCTGTTCTTACAAT 60.295 38.462 0.00 0.00 32.92 2.71
2210 2313 2.874701 CAGACCCTGTCACTGTTTTGAG 59.125 50.000 0.00 0.00 34.60 3.02
2227 2330 7.432059 TGTTTTGAGCATGTGATTTGAATGTA 58.568 30.769 0.00 0.00 0.00 2.29
2251 2358 6.344500 AGTATAGTTGATGAGCAAAGGTCTG 58.656 40.000 0.00 0.00 38.44 3.51
2257 2364 3.262660 TGATGAGCAAAGGTCTGTCTCAT 59.737 43.478 3.05 3.05 40.11 2.90
2258 2365 3.049708 TGAGCAAAGGTCTGTCTCATG 57.950 47.619 0.00 0.00 29.99 3.07
2300 2416 8.128322 AGTATAAGTCCACCTAAGATGCTATG 57.872 38.462 0.00 0.00 0.00 2.23
2301 2417 7.730784 AGTATAAGTCCACCTAAGATGCTATGT 59.269 37.037 0.00 0.00 0.00 2.29
2317 2433 3.059325 GCTATGTCTTGCGAATGTCCATC 60.059 47.826 0.00 0.00 0.00 3.51
2381 2497 6.453092 TGTTCAGTTTTACTAGTCTACTGCC 58.547 40.000 19.46 14.78 36.91 4.85
2396 2512 3.377346 ACTGCCGAGTTATGCTGATAG 57.623 47.619 0.00 0.00 0.00 2.08
2398 2514 1.688735 TGCCGAGTTATGCTGATAGCT 59.311 47.619 2.24 0.00 42.97 3.32
2404 2520 4.381270 CGAGTTATGCTGATAGCTTTCTCG 59.619 45.833 18.55 18.55 42.97 4.04
2415 2531 6.323266 TGATAGCTTTCTCGTGTTCTCTTAC 58.677 40.000 5.74 0.00 0.00 2.34
2686 2802 1.616159 GGTGCCAAAAAGGTAGCTCA 58.384 50.000 0.00 0.00 45.70 4.26
3089 3316 7.507616 TGAACTTGACCCATTTAACCACTTATT 59.492 33.333 0.00 0.00 0.00 1.40
3097 3324 6.332630 CCATTTAACCACTTATTTGGCTCTG 58.667 40.000 0.00 0.00 40.77 3.35
3227 3454 4.624015 CTCGGTACAACTAAGAACACCAA 58.376 43.478 0.00 0.00 0.00 3.67
3336 3566 3.310774 CGAATCCAGCATACAAAGGACAG 59.689 47.826 0.00 0.00 32.04 3.51
3362 3592 1.199624 CGCAAGGTTTGTCTTGTTGC 58.800 50.000 6.48 0.00 44.26 4.17
3375 3605 3.316308 GTCTTGTTGCTTGTCCATCAGTT 59.684 43.478 0.00 0.00 0.00 3.16
3382 3612 4.650734 TGCTTGTCCATCAGTTGTTCATA 58.349 39.130 0.00 0.00 0.00 2.15
3383 3613 4.696877 TGCTTGTCCATCAGTTGTTCATAG 59.303 41.667 0.00 0.00 0.00 2.23
3400 3630 9.840427 TTGTTCATAGCTACTTTATTTCTTTGC 57.160 29.630 0.00 0.00 0.00 3.68
3416 3646 7.426929 TTTCTTTGCTAGACTTCATGTTCTC 57.573 36.000 0.00 0.00 30.90 2.87
3421 3651 5.414360 TGCTAGACTTCATGTTCTCACATC 58.586 41.667 0.00 0.00 42.14 3.06
3429 3659 3.262660 TCATGTTCTCACATCTTCTGCCT 59.737 43.478 0.00 0.00 42.14 4.75
3487 3717 6.473429 TGGAAGATCCCATGGATTGATAAT 57.527 37.500 15.22 0.00 43.27 1.28
3506 3736 7.811282 TGATAATCCAGGTAAGCAAATAGGAA 58.189 34.615 0.00 0.00 0.00 3.36
3509 3739 6.775594 ATCCAGGTAAGCAAATAGGAAAAC 57.224 37.500 0.00 0.00 0.00 2.43
3512 3742 5.105756 CCAGGTAAGCAAATAGGAAAACTGG 60.106 44.000 0.00 0.00 35.24 4.00
3556 3786 3.541632 TGAAGTGGACCTCTTGTCAAAC 58.458 45.455 13.46 0.00 46.38 2.93
3560 3790 4.200092 AGTGGACCTCTTGTCAAACTTTC 58.800 43.478 0.00 0.00 46.38 2.62
3564 3794 5.105917 TGGACCTCTTGTCAAACTTTCAAAC 60.106 40.000 0.00 0.00 46.38 2.93
3566 3796 5.954335 ACCTCTTGTCAAACTTTCAAACAG 58.046 37.500 0.00 0.00 0.00 3.16
3567 3797 5.105756 ACCTCTTGTCAAACTTTCAAACAGG 60.106 40.000 0.00 0.00 32.22 4.00
3571 3801 5.146010 TGTCAAACTTTCAAACAGGCTTT 57.854 34.783 0.00 0.00 0.00 3.51
3572 3802 5.546526 TGTCAAACTTTCAAACAGGCTTTT 58.453 33.333 0.00 0.00 0.00 2.27
3585 3815 4.215109 ACAGGCTTTTACCATGAACTGTT 58.785 39.130 0.00 0.00 34.59 3.16
3592 3822 5.590530 TTTACCATGAACTGTTGCACTTT 57.409 34.783 0.00 0.00 0.00 2.66
3674 3904 4.374689 TGAAGTTTGGCAGGTACCATAA 57.625 40.909 15.94 0.24 40.13 1.90
3675 3905 4.331968 TGAAGTTTGGCAGGTACCATAAG 58.668 43.478 15.94 1.86 40.13 1.73
3687 3918 9.028284 GGCAGGTACCATAAGTTACATATAGTA 57.972 37.037 15.94 0.00 0.00 1.82
3708 3939 7.726033 AGTAGTCTTCTGGAGATACATGTTT 57.274 36.000 2.30 0.00 36.61 2.83
3758 3989 6.969366 TGAAGTACATTTGATGTTGACTTGG 58.031 36.000 11.77 0.00 40.36 3.61
3760 3991 6.808008 AGTACATTTGATGTTGACTTGGAG 57.192 37.500 0.00 0.00 41.63 3.86
3768 3999 3.026630 TGTTGACTTGGAGCTTACTCG 57.973 47.619 0.00 0.00 44.48 4.18
