Multiple sequence alignment - TraesCS1A01G183100

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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 TraesCS1A01G183100 chr1A 100.000 3576 0 0 1 3576 331519917 331516342 0.000000e+00 6604.0
1 TraesCS1A01G183100 chr1A 90.265 113 11 0 2084 2196 22660639 22660527 8.000000e-32 148.0
2 TraesCS1A01G183100 chr1A 97.333 75 2 0 528 602 331519318 331519244 1.040000e-25 128.0
3 TraesCS1A01G183100 chr1A 97.333 75 2 0 600 674 331519390 331519316 1.040000e-25 128.0
4 TraesCS1A01G183100 chr1D 94.277 2953 102 25 625 3566 257476229 257473333 0.000000e+00 4455.0
5 TraesCS1A01G183100 chr1D 77.778 387 70 14 89 461 355673543 355673159 1.290000e-54 224.0
6 TraesCS1A01G183100 chr1D 96.000 50 2 0 553 602 257476229 257476180 8.230000e-12 82.4
7 TraesCS1A01G183100 chr1B 94.002 2851 110 25 600 3435 355154814 355157618 0.000000e+00 4261.0
8 TraesCS1A01G183100 chr1B 82.650 317 48 6 196 509 355154419 355154731 1.260000e-69 274.0
9 TraesCS1A01G183100 chr1B 94.624 93 4 1 510 602 355154796 355154887 3.720000e-30 143.0
10 TraesCS1A01G183100 chr4D 91.957 460 27 4 2907 3366 170196541 170196990 1.400000e-178 636.0
11 TraesCS1A01G183100 chr4D 76.441 399 73 17 79 461 434096215 434095822 2.820000e-46 196.0
12 TraesCS1A01G183100 chr7D 91.379 464 28 6 2907 3368 46554742 46554289 3.030000e-175 625.0
13 TraesCS1A01G183100 chr7D 91.071 112 10 0 2085 2196 179537696 179537585 6.180000e-33 152.0
14 TraesCS1A01G183100 chr6D 91.126 462 31 4 2907 3368 37355487 37355036 5.070000e-173 617.0
15 TraesCS1A01G183100 chr6D 95.833 192 7 1 2591 2782 177655321 177655131 3.470000e-80 309.0
16 TraesCS1A01G183100 chr6D 78.187 353 55 20 90 428 14613265 14613609 4.680000e-49 206.0
17 TraesCS1A01G183100 chr6D 76.413 407 75 18 73 461 312191976 312192379 2.180000e-47 200.0
18 TraesCS1A01G183100 chr2A 89.371 461 36 5 2907 3367 145401125 145400678 5.180000e-158 568.0
19 TraesCS1A01G183100 chr2A 80.420 286 53 3 178 461 183214961 183214677 7.780000e-52 215.0
20 TraesCS1A01G183100 chr2D 96.875 192 6 0 2591 2782 551019616 551019807 4.450000e-84 322.0
21 TraesCS1A01G183100 chr2D 95.337 193 8 1 2591 2782 307552452 307552260 4.490000e-79 305.0
22 TraesCS1A01G183100 chr2D 95.312 192 8 1 2591 2782 364648003 364647813 1.610000e-78 303.0
23 TraesCS1A01G183100 chr2D 90.351 114 11 0 2083 2196 25847407 25847294 2.220000e-32 150.0
24 TraesCS1A01G183100 chr2D 91.011 89 8 0 2085 2173 424722172 424722084 1.740000e-23 121.0
25 TraesCS1A01G183100 chrUn 95.833 192 8 0 2591 2782 79160945 79160754 9.640000e-81 311.0
26 TraesCS1A01G183100 chr5D 94.949 198 10 0 2585 2782 351513352 351513549 9.640000e-81 311.0
27 TraesCS1A01G183100 chr5D 96.296 81 2 1 2907 2987 556136394 556136315 8.060000e-27 132.0
28 TraesCS1A01G183100 chr5D 76.510 149 31 4 1334 1480 525471993 525472139 1.060000e-10 78.7
29 TraesCS1A01G183100 chr3D 94.949 198 10 0 2585 2782 16353027 16353224 9.640000e-81 311.0
30 TraesCS1A01G183100 chr3B 79.938 324 55 9 144 461 100825616 100825297 2.780000e-56 230.0
31 TraesCS1A01G183100 chr3B 98.000 50 1 0 2907 2956 660298636 660298587 1.770000e-13 87.9
32 TraesCS1A01G183100 chr3B 78.095 105 13 6 83 185 193404707 193404803 1.390000e-04 58.4
33 TraesCS1A01G183100 chr6A 76.733 404 71 19 95 489 616863991 616863602 1.680000e-48 204.0
34 TraesCS1A01G183100 chr2B 75.969 387 70 17 95 461 21865810 21866193 1.020000e-40 178.0
35 TraesCS1A01G183100 chr2B 83.696 92 10 4 73 161 378914487 378914576 8.230000e-12 82.4
36 TraesCS1A01G183100 chr7A 89.286 112 12 0 2085 2196 631999617 631999506 1.340000e-29 141.0
37 TraesCS1A01G183100 chr7A 84.932 73 8 3 1 71 218267242 218267171 1.780000e-08 71.3
38 TraesCS1A01G183100 chr7B 97.333 75 2 0 2538 2612 76818946 76819020 1.040000e-25 128.0
39 TraesCS1A01G183100 chr5A 95.062 81 2 2 2117 2196 561130242 561130163 3.750000e-25 126.0
40 TraesCS1A01G183100 chr5B 77.181 149 30 4 1334 1480 659770187 659770333 2.290000e-12 84.2
41 TraesCS1A01G183100 chr5B 74.497 149 30 8 1334 1478 659984143 659984287 1.390000e-04 58.4
42 TraesCS1A01G183100 chr4A 96.774 31 1 0 83 113 643786548 643786578 6.000000e-03 52.8


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 TraesCS1A01G183100 chr1A 331516342 331519917 3575 True 2286.666667 6604 98.222000 1 3576 3 chr1A.!!$R2 3575
1 TraesCS1A01G183100 chr1D 257473333 257476229 2896 True 2268.700000 4455 95.138500 553 3566 2 chr1D.!!$R2 3013
2 TraesCS1A01G183100 chr1B 355154419 355157618 3199 False 1559.333333 4261 90.425333 196 3435 3 chr1B.!!$F1 3239

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
908 979 0.034089 CAACCCAATCTCCTCCACCC 60.034 60.0 0.0 0.0 0.00 4.61 F
1961 2043 0.452784 CGCGAAGGTAACAGCAAAGC 60.453 55.0 0.0 0.0 41.41 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2529 2612 1.464997 GAACTTCCAAGTCCATGTCGC 59.535 52.381 0.0 0.0 38.57 5.19 R
3477 3578 1.008538 GGTTGCCACGCTTTCAGTG 60.009 57.895 0.0 0.0 39.19 3.66 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
34 35 5.977171 TGAATGCATGAATTTGCTTATGC 57.023 34.783 0.00 0.00 44.56 3.14
35 36 4.504826 TGAATGCATGAATTTGCTTATGCG 59.495 37.500 0.00 0.00 46.61 4.73
36 37 3.779271 TGCATGAATTTGCTTATGCGA 57.221 38.095 0.00 0.00 46.61 5.10
37 38 3.697982 TGCATGAATTTGCTTATGCGAG 58.302 40.909 0.00 0.00 46.61 5.03
38 39 3.377798 TGCATGAATTTGCTTATGCGAGA 59.622 39.130 0.00 0.00 46.61 4.04
