Multiple sequence alignment - TraesCS5A01G525800

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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 TraesCS5A01G525800 chr5A 100.000 2279 0 0 1 2279 685989213 685986935 0.000000e+00 4209.0
1 TraesCS5A01G525800 chr5A 98.077 52 1 0 34 85 685989137 685989086 8.670000e-15 91.6
2 TraesCS5A01G525800 chr5A 98.077 52 1 0 77 128 685989180 685989129 8.670000e-15 91.6
3 TraesCS5A01G525800 chr5A 87.037 54 5 2 2055 2107 685982833 685982781 2.440000e-05 60.2
4 TraesCS5A01G525800 chr4D 90.486 1461 79 34 77 1526 502571856 502570445 0.000000e+00 1873.0
5 TraesCS5A01G525800 chr4D 84.157 587 40 19 1720 2279 502569973 502569413 9.330000e-144 520.0
6 TraesCS5A01G525800 chr4B 95.978 721 23 2 77 791 646968771 646968051 0.000000e+00 1166.0
7 TraesCS5A01G525800 chr4B 85.260 597 53 19 829 1421 646968055 646967490 1.170000e-162 582.0
8 TraesCS5A01G525800 chr4B 82.776 598 52 18 1577 2159 646967380 646966819 9.460000e-134 486.0
9 TraesCS5A01G525800 chr4B 89.362 47 3 2 2055 2100 646959688 646959643 8.790000e-05 58.4
10 TraesCS5A01G525800 chr7B 81.795 390 54 10 143 530 478486403 478486777 6.110000e-81 311.0
11 TraesCS5A01G525800 chr1D 80.122 327 57 7 216 538 258984128 258984450 1.050000e-58 237.0
12 TraesCS5A01G525800 chr1B 80.000 325 61 4 216 538 353942298 353941976 1.050000e-58 237.0
13 TraesCS5A01G525800 chr1A 78.594 313 63 4 228 538 341868206 341867896 1.070000e-48 204.0


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 TraesCS5A01G525800 chr5A 685986935 685989213 2278 True 1464.066667 4209 98.718000 1 2279 3 chr5A.!!$R2 2278
1 TraesCS5A01G525800 chr4D 502569413 502571856 2443 True 1196.500000 1873 87.321500 77 2279 2 chr4D.!!$R1 2202
2 TraesCS5A01G525800 chr4B 646966819 646968771 1952 True 744.666667 1166 88.004667 77 2159 3 chr4B.!!$R2 2082

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
60 61 0.035439 AGCCAGGAATACCAACACGG 60.035 55.0 0.0 0.0 42.5 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1552 1626 0.031043 CAGGTGCATTGTGTGTGGTG 59.969 55.0 0.0 0.0 0.0 4.17 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
32 33 8.690203 AATCCGTCAATGATAATCATAAACCA 57.310 30.769 0.00 0.00 35.76 3.67
33 34 7.728847 TCCGTCAATGATAATCATAAACCAG 57.271 36.000 0.00 0.00 35.76 4.00
34 35 7.505258 TCCGTCAATGATAATCATAAACCAGA 58.495 34.615 0.00 0.00 35.76 3.86
35 36 7.441157 TCCGTCAATGATAATCATAAACCAGAC 59.559 37.037 0.00 0.00 35.76 3.51
36 37 7.226523 CCGTCAATGATAATCATAAACCAGACA 59.773 37.037 0.00 0.00 35.76 3.41
37 38 8.278408 CGTCAATGATAATCATAAACCAGACAG 58.722 37.037 0.00 0.00 35.76 3.51
38 39 9.330063 GTCAATGATAATCATAAACCAGACAGA 57.670 33.333 0.00 0.00 35.76 3.41
42 43 9.722184 ATGATAATCATAAACCAGACAGATCAG 57.278 33.333 0.00 0.00 34.88 2.90
43 44 7.658982 TGATAATCATAAACCAGACAGATCAGC 59.341 37.037 0.00 0.00 0.00 4.26
44 45 4.142609 TCATAAACCAGACAGATCAGCC 57.857 45.455 0.00 0.00 0.00 4.85
45 46 3.519107 TCATAAACCAGACAGATCAGCCA 59.481 43.478 0.00 0.00 0.00 4.75
46 47 2.486472 AAACCAGACAGATCAGCCAG 57.514 50.000 0.00 0.00 0.00 4.85
47 48 0.617413 AACCAGACAGATCAGCCAGG 59.383 55.000 0.00 0.00 0.00 4.45
48 49 0.252421 ACCAGACAGATCAGCCAGGA 60.252 55.000 0.00 0.00 0.00 3.86
49 50 0.907486 CCAGACAGATCAGCCAGGAA 59.093 55.000 0.00 0.00 0.00 3.36
50 51 1.489649 CCAGACAGATCAGCCAGGAAT 59.510 52.381 0.00 0.00 0.00 3.01
51 52 2.702478 CCAGACAGATCAGCCAGGAATA 59.298 50.000 0.00 0.00 0.00 1.75
52 53 3.494048 CCAGACAGATCAGCCAGGAATAC 60.494 52.174 0.00 0.00 0.00 1.89
53 54 2.703007 AGACAGATCAGCCAGGAATACC 59.297 50.000 0.00 0.00 0.00 2.73
54 55 2.435805 GACAGATCAGCCAGGAATACCA 59.564 50.000 0.00 0.00 38.94 3.25
55 56 2.846206 ACAGATCAGCCAGGAATACCAA 59.154 45.455 0.00 0.00 38.94 3.67
56 57 3.209410 CAGATCAGCCAGGAATACCAAC 58.791 50.000 0.00 0.00 38.94 3.77
57 58 2.846206 AGATCAGCCAGGAATACCAACA 59.154 45.455 0.00 0.00 38.94 3.33
58 59 2.489938 TCAGCCAGGAATACCAACAC 57.510 50.000 0.00 0.00 38.94 3.32
59 60 1.086696 CAGCCAGGAATACCAACACG 58.913 55.000 0.00 0.00 38.94 4.49
60 61 0.035439 AGCCAGGAATACCAACACGG 60.035 55.000 0.00 0.00 42.50 4.94
61 62 1.029947 GCCAGGAATACCAACACGGG 61.030 60.000 0.00 0.00 40.22 5.28
62 63 0.616371 CCAGGAATACCAACACGGGA 59.384 55.000 0.00 0.00 40.22 5.14
63 64 1.406887 CCAGGAATACCAACACGGGAG 60.407 57.143 0.00 0.00 40.22 4.30
64 65 0.909623 AGGAATACCAACACGGGAGG 59.090 55.000 0.00 0.00 40.22 4.30
65 66 0.746923 GGAATACCAACACGGGAGGC 60.747 60.000 0.00 0.00 40.22 4.70
66 67 1.078708 AATACCAACACGGGAGGCG 60.079 57.895 0.00 0.00 40.22 5.52
67 68 3.675619 ATACCAACACGGGAGGCGC 62.676 63.158 0.00 0.00 40.22 6.53
70 71 3.055719 CAACACGGGAGGCGCAAT 61.056 61.111 10.83 0.00 0.00 3.56
