Multiple sequence alignment - TraesCS7B01G475300

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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 TraesCS7B01G475300 chr7B 100.000 2805 0 0 1 2805 731242223 731245027 0.000000e+00 5180
1 TraesCS7B01G475300 chr7D 92.198 1897 116 14 174 2047 628988437 628986550 0.000000e+00 2654
2 TraesCS7B01G475300 chr7D 92.236 747 52 5 2065 2805 628950585 628949839 0.000000e+00 1053
3 TraesCS7B01G475300 chr7D 92.102 747 53 5 2065 2805 628947959 628947213 0.000000e+00 1048
4 TraesCS7B01G475300 chr7D 91.834 747 55 3 2065 2805 628944022 628943276 0.000000e+00 1037
5 TraesCS7B01G475300 chr7D 91.834 747 54 4 2065 2805 628924393 628923648 0.000000e+00 1035
6 TraesCS7B01G475300 chr7D 91.834 747 54 4 2065 2805 628925704 628924959 0.000000e+00 1035
7 TraesCS7B01G475300 chr7D 91.711 748 54 8 2065 2805 628937503 628936757 0.000000e+00 1031
8 TraesCS7B01G475300 chr7D 91.700 747 54 7 2065 2805 628966817 628966073 0.000000e+00 1029
9 TraesCS7B01G475300 chr7D 91.432 747 58 6 2065 2805 628929637 628928891 0.000000e+00 1020
10 TraesCS7B01G475300 chr7D 91.432 747 58 6 2065 2805 628938796 628938050 0.000000e+00 1020
11 TraesCS7B01G475300 chr7D 80.205 586 80 17 1124 1677 629247964 629248545 9.350000e-110 407
12 TraesCS7B01G475300 chr7A 79.327 624 92 23 1052 1649 725034785 725034173 1.210000e-108 403
13 TraesCS7B01G475300 chr3A 78.764 259 40 12 1268 1523 27543821 27544067 2.890000e-35 159
14 TraesCS7B01G475300 chr2D 74.935 387 74 19 1162 1544 405275798 405276165 3.740000e-34 156
15 TraesCS7B01G475300 chr2B 75.134 374 71 20 1162 1530 480412288 480412644 3.740000e-34 156
16 TraesCS7B01G475300 chr2A 74.799 373 74 18 1162 1530 543308346 543308702 1.740000e-32 150
17 TraesCS7B01G475300 chr3D 77.043 257 48 9 1268 1523 19880856 19881102 1.360000e-28 137


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 TraesCS7B01G475300 chr7B 731242223 731245027 2804 False 5180.0 5180 100.000000 1 2805 1 chr7B.!!$F1 2804
1 TraesCS7B01G475300 chr7D 628986550 628988437 1887 True 2654.0 2654 92.198000 174 2047 1 chr7D.!!$R2 1873
2 TraesCS7B01G475300 chr7D 628943276 628950585 7309 True 1046.0 1053 92.057333 2065 2805 3 chr7D.!!$R5 740
3 TraesCS7B01G475300 chr7D 628923648 628929637 5989 True 1030.0 1035 91.700000 2065 2805 3 chr7D.!!$R3 740
4 TraesCS7B01G475300 chr7D 628966073 628966817 744 True 1029.0 1029 91.700000 2065 2805 1 chr7D.!!$R1 740
5 TraesCS7B01G475300 chr7D 628936757 628938796 2039 True 1025.5 1031 91.571500 2065 2805 2 chr7D.!!$R4 740
6 TraesCS7B01G475300 chr7D 629247964 629248545 581 False 407.0 407 80.205000 1124 1677 1 chr7D.!!$F1 553
7 TraesCS7B01G475300 chr7A 725034173 725034785 612 True 403.0 403 79.327000 1052 1649 1 chr7A.!!$R1 597

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
170 171 0.037605 GTGCGTGTTACCCTGCTAGT 60.038 55.0 0.00 0.0 0.0 2.57 F
936 940 0.249489 CTGGTGGCAGCCGTAGTATC 60.249 60.0 14.97 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1704 1764 0.036448 ACGTGACTCCCTCTCTTCGA 59.964 55.0 0.00 0.00 0.00 3.71 R
2053 2129 0.332972 ATGGTGAAGCCCCTTCTTCC 59.667 55.0 6.54 8.83 41.23 3.46 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
23 24 3.961477 TTGGTCTTTCAATGTCACACG 57.039 42.857 0.00 0.00 0.00 4.49
24 25 2.912771 TGGTCTTTCAATGTCACACGT 58.087 42.857 0.00 0.00 0.00 4.49
25 26 2.869801 TGGTCTTTCAATGTCACACGTC 59.130 45.455 0.00 0.00 0.00 4.34
26 27 2.869801 GGTCTTTCAATGTCACACGTCA 59.130 45.455 0.00 0.00 0.00 4.35
27 28 3.311322 GGTCTTTCAATGTCACACGTCAA 59.689 43.478 0.00 0.00 0.00 3.18
28 29 4.518217 GTCTTTCAATGTCACACGTCAAG 58.482 43.478 0.00 0.00 0.00 3.02
29 30 4.270084 GTCTTTCAATGTCACACGTCAAGA 59.730 41.667 0.00 0.00 0.00 3.02
30 31 5.050091 GTCTTTCAATGTCACACGTCAAGAT 60.050 40.000 0.00 0.00 0.00 2.40
31 32 4.990543 TTCAATGTCACACGTCAAGATC 57.009 40.909 0.00 0.00 0.00 2.75
32 33 4.257267 TCAATGTCACACGTCAAGATCT 57.743 40.909 0.00 0.00 0.00 2.75
33 34 4.631131 TCAATGTCACACGTCAAGATCTT 58.369 39.130 0.88 0.88 0.00 2.40
34 35 4.448732 TCAATGTCACACGTCAAGATCTTG 59.551 41.667 26.56 26.56 41.71 3.02
35 36 2.754472 TGTCACACGTCAAGATCTTGG 58.246 47.619 30.33 19.70 40.78 3.61
36 37 2.364002 TGTCACACGTCAAGATCTTGGA 59.636 45.455 30.33 17.89 40.78 3.53
