Multiple sequence alignment - TraesCS5B01G291300

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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 TraesCS5B01G291300 chr5B 100.000 3465 0 0 1 3465 476918745 476915281 0.000000e+00 6399.0
1 TraesCS5B01G291300 chr5B 86.275 969 122 6 906 1864 476907722 476906755 0.000000e+00 1042.0
2 TraesCS5B01G291300 chr5B 82.065 920 124 16 1253 2134 477984386 477985302 0.000000e+00 747.0
3 TraesCS5B01G291300 chr5B 86.815 675 74 8 1879 2541 476906705 476906034 0.000000e+00 739.0
4 TraesCS5B01G291300 chr5B 81.878 607 62 12 1939 2541 476903000 476902438 5.240000e-128 468.0
5 TraesCS5B01G291300 chr5B 80.899 178 25 7 205 382 476908824 476908656 7.800000e-27 132.0
6 TraesCS5B01G291300 chr5D 95.303 1022 46 2 862 1882 396947045 396946025 0.000000e+00 1620.0
7 TraesCS5B01G291300 chr5D 94.753 667 31 2 1879 2541 396945999 396945333 0.000000e+00 1035.0
8 TraesCS5B01G291300 chr5D 77.200 1614 318 40 944 2528 397929786 397931378 0.000000e+00 896.0
9 TraesCS5B01G291300 chr5D 95.415 349 11 2 386 730 396947563 396947216 5.050000e-153 551.0
10 TraesCS5B01G291300 chr5D 78.228 914 149 29 1528 2400 397941409 397942313 1.090000e-149 540.0
11 TraesCS5B01G291300 chr5D 90.351 228 16 4 164 391 396947830 396947609 9.400000e-76 294.0
12 TraesCS5B01G291300 chr5D 81.404 285 45 4 1253 1531 397940973 397941255 3.480000e-55 226.0
13 TraesCS5B01G291300 chr3B 91.251 903 48 11 2590 3465 548041910 548041012 0.000000e+00 1201.0
14 TraesCS5B01G291300 chr3B 88.759 427 24 10 3063 3465 31525959 31525533 5.160000e-138 501.0
15 TraesCS5B01G291300 chr1B 89.845 906 56 13 2590 3465 542689309 542690208 0.000000e+00 1131.0
16 TraesCS5B01G291300 chr1B 94.294 333 19 0 3133 3465 647181051 647180719 8.580000e-141 510.0
17 TraesCS5B01G291300 chr1B 88.837 430 24 13 3060 3465 56995202 56995631 1.110000e-139 507.0
18 TraesCS5B01G291300 chr7B 90.593 776 48 12 2699 3450 551900827 551900053 0.000000e+00 1005.0
19 TraesCS5B01G291300 chr7B 88.328 317 33 2 2695 3008 60337325 60337010 9.080000e-101 377.0
20 TraesCS5B01G291300 chr5A 85.582 971 109 20 906 1864 502501084 502500133 0.000000e+00 989.0
21 TraesCS5B01G291300 chr5A 77.170 1590 309 37 968 2528 503050094 503051658 0.000000e+00 876.0
22 TraesCS5B01G291300 chr5A 79.926 1076 168 25 1367 2400 503060801 503061870 0.000000e+00 747.0
23 TraesCS5B01G291300 chr5A 84.663 652 89 5 1879 2520 502500083 502499433 1.050000e-179 640.0
24 TraesCS5B01G291300 chr1D 89.429 473 38 5 2590 3057 448612148 448612613 1.390000e-163 586.0
25 TraesCS5B01G291300 chr1D 88.865 458 27 8 2589 3042 76086246 76085809 3.040000e-150 542.0
26 TraesCS5B01G291300 chr1D 93.694 333 21 0 3133 3465 25674751 25674419 1.860000e-137 499.0
27 TraesCS5B01G291300 chr1D 88.056 427 27 1 3063 3465 11318496 11318070 5.200000e-133 484.0
28 TraesCS5B01G291300 chr1D 89.024 246 18 2 2815 3057 447476163 447475924 2.610000e-76 296.0
29 TraesCS5B01G291300 chrUn 92.308 403 22 2 3063 3465 24306690 24306297 6.490000e-157 564.0
30 TraesCS5B01G291300 chr6B 89.041 438 35 8 2589 3021 476121192 476120763 6.580000e-147 531.0
31 TraesCS5B01G291300 chr4B 88.372 430 26 6 3060 3465 132344112 132344541 2.400000e-136 496.0
32 TraesCS5B01G291300 chr4B 93.393 333 22 0 3133 3465 2506914 2507246 8.640000e-136 494.0
33 TraesCS5B01G291300 chr4B 86.667 420 32 8 3063 3458 58751149 58751568 8.820000e-121 444.0
34 TraesCS5B01G291300 chr7D 88.140 430 27 7 3060 3465 108353597 108354026 1.120000e-134 490.0
35 TraesCS5B01G291300 chr7D 87.907 430 28 6 3060 3465 108379127 108379556 5.200000e-133 484.0
36 TraesCS5B01G291300 chr7D 92.793 333 24 0 3133 3465 20004022 20004354 1.870000e-132 483.0
37 TraesCS5B01G291300 chr7D 87.089 426 31 9 3060 3461 108375086 108375511 8.760000e-126 460.0
38 TraesCS5B01G291300 chr7D 90.909 44 4 0 588 631 123223903 123223860 3.730000e-05 60.2
39 TraesCS5B01G291300 chr6D 93.313 329 22 0 3137 3465 12555681 12555353 1.450000e-133 486.0
40 TraesCS5B01G291300 chr6D 93.617 94 3 2 770 861 217177387 217177295 1.680000e-28 137.0
41 TraesCS5B01G291300 chr7A 86.105 439 39 15 2589 3021 627012012 627012434 1.470000e-123 453.0
42 TraesCS5B01G291300 chr7A 90.159 315 24 6 2702 3012 627049790 627050101 1.500000e-108 403.0
43 TraesCS5B01G291300 chr4A 91.900 321 26 0 3145 3465 625258635 625258315 1.900000e-122 449.0
44 TraesCS5B01G291300 chr3A 78.992 119 11 2 528 632 582348622 582348740 6.210000e-08 69.4


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 TraesCS5B01G291300 chr5B 476915281 476918745 3464 True 6399.00 6399 100.00000 1 3465 1 chr5B.!!$R1 3464
1 TraesCS5B01G291300 chr5B 477984386 477985302 916 False 747.00 747 82.06500 1253 2134 1 chr5B.!!$F1 881
2 TraesCS5B01G291300 chr5B 476902438 476908824 6386 True 595.25 1042 83.96675 205 2541 4 chr5B.!!$R2 2336
3 TraesCS5B01G291300 chr5D 397929786 397931378 1592 False 896.00 896 77.20000 944 2528 1 chr5D.!!$F1 1584
4 TraesCS5B01G291300 chr5D 396945333 396947830 2497 True 875.00 1620 93.95550 164 2541 4 chr5D.!!$R1 2377
5 TraesCS5B01G291300 chr5D 397940973 397942313 1340 False 383.00 540 79.81600 1253 2400 2 chr5D.!!$F2 1147
6 TraesCS5B01G291300 chr3B 548041012 548041910 898 True 1201.00 1201 91.25100 2590 3465 1 chr3B.!!$R2 875
7 TraesCS5B01G291300 chr1B 542689309 542690208 899 False 1131.00 1131 89.84500 2590 3465 1 chr1B.!!$F2 875
