Multiple sequence alignment - TraesCS7A01G209000

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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 TraesCS7A01G209000 chr7A 100.000 5248 0 0 1 5248 171431437 171436684 0.000000e+00 9692
1 TraesCS7A01G209000 chr7A 86.429 560 40 19 4096 4624 171943883 171944437 9.800000e-162 580
2 TraesCS7A01G209000 chr7A 84.516 620 56 18 4294 4897 171552542 171553137 1.270000e-160 577
3 TraesCS7A01G209000 chr7A 92.328 378 26 3 3895 4270 171552117 171552493 7.740000e-148 534
4 TraesCS7A01G209000 chr7A 88.938 226 17 4 1739 1964 515164080 515164297 6.700000e-69 272
5 TraesCS7A01G209000 chr7A 88.106 227 25 2 5020 5244 171553212 171553438 8.660000e-68 268
6 TraesCS7A01G209000 chr7A 87.288 236 24 3 5019 5248 171944850 171945085 1.120000e-66 265
7 TraesCS7A01G209000 chr7A 92.562 121 9 0 3778 3898 171551919 171552039 1.940000e-39 174
8 TraesCS7A01G209000 chr7A 94.118 85 4 1 4898 4982 223266106 223266023 1.530000e-25 128
9 TraesCS7A01G209000 chr7B 95.417 2815 91 20 1964 4759 134629217 134632012 0.000000e+00 4449
10 TraesCS7A01G209000 chr7B 98.734 948 12 0 1 948 68110225 68111172 0.000000e+00 1685
11 TraesCS7A01G209000 chr7B 99.467 563 3 0 3 565 528912899 528913461 0.000000e+00 1024
12 TraesCS7A01G209000 chr7B 88.266 767 52 16 968 1730 134628480 134629212 0.000000e+00 883
13 TraesCS7A01G209000 chr7B 89.908 218 21 1 5019 5236 128441921 128441705 4.000000e-71 279
14 TraesCS7A01G209000 chr7B 90.698 86 2 4 4815 4897 134632017 134632099 5.560000e-20 110
15 TraesCS7A01G209000 chr7D 94.715 1911 66 17 2999 4897 169416541 169418428 0.000000e+00 2937
16 TraesCS7A01G209000 chr7D 92.736 1060 65 7 1964 3014 169415417 169416473 0.000000e+00 1520
17 TraesCS7A01G209000 chr7D 92.680 765 35 10 968 1730 169414667 169415412 0.000000e+00 1083
18 TraesCS7A01G209000 chr7D 85.808 1064 77 43 3867 4897 169538235 169539257 0.000000e+00 1061
19 TraesCS7A01G209000 chr7D 88.057 628 47 14 4274 4897 169427836 169428439 0.000000e+00 719
20 TraesCS7A01G209000 chr7D 89.703 505 44 7 3875 4375 169480488 169480988 5.730000e-179 638
21 TraesCS7A01G209000 chr7D 89.655 406 35 7 3875 4275 169427393 169427796 1.300000e-140 510
22 TraesCS7A01G209000 chr7D 93.511 262 15 2 4988 5248 169482971 169483231 6.370000e-104 388
23 TraesCS7A01G209000 chr7D 88.991 218 23 1 5019 5236 165138101 165137885 8.660000e-68 268
24 TraesCS7A01G209000 chr7D 88.667 150 15 1 4668 4815 169481037 169481186 1.160000e-41 182
25 TraesCS7A01G209000 chr2A 99.262 948 7 0 1 948 719466593 719467540 0.000000e+00 1712
26 TraesCS7A01G209000 chr2A 98.714 933 11 1 23 954 43393103 43394035 0.000000e+00 1655
27 TraesCS7A01G209000 chr6B 98.944 947 10 0 1 947 408674761 408675707 0.000000e+00 1694
28 TraesCS7A01G209000 chr6B 98.429 955 15 0 1 955 704837876 704836922 0.000000e+00 1681
29 TraesCS7A01G209000 chr6B 94.048 84 4 1 4899 4982 642460089 642460171 5.520000e-25 126
30 TraesCS7A01G209000 chr5B 98.312 948 14 2 1 947 420730003 420730949 0.000000e+00 1661
31 TraesCS7A01G209000 chr5B 98.307 945 16 0 3 947 179240260 179241204 0.000000e+00 1657
32 TraesCS7A01G209000 chr3B 97.374 952 23 2 1 951 552490932 552491882 0.000000e+00 1618
33 TraesCS7A01G209000 chr3B 94.118 85 4 1 4898 4982 12420529 12420612 1.530000e-25 128
34 TraesCS7A01G209000 chr4B 94.937 948 14 4 1 947 194231923 194232837 0.000000e+00 1454
35 TraesCS7A01G209000 chr4B 89.868 227 19 4 1736 1961 640809792 640810015 6.650000e-74 289
36 TraesCS7A01G209000 chr6A 94.810 501 22 3 3778 4275 124314053 124313554 0.000000e+00 778
37 TraesCS7A01G209000 chr6A 89.491 609 42 13 4294 4897 124426695 124426104 0.000000e+00 750
38 TraesCS7A01G209000 chr6A 86.864 609 41 19 4294 4897 124913993 124914567 0.000000e+00 645
39 TraesCS7A01G209000 chr6A 89.189 407 38 4 3875 4275 124427148 124426742 2.180000e-138 503
40 TraesCS7A01G209000 chr6A 89.189 407 38 4 3875 4275 124913540 124913946 2.180000e-138 503
41 TraesCS7A01G209000 chr6A 95.408 196 8 1 1770 1964 74233288 74233483 1.420000e-80 311
42 TraesCS7A01G209000 chrUn 86.429 560 40 19 4096 4624 293555437 293554883 9.800000e-162 580
43 TraesCS7A01G209000 chrUn 86.429 560 40 19 4096 4624 314488199 314487645 9.800000e-162 580
44 TraesCS7A01G209000 chrUn 86.429 560 40 19 4096 4624 325381535 325382089 9.800000e-162 580
45 TraesCS7A01G209000 chrUn 84.516 620 56 18 4294 4897 82710485 82711080 1.270000e-160 577
46 TraesCS7A01G209000 chrUn 92.328 378 26 3 3895 4270 82710060 82710436 7.740000e-148 534
47 TraesCS7A01G209000 chrUn 88.106 227 25 2 5020 5244 82711155 82711381 8.660000e-68 268
48 TraesCS7A01G209000 chrUn 87.288 236 24 3 5019 5248 293554470 293554235 1.120000e-66 265
49 TraesCS7A01G209000 chrUn 87.288 236 24 3 5019 5248 314487232 314486997 1.120000e-66 265
50 TraesCS7A01G209000 chrUn 87.288 236 24 3 5019 5248 325382502 325382737 1.120000e-66 265
51 TraesCS7A01G209000 chrUn 92.562 121 9 0 3778 3898 82709862 82709982 1.940000e-39 174
52 TraesCS7A01G209000 chr1A 94.805 231 11 1 1734 1963 482834462 482834232 5.000000e-95 359
53 TraesCS7A01G209000 chr1A 93.506 231 14 1 1734 1963 586137735 586137505 5.030000e-90 342
54 TraesCS7A01G209000 chr4A 89.868 227 21 2 1739 1964 682738695 682738920 1.850000e-74 291
55 TraesCS7A01G209000 chr3A 90.222 225 16 2 1738 1962 683348120 683348338 6.650000e-74 289
