Multiple sequence alignment - TraesCS3A01G534200

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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 TraesCS3A01G534200 chr3A 100.000 3146 0 0 1 3146 746261554 746264699 0.000000e+00 5810.0
1 TraesCS3A01G534200 chr3A 79.904 209 35 4 1289 1490 746289884 746290092 2.530000e-31 147.0
2 TraesCS3A01G534200 chr3B 94.706 1530 70 6 1329 2848 829114257 829115785 0.000000e+00 2366.0
3 TraesCS3A01G534200 chr3B 89.749 478 22 10 1 458 829113147 829113617 1.260000e-163 586.0
4 TraesCS3A01G534200 chr3B 79.634 766 61 45 426 1181 829113525 829114205 2.210000e-126 462.0
5 TraesCS3A01G534200 chr3B 75.422 651 123 26 2309 2934 829124064 829124702 6.640000e-72 281.0
6 TraesCS3A01G534200 chr3B 80.096 417 48 16 1650 2036 829123143 829123554 8.590000e-71 278.0
7 TraesCS3A01G534200 chr3B 98.261 115 2 0 3032 3146 829115785 829115899 5.320000e-48 202.0
8 TraesCS3A01G534200 chr3B 87.500 112 8 3 1682 1790 829234008 829234116 1.180000e-24 124.0
9 TraesCS3A01G534200 chr3B 92.593 54 4 0 1220 1273 829114202 829114255 9.360000e-11 78.7
10 TraesCS3A01G534200 chr3D 96.995 832 24 1 2315 3146 611409605 611410435 0.000000e+00 1397.0
11 TraesCS3A01G534200 chr3D 95.953 766 25 5 1304 2065 611408595 611409358 0.000000e+00 1238.0
12 TraesCS3A01G534200 chr3D 94.783 460 24 0 1 460 611407474 611407933 0.000000e+00 717.0
13 TraesCS3A01G534200 chr3D 85.154 714 51 21 473 1181 611407883 611408546 0.000000e+00 680.0
14 TraesCS3A01G534200 chr3D 77.402 916 127 39 1634 2496 611412133 611413021 3.670000e-129 472.0
15 TraesCS3A01G534200 chr3D 97.154 246 5 2 2030 2274 611409360 611409604 6.280000e-112 414.0
16 TraesCS3A01G534200 chr3D 94.444 54 3 0 1220 1273 611408543 611408596 2.010000e-12 84.2
17 TraesCS3A01G534200 chr6D 84.746 354 35 15 1 349 16529369 16529030 1.400000e-88 337.0
18 TraesCS3A01G534200 chr6D 83.377 379 40 15 1 373 24001724 24002085 2.340000e-86 329.0
19 TraesCS3A01G534200 chr6D 91.071 224 19 1 126 349 16389826 16389604 5.100000e-78 302.0
20 TraesCS3A01G534200 chr6D 91.204 216 19 0 134 349 16306965 16306750 8.530000e-76 294.0
21 TraesCS3A01G534200 chr6D 93.023 43 1 2 1522 1564 267129850 267129810 9.420000e-06 62.1
22 TraesCS3A01G534200 chr6B 83.554 377 44 14 1 373 38877885 38878247 1.400000e-88 337.0
23 TraesCS3A01G534200 chr6B 83.476 351 41 14 1 349 28256479 28256144 8.470000e-81 311.0
24 TraesCS3A01G534200 chr6B 83.286 353 39 14 1 349 59232949 59233285 1.100000e-79 307.0
25 TraesCS3A01G534200 chr6B 83.191 351 43 11 1 349 59295095 59295431 1.100000e-79 307.0
26 TraesCS3A01G534200 chr6B 83.099 355 40 15 1 349 28517181 28516841 3.940000e-79 305.0
27 TraesCS3A01G534200 chr6B 82.303 356 46 12 1 349 58812547 58812892 3.070000e-75 292.0
28 TraesCS3A01G534200 chr1A 90.351 228 20 2 133 359 21023099 21023325 6.600000e-77 298.0
29 TraesCS3A01G534200 chr7D 82.883 111 19 0 1355 1465 52623761 52623871 2.000000e-17 100.0
30 TraesCS3A01G534200 chr2D 81.982 111 20 0 1358 1468 56184618 56184508 9.290000e-16 95.3
31 TraesCS3A01G534200 chr5D 81.081 111 21 0 1355 1465 213079865 213079975 4.320000e-14 89.8
32 TraesCS3A01G534200 chr5D 81.522 92 15 2 1522 1613 213080067 213080156 1.210000e-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 TraesCS3A01G534200 chr3A 746261554 746264699 3145 False 5810.00 5810 100.000000 1 3146 1 chr3A.!!$F1 3145
1 TraesCS3A01G534200 chr3B 829113147 829115899 2752 False 738.94 2366 90.988600 1 3146 5 chr3B.!!$F2 3145
2 TraesCS3A01G534200 chr3B 829123143 829124702 1559 False 279.50 281 77.759000 1650 2934 2 chr3B.!!$F3 1284
3 TraesCS3A01G534200 chr3D 611407474 611413021 5547 False 714.60 1397 91.697857 1 3146 7 chr3D.!!$F1 3145

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
652 672 0.038159 GTCTGGAGTCCGAACTGGTG 60.038 60.0 4.3 0.0 39.52 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 2327 0.036765 GTACATGTCCAGGGCACGAA 60.037 55.0 0.0 0.0 0.0 3.85 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
52 57 0.393402 GGTAACCACCCAACCGATCC 60.393 60.000 0.00 0.00 39.11 3.36