8 TraesCS5B01G291300 chr7B 551900053 551900827 774 True 1005.00 1005 90.59300 2699 3450 1 chr7B.!!$R2 751
9 TraesCS5B01G291300 chr5A 503050094 503051658 1564 False 876.00 876 77.17000 968 2528 1 chr5A.!!$F1 1560
10 TraesCS5B01G291300 chr5A 502499433 502501084 1651 True 814.50 989 85.12250 906 2520 2 chr5A.!!$R1 1614
11 TraesCS5B01G291300 chr5A 503060801 503061870 1069 False 747.00 747 79.92600 1367 2400 1 chr5A.!!$F2 1033
12 TraesCS5B01G291300 chr7D 108375086 108379556 4470 False 472.00 484 87.49800 3060 3465 2 chr7D.!!$F3 405

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
59 60 0.035458 CAGGGAAGGAACTCGCAGTT 59.965 55.0 1.82 1.82 41.95 3.16 F
782 1276 0.104409 ACACTCCCAACCCCTTCTCT 60.104 55.0 0.00 0.00 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1305 1880 0.250234 TCTCAGGAATCGCAAGGGTG 59.750 55.0 0.0 0.0 38.47 4.61 R
2566 6999 0.399233 CGGGAGGAGAGAGGGGAATT 60.399 60.0 0.0 0.0 0.00 2.17 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
19 20 2.851805 CGAGATGATGGTTCTCACGA 57.148 50.000 0.00 0.00 39.69 4.35
20 21 3.361794 CGAGATGATGGTTCTCACGAT 57.638 47.619 0.00 0.00 39.69 3.73
21 22 4.489679 CGAGATGATGGTTCTCACGATA 57.510 45.455 0.00 0.00 39.69 2.92
22 23 4.471373 CGAGATGATGGTTCTCACGATAG 58.529 47.826 0.00 0.00 39.69 2.08
23 24 4.233789 GAGATGATGGTTCTCACGATAGC 58.766 47.826 0.00 0.00 39.54 2.97
24 25 3.638627 AGATGATGGTTCTCACGATAGCA 59.361 43.478 0.00 0.00 42.67 3.49
25 26 3.885724 TGATGGTTCTCACGATAGCAA 57.114 42.857 0.00 0.00 42.67 3.91
26 27 4.200838 TGATGGTTCTCACGATAGCAAA 57.799 40.909 0.00 0.00 42.67 3.68
27 28 4.574892 TGATGGTTCTCACGATAGCAAAA 58.425 39.130 0.00 0.00 42.67 2.44
28 29 4.631377 TGATGGTTCTCACGATAGCAAAAG 59.369 41.667 0.00 0.00 42.67 2.27
29 30 4.265904 TGGTTCTCACGATAGCAAAAGA 57.734 40.909 0.00 0.00 42.67 2.52
30 31 4.637276 TGGTTCTCACGATAGCAAAAGAA 58.363 39.130 0.00 0.00 42.67 2.52
31 32 4.690748 TGGTTCTCACGATAGCAAAAGAAG 59.309 41.667 0.00 0.00 42.67 2.85
32 33 4.093556 GGTTCTCACGATAGCAAAAGAAGG 59.906 45.833 0.00 0.00 42.67 3.46
33 34 3.861840 TCTCACGATAGCAAAAGAAGGG 58.138 45.455 0.00 0.00 42.67 3.95
34 35 2.939103 CTCACGATAGCAAAAGAAGGGG 59.061 50.000 0.00 0.00 42.67 4.79
35 36 2.017049 CACGATAGCAAAAGAAGGGGG 58.983 52.381 0.00 0.00 42.67 5.40
36 37 1.633945 ACGATAGCAAAAGAAGGGGGT 59.366 47.619 0.00 0.00 42.67 4.95
37 38 2.289565 CGATAGCAAAAGAAGGGGGTC 58.710 52.381 0.00 0.00 0.00 4.46
38 39 2.092914 CGATAGCAAAAGAAGGGGGTCT 60.093 50.000 0.00 0.00 0.00 3.85
39 40 3.622455 CGATAGCAAAAGAAGGGGGTCTT 60.622 47.826 0.00 0.00 39.60 3.01
40 41 7.829962 ACGATAGCAAAAGAAGGGGGTCTTC 62.830 48.000 0.00 0.00 46.11 2.87
47 48 2.792635 AAGGGGGTCTTCAGGGAAG 58.207 57.895 0.00 0.00 40.65 3.46
48 49 0.846870 AAGGGGGTCTTCAGGGAAGG 60.847 60.000 6.17 0.00 39.82 3.46
49 50 1.229853 GGGGGTCTTCAGGGAAGGA 60.230 63.158 6.17 0.00 39.82 3.36
50 51 0.845102 GGGGGTCTTCAGGGAAGGAA 60.845 60.000 6.17 0.00 39.82 3.36
51 52 0.328592 GGGGTCTTCAGGGAAGGAAC 59.671 60.000 6.17 0.00 39.82 3.62
53 54 1.279558 GGGTCTTCAGGGAAGGAACTC 59.720 57.143 6.17 0.00 38.49 3.01
54 55 1.066787 GGTCTTCAGGGAAGGAACTCG 60.067 57.143 6.17 0.00 38.49 4.18
55 56 0.608640 TCTTCAGGGAAGGAACTCGC 59.391 55.000 6.17 0.00 38.49 5.03
56 57 0.321671 CTTCAGGGAAGGAACTCGCA 59.678 55.000 0.00 0.00 38.49 5.10
57 58 0.321671 TTCAGGGAAGGAACTCGCAG 59.678 55.000 0.00 0.00 38.49 5.18
58 59 0.832135 TCAGGGAAGGAACTCGCAGT 60.832 55.000 0.00 0.00 38.49 4.40
59 60 0.035458 CAGGGAAGGAACTCGCAGTT 59.965 55.000 1.82 1.82 41.95 3.16
66 67 2.533318 GAACTCGCAGTTCCACAGG 58.467 57.895 14.47 0.00 46.68 4.00
67 68 0.249911 GAACTCGCAGTTCCACAGGT 60.250 55.000 14.47 0.00 46.68 4.00
68 69 1.000506 GAACTCGCAGTTCCACAGGTA 59.999 52.381 14.47 0.00 46.68 3.08
69 70 1.045407 ACTCGCAGTTCCACAGGTAA 58.955 50.000 0.00 0.00 0.00 2.85
70 71 1.270147 ACTCGCAGTTCCACAGGTAAC 60.270 52.381 0.00 0.00 0.00 2.50
71 72 0.753867 TCGCAGTTCCACAGGTAACA 59.246 50.000 0.00 0.00 41.41 2.41
72 73 0.865769 CGCAGTTCCACAGGTAACAC 59.134 55.000 0.00 0.00 41.41 3.32
73 74 1.808512 CGCAGTTCCACAGGTAACACA 60.809 52.381 0.00 0.00 41.41 3.72
74 75 2.504367 GCAGTTCCACAGGTAACACAT 58.496 47.619 0.00 0.00 41.41 3.21
75 76 2.484264 GCAGTTCCACAGGTAACACATC 59.516 50.000 0.00 0.00 41.41 3.06
76 77 3.074412 CAGTTCCACAGGTAACACATCC 58.926 50.000 0.00 0.00 41.41 3.51
77 78 2.979678 AGTTCCACAGGTAACACATCCT 59.020 45.455 0.00 0.00 41.41 3.24
78 79 3.394606 AGTTCCACAGGTAACACATCCTT 59.605 43.478 0.00 0.00 41.41 3.36
79 80 3.695830 TCCACAGGTAACACATCCTTC 57.304 47.619 0.00 0.00 41.41 3.46
80 81 2.304761 TCCACAGGTAACACATCCTTCC 59.695 50.000 0.00 0.00 41.41 3.46
81 82 2.039746 CCACAGGTAACACATCCTTCCA 59.960 50.000 0.00 0.00 41.41 3.53
82 83 3.308402 CCACAGGTAACACATCCTTCCAT 60.308 47.826 0.00 0.00 41.41 3.41
83 84 3.691118 CACAGGTAACACATCCTTCCATG 59.309 47.826 0.00 0.00 41.41 3.66
84 85 3.587061 ACAGGTAACACATCCTTCCATGA 59.413 43.478 0.00 0.00 41.41 3.07
85 86 4.042809 ACAGGTAACACATCCTTCCATGAA 59.957 41.667 0.00 0.00 41.41 2.57
86 87 5.195940 CAGGTAACACATCCTTCCATGAAT 58.804 41.667 0.00 0.00 41.41 2.57
87 88 5.653769 CAGGTAACACATCCTTCCATGAATT 59.346 40.000 0.00 0.00 41.41 2.17
88 89 6.153340 CAGGTAACACATCCTTCCATGAATTT 59.847 38.462 0.00 0.00 41.41 1.82
89 90 6.153340 AGGTAACACATCCTTCCATGAATTTG 59.847 38.462 0.00 0.00 41.41 2.32
90 91 6.152661 GGTAACACATCCTTCCATGAATTTGA 59.847 38.462 0.00 0.00 0.00 2.69
91 92 6.669125 AACACATCCTTCCATGAATTTGAA 57.331 33.333 0.00 0.00 0.00 2.69
