Multiple sequence alignment - TraesCS4B01G228700

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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 TraesCS4B01G228700 chr4B 100.000 2897 0 0 427 3323 479397493 479400389 0.000000e+00 5350.0
1 TraesCS4B01G228700 chr4B 100.000 174 0 0 1 174 479397067 479397240 4.140000e-84 322.0
2 TraesCS4B01G228700 chr4D 94.931 1874 76 8 539 2408 389494484 389496342 0.000000e+00 2916.0
3 TraesCS4B01G228700 chr4D 98.000 50 1 0 427 476 389493623 389493672 1.640000e-13 87.9
4 TraesCS4B01G228700 chr4A 90.337 1987 90 30 469 2408 71165640 71167571 0.000000e+00 2512.0
5 TraesCS4B01G228700 chr4A 89.281 765 69 10 2563 3321 71167554 71168311 0.000000e+00 946.0
6 TraesCS4B01G228700 chr7D 85.345 232 27 7 1060 1289 160629081 160629307 1.990000e-57 233.0
7 TraesCS4B01G228700 chr7D 89.308 159 16 1 2411 2569 79917319 79917162 7.270000e-47 198.0
8 TraesCS4B01G228700 chr7D 88.462 156 17 1 2409 2564 41411372 41411526 1.570000e-43 187.0
9 TraesCS4B01G228700 chr7D 75.000 396 78 18 1921 2310 160629933 160630313 2.650000e-36 163.0
10 TraesCS4B01G228700 chr7B 84.052 232 30 5 1060 1289 121883826 121884052 2.010000e-52 217.0
11 TraesCS4B01G228700 chr7A 83.190 232 33 6 1059 1289 161732265 161732491 1.210000e-49 207.0
12 TraesCS4B01G228700 chr7A 76.322 397 71 17 1921 2310 161733117 161733497 1.220000e-44 191.0
13 TraesCS4B01G228700 chr5D 89.571 163 15 2 2402 2564 337582970 337583130 4.350000e-49 206.0
14 TraesCS4B01G228700 chr5D 88.050 159 18 1 2411 2569 242073011 242073168 1.570000e-43 187.0
15 TraesCS4B01G228700 chr5D 89.655 58 6 0 1735 1792 500453420 500453477 1.280000e-09 75.0
16 TraesCS4B01G228700 chr1D 89.610 154 14 1 2411 2564 406518672 406518823 9.410000e-46 195.0
17 TraesCS4B01G228700 chr1D 88.961 154 16 1 2411 2564 39901358 39901510 4.380000e-44 189.0
18 TraesCS4B01G228700 chr1D 87.195 164 21 0 2411 2574 251299737 251299900 1.570000e-43 187.0
19 TraesCS4B01G228700 chr2B 89.677 155 11 3 2412 2564 785910296 785910447 3.380000e-45 193.0
20 TraesCS4B01G228700 chr6D 88.125 160 18 1 2411 2569 403816512 403816671 4.380000e-44 189.0
21 TraesCS4B01G228700 chr5A 76.316 228 42 9 1063 1290 119028946 119028731 9.750000e-21 111.0
22 TraesCS4B01G228700 chr5A 88.889 54 5 1 2036 2088 27734184 27734237 7.700000e-07 65.8
23 TraesCS4B01G228700 chr6A 75.877 228 43 9 1063 1290 412854395 412854180 4.530000e-19 106.0
24 TraesCS4B01G228700 chr3B 94.872 39 2 0 1076 1114 543582014 543582052 9.950000e-06 62.1


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 TraesCS4B01G228700 chr4B 479397067 479400389 3322 False 2836.00 5350 100.0000 1 3323 2 chr4B.!!$F1 3322
1 TraesCS4B01G228700 chr4D 389493623 389496342 2719 False 1501.95 2916 96.4655 427 2408 2 chr4D.!!$F1 1981
2 TraesCS4B01G228700 chr4A 71165640 71168311 2671 False 1729.00 2512 89.8090 469 3321 2 chr4A.!!$F1 2852

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
633 1390 0.103208 CTGCACATCGGTAGGTCCTC 59.897 60.0 0.0 0.0 0.0 3.71 F
640 1397 0.250858 TCGGTAGGTCCTCAACGTCA 60.251 55.0 0.0 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2217 3017 0.037232 CGGTGGTCTTCTCCTTGGTC 60.037 60.0 0.0 0.0 0.0 4.02 R
2578 3378 0.543749 TTGGCAAACACAAAAGGGGG 59.456 50.0 0.0 0.0 0.0 5.40 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
25 26 5.968251 CGATAGTTTTTCGTTCGCAATTT 57.032 34.783 0.00 0.00 32.08 1.82
26 27 6.357301 CGATAGTTTTTCGTTCGCAATTTT 57.643 33.333 0.00 0.00 32.08 1.82
27 28 6.793227 CGATAGTTTTTCGTTCGCAATTTTT 58.207 32.000 0.00 0.00 32.08 1.94
65 66 5.782893 CCAGTAGGTCAATTTTGTTCCAA 57.217 39.130 8.85 0.00 0.00 3.53
66 67 6.155475 CCAGTAGGTCAATTTTGTTCCAAA 57.845 37.500 8.85 0.00 0.00 3.28
67 68 6.578023 CCAGTAGGTCAATTTTGTTCCAAAA 58.422 36.000 4.76 4.76 0.00 2.44
68 69 7.044798 CCAGTAGGTCAATTTTGTTCCAAAAA 58.955 34.615 6.26 0.00 33.76 1.94
129 130 7.956420 TTTTTGTATCACGTTCATCTACACT 57.044 32.000 0.00 0.00 0.00 3.55
130 131 7.956420 TTTTGTATCACGTTCATCTACACTT 57.044 32.000 0.00 0.00 0.00 3.16
131 132 9.478768 TTTTTGTATCACGTTCATCTACACTTA 57.521 29.630 0.00 0.00 0.00 2.24
132 133 8.683550 TTTGTATCACGTTCATCTACACTTAG 57.316 34.615 0.00 0.00 0.00 2.18
133 134 6.792326 TGTATCACGTTCATCTACACTTAGG 58.208 40.000 0.00 0.00 0.00 2.69
134 135 5.916661 ATCACGTTCATCTACACTTAGGT 57.083 39.130 0.00 0.00 0.00 3.08
135 136 5.306532 TCACGTTCATCTACACTTAGGTC 57.693 43.478 0.00 0.00 0.00 3.85
136 137 4.157289 TCACGTTCATCTACACTTAGGTCC 59.843 45.833 0.00 0.00 0.00 4.46
137 138 4.082408 CACGTTCATCTACACTTAGGTCCA 60.082 45.833 0.00 0.00 0.00 4.02
138 139 4.525487 ACGTTCATCTACACTTAGGTCCAA 59.475 41.667 0.00 0.00 0.00 3.53
139 140 5.011329 ACGTTCATCTACACTTAGGTCCAAA 59.989 40.000 0.00 0.00 0.00 3.28
140 141 5.577164 CGTTCATCTACACTTAGGTCCAAAG 59.423 44.000 0.00 0.00 0.00 2.77
141 142 5.677319 TCATCTACACTTAGGTCCAAAGG 57.323 43.478 0.00 0.00 0.00 3.11
142 143 4.469945 TCATCTACACTTAGGTCCAAAGGG 59.530 45.833 0.00 0.00 33.41 3.95
143 144 3.865571 TCTACACTTAGGTCCAAAGGGT 58.134 45.455 0.00 0.00 43.00 4.34
144 145 5.014534 TCTACACTTAGGTCCAAAGGGTA 57.985 43.478 0.00 0.00 40.90 3.69