39 40 4.142425 TGCATGAATTTGCTTATGCGAGAA 60.142 37.500 0.00 0.00 46.61 2.87
40 41 4.440103 GCATGAATTTGCTTATGCGAGAAG 59.560 41.667 0.00 0.00 43.34 2.85
41 42 5.731406 GCATGAATTTGCTTATGCGAGAAGA 60.731 40.000 0.00 0.00 43.34 2.87
42 43 5.878332 TGAATTTGCTTATGCGAGAAGAA 57.122 34.783 0.00 0.00 43.34 2.52
43 44 6.441093 TGAATTTGCTTATGCGAGAAGAAT 57.559 33.333 0.00 0.00 43.34 2.40
44 45 6.260377 TGAATTTGCTTATGCGAGAAGAATG 58.740 36.000 0.00 0.00 43.34 2.67
45 46 6.093909 TGAATTTGCTTATGCGAGAAGAATGA 59.906 34.615 0.00 0.00 43.34 2.57
46 47 4.864916 TTGCTTATGCGAGAAGAATGAC 57.135 40.909 0.00 0.00 43.34 3.06
47 48 3.198068 TGCTTATGCGAGAAGAATGACC 58.802 45.455 0.00 0.00 43.34 4.02
48 49 2.219674 GCTTATGCGAGAAGAATGACCG 59.780 50.000 0.00 0.00 0.00 4.79
49 50 3.448686 CTTATGCGAGAAGAATGACCGT 58.551 45.455 0.00 0.00 0.00 4.83
50 51 1.645034 ATGCGAGAAGAATGACCGTG 58.355 50.000 0.00 0.00 0.00 4.94
51 52 0.389817 TGCGAGAAGAATGACCGTGG 60.390 55.000 0.00 0.00 0.00 4.94
52 53 1.696832 GCGAGAAGAATGACCGTGGC 61.697 60.000 0.00 0.00 0.00 5.01
53 54 0.108615 CGAGAAGAATGACCGTGGCT 60.109 55.000 0.00 0.00 0.00 4.75
54 55 1.673033 CGAGAAGAATGACCGTGGCTT 60.673 52.381 0.00 0.00 0.00 4.35
55 56 2.427506 GAGAAGAATGACCGTGGCTTT 58.572 47.619 0.00 0.00 0.00 3.51
56 57 2.416893 GAGAAGAATGACCGTGGCTTTC 59.583 50.000 0.00 0.00 0.00 2.62
57 58 1.128692 GAAGAATGACCGTGGCTTTCG 59.871 52.381 0.00 0.00 0.00 3.46
58 59 0.320374 AGAATGACCGTGGCTTTCGA 59.680 50.000 0.00 0.00 0.00 3.71
59 60 1.153353 GAATGACCGTGGCTTTCGAA 58.847 50.000 0.00 0.00 0.00 3.71
60 61 1.533731 GAATGACCGTGGCTTTCGAAA 59.466 47.619 10.71 10.71 0.00 3.46
61 62 1.600023 ATGACCGTGGCTTTCGAAAA 58.400 45.000 12.41 0.00 0.00 2.29
62 63 1.380524 TGACCGTGGCTTTCGAAAAA 58.619 45.000 12.41 0.00 0.00 1.94
63 64 1.064357 TGACCGTGGCTTTCGAAAAAC 59.936 47.619 12.41 9.54 0.00 2.43
64 65 1.064357 GACCGTGGCTTTCGAAAAACA 59.936 47.619 12.41 10.68 0.00 2.83
65 66 1.473278 ACCGTGGCTTTCGAAAAACAA 59.527 42.857 12.41 0.00 0.00 2.83
66 67 2.094649 ACCGTGGCTTTCGAAAAACAAA 60.095 40.909 12.41 0.00 0.00 2.83
67 68 2.924290 CCGTGGCTTTCGAAAAACAAAA 59.076 40.909 12.41 0.00 0.00 2.44
68 69 3.368236 CCGTGGCTTTCGAAAAACAAAAA 59.632 39.130 12.41 0.00 0.00 1.94
89 90 6.916360 AAAAACTTCCTATCATGAAAGGCA 57.084 33.333 0.00 0.00 32.55 4.75
90 91 5.904362 AAACTTCCTATCATGAAAGGCAC 57.096 39.130 0.00 0.00 32.55 5.01
91 92 3.535561 ACTTCCTATCATGAAAGGCACG 58.464 45.455 0.00 0.00 32.55 5.34
92 93 2.620251 TCCTATCATGAAAGGCACGG 57.380 50.000 0.00 0.00 32.55 4.94
93 94 2.115427 TCCTATCATGAAAGGCACGGA 58.885 47.619 0.00 0.00 32.55 4.69
94 95 2.705658 TCCTATCATGAAAGGCACGGAT 59.294 45.455 0.00 0.00 32.55 4.18
95 96 3.136443 TCCTATCATGAAAGGCACGGATT 59.864 43.478 0.00 0.00 32.55 3.01
96 97 3.885297 CCTATCATGAAAGGCACGGATTT 59.115 43.478 0.00 0.00 0.00 2.17
97 98 3.788333 ATCATGAAAGGCACGGATTTG 57.212 42.857 0.00 0.00 0.00 2.32
98 99 1.202114 TCATGAAAGGCACGGATTTGC 59.798 47.619 0.00 0.00 42.18 3.68
99 100 1.203052 CATGAAAGGCACGGATTTGCT 59.797 47.619 0.00 0.00 42.56 3.91
100 101 1.327303 TGAAAGGCACGGATTTGCTT 58.673 45.000 0.00 0.00 42.56 3.91
101 102 1.269448 TGAAAGGCACGGATTTGCTTC 59.731 47.619 0.00 0.00 42.56 3.86
102 103 1.541588 GAAAGGCACGGATTTGCTTCT 59.458 47.619 0.00 0.00 42.56 2.85
103 104 1.168714 AAGGCACGGATTTGCTTCTC 58.831 50.000 0.00 0.00 42.56 2.87
104 105 1.021390 AGGCACGGATTTGCTTCTCG 61.021 55.000 0.00 0.00 42.56 4.04
105 106 1.298859 GGCACGGATTTGCTTCTCGT 61.299 55.000 0.00 0.00 42.56 4.18
106 107 3.955429 CACGGATTTGCTTCTCGTG 57.045 52.632 0.00 0.00 43.58 4.35
107 108 0.443869 CACGGATTTGCTTCTCGTGG 59.556 55.000 0.00 0.00 44.79 4.94
108 109 0.320374 ACGGATTTGCTTCTCGTGGA 59.680 50.000 0.00 0.00 32.60 4.02
109 110 1.002366 CGGATTTGCTTCTCGTGGAG 58.998 55.000 0.00 0.00 0.00 3.86
110 111 1.373570 GGATTTGCTTCTCGTGGAGG 58.626 55.000 0.00 0.00 0.00 4.30
111 112 0.729690 GATTTGCTTCTCGTGGAGGC 59.270 55.000 7.89 7.89 45.68 4.70
114 115 2.811317 GCTTCTCGTGGAGGCACG 60.811 66.667 0.00 0.00 44.96 5.34
120 121 3.177600 CGTGGAGGCACGGATTTG 58.822 61.111 0.00 0.00 44.01 2.32
121 122 1.671054 CGTGGAGGCACGGATTTGT 60.671 57.895 0.00 0.00 44.01 2.83
122 123 1.234615 CGTGGAGGCACGGATTTGTT 61.235 55.000 0.00 0.00 44.01 2.83
123 124 0.958822 GTGGAGGCACGGATTTGTTT 59.041 50.000 0.00 0.00 0.00 2.83
124 125 1.339929 GTGGAGGCACGGATTTGTTTT 59.660 47.619 0.00 0.00 0.00 2.43
125 126 1.611491 TGGAGGCACGGATTTGTTTTC 59.389 47.619 0.00 0.00 0.00 2.29
126 127 1.067846 GGAGGCACGGATTTGTTTTCC 60.068 52.381 0.00 0.00 0.00 3.13
127 128 1.611491 GAGGCACGGATTTGTTTTCCA 59.389 47.619 0.00 0.00 32.45 3.53
128 129 1.339929 AGGCACGGATTTGTTTTCCAC 59.660 47.619 0.00 0.00 32.45 4.02
129 130 1.067821 GGCACGGATTTGTTTTCCACA 59.932 47.619 0.00 0.00 32.45 4.17
130 131 2.482142 GGCACGGATTTGTTTTCCACAA 60.482 45.455 0.00 0.00 44.11 3.33
131 132 2.794350 GCACGGATTTGTTTTCCACAAG 59.206 45.455 0.00 0.00 46.37 3.16
132 133 3.490078 GCACGGATTTGTTTTCCACAAGA 60.490 43.478 0.00 0.00 46.37 3.02
133 134 4.041723 CACGGATTTGTTTTCCACAAGAC 58.958 43.478 0.00 0.00 46.37 3.01
134 135 3.697045 ACGGATTTGTTTTCCACAAGACA 59.303 39.130 0.00 0.00 46.37 3.41
135 136 4.041723 CGGATTTGTTTTCCACAAGACAC 58.958 43.478 0.00 0.00 46.37 3.67
136 137 4.041723 GGATTTGTTTTCCACAAGACACG 58.958 43.478 0.00 0.00 46.37 4.49
137 138 3.495670 TTTGTTTTCCACAAGACACGG 57.504 42.857 0.00 0.00 46.37 4.94
