Multiple sequence alignment - TraesCS7B01G112400

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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 TraesCS7B01G112400 chr7B 100.000 3439 0 0 1 3439 128820872 128824310 0.000000e+00 6351.0
1 TraesCS7B01G112400 chr7D 91.065 2272 112 37 703 2924 165634207 165636437 0.000000e+00 2987.0
2 TraesCS7B01G112400 chr7D 86.214 457 32 17 197 644 165633644 165634078 1.870000e-127 466.0
3 TraesCS7B01G112400 chr7D 95.122 82 3 1 128 209 165633533 165633613 1.000000e-25 128.0
4 TraesCS7B01G112400 chr7D 83.621 116 13 4 1686 1798 262698683 262698571 1.690000e-18 104.0
5 TraesCS7B01G112400 chr7A 90.376 2234 135 31 713 2903 167179188 167181384 0.000000e+00 2861.0
6 TraesCS7B01G112400 chr7A 89.941 507 49 2 2924 3430 194280602 194281106 0.000000e+00 652.0
7 TraesCS7B01G112400 chr7A 87.248 298 22 8 194 475 167178627 167178924 3.310000e-85 326.0
8 TraesCS7B01G112400 chr7A 91.463 82 6 1 128 209 167178519 167178599 1.010000e-20 111.0
9 TraesCS7B01G112400 chr7A 83.621 116 13 4 1686 1798 285576335 285576223 1.690000e-18 104.0
10 TraesCS7B01G112400 chr2D 94.961 516 25 1 2925 3439 639391883 639392398 0.000000e+00 808.0
11 TraesCS7B01G112400 chr2D 89.709 515 52 1 2926 3439 643240380 643239866 0.000000e+00 656.0
12 TraesCS7B01G112400 chr2D 83.594 128 17 4 1457 1582 101872854 101872729 2.170000e-22 117.0
13 TraesCS7B01G112400 chr2D 77.953 127 23 5 1457 1582 101956591 101956469 1.320000e-09 75.0
14 TraesCS7B01G112400 chr1D 93.810 517 30 2 2924 3439 105355680 105356195 0.000000e+00 776.0
15 TraesCS7B01G112400 chr1D 90.495 505 47 1 2926 3430 444483566 444484069 0.000000e+00 665.0
16 TraesCS7B01G112400 chr6A 90.514 506 46 2 2925 3430 28948355 28948858 0.000000e+00 667.0
17 TraesCS7B01G112400 chr6A 82.292 384 48 14 1210 1591 525992597 525992232 7.160000e-82 315.0
18 TraesCS7B01G112400 chr4D 90.495 505 48 0 2926 3430 449394936 449395440 0.000000e+00 667.0
19 TraesCS7B01G112400 chr3B 90.078 514 51 0 2926 3439 780741333 780740820 0.000000e+00 667.0
20 TraesCS7B01G112400 chr5D 89.709 515 51 2 2926 3439 542541867 542541354 0.000000e+00 656.0
21 TraesCS7B01G112400 chr5D 86.594 276 32 3 1832 2103 377280374 377280100 2.010000e-77 300.0
22 TraesCS7B01G112400 chr5D 91.489 141 11 1 1207 1347 319254267 319254406 3.500000e-45 193.0
23 TraesCS7B01G112400 chr6D 79.333 600 92 25 1210 1794 383745563 383744981 3.220000e-105 392.0
24 TraesCS7B01G112400 chr6D 84.097 371 39 6 1832 2201 157661397 157661748 1.180000e-89 340.0
25 TraesCS7B01G112400 chr3D 84.267 375 36 12 1832 2202 105175253 105174898 9.140000e-91 344.0
26 TraesCS7B01G112400 chr3D 84.367 371 37 11 1835 2202 105253028 105252676 9.140000e-91 344.0
27 TraesCS7B01G112400 chr3D 84.097 371 37 6 1835 2202 105197263 105196912 4.250000e-89 339.0
28 TraesCS7B01G112400 chr3D 83.333 372 41 7 1834 2202 105280455 105280102 1.190000e-84 324.0
29 TraesCS7B01G112400 chr6B 81.073 354 52 12 1448 1796 574021257 574020914 5.660000e-68 268.0
30 TraesCS7B01G112400 chr6B 91.034 145 12 1 1210 1354 574021486 574021343 9.740000e-46 195.0
31 TraesCS7B01G112400 chr5B 91.489 141 11 1 1207 1347 369485435 369485574 3.500000e-45 193.0
32 TraesCS7B01G112400 chr5B 89.831 118 12 0 1673 1790 369485858 369485975 5.940000e-33 152.0
33 TraesCS7B01G112400 chr5A 90.780 141 12 1 1207 1347 414934858 414934719 1.630000e-43 187.0
34 TraesCS7B01G112400 chr5A 89.655 116 12 0 1675 1790 414934424 414934309 7.690000e-32 148.0
35 TraesCS7B01G112400 chr4A 97.959 98 2 0 1208 1305 406202731 406202634 1.640000e-38 171.0
36 TraesCS7B01G112400 chr2A 83.594 128 17 4 1457 1582 100826055 100825930 2.170000e-22 117.0
37 TraesCS7B01G112400 chr2A 84.034 119 17 2 1674 1791 696316041 696316158 2.810000e-21 113.0
38 TraesCS7B01G112400 chr2A 80.189 106 18 3 1457 1562 100971516 100971414 3.680000e-10 76.8
39 TraesCS7B01G112400 chr2B 82.812 128 18 4 1457 1582 152844327 152844202 1.010000e-20 111.0
40 TraesCS7B01G112400 chr2B 95.455 44 2 0 1457 1500 153126803 153126760 1.710000e-08 71.3


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 TraesCS7B01G112400 chr7B 128820872 128824310 3438 False 6351.000000 6351 100.000000 1 3439 1 chr7B.!!$F1 3438
1 TraesCS7B01G112400 chr7D 165633533 165636437 2904 False 1193.666667 2987 90.800333 128 2924 3 chr7D.!!$F1 2796
2 TraesCS7B01G112400 chr7A 167178519 167181384 2865 False 1099.333333 2861 89.695667 128 2903 3 chr7A.!!$F2 2775
3 TraesCS7B01G112400 chr7A 194280602 194281106 504 False 652.000000 652 89.941000 2924 3430 1 chr7A.!!$F1 506
4 TraesCS7B01G112400 chr2D 639391883 639392398 515 False 808.000000 808 94.961000 2925 3439 1 chr2D.!!$F1 514
5 TraesCS7B01G112400 chr2D 643239866 643240380 514 True 656.000000 656 89.709000 2926 3439 1 chr2D.!!$R3 513
6 TraesCS7B01G112400 chr1D 105355680 105356195 515 False 776.000000 776 93.810000 2924 3439 1 chr1D.!!$F1 515
7 TraesCS7B01G112400 chr1D 444483566 444484069 503 False 665.000000 665 90.495000 2926 3430 1 chr1D.!!$F2 504
8 TraesCS7B01G112400 chr6A 28948355 28948858 503 False 667.000000 667 90.514000 2925 3430 1 chr6A.!!$F1 505
9 TraesCS7B01G112400 chr4D 449394936 449395440 504 False 667.000000 667 90.495000 2926 3430 1 chr4D.!!$F1 504
10 TraesCS7B01G112400 chr3B 780740820 780741333 513 True 667.000000 667 90.078000 2926 3439 1 chr3B.!!$R1 513