71 72 2.282180 AACACGGGAGGCGCAATT 60.282 55.556 10.83 0.00 0.00 2.32
72 73 2.332654 AACACGGGAGGCGCAATTC 61.333 57.895 10.83 3.16 0.00 2.17
73 74 3.864686 CACGGGAGGCGCAATTCG 61.865 66.667 10.83 10.35 42.12 3.34
74 75 4.388499 ACGGGAGGCGCAATTCGT 62.388 61.111 10.83 11.06 41.07 3.85
75 76 3.564027 CGGGAGGCGCAATTCGTC 61.564 66.667 10.83 0.00 44.51 4.20
109 110 1.078708 AATACCAACACGGGAGGCG 60.079 57.895 0.00 0.00 40.22 5.52
168 169 2.418976 GGCAGAAACTAATGGGAACGAC 59.581 50.000 0.00 0.00 0.00 4.34
206 208 1.679898 GGTCAGAACAGGGGGTCAG 59.320 63.158 0.00 0.00 0.00 3.51
667 677 2.159170 CCGCAAAACCCTAGAGAGAGAG 60.159 54.545 0.00 0.00 0.00 3.20
702 712 1.615262 TCCGGAGAGGAGAGATGCA 59.385 57.895 0.00 0.00 45.98 3.96
784 794 4.710167 AGTTACGTTGGGCCGGGC 62.710 66.667 22.00 22.00 0.00 6.13
809 819 2.430694 GGTTTTGTTCTCAACTTGGGCT 59.569 45.455 0.00 0.00 32.93 5.19
810 820 3.447742 GTTTTGTTCTCAACTTGGGCTG 58.552 45.455 0.00 0.00 32.93 4.85
840 850 3.658398 CCTTTCTGGGTCATGTGCT 57.342 52.632 0.00 0.00 0.00 4.40
851 861 0.609151 TCATGTGCTTTGGCCCAATG 59.391 50.000 0.00 0.00 37.74 2.82
886 896 1.633945 ACAGGCCGAAATACCCTCTTT 59.366 47.619 0.00 0.00 0.00 2.52
887 897 2.841881 ACAGGCCGAAATACCCTCTTTA 59.158 45.455 0.00 0.00 0.00 1.85
888 898 3.458487 ACAGGCCGAAATACCCTCTTTAT 59.542 43.478 0.00 0.00 0.00 1.40
889 899 4.657039 ACAGGCCGAAATACCCTCTTTATA 59.343 41.667 0.00 0.00 0.00 0.98
890 900 5.309806 ACAGGCCGAAATACCCTCTTTATAT 59.690 40.000 0.00 0.00 0.00 0.86
891 901 5.643777 CAGGCCGAAATACCCTCTTTATATG 59.356 44.000 0.00 0.00 0.00 1.78
892 902 5.309806 AGGCCGAAATACCCTCTTTATATGT 59.690 40.000 0.00 0.00 0.00 2.29
893 903 6.499350 AGGCCGAAATACCCTCTTTATATGTA 59.501 38.462 0.00 0.00 0.00 2.29
894 904 7.182206 AGGCCGAAATACCCTCTTTATATGTAT 59.818 37.037 0.00 0.00 0.00 2.29
895 905 7.280205 GGCCGAAATACCCTCTTTATATGTATG 59.720 40.741 0.00 0.00 0.00 2.39
896 906 7.822822 GCCGAAATACCCTCTTTATATGTATGT 59.177 37.037 0.00 0.00 0.00 2.29
923 946 2.901840 CTGGTGGCGTGCTGTGTT 60.902 61.111 0.00 0.00 0.00 3.32
940 963 5.393678 GCTGTGTTCACTTTTTAGGTCCAAA 60.394 40.000 4.59 0.00 0.00 3.28
942 965 5.946972 TGTGTTCACTTTTTAGGTCCAAAGA 59.053 36.000 7.08 0.00 34.60 2.52
943 966 6.434652 TGTGTTCACTTTTTAGGTCCAAAGAA 59.565 34.615 7.08 0.00 34.60 2.52
944 967 6.972901 GTGTTCACTTTTTAGGTCCAAAGAAG 59.027 38.462 7.08 1.53 34.60 2.85
945 968 6.887545 TGTTCACTTTTTAGGTCCAAAGAAGA 59.112 34.615 7.08 2.96 34.60 2.87
946 969 7.559897 TGTTCACTTTTTAGGTCCAAAGAAGAT 59.440 33.333 7.08 0.00 34.60 2.40
947 970 8.414003 GTTCACTTTTTAGGTCCAAAGAAGATT 58.586 33.333 7.08 0.00 34.60 2.40
948 971 8.166422 TCACTTTTTAGGTCCAAAGAAGATTC 57.834 34.615 7.08 0.00 34.60 2.52
949 972 7.230712 TCACTTTTTAGGTCCAAAGAAGATTCC 59.769 37.037 7.08 0.00 34.60 3.01
950 973 6.206829 ACTTTTTAGGTCCAAAGAAGATTCCG 59.793 38.462 7.08 0.00 34.60 4.30
951 974 5.492855 TTTAGGTCCAAAGAAGATTCCGA 57.507 39.130 0.00 0.00 0.00 4.55
952 975 3.336138 AGGTCCAAAGAAGATTCCGAC 57.664 47.619 0.00 0.00 0.00 4.79
953 976 2.000447 GGTCCAAAGAAGATTCCGACG 59.000 52.381 0.00 0.00 0.00 5.12
954 977 2.353406 GGTCCAAAGAAGATTCCGACGA 60.353 50.000 0.00 0.00 0.00 4.20
955 978 2.924290 GTCCAAAGAAGATTCCGACGAG 59.076 50.000 0.00 0.00 0.00 4.18
956 979 1.661112 CCAAAGAAGATTCCGACGAGC 59.339 52.381 0.00 0.00 0.00 5.03
957 980 1.321743 CAAAGAAGATTCCGACGAGCG 59.678 52.381 0.00 0.00 40.47 5.03
958 981 0.809385 AAGAAGATTCCGACGAGCGA 59.191 50.000 0.00 0.00 44.57 4.93
959 982 0.378962 AGAAGATTCCGACGAGCGAG 59.621 55.000 0.00 0.00 44.57 5.03
960 983 0.592754 GAAGATTCCGACGAGCGAGG 60.593 60.000 0.00 0.00 44.57 4.63
961 984 1.030488 AAGATTCCGACGAGCGAGGA 61.030 55.000 0.00 2.39 44.57 3.71
962 985 1.009449 GATTCCGACGAGCGAGGAG 60.009 63.158 0.00 0.00 44.57 3.69
963 986 2.395367 GATTCCGACGAGCGAGGAGG 62.395 65.000 0.00 0.00 44.57 4.30
964 987 3.914579 TTCCGACGAGCGAGGAGGT 62.915 63.158 0.00 0.00 44.57 3.85
965 988 3.878519 CCGACGAGCGAGGAGGTC 61.879 72.222 0.00 0.00 44.57 3.85
966 989 3.878519 CGACGAGCGAGGAGGTCC 61.879 72.222 0.00 0.00 44.07 4.46
967 990 2.750637 GACGAGCGAGGAGGTCCA 60.751 66.667 0.00 0.00 44.07 4.02
968 991 2.752238 ACGAGCGAGGAGGTCCAG 60.752 66.667 0.00 0.00 44.07 3.86
969 992 4.200283 CGAGCGAGGAGGTCCAGC 62.200 72.222 8.05 8.05 44.07 4.85
970 993 3.071206 GAGCGAGGAGGTCCAGCA 61.071 66.667 15.81 0.00 41.98 4.41
1208 1240 4.899239 CGAGGCGGAGGTGGATGC 62.899 72.222 0.00 0.00 0.00 3.91
1215 1247 4.408821 GAGGTGGATGCGGCACCA 62.409 66.667 16.76 16.76 41.22 4.17
1216 1248 3.918253 GAGGTGGATGCGGCACCAA 62.918 63.158 20.60 0.00 41.22 3.67
1251 1283 1.548269 CGCAAGAAGAGGAGGAAGACT 59.452 52.381 0.00 0.00 43.02 3.24
1322 1354 7.675962 TTAAATCCATGTGTTACTGTGGTAC 57.324 36.000 0.00 0.00 33.47 3.34
