Multiple sequence alignment - TraesCS3D01G023500

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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 TraesCS3D01G023500 chr3D 100.000 4444 0 0 1 4444 7432128 7436571 0.000000e+00 8207
1 TraesCS3D01G023500 chr3D 89.252 214 20 3 3719 3932 7440731 7440941 9.480000e-67 265
2 TraesCS3D01G023500 chr3B 93.705 2478 96 21 1729 4173 9440154 9442604 0.000000e+00 3657
3 TraesCS3D01G023500 chr3B 87.120 1545 127 35 236 1733 9438599 9440118 0.000000e+00 1685
4 TraesCS3D01G023500 chr3B 94.488 381 12 6 4068 4444 9443233 9443608 2.980000e-161 579
5 TraesCS3D01G023500 chr3B 81.407 199 34 3 2162 2358 780553318 780553121 4.600000e-35 159
6 TraesCS3D01G023500 chr3B 93.269 104 6 1 112 214 744914059 744913956 7.700000e-33 152
7 TraesCS3D01G023500 chr3B 83.117 154 23 3 1553 1706 9440333 9440483 2.160000e-28 137
8 TraesCS3D01G023500 chr3A 94.632 2217 76 21 1738 3926 12854822 12852621 0.000000e+00 3395
9 TraesCS3D01G023500 chr3A 90.575 626 37 15 849 1462 12855786 12855171 0.000000e+00 809
10 TraesCS3D01G023500 chr3A 88.403 526 28 13 3928 4444 12852524 12852023 1.770000e-168 603
11 TraesCS3D01G023500 chr4D 84.672 411 43 16 988 1396 394151683 394151291 4.170000e-105 392
12 TraesCS3D01G023500 chr4D 88.439 173 20 0 2170 2342 394150461 394150289 4.500000e-50 209
13 TraesCS3D01G023500 chr4A 78.399 662 100 27 2170 2813 75431817 75431181 1.500000e-104 390
14 TraesCS3D01G023500 chr4A 84.223 412 36 19 988 1398 75436040 75435657 1.510000e-99 374
15 TraesCS3D01G023500 chr4B 83.654 416 43 19 988 1398 483769891 483769496 7.020000e-98 368
16 TraesCS3D01G023500 chr4B 90.566 159 15 0 2184 2342 483767635 483767477 1.250000e-50 211
17 TraesCS3D01G023500 chrUn 83.861 316 44 7 3486 3797 216084924 216084612 1.210000e-75 294
18 TraesCS3D01G023500 chrUn 83.861 316 44 7 3486 3797 244197175 244197487 1.210000e-75 294
19 TraesCS3D01G023500 chr7B 83.544 316 45 7 3486 3797 748956537 748956849 5.620000e-74 289
20 TraesCS3D01G023500 chr7B 82.595 316 48 7 3486 3797 749027798 749028110 5.660000e-69 272
21 TraesCS3D01G023500 chr6B 82.866 321 48 7 3481 3797 542383486 542383169 9.410000e-72 281
22 TraesCS3D01G023500 chr6B 90.909 110 9 1 110 218 38755220 38755111 3.580000e-31 147
23 TraesCS3D01G023500 chr2B 77.852 298 52 9 2162 2455 432935042 432935329 5.910000e-39 172
24 TraesCS3D01G023500 chr7D 93.519 108 6 1 112 218 588079514 588079621 4.600000e-35 159
25 TraesCS3D01G023500 chr7D 94.231 104 5 1 112 214 588075302 588075405 1.650000e-34 158
26 TraesCS3D01G023500 chr7D 83.436 163 26 1 2196 2358 466669699 466669538 2.770000e-32 150
27 TraesCS3D01G023500 chr5D 92.593 108 7 1 112 218 426286371 426286264 2.140000e-33 154
28 TraesCS3D01G023500 chr2A 92.453 106 7 1 114 218 504337974 504337869 2.770000e-32 150
29 TraesCS3D01G023500 chr7A 91.667 108 8 1 112 218 724086760 724086653 9.960000e-32 148
30 TraesCS3D01G023500 chr6D 91.667 108 8 1 112 218 23623514 23623407 9.960000e-32 148
31 TraesCS3D01G023500 chr6D 90.741 108 9 1 112 218 23783124 23783017 4.630000e-30 143


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 TraesCS3D01G023500 chr3D 7432128 7436571 4443 False 8207.000000 8207 100.000000 1 4444 1 chr3D.!!$F1 4443
1 TraesCS3D01G023500 chr3B 9438599 9443608 5009 False 1514.500000 3657 89.607500 236 4444 4 chr3B.!!$F1 4208
2 TraesCS3D01G023500 chr3A 12852023 12855786 3763 True 1602.333333 3395 91.203333 849 4444 3 chr3A.!!$R1 3595
3 TraesCS3D01G023500 chr4D 394150289 394151683 1394 True 300.500000 392 86.555500 988 2342 2 chr4D.!!$R1 1354
4 TraesCS3D01G023500 chr4A 75431181 75436040 4859 True 382.000000 390 81.311000 988 2813 2 chr4A.!!$R1 1825
5 TraesCS3D01G023500 chr4B 483767477 483769891 2414 True 289.500000 368 87.110000 988 2342 2 chr4B.!!$R1 1354

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
220 221 0.250513 CTGACCACTGGGCTAGAACC 59.749 60.000 4.33 0.00 37.9 3.62 F
792 820 0.328258 ACCTCCATCGTTTTCCCCTG 59.672 55.000 0.00 0.00 0.0 4.45 F
971 999 0.725133 TTCCCCTCTTCCCCTCATCT 59.275 55.000 0.00 0.00 0.0 2.90 F
1710 4861 1.065551 GAGAAAACTGCGTTTGTGGCT 59.934 47.619 7.30 4.15 35.8 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1225 1256 0.308684 CGTGCCCAATCCATTGATCG 59.691 55.000 0.56 0.0 40.14 3.69 R
1826 5018 1.272704 GGAGAACCCAGAATGCCCTTT 60.273 52.381 0.00 0.0 34.14 3.11 R
2365 6979 1.637035 TCTTAACCAAGGTAAGGGGGC 59.363 52.381 0.00 0.0 32.22 5.80 R
3469 8117 1.136500 GCTCCCGTCCCTAGTAAACAG 59.864 57.143 0.00 0.0 0.00 3.16 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 2.936202 CAGAAGGACAATACATGGGGG 58.064 52.381 0.00 0.00 0.00 5.40
21 22 2.509548 CAGAAGGACAATACATGGGGGA 59.490 50.000 0.00 0.00 0.00 4.81
22 23 3.139025 CAGAAGGACAATACATGGGGGAT 59.861 47.826 0.00 0.00 0.00 3.85
23 24 4.350816 CAGAAGGACAATACATGGGGGATA 59.649 45.833 0.00 0.00 0.00 2.59
24 25 4.351111 AGAAGGACAATACATGGGGGATAC 59.649 45.833 0.00 0.00 0.00 2.24
25 26 3.675613 AGGACAATACATGGGGGATACA 58.324 45.455 0.00 0.00 39.74 2.29
26 27 4.251169 AGGACAATACATGGGGGATACAT 58.749 43.478 0.00 0.00 39.74 2.29
28 29 4.042809 GGACAATACATGGGGGATACATGA 59.957 45.833 11.87 0.00 46.60 3.07
29 30 5.281193 GGACAATACATGGGGGATACATGAT 60.281 44.000 11.87 0.00 46.60 2.45
30 31 6.218195 ACAATACATGGGGGATACATGATT 57.782 37.500 11.87 5.27 46.60 2.57
31 32 6.623329 ACAATACATGGGGGATACATGATTT 58.377 36.000 11.87 3.01 46.60 2.17