11 TraesCS7B01G112400 chr5D 542541354 542541867 513 True 656.000000 656 89.709000 2926 3439 1 chr5D.!!$R2 513
12 TraesCS7B01G112400 chr6D 383744981 383745563 582 True 392.000000 392 79.333000 1210 1794 1 chr6D.!!$R1 584
13 TraesCS7B01G112400 chr6B 574020914 574021486 572 True 231.500000 268 86.053500 1210 1796 2 chr6B.!!$R1 586

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
606 679 0.320374 TTGACATTCTCTTCGGCGGT 59.680 50.0 7.21 0.0 0.00 5.68 F
1206 1376 0.177604 GAGCCATCACTCAGTCAGGG 59.822 60.0 0.00 0.0 36.65 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2386 2611 0.452987 CAAACACCCGAGCATGGATG 59.547 55.0 0.00 0.00 0.0 3.51 R
2478 2709 0.596577 CCACGTCCGGATCGATACAT 59.403 55.0 26.02 6.96 0.0 2.29 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 4.073201 CCACCAGGCCTATGACCT 57.927 61.111 16.20 0.00 38.35 3.85
20 21 3.240670 CCACCAGGCCTATGACCTA 57.759 57.895 16.20 0.00 35.10 3.08
21 22 1.734655 CCACCAGGCCTATGACCTAT 58.265 55.000 16.20 0.00 35.10 2.57
22 23 1.625818 CCACCAGGCCTATGACCTATC 59.374 57.143 16.20 0.00 35.10 2.08
23 24 1.625818 CACCAGGCCTATGACCTATCC 59.374 57.143 3.98 0.00 35.10 2.59
24 25 1.223077 ACCAGGCCTATGACCTATCCA 59.777 52.381 3.98 0.00 35.10 3.41
25 26 1.625818 CCAGGCCTATGACCTATCCAC 59.374 57.143 3.98 0.00 35.10 4.02
26 27 1.273606 CAGGCCTATGACCTATCCACG 59.726 57.143 3.98 0.00 35.10 4.94
27 28 1.147191 AGGCCTATGACCTATCCACGA 59.853 52.381 1.29 0.00 35.10 4.35
28 29 1.968493 GGCCTATGACCTATCCACGAA 59.032 52.381 0.00 0.00 0.00 3.85
29 30 2.367567 GGCCTATGACCTATCCACGAAA 59.632 50.000 0.00 0.00 0.00 3.46
30 31 3.008049 GGCCTATGACCTATCCACGAAAT 59.992 47.826 0.00 0.00 0.00 2.17
31 32 4.246458 GCCTATGACCTATCCACGAAATC 58.754 47.826 0.00 0.00 0.00 2.17
32 33 4.021016 GCCTATGACCTATCCACGAAATCT 60.021 45.833 0.00 0.00 0.00 2.40
33 34 5.511545 GCCTATGACCTATCCACGAAATCTT 60.512 44.000 0.00 0.00 0.00 2.40
34 35 6.159988 CCTATGACCTATCCACGAAATCTTC 58.840 44.000 0.00 0.00 0.00 2.87
50 51 7.861176 GAAATCTTCGAGGTAGACATGATAC 57.139 40.000 0.00 1.82 0.00 2.24
51 52 7.589958 AAATCTTCGAGGTAGACATGATACT 57.410 36.000 0.00 0.00 0.00 2.12
52 53 8.693120 AAATCTTCGAGGTAGACATGATACTA 57.307 34.615 0.00 0.00 0.00 1.82
53 54 8.871629 AATCTTCGAGGTAGACATGATACTAT 57.128 34.615 0.00 0.00 0.00 2.12
54 55 8.871629 ATCTTCGAGGTAGACATGATACTATT 57.128 34.615 0.00 0.00 0.00 1.73
55 56 8.693120 TCTTCGAGGTAGACATGATACTATTT 57.307 34.615 0.00 0.00 0.00 1.40
56 57 9.132923 TCTTCGAGGTAGACATGATACTATTTT 57.867 33.333 0.00 0.00 0.00 1.82
57 58 9.751542 CTTCGAGGTAGACATGATACTATTTTT 57.248 33.333 0.00 0.00 0.00 1.94
58 59 9.745880 TTCGAGGTAGACATGATACTATTTTTC 57.254 33.333 0.00 0.00 0.00 2.29
59 60 9.132923 TCGAGGTAGACATGATACTATTTTTCT 57.867 33.333 0.00 0.00 0.00 2.52
60 61 9.400638 CGAGGTAGACATGATACTATTTTTCTC 57.599 37.037 0.00 2.24 0.00 2.87
61 62 9.400638 GAGGTAGACATGATACTATTTTTCTCG 57.599 37.037 0.00 0.00 0.00 4.04
62 63 8.361139 AGGTAGACATGATACTATTTTTCTCGG 58.639 37.037 0.00 0.00 0.00 4.63
63 64 7.599245 GGTAGACATGATACTATTTTTCTCGGG 59.401 40.741 0.00 0.00 0.00 5.14
64 65 5.992217 AGACATGATACTATTTTTCTCGGGC 59.008 40.000 0.00 0.00 0.00 6.13
65 66 5.063880 ACATGATACTATTTTTCTCGGGCC 58.936 41.667 0.00 0.00 0.00 5.80
66 67 5.163195 ACATGATACTATTTTTCTCGGGCCT 60.163 40.000 0.84 0.00 0.00 5.19
67 68 6.042781 ACATGATACTATTTTTCTCGGGCCTA 59.957 38.462 0.84 0.00 0.00 3.93
68 69 6.097915 TGATACTATTTTTCTCGGGCCTAG 57.902 41.667 0.84 0.00 0.00 3.02
69 70 3.195471 ACTATTTTTCTCGGGCCTAGC 57.805 47.619 0.84 0.00 0.00 3.42
70 71 2.504175 ACTATTTTTCTCGGGCCTAGCA 59.496 45.455 0.84 0.00 0.00 3.49
71 72 2.736670 ATTTTTCTCGGGCCTAGCAT 57.263 45.000 0.84 0.00 0.00 3.79
72 73 3.857157 ATTTTTCTCGGGCCTAGCATA 57.143 42.857 0.84 0.00 0.00 3.14
73 74 2.910688 TTTTCTCGGGCCTAGCATAG 57.089 50.000 0.84 0.00 38.80 2.23
74 75 1.789523 TTTCTCGGGCCTAGCATAGT 58.210 50.000 0.84 0.00 36.82 2.12
75 76 1.789523 TTCTCGGGCCTAGCATAGTT 58.210 50.000 0.84 0.00 36.82 2.24
76 77 2.670019 TCTCGGGCCTAGCATAGTTA 57.330 50.000 0.84 0.00 36.82 2.24
77 78 2.953453 TCTCGGGCCTAGCATAGTTAA 58.047 47.619 0.84 0.00 36.82 2.01
78 79 3.507411 TCTCGGGCCTAGCATAGTTAAT 58.493 45.455 0.84 0.00 36.82 1.40
79 80 3.901844 TCTCGGGCCTAGCATAGTTAATT 59.098 43.478 0.84 0.00 36.82 1.40
80 81 4.347000 TCTCGGGCCTAGCATAGTTAATTT 59.653 41.667 0.84 0.00 36.82 1.82
81 82 4.638304 TCGGGCCTAGCATAGTTAATTTC 58.362 43.478 0.84 0.00 36.82 2.17
82 83 4.347000 TCGGGCCTAGCATAGTTAATTTCT 59.653 41.667 0.84 0.00 36.82 2.52
83 84 5.063880 CGGGCCTAGCATAGTTAATTTCTT 58.936 41.667 0.84 0.00 36.82 2.52
84 85 5.049405 CGGGCCTAGCATAGTTAATTTCTTG 60.049 44.000 0.84 0.00 36.82 3.02
85 86 5.828328 GGGCCTAGCATAGTTAATTTCTTGT 59.172 40.000 0.84 0.00 36.82 3.16
86 87 6.321435 GGGCCTAGCATAGTTAATTTCTTGTT 59.679 38.462 0.84 0.00 36.82 2.83
87 88 7.196331 GGCCTAGCATAGTTAATTTCTTGTTG 58.804 38.462 0.00 0.00 36.82 3.33
88 89 7.067008 GGCCTAGCATAGTTAATTTCTTGTTGA 59.933 37.037 0.00 0.00 36.82 3.18
89 90 8.458843 GCCTAGCATAGTTAATTTCTTGTTGAA 58.541 33.333 0.00 0.00 36.82 2.69
90 91 9.774742 CCTAGCATAGTTAATTTCTTGTTGAAC 57.225 33.333 0.00 0.00 36.82 3.18
97 98 8.084590 AGTTAATTTCTTGTTGAACTAGTCGG 57.915 34.615 6.67 0.00 33.88 4.79
98 99 7.929785 AGTTAATTTCTTGTTGAACTAGTCGGA 59.070 33.333 6.67 0.00 33.88 4.55