56 TraesCS7A01G209000 chr1B 86.842 228 28 2 1738 1964 87973166 87972940 2.430000e-63 254
57 TraesCS7A01G209000 chr6D 90.055 181 10 5 4716 4893 103036694 103036519 1.470000e-55 228
58 TraesCS7A01G209000 chr2B 92.517 147 11 0 1738 1884 103958018 103958164 1.480000e-50 211
59 TraesCS7A01G209000 chr5D 94.118 85 5 0 4898 4982 44052872 44052788 4.270000e-26 130
60 TraesCS7A01G209000 chr5D 91.304 92 7 1 4892 4982 244012116 244012025 1.980000e-24 124
61 TraesCS7A01G209000 chr3D 94.118 85 5 0 4898 4982 23968512 23968428 4.270000e-26 130
62 TraesCS7A01G209000 chr3D 94.186 86 4 1 4898 4982 75614556 75614641 4.270000e-26 130
63 TraesCS7A01G209000 chr3D 90.526 95 7 2 4888 4982 604567754 604567662 1.980000e-24 124
64 TraesCS7A01G209000 chr5A 92.941 85 6 0 4899 4983 632197022 632197106 1.980000e-24 124


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 TraesCS7A01G209000 chr7A 171431437 171436684 5247 False 9692.000000 9692 100.000000 1 5248 1 chr7A.!!$F1 5247
1 TraesCS7A01G209000 chr7A 171943883 171945085 1202 False 422.500000 580 86.858500 4096 5248 2 chr7A.!!$F4 1152
2 TraesCS7A01G209000 chr7A 171551919 171553438 1519 False 388.250000 577 89.378000 3778 5244 4 chr7A.!!$F3 1466
3 TraesCS7A01G209000 chr7B 134628480 134632099 3619 False 1814.000000 4449 91.460333 968 4897 3 chr7B.!!$F3 3929
4 TraesCS7A01G209000 chr7B 68110225 68111172 947 False 1685.000000 1685 98.734000 1 948 1 chr7B.!!$F1 947
5 TraesCS7A01G209000 chr7B 528912899 528913461 562 False 1024.000000 1024 99.467000 3 565 1 chr7B.!!$F2 562
6 TraesCS7A01G209000 chr7D 169414667 169418428 3761 False 1846.666667 2937 93.377000 968 4897 3 chr7D.!!$F2 3929
7 TraesCS7A01G209000 chr7D 169538235 169539257 1022 False 1061.000000 1061 85.808000 3867 4897 1 chr7D.!!$F1 1030
8 TraesCS7A01G209000 chr7D 169427393 169428439 1046 False 614.500000 719 88.856000 3875 4897 2 chr7D.!!$F3 1022
9 TraesCS7A01G209000 chr7D 169480488 169483231 2743 False 402.666667 638 90.627000 3875 5248 3 chr7D.!!$F4 1373
10 TraesCS7A01G209000 chr2A 719466593 719467540 947 False 1712.000000 1712 99.262000 1 948 1 chr2A.!!$F2 947
11 TraesCS7A01G209000 chr2A 43393103 43394035 932 False 1655.000000 1655 98.714000 23 954 1 chr2A.!!$F1 931
12 TraesCS7A01G209000 chr6B 408674761 408675707 946 False 1694.000000 1694 98.944000 1 947 1 chr6B.!!$F1 946
13 TraesCS7A01G209000 chr6B 704836922 704837876 954 True 1681.000000 1681 98.429000 1 955 1 chr6B.!!$R1 954
14 TraesCS7A01G209000 chr5B 420730003 420730949 946 False 1661.000000 1661 98.312000 1 947 1 chr5B.!!$F2 946
15 TraesCS7A01G209000 chr5B 179240260 179241204 944 False 1657.000000 1657 98.307000 3 947 1 chr5B.!!$F1 944
16 TraesCS7A01G209000 chr3B 552490932 552491882 950 False 1618.000000 1618 97.374000 1 951 1 chr3B.!!$F2 950
17 TraesCS7A01G209000 chr4B 194231923 194232837 914 False 1454.000000 1454 94.937000 1 947 1 chr4B.!!$F1 946
18 TraesCS7A01G209000 chr6A 124426104 124427148 1044 True 626.500000 750 89.340000 3875 4897 2 chr6A.!!$R2 1022
19 TraesCS7A01G209000 chr6A 124913540 124914567 1027 False 574.000000 645 88.026500 3875 4897 2 chr6A.!!$F2 1022
20 TraesCS7A01G209000 chrUn 293554235 293555437 1202 True 422.500000 580 86.858500 4096 5248 2 chrUn.!!$R1 1152
21 TraesCS7A01G209000 chrUn 314486997 314488199 1202 True 422.500000 580 86.858500 4096 5248 2 chrUn.!!$R2 1152
22 TraesCS7A01G209000 chrUn 325381535 325382737 1202 False 422.500000 580 86.858500 4096 5248 2 chrUn.!!$F2 1152
23 TraesCS7A01G209000 chrUn 82709862 82711381 1519 False 388.250000 577 89.378000 3778 5244 4 chrUn.!!$F1 1466

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
754 756 1.278127 GAAAATGAGGGGAGACGGACA 59.722 52.381 0.00 0.0 0.00 4.02 F
1751 1759 0.036306 ACAACCTTAGGCCCTGTTCG 59.964 55.000 0.00 0.0 0.00 3.95 F
1772 1780 0.034059 CAGACGTCCACTCCTTGCTT 59.966 55.000 13.01 0.0 0.00 3.91 F
1794 1802 0.107312 CAACTCCCAGCTCCATCCAG 60.107 60.000 0.00 0.0 0.00 3.86 F
2425 2449 0.249398 AAATTCGCACCTCGCTACCT 59.751 50.000 0.00 0.0 39.08 3.08 F
3956 4152 0.462789 AATGTAGGGCGTAGTTCGGG 59.537 55.000 0.00 0.0 40.26 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1753 1761 0.034059 AAGCAAGGAGTGGACGTCTG 59.966 55.000 16.46 4.89 0.00 3.51 R
2650 2674 1.742768 CCAGCTCTACGCCCCTAAG 59.257 63.158 0.00 0.00 40.39 2.18 R
3684 3798 2.794350 TGATACATCACGCATAGCAACG 59.206 45.455 0.00 0.00 0.00 4.10 R
3956 4152 6.481644 TGTTGGTCAAATTTAAACTTGGATGC 59.518 34.615 9.33 0.00 0.00 3.91 R
4169 4376 1.985159 ACCTGAACCATCAAGCTACCA 59.015 47.619 0.00 0.00 34.49 3.25 R
4933 6972 0.673644 ATCGAGTTTTGGAGCACCGG 60.674 55.000 0.00 0.00 39.42 5.28 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
721 723 2.674754 GGATTTGGGGCGGAGTGA 59.325 61.111 0.00 0.00 0.00 3.41
754 756 1.278127 GAAAATGAGGGGAGACGGACA 59.722 52.381 0.00 0.00 0.00 4.02
955 957 9.771534 CACTTTTTAGGATTTGGGATTAAACAA 57.228 29.630 0.00 0.00 0.00 2.83
961 963 7.244886 AGGATTTGGGATTAAACAAAAGAGG 57.755 36.000 7.22 0.00 39.69 3.69
962 964 6.213397 AGGATTTGGGATTAAACAAAAGAGGG 59.787 38.462 7.22 0.00 39.69 4.30
963 965 4.882842 TTGGGATTAAACAAAAGAGGGC 57.117 40.909 0.00 0.00 0.00 5.19
964 966 3.169908 TGGGATTAAACAAAAGAGGGCC 58.830 45.455 0.00 0.00 0.00 5.80
965 967 3.181412 TGGGATTAAACAAAAGAGGGCCT 60.181 43.478 5.25 5.25 0.00 5.19
