Multiple sequence alignment - TraesCS5B01G356400

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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 TraesCS5B01G356400 chr5B 100.000 5052 0 0 1 5052 536056607 536051556 0.000000e+00 9330.0
1 TraesCS5B01G356400 chr5B 78.279 244 39 12 84 321 658651485 658651250 1.470000e-30 145.0
2 TraesCS5B01G356400 chr5B 83.654 104 14 2 219 321 139125724 139125825 1.500000e-15 95.3
3 TraesCS5B01G356400 chr5A 89.281 1614 98 45 2526 4087 556687383 556685793 0.000000e+00 1953.0
4 TraesCS5B01G356400 chr5A 88.970 1641 98 31 835 2419 556689212 556687599 0.000000e+00 1951.0
5 TraesCS5B01G356400 chr5A 88.664 741 42 20 4353 5052 556685019 556684280 0.000000e+00 865.0
6 TraesCS5B01G356400 chr5A 88.235 476 20 8 4608 5052 134457199 134456729 2.070000e-148 536.0
7 TraesCS5B01G356400 chr5D 89.685 1173 51 16 1248 2367 440651402 440650247 0.000000e+00 1432.0
8 TraesCS5B01G356400 chr5D 92.299 844 34 8 2606 3421 440649840 440649000 0.000000e+00 1170.0
9 TraesCS5B01G356400 chr5D 92.493 706 32 10 3436 4128 440648950 440648253 0.000000e+00 990.0
10 TraesCS5B01G356400 chr5D 90.139 720 32 9 4369 5052 440647979 440647263 0.000000e+00 900.0
11 TraesCS5B01G356400 chr5D 87.122 629 55 19 1 619 440653301 440652689 0.000000e+00 689.0
12 TraesCS5B01G356400 chr5D 93.656 331 12 4 818 1144 440651726 440651401 2.110000e-133 486.0
13 TraesCS5B01G356400 chr5D 86.740 362 23 6 1243 1591 481216601 481216950 3.690000e-101 379.0
14 TraesCS5B01G356400 chr5D 90.780 282 16 6 4161 4436 440648257 440647980 7.990000e-98 368.0
15 TraesCS5B01G356400 chr5D 88.889 63 6 1 702 763 440652021 440651959 5.420000e-10 76.8
16 TraesCS5B01G356400 chr3B 85.124 363 24 4 1241 1591 651955453 651955109 1.350000e-90 344.0
17 TraesCS5B01G356400 chr3B 78.000 250 42 10 84 327 402773519 402773761 1.470000e-30 145.0
18 TraesCS5B01G356400 chr3B 80.851 188 29 7 22 205 743786007 743785823 1.900000e-29 141.0
19 TraesCS5B01G356400 chr3B 88.542 96 8 2 233 327 402801125 402801218 4.130000e-21 113.0
20 TraesCS5B01G356400 chr7D 84.298 363 25 8 1241 1591 83969498 83969840 4.880000e-85 326.0
21 TraesCS5B01G356400 chr7D 80.623 289 48 7 42 328 537877460 537877178 3.060000e-52 217.0
22 TraesCS5B01G356400 chr7A 83.196 363 24 16 1242 1591 155497460 155497122 1.060000e-76 298.0
23 TraesCS5B01G356400 chr7A 93.333 45 3 0 4120 4164 81863981 81863937 3.260000e-07 67.6
24 TraesCS5B01G356400 chr3A 82.418 364 38 9 1241 1591 370986515 370986165 1.380000e-75 294.0
25 TraesCS5B01G356400 chr2D 82.418 364 29 10 1241 1591 41230565 41230906 8.280000e-73 285.0
26 TraesCS5B01G356400 chr2D 77.578 223 42 7 90 309 508611550 508611333 1.480000e-25 128.0
27 TraesCS5B01G356400 chr2D 90.909 44 3 1 4134 4177 38066365 38066323 1.960000e-04 58.4
28 TraesCS5B01G356400 chr1A 82.857 350 29 11 1257 1591 139504841 139505174 8.280000e-73 285.0
29 TraesCS5B01G356400 chr1A 85.714 98 11 2 228 324 144330977 144330882 3.220000e-17 100.0
30 TraesCS5B01G356400 chr2A 82.253 293 30 4 1322 1602 232451948 232452230 3.040000e-57 233.0
31 TraesCS5B01G356400 chr1D 83.465 254 34 7 83 331 314831766 314832016 3.930000e-56 230.0
32 TraesCS5B01G356400 chr3D 80.405 296 44 11 25 318 397216773 397217056 3.960000e-51 213.0
33 TraesCS5B01G356400 chr4B 78.275 313 58 10 15 321 419711670 419711978 5.160000e-45 193.0
34 TraesCS5B01G356400 chr1B 88.060 134 7 3 1327 1451 46568648 46568781 3.150000e-32 150.0


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 TraesCS5B01G356400 chr5B 536051556 536056607 5051 True 9330.000000 9330 100.000000 1 5052 1 chr5B.!!$R1 5051
1 TraesCS5B01G356400 chr5A 556684280 556689212 4932 True 1589.666667 1953 88.971667 835 5052 3 chr5A.!!$R2 4217
2 TraesCS5B01G356400 chr5D 440647263 440653301 6038 True 763.975000 1432 90.632875 1 5052 8 chr5D.!!$R1 5051

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
763 1360 0.181824 ACCCAACACGGCAACTTAGT 59.818 50.000 0.0 0.0 0.00 2.24 F
1669 2514 0.173935 TTATCTACCGTGCGTGTGGG 59.826 55.000 0.0 0.0 0.00 4.61 F
1670 2515 0.966875 TATCTACCGTGCGTGTGGGT 60.967 55.000 0.0 0.0 37.84 4.51 F
3346 4466 1.002033 CCCTCGACCCGTTAATACTCG 60.002 57.143 0.0 0.0 0.00 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 2825 0.107945 GAACTCTGAAGATGGCGCCT 60.108 55.0 29.7 13.55 0.00 5.52 R
3650 4834 0.250252 TTGCTGTGCCGATGTCTTGA 60.250 50.0 0.0 0.00 0.00 3.02 R
3652 4836 1.089920 GATTGCTGTGCCGATGTCTT 58.910 50.0 0.0 0.00 0.00 3.01 R
4384 6207 0.100325 CGTGCTTGGCAGTTTTGTCA 59.900 50.0 0.0 0.00 40.08 3.58 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
57 58 6.638610 AGAAATTGATCACTCTCCAGTACAG 58.361 40.000 0.00 0.00 0.00 2.74
72 73 7.604164 TCTCCAGTACAGAATGAAAATTCAGAC 59.396 37.037 1.98 0.00 41.08 3.51
73 74 7.223584 TCCAGTACAGAATGAAAATTCAGACA 58.776 34.615 1.98 0.00 41.08 3.41
74 75 7.388776 TCCAGTACAGAATGAAAATTCAGACAG 59.611 37.037 1.98 0.00 41.08 3.51
75 76 7.173907 CCAGTACAGAATGAAAATTCAGACAGT 59.826 37.037 1.98 4.47 41.08 3.55
77 78 6.323203 ACAGAATGAAAATTCAGACAGTGG 57.677 37.500 1.98 0.00 41.08 4.00