1323 1355 5.499004 AATCCATGTGTTACTGTGGTACT 57.501 39.130 0.00 0.00 33.47 2.73
1325 1357 3.007506 TCCATGTGTTACTGTGGTACTGG 59.992 47.826 0.00 0.00 33.47 4.00
1327 1359 4.020928 CCATGTGTTACTGTGGTACTGGTA 60.021 45.833 0.00 0.00 0.00 3.25
1328 1360 4.859304 TGTGTTACTGTGGTACTGGTAG 57.141 45.455 0.00 0.00 0.00 3.18
1329 1361 3.006110 TGTGTTACTGTGGTACTGGTAGC 59.994 47.826 3.35 3.35 0.00 3.58
1331 1363 3.899360 TGTTACTGTGGTACTGGTAGCTT 59.101 43.478 10.58 0.00 34.84 3.74
1332 1364 4.243270 GTTACTGTGGTACTGGTAGCTTG 58.757 47.826 10.58 4.51 34.84 4.01
1333 1365 1.002087 ACTGTGGTACTGGTAGCTTGC 59.998 52.381 10.58 0.00 34.84 4.01
1345 1377 2.226674 GGTAGCTTGCCTGTTGTTCTTC 59.773 50.000 0.00 0.00 0.00 2.87
1391 1423 9.559732 TTACTGTGGTAGCGACTAGTAATAATA 57.440 33.333 13.43 0.00 29.68 0.98
1393 1425 9.730705 ACTGTGGTAGCGACTAGTAATAATATA 57.269 33.333 0.00 0.00 0.00 0.86
1442 1474 0.955428 TCATTTGGGACGAGCTGTGC 60.955 55.000 0.00 0.00 38.37 4.57
1443 1475 0.957395 CATTTGGGACGAGCTGTGCT 60.957 55.000 0.00 0.00 43.88 4.40
1444 1476 0.957395 ATTTGGGACGAGCTGTGCTG 60.957 55.000 0.00 0.00 39.88 4.41
1445 1477 2.324014 TTTGGGACGAGCTGTGCTGT 62.324 55.000 0.00 0.00 39.88 4.40
1446 1478 2.740055 GGGACGAGCTGTGCTGTG 60.740 66.667 0.00 0.00 39.88 3.66
1447 1479 2.029666 GGACGAGCTGTGCTGTGT 59.970 61.111 0.00 0.00 39.88 3.72
1448 1480 2.024319 GGACGAGCTGTGCTGTGTC 61.024 63.158 0.00 10.97 39.88 3.67
1476 1508 3.070018 GTGATGTATGTATCCTGCTGCC 58.930 50.000 0.00 0.00 0.00 4.85
1505 1579 6.197096 GCTACATTTTATTTCAGTGCAATCGG 59.803 38.462 0.00 0.00 0.00 4.18
1512 1586 1.603456 TCAGTGCAATCGGCTGAAAA 58.397 45.000 0.00 0.00 45.15 2.29
1520 1594 3.308530 CAATCGGCTGAAAACTTTCACC 58.691 45.455 0.00 7.11 41.88 4.02
1526 1600 1.676006 CTGAAAACTTTCACCGCCACT 59.324 47.619 0.69 0.00 41.88 4.00
1527 1601 1.673920 TGAAAACTTTCACCGCCACTC 59.326 47.619 0.69 0.00 41.88 3.51
1528 1602 1.001706 GAAAACTTTCACCGCCACTCC 60.002 52.381 0.00 0.00 37.15 3.85
1529 1603 0.106918 AAACTTTCACCGCCACTCCA 60.107 50.000 0.00 0.00 0.00 3.86
1530 1604 0.106918 AACTTTCACCGCCACTCCAA 60.107 50.000 0.00 0.00 0.00 3.53
1531 1605 0.535102 ACTTTCACCGCCACTCCAAG 60.535 55.000 0.00 0.00 0.00 3.61
1532 1606 0.250295 CTTTCACCGCCACTCCAAGA 60.250 55.000 0.00 0.00 0.00 3.02
1533 1607 0.250295 TTTCACCGCCACTCCAAGAG 60.250 55.000 0.00 0.00 35.52 2.85
1534 1608 1.118965 TTCACCGCCACTCCAAGAGA 61.119 55.000 0.00 0.00 33.32 3.10
1536 1610 1.228894 ACCGCCACTCCAAGAGAGA 60.229 57.895 0.00 0.00 46.50 3.10
1537 1611 1.216710 CCGCCACTCCAAGAGAGAC 59.783 63.158 0.00 0.00 46.50 3.36
1538 1612 1.536073 CCGCCACTCCAAGAGAGACA 61.536 60.000 0.00 0.00 46.50 3.41
1539 1613 0.108898 CGCCACTCCAAGAGAGACAG 60.109 60.000 0.00 0.00 46.50 3.51
1540 1614 1.261480 GCCACTCCAAGAGAGACAGA 58.739 55.000 0.00 0.00 46.50 3.41
1541 1615 1.204467 GCCACTCCAAGAGAGACAGAG 59.796 57.143 0.00 0.00 46.50 3.35
1542 1616 2.801483 CCACTCCAAGAGAGACAGAGA 58.199 52.381 0.00 0.00 46.50 3.10
1543 1617 3.161067 CCACTCCAAGAGAGACAGAGAA 58.839 50.000 0.00 0.00 46.50 2.87
1544 1618 3.193267 CCACTCCAAGAGAGACAGAGAAG 59.807 52.174 0.00 0.00 46.50 2.85
1545 1619 4.078537 CACTCCAAGAGAGACAGAGAAGA 58.921 47.826 0.00 0.00 46.50 2.87
1546 1620 4.079253 ACTCCAAGAGAGACAGAGAAGAC 58.921 47.826 0.00 0.00 46.50 3.01
1547 1621 4.202567 ACTCCAAGAGAGACAGAGAAGACT 60.203 45.833 0.00 0.00 46.50 3.24
1548 1622 4.078537 TCCAAGAGAGACAGAGAAGACTG 58.921 47.826 0.00 0.00 42.78 3.51
1549 1623 3.367292 CCAAGAGAGACAGAGAAGACTGC 60.367 52.174 0.00 0.00 41.06 4.40
1550 1624 3.153369 AGAGAGACAGAGAAGACTGCA 57.847 47.619 0.00 0.00 41.06 4.41
1551 1625 3.084039 AGAGAGACAGAGAAGACTGCAG 58.916 50.000 13.48 13.48 41.06 4.41
1552 1626 1.545582 AGAGACAGAGAAGACTGCAGC 59.454 52.381 15.27 6.85 41.06 5.25
1553 1627 1.271934 GAGACAGAGAAGACTGCAGCA 59.728 52.381 15.27 0.00 41.06 4.41
1554 1628 1.000731 AGACAGAGAAGACTGCAGCAC 59.999 52.381 15.27 8.60 41.06 4.40
1555 1629 0.034616 ACAGAGAAGACTGCAGCACC 59.965 55.000 15.27 3.20 41.06 5.01
1556 1630 0.034476 CAGAGAAGACTGCAGCACCA 59.966 55.000 15.27 0.00 0.00 4.17
1557 1631 0.034616 AGAGAAGACTGCAGCACCAC 59.965 55.000 15.27 1.92 0.00 4.16
1558 1632 0.250038 GAGAAGACTGCAGCACCACA 60.250 55.000 15.27 0.00 0.00 4.17
1559 1633 0.533755 AGAAGACTGCAGCACCACAC 60.534 55.000 15.27 0.00 0.00 3.82
1560 1634 0.815213 GAAGACTGCAGCACCACACA 60.815 55.000 15.27 0.00 0.00 3.72
1561 1635 1.097547 AAGACTGCAGCACCACACAC 61.098 55.000 15.27 0.00 0.00 3.82
1562 1636 1.819208 GACTGCAGCACCACACACA 60.819 57.895 15.27 0.00 0.00 3.72
1572 1646 0.106769 ACCACACACAATGCACCTGA 60.107 50.000 4.68 0.00 0.00 3.86
1573 1647 1.031235 CCACACACAATGCACCTGAA 58.969 50.000 4.68 0.00 0.00 3.02