138 139 0.736053 TGTTTTCCACAAGACACGGC 59.264 50.000 0.00 0.00 29.87 5.68
139 140 1.021968 GTTTTCCACAAGACACGGCT 58.978 50.000 0.00 0.00 0.00 5.52
140 141 1.021202 TTTTCCACAAGACACGGCTG 58.979 50.000 0.00 0.00 0.00 4.85
141 142 1.444119 TTTCCACAAGACACGGCTGC 61.444 55.000 0.00 0.00 0.00 5.25
142 143 3.716006 CCACAAGACACGGCTGCG 61.716 66.667 0.00 0.00 0.00 5.18
143 144 4.374702 CACAAGACACGGCTGCGC 62.375 66.667 0.00 0.00 0.00 6.09
153 154 2.742372 GGCTGCGCCTCTCGAAAA 60.742 61.111 4.18 0.00 46.69 2.29
154 155 2.325082 GGCTGCGCCTCTCGAAAAA 61.325 57.895 4.18 0.00 46.69 1.94
155 156 1.133458 GCTGCGCCTCTCGAAAAAG 59.867 57.895 4.18 0.00 41.67 2.27
156 157 1.291877 GCTGCGCCTCTCGAAAAAGA 61.292 55.000 4.18 0.00 41.67 2.52
157 158 1.148310 CTGCGCCTCTCGAAAAAGAA 58.852 50.000 4.18 0.00 41.67 2.52
158 159 1.531149 CTGCGCCTCTCGAAAAAGAAA 59.469 47.619 4.18 0.00 41.67 2.52
159 160 1.944024 TGCGCCTCTCGAAAAAGAAAA 59.056 42.857 4.18 0.00 41.67 2.29
160 161 2.356382 TGCGCCTCTCGAAAAAGAAAAA 59.644 40.909 4.18 0.00 41.67 1.94
219 220 0.888619 TACTTCTCGTGGAGGCACAG 59.111 55.000 0.00 0.00 0.00 3.66
222 223 0.976641 TTCTCGTGGAGGCACAGATT 59.023 50.000 0.00 0.00 0.00 2.40
262 263 0.685097 TTGTGTCTCTCGGAAAGGGG 59.315 55.000 0.00 0.00 0.00 4.79
267 269 2.642807 TGTCTCTCGGAAAGGGGAAAAT 59.357 45.455 0.00 0.00 0.00 1.82
268 270 3.010420 GTCTCTCGGAAAGGGGAAAATG 58.990 50.000 0.00 0.00 0.00 2.32
277 279 4.734652 GGGAAAATGTGCTCCCGA 57.265 55.556 0.00 0.00 42.03 5.14
314 316 5.171337 CGTGAAAACTTTTCATCGAAACCTG 59.829 40.000 17.84 0.00 30.83 4.00
347 349 7.158099 TGATCTAGTTTTGAAGATCTCGACA 57.842 36.000 12.19 0.00 38.30 4.35
361 363 2.785713 TCGACACGAGAAATCACACA 57.214 45.000 0.00 0.00 0.00 3.72
362 364 3.086818 TCGACACGAGAAATCACACAA 57.913 42.857 0.00 0.00 0.00 3.33
370 372 5.113975 CACGAGAAATCACACAATGAAAACG 59.886 40.000 0.00 0.00 41.93 3.60
375 377 3.326733 TCACACAATGAAAACGGTTCG 57.673 42.857 0.00 0.00 33.02 3.95
385 387 3.872182 TGAAAACGGTTCGAGATTTGACA 59.128 39.130 0.00 0.00 0.00 3.58
386 388 4.513692 TGAAAACGGTTCGAGATTTGACAT 59.486 37.500 0.00 0.00 0.00 3.06
460 462 6.094325 TGAAACTTACAGGTTACAACAAGTGG 59.906 38.462 0.00 0.00 0.00 4.00
461 463 5.362105 ACTTACAGGTTACAACAAGTGGA 57.638 39.130 0.00 0.00 0.00 4.02
463 465 5.763204 ACTTACAGGTTACAACAAGTGGATG 59.237 40.000 0.00 0.00 0.00 3.51
464 466 3.486383 ACAGGTTACAACAAGTGGATGG 58.514 45.455 0.00 0.00 0.00 3.51
465 467 3.137544 ACAGGTTACAACAAGTGGATGGA 59.862 43.478 0.00 0.00 0.00 3.41
466 468 3.753272 CAGGTTACAACAAGTGGATGGAG 59.247 47.826 0.00 0.00 0.00 3.86
475 477 3.244875 ACAAGTGGATGGAGCACATGTAA 60.245 43.478 0.00 0.00 40.72 2.41
496 500 1.378882 GCGATGCTTGCCAATCTGGA 61.379 55.000 0.00 0.00 40.96 3.86
499 503 2.100252 CGATGCTTGCCAATCTGGAAAT 59.900 45.455 0.00 0.00 40.96 2.17
500 504 3.454375 GATGCTTGCCAATCTGGAAATG 58.546 45.455 0.00 0.00 40.96 2.32
504 508 1.559368 TGCCAATCTGGAAATGTGGG 58.441 50.000 0.00 0.00 40.96 4.61
573 641 3.239712 CGCTTCGAAACCACTTTTTGAAC 59.760 43.478 0.00 0.00 41.07 3.18
602 670 0.395724 CTTTCTATTGGGCCGGGCTT 60.396 55.000 28.80 15.28 0.00 4.35
603 671 0.920438 TTTCTATTGGGCCGGGCTTA 59.080 50.000 28.80 16.28 0.00 3.09
604 672 0.920438 TTCTATTGGGCCGGGCTTAA 59.080 50.000 28.80 22.34 0.00 1.85
605 673 1.145571 TCTATTGGGCCGGGCTTAAT 58.854 50.000 28.80 26.72 0.00 1.40
606 674 1.202879 TCTATTGGGCCGGGCTTAATG 60.203 52.381 28.80 19.49 0.00 1.90
607 675 0.825840 TATTGGGCCGGGCTTAATGC 60.826 55.000 28.80 10.51 41.94 3.56
609 677 4.868116 GGGCCGGGCTTAATGCGA 62.868 66.667 28.80 0.00 44.05 5.10
610 678 3.279875 GGCCGGGCTTAATGCGAG 61.280 66.667 22.87 0.00 44.05 5.03
611 679 2.203015 GCCGGGCTTAATGCGAGA 60.203 61.111 12.87 0.00 44.05 4.04
612 680 2.534903 GCCGGGCTTAATGCGAGAC 61.535 63.158 12.87 0.00 44.05 3.36
613 681 1.153449 CCGGGCTTAATGCGAGACA 60.153 57.895 0.00 0.00 44.05 3.41
614 682 1.429148 CCGGGCTTAATGCGAGACAC 61.429 60.000 0.00 0.00 44.05 3.67
615 683 0.739462 CGGGCTTAATGCGAGACACA 60.739 55.000 0.00 0.00 44.05 3.72
616 684 1.009829 GGGCTTAATGCGAGACACAG 58.990 55.000 0.00 0.00 44.05 3.66
617 685 1.676014 GGGCTTAATGCGAGACACAGT 60.676 52.381 0.00 0.00 44.05 3.55
618 686 1.394917 GGCTTAATGCGAGACACAGTG 59.605 52.381 0.00 0.00 44.05 3.66
619 687 1.201965 GCTTAATGCGAGACACAGTGC 60.202 52.381 0.00 0.00 0.00 4.40
620 688 2.341257 CTTAATGCGAGACACAGTGCT 58.659 47.619 0.00 0.00 0.00 4.40
621 689 1.996292 TAATGCGAGACACAGTGCTC 58.004 50.000 0.00 7.61 0.00 4.26
624 692 3.168604 CGAGACACAGTGCTCGCG 61.169 66.667 24.63 18.59 45.97 5.87
625 693 3.474034 GAGACACAGTGCTCGCGC 61.474 66.667 0.00 0.00 0.00 6.86
626 694 3.905705 GAGACACAGTGCTCGCGCT 62.906 63.158 5.56 0.00 37.24 5.92
627 695 3.038417 GACACAGTGCTCGCGCTT 61.038 61.111 5.56 0.00 34.14 4.68
628 696 3.004734 GACACAGTGCTCGCGCTTC 62.005 63.158 5.56 0.00 34.14 3.86
629 697 4.126390 CACAGTGCTCGCGCTTCG 62.126 66.667 5.56 0.00 34.14 3.79
630 698 4.342987 ACAGTGCTCGCGCTTCGA 62.343 61.111 5.56 0.00 46.29 3.71
637 705 2.028484 TCGCGCTTCGAAACCACT 59.972 55.556 5.56 0.00 45.36 4.00
638 706 1.593209 TCGCGCTTCGAAACCACTT 60.593 52.632 5.56 0.00 45.36 3.16
639 707 1.154654 CGCGCTTCGAAACCACTTC 60.155 57.895 5.56 0.00 41.67 3.01
640 708 1.557443 CGCGCTTCGAAACCACTTCT 61.557 55.000 5.56 0.00 41.67 2.85
641 709 0.586802 GCGCTTCGAAACCACTTCTT 59.413 50.000 0.00 0.00 31.20 2.52
642 710 1.660333 GCGCTTCGAAACCACTTCTTG 60.660 52.381 0.00 0.00 31.20 3.02