99 100 8.718734 GTTAATTTCTTGTTGAACTAGTCGGAT 58.281 33.333 6.67 0.00 33.88 4.18
100 101 6.727824 ATTTCTTGTTGAACTAGTCGGATG 57.272 37.500 6.67 0.00 33.88 3.51
101 102 3.585862 TCTTGTTGAACTAGTCGGATGC 58.414 45.455 6.67 0.00 0.00 3.91
102 103 3.006430 TCTTGTTGAACTAGTCGGATGCA 59.994 43.478 6.67 0.00 0.00 3.96
103 104 2.683968 TGTTGAACTAGTCGGATGCAC 58.316 47.619 0.00 0.00 0.00 4.57
104 105 2.036604 TGTTGAACTAGTCGGATGCACA 59.963 45.455 0.00 0.00 0.00 4.57
105 106 3.064207 GTTGAACTAGTCGGATGCACAA 58.936 45.455 0.00 0.00 0.00 3.33
106 107 3.394674 TGAACTAGTCGGATGCACAAA 57.605 42.857 0.00 0.00 0.00 2.83
107 108 3.937814 TGAACTAGTCGGATGCACAAAT 58.062 40.909 0.00 0.00 0.00 2.32
108 109 4.323417 TGAACTAGTCGGATGCACAAATT 58.677 39.130 0.00 0.00 0.00 1.82
109 110 4.759693 TGAACTAGTCGGATGCACAAATTT 59.240 37.500 0.00 0.00 0.00 1.82
110 111 4.685169 ACTAGTCGGATGCACAAATTTG 57.315 40.909 16.67 16.67 0.00 2.32
111 112 3.440173 ACTAGTCGGATGCACAAATTTGG 59.560 43.478 21.74 11.81 0.00 3.28
112 113 2.238521 AGTCGGATGCACAAATTTGGT 58.761 42.857 21.74 5.40 0.00 3.67
113 114 3.417101 AGTCGGATGCACAAATTTGGTA 58.583 40.909 21.74 10.77 0.00 3.25
114 115 4.016444 AGTCGGATGCACAAATTTGGTAT 58.984 39.130 21.74 14.60 0.00 2.73
115 116 5.189928 AGTCGGATGCACAAATTTGGTATA 58.810 37.500 21.74 6.20 0.00 1.47
116 117 5.650266 AGTCGGATGCACAAATTTGGTATAA 59.350 36.000 21.74 3.80 0.00 0.98
117 118 6.321181 AGTCGGATGCACAAATTTGGTATAAT 59.679 34.615 21.74 8.18 0.00 1.28
118 119 6.978080 GTCGGATGCACAAATTTGGTATAATT 59.022 34.615 21.74 0.00 0.00 1.40
119 120 7.491048 GTCGGATGCACAAATTTGGTATAATTT 59.509 33.333 21.74 0.00 38.02 1.82
157 158 3.830755 AGCTCCTCAAATTGCATCAAACT 59.169 39.130 0.00 0.00 0.00 2.66
194 195 5.607119 AAACTATACAGCAAGAAACACGG 57.393 39.130 0.00 0.00 0.00 4.94
202 203 0.788391 CAAGAAACACGGCGTAGGAC 59.212 55.000 14.22 5.25 0.00 3.85
215 259 3.901667 CGTAGGACGCATTTTACTGTC 57.098 47.619 0.00 0.00 33.65 3.51
222 266 4.909880 GGACGCATTTTACTGTCTGTTTTC 59.090 41.667 0.00 0.00 0.00 2.29
235 279 5.232463 TGTCTGTTTTCCGTTGACCTATAC 58.768 41.667 0.00 0.00 0.00 1.47
240 289 7.118680 TCTGTTTTCCGTTGACCTATACAATTC 59.881 37.037 0.00 0.00 0.00 2.17
243 292 8.885722 GTTTTCCGTTGACCTATACAATTCATA 58.114 33.333 0.00 0.00 0.00 2.15
248 297 9.051679 CCGTTGACCTATACAATTCATATTTCA 57.948 33.333 0.00 0.00 0.00 2.69
260 309 5.930837 TTCATATTTCAATTGACCCCCAC 57.069 39.130 7.89 0.00 0.00 4.61
301 357 3.256879 TGACTTCACCAGAGCTAGTTCAG 59.743 47.826 9.43 0.40 0.00 3.02
339 395 2.806244 CTCCAACAAAAGACCCACGTAG 59.194 50.000 0.00 0.00 0.00 3.51
355 411 1.066143 CGTAGCAAATCCACCTCCTGT 60.066 52.381 0.00 0.00 0.00 4.00
381 439 4.518249 CATCTAAAAGGAGAGGGGTGAAC 58.482 47.826 0.00 0.00 0.00 3.18
382 440 2.565834 TCTAAAAGGAGAGGGGTGAACG 59.434 50.000 0.00 0.00 0.00 3.95
383 441 1.137697 AAAAGGAGAGGGGTGAACGT 58.862 50.000 0.00 0.00 0.00 3.99
459 518 1.134788 AGGGTACGCGGAGAAGATTTG 60.135 52.381 12.47 0.00 0.00 2.32
469 528 3.426695 CGGAGAAGATTTGCATGTCAACC 60.427 47.826 0.00 0.00 33.73 3.77
475 534 3.820467 AGATTTGCATGTCAACCTCGAAA 59.180 39.130 0.00 0.00 33.73 3.46
476 535 4.278170 AGATTTGCATGTCAACCTCGAAAA 59.722 37.500 0.00 0.00 33.73 2.29
477 536 3.624326 TTGCATGTCAACCTCGAAAAG 57.376 42.857 0.00 0.00 0.00 2.27
479 538 2.548057 TGCATGTCAACCTCGAAAAGTC 59.452 45.455 0.00 0.00 0.00 3.01
480 539 2.095718 GCATGTCAACCTCGAAAAGTCC 60.096 50.000 0.00 0.00 0.00 3.85
510 582 6.816616 TTTTTGGGGGAAAAAGTGATTACT 57.183 33.333 0.00 0.00 38.38 2.24
512 584 7.916077 TTTTGGGGGAAAAAGTGATTACTTA 57.084 32.000 2.94 0.00 46.14 2.24
513 585 8.499288 TTTTGGGGGAAAAAGTGATTACTTAT 57.501 30.769 2.94 0.00 46.14 1.73
514 586 8.499288 TTTGGGGGAAAAAGTGATTACTTATT 57.501 30.769 2.94 0.00 46.14 1.40
515 587 9.603189 TTTGGGGGAAAAAGTGATTACTTATTA 57.397 29.630 2.94 0.00 46.14 0.98
516 588 8.817092 TGGGGGAAAAAGTGATTACTTATTAG 57.183 34.615 2.94 0.00 46.14 1.73
517 589 7.340999 TGGGGGAAAAAGTGATTACTTATTAGC 59.659 37.037 2.94 0.00 46.14 3.09
518 590 7.340999 GGGGGAAAAAGTGATTACTTATTAGCA 59.659 37.037 2.94 0.00 46.14 3.49
519 591 8.188799 GGGGAAAAAGTGATTACTTATTAGCAC 58.811 37.037 2.94 0.00 46.14 4.40
520 592 7.908601 GGGAAAAAGTGATTACTTATTAGCACG 59.091 37.037 2.94 0.00 46.14 5.34
521 593 8.448615 GGAAAAAGTGATTACTTATTAGCACGT 58.551 33.333 2.94 0.00 46.14 4.49
522 594 9.474249 GAAAAAGTGATTACTTATTAGCACGTC 57.526 33.333 2.94 0.00 46.14 4.34
554 627 5.646360 GGATTTAAGATTTGTGAAGGGTCGA 59.354 40.000 0.00 0.00 0.00 4.20
600 673 5.465935 AGAGTTCTCGTTGACATTCTCTTC 58.534 41.667 0.00 0.00 0.00 2.87
606 679 0.320374 TTGACATTCTCTTCGGCGGT 59.680 50.000 7.21 0.00 0.00 5.68
615 688 4.388499 TTCGGCGGTTCTCCCTGC 62.388 66.667 7.21 0.00 33.64 4.85
644 717 4.270008 GGGAGCTTAATTAAGAGTGGCAA 58.730 43.478 26.00 0.00 35.33 4.52
646 719 5.185056 GGGAGCTTAATTAAGAGTGGCAAAA 59.815 40.000 26.00 0.00 35.33 2.44
647 720 6.093404 GGAGCTTAATTAAGAGTGGCAAAAC 58.907 40.000 26.00 6.70 35.33 2.43
649 722 5.472137 AGCTTAATTAAGAGTGGCAAAACGA 59.528 36.000 26.00 0.00 35.33 3.85
650 723 6.151144 AGCTTAATTAAGAGTGGCAAAACGAT 59.849 34.615 26.00 0.00 35.33 3.73
652 725 7.626452 GCTTAATTAAGAGTGGCAAAACGATCT 60.626 37.037 26.00 0.00 35.33 2.75
654 727 7.681939 AATTAAGAGTGGCAAAACGATCTTA 57.318 32.000 0.00 0.00 0.00 2.10
655 728 6.476243 TTAAGAGTGGCAAAACGATCTTAC 57.524 37.500 0.00 0.00 31.04 2.34