1579 1653 2.624838 ACACAATGCACCTGAAGGAAAG 59.375 45.455 2.62 0.00 38.94 2.62
1580 1654 2.886523 CACAATGCACCTGAAGGAAAGA 59.113 45.455 2.62 0.00 38.94 2.52
1581 1655 2.887152 ACAATGCACCTGAAGGAAAGAC 59.113 45.455 2.62 0.00 38.94 3.01
1582 1656 1.813513 ATGCACCTGAAGGAAAGACG 58.186 50.000 2.62 0.00 38.94 4.18
1583 1657 0.468226 TGCACCTGAAGGAAAGACGT 59.532 50.000 2.62 0.00 38.94 4.34
1584 1658 1.149148 GCACCTGAAGGAAAGACGTC 58.851 55.000 7.70 7.70 38.94 4.34
1585 1659 1.270358 GCACCTGAAGGAAAGACGTCT 60.270 52.381 13.58 13.58 38.94 4.18
1586 1660 2.408050 CACCTGAAGGAAAGACGTCTG 58.592 52.381 20.85 5.48 38.94 3.51
1587 1661 2.035961 CACCTGAAGGAAAGACGTCTGA 59.964 50.000 20.85 0.00 38.94 3.27
1600 1674 1.069204 ACGTCTGATGAGCTTGTGTGT 59.931 47.619 3.44 0.00 0.00 3.72
1618 1692 2.880890 GTGTTGTGCTCTTCAGTCCATT 59.119 45.455 0.00 0.00 0.00 3.16
1690 1769 3.271729 TGTTTTAGTTGGACGTTGAGCA 58.728 40.909 0.00 0.00 0.00 4.26
1694 1773 5.508200 TTTAGTTGGACGTTGAGCATTTT 57.492 34.783 0.00 0.00 0.00 1.82
1701 1780 5.277825 TGGACGTTGAGCATTTTAGTTTTG 58.722 37.500 0.00 0.00 0.00 2.44
1707 1786 7.148490 ACGTTGAGCATTTTAGTTTTGCTTTTT 60.148 29.630 0.00 0.00 46.21 1.94
1709 1788 9.980780 GTTGAGCATTTTAGTTTTGCTTTTTAA 57.019 25.926 0.00 0.00 46.21 1.52
1718 1797 4.627900 AGTTTTGCTTTTTAACCACAACCG 59.372 37.500 0.00 0.00 0.00 4.44
1735 2126 4.235360 CAACCGAACTCTGTAGTAAGGTG 58.765 47.826 5.86 0.00 41.81 4.00
1738 2129 2.230508 CGAACTCTGTAGTAAGGTGCCA 59.769 50.000 0.00 0.00 33.75 4.92
1755 2146 1.728971 GCCATTGTCTCTTGTCTGTCG 59.271 52.381 0.00 0.00 0.00 4.35
1814 2205 4.576873 TGTCGCTGTTAATTTGGTTCTGAA 59.423 37.500 0.00 0.00 0.00 3.02
1838 2229 0.865769 GAACTCGTGTGCGTTGGAAT 59.134 50.000 0.00 0.00 39.49 3.01
1858 2249 6.652481 TGGAATTTCAGTGTCTGATTTCTCTC 59.348 38.462 15.60 6.73 40.39 3.20
1862 2253 3.441922 TCAGTGTCTGATTTCTCTCTCGG 59.558 47.826 0.00 0.00 35.39 4.63
1863 2254 2.757868 AGTGTCTGATTTCTCTCTCGGG 59.242 50.000 0.00 0.00 0.00 5.14
1864 2255 2.103373 TGTCTGATTTCTCTCTCGGGG 58.897 52.381 0.00 0.00 0.00 5.73
1865 2256 1.115467 TCTGATTTCTCTCTCGGGGC 58.885 55.000 0.00 0.00 0.00 5.80
1866 2257 0.105778 CTGATTTCTCTCTCGGGGCC 59.894 60.000 0.00 0.00 0.00 5.80
1867 2258 0.325671 TGATTTCTCTCTCGGGGCCT 60.326 55.000 0.84 0.00 0.00 5.19
1868 2259 0.833949 GATTTCTCTCTCGGGGCCTT 59.166 55.000 0.84 0.00 0.00 4.35
1912 2303 4.202010 TGTTGTTTTAGCACCTTTCAGCTC 60.202 41.667 0.00 0.00 42.05 4.09
1959 2356 2.133281 TCCCATTGGCTCAGACATTG 57.867 50.000 0.00 0.00 0.00 2.82
2037 2434 2.125326 GGCCGGCAAGTAAATCCCC 61.125 63.158 30.85 1.22 0.00 4.81
2039 2436 1.384222 GCCGGCAAGTAAATCCCCAG 61.384 60.000 24.80 0.00 0.00 4.45
2053 2450 1.213182 TCCCCAGGCAAATACGCAATA 59.787 47.619 0.00 0.00 0.00 1.90
2084 2488 1.374252 GTCAGCCGTCACGTTCCAT 60.374 57.895 0.00 0.00 0.00 3.41
2092 2496 2.094258 CCGTCACGTTCCATGAAGATTG 59.906 50.000 0.00 0.00 0.00 2.67
2116 2520 0.473755 AGTCAGCCACACAATCCACA 59.526 50.000 0.00 0.00 0.00 4.17
2117 2521 0.593128 GTCAGCCACACAATCCACAC 59.407 55.000 0.00 0.00 0.00 3.82
2133 2537 1.955778 CACACAGTCCAGGCAAATTCA 59.044 47.619 0.00 0.00 0.00 2.57
2195 2611 4.157105 TGTGCTTGTGCTATAACTCGTCTA 59.843 41.667 0.00 0.00 40.48 2.59
2208 2624 2.563179 ACTCGTCTACATTGGCAGTTCT 59.437 45.455 0.00 0.00 0.00 3.01
2211 2627 1.394917 GTCTACATTGGCAGTTCTGCG 59.605 52.381 16.84 7.17 35.24 5.18
2212 2628 1.001974 TCTACATTGGCAGTTCTGCGT 59.998 47.619 16.84 11.94 35.24 5.24
2213 2629 2.232696 TCTACATTGGCAGTTCTGCGTA 59.767 45.455 16.84 12.36 35.24 4.42
2214 2630 2.113860 ACATTGGCAGTTCTGCGTAT 57.886 45.000 16.84 10.49 35.24 3.06
2216 2632 2.009051 CATTGGCAGTTCTGCGTATCA 58.991 47.619 16.84 7.80 35.24 2.15
2218 2634 1.655484 TGGCAGTTCTGCGTATCATG 58.345 50.000 16.84 0.00 35.24 3.07
2219 2635 1.066215 TGGCAGTTCTGCGTATCATGT 60.066 47.619 16.84 0.00 35.24 3.21
2220 2636 2.167487 TGGCAGTTCTGCGTATCATGTA 59.833 45.455 16.84 0.00 35.24 2.29
2221 2637 2.540101 GGCAGTTCTGCGTATCATGTAC 59.460 50.000 16.84 0.00 35.24 2.90
2222 2638 2.216488 GCAGTTCTGCGTATCATGTACG 59.784 50.000 17.82 17.82 43.13 3.67
2223 2639 3.435566 CAGTTCTGCGTATCATGTACGT 58.564 45.455 20.90 0.00 42.35 3.57
2224 2640 4.594136 CAGTTCTGCGTATCATGTACGTA 58.406 43.478 20.90 17.60 42.35 3.57
2225 2641 5.212934 CAGTTCTGCGTATCATGTACGTAT 58.787 41.667 20.90 6.76 42.35 3.06
2226 2642 5.339875 CAGTTCTGCGTATCATGTACGTATC 59.660 44.000 20.90 13.43 42.35 2.24
2227 2643 5.238868 AGTTCTGCGTATCATGTACGTATCT 59.761 40.000 20.90 14.68 42.35 1.98
2228 2644 5.278964 TCTGCGTATCATGTACGTATCTC 57.721 43.478 20.90 10.33 42.35 2.75
2235 2663 8.176365 GCGTATCATGTACGTATCTCTTAGATT 58.824 37.037 20.90 0.00 42.35 2.40
2245 2673 7.936584 ACGTATCTCTTAGATTCCTTGAGAAG 58.063 38.462 0.00 0.00 38.07 2.85
