Multiple sequence alignment - TraesCS2B01G468100

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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 TraesCS2B01G468100 chr2B 100.000 8143 0 0 1 8143 664125951 664134093 0.000000e+00 15038.0
1 TraesCS2B01G468100 chr2B 84.436 257 20 2 83 319 110537608 110537864 1.370000e-57 235.0
2 TraesCS2B01G468100 chr7D 91.326 4231 252 62 1894 6103 606961863 606965999 0.000000e+00 5674.0
3 TraesCS2B01G468100 chr7D 89.655 928 73 14 6110 7027 606966162 606967076 0.000000e+00 1160.0
4 TraesCS2B01G468100 chr7D 90.421 428 22 10 1016 1443 606961317 606961725 5.560000e-151 545.0
5 TraesCS2B01G468100 chr7B 93.161 3290 189 22 2130 5402 692838527 692835257 0.000000e+00 4796.0
6 TraesCS2B01G468100 chr7B 86.953 1211 94 18 6110 7306 692834429 692833269 0.000000e+00 1303.0
7 TraesCS2B01G468100 chr7B 86.475 695 68 17 5422 6106 692835266 692834588 0.000000e+00 739.0
8 TraesCS2B01G468100 chr7B 93.687 396 21 3 1050 1445 692838950 692838559 2.530000e-164 590.0
9 TraesCS2B01G468100 chr7B 87.624 202 25 0 83 284 476197579 476197780 1.370000e-57 235.0
10 TraesCS2B01G468100 chr7B 84.047 257 21 5 83 319 642501785 642501529 6.360000e-56 230.0
11 TraesCS2B01G468100 chr7B 83.268 257 22 10 83 319 670244736 670244481 4.950000e-52 217.0
12 TraesCS2B01G468100 chr7B 92.857 56 4 0 264 319 717552273 717552218 1.880000e-11 82.4
13 TraesCS2B01G468100 chr2D 94.860 2568 103 17 2864 5414 556927340 556929895 0.000000e+00 3984.0
14 TraesCS2B01G468100 chr2D 92.360 2042 112 15 6110 8143 556930690 556932695 0.000000e+00 2867.0
15 TraesCS2B01G468100 chr2D 94.179 1151 47 9 1008 2157 556925299 556926430 0.000000e+00 1736.0
16 TraesCS2B01G468100 chr2D 87.179 663 64 16 5454 6106 556929904 556930555 0.000000e+00 734.0
17 TraesCS2B01G468100 chr2D 94.919 433 12 3 2156 2584 556926512 556926938 0.000000e+00 669.0
18 TraesCS2B01G468100 chr2D 97.984 248 4 1 2578 2825 556927092 556927338 5.840000e-116 429.0
19 TraesCS2B01G468100 chr2A 94.382 2563 105 17 4639 7179 696852537 696855082 0.000000e+00 3899.0
20 TraesCS2B01G468100 chr2A 93.712 1654 85 12 3026 4667 696850873 696852519 0.000000e+00 2460.0
21 TraesCS2B01G468100 chr2A 94.974 1333 56 7 1703 3030 696849392 696850718 0.000000e+00 2080.0
22 TraesCS2B01G468100 chr2A 88.744 995 70 15 7178 8142 696855115 696856097 0.000000e+00 1179.0
23 TraesCS2B01G468100 chr2A 90.169 651 39 9 1014 1658 696848762 696849393 0.000000e+00 824.0
24 TraesCS2B01G468100 chr1B 88.966 1006 91 10 1 992 673408988 673409987 0.000000e+00 1225.0
25 TraesCS2B01G468100 chr5B 90.336 745 58 6 1 733 527296599 527295857 0.000000e+00 965.0
26 TraesCS2B01G468100 chr4D 88.520 662 50 14 1927 2582 504510716 504511357 0.000000e+00 778.0
27 TraesCS2B01G468100 chr5D 84.459 296 28 12 440 730 46064798 46065080 8.050000e-70 276.0
28 TraesCS2B01G468100 chr5D 83.571 140 19 4 83 221 46064441 46064577 2.390000e-25 128.0
29 TraesCS2B01G468100 chr5D 98.148 54 0 1 265 318 46064527 46064579 8.700000e-15 93.5
30 TraesCS2B01G468100 chr4B 80.233 258 30 11 83 319 192061449 192061192 3.020000e-39 174.0
31 TraesCS2B01G468100 chr6B 86.179 123 14 3 83 204 504157209 504157089 6.630000e-26 130.0
32 TraesCS2B01G468100 chr5A 90.217 92 9 0 83 174 37069365 37069456 3.990000e-23 121.0
33 TraesCS2B01G468100 chr3B 100.000 28 0 0 937 964 819848854 819848827 1.500000e-02 52.8


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 TraesCS2B01G468100 chr2B 664125951 664134093 8142 False 15038.000000 15038 100.000000 1 8143 1 chr2B.!!$F2 8142
1 TraesCS2B01G468100 chr7D 606961317 606967076 5759 False 2459.666667 5674 90.467333 1016 7027 3 chr7D.!!$F1 6011
2 TraesCS2B01G468100 chr7B 692833269 692838950 5681 True 1857.000000 4796 90.069000 1050 7306 4 chr7B.!!$R4 6256
3 TraesCS2B01G468100 chr2D 556925299 556932695 7396 False 1736.500000 3984 93.580167 1008 8143 6 chr2D.!!$F1 7135
4 TraesCS2B01G468100 chr2A 696848762 696856097 7335 False 2088.400000 3899 92.396200 1014 8142 5 chr2A.!!$F1 7128
5 TraesCS2B01G468100 chr1B 673408988 673409987 999 False 1225.000000 1225 88.966000 1 992 1 chr1B.!!$F1 991
6 TraesCS2B01G468100 chr5B 527295857 527296599 742 True 965.000000 965 90.336000 1 733 1 chr5B.!!$R1 732
7 TraesCS2B01G468100 chr4D 504510716 504511357 641 False 778.000000 778 88.520000 1927 2582 1 chr4D.!!$F1 655

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
188 190 0.178301 TTGCTACCAACGACACCACA 59.822 50.000 0.00 0.0 0.00 4.17 F
1081 1099 0.036294 GCAAAACCCTAGCTCCGACT 60.036 55.000 0.00 0.0 0.00 4.18 F
1484 1516 0.105964 TCTGTGGCGCTTAACTGTGT 59.894 50.000 7.64 0.0 0.00 3.72 F
