Multiple sequence alignment - TraesCS4B01G143800

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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 TraesCS4B01G143800 chr4B 100.000 3617 0 0 1 3617 191787332 191790948 0.000000e+00 6680.0
1 TraesCS4B01G143800 chr3A 93.084 2993 156 24 646 3617 10290360 10293322 0.000000e+00 4333.0
2 TraesCS4B01G143800 chr4D 93.166 2956 151 23 681 3617 127927843 127930766 0.000000e+00 4292.0
3 TraesCS4B01G143800 chr4D 87.949 390 37 2 264 643 108233945 108233556 5.510000e-123 451.0
4 TraesCS4B01G143800 chr4D 87.565 386 38 4 264 640 10101971 10101587 4.290000e-119 438.0
5 TraesCS4B01G143800 chr4D 85.185 297 35 7 2813 3104 85627636 85627928 2.730000e-76 296.0
6 TraesCS4B01G143800 chr4A 93.813 1988 98 11 646 2611 440255529 440253545 0.000000e+00 2966.0
7 TraesCS4B01G143800 chr7A 88.156 667 72 6 2955 3617 8585251 8585914 0.000000e+00 787.0
8 TraesCS4B01G143800 chr7A 74.667 1350 246 52 1256 2581 126919188 126917911 8.960000e-141 510.0
9 TraesCS4B01G143800 chr2D 82.690 803 128 9 2817 3616 393209604 393210398 0.000000e+00 702.0
10 TraesCS4B01G143800 chr2D 98.872 266 3 0 1 266 49117277 49117542 3.270000e-130 475.0
11 TraesCS4B01G143800 chr2D 96.441 281 8 2 2 281 52336018 52335739 2.540000e-126 462.0
12 TraesCS4B01G143800 chr2D 87.760 384 33 8 264 640 50845522 50845898 1.540000e-118 436.0
13 TraesCS4B01G143800 chr5B 81.718 815 125 19 2819 3615 222296573 222295765 0.000000e+00 658.0
14 TraesCS4B01G143800 chr5B 79.044 816 149 19 2814 3617 288946391 288945586 1.140000e-149 540.0
15 TraesCS4B01G143800 chr5B 87.927 381 37 5 264 640 426057903 426058278 1.190000e-119 440.0
16 TraesCS4B01G143800 chr5B 87.599 379 42 3 264 640 426062358 426062733 5.550000e-118 435.0
17 TraesCS4B01G143800 chr5B 87.335 379 43 3 264 640 426060130 426060505 2.580000e-116 429.0
18 TraesCS4B01G143800 chr5B 84.722 72 8 3 2817 2887 262709667 262709598 6.480000e-08 69.4
19 TraesCS4B01G143800 chr2A 82.134 778 122 12 2817 3583 662749848 662750619 0.000000e+00 651.0
20 TraesCS4B01G143800 chr2A 98.876 267 3 0 1 267 500166940 500166674 9.090000e-131 477.0
21 TraesCS4B01G143800 chr7B 75.356 1335 266 43 1256 2581 86165885 86164605 5.200000e-163 584.0
22 TraesCS4B01G143800 chr7B 87.339 387 38 6 264 640 664211237 664211622 1.990000e-117 433.0
23 TraesCS4B01G143800 chr3B 79.730 814 138 17 2818 3616 446061636 446060835 6.780000e-157 564.0
24 TraesCS4B01G143800 chr7D 75.354 1270 239 46 1463 2718 124504799 124503590 8.830000e-151 544.0
25 TraesCS4B01G143800 chr7D 82.160 611 97 10 3011 3615 393941294 393940690 6.930000e-142 514.0
26 TraesCS4B01G143800 chr5D 98.868 265 3 0 1 265 96016909 96016645 1.180000e-129 473.0
27 TraesCS4B01G143800 chr5D 98.502 267 4 0 1 267 904180 904446 4.230000e-129 472.0
28 TraesCS4B01G143800 chr5D 96.454 282 7 3 1 281 130511561 130511282 2.540000e-126 462.0
29 TraesCS4B01G143800 chr2B 98.513 269 3 1 1 269 718857219 718857486 1.180000e-129 473.0
30 TraesCS4B01G143800 chr2B 71.940 531 144 5 3089 3617 245122185 245121658 2.250000e-32 150.0
31 TraesCS4B01G143800 chr2B 89.831 59 5 1 2816 2874 326850459 326850516 1.390000e-09 75.0
32 TraesCS4B01G143800 chr1D 98.868 265 3 0 1 265 40929732 40929468 1.180000e-129 473.0
33 TraesCS4B01G143800 chr1D 85.294 68 7 3 2818 2884 199626185 199626250 2.330000e-07 67.6
34 TraesCS4B01G143800 chr6D 98.507 268 3 1 1 267 112972542 112972275 4.230000e-129 472.0
35 TraesCS4B01G143800 chr6D 87.990 383 39 5 264 640 363279132 363278751 2.560000e-121 446.0
36 TraesCS4B01G143800 chr6D 79.114 158 21 8 2342 2493 410040018 410039867 8.270000e-17 99.0
37 TraesCS4B01G143800 chr3D 87.339 387 39 7 264 641 541350223 541350608 5.550000e-118 435.0
38 TraesCS4B01G143800 chr6B 78.344 157 24 6 2342 2493 616426899 616426748 3.850000e-15 93.5


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 TraesCS4B01G143800 chr4B 191787332 191790948 3616 False 6680.000000 6680 100.000000 1 3617 1 chr4B.!!$F1 3616
1 TraesCS4B01G143800 chr3A 10290360 10293322 2962 False 4333.000000 4333 93.084000 646 3617 1 chr3A.!!$F1 2971
2 TraesCS4B01G143800 chr4D 127927843 127930766 2923 False 4292.000000 4292 93.166000 681 3617 1 chr4D.!!$F2 2936
3 TraesCS4B01G143800 chr4A 440253545 440255529 1984 True 2966.000000 2966 93.813000 646 2611 1 chr4A.!!$R1 1965
4 TraesCS4B01G143800 chr7A 8585251 8585914 663 False 787.000000 787 88.156000 2955 3617 1 chr7A.!!$F1 662
5 TraesCS4B01G143800 chr7A 126917911 126919188 1277 True 510.000000 510 74.667000 1256 2581 1 chr7A.!!$R1 1325
6 TraesCS4B01G143800 chr2D 393209604 393210398 794 False 702.000000 702 82.690000 2817 3616 1 chr2D.!!$F3 799
7 TraesCS4B01G143800 chr5B 222295765 222296573 808 True 658.000000 658 81.718000 2819 3615 1 chr5B.!!$R1 796
8 TraesCS4B01G143800 chr5B 288945586 288946391 805 True 540.000000 540 79.044000 2814 3617 1 chr5B.!!$R3 803
9 TraesCS4B01G143800 chr5B 426057903 426062733 4830 False 434.666667 440 87.620333 264 640 3 chr5B.!!$F1 376