2264 2694 7.497595 TGAGAAGGACATATGTATGTAACACC 58.502 38.462 8.71 3.05 46.20 4.16
2269 2699 7.280356 AGGACATATGTATGTAACACCTTTCC 58.720 38.462 8.71 0.34 46.20 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.785982 TGGTTTATGATTATCATTGACGGATTA 57.214 29.630 13.25 0.00 38.26 1.75
7 8 8.690203 TGGTTTATGATTATCATTGACGGATT 57.310 30.769 13.25 0.00 38.26 3.01
8 9 8.156820 TCTGGTTTATGATTATCATTGACGGAT 58.843 33.333 13.25 0.00 38.26 4.18
9 10 7.441157 GTCTGGTTTATGATTATCATTGACGGA 59.559 37.037 13.25 9.02 38.26 4.69
10 11 7.226523 TGTCTGGTTTATGATTATCATTGACGG 59.773 37.037 13.25 7.07 38.26 4.79
11 12 8.141835 TGTCTGGTTTATGATTATCATTGACG 57.858 34.615 13.25 2.28 38.26 4.35
12 13 9.330063 TCTGTCTGGTTTATGATTATCATTGAC 57.670 33.333 13.25 11.45 38.26 3.18
16 17 9.722184 CTGATCTGTCTGGTTTATGATTATCAT 57.278 33.333 12.62 12.62 40.72 2.45
17 18 7.658982 GCTGATCTGTCTGGTTTATGATTATCA 59.341 37.037 0.00 0.00 0.00 2.15
18 19 7.118971 GGCTGATCTGTCTGGTTTATGATTATC 59.881 40.741 1.27 0.00 0.00 1.75
19 20 6.939163 GGCTGATCTGTCTGGTTTATGATTAT 59.061 38.462 1.27 0.00 0.00 1.28
20 21 6.126796 TGGCTGATCTGTCTGGTTTATGATTA 60.127 38.462 5.76 0.00 0.00 1.75
21 22 5.128919 GGCTGATCTGTCTGGTTTATGATT 58.871 41.667 1.27 0.00 0.00 2.57
22 23 4.164796 TGGCTGATCTGTCTGGTTTATGAT 59.835 41.667 5.76 0.00 0.00 2.45
23 24 3.519107 TGGCTGATCTGTCTGGTTTATGA 59.481 43.478 5.76 0.00 0.00 2.15
24 25 3.875727 CTGGCTGATCTGTCTGGTTTATG 59.124 47.826 5.76 0.00 0.00 1.90
25 26 3.118112 CCTGGCTGATCTGTCTGGTTTAT 60.118 47.826 18.29 0.00 0.00 1.40
26 27 2.237143 CCTGGCTGATCTGTCTGGTTTA 59.763 50.000 18.29 0.00 0.00 2.01
27 28 1.004044 CCTGGCTGATCTGTCTGGTTT 59.996 52.381 18.29 0.00 0.00 3.27
28 29 0.617413 CCTGGCTGATCTGTCTGGTT 59.383 55.000 18.29 0.00 0.00 3.67
29 30 0.252421 TCCTGGCTGATCTGTCTGGT 60.252 55.000 23.25 0.00 33.28 4.00
30 31 0.907486 TTCCTGGCTGATCTGTCTGG 59.093 55.000 19.87 19.87 32.86 3.86
31 32 3.494048 GGTATTCCTGGCTGATCTGTCTG 60.494 52.174 5.76 5.04 0.00 3.51
32 33 2.703007 GGTATTCCTGGCTGATCTGTCT 59.297 50.000 5.76 0.00 0.00 3.41
33 34 2.435805 TGGTATTCCTGGCTGATCTGTC 59.564 50.000 0.00 0.00 34.23 3.51
34 35 2.481441 TGGTATTCCTGGCTGATCTGT 58.519 47.619 1.27 0.00 34.23 3.41
35 36 3.209410 GTTGGTATTCCTGGCTGATCTG 58.791 50.000 0.00 0.00 34.23 2.90
36 37 2.846206 TGTTGGTATTCCTGGCTGATCT 59.154 45.455 0.00 0.00 34.23 2.75
37 38 2.945668 GTGTTGGTATTCCTGGCTGATC 59.054 50.000 0.00 0.00 34.23 2.92
38 39 2.680805 CGTGTTGGTATTCCTGGCTGAT 60.681 50.000 0.00 0.00 34.23 2.90
39 40 1.338674 CGTGTTGGTATTCCTGGCTGA 60.339 52.381 0.00 0.00 34.23 4.26
40 41 1.086696 CGTGTTGGTATTCCTGGCTG 58.913 55.000 0.00 0.00 34.23 4.85
41 42 0.035439 CCGTGTTGGTATTCCTGGCT 60.035 55.000 0.00 0.00 34.23 4.75
42 43 1.029947 CCCGTGTTGGTATTCCTGGC 61.030 60.000 0.00 0.00 35.15 4.85
43 44 0.616371 TCCCGTGTTGGTATTCCTGG 59.384 55.000 0.00 0.00 35.15 4.45
44 45 1.406887 CCTCCCGTGTTGGTATTCCTG 60.407 57.143 0.00 0.00 35.15 3.86
45 46 0.909623 CCTCCCGTGTTGGTATTCCT 59.090 55.000 0.00 0.00 35.15 3.36
46 47 0.746923 GCCTCCCGTGTTGGTATTCC 60.747 60.000 0.00 0.00 35.15 3.01
47 48 1.087771 CGCCTCCCGTGTTGGTATTC 61.088 60.000 0.00 0.00 35.15 1.75
48 49 1.078708 CGCCTCCCGTGTTGGTATT 60.079 57.895 0.00 0.00 35.15 1.89
49 50 2.582436 CGCCTCCCGTGTTGGTAT 59.418 61.111 0.00 0.00 35.15 2.73
50 51 4.382320 GCGCCTCCCGTGTTGGTA 62.382 66.667 0.00 0.00 39.71 3.25
53 54 2.527547 GAATTGCGCCTCCCGTGTTG 62.528 60.000 4.18 0.00 39.71 3.33
54 55 2.282180 AATTGCGCCTCCCGTGTT 60.282 55.556 4.18 0.00 39.71 3.32
55 56 2.746277 GAATTGCGCCTCCCGTGT 60.746 61.111 4.18 0.00 39.71 4.49
56 57 3.864686 CGAATTGCGCCTCCCGTG 61.865 66.667 4.18 0.00 39.71 4.94
57 58 4.388499 ACGAATTGCGCCTCCCGT 62.388 61.111 4.18 7.09 46.04 5.28
58 59 3.564027 GACGAATTGCGCCTCCCG 61.564 66.667 4.18 6.36 46.04 5.14
59 60 3.564027 CGACGAATTGCGCCTCCC 61.564 66.667 4.18 0.00 46.04 4.30
60 61 2.508439 TCGACGAATTGCGCCTCC 60.508 61.111 4.18 0.00 46.04 4.30
61 62 2.014093 CTGTCGACGAATTGCGCCTC 62.014 60.000 11.62 0.00 46.04 4.70
62 63 2.048597 TGTCGACGAATTGCGCCT 60.049 55.556 11.62 0.00 46.04 5.52
63 64 1.421410 ATCTGTCGACGAATTGCGCC 61.421 55.000 11.62 0.00 46.04 6.53
64 65 0.043822 GATCTGTCGACGAATTGCGC 60.044 55.000 11.62 0.00 46.04 6.09
66 67 1.005557 GCTGATCTGTCGACGAATTGC 60.006 52.381 11.62 10.96 0.00 3.56
67 68 1.590238 GGCTGATCTGTCGACGAATTG 59.410 52.381 11.62 5.55 0.00 2.32
68 69 1.204704 TGGCTGATCTGTCGACGAATT 59.795 47.619 11.62 0.00 0.00 2.17
69 70 0.817654 TGGCTGATCTGTCGACGAAT 59.182 50.000 11.62 6.63 0.00 3.34
70 71 0.171231 CTGGCTGATCTGTCGACGAA 59.829 55.000 11.62 1.11 0.00 3.85
71 72 1.657751 CCTGGCTGATCTGTCGACGA 61.658 60.000 11.62 11.52 0.00 4.20