92 93 6.862469 ACACATCCTTCCATGAATTTGAAT 57.138 33.333 0.00 0.00 0.00 2.57
93 94 6.636705 ACACATCCTTCCATGAATTTGAATG 58.363 36.000 0.00 0.00 0.00 2.67
94 95 6.046593 CACATCCTTCCATGAATTTGAATGG 58.953 40.000 0.00 8.68 44.06 3.16
95 96 4.741321 TCCTTCCATGAATTTGAATGGC 57.259 40.909 9.71 0.00 42.67 4.40
96 97 4.095211 TCCTTCCATGAATTTGAATGGCA 58.905 39.130 9.71 0.00 42.67 4.92
97 98 4.081531 TCCTTCCATGAATTTGAATGGCAC 60.082 41.667 9.71 0.00 42.67 5.01
110 111 3.238232 TGGCACAAGCTGATCTGAC 57.762 52.632 3.42 0.00 41.70 3.51
111 112 0.671472 TGGCACAAGCTGATCTGACG 60.671 55.000 3.42 0.00 41.70 4.35
112 113 0.390340 GGCACAAGCTGATCTGACGA 60.390 55.000 3.42 0.00 41.70 4.20
113 114 0.718343 GCACAAGCTGATCTGACGAC 59.282 55.000 3.42 0.00 37.91 4.34
114 115 1.354040 CACAAGCTGATCTGACGACC 58.646 55.000 3.42 0.00 0.00 4.79
115 116 1.067283 CACAAGCTGATCTGACGACCT 60.067 52.381 3.42 0.00 0.00 3.85
116 117 2.164422 CACAAGCTGATCTGACGACCTA 59.836 50.000 3.42 0.00 0.00 3.08
117 118 3.027412 ACAAGCTGATCTGACGACCTAT 58.973 45.455 3.42 0.00 0.00 2.57
118 119 3.181482 ACAAGCTGATCTGACGACCTATG 60.181 47.826 3.42 0.00 0.00 2.23
119 120 1.339610 AGCTGATCTGACGACCTATGC 59.660 52.381 3.42 0.00 0.00 3.14
120 121 1.339610 GCTGATCTGACGACCTATGCT 59.660 52.381 3.42 0.00 0.00 3.79
121 122 2.554462 GCTGATCTGACGACCTATGCTA 59.446 50.000 3.42 0.00 0.00 3.49
122 123 3.365868 GCTGATCTGACGACCTATGCTAG 60.366 52.174 3.42 0.00 0.00 3.42
123 124 2.554462 TGATCTGACGACCTATGCTAGC 59.446 50.000 8.10 8.10 0.00 3.42
124 125 2.350057 TCTGACGACCTATGCTAGCT 57.650 50.000 17.23 4.07 0.00 3.32
125 126 3.487120 TCTGACGACCTATGCTAGCTA 57.513 47.619 17.23 2.58 0.00 3.32
126 127 3.403968 TCTGACGACCTATGCTAGCTAG 58.596 50.000 16.84 16.84 0.00 3.42
166 167 8.508800 TTTACTGTATTTATTTTTGCGTGTGG 57.491 30.769 0.00 0.00 0.00 4.17
167 168 6.079424 ACTGTATTTATTTTTGCGTGTGGT 57.921 33.333 0.00 0.00 0.00 4.16
180 181 1.089920 GTGTGGTCCTGCTGCATTAG 58.910 55.000 1.31 0.00 0.00 1.73
192 193 5.182001 CCTGCTGCATTAGTACTTCTGTTTT 59.818 40.000 1.31 0.00 0.00 2.43
209 210 6.991938 TCTGTTTTATTCCAATTGTTCCAGG 58.008 36.000 4.43 0.00 0.00 4.45
210 211 6.780031 TCTGTTTTATTCCAATTGTTCCAGGA 59.220 34.615 4.43 0.00 0.00 3.86
213 214 8.093927 TGTTTTATTCCAATTGTTCCAGGATTC 58.906 33.333 4.43 0.00 0.00 2.52
214 215 7.789202 TTTATTCCAATTGTTCCAGGATTCA 57.211 32.000 4.43 0.00 0.00 2.57
215 216 7.976414 TTATTCCAATTGTTCCAGGATTCAT 57.024 32.000 4.43 0.00 0.00 2.57
216 217 5.920193 TTCCAATTGTTCCAGGATTCATC 57.080 39.130 4.43 0.00 0.00 2.92
217 218 5.197224 TCCAATTGTTCCAGGATTCATCT 57.803 39.130 4.43 0.00 0.00 2.90
218 219 5.195940 TCCAATTGTTCCAGGATTCATCTC 58.804 41.667 4.43 0.00 0.00 2.75
219 220 4.340381 CCAATTGTTCCAGGATTCATCTCC 59.660 45.833 4.43 0.00 35.37 3.71
220 221 2.988010 TGTTCCAGGATTCATCTCCG 57.012 50.000 0.00 0.00 40.46 4.63
221 222 1.134401 TGTTCCAGGATTCATCTCCGC 60.134 52.381 0.00 0.00 40.46 5.54
223 224 1.043116 TCCAGGATTCATCTCCGCGT 61.043 55.000 4.92 0.00 40.46 6.01
267 268 8.495949 CGAGTCTTGTTAAAGAGCAGAAAATTA 58.504 33.333 0.00 0.00 43.13 1.40
291 292 3.141398 TGTTCTGTTCCAGATTCAGTGC 58.859 45.455 0.00 0.00 40.39 4.40
365 366 6.590068 TCAGATTCTGGAGATTTCTGATTCC 58.410 40.000 13.59 0.00 38.07 3.01
382 383 2.380064 TCCCATGTTCAACAGCCTTT 57.620 45.000 0.00 0.00 0.00 3.11
384 385 1.001181 CCCATGTTCAACAGCCTTTGG 59.999 52.381 0.00 0.00 0.00 3.28
433 507 6.923508 CACAAACTTTCTCCAGATTAAAACCC 59.076 38.462 0.00 0.00 0.00 4.11
435 509 6.650427 AACTTTCTCCAGATTAAAACCCAC 57.350 37.500 0.00 0.00 0.00 4.61
483 557 5.273944 GTCGCAAATGAACTTCAGAACTTT 58.726 37.500 0.00 0.00 0.00 2.66
573 651 8.894768 AATCGAAGTTCTAGGATTTCCATAAG 57.105 34.615 0.56 0.00 38.89 1.73
620 698 8.594881 AATCCACAAAGATCTACGATATCAAC 57.405 34.615 3.12 0.00 0.00 3.18
625 703 9.684448 CACAAAGATCTACGATATCAACTATGT 57.316 33.333 3.12 0.00 0.00 2.29
672 780 8.923683 GGTAGTAGAACTTAGTAAAGCTTTGTG 58.076 37.037 22.02 9.09 36.05 3.33
709 1014 7.543868 CAGTTGTCAGAGGTAGTAAATCTTCTG 59.456 40.741 0.00 0.00 32.70 3.02
735 1040 7.953158 TCTTAGTGATCAAAAGTTGTCAGAG 57.047 36.000 15.24 0.00 0.00 3.35
736 1041 6.931281 TCTTAGTGATCAAAAGTTGTCAGAGG 59.069 38.462 15.24 0.00 0.00 3.69
738 1043 6.174720 AGTGATCAAAAGTTGTCAGAGGTA 57.825 37.500 0.00 0.00 0.00 3.08
740 1045 5.992217 GTGATCAAAAGTTGTCAGAGGTAGT 59.008 40.000 0.00 0.00 0.00 2.73
741 1046 5.991606 TGATCAAAAGTTGTCAGAGGTAGTG 59.008 40.000 0.00 0.00 0.00 2.74
769 1263 5.005779 CGCTATTGTTGACTCATAACACTCC 59.994 44.000 0.00 0.00 37.73 3.85
770 1264 5.294552 GCTATTGTTGACTCATAACACTCCC 59.705 44.000 0.00 0.00 37.73 4.30
771 1265 4.698201 TTGTTGACTCATAACACTCCCA 57.302 40.909 0.00 0.00 37.73 4.37
773 1267 4.385825 TGTTGACTCATAACACTCCCAAC 58.614 43.478 0.00 0.00 33.43 3.77
774 1268 3.695830 TGACTCATAACACTCCCAACC 57.304 47.619 0.00 0.00 0.00 3.77
775 1269 2.304761 TGACTCATAACACTCCCAACCC 59.695 50.000 0.00 0.00 0.00 4.11
776 1270 1.633945 ACTCATAACACTCCCAACCCC 59.366 52.381 0.00 0.00 0.00 4.95
778 1272 2.308866 CTCATAACACTCCCAACCCCTT 59.691 50.000 0.00 0.00 0.00 3.95
779 1273 2.307686 TCATAACACTCCCAACCCCTTC 59.692 50.000 0.00 0.00 0.00 3.46
780 1274 2.127651 TAACACTCCCAACCCCTTCT 57.872 50.000 0.00 0.00 0.00 2.85
781 1275 0.771755 AACACTCCCAACCCCTTCTC 59.228 55.000 0.00 0.00 0.00 2.87
782 1276 0.104409 ACACTCCCAACCCCTTCTCT 60.104 55.000 0.00 0.00 0.00 3.10
783 1277 1.068121 CACTCCCAACCCCTTCTCTT 58.932 55.000 0.00 0.00 0.00 2.85