145 146 5.596763 TCTACACTTAGGTCCAAAGGGTAT 58.403 41.667 0.00 0.00 40.94 2.73
146 147 6.027482 TCTACACTTAGGTCCAAAGGGTATT 58.973 40.000 0.00 0.00 40.94 1.89
147 148 5.594199 ACACTTAGGTCCAAAGGGTATTT 57.406 39.130 0.00 0.00 38.80 1.40
148 149 5.960704 ACACTTAGGTCCAAAGGGTATTTT 58.039 37.500 0.00 0.00 38.80 1.82
149 150 6.008331 ACACTTAGGTCCAAAGGGTATTTTC 58.992 40.000 0.00 0.00 38.80 2.29
150 151 5.417894 CACTTAGGTCCAAAGGGTATTTTCC 59.582 44.000 0.00 0.00 34.93 3.13
151 152 5.315109 ACTTAGGTCCAAAGGGTATTTTCCT 59.685 40.000 0.00 0.00 35.88 3.36
152 153 4.317530 AGGTCCAAAGGGTATTTTCCTC 57.682 45.455 0.00 0.00 32.59 3.71
153 154 3.011369 AGGTCCAAAGGGTATTTTCCTCC 59.989 47.826 0.00 0.00 32.59 4.30
154 155 3.011369 GGTCCAAAGGGTATTTTCCTCCT 59.989 47.826 0.00 0.00 32.59 3.69
155 156 4.510386 GGTCCAAAGGGTATTTTCCTCCTT 60.510 45.833 0.00 0.00 40.94 3.36
156 157 4.462834 GTCCAAAGGGTATTTTCCTCCTTG 59.537 45.833 0.00 0.00 39.33 3.61
157 158 3.195610 CCAAAGGGTATTTTCCTCCTTGC 59.804 47.826 0.00 0.00 39.33 4.01
158 159 2.828661 AGGGTATTTTCCTCCTTGCC 57.171 50.000 0.00 0.00 0.00 4.52
159 160 2.288525 AGGGTATTTTCCTCCTTGCCT 58.711 47.619 0.00 0.00 0.00 4.75
160 161 2.242452 AGGGTATTTTCCTCCTTGCCTC 59.758 50.000 0.00 0.00 0.00 4.70
161 162 2.242452 GGGTATTTTCCTCCTTGCCTCT 59.758 50.000 0.00 0.00 0.00 3.69
162 163 3.546724 GGTATTTTCCTCCTTGCCTCTC 58.453 50.000 0.00 0.00 0.00 3.20
163 164 3.201045 GGTATTTTCCTCCTTGCCTCTCT 59.799 47.826 0.00 0.00 0.00 3.10
164 165 3.643199 ATTTTCCTCCTTGCCTCTCTC 57.357 47.619 0.00 0.00 0.00 3.20
165 166 2.334006 TTTCCTCCTTGCCTCTCTCT 57.666 50.000 0.00 0.00 0.00 3.10
166 167 3.474798 TTTCCTCCTTGCCTCTCTCTA 57.525 47.619 0.00 0.00 0.00 2.43
167 168 2.445682 TCCTCCTTGCCTCTCTCTAC 57.554 55.000 0.00 0.00 0.00 2.59
168 169 1.926665 TCCTCCTTGCCTCTCTCTACT 59.073 52.381 0.00 0.00 0.00 2.57
169 170 2.313342 TCCTCCTTGCCTCTCTCTACTT 59.687 50.000 0.00 0.00 0.00 2.24
170 171 2.693074 CCTCCTTGCCTCTCTCTACTTC 59.307 54.545 0.00 0.00 0.00 3.01
171 172 2.693074 CTCCTTGCCTCTCTCTACTTCC 59.307 54.545 0.00 0.00 0.00 3.46
172 173 1.760029 CCTTGCCTCTCTCTACTTCCC 59.240 57.143 0.00 0.00 0.00 3.97
173 174 2.625617 CCTTGCCTCTCTCTACTTCCCT 60.626 54.545 0.00 0.00 0.00 4.20
458 459 5.817296 TCAAGAATATTCGGTCCAACATCAG 59.183 40.000 9.78 0.00 0.00 2.90
480 497 2.024273 CCTAGACAACCTCCCCTCTACA 60.024 54.545 0.00 0.00 0.00 2.74
497 514 5.011125 CCTCTACACCCTAAATCGATGATGT 59.989 44.000 0.00 0.44 0.00 3.06
498 515 5.842907 TCTACACCCTAAATCGATGATGTG 58.157 41.667 0.00 5.54 0.00 3.21
533 558 5.291971 CCATTGGGCTAATATTTTGCTGAC 58.708 41.667 0.00 5.28 0.00 3.51
537 562 4.769488 TGGGCTAATATTTTGCTGACACAA 59.231 37.500 11.26 0.00 0.00 3.33
542 567 8.720562 GGCTAATATTTTGCTGACACAATTTTT 58.279 29.630 11.26 0.00 29.26 1.94
567 1317 4.918810 TTGAAGAAAGAAAGAAGGCCAC 57.081 40.909 5.01 0.00 0.00 5.01
573 1323 3.356529 AAGAAAGAAGGCCACGATCAT 57.643 42.857 5.01 0.00 0.00 2.45
588 1338 3.372206 ACGATCATGTTGCTTTGCTCTAC 59.628 43.478 0.00 0.00 0.00 2.59
632 1389 0.614979 ACTGCACATCGGTAGGTCCT 60.615 55.000 0.00 0.00 31.06 3.85
633 1390 0.103208 CTGCACATCGGTAGGTCCTC 59.897 60.000 0.00 0.00 0.00 3.71
634 1391 0.613572 TGCACATCGGTAGGTCCTCA 60.614 55.000 0.00 0.00 0.00 3.86
635 1392 0.535335 GCACATCGGTAGGTCCTCAA 59.465 55.000 0.00 0.00 0.00 3.02
636 1393 1.739371 GCACATCGGTAGGTCCTCAAC 60.739 57.143 0.00 0.00 0.00 3.18
637 1394 0.815734 ACATCGGTAGGTCCTCAACG 59.184 55.000 0.00 0.00 0.00 4.10
638 1395 0.815734 CATCGGTAGGTCCTCAACGT 59.184 55.000 0.00 0.00 0.00 3.99
639 1396 1.101331 ATCGGTAGGTCCTCAACGTC 58.899 55.000 0.00 0.00 0.00 4.34
640 1397 0.250858 TCGGTAGGTCCTCAACGTCA 60.251 55.000 0.00 0.00 0.00 4.35
641 1398 0.599558 CGGTAGGTCCTCAACGTCAA 59.400 55.000 0.00 0.00 0.00 3.18
642 1399 1.668047 CGGTAGGTCCTCAACGTCAAC 60.668 57.143 0.00 0.00 0.00 3.18
643 1400 1.337541 GGTAGGTCCTCAACGTCAACC 60.338 57.143 0.00 0.00 0.00 3.77
644 1401 1.617357 GTAGGTCCTCAACGTCAACCT 59.383 52.381 0.00 10.75 42.78 3.50
645 1402 0.393077 AGGTCCTCAACGTCAACCTG 59.607 55.000 6.52 0.00 38.88 4.00
646 1403 0.391597 GGTCCTCAACGTCAACCTGA 59.608 55.000 0.00 0.00 0.00 3.86
647 1404 1.202604 GGTCCTCAACGTCAACCTGAA 60.203 52.381 0.00 0.00 0.00 3.02
648 1405 2.557317 GTCCTCAACGTCAACCTGAAA 58.443 47.619 0.00 0.00 0.00 2.69
649 1406 3.139077 GTCCTCAACGTCAACCTGAAAT 58.861 45.455 0.00 0.00 0.00 2.17
650 1407 3.186613 GTCCTCAACGTCAACCTGAAATC 59.813 47.826 0.00 0.00 0.00 2.17
660 1417 7.093992 ACGTCAACCTGAAATCAAAAGAAAAA 58.906 30.769 0.00 0.00 0.00 1.94
661 1418 7.275560 ACGTCAACCTGAAATCAAAAGAAAAAG 59.724 33.333 0.00 0.00 0.00 2.27
662 1419 7.487829 CGTCAACCTGAAATCAAAAGAAAAAGA 59.512 33.333 0.00 0.00 0.00 2.52
664 1421 9.369904 TCAACCTGAAATCAAAAGAAAAAGAAG 57.630 29.630 0.00 0.00 0.00 2.85
749 1506 4.503910 GCCCCCTTTTCATTCAAACATAC 58.496 43.478 0.00 0.00 0.00 2.39
750 1507 4.222810 GCCCCCTTTTCATTCAAACATACT 59.777 41.667 0.00 0.00 0.00 2.12
751 1508 5.420739 GCCCCCTTTTCATTCAAACATACTA 59.579 40.000 0.00 0.00 0.00 1.82
753 1510 6.096846 CCCCCTTTTCATTCAAACATACTAGG 59.903 42.308 0.00 0.00 0.00 3.02
754 1511 6.663523 CCCCTTTTCATTCAAACATACTAGGT 59.336 38.462 0.00 0.00 0.00 3.08
