Multiple sequence alignment - TraesCS4D01G273000

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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 TraesCS4D01G273000 chr4D 100.000 3355 0 0 1 3355 442901431 442898077 0.000000e+00 6196
1 TraesCS4D01G273000 chr4D 93.913 115 3 4 355 465 102160949 102160835 1.600000e-38 171
2 TraesCS4D01G273000 chr4A 88.867 2542 138 70 884 3355 24762586 24765052 0.000000e+00 2992
3 TraesCS4D01G273000 chr4A 93.571 140 9 0 3216 3355 621564731 621564870 3.390000e-50 209
4 TraesCS4D01G273000 chr4A 90.000 160 16 0 2570 2729 621564031 621564190 1.220000e-49 207
5 TraesCS4D01G273000 chr4A 92.969 128 5 3 346 469 24759695 24759822 2.060000e-42 183
6 TraesCS4D01G273000 chr4B 89.950 2398 107 59 775 3103 552019676 552017344 0.000000e+00 2970
7 TraesCS4D01G273000 chr4B 90.785 293 22 5 430 720 552020181 552019892 1.460000e-103 387
8 TraesCS4D01G273000 chr4B 91.845 233 15 3 119 351 552026039 552025811 4.180000e-84 322
9 TraesCS4D01G273000 chr4B 94.203 207 11 1 349 555 552025619 552025414 6.990000e-82 315
10 TraesCS4D01G273000 chr4B 95.408 196 3 3 3163 3355 552017328 552017136 1.170000e-79 307
11 TraesCS4D01G273000 chrUn 94.286 140 8 0 3216 3355 68495883 68496022 7.290000e-52 215
12 TraesCS4D01G273000 chrUn 89.375 160 17 0 2570 2729 68495178 68495337 5.680000e-48 202
13 TraesCS4D01G273000 chrUn 90.805 87 6 2 688 774 97273089 97273173 7.610000e-22 115
14 TraesCS4D01G273000 chr5D 94.286 140 8 0 3216 3355 547607974 547608113 7.290000e-52 215
15 TraesCS4D01G273000 chr5D 90.000 160 16 0 2570 2729 547607269 547607428 1.220000e-49 207
16 TraesCS4D01G273000 chr5D 95.413 109 2 3 361 466 233159012 233158904 1.600000e-38 171
17 TraesCS4D01G273000 chr5D 95.370 108 3 2 356 463 519411748 519411643 1.600000e-38 171
18 TraesCS4D01G273000 chr5D 96.000 75 3 0 700 774 74461657 74461731 4.550000e-24 122
19 TraesCS4D01G273000 chr5B 93.571 140 9 0 3216 3355 690908801 690908662 3.390000e-50 209
20 TraesCS4D01G273000 chr5B 86.034 179 25 0 2570 2748 690909500 690909322 3.420000e-45 193
21 TraesCS4D01G273000 chr5B 92.793 111 4 4 358 465 653786157 653786048 1.250000e-34 158
22 TraesCS4D01G273000 chr7A 97.030 101 1 2 364 463 550276973 550277072 5.760000e-38 169
23 TraesCS4D01G273000 chr5A 93.162 117 3 4 354 466 321891680 321891795 2.070000e-37 167
24 TraesCS4D01G273000 chr5A 92.035 113 6 3 354 464 645980763 645980652 4.480000e-34 156
25 TraesCS4D01G273000 chr5A 90.426 94 8 1 682 774 626964492 626964585 4.550000e-24 122
26 TraesCS4D01G273000 chr7B 94.872 78 4 0 697 774 534830144 534830221 4.550000e-24 122
27 TraesCS4D01G273000 chr7B 88.421 95 10 1 681 774 489323057 489323151 2.740000e-21 113
28 TraesCS4D01G273000 chr6A 96.000 75 3 0 700 774 616205841 616205767 4.550000e-24 122
29 TraesCS4D01G273000 chr7D 91.667 84 7 0 691 774 163634718 163634801 2.110000e-22 117
30 TraesCS4D01G273000 chr6D 89.130 92 9 1 683 774 155146764 155146854 2.740000e-21 113
31 TraesCS4D01G273000 chr2B 89.773 88 9 0 687 774 466505682 466505595 2.740000e-21 113


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 TraesCS4D01G273000 chr4D 442898077 442901431 3354 True 6196.000000 6196 100.000000 1 3355 1 chr4D.!!$R2 3354
1 TraesCS4D01G273000 chr4A 24759695 24765052 5357 False 1587.500000 2992 90.918000 346 3355 2 chr4A.!!$F1 3009
2 TraesCS4D01G273000 chr4A 621564031 621564870 839 False 208.000000 209 91.785500 2570 3355 2 chr4A.!!$F2 785
3 TraesCS4D01G273000 chr4B 552017136 552020181 3045 True 1221.333333 2970 92.047667 430 3355 3 chr4B.!!$R1 2925
4 TraesCS4D01G273000 chr4B 552025414 552026039 625 True 318.500000 322 93.024000 119 555 2 chr4B.!!$R2 436
5 TraesCS4D01G273000 chrUn 68495178 68496022 844 False 208.500000 215 91.830500 2570 3355 2 chrUn.!!$F2 785
6 TraesCS4D01G273000 chr5D 547607269 547608113 844 False 211.000000 215 92.143000 2570 3355 2 chr5D.!!$F2 785
7 TraesCS4D01G273000 chr5B 690908662 690909500 838 True 201.000000 209 89.802500 2570 3355 2 chr5B.!!$R2 785

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
303 304 0.036952 TTCTTCTCTTCTGCCAGCCG 60.037 55.0 0.00 0.0 0.0 5.52 F
1956 4790 0.332293 TCTTGGCTTGGGATGCATCA 59.668 50.0 27.25 6.5 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2205 5063 1.066908 TGGCACGCAAGAAAAAGGAAG 59.933 47.619 0.0 0.0 43.62 3.46 R
3152 6102 1.227527 TCAACACCGTGCCAGACAG 60.228 57.895 0.0 0.0 0.00 3.51 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
22 23 4.265904 ACGTCCAACATGTACAATCTCA 57.734 40.909 0.00 0.00 0.00 3.27
23 24 4.245660 ACGTCCAACATGTACAATCTCAG 58.754 43.478 0.00 0.00 0.00 3.35
24 25 4.245660 CGTCCAACATGTACAATCTCAGT 58.754 43.478 0.00 0.00 0.00 3.41
