Multiple sequence alignment - TraesCS7A01G046100

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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 TraesCS7A01G046100 chr7A 100.000 3029 0 0 1 3029 20965303 20968331 0.000000e+00 5594.0
1 TraesCS7A01G046100 chr7A 92.179 2455 171 10 596 3029 20482404 20484858 0.000000e+00 3450.0
2 TraesCS7A01G046100 chr7A 91.191 2418 178 21 596 2983 20554710 20557122 0.000000e+00 3253.0
3 TraesCS7A01G046100 chr7A 87.403 2461 256 31 596 3029 20588354 20590787 0.000000e+00 2778.0
4 TraesCS7A01G046100 chr7A 85.434 2142 289 18 894 3027 20910611 20912737 0.000000e+00 2206.0
5 TraesCS7A01G046100 chr7A 84.259 2268 327 17 730 2983 20980351 20982602 0.000000e+00 2183.0
6 TraesCS7A01G046100 chr7A 84.133 2231 329 20 814 3029 20659483 20661703 0.000000e+00 2135.0
7 TraesCS7A01G046100 chr7A 90.116 344 17 9 117 459 20587990 20588317 6.000000e-117 431.0
8 TraesCS7A01G046100 chr7A 79.710 345 21 25 117 459 20482062 20482359 1.420000e-48 204.0
9 TraesCS7A01G046100 chr7A 84.252 127 13 5 479 600 730565686 730565810 1.910000e-22 117.0
10 TraesCS7A01G046100 chr7D 91.548 2449 187 10 596 3027 20310456 20312901 0.000000e+00 3358.0
11 TraesCS7A01G046100 chr7D 87.989 2098 237 13 894 2983 20485536 20487626 0.000000e+00 2464.0
12 TraesCS7A01G046100 chr7D 83.989 2236 328 25 764 2983 20442235 20444456 0.000000e+00 2119.0
13 TraesCS7A01G046100 chr4A 90.441 544 33 9 596 1121 669352153 669352695 0.000000e+00 699.0
14 TraesCS7A01G046100 chr4A 86.337 344 21 5 117 459 669351798 669352116 4.800000e-93 351.0
15 TraesCS7A01G046100 chr7B 93.103 116 8 0 1 116 696679703 696679588 1.440000e-38 171.0
16 TraesCS7A01G046100 chr7B 92.241 116 9 0 1 116 696707509 696707394 6.720000e-37 165.0
17 TraesCS7A01G046100 chr5A 85.950 121 14 3 479 596 46575428 46575548 3.170000e-25 126.0
18 TraesCS7A01G046100 chr5A 83.673 98 12 3 474 568 599486732 599486828 4.160000e-14 89.8
19 TraesCS7A01G046100 chrUn 83.333 126 17 4 473 595 43363145 43363269 2.470000e-21 113.0
20 TraesCS7A01G046100 chrUn 86.598 97 12 1 475 571 84439545 84439450 4.130000e-19 106.0
21 TraesCS7A01G046100 chr2B 92.105 76 6 0 473 548 801156742 801156817 1.150000e-19 108.0
22 TraesCS7A01G046100 chr1B 92.105 76 6 0 473 548 49318987 49319062 1.150000e-19 108.0
23 TraesCS7A01G046100 chr3D 91.429 70 6 0 479 548 587081194 587081263 2.490000e-16 97.1
24 TraesCS7A01G046100 chr6A 88.732 71 8 0 478 548 4537222 4537152 1.500000e-13 87.9
25 TraesCS7A01G046100 chr6D 86.792 53 4 2 544 593 82905568 82905516 4.220000e-04 56.5


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 TraesCS7A01G046100 chr7A 20965303 20968331 3028 False 5594.0 5594 100.0000 1 3029 1 chr7A.!!$F4 3028
1 TraesCS7A01G046100 chr7A 20554710 20557122 2412 False 3253.0 3253 91.1910 596 2983 1 chr7A.!!$F1 2387
2 TraesCS7A01G046100 chr7A 20910611 20912737 2126 False 2206.0 2206 85.4340 894 3027 1 chr7A.!!$F3 2133
3 TraesCS7A01G046100 chr7A 20980351 20982602 2251 False 2183.0 2183 84.2590 730 2983 1 chr7A.!!$F5 2253
4 TraesCS7A01G046100 chr7A 20659483 20661703 2220 False 2135.0 2135 84.1330 814 3029 1 chr7A.!!$F2 2215
5 TraesCS7A01G046100 chr7A 20482062 20484858 2796 False 1827.0 3450 85.9445 117 3029 2 chr7A.!!$F7 2912
6 TraesCS7A01G046100 chr7A 20587990 20590787 2797 False 1604.5 2778 88.7595 117 3029 2 chr7A.!!$F8 2912
7 TraesCS7A01G046100 chr7D 20310456 20312901 2445 False 3358.0 3358 91.5480 596 3027 1 chr7D.!!$F1 2431
8 TraesCS7A01G046100 chr7D 20485536 20487626 2090 False 2464.0 2464 87.9890 894 2983 1 chr7D.!!$F3 2089
9 TraesCS7A01G046100 chr7D 20442235 20444456 2221 False 2119.0 2119 83.9890 764 2983 1 chr7D.!!$F2 2219
10 TraesCS7A01G046100 chr4A 669351798 669352695 897 False 525.0 699 88.3890 117 1121 2 chr4A.!!$F1 1004

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
577 579 0.027586 CCGGCGCTATTTTGCTACAC 59.972 55.0 7.64 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2366 2456 1.207791 CCCCTCTGCTGTCCATAACT 58.792 55.0 0.0 0.0 0.0 2.24 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
21 22 1.766494 TTTCCGTCGGTATCTAGCCA 58.234 50.000 11.88 0.00 0.00 4.75
22 23 1.315690 TTCCGTCGGTATCTAGCCAG 58.684 55.000 11.88 0.00 0.00 4.85
23 24 1.170919 TCCGTCGGTATCTAGCCAGC 61.171 60.000 11.88 0.00 0.00 4.85
24 25 1.286260 CGTCGGTATCTAGCCAGCC 59.714 63.158 0.00 0.00 0.00 4.85
25 26 1.666580 GTCGGTATCTAGCCAGCCC 59.333 63.158 0.00 0.00 0.00 5.19
26 27 1.113517 GTCGGTATCTAGCCAGCCCA 61.114 60.000 0.00 0.00 0.00 5.36
27 28 1.113517 TCGGTATCTAGCCAGCCCAC 61.114 60.000 0.00 0.00 0.00 4.61
28 29 1.399744 CGGTATCTAGCCAGCCCACA 61.400 60.000 0.00 0.00 0.00 4.17
29 30 0.394565 GGTATCTAGCCAGCCCACAG 59.605 60.000 0.00 0.00 0.00 3.66
30 31 0.394565 GTATCTAGCCAGCCCACAGG 59.605 60.000 0.00 0.00 0.00 4.00
31 32 0.264657 TATCTAGCCAGCCCACAGGA 59.735 55.000 0.00 0.00 33.47 3.86
32 33 0.621571 ATCTAGCCAGCCCACAGGAA 60.622 55.000 0.00 0.00 33.47 3.36