72 73 1.226802 CCTGGCTGATCTGTCGACG 60.227 63.158 11.62 6.07 0.00 5.12
73 74 0.532573 TTCCTGGCTGATCTGTCGAC 59.467 55.000 9.11 9.11 0.00 4.20
74 75 1.489481 ATTCCTGGCTGATCTGTCGA 58.511 50.000 0.00 0.00 0.00 4.20
75 76 2.546795 GGTATTCCTGGCTGATCTGTCG 60.547 54.545 0.00 0.00 0.00 4.35
116 117 0.438830 GGTTGCGTTGATCTGTCGAC 59.561 55.000 9.11 9.11 35.71 4.20
168 169 2.029728 CCGCTTCTCTGAATTTACTGCG 59.970 50.000 0.00 0.00 40.44 5.18
206 208 1.281287 GAGAAAACCCTACCCCTCCAC 59.719 57.143 0.00 0.00 0.00 4.02
686 696 0.953727 CTCTGCATCTCTCCTCTCCG 59.046 60.000 0.00 0.00 0.00 4.63
702 712 0.116541 TCCGTCTTTTCCCCTCCTCT 59.883 55.000 0.00 0.00 0.00 3.69
784 794 4.370917 CCAAGTTGAGAACAAAACCCATG 58.629 43.478 3.87 0.00 37.77 3.66
809 819 0.404040 AGAAAGGGGCGTTCATTCCA 59.596 50.000 0.00 0.00 0.00 3.53
810 820 0.811281 CAGAAAGGGGCGTTCATTCC 59.189 55.000 0.00 0.00 0.00 3.01
840 850 2.692557 CCATACGAATCATTGGGCCAAA 59.307 45.455 24.97 8.29 0.00 3.28
851 861 2.143925 GCCTGTTAGCCCATACGAATC 58.856 52.381 0.00 0.00 0.00 2.52
879 889 7.829211 CCCACCATAACATACATATAAAGAGGG 59.171 40.741 0.00 0.00 0.00 4.30
886 896 5.550011 ACCAGCCCACCATAACATACATATA 59.450 40.000 0.00 0.00 0.00 0.86
887 897 4.353788 ACCAGCCCACCATAACATACATAT 59.646 41.667 0.00 0.00 0.00 1.78
888 898 3.719479 ACCAGCCCACCATAACATACATA 59.281 43.478 0.00 0.00 0.00 2.29
889 899 2.513738 ACCAGCCCACCATAACATACAT 59.486 45.455 0.00 0.00 0.00 2.29
890 900 1.919654 ACCAGCCCACCATAACATACA 59.080 47.619 0.00 0.00 0.00 2.29
891 901 2.297701 CACCAGCCCACCATAACATAC 58.702 52.381 0.00 0.00 0.00 2.39
892 902 1.214175 CCACCAGCCCACCATAACATA 59.786 52.381 0.00 0.00 0.00 2.29
893 903 0.033208 CCACCAGCCCACCATAACAT 60.033 55.000 0.00 0.00 0.00 2.71
894 904 1.382240 CCACCAGCCCACCATAACA 59.618 57.895 0.00 0.00 0.00 2.41
895 905 2.052104 GCCACCAGCCCACCATAAC 61.052 63.158 0.00 0.00 34.35 1.89
896 906 2.358619 GCCACCAGCCCACCATAA 59.641 61.111 0.00 0.00 34.35 1.90
923 946 7.230712 GGAATCTTCTTTGGACCTAAAAAGTGA 59.769 37.037 2.32 3.82 35.38 3.41
940 963 0.378962 CTCGCTCGTCGGAATCTTCT 59.621 55.000 0.00 0.00 39.05 2.85
942 965 1.030488 TCCTCGCTCGTCGGAATCTT 61.030 55.000 0.00 0.00 39.05 2.40
943 966 1.440938 CTCCTCGCTCGTCGGAATCT 61.441 60.000 0.00 0.00 39.05 2.40
944 967 1.009449 CTCCTCGCTCGTCGGAATC 60.009 63.158 0.00 0.00 39.05 2.52
945 968 2.482333 CCTCCTCGCTCGTCGGAAT 61.482 63.158 0.00 0.00 39.05 3.01
946 969 3.132139 CCTCCTCGCTCGTCGGAA 61.132 66.667 0.00 0.00 39.05 4.30
947 970 4.405671 ACCTCCTCGCTCGTCGGA 62.406 66.667 0.00 3.90 39.05 4.55
948 971 3.878519 GACCTCCTCGCTCGTCGG 61.879 72.222 0.00 0.00 39.05 4.79
949 972 3.878519 GGACCTCCTCGCTCGTCG 61.879 72.222 0.00 0.00 40.15 5.12
950 973 2.750637 TGGACCTCCTCGCTCGTC 60.751 66.667 0.00 0.00 36.82 4.20
951 974 2.752238 CTGGACCTCCTCGCTCGT 60.752 66.667 0.00 0.00 36.82 4.18
952 975 4.200283 GCTGGACCTCCTCGCTCG 62.200 72.222 0.00 0.00 36.82 5.03
953 976 3.071206 TGCTGGACCTCCTCGCTC 61.071 66.667 0.00 0.00 35.31 5.03
954 977 3.386237 GTGCTGGACCTCCTCGCT 61.386 66.667 0.00 0.00 35.31 4.93
955 978 3.363844 GAGTGCTGGACCTCCTCGC 62.364 68.421 0.00 0.00 36.82 5.03
956 979 2.888863 GAGTGCTGGACCTCCTCG 59.111 66.667 0.00 0.00 36.82 4.63
957 980 1.662438 CTCGAGTGCTGGACCTCCTC 61.662 65.000 3.62 0.00 36.82 3.71
958 981 1.680651 CTCGAGTGCTGGACCTCCT 60.681 63.158 3.62 0.00 36.82 3.69
959 982 2.888863 CTCGAGTGCTGGACCTCC 59.111 66.667 3.62 0.00 0.00 4.30
960 983 2.183046 GCTCGAGTGCTGGACCTC 59.817 66.667 15.13 0.00 0.00 3.85
961 984 3.753434 CGCTCGAGTGCTGGACCT 61.753 66.667 13.91 0.00 0.00 3.85
962 985 4.803426 CCGCTCGAGTGCTGGACC 62.803 72.222 20.61 0.00 0.00 4.46
1212 1244 3.764466 CGCTCCTCTCCGCTTGGT 61.764 66.667 0.00 0.00 0.00 3.67
1251 1283 4.980805 GACACACCTTCGCGCCCA 62.981 66.667 0.00 0.00 0.00 5.36
1292 1324 5.020795 AGTAACACATGGATTTAAACCCCC 58.979 41.667 0.00 0.00 0.00 5.40
1293 1325 5.479027 ACAGTAACACATGGATTTAAACCCC 59.521 40.000 0.00 0.00 0.00 4.95
1294 1326 6.386654 CACAGTAACACATGGATTTAAACCC 58.613 40.000 0.00 0.00 0.00 4.11
1295 1327 6.015772 ACCACAGTAACACATGGATTTAAACC 60.016 38.462 0.00 0.00 36.04 3.27
1296 1328 6.977213 ACCACAGTAACACATGGATTTAAAC 58.023 36.000 0.00 0.00 36.04 2.01
1297 1329 7.940137 AGTACCACAGTAACACATGGATTTAAA 59.060 33.333 0.00 0.00 36.04 1.52
1298 1330 7.389330 CAGTACCACAGTAACACATGGATTTAA 59.611 37.037 0.00 0.00 36.04 1.52
1299 1331 6.876789 CAGTACCACAGTAACACATGGATTTA 59.123 38.462 0.00 0.00 36.04 1.40
1322 1354 1.537202 GAACAACAGGCAAGCTACCAG 59.463 52.381 8.33 2.82 0.00 4.00
1323 1355 1.142870 AGAACAACAGGCAAGCTACCA 59.857 47.619 8.33 0.00 0.00 3.25
1325 1357 2.878406 TGAAGAACAACAGGCAAGCTAC 59.122 45.455 0.00 0.00 0.00 3.58
1327 1359 2.057137 TGAAGAACAACAGGCAAGCT 57.943 45.000 0.00 0.00 0.00 3.74
