Multiple sequence alignment - TraesCS3D01G261600

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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 TraesCS3D01G261600 chr3D 100.000 2288 0 0 1 2288 363592703 363594990 0.000000e+00 4226
1 TraesCS3D01G261600 chr3A 93.169 688 36 5 1608 2286 484634591 484635276 0.000000e+00 1000
2 TraesCS3D01G261600 chr3A 90.808 631 40 9 758 1375 484633877 484634502 0.000000e+00 828
3 TraesCS3D01G261600 chr3A 95.335 343 14 2 231 573 484633186 484633526 5.560000e-151 544
4 TraesCS3D01G261600 chr3A 95.588 204 9 0 1 204 484631648 484631851 6.090000e-86 327
5 TraesCS3D01G261600 chr3B 89.481 694 55 11 1608 2286 473692024 473692714 0.000000e+00 861
6 TraesCS3D01G261600 chr3B 89.921 635 36 11 758 1375 473691324 473691947 0.000000e+00 793
7 TraesCS3D01G261600 chr3B 92.429 317 14 3 257 573 473690655 473690961 5.800000e-121 444
8 TraesCS3D01G261600 chr3B 95.588 204 9 0 1 204 473689103 473689306 6.090000e-86 327
9 TraesCS3D01G261600 chr3B 92.500 80 6 0 1423 1502 473691945 473692024 5.170000e-22 115


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 TraesCS3D01G261600 chr3D 363592703 363594990 2287 False 4226.00 4226 100.0000 1 2288 1 chr3D.!!$F1 2287
1 TraesCS3D01G261600 chr3A 484631648 484635276 3628 False 674.75 1000 93.7250 1 2286 4 chr3A.!!$F1 2285
2 TraesCS3D01G261600 chr3B 473689103 473692714 3611 False 508.00 861 91.9838 1 2286 5 chr3B.!!$F1 2285

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
673 2176 0.034337 TTCAACACCGGTCACTAGGC 59.966 55.0 2.59 0.0 0.0 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1551 3117 0.035152 TAAGGTGCCTGGTGAGCATG 60.035 55.0 0.0 0.0 43.29 4.06 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
33 34 4.041567 TCATTGGTGTCACAGTGGATACTT 59.958 41.667 5.12 0.00 34.07 2.24
66 67 9.491406 AGATTATAGCATCAGAGGTATTCTCAT 57.509 33.333 0.00 0.00 44.81 2.90
82 83 7.547370 GGTATTCTCATATAGATTGCTTCGCTT 59.453 37.037 0.00 0.00 33.05 4.68
100 101 5.230182 TCGCTTATGGAGTATGCTTGTATG 58.770 41.667 0.00 0.00 32.75 2.39
166 167 5.593909 TGAACTCAACTGGTGTTTCATCAAT 59.406 36.000 7.96 0.00 33.60 2.57
204 205 5.640732 ACTTGGTTCGTGCAATCATATTTC 58.359 37.500 0.00 0.00 0.00 2.17
211 480 4.332543 TCGTGCAATCATATTTCCTCACAC 59.667 41.667 0.00 0.00 0.00 3.82
245 1558 0.754957 TATTTGGAATGGCCCTGCGG 60.755 55.000 0.00 0.00 34.97 5.69
263 1576 1.887242 GCGTGCAGTCTGTGGTCAA 60.887 57.895 0.93 0.00 0.00 3.18
274 1587 0.251297 TGTGGTCAAGATTGCTGGGG 60.251 55.000 0.00 0.00 0.00 4.96
280 1593 3.091545 GTCAAGATTGCTGGGGAAATGA 58.908 45.455 0.00 0.00 0.00 2.57
305 1618 0.865111 CATGACTTCACGCGTTTGGA 59.135 50.000 10.22 0.00 0.00 3.53
351 1664 5.181748 AGATGTCTGATCTGTTTAGTTGCC 58.818 41.667 0.00 0.00 0.00 4.52
471 1784 4.030216 GCAATTGAGGGAGGGGAATAAAA 58.970 43.478 10.34 0.00 0.00 1.52
513 1826 5.772825 TCCTTCAACCAGATGTTTTCTTG 57.227 39.130 0.00 0.00 34.00 3.02
523 1836 3.073650 AGATGTTTTCTTGGTCAGAGCCT 59.926 43.478 0.00 0.00 31.12 4.58
573 1886 5.428253 CCAGTAGTTTATGCCAGAAGCTTA 58.572 41.667 0.00 0.00 44.23 3.09
575 1888 5.874810 CAGTAGTTTATGCCAGAAGCTTACA 59.125 40.000 0.00 0.00 44.23 2.41
576 1889 5.875359 AGTAGTTTATGCCAGAAGCTTACAC 59.125 40.000 0.00 0.00 44.23 2.90
582 1895 1.727335 GCCAGAAGCTTACACGAACTC 59.273 52.381 0.00 0.00 38.99 3.01
583 1896 2.610727 GCCAGAAGCTTACACGAACTCT 60.611 50.000 0.00 0.00 38.99 3.24
584 1897 3.246619 CCAGAAGCTTACACGAACTCTC 58.753 50.000 0.00 0.00 0.00 3.20
586 1899 2.095161 AGAAGCTTACACGAACTCTCCG 60.095 50.000 0.00 0.00 0.00 4.63
587 1900 1.531423 AGCTTACACGAACTCTCCGA 58.469 50.000 0.00 0.00 0.00 4.55
588 1901 1.199558 AGCTTACACGAACTCTCCGAC 59.800 52.381 0.00 0.00 0.00 4.79
597 2091 2.432628 CTCTCCGACGGTGTTGCC 60.433 66.667 14.79 0.00 0.00 4.52
609 2103 0.324943 GTGTTGCCTCTTAGCCTCCA 59.675 55.000 0.00 0.00 0.00 3.86
614 2108 3.777106 TGCCTCTTAGCCTCCATATTG 57.223 47.619 0.00 0.00 0.00 1.90
622 2116 3.659183 AGCCTCCATATTGCAGAAACT 57.341 42.857 0.00 0.00 0.00 2.66
641 2144 2.076100 CTACTTCGCCATTGCTCAACA 58.924 47.619 0.00 0.00 34.43 3.33
644 2147 2.297033 ACTTCGCCATTGCTCAACATTT 59.703 40.909 0.00 0.00 34.43 2.32
663 2166 5.748152 ACATTTGAAAATCTGTTCAACACCG 59.252 36.000 0.01 0.00 44.96 4.94
666 2169 3.314080 TGAAAATCTGTTCAACACCGGTC 59.686 43.478 2.59 0.00 34.59 4.79
667 2170 2.631160 AATCTGTTCAACACCGGTCA 57.369 45.000 2.59 0.00 0.00 4.02
668 2171 1.878953 ATCTGTTCAACACCGGTCAC 58.121 50.000 2.59 0.00 0.00 3.67
669 2172 0.828022 TCTGTTCAACACCGGTCACT 59.172 50.000 2.59 0.00 0.00 3.41