657 730 4.246458 AGAGTGGCAAAACGATCTTACTC 58.754 43.478 0.00 0.00 34.92 2.59
658 731 3.335579 AGTGGCAAAACGATCTTACTCC 58.664 45.455 0.00 0.00 0.00 3.85
659 732 3.008049 AGTGGCAAAACGATCTTACTCCT 59.992 43.478 0.00 0.00 0.00 3.69
660 733 4.222145 AGTGGCAAAACGATCTTACTCCTA 59.778 41.667 0.00 0.00 0.00 2.94
661 734 5.104900 AGTGGCAAAACGATCTTACTCCTAT 60.105 40.000 0.00 0.00 0.00 2.57
663 736 6.093633 GTGGCAAAACGATCTTACTCCTATTT 59.906 38.462 0.00 0.00 0.00 1.40
664 737 7.279313 GTGGCAAAACGATCTTACTCCTATTTA 59.721 37.037 0.00 0.00 0.00 1.40
665 738 7.990886 TGGCAAAACGATCTTACTCCTATTTAT 59.009 33.333 0.00 0.00 0.00 1.40
666 739 9.485206 GGCAAAACGATCTTACTCCTATTTATA 57.515 33.333 0.00 0.00 0.00 0.98
673 746 8.944029 CGATCTTACTCCTATTTATAAGACGGA 58.056 37.037 0.00 0.00 36.69 4.69
675 748 8.632906 TCTTACTCCTATTTATAAGACGGAGG 57.367 38.462 20.71 10.36 41.72 4.30
676 749 8.223330 TCTTACTCCTATTTATAAGACGGAGGT 58.777 37.037 20.71 13.24 41.72 3.85
677 750 9.512588 CTTACTCCTATTTATAAGACGGAGGTA 57.487 37.037 20.71 12.63 41.72 3.08
678 751 7.999450 ACTCCTATTTATAAGACGGAGGTAG 57.001 40.000 20.71 10.98 41.72 3.18
679 752 7.525165 ACTCCTATTTATAAGACGGAGGTAGT 58.475 38.462 20.71 11.36 41.72 2.73
680 753 8.664079 ACTCCTATTTATAAGACGGAGGTAGTA 58.336 37.037 20.71 0.00 41.72 1.82
681 754 9.165035 CTCCTATTTATAAGACGGAGGTAGTAG 57.835 40.741 13.88 0.00 35.54 2.57
682 755 7.609532 TCCTATTTATAAGACGGAGGTAGTAGC 59.390 40.741 0.00 0.00 0.00 3.58
683 756 7.611079 CCTATTTATAAGACGGAGGTAGTAGCT 59.389 40.741 0.36 0.36 0.00 3.32
685 758 7.976135 TTTATAAGACGGAGGTAGTAGCTAG 57.024 40.000 0.89 2.51 0.00 3.42
686 759 2.934886 AGACGGAGGTAGTAGCTAGG 57.065 55.000 0.89 0.00 0.00 3.02
688 761 2.981081 AGACGGAGGTAGTAGCTAGGAT 59.019 50.000 0.89 0.00 0.00 3.24
704 777 6.448207 GCTAGGATGAGCTCTTTTGAATTT 57.552 37.500 16.19 0.00 39.50 1.82
705 778 6.861144 GCTAGGATGAGCTCTTTTGAATTTT 58.139 36.000 16.19 0.00 39.50 1.82
706 779 7.318893 GCTAGGATGAGCTCTTTTGAATTTTT 58.681 34.615 16.19 0.00 39.50 1.94
721 794 3.957383 TTTTTGACGCTTTGGCTCC 57.043 47.368 0.00 0.00 36.09 4.70
722 795 1.398692 TTTTTGACGCTTTGGCTCCT 58.601 45.000 0.00 0.00 36.09 3.69
735 886 6.042777 GCTTTGGCTCCTTATGGAATTTTAC 58.957 40.000 0.00 0.00 42.66 2.01
802 955 1.922545 GTTTGGAGCGACGTACATACC 59.077 52.381 0.00 0.00 0.00 2.73
804 957 0.736636 TGGAGCGACGTACATACCTG 59.263 55.000 0.00 0.00 0.00 4.00
805 958 1.019673 GGAGCGACGTACATACCTGA 58.980 55.000 0.00 0.00 0.00 3.86
806 959 1.002684 GGAGCGACGTACATACCTGAG 60.003 57.143 0.00 0.00 0.00 3.35
828 984 4.448537 CTGAGAGTTCAGTTACTGGGAG 57.551 50.000 12.79 0.00 44.74 4.30
829 985 4.082845 CTGAGAGTTCAGTTACTGGGAGA 58.917 47.826 12.79 0.00 44.74 3.71
830 986 4.480115 TGAGAGTTCAGTTACTGGGAGAA 58.520 43.478 12.79 0.00 31.51 2.87
831 987 4.281182 TGAGAGTTCAGTTACTGGGAGAAC 59.719 45.833 12.79 9.23 38.99 3.01
832 988 3.579151 AGAGTTCAGTTACTGGGAGAACC 59.421 47.826 12.79 4.36 39.39 3.62
868 1024 4.134379 AGGATGAGCAGTGAACATAGTG 57.866 45.455 0.00 0.00 0.00 2.74
994 1158 1.592400 CTCTCTTCCCGCCACGTACA 61.592 60.000 0.00 0.00 0.00 2.90
1025 1189 1.827681 CAACGTCTCTCTCTCCCTCA 58.172 55.000 0.00 0.00 0.00 3.86
1034 1202 2.680352 TCTCCCTCACTCCACCGC 60.680 66.667 0.00 0.00 0.00 5.68
1051 1219 2.878429 CGACCTGACTGACCCTCG 59.122 66.667 0.00 0.00 0.00 4.63
1082 1252 4.767255 GGAGCTCTGGTGCACCGG 62.767 72.222 35.06 35.06 43.86 5.28
1118 1288 4.680237 CAGGCAGGCCGTCGTCAA 62.680 66.667 4.37 0.00 41.95 3.18
1119 1289 3.936203 AGGCAGGCCGTCGTCAAA 61.936 61.111 4.37 0.00 41.95 2.69
1199 1369 1.066422 GCGATCGAGCCATCACTCA 59.934 57.895 21.57 0.00 36.42 3.41
1203 1373 1.406898 GATCGAGCCATCACTCAGTCA 59.593 52.381 0.00 0.00 36.42 3.41
1205 1375 0.179116 CGAGCCATCACTCAGTCAGG 60.179 60.000 0.00 0.00 36.42 3.86
1206 1376 0.177604 GAGCCATCACTCAGTCAGGG 59.822 60.000 0.00 0.00 36.65 4.45
1396 1574 1.079490 TGGAACCCATCAGTCCTCTCT 59.921 52.381 0.00 0.00 0.00 3.10
1659 1848 2.903855 GCTCATGGACCATGCCCG 60.904 66.667 27.02 18.33 41.18 6.13
1806 2010 4.473520 CCGCCCGCTGGATCAAGT 62.474 66.667 0.00 0.00 0.00 3.16
1808 2012 3.512516 GCCCGCTGGATCAAGTGC 61.513 66.667 5.02 0.00 0.00 4.40
1815 2019 2.190578 GGATCAAGTGCCCCCTCG 59.809 66.667 0.00 0.00 0.00 4.63
1896 2100 2.667536 CGAGCACTGCCAGCAAGT 60.668 61.111 0.00 0.00 0.00 3.16
1975 2179 3.376078 CCCACCGCAAGCAGCAAT 61.376 61.111 0.00 0.00 46.13 3.56
2000 2204 3.702048 TTTCCCCTGCCTCGGTCG 61.702 66.667 0.00 0.00 0.00 4.79
2083 2290 0.398522 TGTACCTCCTCGGCATGGAT 60.399 55.000 0.00 0.00 35.61 3.41
2098 2305 0.255604 TGGATGGCATCATGGACGTT 59.744 50.000 27.39 0.00 32.98 3.99
2104 2311 2.009108 CATCATGGACGTTGGCTCG 58.991 57.895 0.00 1.70 0.00 5.03
2176 2383 1.309006 CCACTACTACCCGGACCCT 59.691 63.158 0.73 0.00 0.00 4.34
2179 2386 1.380785 CTACTACCCGGACCCTGCA 60.381 63.158 0.73 0.00 0.00 4.41
2188 2395 2.586792 GACCCTGCAGGCTTCGAT 59.413 61.111 28.39 7.39 40.58 3.59
2202 2409 0.615331 TTCGATCAAGAAGCCTGGCT 59.385 50.000 17.22 17.22 42.56 4.75
2205 2412 1.134699 CGATCAAGAAGCCTGGCTGTA 60.135 52.381 24.16 6.56 39.62 2.74
2219 2426 1.305219 GCTGTAACGCCATCCTTGCA 61.305 55.000 0.00 0.00 0.00 4.08
2220 2427 0.729116 CTGTAACGCCATCCTTGCAG 59.271 55.000 0.00 0.00 0.00 4.41
2238 2446 1.012086 AGCAGCAATGCACATAGACG 58.988 50.000 8.35 0.00 37.25 4.18