25 26 4.327357 CGTCCAACATGTACAATCTCAGTC 59.673 45.833 0.00 0.00 0.00 3.51
26 27 5.482908 GTCCAACATGTACAATCTCAGTCT 58.517 41.667 0.00 0.00 0.00 3.24
27 28 5.349817 GTCCAACATGTACAATCTCAGTCTG 59.650 44.000 0.00 0.00 0.00 3.51
28 29 5.245977 TCCAACATGTACAATCTCAGTCTGA 59.754 40.000 0.00 1.78 0.00 3.27
29 30 5.934043 CCAACATGTACAATCTCAGTCTGAA 59.066 40.000 0.00 0.00 0.00 3.02
30 31 6.596888 CCAACATGTACAATCTCAGTCTGAAT 59.403 38.462 0.00 0.00 0.00 2.57
31 32 7.413767 CCAACATGTACAATCTCAGTCTGAATG 60.414 40.741 0.00 4.87 0.00 2.67
32 33 6.939622 ACATGTACAATCTCAGTCTGAATGA 58.060 36.000 7.64 7.64 0.00 2.57
33 34 7.389232 ACATGTACAATCTCAGTCTGAATGAA 58.611 34.615 9.25 1.51 0.00 2.57
34 35 7.332926 ACATGTACAATCTCAGTCTGAATGAAC 59.667 37.037 9.25 4.14 0.00 3.18
35 36 6.997655 TGTACAATCTCAGTCTGAATGAACT 58.002 36.000 9.25 0.00 0.00 3.01
36 37 7.445121 TGTACAATCTCAGTCTGAATGAACTT 58.555 34.615 9.25 3.11 0.00 2.66
37 38 6.798315 ACAATCTCAGTCTGAATGAACTTG 57.202 37.500 19.26 19.26 0.00 3.16
38 39 5.704515 ACAATCTCAGTCTGAATGAACTTGG 59.295 40.000 22.26 8.72 0.00 3.61
39 40 4.963318 TCTCAGTCTGAATGAACTTGGT 57.037 40.909 9.25 0.00 0.00 3.67
40 41 6.611613 ATCTCAGTCTGAATGAACTTGGTA 57.388 37.500 9.25 0.00 0.00 3.25
41 42 5.784177 TCTCAGTCTGAATGAACTTGGTAC 58.216 41.667 9.25 0.00 0.00 3.34
42 43 5.540337 TCTCAGTCTGAATGAACTTGGTACT 59.460 40.000 9.25 0.00 0.00 2.73
43 44 5.541845 TCAGTCTGAATGAACTTGGTACTG 58.458 41.667 5.19 0.00 34.54 2.74
44 45 4.692625 CAGTCTGAATGAACTTGGTACTGG 59.307 45.833 0.00 0.00 0.00 4.00
45 46 4.593206 AGTCTGAATGAACTTGGTACTGGA 59.407 41.667 0.00 0.00 0.00 3.86
46 47 5.249393 AGTCTGAATGAACTTGGTACTGGAT 59.751 40.000 0.00 0.00 0.00 3.41
47 48 5.940470 GTCTGAATGAACTTGGTACTGGATT 59.060 40.000 0.00 0.00 0.00 3.01
48 49 6.431234 GTCTGAATGAACTTGGTACTGGATTT 59.569 38.462 0.00 0.00 0.00 2.17
49 50 7.606456 GTCTGAATGAACTTGGTACTGGATTTA 59.394 37.037 0.00 0.00 0.00 1.40
50 51 8.160765 TCTGAATGAACTTGGTACTGGATTTAA 58.839 33.333 0.00 0.00 0.00 1.52
51 52 8.698973 TGAATGAACTTGGTACTGGATTTAAA 57.301 30.769 0.00 0.00 0.00 1.52
52 53 8.573035 TGAATGAACTTGGTACTGGATTTAAAC 58.427 33.333 0.00 0.00 0.00 2.01
53 54 8.706322 AATGAACTTGGTACTGGATTTAAACT 57.294 30.769 0.00 0.00 0.00 2.66
54 55 8.706322 ATGAACTTGGTACTGGATTTAAACTT 57.294 30.769 0.00 0.00 0.00 2.66
55 56 7.936584 TGAACTTGGTACTGGATTTAAACTTG 58.063 34.615 0.00 0.00 0.00 3.16
56 57 7.776030 TGAACTTGGTACTGGATTTAAACTTGA 59.224 33.333 0.00 0.00 0.00 3.02
57 58 8.706322 AACTTGGTACTGGATTTAAACTTGAT 57.294 30.769 0.00 0.00 0.00 2.57
58 59 8.110860 ACTTGGTACTGGATTTAAACTTGATG 57.889 34.615 0.00 0.00 0.00 3.07
59 60 6.509418 TGGTACTGGATTTAAACTTGATGC 57.491 37.500 0.00 0.00 0.00 3.91
60 61 5.417580 TGGTACTGGATTTAAACTTGATGCC 59.582 40.000 0.00 0.00 0.00 4.40
61 62 5.417580 GGTACTGGATTTAAACTTGATGCCA 59.582 40.000 0.00 0.00 0.00 4.92
62 63 5.391312 ACTGGATTTAAACTTGATGCCAC 57.609 39.130 0.00 0.00 0.00 5.01
63 64 4.082787 ACTGGATTTAAACTTGATGCCACG 60.083 41.667 0.00 0.00 0.00 4.94
64 65 3.192422 TGGATTTAAACTTGATGCCACGG 59.808 43.478 0.00 0.00 0.00 4.94
65 66 3.442273 GGATTTAAACTTGATGCCACGGA 59.558 43.478 0.00 0.00 0.00 4.69
66 67 4.082463 GGATTTAAACTTGATGCCACGGAA 60.082 41.667 0.00 0.00 0.00 4.30
67 68 4.497473 TTTAAACTTGATGCCACGGAAG 57.503 40.909 0.00 0.00 0.00 3.46
68 69 2.270352 AAACTTGATGCCACGGAAGA 57.730 45.000 0.00 0.00 0.00 2.87
69 70 1.813513 AACTTGATGCCACGGAAGAG 58.186 50.000 0.00 0.00 0.00 2.85
70 71 0.976641 ACTTGATGCCACGGAAGAGA 59.023 50.000 0.00 0.00 0.00 3.10
71 72 1.556911 ACTTGATGCCACGGAAGAGAT 59.443 47.619 0.00 0.00 0.00 2.75
72 73 2.208431 CTTGATGCCACGGAAGAGATC 58.792 52.381 0.00 0.00 0.00 2.75
73 74 1.194218 TGATGCCACGGAAGAGATCA 58.806 50.000 0.00 0.00 0.00 2.92
74 75 1.134699 TGATGCCACGGAAGAGATCAC 60.135 52.381 0.00 0.00 0.00 3.06
75 76 0.179000 ATGCCACGGAAGAGATCACC 59.821 55.000 0.00 0.00 0.00 4.02
76 77 1.153349 GCCACGGAAGAGATCACCC 60.153 63.158 0.00 0.00 0.00 4.61
77 78 1.141881 CCACGGAAGAGATCACCCG 59.858 63.158 11.69 11.69 46.65 5.28
78 79 1.519455 CACGGAAGAGATCACCCGC 60.519 63.158 12.76 0.00 45.29 6.13
79 80 1.982395 ACGGAAGAGATCACCCGCA 60.982 57.895 12.76 0.00 45.29 5.69
80 81 1.218047 CGGAAGAGATCACCCGCAA 59.782 57.895 0.00 0.00 35.29 4.85
81 82 0.391130 CGGAAGAGATCACCCGCAAA 60.391 55.000 0.00 0.00 35.29 3.68
82 83 1.821216 GGAAGAGATCACCCGCAAAA 58.179 50.000 0.00 0.00 0.00 2.44
83 84 2.159382 GGAAGAGATCACCCGCAAAAA 58.841 47.619 0.00 0.00 0.00 1.94
84 85 2.162408 GGAAGAGATCACCCGCAAAAAG 59.838 50.000 0.00 0.00 0.00 2.27
85 86 1.826385 AGAGATCACCCGCAAAAAGG 58.174 50.000 0.00 0.00 0.00 3.11