37 38 2.731976 GTCACACGTCAAGATCTTGGAC 59.268 50.000 30.33 23.68 40.78 4.02
38 39 2.069273 CACACGTCAAGATCTTGGACC 58.931 52.381 30.33 18.93 40.78 4.46
39 40 1.002087 ACACGTCAAGATCTTGGACCC 59.998 52.381 30.33 16.86 40.78 4.46
40 41 0.613777 ACGTCAAGATCTTGGACCCC 59.386 55.000 30.33 14.82 40.78 4.95
41 42 0.613260 CGTCAAGATCTTGGACCCCA 59.387 55.000 30.33 11.32 40.78 4.96
42 43 1.003118 CGTCAAGATCTTGGACCCCAA 59.997 52.381 30.33 10.64 41.69 4.12
43 44 2.437413 GTCAAGATCTTGGACCCCAAC 58.563 52.381 30.33 17.74 38.75 3.77
44 45 2.040412 GTCAAGATCTTGGACCCCAACT 59.960 50.000 30.33 0.00 38.75 3.16
45 46 2.716424 TCAAGATCTTGGACCCCAACTT 59.284 45.455 30.33 0.00 38.75 2.66
46 47 3.913799 TCAAGATCTTGGACCCCAACTTA 59.086 43.478 30.33 8.09 38.75 2.24
47 48 4.019321 TCAAGATCTTGGACCCCAACTTAG 60.019 45.833 30.33 4.69 38.75 2.18
48 49 3.532102 AGATCTTGGACCCCAACTTAGT 58.468 45.455 0.00 0.00 38.75 2.24
49 50 4.695606 AGATCTTGGACCCCAACTTAGTA 58.304 43.478 0.00 0.00 38.75 1.82
50 51 4.470304 AGATCTTGGACCCCAACTTAGTAC 59.530 45.833 0.00 0.00 38.75 2.73
51 52 3.589641 TCTTGGACCCCAACTTAGTACA 58.410 45.455 0.00 0.00 38.75 2.90
52 53 4.172807 TCTTGGACCCCAACTTAGTACAT 58.827 43.478 0.00 0.00 38.75 2.29
53 54 5.343715 TCTTGGACCCCAACTTAGTACATA 58.656 41.667 0.00 0.00 38.75 2.29
54 55 5.968167 TCTTGGACCCCAACTTAGTACATAT 59.032 40.000 0.00 0.00 38.75 1.78
55 56 7.134162 TCTTGGACCCCAACTTAGTACATATA 58.866 38.462 0.00 0.00 38.75 0.86
56 57 6.989155 TGGACCCCAACTTAGTACATATAG 57.011 41.667 0.00 0.00 0.00 1.31
57 58 5.842328 TGGACCCCAACTTAGTACATATAGG 59.158 44.000 0.00 0.00 0.00 2.57
58 59 6.080009 GGACCCCAACTTAGTACATATAGGA 58.920 44.000 0.00 0.00 0.00 2.94
59 60 6.556116 GGACCCCAACTTAGTACATATAGGAA 59.444 42.308 0.00 0.00 0.00 3.36
60 61 7.370905 ACCCCAACTTAGTACATATAGGAAC 57.629 40.000 0.00 0.00 0.00 3.62
61 62 6.904654 ACCCCAACTTAGTACATATAGGAACA 59.095 38.462 0.00 0.00 0.00 3.18
62 63 7.571357 ACCCCAACTTAGTACATATAGGAACAT 59.429 37.037 0.00 0.00 0.00 2.71
63 64 9.096823 CCCCAACTTAGTACATATAGGAACATA 57.903 37.037 0.00 0.00 0.00 2.29
126 127 9.463443 AAAGAAAAGAAAAGAACATAACATCGG 57.537 29.630 0.00 0.00 0.00 4.18
127 128 8.391075 AGAAAAGAAAAGAACATAACATCGGA 57.609 30.769 0.00 0.00 0.00 4.55
128 129 8.846211 AGAAAAGAAAAGAACATAACATCGGAA 58.154 29.630 0.00 0.00 0.00 4.30
129 130 9.626045 GAAAAGAAAAGAACATAACATCGGAAT 57.374 29.630 0.00 0.00 0.00 3.01
132 133 8.786826 AGAAAAGAACATAACATCGGAATACA 57.213 30.769 0.00 0.00 0.00 2.29
133 134 9.396022 AGAAAAGAACATAACATCGGAATACAT 57.604 29.630 0.00 0.00 0.00 2.29
134 135 9.438291 GAAAAGAACATAACATCGGAATACATG 57.562 33.333 0.00 0.00 0.00 3.21
135 136 7.496529 AAGAACATAACATCGGAATACATGG 57.503 36.000 0.00 0.00 0.00 3.66
136 137 6.591935 AGAACATAACATCGGAATACATGGT 58.408 36.000 0.00 0.00 0.00 3.55
137 138 6.706270 AGAACATAACATCGGAATACATGGTC 59.294 38.462 0.00 0.00 0.00 4.02
138 139 6.174720 ACATAACATCGGAATACATGGTCT 57.825 37.500 0.00 0.00 0.00 3.85
139 140 7.297936 ACATAACATCGGAATACATGGTCTA 57.702 36.000 0.00 0.00 0.00 2.59
140 141 7.378966 ACATAACATCGGAATACATGGTCTAG 58.621 38.462 0.00 0.00 0.00 2.43
141 142 4.258702 ACATCGGAATACATGGTCTAGC 57.741 45.455 0.00 0.00 0.00 3.42
142 143 3.006967 ACATCGGAATACATGGTCTAGCC 59.993 47.826 0.00 0.00 37.90 3.93
143 144 1.611977 TCGGAATACATGGTCTAGCCG 59.388 52.381 0.00 0.00 41.21 5.52
144 145 1.797025 GGAATACATGGTCTAGCCGC 58.203 55.000 0.00 0.00 41.21 6.53
145 146 1.419374 GAATACATGGTCTAGCCGCG 58.581 55.000 0.00 0.00 41.21 6.46
146 147 0.600255 AATACATGGTCTAGCCGCGC 60.600 55.000 0.00 0.00 41.21 6.86
147 148 1.744320 ATACATGGTCTAGCCGCGCA 61.744 55.000 8.75 0.00 41.21 6.09
148 149 1.950973 TACATGGTCTAGCCGCGCAA 61.951 55.000 8.75 0.00 41.21 4.85
149 150 2.106074 CATGGTCTAGCCGCGCAAA 61.106 57.895 8.75 0.00 41.21 3.68
150 151 1.153168 ATGGTCTAGCCGCGCAAAT 60.153 52.632 8.75 0.00 41.21 2.32
151 152 1.439353 ATGGTCTAGCCGCGCAAATG 61.439 55.000 8.75 0.00 41.21 2.32
152 153 2.106683 GGTCTAGCCGCGCAAATGT 61.107 57.895 8.75 0.00 0.00 2.71
153 154 1.060937 GTCTAGCCGCGCAAATGTG 59.939 57.895 8.75 0.00 0.00 3.21
163 164 3.101019 GCAAATGTGCGTGTTACCC 57.899 52.632 0.00 0.00 41.93 3.69
164 165 0.596082 GCAAATGTGCGTGTTACCCT 59.404 50.000 0.00 0.00 41.93 4.34
