Multiple sequence alignment - TraesCS7B01G127200

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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 TraesCS7B01G127200 chr7B 100.000 6194 0 0 1 6194 151434482 151428289 0.000000e+00 11439.0
1 TraesCS7B01G127200 chr7B 84.239 1288 186 14 4011 5288 134560067 134558787 0.000000e+00 1238.0
2 TraesCS7B01G127200 chr7B 85.935 583 70 11 2752 3328 134561137 134560561 4.100000e-171 612.0
3 TraesCS7B01G127200 chr7B 84.964 419 51 9 4 421 396049000 396048593 1.240000e-111 414.0
4 TraesCS7B01G127200 chr7B 80.912 351 50 11 1048 1382 134562827 134562478 1.710000e-65 261.0
5 TraesCS7B01G127200 chr7B 91.729 133 9 2 1636 1766 372834983 372835115 3.810000e-42 183.0
6 TraesCS7B01G127200 chr7B 89.928 139 10 4 1631 1765 551815408 551815270 6.380000e-40 176.0
7 TraesCS7B01G127200 chr7A 94.877 2479 98 10 3497 5958 188660178 188662644 0.000000e+00 3847.0
8 TraesCS7B01G127200 chr7A 96.614 1595 44 7 1876 3462 188658596 188660188 0.000000e+00 2638.0
9 TraesCS7B01G127200 chr7A 96.009 877 22 3 766 1638 188657654 188658521 0.000000e+00 1413.0
10 TraesCS7B01G127200 chr7A 84.022 1283 191 9 4014 5288 171386411 171385135 0.000000e+00 1221.0
11 TraesCS7B01G127200 chr7A 85.445 584 79 6 2748 3328 171387491 171386911 2.470000e-168 603.0
12 TraesCS7B01G127200 chr7A 88.415 328 28 7 441 764 40794557 40794878 2.710000e-103 387.0
13 TraesCS7B01G127200 chr7A 94.142 239 14 0 5956 6194 188662766 188663004 1.270000e-96 364.0
14 TraesCS7B01G127200 chr7A 89.121 239 17 5 3397 3632 341444525 341444293 7.860000e-74 289.0
15 TraesCS7B01G127200 chr7A 81.564 358 45 11 1048 1385 171389129 171388773 6.120000e-70 276.0
16 TraesCS7B01G127200 chr7A 96.842 95 2 1 1757 1851 188658518 188658611 2.310000e-34 158.0
17 TraesCS7B01G127200 chr7A 97.436 39 1 0 1833 1871 188658532 188658570 4.010000e-07 67.6
18 TraesCS7B01G127200 chr7D 94.241 2483 95 15 3497 5958 183027574 183025119 0.000000e+00 3749.0
19 TraesCS7B01G127200 chr7D 96.673 1593 39 6 1876 3462 183029148 183027564 0.000000e+00 2636.0
20 TraesCS7B01G127200 chr7D 95.144 1627 68 5 2 1626 183031244 183029627 0.000000e+00 2556.0
21 TraesCS7B01G127200 chr7D 84.688 1280 188 8 4014 5288 169388090 169386814 0.000000e+00 1271.0
22 TraesCS7B01G127200 chr7D 85.616 584 78 6 2748 3328 169389169 169388589 5.310000e-170 608.0
23 TraesCS7B01G127200 chr7D 88.889 324 28 3 441 762 42920240 42920557 5.820000e-105 392.0
24 TraesCS7B01G127200 chr7D 83.452 423 53 7 9 421 57598333 57598748 1.630000e-100 377.0
25 TraesCS7B01G127200 chr7D 83.684 380 42 7 4 365 87462520 87462897 2.140000e-89 340.0
26 TraesCS7B01G127200 chr7D 89.627 241 21 3 5958 6194 183024995 183024755 2.810000e-78 303.0
27 TraesCS7B01G127200 chr7D 81.006 358 47 13 1048 1385 169390807 169390451 1.320000e-66 265.0
28 TraesCS7B01G127200 chr1A 84.773 440 50 6 4 428 34194732 34195169 5.740000e-115 425.0
29 TraesCS7B01G127200 chr1A 79.264 299 36 16 144 421 33069421 33069714 1.060000e-42 185.0
30 TraesCS7B01G127200 chr2D 84.668 437 46 7 4 424 139023840 139024271 3.450000e-112 416.0
31 TraesCS7B01G127200 chr2D 83.753 437 48 8 4 423 633573849 633574279 5.820000e-105 392.0
32 TraesCS7B01G127200 chr2D 91.852 135 7 4 1636 1766 602705878 602705744 1.060000e-42 185.0
33 TraesCS7B01G127200 chr4D 85.343 423 37 10 4 424 493877592 493877991 1.240000e-111 414.0
34 TraesCS7B01G127200 chr4D 83.827 439 45 6 4 421 74263111 74263544 1.620000e-105 394.0
35 TraesCS7B01G127200 chr4D 90.119 253 19 4 3395 3642 319269607 319269858 2.150000e-84 324.0
36 TraesCS7B01G127200 chr4D 93.798 129 5 3 1636 1761 439129801 439129929 2.280000e-44 191.0
37 TraesCS7B01G127200 chr4B 88.720 328 27 4 442 765 427519053 427518732 5.820000e-105 392.0
38 TraesCS7B01G127200 chr4B 89.683 252 21 3 3395 3642 396716026 396716276 3.600000e-82 316.0
39 TraesCS7B01G127200 chr4B 82.372 312 24 15 139 424 609312133 609311827 6.200000e-60 243.0
40 TraesCS7B01G127200 chr3A 88.685 327 28 6 441 764 603273456 603273136 2.090000e-104 390.0
41 TraesCS7B01G127200 chr5B 88.379 327 29 6 441 764 82463954 82463634 9.740000e-103 385.0
42 TraesCS7B01G127200 chr4A 88.073 327 30 6 441 764 97813938 97814258 4.530000e-101 379.0
43 TraesCS7B01G127200 chr3D 87.768 327 32 3 441 765 591660979 591660659 5.860000e-100 375.0
44 TraesCS7B01G127200 chr3D 81.481 243 32 10 5962 6193 583233364 583233124 2.950000e-43 187.0
45 TraesCS7B01G127200 chr3D 92.248 129 7 3 1636 1761 210622549 210622421 4.930000e-41 180.0
46 TraesCS7B01G127200 chr3D 75.449 167 38 3 265 429 463695432 463695267 1.850000e-10 78.7
47 TraesCS7B01G127200 chr2B 87.805 328 30 3 441 766 4461544 4461225 5.860000e-100 375.0
48 TraesCS7B01G127200 chr2B 82.705 451 43 11 4 427 711305916 711306358 9.810000e-98 368.0
49 TraesCS7B01G127200 chr2B 84.635 384 41 8 4 387 411499293 411498928 3.530000e-97 366.0
50 TraesCS7B01G127200 chr1B 79.909 438 69 10 2 423 538993992 538993558 2.810000e-78 303.0
51 TraesCS7B01G127200 chr6D 79.730 444 53 22 3 423 82133591 82134020 2.830000e-73 287.0
52 TraesCS7B01G127200 chr6D 91.304 138 7 5 1636 1768 54003300 54003163 3.810000e-42 183.0
53 TraesCS7B01G127200 chrUn 86.561 253 26 5 3390 3638 91107468 91107716 7.910000e-69 272.0
54 TraesCS7B01G127200 chrUn 86.561 253 27 5 3390 3638 135321613 135321364 7.910000e-69 272.0