86 87 1.351017 AGAGATCACCCGCAAAAAGGA 59.649 47.619 0.00 0.00 0.00 3.36
87 88 2.159382 GAGATCACCCGCAAAAAGGAA 58.841 47.619 0.00 0.00 0.00 3.36
88 89 2.556622 GAGATCACCCGCAAAAAGGAAA 59.443 45.455 0.00 0.00 0.00 3.13
89 90 2.962421 AGATCACCCGCAAAAAGGAAAA 59.038 40.909 0.00 0.00 0.00 2.29
90 91 2.880963 TCACCCGCAAAAAGGAAAAG 57.119 45.000 0.00 0.00 0.00 2.27
91 92 1.202475 TCACCCGCAAAAAGGAAAAGC 60.202 47.619 0.00 0.00 0.00 3.51
93 94 1.556591 CCCGCAAAAAGGAAAAGCGC 61.557 55.000 0.00 0.00 46.33 5.92
94 95 1.556591 CCGCAAAAAGGAAAAGCGCC 61.557 55.000 2.29 0.00 46.33 6.53
95 96 1.556591 CGCAAAAAGGAAAAGCGCCC 61.557 55.000 2.29 0.00 41.95 6.13
96 97 1.556591 GCAAAAAGGAAAAGCGCCCG 61.557 55.000 2.29 0.00 0.00 6.13
97 98 0.943835 CAAAAAGGAAAAGCGCCCGG 60.944 55.000 2.29 0.00 0.00 5.73
98 99 2.709125 AAAAAGGAAAAGCGCCCGGC 62.709 55.000 2.29 0.00 44.05 6.13
102 103 4.717629 GAAAAGCGCCCGGCCAAC 62.718 66.667 2.29 0.00 45.17 3.77
110 111 4.351054 CCCGGCCAACTCCAAGCT 62.351 66.667 2.24 0.00 0.00 3.74
111 112 3.058160 CCGGCCAACTCCAAGCTG 61.058 66.667 2.24 0.00 0.00 4.24
112 113 2.032528 CGGCCAACTCCAAGCTGA 59.967 61.111 2.24 0.00 34.73 4.26
113 114 1.377725 CGGCCAACTCCAAGCTGAT 60.378 57.895 2.24 0.00 34.73 2.90
114 115 1.372087 CGGCCAACTCCAAGCTGATC 61.372 60.000 2.24 0.00 34.73 2.92
115 116 0.322816 GGCCAACTCCAAGCTGATCA 60.323 55.000 0.00 0.00 0.00 2.92
116 117 1.093159 GCCAACTCCAAGCTGATCAG 58.907 55.000 18.84 18.84 0.00 2.90
146 147 3.211963 GCCAAGGCCTACGCATGG 61.212 66.667 15.11 15.11 43.12 3.66
162 163 1.608717 ATGGAGGGCGTCAGTCAGAC 61.609 60.000 9.66 0.00 44.02 3.51
168 169 1.078759 GGCGTCAGTCAGACCATTCG 61.079 60.000 0.00 0.00 44.66 3.34
206 207 3.674997 ACAGTATTGGAATGCGTCAGTT 58.325 40.909 0.00 0.00 0.00 3.16
253 254 1.067425 CCGATTACGTTCAGTCCACCA 60.067 52.381 0.00 0.00 37.88 4.17
266 267 1.818674 GTCCACCATTGCCAAAGTAGG 59.181 52.381 0.00 0.00 0.00 3.18
270 271 4.023291 CCACCATTGCCAAAGTAGGTATT 58.977 43.478 0.00 0.00 0.00 1.89
271 272 4.142182 CCACCATTGCCAAAGTAGGTATTG 60.142 45.833 0.00 0.00 0.00 1.90
272 273 4.462483 CACCATTGCCAAAGTAGGTATTGT 59.538 41.667 0.00 0.00 0.00 2.71
273 274 4.705023 ACCATTGCCAAAGTAGGTATTGTC 59.295 41.667 0.00 0.00 0.00 3.18
281 282 5.237815 CAAAGTAGGTATTGTCTGTCAGCA 58.762 41.667 0.00 0.00 0.00 4.41
292 293 3.386078 TGTCTGTCAGCAGTTTCTTCTCT 59.614 43.478 0.00 0.00 43.05 3.10
303 304 0.036952 TTCTTCTCTTCTGCCAGCCG 60.037 55.000 0.00 0.00 0.00 5.52
327 328 2.036475 GGATAGCCTGAAGAATCTCGCA 59.964 50.000 0.00 0.00 0.00 5.10
333 334 3.376546 GCCTGAAGAATCTCGCAAAAGAT 59.623 43.478 0.00 0.00 37.61 2.40
337 338 7.680588 GCCTGAAGAATCTCGCAAAAGATAAAT 60.681 37.037 0.00 0.00 34.90 1.40
347 348 8.397906 TCTCGCAAAAGATAAATTATTGTCAGG 58.602 33.333 0.00 0.00 0.00 3.86
472 667 2.793933 CCATCCTGACTTGTACGTACG 58.206 52.381 20.18 15.01 0.00 3.67
539 778 9.716531 CATGATATTGTATACAGTCCATCACTT 57.283 33.333 13.18 0.94 30.26 3.16
575 815 2.613730 TTGTCGTTGTTGTTGCGAAA 57.386 40.000 0.00 0.00 36.37 3.46
592 832 7.813627 TGTTGCGAAAGTGTACATATACTTGTA 59.186 33.333 0.00 0.00 37.64 2.41
602 842 8.639761 GTGTACATATACTTGTAGAACTCCCAT 58.360 37.037 0.00 0.00 32.92 4.00
655 895 4.793071 TCAACGCGAACATTCATGAATTT 58.207 34.783 18.41 14.95 0.00 1.82
709 949 8.480643 AAAATTGAAACATACTACTCTCTCGG 57.519 34.615 0.00 0.00 0.00 4.63
710 950 6.777213 ATTGAAACATACTACTCTCTCGGT 57.223 37.500 0.00 0.00 0.00 4.69
712 952 6.192234 TGAAACATACTACTCTCTCGGTTC 57.808 41.667 0.00 0.00 0.00 3.62
713 953 5.125097 TGAAACATACTACTCTCTCGGTTCC 59.875 44.000 0.00 0.00 0.00 3.62
715 955 4.597004 ACATACTACTCTCTCGGTTCCAA 58.403 43.478 0.00 0.00 0.00 3.53
717 957 5.479375 ACATACTACTCTCTCGGTTCCAAAA 59.521 40.000 0.00 0.00 0.00 2.44
722 971 5.941555 ACTCTCTCGGTTCCAAAATAGAT 57.058 39.130 0.00 0.00 0.00 1.98
723 972 5.665459 ACTCTCTCGGTTCCAAAATAGATG 58.335 41.667 0.00 0.00 0.00 2.90
724 973 5.422331 ACTCTCTCGGTTCCAAAATAGATGA 59.578 40.000 0.00 0.00 0.00 2.92
725 974 5.661458 TCTCTCGGTTCCAAAATAGATGAC 58.339 41.667 0.00 0.00 0.00 3.06
731 980 5.127031 CGGTTCCAAAATAGATGACCCAATT 59.873 40.000 0.00 0.00 0.00 2.32
732 981 6.350949 CGGTTCCAAAATAGATGACCCAATTT 60.351 38.462 0.00 0.00 0.00 1.82
733 982 7.394016 GGTTCCAAAATAGATGACCCAATTTT 58.606 34.615 0.00 0.00 33.07 1.82
764 1013 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
765 1014 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
766 1015 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
767 1016 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
768 1017 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
770 1019 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