33 34 0.840288 TCTAGCCAGCCCACAGGAAA 60.840 55.000 0.00 0.00 33.47 3.13
34 35 0.038166 CTAGCCAGCCCACAGGAAAA 59.962 55.000 0.00 0.00 33.47 2.29
35 36 0.704076 TAGCCAGCCCACAGGAAAAT 59.296 50.000 0.00 0.00 33.47 1.82
36 37 0.901580 AGCCAGCCCACAGGAAAATG 60.902 55.000 0.00 0.00 33.47 2.32
37 38 1.187567 GCCAGCCCACAGGAAAATGT 61.188 55.000 0.00 0.00 33.47 2.71
38 39 1.341080 CCAGCCCACAGGAAAATGTT 58.659 50.000 0.00 0.00 33.47 2.71
39 40 1.001181 CCAGCCCACAGGAAAATGTTG 59.999 52.381 0.00 0.00 33.47 3.33
40 41 0.681175 AGCCCACAGGAAAATGTTGC 59.319 50.000 0.00 0.00 33.47 4.17
41 42 0.392336 GCCCACAGGAAAATGTTGCA 59.608 50.000 0.00 0.00 33.47 4.08
42 43 1.002315 GCCCACAGGAAAATGTTGCAT 59.998 47.619 0.00 0.00 33.47 3.96
43 44 2.550639 GCCCACAGGAAAATGTTGCATT 60.551 45.455 0.00 0.00 33.47 3.56
44 45 3.328505 CCCACAGGAAAATGTTGCATTC 58.671 45.455 0.00 0.00 33.47 2.67
45 46 3.007182 CCCACAGGAAAATGTTGCATTCT 59.993 43.478 0.00 0.00 33.47 2.40
46 47 4.240096 CCACAGGAAAATGTTGCATTCTC 58.760 43.478 0.00 0.00 0.00 2.87
47 48 4.240096 CACAGGAAAATGTTGCATTCTCC 58.760 43.478 6.19 6.19 0.00 3.71
48 49 4.021719 CACAGGAAAATGTTGCATTCTCCT 60.022 41.667 10.09 10.09 31.94 3.69
49 50 4.491676 CAGGAAAATGTTGCATTCTCCTG 58.508 43.478 22.17 22.17 41.72 3.86
50 51 4.410099 AGGAAAATGTTGCATTCTCCTGA 58.590 39.130 13.97 0.00 30.63 3.86
51 52 4.461781 AGGAAAATGTTGCATTCTCCTGAG 59.538 41.667 13.97 0.00 30.63 3.35
52 53 4.219288 GGAAAATGTTGCATTCTCCTGAGT 59.781 41.667 6.90 0.00 0.00 3.41
53 54 4.778534 AAATGTTGCATTCTCCTGAGTG 57.221 40.909 0.00 0.00 33.70 3.51
54 55 2.936919 TGTTGCATTCTCCTGAGTGT 57.063 45.000 0.00 0.00 33.21 3.55
55 56 3.213206 TGTTGCATTCTCCTGAGTGTT 57.787 42.857 0.00 0.00 33.21 3.32
56 57 2.880268 TGTTGCATTCTCCTGAGTGTTG 59.120 45.455 0.00 0.00 33.21 3.33
57 58 2.189594 TGCATTCTCCTGAGTGTTGG 57.810 50.000 0.00 0.00 33.21 3.77
58 59 1.421268 TGCATTCTCCTGAGTGTTGGT 59.579 47.619 0.00 0.00 33.21 3.67
59 60 2.158623 TGCATTCTCCTGAGTGTTGGTT 60.159 45.455 0.00 0.00 33.21 3.67
60 61 2.227388 GCATTCTCCTGAGTGTTGGTTG 59.773 50.000 0.00 0.00 33.21 3.77
61 62 1.967319 TTCTCCTGAGTGTTGGTTGC 58.033 50.000 0.00 0.00 0.00 4.17
62 63 0.249868 TCTCCTGAGTGTTGGTTGCG 60.250 55.000 0.00 0.00 0.00 4.85
63 64 1.227823 TCCTGAGTGTTGGTTGCGG 60.228 57.895 0.00 0.00 0.00 5.69
64 65 2.260869 CCTGAGTGTTGGTTGCGGG 61.261 63.158 0.00 0.00 0.00 6.13
65 66 2.904866 TGAGTGTTGGTTGCGGGC 60.905 61.111 0.00 0.00 0.00 6.13
66 67 3.670377 GAGTGTTGGTTGCGGGCC 61.670 66.667 0.00 0.00 0.00 5.80
78 79 3.053896 CGGGCCCGACAGGAAAAC 61.054 66.667 41.82 0.00 42.83 2.43
79 80 2.114411 GGGCCCGACAGGAAAACA 59.886 61.111 5.69 0.00 41.02 2.83
80 81 1.529713 GGGCCCGACAGGAAAACAA 60.530 57.895 5.69 0.00 41.02 2.83
81 82 0.898326 GGGCCCGACAGGAAAACAAT 60.898 55.000 5.69 0.00 41.02 2.71
82 83 0.526211 GGCCCGACAGGAAAACAATC 59.474 55.000 0.00 0.00 41.02 2.67
83 84 0.526211 GCCCGACAGGAAAACAATCC 59.474 55.000 0.00 0.00 41.02 3.01
84 85 0.802494 CCCGACAGGAAAACAATCCG 59.198 55.000 0.00 0.00 44.60 4.18
85 86 0.802494 CCGACAGGAAAACAATCCGG 59.198 55.000 0.00 0.00 44.60 5.14
86 87 0.168128 CGACAGGAAAACAATCCGGC 59.832 55.000 0.00 0.00 44.60 6.13
87 88 0.526211 GACAGGAAAACAATCCGGCC 59.474 55.000 0.00 0.00 44.60 6.13
88 89 0.898326 ACAGGAAAACAATCCGGCCC 60.898 55.000 0.00 0.00 44.60 5.80
89 90 0.897863 CAGGAAAACAATCCGGCCCA 60.898 55.000 0.00 0.00 44.60 5.36
90 91 0.898326 AGGAAAACAATCCGGCCCAC 60.898 55.000 0.00 0.00 44.60 4.61
91 92 1.182385 GGAAAACAATCCGGCCCACA 61.182 55.000 0.00 0.00 0.00 4.17
92 93 0.243636 GAAAACAATCCGGCCCACAG 59.756 55.000 0.00 0.00 0.00 3.66
93 94 0.178975 AAAACAATCCGGCCCACAGA 60.179 50.000 0.00 0.00 0.00 3.41
94 95 0.178975 AAACAATCCGGCCCACAGAA 60.179 50.000 0.00 0.00 0.00 3.02
95 96 0.178975 AACAATCCGGCCCACAGAAA 60.179 50.000 0.00 0.00 0.00 2.52
96 97 0.039618 ACAATCCGGCCCACAGAAAT 59.960 50.000 0.00 0.00 0.00 2.17
97 98 1.283613 ACAATCCGGCCCACAGAAATA 59.716 47.619 0.00 0.00 0.00 1.40
98 99 2.091885 ACAATCCGGCCCACAGAAATAT 60.092 45.455 0.00 0.00 0.00 1.28
99 100 2.958355 CAATCCGGCCCACAGAAATATT 59.042 45.455 0.00 0.00 0.00 1.28
100 101 2.341846 TCCGGCCCACAGAAATATTC 57.658 50.000 0.00 0.00 0.00 1.75
101 102 0.944386 CCGGCCCACAGAAATATTCG 59.056 55.000 0.00 0.00 34.02 3.34
102 103 1.474320 CCGGCCCACAGAAATATTCGA 60.474 52.381 0.00 0.00 34.02 3.71
103 104 1.867233 CGGCCCACAGAAATATTCGAG 59.133 52.381 0.00 0.00 34.02 4.04
104 105 2.741878 CGGCCCACAGAAATATTCGAGT 60.742 50.000 0.00 0.00 34.02 4.18
105 106 3.279434 GGCCCACAGAAATATTCGAGTT 58.721 45.455 0.00 0.00 34.02 3.01
106 107 3.694566 GGCCCACAGAAATATTCGAGTTT 59.305 43.478 0.00 0.00 34.02 2.66
107 108 4.201920 GGCCCACAGAAATATTCGAGTTTC 60.202 45.833 0.00 10.32 35.18 2.78
108 109 4.636206 GCCCACAGAAATATTCGAGTTTCT 59.364 41.667 13.48 13.48 43.44 2.52
174 175 7.807977 TTCTCCTAATGATTCCTAATGCAAC 57.192 36.000 0.00 0.00 0.00 4.17