966 968 4.044825 TGGGATTAAACAAAAGAGGGCCTA 59.955 41.667 5.73 0.00 0.00 3.93
969 971 6.406961 GGGATTAAACAAAAGAGGGCCTAATG 60.407 42.308 5.73 5.89 0.00 1.90
986 988 3.497031 GTTAGTGGAAGGCGCGCC 61.497 66.667 42.34 42.34 0.00 6.53
1355 1361 4.414956 TGAGGGCGAGGGGTGGAT 62.415 66.667 0.00 0.00 0.00 3.41
1485 1491 3.467119 CGGAAGGCGACGTCGTTG 61.467 66.667 35.48 16.98 40.00 4.10
1548 1554 3.317149 TCGTCCTCATATTTGGTACGGAG 59.683 47.826 0.00 0.00 32.22 4.63
1553 1559 5.479375 TCCTCATATTTGGTACGGAGGTATC 59.521 44.000 0.00 0.00 37.96 2.24
1562 1568 2.201771 GGAGGTATCCGGCTCCCT 59.798 66.667 13.38 9.56 35.37 4.20
1564 1570 2.203509 AGGTATCCGGCTCCCTCG 60.204 66.667 0.00 0.00 0.00 4.63
1581 1587 2.141517 CTCGCCCTGCATTTCTGATAG 58.858 52.381 0.00 0.00 0.00 2.08
1582 1588 1.762370 TCGCCCTGCATTTCTGATAGA 59.238 47.619 0.00 0.00 0.00 1.98
1584 1590 2.484417 CGCCCTGCATTTCTGATAGAGT 60.484 50.000 0.00 0.00 0.00 3.24
1585 1591 3.243873 CGCCCTGCATTTCTGATAGAGTA 60.244 47.826 0.00 0.00 0.00 2.59
1586 1592 4.562347 CGCCCTGCATTTCTGATAGAGTAT 60.562 45.833 0.00 0.00 0.00 2.12
1593 1601 7.500141 TGCATTTCTGATAGAGTATTACTGCA 58.500 34.615 0.00 0.00 0.00 4.41
1594 1602 7.439356 TGCATTTCTGATAGAGTATTACTGCAC 59.561 37.037 0.00 0.00 0.00 4.57
1647 1655 3.420482 AAATGGCGAGGGGAGGGG 61.420 66.667 0.00 0.00 0.00 4.79
1654 1662 4.825679 GAGGGGAGGGGTCTGGGG 62.826 77.778 0.00 0.00 0.00 4.96
1658 1666 2.689034 GGAGGGGTCTGGGGTCTG 60.689 72.222 0.00 0.00 0.00 3.51
1668 1676 3.034635 GTCTGGGGTCTGTCATATCTGT 58.965 50.000 0.00 0.00 0.00 3.41
1670 1678 2.768527 CTGGGGTCTGTCATATCTGTGT 59.231 50.000 0.00 0.00 0.00 3.72
1671 1679 2.766263 TGGGGTCTGTCATATCTGTGTC 59.234 50.000 0.00 0.00 0.00 3.67
1672 1680 2.766263 GGGGTCTGTCATATCTGTGTCA 59.234 50.000 0.00 0.00 0.00 3.58
1673 1681 3.389329 GGGGTCTGTCATATCTGTGTCAT 59.611 47.826 0.00 0.00 0.00 3.06
1674 1682 4.588951 GGGGTCTGTCATATCTGTGTCATA 59.411 45.833 0.00 0.00 0.00 2.15
1675 1683 5.247110 GGGGTCTGTCATATCTGTGTCATAT 59.753 44.000 0.00 0.00 0.00 1.78
1676 1684 6.393990 GGGTCTGTCATATCTGTGTCATATC 58.606 44.000 0.00 0.00 0.00 1.63
1731 1739 5.407502 GTGGGTTATTTCAATACCACAAGC 58.592 41.667 11.74 0.00 45.72 4.01
1732 1740 5.047660 GTGGGTTATTTCAATACCACAAGCA 60.048 40.000 11.74 0.00 45.72 3.91
1733 1741 5.047660 TGGGTTATTTCAATACCACAAGCAC 60.048 40.000 0.00 0.00 0.00 4.40
1734 1742 5.047660 GGGTTATTTCAATACCACAAGCACA 60.048 40.000 0.00 0.00 0.00 4.57
1735 1743 6.451393 GGTTATTTCAATACCACAAGCACAA 58.549 36.000 0.00 0.00 0.00 3.33
1736 1744 6.364976 GGTTATTTCAATACCACAAGCACAAC 59.635 38.462 0.00 0.00 0.00 3.32
1737 1745 4.314740 TTTCAATACCACAAGCACAACC 57.685 40.909 0.00 0.00 0.00 3.77
1738 1746 3.222173 TCAATACCACAAGCACAACCT 57.778 42.857 0.00 0.00 0.00 3.50
1739 1747 3.561143 TCAATACCACAAGCACAACCTT 58.439 40.909 0.00 0.00 0.00 3.50
1740 1748 4.720046 TCAATACCACAAGCACAACCTTA 58.280 39.130 0.00 0.00 0.00 2.69
1741 1749 4.759693 TCAATACCACAAGCACAACCTTAG 59.240 41.667 0.00 0.00 0.00 2.18
1742 1750 1.981256 ACCACAAGCACAACCTTAGG 58.019 50.000 0.00 0.00 0.00 2.69
1743 1751 0.598065 CCACAAGCACAACCTTAGGC 59.402 55.000 0.00 0.00 0.00 3.93
1744 1752 0.598065 CACAAGCACAACCTTAGGCC 59.402 55.000 0.00 0.00 0.00 5.19
1745 1753 0.539669 ACAAGCACAACCTTAGGCCC 60.540 55.000 0.00 0.00 0.00 5.80
1746 1754 0.251341 CAAGCACAACCTTAGGCCCT 60.251 55.000 0.00 0.00 0.00 5.19
1747 1755 0.251341 AAGCACAACCTTAGGCCCTG 60.251 55.000 0.00 0.00 0.00 4.45
1748 1756 1.074951 GCACAACCTTAGGCCCTGT 59.925 57.895 0.00 0.00 0.00 4.00
1749 1757 0.539669 GCACAACCTTAGGCCCTGTT 60.540 55.000 0.00 0.00 0.00 3.16
1750 1758 1.534729 CACAACCTTAGGCCCTGTTC 58.465 55.000 0.00 0.00 0.00 3.18
1751 1759 0.036306 ACAACCTTAGGCCCTGTTCG 59.964 55.000 0.00 0.00 0.00 3.95
1752 1760 0.676782 CAACCTTAGGCCCTGTTCGG 60.677 60.000 0.00 0.00 0.00 4.30
1763 1771 2.028484 TGTTCGGCAGACGTCCAC 59.972 61.111 13.01 4.19 44.69 4.02
1764 1772 2.338984 GTTCGGCAGACGTCCACT 59.661 61.111 13.01 0.00 44.69 4.00
1765 1773 1.733399 GTTCGGCAGACGTCCACTC 60.733 63.158 13.01 0.00 44.69 3.51
1766 1774 2.927580 TTCGGCAGACGTCCACTCC 61.928 63.158 13.01 7.39 44.69 3.85
1767 1775 3.374402 CGGCAGACGTCCACTCCT 61.374 66.667 13.01 0.00 37.93 3.69
1768 1776 2.932234 CGGCAGACGTCCACTCCTT 61.932 63.158 13.01 0.00 37.93 3.36
1769 1777 1.374758 GGCAGACGTCCACTCCTTG 60.375 63.158 13.01 2.92 0.00 3.61
1770 1778 2.029844 GCAGACGTCCACTCCTTGC 61.030 63.158 13.01 9.98 0.00 4.01
1771 1779 1.668294 CAGACGTCCACTCCTTGCT 59.332 57.895 13.01 0.00 0.00 3.91
1772 1780 0.034059 CAGACGTCCACTCCTTGCTT 59.966 55.000 13.01 0.00 0.00 3.91
1773 1781 0.759346 AGACGTCCACTCCTTGCTTT 59.241 50.000 13.01 0.00 0.00 3.51
1774 1782 1.149148 GACGTCCACTCCTTGCTTTC 58.851 55.000 3.51 0.00 0.00 2.62
1775 1783 0.250338 ACGTCCACTCCTTGCTTTCC 60.250 55.000 0.00 0.00 0.00 3.13
1776 1784 0.250295 CGTCCACTCCTTGCTTTCCA 60.250 55.000 0.00 0.00 0.00 3.53
1777 1785 1.813862 CGTCCACTCCTTGCTTTCCAA 60.814 52.381 0.00 0.00 0.00 3.53
1778 1786 1.609072 GTCCACTCCTTGCTTTCCAAC 59.391 52.381 0.00 0.00 0.00 3.77
1779 1787 1.494721 TCCACTCCTTGCTTTCCAACT 59.505 47.619 0.00 0.00 0.00 3.16
1780 1788 1.882623 CCACTCCTTGCTTTCCAACTC 59.117 52.381 0.00 0.00 0.00 3.01
1781 1789 1.882623 CACTCCTTGCTTTCCAACTCC 59.117 52.381 0.00 0.00 0.00 3.85
1782 1790 1.202940 ACTCCTTGCTTTCCAACTCCC 60.203 52.381 0.00 0.00 0.00 4.30