771 1020 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
772 1021 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
802 1206 7.147312 TCTGAATTGCGAAAACAAAGATCATT 58.853 30.769 0.00 0.00 32.27 2.57
852 1272 1.812922 CTGTTGCTAGGCAGGCTCG 60.813 63.158 0.00 0.00 40.61 5.03
854 1274 3.705289 TTGCTAGGCAGGCTCGCA 61.705 61.111 18.21 18.21 40.61 5.10
895 3705 2.811317 CACGGACAAGGAGCGAGC 60.811 66.667 0.00 0.00 0.00 5.03
936 3746 1.447217 CGGTGGATATGAGGCTGCA 59.553 57.895 0.50 0.00 0.00 4.41
937 3747 0.602106 CGGTGGATATGAGGCTGCAG 60.602 60.000 10.11 10.11 0.00 4.41
938 3748 0.471617 GGTGGATATGAGGCTGCAGT 59.528 55.000 16.64 0.00 0.00 4.40
939 3749 1.542108 GGTGGATATGAGGCTGCAGTC 60.542 57.143 11.28 11.28 0.00 3.51
977 3787 1.219393 CGACTCTCAAGGGGAAGGC 59.781 63.158 0.00 0.00 0.00 4.35
978 3788 1.604915 GACTCTCAAGGGGAAGGCC 59.395 63.158 0.00 0.00 0.00 5.19
1406 4228 3.519930 GCCTCCTCCTCGTCGTCC 61.520 72.222 0.00 0.00 0.00 4.79
1407 4229 3.203412 CCTCCTCCTCGTCGTCCG 61.203 72.222 0.00 0.00 38.13 4.79
1408 4230 3.203412 CTCCTCCTCGTCGTCCGG 61.203 72.222 0.00 0.00 37.11 5.14
1466 4288 1.970114 GGACGTGGACTCGGACTCA 60.970 63.158 0.00 0.00 34.94 3.41
1475 4297 1.009900 CTCGGACTCATACGACGCC 60.010 63.158 0.00 0.00 35.77 5.68
1901 4735 4.873129 ATCTACAGCACCGCGCCG 62.873 66.667 0.00 0.00 44.04 6.46
1939 4773 0.597072 GACCAGGTTCGTTCGTCTCT 59.403 55.000 0.00 0.00 0.00 3.10
1940 4774 1.000496 GACCAGGTTCGTTCGTCTCTT 60.000 52.381 0.00 0.00 0.00 2.85
1941 4775 1.269621 ACCAGGTTCGTTCGTCTCTTG 60.270 52.381 0.00 0.00 0.00 3.02
1942 4776 1.419374 CAGGTTCGTTCGTCTCTTGG 58.581 55.000 0.00 0.00 0.00 3.61
1956 4790 0.332293 TCTTGGCTTGGGATGCATCA 59.668 50.000 27.25 6.50 0.00 3.07
1957 4791 1.063492 TCTTGGCTTGGGATGCATCAT 60.063 47.619 27.25 0.00 0.00 2.45
1958 4792 1.340248 CTTGGCTTGGGATGCATCATC 59.660 52.381 27.25 18.46 39.87 2.92
1984 4842 5.138125 TCGCATTGCTCACTGATGATATA 57.862 39.130 7.12 0.00 33.22 0.86
1988 4846 5.448768 GCATTGCTCACTGATGATATATGGC 60.449 44.000 0.16 0.00 33.22 4.40
2053 4911 0.976073 GAGGATGGGGTTCGAGGACA 60.976 60.000 0.00 0.00 0.00 4.02
2172 5030 4.432741 GGCAAGGAGTGGAGGGGC 62.433 72.222 0.00 0.00 0.00 5.80
2204 5062 1.855978 CGAGCACGACAACTTGTAACA 59.144 47.619 0.00 0.00 42.66 2.41
2205 5063 2.347292 CGAGCACGACAACTTGTAACAC 60.347 50.000 0.00 0.00 42.66 3.32
2208 5066 3.308866 AGCACGACAACTTGTAACACTTC 59.691 43.478 0.00 0.00 0.00 3.01
2209 5067 3.545426 GCACGACAACTTGTAACACTTCC 60.545 47.826 0.00 0.00 0.00 3.46
2235 5093 1.195448 CTTGCGTGCCAACAGAGTTAG 59.805 52.381 0.00 0.00 0.00 2.34
2237 5095 1.071605 GCGTGCCAACAGAGTTAGAG 58.928 55.000 0.00 0.00 0.00 2.43
2239 5097 2.600731 CGTGCCAACAGAGTTAGAGAG 58.399 52.381 0.00 0.00 0.00 3.20
2261 5119 9.118300 GAGAGGAAATCAATCATGTACATTCTT 57.882 33.333 5.37 0.00 0.00 2.52
2292 5150 3.378427 GGATGAATCTTGTAACTGCCCAC 59.622 47.826 0.00 0.00 0.00 4.61
2316 5174 2.860136 CGATCAATCTGTACACATGCGT 59.140 45.455 0.00 0.00 0.00 5.24
2317 5175 4.041723 CGATCAATCTGTACACATGCGTA 58.958 43.478 0.00 0.00 0.00 4.42
2318 5176 4.147133 CGATCAATCTGTACACATGCGTAG 59.853 45.833 0.00 0.00 0.00 3.51
2319 5177 4.450082 TCAATCTGTACACATGCGTAGT 57.550 40.909 0.00 0.00 0.00 2.73
2321 5179 5.578776 TCAATCTGTACACATGCGTAGTAG 58.421 41.667 0.00 0.00 0.00 2.57
2325 5183 4.937015 TCTGTACACATGCGTAGTAGTACA 59.063 41.667 8.43 11.94 39.36 2.90
2326 5184 5.412286 TCTGTACACATGCGTAGTAGTACAA 59.588 40.000 8.43 0.00 40.59 2.41
2379 5248 0.603707 ACATGGGCGTGTGTGAAGAG 60.604 55.000 0.00 0.00 0.00 2.85
2407 5295 1.658994 AACCTCAAACGAACGAGCAA 58.341 45.000 0.14 0.00 0.00 3.91
2419 5309 4.454504 ACGAACGAGCAATAAAAATGGACT 59.545 37.500 0.14 0.00 0.00 3.85
2462 5352 4.497006 GCATCAGCTCAACATAATCCACAC 60.497 45.833 0.00 0.00 37.91 3.82
2536 5426 3.961477 ACATAATCAAATAAGCGCGCA 57.039 38.095 35.10 14.88 0.00 6.09
2567 5457 4.331968 CCACCTATTTCTGCCAGTAAACA 58.668 43.478 0.00 0.00 0.00 2.83
2737 5627 1.145738 AGCTCCTGTCACCACCAAAAT 59.854 47.619 0.00 0.00 0.00 1.82
2762 5660 4.009675 CAGTTAGGCCACAAGATAAGCAA 58.990 43.478 5.01 0.00 0.00 3.91
2782 5682 4.625742 GCAACTCTACTCAACAGCGATTAA 59.374 41.667 0.00 0.00 0.00 1.40
2785 5685 5.642686 ACTCTACTCAACAGCGATTAACTC 58.357 41.667 0.00 0.00 0.00 3.01
2795 5695 5.488341 ACAGCGATTAACTCATAAACTGGT 58.512 37.500 0.00 0.00 31.95 4.00
2799 5699 9.424319 CAGCGATTAACTCATAAACTGGTATAT 57.576 33.333 0.00 0.00 0.00 0.86
2841 5775 8.299570 GTGTCCAACTGATAAATCATGAAAACT 58.700 33.333 0.00 0.00 36.02 2.66
2888 5822 6.180472 TCTCCAGAAATAGGAAATCACAACC 58.820 40.000 0.00 0.00 34.08 3.77
2892 5826 6.094603 CCAGAAATAGGAAATCACAACCTCTG 59.905 42.308 0.00 0.00 35.52 3.35
