Multiple sequence alignment - TraesCS7B01G209000

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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 TraesCS7B01G209000 chr7B 100.000 7721 0 0 1 7721 382220953 382228673 0.000000e+00 14259.0
1 TraesCS7B01G209000 chr7B 92.188 64 4 1 1672 1735 379114997 379114935 1.070000e-13 89.8
2 TraesCS7B01G209000 chr7B 96.226 53 1 1 1258 1310 115288 115237 1.380000e-12 86.1
3 TraesCS7B01G209000 chr7D 95.619 5478 143 27 1735 7124 386915144 386920612 0.000000e+00 8696.0
4 TraesCS7B01G209000 chr7D 87.071 1400 84 28 320 1686 386913824 386915159 0.000000e+00 1493.0
5 TraesCS7B01G209000 chr7D 91.751 594 46 3 7126 7717 266210256 266210848 0.000000e+00 822.0
6 TraesCS7B01G209000 chr7D 90.941 287 15 4 1 276 386913446 386913732 7.320000e-100 375.0
7 TraesCS7B01G209000 chr7A 96.125 4722 118 27 1735 6397 437053290 437058005 0.000000e+00 7646.0
8 TraesCS7B01G209000 chr7A 97.268 732 14 4 6395 7124 437058145 437058872 0.000000e+00 1236.0
9 TraesCS7B01G209000 chr7A 89.437 871 38 12 834 1686 437052471 437053305 0.000000e+00 1050.0
10 TraesCS7B01G209000 chr7A 91.275 596 48 4 7127 7721 677852303 677852895 0.000000e+00 809.0
11 TraesCS7B01G209000 chr7A 85.520 442 25 15 378 783 437051680 437052118 7.160000e-115 425.0
12 TraesCS7B01G209000 chr7A 88.811 286 22 2 1 276 437051341 437051626 7.420000e-90 342.0
13 TraesCS7B01G209000 chr7A 95.082 61 2 1 1675 1735 632597339 632597398 2.290000e-15 95.3
14 TraesCS7B01G209000 chr7A 90.164 61 6 0 277 337 646101526 646101466 6.420000e-11 80.5
15 TraesCS7B01G209000 chr6D 91.290 597 49 3 7126 7721 436318485 436319079 0.000000e+00 811.0
16 TraesCS7B01G209000 chr6D 90.620 597 52 4 7126 7721 54789421 54788828 0.000000e+00 789.0
17 TraesCS7B01G209000 chr6D 91.667 60 4 1 277 335 36692815 36692874 1.790000e-11 82.4
18 TraesCS7B01G209000 chr3D 91.137 598 50 3 7126 7721 567658468 567659064 0.000000e+00 808.0
19 TraesCS7B01G209000 chr3D 91.667 60 4 1 277 335 271512634 271512575 1.790000e-11 82.4
20 TraesCS7B01G209000 chr2B 91.207 580 41 8 7143 7721 383635858 383636428 0.000000e+00 780.0
21 TraesCS7B01G209000 chr2B 91.228 57 4 1 1244 1299 796974924 796974868 8.310000e-10 76.8
22 TraesCS7B01G209000 chr4D 89.447 597 59 4 7126 7721 406645281 406645874 0.000000e+00 750.0
23 TraesCS7B01G209000 chr4D 100.000 49 0 0 1687 1735 392738238 392738190 2.970000e-14 91.6
24 TraesCS7B01G209000 chr4D 92.982 57 1 3 1252 1305 427262402 427262346 6.420000e-11 80.5
25 TraesCS7B01G209000 chr2D 91.667 504 40 2 7126 7628 131052099 131051597 0.000000e+00 697.0
26 TraesCS7B01G209000 chr2D 96.429 56 2 0 279 334 217050451 217050506 8.250000e-15 93.5
27 TraesCS7B01G209000 chr2D 94.545 55 3 0 277 331 619321042 619321096 1.380000e-12 86.1
28 TraesCS7B01G209000 chr2D 96.078 51 2 0 1258 1308 640366688 640366738 4.970000e-12 84.2
29 TraesCS7B01G209000 chr2D 91.667 60 4 1 277 335 480173375 480173316 1.790000e-11 82.4
30 TraesCS7B01G209000 chr3B 84.942 518 75 3 7136 7652 564047923 564047408 8.880000e-144 521.0
31 TraesCS7B01G209000 chr3B 96.552 58 1 1 1678 1735 627207019 627207075 2.290000e-15 95.3
32 TraesCS7B01G209000 chr3B 92.308 65 4 1 1671 1735 302245036 302245099 2.970000e-14 91.6
33 TraesCS7B01G209000 chr1B 100.000 53 0 0 1683 1735 512688519 512688467 1.770000e-16 99.0
34 TraesCS7B01G209000 chr1B 93.103 58 4 0 277 334 518259051 518258994 1.380000e-12 86.1
35 TraesCS7B01G209000 chr6B 100.000 52 0 0 1684 1735 454733277 454733328 6.380000e-16 97.1
36 TraesCS7B01G209000 chr6A 96.491 57 1 1 1679 1735 356206159 356206104 8.250000e-15 93.5
37 TraesCS7B01G209000 chrUn 100.000 47 0 0 1689 1735 83503007 83502961 3.840000e-13 87.9
38 TraesCS7B01G209000 chrUn 100.000 45 0 0 1256 1300 37028998 37028954 4.970000e-12 84.2
39 TraesCS7B01G209000 chr5D 94.545 55 3 0 277 331 111788677 111788731 1.380000e-12 86.1