55 TraesCS7B01G127200 chrUn 86.561 253 27 5 3390 3638 135354767 135354518 7.910000e-69 272.0
56 TraesCS7B01G127200 chrUn 86.561 253 27 5 3390 3638 239422219 239421970 7.910000e-69 272.0
57 TraesCS7B01G127200 chr1D 93.130 131 6 3 1633 1760 469018555 469018685 8.200000e-44 189.0
58 TraesCS7B01G127200 chr1D 90.845 142 7 6 1622 1760 478911663 478911801 1.060000e-42 185.0
59 TraesCS7B01G127200 chr6B 82.018 228 32 7 1159 1381 569820886 569821109 1.060000e-42 185.0
60 TraesCS7B01G127200 chr5D 93.023 129 6 3 1635 1760 382508097 382507969 1.060000e-42 185.0
61 TraesCS7B01G127200 chr6A 81.944 216 29 8 1170 1381 522641441 522641232 2.300000e-39 174.0


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 TraesCS7B01G127200 chr7B 151428289 151434482 6193 True 11439.000000 11439 100.000000 1 6194 1 chr7B.!!$R1 6193
1 TraesCS7B01G127200 chr7B 134558787 134562827 4040 True 703.666667 1238 83.695333 1048 5288 3 chr7B.!!$R4 4240
2 TraesCS7B01G127200 chr7A 188657654 188663004 5350 False 1414.600000 3847 95.986667 766 6194 6 chr7A.!!$F2 5428
3 TraesCS7B01G127200 chr7A 171385135 171389129 3994 True 700.000000 1221 83.677000 1048 5288 3 chr7A.!!$R2 4240
4 TraesCS7B01G127200 chr7D 183024755 183031244 6489 True 2311.000000 3749 93.921250 2 6194 4 chr7D.!!$R2 6192
5 TraesCS7B01G127200 chr7D 169386814 169390807 3993 True 714.666667 1271 83.770000 1048 5288 3 chr7D.!!$R1 4240

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
165 166 1.135431 GTTTGATGCATTGCCTACGCA 60.135 47.619 6.12 0.0 45.49 5.24 F
1398 1422 0.179181 GTACGCACGTTCCGATCTGA 60.179 55.000 11.82 0.0 0.00 3.27 F
2078 2814 1.228245 TTGGACCAGCTGCAGAACC 60.228 57.895 20.43 12.4 0.00 3.62 F
3444 4204 0.039256 CAAACACATGGCAACTCCCG 60.039 55.000 0.00 0.0 37.61 5.14 F
3471 4231 0.249531 TGGCAAGTTTAGTGACGCGA 60.250 50.000 15.93 0.0 0.00 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1870 2603 1.632589 AAAACAGAATCTGCACCCCC 58.367 50.000 10.62 0.0 34.37 5.40 R
2901 3659 1.233019 CCAACAGTGAAGGTGCTCAG 58.767 55.000 0.00 0.0 0.00 3.35 R
3464 4224 0.317160 AAGTTGACATCCTCGCGTCA 59.683 50.000 5.77 0.0 40.30 4.35 R
4589 5784 0.463116 AACGTTGTTCCCAAGCTCGT 60.463 50.000 0.00 0.0 33.75 4.18 R
5446 6641 3.482110 GCACAACTTTCAATCGAACACAC 59.518 43.478 0.00 0.0 0.00 3.82 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
18 19 4.947147 GTGCCAACTCCCACGCCA 62.947 66.667 0.00 0.00 0.00 5.69
62 63 1.953138 GCGATGATGCCTCCACGAG 60.953 63.158 8.49 0.00 0.00 4.18
115 116 3.345808 CACACACGCCAACTCCCG 61.346 66.667 0.00 0.00 0.00 5.14
165 166 1.135431 GTTTGATGCATTGCCTACGCA 60.135 47.619 6.12 0.00 45.49 5.24
177 178 2.237643 TGCCTACGCATCCTTCCTTTTA 59.762 45.455 0.00 0.00 41.12 1.52
226 227 2.422597 CGAACTGTGGCAAGGTAATCA 58.577 47.619 0.00 0.00 0.00 2.57
304 305 6.057321 TGAATTTATGACGTCTTTAGGGGT 57.943 37.500 17.92 0.00 0.00 4.95
380 381 3.897819 CGAAGGGTCAAAATAGCGC 57.102 52.632 0.00 0.00 0.00 5.92
408 409 3.053896 GTTTGGGGGCCGAACGAG 61.054 66.667 0.00 0.00 38.03 4.18
430 431 2.402305 GGAGATGCTCTTAGTCATGCG 58.598 52.381 0.00 0.00 0.00 4.73
619 621 7.394359 ACTCACATGGTTACTTATTTGAGCATT 59.606 33.333 12.49 0.00 33.92 3.56
713 715 9.597999 GAAAATTTCAGAATAACATTTTGGCAC 57.402 29.630 7.66 0.00 29.27 5.01
733 735 5.302823 GGCACAATTCAAAATATAGGGCTCT 59.697 40.000 0.00 0.00 0.00 4.09
745 747 1.819632 GGGCTCTAATGCACCCGTG 60.820 63.158 0.00 0.00 31.32 4.94
847 849 3.340034 TGCGTAATGATTCCCTTCGTTT 58.660 40.909 0.00 0.00 0.00 3.60
868 870 1.777101 CTAAGCTAGTGATCAGCCGC 58.223 55.000 0.00 0.00 39.99 6.53
989 995 1.153745 GATCCTCGTGCAAGCGACT 60.154 57.895 0.00 0.00 36.80 4.18
1396 1420 1.138247 GGTACGCACGTTCCGATCT 59.862 57.895 11.82 0.00 0.00 2.75
1398 1422 0.179181 GTACGCACGTTCCGATCTGA 60.179 55.000 11.82 0.00 0.00 3.27
1536 1631 4.096382 CCTGGAGCATGGTAATGTTAACAC 59.904 45.833 11.22 0.00 32.34 3.32
1544 1639 6.905076 GCATGGTAATGTTAACACTATGTTCG 59.095 38.462 11.22 0.00 37.66 3.95
1634 2004 6.877611 AGTTACAGGTGTTTCTATGGTTTG 57.122 37.500 0.00 0.00 0.00 2.93
1635 2005 6.362248 AGTTACAGGTGTTTCTATGGTTTGT 58.638 36.000 0.00 0.00 0.00 2.83
1636 2006 7.511268 AGTTACAGGTGTTTCTATGGTTTGTA 58.489 34.615 0.00 0.00 0.00 2.41
1637 2007 7.443272 AGTTACAGGTGTTTCTATGGTTTGTAC 59.557 37.037 0.00 0.00 0.00 2.90
1638 2008 5.937111 ACAGGTGTTTCTATGGTTTGTACT 58.063 37.500 0.00 0.00 0.00 2.73
1639 2009 6.362248 ACAGGTGTTTCTATGGTTTGTACTT 58.638 36.000 0.00 0.00 0.00 2.24
1640 2010 6.485648 ACAGGTGTTTCTATGGTTTGTACTTC 59.514 38.462 0.00 0.00 0.00 3.01
1641 2011 6.002082 AGGTGTTTCTATGGTTTGTACTTCC 58.998 40.000 0.00 0.00 0.00 3.46
1642 2012 6.002082 GGTGTTTCTATGGTTTGTACTTCCT 58.998 40.000 0.00 0.00 0.00 3.36
1643 2013 6.148976 GGTGTTTCTATGGTTTGTACTTCCTC 59.851 42.308 0.00 0.00 0.00 3.71
1644 2014 6.148976 GTGTTTCTATGGTTTGTACTTCCTCC 59.851 42.308 0.00 0.00 0.00 4.30
1645 2015 4.730949 TCTATGGTTTGTACTTCCTCCG 57.269 45.455 0.00 0.00 0.00 4.63
1646 2016 4.091549 TCTATGGTTTGTACTTCCTCCGT 58.908 43.478 0.00 0.00 0.00 4.69
1647 2017 2.825861 TGGTTTGTACTTCCTCCGTC 57.174 50.000 0.00 0.00 0.00 4.79
1648 2018 1.345415 TGGTTTGTACTTCCTCCGTCC 59.655 52.381 0.00 0.00 0.00 4.79
1649 2019 1.338484 GGTTTGTACTTCCTCCGTCCC 60.338 57.143 0.00 0.00 0.00 4.46