2299 2512 1.373044 CCTCCCCTCCCCTAGCTAGT 61.373 65.000 19.31 0.00 0.00 2.57
2341 2554 0.179065 GTTACCGCCATACCCACCTC 60.179 60.000 0.00 0.00 0.00 3.85
2358 2571 3.633986 CACCTCAGCTTTTCTTGGAACTT 59.366 43.478 0.00 0.00 0.00 2.66
2376 2601 4.627611 ACTTGGAAGAAATGCATGATCG 57.372 40.909 0.00 0.00 0.00 3.69
2384 2609 0.468585 AATGCATGATCGGGCCATGT 60.469 50.000 4.39 0.00 42.39 3.21
2386 2611 2.263741 GCATGATCGGGCCATGTCC 61.264 63.158 4.39 0.00 42.39 4.02
2442 2667 8.348285 TCGATAAAGAAAGTGGAAATGGAAAT 57.652 30.769 0.00 0.00 0.00 2.17
2455 2680 1.079612 GGAAATCCCGACGACCGTT 60.080 57.895 0.00 0.00 36.31 4.44
2478 2709 1.153369 GATGCGAGCAAGGCTGGTA 60.153 57.895 0.57 0.00 39.88 3.25
2491 2722 1.135083 GGCTGGTATGTATCGATCCGG 60.135 57.143 0.00 2.50 0.00 5.14
2500 2735 1.808945 GTATCGATCCGGACGTGGTAT 59.191 52.381 20.62 12.30 0.00 2.73
2526 2761 0.943359 CTCTTGGCGAGATCGATGGC 60.943 60.000 0.54 3.13 42.62 4.40
2529 2764 1.960040 TTGGCGAGATCGATGGCTGT 61.960 55.000 0.54 0.00 43.02 4.40
2531 2766 1.227089 GCGAGATCGATGGCTGTGT 60.227 57.895 0.54 0.00 43.02 3.72
2612 2847 0.238553 GGTGCAGGAGACTTTTTCGC 59.761 55.000 0.00 0.00 40.21 4.70
2629 2865 1.068921 GCTCCGAGAAGGGCTGATC 59.931 63.158 0.00 0.00 41.52 2.92
2652 2888 2.788176 CGATTGTCATGACGCGCGT 61.788 57.895 38.52 38.52 0.00 6.01
2653 2889 1.468340 CGATTGTCATGACGCGCGTA 61.468 55.000 37.91 23.62 0.00 4.42
2756 3000 1.334556 GTGGTTCACCCCGTTTGTTAC 59.665 52.381 0.00 0.00 34.29 2.50
2797 3045 9.846248 AGTTGACTAATTTTACAAGATCATTGC 57.154 29.630 0.00 0.00 0.00 3.56
2798 3046 9.624697 GTTGACTAATTTTACAAGATCATTGCA 57.375 29.630 0.00 0.00 0.00 4.08
2827 3075 2.108514 CCGGCTGTGTGCATACAGG 61.109 63.158 35.32 23.40 46.32 4.00
2851 3099 1.000607 GAACAGTAGCGAGACCACACA 60.001 52.381 0.00 0.00 0.00 3.72
2852 3100 0.314302 ACAGTAGCGAGACCACACAC 59.686 55.000 0.00 0.00 0.00 3.82
2853 3101 0.313987 CAGTAGCGAGACCACACACA 59.686 55.000 0.00 0.00 0.00 3.72
2854 3102 0.314302 AGTAGCGAGACCACACACAC 59.686 55.000 0.00 0.00 0.00 3.82
2856 3104 0.031585 TAGCGAGACCACACACACAC 59.968 55.000 0.00 0.00 0.00 3.82
2924 3172 1.304464 CAGAGGGCAAAGGTTCCCC 60.304 63.158 0.00 0.00 43.67 4.81
3003 3251 5.930135 CCTACACAAGCTAGGGATATTGTT 58.070 41.667 0.00 0.00 33.76 2.83
3177 3425 3.121030 CGAGCGGTCTTGGCTTGG 61.121 66.667 13.48 0.00 41.72 3.61
3228 3476 0.733150 TCGCTCTCGACGATGAATGT 59.267 50.000 0.00 0.00 40.21 2.71
3244 3492 0.745845 ATGTCAGCTCGGTCCATTGC 60.746 55.000 0.00 0.00 0.00 3.56
3279 3527 2.036098 CTCCATGCACCCAGCCAA 59.964 61.111 0.00 0.00 44.83 4.52
3341 3589 0.106335 CGCAGAGAAGATGATGCCCT 59.894 55.000 0.00 0.00 35.22 5.19
3403 3651 1.203428 TCCTCATGGGAGAAGGAACCA 60.203 52.381 0.00 0.00 44.26 3.67
3432 3680 1.301716 GCTTCGTCCAGTTGGCAGA 60.302 57.895 0.00 0.00 34.44 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.625818 GATAGGTCATAGGCCTGGTGG 59.374 57.143 17.99 1.55 37.54 4.61
4 5 1.223077 TGGATAGGTCATAGGCCTGGT 59.777 52.381 17.99 0.00 37.54 4.00
5 6 1.625818 GTGGATAGGTCATAGGCCTGG 59.374 57.143 17.99 7.85 37.54 4.45
6 7 1.273606 CGTGGATAGGTCATAGGCCTG 59.726 57.143 17.99 0.00 37.54 4.85
7 8 1.147191 TCGTGGATAGGTCATAGGCCT 59.853 52.381 11.78 11.78 40.00 5.19
8 9 1.629043 TCGTGGATAGGTCATAGGCC 58.371 55.000 0.00 0.00 0.00 5.19
9 10 3.746045 TTTCGTGGATAGGTCATAGGC 57.254 47.619 0.00 0.00 0.00 3.93
10 11 5.730296 AGATTTCGTGGATAGGTCATAGG 57.270 43.478 0.00 0.00 0.00 2.57
26 27 7.653647 AGTATCATGTCTACCTCGAAGATTTC 58.346 38.462 0.00 0.00 33.89 2.17
27 28 7.589958 AGTATCATGTCTACCTCGAAGATTT 57.410 36.000 0.00 0.00 33.89 2.17
28 29 8.871629 ATAGTATCATGTCTACCTCGAAGATT 57.128 34.615 0.00 0.00 33.89 2.40
29 30 8.871629 AATAGTATCATGTCTACCTCGAAGAT 57.128 34.615 0.00 0.00 33.89 2.40
30 31 8.693120 AAATAGTATCATGTCTACCTCGAAGA 57.307 34.615 0.00 0.00 0.00 2.87
31 32 9.751542 AAAAATAGTATCATGTCTACCTCGAAG 57.248 33.333 0.00 0.00 0.00 3.79
32 33 9.745880 GAAAAATAGTATCATGTCTACCTCGAA 57.254 33.333 0.00 0.00 0.00 3.71
33 34 9.132923 AGAAAAATAGTATCATGTCTACCTCGA 57.867 33.333 0.00 0.00 0.00 4.04
34 35 9.400638 GAGAAAAATAGTATCATGTCTACCTCG 57.599 37.037 0.00 0.00 0.00 4.63
35 36 9.400638 CGAGAAAAATAGTATCATGTCTACCTC 57.599 37.037 0.00 0.00 0.00 3.85
36 37 8.361139 CCGAGAAAAATAGTATCATGTCTACCT 58.639 37.037 0.00 0.00 0.00 3.08
37 38 7.599245 CCCGAGAAAAATAGTATCATGTCTACC 59.401 40.741 0.00 0.00 0.00 3.18
38 39 7.116519 GCCCGAGAAAAATAGTATCATGTCTAC 59.883 40.741 0.00 0.00 0.00 2.59
39 40 7.152645 GCCCGAGAAAAATAGTATCATGTCTA 58.847 38.462 0.00 0.00 0.00 2.59
40 41 5.992217 GCCCGAGAAAAATAGTATCATGTCT 59.008 40.000 0.00 0.00 0.00 3.41
41 42 5.179555 GGCCCGAGAAAAATAGTATCATGTC 59.820 44.000 0.00 0.00 0.00 3.06
42 43 5.063880 GGCCCGAGAAAAATAGTATCATGT 58.936 41.667 0.00 0.00 0.00 3.21
43 44 5.308825 AGGCCCGAGAAAAATAGTATCATG 58.691 41.667 0.00 0.00 0.00 3.07
44 45 5.568620 AGGCCCGAGAAAAATAGTATCAT 57.431 39.130 0.00 0.00 0.00 2.45
45 46 5.510861 GCTAGGCCCGAGAAAAATAGTATCA 60.511 44.000 0.00 0.00 0.00 2.15
46 47 4.930405 GCTAGGCCCGAGAAAAATAGTATC 59.070 45.833 0.00 0.00 0.00 2.24
47 48 4.347000 TGCTAGGCCCGAGAAAAATAGTAT 59.653 41.667 0.00 0.00 0.00 2.12
48 49 3.707611 TGCTAGGCCCGAGAAAAATAGTA 59.292 43.478 0.00 0.00 0.00 1.82
49 50 2.504175 TGCTAGGCCCGAGAAAAATAGT 59.496 45.455 0.00 0.00 0.00 2.12
50 51 3.194005 TGCTAGGCCCGAGAAAAATAG 57.806 47.619 0.00 0.00 0.00 1.73