40 TraesCS7B01G209000 chr5D 95.918 49 2 0 1259 1307 543223110 543223158 6.420000e-11 80.5
41 TraesCS7B01G209000 chr1D 100.000 45 0 0 1256 1300 363509574 363509530 4.970000e-12 84.2
42 TraesCS7B01G209000 chr1A 91.667 60 4 1 278 336 108312649 108312590 1.790000e-11 82.4
43 TraesCS7B01G209000 chr5B 90.476 63 1 5 1259 1319 471409344 471409285 2.310000e-10 78.7
44 TraesCS7B01G209000 chr4A 91.525 59 2 3 1242 1298 742468061 742468004 2.310000e-10 78.7


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 TraesCS7B01G209000 chr7B 382220953 382228673 7720 False 14259.000000 14259 100.000000 1 7721 1 chr7B.!!$F1 7720
1 TraesCS7B01G209000 chr7D 386913446 386920612 7166 False 3521.333333 8696 91.210333 1 7124 3 chr7D.!!$F2 7123
2 TraesCS7B01G209000 chr7D 266210256 266210848 592 False 822.000000 822 91.751000 7126 7717 1 chr7D.!!$F1 591
3 TraesCS7B01G209000 chr7A 437051341 437058872 7531 False 2139.800000 7646 91.432200 1 7124 5 chr7A.!!$F3 7123
4 TraesCS7B01G209000 chr7A 677852303 677852895 592 False 809.000000 809 91.275000 7127 7721 1 chr7A.!!$F2 594
5 TraesCS7B01G209000 chr6D 436318485 436319079 594 False 811.000000 811 91.290000 7126 7721 1 chr6D.!!$F2 595
6 TraesCS7B01G209000 chr6D 54788828 54789421 593 True 789.000000 789 90.620000 7126 7721 1 chr6D.!!$R1 595
7 TraesCS7B01G209000 chr3D 567658468 567659064 596 False 808.000000 808 91.137000 7126 7721 1 chr3D.!!$F1 595
8 TraesCS7B01G209000 chr2B 383635858 383636428 570 False 780.000000 780 91.207000 7143 7721 1 chr2B.!!$F1 578
9 TraesCS7B01G209000 chr4D 406645281 406645874 593 False 750.000000 750 89.447000 7126 7721 1 chr4D.!!$F1 595
10 TraesCS7B01G209000 chr2D 131051597 131052099 502 True 697.000000 697 91.667000 7126 7628 1 chr2D.!!$R1 502
11 TraesCS7B01G209000 chr3B 564047408 564047923 515 True 521.000000 521 84.942000 7136 7652 1 chr3B.!!$R1 516

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
643 746 0.033011 ACCTCGTAGGCATCTGACCT 60.033 55.000 1.36 0.0 39.63 3.85 F
894 1303 0.526662 CCTGAGTCCGAACTTAGCGT 59.473 55.000 0.00 0.0 37.70 5.07 F
1377 1804 1.445754 CAGCTCTGACGGCTCTGTG 60.446 63.158 0.00 0.0 38.03 3.66 F
1736 2163 0.187361 AAGCAAGTTGGGGTAGGCAA 59.813 50.000 4.75 0.0 0.00 4.52 F
2288 2718 0.237761 GCTGCTTTGTGCTCTGACAG 59.762 55.000 0.00 0.0 43.37 3.51 F
3567 4001 0.038310 CCTCCCCAGGTTTTGAGGAC 59.962 60.000 5.90 0.0 45.93 3.85 F
4390 4902 0.546122 ACCTAATTGCATGCGGGAGA 59.454 50.000 14.09 0.0 0.00 3.71 F
4593 5106 1.619332 TCGGCATACACACAAGTACCA 59.381 47.619 0.00 0.0 0.00 3.25 F
5735 6272 2.159099 TGTCGAATCCTGTAGTGCATCC 60.159 50.000 0.00 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1717 2144 0.187361 TTGCCTACCCCAACTTGCTT 59.813 50.000 0.00 0.00 0.00 3.91 R
1718 2145 0.409484 ATTGCCTACCCCAACTTGCT 59.591 50.000 0.00 0.00 0.00 3.91 R
3340 3774 0.253044 TCAACTGATAGGCCACCTGC 59.747 55.000 5.01 0.00 34.61 4.85 R
3489 3923 1.198713 TTTGCAGGCCTTCAAACCAA 58.801 45.000 24.30 4.83 0.00 3.67 R
3949 4434 2.290577 ACTCCAGATGCCACTTCCTTTC 60.291 50.000 0.00 0.00 0.00 2.62 R
4593 5106 1.075482 CCAGCCACAGTTGACCCAT 59.925 57.895 0.00 0.00 0.00 4.00 R
5650 6187 2.263077 CTGAAGGCACAGCTAGTTACG 58.737 52.381 0.00 0.00 0.00 3.18 R
6492 7171 0.318441 TCACTGCTTTCTGGTCCTCG 59.682 55.000 0.00 0.00 0.00 4.63 R
7654 8338 0.178953 AGAACATTGGGCAAGTGGCT 60.179 50.000 4.74 0.00 44.01 4.75 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
75 86 3.117663 ACAAGCCTTTCCACTCAACCTAA 60.118 43.478 0.00 0.00 0.00 2.69
95 106 3.353836 GAAGGCCGCAACGCAGAA 61.354 61.111 0.00 0.00 0.00 3.02
100 111 2.252260 CCGCAACGCAGAAAGGTG 59.748 61.111 0.00 0.00 0.00 4.00
133 144 2.418746 GCTCATTTCTAAGCGAGGTCCA 60.419 50.000 0.00 0.00 0.00 4.02
139 150 2.457598 TCTAAGCGAGGTCCATGAAGT 58.542 47.619 0.00 0.00 0.00 3.01
142 153 0.904865 AGCGAGGTCCATGAAGTCCA 60.905 55.000 0.00 0.00 0.00 4.02