1328 1360 2.669364 CATGAAGAACAACAGGCAAGC 58.331 47.619 0.00 0.00 0.00 4.01
1329 1361 2.295349 AGCATGAAGAACAACAGGCAAG 59.705 45.455 0.00 0.00 44.45 4.01
1331 1363 1.610038 CAGCATGAAGAACAACAGGCA 59.390 47.619 0.00 0.00 44.45 4.75
1332 1364 1.610522 ACAGCATGAAGAACAACAGGC 59.389 47.619 0.00 0.00 42.77 4.85
1333 1365 3.996150 AACAGCATGAAGAACAACAGG 57.004 42.857 0.00 0.00 39.69 4.00
1345 1377 7.814107 ACAGTAACAAATGGATTTAACAGCATG 59.186 33.333 0.00 0.00 46.00 4.06
1391 1423 4.832248 ACATCGTGAACAACACCAGATAT 58.168 39.130 0.00 0.00 45.73 1.63
1393 1425 3.126001 ACATCGTGAACAACACCAGAT 57.874 42.857 0.00 0.00 45.73 2.90
1403 1435 8.950961 CAAATGATGAAATGATACATCGTGAAC 58.049 33.333 0.00 0.00 43.74 3.18
1413 1445 5.239306 GCTCGTCCCAAATGATGAAATGATA 59.761 40.000 0.00 0.00 30.21 2.15
1414 1446 4.037208 GCTCGTCCCAAATGATGAAATGAT 59.963 41.667 0.00 0.00 30.21 2.45
1415 1447 3.378112 GCTCGTCCCAAATGATGAAATGA 59.622 43.478 0.00 0.00 30.21 2.57
1416 1448 3.379372 AGCTCGTCCCAAATGATGAAATG 59.621 43.478 0.00 0.00 30.21 2.32
1417 1449 3.379372 CAGCTCGTCCCAAATGATGAAAT 59.621 43.478 0.00 0.00 30.21 2.17
1418 1450 2.749076 CAGCTCGTCCCAAATGATGAAA 59.251 45.455 0.00 0.00 30.21 2.69
1419 1451 2.290260 ACAGCTCGTCCCAAATGATGAA 60.290 45.455 0.00 0.00 30.21 2.57
1420 1452 1.278985 ACAGCTCGTCCCAAATGATGA 59.721 47.619 0.00 0.00 0.00 2.92
1442 1474 4.751600 ACATACATCACACACAAGACACAG 59.248 41.667 0.00 0.00 0.00 3.66
1443 1475 4.702831 ACATACATCACACACAAGACACA 58.297 39.130 0.00 0.00 0.00 3.72
1444 1476 6.036083 GGATACATACATCACACACAAGACAC 59.964 42.308 0.00 0.00 0.00 3.67
1445 1477 6.070824 AGGATACATACATCACACACAAGACA 60.071 38.462 0.00 0.00 41.41 3.41
1446 1478 6.256539 CAGGATACATACATCACACACAAGAC 59.743 42.308 0.00 0.00 41.41 3.01
1447 1479 6.340522 CAGGATACATACATCACACACAAGA 58.659 40.000 0.00 0.00 41.41 3.02
1448 1480 5.007039 GCAGGATACATACATCACACACAAG 59.993 44.000 0.00 0.00 41.41 3.16
1476 1508 4.733523 GCACTGAAATAAAATGTAGCCCCG 60.734 45.833 0.00 0.00 0.00 5.73
1512 1586 0.535102 CTTGGAGTGGCGGTGAAAGT 60.535 55.000 0.00 0.00 0.00 2.66
1520 1594 0.108898 CTGTCTCTCTTGGAGTGGCG 60.109 60.000 0.00 0.00 42.40 5.69
1526 1600 4.078537 CAGTCTTCTCTGTCTCTCTTGGA 58.921 47.826 0.00 0.00 0.00 3.53
1527 1601 3.367292 GCAGTCTTCTCTGTCTCTCTTGG 60.367 52.174 0.00 0.00 37.70 3.61
1528 1602 3.255395 TGCAGTCTTCTCTGTCTCTCTTG 59.745 47.826 0.00 0.00 37.70 3.02
1529 1603 3.495331 TGCAGTCTTCTCTGTCTCTCTT 58.505 45.455 0.00 0.00 37.70 2.85
1530 1604 3.084039 CTGCAGTCTTCTCTGTCTCTCT 58.916 50.000 5.25 0.00 37.70 3.10
1531 1605 2.415893 GCTGCAGTCTTCTCTGTCTCTC 60.416 54.545 16.64 0.00 37.70 3.20
1532 1606 1.545582 GCTGCAGTCTTCTCTGTCTCT 59.454 52.381 16.64 0.00 37.70 3.10
1533 1607 1.271934 TGCTGCAGTCTTCTCTGTCTC 59.728 52.381 16.64 0.00 37.70 3.36
1534 1608 1.000731 GTGCTGCAGTCTTCTCTGTCT 59.999 52.381 16.64 0.00 37.70 3.41
1535 1609 1.427435 GTGCTGCAGTCTTCTCTGTC 58.573 55.000 16.64 0.00 37.70 3.51
1536 1610 0.034616 GGTGCTGCAGTCTTCTCTGT 59.965 55.000 16.64 0.00 37.70 3.41
1537 1611 0.034476 TGGTGCTGCAGTCTTCTCTG 59.966 55.000 16.64 0.00 38.35 3.35
1538 1612 0.034616 GTGGTGCTGCAGTCTTCTCT 59.965 55.000 16.64 0.00 0.00 3.10
1539 1613 0.250038 TGTGGTGCTGCAGTCTTCTC 60.250 55.000 16.64 0.00 0.00 2.87
1540 1614 0.533755 GTGTGGTGCTGCAGTCTTCT 60.534 55.000 16.64 0.00 0.00 2.85
1541 1615 0.815213 TGTGTGGTGCTGCAGTCTTC 60.815 55.000 16.64 0.00 0.00 2.87
1542 1616 1.097547 GTGTGTGGTGCTGCAGTCTT 61.098 55.000 16.64 0.00 0.00 3.01
1543 1617 1.524621 GTGTGTGGTGCTGCAGTCT 60.525 57.895 16.64 0.00 0.00 3.24
1544 1618 1.375853 TTGTGTGTGGTGCTGCAGTC 61.376 55.000 16.64 8.39 0.00 3.51
1545 1619 0.752743 ATTGTGTGTGGTGCTGCAGT 60.753 50.000 16.64 0.00 0.00 4.40
1546 1620 0.318360 CATTGTGTGTGGTGCTGCAG 60.318 55.000 10.11 10.11 0.00 4.41
1547 1621 1.734748 CATTGTGTGTGGTGCTGCA 59.265 52.632 0.00 0.00 0.00 4.41
1548 1622 1.662446 GCATTGTGTGTGGTGCTGC 60.662 57.895 0.00 0.00 34.85 5.25
1549 1623 0.595567 GTGCATTGTGTGTGGTGCTG 60.596 55.000 0.00 0.00 38.37 4.41
1550 1624 1.735360 GTGCATTGTGTGTGGTGCT 59.265 52.632 0.00 0.00 38.37 4.40
1551 1625 1.300080 GGTGCATTGTGTGTGGTGC 60.300 57.895 0.00 0.00 38.05 5.01
1552 1626 0.031043 CAGGTGCATTGTGTGTGGTG 59.969 55.000 0.00 0.00 0.00 4.17
1553 1627 0.106769 TCAGGTGCATTGTGTGTGGT 60.107 50.000 0.00 0.00 0.00 4.16
1554 1628 1.001048 CTTCAGGTGCATTGTGTGTGG 60.001 52.381 0.00 0.00 0.00 4.17
1555 1629 1.001048 CCTTCAGGTGCATTGTGTGTG 60.001 52.381 0.00 0.00 0.00 3.82
1556 1630 1.133823 TCCTTCAGGTGCATTGTGTGT 60.134 47.619 0.00 0.00 36.34 3.72
1557 1631 1.608055 TCCTTCAGGTGCATTGTGTG 58.392 50.000 0.00 0.00 36.34 3.82
1558 1632 2.363306 TTCCTTCAGGTGCATTGTGT 57.637 45.000 0.00 0.00 36.34 3.72