212 214 9.415544 ACTTATTCATTTTCTTGACTGCAAATC 57.584 29.630 0.00 0.00 32.73 2.17
213 215 9.635520 CTTATTCATTTTCTTGACTGCAAATCT 57.364 29.630 0.00 0.00 32.73 2.40
214 216 7.884816 ATTCATTTTCTTGACTGCAAATCTG 57.115 32.000 0.00 0.00 32.73 2.90
235 237 4.708726 GCAATACATCTTCCTTGCAACT 57.291 40.909 0.00 0.00 42.66 3.16
236 238 4.666237 GCAATACATCTTCCTTGCAACTC 58.334 43.478 0.00 0.00 42.66 3.01
237 239 4.156556 GCAATACATCTTCCTTGCAACTCA 59.843 41.667 0.00 0.00 42.66 3.41
238 240 5.335897 GCAATACATCTTCCTTGCAACTCAA 60.336 40.000 0.00 0.00 42.66 3.02
369 371 7.316640 TCACATTAGCTAACTCTCTGAAAGTC 58.683 38.462 8.70 0.00 33.76 3.01
395 397 4.942761 ATTTATTTCGGCAATCTGGCAT 57.057 36.364 0.94 0.00 43.94 4.40
414 416 2.036958 TGTATGCCAGATTGGTTCCG 57.963 50.000 0.00 0.00 40.46 4.30
449 451 4.428294 TCAAATTTCAACATTTGGGGCA 57.572 36.364 6.36 0.00 42.28 5.36
450 452 4.133078 TCAAATTTCAACATTTGGGGCAC 58.867 39.130 6.36 0.00 42.28 5.01
451 453 4.136051 CAAATTTCAACATTTGGGGCACT 58.864 39.130 0.00 0.00 39.53 4.40
452 454 4.436113 AATTTCAACATTTGGGGCACTT 57.564 36.364 0.00 0.00 0.00 3.16
453 455 3.922171 TTTCAACATTTGGGGCACTTT 57.078 38.095 0.00 0.00 0.00 2.66
454 456 3.467374 TTCAACATTTGGGGCACTTTC 57.533 42.857 0.00 0.00 0.00 2.62
455 457 2.392662 TCAACATTTGGGGCACTTTCA 58.607 42.857 0.00 0.00 0.00 2.69
456 458 2.768527 TCAACATTTGGGGCACTTTCAA 59.231 40.909 0.00 0.00 0.00 2.69
457 459 2.871633 CAACATTTGGGGCACTTTCAAC 59.128 45.455 0.00 0.00 0.00 3.18
458 460 1.416030 ACATTTGGGGCACTTTCAACC 59.584 47.619 0.00 0.00 0.00 3.77
459 461 1.415659 CATTTGGGGCACTTTCAACCA 59.584 47.619 0.00 0.00 0.00 3.67
460 462 0.827368 TTTGGGGCACTTTCAACCAC 59.173 50.000 0.00 0.00 0.00 4.16
461 463 0.032615 TTGGGGCACTTTCAACCACT 60.033 50.000 0.00 0.00 0.00 4.00
462 464 0.754957 TGGGGCACTTTCAACCACTG 60.755 55.000 0.00 0.00 0.00 3.66
463 465 0.755327 GGGGCACTTTCAACCACTGT 60.755 55.000 0.00 0.00 0.00 3.55
464 466 1.477923 GGGGCACTTTCAACCACTGTA 60.478 52.381 0.00 0.00 0.00 2.74
465 467 2.303175 GGGCACTTTCAACCACTGTAA 58.697 47.619 0.00 0.00 0.00 2.41
466 468 2.890945 GGGCACTTTCAACCACTGTAAT 59.109 45.455 0.00 0.00 0.00 1.89
467 469 4.076394 GGGCACTTTCAACCACTGTAATA 58.924 43.478 0.00 0.00 0.00 0.98
468 470 4.521256 GGGCACTTTCAACCACTGTAATAA 59.479 41.667 0.00 0.00 0.00 1.40
469 471 5.010213 GGGCACTTTCAACCACTGTAATAAA 59.990 40.000 0.00 0.00 0.00 1.40
470 472 6.295067 GGGCACTTTCAACCACTGTAATAAAT 60.295 38.462 0.00 0.00 0.00 1.40
471 473 7.094118 GGGCACTTTCAACCACTGTAATAAATA 60.094 37.037 0.00 0.00 0.00 1.40
472 474 7.968405 GGCACTTTCAACCACTGTAATAAATAG 59.032 37.037 0.00 0.00 0.00 1.73
473 475 7.484959 GCACTTTCAACCACTGTAATAAATAGC 59.515 37.037 0.00 0.00 0.00 2.97
474 476 7.968405 CACTTTCAACCACTGTAATAAATAGCC 59.032 37.037 0.00 0.00 0.00 3.93
475 477 6.671614 TTCAACCACTGTAATAAATAGCCG 57.328 37.500 0.00 0.00 0.00 5.52
476 478 4.573201 TCAACCACTGTAATAAATAGCCGC 59.427 41.667 0.00 0.00 0.00 6.53
477 479 4.417426 ACCACTGTAATAAATAGCCGCT 57.583 40.909 0.00 0.00 0.00 5.52
478 480 5.540400 ACCACTGTAATAAATAGCCGCTA 57.460 39.130 1.73 1.73 0.00 4.26
479 481 5.920903 ACCACTGTAATAAATAGCCGCTAA 58.079 37.500 3.73 0.00 0.00 3.09
480 482 6.531021 ACCACTGTAATAAATAGCCGCTAAT 58.469 36.000 3.73 0.00 0.00 1.73
481 483 7.673180 ACCACTGTAATAAATAGCCGCTAATA 58.327 34.615 3.73 1.68 0.00 0.98
482 484 7.817962 ACCACTGTAATAAATAGCCGCTAATAG 59.182 37.037 3.73 0.00 0.00 1.73
483 485 7.201530 CCACTGTAATAAATAGCCGCTAATAGC 60.202 40.741 3.73 1.41 38.02 2.97
484 486 7.330946 CACTGTAATAAATAGCCGCTAATAGCA 59.669 37.037 13.15 0.00 42.58 3.49
485 487 7.331193 ACTGTAATAAATAGCCGCTAATAGCAC 59.669 37.037 13.15 3.67 42.58 4.40
486 488 5.779806 AATAAATAGCCGCTAATAGCACG 57.220 39.130 13.15 2.62 42.58 5.34
487 489 1.429463 AATAGCCGCTAATAGCACGC 58.571 50.000 13.15 12.48 42.58 5.34
488 490 0.603569 ATAGCCGCTAATAGCACGCT 59.396 50.000 22.11 22.11 45.12 5.07
489 491 1.241165 TAGCCGCTAATAGCACGCTA 58.759 50.000 20.49 20.49 42.50 4.26
490 492 0.387929 AGCCGCTAATAGCACGCTAA 59.612 50.000 18.61 0.00 42.50 3.09
491 493 1.202486 AGCCGCTAATAGCACGCTAAA 60.202 47.619 18.61 0.00 42.50 1.85
492 494 1.192534 GCCGCTAATAGCACGCTAAAG 59.807 52.381 13.15 5.30 42.58 1.85
493 495 1.192534 CCGCTAATAGCACGCTAAAGC 59.807 52.381 19.33 19.33 42.58 3.51
494 496 1.858458 CGCTAATAGCACGCTAAAGCA 59.142 47.619 24.63 0.42 42.58 3.91
495 497 2.476619 CGCTAATAGCACGCTAAAGCAT 59.523 45.455 24.63 2.51 42.58 3.79
496 498 3.422343 CGCTAATAGCACGCTAAAGCATC 60.422 47.826 24.63 7.30 42.58 3.91
497 499 3.120511 GCTAATAGCACGCTAAAGCATCC 60.121 47.826 22.24 3.27 41.89 3.51
498 500 2.918712 ATAGCACGCTAAAGCATCCT 57.081 45.000 2.32 0.00 42.21 3.24
499 501 1.939974 TAGCACGCTAAAGCATCCTG 58.060 50.000 2.44 0.00 42.21 3.86
500 502 0.250234 AGCACGCTAAAGCATCCTGA 59.750 50.000 2.44 0.00 42.21 3.86
501 503 0.654683 GCACGCTAAAGCATCCTGAG 59.345 55.000 2.44 0.00 42.21 3.35