670 2173 2.033372 TCTGTTCAACACCGGTCACTA 58.967 47.619 2.59 0.00 0.00 2.74
671 2174 2.035449 TCTGTTCAACACCGGTCACTAG 59.965 50.000 2.59 0.00 0.00 2.57
672 2175 1.069513 TGTTCAACACCGGTCACTAGG 59.930 52.381 2.59 0.00 0.00 3.02
673 2176 0.034337 TTCAACACCGGTCACTAGGC 59.966 55.000 2.59 0.00 0.00 3.93
674 2177 0.830444 TCAACACCGGTCACTAGGCT 60.830 55.000 2.59 0.00 0.00 4.58
675 2178 0.389948 CAACACCGGTCACTAGGCTC 60.390 60.000 2.59 0.00 0.00 4.70
676 2179 1.874345 AACACCGGTCACTAGGCTCG 61.874 60.000 2.59 0.00 0.00 5.03
677 2180 2.044555 CACCGGTCACTAGGCTCGA 61.045 63.158 2.59 0.00 0.00 4.04
678 2181 2.045131 ACCGGTCACTAGGCTCGAC 61.045 63.158 0.00 0.00 0.00 4.20
679 2182 2.044555 CCGGTCACTAGGCTCGACA 61.045 63.158 12.09 0.00 0.00 4.35
680 2183 1.136984 CGGTCACTAGGCTCGACAC 59.863 63.158 12.09 0.30 0.00 3.67
681 2184 1.306642 CGGTCACTAGGCTCGACACT 61.307 60.000 12.09 0.00 0.00 3.55
682 2185 1.747709 GGTCACTAGGCTCGACACTA 58.252 55.000 12.09 0.00 0.00 2.74
722 2225 2.805671 CAGACACTTTTATCGGTGTGCA 59.194 45.455 3.42 0.00 45.17 4.57
723 2226 3.067106 AGACACTTTTATCGGTGTGCAG 58.933 45.455 3.42 0.00 45.17 4.41
743 2255 8.084684 TGTGCAGCACATTATTAATAACAAACA 58.915 29.630 24.84 0.00 39.62 2.83
759 2294 5.235305 ACAAACATAATCTTTGCTAGGCG 57.765 39.130 0.00 0.00 32.71 5.52
867 2406 2.729360 GCAACCGTGTAATTCAAAAGCC 59.271 45.455 0.00 0.00 0.00 4.35
873 2415 6.807789 ACCGTGTAATTCAAAAGCCTTAAAA 58.192 32.000 0.00 0.00 0.00 1.52
886 2428 3.257127 AGCCTTAAAATTTTAGCGGCACA 59.743 39.130 32.53 12.96 40.49 4.57
887 2429 3.991121 GCCTTAAAATTTTAGCGGCACAA 59.009 39.130 29.54 11.27 39.15 3.33
890 2432 6.348132 GCCTTAAAATTTTAGCGGCACAATTT 60.348 34.615 29.54 6.83 39.15 1.82
895 2437 3.552604 TTTAGCGGCACAATTTCAGAC 57.447 42.857 1.45 0.00 0.00 3.51
911 2455 3.952508 ACAGCATGGCACGGGTGA 61.953 61.111 22.17 0.00 43.62 4.02
936 2487 5.232414 CGGCTTCTCTTGCTACAAATAGTAC 59.768 44.000 0.00 0.00 0.00 2.73
937 2488 6.106673 GGCTTCTCTTGCTACAAATAGTACA 58.893 40.000 0.00 0.00 0.00 2.90
942 2493 7.097192 TCTCTTGCTACAAATAGTACACCAAG 58.903 38.462 0.00 0.00 33.68 3.61
947 2498 4.634012 ACAAATAGTACACCAAGCCTCA 57.366 40.909 0.00 0.00 0.00 3.86
966 2517 1.480137 CACTTGTGCTCCCAAAACCAA 59.520 47.619 0.00 0.00 0.00 3.67
985 2536 2.191128 AACAGAGTCCACTGCAATCC 57.809 50.000 0.00 0.00 41.06 3.01
986 2537 0.036952 ACAGAGTCCACTGCAATCCG 60.037 55.000 0.00 0.00 41.06 4.18
987 2538 0.036952 CAGAGTCCACTGCAATCCGT 60.037 55.000 0.00 0.00 0.00 4.69
988 2539 0.036952 AGAGTCCACTGCAATCCGTG 60.037 55.000 0.00 0.00 0.00 4.94
1042 2593 2.986979 TCGTAGCCGTGCTCACCA 60.987 61.111 1.46 0.00 40.44 4.17
1372 2926 1.289380 GCCGTCTCCGTTTCTGACT 59.711 57.895 0.00 0.00 0.00 3.41
1373 2927 1.009389 GCCGTCTCCGTTTCTGACTG 61.009 60.000 0.00 0.00 0.00 3.51
1374 2928 1.009389 CCGTCTCCGTTTCTGACTGC 61.009 60.000 0.00 0.00 0.00 4.40
1375 2929 1.009389 CGTCTCCGTTTCTGACTGCC 61.009 60.000 0.00 0.00 0.00 4.85
1376 2930 1.009389 GTCTCCGTTTCTGACTGCCG 61.009 60.000 0.00 0.00 0.00 5.69
1377 2931 1.738099 CTCCGTTTCTGACTGCCGG 60.738 63.158 0.00 0.00 39.98 6.13
1378 2932 2.742372 CCGTTTCTGACTGCCGGG 60.742 66.667 2.18 0.00 35.11 5.73
1379 2933 2.030562 CGTTTCTGACTGCCGGGT 59.969 61.111 2.18 0.00 0.00 5.28
1380 2934 2.317609 CGTTTCTGACTGCCGGGTG 61.318 63.158 2.18 0.00 0.00 4.61
1381 2935 1.070786 GTTTCTGACTGCCGGGTGA 59.929 57.895 2.18 0.00 0.00 4.02
1382 2936 0.321653 GTTTCTGACTGCCGGGTGAT 60.322 55.000 2.18 0.00 0.00 3.06
1383 2937 0.321564 TTTCTGACTGCCGGGTGATG 60.322 55.000 2.18 0.00 0.00 3.07
1384 2938 1.480212 TTCTGACTGCCGGGTGATGT 61.480 55.000 2.18 0.00 0.00 3.06
1385 2939 1.742880 CTGACTGCCGGGTGATGTG 60.743 63.158 2.18 0.00 0.00 3.21
1386 2940 2.436646 GACTGCCGGGTGATGTGG 60.437 66.667 2.18 0.00 0.00 4.17
1387 2941 3.249189 ACTGCCGGGTGATGTGGT 61.249 61.111 2.18 0.00 0.00 4.16
1388 2942 2.747460 CTGCCGGGTGATGTGGTG 60.747 66.667 2.18 0.00 0.00 4.17
1389 2943 3.551496 CTGCCGGGTGATGTGGTGT 62.551 63.158 2.18 0.00 0.00 4.16
1390 2944 2.746277 GCCGGGTGATGTGGTGTC 60.746 66.667 2.18 0.00 0.00 3.67
1391 2945 2.747022 CCGGGTGATGTGGTGTCA 59.253 61.111 0.00 0.00 0.00 3.58
1392 2946 1.375908 CCGGGTGATGTGGTGTCAG 60.376 63.158 0.00 0.00 0.00 3.51
1393 2947 1.671166 CGGGTGATGTGGTGTCAGA 59.329 57.895 0.00 0.00 0.00 3.27
1394 2948 0.670546 CGGGTGATGTGGTGTCAGAC 60.671 60.000 0.00 0.00 0.00 3.51
1395 2949 0.396435 GGGTGATGTGGTGTCAGACA 59.604 55.000 0.00 0.00 0.00 3.41
1396 2950 1.202758 GGGTGATGTGGTGTCAGACAA 60.203 52.381 4.32 0.00 0.00 3.18