755 1512 7.832187 CCCCTTTTCATTCAAACATACTAGGTA 59.168 37.037 0.00 0.00 0.00 3.08
756 1513 8.674607 CCCTTTTCATTCAAACATACTAGGTAC 58.325 37.037 0.00 0.00 0.00 3.34
760 1517 8.997621 TTCATTCAAACATACTAGGTACTCAC 57.002 34.615 0.00 0.00 41.75 3.51
876 1654 2.185004 ATTCAACTCTTCACACCCCG 57.815 50.000 0.00 0.00 0.00 5.73
877 1655 0.534203 TTCAACTCTTCACACCCCGC 60.534 55.000 0.00 0.00 0.00 6.13
1110 1910 2.415010 CCGATCTCGCTGGACCTG 59.585 66.667 0.00 0.00 38.18 4.00
1153 1953 1.000521 ACGGGGATCACCTACGACA 60.001 57.895 13.38 0.00 40.03 4.35
1176 1976 4.827087 AGCATCGAGGCGTGGCTG 62.827 66.667 17.28 0.00 36.46 4.85
1248 2048 2.656069 CGACCTCGTCCCCAACCAT 61.656 63.158 0.00 0.00 34.11 3.55
1337 2137 1.995626 CCAAGATCCCCGTCACCCT 60.996 63.158 0.00 0.00 0.00 4.34
1567 2367 1.764571 CGGGGGTGTTCTTGAGGACA 61.765 60.000 0.00 0.00 0.00 4.02
1569 2369 1.340114 GGGGGTGTTCTTGAGGACATC 60.340 57.143 0.00 0.00 0.00 3.06
1723 2523 0.895530 GATCAAGGAGGTCGTGTCCA 59.104 55.000 3.81 0.00 36.43 4.02
1800 2600 2.295885 CTGGTCAAGATCATCAAGGCC 58.704 52.381 0.00 0.00 0.00 5.19
1809 2609 0.920763 TCATCAAGGCCCCCATCTGT 60.921 55.000 0.00 0.00 0.00 3.41
1812 2612 3.411517 AAGGCCCCCATCTGTCCG 61.412 66.667 0.00 0.00 0.00 4.79
2065 2865 3.215597 ATGTTCCGCGTGTCCGACA 62.216 57.895 4.92 0.00 35.63 4.35
2151 2951 1.741770 AGCGACGAAATGCCTGGTC 60.742 57.895 0.00 0.00 0.00 4.02
2418 3218 8.507249 AGATGTAAATTCTTCTTTTGAGAACGG 58.493 33.333 0.00 0.00 0.00 4.44
2419 3219 7.795482 TGTAAATTCTTCTTTTGAGAACGGA 57.205 32.000 0.00 0.00 0.00 4.69
2420 3220 7.861630 TGTAAATTCTTCTTTTGAGAACGGAG 58.138 34.615 0.00 0.00 0.00 4.63
2421 3221 5.948992 AATTCTTCTTTTGAGAACGGAGG 57.051 39.130 0.00 0.00 0.00 4.30
2422 3222 3.402628 TCTTCTTTTGAGAACGGAGGG 57.597 47.619 0.00 0.00 0.00 4.30
2423 3223 1.807142 CTTCTTTTGAGAACGGAGGGC 59.193 52.381 0.00 0.00 0.00 5.19
2424 3224 0.762418 TCTTTTGAGAACGGAGGGCA 59.238 50.000 0.00 0.00 0.00 5.36
2425 3225 1.160137 CTTTTGAGAACGGAGGGCAG 58.840 55.000 0.00 0.00 0.00 4.85
2426 3226 0.889186 TTTTGAGAACGGAGGGCAGC 60.889 55.000 0.00 0.00 0.00 5.25
2427 3227 1.768684 TTTGAGAACGGAGGGCAGCT 61.769 55.000 0.00 0.00 0.00 4.24
2428 3228 2.172483 TTGAGAACGGAGGGCAGCTC 62.172 60.000 0.00 0.00 0.00 4.09
2429 3229 2.604686 AGAACGGAGGGCAGCTCA 60.605 61.111 0.00 0.00 0.00 4.26
2430 3230 2.125350 GAACGGAGGGCAGCTCAG 60.125 66.667 0.00 0.00 0.00 3.35
2431 3231 2.925170 AACGGAGGGCAGCTCAGT 60.925 61.111 0.00 0.00 0.00 3.41
2432 3232 2.456287 GAACGGAGGGCAGCTCAGTT 62.456 60.000 8.51 8.51 40.74 3.16
2433 3233 2.435586 CGGAGGGCAGCTCAGTTG 60.436 66.667 0.00 0.00 0.00 3.16
2434 3234 2.045536 GGAGGGCAGCTCAGTTGG 60.046 66.667 0.00 0.00 0.00 3.77
2435 3235 2.749441 GAGGGCAGCTCAGTTGGC 60.749 66.667 6.51 6.51 38.47 4.52
2436 3236 3.557903 GAGGGCAGCTCAGTTGGCA 62.558 63.158 17.08 0.00 40.70 4.92
2437 3237 2.598394 GGGCAGCTCAGTTGGCAA 60.598 61.111 17.08 0.00 40.70 4.52
2438 3238 2.633509 GGGCAGCTCAGTTGGCAAG 61.634 63.158 17.08 0.00 40.70 4.01
2439 3239 2.257676 GCAGCTCAGTTGGCAAGC 59.742 61.111 0.00 0.00 36.27 4.01
2440 3240 2.266627 GCAGCTCAGTTGGCAAGCT 61.267 57.895 5.60 5.60 46.98 3.74
2441 3241 4.076244 AGCTCAGTTGGCAAGCTG 57.924 55.556 10.46 14.88 44.41 4.24
2442 3242 2.257676 GCTCAGTTGGCAAGCTGC 59.742 61.111 18.78 10.43 44.08 5.25
2443 3243 2.559840 CTCAGTTGGCAAGCTGCG 59.440 61.111 18.78 12.50 46.21 5.18
2444 3244 2.974489 CTCAGTTGGCAAGCTGCGG 61.974 63.158 18.78 12.71 46.21 5.69
2445 3245 4.047059 CAGTTGGCAAGCTGCGGG 62.047 66.667 0.00 0.00 46.21 6.13
2446 3246 4.269523 AGTTGGCAAGCTGCGGGA 62.270 61.111 0.00 0.00 46.21 5.14
2447 3247 3.741476 GTTGGCAAGCTGCGGGAG 61.741 66.667 0.00 0.00 46.21 4.30
2448 3248 4.269523 TTGGCAAGCTGCGGGAGT 62.270 61.111 0.00 0.00 46.21 3.85
2449 3249 3.790416 TTGGCAAGCTGCGGGAGTT 62.790 57.895 0.00 0.00 46.21 3.01
2450 3250 3.435186 GGCAAGCTGCGGGAGTTC 61.435 66.667 0.00 0.00 46.21 3.01
2451 3251 3.793144 GCAAGCTGCGGGAGTTCG 61.793 66.667 0.00 0.00 31.71 3.95
2459 3259 2.583593 CGGGAGTTCGCAGCTAGC 60.584 66.667 6.62 6.62 40.87 3.42
2460 3260 2.202946 GGGAGTTCGCAGCTAGCC 60.203 66.667 12.13 0.00 41.38 3.93
2461 3261 2.202946 GGAGTTCGCAGCTAGCCC 60.203 66.667 12.13 1.56 41.38 5.19
2462 3262 2.579201 GAGTTCGCAGCTAGCCCA 59.421 61.111 12.13 0.00 41.38 5.36
2463 3263 1.144936 GAGTTCGCAGCTAGCCCAT 59.855 57.895 12.13 0.00 41.38 4.00
2464 3264 0.878086 GAGTTCGCAGCTAGCCCATC 60.878 60.000 12.13 0.00 41.38 3.51
2465 3265 1.153369 GTTCGCAGCTAGCCCATCA 60.153 57.895 12.13 0.00 41.38 3.07
2466 3266 1.144716 TTCGCAGCTAGCCCATCAG 59.855 57.895 12.13 0.00 41.38 2.90
2467 3267 2.280660 CGCAGCTAGCCCATCAGG 60.281 66.667 12.13 0.00 41.38 3.86
2481 3281 4.243007 CCATCAGGGTTCAAGTTTTGAC 57.757 45.455 0.00 0.00 39.87 3.18
2482 3282 3.891366 CCATCAGGGTTCAAGTTTTGACT 59.109 43.478 0.00 0.00 39.87 3.41
2483 3283 4.022849 CCATCAGGGTTCAAGTTTTGACTC 60.023 45.833 0.00 0.00 39.87 3.36
2484 3284 3.202906 TCAGGGTTCAAGTTTTGACTCG 58.797 45.455 0.00 0.00 39.87 4.18
2485 3285 3.118555 TCAGGGTTCAAGTTTTGACTCGA 60.119 43.478 0.00 0.00 39.87 4.04
2486 3286 3.248602 CAGGGTTCAAGTTTTGACTCGAG 59.751 47.826 11.84 11.84 39.87 4.04