502 504 1.740380 GCACGCTAAAGCATCCTGAGA 60.740 52.381 2.44 0.00 42.21 3.27
503 505 2.621338 CACGCTAAAGCATCCTGAGAA 58.379 47.619 2.44 0.00 42.21 2.87
504 506 3.201290 CACGCTAAAGCATCCTGAGAAT 58.799 45.455 2.44 0.00 42.21 2.40
505 507 3.624861 CACGCTAAAGCATCCTGAGAATT 59.375 43.478 2.44 0.00 42.21 2.17
506 508 3.624861 ACGCTAAAGCATCCTGAGAATTG 59.375 43.478 2.44 0.00 42.21 2.32
507 509 3.624861 CGCTAAAGCATCCTGAGAATTGT 59.375 43.478 2.44 0.00 42.21 2.71
508 510 4.260538 CGCTAAAGCATCCTGAGAATTGTC 60.261 45.833 2.44 0.00 42.21 3.18
509 511 4.880696 GCTAAAGCATCCTGAGAATTGTCT 59.119 41.667 4.03 0.00 41.59 3.41
510 512 5.007528 GCTAAAGCATCCTGAGAATTGTCTC 59.992 44.000 4.03 0.00 44.66 3.36
511 513 8.145106 GCTAAAGCATCCTGAGAATTGTCTCG 62.145 46.154 4.03 0.00 45.98 4.04
525 527 8.723942 AGAATTGTCTCGCTAAATAAATCAGT 57.276 30.769 0.00 0.00 0.00 3.41
526 528 8.607459 AGAATTGTCTCGCTAAATAAATCAGTG 58.393 33.333 0.00 0.00 0.00 3.66
527 529 7.849804 ATTGTCTCGCTAAATAAATCAGTGT 57.150 32.000 0.00 0.00 0.00 3.55
528 530 8.942338 ATTGTCTCGCTAAATAAATCAGTGTA 57.058 30.769 0.00 0.00 0.00 2.90
529 531 8.942338 TTGTCTCGCTAAATAAATCAGTGTAT 57.058 30.769 0.00 0.00 0.00 2.29
540 542 9.547753 AAATAAATCAGTGTATAATGTCTCGCT 57.452 29.630 0.00 0.00 0.00 4.93
545 547 9.847706 AATCAGTGTATAATGTCTCGCTAATAG 57.152 33.333 0.00 0.00 0.00 1.73
546 548 7.306213 TCAGTGTATAATGTCTCGCTAATAGC 58.694 38.462 1.41 1.41 38.02 2.97
547 549 7.040686 TCAGTGTATAATGTCTCGCTAATAGCA 60.041 37.037 13.15 0.00 42.58 3.49
548 550 7.757173 CAGTGTATAATGTCTCGCTAATAGCAT 59.243 37.037 13.15 0.00 42.58 3.79
549 551 8.957466 AGTGTATAATGTCTCGCTAATAGCATA 58.043 33.333 13.15 0.00 42.58 3.14
550 552 9.737427 GTGTATAATGTCTCGCTAATAGCATAT 57.263 33.333 13.15 0.00 42.58 1.78
557 559 8.534333 TGTCTCGCTAATAGCATATTTTAAGG 57.466 34.615 13.15 0.00 42.58 2.69
558 560 7.117812 TGTCTCGCTAATAGCATATTTTAAGGC 59.882 37.037 13.15 0.00 42.58 4.35
559 561 6.594159 TCTCGCTAATAGCATATTTTAAGGCC 59.406 38.462 13.15 0.00 42.58 5.19
560 562 5.350365 TCGCTAATAGCATATTTTAAGGCCG 59.650 40.000 13.15 0.00 42.58 6.13
561 563 5.447279 CGCTAATAGCATATTTTAAGGCCGG 60.447 44.000 13.15 0.00 42.58 6.13
562 564 4.783764 AATAGCATATTTTAAGGCCGGC 57.216 40.909 21.18 21.18 0.00 6.13
563 565 0.951558 AGCATATTTTAAGGCCGGCG 59.048 50.000 22.54 0.00 0.00 6.46
564 566 0.663269 GCATATTTTAAGGCCGGCGC 60.663 55.000 22.54 13.90 0.00 6.53
565 567 0.951558 CATATTTTAAGGCCGGCGCT 59.048 50.000 22.54 16.21 34.44 5.92
566 568 2.147958 CATATTTTAAGGCCGGCGCTA 58.852 47.619 22.54 11.45 34.44 4.26
567 569 2.554370 TATTTTAAGGCCGGCGCTAT 57.446 45.000 22.54 11.13 34.44 2.97
568 570 1.687563 ATTTTAAGGCCGGCGCTATT 58.312 45.000 22.54 14.72 34.44 1.73
569 571 1.465794 TTTTAAGGCCGGCGCTATTT 58.534 45.000 22.54 11.76 34.44 1.40
570 572 1.465794 TTTAAGGCCGGCGCTATTTT 58.534 45.000 22.54 9.96 34.44 1.82
571 573 0.736053 TTAAGGCCGGCGCTATTTTG 59.264 50.000 22.54 0.00 34.44 2.44
572 574 1.720694 TAAGGCCGGCGCTATTTTGC 61.721 55.000 22.54 2.36 34.44 3.68
573 575 3.518068 GGCCGGCGCTATTTTGCT 61.518 61.111 22.54 0.00 34.44 3.91
574 576 2.184167 GGCCGGCGCTATTTTGCTA 61.184 57.895 22.54 0.00 34.44 3.49
575 577 1.010013 GCCGGCGCTATTTTGCTAC 60.010 57.895 12.58 0.00 0.00 3.58
576 578 1.711060 GCCGGCGCTATTTTGCTACA 61.711 55.000 12.58 0.00 0.00 2.74
577 579 0.027586 CCGGCGCTATTTTGCTACAC 59.972 55.000 7.64 0.00 0.00 2.90
578 580 0.315059 CGGCGCTATTTTGCTACACG 60.315 55.000 7.64 0.00 0.00 4.49
579 581 0.588980 GGCGCTATTTTGCTACACGC 60.589 55.000 7.64 0.00 43.80 5.34
580 582 0.373716 GCGCTATTTTGCTACACGCT 59.626 50.000 0.00 0.00 41.50 5.07
581 583 1.591158 GCGCTATTTTGCTACACGCTA 59.409 47.619 0.00 0.00 41.50 4.26
582 584 2.221055 GCGCTATTTTGCTACACGCTAT 59.779 45.455 0.00 0.00 41.50 2.97
583 585 3.303132 GCGCTATTTTGCTACACGCTATT 60.303 43.478 0.00 0.00 41.50 1.73
584 586 4.785341 GCGCTATTTTGCTACACGCTATTT 60.785 41.667 0.00 0.00 41.50 1.40
585 587 5.263185 CGCTATTTTGCTACACGCTATTTT 58.737 37.500 0.00 0.00 40.11 1.82
586 588 5.737290 CGCTATTTTGCTACACGCTATTTTT 59.263 36.000 0.00 0.00 40.11 1.94
643 698 4.814234 CGAAGCATGGCTAGTTATTTGGTA 59.186 41.667 0.00 0.00 38.25 3.25
651 706 5.720041 TGGCTAGTTATTTGGTAGAGTGTCT 59.280 40.000 0.00 0.00 0.00 3.41
693 748 3.058293 TCAAATTTGCCGCAGTTGACTAG 60.058 43.478 13.54 0.00 0.00 2.57
694 749 0.804989 ATTTGCCGCAGTTGACTAGC 59.195 50.000 0.00 0.00 0.00 3.42
695 750 0.533978 TTTGCCGCAGTTGACTAGCA 60.534 50.000 0.00 0.00 0.00 3.49
727 785 5.946377 AGTGTTCTTAAATTCTCATGGACCC 59.054 40.000 0.00 0.00 0.00 4.46
854 934 5.659463 TGGTTGGAGATTTTTGAAGTGTTG 58.341 37.500 0.00 0.00 0.00 3.33
879 959 4.141914 GGCAAGTGCTTACTACTACCAGAT 60.142 45.833 2.85 0.00 41.70 2.90
939 1027 6.935167 TGCAGTGAACTTTCTGATGATACTA 58.065 36.000 0.00 0.00 34.02 1.82
1121 1209 2.826128 CACAACTACTGGAGCTACAGGA 59.174 50.000 29.50 21.49 42.75 3.86
1152 1240 2.347490 GTTGCCAGGGAGCTTCGA 59.653 61.111 0.00 0.00 0.00 3.71