1783 1791 0.850100 TCCTTGCTTTCCAACTCCCA 59.150 50.000 0.00 0.00 0.00 4.37
1784 1792 1.202927 TCCTTGCTTTCCAACTCCCAG 60.203 52.381 0.00 0.00 0.00 4.45
1785 1793 0.600057 CTTGCTTTCCAACTCCCAGC 59.400 55.000 0.00 0.00 0.00 4.85
1786 1794 0.185901 TTGCTTTCCAACTCCCAGCT 59.814 50.000 0.00 0.00 0.00 4.24
1787 1795 0.250901 TGCTTTCCAACTCCCAGCTC 60.251 55.000 0.00 0.00 0.00 4.09
1788 1796 0.962855 GCTTTCCAACTCCCAGCTCC 60.963 60.000 0.00 0.00 0.00 4.70
1789 1797 0.401738 CTTTCCAACTCCCAGCTCCA 59.598 55.000 0.00 0.00 0.00 3.86
1790 1798 1.005215 CTTTCCAACTCCCAGCTCCAT 59.995 52.381 0.00 0.00 0.00 3.41
1791 1799 0.620556 TTCCAACTCCCAGCTCCATC 59.379 55.000 0.00 0.00 0.00 3.51
1792 1800 1.225704 CCAACTCCCAGCTCCATCC 59.774 63.158 0.00 0.00 0.00 3.51
1793 1801 1.565390 CCAACTCCCAGCTCCATCCA 61.565 60.000 0.00 0.00 0.00 3.41
1794 1802 0.107312 CAACTCCCAGCTCCATCCAG 60.107 60.000 0.00 0.00 0.00 3.86
1795 1803 0.252881 AACTCCCAGCTCCATCCAGA 60.253 55.000 0.00 0.00 0.00 3.86
1796 1804 0.252881 ACTCCCAGCTCCATCCAGAA 60.253 55.000 0.00 0.00 0.00 3.02
1797 1805 0.469070 CTCCCAGCTCCATCCAGAAG 59.531 60.000 0.00 0.00 0.00 2.85
1798 1806 1.153005 CCCAGCTCCATCCAGAAGC 60.153 63.158 0.00 0.00 0.00 3.86
1799 1807 1.523258 CCAGCTCCATCCAGAAGCG 60.523 63.158 0.00 0.00 0.00 4.68
1800 1808 1.523258 CAGCTCCATCCAGAAGCGG 60.523 63.158 0.00 0.00 0.00 5.52
1801 1809 1.687146 AGCTCCATCCAGAAGCGGA 60.687 57.895 0.00 0.00 40.07 5.54
1802 1810 1.227497 GCTCCATCCAGAAGCGGAG 60.227 63.158 0.00 0.00 46.53 4.63
1821 1829 3.660111 GCACGGAGCGGCACTTTT 61.660 61.111 1.45 0.00 0.00 2.27
1822 1830 2.252260 CACGGAGCGGCACTTTTG 59.748 61.111 1.45 0.00 0.00 2.44
1839 1847 5.707411 CTTTTGCAACTCTGAAAAAGTGG 57.293 39.130 0.00 0.00 46.79 4.00
1840 1848 2.869233 TGCAACTCTGAAAAAGTGGC 57.131 45.000 0.00 0.00 42.89 5.01
1841 1849 1.408702 TGCAACTCTGAAAAAGTGGCC 59.591 47.619 0.00 0.00 42.07 5.36
1842 1850 1.683385 GCAACTCTGAAAAAGTGGCCT 59.317 47.619 3.32 0.00 37.67 5.19
1843 1851 2.884639 GCAACTCTGAAAAAGTGGCCTA 59.115 45.455 3.32 0.00 37.67 3.93
1844 1852 3.304726 GCAACTCTGAAAAAGTGGCCTAC 60.305 47.826 3.32 0.00 37.67 3.18
1845 1853 3.857157 ACTCTGAAAAAGTGGCCTACA 57.143 42.857 3.32 0.00 0.00 2.74
1846 1854 4.164843 ACTCTGAAAAAGTGGCCTACAA 57.835 40.909 3.32 0.00 0.00 2.41
1847 1855 4.137543 ACTCTGAAAAAGTGGCCTACAAG 58.862 43.478 3.32 0.00 0.00 3.16
1848 1856 2.884639 TCTGAAAAAGTGGCCTACAAGC 59.115 45.455 3.32 0.00 0.00 4.01
1857 1865 4.148825 CCTACAAGCCGCTCCGCT 62.149 66.667 0.00 0.00 42.22 5.52
1858 1866 2.583593 CTACAAGCCGCTCCGCTC 60.584 66.667 0.00 0.00 38.44 5.03
1859 1867 4.143333 TACAAGCCGCTCCGCTCC 62.143 66.667 0.00 0.00 38.44 4.70
1874 1882 4.382541 TCCGCTCTGGGAGAGGCA 62.383 66.667 11.51 0.48 46.68 4.75
1875 1883 3.160047 CCGCTCTGGGAGAGGCAT 61.160 66.667 4.55 0.00 42.15 4.40
1876 1884 2.108566 CGCTCTGGGAGAGGCATG 59.891 66.667 2.88 0.00 42.54 4.06
1877 1885 2.509916 GCTCTGGGAGAGGCATGG 59.490 66.667 2.88 0.00 42.54 3.66
1878 1886 2.068821 GCTCTGGGAGAGGCATGGA 61.069 63.158 2.88 0.00 42.54 3.41
1879 1887 2.042404 GCTCTGGGAGAGGCATGGAG 62.042 65.000 2.88 0.00 42.54 3.86
1880 1888 2.042404 CTCTGGGAGAGGCATGGAGC 62.042 65.000 0.00 0.00 38.67 4.70
1890 1898 3.869272 CATGGAGCCAGCGCGTTC 61.869 66.667 8.43 0.00 41.18 3.95
1904 1912 4.980805 GTTCGGTGCCACTCCGCA 62.981 66.667 3.33 0.00 46.49 5.69
1905 1913 4.680237 TTCGGTGCCACTCCGCAG 62.680 66.667 3.33 0.00 46.49 5.18
1911 1919 4.828925 GCCACTCCGCAGCTCCTC 62.829 72.222 0.00 0.00 0.00 3.71
1912 1920 4.154347 CCACTCCGCAGCTCCTCC 62.154 72.222 0.00 0.00 0.00 4.30
1913 1921 3.385384 CACTCCGCAGCTCCTCCA 61.385 66.667 0.00 0.00 0.00 3.86
1914 1922 3.073735 ACTCCGCAGCTCCTCCAG 61.074 66.667 0.00 0.00 0.00 3.86
1923 1931 3.847602 CTCCTCCAGCCGCTCCAG 61.848 72.222 0.00 0.00 0.00 3.86
1926 1934 3.847602 CTCCAGCCGCTCCAGGAG 61.848 72.222 12.81 12.81 41.43 3.69
1984 1996 3.417069 TTGTGTACCTGCATGCTAGTT 57.583 42.857 20.33 5.87 0.00 2.24
2099 2117 6.435430 TTCAGGTATACATTGTGTGATTGC 57.565 37.500 5.01 0.00 0.00 3.56
2122 2140 7.774134 TGCAATTCTCACATAATATTGTTGCT 58.226 30.769 0.00 0.00 30.80 3.91
2163 2182 9.828039 ATCCTATGTATATTGTGATAGTGCATG 57.172 33.333 0.00 0.00 0.00 4.06
2200 2219 6.480763 TGTTGTATCTATCCTTTTTGCCTGA 58.519 36.000 0.00 0.00 0.00 3.86
2211 2230 4.280174 CCTTTTTGCCTGATATAGCATGCT 59.720 41.667 25.99 25.99 39.11 3.79
2218 2237 6.479006 TGCCTGATATAGCATGCTAATTCTT 58.521 36.000 30.06 16.30 33.08 2.52
2240 2260 6.931840 TCTTCTCTTTTTGTTCTCTAAGGCTC 59.068 38.462 0.00 0.00 0.00 4.70
2262 2282 4.641541 TCTGCCATCAAATATGGAGTGTTG 59.358 41.667 8.20 0.00 41.64 3.33
2321 2344 0.740737 GTCCATGCTCCATTTTCCGG 59.259 55.000 0.00 0.00 0.00 5.14
2380 2403 7.425606 AGTAGTGTGATTTGGAAAATGTGAAC 58.574 34.615 0.00 0.00 0.00 3.18
2425 2449 0.249398 AAATTCGCACCTCGCTACCT 59.751 50.000 0.00 0.00 39.08 3.08
2436 2460 5.163652 GCACCTCGCTACCTGATTTTAAATT 60.164 40.000 0.00 0.00 37.77 1.82
2544 2568 6.642131 GCAACATTTCTATTGTCAAAGAAGCA 59.358 34.615 8.95 0.55 33.49 3.91
2650 2674 3.812053 ACTCAGAGACATGCAAGTTGTTC 59.188 43.478 3.79 0.00 0.00 3.18
2700 2724 0.984230 CCTTGGCCTACCTCACTCAA 59.016 55.000 3.32 0.00 36.63 3.02
2798 2822 6.592870 AGCTTAGTCCATAAAGTATTCCCAC 58.407 40.000 0.00 0.00 0.00 4.61
3165 3273 6.321848 TGCACATATCATGTTGATTGATCC 57.678 37.500 0.00 0.00 42.70 3.36
3361 3471 9.649167 CTTGCATTTATCTCTGAAAATTTTCCT 57.351 29.630 24.51 9.45 36.36 3.36