1810 1854 0.755327 AAACAGCAGTGGACCAACCC 60.755 55.000 0.00 0.0 38.00 4.11 F
3234 3707 0.995024 CCTTCATTGGACCAGGGAGT 59.005 55.000 0.00 0.0 0.00 3.85 F
3813 4287 1.070914 TGCAGGTCCGTGTTTATGACA 59.929 47.619 0.00 0.0 35.42 3.58 F
4290 4784 1.461127 GAACTGTTGAGATGCCACGTC 59.539 52.381 0.00 0.0 0.00 4.34 F
5330 5875 0.606401 ACAAGCACGATGGGAAGGTG 60.606 55.000 0.00 0.0 34.85 4.00 F
6125 6841 0.107017 ACAATGGCTCCTTGGATCGG 60.107 55.000 0.00 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1593 1637 0.178953 AATTGCACCTGAGCACCCTT 60.179 50.000 0.00 0.0 45.61 3.95 R
2982 3291 0.696485 TAACTAGCCCCATCCCCCAC 60.696 60.000 0.00 0.0 0.00 4.61 R
3234 3707 0.680618 CCAAACAAGCCAAGATGCCA 59.319 50.000 0.00 0.0 0.00 4.92 R
3315 3788 1.221466 ACCATATGCGCACGATTCCG 61.221 55.000 14.90 0.0 42.50 4.30 R
4316 4810 0.472352 TCCTTAGAACACCCACCGGT 60.472 55.000 0.00 0.0 46.31 5.28 R
5197 5740 0.824595 GTTACACCACCCAACACCCC 60.825 60.000 0.00 0.0 0.00 4.95 R
5628 6179 1.978782 GCAAGTCGCAAATTAGCACAC 59.021 47.619 0.00 0.0 41.79 3.82 R
6731 7462 0.246635 CGGGTCAAGGTGTAGTCCAG 59.753 60.000 0.00 0.0 0.00 3.86 R
7593 8381 0.037790 AGCTTCTGTCGAAGTCCTGC 60.038 55.000 4.26 0.0 46.65 4.85 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
33 35 0.951558 GCGTCAATGGTGAGGTTTGT 59.048 50.000 0.00 0.00 40.93 2.83
113 115 3.558475 ACCGTGGGTGCTACAAGT 58.442 55.556 0.00 0.00 32.98 3.16
116 118 0.534203 CCGTGGGTGCTACAAGTTGT 60.534 55.000 14.05 14.05 0.00 3.32
121 123 0.882927 GGTGCTACAAGTTGTCGGCA 60.883 55.000 23.71 23.71 37.07 5.69
128 130 0.586319 CAAGTTGTCGGCATCGTTGT 59.414 50.000 0.00 0.00 37.69 3.32
163 165 1.003718 AGGAGCTACAACCGGCAAC 60.004 57.895 0.00 0.00 0.00 4.17
188 190 0.178301 TTGCTACCAACGACACCACA 59.822 50.000 0.00 0.00 0.00 4.17
201 203 3.347216 GACACCACAATATGCTGGAACT 58.653 45.455 6.02 0.00 0.00 3.01
218 220 2.065899 ACTGGCCAACTGTTTTGCTA 57.934 45.000 7.01 5.13 0.00 3.49
228 230 1.269448 CTGTTTTGCTACAACCGGCAT 59.731 47.619 0.00 0.00 38.30 4.40
230 232 0.600557 TTTTGCTACAACCGGCATGG 59.399 50.000 0.00 0.00 46.41 3.66
403 405 3.225104 AGAAAAGCTTCAACCAGCATCA 58.775 40.909 0.00 0.00 42.84 3.07
436 438 2.375146 ACCCGTGTGAAAAAGAGCTTT 58.625 42.857 0.00 0.00 0.00 3.51
540 554 1.410517 CTGGCTGACGATGGTATGAGT 59.589 52.381 0.00 0.00 0.00 3.41
607 621 1.661197 GTGTTACGACGGTGGCGAA 60.661 57.895 0.00 0.00 0.00 4.70
622 636 2.235155 TGGCGAATAGTTGCTACAAGGA 59.765 45.455 1.87 0.00 0.00 3.36
634 648 2.158842 GCTACAAGGACAGAGGCATCAT 60.159 50.000 0.00 0.00 0.00 2.45
655 669 0.368907 CGTTCTACAAATGGCGGACG 59.631 55.000 0.00 0.00 0.00 4.79
658 672 2.995258 GTTCTACAAATGGCGGACGTTA 59.005 45.455 0.00 0.00 0.00 3.18
682 696 2.359850 GGGCGACAACTGGATGCA 60.360 61.111 0.00 0.00 0.00 3.96
688 702 4.170062 CAACTGGATGCAGCGGCG 62.170 66.667 14.95 0.51 45.35 6.46
749 763 3.637273 GGTGGGGAAGGCGAGTGT 61.637 66.667 0.00 0.00 0.00 3.55
790 804 3.766691 GTGGGGGCGCTCTCGTAA 61.767 66.667 7.48 0.00 38.14 3.18
797 811 2.526120 GCGCTCTCGTAACCATGGC 61.526 63.158 13.04 0.00 38.14 4.40
798 812 1.153647 CGCTCTCGTAACCATGGCA 60.154 57.895 13.04 0.00 0.00 4.92
800 814 1.668419 GCTCTCGTAACCATGGCAAT 58.332 50.000 13.04 0.41 0.00 3.56
811 825 3.505386 ACCATGGCAATCAAGGTTGTTA 58.495 40.909 13.04 0.00 44.22 2.41
812 826 3.511146 ACCATGGCAATCAAGGTTGTTAG 59.489 43.478 13.04 0.00 44.22 2.34
813 827 3.119029 CCATGGCAATCAAGGTTGTTAGG 60.119 47.826 0.00 0.00 30.07 2.69
814 828 3.517296 TGGCAATCAAGGTTGTTAGGA 57.483 42.857 0.00 0.00 0.00 2.94
815 829 3.838565 TGGCAATCAAGGTTGTTAGGAA 58.161 40.909 0.00 0.00 0.00 3.36
816 830 3.572255 TGGCAATCAAGGTTGTTAGGAAC 59.428 43.478 0.00 0.00 0.00 3.62
817 831 3.365969 GGCAATCAAGGTTGTTAGGAACG 60.366 47.826 0.00 0.00 0.00 3.95
818 832 3.252458 GCAATCAAGGTTGTTAGGAACGT 59.748 43.478 0.00 0.00 0.00 3.99
819 833 4.612939 GCAATCAAGGTTGTTAGGAACGTC 60.613 45.833 0.00 0.00 0.00 4.34
873 889 5.561532 CGTTGAAAGAGTAACAGGTAGACGA 60.562 44.000 0.00 0.00 0.00 4.20
916 932 8.933807 TCAATCGTACGGTATGAATTGTTTTAA 58.066 29.630 16.52 0.00 0.00 1.52
981 997 4.527157 GCGCGTAGTACTCGCCGT 62.527 66.667 23.59 0.00 45.44 5.68
984 1000 3.604130 GCGTAGTACTCGCCGTAAA 57.396 52.632 21.53 0.00 46.61 2.01
1028 1044 3.833070 TCTCGAGCTCTTAAACCCTTCTT 59.167 43.478 12.85 0.00 0.00 2.52
1038 1054 1.076438 AACCCTTCTTCCCCCTTCTG 58.924 55.000 0.00 0.00 0.00 3.02
1081 1099 0.036294 GCAAAACCCTAGCTCCGACT 60.036 55.000 0.00 0.00 0.00 4.18
1363 1387 2.037367 CTGTCCCCCGACTCCAGA 59.963 66.667 0.00 0.00 39.94 3.86
1484 1516 0.105964 TCTGTGGCGCTTAACTGTGT 59.894 50.000 7.64 0.00 0.00 3.72