1204 1292 0.886938 TCGGAACCGCAGCAATCAAA 60.887 50.000 8.48 0.00 39.59 2.69
1299 1387 5.661056 ATCTAGTTGGTCGAGAACATGAA 57.339 39.130 0.00 0.00 32.03 2.57
1307 1395 5.556915 TGGTCGAGAACATGAAATAGGTTT 58.443 37.500 0.00 0.00 32.65 3.27
1310 1398 7.662258 TGGTCGAGAACATGAAATAGGTTTTTA 59.338 33.333 0.00 0.00 32.65 1.52
1353 1443 3.254166 TCAAAAAGCCAAGATCACTGCTC 59.746 43.478 0.00 0.00 32.62 4.26
1603 1693 2.704464 TGATCAGGAATGCTCTGTGG 57.296 50.000 0.00 0.00 34.15 4.17
1617 1707 2.290122 CTGTGGTAGCTCTGCTCGGG 62.290 65.000 0.00 0.00 40.44 5.14
1652 1742 4.229876 GGTAAAACTGCTTTAGCTGCAAG 58.770 43.478 1.02 0.00 42.33 4.01
1662 1752 4.024048 GCTTTAGCTGCAAGTGTCTACAAA 60.024 41.667 1.02 0.00 38.21 2.83
1962 2052 0.250295 TCACAACAAGAGAAGCCCGG 60.250 55.000 0.00 0.00 0.00 5.73
2012 2102 6.588756 CGTATCTTAACACTGGAAGCTTTACA 59.411 38.462 0.00 2.25 37.60 2.41
2028 2118 4.216257 GCTTTACAAGAAGACAAGGCATGA 59.784 41.667 0.00 0.00 0.00 3.07
2081 2171 6.996879 AGAGATACAAATCATGAATGTCCCAG 59.003 38.462 17.77 0.00 34.28 4.45
2114 2204 4.272748 GCCATCGTCCAAGGAAATAGTTAC 59.727 45.833 0.00 0.00 0.00 2.50
2127 2217 5.243060 GGAAATAGTTACCAAGTGCAAAGGT 59.757 40.000 10.40 10.40 39.41 3.50
2292 2382 1.482593 AGCTTCATCTACCTCCCAACG 59.517 52.381 0.00 0.00 0.00 4.10
2311 2401 7.028361 CCCAACGTACTTAAAAAGTTGTTTCA 58.972 34.615 12.21 0.00 42.81 2.69
2433 2523 4.042187 ACATTAGAAGAAGTGGCAGAAGGT 59.958 41.667 0.00 0.00 0.00 3.50
2595 2694 7.516198 ACATATGAGAATAAATGTGAAGGGC 57.484 36.000 10.38 0.00 31.56 5.19
2643 2742 6.554334 TGGTACTGCACAAACTAAAAGATC 57.446 37.500 0.00 0.00 0.00 2.75
2727 2826 6.804677 AGCAAGTCATCATTCACTCTACTAG 58.195 40.000 0.00 0.00 0.00 2.57
2812 2911 4.637387 AGATTCCAGATGCTATTGGAGG 57.363 45.455 4.31 0.00 43.89 4.30
2900 2999 6.042143 TGAGAAGCTTTCAAATTTGTTGACC 58.958 36.000 17.47 4.68 0.00 4.02
2910 3009 4.670896 AATTTGTTGACCTTGGACCTTG 57.329 40.909 0.00 0.00 0.00 3.61
2930 3029 3.937814 TGGTGGTTCTGACATACATGAC 58.062 45.455 0.00 0.00 0.00 3.06
2991 3090 7.036220 GCACTTATTTGCTGAGAGAGTAACTA 58.964 38.462 0.00 0.00 39.59 2.24
2997 3096 5.584253 TGCTGAGAGAGTAACTAATCCAC 57.416 43.478 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.489355 TGGCTAGATACCGACGGAAATA 58.511 45.455 23.38 2.51 0.00 1.40
1 2 2.296471 CTGGCTAGATACCGACGGAAAT 59.704 50.000 23.38 13.53 0.00 2.17
2 3 1.679680 CTGGCTAGATACCGACGGAAA 59.320 52.381 23.38 8.65 0.00 3.13
3 4 1.315690 CTGGCTAGATACCGACGGAA 58.684 55.000 23.38 0.00 0.00 4.30
4 5 1.170919 GCTGGCTAGATACCGACGGA 61.171 60.000 23.38 4.52 0.00 4.69
5 6 1.286260 GCTGGCTAGATACCGACGG 59.714 63.158 13.61 13.61 0.00 4.79
6 7 1.286260 GGCTGGCTAGATACCGACG 59.714 63.158 0.00 0.00 0.00 5.12
7 8 1.113517 TGGGCTGGCTAGATACCGAC 61.114 60.000 0.00 0.00 0.00 4.79
8 9 1.113517 GTGGGCTGGCTAGATACCGA 61.114 60.000 0.00 0.00 0.00 4.69
9 10 1.367840 GTGGGCTGGCTAGATACCG 59.632 63.158 0.00 0.00 0.00 4.02
10 11 0.394565 CTGTGGGCTGGCTAGATACC 59.605 60.000 0.00 0.00 0.00 2.73
11 12 0.394565 CCTGTGGGCTGGCTAGATAC 59.605 60.000 0.00 0.00 0.00 2.24
12 13 0.264657 TCCTGTGGGCTGGCTAGATA 59.735 55.000 0.00 0.00 34.18 1.98
13 14 0.621571 TTCCTGTGGGCTGGCTAGAT 60.622 55.000 0.00 0.00 34.18 1.98
14 15 0.840288 TTTCCTGTGGGCTGGCTAGA 60.840 55.000 0.00 0.00 34.18 2.43
15 16 0.038166 TTTTCCTGTGGGCTGGCTAG 59.962 55.000 0.00 0.00 34.18 3.42
16 17 0.704076 ATTTTCCTGTGGGCTGGCTA 59.296 50.000 0.00 0.00 34.18 3.93
17 18 0.901580 CATTTTCCTGTGGGCTGGCT 60.902 55.000 0.00 0.00 34.18 4.75
18 19 1.187567 ACATTTTCCTGTGGGCTGGC 61.188 55.000 0.00 0.00 34.18 4.85
19 20 1.001181 CAACATTTTCCTGTGGGCTGG 59.999 52.381 0.00 0.00 35.32 4.85
20 21 1.606224 GCAACATTTTCCTGTGGGCTG 60.606 52.381 0.00 0.00 31.29 4.85
21 22 0.681175 GCAACATTTTCCTGTGGGCT 59.319 50.000 0.00 0.00 31.29 5.19
22 23 0.392336 TGCAACATTTTCCTGTGGGC 59.608 50.000 0.00 0.00 33.34 5.36
23 24 3.007182 AGAATGCAACATTTTCCTGTGGG 59.993 43.478 0.00 0.00 0.00 4.61
24 25 4.240096 GAGAATGCAACATTTTCCTGTGG 58.760 43.478 0.00 0.00 0.00 4.17
25 26 4.021719 AGGAGAATGCAACATTTTCCTGTG 60.022 41.667 24.00 0.00 40.02 3.66
26 27 4.021719 CAGGAGAATGCAACATTTTCCTGT 60.022 41.667 32.04 14.65 46.70 4.00
27 28 4.491676 CAGGAGAATGCAACATTTTCCTG 58.508 43.478 29.99 29.99 46.73 3.86
28 29 4.410099 TCAGGAGAATGCAACATTTTCCT 58.590 39.130 20.80 20.80 41.57 3.36
29 30 4.219288 ACTCAGGAGAATGCAACATTTTCC 59.781 41.667 17.71 17.71 33.79 3.13
30 31 5.159209 CACTCAGGAGAATGCAACATTTTC 58.841 41.667 2.79 3.01 0.00 2.29
31 32 4.586001 ACACTCAGGAGAATGCAACATTTT 59.414 37.500 2.79 0.00 0.00 1.82
32 33 4.147321 ACACTCAGGAGAATGCAACATTT 58.853 39.130 2.79 0.00 0.00 2.32
33 34 3.759581 ACACTCAGGAGAATGCAACATT 58.240 40.909 2.79 0.00 0.00 2.71
34 35 3.430042 ACACTCAGGAGAATGCAACAT 57.570 42.857 2.79 0.00 0.00 2.71
35 36 2.880268 CAACACTCAGGAGAATGCAACA 59.120 45.455 2.79 0.00 0.00 3.33
36 37 2.227388 CCAACACTCAGGAGAATGCAAC 59.773 50.000 2.79 0.00 0.00 4.17