165 166 1.665735 GCAAATGTGCGTGTTACCCTG 60.666 52.381 0.00 0.00 41.93 4.45
166 167 0.596082 AAATGTGCGTGTTACCCTGC 59.404 50.000 0.00 0.00 0.00 4.85
167 168 0.250727 AATGTGCGTGTTACCCTGCT 60.251 50.000 0.00 0.00 0.00 4.24
168 169 0.611200 ATGTGCGTGTTACCCTGCTA 59.389 50.000 0.00 0.00 0.00 3.49
169 170 0.037697 TGTGCGTGTTACCCTGCTAG 60.038 55.000 0.00 0.00 0.00 3.42
170 171 0.037605 GTGCGTGTTACCCTGCTAGT 60.038 55.000 0.00 0.00 0.00 2.57
171 172 0.682852 TGCGTGTTACCCTGCTAGTT 59.317 50.000 0.00 0.00 0.00 2.24
172 173 1.337447 TGCGTGTTACCCTGCTAGTTC 60.337 52.381 0.00 0.00 0.00 3.01
181 182 4.844349 ACCCTGCTAGTTCATGTTACAT 57.156 40.909 0.00 0.00 0.00 2.29
268 269 9.920946 ACCATATGTCAAATTGTAATTCTAGGT 57.079 29.630 1.24 0.00 0.00 3.08
275 276 9.744468 GTCAAATTGTAATTCTAGGTGTTGTTT 57.256 29.630 0.00 0.00 0.00 2.83
323 324 4.565166 TGAATCTAATAGCGGTGAACAACG 59.435 41.667 7.92 7.92 45.82 4.10
325 326 4.380841 TCTAATAGCGGTGAACAACGAT 57.619 40.909 16.40 12.34 45.97 3.73
395 396 5.003160 TGTTGTCATGGTCGAATGAAAGAT 58.997 37.500 1.39 0.00 38.28 2.40
406 409 3.778718 CGAATGAAAGATACCGCAAAACG 59.221 43.478 0.00 0.00 43.15 3.60
434 437 2.427812 TCGGGCATAAGTTATCGTGTGA 59.572 45.455 0.00 0.00 0.00 3.58
452 455 4.278419 GTGTGAATAGCAACCCTCAAACTT 59.722 41.667 0.00 0.00 0.00 2.66
480 483 6.365520 AGGCCCGTGATTATTTATTTTCTCT 58.634 36.000 0.00 0.00 0.00 3.10
490 493 9.604626 GATTATTTATTTTCTCTCTGGAATGCG 57.395 33.333 0.00 0.00 0.00 4.73
527 530 0.456312 GTTCGTCCTACTCCACGCTG 60.456 60.000 0.00 0.00 35.93 5.18
562 565 3.368427 CCACTTGATCTTAGCTTCGGTCA 60.368 47.826 0.00 0.00 0.00 4.02
580 583 4.261572 CGGTCATCAGGTTGATTTTGTGTT 60.262 41.667 0.00 0.00 34.28 3.32
647 650 1.295357 TGCGTTGGTTAGGACATGCG 61.295 55.000 0.00 0.00 0.00 4.73
666 669 2.287769 CGTGTATGGCATCATCCAACA 58.712 47.619 1.65 0.00 39.96 3.33
690 693 2.188817 ACCAAACCTAGGCAGGACTAG 58.811 52.381 18.68 2.01 45.91 2.57
717 720 1.731709 CTTTCACGACATCATTGCGGA 59.268 47.619 0.00 0.00 0.00 5.54
750 753 4.134379 TGTCAACACATGCAAAAACCAT 57.866 36.364 0.00 0.00 0.00 3.55
784 788 2.667473 AAGCTGCGTACGGATTACTT 57.333 45.000 18.39 14.60 0.00 2.24
788 792 5.044428 AGCTGCGTACGGATTACTTATAG 57.956 43.478 18.39 0.00 0.00 1.31
850 854 0.745845 AGACGAAGCCATGCACCATC 60.746 55.000 0.00 0.00 0.00 3.51
890 894 4.905456 TCCAAGTTGGAGAAGTTCCTTAGA 59.095 41.667 21.05 0.00 42.67 2.10
933 937 3.706373 CCTGGTGGCAGCCGTAGT 61.706 66.667 14.97 0.00 0.00 2.73
934 938 2.355986 CCTGGTGGCAGCCGTAGTA 61.356 63.158 14.97 0.00 0.00 1.82
935 939 1.686325 CCTGGTGGCAGCCGTAGTAT 61.686 60.000 14.97 0.00 0.00 2.12
936 940 0.249489 CTGGTGGCAGCCGTAGTATC 60.249 60.000 14.97 0.00 0.00 2.24
937 941 1.299926 GGTGGCAGCCGTAGTATCG 60.300 63.158 7.03 0.00 0.00 2.92
938 942 1.436336 GTGGCAGCCGTAGTATCGT 59.564 57.895 7.03 0.00 0.00 3.73
939 943 0.664761 GTGGCAGCCGTAGTATCGTA 59.335 55.000 7.03 0.00 0.00 3.43
940 944 0.664761 TGGCAGCCGTAGTATCGTAC 59.335 55.000 7.03 0.00 0.00 3.67
973 977 4.980805 TCGACACCCGCACAAGGC 62.981 66.667 0.00 0.00 38.37 4.35
1008 1012 2.331194 TCTCTAACGTTAGTTTGCCGC 58.669 47.619 29.36 0.00 41.49 6.53
1024 1028 0.392998 CCGCCCTGTTCTTGCATACT 60.393 55.000 0.00 0.00 0.00 2.12
1040 1044 3.324846 GCATACTGATGGTAGTGATGGGA 59.675 47.826 0.00 0.00 33.51 4.37
1044 1048 3.303938 CTGATGGTAGTGATGGGAGACT 58.696 50.000 0.00 0.00 0.00 3.24
1079 1083 2.159282 CGGCAGAGACGTGGTTATTAGT 60.159 50.000 0.00 0.00 0.00 2.24
1126 1139 0.811616 GAGGATAACAGCACGGCCAG 60.812 60.000 2.24 0.00 0.00 4.85
1151 1164 0.462581 CCATCATCTCGGTGGTGGTG 60.463 60.000 1.17 0.00 43.88 4.17
1155 1168 2.515979 ATCTCGGTGGTGGTGTGCA 61.516 57.895 0.00 0.00 0.00 4.57
1179 1192 1.074752 GTTCCTGCTGCTCTTCTTCG 58.925 55.000 0.00 0.00 0.00 3.79
1292 1320 4.572571 AAGCGCGGGTTGGACCAA 62.573 61.111 8.83 1.69 41.02 3.67
1313 1341 4.980805 GTGCTGGCGACGTTCCCA 62.981 66.667 7.74 7.74 0.00 4.37
1314 1342 4.243008 TGCTGGCGACGTTCCCAA 62.243 61.111 9.08 0.00 0.00 4.12
1394 1434 4.269523 TGCCCTGTGTGCCTGACC 62.270 66.667 0.00 0.00 0.00 4.02
1456 1496 4.922026 GCACGTGTTCCACCCGGT 62.922 66.667 18.38 0.00 0.00 5.28
1478 1518 2.064628 CATCGATCCCTGGCTCCAT 58.935 57.895 0.00 0.00 0.00 3.41
1480 1520 0.472543 ATCGATCCCTGGCTCCATCA 60.473 55.000 0.00 0.00 0.00 3.07