1493 1525 2.611971 CGCTTAACTGTGTTGCCTCCTA 60.612 50.000 0.00 0.00 0.00 2.94
1537 1581 6.299805 TGCTAATCGCATCCTAATCCTAAT 57.700 37.500 0.00 0.00 45.47 1.73
1577 1621 2.738846 CCTCGCTCCCAATTTCATATCG 59.261 50.000 0.00 0.00 0.00 2.92
1616 1660 2.298729 GGGTGCTCAGGTGCAATTTTTA 59.701 45.455 0.00 0.00 45.12 1.52
1631 1675 4.717233 ATTTTTAGCGCATGTGGAATCA 57.283 36.364 11.47 0.00 0.00 2.57
1638 1682 2.030540 GCGCATGTGGAATCAAGCATAT 60.031 45.455 8.62 0.00 32.57 1.78
1723 1767 6.528537 TTCAAATAGGGTGGTGAATGAATG 57.471 37.500 0.00 0.00 0.00 2.67
1746 1790 0.755686 GCCCGATCACCTTCTCAGAT 59.244 55.000 0.00 0.00 0.00 2.90
1753 1797 5.418524 CCGATCACCTTCTCAGATATCTCAT 59.581 44.000 1.03 0.00 0.00 2.90
1777 1821 3.079960 TCAAGAGATACTAAAGCGCCG 57.920 47.619 2.29 0.00 0.00 6.46
1781 1825 1.066605 GAGATACTAAAGCGCCGTGGA 59.933 52.381 2.29 0.00 0.00 4.02
1810 1854 0.755327 AAACAGCAGTGGACCAACCC 60.755 55.000 0.00 0.00 38.00 4.11
1899 1943 6.204882 ACCTTCTTATGGAAACGCATAATAGC 59.795 38.462 0.00 0.00 33.07 2.97
1907 1951 5.753438 TGGAAACGCATAATAGCTAGTTCTG 59.247 40.000 0.00 0.00 0.00 3.02
1930 1974 6.744112 TGGAAAATTTACCTAGCTTGTGTTG 58.256 36.000 0.00 0.00 0.00 3.33
1940 1984 4.819630 CCTAGCTTGTGTTGTTGGAAGTAA 59.180 41.667 0.00 0.00 0.00 2.24
2114 2158 3.495193 CTGTGCATCAATTCCTGTTTCG 58.505 45.455 0.00 0.00 0.00 3.46
2497 2636 9.110502 GGAGATAAATTACTTAAGTGAACAGGG 57.889 37.037 18.56 0.00 0.00 4.45
2629 2929 7.200455 GCGGTATTTACAGCCTCATTATTTTT 58.800 34.615 1.95 0.00 40.71 1.94
2739 3039 5.101628 GCACATTTTTCAACAGTGACTTCA 58.898 37.500 0.00 0.00 31.90 3.02
2907 3207 4.657013 TGCATGAGTACCATTGGTTTGTA 58.343 39.130 14.78 1.97 37.09 2.41
2914 3214 6.266558 TGAGTACCATTGGTTTGTAATTGCTT 59.733 34.615 14.78 0.00 37.09 3.91
2928 3228 5.359576 TGTAATTGCTTGACACTGGAAAAGT 59.640 36.000 0.00 0.00 40.93 2.66
2948 3256 4.388485 AGTTGGGGTTTGAAATTGATTGC 58.612 39.130 0.00 0.00 0.00 3.56
2949 3257 4.133078 GTTGGGGTTTGAAATTGATTGCA 58.867 39.130 0.00 0.00 0.00 4.08
2981 3290 9.991906 CATAAAATAAATGATCTTCATGGCCTT 57.008 29.630 3.32 0.00 37.15 4.35
2982 3291 9.991906 ATAAAATAAATGATCTTCATGGCCTTG 57.008 29.630 12.41 12.41 37.15 3.61
3063 3533 3.664107 TGGCTAGCATTCCGATATTCAC 58.336 45.455 18.24 0.00 0.00 3.18
3109 3579 2.923121 TGCATATTTCTGTCCTGAGCC 58.077 47.619 0.00 0.00 0.00 4.70
3168 3641 3.104512 TGTGTGGGATCTTCGGAAGTAT 58.895 45.455 16.78 9.45 0.00 2.12
3234 3707 0.995024 CCTTCATTGGACCAGGGAGT 59.005 55.000 0.00 0.00 0.00 3.85
3315 3788 1.219646 TTCTTACGGTTGGTGAACGC 58.780 50.000 0.00 0.00 32.28 4.84
3383 3856 8.397906 TGCATATACAGTTCTTAAATGCTTCAC 58.602 33.333 0.00 0.00 39.13 3.18
3445 3918 2.736579 ATTCCACAGCGCTGTCTGCA 62.737 55.000 38.87 23.52 42.83 4.41
3513 3986 3.388350 AGGAATCTAGAAGGGGCTTTACG 59.612 47.826 0.00 0.00 0.00 3.18
3521 3994 2.098618 AGGGGCTTTACGGCTACTAT 57.901 50.000 0.00 0.00 38.46 2.12
3555 4028 7.501559 CCAGATGATCAAGGAATTCTATGTGTT 59.498 37.037 0.00 0.00 0.00 3.32
3558 4031 8.682936 ATGATCAAGGAATTCTATGTGTTACC 57.317 34.615 0.00 0.00 0.00 2.85
3672 4145 7.121974 TGACGAGATTCTTGATTTGAAGTTC 57.878 36.000 7.95 0.00 0.00 3.01
3702 4175 5.649831 GGAAGAGGAACAATATCTTGCTGTT 59.350 40.000 0.00 0.00 38.10 3.16
3708 4181 2.493278 ACAATATCTTGCTGTTGCCACC 59.507 45.455 0.00 0.00 38.71 4.61
3788 4262 4.901250 ACCAATTTCTCACACCATTTCCTT 59.099 37.500 0.00 0.00 0.00 3.36
3813 4287 1.070914 TGCAGGTCCGTGTTTATGACA 59.929 47.619 0.00 0.00 35.42 3.58
3875 4349 4.869861 ACTGAAATTGTTGTTTGCCTTGAC 59.130 37.500 0.00 0.00 0.00 3.18
4095 4570 3.118592 AGAGAAGCTGTATTGGTACTGGC 60.119 47.826 0.00 0.00 33.65 4.85
4217 4692 6.656902 TCCATTTCAGAGCTGAGTGATATTT 58.343 36.000 13.26 0.00 41.13 1.40
4218 4693 7.114754 TCCATTTCAGAGCTGAGTGATATTTT 58.885 34.615 13.26 0.00 41.13 1.82
4219 4694 7.613022 TCCATTTCAGAGCTGAGTGATATTTTT 59.387 33.333 13.26 0.00 41.13 1.94
4290 4784 1.461127 GAACTGTTGAGATGCCACGTC 59.539 52.381 0.00 0.00 0.00 4.34
4316 4810 3.448093 TGGGTTTTGCATGTCTATGGA 57.552 42.857 0.00 0.00 34.79 3.41
4318 4812 2.427095 GGGTTTTGCATGTCTATGGACC 59.573 50.000 6.77 0.00 41.47 4.46
4351 4845 6.976934 TCTAAGGAAATTGACTTTGCCTTT 57.023 33.333 1.89 0.00 36.55 3.11
4361 4856 6.757897 TTGACTTTGCCTTTTGATATCGAT 57.242 33.333 2.16 2.16 0.00 3.59
4392 4887 2.566833 AGCAGTGTAGGCATTGAACA 57.433 45.000 0.00 0.00 34.71 3.18
4399 4894 4.994744 GGCATTGAACAGCCCAAC 57.005 55.556 0.00 0.00 45.18 3.77
4422 4917 1.678101 GTCAACTAGCCATGGGAATGC 59.322 52.381 15.13 0.00 0.00 3.56
4511 5007 2.819019 TGTGGATGCAAACATGTCGAAT 59.181 40.909 0.00 0.00 36.35 3.34
4520 5016 4.085107 GCAAACATGTCGAATTGAACCAAC 60.085 41.667 11.33 0.00 0.00 3.77
