Multiple sequence alignment - TraesCS2B01G025400

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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 TraesCS2B01G025400 chr2B 100.000 3589 0 0 1 3589 11560603 11557015 0.000000e+00 6628.0
1 TraesCS2B01G025400 chr2B 96.567 2738 87 5 858 3589 12914380 12917116 0.000000e+00 4529.0
2 TraesCS2B01G025400 chr2B 93.947 1933 93 14 683 2598 11574041 11572116 0.000000e+00 2900.0
3 TraesCS2B01G025400 chr2B 79.753 1541 267 32 1042 2559 12422311 12423829 0.000000e+00 1075.0
4 TraesCS2B01G025400 chr2B 87.771 507 60 2 3081 3586 601187728 601188233 3.090000e-165 592.0
5 TraesCS2B01G025400 chr2B 87.549 506 59 4 3083 3586 168845052 168845555 1.860000e-162 582.0
6 TraesCS2B01G025400 chr2B 95.565 248 11 0 580 827 12914136 12914383 7.220000e-107 398.0
7 TraesCS2B01G025400 chr2A 90.961 2445 147 32 683 3080 8627056 8629473 0.000000e+00 3223.0
8 TraesCS2B01G025400 chr2A 82.067 1461 233 13 1022 2475 7727378 7728816 0.000000e+00 1219.0
9 TraesCS2B01G025400 chr2A 80.254 1575 261 31 1018 2576 8630933 8632473 0.000000e+00 1140.0
10 TraesCS2B01G025400 chr2A 80.400 1551 254 26 1043 2579 9944092 9945606 0.000000e+00 1134.0
11 TraesCS2B01G025400 chr2A 91.667 108 9 0 376 483 677418396 677418503 2.230000e-32 150.0
12 TraesCS2B01G025400 chr2D 91.803 2147 135 15 488 2630 9370984 9373093 0.000000e+00 2952.0
13 TraesCS2B01G025400 chr2D 87.259 2229 218 40 883 3080 9277335 9279528 0.000000e+00 2483.0
14 TraesCS2B01G025400 chr2D 88.706 1576 155 10 1022 2584 9502197 9503762 0.000000e+00 1903.0
15 TraesCS2B01G025400 chr2D 82.428 1565 242 17 1022 2574 8686448 8687991 0.000000e+00 1336.0
16 TraesCS2B01G025400 chr2D 82.660 1534 231 16 1018 2538 8659771 8661282 0.000000e+00 1327.0
17 TraesCS2B01G025400 chr2D 87.255 510 63 2 3081 3589 4451872 4451364 6.680000e-162 580.0
18 TraesCS2B01G025400 chr2D 81.236 437 45 18 488 915 9501255 9501663 5.780000e-83 318.0
19 TraesCS2B01G025400 chr2D 84.470 264 30 7 568 827 9276994 9277250 2.140000e-62 250.0
20 TraesCS2B01G025400 chr2D 91.045 67 3 3 2685 2748 30473311 30473377 1.780000e-13 87.9
21 TraesCS2B01G025400 chr5D 87.377 507 62 2 3081 3586 292147932 292148437 6.680000e-162 580.0
22 TraesCS2B01G025400 chr5D 78.740 127 16 7 2948 3071 205596791 205596673 1.380000e-09 75.0
23 TraesCS2B01G025400 chr5D 93.333 45 3 0 1 45 416971801 416971757 2.310000e-07 67.6
24 TraesCS2B01G025400 chr4A 87.255 510 63 2 3081 3589 164877785 164877277 6.680000e-162 580.0
25 TraesCS2B01G025400 chr3D 87.255 510 63 2 3081 3589 262995627 262995119 6.680000e-162 580.0
26 TraesCS2B01G025400 chr1A 87.255 510 63 2 3081 3589 292063085 292062577 6.680000e-162 580.0
27 TraesCS2B01G025400 chr5A 87.377 507 61 3 3081 3586 111614632 111615136 2.400000e-161 579.0
28 TraesCS2B01G025400 chr5A 89.041 73 4 3 2681 2749 706219321 706219393 1.780000e-13 87.9
29 TraesCS2B01G025400 chr5A 97.561 41 1 0 1 41 698618722 698618762 1.790000e-08 71.3
30 TraesCS2B01G025400 chr7A 92.537 67 2 3 2684 2747 679067122 679067056 3.820000e-15 93.5
31 TraesCS2B01G025400 chr4B 91.304 69 3 2 2684 2749 546830755 546830687 1.370000e-14 91.6
32 TraesCS2B01G025400 chr7D 91.045 67 3 2 2684 2747 587169263 587169197 1.780000e-13 87.9
33 TraesCS2B01G025400 chrUn 88.889 72 5 2 2681 2749 29748474 29748545 6.380000e-13 86.1
34 TraesCS2B01G025400 chrUn 97.436 39 1 0 1 39 108959511 108959473 2.310000e-07 67.6
35 TraesCS2B01G025400 chr1D 100.000 43 0 0 1 43 99696460 99696502 2.970000e-11 80.5
36 TraesCS2B01G025400 chr6D 97.500 40 1 0 1 40 433692597 433692636 6.430000e-08 69.4
37 TraesCS2B01G025400 chr5B 95.349 43 2 0 1 43 623119547 623119589 6.430000e-08 69.4
38 TraesCS2B01G025400 chr5B 95.349 43 2 0 1 43 626787498 626787540 6.430000e-08 69.4
39 TraesCS2B01G025400 chr1B 95.349 43 2 0 1 43 59425323 59425365 6.430000e-08 69.4
40 TraesCS2B01G025400 chr3B 90.196 51 4 1 1 50 7153198 7153148 8.320000e-07 65.8


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 TraesCS2B01G025400 chr2B 11557015 11560603 3588 True 6628.0 6628 100.0000 1 3589 1 chr2B.!!$R1 3588
1 TraesCS2B01G025400 chr2B 11572116 11574041 1925 True 2900.0 2900 93.9470 683 2598 1 chr2B.!!$R2 1915
2 TraesCS2B01G025400 chr2B 12914136 12917116 2980 False 2463.5 4529 96.0660 580 3589 2 chr2B.!!$F4 3009
3 TraesCS2B01G025400 chr2B 12422311 12423829 1518 False 1075.0 1075 79.7530 1042 2559 1 chr2B.!!$F1 1517
4 TraesCS2B01G025400 chr2B 601187728 601188233 505 False 592.0 592 87.7710 3081 3586 1 chr2B.!!$F3 505
5 TraesCS2B01G025400 chr2B 168845052 168845555 503 False 582.0 582 87.5490 3083 3586 1 chr2B.!!$F2 503
6 TraesCS2B01G025400 chr2A 8627056 8632473 5417 False 2181.5 3223 85.6075 683 3080 2 chr2A.!!$F4 2397
7 TraesCS2B01G025400 chr2A 7727378 7728816 1438 False 1219.0 1219 82.0670 1022 2475 1 chr2A.!!$F1 1453
8 TraesCS2B01G025400 chr2A 9944092 9945606 1514 False 1134.0 1134 80.4000 1043 2579 1 chr2A.!!$F2 1536
9 TraesCS2B01G025400 chr2D 9370984 9373093 2109 False 2952.0 2952 91.8030 488 2630 1 chr2D.!!$F3 2142
10 TraesCS2B01G025400 chr2D 9276994 9279528 2534 False 1366.5 2483 85.8645 568 3080 2 chr2D.!!$F5 2512
11 TraesCS2B01G025400 chr2D 8686448 8687991 1543 False 1336.0 1336 82.4280 1022 2574 1 chr2D.!!$F2 1552
12 TraesCS2B01G025400 chr2D 8659771 8661282 1511 False 1327.0 1327 82.6600 1018 2538 1 chr2D.!!$F1 1520
