Multiple sequence alignment - TraesCS3D01G421300

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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 TraesCS3D01G421300 chr3D 100.000 4495 0 0 1 4495 533722741 533727235 0.000000e+00 8301.0
1 TraesCS3D01G421300 chr3D 90.504 853 63 9 3651 4495 506169993 506170835 0.000000e+00 1110.0
2 TraesCS3D01G421300 chr3A 91.678 2307 77 33 1417 3646 669602360 669604628 0.000000e+00 3090.0
3 TraesCS3D01G421300 chr3A 89.231 1170 93 15 124 1277 669601204 669602356 0.000000e+00 1432.0
4 TraesCS3D01G421300 chr3A 95.775 142 4 2 1286 1425 643281395 643281536 1.260000e-55 228.0
5 TraesCS3D01G421300 chr3A 91.139 79 7 0 2034 2112 669603052 669603130 1.710000e-19 108.0
6 TraesCS3D01G421300 chr3B 95.924 1472 49 6 2034 3505 705589282 705590742 0.000000e+00 2375.0
7 TraesCS3D01G421300 chr3B 89.013 892 59 19 125 997 705587597 705588468 0.000000e+00 1068.0
8 TraesCS3D01G421300 chr3B 90.660 621 39 9 1538 2154 705588755 705589360 0.000000e+00 808.0
9 TraesCS3D01G421300 chr3B 84.889 225 15 8 3444 3652 705591841 705592062 4.560000e-50 209.0
10 TraesCS3D01G421300 chr3B 96.000 50 2 0 2063 2112 705589353 705589402 1.040000e-11 82.4
11 TraesCS3D01G421300 chr5B 90.962 852 66 7 3653 4495 642345247 642346096 0.000000e+00 1136.0
12 TraesCS3D01G421300 chr5B 90.129 851 74 6 3654 4495 642009353 642008504 0.000000e+00 1098.0
13 TraesCS3D01G421300 chr4D 88.070 855 92 5 3650 4495 450647913 450647060 0.000000e+00 1005.0
14 TraesCS3D01G421300 chr4D 81.000 800 137 14 3650 4442 503508168 503508959 4.940000e-174 621.0
15 TraesCS3D01G421300 chr1D 81.839 859 137 13 3650 4495 31907207 31908059 0.000000e+00 704.0
16 TraesCS3D01G421300 chr6B 80.168 832 140 23 3650 4468 508601798 508600979 2.310000e-167 599.0
17 TraesCS3D01G421300 chr6B 79.710 828 151 14 3650 4468 670908976 670908157 2.330000e-162 582.0
18 TraesCS3D01G421300 chr6B 92.647 136 9 1 1288 1422 663547312 663547177 1.280000e-45 195.0
19 TraesCS3D01G421300 chr6B 91.111 135 10 2 1288 1421 31958842 31958709 9.930000e-42 182.0
20 TraesCS3D01G421300 chr2A 79.783 831 148 16 3648 4468 630741780 630742600 1.800000e-163 586.0
21 TraesCS3D01G421300 chr2A 91.603 131 10 1 1288 1417 205193498 205193368 3.570000e-41 180.0
22 TraesCS3D01G421300 chr5A 90.345 145 12 2 1279 1422 104977122 104976979 5.940000e-44 189.0
23 TraesCS3D01G421300 chr7B 91.304 138 11 1 1286 1422 542985562 542985699 2.130000e-43 187.0
24 TraesCS3D01G421300 chr1B 91.304 138 11 1 1286 1422 522748807 522748670 2.130000e-43 187.0
25 TraesCS3D01G421300 chr6A 91.603 131 10 1 1288 1417 586992310 586992440 3.570000e-41 180.0
26 TraesCS3D01G421300 chr1A 90.441 136 11 2 1288 1422 108916721 108916587 1.280000e-40 178.0


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 TraesCS3D01G421300 chr3D 533722741 533727235 4494 False 8301.000000 8301 100.000000 1 4495 1 chr3D.!!$F2 4494
1 TraesCS3D01G421300 chr3D 506169993 506170835 842 False 1110.000000 1110 90.504000 3651 4495 1 chr3D.!!$F1 844
2 TraesCS3D01G421300 chr3A 669601204 669604628 3424 False 1543.333333 3090 90.682667 124 3646 3 chr3A.!!$F2 3522
3 TraesCS3D01G421300 chr3B 705587597 705592062 4465 False 908.480000 2375 91.297200 125 3652 5 chr3B.!!$F1 3527
4 TraesCS3D01G421300 chr5B 642345247 642346096 849 False 1136.000000 1136 90.962000 3653 4495 1 chr5B.!!$F1 842
5 TraesCS3D01G421300 chr5B 642008504 642009353 849 True 1098.000000 1098 90.129000 3654 4495 1 chr5B.!!$R1 841
6 TraesCS3D01G421300 chr4D 450647060 450647913 853 True 1005.000000 1005 88.070000 3650 4495 1 chr4D.!!$R1 845
7 TraesCS3D01G421300 chr4D 503508168 503508959 791 False 621.000000 621 81.000000 3650 4442 1 chr4D.!!$F1 792
8 TraesCS3D01G421300 chr1D 31907207 31908059 852 False 704.000000 704 81.839000 3650 4495 1 chr1D.!!$F1 845
9 TraesCS3D01G421300 chr6B 508600979 508601798 819 True 599.000000 599 80.168000 3650 4468 1 chr6B.!!$R2 818
10 TraesCS3D01G421300 chr6B 670908157 670908976 819 True 582.000000 582 79.710000 3650 4468 1 chr6B.!!$R4 818
11 TraesCS3D01G421300 chr2A 630741780 630742600 820 False 586.000000 586 79.783000 3648 4468 1 chr2A.!!$F1 820

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
585 611 0.040157 TCCGTTACGTCTCGGTTGTG 60.040 55.0 23.69 5.56 45.88 3.33 F
1335 1373 0.032615 AGTGGTTTGGCAGGGTTTGA 60.033 50.0 0.00 0.00 0.00 2.69 F
1387 1425 0.033109 CCAAATCCCCTCCAACCCTC 60.033 60.0 0.00 0.00 0.00 4.30 F
1413 1451 0.037605 AGAGGCGTAACCGAACAAGG 60.038 55.0 0.00 0.00 46.52 3.61 F
2189 2318 0.109504 GCGAGGTCAGTCAGTCAGTC 60.110 60.0 0.00 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1838 1896 0.025001 GTGACGCGAAATGTGATCGG 59.975 55.000 15.93 0.0 40.54 4.18 R
2232 2361 0.317269 CACTGGTTCTGCAAGCAACG 60.317 55.000 0.00 0.0 39.51 4.10 R
3026 3156 0.669318 CGCAGTACCCGAGCTTGAAA 60.669 55.000 1.22 0.0 0.00 2.69 R
3063 3193 2.202388 GACGATGCCGACGTTCGA 60.202 61.111 13.09 0.0 43.74 3.71 R
4135 5478 0.460284 CGAAGGGTGGGTGAAGATCG 60.460 60.000 0.00 0.0 0.00 3.69 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
37 38 8.538409 AAAAGATAAAAATGACACCTCATTGC 57.462 30.769 0.00 0.00 44.93 3.56
38 39 6.839124 AGATAAAAATGACACCTCATTGCA 57.161 33.333 0.00 0.00 44.93 4.08