1397 2951 2.146342 GGTGATGTGGTGTCAGACAAG 58.854 52.381 4.32 0.00 0.00 3.16
1398 2952 2.224281 GGTGATGTGGTGTCAGACAAGA 60.224 50.000 4.32 0.00 0.00 3.02
1399 2953 3.466836 GTGATGTGGTGTCAGACAAGAA 58.533 45.455 4.32 0.00 0.00 2.52
1400 2954 3.496130 GTGATGTGGTGTCAGACAAGAAG 59.504 47.826 4.32 0.00 0.00 2.85
1401 2955 3.387699 TGATGTGGTGTCAGACAAGAAGA 59.612 43.478 4.32 0.00 0.00 2.87
1402 2956 3.459232 TGTGGTGTCAGACAAGAAGAG 57.541 47.619 4.32 0.00 0.00 2.85
1403 2957 2.766263 TGTGGTGTCAGACAAGAAGAGT 59.234 45.455 4.32 0.00 0.00 3.24
1404 2958 3.197766 TGTGGTGTCAGACAAGAAGAGTT 59.802 43.478 4.32 0.00 0.00 3.01
1405 2959 3.557595 GTGGTGTCAGACAAGAAGAGTTG 59.442 47.826 4.32 0.00 0.00 3.16
1406 2960 3.197766 TGGTGTCAGACAAGAAGAGTTGT 59.802 43.478 4.32 0.00 43.49 3.32
1407 2961 3.557595 GGTGTCAGACAAGAAGAGTTGTG 59.442 47.826 4.32 0.00 40.83 3.33
1408 2962 4.433615 GTGTCAGACAAGAAGAGTTGTGA 58.566 43.478 4.32 0.00 40.83 3.58
1409 2963 5.053145 GTGTCAGACAAGAAGAGTTGTGAT 58.947 41.667 4.32 0.00 40.83 3.06
1410 2964 6.216569 GTGTCAGACAAGAAGAGTTGTGATA 58.783 40.000 4.32 0.00 40.83 2.15
1411 2965 6.701841 GTGTCAGACAAGAAGAGTTGTGATAA 59.298 38.462 4.32 0.00 40.83 1.75
1412 2966 6.701841 TGTCAGACAAGAAGAGTTGTGATAAC 59.298 38.462 0.00 0.00 40.83 1.89
1413 2967 5.920840 TCAGACAAGAAGAGTTGTGATAACG 59.079 40.000 0.00 0.00 40.83 3.18
1414 2968 5.119279 CAGACAAGAAGAGTTGTGATAACGG 59.881 44.000 0.00 0.00 40.83 4.44
1415 2969 5.010719 AGACAAGAAGAGTTGTGATAACGGA 59.989 40.000 0.00 0.00 40.83 4.69
1416 2970 4.989168 ACAAGAAGAGTTGTGATAACGGAC 59.011 41.667 0.00 0.00 39.25 4.79
1417 2971 3.834610 AGAAGAGTTGTGATAACGGACG 58.165 45.455 0.00 0.00 0.00 4.79
1418 2972 2.649331 AGAGTTGTGATAACGGACGG 57.351 50.000 0.00 0.00 0.00 4.79
1419 2973 0.997196 GAGTTGTGATAACGGACGGC 59.003 55.000 0.00 0.00 0.00 5.68
1420 2974 0.390735 AGTTGTGATAACGGACGGCC 60.391 55.000 0.00 0.00 0.00 6.13
1421 2975 0.390735 GTTGTGATAACGGACGGCCT 60.391 55.000 5.33 0.00 0.00 5.19
1424 2978 0.390735 GTGATAACGGACGGCCTTGT 60.391 55.000 5.33 0.00 0.00 3.16
1470 3025 0.458889 ATGCCATCAAATGTGCGTGC 60.459 50.000 0.00 0.00 31.73 5.34
1490 3051 2.029244 GCGGTGATCGTGTCTTATTGTG 59.971 50.000 0.00 0.00 41.72 3.33
1491 3052 2.029244 CGGTGATCGTGTCTTATTGTGC 59.971 50.000 0.00 0.00 0.00 4.57
1501 3067 5.330498 CGTGTCTTATTGTGCGTTTGTTTTC 60.330 40.000 0.00 0.00 0.00 2.29
1502 3068 5.038033 TGTCTTATTGTGCGTTTGTTTTCC 58.962 37.500 0.00 0.00 0.00 3.13
1503 3069 5.163602 TGTCTTATTGTGCGTTTGTTTTCCT 60.164 36.000 0.00 0.00 0.00 3.36
1504 3070 5.173131 GTCTTATTGTGCGTTTGTTTTCCTG 59.827 40.000 0.00 0.00 0.00 3.86
1505 3071 3.518634 ATTGTGCGTTTGTTTTCCTGT 57.481 38.095 0.00 0.00 0.00 4.00
1506 3072 2.270275 TGTGCGTTTGTTTTCCTGTG 57.730 45.000 0.00 0.00 0.00 3.66
1507 3073 1.135257 TGTGCGTTTGTTTTCCTGTGG 60.135 47.619 0.00 0.00 0.00 4.17
1508 3074 0.457851 TGCGTTTGTTTTCCTGTGGG 59.542 50.000 0.00 0.00 0.00 4.61
1509 3075 0.249280 GCGTTTGTTTTCCTGTGGGG 60.249 55.000 0.00 0.00 0.00 4.96
1510 3076 1.107945 CGTTTGTTTTCCTGTGGGGT 58.892 50.000 0.00 0.00 36.25 4.95
1511 3077 1.478916 CGTTTGTTTTCCTGTGGGGTT 59.521 47.619 0.00 0.00 36.25 4.11
1512 3078 2.737039 CGTTTGTTTTCCTGTGGGGTTG 60.737 50.000 0.00 0.00 36.25 3.77
1513 3079 0.827368 TTGTTTTCCTGTGGGGTTGC 59.173 50.000 0.00 0.00 36.25 4.17
1514 3080 1.362355 GTTTTCCTGTGGGGTTGCG 59.638 57.895 0.00 0.00 36.25 4.85
1515 3081 1.830408 TTTTCCTGTGGGGTTGCGG 60.830 57.895 0.00 0.00 36.25 5.69
1516 3082 2.575455 TTTTCCTGTGGGGTTGCGGT 62.575 55.000 0.00 0.00 36.25 5.68
1517 3083 3.783362 TTCCTGTGGGGTTGCGGTG 62.783 63.158 0.00 0.00 36.25 4.94
1530 3096 0.449786 TGCGGTGGCATAATTTGACG 59.550 50.000 0.00 0.00 46.21 4.35
1531 3097 0.730265 GCGGTGGCATAATTTGACGA 59.270 50.000 0.00 0.00 35.37 4.20
1532 3098 1.131504 GCGGTGGCATAATTTGACGAA 59.868 47.619 0.00 0.00 35.37 3.85
1533 3099 2.791158 GCGGTGGCATAATTTGACGAAG 60.791 50.000 0.00 0.00 35.37 3.79
1534 3100 5.264448 GCGGTGGCATAATTTGACGAAGT 62.264 47.826 0.00 0.00 41.98 3.01
1535 3101 6.671045 GCGGTGGCATAATTTGACGAAGTT 62.671 45.833 0.00 0.00 39.70 2.66
1550 3116 3.692791 GAAGTTGTTGTTCTTCGCCTT 57.307 42.857 0.00 0.00 32.34 4.35
1551 3117 3.618698 GAAGTTGTTGTTCTTCGCCTTC 58.381 45.455 0.00 0.00 32.34 3.46
1552 3118 2.639065 AGTTGTTGTTCTTCGCCTTCA 58.361 42.857 0.00 0.00 0.00 3.02
1553 3119 3.214328 AGTTGTTGTTCTTCGCCTTCAT 58.786 40.909 0.00 0.00 0.00 2.57
1554 3120 3.003689 AGTTGTTGTTCTTCGCCTTCATG 59.996 43.478 0.00 0.00 0.00 3.07
1555 3121 1.266718 TGTTGTTCTTCGCCTTCATGC 59.733 47.619 0.00 0.00 0.00 4.06