784 1278 1.425448 CACTCCCAACCCCTTCTCTTT 59.575 52.381 0.00 0.00 0.00 2.52
785 1279 2.144450 ACTCCCAACCCCTTCTCTTTT 58.856 47.619 0.00 0.00 0.00 2.27
786 1280 2.518407 ACTCCCAACCCCTTCTCTTTTT 59.482 45.455 0.00 0.00 0.00 1.94
787 1281 3.157881 CTCCCAACCCCTTCTCTTTTTC 58.842 50.000 0.00 0.00 0.00 2.29
788 1282 2.516277 TCCCAACCCCTTCTCTTTTTCA 59.484 45.455 0.00 0.00 0.00 2.69
789 1283 3.142028 TCCCAACCCCTTCTCTTTTTCAT 59.858 43.478 0.00 0.00 0.00 2.57
790 1284 4.355588 TCCCAACCCCTTCTCTTTTTCATA 59.644 41.667 0.00 0.00 0.00 2.15
791 1285 5.083821 CCCAACCCCTTCTCTTTTTCATAA 58.916 41.667 0.00 0.00 0.00 1.90
792 1286 5.185828 CCCAACCCCTTCTCTTTTTCATAAG 59.814 44.000 0.00 0.00 0.00 1.73
793 1287 6.010219 CCAACCCCTTCTCTTTTTCATAAGA 58.990 40.000 0.00 0.00 33.33 2.10
794 1288 6.071896 CCAACCCCTTCTCTTTTTCATAAGAC 60.072 42.308 0.00 0.00 31.19 3.01
795 1289 6.455690 ACCCCTTCTCTTTTTCATAAGACT 57.544 37.500 0.00 0.00 31.19 3.24
796 1290 6.241645 ACCCCTTCTCTTTTTCATAAGACTG 58.758 40.000 0.00 0.00 31.19 3.51
797 1291 6.044404 ACCCCTTCTCTTTTTCATAAGACTGA 59.956 38.462 0.00 0.00 31.19 3.41
798 1292 6.597280 CCCCTTCTCTTTTTCATAAGACTGAG 59.403 42.308 0.00 0.00 31.19 3.35
799 1293 6.597280 CCCTTCTCTTTTTCATAAGACTGAGG 59.403 42.308 0.00 0.00 31.19 3.86
800 1294 7.164803 CCTTCTCTTTTTCATAAGACTGAGGT 58.835 38.462 0.00 0.00 31.19 3.85
801 1295 8.314751 CCTTCTCTTTTTCATAAGACTGAGGTA 58.685 37.037 0.00 0.00 31.19 3.08
802 1296 9.883142 CTTCTCTTTTTCATAAGACTGAGGTAT 57.117 33.333 0.00 0.00 31.19 2.73
805 1299 9.757227 CTCTTTTTCATAAGACTGAGGTATAGG 57.243 37.037 0.00 0.00 31.19 2.57
806 1300 9.268282 TCTTTTTCATAAGACTGAGGTATAGGT 57.732 33.333 0.00 0.00 0.00 3.08
809 1303 8.707796 TTTCATAAGACTGAGGTATAGGTAGG 57.292 38.462 0.00 0.00 0.00 3.18
810 1304 6.791371 TCATAAGACTGAGGTATAGGTAGGG 58.209 44.000 0.00 0.00 0.00 3.53
811 1305 3.529216 AGACTGAGGTATAGGTAGGGC 57.471 52.381 0.00 0.00 0.00 5.19
812 1306 3.065175 AGACTGAGGTATAGGTAGGGCT 58.935 50.000 0.00 0.00 0.00 5.19
813 1307 4.249490 AGACTGAGGTATAGGTAGGGCTA 58.751 47.826 0.00 0.00 0.00 3.93
814 1308 4.668812 AGACTGAGGTATAGGTAGGGCTAA 59.331 45.833 0.00 0.00 0.00 3.09
815 1309 5.135705 AGACTGAGGTATAGGTAGGGCTAAA 59.864 44.000 0.00 0.00 0.00 1.85
816 1310 5.785123 ACTGAGGTATAGGTAGGGCTAAAA 58.215 41.667 0.00 0.00 0.00 1.52
817 1311 6.207532 ACTGAGGTATAGGTAGGGCTAAAAA 58.792 40.000 0.00 0.00 0.00 1.94
841 1335 6.934561 AAGCAAAATAAAGAGTCAAATCGC 57.065 33.333 0.00 0.00 0.00 4.58
842 1336 6.012658 AGCAAAATAAAGAGTCAAATCGCA 57.987 33.333 0.00 0.00 0.00 5.10
843 1337 5.858581 AGCAAAATAAAGAGTCAAATCGCAC 59.141 36.000 0.00 0.00 0.00 5.34
844 1338 5.060940 GCAAAATAAAGAGTCAAATCGCACC 59.939 40.000 0.00 0.00 0.00 5.01
845 1339 5.957842 AAATAAAGAGTCAAATCGCACCA 57.042 34.783 0.00 0.00 0.00 4.17
846 1340 5.957842 AATAAAGAGTCAAATCGCACCAA 57.042 34.783 0.00 0.00 0.00 3.67
847 1341 3.626028 AAAGAGTCAAATCGCACCAAC 57.374 42.857 0.00 0.00 0.00 3.77
848 1342 2.550830 AGAGTCAAATCGCACCAACT 57.449 45.000 0.00 0.00 0.00 3.16
849 1343 2.417719 AGAGTCAAATCGCACCAACTC 58.582 47.619 0.00 0.00 34.69 3.01
850 1344 2.037772 AGAGTCAAATCGCACCAACTCT 59.962 45.455 0.00 0.00 38.82 3.24
851 1345 3.258372 AGAGTCAAATCGCACCAACTCTA 59.742 43.478 1.20 0.00 41.11 2.43
852 1346 4.081420 AGAGTCAAATCGCACCAACTCTAT 60.081 41.667 1.20 0.00 41.11 1.98
853 1347 5.127194 AGAGTCAAATCGCACCAACTCTATA 59.873 40.000 1.20 0.00 41.11 1.31
854 1348 5.730550 AGTCAAATCGCACCAACTCTATAA 58.269 37.500 0.00 0.00 0.00 0.98
855 1349 6.349300 AGTCAAATCGCACCAACTCTATAAT 58.651 36.000 0.00 0.00 0.00 1.28
856 1350 7.497595 AGTCAAATCGCACCAACTCTATAATA 58.502 34.615 0.00 0.00 0.00 0.98
857 1351 7.985184 AGTCAAATCGCACCAACTCTATAATAA 59.015 33.333 0.00 0.00 0.00 1.40
858 1352 8.276325 GTCAAATCGCACCAACTCTATAATAAG 58.724 37.037 0.00 0.00 0.00 1.73
859 1353 7.985184 TCAAATCGCACCAACTCTATAATAAGT 59.015 33.333 0.00 0.00 0.00 2.24
860 1354 9.256477 CAAATCGCACCAACTCTATAATAAGTA 57.744 33.333 0.00 0.00 0.00 2.24
861 1355 9.477484 AAATCGCACCAACTCTATAATAAGTAG 57.523 33.333 0.00 0.00 0.00 2.57
862 1356 6.978338 TCGCACCAACTCTATAATAAGTAGG 58.022 40.000 0.00 0.00 0.00 3.18
863 1357 6.015688 TCGCACCAACTCTATAATAAGTAGGG 60.016 42.308 0.00 0.00 0.00 3.53
864 1358 6.015688 CGCACCAACTCTATAATAAGTAGGGA 60.016 42.308 0.00 0.00 0.00 4.20
865 1359 7.470981 CGCACCAACTCTATAATAAGTAGGGAA 60.471 40.741 0.00 0.00 0.00 3.97
866 1360 8.208903 GCACCAACTCTATAATAAGTAGGGAAA 58.791 37.037 0.00 0.00 0.00 3.13
1055 1626 1.363807 CGATACGAGATGCTGCCCA 59.636 57.895 0.00 0.00 0.00 5.36
1081 1652 0.647410 CTGCGTATCTCGTGCCTTTG 59.353 55.000 0.00 0.00 42.13 2.77
1096 1667 3.772025 TGCCTTTGGAAGTTCTTGGAAAA 59.228 39.130 2.25 0.00 0.00 2.29
1162 1733 0.971959 TGGCATGGATTTCACCTGCC 60.972 55.000 15.70 15.70 45.43 4.85
1191 1763 7.111247 TGATCACATTTTGGAAAAACACTCT 57.889 32.000 0.00 0.00 0.00 3.24
1207 1779 1.651240 CTCTGGCATTGGCGTGAAGG 61.651 60.000 5.68 0.00 42.47 3.46
1224 1796 5.402398 GTGAAGGCATTCGAGCTTAATTTT 58.598 37.500 6.62 0.00 38.34 1.82
1247 1819 5.560724 TCCCTTTTTCTACAAGTCTGATGG 58.439 41.667 0.00 0.00 0.00 3.51
1305 1880 5.465390 GGTTAAACCTGGCATTGAAAAACTC 59.535 40.000 0.00 0.00 34.73 3.01
1443 2029 3.118261 TCAGTCTTGGTTGCTTGAGAAGT 60.118 43.478 0.00 0.00 0.00 3.01
1444 2030 3.629398 CAGTCTTGGTTGCTTGAGAAGTT 59.371 43.478 0.00 0.00 0.00 2.66
1464 2050 1.852942 TGACAGTGCTGTTTCTCGAC 58.147 50.000 6.28 0.00 45.05 4.20