3790 4021 1.674322 GCAGGTAAAAGCCGGCTCA 60.674 57.895 32.93 15.78 44.47 4.26
3793 4024 1.066430 CAGGTAAAAGCCGGCTCAGTA 60.066 52.381 32.93 19.01 0.00 2.74
3826 4057 0.035915 TCATTTGCGATGACCCGGAA 60.036 50.000 0.73 0.00 38.07 4.30
3878 4109 2.681344 GGTGCAAATAAGGAGGTAACCG 59.319 50.000 0.00 0.00 34.73 4.44
3900 4131 5.092781 CGCACATGTTTACTGAATTAACCC 58.907 41.667 0.00 0.00 0.00 4.11
3904 4135 6.531240 CACATGTTTACTGAATTAACCCATGC 59.469 38.462 0.00 0.00 30.52 4.06
3916 4147 0.403271 ACCCATGCTGCTGATATCCC 59.597 55.000 0.00 0.00 0.00 3.85
3917 4148 0.402887 CCCATGCTGCTGATATCCCA 59.597 55.000 0.00 0.00 0.00 4.37
3933 4164 8.079211 TGATATCCCATAAGCAGTATCTTACC 57.921 38.462 0.00 0.00 32.02 2.85
4003 4234 5.142806 AGGAGAGGAAAGCTAGAGAAGAT 57.857 43.478 0.00 0.00 0.00 2.40
4067 4298 3.350219 TTATGTCCTTGAGGCAGAACC 57.650 47.619 0.00 0.00 39.61 3.62
4078 4309 1.963515 AGGCAGAACCGCAAAAGAATT 59.036 42.857 0.00 0.00 46.52 2.17
4085 4316 3.806316 ACCGCAAAAGAATTACTGTCG 57.194 42.857 0.00 0.00 0.00 4.35
4225 4456 6.402222 AGGACAGATACAAAAGAGTAAGCTG 58.598 40.000 0.00 0.00 36.92 4.24
4230 4461 8.531982 ACAGATACAAAAGAGTAAGCTGACATA 58.468 33.333 3.43 0.00 35.65 2.29
4302 4537 4.399483 TCTGACTACCACCCTAGAACTT 57.601 45.455 0.00 0.00 0.00 2.66
4317 4552 9.642343 ACCCTAGAACTTTTTGAAGTCTTATTT 57.358 29.630 0.00 0.00 31.53 1.40
4348 4585 5.046591 TCCCTTAACACACCTATTGACTGAG 60.047 44.000 0.00 0.00 0.00 3.35
4350 4587 5.046591 CCTTAACACACCTATTGACTGAGGA 60.047 44.000 0.00 0.00 36.61 3.71
4352 4589 5.505181 AACACACCTATTGACTGAGGAAT 57.495 39.130 0.00 0.00 36.61 3.01
4353 4590 5.091261 ACACACCTATTGACTGAGGAATC 57.909 43.478 0.00 0.00 36.61 2.52
4358 4596 6.015856 ACACCTATTGACTGAGGAATCTATCG 60.016 42.308 0.00 0.00 36.61 2.92
4410 4649 9.326413 AGACATTGCTATATGGTAAACAAGTAC 57.674 33.333 0.00 0.00 0.00 2.73
4411 4650 9.326413 GACATTGCTATATGGTAAACAAGTACT 57.674 33.333 0.00 0.00 0.00 2.73
4412 4651 9.326413 ACATTGCTATATGGTAAACAAGTACTC 57.674 33.333 0.00 0.00 0.00 2.59
4413 4652 8.774586 CATTGCTATATGGTAAACAAGTACTCC 58.225 37.037 0.00 0.00 0.00 3.85
4414 4653 6.823497 TGCTATATGGTAAACAAGTACTCCC 58.177 40.000 0.00 0.00 0.00 4.30
4415 4654 6.614087 TGCTATATGGTAAACAAGTACTCCCT 59.386 38.462 0.00 0.00 0.00 4.20
4416 4655 7.153315 GCTATATGGTAAACAAGTACTCCCTC 58.847 42.308 0.00 0.00 0.00 4.30
4417 4656 7.015389 GCTATATGGTAAACAAGTACTCCCTCT 59.985 40.741 0.00 0.00 0.00 3.69
4418 4657 4.884668 TGGTAAACAAGTACTCCCTCTG 57.115 45.455 0.00 0.00 0.00 3.35
4419 4658 4.228824 TGGTAAACAAGTACTCCCTCTGT 58.771 43.478 0.00 0.00 0.00 3.41
4420 4659 4.282703 TGGTAAACAAGTACTCCCTCTGTC 59.717 45.833 0.00 0.00 0.00 3.51
4421 4660 4.527427 GGTAAACAAGTACTCCCTCTGTCT 59.473 45.833 0.00 0.00 0.00 3.41
4422 4661 4.875561 AAACAAGTACTCCCTCTGTCTC 57.124 45.455 0.00 0.00 0.00 3.36
4423 4662 3.527507 ACAAGTACTCCCTCTGTCTCA 57.472 47.619 0.00 0.00 0.00 3.27
4424 4663 3.845860 ACAAGTACTCCCTCTGTCTCAA 58.154 45.455 0.00 0.00 0.00 3.02
4425 4664 4.223953 ACAAGTACTCCCTCTGTCTCAAA 58.776 43.478 0.00 0.00 0.00 2.69
4426 4665 4.654262 ACAAGTACTCCCTCTGTCTCAAAA 59.346 41.667 0.00 0.00 0.00 2.44
4427 4666 5.308237 ACAAGTACTCCCTCTGTCTCAAAAT 59.692 40.000 0.00 0.00 0.00 1.82
4428 4667 6.497259 ACAAGTACTCCCTCTGTCTCAAAATA 59.503 38.462 0.00 0.00 0.00 1.40
4429 4668 6.532988 AGTACTCCCTCTGTCTCAAAATAC 57.467 41.667 0.00 0.00 0.00 1.89
4430 4669 6.017192 AGTACTCCCTCTGTCTCAAAATACA 58.983 40.000 0.00 0.00 0.00 2.29
4431 4670 5.413309 ACTCCCTCTGTCTCAAAATACAG 57.587 43.478 0.00 0.00 43.63 2.74
4432 4671 4.223923 ACTCCCTCTGTCTCAAAATACAGG 59.776 45.833 0.00 0.00 42.72 4.00
4433 4672 3.519510 TCCCTCTGTCTCAAAATACAGGG 59.480 47.826 0.00 0.00 42.72 4.45