13 TraesCS2B01G025400 chr2D 9501255 9503762 2507 False 1110.5 1903 84.9710 488 2584 2 chr2D.!!$F6 2096
14 TraesCS2B01G025400 chr2D 4451364 4451872 508 True 580.0 580 87.2550 3081 3589 1 chr2D.!!$R1 508
15 TraesCS2B01G025400 chr5D 292147932 292148437 505 False 580.0 580 87.3770 3081 3586 1 chr5D.!!$F1 505
16 TraesCS2B01G025400 chr4A 164877277 164877785 508 True 580.0 580 87.2550 3081 3589 1 chr4A.!!$R1 508
17 TraesCS2B01G025400 chr3D 262995119 262995627 508 True 580.0 580 87.2550 3081 3589 1 chr3D.!!$R1 508
18 TraesCS2B01G025400 chr1A 292062577 292063085 508 True 580.0 580 87.2550 3081 3589 1 chr1A.!!$R1 508
19 TraesCS2B01G025400 chr5A 111614632 111615136 504 False 579.0 579 87.3770 3081 3586 1 chr5A.!!$F1 505

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
383 384 0.035630 CTAGCCTGCAGAGCCTTGTT 60.036 55.0 17.39 3.38 0.00 2.83 F
419 420 0.105349 CCGGGGAGGTTAGGATGGTA 60.105 60.0 0.00 0.00 34.51 3.25 F
1802 2286 0.548926 TACTTGGTGATGGGAGGGCA 60.549 55.0 0.00 0.00 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 2377 0.323725 TTGCTTCCTCTGCCCATTCC 60.324 55.0 0.00 0.00 0.00 3.01 R
2040 2530 0.533491 TGTACTAGCCGCGGATGTTT 59.467 50.0 33.48 14.24 0.00 2.83 R
3138 3746 0.249031 GTGCGTGGAAGCTTGCTTTT 60.249 50.0 19.34 0.00 38.13 2.27 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
29 30 3.249999 ACGGTTGTGATTTCGCGG 58.750 55.556 6.13 0.00 0.00 6.46
30 31 2.322081 ACGGTTGTGATTTCGCGGG 61.322 57.895 6.13 0.00 0.00 6.13
31 32 2.030401 CGGTTGTGATTTCGCGGGA 61.030 57.895 6.13 0.00 0.00 5.14
32 33 1.794222 GGTTGTGATTTCGCGGGAG 59.206 57.895 6.13 0.00 0.00 4.30
33 34 1.644786 GGTTGTGATTTCGCGGGAGG 61.645 60.000 6.13 0.00 0.00 4.30
34 35 2.038269 TTGTGATTTCGCGGGAGGC 61.038 57.895 6.13 0.00 38.69 4.70
35 36 2.435938 GTGATTTCGCGGGAGGCA 60.436 61.111 6.13 0.00 43.84 4.75
36 37 2.435938 TGATTTCGCGGGAGGCAC 60.436 61.111 6.13 0.00 43.84 5.01
37 38 3.564027 GATTTCGCGGGAGGCACG 61.564 66.667 6.13 0.00 43.84 5.34
50 51 2.900273 GCACGGCCATACTCCTCA 59.100 61.111 2.24 0.00 0.00 3.86
51 52 1.220749 GCACGGCCATACTCCTCAA 59.779 57.895 2.24 0.00 0.00 3.02
52 53 0.179045 GCACGGCCATACTCCTCAAT 60.179 55.000 2.24 0.00 0.00 2.57
53 54 1.747206 GCACGGCCATACTCCTCAATT 60.747 52.381 2.24 0.00 0.00 2.32
54 55 2.484770 GCACGGCCATACTCCTCAATTA 60.485 50.000 2.24 0.00 0.00 1.40
55 56 3.393800 CACGGCCATACTCCTCAATTAG 58.606 50.000 2.24 0.00 0.00 1.73
56 57 3.039011 ACGGCCATACTCCTCAATTAGT 58.961 45.455 2.24 0.00 0.00 2.24
57 58 3.181465 ACGGCCATACTCCTCAATTAGTG 60.181 47.826 2.24 0.00 0.00 2.74
58 59 3.069586 CGGCCATACTCCTCAATTAGTGA 59.930 47.826 2.24 0.00 34.17 3.41
59 60 4.262635 CGGCCATACTCCTCAATTAGTGAT 60.263 45.833 2.24 0.00 35.07 3.06
60 61 5.625150 GGCCATACTCCTCAATTAGTGATT 58.375 41.667 0.00 0.00 35.07 2.57
61 62 6.064717 GGCCATACTCCTCAATTAGTGATTT 58.935 40.000 0.00 0.00 35.07 2.17
62 63 6.205658 GGCCATACTCCTCAATTAGTGATTTC 59.794 42.308 0.00 0.00 35.07 2.17
63 64 6.073548 GCCATACTCCTCAATTAGTGATTTCG 60.074 42.308 0.00 0.00 35.07 3.46
64 65 6.986817 CCATACTCCTCAATTAGTGATTTCGT 59.013 38.462 0.00 0.00 35.07 3.85
65 66 7.169982 CCATACTCCTCAATTAGTGATTTCGTC 59.830 40.741 0.00 0.00 35.07 4.20
66 67 6.287589 ACTCCTCAATTAGTGATTTCGTCT 57.712 37.500 0.00 0.00 35.07 4.18
67 68 6.334202 ACTCCTCAATTAGTGATTTCGTCTC 58.666 40.000 0.00 0.00 35.07 3.36
68 69 6.153680 ACTCCTCAATTAGTGATTTCGTCTCT 59.846 38.462 0.00 0.00 35.07 3.10
69 70 6.936279 TCCTCAATTAGTGATTTCGTCTCTT 58.064 36.000 0.00 0.00 35.07 2.85
70 71 7.036220 TCCTCAATTAGTGATTTCGTCTCTTC 58.964 38.462 0.00 0.00 35.07 2.87
71 72 6.020281 CCTCAATTAGTGATTTCGTCTCTTCG 60.020 42.308 0.00 0.00 35.07 3.79
72 73 5.288712 TCAATTAGTGATTTCGTCTCTTCGC 59.711 40.000 0.00 0.00 33.08 4.70
73 74 4.436242 TTAGTGATTTCGTCTCTTCGCT 57.564 40.909 0.00 0.00 33.08 4.93
74 75 5.556355 TTAGTGATTTCGTCTCTTCGCTA 57.444 39.130 0.00 0.00 33.08 4.26
75 76 4.022464 AGTGATTTCGTCTCTTCGCTAG 57.978 45.455 0.00 0.00 0.00 3.42
76 77 3.440872 AGTGATTTCGTCTCTTCGCTAGT 59.559 43.478 0.00 0.00 0.00 2.57
77 78 4.082679 AGTGATTTCGTCTCTTCGCTAGTT 60.083 41.667 0.00 0.00 0.00 2.24
78 79 4.263443 GTGATTTCGTCTCTTCGCTAGTTC 59.737 45.833 0.00 0.00 0.00 3.01
79 80 2.915738 TTCGTCTCTTCGCTAGTTCC 57.084 50.000 0.00 0.00 0.00 3.62
80 81 1.093159 TCGTCTCTTCGCTAGTTCCC 58.907 55.000 0.00 0.00 0.00 3.97
81 82 1.096416 CGTCTCTTCGCTAGTTCCCT 58.904 55.000 0.00 0.00 0.00 4.20
82 83 1.473278 CGTCTCTTCGCTAGTTCCCTT 59.527 52.381 0.00 0.00 0.00 3.95
83 84 2.732597 CGTCTCTTCGCTAGTTCCCTTG 60.733 54.545 0.00 0.00 0.00 3.61
84 85 2.231721 GTCTCTTCGCTAGTTCCCTTGT 59.768 50.000 0.00 0.00 0.00 3.16
85 86 2.897969 TCTCTTCGCTAGTTCCCTTGTT 59.102 45.455 0.00 0.00 0.00 2.83
86 87 3.323979 TCTCTTCGCTAGTTCCCTTGTTT 59.676 43.478 0.00 0.00 0.00 2.83
87 88 4.065789 CTCTTCGCTAGTTCCCTTGTTTT 58.934 43.478 0.00 0.00 0.00 2.43
88 89 4.062991 TCTTCGCTAGTTCCCTTGTTTTC 58.937 43.478 0.00 0.00 0.00 2.29
89 90 3.478857 TCGCTAGTTCCCTTGTTTTCA 57.521 42.857 0.00 0.00 0.00 2.69
90 91 3.135994 TCGCTAGTTCCCTTGTTTTCAC 58.864 45.455 0.00 0.00 0.00 3.18
91 92 3.139077 CGCTAGTTCCCTTGTTTTCACT 58.861 45.455 0.00 0.00 0.00 3.41
92 93 3.058914 CGCTAGTTCCCTTGTTTTCACTG 60.059 47.826 0.00 0.00 0.00 3.66
93 94 3.883489 GCTAGTTCCCTTGTTTTCACTGT 59.117 43.478 0.00 0.00 0.00 3.55
94 95 4.338400 GCTAGTTCCCTTGTTTTCACTGTT 59.662 41.667 0.00 0.00 0.00 3.16
95 96 5.163550 GCTAGTTCCCTTGTTTTCACTGTTT 60.164 40.000 0.00 0.00 0.00 2.83