32 33 6.494491 ACAATACATGGGGGATACATGATTTG 59.506 38.462 11.87 14.41 46.60 2.32
33 34 3.848303 ACATGGGGGATACATGATTTGG 58.152 45.455 11.87 0.00 46.60 3.28
34 35 3.167485 CATGGGGGATACATGATTTGGG 58.833 50.000 0.00 0.00 46.60 4.12
35 36 2.508156 TGGGGGATACATGATTTGGGA 58.492 47.619 0.00 0.00 39.74 4.37
36 37 2.861957 TGGGGGATACATGATTTGGGAA 59.138 45.455 0.00 0.00 39.74 3.97
37 38 3.230976 GGGGGATACATGATTTGGGAAC 58.769 50.000 0.00 0.00 39.74 3.62
38 39 3.373658 GGGGGATACATGATTTGGGAACA 60.374 47.826 0.00 0.00 36.89 3.18
39 40 3.891366 GGGGATACATGATTTGGGAACAG 59.109 47.826 0.00 0.00 40.00 3.16
40 41 4.536765 GGGATACATGATTTGGGAACAGT 58.463 43.478 0.00 0.00 40.00 3.55
41 42 5.398581 GGGGATACATGATTTGGGAACAGTA 60.399 44.000 0.00 0.00 40.00 2.74
42 43 5.531287 GGGATACATGATTTGGGAACAGTAC 59.469 44.000 0.00 0.00 40.00 2.73
43 44 6.357367 GGATACATGATTTGGGAACAGTACT 58.643 40.000 0.00 0.00 44.54 2.73
44 45 6.828785 GGATACATGATTTGGGAACAGTACTT 59.171 38.462 0.00 0.00 44.54 2.24
45 46 7.339466 GGATACATGATTTGGGAACAGTACTTT 59.661 37.037 0.00 0.00 44.54 2.66
46 47 9.391006 GATACATGATTTGGGAACAGTACTTTA 57.609 33.333 0.00 0.00 44.54 1.85
47 48 7.448748 ACATGATTTGGGAACAGTACTTTAC 57.551 36.000 0.00 0.00 44.54 2.01
48 49 7.001674 ACATGATTTGGGAACAGTACTTTACA 58.998 34.615 0.00 0.00 44.54 2.41
49 50 6.870971 TGATTTGGGAACAGTACTTTACAC 57.129 37.500 0.00 0.00 44.54 2.90
50 51 6.597562 TGATTTGGGAACAGTACTTTACACT 58.402 36.000 0.00 0.00 44.54 3.55
51 52 7.057894 TGATTTGGGAACAGTACTTTACACTT 58.942 34.615 0.00 0.00 44.54 3.16
52 53 6.687081 TTTGGGAACAGTACTTTACACTTG 57.313 37.500 0.00 0.00 44.54 3.16
53 54 4.131596 TGGGAACAGTACTTTACACTTGC 58.868 43.478 0.00 0.00 35.01 4.01
54 55 3.501062 GGGAACAGTACTTTACACTTGCC 59.499 47.826 0.00 0.00 0.00 4.52
55 56 4.131596 GGAACAGTACTTTACACTTGCCA 58.868 43.478 0.00 0.00 0.00 4.92
56 57 4.760204 GGAACAGTACTTTACACTTGCCAT 59.240 41.667 0.00 0.00 0.00 4.40
57 58 5.106673 GGAACAGTACTTTACACTTGCCATC 60.107 44.000 0.00 0.00 0.00 3.51
58 59 4.968259 ACAGTACTTTACACTTGCCATCA 58.032 39.130 0.00 0.00 0.00 3.07
59 60 4.755123 ACAGTACTTTACACTTGCCATCAC 59.245 41.667 0.00 0.00 0.00 3.06
60 61 4.754618 CAGTACTTTACACTTGCCATCACA 59.245 41.667 0.00 0.00 0.00 3.58
61 62 4.997395 AGTACTTTACACTTGCCATCACAG 59.003 41.667 0.00 0.00 0.00 3.66
62 63 4.085357 ACTTTACACTTGCCATCACAGA 57.915 40.909 0.00 0.00 0.00 3.41
63 64 4.460263 ACTTTACACTTGCCATCACAGAA 58.540 39.130 0.00 0.00 0.00 3.02
64 65 4.887071 ACTTTACACTTGCCATCACAGAAA 59.113 37.500 0.00 0.00 0.00 2.52
65 66 5.009010 ACTTTACACTTGCCATCACAGAAAG 59.991 40.000 0.00 0.00 0.00 2.62
66 67 1.610522 ACACTTGCCATCACAGAAAGC 59.389 47.619 0.00 0.00 0.00 3.51
67 68 1.610038 CACTTGCCATCACAGAAAGCA 59.390 47.619 0.00 0.00 0.00 3.91
68 69 1.610522 ACTTGCCATCACAGAAAGCAC 59.389 47.619 0.00 0.00 32.18 4.40
69 70 1.884579 CTTGCCATCACAGAAAGCACT 59.115 47.619 0.00 0.00 32.18 4.40
70 71 1.985473 TGCCATCACAGAAAGCACTT 58.015 45.000 0.00 0.00 0.00 3.16
71 72 1.610038 TGCCATCACAGAAAGCACTTG 59.390 47.619 0.00 0.00 0.00 3.16
72 73 1.610522 GCCATCACAGAAAGCACTTGT 59.389 47.619 0.00 0.00 0.00 3.16
73 74 2.813754 GCCATCACAGAAAGCACTTGTA 59.186 45.455 0.00 0.00 0.00 2.41
74 75 3.253188 GCCATCACAGAAAGCACTTGTAA 59.747 43.478 0.00 0.00 0.00 2.41
75 76 4.082571 GCCATCACAGAAAGCACTTGTAAT 60.083 41.667 0.00 0.00 0.00 1.89
76 77 5.123820 GCCATCACAGAAAGCACTTGTAATA 59.876 40.000 0.00 0.00 0.00 0.98
77 78 6.546395 CCATCACAGAAAGCACTTGTAATAC 58.454 40.000 0.00 0.00 0.00 1.89
78 79 6.403636 CCATCACAGAAAGCACTTGTAATACC 60.404 42.308 0.00 0.00 0.00 2.73
79 80 5.865085 TCACAGAAAGCACTTGTAATACCT 58.135 37.500 0.00 0.00 0.00 3.08
80 81 5.700832 TCACAGAAAGCACTTGTAATACCTG 59.299 40.000 0.00 0.00 0.00 4.00
81 82 5.003804 ACAGAAAGCACTTGTAATACCTGG 58.996 41.667 0.00 0.00 0.00 4.45
82 83 5.003804 CAGAAAGCACTTGTAATACCTGGT 58.996 41.667 4.05 4.05 0.00 4.00
83 84 6.170506 CAGAAAGCACTTGTAATACCTGGTA 58.829 40.000 9.36 9.36 0.00 3.25
84 85 6.823689 CAGAAAGCACTTGTAATACCTGGTAT 59.176 38.462 13.60 13.60 0.00 2.73
85 86 6.823689 AGAAAGCACTTGTAATACCTGGTATG 59.176 38.462 19.61 9.46 0.00 2.39
86 87 5.950544 AGCACTTGTAATACCTGGTATGA 57.049 39.130 19.61 10.02 0.00 2.15
87 88 6.308015 AGCACTTGTAATACCTGGTATGAA 57.692 37.500 19.61 11.73 0.00 2.57
88 89 6.113411 AGCACTTGTAATACCTGGTATGAAC 58.887 40.000 19.61 19.11 0.00 3.18
89 90 5.878116 GCACTTGTAATACCTGGTATGAACA 59.122 40.000 19.61 21.11 0.00 3.18
90 91 6.373216 GCACTTGTAATACCTGGTATGAACAA 59.627 38.462 28.42 28.42 35.15 2.83
91 92 7.094549 GCACTTGTAATACCTGGTATGAACAAA 60.095 37.037 29.17 20.34 36.12 2.83
92 93 8.956426 CACTTGTAATACCTGGTATGAACAAAT 58.044 33.333 29.17 23.56 36.12 2.32
99 100 8.980481 ATACCTGGTATGAACAAATAAGAAGG 57.020 34.615 18.31 0.00 0.00 3.46
100 101 6.790319 ACCTGGTATGAACAAATAAGAAGGT 58.210 36.000 0.00 0.00 0.00 3.50
101 102 7.924541 ACCTGGTATGAACAAATAAGAAGGTA 58.075 34.615 0.00 0.00 0.00 3.08
102 103 8.557450 ACCTGGTATGAACAAATAAGAAGGTAT 58.443 33.333 0.00 0.00 0.00 2.73
103 104 8.840321 CCTGGTATGAACAAATAAGAAGGTATG 58.160 37.037 0.00 0.00 0.00 2.39
104 105 9.613428 CTGGTATGAACAAATAAGAAGGTATGA 57.387 33.333 0.00 0.00 0.00 2.15
105 106 9.967451 TGGTATGAACAAATAAGAAGGTATGAA 57.033 29.630 0.00 0.00 0.00 2.57
131 132 8.697507 AAAATGACCTTACTTGAACAAGATCT 57.302 30.769 19.35 0.00 40.79 2.75
132 133 7.678947 AATGACCTTACTTGAACAAGATCTG 57.321 36.000 19.35 8.71 40.79 2.90
133 134 6.174720 TGACCTTACTTGAACAAGATCTGT 57.825 37.500 19.35 11.25 40.79 3.41