1599 1642 1.826024 CACGATGGGAAGGAGGAGG 59.174 63.158 0.00 0.00 0.00 4.30
1600 1643 0.687757 CACGATGGGAAGGAGGAGGA 60.688 60.000 0.00 0.00 0.00 3.71
1613 1662 2.381941 GGAGGAGGCCATGGAGCTT 61.382 63.158 18.40 0.00 0.00 3.74
1653 1702 2.109181 GGGCGGCAAGGCTACTAG 59.891 66.667 12.47 0.00 45.89 2.57
1708 1768 0.176680 GAGCCTTCTGCCATCTCGAA 59.823 55.000 0.00 0.00 42.71 3.71
1724 1784 0.169230 CGAAGAGAGGGAGTCACGTG 59.831 60.000 9.94 9.94 0.00 4.49
1778 1838 5.472137 AGGTTGTTTGCGTGATACTATTTGT 59.528 36.000 0.00 0.00 0.00 2.83
1802 1862 1.944709 GTTCAGCCCAAGTTGTTACGT 59.055 47.619 1.45 0.00 0.00 3.57
1831 1894 0.391793 TGACGGGCATATTTCGCACA 60.392 50.000 0.00 0.00 31.27 4.57
1844 1920 7.744715 GCATATTTCGCACATGTAAAGTATACC 59.255 37.037 0.00 0.00 0.00 2.73
1905 1981 3.012047 TCCTCCCTTGTTAGCTACCAGTA 59.988 47.826 0.00 0.00 0.00 2.74
1917 1993 2.032204 GCTACCAGTACATCCTCGTACG 60.032 54.545 9.53 9.53 45.25 3.67
1925 2001 1.135859 ACATCCTCGTACGTGTCGTTC 60.136 52.381 16.05 0.00 41.54 3.95
1971 2047 2.762535 ACTTGATCGGATTCGTTGGT 57.237 45.000 0.00 0.00 37.69 3.67
1972 2048 3.053831 ACTTGATCGGATTCGTTGGTT 57.946 42.857 0.00 0.00 37.69 3.67
1974 2050 2.753055 TGATCGGATTCGTTGGTTGA 57.247 45.000 0.00 0.00 37.69 3.18
1975 2051 3.046968 TGATCGGATTCGTTGGTTGAA 57.953 42.857 0.00 0.00 37.69 2.69
1987 2063 6.687081 TCGTTGGTTGAACTTGTTTCTATT 57.313 33.333 0.00 0.00 34.97 1.73
2029 2105 9.802039 ATATACCTTGTTAGTCCTTGTTTGAAA 57.198 29.630 0.00 0.00 0.00 2.69
2031 2107 6.863275 ACCTTGTTAGTCCTTGTTTGAAAAG 58.137 36.000 0.00 0.00 0.00 2.27
2033 2109 6.405842 CCTTGTTAGTCCTTGTTTGAAAAGCT 60.406 38.462 0.00 0.00 0.00 3.74
2052 2128 4.071875 GCTTCAAAGAGCTCGTTTAAGG 57.928 45.455 26.81 15.00 39.57 2.69
2053 2129 3.120165 GCTTCAAAGAGCTCGTTTAAGGG 60.120 47.826 26.81 12.38 39.57 3.95
2054 2130 3.053831 TCAAAGAGCTCGTTTAAGGGG 57.946 47.619 12.50 0.70 0.00 4.79
2055 2131 2.635915 TCAAAGAGCTCGTTTAAGGGGA 59.364 45.455 12.50 3.15 0.00 4.81
2056 2132 3.071892 TCAAAGAGCTCGTTTAAGGGGAA 59.928 43.478 12.50 0.00 0.00 3.97
2057 2133 3.336138 AAGAGCTCGTTTAAGGGGAAG 57.664 47.619 8.37 0.00 0.00 3.46
2058 2134 2.537143 AGAGCTCGTTTAAGGGGAAGA 58.463 47.619 8.37 0.00 0.00 2.87
2059 2135 2.904434 AGAGCTCGTTTAAGGGGAAGAA 59.096 45.455 8.37 0.00 0.00 2.52
2060 2136 3.055747 AGAGCTCGTTTAAGGGGAAGAAG 60.056 47.826 8.37 0.00 0.00 2.85
2061 2137 2.027100 AGCTCGTTTAAGGGGAAGAAGG 60.027 50.000 0.00 0.00 0.00 3.46
2062 2138 2.940083 GCTCGTTTAAGGGGAAGAAGGG 60.940 54.545 0.00 0.00 0.00 3.95
2063 2139 1.631898 TCGTTTAAGGGGAAGAAGGGG 59.368 52.381 0.00 0.00 0.00 4.79
2077 2153 2.043526 AGAAGGGGCTTCACCATTTCAT 59.956 45.455 0.00 0.00 42.37 2.57
2084 2160 3.509575 GGCTTCACCATTTCATTACCACA 59.490 43.478 0.00 0.00 38.86 4.17
2124 2200 1.758280 TCACGGCCATCGGTATTACTT 59.242 47.619 2.24 0.00 44.45 2.24
2145 3514 3.508845 TTTCCTCCCTTTTCCTGTCTG 57.491 47.619 0.00 0.00 0.00 3.51
2153 3522 3.195825 CCCTTTTCCTGTCTGTATCGACT 59.804 47.826 0.00 0.00 35.00 4.18
2155 3524 4.425520 CTTTTCCTGTCTGTATCGACTCC 58.574 47.826 0.00 0.00 35.00 3.85
2181 3550 4.941609 GAGAGAATCCAGCGCCAA 57.058 55.556 2.29 0.00 33.66 4.52
2237 3606 0.676466 TTGGTAGTTGCATCTGCCCG 60.676 55.000 24.02 0.00 39.01 6.13
2315 3684 2.519377 ACGTCATTCTTTGGTCGTGA 57.481 45.000 0.00 0.00 35.93 4.35
2351 5034 3.181485 GGTGAGATCTACTCCAGTTTCCG 60.181 52.174 0.00 0.00 44.34 4.30
2417 5100 5.219343 TGCTATGTATCTTGTGGATGAGG 57.781 43.478 0.00 0.00 35.98 3.86
2500 11748 6.237901 TGTGCACATTAAGACCAGATTTAGT 58.762 36.000 17.42 0.00 0.00 2.24
2524 11772 5.075858 ACTTTCATTCGTATCACCGGTTA 57.924 39.130 2.97 0.00 0.00 2.85
2535 11783 5.121142 CGTATCACCGGTTATGAACAAACTT 59.879 40.000 2.97 0.00 0.00 2.66
2583 11831 5.713025 CAATTTGTAGAACCTTGTGGATGG 58.287 41.667 0.00 0.00 37.04 3.51
2611 11859 5.671493 AGGGATGAGTACGAAGGTTTTATG 58.329 41.667 0.00 0.00 0.00 1.90
2612 11860 4.272748 GGGATGAGTACGAAGGTTTTATGC 59.727 45.833 0.00 0.00 0.00 3.14
2619 11867 4.759516 ACGAAGGTTTTATGCGTTTCAT 57.240 36.364 0.00 0.00 39.17 2.57
2620 11868 5.116069 ACGAAGGTTTTATGCGTTTCATT 57.884 34.783 0.00 0.00 36.63 2.57
2669 11917 7.447374 TGTCTTAGTAATTTGGTTCACATGG 57.553 36.000 0.00 0.00 0.00 3.66