10 TraesCS4B01G143800 chr2A 662749848 662750619 771 False 651.000000 651 82.134000 2817 3583 1 chr2A.!!$F1 766
11 TraesCS4B01G143800 chr7B 86164605 86165885 1280 True 584.000000 584 75.356000 1256 2581 1 chr7B.!!$R1 1325
12 TraesCS4B01G143800 chr3B 446060835 446061636 801 True 564.000000 564 79.730000 2818 3616 1 chr3B.!!$R1 798
13 TraesCS4B01G143800 chr7D 124503590 124504799 1209 True 544.000000 544 75.354000 1463 2718 1 chr7D.!!$R1 1255
14 TraesCS4B01G143800 chr7D 393940690 393941294 604 True 514.000000 514 82.160000 3011 3615 1 chr7D.!!$R2 604

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
73 74 0.111089 CGAAAGCACTTCTGTGACGC 60.111 55.0 0.00 0.00 46.55 5.19 F
74 75 0.111089 GAAAGCACTTCTGTGACGCG 60.111 55.0 3.53 3.53 46.55 6.01 F
1335 2655 0.261991 CCTACCTGGTGGAGAGGCTA 59.738 60.0 12.27 0.00 34.79 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1138 1164 0.972983 CACCAGATCAGAGGGTCGGT 60.973 60.0 0.0 0.0 31.03 4.69 R
1555 3494 1.333177 GGCTCATGGACGAGTAGGAT 58.667 55.0 0.0 0.0 35.33 3.24 R
2626 6157 0.038526 GGGTCGTCCATATGCCGTAG 60.039 60.0 11.3 0.0 35.00 3.51 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.455786 CGATAGCTTAATGGCGTTCCG 59.544 52.381 0.00 0.00 37.29 4.30
21 22 2.480845 GATAGCTTAATGGCGTTCCGT 58.519 47.619 0.00 0.00 37.29 4.69
22 23 2.389962 TAGCTTAATGGCGTTCCGTT 57.610 45.000 0.00 0.00 43.70 4.44
23 24 2.389962 AGCTTAATGGCGTTCCGTTA 57.610 45.000 0.00 0.00 41.63 3.18
24 25 2.004733 AGCTTAATGGCGTTCCGTTAC 58.995 47.619 0.00 0.00 42.06 2.50
25 26 1.267186 GCTTAATGGCGTTCCGTTACG 60.267 52.381 0.00 0.00 42.06 3.18
35 36 2.266372 CCGTTACGGTGGATGCCA 59.734 61.111 16.53 0.00 42.73 4.92
43 44 3.118454 GTGGATGCCACGTGTCGG 61.118 66.667 15.65 0.00 44.95 4.79
44 45 3.621805 TGGATGCCACGTGTCGGT 61.622 61.111 15.65 0.00 0.00 4.69
45 46 2.813908 GGATGCCACGTGTCGGTC 60.814 66.667 15.65 4.01 0.00 4.79
46 47 2.048597 GATGCCACGTGTCGGTCA 60.049 61.111 15.65 4.62 0.00 4.02
47 48 2.357034 ATGCCACGTGTCGGTCAC 60.357 61.111 15.65 0.00 43.03 3.67
48 49 3.876589 ATGCCACGTGTCGGTCACC 62.877 63.158 15.65 0.00 43.51 4.02
50 51 3.612681 CCACGTGTCGGTCACCCT 61.613 66.667 15.65 0.00 43.51 4.34
51 52 2.420043 CACGTGTCGGTCACCCTT 59.580 61.111 7.58 0.00 43.51 3.95
52 53 1.954146 CACGTGTCGGTCACCCTTG 60.954 63.158 7.58 0.00 43.51 3.61
53 54 2.129146 ACGTGTCGGTCACCCTTGA 61.129 57.895 0.00 0.00 43.51 3.02
61 62 3.000815 GTCACCCTTGACGAAAGCA 57.999 52.632 0.00 0.00 42.86 3.91
62 63 0.586802 GTCACCCTTGACGAAAGCAC 59.413 55.000 0.00 0.00 42.86 4.40
63 64 0.468226 TCACCCTTGACGAAAGCACT 59.532 50.000 0.00 0.00 34.24 4.40
64 65 1.134220 TCACCCTTGACGAAAGCACTT 60.134 47.619 0.00 0.00 34.24 3.16
65 66 1.264288 CACCCTTGACGAAAGCACTTC 59.736 52.381 0.00 0.00 34.24 3.01
66 67 1.141053 ACCCTTGACGAAAGCACTTCT 59.859 47.619 0.00 0.00 34.24 2.85
67 68 1.532868 CCCTTGACGAAAGCACTTCTG 59.467 52.381 0.00 0.00 34.24 3.02
68 69 2.213499 CCTTGACGAAAGCACTTCTGT 58.787 47.619 0.00 0.00 34.24 3.41
69 70 2.032549 CCTTGACGAAAGCACTTCTGTG 60.033 50.000 0.00 0.00 46.37 3.66
70 71 2.595124 TGACGAAAGCACTTCTGTGA 57.405 45.000 0.00 0.00 46.55 3.58
71 72 2.201732 TGACGAAAGCACTTCTGTGAC 58.798 47.619 0.00 0.00 46.55 3.67
72 73 1.190323 GACGAAAGCACTTCTGTGACG 59.810 52.381 0.00 0.00 46.55 4.35
73 74 0.111089 CGAAAGCACTTCTGTGACGC 60.111 55.000 0.00 0.00 46.55 5.19
74 75 0.111089 GAAAGCACTTCTGTGACGCG 60.111 55.000 3.53 3.53 46.55 6.01
75 76 2.105960 AAAGCACTTCTGTGACGCGC 62.106 55.000 5.73 0.00 46.55 6.86
76 77 4.415501 GCACTTCTGTGACGCGCG 62.416 66.667 30.96 30.96 46.55 6.86
77 78 2.729491 CACTTCTGTGACGCGCGA 60.729 61.111 39.36 13.15 46.55 5.87
78 79 2.088763 CACTTCTGTGACGCGCGAT 61.089 57.895 39.36 21.24 46.55 4.58
79 80 1.372997 ACTTCTGTGACGCGCGATT 60.373 52.632 39.36 16.45 0.00 3.34
80 81 0.944311 ACTTCTGTGACGCGCGATTT 60.944 50.000 39.36 15.50 0.00 2.17
81 82 0.989164 CTTCTGTGACGCGCGATTTA 59.011 50.000 39.36 18.32 0.00 1.40
82 83 1.588404 CTTCTGTGACGCGCGATTTAT 59.412 47.619 39.36 14.54 0.00 1.40
83 84 1.197055 TCTGTGACGCGCGATTTATC 58.803 50.000 39.36 23.49 0.00 1.75
96 97 4.715520 CGATTTATCGTCATGGAAGTGG 57.284 45.455 4.03 0.00 44.74 4.00
97 98 4.368315 CGATTTATCGTCATGGAAGTGGA 58.632 43.478 4.03 0.00 44.74 4.02
98 99 4.209288 CGATTTATCGTCATGGAAGTGGAC 59.791 45.833 4.03 0.00 44.74 4.02
99 100 4.545208 TTTATCGTCATGGAAGTGGACA 57.455 40.909 0.00 0.00 0.00 4.02
100 101 2.386661 ATCGTCATGGAAGTGGACAC 57.613 50.000 0.00 0.00 0.00 3.67
101 102 1.338107 TCGTCATGGAAGTGGACACT 58.662 50.000 0.00 0.00 44.94 3.55
110 111 3.914984 AGTGGACACTTCCGTGATG 57.085 52.632 0.00 0.00 46.37 3.07
111 112 1.338107 AGTGGACACTTCCGTGATGA 58.662 50.000 0.00 0.00 46.37 2.92
112 113 1.902508 AGTGGACACTTCCGTGATGAT 59.097 47.619 0.00 0.00 46.37 2.45
113 114 3.096852 AGTGGACACTTCCGTGATGATA 58.903 45.455 0.00 0.00 46.37 2.15
114 115 3.513912 AGTGGACACTTCCGTGATGATAA 59.486 43.478 0.00 0.00 46.37 1.75
115 116 4.162320 AGTGGACACTTCCGTGATGATAAT 59.838 41.667 0.00 0.00 46.37 1.28