1556 3122 1.537202 GTTGTTCTTCGCCTTCATGCT 59.463 47.619 0.00 0.00 0.00 3.79
1557 3123 1.442769 TGTTCTTCGCCTTCATGCTC 58.557 50.000 0.00 0.00 0.00 4.26
1558 3124 1.270785 TGTTCTTCGCCTTCATGCTCA 60.271 47.619 0.00 0.00 0.00 4.26
1559 3125 1.129437 GTTCTTCGCCTTCATGCTCAC 59.871 52.381 0.00 0.00 0.00 3.51
1560 3126 0.391661 TCTTCGCCTTCATGCTCACC 60.392 55.000 0.00 0.00 0.00 4.02
1561 3127 0.674581 CTTCGCCTTCATGCTCACCA 60.675 55.000 0.00 0.00 0.00 4.17
1562 3128 0.674581 TTCGCCTTCATGCTCACCAG 60.675 55.000 0.00 0.00 0.00 4.00
1563 3129 2.110967 CGCCTTCATGCTCACCAGG 61.111 63.158 0.00 0.00 0.00 4.45
1564 3130 2.413142 GCCTTCATGCTCACCAGGC 61.413 63.158 0.00 0.00 43.26 4.85
1565 3131 1.001764 CCTTCATGCTCACCAGGCA 60.002 57.895 0.00 0.00 44.05 4.75
1566 3132 1.310933 CCTTCATGCTCACCAGGCAC 61.311 60.000 0.00 0.00 42.69 5.01
1567 3133 1.303561 TTCATGCTCACCAGGCACC 60.304 57.895 0.00 0.00 42.69 5.01
1568 3134 1.782201 TTCATGCTCACCAGGCACCT 61.782 55.000 0.00 0.00 42.69 4.00
1569 3135 1.303888 CATGCTCACCAGGCACCTT 60.304 57.895 0.00 0.00 42.69 3.50
1570 3136 0.035152 CATGCTCACCAGGCACCTTA 60.035 55.000 0.00 0.00 42.69 2.69
1571 3137 0.698238 ATGCTCACCAGGCACCTTAA 59.302 50.000 0.00 0.00 42.69 1.85
1572 3138 0.698238 TGCTCACCAGGCACCTTAAT 59.302 50.000 0.00 0.00 34.56 1.40
1573 3139 1.075374 TGCTCACCAGGCACCTTAATT 59.925 47.619 0.00 0.00 34.56 1.40
1574 3140 2.171003 GCTCACCAGGCACCTTAATTT 58.829 47.619 0.00 0.00 0.00 1.82
1575 3141 2.094545 GCTCACCAGGCACCTTAATTTG 60.095 50.000 0.00 0.00 0.00 2.32
1576 3142 3.420893 CTCACCAGGCACCTTAATTTGA 58.579 45.455 0.00 0.00 0.00 2.69
1577 3143 3.420893 TCACCAGGCACCTTAATTTGAG 58.579 45.455 0.00 0.00 0.00 3.02
1578 3144 2.094545 CACCAGGCACCTTAATTTGAGC 60.095 50.000 0.00 0.00 0.00 4.26
1579 3145 1.133025 CCAGGCACCTTAATTTGAGCG 59.867 52.381 0.00 0.00 0.00 5.03
1580 3146 1.812571 CAGGCACCTTAATTTGAGCGT 59.187 47.619 0.00 0.00 0.00 5.07
1581 3147 2.084546 AGGCACCTTAATTTGAGCGTC 58.915 47.619 0.00 0.00 0.00 5.19
1582 3148 2.084546 GGCACCTTAATTTGAGCGTCT 58.915 47.619 0.00 0.00 0.00 4.18
1583 3149 2.096013 GGCACCTTAATTTGAGCGTCTC 59.904 50.000 0.58 0.58 0.00 3.36
1584 3150 2.222819 GCACCTTAATTTGAGCGTCTCG 60.223 50.000 3.08 0.00 32.35 4.04
1585 3151 3.250744 CACCTTAATTTGAGCGTCTCGA 58.749 45.455 3.08 0.00 32.35 4.04
1586 3152 3.304559 CACCTTAATTTGAGCGTCTCGAG 59.695 47.826 5.93 5.93 32.35 4.04
1587 3153 3.192844 ACCTTAATTTGAGCGTCTCGAGA 59.807 43.478 12.08 12.08 32.35 4.04
1588 3154 4.142138 ACCTTAATTTGAGCGTCTCGAGAT 60.142 41.667 19.90 1.81 32.35 2.75
1589 3155 5.067413 ACCTTAATTTGAGCGTCTCGAGATA 59.933 40.000 19.90 0.07 32.35 1.98
1590 3156 6.153067 CCTTAATTTGAGCGTCTCGAGATAT 58.847 40.000 19.90 7.57 32.35 1.63
1591 3157 6.642950 CCTTAATTTGAGCGTCTCGAGATATT 59.357 38.462 19.90 6.82 32.35 1.28
1592 3158 7.169982 CCTTAATTTGAGCGTCTCGAGATATTT 59.830 37.037 19.90 4.90 32.35 1.40
1593 3159 5.896922 ATTTGAGCGTCTCGAGATATTTG 57.103 39.130 19.90 7.71 32.35 2.32
1594 3160 4.371855 TTGAGCGTCTCGAGATATTTGT 57.628 40.909 19.90 0.31 32.35 2.83
1595 3161 3.695816 TGAGCGTCTCGAGATATTTGTG 58.304 45.455 19.90 4.24 32.35 3.33
1596 3162 3.128764 TGAGCGTCTCGAGATATTTGTGT 59.871 43.478 19.90 0.00 32.35 3.72
1597 3163 3.439293 AGCGTCTCGAGATATTTGTGTG 58.561 45.455 19.90 1.87 0.00 3.82
1598 3164 3.119459 AGCGTCTCGAGATATTTGTGTGT 60.119 43.478 19.90 0.00 0.00 3.72
1599 3165 3.240861 GCGTCTCGAGATATTTGTGTGTC 59.759 47.826 19.90 0.00 0.00 3.67
1600 3166 4.663166 CGTCTCGAGATATTTGTGTGTCT 58.337 43.478 19.90 0.00 0.00 3.41
1601 3167 4.731000 CGTCTCGAGATATTTGTGTGTCTC 59.269 45.833 19.90 0.00 34.23 3.36
1602 3168 5.641709 GTCTCGAGATATTTGTGTGTCTCA 58.358 41.667 19.90 0.00 36.49 3.27
1603 3169 6.093404 GTCTCGAGATATTTGTGTGTCTCAA 58.907 40.000 19.90 0.00 36.49 3.02
1604 3170 6.034044 GTCTCGAGATATTTGTGTGTCTCAAC 59.966 42.308 19.90 0.00 36.49 3.18
1605 3171 5.778862 TCGAGATATTTGTGTGTCTCAACA 58.221 37.500 0.00 0.00 36.49 3.33
1606 3172 6.220201 TCGAGATATTTGTGTGTCTCAACAA 58.780 36.000 0.00 0.00 36.49 2.83
1613 3179 4.354071 TGTGTGTCTCAACAACAACATG 57.646 40.909 0.00 0.00 37.08 3.21
1622 3188 4.946445 TCAACAACAACATGTGATTGCAT 58.054 34.783 17.92 8.20 32.81 3.96
1626 3192 5.543714 ACAACAACATGTGATTGCATGAAT 58.456 33.333 17.92 0.00 46.65 2.57
1637 3203 8.510243 TGTGATTGCATGAATAAGTTATCTGT 57.490 30.769 0.00 0.00 0.00 3.41
1651 3223 6.963083 AGTTATCTGTCACCAGTCCTATAC 57.037 41.667 0.00 0.00 39.82 1.47
1663 3235 5.962031 ACCAGTCCTATACCTGACAATAACA 59.038 40.000 0.00 0.00 33.89 2.41