51 52 3.857157 ATGCTAGGCCCGAGAAAAATA 57.143 42.857 0.00 0.00 0.00 1.40
52 53 2.736670 ATGCTAGGCCCGAGAAAAAT 57.263 45.000 0.00 0.00 0.00 1.82
53 54 2.504175 ACTATGCTAGGCCCGAGAAAAA 59.496 45.455 0.00 0.00 0.00 1.94
54 55 2.116238 ACTATGCTAGGCCCGAGAAAA 58.884 47.619 0.00 0.00 0.00 2.29
55 56 1.789523 ACTATGCTAGGCCCGAGAAA 58.210 50.000 0.00 0.00 0.00 2.52
56 57 1.789523 AACTATGCTAGGCCCGAGAA 58.210 50.000 0.00 0.00 0.00 2.87
57 58 2.670019 TAACTATGCTAGGCCCGAGA 57.330 50.000 0.00 0.00 0.00 4.04
58 59 3.963428 ATTAACTATGCTAGGCCCGAG 57.037 47.619 0.00 0.00 0.00 4.63
59 60 4.347000 AGAAATTAACTATGCTAGGCCCGA 59.653 41.667 0.00 0.00 0.00 5.14
60 61 4.642429 AGAAATTAACTATGCTAGGCCCG 58.358 43.478 0.00 0.00 0.00 6.13
61 62 5.828328 ACAAGAAATTAACTATGCTAGGCCC 59.172 40.000 0.00 0.00 0.00 5.80
62 63 6.944234 ACAAGAAATTAACTATGCTAGGCC 57.056 37.500 0.00 0.00 0.00 5.19
63 64 7.985476 TCAACAAGAAATTAACTATGCTAGGC 58.015 34.615 0.00 0.00 0.00 3.93
64 65 9.774742 GTTCAACAAGAAATTAACTATGCTAGG 57.225 33.333 0.00 0.00 38.13 3.02
71 72 9.199982 CCGACTAGTTCAACAAGAAATTAACTA 57.800 33.333 0.00 0.00 38.13 2.24
72 73 7.929785 TCCGACTAGTTCAACAAGAAATTAACT 59.070 33.333 0.00 0.00 38.13 2.24
73 74 8.080083 TCCGACTAGTTCAACAAGAAATTAAC 57.920 34.615 0.00 0.00 38.13 2.01
74 75 8.717821 CATCCGACTAGTTCAACAAGAAATTAA 58.282 33.333 0.00 0.00 38.13 1.40
75 76 7.148474 GCATCCGACTAGTTCAACAAGAAATTA 60.148 37.037 0.00 0.00 38.13 1.40
76 77 6.348540 GCATCCGACTAGTTCAACAAGAAATT 60.349 38.462 0.00 0.00 38.13 1.82
77 78 5.122396 GCATCCGACTAGTTCAACAAGAAAT 59.878 40.000 0.00 0.00 38.13 2.17
78 79 4.451096 GCATCCGACTAGTTCAACAAGAAA 59.549 41.667 0.00 0.00 38.13 2.52
79 80 3.994392 GCATCCGACTAGTTCAACAAGAA 59.006 43.478 0.00 0.00 0.00 2.52
80 81 3.006430 TGCATCCGACTAGTTCAACAAGA 59.994 43.478 0.00 0.00 0.00 3.02
81 82 3.123621 GTGCATCCGACTAGTTCAACAAG 59.876 47.826 0.00 0.00 0.00 3.16
82 83 3.064207 GTGCATCCGACTAGTTCAACAA 58.936 45.455 0.00 0.00 0.00 2.83
83 84 2.036604 TGTGCATCCGACTAGTTCAACA 59.963 45.455 0.00 0.00 0.00 3.33
84 85 2.683968 TGTGCATCCGACTAGTTCAAC 58.316 47.619 0.00 0.00 0.00 3.18
85 86 3.394674 TTGTGCATCCGACTAGTTCAA 57.605 42.857 0.00 0.00 0.00 2.69
86 87 3.394674 TTTGTGCATCCGACTAGTTCA 57.605 42.857 0.00 0.00 0.00 3.18
87 88 4.946784 AATTTGTGCATCCGACTAGTTC 57.053 40.909 0.00 0.00 0.00 3.01
88 89 4.082787 CCAAATTTGTGCATCCGACTAGTT 60.083 41.667 16.73 0.00 0.00 2.24
89 90 3.440173 CCAAATTTGTGCATCCGACTAGT 59.560 43.478 16.73 0.00 0.00 2.57
90 91 3.440173 ACCAAATTTGTGCATCCGACTAG 59.560 43.478 16.73 0.00 0.00 2.57
91 92 3.417101 ACCAAATTTGTGCATCCGACTA 58.583 40.909 16.73 0.00 0.00 2.59
92 93 2.238521 ACCAAATTTGTGCATCCGACT 58.761 42.857 16.73 0.00 0.00 4.18
93 94 2.723124 ACCAAATTTGTGCATCCGAC 57.277 45.000 16.73 0.00 0.00 4.79
94 95 6.707440 ATTATACCAAATTTGTGCATCCGA 57.293 33.333 16.73 0.00 0.00 4.55
95 96 7.620215 CAAATTATACCAAATTTGTGCATCCG 58.380 34.615 16.73 2.48 45.46 4.18
114 115 9.316730 GGAGCTTCATGCATATTTTTCAAATTA 57.683 29.630 0.00 0.00 45.94 1.40
115 116 8.044908 AGGAGCTTCATGCATATTTTTCAAATT 58.955 29.630 0.00 0.00 45.94 1.82
116 117 7.562135 AGGAGCTTCATGCATATTTTTCAAAT 58.438 30.769 0.00 0.00 45.94 2.32
117 118 6.938507 AGGAGCTTCATGCATATTTTTCAAA 58.061 32.000 0.00 0.00 45.94 2.69
118 119 6.153170 TGAGGAGCTTCATGCATATTTTTCAA 59.847 34.615 0.00 0.00 45.94 2.69
119 120 5.653330 TGAGGAGCTTCATGCATATTTTTCA 59.347 36.000 0.00 0.00 45.94 2.69
120 121 6.140303 TGAGGAGCTTCATGCATATTTTTC 57.860 37.500 0.00 0.00 45.94 2.29
121 122 6.534475 TTGAGGAGCTTCATGCATATTTTT 57.466 33.333 0.00 0.00 45.94 1.94
122 123 6.534475 TTTGAGGAGCTTCATGCATATTTT 57.466 33.333 0.00 0.00 45.94 1.82
123 124 6.726490 ATTTGAGGAGCTTCATGCATATTT 57.274 33.333 0.00 0.00 45.94 1.40
124 125 6.513180 CAATTTGAGGAGCTTCATGCATATT 58.487 36.000 0.00 0.00 45.94 1.28
125 126 5.509163 GCAATTTGAGGAGCTTCATGCATAT 60.509 40.000 0.00 0.00 45.94 1.78
126 127 4.202080 GCAATTTGAGGAGCTTCATGCATA 60.202 41.667 0.00 0.00 45.94 3.14
157 158 6.056236 TGTATAGTTTACACCAGTTGCACAA 58.944 36.000 0.00 0.00 0.00 3.33
202 203 3.906008 CGGAAAACAGACAGTAAAATGCG 59.094 43.478 0.00 0.00 0.00 4.73
203 204 4.855531 ACGGAAAACAGACAGTAAAATGC 58.144 39.130 0.00 0.00 0.00 3.56
204 205 6.413818 GTCAACGGAAAACAGACAGTAAAATG 59.586 38.462 0.00 0.00 0.00 2.32
215 259 6.737254 ATTGTATAGGTCAACGGAAAACAG 57.263 37.500 0.00 0.00 0.00 3.16
222 266 9.051679 TGAAATATGAATTGTATAGGTCAACGG 57.948 33.333 0.00 0.00 0.00 4.44
235 279 6.762661 GTGGGGGTCAATTGAAATATGAATTG 59.237 38.462 10.35 0.00 39.79 2.32
240 289 3.951037 TCGTGGGGGTCAATTGAAATATG 59.049 43.478 10.35 1.59 0.00 1.78
243 292 2.167662 GTCGTGGGGGTCAATTGAAAT 58.832 47.619 10.35 0.00 0.00 2.17
248 297 1.189524 TCGAGTCGTGGGGGTCAATT 61.190 55.000 13.12 0.00 0.00 2.32
250 299 1.601419 GATCGAGTCGTGGGGGTCAA 61.601 60.000 13.12 0.00 0.00 3.18
260 309 0.100682 ACGTCCCATTGATCGAGTCG 59.899 55.000 6.09 6.09 0.00 4.18
301 357 2.037251 TGGAGTGGAGTACAGCTTTGTC 59.963 50.000 0.00 0.00 0.00 3.18
339 395 0.244721 GCAACAGGAGGTGGATTTGC 59.755 55.000 0.00 0.00 30.94 3.68
355 411 2.242196 CCCCTCTCCTTTTAGATGGCAA 59.758 50.000 0.00 0.00 31.78 4.52
381 439 2.472934 GCCCTTTACGTGCGAACG 59.527 61.111 16.06 16.06 39.31 3.95
459 518 2.095718 GGACTTTTCGAGGTTGACATGC 60.096 50.000 0.00 0.00 0.00 4.06