183 195 1.542472 CCAACCAACCCAATTCGTACC 59.458 52.381 0.00 0.00 0.00 3.34
322 390 9.525826 AAATGCTCTTATATTATTGGAAGGAGG 57.474 33.333 0.00 0.00 0.00 4.30
323 391 7.020827 TGCTCTTATATTATTGGAAGGAGGG 57.979 40.000 0.00 0.00 0.00 4.30
324 392 6.792473 TGCTCTTATATTATTGGAAGGAGGGA 59.208 38.462 0.00 0.00 0.00 4.20
325 393 7.038017 TGCTCTTATATTATTGGAAGGAGGGAG 60.038 40.741 0.00 0.00 0.00 4.30
326 394 7.037945 GCTCTTATATTATTGGAAGGAGGGAGT 60.038 40.741 0.00 0.00 0.00 3.85
327 395 9.548631 CTCTTATATTATTGGAAGGAGGGAGTA 57.451 37.037 0.00 0.00 0.00 2.59
414 482 7.517614 TTAAAACTGTTCACCAGATGCATTA 57.482 32.000 0.00 0.00 44.49 1.90
415 483 6.594788 AAAACTGTTCACCAGATGCATTAT 57.405 33.333 0.00 0.00 44.49 1.28
479 547 7.148639 ACGTGTGCTACAATATTTGTCAACTAG 60.149 37.037 0.00 0.00 44.12 2.57
601 703 6.480524 AAAAAGAAACAGTGAAAAAGGTGC 57.519 33.333 0.00 0.00 0.00 5.01
602 704 3.420839 AGAAACAGTGAAAAAGGTGCG 57.579 42.857 0.00 0.00 0.00 5.34
638 740 2.435693 GCCCACCTCGTAGGCATCT 61.436 63.158 0.00 0.00 46.34 2.90
640 742 1.043116 CCCACCTCGTAGGCATCTGA 61.043 60.000 1.36 0.00 39.63 3.27
643 746 0.033011 ACCTCGTAGGCATCTGACCT 60.033 55.000 1.36 0.00 39.63 3.85
722 829 2.656069 GCCTCCACGACTGGCCTAA 61.656 63.158 3.32 0.00 40.71 2.69
815 922 2.269241 CGTCCTCCCCTTGCTTCC 59.731 66.667 0.00 0.00 0.00 3.46
822 929 4.766632 CCCTTGCTTCCCAGCCCC 62.767 72.222 0.00 0.00 46.74 5.80
823 930 3.665971 CCTTGCTTCCCAGCCCCT 61.666 66.667 0.00 0.00 46.74 4.79
825 932 1.077429 CTTGCTTCCCAGCCCCTAC 60.077 63.158 0.00 0.00 46.74 3.18
827 934 2.692741 GCTTCCCAGCCCCTACCT 60.693 66.667 0.00 0.00 40.61 3.08
894 1303 0.526662 CCTGAGTCCGAACTTAGCGT 59.473 55.000 0.00 0.00 37.70 5.07
939 1348 4.685030 GCCTTATTGTCCATTTCTACCGGA 60.685 45.833 9.46 0.00 0.00 5.14
944 1353 1.757699 GTCCATTTCTACCGGAGAGCT 59.242 52.381 9.46 0.00 34.93 4.09
958 1367 2.600769 AGCTCCGAGTGGGACGTT 60.601 61.111 0.00 0.00 40.94 3.99
1281 1708 9.725206 AGGTACTCCCTCTGTAAAGAAATATAA 57.275 33.333 0.00 0.00 40.71 0.98
1282 1709 9.984190 GGTACTCCCTCTGTAAAGAAATATAAG 57.016 37.037 0.00 0.00 0.00 1.73
1285 1712 8.425703 ACTCCCTCTGTAAAGAAATATAAGAGC 58.574 37.037 0.00 0.00 0.00 4.09
1286 1713 7.434492 TCCCTCTGTAAAGAAATATAAGAGCG 58.566 38.462 0.00 0.00 0.00 5.03
1287 1714 7.069578 TCCCTCTGTAAAGAAATATAAGAGCGT 59.930 37.037 0.00 0.00 0.00 5.07
1288 1715 7.711339 CCCTCTGTAAAGAAATATAAGAGCGTT 59.289 37.037 0.00 0.00 0.00 4.84
1289 1716 9.099454 CCTCTGTAAAGAAATATAAGAGCGTTT 57.901 33.333 0.00 0.00 0.00 3.60
1312 1739 9.575783 GTTTAGATCACTAACCTCTCTAGTTTG 57.424 37.037 0.00 0.00 38.18 2.93
1327 1754 5.423015 TCTAGTTTGCTCTTAGCCATTGAG 58.577 41.667 0.00 0.00 41.51 3.02
1329 1756 5.165961 AGTTTGCTCTTAGCCATTGAGTA 57.834 39.130 0.00 0.00 41.51 2.59
1374 1801 4.127040 CGCAGCTCTGACGGCTCT 62.127 66.667 0.29 0.00 38.03 4.09
1375 1802 2.508887 GCAGCTCTGACGGCTCTG 60.509 66.667 0.29 0.00 38.03 3.35
1376 1803 2.969016 CAGCTCTGACGGCTCTGT 59.031 61.111 0.00 0.00 38.03 3.41
1377 1804 1.445754 CAGCTCTGACGGCTCTGTG 60.446 63.158 0.00 0.00 38.03 3.66
1378 1805 2.125753 GCTCTGACGGCTCTGTGG 60.126 66.667 0.00 0.00 0.00 4.17
1379 1806 2.125753 CTCTGACGGCTCTGTGGC 60.126 66.667 0.00 0.00 37.94 5.01
1446 1873 9.512435 CTCTTACATTTCATCAAATCCACATTC 57.488 33.333 0.00 0.00 28.97 2.67
1476 1903 6.419710 CACTCGAAGGTAATATCACGCATTTA 59.580 38.462 0.00 0.00 0.00 1.40
1491 1918 3.953853 CGCATTTAAATCGCAAGTCGTAG 59.046 43.478 17.14 0.00 39.67 3.51
1673 2100 4.836175 ACAAAGGGGACGGTTATTTTCAAT 59.164 37.500 0.00 0.00 0.00 2.57
1674 2101 6.011481 ACAAAGGGGACGGTTATTTTCAATA 58.989 36.000 0.00 0.00 0.00 1.90
1675 2102 6.494146 ACAAAGGGGACGGTTATTTTCAATAA 59.506 34.615 0.00 0.00 0.00 1.40
1676 2103 7.015389 ACAAAGGGGACGGTTATTTTCAATAAA 59.985 33.333 0.00 0.00 0.00 1.40
1677 2104 7.727578 AAGGGGACGGTTATTTTCAATAAAT 57.272 32.000 0.00 0.00 0.00 1.40