1681 2426 7.164230 AGGTTTCACTTTACAACATTTCACA 57.836 32.000 0.00 0.00 0.00 3.58
2043 2849 1.003580 TCTTTTCTTGATGCCGCTCCT 59.996 47.619 0.00 0.00 0.00 3.69
2077 2888 3.678056 TCACACTGAATGTAGGTCACC 57.322 47.619 0.00 0.00 40.64 4.02
2113 2928 7.922278 GCAAATATTCTTGAATGCACTTATCCA 59.078 33.333 6.15 0.00 34.10 3.41
2125 2940 9.169468 GAATGCACTTATCCAACAAATATAACG 57.831 33.333 0.00 0.00 0.00 3.18
2220 3040 8.192068 CAAGAATGCATTGATGAATTGCTTTA 57.808 30.769 18.59 0.00 36.18 1.85
2235 3055 2.869801 TGCTTTATAAAGATCCGCCACG 59.130 45.455 26.00 0.05 38.28 4.94
2258 6678 4.081087 GTCTAAGGAAGTTGCCAGGATACA 60.081 45.833 0.00 0.00 41.41 2.29
2345 6768 3.179048 GCGTGCCATATTCTTGAAAACC 58.821 45.455 0.00 0.00 0.00 3.27
2438 6871 2.559440 CTCCTTCTTGCATAGAGCCAC 58.441 52.381 0.00 0.00 44.83 5.01
2493 6926 2.249844 ACATCGTGGGAAAAGTTCGT 57.750 45.000 0.00 0.00 0.00 3.85
2505 6938 7.225341 GTGGGAAAAGTTCGTTCTAGAGTTAAA 59.775 37.037 0.00 0.00 0.00 1.52
2529 6962 1.547372 GATGTTGTGGAGCCTTGCATT 59.453 47.619 0.00 0.00 0.00 3.56
2547 6980 2.851263 TTTGGTGCCATACGAGAGTT 57.149 45.000 0.00 0.00 46.40 3.01
2548 6981 2.851263 TTGGTGCCATACGAGAGTTT 57.149 45.000 0.00 0.00 46.40 2.66
2549 6982 2.851263 TGGTGCCATACGAGAGTTTT 57.149 45.000 0.00 0.00 46.40 2.43
2550 6983 3.134574 TGGTGCCATACGAGAGTTTTT 57.865 42.857 0.00 0.00 46.40 1.94
2576 7009 4.453480 TCAACTTGTGAAATTCCCCTCT 57.547 40.909 0.00 0.00 31.51 3.69
2577 7010 4.398319 TCAACTTGTGAAATTCCCCTCTC 58.602 43.478 0.00 0.00 31.51 3.20
2578 7011 4.104738 TCAACTTGTGAAATTCCCCTCTCT 59.895 41.667 0.00 0.00 31.51 3.10
2579 7012 4.293662 ACTTGTGAAATTCCCCTCTCTC 57.706 45.455 0.00 0.00 0.00 3.20
2580 7013 3.009584 ACTTGTGAAATTCCCCTCTCTCC 59.990 47.826 0.00 0.00 0.00 3.71
2581 7014 2.921221 TGTGAAATTCCCCTCTCTCCT 58.079 47.619 0.00 0.00 0.00 3.69
2582 7015 2.840651 TGTGAAATTCCCCTCTCTCCTC 59.159 50.000 0.00 0.00 0.00 3.71
2583 7016 2.171659 GTGAAATTCCCCTCTCTCCTCC 59.828 54.545 0.00 0.00 0.00 4.30
2584 7017 1.771854 GAAATTCCCCTCTCTCCTCCC 59.228 57.143 0.00 0.00 0.00 4.30
2585 7018 0.399233 AATTCCCCTCTCTCCTCCCG 60.399 60.000 0.00 0.00 0.00 5.14
2586 7019 1.595058 ATTCCCCTCTCTCCTCCCGT 61.595 60.000 0.00 0.00 0.00 5.28
2587 7020 2.443016 CCCCTCTCTCCTCCCGTG 60.443 72.222 0.00 0.00 0.00 4.94
2588 7021 2.360980 CCCTCTCTCCTCCCGTGT 59.639 66.667 0.00 0.00 0.00 4.49
3151 7614 3.289834 CAGGCGTGGTTGCTGCTT 61.290 61.111 0.00 0.00 34.52 3.91
3156 7619 2.980233 GTGGTTGCTGCTTCGGCT 60.980 61.111 0.00 0.00 42.37 5.52
3203 7666 3.688159 GCCTACCGGTGTCGTGGT 61.688 66.667 19.93 0.00 42.34 4.16
3271 7734 2.970324 GGCGTCGGTTTGTCTGCA 60.970 61.111 0.00 0.00 0.00 4.41
3348 7811 2.610859 GGGCTGGTCCTCTCCCAA 60.611 66.667 8.29 0.00 38.62 4.12
3403 11907 2.258591 GGCAGAACTCGTCTCGCA 59.741 61.111 0.00 0.00 32.70 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.851805 TCGTGAGAACCATCATCTCG 57.148 50.000 0.00 0.00 45.05 4.04
13 14 2.939103 CCCCTTCTTTTGCTATCGTGAG 59.061 50.000 0.00 0.00 0.00 3.51
14 15 2.355716 CCCCCTTCTTTTGCTATCGTGA 60.356 50.000 0.00 0.00 0.00 4.35
15 16 2.017049 CCCCCTTCTTTTGCTATCGTG 58.983 52.381 0.00 0.00 0.00 4.35
16 17 1.633945 ACCCCCTTCTTTTGCTATCGT 59.366 47.619 0.00 0.00 0.00 3.73
17 18 2.092914 AGACCCCCTTCTTTTGCTATCG 60.093 50.000 0.00 0.00 0.00 2.92
18 19 3.653835 AGACCCCCTTCTTTTGCTATC 57.346 47.619 0.00 0.00 0.00 2.08
19 20 3.969553 GAAGACCCCCTTCTTTTGCTAT 58.030 45.455 0.00 0.00 46.03 2.97
20 21 3.434940 GAAGACCCCCTTCTTTTGCTA 57.565 47.619 0.00 0.00 46.03 3.49
21 22 2.294449 GAAGACCCCCTTCTTTTGCT 57.706 50.000 0.00 0.00 46.03 3.91
29 30 0.846870 CCTTCCCTGAAGACCCCCTT 60.847 60.000 5.43 0.00 41.71 3.95
30 31 1.229984 CCTTCCCTGAAGACCCCCT 60.230 63.158 5.43 0.00 41.71 4.79
31 32 0.845102 TTCCTTCCCTGAAGACCCCC 60.845 60.000 5.43 0.00 41.71 5.40
32 33 0.328592 GTTCCTTCCCTGAAGACCCC 59.671 60.000 5.43 0.00 41.71 4.95
33 34 1.279558 GAGTTCCTTCCCTGAAGACCC 59.720 57.143 5.43 0.00 41.71 4.46
34 35 1.066787 CGAGTTCCTTCCCTGAAGACC 60.067 57.143 5.43 0.00 41.71 3.85
35 36 1.673329 GCGAGTTCCTTCCCTGAAGAC 60.673 57.143 5.43 0.00 41.71 3.01
36 37 0.608640 GCGAGTTCCTTCCCTGAAGA 59.391 55.000 5.43 0.00 41.71 2.87
37 38 0.321671 TGCGAGTTCCTTCCCTGAAG 59.678 55.000 0.00 0.00 39.17 3.02
38 39 0.321671 CTGCGAGTTCCTTCCCTGAA 59.678 55.000 0.00 0.00 0.00 3.02
39 40 0.832135 ACTGCGAGTTCCTTCCCTGA 60.832 55.000 0.00 0.00 0.00 3.86
40 41 0.035458 AACTGCGAGTTCCTTCCCTG 59.965 55.000 0.00 0.00 31.77 4.45
41 42 0.321996 GAACTGCGAGTTCCTTCCCT 59.678 55.000 14.47 0.00 46.68 4.20
42 43 2.842320 GAACTGCGAGTTCCTTCCC 58.158 57.895 14.47 0.00 46.68 3.97
49 50 1.045407 TACCTGTGGAACTGCGAGTT 58.955 50.000 1.82 1.82 41.95 3.01
50 51 1.045407 TTACCTGTGGAACTGCGAGT 58.955 50.000 0.00 0.00 38.04 4.18
51 52 1.270094 TGTTACCTGTGGAACTGCGAG 60.270 52.381 0.00 0.00 38.04 5.03
52 53 0.753867 TGTTACCTGTGGAACTGCGA 59.246 50.000 0.00 0.00 38.04 5.10
53 54 0.865769 GTGTTACCTGTGGAACTGCG 59.134 55.000 0.00 0.00 38.04 5.18
54 55 1.961793 TGTGTTACCTGTGGAACTGC 58.038 50.000 0.00 0.00 38.04 4.40
55 56 3.074412 GGATGTGTTACCTGTGGAACTG 58.926 50.000 0.00 0.00 38.04 3.16
56 57 2.979678 AGGATGTGTTACCTGTGGAACT 59.020 45.455 0.00 0.00 38.04 3.01
57 58 3.418684 AGGATGTGTTACCTGTGGAAC 57.581 47.619 0.00 0.00 34.99 3.62
58 59 3.244770 GGAAGGATGTGTTACCTGTGGAA 60.245 47.826 0.00 0.00 36.56 3.53
59 60 2.304761 GGAAGGATGTGTTACCTGTGGA 59.695 50.000 0.00 0.00 36.56 4.02