643 711 1.864711 CGCTTCGAAACCACTTCTTGA 59.135 47.619 0.00 0.00 31.20 3.02
644 712 2.286833 CGCTTCGAAACCACTTCTTGAA 59.713 45.455 0.00 0.00 31.20 2.69
645 713 3.618698 GCTTCGAAACCACTTCTTGAAC 58.381 45.455 0.00 0.00 31.20 3.18
646 714 3.844943 GCTTCGAAACCACTTCTTGAACG 60.845 47.826 0.00 0.00 31.20 3.95
647 715 3.167921 TCGAAACCACTTCTTGAACGA 57.832 42.857 0.00 0.00 31.20 3.85
648 716 3.523547 TCGAAACCACTTCTTGAACGAA 58.476 40.909 0.00 0.00 31.20 3.85
649 717 3.933955 TCGAAACCACTTCTTGAACGAAA 59.066 39.130 0.00 0.00 31.20 3.46
650 718 4.392445 TCGAAACCACTTCTTGAACGAAAA 59.608 37.500 0.00 0.00 31.20 2.29
651 719 5.065474 TCGAAACCACTTCTTGAACGAAAAT 59.935 36.000 0.00 0.00 31.20 1.82
652 720 6.258287 TCGAAACCACTTCTTGAACGAAAATA 59.742 34.615 0.00 0.00 31.20 1.40
653 721 6.908284 CGAAACCACTTCTTGAACGAAAATAA 59.092 34.615 0.00 0.00 31.20 1.40
654 722 7.589954 CGAAACCACTTCTTGAACGAAAATAAT 59.410 33.333 0.00 0.00 31.20 1.28
655 723 8.797266 AAACCACTTCTTGAACGAAAATAATC 57.203 30.769 0.00 0.00 0.00 1.75
656 724 7.745620 ACCACTTCTTGAACGAAAATAATCT 57.254 32.000 0.00 0.00 0.00 2.40
657 725 8.166422 ACCACTTCTTGAACGAAAATAATCTT 57.834 30.769 0.00 0.00 0.00 2.40
658 726 8.630037 ACCACTTCTTGAACGAAAATAATCTTT 58.370 29.630 0.00 0.00 0.00 2.52
667 735 9.959749 TGAACGAAAATAATCTTTATATTGGGC 57.040 29.630 0.00 0.00 0.00 5.36
668 736 9.406828 GAACGAAAATAATCTTTATATTGGGCC 57.593 33.333 0.00 0.00 0.00 5.80
669 737 7.590279 ACGAAAATAATCTTTATATTGGGCCG 58.410 34.615 0.00 0.00 0.00 6.13
670 738 7.027161 CGAAAATAATCTTTATATTGGGCCGG 58.973 38.462 0.00 0.00 0.00 6.13
671 739 6.850752 AAATAATCTTTATATTGGGCCGGG 57.149 37.500 2.18 0.00 0.00 5.73
672 740 2.215942 ATCTTTATATTGGGCCGGGC 57.784 50.000 22.00 22.00 0.00 6.13
673 741 1.145571 TCTTTATATTGGGCCGGGCT 58.854 50.000 28.80 11.06 0.00 5.19
678 746 3.875147 TATATTGGGCCGGGCTCTCCA 62.875 57.143 28.80 15.80 34.36 3.86
711 779 3.025262 CCGTCTATAGGCTCCCTAATCC 58.975 54.545 2.29 0.00 39.77 3.01
718 786 9.490083 GTCTATAGGCTCCCTAATCCTTTATAA 57.510 37.037 0.00 0.00 39.77 0.98
735 803 6.653320 CCTTTATAATGCCGGCTACTATTTGA 59.347 38.462 29.70 3.35 0.00 2.69
782 850 2.618045 CCCAAATCTAGGTTGAAGGCGT 60.618 50.000 8.23 0.00 0.00 5.68
908 979 0.034089 CAACCCAATCTCCTCCACCC 60.034 60.000 0.00 0.00 0.00 4.61
957 1028 1.152943 CTCCCTCGGATCGACCAGA 60.153 63.158 0.00 0.00 38.90 3.86
1285 1356 3.186047 CCGGCGTGGATTGACGTC 61.186 66.667 9.11 9.11 42.00 4.34
1602 1673 8.429641 AGTTTGGTTACAGAGTTGAAGATTCTA 58.570 33.333 0.00 0.00 0.00 2.10
1608 1680 9.959749 GTTACAGAGTTGAAGATTCTATCTAGG 57.040 37.037 0.00 0.00 39.08 3.02
1609 1681 7.049799 ACAGAGTTGAAGATTCTATCTAGGC 57.950 40.000 0.00 0.00 39.08 3.93
1736 1808 5.030874 GTGCTAAACACTTAAACAGCGAT 57.969 39.130 0.00 0.00 46.41 4.58
1817 1889 5.827797 TGTACAATCCTTTCAGCTTTCAGTT 59.172 36.000 0.00 0.00 0.00 3.16
1945 2027 2.867456 ATTTTTCGTGTAACCTCGCG 57.133 45.000 0.00 0.00 41.75 5.87
1961 2043 0.452784 CGCGAAGGTAACAGCAAAGC 60.453 55.000 0.00 0.00 41.41 3.51
2024 2106 1.155889 CGGCAGTGCACTTGACAATA 58.844 50.000 18.94 0.00 0.00 1.90
2035 2117 6.197096 GTGCACTTGACAATACTTTTCAGTTG 59.803 38.462 10.32 0.00 34.06 3.16
2250 2332 4.804868 TTTGATGAAATGTCCATGTGGG 57.195 40.909 0.00 0.00 35.41 4.61
2251 2333 3.735720 TGATGAAATGTCCATGTGGGA 57.264 42.857 0.00 0.00 45.89 4.37
2279 2361 1.516161 TCACTTGCACTGCATGACTC 58.484 50.000 20.62 0.00 38.76 3.36
2359 2442 4.452455 GGGTATTCTTGTCAGTTGTCACAG 59.548 45.833 0.00 0.00 0.00 3.66
2369 2452 2.029020 CAGTTGTCACAGGTAGCTGCTA 60.029 50.000 21.58 5.02 0.00 3.49
2406 2489 9.331282 AGAAGATAACAATATTACAGCTGTTCC 57.669 33.333 27.06 0.68 34.08 3.62
2467 2550 4.319046 GCAAAGACCATATATGCTGTGTCG 60.319 45.833 7.24 0.00 34.29 4.35
2873 2956 2.600867 GAGCTTAAACTGCTACTGCTCG 59.399 50.000 0.00 0.00 41.30 5.03
2891 2983 4.822896 TGCTCGGTGGTTTTGTAATAGTTT 59.177 37.500 0.00 0.00 0.00 2.66
2892 2984 5.049267 TGCTCGGTGGTTTTGTAATAGTTTC 60.049 40.000 0.00 0.00 0.00 2.78
2893 2985 5.180680 GCTCGGTGGTTTTGTAATAGTTTCT 59.819 40.000 0.00 0.00 0.00 2.52
2894 2986 6.548441 TCGGTGGTTTTGTAATAGTTTCTG 57.452 37.500 0.00 0.00 0.00 3.02
2895 2987 6.056884 TCGGTGGTTTTGTAATAGTTTCTGT 58.943 36.000 0.00 0.00 0.00 3.41
2896 2988 6.543100 TCGGTGGTTTTGTAATAGTTTCTGTT 59.457 34.615 0.00 0.00 0.00 3.16
2897 2989 7.067251 TCGGTGGTTTTGTAATAGTTTCTGTTT 59.933 33.333 0.00 0.00 0.00 2.83
2898 2990 7.703197 CGGTGGTTTTGTAATAGTTTCTGTTTT 59.297 33.333 0.00 0.00 0.00 2.43
2899 2991 9.373603 GGTGGTTTTGTAATAGTTTCTGTTTTT 57.626 29.630 0.00 0.00 0.00 1.94
2975 3067 0.740737 GGTGTTGTGCTTGTTCTGCT 59.259 50.000 0.00 0.00 0.00 4.24
3129 3224 5.051816 ACATGAAAACAGACTTGGCAAATG 58.948 37.500 0.00 3.33 0.00 2.32
3165 3260 9.262358 GTTTTTCTTTGTCTTTAGAGAGAGCTA 57.738 33.333 0.00 0.00 31.07 3.32
3207 3302 8.629986 CAATATTAGCAGTTGTTTTGACTTTCG 58.370 33.333 0.00 0.00 0.00 3.46
3209 3304 4.278678 AGCAGTTGTTTTGACTTTCGAG 57.721 40.909 0.00 0.00 0.00 4.04
3224 3319 8.516811 TGACTTTCGAGTACTATTGTTCTTTC 57.483 34.615 0.00 0.00 0.00 2.62
3310 3405 4.686191 AATTTCCTTTGCATCACCACAA 57.314 36.364 0.00 0.00 0.00 3.33
3317 3412 7.041635 TCCTTTGCATCACCACAATTATATG 57.958 36.000 0.00 0.00 0.00 1.78
3320 3415 8.579006 CCTTTGCATCACCACAATTATATGTAT 58.421 33.333 0.00 0.00 30.84 2.29
3322 3417 7.451501 TGCATCACCACAATTATATGTATGG 57.548 36.000 0.00 0.00 30.84 2.74
3376 3471 9.896645 GATTATGATAATTCTGCCAGGATTAGA 57.103 33.333 11.04 1.45 0.00 2.10