1650 2020 1.345415 GTTTGTACTTCCTCCGTCCCA 59.655 52.381 0.00 0.00 0.00 4.37
1651 2021 1.719529 TTGTACTTCCTCCGTCCCAA 58.280 50.000 0.00 0.00 0.00 4.12
1652 2022 1.719529 TGTACTTCCTCCGTCCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
1653 2023 2.048601 TGTACTTCCTCCGTCCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
1654 2024 2.640826 TGTACTTCCTCCGTCCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
1655 2025 2.971901 ACTTCCTCCGTCCCAAAATT 57.028 45.000 0.00 0.00 0.00 1.82
1656 2026 2.791655 ACTTCCTCCGTCCCAAAATTC 58.208 47.619 0.00 0.00 0.00 2.17
1657 2027 2.375509 ACTTCCTCCGTCCCAAAATTCT 59.624 45.455 0.00 0.00 0.00 2.40
1658 2028 3.181433 ACTTCCTCCGTCCCAAAATTCTT 60.181 43.478 0.00 0.00 0.00 2.52
1659 2029 2.790433 TCCTCCGTCCCAAAATTCTTG 58.210 47.619 0.00 0.00 0.00 3.02
1660 2030 2.107552 TCCTCCGTCCCAAAATTCTTGT 59.892 45.455 0.00 0.00 0.00 3.16
1661 2031 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
1662 2032 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
1663 2033 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
1664 2034 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
1665 2035 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
1666 2036 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
1667 2037 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
1668 2038 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
1669 2039 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
1670 2040 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
1671 2041 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
1672 2042 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
1673 2043 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
1681 2051 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
1682 2052 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
1684 2054 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
1685 2055 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
1692 2062 9.832445 ATTTGTCTAAATACGGATGTATCAAGT 57.168 29.630 0.00 0.00 40.42 3.16
1693 2063 8.867112 TTGTCTAAATACGGATGTATCAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
1694 2064 8.002984 TGTCTAAATACGGATGTATCAAGTCA 57.997 34.615 0.00 0.00 40.42 3.41
1695 2065 7.919091 TGTCTAAATACGGATGTATCAAGTCAC 59.081 37.037 0.00 0.00 40.42 3.67
1696 2066 7.919091 GTCTAAATACGGATGTATCAAGTCACA 59.081 37.037 0.00 0.00 40.42 3.58
1697 2067 8.638873 TCTAAATACGGATGTATCAAGTCACAT 58.361 33.333 0.00 0.00 40.42 3.21
1698 2068 9.261180 CTAAATACGGATGTATCAAGTCACATT 57.739 33.333 0.00 0.00 40.42 2.71
1699 2069 8.506168 AAATACGGATGTATCAAGTCACATTT 57.494 30.769 0.00 0.00 40.42 2.32
1700 2070 8.506168 AATACGGATGTATCAAGTCACATTTT 57.494 30.769 0.00 0.00 40.42 1.82
1701 2071 9.607988 AATACGGATGTATCAAGTCACATTTTA 57.392 29.630 0.00 0.00 40.42 1.52
1702 2072 7.539712 ACGGATGTATCAAGTCACATTTTAG 57.460 36.000 0.00 0.00 35.55 1.85
1703 2073 7.103641 ACGGATGTATCAAGTCACATTTTAGT 58.896 34.615 0.00 0.00 35.55 2.24
1704 2074 8.255206 ACGGATGTATCAAGTCACATTTTAGTA 58.745 33.333 0.00 0.00 35.55 1.82
1705 2075 9.261180 CGGATGTATCAAGTCACATTTTAGTAT 57.739 33.333 0.00 0.00 35.55 2.12
1737 2107 8.752187 ACATCCGTACCTAAATAAGTTAAGACA 58.248 33.333 0.00 0.00 0.00 3.41
1738 2108 9.245962 CATCCGTACCTAAATAAGTTAAGACAG 57.754 37.037 0.00 0.00 0.00 3.51
1739 2109 8.579850 TCCGTACCTAAATAAGTTAAGACAGA 57.420 34.615 0.00 0.00 0.00 3.41
1740 2110 9.023962 TCCGTACCTAAATAAGTTAAGACAGAA 57.976 33.333 0.00 0.00 0.00 3.02
1741 2111 9.813446 CCGTACCTAAATAAGTTAAGACAGAAT 57.187 33.333 0.00 0.00 0.00 2.40
1749 2119 9.893305 AAATAAGTTAAGACAGAATTTTGGACG 57.107 29.630 0.57 0.00 0.00 4.79
1750 2120 5.941948 AGTTAAGACAGAATTTTGGACGG 57.058 39.130 0.57 0.00 0.00 4.79
1751 2121 5.617252 AGTTAAGACAGAATTTTGGACGGA 58.383 37.500 0.57 0.00 0.00 4.69
1752 2122 6.059484 AGTTAAGACAGAATTTTGGACGGAA 58.941 36.000 0.57 0.00 0.00 4.30
1753 2123 6.204882 AGTTAAGACAGAATTTTGGACGGAAG 59.795 38.462 0.57 0.00 0.00 3.46
1754 2124 3.412386 AGACAGAATTTTGGACGGAAGG 58.588 45.455 0.57 0.00 0.00 3.46
1755 2125 3.072476 AGACAGAATTTTGGACGGAAGGA 59.928 43.478 0.57 0.00 0.00 3.36
1810 2180 5.652994 TTCTTTTTGAATAATCACCGGGG 57.347 39.130 6.32 0.00 34.61 5.73
1842 2575 2.026822 CCCACCTGTCTACTTGCAGATT 60.027 50.000 0.00 0.00 34.87 2.40
1843 2576 3.265791 CCACCTGTCTACTTGCAGATTC 58.734 50.000 0.00 0.00 34.87 2.52
1844 2577 3.055530 CCACCTGTCTACTTGCAGATTCT 60.056 47.826 0.00 0.00 34.87 2.40
1845 2578 3.931468 CACCTGTCTACTTGCAGATTCTG 59.069 47.826 9.40 9.40 34.87 3.02
1846 2579 3.580458 ACCTGTCTACTTGCAGATTCTGT 59.420 43.478 14.90 0.00 34.87 3.41
1847 2580 4.040952 ACCTGTCTACTTGCAGATTCTGTT 59.959 41.667 14.90 0.92 34.87 3.16
1848 2581 4.999950 CCTGTCTACTTGCAGATTCTGTTT 59.000 41.667 14.90 0.60 34.87 2.83
1849 2582 5.471456 CCTGTCTACTTGCAGATTCTGTTTT 59.529 40.000 14.90 0.92 34.87 2.43
1850 2583 6.016777 CCTGTCTACTTGCAGATTCTGTTTTT 60.017 38.462 14.90 1.25 34.87 1.94
1851 2584 6.959361 TGTCTACTTGCAGATTCTGTTTTTC 58.041 36.000 14.90 0.00 33.43 2.29
1852 2585 6.767902 TGTCTACTTGCAGATTCTGTTTTTCT 59.232 34.615 14.90 0.00 33.43 2.52
1853 2586 7.283127 TGTCTACTTGCAGATTCTGTTTTTCTT 59.717 33.333 14.90 0.00 33.43 2.52
1854 2587 8.131731 GTCTACTTGCAGATTCTGTTTTTCTTT 58.868 33.333 14.90 0.00 33.43 2.52