1680 3252 9.683069 GACAATAACAAAATGAAGTTCTCATGT 57.317 29.630 4.17 1.91 44.43 3.21
1727 3301 2.739913 CAAATCCAAAAGCAGGTGCATG 59.260 45.455 4.48 0.46 45.16 4.06
1742 3316 2.095059 GTGCATGTCCCTGAACATTGTC 60.095 50.000 0.00 0.00 37.78 3.18
1769 3349 2.544685 CATGTCTTCTACGCTTCAGGG 58.455 52.381 0.00 0.00 0.00 4.45
1771 3351 1.183549 GTCTTCTACGCTTCAGGGGA 58.816 55.000 0.00 0.00 0.00 4.81
2019 3599 1.139058 ACCTTGACGTGTCTCTTTGCT 59.861 47.619 0.00 0.00 0.00 3.91
2022 3602 2.423926 TGACGTGTCTCTTTGCTCTC 57.576 50.000 0.00 0.00 0.00 3.20
2130 3710 1.215673 TCGTAGCCATCTCTCTCCCTT 59.784 52.381 0.00 0.00 0.00 3.95
2136 3716 0.179089 CATCTCTCTCCCTTGCACCG 60.179 60.000 0.00 0.00 0.00 4.94
2190 3770 4.277672 CCAACATCAGATATCTTTGGGCAG 59.722 45.833 19.87 2.67 30.35 4.85
2196 3776 3.044156 AGATATCTTTGGGCAGAGCTCA 58.956 45.455 17.77 0.00 37.19 4.26
2241 3821 2.131776 TGATGCTGATGTTCATGCCA 57.868 45.000 0.00 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.431416 AAAAGTATCCACTGTGACACCA 57.569 40.909 9.86 0.00 34.36 4.17
100 101 5.405571 CCAGATGTACGATACCTGTTAATGC 59.594 44.000 0.00 0.00 0.00 3.56
107 108 3.256879 AGCATCCAGATGTACGATACCTG 59.743 47.826 9.29 0.00 40.80 4.00
113 114 2.294512 CTGCTAGCATCCAGATGTACGA 59.705 50.000 19.72 0.00 40.80 3.43
166 167 2.304761 ACCAAGTCCCAGATAAGCGAAA 59.695 45.455 0.00 0.00 0.00 3.46
204 205 9.871238 AAATAGTATAACAAGTAGTGTGTGAGG 57.129 33.333 0.00 0.00 40.60 3.86
245 1558 1.835483 CTTGACCACAGACTGCACGC 61.835 60.000 1.25 0.00 0.00 5.34
251 1564 2.551721 CCAGCAATCTTGACCACAGACT 60.552 50.000 0.00 0.00 0.00 3.24
255 1568 0.251297 CCCCAGCAATCTTGACCACA 60.251 55.000 0.00 0.00 0.00 4.17
263 1576 1.687368 GCCTCATTTCCCCAGCAATCT 60.687 52.381 0.00 0.00 0.00 2.40
274 1587 1.064654 GAAGTCATGCCGCCTCATTTC 59.935 52.381 0.00 0.00 0.00 2.17
280 1593 2.434884 CGTGAAGTCATGCCGCCT 60.435 61.111 0.00 0.00 0.00 5.52
305 1618 8.408043 TCTAACAAATCAATCAGGTGAACATT 57.592 30.769 0.00 0.00 0.00 2.71
351 1664 4.271687 GTGCCTATAAAGACGCAATTTCG 58.728 43.478 0.00 0.00 32.04 3.46
446 1759 1.153086 CCCCTCCCTCAATTGCTCG 60.153 63.158 0.00 0.00 0.00 5.03
471 1784 4.431131 CCCTTGCCCTGCATCCGT 62.431 66.667 0.00 0.00 38.76 4.69
513 1826 2.621526 GCTTCTAGTCTAGGCTCTGACC 59.378 54.545 0.00 0.00 34.02 4.02
523 1836 6.591750 ACAGCTAAACTTGCTTCTAGTCTA 57.408 37.500 0.00 0.00 38.92 2.59
573 1886 1.895707 ACCGTCGGAGAGTTCGTGT 60.896 57.895 20.51 0.00 36.95 4.49
575 1888 1.450531 AACACCGTCGGAGAGTTCGT 61.451 55.000 20.51 0.14 36.95 3.85
576 1889 1.002250 CAACACCGTCGGAGAGTTCG 61.002 60.000 20.51 10.12 36.95 3.95
582 1895 2.432628 GAGGCAACACCGTCGGAG 60.433 66.667 20.51 13.51 46.52 4.63
583 1896 1.180456 TAAGAGGCAACACCGTCGGA 61.180 55.000 20.51 0.00 46.52 4.55
584 1897 0.736325 CTAAGAGGCAACACCGTCGG 60.736 60.000 10.48 10.48 46.52 4.79
586 1899 1.019805 GGCTAAGAGGCAACACCGTC 61.020 60.000 0.00 0.00 46.52 4.79
587 1900 1.003718 GGCTAAGAGGCAACACCGT 60.004 57.895 0.00 0.00 46.52 4.83
588 1901 0.741221 GAGGCTAAGAGGCAACACCG 60.741 60.000 2.66 0.00 46.52 4.94
597 2091 4.613925 TCTGCAATATGGAGGCTAAGAG 57.386 45.455 0.00 0.00 36.40 2.85
609 2103 4.513442 TGGCGAAGTAGTTTCTGCAATAT 58.487 39.130 0.00 0.00 37.19 1.28
614 2108 2.729156 GCAATGGCGAAGTAGTTTCTGC 60.729 50.000 0.00 0.00 35.79 4.26
641 2144 5.163457 ACCGGTGTTGAACAGATTTTCAAAT 60.163 36.000 6.12 0.00 44.96 2.32
644 2147 3.283751 ACCGGTGTTGAACAGATTTTCA 58.716 40.909 6.12 0.00 33.55 2.69
663 2166 1.671845 CTAGTGTCGAGCCTAGTGACC 59.328 57.143 9.24 0.00 0.00 4.02
666 2169 1.752683 ACCTAGTGTCGAGCCTAGTG 58.247 55.000 14.17 9.69 30.79 2.74
667 2170 2.093106 CAACCTAGTGTCGAGCCTAGT 58.907 52.381 14.17 3.84 30.79 2.57
668 2171 2.356382 CTCAACCTAGTGTCGAGCCTAG 59.644 54.545 10.13 10.13 0.00 3.02
669 2172 2.290768 ACTCAACCTAGTGTCGAGCCTA 60.291 50.000 0.00 0.00 0.00 3.93
670 2173 1.178276 CTCAACCTAGTGTCGAGCCT 58.822 55.000 0.00 0.00 0.00 4.58
671 2174 0.889306 ACTCAACCTAGTGTCGAGCC 59.111 55.000 0.00 0.00 0.00 4.70
672 2175 1.983972 CACTCAACCTAGTGTCGAGC 58.016 55.000 0.00 0.00 41.63 5.03
679 2182 4.652421 TGGTCTGTAAACACTCAACCTAGT 59.348 41.667 0.00 0.00 0.00 2.57
680 2183 5.010719 TCTGGTCTGTAAACACTCAACCTAG 59.989 44.000 0.00 0.00 0.00 3.02
681 2184 4.897076 TCTGGTCTGTAAACACTCAACCTA 59.103 41.667 0.00 0.00 0.00 3.08
682 2185 3.709653 TCTGGTCTGTAAACACTCAACCT 59.290 43.478 0.00 0.00 0.00 3.50
696 2199 3.679980 CACCGATAAAAGTGTCTGGTCTG 59.320 47.826 0.00 0.00 0.00 3.51
733 2236 7.915397 CGCCTAGCAAAGATTATGTTTGTTATT 59.085 33.333 14.72 3.66 37.25 1.40