1559 1633 2.886523 TCTTTCCTTCAGGTGCATTGTG 59.113 45.455 0.00 0.00 36.34 3.33
1560 1634 2.887152 GTCTTTCCTTCAGGTGCATTGT 59.113 45.455 0.00 0.00 36.34 2.71
1561 1635 2.095567 CGTCTTTCCTTCAGGTGCATTG 60.096 50.000 0.00 0.00 36.34 2.82
1562 1636 2.154462 CGTCTTTCCTTCAGGTGCATT 58.846 47.619 0.00 0.00 36.34 3.56
1572 1646 2.564947 AGCTCATCAGACGTCTTTCCTT 59.435 45.455 17.26 0.00 0.00 3.36
1573 1647 2.175202 AGCTCATCAGACGTCTTTCCT 58.825 47.619 17.26 3.83 0.00 3.36
1579 1653 1.723542 CACACAAGCTCATCAGACGTC 59.276 52.381 7.70 7.70 0.00 4.34
1580 1654 1.069204 ACACACAAGCTCATCAGACGT 59.931 47.619 0.00 0.00 0.00 4.34
1581 1655 1.788258 ACACACAAGCTCATCAGACG 58.212 50.000 0.00 0.00 0.00 4.18
1582 1656 2.874701 ACAACACACAAGCTCATCAGAC 59.125 45.455 0.00 0.00 0.00 3.51
1583 1657 2.874086 CACAACACACAAGCTCATCAGA 59.126 45.455 0.00 0.00 0.00 3.27
1584 1658 2.603892 GCACAACACACAAGCTCATCAG 60.604 50.000 0.00 0.00 0.00 2.90
1585 1659 1.334556 GCACAACACACAAGCTCATCA 59.665 47.619 0.00 0.00 0.00 3.07
1586 1660 1.605710 AGCACAACACACAAGCTCATC 59.394 47.619 0.00 0.00 0.00 2.92
1587 1661 1.683943 AGCACAACACACAAGCTCAT 58.316 45.000 0.00 0.00 0.00 2.90
1600 1674 4.623932 AGTAATGGACTGAAGAGCACAA 57.376 40.909 0.00 0.00 36.87 3.33
1618 1692 0.618458 GGACAACAGGGGATGCAGTA 59.382 55.000 0.00 0.00 0.00 2.74
1623 1697 2.162681 GTTCAAGGACAACAGGGGATG 58.837 52.381 0.00 0.00 0.00 3.51
1665 1742 5.473796 TCAACGTCCAACTAAAACAGTTC 57.526 39.130 0.00 0.00 44.48 3.01
1670 1747 3.955771 TGCTCAACGTCCAACTAAAAC 57.044 42.857 0.00 0.00 0.00 2.43
1701 1780 4.036567 AGTTCGGTTGTGGTTAAAAAGC 57.963 40.909 0.00 0.00 0.00 3.51
1707 1786 3.638160 ACTACAGAGTTCGGTTGTGGTTA 59.362 43.478 0.00 0.00 33.51 2.85
1709 1788 2.037144 ACTACAGAGTTCGGTTGTGGT 58.963 47.619 0.00 0.00 32.62 4.16
1718 1797 3.955650 TGGCACCTTACTACAGAGTTC 57.044 47.619 0.00 0.00 37.10 3.01
1735 2126 1.728971 CGACAGACAAGAGACAATGGC 59.271 52.381 0.00 0.00 0.00 4.40
1738 2129 2.289072 CCACCGACAGACAAGAGACAAT 60.289 50.000 0.00 0.00 0.00 2.71
1755 2146 0.332972 AAAATCAGGGAGGCTCCACC 59.667 55.000 33.27 18.03 38.64 4.61
1814 2205 0.102481 AACGCACACGAGTTCAGACT 59.898 50.000 0.00 0.00 43.93 3.24
1838 2229 5.465051 CGAGAGAGAAATCAGACACTGAAA 58.535 41.667 5.57 0.00 44.04 2.69
1858 2249 0.107945 CTCTTTCTCAAGGCCCCGAG 60.108 60.000 11.97 11.97 0.00 4.63
1862 2253 0.391793 CCGTCTCTTTCTCAAGGCCC 60.392 60.000 0.00 0.00 0.00 5.80
1863 2254 0.608640 TCCGTCTCTTTCTCAAGGCC 59.391 55.000 0.00 0.00 0.00 5.19
1864 2255 2.682155 ATCCGTCTCTTTCTCAAGGC 57.318 50.000 0.00 0.00 0.00 4.35
1865 2256 4.993029 AGTATCCGTCTCTTTCTCAAGG 57.007 45.455 0.00 0.00 0.00 3.61
1866 2257 5.574830 CACAAGTATCCGTCTCTTTCTCAAG 59.425 44.000 0.00 0.00 0.00 3.02
1867 2258 5.010719 ACACAAGTATCCGTCTCTTTCTCAA 59.989 40.000 0.00 0.00 0.00 3.02
1868 2259 4.523173 ACACAAGTATCCGTCTCTTTCTCA 59.477 41.667 0.00 0.00 0.00 3.27
1912 2303 3.839293 AGCTTGAGTAACGTTCTAGCTG 58.161 45.455 19.30 4.43 46.74 4.24
1959 2356 4.323553 AACTTGTGTACTCACTCTCACC 57.676 45.455 0.00 0.00 44.14 4.02
2029 2426 2.303175 GCGTATTTGCCTGGGGATTTA 58.697 47.619 0.00 0.00 0.00 1.40
2031 2428 0.033601 TGCGTATTTGCCTGGGGATT 60.034 50.000 0.00 0.00 0.00 3.01
2037 2434 5.173774 AGATGTTATTGCGTATTTGCCTG 57.826 39.130 0.00 0.00 0.00 4.85
2039 2436 5.168526 TGAGATGTTATTGCGTATTTGCC 57.831 39.130 0.00 0.00 0.00 4.52
2053 2450 1.134580 CGGCTGACTGGATGAGATGTT 60.135 52.381 0.00 0.00 0.00 2.71
2116 2520 2.233271 CACTGAATTTGCCTGGACTGT 58.767 47.619 0.00 0.00 0.00 3.55
2117 2521 1.068055 GCACTGAATTTGCCTGGACTG 60.068 52.381 0.00 0.00 33.58 3.51
2133 2537 1.296715 GACTGGACCGGATTGCACT 59.703 57.895 9.46 0.00 0.00 4.40
2208 2624 5.684550 AAGAGATACGTACATGATACGCA 57.315 39.130 20.41 12.75 43.97 5.24
2211 2627 9.991388 GGAATCTAAGAGATACGTACATGATAC 57.009 37.037 0.00 0.00 32.89 2.24
2212 2628 9.961264 AGGAATCTAAGAGATACGTACATGATA 57.039 33.333 0.00 0.00 32.89 2.15
2213 2629 8.871629 AGGAATCTAAGAGATACGTACATGAT 57.128 34.615 0.00 0.00 32.89 2.45
2214 2630 8.568794 CAAGGAATCTAAGAGATACGTACATGA 58.431 37.037 0.00 0.00 32.89 3.07
2216 2632 8.693120 TCAAGGAATCTAAGAGATACGTACAT 57.307 34.615 0.00 0.00 32.89 2.29
2218 2634 8.380743 TCTCAAGGAATCTAAGAGATACGTAC 57.619 38.462 0.00 0.00 32.89 3.67
2219 2635 8.975663 TTCTCAAGGAATCTAAGAGATACGTA 57.024 34.615 0.00 0.00 32.89 3.57
2220 2636 7.883391 TTCTCAAGGAATCTAAGAGATACGT 57.117 36.000 0.00 0.00 32.89 3.57
2245 2673 7.012044 GTGGAAAGGTGTTACATACATATGTCC 59.988 40.741 12.68 4.72 45.11 4.02
2248 2676 7.768582 TCAGTGGAAAGGTGTTACATACATATG 59.231 37.037 0.00 0.00 39.39 1.78


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

AutoCloner maintained by Alex Coulton.