4435 4674 4.826274 CTCTGTCTCAAAATACAGGGGA 57.174 45.455 0.00 0.00 42.72 4.81
4436 4675 5.165961 CTCTGTCTCAAAATACAGGGGAA 57.834 43.478 0.00 0.00 42.72 3.97
4437 4676 5.560724 CTCTGTCTCAAAATACAGGGGAAA 58.439 41.667 0.00 0.00 42.72 3.13
4438 4677 5.947663 TCTGTCTCAAAATACAGGGGAAAA 58.052 37.500 0.00 0.00 42.72 2.29
4439 4678 6.369629 TCTGTCTCAAAATACAGGGGAAAAA 58.630 36.000 0.00 0.00 42.72 1.94
4472 4711 7.113658 TGAGACAGAGGGAGTATAATTGAAC 57.886 40.000 0.00 0.00 0.00 3.18
4497 4736 7.557719 ACATGTTCTAATTCTGGTAATCTTGGG 59.442 37.037 0.00 0.00 0.00 4.12
4499 4738 7.695055 TGTTCTAATTCTGGTAATCTTGGGAA 58.305 34.615 0.00 0.00 0.00 3.97
4502 4741 4.870021 ATTCTGGTAATCTTGGGAAGCT 57.130 40.909 0.00 0.00 0.00 3.74
4737 4986 9.632638 AGATAACATGTGGCTTATAACATTCTT 57.367 29.630 0.00 0.00 34.81 2.52
4804 5054 2.418669 TCTTCCAAGGAGAAACTGGGT 58.581 47.619 0.00 0.00 33.02 4.51
4813 5063 3.020984 GGAGAAACTGGGTTTTGACACA 58.979 45.455 0.00 0.00 35.77 3.72
4914 5164 5.596772 TGACCACGAAGATCATTCCTATGTA 59.403 40.000 0.00 0.00 33.34 2.29
4944 5194 4.878397 GGACAGACAATTCCACTTATCCTG 59.122 45.833 0.00 0.00 0.00 3.86
4945 5195 4.848357 ACAGACAATTCCACTTATCCTGG 58.152 43.478 0.00 0.00 0.00 4.45
4979 5229 2.580815 GCCTTGGCCCTGAAATGC 59.419 61.111 0.00 0.00 0.00 3.56
4989 5239 1.541147 CCCTGAAATGCGATGTTGTGT 59.459 47.619 0.00 0.00 0.00 3.72
5021 5271 1.933021 TGGTCGGTGATGTACTTCCT 58.067 50.000 6.32 0.00 0.00 3.36
5093 5343 9.800433 TCCATATTTATTGCATAACACAAACAG 57.200 29.630 0.00 0.00 0.00 3.16
5097 5347 2.420628 TGCATAACACAAACAGCTGC 57.579 45.000 15.27 0.00 0.00 5.25
5129 5379 4.256140 GAGTTCTCACTCGATTTGCATG 57.744 45.455 0.00 0.00 40.30 4.06
5130 5380 3.928992 GAGTTCTCACTCGATTTGCATGA 59.071 43.478 0.00 0.00 40.30 3.07
5133 5383 5.413833 AGTTCTCACTCGATTTGCATGAAAT 59.586 36.000 0.00 0.00 36.94 2.17
5189 5439 2.545946 CGCCTGCTAGAATTTAGCTTCC 59.454 50.000 15.79 7.17 40.95 3.46
5219 5470 3.056393 TGAAAAGAAAGCATGCATCCAGG 60.056 43.478 21.98 0.00 0.00 4.45
5322 5631 6.759272 TGGTATACCAGAATAGCATCAGAAC 58.241 40.000 21.05 0.00 42.01 3.01
5355 5664 1.078918 GATGCAAAAGGGGCAAGGC 60.079 57.895 0.00 0.00 45.60 4.35
5361 5670 2.351924 AAAAGGGGCAAGGCGACTCA 62.352 55.000 0.00 0.00 42.68 3.41
5365 5674 3.123620 GGCAAGGCGACTCAGCAG 61.124 66.667 16.41 0.00 42.68 4.24
5369 5678 0.038251 CAAGGCGACTCAGCAGTGTA 60.038 55.000 0.00 0.00 42.68 2.90
5398 5707 5.715279 AGAACAAGTCTGCTGTATACCTGTA 59.285 40.000 0.00 0.00 34.29 2.74
5399 5708 5.326200 ACAAGTCTGCTGTATACCTGTAC 57.674 43.478 0.00 0.00 0.00 2.90
5496 5805 7.936496 TCCACATATGAAAAGCAACATCTTA 57.064 32.000 10.38 0.00 0.00 2.10
5497 5806 8.347004 TCCACATATGAAAAGCAACATCTTAA 57.653 30.769 10.38 0.00 0.00 1.85
5517 5826 8.948631 TCTTAATTTATGGCTTGAGTCTACAG 57.051 34.615 0.00 0.00 0.00 2.74
5602 5999 9.434420 CTTCTCATTCCTTTACATGATATCCTC 57.566 37.037 0.00 0.00 0.00 3.71
5620 6017 5.388599 TCCTCCATAAAAAGATCCCCTTC 57.611 43.478 0.00 0.00 33.02 3.46
5626 6023 5.066505 CCATAAAAAGATCCCCTTCTGTTCG 59.933 44.000 0.00 0.00 33.02 3.95
5657 6061 4.371855 TGCATCTACAAGTCGAGGTAAG 57.628 45.455 0.00 0.00 0.00 2.34
5693 6097 4.259356 CATCTGAGATGACCAAAGAAGCA 58.741 43.478 17.28 0.00 0.00 3.91
5705 6109 2.489329 CAAAGAAGCACATACCACCAGG 59.511 50.000 0.00 0.00 42.21 4.45
5745 6149 7.282585 AGTATAGCATTGTGTCAACATGGTAT 58.717 34.615 16.08 16.08 39.31 2.73
5746 6150 4.707030 AGCATTGTGTCAACATGGTATG 57.293 40.909 0.00 0.00 35.83 2.39
5747 6151 3.444742 AGCATTGTGTCAACATGGTATGG 59.555 43.478 0.00 0.00 35.83 2.74
5753 6157 6.961360 TGTGTCAACATGGTATGGTTTTAA 57.039 33.333 0.00 0.00 33.60 1.52
5754 6158 7.531857 TGTGTCAACATGGTATGGTTTTAAT 57.468 32.000 0.00 0.00 33.60 1.40
5756 6160 8.085296 TGTGTCAACATGGTATGGTTTTAATTC 58.915 33.333 0.00 0.00 33.60 2.17