60 65 2.579201 CAACCGATCCCGTGCTCT 59.421 61.111 0.00 0.00 0.00 4.09
67 72 0.179097 GATCCCGTGCTCTGTTCCTC 60.179 60.000 0.00 0.00 0.00 3.71
69 74 2.266055 CCGTGCTCTGTTCCTCCC 59.734 66.667 0.00 0.00 0.00 4.30
72 77 1.599576 GTGCTCTGTTCCTCCCCTC 59.400 63.158 0.00 0.00 0.00 4.30
102 107 4.803426 CTCGCCGGAGTGCTGACC 62.803 72.222 5.05 0.00 35.48 4.02
130 140 3.772572 TGTCTCGGTTCTTTGGATGGATA 59.227 43.478 0.00 0.00 0.00 2.59
131 141 4.224147 TGTCTCGGTTCTTTGGATGGATAA 59.776 41.667 0.00 0.00 0.00 1.75
427 446 2.809601 CCGCCGACAAGAAGACCG 60.810 66.667 0.00 0.00 0.00 4.79
445 464 4.735132 CCGCCGCCGACAAGAAGA 62.735 66.667 0.00 0.00 36.29 2.87
446 465 3.479269 CGCCGCCGACAAGAAGAC 61.479 66.667 0.00 0.00 36.29 3.01
447 466 3.119096 GCCGCCGACAAGAAGACC 61.119 66.667 0.00 0.00 0.00 3.85
448 467 2.809601 CCGCCGACAAGAAGACCG 60.810 66.667 0.00 0.00 0.00 4.79
449 468 3.479269 CGCCGACAAGAAGACCGC 61.479 66.667 0.00 0.00 0.00 5.68
450 469 3.119096 GCCGACAAGAAGACCGCC 61.119 66.667 0.00 0.00 0.00 6.13
488 507 2.383527 CCGCCGCTGACAAGAAGAC 61.384 63.158 0.00 0.00 0.00 3.01
489 508 2.383527 CGCCGCTGACAAGAAGACC 61.384 63.158 0.00 0.00 0.00 3.85
490 509 2.383527 GCCGCTGACAAGAAGACCG 61.384 63.158 0.00 0.00 0.00 4.79
491 510 2.383527 CCGCTGACAAGAAGACCGC 61.384 63.158 0.00 0.00 0.00 5.68
492 511 2.383527 CGCTGACAAGAAGACCGCC 61.384 63.158 0.00 0.00 0.00 6.13
493 512 2.383527 GCTGACAAGAAGACCGCCG 61.384 63.158 0.00 0.00 0.00 6.46
494 513 2.357034 TGACAAGAAGACCGCCGC 60.357 61.111 0.00 0.00 0.00 6.53
495 514 3.119096 GACAAGAAGACCGCCGCC 61.119 66.667 0.00 0.00 0.00 6.13
551 570 4.883300 CGCCGCCGACGAGTAGAC 62.883 72.222 0.00 0.00 43.93 2.59
557 576 2.044555 CCGACGAGTAGACAGGGCA 61.045 63.158 0.00 0.00 0.00 5.36
652 672 0.038159 GTCTGGAGTCCGAACTGGTG 60.038 60.000 4.30 0.00 39.52 4.17
667 687 1.132643 CTGGTGGTAGTCTGTAGCGTC 59.867 57.143 0.00 0.00 0.00 5.19
668 688 0.098376 GGTGGTAGTCTGTAGCGTCG 59.902 60.000 0.00 0.00 0.00 5.12
669 689 1.081892 GTGGTAGTCTGTAGCGTCGA 58.918 55.000 0.00 0.00 0.00 4.20
670 690 1.669779 GTGGTAGTCTGTAGCGTCGAT 59.330 52.381 0.00 0.00 0.00 3.59
671 691 2.097142 GTGGTAGTCTGTAGCGTCGATT 59.903 50.000 0.00 0.00 0.00 3.34
672 692 2.096980 TGGTAGTCTGTAGCGTCGATTG 59.903 50.000 0.00 0.00 0.00 2.67
673 693 2.353889 GGTAGTCTGTAGCGTCGATTGA 59.646 50.000 0.00 0.00 0.00 2.57
674 694 3.003482 GGTAGTCTGTAGCGTCGATTGAT 59.997 47.826 0.00 0.00 0.00 2.57
675 695 3.341857 AGTCTGTAGCGTCGATTGATC 57.658 47.619 0.00 0.00 0.00 2.92
676 696 2.946329 AGTCTGTAGCGTCGATTGATCT 59.054 45.455 0.00 0.00 0.00 2.75
677 697 3.378742 AGTCTGTAGCGTCGATTGATCTT 59.621 43.478 0.00 0.00 0.00 2.40
678 698 3.483922 GTCTGTAGCGTCGATTGATCTTG 59.516 47.826 0.00 0.00 0.00 3.02
679 699 3.377172 TCTGTAGCGTCGATTGATCTTGA 59.623 43.478 0.00 0.00 0.00 3.02
680 700 4.104696 TGTAGCGTCGATTGATCTTGAA 57.895 40.909 0.00 0.00 0.00 2.69
681 701 4.682787 TGTAGCGTCGATTGATCTTGAAT 58.317 39.130 0.00 0.00 0.00 2.57
682 702 4.740205 TGTAGCGTCGATTGATCTTGAATC 59.260 41.667 0.00 0.00 0.00 2.52
683 703 3.785486 AGCGTCGATTGATCTTGAATCA 58.215 40.909 0.00 0.00 31.26 2.57
684 704 3.553511 AGCGTCGATTGATCTTGAATCAC 59.446 43.478 0.00 0.00 31.26 3.06
685 705 3.553511 GCGTCGATTGATCTTGAATCACT 59.446 43.478 0.00 0.00 31.26 3.41
686 706 4.033358 GCGTCGATTGATCTTGAATCACTT 59.967 41.667 0.00 0.00 31.26 3.16
687 707 5.722237 CGTCGATTGATCTTGAATCACTTC 58.278 41.667 0.00 0.00 31.26 3.01
688 708 5.518128 CGTCGATTGATCTTGAATCACTTCT 59.482 40.000 0.00 0.00 31.26 2.85
689 709 6.507614 CGTCGATTGATCTTGAATCACTTCTG 60.508 42.308 0.00 0.00 31.26 3.02
690 710 6.312426 GTCGATTGATCTTGAATCACTTCTGT 59.688 38.462 0.00 0.00 31.26 3.41
691 711 7.489435 GTCGATTGATCTTGAATCACTTCTGTA 59.511 37.037 0.00 0.00 31.26 2.74
692 712 7.704047 TCGATTGATCTTGAATCACTTCTGTAG 59.296 37.037 0.00 0.00 31.26 2.74
693 713 6.974932 TTGATCTTGAATCACTTCTGTAGC 57.025 37.500 0.00 0.00 32.29 3.58
694 714 5.105063 TGATCTTGAATCACTTCTGTAGCG 58.895 41.667 0.00 0.00 32.29 4.26
695 715 4.521130 TCTTGAATCACTTCTGTAGCGT 57.479 40.909 0.00 0.00 32.29 5.07
