Multiple sequence alignment - TraesCS1D01G404300

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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 TraesCS1D01G404300 chr1D 100.000 3418 0 0 1 3418 469051620 469055037 0.000000e+00 6312
1 TraesCS1D01G404300 chr1D 85.000 760 90 9 1 748 211302028 211302775 0.000000e+00 750
2 TraesCS1D01G404300 chr1A 89.686 2259 103 60 783 2985 562042053 562044237 0.000000e+00 2761
3 TraesCS1D01G404300 chr1A 85.771 752 73 6 1 748 386502963 386502242 0.000000e+00 765
4 TraesCS1D01G404300 chr1A 97.305 334 8 1 3086 3418 562044862 562045195 1.780000e-157 566
5 TraesCS1D01G404300 chr1A 94.805 77 4 0 2885 2961 562044339 562044415 1.670000e-23 121
6 TraesCS1D01G404300 chr1B 86.432 2049 127 75 792 2778 648594583 648592624 0.000000e+00 2104
7 TraesCS1D01G404300 chr1B 93.093 333 19 3 3086 3415 648592372 648592041 5.130000e-133 484
8 TraesCS1D01G404300 chr5D 87.682 755 70 10 2 746 176088986 176089727 0.000000e+00 857
9 TraesCS1D01G404300 chr5D 83.718 780 76 17 1 747 36482848 36483609 0.000000e+00 689
10 TraesCS1D01G404300 chr5D 79.154 331 56 13 1787 2109 37202355 37202680 2.070000e-52 217
11 TraesCS1D01G404300 chr5D 85.128 195 27 2 1467 1660 37202115 37202308 7.480000e-47 198
12 TraesCS1D01G404300 chr5D 82.286 175 26 3 1203 1373 37201849 37202022 2.750000e-31 147
13 TraesCS1D01G404300 chr5D 93.827 81 4 1 1293 1373 508999696 508999775 1.670000e-23 121
14 TraesCS1D01G404300 chr7D 86.873 777 59 19 1 748 403542541 403543303 0.000000e+00 830
15 TraesCS1D01G404300 chr7D 80.380 790 103 26 1 748 19325159 19325938 1.390000e-153 553
16 TraesCS1D01G404300 chr7D 86.154 195 25 2 1467 1660 31119639 31119832 3.460000e-50 209
17 TraesCS1D01G404300 chr7D 77.586 348 62 12 1786 2122 58842626 58842284 2.690000e-46 196
18 TraesCS1D01G404300 chr2D 86.728 761 61 15 1 739 560967410 560966668 0.000000e+00 809
19 TraesCS1D01G404300 chr2D 85.237 779 75 18 1 750 644675793 644675026 0.000000e+00 765
20 TraesCS1D01G404300 chr6D 86.561 759 66 10 1 736 107769200 107769945 0.000000e+00 804
21 TraesCS1D01G404300 chr6D 93.035 201 10 3 1467 1665 466908805 466908607 1.200000e-74 291
22 TraesCS1D01G404300 chr7B 85.263 760 84 13 1 742 524890400 524889651 0.000000e+00 758
23 TraesCS1D01G404300 chr7B 82.470 753 86 25 3 748 579479485 579478772 4.850000e-173 617
24 TraesCS1D01G404300 chr7B 84.594 357 39 5 397 748 6126683 6127028 1.170000e-89 340
25 TraesCS1D01G404300 chr4D 87.097 682 60 16 1 674 374784734 374784073 0.000000e+00 747
26 TraesCS1D01G404300 chr4D 82.886 783 88 21 3 751 312572749 312571979 0.000000e+00 662
27 TraesCS1D01G404300 chr7A 83.812 766 80 19 1 755 461923790 461924522 0.000000e+00 688
28 TraesCS1D01G404300 chr7A 85.128 195 27 2 1467 1660 31592098 31592291 7.480000e-47 198
29 TraesCS1D01G404300 chr7A 78.107 338 55 15 1786 2109 31592337 31592669 2.690000e-46 196
30 TraesCS1D01G404300 chr7A 76.093 343 62 17 1793 2122 63383749 63383414 9.820000e-36 161
31 TraesCS1D01G404300 chr7A 76.190 336 60 17 1787 2109 63378659 63378987 3.530000e-35 159
32 TraesCS1D01G404300 chr7A 80.571 175 29 4 1203 1373 31591820 31591993 2.770000e-26 130
33 TraesCS1D01G404300 chr4B 82.461 764 78 27 1 747 125453788 125454512 4.850000e-173 617
34 TraesCS1D01G404300 chr3B 80.107 749 99 32 1 734 802310768 802311481 2.350000e-141 512
35 TraesCS1D01G404300 chr6A 83.801 463 64 7 1 457 208873135 208873592 2.440000e-116 429
36 TraesCS1D01G404300 chr6A 93.532 201 9 3 1467 1665 613237617 613237419 2.580000e-76 296
37 TraesCS1D01G404300 chr6B 93.532 201 9 3 1467 1665 712103720 712103918 2.580000e-76 296
38 TraesCS1D01G404300 chr6B 91.509 106 7 2 1269 1373 712103523 712103627 9.890000e-31 145
39 TraesCS1D01G404300 chr5B 78.743 334 57 13 1786 2109 27813572 27813901 9.610000e-51 211
40 TraesCS1D01G404300 chr5B 85.641 195 26 2 1467 1660 27813333 27813526 1.610000e-48 204
41 TraesCS1D01G404300 chr5B 82.286 175 26 3 1203 1373 27813083 27813256 2.750000e-31 147
42 TraesCS1D01G404300 chr4A 77.437 359 65 12 1775 2122 675954866 675954513 2.080000e-47 200
43 TraesCS1D01G404300 chr4A 76.369 347 68 13 1787 2123 675932852 675933194 1.260000e-39 174
44 TraesCS1D01G404300 chr3D 75.873 315 59 10 1814 2124 47740874 47740573 9.890000e-31 145


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 TraesCS1D01G404300 chr1D 469051620 469055037 3417 False 6312.000000 6312 100.0000 1 3418 1 chr1D.!!$F2 3417
1 TraesCS1D01G404300 chr1D 211302028 211302775 747 False 750.000000 750 85.0000 1 748 1 chr1D.!!$F1 747
2 TraesCS1D01G404300 chr1A 562042053 562045195 3142 False 1149.333333 2761 93.9320 783 3418 3 chr1A.!!$F1 2635
3 TraesCS1D01G404300 chr1A 386502242 386502963 721 True 765.000000 765 85.7710 1 748 1 chr1A.!!$R1 747
4 TraesCS1D01G404300 chr1B 648592041 648594583 2542 True 1294.000000 2104 89.7625 792 3415 2 chr1B.!!$R1 2623
5 TraesCS1D01G404300 chr5D 176088986 176089727 741 False 857.000000 857 87.6820 2 746 1 chr5D.!!$F2 744