60 61 2.039746 TGGAAGGATGTGTTACCTGTGG 59.960 50.000 0.00 0.00 36.56 4.17
61 62 3.417069 TGGAAGGATGTGTTACCTGTG 57.583 47.619 0.00 0.00 36.56 3.66
62 63 3.587061 TCATGGAAGGATGTGTTACCTGT 59.413 43.478 0.00 0.00 36.56 4.00
63 64 4.220693 TCATGGAAGGATGTGTTACCTG 57.779 45.455 0.00 0.00 36.56 4.00
64 65 4.927267 TTCATGGAAGGATGTGTTACCT 57.073 40.909 0.00 0.00 38.23 3.08
65 66 6.152661 TCAAATTCATGGAAGGATGTGTTACC 59.847 38.462 0.00 0.00 0.00 2.85
66 67 7.156876 TCAAATTCATGGAAGGATGTGTTAC 57.843 36.000 0.00 0.00 0.00 2.50
67 68 7.773489 TTCAAATTCATGGAAGGATGTGTTA 57.227 32.000 0.00 0.00 0.00 2.41
68 69 6.669125 TTCAAATTCATGGAAGGATGTGTT 57.331 33.333 0.00 0.00 0.00 3.32
69 70 6.351541 CCATTCAAATTCATGGAAGGATGTGT 60.352 38.462 5.64 0.00 42.49 3.72
70 71 6.046593 CCATTCAAATTCATGGAAGGATGTG 58.953 40.000 5.64 0.00 42.49 3.21
71 72 5.395990 GCCATTCAAATTCATGGAAGGATGT 60.396 40.000 13.14 0.00 42.49 3.06
72 73 5.054477 GCCATTCAAATTCATGGAAGGATG 58.946 41.667 13.14 0.00 42.49 3.51
73 74 4.717778 TGCCATTCAAATTCATGGAAGGAT 59.282 37.500 13.14 0.00 42.49 3.24
74 75 4.081531 GTGCCATTCAAATTCATGGAAGGA 60.082 41.667 13.14 0.00 42.49 3.36
75 76 4.186159 GTGCCATTCAAATTCATGGAAGG 58.814 43.478 13.14 0.00 42.49 3.46
76 77 4.823157 TGTGCCATTCAAATTCATGGAAG 58.177 39.130 13.14 0.00 42.49 3.46
77 78 4.886496 TGTGCCATTCAAATTCATGGAA 57.114 36.364 13.14 2.55 42.49 3.53
78 79 4.823157 CTTGTGCCATTCAAATTCATGGA 58.177 39.130 13.14 0.00 42.49 3.41
79 80 3.372822 GCTTGTGCCATTCAAATTCATGG 59.627 43.478 6.83 6.83 42.73 3.66
80 81 4.092821 CAGCTTGTGCCATTCAAATTCATG 59.907 41.667 0.00 0.00 40.80 3.07
81 82 4.020928 TCAGCTTGTGCCATTCAAATTCAT 60.021 37.500 0.00 0.00 40.80 2.57
82 83 3.321396 TCAGCTTGTGCCATTCAAATTCA 59.679 39.130 0.00 0.00 40.80 2.57
83 84 3.916761 TCAGCTTGTGCCATTCAAATTC 58.083 40.909 0.00 0.00 40.80 2.17
84 85 4.222145 AGATCAGCTTGTGCCATTCAAATT 59.778 37.500 0.00 0.00 40.80 1.82
85 86 3.767673 AGATCAGCTTGTGCCATTCAAAT 59.232 39.130 0.00 0.00 40.80 2.32
86 87 3.057104 CAGATCAGCTTGTGCCATTCAAA 60.057 43.478 0.00 0.00 40.80 2.69
87 88 2.490509 CAGATCAGCTTGTGCCATTCAA 59.509 45.455 0.00 0.00 40.80 2.69
88 89 2.089201 CAGATCAGCTTGTGCCATTCA 58.911 47.619 0.00 0.00 40.80 2.57
89 90 2.097142 GTCAGATCAGCTTGTGCCATTC 59.903 50.000 0.00 0.00 40.80 2.67
90 91 2.089980 GTCAGATCAGCTTGTGCCATT 58.910 47.619 0.00 0.00 40.80 3.16
91 92 1.747709 GTCAGATCAGCTTGTGCCAT 58.252 50.000 0.00 0.00 40.80 4.40
92 93 0.671472 CGTCAGATCAGCTTGTGCCA 60.671 55.000 0.00 0.00 40.80 4.92
93 94 0.390340 TCGTCAGATCAGCTTGTGCC 60.390 55.000 0.00 0.00 40.80 5.01
94 95 0.718343 GTCGTCAGATCAGCTTGTGC 59.282 55.000 0.00 0.00 40.05 4.57
95 96 1.067283 AGGTCGTCAGATCAGCTTGTG 60.067 52.381 0.00 0.00 0.00 3.33
96 97 1.261480 AGGTCGTCAGATCAGCTTGT 58.739 50.000 0.00 0.00 0.00 3.16
97 98 3.379240 CATAGGTCGTCAGATCAGCTTG 58.621 50.000 0.00 0.00 0.00 4.01
98 99 2.223923 GCATAGGTCGTCAGATCAGCTT 60.224 50.000 0.00 0.00 0.00 3.74
99 100 1.339610 GCATAGGTCGTCAGATCAGCT 59.660 52.381 0.00 0.00 0.00 4.24
100 101 1.339610 AGCATAGGTCGTCAGATCAGC 59.660 52.381 0.00 0.00 0.00 4.26
101 102 3.365868 GCTAGCATAGGTCGTCAGATCAG 60.366 52.174 10.63 0.00 39.70 2.90
102 103 2.554462 GCTAGCATAGGTCGTCAGATCA 59.446 50.000 10.63 0.00 39.70 2.92
103 104 3.210358 GCTAGCATAGGTCGTCAGATC 57.790 52.381 10.63 0.00 39.70 2.75
140 141 9.134734 CCACACGCAAAAATAAATACAGTAAAT 57.865 29.630 0.00 0.00 0.00 1.40
141 142 8.136165 ACCACACGCAAAAATAAATACAGTAAA 58.864 29.630 0.00 0.00 0.00 2.01
142 143 7.649973 ACCACACGCAAAAATAAATACAGTAA 58.350 30.769 0.00 0.00 0.00 2.24
143 144 7.204496 ACCACACGCAAAAATAAATACAGTA 57.796 32.000 0.00 0.00 0.00 2.74
144 145 6.079424 ACCACACGCAAAAATAAATACAGT 57.921 33.333 0.00 0.00 0.00 3.55
145 146 5.571357 GGACCACACGCAAAAATAAATACAG 59.429 40.000 0.00 0.00 0.00 2.74
146 147 5.241949 AGGACCACACGCAAAAATAAATACA 59.758 36.000 0.00 0.00 0.00 2.29
147 148 5.571357 CAGGACCACACGCAAAAATAAATAC 59.429 40.000 0.00 0.00 0.00 1.89
148 149 5.704888 CAGGACCACACGCAAAAATAAATA 58.295 37.500 0.00 0.00 0.00 1.40
149 150 4.555262 CAGGACCACACGCAAAAATAAAT 58.445 39.130 0.00 0.00 0.00 1.40
150 151 3.797184 GCAGGACCACACGCAAAAATAAA 60.797 43.478 0.00 0.00 0.00 1.40
151 152 2.287909 GCAGGACCACACGCAAAAATAA 60.288 45.455 0.00 0.00 0.00 1.40
152 153 1.268352 GCAGGACCACACGCAAAAATA 59.732 47.619 0.00 0.00 0.00 1.40
153 154 0.031994 GCAGGACCACACGCAAAAAT 59.968 50.000 0.00 0.00 0.00 1.82
154 155 1.034838 AGCAGGACCACACGCAAAAA 61.035 50.000 0.00 0.00 0.00 1.94
155 156 1.453015 AGCAGGACCACACGCAAAA 60.453 52.632 0.00 0.00 0.00 2.44
156 157 2.186160 CAGCAGGACCACACGCAAA 61.186 57.895 0.00 0.00 0.00 3.68
157 158 2.591429 CAGCAGGACCACACGCAA 60.591 61.111 0.00 0.00 0.00 4.85
160 161 0.673333 TAATGCAGCAGGACCACACG 60.673 55.000 0.00 0.00 0.00 4.49
161 162 1.089920 CTAATGCAGCAGGACCACAC 58.910 55.000 0.00 0.00 0.00 3.82
162 163 0.692476 ACTAATGCAGCAGGACCACA 59.308 50.000 0.00 0.00 0.00 4.17
163 164 2.093447 AGTACTAATGCAGCAGGACCAC 60.093 50.000 0.00 0.00 0.00 4.16
164 165 2.187958 AGTACTAATGCAGCAGGACCA 58.812 47.619 0.00 0.00 0.00 4.02
165 166 2.990066 AGTACTAATGCAGCAGGACC 57.010 50.000 0.00 0.00 0.00 4.46
166 167 3.868077 CAGAAGTACTAATGCAGCAGGAC 59.132 47.826 0.00 4.81 0.00 3.85
167 168 3.515502 ACAGAAGTACTAATGCAGCAGGA 59.484 43.478 0.00 0.00 0.00 3.86
180 181 9.406828 GGAACAATTGGAATAAAACAGAAGTAC 57.593 33.333 10.83 0.00 0.00 2.73