78 79 6.064060 ACAGAATGAAAATTCAGACAGTGGA 58.936 36.000 1.98 0.00 41.08 4.02
79 80 6.718454 ACAGAATGAAAATTCAGACAGTGGAT 59.282 34.615 1.98 0.00 41.08 3.41
80 81 7.027760 CAGAATGAAAATTCAGACAGTGGATG 58.972 38.462 1.98 0.00 41.08 3.51
81 82 6.944290 AGAATGAAAATTCAGACAGTGGATGA 59.056 34.615 1.98 0.00 41.08 2.92
82 83 7.449395 AGAATGAAAATTCAGACAGTGGATGAA 59.551 33.333 12.86 12.86 41.08 2.57
83 84 6.957920 TGAAAATTCAGACAGTGGATGAAA 57.042 33.333 14.06 0.00 36.59 2.69
138 139 2.739913 CAAGCATTTGCAACATCCCAAG 59.260 45.455 0.00 0.00 45.16 3.61
145 146 3.517296 TGCAACATCCCAAGGTCTTAA 57.483 42.857 0.00 0.00 0.00 1.85
146 147 3.420893 TGCAACATCCCAAGGTCTTAAG 58.579 45.455 0.00 0.00 0.00 1.85
150 151 4.034285 ACATCCCAAGGTCTTAAGTTGG 57.966 45.455 13.82 13.82 40.49 3.77
154 155 1.535462 CCAAGGTCTTAAGTTGGCACG 59.465 52.381 9.65 0.00 34.65 5.34
157 158 3.202829 AGGTCTTAAGTTGGCACGAAA 57.797 42.857 1.63 0.00 0.00 3.46
158 159 3.547746 AGGTCTTAAGTTGGCACGAAAA 58.452 40.909 1.63 0.00 0.00 2.29
159 160 3.314357 AGGTCTTAAGTTGGCACGAAAAC 59.686 43.478 1.63 0.00 0.00 2.43
160 161 3.065648 GGTCTTAAGTTGGCACGAAAACA 59.934 43.478 1.63 0.00 0.00 2.83
161 162 4.439016 GGTCTTAAGTTGGCACGAAAACAA 60.439 41.667 1.63 0.00 0.00 2.83
162 163 5.096849 GTCTTAAGTTGGCACGAAAACAAA 58.903 37.500 1.63 0.00 0.00 2.83
163 164 5.573669 GTCTTAAGTTGGCACGAAAACAAAA 59.426 36.000 1.63 0.00 0.00 2.44
164 165 6.254804 GTCTTAAGTTGGCACGAAAACAAAAT 59.745 34.615 1.63 0.00 0.00 1.82
213 214 6.754702 ATAGCAATAATTATGCAGGCTCAG 57.245 37.500 16.83 0.00 46.22 3.35
224 226 1.494824 CAGGCTCAGCAAACAAAAGC 58.505 50.000 0.00 0.00 0.00 3.51
226 228 1.202452 AGGCTCAGCAAACAAAAGCAC 60.202 47.619 0.00 0.00 34.65 4.40
230 232 3.310501 GCTCAGCAAACAAAAGCACAAAT 59.689 39.130 0.00 0.00 33.21 2.32
257 259 6.731292 AAGATAAATATTGGGTTGCCTTCC 57.269 37.500 0.00 0.00 0.00 3.46
281 283 5.072040 ACAAGTGCTATTGTTTAATGCCC 57.928 39.130 1.81 0.00 40.47 5.36
282 284 4.081697 ACAAGTGCTATTGTTTAATGCCCC 60.082 41.667 1.81 0.00 40.47 5.80
289 291 3.730215 TTGTTTAATGCCCCTCTAGCA 57.270 42.857 0.00 0.00 45.94 3.49
384 386 0.469917 ATCCACATGGCTCCTTACGG 59.530 55.000 0.00 0.00 34.44 4.02
434 436 6.664428 AGGATCTATAGACAAAGAGCTTCC 57.336 41.667 4.10 4.93 0.00 3.46
449 451 8.517878 CAAAGAGCTTCCAGAATTCTCAAAATA 58.482 33.333 4.57 0.00 0.00 1.40
526 528 8.723942 AGAACTCATACGCTTCAAATTAGAAT 57.276 30.769 0.00 0.00 0.00 2.40
530 532 9.046296 ACTCATACGCTTCAAATTAGAATTAGG 57.954 33.333 0.00 0.00 0.00 2.69
532 534 9.261180 TCATACGCTTCAAATTAGAATTAGGAG 57.739 33.333 0.00 0.00 0.00 3.69
556 567 9.965824 GAGTTTCTCCATTTTTACTCAAATCAA 57.034 29.630 0.00 0.00 33.86 2.57
599 610 9.736023 AACACTCAGTTTATCAAGAATTTGAAC 57.264 29.630 0.00 0.00 41.19 3.18
633 658 2.064581 CGGGAGGAGGTACCCCAAG 61.065 68.421 18.39 4.34 42.86 3.61
639 1155 1.057471 GGAGGTACCCCAAGGATAGC 58.943 60.000 8.74 0.00 36.73 2.97
641 1157 1.694696 GAGGTACCCCAAGGATAGCAG 59.305 57.143 8.74 0.00 36.73 4.24
642 1158 1.009675 AGGTACCCCAAGGATAGCAGT 59.990 52.381 8.74 0.00 36.73 4.40
646 1162 3.933861 ACCCCAAGGATAGCAGTAAAG 57.066 47.619 0.00 0.00 36.73 1.85
647 1163 2.092375 ACCCCAAGGATAGCAGTAAAGC 60.092 50.000 0.00 0.00 36.73 3.51
652 1168 5.189180 CCAAGGATAGCAGTAAAGCTTTCT 58.811 41.667 16.57 9.14 43.70 2.52
655 1171 5.912892 AGGATAGCAGTAAAGCTTTCTCTC 58.087 41.667 16.57 8.48 43.70 3.20
661 1177 7.608308 AGCAGTAAAGCTTTCTCTCAATTAG 57.392 36.000 16.57 4.27 43.70 1.73
662 1178 7.390027 AGCAGTAAAGCTTTCTCTCAATTAGA 58.610 34.615 16.57 0.00 43.70 2.10
664 1180 7.960195 GCAGTAAAGCTTTCTCTCAATTAGAAC 59.040 37.037 16.57 3.36 32.81 3.01
665 1181 8.447053 CAGTAAAGCTTTCTCTCAATTAGAACC 58.553 37.037 16.57 0.00 32.81 3.62
671 1190 6.207614 GCTTTCTCTCAATTAGAACCAAGGTT 59.792 38.462 3.73 3.73 41.54 3.50
675 1194 9.449719 TTCTCTCAATTAGAACCAAGGTTTATC 57.550 33.333 5.87 0.00 38.60 1.75
679 1198 8.036273 TCAATTAGAACCAAGGTTTATCGAAC 57.964 34.615 5.87 0.00 38.60 3.95
692 1211 5.209977 GTTTATCGAACCGACAAAAGCTTT 58.790 37.500 5.69 5.69 34.14 3.51
695 1214 4.461992 TCGAACCGACAAAAGCTTTTAG 57.538 40.909 23.44 18.70 0.00 1.85
705 1301 6.202188 CGACAAAAGCTTTTAGACTACCAAGA 59.798 38.462 23.44 0.00 0.00 3.02
715 1311 8.547967 TTTTAGACTACCAAGATAAGCAACAG 57.452 34.615 0.00 0.00 0.00 3.16
716 1312 4.508662 AGACTACCAAGATAAGCAACAGC 58.491 43.478 0.00 0.00 0.00 4.40
731 1327 2.282701 ACAGCTGCACACAAACAAAG 57.717 45.000 15.27 0.00 0.00 2.77
732 1328 1.545582 ACAGCTGCACACAAACAAAGT 59.454 42.857 15.27 0.00 0.00 2.66
763 1360 0.181824 ACCCAACACGGCAACTTAGT 59.818 50.000 0.00 0.00 0.00 2.24
764 1361 1.417145 ACCCAACACGGCAACTTAGTA 59.583 47.619 0.00 0.00 0.00 1.82
777 1565 5.484715 GCAACTTAGTAGGATTGTACACCA 58.515 41.667 0.00 0.00 0.00 4.17
779 1567 6.460781 CAACTTAGTAGGATTGTACACCACA 58.539 40.000 0.00 0.00 34.51 4.17
782 1570 6.269307 ACTTAGTAGGATTGTACACCACAGTT 59.731 38.462 0.00 0.00 38.72 3.16
798 1586 3.734231 CACAGTTGAACGTATTGTCTCGT 59.266 43.478 0.00 0.00 42.12 4.18
833 1621 6.683974 TTCTTTCTTCCTTTTCACTCTGTG 57.316 37.500 0.00 0.00 34.45 3.66