96 97 5.324784 AGTTCCCTTGTTTTCACTGTTTC 57.675 39.130 0.00 0.00 0.00 2.78
97 98 5.016831 AGTTCCCTTGTTTTCACTGTTTCT 58.983 37.500 0.00 0.00 0.00 2.52
98 99 5.480422 AGTTCCCTTGTTTTCACTGTTTCTT 59.520 36.000 0.00 0.00 0.00 2.52
99 100 5.993748 TCCCTTGTTTTCACTGTTTCTTT 57.006 34.783 0.00 0.00 0.00 2.52
100 101 7.177744 AGTTCCCTTGTTTTCACTGTTTCTTTA 59.822 33.333 0.00 0.00 0.00 1.85
101 102 7.654022 TCCCTTGTTTTCACTGTTTCTTTAT 57.346 32.000 0.00 0.00 0.00 1.40
102 103 8.073467 TCCCTTGTTTTCACTGTTTCTTTATT 57.927 30.769 0.00 0.00 0.00 1.40
103 104 7.978975 TCCCTTGTTTTCACTGTTTCTTTATTG 59.021 33.333 0.00 0.00 0.00 1.90
104 105 7.763985 CCCTTGTTTTCACTGTTTCTTTATTGT 59.236 33.333 0.00 0.00 0.00 2.71
105 106 9.150348 CCTTGTTTTCACTGTTTCTTTATTGTT 57.850 29.630 0.00 0.00 0.00 2.83
111 112 9.495572 TTTCACTGTTTCTTTATTGTTTTTGGT 57.504 25.926 0.00 0.00 0.00 3.67
112 113 9.495572 TTCACTGTTTCTTTATTGTTTTTGGTT 57.504 25.926 0.00 0.00 0.00 3.67
113 114 9.495572 TCACTGTTTCTTTATTGTTTTTGGTTT 57.504 25.926 0.00 0.00 0.00 3.27
121 122 9.936759 TCTTTATTGTTTTTGGTTTTCTTCTGT 57.063 25.926 0.00 0.00 0.00 3.41
127 128 9.495572 TTGTTTTTGGTTTTCTTCTGTTATTGT 57.504 25.926 0.00 0.00 0.00 2.71
128 129 8.930760 TGTTTTTGGTTTTCTTCTGTTATTGTG 58.069 29.630 0.00 0.00 0.00 3.33
129 130 8.931775 GTTTTTGGTTTTCTTCTGTTATTGTGT 58.068 29.630 0.00 0.00 0.00 3.72
130 131 8.472683 TTTTGGTTTTCTTCTGTTATTGTGTG 57.527 30.769 0.00 0.00 0.00 3.82
131 132 5.587289 TGGTTTTCTTCTGTTATTGTGTGC 58.413 37.500 0.00 0.00 0.00 4.57
132 133 5.359576 TGGTTTTCTTCTGTTATTGTGTGCT 59.640 36.000 0.00 0.00 0.00 4.40
133 134 6.127479 TGGTTTTCTTCTGTTATTGTGTGCTT 60.127 34.615 0.00 0.00 0.00 3.91
134 135 6.417930 GGTTTTCTTCTGTTATTGTGTGCTTC 59.582 38.462 0.00 0.00 0.00 3.86
135 136 6.942532 TTTCTTCTGTTATTGTGTGCTTCT 57.057 33.333 0.00 0.00 0.00 2.85
136 137 6.942532 TTCTTCTGTTATTGTGTGCTTCTT 57.057 33.333 0.00 0.00 0.00 2.52
137 138 6.942532 TCTTCTGTTATTGTGTGCTTCTTT 57.057 33.333 0.00 0.00 0.00 2.52
138 139 7.333528 TCTTCTGTTATTGTGTGCTTCTTTT 57.666 32.000 0.00 0.00 0.00 2.27
139 140 7.417612 TCTTCTGTTATTGTGTGCTTCTTTTC 58.582 34.615 0.00 0.00 0.00 2.29
140 141 6.942532 TCTGTTATTGTGTGCTTCTTTTCT 57.057 33.333 0.00 0.00 0.00 2.52
141 142 7.333528 TCTGTTATTGTGTGCTTCTTTTCTT 57.666 32.000 0.00 0.00 0.00 2.52
142 143 7.195646 TCTGTTATTGTGTGCTTCTTTTCTTG 58.804 34.615 0.00 0.00 0.00 3.02
143 144 6.272318 TGTTATTGTGTGCTTCTTTTCTTGG 58.728 36.000 0.00 0.00 0.00 3.61
144 145 6.127479 TGTTATTGTGTGCTTCTTTTCTTGGT 60.127 34.615 0.00 0.00 0.00 3.67
145 146 4.799564 TTGTGTGCTTCTTTTCTTGGTT 57.200 36.364 0.00 0.00 0.00 3.67
146 147 4.799564 TGTGTGCTTCTTTTCTTGGTTT 57.200 36.364 0.00 0.00 0.00 3.27
147 148 5.146010 TGTGTGCTTCTTTTCTTGGTTTT 57.854 34.783 0.00 0.00 0.00 2.43
148 149 6.274157 TGTGTGCTTCTTTTCTTGGTTTTA 57.726 33.333 0.00 0.00 0.00 1.52
149 150 6.872920 TGTGTGCTTCTTTTCTTGGTTTTAT 58.127 32.000 0.00 0.00 0.00 1.40
150 151 6.978080 TGTGTGCTTCTTTTCTTGGTTTTATC 59.022 34.615 0.00 0.00 0.00 1.75
151 152 6.978080 GTGTGCTTCTTTTCTTGGTTTTATCA 59.022 34.615 0.00 0.00 0.00 2.15
152 153 7.653311 GTGTGCTTCTTTTCTTGGTTTTATCAT 59.347 33.333 0.00 0.00 0.00 2.45
153 154 8.203485 TGTGCTTCTTTTCTTGGTTTTATCATT 58.797 29.630 0.00 0.00 0.00 2.57
154 155 9.045223 GTGCTTCTTTTCTTGGTTTTATCATTT 57.955 29.630 0.00 0.00 0.00 2.32
155 156 9.612066 TGCTTCTTTTCTTGGTTTTATCATTTT 57.388 25.926 0.00 0.00 0.00 1.82
158 159 9.554395 TTCTTTTCTTGGTTTTATCATTTTCCC 57.446 29.630 0.00 0.00 0.00 3.97
159 160 8.709308 TCTTTTCTTGGTTTTATCATTTTCCCA 58.291 29.630 0.00 0.00 0.00 4.37
160 161 9.336171 CTTTTCTTGGTTTTATCATTTTCCCAA 57.664 29.630 0.00 0.00 0.00 4.12
161 162 9.686683 TTTTCTTGGTTTTATCATTTTCCCAAA 57.313 25.926 0.00 0.00 30.72 3.28
162 163 9.686683 TTTCTTGGTTTTATCATTTTCCCAAAA 57.313 25.926 0.00 0.00 30.72 2.44
163 164 9.686683 TTCTTGGTTTTATCATTTTCCCAAAAA 57.313 25.926 0.00 0.00 38.66 1.94
186 187 8.731275 AAAAATCCGGATTTTCTTCTTGTTTT 57.269 26.923 41.03 25.48 46.76 2.43
187 188 8.731275 AAAATCCGGATTTTCTTCTTGTTTTT 57.269 26.923 37.92 19.82 44.98 1.94
233 234 9.847224 TTTACCTTCAGTGTTTATTCTTCTTCT 57.153 29.630 0.00 0.00 0.00 2.85
234 235 9.847224 TTACCTTCAGTGTTTATTCTTCTTCTT 57.153 29.630 0.00 0.00 0.00 2.52
235 236 8.753497 ACCTTCAGTGTTTATTCTTCTTCTTT 57.247 30.769 0.00 0.00 0.00 2.52
236 237 9.190317 ACCTTCAGTGTTTATTCTTCTTCTTTT 57.810 29.630 0.00 0.00 0.00 2.27
237 238 9.670719 CCTTCAGTGTTTATTCTTCTTCTTTTC 57.329 33.333 0.00 0.00 0.00 2.29
243 244 9.803315 GTGTTTATTCTTCTTCTTTTCTTTGGT 57.197 29.630 0.00 0.00 0.00 3.67
249 250 9.725019 ATTCTTCTTCTTTTCTTTGGTTTTGTT 57.275 25.926 0.00 0.00 0.00 2.83
250 251 9.554395 TTCTTCTTCTTTTCTTTGGTTTTGTTT 57.446 25.926 0.00 0.00 0.00 2.83
251 252 9.203421 TCTTCTTCTTTTCTTTGGTTTTGTTTC 57.797 29.630 0.00 0.00 0.00 2.78
252 253 8.894768 TTCTTCTTTTCTTTGGTTTTGTTTCA 57.105 26.923 0.00 0.00 0.00 2.69
253 254 9.500785 TTCTTCTTTTCTTTGGTTTTGTTTCAT 57.499 25.926 0.00 0.00 0.00 2.57
254 255 8.934825 TCTTCTTTTCTTTGGTTTTGTTTCATG 58.065 29.630 0.00 0.00 0.00 3.07
255 256 8.614469 TTCTTTTCTTTGGTTTTGTTTCATGT 57.386 26.923 0.00 0.00 0.00 3.21
256 257 8.614469 TCTTTTCTTTGGTTTTGTTTCATGTT 57.386 26.923 0.00 0.00 0.00 2.71
257 258 9.061435 TCTTTTCTTTGGTTTTGTTTCATGTTT 57.939 25.926 0.00 0.00 0.00 2.83
258 259 9.328721 CTTTTCTTTGGTTTTGTTTCATGTTTC 57.671 29.630 0.00 0.00 0.00 2.78
259 260 8.614469 TTTCTTTGGTTTTGTTTCATGTTTCT 57.386 26.923 0.00 0.00 0.00 2.52