2487 3287 3.118371 AGGGTTCAAGTTTTGACTCGAGT 60.118 43.478 20.18 20.18 39.87 4.18
2488 3288 3.002348 GGGTTCAAGTTTTGACTCGAGTG 59.998 47.826 25.58 5.89 39.87 3.51
2489 3289 3.546218 GGTTCAAGTTTTGACTCGAGTGC 60.546 47.826 25.58 14.85 39.87 4.40
2490 3290 3.179443 TCAAGTTTTGACTCGAGTGCT 57.821 42.857 25.58 9.82 34.08 4.40
2491 3291 3.531538 TCAAGTTTTGACTCGAGTGCTT 58.468 40.909 25.58 14.96 34.08 3.91
2492 3292 3.309682 TCAAGTTTTGACTCGAGTGCTTG 59.690 43.478 25.58 23.85 34.08 4.01
2493 3293 3.179443 AGTTTTGACTCGAGTGCTTGA 57.821 42.857 25.58 1.77 0.00 3.02
2494 3294 3.733337 AGTTTTGACTCGAGTGCTTGAT 58.267 40.909 25.58 1.65 0.00 2.57
2495 3295 3.496130 AGTTTTGACTCGAGTGCTTGATG 59.504 43.478 25.58 0.00 0.00 3.07
2496 3296 1.432514 TTGACTCGAGTGCTTGATGC 58.567 50.000 25.58 6.22 43.25 3.91
2497 3297 0.605083 TGACTCGAGTGCTTGATGCT 59.395 50.000 25.58 0.00 43.37 3.79
2498 3298 1.276415 GACTCGAGTGCTTGATGCTC 58.724 55.000 25.58 0.00 43.37 4.26
2499 3299 0.605083 ACTCGAGTGCTTGATGCTCA 59.395 50.000 19.30 0.00 43.37 4.26
2500 3300 0.997932 CTCGAGTGCTTGATGCTCAC 59.002 55.000 3.62 0.00 43.37 3.51
2501 3301 0.733909 TCGAGTGCTTGATGCTCACG 60.734 55.000 6.03 6.03 45.50 4.35
2502 3302 1.690283 CGAGTGCTTGATGCTCACGG 61.690 60.000 4.79 0.00 42.39 4.94
2503 3303 0.390340 GAGTGCTTGATGCTCACGGA 60.390 55.000 0.00 0.00 43.37 4.69
2504 3304 0.390866 AGTGCTTGATGCTCACGGAG 60.391 55.000 0.00 0.00 43.37 4.63
2505 3305 0.671781 GTGCTTGATGCTCACGGAGT 60.672 55.000 3.38 0.00 42.92 3.85
2506 3306 0.035317 TGCTTGATGCTCACGGAGTT 59.965 50.000 3.38 0.00 40.69 3.01
2507 3307 1.160137 GCTTGATGCTCACGGAGTTT 58.840 50.000 3.38 0.00 37.40 2.66
2508 3308 1.537202 GCTTGATGCTCACGGAGTTTT 59.463 47.619 3.38 0.00 37.40 2.43
2509 3309 2.413371 GCTTGATGCTCACGGAGTTTTC 60.413 50.000 3.38 0.28 37.40 2.29
2510 3310 2.839486 TGATGCTCACGGAGTTTTCT 57.161 45.000 3.38 0.00 41.61 2.52
2511 3311 3.126001 TGATGCTCACGGAGTTTTCTT 57.874 42.857 3.38 0.00 41.61 2.52
2512 3312 3.067106 TGATGCTCACGGAGTTTTCTTC 58.933 45.455 3.38 0.00 41.61 2.87
2513 3313 2.910688 TGCTCACGGAGTTTTCTTCT 57.089 45.000 3.38 0.00 41.61 2.85
2514 3314 4.021456 TGATGCTCACGGAGTTTTCTTCTA 60.021 41.667 3.38 0.00 41.61 2.10
2515 3315 4.537135 TGCTCACGGAGTTTTCTTCTAT 57.463 40.909 3.38 0.00 41.61 1.98
2516 3316 4.495422 TGCTCACGGAGTTTTCTTCTATC 58.505 43.478 3.38 0.00 41.61 2.08
2517 3317 4.021456 TGCTCACGGAGTTTTCTTCTATCA 60.021 41.667 3.38 0.00 41.61 2.15
2518 3318 4.929808 GCTCACGGAGTTTTCTTCTATCAA 59.070 41.667 3.38 0.00 41.61 2.57
2519 3319 5.408604 GCTCACGGAGTTTTCTTCTATCAAA 59.591 40.000 3.38 0.00 41.61 2.69
2520 3320 6.073222 GCTCACGGAGTTTTCTTCTATCAAAA 60.073 38.462 3.38 0.00 41.61 2.44
2521 3321 7.519970 GCTCACGGAGTTTTCTTCTATCAAAAA 60.520 37.037 3.38 0.00 41.61 1.94
2550 3350 3.951765 GCTAGTCTAGCCCGGGTT 58.048 61.111 24.63 20.60 45.95 4.11
2551 3351 1.442148 GCTAGTCTAGCCCGGGTTG 59.558 63.158 24.63 12.73 45.95 3.77
2552 3352 2.029307 GCTAGTCTAGCCCGGGTTGG 62.029 65.000 24.63 19.66 45.95 3.77
2553 3353 0.686769 CTAGTCTAGCCCGGGTTGGT 60.687 60.000 24.63 5.63 35.15 3.67
2554 3354 0.685458 TAGTCTAGCCCGGGTTGGTC 60.685 60.000 24.63 16.39 35.15 4.02
2555 3355 1.988406 GTCTAGCCCGGGTTGGTCT 60.988 63.158 24.63 12.87 35.15 3.85
2556 3356 1.684734 TCTAGCCCGGGTTGGTCTC 60.685 63.158 24.63 2.54 35.15 3.36
2557 3357 3.072468 TAGCCCGGGTTGGTCTCG 61.072 66.667 24.63 0.00 40.13 4.04
2558 3358 3.892104 TAGCCCGGGTTGGTCTCGT 62.892 63.158 24.63 0.00 38.54 4.18
2559 3359 4.324991 GCCCGGGTTGGTCTCGTT 62.325 66.667 24.63 0.00 38.54 3.85
2560 3360 2.428622 CCCGGGTTGGTCTCGTTT 59.571 61.111 14.18 0.00 38.54 3.60
2561 3361 1.228033 CCCGGGTTGGTCTCGTTTT 60.228 57.895 14.18 0.00 38.54 2.43
2562 3362 0.820482 CCCGGGTTGGTCTCGTTTTT 60.820 55.000 14.18 0.00 38.54 1.94
2597 3397 0.543749 CCCCCTTTTGTGTTTGCCAA 59.456 50.000 0.00 0.00 0.00 4.52
2600 3400 2.432510 CCCCTTTTGTGTTTGCCAAGTA 59.567 45.455 0.00 0.00 0.00 2.24
2608 3408 7.461182 TTTGTGTTTGCCAAGTATTAGCTAT 57.539 32.000 0.00 0.00 0.00 2.97
2611 3411 8.153479 TGTGTTTGCCAAGTATTAGCTATATG 57.847 34.615 0.00 0.00 0.00 1.78
2641 3443 3.955771 TTTTAGAAACGCTTGAACGCT 57.044 38.095 0.00 0.00 36.19 5.07
2642 3444 5.406767 TTTTTAGAAACGCTTGAACGCTA 57.593 34.783 0.00 0.00 36.19 4.26
2652 3454 2.924290 GCTTGAACGCTACTACTTGAGG 59.076 50.000 0.00 0.00 0.00 3.86
2657 3459 4.219944 TGAACGCTACTACTTGAGGAACAT 59.780 41.667 0.00 0.00 0.00 2.71
2682 3484 7.660030 ATAAAAGGCTTAGGTACAATGCAAT 57.340 32.000 0.00 0.00 0.00 3.56
2704 3506 7.550196 GCAATTGTCATTGGATGAAAAACCTAT 59.450 33.333 7.40 0.00 39.76 2.57
2708 3510 8.187913 TGTCATTGGATGAAAAACCTATGAAA 57.812 30.769 0.00 0.00 44.70 2.69
2742 3544 2.697654 CCTGCTTTCCTCACTCTTCTG 58.302 52.381 0.00 0.00 0.00 3.02
2746 3548 5.336150 TGCTTTCCTCACTCTTCTGATAG 57.664 43.478 0.00 0.00 0.00 2.08
2752 3554 7.873719 TTCCTCACTCTTCTGATAGTTCTAG 57.126 40.000 0.00 0.00 0.00 2.43
2759 3561 8.690884 CACTCTTCTGATAGTTCTAGGAATTGA 58.309 37.037 0.00 0.00 0.00 2.57
2763 3565 9.829507 CTTCTGATAGTTCTAGGAATTGATGTT 57.170 33.333 0.00 0.00 0.00 2.71
2766 3568 9.775854 CTGATAGTTCTAGGAATTGATGTTGAT 57.224 33.333 0.00 0.00 0.00 2.57