734 2237 7.417612 CGCCTAGCAAAGATTATGTTTGTTAT 58.582 34.615 14.72 5.87 37.25 1.89
743 2255 2.498167 CTGCCGCCTAGCAAAGATTAT 58.502 47.619 0.00 0.00 43.52 1.28
830 2369 0.604243 TTGCGTAAACGGTGGAGCAT 60.604 50.000 4.49 0.00 40.23 3.79
859 2398 5.407084 GCCGCTAAAATTTTAAGGCTTTTGA 59.593 36.000 30.45 6.30 40.42 2.69
867 2406 7.791949 TGAAATTGTGCCGCTAAAATTTTAAG 58.208 30.769 11.62 8.60 33.54 1.85
873 2415 4.022416 TGTCTGAAATTGTGCCGCTAAAAT 60.022 37.500 0.00 0.00 0.00 1.82
886 2428 1.200716 CGTGCCATGCTGTCTGAAATT 59.799 47.619 0.00 0.00 0.00 1.82
887 2429 0.806868 CGTGCCATGCTGTCTGAAAT 59.193 50.000 0.00 0.00 0.00 2.17
890 2432 2.046988 CCGTGCCATGCTGTCTGA 60.047 61.111 0.00 0.00 0.00 3.27
895 2437 3.434319 GTCACCCGTGCCATGCTG 61.434 66.667 0.00 0.00 0.00 4.41
904 2448 2.207924 AAGAGAAGCCGTCACCCGT 61.208 57.895 0.00 0.00 33.66 5.28
911 2455 2.543777 TTTGTAGCAAGAGAAGCCGT 57.456 45.000 0.00 0.00 0.00 5.68
915 2459 7.097192 TGGTGTACTATTTGTAGCAAGAGAAG 58.903 38.462 0.00 0.00 0.00 2.85
942 2493 0.823356 TTTGGGAGCACAAGTGAGGC 60.823 55.000 4.04 0.00 0.00 4.70
947 2498 1.859302 TTGGTTTTGGGAGCACAAGT 58.141 45.000 0.00 0.00 0.00 3.16
966 2517 1.609061 CGGATTGCAGTGGACTCTGTT 60.609 52.381 3.02 0.00 37.70 3.16
985 2536 1.998315 CTTCATGGCTTCTCAGTCACG 59.002 52.381 0.00 0.00 37.50 4.35
986 2537 1.736681 GCTTCATGGCTTCTCAGTCAC 59.263 52.381 0.00 0.00 37.50 3.67
987 2538 1.339438 GGCTTCATGGCTTCTCAGTCA 60.339 52.381 0.00 0.00 39.60 3.41
988 2539 1.377536 GGCTTCATGGCTTCTCAGTC 58.622 55.000 0.00 0.00 38.32 3.51
1372 2926 3.545124 GACACCACATCACCCGGCA 62.545 63.158 0.00 0.00 0.00 5.69
1373 2927 2.746277 GACACCACATCACCCGGC 60.746 66.667 0.00 0.00 0.00 6.13
1374 2928 1.375908 CTGACACCACATCACCCGG 60.376 63.158 0.00 0.00 0.00 5.73
1375 2929 0.670546 GTCTGACACCACATCACCCG 60.671 60.000 2.24 0.00 0.00 5.28
1376 2930 0.396435 TGTCTGACACCACATCACCC 59.604 55.000 6.36 0.00 0.00 4.61
1377 2931 2.146342 CTTGTCTGACACCACATCACC 58.854 52.381 10.56 0.00 0.00 4.02
1378 2932 3.111853 TCTTGTCTGACACCACATCAC 57.888 47.619 10.56 0.00 0.00 3.06
1379 2933 3.387699 TCTTCTTGTCTGACACCACATCA 59.612 43.478 10.56 0.00 0.00 3.07
1380 2934 3.993081 CTCTTCTTGTCTGACACCACATC 59.007 47.826 10.56 0.00 0.00 3.06
1381 2935 3.389329 ACTCTTCTTGTCTGACACCACAT 59.611 43.478 10.56 0.00 0.00 3.21
1382 2936 2.766263 ACTCTTCTTGTCTGACACCACA 59.234 45.455 10.56 0.00 0.00 4.17
1383 2937 3.460857 ACTCTTCTTGTCTGACACCAC 57.539 47.619 10.56 0.00 0.00 4.16
1384 2938 3.197766 ACAACTCTTCTTGTCTGACACCA 59.802 43.478 10.56 0.00 27.41 4.17
1385 2939 3.557595 CACAACTCTTCTTGTCTGACACC 59.442 47.826 10.56 0.00 31.73 4.16
1386 2940 4.433615 TCACAACTCTTCTTGTCTGACAC 58.566 43.478 10.56 0.00 31.73 3.67
1387 2941 4.736126 TCACAACTCTTCTTGTCTGACA 57.264 40.909 6.36 6.36 31.73 3.58
1388 2942 6.129062 CGTTATCACAACTCTTCTTGTCTGAC 60.129 42.308 0.00 0.00 31.73 3.51
1389 2943 5.920840 CGTTATCACAACTCTTCTTGTCTGA 59.079 40.000 0.00 0.00 31.73 3.27
1390 2944 5.119279 CCGTTATCACAACTCTTCTTGTCTG 59.881 44.000 0.00 0.00 31.73 3.51
1391 2945 5.010719 TCCGTTATCACAACTCTTCTTGTCT 59.989 40.000 0.00 0.00 31.73 3.41
1392 2946 5.118817 GTCCGTTATCACAACTCTTCTTGTC 59.881 44.000 0.00 0.00 31.73 3.18
1393 2947 4.989168 GTCCGTTATCACAACTCTTCTTGT 59.011 41.667 0.00 0.00 34.56 3.16
1394 2948 4.090066 CGTCCGTTATCACAACTCTTCTTG 59.910 45.833 0.00 0.00 0.00 3.02
1395 2949 4.235360 CGTCCGTTATCACAACTCTTCTT 58.765 43.478 0.00 0.00 0.00 2.52
1396 2950 3.367087 CCGTCCGTTATCACAACTCTTCT 60.367 47.826 0.00 0.00 0.00 2.85
1397 2951 2.921754 CCGTCCGTTATCACAACTCTTC 59.078 50.000 0.00 0.00 0.00 2.87
1398 2952 2.929592 GCCGTCCGTTATCACAACTCTT 60.930 50.000 0.00 0.00 0.00 2.85
1399 2953 1.403780 GCCGTCCGTTATCACAACTCT 60.404 52.381 0.00 0.00 0.00 3.24
1400 2954 0.997196 GCCGTCCGTTATCACAACTC 59.003 55.000 0.00 0.00 0.00 3.01
1401 2955 0.390735 GGCCGTCCGTTATCACAACT 60.391 55.000 0.00 0.00 0.00 3.16
1402 2956 0.390735 AGGCCGTCCGTTATCACAAC 60.391 55.000 0.00 0.00 37.47 3.32
1403 2957 0.322322 AAGGCCGTCCGTTATCACAA 59.678 50.000 0.00 0.00 37.47 3.33
1404 2958 0.390603 CAAGGCCGTCCGTTATCACA 60.391 55.000 0.00 0.00 37.47 3.58
1405 2959 0.390735 ACAAGGCCGTCCGTTATCAC 60.391 55.000 0.00 0.00 37.47 3.06
1406 2960 0.322322 AACAAGGCCGTCCGTTATCA 59.678 50.000 0.00 0.00 37.47 2.15
1407 2961 2.199236 CTAACAAGGCCGTCCGTTATC 58.801 52.381 0.00 0.00 37.47 1.75
1408 2962 1.741394 GCTAACAAGGCCGTCCGTTAT 60.741 52.381 0.00 0.00 37.47 1.89
1409 2963 0.390209 GCTAACAAGGCCGTCCGTTA 60.390 55.000 0.00 3.20 37.47 3.18