1855 2588 8.686334 TCTACTTGCAGATTCTGTTTTTCTTTT 58.314 29.630 14.90 0.00 33.43 2.27
1856 2589 9.305925 CTACTTGCAGATTCTGTTTTTCTTTTT 57.694 29.630 14.90 0.00 33.43 1.94
1857 2590 7.967178 ACTTGCAGATTCTGTTTTTCTTTTTG 58.033 30.769 14.90 0.00 33.43 2.44
1858 2591 7.818930 ACTTGCAGATTCTGTTTTTCTTTTTGA 59.181 29.630 14.90 0.00 33.43 2.69
1859 2592 8.545229 TTGCAGATTCTGTTTTTCTTTTTGAA 57.455 26.923 14.90 0.00 33.43 2.69
1860 2593 8.721019 TGCAGATTCTGTTTTTCTTTTTGAAT 57.279 26.923 14.90 0.00 32.44 2.57
1861 2594 9.814899 TGCAGATTCTGTTTTTCTTTTTGAATA 57.185 25.926 14.90 0.00 32.44 1.75
1869 2602 9.848172 CTGTTTTTCTTTTTGAATAATCAACGG 57.152 29.630 0.00 0.00 45.01 4.44
1870 2603 8.821894 TGTTTTTCTTTTTGAATAATCAACGGG 58.178 29.630 0.00 0.00 45.01 5.28
1871 2604 7.954788 TTTTCTTTTTGAATAATCAACGGGG 57.045 32.000 0.00 0.00 45.01 5.73
1872 2605 5.652994 TCTTTTTGAATAATCAACGGGGG 57.347 39.130 0.00 0.00 45.01 5.40
1961 2695 5.181009 CACTCTGAATATTGAGCCTGTTGA 58.819 41.667 0.00 0.00 33.92 3.18
2078 2814 1.228245 TTGGACCAGCTGCAGAACC 60.228 57.895 20.43 12.40 0.00 3.62
2246 2984 6.073331 GCTTGCTGATCTTTCATAGTATCACC 60.073 42.308 0.00 0.00 0.00 4.02
2259 2997 3.262420 AGTATCACCGTGATGCAGAAAC 58.738 45.455 25.61 14.56 41.14 2.78
2286 3025 4.023536 CCTTAATGGTAGCGTTGTTTGTGT 60.024 41.667 9.64 0.00 0.00 3.72
2354 3111 8.198109 TCTAGCTCCATACTTGAAGTTGTTATC 58.802 37.037 1.97 0.00 0.00 1.75
2704 3462 2.702478 CCTGCCTCTCACTGATATGGAA 59.298 50.000 0.00 0.00 0.00 3.53
2743 3501 9.558396 AATTTCATGGTGTGTACATTCAAAAAT 57.442 25.926 0.00 6.44 0.00 1.82
2901 3659 7.976175 GGGAAATGGAAGAAGTGATTATTGTTC 59.024 37.037 0.00 0.00 31.13 3.18
3079 3837 6.205464 AGCCTTATGAATATGGATTTCGTGTG 59.795 38.462 6.46 0.00 31.18 3.82
3091 3849 3.579147 TTTCGTGTGTTCTTGCTAACG 57.421 42.857 0.00 0.00 31.76 3.18
3180 3938 1.250328 TTCATTGCTCTTGGTGCTGG 58.750 50.000 0.00 0.00 0.00 4.85
3280 4038 2.137523 GCTGGTGTTGCAAATTCCTTG 58.862 47.619 0.00 3.42 38.15 3.61
3370 4130 1.402456 GCACAAGCCTTGCATCTCTTG 60.402 52.381 3.88 16.09 39.93 3.02
3388 4148 9.269453 CATCTCTTGATGCATTGATAGTAGAAA 57.731 33.333 0.00 0.00 42.83 2.52
3443 4203 1.039856 ACAAACACATGGCAACTCCC 58.960 50.000 0.00 0.00 37.61 4.30
3444 4204 0.039256 CAAACACATGGCAACTCCCG 60.039 55.000 0.00 0.00 37.61 5.14
3445 4205 0.467290 AAACACATGGCAACTCCCGT 60.467 50.000 0.00 0.00 37.61 5.28
3446 4206 0.467290 AACACATGGCAACTCCCGTT 60.467 50.000 0.00 0.00 37.61 4.44
3447 4207 0.467290 ACACATGGCAACTCCCGTTT 60.467 50.000 0.00 0.00 37.61 3.60
3469 4229 4.413495 TTTATGGCAAGTTTAGTGACGC 57.587 40.909 0.00 0.00 0.00 5.19
3470 4230 0.796312 ATGGCAAGTTTAGTGACGCG 59.204 50.000 3.53 3.53 0.00 6.01
3471 4231 0.249531 TGGCAAGTTTAGTGACGCGA 60.250 50.000 15.93 0.00 0.00 5.87
3472 4232 0.438830 GGCAAGTTTAGTGACGCGAG 59.561 55.000 15.93 0.00 0.00 5.03
3473 4233 0.438830 GCAAGTTTAGTGACGCGAGG 59.561 55.000 15.93 0.00 0.00 4.63
3474 4234 1.933500 GCAAGTTTAGTGACGCGAGGA 60.934 52.381 15.93 0.00 0.00 3.71
3475 4235 2.607187 CAAGTTTAGTGACGCGAGGAT 58.393 47.619 15.93 0.00 0.00 3.24
3476 4236 2.279582 AGTTTAGTGACGCGAGGATG 57.720 50.000 15.93 0.00 0.00 3.51
3477 4237 1.544691 AGTTTAGTGACGCGAGGATGT 59.455 47.619 15.93 0.00 0.00 3.06
3478 4238 1.918609 GTTTAGTGACGCGAGGATGTC 59.081 52.381 15.93 0.00 35.67 3.06
3479 4239 1.170442 TTAGTGACGCGAGGATGTCA 58.830 50.000 15.93 0.73 42.49 3.58
3480 4240 1.170442 TAGTGACGCGAGGATGTCAA 58.830 50.000 15.93 0.00 45.84 3.18
3481 4241 0.388649 AGTGACGCGAGGATGTCAAC 60.389 55.000 15.93 0.00 45.84 3.18
3482 4242 0.388649 GTGACGCGAGGATGTCAACT 60.389 55.000 15.93 0.00 45.84 3.16
3483 4243 0.317160 TGACGCGAGGATGTCAACTT 59.683 50.000 15.93 0.00 41.82 2.66
3484 4244 1.270094 TGACGCGAGGATGTCAACTTT 60.270 47.619 15.93 0.00 41.82 2.66
3485 4245 2.029739 TGACGCGAGGATGTCAACTTTA 60.030 45.455 15.93 0.00 41.82 1.85
3486 4246 2.334838 ACGCGAGGATGTCAACTTTAC 58.665 47.619 15.93 0.00 0.00 2.01
3487 4247 2.029290 ACGCGAGGATGTCAACTTTACT 60.029 45.455 15.93 0.00 0.00 2.24
3488 4248 2.993899 CGCGAGGATGTCAACTTTACTT 59.006 45.455 0.00 0.00 0.00 2.24
3489 4249 4.171005 CGCGAGGATGTCAACTTTACTTA 58.829 43.478 0.00 0.00 0.00 2.24
3490 4250 4.804139 CGCGAGGATGTCAACTTTACTTAT 59.196 41.667 0.00 0.00 0.00 1.73
3491 4251 5.051641 CGCGAGGATGTCAACTTTACTTATC 60.052 44.000 0.00 0.00 0.00 1.75
3492 4252 5.810587 GCGAGGATGTCAACTTTACTTATCA 59.189 40.000 0.00 0.00 0.00 2.15
3493 4253 6.312918 GCGAGGATGTCAACTTTACTTATCAA 59.687 38.462 0.00 0.00 0.00 2.57
3494 4254 7.464710 GCGAGGATGTCAACTTTACTTATCAAG 60.465 40.741 0.00 0.00 0.00 3.02
3495 4255 7.759886 CGAGGATGTCAACTTTACTTATCAAGA 59.240 37.037 0.00 0.00 0.00 3.02
3690 4450 3.643159 AAAATTCGAAGCAACACTCCC 57.357 42.857 3.35 0.00 0.00 4.30
3782 4547 3.561143 TGGTATTGTCAAGCAAGTTGGT 58.439 40.909 0.63 0.63 40.86 3.67
3794 4559 2.159435 GCAAGTTGGTGACGTTGAGTTT 60.159 45.455 4.75 0.00 0.00 2.66
3796 4561 4.437659 GCAAGTTGGTGACGTTGAGTTTTA 60.438 41.667 4.75 0.00 0.00 1.52
3802 4567 4.636648 TGGTGACGTTGAGTTTTATGTTGT 59.363 37.500 0.00 0.00 0.00 3.32
3804 4569 4.896238 GTGACGTTGAGTTTTATGTTGTCG 59.104 41.667 0.00 0.00 0.00 4.35
3927 4692 5.729510 TGATGTCACTAATCCACGAAATCA 58.270 37.500 0.00 0.00 31.22 2.57
3962 4728 9.492973 CTCATGTTGAATTGTTTAAATTTCCCT 57.507 29.630 0.00 0.00 0.00 4.20