5237 5782 2.540101 CTCGGTTGACTCTTGTTGTGAC 59.460 50.000 0.00 0.00 0.00 3.67
5330 5875 0.606401 ACAAGCACGATGGGAAGGTG 60.606 55.000 0.00 0.00 34.85 4.00
5367 5913 6.038603 TCTGCCTTGTTTATCATCTGTAATGC 59.961 38.462 0.00 0.00 0.00 3.56
5393 5939 6.421485 AGCTCAGTAGATCATCCACATTTTT 58.579 36.000 0.00 0.00 0.00 1.94
5447 5994 4.415596 TGTTGAAAGTCTTTATGGGGCAT 58.584 39.130 0.00 0.00 0.00 4.40
5448 5995 4.837860 TGTTGAAAGTCTTTATGGGGCATT 59.162 37.500 0.00 0.00 0.00 3.56
5449 5996 5.306678 TGTTGAAAGTCTTTATGGGGCATTT 59.693 36.000 0.00 0.00 0.00 2.32
5479 6026 7.253883 GCAGCTAAAACACTATGCATTGAATTC 60.254 37.037 15.23 0.00 33.92 2.17
5490 6039 3.055021 TGCATTGAATTCCTGTACCGGTA 60.055 43.478 11.16 11.16 0.00 4.02
5493 6042 5.277828 GCATTGAATTCCTGTACCGGTATTC 60.278 44.000 19.19 21.28 39.74 1.75
5539 6089 6.515272 ACTTGTGTTCAGTGAAACAGAAAT 57.485 33.333 7.25 0.90 44.12 2.17
5561 6111 3.554934 TGCTGGTGTTCTGTTTCATTCT 58.445 40.909 0.00 0.00 0.00 2.40
5581 6131 5.268118 TCTAGAGCAGTGTGATAATGTGG 57.732 43.478 0.00 0.00 0.00 4.17
5610 6160 2.279741 TGTGTGATTCATTAGCCTCGC 58.720 47.619 0.00 0.00 0.00 5.03
5628 6179 1.727880 CGCCAGTTGCCATCATTTTTG 59.272 47.619 0.00 0.00 36.24 2.44
5633 6184 3.059461 CAGTTGCCATCATTTTTGTGTGC 60.059 43.478 0.00 0.00 0.00 4.57
5786 6338 6.861065 AAATACCATTCGTAGGCAATACAG 57.139 37.500 0.00 0.00 33.65 2.74
5789 6341 3.054655 ACCATTCGTAGGCAATACAGGTT 60.055 43.478 0.00 0.00 33.65 3.50
5839 6391 2.593026 GGTTCCCCAACTGATTGTCAA 58.407 47.619 0.00 0.00 33.60 3.18
6124 6840 2.620251 TACAATGGCTCCTTGGATCG 57.380 50.000 0.00 0.00 0.00 3.69
6125 6841 0.107017 ACAATGGCTCCTTGGATCGG 60.107 55.000 0.00 0.00 0.00 4.18
6149 6865 6.813152 GGTGTGCAATACTTATCTGCATTTTT 59.187 34.615 0.00 0.00 46.90 1.94
6295 7011 2.462456 TCTCACAGCTTTGCAGGTAG 57.538 50.000 0.00 0.00 0.00 3.18
6391 7116 5.841237 TGATCCAGAGGACCCTATAGAAAAG 59.159 44.000 0.00 0.00 32.98 2.27
6542 7267 4.656112 CCACTGATATCCTGGAGGTACTTT 59.344 45.833 9.95 0.00 41.55 2.66
6543 7268 5.839063 CCACTGATATCCTGGAGGTACTTTA 59.161 44.000 9.95 0.00 41.55 1.85
6579 7305 5.610398 TGAAGAGTTGTATTGAAGAGCACA 58.390 37.500 0.00 0.00 0.00 4.57
6670 7401 2.762043 GAGCTCCTCGAGGGCCTT 60.762 66.667 30.80 17.12 33.61 4.35
6706 7437 1.268352 AGACACTTCAGCAGAGTCGAC 59.732 52.381 7.70 7.70 45.27 4.20
6731 7462 1.764851 TGTACGCAGCACATTTTTGC 58.235 45.000 0.00 0.00 43.34 3.68
6809 7540 5.124138 ACAACCAAAGATGTTACAAACGACA 59.876 36.000 0.00 0.00 0.00 4.35
6834 7565 4.393062 GTCAATGGACAATGTTGAGATCGT 59.607 41.667 0.00 0.00 43.73 3.73
6836 7567 3.676291 TGGACAATGTTGAGATCGTGA 57.324 42.857 0.00 0.00 0.00 4.35
6869 7600 1.900486 CACTAAAGACCCCGGAGAAGT 59.100 52.381 0.73 0.00 0.00 3.01
6872 7603 0.541296 AAAGACCCCGGAGAAGTCGA 60.541 55.000 0.73 0.00 35.12 4.20
6943 7677 2.816672 CAAGAAGGTGAAGGCTTCTTCC 59.183 50.000 26.26 24.97 44.66 3.46
6949 7689 0.250727 TGAAGGCTTCTTCCAACGGG 60.251 55.000 26.26 0.00 44.66 5.28
6999 7739 4.643387 AGTTGACACTGGCCGGGC 62.643 66.667 23.42 23.42 0.00 6.13
7168 7911 0.615331 TTCTGATGGAGTCCACAGCC 59.385 55.000 25.21 13.40 35.80 4.85
7201 7978 1.340889 TCAGAAATTGTTGCAGGCCAC 59.659 47.619 5.01 0.00 0.00 5.01
7212 7989 1.224592 CAGGCCACCTTATCCGCTT 59.775 57.895 5.01 0.00 0.00 4.68
7214 7991 2.481471 GGCCACCTTATCCGCTTGC 61.481 63.158 0.00 0.00 0.00 4.01
7246 8026 0.250513 GATTGTCTTCCACGGAGGCT 59.749 55.000 0.00 0.00 37.29 4.58
7275 8055 1.315257 CCAGCCATAAAGCCGCTTGT 61.315 55.000 6.34 0.00 0.00 3.16
7371 8151 2.122413 TGGCTGAGTGGGGAGTGT 60.122 61.111 0.00 0.00 0.00 3.55
7376 8156 1.383943 TGAGTGGGGAGTGTGGTGT 60.384 57.895 0.00 0.00 0.00 4.16
7414 8202 6.806249 CCACGTTTTGCAAGTTGTGATATAAT 59.194 34.615 21.42 0.00 0.00 1.28
7455 8243 3.372897 ACGTAAACCTTTTGGGGGAAAA 58.627 40.909 0.00 0.00 46.08 2.29
7457 8245 3.735591 GTAAACCTTTTGGGGGAAAAGC 58.264 45.455 0.00 0.00 46.46 3.51
7458 8246 1.886422 AACCTTTTGGGGGAAAAGCA 58.114 45.000 0.00 0.00 46.46 3.91
7459 8247 2.116869 ACCTTTTGGGGGAAAAGCAT 57.883 45.000 0.00 0.00 46.46 3.79
7460 8248 1.977854 ACCTTTTGGGGGAAAAGCATC 59.022 47.619 0.00 0.00 46.46 3.91
7462 8250 2.639347 CCTTTTGGGGGAAAAGCATCTT 59.361 45.455 0.00 0.00 46.46 2.40
7463 8251 3.837731 CCTTTTGGGGGAAAAGCATCTTA 59.162 43.478 0.00 0.00 46.46 2.10
7464 8252 4.471025 CCTTTTGGGGGAAAAGCATCTTAT 59.529 41.667 0.00 0.00 46.46 1.73
7465 8253 5.419239 TTTTGGGGGAAAAGCATCTTATG 57.581 39.130 0.00 0.00 0.00 1.90
7466 8254 3.756082 TGGGGGAAAAGCATCTTATGT 57.244 42.857 0.00 0.00 0.00 2.29
7485 8273 4.742438 TGTTTAGTTGTCATCGCCTTTC 57.258 40.909 0.00 0.00 0.00 2.62
7545 8333 0.884704 GGTGCTTTCAGTTCGGCAGA 60.885 55.000 0.00 0.00 35.29 4.26