494 566 7.908601 CGTGCTAATAAGTAATCACTTTTTCCC 59.091 37.037 0.00 0.00 42.51 3.97
496 568 9.474249 GACGTGCTAATAAGTAATCACTTTTTC 57.526 33.333 0.00 0.00 42.51 2.29
497 569 8.166706 CGACGTGCTAATAAGTAATCACTTTTT 58.833 33.333 0.00 0.00 42.51 1.94
498 570 7.201496 CCGACGTGCTAATAAGTAATCACTTTT 60.201 37.037 0.00 0.00 42.51 2.27
499 571 6.255020 CCGACGTGCTAATAAGTAATCACTTT 59.745 38.462 0.00 0.00 42.51 2.66
500 572 5.747197 CCGACGTGCTAATAAGTAATCACTT 59.253 40.000 0.00 0.00 46.77 3.16
502 574 5.276270 TCCGACGTGCTAATAAGTAATCAC 58.724 41.667 0.00 0.00 0.00 3.06
503 575 5.066893 ACTCCGACGTGCTAATAAGTAATCA 59.933 40.000 0.00 0.00 0.00 2.57
504 576 5.517904 ACTCCGACGTGCTAATAAGTAATC 58.482 41.667 0.00 0.00 0.00 1.75
505 577 5.511234 ACTCCGACGTGCTAATAAGTAAT 57.489 39.130 0.00 0.00 0.00 1.89
506 578 4.970662 ACTCCGACGTGCTAATAAGTAA 57.029 40.909 0.00 0.00 0.00 2.24
507 579 4.970662 AACTCCGACGTGCTAATAAGTA 57.029 40.909 0.00 0.00 0.00 2.24
508 580 3.863142 AACTCCGACGTGCTAATAAGT 57.137 42.857 0.00 0.00 0.00 2.24
509 581 3.306166 CCAAACTCCGACGTGCTAATAAG 59.694 47.826 0.00 0.00 0.00 1.73
510 582 3.056678 TCCAAACTCCGACGTGCTAATAA 60.057 43.478 0.00 0.00 0.00 1.40
511 583 2.492881 TCCAAACTCCGACGTGCTAATA 59.507 45.455 0.00 0.00 0.00 0.98
512 584 1.274167 TCCAAACTCCGACGTGCTAAT 59.726 47.619 0.00 0.00 0.00 1.73
513 585 0.675083 TCCAAACTCCGACGTGCTAA 59.325 50.000 0.00 0.00 0.00 3.09
514 586 0.892755 ATCCAAACTCCGACGTGCTA 59.107 50.000 0.00 0.00 0.00 3.49
515 587 0.034896 AATCCAAACTCCGACGTGCT 59.965 50.000 0.00 0.00 0.00 4.40
516 588 0.872388 AAATCCAAACTCCGACGTGC 59.128 50.000 0.00 0.00 0.00 5.34
517 589 3.991773 TCTTAAATCCAAACTCCGACGTG 59.008 43.478 0.00 0.00 0.00 4.49
518 590 4.261578 TCTTAAATCCAAACTCCGACGT 57.738 40.909 0.00 0.00 0.00 4.34
519 591 5.796350 AATCTTAAATCCAAACTCCGACG 57.204 39.130 0.00 0.00 0.00 5.12
520 592 6.801862 CACAAATCTTAAATCCAAACTCCGAC 59.198 38.462 0.00 0.00 0.00 4.79
521 593 6.712998 TCACAAATCTTAAATCCAAACTCCGA 59.287 34.615 0.00 0.00 0.00 4.55
522 594 6.908825 TCACAAATCTTAAATCCAAACTCCG 58.091 36.000 0.00 0.00 0.00 4.63
554 627 3.782523 TCTAGGGAAGAGGCAACATCATT 59.217 43.478 0.00 0.00 41.41 2.57
578 651 4.322274 CGAAGAGAATGTCAACGAGAACTC 59.678 45.833 0.00 0.00 0.00 3.01
579 652 4.230657 CGAAGAGAATGTCAACGAGAACT 58.769 43.478 0.00 0.00 0.00 3.01
580 653 3.365220 CCGAAGAGAATGTCAACGAGAAC 59.635 47.826 0.00 0.00 0.00 3.01
600 673 4.697756 TTGCAGGGAGAACCGCCG 62.698 66.667 0.00 0.00 46.96 6.46
615 688 6.317391 CACTCTTAATTAAGCTCCCCTCTTTG 59.683 42.308 18.68 2.19 33.40 2.77
646 719 8.728833 CCGTCTTATAAATAGGAGTAAGATCGT 58.271 37.037 0.00 0.00 36.09 3.73
647 720 8.944029 TCCGTCTTATAAATAGGAGTAAGATCG 58.056 37.037 0.00 0.00 36.09 3.69
649 722 9.245481 CCTCCGTCTTATAAATAGGAGTAAGAT 57.755 37.037 19.74 0.00 42.59 2.40
650 723 8.223330 ACCTCCGTCTTATAAATAGGAGTAAGA 58.777 37.037 19.74 0.00 42.59 2.10
652 725 9.512588 CTACCTCCGTCTTATAAATAGGAGTAA 57.487 37.037 19.74 11.49 42.59 2.24
654 727 7.525165 ACTACCTCCGTCTTATAAATAGGAGT 58.475 38.462 19.74 13.78 42.59 3.85
655 728 7.999450 ACTACCTCCGTCTTATAAATAGGAG 57.001 40.000 16.75 16.75 43.46 3.69
657 730 7.611079 AGCTACTACCTCCGTCTTATAAATAGG 59.389 40.741 0.00 0.00 0.00 2.57
658 731 8.564509 AGCTACTACCTCCGTCTTATAAATAG 57.435 38.462 0.00 0.00 0.00 1.73
659 732 9.664332 CTAGCTACTACCTCCGTCTTATAAATA 57.336 37.037 0.00 0.00 0.00 1.40
660 733 7.611079 CCTAGCTACTACCTCCGTCTTATAAAT 59.389 40.741 0.00 0.00 0.00 1.40
661 734 6.939163 CCTAGCTACTACCTCCGTCTTATAAA 59.061 42.308 0.00 0.00 0.00 1.40
663 736 5.782331 TCCTAGCTACTACCTCCGTCTTATA 59.218 44.000 0.00 0.00 0.00 0.98
664 737 4.596643 TCCTAGCTACTACCTCCGTCTTAT 59.403 45.833 0.00 0.00 0.00 1.73
665 738 3.969976 TCCTAGCTACTACCTCCGTCTTA 59.030 47.826 0.00 0.00 0.00 2.10
666 739 2.776536 TCCTAGCTACTACCTCCGTCTT 59.223 50.000 0.00 0.00 0.00 3.01
667 740 2.406559 TCCTAGCTACTACCTCCGTCT 58.593 52.381 0.00 0.00 0.00 4.18
681 754 6.448207 AAATTCAAAAGAGCTCATCCTAGC 57.552 37.500 17.77 0.00 43.11 3.42
703 776 1.398692 AGGAGCCAAAGCGTCAAAAA 58.601 45.000 0.00 0.00 46.67 1.94
704 777 1.398692 AAGGAGCCAAAGCGTCAAAA 58.601 45.000 0.00 0.00 46.67 2.44
705 778 2.264005 TAAGGAGCCAAAGCGTCAAA 57.736 45.000 0.00 0.00 46.67 2.69
706 779 2.083774 CATAAGGAGCCAAAGCGTCAA 58.916 47.619 0.00 0.00 46.67 3.18
707 780 1.678728 CCATAAGGAGCCAAAGCGTCA 60.679 52.381 0.00 0.00 46.67 4.35
709 782 0.618458 TCCATAAGGAGCCAAAGCGT 59.382 50.000 0.00 0.00 46.67 5.07
710 783 1.750193 TTCCATAAGGAGCCAAAGCG 58.250 50.000 0.00 0.00 46.74 4.68
713 786 5.946972 TCGTAAAATTCCATAAGGAGCCAAA 59.053 36.000 0.00 0.00 46.74 3.28
714 787 5.502079 TCGTAAAATTCCATAAGGAGCCAA 58.498 37.500 0.00 0.00 46.74 4.52
715 788 5.105567 TCGTAAAATTCCATAAGGAGCCA 57.894 39.130 0.00 0.00 46.74 4.75
716 789 4.515567 CCTCGTAAAATTCCATAAGGAGCC 59.484 45.833 0.00 0.00 46.74 4.70
718 791 7.272978 TCTTCCTCGTAAAATTCCATAAGGAG 58.727 38.462 0.00 0.00 46.74 3.69
719 792 7.125204 TCTCTTCCTCGTAAAATTCCATAAGGA 59.875 37.037 0.00 0.00 43.93 3.36
721 794 8.718102 TTCTCTTCCTCGTAAAATTCCATAAG 57.282 34.615 0.00 0.00 0.00 1.73
722 795 9.509956 TTTTCTCTTCCTCGTAAAATTCCATAA 57.490 29.630 0.00 0.00 0.00 1.90
735 886 4.092091 CCGAAGACATTTTTCTCTTCCTCG 59.908 45.833 0.00 0.00 36.25 4.63
825 981 1.893801 TCTGACTTTCTCCGGTTCTCC 59.106 52.381 0.00 0.00 0.00 3.71