39 40 7.414222 AGATAAAAATGACACCTCATTGCAT 57.586 32.000 0.00 0.00 44.93 3.96
40 41 7.486647 AGATAAAAATGACACCTCATTGCATC 58.513 34.615 0.00 2.00 44.93 3.91
41 42 5.733620 AAAAATGACACCTCATTGCATCT 57.266 34.783 0.00 0.00 44.93 2.90
42 43 4.978083 AAATGACACCTCATTGCATCTC 57.022 40.909 0.00 0.00 44.93 2.75
43 44 3.928005 ATGACACCTCATTGCATCTCT 57.072 42.857 0.00 0.00 32.79 3.10
44 45 3.708403 TGACACCTCATTGCATCTCTT 57.292 42.857 0.00 0.00 0.00 2.85
45 46 3.603532 TGACACCTCATTGCATCTCTTC 58.396 45.455 0.00 0.00 0.00 2.87
46 47 3.262660 TGACACCTCATTGCATCTCTTCT 59.737 43.478 0.00 0.00 0.00 2.85
47 48 4.260170 GACACCTCATTGCATCTCTTCTT 58.740 43.478 0.00 0.00 0.00 2.52
48 49 5.046376 TGACACCTCATTGCATCTCTTCTTA 60.046 40.000 0.00 0.00 0.00 2.10
49 50 5.999044 ACACCTCATTGCATCTCTTCTTAT 58.001 37.500 0.00 0.00 0.00 1.73
50 51 6.421485 ACACCTCATTGCATCTCTTCTTATT 58.579 36.000 0.00 0.00 0.00 1.40
51 52 7.568349 ACACCTCATTGCATCTCTTCTTATTA 58.432 34.615 0.00 0.00 0.00 0.98
52 53 8.049117 ACACCTCATTGCATCTCTTCTTATTAA 58.951 33.333 0.00 0.00 0.00 1.40
53 54 8.341173 CACCTCATTGCATCTCTTCTTATTAAC 58.659 37.037 0.00 0.00 0.00 2.01
54 55 8.049117 ACCTCATTGCATCTCTTCTTATTAACA 58.951 33.333 0.00 0.00 0.00 2.41
55 56 8.896744 CCTCATTGCATCTCTTCTTATTAACAA 58.103 33.333 0.00 0.00 0.00 2.83
93 94 5.371115 AGAACCAATAAAACATGACCACG 57.629 39.130 0.00 0.00 0.00 4.94
94 95 5.067273 AGAACCAATAAAACATGACCACGA 58.933 37.500 0.00 0.00 0.00 4.35
95 96 5.181245 AGAACCAATAAAACATGACCACGAG 59.819 40.000 0.00 0.00 0.00 4.18
96 97 4.647611 ACCAATAAAACATGACCACGAGA 58.352 39.130 0.00 0.00 0.00 4.04
97 98 5.067273 ACCAATAAAACATGACCACGAGAA 58.933 37.500 0.00 0.00 0.00 2.87
98 99 5.710099 ACCAATAAAACATGACCACGAGAAT 59.290 36.000 0.00 0.00 0.00 2.40
99 100 6.128007 ACCAATAAAACATGACCACGAGAATC 60.128 38.462 0.00 0.00 0.00 2.52
100 101 6.258160 CAATAAAACATGACCACGAGAATCC 58.742 40.000 0.00 0.00 0.00 3.01
101 102 3.703001 AAACATGACCACGAGAATCCT 57.297 42.857 0.00 0.00 0.00 3.24
102 103 3.703001 AACATGACCACGAGAATCCTT 57.297 42.857 0.00 0.00 0.00 3.36
103 104 4.819105 AACATGACCACGAGAATCCTTA 57.181 40.909 0.00 0.00 0.00 2.69
104 105 4.819105 ACATGACCACGAGAATCCTTAA 57.181 40.909 0.00 0.00 0.00 1.85
105 106 5.160607 ACATGACCACGAGAATCCTTAAA 57.839 39.130 0.00 0.00 0.00 1.52
106 107 4.935808 ACATGACCACGAGAATCCTTAAAC 59.064 41.667 0.00 0.00 0.00 2.01
107 108 3.934068 TGACCACGAGAATCCTTAAACC 58.066 45.455 0.00 0.00 0.00 3.27
108 109 3.581332 TGACCACGAGAATCCTTAAACCT 59.419 43.478 0.00 0.00 0.00 3.50
109 110 4.182339 GACCACGAGAATCCTTAAACCTC 58.818 47.826 0.00 0.00 0.00 3.85
110 111 3.055312 ACCACGAGAATCCTTAAACCTCC 60.055 47.826 0.00 0.00 0.00 4.30
111 112 3.187700 CACGAGAATCCTTAAACCTCCG 58.812 50.000 0.00 0.00 0.00 4.63
112 113 2.830321 ACGAGAATCCTTAAACCTCCGT 59.170 45.455 0.00 0.00 0.00 4.69
113 114 3.260128 ACGAGAATCCTTAAACCTCCGTT 59.740 43.478 0.00 0.00 0.00 4.44
114 115 4.251268 CGAGAATCCTTAAACCTCCGTTT 58.749 43.478 0.00 0.00 44.44 3.60
115 116 5.047092 ACGAGAATCCTTAAACCTCCGTTTA 60.047 40.000 0.00 0.00 42.29 2.01
116 117 5.870978 CGAGAATCCTTAAACCTCCGTTTAA 59.129 40.000 7.68 7.68 47.00 1.52
205 206 1.607148 GTAAGAATGCAATACCGCCCC 59.393 52.381 0.00 0.00 0.00 5.80
275 277 8.940397 AAAATATCCCTCCATTACCATTACTG 57.060 34.615 0.00 0.00 0.00 2.74
279 281 3.496870 CCCTCCATTACCATTACTGCTCC 60.497 52.174 0.00 0.00 0.00 4.70
393 397 4.933064 CGCCTCCGATCACGAGCC 62.933 72.222 0.00 0.00 42.66 4.70
395 399 2.835431 CCTCCGATCACGAGCCCT 60.835 66.667 0.00 0.00 42.66 5.19
396 400 2.427245 CCTCCGATCACGAGCCCTT 61.427 63.158 0.00 0.00 42.66 3.95
492 511 2.972625 TGGTAAGCCGTTCTTGATCTG 58.027 47.619 0.00 0.00 36.25 2.90
576 602 1.203052 TGGATGGAGTTCCGTTACGTC 59.797 52.381 3.52 0.00 38.74 4.34
582 608 0.954452 AGTTCCGTTACGTCTCGGTT 59.046 50.000 23.69 12.60 45.88 4.44
583 609 1.055338 GTTCCGTTACGTCTCGGTTG 58.945 55.000 23.69 6.13 45.88 3.77
585 611 0.040157 TCCGTTACGTCTCGGTTGTG 60.040 55.000 23.69 5.56 45.88 3.33
671 699 1.635663 GCCGAGTCGTTGGGTTCATG 61.636 60.000 12.31 0.00 0.00 3.07
725 753 3.382832 CCGAGCTCGTGGGTTCCT 61.383 66.667 32.41 0.00 37.74 3.36
727 755 2.266055 GAGCTCGTGGGTTCCTGG 59.734 66.667 0.00 0.00 0.00 4.45
757 785 2.048597 TTGTCAGAATCCGCGCGT 60.049 55.556 29.95 10.71 0.00 6.01
792 826 0.598680 GAGGTGATGATTCGCGGAGG 60.599 60.000 6.13 0.00 32.95 4.30
802 836 1.632046 TTCGCGGAGGATTGTTTCGC 61.632 55.000 6.13 0.00 42.51 4.70
820 854 1.466866 CGCGTCGTCTTCTTGTATGGA 60.467 52.381 0.00 0.00 0.00 3.41
825 859 4.027621 CGTCGTCTTCTTGTATGGAATTCG 60.028 45.833 0.00 0.00 0.00 3.34
848 882 4.797471 CTGAATTGCGTTCAAGATTGGAA 58.203 39.130 5.93 0.00 45.74 3.53
874 909 4.253685 TGGAATTCTCGGAATCAACTGTC 58.746 43.478 5.23 0.00 0.00 3.51
877 912 3.380479 TTCTCGGAATCAACTGTCGTT 57.620 42.857 0.00 0.00 0.00 3.85
892 927 0.325602 TCGTTGGGGGTTTTATCGCT 59.674 50.000 0.00 0.00 0.00 4.93
909 944 0.653114 GCTTTTCTCGCGAGGAATCC 59.347 55.000 33.98 21.22 0.00 3.01
942 977 2.125147 CGCTCCGGCAATTCTCCA 60.125 61.111 0.00 0.00 38.60 3.86
971 1006 8.024146 ACGCGCTTTCCATTTTTATAAAATTT 57.976 26.923 5.73 0.45 0.00 1.82
1090 1125 9.693739 TTTGGTTCCATTTTATTAGCTCTGATA 57.306 29.630 0.00 0.00 0.00 2.15
1107 1142 4.512571 TCTGATACATTGCATGTGAATCCG 59.487 41.667 10.77 5.25 44.60 4.18