7551 8339 0.321671 TTCAGTTCGGCAGAAGGAGG 59.678 55.000 0.00 0.00 36.99 4.30
7554 8342 1.122019 AGTTCGGCAGAAGGAGGTGT 61.122 55.000 0.00 0.00 36.99 4.16
7580 8368 4.401022 TGCTGCCAGAATAAGGATATTGG 58.599 43.478 0.00 0.00 31.83 3.16
7593 8381 3.312421 AGGATATTGGTGTGCGAATTTCG 59.688 43.478 14.33 14.33 43.89 3.46
7605 8397 1.059264 CGAATTTCGCAGGACTTCGAC 59.941 52.381 5.78 0.00 38.72 4.20
7621 8413 3.319137 TCGACAGAAGCTGCTTGTAAT 57.681 42.857 21.25 7.41 34.37 1.89
7622 8414 4.450082 TCGACAGAAGCTGCTTGTAATA 57.550 40.909 21.25 0.00 34.37 0.98
7623 8415 4.816392 TCGACAGAAGCTGCTTGTAATAA 58.184 39.130 21.25 0.00 34.37 1.40
7624 8416 5.234752 TCGACAGAAGCTGCTTGTAATAAA 58.765 37.500 21.25 0.00 34.37 1.40
7785 8577 1.682849 CCATCCGGGGTCTTTCACA 59.317 57.895 0.00 0.00 0.00 3.58
7787 8579 0.613260 CATCCGGGGTCTTTCACAGA 59.387 55.000 0.00 0.00 0.00 3.41
7794 8586 3.494398 CGGGGTCTTTCACAGAAAAGAGA 60.494 47.826 0.00 0.00 43.88 3.10
7795 8587 4.068599 GGGGTCTTTCACAGAAAAGAGAG 58.931 47.826 0.00 0.00 43.88 3.20
7796 8588 3.500299 GGGTCTTTCACAGAAAAGAGAGC 59.500 47.826 0.00 0.00 43.88 4.09
7797 8589 4.384940 GGTCTTTCACAGAAAAGAGAGCT 58.615 43.478 0.00 0.00 43.88 4.09
7801 8593 4.944619 TTCACAGAAAAGAGAGCTGAGA 57.055 40.909 0.00 0.00 33.94 3.27
7802 8594 5.480642 TTCACAGAAAAGAGAGCTGAGAT 57.519 39.130 0.00 0.00 31.22 2.75
7803 8595 5.070770 TCACAGAAAAGAGAGCTGAGATC 57.929 43.478 0.00 0.00 33.94 2.75
7804 8596 4.525874 TCACAGAAAAGAGAGCTGAGATCA 59.474 41.667 0.00 0.00 33.94 2.92
7805 8597 4.626604 CACAGAAAAGAGAGCTGAGATCAC 59.373 45.833 0.00 0.00 33.94 3.06
7806 8598 4.282957 ACAGAAAAGAGAGCTGAGATCACA 59.717 41.667 0.00 0.00 33.94 3.58
7885 8677 3.813166 GCAACTGTTGAGCCTAGTTTGTA 59.187 43.478 23.81 0.00 32.69 2.41
7987 8793 3.811083 ACGAACCAAGAAACACCACATA 58.189 40.909 0.00 0.00 0.00 2.29
8002 8809 2.367486 CACATATGACATGCCCACACA 58.633 47.619 10.38 0.00 0.00 3.72
8015 8822 2.348411 CCACACAAGATATGGGGTCC 57.652 55.000 0.00 0.00 36.45 4.46
8091 8899 4.759516 AATTACACGAAACCACCACATC 57.240 40.909 0.00 0.00 0.00 3.06
8103 8911 1.379044 CCACATCAAGGGCTGGGTC 60.379 63.158 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 78 2.751436 CCGGTTCCAGCACCCATG 60.751 66.667 0.00 0.00 32.48 3.66
113 115 0.533085 TCCAACAACGATGCCGACAA 60.533 50.000 0.00 0.00 39.50 3.18
116 118 1.231958 GGTTCCAACAACGATGCCGA 61.232 55.000 0.00 0.00 39.50 5.54
121 123 1.238439 CTGCAGGTTCCAACAACGAT 58.762 50.000 5.57 0.00 0.00 3.73
188 190 2.102578 GTTGGCCAGTTCCAGCATATT 58.897 47.619 5.11 0.00 37.31 1.28
201 203 1.769026 TGTAGCAAAACAGTTGGCCA 58.231 45.000 0.00 0.00 33.71 5.36
241 243 2.426261 CGTCGCAGTTCGTCGTCA 60.426 61.111 0.00 0.00 42.87 4.35
246 248 1.426041 AACTTTGCGTCGCAGTTCGT 61.426 50.000 20.65 12.60 40.61 3.85
283 285 5.441718 AATTCCATCAGTTCCAGCTTCTA 57.558 39.130 0.00 0.00 0.00 2.10
359 361 3.497262 CCACGTTTGAACCTTTCCTCTAC 59.503 47.826 0.00 0.00 0.00 2.59
365 367 4.625972 TTTCTCCACGTTTGAACCTTTC 57.374 40.909 0.00 0.00 0.00 2.62
403 405 2.099098 CACACGGGTTGAAGCTTTTCTT 59.901 45.455 0.00 0.00 37.83 2.52
521 535 1.136891 CACTCATACCATCGTCAGCCA 59.863 52.381 0.00 0.00 0.00 4.75
569 583 4.012895 CCGTCGCAGCAACACCAC 62.013 66.667 0.00 0.00 0.00 4.16
601 615 2.235155 TCCTTGTAGCAACTATTCGCCA 59.765 45.455 0.00 0.00 0.00 5.69
607 621 3.118592 GCCTCTGTCCTTGTAGCAACTAT 60.119 47.826 0.00 0.00 0.00 2.12
622 636 0.251354 AGAACGCATGATGCCTCTGT 59.749 50.000 12.40 0.45 41.12 3.41
634 648 0.320858 TCCGCCATTTGTAGAACGCA 60.321 50.000 0.00 0.00 0.00 5.24
655 669 1.200948 AGTTGTCGCCCTCGTAGTAAC 59.799 52.381 0.00 0.00 36.96 2.50
658 672 1.585006 CAGTTGTCGCCCTCGTAGT 59.415 57.895 0.00 0.00 36.96 2.73
731 745 4.760047 CACTCGCCTTCCCCACCG 62.760 72.222 0.00 0.00 0.00 4.94
734 748 3.691342 CGACACTCGCCTTCCCCA 61.691 66.667 0.00 0.00 31.14 4.96
756 770 0.670546 CACCTTGAAGTGTCGCCGAT 60.671 55.000 0.00 0.00 32.89 4.18
762 776 1.603739 GCCCCCACCTTGAAGTGTC 60.604 63.158 0.00 0.00 35.93 3.67
763 777 2.520968 GCCCCCACCTTGAAGTGT 59.479 61.111 0.00 0.00 35.93 3.55
797 811 4.513692 TGACGTTCCTAACAACCTTGATTG 59.486 41.667 0.00 0.00 35.59 2.67
798 812 4.710324 TGACGTTCCTAACAACCTTGATT 58.290 39.130 0.00 0.00 0.00 2.57
800 814 3.823281 TGACGTTCCTAACAACCTTGA 57.177 42.857 0.00 0.00 0.00 3.02
811 825 1.347707 TCTTCTGCCATTGACGTTCCT 59.652 47.619 0.00 0.00 0.00 3.36
812 826 1.734465 CTCTTCTGCCATTGACGTTCC 59.266 52.381 0.00 0.00 0.00 3.62
813 827 2.670414 CTCTCTTCTGCCATTGACGTTC 59.330 50.000 0.00 0.00 0.00 3.95
814 828 2.300152 TCTCTCTTCTGCCATTGACGTT 59.700 45.455 0.00 0.00 0.00 3.99
815 829 1.895798 TCTCTCTTCTGCCATTGACGT 59.104 47.619 0.00 0.00 0.00 4.34