2924 5859 6.660887 AAATGAAAATGAGCAAACAAACGT 57.339 29.167 0.00 0.00 0.00 3.99
2925 5860 5.640218 ATGAAAATGAGCAAACAAACGTG 57.360 34.783 0.00 0.00 0.00 4.49
2926 5861 4.738124 TGAAAATGAGCAAACAAACGTGA 58.262 34.783 0.00 0.00 0.00 4.35
2927 5862 4.560819 TGAAAATGAGCAAACAAACGTGAC 59.439 37.500 0.00 0.00 0.00 3.67
2928 5863 3.773860 AATGAGCAAACAAACGTGACA 57.226 38.095 0.00 0.00 0.00 3.58
2929 5864 3.988379 ATGAGCAAACAAACGTGACAT 57.012 38.095 0.00 0.00 0.00 3.06
2930 5865 3.332761 TGAGCAAACAAACGTGACATC 57.667 42.857 0.00 0.00 0.00 3.06
2931 5866 2.942376 TGAGCAAACAAACGTGACATCT 59.058 40.909 0.00 0.00 0.00 2.90
3033 5982 3.144506 CTGGTTCTGCTGACAAGTTCAT 58.855 45.455 0.00 0.00 32.17 2.57
3034 5983 3.141398 TGGTTCTGCTGACAAGTTCATC 58.859 45.455 0.00 0.00 32.17 2.92
3060 6009 4.010349 AGGCTAGAACAAACAGGCATTAC 58.990 43.478 0.00 0.00 37.32 1.89
3091 6040 3.925688 ATGTAGCGTGTTTGCTTATCG 57.074 42.857 0.00 0.00 44.46 2.92
3095 6044 1.665679 AGCGTGTTTGCTTATCGATGG 59.334 47.619 8.54 1.88 44.46 3.51
3096 6045 1.396996 GCGTGTTTGCTTATCGATGGT 59.603 47.619 8.54 0.00 0.00 3.55
3113 6062 4.695455 CGATGGTTAACAGGTTCAATCTGT 59.305 41.667 8.10 0.00 46.22 3.41
3141 6091 9.619842 ATTATCCCAAGCCATTTAATTCCTATT 57.380 29.630 0.00 0.00 0.00 1.73
3148 6098 7.272037 AGCCATTTAATTCCTATTAACACCG 57.728 36.000 0.00 0.00 36.27 4.94
3149 6099 5.918576 GCCATTTAATTCCTATTAACACCGC 59.081 40.000 0.00 0.00 36.27 5.68
3150 6100 6.140110 CCATTTAATTCCTATTAACACCGCG 58.860 40.000 0.00 0.00 36.27 6.46
3152 6102 5.971895 TTAATTCCTATTAACACCGCGAC 57.028 39.130 8.23 0.00 32.60 5.19
3159 6109 0.319211 TTAACACCGCGACTGTCTGG 60.319 55.000 8.23 12.65 0.00 3.86
3178 6135 1.132262 GGCACGGTGTTGACCAATATG 59.868 52.381 10.24 0.00 43.33 1.78
3179 6136 1.467374 GCACGGTGTTGACCAATATGC 60.467 52.381 10.24 0.00 43.33 3.14
3202 6164 8.240267 TGCTACAGTGGTGTATGTACATAATA 57.760 34.615 17.07 7.02 38.51 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.047590 ACTGAGATTGTACATGTTGGACGTA 60.048 40.000 2.30 0.00 32.63 3.57
1 2 4.245660 CTGAGATTGTACATGTTGGACGT 58.754 43.478 2.30 0.00 32.63 4.34
2 3 4.245660 ACTGAGATTGTACATGTTGGACG 58.754 43.478 2.30 0.00 32.63 4.79
3 4 5.349817 CAGACTGAGATTGTACATGTTGGAC 59.650 44.000 2.30 0.00 0.00 4.02
4 5 5.245977 TCAGACTGAGATTGTACATGTTGGA 59.754 40.000 2.30 0.00 0.00 3.53
5 6 5.482006 TCAGACTGAGATTGTACATGTTGG 58.518 41.667 2.30 0.00 0.00 3.77
6 7 7.332678 TCATTCAGACTGAGATTGTACATGTTG 59.667 37.037 2.30 0.00 0.00 3.33
7 8 7.389232 TCATTCAGACTGAGATTGTACATGTT 58.611 34.615 2.30 0.00 0.00 2.71
8 9 6.939622 TCATTCAGACTGAGATTGTACATGT 58.060 36.000 2.69 2.69 0.00 3.21
9 10 7.548427 AGTTCATTCAGACTGAGATTGTACATG 59.452 37.037 5.10 4.43 0.00 3.21
10 11 7.619050 AGTTCATTCAGACTGAGATTGTACAT 58.381 34.615 5.10 0.00 0.00 2.29
11 12 6.997655 AGTTCATTCAGACTGAGATTGTACA 58.002 36.000 5.10 0.00 0.00 2.90
12 13 7.148507 CCAAGTTCATTCAGACTGAGATTGTAC 60.149 40.741 5.10 8.89 0.00 2.90
13 14 6.875726 CCAAGTTCATTCAGACTGAGATTGTA 59.124 38.462 5.10 0.00 0.00 2.41
14 15 5.704515 CCAAGTTCATTCAGACTGAGATTGT 59.295 40.000 5.10 0.00 0.00 2.71
15 16 5.704515 ACCAAGTTCATTCAGACTGAGATTG 59.295 40.000 5.10 5.66 0.00 2.67
16 17 5.874093 ACCAAGTTCATTCAGACTGAGATT 58.126 37.500 5.10 0.00 0.00 2.40
17 18 5.495926 ACCAAGTTCATTCAGACTGAGAT 57.504 39.130 5.10 0.28 0.00 2.75
18 19 4.963318 ACCAAGTTCATTCAGACTGAGA 57.037 40.909 5.10 0.00 0.00 3.27
19 20 5.636965 CAGTACCAAGTTCATTCAGACTGAG 59.363 44.000 5.10 0.00 34.98 3.35
20 21 5.511373 CCAGTACCAAGTTCATTCAGACTGA 60.511 44.000 0.00 0.00 34.98 3.41
21 22 4.692625 CCAGTACCAAGTTCATTCAGACTG 59.307 45.833 0.00 0.00 33.25 3.51
22 23 4.593206 TCCAGTACCAAGTTCATTCAGACT 59.407 41.667 0.00 0.00 0.00 3.24
23 24 4.894784 TCCAGTACCAAGTTCATTCAGAC 58.105 43.478 0.00 0.00 0.00 3.51
24 25 5.762179 ATCCAGTACCAAGTTCATTCAGA 57.238 39.130 0.00 0.00 0.00 3.27
25 26 6.824305 AAATCCAGTACCAAGTTCATTCAG 57.176 37.500 0.00 0.00 0.00 3.02
26 27 8.573035 GTTTAAATCCAGTACCAAGTTCATTCA 58.427 33.333 0.00 0.00 0.00 2.57
27 28 8.793592 AGTTTAAATCCAGTACCAAGTTCATTC 58.206 33.333 0.00 0.00 0.00 2.67
28 29 8.706322 AGTTTAAATCCAGTACCAAGTTCATT 57.294 30.769 0.00 0.00 0.00 2.57
29 30 8.576442 CAAGTTTAAATCCAGTACCAAGTTCAT 58.424 33.333 0.00 0.00 0.00 2.57
30 31 7.776030 TCAAGTTTAAATCCAGTACCAAGTTCA 59.224 33.333 0.00 0.00 0.00 3.18
31 32 8.161699 TCAAGTTTAAATCCAGTACCAAGTTC 57.838 34.615 0.00 0.00 0.00 3.01
32 33 8.576442 CATCAAGTTTAAATCCAGTACCAAGTT 58.424 33.333 0.00 0.00 0.00 2.66
33 34 7.309194 GCATCAAGTTTAAATCCAGTACCAAGT 60.309 37.037 0.00 0.00 0.00 3.16
34 35 7.029563 GCATCAAGTTTAAATCCAGTACCAAG 58.970 38.462 0.00 0.00 0.00 3.61
35 36 6.071616 GGCATCAAGTTTAAATCCAGTACCAA 60.072 38.462 0.00 0.00 0.00 3.67