3398 3493 7.840342 AGATGTTTTAGACTAATCAGTGCTG 57.160 36.000 0.00 0.00 34.21 4.41
3399 3494 7.390027 AGATGTTTTAGACTAATCAGTGCTGT 58.610 34.615 0.00 0.00 34.21 4.40
3490 3591 6.923508 TCAGAATATATACACTGAAAGCGTGG 59.076 38.462 14.42 0.00 37.60 4.94
3492 3593 2.753055 TATACACTGAAAGCGTGGCA 57.247 45.000 0.00 0.00 37.60 4.92
3493 3594 1.890876 ATACACTGAAAGCGTGGCAA 58.109 45.000 0.00 0.00 37.60 4.52
3494 3595 0.941542 TACACTGAAAGCGTGGCAAC 59.058 50.000 0.00 0.00 37.60 4.17
3495 3596 1.008538 CACTGAAAGCGTGGCAACC 60.009 57.895 0.00 0.00 37.60 3.77
3496 3597 1.453015 ACTGAAAGCGTGGCAACCA 60.453 52.632 0.00 0.00 37.60 3.67
3497 3598 0.823356 ACTGAAAGCGTGGCAACCAT 60.823 50.000 0.00 0.00 37.60 3.55
3498 3599 1.164411 CTGAAAGCGTGGCAACCATA 58.836 50.000 0.00 0.00 35.28 2.74
3499 3600 0.878416 TGAAAGCGTGGCAACCATAC 59.122 50.000 0.00 0.00 35.28 2.39
3500 3601 0.179200 GAAAGCGTGGCAACCATACG 60.179 55.000 0.00 0.00 40.52 3.06
3501 3602 0.604243 AAAGCGTGGCAACCATACGA 60.604 50.000 0.00 0.00 40.01 3.43
3502 3603 0.392461 AAGCGTGGCAACCATACGAT 60.392 50.000 0.00 0.00 40.01 3.73
3503 3604 0.462375 AGCGTGGCAACCATACGATA 59.538 50.000 0.00 0.00 40.01 2.92
3504 3605 0.859232 GCGTGGCAACCATACGATAG 59.141 55.000 0.00 0.00 40.01 2.08
3505 3606 0.859232 CGTGGCAACCATACGATAGC 59.141 55.000 0.00 0.00 40.01 2.97
3506 3607 1.804746 CGTGGCAACCATACGATAGCA 60.805 52.381 0.00 0.00 40.01 3.49
3507 3608 2.494059 GTGGCAACCATACGATAGCAT 58.506 47.619 0.00 0.00 35.77 3.79
3527 3628 4.437390 GCATAATTTGACTTGTCTCCACGG 60.437 45.833 2.35 0.00 0.00 4.94
3566 3667 2.161609 CCCAACTGAGTTTATTCGCCAC 59.838 50.000 0.00 0.00 0.00 5.01
3567 3668 2.811431 CCAACTGAGTTTATTCGCCACA 59.189 45.455 0.00 0.00 0.00 4.17
3568 3669 3.120199 CCAACTGAGTTTATTCGCCACAG 60.120 47.826 0.00 0.00 0.00 3.66
3569 3670 3.402628 ACTGAGTTTATTCGCCACAGT 57.597 42.857 0.00 0.00 33.29 3.55
3570 3671 4.530710 ACTGAGTTTATTCGCCACAGTA 57.469 40.909 0.00 0.00 35.77 2.74
3571 3672 4.890088 ACTGAGTTTATTCGCCACAGTAA 58.110 39.130 0.00 0.00 35.77 2.24
3572 3673 5.302360 ACTGAGTTTATTCGCCACAGTAAA 58.698 37.500 0.00 0.00 35.77 2.01
3573 3674 5.178809 ACTGAGTTTATTCGCCACAGTAAAC 59.821 40.000 0.00 0.00 37.32 2.01
3574 3675 5.057819 TGAGTTTATTCGCCACAGTAAACA 58.942 37.500 8.87 0.00 38.72 2.83
3575 3676 5.703592 TGAGTTTATTCGCCACAGTAAACAT 59.296 36.000 8.87 0.00 38.72 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.956233 TCTCGCATAAGCAAATTCATGC 58.044 40.909 0.00 0.00 46.78 4.06
18 19 5.813717 TCTTCTCGCATAAGCAAATTCATG 58.186 37.500 0.00 0.00 42.27 3.07
19 20 6.441093 TTCTTCTCGCATAAGCAAATTCAT 57.559 33.333 0.00 0.00 42.27 2.57
20 21 5.878332 TTCTTCTCGCATAAGCAAATTCA 57.122 34.783 0.00 0.00 42.27 2.57
21 22 6.413235 GTCATTCTTCTCGCATAAGCAAATTC 59.587 38.462 0.00 0.00 42.27 2.17
22 23 6.261118 GTCATTCTTCTCGCATAAGCAAATT 58.739 36.000 0.00 0.00 42.27 1.82
23 24 5.220931 GGTCATTCTTCTCGCATAAGCAAAT 60.221 40.000 0.00 0.00 42.27 2.32
24 25 4.094887 GGTCATTCTTCTCGCATAAGCAAA 59.905 41.667 0.00 0.00 42.27 3.68
25 26 3.623060 GGTCATTCTTCTCGCATAAGCAA 59.377 43.478 0.00 0.00 42.27 3.91
26 27 3.198068 GGTCATTCTTCTCGCATAAGCA 58.802 45.455 0.00 0.00 42.27 3.91
27 28 2.219674 CGGTCATTCTTCTCGCATAAGC 59.780 50.000 0.00 0.00 37.42 3.09
28 29 3.243877 CACGGTCATTCTTCTCGCATAAG 59.756 47.826 0.00 0.00 0.00 1.73
29 30 3.186909 CACGGTCATTCTTCTCGCATAA 58.813 45.455 0.00 0.00 0.00 1.90
30 31 2.481276 CCACGGTCATTCTTCTCGCATA 60.481 50.000 0.00 0.00 0.00 3.14
31 32 1.645034 CACGGTCATTCTTCTCGCAT 58.355 50.000 0.00 0.00 0.00 4.73
32 33 0.389817 CCACGGTCATTCTTCTCGCA 60.390 55.000 0.00 0.00 0.00 5.10
33 34 1.696832 GCCACGGTCATTCTTCTCGC 61.697 60.000 0.00 0.00 0.00 5.03
34 35 0.108615 AGCCACGGTCATTCTTCTCG 60.109 55.000 0.00 0.00 0.00 4.04
35 36 2.100605 AAGCCACGGTCATTCTTCTC 57.899 50.000 0.00 0.00 0.00 2.87
36 37 2.427506 GAAAGCCACGGTCATTCTTCT 58.572 47.619 0.00 0.00 0.00 2.85
37 38 1.128692 CGAAAGCCACGGTCATTCTTC 59.871 52.381 0.00 0.00 0.00 2.87
38 39 1.156736 CGAAAGCCACGGTCATTCTT 58.843 50.000 0.00 0.00 0.00 2.52
39 40 0.320374 TCGAAAGCCACGGTCATTCT 59.680 50.000 0.00 0.00 0.00 2.40
40 41 1.153353 TTCGAAAGCCACGGTCATTC 58.847 50.000 0.00 0.00 0.00 2.67
41 42 1.600023 TTTCGAAAGCCACGGTCATT 58.400 45.000 6.47 0.00 0.00 2.57
42 43 1.600023 TTTTCGAAAGCCACGGTCAT 58.400 45.000 10.98 0.00 0.00 3.06
43 44 1.064357 GTTTTTCGAAAGCCACGGTCA 59.936 47.619 10.98 0.00 0.00 4.02
44 45 1.064357 TGTTTTTCGAAAGCCACGGTC 59.936 47.619 10.98 0.00 0.00 4.79
45 46 1.096416 TGTTTTTCGAAAGCCACGGT 58.904 45.000 10.98 0.00 0.00 4.83
46 47 2.196295 TTGTTTTTCGAAAGCCACGG 57.804 45.000 10.98 0.00 0.00 4.94
47 48 4.569801 TTTTTGTTTTTCGAAAGCCACG 57.430 36.364 10.98 0.00 31.89 4.94
66 67 6.570378 CGTGCCTTTCATGATAGGAAGTTTTT 60.570 38.462 29.92 0.00 32.13 1.94
67 68 5.106157 CGTGCCTTTCATGATAGGAAGTTTT 60.106 40.000 29.92 0.00 32.13 2.43
68 69 4.396166 CGTGCCTTTCATGATAGGAAGTTT 59.604 41.667 29.92 0.00 32.13 2.66
69 70 3.941483 CGTGCCTTTCATGATAGGAAGTT 59.059 43.478 29.92 0.00 32.13 2.66
70 71 3.535561 CGTGCCTTTCATGATAGGAAGT 58.464 45.455 29.92 0.00 32.13 3.01
71 72 2.874701 CCGTGCCTTTCATGATAGGAAG 59.125 50.000 29.92 19.97 32.13 3.46
72 73 2.503765 TCCGTGCCTTTCATGATAGGAA 59.496 45.455 29.92 20.52 32.13 3.36
73 74 2.115427 TCCGTGCCTTTCATGATAGGA 58.885 47.619 29.92 15.45 32.13 2.94
74 75 2.620251 TCCGTGCCTTTCATGATAGG 57.380 50.000 23.67 23.67 33.49 2.57
