Multiple sequence alignment - TraesCS6B01G019300

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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 TraesCS6B01G019300 chr6B 100.000 6312 0 0 1 6312 11611841 11618152 0.000000e+00 11657.0
1 TraesCS6B01G019300 chr6B 90.768 1928 117 21 1 1887 11741536 11743443 0.000000e+00 2518.0
2 TraesCS6B01G019300 chr6B 97.915 1247 8 1 5084 6312 11746848 11748094 0.000000e+00 2143.0
3 TraesCS6B01G019300 chr6B 95.097 1183 18 14 3893 5052 11745687 11746852 0.000000e+00 1827.0
4 TraesCS6B01G019300 chr6B 94.881 1172 50 2 2169 3330 11743956 11745127 0.000000e+00 1823.0
5 TraesCS6B01G019300 chr6B 97.653 426 8 2 3473 3896 11745139 11745564 0.000000e+00 730.0
6 TraesCS6B01G019300 chr6B 95.793 309 9 3 1864 2171 11743622 11743927 4.400000e-136 496.0
7 TraesCS6B01G019300 chr6B 79.869 611 107 15 2174 2776 11719975 11719373 3.500000e-117 433.0
8 TraesCS6B01G019300 chr6B 80.913 482 70 13 1 464 11721117 11721594 1.670000e-95 361.0
9 TraesCS6B01G019300 chr6B 78.479 539 88 13 3096 3610 43387687 43387153 1.700000e-85 327.0
10 TraesCS6B01G019300 chr6B 82.394 284 42 7 3331 3610 20240683 20240404 2.270000e-59 241.0
11 TraesCS6B01G019300 chr6B 82.609 276 40 6 3331 3602 719421187 719420916 2.940000e-58 237.0
12 TraesCS6B01G019300 chr6B 83.200 250 38 4 2534 2781 11610304 11610057 6.370000e-55 226.0
13 TraesCS6B01G019300 chr6B 87.324 71 9 0 5775 5845 19120540 19120470 1.460000e-11 82.4
14 TraesCS6B01G019300 chr7D 79.940 668 104 15 2966 3610 474540584 474539924 1.240000e-126 464.0
15 TraesCS6B01G019300 chr7D 77.151 674 97 33 2956 3604 563514825 563515466 7.840000e-89 339.0
16 TraesCS6B01G019300 chr5B 79.822 674 104 14 2955 3604 101352127 101352792 4.460000e-126 462.0
17 TraesCS6B01G019300 chr3D 79.118 680 97 19 2956 3610 4185728 4185069 1.630000e-115 427.0
18 TraesCS6B01G019300 chr3B 78.498 679 103 14 2956 3610 6675814 6675155 7.620000e-109 405.0
19 TraesCS6B01G019300 chr5A 83.755 277 38 5 3332 3604 87980927 87981200 8.120000e-64 255.0
20 TraesCS6B01G019300 chr1D 84.259 216 30 3 1396 1609 466387959 466387746 2.310000e-49 207.0
21 TraesCS6B01G019300 chr7A 84.694 98 13 2 5750 5846 728088680 728088776 5.210000e-16 97.1
22 TraesCS6B01G019300 chr7A 82.828 99 15 2 5749 5846 728055633 728055730 3.130000e-13 87.9
23 TraesCS6B01G019300 chr6D 85.227 88 13 0 5758 5845 10344493 10344580 2.420000e-14 91.6
24 TraesCS6B01G019300 chr7B 82.022 89 14 2 5759 5846 738817561 738817474 2.440000e-09 75.0


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 TraesCS6B01G019300 chr6B 11611841 11618152 6311 False 11657.0 11657 100.000000 1 6312 1 chr6B.!!$F1 6311
1 TraesCS6B01G019300 chr6B 11741536 11748094 6558 False 1589.5 2518 95.351167 1 6312 6 chr6B.!!$F3 6311
2 TraesCS6B01G019300 chr6B 11719373 11719975 602 True 433.0 433 79.869000 2174 2776 1 chr6B.!!$R2 602
3 TraesCS6B01G019300 chr6B 43387153 43387687 534 True 327.0 327 78.479000 3096 3610 1 chr6B.!!$R5 514
4 TraesCS6B01G019300 chr7D 474539924 474540584 660 True 464.0 464 79.940000 2966 3610 1 chr7D.!!$R1 644
5 TraesCS6B01G019300 chr7D 563514825 563515466 641 False 339.0 339 77.151000 2956 3604 1 chr7D.!!$F1 648
6 TraesCS6B01G019300 chr5B 101352127 101352792 665 False 462.0 462 79.822000 2955 3604 1 chr5B.!!$F1 649
7 TraesCS6B01G019300 chr3D 4185069 4185728 659 True 427.0 427 79.118000 2956 3610 1 chr3D.!!$R1 654
8 TraesCS6B01G019300 chr3B 6675155 6675814 659 True 405.0 405 78.498000 2956 3610 1 chr3B.!!$R1 654

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
238 248 0.251354 TGCCTGAGCTGGACAAGATC 59.749 55.0 0.00 0.00 41.95 2.75 F
1116 1138 0.180406 TATCTTCCTCCCGGCTTTGC 59.820 55.0 0.00 0.00 0.00 3.68 F
1187 1222 0.323360 GGGGTGGCTATCAGCAAACA 60.323 55.0 0.00 0.00 44.75 2.83 F
2990 3264 0.961358 AACTCGGTCGGTCTCCTCTG 60.961 60.0 0.00 0.00 0.00 3.35 F
3388 3690 0.249657 CTTGGATCTAGCCGCTGACC 60.250 60.0 2.16 1.89 0.00 4.02 F
3410 3713 0.535797 GAGTTCCGATCTTCCCCGTT 59.464 55.0 0.00 0.00 0.00 4.44 F
3423 3726 0.673985 CCCCGTTCGAGATCTATGCA 59.326 55.0 0.00 0.00 0.00 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1478 1519 0.251564 ATTGGTGATGGCCGGTTTGA 60.252 50.000 1.9 0.0 0.0 2.69 R
3054 3328 0.976641 TCGCCATCACCTCAAAGAGT 59.023 50.000 0.0 0.0 0.0 3.24 R
3140 3414 1.765597 GACTCCCAGACCCACCGTTT 61.766 60.000 0.0 0.0 0.0 3.60 R
4699 5158 2.060326 TAGGTTTCGAGCACAAGACG 57.940 50.000 0.0 0.0 0.0 4.18 R
5027 5486 1.151777 ACCGTTGAACTGTGACTGCG 61.152 55.000 0.0 0.0 0.0 5.18 R