5757 6161 8.303876 GTGTCAACATGGTATGGTTTTAATTCT 58.696 33.333 0.00 0.00 33.60 2.40
5758 6162 8.303156 TGTCAACATGGTATGGTTTTAATTCTG 58.697 33.333 0.00 0.00 33.60 3.02
5759 6163 8.519526 GTCAACATGGTATGGTTTTAATTCTGA 58.480 33.333 0.00 0.00 33.60 3.27
5762 6166 9.705290 AACATGGTATGGTTTTAATTCTGAAAC 57.295 29.630 0.00 4.35 35.54 2.78
5763 6167 8.865090 ACATGGTATGGTTTTAATTCTGAAACA 58.135 29.630 0.00 2.71 37.46 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 60 5.718146 TCTAATATCTGCACTAGCTCATGC 58.282 41.667 13.84 13.84 42.74 4.06
81 84 5.336213 GCCTGTTTTCAGTGATGATGAATGT 60.336 40.000 0.00 0.00 45.68 2.71
82 85 5.100259 GCCTGTTTTCAGTGATGATGAATG 58.900 41.667 0.00 0.00 45.68 2.67
103 108 6.927294 AACAGCTTATGACTTATAACAGCC 57.073 37.500 0.00 0.00 0.00 4.85
111 116 6.065374 TGGGTTTCAAACAGCTTATGACTTA 58.935 36.000 1.93 0.00 0.00 2.24
112 117 4.892934 TGGGTTTCAAACAGCTTATGACTT 59.107 37.500 1.93 0.00 0.00 3.01
113 118 4.469657 TGGGTTTCAAACAGCTTATGACT 58.530 39.130 1.93 0.00 0.00 3.41
114 119 4.846779 TGGGTTTCAAACAGCTTATGAC 57.153 40.909 1.93 0.00 0.00 3.06
116 121 4.463891 AGGATGGGTTTCAAACAGCTTATG 59.536 41.667 1.93 0.00 0.00 1.90
121 126 3.572255 TGTAAGGATGGGTTTCAAACAGC 59.428 43.478 1.93 0.00 0.00 4.40
222 232 2.412065 CGTAAGTTCAAGAGCAAGCAGC 60.412 50.000 0.00 0.00 46.19 5.25
223 233 3.446184 CGTAAGTTCAAGAGCAAGCAG 57.554 47.619 0.00 0.00 0.00 4.24
399 414 0.899720 TAGAATTCCACCGCGGTTCT 59.100 50.000 32.11 29.13 35.05 3.01
426 441 0.465705 TGCTACTGGACTAGGCATGC 59.534 55.000 9.90 9.90 0.00 4.06
428 443 1.123928 GGTGCTACTGGACTAGGCAT 58.876 55.000 0.00 0.00 35.37 4.40
429 444 0.252057 TGGTGCTACTGGACTAGGCA 60.252 55.000 0.00 0.00 34.78 4.75
431 446 0.456221 CGTGGTGCTACTGGACTAGG 59.544 60.000 0.00 0.00 34.78 3.02
433 448 1.460504 CTCGTGGTGCTACTGGACTA 58.539 55.000 0.00 0.00 34.78 2.59
435 450 1.446272 GCTCGTGGTGCTACTGGAC 60.446 63.158 0.00 0.00 0.00 4.02
437 452 2.125512 GGCTCGTGGTGCTACTGG 60.126 66.667 0.00 0.00 0.00 4.00
438 453 2.507102 CGGCTCGTGGTGCTACTG 60.507 66.667 0.00 0.00 0.00 2.74
439 454 4.436998 GCGGCTCGTGGTGCTACT 62.437 66.667 0.00 0.00 0.00 2.57
593 612 1.094785 TTAGCAAATGAAGCTCGGCC 58.905 50.000 0.00 0.00 42.32 6.13
611 630 1.001520 GCCCCACTTTTTAATGCGGTT 59.998 47.619 0.00 0.00 0.00 4.44
612 631 0.606096 GCCCCACTTTTTAATGCGGT 59.394 50.000 0.00 0.00 0.00 5.68
790 821 2.752903 GGTGGCATCCTTGTAAATTCGT 59.247 45.455 0.00 0.00 0.00 3.85
797 828 2.125310 CGCGGTGGCATCCTTGTA 60.125 61.111 0.00 0.00 39.92 2.41
812 843 4.241555 ATCGGGTGATGGGAGCGC 62.242 66.667 0.00 0.00 32.21 5.92
857 902 1.134640 TGTGGCGCTTATTCACGGTAT 60.135 47.619 7.64 0.00 34.43 2.73
960 1005 3.787013 AGAAGAGGAGTAGGTAGTGGCTA 59.213 47.826 0.00 0.00 0.00 3.93
967 1012 2.092538 CACCGGAGAAGAGGAGTAGGTA 60.093 54.545 9.46 0.00 0.00 3.08
969 1014 1.064611 TCACCGGAGAAGAGGAGTAGG 60.065 57.143 9.46 0.00 0.00 3.18
971 1016 1.682394 GCTCACCGGAGAAGAGGAGTA 60.682 57.143 9.46 0.00 44.26 2.59
972 1017 0.968393 GCTCACCGGAGAAGAGGAGT 60.968 60.000 9.46 0.00 44.26 3.85
973 1018 1.671901 GGCTCACCGGAGAAGAGGAG 61.672 65.000 9.46 4.23 44.26 3.69
1118 1183 2.045536 GCTGGGAAGTGGGAGCAG 60.046 66.667 0.00 0.00 0.00 4.24
1156 1229 1.963338 GGTGCGATAGGGAGCATGC 60.963 63.158 10.51 10.51 45.69 4.06
1158 1231 1.050988 ACAGGTGCGATAGGGAGCAT 61.051 55.000 0.00 0.00 45.69 3.79
1160 1233 0.969894 ATACAGGTGCGATAGGGAGC 59.030 55.000 0.00 0.00 34.29 4.70
1162 1235 2.082140 ACATACAGGTGCGATAGGGA 57.918 50.000 0.00 0.00 0.00 4.20
1163 1236 2.029290 GGTACATACAGGTGCGATAGGG 60.029 54.545 0.00 0.00 0.00 3.53
1164 1237 2.891580 AGGTACATACAGGTGCGATAGG 59.108 50.000 0.00 0.00 0.00 2.57
1165 1238 3.857383 GCAGGTACATACAGGTGCGATAG 60.857 52.174 0.00 0.00 0.00 2.08