146 147 7.906199 AACAAGATCTGTTCTATAGGCTAGT 57.094 36.000 0.00 0.00 45.50 2.57
147 148 8.998277 AACAAGATCTGTTCTATAGGCTAGTA 57.002 34.615 0.00 0.00 45.50 1.82
148 149 8.398878 ACAAGATCTGTTCTATAGGCTAGTAC 57.601 38.462 0.00 0.00 32.99 2.73
149 150 7.449086 ACAAGATCTGTTCTATAGGCTAGTACC 59.551 40.741 0.00 0.00 32.99 3.34
150 151 6.174760 AGATCTGTTCTATAGGCTAGTACCG 58.825 44.000 0.00 0.00 30.96 4.02
151 152 5.301835 TCTGTTCTATAGGCTAGTACCGT 57.698 43.478 0.00 0.00 33.69 4.83
152 153 5.688807 TCTGTTCTATAGGCTAGTACCGTT 58.311 41.667 0.00 0.00 33.69 4.44
153 154 5.530171 TCTGTTCTATAGGCTAGTACCGTTG 59.470 44.000 0.00 0.00 33.69 4.10
154 155 4.037208 TGTTCTATAGGCTAGTACCGTTGC 59.963 45.833 0.00 0.00 33.69 4.17
155 156 3.152341 TCTATAGGCTAGTACCGTTGCC 58.848 50.000 0.00 7.64 45.21 4.52
157 158 4.829588 GGCTAGTACCGTTGCCTC 57.170 61.111 8.26 0.00 41.92 4.70
158 159 1.143401 GGCTAGTACCGTTGCCTCC 59.857 63.158 8.26 0.00 41.92 4.30
159 160 1.328430 GGCTAGTACCGTTGCCTCCT 61.328 60.000 8.26 0.00 41.92 3.69
160 161 0.535797 GCTAGTACCGTTGCCTCCTT 59.464 55.000 0.00 0.00 0.00 3.36
161 162 1.066358 GCTAGTACCGTTGCCTCCTTT 60.066 52.381 0.00 0.00 0.00 3.11
162 163 2.167075 GCTAGTACCGTTGCCTCCTTTA 59.833 50.000 0.00 0.00 0.00 1.85
163 164 2.756840 AGTACCGTTGCCTCCTTTAC 57.243 50.000 0.00 0.00 0.00 2.01
164 165 1.277273 AGTACCGTTGCCTCCTTTACC 59.723 52.381 0.00 0.00 0.00 2.85
165 166 1.002315 GTACCGTTGCCTCCTTTACCA 59.998 52.381 0.00 0.00 0.00 3.25
166 167 0.475044 ACCGTTGCCTCCTTTACCAA 59.525 50.000 0.00 0.00 0.00 3.67
167 168 1.074889 ACCGTTGCCTCCTTTACCAAT 59.925 47.619 0.00 0.00 0.00 3.16
168 169 2.306512 ACCGTTGCCTCCTTTACCAATA 59.693 45.455 0.00 0.00 0.00 1.90
169 170 3.244981 ACCGTTGCCTCCTTTACCAATAA 60.245 43.478 0.00 0.00 0.00 1.40
170 171 3.377172 CCGTTGCCTCCTTTACCAATAAG 59.623 47.826 0.00 0.00 0.00 1.73
171 172 3.377172 CGTTGCCTCCTTTACCAATAAGG 59.623 47.826 0.00 0.00 42.89 2.69
172 173 4.595986 GTTGCCTCCTTTACCAATAAGGA 58.404 43.478 0.00 0.00 46.77 3.36
177 178 4.938575 TCCTTTACCAATAAGGAGGCAA 57.061 40.909 0.00 0.00 44.72 4.52
178 179 4.855340 TCCTTTACCAATAAGGAGGCAAG 58.145 43.478 0.00 0.00 44.72 4.01
179 180 3.381590 CCTTTACCAATAAGGAGGCAAGC 59.618 47.826 0.00 0.00 44.01 4.01
180 181 3.730215 TTACCAATAAGGAGGCAAGCA 57.270 42.857 0.00 0.00 41.22 3.91
181 182 1.839424 ACCAATAAGGAGGCAAGCAC 58.161 50.000 0.00 0.00 41.22 4.40
182 183 1.355720 ACCAATAAGGAGGCAAGCACT 59.644 47.619 0.00 0.00 41.22 4.40
183 184 2.019984 CCAATAAGGAGGCAAGCACTC 58.980 52.381 0.00 0.00 41.22 3.51
184 185 2.618816 CCAATAAGGAGGCAAGCACTCA 60.619 50.000 11.01 0.00 41.22 3.41
185 186 3.084039 CAATAAGGAGGCAAGCACTCAA 58.916 45.455 11.01 0.22 36.70 3.02
186 187 3.659183 ATAAGGAGGCAAGCACTCAAT 57.341 42.857 11.01 4.00 36.70 2.57
187 188 1.831580 AAGGAGGCAAGCACTCAATC 58.168 50.000 11.01 0.00 36.70 2.67
188 189 0.990374 AGGAGGCAAGCACTCAATCT 59.010 50.000 11.01 0.13 36.70 2.40
189 190 1.093159 GGAGGCAAGCACTCAATCTG 58.907 55.000 11.01 0.00 36.70 2.90
190 191 1.093159 GAGGCAAGCACTCAATCTGG 58.907 55.000 0.00 0.00 35.09 3.86
191 192 0.403271 AGGCAAGCACTCAATCTGGT 59.597 50.000 0.00 0.00 0.00 4.00
192 193 1.202976 AGGCAAGCACTCAATCTGGTT 60.203 47.619 0.00 0.00 0.00 3.67
193 194 1.068055 GGCAAGCACTCAATCTGGTTG 60.068 52.381 6.07 6.07 45.71 3.77
194 195 1.881973 GCAAGCACTCAATCTGGTTGA 59.118 47.619 13.10 2.96 45.79 3.18
195 196 2.490903 GCAAGCACTCAATCTGGTTGAT 59.509 45.455 13.10 0.00 45.79 2.57
196 197 3.672511 GCAAGCACTCAATCTGGTTGATG 60.673 47.826 13.10 6.32 45.79 3.07
197 198 2.089980 AGCACTCAATCTGGTTGATGC 58.910 47.619 20.59 20.59 45.36 3.91
198 199 1.814394 GCACTCAATCTGGTTGATGCA 59.186 47.619 22.02 0.00 45.36 3.96
199 200 2.426024 GCACTCAATCTGGTTGATGCAT 59.574 45.455 22.02 0.00 45.36 3.96
200 201 3.119245 GCACTCAATCTGGTTGATGCATT 60.119 43.478 22.02 0.00 45.36 3.56
201 202 4.669318 CACTCAATCTGGTTGATGCATTC 58.331 43.478 3.44 0.00 45.36 2.67
202 203 4.398358 CACTCAATCTGGTTGATGCATTCT 59.602 41.667 3.44 0.00 45.36 2.40
203 204 4.398358 ACTCAATCTGGTTGATGCATTCTG 59.602 41.667 3.44 0.00 45.36 3.02
204 205 4.591929 TCAATCTGGTTGATGCATTCTGA 58.408 39.130 0.00 1.90 41.79 3.27
205 206 4.397103 TCAATCTGGTTGATGCATTCTGAC 59.603 41.667 0.00 0.00 41.79 3.51
206 207 2.715046 TCTGGTTGATGCATTCTGACC 58.285 47.619 0.00 7.64 34.06 4.02
207 208 2.040145 TCTGGTTGATGCATTCTGACCA 59.960 45.455 17.71 17.71 38.26 4.02
208 209 2.161855 TGGTTGATGCATTCTGACCAC 58.838 47.619 15.89 0.65 36.77 4.16
209 210 2.224843 TGGTTGATGCATTCTGACCACT 60.225 45.455 15.89 0.00 36.77 4.00
210 211 2.163010 GGTTGATGCATTCTGACCACTG 59.837 50.000 0.00 0.00 33.81 3.66
211 212 2.118313 TGATGCATTCTGACCACTGG 57.882 50.000 0.00 0.00 0.00 4.00
212 213 1.340308 TGATGCATTCTGACCACTGGG 60.340 52.381 0.00 0.00 41.29 4.45
213 214 0.682209 ATGCATTCTGACCACTGGGC 60.682 55.000 0.00 0.00 37.90 5.36
214 215 1.001641 GCATTCTGACCACTGGGCT 60.002 57.895 1.57 0.00 37.90 5.19
215 216 0.253044 GCATTCTGACCACTGGGCTA 59.747 55.000 1.57 0.00 37.90 3.93
216 217 1.745141 GCATTCTGACCACTGGGCTAG 60.745 57.143 1.57 0.00 37.90 3.42
217 218 1.833630 CATTCTGACCACTGGGCTAGA 59.166 52.381 4.33 0.79 37.90 2.43
218 219 2.024176 TTCTGACCACTGGGCTAGAA 57.976 50.000 4.33 7.05 37.20 2.10
219 220 1.267121 TCTGACCACTGGGCTAGAAC 58.733 55.000 4.33 0.00 37.90 3.01
220 221 0.250513 CTGACCACTGGGCTAGAACC 59.749 60.000 4.33 0.00 37.90 3.62