1678 2105 7.727578 AGGGGACGGTTATTTTCAATAAATT 57.272 32.000 0.00 0.00 0.00 1.82
1679 2106 8.141298 AGGGGACGGTTATTTTCAATAAATTT 57.859 30.769 0.00 0.00 0.00 1.82
1680 2107 8.255206 AGGGGACGGTTATTTTCAATAAATTTC 58.745 33.333 0.00 0.00 0.00 2.17
1681 2108 7.221259 GGGGACGGTTATTTTCAATAAATTTCG 59.779 37.037 0.00 0.00 0.00 3.46
1682 2109 7.756272 GGGACGGTTATTTTCAATAAATTTCGT 59.244 33.333 0.00 0.00 0.00 3.85
1683 2110 9.771915 GGACGGTTATTTTCAATAAATTTCGTA 57.228 29.630 0.00 0.00 0.00 3.43
1699 2126 8.467402 AAATTTCGTAATCAACAACAACAACA 57.533 26.923 0.00 0.00 0.00 3.33
1700 2127 8.467402 AATTTCGTAATCAACAACAACAACAA 57.533 26.923 0.00 0.00 0.00 2.83
1701 2128 6.856494 TTCGTAATCAACAACAACAACAAC 57.144 33.333 0.00 0.00 0.00 3.32
1702 2129 5.939457 TCGTAATCAACAACAACAACAACA 58.061 33.333 0.00 0.00 0.00 3.33
1703 2130 6.379386 TCGTAATCAACAACAACAACAACAA 58.621 32.000 0.00 0.00 0.00 2.83
1704 2131 6.861572 TCGTAATCAACAACAACAACAACAAA 59.138 30.769 0.00 0.00 0.00 2.83
1705 2132 7.061210 TCGTAATCAACAACAACAACAACAAAG 59.939 33.333 0.00 0.00 0.00 2.77
1706 2133 4.981389 TCAACAACAACAACAACAAAGC 57.019 36.364 0.00 0.00 0.00 3.51
1707 2134 3.743396 TCAACAACAACAACAACAAAGCC 59.257 39.130 0.00 0.00 0.00 4.35
1708 2135 3.676291 ACAACAACAACAACAAAGCCT 57.324 38.095 0.00 0.00 0.00 4.58
1709 2136 4.001618 ACAACAACAACAACAAAGCCTT 57.998 36.364 0.00 0.00 0.00 4.35
1710 2137 4.384940 ACAACAACAACAACAAAGCCTTT 58.615 34.783 0.00 0.00 0.00 3.11
1711 2138 5.542779 ACAACAACAACAACAAAGCCTTTA 58.457 33.333 0.00 0.00 0.00 1.85
1712 2139 5.637387 ACAACAACAACAACAAAGCCTTTAG 59.363 36.000 0.00 0.00 0.00 1.85
1713 2140 5.400066 ACAACAACAACAAAGCCTTTAGT 57.600 34.783 0.00 0.00 0.00 2.24
1714 2141 5.407502 ACAACAACAACAAAGCCTTTAGTC 58.592 37.500 0.00 0.00 0.00 2.59
1715 2142 4.649088 ACAACAACAAAGCCTTTAGTCC 57.351 40.909 0.00 0.00 0.00 3.85
1716 2143 3.383505 ACAACAACAAAGCCTTTAGTCCC 59.616 43.478 0.00 0.00 0.00 4.46
1717 2144 3.306472 ACAACAAAGCCTTTAGTCCCA 57.694 42.857 0.00 0.00 0.00 4.37
1718 2145 3.637769 ACAACAAAGCCTTTAGTCCCAA 58.362 40.909 0.00 0.00 0.00 4.12
1719 2146 3.636764 ACAACAAAGCCTTTAGTCCCAAG 59.363 43.478 0.00 0.00 0.00 3.61
1720 2147 2.239400 ACAAAGCCTTTAGTCCCAAGC 58.761 47.619 0.00 0.00 0.00 4.01
1721 2148 2.238521 CAAAGCCTTTAGTCCCAAGCA 58.761 47.619 0.00 0.00 0.00 3.91
1722 2149 2.627699 CAAAGCCTTTAGTCCCAAGCAA 59.372 45.455 0.00 0.00 0.00 3.91
1723 2150 2.206576 AGCCTTTAGTCCCAAGCAAG 57.793 50.000 0.00 0.00 0.00 4.01
1724 2151 1.425448 AGCCTTTAGTCCCAAGCAAGT 59.575 47.619 0.00 0.00 0.00 3.16
1725 2152 2.158460 AGCCTTTAGTCCCAAGCAAGTT 60.158 45.455 0.00 0.00 0.00 2.66
1726 2153 2.029918 GCCTTTAGTCCCAAGCAAGTTG 60.030 50.000 0.00 0.00 35.71 3.16
1734 2161 2.267045 CAAGCAAGTTGGGGTAGGC 58.733 57.895 4.75 0.00 31.82 3.93
1735 2162 0.539438 CAAGCAAGTTGGGGTAGGCA 60.539 55.000 4.75 0.00 31.82 4.75
1736 2163 0.187361 AAGCAAGTTGGGGTAGGCAA 59.813 50.000 4.75 0.00 0.00 4.52
1819 2246 5.724370 TCCAGGAGTCTTGTGGTATTTCATA 59.276 40.000 1.16 0.00 32.73 2.15
1903 2330 8.832521 TGTACACAGTTACAAATAGTTTTCCAG 58.167 33.333 0.00 0.00 0.00 3.86
2004 2433 8.787852 CAAGGATAATTTTGGCTATTCCTAGAC 58.212 37.037 0.00 0.00 33.12 2.59
2071 2501 7.880713 TCAGTGGTTATTGCTGTCTGTTAATTA 59.119 33.333 0.00 0.00 0.00 1.40
2205 2635 3.773418 TGAAACATTAGACGGGGACAA 57.227 42.857 0.00 0.00 0.00 3.18
2230 2660 6.698766 ACAAACATTCAGCTGCTTTTAGAAAG 59.301 34.615 9.47 0.17 0.00 2.62
2280 2710 2.159327 AAAATCTGGCTGCTTTGTGC 57.841 45.000 0.00 0.00 43.25 4.57
2288 2718 0.237761 GCTGCTTTGTGCTCTGACAG 59.762 55.000 0.00 0.00 43.37 3.51
2593 3023 6.003950 TCTTTTTATTCTGTCTTCACTGGGG 58.996 40.000 0.00 0.00 0.00 4.96
2598 3028 1.630369 TCTGTCTTCACTGGGGGAATG 59.370 52.381 0.00 0.00 0.00 2.67
2607 3037 0.748005 CTGGGGGAATGCAAGTACCG 60.748 60.000 0.00 0.00 0.00 4.02
2620 3054 6.169557 TGCAAGTACCGGTATTTCAGATAT 57.830 37.500 19.19 0.00 0.00 1.63