1134 1169 8.524870 AATTTGAAATCTCTTTCCATTTCGTG 57.475 30.769 0.00 0.00 40.50 4.35
1164 1199 0.165944 GTGCCAATTCGACTGGAACG 59.834 55.000 15.47 0.00 37.50 3.95
1173 1208 0.515564 CGACTGGAACGGCGAAATTT 59.484 50.000 16.62 0.00 39.14 1.82
1191 1227 9.528847 GCGAAATTTTCTGTGAAATTTTTATCC 57.471 29.630 7.50 5.37 44.74 2.59
1219 1255 3.288243 CACGTTTTGCTGCTTTTTGAC 57.712 42.857 0.00 0.00 0.00 3.18
1249 1286 2.906389 TCTATGAGTGCCACAGAGGTTT 59.094 45.455 0.00 0.00 40.61 3.27
1251 1288 1.679139 TGAGTGCCACAGAGGTTTTG 58.321 50.000 0.00 0.00 40.61 2.44
1253 1290 2.024414 GAGTGCCACAGAGGTTTTGTT 58.976 47.619 0.00 0.00 40.61 2.83
1277 1315 3.744660 CTGTTGCAGAGTTCTTAACCCT 58.255 45.455 0.00 0.00 32.44 4.34
1281 1319 2.115343 CAGAGTTCTTAACCCTGCCC 57.885 55.000 0.00 0.00 30.37 5.36
1282 1320 1.630878 CAGAGTTCTTAACCCTGCCCT 59.369 52.381 0.00 0.00 30.37 5.19
1283 1321 1.630878 AGAGTTCTTAACCCTGCCCTG 59.369 52.381 0.00 0.00 0.00 4.45
1284 1322 0.698818 AGTTCTTAACCCTGCCCTGG 59.301 55.000 0.00 0.00 0.00 4.45
1285 1323 0.404426 GTTCTTAACCCTGCCCTGGT 59.596 55.000 0.00 0.00 37.85 4.00
1286 1324 0.404040 TTCTTAACCCTGCCCTGGTG 59.596 55.000 0.00 0.00 35.88 4.17
1287 1325 0.474854 TCTTAACCCTGCCCTGGTGA 60.475 55.000 0.00 0.00 35.88 4.02
1288 1326 0.035056 CTTAACCCTGCCCTGGTGAG 60.035 60.000 0.00 0.00 35.88 3.51
1289 1327 1.497309 TTAACCCTGCCCTGGTGAGG 61.497 60.000 1.94 1.94 39.42 3.86
1295 1333 3.971702 GCCCTGGTGAGGCCTTGT 61.972 66.667 6.77 0.00 45.16 3.16
1296 1334 2.846532 CCCTGGTGAGGCCTTGTT 59.153 61.111 6.77 0.00 38.17 2.83
1297 1335 1.303643 CCCTGGTGAGGCCTTGTTC 60.304 63.158 6.77 0.00 38.17 3.18
1298 1336 1.672356 CCTGGTGAGGCCTTGTTCG 60.672 63.158 6.77 0.00 38.35 3.95
1299 1337 1.672356 CTGGTGAGGCCTTGTTCGG 60.672 63.158 6.77 0.00 38.35 4.30
1300 1338 2.397413 CTGGTGAGGCCTTGTTCGGT 62.397 60.000 6.77 0.00 38.35 4.69
1301 1339 1.228154 GGTGAGGCCTTGTTCGGTT 60.228 57.895 6.77 0.00 0.00 4.44
1302 1340 0.035739 GGTGAGGCCTTGTTCGGTTA 59.964 55.000 6.77 0.00 0.00 2.85
1303 1341 1.543871 GGTGAGGCCTTGTTCGGTTAA 60.544 52.381 6.77 0.00 0.00 2.01
1304 1342 1.534163 GTGAGGCCTTGTTCGGTTAAC 59.466 52.381 6.77 0.00 38.67 2.01
1305 1343 1.141254 TGAGGCCTTGTTCGGTTAACA 59.859 47.619 6.77 0.00 46.41 2.41
1315 1353 4.581868 TGTTCGGTTAACAGGGATTTAGG 58.418 43.478 8.10 0.00 43.22 2.69
1316 1354 4.286549 TGTTCGGTTAACAGGGATTTAGGA 59.713 41.667 8.10 0.00 43.22 2.94
1317 1355 4.748277 TCGGTTAACAGGGATTTAGGAG 57.252 45.455 8.10 0.00 0.00 3.69
1318 1356 4.098894 TCGGTTAACAGGGATTTAGGAGT 58.901 43.478 8.10 0.00 0.00 3.85
1319 1357 4.081309 TCGGTTAACAGGGATTTAGGAGTG 60.081 45.833 8.10 0.00 0.00 3.51
1320 1358 4.524053 GGTTAACAGGGATTTAGGAGTGG 58.476 47.826 8.10 0.00 0.00 4.00
1321 1359 4.018688 GGTTAACAGGGATTTAGGAGTGGT 60.019 45.833 8.10 0.00 0.00 4.16
1322 1360 5.516062 GGTTAACAGGGATTTAGGAGTGGTT 60.516 44.000 8.10 0.00 0.00 3.67
1323 1361 4.741928 AACAGGGATTTAGGAGTGGTTT 57.258 40.909 0.00 0.00 0.00 3.27
1324 1362 4.034285 ACAGGGATTTAGGAGTGGTTTG 57.966 45.455 0.00 0.00 0.00 2.93
1325 1363 3.245264 ACAGGGATTTAGGAGTGGTTTGG 60.245 47.826 0.00 0.00 0.00 3.28
1326 1364 2.100197 GGGATTTAGGAGTGGTTTGGC 58.900 52.381 0.00 0.00 0.00 4.52
1327 1365 2.556559 GGGATTTAGGAGTGGTTTGGCA 60.557 50.000 0.00 0.00 0.00 4.92
1328 1366 2.755103 GGATTTAGGAGTGGTTTGGCAG 59.245 50.000 0.00 0.00 0.00 4.85
1329 1367 2.286365 TTTAGGAGTGGTTTGGCAGG 57.714 50.000 0.00 0.00 0.00 4.85
1330 1368 0.404040 TTAGGAGTGGTTTGGCAGGG 59.596 55.000 0.00 0.00 0.00 4.45
1331 1369 0.770557 TAGGAGTGGTTTGGCAGGGT 60.771 55.000 0.00 0.00 0.00 4.34
1332 1370 1.152546 GGAGTGGTTTGGCAGGGTT 60.153 57.895 0.00 0.00 0.00 4.11
1333 1371 0.759060 GGAGTGGTTTGGCAGGGTTT 60.759 55.000 0.00 0.00 0.00 3.27
1334 1372 0.389025 GAGTGGTTTGGCAGGGTTTG 59.611 55.000 0.00 0.00 0.00 2.93
1335 1373 0.032615 AGTGGTTTGGCAGGGTTTGA 60.033 50.000 0.00 0.00 0.00 2.69
1336 1374 0.389025 GTGGTTTGGCAGGGTTTGAG 59.611 55.000 0.00 0.00 0.00 3.02
1337 1375 0.758685 TGGTTTGGCAGGGTTTGAGG 60.759 55.000 0.00 0.00 0.00 3.86
1338 1376 0.759060 GGTTTGGCAGGGTTTGAGGT 60.759 55.000 0.00 0.00 0.00 3.85
1339 1377 0.389025 GTTTGGCAGGGTTTGAGGTG 59.611 55.000 0.00 0.00 0.00 4.00
1340 1378 0.758685 TTTGGCAGGGTTTGAGGTGG 60.759 55.000 0.00 0.00 0.00 4.61
1341 1379 1.650242 TTGGCAGGGTTTGAGGTGGA 61.650 55.000 0.00 0.00 0.00 4.02
1342 1380 1.384191 GGCAGGGTTTGAGGTGGAT 59.616 57.895 0.00 0.00 0.00 3.41
1343 1381 0.623723 GGCAGGGTTTGAGGTGGATA 59.376 55.000 0.00 0.00 0.00 2.59
1344 1382 1.682087 GGCAGGGTTTGAGGTGGATAC 60.682 57.143 0.00 0.00 0.00 2.24
1368 1406 7.886338 ACAATCTTCTAAAGTCAAAATCCACC 58.114 34.615 0.00 0.00 0.00 4.61
1369 1407 7.039714 ACAATCTTCTAAAGTCAAAATCCACCC 60.040 37.037 0.00 0.00 0.00 4.61
1370 1408 5.947663 TCTTCTAAAGTCAAAATCCACCCA 58.052 37.500 0.00 0.00 0.00 4.51
1371 1409 6.369629 TCTTCTAAAGTCAAAATCCACCCAA 58.630 36.000 0.00 0.00 0.00 4.12
1372 1410 6.836527 TCTTCTAAAGTCAAAATCCACCCAAA 59.163 34.615 0.00 0.00 0.00 3.28
1373 1411 7.508977 TCTTCTAAAGTCAAAATCCACCCAAAT 59.491 33.333 0.00 0.00 0.00 2.32
1374 1412 7.227049 TCTAAAGTCAAAATCCACCCAAATC 57.773 36.000 0.00 0.00 0.00 2.17
1375 1413 4.890158 AAGTCAAAATCCACCCAAATCC 57.110 40.909 0.00 0.00 0.00 3.01