260 261 7.826260 TCTTTGGTTTTGTTTCATGTTTCTC 57.174 32.000 0.00 0.00 0.00 2.87
261 262 6.529829 TCTTTGGTTTTGTTTCATGTTTCTCG 59.470 34.615 0.00 0.00 0.00 4.04
262 263 5.317733 TGGTTTTGTTTCATGTTTCTCGT 57.682 34.783 0.00 0.00 0.00 4.18
263 264 5.715070 TGGTTTTGTTTCATGTTTCTCGTT 58.285 33.333 0.00 0.00 0.00 3.85
264 265 6.159988 TGGTTTTGTTTCATGTTTCTCGTTT 58.840 32.000 0.00 0.00 0.00 3.60
265 266 6.647067 TGGTTTTGTTTCATGTTTCTCGTTTT 59.353 30.769 0.00 0.00 0.00 2.43
266 267 7.171678 TGGTTTTGTTTCATGTTTCTCGTTTTT 59.828 29.630 0.00 0.00 0.00 1.94
307 308 8.961294 TTTTTCATTGTGGTTCATGATTTTCT 57.039 26.923 0.00 0.00 0.00 2.52
308 309 8.961294 TTTTCATTGTGGTTCATGATTTTCTT 57.039 26.923 0.00 0.00 0.00 2.52
309 310 8.592105 TTTCATTGTGGTTCATGATTTTCTTC 57.408 30.769 0.00 0.00 0.00 2.87
310 311 7.528996 TCATTGTGGTTCATGATTTTCTTCT 57.471 32.000 0.00 0.00 0.00 2.85
311 312 7.372714 TCATTGTGGTTCATGATTTTCTTCTG 58.627 34.615 0.00 0.00 0.00 3.02
312 313 6.713762 TTGTGGTTCATGATTTTCTTCTGT 57.286 33.333 0.00 0.00 0.00 3.41
313 314 6.713762 TGTGGTTCATGATTTTCTTCTGTT 57.286 33.333 0.00 0.00 0.00 3.16
314 315 7.111247 TGTGGTTCATGATTTTCTTCTGTTT 57.889 32.000 0.00 0.00 0.00 2.83
315 316 7.555087 TGTGGTTCATGATTTTCTTCTGTTTT 58.445 30.769 0.00 0.00 0.00 2.43
316 317 7.492020 TGTGGTTCATGATTTTCTTCTGTTTTG 59.508 33.333 0.00 0.00 0.00 2.44
317 318 7.492344 GTGGTTCATGATTTTCTTCTGTTTTGT 59.508 33.333 0.00 0.00 0.00 2.83
318 319 7.706179 TGGTTCATGATTTTCTTCTGTTTTGTC 59.294 33.333 0.00 0.00 0.00 3.18
319 320 7.922811 GGTTCATGATTTTCTTCTGTTTTGTCT 59.077 33.333 0.00 0.00 0.00 3.41
320 321 8.749499 GTTCATGATTTTCTTCTGTTTTGTCTG 58.251 33.333 0.00 0.00 0.00 3.51
321 322 7.999679 TCATGATTTTCTTCTGTTTTGTCTGT 58.000 30.769 0.00 0.00 0.00 3.41
322 323 8.469200 TCATGATTTTCTTCTGTTTTGTCTGTT 58.531 29.630 0.00 0.00 0.00 3.16
323 324 9.090692 CATGATTTTCTTCTGTTTTGTCTGTTT 57.909 29.630 0.00 0.00 0.00 2.83
324 325 9.657419 ATGATTTTCTTCTGTTTTGTCTGTTTT 57.343 25.926 0.00 0.00 0.00 2.43
325 326 9.139174 TGATTTTCTTCTGTTTTGTCTGTTTTC 57.861 29.630 0.00 0.00 0.00 2.29
326 327 7.883229 TTTTCTTCTGTTTTGTCTGTTTTCC 57.117 32.000 0.00 0.00 0.00 3.13
327 328 6.582677 TTCTTCTGTTTTGTCTGTTTTCCA 57.417 33.333 0.00 0.00 0.00 3.53
328 329 6.582677 TCTTCTGTTTTGTCTGTTTTCCAA 57.417 33.333 0.00 0.00 0.00 3.53
329 330 7.169158 TCTTCTGTTTTGTCTGTTTTCCAAT 57.831 32.000 0.00 0.00 0.00 3.16
330 331 8.287439 TCTTCTGTTTTGTCTGTTTTCCAATA 57.713 30.769 0.00 0.00 0.00 1.90
331 332 8.912988 TCTTCTGTTTTGTCTGTTTTCCAATAT 58.087 29.630 0.00 0.00 0.00 1.28
340 341 9.832445 TTGTCTGTTTTCCAATATATCTCTACC 57.168 33.333 0.00 0.00 0.00 3.18
341 342 9.213777 TGTCTGTTTTCCAATATATCTCTACCT 57.786 33.333 0.00 0.00 0.00 3.08
368 369 8.795786 TTTTACACACAATTGTCATTTCTAGC 57.204 30.769 8.48 0.00 31.66 3.42
369 370 5.376854 ACACACAATTGTCATTTCTAGCC 57.623 39.130 8.48 0.00 31.66 3.93
370 371 5.072741 ACACACAATTGTCATTTCTAGCCT 58.927 37.500 8.48 0.00 31.66 4.58
371 372 5.048504 ACACACAATTGTCATTTCTAGCCTG 60.049 40.000 8.48 0.00 31.66 4.85
372 373 4.082571 ACACAATTGTCATTTCTAGCCTGC 60.083 41.667 8.48 0.00 0.00 4.85
373 374 4.081406 ACAATTGTCATTTCTAGCCTGCA 58.919 39.130 4.92 0.00 0.00 4.41
374 375 4.157289 ACAATTGTCATTTCTAGCCTGCAG 59.843 41.667 6.78 6.78 0.00 4.41
375 376 3.701205 TTGTCATTTCTAGCCTGCAGA 57.299 42.857 17.39 0.00 0.00 4.26
376 377 3.257469 TGTCATTTCTAGCCTGCAGAG 57.743 47.619 17.39 4.72 0.00 3.35
377 378 1.939255 GTCATTTCTAGCCTGCAGAGC 59.061 52.381 17.39 16.92 0.00 4.09
378 379 1.134280 TCATTTCTAGCCTGCAGAGCC 60.134 52.381 17.39 2.86 0.00 4.70
379 380 1.134159 CATTTCTAGCCTGCAGAGCCT 60.134 52.381 17.39 10.82 0.00 4.58
380 381 0.987294 TTTCTAGCCTGCAGAGCCTT 59.013 50.000 17.39 4.82 0.00 4.35
381 382 0.251354 TTCTAGCCTGCAGAGCCTTG 59.749 55.000 17.39 9.39 0.00 3.61
382 383 0.906756 TCTAGCCTGCAGAGCCTTGT 60.907 55.000 17.39 3.75 0.00 3.16
383 384 0.035630 CTAGCCTGCAGAGCCTTGTT 60.036 55.000 17.39 3.38 0.00 2.83
384 385 0.321919 TAGCCTGCAGAGCCTTGTTG 60.322 55.000 17.39 0.00 0.00 3.33
385 386 2.960170 CCTGCAGAGCCTTGTTGC 59.040 61.111 17.39 0.00 38.30 4.17
386 387 2.559840 CTGCAGAGCCTTGTTGCG 59.440 61.111 8.42 0.00 40.62 4.85
387 388 2.974489 CTGCAGAGCCTTGTTGCGG 61.974 63.158 8.42 0.00 40.62 5.69
411 412 3.777910 GAAGCGCCGGGGAGGTTA 61.778 66.667 24.68 0.00 43.70 2.85
412 413 3.735037 GAAGCGCCGGGGAGGTTAG 62.735 68.421 24.68 0.00 43.70 2.34
415 416 2.842936 CGCCGGGGAGGTTAGGAT 60.843 66.667 14.46 0.00 43.70 3.24
416 417 2.829592 GCCGGGGAGGTTAGGATG 59.170 66.667 2.18 0.00 43.70 3.51
417 418 2.819284 GCCGGGGAGGTTAGGATGG 61.819 68.421 2.18 0.00 43.70 3.51
418 419 1.384082 CCGGGGAGGTTAGGATGGT 60.384 63.158 0.00 0.00 34.51 3.55
419 420 0.105349 CCGGGGAGGTTAGGATGGTA 60.105 60.000 0.00 0.00 34.51 3.25
420 421 1.046204 CGGGGAGGTTAGGATGGTAC 58.954 60.000 0.00 0.00 0.00 3.34
421 422 1.432056 GGGGAGGTTAGGATGGTACC 58.568 60.000 4.43 4.43 0.00 3.34
422 423 1.344701 GGGGAGGTTAGGATGGTACCA 60.345 57.143 18.99 18.99 34.32 3.25
423 424 2.699281 GGGGAGGTTAGGATGGTACCAT 60.699 54.545 27.70 27.70 39.69 3.55
424 425 3.053826 GGGAGGTTAGGATGGTACCATT 58.946 50.000 27.97 15.94 36.70 3.16
425 426 3.072622 GGGAGGTTAGGATGGTACCATTC 59.927 52.174 27.97 25.94 36.70 2.67
426 427 3.244112 GGAGGTTAGGATGGTACCATTCG 60.244 52.174 27.97 0.00 37.04 3.34
427 428 2.704065 AGGTTAGGATGGTACCATTCGG 59.296 50.000 27.97 0.00 37.04 4.30
467 468 3.520862 GGCATGGGTGTCGCCATG 61.521 66.667 13.62 13.62 45.52 3.66