2816 3618 5.821516 ACCATGTTGTTGTCGACTTTTTA 57.178 34.783 17.92 0.00 0.00 1.52
2825 3627 6.556212 TGTTGTCGACTTTTTAATCAAGCAA 58.444 32.000 17.92 0.00 0.00 3.91
2830 3632 4.385748 CGACTTTTTAATCAAGCAAAGGCC 59.614 41.667 0.00 0.00 42.56 5.19
2848 3650 0.397941 CCCAGTATCACATGGCGGAT 59.602 55.000 0.00 0.00 35.10 4.18
2857 3659 0.966179 ACATGGCGGATGCGATAGTA 59.034 50.000 12.10 0.00 44.10 1.82
2859 3661 0.532573 ATGGCGGATGCGATAGTAGG 59.467 55.000 12.10 0.00 44.10 3.18
2862 3664 1.154016 CGGATGCGATAGTAGGGCG 60.154 63.158 0.00 0.00 39.35 6.13
2867 3669 1.729838 GCGATAGTAGGGCGCTTCG 60.730 63.158 9.23 13.35 46.53 3.79
2885 3687 2.306847 TCGCCATCATACAGCTAGTGA 58.693 47.619 0.00 0.00 0.00 3.41
2889 3691 4.697514 GCCATCATACAGCTAGTGAAAGA 58.302 43.478 0.00 0.00 0.00 2.52
2915 3717 5.355910 ACAACCACGACTTGAATACAAACTT 59.644 36.000 0.00 0.00 35.49 2.66
2918 3720 7.739498 ACCACGACTTGAATACAAACTTAAT 57.261 32.000 0.00 0.00 35.49 1.40
2944 3746 1.619332 GTCTCTCACCTCTTCCGGTTT 59.381 52.381 0.00 0.00 34.29 3.27
2961 3763 5.046591 TCCGGTTTGTTAGTCTCATCTCAAT 60.047 40.000 0.00 0.00 0.00 2.57
2964 3766 7.495934 CCGGTTTGTTAGTCTCATCTCAATATT 59.504 37.037 0.00 0.00 0.00 1.28
2994 3796 4.764050 TCCGGTTTATAAGGCTCATTGA 57.236 40.909 0.00 0.00 0.00 2.57
2997 3799 6.126409 TCCGGTTTATAAGGCTCATTGATTT 58.874 36.000 0.00 0.00 0.00 2.17
3000 3802 7.416213 CCGGTTTATAAGGCTCATTGATTTGAA 60.416 37.037 0.00 0.00 0.00 2.69
3023 3825 1.379527 AGGCAAACGTTAGCTATGGC 58.620 50.000 13.79 13.79 36.88 4.40
3025 3827 1.676006 GGCAAACGTTAGCTATGGCAT 59.324 47.619 16.02 4.88 41.70 4.40
3073 3875 1.771854 TGTTTGTCTAGACTTGGGCCA 59.228 47.619 23.01 0.00 0.00 5.36
3080 3882 2.834549 TCTAGACTTGGGCCAGAAAGAG 59.165 50.000 16.47 3.00 0.00 2.85
3100 3902 4.910304 AGAGCCCAGATAAACATGGTCTAT 59.090 41.667 0.00 0.00 34.58 1.98
3105 3907 6.998673 GCCCAGATAAACATGGTCTATAAACT 59.001 38.462 0.00 0.00 34.58 2.66
3106 3908 7.502561 GCCCAGATAAACATGGTCTATAAACTT 59.497 37.037 0.00 0.00 34.58 2.66
3147 3949 3.492337 AGAAATGTTTGGTTCCGCCTAA 58.508 40.909 0.00 0.00 38.35 2.69
3158 3960 0.177141 TCCGCCTAAGTTCCCATTCG 59.823 55.000 0.00 0.00 0.00 3.34
3159 3961 0.177141 CCGCCTAAGTTCCCATTCGA 59.823 55.000 0.00 0.00 0.00 3.71
3170 3973 7.891183 AAGTTCCCATTCGATTTCTATATCG 57.109 36.000 0.00 0.00 46.63 2.92
3206 4010 9.213819 GTTTCCAATAATTTTCGTAATACGTCC 57.786 33.333 12.78 0.00 43.14 4.79
3211 4015 8.730427 CAATAATTTTCGTAATACGTCCTTTGC 58.270 33.333 12.78 0.00 43.14 3.68
3218 4022 4.435121 CGTAATACGTCCTTTGCTTGGTTC 60.435 45.833 4.41 0.00 36.74 3.62
3221 4025 0.041312 CGTCCTTTGCTTGGTTCGTG 60.041 55.000 0.00 0.00 0.00 4.35
3239 4043 1.668151 GCGGCCGAGTCTCAGTTTT 60.668 57.895 33.48 0.00 0.00 2.43
3245 4049 4.254492 GGCCGAGTCTCAGTTTTTAATCT 58.746 43.478 0.00 0.00 0.00 2.40
3267 4071 6.597562 TCTGCTCCAGTTTAGAAGGTTTTAA 58.402 36.000 0.00 0.00 32.61 1.52
3282 4086 7.565768 AGAAGGTTTTAATTTTGTGAAGGGGTA 59.434 33.333 0.00 0.00 0.00 3.69
3287 4091 9.811995 GTTTTAATTTTGTGAAGGGGTATATCC 57.188 33.333 0.00 0.00 0.00 2.59
3312 4116 2.228582 AGCACGCTTAAAACATCATGCA 59.771 40.909 0.00 0.00 34.27 3.96
3321 4125 6.292061 GCTTAAAACATCATGCACGAAACAAA 60.292 34.615 0.00 0.00 0.00 2.83
3322 4126 7.525688 TTAAAACATCATGCACGAAACAAAA 57.474 28.000 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 6.652053 ACCTACTGGTGTACTTGTGTAAAAA 58.348 36.000 0.00 0.00 46.51 1.94
28 29 6.237887 ACCTACTGGTGTACTTGTGTAAAA 57.762 37.500 0.00 0.00 46.51 1.52
29 30 5.874897 ACCTACTGGTGTACTTGTGTAAA 57.125 39.130 0.00 0.00 46.51 2.01
38 39 8.599294 TGGAACAAAATTGACCTACTGGTGTAC 61.599 40.741 0.00 0.00 41.36 2.90
39 40 6.635185 TGGAACAAAATTGACCTACTGGTGTA 60.635 38.462 0.00 0.00 41.36 2.90
40 41 5.867151 TGGAACAAAATTGACCTACTGGTGT 60.867 40.000 0.00 0.00 41.36 4.16
41 42 4.582656 TGGAACAAAATTGACCTACTGGTG 59.417 41.667 0.00 0.00 41.36 4.17
42 43 4.798882 TGGAACAAAATTGACCTACTGGT 58.201 39.130 0.00 0.00 43.55 4.00
105 106 7.956420 AGTGTAGATGAACGTGATACAAAAA 57.044 32.000 0.00 0.00 0.00 1.94
106 107 7.956420 AAGTGTAGATGAACGTGATACAAAA 57.044 32.000 0.00 0.00 0.00 2.44
107 108 7.758076 CCTAAGTGTAGATGAACGTGATACAAA 59.242 37.037 0.00 0.00 0.00 2.83
108 109 7.094075 ACCTAAGTGTAGATGAACGTGATACAA 60.094 37.037 0.00 0.00 0.00 2.41
109 110 6.376299 ACCTAAGTGTAGATGAACGTGATACA 59.624 38.462 0.00 0.00 0.00 2.29
110 111 6.793349 ACCTAAGTGTAGATGAACGTGATAC 58.207 40.000 0.00 0.00 0.00 2.24
111 112 6.039047 GGACCTAAGTGTAGATGAACGTGATA 59.961 42.308 0.00 0.00 0.00 2.15
112 113 5.163540 GGACCTAAGTGTAGATGAACGTGAT 60.164 44.000 0.00 0.00 0.00 3.06
113 114 4.157289 GGACCTAAGTGTAGATGAACGTGA 59.843 45.833 0.00 0.00 0.00 4.35
114 115 4.082408 TGGACCTAAGTGTAGATGAACGTG 60.082 45.833 0.00 0.00 0.00 4.49
115 116 4.084287 TGGACCTAAGTGTAGATGAACGT 58.916 43.478 0.00 0.00 0.00 3.99
116 117 4.713824 TGGACCTAAGTGTAGATGAACG 57.286 45.455 0.00 0.00 0.00 3.95
117 118 5.875359 CCTTTGGACCTAAGTGTAGATGAAC 59.125 44.000 13.63 0.00 0.00 3.18
118 119 5.045869 CCCTTTGGACCTAAGTGTAGATGAA 60.046 44.000 13.63 0.00 0.00 2.57
119 120 4.469945 CCCTTTGGACCTAAGTGTAGATGA 59.530 45.833 13.63 0.00 0.00 2.92
120 121 4.225267 ACCCTTTGGACCTAAGTGTAGATG 59.775 45.833 13.63 0.00 34.81 2.90