36 37 5.417580 GGCATCAAGTTTAAATCCAGTACCA 59.582 40.000 0.00 0.00 0.00 3.25
37 38 5.417580 TGGCATCAAGTTTAAATCCAGTACC 59.582 40.000 0.00 0.00 0.00 3.34
38 39 6.322491 GTGGCATCAAGTTTAAATCCAGTAC 58.678 40.000 0.00 0.00 0.00 2.73
39 40 5.123186 CGTGGCATCAAGTTTAAATCCAGTA 59.877 40.000 0.00 0.00 0.00 2.74
40 41 4.082787 CGTGGCATCAAGTTTAAATCCAGT 60.083 41.667 0.00 0.00 0.00 4.00
41 42 4.414852 CGTGGCATCAAGTTTAAATCCAG 58.585 43.478 0.00 0.00 0.00 3.86
42 43 3.192422 CCGTGGCATCAAGTTTAAATCCA 59.808 43.478 0.00 0.00 0.00 3.41
43 44 3.442273 TCCGTGGCATCAAGTTTAAATCC 59.558 43.478 0.00 0.00 0.00 3.01
44 45 4.695217 TCCGTGGCATCAAGTTTAAATC 57.305 40.909 0.00 0.00 0.00 2.17
45 46 4.764823 TCTTCCGTGGCATCAAGTTTAAAT 59.235 37.500 0.00 0.00 0.00 1.40
46 47 4.138290 TCTTCCGTGGCATCAAGTTTAAA 58.862 39.130 0.00 0.00 0.00 1.52
47 48 3.745799 TCTTCCGTGGCATCAAGTTTAA 58.254 40.909 0.00 0.00 0.00 1.52
48 49 3.007506 TCTCTTCCGTGGCATCAAGTTTA 59.992 43.478 0.00 0.00 0.00 2.01
49 50 2.154462 CTCTTCCGTGGCATCAAGTTT 58.846 47.619 0.00 0.00 0.00 2.66
50 51 1.347707 TCTCTTCCGTGGCATCAAGTT 59.652 47.619 0.00 0.00 0.00 2.66
51 52 0.976641 TCTCTTCCGTGGCATCAAGT 59.023 50.000 0.00 0.00 0.00 3.16
52 53 2.208431 GATCTCTTCCGTGGCATCAAG 58.792 52.381 0.00 0.00 0.00 3.02
53 54 1.554617 TGATCTCTTCCGTGGCATCAA 59.445 47.619 0.00 0.00 0.00 2.57
54 55 1.134699 GTGATCTCTTCCGTGGCATCA 60.135 52.381 0.00 0.00 0.00 3.07
55 56 1.576356 GTGATCTCTTCCGTGGCATC 58.424 55.000 0.00 0.00 0.00 3.91
56 57 0.179000 GGTGATCTCTTCCGTGGCAT 59.821 55.000 0.00 0.00 0.00 4.40
57 58 1.596934 GGTGATCTCTTCCGTGGCA 59.403 57.895 0.00 0.00 0.00 4.92
58 59 1.153349 GGGTGATCTCTTCCGTGGC 60.153 63.158 0.00 0.00 0.00 5.01
59 60 1.141881 CGGGTGATCTCTTCCGTGG 59.858 63.158 0.00 0.00 37.92 4.94
60 61 1.519455 GCGGGTGATCTCTTCCGTG 60.519 63.158 12.14 1.18 43.87 4.94
61 62 1.541310 TTGCGGGTGATCTCTTCCGT 61.541 55.000 12.14 0.00 43.87 4.69
62 63 0.391130 TTTGCGGGTGATCTCTTCCG 60.391 55.000 7.77 7.77 44.70 4.30
63 64 1.821216 TTTTGCGGGTGATCTCTTCC 58.179 50.000 0.00 0.00 0.00 3.46
64 65 2.162408 CCTTTTTGCGGGTGATCTCTTC 59.838 50.000 0.00 0.00 0.00 2.87
65 66 2.162681 CCTTTTTGCGGGTGATCTCTT 58.837 47.619 0.00 0.00 0.00 2.85
66 67 1.351017 TCCTTTTTGCGGGTGATCTCT 59.649 47.619 0.00 0.00 0.00 3.10
67 68 1.821216 TCCTTTTTGCGGGTGATCTC 58.179 50.000 0.00 0.00 0.00 2.75
68 69 2.286365 TTCCTTTTTGCGGGTGATCT 57.714 45.000 0.00 0.00 0.00 2.75
69 70 3.317150 CTTTTCCTTTTTGCGGGTGATC 58.683 45.455 0.00 0.00 0.00 2.92
70 71 2.547855 GCTTTTCCTTTTTGCGGGTGAT 60.548 45.455 0.00 0.00 0.00 3.06
71 72 1.202475 GCTTTTCCTTTTTGCGGGTGA 60.202 47.619 0.00 0.00 0.00 4.02
72 73 1.217001 GCTTTTCCTTTTTGCGGGTG 58.783 50.000 0.00 0.00 0.00 4.61
73 74 0.249280 CGCTTTTCCTTTTTGCGGGT 60.249 50.000 0.00 0.00 42.46 5.28
74 75 1.556591 GCGCTTTTCCTTTTTGCGGG 61.557 55.000 0.00 0.00 45.65 6.13
75 76 1.556591 GGCGCTTTTCCTTTTTGCGG 61.557 55.000 7.64 0.00 45.65 5.69
77 78 1.556591 CGGGCGCTTTTCCTTTTTGC 61.557 55.000 7.64 0.00 0.00 3.68
78 79 0.943835 CCGGGCGCTTTTCCTTTTTG 60.944 55.000 7.64 0.00 0.00 2.44
79 80 1.365999 CCGGGCGCTTTTCCTTTTT 59.634 52.632 7.64 0.00 0.00 1.94
80 81 3.047735 CCGGGCGCTTTTCCTTTT 58.952 55.556 7.64 0.00 0.00 2.27
81 82 3.680786 GCCGGGCGCTTTTCCTTT 61.681 61.111 7.64 0.00 0.00 3.11
85 86 4.717629 GTTGGCCGGGCGCTTTTC 62.718 66.667 24.45 5.88 37.74 2.29
93 94 4.351054 AGCTTGGAGTTGGCCGGG 62.351 66.667 2.18 0.00 0.00 5.73
94 95 2.826777 ATCAGCTTGGAGTTGGCCGG 62.827 60.000 0.00 0.00 0.00 6.13
95 96 1.372087 GATCAGCTTGGAGTTGGCCG 61.372 60.000 0.00 0.00 0.00 6.13
96 97 0.322816 TGATCAGCTTGGAGTTGGCC 60.323 55.000 0.00 0.00 0.00 5.36
97 98 1.093159 CTGATCAGCTTGGAGTTGGC 58.907 55.000 10.38 0.00 0.00 4.52
109 110 1.440893 CTCTCCCGTGGCTGATCAG 59.559 63.158 18.84 18.84 0.00 2.90
110 111 2.060383 CCTCTCCCGTGGCTGATCA 61.060 63.158 0.00 0.00 0.00 2.92
111 112 2.801631 CCCTCTCCCGTGGCTGATC 61.802 68.421 0.00 0.00 0.00 2.92
112 113 2.765807 CCCTCTCCCGTGGCTGAT 60.766 66.667 0.00 0.00 0.00 2.90
117 118 4.101448 CTTGGCCCTCTCCCGTGG 62.101 72.222 0.00 0.00 0.00 4.94
146 147 1.608717 ATGGTCTGACTGACGCCCTC 61.609 60.000 7.85 0.00 46.24 4.30
162 163 0.379669 GAGCCATGTTCAGCGAATGG 59.620 55.000 0.00 0.00 43.18 3.16
168 169 2.109126 GTCCGGAGCCATGTTCAGC 61.109 63.158 3.06 0.00 0.00 4.26
206 207 1.301401 CGGTGAGAAACGGCTGGAA 60.301 57.895 0.00 0.00 0.00 3.53
253 254 5.570320 ACAGACAATACCTACTTTGGCAAT 58.430 37.500 0.00 0.00 33.09 3.56
281 282 2.551938 GGCTGGCAGAAGAGAAGAAACT 60.552 50.000 20.86 0.00 0.00 2.66
292 293 1.040646 CTATCCTACGGCTGGCAGAA 58.959 55.000 20.86 0.00 0.00 3.02