861 1649 2.819595 GCTGCTGCGGAATTCGGA 60.820 61.111 13.72 4.50 39.69 4.55
948 1740 2.474410 AAATGTCTTCCACGAGGACC 57.526 50.000 0.00 0.00 45.73 4.46
983 1780 4.778143 ACCCGCCACGCCATCTTC 62.778 66.667 0.00 0.00 0.00 2.87
1169 1981 2.844839 CCGTCCTCCTCCCATCCC 60.845 72.222 0.00 0.00 0.00 3.85
1173 1985 3.164269 CCTCCTCCCATCCCCACG 61.164 72.222 0.00 0.00 0.00 4.94
1214 2026 1.693152 CCCCTCCCTACTAAACCCGC 61.693 65.000 0.00 0.00 0.00 6.13
1215 2027 1.693152 CCCTCCCTACTAAACCCGCC 61.693 65.000 0.00 0.00 0.00 6.13
1216 2028 1.693152 CCTCCCTACTAAACCCGCCC 61.693 65.000 0.00 0.00 0.00 6.13
1217 2029 2.024590 CTCCCTACTAAACCCGCCCG 62.025 65.000 0.00 0.00 0.00 6.13
1503 2342 1.474478 GTGTCGGAGCTGAGATTCTGA 59.526 52.381 0.00 0.00 0.00 3.27
1524 2363 0.782384 GCCGTAGAATAATCGCCGTG 59.218 55.000 0.00 0.00 0.00 4.94
1634 2479 1.290009 GTTGCAACCATGGTGCTCC 59.710 57.895 28.04 19.07 0.00 4.70
1669 2514 0.173935 TTATCTACCGTGCGTGTGGG 59.826 55.000 0.00 0.00 0.00 4.61
1670 2515 0.966875 TATCTACCGTGCGTGTGGGT 60.967 55.000 0.00 0.00 37.84 4.51
1676 2521 3.737172 GTGCGTGTGGGTGGATGC 61.737 66.667 0.00 0.00 0.00 3.91
1709 2554 8.608844 ATTCAGGATCGAAATTAGTGGATAAC 57.391 34.615 0.00 0.00 0.00 1.89
1779 2624 2.359214 TGGTTTAAACGCATGTTGCTGA 59.641 40.909 12.07 0.00 42.25 4.26
1790 2635 2.831685 TGTTGCTGACCGAATACACT 57.168 45.000 0.00 0.00 0.00 3.55
1974 2829 5.592054 TGAAGAACAGAGTATGAATAGGCG 58.408 41.667 0.00 0.00 0.00 5.52
1975 2830 3.983741 AGAACAGAGTATGAATAGGCGC 58.016 45.455 0.00 0.00 0.00 6.53
2025 2880 6.766084 GCATATGCATTTAGAACCGAGATAC 58.234 40.000 22.84 0.00 41.59 2.24
2030 2885 4.508124 GCATTTAGAACCGAGATACTGTGG 59.492 45.833 0.00 0.00 0.00 4.17
2042 2897 3.891366 AGATACTGTGGTTTGCTTGCTTT 59.109 39.130 0.00 0.00 0.00 3.51
2100 2972 5.012046 ACCTGATATCTGTCACTGTTCAACA 59.988 40.000 3.98 0.00 0.00 3.33
2103 2975 6.287525 TGATATCTGTCACTGTTCAACAACA 58.712 36.000 3.98 0.00 40.40 3.33
2116 2988 8.977505 ACTGTTCAACAACACAAAATTATATGC 58.022 29.630 0.00 0.00 37.61 3.14
2118 2990 7.386299 TGTTCAACAACACAAAATTATATGCCC 59.614 33.333 0.00 0.00 37.61 5.36
2119 2991 7.238486 TCAACAACACAAAATTATATGCCCT 57.762 32.000 0.00 0.00 0.00 5.19
2139 3011 6.070136 TGCCCTATAACATTTGTAGGTGTGTA 60.070 38.462 7.66 0.00 41.45 2.90
2180 3052 6.929049 TCGTTTTTCACTAATCTGTGTCATCT 59.071 34.615 0.00 0.00 38.90 2.90
2211 3083 1.973281 CGGTTGCCTTGTGGAGCAT 60.973 57.895 0.00 0.00 39.11 3.79
2272 3144 3.551846 GCTTATGGCCTTTGGTAAGCTA 58.448 45.455 20.13 0.00 43.38 3.32
2274 3146 5.757581 GCTTATGGCCTTTGGTAAGCTACC 61.758 50.000 20.13 5.65 43.38 3.18
2292 3164 4.378459 GCTACCTTTGACGAGTCCATTTTG 60.378 45.833 0.34 0.00 0.00 2.44
2297 3169 3.201353 TGACGAGTCCATTTTGTTGGA 57.799 42.857 0.34 0.00 43.56 3.53
2329 3201 3.804036 CTTTCTGGTGTTGTCTGTACCA 58.196 45.455 0.00 0.00 41.90 3.25
2406 3278 9.158233 TGTTTTTCTTGCCTGTATATGTAGTAC 57.842 33.333 0.00 0.00 0.00 2.73
2423 3295 8.650143 ATGTAGTACCAAAATCAATTTCCTGT 57.350 30.769 0.00 0.00 0.00 4.00
2424 3296 8.106247 TGTAGTACCAAAATCAATTTCCTGTC 57.894 34.615 0.00 0.00 0.00 3.51
2425 3297 7.721842 TGTAGTACCAAAATCAATTTCCTGTCA 59.278 33.333 0.00 0.00 0.00 3.58
2426 3298 7.595819 AGTACCAAAATCAATTTCCTGTCAA 57.404 32.000 0.00 0.00 0.00 3.18
2427 3299 8.017418 AGTACCAAAATCAATTTCCTGTCAAA 57.983 30.769 0.00 0.00 0.00 2.69
2428 3300 8.482128 AGTACCAAAATCAATTTCCTGTCAAAA 58.518 29.630 0.00 0.00 0.00 2.44
2429 3301 9.103861 GTACCAAAATCAATTTCCTGTCAAAAA 57.896 29.630 0.00 0.00 0.00 1.94
2477 3349 8.573885 CGTCCATAGGAAGTATGTACAGAATTA 58.426 37.037 2.80 0.00 37.42 1.40
2512 3384 5.726980 ATTTGTGGTGTGAAACTGCATAT 57.273 34.783 0.00 0.00 38.04 1.78
2513 3385 4.502171 TTGTGGTGTGAAACTGCATATG 57.498 40.909 0.00 0.00 38.04 1.78
2592 3648 5.161358 GGATTGCTCCTTTCCTTTTTAACG 58.839 41.667 0.00 0.00 38.65 3.18
2627 3714 6.606234 TTCTCTCTCTAATGCACTAGTACG 57.394 41.667 1.57 0.00 0.00 3.67
2898 3994 1.032014 TGGCCAAGTGAGTGAAAAGC 58.968 50.000 0.61 0.00 0.00 3.51
2907 4003 3.755378 AGTGAGTGAAAAGCAGCCTAATG 59.245 43.478 0.00 0.00 0.00 1.90
2910 4006 2.171003 GTGAAAAGCAGCCTAATGGGT 58.829 47.619 0.00 0.00 46.37 4.51
2928 4024 7.716799 AATGGGTCAATTCATGCTTAACTTA 57.283 32.000 0.00 0.00 0.00 2.24
3014 4110 1.283321 GAGCAAGAATGAAGACCCCCT 59.717 52.381 0.00 0.00 0.00 4.79
3085 4181 7.550712 TGGATGATATACCATTCGATTCTCTG 58.449 38.462 0.00 0.00 0.00 3.35
3209 4329 9.317936 CATCATAAGCTTCTTACATCTGTACAA 57.682 33.333 0.00 0.00 0.00 2.41
3211 4331 9.719355 TCATAAGCTTCTTACATCTGTACAAAA 57.281 29.630 0.00 0.00 0.00 2.44
3285 4405 6.701145 TGCACAATAAACAAGAGGTACAAA 57.299 33.333 0.00 0.00 0.00 2.83
3296 4416 6.533730 ACAAGAGGTACAAATCACTTCATCA 58.466 36.000 0.00 0.00 0.00 3.07
3335 4455 1.343069 AGATCAATAGCCCTCGACCC 58.657 55.000 0.00 0.00 0.00 4.46
3342 4462 2.363306 TAGCCCTCGACCCGTTAATA 57.637 50.000 0.00 0.00 0.00 0.98
3346 4466 1.002033 CCCTCGACCCGTTAATACTCG 60.002 57.143 0.00 0.00 0.00 4.18
3347 4467 1.942657 CCTCGACCCGTTAATACTCGA 59.057 52.381 0.00 0.00 30.74 4.04