2689 11937 4.724399 TGGTTTTCCTACATTGCTTGAGA 58.276 39.130 0.00 0.00 41.38 3.27
2697 11945 5.643777 TCCTACATTGCTTGAGAAAAGTAGC 59.356 40.000 8.10 0.00 34.91 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.529430 ACGTGTGACATTGAAAGACCAAATA 59.471 36.000 0.00 0.00 0.00 1.40
1 2 4.338118 ACGTGTGACATTGAAAGACCAAAT 59.662 37.500 0.00 0.00 0.00 2.32
2 3 3.692101 ACGTGTGACATTGAAAGACCAAA 59.308 39.130 0.00 0.00 0.00 3.28
3 4 3.275143 ACGTGTGACATTGAAAGACCAA 58.725 40.909 0.00 0.00 0.00 3.67
4 5 2.869801 GACGTGTGACATTGAAAGACCA 59.130 45.455 0.00 0.00 0.00 4.02
5 6 2.869801 TGACGTGTGACATTGAAAGACC 59.130 45.455 0.00 0.00 0.00 3.85
6 7 4.270084 TCTTGACGTGTGACATTGAAAGAC 59.730 41.667 0.00 0.00 0.00 3.01
7 8 4.438148 TCTTGACGTGTGACATTGAAAGA 58.562 39.130 0.00 0.00 0.00 2.52
8 9 4.794248 TCTTGACGTGTGACATTGAAAG 57.206 40.909 0.00 0.00 0.00 2.62
9 10 5.056480 AGATCTTGACGTGTGACATTGAAA 58.944 37.500 0.00 0.00 0.00 2.69
10 11 4.631131 AGATCTTGACGTGTGACATTGAA 58.369 39.130 0.00 0.00 0.00 2.69
11 12 4.257267 AGATCTTGACGTGTGACATTGA 57.743 40.909 0.00 0.00 0.00 2.57
12 13 4.377738 CCAAGATCTTGACGTGTGACATTG 60.378 45.833 32.49 10.42 42.93 2.82
13 14 3.748048 CCAAGATCTTGACGTGTGACATT 59.252 43.478 32.49 0.00 42.93 2.71
14 15 3.006859 TCCAAGATCTTGACGTGTGACAT 59.993 43.478 32.49 0.00 42.93 3.06
15 16 2.364002 TCCAAGATCTTGACGTGTGACA 59.636 45.455 32.49 5.70 42.93 3.58
16 17 2.731976 GTCCAAGATCTTGACGTGTGAC 59.268 50.000 32.49 24.50 42.93 3.67
17 18 2.288825 GGTCCAAGATCTTGACGTGTGA 60.289 50.000 32.49 18.68 42.93 3.58
18 19 2.069273 GGTCCAAGATCTTGACGTGTG 58.931 52.381 32.49 16.84 42.93 3.82
19 20 1.002087 GGGTCCAAGATCTTGACGTGT 59.998 52.381 32.49 0.00 42.93 4.49
20 21 1.676014 GGGGTCCAAGATCTTGACGTG 60.676 57.143 32.49 17.84 42.93 4.49
21 22 0.613777 GGGGTCCAAGATCTTGACGT 59.386 55.000 32.49 0.00 42.93 4.34
22 23 0.613260 TGGGGTCCAAGATCTTGACG 59.387 55.000 32.49 18.83 42.93 4.35
23 24 2.040412 AGTTGGGGTCCAAGATCTTGAC 59.960 50.000 32.49 25.63 44.82 3.18
24 25 2.348472 AGTTGGGGTCCAAGATCTTGA 58.652 47.619 32.49 17.73 44.82 3.02
25 26 2.887151 AGTTGGGGTCCAAGATCTTG 57.113 50.000 25.75 25.75 44.82 3.02
26 27 3.916989 ACTAAGTTGGGGTCCAAGATCTT 59.083 43.478 0.88 0.88 44.82 2.40
27 28 3.532102 ACTAAGTTGGGGTCCAAGATCT 58.468 45.455 0.00 0.00 44.82 2.75
28 29 4.224370 TGTACTAAGTTGGGGTCCAAGATC 59.776 45.833 0.00 0.00 44.82 2.75
29 30 4.172807 TGTACTAAGTTGGGGTCCAAGAT 58.827 43.478 0.00 0.00 44.82 2.40
30 31 3.589641 TGTACTAAGTTGGGGTCCAAGA 58.410 45.455 0.00 0.00 44.82 3.02
31 32 4.569719 ATGTACTAAGTTGGGGTCCAAG 57.430 45.455 0.00 0.00 44.82 3.61
32 33 6.328148 CCTATATGTACTAAGTTGGGGTCCAA 59.672 42.308 0.00 0.00 41.69 3.53
33 34 5.842328 CCTATATGTACTAAGTTGGGGTCCA 59.158 44.000 0.00 0.00 0.00 4.02
34 35 6.080009 TCCTATATGTACTAAGTTGGGGTCC 58.920 44.000 0.00 0.00 0.00 4.46
35 36 7.070322 TGTTCCTATATGTACTAAGTTGGGGTC 59.930 40.741 0.00 0.00 0.00 4.46
36 37 6.904654 TGTTCCTATATGTACTAAGTTGGGGT 59.095 38.462 0.00 0.00 0.00 4.95
37 38 7.369551 TGTTCCTATATGTACTAAGTTGGGG 57.630 40.000 0.00 0.00 0.00 4.96
100 101 9.463443 CCGATGTTATGTTCTTTTCTTTTCTTT 57.537 29.630 0.00 0.00 0.00 2.52
101 102 8.846211 TCCGATGTTATGTTCTTTTCTTTTCTT 58.154 29.630 0.00 0.00 0.00 2.52
102 103 8.391075 TCCGATGTTATGTTCTTTTCTTTTCT 57.609 30.769 0.00 0.00 0.00 2.52
103 104 9.626045 ATTCCGATGTTATGTTCTTTTCTTTTC 57.374 29.630 0.00 0.00 0.00 2.29
106 107 9.226606 TGTATTCCGATGTTATGTTCTTTTCTT 57.773 29.630 0.00 0.00 0.00 2.52
107 108 8.786826 TGTATTCCGATGTTATGTTCTTTTCT 57.213 30.769 0.00 0.00 0.00 2.52
108 109 9.438291 CATGTATTCCGATGTTATGTTCTTTTC 57.562 33.333 0.00 0.00 0.00 2.29
109 110 8.405531 CCATGTATTCCGATGTTATGTTCTTTT 58.594 33.333 0.00 0.00 0.00 2.27
110 111 7.556275 ACCATGTATTCCGATGTTATGTTCTTT 59.444 33.333 0.00 0.00 0.00 2.52
111 112 7.054124 ACCATGTATTCCGATGTTATGTTCTT 58.946 34.615 0.00 0.00 0.00 2.52
112 113 6.591935 ACCATGTATTCCGATGTTATGTTCT 58.408 36.000 0.00 0.00 0.00 3.01
113 114 6.706270 AGACCATGTATTCCGATGTTATGTTC 59.294 38.462 0.00 0.00 0.00 3.18
114 115 6.591935 AGACCATGTATTCCGATGTTATGTT 58.408 36.000 0.00 0.00 0.00 2.71
115 116 6.174720 AGACCATGTATTCCGATGTTATGT 57.825 37.500 0.00 0.00 0.00 2.29
116 117 6.311445 GCTAGACCATGTATTCCGATGTTATG 59.689 42.308 0.00 0.00 0.00 1.90