5265 5724 4.734398 ATTTGTTTGGTGAGTTTGCAGA 57.266 36.364 0.0 0.0 0.0 4.26 R
5575 6034 9.964354 TTCTCTAAGATGATTTTGAAAGGATGA 57.036 29.630 0.0 0.0 0.0 2.92 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
23 24 2.625314 GCAGCCTTTCTTCCAAGAAGTT 59.375 45.455 4.38 0.00 45.01 2.66
37 38 5.067674 TCCAAGAAGTTTGAGTTGGAATGTG 59.932 40.000 0.11 0.00 44.33 3.21
47 48 2.024655 AGTTGGAATGTGGGATGCTCAT 60.025 45.455 0.00 0.00 0.00 2.90
106 107 5.181009 CAGTGTTATCACATCCACACATCT 58.819 41.667 6.70 0.00 46.01 2.90
160 170 2.677325 CGAAGACCTCCTCGAGTCTGTA 60.677 54.545 12.31 0.00 0.00 2.74
170 180 4.158025 TCCTCGAGTCTGTAAATCTTGTCC 59.842 45.833 12.31 0.00 0.00 4.02
171 181 4.082190 CCTCGAGTCTGTAAATCTTGTCCA 60.082 45.833 12.31 0.00 0.00 4.02
207 217 5.104693 TCCAGTTTTTATCTCCTAATCCGCA 60.105 40.000 0.00 0.00 0.00 5.69
213 223 1.195115 TCTCCTAATCCGCAACTGCT 58.805 50.000 0.00 0.00 39.32 4.24
232 242 4.074526 TCGCTGCCTGAGCTGGAC 62.075 66.667 0.00 0.00 46.64 4.02
233 243 4.383861 CGCTGCCTGAGCTGGACA 62.384 66.667 0.00 0.00 46.64 4.02
234 244 2.033141 GCTGCCTGAGCTGGACAA 59.967 61.111 0.00 0.00 45.21 3.18
235 245 2.039405 GCTGCCTGAGCTGGACAAG 61.039 63.158 0.00 0.00 45.21 3.16
236 246 1.675801 CTGCCTGAGCTGGACAAGA 59.324 57.895 0.00 0.00 40.80 3.02
237 247 0.252479 CTGCCTGAGCTGGACAAGAT 59.748 55.000 0.00 0.00 40.80 2.40
238 248 0.251354 TGCCTGAGCTGGACAAGATC 59.749 55.000 0.00 0.00 41.95 2.75
242 252 2.996249 TGAGCTGGACAAGATCATCC 57.004 50.000 0.00 0.00 46.25 3.51
243 253 2.475155 TGAGCTGGACAAGATCATCCT 58.525 47.619 10.89 0.00 46.25 3.24
244 254 2.169978 TGAGCTGGACAAGATCATCCTG 59.830 50.000 10.89 11.01 46.25 3.86
245 255 1.489649 AGCTGGACAAGATCATCCTGG 59.510 52.381 15.01 0.00 35.86 4.45
246 256 1.964552 CTGGACAAGATCATCCTGGC 58.035 55.000 10.89 0.00 35.86 4.85
266 276 6.316390 CCTGGCTTGTTCTACTCGATATTTTT 59.684 38.462 0.00 0.00 0.00 1.94
277 287 7.987458 TCTACTCGATATTTTTCAGCAGGAATT 59.013 33.333 0.00 0.00 34.91 2.17
279 289 6.135290 TCGATATTTTTCAGCAGGAATTGG 57.865 37.500 0.00 0.00 34.91 3.16
302 312 1.277557 AGAGATCTTCCACACCAGTGC 59.722 52.381 0.00 0.00 44.53 4.40
330 340 0.745845 ATGTCTCAGCGTGGAATGGC 60.746 55.000 0.00 0.00 0.00 4.40
353 363 2.996621 CACTGGTCCAAGATTCTCGTTC 59.003 50.000 0.00 0.00 0.00 3.95
382 392 5.316167 TGTGACTGGCTTTCAGAATGTATT 58.684 37.500 0.00 0.00 46.18 1.89
398 408 7.010830 CAGAATGTATTGTGTGGACATGACTAG 59.989 40.741 0.00 0.00 34.10 2.57
404 414 4.883083 TGTGTGGACATGACTAGTTTCTC 58.117 43.478 0.00 0.00 0.00 2.87
412 422 6.146347 GGACATGACTAGTTTCTCTGTGTTTC 59.854 42.308 0.00 0.00 0.00 2.78
425 435 6.436027 TCTCTGTGTTTCCTGGATAGAGTAT 58.564 40.000 0.00 0.00 33.68 2.12
435 445 8.582657 TTCCTGGATAGAGTATATGTTAGAGC 57.417 38.462 0.00 0.00 0.00 4.09
436 446 7.699878 TCCTGGATAGAGTATATGTTAGAGCA 58.300 38.462 0.00 0.00 0.00 4.26
448 458 2.497675 TGTTAGAGCAGGCCAACTAGAG 59.502 50.000 5.01 0.00 0.00 2.43
449 459 2.761208 GTTAGAGCAGGCCAACTAGAGA 59.239 50.000 5.01 0.00 0.00 3.10
457 467 4.437239 CAGGCCAACTAGAGACTTGTATG 58.563 47.826 5.01 0.00 0.00 2.39
458 468 4.081420 CAGGCCAACTAGAGACTTGTATGT 60.081 45.833 5.01 0.00 0.00 2.29
463 473 6.418226 GCCAACTAGAGACTTGTATGTATTCG 59.582 42.308 0.00 0.00 0.00 3.34
465 475 7.644551 CCAACTAGAGACTTGTATGTATTCGAC 59.355 40.741 0.00 0.00 0.00 4.20
475 485 8.467598 ACTTGTATGTATTCGACTGACAACTAT 58.532 33.333 0.00 0.00 32.94 2.12
484 494 5.891451 TCGACTGACAACTATAGAACATGG 58.109 41.667 6.78 0.00 0.00 3.66
588 598 5.616204 GCACAACAAAGATAAGGTAACGGTC 60.616 44.000 0.00 0.00 46.39 4.79
637 647 0.732880 CGGCAAGACACCTCTACACG 60.733 60.000 0.00 0.00 0.00 4.49
640 650 2.593257 GCAAGACACCTCTACACGTAC 58.407 52.381 0.00 0.00 0.00 3.67
650 660 3.414464 CTCTACACGTACACTAACGCAG 58.586 50.000 0.00 0.00 46.71 5.18
693 704 3.691118 TCACTGAAAATACTCATGGCAGC 59.309 43.478 0.00 0.00 0.00 5.25
749 760 2.434185 GCCGCAACGATCCTGTCA 60.434 61.111 0.00 0.00 0.00 3.58
793 804 4.573201 CGGCGGATTTGGAGATAAAAACTA 59.427 41.667 0.00 0.00 0.00 2.24
797 808 7.187480 GCGGATTTGGAGATAAAAACTAGAAC 58.813 38.462 0.00 0.00 0.00 3.01
822 833 3.553508 GCGGTAACTGACAAGGTTGACTA 60.554 47.826 0.00 0.00 0.00 2.59
885 896 9.857656 TTAAGATAAGGCATGAGATTTTCAGAT 57.142 29.630 0.00 0.00 39.68 2.90
887 898 4.650754 AAGGCATGAGATTTTCAGATGC 57.349 40.909 0.00 0.00 39.84 3.91
913 924 5.998981 TGGATGTGATAACGGTGTAAAAGTT 59.001 36.000 0.00 0.00 0.00 2.66
961 972 3.137913 AGCTGAGCATCCTACATTCCAAT 59.862 43.478 7.39 0.00 0.00 3.16