3584 4768 3.530265 ATCGACAACCATTTAGCCGTA 57.470 42.857 0.00 0.00 0.00 4.02
3601 4785 2.618045 CCGTATGAGCTTGGGAAGGTTT 60.618 50.000 0.00 0.00 39.77 3.27
3650 4834 2.230660 GCTCTTGTTAAACACCAGCCT 58.769 47.619 0.00 0.00 30.49 4.58
3652 4836 3.476552 CTCTTGTTAAACACCAGCCTCA 58.523 45.455 0.00 0.00 0.00 3.86
3677 4861 1.246649 TCGGCACAGCAATCACATTT 58.753 45.000 0.00 0.00 0.00 2.32
3767 4951 3.181496 GGTAGATTGTTTAAGCTGCTGCC 60.181 47.826 12.44 0.00 40.80 4.85
3957 5141 2.993937 TGTTTTTCCGACTGTTCCTGT 58.006 42.857 0.00 0.00 0.00 4.00
4002 5186 7.173218 GTGTGGGAAATATACTGTGATACCATG 59.827 40.741 0.00 0.00 0.00 3.66
4003 5187 7.071824 TGTGGGAAATATACTGTGATACCATGA 59.928 37.037 0.00 0.00 0.00 3.07
4004 5188 8.103305 GTGGGAAATATACTGTGATACCATGAT 58.897 37.037 0.00 0.00 0.00 2.45
4005 5189 8.102676 TGGGAAATATACTGTGATACCATGATG 58.897 37.037 0.00 0.00 0.00 3.07
4006 5190 8.103305 GGGAAATATACTGTGATACCATGATGT 58.897 37.037 0.00 0.00 0.00 3.06
4014 5198 8.837788 ACTGTGATACCATGATGTATTACATG 57.162 34.615 13.93 12.74 42.90 3.21
4079 5272 6.990341 TTCTGAATGTTCACAGGACATATG 57.010 37.500 0.00 0.00 36.76 1.78
4087 5280 7.898014 TGTTCACAGGACATATGTCTACTAT 57.102 36.000 29.87 10.79 44.20 2.12
4088 5281 7.941919 TGTTCACAGGACATATGTCTACTATC 58.058 38.462 29.87 15.50 44.20 2.08
4089 5282 7.780271 TGTTCACAGGACATATGTCTACTATCT 59.220 37.037 29.87 17.26 44.20 1.98
4090 5283 8.634444 GTTCACAGGACATATGTCTACTATCTT 58.366 37.037 29.87 9.80 44.20 2.40
4091 5284 8.768501 TCACAGGACATATGTCTACTATCTTT 57.231 34.615 29.87 11.77 44.20 2.52
4092 5285 8.851145 TCACAGGACATATGTCTACTATCTTTC 58.149 37.037 29.87 12.97 44.20 2.62
4093 5286 8.633561 CACAGGACATATGTCTACTATCTTTCA 58.366 37.037 29.87 0.00 44.20 2.69
4094 5287 9.201989 ACAGGACATATGTCTACTATCTTTCAA 57.798 33.333 29.87 0.00 44.20 2.69
4133 5768 6.588719 CAAATTTGGATTTGTACTCCCTCA 57.411 37.500 10.49 0.00 44.52 3.86
4134 5769 6.389906 CAAATTTGGATTTGTACTCCCTCAC 58.610 40.000 10.49 0.00 44.52 3.51
4135 5770 3.328382 TTGGATTTGTACTCCCTCACG 57.672 47.619 0.00 0.00 31.32 4.35
4136 5771 1.066430 TGGATTTGTACTCCCTCACGC 60.066 52.381 0.00 0.00 31.32 5.34
4137 5772 1.207329 GGATTTGTACTCCCTCACGCT 59.793 52.381 0.00 0.00 0.00 5.07
4138 5773 2.541556 GATTTGTACTCCCTCACGCTC 58.458 52.381 0.00 0.00 0.00 5.03
4139 5774 1.629043 TTTGTACTCCCTCACGCTCT 58.371 50.000 0.00 0.00 0.00 4.09
4140 5775 1.629043 TTGTACTCCCTCACGCTCTT 58.371 50.000 0.00 0.00 0.00 2.85
4141 5776 2.502142 TGTACTCCCTCACGCTCTTA 57.498 50.000 0.00 0.00 0.00 2.10
4142 5777 3.014304 TGTACTCCCTCACGCTCTTAT 57.986 47.619 0.00 0.00 0.00 1.73
4143 5778 4.160642 TGTACTCCCTCACGCTCTTATA 57.839 45.455 0.00 0.00 0.00 0.98
4144 5779 4.726583 TGTACTCCCTCACGCTCTTATAT 58.273 43.478 0.00 0.00 0.00 0.86
4145 5780 5.138276 TGTACTCCCTCACGCTCTTATATT 58.862 41.667 0.00 0.00 0.00 1.28
4146 5781 5.597182 TGTACTCCCTCACGCTCTTATATTT 59.403 40.000 0.00 0.00 0.00 1.40
4147 5782 5.203060 ACTCCCTCACGCTCTTATATTTC 57.797 43.478 0.00 0.00 0.00 2.17
4148 5783 4.896482 ACTCCCTCACGCTCTTATATTTCT 59.104 41.667 0.00 0.00 0.00 2.52
4149 5784 5.364157 ACTCCCTCACGCTCTTATATTTCTT 59.636 40.000 0.00 0.00 0.00 2.52
4150 5785 6.127026 ACTCCCTCACGCTCTTATATTTCTTT 60.127 38.462 0.00 0.00 0.00 2.52
4151 5786 7.069578 ACTCCCTCACGCTCTTATATTTCTTTA 59.930 37.037 0.00 0.00 0.00 1.85
4152 5787 7.963532 TCCCTCACGCTCTTATATTTCTTTAT 58.036 34.615 0.00 0.00 0.00 1.40
4153 5788 7.872993 TCCCTCACGCTCTTATATTTCTTTATG 59.127 37.037 0.00 0.00 0.00 1.90
4154 5789 7.118390 CCCTCACGCTCTTATATTTCTTTATGG 59.882 40.741 0.00 0.00 0.00 2.74
4155 5790 7.360438 CCTCACGCTCTTATATTTCTTTATGGC 60.360 40.741 0.00 0.00 0.00 4.40
4156 5791 6.145534 TCACGCTCTTATATTTCTTTATGGCG 59.854 38.462 0.00 0.00 42.65 5.69
4157 5792 5.408604 ACGCTCTTATATTTCTTTATGGCGG 59.591 40.000 0.00 0.00 41.56 6.13
4158 5793 5.163854 CGCTCTTATATTTCTTTATGGCGGG 60.164 44.000 0.00 0.00 35.20 6.13
4159 5794 5.938125 GCTCTTATATTTCTTTATGGCGGGA 59.062 40.000 0.00 0.00 0.00 5.14
4160 5795 6.092807 GCTCTTATATTTCTTTATGGCGGGAG 59.907 42.308 0.00 0.00 0.00 4.30
4161 5796 7.074653 TCTTATATTTCTTTATGGCGGGAGT 57.925 36.000 0.00 0.00 0.00 3.85
4162 5797 8.197592 TCTTATATTTCTTTATGGCGGGAGTA 57.802 34.615 0.00 0.00 0.00 2.59
4163 5798 8.092687 TCTTATATTTCTTTATGGCGGGAGTAC 58.907 37.037 0.00 0.00 0.00 2.73
4177 5812 4.867047 GCGGGAGTACTTTTTACTAAGGAC 59.133 45.833 0.00 0.00 38.93 3.85
4202 5842 4.500265 ACATGCCTTGTGACACCC 57.500 55.556 2.45 0.00 37.11 4.61
4303 5943 1.402968 CCGTGCAAGCTTATTCATGCT 59.597 47.619 0.00 0.00 41.82 3.79
4372 6127 3.090790 GGTATAAGGCAACCGGGAAAAA 58.909 45.455 6.32 0.00 37.17 1.94
4384 6207 4.086457 ACCGGGAAAAAGAATAAGCACAT 58.914 39.130 6.32 0.00 0.00 3.21
4391 6214 7.440856 GGGAAAAAGAATAAGCACATGACAAAA 59.559 33.333 0.00 0.00 0.00 2.44
4392 6215 8.275632 GGAAAAAGAATAAGCACATGACAAAAC 58.724 33.333 0.00 0.00 0.00 2.43
4436 6259 4.501559 CAGTTCATGACAAAGTTGCAACTG 59.498 41.667 31.73 22.77 39.66 3.16
4440 6263 3.485947 TGACAAAGTTGCAACTGTGAC 57.514 42.857 42.62 37.28 45.23 3.67
4446 6269 5.405269 ACAAAGTTGCAACTGTGACTTTTTC 59.595 36.000 42.62 11.24 45.23 2.29