1167 1240 1.202533 GCAGGTACATACAGGTGCGAT 60.203 52.381 0.00 0.00 0.00 4.58
1168 1241 0.174845 GCAGGTACATACAGGTGCGA 59.825 55.000 0.00 0.00 0.00 5.10
1169 1242 0.175760 AGCAGGTACATACAGGTGCG 59.824 55.000 0.00 0.00 35.43 5.34
1171 1244 1.208052 AGCAGCAGGTACATACAGGTG 59.792 52.381 0.00 7.95 35.66 4.00
1172 1245 1.573108 AGCAGCAGGTACATACAGGT 58.427 50.000 0.00 0.00 0.00 4.00
1173 1246 4.342862 AATAGCAGCAGGTACATACAGG 57.657 45.455 0.00 0.00 0.00 4.00
1174 1247 5.464722 CAGAAATAGCAGCAGGTACATACAG 59.535 44.000 0.00 0.00 0.00 2.74
1175 1248 5.104941 ACAGAAATAGCAGCAGGTACATACA 60.105 40.000 0.00 0.00 0.00 2.29
1176 1249 5.235186 CACAGAAATAGCAGCAGGTACATAC 59.765 44.000 0.00 0.00 0.00 2.39
1177 1250 5.359756 CACAGAAATAGCAGCAGGTACATA 58.640 41.667 0.00 0.00 0.00 2.29
1178 1251 4.194640 CACAGAAATAGCAGCAGGTACAT 58.805 43.478 0.00 0.00 0.00 2.29
1218 1304 0.464373 TGGGAGCAGCGAATCCAATC 60.464 55.000 1.79 0.00 37.33 2.67
1220 1306 0.251121 TTTGGGAGCAGCGAATCCAA 60.251 50.000 1.79 4.94 37.33 3.53
1305 1393 3.260380 CCCAAGGGCATGAACAAAATACA 59.740 43.478 0.00 0.00 0.00 2.29
1389 1477 2.636830 CACTCAATTCCTTGCTCGGAT 58.363 47.619 0.00 0.00 32.02 4.18
1390 1478 1.339055 CCACTCAATTCCTTGCTCGGA 60.339 52.381 0.00 0.00 32.11 4.55
1483 1571 5.712917 TCAACTTAAATACCCAATCCCACAC 59.287 40.000 0.00 0.00 0.00 3.82
1484 1572 5.893500 TCAACTTAAATACCCAATCCCACA 58.106 37.500 0.00 0.00 0.00 4.17
1546 1643 0.524862 CAGCAATTCACTGGCCACTC 59.475 55.000 0.00 0.00 0.00 3.51
1567 1666 1.474332 AAGCAAACCACCAGGCCATG 61.474 55.000 5.01 0.00 39.06 3.66
1568 1667 1.152269 AAGCAAACCACCAGGCCAT 60.152 52.632 5.01 0.00 39.06 4.40
1569 1668 2.132996 CAAGCAAACCACCAGGCCA 61.133 57.895 5.01 0.00 39.06 5.36
1571 1670 1.109323 AGTCAAGCAAACCACCAGGC 61.109 55.000 0.00 0.00 39.06 4.85
1572 1671 1.402787 AAGTCAAGCAAACCACCAGG 58.597 50.000 0.00 0.00 42.21 4.45
1573 1672 2.030805 GCTAAGTCAAGCAAACCACCAG 60.031 50.000 0.00 0.00 42.30 4.00
1574 1673 1.953686 GCTAAGTCAAGCAAACCACCA 59.046 47.619 0.00 0.00 42.30 4.17
1575 1674 2.030805 CAGCTAAGTCAAGCAAACCACC 60.031 50.000 0.00 0.00 45.30 4.61
1576 1675 2.605580 GCAGCTAAGTCAAGCAAACCAC 60.606 50.000 0.00 0.00 45.30 4.16
1631 1730 3.733337 AGACAACTAGAAACCAGCAGTG 58.267 45.455 0.00 0.00 0.00 3.66
1647 1746 8.100164 TCTGAAACATACAACCATATGAGACAA 58.900 33.333 3.65 0.00 36.27 3.18
1695 1794 3.487544 CGCTCCTTTTCCAATCGGATTTC 60.488 47.826 0.00 0.00 42.41 2.17
1710 1809 1.002011 GGCTTTCCCTTCGCTCCTT 60.002 57.895 0.00 0.00 0.00 3.36
1712 1811 2.820037 CGGCTTTCCCTTCGCTCC 60.820 66.667 0.00 0.00 0.00 4.70
1733 1832 1.210931 CCTGCCGTGTGCTTGAATG 59.789 57.895 0.00 0.00 42.00 2.67
1734 1833 0.537143 TTCCTGCCGTGTGCTTGAAT 60.537 50.000 0.00 0.00 42.00 2.57
1761 1860 2.169352 ACCTTTGTCATCAGGATCTCCG 59.831 50.000 5.72 0.00 42.08 4.63
1791 1890 8.408601 CAATTAAACAAGAAGTATGAGGGATGG 58.591 37.037 0.00 0.00 0.00 3.51
1819 1922 2.423185 TGCGACCAAAACATCATCATCC 59.577 45.455 0.00 0.00 0.00 3.51
1830 1933 3.577649 TTGTTTGACTTGCGACCAAAA 57.422 38.095 0.00 0.00 32.44 2.44
1841 1944 5.297029 GTCCTAAGCAAGAGTTTGTTTGACT 59.703 40.000 0.53 0.00 38.09 3.41
1848 1951 3.406764 AGCTGTCCTAAGCAAGAGTTTG 58.593 45.455 0.00 0.00 46.08 2.93
1855 1958 4.943705 CCAGAATTAAGCTGTCCTAAGCAA 59.056 41.667 0.00 0.00 46.08 3.91
1861 1964 3.201708 AGCATCCAGAATTAAGCTGTCCT 59.798 43.478 0.00 0.00 0.00 3.85
1862 1965 3.314635 CAGCATCCAGAATTAAGCTGTCC 59.685 47.826 0.00 0.00 43.16 4.02
1881 1984 7.327032 GTGAATAAAACAAAAGGATCAGACAGC 59.673 37.037 0.00 0.00 0.00 4.40
1895 1998 5.527951 TGCCTAGAACACGTGAATAAAACAA 59.472 36.000 25.01 0.00 0.00 2.83
1900 2003 5.483811 TGAATGCCTAGAACACGTGAATAA 58.516 37.500 25.01 3.89 0.00 1.40