6 TraesCS1D01G404300 chr5D 36482848 36483609 761 False 689.000000 689 83.7180 1 747 1 chr5D.!!$F1 746
7 TraesCS1D01G404300 chr7D 403542541 403543303 762 False 830.000000 830 86.8730 1 748 1 chr7D.!!$F3 747
8 TraesCS1D01G404300 chr7D 19325159 19325938 779 False 553.000000 553 80.3800 1 748 1 chr7D.!!$F1 747
9 TraesCS1D01G404300 chr2D 560966668 560967410 742 True 809.000000 809 86.7280 1 739 1 chr2D.!!$R1 738
10 TraesCS1D01G404300 chr2D 644675026 644675793 767 True 765.000000 765 85.2370 1 750 1 chr2D.!!$R2 749
11 TraesCS1D01G404300 chr6D 107769200 107769945 745 False 804.000000 804 86.5610 1 736 1 chr6D.!!$F1 735
12 TraesCS1D01G404300 chr7B 524889651 524890400 749 True 758.000000 758 85.2630 1 742 1 chr7B.!!$R1 741
13 TraesCS1D01G404300 chr7B 579478772 579479485 713 True 617.000000 617 82.4700 3 748 1 chr7B.!!$R2 745
14 TraesCS1D01G404300 chr4D 374784073 374784734 661 True 747.000000 747 87.0970 1 674 1 chr4D.!!$R2 673
15 TraesCS1D01G404300 chr4D 312571979 312572749 770 True 662.000000 662 82.8860 3 751 1 chr4D.!!$R1 748
16 TraesCS1D01G404300 chr7A 461923790 461924522 732 False 688.000000 688 83.8120 1 755 1 chr7A.!!$F2 754
17 TraesCS1D01G404300 chr4B 125453788 125454512 724 False 617.000000 617 82.4610 1 747 1 chr4B.!!$F1 746
18 TraesCS1D01G404300 chr3B 802310768 802311481 713 False 512.000000 512 80.1070 1 734 1 chr3B.!!$F1 733

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
396 468 0.105709 CTCCTCCTCCTCTCTTCCCC 60.106 65.0 0.0 0.0 0.0 4.81 F
1683 1880 0.173708 TGTACGCACGCACATATCCA 59.826 50.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1685 1882 0.034186 GATGCAAGATGGTGTGGGGA 60.034 55.0 0.0 0.0 0.0 4.81 R
2658 2927 0.601841 AACTAACGTGCCAACTCCCG 60.602 55.0 0.0 0.0 0.0 5.14 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
224 249 1.531748 CCGGTTGGCCTCCACATAT 59.468 57.895 3.32 0.00 30.78 1.78
344 382 2.055042 CACCTGCTAGTCCGGCTCT 61.055 63.158 0.00 0.00 0.00 4.09
390 462 1.203050 CCATCTCCTCCTCCTCCTCTC 60.203 61.905 0.00 0.00 0.00 3.20
392 464 1.994399 TCTCCTCCTCCTCCTCTCTT 58.006 55.000 0.00 0.00 0.00 2.85
396 468 0.105709 CTCCTCCTCCTCTCTTCCCC 60.106 65.000 0.00 0.00 0.00 4.81
398 470 1.706575 CTCCTCCTCTCTTCCCCCA 59.293 63.158 0.00 0.00 0.00 4.96
399 471 0.398381 CTCCTCCTCTCTTCCCCCAG 60.398 65.000 0.00 0.00 0.00 4.45
405 534 0.263172 CTCTCTTCCCCCAGCTCCTA 59.737 60.000 0.00 0.00 0.00 2.94
410 542 1.528341 TTCCCCCAGCTCCTACTCCT 61.528 60.000 0.00 0.00 0.00 3.69
411 543 1.458588 CCCCCAGCTCCTACTCCTC 60.459 68.421 0.00 0.00 0.00 3.71
556 690 0.911769 TGATCTTGCTCCGGACCATT 59.088 50.000 0.00 0.00 0.00 3.16
558 692 0.911769 ATCTTGCTCCGGACCATTGA 59.088 50.000 0.00 2.61 0.00 2.57
618 771 2.124695 GGAGGTGGATGGGTTCGC 60.125 66.667 0.00 0.00 0.00 4.70
764 924 4.910585 GGCCCGCCTGGACGTATG 62.911 72.222 0.00 0.00 37.49 2.39
765 925 3.845259 GCCCGCCTGGACGTATGA 61.845 66.667 0.00 0.00 37.49 2.15
766 926 2.417516 CCCGCCTGGACGTATGAG 59.582 66.667 0.00 0.00 37.49 2.90
767 927 2.125326 CCCGCCTGGACGTATGAGA 61.125 63.158 0.00 0.00 37.49 3.27
768 928 1.065928 CCGCCTGGACGTATGAGAC 59.934 63.158 0.00 0.00 37.49 3.36
781 941 4.981389 GTATGAGACGGATTTGATGCTC 57.019 45.455 0.00 0.00 0.00 4.26
782 942 3.834489 ATGAGACGGATTTGATGCTCT 57.166 42.857 0.00 0.00 0.00 4.09
783 943 3.616956 TGAGACGGATTTGATGCTCTT 57.383 42.857 0.00 0.00 0.00 2.85
784 944 4.736126 TGAGACGGATTTGATGCTCTTA 57.264 40.909 0.00 0.00 0.00 2.10
785 945 4.686972 TGAGACGGATTTGATGCTCTTAG 58.313 43.478 0.00 0.00 0.00 2.18
786 946 4.160439 TGAGACGGATTTGATGCTCTTAGT 59.840 41.667 0.00 0.00 0.00 2.24
787 947 5.359860 TGAGACGGATTTGATGCTCTTAGTA 59.640 40.000 0.00 0.00 0.00 1.82
788 948 5.593010 AGACGGATTTGATGCTCTTAGTAC 58.407 41.667 0.00 0.00 0.00 2.73
831 1003 2.364317 CCCCTCTCCTCTCGGCAA 60.364 66.667 0.00 0.00 0.00 4.52
854 1026 1.566211 ACTACACCAGCAGAGCAGAT 58.434 50.000 0.00 0.00 0.00 2.90
901 1074 1.566018 AAGGAAAGTTTCGCGCTCCG 61.566 55.000 5.56 0.00 38.61 4.63
914 1087 3.691342 CTCCGCCCGACAGAACCA 61.691 66.667 0.00 0.00 0.00 3.67
1014 1187 2.359107 CAGACCGCACAGCACCAT 60.359 61.111 0.00 0.00 0.00 3.55
1018 1191 2.669229 CCGCACAGCACCATCACA 60.669 61.111 0.00 0.00 0.00 3.58
1019 1192 2.557805 CGCACAGCACCATCACAC 59.442 61.111 0.00 0.00 0.00 3.82
1121 1300 1.687493 GTCCCTCTCCCTCCACCTG 60.687 68.421 0.00 0.00 0.00 4.00
1260 1439 4.103103 CGCTCACGCTCGACCAGA 62.103 66.667 0.00 0.00 0.00 3.86
1380 1559 1.132643 CCTCCTTCTACGTGAGTTCCG 59.867 57.143 0.00 0.00 46.40 4.30
1418 1607 1.115467 GAGGAGCAAGGGATCGAAGA 58.885 55.000 0.00 0.00 45.75 2.87
1419 1608 0.827368 AGGAGCAAGGGATCGAAGAC 59.173 55.000 0.00 0.00 42.51 3.01
1420 1609 0.179070 GGAGCAAGGGATCGAAGACC 60.179 60.000 0.00 0.00 42.51 3.85
1421 1610 0.537188 GAGCAAGGGATCGAAGACCA 59.463 55.000 6.24 0.00 42.51 4.02
1422 1611 1.139853 GAGCAAGGGATCGAAGACCAT 59.860 52.381 6.24 0.00 42.51 3.55