4150 5338 7.225784 TCAAGCTTCTGATGATCCTCTATAC 57.774 40.000 0.00 0.00 0.00 1.47
4409 5598 1.450134 CTTCGCAGCCATGGCACTA 60.450 57.895 37.18 18.66 44.88 2.74
4457 5646 9.700831 ATTCAGGTTTGCTAATATAGTTTCCTT 57.299 29.630 0.00 0.00 0.00 3.36
4461 5650 8.329502 AGGTTTGCTAATATAGTTTCCTTGACT 58.670 33.333 0.00 0.00 0.00 3.41
4483 5672 2.760092 ACCTGTTGAAGTTGTGCATGTT 59.240 40.909 0.00 0.00 0.00 2.71
4521 5716 8.880244 ACTATATACATCTGATTTTAGGCACCA 58.120 33.333 0.00 0.00 0.00 4.17
4522 5717 9.896645 CTATATACATCTGATTTTAGGCACCAT 57.103 33.333 0.00 0.00 0.00 3.55
4589 5784 4.023792 CAGAGAATGTGCTAAAGTGTTGCA 60.024 41.667 0.00 0.00 0.00 4.08
4839 6034 2.420628 TTGCTGATCAAACTTTGGCG 57.579 45.000 0.00 0.00 0.00 5.69
5091 6286 3.248602 ACGCATTTGAAGAACTGAGTGAC 59.751 43.478 0.00 0.00 0.00 3.67
5250 6445 0.521735 GCCTTGTCGCCCACTTTTAG 59.478 55.000 0.00 0.00 0.00 1.85
5297 6492 1.824852 ACCACGATATGCAGTGAGACA 59.175 47.619 5.44 0.00 40.56 3.41
5373 6568 2.749621 CAACAGGGAAAGGTAGATGTGC 59.250 50.000 0.00 0.00 0.00 4.57
5440 6635 3.591023 TGCTTTCAATGCATTGATGTGG 58.409 40.909 35.87 25.79 45.30 4.17
5441 6636 3.007074 TGCTTTCAATGCATTGATGTGGT 59.993 39.130 35.87 0.00 45.30 4.16
5446 6641 4.316645 TCAATGCATTGATGTGGTTTTGG 58.683 39.130 33.08 7.98 41.51 3.28
5451 6646 3.740764 GCATTGATGTGGTTTTGGTGTGT 60.741 43.478 0.00 0.00 0.00 3.72
5476 6671 2.565210 TGAAAGTTGTGCTGTTGCTG 57.435 45.000 0.00 0.00 40.48 4.41
5482 6677 2.493278 AGTTGTGCTGTTGCTGAAAACT 59.507 40.909 0.00 0.00 40.48 2.66
5527 6722 1.537776 GCAGATGATAGTCACGCAGCT 60.538 52.381 0.00 0.00 0.00 4.24
5530 6725 3.251972 CAGATGATAGTCACGCAGCTCTA 59.748 47.826 0.00 0.00 0.00 2.43
5536 6733 0.794981 GTCACGCAGCTCTAGACACG 60.795 60.000 0.00 0.00 0.00 4.49
5557 6754 3.068165 CGGAGCTCTGTACAACCATGATA 59.932 47.826 14.84 0.00 0.00 2.15
5621 6827 2.490903 ACGACCGCTGTTGTAGATTAGT 59.509 45.455 0.00 0.00 37.33 2.24
5642 6849 1.053424 TGTTTTCCAGGAGTAGCCGT 58.947 50.000 0.00 0.00 43.43 5.68
5661 6868 5.092781 GCCGTATTTGATTTGTGTTAGTGG 58.907 41.667 0.00 0.00 0.00 4.00
5670 6877 1.301423 TGTGTTAGTGGCGTTGGAAC 58.699 50.000 0.00 0.00 0.00 3.62
5812 7022 2.698855 TCAGTCTTGGAGCTATTGGC 57.301 50.000 0.00 0.00 42.19 4.52
5819 7029 0.034186 TGGAGCTATTGGCCTGGTTG 60.034 55.000 3.32 0.00 43.05 3.77
5866 7076 8.218488 GGGGAGTATTTTATACTCAATCAACCT 58.782 37.037 21.80 0.00 44.18 3.50
5902 7112 1.414158 TGGCTCTATCTGCTACCCAC 58.586 55.000 0.00 0.00 0.00 4.61
5903 7113 1.342975 TGGCTCTATCTGCTACCCACA 60.343 52.381 0.00 0.00 0.00 4.17
5904 7114 1.974236 GGCTCTATCTGCTACCCACAT 59.026 52.381 0.00 0.00 0.00 3.21
5905 7115 2.289320 GGCTCTATCTGCTACCCACATG 60.289 54.545 0.00 0.00 0.00 3.21
5906 7116 2.289320 GCTCTATCTGCTACCCACATGG 60.289 54.545 0.00 0.00 41.37 3.66
5945 7155 3.012518 CAATGCCTTGGAGGTGAACTAG 58.987 50.000 0.00 0.00 37.80 2.57
5949 7159 3.075148 GCCTTGGAGGTGAACTAGTTTC 58.925 50.000 10.02 2.98 37.80 2.78
5950 7160 3.496160 GCCTTGGAGGTGAACTAGTTTCA 60.496 47.826 10.02 6.61 37.62 2.69
5951 7161 4.319177 CCTTGGAGGTGAACTAGTTTCAG 58.681 47.826 10.02 0.00 45.23 3.02
5953 7163 3.583228 TGGAGGTGAACTAGTTTCAGGA 58.417 45.455 10.02 0.00 45.23 3.86
5954 7164 4.168101 TGGAGGTGAACTAGTTTCAGGAT 58.832 43.478 10.02 0.00 45.23 3.24
6022 7361 1.425412 GTACACACATGACACGGACC 58.575 55.000 0.00 0.00 0.00 4.46
6043 7382 0.976641 AAGAGGCGTGAACATGGAGA 59.023 50.000 0.00 0.00 0.00 3.71
6123 7462 4.202151 GCTGACCAAAGAAACAATCCAACT 60.202 41.667 0.00 0.00 0.00 3.16
6142 7481 5.106830 CCAACTAACAATTAGACGACCAACC 60.107 44.000 2.65 0.00 36.73 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.947147 GGCGTGGGAGTTGGCACA 62.947 66.667 0.00 0.00 0.00 4.57
31 32 3.449227 ATCGCTCGGGCTTGACGA 61.449 61.111 5.36 0.00 38.79 4.20
34 35 1.227350 CATCATCGCTCGGGCTTGA 60.227 57.895 5.36 9.16 34.47 3.02
108 109 3.692406 GTCGGACTGGCGGGAGTT 61.692 66.667 0.00 0.00 0.00 3.01
139 140 2.160221 CAATGCATCAAACGGCCGC 61.160 57.895 28.58 7.43 0.00 6.53
141 142 1.810853 GGCAATGCATCAAACGGCC 60.811 57.895 7.79 3.21 0.00 6.13
165 166 3.062122 TCGGCGTTTAAAAGGAAGGAT 57.938 42.857 6.85 0.00 0.00 3.24
204 205 0.470766 TTACCTTGCCACAGTTCGGT 59.529 50.000 0.00 0.00 0.00 4.69
267 268 7.273381 CGTCATAAATTCAAACTTGTCATTCCC 59.727 37.037 0.00 0.00 0.00 3.97
324 325 2.317040 CCTAGGGGCGATCTAGTTTCA 58.683 52.381 0.00 0.00 34.06 2.69
387 388 4.669809 TTCGGCCCCCAAACGCAT 62.670 61.111 0.00 0.00 0.00 4.73
413 414 2.814269 TCACGCATGACTAAGAGCATC 58.186 47.619 0.00 0.00 0.00 3.91
430 431 1.344438 TCCATATGATCTGGGCGTCAC 59.656 52.381 3.65 0.00 34.36 3.67
691 693 8.851541 ATTGTGCCAAAATGTTATTCTGAAAT 57.148 26.923 0.00 0.00 0.00 2.17
692 694 8.674263 AATTGTGCCAAAATGTTATTCTGAAA 57.326 26.923 0.00 0.00 0.00 2.69
697 699 9.896263 ATTTTGAATTGTGCCAAAATGTTATTC 57.104 25.926 12.34 0.00 45.65 1.75
702 704 9.165035 CCTATATTTTGAATTGTGCCAAAATGT 57.835 29.630 18.66 15.89 46.35 2.71
713 715 8.579006 TGCATTAGAGCCCTATATTTTGAATTG 58.421 33.333 0.00 0.00 0.00 2.32
745 747 3.118542 CTGCAAAAAGTCACTTTGGAGC 58.881 45.455 2.78 8.99 42.68 4.70
748 750 3.492011 GCATCTGCAAAAAGTCACTTTGG 59.508 43.478 2.78 0.57 41.59 3.28
807 809 0.037326 AGACGCGCCAGATTCTTCAA 60.037 50.000 5.73 0.00 0.00 2.69
847 849 1.067669 CGGCTGATCACTAGCTTAGCA 59.932 52.381 7.07 0.00 40.92 3.49