1905 2008 3.249799 TGTTTGAATGCCTAGAACACGTG 59.750 43.478 15.48 15.48 0.00 4.49
1906 2009 3.472652 TGTTTGAATGCCTAGAACACGT 58.527 40.909 0.00 0.00 0.00 4.49
1907 2010 4.219033 GTTGTTTGAATGCCTAGAACACG 58.781 43.478 0.00 0.00 30.71 4.49
1911 2014 7.994425 TCTATTGTTGTTTGAATGCCTAGAA 57.006 32.000 0.00 0.00 0.00 2.10
1969 2072 1.822506 GGCCCTTGTTACTGAACTCC 58.177 55.000 0.00 0.00 36.45 3.85
1990 2093 3.075283 TGGAATACTGGACCACCAATGTT 59.925 43.478 0.00 0.00 46.32 2.71
2008 2111 6.916360 ATTTCCTGCTCAAACTTTATGGAA 57.084 33.333 0.00 0.00 0.00 3.53
2068 2171 7.441157 CCGCTATATTTCTTCTGGTTGACATAA 59.559 37.037 0.00 0.00 0.00 1.90
2130 2233 1.611491 GAACAGGAAATTCAACGGGCA 59.389 47.619 0.00 0.00 0.00 5.36
2131 2234 1.886542 AGAACAGGAAATTCAACGGGC 59.113 47.619 0.00 0.00 0.00 6.13
2143 2246 4.288366 TGGTGGATCATTGTAAGAACAGGA 59.712 41.667 0.00 0.00 36.83 3.86
2145 2248 6.558009 CAATGGTGGATCATTGTAAGAACAG 58.442 40.000 4.69 0.00 45.21 3.16
2157 2260 3.719268 ACTAACAGCAATGGTGGATCA 57.281 42.857 17.16 0.00 35.13 2.92
2210 2313 9.655769 CAACTATACTACATTCAAATCACATGC 57.344 33.333 0.00 0.00 0.00 4.06
2227 2330 6.070538 ACAGACCTTTGCTCATCAACTATACT 60.071 38.462 0.00 0.00 33.73 2.12
2273 2380 9.998752 ATAGCATCTTAGGTGGACTTATACTAT 57.001 33.333 0.00 0.00 0.00 2.12
2276 2383 7.897864 ACATAGCATCTTAGGTGGACTTATAC 58.102 38.462 0.00 0.00 0.00 1.47
2317 2433 4.654091 ATTCATTTCGCCTTAACCATGG 57.346 40.909 11.19 11.19 0.00 3.66
2381 2497 4.381270 CGAGAAAGCTATCAGCATAACTCG 59.619 45.833 15.95 15.95 45.56 4.18
2396 2512 2.090812 GCGTAAGAGAACACGAGAAAGC 59.909 50.000 0.00 0.00 40.56 3.51
2398 2514 3.305964 CTGCGTAAGAGAACACGAGAAA 58.694 45.455 0.00 0.00 40.56 2.52
2404 2520 2.404215 TCAAGCTGCGTAAGAGAACAC 58.596 47.619 0.00 0.00 43.02 3.32
2415 2531 1.444895 GCCCAAACATCAAGCTGCG 60.445 57.895 0.00 0.00 0.00 5.18
2810 3032 9.932207 CAAATTCACATAATAATGTATGGGCAT 57.068 29.630 0.00 0.00 44.70 4.40
3015 3242 8.363390 TGATGCATTACCAAATAAGTCAAAACA 58.637 29.630 0.00 0.00 0.00 2.83
3089 3316 3.370840 AGACCAAATATGCAGAGCCAA 57.629 42.857 0.00 0.00 0.00 4.52
3097 3324 2.945447 TGCAGCAAGACCAAATATGC 57.055 45.000 0.00 0.00 39.06 3.14
3227 3454 9.471084 CACAACATGCATATATTTGTCATCATT 57.529 29.630 0.00 0.00 0.00 2.57
3336 3566 0.317854 GACAAACCTTGCGCTTCCAC 60.318 55.000 9.73 0.00 0.00 4.02
3362 3592 4.940046 AGCTATGAACAACTGATGGACAAG 59.060 41.667 0.00 0.00 0.00 3.16
3375 3605 9.231297 AGCAAAGAAATAAAGTAGCTATGAACA 57.769 29.630 0.00 0.00 0.00 3.18
3382 3612 9.157104 GAAGTCTAGCAAAGAAATAAAGTAGCT 57.843 33.333 0.00 0.00 35.47 3.32
3383 3613 8.936864 TGAAGTCTAGCAAAGAAATAAAGTAGC 58.063 33.333 0.00 0.00 35.47 3.58
3400 3630 7.488792 CAGAAGATGTGAGAACATGAAGTCTAG 59.511 40.741 0.00 0.00 0.00 2.43
3487 3717 5.710099 CAGTTTTCCTATTTGCTTACCTGGA 59.290 40.000 0.00 0.00 0.00 3.86
3506 3736 3.323979 AGTGTCGAGTCCAATACCAGTTT 59.676 43.478 0.00 0.00 0.00 2.66
3509 3739 3.056821 TCAAGTGTCGAGTCCAATACCAG 60.057 47.826 0.00 0.00 0.00 4.00
3512 3742 6.147164 TCAAAATCAAGTGTCGAGTCCAATAC 59.853 38.462 0.00 0.00 0.00 1.89
3556 3786 5.841810 TCATGGTAAAAGCCTGTTTGAAAG 58.158 37.500 0.00 0.00 0.00 2.62
3560 3790 4.984161 CAGTTCATGGTAAAAGCCTGTTTG 59.016 41.667 0.00 0.00 0.00 2.93
3564 3794 4.549458 CAACAGTTCATGGTAAAAGCCTG 58.451 43.478 0.00 0.00 0.00 4.85
3566 3796 3.243704 TGCAACAGTTCATGGTAAAAGCC 60.244 43.478 0.00 0.00 0.00 4.35
3567 3797 3.735746 GTGCAACAGTTCATGGTAAAAGC 59.264 43.478 0.00 0.00 36.32 3.51
3571 3801 5.347342 CAAAAGTGCAACAGTTCATGGTAA 58.653 37.500 0.00 0.00 41.43 2.85
3572 3802 4.930963 CAAAAGTGCAACAGTTCATGGTA 58.069 39.130 0.00 0.00 41.43 3.25
3592 3822 3.009363 TGGATCATCCTCAAACTCTGCAA 59.991 43.478 4.96 0.00 37.46 4.08
3636 3866 9.793252 CCAAACTTCAATTCCAATATACTTCAG 57.207 33.333 0.00 0.00 0.00 3.02