967 978 5.128919 AGCATCCTACATTCCAATTCACTC 58.871 41.667 0.00 0.00 0.00 3.51
968 979 4.024556 GCATCCTACATTCCAATTCACTCG 60.025 45.833 0.00 0.00 0.00 4.18
969 980 3.531538 TCCTACATTCCAATTCACTCGC 58.468 45.455 0.00 0.00 0.00 5.03
970 981 2.614057 CCTACATTCCAATTCACTCGCC 59.386 50.000 0.00 0.00 0.00 5.54
972 983 1.812571 ACATTCCAATTCACTCGCCAC 59.187 47.619 0.00 0.00 0.00 5.01
973 984 1.811965 CATTCCAATTCACTCGCCACA 59.188 47.619 0.00 0.00 0.00 4.17
974 985 1.522668 TTCCAATTCACTCGCCACAG 58.477 50.000 0.00 0.00 0.00 3.66
975 986 0.684535 TCCAATTCACTCGCCACAGA 59.315 50.000 0.00 0.00 0.00 3.41
978 989 1.197721 CAATTCACTCGCCACAGAACC 59.802 52.381 0.00 0.00 0.00 3.62
980 991 2.358737 CACTCGCCACAGAACCCC 60.359 66.667 0.00 0.00 0.00 4.95
981 992 2.526873 ACTCGCCACAGAACCCCT 60.527 61.111 0.00 0.00 0.00 4.79
991 1008 2.612746 GAACCCCTGGCCCTGGTA 60.613 66.667 0.00 0.00 0.00 3.25
1013 1030 0.613012 AGGACCATGCAAGAAAGGCC 60.613 55.000 0.00 0.00 0.00 5.19
1020 1037 3.039134 CAAGAAAGGCCGCCGTTT 58.961 55.556 12.13 9.00 0.00 3.60
1037 1054 4.529219 TTGCGCGATCAGGCCGAT 62.529 61.111 12.10 9.42 36.91 4.18
1063 1081 3.268334 AGGTACTCTGTCTCCTGATCAGT 59.732 47.826 21.11 2.98 0.00 3.41
1065 1083 4.577283 GGTACTCTGTCTCCTGATCAGTAC 59.423 50.000 21.11 15.54 34.34 2.73
1066 1084 4.308526 ACTCTGTCTCCTGATCAGTACA 57.691 45.455 21.11 18.74 0.00 2.90
1074 1096 3.865446 TCCTGATCAGTACACATGCTTG 58.135 45.455 21.11 0.00 0.00 4.01
1083 1105 5.585844 TCAGTACACATGCTTGATTACCATG 59.414 40.000 6.60 0.00 41.49 3.66
1088 1110 7.408756 ACACATGCTTGATTACCATGTATTT 57.591 32.000 6.60 0.00 45.49 1.40
1093 1115 5.421693 TGCTTGATTACCATGTATTTTGGCT 59.578 36.000 0.00 0.00 37.81 4.75
1096 1118 7.334171 GCTTGATTACCATGTATTTTGGCTTTT 59.666 33.333 0.00 0.00 37.81 2.27
1110 1132 2.298610 GGCTTTTTATCTTCCTCCCGG 58.701 52.381 0.00 0.00 0.00 5.73
1116 1138 0.180406 TATCTTCCTCCCGGCTTTGC 59.820 55.000 0.00 0.00 0.00 3.68
1135 1157 6.394025 TTTGCCTTTATTTGGTTCGTTACT 57.606 33.333 0.00 0.00 0.00 2.24
1151 1173 6.312399 TCGTTACTTCAAGCATTTCACAAT 57.688 33.333 0.00 0.00 0.00 2.71
1152 1174 6.734137 TCGTTACTTCAAGCATTTCACAATT 58.266 32.000 0.00 0.00 0.00 2.32
1153 1175 7.866729 TCGTTACTTCAAGCATTTCACAATTA 58.133 30.769 0.00 0.00 0.00 1.40
1154 1176 8.346300 TCGTTACTTCAAGCATTTCACAATTAA 58.654 29.630 0.00 0.00 0.00 1.40
1157 1179 7.713764 ACTTCAAGCATTTCACAATTAAACC 57.286 32.000 0.00 0.00 0.00 3.27
1170 1205 8.801882 TCACAATTAAACCTCTAATAACTGGG 57.198 34.615 0.00 0.00 0.00 4.45
1187 1222 0.323360 GGGGTGGCTATCAGCAAACA 60.323 55.000 0.00 0.00 44.75 2.83
1193 1228 2.553602 TGGCTATCAGCAAACACACTTG 59.446 45.455 0.00 0.00 44.75 3.16
1201 1237 2.671130 CAAACACACTTGCAGGGTTT 57.329 45.000 0.00 0.00 21.60 3.27
1208 1244 2.174854 ACACTTGCAGGGTTTAACCTCT 59.825 45.455 14.27 6.69 39.34 3.69
1263 1303 4.873746 ACTTCTTTTCTGAGTGGATCGA 57.126 40.909 0.00 0.00 0.00 3.59
1268 1308 6.300354 TCTTTTCTGAGTGGATCGAAAAAC 57.700 37.500 0.00 0.00 38.60 2.43
1281 1321 8.850452 GTGGATCGAAAAACTTTATTGTTCATC 58.150 33.333 0.00 0.00 0.00 2.92
1282 1322 8.572185 TGGATCGAAAAACTTTATTGTTCATCA 58.428 29.630 0.00 0.00 0.00 3.07
1293 1333 8.873830 ACTTTATTGTTCATCAGAGTATGTTCG 58.126 33.333 0.00 0.00 0.00 3.95
1294 1334 8.996024 TTTATTGTTCATCAGAGTATGTTCGA 57.004 30.769 0.00 0.00 0.00 3.71
1296 1336 5.385509 TGTTCATCAGAGTATGTTCGACA 57.614 39.130 0.00 0.00 0.00 4.35
1301 1341 3.617284 TCAGAGTATGTTCGACAGGCTA 58.383 45.455 0.00 0.00 0.00 3.93
1310 1350 4.430007 TGTTCGACAGGCTATGAACATAC 58.570 43.478 18.64 1.60 44.01 2.39
1315 1355 2.505407 ACAGGCTATGAACATACTGGCA 59.495 45.455 13.22 0.00 0.00 4.92
1316 1356 3.054434 ACAGGCTATGAACATACTGGCAA 60.054 43.478 13.22 0.00 0.00 4.52
1317 1357 3.947196 CAGGCTATGAACATACTGGCAAA 59.053 43.478 0.00 0.00 0.00 3.68
1333 1373 5.812127 ACTGGCAAAAGTGTTCATTCTTTTC 59.188 36.000 0.00 0.00 40.43 2.29
1358 1399 3.678056 TGCAGGTAACGAAGTCAATCT 57.322 42.857 0.00 0.00 45.00 2.40
1360 1401 2.673368 GCAGGTAACGAAGTCAATCTGG 59.327 50.000 0.00 0.00 45.00 3.86
1361 1402 3.262420 CAGGTAACGAAGTCAATCTGGG 58.738 50.000 0.00 0.00 45.00 4.45
1363 1404 3.195825 AGGTAACGAAGTCAATCTGGGAG 59.804 47.826 0.00 0.00 45.00 4.30
1393 1434 3.458189 GCCGTGCTTCTACTATTGTCAT 58.542 45.455 0.00 0.00 0.00 3.06
1398 1439 5.520632 GTGCTTCTACTATTGTCATCGCTA 58.479 41.667 0.00 0.00 0.00 4.26
1418 1459 5.451937 CGCTACTCATTTCCTATGGAGTTGA 60.452 44.000 0.00 0.00 40.76 3.18
1421 1462 5.738909 ACTCATTTCCTATGGAGTTGACAG 58.261 41.667 0.00 0.00 37.31 3.51