116 117 4.876107 GTGGACACTTCCGTGATGATAATT 59.124 41.667 0.00 0.00 46.37 1.40
117 118 5.354234 GTGGACACTTCCGTGATGATAATTT 59.646 40.000 0.00 0.00 46.37 1.82
118 119 5.943416 TGGACACTTCCGTGATGATAATTTT 59.057 36.000 0.00 0.00 46.37 1.82
119 120 6.128035 TGGACACTTCCGTGATGATAATTTTG 60.128 38.462 0.00 0.00 46.37 2.44
120 121 6.194796 ACACTTCCGTGATGATAATTTTGG 57.805 37.500 0.00 0.00 43.97 3.28
121 122 5.710099 ACACTTCCGTGATGATAATTTTGGT 59.290 36.000 0.00 0.00 43.97 3.67
122 123 6.882140 ACACTTCCGTGATGATAATTTTGGTA 59.118 34.615 0.00 0.00 43.97 3.25
123 124 7.392113 ACACTTCCGTGATGATAATTTTGGTAA 59.608 33.333 0.00 0.00 43.97 2.85
124 125 8.405531 CACTTCCGTGATGATAATTTTGGTAAT 58.594 33.333 0.00 0.00 43.97 1.89
125 126 8.405531 ACTTCCGTGATGATAATTTTGGTAATG 58.594 33.333 0.00 0.00 0.00 1.90
126 127 7.873719 TCCGTGATGATAATTTTGGTAATGT 57.126 32.000 0.00 0.00 0.00 2.71
127 128 7.925993 TCCGTGATGATAATTTTGGTAATGTC 58.074 34.615 0.00 0.00 0.00 3.06
128 129 7.554476 TCCGTGATGATAATTTTGGTAATGTCA 59.446 33.333 0.00 0.00 0.00 3.58
129 130 8.352201 CCGTGATGATAATTTTGGTAATGTCAT 58.648 33.333 0.00 0.00 0.00 3.06
130 131 9.172820 CGTGATGATAATTTTGGTAATGTCATG 57.827 33.333 0.00 0.00 0.00 3.07
131 132 9.467258 GTGATGATAATTTTGGTAATGTCATGG 57.533 33.333 0.00 0.00 0.00 3.66
132 133 9.418839 TGATGATAATTTTGGTAATGTCATGGA 57.581 29.630 0.00 0.00 0.00 3.41
148 149 2.433868 TGGAACACTTCTACGACAGC 57.566 50.000 0.00 0.00 0.00 4.40
149 150 1.684450 TGGAACACTTCTACGACAGCA 59.316 47.619 0.00 0.00 0.00 4.41
150 151 2.059541 GGAACACTTCTACGACAGCAC 58.940 52.381 0.00 0.00 0.00 4.40
151 152 2.545113 GGAACACTTCTACGACAGCACA 60.545 50.000 0.00 0.00 0.00 4.57
152 153 3.318017 GAACACTTCTACGACAGCACAT 58.682 45.455 0.00 0.00 0.00 3.21
153 154 2.677199 ACACTTCTACGACAGCACATG 58.323 47.619 0.00 0.00 0.00 3.21
155 156 3.254903 ACACTTCTACGACAGCACATGTA 59.745 43.478 0.00 0.00 44.17 2.29
156 157 4.082190 ACACTTCTACGACAGCACATGTAT 60.082 41.667 0.00 0.00 44.17 2.29
157 158 4.266265 CACTTCTACGACAGCACATGTATG 59.734 45.833 0.00 3.11 44.17 2.39
158 159 4.157840 ACTTCTACGACAGCACATGTATGA 59.842 41.667 15.20 0.00 44.17 2.15
159 160 4.028852 TCTACGACAGCACATGTATGAC 57.971 45.455 15.20 9.20 44.17 3.06
160 161 3.694566 TCTACGACAGCACATGTATGACT 59.305 43.478 15.20 1.35 44.17 3.41
161 162 4.879545 TCTACGACAGCACATGTATGACTA 59.120 41.667 15.20 5.18 44.17 2.59
162 163 4.655762 ACGACAGCACATGTATGACTAT 57.344 40.909 15.20 0.00 44.17 2.12
163 164 4.611943 ACGACAGCACATGTATGACTATC 58.388 43.478 15.20 2.34 44.17 2.08
164 165 4.339530 ACGACAGCACATGTATGACTATCT 59.660 41.667 15.20 0.00 44.17 1.98
165 166 5.163509 ACGACAGCACATGTATGACTATCTT 60.164 40.000 15.20 0.00 44.17 2.40
166 167 5.174579 CGACAGCACATGTATGACTATCTTG 59.825 44.000 15.20 0.00 44.17 3.02
167 168 6.225981 ACAGCACATGTATGACTATCTTGA 57.774 37.500 15.20 0.00 41.60 3.02
168 169 6.824553 ACAGCACATGTATGACTATCTTGAT 58.175 36.000 15.20 0.00 41.60 2.57
169 170 7.278135 ACAGCACATGTATGACTATCTTGATT 58.722 34.615 15.20 0.00 41.60 2.57
170 171 7.440556 ACAGCACATGTATGACTATCTTGATTC 59.559 37.037 15.20 0.00 41.60 2.52
171 172 7.656542 CAGCACATGTATGACTATCTTGATTCT 59.343 37.037 0.00 0.00 0.00 2.40
172 173 7.656542 AGCACATGTATGACTATCTTGATTCTG 59.343 37.037 0.00 0.00 0.00 3.02
173 174 7.440556 GCACATGTATGACTATCTTGATTCTGT 59.559 37.037 0.00 0.00 0.00 3.41
174 175 8.976471 CACATGTATGACTATCTTGATTCTGTC 58.024 37.037 0.00 0.00 0.00 3.51
175 176 8.699130 ACATGTATGACTATCTTGATTCTGTCA 58.301 33.333 0.00 12.36 38.52 3.58
176 177 9.708092 CATGTATGACTATCTTGATTCTGTCAT 57.292 33.333 19.47 19.47 44.19 3.06
184 185 9.823647 ACTATCTTGATTCTGTCATAAAATCGT 57.176 29.630 0.00 0.00 36.54 3.73
186 187 8.722480 ATCTTGATTCTGTCATAAAATCGTCA 57.278 30.769 0.00 0.00 36.54 4.35
187 188 8.722480 TCTTGATTCTGTCATAAAATCGTCAT 57.278 30.769 0.00 0.00 36.54 3.06
188 189 8.606602 TCTTGATTCTGTCATAAAATCGTCATG 58.393 33.333 0.00 0.00 36.54 3.07
189 190 7.250445 TGATTCTGTCATAAAATCGTCATGG 57.750 36.000 0.00 0.00 33.13 3.66
190 191 7.047271 TGATTCTGTCATAAAATCGTCATGGA 58.953 34.615 0.00 0.00 33.13 3.41
191 192 7.716560 TGATTCTGTCATAAAATCGTCATGGAT 59.283 33.333 0.00 0.00 33.13 3.41
192 193 6.849588 TCTGTCATAAAATCGTCATGGATG 57.150 37.500 0.00 0.00 0.00 3.51
193 194 6.348498 TCTGTCATAAAATCGTCATGGATGT 58.652 36.000 0.00 0.00 0.00 3.06
194 195 7.496747 TCTGTCATAAAATCGTCATGGATGTA 58.503 34.615 0.00 0.00 0.00 2.29
195 196 7.438160 TCTGTCATAAAATCGTCATGGATGTAC 59.562 37.037 0.00 0.00 0.00 2.90
196 197 7.044798 TGTCATAAAATCGTCATGGATGTACA 58.955 34.615 0.00 0.00 0.00 2.90
197 198 7.714813 TGTCATAAAATCGTCATGGATGTACAT 59.285 33.333 8.43 8.43 0.00 2.29
199 200 4.818534 AAATCGTCATGGATGTACATGC 57.181 40.909 19.53 19.53 46.02 4.06
200 201 2.977772 TCGTCATGGATGTACATGCA 57.022 45.000 29.03 29.03 46.02 3.96
208 209 5.918426 ATGGATGTACATGCATGACAAAA 57.082 34.783 33.87 18.90 46.05 2.44
209 210 5.718724 TGGATGTACATGCATGACAAAAA 57.281 34.783 32.75 16.53 34.14 1.94
225 226 2.228138 AAAAACGCGACCTACTGTGA 57.772 45.000 15.93 0.00 0.00 3.58