37 38 2.158623 ACCAACACTCAGGAGAATGCAA 60.159 45.455 2.79 0.00 0.00 4.08
38 39 1.421268 ACCAACACTCAGGAGAATGCA 59.579 47.619 2.79 0.00 0.00 3.96
39 40 2.191128 ACCAACACTCAGGAGAATGC 57.809 50.000 2.79 0.00 0.00 3.56
40 41 2.227388 GCAACCAACACTCAGGAGAATG 59.773 50.000 2.79 0.00 0.00 2.67
41 42 2.508526 GCAACCAACACTCAGGAGAAT 58.491 47.619 2.79 0.00 0.00 2.40
42 43 1.810031 CGCAACCAACACTCAGGAGAA 60.810 52.381 2.79 0.00 0.00 2.87
43 44 0.249868 CGCAACCAACACTCAGGAGA 60.250 55.000 2.79 0.00 0.00 3.71
44 45 1.230635 CCGCAACCAACACTCAGGAG 61.231 60.000 0.00 0.00 0.00 3.69
45 46 1.227823 CCGCAACCAACACTCAGGA 60.228 57.895 0.00 0.00 0.00 3.86
46 47 2.260869 CCCGCAACCAACACTCAGG 61.261 63.158 0.00 0.00 0.00 3.86
47 48 2.908073 GCCCGCAACCAACACTCAG 61.908 63.158 0.00 0.00 0.00 3.35
48 49 2.904866 GCCCGCAACCAACACTCA 60.905 61.111 0.00 0.00 0.00 3.41
49 50 3.670377 GGCCCGCAACCAACACTC 61.670 66.667 0.00 0.00 0.00 3.51
61 62 3.053896 GTTTTCCTGTCGGGCCCG 61.054 66.667 39.13 39.13 41.35 6.13
62 63 0.898326 ATTGTTTTCCTGTCGGGCCC 60.898 55.000 13.57 13.57 34.39 5.80
63 64 0.526211 GATTGTTTTCCTGTCGGGCC 59.474 55.000 0.00 0.00 34.39 5.80
64 65 0.526211 GGATTGTTTTCCTGTCGGGC 59.474 55.000 0.00 0.00 32.68 6.13
65 66 0.802494 CGGATTGTTTTCCTGTCGGG 59.198 55.000 0.00 0.00 33.30 5.14
66 67 0.802494 CCGGATTGTTTTCCTGTCGG 59.198 55.000 0.00 0.00 33.30 4.79
67 68 0.168128 GCCGGATTGTTTTCCTGTCG 59.832 55.000 5.05 0.00 33.30 4.35
68 69 0.526211 GGCCGGATTGTTTTCCTGTC 59.474 55.000 5.05 0.00 33.30 3.51
69 70 0.898326 GGGCCGGATTGTTTTCCTGT 60.898 55.000 5.05 0.00 33.30 4.00
70 71 0.897863 TGGGCCGGATTGTTTTCCTG 60.898 55.000 5.05 0.00 33.30 3.86
71 72 0.898326 GTGGGCCGGATTGTTTTCCT 60.898 55.000 5.05 0.00 33.30 3.36
72 73 1.182385 TGTGGGCCGGATTGTTTTCC 61.182 55.000 5.05 0.00 0.00 3.13
73 74 0.243636 CTGTGGGCCGGATTGTTTTC 59.756 55.000 5.05 0.00 0.00 2.29
74 75 0.178975 TCTGTGGGCCGGATTGTTTT 60.179 50.000 5.05 0.00 0.00 2.43
75 76 0.178975 TTCTGTGGGCCGGATTGTTT 60.179 50.000 5.05 0.00 0.00 2.83
76 77 0.178975 TTTCTGTGGGCCGGATTGTT 60.179 50.000 5.05 0.00 0.00 2.83
77 78 0.039618 ATTTCTGTGGGCCGGATTGT 59.960 50.000 5.05 0.00 0.00 2.71
78 79 2.051334 TATTTCTGTGGGCCGGATTG 57.949 50.000 5.05 0.00 0.00 2.67
79 80 3.222603 GAATATTTCTGTGGGCCGGATT 58.777 45.455 5.05 0.00 0.00 3.01
80 81 2.810400 CGAATATTTCTGTGGGCCGGAT 60.810 50.000 5.05 0.00 0.00 4.18
81 82 1.474320 CGAATATTTCTGTGGGCCGGA 60.474 52.381 5.05 0.00 0.00 5.14
82 83 0.944386 CGAATATTTCTGTGGGCCGG 59.056 55.000 0.00 0.00 0.00 6.13
83 84 1.867233 CTCGAATATTTCTGTGGGCCG 59.133 52.381 0.00 0.00 0.00 6.13
84 85 2.919228 ACTCGAATATTTCTGTGGGCC 58.081 47.619 0.00 0.00 0.00 5.80
85 86 4.636206 AGAAACTCGAATATTTCTGTGGGC 59.364 41.667 14.81 0.00 42.27 5.36
91 92 7.612677 ACACTACCAGAAACTCGAATATTTCT 58.387 34.615 11.35 11.35 44.19 2.52
92 93 7.760340 AGACACTACCAGAAACTCGAATATTTC 59.240 37.037 7.91 7.91 35.46 2.17
93 94 7.545965 CAGACACTACCAGAAACTCGAATATTT 59.454 37.037 0.00 0.00 0.00 1.40
94 95 7.036220 CAGACACTACCAGAAACTCGAATATT 58.964 38.462 0.00 0.00 0.00 1.28
95 96 6.153000 ACAGACACTACCAGAAACTCGAATAT 59.847 38.462 0.00 0.00 0.00 1.28
96 97 5.475909 ACAGACACTACCAGAAACTCGAATA 59.524 40.000 0.00 0.00 0.00 1.75
97 98 4.281182 ACAGACACTACCAGAAACTCGAAT 59.719 41.667 0.00 0.00 0.00 3.34
98 99 3.635373 ACAGACACTACCAGAAACTCGAA 59.365 43.478 0.00 0.00 0.00 3.71
99 100 3.220110 ACAGACACTACCAGAAACTCGA 58.780 45.455 0.00 0.00 0.00 4.04
100 101 3.644884 ACAGACACTACCAGAAACTCG 57.355 47.619 0.00 0.00 0.00 4.18
101 102 4.022242 TGCTACAGACACTACCAGAAACTC 60.022 45.833 0.00 0.00 0.00 3.01
102 103 3.895656 TGCTACAGACACTACCAGAAACT 59.104 43.478 0.00 0.00 0.00 2.66
103 104 4.252971 TGCTACAGACACTACCAGAAAC 57.747 45.455 0.00 0.00 0.00 2.78
104 105 5.715279 ACTATGCTACAGACACTACCAGAAA 59.285 40.000 0.00 0.00 0.00 2.52
105 106 5.262009 ACTATGCTACAGACACTACCAGAA 58.738 41.667 0.00 0.00 0.00 3.02
106 107 4.856509 ACTATGCTACAGACACTACCAGA 58.143 43.478 0.00 0.00 0.00 3.86
107 108 5.105716 ACAACTATGCTACAGACACTACCAG 60.106 44.000 0.00 0.00 0.00 4.00
108 109 4.770531 ACAACTATGCTACAGACACTACCA 59.229 41.667 0.00 0.00 0.00 3.25
109 110 5.326200 ACAACTATGCTACAGACACTACC 57.674 43.478 0.00 0.00 0.00 3.18
110 111 6.387465 TGAACAACTATGCTACAGACACTAC 58.613 40.000 0.00 0.00 0.00 2.73
111 112 6.584185 TGAACAACTATGCTACAGACACTA 57.416 37.500 0.00 0.00 0.00 2.74
112 113 5.468540 TGAACAACTATGCTACAGACACT 57.531 39.130 0.00 0.00 0.00 3.55
113 114 7.827819 TTATGAACAACTATGCTACAGACAC 57.172 36.000 0.00 0.00 0.00 3.67
114 115 8.257306 TCATTATGAACAACTATGCTACAGACA 58.743 33.333 0.00 0.00 0.00 3.41
115 116 8.648557 TCATTATGAACAACTATGCTACAGAC 57.351 34.615 0.00 0.00 0.00 3.51
214 216 4.156556 TGAGTTGCAAGGAAGATGTATTGC 59.843 41.667 0.00 1.96 46.36 3.56
215 217 5.885230 TGAGTTGCAAGGAAGATGTATTG 57.115 39.130 0.00 0.00 0.00 1.90
234 236 7.763528 AGCTATAGTTGTTGATTGAGACTTGAG 59.236 37.037 0.84 0.00 0.00 3.02