1426 1467 3.106827 TCCTATGGAGTTGACAGCATCA 58.893 45.455 0.00 0.00 34.65 3.07
1478 1519 5.527951 CAGACATGCTCTCATTGCTAGATTT 59.472 40.000 0.00 0.00 0.00 2.17
1483 1524 6.187125 TGCTCTCATTGCTAGATTTCAAAC 57.813 37.500 0.00 0.00 0.00 2.93
1484 1525 5.124457 TGCTCTCATTGCTAGATTTCAAACC 59.876 40.000 0.00 0.00 0.00 3.27
1578 1619 2.974698 AACTGCAGCCTGACGCAC 60.975 61.111 15.27 0.00 41.38 5.34
1618 1659 2.091541 TCAATCTCACCCGCCAAAATC 58.908 47.619 0.00 0.00 0.00 2.17
1786 1827 2.156098 GGTTCAACCCTGACGCAATTA 58.844 47.619 0.00 0.00 30.04 1.40
1920 2162 3.675348 AATTTCTCTGGCATCATCCCA 57.325 42.857 0.00 0.00 0.00 4.37
1926 2168 1.848388 TCTGGCATCATCCCATCAAGT 59.152 47.619 0.00 0.00 0.00 3.16
1988 2230 3.440522 GGTAATCAGTTTGAAGGGAGCAC 59.559 47.826 0.00 0.00 0.00 4.40
2040 2282 3.271225 TGTCTCAGTTGTATCTAGGGGGA 59.729 47.826 0.00 0.00 0.00 4.81
2042 2284 4.902448 GTCTCAGTTGTATCTAGGGGGAAT 59.098 45.833 0.00 0.00 0.00 3.01
2043 2285 6.075984 GTCTCAGTTGTATCTAGGGGGAATA 58.924 44.000 0.00 0.00 0.00 1.75
2044 2286 6.209788 GTCTCAGTTGTATCTAGGGGGAATAG 59.790 46.154 0.00 0.00 0.00 1.73
2046 2288 4.020128 CAGTTGTATCTAGGGGGAATAGGC 60.020 50.000 0.00 0.00 0.00 3.93
2047 2289 4.140423 AGTTGTATCTAGGGGGAATAGGCT 60.140 45.833 0.00 0.00 0.00 4.58
2048 2290 5.077441 AGTTGTATCTAGGGGGAATAGGCTA 59.923 44.000 0.00 0.00 0.00 3.93
2049 2291 5.833413 TGTATCTAGGGGGAATAGGCTAT 57.167 43.478 0.00 0.00 0.00 2.97
2050 2292 5.778542 TGTATCTAGGGGGAATAGGCTATC 58.221 45.833 7.63 1.74 0.00 2.08
2051 2293 4.994411 ATCTAGGGGGAATAGGCTATCA 57.006 45.455 7.63 0.00 0.00 2.15
2064 2306 3.515562 AGGCTATCAGGTAGAATCCCAG 58.484 50.000 0.00 0.00 31.71 4.45
2075 2317 5.047092 AGGTAGAATCCCAGCAACAATTTTG 60.047 40.000 0.00 0.00 0.00 2.44
2123 2365 9.450807 CTTGACTTGAATTCAAATTTTCTACGT 57.549 29.630 20.82 12.01 35.15 3.57
2284 2557 5.104235 GGGGAGGCTTATTAACCTGAACTAA 60.104 44.000 0.00 0.00 36.05 2.24
2302 2575 5.416271 ACTAATTAGGACTTGCGGAGAAA 57.584 39.130 16.73 0.00 0.00 2.52
2381 2654 2.428890 AGTTATCTGGAAGTGCTCTCCG 59.571 50.000 0.00 0.00 33.76 4.63
2395 2668 4.570772 GTGCTCTCCGTATAAAGCAATCAA 59.429 41.667 0.00 0.00 45.55 2.57
2438 2711 1.021968 AGTTGGAAAGTTGTCGCCAC 58.978 50.000 0.00 0.00 0.00 5.01
2480 2753 7.360946 CGTTAGAAAGAAATTACTTGTCTGGGG 60.361 40.741 0.00 0.00 0.00 4.96
2817 3090 4.114794 ACATATCCGTTAAGCGTTGGTAC 58.885 43.478 0.00 0.00 39.32 3.34
2844 3117 3.438297 AGAATAACCATCGGTGAGACG 57.562 47.619 0.00 0.00 35.34 4.18
2856 3130 2.000447 GGTGAGACGATCCGGAAAAAG 59.000 52.381 9.01 2.40 0.00 2.27
2990 3264 0.961358 AACTCGGTCGGTCTCCTCTG 60.961 60.000 0.00 0.00 0.00 3.35
3105 3379 2.564561 TTTGGGCGGCATCATGGCTA 62.565 55.000 12.47 0.00 41.25 3.93
3162 3436 1.536662 GGTGGGTCTGGGAGTCACT 60.537 63.158 0.00 0.00 0.00 3.41
3253 3528 1.744741 TTGCGAGCGGAATGATGCA 60.745 52.632 0.00 0.00 0.00 3.96
3378 3680 3.885901 CAGATGTCGACCTCTTGGATCTA 59.114 47.826 19.23 0.00 37.04 1.98
3388 3690 0.249657 CTTGGATCTAGCCGCTGACC 60.250 60.000 2.16 1.89 0.00 4.02
3389 3691 0.687757 TTGGATCTAGCCGCTGACCT 60.688 55.000 2.16 0.00 0.00 3.85
3390 3692 1.109920 TGGATCTAGCCGCTGACCTC 61.110 60.000 2.16 0.00 0.00 3.85
3410 3713 0.535797 GAGTTCCGATCTTCCCCGTT 59.464 55.000 0.00 0.00 0.00 4.44
3411 3714 0.535797 AGTTCCGATCTTCCCCGTTC 59.464 55.000 0.00 0.00 0.00 3.95
3423 3726 0.673985 CCCCGTTCGAGATCTATGCA 59.326 55.000 0.00 0.00 0.00 3.96
3424 3727 1.068588 CCCCGTTCGAGATCTATGCAA 59.931 52.381 0.00 0.00 0.00 4.08
3447 3751 2.111043 CGTATGCCGCCCTGGATT 59.889 61.111 0.00 0.00 42.00 3.01
3611 3920 1.064621 CCATGGCGGCTTCGATTTG 59.935 57.895 11.43 0.00 35.61 2.32
3645 3954 2.743553 ACTAGGGACGGCTTAGCTTAA 58.256 47.619 3.59 0.00 0.00 1.85
3646 3955 2.429971 ACTAGGGACGGCTTAGCTTAAC 59.570 50.000 3.59 0.00 0.00 2.01
3725 4035 6.088016 TGTATTGTAGTGTACGTTTGGACT 57.912 37.500 0.00 0.00 0.00 3.85
3899 4337 6.038603 GCAGATGTTAAAGCATTACTCCATGA 59.961 38.462 0.00 0.00 0.00 3.07
3943 4381 8.461222 CCTACTTTTGCAATCAAGATGATGTAA 58.539 33.333 16.01 0.00 37.15 2.41
4264 4723 2.362120 AGGCCCACATTCAGCAGC 60.362 61.111 0.00 0.00 0.00 5.25
4266 4725 2.570181 GCCCACATTCAGCAGCAC 59.430 61.111 0.00 0.00 0.00 4.40
4357 4816 4.206375 TGCATCAAAACTCAACTCTTCCA 58.794 39.130 0.00 0.00 0.00 3.53
4359 4818 5.218139 GCATCAAAACTCAACTCTTCCAAG 58.782 41.667 0.00 0.00 0.00 3.61
4360 4819 4.900635 TCAAAACTCAACTCTTCCAAGC 57.099 40.909 0.00 0.00 0.00 4.01
4364 4823 6.260936 TCAAAACTCAACTCTTCCAAGCTAAG 59.739 38.462 0.00 0.00 0.00 2.18