192 193 7.356680 AGATGAATCCTGGAACAATTGGAATA 58.643 34.615 10.83 0.00 38.70 1.75
209 210 2.209838 TTCTGACGCGGAGATGAATC 57.790 50.000 12.47 0.00 0.00 2.52
210 211 2.672961 TTTCTGACGCGGAGATGAAT 57.327 45.000 12.47 0.00 0.00 2.57
213 214 1.714794 AGTTTTCTGACGCGGAGATG 58.285 50.000 12.47 0.00 0.00 2.90
291 292 7.491682 AGTTTGCTTAAGGGCATAATATGTTG 58.508 34.615 4.29 0.00 42.09 3.33
319 320 1.586154 AAAGCGACATCCCAAAGGCG 61.586 55.000 0.00 0.00 0.00 5.52
344 345 5.688807 TGGGAATCAGAAATCTCCAGAATC 58.311 41.667 0.00 0.00 0.00 2.52
365 366 1.962807 TCCAAAGGCTGTTGAACATGG 59.037 47.619 8.26 8.26 0.00 3.66
382 383 0.106769 TTTGTGGCACTTCTGCTCCA 60.107 50.000 19.83 0.00 43.66 3.86
384 385 1.265365 GTCTTTGTGGCACTTCTGCTC 59.735 52.381 19.83 0.10 43.66 4.26
433 507 2.390938 CATTTGAGTGCAAGCAGTGTG 58.609 47.619 7.19 0.00 35.04 3.82
435 509 1.415374 GCATTTGAGTGCAAGCAGTG 58.585 50.000 7.19 0.00 44.43 3.66
462 536 7.617935 GCATTAAAGTTCTGAAGTTCATTTGCG 60.618 37.037 5.91 0.00 0.00 4.85
730 1035 2.502142 TAGCGGTTCACTACCTCTGA 57.498 50.000 0.00 0.00 41.99 3.27
731 1036 3.119101 ACAATAGCGGTTCACTACCTCTG 60.119 47.826 0.00 0.00 41.99 3.35
733 1038 3.521947 ACAATAGCGGTTCACTACCTC 57.478 47.619 0.00 0.00 45.40 3.85
734 1039 3.259876 TCAACAATAGCGGTTCACTACCT 59.740 43.478 0.00 0.00 45.40 3.08
735 1040 3.370061 GTCAACAATAGCGGTTCACTACC 59.630 47.826 0.00 0.00 44.03 3.18
736 1041 4.243270 AGTCAACAATAGCGGTTCACTAC 58.757 43.478 0.00 0.00 27.24 2.73
738 1043 3.244078 TGAGTCAACAATAGCGGTTCACT 60.244 43.478 0.00 0.00 31.99 3.41
740 1045 3.394674 TGAGTCAACAATAGCGGTTCA 57.605 42.857 0.00 0.00 0.00 3.18
741 1046 5.350365 TGTTATGAGTCAACAATAGCGGTTC 59.650 40.000 0.00 0.00 33.11 3.62
769 1263 6.010219 TCTTATGAAAAAGAGAAGGGGTTGG 58.990 40.000 0.00 0.00 31.85 3.77
770 1264 6.717084 AGTCTTATGAAAAAGAGAAGGGGTTG 59.283 38.462 0.00 0.00 36.19 3.77
771 1265 6.717084 CAGTCTTATGAAAAAGAGAAGGGGTT 59.283 38.462 0.00 0.00 36.19 4.11
773 1267 6.476378 TCAGTCTTATGAAAAAGAGAAGGGG 58.524 40.000 0.00 0.00 36.19 4.79
774 1268 6.597280 CCTCAGTCTTATGAAAAAGAGAAGGG 59.403 42.308 0.00 0.00 36.19 3.95
775 1269 7.164803 ACCTCAGTCTTATGAAAAAGAGAAGG 58.835 38.462 0.00 0.00 36.19 3.46
776 1270 9.883142 ATACCTCAGTCTTATGAAAAAGAGAAG 57.117 33.333 0.00 0.00 36.19 2.85
779 1273 9.757227 CCTATACCTCAGTCTTATGAAAAAGAG 57.243 37.037 0.00 0.00 36.19 2.85
780 1274 9.268282 ACCTATACCTCAGTCTTATGAAAAAGA 57.732 33.333 0.00 0.00 33.10 2.52
783 1277 9.144298 CCTACCTATACCTCAGTCTTATGAAAA 57.856 37.037 0.00 0.00 0.00 2.29
784 1278 7.728981 CCCTACCTATACCTCAGTCTTATGAAA 59.271 40.741 0.00 0.00 0.00 2.69
785 1279 7.239438 CCCTACCTATACCTCAGTCTTATGAA 58.761 42.308 0.00 0.00 0.00 2.57
786 1280 6.750351 GCCCTACCTATACCTCAGTCTTATGA 60.750 46.154 0.00 0.00 0.00 2.15
787 1281 5.419471 GCCCTACCTATACCTCAGTCTTATG 59.581 48.000 0.00 0.00 0.00 1.90
788 1282 5.316453 AGCCCTACCTATACCTCAGTCTTAT 59.684 44.000 0.00 0.00 0.00 1.73
789 1283 4.668812 AGCCCTACCTATACCTCAGTCTTA 59.331 45.833 0.00 0.00 0.00 2.10
790 1284 3.467863 AGCCCTACCTATACCTCAGTCTT 59.532 47.826 0.00 0.00 0.00 3.01
791 1285 3.065175 AGCCCTACCTATACCTCAGTCT 58.935 50.000 0.00 0.00 0.00 3.24
792 1286 3.529216 AGCCCTACCTATACCTCAGTC 57.471 52.381 0.00 0.00 0.00 3.51
793 1287 5.414133 TTTAGCCCTACCTATACCTCAGT 57.586 43.478 0.00 0.00 0.00 3.41
794 1288 6.742559 TTTTTAGCCCTACCTATACCTCAG 57.257 41.667 0.00 0.00 0.00 3.35
815 1309 8.275632 GCGATTTGACTCTTTATTTTGCTTTTT 58.724 29.630 0.00 0.00 0.00 1.94
816 1310 7.437862 TGCGATTTGACTCTTTATTTTGCTTTT 59.562 29.630 0.00 0.00 0.00 2.27
817 1311 6.922957 TGCGATTTGACTCTTTATTTTGCTTT 59.077 30.769 0.00 0.00 0.00 3.51
818 1312 6.363357 GTGCGATTTGACTCTTTATTTTGCTT 59.637 34.615 0.00 0.00 0.00 3.91
819 1313 5.858581 GTGCGATTTGACTCTTTATTTTGCT 59.141 36.000 0.00 0.00 0.00 3.91
820 1314 5.060940 GGTGCGATTTGACTCTTTATTTTGC 59.939 40.000 0.00 0.00 0.00 3.68
821 1315 6.148948 TGGTGCGATTTGACTCTTTATTTTG 58.851 36.000 0.00 0.00 0.00 2.44
822 1316 6.325919 TGGTGCGATTTGACTCTTTATTTT 57.674 33.333 0.00 0.00 0.00 1.82
823 1317 5.957842 TGGTGCGATTTGACTCTTTATTT 57.042 34.783 0.00 0.00 0.00 1.40
824 1318 5.473504 AGTTGGTGCGATTTGACTCTTTATT 59.526 36.000 0.00 0.00 0.00 1.40
825 1319 5.003804 AGTTGGTGCGATTTGACTCTTTAT 58.996 37.500 0.00 0.00 0.00 1.40
826 1320 4.385825 AGTTGGTGCGATTTGACTCTTTA 58.614 39.130 0.00 0.00 0.00 1.85
827 1321 3.214328 AGTTGGTGCGATTTGACTCTTT 58.786 40.909 0.00 0.00 0.00 2.52
828 1322 2.808543 GAGTTGGTGCGATTTGACTCTT 59.191 45.455 0.00 0.00 32.79 2.85
829 1323 2.037772 AGAGTTGGTGCGATTTGACTCT 59.962 45.455 0.00 0.00 39.07 3.24
830 1324 2.417719 AGAGTTGGTGCGATTTGACTC 58.582 47.619 0.00 0.00 35.06 3.36
831 1325 2.550830 AGAGTTGGTGCGATTTGACT 57.449 45.000 0.00 0.00 0.00 3.41
832 1326 6.604735 ATTATAGAGTTGGTGCGATTTGAC 57.395 37.500 0.00 0.00 0.00 3.18
833 1327 7.985184 ACTTATTATAGAGTTGGTGCGATTTGA 59.015 33.333 0.00 0.00 0.00 2.69
834 1328 8.142994 ACTTATTATAGAGTTGGTGCGATTTG 57.857 34.615 0.00 0.00 0.00 2.32
835 1329 9.477484 CTACTTATTATAGAGTTGGTGCGATTT 57.523 33.333 0.00 0.00 0.00 2.17
836 1330 8.088981 CCTACTTATTATAGAGTTGGTGCGATT 58.911 37.037 0.00 0.00 35.13 3.34
837 1331 7.309867 CCCTACTTATTATAGAGTTGGTGCGAT 60.310 40.741 0.00 0.00 37.16 4.58
838 1332 6.015688 CCCTACTTATTATAGAGTTGGTGCGA 60.016 42.308 0.00 0.00 37.16 5.10
839 1333 6.015688 TCCCTACTTATTATAGAGTTGGTGCG 60.016 42.308 10.31 0.00 37.16 5.34