2699 3133 9.658475 TTTATCACATTAAAGAAGTGAAACACG 57.342 29.630 0.00 0.00 44.47 4.49
2704 3138 7.164171 CACATTAAAGAAGTGAAACACGACTTG 59.836 37.037 13.26 7.62 41.43 3.16
2732 3166 2.168106 TGGGAATACAATGCAATGCCAC 59.832 45.455 1.53 0.00 0.00 5.01
2755 3189 5.105797 ACGCACAATGGAATATGTGTCAAAT 60.106 36.000 7.62 0.00 46.68 2.32
2827 3261 4.898829 TGGTTTGTCTGTTTGATGAGTG 57.101 40.909 0.00 0.00 0.00 3.51
2942 3376 2.035632 CAGGGGTAAGCTCTAGACAGG 58.964 57.143 0.00 0.00 0.00 4.00
3021 3455 7.065085 GCACTTAAGATTCTCTAGAATGTTGCA 59.935 37.037 19.78 9.40 44.44 4.08
3131 3565 7.994425 TTGAGTGCAGAACCTATTGAAAATA 57.006 32.000 0.00 0.00 0.00 1.40
3134 3568 9.679661 TGAGTGCAGAACCTATTGAAAATATTA 57.320 29.630 0.00 0.00 0.00 0.98
3272 3706 9.051027 CGTGCAACTTATTTTACTAAACATCAG 57.949 33.333 0.00 0.00 31.75 2.90
3366 3800 3.072184 GTGGCCTATCAGTTGATGAGGAT 59.928 47.826 3.32 0.00 42.53 3.24
3489 3923 6.045106 TCCCTTGGGTTCTAAGTTTACTCATT 59.955 38.462 5.51 0.00 0.00 2.57
3567 4001 0.038310 CCTCCCCAGGTTTTGAGGAC 59.962 60.000 5.90 0.00 45.93 3.85
3621 4055 4.262036 CCTGCTGCATCATTTTATCATGCT 60.262 41.667 1.31 0.00 42.91 3.79
3645 4079 9.299963 GCTGCTGAAGATTGTCTATATATAGTG 57.700 37.037 17.44 0.00 0.00 2.74
3735 4169 6.070824 TCACTGGCTACTGAGATTTCATACAA 60.071 38.462 0.00 0.00 31.68 2.41
3783 4241 6.256975 GGTGGTTGGTGTCAATTAAAGTTTTC 59.743 38.462 0.00 0.00 35.10 2.29
3811 4269 4.826733 TGTTCCTTTGTCTTGTACATGCAT 59.173 37.500 0.00 0.00 38.10 3.96
3928 4413 2.037251 TGGAAGAAGGTTTCTGGAGACG 59.963 50.000 0.00 0.00 40.59 4.18
3949 4434 7.042335 AGACGGTTTATCCAGTCTTCAATAAG 58.958 38.462 0.00 0.00 42.62 1.73
3961 4446 5.707764 AGTCTTCAATAAGAAAGGAAGTGGC 59.292 40.000 0.00 0.00 43.30 5.01
3962 4447 5.473504 GTCTTCAATAAGAAAGGAAGTGGCA 59.526 40.000 0.00 0.00 43.30 4.92
4049 4534 5.914635 GCTTCAAACATTCAAGATTTCGACA 59.085 36.000 0.00 0.00 0.00 4.35
4081 4566 2.369532 AGTGTTTCCATGGCATTTGCTT 59.630 40.909 6.96 0.00 41.70 3.91
4116 4601 7.526142 AGGACGATTTATTAGTAGCAGATCA 57.474 36.000 0.00 0.00 0.00 2.92
4153 4638 6.380414 TCTATTCATCTCCTCCATCTTGTCT 58.620 40.000 0.00 0.00 0.00 3.41
4218 4704 3.760684 GCTTCAGTTGGATGGTTTCATCT 59.239 43.478 6.37 0.00 46.70 2.90
4266 4752 2.119457 GTTTTGCACTGTTGTAGCTGC 58.881 47.619 0.00 0.00 35.42 5.25
4344 4830 8.231692 TCAGGTTCAGTTTGATTTTGACATTA 57.768 30.769 0.00 0.00 0.00 1.90
4390 4902 0.546122 ACCTAATTGCATGCGGGAGA 59.454 50.000 14.09 0.00 0.00 3.71
4401 4913 2.889617 CGGGAGATACGTGCACCA 59.110 61.111 12.15 0.00 0.00 4.17
4538 5051 6.479990 TCTTCCATCAATGTCATTCGATGTAC 59.520 38.462 22.59 0.00 34.70 2.90
4585 5098 5.037015 TGTTATTGTTTCGGCATACACAC 57.963 39.130 0.00 0.00 0.00 3.82
4593 5106 1.619332 TCGGCATACACACAAGTACCA 59.381 47.619 0.00 0.00 0.00 3.25
4629 5142 3.614870 GCTGGCTTTACTTTGGGACATTG 60.615 47.826 0.00 0.00 39.30 2.82
4638 5151 3.320826 ACTTTGGGACATTGCAAACCTAC 59.679 43.478 1.71 0.00 39.30 3.18
5059 5572 2.217510 AGAGTCAGACCGTACCACAT 57.782 50.000 0.00 0.00 0.00 3.21
5137 5650 5.163141 TGACTTGGATACCAAAGAAACCTCA 60.163 40.000 4.78 0.00 43.44 3.86
5650 6187 2.290577 ACCTCTGCTTTCCACATTCCTC 60.291 50.000 0.00 0.00 0.00 3.71
5703 6240 6.375736 TGATTTTGAGTTGACAACACAGGTTA 59.624 34.615 20.08 2.75 34.87 2.85
5735 6272 2.159099 TGTCGAATCCTGTAGTGCATCC 60.159 50.000 0.00 0.00 0.00 3.51
6053 6590 2.367567 AGGTAAAGCACTTCTTGTCCGA 59.632 45.455 0.00 0.00 35.18 4.55
6057 6594 2.839486 AGCACTTCTTGTCCGATTCA 57.161 45.000 0.00 0.00 0.00 2.57
6335 6872 2.665000 CTGGGACATGCGAGGTGT 59.335 61.111 0.00 0.00 38.20 4.16
6492 7171 2.851104 CGAACGAAAGCGGACCAC 59.149 61.111 0.00 0.00 43.17 4.16
6587 7266 1.469308 GACGGAGAATCACAGAGACGT 59.531 52.381 0.00 0.00 36.25 4.34
6692 7371 1.448540 CCATCAGCACCGAGTCCAC 60.449 63.158 0.00 0.00 0.00 4.02
6728 7407 5.008118 GCATCACTTTAGAGTAGCCATTTCC 59.992 44.000 0.00 0.00 33.90 3.13
6929 7609 5.505173 AGCGAGGATTAATGAAACATTGG 57.495 39.130 7.16 0.00 0.00 3.16