4366 4825 3.326297 ACTCAACTCTTCCAAGCTAAGCT 59.674 43.478 0.00 0.00 42.56 3.74
4380 4839 5.798125 AGCTAAGCTTATGTATCTGCTCA 57.202 39.130 6.64 0.00 33.89 4.26
4406 4865 3.266510 TGCGATATAGGGAATGGATGC 57.733 47.619 0.00 0.00 0.00 3.91
4506 4965 7.826252 ACTACCAGCTAATATAGGAAATGCATG 59.174 37.037 0.00 0.00 0.00 4.06
4524 4983 5.491070 TGCATGTCATTACTAGTGCTCTTT 58.509 37.500 5.39 0.00 33.38 2.52
4534 4993 3.838317 ACTAGTGCTCTTTCATGGTACCA 59.162 43.478 18.99 18.99 0.00 3.25
4543 5002 4.473196 TCTTTCATGGTACCAGCCTCATAA 59.527 41.667 21.41 6.49 0.00 1.90
4880 5339 7.562135 TGTTAACTAGGATTATTCACTGGTCC 58.438 38.462 7.22 0.00 0.00 4.46
4881 5340 5.632034 AACTAGGATTATTCACTGGTCCC 57.368 43.478 0.00 0.00 0.00 4.46
4882 5341 4.897051 ACTAGGATTATTCACTGGTCCCT 58.103 43.478 0.00 0.00 0.00 4.20
4883 5342 5.289510 ACTAGGATTATTCACTGGTCCCTT 58.710 41.667 0.00 0.00 0.00 3.95
4884 5343 4.510167 AGGATTATTCACTGGTCCCTTG 57.490 45.455 0.00 0.00 0.00 3.61
4885 5344 3.852578 AGGATTATTCACTGGTCCCTTGT 59.147 43.478 0.00 0.00 0.00 3.16
4886 5345 3.947834 GGATTATTCACTGGTCCCTTGTG 59.052 47.826 4.45 4.45 0.00 3.33
4887 5346 2.489938 TATTCACTGGTCCCTTGTGC 57.510 50.000 5.55 0.00 0.00 4.57
5027 5486 7.601886 ACTCACATACATAATAGCTTGAGCATC 59.398 37.037 5.70 0.00 45.16 3.91
5048 5507 1.525619 GCAGTCACAGTTCAACGGTAC 59.474 52.381 0.00 0.00 0.00 3.34
5068 5527 7.775397 GGTACGATGCTAACCTGTAAATAAA 57.225 36.000 0.00 0.00 0.00 1.40
5069 5528 7.848491 GGTACGATGCTAACCTGTAAATAAAG 58.152 38.462 0.00 0.00 0.00 1.85
5070 5529 6.359480 ACGATGCTAACCTGTAAATAAAGC 57.641 37.500 0.00 0.00 0.00 3.51
5071 5530 5.878116 ACGATGCTAACCTGTAAATAAAGCA 59.122 36.000 0.00 0.00 42.14 3.91
5072 5531 6.373216 ACGATGCTAACCTGTAAATAAAGCAA 59.627 34.615 0.00 0.00 41.36 3.91
5073 5532 7.094549 ACGATGCTAACCTGTAAATAAAGCAAA 60.095 33.333 0.00 0.00 41.36 3.68
5074 5533 7.753132 CGATGCTAACCTGTAAATAAAGCAAAA 59.247 33.333 0.00 0.00 41.36 2.44
5075 5534 9.418045 GATGCTAACCTGTAAATAAAGCAAAAA 57.582 29.630 0.00 0.00 41.36 1.94
5124 5583 5.552870 AGGAAGCTAAAGTTTCAGACTGA 57.447 39.130 0.00 0.00 39.00 3.41
5575 6034 2.751166 ACGAAGTAAGAGCAGCACAT 57.249 45.000 0.00 0.00 41.94 3.21
5635 6094 7.678947 ATGATGTTGAACTGGTTCTCTAAAG 57.321 36.000 13.54 0.00 40.14 1.85
6290 6767 6.390721 AGCATAGGTTTACTGTCATATAGCG 58.609 40.000 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.170166 GCATCCCACATTCCAACTCAA 58.830 47.619 0.00 0.00 0.00 3.02
37 38 0.250381 CTCAGCCAGATGAGCATCCC 60.250 60.000 6.84 0.00 40.26 3.85
47 48 2.680352 GACGGGACCTCAGCCAGA 60.680 66.667 0.00 0.00 0.00 3.86
106 107 3.994392 GGTCACGCTTAAGATGACTTTCA 59.006 43.478 26.62 1.84 42.00 2.69
160 170 1.400494 GCGCGGTAATGGACAAGATTT 59.600 47.619 8.83 0.00 0.00 2.17
170 180 1.632046 AACTGGAACGCGCGGTAATG 61.632 55.000 35.22 21.95 0.00 1.90
171 181 0.952010 AAACTGGAACGCGCGGTAAT 60.952 50.000 35.22 17.14 0.00 1.89
232 242 3.618351 AGAACAAGCCAGGATGATCTTG 58.382 45.455 0.00 0.00 45.38 3.02
233 243 4.472833 AGTAGAACAAGCCAGGATGATCTT 59.527 41.667 9.76 0.00 39.69 2.40
234 244 4.036518 AGTAGAACAAGCCAGGATGATCT 58.963 43.478 9.50 9.50 39.69 2.75
235 245 4.376146 GAGTAGAACAAGCCAGGATGATC 58.624 47.826 0.00 0.00 39.69 2.92
236 246 3.181471 CGAGTAGAACAAGCCAGGATGAT 60.181 47.826 0.00 0.00 39.69 2.45
237 247 2.166459 CGAGTAGAACAAGCCAGGATGA 59.834 50.000 0.00 0.00 39.69 2.92
238 248 2.166459 TCGAGTAGAACAAGCCAGGATG 59.834 50.000 0.00 0.00 0.00 3.51
239 249 2.457598 TCGAGTAGAACAAGCCAGGAT 58.542 47.619 0.00 0.00 0.00 3.24
240 250 1.919240 TCGAGTAGAACAAGCCAGGA 58.081 50.000 0.00 0.00 0.00 3.86
241 251 2.969628 ATCGAGTAGAACAAGCCAGG 57.030 50.000 0.00 0.00 0.00 4.45
242 252 6.910536 AAAATATCGAGTAGAACAAGCCAG 57.089 37.500 0.00 0.00 0.00 4.85
243 253 6.876789 TGAAAAATATCGAGTAGAACAAGCCA 59.123 34.615 0.00 0.00 0.00 4.75
244 254 7.303634 TGAAAAATATCGAGTAGAACAAGCC 57.696 36.000 0.00 0.00 0.00 4.35
245 255 6.902417 GCTGAAAAATATCGAGTAGAACAAGC 59.098 38.462 0.00 0.00 0.00 4.01
246 256 7.963981 TGCTGAAAAATATCGAGTAGAACAAG 58.036 34.615 0.00 0.00 0.00 3.16
266 276 2.259917 TCTCTGTCCAATTCCTGCTGA 58.740 47.619 0.00 0.00 0.00 4.26
277 287 1.902508 GGTGTGGAAGATCTCTGTCCA 59.097 52.381 10.09 10.09 39.14 4.02
279 289 2.564947 ACTGGTGTGGAAGATCTCTGTC 59.435 50.000 0.00 0.00 0.00 3.51
302 312 1.067565 ACGCTGAGACATGTGGTAGTG 60.068 52.381 1.15 7.42 0.00 2.74
330 340 2.232452 ACGAGAATCTTGGACCAGTGAG 59.768 50.000 2.15 0.00 0.00 3.51
382 392 4.588951 AGAGAAACTAGTCATGTCCACACA 59.411 41.667 0.00 0.00 36.78 3.72