743 763 2.807967 TGAAGCTGGAAACTTGATCGTG 59.192 45.455 0.00 0.00 0.00 4.35
761 781 4.331968 TCGTGTAGCCAATTCCAATCTTT 58.668 39.130 0.00 0.00 0.00 2.52
773 793 5.782893 TTCCAATCTTTTCCGTGTCAATT 57.217 34.783 0.00 0.00 0.00 2.32
775 795 6.155475 TCCAATCTTTTCCGTGTCAATTTT 57.845 33.333 0.00 0.00 0.00 1.82
781 801 3.422417 TTCCGTGTCAATTTTGCGAAA 57.578 38.095 0.53 0.53 0.00 3.46
788 808 4.670175 GTGTCAATTTTGCGAAATTTTGCC 59.330 37.500 24.46 9.40 42.14 4.52
798 818 1.798223 GAAATTTTGCCGGTTCTTGCC 59.202 47.619 1.90 0.00 0.00 4.52
819 845 1.348064 TGATCCCCTTGTTCGTCTGT 58.652 50.000 0.00 0.00 0.00 3.41
830 856 5.412526 TTGTTCGTCTGTACATTTGTTCC 57.587 39.130 0.00 0.00 0.00 3.62
842 868 4.702831 ACATTTGTTCCCACAATTTCACC 58.297 39.130 0.00 0.00 42.66 4.02
843 869 4.408596 ACATTTGTTCCCACAATTTCACCT 59.591 37.500 0.00 0.00 42.66 4.00
889 915 3.826524 TGGCAATAACTTGGTTCAGTGA 58.173 40.909 0.00 0.00 32.72 3.41
894 920 4.706842 ATAACTTGGTTCAGTGAGGTGT 57.293 40.909 0.00 0.00 0.00 4.16
899 925 1.283613 TGGTTCAGTGAGGTGTGGTTT 59.716 47.619 0.00 0.00 0.00 3.27
912 938 6.378564 TGAGGTGTGGTTTGTGAAATTTCTTA 59.621 34.615 18.64 5.43 0.00 2.10
944 970 2.628187 ATCTGCGGGGAAGGGGATCT 62.628 60.000 0.00 0.00 0.00 2.75
945 971 3.089874 TGCGGGGAAGGGGATCTG 61.090 66.667 0.00 0.00 0.00 2.90
949 975 2.376842 GGGAAGGGGATCTGGGGA 59.623 66.667 0.00 0.00 0.00 4.81
950 976 1.072616 GGGAAGGGGATCTGGGGAT 60.073 63.158 0.00 0.00 34.45 3.85
991 1018 2.236766 TCTAGGGTTCGTAGCATAGGC 58.763 52.381 11.98 0.00 36.92 3.93
1063 1090 2.753043 CGGGCAAGCTGCTGGATT 60.753 61.111 8.57 0.00 44.28 3.01
1087 1114 2.815647 CCGCTTTCTCGTCAGGCC 60.816 66.667 0.00 0.00 0.00 5.19
1156 1183 1.557832 TCCTGGTATTCGGTTTGGGAG 59.442 52.381 0.00 0.00 0.00 4.30
1163 1190 4.320714 GGTATTCGGTTTGGGAGTTTGTTC 60.321 45.833 0.00 0.00 0.00 3.18
1181 1208 2.046285 CGGTGCTTGGACCCCAATC 61.046 63.158 5.74 0.00 43.07 2.67
1183 1210 0.251787 GGTGCTTGGACCCCAATCTT 60.252 55.000 0.00 0.00 43.07 2.40
1184 1211 1.632589 GTGCTTGGACCCCAATCTTT 58.367 50.000 0.00 0.00 43.07 2.52
1185 1212 1.546029 GTGCTTGGACCCCAATCTTTC 59.454 52.381 0.00 0.00 43.07 2.62
1186 1213 1.186200 GCTTGGACCCCAATCTTTCC 58.814 55.000 0.00 0.00 43.07 3.13
1187 1214 1.272704 GCTTGGACCCCAATCTTTCCT 60.273 52.381 0.00 0.00 43.07 3.36
1188 1215 2.450476 CTTGGACCCCAATCTTTCCTG 58.550 52.381 0.00 0.00 43.07 3.86
1189 1216 1.455822 TGGACCCCAATCTTTCCTGT 58.544 50.000 0.00 0.00 0.00 4.00
1190 1217 1.075374 TGGACCCCAATCTTTCCTGTG 59.925 52.381 0.00 0.00 0.00 3.66
1191 1218 1.075536 GGACCCCAATCTTTCCTGTGT 59.924 52.381 0.00 0.00 0.00 3.72
1192 1219 2.490902 GGACCCCAATCTTTCCTGTGTT 60.491 50.000 0.00 0.00 0.00 3.32
1193 1220 2.820197 GACCCCAATCTTTCCTGTGTTC 59.180 50.000 0.00 0.00 0.00 3.18
1194 1221 1.812571 CCCCAATCTTTCCTGTGTTCG 59.187 52.381 0.00 0.00 0.00 3.95
1195 1222 2.552155 CCCCAATCTTTCCTGTGTTCGA 60.552 50.000 0.00 0.00 0.00 3.71
1196 1223 2.744202 CCCAATCTTTCCTGTGTTCGAG 59.256 50.000 0.00 0.00 0.00 4.04
1197 1224 3.557054 CCCAATCTTTCCTGTGTTCGAGA 60.557 47.826 0.00 0.00 0.00 4.04
1198 1225 4.256920 CCAATCTTTCCTGTGTTCGAGAT 58.743 43.478 0.00 0.00 0.00 2.75
1199 1226 4.331168 CCAATCTTTCCTGTGTTCGAGATC 59.669 45.833 0.00 0.00 0.00 2.75
1200 1227 5.174395 CAATCTTTCCTGTGTTCGAGATCT 58.826 41.667 0.00 0.00 0.00 2.75
1201 1228 4.179926 TCTTTCCTGTGTTCGAGATCTG 57.820 45.455 0.00 0.00 0.00 2.90
1202 1229 3.056536 TCTTTCCTGTGTTCGAGATCTGG 60.057 47.826 0.00 0.00 0.00 3.86
1203 1230 0.532573 TCCTGTGTTCGAGATCTGGC 59.467 55.000 0.00 0.00 0.00 4.85
1204 1231 0.803768 CCTGTGTTCGAGATCTGGCG 60.804 60.000 0.00 0.00 0.00 5.69
1205 1232 0.803768 CTGTGTTCGAGATCTGGCGG 60.804 60.000 0.00 0.00 0.00 6.13
1206 1233 1.519455 GTGTTCGAGATCTGGCGGG 60.519 63.158 0.00 0.00 0.00 6.13
1207 1234 1.982395 TGTTCGAGATCTGGCGGGT 60.982 57.895 0.00 0.00 0.00 5.28
1208 1235 1.519455 GTTCGAGATCTGGCGGGTG 60.519 63.158 0.00 0.00 0.00 4.61
1209 1236 1.982395 TTCGAGATCTGGCGGGTGT 60.982 57.895 0.00 0.00 0.00 4.16