221 222 1.218316 GACCACTGGGCTAGAACCG 59.782 63.158 4.33 0.00 37.90 4.44
222 223 2.240162 GACCACTGGGCTAGAACCGG 62.240 65.000 4.33 0.00 40.32 5.28
223 224 1.987855 CCACTGGGCTAGAACCGGA 60.988 63.158 9.46 0.00 37.80 5.14
224 225 1.338136 CCACTGGGCTAGAACCGGAT 61.338 60.000 9.46 0.00 37.80 4.18
225 226 1.410004 CACTGGGCTAGAACCGGATA 58.590 55.000 9.46 0.00 37.80 2.59
226 227 1.068741 CACTGGGCTAGAACCGGATAC 59.931 57.143 9.46 0.00 37.80 2.24
227 228 1.342674 ACTGGGCTAGAACCGGATACA 60.343 52.381 9.46 0.00 37.80 2.29
228 229 1.341531 CTGGGCTAGAACCGGATACAG 59.658 57.143 9.46 0.36 36.43 2.74
229 230 1.063492 TGGGCTAGAACCGGATACAGA 60.063 52.381 9.46 0.00 0.00 3.41
230 231 1.614413 GGGCTAGAACCGGATACAGAG 59.386 57.143 9.46 0.00 0.00 3.35
231 232 2.584236 GGCTAGAACCGGATACAGAGA 58.416 52.381 9.46 0.00 0.00 3.10
232 233 2.293955 GGCTAGAACCGGATACAGAGAC 59.706 54.545 9.46 0.00 0.00 3.36
233 234 2.950309 GCTAGAACCGGATACAGAGACA 59.050 50.000 9.46 0.00 0.00 3.41
234 235 3.243134 GCTAGAACCGGATACAGAGACAC 60.243 52.174 9.46 0.00 0.00 3.67
240 241 3.070446 ACCGGATACAGAGACACACAAAA 59.930 43.478 9.46 0.00 0.00 2.44
298 299 7.546358 TGAGCAAACTTTTTATACATGATGGG 58.454 34.615 0.00 0.00 0.00 4.00
345 347 5.559148 TTTTTGTATGGGGTGCTCATTTT 57.441 34.783 0.00 0.00 0.00 1.82
376 378 7.937649 ACAACAAGATAAACCCTCTTTTGTAC 58.062 34.615 0.00 0.00 35.14 2.90
378 380 6.527423 ACAAGATAAACCCTCTTTTGTACGA 58.473 36.000 0.00 0.00 30.60 3.43
413 417 7.552050 TCCAAAATATGTGAGGGACATTTTT 57.448 32.000 0.00 0.00 43.20 1.94
424 428 8.739039 TGTGAGGGACATTTTTAAAGTATGATG 58.261 33.333 15.35 7.36 0.00 3.07
425 429 8.739972 GTGAGGGACATTTTTAAAGTATGATGT 58.260 33.333 15.35 9.68 0.00 3.06
426 430 9.967451 TGAGGGACATTTTTAAAGTATGATGTA 57.033 29.630 15.35 0.49 0.00 2.29
520 525 7.936584 TCTTTAAATAGGCATTGAATAACCGG 58.063 34.615 0.00 0.00 0.00 5.28
524 529 2.099405 AGGCATTGAATAACCGGGTTG 58.901 47.619 22.44 5.54 0.00 3.77
529 534 5.175127 GCATTGAATAACCGGGTTGAATTT 58.825 37.500 22.44 10.22 0.00 1.82
566 571 8.854979 AATAAAAGCCAAACAATTTTGAAAGC 57.145 26.923 0.00 0.00 44.38 3.51
648 656 8.256611 AGAAAGGAAAACAAGAAAAGAAAAGC 57.743 30.769 0.00 0.00 0.00 3.51
651 659 8.565896 AAGGAAAACAAGAAAAGAAAAGCAAT 57.434 26.923 0.00 0.00 0.00 3.56
652 660 9.665719 AAGGAAAACAAGAAAAGAAAAGCAATA 57.334 25.926 0.00 0.00 0.00 1.90
653 661 9.836864 AGGAAAACAAGAAAAGAAAAGCAATAT 57.163 25.926 0.00 0.00 0.00 1.28
698 726 2.086610 AAAGGGAGAAAGCTTGCCAA 57.913 45.000 0.00 0.00 0.00 4.52
726 754 0.902516 AGGTCAGTCAGAGTCCAGGC 60.903 60.000 0.00 0.00 0.00 4.85
776 804 8.270137 AGAAAATTAAATTACCAACCCAACCT 57.730 30.769 0.00 0.00 0.00 3.50
792 820 0.328258 ACCTCCATCGTTTTCCCCTG 59.672 55.000 0.00 0.00 0.00 4.45
811 839 2.209315 CCAACCCAACCAAGCCCAG 61.209 63.158 0.00 0.00 0.00 4.45
923 951 1.340405 CCCCAAACACCTCATCCTCTG 60.340 57.143 0.00 0.00 0.00 3.35
930 958 4.519437 CTCATCCTCTGGCGCGCA 62.519 66.667 34.42 17.93 0.00 6.09
971 999 0.725133 TTCCCCTCTTCCCCTCATCT 59.275 55.000 0.00 0.00 0.00 2.90
1225 1256 2.202676 CTCGCTCTCCCGTTCTGC 60.203 66.667 0.00 0.00 0.00 4.26
1431 1469 3.805422 TGCAGTTTCAGTTCGTATTTCGT 59.195 39.130 0.00 0.00 40.80 3.85
1461 1505 6.352222 GGACTATCTGAAAAGTGAGATTGGGA 60.352 42.308 1.26 0.00 31.29 4.37
1462 1506 7.020827 ACTATCTGAAAAGTGAGATTGGGAA 57.979 36.000 0.00 0.00 31.29 3.97
1469 1513 5.584551 AAAGTGAGATTGGGAAAGGTAGT 57.415 39.130 0.00 0.00 0.00 2.73
1554 4704 2.092212 CCCCCTAGCACAGTGAATCAAT 60.092 50.000 4.15 0.00 0.00 2.57
1577 4728 8.456471 CAATGTGTGAATTCAGTACTGATGATT 58.544 33.333 25.68 21.64 39.64 2.57
1584 4735 6.615264 ATTCAGTACTGATGATTGATGTGC 57.385 37.500 25.68 0.00 39.64 4.57
1604 4755 4.335594 GTGCTTTGTCTTTGGACTGTACTT 59.664 41.667 0.00 0.00 42.54 2.24
1605 4756 4.335315 TGCTTTGTCTTTGGACTGTACTTG 59.665 41.667 0.00 0.00 42.54 3.16
1606 4757 4.574828 GCTTTGTCTTTGGACTGTACTTGA 59.425 41.667 0.00 0.00 42.54 3.02
1607 4758 5.239525 GCTTTGTCTTTGGACTGTACTTGAT 59.760 40.000 0.00 0.00 42.54 2.57
1608 4759 6.238759 GCTTTGTCTTTGGACTGTACTTGATT 60.239 38.462 0.00 0.00 42.54 2.57
1609 4760 7.041372 GCTTTGTCTTTGGACTGTACTTGATTA 60.041 37.037 0.00 0.00 42.54 1.75
1610 4761 7.724305 TTGTCTTTGGACTGTACTTGATTAC 57.276 36.000 0.00 0.00 42.54 1.89
1611 4762 7.062749 TGTCTTTGGACTGTACTTGATTACT 57.937 36.000 0.00 0.00 42.54 2.24
1634 4785 5.835113 TGCTTTTTGCTAGAAGTTGTTCT 57.165 34.783 0.00 0.00 41.92 3.01
1686 4837 7.148967 GCGGTTCAGAAATTACATCTTTGTTTC 60.149 37.037 0.00 0.00 37.28 2.78
1710 4861 1.065551 GAGAAAACTGCGTTTGTGGCT 59.934 47.619 7.30 4.15 35.80 4.75
1730 4881 2.627699 CTGGTTTTGGCCTCTGCTTAAA 59.372 45.455 3.32 0.00 37.74 1.52
1733 4884 4.102367 TGGTTTTGGCCTCTGCTTAAAAAT 59.898 37.500 3.32 0.00 36.25 1.82
1734 4885 5.063204 GGTTTTGGCCTCTGCTTAAAAATT 58.937 37.500 3.32 0.00 36.25 1.82
1782 4973 1.627297 AAGAATGGAGGAGGGGCGAC 61.627 60.000 0.00 0.00 0.00 5.19
1783 4974 2.041265 AATGGAGGAGGGGCGACT 59.959 61.111 0.00 0.00 0.00 4.18
1826 5018 1.065564 TGCTGTATGCCTGTATGTGCA 60.066 47.619 0.00 0.00 42.52 4.57
1961 5161 4.651503 TGGTTTCTTTGGACCATGCTTTTA 59.348 37.500 0.00 0.00 40.85 1.52
1988 5314 9.990360 TTTTTGTTAGAAGTTGTTCTTTTCCTT 57.010 25.926 0.00 0.00 40.35 3.36
2129 6371 7.859325 AGTTTTGTGTTAGTTCTAGAAAGCA 57.141 32.000 6.78 0.00 0.00 3.91
2468 7087 6.537301 CCGTTAATACCACTGCATTTAAGAGA 59.463 38.462 0.00 0.00 0.00 3.10
2545 7164 7.100409 AGGAAATAGAGAAAACAGTAGCACTC 58.900 38.462 0.00 0.00 0.00 3.51