398 408 5.794894 TCTATCCAGGAAACACAGAGAAAC 58.205 41.667 0.00 0.00 0.00 2.78
404 414 7.957002 ACATATACTCTATCCAGGAAACACAG 58.043 38.462 0.00 0.00 0.00 3.66
412 422 7.068103 CCTGCTCTAACATATACTCTATCCAGG 59.932 44.444 0.00 0.00 0.00 4.45
425 435 4.286707 TCTAGTTGGCCTGCTCTAACATA 58.713 43.478 3.32 0.00 0.00 2.29
435 445 4.081420 ACATACAAGTCTCTAGTTGGCCTG 60.081 45.833 3.32 0.00 39.89 4.85
436 446 4.097418 ACATACAAGTCTCTAGTTGGCCT 58.903 43.478 3.32 0.00 39.89 5.19
448 458 6.807230 AGTTGTCAGTCGAATACATACAAGTC 59.193 38.462 0.00 0.00 35.42 3.01
449 459 6.688578 AGTTGTCAGTCGAATACATACAAGT 58.311 36.000 0.00 0.00 36.34 3.16
457 467 8.959058 CATGTTCTATAGTTGTCAGTCGAATAC 58.041 37.037 0.00 0.00 0.00 1.89
458 468 8.135529 CCATGTTCTATAGTTGTCAGTCGAATA 58.864 37.037 0.00 0.00 0.00 1.75
463 473 7.101652 TCTCCATGTTCTATAGTTGTCAGTC 57.898 40.000 0.00 0.00 0.00 3.51
465 475 6.423302 GCATCTCCATGTTCTATAGTTGTCAG 59.577 42.308 0.00 0.00 31.86 3.51
475 485 1.473257 GCACGGCATCTCCATGTTCTA 60.473 52.381 0.00 0.00 28.94 2.10
479 489 2.124570 GGCACGGCATCTCCATGT 60.125 61.111 0.00 0.00 28.94 3.21
611 621 2.567615 AGAGGTGTCTTGCCGTAGAAAT 59.432 45.455 0.00 0.00 0.00 2.17
619 629 0.317479 ACGTGTAGAGGTGTCTTGCC 59.683 55.000 0.00 0.00 33.84 4.52
620 630 2.030540 TGTACGTGTAGAGGTGTCTTGC 60.031 50.000 0.00 0.00 33.84 4.01
637 647 3.571571 TGACATGTCTGCGTTAGTGTAC 58.428 45.455 25.55 0.00 0.00 2.90
640 650 3.305361 CAGATGACATGTCTGCGTTAGTG 59.695 47.826 25.55 8.73 36.95 2.74
650 660 4.047822 GAGAATCCGACAGATGACATGTC 58.952 47.826 19.27 19.27 42.94 3.06
693 704 2.180131 GAGTGCTGCCGCTTGTTCTG 62.180 60.000 0.70 0.00 36.97 3.02
709 720 1.698506 CCCAGCCTCGAATCTAGAGT 58.301 55.000 0.00 0.00 34.08 3.24
749 760 1.963338 GCTGTCGCTGCCTGAGTTT 60.963 57.895 0.00 0.00 0.00 2.66
779 790 3.615496 GCGCGTTCTAGTTTTTATCTCCA 59.385 43.478 8.43 0.00 0.00 3.86
793 804 1.731969 GTCAGTTACCGCGCGTTCT 60.732 57.895 29.95 17.11 0.00 3.01
797 808 2.726691 CCTTGTCAGTTACCGCGCG 61.727 63.158 25.67 25.67 0.00 6.86
822 833 1.375326 GCAAAGACCTCCTCGGGTT 59.625 57.895 0.00 0.00 40.06 4.11
825 836 1.376037 GGTGCAAAGACCTCCTCGG 60.376 63.158 0.00 0.00 39.35 4.63
858 869 9.857656 TCTGAAAATCTCATGCCTTATCTTAAT 57.142 29.630 0.00 0.00 32.14 1.40
885 896 0.248012 ACCGTTATCACATCCACGCA 59.752 50.000 0.00 0.00 0.00 5.24
887 898 2.004583 ACACCGTTATCACATCCACG 57.995 50.000 0.00 0.00 0.00 4.94
961 972 1.070786 GGGTTCTGTGGCGAGTGAA 59.929 57.895 0.00 0.00 0.00 3.18
969 980 4.366684 GGGCCAGGGGTTCTGTGG 62.367 72.222 4.39 0.00 41.83 4.17
970 981 3.260100 AGGGCCAGGGGTTCTGTG 61.260 66.667 6.18 0.00 41.83 3.66
972 983 4.052518 CCAGGGCCAGGGGTTCTG 62.053 72.222 7.16 0.00 43.00 3.02
973 984 2.723334 TTACCAGGGCCAGGGGTTCT 62.723 60.000 20.20 0.00 36.14 3.01
974 985 1.795951 TTTACCAGGGCCAGGGGTTC 61.796 60.000 20.20 0.00 36.14 3.62
975 986 1.373044 TTTTACCAGGGCCAGGGGTT 61.373 55.000 20.20 0.43 36.14 4.11
978 989 1.000359 CCTTTTACCAGGGCCAGGG 60.000 63.158 20.20 16.03 0.00 4.45
980 991 3.266240 GTCCTTTTACCAGGGCCAG 57.734 57.895 6.18 0.00 31.59 4.85
991 1008 2.037641 GCCTTTCTTGCATGGTCCTTTT 59.962 45.455 0.00 0.00 0.00 2.27
1020 1037 2.636778 TTATCGGCCTGATCGCGCAA 62.637 55.000 8.75 0.00 38.57 4.85
1037 1054 5.191921 TGATCAGGAGACAGAGTACCTCTTA 59.808 44.000 0.00 0.00 38.99 2.10
1056 1074 5.817296 GGTAATCAAGCATGTGTACTGATCA 59.183 40.000 0.00 0.00 0.00 2.92
1083 1105 7.265673 GGGAGGAAGATAAAAAGCCAAAATAC 58.734 38.462 0.00 0.00 0.00 1.89
1084 1106 6.096282 CGGGAGGAAGATAAAAAGCCAAAATA 59.904 38.462 0.00 0.00 0.00 1.40
1088 1110 3.352648 CGGGAGGAAGATAAAAAGCCAA 58.647 45.455 0.00 0.00 0.00 4.52
1110 1132 3.649073 ACGAACCAAATAAAGGCAAAGC 58.351 40.909 0.00 0.00 0.00 3.51
1116 1138 6.581166 GCTTGAAGTAACGAACCAAATAAAGG 59.419 38.462 0.00 0.00 0.00 3.11
1124 1146 4.576873 TGAAATGCTTGAAGTAACGAACCA 59.423 37.500 0.00 0.00 0.00 3.67
1126 1148 5.507077 TGTGAAATGCTTGAAGTAACGAAC 58.493 37.500 0.00 0.00 0.00 3.95
1128 1150 5.743026 TTGTGAAATGCTTGAAGTAACGA 57.257 34.783 0.00 0.00 0.00 3.85
1135 1157 7.725251 AGAGGTTTAATTGTGAAATGCTTGAA 58.275 30.769 0.00 0.00 0.00 2.69
1151 1173 5.574120 GCCACCCCAGTTATTAGAGGTTTAA 60.574 44.000 0.00 0.00 0.00 1.52
1152 1174 4.080186 GCCACCCCAGTTATTAGAGGTTTA 60.080 45.833 0.00 0.00 0.00 2.01
1153 1175 3.308904 GCCACCCCAGTTATTAGAGGTTT 60.309 47.826 0.00 0.00 0.00 3.27
1154 1176 2.241430 GCCACCCCAGTTATTAGAGGTT 59.759 50.000 0.00 0.00 0.00 3.50
1156 1178 2.127708 AGCCACCCCAGTTATTAGAGG 58.872 52.381 0.00 0.00 0.00 3.69