469 470 2.438975 CATGGGTGTCGCCATGCT 60.439 61.111 4.48 0.00 37.57 3.79
470 471 2.124570 ATGGGTGTCGCCATGCTC 60.125 61.111 4.48 0.00 39.65 4.26
471 472 3.704231 ATGGGTGTCGCCATGCTCC 62.704 63.158 4.48 0.00 39.65 4.70
472 473 4.408821 GGGTGTCGCCATGCTCCA 62.409 66.667 4.48 0.00 39.65 3.86
473 474 3.127533 GGTGTCGCCATGCTCCAC 61.128 66.667 0.00 0.00 37.17 4.02
474 475 2.358615 GTGTCGCCATGCTCCACA 60.359 61.111 0.00 0.00 30.83 4.17
475 476 1.746615 GTGTCGCCATGCTCCACAT 60.747 57.895 0.00 0.00 40.66 3.21
483 484 2.310251 ATGCTCCACATGGGCTACA 58.690 52.632 11.21 0.00 37.70 2.74
484 485 0.848735 ATGCTCCACATGGGCTACAT 59.151 50.000 11.21 0.00 41.57 2.29
497 498 3.274288 GGGCTACATGGAAAGACTGAAG 58.726 50.000 0.00 0.00 0.00 3.02
502 503 1.466167 CATGGAAAGACTGAAGTGGCG 59.534 52.381 0.00 0.00 0.00 5.69
503 504 0.884704 TGGAAAGACTGAAGTGGCGC 60.885 55.000 0.00 0.00 0.00 6.53
507 508 1.388547 AAGACTGAAGTGGCGCAAAA 58.611 45.000 10.83 0.00 0.00 2.44
515 516 0.899717 AGTGGCGCAAAATGGACCAT 60.900 50.000 10.83 0.00 31.99 3.55
527 528 5.606348 AAATGGACCATAGAGAGACTGAC 57.394 43.478 7.59 0.00 0.00 3.51
541 542 3.513515 GAGACTGACTGGGTTCTGAAGAT 59.486 47.826 0.00 0.00 0.00 2.40
674 678 0.672091 TGCGCGATGCTTTTCCACTA 60.672 50.000 12.10 0.00 46.63 2.74
694 701 6.205658 CCACTAAAGTTCCTCTGGAAAGAAAG 59.794 42.308 0.12 0.78 43.86 2.62
1802 2286 0.548926 TACTTGGTGATGGGAGGGCA 60.549 55.000 0.00 0.00 0.00 5.36
1807 2291 0.753111 GGTGATGGGAGGGCAATGAC 60.753 60.000 0.00 0.00 0.00 3.06
1887 2377 8.186821 GGAAAACATTCCACTCATTTCTCATAG 58.813 37.037 2.78 0.00 40.79 2.23
2040 2530 0.037326 CGGAAGTGTAGAGCCAGCAA 60.037 55.000 0.00 0.00 0.00 3.91
2352 2847 4.320861 CGGAATTGCCAAGTGTGACATTTA 60.321 41.667 0.00 0.00 35.94 1.40
2739 3258 8.964476 ACAATTCGGACTACTATTCATCAAAT 57.036 30.769 0.00 0.00 0.00 2.32
2798 3322 5.333568 GCATTTCTTTGTGAAACTTCATGCC 60.334 40.000 0.00 0.00 46.08 4.40
2924 3449 8.085296 TCCACGTTCAACAGCAAATATAAAAAT 58.915 29.630 0.00 0.00 0.00 1.82
2984 3520 6.126332 ACCAAGTTTGATACCCCCAAAATTTT 60.126 34.615 0.00 0.00 39.00 1.82
3055 3592 1.344114 GGTGCATGTGGAACCATGTTT 59.656 47.619 0.00 0.00 43.33 2.83
3092 3700 5.132043 ACTATTCAGTGGTAGGCTAGAGT 57.868 43.478 0.00 0.00 32.25 3.24
3123 3731 5.050091 CCATAAGATATCGCAACCAACTCAC 60.050 44.000 0.00 0.00 0.00 3.51
3138 3746 5.056480 CCAACTCACAGTTCTAACACATGA 58.944 41.667 0.00 0.00 36.03 3.07
3234 3842 3.610911 GGACTCCTCCGATGTCAAATTT 58.389 45.455 0.00 0.00 32.84 1.82
3235 3843 4.766375 GGACTCCTCCGATGTCAAATTTA 58.234 43.478 0.00 0.00 32.84 1.40
3264 3872 3.384789 CCCGACCTCTCTTGACATTATCA 59.615 47.826 0.00 0.00 34.65 2.15
3306 3914 2.701780 GGAGCGACGCTTCTGGAGA 61.702 63.158 25.30 0.00 39.88 3.71
3445 4057 2.956333 CCATGCATCCATCTCAACATGT 59.044 45.455 0.00 0.00 34.49 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.670546 AATCACAACCGTGCCTCTCG 60.671 55.000 0.00 0.00 43.28 4.04
5 6 1.464997 GAAATCACAACCGTGCCTCTC 59.535 52.381 0.00 0.00 43.28 3.20
6 7 1.523758 GAAATCACAACCGTGCCTCT 58.476 50.000 0.00 0.00 43.28 3.69
7 8 0.165944 CGAAATCACAACCGTGCCTC 59.834 55.000 0.00 0.00 43.28 4.70
8 9 1.852067 GCGAAATCACAACCGTGCCT 61.852 55.000 0.00 0.00 43.28 4.75
9 10 1.442017 GCGAAATCACAACCGTGCC 60.442 57.895 0.00 0.00 43.28 5.01
10 11 1.792057 CGCGAAATCACAACCGTGC 60.792 57.895 0.00 0.00 43.28 5.34
11 12 1.154488 CCGCGAAATCACAACCGTG 60.154 57.895 8.23 0.00 45.08 4.94
12 13 2.322081 CCCGCGAAATCACAACCGT 61.322 57.895 8.23 0.00 0.00 4.83
13 14 1.966493 CTCCCGCGAAATCACAACCG 61.966 60.000 8.23 0.00 0.00 4.44
14 15 1.644786 CCTCCCGCGAAATCACAACC 61.645 60.000 8.23 0.00 0.00 3.77
15 16 1.794222 CCTCCCGCGAAATCACAAC 59.206 57.895 8.23 0.00 0.00 3.32
16 17 2.038269 GCCTCCCGCGAAATCACAA 61.038 57.895 8.23 0.00 0.00 3.33
17 18 2.435938 GCCTCCCGCGAAATCACA 60.436 61.111 8.23 0.00 0.00 3.58
18 19 2.435938 TGCCTCCCGCGAAATCAC 60.436 61.111 8.23 0.00 42.08 3.06
19 20 2.435938 GTGCCTCCCGCGAAATCA 60.436 61.111 8.23 0.00 42.08 2.57
33 34 0.179045 ATTGAGGAGTATGGCCGTGC 60.179 55.000 8.05 6.26 0.00 5.34
34 35 2.332063 AATTGAGGAGTATGGCCGTG 57.668 50.000 8.05 0.00 0.00 4.94
35 36 3.039011 ACTAATTGAGGAGTATGGCCGT 58.961 45.455 1.35 1.35 0.00 5.68
36 37 3.069586 TCACTAATTGAGGAGTATGGCCG 59.930 47.826 0.00 0.00 0.00 6.13
37 38 4.689612 TCACTAATTGAGGAGTATGGCC 57.310 45.455 0.00 0.00 0.00 5.36
38 39 6.073548 CGAAATCACTAATTGAGGAGTATGGC 60.074 42.308 0.00 0.00 37.77 4.40
39 40 6.986817 ACGAAATCACTAATTGAGGAGTATGG 59.013 38.462 0.00 0.00 37.77 2.74
40 41 7.923344 AGACGAAATCACTAATTGAGGAGTATG 59.077 37.037 0.00 0.00 37.77 2.39
41 42 8.012957 AGACGAAATCACTAATTGAGGAGTAT 57.987 34.615 0.00 0.00 37.77 2.12
42 43 7.339721 AGAGACGAAATCACTAATTGAGGAGTA 59.660 37.037 0.00 0.00 37.77 2.59
43 44 6.153680 AGAGACGAAATCACTAATTGAGGAGT 59.846 38.462 0.00 0.00 37.77 3.85
44 45 6.568869 AGAGACGAAATCACTAATTGAGGAG 58.431 40.000 0.00 0.00 37.77 3.69
45 46 6.531503 AGAGACGAAATCACTAATTGAGGA 57.468 37.500 0.00 0.00 37.77 3.71
46 47 6.020281 CGAAGAGACGAAATCACTAATTGAGG 60.020 42.308 0.00 0.00 34.68 3.86
47 48 6.507141 GCGAAGAGACGAAATCACTAATTGAG 60.507 42.308 0.00 0.00 34.68 3.02
48 49 5.288712 GCGAAGAGACGAAATCACTAATTGA 59.711 40.000 0.00 0.00 35.33 2.57
49 50 5.289675 AGCGAAGAGACGAAATCACTAATTG 59.710 40.000 0.00 0.00 35.09 2.32
50 51 5.411781 AGCGAAGAGACGAAATCACTAATT 58.588 37.500 0.00 0.00 35.09 1.40