6958 7638 2.025793 TGTCTGAGAATCGAGGAGGTCT 60.026 50.000 0.00 0.00 38.61 3.85
7042 7723 5.612725 AAGACACATGGGTTGTTTGATTT 57.387 34.783 0.00 0.00 36.00 2.17
7152 7833 3.005367 TCCGAAATGGAGGCAAAAGTTTC 59.995 43.478 0.00 0.00 43.74 2.78
7205 7886 4.142790 TGCCCAGTTAATTACGGAAAACA 58.857 39.130 0.00 0.00 0.00 2.83
7229 7910 5.420739 AGGGCGAAAACCAATACAAATACAT 59.579 36.000 0.00 0.00 0.00 2.29
7296 7977 6.071334 ACGATCGATCCAATAGACATAACCAT 60.071 38.462 24.34 0.00 0.00 3.55
7297 7979 6.254373 CGATCGATCCAATAGACATAACCATG 59.746 42.308 19.51 0.00 38.21 3.66
7339 8021 7.607250 TCACACTTTTAAAACACAATGGAACT 58.393 30.769 0.00 0.00 0.00 3.01
7378 8061 0.828022 TGAAGACAACGGACACCACT 59.172 50.000 0.00 0.00 0.00 4.00
7443 8126 2.510918 GACGCCTTTCCTACGGCC 60.511 66.667 0.00 0.00 43.38 6.13
7490 8173 5.652994 AGAGCTTTTTCTACAGTCTCGAT 57.347 39.130 0.00 0.00 0.00 3.59
7504 8187 1.265635 TCTCGATTTTTGCCCGTTGTG 59.734 47.619 0.00 0.00 0.00 3.33
7520 8203 1.966451 GTGGCCTTGTTCGTCAGGG 60.966 63.158 3.32 7.02 44.80 4.45
7612 8295 2.928757 CGTGAAGAGAGCCTCAGAATTG 59.071 50.000 0.00 0.00 32.06 2.32
7619 8303 2.373169 AGAGCCTCAGAATTGGTTGTCA 59.627 45.455 0.00 0.00 0.00 3.58
7654 8338 2.054021 TCAACCTCATCACCCACAGAA 58.946 47.619 0.00 0.00 0.00 3.02
7655 8339 2.038952 TCAACCTCATCACCCACAGAAG 59.961 50.000 0.00 0.00 0.00 2.85
7706 8390 1.732259 CCTTCATGACGCCAGTAACAC 59.268 52.381 0.00 0.00 0.00 3.32
7713 8397 0.602905 ACGCCAGTAACACTCTTGCC 60.603 55.000 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 4.640771 TGAGTGGAAAGGCTTGTTCTAT 57.359 40.909 0.00 0.00 0.00 1.98
60 71 3.399330 CTTCGCTTAGGTTGAGTGGAAA 58.601 45.455 0.00 0.00 0.00 3.13
100 111 7.921734 GCTTAGAAATGAGCTTGCATGATTGC 61.922 42.308 3.33 0.00 41.23 3.56
142 153 4.963628 TGGTTTTAGGTAGGCCAAAGTTTT 59.036 37.500 5.01 0.00 37.19 2.43
154 165 3.967467 TGGGTTGGTTGGTTTTAGGTA 57.033 42.857 0.00 0.00 0.00 3.08
299 367 6.792473 TCCCTCCTTCCAATAATATAAGAGCA 59.208 38.462 0.00 0.00 0.00 4.26
300 368 7.037945 ACTCCCTCCTTCCAATAATATAAGAGC 60.038 40.741 0.00 0.00 0.00 4.09
336 404 9.421399 CATATGAACCTTTATTTTTAGACCCCT 57.579 33.333 0.00 0.00 0.00 4.79
373 441 8.875803 ACAGTTTTAAATATGAAATGCATGCTG 58.124 29.630 20.33 4.32 37.87 4.41
374 442 9.439500 AACAGTTTTAAATATGAAATGCATGCT 57.561 25.926 20.33 0.00 37.87 3.79
375 443 9.693157 GAACAGTTTTAAATATGAAATGCATGC 57.307 29.630 11.82 11.82 37.87 4.06
433 501 6.260050 ACACGTGAACAACTCTTATCAAATGT 59.740 34.615 25.01 0.00 0.00 2.71
444 512 2.198406 TGTAGCACACGTGAACAACTC 58.802 47.619 25.01 6.75 0.00 3.01
454 522 5.927030 AGTTGACAAATATTGTAGCACACG 58.073 37.500 0.00 0.00 45.52 4.49
590 692 1.388547 ACTTCTGCGCACCTTTTTCA 58.611 45.000 5.66 0.00 0.00 2.69
601 703 1.714899 CCGGCCCAATAACTTCTGCG 61.715 60.000 0.00 0.00 0.00 5.18
602 704 2.004808 GCCGGCCCAATAACTTCTGC 62.005 60.000 18.11 0.00 0.00 4.26
627 729 1.103803 GACAGGTCAGATGCCTACGA 58.896 55.000 0.00 0.00 34.45 3.43
638 740 2.741092 GGCGAACAGGACAGGTCA 59.259 61.111 1.41 0.00 0.00 4.02
640 742 2.710724 GAACGGCGAACAGGACAGGT 62.711 60.000 16.62 0.00 0.00 4.00
643 746 2.029964 GGAACGGCGAACAGGACA 59.970 61.111 16.62 0.00 0.00 4.02
793 900 2.584391 GCAAGGGGAGGACGACTGT 61.584 63.158 0.00 0.00 0.00 3.55
815 922 4.798682 ACGGGAGGTAGGGGCTGG 62.799 72.222 0.00 0.00 0.00 4.85
822 929 2.280823 GACGGCTGAACGGGAGGTAG 62.281 65.000 0.00 0.00 38.39 3.18
823 930 2.283388 ACGGCTGAACGGGAGGTA 60.283 61.111 0.00 0.00 38.39 3.08
825 932 4.452733 GGACGGCTGAACGGGAGG 62.453 72.222 0.00 0.00 38.39 4.30
827 934 1.607178 TTAGGACGGCTGAACGGGA 60.607 57.895 0.00 0.00 38.39 5.14
894 1303 3.443925 CTGCTCGTGCTCGGAGGA 61.444 66.667 11.19 0.00 40.48 3.71
919 1328 5.684030 GCTCTCCGGTAGAAATGGACAATAA 60.684 44.000 0.00 0.00 32.46 1.40
921 1330 3.432326 GCTCTCCGGTAGAAATGGACAAT 60.432 47.826 0.00 0.00 32.46 2.71