1423 1612 1.134280 AGCAAGGGATCGAAGACCATG 60.134 52.381 6.24 5.48 42.51 3.66
1424 1613 1.959042 CAAGGGATCGAAGACCATGG 58.041 55.000 11.19 11.19 42.51 3.66
1437 1628 3.238232 CCATGGTGGTCTGACTGTG 57.762 57.895 2.57 0.58 31.35 3.66
1438 1629 0.321919 CCATGGTGGTCTGACTGTGG 60.322 60.000 2.57 5.61 31.35 4.17
1439 1630 0.397941 CATGGTGGTCTGACTGTGGT 59.602 55.000 7.85 0.00 0.00 4.16
1454 1645 1.339247 TGTGGTTGGTTGACTCGTGTT 60.339 47.619 0.00 0.00 0.00 3.32
1460 1651 4.751098 GGTTGGTTGACTCGTGTTTGTATA 59.249 41.667 0.00 0.00 0.00 1.47
1542 1733 3.227276 CTCAGCGGCGACCCCTAT 61.227 66.667 12.98 0.00 0.00 2.57
1672 1869 2.095853 CCCAAGAACATCATGTACGCAC 59.904 50.000 0.00 0.00 0.00 5.34
1673 1870 2.222796 CCAAGAACATCATGTACGCACG 60.223 50.000 0.00 0.00 0.00 5.34
1674 1871 0.999406 AGAACATCATGTACGCACGC 59.001 50.000 0.00 0.00 0.00 5.34
1675 1872 0.718904 GAACATCATGTACGCACGCA 59.281 50.000 0.00 0.00 0.00 5.24
1676 1873 0.442310 AACATCATGTACGCACGCAC 59.558 50.000 0.00 0.00 0.00 5.34
1677 1874 0.669012 ACATCATGTACGCACGCACA 60.669 50.000 0.00 0.00 0.00 4.57
1678 1875 0.652071 CATCATGTACGCACGCACAT 59.348 50.000 3.11 3.11 35.79 3.21
1679 1876 1.857837 CATCATGTACGCACGCACATA 59.142 47.619 8.47 0.00 33.66 2.29
1680 1877 2.217429 TCATGTACGCACGCACATAT 57.783 45.000 8.47 0.00 33.66 1.78
1681 1878 2.124122 TCATGTACGCACGCACATATC 58.876 47.619 8.47 0.00 33.66 1.63
1682 1879 1.192312 CATGTACGCACGCACATATCC 59.808 52.381 8.47 0.00 33.66 2.59
1683 1880 0.173708 TGTACGCACGCACATATCCA 59.826 50.000 0.00 0.00 0.00 3.41
1684 1881 1.202475 TGTACGCACGCACATATCCAT 60.202 47.619 0.00 0.00 0.00 3.41
1685 1882 1.864711 GTACGCACGCACATATCCATT 59.135 47.619 0.00 0.00 0.00 3.16
1686 1883 0.937304 ACGCACGCACATATCCATTC 59.063 50.000 0.00 0.00 0.00 2.67
1687 1884 0.235665 CGCACGCACATATCCATTCC 59.764 55.000 0.00 0.00 0.00 3.01
1688 1885 0.593128 GCACGCACATATCCATTCCC 59.407 55.000 0.00 0.00 0.00 3.97
1689 1886 1.238439 CACGCACATATCCATTCCCC 58.762 55.000 0.00 0.00 0.00 4.81
1690 1887 0.843309 ACGCACATATCCATTCCCCA 59.157 50.000 0.00 0.00 0.00 4.96
1691 1888 1.238439 CGCACATATCCATTCCCCAC 58.762 55.000 0.00 0.00 0.00 4.61
1692 1889 1.476652 CGCACATATCCATTCCCCACA 60.477 52.381 0.00 0.00 0.00 4.17
1717 1920 3.084039 TCTTGCATCCAAGTTCCATGTC 58.916 45.455 0.00 0.00 46.74 3.06
1718 1921 2.885135 TGCATCCAAGTTCCATGTCT 57.115 45.000 0.00 0.00 0.00 3.41
1722 1925 5.263599 TGCATCCAAGTTCCATGTCTAATT 58.736 37.500 0.00 0.00 0.00 1.40
1724 1927 5.591877 GCATCCAAGTTCCATGTCTAATTCT 59.408 40.000 0.00 0.00 0.00 2.40
1730 1933 7.201767 CCAAGTTCCATGTCTAATTCTTCCATC 60.202 40.741 0.00 0.00 0.00 3.51
1734 1937 6.226052 TCCATGTCTAATTCTTCCATCGATG 58.774 40.000 18.76 18.76 0.00 3.84
1736 1939 6.484643 CCATGTCTAATTCTTCCATCGATGTT 59.515 38.462 23.27 12.42 0.00 2.71
1740 1975 9.443323 TGTCTAATTCTTCCATCGATGTTAAAA 57.557 29.630 23.27 12.59 0.00 1.52
1934 2169 2.797278 CCGCGGCTACTCCTCCAAT 61.797 63.158 14.67 0.00 0.00 3.16
1997 2232 2.019408 CGACGCGTGGATGAACACA 61.019 57.895 20.70 0.00 41.38 3.72
2127 2362 0.734889 CAACCGCAACTGATCCATCC 59.265 55.000 0.00 0.00 0.00 3.51
2128 2363 0.620556 AACCGCAACTGATCCATCCT 59.379 50.000 0.00 0.00 0.00 3.24
2129 2364 0.179000 ACCGCAACTGATCCATCCTC 59.821 55.000 0.00 0.00 0.00 3.71
2130 2365 0.533755 CCGCAACTGATCCATCCTCC 60.534 60.000 0.00 0.00 0.00 4.30
2131 2366 0.533755 CGCAACTGATCCATCCTCCC 60.534 60.000 0.00 0.00 0.00 4.30
2132 2367 0.179006 GCAACTGATCCATCCTCCCC 60.179 60.000 0.00 0.00 0.00 4.81
2133 2368 1.216064 CAACTGATCCATCCTCCCCA 58.784 55.000 0.00 0.00 0.00 4.96
2134 2369 1.779092 CAACTGATCCATCCTCCCCAT 59.221 52.381 0.00 0.00 0.00 4.00
2140 2375 0.837691 TCCATCCTCCCCATGGATCG 60.838 60.000 15.22 0.00 44.17 3.69
2141 2376 1.130054 CCATCCTCCCCATGGATCGT 61.130 60.000 15.22 0.00 43.32 3.73
2142 2377 0.322975 CATCCTCCCCATGGATCGTC 59.677 60.000 15.22 0.00 41.94 4.20
2170 2405 5.772169 CAGTTTCTTCCTTTCATCCTTCCTT 59.228 40.000 0.00 0.00 0.00 3.36
2171 2406 6.007076 AGTTTCTTCCTTTCATCCTTCCTTC 58.993 40.000 0.00 0.00 0.00 3.46
2172 2407 4.576330 TCTTCCTTTCATCCTTCCTTCC 57.424 45.455 0.00 0.00 0.00 3.46
2173 2408 4.179133 TCTTCCTTTCATCCTTCCTTCCT 58.821 43.478 0.00 0.00 0.00 3.36
2174 2409 4.226168 TCTTCCTTTCATCCTTCCTTCCTC 59.774 45.833 0.00 0.00 0.00 3.71
2175 2410 2.501723 TCCTTTCATCCTTCCTTCCTCG 59.498 50.000 0.00 0.00 0.00 4.63
2176 2411 2.237392 CCTTTCATCCTTCCTTCCTCGT 59.763 50.000 0.00 0.00 0.00 4.18
2177 2412 3.526534 CTTTCATCCTTCCTTCCTCGTC 58.473 50.000 0.00 0.00 0.00 4.20
2178 2413 2.231716 TCATCCTTCCTTCCTCGTCA 57.768 50.000 0.00 0.00 0.00 4.35
2179 2414 2.752030 TCATCCTTCCTTCCTCGTCAT 58.248 47.619 0.00 0.00 0.00 3.06
2180 2415 3.107601 TCATCCTTCCTTCCTCGTCATT 58.892 45.455 0.00 0.00 0.00 2.57
2181 2416 3.118629 TCATCCTTCCTTCCTCGTCATTG 60.119 47.826 0.00 0.00 0.00 2.82
2182 2417 2.536066 TCCTTCCTTCCTCGTCATTGA 58.464 47.619 0.00 0.00 0.00 2.57
2183 2418 3.107601 TCCTTCCTTCCTCGTCATTGAT 58.892 45.455 0.00 0.00 0.00 2.57