3060 7697 3.560068 GGTGAAATAACTGCGTAGGGATG 59.440 47.826 5.26 0.00 0.00 3.51
3235 7878 4.789481 GCAGAATGAAACTTTCGTTGCTGA 60.789 41.667 23.32 1.29 39.69 4.26
3419 8067 4.265073 GAATCAATAACCTGTCCACTGCT 58.735 43.478 0.00 0.00 0.00 4.24
3468 8116 0.752743 TGCTGCTGCTGAGGTGTTTT 60.753 50.000 17.00 0.00 40.48 2.43
3469 8117 0.039708 GCTGCTGCTGAGGTGTTTTC 60.040 55.000 10.92 0.00 36.03 2.29
3470 8118 1.602311 CTGCTGCTGAGGTGTTTTCT 58.398 50.000 0.00 0.00 0.00 2.52
3471 8119 1.266175 CTGCTGCTGAGGTGTTTTCTG 59.734 52.381 0.00 0.00 0.00 3.02
3472 8120 1.312815 GCTGCTGAGGTGTTTTCTGT 58.687 50.000 0.00 0.00 0.00 3.41
3473 8121 1.678101 GCTGCTGAGGTGTTTTCTGTT 59.322 47.619 0.00 0.00 0.00 3.16
3474 8122 2.099756 GCTGCTGAGGTGTTTTCTGTTT 59.900 45.455 0.00 0.00 0.00 2.83
3558 8206 1.205820 GTTGTTCGTTACCTGCGGC 59.794 57.895 0.00 0.00 0.00 6.53
3617 8265 2.407090 GCAAAAAGCTGACATGGGAAC 58.593 47.619 0.00 0.00 41.15 3.62
3650 8298 7.799081 TCTCTCCTGTTGTTCATATGATGATT 58.201 34.615 6.17 0.00 39.39 2.57
3662 8310 6.944096 TCATATGATGATTCAGAGGATGGTC 58.056 40.000 0.00 0.00 29.68 4.02
3671 8319 3.017442 TCAGAGGATGGTCTCGTTACAG 58.983 50.000 0.00 0.00 38.71 2.74
3687 8338 6.913170 TCGTTACAGTTTACTAGGTGGTAAG 58.087 40.000 0.00 0.00 33.90 2.34
3716 8367 4.378978 CGTTTGATTTTCATAGAACCGCCA 60.379 41.667 0.00 0.00 0.00 5.69
3749 8400 9.065871 GTGCTTATGTTACACAAAAGAATGATC 57.934 33.333 7.75 0.00 34.43 2.92
3762 8413 4.824479 AGAATGATCGGGCCAAAATTTT 57.176 36.364 4.39 0.00 0.00 1.82
3770 8421 2.799917 CGGGCCAAAATTTTGACGTTCA 60.800 45.455 28.44 0.00 40.55 3.18
3810 8468 6.974048 TCCTTGCAAATGATTGTGATTTATCG 59.026 34.615 0.00 0.00 38.85 2.92
3827 8485 2.455674 TCGCACAGTGATTTAGCAGT 57.544 45.000 4.15 0.00 0.00 4.40
3832 8490 3.372206 GCACAGTGATTTAGCAGTAGGTG 59.628 47.826 4.15 0.00 0.00 4.00
3844 8502 2.350522 CAGTAGGTGTTCACATGAGGC 58.649 52.381 0.00 0.00 0.00 4.70
3850 8508 0.107643 TGTTCACATGAGGCGGTTGA 59.892 50.000 0.00 0.00 0.00 3.18
3869 8527 5.279456 GGTTGAAATACCAAGCTCCAAATGT 60.279 40.000 0.00 0.00 40.32 2.71
3926 8584 3.365868 GCACAATGCATCCGTTCTGTTAA 60.366 43.478 0.00 0.00 44.26 2.01
4037 8790 8.601845 AATAACAGCTAAATATACATGCACGA 57.398 30.769 0.00 0.00 0.00 4.35
4243 9722 1.130054 TGGAGGCTGGGCTCCATATC 61.130 60.000 32.63 13.90 44.02 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.509548 TCCCCCATGTATTGTCCTTCTG 59.490 50.000 0.00 0.00 0.00 3.02
1 2 2.858644 TCCCCCATGTATTGTCCTTCT 58.141 47.619 0.00 0.00 0.00 2.85
2 3 3.884037 ATCCCCCATGTATTGTCCTTC 57.116 47.619 0.00 0.00 0.00 3.46
3 4 4.051478 TGTATCCCCCATGTATTGTCCTT 58.949 43.478 0.00 0.00 0.00 3.36
4 5 3.675613 TGTATCCCCCATGTATTGTCCT 58.324 45.455 0.00 0.00 0.00 3.85
5 6 4.042809 TCATGTATCCCCCATGTATTGTCC 59.957 45.833 0.00 0.00 40.43 4.02
6 7 5.241403 TCATGTATCCCCCATGTATTGTC 57.759 43.478 0.00 0.00 40.43 3.18
7 8 5.865977 ATCATGTATCCCCCATGTATTGT 57.134 39.130 0.00 0.00 40.43 2.71
8 9 6.071221 CCAAATCATGTATCCCCCATGTATTG 60.071 42.308 0.00 0.00 40.43 1.90
9 10 6.018469 CCAAATCATGTATCCCCCATGTATT 58.982 40.000 0.00 0.00 40.43 1.89
10 11 5.518904 CCCAAATCATGTATCCCCCATGTAT 60.519 44.000 0.00 0.00 40.43 2.29
11 12 4.202663 CCCAAATCATGTATCCCCCATGTA 60.203 45.833 0.00 0.00 40.43 2.29
12 13 3.438372 CCCAAATCATGTATCCCCCATGT 60.438 47.826 0.00 0.00 40.43 3.21
13 14 3.167485 CCCAAATCATGTATCCCCCATG 58.833 50.000 0.00 0.00 40.82 3.66
14 15 3.070543 TCCCAAATCATGTATCCCCCAT 58.929 45.455 0.00 0.00 0.00 4.00
15 16 2.508156 TCCCAAATCATGTATCCCCCA 58.492 47.619 0.00 0.00 0.00 4.96
16 17 3.230976 GTTCCCAAATCATGTATCCCCC 58.769 50.000 0.00 0.00 0.00 5.40
17 18 3.891366 CTGTTCCCAAATCATGTATCCCC 59.109 47.826 0.00 0.00 0.00 4.81
18 19 4.536765 ACTGTTCCCAAATCATGTATCCC 58.463 43.478 0.00 0.00 0.00 3.85
19 20 6.357367 AGTACTGTTCCCAAATCATGTATCC 58.643 40.000 0.00 0.00 0.00 2.59
20 21 7.865706 AAGTACTGTTCCCAAATCATGTATC 57.134 36.000 0.00 0.00 0.00 2.24
21 22 9.174166 GTAAAGTACTGTTCCCAAATCATGTAT 57.826 33.333 0.00 0.00 0.00 2.29
22 23 8.158132 TGTAAAGTACTGTTCCCAAATCATGTA 58.842 33.333 0.00 0.00 0.00 2.29
23 24 7.001674 TGTAAAGTACTGTTCCCAAATCATGT 58.998 34.615 0.00 0.00 0.00 3.21
24 25 7.174946 AGTGTAAAGTACTGTTCCCAAATCATG 59.825 37.037 0.00 0.00 0.00 3.07
25 26 7.231467 AGTGTAAAGTACTGTTCCCAAATCAT 58.769 34.615 0.00 0.00 0.00 2.45
26 27 6.597562 AGTGTAAAGTACTGTTCCCAAATCA 58.402 36.000 0.00 0.00 0.00 2.57
27 28 7.360361 CAAGTGTAAAGTACTGTTCCCAAATC 58.640 38.462 0.00 0.00 0.00 2.17
28 29 6.238925 GCAAGTGTAAAGTACTGTTCCCAAAT 60.239 38.462 0.00 0.00 0.00 2.32
29 30 5.066764 GCAAGTGTAAAGTACTGTTCCCAAA 59.933 40.000 0.00 0.00 0.00 3.28
30 31 4.577283 GCAAGTGTAAAGTACTGTTCCCAA 59.423 41.667 0.00 0.00 0.00 4.12
31 32 4.131596 GCAAGTGTAAAGTACTGTTCCCA 58.868 43.478 0.00 0.00 0.00 4.37
32 33 3.501062 GGCAAGTGTAAAGTACTGTTCCC 59.499 47.826 0.00 0.00 0.00 3.97
33 34 4.131596 TGGCAAGTGTAAAGTACTGTTCC 58.868 43.478 0.00 0.00 0.00 3.62
34 35 5.468746 TGATGGCAAGTGTAAAGTACTGTTC 59.531 40.000 0.00 0.00 0.00 3.18
35 36 5.238650 GTGATGGCAAGTGTAAAGTACTGTT 59.761 40.000 0.00 0.00 0.00 3.16
36 37 4.755123 GTGATGGCAAGTGTAAAGTACTGT 59.245 41.667 0.00 0.00 0.00 3.55
37 38 4.754618 TGTGATGGCAAGTGTAAAGTACTG 59.245 41.667 0.00 0.00 0.00 2.74
38 39 4.968259 TGTGATGGCAAGTGTAAAGTACT 58.032 39.130 0.00 0.00 0.00 2.73
39 40 4.994852 TCTGTGATGGCAAGTGTAAAGTAC 59.005 41.667 0.00 0.00 0.00 2.73
40 41 5.222079 TCTGTGATGGCAAGTGTAAAGTA 57.778 39.130 0.00 0.00 0.00 2.24