121 122 4.436079 ACCCTTTGGACCTAAGTGTAGAT 58.564 43.478 13.63 0.00 34.81 1.98
122 123 3.865571 ACCCTTTGGACCTAAGTGTAGA 58.134 45.455 13.63 0.00 34.81 2.59
123 124 5.952347 ATACCCTTTGGACCTAAGTGTAG 57.048 43.478 14.17 4.67 34.81 2.74
124 125 6.707273 AAATACCCTTTGGACCTAAGTGTA 57.293 37.500 11.95 11.95 34.81 2.90
125 126 5.594199 AAATACCCTTTGGACCTAAGTGT 57.406 39.130 13.63 11.11 34.81 3.55
126 127 5.417894 GGAAAATACCCTTTGGACCTAAGTG 59.582 44.000 13.63 5.86 34.81 3.16
127 128 5.315109 AGGAAAATACCCTTTGGACCTAAGT 59.685 40.000 13.63 1.18 34.81 2.24
128 129 5.827756 AGGAAAATACCCTTTGGACCTAAG 58.172 41.667 8.56 8.56 34.81 2.18
129 130 5.281349 GGAGGAAAATACCCTTTGGACCTAA 60.281 44.000 0.00 0.00 33.36 2.69
130 131 4.228895 GGAGGAAAATACCCTTTGGACCTA 59.771 45.833 0.00 0.00 33.36 3.08
131 132 3.011369 GGAGGAAAATACCCTTTGGACCT 59.989 47.826 0.00 0.00 33.36 3.85
132 133 3.011369 AGGAGGAAAATACCCTTTGGACC 59.989 47.826 0.00 0.00 33.36 4.46
133 134 4.317530 AGGAGGAAAATACCCTTTGGAC 57.682 45.455 0.00 0.00 33.36 4.02
134 135 4.672899 CAAGGAGGAAAATACCCTTTGGA 58.327 43.478 0.00 0.00 36.93 3.53
135 136 3.195610 GCAAGGAGGAAAATACCCTTTGG 59.804 47.826 0.00 0.00 36.93 3.28
136 137 3.195610 GGCAAGGAGGAAAATACCCTTTG 59.804 47.826 0.00 0.00 36.93 2.77
137 138 3.077543 AGGCAAGGAGGAAAATACCCTTT 59.922 43.478 0.00 0.00 36.93 3.11
138 139 2.654896 AGGCAAGGAGGAAAATACCCTT 59.345 45.455 0.00 0.00 39.42 3.95
139 140 2.242452 GAGGCAAGGAGGAAAATACCCT 59.758 50.000 0.00 0.00 36.57 4.34
140 141 2.242452 AGAGGCAAGGAGGAAAATACCC 59.758 50.000 0.00 0.00 0.00 3.69
141 142 3.201045 AGAGAGGCAAGGAGGAAAATACC 59.799 47.826 0.00 0.00 0.00 2.73
142 143 4.163268 AGAGAGAGGCAAGGAGGAAAATAC 59.837 45.833 0.00 0.00 0.00 1.89
143 144 4.366267 AGAGAGAGGCAAGGAGGAAAATA 58.634 43.478 0.00 0.00 0.00 1.40
144 145 3.188773 AGAGAGAGGCAAGGAGGAAAAT 58.811 45.455 0.00 0.00 0.00 1.82
145 146 2.625639 AGAGAGAGGCAAGGAGGAAAA 58.374 47.619 0.00 0.00 0.00 2.29
146 147 2.334006 AGAGAGAGGCAAGGAGGAAA 57.666 50.000 0.00 0.00 0.00 3.13
147 148 2.313342 AGTAGAGAGAGGCAAGGAGGAA 59.687 50.000 0.00 0.00 0.00 3.36
148 149 1.926665 AGTAGAGAGAGGCAAGGAGGA 59.073 52.381 0.00 0.00 0.00 3.71
149 150 2.452600 AGTAGAGAGAGGCAAGGAGG 57.547 55.000 0.00 0.00 0.00 4.30
150 151 2.693074 GGAAGTAGAGAGAGGCAAGGAG 59.307 54.545 0.00 0.00 0.00 3.69
151 152 2.624557 GGGAAGTAGAGAGAGGCAAGGA 60.625 54.545 0.00 0.00 0.00 3.36
152 153 1.760029 GGGAAGTAGAGAGAGGCAAGG 59.240 57.143 0.00 0.00 0.00 3.61
153 154 2.745968 AGGGAAGTAGAGAGAGGCAAG 58.254 52.381 0.00 0.00 0.00 4.01
154 155 2.930109 AGGGAAGTAGAGAGAGGCAA 57.070 50.000 0.00 0.00 0.00 4.52
458 459 0.325765 AGAGGGGAGGTTGTCTAGGC 60.326 60.000 0.00 0.00 0.00 3.93
480 497 2.806745 CGGCACATCATCGATTTAGGGT 60.807 50.000 0.00 0.00 0.00 4.34
497 514 0.969917 CCAATGGGGTTTCATCGGCA 60.970 55.000 0.00 0.00 0.00 5.69
498 515 1.815866 CCAATGGGGTTTCATCGGC 59.184 57.895 0.00 0.00 0.00 5.54
542 567 7.433680 GTGGCCTTCTTTCTTTCTTCAAATAA 58.566 34.615 3.32 0.00 0.00 1.40
552 1302 3.140325 TGATCGTGGCCTTCTTTCTTT 57.860 42.857 3.32 0.00 0.00 2.52
567 1317 3.371898 TGTAGAGCAAAGCAACATGATCG 59.628 43.478 0.00 0.00 37.07 3.69
573 1323 5.574891 TTCTTTTGTAGAGCAAAGCAACA 57.425 34.783 0.00 0.00 46.40 3.33
632 1389 5.355630 TCTTTTGATTTCAGGTTGACGTTGA 59.644 36.000 0.00 0.00 0.00 3.18
633 1390 5.577835 TCTTTTGATTTCAGGTTGACGTTG 58.422 37.500 0.00 0.00 0.00 4.10
634 1391 5.828299 TCTTTTGATTTCAGGTTGACGTT 57.172 34.783 0.00 0.00 0.00 3.99
635 1392 5.828299 TTCTTTTGATTTCAGGTTGACGT 57.172 34.783 0.00 0.00 0.00 4.34
636 1393 7.487829 TCTTTTTCTTTTGATTTCAGGTTGACG 59.512 33.333 0.00 0.00 0.00 4.35
637 1394 8.702163 TCTTTTTCTTTTGATTTCAGGTTGAC 57.298 30.769 0.00 0.00 0.00 3.18
638 1395 9.369904 CTTCTTTTTCTTTTGATTTCAGGTTGA 57.630 29.630 0.00 0.00 0.00 3.18
639 1396 9.369904 TCTTCTTTTTCTTTTGATTTCAGGTTG 57.630 29.630 0.00 0.00 0.00 3.77
640 1397 9.942850 TTCTTCTTTTTCTTTTGATTTCAGGTT 57.057 25.926 0.00 0.00 0.00 3.50
641 1398 9.942850 TTTCTTCTTTTTCTTTTGATTTCAGGT 57.057 25.926 0.00 0.00 0.00 4.00
660 1417 5.368989 ACCGATGTTCACTTCTTTTCTTCT 58.631 37.500 0.00 0.00 0.00 2.85
661 1418 5.674933 ACCGATGTTCACTTCTTTTCTTC 57.325 39.130 0.00 0.00 0.00 2.87
662 1419 6.204882 CCTTACCGATGTTCACTTCTTTTCTT 59.795 38.462 0.00 0.00 0.00 2.52
664 1421 5.617087 GCCTTACCGATGTTCACTTCTTTTC 60.617 44.000 0.00 0.00 0.00 2.29
754 1511 4.229096 GTTGAATGGAACGTACGTGAGTA 58.771 43.478 23.57 9.42 46.88 2.59
755 1512 4.394965 CGTTGAATGGAACGTACGTGAGT 61.395 47.826 23.57 6.17 42.99 3.41
756 1513 2.090041 CGTTGAATGGAACGTACGTGAG 59.910 50.000 23.57 0.58 42.99 3.51
779 1536 2.791655 AGGTTTGAATCGGGAAGGTTC 58.208 47.619 0.00 0.00 40.35 3.62
925 1714 1.001406 GGATGGGTGATGGAGACGATC 59.999 57.143 0.00 0.00 0.00 3.69
1104 1904 2.125106 GGGTCACGCATCAGGTCC 60.125 66.667 0.00 0.00 0.00 4.46
1153 1953 3.222855 CGCCTCGATGCTCTCCCT 61.223 66.667 11.00 0.00 0.00 4.20
1730 2530 2.690778 AAATTCGTGCAGGCTCCGC 61.691 57.895 0.35 0.00 0.00 5.54
1737 2537 0.953471 TCCCGTCCAAATTCGTGCAG 60.953 55.000 0.00 0.00 0.00 4.41
1744 2544 4.434483 GGCCTTCCCGTCCAAATT 57.566 55.556 0.00 0.00 0.00 1.82