1376 1414 3.173151 AGTCAAAATCCACCCAAATCCC 58.827 45.455 0.00 0.00 0.00 3.85
1377 1415 2.236146 GTCAAAATCCACCCAAATCCCC 59.764 50.000 0.00 0.00 0.00 4.81
1378 1416 2.113414 TCAAAATCCACCCAAATCCCCT 59.887 45.455 0.00 0.00 0.00 4.79
1379 1417 2.501316 CAAAATCCACCCAAATCCCCTC 59.499 50.000 0.00 0.00 0.00 4.30
1380 1418 0.636647 AATCCACCCAAATCCCCTCC 59.363 55.000 0.00 0.00 0.00 4.30
1381 1419 0.554865 ATCCACCCAAATCCCCTCCA 60.555 55.000 0.00 0.00 0.00 3.86
1382 1420 0.778078 TCCACCCAAATCCCCTCCAA 60.778 55.000 0.00 0.00 0.00 3.53
1383 1421 0.614697 CCACCCAAATCCCCTCCAAC 60.615 60.000 0.00 0.00 0.00 3.77
1384 1422 0.614697 CACCCAAATCCCCTCCAACC 60.615 60.000 0.00 0.00 0.00 3.77
1385 1423 1.001631 CCCAAATCCCCTCCAACCC 59.998 63.158 0.00 0.00 0.00 4.11
1386 1424 1.518431 CCCAAATCCCCTCCAACCCT 61.518 60.000 0.00 0.00 0.00 4.34
1387 1425 0.033109 CCAAATCCCCTCCAACCCTC 60.033 60.000 0.00 0.00 0.00 4.30
1388 1426 1.002857 CAAATCCCCTCCAACCCTCT 58.997 55.000 0.00 0.00 0.00 3.69
1389 1427 1.359130 CAAATCCCCTCCAACCCTCTT 59.641 52.381 0.00 0.00 0.00 2.85
1390 1428 1.002857 AATCCCCTCCAACCCTCTTG 58.997 55.000 0.00 0.00 0.00 3.02
1391 1429 0.921256 ATCCCCTCCAACCCTCTTGG 60.921 60.000 0.00 0.00 40.87 3.61
1405 1443 0.611714 TCTTGGGAAGAGGCGTAACC 59.388 55.000 0.00 0.00 39.61 2.85
1406 1444 0.739813 CTTGGGAAGAGGCGTAACCG 60.740 60.000 0.00 0.00 46.52 4.44
1407 1445 1.186917 TTGGGAAGAGGCGTAACCGA 61.187 55.000 0.00 0.00 46.52 4.69
1408 1446 1.186917 TGGGAAGAGGCGTAACCGAA 61.187 55.000 0.00 0.00 46.52 4.30
1409 1447 0.738762 GGGAAGAGGCGTAACCGAAC 60.739 60.000 0.00 0.00 46.52 3.95
1410 1448 0.037975 GGAAGAGGCGTAACCGAACA 60.038 55.000 0.00 0.00 46.52 3.18
1411 1449 1.606224 GGAAGAGGCGTAACCGAACAA 60.606 52.381 0.00 0.00 46.52 2.83
1412 1450 1.725164 GAAGAGGCGTAACCGAACAAG 59.275 52.381 0.00 0.00 46.52 3.16
1413 1451 0.037605 AGAGGCGTAACCGAACAAGG 60.038 55.000 0.00 0.00 46.52 3.61
1414 1452 1.632948 GAGGCGTAACCGAACAAGGC 61.633 60.000 0.00 0.00 46.52 4.35
1415 1453 2.683859 GGCGTAACCGAACAAGGCC 61.684 63.158 0.00 0.00 37.05 5.19
1484 1522 0.394899 GCCTTGGCATAGCTTCACCT 60.395 55.000 6.79 0.00 0.00 4.00
1558 1608 3.245519 GCTTGGTTAATCCGATCGAGTTC 59.754 47.826 18.66 1.75 39.52 3.01
1582 1632 4.853196 CACATTGCTTTACCTCGTTCAATG 59.147 41.667 10.17 10.17 43.56 2.82
1661 1711 1.300620 TTGGTTCTGACGGCTCGTG 60.301 57.895 4.94 0.00 41.37 4.35
1662 1712 2.432628 GGTTCTGACGGCTCGTGG 60.433 66.667 4.94 0.00 41.37 4.94
1787 1843 1.296392 TCCATCACAAGGAGGTGCG 59.704 57.895 0.00 0.00 38.66 5.34
1788 1844 1.003355 CCATCACAAGGAGGTGCGT 60.003 57.895 0.00 0.00 38.66 5.24
1803 1859 1.092345 TGCGTGTGCTGTTTGCTGTA 61.092 50.000 0.00 0.00 43.34 2.74
1807 1863 0.662619 TGTGCTGTTTGCTGTACTGC 59.337 50.000 17.07 17.07 43.37 4.40
1808 1864 0.662619 GTGCTGTTTGCTGTACTGCA 59.337 50.000 21.93 21.93 44.63 4.41
1809 1865 0.662619 TGCTGTTTGCTGTACTGCAC 59.337 50.000 24.99 15.83 42.85 4.57
1810 1866 0.947244 GCTGTTTGCTGTACTGCACT 59.053 50.000 24.99 0.00 43.20 4.40
1812 1868 1.942657 CTGTTTGCTGTACTGCACTGT 59.057 47.619 24.99 0.00 43.20 3.55
1813 1869 3.130633 CTGTTTGCTGTACTGCACTGTA 58.869 45.455 24.99 9.58 43.20 2.74
1814 1870 3.130633 TGTTTGCTGTACTGCACTGTAG 58.869 45.455 24.99 0.00 43.20 2.74
1815 1871 3.181470 TGTTTGCTGTACTGCACTGTAGA 60.181 43.478 24.99 8.51 43.20 2.59
1816 1872 3.961480 TTGCTGTACTGCACTGTAGAT 57.039 42.857 24.99 0.00 43.20 1.98
1838 1896 7.478322 AGATTAACTGAACATGATGTTGATGC 58.522 34.615 16.52 1.58 41.28 3.91
1839 1897 4.445452 AACTGAACATGATGTTGATGCC 57.555 40.909 16.52 1.19 41.28 4.40
1921 1981 3.365265 GGTTGTTGCCCCGCAGAG 61.365 66.667 0.00 0.00 40.61 3.35
1970 2030 2.105128 CTGGCCGCTAACGAGGAG 59.895 66.667 0.00 0.00 43.93 3.69
1971 2031 2.678934 TGGCCGCTAACGAGGAGT 60.679 61.111 0.00 0.00 43.93 3.85
1972 2032 2.104530 GGCCGCTAACGAGGAGTC 59.895 66.667 0.00 0.00 43.93 3.36
1987 2047 2.804090 GTCGTCGTTCAGGTCCGC 60.804 66.667 0.00 0.00 0.00 5.54
2124 2253 3.598715 TGGAACAGGCGACGACGT 61.599 61.111 9.33 0.00 41.98 4.34
2188 2317 0.823769 TGCGAGGTCAGTCAGTCAGT 60.824 55.000 0.00 0.00 0.00 3.41
2189 2318 0.109504 GCGAGGTCAGTCAGTCAGTC 60.110 60.000 0.00 0.00 0.00 3.51
2190 2319 1.239347 CGAGGTCAGTCAGTCAGTCA 58.761 55.000 0.00 0.00 0.00 3.41
2191 2320 1.198867 CGAGGTCAGTCAGTCAGTCAG 59.801 57.143 0.00 0.00 0.00 3.51
2218 2347 6.201517 ACACATTGATTTCAGTTTCAGAACG 58.798 36.000 0.00 0.00 40.75 3.95
2232 2361 0.663153 AGAACGCTTGCTGAACAACC 59.337 50.000 0.00 0.00 33.68 3.77
2465 2594 1.675552 TGCATGCATGATCACTCAGG 58.324 50.000 30.64 1.70 36.27 3.86
2466 2595 1.064979 TGCATGCATGATCACTCAGGT 60.065 47.619 30.64 0.00 35.62 4.00
2514 2644 1.320555 CTTAACTGTTCGCCGTGATCG 59.679 52.381 0.00 0.00 0.00 3.69
2885 3015 2.098831 GTTCTACAAGACGGCCGGC 61.099 63.158 31.76 30.01 0.00 6.13
3242 3375 5.163713 GCAGATATTCAACAAGAGGTGGAAC 60.164 44.000 0.00 0.00 42.18 3.62
3278 3411 2.607750 ATGTGCTGGACGGACCCT 60.608 61.111 0.00 0.00 38.00 4.34
3314 3447 4.467084 GCGACGCCCAAGGGATGA 62.467 66.667 9.14 0.00 37.50 2.92
3315 3448 2.511600 CGACGCCCAAGGGATGAC 60.512 66.667 9.92 0.00 37.50 3.06
3316 3449 2.124695 GACGCCCAAGGGATGACC 60.125 66.667 9.92 0.00 37.50 4.02
3436 3578 4.339530 TCATGTACAGATCTCTTTCTCCCG 59.660 45.833 0.33 0.00 0.00 5.14