41 42 4.085357 TCTGTGATGGCAAGTGTAAAGT 57.915 40.909 0.00 0.00 0.00 2.66
42 43 5.437289 TTTCTGTGATGGCAAGTGTAAAG 57.563 39.130 0.00 0.00 0.00 1.85
43 44 4.261572 GCTTTCTGTGATGGCAAGTGTAAA 60.262 41.667 0.00 0.00 0.00 2.01
44 45 3.253188 GCTTTCTGTGATGGCAAGTGTAA 59.747 43.478 0.00 0.00 0.00 2.41
45 46 2.813754 GCTTTCTGTGATGGCAAGTGTA 59.186 45.455 0.00 0.00 0.00 2.90
46 47 1.610522 GCTTTCTGTGATGGCAAGTGT 59.389 47.619 0.00 0.00 0.00 3.55
47 48 1.610038 TGCTTTCTGTGATGGCAAGTG 59.390 47.619 0.00 0.00 0.00 3.16
48 49 1.610522 GTGCTTTCTGTGATGGCAAGT 59.389 47.619 0.00 0.00 34.65 3.16
49 50 1.884579 AGTGCTTTCTGTGATGGCAAG 59.115 47.619 0.00 0.00 34.65 4.01
50 51 1.985473 AGTGCTTTCTGTGATGGCAA 58.015 45.000 0.00 0.00 34.65 4.52
51 52 1.610038 CAAGTGCTTTCTGTGATGGCA 59.390 47.619 0.00 0.00 0.00 4.92
52 53 1.610522 ACAAGTGCTTTCTGTGATGGC 59.389 47.619 0.00 0.00 0.00 4.40
53 54 5.633830 ATTACAAGTGCTTTCTGTGATGG 57.366 39.130 0.00 0.00 0.00 3.51
54 55 6.372659 AGGTATTACAAGTGCTTTCTGTGATG 59.627 38.462 0.00 0.00 0.00 3.07
55 56 6.372659 CAGGTATTACAAGTGCTTTCTGTGAT 59.627 38.462 0.00 0.00 0.00 3.06
56 57 5.700832 CAGGTATTACAAGTGCTTTCTGTGA 59.299 40.000 0.00 0.00 0.00 3.58
57 58 5.106555 CCAGGTATTACAAGTGCTTTCTGTG 60.107 44.000 0.00 0.00 0.00 3.66
58 59 5.003804 CCAGGTATTACAAGTGCTTTCTGT 58.996 41.667 0.00 0.00 0.00 3.41
59 60 5.003804 ACCAGGTATTACAAGTGCTTTCTG 58.996 41.667 0.00 0.00 0.00 3.02
60 61 5.242795 ACCAGGTATTACAAGTGCTTTCT 57.757 39.130 0.00 0.00 0.00 2.52
61 62 6.821665 TCATACCAGGTATTACAAGTGCTTTC 59.178 38.462 9.67 0.00 0.00 2.62
62 63 6.717289 TCATACCAGGTATTACAAGTGCTTT 58.283 36.000 9.67 0.00 0.00 3.51
63 64 6.308015 TCATACCAGGTATTACAAGTGCTT 57.692 37.500 9.67 0.00 0.00 3.91
64 65 5.950544 TCATACCAGGTATTACAAGTGCT 57.049 39.130 9.67 0.00 0.00 4.40
65 66 5.878116 TGTTCATACCAGGTATTACAAGTGC 59.122 40.000 16.89 3.99 0.00 4.40
66 67 7.915293 TTGTTCATACCAGGTATTACAAGTG 57.085 36.000 22.42 9.38 31.52 3.16
73 74 9.408648 CCTTCTTATTTGTTCATACCAGGTATT 57.591 33.333 9.67 0.00 0.00 1.89
74 75 8.557450 ACCTTCTTATTTGTTCATACCAGGTAT 58.443 33.333 6.25 6.25 0.00 2.73
75 76 7.924541 ACCTTCTTATTTGTTCATACCAGGTA 58.075 34.615 0.39 0.39 0.00 3.08
76 77 6.790319 ACCTTCTTATTTGTTCATACCAGGT 58.210 36.000 0.00 0.00 0.00 4.00
77 78 8.840321 CATACCTTCTTATTTGTTCATACCAGG 58.160 37.037 0.00 0.00 0.00 4.45
78 79 9.613428 TCATACCTTCTTATTTGTTCATACCAG 57.387 33.333 0.00 0.00 0.00 4.00
79 80 9.967451 TTCATACCTTCTTATTTGTTCATACCA 57.033 29.630 0.00 0.00 0.00 3.25
105 106 9.136323 AGATCTTGTTCAAGTAAGGTCATTTTT 57.864 29.630 11.52 0.00 36.68 1.94
106 107 8.571336 CAGATCTTGTTCAAGTAAGGTCATTTT 58.429 33.333 11.52 0.00 36.68 1.82
107 108 7.721399 ACAGATCTTGTTCAAGTAAGGTCATTT 59.279 33.333 11.52 0.00 36.68 2.32
108 109 7.227156 ACAGATCTTGTTCAAGTAAGGTCATT 58.773 34.615 11.52 0.00 36.68 2.57
109 110 6.773638 ACAGATCTTGTTCAAGTAAGGTCAT 58.226 36.000 11.52 0.00 36.68 3.06
110 111 6.174720 ACAGATCTTGTTCAAGTAAGGTCA 57.825 37.500 11.52 0.00 36.68 4.02
123 124 7.449086 GGTACTAGCCTATAGAACAGATCTTGT 59.551 40.741 0.00 0.00 43.45 3.16
124 125 7.361371 CGGTACTAGCCTATAGAACAGATCTTG 60.361 44.444 0.00 0.00 39.71 3.02
125 126 6.655848 CGGTACTAGCCTATAGAACAGATCTT 59.344 42.308 0.00 0.00 39.71 2.40
126 127 6.174760 CGGTACTAGCCTATAGAACAGATCT 58.825 44.000 0.00 0.00 42.48 2.75
127 128 5.939296 ACGGTACTAGCCTATAGAACAGATC 59.061 44.000 0.00 0.00 0.00 2.75
128 129 5.878627 ACGGTACTAGCCTATAGAACAGAT 58.121 41.667 0.00 0.00 0.00 2.90
129 130 5.301835 ACGGTACTAGCCTATAGAACAGA 57.698 43.478 0.00 0.00 0.00 3.41
130 131 5.759963 CAACGGTACTAGCCTATAGAACAG 58.240 45.833 0.00 0.00 0.00 3.16
131 132 4.037208 GCAACGGTACTAGCCTATAGAACA 59.963 45.833 0.00 0.00 0.00 3.18
132 133 4.544651 GCAACGGTACTAGCCTATAGAAC 58.455 47.826 0.00 0.00 0.00 3.01
133 134 3.571401 GGCAACGGTACTAGCCTATAGAA 59.429 47.826 0.00 0.00 43.70 2.10
134 135 3.152341 GGCAACGGTACTAGCCTATAGA 58.848 50.000 0.00 0.00 43.70 1.98
135 136 3.572604 GGCAACGGTACTAGCCTATAG 57.427 52.381 9.93 0.00 43.70 1.31
141 142 0.535797 AAGGAGGCAACGGTACTAGC 59.464 55.000 0.00 0.00 46.39 3.42
142 143 3.429960 GGTAAAGGAGGCAACGGTACTAG 60.430 52.174 0.00 0.00 46.39 2.57
143 144 2.497273 GGTAAAGGAGGCAACGGTACTA 59.503 50.000 0.00 0.00 46.39 1.82
144 145 1.277273 GGTAAAGGAGGCAACGGTACT 59.723 52.381 0.00 0.00 46.39 2.73
145 146 1.002315 TGGTAAAGGAGGCAACGGTAC 59.998 52.381 0.00 0.00 46.39 3.34
146 147 1.350071 TGGTAAAGGAGGCAACGGTA 58.650 50.000 0.00 0.00 46.39 4.02
147 148 0.475044 TTGGTAAAGGAGGCAACGGT 59.525 50.000 0.00 0.00 46.39 4.83
148 149 1.834188 ATTGGTAAAGGAGGCAACGG 58.166 50.000 0.00 0.00 46.39 4.44
149 150 3.377172 CCTTATTGGTAAAGGAGGCAACG 59.623 47.826 0.00 0.00 45.41 4.10
150 151 4.595986 TCCTTATTGGTAAAGGAGGCAAC 58.404 43.478 0.43 0.00 45.97 4.17
151 152 4.938575 TCCTTATTGGTAAAGGAGGCAA 57.061 40.909 0.43 0.00 45.97 4.52
157 158 3.381590 GCTTGCCTCCTTATTGGTAAAGG 59.618 47.826 0.00 0.00 44.17 3.11
158 159 4.016444 TGCTTGCCTCCTTATTGGTAAAG 58.984 43.478 0.00 0.00 37.07 1.85
159 160 3.761752 GTGCTTGCCTCCTTATTGGTAAA 59.238 43.478 0.00 0.00 37.07 2.01
160 161 3.010138 AGTGCTTGCCTCCTTATTGGTAA 59.990 43.478 0.00 0.00 37.07 2.85
161 162 2.576191 AGTGCTTGCCTCCTTATTGGTA 59.424 45.455 0.00 0.00 37.07 3.25
162 163 1.355720 AGTGCTTGCCTCCTTATTGGT 59.644 47.619 0.00 0.00 37.07 3.67
163 164 2.019984 GAGTGCTTGCCTCCTTATTGG 58.980 52.381 0.00 0.00 37.10 3.16