51 52 5.000012 AGCGAAGAGACGAAATCACTAAT 58.000 39.130 0.00 0.00 35.09 1.73
52 53 4.436242 AGCGAAGAGACGAAATCACTAA 57.564 40.909 0.00 0.00 35.09 2.24
53 54 4.634883 ACTAGCGAAGAGACGAAATCACTA 59.365 41.667 0.00 0.00 35.09 2.74
54 55 3.440872 ACTAGCGAAGAGACGAAATCACT 59.559 43.478 0.00 0.00 35.09 3.41
55 56 3.760537 ACTAGCGAAGAGACGAAATCAC 58.239 45.455 0.00 0.00 35.09 3.06
56 57 4.413087 GAACTAGCGAAGAGACGAAATCA 58.587 43.478 0.00 0.00 35.09 2.57
57 58 3.792421 GGAACTAGCGAAGAGACGAAATC 59.208 47.826 0.00 0.00 35.09 2.17
58 59 3.429135 GGGAACTAGCGAAGAGACGAAAT 60.429 47.826 0.00 0.00 35.09 2.17
59 60 2.094854 GGGAACTAGCGAAGAGACGAAA 60.095 50.000 0.00 0.00 35.09 3.46
60 61 1.471684 GGGAACTAGCGAAGAGACGAA 59.528 52.381 0.00 0.00 35.09 3.85
61 62 1.093159 GGGAACTAGCGAAGAGACGA 58.907 55.000 0.00 0.00 35.09 4.20
62 63 1.096416 AGGGAACTAGCGAAGAGACG 58.904 55.000 0.00 0.00 40.61 4.18
63 64 2.231721 ACAAGGGAACTAGCGAAGAGAC 59.768 50.000 0.00 0.00 42.68 3.36
64 65 2.526432 ACAAGGGAACTAGCGAAGAGA 58.474 47.619 0.00 0.00 42.68 3.10
65 66 3.320673 AACAAGGGAACTAGCGAAGAG 57.679 47.619 0.00 0.00 42.68 2.85
66 67 3.764237 AAACAAGGGAACTAGCGAAGA 57.236 42.857 0.00 0.00 42.68 2.87
67 68 3.813166 TGAAAACAAGGGAACTAGCGAAG 59.187 43.478 0.00 0.00 42.68 3.79
68 69 3.562557 GTGAAAACAAGGGAACTAGCGAA 59.437 43.478 0.00 0.00 42.68 4.70
69 70 3.135994 GTGAAAACAAGGGAACTAGCGA 58.864 45.455 0.00 0.00 42.68 4.93
70 71 3.058914 CAGTGAAAACAAGGGAACTAGCG 60.059 47.826 0.00 0.00 42.68 4.26
71 72 3.883489 ACAGTGAAAACAAGGGAACTAGC 59.117 43.478 0.00 0.00 42.68 3.42
72 73 6.318900 AGAAACAGTGAAAACAAGGGAACTAG 59.681 38.462 0.00 0.00 42.68 2.57
73 74 6.184789 AGAAACAGTGAAAACAAGGGAACTA 58.815 36.000 0.00 0.00 42.68 2.24
75 76 5.324784 AGAAACAGTGAAAACAAGGGAAC 57.675 39.130 0.00 0.00 0.00 3.62
76 77 5.993748 AAGAAACAGTGAAAACAAGGGAA 57.006 34.783 0.00 0.00 0.00 3.97
77 78 5.993748 AAAGAAACAGTGAAAACAAGGGA 57.006 34.783 0.00 0.00 0.00 4.20
78 79 7.763985 ACAATAAAGAAACAGTGAAAACAAGGG 59.236 33.333 0.00 0.00 0.00 3.95
79 80 8.702163 ACAATAAAGAAACAGTGAAAACAAGG 57.298 30.769 0.00 0.00 0.00 3.61
85 86 9.495572 ACCAAAAACAATAAAGAAACAGTGAAA 57.504 25.926 0.00 0.00 0.00 2.69
86 87 9.495572 AACCAAAAACAATAAAGAAACAGTGAA 57.504 25.926 0.00 0.00 0.00 3.18
87 88 9.495572 AAACCAAAAACAATAAAGAAACAGTGA 57.504 25.926 0.00 0.00 0.00 3.41
95 96 9.936759 ACAGAAGAAAACCAAAAACAATAAAGA 57.063 25.926 0.00 0.00 0.00 2.52
101 102 9.495572 ACAATAACAGAAGAAAACCAAAAACAA 57.504 25.926 0.00 0.00 0.00 2.83
102 103 8.930760 CACAATAACAGAAGAAAACCAAAAACA 58.069 29.630 0.00 0.00 0.00 2.83
103 104 8.931775 ACACAATAACAGAAGAAAACCAAAAAC 58.068 29.630 0.00 0.00 0.00 2.43
104 105 8.930760 CACACAATAACAGAAGAAAACCAAAAA 58.069 29.630 0.00 0.00 0.00 1.94
105 106 7.064016 GCACACAATAACAGAAGAAAACCAAAA 59.936 33.333 0.00 0.00 0.00 2.44
106 107 6.533367 GCACACAATAACAGAAGAAAACCAAA 59.467 34.615 0.00 0.00 0.00 3.28
107 108 6.039616 GCACACAATAACAGAAGAAAACCAA 58.960 36.000 0.00 0.00 0.00 3.67
108 109 5.359576 AGCACACAATAACAGAAGAAAACCA 59.640 36.000 0.00 0.00 0.00 3.67
109 110 5.831997 AGCACACAATAACAGAAGAAAACC 58.168 37.500 0.00 0.00 0.00 3.27
110 111 7.196331 AGAAGCACACAATAACAGAAGAAAAC 58.804 34.615 0.00 0.00 0.00 2.43
111 112 7.333528 AGAAGCACACAATAACAGAAGAAAA 57.666 32.000 0.00 0.00 0.00 2.29
112 113 6.942532 AGAAGCACACAATAACAGAAGAAA 57.057 33.333 0.00 0.00 0.00 2.52
113 114 6.942532 AAGAAGCACACAATAACAGAAGAA 57.057 33.333 0.00 0.00 0.00 2.52
114 115 6.942532 AAAGAAGCACACAATAACAGAAGA 57.057 33.333 0.00 0.00 0.00 2.87
115 116 7.420800 AGAAAAGAAGCACACAATAACAGAAG 58.579 34.615 0.00 0.00 0.00 2.85
116 117 7.333528 AGAAAAGAAGCACACAATAACAGAA 57.666 32.000 0.00 0.00 0.00 3.02
117 118 6.942532 AGAAAAGAAGCACACAATAACAGA 57.057 33.333 0.00 0.00 0.00 3.41
118 119 6.418819 CCAAGAAAAGAAGCACACAATAACAG 59.581 38.462 0.00 0.00 0.00 3.16
119 120 6.127479 ACCAAGAAAAGAAGCACACAATAACA 60.127 34.615 0.00 0.00 0.00 2.41
120 121 6.273071 ACCAAGAAAAGAAGCACACAATAAC 58.727 36.000 0.00 0.00 0.00 1.89
121 122 6.463995 ACCAAGAAAAGAAGCACACAATAA 57.536 33.333 0.00 0.00 0.00 1.40
122 123 6.463995 AACCAAGAAAAGAAGCACACAATA 57.536 33.333 0.00 0.00 0.00 1.90
123 124 5.343307 AACCAAGAAAAGAAGCACACAAT 57.657 34.783 0.00 0.00 0.00 2.71
124 125 4.799564 AACCAAGAAAAGAAGCACACAA 57.200 36.364 0.00 0.00 0.00 3.33
125 126 4.799564 AAACCAAGAAAAGAAGCACACA 57.200 36.364 0.00 0.00 0.00 3.72
126 127 6.978080 TGATAAAACCAAGAAAAGAAGCACAC 59.022 34.615 0.00 0.00 0.00 3.82
127 128 7.106439 TGATAAAACCAAGAAAAGAAGCACA 57.894 32.000 0.00 0.00 0.00 4.57
128 129 8.593492 AATGATAAAACCAAGAAAAGAAGCAC 57.407 30.769 0.00 0.00 0.00 4.40
129 130 9.612066 AAAATGATAAAACCAAGAAAAGAAGCA 57.388 25.926 0.00 0.00 0.00 3.91
132 133 9.554395 GGGAAAATGATAAAACCAAGAAAAGAA 57.446 29.630 0.00 0.00 0.00 2.52
133 134 8.709308 TGGGAAAATGATAAAACCAAGAAAAGA 58.291 29.630 0.00 0.00 0.00 2.52
134 135 8.900983 TGGGAAAATGATAAAACCAAGAAAAG 57.099 30.769 0.00 0.00 0.00 2.27
135 136 9.686683 TTTGGGAAAATGATAAAACCAAGAAAA 57.313 25.926 0.00 0.00 37.74 2.29
136 137 9.686683 TTTTGGGAAAATGATAAAACCAAGAAA 57.313 25.926 0.00 0.00 37.74 2.52
137 138 9.686683 TTTTTGGGAAAATGATAAAACCAAGAA 57.313 25.926 0.00 0.00 37.74 2.52
207 208 9.847224 AGAAGAAGAATAAACACTGAAGGTAAA 57.153 29.630 0.00 0.00 0.00 2.01
208 209 9.847224 AAGAAGAAGAATAAACACTGAAGGTAA 57.153 29.630 0.00 0.00 0.00 2.85
209 210 9.847224 AAAGAAGAAGAATAAACACTGAAGGTA 57.153 29.630 0.00 0.00 0.00 3.08