226 227 1.494824 AAAACGCGACCTACTGTGAC 58.505 50.000 15.93 0.00 0.00 3.67
227 228 0.386476 AAACGCGACCTACTGTGACA 59.614 50.000 15.93 0.00 0.00 3.58
228 229 0.386476 AACGCGACCTACTGTGACAA 59.614 50.000 15.93 0.00 0.00 3.18
229 230 0.386476 ACGCGACCTACTGTGACAAA 59.614 50.000 15.93 0.00 0.00 2.83
230 231 0.782384 CGCGACCTACTGTGACAAAC 59.218 55.000 0.00 0.00 0.00 2.93
231 232 1.860676 GCGACCTACTGTGACAAACA 58.139 50.000 0.00 0.00 37.22 2.83
232 233 2.413837 GCGACCTACTGTGACAAACAT 58.586 47.619 0.00 0.00 38.39 2.71
233 234 2.157668 GCGACCTACTGTGACAAACATG 59.842 50.000 0.00 0.00 38.39 3.21
234 235 3.390135 CGACCTACTGTGACAAACATGT 58.610 45.455 0.00 0.00 38.39 3.21
235 236 4.552355 CGACCTACTGTGACAAACATGTA 58.448 43.478 0.00 0.00 38.39 2.29
236 237 5.168569 CGACCTACTGTGACAAACATGTAT 58.831 41.667 0.00 0.00 38.39 2.29
237 238 5.288712 CGACCTACTGTGACAAACATGTATC 59.711 44.000 0.00 0.00 38.39 2.24
238 239 6.109156 ACCTACTGTGACAAACATGTATCA 57.891 37.500 0.00 0.59 38.39 2.15
239 240 6.711277 ACCTACTGTGACAAACATGTATCAT 58.289 36.000 0.00 0.00 38.39 2.45
240 241 6.818644 ACCTACTGTGACAAACATGTATCATC 59.181 38.462 0.00 0.00 38.39 2.92
241 242 6.818142 CCTACTGTGACAAACATGTATCATCA 59.182 38.462 0.00 0.00 38.39 3.07
242 243 6.486253 ACTGTGACAAACATGTATCATCAC 57.514 37.500 18.50 18.50 38.39 3.06
243 244 5.997129 ACTGTGACAAACATGTATCATCACA 59.003 36.000 23.08 23.08 41.85 3.58
244 245 6.484818 TGTGACAAACATGTATCATCACAG 57.515 37.500 21.77 1.77 39.87 3.66
245 246 6.229733 TGTGACAAACATGTATCATCACAGA 58.770 36.000 21.77 8.64 39.87 3.41
246 247 6.709846 TGTGACAAACATGTATCATCACAGAA 59.290 34.615 21.77 8.14 39.87 3.02
247 248 7.095102 TGTGACAAACATGTATCATCACAGAAG 60.095 37.037 21.77 0.00 39.87 2.85
248 249 6.936335 TGACAAACATGTATCATCACAGAAGT 59.064 34.615 0.00 0.00 0.00 3.01
250 251 6.712095 ACAAACATGTATCATCACAGAAGTGT 59.288 34.615 0.00 0.00 46.01 3.55
251 252 7.877612 ACAAACATGTATCATCACAGAAGTGTA 59.122 33.333 0.00 0.00 46.01 2.90
252 253 8.886719 CAAACATGTATCATCACAGAAGTGTAT 58.113 33.333 0.00 0.00 46.01 2.29
253 254 9.453572 AAACATGTATCATCACAGAAGTGTATT 57.546 29.630 0.00 0.00 46.01 1.89
254 255 9.453572 AACATGTATCATCACAGAAGTGTATTT 57.546 29.630 0.00 0.00 46.01 1.40
255 256 9.453572 ACATGTATCATCACAGAAGTGTATTTT 57.546 29.630 0.00 0.00 46.01 1.82
283 286 1.801512 CTGACGATGCGCTTCGACA 60.802 57.895 40.83 37.31 41.62 4.35
293 296 1.216710 GCTTCGACAGGGGTCAGAG 59.783 63.158 0.00 0.00 44.54 3.35
340 343 0.476338 CCATCGGAGGAGAGGAGAGA 59.524 60.000 0.00 0.00 0.00 3.10
349 352 2.520741 GAGGAGAGAGAGGGGCGG 60.521 72.222 0.00 0.00 0.00 6.13
380 383 4.308458 CGGTGGGAACAGTGCGGA 62.308 66.667 0.00 0.00 44.46 5.54
413 416 1.763545 GAGTGGGAGGGGAGTTATGAC 59.236 57.143 0.00 0.00 0.00 3.06
553 556 0.589223 TGCTTTAAGTTTCGTGCGGG 59.411 50.000 0.00 0.00 0.00 6.13
554 557 0.728129 GCTTTAAGTTTCGTGCGGGC 60.728 55.000 0.00 0.00 0.00 6.13
557 560 0.606944 TTAAGTTTCGTGCGGGCCAT 60.607 50.000 4.39 0.00 0.00 4.40
601 604 0.827507 AAACAGGCCACACACATCCC 60.828 55.000 5.01 0.00 0.00 3.85
602 605 2.747460 CAGGCCACACACATCCCG 60.747 66.667 5.01 0.00 0.00 5.14
603 606 3.249189 AGGCCACACACATCCCGT 61.249 61.111 5.01 0.00 0.00 5.28
604 607 1.916273 AGGCCACACACATCCCGTA 60.916 57.895 5.01 0.00 0.00 4.02
618 621 3.697747 CGTACGGGGGTGCTTGGA 61.698 66.667 7.57 0.00 0.00 3.53
619 622 2.046604 GTACGGGGGTGCTTGGAC 60.047 66.667 0.00 0.00 0.00 4.02
626 629 1.604593 GGGTGCTTGGACTGCATGT 60.605 57.895 0.00 0.00 42.69 3.21
630 633 2.998279 GCTTGGACTGCATGTGGGC 61.998 63.158 0.00 0.00 0.00 5.36
782 787 9.360093 GTATATTGCTGGAGTAGTAATTAGCTG 57.640 37.037 0.00 0.00 41.25 4.24
829 834 5.358160 GGTCAGACTATTCCAAATCCAAAGG 59.642 44.000 0.00 0.00 0.00 3.11
851 856 5.780793 AGGTAGAAAAGAGAGGAAAGCAGTA 59.219 40.000 0.00 0.00 0.00 2.74
853 858 7.037945 AGGTAGAAAAGAGAGGAAAGCAGTAAT 60.038 37.037 0.00 0.00 0.00 1.89
872 877 7.437748 CAGTAATGTTCCTAGACAGAATAGGG 58.562 42.308 0.00 0.00 40.30 3.53
895 900 5.661312 GGAGCAAATAATTACTTCCCCCTTT 59.339 40.000 0.00 0.00 0.00 3.11
902 907 3.639672 TTACTTCCCCCTTTCGAATCC 57.360 47.619 0.00 0.00 0.00 3.01
954 961 6.660521 TGTATGCAAAAAGGATGATGTCTCTT 59.339 34.615 0.00 0.00 0.00 2.85
975 982 0.383231 CCTCCATTCGGCAGCAAATC 59.617 55.000 0.00 0.00 0.00 2.17
1017 1040 3.643320 TGATAATGGAAGGAGATCTGCGT 59.357 43.478 8.74 5.34 0.00 5.24
1024 1047 0.753479 AGGAGATCTGCGTGGTCGAT 60.753 55.000 8.74 0.00 39.71 3.59
1047 1073 1.884444 GGAGGCGAGAGAGAAACGT 59.116 57.895 0.00 0.00 0.00 3.99
1075 1101 4.776322 CCAGTTCGGCCGCCATCA 62.776 66.667 23.51 0.00 0.00 3.07
1090 1116 3.813724 CGCCATCATCATCATCTTCTTGT 59.186 43.478 0.00 0.00 0.00 3.16
1309 2629 2.306255 GAAGCCCACGCGATTCCCTA 62.306 60.000 15.93 0.00 41.18 3.53
1335 2655 0.261991 CCTACCTGGTGGAGAGGCTA 59.738 60.000 12.27 0.00 34.79 3.93
1339 2659 0.618968 CCTGGTGGAGAGGCTAAGGT 60.619 60.000 0.00 0.00 34.57 3.50
1476 2916 3.517602 TCATACATGCAAGTACGTGGTC 58.482 45.455 10.87 0.00 0.00 4.02
1560 3499 2.125326 CCTCACCGACCGCATCCTA 61.125 63.158 0.00 0.00 0.00 2.94