1210 1237 1.945354 TTCGAGATCTGGCGGGTGTC 61.945 60.000 0.00 0.00 0.00 3.67
1211 1238 2.501610 GAGATCTGGCGGGTGTCC 59.498 66.667 0.00 0.00 0.00 4.02
1212 1239 2.039624 AGATCTGGCGGGTGTCCT 59.960 61.111 0.00 0.00 0.00 3.85
1213 1240 0.755698 GAGATCTGGCGGGTGTCCTA 60.756 60.000 0.00 0.00 0.00 2.94
1214 1241 0.105453 AGATCTGGCGGGTGTCCTAT 60.105 55.000 0.00 0.00 0.00 2.57
1215 1242 1.147191 AGATCTGGCGGGTGTCCTATA 59.853 52.381 0.00 0.00 0.00 1.31
1216 1243 2.180276 GATCTGGCGGGTGTCCTATAT 58.820 52.381 0.00 0.00 0.00 0.86
1217 1244 1.338107 TCTGGCGGGTGTCCTATATG 58.662 55.000 0.00 0.00 0.00 1.78
1218 1245 0.321671 CTGGCGGGTGTCCTATATGG 59.678 60.000 0.00 0.00 37.10 2.74
1219 1246 1.003718 GGCGGGTGTCCTATATGGC 60.004 63.158 0.00 0.00 35.26 4.40
1220 1247 1.752198 GCGGGTGTCCTATATGGCA 59.248 57.895 0.00 0.00 35.26 4.92
1221 1248 0.107831 GCGGGTGTCCTATATGGCAA 59.892 55.000 0.00 0.00 35.26 4.52
1222 1249 1.271379 GCGGGTGTCCTATATGGCAAT 60.271 52.381 0.00 0.00 35.26 3.56
1223 1250 2.814097 GCGGGTGTCCTATATGGCAATT 60.814 50.000 0.00 0.00 35.26 2.32
1224 1251 3.486383 CGGGTGTCCTATATGGCAATTT 58.514 45.455 0.00 0.00 35.26 1.82
1225 1252 3.253188 CGGGTGTCCTATATGGCAATTTG 59.747 47.826 0.00 0.00 35.26 2.32
1226 1253 3.005791 GGGTGTCCTATATGGCAATTTGC 59.994 47.826 13.04 13.04 44.08 3.68
1227 1254 3.891366 GGTGTCCTATATGGCAATTTGCT 59.109 43.478 20.06 4.94 44.28 3.91
1228 1255 5.070001 GGTGTCCTATATGGCAATTTGCTA 58.930 41.667 20.06 15.33 44.28 3.49
1229 1256 5.534654 GGTGTCCTATATGGCAATTTGCTAA 59.465 40.000 20.06 10.06 44.28 3.09
1230 1257 6.438763 GTGTCCTATATGGCAATTTGCTAAC 58.561 40.000 20.06 9.23 44.28 2.34
1231 1258 5.534654 TGTCCTATATGGCAATTTGCTAACC 59.465 40.000 20.06 5.02 44.28 2.85
1232 1259 4.759693 TCCTATATGGCAATTTGCTAACCG 59.240 41.667 20.06 5.73 44.28 4.44
1233 1260 4.082787 CCTATATGGCAATTTGCTAACCGG 60.083 45.833 20.06 0.00 44.28 5.28
1273 1300 2.048444 TCCTCAATCATCCTGCTTGC 57.952 50.000 0.00 0.00 0.00 4.01
1274 1301 1.562942 TCCTCAATCATCCTGCTTGCT 59.437 47.619 0.00 0.00 0.00 3.91
1275 1302 1.676529 CCTCAATCATCCTGCTTGCTG 59.323 52.381 0.00 0.00 0.00 4.41
1276 1303 2.366533 CTCAATCATCCTGCTTGCTGT 58.633 47.619 0.00 0.00 0.00 4.40
1277 1304 2.753452 CTCAATCATCCTGCTTGCTGTT 59.247 45.455 0.00 0.00 0.00 3.16
1278 1305 3.159472 TCAATCATCCTGCTTGCTGTTT 58.841 40.909 0.00 0.00 0.00 2.83
1279 1306 3.057104 TCAATCATCCTGCTTGCTGTTTG 60.057 43.478 0.00 0.00 0.00 2.93
1280 1307 0.599558 TCATCCTGCTTGCTGTTTGC 59.400 50.000 0.00 0.00 43.25 3.68
1281 1308 0.601558 CATCCTGCTTGCTGTTTGCT 59.398 50.000 0.00 0.00 43.37 3.91
1282 1309 1.814394 CATCCTGCTTGCTGTTTGCTA 59.186 47.619 0.00 0.00 43.37 3.49
1283 1310 1.527034 TCCTGCTTGCTGTTTGCTAG 58.473 50.000 0.00 0.00 45.12 3.42
1294 1321 5.752098 GCTGTTTGCTAGCAAAAATAGTG 57.248 39.130 37.37 23.63 45.86 2.74
1295 1322 4.090498 GCTGTTTGCTAGCAAAAATAGTGC 59.910 41.667 37.37 28.09 45.86 4.40
1296 1323 5.193663 TGTTTGCTAGCAAAAATAGTGCA 57.806 34.783 37.37 27.04 45.86 4.57
1297 1324 5.782047 TGTTTGCTAGCAAAAATAGTGCAT 58.218 33.333 37.37 0.00 45.86 3.96
1298 1325 6.222389 TGTTTGCTAGCAAAAATAGTGCATT 58.778 32.000 37.37 0.00 45.86 3.56
1299 1326 7.374272 TGTTTGCTAGCAAAAATAGTGCATTA 58.626 30.769 37.37 14.09 45.86 1.90
1300 1327 8.034215 TGTTTGCTAGCAAAAATAGTGCATTAT 58.966 29.630 37.37 0.00 45.86 1.28
1301 1328 8.872845 GTTTGCTAGCAAAAATAGTGCATTATT 58.127 29.630 37.37 8.55 45.86 1.40
1302 1329 8.633075 TTGCTAGCAAAAATAGTGCATTATTC 57.367 30.769 27.50 3.18 44.74 1.75
1303 1330 7.999679 TGCTAGCAAAAATAGTGCATTATTCT 58.000 30.769 16.84 9.69 44.74 2.40
1304 1331 7.916977 TGCTAGCAAAAATAGTGCATTATTCTG 59.083 33.333 16.84 14.43 44.74 3.02
1305 1332 7.917505 GCTAGCAAAAATAGTGCATTATTCTGT 59.082 33.333 14.11 8.60 44.74 3.41
1306 1333 9.443283 CTAGCAAAAATAGTGCATTATTCTGTC 57.557 33.333 14.11 10.60 44.74 3.51
1334 1361 1.444119 TTGGTGCAAACGCTCTGTCC 61.444 55.000 0.00 0.00 0.00 4.02
1343 1370 2.839486 ACGCTCTGTCCAATCTGAAA 57.161 45.000 0.00 0.00 0.00 2.69
1375 1402 5.486526 AGTGCTAGGAGAAATCTGTTTGAG 58.513 41.667 0.00 0.00 0.00 3.02