2184 2419 3.133003 TCCTTCCTTCCTCGTCATTGATC 59.867 47.826 0.00 0.00 0.00 2.92
2185 2420 2.871182 TCCTTCCTCGTCATTGATCG 57.129 50.000 0.00 0.00 0.00 3.69
2186 2421 2.375146 TCCTTCCTCGTCATTGATCGA 58.625 47.619 9.75 9.75 34.88 3.59
2221 2456 2.526077 CATTCGATTCGAGACGGACAA 58.474 47.619 8.98 0.00 37.14 3.18
2233 2468 0.105408 ACGGACAAACGTTACTGCCT 59.895 50.000 0.00 0.00 46.25 4.75
2236 2471 2.801679 CGGACAAACGTTACTGCCTTTA 59.198 45.455 0.00 0.00 0.00 1.85
2238 2473 3.811497 GGACAAACGTTACTGCCTTTAGT 59.189 43.478 0.00 0.00 34.71 2.24
2246 2482 5.995897 ACGTTACTGCCTTTAGTTCATTTCT 59.004 36.000 0.00 0.00 32.19 2.52
2291 2533 6.519353 TTGATTGTTACAGTGAGTGTTACG 57.481 37.500 0.00 0.00 40.86 3.18
2329 2573 4.407365 AGAATTAAGGTGGGTTCTTGTGG 58.593 43.478 0.00 0.00 0.00 4.17
2330 2574 2.668144 TTAAGGTGGGTTCTTGTGGG 57.332 50.000 0.00 0.00 0.00 4.61
2390 2635 7.477144 TGTGATCAATCGGTTATGTATGAAC 57.523 36.000 0.00 0.00 0.00 3.18
2396 2646 6.882140 TCAATCGGTTATGTATGAACAAACCT 59.118 34.615 14.69 2.50 40.65 3.50
2443 2697 9.603921 TTGCATCTCTTTTTCTTTTCTTTTGAT 57.396 25.926 0.00 0.00 0.00 2.57
2483 2737 6.214191 TCTCTCTGAGATATTGTTGTGGAC 57.786 41.667 8.00 0.00 33.35 4.02
2487 2741 6.096141 TCTCTGAGATATTGTTGTGGACTCTC 59.904 42.308 2.58 0.00 0.00 3.20
2491 2746 6.096141 TGAGATATTGTTGTGGACTCTCTCTC 59.904 42.308 0.00 0.00 30.92 3.20
2528 2783 1.290639 GAGCTATCCGCCTGGCTAC 59.709 63.158 17.92 0.00 40.39 3.58
2531 2786 0.035458 GCTATCCGCCTGGCTACATT 59.965 55.000 17.92 0.00 34.14 2.71
2546 2801 5.008613 TGGCTACATTCTTGTGAGTTTGAAC 59.991 40.000 0.00 0.00 36.53 3.18
2575 2830 0.657840 GTGACGCAAGCAGACAAGTT 59.342 50.000 0.00 0.00 45.62 2.66
2619 2874 1.702886 CTGGCTTCAGTCGTACACAG 58.297 55.000 0.00 0.00 33.96 3.66
2622 2877 1.269621 GGCTTCAGTCGTACACAGTGT 60.270 52.381 11.87 11.87 0.00 3.55
2629 2884 4.157817 GTACACAGTGTACGGCCG 57.842 61.111 26.86 26.86 42.99 6.13
2658 2927 1.527034 TGCTCTGCCATGTTCAAGAC 58.473 50.000 0.00 0.00 0.00 3.01
2662 2931 0.321564 CTGCCATGTTCAAGACGGGA 60.322 55.000 0.00 0.00 0.00 5.14
2663 2932 0.321564 TGCCATGTTCAAGACGGGAG 60.322 55.000 0.00 0.00 0.00 4.30
2674 2943 3.140506 ACGGGAGTTGGCACGTTA 58.859 55.556 0.00 0.00 43.33 3.18
2675 2944 1.005394 ACGGGAGTTGGCACGTTAG 60.005 57.895 0.00 0.00 43.33 2.34
2676 2945 1.005394 CGGGAGTTGGCACGTTAGT 60.005 57.895 0.00 0.00 0.00 2.24
2677 2946 0.601841 CGGGAGTTGGCACGTTAGTT 60.602 55.000 0.00 0.00 0.00 2.24
2678 2947 0.872388 GGGAGTTGGCACGTTAGTTG 59.128 55.000 0.00 0.00 0.00 3.16
2679 2948 0.872388 GGAGTTGGCACGTTAGTTGG 59.128 55.000 0.00 0.00 0.00 3.77
2680 2949 1.589803 GAGTTGGCACGTTAGTTGGT 58.410 50.000 0.00 0.00 0.00 3.67
2682 2951 1.134340 AGTTGGCACGTTAGTTGGTGA 60.134 47.619 0.00 0.00 36.25 4.02
2683 2952 1.671845 GTTGGCACGTTAGTTGGTGAA 59.328 47.619 0.00 0.00 36.25 3.18
2684 2953 2.264005 TGGCACGTTAGTTGGTGAAT 57.736 45.000 0.00 0.00 36.25 2.57
2686 2955 1.199097 GGCACGTTAGTTGGTGAATGG 59.801 52.381 0.00 0.00 36.25 3.16
2688 2957 2.350388 GCACGTTAGTTGGTGAATGGTG 60.350 50.000 0.00 0.00 36.25 4.17
2689 2958 3.135225 CACGTTAGTTGGTGAATGGTGA 58.865 45.455 0.00 0.00 36.25 4.02
2690 2959 3.059188 CACGTTAGTTGGTGAATGGTGAC 60.059 47.826 0.00 0.00 36.25 3.67
2691 2960 3.181458 ACGTTAGTTGGTGAATGGTGACT 60.181 43.478 0.00 0.00 0.00 3.41
2692 2961 4.039488 ACGTTAGTTGGTGAATGGTGACTA 59.961 41.667 0.00 0.00 0.00 2.59
2693 2962 5.175859 CGTTAGTTGGTGAATGGTGACTAT 58.824 41.667 0.00 0.00 0.00 2.12
2694 2963 5.063438 CGTTAGTTGGTGAATGGTGACTATG 59.937 44.000 0.00 0.00 0.00 2.23
2699 2968 4.979335 TGGTGAATGGTGACTATGTTCAA 58.021 39.130 0.00 0.00 31.38 2.69
2741 3011 4.214310 TCTTGACCTGGCTGAATTTGAAA 58.786 39.130 0.00 0.00 0.00 2.69
2779 3053 3.598264 TGAAAGAGAGAAAAGGAGGGGA 58.402 45.455 0.00 0.00 0.00 4.81
2928 3408 4.047627 AGGCAAAATTTGTAGGGCTAGT 57.952 40.909 7.60 0.00 32.13 2.57
2930 3410 4.838423 AGGCAAAATTTGTAGGGCTAGTTT 59.162 37.500 7.60 0.00 32.13 2.66
2961 3441 9.581289 TTTAGGATTGGTTCTCTACAAAATTCA 57.419 29.630 0.00 0.00 0.00 2.57
2962 3442 9.753674 TTAGGATTGGTTCTCTACAAAATTCAT 57.246 29.630 0.00 0.00 0.00 2.57
2963 3443 8.059798 AGGATTGGTTCTCTACAAAATTCATG 57.940 34.615 0.00 0.00 0.00 3.07
2985 3865 8.668353 TCATGTAGAACTTATGATTTGAGTTGC 58.332 33.333 0.00 0.00 34.02 4.17
2987 3867 5.904362 AGAACTTATGATTTGAGTTGCCC 57.096 39.130 0.00 0.00 34.02 5.36
2995 3875 3.571828 TGATTTGAGTTGCCCGATGAAAA 59.428 39.130 0.00 0.00 0.00 2.29
2996 3876 3.363341 TTTGAGTTGCCCGATGAAAAC 57.637 42.857 0.00 0.00 0.00 2.43
3000 3880 3.320541 TGAGTTGCCCGATGAAAACAATT 59.679 39.130 0.00 0.00 0.00 2.32
3003 3883 4.021192 AGTTGCCCGATGAAAACAATTCAT 60.021 37.500 3.48 3.48 41.43 2.57
3004 3884 4.533919 TGCCCGATGAAAACAATTCATT 57.466 36.364 5.27 0.00 39.08 2.57
3005 3885 4.493547 TGCCCGATGAAAACAATTCATTC 58.506 39.130 5.27 0.00 39.08 2.67
3006 3886 3.865164 GCCCGATGAAAACAATTCATTCC 59.135 43.478 5.27 0.00 39.08 3.01