3644 3874 4.837860 ACCTGCCAAACTTCAATTCCAATA 59.162 37.500 0.00 0.00 0.00 1.90
3687 3918 6.611613 TGAAACATGTATCTCCAGAAGACT 57.388 37.500 0.00 0.00 36.65 3.24
3690 3921 9.551734 TTATGATGAAACATGTATCTCCAGAAG 57.448 33.333 0.00 0.00 0.00 2.85
3721 3952 9.288576 TCAAATGTACTTCATTCAGAACAATCT 57.711 29.630 0.00 0.00 44.85 2.40
3723 3954 9.850628 CATCAAATGTACTTCATTCAGAACAAT 57.149 29.630 0.00 0.00 44.85 2.71
3738 3969 5.182001 AGCTCCAAGTCAACATCAAATGTAC 59.818 40.000 0.00 0.00 44.07 2.90
3739 3970 5.316167 AGCTCCAAGTCAACATCAAATGTA 58.684 37.500 0.00 0.00 44.07 2.29
3749 3980 2.731976 CACGAGTAAGCTCCAAGTCAAC 59.268 50.000 0.00 0.00 38.49 3.18
3757 3988 0.737715 CCTGCACACGAGTAAGCTCC 60.738 60.000 0.00 0.00 38.49 4.70
3758 3989 0.038159 ACCTGCACACGAGTAAGCTC 60.038 55.000 0.00 0.00 38.35 4.09
3760 3991 2.074547 TTACCTGCACACGAGTAAGC 57.925 50.000 0.00 0.00 0.00 3.09
3768 3999 1.579429 CCGGCTTTTACCTGCACAC 59.421 57.895 0.00 0.00 0.00 3.82
3787 4018 9.338291 CAAATGAGAATGTTGTCAAATACTGAG 57.662 33.333 0.00 0.00 33.95 3.35
3790 4021 6.803320 CGCAAATGAGAATGTTGTCAAATACT 59.197 34.615 0.00 0.00 33.95 2.12
3793 4024 5.771469 TCGCAAATGAGAATGTTGTCAAAT 58.229 33.333 0.00 0.00 33.95 2.32
3878 4109 6.019779 TGGGTTAATTCAGTAAACATGTGC 57.980 37.500 0.00 0.00 0.00 4.57
3900 4131 3.377485 GCTTATGGGATATCAGCAGCATG 59.623 47.826 4.83 0.00 40.87 4.06
3916 4147 9.988815 ATACAGAAAGGTAAGATACTGCTTATG 57.011 33.333 0.00 0.00 33.34 1.90
3943 4174 5.394562 AAGCCTCCTTTTCAGCCTATAAT 57.605 39.130 0.00 0.00 0.00 1.28
4052 4283 2.050836 TTGCGGTTCTGCCTCAAGGA 62.051 55.000 0.00 0.00 37.07 3.36
4067 4298 4.375698 CACAACGACAGTAATTCTTTTGCG 59.624 41.667 0.00 0.00 0.00 4.85
4078 4309 4.054780 AGCTTCTTTCACAACGACAGTA 57.945 40.909 0.00 0.00 0.00 2.74
4085 4316 7.113544 GCAGTTATGTTTAGCTTCTTTCACAAC 59.886 37.037 0.00 0.00 0.00 3.32
4187 4418 4.069312 TCTGTCCTTGTAATGGTCCCTA 57.931 45.455 0.00 0.00 31.98 3.53
4225 4456 2.347755 GGAAGAAAGCGAACGGTATGTC 59.652 50.000 0.00 0.00 0.00 3.06
4230 4461 0.391597 TCAGGAAGAAAGCGAACGGT 59.608 50.000 0.00 0.00 0.00 4.83
4302 4537 7.233348 AGGGAATCAGCAAATAAGACTTCAAAA 59.767 33.333 0.00 0.00 0.00 2.44
4317 4552 2.375174 AGGTGTGTTAAGGGAATCAGCA 59.625 45.455 0.00 0.00 0.00 4.41
4353 4590 8.433421 ACTTGGGTTTTGTAATATGTCGATAG 57.567 34.615 0.00 0.00 0.00 2.08
4358 4596 7.175990 TCAAGGACTTGGGTTTTGTAATATGTC 59.824 37.037 11.76 0.00 40.78 3.06
4410 4649 4.383552 CCCTGTATTTTGAGACAGAGGGAG 60.384 50.000 0.00 0.00 44.88 4.30
4411 4650 3.519510 CCCTGTATTTTGAGACAGAGGGA 59.480 47.826 0.00 0.00 44.88 4.20
4412 4651 3.370953 CCCCTGTATTTTGAGACAGAGGG 60.371 52.174 11.64 11.64 44.88 4.30
4413 4652 3.519510 TCCCCTGTATTTTGAGACAGAGG 59.480 47.826 3.64 0.06 44.88 3.69
4414 4653 4.826274 TCCCCTGTATTTTGAGACAGAG 57.174 45.455 3.64 0.00 44.88 3.35
4415 4654 5.576563 TTTCCCCTGTATTTTGAGACAGA 57.423 39.130 3.64 0.00 44.88 3.41
4416 4655 6.648879 TTTTTCCCCTGTATTTTGAGACAG 57.351 37.500 0.00 0.00 42.29 3.51
4436 4675 8.166726 ACTCCCTCTGTCTCAAAATATCTTTTT 58.833 33.333 0.00 0.00 32.21 1.94
4437 4676 7.694093 ACTCCCTCTGTCTCAAAATATCTTTT 58.306 34.615 0.00 0.00 34.90 2.27
4438 4677 7.264294 ACTCCCTCTGTCTCAAAATATCTTT 57.736 36.000 0.00 0.00 0.00 2.52
4439 4678 6.882768 ACTCCCTCTGTCTCAAAATATCTT 57.117 37.500 0.00 0.00 0.00 2.40
4440 4679 9.661954 TTATACTCCCTCTGTCTCAAAATATCT 57.338 33.333 0.00 0.00 0.00 1.98
4444 4683 8.772250 TCAATTATACTCCCTCTGTCTCAAAAT 58.228 33.333 0.00 0.00 0.00 1.82
4445 4684 8.146053 TCAATTATACTCCCTCTGTCTCAAAA 57.854 34.615 0.00 0.00 0.00 2.44
4446 4685 7.733773 TCAATTATACTCCCTCTGTCTCAAA 57.266 36.000 0.00 0.00 0.00 2.69
4447 4686 7.180229 TGTTCAATTATACTCCCTCTGTCTCAA 59.820 37.037 0.00 0.00 0.00 3.02