235 237 7.615403 AGCTATAGTTGTTGATTGAGACTTGA 58.385 34.615 0.84 0.00 0.00 3.02
236 238 7.840342 AGCTATAGTTGTTGATTGAGACTTG 57.160 36.000 0.84 0.00 0.00 3.16
369 371 6.700960 TGCCAGATTGCCGAAATAAATATTTG 59.299 34.615 11.05 0.00 36.13 2.32
395 397 1.280710 ACGGAACCAATCTGGCATACA 59.719 47.619 0.00 0.00 42.67 2.29
414 416 7.330700 TGTTGAAATTTGAACCAAGACAAAGAC 59.669 33.333 16.42 0.00 38.94 3.01
449 451 7.148306 CGGCTATTTATTACAGTGGTTGAAAGT 60.148 37.037 0.00 0.00 0.00 2.66
450 452 7.186804 CGGCTATTTATTACAGTGGTTGAAAG 58.813 38.462 0.00 0.00 0.00 2.62
451 453 6.403855 GCGGCTATTTATTACAGTGGTTGAAA 60.404 38.462 0.00 0.00 0.00 2.69
452 454 5.065474 GCGGCTATTTATTACAGTGGTTGAA 59.935 40.000 0.00 0.00 0.00 2.69
453 455 4.573201 GCGGCTATTTATTACAGTGGTTGA 59.427 41.667 0.00 0.00 0.00 3.18
454 456 4.574828 AGCGGCTATTTATTACAGTGGTTG 59.425 41.667 0.00 0.00 0.00 3.77
455 457 4.777463 AGCGGCTATTTATTACAGTGGTT 58.223 39.130 0.00 0.00 0.00 3.67
456 458 4.417426 AGCGGCTATTTATTACAGTGGT 57.583 40.909 0.00 0.00 0.00 4.16
457 459 7.201530 GCTATTAGCGGCTATTTATTACAGTGG 60.202 40.741 11.04 0.00 0.00 4.00
458 460 7.330946 TGCTATTAGCGGCTATTTATTACAGTG 59.669 37.037 11.04 0.00 46.26 3.66
459 461 7.331193 GTGCTATTAGCGGCTATTTATTACAGT 59.669 37.037 11.04 0.00 46.26 3.55
460 462 7.462856 CGTGCTATTAGCGGCTATTTATTACAG 60.463 40.741 11.04 2.21 46.26 2.74
461 463 6.309494 CGTGCTATTAGCGGCTATTTATTACA 59.691 38.462 11.04 1.44 46.26 2.41
462 464 6.693342 CGTGCTATTAGCGGCTATTTATTAC 58.307 40.000 11.04 5.80 46.26 1.89
463 465 5.290158 GCGTGCTATTAGCGGCTATTTATTA 59.710 40.000 18.79 0.00 46.26 0.98
464 466 4.092968 GCGTGCTATTAGCGGCTATTTATT 59.907 41.667 18.79 0.00 46.26 1.40
465 467 3.617263 GCGTGCTATTAGCGGCTATTTAT 59.383 43.478 18.79 4.28 46.26 1.40
466 468 2.991190 GCGTGCTATTAGCGGCTATTTA 59.009 45.455 18.79 5.42 46.26 1.40
467 469 1.798813 GCGTGCTATTAGCGGCTATTT 59.201 47.619 18.79 4.49 46.26 1.40
468 470 1.000955 AGCGTGCTATTAGCGGCTATT 59.999 47.619 24.23 9.96 46.86 1.73
469 471 0.603569 AGCGTGCTATTAGCGGCTAT 59.396 50.000 24.23 8.98 46.86 2.97
470 472 1.241165 TAGCGTGCTATTAGCGGCTA 58.759 50.000 25.29 25.29 46.86 3.93
471 473 2.815308 AGCGTGCTATTAGCGGCT 59.185 55.556 21.53 21.53 46.26 5.52
472 474 1.192534 CTTTAGCGTGCTATTAGCGGC 59.807 52.381 18.55 18.55 46.26 6.53
473 475 1.192534 GCTTTAGCGTGCTATTAGCGG 59.807 52.381 15.94 6.68 46.26 5.52
474 476 1.858458 TGCTTTAGCGTGCTATTAGCG 59.142 47.619 21.38 0.00 44.30 4.26
475 477 3.120511 GGATGCTTTAGCGTGCTATTAGC 60.121 47.826 20.67 20.67 43.75 3.09
476 478 4.653806 GGATGCTTTAGCGTGCTATTAG 57.346 45.455 8.04 5.03 43.75 1.73
482 484 0.654683 CTCAGGATGCTTTAGCGTGC 59.345 55.000 7.30 7.30 46.85 5.34
483 485 2.299993 TCTCAGGATGCTTTAGCGTG 57.700 50.000 0.31 0.00 45.83 5.34
484 486 3.550437 ATTCTCAGGATGCTTTAGCGT 57.450 42.857 0.00 0.00 45.83 5.07
485 487 3.624861 ACAATTCTCAGGATGCTTTAGCG 59.375 43.478 0.00 0.00 45.83 4.26
486 488 4.880696 AGACAATTCTCAGGATGCTTTAGC 59.119 41.667 0.00 0.00 42.50 3.09
487 489 6.601741 GAGACAATTCTCAGGATGCTTTAG 57.398 41.667 0.00 0.00 46.84 1.85
499 501 8.821894 ACTGATTTATTTAGCGAGACAATTCTC 58.178 33.333 0.00 0.00 44.50 2.87
500 502 8.607459 CACTGATTTATTTAGCGAGACAATTCT 58.393 33.333 0.00 0.00 33.37 2.40
501 503 8.391106 ACACTGATTTATTTAGCGAGACAATTC 58.609 33.333 0.00 0.00 0.00 2.17
502 504 8.268850 ACACTGATTTATTTAGCGAGACAATT 57.731 30.769 0.00 0.00 0.00 2.32
503 505 7.849804 ACACTGATTTATTTAGCGAGACAAT 57.150 32.000 0.00 0.00 0.00 2.71
504 506 8.942338 ATACACTGATTTATTTAGCGAGACAA 57.058 30.769 0.00 0.00 0.00 3.18
514 516 9.547753 AGCGAGACATTATACACTGATTTATTT 57.452 29.630 0.00 0.00 0.00 1.40
519 521 9.847706 CTATTAGCGAGACATTATACACTGATT 57.152 33.333 0.00 0.00 0.00 2.57
520 522 7.971168 GCTATTAGCGAGACATTATACACTGAT 59.029 37.037 0.00 0.00 0.00 2.90
521 523 7.040686 TGCTATTAGCGAGACATTATACACTGA 60.041 37.037 10.94 0.00 46.26 3.41
522 524 7.084486 TGCTATTAGCGAGACATTATACACTG 58.916 38.462 10.94 0.00 46.26 3.66
523 525 7.215719 TGCTATTAGCGAGACATTATACACT 57.784 36.000 10.94 0.00 46.26 3.55
524 526 9.737427 ATATGCTATTAGCGAGACATTATACAC 57.263 33.333 10.94 0.00 46.26 2.90
531 533 9.155975 CCTTAAAATATGCTATTAGCGAGACAT 57.844 33.333 10.94 1.55 46.26 3.06
532 534 7.117812 GCCTTAAAATATGCTATTAGCGAGACA 59.882 37.037 10.94 0.00 46.26 3.41
533 535 7.413109 GGCCTTAAAATATGCTATTAGCGAGAC 60.413 40.741 10.94 0.00 46.26 3.36
534 536 6.594159 GGCCTTAAAATATGCTATTAGCGAGA 59.406 38.462 10.94 0.00 46.26 4.04
535 537 6.455646 CGGCCTTAAAATATGCTATTAGCGAG 60.456 42.308 10.94 0.02 46.26 5.03
536 538 5.350365 CGGCCTTAAAATATGCTATTAGCGA 59.650 40.000 10.94 2.18 46.26 4.93
537 539 5.447279 CCGGCCTTAAAATATGCTATTAGCG 60.447 44.000 10.94 0.00 46.26 4.26
538 540 5.676331 GCCGGCCTTAAAATATGCTATTAGC 60.676 44.000 18.11 8.80 42.82 3.09
539 541 5.447279 CGCCGGCCTTAAAATATGCTATTAG 60.447 44.000 23.46 0.00 0.00 1.73
540 542 4.393680 CGCCGGCCTTAAAATATGCTATTA 59.606 41.667 23.46 0.00 0.00 0.98