4457 6291 2.033424 GTGACTTTTTCTCACAGTGGGC 59.967 50.000 0.00 0.00 38.36 5.36
4458 6292 1.609072 GACTTTTTCTCACAGTGGGCC 59.391 52.381 0.00 0.00 0.00 5.80
4473 6307 1.593265 GGCCCATGGAAGCAAACAG 59.407 57.895 15.22 0.00 0.00 3.16
4477 6311 1.068333 CCCATGGAAGCAAACAGTTCG 60.068 52.381 15.22 0.00 0.00 3.95
4483 6317 1.947456 GAAGCAAACAGTTCGGGTTCT 59.053 47.619 16.72 0.00 35.51 3.01
4580 6415 2.427095 ACTGGCAAAGGAGACACAAAAC 59.573 45.455 0.00 0.00 0.00 2.43
4803 6641 5.627499 ATGCACACGAAAATTACATGACT 57.373 34.783 0.00 0.00 0.00 3.41
4825 6663 1.919240 TAACTCAGCGAAGGAGGACA 58.081 50.000 0.00 0.00 36.70 4.02
4842 6680 2.505405 GACAGGAAGGTTTCTGGGAAC 58.495 52.381 3.05 0.00 35.47 3.62
4881 6720 1.272781 GCGTCACTCAAAGATCCTCG 58.727 55.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 9.354673 TGGAGAGTGATCAATTTCTAACTTTTT 57.645 29.630 12.69 0.00 0.00 1.94
27 28 8.160106 ACTGGAGAGTGATCAATTTCTAACTTT 58.840 33.333 12.69 0.00 0.00 2.66
28 29 7.684529 ACTGGAGAGTGATCAATTTCTAACTT 58.315 34.615 12.69 0.00 0.00 2.66
29 30 7.251321 ACTGGAGAGTGATCAATTTCTAACT 57.749 36.000 12.69 0.00 0.00 2.24
30 31 8.035394 TGTACTGGAGAGTGATCAATTTCTAAC 58.965 37.037 12.69 4.73 33.21 2.34
47 48 7.388776 TGTCTGAATTTTCATTCTGTACTGGAG 59.611 37.037 0.00 0.00 39.81 3.86
50 51 8.013947 CACTGTCTGAATTTTCATTCTGTACTG 58.986 37.037 0.00 0.00 39.81 2.74
57 58 7.149569 TCATCCACTGTCTGAATTTTCATTC 57.850 36.000 0.00 0.00 39.58 2.67
82 83 8.715191 TTCTGTGCAGAAACATAAACATTTTT 57.285 26.923 11.72 0.00 43.79 1.94
99 100 4.824537 TGCTTGTTTATTAGGTTCTGTGCA 59.175 37.500 0.00 0.00 0.00 4.57
100 101 5.371115 TGCTTGTTTATTAGGTTCTGTGC 57.629 39.130 0.00 0.00 0.00 4.57
101 102 7.148755 GCAAATGCTTGTTTATTAGGTTCTGTG 60.149 37.037 0.00 0.00 38.21 3.66
102 103 6.868339 GCAAATGCTTGTTTATTAGGTTCTGT 59.132 34.615 0.00 0.00 38.21 3.41
103 104 6.867816 TGCAAATGCTTGTTTATTAGGTTCTG 59.132 34.615 6.97 0.00 42.66 3.02
104 105 6.991938 TGCAAATGCTTGTTTATTAGGTTCT 58.008 32.000 6.97 0.00 42.66 3.01
105 106 7.170658 TGTTGCAAATGCTTGTTTATTAGGTTC 59.829 33.333 0.00 0.00 42.66 3.62
138 139 3.065648 TGTTTTCGTGCCAACTTAAGACC 59.934 43.478 10.09 0.00 0.00 3.85
145 146 6.814146 TCTTTTATTTTGTTTTCGTGCCAACT 59.186 30.769 0.00 0.00 0.00 3.16
146 147 6.994992 TCTTTTATTTTGTTTTCGTGCCAAC 58.005 32.000 0.00 0.00 0.00 3.77
205 206 1.202440 TGCTTTTGTTTGCTGAGCCTG 60.202 47.619 0.23 0.00 32.53 4.85
213 214 8.839947 ATCTTTAAATTTGTGCTTTTGTTTGC 57.160 26.923 0.00 0.00 0.00 3.68
247 249 0.249447 GCACTTGTTGGAAGGCAACC 60.249 55.000 0.00 0.00 37.17 3.77
255 257 6.155827 GCATTAAACAATAGCACTTGTTGGA 58.844 36.000 14.90 8.84 45.98 3.53
257 259 5.348451 GGGCATTAAACAATAGCACTTGTTG 59.652 40.000 14.90 6.85 45.98 3.33
264 266 4.249638 AGAGGGGCATTAAACAATAGCA 57.750 40.909 0.00 0.00 0.00 3.49
265 267 4.216472 GCTAGAGGGGCATTAAACAATAGC 59.784 45.833 0.00 0.00 0.00 2.97
281 283 2.854963 TGCATTATGCCTTGCTAGAGG 58.145 47.619 15.06 0.00 44.23 3.69
282 284 4.421033 CATGCATTATGCCTTGCTAGAG 57.579 45.455 15.06 0.00 44.23 2.43
328 330 7.773690 TCTTCACTTAAAAAGAGCTGGTAAAGT 59.226 33.333 0.00 0.00 0.00 2.66
334 336 7.880105 AGAAATCTTCACTTAAAAAGAGCTGG 58.120 34.615 0.00 0.00 35.13 4.85
337 339 9.736023 TGAAAGAAATCTTCACTTAAAAAGAGC 57.264 29.630 0.00 0.00 35.13 4.09
347 349 7.587037 TGTGGATTTGAAAGAAATCTTCACT 57.413 32.000 0.00 0.00 36.97 3.41
412 414 6.266558 TCTGGAAGCTCTTTGTCTATAGATCC 59.733 42.308 5.57 6.05 0.00 3.36
419 421 6.014242 TGAGAATTCTGGAAGCTCTTTGTCTA 60.014 38.462 14.00 0.00 31.22 2.59
423 425 5.954296 TTGAGAATTCTGGAAGCTCTTTG 57.046 39.130 14.00 0.00 31.22 2.77
492 494 9.594478 TTGAAGCGTATGAGTTCTCATTTAATA 57.406 29.630 18.43 0.23 0.00 0.98
493 495 8.492673 TTGAAGCGTATGAGTTCTCATTTAAT 57.507 30.769 18.43 4.65 0.00 1.40
530 532 9.965824 TTGATTTGAGTAAAAATGGAGAAACTC 57.034 29.630 0.00 0.00 35.13 3.01
581 592 7.896811 AGAAGGGGTTCAAATTCTTGATAAAC 58.103 34.615 0.00 0.00 41.22 2.01
633 658 5.665459 TGAGAGAAAGCTTTACTGCTATCC 58.335 41.667 12.68 0.00 43.24 2.59
639 1155 8.447053 GGTTCTAATTGAGAGAAAGCTTTACTG 58.553 37.037 12.68 2.66 34.78 2.74
641 1157 8.324163 TGGTTCTAATTGAGAGAAAGCTTTAC 57.676 34.615 12.68 9.56 34.78 2.01
642 1158 8.918202 TTGGTTCTAATTGAGAGAAAGCTTTA 57.082 30.769 12.68 0.00 34.78 1.85
646 1162 5.707764 ACCTTGGTTCTAATTGAGAGAAAGC 59.292 40.000 0.00 0.00 34.78 3.51
647 1163 7.751768 AACCTTGGTTCTAATTGAGAGAAAG 57.248 36.000 0.00 0.00 34.78 2.62
652 1168 7.617225 TCGATAAACCTTGGTTCTAATTGAGA 58.383 34.615 5.43 0.00 0.00 3.27
671 1190 5.427036 AAAAGCTTTTGTCGGTTCGATAA 57.573 34.783 23.30 0.00 38.42 1.75
675 1194 4.025145 AGTCTAAAAGCTTTTGTCGGTTCG 60.025 41.667 30.21 10.84 0.00 3.95
679 1198 4.753107 TGGTAGTCTAAAAGCTTTTGTCGG 59.247 41.667 30.21 18.08 0.00 4.79
681 1200 7.492352 TCTTGGTAGTCTAAAAGCTTTTGTC 57.508 36.000 30.21 19.94 0.00 3.18
682 1201 9.569122 TTATCTTGGTAGTCTAAAAGCTTTTGT 57.431 29.630 30.21 16.10 0.00 2.83
684 1203 8.731605 GCTTATCTTGGTAGTCTAAAAGCTTTT 58.268 33.333 26.50 26.50 0.00 2.27
685 1204 7.883311 TGCTTATCTTGGTAGTCTAAAAGCTTT 59.117 33.333 5.69 5.69 0.00 3.51