75 76 4.790766 GCAAATCCGTGCCTTTCATGATAG 60.791 45.833 6.21 6.21 38.66 2.08
76 77 3.066621 GCAAATCCGTGCCTTTCATGATA 59.933 43.478 0.00 0.00 38.66 2.15
77 78 2.159198 GCAAATCCGTGCCTTTCATGAT 60.159 45.455 0.00 0.00 38.66 2.45
78 79 1.202114 GCAAATCCGTGCCTTTCATGA 59.798 47.619 0.00 0.00 38.66 3.07
79 80 1.203052 AGCAAATCCGTGCCTTTCATG 59.797 47.619 0.00 0.00 46.14 3.07
80 81 1.549203 AGCAAATCCGTGCCTTTCAT 58.451 45.000 0.00 0.00 46.14 2.57
81 82 1.269448 GAAGCAAATCCGTGCCTTTCA 59.731 47.619 0.00 0.00 46.14 2.69
82 83 1.541588 AGAAGCAAATCCGTGCCTTTC 59.458 47.619 0.00 0.00 46.14 2.62
83 84 1.541588 GAGAAGCAAATCCGTGCCTTT 59.458 47.619 0.00 0.00 46.14 3.11
84 85 1.168714 GAGAAGCAAATCCGTGCCTT 58.831 50.000 0.00 0.00 46.14 4.35
85 86 1.021390 CGAGAAGCAAATCCGTGCCT 61.021 55.000 0.00 0.00 46.14 4.75
86 87 1.298859 ACGAGAAGCAAATCCGTGCC 61.299 55.000 0.00 0.00 46.14 5.01
87 88 0.179215 CACGAGAAGCAAATCCGTGC 60.179 55.000 0.00 0.00 42.83 5.34
88 89 0.443869 CCACGAGAAGCAAATCCGTG 59.556 55.000 0.00 0.00 46.83 4.94
89 90 0.320374 TCCACGAGAAGCAAATCCGT 59.680 50.000 0.00 0.00 0.00 4.69
90 91 1.002366 CTCCACGAGAAGCAAATCCG 58.998 55.000 0.00 0.00 0.00 4.18
91 92 1.373570 CCTCCACGAGAAGCAAATCC 58.626 55.000 0.00 0.00 0.00 3.01
92 93 0.729690 GCCTCCACGAGAAGCAAATC 59.270 55.000 0.00 0.00 0.00 2.17
93 94 0.036732 TGCCTCCACGAGAAGCAAAT 59.963 50.000 0.00 0.00 0.00 2.32
94 95 0.884704 GTGCCTCCACGAGAAGCAAA 60.885 55.000 5.32 0.00 31.08 3.68
95 96 1.301716 GTGCCTCCACGAGAAGCAA 60.302 57.895 5.32 0.00 31.08 3.91
96 97 2.343758 GTGCCTCCACGAGAAGCA 59.656 61.111 0.00 0.00 31.34 3.91
104 105 0.958822 AAACAAATCCGTGCCTCCAC 59.041 50.000 0.00 0.00 38.62 4.02
105 106 1.611491 GAAAACAAATCCGTGCCTCCA 59.389 47.619 0.00 0.00 0.00 3.86
106 107 1.067846 GGAAAACAAATCCGTGCCTCC 60.068 52.381 0.00 0.00 0.00 4.30
107 108 1.611491 TGGAAAACAAATCCGTGCCTC 59.389 47.619 0.00 0.00 39.98 4.70
108 109 1.339929 GTGGAAAACAAATCCGTGCCT 59.660 47.619 0.00 0.00 39.98 4.75
109 110 1.067821 TGTGGAAAACAAATCCGTGCC 59.932 47.619 0.00 0.00 39.98 5.01
110 111 2.500509 TGTGGAAAACAAATCCGTGC 57.499 45.000 0.00 0.00 39.98 5.34
111 112 4.041723 GTCTTGTGGAAAACAAATCCGTG 58.958 43.478 0.00 0.00 44.97 4.94
112 113 3.697045 TGTCTTGTGGAAAACAAATCCGT 59.303 39.130 0.00 0.00 44.97 4.69
113 114 4.041723 GTGTCTTGTGGAAAACAAATCCG 58.958 43.478 0.00 0.00 44.97 4.18
114 115 4.041723 CGTGTCTTGTGGAAAACAAATCC 58.958 43.478 0.00 0.00 44.97 3.01
115 116 4.041723 CCGTGTCTTGTGGAAAACAAATC 58.958 43.478 0.00 0.00 44.97 2.17
116 117 3.736740 GCCGTGTCTTGTGGAAAACAAAT 60.737 43.478 0.00 0.00 44.97 2.32
117 118 2.416162 GCCGTGTCTTGTGGAAAACAAA 60.416 45.455 0.00 0.00 44.97 2.83
118 119 1.133407 GCCGTGTCTTGTGGAAAACAA 59.867 47.619 0.00 0.00 44.97 2.83
119 120 0.736053 GCCGTGTCTTGTGGAAAACA 59.264 50.000 0.00 0.00 36.85 2.83
120 121 1.021968 AGCCGTGTCTTGTGGAAAAC 58.978 50.000 0.00 0.00 0.00 2.43
121 122 1.021202 CAGCCGTGTCTTGTGGAAAA 58.979 50.000 0.00 0.00 0.00 2.29
122 123 1.444119 GCAGCCGTGTCTTGTGGAAA 61.444 55.000 0.00 0.00 0.00 3.13
123 124 1.891919 GCAGCCGTGTCTTGTGGAA 60.892 57.895 0.00 0.00 0.00 3.53
124 125 2.280797 GCAGCCGTGTCTTGTGGA 60.281 61.111 0.00 0.00 0.00 4.02
125 126 3.716006 CGCAGCCGTGTCTTGTGG 61.716 66.667 0.00 0.00 0.00 4.17
138 139 1.148310 TTCTTTTTCGAGAGGCGCAG 58.852 50.000 10.83 0.00 40.61 5.18
139 140 1.588674 TTTCTTTTTCGAGAGGCGCA 58.411 45.000 10.83 0.00 40.61 6.09
140 141 2.681152 TTTTCTTTTTCGAGAGGCGC 57.319 45.000 0.00 0.00 40.61 6.53
182 183 9.197694 CGAGAAGTAAATTTATACCTCTCATGG 57.802 37.037 15.30 2.03 40.81 3.66
183 184 9.751542 ACGAGAAGTAAATTTATACCTCTCATG 57.248 33.333 15.30 6.73 40.81 3.07
184 185 9.751542 CACGAGAAGTAAATTTATACCTCTCAT 57.248 33.333 15.30 2.90 40.81 2.90
185 186 8.195436 CCACGAGAAGTAAATTTATACCTCTCA 58.805 37.037 15.30 0.00 40.81 3.27
186 187 8.411683 TCCACGAGAAGTAAATTTATACCTCTC 58.588 37.037 0.31 5.58 38.87 3.20
187 188 8.302515 TCCACGAGAAGTAAATTTATACCTCT 57.697 34.615 0.31 0.00 30.95 3.69
188 189 7.652507 CCTCCACGAGAAGTAAATTTATACCTC 59.347 40.741 0.31 7.24 0.00 3.85
189 190 7.498443 CCTCCACGAGAAGTAAATTTATACCT 58.502 38.462 0.31 0.00 0.00 3.08
190 191 6.202379 GCCTCCACGAGAAGTAAATTTATACC 59.798 42.308 0.31 0.00 0.00 2.73
191 192 6.759827 TGCCTCCACGAGAAGTAAATTTATAC 59.240 38.462 0.31 0.00 0.00 1.47
192 193 6.759827 GTGCCTCCACGAGAAGTAAATTTATA 59.240 38.462 0.31 0.00 31.34 0.98
193 194 5.585047 GTGCCTCCACGAGAAGTAAATTTAT 59.415 40.000 0.31 0.00 31.34 1.40
194 195 4.933400 GTGCCTCCACGAGAAGTAAATTTA 59.067 41.667 0.00 0.00 31.34 1.40
242 243 1.608283 CCCCTTTCCGAGAGACACAAC 60.608 57.143 0.00 0.00 0.00 3.32
243 244 0.685097 CCCCTTTCCGAGAGACACAA 59.315 55.000 0.00 0.00 0.00 3.33
244 245 0.178944 TCCCCTTTCCGAGAGACACA 60.179 55.000 0.00 0.00 0.00 3.72
253 254 1.202348 GAGCACATTTTCCCCTTTCCG 59.798 52.381 0.00 0.00 0.00 4.30
262 263 2.879826 CCAAATCGGGAGCACATTTTC 58.120 47.619 0.00 0.00 0.00 2.29
288 290 5.740099 GGTTTCGATGAAAAGTTTTCACGAA 59.260 36.000 34.21 34.21 38.64 3.85
290 292 5.171337 CAGGTTTCGATGAAAAGTTTTCACG 59.829 40.000 28.62 28.39 33.14 4.35
294 296 6.202516 TGACAGGTTTCGATGAAAAGTTTT 57.797 33.333 0.00 0.00 33.14 2.43
297 299 7.687941 ATATTGACAGGTTTCGATGAAAAGT 57.312 32.000 0.00 0.00 33.14 2.66
298 300 9.655769 CATATATTGACAGGTTTCGATGAAAAG 57.344 33.333 0.00 0.00 33.14 2.27
347 349 5.204833 CGTTTTCATTGTGTGATTTCTCGT 58.795 37.500 0.00 0.00 36.54 4.18