3444 3586 0.837272 CTCTTTCTCCCGGGCCAATA 59.163 55.000 18.49 0.00 0.00 1.90
3445 3587 1.211949 CTCTTTCTCCCGGGCCAATAA 59.788 52.381 18.49 4.38 0.00 1.40
3446 3588 1.211949 TCTTTCTCCCGGGCCAATAAG 59.788 52.381 18.49 14.16 0.00 1.73
3447 3589 0.996583 TTTCTCCCGGGCCAATAAGT 59.003 50.000 18.49 0.00 0.00 2.24
3579 4915 5.994054 CGAATTGGATAACTGATGGACTCAT 59.006 40.000 0.00 0.00 36.09 2.90
3632 4975 0.534203 TTGTCCGGCTCAACTTCCAC 60.534 55.000 0.00 0.00 0.00 4.02
3648 4991 7.279758 TCAACTTCCACAAAATTGAATCAAACC 59.720 33.333 0.00 0.00 0.00 3.27
3729 5072 2.089980 GCACAAGATCAGTCAGCCATT 58.910 47.619 0.00 0.00 0.00 3.16
3751 5094 8.694540 CCATTCAGGGATTGTTTCATACATAAA 58.305 33.333 0.00 0.00 36.44 1.40
3826 5169 2.575893 TAAGACGGCTGGCGAACCA 61.576 57.895 30.58 9.43 46.51 3.67
3839 5182 2.223377 GGCGAACCATAGCTTAAATCCG 59.777 50.000 0.00 0.00 35.26 4.18
3845 5188 5.813080 ACCATAGCTTAAATCCGTGAAAC 57.187 39.130 0.00 0.00 0.00 2.78
3914 5257 2.861730 TGTGGAGCCTCCCAGAGA 59.138 61.111 8.62 0.00 36.78 3.10
3919 5262 1.104577 GGAGCCTCCCAGAGACGTAG 61.105 65.000 0.00 0.00 0.00 3.51
4048 5391 1.544825 CCCTCGAACCTTGAGCCTCA 61.545 60.000 0.00 0.00 31.98 3.86
4135 5478 5.065218 CCAAGTGTGTAGCTCCATTTGTATC 59.935 44.000 12.19 0.00 29.31 2.24
4238 5581 2.359214 AGCTCGCACGATCTCTTCAATA 59.641 45.455 0.00 0.00 0.00 1.90
4254 5597 7.930325 TCTCTTCAATAATGATCATGGAGTGAC 59.070 37.037 16.40 0.00 40.28 3.67
4304 5647 1.195115 AGCTATTCCTCGAGTGCCAA 58.805 50.000 12.31 0.00 0.00 4.52
4327 5670 1.665679 CGCCCACATCACAGTAATCAC 59.334 52.381 0.00 0.00 0.00 3.06
4343 5686 1.402787 TCACGATAGCAGCCTCATCA 58.597 50.000 0.00 0.00 42.67 3.07
4394 5737 1.656652 GAGACCATGTCCGTGGATTG 58.343 55.000 12.42 0.00 42.02 2.67
4447 5790 4.845580 CGCCTCCCAGAAGCGCAT 62.846 66.667 11.47 0.00 43.72 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.928005 AGAGATGCAATGAGGTGTCAT 57.072 42.857 0.00 0.00 46.01 3.06
24 25 3.262660 AGAAGAGATGCAATGAGGTGTCA 59.737 43.478 0.00 0.00 37.02 3.58
25 26 3.871485 AGAAGAGATGCAATGAGGTGTC 58.129 45.455 0.00 0.00 0.00 3.67
26 27 3.996921 AGAAGAGATGCAATGAGGTGT 57.003 42.857 0.00 0.00 0.00 4.16
27 28 6.939132 AATAAGAAGAGATGCAATGAGGTG 57.061 37.500 0.00 0.00 0.00 4.00
28 29 8.049117 TGTTAATAAGAAGAGATGCAATGAGGT 58.951 33.333 0.00 0.00 0.00 3.85
29 30 8.442632 TGTTAATAAGAAGAGATGCAATGAGG 57.557 34.615 0.00 0.00 0.00 3.86
67 68 8.026607 CGTGGTCATGTTTTATTGGTTCTTATT 58.973 33.333 0.00 0.00 0.00 1.40
68 69 7.392113 TCGTGGTCATGTTTTATTGGTTCTTAT 59.608 33.333 0.00 0.00 0.00 1.73
69 70 6.711194 TCGTGGTCATGTTTTATTGGTTCTTA 59.289 34.615 0.00 0.00 0.00 2.10
70 71 5.533154 TCGTGGTCATGTTTTATTGGTTCTT 59.467 36.000 0.00 0.00 0.00 2.52
71 72 5.067273 TCGTGGTCATGTTTTATTGGTTCT 58.933 37.500 0.00 0.00 0.00 3.01
72 73 5.180492 TCTCGTGGTCATGTTTTATTGGTTC 59.820 40.000 0.00 0.00 0.00 3.62
73 74 5.067273 TCTCGTGGTCATGTTTTATTGGTT 58.933 37.500 0.00 0.00 0.00 3.67
74 75 4.647611 TCTCGTGGTCATGTTTTATTGGT 58.352 39.130 0.00 0.00 0.00 3.67
75 76 5.621197 TTCTCGTGGTCATGTTTTATTGG 57.379 39.130 0.00 0.00 0.00 3.16
76 77 6.094048 AGGATTCTCGTGGTCATGTTTTATTG 59.906 38.462 0.00 0.00 0.00 1.90
77 78 6.180472 AGGATTCTCGTGGTCATGTTTTATT 58.820 36.000 0.00 0.00 0.00 1.40
78 79 5.745227 AGGATTCTCGTGGTCATGTTTTAT 58.255 37.500 0.00 0.00 0.00 1.40
79 80 5.160607 AGGATTCTCGTGGTCATGTTTTA 57.839 39.130 0.00 0.00 0.00 1.52
80 81 4.021102 AGGATTCTCGTGGTCATGTTTT 57.979 40.909 0.00 0.00 0.00 2.43
81 82 3.703001 AGGATTCTCGTGGTCATGTTT 57.297 42.857 0.00 0.00 0.00 2.83
82 83 3.703001 AAGGATTCTCGTGGTCATGTT 57.297 42.857 0.00 0.00 0.00 2.71
83 84 4.819105 TTAAGGATTCTCGTGGTCATGT 57.181 40.909 0.00 0.00 0.00 3.21
84 85 4.332819 GGTTTAAGGATTCTCGTGGTCATG 59.667 45.833 0.00 0.00 0.00 3.07
85 86 4.225267 AGGTTTAAGGATTCTCGTGGTCAT 59.775 41.667 0.00 0.00 0.00 3.06
86 87 3.581332 AGGTTTAAGGATTCTCGTGGTCA 59.419 43.478 0.00 0.00 0.00 4.02
87 88 4.182339 GAGGTTTAAGGATTCTCGTGGTC 58.818 47.826 0.00 0.00 0.00 4.02
88 89 3.055312 GGAGGTTTAAGGATTCTCGTGGT 60.055 47.826 0.00 0.00 0.00 4.16
89 90 3.532542 GGAGGTTTAAGGATTCTCGTGG 58.467 50.000 0.00 0.00 0.00 4.94
90 91 3.187700 CGGAGGTTTAAGGATTCTCGTG 58.812 50.000 0.00 0.00 0.00 4.35
91 92 2.830321 ACGGAGGTTTAAGGATTCTCGT 59.170 45.455 0.00 0.00 0.00 4.18
92 93 3.521947 ACGGAGGTTTAAGGATTCTCG 57.478 47.619 0.00 0.00 0.00 4.04
120 121 6.270000 CCTGAAAAGGGTTTAAGGATTCCTTT 59.730 38.462 22.63 7.79 45.50 3.11
121 122 5.780282 CCTGAAAAGGGTTTAAGGATTCCTT 59.220 40.000 21.31 21.31 45.50 3.36
122 123 5.333581 CCTGAAAAGGGTTTAAGGATTCCT 58.666 41.667 0.00 0.00 45.50 3.36
190 191 0.681564 TTTCGGGGCGGTATTGCATT 60.682 50.000 0.00 0.00 36.28 3.56
192 193 2.041686 GTTTCGGGGCGGTATTGCA 61.042 57.895 0.00 0.00 36.28 4.08
205 206 0.388907 TAGCCTTCGGTTCCGTTTCG 60.389 55.000 11.04 0.00 0.00 3.46
231 233 5.400066 TTTTTAATGCTTTAGCCCCTCAC 57.600 39.130 0.00 0.00 41.18 3.51
275 277 1.414866 GGAGGGAGATGGAAGGGAGC 61.415 65.000 0.00 0.00 0.00 4.70
279 281 0.548510 GTTGGGAGGGAGATGGAAGG 59.451 60.000 0.00 0.00 0.00 3.46
393 397 1.449601 CGACCATTGACGGGGAAGG 60.450 63.158 0.00 0.00 0.00 3.46
395 399 2.046700 GCGACCATTGACGGGGAA 60.047 61.111 0.00 0.00 0.00 3.97
396 400 4.090588 GGCGACCATTGACGGGGA 62.091 66.667 0.00 0.00 0.00 4.81