686 1205 7.394816 TGCTTATCTTGGTAGTCTAAAAGCTT 58.605 34.615 0.00 0.00 0.00 3.74
687 1206 6.947464 TGCTTATCTTGGTAGTCTAAAAGCT 58.053 36.000 0.00 0.00 0.00 3.74
692 1211 6.106673 GCTGTTGCTTATCTTGGTAGTCTAA 58.893 40.000 0.00 0.00 36.03 2.10
695 1214 4.866682 GCTGTTGCTTATCTTGGTAGTC 57.133 45.455 0.00 0.00 36.03 2.59
715 1311 5.717038 ATTTTACTTTGTTTGTGTGCAGC 57.283 34.783 0.00 0.00 0.00 5.25
716 1312 7.985634 AGTATTTTACTTTGTTTGTGTGCAG 57.014 32.000 0.00 0.00 34.86 4.41
731 1327 4.223659 CGTGTTGGGTGCAAGTATTTTAC 58.776 43.478 0.00 0.00 0.00 2.01
732 1328 3.253677 CCGTGTTGGGTGCAAGTATTTTA 59.746 43.478 0.00 0.00 0.00 1.52
763 1360 5.302360 GTTCAACTGTGGTGTACAATCCTA 58.698 41.667 0.00 0.00 39.20 2.94
764 1361 4.134563 GTTCAACTGTGGTGTACAATCCT 58.865 43.478 0.00 0.00 39.20 3.24
777 1565 3.973657 ACGAGACAATACGTTCAACTGT 58.026 40.909 0.00 0.00 39.75 3.55
801 1589 7.065683 GTGAAAAGGAAGAAAGAAAATGGCAAA 59.934 33.333 0.00 0.00 0.00 3.68
802 1590 6.538381 GTGAAAAGGAAGAAAGAAAATGGCAA 59.462 34.615 0.00 0.00 0.00 4.52
804 1592 6.283694 AGTGAAAAGGAAGAAAGAAAATGGC 58.716 36.000 0.00 0.00 0.00 4.40
805 1593 7.650903 CAGAGTGAAAAGGAAGAAAGAAAATGG 59.349 37.037 0.00 0.00 0.00 3.16
806 1594 8.193438 ACAGAGTGAAAAGGAAGAAAGAAAATG 58.807 33.333 0.00 0.00 0.00 2.32
807 1595 8.193438 CACAGAGTGAAAAGGAAGAAAGAAAAT 58.807 33.333 0.00 0.00 35.23 1.82
808 1596 7.538575 CACAGAGTGAAAAGGAAGAAAGAAAA 58.461 34.615 0.00 0.00 35.23 2.29
809 1597 6.404734 GCACAGAGTGAAAAGGAAGAAAGAAA 60.405 38.462 0.58 0.00 35.23 2.52
810 1598 5.066505 GCACAGAGTGAAAAGGAAGAAAGAA 59.933 40.000 0.58 0.00 35.23 2.52
811 1599 4.576463 GCACAGAGTGAAAAGGAAGAAAGA 59.424 41.667 0.58 0.00 35.23 2.52
812 1600 4.336433 TGCACAGAGTGAAAAGGAAGAAAG 59.664 41.667 0.58 0.00 35.23 2.62
813 1601 4.269183 TGCACAGAGTGAAAAGGAAGAAA 58.731 39.130 0.58 0.00 35.23 2.52
814 1602 3.884895 TGCACAGAGTGAAAAGGAAGAA 58.115 40.909 0.58 0.00 35.23 2.52
815 1603 3.558931 TGCACAGAGTGAAAAGGAAGA 57.441 42.857 0.58 0.00 35.23 2.87
816 1604 3.817084 TCATGCACAGAGTGAAAAGGAAG 59.183 43.478 0.58 0.00 35.23 3.46
833 1621 1.513586 GCAGCAGCGAAGTTCATGC 60.514 57.895 18.02 18.02 38.97 4.06
856 1644 5.417580 CCTCATTTTCCCATTACTTTCCGAA 59.582 40.000 0.00 0.00 0.00 4.30
857 1645 4.947388 CCTCATTTTCCCATTACTTTCCGA 59.053 41.667 0.00 0.00 0.00 4.55
858 1646 4.440112 GCCTCATTTTCCCATTACTTTCCG 60.440 45.833 0.00 0.00 0.00 4.30
859 1647 4.440112 CGCCTCATTTTCCCATTACTTTCC 60.440 45.833 0.00 0.00 0.00 3.13
860 1648 4.398044 TCGCCTCATTTTCCCATTACTTTC 59.602 41.667 0.00 0.00 0.00 2.62
861 1649 4.340617 TCGCCTCATTTTCCCATTACTTT 58.659 39.130 0.00 0.00 0.00 2.66
926 1718 3.058224 GGTCCTCGTGGAAGACATTTTTG 60.058 47.826 7.99 0.00 45.18 2.44
938 1730 0.602905 GGTGTCTTTGGTCCTCGTGG 60.603 60.000 0.00 0.00 0.00 4.94
948 1740 3.007635 GGGTTTATCCTCGGTGTCTTTG 58.992 50.000 0.00 0.00 36.25 2.77
983 1780 1.202405 GCGCTGGATAAACAATTGGGG 60.202 52.381 10.83 0.00 0.00 4.96
1173 1985 4.279043 GTTGGTTGGTGGCGTGGC 62.279 66.667 0.00 0.00 0.00 5.01
1199 2011 2.059786 CGGGCGGGTTTAGTAGGGA 61.060 63.158 0.00 0.00 0.00 4.20
1200 2012 2.059786 TCGGGCGGGTTTAGTAGGG 61.060 63.158 0.00 0.00 0.00 3.53
1201 2013 1.142531 GTCGGGCGGGTTTAGTAGG 59.857 63.158 0.00 0.00 0.00 3.18
1215 2027 4.899239 GAGGAGCATGGCGGTCGG 62.899 72.222 0.00 0.00 43.39 4.79
1216 2028 4.899239 GGAGGAGCATGGCGGTCG 62.899 72.222 0.00 0.00 43.39 4.79
1217 2029 3.453070 GAGGAGGAGCATGGCGGTC 62.453 68.421 0.00 0.00 41.64 4.79
1503 2342 0.038526 CGGCGATTATTCTACGGCCT 60.039 55.000 0.00 0.00 46.71 5.19
1524 2363 0.946221 CGCGCTAGATGGTTCCATCC 60.946 60.000 23.22 10.95 42.61 3.51
1634 2479 4.592485 AGATAATTGTGCTAGGGAGACG 57.408 45.455 0.00 0.00 0.00 4.18
1669 2514 1.159713 TGAATCGATGCCGCATCCAC 61.160 55.000 24.44 14.50 37.57 4.02
1670 2515 0.881600 CTGAATCGATGCCGCATCCA 60.882 55.000 24.44 14.86 37.57 3.41
1707 2552 6.899393 TTATCTCATGAAACCAAAGCTGTT 57.101 33.333 0.00 0.00 0.00 3.16
1779 2624 2.498885 GGTGGTTAGGAGTGTATTCGGT 59.501 50.000 0.00 0.00 0.00 4.69
1790 2635 0.906066 TGCATTAGCGGTGGTTAGGA 59.094 50.000 0.00 0.00 46.23 2.94
1970 2825 0.107945 GAACTCTGAAGATGGCGCCT 60.108 55.000 29.70 13.55 0.00 5.52
1971 2826 0.391661 TGAACTCTGAAGATGGCGCC 60.392 55.000 22.73 22.73 0.00 6.53
1972 2827 1.005340 CTGAACTCTGAAGATGGCGC 58.995 55.000 0.00 0.00 0.00 6.53
1973 2828 2.266554 GTCTGAACTCTGAAGATGGCG 58.733 52.381 0.00 0.00 0.00 5.69
1974 2829 3.325293 TGTCTGAACTCTGAAGATGGC 57.675 47.619 0.00 0.00 0.00 4.40
1975 2830 7.011202 CACATATTGTCTGAACTCTGAAGATGG 59.989 40.741 0.00 0.00 0.00 3.51
2013 2868 3.864921 GCAAACCACAGTATCTCGGTTCT 60.865 47.826 0.00 0.00 40.84 3.01
2025 2880 2.582728 TCAAAGCAAGCAAACCACAG 57.417 45.000 0.00 0.00 0.00 3.66
2030 2885 2.211806 TGGCATTCAAAGCAAGCAAAC 58.788 42.857 0.00 0.00 0.00 2.93
2116 2988 8.974060 AATACACACCTACAAATGTTATAGGG 57.026 34.615 5.97 0.00 39.96 3.53
2139 3011 7.597369 GTGAAAAACGAATGGGTAAAAGCTAAT 59.403 33.333 0.00 0.00 0.00 1.73
2180 3052 1.677052 GGCAACCGACAACCTACAAAA 59.323 47.619 0.00 0.00 0.00 2.44