1157 1179 4.593206 TGATAGCCACCCCAGTTATTAGAG 59.407 45.833 0.00 0.00 0.00 2.43
1170 1205 1.200020 GTGTGTTTGCTGATAGCCACC 59.800 52.381 0.00 0.00 41.51 4.61
1187 1222 2.174854 AGAGGTTAAACCCTGCAAGTGT 59.825 45.455 0.00 0.00 39.75 3.55
1233 1269 9.490379 TCCACTCAGAAAAGAAGTAAAGAATAC 57.510 33.333 0.00 0.00 0.00 1.89
1268 1308 9.087424 TCGAACATACTCTGATGAACAATAAAG 57.913 33.333 0.00 0.00 0.00 1.85
1281 1321 2.949451 AGCCTGTCGAACATACTCTG 57.051 50.000 0.00 0.00 0.00 3.35
1282 1322 4.207955 TCATAGCCTGTCGAACATACTCT 58.792 43.478 0.00 0.00 0.00 3.24
1293 1333 3.134458 GCCAGTATGTTCATAGCCTGTC 58.866 50.000 8.54 0.00 0.00 3.51
1294 1334 2.505407 TGCCAGTATGTTCATAGCCTGT 59.495 45.455 8.54 0.00 0.00 4.00
1296 1336 3.931907 TTGCCAGTATGTTCATAGCCT 57.068 42.857 0.00 0.00 0.00 4.58
1301 1341 5.301551 TGAACACTTTTGCCAGTATGTTCAT 59.698 36.000 15.08 0.00 35.95 2.57
1310 1350 5.811613 TGAAAAGAATGAACACTTTTGCCAG 59.188 36.000 0.00 0.00 43.36 4.85
1333 1373 2.869801 TGACTTCGTTACCTGCAAAGTG 59.130 45.455 2.54 0.00 30.68 3.16
1352 1393 2.368439 CCATTTTCGCTCCCAGATTGA 58.632 47.619 0.00 0.00 0.00 2.57
1358 1399 2.749839 CGGCCATTTTCGCTCCCA 60.750 61.111 2.24 0.00 0.00 4.37
1360 1401 2.485122 CACGGCCATTTTCGCTCC 59.515 61.111 2.24 0.00 0.00 4.70
1361 1402 2.200170 AAGCACGGCCATTTTCGCTC 62.200 55.000 2.24 0.00 0.00 5.03
1363 1404 1.801512 GAAGCACGGCCATTTTCGC 60.802 57.895 2.24 0.00 0.00 4.70
1393 1434 4.215908 ACTCCATAGGAAATGAGTAGCGA 58.784 43.478 0.00 0.00 0.00 4.93
1398 1439 5.738909 CTGTCAACTCCATAGGAAATGAGT 58.261 41.667 0.00 0.00 30.49 3.41
1426 1467 1.002134 CAGGGACCGTGGAGCATTT 60.002 57.895 6.27 0.00 0.00 2.32
1455 1496 4.959560 ATCTAGCAATGAGAGCATGTCT 57.040 40.909 0.00 0.00 38.71 3.41
1467 1508 2.427095 GGCCGGTTTGAAATCTAGCAAT 59.573 45.455 1.90 0.00 0.00 3.56
1478 1519 0.251564 ATTGGTGATGGCCGGTTTGA 60.252 50.000 1.90 0.00 0.00 2.69
1483 1524 1.174712 GGATCATTGGTGATGGCCGG 61.175 60.000 0.00 0.00 44.96 6.13
1484 1525 1.509644 CGGATCATTGGTGATGGCCG 61.510 60.000 0.00 4.76 44.96 6.13
1578 1619 2.590575 ACCGTGACACGCCCTTTG 60.591 61.111 22.46 10.05 40.91 2.77
1786 1827 1.073897 GGAGGCTGGAGCAGTTTGT 59.926 57.895 0.00 0.00 44.36 2.83
1907 2149 2.158652 AGACTTGATGGGATGATGCCAG 60.159 50.000 12.23 0.00 42.59 4.85
1988 2230 4.785453 GCCCAAGCTGTCCCGGAG 62.785 72.222 0.73 0.00 35.50 4.63
2040 2282 5.665701 TGGGATTCTACCTGATAGCCTATT 58.334 41.667 0.00 0.00 0.00 1.73
2042 2284 4.678256 CTGGGATTCTACCTGATAGCCTA 58.322 47.826 0.00 0.00 0.00 3.93
2043 2285 3.515562 CTGGGATTCTACCTGATAGCCT 58.484 50.000 0.00 0.00 0.00 4.58
2044 2286 2.027653 GCTGGGATTCTACCTGATAGCC 60.028 54.545 0.00 0.00 0.00 3.93
2046 2288 4.101585 TGTTGCTGGGATTCTACCTGATAG 59.898 45.833 0.00 0.00 0.00 2.08
2047 2289 4.037222 TGTTGCTGGGATTCTACCTGATA 58.963 43.478 0.00 0.00 0.00 2.15
2048 2290 2.846206 TGTTGCTGGGATTCTACCTGAT 59.154 45.455 0.00 0.00 0.00 2.90
2049 2291 2.265367 TGTTGCTGGGATTCTACCTGA 58.735 47.619 0.00 0.00 0.00 3.86
2050 2292 2.787473 TGTTGCTGGGATTCTACCTG 57.213 50.000 0.00 0.00 0.00 4.00
2051 2293 4.322057 AATTGTTGCTGGGATTCTACCT 57.678 40.909 0.00 0.00 0.00 3.08
2064 2306 6.018507 AGAGCAGAATTGTTCAAAATTGTTGC 60.019 34.615 0.00 0.00 37.04 4.17
2284 2557 3.440522 GCTTTTTCTCCGCAAGTCCTAAT 59.559 43.478 0.00 0.00 0.00 1.73
2302 2575 3.080319 GCTGTCATTCTCTTCCAGCTTT 58.920 45.455 0.00 0.00 43.89 3.51
2359 2632 3.632604 CGGAGAGCACTTCCAGATAACTA 59.367 47.826 2.68 0.00 0.00 2.24
2381 2654 8.131731 GGATCCTTTCAGTTGATTGCTTTATAC 58.868 37.037 3.84 0.00 0.00 1.47
2395 2668 4.946160 TTTGGGTATGGATCCTTTCAGT 57.054 40.909 14.23 0.00 0.00 3.41
2438 2711 4.733850 TCTAACGATAGATATGCAAGGCG 58.266 43.478 0.00 0.00 41.38 5.52
2480 2753 3.031736 TCCCTATACTGTCTGGAACTGC 58.968 50.000 0.00 0.00 0.00 4.40
2532 2805 3.181449 TGGACCGGAGAGATTGTTTTGAA 60.181 43.478 9.46 0.00 0.00 2.69
2584 2857 2.093973 TGCAAGAGCTAACACTCCTAGC 60.094 50.000 0.00 0.00 41.80 3.42
2610 2883 1.132453 GAATCGGCCCAGCAAAGTTAC 59.868 52.381 0.00 0.00 0.00 2.50
2817 3090 5.775686 TCACCGATGGTTATTCTATTACCG 58.224 41.667 0.00 0.00 31.02 4.02
2870 3144 2.358247 CCTTGTTGGGGGACGACG 60.358 66.667 0.00 0.00 36.17 5.12
2882 3156 1.078848 GATGCCAGAGTCGCCTTGT 60.079 57.895 0.00 0.00 0.00 3.16
3054 3328 0.976641 TCGCCATCACCTCAAAGAGT 59.023 50.000 0.00 0.00 0.00 3.24
3060 3334 2.265739 GCAGTCGCCATCACCTCA 59.734 61.111 0.00 0.00 0.00 3.86
3105 3379 2.046892 CGTGTAGCCTGCAAGCCT 60.047 61.111 3.00 0.00 0.00 4.58
3140 3414 1.765597 GACTCCCAGACCCACCGTTT 61.766 60.000 0.00 0.00 0.00 3.60