303 304 4.617298 GCGAGATTCTTCAGGCTATCCTAC 60.617 50.000 0.00 0.00 41.93 3.18
337 338 8.415950 TTCCTTGCTTAATTTCCTGACAATAA 57.584 30.769 0.00 0.00 0.00 1.40
339 340 6.916360 TTCCTTGCTTAATTTCCTGACAAT 57.084 33.333 0.00 0.00 0.00 2.71
472 667 5.716094 ACATTAAGGCATTAAAACCGAACC 58.284 37.500 7.74 0.00 34.62 3.62
539 778 9.263538 ACAACGACAAAAGACAAGTATATGTAA 57.736 29.630 0.00 0.00 32.57 2.41
560 800 1.889891 ACACTTTCGCAACAACAACG 58.110 45.000 0.00 0.00 0.00 4.10
575 815 7.837689 TGGGAGTTCTACAAGTATATGTACACT 59.162 37.037 0.00 0.00 34.75 3.55
592 832 2.840651 ACGGATCTCAAATGGGAGTTCT 59.159 45.455 0.00 0.00 35.13 3.01
599 839 4.137116 TGTAGGAACGGATCTCAAATGG 57.863 45.455 0.00 0.00 0.00 3.16
602 842 4.884668 ACTTGTAGGAACGGATCTCAAA 57.115 40.909 0.00 0.00 0.00 2.69
655 895 0.747255 GAACTCTGAGGCCGATGCTA 59.253 55.000 9.85 0.00 37.74 3.49
688 928 6.349944 GGAACCGAGAGAGTAGTATGTTTCAA 60.350 42.308 0.00 0.00 0.00 2.69
702 942 5.395324 GGTCATCTATTTTGGAACCGAGAGA 60.395 44.000 0.00 0.00 0.00 3.10
703 943 4.811557 GGTCATCTATTTTGGAACCGAGAG 59.188 45.833 0.00 0.00 0.00 3.20
704 944 4.383770 GGGTCATCTATTTTGGAACCGAGA 60.384 45.833 0.00 0.00 0.00 4.04
705 945 3.877508 GGGTCATCTATTTTGGAACCGAG 59.122 47.826 0.00 0.00 0.00 4.63
706 946 3.264706 TGGGTCATCTATTTTGGAACCGA 59.735 43.478 0.00 0.00 40.06 4.69
707 947 3.616219 TGGGTCATCTATTTTGGAACCG 58.384 45.455 0.00 0.00 40.06 4.44
708 948 6.544928 AATTGGGTCATCTATTTTGGAACC 57.455 37.500 0.00 0.00 37.64 3.62
737 986 8.983702 ATGACCCAACTTTGTACTAACTTTAA 57.016 30.769 0.00 0.00 0.00 1.52
738 987 8.434392 AGATGACCCAACTTTGTACTAACTTTA 58.566 33.333 0.00 0.00 0.00 1.85
740 989 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
742 991 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
743 992 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
744 993 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
747 996 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
748 997 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
755 1004 6.434028 CAGAAACTTCCAAAATAGATGACCCA 59.566 38.462 0.00 0.00 0.00 4.51
760 1009 8.866956 GCAATTCAGAAACTTCCAAAATAGATG 58.133 33.333 0.00 0.00 0.00 2.90
764 1013 6.976088 TCGCAATTCAGAAACTTCCAAAATA 58.024 32.000 0.00 0.00 0.00 1.40
765 1014 5.841810 TCGCAATTCAGAAACTTCCAAAAT 58.158 33.333 0.00 0.00 0.00 1.82
766 1015 5.255710 TCGCAATTCAGAAACTTCCAAAA 57.744 34.783 0.00 0.00 0.00 2.44
767 1016 4.909696 TCGCAATTCAGAAACTTCCAAA 57.090 36.364 0.00 0.00 0.00 3.28
768 1017 4.909696 TTCGCAATTCAGAAACTTCCAA 57.090 36.364 0.00 0.00 0.00 3.53
770 1019 5.040635 TGTTTTCGCAATTCAGAAACTTCC 58.959 37.500 4.79 0.00 36.26 3.46
771 1020 6.567769 TTGTTTTCGCAATTCAGAAACTTC 57.432 33.333 4.79 1.67 36.26 3.01
772 1021 6.811170 TCTTTGTTTTCGCAATTCAGAAACTT 59.189 30.769 4.79 0.00 36.26 2.66
802 1206 4.616604 CGGAATGAGCATGCAGAAAAGAAA 60.617 41.667 21.98 0.00 0.00 2.52
852 1272 3.024782 CTTGCTCTGCTGCGACTGC 62.025 63.158 0.00 0.00 43.20 4.40
854 1274 2.047465 CCTTGCTCTGCTGCGACT 60.047 61.111 0.00 0.00 35.36 4.18
895 3705 0.174845 TGAGGATAGGTGGTTTCGCG 59.825 55.000 0.00 0.00 0.00 5.87
897 3707 2.280628 GCTTGAGGATAGGTGGTTTCG 58.719 52.381 0.00 0.00 0.00 3.46
936 3746 0.321671 CCGATTGGGTGTCACTGACT 59.678 55.000 10.54 0.00 33.15 3.41
937 3747 1.298859 GCCGATTGGGTGTCACTGAC 61.299 60.000 0.00 1.86 38.44 3.51
938 3748 1.003839 GCCGATTGGGTGTCACTGA 60.004 57.895 0.00 0.00 38.44 3.41
939 3749 2.040544 GGCCGATTGGGTGTCACTG 61.041 63.158 0.00 0.00 38.44 3.66
962 3772 1.606531 CTGGCCTTCCCCTTGAGAG 59.393 63.158 3.32 0.00 0.00 3.20
977 3787 1.301293 GAGAAGGGGAAGGTGCTGG 59.699 63.158 0.00 0.00 0.00 4.85
978 3788 1.301293 GGAGAAGGGGAAGGTGCTG 59.699 63.158 0.00 0.00 0.00 4.41
1028 3847 2.031768 GAGGAGGCGGCCATCATC 59.968 66.667 23.09 17.69 0.00 2.92
1029 3848 3.564218 GGAGGAGGCGGCCATCAT 61.564 66.667 23.09 13.22 0.00 2.45
1030 3849 4.804420 AGGAGGAGGCGGCCATCA 62.804 66.667 23.09 0.00 0.00 3.07
1865 4699 1.226831 GCGCTTCTTCCTCTCCTCG 60.227 63.158 0.00 0.00 0.00 4.63
1901 4735 1.156736 CGATGGTGGTGAACTTGGAC 58.843 55.000 0.00 0.00 0.00 4.02
1939 4773 1.405872 GATGATGCATCCCAAGCCAA 58.594 50.000 23.67 2.79 35.07 4.52
1940 4774 3.120796 GATGATGCATCCCAAGCCA 57.879 52.632 23.67 4.28 35.07 4.75
1956 4790 1.674441 CAGTGAGCAATGCGAATGGAT 59.326 47.619 0.00 0.00 0.00 3.41
1957 4791 1.089112 CAGTGAGCAATGCGAATGGA 58.911 50.000 0.00 0.00 0.00 3.41
1958 4792 1.089112 TCAGTGAGCAATGCGAATGG 58.911 50.000 0.00 0.00 0.00 3.16
1960 4794 2.635714 TCATCAGTGAGCAATGCGAAT 58.364 42.857 0.00 0.00 0.00 3.34
1984 4842 2.028748 GTCCAAGCAAATCACAAGCCAT 60.029 45.455 0.00 0.00 0.00 4.40