868 870 1.724545 TACCCTTGGATATGGACGGG 58.275 55.000 0.00 0.00 37.70 5.28
894 896 6.596106 GGAGACACGAGAGATTATATAGAGCA 59.404 42.308 0.00 0.00 0.00 4.26
1634 2004 2.845363 TTTTGGGACGGAGGAAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
1635 2005 3.585732 AGAATTTTGGGACGGAGGAAGTA 59.414 43.478 0.00 0.00 0.00 2.24
1636 2006 2.375509 AGAATTTTGGGACGGAGGAAGT 59.624 45.455 0.00 0.00 0.00 3.01
1637 2007 3.073274 AGAATTTTGGGACGGAGGAAG 57.927 47.619 0.00 0.00 0.00 3.46
1638 2008 3.153919 CAAGAATTTTGGGACGGAGGAA 58.846 45.455 0.00 0.00 0.00 3.36
1639 2009 2.107552 ACAAGAATTTTGGGACGGAGGA 59.892 45.455 0.00 0.00 0.00 3.71
1640 2010 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
1641 2011 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
1642 2012 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
1643 2013 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
1644 2014 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
1645 2015 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
1646 2016 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
1647 2017 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
1655 2025 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
1656 2026 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
1658 2028 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
1659 2029 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
1666 2036 9.832445 ACTTGATACATCCGTATTTAGACAAAT 57.168 29.630 0.00 0.00 38.48 2.32
1667 2037 9.309516 GACTTGATACATCCGTATTTAGACAAA 57.690 33.333 0.00 0.00 38.48 2.83
1668 2038 8.471609 TGACTTGATACATCCGTATTTAGACAA 58.528 33.333 0.00 0.00 38.48 3.18
1669 2039 7.919091 GTGACTTGATACATCCGTATTTAGACA 59.081 37.037 0.00 0.00 38.48 3.41
1670 2040 7.919091 TGTGACTTGATACATCCGTATTTAGAC 59.081 37.037 0.00 0.00 38.48 2.59
1671 2041 8.002984 TGTGACTTGATACATCCGTATTTAGA 57.997 34.615 0.00 0.00 38.48 2.10
1672 2042 8.818141 ATGTGACTTGATACATCCGTATTTAG 57.182 34.615 0.00 0.00 38.48 1.85
1673 2043 9.607988 AAATGTGACTTGATACATCCGTATTTA 57.392 29.630 0.00 0.00 38.48 1.40
1674 2044 8.506168 AAATGTGACTTGATACATCCGTATTT 57.494 30.769 0.00 0.00 38.48 1.40
1675 2045 8.506168 AAAATGTGACTTGATACATCCGTATT 57.494 30.769 0.00 0.00 38.48 1.89
1676 2046 9.261180 CTAAAATGTGACTTGATACATCCGTAT 57.739 33.333 0.00 0.00 41.16 3.06
1677 2047 8.255206 ACTAAAATGTGACTTGATACATCCGTA 58.745 33.333 0.00 0.00 36.56 4.02
1678 2048 7.103641 ACTAAAATGTGACTTGATACATCCGT 58.896 34.615 0.00 0.00 36.56 4.69
1679 2049 7.539712 ACTAAAATGTGACTTGATACATCCG 57.460 36.000 0.00 0.00 36.56 4.18
1711 2081 8.752187 TGTCTTAACTTATTTAGGTACGGATGT 58.248 33.333 0.00 0.00 0.00 3.06
1712 2082 9.245962 CTGTCTTAACTTATTTAGGTACGGATG 57.754 37.037 0.00 0.00 0.00 3.51
1713 2083 9.193806 TCTGTCTTAACTTATTTAGGTACGGAT 57.806 33.333 0.00 0.00 0.00 4.18
1714 2084 8.579850 TCTGTCTTAACTTATTTAGGTACGGA 57.420 34.615 0.00 0.00 0.00 4.69
1715 2085 9.813446 ATTCTGTCTTAACTTATTTAGGTACGG 57.187 33.333 0.00 0.00 0.00 4.02
1723 2093 9.893305 CGTCCAAAATTCTGTCTTAACTTATTT 57.107 29.630 0.00 0.00 0.00 1.40
1724 2094 8.512138 CCGTCCAAAATTCTGTCTTAACTTATT 58.488 33.333 0.00 0.00 0.00 1.40
1725 2095 7.881232 TCCGTCCAAAATTCTGTCTTAACTTAT 59.119 33.333 0.00 0.00 0.00 1.73
1726 2096 7.218614 TCCGTCCAAAATTCTGTCTTAACTTA 58.781 34.615 0.00 0.00 0.00 2.24
1727 2097 6.059484 TCCGTCCAAAATTCTGTCTTAACTT 58.941 36.000 0.00 0.00 0.00 2.66
1728 2098 5.617252 TCCGTCCAAAATTCTGTCTTAACT 58.383 37.500 0.00 0.00 0.00 2.24
1729 2099 5.934935 TCCGTCCAAAATTCTGTCTTAAC 57.065 39.130 0.00 0.00 0.00 2.01
1730 2100 5.472137 CCTTCCGTCCAAAATTCTGTCTTAA 59.528 40.000 0.00 0.00 0.00 1.85
1731 2101 5.001232 CCTTCCGTCCAAAATTCTGTCTTA 58.999 41.667 0.00 0.00 0.00 2.10
1732 2102 3.821033 CCTTCCGTCCAAAATTCTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
1733 2103 3.072476 TCCTTCCGTCCAAAATTCTGTCT 59.928 43.478 0.00 0.00 0.00 3.41
1734 2104 3.408634 TCCTTCCGTCCAAAATTCTGTC 58.591 45.455 0.00 0.00 0.00 3.51
1735 2105 3.181443 ACTCCTTCCGTCCAAAATTCTGT 60.181 43.478 0.00 0.00 0.00 3.41
1736 2106 3.412386 ACTCCTTCCGTCCAAAATTCTG 58.588 45.455 0.00 0.00 0.00 3.02
1737 2107 3.790089 ACTCCTTCCGTCCAAAATTCT 57.210 42.857 0.00 0.00 0.00 2.40
1738 2108 4.320870 TGTACTCCTTCCGTCCAAAATTC 58.679 43.478 0.00 0.00 0.00 2.17
1739 2109 4.202430 ACTGTACTCCTTCCGTCCAAAATT 60.202 41.667 0.00 0.00 0.00 1.82
1740 2110 3.326880 ACTGTACTCCTTCCGTCCAAAAT 59.673 43.478 0.00 0.00 0.00 1.82
1741 2111 2.701951 ACTGTACTCCTTCCGTCCAAAA 59.298 45.455 0.00 0.00 0.00 2.44
1742 2112 2.322658 ACTGTACTCCTTCCGTCCAAA 58.677 47.619 0.00 0.00 0.00 3.28
1743 2113 2.005370 ACTGTACTCCTTCCGTCCAA 57.995 50.000 0.00 0.00 0.00 3.53
1744 2114 2.885135 TACTGTACTCCTTCCGTCCA 57.115 50.000 0.00 0.00 0.00 4.02
1745 2115 3.446516 ACAATACTGTACTCCTTCCGTCC 59.553 47.826 0.00 0.00 32.54 4.79
1746 2116 4.157289 TCACAATACTGTACTCCTTCCGTC 59.843 45.833 0.00 0.00 33.22 4.79
1747 2117 4.084287 TCACAATACTGTACTCCTTCCGT 58.916 43.478 0.00 0.00 33.22 4.69
1748 2118 4.713824 TCACAATACTGTACTCCTTCCG 57.286 45.455 0.00 0.00 33.22 4.30
1749 2119 6.038997 AGTTCACAATACTGTACTCCTTCC 57.961 41.667 0.00 0.00 33.22 3.46
1750 2120 6.128526 GCAAGTTCACAATACTGTACTCCTTC 60.129 42.308 0.00 0.00 33.22 3.46
1751 2121 5.701290 GCAAGTTCACAATACTGTACTCCTT 59.299 40.000 0.00 0.00 33.22 3.36