3007 3887 4.381932 GCCCGATGAAAACAATTCATTCCT 60.382 41.667 5.27 0.00 39.08 3.36
3008 3888 5.163561 GCCCGATGAAAACAATTCATTCCTA 60.164 40.000 5.27 0.00 39.08 2.94
3009 3889 6.461509 GCCCGATGAAAACAATTCATTCCTAT 60.462 38.462 5.27 0.00 39.08 2.57
3010 3890 7.491682 CCCGATGAAAACAATTCATTCCTATT 58.508 34.615 5.27 0.00 39.08 1.73
3011 3891 7.649306 CCCGATGAAAACAATTCATTCCTATTC 59.351 37.037 5.27 0.00 39.08 1.75
3012 3892 7.649306 CCGATGAAAACAATTCATTCCTATTCC 59.351 37.037 5.27 0.00 39.08 3.01
3013 3893 8.190122 CGATGAAAACAATTCATTCCTATTCCA 58.810 33.333 5.27 0.00 39.08 3.53
3016 3896 9.033711 TGAAAACAATTCATTCCTATTCCATCA 57.966 29.630 0.00 0.00 0.00 3.07
3017 3897 9.874205 GAAAACAATTCATTCCTATTCCATCAA 57.126 29.630 0.00 0.00 0.00 2.57
3026 3906 9.524496 TCATTCCTATTCCATCAATTTCATAGG 57.476 33.333 0.00 0.00 36.20 2.57
3027 3907 7.765695 TTCCTATTCCATCAATTTCATAGGC 57.234 36.000 0.00 0.00 35.25 3.93
3028 3908 6.851318 TCCTATTCCATCAATTTCATAGGCA 58.149 36.000 0.00 0.00 35.25 4.75
3029 3909 7.296856 TCCTATTCCATCAATTTCATAGGCAA 58.703 34.615 0.00 0.00 35.25 4.52
3030 3910 7.784073 TCCTATTCCATCAATTTCATAGGCAAA 59.216 33.333 0.00 0.00 35.25 3.68
3031 3911 8.591072 CCTATTCCATCAATTTCATAGGCAAAT 58.409 33.333 0.00 0.00 29.72 2.32
3032 3912 9.635520 CTATTCCATCAATTTCATAGGCAAATC 57.364 33.333 0.00 0.00 0.00 2.17
3033 3913 6.075762 TCCATCAATTTCATAGGCAAATCG 57.924 37.500 0.00 0.00 0.00 3.34
3034 3914 5.827267 TCCATCAATTTCATAGGCAAATCGA 59.173 36.000 0.00 0.00 0.00 3.59
3035 3915 5.916883 CCATCAATTTCATAGGCAAATCGAC 59.083 40.000 0.00 0.00 0.00 4.20
3036 3916 6.459985 CCATCAATTTCATAGGCAAATCGACA 60.460 38.462 0.00 0.00 0.00 4.35
3037 3917 6.698008 TCAATTTCATAGGCAAATCGACAT 57.302 33.333 0.00 0.00 0.00 3.06
3038 3918 6.497437 TCAATTTCATAGGCAAATCGACATG 58.503 36.000 0.00 0.00 0.00 3.21
3039 3919 3.969117 TTCATAGGCAAATCGACATGC 57.031 42.857 14.23 14.23 41.82 4.06
3040 3920 3.198409 TCATAGGCAAATCGACATGCT 57.802 42.857 19.94 11.02 42.20 3.79
3041 3921 3.133691 TCATAGGCAAATCGACATGCTC 58.866 45.455 19.94 12.21 42.20 4.26
3042 3922 1.953559 TAGGCAAATCGACATGCTCC 58.046 50.000 19.94 7.92 42.20 4.70
3043 3923 0.749454 AGGCAAATCGACATGCTCCC 60.749 55.000 19.94 7.34 42.20 4.30
3044 3924 1.728490 GGCAAATCGACATGCTCCCC 61.728 60.000 19.94 4.02 42.20 4.81
3045 3925 1.728490 GCAAATCGACATGCTCCCCC 61.728 60.000 15.07 0.00 39.46 5.40
3072 3952 4.350368 CCCCCAAAAAGTATTGCTTTGT 57.650 40.909 0.24 0.00 45.91 2.83
3073 3953 5.476091 CCCCCAAAAAGTATTGCTTTGTA 57.524 39.130 0.24 0.00 45.91 2.41
3074 3954 6.048732 CCCCCAAAAAGTATTGCTTTGTAT 57.951 37.500 0.24 0.00 45.91 2.29
3075 3955 6.472016 CCCCCAAAAAGTATTGCTTTGTATT 58.528 36.000 0.24 0.00 45.91 1.89
3076 3956 6.939730 CCCCCAAAAAGTATTGCTTTGTATTT 59.060 34.615 0.24 0.00 45.91 1.40
3077 3957 7.446931 CCCCCAAAAAGTATTGCTTTGTATTTT 59.553 33.333 0.24 0.00 45.91 1.82
3078 3958 8.845227 CCCCAAAAAGTATTGCTTTGTATTTTT 58.155 29.630 0.24 0.00 45.91 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
309 335 1.077787 TGCCGGCCTTCAACATAGG 60.078 57.895 26.77 0.00 35.80 2.57
311 337 1.377987 GGTGCCGGCCTTCAACATA 60.378 57.895 26.77 0.00 0.00 2.29
344 382 2.683933 GAGGTGGAGGAGGCGGAA 60.684 66.667 0.00 0.00 0.00 4.30
390 462 1.051556 GGAGTAGGAGCTGGGGGAAG 61.052 65.000 0.00 0.00 0.00 3.46
392 464 1.941820 AGGAGTAGGAGCTGGGGGA 60.942 63.158 0.00 0.00 0.00 4.81
396 468 0.469144 GGAGGAGGAGTAGGAGCTGG 60.469 65.000 0.00 0.00 0.00 4.85
398 470 1.534697 CGGAGGAGGAGTAGGAGCT 59.465 63.158 0.00 0.00 0.00 4.09
399 471 4.167597 CGGAGGAGGAGTAGGAGC 57.832 66.667 0.00 0.00 0.00 4.70
556 690 2.601666 ACGCTCTGGCACTCCTCA 60.602 61.111 0.00 0.00 38.60 3.86
558 692 3.699894 CCACGCTCTGGCACTCCT 61.700 66.667 0.00 0.00 38.60 3.69
684 842 1.535462 CTCGTCGCCCAAGACAAAATT 59.465 47.619 0.00 0.00 40.98 1.82
748 908 3.792053 CTCATACGTCCAGGCGGGC 62.792 68.421 0.00 0.00 36.21 6.13
750 910 1.065928 GTCTCATACGTCCAGGCGG 59.934 63.158 0.00 0.00 35.98 6.13
752 912 4.711980 CGTCTCATACGTCCAGGC 57.288 61.111 0.00 0.00 46.72 4.85
757 917 6.791922 GAGCATCAAATCCGTCTCATACGTC 61.792 48.000 0.00 0.00 42.47 4.34
758 918 5.029190 GAGCATCAAATCCGTCTCATACGT 61.029 45.833 0.00 0.00 42.47 3.57
759 919 3.426859 GAGCATCAAATCCGTCTCATACG 59.573 47.826 0.00 0.00 43.23 3.06
760 920 4.626042 AGAGCATCAAATCCGTCTCATAC 58.374 43.478 0.00 0.00 37.82 2.39
761 921 4.944619 AGAGCATCAAATCCGTCTCATA 57.055 40.909 0.00 0.00 37.82 2.15
762 922 3.834489 AGAGCATCAAATCCGTCTCAT 57.166 42.857 0.00 0.00 37.82 2.90
763 923 3.616956 AAGAGCATCAAATCCGTCTCA 57.383 42.857 0.00 0.00 37.82 3.27
764 924 4.688021 ACTAAGAGCATCAAATCCGTCTC 58.312 43.478 0.00 0.00 37.82 3.36
765 925 4.744795 ACTAAGAGCATCAAATCCGTCT 57.255 40.909 0.00 0.00 37.82 4.18
766 926 4.745620 GGTACTAAGAGCATCAAATCCGTC 59.254 45.833 0.00 0.00 37.82 4.79
767 927 4.694339 GGTACTAAGAGCATCAAATCCGT 58.306 43.478 0.00 0.00 37.82 4.69
768 928 3.736252 CGGTACTAAGAGCATCAAATCCG 59.264 47.826 0.00 0.00 37.82 4.18