352 354 4.737765 CGAACCGTTTTCATTGTGTGATTT 59.262 37.500 0.00 0.00 36.54 2.17
354 356 3.562141 TCGAACCGTTTTCATTGTGTGAT 59.438 39.130 0.00 0.00 36.54 3.06
356 358 3.001838 TCTCGAACCGTTTTCATTGTGTG 59.998 43.478 0.00 0.00 0.00 3.82
357 359 3.199677 TCTCGAACCGTTTTCATTGTGT 58.800 40.909 0.00 0.00 0.00 3.72
361 363 5.008217 TGTCAAATCTCGAACCGTTTTCATT 59.992 36.000 0.00 0.00 0.00 2.57
362 364 4.513692 TGTCAAATCTCGAACCGTTTTCAT 59.486 37.500 0.00 0.00 0.00 2.57
370 372 3.518590 ACCGTATGTCAAATCTCGAACC 58.481 45.455 0.00 0.00 0.00 3.62
375 377 6.100004 TCTCTCAAACCGTATGTCAAATCTC 58.900 40.000 0.00 0.00 0.00 2.75
433 435 6.882678 ACTTGTTGTAACCTGTAAGTTTCACT 59.117 34.615 0.00 0.00 28.28 3.41
435 437 6.094325 CCACTTGTTGTAACCTGTAAGTTTCA 59.906 38.462 0.00 0.00 0.00 2.69
436 438 6.316890 TCCACTTGTTGTAACCTGTAAGTTTC 59.683 38.462 0.00 0.00 0.00 2.78
442 444 4.348461 TCCATCCACTTGTTGTAACCTGTA 59.652 41.667 0.00 0.00 0.00 2.74
450 452 1.133823 TGTGCTCCATCCACTTGTTGT 60.134 47.619 0.00 0.00 34.38 3.32
451 453 1.608055 TGTGCTCCATCCACTTGTTG 58.392 50.000 0.00 0.00 34.38 3.33
452 454 2.165167 CATGTGCTCCATCCACTTGTT 58.835 47.619 0.00 0.00 35.11 2.83
457 459 2.033801 GCATTACATGTGCTCCATCCAC 59.966 50.000 9.11 0.00 39.45 4.02
460 462 2.212652 TCGCATTACATGTGCTCCATC 58.787 47.619 9.11 0.00 40.37 3.51
461 463 2.330440 TCGCATTACATGTGCTCCAT 57.670 45.000 9.11 0.00 40.37 3.41
463 465 1.334419 GCATCGCATTACATGTGCTCC 60.334 52.381 9.11 0.00 40.37 4.70
464 466 1.600957 AGCATCGCATTACATGTGCTC 59.399 47.619 9.11 0.00 35.91 4.26
465 467 1.671979 AGCATCGCATTACATGTGCT 58.328 45.000 9.11 2.70 40.37 4.40
466 468 2.114056 CAAGCATCGCATTACATGTGC 58.886 47.619 9.11 2.24 40.47 4.57
475 477 0.384309 CAGATTGGCAAGCATCGCAT 59.616 50.000 18.69 0.00 0.00 4.73
481 483 2.028839 CACATTTCCAGATTGGCAAGCA 60.029 45.455 18.69 0.00 37.47 3.91
482 484 2.613691 CACATTTCCAGATTGGCAAGC 58.386 47.619 7.54 7.54 37.47 4.01
487 489 2.756760 CACTCCCACATTTCCAGATTGG 59.243 50.000 0.00 0.00 39.43 3.16
496 500 2.489073 GGTTCTCCACACTCCCACATTT 60.489 50.000 0.00 0.00 0.00 2.32
499 503 0.692756 TGGTTCTCCACACTCCCACA 60.693 55.000 0.00 0.00 39.03 4.17
500 504 2.142220 TGGTTCTCCACACTCCCAC 58.858 57.895 0.00 0.00 39.03 4.61
573 641 6.142817 CGGCCCAATAGAAAGATTATTTTCG 58.857 40.000 0.00 0.00 40.99 3.46
602 670 1.732405 CGAGCACTGTGTCTCGCATTA 60.732 52.381 27.96 0.00 44.30 1.90
603 671 1.010935 CGAGCACTGTGTCTCGCATT 61.011 55.000 27.96 1.96 44.30 3.56
604 672 1.445066 CGAGCACTGTGTCTCGCAT 60.445 57.895 27.96 3.68 44.30 4.73
605 673 2.050077 CGAGCACTGTGTCTCGCA 60.050 61.111 27.96 0.00 44.30 5.10
621 689 1.154654 GAAGTGGTTTCGAAGCGCG 60.155 57.895 0.00 0.00 43.67 6.86
622 690 0.586802 AAGAAGTGGTTTCGAAGCGC 59.413 50.000 0.00 0.00 40.86 5.92
623 691 1.864711 TCAAGAAGTGGTTTCGAAGCG 59.135 47.619 5.89 0.00 40.86 4.68
624 692 3.618698 GTTCAAGAAGTGGTTTCGAAGC 58.381 45.455 3.02 3.02 40.86 3.86
625 693 3.554324 TCGTTCAAGAAGTGGTTTCGAAG 59.446 43.478 0.00 0.00 40.86 3.79
626 694 3.523547 TCGTTCAAGAAGTGGTTTCGAA 58.476 40.909 0.00 0.00 40.86 3.71
627 695 3.167921 TCGTTCAAGAAGTGGTTTCGA 57.832 42.857 0.00 0.00 40.86 3.71
628 696 3.936902 TTCGTTCAAGAAGTGGTTTCG 57.063 42.857 0.00 0.00 40.86 3.46
629 697 8.797266 ATTATTTTCGTTCAAGAAGTGGTTTC 57.203 30.769 0.00 0.00 35.97 2.78
630 698 8.630037 AGATTATTTTCGTTCAAGAAGTGGTTT 58.370 29.630 0.00 0.00 0.00 3.27
631 699 8.166422 AGATTATTTTCGTTCAAGAAGTGGTT 57.834 30.769 0.00 0.00 0.00 3.67
632 700 7.745620 AGATTATTTTCGTTCAAGAAGTGGT 57.254 32.000 0.00 0.00 0.00 4.16
641 709 9.959749 GCCCAATATAAAGATTATTTTCGTTCA 57.040 29.630 0.00 0.00 0.00 3.18
642 710 9.406828 GGCCCAATATAAAGATTATTTTCGTTC 57.593 33.333 0.00 0.00 0.00 3.95
643 711 8.079809 CGGCCCAATATAAAGATTATTTTCGTT 58.920 33.333 0.00 0.00 0.00 3.85
644 712 7.308951 CCGGCCCAATATAAAGATTATTTTCGT 60.309 37.037 0.00 0.00 0.00 3.85
645 713 7.027161 CCGGCCCAATATAAAGATTATTTTCG 58.973 38.462 0.00 0.00 0.00 3.46
646 714 7.320399 CCCGGCCCAATATAAAGATTATTTTC 58.680 38.462 0.00 0.00 0.00 2.29
647 715 6.295632 GCCCGGCCCAATATAAAGATTATTTT 60.296 38.462 0.00 0.00 0.00 1.82
648 716 5.186992 GCCCGGCCCAATATAAAGATTATTT 59.813 40.000 0.00 0.00 0.00 1.40
649 717 4.709886 GCCCGGCCCAATATAAAGATTATT 59.290 41.667 0.00 0.00 0.00 1.40
650 718 4.017499 AGCCCGGCCCAATATAAAGATTAT 60.017 41.667 5.55 0.00 0.00 1.28
651 719 3.332485 AGCCCGGCCCAATATAAAGATTA 59.668 43.478 5.55 0.00 0.00 1.75
652 720 2.110011 AGCCCGGCCCAATATAAAGATT 59.890 45.455 5.55 0.00 0.00 2.40
653 721 1.710809 AGCCCGGCCCAATATAAAGAT 59.289 47.619 5.55 0.00 0.00 2.40
654 722 1.073284 GAGCCCGGCCCAATATAAAGA 59.927 52.381 5.55 0.00 0.00 2.52
655 723 1.073923 AGAGCCCGGCCCAATATAAAG 59.926 52.381 5.55 0.00 0.00 1.85
656 724 1.073284 GAGAGCCCGGCCCAATATAAA 59.927 52.381 5.55 0.00 0.00 1.40
657 725 0.690762 GAGAGCCCGGCCCAATATAA 59.309 55.000 5.55 0.00 0.00 0.98
658 726 1.198759 GGAGAGCCCGGCCCAATATA 61.199 60.000 5.55 0.00 0.00 0.86
659 727 2.529744 GGAGAGCCCGGCCCAATAT 61.530 63.158 5.55 0.00 0.00 1.28
660 728 3.168528 GGAGAGCCCGGCCCAATA 61.169 66.667 5.55 0.00 0.00 1.90
663 731 3.792325 ATATGGAGAGCCCGGCCCA 62.792 63.158 5.55 7.10 37.93 5.36
664 732 1.198759 TAATATGGAGAGCCCGGCCC 61.199 60.000 5.55 0.34 37.93 5.80
665 733 0.250513 CTAATATGGAGAGCCCGGCC 59.749 60.000 5.55 0.00 37.93 6.13
666 734 0.391793 GCTAATATGGAGAGCCCGGC 60.392 60.000 0.00 0.00 37.93 6.13
667 735 0.976641 TGCTAATATGGAGAGCCCGG 59.023 55.000 0.00 0.00 37.93 5.73