1410 2964 1.670083 GCTAACAAGGCCGTCCGTT 60.670 57.895 0.00 2.03 37.47 4.44
1411 2965 2.047560 GCTAACAAGGCCGTCCGT 60.048 61.111 0.00 0.00 37.47 4.69
1412 2966 2.818274 GGCTAACAAGGCCGTCCG 60.818 66.667 0.00 0.00 40.19 4.79
1418 2972 2.098117 CACTGCTAATGGCTAACAAGGC 59.902 50.000 0.00 0.00 42.39 4.35
1419 2973 2.098117 GCACTGCTAATGGCTAACAAGG 59.902 50.000 0.00 0.00 42.39 3.61
1420 2974 3.012518 AGCACTGCTAATGGCTAACAAG 58.987 45.455 0.21 0.00 42.39 3.16
1421 2975 3.071874 AGCACTGCTAATGGCTAACAA 57.928 42.857 0.21 0.00 42.39 2.83
1424 2978 3.191162 CACAAAGCACTGCTAATGGCTAA 59.809 43.478 16.87 0.00 38.25 3.09
1429 2983 3.003585 TGACACACAAAGCACTGCTAATG 59.996 43.478 3.33 9.33 38.25 1.90
1470 3025 2.029244 GCACAATAAGACACGATCACCG 59.971 50.000 0.00 0.00 45.44 4.94
1490 3051 0.249280 CCCCACAGGAAAACAAACGC 60.249 55.000 0.00 0.00 38.24 4.84
1491 3052 1.107945 ACCCCACAGGAAAACAAACG 58.892 50.000 0.00 0.00 39.89 3.60
1512 3078 0.730265 TCGTCAAATTATGCCACCGC 59.270 50.000 0.00 0.00 0.00 5.68
1513 3079 2.418628 ACTTCGTCAAATTATGCCACCG 59.581 45.455 0.00 0.00 0.00 4.94
1514 3080 4.165779 CAACTTCGTCAAATTATGCCACC 58.834 43.478 0.00 0.00 0.00 4.61
1515 3081 4.794169 ACAACTTCGTCAAATTATGCCAC 58.206 39.130 0.00 0.00 0.00 5.01
1516 3082 5.218885 CAACAACTTCGTCAAATTATGCCA 58.781 37.500 0.00 0.00 0.00 4.92
1517 3083 5.219633 ACAACAACTTCGTCAAATTATGCC 58.780 37.500 0.00 0.00 0.00 4.40
1518 3084 6.636850 AGAACAACAACTTCGTCAAATTATGC 59.363 34.615 0.00 0.00 0.00 3.14
1519 3085 8.560576 AAGAACAACAACTTCGTCAAATTATG 57.439 30.769 0.00 0.00 0.00 1.90
1520 3086 8.782533 GAAGAACAACAACTTCGTCAAATTAT 57.217 30.769 0.00 0.00 34.30 1.28
1530 3096 3.064820 TGAAGGCGAAGAACAACAACTTC 59.935 43.478 0.00 0.00 39.05 3.01
1531 3097 3.013921 TGAAGGCGAAGAACAACAACTT 58.986 40.909 0.00 0.00 0.00 2.66
1532 3098 2.639065 TGAAGGCGAAGAACAACAACT 58.361 42.857 0.00 0.00 0.00 3.16
1533 3099 3.300009 CATGAAGGCGAAGAACAACAAC 58.700 45.455 0.00 0.00 0.00 3.32
1534 3100 2.287547 GCATGAAGGCGAAGAACAACAA 60.288 45.455 0.00 0.00 0.00 2.83
1535 3101 1.266718 GCATGAAGGCGAAGAACAACA 59.733 47.619 0.00 0.00 0.00 3.33
1536 3102 1.537202 AGCATGAAGGCGAAGAACAAC 59.463 47.619 0.00 0.00 39.27 3.32
1537 3103 1.806542 GAGCATGAAGGCGAAGAACAA 59.193 47.619 0.00 0.00 39.27 2.83
1538 3104 1.270785 TGAGCATGAAGGCGAAGAACA 60.271 47.619 0.00 0.00 39.27 3.18
1539 3105 1.129437 GTGAGCATGAAGGCGAAGAAC 59.871 52.381 0.00 0.00 39.27 3.01
1540 3106 1.442769 GTGAGCATGAAGGCGAAGAA 58.557 50.000 0.00 0.00 39.27 2.52
1541 3107 0.391661 GGTGAGCATGAAGGCGAAGA 60.392 55.000 0.00 0.00 39.27 2.87
1542 3108 0.674581 TGGTGAGCATGAAGGCGAAG 60.675 55.000 0.00 0.00 39.27 3.79
1543 3109 0.674581 CTGGTGAGCATGAAGGCGAA 60.675 55.000 0.00 0.00 39.27 4.70
1544 3110 1.078918 CTGGTGAGCATGAAGGCGA 60.079 57.895 0.00 0.00 39.27 5.54
1545 3111 2.110967 CCTGGTGAGCATGAAGGCG 61.111 63.158 0.00 0.00 39.27 5.52
1546 3112 2.413142 GCCTGGTGAGCATGAAGGC 61.413 63.158 0.00 0.45 46.04 4.35
1547 3113 1.001764 TGCCTGGTGAGCATGAAGG 60.002 57.895 0.00 0.00 34.69 3.46
1548 3114 1.310933 GGTGCCTGGTGAGCATGAAG 61.311 60.000 0.00 0.00 43.29 3.02
1549 3115 1.303561 GGTGCCTGGTGAGCATGAA 60.304 57.895 0.00 0.00 43.29 2.57
1550 3116 1.782201 AAGGTGCCTGGTGAGCATGA 61.782 55.000 0.00 0.00 43.29 3.07
1551 3117 0.035152 TAAGGTGCCTGGTGAGCATG 60.035 55.000 0.00 0.00 43.29 4.06
1552 3118 0.698238 TTAAGGTGCCTGGTGAGCAT 59.302 50.000 0.00 0.00 43.29 3.79
1553 3119 0.698238 ATTAAGGTGCCTGGTGAGCA 59.302 50.000 0.00 0.00 38.08 4.26
1554 3120 1.839424 AATTAAGGTGCCTGGTGAGC 58.161 50.000 0.00 0.00 0.00 4.26
1555 3121 3.420893 TCAAATTAAGGTGCCTGGTGAG 58.579 45.455 0.00 0.00 0.00 3.51
1556 3122 3.420893 CTCAAATTAAGGTGCCTGGTGA 58.579 45.455 0.00 0.00 0.00 4.02
1557 3123 2.094545 GCTCAAATTAAGGTGCCTGGTG 60.095 50.000 0.00 0.00 0.00 4.17
1558 3124 2.171003 GCTCAAATTAAGGTGCCTGGT 58.829 47.619 0.00 0.00 0.00 4.00
1559 3125 1.133025 CGCTCAAATTAAGGTGCCTGG 59.867 52.381 0.00 0.00 0.00 4.45
1560 3126 1.812571 ACGCTCAAATTAAGGTGCCTG 59.187 47.619 0.00 0.00 0.00 4.85
1561 3127 2.084546 GACGCTCAAATTAAGGTGCCT 58.915 47.619 0.00 0.00 0.00 4.75
1562 3128 2.084546 AGACGCTCAAATTAAGGTGCC 58.915 47.619 0.00 0.00 0.00 5.01
1563 3129 2.222819 CGAGACGCTCAAATTAAGGTGC 60.223 50.000 7.47 0.00 0.00 5.01
1564 3130 3.250744 TCGAGACGCTCAAATTAAGGTG 58.749 45.455 7.47 0.00 0.00 4.00
1565 3131 3.192844 TCTCGAGACGCTCAAATTAAGGT 59.807 43.478 12.08 0.00 0.00 3.50
1566 3132 3.770666 TCTCGAGACGCTCAAATTAAGG 58.229 45.455 12.08 0.00 0.00 2.69