3489 3599 6.435904 TGTGGTACCCTGGAATTTAAAATCAG 59.564 38.462 10.07 7.09 0.00 2.90
3612 3722 3.206150 AGTAACTAATCTTGCCATGCCG 58.794 45.455 0.00 0.00 0.00 5.69
3862 3976 3.624861 CACCACATTCTCAGCTACATTCC 59.375 47.826 0.00 0.00 0.00 3.01
3864 3978 3.525537 CACATTCTCAGCTACATTCCGT 58.474 45.455 0.00 0.00 0.00 4.69
3956 4152 0.462789 AATGTAGGGCGTAGTTCGGG 59.537 55.000 0.00 0.00 40.26 5.14
4169 4376 6.515272 TGACTCTTGTTTTTCTTTTCAGCT 57.485 33.333 0.00 0.00 0.00 4.24
4308 4556 3.934457 TCAGTTGATCACTACTGCGAA 57.066 42.857 18.80 3.71 44.83 4.70
4416 4680 1.472480 CTGACAAAAATAGGGGTGGCG 59.528 52.381 0.00 0.00 0.00 5.69
4417 4681 1.202952 TGACAAAAATAGGGGTGGCGT 60.203 47.619 0.00 0.00 0.00 5.68
4418 4682 1.201414 GACAAAAATAGGGGTGGCGTG 59.799 52.381 0.00 0.00 0.00 5.34
4419 4683 0.530288 CAAAAATAGGGGTGGCGTGG 59.470 55.000 0.00 0.00 0.00 4.94
4420 4684 1.254975 AAAAATAGGGGTGGCGTGGC 61.255 55.000 0.00 0.00 0.00 5.01
4627 4901 9.264719 TGTAATAGATTACTTCATGCTGACATG 57.735 33.333 12.42 0.00 46.07 3.21
4628 4902 9.481340 GTAATAGATTACTTCATGCTGACATGA 57.519 33.333 0.00 4.67 46.50 3.07
4641 4915 6.968131 TGCTGACATGAAACTAGATTGTAC 57.032 37.500 0.00 0.00 0.00 2.90
4665 4982 7.864686 ACCAACCTTTGTTTTAGTACGTTATC 58.135 34.615 0.00 0.00 30.42 1.75
4714 5094 8.880750 GTCCATAAAACTAGATTGTACCAACTC 58.119 37.037 0.00 0.00 0.00 3.01
4723 5103 6.605471 AGATTGTACCAACTCACACATAGA 57.395 37.500 0.00 0.00 0.00 1.98
4897 6936 4.972440 GCAAGAAGTAGAGCAACAGTTTTG 59.028 41.667 0.00 0.00 0.00 2.44
4898 6937 5.514279 CAAGAAGTAGAGCAACAGTTTTGG 58.486 41.667 0.00 0.00 0.00 3.28
4899 6938 4.137543 AGAAGTAGAGCAACAGTTTTGGG 58.862 43.478 0.00 0.00 0.00 4.12
4900 6939 2.863809 AGTAGAGCAACAGTTTTGGGG 58.136 47.619 0.00 0.00 0.00 4.96
4901 6940 2.441750 AGTAGAGCAACAGTTTTGGGGA 59.558 45.455 0.00 0.00 0.00 4.81
4902 6941 2.452600 AGAGCAACAGTTTTGGGGAA 57.547 45.000 0.00 0.00 0.00 3.97
4903 6942 2.745968 AGAGCAACAGTTTTGGGGAAA 58.254 42.857 0.00 0.00 0.00 3.13
4905 6944 4.479158 AGAGCAACAGTTTTGGGGAAATA 58.521 39.130 0.00 0.00 0.00 1.40
4906 6945 5.086621 AGAGCAACAGTTTTGGGGAAATAT 58.913 37.500 0.00 0.00 0.00 1.28
4907 6946 5.185828 AGAGCAACAGTTTTGGGGAAATATC 59.814 40.000 0.00 0.00 0.00 1.63
4910 6949 5.723295 CAACAGTTTTGGGGAAATATCTGG 58.277 41.667 0.00 0.00 0.00 3.86
4911 6950 5.010708 ACAGTTTTGGGGAAATATCTGGT 57.989 39.130 0.00 0.00 0.00 4.00
4912 6951 6.147437 ACAGTTTTGGGGAAATATCTGGTA 57.853 37.500 0.00 0.00 0.00 3.25
4913 6952 5.949952 ACAGTTTTGGGGAAATATCTGGTAC 59.050 40.000 0.00 0.00 0.00 3.34
4914 6953 6.187682 CAGTTTTGGGGAAATATCTGGTACT 58.812 40.000 0.00 0.00 0.00 2.73
4915 6954 6.318900 CAGTTTTGGGGAAATATCTGGTACTC 59.681 42.308 0.00 0.00 0.00 2.59
4916 6955 5.382664 TTTGGGGAAATATCTGGTACTCC 57.617 43.478 0.00 0.00 0.00 3.85
4917 6956 3.323775 TGGGGAAATATCTGGTACTCCC 58.676 50.000 7.99 7.99 37.19 4.30
4918 6957 3.311778 TGGGGAAATATCTGGTACTCCCA 60.312 47.826 15.47 7.12 38.64 4.37
4919 6958 3.072622 GGGGAAATATCTGGTACTCCCAC 59.927 52.174 15.47 5.14 38.64 4.61
4920 6959 3.072622 GGGAAATATCTGGTACTCCCACC 59.927 52.174 10.69 0.00 38.72 4.61
4921 6960 3.072622 GGAAATATCTGGTACTCCCACCC 59.927 52.174 0.00 0.00 38.72 4.61
4922 6961 2.417719 ATATCTGGTACTCCCACCCC 57.582 55.000 0.00 0.00 38.72 4.95
4923 6962 1.326055 TATCTGGTACTCCCACCCCT 58.674 55.000 0.00 0.00 38.72 4.79
4924 6963 1.326055 ATCTGGTACTCCCACCCCTA 58.674 55.000 0.00 0.00 38.72 3.53
4925 6964 0.635009 TCTGGTACTCCCACCCCTAG 59.365 60.000 0.00 0.00 38.72 3.02
4944 6983 4.329545 GTGCTCCCGGTGCTCCAA 62.330 66.667 16.01 0.00 0.00 3.53
4945 6984 3.565214 TGCTCCCGGTGCTCCAAA 61.565 61.111 16.01 0.00 0.00 3.28
4946 6985 2.282180 GCTCCCGGTGCTCCAAAA 60.282 61.111 0.00 0.00 0.00 2.44
4947 6986 2.626780 GCTCCCGGTGCTCCAAAAC 61.627 63.158 0.00 0.00 0.00 2.43
4948 6987 1.073199 CTCCCGGTGCTCCAAAACT 59.927 57.895 0.00 0.00 0.00 2.66
4949 6988 0.955919 CTCCCGGTGCTCCAAAACTC 60.956 60.000 0.00 0.00 0.00 3.01
4950 6989 2.325082 CCCGGTGCTCCAAAACTCG 61.325 63.158 0.00 0.00 0.00 4.18
4951 6990 1.301401 CCGGTGCTCCAAAACTCGA 60.301 57.895 5.52 0.00 0.00 4.04
4952 6991 0.673644 CCGGTGCTCCAAAACTCGAT 60.674 55.000 5.52 0.00 0.00 3.59
4953 6992 1.404986 CCGGTGCTCCAAAACTCGATA 60.405 52.381 5.52 0.00 0.00 2.92
4954 6993 1.927174 CGGTGCTCCAAAACTCGATAG 59.073 52.381 5.52 0.00 0.00 2.08
4955 6994 1.666189 GGTGCTCCAAAACTCGATAGC 59.334 52.381 0.00 0.00 0.00 2.97
4956 6995 2.346803 GTGCTCCAAAACTCGATAGCA 58.653 47.619 0.00 0.00 37.62 3.49
4957 6996 2.939103 GTGCTCCAAAACTCGATAGCAT 59.061 45.455 0.00 0.00 41.53 3.79
4958 6997 2.938451 TGCTCCAAAACTCGATAGCATG 59.062 45.455 0.00 0.00 35.20 4.06
4959 6998 2.939103 GCTCCAAAACTCGATAGCATGT 59.061 45.455 0.00 0.00 0.00 3.21
4960 6999 3.375299 GCTCCAAAACTCGATAGCATGTT 59.625 43.478 0.00 0.00 0.00 2.71
4961 7000 4.142600 GCTCCAAAACTCGATAGCATGTTT 60.143 41.667 0.00 0.00 36.11 2.83
4962 7001 5.619981 GCTCCAAAACTCGATAGCATGTTTT 60.620 40.000 5.42 5.42 40.96 2.43
4963 7002 6.403200 GCTCCAAAACTCGATAGCATGTTTTA 60.403 38.462 9.70 0.00 39.59 1.52
4964 7003 7.441890 TCCAAAACTCGATAGCATGTTTTAA 57.558 32.000 9.70 1.54 39.59 1.52
4965 7004 7.877003 TCCAAAACTCGATAGCATGTTTTAAA 58.123 30.769 9.70 0.00 39.59 1.52
4966 7005 8.353684 TCCAAAACTCGATAGCATGTTTTAAAA 58.646 29.630 9.70 0.00 39.59 1.52