2272 3144 3.551846 ACAAAATGGACTCGTCAAAGGT 58.448 40.909 0.00 0.00 0.00 3.50
2274 3146 4.036262 TCCAACAAAATGGACTCGTCAAAG 59.964 41.667 0.00 0.00 44.52 2.77
2292 3164 5.533903 ACCAGAAAGCATGATCATATCCAAC 59.466 40.000 8.15 0.00 0.00 3.77
2297 3169 5.889853 ACAACACCAGAAAGCATGATCATAT 59.110 36.000 8.15 0.00 0.00 1.78
2301 3173 3.755378 AGACAACACCAGAAAGCATGATC 59.245 43.478 0.00 0.00 0.00 2.92
2306 3178 2.418368 ACAGACAACACCAGAAAGCA 57.582 45.000 0.00 0.00 0.00 3.91
2329 3201 1.227764 CCATGCAGCTCGCCAGTAT 60.228 57.895 0.00 0.00 41.33 2.12
2375 3247 9.019656 ACATATACAGGCAAGAAAAACATGTTA 57.980 29.630 12.39 0.00 0.00 2.41
2376 3248 7.895759 ACATATACAGGCAAGAAAAACATGTT 58.104 30.769 4.92 4.92 0.00 2.71
2377 3249 7.466746 ACATATACAGGCAAGAAAAACATGT 57.533 32.000 0.00 0.00 0.00 3.21
2378 3250 8.677300 ACTACATATACAGGCAAGAAAAACATG 58.323 33.333 0.00 0.00 0.00 3.21
2379 3251 8.807948 ACTACATATACAGGCAAGAAAAACAT 57.192 30.769 0.00 0.00 0.00 2.71
2380 3252 9.158233 GTACTACATATACAGGCAAGAAAAACA 57.842 33.333 0.00 0.00 0.00 2.83
2381 3253 8.610035 GGTACTACATATACAGGCAAGAAAAAC 58.390 37.037 0.00 0.00 0.00 2.43
2382 3254 8.322828 TGGTACTACATATACAGGCAAGAAAAA 58.677 33.333 0.00 0.00 0.00 1.94
2429 3301 9.251792 GGACGTAAAATTCATTTTGGTACTTTT 57.748 29.630 7.63 0.00 40.00 2.27
2430 3302 8.414778 TGGACGTAAAATTCATTTTGGTACTTT 58.585 29.630 7.63 0.00 40.00 2.66
2431 3303 7.942990 TGGACGTAAAATTCATTTTGGTACTT 58.057 30.769 7.63 0.00 40.00 2.24
2432 3304 7.513371 TGGACGTAAAATTCATTTTGGTACT 57.487 32.000 7.63 0.00 40.00 2.73
2436 3308 7.767261 TCCTATGGACGTAAAATTCATTTTGG 58.233 34.615 7.63 3.05 40.00 3.28
2443 3315 8.658499 ACATACTTCCTATGGACGTAAAATTC 57.342 34.615 6.97 0.00 39.33 2.17
2477 3349 6.264292 TCACACCACAAATAGTACAAGCAAAT 59.736 34.615 0.00 0.00 0.00 2.32
2512 3384 7.609918 ACACCATTGCTGTAACATATAAAGACA 59.390 33.333 0.00 0.00 0.00 3.41
2513 3385 7.985476 ACACCATTGCTGTAACATATAAAGAC 58.015 34.615 0.00 0.00 0.00 3.01
2585 3641 8.373220 AGAGAGAAAATAAGAGGTCCGTTAAAA 58.627 33.333 0.00 0.00 0.00 1.52
2592 3648 7.655732 GCATTAGAGAGAGAAAATAAGAGGTCC 59.344 40.741 0.00 0.00 0.00 4.46
2898 3994 3.243636 GCATGAATTGACCCATTAGGCTG 60.244 47.826 0.00 0.00 40.58 4.85
2907 4003 8.682710 TGTATTAAGTTAAGCATGAATTGACCC 58.317 33.333 0.00 0.00 0.00 4.46
3014 4110 1.550524 CTCGGATCCAGGTGAGAAACA 59.449 52.381 13.41 0.00 0.00 2.83
3059 4155 8.037166 CAGAGAATCGAATGGTATATCATCCAA 58.963 37.037 0.00 0.00 42.67 3.53
3085 4181 4.795278 GTGACGATGATTGAAGAAAATGCC 59.205 41.667 0.00 0.00 0.00 4.40
3123 4219 0.842467 CTTGAACTGGAGGAGGGGGT 60.842 60.000 0.00 0.00 0.00 4.95
3151 4249 7.389053 AGACTGAAAACTATAACTTGCTGGAAG 59.611 37.037 7.41 7.41 37.73 3.46
3155 4253 9.173939 CAAAAGACTGAAAACTATAACTTGCTG 57.826 33.333 0.00 0.00 0.00 4.41
3209 4329 8.959548 TGACATCTTCAATATACTGCAACATTT 58.040 29.630 0.00 0.00 0.00 2.32
3211 4331 8.510243 TTGACATCTTCAATATACTGCAACAT 57.490 30.769 0.00 0.00 39.45 2.71
3285 4405 2.651455 CACAGGCCATGATGAAGTGAT 58.349 47.619 5.01 0.00 0.00 3.06
3296 4416 1.302511 GACAACGACCACAGGCCAT 60.303 57.895 5.01 0.00 0.00 4.40
3335 4455 6.332504 AGCAAATGTTCTCGAGTATTAACG 57.667 37.500 13.13 6.06 0.00 3.18
3342 4462 4.083802 GCAAACTAGCAAATGTTCTCGAGT 60.084 41.667 13.13 0.00 0.00 4.18
3346 4466 7.201384 GCAAATAGCAAACTAGCAAATGTTCTC 60.201 37.037 0.00 0.00 44.79 2.87
3347 4467 6.587608 GCAAATAGCAAACTAGCAAATGTTCT 59.412 34.615 0.00 0.00 44.79 3.01
3517 4701 1.754234 GCCCCGATCCTGCAAATGT 60.754 57.895 0.00 0.00 0.00 2.71
3518 4702 2.492773 GGCCCCGATCCTGCAAATG 61.493 63.158 0.00 0.00 0.00 2.32
3584 4768 2.376518 TCTCAAACCTTCCCAAGCTCAT 59.623 45.455 0.00 0.00 0.00 2.90
3601 4785 0.609957 ATGTACCACGACGGGTCTCA 60.610 55.000 10.72 11.50 42.42 3.27
3650 4834 0.250252 TTGCTGTGCCGATGTCTTGA 60.250 50.000 0.00 0.00 0.00 3.02
3652 4836 1.089920 GATTGCTGTGCCGATGTCTT 58.910 50.000 0.00 0.00 0.00 3.01
3677 4861 1.015109 GACCAGCTCTATCGACGACA 58.985 55.000 0.00 0.00 0.00 4.35
3767 4951 5.920273 AGAAACACAAGCATTTACAATTCCG 59.080 36.000 0.00 0.00 0.00 4.30
3840 5024 4.122046 TGCACCATCTATTGAATCACTCG 58.878 43.478 0.00 0.00 0.00 4.18
3957 5141 6.485313 CCCACACATTGTAACTGAAGAGTTTA 59.515 38.462 0.00 0.00 39.56 2.01
4087 5280 9.650539 TTTGAAACACAGATGATTTTTGAAAGA 57.349 25.926 0.00 0.00 0.00 2.52
4092 5285 9.440784 CCAAATTTGAAACACAGATGATTTTTG 57.559 29.630 19.86 0.00 0.00 2.44
4093 5286 9.393512 TCCAAATTTGAAACACAGATGATTTTT 57.606 25.926 19.86 0.00 0.00 1.94
4094 5287 8.961294 TCCAAATTTGAAACACAGATGATTTT 57.039 26.923 19.86 0.00 0.00 1.82
4095 5288 9.563748 AATCCAAATTTGAAACACAGATGATTT 57.436 25.926 19.86 0.00 0.00 2.17
4096 5289 9.563748 AAATCCAAATTTGAAACACAGATGATT 57.436 25.926 19.86 11.74 33.78 2.57
4128 5763 7.118390 CCATAAAGAAATATAAGAGCGTGAGGG 59.882 40.741 0.00 0.00 0.00 4.30
4129 5764 7.360438 GCCATAAAGAAATATAAGAGCGTGAGG 60.360 40.741 0.00 0.00 0.00 3.86
4130 5765 7.513968 GCCATAAAGAAATATAAGAGCGTGAG 58.486 38.462 0.00 0.00 0.00 3.51
4131 5766 6.145534 CGCCATAAAGAAATATAAGAGCGTGA 59.854 38.462 0.00 0.00 34.42 4.35