164 165 2.715046 TGAGTGCTTGCCTCCTTATTG 58.285 47.619 8.04 0.00 0.00 1.90
165 166 3.439857 TTGAGTGCTTGCCTCCTTATT 57.560 42.857 8.04 0.00 0.00 1.40
166 167 3.201708 AGATTGAGTGCTTGCCTCCTTAT 59.798 43.478 8.04 1.91 0.00 1.73
167 168 2.573462 AGATTGAGTGCTTGCCTCCTTA 59.427 45.455 8.04 0.00 0.00 2.69
168 169 1.353694 AGATTGAGTGCTTGCCTCCTT 59.646 47.619 8.04 0.00 0.00 3.36
169 170 0.990374 AGATTGAGTGCTTGCCTCCT 59.010 50.000 8.04 0.00 0.00 3.69
170 171 1.093159 CAGATTGAGTGCTTGCCTCC 58.907 55.000 8.04 0.00 0.00 4.30
171 172 1.093159 CCAGATTGAGTGCTTGCCTC 58.907 55.000 4.81 4.81 0.00 4.70
172 173 0.403271 ACCAGATTGAGTGCTTGCCT 59.597 50.000 0.00 0.00 0.00 4.75
173 174 1.068055 CAACCAGATTGAGTGCTTGCC 60.068 52.381 0.00 0.00 41.23 4.52
174 175 1.881973 TCAACCAGATTGAGTGCTTGC 59.118 47.619 0.00 0.00 42.62 4.01
179 180 7.790988 TCAGAATGCATCAACCAGATTGAGTG 61.791 42.308 0.00 0.00 43.45 3.51
180 181 5.805424 TCAGAATGCATCAACCAGATTGAGT 60.805 40.000 0.00 0.00 43.45 3.41
181 182 4.638865 TCAGAATGCATCAACCAGATTGAG 59.361 41.667 0.00 0.00 43.45 3.02
182 183 4.397103 GTCAGAATGCATCAACCAGATTGA 59.603 41.667 0.00 0.00 44.03 2.57
183 184 4.439700 GGTCAGAATGCATCAACCAGATTG 60.440 45.833 0.00 0.00 36.58 2.67
184 185 3.698040 GGTCAGAATGCATCAACCAGATT 59.302 43.478 0.00 0.00 36.58 2.40
185 186 3.285484 GGTCAGAATGCATCAACCAGAT 58.715 45.455 0.00 0.00 36.58 2.90
186 187 2.040145 TGGTCAGAATGCATCAACCAGA 59.960 45.455 14.81 0.80 39.72 3.86
187 188 2.163010 GTGGTCAGAATGCATCAACCAG 59.837 50.000 17.71 0.50 43.05 4.00
188 189 2.161855 GTGGTCAGAATGCATCAACCA 58.838 47.619 14.81 14.81 41.32 3.67
189 190 2.163010 CAGTGGTCAGAATGCATCAACC 59.837 50.000 0.00 6.24 36.92 3.77
190 191 2.163010 CCAGTGGTCAGAATGCATCAAC 59.837 50.000 0.00 0.00 34.76 3.18
191 192 2.439409 CCAGTGGTCAGAATGCATCAA 58.561 47.619 0.00 0.00 34.76 2.57
192 193 1.340308 CCCAGTGGTCAGAATGCATCA 60.340 52.381 8.74 0.00 34.76 3.07
193 194 1.386533 CCCAGTGGTCAGAATGCATC 58.613 55.000 8.74 0.00 34.76 3.91
194 195 0.682209 GCCCAGTGGTCAGAATGCAT 60.682 55.000 8.74 0.00 34.76 3.96
195 196 1.303561 GCCCAGTGGTCAGAATGCA 60.304 57.895 8.74 0.00 34.76 3.96
196 197 0.253044 TAGCCCAGTGGTCAGAATGC 59.747 55.000 8.74 2.06 34.76 3.56
197 198 1.833630 TCTAGCCCAGTGGTCAGAATG 59.166 52.381 8.74 0.00 37.54 2.67
198 199 2.237392 GTTCTAGCCCAGTGGTCAGAAT 59.763 50.000 16.18 0.00 36.55 2.40
199 200 1.623811 GTTCTAGCCCAGTGGTCAGAA 59.376 52.381 8.74 10.39 33.70 3.02
200 201 1.267121 GTTCTAGCCCAGTGGTCAGA 58.733 55.000 8.74 4.51 0.00 3.27
201 202 0.250513 GGTTCTAGCCCAGTGGTCAG 59.749 60.000 8.74 1.99 0.00 3.51
202 203 1.541310 CGGTTCTAGCCCAGTGGTCA 61.541 60.000 8.74 0.00 0.00 4.02
203 204 1.218316 CGGTTCTAGCCCAGTGGTC 59.782 63.158 8.74 0.00 0.00 4.02
204 205 2.291043 CCGGTTCTAGCCCAGTGGT 61.291 63.158 8.74 0.00 0.00 4.16
205 206 1.338136 ATCCGGTTCTAGCCCAGTGG 61.338 60.000 0.63 0.63 0.00 4.00
206 207 1.068741 GTATCCGGTTCTAGCCCAGTG 59.931 57.143 0.00 0.00 0.00 3.66
207 208 1.342674 TGTATCCGGTTCTAGCCCAGT 60.343 52.381 0.00 0.00 0.00 4.00
208 209 1.341531 CTGTATCCGGTTCTAGCCCAG 59.658 57.143 0.00 0.00 0.00 4.45
209 210 1.063492 TCTGTATCCGGTTCTAGCCCA 60.063 52.381 0.00 0.00 0.00 5.36
210 211 1.614413 CTCTGTATCCGGTTCTAGCCC 59.386 57.143 0.00 0.00 0.00 5.19
211 212 2.293955 GTCTCTGTATCCGGTTCTAGCC 59.706 54.545 0.00 0.00 0.00 3.93
212 213 2.950309 TGTCTCTGTATCCGGTTCTAGC 59.050 50.000 0.00 0.00 0.00 3.42
213 214 3.945921 TGTGTCTCTGTATCCGGTTCTAG 59.054 47.826 0.00 0.00 0.00 2.43
214 215 3.693085 GTGTGTCTCTGTATCCGGTTCTA 59.307 47.826 0.00 0.00 0.00 2.10
215 216 2.492484 GTGTGTCTCTGTATCCGGTTCT 59.508 50.000 0.00 0.00 0.00 3.01
216 217 2.230508 TGTGTGTCTCTGTATCCGGTTC 59.769 50.000 0.00 0.00 0.00 3.62
217 218 2.244695 TGTGTGTCTCTGTATCCGGTT 58.755 47.619 0.00 0.00 0.00 4.44
218 219 1.919240 TGTGTGTCTCTGTATCCGGT 58.081 50.000 0.00 0.00 0.00 5.28
219 220 3.313012 TTTGTGTGTCTCTGTATCCGG 57.687 47.619 0.00 0.00 0.00 5.14
275 276 6.070881 TGCCCATCATGTATAAAAAGTTTGCT 60.071 34.615 0.00 0.00 0.00 3.91
276 277 6.035975 GTGCCCATCATGTATAAAAAGTTTGC 59.964 38.462 0.00 0.00 0.00 3.68
281 282 9.868277 TTTTTAGTGCCCATCATGTATAAAAAG 57.132 29.630 0.00 0.00 31.14 2.27
358 360 6.128117 TGCAATCGTACAAAAGAGGGTTTATC 60.128 38.462 0.00 0.00 0.00 1.75
359 361 5.708230 TGCAATCGTACAAAAGAGGGTTTAT 59.292 36.000 0.00 0.00 0.00 1.40
360 362 5.064558 TGCAATCGTACAAAAGAGGGTTTA 58.935 37.500 0.00 0.00 0.00 2.01
362 364 3.482436 TGCAATCGTACAAAAGAGGGTT 58.518 40.909 0.00 0.00 0.00 4.11
363 365 3.134574 TGCAATCGTACAAAAGAGGGT 57.865 42.857 0.00 0.00 0.00 4.34
390 392 9.717942 TTTAAAAATGTCCCTCACATATTTTGG 57.282 29.630 12.68 0.00 45.77 3.28
504 509 2.099405 CAACCCGGTTATTCAATGCCT 58.901 47.619 1.43 0.00 0.00 4.75
505 510 2.096248 TCAACCCGGTTATTCAATGCC 58.904 47.619 1.43 0.00 0.00 4.40
545 550 5.893897 TGCTTTCAAAATTGTTTGGCTTT 57.106 30.435 0.00 0.00 43.70 3.51
547 552 5.589452 TCATTGCTTTCAAAATTGTTTGGCT 59.411 32.000 0.00 0.00 43.70 4.75
624 632 8.028540 TGCTTTTCTTTTCTTGTTTTCCTTTC 57.971 30.769 0.00 0.00 0.00 2.62
672 700 5.047021 GGCAAGCTTTCTCCCTTTTTCTATT 60.047 40.000 0.00 0.00 0.00 1.73
674 702 3.826729 GGCAAGCTTTCTCCCTTTTTCTA 59.173 43.478 0.00 0.00 0.00 2.10
678 706 2.086610 TGGCAAGCTTTCTCCCTTTT 57.913 45.000 0.00 0.00 0.00 2.27
681 709 0.540597 GGTTGGCAAGCTTTCTCCCT 60.541 55.000 21.39 0.00 0.00 4.20
682 710 1.866853 CGGTTGGCAAGCTTTCTCCC 61.867 60.000 25.03 8.35 0.00 4.30
683 711 1.172812 ACGGTTGGCAAGCTTTCTCC 61.173 55.000 25.03 9.06 0.00 3.71