1599 4200 0.043940 AGATGGAGGGCCTCTTCTGT 59.956 55.000 31.39 13.03 34.31 3.41
1808 4740 0.878961 ACCGTGTTTCTTCTCACCGC 60.879 55.000 0.00 0.00 0.00 5.68
1815 4747 2.797866 TTCTTCTCACCGCGAGCGTC 62.798 60.000 8.23 0.00 41.98 5.19
1859 4791 3.680786 CTGCGACGAGGACCACCA 61.681 66.667 0.00 0.00 38.94 4.17
2097 5029 3.502455 CTCGGCATGCATGTGCGT 61.502 61.111 26.79 0.00 45.97 5.24
2136 5068 1.819632 GCCGCCCGAGATCATGTTT 60.820 57.895 0.00 0.00 0.00 2.83
2235 5203 4.311606 AGGCGAAGAAGAAGAAGAAGAAC 58.688 43.478 0.00 0.00 0.00 3.01
2597 6128 3.722295 CACGCATCCGCAACCGTT 61.722 61.111 0.00 0.00 38.40 4.44
2614 6145 1.156736 GTTATTGCTCACGTGCCAGT 58.843 50.000 11.67 9.71 0.00 4.00
2628 6159 4.872574 CAGTAGGGGGCCGGGCTA 62.873 72.222 28.80 9.89 0.00 3.93
2708 6239 1.719600 CTTGGTCTCAAGCTCTTCGG 58.280 55.000 0.00 0.00 43.10 4.30
2731 6262 5.181433 GGTTGAGCTAAAAACTTACTCCAGG 59.819 44.000 0.00 0.00 0.00 4.45
2796 6327 4.766891 GGAAATCATTTCACCACTCTTCCA 59.233 41.667 12.27 0.00 41.43 3.53
2806 6337 1.238439 CACTCTTCCACCAAACGCAT 58.762 50.000 0.00 0.00 0.00 4.73
2807 6338 1.197721 CACTCTTCCACCAAACGCATC 59.802 52.381 0.00 0.00 0.00 3.91
2874 6405 1.609208 AAAGCCATCAGACAGCGTTT 58.391 45.000 0.00 0.00 0.00 3.60
2894 6425 2.653726 TCAGACAAACCACACAGCAAT 58.346 42.857 0.00 0.00 0.00 3.56
2900 6443 0.832983 AACCACACAGCAATGGCCAT 60.833 50.000 14.09 14.09 42.56 4.40
2902 6445 1.537814 CCACACAGCAATGGCCATGT 61.538 55.000 21.63 12.01 42.56 3.21
3003 6557 6.472686 AGATAAGAGCTAACACCGAAGAAT 57.527 37.500 0.00 0.00 0.00 2.40
3023 6577 1.589803 ACACGAAGCCACCAACTAAC 58.410 50.000 0.00 0.00 0.00 2.34
3060 6615 4.026744 AGACAACTATTCAGCTGGCTCTA 58.973 43.478 15.13 0.00 29.79 2.43
3126 6681 0.391263 ATCAAAAGCGTCCCGGTCTC 60.391 55.000 0.00 0.00 36.27 3.36
3145 6702 3.637229 TCTCCCGTCTTAGTCAATGATCC 59.363 47.826 0.00 0.00 0.00 3.36
3152 6709 5.011125 CGTCTTAGTCAATGATCCCCACTAT 59.989 44.000 0.00 0.00 0.00 2.12
3296 6855 0.035725 GCCGCTTAGTAACCCCAACT 60.036 55.000 0.00 0.00 0.00 3.16
3322 6881 4.083862 GGCGAGGACCCGAAGCTT 62.084 66.667 0.00 0.00 0.00 3.74
3363 6922 1.356124 AGACACCTGAAGCCATGACT 58.644 50.000 0.00 0.00 0.00 3.41
3378 6937 5.539955 AGCCATGACTTAAAACAACTCCAAT 59.460 36.000 0.00 0.00 0.00 3.16
3399 6958 1.966451 AGTTTAGCCAGCGCACACC 60.966 57.895 11.47 0.00 37.52 4.16
3444 7004 1.676635 AAGGCATCGCACAGTGCAT 60.677 52.632 25.19 14.30 45.36 3.96
3552 7112 3.322254 CACTTTAGGAGGGATACGAGCAT 59.678 47.826 0.00 0.00 37.60 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.583276 GACCGACACGTGGCATCCA 62.583 63.158 23.63 0.00 0.00 3.41
28 29 2.813908 GACCGACACGTGGCATCC 60.814 66.667 23.63 5.09 0.00 3.51
29 30 2.048597 TGACCGACACGTGGCATC 60.049 61.111 23.63 18.45 0.00 3.91
30 31 2.357034 GTGACCGACACGTGGCAT 60.357 61.111 23.63 8.84 39.78 4.40
44 45 0.468226 AGTGCTTTCGTCAAGGGTGA 59.532 50.000 0.00 0.00 32.37 4.02
45 46 1.264288 GAAGTGCTTTCGTCAAGGGTG 59.736 52.381 0.00 0.00 32.37 4.61
46 47 1.141053 AGAAGTGCTTTCGTCAAGGGT 59.859 47.619 0.00 0.00 40.86 4.34
47 48 1.532868 CAGAAGTGCTTTCGTCAAGGG 59.467 52.381 0.00 0.00 40.86 3.95
48 49 2.032549 CACAGAAGTGCTTTCGTCAAGG 60.033 50.000 0.00 0.00 40.86 3.61
49 50 2.866156 TCACAGAAGTGCTTTCGTCAAG 59.134 45.455 0.00 0.00 45.49 3.02
50 51 2.607635 GTCACAGAAGTGCTTTCGTCAA 59.392 45.455 0.00 0.00 45.49 3.18
51 52 2.201732 GTCACAGAAGTGCTTTCGTCA 58.798 47.619 0.00 0.00 45.49 4.35
52 53 1.190323 CGTCACAGAAGTGCTTTCGTC 59.810 52.381 0.00 0.00 45.49 4.20
53 54 1.209128 CGTCACAGAAGTGCTTTCGT 58.791 50.000 0.00 0.00 45.49 3.85
54 55 0.111089 GCGTCACAGAAGTGCTTTCG 60.111 55.000 0.00 0.00 45.49 3.46
55 56 0.111089 CGCGTCACAGAAGTGCTTTC 60.111 55.000 0.00 0.00 45.49 2.62
56 57 1.934463 CGCGTCACAGAAGTGCTTT 59.066 52.632 0.00 0.00 45.49 3.51
57 58 2.598632 GCGCGTCACAGAAGTGCTT 61.599 57.895 8.43 0.00 45.49 3.91
58 59 3.038417 GCGCGTCACAGAAGTGCT 61.038 61.111 8.43 0.00 45.49 4.40
59 60 4.415501 CGCGCGTCACAGAAGTGC 62.416 66.667 24.19 8.13 45.49 4.40
61 62 0.944311 AAATCGCGCGTCACAGAAGT 60.944 50.000 30.98 4.30 0.00 3.01
62 63 0.989164 TAAATCGCGCGTCACAGAAG 59.011 50.000 30.98 0.00 0.00 2.85
63 64 1.586578 GATAAATCGCGCGTCACAGAA 59.413 47.619 30.98 8.92 0.00 3.02
64 65 1.197055 GATAAATCGCGCGTCACAGA 58.803 50.000 30.98 9.80 0.00 3.41
65 66 0.112137 CGATAAATCGCGCGTCACAG 60.112 55.000 30.98 12.40 43.84 3.66
66 67 1.914389 CGATAAATCGCGCGTCACA 59.086 52.632 30.98 11.14 43.84 3.58
67 68 4.752565 CGATAAATCGCGCGTCAC 57.247 55.556 30.98 14.60 43.84 3.67
76 77 5.006746 GTGTCCACTTCCATGACGATAAATC 59.993 44.000 0.00 0.00 0.00 2.17
77 78 4.876107 GTGTCCACTTCCATGACGATAAAT 59.124 41.667 0.00 0.00 0.00 1.40
78 79 4.020573 AGTGTCCACTTCCATGACGATAAA 60.021 41.667 0.00 0.00 38.83 1.40
79 80 3.513912 AGTGTCCACTTCCATGACGATAA 59.486 43.478 0.00 0.00 38.83 1.75
80 81 3.096852 AGTGTCCACTTCCATGACGATA 58.903 45.455 0.00 0.00 38.83 2.92
81 82 1.902508 AGTGTCCACTTCCATGACGAT 59.097 47.619 0.00 0.00 38.83 3.73
82 83 1.338107 AGTGTCCACTTCCATGACGA 58.662 50.000 0.00 0.00 38.83 4.20