541 543 3.190535 CGCCGGCCTTAAAATATGCTATT 59.809 43.478 23.46 0.00 0.00 1.73
542 544 2.747446 CGCCGGCCTTAAAATATGCTAT 59.253 45.455 23.46 0.00 0.00 2.97
543 545 2.147958 CGCCGGCCTTAAAATATGCTA 58.852 47.619 23.46 0.00 0.00 3.49
544 546 0.951558 CGCCGGCCTTAAAATATGCT 59.048 50.000 23.46 0.00 0.00 3.79
545 547 0.663269 GCGCCGGCCTTAAAATATGC 60.663 55.000 23.46 10.64 0.00 3.14
546 548 0.951558 AGCGCCGGCCTTAAAATATG 59.048 50.000 23.46 3.17 41.24 1.78
547 549 2.554370 TAGCGCCGGCCTTAAAATAT 57.446 45.000 23.46 0.00 41.24 1.28
548 550 2.554370 ATAGCGCCGGCCTTAAAATA 57.446 45.000 23.46 3.04 41.24 1.40
549 551 1.687563 AATAGCGCCGGCCTTAAAAT 58.312 45.000 23.46 6.48 41.24 1.82
550 552 1.465794 AAATAGCGCCGGCCTTAAAA 58.534 45.000 23.46 4.19 41.24 1.52
551 553 1.133407 CAAAATAGCGCCGGCCTTAAA 59.867 47.619 23.46 4.57 41.24 1.52
552 554 0.736053 CAAAATAGCGCCGGCCTTAA 59.264 50.000 23.46 4.08 41.24 1.85
553 555 1.720694 GCAAAATAGCGCCGGCCTTA 61.721 55.000 23.46 14.16 41.24 2.69
554 556 3.063743 GCAAAATAGCGCCGGCCTT 62.064 57.895 23.46 12.10 41.24 4.35
555 557 2.602746 TAGCAAAATAGCGCCGGCCT 62.603 55.000 23.46 21.00 41.24 5.19
556 558 2.184167 TAGCAAAATAGCGCCGGCC 61.184 57.895 23.46 14.23 41.24 6.13
557 559 1.010013 GTAGCAAAATAGCGCCGGC 60.010 57.895 19.07 19.07 40.15 6.13
558 560 0.027586 GTGTAGCAAAATAGCGCCGG 59.972 55.000 2.29 0.00 40.15 6.13
559 561 0.315059 CGTGTAGCAAAATAGCGCCG 60.315 55.000 2.29 0.00 40.15 6.46
560 562 3.509266 CGTGTAGCAAAATAGCGCC 57.491 52.632 2.29 0.00 40.15 6.53
585 587 8.923270 ACATCTCAGGTTAAAATCAAGGAAAAA 58.077 29.630 0.00 0.00 0.00 1.94
586 588 8.477419 ACATCTCAGGTTAAAATCAAGGAAAA 57.523 30.769 0.00 0.00 0.00 2.29
587 589 8.477419 AACATCTCAGGTTAAAATCAAGGAAA 57.523 30.769 0.00 0.00 0.00 3.13
588 590 7.176690 GGAACATCTCAGGTTAAAATCAAGGAA 59.823 37.037 0.00 0.00 0.00 3.36
589 591 6.659242 GGAACATCTCAGGTTAAAATCAAGGA 59.341 38.462 0.00 0.00 0.00 3.36
590 592 6.660949 AGGAACATCTCAGGTTAAAATCAAGG 59.339 38.462 0.00 0.00 0.00 3.61
591 593 7.693969 AGGAACATCTCAGGTTAAAATCAAG 57.306 36.000 0.00 0.00 0.00 3.02
619 621 3.876914 CCAAATAACTAGCCATGCTTCGA 59.123 43.478 0.00 0.00 40.44 3.71
620 622 3.627577 ACCAAATAACTAGCCATGCTTCG 59.372 43.478 0.00 0.00 40.44 3.79
651 706 9.739276 AATTTGATGTTATTACCTGACAAGAGA 57.261 29.630 0.00 0.00 0.00 3.10
693 748 4.911514 TTTAAGAACACTTGGGACTTGC 57.088 40.909 0.00 0.00 0.00 4.01
694 749 7.013274 TGAGAATTTAAGAACACTTGGGACTTG 59.987 37.037 0.00 0.00 0.00 3.16
695 750 7.060421 TGAGAATTTAAGAACACTTGGGACTT 58.940 34.615 0.00 0.00 0.00 3.01
727 785 3.303990 CCACTGATCCAACAAAACAGTCG 60.304 47.826 0.00 0.00 39.33 4.18
799 871 9.661187 GAAAAGTGTAAGTAGAAGCCTTTAAAC 57.339 33.333 0.00 0.00 0.00 2.01
854 934 3.259902 GGTAGTAGTAAGCACTTGCCAC 58.740 50.000 0.00 0.00 43.38 5.01
939 1027 5.394993 GGCGTCCTAGTTGTATACTTTCCTT 60.395 44.000 4.17 0.00 38.33 3.36
1121 1209 0.748005 GGCAACACGACCCATGCTAT 60.748 55.000 0.00 0.00 38.79 2.97
1152 1240 6.822667 TGACAAAGAACATCATGCATTACT 57.177 33.333 0.00 0.00 0.00 2.24
1188 1276 6.000891 TCATATATTTGATTGCTGCGGTTC 57.999 37.500 0.00 0.00 0.00 3.62
1204 1292 5.276440 CTCCTCTAACCAGCCCTCATATAT 58.724 45.833 0.00 0.00 0.00 0.86
1353 1443 6.571605 TCTGAGAGCTATCTGATTCAAACAG 58.428 40.000 13.25 0.00 35.30 3.16
1603 1693 1.365633 CCATCCCGAGCAGAGCTAC 59.634 63.158 0.00 0.00 39.88 3.58
1617 1707 4.010349 CAGTTTTACCAAGACCTCCCATC 58.990 47.826 0.00 0.00 0.00 3.51
1652 1742 4.283722 TCTCCCTCTCCTTTTTGTAGACAC 59.716 45.833 0.00 0.00 0.00 3.67
1662 1752 3.919554 ACTGGAATTTCTCCCTCTCCTTT 59.080 43.478 0.00 0.00 44.69 3.11
1750 1840 7.425606 ACACTGGCAGTATCTTTAAAAAGTTG 58.574 34.615 21.59 4.44 37.31 3.16
1766 1856 5.825679 AGAGTACTAGATAGAACACTGGCAG 59.174 44.000 14.16 14.16 0.00 4.85
1962 2052 1.860484 GAGAGGCAAGTGCAGCAACC 61.860 60.000 0.00 0.00 44.36 3.77
2012 2102 4.470664 AGAGATCTCATGCCTTGTCTTCTT 59.529 41.667 24.39 0.00 0.00 2.52
2028 2118 7.175816 GGAAAGGCTTTCTTACAAAAGAGATCT 59.824 37.037 32.28 0.00 42.60 2.75
2081 2171 2.632377 TGGACGATGGCTTCAATTCTC 58.368 47.619 0.00 0.00 0.00 2.87
2311 2401 5.102953 TCTGGAAATAAGCTGCAGTACAT 57.897 39.130 16.64 2.90 34.19 2.29
2366 2456 1.207791 CCCCTCTGCTGTCCATAACT 58.792 55.000 0.00 0.00 0.00 2.24
2727 2826 6.545504 TCTTGACTCATTACACAAAAGAGC 57.454 37.500 0.00 0.00 0.00 4.09
2812 2911 5.102313 CCAAATGGCGGAGATTAAAAAGAC 58.898 41.667 0.00 0.00 0.00 3.01
2910 3009 4.207891 AGTCATGTATGTCAGAACCACC 57.792 45.455 0.00 0.00 0.00 4.61
2915 3014 4.558226 AGGCAAGTCATGTATGTCAGAA 57.442 40.909 0.00 0.00 0.00 3.02
2930 3029 2.787473 TCACAATCCCACTAGGCAAG 57.213 50.000 0.00 0.00 34.51 4.01
2991 3090 8.659527 ACATTTAAATTCTTTCCCTTGTGGATT 58.340 29.630 0.00 0.00 44.66 3.01
2997 3096 6.155827 TGCGACATTTAAATTCTTTCCCTTG 58.844 36.000 0.00 0.00 0.00 3.61
3004 3103 5.705609 ACCACTGCGACATTTAAATTCTT 57.294 34.783 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.