668 736 1.066573 CCTGCTAATATGGAGAGCCCG 60.067 57.143 0.00 0.00 37.93 6.13
669 737 1.280421 CCCTGCTAATATGGAGAGCCC 59.720 57.143 0.00 0.00 35.24 5.19
670 738 1.339535 GCCCTGCTAATATGGAGAGCC 60.340 57.143 0.00 0.00 35.24 4.70
671 739 1.339535 GGCCCTGCTAATATGGAGAGC 60.340 57.143 0.00 0.00 36.72 4.09
672 740 1.066573 CGGCCCTGCTAATATGGAGAG 60.067 57.143 0.00 0.00 0.00 3.20
673 741 0.976641 CGGCCCTGCTAATATGGAGA 59.023 55.000 0.00 0.00 0.00 3.71
678 746 3.961408 CCTATAGACGGCCCTGCTAATAT 59.039 47.826 0.00 0.00 0.00 1.28
704 772 4.589908 AGCCGGCATTATAAAGGATTAGG 58.410 43.478 31.54 0.00 0.00 2.69
705 773 6.407202 AGTAGCCGGCATTATAAAGGATTAG 58.593 40.000 31.54 0.00 0.00 1.73
706 774 6.368779 AGTAGCCGGCATTATAAAGGATTA 57.631 37.500 31.54 3.86 0.00 1.75
708 776 4.910458 AGTAGCCGGCATTATAAAGGAT 57.090 40.909 31.54 5.27 0.00 3.24
709 777 6.368779 AATAGTAGCCGGCATTATAAAGGA 57.631 37.500 31.54 2.05 0.00 3.36
710 778 6.653320 TCAAATAGTAGCCGGCATTATAAAGG 59.347 38.462 31.54 10.93 0.00 3.11
711 779 7.667043 TCAAATAGTAGCCGGCATTATAAAG 57.333 36.000 31.54 12.80 0.00 1.85
718 786 3.815401 GTGAATCAAATAGTAGCCGGCAT 59.185 43.478 31.54 16.84 0.00 4.40
719 787 3.202906 GTGAATCAAATAGTAGCCGGCA 58.797 45.455 31.54 12.31 0.00 5.69
735 803 1.366319 AAGAGGCCCAGTCTGTGAAT 58.634 50.000 0.00 0.00 0.00 2.57
782 850 0.953471 CCGCGTCCAGTTGAAATCCA 60.953 55.000 4.92 0.00 0.00 3.41
1066 1137 1.618888 GGTTAAAAGGGGAGGGGAAGC 60.619 57.143 0.00 0.00 0.00 3.86
1068 1139 1.086565 GGGTTAAAAGGGGAGGGGAA 58.913 55.000 0.00 0.00 0.00 3.97
1069 1140 0.852232 GGGGTTAAAAGGGGAGGGGA 60.852 60.000 0.00 0.00 0.00 4.81
1736 1808 2.081787 TGCTTCTGAACCCACCCCA 61.082 57.895 0.00 0.00 0.00 4.96
1817 1889 3.513680 ACGCGTATGAACATCCTAACA 57.486 42.857 11.67 0.00 0.00 2.41
1945 2027 2.742053 TCATCGCTTTGCTGTTACCTTC 59.258 45.455 0.00 0.00 0.00 3.46
1961 2043 6.803320 ACTGAATTGCACTTTTGTATTCATCG 59.197 34.615 7.88 1.94 36.33 3.84
2024 2106 5.741011 TCTAACCACTGACAACTGAAAAGT 58.259 37.500 0.00 0.00 0.00 2.66
2100 2182 3.433274 CCTAATATACACGTGCATGGCAG 59.567 47.826 17.22 6.63 40.08 4.85
2200 2282 7.639113 AAAAACGCTATCCCATGAAATCTAA 57.361 32.000 0.00 0.00 0.00 2.10
2250 2332 5.052481 TGCAGTGCAAGTGATATGTATCTC 58.948 41.667 17.26 0.00 40.62 2.75
2251 2333 5.027293 TGCAGTGCAAGTGATATGTATCT 57.973 39.130 17.26 0.00 40.62 1.98
2258 2340 3.264947 GAGTCATGCAGTGCAAGTGATA 58.735 45.455 23.90 0.00 43.62 2.15
2359 2442 6.651975 TCTTAGGAATTAGTAGCAGCTACC 57.348 41.667 26.20 12.03 37.65 3.18
2529 2612 1.464997 GAACTTCCAAGTCCATGTCGC 59.535 52.381 0.00 0.00 38.57 5.19
2641 2724 4.722855 GCACCAGCGCCGCATTTT 62.723 61.111 13.36 0.00 0.00 1.82
2873 2956 8.936070 AAAACAGAAACTATTACAAAACCACC 57.064 30.769 0.00 0.00 0.00 4.61
2920 3012 3.918294 TCATGCTCCATGATTGACTGA 57.082 42.857 3.91 0.00 44.60 3.41
3129 3224 8.528917 AAAGACAAAGAAAAACAGGTTTGTAC 57.471 30.769 0.00 0.00 41.90 2.90
3317 3412 8.986477 AAGCTAAATGACAACAAATTCCATAC 57.014 30.769 0.00 0.00 0.00 2.39
3320 3415 6.202570 GCAAAGCTAAATGACAACAAATTCCA 59.797 34.615 0.00 0.00 0.00 3.53
3322 3417 7.176285 TGCAAAGCTAAATGACAACAAATTC 57.824 32.000 0.00 0.00 0.00 2.17
3331 3426 9.304731 TCATAATCAAATGCAAAGCTAAATGAC 57.695 29.630 0.00 0.00 0.00 3.06
3376 3471 6.936900 ACACAGCACTGATTAGTCTAAAACAT 59.063 34.615 4.31 0.00 34.07 2.71
3398 3493 2.820845 AAAAACTGGGAGGGCACAC 58.179 52.632 0.00 0.00 0.00 3.82
3420 3521 9.738832 GTACTTGTTTGTTAGCAATTTAAGGAA 57.261 29.630 12.10 2.42 34.18 3.36
3421 3522 8.904834 TGTACTTGTTTGTTAGCAATTTAAGGA 58.095 29.630 12.10 4.58 34.18 3.36
3422 3523 9.180678 CTGTACTTGTTTGTTAGCAATTTAAGG 57.819 33.333 12.10 0.00 34.18 2.69
3445 3546 8.500753 TTCTGAAACACACAAATAAGTACTGT 57.499 30.769 0.00 0.00 0.00 3.55
3474 3575 1.535462 GTTGCCACGCTTTCAGTGTAT 59.465 47.619 0.00 0.00 36.71 2.29
3477 3578 1.008538 GGTTGCCACGCTTTCAGTG 60.009 57.895 0.00 0.00 39.19 3.66
3490 3591 6.797033 GTCAAATTATGCTATCGTATGGTTGC 59.203 38.462 0.00 0.00 0.00 4.17
3492 3593 8.559536 CAAGTCAAATTATGCTATCGTATGGTT 58.440 33.333 0.00 0.00 0.00 3.67
3493 3594 7.715249 ACAAGTCAAATTATGCTATCGTATGGT 59.285 33.333 0.00 0.00 0.00 3.55
3494 3595 8.087982 ACAAGTCAAATTATGCTATCGTATGG 57.912 34.615 0.00 0.00 0.00 2.74
3495 3596 8.982685 AGACAAGTCAAATTATGCTATCGTATG 58.017 33.333 2.72 0.00 0.00 2.39
3496 3597 9.197694 GAGACAAGTCAAATTATGCTATCGTAT 57.802 33.333 2.72 0.00 0.00 3.06
3497 3598 7.652105 GGAGACAAGTCAAATTATGCTATCGTA 59.348 37.037 2.72 0.00 0.00 3.43
3498 3599 6.480320 GGAGACAAGTCAAATTATGCTATCGT 59.520 38.462 2.72 0.00 0.00 3.73
3499 3600 6.479990 TGGAGACAAGTCAAATTATGCTATCG 59.520 38.462 2.72 0.00 37.44 2.92
3500 3601 7.517417 CGTGGAGACAAGTCAAATTATGCTATC 60.517 40.741 2.72 0.00 46.06 2.08
3501 3602 6.258727 CGTGGAGACAAGTCAAATTATGCTAT 59.741 38.462 2.72 0.00 46.06 2.97
3502 3603 5.580691 CGTGGAGACAAGTCAAATTATGCTA 59.419 40.000 2.72 0.00 46.06 3.49
3503 3604 4.393062 CGTGGAGACAAGTCAAATTATGCT 59.607 41.667 2.72 0.00 46.06 3.79
3504 3605 4.437390 CCGTGGAGACAAGTCAAATTATGC 60.437 45.833 2.72 0.00 46.06 3.14
3505 3606 4.437390 GCCGTGGAGACAAGTCAAATTATG 60.437 45.833 2.72 0.00 46.06 1.90
3506 3607 3.689649 GCCGTGGAGACAAGTCAAATTAT 59.310 43.478 2.72 0.00 46.06 1.28
3507 3608 3.071479 GCCGTGGAGACAAGTCAAATTA 58.929 45.455 2.72 0.00 46.06 1.40
3527 3628 4.513198 TGGGTTTAGTATTGTGCTTTGC 57.487 40.909 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.