769 929 4.945246 TCGGTACTAAGAGCATCAAATCC 58.055 43.478 0.00 0.00 37.82 3.01
770 930 6.903883 TTTCGGTACTAAGAGCATCAAATC 57.096 37.500 0.00 0.00 37.82 2.17
771 931 7.865706 ATTTTCGGTACTAAGAGCATCAAAT 57.134 32.000 0.00 0.00 37.82 2.32
772 932 7.389330 TCAATTTTCGGTACTAAGAGCATCAAA 59.611 33.333 0.00 0.00 37.82 2.69
773 933 6.876789 TCAATTTTCGGTACTAAGAGCATCAA 59.123 34.615 0.00 0.00 37.82 2.57
774 934 6.403049 TCAATTTTCGGTACTAAGAGCATCA 58.597 36.000 0.00 0.00 37.82 3.07
775 935 6.903883 TCAATTTTCGGTACTAAGAGCATC 57.096 37.500 0.00 0.00 0.00 3.91
776 936 7.865706 ATTCAATTTTCGGTACTAAGAGCAT 57.134 32.000 0.00 0.00 0.00 3.79
777 937 8.958119 ATATTCAATTTTCGGTACTAAGAGCA 57.042 30.769 0.00 0.00 0.00 4.26
778 938 8.496751 GGATATTCAATTTTCGGTACTAAGAGC 58.503 37.037 0.00 0.00 0.00 4.09
779 939 9.542462 TGGATATTCAATTTTCGGTACTAAGAG 57.458 33.333 0.00 0.00 0.00 2.85
780 940 9.893634 TTGGATATTCAATTTTCGGTACTAAGA 57.106 29.630 0.00 0.00 0.00 2.10
782 942 9.893634 TCTTGGATATTCAATTTTCGGTACTAA 57.106 29.630 0.00 0.00 0.00 2.24
783 943 9.321562 GTCTTGGATATTCAATTTTCGGTACTA 57.678 33.333 0.00 0.00 0.00 1.82
784 944 7.827236 TGTCTTGGATATTCAATTTTCGGTACT 59.173 33.333 0.00 0.00 0.00 2.73
785 945 7.981142 TGTCTTGGATATTCAATTTTCGGTAC 58.019 34.615 0.00 0.00 0.00 3.34
786 946 8.746052 ATGTCTTGGATATTCAATTTTCGGTA 57.254 30.769 0.00 0.00 0.00 4.02
787 947 7.467267 CGATGTCTTGGATATTCAATTTTCGGT 60.467 37.037 0.00 0.00 0.00 4.69
788 948 6.852853 CGATGTCTTGGATATTCAATTTTCGG 59.147 38.462 0.00 0.00 0.00 4.30
831 1003 0.038159 GCTCTGCTGGTGTAGTTCGT 60.038 55.000 0.00 0.00 0.00 3.85
833 1005 1.273606 TCTGCTCTGCTGGTGTAGTTC 59.726 52.381 0.00 0.00 0.00 3.01
843 1015 1.415659 GGTATGGTGATCTGCTCTGCT 59.584 52.381 0.00 0.00 0.00 4.24
854 1026 2.305607 GCAGGGGTGGGTATGGTGA 61.306 63.158 0.00 0.00 0.00 4.02
901 1074 1.212751 GCAAATGGTTCTGTCGGGC 59.787 57.895 0.00 0.00 0.00 6.13
938 1111 0.800683 GTGTGCACGCTACGCTATGA 60.801 55.000 22.93 0.00 0.00 2.15
1014 1187 4.168291 TGCTGTGCGGTGGTGTGA 62.168 61.111 0.00 0.00 0.00 3.58
1018 1191 4.626081 GGAGTGCTGTGCGGTGGT 62.626 66.667 0.00 0.00 0.00 4.16
1019 1192 4.624364 TGGAGTGCTGTGCGGTGG 62.624 66.667 0.00 0.00 0.00 4.61
1380 1559 6.915300 GCTCCTCTGAAAAGAAAAGAAAAGAC 59.085 38.462 0.00 0.00 0.00 3.01
1419 1608 0.321919 CCACAGTCAGACCACCATGG 60.322 60.000 11.19 11.19 45.02 3.66
1420 1609 0.397941 ACCACAGTCAGACCACCATG 59.602 55.000 0.00 0.00 0.00 3.66
1421 1610 1.140312 AACCACAGTCAGACCACCAT 58.860 50.000 0.00 0.00 0.00 3.55
1422 1611 0.180171 CAACCACAGTCAGACCACCA 59.820 55.000 0.00 0.00 0.00 4.17
1423 1612 0.535102 CCAACCACAGTCAGACCACC 60.535 60.000 0.00 0.00 0.00 4.61
1424 1613 0.180406 ACCAACCACAGTCAGACCAC 59.820 55.000 0.00 0.00 0.00 4.16
1436 1627 1.740585 CAAACACGAGTCAACCAACCA 59.259 47.619 0.00 0.00 0.00 3.67
1437 1628 1.741145 ACAAACACGAGTCAACCAACC 59.259 47.619 0.00 0.00 0.00 3.77
1438 1629 4.806342 ATACAAACACGAGTCAACCAAC 57.194 40.909 0.00 0.00 0.00 3.77
1439 1630 5.358090 TGTATACAAACACGAGTCAACCAA 58.642 37.500 2.20 0.00 0.00 3.67
1454 1645 5.038683 CGGACGTCAGCTATTTGTATACAA 58.961 41.667 18.91 14.35 0.00 2.41
1460 1651 0.108329 CCCGGACGTCAGCTATTTGT 60.108 55.000 18.91 0.00 0.00 2.83
1672 1869 1.238439 GTGGGGAATGGATATGTGCG 58.762 55.000 0.00 0.00 0.00 5.34
1673 1870 1.956477 GTGTGGGGAATGGATATGTGC 59.044 52.381 0.00 0.00 0.00 4.57
1674 1871 2.091939 TGGTGTGGGGAATGGATATGTG 60.092 50.000 0.00 0.00 0.00 3.21
1675 1872 2.213310 TGGTGTGGGGAATGGATATGT 58.787 47.619 0.00 0.00 0.00 2.29
1676 1873 3.074985 AGATGGTGTGGGGAATGGATATG 59.925 47.826 0.00 0.00 0.00 1.78
1677 1874 3.339470 AGATGGTGTGGGGAATGGATAT 58.661 45.455 0.00 0.00 0.00 1.63
1678 1875 2.787956 AGATGGTGTGGGGAATGGATA 58.212 47.619 0.00 0.00 0.00 2.59
1679 1876 1.612035 AGATGGTGTGGGGAATGGAT 58.388 50.000 0.00 0.00 0.00 3.41
1680 1877 1.005805 CAAGATGGTGTGGGGAATGGA 59.994 52.381 0.00 0.00 0.00 3.41
1681 1878 1.477553 CAAGATGGTGTGGGGAATGG 58.522 55.000 0.00 0.00 0.00 3.16
1682 1879 0.819582 GCAAGATGGTGTGGGGAATG 59.180 55.000 0.00 0.00 0.00 2.67
1683 1880 0.409092 TGCAAGATGGTGTGGGGAAT 59.591 50.000 0.00 0.00 0.00 3.01
1684 1881 0.409092 ATGCAAGATGGTGTGGGGAA 59.591 50.000 0.00 0.00 0.00 3.97
1685 1882 0.034186 GATGCAAGATGGTGTGGGGA 60.034 55.000 0.00 0.00 0.00 4.81
1686 1883 1.039233 GGATGCAAGATGGTGTGGGG 61.039 60.000 0.00 0.00 0.00 4.96
1687 1884 0.323633 TGGATGCAAGATGGTGTGGG 60.324 55.000 0.00 0.00 0.00 4.61
1688 1885 1.475280 CTTGGATGCAAGATGGTGTGG 59.525 52.381 21.36 0.00 34.26 4.17
1689 1886 2.165167 ACTTGGATGCAAGATGGTGTG 58.835 47.619 30.84 5.55 36.16 3.82
1690 1887 2.592102 ACTTGGATGCAAGATGGTGT 57.408 45.000 30.84 7.67 36.16 4.16
1691 1888 2.165030 GGAACTTGGATGCAAGATGGTG 59.835 50.000 30.84 7.01 36.16 4.17
1692 1889 2.225091 TGGAACTTGGATGCAAGATGGT 60.225 45.455 30.84 13.96 36.16 3.55
1722 1925 8.737168 AATCTGATTTTAACATCGATGGAAGA 57.263 30.769 28.09 16.86 0.00 2.87
1724 1927 7.555914 TGGAATCTGATTTTAACATCGATGGAA 59.444 33.333 28.09 18.58 0.00 3.53