210 211 8.753497 AAAGAAGAAGAATAAACACTGAAGGT 57.247 30.769 0.00 0.00 0.00 3.50
211 212 9.670719 GAAAAGAAGAAGAATAAACACTGAAGG 57.329 33.333 0.00 0.00 0.00 3.46
217 218 9.803315 ACCAAAGAAAAGAAGAAGAATAAACAC 57.197 29.630 0.00 0.00 0.00 3.32
223 224 9.725019 AACAAAACCAAAGAAAAGAAGAAGAAT 57.275 25.926 0.00 0.00 0.00 2.40
224 225 9.554395 AAACAAAACCAAAGAAAAGAAGAAGAA 57.446 25.926 0.00 0.00 0.00 2.52
225 226 9.203421 GAAACAAAACCAAAGAAAAGAAGAAGA 57.797 29.630 0.00 0.00 0.00 2.87
226 227 8.987890 TGAAACAAAACCAAAGAAAAGAAGAAG 58.012 29.630 0.00 0.00 0.00 2.85
227 228 8.894768 TGAAACAAAACCAAAGAAAAGAAGAA 57.105 26.923 0.00 0.00 0.00 2.52
228 229 8.934825 CATGAAACAAAACCAAAGAAAAGAAGA 58.065 29.630 0.00 0.00 0.00 2.87
229 230 8.720562 ACATGAAACAAAACCAAAGAAAAGAAG 58.279 29.630 0.00 0.00 0.00 2.85
230 231 8.614469 ACATGAAACAAAACCAAAGAAAAGAA 57.386 26.923 0.00 0.00 0.00 2.52
231 232 8.614469 AACATGAAACAAAACCAAAGAAAAGA 57.386 26.923 0.00 0.00 0.00 2.52
232 233 9.328721 GAAACATGAAACAAAACCAAAGAAAAG 57.671 29.630 0.00 0.00 0.00 2.27
233 234 9.061435 AGAAACATGAAACAAAACCAAAGAAAA 57.939 25.926 0.00 0.00 0.00 2.29
234 235 8.614469 AGAAACATGAAACAAAACCAAAGAAA 57.386 26.923 0.00 0.00 0.00 2.52
235 236 7.062839 CGAGAAACATGAAACAAAACCAAAGAA 59.937 33.333 0.00 0.00 0.00 2.52
236 237 6.529829 CGAGAAACATGAAACAAAACCAAAGA 59.470 34.615 0.00 0.00 0.00 2.52
237 238 6.310224 ACGAGAAACATGAAACAAAACCAAAG 59.690 34.615 0.00 0.00 0.00 2.77
238 239 6.159988 ACGAGAAACATGAAACAAAACCAAA 58.840 32.000 0.00 0.00 0.00 3.28
239 240 5.715070 ACGAGAAACATGAAACAAAACCAA 58.285 33.333 0.00 0.00 0.00 3.67
240 241 5.317733 ACGAGAAACATGAAACAAAACCA 57.682 34.783 0.00 0.00 0.00 3.67
241 242 6.641176 AAACGAGAAACATGAAACAAAACC 57.359 33.333 0.00 0.00 0.00 3.27
282 283 8.961294 AGAAAATCATGAACCACAATGAAAAA 57.039 26.923 0.00 0.00 0.00 1.94
283 284 8.961294 AAGAAAATCATGAACCACAATGAAAA 57.039 26.923 0.00 0.00 0.00 2.29
284 285 8.423349 AGAAGAAAATCATGAACCACAATGAAA 58.577 29.630 0.00 0.00 0.00 2.69
285 286 7.868922 CAGAAGAAAATCATGAACCACAATGAA 59.131 33.333 0.00 0.00 0.00 2.57
286 287 7.014518 ACAGAAGAAAATCATGAACCACAATGA 59.985 33.333 0.00 0.00 0.00 2.57
287 288 7.149973 ACAGAAGAAAATCATGAACCACAATG 58.850 34.615 0.00 0.00 0.00 2.82
288 289 7.294017 ACAGAAGAAAATCATGAACCACAAT 57.706 32.000 0.00 0.00 0.00 2.71
289 290 6.713762 ACAGAAGAAAATCATGAACCACAA 57.286 33.333 0.00 0.00 0.00 3.33
290 291 6.713762 AACAGAAGAAAATCATGAACCACA 57.286 33.333 0.00 0.00 0.00 4.17
291 292 7.492344 ACAAAACAGAAGAAAATCATGAACCAC 59.508 33.333 0.00 0.00 0.00 4.16
292 293 7.555087 ACAAAACAGAAGAAAATCATGAACCA 58.445 30.769 0.00 0.00 0.00 3.67
293 294 7.922811 AGACAAAACAGAAGAAAATCATGAACC 59.077 33.333 0.00 0.00 0.00 3.62
294 295 8.749499 CAGACAAAACAGAAGAAAATCATGAAC 58.251 33.333 0.00 0.00 0.00 3.18
295 296 8.469200 ACAGACAAAACAGAAGAAAATCATGAA 58.531 29.630 0.00 0.00 0.00 2.57
296 297 7.999679 ACAGACAAAACAGAAGAAAATCATGA 58.000 30.769 0.00 0.00 0.00 3.07
297 298 8.638685 AACAGACAAAACAGAAGAAAATCATG 57.361 30.769 0.00 0.00 0.00 3.07
298 299 9.657419 AAAACAGACAAAACAGAAGAAAATCAT 57.343 25.926 0.00 0.00 0.00 2.45
299 300 9.139174 GAAAACAGACAAAACAGAAGAAAATCA 57.861 29.630 0.00 0.00 0.00 2.57
300 301 8.595533 GGAAAACAGACAAAACAGAAGAAAATC 58.404 33.333 0.00 0.00 0.00 2.17
301 302 8.093927 TGGAAAACAGACAAAACAGAAGAAAAT 58.906 29.630 0.00 0.00 0.00 1.82
302 303 7.437748 TGGAAAACAGACAAAACAGAAGAAAA 58.562 30.769 0.00 0.00 0.00 2.29
303 304 6.987386 TGGAAAACAGACAAAACAGAAGAAA 58.013 32.000 0.00 0.00 0.00 2.52
304 305 6.582677 TGGAAAACAGACAAAACAGAAGAA 57.417 33.333 0.00 0.00 0.00 2.52
305 306 6.582677 TTGGAAAACAGACAAAACAGAAGA 57.417 33.333 0.00 0.00 0.00 2.87
314 315 9.832445 GGTAGAGATATATTGGAAAACAGACAA 57.168 33.333 0.00 0.00 0.00 3.18
315 316 9.213777 AGGTAGAGATATATTGGAAAACAGACA 57.786 33.333 0.00 0.00 0.00 3.41
342 343 9.243637 GCTAGAAATGACAATTGTGTGTAAAAA 57.756 29.630 17.58 0.00 38.41 1.94
343 344 7.865385 GGCTAGAAATGACAATTGTGTGTAAAA 59.135 33.333 17.58 0.00 38.41 1.52
344 345 7.230510 AGGCTAGAAATGACAATTGTGTGTAAA 59.769 33.333 17.58 0.00 38.41 2.01
345 346 6.714810 AGGCTAGAAATGACAATTGTGTGTAA 59.285 34.615 17.58 0.00 38.41 2.41
346 347 6.149308 CAGGCTAGAAATGACAATTGTGTGTA 59.851 38.462 17.58 0.00 38.41 2.90
347 348 5.048504 CAGGCTAGAAATGACAATTGTGTGT 60.049 40.000 17.58 0.00 38.41 3.72
348 349 5.396484 CAGGCTAGAAATGACAATTGTGTG 58.604 41.667 17.58 0.00 38.41 3.82
349 350 4.082571 GCAGGCTAGAAATGACAATTGTGT 60.083 41.667 17.58 1.09 42.10 3.72
350 351 4.082625 TGCAGGCTAGAAATGACAATTGTG 60.083 41.667 17.58 0.00 0.00 3.33
351 352 4.081406 TGCAGGCTAGAAATGACAATTGT 58.919 39.130 11.78 11.78 0.00 2.71
352 353 4.397103 TCTGCAGGCTAGAAATGACAATTG 59.603 41.667 15.13 3.24 0.00 2.32
353 354 4.592942 TCTGCAGGCTAGAAATGACAATT 58.407 39.130 15.13 0.00 0.00 2.32
354 355 4.197750 CTCTGCAGGCTAGAAATGACAAT 58.802 43.478 15.13 0.00 0.00 2.71
355 356 3.603532 CTCTGCAGGCTAGAAATGACAA 58.396 45.455 15.13 0.00 0.00 3.18
356 357 2.679059 GCTCTGCAGGCTAGAAATGACA 60.679 50.000 15.13 0.00 0.00 3.58
357 358 1.939255 GCTCTGCAGGCTAGAAATGAC 59.061 52.381 15.13 0.00 0.00 3.06
358 359 1.134280 GGCTCTGCAGGCTAGAAATGA 60.134 52.381 21.48 0.00 42.14 2.57
359 360 1.307097 GGCTCTGCAGGCTAGAAATG 58.693 55.000 21.48 0.00 42.14 2.32
360 361 3.796764 GGCTCTGCAGGCTAGAAAT 57.203 52.632 21.48 0.00 42.14 2.17
367 368 2.960170 CAACAAGGCTCTGCAGGC 59.040 61.111 15.13 15.77 45.92 4.85