3253 3528 1.609061 CGGACAAAGGTCAGTGATGCT 60.609 52.381 0.00 0.00 46.17 3.79
3343 3645 2.354103 CGACATCTGGCAGAAAGAGGAA 60.354 50.000 22.84 0.00 0.00 3.36
3346 3648 2.266554 GTCGACATCTGGCAGAAAGAG 58.733 52.381 22.84 13.83 0.00 2.85
3378 3680 2.992114 AACTCGAGGTCAGCGGCT 60.992 61.111 18.41 0.00 0.00 5.52
3390 3692 1.065928 CGGGGAAGATCGGAACTCG 59.934 63.158 0.00 0.00 40.90 4.18
3410 3713 2.802247 CGCCAATTTGCATAGATCTCGA 59.198 45.455 0.00 0.00 0.00 4.04
3411 3714 2.545526 ACGCCAATTTGCATAGATCTCG 59.454 45.455 0.00 0.00 0.00 4.04
3531 3838 2.747022 TGTCCCATGACACCGGTG 59.253 61.111 32.83 32.83 46.40 4.94
3611 3920 2.504175 TCCCTAGTTGGTTAGGTCATGC 59.496 50.000 0.00 0.00 38.86 4.06
3645 3954 0.613777 AATCGCCTCTCGGAAAAGGT 59.386 50.000 7.66 0.00 39.05 3.50
3646 3955 1.009829 CAATCGCCTCTCGGAAAAGG 58.990 55.000 2.46 2.46 39.05 3.11
3899 4337 5.953571 AGTAGGGACCTGATTTTCAGTTTT 58.046 37.500 0.00 0.00 42.80 2.43
3943 4381 6.719370 TCATGGGTGTTTAGCAGTTTAATCTT 59.281 34.615 0.00 0.00 0.00 2.40
3993 4452 4.678509 TCTTGATTGCGGTTCACAATAC 57.321 40.909 0.00 0.00 37.85 1.89
4264 4723 2.821378 TGCAGGATGAAATGGTGAAGTG 59.179 45.455 0.00 0.00 39.69 3.16
4266 4725 4.524316 TTTGCAGGATGAAATGGTGAAG 57.476 40.909 0.00 0.00 39.69 3.02
4359 4818 8.539770 TTTATGAGCAGATACATAAGCTTAGC 57.460 34.615 12.54 7.82 39.20 3.09
4364 4823 6.740002 CGCATTTTATGAGCAGATACATAAGC 59.260 38.462 0.00 0.00 39.20 3.09
4366 4825 7.961325 TCGCATTTTATGAGCAGATACATAA 57.039 32.000 0.00 0.00 37.25 1.90
4367 4826 9.822185 ATATCGCATTTTATGAGCAGATACATA 57.178 29.630 0.00 0.00 31.76 2.29
4368 4827 8.728337 ATATCGCATTTTATGAGCAGATACAT 57.272 30.769 0.00 0.00 31.76 2.29
4369 4828 9.305925 CTATATCGCATTTTATGAGCAGATACA 57.694 33.333 0.00 0.00 31.76 2.29
4370 4829 8.759641 CCTATATCGCATTTTATGAGCAGATAC 58.240 37.037 0.00 0.00 31.76 2.24
4371 4830 7.928167 CCCTATATCGCATTTTATGAGCAGATA 59.072 37.037 0.00 0.00 32.67 1.98
4372 4831 6.765036 CCCTATATCGCATTTTATGAGCAGAT 59.235 38.462 0.00 0.00 0.00 2.90
4373 4832 6.070824 TCCCTATATCGCATTTTATGAGCAGA 60.071 38.462 0.00 0.00 0.00 4.26
4374 4833 6.108687 TCCCTATATCGCATTTTATGAGCAG 58.891 40.000 0.00 0.00 0.00 4.24
4375 4834 6.048732 TCCCTATATCGCATTTTATGAGCA 57.951 37.500 0.00 0.00 0.00 4.26
4376 4835 6.985188 TTCCCTATATCGCATTTTATGAGC 57.015 37.500 0.00 0.00 0.00 4.26
4377 4836 7.770433 TCCATTCCCTATATCGCATTTTATGAG 59.230 37.037 0.00 0.00 0.00 2.90
4378 4837 7.629157 TCCATTCCCTATATCGCATTTTATGA 58.371 34.615 0.00 0.00 0.00 2.15
4379 4838 7.864108 TCCATTCCCTATATCGCATTTTATG 57.136 36.000 0.00 0.00 0.00 1.90
4380 4839 7.013655 GCATCCATTCCCTATATCGCATTTTAT 59.986 37.037 0.00 0.00 0.00 1.40
4406 4865 4.665833 TTAGGATGTTATGTGACGGGAG 57.334 45.455 0.00 0.00 0.00 4.30
4506 4965 6.109359 ACCATGAAAGAGCACTAGTAATGAC 58.891 40.000 0.00 0.00 0.00 3.06
4524 4983 5.221843 GGTATTTATGAGGCTGGTACCATGA 60.222 44.000 16.75 0.00 32.41 3.07
4534 4993 5.302823 GCTTTTGGATGGTATTTATGAGGCT 59.697 40.000 0.00 0.00 0.00 4.58
4543 5002 3.269381 TCAGGAGGCTTTTGGATGGTATT 59.731 43.478 0.00 0.00 0.00 1.89
4699 5158 2.060326 TAGGTTTCGAGCACAAGACG 57.940 50.000 0.00 0.00 0.00 4.18
5027 5486 1.151777 ACCGTTGAACTGTGACTGCG 61.152 55.000 0.00 0.00 0.00 5.18
5048 5507 6.358118 TGCTTTATTTACAGGTTAGCATCG 57.642 37.500 0.00 0.00 32.73 3.84
5049 5508 8.980143 TTTTGCTTTATTTACAGGTTAGCATC 57.020 30.769 0.00 0.00 37.06 3.91
5078 5537 9.135189 CCTATTTCTCAAAATCAATCATGGGTA 57.865 33.333 0.00 0.00 36.49 3.69
5079 5538 7.840716 TCCTATTTCTCAAAATCAATCATGGGT 59.159 33.333 0.00 0.00 36.49 4.51
5080 5539 8.241497 TCCTATTTCTCAAAATCAATCATGGG 57.759 34.615 0.00 0.00 36.49 4.00
5081 5540 9.745880 CTTCCTATTTCTCAAAATCAATCATGG 57.254 33.333 0.00 0.00 36.49 3.66
5082 5541 9.245962 GCTTCCTATTTCTCAAAATCAATCATG 57.754 33.333 0.00 0.00 36.49 3.07
5083 5542 9.198475 AGCTTCCTATTTCTCAAAATCAATCAT 57.802 29.630 0.00 0.00 36.49 2.45
5124 5583 5.716228 TCTGAAATAGCATCACAAACCCATT 59.284 36.000 0.00 0.00 0.00 3.16
5265 5724 4.734398 ATTTGTTTGGTGAGTTTGCAGA 57.266 36.364 0.00 0.00 0.00 4.26
5575 6034 9.964354 TTCTCTAAGATGATTTTGAAAGGATGA 57.036 29.630 0.00 0.00 0.00 2.92
5635 6094 6.367969 GGTATATGATTGGTTCCATACGTCAC 59.632 42.308 0.00 0.00 0.00 3.67
5725 6184 2.231478 TCTTCTCTTGGCTGAGGTTACG 59.769 50.000 7.90 0.00 34.98 3.18
5821 6280 6.645790 ATCCATCCTTTTATGATGTTCTGC 57.354 37.500 0.00 0.00 38.32 4.26
6290 6767 3.676093 CCACCACTAAAACCTCTTCTCC 58.324 50.000 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.