4967 7006 9.139174 CCAAAACTCGATAGCATGTTTTAAAAT 57.861 29.630 3.52 0.00 39.59 1.82
4968 7007 9.941991 CAAAACTCGATAGCATGTTTTAAAATG 57.058 29.630 3.52 0.57 39.59 2.32
4969 7008 9.691362 AAAACTCGATAGCATGTTTTAAAATGT 57.309 25.926 3.52 0.00 39.70 2.71
4970 7009 9.691362 AAACTCGATAGCATGTTTTAAAATGTT 57.309 25.926 3.52 0.34 32.85 2.71
4971 7010 8.895932 ACTCGATAGCATGTTTTAAAATGTTC 57.104 30.769 3.52 0.00 0.00 3.18
4972 7011 8.511321 ACTCGATAGCATGTTTTAAAATGTTCA 58.489 29.630 3.52 0.00 0.00 3.18
4973 7012 9.340695 CTCGATAGCATGTTTTAAAATGTTCAA 57.659 29.630 3.52 0.00 0.00 2.69
4974 7013 9.684448 TCGATAGCATGTTTTAAAATGTTCAAA 57.316 25.926 3.52 0.00 0.00 2.69
5001 7040 6.763715 TTCTATCAATGGCTACCCTTGTAT 57.236 37.500 2.25 0.00 0.00 2.29
5046 7085 7.058525 TCAACTCCTTCTATCAATGCAATGAT 58.941 34.615 20.55 20.55 42.52 2.45
5047 7086 7.228108 TCAACTCCTTCTATCAATGCAATGATC 59.772 37.037 20.35 0.00 40.44 2.92
5141 7184 8.942338 ACTTTCTAAATGCATAAGTACATCGA 57.058 30.769 9.54 0.00 0.00 3.59
5152 7195 7.170828 TGCATAAGTACATCGAACCATCAATAC 59.829 37.037 0.00 0.00 0.00 1.89
5239 7285 1.202582 CCACACCAAAACCGAACAACA 59.797 47.619 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
721 723 4.275936 CCCTCATTTTCGAAACTGTTCACT 59.724 41.667 22.74 0.00 32.89 3.41
754 756 0.406361 ACCACTTCCTCTCCTCTCGT 59.594 55.000 0.00 0.00 0.00 4.18
881 883 4.406173 CACGTCTCTGCGCCGTCT 62.406 66.667 4.18 0.00 34.88 4.18
955 957 3.850173 TCCACTAACATTAGGCCCTCTTT 59.150 43.478 0.00 0.00 35.08 2.52
956 958 3.460825 TCCACTAACATTAGGCCCTCTT 58.539 45.455 0.00 0.00 35.08 2.85
957 959 3.130734 TCCACTAACATTAGGCCCTCT 57.869 47.619 0.00 0.00 35.08 3.69
958 960 3.433740 CCTTCCACTAACATTAGGCCCTC 60.434 52.174 0.00 0.00 35.08 4.30
959 961 2.509964 CCTTCCACTAACATTAGGCCCT 59.490 50.000 0.00 0.00 35.08 5.19
960 962 2.932261 CCTTCCACTAACATTAGGCCC 58.068 52.381 0.00 0.00 35.08 5.80
961 963 2.298610 GCCTTCCACTAACATTAGGCC 58.701 52.381 0.00 0.00 41.74 5.19
962 964 1.940613 CGCCTTCCACTAACATTAGGC 59.059 52.381 0.00 0.00 43.60 3.93
963 965 1.940613 GCGCCTTCCACTAACATTAGG 59.059 52.381 0.00 0.00 35.08 2.69
964 966 1.593006 CGCGCCTTCCACTAACATTAG 59.407 52.381 0.00 0.00 36.82 1.73
965 967 1.647346 CGCGCCTTCCACTAACATTA 58.353 50.000 0.00 0.00 0.00 1.90
966 968 1.644786 GCGCGCCTTCCACTAACATT 61.645 55.000 23.24 0.00 0.00 2.71
969 971 3.497031 GGCGCGCCTTCCACTAAC 61.497 66.667 41.71 12.20 0.00 2.34
986 988 4.697756 ACATGCGTGGGACGGTGG 62.698 66.667 11.36 0.00 42.82 4.61
1078 1084 2.105128 GACGATCGAGCTGGGGTG 59.895 66.667 24.34 0.00 0.00 4.61
1548 1554 3.992317 GCGAGGGAGCCGGATACC 61.992 72.222 15.11 15.11 0.00 2.73
1562 1568 1.762370 TCTATCAGAAATGCAGGGCGA 59.238 47.619 0.00 0.00 0.00 5.54
1564 1570 3.205784 ACTCTATCAGAAATGCAGGGC 57.794 47.619 0.00 0.00 0.00 5.19
1593 1601 3.697439 AACAGGTGGTGTGCAGCGT 62.697 57.895 0.00 0.00 40.26 5.07
1594 1602 2.896801 GAACAGGTGGTGTGCAGCG 61.897 63.158 0.00 0.00 40.26 5.18
1647 1655 3.034635 ACAGATATGACAGACCCCAGAC 58.965 50.000 0.00 0.00 0.00 3.51
1649 1657 2.768527 ACACAGATATGACAGACCCCAG 59.231 50.000 0.00 0.00 0.00 4.45
1652 1660 4.679373 ATGACACAGATATGACAGACCC 57.321 45.455 0.00 0.00 0.00 4.46
1653 1661 6.210385 AGGATATGACACAGATATGACAGACC 59.790 42.308 0.00 0.00 0.00 3.85
1654 1662 7.089538 CAGGATATGACACAGATATGACAGAC 58.910 42.308 0.00 0.00 0.00 3.51
1658 1666 5.337894 CCCCAGGATATGACACAGATATGAC 60.338 48.000 0.00 0.00 0.00 3.06
1668 1676 2.705658 GACATCACCCCAGGATATGACA 59.294 50.000 0.00 0.00 0.00 3.58
1670 1678 3.350992 AGACATCACCCCAGGATATGA 57.649 47.619 0.00 0.00 0.00 2.15
1671 1679 3.649981 AGAAGACATCACCCCAGGATATG 59.350 47.826 0.00 0.00 0.00 1.78
1672 1680 3.906846 GAGAAGACATCACCCCAGGATAT 59.093 47.826 0.00 0.00 0.00 1.63
1673 1681 3.309296 GAGAAGACATCACCCCAGGATA 58.691 50.000 0.00 0.00 0.00 2.59
1674 1682 2.122768 GAGAAGACATCACCCCAGGAT 58.877 52.381 0.00 0.00 0.00 3.24
1675 1683 1.573108 GAGAAGACATCACCCCAGGA 58.427 55.000 0.00 0.00 0.00 3.86
1676 1684 0.176680 CGAGAAGACATCACCCCAGG 59.823 60.000 0.00 0.00 0.00 4.45
1730 1738 0.539669 AACAGGGCCTAAGGTTGTGC 60.540 55.000 5.28 0.00 0.00 4.57
1731 1739 1.534729 GAACAGGGCCTAAGGTTGTG 58.465 55.000 5.28 0.00 0.00 3.33
1732 1740 0.036306 CGAACAGGGCCTAAGGTTGT 59.964 55.000 5.28 0.00 0.00 3.32
1733 1741 0.676782 CCGAACAGGGCCTAAGGTTG 60.677 60.000 5.28 0.00 35.97 3.77
1734 1742 1.683441 CCGAACAGGGCCTAAGGTT 59.317 57.895 5.28 6.58 35.97 3.50
1735 1743 3.400188 CCGAACAGGGCCTAAGGT 58.600 61.111 5.28 0.00 35.97 3.50
1746 1754 2.028484 GTGGACGTCTGCCGAACA 59.972 61.111 16.46 0.00 40.70 3.18
1747 1755 1.733399 GAGTGGACGTCTGCCGAAC 60.733 63.158 16.46 4.93 40.70 3.95
1748 1756 2.649034 GAGTGGACGTCTGCCGAA 59.351 61.111 16.46 0.00 40.70 4.30
1749 1757 3.371063 GGAGTGGACGTCTGCCGA 61.371 66.667 16.46 0.00 40.70 5.54
1750 1758 2.932234 AAGGAGTGGACGTCTGCCG 61.932 63.158 16.46 0.00 44.03 5.69
1751 1759 1.374758 CAAGGAGTGGACGTCTGCC 60.375 63.158 16.46 11.39 0.00 4.85
1752 1760 2.029844 GCAAGGAGTGGACGTCTGC 61.030 63.158 16.46 11.61 0.00 4.26
1753 1761 0.034059 AAGCAAGGAGTGGACGTCTG 59.966 55.000 16.46 4.89 0.00 3.51
1754 1762 0.759346 AAAGCAAGGAGTGGACGTCT 59.241 50.000 16.46 0.00 0.00 4.18
1755 1763 1.149148 GAAAGCAAGGAGTGGACGTC 58.851 55.000 7.13 7.13 0.00 4.34
1756 1764 0.250338 GGAAAGCAAGGAGTGGACGT 60.250 55.000 0.00 0.00 0.00 4.34