1752 2122 5.221641 TGCAAGTTCACAATACTGTACTCCT 60.222 40.000 0.00 0.00 33.22 3.69
1753 2123 4.994852 TGCAAGTTCACAATACTGTACTCC 59.005 41.667 0.00 0.00 33.22 3.85
1754 2124 5.926542 TCTGCAAGTTCACAATACTGTACTC 59.073 40.000 0.00 0.00 31.57 2.59
1755 2125 5.853936 TCTGCAAGTTCACAATACTGTACT 58.146 37.500 0.00 0.00 31.57 2.73
1843 2576 9.848172 CCGTTGATTATTCAAAAAGAAAAACAG 57.152 29.630 1.74 0.00 43.29 3.16
1844 2577 8.821894 CCCGTTGATTATTCAAAAAGAAAAACA 58.178 29.630 1.74 0.00 43.29 2.83
1845 2578 8.279800 CCCCGTTGATTATTCAAAAAGAAAAAC 58.720 33.333 1.74 0.00 43.29 2.43
1846 2579 7.442666 CCCCCGTTGATTATTCAAAAAGAAAAA 59.557 33.333 1.74 0.00 43.29 1.94
1847 2580 6.931840 CCCCCGTTGATTATTCAAAAAGAAAA 59.068 34.615 1.74 0.00 43.29 2.29
1848 2581 6.459923 CCCCCGTTGATTATTCAAAAAGAAA 58.540 36.000 1.74 0.00 43.29 2.52
1849 2582 6.031751 CCCCCGTTGATTATTCAAAAAGAA 57.968 37.500 1.74 0.00 43.29 2.52
1850 2583 5.652994 CCCCCGTTGATTATTCAAAAAGA 57.347 39.130 1.74 0.00 43.29 2.52
1870 2603 1.632589 AAAACAGAATCTGCACCCCC 58.367 50.000 10.62 0.00 34.37 5.40
1910 2644 1.777272 AGAAGCCCAGAACCAGTTCTT 59.223 47.619 10.32 0.00 46.95 2.52
1961 2695 4.532834 TGGTGCTTCCTTACAGAAAAAGT 58.467 39.130 0.80 0.00 37.07 2.66
2078 2814 7.279615 TGGGTGTGTCTACCATTTCATAATAG 58.720 38.462 0.00 0.00 42.69 1.73
2246 2984 1.238439 AGGTTGGTTTCTGCATCACG 58.762 50.000 0.00 0.00 0.00 4.35
2331 3088 6.711277 TGATAACAACTTCAAGTATGGAGCT 58.289 36.000 0.00 0.00 35.34 4.09
2679 3437 4.101585 CCATATCAGTGAGAGGCAGGTAAA 59.898 45.833 0.00 0.00 0.00 2.01
2704 3462 9.206870 CACACCATGAAATTTAGCATTAAAAGT 57.793 29.630 0.00 0.00 32.80 2.66
2743 3501 8.646900 GGACCAAATTAATGAAGGGCAATAATA 58.353 33.333 8.65 0.00 32.70 0.98
2901 3659 1.233019 CCAACAGTGAAGGTGCTCAG 58.767 55.000 0.00 0.00 0.00 3.35
2969 3727 8.100791 AGCCAATAGACAACAAGTTAGATACAA 58.899 33.333 0.00 0.00 0.00 2.41
3079 3837 4.151157 ACATAACCGAACGTTAGCAAGAAC 59.849 41.667 0.00 0.00 40.27 3.01
3091 3849 3.865745 CAGAGACCATGACATAACCGAAC 59.134 47.826 0.00 0.00 0.00 3.95
3180 3938 6.226787 CCTATATTGATTCCCAGACTGACAC 58.773 44.000 3.32 0.00 0.00 3.67
3393 4153 2.706190 GTGGCACTTATCAGGGTCCTAT 59.294 50.000 11.13 0.00 0.00 2.57
3426 4186 0.467290 ACGGGAGTTGCCATGTGTTT 60.467 50.000 0.00 0.00 43.33 2.83
3446 4206 5.216648 GCGTCACTAAACTTGCCATAAAAA 58.783 37.500 0.00 0.00 0.00 1.94
3447 4207 4.611807 CGCGTCACTAAACTTGCCATAAAA 60.612 41.667 0.00 0.00 0.00 1.52
3451 4211 0.796312 CGCGTCACTAAACTTGCCAT 59.204 50.000 0.00 0.00 0.00 4.40
3453 4213 0.438830 CTCGCGTCACTAAACTTGCC 59.561 55.000 5.77 0.00 0.00 4.52
3454 4214 0.438830 CCTCGCGTCACTAAACTTGC 59.561 55.000 5.77 0.00 0.00 4.01
3455 4215 2.060326 TCCTCGCGTCACTAAACTTG 57.940 50.000 5.77 0.00 0.00 3.16
3456 4216 2.029290 ACATCCTCGCGTCACTAAACTT 60.029 45.455 5.77 0.00 0.00 2.66
3457 4217 1.544691 ACATCCTCGCGTCACTAAACT 59.455 47.619 5.77 0.00 0.00 2.66
3458 4218 1.918609 GACATCCTCGCGTCACTAAAC 59.081 52.381 5.77 0.00 32.24 2.01
3459 4219 1.542472 TGACATCCTCGCGTCACTAAA 59.458 47.619 5.77 0.00 37.23 1.85
3460 4220 1.170442 TGACATCCTCGCGTCACTAA 58.830 50.000 5.77 0.00 37.23 2.24
3461 4221 1.135489 GTTGACATCCTCGCGTCACTA 60.135 52.381 5.77 0.00 41.67 2.74
3462 4222 0.388649 GTTGACATCCTCGCGTCACT 60.389 55.000 5.77 0.00 41.67 3.41
3463 4223 0.388649 AGTTGACATCCTCGCGTCAC 60.389 55.000 5.77 0.00 41.67 3.67
3464 4224 0.317160 AAGTTGACATCCTCGCGTCA 59.683 50.000 5.77 0.00 40.30 4.35
3465 4225 1.429463 AAAGTTGACATCCTCGCGTC 58.571 50.000 5.77 0.00 0.00 5.19
3466 4226 2.029290 AGTAAAGTTGACATCCTCGCGT 60.029 45.455 5.77 0.00 0.00 6.01
3467 4227 2.607187 AGTAAAGTTGACATCCTCGCG 58.393 47.619 0.00 0.00 0.00 5.87
3468 4228 5.810587 TGATAAGTAAAGTTGACATCCTCGC 59.189 40.000 0.00 0.00 0.00 5.03
3469 4229 7.759886 TCTTGATAAGTAAAGTTGACATCCTCG 59.240 37.037 0.00 0.00 0.00 4.63
3470 4230 9.436957 TTCTTGATAAGTAAAGTTGACATCCTC 57.563 33.333 0.00 0.00 0.00 3.71
3471 4231 9.965902 ATTCTTGATAAGTAAAGTTGACATCCT 57.034 29.630 0.00 0.00 0.00 3.24
3472 4232 9.994432 CATTCTTGATAAGTAAAGTTGACATCC 57.006 33.333 0.00 0.00 0.00 3.51
3473 4233 9.994432 CCATTCTTGATAAGTAAAGTTGACATC 57.006 33.333 0.00 0.00 0.00 3.06
3474 4234 8.462016 GCCATTCTTGATAAGTAAAGTTGACAT 58.538 33.333 0.00 0.00 0.00 3.06
3475 4235 7.446931 TGCCATTCTTGATAAGTAAAGTTGACA 59.553 33.333 0.00 0.00 0.00 3.58
3476 4236 7.816640 TGCCATTCTTGATAAGTAAAGTTGAC 58.183 34.615 0.00 0.00 0.00 3.18
3477 4237 7.994425 TGCCATTCTTGATAAGTAAAGTTGA 57.006 32.000 0.00 0.00 0.00 3.18
3478 4238 8.299570 AGTTGCCATTCTTGATAAGTAAAGTTG 58.700 33.333 0.00 0.00 0.00 3.16
3479 4239 8.409358 AGTTGCCATTCTTGATAAGTAAAGTT 57.591 30.769 0.00 0.00 0.00 2.66
3480 4240 8.409358 AAGTTGCCATTCTTGATAAGTAAAGT 57.591 30.769 0.00 0.00 0.00 2.66
3481 4241 9.346725 GAAAGTTGCCATTCTTGATAAGTAAAG 57.653 33.333 0.00 0.00 0.00 1.85
3482 4242 9.077885 AGAAAGTTGCCATTCTTGATAAGTAAA 57.922 29.630 0.00 0.00 32.05 2.01
3483 4243 8.635765 AGAAAGTTGCCATTCTTGATAAGTAA 57.364 30.769 0.00 0.00 32.05 2.24
3484 4244 8.635765 AAGAAAGTTGCCATTCTTGATAAGTA 57.364 30.769 0.34 0.00 42.62 2.24
3485 4245 7.530426 AAGAAAGTTGCCATTCTTGATAAGT 57.470 32.000 0.34 0.00 42.62 2.24
3486 4246 8.822652 AAAAGAAAGTTGCCATTCTTGATAAG 57.177 30.769 1.90 0.00 43.24 1.73