826 982 3.662247 TTCTGACTTTCTCCGGTTCTC 57.338 47.619 0.00 0.00 0.00 2.87
827 983 3.244249 CCTTTCTGACTTTCTCCGGTTCT 60.244 47.826 0.00 0.00 0.00 3.01
828 984 3.067833 CCTTTCTGACTTTCTCCGGTTC 58.932 50.000 0.00 0.00 0.00 3.62
829 985 2.704065 TCCTTTCTGACTTTCTCCGGTT 59.296 45.455 0.00 0.00 0.00 4.44
830 986 2.326428 TCCTTTCTGACTTTCTCCGGT 58.674 47.619 0.00 0.00 0.00 5.28
831 987 3.055819 TCATCCTTTCTGACTTTCTCCGG 60.056 47.826 0.00 0.00 0.00 5.14
832 988 4.180057 CTCATCCTTTCTGACTTTCTCCG 58.820 47.826 0.00 0.00 0.00 4.63
868 1024 2.273449 CCACCATGCACCTCCTCC 59.727 66.667 0.00 0.00 0.00 4.30
1025 1189 3.681835 GTCAGGTCGCGGTGGAGT 61.682 66.667 6.13 0.00 0.00 3.85
1034 1202 1.924320 GACGAGGGTCAGTCAGGTCG 61.924 65.000 0.00 0.00 42.91 4.79
1051 1219 4.551388 CAGAGCTCCATTTATAGACGGAC 58.449 47.826 10.93 0.00 0.00 4.79
1082 1252 3.576648 CTGTCTCCGTTCCAAGTAAGAC 58.423 50.000 0.00 0.00 34.98 3.01
1118 1288 0.742990 CGACTGTGTGTGGGTGTGTT 60.743 55.000 0.00 0.00 0.00 3.32
1119 1289 1.153449 CGACTGTGTGTGGGTGTGT 60.153 57.895 0.00 0.00 0.00 3.72
1156 1326 1.272480 CCCTTCTCACCCGGGAATTTT 60.272 52.381 32.02 0.00 40.55 1.82
1199 1369 2.693864 CCCCATCTGCCCCTGACT 60.694 66.667 0.00 0.00 0.00 3.41
1205 1375 4.201122 CTGCCTCCCCATCTGCCC 62.201 72.222 0.00 0.00 0.00 5.36
1206 1376 4.891037 GCTGCCTCCCCATCTGCC 62.891 72.222 0.00 0.00 0.00 4.85
1350 1521 1.958715 CATGCACACGTTCGGGTCA 60.959 57.895 0.00 0.11 0.00 4.02
1356 1530 4.463597 CATGGCATGCACACGTTC 57.536 55.556 21.36 0.00 0.00 3.95
1396 1574 2.357034 GAACGTCAAGCCGGAGCA 60.357 61.111 5.05 0.00 43.56 4.26
1446 1628 3.774528 CGCACCTCAGCAGCCCTA 61.775 66.667 0.00 0.00 0.00 3.53
1640 1829 3.589881 GGCATGGTCCATGAGCGC 61.590 66.667 32.16 18.02 43.81 5.92
1641 1830 2.903855 GGGCATGGTCCATGAGCG 60.904 66.667 32.16 9.16 43.81 5.03
1642 1831 2.903855 CGGGCATGGTCCATGAGC 60.904 66.667 32.16 19.06 43.81 4.26
1801 2005 3.319198 GGACGAGGGGGCACTTGA 61.319 66.667 0.00 0.00 0.00 3.02
1884 2088 1.495579 ATCCTCCACTTGCTGGCAGT 61.496 55.000 17.16 0.00 40.39 4.40
1887 2091 0.747283 CTCATCCTCCACTTGCTGGC 60.747 60.000 0.00 0.00 40.39 4.85
1896 2100 1.186200 CTTCACGTCCTCATCCTCCA 58.814 55.000 0.00 0.00 0.00 3.86
1903 2107 2.915659 ACCGCCTTCACGTCCTCA 60.916 61.111 0.00 0.00 0.00 3.86
1975 2179 1.228552 GGCAGGGGAAACAGAGCAA 60.229 57.895 0.00 0.00 0.00 3.91
2000 2204 4.500116 GGAGCAGGACGGCGAGAC 62.500 72.222 16.62 2.55 39.27 3.36
2083 2290 2.045708 GCCAACGTCCATGATGCCA 61.046 57.895 0.00 0.00 0.00 4.92
2176 2383 1.730501 CTTCTTGATCGAAGCCTGCA 58.269 50.000 0.00 0.00 34.59 4.41
2188 2395 1.608025 CGTTACAGCCAGGCTTCTTGA 60.608 52.381 12.86 0.00 36.40 3.02
2202 2409 1.305219 GCTGCAAGGATGGCGTTACA 61.305 55.000 0.00 0.00 38.51 2.41
2205 2412 2.282391 TGCTGCAAGGATGGCGTT 60.282 55.556 0.00 0.00 38.51 4.84
2238 2446 3.923461 CGAAAGAAGCGGATCTATGATCC 59.077 47.826 14.71 14.71 34.90 3.36
2299 2512 4.811969 TTTCGACATGGAAGCTAACCTA 57.188 40.909 10.52 0.00 0.00 3.08
2302 2515 4.946784 ACATTTCGACATGGAAGCTAAC 57.053 40.909 15.58 0.00 0.00 2.34
2341 2554 4.339247 TCTTCCAAGTTCCAAGAAAAGCTG 59.661 41.667 0.00 0.00 0.00 4.24
2358 2571 2.300433 CCCGATCATGCATTTCTTCCA 58.700 47.619 0.00 0.00 0.00 3.53
2376 2601 2.205152 GCATGGATGGACATGGCCC 61.205 63.158 17.19 7.34 46.40 5.80
2384 2609 1.561769 AACACCCGAGCATGGATGGA 61.562 55.000 0.00 0.00 0.00 3.41
2386 2611 0.452987 CAAACACCCGAGCATGGATG 59.547 55.000 0.00 0.00 0.00 3.51
2442 2667 2.595463 ACAGAACGGTCGTCGGGA 60.595 61.111 0.00 0.00 44.45 5.14
2455 2680 1.742880 GCCTTGCTCGCATCACAGA 60.743 57.895 0.00 0.00 0.00 3.41
2478 2709 0.596577 CCACGTCCGGATCGATACAT 59.403 55.000 26.02 6.96 0.00 2.29
2526 2761 2.772189 GCAGTTAGCGCGACACAG 59.228 61.111 12.10 0.00 0.00 3.66
2612 2847 1.361993 CGATCAGCCCTTCTCGGAG 59.638 63.158 0.00 0.00 33.16 4.63
2629 2865 2.321060 GTCATGACAATCGGCGCG 59.679 61.111 21.07 0.00 0.00 6.86
2789 3037 2.288030 GGTGGCTAGCAATGCAATGATC 60.288 50.000 18.24 0.00 0.00 2.92
2793 3041 1.386525 CCGGTGGCTAGCAATGCAAT 61.387 55.000 18.24 0.00 0.00 3.56
2794 3042 2.045708 CCGGTGGCTAGCAATGCAA 61.046 57.895 18.24 0.00 0.00 4.08
2795 3043 2.438254 CCGGTGGCTAGCAATGCA 60.438 61.111 18.24 1.68 0.00 3.96
2796 3044 3.892581 GCCGGTGGCTAGCAATGC 61.893 66.667 18.24 6.27 46.69 3.56
2827 3075 1.071567 GGTCTCGCTACTGTTCGTGC 61.072 60.000 0.00 0.00 0.00 5.34
2851 3099 5.104374 CACTTCAGAAAGCATTTTGTGTGT 58.896 37.500 10.39 3.75 39.27 3.72
2852 3100 4.026310 GCACTTCAGAAAGCATTTTGTGTG 60.026 41.667 12.64 12.64 39.27 3.82
2853 3101 4.114794 GCACTTCAGAAAGCATTTTGTGT 58.885 39.130 3.03 0.00 39.27 3.72
2854 3102 4.114073 TGCACTTCAGAAAGCATTTTGTG 58.886 39.130 5.96 0.00 39.27 3.33
2856 3104 3.183775 GCTGCACTTCAGAAAGCATTTTG 59.816 43.478 9.68 1.68 45.72 2.44
2924 3172 4.932799 CCCTTTTACCCCGCAAATAAAAAG 59.067 41.667 0.00 0.00 34.99 2.27
2930 3178 2.543037 ATCCCTTTTACCCCGCAAAT 57.457 45.000 0.00 0.00 0.00 2.32
3177 3425 1.035932 AGTGCAGCTGATCAATGCCC 61.036 55.000 20.43 15.43 39.22 5.36
3228 3476 1.078918 CTGCAATGGACCGAGCTGA 60.079 57.895 0.00 0.00 0.00 4.26
3279 3527 1.490574 GGACCCTCTACATGCTGAGT 58.509 55.000 12.61 0.00 0.00 3.41
3341 3589 3.760035 GCTCCGCGACCAGGAAGA 61.760 66.667 8.23 0.00 37.32 2.87
3403 3651 1.278985 TGGACGAAGCTGAATGTGGAT 59.721 47.619 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.