939 1348 2.752238 CGTCCCACTCGGAGCTCT 60.752 66.667 14.64 0.00 43.19 4.09
944 1353 0.824595 TTCAGAACGTCCCACTCGGA 60.825 55.000 0.00 0.00 38.83 4.55
958 1367 2.571653 CAGTGGGGTTCAGGTATTCAGA 59.428 50.000 0.00 0.00 0.00 3.27
1153 1562 3.849951 GATGGAAGAGCCGGCCGA 61.850 66.667 30.73 4.97 40.66 5.54
1215 1642 2.787249 GTCGTAGTCGTAGCCGCA 59.213 61.111 0.00 0.00 38.33 5.69
1222 1649 2.105466 GGGCTCTCGTCGTAGTCGT 61.105 63.158 0.00 0.00 40.43 4.34
1260 1687 7.596995 CGCTCTTATATTTCTTTACAGAGGGAG 59.403 40.741 4.76 0.00 40.49 4.30
1261 1688 7.069578 ACGCTCTTATATTTCTTTACAGAGGGA 59.930 37.037 14.96 0.00 40.49 4.20
1262 1689 7.210873 ACGCTCTTATATTTCTTTACAGAGGG 58.789 38.462 8.36 8.36 42.53 4.30
1263 1690 8.649973 AACGCTCTTATATTTCTTTACAGAGG 57.350 34.615 0.00 0.00 0.00 3.69
1275 1702 9.694137 GGTTAGTGATCTAAACGCTCTTATATT 57.306 33.333 0.00 0.00 37.81 1.28
1276 1703 9.080097 AGGTTAGTGATCTAAACGCTCTTATAT 57.920 33.333 0.00 0.00 45.47 0.86
1277 1704 8.461249 AGGTTAGTGATCTAAACGCTCTTATA 57.539 34.615 0.00 0.00 45.47 0.98
1278 1705 7.285858 AGAGGTTAGTGATCTAAACGCTCTTAT 59.714 37.037 4.07 0.00 45.87 1.73
1279 1706 6.602406 AGAGGTTAGTGATCTAAACGCTCTTA 59.398 38.462 4.07 0.00 45.87 2.10
1280 1707 5.419471 AGAGGTTAGTGATCTAAACGCTCTT 59.581 40.000 4.07 0.00 45.87 2.85
1281 1708 4.951094 AGAGGTTAGTGATCTAAACGCTCT 59.049 41.667 4.07 13.76 45.87 4.09
1282 1709 5.251601 AGAGGTTAGTGATCTAAACGCTC 57.748 43.478 4.07 5.40 45.87 5.03
1284 1711 5.251601 AGAGAGGTTAGTGATCTAAACGC 57.748 43.478 0.00 0.00 45.47 4.84
1285 1712 7.556733 ACTAGAGAGGTTAGTGATCTAAACG 57.443 40.000 0.00 0.00 45.47 3.60
1286 1713 9.575783 CAAACTAGAGAGGTTAGTGATCTAAAC 57.424 37.037 0.00 0.00 42.37 2.01
1287 1714 8.251721 GCAAACTAGAGAGGTTAGTGATCTAAA 58.748 37.037 0.00 0.00 37.81 1.85
1288 1715 7.616150 AGCAAACTAGAGAGGTTAGTGATCTAA 59.384 37.037 0.00 0.00 28.82 2.10
1289 1716 7.120051 AGCAAACTAGAGAGGTTAGTGATCTA 58.880 38.462 0.00 0.00 28.82 1.98
1290 1717 5.955355 AGCAAACTAGAGAGGTTAGTGATCT 59.045 40.000 0.00 0.00 28.82 2.75
1291 1718 6.096282 AGAGCAAACTAGAGAGGTTAGTGATC 59.904 42.308 0.00 0.00 28.82 2.92
1292 1719 5.955355 AGAGCAAACTAGAGAGGTTAGTGAT 59.045 40.000 0.00 0.00 28.82 3.06
1293 1720 5.326069 AGAGCAAACTAGAGAGGTTAGTGA 58.674 41.667 0.00 0.00 28.82 3.41
1294 1721 5.652994 AGAGCAAACTAGAGAGGTTAGTG 57.347 43.478 0.00 0.00 28.82 2.74
1295 1722 6.127563 GCTAAGAGCAAACTAGAGAGGTTAGT 60.128 42.308 0.00 0.00 41.89 2.24
1296 1723 6.270064 GCTAAGAGCAAACTAGAGAGGTTAG 58.730 44.000 0.00 0.00 41.89 2.34
1297 1724 5.127356 GGCTAAGAGCAAACTAGAGAGGTTA 59.873 44.000 0.00 0.00 44.75 2.85
1298 1725 4.081365 GGCTAAGAGCAAACTAGAGAGGTT 60.081 45.833 0.00 0.00 44.75 3.50
1299 1726 3.449377 GGCTAAGAGCAAACTAGAGAGGT 59.551 47.826 0.00 0.00 44.75 3.85
1327 1754 1.134189 AGGGCGGCTTTGTTAGGATAC 60.134 52.381 9.56 0.00 0.00 2.24
1329 1756 0.107165 GAGGGCGGCTTTGTTAGGAT 60.107 55.000 9.56 0.00 0.00 3.24
1378 1805 2.743928 CTCACTTGAGGCGGTGGC 60.744 66.667 0.00 0.00 38.48 5.01
1379 1806 1.079543 CTCTCACTTGAGGCGGTGG 60.080 63.158 6.40 0.00 42.30 4.61
1380 1807 0.888619 TACTCTCACTTGAGGCGGTG 59.111 55.000 6.40 0.00 42.30 4.94
1381 1808 0.889306 GTACTCTCACTTGAGGCGGT 59.111 55.000 6.40 6.16 42.30 5.68
1382 1809 0.888619 TGTACTCTCACTTGAGGCGG 59.111 55.000 6.40 0.91 42.30 6.13
1383 1810 1.402984 GGTGTACTCTCACTTGAGGCG 60.403 57.143 6.40 1.42 42.30 5.52
1384 1811 1.066787 GGGTGTACTCTCACTTGAGGC 60.067 57.143 6.40 0.00 42.30 4.70
1385 1812 2.028930 GTGGGTGTACTCTCACTTGAGG 60.029 54.545 18.52 0.56 42.30 3.86
1386 1813 2.028930 GGTGGGTGTACTCTCACTTGAG 60.029 54.545 23.31 0.00 43.36 3.02
1387 1814 1.968493 GGTGGGTGTACTCTCACTTGA 59.032 52.381 23.31 0.00 38.28 3.02
1388 1815 1.971357 AGGTGGGTGTACTCTCACTTG 59.029 52.381 23.31 0.00 38.28 3.16
1446 1873 3.317149 TGATATTACCTTCGAGTGTCCCG 59.683 47.826 0.00 0.00 0.00 5.14
1476 1903 3.551890 CAGTATGCTACGACTTGCGATTT 59.448 43.478 0.00 0.00 44.57 2.17