1988 4846 3.567164 AGACTGTCCAAGCAAATCACAAG 59.433 43.478 3.76 0.00 0.00 3.16
2053 4911 2.735772 CCGGGCTGCTCAGGTACAT 61.736 63.158 0.00 0.00 0.00 2.29
2175 5033 3.996614 TCGTGCTCGATGACCTGA 58.003 55.556 6.80 0.00 41.35 3.86
2204 5062 1.067060 GGCACGCAAGAAAAAGGAAGT 59.933 47.619 0.00 0.00 43.62 3.01
2205 5063 1.066908 TGGCACGCAAGAAAAAGGAAG 59.933 47.619 0.00 0.00 43.62 3.46
2208 5066 1.208259 GTTGGCACGCAAGAAAAAGG 58.792 50.000 0.00 0.00 43.62 3.11
2209 5067 1.854126 CTGTTGGCACGCAAGAAAAAG 59.146 47.619 0.00 0.00 43.62 2.27
2235 5093 8.674263 AGAATGTACATGATTGATTTCCTCTC 57.326 34.615 9.63 0.00 0.00 3.20
2239 5097 9.722056 GTGTAAGAATGTACATGATTGATTTCC 57.278 33.333 9.63 0.00 36.42 3.13
2261 5119 4.860802 ACAAGATTCATCCCCATGTGTA 57.139 40.909 0.00 0.00 0.00 2.90
2292 5150 3.302935 GCATGTGTACAGATTGATCGCAG 60.303 47.826 2.09 0.00 0.00 5.18
2347 5216 3.119990 ACGCCCATGTAATTTCGTTTGAG 60.120 43.478 0.00 0.00 0.00 3.02
2353 5222 1.466950 ACACACGCCCATGTAATTTCG 59.533 47.619 0.00 0.00 0.00 3.46
2379 5248 4.348656 GTTCGTTTGAGGTTTTCAAGTCC 58.651 43.478 0.00 0.00 46.01 3.85
2407 5295 7.937700 TCTATGAGGGAGAGTCCATTTTTAT 57.062 36.000 0.00 0.00 38.64 1.40
2419 5309 3.897505 TGCGATGAATTCTATGAGGGAGA 59.102 43.478 7.05 0.00 0.00 3.71
2462 5352 2.483106 CAGATGCTTGTGTCTGGAGTTG 59.517 50.000 0.00 0.00 38.50 3.16
2536 5426 2.166254 CAGAAATAGGTGGCGGCAAATT 59.834 45.455 15.50 11.35 0.00 1.82
2737 5627 4.700213 GCTTATCTTGTGGCCTAACTGAAA 59.300 41.667 3.32 0.00 0.00 2.69
2762 5660 5.183331 TGAGTTAATCGCTGTTGAGTAGAGT 59.817 40.000 0.00 0.00 0.00 3.24
2802 5702 7.433708 TCAGTTGGACACATAATAAGTTGTG 57.566 36.000 1.74 1.74 46.76 3.33
2810 5710 9.631257 TCATGATTTATCAGTTGGACACATAAT 57.369 29.630 0.00 0.00 40.64 1.28
2813 5713 7.943079 TTCATGATTTATCAGTTGGACACAT 57.057 32.000 0.00 0.00 40.64 3.21
2815 5715 8.299570 AGTTTTCATGATTTATCAGTTGGACAC 58.700 33.333 0.00 0.00 40.64 3.67
2816 5716 8.408043 AGTTTTCATGATTTATCAGTTGGACA 57.592 30.769 0.00 0.00 40.64 4.02
2819 5719 9.956720 GGATAGTTTTCATGATTTATCAGTTGG 57.043 33.333 0.00 0.00 40.64 3.77
2861 5795 8.743714 GTTGTGATTTCCTATTTCTGGAGATTT 58.256 33.333 0.00 0.00 34.76 2.17
2902 5836 5.809562 TCACGTTTGTTTGCTCATTTTCATT 59.190 32.000 0.00 0.00 0.00 2.57
2903 5837 5.231991 GTCACGTTTGTTTGCTCATTTTCAT 59.768 36.000 0.00 0.00 0.00 2.57
2904 5838 4.560819 GTCACGTTTGTTTGCTCATTTTCA 59.439 37.500 0.00 0.00 0.00 2.69
2910 5844 2.942376 AGATGTCACGTTTGTTTGCTCA 59.058 40.909 0.00 0.00 0.00 4.26
2913 5847 7.240674 TGATTATAGATGTCACGTTTGTTTGC 58.759 34.615 0.00 0.00 0.00 3.68
2920 5855 8.317891 TGTTTGTTGATTATAGATGTCACGTT 57.682 30.769 0.00 0.00 0.00 3.99
2921 5856 7.899178 TGTTTGTTGATTATAGATGTCACGT 57.101 32.000 0.00 0.00 0.00 4.49
2922 5857 9.213819 CATTGTTTGTTGATTATAGATGTCACG 57.786 33.333 0.00 0.00 0.00 4.35
2924 5859 9.241919 ACCATTGTTTGTTGATTATAGATGTCA 57.758 29.630 0.00 0.00 0.00 3.58
2925 5860 9.722056 GACCATTGTTTGTTGATTATAGATGTC 57.278 33.333 0.00 0.00 0.00 3.06
2926 5861 9.241919 TGACCATTGTTTGTTGATTATAGATGT 57.758 29.630 0.00 0.00 0.00 3.06
2927 5862 9.507280 GTGACCATTGTTTGTTGATTATAGATG 57.493 33.333 0.00 0.00 0.00 2.90
2928 5863 9.241919 TGTGACCATTGTTTGTTGATTATAGAT 57.758 29.630 0.00 0.00 0.00 1.98
2929 5864 8.628630 TGTGACCATTGTTTGTTGATTATAGA 57.371 30.769 0.00 0.00 0.00 1.98
2930 5865 9.507280 GATGTGACCATTGTTTGTTGATTATAG 57.493 33.333 0.00 0.00 0.00 1.31
2931 5866 9.018582 TGATGTGACCATTGTTTGTTGATTATA 57.981 29.630 0.00 0.00 0.00 0.98
3033 5982 3.307480 GCCTGTTTGTTCTAGCCTAAGGA 60.307 47.826 0.00 0.00 0.00 3.36
3034 5983 3.010420 GCCTGTTTGTTCTAGCCTAAGG 58.990 50.000 0.00 0.00 0.00 2.69
3060 6009 5.450376 AACACGCTACATTTAGTCAATCG 57.550 39.130 0.00 0.00 0.00 3.34
3091 6040 5.705441 TGACAGATTGAACCTGTTAACCATC 59.295 40.000 2.48 0.00 44.14 3.51
3095 6044 8.398665 GGATAATGACAGATTGAACCTGTTAAC 58.601 37.037 0.00 0.00 44.14 2.01
3096 6045 7.556275 GGGATAATGACAGATTGAACCTGTTAA 59.444 37.037 0.00 0.00 44.14 2.01
3113 6062 7.075148 AGGAATTAAATGGCTTGGGATAATGA 58.925 34.615 0.00 0.00 0.00 2.57
3141 6091 1.287815 CCAGACAGTCGCGGTGTTA 59.712 57.895 14.89 0.00 0.00 2.41
3148 6098 4.664677 ACCGTGCCAGACAGTCGC 62.665 66.667 0.00 0.00 0.00 5.19
3149 6099 2.734723 CACCGTGCCAGACAGTCG 60.735 66.667 0.00 0.00 0.00 4.18
3150 6100 1.227556 AACACCGTGCCAGACAGTC 60.228 57.895 0.00 0.00 0.00 3.51
3152 6102 1.227527 TCAACACCGTGCCAGACAG 60.228 57.895 0.00 0.00 0.00 3.51
3178 6135 8.573885 TCTATTATGTACATACACCACTGTAGC 58.426 37.037 15.20 0.00 39.30 3.58
3179 6136 9.894783 GTCTATTATGTACATACACCACTGTAG 57.105 37.037 15.20 7.78 39.30 2.74


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

AutoCloner maintained by Alex Coulton.