1887 2687 2.263852 GGGACGAGACCGGTTTCC 59.736 66.667 18.75 16.19 40.78 3.13
1902 2702 4.477975 GACTCGACGAGCACCGGG 62.478 72.222 24.38 0.33 43.93 5.73
2217 3017 0.037232 CGGTGGTCTTCTCCTTGGTC 60.037 60.000 0.00 0.00 0.00 4.02
2408 3208 1.302511 GCTGCCCTCCGTTCTCAAA 60.303 57.895 0.00 0.00 0.00 2.69
2409 3209 2.172483 GAGCTGCCCTCCGTTCTCAA 62.172 60.000 0.00 0.00 34.35 3.02
2410 3210 2.604686 AGCTGCCCTCCGTTCTCA 60.605 61.111 0.00 0.00 0.00 3.27
2411 3211 2.185608 GAGCTGCCCTCCGTTCTC 59.814 66.667 0.00 0.00 34.35 2.87
2412 3212 2.604686 TGAGCTGCCCTCCGTTCT 60.605 61.111 0.00 0.00 39.98 3.01
2413 3213 2.125350 CTGAGCTGCCCTCCGTTC 60.125 66.667 0.00 0.00 39.98 3.95
2414 3214 2.520536 AACTGAGCTGCCCTCCGTT 61.521 57.895 0.00 5.76 41.40 4.44
2415 3215 2.925170 AACTGAGCTGCCCTCCGT 60.925 61.111 0.00 0.00 39.36 4.69
2416 3216 2.435586 CAACTGAGCTGCCCTCCG 60.436 66.667 0.00 0.00 39.98 4.63
2417 3217 2.045536 CCAACTGAGCTGCCCTCC 60.046 66.667 0.00 0.00 39.98 4.30
2418 3218 2.749441 GCCAACTGAGCTGCCCTC 60.749 66.667 0.00 0.00 41.15 4.30
2419 3219 3.137385 TTGCCAACTGAGCTGCCCT 62.137 57.895 0.00 0.00 0.00 5.19
2420 3220 2.598394 TTGCCAACTGAGCTGCCC 60.598 61.111 0.00 0.00 0.00 5.36
2421 3221 2.960170 CTTGCCAACTGAGCTGCC 59.040 61.111 0.00 0.00 0.00 4.85
2422 3222 2.257676 GCTTGCCAACTGAGCTGC 59.742 61.111 0.00 0.00 33.72 5.25
2423 3223 4.076244 AGCTTGCCAACTGAGCTG 57.924 55.556 0.00 0.00 44.53 4.24
2425 3225 2.257676 GCAGCTTGCCAACTGAGC 59.742 61.111 10.06 0.00 37.42 4.26
2426 3226 2.559840 CGCAGCTTGCCAACTGAG 59.440 61.111 10.06 4.48 41.12 3.35
2427 3227 2.979676 CCGCAGCTTGCCAACTGA 60.980 61.111 10.06 0.00 41.12 3.41
2428 3228 4.047059 CCCGCAGCTTGCCAACTG 62.047 66.667 3.09 3.57 41.12 3.16
2429 3229 4.269523 TCCCGCAGCTTGCCAACT 62.270 61.111 3.09 0.00 41.12 3.16
2430 3230 3.741476 CTCCCGCAGCTTGCCAAC 61.741 66.667 3.09 0.00 41.12 3.77
2431 3231 3.790416 AACTCCCGCAGCTTGCCAA 62.790 57.895 3.09 0.00 41.12 4.52
2432 3232 4.269523 AACTCCCGCAGCTTGCCA 62.270 61.111 3.09 0.00 41.12 4.92
2433 3233 3.435186 GAACTCCCGCAGCTTGCC 61.435 66.667 3.09 0.00 41.12 4.52
2434 3234 3.793144 CGAACTCCCGCAGCTTGC 61.793 66.667 0.00 0.00 40.69 4.01
2442 3242 2.583593 GCTAGCTGCGAACTCCCG 60.584 66.667 7.70 0.00 0.00 5.14
2443 3243 2.202946 GGCTAGCTGCGAACTCCC 60.203 66.667 15.72 0.00 44.05 4.30
2444 3244 2.202946 GGGCTAGCTGCGAACTCC 60.203 66.667 15.72 0.13 44.05 3.85
2445 3245 0.878086 GATGGGCTAGCTGCGAACTC 60.878 60.000 15.72 0.00 44.05 3.01
2446 3246 1.144936 GATGGGCTAGCTGCGAACT 59.855 57.895 15.72 0.00 44.05 3.01
2447 3247 1.153369 TGATGGGCTAGCTGCGAAC 60.153 57.895 15.72 0.00 44.05 3.95
2448 3248 1.144716 CTGATGGGCTAGCTGCGAA 59.855 57.895 15.72 0.00 44.05 4.70
2449 3249 2.800541 CCTGATGGGCTAGCTGCGA 61.801 63.158 15.72 0.00 44.05 5.10
2450 3250 2.280660 CCTGATGGGCTAGCTGCG 60.281 66.667 15.72 0.00 44.05 5.18
2456 3256 7.460623 TCAAAACTTGAACCCTGATGGGCTA 62.461 44.000 0.28 0.00 45.60 3.93
2457 3257 6.776707 TCAAAACTTGAACCCTGATGGGCT 62.777 45.833 0.28 0.00 45.60 5.19
2458 3258 4.567451 TCAAAACTTGAACCCTGATGGGC 61.567 47.826 0.28 0.00 45.60 5.36
2459 3259 3.005791 GTCAAAACTTGAACCCTGATGGG 59.994 47.826 0.00 0.00 46.43 4.00
2460 3260 3.891366 AGTCAAAACTTGAACCCTGATGG 59.109 43.478 0.00 0.00 42.15 3.51
2461 3261 4.319766 CGAGTCAAAACTTGAACCCTGATG 60.320 45.833 0.00 0.00 42.15 3.07
2462 3262 3.815401 CGAGTCAAAACTTGAACCCTGAT 59.185 43.478 0.00 0.00 42.15 2.90
2463 3263 3.118555 TCGAGTCAAAACTTGAACCCTGA 60.119 43.478 0.00 0.00 41.96 3.86
2464 3264 3.202906 TCGAGTCAAAACTTGAACCCTG 58.797 45.455 0.00 0.00 41.96 4.45
2465 3265 3.118371 ACTCGAGTCAAAACTTGAACCCT 60.118 43.478 13.58 0.00 43.81 4.34
2466 3266 3.002348 CACTCGAGTCAAAACTTGAACCC 59.998 47.826 16.96 0.00 43.81 4.11
2467 3267 3.546218 GCACTCGAGTCAAAACTTGAACC 60.546 47.826 16.96 0.00 43.81 3.62
2468 3268 3.309954 AGCACTCGAGTCAAAACTTGAAC 59.690 43.478 16.96 0.00 43.81 3.18
2469 3269 3.531538 AGCACTCGAGTCAAAACTTGAA 58.468 40.909 16.96 0.00 43.81 2.69
2470 3270 3.179443 AGCACTCGAGTCAAAACTTGA 57.821 42.857 16.96 0.00 42.55 3.02
2471 3271 3.309682 TCAAGCACTCGAGTCAAAACTTG 59.690 43.478 16.96 21.05 38.14 3.16
2472 3272 3.531538 TCAAGCACTCGAGTCAAAACTT 58.468 40.909 16.96 11.25 35.28 2.66
2473 3273 3.179443 TCAAGCACTCGAGTCAAAACT 57.821 42.857 16.96 5.45 38.88 2.66
2474 3274 3.803555 CATCAAGCACTCGAGTCAAAAC 58.196 45.455 16.96 3.03 0.00 2.43
2475 3275 2.224079 GCATCAAGCACTCGAGTCAAAA 59.776 45.455 16.96 0.61 44.79 2.44
2476 3276 1.800586 GCATCAAGCACTCGAGTCAAA 59.199 47.619 16.96 0.00 44.79 2.69
2477 3277 1.432514 GCATCAAGCACTCGAGTCAA 58.567 50.000 16.96 0.00 44.79 3.18
2478 3278 3.128259 GCATCAAGCACTCGAGTCA 57.872 52.632 16.96 0.00 44.79 3.41
2479 3279 1.403382 TGAGCATCAAGCACTCGAGTC 60.403 52.381 16.96 10.84 45.97 3.36
2480 3280 0.605083 TGAGCATCAAGCACTCGAGT 59.395 50.000 13.58 13.58 45.97 4.18
2481 3281 3.430779 TGAGCATCAAGCACTCGAG 57.569 52.632 11.84 11.84 45.97 4.04
2492 3292 3.330267 AGAAGAAAACTCCGTGAGCATC 58.670 45.455 1.36 0.00 32.04 3.91
2493 3293 3.409026 AGAAGAAAACTCCGTGAGCAT 57.591 42.857 1.36 0.00 32.04 3.79
2494 3294 2.910688 AGAAGAAAACTCCGTGAGCA 57.089 45.000 1.36 0.00 32.04 4.26