456 460 2.415010 CATGGCGAGGACCGAGAG 59.585 66.667 0.00 0.00 41.76 3.20
457 461 2.561467 TACCATGGCGAGGACCGAGA 62.561 60.000 13.04 0.00 41.76 4.04
458 462 1.672854 TTACCATGGCGAGGACCGAG 61.673 60.000 13.04 0.00 41.76 4.63
459 463 1.672854 CTTACCATGGCGAGGACCGA 61.673 60.000 13.04 0.00 41.76 4.69
460 464 1.227263 CTTACCATGGCGAGGACCG 60.227 63.158 13.04 0.00 42.21 4.79
461 465 1.523938 GCTTACCATGGCGAGGACC 60.524 63.158 13.04 0.00 0.00 4.46
462 466 1.523938 GGCTTACCATGGCGAGGAC 60.524 63.158 13.04 0.00 35.26 3.85
463 467 2.908015 GGCTTACCATGGCGAGGA 59.092 61.111 13.04 0.00 35.26 3.71
510 530 1.302511 CTCCGGCGGGGAATTATGG 60.303 63.158 24.59 0.00 46.61 2.74
546 566 1.633774 ACTCCATCCACGTCTCAAGT 58.366 50.000 0.00 0.00 0.00 3.16
548 568 1.275291 GGAACTCCATCCACGTCTCAA 59.725 52.381 0.00 0.00 39.42 3.02
549 569 0.895530 GGAACTCCATCCACGTCTCA 59.104 55.000 0.00 0.00 39.42 3.27
550 570 0.179134 CGGAACTCCATCCACGTCTC 60.179 60.000 0.00 0.00 39.61 3.36
551 571 0.898789 ACGGAACTCCATCCACGTCT 60.899 55.000 0.00 0.00 39.61 4.18
725 753 1.270785 TGACAAGAGAATTCAGCGCCA 60.271 47.619 2.29 0.00 0.00 5.69
727 755 2.341257 TCTGACAAGAGAATTCAGCGC 58.659 47.619 8.44 0.00 37.31 5.92
757 785 1.272536 ACCTCGTCAGGGAAAGCTCTA 60.273 52.381 0.00 0.00 45.53 2.43
768 796 1.203928 GCGAATCATCACCTCGTCAG 58.796 55.000 0.00 0.00 35.06 3.51
792 826 1.719780 AGAAGACGACGCGAAACAATC 59.280 47.619 15.93 4.22 0.00 2.67
802 836 4.027621 CGAATTCCATACAAGAAGACGACG 60.028 45.833 0.00 0.00 31.86 5.12
848 882 6.209391 ACAGTTGATTCCGAGAATTCCAAAAT 59.791 34.615 0.65 0.00 0.00 1.82
874 909 1.170442 AAGCGATAAAACCCCCAACG 58.830 50.000 0.00 0.00 0.00 4.10
877 912 3.086282 GAGAAAAGCGATAAAACCCCCA 58.914 45.455 0.00 0.00 0.00 4.96
892 927 0.611200 TGGGATTCCTCGCGAGAAAA 59.389 50.000 36.59 27.70 41.32 2.29
971 1006 2.237143 AGAGCACCTGCAATAGCTACAA 59.763 45.455 0.00 0.00 45.16 2.41
997 1032 0.820226 CTGATTCACTCGAGCCTGGA 59.180 55.000 13.61 0.00 0.00 3.86
999 1034 2.662006 TTCTGATTCACTCGAGCCTG 57.338 50.000 13.61 4.30 0.00 4.85
1107 1142 9.626045 ACGAAATGGAAAGAGATTTCAAATTAC 57.374 29.630 0.00 0.00 38.12 1.89
1134 1169 2.798148 AATTGGCACGACCTCGGTCC 62.798 60.000 10.34 2.44 44.95 4.46
1164 1199 9.528847 GATAAAAATTTCACAGAAAATTTCGCC 57.471 29.630 7.55 0.00 44.17 5.54
1173 1208 6.072175 CGTGGAGGGATAAAAATTTCACAGAA 60.072 38.462 0.00 0.00 0.00 3.02
1191 1227 2.051345 GCAAAACGTGCGTGGAGG 60.051 61.111 0.00 0.00 45.10 4.30
1231 1267 2.233271 CAAAACCTCTGTGGCACTCAT 58.767 47.619 19.83 0.00 40.22 2.90
1249 1286 2.754552 AGAACTCTGCAACAGCAAACAA 59.245 40.909 0.00 0.00 37.91 2.83
1251 1288 3.427161 AAGAACTCTGCAACAGCAAAC 57.573 42.857 0.00 0.00 37.91 2.93
1253 1290 3.315191 GGTTAAGAACTCTGCAACAGCAA 59.685 43.478 0.00 0.00 37.91 3.91
1279 1317 1.303643 GAACAAGGCCTCACCAGGG 60.304 63.158 5.23 0.00 43.14 4.45
1280 1318 1.672356 CGAACAAGGCCTCACCAGG 60.672 63.158 5.23 0.00 43.14 4.45
1281 1319 1.672356 CCGAACAAGGCCTCACCAG 60.672 63.158 5.23 0.00 43.14 4.00
1282 1320 1.990160 AACCGAACAAGGCCTCACCA 61.990 55.000 5.23 0.00 43.14 4.17
1283 1321 0.035739 TAACCGAACAAGGCCTCACC 59.964 55.000 5.23 0.00 39.61 4.02
1284 1322 1.534163 GTTAACCGAACAAGGCCTCAC 59.466 52.381 5.23 0.00 38.02 3.51
1285 1323 1.141254 TGTTAACCGAACAAGGCCTCA 59.859 47.619 5.23 0.00 45.23 3.86
1286 1324 1.886886 TGTTAACCGAACAAGGCCTC 58.113 50.000 5.23 0.00 45.23 4.70
1293 1331 4.286549 TCCTAAATCCCTGTTAACCGAACA 59.713 41.667 2.48 0.00 46.03 3.18
1294 1332 4.835678 TCCTAAATCCCTGTTAACCGAAC 58.164 43.478 2.48 0.00 38.65 3.95
1295 1333 4.533311 ACTCCTAAATCCCTGTTAACCGAA 59.467 41.667 2.48 0.00 0.00 4.30
1296 1334 4.081309 CACTCCTAAATCCCTGTTAACCGA 60.081 45.833 2.48 0.00 0.00 4.69
1297 1335 4.189231 CACTCCTAAATCCCTGTTAACCG 58.811 47.826 2.48 0.00 0.00 4.44
1298 1336 4.018688 ACCACTCCTAAATCCCTGTTAACC 60.019 45.833 2.48 0.00 0.00 2.85
1299 1337 5.175388 ACCACTCCTAAATCCCTGTTAAC 57.825 43.478 0.00 0.00 0.00 2.01
1300 1338 5.853572 AACCACTCCTAAATCCCTGTTAA 57.146 39.130 0.00 0.00 0.00 2.01
1301 1339 5.515886 CCAAACCACTCCTAAATCCCTGTTA 60.516 44.000 0.00 0.00 0.00 2.41
1302 1340 4.407365 CAAACCACTCCTAAATCCCTGTT 58.593 43.478 0.00 0.00 0.00 3.16
1303 1341 3.245264 CCAAACCACTCCTAAATCCCTGT 60.245 47.826 0.00 0.00 0.00 4.00
1304 1342 3.356290 CCAAACCACTCCTAAATCCCTG 58.644 50.000 0.00 0.00 0.00 4.45
1305 1343 2.291605 GCCAAACCACTCCTAAATCCCT 60.292 50.000 0.00 0.00 0.00 4.20
1306 1344 2.100197 GCCAAACCACTCCTAAATCCC 58.900 52.381 0.00 0.00 0.00 3.85
1307 1345 2.755103 CTGCCAAACCACTCCTAAATCC 59.245 50.000 0.00 0.00 0.00 3.01
1308 1346 2.755103 CCTGCCAAACCACTCCTAAATC 59.245 50.000 0.00 0.00 0.00 2.17
1309 1347 2.557452 CCCTGCCAAACCACTCCTAAAT 60.557 50.000 0.00 0.00 0.00 1.40
1310 1348 1.203001 CCCTGCCAAACCACTCCTAAA 60.203 52.381 0.00 0.00 0.00 1.85
1311 1349 0.404040 CCCTGCCAAACCACTCCTAA 59.596 55.000 0.00 0.00 0.00 2.69
1312 1350 0.770557 ACCCTGCCAAACCACTCCTA 60.771 55.000 0.00 0.00 0.00 2.94
1313 1351 1.655114 AACCCTGCCAAACCACTCCT 61.655 55.000 0.00 0.00 0.00 3.69
1314 1352 0.759060 AAACCCTGCCAAACCACTCC 60.759 55.000 0.00 0.00 0.00 3.85
1315 1353 0.389025 CAAACCCTGCCAAACCACTC 59.611 55.000 0.00 0.00 0.00 3.51
1316 1354 0.032615 TCAAACCCTGCCAAACCACT 60.033 50.000 0.00 0.00 0.00 4.00