1757 1765 0.250295 TGGAAAGCAAGGAGTGGACG 60.250 55.000 0.00 0.00 0.00 4.79
1758 1766 1.609072 GTTGGAAAGCAAGGAGTGGAC 59.391 52.381 0.00 0.00 0.00 4.02
1759 1767 1.494721 AGTTGGAAAGCAAGGAGTGGA 59.505 47.619 0.00 0.00 0.00 4.02
1760 1768 1.882623 GAGTTGGAAAGCAAGGAGTGG 59.117 52.381 0.00 0.00 0.00 4.00
1761 1769 1.882623 GGAGTTGGAAAGCAAGGAGTG 59.117 52.381 0.00 0.00 0.00 3.51
1762 1770 1.202940 GGGAGTTGGAAAGCAAGGAGT 60.203 52.381 0.00 0.00 0.00 3.85
1763 1771 1.202927 TGGGAGTTGGAAAGCAAGGAG 60.203 52.381 0.00 0.00 0.00 3.69
1764 1772 0.850100 TGGGAGTTGGAAAGCAAGGA 59.150 50.000 0.00 0.00 0.00 3.36
1765 1773 1.251251 CTGGGAGTTGGAAAGCAAGG 58.749 55.000 0.00 0.00 0.00 3.61
1766 1774 0.600057 GCTGGGAGTTGGAAAGCAAG 59.400 55.000 0.00 0.00 34.01 4.01
1767 1775 0.185901 AGCTGGGAGTTGGAAAGCAA 59.814 50.000 0.00 0.00 36.32 3.91
1768 1776 0.250901 GAGCTGGGAGTTGGAAAGCA 60.251 55.000 0.00 0.00 36.32 3.91
1769 1777 0.962855 GGAGCTGGGAGTTGGAAAGC 60.963 60.000 0.00 0.00 0.00 3.51
1770 1778 0.401738 TGGAGCTGGGAGTTGGAAAG 59.598 55.000 0.00 0.00 0.00 2.62
1771 1779 1.004745 GATGGAGCTGGGAGTTGGAAA 59.995 52.381 0.00 0.00 0.00 3.13
1772 1780 0.620556 GATGGAGCTGGGAGTTGGAA 59.379 55.000 0.00 0.00 0.00 3.53
1773 1781 1.274703 GGATGGAGCTGGGAGTTGGA 61.275 60.000 0.00 0.00 0.00 3.53
1774 1782 1.225704 GGATGGAGCTGGGAGTTGG 59.774 63.158 0.00 0.00 0.00 3.77
1775 1783 0.107312 CTGGATGGAGCTGGGAGTTG 60.107 60.000 0.00 0.00 0.00 3.16
1776 1784 0.252881 TCTGGATGGAGCTGGGAGTT 60.253 55.000 0.00 0.00 0.00 3.01
1777 1785 0.252881 TTCTGGATGGAGCTGGGAGT 60.253 55.000 0.00 0.00 0.00 3.85
1778 1786 0.469070 CTTCTGGATGGAGCTGGGAG 59.531 60.000 0.00 0.00 0.00 4.30
1779 1787 1.630126 GCTTCTGGATGGAGCTGGGA 61.630 60.000 0.00 0.00 0.00 4.37
1780 1788 1.153005 GCTTCTGGATGGAGCTGGG 60.153 63.158 0.00 0.00 0.00 4.45
1781 1789 1.523258 CGCTTCTGGATGGAGCTGG 60.523 63.158 0.00 0.00 0.00 4.85
1782 1790 1.523258 CCGCTTCTGGATGGAGCTG 60.523 63.158 0.00 0.00 0.00 4.24
1783 1791 1.684386 CTCCGCTTCTGGATGGAGCT 61.684 60.000 0.00 0.00 41.36 4.09
1784 1792 1.227497 CTCCGCTTCTGGATGGAGC 60.227 63.158 0.00 0.00 41.36 4.70
1786 1794 2.903357 GCTCCGCTTCTGGATGGA 59.097 61.111 0.00 0.00 37.41 3.41
1787 1795 2.587194 CGCTCCGCTTCTGGATGG 60.587 66.667 0.00 0.00 37.41 3.51
1804 1812 3.660111 AAAAGTGCCGCTCCGTGC 61.660 61.111 0.00 0.00 38.57 5.34
1805 1813 2.252260 CAAAAGTGCCGCTCCGTG 59.748 61.111 0.00 0.00 0.00 4.94
1806 1814 3.660111 GCAAAAGTGCCGCTCCGT 61.660 61.111 0.00 0.00 45.68 4.69
1817 1825 4.033243 GCCACTTTTTCAGAGTTGCAAAAG 59.967 41.667 0.00 9.68 46.33 2.27
1818 1826 3.932089 GCCACTTTTTCAGAGTTGCAAAA 59.068 39.130 0.00 0.00 36.22 2.44
1819 1827 3.520569 GCCACTTTTTCAGAGTTGCAAA 58.479 40.909 0.00 0.00 36.22 3.68
1820 1828 2.159114 GGCCACTTTTTCAGAGTTGCAA 60.159 45.455 0.00 0.00 37.48 4.08
1821 1829 1.408702 GGCCACTTTTTCAGAGTTGCA 59.591 47.619 0.00 0.00 37.48 4.08
1822 1830 1.683385 AGGCCACTTTTTCAGAGTTGC 59.317 47.619 5.01 0.00 35.65 4.17
1823 1831 3.882888 TGTAGGCCACTTTTTCAGAGTTG 59.117 43.478 5.01 0.00 0.00 3.16
1824 1832 4.164843 TGTAGGCCACTTTTTCAGAGTT 57.835 40.909 5.01 0.00 0.00 3.01
1825 1833 3.857157 TGTAGGCCACTTTTTCAGAGT 57.143 42.857 5.01 0.00 0.00 3.24
1826 1834 3.057946 GCTTGTAGGCCACTTTTTCAGAG 60.058 47.826 5.01 0.00 0.00 3.35
1827 1835 2.884639 GCTTGTAGGCCACTTTTTCAGA 59.115 45.455 5.01 0.00 0.00 3.27
1828 1836 3.288809 GCTTGTAGGCCACTTTTTCAG 57.711 47.619 5.01 0.00 0.00 3.02
1857 1865 3.686098 ATGCCTCTCCCAGAGCGGA 62.686 63.158 4.82 0.00 40.98 5.54
1858 1866 3.160047 ATGCCTCTCCCAGAGCGG 61.160 66.667 0.00 0.00 40.98 5.52
1859 1867 2.108566 CATGCCTCTCCCAGAGCG 59.891 66.667 0.00 0.00 40.98 5.03
1860 1868 2.042404 CTCCATGCCTCTCCCAGAGC 62.042 65.000 0.00 0.00 40.98 4.09
1861 1869 2.042404 GCTCCATGCCTCTCCCAGAG 62.042 65.000 0.00 0.00 41.96 3.35
1862 1870 2.068821 GCTCCATGCCTCTCCCAGA 61.069 63.158 0.00 0.00 35.15 3.86
1863 1871 2.509916 GCTCCATGCCTCTCCCAG 59.490 66.667 0.00 0.00 35.15 4.45
1873 1881 3.869272 GAACGCGCTGGCTCCATG 61.869 66.667 5.73 0.00 36.88 3.66
1894 1902 4.828925 GAGGAGCTGCGGAGTGGC 62.829 72.222 5.62 0.00 0.00 5.01
1895 1903 4.154347 GGAGGAGCTGCGGAGTGG 62.154 72.222 5.62 0.00 0.00 4.00
1896 1904 3.368190 CTGGAGGAGCTGCGGAGTG 62.368 68.421 5.62 0.00 29.37 3.51
1897 1905 3.073735 CTGGAGGAGCTGCGGAGT 61.074 66.667 5.62 0.00 29.37 3.85
1898 1906 4.527583 GCTGGAGGAGCTGCGGAG 62.528 72.222 0.00 0.00 45.21 4.63
1906 1914 3.847602 CTGGAGCGGCTGGAGGAG 61.848 72.222 7.50 0.00 0.00 3.69
1909 1917 3.847602 CTCCTGGAGCGGCTGGAG 61.848 72.222 17.36 17.36 39.87 3.86
1926 1934 4.567385 CTCCGCTCCGAGCTCAGC 62.567 72.222 18.14 14.90 39.60 4.26
1927 1935 3.898509 CCTCCGCTCCGAGCTCAG 61.899 72.222 18.14 12.51 39.60 3.35
1949 1957 2.900122 CACAATAAGTGCCTGTTCGG 57.100 50.000 0.00 0.00 42.15 4.30
1959 1967 3.955471 AGCATGCAGGTACACAATAAGT 58.045 40.909 21.98 0.00 0.00 2.24
1960 1968 5.118990 ACTAGCATGCAGGTACACAATAAG 58.881 41.667 21.98 0.78 0.00 1.73
1961 1969 5.097742 ACTAGCATGCAGGTACACAATAA 57.902 39.130 21.98 0.00 0.00 1.40
1962 1970 4.753516 ACTAGCATGCAGGTACACAATA 57.246 40.909 21.98 0.00 0.00 1.90
2024 2036 6.650427 TCTATGAATGAAGCCATAGTACGT 57.350 37.500 0.00 0.00 41.63 3.57
2070 2082 7.394016 TCACACAATGTATACCTGAAATGACT 58.606 34.615 8.61 0.00 0.00 3.41
2072 2084 8.676401 CAATCACACAATGTATACCTGAAATGA 58.324 33.333 8.61 8.59 0.00 2.57