2495 3295 4.495422 TGATAGAAGAAAACTCCGTGAGC 58.505 43.478 1.36 0.00 32.04 4.26
2496 3296 7.421530 TTTTGATAGAAGAAAACTCCGTGAG 57.578 36.000 0.03 0.03 35.52 3.51
2497 3297 7.795482 TTTTTGATAGAAGAAAACTCCGTGA 57.205 32.000 0.00 0.00 0.00 4.35
2534 3334 0.686769 ACCAACCCGGGCTAGACTAG 60.687 60.000 24.08 5.03 40.22 2.57
2535 3335 0.685458 GACCAACCCGGGCTAGACTA 60.685 60.000 24.08 0.00 41.26 2.59
2536 3336 1.988406 GACCAACCCGGGCTAGACT 60.988 63.158 24.08 0.00 41.26 3.24
2537 3337 2.582978 GACCAACCCGGGCTAGAC 59.417 66.667 24.08 5.60 41.26 2.59
2543 3343 0.820482 AAAAACGAGACCAACCCGGG 60.820 55.000 22.25 22.25 40.22 5.73
2544 3344 2.710440 AAAAACGAGACCAACCCGG 58.290 52.632 0.00 0.00 42.50 5.73
2578 3378 0.543749 TTGGCAAACACAAAAGGGGG 59.456 50.000 0.00 0.00 0.00 5.40
2579 3379 1.209261 ACTTGGCAAACACAAAAGGGG 59.791 47.619 0.00 0.00 0.00 4.79
2580 3380 2.689553 ACTTGGCAAACACAAAAGGG 57.310 45.000 0.00 0.00 0.00 3.95
2581 3381 5.405269 GCTAATACTTGGCAAACACAAAAGG 59.595 40.000 0.00 0.00 37.09 3.11
2582 3382 6.215845 AGCTAATACTTGGCAAACACAAAAG 58.784 36.000 0.00 0.00 39.92 2.27
2588 3388 6.770303 TGCATATAGCTAATACTTGGCAAACA 59.230 34.615 0.00 0.00 45.94 2.83
2626 3428 2.985139 AGTAGTAGCGTTCAAGCGTTTC 59.015 45.455 0.00 0.00 43.00 2.78
2628 3430 2.719426 AGTAGTAGCGTTCAAGCGTT 57.281 45.000 0.00 0.00 43.00 4.84
2640 3442 9.262358 GCCTTTTATATGTTCCTCAAGTAGTAG 57.738 37.037 0.00 0.00 0.00 2.57
2641 3443 8.989131 AGCCTTTTATATGTTCCTCAAGTAGTA 58.011 33.333 0.00 0.00 0.00 1.82
2642 3444 7.862675 AGCCTTTTATATGTTCCTCAAGTAGT 58.137 34.615 0.00 0.00 0.00 2.73
2657 3459 8.760980 ATTGCATTGTACCTAAGCCTTTTATA 57.239 30.769 0.00 0.00 0.00 0.98
2682 3484 7.773489 TCATAGGTTTTTCATCCAATGACAA 57.227 32.000 0.00 0.00 39.39 3.18
2708 3510 8.320617 TGAGGAAAGCAGGCAATTTATTTATTT 58.679 29.630 0.00 0.00 0.00 1.40
2712 3514 5.246883 AGTGAGGAAAGCAGGCAATTTATTT 59.753 36.000 0.00 0.00 0.00 1.40
2773 3575 3.814577 GCTCAGGCGTACTCTTGAA 57.185 52.632 0.00 0.00 0.00 2.69
2788 3590 1.126113 CGACAACAACATGGTACGCTC 59.874 52.381 0.00 0.00 0.00 5.03
2789 3591 1.144969 CGACAACAACATGGTACGCT 58.855 50.000 0.00 0.00 0.00 5.07
2792 3594 4.806342 AAAGTCGACAACAACATGGTAC 57.194 40.909 19.50 0.00 0.00 3.34
2816 3618 2.603075 TACTGGGCCTTTGCTTGATT 57.397 45.000 4.53 0.00 37.74 2.57
2825 3627 0.106519 GCCATGTGATACTGGGCCTT 60.107 55.000 4.53 0.00 38.70 4.35
2830 3632 1.516161 CATCCGCCATGTGATACTGG 58.484 55.000 0.00 0.00 35.53 4.00
2867 3669 4.509600 GTCTTTCACTAGCTGTATGATGGC 59.490 45.833 0.00 0.00 0.00 4.40
2869 3671 6.101997 TGTGTCTTTCACTAGCTGTATGATG 58.898 40.000 0.00 0.00 46.27 3.07
2870 3672 6.286240 TGTGTCTTTCACTAGCTGTATGAT 57.714 37.500 0.00 0.00 46.27 2.45
2871 3673 5.722021 TGTGTCTTTCACTAGCTGTATGA 57.278 39.130 0.00 0.00 46.27 2.15
2885 3687 2.980568 TCAAGTCGTGGTTGTGTCTTT 58.019 42.857 0.00 0.00 0.00 2.52
2889 3691 3.799366 TGTATTCAAGTCGTGGTTGTGT 58.201 40.909 0.00 0.00 0.00 3.72
2936 3738 4.282449 TGAGATGAGACTAACAAACCGGAA 59.718 41.667 9.46 0.00 0.00 4.30
2939 3741 8.425577 AATATTGAGATGAGACTAACAAACCG 57.574 34.615 0.00 0.00 0.00 4.44
2944 3746 9.739276 ACCAAAAATATTGAGATGAGACTAACA 57.261 29.630 0.00 0.00 0.00 2.41
2961 3763 7.818446 GCCTTATAAACCGGAAAACCAAAAATA 59.182 33.333 9.46 0.00 0.00 1.40
2964 3766 5.304871 AGCCTTATAAACCGGAAAACCAAAA 59.695 36.000 9.46 0.00 0.00 2.44
2994 3796 6.687604 AGCTAACGTTTGCCTATTTTCAAAT 58.312 32.000 27.08 5.17 35.06 2.32
2997 3799 6.183360 CCATAGCTAACGTTTGCCTATTTTCA 60.183 38.462 27.08 6.70 0.00 2.69
3000 3802 4.036380 GCCATAGCTAACGTTTGCCTATTT 59.964 41.667 27.08 13.52 35.50 1.40
3073 3875 4.018050 ACCATGTTTATCTGGGCTCTTTCT 60.018 41.667 0.00 0.00 36.82 2.52
3080 3882 6.998673 AGTTTATAGACCATGTTTATCTGGGC 59.001 38.462 0.00 0.00 41.21 5.36
3100 3902 6.014755 TCCCATGCAATTCAATGACAAGTTTA 60.015 34.615 0.00 0.00 0.00 2.01
3105 3907 4.527427 TCTTCCCATGCAATTCAATGACAA 59.473 37.500 0.00 0.00 0.00 3.18
3106 3908 4.087907 TCTTCCCATGCAATTCAATGACA 58.912 39.130 0.00 0.00 0.00 3.58
3158 3960 5.471257 ACTTCGCTTCCCGATATAGAAATC 58.529 41.667 0.00 0.00 46.81 2.17
3159 3961 5.470047 ACTTCGCTTCCCGATATAGAAAT 57.530 39.130 0.00 0.00 46.81 2.17
3170 3973 4.983671 ATTATTGGAAACTTCGCTTCCC 57.016 40.909 0.00 0.00 41.54 3.97
3189 3992 6.490566 AGCAAAGGACGTATTACGAAAATT 57.509 33.333 22.18 9.13 46.05 1.82
3206 4010 1.370414 CCGCACGAACCAAGCAAAG 60.370 57.895 0.00 0.00 0.00 2.77
3221 4025 1.228657 AAAAACTGAGACTCGGCCGC 61.229 55.000 23.51 6.72 0.00 6.53
3234 4038 8.691661 TTCTAAACTGGAGCAGATTAAAAACT 57.308 30.769 0.00 0.00 35.18 2.66
3239 4043 6.374417 ACCTTCTAAACTGGAGCAGATTAA 57.626 37.500 0.00 0.00 35.18 1.40
3245 4049 7.833285 AATTAAAACCTTCTAAACTGGAGCA 57.167 32.000 0.00 0.00 0.00 4.26
3267 4071 5.640158 TCGGATATACCCCTTCACAAAAT 57.360 39.130 0.00 0.00 34.64 1.82
3277 4081 1.792006 CGTGCTTTCGGATATACCCC 58.208 55.000 0.00 0.00 34.64 4.95
3282 4086 4.393680 TGTTTTAAGCGTGCTTTCGGATAT 59.606 37.500 12.93 0.00 37.47 1.63
3287 4091 3.550561 TGATGTTTTAAGCGTGCTTTCG 58.449 40.909 12.93 0.00 37.47 3.46


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

AutoCloner maintained by Alex Coulton.