1317 1355 0.389025 CTCAAACCCTGCCAAACCAC 59.611 55.000 0.00 0.00 0.00 4.16
1318 1356 0.758685 CCTCAAACCCTGCCAAACCA 60.759 55.000 0.00 0.00 0.00 3.67
1319 1357 0.759060 ACCTCAAACCCTGCCAAACC 60.759 55.000 0.00 0.00 0.00 3.27
1320 1358 0.389025 CACCTCAAACCCTGCCAAAC 59.611 55.000 0.00 0.00 0.00 2.93
1321 1359 0.758685 CCACCTCAAACCCTGCCAAA 60.759 55.000 0.00 0.00 0.00 3.28
1322 1360 1.152567 CCACCTCAAACCCTGCCAA 60.153 57.895 0.00 0.00 0.00 4.52
1323 1361 1.434513 ATCCACCTCAAACCCTGCCA 61.435 55.000 0.00 0.00 0.00 4.92
1324 1362 0.623723 TATCCACCTCAAACCCTGCC 59.376 55.000 0.00 0.00 0.00 4.85
1325 1363 1.004277 TGTATCCACCTCAAACCCTGC 59.996 52.381 0.00 0.00 0.00 4.85
1326 1364 3.433306 TTGTATCCACCTCAAACCCTG 57.567 47.619 0.00 0.00 0.00 4.45
1327 1365 3.852578 AGATTGTATCCACCTCAAACCCT 59.147 43.478 0.00 0.00 0.00 4.34
1328 1366 4.236527 AGATTGTATCCACCTCAAACCC 57.763 45.455 0.00 0.00 0.00 4.11
1329 1367 5.501156 AGAAGATTGTATCCACCTCAAACC 58.499 41.667 0.00 0.00 0.00 3.27
1330 1368 8.561738 TTTAGAAGATTGTATCCACCTCAAAC 57.438 34.615 0.00 0.00 0.00 2.93
1331 1369 8.383175 ACTTTAGAAGATTGTATCCACCTCAAA 58.617 33.333 0.00 0.00 0.00 2.69
1332 1370 7.918076 ACTTTAGAAGATTGTATCCACCTCAA 58.082 34.615 0.00 0.00 0.00 3.02
1333 1371 7.180229 TGACTTTAGAAGATTGTATCCACCTCA 59.820 37.037 0.00 0.00 0.00 3.86
1334 1372 7.556844 TGACTTTAGAAGATTGTATCCACCTC 58.443 38.462 0.00 0.00 0.00 3.85
1335 1373 7.496346 TGACTTTAGAAGATTGTATCCACCT 57.504 36.000 0.00 0.00 0.00 4.00
1336 1374 8.561738 TTTGACTTTAGAAGATTGTATCCACC 57.438 34.615 0.00 0.00 0.00 4.61
1342 1380 9.010029 GGTGGATTTTGACTTTAGAAGATTGTA 57.990 33.333 0.00 0.00 0.00 2.41
1343 1381 7.039714 GGGTGGATTTTGACTTTAGAAGATTGT 60.040 37.037 0.00 0.00 0.00 2.71
1344 1382 7.039784 TGGGTGGATTTTGACTTTAGAAGATTG 60.040 37.037 0.00 0.00 0.00 2.67
1345 1383 7.010160 TGGGTGGATTTTGACTTTAGAAGATT 58.990 34.615 0.00 0.00 0.00 2.40
1346 1384 6.552008 TGGGTGGATTTTGACTTTAGAAGAT 58.448 36.000 0.00 0.00 0.00 2.40
1347 1385 5.947663 TGGGTGGATTTTGACTTTAGAAGA 58.052 37.500 0.00 0.00 0.00 2.87
1348 1386 6.648879 TTGGGTGGATTTTGACTTTAGAAG 57.351 37.500 0.00 0.00 0.00 2.85
1349 1387 7.256154 GGATTTGGGTGGATTTTGACTTTAGAA 60.256 37.037 0.00 0.00 0.00 2.10
1350 1388 6.210584 GGATTTGGGTGGATTTTGACTTTAGA 59.789 38.462 0.00 0.00 0.00 2.10
1351 1389 6.398095 GGATTTGGGTGGATTTTGACTTTAG 58.602 40.000 0.00 0.00 0.00 1.85
1352 1390 5.247337 GGGATTTGGGTGGATTTTGACTTTA 59.753 40.000 0.00 0.00 0.00 1.85
1353 1391 4.041567 GGGATTTGGGTGGATTTTGACTTT 59.958 41.667 0.00 0.00 0.00 2.66
1354 1392 3.582647 GGGATTTGGGTGGATTTTGACTT 59.417 43.478 0.00 0.00 0.00 3.01
1355 1393 3.173151 GGGATTTGGGTGGATTTTGACT 58.827 45.455 0.00 0.00 0.00 3.41
1356 1394 2.236146 GGGGATTTGGGTGGATTTTGAC 59.764 50.000 0.00 0.00 0.00 3.18
1357 1395 2.113414 AGGGGATTTGGGTGGATTTTGA 59.887 45.455 0.00 0.00 0.00 2.69
1358 1396 2.501316 GAGGGGATTTGGGTGGATTTTG 59.499 50.000 0.00 0.00 0.00 2.44
1359 1397 2.561984 GGAGGGGATTTGGGTGGATTTT 60.562 50.000 0.00 0.00 0.00 1.82
1360 1398 1.008327 GGAGGGGATTTGGGTGGATTT 59.992 52.381 0.00 0.00 0.00 2.17
1361 1399 0.636647 GGAGGGGATTTGGGTGGATT 59.363 55.000 0.00 0.00 0.00 3.01
1362 1400 0.554865 TGGAGGGGATTTGGGTGGAT 60.555 55.000 0.00 0.00 0.00 3.41
1363 1401 0.778078 TTGGAGGGGATTTGGGTGGA 60.778 55.000 0.00 0.00 0.00 4.02
1364 1402 0.614697 GTTGGAGGGGATTTGGGTGG 60.615 60.000 0.00 0.00 0.00 4.61
1365 1403 0.614697 GGTTGGAGGGGATTTGGGTG 60.615 60.000 0.00 0.00 0.00 4.61
1366 1404 1.781001 GGTTGGAGGGGATTTGGGT 59.219 57.895 0.00 0.00 0.00 4.51
1367 1405 1.001631 GGGTTGGAGGGGATTTGGG 59.998 63.158 0.00 0.00 0.00 4.12
1368 1406 0.033109 GAGGGTTGGAGGGGATTTGG 60.033 60.000 0.00 0.00 0.00 3.28
1369 1407 1.002857 AGAGGGTTGGAGGGGATTTG 58.997 55.000 0.00 0.00 0.00 2.32
1370 1408 1.359130 CAAGAGGGTTGGAGGGGATTT 59.641 52.381 0.00 0.00 0.00 2.17
1371 1409 1.002857 CAAGAGGGTTGGAGGGGATT 58.997 55.000 0.00 0.00 0.00 3.01
1372 1410 0.921256 CCAAGAGGGTTGGAGGGGAT 60.921 60.000 0.00 0.00 42.06 3.85
1373 1411 1.541368 CCAAGAGGGTTGGAGGGGA 60.541 63.158 0.00 0.00 42.06 4.81
1374 1412 3.090765 CCAAGAGGGTTGGAGGGG 58.909 66.667 0.00 0.00 42.06 4.79
1386 1424 0.611714 GGTTACGCCTCTTCCCAAGA 59.388 55.000 0.00 0.00 35.87 3.02
1387 1425 0.739813 CGGTTACGCCTCTTCCCAAG 60.740 60.000 0.00 0.00 34.25 3.61
1388 1426 1.186917 TCGGTTACGCCTCTTCCCAA 61.187 55.000 0.00 0.00 40.69 4.12
1389 1427 1.186917 TTCGGTTACGCCTCTTCCCA 61.187 55.000 0.00 0.00 40.69 4.37
1390 1428 0.738762 GTTCGGTTACGCCTCTTCCC 60.739 60.000 0.00 0.00 40.69 3.97
1391 1429 0.037975 TGTTCGGTTACGCCTCTTCC 60.038 55.000 0.00 0.00 40.69 3.46
1392 1430 1.725164 CTTGTTCGGTTACGCCTCTTC 59.275 52.381 0.00 0.00 40.69 2.87
1393 1431 1.607251 CCTTGTTCGGTTACGCCTCTT 60.607 52.381 0.00 0.00 40.69 2.85
1394 1432 0.037605 CCTTGTTCGGTTACGCCTCT 60.038 55.000 0.00 0.00 40.69 3.69
1395 1433 1.632948 GCCTTGTTCGGTTACGCCTC 61.633 60.000 0.00 0.00 40.69 4.70
1396 1434 1.670083 GCCTTGTTCGGTTACGCCT 60.670 57.895 0.00 0.00 40.69 5.52
1397 1435 2.683859 GGCCTTGTTCGGTTACGCC 61.684 63.158 0.00 0.00 40.69 5.68
1398 1436 1.670083 AGGCCTTGTTCGGTTACGC 60.670 57.895 0.00 0.00 40.69 4.42
1399 1437 0.320073 TCAGGCCTTGTTCGGTTACG 60.320 55.000 0.00 0.00 42.74 3.18