83 84 3.914984 AGTGTCCACTTCCATGACG 57.085 52.632 0.00 0.00 38.83 4.35
100 101 8.405531 ACATTACCAAAATTATCATCACGGAAG 58.594 33.333 0.00 0.00 0.00 3.46
101 102 8.287439 ACATTACCAAAATTATCATCACGGAA 57.713 30.769 0.00 0.00 0.00 4.30
102 103 7.554476 TGACATTACCAAAATTATCATCACGGA 59.446 33.333 0.00 0.00 0.00 4.69
103 104 7.702386 TGACATTACCAAAATTATCATCACGG 58.298 34.615 0.00 0.00 0.00 4.94
104 105 9.172820 CATGACATTACCAAAATTATCATCACG 57.827 33.333 0.00 0.00 0.00 4.35
105 106 9.467258 CCATGACATTACCAAAATTATCATCAC 57.533 33.333 0.00 0.00 0.00 3.06
106 107 9.418839 TCCATGACATTACCAAAATTATCATCA 57.581 29.630 0.00 0.00 0.00 3.07
109 110 9.029368 TGTTCCATGACATTACCAAAATTATCA 57.971 29.630 0.00 0.00 0.00 2.15
110 111 9.301153 GTGTTCCATGACATTACCAAAATTATC 57.699 33.333 0.00 0.00 0.00 1.75
111 112 9.034800 AGTGTTCCATGACATTACCAAAATTAT 57.965 29.630 0.00 0.00 0.00 1.28
112 113 8.415950 AGTGTTCCATGACATTACCAAAATTA 57.584 30.769 0.00 0.00 0.00 1.40
113 114 7.301868 AGTGTTCCATGACATTACCAAAATT 57.698 32.000 0.00 0.00 0.00 1.82
114 115 6.916360 AGTGTTCCATGACATTACCAAAAT 57.084 33.333 0.00 0.00 0.00 1.82
115 116 6.549364 AGAAGTGTTCCATGACATTACCAAAA 59.451 34.615 0.00 0.00 0.00 2.44
116 117 6.068010 AGAAGTGTTCCATGACATTACCAAA 58.932 36.000 0.00 0.00 0.00 3.28
117 118 5.630121 AGAAGTGTTCCATGACATTACCAA 58.370 37.500 0.00 0.00 0.00 3.67
118 119 5.241403 AGAAGTGTTCCATGACATTACCA 57.759 39.130 0.00 0.00 0.00 3.25
119 120 5.291128 CGTAGAAGTGTTCCATGACATTACC 59.709 44.000 0.00 0.00 0.00 2.85
120 121 6.034683 GTCGTAGAAGTGTTCCATGACATTAC 59.965 42.308 0.00 0.00 39.69 1.89
121 122 6.097356 GTCGTAGAAGTGTTCCATGACATTA 58.903 40.000 0.00 0.00 39.69 1.90
122 123 4.929808 GTCGTAGAAGTGTTCCATGACATT 59.070 41.667 0.00 0.00 39.69 2.71
123 124 4.021456 TGTCGTAGAAGTGTTCCATGACAT 60.021 41.667 6.17 0.00 40.63 3.06
124 125 3.319689 TGTCGTAGAAGTGTTCCATGACA 59.680 43.478 6.17 6.17 42.33 3.58
125 126 3.909430 TGTCGTAGAAGTGTTCCATGAC 58.091 45.455 0.00 1.80 39.69 3.06
126 127 3.614150 GCTGTCGTAGAAGTGTTCCATGA 60.614 47.826 0.00 0.00 39.69 3.07
127 128 2.668457 GCTGTCGTAGAAGTGTTCCATG 59.332 50.000 0.00 0.00 39.69 3.66
128 129 2.299013 TGCTGTCGTAGAAGTGTTCCAT 59.701 45.455 0.00 0.00 39.69 3.41
129 130 1.684450 TGCTGTCGTAGAAGTGTTCCA 59.316 47.619 0.00 0.00 39.69 3.53
130 131 2.059541 GTGCTGTCGTAGAAGTGTTCC 58.940 52.381 0.00 0.00 39.69 3.62
131 132 2.739292 TGTGCTGTCGTAGAAGTGTTC 58.261 47.619 0.00 0.00 39.69 3.18
132 133 2.882927 TGTGCTGTCGTAGAAGTGTT 57.117 45.000 0.00 0.00 39.69 3.32
133 134 2.035961 ACATGTGCTGTCGTAGAAGTGT 59.964 45.455 0.00 0.00 39.69 3.55
134 135 2.677199 ACATGTGCTGTCGTAGAAGTG 58.323 47.619 0.00 0.00 39.69 3.16
135 136 4.157840 TCATACATGTGCTGTCGTAGAAGT 59.842 41.667 9.11 0.00 39.69 3.01
136 137 4.500837 GTCATACATGTGCTGTCGTAGAAG 59.499 45.833 9.11 0.00 39.69 2.85
137 138 4.157840 AGTCATACATGTGCTGTCGTAGAA 59.842 41.667 9.11 0.00 39.69 2.10
138 139 3.694566 AGTCATACATGTGCTGTCGTAGA 59.305 43.478 9.11 0.00 39.39 2.59
139 140 4.033990 AGTCATACATGTGCTGTCGTAG 57.966 45.455 9.11 0.00 39.39 3.51
140 141 5.531287 AGATAGTCATACATGTGCTGTCGTA 59.469 40.000 9.11 1.15 39.39 3.43
141 142 4.339530 AGATAGTCATACATGTGCTGTCGT 59.660 41.667 9.11 0.00 39.39 4.34
142 143 4.864633 AGATAGTCATACATGTGCTGTCG 58.135 43.478 9.11 0.00 39.39 4.35
143 144 6.276091 TCAAGATAGTCATACATGTGCTGTC 58.724 40.000 9.11 8.96 39.39 3.51
144 145 6.225981 TCAAGATAGTCATACATGTGCTGT 57.774 37.500 9.11 0.00 42.13 4.40
145 146 7.656542 AGAATCAAGATAGTCATACATGTGCTG 59.343 37.037 9.11 6.26 0.00 4.41
146 147 7.656542 CAGAATCAAGATAGTCATACATGTGCT 59.343 37.037 9.11 4.10 0.00 4.40
147 148 7.440556 ACAGAATCAAGATAGTCATACATGTGC 59.559 37.037 9.11 0.00 0.00 4.57
148 149 8.883954 ACAGAATCAAGATAGTCATACATGTG 57.116 34.615 9.11 0.00 0.00 3.21
149 150 8.699130 TGACAGAATCAAGATAGTCATACATGT 58.301 33.333 2.69 2.69 33.02 3.21
150 151 9.708092 ATGACAGAATCAAGATAGTCATACATG 57.292 33.333 16.97 0.00 42.83 3.21
158 159 9.823647 ACGATTTTATGACAGAATCAAGATAGT 57.176 29.630 0.00 0.00 41.93 2.12
160 161 9.816354 TGACGATTTTATGACAGAATCAAGATA 57.184 29.630 0.00 0.00 41.93 1.98
161 162 8.722480 TGACGATTTTATGACAGAATCAAGAT 57.278 30.769 0.00 0.00 41.93 2.40
162 163 8.606602 CATGACGATTTTATGACAGAATCAAGA 58.393 33.333 0.00 0.00 41.93 3.02
163 164 7.854422 CCATGACGATTTTATGACAGAATCAAG 59.146 37.037 0.00 0.00 41.93 3.02
164 165 7.552330 TCCATGACGATTTTATGACAGAATCAA 59.448 33.333 0.00 0.00 41.93 2.57
165 166 7.047271 TCCATGACGATTTTATGACAGAATCA 58.953 34.615 0.00 0.00 43.13 2.57
166 167 7.482654 TCCATGACGATTTTATGACAGAATC 57.517 36.000 0.00 0.00 0.00 2.52
167 168 7.500227 ACATCCATGACGATTTTATGACAGAAT 59.500 33.333 0.00 0.00 0.00 2.40
168 169 6.823182 ACATCCATGACGATTTTATGACAGAA 59.177 34.615 0.00 0.00 0.00 3.02
169 170 6.348498 ACATCCATGACGATTTTATGACAGA 58.652 36.000 0.00 0.00 0.00 3.41
170 171 6.609237 ACATCCATGACGATTTTATGACAG 57.391 37.500 0.00 0.00 0.00 3.51
171 172 7.044798 TGTACATCCATGACGATTTTATGACA 58.955 34.615 0.00 0.00 0.00 3.58