3487 4247 8.641541 AGAAAAGAAAGTTGCCATTCTTGATAA 58.358 29.630 1.90 0.00 43.24 1.75
3488 4248 8.084073 CAGAAAAGAAAGTTGCCATTCTTGATA 58.916 33.333 1.90 0.00 43.24 2.15
3489 4249 6.927381 CAGAAAAGAAAGTTGCCATTCTTGAT 59.073 34.615 1.90 0.00 43.24 2.57
3490 4250 6.096705 TCAGAAAAGAAAGTTGCCATTCTTGA 59.903 34.615 1.90 0.00 43.24 3.02
3491 4251 6.275335 TCAGAAAAGAAAGTTGCCATTCTTG 58.725 36.000 1.90 0.00 43.24 3.02
3492 4252 6.469782 TCAGAAAAGAAAGTTGCCATTCTT 57.530 33.333 0.00 0.00 45.30 2.52
3493 4253 6.453092 CATCAGAAAAGAAAGTTGCCATTCT 58.547 36.000 0.00 0.00 37.49 2.40
3494 4254 5.636543 CCATCAGAAAAGAAAGTTGCCATTC 59.363 40.000 0.00 0.00 0.00 2.67
3495 4255 5.544650 CCATCAGAAAAGAAAGTTGCCATT 58.455 37.500 0.00 0.00 0.00 3.16
3584 4344 0.396695 ATGAAGCAATCTGGCCCTGG 60.397 55.000 0.00 0.00 0.00 4.45
3660 4420 3.504520 TGCTTCGAATTTTTAGGGGTGAC 59.495 43.478 0.00 0.00 0.00 3.67
3763 4528 4.537015 GTCACCAACTTGCTTGACAATAC 58.463 43.478 13.27 0.00 38.60 1.89
3782 4547 4.804665 TCGACAACATAAAACTCAACGTCA 59.195 37.500 0.00 0.00 0.00 4.35
3794 4559 2.333926 CTGCCGTCTTCGACAACATAA 58.666 47.619 0.00 0.00 39.71 1.90
3796 4561 1.291877 GCTGCCGTCTTCGACAACAT 61.292 55.000 0.00 0.00 39.71 2.71
3802 4567 1.070786 AAAAGGCTGCCGTCTTCGA 59.929 52.632 13.96 0.00 32.99 3.71
3804 4569 1.081175 GCAAAAGGCTGCCGTCTTC 60.081 57.895 13.96 0.15 40.25 2.87
4150 5338 1.264749 TAGCTGCCCTGTACCCACTG 61.265 60.000 0.00 0.00 0.00 3.66
4457 5646 3.202906 GCACAACTTCAACAGGTAGTCA 58.797 45.455 0.00 0.00 0.00 3.41
4461 5650 3.550820 ACATGCACAACTTCAACAGGTA 58.449 40.909 0.00 0.00 0.00 3.08
4502 5691 3.879295 CGATGGTGCCTAAAATCAGATGT 59.121 43.478 0.00 0.00 0.00 3.06
4503 5692 3.251729 CCGATGGTGCCTAAAATCAGATG 59.748 47.826 0.00 0.00 0.00 2.90
4521 5716 3.425162 AAGACCTTTCTGCTTTCCGAT 57.575 42.857 0.00 0.00 29.98 4.18
4522 5717 2.930826 AAGACCTTTCTGCTTTCCGA 57.069 45.000 0.00 0.00 29.98 4.55
4589 5784 0.463116 AACGTTGTTCCCAAGCTCGT 60.463 50.000 0.00 0.00 33.75 4.18
4839 6034 5.823045 AGCAGCAAAGGTCTTATAATGGTAC 59.177 40.000 0.00 0.00 0.00 3.34
5067 6262 4.686091 TCACTCAGTTCTTCAAATGCGTAG 59.314 41.667 0.00 0.00 0.00 3.51
5250 6445 7.414540 CCAGAATAACTAAACAGAACTGGATGC 60.415 40.741 0.00 0.00 43.12 3.91
5297 6492 3.590824 GCAGTACCGCCAGCAATT 58.409 55.556 0.00 0.00 0.00 2.32
5373 6568 8.508062 AGACGACTAATAATGAGCATACTACAG 58.492 37.037 0.00 0.00 0.00 2.74
5440 6635 5.099575 ACTTTCAATCGAACACACCAAAAC 58.900 37.500 0.00 0.00 0.00 2.43
5441 6636 5.317733 ACTTTCAATCGAACACACCAAAA 57.682 34.783 0.00 0.00 0.00 2.44
5446 6641 3.482110 GCACAACTTTCAATCGAACACAC 59.518 43.478 0.00 0.00 0.00 3.82
5451 6646 4.350346 CAACAGCACAACTTTCAATCGAA 58.650 39.130 0.00 0.00 0.00 3.71
5476 6671 5.805728 TCCTCAGGAAATCTACCAGTTTTC 58.194 41.667 0.00 2.48 34.68 2.29
5527 6722 2.027469 TGTACAGAGCTCCGTGTCTAGA 60.027 50.000 12.99 0.00 0.00 2.43
5530 6725 1.269998 GTTGTACAGAGCTCCGTGTCT 59.730 52.381 12.99 0.00 0.00 3.41
5536 6733 3.550437 ATCATGGTTGTACAGAGCTCC 57.450 47.619 10.93 0.00 0.00 4.70
5621 6827 2.158726 ACGGCTACTCCTGGAAAACAAA 60.159 45.455 0.00 0.00 0.00 2.83
5642 6849 5.950758 ACGCCACTAACACAAATCAAATA 57.049 34.783 0.00 0.00 0.00 1.40
5661 6868 2.206750 TCACACTTACAGTTCCAACGC 58.793 47.619 0.00 0.00 0.00 4.84
5802 7012 1.952296 CATCAACCAGGCCAATAGCTC 59.048 52.381 5.01 0.00 43.05 4.09
5803 7013 1.565759 TCATCAACCAGGCCAATAGCT 59.434 47.619 5.01 0.00 43.05 3.32
5809 7019 2.290641 ACGTATTTCATCAACCAGGCCA 60.291 45.455 5.01 0.00 0.00 5.36
5810 7020 2.365582 ACGTATTTCATCAACCAGGCC 58.634 47.619 0.00 0.00 0.00 5.19
5812 7022 5.872617 TGACTTACGTATTTCATCAACCAGG 59.127 40.000 0.00 0.00 0.00 4.45
5819 7029 5.696724 CCCCTGATGACTTACGTATTTCATC 59.303 44.000 25.89 25.89 43.14 2.92
5840 7050 8.218488 AGGTTGATTGAGTATAAAATACTCCCC 58.782 37.037 19.37 11.47 42.32 4.81
5841 7051 9.274206 GAGGTTGATTGAGTATAAAATACTCCC 57.726 37.037 19.37 13.63 42.32 4.30
5842 7052 8.979574 CGAGGTTGATTGAGTATAAAATACTCC 58.020 37.037 19.37 8.81 42.32 3.85
5843 7053 9.530633 ACGAGGTTGATTGAGTATAAAATACTC 57.469 33.333 16.64 16.64 43.06 2.59
5866 7076 4.588951 AGAGCCATTCTACATTATCCACGA 59.411 41.667 0.00 0.00 33.23 4.35
5902 7112 4.119136 GTGGTTTCTTGTTTGTTCCCATG 58.881 43.478 0.00 0.00 0.00 3.66
5903 7113 3.772025 TGTGGTTTCTTGTTTGTTCCCAT 59.228 39.130 0.00 0.00 0.00 4.00
5904 7114 3.165875 TGTGGTTTCTTGTTTGTTCCCA 58.834 40.909 0.00 0.00 0.00 4.37
5905 7115 3.878160 TGTGGTTTCTTGTTTGTTCCC 57.122 42.857 0.00 0.00 0.00 3.97
5906 7116 4.033932 GCATTGTGGTTTCTTGTTTGTTCC 59.966 41.667 0.00 0.00 0.00 3.62
5945 7155 4.678509 TGATACGCAAACATCCTGAAAC 57.321 40.909 0.00 0.00 0.00 2.78
5949 7159 7.914871 TCAATAAAATGATACGCAAACATCCTG 59.085 33.333 0.00 0.00 0.00 3.86
5950 7160 7.995289 TCAATAAAATGATACGCAAACATCCT 58.005 30.769 0.00 0.00 0.00 3.24
5951 7161 8.801715 ATCAATAAAATGATACGCAAACATCC 57.198 30.769 0.00 0.00 38.25 3.51
5978 7313 7.162082 CCACCTCTTGTACTCAATCTAACTTT 58.838 38.462 0.00 0.00 32.82 2.66
6022 7361 0.321564 TCCATGTTCACGCCTCTTGG 60.322 55.000 0.00 0.00 0.00 3.61
6043 7382 0.610174 TCATGCCTCTCTGCTTCGTT 59.390 50.000 0.00 0.00 0.00 3.85
6123 7462 5.337009 GGAGAGGTTGGTCGTCTAATTGTTA 60.337 44.000 0.00 0.00 40.72 2.41
6142 7481 0.250234 TCGGTGCTGGATTTGGAGAG 59.750 55.000 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.