2073 2085 7.433131 GCAATCACACAATGTATACCTGAAATG 59.567 37.037 8.61 4.71 0.00 2.32
2086 2098 5.224135 TGTGAGAATTGCAATCACACAATG 58.776 37.500 27.64 0.00 46.17 2.82
2139 2157 7.011763 GGCATGCACTATCACAATATACATAGG 59.988 40.741 21.36 0.00 0.00 2.57
2148 2166 4.463539 TGAAAAGGCATGCACTATCACAAT 59.536 37.500 21.36 0.00 0.00 2.71
2156 2175 1.927487 TCCATGAAAAGGCATGCACT 58.073 45.000 21.36 11.46 43.30 4.40
2163 2182 5.841957 AGATACAACATCCATGAAAAGGC 57.158 39.130 0.00 0.00 0.00 4.35
2218 2237 6.226787 CAGAGCCTTAGAGAACAAAAAGAGA 58.773 40.000 0.00 0.00 0.00 3.10
2240 2260 4.735578 GCAACACTCCATATTTGATGGCAG 60.736 45.833 0.00 1.23 39.01 4.85
2262 2282 7.475840 AGCAAGCACTAAAGAAATATAACAGC 58.524 34.615 0.00 0.00 0.00 4.40
2321 2344 7.307493 TGACACTCATTCTATGTGCAATAAC 57.693 36.000 0.00 0.00 35.33 1.89
2368 2391 7.652909 TCATCTGAAATTGTGTTCACATTTTCC 59.347 33.333 29.30 20.15 38.32 3.13
2425 2449 9.844790 CAGCAGTACTCATCAAATTTAAAATCA 57.155 29.630 0.00 0.00 0.00 2.57
2436 2460 4.560128 GAGTGTTCAGCAGTACTCATCAA 58.440 43.478 0.00 0.00 39.39 2.57
2453 2477 5.512232 GGAGAAAATCTCAGACAAGGAGTGT 60.512 44.000 9.40 0.00 45.12 3.55
2544 2568 3.452627 GGTCAGGATCCAACATAGTCTGT 59.547 47.826 15.82 0.00 40.84 3.41
2650 2674 1.742768 CCAGCTCTACGCCCCTAAG 59.257 63.158 0.00 0.00 40.39 2.18
2700 2724 6.808321 TCAGCTGTAACTAACCCAATAGAT 57.192 37.500 14.67 0.00 0.00 1.98
3165 3273 2.999507 AAGACAGTACGCAGAGACAG 57.000 50.000 0.00 0.00 0.00 3.51
3371 3481 6.463995 ACCAATTTTTAGAACACTTGCTCA 57.536 33.333 0.00 0.00 0.00 4.26
3489 3599 4.003648 CTGAATAACTCTGTTGGTGTCCC 58.996 47.826 0.00 0.00 0.00 4.46
3612 3722 8.862550 AAACTGACATCAAACTGAAAAGAATC 57.137 30.769 0.00 0.00 0.00 2.52
3684 3798 2.794350 TGATACATCACGCATAGCAACG 59.206 45.455 0.00 0.00 0.00 4.10
3956 4152 6.481644 TGTTGGTCAAATTTAAACTTGGATGC 59.518 34.615 9.33 0.00 0.00 3.91
4169 4376 1.985159 ACCTGAACCATCAAGCTACCA 59.015 47.619 0.00 0.00 34.49 3.25
4308 4556 5.587388 TGCTAACTACTTGGCGTATTACT 57.413 39.130 0.00 0.00 36.67 2.24
4416 4680 3.958860 AGGCCACCAGTGAGCCAC 61.959 66.667 23.47 6.35 44.21 5.01
4417 4681 3.957586 CAGGCCACCAGTGAGCCA 61.958 66.667 23.47 0.00 44.21 4.75
4418 4682 3.618780 CTCAGGCCACCAGTGAGCC 62.619 68.421 17.51 17.51 43.02 4.70
4419 4683 2.046507 CTCAGGCCACCAGTGAGC 60.047 66.667 5.01 1.23 31.83 4.26
4420 4684 2.046507 GCTCAGGCCACCAGTGAG 60.047 66.667 13.31 13.31 40.66 3.51
4471 4735 6.600822 CCATTTTCTGTAGATGTGTTCTCCAT 59.399 38.462 0.00 0.00 35.79 3.41
4512 4776 2.167900 AGGCTACCCTAAGCGTTTAGTG 59.832 50.000 16.51 8.88 43.74 2.74
4639 4913 8.900983 ATAACGTACTAAAACAAAGGTTGGTA 57.099 30.769 0.00 0.00 37.30 3.25
4641 4915 7.011189 CGATAACGTACTAAAACAAAGGTTGG 58.989 38.462 0.00 0.00 34.38 3.77
4665 4982 5.871524 ACATATATCTAGCTGGCAATGAACG 59.128 40.000 0.00 0.00 0.00 3.95
4714 5094 8.347771 CCATGGAGAATTTGTAATCTATGTGTG 58.652 37.037 5.56 0.00 31.01 3.82
4723 5103 6.914665 TCTGATCCCATGGAGAATTTGTAAT 58.085 36.000 15.22 0.00 34.05 1.89
4897 6936 3.323775 TGGGAGTACCAGATATTTCCCC 58.676 50.000 9.42 0.00 46.80 4.81
4927 6966 3.842925 TTTGGAGCACCGGGAGCAC 62.843 63.158 21.10 15.32 39.42 4.40
4928 6967 3.126703 TTTTGGAGCACCGGGAGCA 62.127 57.895 21.10 0.19 39.42 4.26
4929 6968 2.282180 TTTTGGAGCACCGGGAGC 60.282 61.111 6.32 10.14 39.42 4.70
4930 6969 0.955919 GAGTTTTGGAGCACCGGGAG 60.956 60.000 6.32 0.00 39.42 4.30
4932 6971 2.325082 CGAGTTTTGGAGCACCGGG 61.325 63.158 6.32 0.00 39.42 5.73
4933 6972 0.673644 ATCGAGTTTTGGAGCACCGG 60.674 55.000 0.00 0.00 39.42 5.28
4935 6974 1.666189 GCTATCGAGTTTTGGAGCACC 59.334 52.381 0.00 0.00 0.00 5.01
4936 6975 2.346803 TGCTATCGAGTTTTGGAGCAC 58.653 47.619 0.00 0.00 35.12 4.40
4937 6976 2.760634 TGCTATCGAGTTTTGGAGCA 57.239 45.000 0.00 0.00 37.58 4.26
4939 6978 5.551760 AAACATGCTATCGAGTTTTGGAG 57.448 39.130 0.00 0.00 30.64 3.86
4940 6979 5.957842 AAAACATGCTATCGAGTTTTGGA 57.042 34.783 9.37 0.00 41.18 3.53
4941 6980 8.514136 TTTTAAAACATGCTATCGAGTTTTGG 57.486 30.769 16.67 0.00 42.27 3.28
4942 6981 9.941991 CATTTTAAAACATGCTATCGAGTTTTG 57.058 29.630 16.67 3.29 42.27 2.44
4944 6983 9.691362 AACATTTTAAAACATGCTATCGAGTTT 57.309 25.926 1.97 0.00 35.87 2.66
4945 6984 9.341899 GAACATTTTAAAACATGCTATCGAGTT 57.658 29.630 1.97 0.00 0.00 3.01
4946 6985 8.511321 TGAACATTTTAAAACATGCTATCGAGT 58.489 29.630 1.97 0.00 0.00 4.18
4947 6986 8.894409 TGAACATTTTAAAACATGCTATCGAG 57.106 30.769 1.97 0.00 0.00 4.04
4948 6987 9.684448 TTTGAACATTTTAAAACATGCTATCGA 57.316 25.926 1.97 0.00 0.00 3.59
4973 7012 7.400052 ACAAGGGTAGCCATTGATAGAATTTTT 59.600 33.333 22.02 0.00 46.65 1.94
4974 7013 6.897413 ACAAGGGTAGCCATTGATAGAATTTT 59.103 34.615 22.02 0.08 46.65 1.82
4975 7014 6.435164 ACAAGGGTAGCCATTGATAGAATTT 58.565 36.000 22.02 0.26 46.65 1.82
4976 7015 6.018433 ACAAGGGTAGCCATTGATAGAATT 57.982 37.500 22.02 0.70 46.65 2.17
4977 7016 5.653255 ACAAGGGTAGCCATTGATAGAAT 57.347 39.130 22.02 4.09 46.65 2.40
4978 7017 6.763715 ATACAAGGGTAGCCATTGATAGAA 57.236 37.500 22.02 8.53 46.65 2.10
4979 7018 6.360370 GATACAAGGGTAGCCATTGATAGA 57.640 41.667 22.02 10.05 46.65 1.98
5001 7040 6.044404 AGTTGAAAGATAGGAGTTGAAAGGGA 59.956 38.462 0.00 0.00 0.00 4.20
5139 7182 5.996219 TGAAAGTTGTGTATTGATGGTTCG 58.004 37.500 0.00 0.00 0.00 3.95
5152 7195 9.409312 TGCATCTTGTTATATTTGAAAGTTGTG 57.591 29.630 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.