1382 1409 3.829948 AGAAATCTGTTTGAGCATTGCG 58.170 40.909 2.38 0.00 0.00 4.85
1516 1545 7.432148 TTTATCCAGGTCATGCTAGTTTCTA 57.568 36.000 0.00 0.00 0.00 2.10
1566 1598 7.151999 AGCACAATGTATTTATTTCGTCCAA 57.848 32.000 0.00 0.00 0.00 3.53
1636 1672 6.220930 TGTTAGGAAGTATCTGTGTGAACAC 58.779 40.000 6.63 6.63 46.59 3.32
1793 1831 3.131396 GGCGATGTTATCCAAGGTACAG 58.869 50.000 0.00 0.00 0.00 2.74
1937 1996 3.071747 AGTTCTCCTCGGAAAAAGAAGCT 59.928 43.478 0.00 0.00 0.00 3.74
1985 2044 5.446473 CGATGAGGTAAGAATTGTGCTTCAC 60.446 44.000 0.00 0.00 34.56 3.18
2208 2314 5.344933 GGTCTTTGTTTGTTGTGTTCAGAAC 59.655 40.000 6.32 6.32 0.00 3.01
2312 2418 7.327214 ACTTCAAATAGACCAGTCTTCTGATC 58.673 38.462 5.49 0.00 43.76 2.92
2328 2435 8.510505 GTCTTCTGATCTTTTAGCTTGACATTT 58.489 33.333 0.00 0.00 0.00 2.32
2377 2485 3.138283 TGAAAACCAGAGGAACACCTGAT 59.862 43.478 0.00 0.00 34.13 2.90
2397 2505 7.050377 CCTGATTGGTTAGCTAATTCTCTTCA 58.950 38.462 9.88 7.78 0.00 3.02
2776 3194 4.781934 AGGGAGATGTTAAAGGAATTCCG 58.218 43.478 18.82 0.00 42.08 4.30
2789 3207 3.326880 AGGAATTCCGTATTTATCCGGCT 59.673 43.478 18.82 0.00 43.87 5.52
2826 3244 8.388484 AGGCTTAAGAATTTATATGAGCAGTG 57.612 34.615 6.67 0.00 0.00 3.66
2848 3266 4.224147 TGGCTCAACTAGTGTAGGCATAAA 59.776 41.667 22.64 7.20 36.07 1.40
2849 3267 5.183228 GGCTCAACTAGTGTAGGCATAAAA 58.817 41.667 20.24 0.00 33.23 1.52
2894 3312 3.126171 GCAAGTGACACGCCACATAATTA 59.874 43.478 0.00 0.00 39.42 1.40
2907 3325 7.229306 ACGCCACATAATTATCATTCATCAAGT 59.771 33.333 0.00 0.00 0.00 3.16
2918 3336 4.100035 TCATTCATCAAGTAGCATCCGACT 59.900 41.667 0.00 0.00 0.00 4.18
2973 3391 4.147321 CCACCTCCTTATTCCCATTCATG 58.853 47.826 0.00 0.00 0.00 3.07
2981 3399 6.156602 TCCTTATTCCCATTCATGCATGTTTT 59.843 34.615 25.43 9.46 0.00 2.43
3028 3446 4.291513 TGAACCTAAGGTAGACTCTCCAGA 59.708 45.833 0.00 0.00 33.12 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 57 2.266055 GGGAGGAACAGAGCACGG 59.734 66.667 0.00 0.00 0.00 4.94
60 65 2.907042 GAGAAAGAAGAGGGGAGGAACA 59.093 50.000 0.00 0.00 0.00 3.18
67 72 1.811679 GCGCGAGAAAGAAGAGGGG 60.812 63.158 12.10 0.00 0.00 4.79
69 74 1.136872 CGAGCGCGAGAAAGAAGAGG 61.137 60.000 12.10 0.00 40.82 3.69
72 77 2.692109 GCGAGCGCGAGAAAGAAG 59.308 61.111 15.92 0.00 40.82 2.85
95 100 0.171231 CGAGACAAGATCGGTCAGCA 59.829 55.000 18.66 0.00 37.74 4.41
102 107 2.668457 CCAAAGAACCGAGACAAGATCG 59.332 50.000 0.00 0.00 39.86 3.69
274 284 1.306296 CGGGGTTGATGTTGGGGAT 59.694 57.895 0.00 0.00 0.00 3.85
378 394 4.699522 GTCTTCTTGGCGGCGGGT 62.700 66.667 9.78 0.00 0.00 5.28
449 468 4.735132 TCTTCTTGTCGGCGGCGG 62.735 66.667 31.73 15.35 0.00 6.13
450 469 3.479269 GTCTTCTTGTCGGCGGCG 61.479 66.667 27.15 27.15 0.00 6.46
557 576 0.505655 GAACTACGCGACGCAACTTT 59.494 50.000 21.35 7.04 0.00 2.66
652 672 2.353889 TCAATCGACGCTACAGACTACC 59.646 50.000 0.00 0.00 0.00 3.18
667 687 6.659361 ACAGAAGTGATTCAAGATCAATCG 57.341 37.500 0.00 0.00 33.57 3.34
668 688 7.516470 CGCTACAGAAGTGATTCAAGATCAATC 60.516 40.741 0.00 0.00 37.99 2.67
669 689 6.257411 CGCTACAGAAGTGATTCAAGATCAAT 59.743 38.462 0.00 0.00 37.99 2.57
670 690 5.578336 CGCTACAGAAGTGATTCAAGATCAA 59.422 40.000 0.00 0.00 37.99 2.57
671 691 5.105063 CGCTACAGAAGTGATTCAAGATCA 58.895 41.667 0.00 0.00 37.99 2.92
672 692 5.105752 ACGCTACAGAAGTGATTCAAGATC 58.894 41.667 0.00 0.00 39.15 2.75
673 693 5.078411 ACGCTACAGAAGTGATTCAAGAT 57.922 39.130 0.00 0.00 39.15 2.40
674 694 4.486090 GACGCTACAGAAGTGATTCAAGA 58.514 43.478 0.00 0.00 39.15 3.02
675 695 3.301906 CGACGCTACAGAAGTGATTCAAG 59.698 47.826 0.00 0.00 39.15 3.02
676 696 3.057806 TCGACGCTACAGAAGTGATTCAA 60.058 43.478 0.00 0.00 39.15 2.69
677 697 2.486592 TCGACGCTACAGAAGTGATTCA 59.513 45.455 0.00 0.00 39.15 2.57
678 698 3.132629 TCGACGCTACAGAAGTGATTC 57.867 47.619 0.00 0.00 39.15 2.52
679 699 3.784701 ATCGACGCTACAGAAGTGATT 57.215 42.857 0.00 0.00 39.15 2.57
680 700 3.128764 TCAATCGACGCTACAGAAGTGAT 59.871 43.478 0.00 0.00 39.15 3.06
681 701 2.486592 TCAATCGACGCTACAGAAGTGA 59.513 45.455 0.00 0.00 39.15 3.41
682 702 2.863739 TCAATCGACGCTACAGAAGTG 58.136 47.619 0.00 0.00 41.76 3.16