816 830 2.662006 TCTCTCTTCTGCCATTGACG 57.338 50.000 0.00 0.00 0.00 4.35
817 831 5.893897 AAAATCTCTCTTCTGCCATTGAC 57.106 39.130 0.00 0.00 0.00 3.18
818 832 6.243900 AGAAAAATCTCTCTTCTGCCATTGA 58.756 36.000 0.00 0.00 0.00 2.57
819 833 6.512342 AGAAAAATCTCTCTTCTGCCATTG 57.488 37.500 0.00 0.00 0.00 2.82
846 862 3.378339 ACCTGTTACTCTTTCAACGACG 58.622 45.455 0.00 0.00 0.00 5.12
889 905 6.971527 AACAATTCATACCGTACGATTGAA 57.028 33.333 23.69 22.46 0.00 2.69
899 915 6.142161 CCGCATGATTAAAACAATTCATACCG 59.858 38.462 0.00 0.00 0.00 4.02
900 916 6.074356 GCCGCATGATTAAAACAATTCATACC 60.074 38.462 0.00 0.00 0.00 2.73
901 917 6.697019 AGCCGCATGATTAAAACAATTCATAC 59.303 34.615 0.00 0.00 0.00 2.39
984 1000 6.121590 AGAGTGGGCAAAATTTCATGTTTTT 58.878 32.000 0.00 0.00 0.00 1.94
988 1004 3.057315 CGAGAGTGGGCAAAATTTCATGT 60.057 43.478 0.00 0.00 0.00 3.21
989 1005 3.191162 TCGAGAGTGGGCAAAATTTCATG 59.809 43.478 0.00 0.00 0.00 3.07
990 1006 3.420893 TCGAGAGTGGGCAAAATTTCAT 58.579 40.909 0.00 0.00 0.00 2.57
991 1007 2.813754 CTCGAGAGTGGGCAAAATTTCA 59.186 45.455 6.58 0.00 0.00 2.69
992 1008 2.414691 GCTCGAGAGTGGGCAAAATTTC 60.415 50.000 18.75 0.00 0.00 2.17
993 1009 1.541588 GCTCGAGAGTGGGCAAAATTT 59.458 47.619 18.75 0.00 0.00 1.82
994 1010 1.168714 GCTCGAGAGTGGGCAAAATT 58.831 50.000 18.75 0.00 0.00 1.82
995 1011 0.326264 AGCTCGAGAGTGGGCAAAAT 59.674 50.000 18.75 0.00 0.00 1.82
996 1012 0.320771 GAGCTCGAGAGTGGGCAAAA 60.321 55.000 18.75 0.00 0.00 2.44
997 1013 1.188219 AGAGCTCGAGAGTGGGCAAA 61.188 55.000 18.75 0.00 0.00 3.68
998 1014 1.188219 AAGAGCTCGAGAGTGGGCAA 61.188 55.000 18.75 0.00 0.00 4.52
999 1015 0.323451 TAAGAGCTCGAGAGTGGGCA 60.323 55.000 18.75 0.00 0.00 5.36
1000 1016 0.818296 TTAAGAGCTCGAGAGTGGGC 59.182 55.000 18.75 0.00 0.00 5.36
1001 1017 2.417515 GGTTTAAGAGCTCGAGAGTGGG 60.418 54.545 18.75 0.00 0.00 4.61
1002 1018 2.417515 GGGTTTAAGAGCTCGAGAGTGG 60.418 54.545 18.75 0.00 0.00 4.00
1003 1019 2.494073 AGGGTTTAAGAGCTCGAGAGTG 59.506 50.000 18.75 0.00 0.00 3.51
1004 1020 2.810164 AGGGTTTAAGAGCTCGAGAGT 58.190 47.619 18.75 1.10 0.00 3.24
1005 1021 3.445805 AGAAGGGTTTAAGAGCTCGAGAG 59.554 47.826 18.75 0.00 0.00 3.20
1006 1022 3.432378 AGAAGGGTTTAAGAGCTCGAGA 58.568 45.455 18.75 0.00 0.00 4.04
1057 1075 0.321298 GAGCTAGGGTTTTGCGGTGA 60.321 55.000 0.00 0.00 0.00 4.02
1223 1247 4.755614 GAACGTCTCGGCGTCGCT 62.756 66.667 18.11 2.09 45.00 4.93
1361 1385 0.324285 CCAGCAGCAAAGAGGAGTCT 59.676 55.000 0.00 0.00 32.81 3.24
1363 1387 1.303155 GCCAGCAGCAAAGAGGAGT 60.303 57.895 0.00 0.00 42.97 3.85
1484 1516 3.696051 GCAACATTTCAGATAGGAGGCAA 59.304 43.478 0.00 0.00 0.00 4.52
1534 1578 6.323737 AGGAGCTCCTTAATAGTAGGCATTA 58.676 40.000 30.40 0.00 46.09 1.90
1537 1581 4.200447 AGGAGCTCCTTAATAGTAGGCA 57.800 45.455 30.40 0.00 46.09 4.75
1577 1621 5.710567 AGCACCCTTTCTTATTAGTTTCACC 59.289 40.000 0.00 0.00 0.00 4.02
1593 1637 0.178953 AATTGCACCTGAGCACCCTT 60.179 50.000 0.00 0.00 45.61 3.95
1616 1660 0.961857 TGCTTGATTCCACATGCGCT 60.962 50.000 9.73 0.00 41.62 5.92
1631 1675 7.866898 TGCGCATAAAATTGATACAATATGCTT 59.133 29.630 5.66 7.26 41.97 3.91
1638 1682 6.558909 TCACATGCGCATAAAATTGATACAA 58.441 32.000 24.84 0.00 0.00 2.41
1723 1767 0.250081 GAGAAGGTGATCGGGCATCC 60.250 60.000 0.00 0.00 0.00 3.51
1753 1797 5.050490 GGCGCTTTAGTATCTCTTGATTCA 58.950 41.667 7.64 0.00 34.32 2.57
1777 1821 4.202151 ACTGCTGTTTCCTGATTTTTCCAC 60.202 41.667 0.00 0.00 0.00 4.02
1781 1825 3.960102 TCCACTGCTGTTTCCTGATTTTT 59.040 39.130 0.00 0.00 0.00 1.94
1810 1854 3.674528 ATATCTCGGGTGAAGAGCATG 57.325 47.619 0.00 0.00 35.79 4.06
1899 1943 8.669243 CAAGCTAGGTAAATTTTCCAGAACTAG 58.331 37.037 15.37 10.30 0.00 2.57
1907 1951 6.745116 ACAACACAAGCTAGGTAAATTTTCC 58.255 36.000 5.74 5.74 0.00 3.13
2114 2158 1.068588 TGTCACTGCTGTCACCACTAC 59.931 52.381 0.00 0.00 0.00 2.73
2205 2336 3.025322 TGAGGAACAAAAGGAAGGCAA 57.975 42.857 0.00 0.00 0.00 4.52
2213 2344 7.829725 TGGATGTCAATATTGAGGAACAAAAG 58.170 34.615 18.47 0.00 42.03 2.27
2260 2391 5.185056 CCATCATGTCCCTGTACGACATATA 59.815 44.000 12.66 6.75 46.68 0.86
2261 2392 4.021104 CCATCATGTCCCTGTACGACATAT 60.021 45.833 12.66 6.56 46.68 1.78
2592 2892 6.364165 GCTGTAAATACCGCGAATACATAGAA 59.636 38.462 8.23 0.00 0.00 2.10
2629 2929 8.311836 ACTTCCTGAAAATAACTAGACATCGAA 58.688 33.333 0.00 0.00 0.00 3.71
2739 3039 3.830755 GCCCATCTTCTGATAATGCCAAT 59.169 43.478 0.00 0.00 0.00 3.16
2862 3162 6.617317 GCATCATCAAAGTATAAGCTAGCACG 60.617 42.308 18.83 0.00 0.00 5.34
2907 3207 5.111293 CAACTTTTCCAGTGTCAAGCAATT 58.889 37.500 0.00 0.00 35.12 2.32