1730 1933 6.458751 CCACCTGGAATCTGATTTTAACATCG 60.459 42.308 0.00 0.00 37.39 3.84
1997 2232 4.443266 GCCTTGCCGTCGAGCTCT 62.443 66.667 12.85 0.00 0.00 4.09
2140 2375 5.124617 GGATGAAAGGAAGAAACTGATGGAC 59.875 44.000 0.00 0.00 0.00 4.02
2141 2376 5.014544 AGGATGAAAGGAAGAAACTGATGGA 59.985 40.000 0.00 0.00 0.00 3.41
2142 2377 5.259632 AGGATGAAAGGAAGAAACTGATGG 58.740 41.667 0.00 0.00 0.00 3.51
2148 2383 5.184096 GGAAGGAAGGATGAAAGGAAGAAAC 59.816 44.000 0.00 0.00 0.00 2.78
2170 2405 3.381590 AGAACATCGATCAATGACGAGGA 59.618 43.478 20.00 2.85 41.63 3.71
2171 2406 3.711086 AGAACATCGATCAATGACGAGG 58.289 45.455 14.53 14.53 43.97 4.63
2172 2407 4.564372 ACAAGAACATCGATCAATGACGAG 59.436 41.667 0.00 7.88 41.63 4.18
2173 2408 4.494484 ACAAGAACATCGATCAATGACGA 58.506 39.130 0.00 9.52 42.49 4.20
2174 2409 4.847365 ACAAGAACATCGATCAATGACG 57.153 40.909 0.00 0.00 0.00 4.35
2175 2410 6.373779 ACAAACAAGAACATCGATCAATGAC 58.626 36.000 0.00 0.00 0.00 3.06
2176 2411 6.348458 GGACAAACAAGAACATCGATCAATGA 60.348 38.462 0.00 0.00 0.00 2.57
2177 2412 5.796935 GGACAAACAAGAACATCGATCAATG 59.203 40.000 0.00 0.00 0.00 2.82
2178 2413 5.473162 TGGACAAACAAGAACATCGATCAAT 59.527 36.000 0.00 0.00 0.00 2.57
2179 2414 4.819088 TGGACAAACAAGAACATCGATCAA 59.181 37.500 0.00 0.00 0.00 2.57
2180 2415 4.384940 TGGACAAACAAGAACATCGATCA 58.615 39.130 0.00 0.00 0.00 2.92
2181 2416 5.551760 ATGGACAAACAAGAACATCGATC 57.448 39.130 0.00 0.00 0.00 3.69
2182 2417 5.390885 CGAATGGACAAACAAGAACATCGAT 60.391 40.000 0.00 0.00 0.00 3.59
2183 2418 4.084066 CGAATGGACAAACAAGAACATCGA 60.084 41.667 0.00 0.00 0.00 3.59
2184 2419 4.084066 TCGAATGGACAAACAAGAACATCG 60.084 41.667 0.00 0.00 0.00 3.84
2185 2420 5.356882 TCGAATGGACAAACAAGAACATC 57.643 39.130 0.00 0.00 0.00 3.06
2186 2421 5.964958 ATCGAATGGACAAACAAGAACAT 57.035 34.783 0.00 0.00 0.00 2.71
2221 2456 6.485648 AGAAATGAACTAAAGGCAGTAACGTT 59.514 34.615 5.88 5.88 0.00 3.99
2236 2471 7.448161 TGGTGAAATGTACATGAGAAATGAACT 59.552 33.333 9.63 0.00 0.00 3.01
2238 2473 7.757941 TGGTGAAATGTACATGAGAAATGAA 57.242 32.000 9.63 0.00 0.00 2.57
2246 2482 6.662663 TCAAATCCATGGTGAAATGTACATGA 59.337 34.615 12.58 0.00 42.39 3.07
2291 2533 8.312564 ACCTTAATTCTCTCTGTAACAGTAACC 58.687 37.037 0.00 0.00 32.61 2.85
2409 2663 8.902040 AAAGAAAAAGAGATGCAACGATTATC 57.098 30.769 0.00 0.00 0.00 1.75
2416 2670 8.872845 TCAAAAGAAAAGAAAAAGAGATGCAAC 58.127 29.630 0.00 0.00 0.00 4.17
2478 2732 3.509575 ACATGTTCAGAGAGAGAGTCCAC 59.490 47.826 0.00 0.00 0.00 4.02
2483 2737 4.433186 ACGAACATGTTCAGAGAGAGAG 57.567 45.455 32.06 17.76 39.46 3.20
2487 2741 4.376413 CCGAAAACGAACATGTTCAGAGAG 60.376 45.833 32.06 20.21 39.46 3.20
2491 2746 3.799035 CTCCGAAAACGAACATGTTCAG 58.201 45.455 32.06 26.09 39.46 3.02
2520 2775 3.340814 ACTCACAAGAATGTAGCCAGG 57.659 47.619 0.00 0.00 37.82 4.45
2528 2783 5.967674 GTGACAGTTCAAACTCACAAGAATG 59.032 40.000 9.25 0.00 37.08 2.67
2531 2786 3.938963 GGTGACAGTTCAAACTCACAAGA 59.061 43.478 13.82 0.00 36.42 3.02
2619 2874 2.014335 AAGTAAATCCGGCCGTACAC 57.986 50.000 26.12 13.88 0.00 2.90
2622 2877 1.065998 AGCAAAGTAAATCCGGCCGTA 60.066 47.619 26.12 9.32 0.00 4.02
2629 2884 3.445096 ACATGGCAGAGCAAAGTAAATCC 59.555 43.478 0.00 0.00 0.00 3.01
2658 2927 0.601841 AACTAACGTGCCAACTCCCG 60.602 55.000 0.00 0.00 0.00 5.14
2662 2931 1.134340 TCACCAACTAACGTGCCAACT 60.134 47.619 0.00 0.00 0.00 3.16
2663 2932 1.301423 TCACCAACTAACGTGCCAAC 58.699 50.000 0.00 0.00 0.00 3.77
2664 2933 2.039818 TTCACCAACTAACGTGCCAA 57.960 45.000 0.00 0.00 0.00 4.52
2668 2937 3.059188 GTCACCATTCACCAACTAACGTG 60.059 47.826 0.00 0.00 0.00 4.49
2669 2938 3.135994 GTCACCATTCACCAACTAACGT 58.864 45.455 0.00 0.00 0.00 3.99
2670 2939 3.399330 AGTCACCATTCACCAACTAACG 58.601 45.455 0.00 0.00 0.00 3.18
2671 2940 5.938125 ACATAGTCACCATTCACCAACTAAC 59.062 40.000 0.00 0.00 0.00 2.34
2672 2941 6.121776 ACATAGTCACCATTCACCAACTAA 57.878 37.500 0.00 0.00 0.00 2.24
2673 2942 5.755409 ACATAGTCACCATTCACCAACTA 57.245 39.130 0.00 0.00 0.00 2.24
2674 2943 4.640771 ACATAGTCACCATTCACCAACT 57.359 40.909 0.00 0.00 0.00 3.16
2675 2944 4.759693 TGAACATAGTCACCATTCACCAAC 59.240 41.667 0.00 0.00 0.00 3.77
2676 2945 4.979335 TGAACATAGTCACCATTCACCAA 58.021 39.130 0.00 0.00 0.00 3.67
2677 2946 4.632327 TGAACATAGTCACCATTCACCA 57.368 40.909 0.00 0.00 0.00 4.17
2678 2947 5.003804 ACTTGAACATAGTCACCATTCACC 58.996 41.667 0.00 0.00 0.00 4.02
2679 2948 5.700832 TGACTTGAACATAGTCACCATTCAC 59.299 40.000 0.00 0.00 45.15 3.18
2680 2949 5.863965 TGACTTGAACATAGTCACCATTCA 58.136 37.500 0.00 0.00 45.15 2.57
2682 2951 5.869579 ACTGACTTGAACATAGTCACCATT 58.130 37.500 0.00 0.00 45.15 3.16
2683 2952 5.489792 ACTGACTTGAACATAGTCACCAT 57.510 39.130 0.00 0.00 45.15 3.55
2684 2953 4.955811 ACTGACTTGAACATAGTCACCA 57.044 40.909 0.00 0.00 45.15 4.17
2686 2955 8.230486 CCAATTTACTGACTTGAACATAGTCAC 58.770 37.037 0.00 0.00 45.15 3.67