684 712 0.040067 CACGGTTGGCAAGCTTTCTC 60.040 55.000 25.03 0.53 0.00 2.87
685 713 0.751643 ACACGGTTGGCAAGCTTTCT 60.752 50.000 25.03 2.81 0.00 2.52
686 714 0.948678 TACACGGTTGGCAAGCTTTC 59.051 50.000 25.03 2.02 0.00 2.62
698 726 2.296471 CTCTGACTGACCTTTACACGGT 59.704 50.000 0.00 0.00 37.50 4.83
726 754 4.729918 GGTGGGCTGGGCTGACTG 62.730 72.222 0.00 0.00 0.00 3.51
773 801 0.328258 CAGGGGAAAACGATGGAGGT 59.672 55.000 0.00 0.00 0.00 3.85
776 804 1.001393 GGCAGGGGAAAACGATGGA 60.001 57.895 0.00 0.00 0.00 3.41
792 820 3.625897 GGGCTTGGTTGGGTTGGC 61.626 66.667 0.00 0.00 0.00 4.52
816 844 4.124351 CGGCGGCGGACTGTAGAA 62.124 66.667 25.36 0.00 0.00 2.10
1225 1256 0.308684 CGTGCCCAATCCATTGATCG 59.691 55.000 0.56 0.00 40.14 3.69
1253 1290 1.731709 CACGAAACCGCATCAATCAGA 59.268 47.619 0.00 0.00 0.00 3.27
1431 1469 6.826668 TCTCACTTTTCAGATAGTCCAACAA 58.173 36.000 0.00 0.00 0.00 2.83
1461 1505 5.659525 AGCAAAGTTACCCAAAACTACCTTT 59.340 36.000 0.00 0.00 38.76 3.11
1462 1506 5.068591 CAGCAAAGTTACCCAAAACTACCTT 59.931 40.000 0.00 0.00 38.76 3.50
1469 1513 4.877282 GCATACAGCAAAGTTACCCAAAA 58.123 39.130 0.00 0.00 44.79 2.44
1537 4687 4.692155 TCACACATTGATTCACTGTGCTAG 59.308 41.667 27.51 20.13 44.93 3.42
1548 4698 7.984422 TCAGTACTGAATTCACACATTGATT 57.016 32.000 23.24 0.00 36.53 2.57
1554 4704 7.160726 TCAATCATCAGTACTGAATTCACACA 58.839 34.615 28.43 3.57 43.58 3.72
1577 4728 3.316029 CAGTCCAAAGACAAAGCACATCA 59.684 43.478 0.00 0.00 46.15 3.07
1584 4735 6.867662 ATCAAGTACAGTCCAAAGACAAAG 57.132 37.500 0.00 0.00 46.15 2.77
1608 4759 7.067008 AGAACAACTTCTAGCAAAAAGCAAGTA 59.933 33.333 0.00 0.00 36.36 2.24
1609 4760 6.127619 AGAACAACTTCTAGCAAAAAGCAAGT 60.128 34.615 0.00 0.00 38.27 3.16
1610 4761 6.268566 AGAACAACTTCTAGCAAAAAGCAAG 58.731 36.000 0.00 0.00 37.87 4.01
1611 4762 6.207691 AGAACAACTTCTAGCAAAAAGCAA 57.792 33.333 0.00 0.00 37.87 3.91
1642 4793 3.199071 ACCGCATATTCCTAAGTTCCACA 59.801 43.478 0.00 0.00 0.00 4.17
1710 4861 2.373335 TTAAGCAGAGGCCAAAACCA 57.627 45.000 5.01 0.00 42.56 3.67
1782 4973 6.575162 AAGTACCCAAAAACTGCAAGATAG 57.425 37.500 0.00 0.00 37.43 2.08
1783 4974 6.737346 GCAAAGTACCCAAAAACTGCAAGATA 60.737 38.462 0.00 0.00 37.43 1.98
1826 5018 1.272704 GGAGAACCCAGAATGCCCTTT 60.273 52.381 0.00 0.00 34.14 3.11
1899 5092 4.483950 TGGATTAACAATTTGGACCACCA 58.516 39.130 0.00 2.67 45.34 4.17
1988 5314 5.018539 ACGCATATACCTAAGCTTCACAA 57.981 39.130 0.00 0.00 0.00 3.33
2129 6371 4.344679 TGAAAATGCACAAATGAACCCTCT 59.655 37.500 0.00 0.00 0.00 3.69
2365 6979 1.637035 TCTTAACCAAGGTAAGGGGGC 59.363 52.381 0.00 0.00 32.22 5.80
2498 7117 2.226437 CGAGAAAGGCTAGCTGCAAAAA 59.774 45.455 15.72 0.00 45.15 1.94
2545 7164 9.023967 CAGTTCTTTACATCTTCAAAAACCAAG 57.976 33.333 0.00 0.00 0.00 3.61
3157 7795 7.306225 GCAGCACTGAGATGAAAAGTTTTAAAC 60.306 37.037 0.00 0.00 35.00 2.01
3235 7878 2.222027 CAGTTCGAAAGAGCCCAAACT 58.778 47.619 0.00 0.00 42.90 2.66
3419 8067 6.794534 TCATATAGCTGGATCTTCTAGGTCA 58.205 40.000 0.00 0.00 36.99 4.02
3468 8116 2.731572 CTCCCGTCCCTAGTAAACAGA 58.268 52.381 0.00 0.00 0.00 3.41
3469 8117 1.136500 GCTCCCGTCCCTAGTAAACAG 59.864 57.143 0.00 0.00 0.00 3.16
3470 8118 1.188863 GCTCCCGTCCCTAGTAAACA 58.811 55.000 0.00 0.00 0.00 2.83
3471 8119 1.482954 AGCTCCCGTCCCTAGTAAAC 58.517 55.000 0.00 0.00 0.00 2.01
3472 8120 2.242882 AAGCTCCCGTCCCTAGTAAA 57.757 50.000 0.00 0.00 0.00 2.01
3473 8121 2.423947 CCTAAGCTCCCGTCCCTAGTAA 60.424 54.545 0.00 0.00 0.00 2.24
3474 8122 1.144503 CCTAAGCTCCCGTCCCTAGTA 59.855 57.143 0.00 0.00 0.00 1.82
3558 8206 3.251729 AGCAGTGTGTTCAAATAGTGCAG 59.748 43.478 0.00 0.00 31.98 4.41
3563 8211 6.264832 TGAAACAAGCAGTGTGTTCAAATAG 58.735 36.000 0.06 0.00 40.60 1.73
3566 8214 4.511617 TGAAACAAGCAGTGTGTTCAAA 57.488 36.364 0.06 0.00 40.60 2.69
3617 8265 2.760374 ACAACAGGAGAGAGCGAAAAG 58.240 47.619 0.00 0.00 0.00 2.27
3650 8298 3.017442 CTGTAACGAGACCATCCTCTGA 58.983 50.000 0.00 0.00 0.00 3.27
3662 8310 5.382618 ACCACCTAGTAAACTGTAACGAG 57.617 43.478 0.00 0.00 0.00 4.18
3671 8319 5.985530 ACGAAACACTTACCACCTAGTAAAC 59.014 40.000 0.00 0.00 32.02 2.01
3687 8338 7.149192 CGGTTCTATGAAAATCAAACGAAACAC 60.149 37.037 0.00 0.00 0.00 3.32
3716 8367 4.393834 TGTGTAACATAAGCACCACACAT 58.606 39.130 1.48 0.00 45.67 3.21
3749 8400 1.790043 GAACGTCAAAATTTTGGCCCG 59.210 47.619 25.56 24.64 39.52 6.13
3762 8413 6.293407 GGAGAAAGAACATGAATTGAACGTCA 60.293 38.462 0.00 0.00 0.00 4.35
3770 8421 6.409524 TTGCAAGGAGAAAGAACATGAATT 57.590 33.333 0.00 0.00 0.00 2.17
3810 8468 3.372206 CACCTACTGCTAAATCACTGTGC 59.628 47.826 2.12 0.00 0.00 4.57
3827 8485 0.249120 CCGCCTCATGTGAACACCTA 59.751 55.000 2.46 0.00 0.00 3.08
3832 8490 1.234821 TTCAACCGCCTCATGTGAAC 58.765 50.000 0.00 0.00 0.00 3.18
3844 8502 2.432444 TGGAGCTTGGTATTTCAACCG 58.568 47.619 0.00 0.00 42.91 4.44
3850 8508 6.173427 ACAAACATTTGGAGCTTGGTATTT 57.827 33.333 9.09 0.00 42.34 1.40
4037 8790 3.826729 GCCTGGTTTCTTATGGTTTCAGT 59.173 43.478 0.00 0.00 0.00 3.41
4077 9556 8.893219 AGGCTTTCATTTTAAAAGGAGAAAAG 57.107 30.769 14.27 15.23 34.88 2.27
4162 9641 4.853924 ATCCAATTTGCCTTATAAGCCG 57.146 40.909 6.99 0.00 0.00 5.52
4192 9671 3.702548 ACTAGTGTTTGGTTGGGTTTTCC 59.297 43.478 0.00 0.00 39.75 3.13
4243 9722 8.989653 TTATTTTATTTAGAAAAACAGGCCCG 57.010 30.769 0.00 0.00 32.29 6.13


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

AutoCloner maintained by Alex Coulton.