1400 1438 1.804748 CTTCAGGCCTTGTTCGGTTAC 59.195 52.381 0.00 0.00 0.00 2.50
1401 1439 1.271163 CCTTCAGGCCTTGTTCGGTTA 60.271 52.381 0.00 0.00 0.00 2.85
1402 1440 0.537371 CCTTCAGGCCTTGTTCGGTT 60.537 55.000 0.00 0.00 0.00 4.44
1403 1441 1.073199 CCTTCAGGCCTTGTTCGGT 59.927 57.895 0.00 0.00 0.00 4.69
1404 1442 0.537371 AACCTTCAGGCCTTGTTCGG 60.537 55.000 0.00 1.68 39.32 4.30
1405 1443 1.266989 GAAACCTTCAGGCCTTGTTCG 59.733 52.381 0.00 0.00 39.32 3.95
1406 1444 2.587522 AGAAACCTTCAGGCCTTGTTC 58.412 47.619 0.00 0.39 39.32 3.18
1407 1445 2.755952 AGAAACCTTCAGGCCTTGTT 57.244 45.000 0.00 1.12 39.32 2.83
1408 1446 2.695147 CAAAGAAACCTTCAGGCCTTGT 59.305 45.455 0.00 0.00 39.32 3.16
1409 1447 2.546584 GCAAAGAAACCTTCAGGCCTTG 60.547 50.000 0.00 0.00 39.32 3.61
1410 1448 1.688735 GCAAAGAAACCTTCAGGCCTT 59.311 47.619 0.00 0.00 39.32 4.35
1411 1449 1.133356 AGCAAAGAAACCTTCAGGCCT 60.133 47.619 0.00 0.00 39.32 5.19
1412 1450 1.332195 AGCAAAGAAACCTTCAGGCC 58.668 50.000 0.00 0.00 39.32 5.19
1413 1451 2.546584 CCAAGCAAAGAAACCTTCAGGC 60.547 50.000 0.00 0.00 39.32 4.85
1414 1452 2.036346 CCCAAGCAAAGAAACCTTCAGG 59.964 50.000 0.00 0.00 42.17 3.86
1415 1453 2.036346 CCCCAAGCAAAGAAACCTTCAG 59.964 50.000 0.00 0.00 0.00 3.02
1558 1608 2.811431 TGAACGAGGTAAAGCAATGTGG 59.189 45.455 0.00 0.00 0.00 4.17
1803 1859 5.853936 TGTTCAGTTAATCTACAGTGCAGT 58.146 37.500 0.00 0.00 0.00 4.40
1807 1863 8.484641 ACATCATGTTCAGTTAATCTACAGTG 57.515 34.615 0.00 0.00 0.00 3.66
1808 1864 8.939929 CAACATCATGTTCAGTTAATCTACAGT 58.060 33.333 0.00 0.00 38.77 3.55
1809 1865 9.154847 TCAACATCATGTTCAGTTAATCTACAG 57.845 33.333 0.00 0.00 38.77 2.74
1810 1866 9.671279 ATCAACATCATGTTCAGTTAATCTACA 57.329 29.630 0.00 0.00 38.77 2.74
1812 1868 8.615211 GCATCAACATCATGTTCAGTTAATCTA 58.385 33.333 0.00 0.00 38.77 1.98
1813 1869 7.415989 GGCATCAACATCATGTTCAGTTAATCT 60.416 37.037 0.00 0.00 38.77 2.40
1814 1870 6.694411 GGCATCAACATCATGTTCAGTTAATC 59.306 38.462 0.00 0.00 38.77 1.75
1815 1871 6.567050 GGCATCAACATCATGTTCAGTTAAT 58.433 36.000 0.00 0.00 38.77 1.40
1816 1872 5.391843 CGGCATCAACATCATGTTCAGTTAA 60.392 40.000 0.00 0.00 38.77 2.01
1838 1896 0.025001 GTGACGCGAAATGTGATCGG 59.975 55.000 15.93 0.00 40.54 4.18
1839 1897 0.313469 CGTGACGCGAAATGTGATCG 60.313 55.000 15.93 0.28 44.77 3.69
1915 1975 0.593518 CAGTATCGACAGGCTCTGCG 60.594 60.000 0.00 7.19 34.37 5.18
1921 1981 4.427394 CCTGCAGTATCGACAGGC 57.573 61.111 13.81 0.16 44.16 4.85
1970 2030 2.804090 GCGGACCTGAACGACGAC 60.804 66.667 0.00 0.00 0.00 4.34
1971 2031 4.394078 CGCGGACCTGAACGACGA 62.394 66.667 0.00 0.00 33.74 4.20
2124 2253 2.591311 GCGTCGTTTGCTCAACCGA 61.591 57.895 0.00 0.00 30.65 4.69
2188 2317 6.767423 TGAAACTGAAATCAATGTGTCTCTGA 59.233 34.615 0.00 0.00 0.00 3.27
2189 2318 6.962686 TGAAACTGAAATCAATGTGTCTCTG 58.037 36.000 0.00 0.00 0.00 3.35
2190 2319 6.994496 TCTGAAACTGAAATCAATGTGTCTCT 59.006 34.615 0.00 0.00 0.00 3.10
2191 2320 7.194607 TCTGAAACTGAAATCAATGTGTCTC 57.805 36.000 0.00 0.00 0.00 3.36
2232 2361 0.317269 CACTGGTTCTGCAAGCAACG 60.317 55.000 0.00 0.00 39.51 4.10
2490 2620 1.196808 CACGGCGAACAGTTAAGCATT 59.803 47.619 16.62 0.00 0.00 3.56
2627 2757 1.301716 CCACTTGGTCTGGTCCACG 60.302 63.158 0.00 0.00 37.20 4.94
3026 3156 0.669318 CGCAGTACCCGAGCTTGAAA 60.669 55.000 1.22 0.00 0.00 2.69
3063 3193 2.202388 GACGATGCCGACGTTCGA 60.202 61.111 13.09 0.00 43.74 3.71
3191 3324 2.742710 TATACGATCGCAGCCGCACC 62.743 60.000 16.60 0.00 38.40 5.01
3403 3545 8.242729 AGAGATCTGTACATGACATGTTATCA 57.757 34.615 25.34 19.06 41.63 2.15
3436 3578 5.937111 TGAACCTATCTTACTTATTGGCCC 58.063 41.667 0.00 0.00 0.00 5.80
3444 3586 7.612677 ACATCGTCTTTGAACCTATCTTACTT 58.387 34.615 0.00 0.00 0.00 2.24
3445 3587 7.171630 ACATCGTCTTTGAACCTATCTTACT 57.828 36.000 0.00 0.00 0.00 2.24
3446 3588 8.922058 TTACATCGTCTTTGAACCTATCTTAC 57.078 34.615 0.00 0.00 0.00 2.34
3592 4935 5.538433 ACAATTTTGGAAAGCCTGCTAAGTA 59.462 36.000 0.00 0.00 34.31 2.24
3729 5072 8.821686 ATGTTTATGTATGAAACAATCCCTGA 57.178 30.769 5.16 0.00 46.70 3.86
3808 5151 2.263540 GGTTCGCCAGCCGTCTTA 59.736 61.111 0.00 0.00 38.35 2.10
3826 5169 5.944007 ACCTTGTTTCACGGATTTAAGCTAT 59.056 36.000 0.00 0.00 0.00 2.97
3839 5182 4.642429 AGGTGATGAGTACCTTGTTTCAC 58.358 43.478 0.00 0.00 46.13 3.18
3914 5257 3.065510 CAGATTGTCACGAGATCCTACGT 59.934 47.826 0.00 0.00 43.50 3.57
3919 5262 4.245660 TGAAACAGATTGTCACGAGATCC 58.754 43.478 0.00 0.00 0.00 3.36
4048 5391 3.552875 CATGGATCCTTTGTGAGAGCAT 58.447 45.455 14.23 0.00 0.00 3.79
4057 5400 2.615447 CGTGATCACCATGGATCCTTTG 59.385 50.000 21.47 10.56 42.41 2.77
4135 5478 0.460284 CGAAGGGTGGGTGAAGATCG 60.460 60.000 0.00 0.00 0.00 3.69
4238 5581 2.237143 ACCGTGTCACTCCATGATCATT 59.763 45.455 5.16 0.00 40.28 2.57
4304 5647 0.398696 TTACTGTGATGTGGGCGGTT 59.601 50.000 0.00 0.00 0.00 4.44
4327 5670 1.077123 GCATGATGAGGCTGCTATCG 58.923 55.000 0.00 0.00 33.15 2.92
4343 5686 3.705051 AGATCATGGGTTGTTCAAGCAT 58.295 40.909 14.96 5.76 0.00 3.79
4394 5737 7.556844 TCTTTGATATAAATATCCCGAGGCTC 58.443 38.462 3.87 3.87 38.66 4.70
4447 5790 0.104855 GATGGAGTGCGACCATGCTA 59.895 55.000 12.60 0.00 46.48 3.49


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

AutoCloner maintained by Alex Coulton.