2914 3214 1.286553 ACCCCAACTTTTCCAGTGTCA 59.713 47.619 0.00 0.00 35.12 3.58
2928 3228 4.428294 TGCAATCAATTTCAAACCCCAA 57.572 36.364 0.00 0.00 0.00 4.12
2964 3273 3.028850 CCACAAGGCCATGAAGATCATT 58.971 45.455 16.33 0.00 34.28 2.57
2981 3290 2.368192 CTAGCCCCATCCCCCACA 60.368 66.667 0.00 0.00 0.00 4.17
2982 3291 0.696485 TAACTAGCCCCATCCCCCAC 60.696 60.000 0.00 0.00 0.00 4.61
3086 3556 5.065914 GGCTCAGGACAGAAATATGCATTA 58.934 41.667 3.54 0.00 0.00 1.90
3109 3579 4.852134 TCATCCACTCAAATTGTTGGTG 57.148 40.909 13.38 10.88 36.48 4.17
3168 3641 4.326826 CTGGTATTGTCTTCTTTGAGGCA 58.673 43.478 0.00 0.00 0.00 4.75
3234 3707 0.680618 CCAAACAAGCCAAGATGCCA 59.319 50.000 0.00 0.00 0.00 4.92
3285 3758 4.998672 CCAACCGTAAGAAAGTAACCATCA 59.001 41.667 0.00 0.00 43.02 3.07
3294 3767 2.349155 GCGTTCACCAACCGTAAGAAAG 60.349 50.000 0.00 0.00 43.02 2.62
3315 3788 1.221466 ACCATATGCGCACGATTCCG 61.221 55.000 14.90 0.00 42.50 4.30
3377 3850 4.662468 TCTAGATGGACATGAGTGAAGC 57.338 45.455 0.00 0.00 0.00 3.86
3383 3856 6.711194 AGAAATGCATTCTAGATGGACATGAG 59.289 38.462 13.38 0.00 46.65 2.90
3445 3918 2.747989 CAGATGACTGCTGCTCAAACAT 59.252 45.455 0.00 0.02 37.33 2.71
3555 4028 5.446143 ACAAAAATTGTTGATCAGCGGTA 57.554 34.783 15.43 0.00 42.22 4.02
3672 4145 2.200373 ATTGTTCCTCTTCCCCAACG 57.800 50.000 0.00 0.00 0.00 4.10
3702 4175 1.529010 CTGCTCCAAGTTGGTGGCA 60.529 57.895 28.91 28.91 41.70 4.92
3708 4181 1.893808 ACGCACCTGCTCCAAGTTG 60.894 57.895 0.00 0.00 39.32 3.16
3759 4232 4.141287 TGGTGTGAGAAATTGGTTACAGG 58.859 43.478 0.00 0.00 0.00 4.00
3788 4262 1.686355 AAACACGGACCTGCAAATGA 58.314 45.000 0.00 0.00 0.00 2.57
3813 4287 7.704899 CACATAAGAACATGACATTGATGCAAT 59.295 33.333 0.00 0.00 34.04 3.56
3875 4349 2.141517 CCAGAAGCAGAGACACAAGTG 58.858 52.381 0.00 0.00 0.00 3.16
4017 4491 5.184711 CCAAATGTTACATCCAAAATGGGG 58.815 41.667 0.00 0.00 38.32 4.96
4095 4570 4.070716 CAATAGCTCCTAGATGGCCTTTG 58.929 47.826 3.32 0.00 35.26 2.77
4217 4692 5.179368 GTCACGATTGATCACTGAGGAAAAA 59.821 40.000 0.00 0.00 33.11 1.94
4218 4693 4.690748 GTCACGATTGATCACTGAGGAAAA 59.309 41.667 0.00 0.00 33.11 2.29
4219 4694 4.021104 AGTCACGATTGATCACTGAGGAAA 60.021 41.667 0.00 0.00 33.11 3.13
4290 4784 2.102925 AGACATGCAAAACCCAACCAAG 59.897 45.455 0.00 0.00 0.00 3.61
4316 4810 0.472352 TCCTTAGAACACCCACCGGT 60.472 55.000 0.00 0.00 46.31 5.28
4318 4812 2.554370 TTTCCTTAGAACACCCACCG 57.446 50.000 0.00 0.00 0.00 4.94
4361 4856 6.645306 TGCCTACACTGCTACATACAATAAA 58.355 36.000 0.00 0.00 0.00 1.40
4392 4887 1.555533 GGCTAGTTGACTAGTTGGGCT 59.444 52.381 17.02 0.00 45.85 5.19
4399 4894 4.384056 CATTCCCATGGCTAGTTGACTAG 58.616 47.826 6.09 12.72 46.63 2.57
4422 4917 1.066858 AGGTCACGAGTTGCCTACATG 60.067 52.381 0.00 0.00 31.97 3.21
4442 4937 4.141287 ACCGATGAACAAATCACCAAGAA 58.859 39.130 0.00 0.00 41.93 2.52
4511 5007 1.305201 GGACTTGAGCGTTGGTTCAA 58.695 50.000 0.00 0.00 40.49 2.69
4564 5060 1.151668 CTGCGGTGAAGAAAGACTGG 58.848 55.000 0.00 0.00 0.00 4.00
4861 5404 4.464008 TCAATGAGGCAAGTCAAAAGAGT 58.536 39.130 0.00 0.00 0.00 3.24
4983 5526 2.664402 ACTCAACTGACCAAATGCCT 57.336 45.000 0.00 0.00 0.00 4.75
5094 5637 1.201647 ACACTTGACGTATGACCCTCG 59.798 52.381 0.00 0.00 0.00 4.63
5197 5740 0.824595 GTTACACCACCCAACACCCC 60.825 60.000 0.00 0.00 0.00 4.95
5237 5782 4.440250 CCATCACTTCCTACAGTAAGGACG 60.440 50.000 0.00 0.00 45.49 4.79
5367 5913 2.620585 TGTGGATGATCTACTGAGCTCG 59.379 50.000 9.64 6.63 0.00 5.03
5420 5967 7.284489 TGCCCCATAAAGACTTTCAACATATAC 59.716 37.037 3.07 0.00 0.00 1.47
5430 5977 5.559770 CCAAAAATGCCCCATAAAGACTTT 58.440 37.500 5.62 5.62 0.00 2.66
5447 5994 4.987912 GCATAGTGTTTTAGCTGCCAAAAA 59.012 37.500 7.53 6.93 0.00 1.94
5448 5995 4.038522 TGCATAGTGTTTTAGCTGCCAAAA 59.961 37.500 1.85 1.85 0.00 2.44
5449 5996 3.571828 TGCATAGTGTTTTAGCTGCCAAA 59.428 39.130 0.00 0.00 0.00 3.28
5479 6026 4.730949 TTCTCTTGAATACCGGTACAGG 57.269 45.455 18.55 12.07 37.30 4.00
5490 6039 7.173722 AGGTTCATCACTCAATTCTCTTGAAT 58.826 34.615 0.00 0.00 44.08 2.57
5493 6042 7.102346 AGTAGGTTCATCACTCAATTCTCTTG 58.898 38.462 0.00 0.00 0.00 3.02
5539 6089 3.953612 AGAATGAAACAGAACACCAGCAA 59.046 39.130 0.00 0.00 0.00 3.91
5561 6111 3.197549 TGCCACATTATCACACTGCTCTA 59.802 43.478 0.00 0.00 0.00 2.43
5581 6131 2.728690 TGAATCACACAGCCAAATGC 57.271 45.000 0.00 0.00 41.71 3.56
5610 6160 3.495377 CACACAAAAATGATGGCAACTGG 59.505 43.478 0.00 0.00 37.61 4.00
5628 6179 1.978782 GCAAGTCGCAAATTAGCACAC 59.021 47.619 0.00 0.00 41.79 3.82
5633 6184 4.606457 AGCTAAGCAAGTCGCAAATTAG 57.394 40.909 0.00 0.00 46.13 1.73
5763 6315 5.763204 CCTGTATTGCCTACGAATGGTATTT 59.237 40.000 0.00 0.00 32.61 1.40