172 173 7.477144 TGTACATCCATGACGATTTTATGAC 57.523 36.000 0.00 0.00 0.00 3.06
173 174 7.307930 GCATGTACATCCATGACGATTTTATGA 60.308 37.037 5.07 0.00 43.99 2.15
174 175 6.798476 GCATGTACATCCATGACGATTTTATG 59.202 38.462 5.07 0.00 43.99 1.90
175 176 6.486320 TGCATGTACATCCATGACGATTTTAT 59.514 34.615 5.07 0.00 43.99 1.40
176 177 5.819901 TGCATGTACATCCATGACGATTTTA 59.180 36.000 5.07 0.00 43.99 1.52
177 178 4.639755 TGCATGTACATCCATGACGATTTT 59.360 37.500 5.07 0.00 43.99 1.82
178 179 4.198530 TGCATGTACATCCATGACGATTT 58.801 39.130 5.07 0.00 43.99 2.17
179 180 3.807553 TGCATGTACATCCATGACGATT 58.192 40.909 5.07 0.00 43.99 3.34
180 181 3.473923 TGCATGTACATCCATGACGAT 57.526 42.857 5.07 0.00 43.99 3.73
181 182 2.977772 TGCATGTACATCCATGACGA 57.022 45.000 5.07 0.00 43.99 4.20
182 183 3.132925 TCATGCATGTACATCCATGACG 58.867 45.455 30.25 12.42 43.99 4.35
184 185 4.153673 TGTCATGCATGTACATCCATGA 57.846 40.909 30.25 30.25 43.99 3.07
185 186 4.904253 TTGTCATGCATGTACATCCATG 57.096 40.909 27.23 27.23 44.07 3.66
186 187 5.918426 TTTTGTCATGCATGTACATCCAT 57.082 34.783 25.43 6.44 0.00 3.41
187 188 5.718724 TTTTTGTCATGCATGTACATCCA 57.281 34.783 25.43 2.99 0.00 3.41
206 207 1.862827 GTCACAGTAGGTCGCGTTTTT 59.137 47.619 5.77 0.00 0.00 1.94
207 208 1.202440 TGTCACAGTAGGTCGCGTTTT 60.202 47.619 5.77 0.00 0.00 2.43
208 209 0.386476 TGTCACAGTAGGTCGCGTTT 59.614 50.000 5.77 0.00 0.00 3.60
209 210 0.386476 TTGTCACAGTAGGTCGCGTT 59.614 50.000 5.77 0.00 0.00 4.84
210 211 0.386476 TTTGTCACAGTAGGTCGCGT 59.614 50.000 5.77 0.00 0.00 6.01
211 212 0.782384 GTTTGTCACAGTAGGTCGCG 59.218 55.000 0.00 0.00 0.00 5.87
212 213 1.860676 TGTTTGTCACAGTAGGTCGC 58.139 50.000 0.00 0.00 0.00 5.19
213 214 3.390135 ACATGTTTGTCACAGTAGGTCG 58.610 45.455 0.00 0.00 39.40 4.79
214 215 6.163476 TGATACATGTTTGTCACAGTAGGTC 58.837 40.000 2.30 0.00 39.40 3.85
215 216 6.109156 TGATACATGTTTGTCACAGTAGGT 57.891 37.500 2.30 0.00 39.40 3.08
216 217 6.818142 TGATGATACATGTTTGTCACAGTAGG 59.182 38.462 2.30 0.00 39.40 3.18
217 218 7.331687 TGTGATGATACATGTTTGTCACAGTAG 59.668 37.037 21.68 0.00 39.40 2.57
218 219 7.158021 TGTGATGATACATGTTTGTCACAGTA 58.842 34.615 21.68 8.64 39.40 2.74
219 220 5.997129 TGTGATGATACATGTTTGTCACAGT 59.003 36.000 21.68 6.13 39.40 3.55
220 221 6.369615 TCTGTGATGATACATGTTTGTCACAG 59.630 38.462 31.62 31.62 45.67 3.66
221 222 6.229733 TCTGTGATGATACATGTTTGTCACA 58.770 36.000 22.94 22.94 40.71 3.58
222 223 6.726258 TCTGTGATGATACATGTTTGTCAC 57.274 37.500 18.54 18.54 37.28 3.67
223 224 6.936335 ACTTCTGTGATGATACATGTTTGTCA 59.064 34.615 2.30 7.19 37.28 3.58
224 225 7.095060 ACACTTCTGTGATGATACATGTTTGTC 60.095 37.037 2.30 0.95 46.55 3.18
225 226 6.712095 ACACTTCTGTGATGATACATGTTTGT 59.288 34.615 2.30 0.00 46.55 2.83
226 227 7.137490 ACACTTCTGTGATGATACATGTTTG 57.863 36.000 2.30 0.00 46.55 2.93
227 228 9.453572 AATACACTTCTGTGATGATACATGTTT 57.546 29.630 2.30 0.00 46.55 2.83
228 229 9.453572 AAATACACTTCTGTGATGATACATGTT 57.546 29.630 2.30 0.00 46.55 2.71
229 230 9.453572 AAAATACACTTCTGTGATGATACATGT 57.546 29.630 2.69 2.69 46.55 3.21
254 255 2.096466 CGCATCGTCAGCACTACAAAAA 60.096 45.455 0.00 0.00 0.00 1.94
255 256 1.459209 CGCATCGTCAGCACTACAAAA 59.541 47.619 0.00 0.00 0.00 2.44
256 257 1.067693 CGCATCGTCAGCACTACAAA 58.932 50.000 0.00 0.00 0.00 2.83
257 258 1.351430 GCGCATCGTCAGCACTACAA 61.351 55.000 0.30 0.00 0.00 2.41
258 259 1.805539 GCGCATCGTCAGCACTACA 60.806 57.895 0.30 0.00 0.00 2.74
259 260 1.078759 AAGCGCATCGTCAGCACTAC 61.079 55.000 11.47 0.00 0.00 2.73
260 261 0.802222 GAAGCGCATCGTCAGCACTA 60.802 55.000 11.47 0.00 0.00 2.74
261 262 2.047844 AAGCGCATCGTCAGCACT 60.048 55.556 11.47 0.00 0.00 4.40
262 263 2.397252 GAAGCGCATCGTCAGCAC 59.603 61.111 11.47 0.00 0.00 4.40
268 269 2.507102 CCTGTCGAAGCGCATCGT 60.507 61.111 30.86 3.62 43.19 3.73
269 270 3.257561 CCCTGTCGAAGCGCATCG 61.258 66.667 27.51 27.51 44.04 3.84
312 315 2.511452 CCTCCGATGGATCCGCCTT 61.511 63.158 7.39 0.00 37.63 4.35
316 319 1.247419 CCTCTCCTCCGATGGATCCG 61.247 65.000 7.39 0.00 35.30 4.18
320 323 0.476338 CTCTCCTCTCCTCCGATGGA 59.524 60.000 0.00 0.00 34.52 3.41
349 352 4.436998 ACCGCTAGCACGCCTCAC 62.437 66.667 16.45 0.00 0.00 3.51
356 359 1.741770 CTGTTCCCACCGCTAGCAC 60.742 63.158 16.45 3.75 0.00 4.40
357 360 2.214216 ACTGTTCCCACCGCTAGCA 61.214 57.895 16.45 0.00 0.00 3.49
358 361 1.741770 CACTGTTCCCACCGCTAGC 60.742 63.158 4.06 4.06 0.00 3.42
359 362 1.741770 GCACTGTTCCCACCGCTAG 60.742 63.158 0.00 0.00 0.00 3.42
360 363 2.345991 GCACTGTTCCCACCGCTA 59.654 61.111 0.00 0.00 0.00 4.26
380 383 0.757188 CCCACTCTCCTATCACCGCT 60.757 60.000 0.00 0.00 0.00 5.52
382 385 1.323412 CTCCCACTCTCCTATCACCG 58.677 60.000 0.00 0.00 0.00 4.94
383 386 1.710816 CCTCCCACTCTCCTATCACC 58.289 60.000 0.00 0.00 0.00 4.02
388 391 0.555369 ACTCCCCTCCCACTCTCCTA 60.555 60.000 0.00 0.00 0.00 2.94
390 393 0.338814 TAACTCCCCTCCCACTCTCC 59.661 60.000 0.00 0.00 0.00 3.71
413 416 3.450115 GGAGACGGAGGGGACGTG 61.450 72.222 0.00 0.00 45.68 4.49