4448 4687 6.667848 TGTTCAATTATACTCCCTCTGTCTCA 59.332 38.462 0.00 0.00 0.00 3.27
4449 4688 7.113658 TGTTCAATTATACTCCCTCTGTCTC 57.886 40.000 0.00 0.00 0.00 3.36
4450 4689 7.126421 ACATGTTCAATTATACTCCCTCTGTCT 59.874 37.037 0.00 0.00 0.00 3.41
4451 4690 7.275920 ACATGTTCAATTATACTCCCTCTGTC 58.724 38.462 0.00 0.00 0.00 3.51
4452 4691 7.200434 ACATGTTCAATTATACTCCCTCTGT 57.800 36.000 0.00 0.00 0.00 3.41
4453 4692 7.989741 AGAACATGTTCAATTATACTCCCTCTG 59.010 37.037 33.92 0.00 41.84 3.35
4454 4693 8.095452 AGAACATGTTCAATTATACTCCCTCT 57.905 34.615 33.92 10.07 41.84 3.69
4455 4694 9.832445 TTAGAACATGTTCAATTATACTCCCTC 57.168 33.333 33.92 7.98 41.84 4.30
4472 4711 7.775093 TCCCAAGATTACCAGAATTAGAACATG 59.225 37.037 0.00 0.00 0.00 3.21
4483 4722 2.912956 ACAGCTTCCCAAGATTACCAGA 59.087 45.455 0.00 0.00 0.00 3.86
4490 4729 0.773644 ACACCACAGCTTCCCAAGAT 59.226 50.000 0.00 0.00 0.00 2.40
4497 4736 1.103398 AGGCAACACACCACAGCTTC 61.103 55.000 0.00 0.00 41.41 3.86
4499 4738 1.076777 AAGGCAACACACCACAGCT 60.077 52.632 0.00 0.00 41.41 4.24
4502 4741 1.943116 GCACAAGGCAACACACCACA 61.943 55.000 0.00 0.00 43.97 4.17
4550 4789 5.109903 GTCTTACACAGTCACAGTTTCACT 58.890 41.667 0.00 0.00 0.00 3.41
4737 4986 3.149196 GCTCATCCTGAACAAGAAACCA 58.851 45.455 0.00 0.00 0.00 3.67
4775 5024 7.176340 CAGTTTCTCCTTGGAAGAATTGAAGAT 59.824 37.037 0.00 0.00 33.01 2.40
4813 5063 7.744087 TTGAAGCAACTATAACACAATGTCT 57.256 32.000 0.00 0.00 0.00 3.41
4914 5164 2.158623 TGGAATTGTCTGTCCTGCTGTT 60.159 45.455 0.00 0.00 34.77 3.16
4979 5229 4.045783 TGTACACTACACACACAACATCG 58.954 43.478 0.00 0.00 32.89 3.84
4989 5239 2.029739 CACCGACCATGTACACTACACA 60.030 50.000 0.00 0.00 42.23 3.72
5093 5343 1.502163 AACTCGTCAGCAACAGCAGC 61.502 55.000 0.00 0.00 0.00 5.25
5097 5347 1.789464 GTGAGAACTCGTCAGCAACAG 59.211 52.381 0.00 0.00 0.00 3.16
5189 5439 4.616835 GCATGCTTTCTTTTCACTACCTGG 60.617 45.833 11.37 0.00 0.00 4.45
5219 5470 8.765219 TGAAAGAAACGCTAATATATGCTTCTC 58.235 33.333 0.00 0.00 0.00 2.87
5271 5580 7.885297 TCAATTAATCAAGGAAGTTCCAAGTG 58.115 34.615 23.87 16.02 39.61 3.16
5322 5631 4.418013 TTGCATCAATGTGTTTAGACGG 57.582 40.909 0.00 0.00 0.00 4.79
5355 5664 0.108662 TGCCATACACTGCTGAGTCG 60.109 55.000 0.00 0.00 0.00 4.18
5361 5670 2.224621 ACTTGTTCTGCCATACACTGCT 60.225 45.455 0.00 0.00 0.00 4.24
5386 5695 4.465632 TGTTGCCAGTACAGGTATACAG 57.534 45.455 6.14 0.00 0.00 2.74
5392 5701 2.884639 GTGAATTGTTGCCAGTACAGGT 59.115 45.455 6.14 0.00 0.00 4.00
5398 5707 2.162208 CGCATAGTGAATTGTTGCCAGT 59.838 45.455 0.00 0.00 0.00 4.00
5399 5708 2.162208 ACGCATAGTGAATTGTTGCCAG 59.838 45.455 0.00 0.00 0.00 4.85
5418 5727 6.035112 GCTCCTTCTATTTGTCTTGAAGTACG 59.965 42.308 0.00 0.00 35.47 3.67
5421 5730 5.869579 TGCTCCTTCTATTTGTCTTGAAGT 58.130 37.500 0.00 0.00 35.47 3.01
5490 5799 9.330063 TGTAGACTCAAGCCATAAATTAAGATG 57.670 33.333 0.00 0.00 0.00 2.90
5496 5805 9.553064 CTAATCTGTAGACTCAAGCCATAAATT 57.447 33.333 0.00 0.00 0.00 1.82
5497 5806 8.928448 TCTAATCTGTAGACTCAAGCCATAAAT 58.072 33.333 0.00 0.00 0.00 1.40
5503 5812 8.172352 TCTATTCTAATCTGTAGACTCAAGCC 57.828 38.462 0.00 0.00 0.00 4.35
5602 5999 5.066505 CGAACAGAAGGGGATCTTTTTATGG 59.933 44.000 0.00 0.00 35.50 2.74
5613 6010 3.780804 TTCATTTCGAACAGAAGGGGA 57.219 42.857 0.00 0.00 40.40 4.81
5626 6023 5.961843 CGACTTGTAGATGCATGTTCATTTC 59.038 40.000 2.46 3.05 0.00 2.17
5643 6047 3.506844 GGAGTTCTCTTACCTCGACTTGT 59.493 47.826 0.00 0.00 0.00 3.16
5657 6061 3.766591 TCTCAGATGTGAAGGGAGTTCTC 59.233 47.826 0.00 0.00 35.99 2.87
5705 6109 8.915654 CAATGCTATACTTTCAGTTTTGGAAAC 58.084 33.333 0.00 0.00 31.44 2.78


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

AutoCloner maintained by Alex Coulton.