840 1334 7.299246 TCCCTACTTATTATAGAGTTGGTGC 57.701 40.000 10.31 0.00 37.16 5.01
866 1360 6.491403 ACTGAGCATTGGATAGACAAGTTTTT 59.509 34.615 0.00 0.00 33.23 1.94
867 1361 6.006449 ACTGAGCATTGGATAGACAAGTTTT 58.994 36.000 0.00 0.00 33.23 2.43
998 1569 2.291209 ACACCAAATGTCCTGCATCA 57.709 45.000 0.00 0.00 36.54 3.07
1039 1610 0.604780 GCATGGGCAGCATCTCGTAT 60.605 55.000 0.00 0.00 40.72 3.06
1055 1626 1.300465 CGAGATACGCAGGCAGCAT 60.300 57.895 1.96 0.00 46.13 3.79
1081 1652 4.399618 GGGATAGCTTTTCCAAGAACTTCC 59.600 45.833 15.17 0.00 34.77 3.46
1096 1667 9.117223 AGTATTAAATATGAGGTTGGGATAGCT 57.883 33.333 0.00 0.00 0.00 3.32
1162 1733 6.475076 TGTTTTTCCAAAATGTGATCAACTCG 59.525 34.615 0.00 0.00 0.00 4.18
1191 1763 3.372730 GCCTTCACGCCAATGCCA 61.373 61.111 0.00 0.00 0.00 4.92
1207 1779 4.639135 AGGGAAAATTAAGCTCGAATGC 57.361 40.909 0.00 0.00 0.00 3.56
1224 1796 5.560724 CCATCAGACTTGTAGAAAAAGGGA 58.439 41.667 0.00 0.00 0.00 4.20
1242 1814 8.708378 CACCTATGGAGATATTTATAGCCATCA 58.292 37.037 0.00 0.00 37.34 3.07
1305 1880 0.250234 TCTCAGGAATCGCAAGGGTG 59.750 55.000 0.00 0.00 38.47 4.61
1443 2029 2.607635 GTCGAGAAACAGCACTGTCAAA 59.392 45.455 3.32 0.00 44.13 2.69
1444 2030 2.159099 AGTCGAGAAACAGCACTGTCAA 60.159 45.455 3.32 0.00 44.13 3.18
1464 2050 2.093306 TCCCTGTAATTCGCACACAG 57.907 50.000 0.00 0.00 39.50 3.66
1814 2560 7.259088 AGAGTTTTAGAACATACCTCATGGT 57.741 36.000 0.00 0.00 42.92 3.55
2043 2849 3.390967 TCAGTGTGAACATCTCCAAGGAA 59.609 43.478 0.00 0.00 0.00 3.36
2054 2860 4.377021 GTGACCTACATTCAGTGTGAACA 58.623 43.478 0.00 0.00 39.45 3.18
2077 2888 6.122850 TCAAGAATATTTGCAGGATGAACG 57.877 37.500 0.00 0.00 39.69 3.95
2113 2928 6.875076 ACTACAGAGGCTCGTTATATTTGTT 58.125 36.000 15.14 0.00 0.00 2.83
2125 2940 3.618690 ATGGTTCAACTACAGAGGCTC 57.381 47.619 6.34 6.34 0.00 4.70
2220 3040 3.243771 CCTTAGACGTGGCGGATCTTTAT 60.244 47.826 0.00 0.00 0.00 1.40
2235 3055 3.636153 ATCCTGGCAACTTCCTTAGAC 57.364 47.619 0.00 0.00 37.61 2.59
2345 6768 1.703438 GCAAGACGCTCTGATGCTGG 61.703 60.000 0.00 0.00 37.77 4.85
2438 6871 2.666190 CCGCTGTATGGGCATCCG 60.666 66.667 0.00 0.00 35.24 4.18
2493 6926 9.085645 TCCACAACATCTAGTTTAACTCTAGAA 57.914 33.333 15.85 5.32 44.29 2.10
2505 6938 2.616510 GCAAGGCTCCACAACATCTAGT 60.617 50.000 0.00 0.00 0.00 2.57
2529 6962 2.851263 AAACTCTCGTATGGCACCAA 57.149 45.000 0.00 0.00 0.00 3.67
2547 6980 7.766738 GGGGAATTTCACAAGTTGAACTAAAAA 59.233 33.333 10.54 0.00 44.28 1.94
2548 6981 7.125053 AGGGGAATTTCACAAGTTGAACTAAAA 59.875 33.333 10.54 0.00 44.28 1.52
2549 6982 6.609616 AGGGGAATTTCACAAGTTGAACTAAA 59.390 34.615 10.54 4.75 44.28 1.85
2550 6983 6.133356 AGGGGAATTTCACAAGTTGAACTAA 58.867 36.000 10.54 0.00 44.28 2.24
2551 6984 5.701224 AGGGGAATTTCACAAGTTGAACTA 58.299 37.500 10.54 0.00 44.28 2.24
2552 6985 4.546674 AGGGGAATTTCACAAGTTGAACT 58.453 39.130 10.54 0.00 44.28 3.01
2553 6986 4.584743 AGAGGGGAATTTCACAAGTTGAAC 59.415 41.667 10.54 0.00 44.28 3.18
2554 6987 4.803452 AGAGGGGAATTTCACAAGTTGAA 58.197 39.130 10.54 0.00 42.83 2.69
2555 6988 4.104738 AGAGAGGGGAATTTCACAAGTTGA 59.895 41.667 10.54 0.00 0.00 3.18
2556 6989 4.401925 AGAGAGGGGAATTTCACAAGTTG 58.598 43.478 0.00 0.00 0.00 3.16
2557 6990 4.507512 GGAGAGAGGGGAATTTCACAAGTT 60.508 45.833 0.29 0.00 0.00 2.66
2558 6991 3.009584 GGAGAGAGGGGAATTTCACAAGT 59.990 47.826 0.29 0.00 0.00 3.16
2559 6992 3.265479 AGGAGAGAGGGGAATTTCACAAG 59.735 47.826 0.29 0.00 0.00 3.16
2560 6993 3.260205 AGGAGAGAGGGGAATTTCACAA 58.740 45.455 0.29 0.00 0.00 3.33
2561 6994 2.840651 GAGGAGAGAGGGGAATTTCACA 59.159 50.000 0.29 0.00 0.00 3.58
2562 6995 2.171659 GGAGGAGAGAGGGGAATTTCAC 59.828 54.545 0.00 0.00 0.00 3.18
2563 6996 2.482494 GGAGGAGAGAGGGGAATTTCA 58.518 52.381 0.00 0.00 0.00 2.69
2564 6997 1.771854 GGGAGGAGAGAGGGGAATTTC 59.228 57.143 0.00 0.00 0.00 2.17
2565 6998 1.900254 GGGAGGAGAGAGGGGAATTT 58.100 55.000 0.00 0.00 0.00 1.82
2566 6999 0.399233 CGGGAGGAGAGAGGGGAATT 60.399 60.000 0.00 0.00 0.00 2.17
2567 7000 1.234529 CGGGAGGAGAGAGGGGAAT 59.765 63.158 0.00 0.00 0.00 3.01
2568 7001 2.246874 ACGGGAGGAGAGAGGGGAA 61.247 63.158 0.00 0.00 0.00 3.97
2569 7002 2.617538 ACGGGAGGAGAGAGGGGA 60.618 66.667 0.00 0.00 0.00 4.81
2570 7003 2.443016 CACGGGAGGAGAGAGGGG 60.443 72.222 0.00 0.00 0.00 4.79
2571 7004 1.755008 GACACGGGAGGAGAGAGGG 60.755 68.421 0.00 0.00 0.00 4.30
2572 7005 1.755008 GGACACGGGAGGAGAGAGG 60.755 68.421 0.00 0.00 0.00 3.69
2573 7006 1.755008 GGGACACGGGAGGAGAGAG 60.755 68.421 0.00 0.00 0.00 3.20
2574 7007 2.359404 GGGACACGGGAGGAGAGA 59.641 66.667 0.00 0.00 0.00 3.10
2575 7008 2.760385 GGGGACACGGGAGGAGAG 60.760 72.222 0.00 0.00 0.00 3.20
2576 7009 4.393778 GGGGGACACGGGAGGAGA 62.394 72.222 0.00 0.00 0.00 3.71
3135 7574 2.980233 GAAGCAGCAACCACGCCT 60.980 61.111 0.00 0.00 0.00 5.52
3143 7606 2.979676 CCACAGCCGAAGCAGCAA 60.980 61.111 0.00 0.00 43.56 3.91
3203 7666 2.107041 ATCGAGCCACCGTGAAACCA 62.107 55.000 0.00 0.00 0.00 3.67
3271 7734 3.834799 GGTCGAGACGGCCCGAAT 61.835 66.667 11.71 0.00 46.90 3.34
3374 7837 2.958281 TTCTGCCCTGCTGCATCGA 61.958 57.895 1.31 0.00 41.16 3.59
3387 11891 1.371758 TGTGCGAGACGAGTTCTGC 60.372 57.895 0.00 0.00 33.22 4.26
3403 11907 1.667830 CGGTCCTGTTGCATCGTGT 60.668 57.895 0.00 0.00 0.00 4.49
3413 11917 2.034376 AGACGAGCTCGGTCCTGT 59.966 61.111 36.93 17.55 44.95 4.00


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

AutoCloner maintained by Alex Coulton.