5833 6385 6.520272 CCCAAACCTGTTGAATAATTGACAA 58.480 36.000 0.00 0.00 0.00 3.18
5839 6391 5.490159 CAATGCCCAAACCTGTTGAATAAT 58.510 37.500 0.00 0.00 0.00 1.28
6012 6568 4.935885 AACAAAGACAAGATCTCGCATC 57.064 40.909 0.00 0.00 36.27 3.91
6094 6654 5.128919 AGGAGCCATTGTAAAGATCATGTC 58.871 41.667 0.00 0.00 0.00 3.06
6149 6865 3.330701 ACTTCCTCCTCCTGCAACAATAA 59.669 43.478 0.00 0.00 0.00 1.40
6150 6866 2.912956 ACTTCCTCCTCCTGCAACAATA 59.087 45.455 0.00 0.00 0.00 1.90
6295 7011 4.278975 AGTGACCTCCTTCAAAGATGAC 57.721 45.455 0.00 0.00 34.61 3.06
6579 7305 8.730680 GGTAACAGTTTGTCACAGATTATCAAT 58.269 33.333 0.00 0.00 0.00 2.57
6670 7401 6.821160 TGAAGTGTCTTTGCGAATATGGAATA 59.179 34.615 0.00 0.00 0.00 1.75
6706 7437 1.432514 ATGTGCTGCGTACAAGTCTG 58.567 50.000 3.99 0.00 31.17 3.51
6731 7462 0.246635 CGGGTCAAGGTGTAGTCCAG 59.753 60.000 0.00 0.00 0.00 3.86
6809 7540 3.738982 TCTCAACATTGTCCATTGACGT 58.261 40.909 0.00 0.00 44.86 4.34
6854 7585 0.966370 CTCGACTTCTCCGGGGTCTT 60.966 60.000 0.00 0.00 0.00 3.01
6869 7600 4.248859 CTGGATTTTCTCTTCTTGCTCGA 58.751 43.478 0.00 0.00 0.00 4.04
6872 7603 3.759581 TGCTGGATTTTCTCTTCTTGCT 58.240 40.909 0.00 0.00 0.00 3.91
6943 7677 1.156736 CAGCTTTACTGTCCCCGTTG 58.843 55.000 0.00 0.00 41.86 4.10
6999 7739 2.859273 ATTGGTGGCGCGAAGAGAGG 62.859 60.000 12.10 0.00 0.00 3.69
7168 7911 7.847564 GCAACAATTTCTGAAACTAAAAGCTTG 59.152 33.333 4.73 6.20 0.00 4.01
7201 7978 1.463674 AACCAAGCAAGCGGATAAGG 58.536 50.000 0.00 0.00 0.00 2.69
7212 7989 1.761784 ACAATCAAGGCAAACCAAGCA 59.238 42.857 0.00 0.00 39.06 3.91
7214 7991 4.301628 GAAGACAATCAAGGCAAACCAAG 58.698 43.478 0.00 0.00 39.06 3.61
7268 8048 0.314935 ATTGCAAGTGGAACAAGCGG 59.685 50.000 4.94 0.00 44.16 5.52
7275 8055 3.896888 AGATCCAACAATTGCAAGTGGAA 59.103 39.130 28.40 12.43 0.00 3.53
7371 8151 3.298686 TGGGACACAATTGTTACACCA 57.701 42.857 8.77 12.06 35.47 4.17
7414 8202 4.096833 ACGTTACACGACTGCTATGGAATA 59.903 41.667 2.75 0.00 46.05 1.75
7446 8234 3.756082 ACATAAGATGCTTTTCCCCCA 57.244 42.857 0.00 0.00 0.00 4.96
7455 8243 6.238211 GCGATGACAACTAAACATAAGATGCT 60.238 38.462 0.00 0.00 0.00 3.79
7456 8244 5.904080 GCGATGACAACTAAACATAAGATGC 59.096 40.000 0.00 0.00 0.00 3.91
7457 8245 6.258727 AGGCGATGACAACTAAACATAAGATG 59.741 38.462 0.00 0.00 0.00 2.90
7458 8246 6.349300 AGGCGATGACAACTAAACATAAGAT 58.651 36.000 0.00 0.00 0.00 2.40
7459 8247 5.730550 AGGCGATGACAACTAAACATAAGA 58.269 37.500 0.00 0.00 0.00 2.10
7460 8248 6.422776 AAGGCGATGACAACTAAACATAAG 57.577 37.500 0.00 0.00 0.00 1.73
7462 8250 5.062934 CGAAAGGCGATGACAACTAAACATA 59.937 40.000 0.00 0.00 44.57 2.29
7463 8251 4.142902 CGAAAGGCGATGACAACTAAACAT 60.143 41.667 0.00 0.00 44.57 2.71
7464 8252 3.185594 CGAAAGGCGATGACAACTAAACA 59.814 43.478 0.00 0.00 44.57 2.83
7465 8253 3.732943 CGAAAGGCGATGACAACTAAAC 58.267 45.455 0.00 0.00 44.57 2.01
7499 8287 2.193306 TACCGGCGATTAAACTCGTC 57.807 50.000 9.30 0.00 40.73 4.20
7545 8333 0.610232 GGCAGCATCAACACCTCCTT 60.610 55.000 0.00 0.00 0.00 3.36
7551 8339 3.181493 CCTTATTCTGGCAGCATCAACAC 60.181 47.826 10.34 0.00 0.00 3.32
7554 8342 3.650281 TCCTTATTCTGGCAGCATCAA 57.350 42.857 10.34 0.00 0.00 2.57
7593 8381 0.037790 AGCTTCTGTCGAAGTCCTGC 60.038 55.000 4.26 0.00 46.65 4.85
7605 8397 5.886960 AGGTTTATTACAAGCAGCTTCTG 57.113 39.130 4.07 0.00 34.12 3.02
7621 8413 2.562298 ACACCGGACGTTGATAGGTTTA 59.438 45.455 9.46 0.00 32.04 2.01
7622 8414 1.345415 ACACCGGACGTTGATAGGTTT 59.655 47.619 9.46 0.00 32.04 3.27
7623 8415 0.971386 ACACCGGACGTTGATAGGTT 59.029 50.000 9.46 0.00 32.04 3.50
7624 8416 0.245539 CACACCGGACGTTGATAGGT 59.754 55.000 9.46 0.00 35.24 3.08
7785 8577 5.395546 GGATGTGATCTCAGCTCTCTTTTCT 60.396 44.000 12.29 0.00 0.00 2.52
7787 8579 4.224594 TGGATGTGATCTCAGCTCTCTTTT 59.775 41.667 12.29 0.00 0.00 2.27
7794 8586 3.181453 CCTGAATGGATGTGATCTCAGCT 60.181 47.826 12.29 0.00 38.35 4.24
7795 8587 3.139850 CCTGAATGGATGTGATCTCAGC 58.860 50.000 4.47 4.47 38.35 4.26
7796 8588 4.684484 TCCTGAATGGATGTGATCTCAG 57.316 45.455 3.58 1.00 40.56 3.35
7885 8677 5.736813 TCATTTTAGCGTAGGGTAACATGT 58.263 37.500 22.71 0.00 41.55 3.21
7987 8793 2.519771 ATCTTGTGTGGGCATGTCAT 57.480 45.000 0.00 0.00 0.00 3.06
8002 8809 2.108250 CGGATTTGGGACCCCATATCTT 59.892 50.000 26.60 4.67 46.62 2.40
8049 8856 9.493206 GTAATTAACTCGTGTTTTCAAGTTCAA 57.507 29.630 8.32 0.00 37.59 2.69
8091 8899 2.360852 CTGCAGACCCAGCCCTTG 60.361 66.667 8.42 0.00 0.00 3.61
8103 8911 0.817634 TGAACCGGTGGTTTCTGCAG 60.818 55.000 8.52 7.63 46.95 4.41


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

AutoCloner maintained by Alex Coulton.