117 118 6.398918 GCTAGACCATGTATTCCGATGTTAT 58.601 40.000 0.00 0.00 0.00 1.89
118 119 5.279306 GGCTAGACCATGTATTCCGATGTTA 60.279 44.000 0.00 0.00 38.86 2.41
119 120 4.503296 GGCTAGACCATGTATTCCGATGTT 60.503 45.833 0.00 0.00 38.86 2.71
120 121 3.006967 GGCTAGACCATGTATTCCGATGT 59.993 47.826 0.00 0.00 38.86 3.06
121 122 3.589988 GGCTAGACCATGTATTCCGATG 58.410 50.000 0.00 0.00 38.86 3.84
122 123 2.231478 CGGCTAGACCATGTATTCCGAT 59.769 50.000 0.00 0.00 39.03 4.18
123 124 1.611977 CGGCTAGACCATGTATTCCGA 59.388 52.381 0.00 0.00 39.03 4.55
124 125 1.935300 GCGGCTAGACCATGTATTCCG 60.935 57.143 0.00 0.00 39.03 4.30
125 126 1.797025 GCGGCTAGACCATGTATTCC 58.203 55.000 0.00 0.00 39.03 3.01
126 127 1.419374 CGCGGCTAGACCATGTATTC 58.581 55.000 0.00 0.00 39.03 1.75
127 128 0.600255 GCGCGGCTAGACCATGTATT 60.600 55.000 8.83 0.00 39.03 1.89
128 129 1.006102 GCGCGGCTAGACCATGTAT 60.006 57.895 8.83 0.00 39.03 2.29
129 130 1.950973 TTGCGCGGCTAGACCATGTA 61.951 55.000 8.83 0.00 39.03 2.29
130 131 2.796483 TTTGCGCGGCTAGACCATGT 62.796 55.000 8.83 0.00 39.03 3.21
131 132 1.439353 ATTTGCGCGGCTAGACCATG 61.439 55.000 8.83 0.00 39.03 3.66
132 133 1.153168 ATTTGCGCGGCTAGACCAT 60.153 52.632 8.83 0.00 39.03 3.55
133 134 2.106074 CATTTGCGCGGCTAGACCA 61.106 57.895 8.83 0.00 39.03 4.02
134 135 2.106683 ACATTTGCGCGGCTAGACC 61.107 57.895 8.83 0.00 0.00 3.85
135 136 1.060937 CACATTTGCGCGGCTAGAC 59.939 57.895 8.83 0.00 0.00 2.59
136 137 2.749865 GCACATTTGCGCGGCTAGA 61.750 57.895 8.83 0.00 39.50 2.43
137 138 2.277501 GCACATTTGCGCGGCTAG 60.278 61.111 8.83 0.00 39.50 3.42
145 146 0.596082 AGGGTAACACGCACATTTGC 59.404 50.000 0.00 0.00 42.22 3.68
146 147 1.665735 GCAGGGTAACACGCACATTTG 60.666 52.381 0.00 0.00 39.74 2.32
147 148 0.596082 GCAGGGTAACACGCACATTT 59.404 50.000 0.00 0.00 39.74 2.32
148 149 0.250727 AGCAGGGTAACACGCACATT 60.251 50.000 0.00 0.00 39.74 2.71
149 150 0.611200 TAGCAGGGTAACACGCACAT 59.389 50.000 0.00 0.00 39.74 3.21
150 151 0.037697 CTAGCAGGGTAACACGCACA 60.038 55.000 0.00 0.00 39.74 4.57
151 152 0.037605 ACTAGCAGGGTAACACGCAC 60.038 55.000 0.00 0.00 39.74 5.34
152 153 0.682852 AACTAGCAGGGTAACACGCA 59.317 50.000 0.00 0.00 39.74 5.24
153 154 1.337447 TGAACTAGCAGGGTAACACGC 60.337 52.381 0.00 0.00 39.74 5.34
154 155 2.736144 TGAACTAGCAGGGTAACACG 57.264 50.000 0.00 0.00 39.74 4.49
155 156 3.939066 ACATGAACTAGCAGGGTAACAC 58.061 45.455 0.00 0.00 39.74 3.32
156 157 4.634012 AACATGAACTAGCAGGGTAACA 57.366 40.909 0.00 0.00 39.74 2.41
157 158 5.484715 TGTAACATGAACTAGCAGGGTAAC 58.515 41.667 0.00 0.00 0.00 2.50
158 159 5.748670 TGTAACATGAACTAGCAGGGTAA 57.251 39.130 0.00 0.00 0.00 2.85
159 160 5.661312 AGATGTAACATGAACTAGCAGGGTA 59.339 40.000 0.00 0.00 0.00 3.69
160 161 4.471386 AGATGTAACATGAACTAGCAGGGT 59.529 41.667 0.00 0.00 0.00 4.34
161 162 5.028549 AGATGTAACATGAACTAGCAGGG 57.971 43.478 0.00 0.00 0.00 4.45
162 163 6.108687 TGAAGATGTAACATGAACTAGCAGG 58.891 40.000 0.00 0.00 0.00 4.85
163 164 7.601073 TTGAAGATGTAACATGAACTAGCAG 57.399 36.000 0.00 0.00 0.00 4.24
164 165 7.977789 TTTGAAGATGTAACATGAACTAGCA 57.022 32.000 0.00 0.00 0.00 3.49
165 166 8.668353 TGATTTGAAGATGTAACATGAACTAGC 58.332 33.333 0.00 0.00 0.00 3.42
295 296 5.055642 TCACCGCTATTAGATTCATACCG 57.944 43.478 0.00 0.00 0.00 4.02
311 312 0.389948 AGAGGATCGTTGTTCACCGC 60.390 55.000 0.00 0.00 42.67 5.68
316 317 4.752101 CCATCCATAAGAGGATCGTTGTTC 59.248 45.833 0.00 0.00 45.16 3.18
323 324 3.883669 GGATGCCATCCATAAGAGGATC 58.116 50.000 18.99 0.00 45.16 3.36
377 378 4.368315 CGGTATCTTTCATTCGACCATGA 58.632 43.478 0.00 0.00 0.00 3.07
382 383 4.593597 TTTGCGGTATCTTTCATTCGAC 57.406 40.909 0.00 0.00 0.00 4.20
389 390 3.542310 GCATTCGTTTTGCGGTATCTTTC 59.458 43.478 0.00 0.00 41.72 2.62
390 391 3.498082 GCATTCGTTTTGCGGTATCTTT 58.502 40.909 0.00 0.00 41.72 2.52
434 437 5.888161 CCTATCAAGTTTGAGGGTTGCTATT 59.112 40.000 0.74 0.00 41.08 1.73
452 455 7.942341 AGAAAATAAATAATCACGGGCCTATCA 59.058 33.333 0.84 0.00 0.00 2.15
480 483 0.389817 CTTCCGTGACGCATTCCAGA 60.390 55.000 0.00 0.00 0.00 3.86
490 493 0.595095 ACGTACCTGTCTTCCGTGAC 59.405 55.000 0.00 0.00 37.47 3.67
527 530 3.034721 TCAAGTGGTATGTCGTTGGAC 57.965 47.619 0.00 0.00 43.71 4.02
541 544 3.849911 TGACCGAAGCTAAGATCAAGTG 58.150 45.455 0.00 0.00 0.00 3.16