1567 3133 7.630470 AATATCTCGAGACGCTCAAATTAAG 57.370 36.000 19.30 0.00 0.00 1.85
1568 3134 7.491372 ACAAATATCTCGAGACGCTCAAATTAA 59.509 33.333 19.30 0.00 0.00 1.40
1569 3135 6.978659 ACAAATATCTCGAGACGCTCAAATTA 59.021 34.615 19.30 2.99 0.00 1.40
1570 3136 5.812642 ACAAATATCTCGAGACGCTCAAATT 59.187 36.000 19.30 0.39 0.00 1.82
1571 3137 5.233050 CACAAATATCTCGAGACGCTCAAAT 59.767 40.000 19.30 1.20 0.00 2.32
1572 3138 4.562789 CACAAATATCTCGAGACGCTCAAA 59.437 41.667 19.30 0.00 0.00 2.69
1573 3139 4.105486 CACAAATATCTCGAGACGCTCAA 58.895 43.478 19.30 0.00 0.00 3.02
1574 3140 3.128764 ACACAAATATCTCGAGACGCTCA 59.871 43.478 19.30 0.99 0.00 4.26
1575 3141 3.483922 CACACAAATATCTCGAGACGCTC 59.516 47.826 19.30 0.00 0.00 5.03
1576 3142 3.119459 ACACACAAATATCTCGAGACGCT 60.119 43.478 19.30 4.55 0.00 5.07
1577 3143 3.179830 ACACACAAATATCTCGAGACGC 58.820 45.455 19.30 0.00 0.00 5.19
1578 3144 4.663166 AGACACACAAATATCTCGAGACG 58.337 43.478 19.30 6.68 0.00 4.18
1579 3145 5.641709 TGAGACACACAAATATCTCGAGAC 58.358 41.667 19.30 0.00 40.45 3.36
1580 3146 5.897377 TGAGACACACAAATATCTCGAGA 57.103 39.130 19.19 19.19 40.45 4.04
1581 3147 5.863935 TGTTGAGACACACAAATATCTCGAG 59.136 40.000 5.93 5.93 40.45 4.04
1582 3148 5.778862 TGTTGAGACACACAAATATCTCGA 58.221 37.500 0.00 0.00 40.45 4.04
1583 3149 6.073819 TGTTGTTGAGACACACAAATATCTCG 60.074 38.462 0.00 0.00 40.45 4.04
1584 3150 7.189693 TGTTGTTGAGACACACAAATATCTC 57.810 36.000 0.00 0.00 38.46 2.75
1585 3151 7.066887 TGTTGTTGTTGAGACACACAAATATCT 59.933 33.333 8.03 0.00 37.91 1.98
1586 3152 7.192913 TGTTGTTGTTGAGACACACAAATATC 58.807 34.615 8.03 0.00 37.91 1.63
1587 3153 7.094508 TGTTGTTGTTGAGACACACAAATAT 57.905 32.000 8.03 0.00 37.91 1.28
1588 3154 6.502136 TGTTGTTGTTGAGACACACAAATA 57.498 33.333 8.03 1.97 37.91 1.40
1589 3155 5.384063 TGTTGTTGTTGAGACACACAAAT 57.616 34.783 8.03 0.00 37.91 2.32
1590 3156 4.837896 TGTTGTTGTTGAGACACACAAA 57.162 36.364 8.03 0.00 37.91 2.83
1591 3157 4.217334 ACATGTTGTTGTTGAGACACACAA 59.783 37.500 0.00 0.00 35.94 3.33
1592 3158 3.755905 ACATGTTGTTGTTGAGACACACA 59.244 39.130 0.00 0.00 34.98 3.72
1593 3159 4.097714 CACATGTTGTTGTTGAGACACAC 58.902 43.478 0.00 0.00 34.98 3.82
1594 3160 4.006319 TCACATGTTGTTGTTGAGACACA 58.994 39.130 0.00 0.00 34.98 3.72
1595 3161 4.614555 TCACATGTTGTTGTTGAGACAC 57.385 40.909 0.00 0.00 34.98 3.67
1596 3162 5.580661 CAATCACATGTTGTTGTTGAGACA 58.419 37.500 0.00 0.00 28.93 3.41
1597 3163 4.442073 GCAATCACATGTTGTTGTTGAGAC 59.558 41.667 16.93 1.60 28.93 3.36
1598 3164 4.097589 TGCAATCACATGTTGTTGTTGAGA 59.902 37.500 16.93 1.51 28.93 3.27
1599 3165 4.361420 TGCAATCACATGTTGTTGTTGAG 58.639 39.130 16.93 0.00 28.93 3.02
1600 3166 4.382345 TGCAATCACATGTTGTTGTTGA 57.618 36.364 16.93 2.83 28.93 3.18
1601 3167 4.745620 TCATGCAATCACATGTTGTTGTTG 59.254 37.500 16.93 14.88 46.15 3.33
1602 3168 4.946445 TCATGCAATCACATGTTGTTGTT 58.054 34.783 16.93 6.72 46.15 2.83
1603 3169 4.587584 TCATGCAATCACATGTTGTTGT 57.412 36.364 16.93 1.35 46.15 3.32
1604 3170 7.329962 ACTTATTCATGCAATCACATGTTGTTG 59.670 33.333 13.20 13.20 46.15 3.33
1605 3171 7.380536 ACTTATTCATGCAATCACATGTTGTT 58.619 30.769 0.00 0.00 46.15 2.83
1606 3172 6.927416 ACTTATTCATGCAATCACATGTTGT 58.073 32.000 0.00 0.00 46.15 3.32
1613 3179 8.615211 TGACAGATAACTTATTCATGCAATCAC 58.385 33.333 0.00 0.00 0.00 3.06
1637 3203 3.750501 TGTCAGGTATAGGACTGGTGA 57.249 47.619 0.00 0.00 35.47 4.02
1651 3223 8.352201 TGAGAACTTCATTTTGTTATTGTCAGG 58.648 33.333 0.00 0.00 0.00 3.86
1663 3235 6.294397 GGAGAGCAACATGAGAACTTCATTTT 60.294 38.462 0.00 0.00 44.14 1.82
1673 3245 4.511527 GATTTCAGGAGAGCAACATGAGA 58.488 43.478 0.00 0.00 0.00 3.27
1680 3252 3.149196 GTGTTGGATTTCAGGAGAGCAA 58.851 45.455 0.00 0.00 0.00 3.91
1727 3301 3.751698 GGTTGTAGACAATGTTCAGGGAC 59.248 47.826 0.00 0.00 38.24 4.46
1742 3316 4.111375 AGCGTAGAAGACATGGTTGTAG 57.889 45.455 0.00 0.00 35.79 2.74
2019 3599 0.413434 TGGTCCTGGAGATGGTGAGA 59.587 55.000 0.00 0.00 0.00 3.27
2022 3602 1.134280 GTGATGGTCCTGGAGATGGTG 60.134 57.143 0.00 0.00 0.00 4.17
2130 3710 3.932580 GACATCCACTCGCGGTGCA 62.933 63.158 18.57 7.82 44.08 4.57
2142 3722 1.599542 GCAAACCTATGCGAGACATCC 59.400 52.381 0.00 0.00 40.38 3.51
2190 3770 2.616634 TTCTGCTGGATCATGAGCTC 57.383 50.000 11.34 6.82 36.11 4.09
2196 3776 2.569059 CGGAACATTCTGCTGGATCAT 58.431 47.619 0.00 0.00 0.00 2.45
2241 3821 1.591594 CGGCGATGACGGTGCTAAT 60.592 57.895 0.00 0.00 40.15 1.73


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

AutoCloner maintained by Alex Coulton.