683 703 3.378742 AGATCAATCGACGCTACAGAAGT 59.621 43.478 0.00 0.00 0.00 3.01
684 704 3.958704 AGATCAATCGACGCTACAGAAG 58.041 45.455 0.00 0.00 0.00 2.85
685 705 4.105486 CAAGATCAATCGACGCTACAGAA 58.895 43.478 0.00 0.00 0.00 3.02
686 706 3.377172 TCAAGATCAATCGACGCTACAGA 59.623 43.478 0.00 0.00 0.00 3.41
687 707 3.695816 TCAAGATCAATCGACGCTACAG 58.304 45.455 0.00 0.00 0.00 2.74
688 708 3.775661 TCAAGATCAATCGACGCTACA 57.224 42.857 0.00 0.00 0.00 2.74
689 709 4.740205 TGATTCAAGATCAATCGACGCTAC 59.260 41.667 0.00 0.00 33.57 3.58
690 710 4.740205 GTGATTCAAGATCAATCGACGCTA 59.260 41.667 0.00 0.00 33.57 4.26
691 711 3.553511 GTGATTCAAGATCAATCGACGCT 59.446 43.478 0.00 0.00 33.57 5.07
692 712 3.553511 AGTGATTCAAGATCAATCGACGC 59.446 43.478 0.00 0.00 33.57 5.19
693 713 4.549680 GCAGTGATTCAAGATCAATCGACG 60.550 45.833 0.00 0.00 33.57 5.12
694 714 4.569966 AGCAGTGATTCAAGATCAATCGAC 59.430 41.667 0.00 0.00 33.57 4.20
695 715 4.569564 CAGCAGTGATTCAAGATCAATCGA 59.430 41.667 0.00 0.00 33.57 3.59
743 763 4.157840 ACGGAAAAGATTGGAATTGGCTAC 59.842 41.667 0.00 0.00 0.00 3.58
761 781 3.422417 TTTCGCAAAATTGACACGGAA 57.578 38.095 0.00 0.00 0.00 4.30
773 793 1.861575 GAACCGGCAAAATTTCGCAAA 59.138 42.857 0.00 0.00 0.00 3.68
775 795 0.671251 AGAACCGGCAAAATTTCGCA 59.329 45.000 0.00 0.00 0.00 5.10
781 801 1.047801 AAGGCAAGAACCGGCAAAAT 58.952 45.000 0.00 0.00 33.69 1.82
788 808 1.032114 GGGGATCAAGGCAAGAACCG 61.032 60.000 0.00 0.00 33.69 4.44
798 818 2.289694 ACAGACGAACAAGGGGATCAAG 60.290 50.000 0.00 0.00 0.00 3.02
819 845 5.600484 AGGTGAAATTGTGGGAACAAATGTA 59.400 36.000 0.00 0.00 46.06 2.29
842 868 1.271926 CCCCCAAGAACACCTAACCAG 60.272 57.143 0.00 0.00 0.00 4.00
843 869 0.774908 CCCCCAAGAACACCTAACCA 59.225 55.000 0.00 0.00 0.00 3.67
879 905 0.916086 AACCACACCTCACTGAACCA 59.084 50.000 0.00 0.00 0.00 3.67
889 915 5.675684 AAGAAATTTCACAAACCACACCT 57.324 34.783 19.99 0.00 0.00 4.00
894 920 4.591072 CCCCCTAAGAAATTTCACAAACCA 59.409 41.667 19.99 0.00 0.00 3.67
899 925 4.733077 TGACCCCCTAAGAAATTTCACA 57.267 40.909 19.99 6.30 0.00 3.58
912 938 2.670148 GCAGATCGGTTGACCCCCT 61.670 63.158 0.00 0.00 0.00 4.79
944 970 0.550914 CCCAAATCCTTCGATCCCCA 59.449 55.000 0.00 0.00 0.00 4.96
945 971 0.178990 CCCCAAATCCTTCGATCCCC 60.179 60.000 0.00 0.00 0.00 4.81
949 975 6.614657 AGAAATAATCCCCAAATCCTTCGAT 58.385 36.000 0.00 0.00 0.00 3.59
950 976 6.013554 AGAAATAATCCCCAAATCCTTCGA 57.986 37.500 0.00 0.00 0.00 3.71
991 1018 1.532505 CCAATTCAGCATCGCCTTTCG 60.533 52.381 0.00 0.00 40.15 3.46
992 1019 1.202336 CCCAATTCAGCATCGCCTTTC 60.202 52.381 0.00 0.00 0.00 2.62
993 1020 0.819582 CCCAATTCAGCATCGCCTTT 59.180 50.000 0.00 0.00 0.00 3.11
994 1021 1.039233 CCCCAATTCAGCATCGCCTT 61.039 55.000 0.00 0.00 0.00 4.35
995 1022 1.454479 CCCCAATTCAGCATCGCCT 60.454 57.895 0.00 0.00 0.00 5.52
996 1023 1.037030 TTCCCCAATTCAGCATCGCC 61.037 55.000 0.00 0.00 0.00 5.54
997 1024 0.383231 CTTCCCCAATTCAGCATCGC 59.617 55.000 0.00 0.00 0.00 4.58
1005 1032 1.205655 GCAGCCTTTCTTCCCCAATTC 59.794 52.381 0.00 0.00 0.00 2.17
1073 1100 0.250727 TTTGGGGCCTGACGAGAAAG 60.251 55.000 0.84 0.00 0.00 2.62
1087 1114 0.949105 CCTCCGACGAACAGTTTGGG 60.949 60.000 5.48 0.00 31.80 4.12
1156 1183 0.030235 GGTCCAAGCACCGAACAAAC 59.970 55.000 0.00 0.00 0.00 2.93
1181 1208 3.257393 CCAGATCTCGAACACAGGAAAG 58.743 50.000 0.00 0.00 0.00 2.62
1183 1210 1.066858 GCCAGATCTCGAACACAGGAA 60.067 52.381 0.00 0.00 0.00 3.36
1184 1211 0.532573 GCCAGATCTCGAACACAGGA 59.467 55.000 0.00 0.00 0.00 3.86
1185 1212 0.803768 CGCCAGATCTCGAACACAGG 60.804 60.000 0.00 0.00 0.00 4.00
1186 1213 0.803768 CCGCCAGATCTCGAACACAG 60.804 60.000 5.45 0.00 0.00 3.66
1187 1214 1.215382 CCGCCAGATCTCGAACACA 59.785 57.895 5.45 0.00 0.00 3.72
1188 1215 1.519455 CCCGCCAGATCTCGAACAC 60.519 63.158 5.45 0.00 0.00 3.32
1189 1216 1.982395 ACCCGCCAGATCTCGAACA 60.982 57.895 5.45 0.00 0.00 3.18
1190 1217 1.519455 CACCCGCCAGATCTCGAAC 60.519 63.158 5.45 0.00 0.00 3.95
1191 1218 1.945354 GACACCCGCCAGATCTCGAA 61.945 60.000 5.45 0.00 0.00 3.71