562 565 5.596836 ACACAACACAAAATCAACCTGAT 57.403 34.783 0.00 0.00 39.09 2.90
580 583 1.728068 AACAACACACAGCGTACACA 58.272 45.000 0.00 0.00 0.00 3.72
647 650 3.696051 ACTTGTTGGATGATGCCATACAC 59.304 43.478 0.00 0.00 43.04 2.90
666 669 2.305052 GTCCTGCCTAGGTTTGGTACTT 59.695 50.000 11.31 0.00 44.88 2.24
690 693 6.787515 CGCAATGATGTCGTGAAAGATATTAC 59.212 38.462 0.00 0.00 0.00 1.89
717 720 5.633927 CATGTGTTGACATTTCGATGATGT 58.366 37.500 13.01 13.01 41.12 3.06
750 753 2.936993 GCAGCTTTAGACTAGCTTGCCA 60.937 50.000 0.00 0.00 46.42 4.92
784 788 6.155221 GGTCCATCTCCATATTCTGCACTATA 59.845 42.308 0.00 0.00 0.00 1.31
788 792 3.181451 TGGTCCATCTCCATATTCTGCAC 60.181 47.826 0.00 0.00 0.00 4.57
817 821 0.242825 TCGTCTGTAGCCTTTCGGTG 59.757 55.000 0.00 0.00 0.00 4.94
834 838 2.827051 CGGATGGTGCATGGCTTCG 61.827 63.158 0.00 0.00 0.00 3.79
850 854 4.212636 ACTTGGAAAAACAATACTCGTCGG 59.787 41.667 0.00 0.00 0.00 4.79
882 886 4.669318 CTTGCGATACTCGTTCTAAGGAA 58.331 43.478 0.00 0.00 42.81 3.36
885 889 3.696898 AGCTTGCGATACTCGTTCTAAG 58.303 45.455 0.00 0.00 42.81 2.18
890 894 2.263077 CAGAAGCTTGCGATACTCGTT 58.737 47.619 2.10 0.00 42.81 3.85
933 937 9.136323 TCGATGGGATACTACTATAGTACGATA 57.864 37.037 8.59 2.97 43.46 2.92
934 938 7.925483 GTCGATGGGATACTACTATAGTACGAT 59.075 40.741 8.59 5.19 43.46 3.73
935 939 7.093771 TGTCGATGGGATACTACTATAGTACGA 60.094 40.741 8.59 9.79 43.46 3.43
936 940 7.009999 GTGTCGATGGGATACTACTATAGTACG 59.990 44.444 8.59 7.76 43.46 3.67
937 941 7.279758 GGTGTCGATGGGATACTACTATAGTAC 59.720 44.444 8.59 0.00 43.46 2.73
938 942 7.334090 GGTGTCGATGGGATACTACTATAGTA 58.666 42.308 12.05 12.05 44.64 1.82
939 943 6.179040 GGTGTCGATGGGATACTACTATAGT 58.821 44.000 10.87 10.87 42.68 2.12
940 944 5.589452 GGGTGTCGATGGGATACTACTATAG 59.411 48.000 0.00 0.00 37.00 1.31
997 1001 0.109723 AGAACAGGGCGGCAAACTAA 59.890 50.000 12.47 0.00 0.00 2.24
1008 1012 2.947652 CCATCAGTATGCAAGAACAGGG 59.052 50.000 0.00 0.00 34.76 4.45
1024 1028 3.404869 AGTCTCCCATCACTACCATCA 57.595 47.619 0.00 0.00 0.00 3.07
1040 1044 1.437772 CGACGGCGATGAGGTAGTCT 61.438 60.000 16.62 0.00 40.82 3.24
1044 1048 3.896133 GCCGACGGCGATGAGGTA 61.896 66.667 25.24 0.00 39.62 3.08
1126 1139 0.249073 CACCGAGATGATGGTCGACC 60.249 60.000 28.17 28.17 38.50 4.79
1155 1168 2.239150 AGAAGAGCAGCAGGAACATGAT 59.761 45.455 0.00 0.00 0.00 2.45
1179 1192 2.112815 GCCTGTTCATGTACCCGCC 61.113 63.158 0.00 0.00 0.00 6.13
1292 1320 4.373116 AACGTCGCCAGCACCGAT 62.373 61.111 5.13 0.00 37.04 4.18
1313 1341 1.224592 GTCCCTCCACGGCATGATT 59.775 57.895 0.00 0.00 0.00 2.57
1314 1342 2.746375 GGTCCCTCCACGGCATGAT 61.746 63.158 0.00 0.00 35.97 2.45
1339 1367 0.462759 CACCATCGCCCTCTTCTTCC 60.463 60.000 0.00 0.00 0.00 3.46
1382 1422 4.539083 AACGCGGTCAGGCACACA 62.539 61.111 12.47 0.00 0.00 3.72
1402 1442 2.636412 CGGAGACTGTCGCCTTCCA 61.636 63.158 24.80 0.00 33.90 3.53
1456 1496 2.190313 GCCAGGGATCGATGCACA 59.810 61.111 19.14 0.00 0.00 4.57
1544 1584 1.067283 CCCTCTGCTGATATCGCGATT 60.067 52.381 28.81 14.94 0.00 3.34
1599 1642 0.473326 ATCTCAAGCTCCATGGCCTC 59.527 55.000 6.96 0.00 0.00 4.70
1600 1643 0.183014 CATCTCAAGCTCCATGGCCT 59.817 55.000 6.96 2.54 0.00 5.19
1643 1692 3.537874 CCCGCCGCTAGTAGCCTT 61.538 66.667 16.51 0.00 38.18 4.35
1694 1754 1.753649 CCTCTCTTCGAGATGGCAGAA 59.246 52.381 0.00 0.00 42.62 3.02
1698 1758 0.673437 CTCCCTCTCTTCGAGATGGC 59.327 60.000 9.49 0.00 41.90 4.40
1702 1762 1.676314 CGTGACTCCCTCTCTTCGAGA 60.676 57.143 0.00 0.00 42.62 4.04
1704 1764 0.036448 ACGTGACTCCCTCTCTTCGA 59.964 55.000 0.00 0.00 0.00 3.71
1708 1768 2.336478 CGCACGTGACTCCCTCTCT 61.336 63.158 22.23 0.00 0.00 3.10
1724 1784 2.181021 CTCCTCCCACGTGTACGC 59.819 66.667 15.65 0.00 44.43 4.42
1762 1822 6.960468 TGAACAAAACAAATAGTATCACGCA 58.040 32.000 0.00 0.00 0.00 5.24
1778 1838 3.971245 AACAACTTGGGCTGAACAAAA 57.029 38.095 0.00 0.00 0.00 2.44
1802 1862 6.457663 CGAAATATGCCCGTCAAATAGTTTGA 60.458 38.462 1.24 1.24 46.68 2.69
1821 1884 8.719560 TTGGTATACTTTACATGTGCGAAATA 57.280 30.769 9.11 0.00 0.00 1.40
1844 1920 3.066760 GGAGGAAAAGGCAATACCGATTG 59.933 47.826 0.00 0.00 46.52 2.67
1893 1969 3.894759 ACGAGGATGTACTGGTAGCTAA 58.105 45.455 0.00 0.00 0.00 3.09