528 531 3.071479 CACGAAACTTAAAGCAGGCCTA 58.929 45.455 3.98 0.00 0.00 3.93
557 560 2.045143 TGGGCTGCATGCGATTCA 60.045 55.556 14.09 6.36 44.05 2.57
571 574 2.871253 GCCTGTTTGGTTGGCTGGG 61.871 63.158 0.00 0.00 43.05 4.45
590 593 4.178861 CCGTACGGGATGTGTGTG 57.821 61.111 27.00 0.00 38.47 3.82
601 604 3.697747 TCCAAGCACCCCCGTACG 61.698 66.667 8.69 8.69 0.00 3.67
602 605 2.046604 GTCCAAGCACCCCCGTAC 60.047 66.667 0.00 0.00 0.00 3.67
603 606 2.203877 AGTCCAAGCACCCCCGTA 60.204 61.111 0.00 0.00 0.00 4.02
604 607 3.953775 CAGTCCAAGCACCCCCGT 61.954 66.667 0.00 0.00 0.00 5.28
609 612 1.582968 CACATGCAGTCCAAGCACC 59.417 57.895 0.00 0.00 45.95 5.01
610 613 1.582968 CCACATGCAGTCCAAGCAC 59.417 57.895 0.00 0.00 45.95 4.40
613 616 1.180456 TTGCCCACATGCAGTCCAAG 61.180 55.000 0.00 0.00 43.21 3.61
618 621 1.047596 TTTGGTTGCCCACATGCAGT 61.048 50.000 0.00 0.00 43.21 4.40
619 622 0.600782 GTTTGGTTGCCCACATGCAG 60.601 55.000 0.00 0.00 43.21 4.41
626 629 1.693627 AACGTATGTTTGGTTGCCCA 58.306 45.000 0.00 0.00 39.65 5.36
630 633 6.889494 TGTGTACATAACGTATGTTTGGTTG 58.111 36.000 5.48 2.54 46.69 3.77
644 647 9.467796 TTCATGAAATGGGTTATGTGTACATAA 57.532 29.630 5.45 12.18 46.73 1.90
782 787 5.335504 CCCTCCGAGTTATTACGTAAGATCC 60.336 48.000 14.25 3.39 43.62 3.36
829 834 7.604545 ACATTACTGCTTTCCTCTCTTTTCTAC 59.395 37.037 0.00 0.00 0.00 2.59
851 856 5.071115 GCTCCCTATTCTGTCTAGGAACATT 59.929 44.000 6.80 0.00 38.44 2.71
853 858 3.961408 GCTCCCTATTCTGTCTAGGAACA 59.039 47.826 6.80 0.00 38.44 3.18
872 877 6.459710 CGAAAGGGGGAAGTAATTATTTGCTC 60.460 42.308 11.11 7.69 0.00 4.26
902 907 5.169836 GGGCAAAATTACTTGTCCGATAG 57.830 43.478 0.00 0.00 41.04 2.08
1047 1073 2.268920 GAACTGGCTGCATCCCGA 59.731 61.111 3.68 0.00 0.00 5.14
1075 1101 3.624861 GCGACCAACAAGAAGATGATGAT 59.375 43.478 0.00 0.00 0.00 2.45
1119 1145 4.821589 GCGCCGAAGTGGGAGGAG 62.822 72.222 0.00 0.00 38.63 3.69
1138 1164 0.972983 CACCAGATCAGAGGGTCGGT 60.973 60.000 0.00 0.00 31.03 4.69
1335 2655 1.373812 GTTGGCCTCGTACCACCTT 59.626 57.895 3.32 0.00 36.76 3.50
1339 2659 2.745037 GTGGTTGGCCTCGTACCA 59.255 61.111 3.32 9.86 39.53 3.25
1451 2891 4.751600 CCACGTACTTGCATGTATGATGAT 59.248 41.667 28.97 11.34 34.51 2.45
1555 3494 1.333177 GGCTCATGGACGAGTAGGAT 58.667 55.000 0.00 0.00 35.33 3.24
1560 3499 3.083997 GGGGGCTCATGGACGAGT 61.084 66.667 0.00 0.00 35.33 4.18
1666 4267 2.364448 GGAGCGGGAGGAGAAGGT 60.364 66.667 0.00 0.00 0.00 3.50
1859 4791 5.063204 TCCAGTCGAACTTGTTGATCAAAT 58.937 37.500 10.35 0.00 35.48 2.32
1964 4896 4.699522 ACACCGCCCCTTTCGCTC 62.700 66.667 0.00 0.00 0.00 5.03
2097 5029 1.906574 ACCGGGAAGATCTGCTTGTTA 59.093 47.619 6.32 0.00 36.83 2.41
2235 5203 4.379243 AGGACTGCGACGGCCTTG 62.379 66.667 0.00 0.00 38.85 3.61
2597 6128 1.134818 CCTACTGGCACGTGAGCAATA 60.135 52.381 22.23 3.34 35.83 1.90
2622 6153 1.374252 GTCCATATGCCGTAGCCCG 60.374 63.158 0.00 0.00 38.69 6.13
2623 6154 1.374252 CGTCCATATGCCGTAGCCC 60.374 63.158 0.00 0.00 38.69 5.19
2624 6155 0.666577 GTCGTCCATATGCCGTAGCC 60.667 60.000 11.30 0.00 38.69 3.93
2625 6156 0.666577 GGTCGTCCATATGCCGTAGC 60.667 60.000 11.30 6.14 40.48 3.58
2626 6157 0.038526 GGGTCGTCCATATGCCGTAG 60.039 60.000 11.30 0.00 35.00 3.51
2627 6158 1.466025 GGGGTCGTCCATATGCCGTA 61.466 60.000 11.30 0.00 37.22 4.02
2628 6159 2.803817 GGGGTCGTCCATATGCCGT 61.804 63.158 11.30 0.00 37.22 5.68
2708 6239 5.763698 ACCTGGAGTAAGTTTTTAGCTCAAC 59.236 40.000 0.00 0.00 0.00 3.18
2772 6303 4.142600 GGAAGAGTGGTGAAATGATTTCCG 60.143 45.833 14.73 0.00 38.90 4.30
2827 6358 0.534412 AGTCGGGCTCATGTCTCTTG 59.466 55.000 0.00 0.00 0.00 3.02
2874 6405 2.121291 TTGCTGTGTGGTTTGTCTGA 57.879 45.000 0.00 0.00 0.00 3.27
2894 6425 0.918258 TATGCTCTTGGACATGGCCA 59.082 50.000 19.12 19.12 35.78 5.36
2900 6443 4.002906 ACTTTCGTTATGCTCTTGGACA 57.997 40.909 0.00 0.00 0.00 4.02
2902 6445 5.168569 CAGTACTTTCGTTATGCTCTTGGA 58.831 41.667 0.00 0.00 0.00 3.53
2932 6483 1.685224 CATGTGTGCCCTGTACCCT 59.315 57.895 0.00 0.00 0.00 4.34
2965 6516 4.776349 TCTTATCTTATTTTCGGCCTGCA 58.224 39.130 0.00 0.00 0.00 4.41
2974 6525 9.099454 CTTCGGTGTTAGCTCTTATCTTATTTT 57.901 33.333 0.00 0.00 0.00 1.82
3003 6557 2.366266 AGTTAGTTGGTGGCTTCGTGTA 59.634 45.455 0.00 0.00 0.00 2.90
3023 6577 5.130292 AGTTGTCTTGGCATCATTTTGAG 57.870 39.130 0.00 0.00 0.00 3.02
3060 6615 0.179108 GCGTCTTCCTTATCACGGCT 60.179 55.000 0.00 0.00 32.79 5.52
3126 6681 2.224305 GGGGATCATTGACTAAGACGGG 60.224 54.545 0.00 0.00 0.00 5.28
3322 6881 1.062810 GGGCTCCTTCCTCCTTCTCTA 60.063 57.143 0.00 0.00 0.00 2.43
3363 6922 7.430441 GCTAAACTGGATTGGAGTTGTTTTAA 58.570 34.615 0.00 0.00 33.85 1.52
3378 6937 1.671054 GTGCGCTGGCTAAACTGGA 60.671 57.895 9.73 0.00 40.82 3.86
3399 6958 4.040445 ACACAAACCACATTTTCTTCCG 57.960 40.909 0.00 0.00 0.00 4.30
3500 7060 1.075482 CTGGCAAGCCTTCAAGGGA 59.925 57.895 12.96 0.00 35.37 4.20
3579 7139 1.792757 AAGCTCATTGGTGGCTCCCA 61.793 55.000 2.66 0.00 32.85 4.37


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

AutoCloner maintained by Alex Coulton.