1192 1219 2.362503 ACACCCGCCAGATCTCGA 60.363 61.111 5.45 0.00 0.00 4.04
1193 1220 2.105128 GACACCCGCCAGATCTCG 59.895 66.667 0.00 0.00 0.00 4.04
1194 1221 0.755698 TAGGACACCCGCCAGATCTC 60.756 60.000 0.00 0.00 37.58 2.75
1195 1222 0.105453 ATAGGACACCCGCCAGATCT 60.105 55.000 0.00 0.00 37.58 2.75
1196 1223 1.629043 TATAGGACACCCGCCAGATC 58.371 55.000 0.00 0.00 37.58 2.75
1197 1224 1.902508 CATATAGGACACCCGCCAGAT 59.097 52.381 0.00 0.00 37.58 2.90
1198 1225 1.338107 CATATAGGACACCCGCCAGA 58.662 55.000 0.00 0.00 37.58 3.86
1199 1226 0.321671 CCATATAGGACACCCGCCAG 59.678 60.000 0.00 0.00 41.22 4.85
1200 1227 1.764571 GCCATATAGGACACCCGCCA 61.765 60.000 0.00 0.00 41.22 5.69
1201 1228 1.003718 GCCATATAGGACACCCGCC 60.004 63.158 0.00 0.00 41.22 6.13
1202 1229 0.107831 TTGCCATATAGGACACCCGC 59.892 55.000 0.00 0.00 41.22 6.13
1203 1230 2.859165 ATTGCCATATAGGACACCCG 57.141 50.000 0.00 0.00 41.22 5.28
1204 1231 3.005791 GCAAATTGCCATATAGGACACCC 59.994 47.826 6.72 0.00 41.22 4.61
1205 1232 3.891366 AGCAAATTGCCATATAGGACACC 59.109 43.478 15.04 0.00 46.52 4.16
1206 1233 6.438763 GTTAGCAAATTGCCATATAGGACAC 58.561 40.000 15.04 0.00 46.52 3.67
1207 1234 5.534654 GGTTAGCAAATTGCCATATAGGACA 59.465 40.000 15.04 0.00 46.52 4.02
1208 1235 5.334879 CGGTTAGCAAATTGCCATATAGGAC 60.335 44.000 15.04 2.35 46.52 3.85
1209 1236 4.759693 CGGTTAGCAAATTGCCATATAGGA 59.240 41.667 15.04 0.00 46.52 2.94
1210 1237 4.082787 CCGGTTAGCAAATTGCCATATAGG 60.083 45.833 15.04 7.84 46.52 2.57
1211 1238 4.615912 GCCGGTTAGCAAATTGCCATATAG 60.616 45.833 15.04 1.44 46.52 1.31
1212 1239 3.254657 GCCGGTTAGCAAATTGCCATATA 59.745 43.478 15.04 0.00 46.52 0.86
1213 1240 2.035832 GCCGGTTAGCAAATTGCCATAT 59.964 45.455 15.04 0.00 46.52 1.78
1214 1241 1.407258 GCCGGTTAGCAAATTGCCATA 59.593 47.619 15.04 0.00 46.52 2.74
1215 1242 0.175531 GCCGGTTAGCAAATTGCCAT 59.824 50.000 15.04 0.00 46.52 4.40
1216 1243 0.897863 AGCCGGTTAGCAAATTGCCA 60.898 50.000 15.04 0.00 46.52 4.92
1217 1244 0.246360 AAGCCGGTTAGCAAATTGCC 59.754 50.000 15.04 0.00 46.52 4.52
1218 1245 2.479560 CCTAAGCCGGTTAGCAAATTGC 60.480 50.000 10.41 10.41 45.46 3.56
1219 1246 3.013921 TCCTAAGCCGGTTAGCAAATTG 58.986 45.455 11.22 0.00 37.41 2.32
1220 1247 3.359695 TCCTAAGCCGGTTAGCAAATT 57.640 42.857 11.22 0.00 37.41 1.82
1221 1248 3.054655 TCTTCCTAAGCCGGTTAGCAAAT 60.055 43.478 11.22 0.00 37.41 2.32
1222 1249 2.303600 TCTTCCTAAGCCGGTTAGCAAA 59.696 45.455 11.22 7.31 37.41 3.68
1223 1250 1.903860 TCTTCCTAAGCCGGTTAGCAA 59.096 47.619 11.22 3.04 37.41 3.91
1224 1251 1.563924 TCTTCCTAAGCCGGTTAGCA 58.436 50.000 11.22 0.00 37.41 3.49
1225 1252 2.102588 TGATCTTCCTAAGCCGGTTAGC 59.897 50.000 11.22 0.00 37.41 3.09
1226 1253 4.310769 CATGATCTTCCTAAGCCGGTTAG 58.689 47.826 1.90 9.94 38.35 2.34
1227 1254 3.494398 GCATGATCTTCCTAAGCCGGTTA 60.494 47.826 1.90 0.00 0.00 2.85
1228 1255 2.746472 GCATGATCTTCCTAAGCCGGTT 60.746 50.000 1.90 0.00 0.00 4.44
1229 1256 1.202698 GCATGATCTTCCTAAGCCGGT 60.203 52.381 1.90 0.00 0.00 5.28
1230 1257 1.071385 AGCATGATCTTCCTAAGCCGG 59.929 52.381 0.00 0.00 0.00 6.13
1231 1258 2.540265 AGCATGATCTTCCTAAGCCG 57.460 50.000 0.00 0.00 0.00 5.52
1232 1259 4.615588 ACTAGCATGATCTTCCTAAGCC 57.384 45.455 0.00 0.00 0.00 4.35
1233 1260 4.994217 GGAACTAGCATGATCTTCCTAAGC 59.006 45.833 11.42 0.00 0.00 3.09
1273 1300 5.221880 TGCACTATTTTTGCTAGCAAACAG 58.778 37.500 36.23 31.25 44.39 3.16
1274 1301 5.193663 TGCACTATTTTTGCTAGCAAACA 57.806 34.783 36.23 31.24 44.39 2.83
1275 1302 6.710692 AATGCACTATTTTTGCTAGCAAAC 57.289 33.333 36.23 24.49 44.39 2.93
1276 1303 9.086336 GAATAATGCACTATTTTTGCTAGCAAA 57.914 29.630 33.58 33.58 43.23 3.68
1277 1304 8.469200 AGAATAATGCACTATTTTTGCTAGCAA 58.531 29.630 26.06 26.06 40.86 3.91
1278 1305 7.916977 CAGAATAATGCACTATTTTTGCTAGCA 59.083 33.333 14.93 14.93 40.86 3.49
1279 1306 7.917505 ACAGAATAATGCACTATTTTTGCTAGC 59.082 33.333 8.10 8.10 40.86 3.42
1280 1307 9.443283 GACAGAATAATGCACTATTTTTGCTAG 57.557 33.333 1.38 0.00 40.86 3.42
1281 1308 9.177608 AGACAGAATAATGCACTATTTTTGCTA 57.822 29.630 1.38 0.00 40.86 3.49