4132 5767 6.299604 CGCCATAAAGAAATATAAGAGCGTG 58.700 40.000 0.00 0.00 34.42 5.34
4133 5768 5.408604 CCGCCATAAAGAAATATAAGAGCGT 59.591 40.000 0.00 0.00 37.15 5.07
4134 5769 5.163854 CCCGCCATAAAGAAATATAAGAGCG 60.164 44.000 0.00 0.00 38.48 5.03
4135 5770 5.938125 TCCCGCCATAAAGAAATATAAGAGC 59.062 40.000 0.00 0.00 0.00 4.09
4136 5771 7.162082 ACTCCCGCCATAAAGAAATATAAGAG 58.838 38.462 0.00 0.00 0.00 2.85
4137 5772 7.074653 ACTCCCGCCATAAAGAAATATAAGA 57.925 36.000 0.00 0.00 0.00 2.10
4138 5773 8.095169 AGTACTCCCGCCATAAAGAAATATAAG 58.905 37.037 0.00 0.00 0.00 1.73
4139 5774 7.970102 AGTACTCCCGCCATAAAGAAATATAA 58.030 34.615 0.00 0.00 0.00 0.98
4140 5775 7.549147 AGTACTCCCGCCATAAAGAAATATA 57.451 36.000 0.00 0.00 0.00 0.86
4141 5776 6.435292 AGTACTCCCGCCATAAAGAAATAT 57.565 37.500 0.00 0.00 0.00 1.28
4142 5777 5.881923 AGTACTCCCGCCATAAAGAAATA 57.118 39.130 0.00 0.00 0.00 1.40
4143 5778 4.772886 AGTACTCCCGCCATAAAGAAAT 57.227 40.909 0.00 0.00 0.00 2.17
4144 5779 4.563140 AAGTACTCCCGCCATAAAGAAA 57.437 40.909 0.00 0.00 0.00 2.52
4145 5780 4.563140 AAAGTACTCCCGCCATAAAGAA 57.437 40.909 0.00 0.00 0.00 2.52
4146 5781 4.563140 AAAAGTACTCCCGCCATAAAGA 57.437 40.909 0.00 0.00 0.00 2.52
4147 5782 5.878669 AGTAAAAAGTACTCCCGCCATAAAG 59.121 40.000 0.00 0.00 0.00 1.85
4148 5783 5.807909 AGTAAAAAGTACTCCCGCCATAAA 58.192 37.500 0.00 0.00 0.00 1.40
4149 5784 5.425196 AGTAAAAAGTACTCCCGCCATAA 57.575 39.130 0.00 0.00 0.00 1.90
4150 5785 6.407299 CCTTAGTAAAAAGTACTCCCGCCATA 60.407 42.308 0.00 0.00 0.00 2.74
4151 5786 3.994931 AGTAAAAAGTACTCCCGCCAT 57.005 42.857 0.00 0.00 0.00 4.40
4152 5787 4.322953 CCTTAGTAAAAAGTACTCCCGCCA 60.323 45.833 0.00 0.00 0.00 5.69
4153 5788 4.081476 TCCTTAGTAAAAAGTACTCCCGCC 60.081 45.833 0.00 0.00 0.00 6.13
4154 5789 4.867047 GTCCTTAGTAAAAAGTACTCCCGC 59.133 45.833 0.00 0.00 0.00 6.13
4155 5790 6.098017 CAGTCCTTAGTAAAAAGTACTCCCG 58.902 44.000 0.00 0.00 0.00 5.14
4156 5791 7.002250 ACAGTCCTTAGTAAAAAGTACTCCC 57.998 40.000 0.00 0.00 0.00 4.30
4157 5792 9.018582 TCTACAGTCCTTAGTAAAAAGTACTCC 57.981 37.037 0.00 0.00 0.00 3.85
4158 5793 9.838975 GTCTACAGTCCTTAGTAAAAAGTACTC 57.161 37.037 0.00 0.00 0.00 2.59
4159 5794 9.359653 TGTCTACAGTCCTTAGTAAAAAGTACT 57.640 33.333 0.00 0.00 0.00 2.73
4160 5795 9.404348 GTGTCTACAGTCCTTAGTAAAAAGTAC 57.596 37.037 0.00 0.00 0.00 2.73
4161 5796 9.135189 TGTGTCTACAGTCCTTAGTAAAAAGTA 57.865 33.333 0.00 0.00 31.91 2.24
4162 5797 8.015185 TGTGTCTACAGTCCTTAGTAAAAAGT 57.985 34.615 0.00 0.00 31.91 2.66
4163 5798 8.926710 CATGTGTCTACAGTCCTTAGTAAAAAG 58.073 37.037 0.00 0.00 40.79 2.27
4247 5887 7.121611 ACTTGCATTGTGTGAAGATATCAATCA 59.878 33.333 5.32 6.33 40.50 2.57
4248 5888 7.431376 CACTTGCATTGTGTGAAGATATCAATC 59.569 37.037 5.32 3.66 40.50 2.67
4249 5889 7.094075 ACACTTGCATTGTGTGAAGATATCAAT 60.094 33.333 20.47 0.00 45.57 2.57
4250 5890 6.207221 ACACTTGCATTGTGTGAAGATATCAA 59.793 34.615 20.47 0.00 45.57 2.57
4259 5899 2.373224 TCCAACACTTGCATTGTGTGA 58.627 42.857 21.43 14.56 46.46 3.58
4290 5930 6.770746 AAAGAACATGAGCATGAATAAGCT 57.229 33.333 16.70 0.00 45.25 3.74
4303 5943 3.229293 TCATGGTGGCAAAAGAACATGA 58.771 40.909 0.00 0.00 41.45 3.07
4364 6119 5.095490 GTCATGTGCTTATTCTTTTTCCCG 58.905 41.667 0.00 0.00 0.00 5.14
4372 6127 5.464168 GCAGTTTTGTCATGTGCTTATTCT 58.536 37.500 0.00 0.00 0.00 2.40
4384 6207 0.100325 CGTGCTTGGCAGTTTTGTCA 59.900 50.000 0.00 0.00 40.08 3.58
4391 6214 2.045926 GGGATCGTGCTTGGCAGT 60.046 61.111 0.00 0.00 40.08 4.40
4392 6215 1.372087 GAAGGGATCGTGCTTGGCAG 61.372 60.000 0.00 0.00 40.08 4.85
4436 6259 2.033424 GCCCACTGTGAGAAAAAGTCAC 59.967 50.000 9.86 0.00 43.97 3.67
4440 6263 0.961753 GGGCCCACTGTGAGAAAAAG 59.038 55.000 19.95 0.00 0.00 2.27
4446 6269 2.044650 CCATGGGCCCACTGTGAG 60.045 66.667 31.51 12.04 0.00 3.51
4452 6286 1.912763 TTTGCTTCCATGGGCCCAC 60.913 57.895 31.51 14.57 0.00 4.61
4457 6291 1.068333 CGAACTGTTTGCTTCCATGGG 60.068 52.381 13.02 0.00 0.00 4.00
4458 6292 1.068333 CCGAACTGTTTGCTTCCATGG 60.068 52.381 4.97 4.97 0.00 3.66
4473 6307 0.790814 CTTTCTCGCAGAACCCGAAC 59.209 55.000 0.00 0.00 33.26 3.95
4477 6311 2.416893 GACAATCTTTCTCGCAGAACCC 59.583 50.000 0.00 0.00 33.26 4.11
4483 6317 4.562789 CGTCTATTGACAATCTTTCTCGCA 59.437 41.667 3.36 0.00 43.06 5.10
4544 6379 0.109781 CCAGTTGTGCCATGCGTAAC 60.110 55.000 0.00 0.00 0.00 2.50
4580 6415 2.360165 AGAGTTGCTTTTTGCTGGAGTG 59.640 45.455 0.00 0.00 43.37 3.51
4799 6637 2.626266 TCCTTCGCTGAGTTAACAGTCA 59.374 45.455 8.61 2.90 39.73 3.41
4803 6641 2.029290 GTCCTCCTTCGCTGAGTTAACA 60.029 50.000 8.61 0.00 0.00 2.41
4825 6663 0.250770 GCGTTCCCAGAAACCTTCCT 60.251 55.000 0.00 0.00 0.00 3.36
4856 6694 0.601046 TCTTTGAGTGACGCCTGCTG 60.601 55.000 0.00 0.00 0.00 4.41
4857 6695 0.322975 ATCTTTGAGTGACGCCTGCT 59.677 50.000 0.00 0.00 0.00 4.24
4860 6699 1.205893 GAGGATCTTTGAGTGACGCCT 59.794 52.381 0.00 0.00 0.00 5.52
4881 6720 2.438434 CAGGACATCAACGGCCCC 60.438 66.667 0.00 0.00 0.00 5.80


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

AutoCloner maintained by Alex Coulton.