1905 1981 0.877071 AACGACACGTACGAGGATGT 59.123 50.000 24.41 15.77 39.99 3.06
1947 2023 4.083537 CCAACGAATCCGATCAAGTTTTGA 60.084 41.667 0.00 0.00 40.77 2.69
1953 2029 3.000041 TCAACCAACGAATCCGATCAAG 59.000 45.455 0.00 0.00 39.50 3.02
2031 2107 3.120165 CCCTTAAACGAGCTCTTTGAAGC 60.120 47.826 20.06 0.00 42.82 3.86
2033 2109 3.071892 TCCCCTTAAACGAGCTCTTTGAA 59.928 43.478 12.85 7.37 0.00 2.69
2047 2123 1.639108 GAAGCCCCTTCTTCCCCTTAA 59.361 52.381 0.00 0.00 37.49 1.85
2048 2124 1.296002 GAAGCCCCTTCTTCCCCTTA 58.704 55.000 0.00 0.00 37.49 2.69
2049 2125 0.776080 TGAAGCCCCTTCTTCCCCTT 60.776 55.000 6.54 0.00 41.23 3.95
2050 2126 1.151587 TGAAGCCCCTTCTTCCCCT 60.152 57.895 6.54 0.00 41.23 4.79
2051 2127 1.000771 GTGAAGCCCCTTCTTCCCC 60.001 63.158 6.54 0.00 41.23 4.81
2052 2128 1.000771 GGTGAAGCCCCTTCTTCCC 60.001 63.158 6.54 1.30 41.23 3.97
2053 2129 0.332972 ATGGTGAAGCCCCTTCTTCC 59.667 55.000 6.54 8.83 41.23 3.46
2054 2130 2.222227 AATGGTGAAGCCCCTTCTTC 57.778 50.000 6.54 0.00 40.73 2.87
2055 2131 2.158325 TGAAATGGTGAAGCCCCTTCTT 60.158 45.455 6.54 0.00 40.73 2.52
2056 2132 1.428912 TGAAATGGTGAAGCCCCTTCT 59.571 47.619 6.54 0.00 40.73 2.85
2057 2133 1.923356 TGAAATGGTGAAGCCCCTTC 58.077 50.000 0.00 0.00 40.54 3.46
2058 2134 2.629017 ATGAAATGGTGAAGCCCCTT 57.371 45.000 0.00 0.00 36.04 3.95
2059 2135 2.629017 AATGAAATGGTGAAGCCCCT 57.371 45.000 0.00 0.00 36.04 4.79
2060 2136 2.430694 GGTAATGAAATGGTGAAGCCCC 59.569 50.000 0.00 0.00 36.04 5.80
2061 2137 3.096092 TGGTAATGAAATGGTGAAGCCC 58.904 45.455 0.00 0.00 36.04 5.19
2062 2138 3.509575 TGTGGTAATGAAATGGTGAAGCC 59.490 43.478 0.00 0.00 37.90 4.35
2063 2139 4.218417 AGTGTGGTAATGAAATGGTGAAGC 59.782 41.667 0.00 0.00 0.00 3.86
2077 2153 5.232463 GTGATTTTCGGTAGAGTGTGGTAA 58.768 41.667 0.00 0.00 0.00 2.85
2084 2160 2.667473 CCGGTGATTTTCGGTAGAGT 57.333 50.000 0.00 0.00 41.23 3.24
2106 2182 2.994186 AAAGTAATACCGATGGCCGT 57.006 45.000 0.00 0.00 36.31 5.68
2124 2200 3.204382 ACAGACAGGAAAAGGGAGGAAAA 59.796 43.478 0.00 0.00 0.00 2.29
2145 3514 1.337071 TCCGCTTGATGGAGTCGATAC 59.663 52.381 0.00 0.00 0.00 2.24
2153 3522 1.414181 GGATTCTCTCCGCTTGATGGA 59.586 52.381 0.00 0.00 33.29 3.41
2181 3550 2.034879 CGCAACAAGATGCCGACCT 61.035 57.895 0.00 0.00 43.47 3.85
2210 3579 6.433766 GCAGATGCAACTACCAAATTAGATC 58.566 40.000 0.00 0.00 41.59 2.75
2218 3587 0.676466 CGGGCAGATGCAACTACCAA 60.676 55.000 14.64 0.00 44.36 3.67
2281 3650 4.470876 CGTATCACGTGCCGAGTT 57.529 55.556 11.67 0.00 36.74 3.01
2293 3662 4.031426 GTCACGACCAAAGAATGACGTATC 59.969 45.833 0.00 0.00 38.82 2.24
2294 3663 3.924686 GTCACGACCAAAGAATGACGTAT 59.075 43.478 0.00 0.00 38.82 3.06
2296 3665 2.132762 GTCACGACCAAAGAATGACGT 58.867 47.619 0.00 0.00 40.42 4.34
2351 5034 9.161684 ACAATAAAAATAACTCGTCGACAAAAC 57.838 29.630 17.16 0.00 0.00 2.43
2386 5069 9.290988 TCCACAAGATACATAGCAAACTAAAAA 57.709 29.630 0.00 0.00 30.45 1.94
2462 11710 8.686397 TTAATGTGCACAAATAACATGCTAAG 57.314 30.769 25.72 0.00 40.13 2.18
2500 11748 5.075858 ACCGGTGATACGAATGAAAGTTA 57.924 39.130 6.12 0.00 35.47 2.24
2508 11756 5.013568 TGTTCATAACCGGTGATACGAAT 57.986 39.130 8.52 0.00 35.47 3.34
2524 11772 8.006298 TCAACAAGGTTCATAAGTTTGTTCAT 57.994 30.769 0.00 0.00 39.25 2.57
2535 11783 6.127647 GCCTTTCATCATCAACAAGGTTCATA 60.128 38.462 0.00 0.00 37.02 2.15
2583 11831 3.056035 ACCTTCGTACTCATCCCTTTCAC 60.056 47.826 0.00 0.00 0.00 3.18
2649 11897 8.145122 GGAAAACCATGTGAACCAAATTACTAA 58.855 33.333 0.00 0.00 0.00 2.24
2669 11917 7.203218 ACTTTTCTCAAGCAATGTAGGAAAAC 58.797 34.615 0.00 0.00 33.88 2.43
2765 12013 5.487153 TGCTTGTTTGCTAAAAACGTAGA 57.513 34.783 0.00 0.00 33.05 2.59
2766 12014 5.685511 ACATGCTTGTTTGCTAAAAACGTAG 59.314 36.000 0.00 0.00 29.55 3.51
2768 12016 4.429108 ACATGCTTGTTTGCTAAAAACGT 58.571 34.783 0.00 0.00 29.55 3.99
2769 12017 5.231991 AGAACATGCTTGTTTGCTAAAAACG 59.768 36.000 17.99 0.00 46.01 3.60
2770 12018 6.588348 AGAACATGCTTGTTTGCTAAAAAC 57.412 33.333 17.99 3.71 46.01 2.43
2771 12019 6.416455 CGTAGAACATGCTTGTTTGCTAAAAA 59.584 34.615 17.99 0.00 46.01 1.94
2774 12028 4.513692 ACGTAGAACATGCTTGTTTGCTAA 59.486 37.500 17.99 1.85 46.01 3.09


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

AutoCloner maintained by Alex Coulton.