368 369 2.960170 GCAACAAGGCTCTGCAGG 59.040 61.111 15.13 5.82 36.09 4.85
369 370 2.559840 CGCAACAAGGCTCTGCAG 59.440 61.111 7.63 7.63 35.78 4.41
370 371 2.979676 CCGCAACAAGGCTCTGCA 60.980 61.111 14.23 0.00 35.78 4.41
394 395 3.735037 CTAACCTCCCCGGCGCTTC 62.735 68.421 7.64 0.00 35.61 3.86
395 396 3.782443 CTAACCTCCCCGGCGCTT 61.782 66.667 7.64 0.00 35.61 4.68
398 399 2.842936 ATCCTAACCTCCCCGGCG 60.843 66.667 0.00 0.00 35.61 6.46
399 400 2.819284 CCATCCTAACCTCCCCGGC 61.819 68.421 0.00 0.00 35.61 6.13
400 401 0.105349 TACCATCCTAACCTCCCCGG 60.105 60.000 0.00 0.00 39.35 5.73
401 402 1.046204 GTACCATCCTAACCTCCCCG 58.954 60.000 0.00 0.00 0.00 5.73
402 403 1.344701 TGGTACCATCCTAACCTCCCC 60.345 57.143 11.60 0.00 34.23 4.81
403 404 2.185663 TGGTACCATCCTAACCTCCC 57.814 55.000 11.60 0.00 34.23 4.30
404 405 3.244112 CGAATGGTACCATCCTAACCTCC 60.244 52.174 27.49 7.71 35.31 4.30
405 406 3.244112 CCGAATGGTACCATCCTAACCTC 60.244 52.174 27.49 17.42 35.31 3.85
406 407 2.704065 CCGAATGGTACCATCCTAACCT 59.296 50.000 27.49 10.31 35.31 3.50
407 408 3.121738 CCGAATGGTACCATCCTAACC 57.878 52.381 27.49 11.41 35.31 2.85
465 466 0.848735 ATGTAGCCCATGTGGAGCAT 59.151 50.000 12.79 2.85 38.60 3.79
466 467 0.107066 CATGTAGCCCATGTGGAGCA 60.107 55.000 12.79 0.91 44.96 4.26
467 468 2.711711 CATGTAGCCCATGTGGAGC 58.288 57.895 0.00 2.67 44.96 4.70
474 475 2.846206 TCAGTCTTTCCATGTAGCCCAT 59.154 45.455 0.00 0.00 0.00 4.00
475 476 2.265367 TCAGTCTTTCCATGTAGCCCA 58.735 47.619 0.00 0.00 0.00 5.36
476 477 3.274288 CTTCAGTCTTTCCATGTAGCCC 58.726 50.000 0.00 0.00 0.00 5.19
477 478 3.686726 CACTTCAGTCTTTCCATGTAGCC 59.313 47.826 0.00 0.00 0.00 3.93
478 479 3.686726 CCACTTCAGTCTTTCCATGTAGC 59.313 47.826 0.00 0.00 0.00 3.58
479 480 3.686726 GCCACTTCAGTCTTTCCATGTAG 59.313 47.826 0.00 0.00 0.00 2.74
480 481 3.674997 GCCACTTCAGTCTTTCCATGTA 58.325 45.455 0.00 0.00 0.00 2.29
481 482 2.508526 GCCACTTCAGTCTTTCCATGT 58.491 47.619 0.00 0.00 0.00 3.21
482 483 1.466167 CGCCACTTCAGTCTTTCCATG 59.534 52.381 0.00 0.00 0.00 3.66
483 484 1.813513 CGCCACTTCAGTCTTTCCAT 58.186 50.000 0.00 0.00 0.00 3.41
484 485 0.884704 GCGCCACTTCAGTCTTTCCA 60.885 55.000 0.00 0.00 0.00 3.53
485 486 0.884704 TGCGCCACTTCAGTCTTTCC 60.885 55.000 4.18 0.00 0.00 3.13
486 487 0.944386 TTGCGCCACTTCAGTCTTTC 59.056 50.000 4.18 0.00 0.00 2.62
497 498 0.814457 TATGGTCCATTTTGCGCCAC 59.186 50.000 10.33 0.00 31.47 5.01
502 503 4.574013 CAGTCTCTCTATGGTCCATTTTGC 59.426 45.833 10.33 0.00 0.00 3.68
503 504 5.814705 GTCAGTCTCTCTATGGTCCATTTTG 59.185 44.000 10.33 1.42 0.00 2.44
507 508 4.214310 CAGTCAGTCTCTCTATGGTCCAT 58.786 47.826 9.88 9.88 0.00 3.41
515 516 3.330998 TCAGAACCCAGTCAGTCTCTCTA 59.669 47.826 0.00 0.00 0.00 2.43
527 528 5.560724 TCTTTTGGTATCTTCAGAACCCAG 58.439 41.667 6.00 2.06 32.08 4.45
566 567 5.573337 GCTCCATGCTTCAGTAATCTTTT 57.427 39.130 0.00 0.00 38.95 2.27
636 640 2.224079 GCAAGTCATCGTCAAGCAAAGA 59.776 45.455 0.00 0.00 0.00 2.52
641 645 1.225854 GCGCAAGTCATCGTCAAGC 60.226 57.895 0.30 0.00 41.68 4.01
674 678 4.536765 TGCTTTCTTTCCAGAGGAACTTT 58.463 39.130 0.00 0.00 41.87 2.66
694 701 0.031994 ACACGTGGGAATTTGCTTGC 59.968 50.000 21.57 0.00 0.00 4.01
776 789 3.450457 GGTCCAAATCCATTATTGTGCCA 59.550 43.478 0.00 0.00 0.00 4.92
831 844 1.134946 GCATGGAAAAGAATGGACCGG 59.865 52.381 0.00 0.00 0.00 5.28
1802 2286 6.327386 ACTACCAACATTATCCCAGTCATT 57.673 37.500 0.00 0.00 0.00 2.57
1807 2291 7.993183 ACTCAATAACTACCAACATTATCCCAG 59.007 37.037 0.00 0.00 0.00 4.45
1887 2377 0.323725 TTGCTTCCTCTGCCCATTCC 60.324 55.000 0.00 0.00 0.00 3.01
1932 2422 1.100510 GTTCCAAACCGGGCTATTCC 58.899 55.000 6.32 0.00 34.36 3.01
2040 2530 0.533491 TGTACTAGCCGCGGATGTTT 59.467 50.000 33.48 14.24 0.00 2.83
2352 2847 8.625467 ACACTAGGATCTTTTATAAGTTCCCT 57.375 34.615 15.49 11.45 45.49 4.20
2458 2953 7.160049 ACTTTGATATGTATCCTGAGCATGAG 58.840 38.462 0.00 0.00 31.71 2.90
2759 3283 2.649472 ATGCCATGGGGGATTCTGA 58.351 52.632 15.13 0.00 43.67 3.27
2765 3289 1.203288 ACAAAGAAATGCCATGGGGGA 60.203 47.619 15.13 0.00 40.01 4.81
2767 3291 1.901159 TCACAAAGAAATGCCATGGGG 59.099 47.619 15.13 0.00 37.18 4.96
2798 3322 3.499737 GACGACCGGCATGCTTGG 61.500 66.667 22.64 22.64 0.00 3.61
2942 3478 3.755112 TGGTCAACCATTCTACGAACA 57.245 42.857 0.00 0.00 42.01 3.18
2943 3479 4.062991 ACTTGGTCAACCATTCTACGAAC 58.937 43.478 2.03 0.00 46.97 3.95
2945 3481 4.345859 AACTTGGTCAACCATTCTACGA 57.654 40.909 2.03 0.00 46.97 3.43
3092 3700 6.770303 TGGTTGCGATATCTTATGGATTTCAA 59.230 34.615 0.34 0.00 33.80 2.69
3123 3731 5.400485 GCTTGCTTTTCATGTGTTAGAACTG 59.600 40.000 0.00 0.00 0.00 3.16
3138 3746 0.249031 GTGCGTGGAAGCTTGCTTTT 60.249 50.000 19.34 0.00 38.13 2.27
3223 3831 5.522824 GTCGGGGTAGACTAAATTTGACATC 59.477 44.000 0.00 0.00 38.09 3.06
3234 3842 1.890552 AGAGAGGTCGGGGTAGACTA 58.109 55.000 0.00 0.00 40.76 2.59
3235 3843 1.001282 AAGAGAGGTCGGGGTAGACT 58.999 55.000 0.00 0.00 40.76 3.24
3264 3872 0.802494 CGGACGGCTAAAACATTGCT 59.198 50.000 0.00 0.00 0.00 3.91
3289 3897 1.515304 GTCTCCAGAAGCGTCGCTC 60.515 63.158 21.98 13.83 38.25 5.03
3306 3914 1.128200 TGGGCATATTCAGCGTAGGT 58.872 50.000 0.00 0.00 41.48 3.08
3377 3986 6.036844 CCGGAATGACGATATACGAGATAGAA 59.963 42.308 0.00 0.00 45.77 2.10
3445 4057 1.742831 GTTAATTGTGCCGGAGATGCA 59.257 47.619 5.05 0.00 36.12 3.96


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

AutoCloner maintained by Alex Coulton.