1282 1309 7.972277 CAGACAGAATAATGCACTATTTTTGCT 59.028 33.333 1.38 4.06 40.86 3.91
1283 1310 7.221452 CCAGACAGAATAATGCACTATTTTTGC 59.779 37.037 1.38 2.21 40.63 3.68
1284 1311 8.246180 ACCAGACAGAATAATGCACTATTTTTG 58.754 33.333 1.38 6.80 0.00 2.44
1285 1312 8.246180 CACCAGACAGAATAATGCACTATTTTT 58.754 33.333 1.38 0.00 0.00 1.94
1286 1313 7.611467 TCACCAGACAGAATAATGCACTATTTT 59.389 33.333 1.38 0.00 0.00 1.82
1287 1314 7.112122 TCACCAGACAGAATAATGCACTATTT 58.888 34.615 1.38 0.00 0.00 1.40
1288 1315 6.653020 TCACCAGACAGAATAATGCACTATT 58.347 36.000 0.00 0.00 0.00 1.73
1289 1316 6.239217 TCACCAGACAGAATAATGCACTAT 57.761 37.500 0.00 0.00 0.00 2.12
1290 1317 5.675684 TCACCAGACAGAATAATGCACTA 57.324 39.130 0.00 0.00 0.00 2.74
1291 1318 4.558226 TCACCAGACAGAATAATGCACT 57.442 40.909 0.00 0.00 0.00 4.40
1292 1319 5.824904 ATTCACCAGACAGAATAATGCAC 57.175 39.130 0.00 0.00 32.98 4.57
1293 1320 6.350361 CCAAATTCACCAGACAGAATAATGCA 60.350 38.462 0.00 0.00 33.58 3.96
1294 1321 6.038356 CCAAATTCACCAGACAGAATAATGC 58.962 40.000 0.00 0.00 33.58 3.56
1295 1322 7.031372 CACCAAATTCACCAGACAGAATAATG 58.969 38.462 0.00 0.00 33.58 1.90
1296 1323 6.350445 GCACCAAATTCACCAGACAGAATAAT 60.350 38.462 0.00 0.00 33.58 1.28
1297 1324 5.048083 GCACCAAATTCACCAGACAGAATAA 60.048 40.000 0.00 0.00 33.58 1.40
1298 1325 4.458989 GCACCAAATTCACCAGACAGAATA 59.541 41.667 0.00 0.00 33.58 1.75
1299 1326 3.256631 GCACCAAATTCACCAGACAGAAT 59.743 43.478 0.00 0.00 36.09 2.40
1300 1327 2.622942 GCACCAAATTCACCAGACAGAA 59.377 45.455 0.00 0.00 0.00 3.02
1301 1328 2.229792 GCACCAAATTCACCAGACAGA 58.770 47.619 0.00 0.00 0.00 3.41
1302 1329 1.955778 TGCACCAAATTCACCAGACAG 59.044 47.619 0.00 0.00 0.00 3.51
1303 1330 2.064434 TGCACCAAATTCACCAGACA 57.936 45.000 0.00 0.00 0.00 3.41
1304 1331 3.123050 GTTTGCACCAAATTCACCAGAC 58.877 45.455 0.00 0.00 35.74 3.51
1305 1332 2.223688 CGTTTGCACCAAATTCACCAGA 60.224 45.455 0.00 0.00 35.74 3.86
1306 1333 2.126467 CGTTTGCACCAAATTCACCAG 58.874 47.619 0.00 0.00 35.74 4.00
1343 1370 3.492102 TCTCCTAGCACTTGCAGTTTT 57.508 42.857 3.62 0.00 45.16 2.43
1566 1598 1.403249 GCTGCTTGCACGGAATTTCAT 60.403 47.619 0.00 0.00 42.31 2.57
1636 1672 3.488310 GCACAGTTCTTGCATTTGTTCAG 59.512 43.478 0.00 0.00 39.93 3.02
1793 1831 8.189460 AGCAAAAAGATTCAGAGCAGATAAATC 58.811 33.333 0.00 0.00 0.00 2.17
1803 1841 6.183360 CCCCTAATCAGCAAAAAGATTCAGAG 60.183 42.308 0.00 0.00 36.07 3.35
1985 2044 5.473846 TCTTCTGCTATACCTACAGAATCCG 59.526 44.000 5.24 0.00 46.28 4.18
2208 2314 2.412325 GGGCACGAACGAACATTACAAG 60.412 50.000 0.14 0.00 0.00 3.16
2221 2327 0.036765 GTACATGTCCAGGGCACGAA 60.037 55.000 0.00 0.00 0.00 3.85
2223 2329 1.449601 GGTACATGTCCAGGGCACG 60.450 63.158 0.00 0.00 0.00 5.34
2225 2331 1.072266 AAAGGTACATGTCCAGGGCA 58.928 50.000 0.00 0.00 0.00 5.36
2312 2418 8.044060 TGATACAGGAAATGTCAAGCTAAAAG 57.956 34.615 0.00 0.00 42.70 2.27
2377 2485 9.436957 CTTAGTTGAAGAGAATTAGCTAACCAA 57.563 33.333 8.70 2.52 37.33 3.67
2397 2505 9.490379 ACGATGAATTAACTTTCTGTCTTAGTT 57.510 29.630 0.00 0.00 36.23 2.24
2760 3178 8.780249 CGGATAAATACGGAATTCCTTTAACAT 58.220 33.333 22.05 8.72 0.00 2.71
2785 3203 4.965119 AAGCCTTGAAATAAGTAAGCCG 57.035 40.909 0.00 0.00 0.00 5.52
2826 3244 2.990066 ATGCCTACACTAGTTGAGCC 57.010 50.000 0.00 0.00 0.00 4.70
2849 3267 3.792401 TGACGATGTGAACAAGTTCTGT 58.208 40.909 13.49 5.19 41.27 3.41
2894 3312 4.993584 GTCGGATGCTACTTGATGAATGAT 59.006 41.667 0.00 0.00 0.00 2.45
2907 3325 1.687123 GCCTAGGAAAGTCGGATGCTA 59.313 52.381 14.75 0.00 0.00 3.49
2918 3336 3.772572 GCCAAAATAAAGGGCCTAGGAAA 59.227 43.478 14.75 0.00 41.90 3.13
2944 3362 3.039011 GGAATAAGGAGGTGGCTGACTA 58.961 50.000 0.00 0.00 0.00 2.59
2973 3391 2.233676 CCTTTAGTGGGGGAAAACATGC 59.766 50.000 0.00 0.00 0.00 4.06
3028 3446 3.769739 TCTGACCAGTTAACATGTGCT 57.230 42.857 8.61 0.00 0.00 4.40
3081 3499 6.747280 CGAATTAAAACAGATGCCTGGTAAAG 59.253 38.462 0.00 0.00 39.98 1.85


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

AutoCloner maintained by Alex Coulton.