2688 2957 8.547967 TCCAATTTACTGACTTGAACATAGTC 57.452 34.615 0.00 0.00 41.86 2.59
2689 2958 8.157476 ACTCCAATTTACTGACTTGAACATAGT 58.843 33.333 0.00 0.00 0.00 2.12
2690 2959 8.446273 CACTCCAATTTACTGACTTGAACATAG 58.554 37.037 0.00 0.00 0.00 2.23
2691 2960 7.094805 GCACTCCAATTTACTGACTTGAACATA 60.095 37.037 0.00 0.00 0.00 2.29
2692 2961 6.294176 GCACTCCAATTTACTGACTTGAACAT 60.294 38.462 0.00 0.00 0.00 2.71
2693 2962 5.008613 GCACTCCAATTTACTGACTTGAACA 59.991 40.000 0.00 0.00 0.00 3.18
2694 2963 5.008613 TGCACTCCAATTTACTGACTTGAAC 59.991 40.000 0.00 0.00 0.00 3.18
2699 2968 5.171339 AGATGCACTCCAATTTACTGACT 57.829 39.130 0.00 0.00 0.00 3.41
2741 3011 4.759693 TCTTTCATCAGCGGTGTATTTTGT 59.240 37.500 15.22 0.00 0.00 2.83
2779 3053 1.140312 TCTTGCCAGGAACTCAAGGT 58.860 50.000 0.00 0.00 39.72 3.50
2782 3056 2.727123 TGTTCTTGCCAGGAACTCAA 57.273 45.000 18.86 0.00 42.27 3.02
2911 3391 5.775195 AGCTGAAACTAGCCCTACAAATTTT 59.225 36.000 0.00 0.00 44.76 1.82
2923 3403 4.944317 ACCAATCCTAAAGCTGAAACTAGC 59.056 41.667 0.00 0.00 44.01 3.42
2928 3408 5.880901 AGAGAACCAATCCTAAAGCTGAAA 58.119 37.500 0.00 0.00 0.00 2.69
2930 3410 5.483937 TGTAGAGAACCAATCCTAAAGCTGA 59.516 40.000 0.00 0.00 0.00 4.26
2961 3441 7.067494 GGGCAACTCAAATCATAAGTTCTACAT 59.933 37.037 0.00 0.00 31.04 2.29
2962 3442 6.374333 GGGCAACTCAAATCATAAGTTCTACA 59.626 38.462 0.00 0.00 31.04 2.74
2963 3443 6.456988 CGGGCAACTCAAATCATAAGTTCTAC 60.457 42.308 0.00 0.00 31.04 2.59
2968 3848 3.950397 TCGGGCAACTCAAATCATAAGT 58.050 40.909 0.00 0.00 0.00 2.24
2985 3865 5.329035 AGGAATGAATTGTTTTCATCGGG 57.671 39.130 1.62 0.00 38.11 5.14
2987 3867 8.190122 TGGAATAGGAATGAATTGTTTTCATCG 58.810 33.333 1.62 0.00 38.11 3.84
3000 3880 9.524496 CCTATGAAATTGATGGAATAGGAATGA 57.476 33.333 0.00 0.00 39.23 2.57
3003 3883 7.296856 TGCCTATGAAATTGATGGAATAGGAA 58.703 34.615 10.06 0.00 39.23 3.36
3004 3884 6.851318 TGCCTATGAAATTGATGGAATAGGA 58.149 36.000 10.06 0.00 39.23 2.94
3005 3885 7.528996 TTGCCTATGAAATTGATGGAATAGG 57.471 36.000 0.00 0.00 39.67 2.57
3006 3886 9.635520 GATTTGCCTATGAAATTGATGGAATAG 57.364 33.333 0.00 0.00 0.00 1.73
3007 3887 8.298854 CGATTTGCCTATGAAATTGATGGAATA 58.701 33.333 0.00 0.00 0.00 1.75
3008 3888 7.014518 TCGATTTGCCTATGAAATTGATGGAAT 59.985 33.333 0.00 0.00 31.13 3.01
3009 3889 6.320926 TCGATTTGCCTATGAAATTGATGGAA 59.679 34.615 0.00 0.00 31.13 3.53
3010 3890 5.827267 TCGATTTGCCTATGAAATTGATGGA 59.173 36.000 0.00 0.00 31.13 3.41
3011 3891 5.916883 GTCGATTTGCCTATGAAATTGATGG 59.083 40.000 0.00 0.00 36.21 3.51
3012 3892 6.497437 TGTCGATTTGCCTATGAAATTGATG 58.503 36.000 0.00 0.00 36.21 3.07
3013 3893 6.698008 TGTCGATTTGCCTATGAAATTGAT 57.302 33.333 0.00 0.00 36.21 2.57
3014 3894 6.497437 CATGTCGATTTGCCTATGAAATTGA 58.503 36.000 0.00 0.00 32.88 2.57
3015 3895 5.174398 GCATGTCGATTTGCCTATGAAATTG 59.826 40.000 10.49 0.00 32.66 2.32
3016 3896 5.068198 AGCATGTCGATTTGCCTATGAAATT 59.932 36.000 16.19 0.00 39.72 1.82
3017 3897 4.581824 AGCATGTCGATTTGCCTATGAAAT 59.418 37.500 16.19 0.00 39.72 2.17
3018 3898 3.947196 AGCATGTCGATTTGCCTATGAAA 59.053 39.130 16.19 0.00 39.72 2.69
3019 3899 3.544684 AGCATGTCGATTTGCCTATGAA 58.455 40.909 16.19 0.00 39.72 2.57
3020 3900 3.133691 GAGCATGTCGATTTGCCTATGA 58.866 45.455 16.19 0.00 39.72 2.15
3021 3901 2.225019 GGAGCATGTCGATTTGCCTATG 59.775 50.000 16.19 2.90 39.72 2.23
3022 3902 2.498167 GGAGCATGTCGATTTGCCTAT 58.502 47.619 16.19 1.71 39.72 2.57
3023 3903 1.475034 GGGAGCATGTCGATTTGCCTA 60.475 52.381 16.19 0.00 39.72 3.93
3024 3904 0.749454 GGGAGCATGTCGATTTGCCT 60.749 55.000 16.19 6.58 39.72 4.75
3025 3905 1.728490 GGGGAGCATGTCGATTTGCC 61.728 60.000 16.19 9.53 39.72 4.52
3026 3906 1.728490 GGGGGAGCATGTCGATTTGC 61.728 60.000 13.01 13.01 39.17 3.68
3027 3907 2.408333 GGGGGAGCATGTCGATTTG 58.592 57.895 0.00 0.00 0.00 2.32
3028 3908 4.986467 GGGGGAGCATGTCGATTT 57.014 55.556 0.00 0.00 0.00 2.17
3051 3931 4.350368 ACAAAGCAATACTTTTTGGGGG 57.650 40.909 1.88 0.00 46.73 5.40
3052 3932 7.977789 AAATACAAAGCAATACTTTTTGGGG 57.022 32.000 1.88 0.00 46.73 4.96
3077 3957 7.397892 TCAGACCACAAGTGATGTTTAAAAA 57.602 32.000 0.94 0.00 41.46 1.94
3078 3958 7.397892 TTCAGACCACAAGTGATGTTTAAAA 57.602 32.000 0.94 0.00 41.46 1.52
3079 3959 7.581213 ATTCAGACCACAAGTGATGTTTAAA 57.419 32.000 0.94 0.00 41.46 1.52
3080 3960 7.174253 GGTATTCAGACCACAAGTGATGTTTAA 59.826 37.037 0.94 0.00 41.46 1.52
3081 3961 6.653320 GGTATTCAGACCACAAGTGATGTTTA 59.347 38.462 0.94 0.00 41.46 2.01
3082 3962 5.473504 GGTATTCAGACCACAAGTGATGTTT 59.526 40.000 0.94 0.00 41.46 2.83
3083 3963 5.003804 GGTATTCAGACCACAAGTGATGTT 58.996 41.667 0.94 0.00 41.46 2.71
3084 3964 4.579869 GGTATTCAGACCACAAGTGATGT 58.420 43.478 0.94 0.00 45.34 3.06
3147 4030 1.466856 TCTCTGGCCAATCATTGCAC 58.533 50.000 7.01 0.00 0.00 4.57
3187 4070 2.023673 TCAAGTCACTGGCACTTTTGG 58.976 47.619 0.00 0.00 31.40 3.28


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

AutoCloner maintained by Alex Coulton.