1673 2100 9.569167 TGTTGTTGTTGTTGATTACGAAATTTA 57.431 25.926 0.00 0.00 0.00 1.40
1674 2101 8.467402 TGTTGTTGTTGTTGATTACGAAATTT 57.533 26.923 0.00 0.00 0.00 1.82
1675 2102 8.376942 GTTGTTGTTGTTGTTGATTACGAAATT 58.623 29.630 0.00 0.00 0.00 1.82
1676 2103 7.542477 TGTTGTTGTTGTTGTTGATTACGAAAT 59.458 29.630 0.00 0.00 0.00 2.17
1677 2104 6.861572 TGTTGTTGTTGTTGTTGATTACGAAA 59.138 30.769 0.00 0.00 0.00 3.46
1678 2105 6.379386 TGTTGTTGTTGTTGTTGATTACGAA 58.621 32.000 0.00 0.00 0.00 3.85
1679 2106 5.939457 TGTTGTTGTTGTTGTTGATTACGA 58.061 33.333 0.00 0.00 0.00 3.43
1680 2107 6.618770 TTGTTGTTGTTGTTGTTGATTACG 57.381 33.333 0.00 0.00 0.00 3.18
1681 2108 6.953189 GCTTTGTTGTTGTTGTTGTTGATTAC 59.047 34.615 0.00 0.00 0.00 1.89
1682 2109 6.091441 GGCTTTGTTGTTGTTGTTGTTGATTA 59.909 34.615 0.00 0.00 0.00 1.75
1683 2110 5.106752 GGCTTTGTTGTTGTTGTTGTTGATT 60.107 36.000 0.00 0.00 0.00 2.57
1684 2111 4.391523 GGCTTTGTTGTTGTTGTTGTTGAT 59.608 37.500 0.00 0.00 0.00 2.57
1685 2112 3.743396 GGCTTTGTTGTTGTTGTTGTTGA 59.257 39.130 0.00 0.00 0.00 3.18
1686 2113 3.745458 AGGCTTTGTTGTTGTTGTTGTTG 59.255 39.130 0.00 0.00 0.00 3.33
1687 2114 4.001618 AGGCTTTGTTGTTGTTGTTGTT 57.998 36.364 0.00 0.00 0.00 2.83
1688 2115 3.676291 AGGCTTTGTTGTTGTTGTTGT 57.324 38.095 0.00 0.00 0.00 3.32
1689 2116 5.637387 ACTAAAGGCTTTGTTGTTGTTGTTG 59.363 36.000 22.32 0.00 0.00 3.33
1690 2117 5.789521 ACTAAAGGCTTTGTTGTTGTTGTT 58.210 33.333 22.32 0.00 0.00 2.83
1691 2118 5.400066 ACTAAAGGCTTTGTTGTTGTTGT 57.600 34.783 22.32 0.00 0.00 3.32
1692 2119 4.803613 GGACTAAAGGCTTTGTTGTTGTTG 59.196 41.667 22.32 0.00 0.00 3.33
1693 2120 4.142026 GGGACTAAAGGCTTTGTTGTTGTT 60.142 41.667 22.32 0.00 0.00 2.83
1694 2121 3.383505 GGGACTAAAGGCTTTGTTGTTGT 59.616 43.478 22.32 10.58 0.00 3.32
1695 2122 3.383185 TGGGACTAAAGGCTTTGTTGTTG 59.617 43.478 22.32 7.79 0.00 3.33
1696 2123 3.637769 TGGGACTAAAGGCTTTGTTGTT 58.362 40.909 22.32 1.84 0.00 2.83
1697 2124 3.306472 TGGGACTAAAGGCTTTGTTGT 57.694 42.857 22.32 16.69 0.00 3.32
1698 2125 3.552890 GCTTGGGACTAAAGGCTTTGTTG 60.553 47.826 22.32 13.85 0.00 3.33
1699 2126 2.628178 GCTTGGGACTAAAGGCTTTGTT 59.372 45.455 22.32 8.73 0.00 2.83
1700 2127 2.239400 GCTTGGGACTAAAGGCTTTGT 58.761 47.619 22.32 16.86 0.00 2.83
1701 2128 2.238521 TGCTTGGGACTAAAGGCTTTG 58.761 47.619 22.32 13.97 0.00 2.77
1702 2129 2.675658 TGCTTGGGACTAAAGGCTTT 57.324 45.000 17.76 17.76 0.00 3.51
1703 2130 2.158460 ACTTGCTTGGGACTAAAGGCTT 60.158 45.455 0.00 0.00 0.00 4.35
1704 2131 1.425448 ACTTGCTTGGGACTAAAGGCT 59.575 47.619 0.00 0.00 0.00 4.58
1705 2132 1.911057 ACTTGCTTGGGACTAAAGGC 58.089 50.000 0.00 0.00 0.00 4.35
1706 2133 2.558359 CCAACTTGCTTGGGACTAAAGG 59.442 50.000 0.00 0.00 45.46 3.11
1707 2134 3.923017 CCAACTTGCTTGGGACTAAAG 57.077 47.619 0.00 0.00 45.46 1.85
1716 2143 0.539438 TGCCTACCCCAACTTGCTTG 60.539 55.000 0.00 0.00 0.00 4.01
1717 2144 0.187361 TTGCCTACCCCAACTTGCTT 59.813 50.000 0.00 0.00 0.00 3.91
1718 2145 0.409484 ATTGCCTACCCCAACTTGCT 59.591 50.000 0.00 0.00 0.00 3.91
1719 2146 2.137810 TATTGCCTACCCCAACTTGC 57.862 50.000 0.00 0.00 0.00 4.01
1720 2147 5.675684 AATTTATTGCCTACCCCAACTTG 57.324 39.130 0.00 0.00 0.00 3.16
1721 2148 5.105513 CGAAATTTATTGCCTACCCCAACTT 60.106 40.000 0.00 0.00 0.00 2.66
1722 2149 4.401202 CGAAATTTATTGCCTACCCCAACT 59.599 41.667 0.00 0.00 0.00 3.16
1723 2150 4.158949 ACGAAATTTATTGCCTACCCCAAC 59.841 41.667 0.00 0.00 0.00 3.77
1724 2151 4.345854 ACGAAATTTATTGCCTACCCCAA 58.654 39.130 0.00 0.00 0.00 4.12
1725 2152 3.970842 ACGAAATTTATTGCCTACCCCA 58.029 40.909 0.00 0.00 0.00 4.96
1726 2153 6.443792 CATTACGAAATTTATTGCCTACCCC 58.556 40.000 0.00 0.00 0.00 4.95
1727 2154 5.918576 GCATTACGAAATTTATTGCCTACCC 59.081 40.000 0.00 0.00 0.00 3.69
1728 2155 6.735130 AGCATTACGAAATTTATTGCCTACC 58.265 36.000 0.00 0.00 0.00 3.18
1729 2156 7.913297 TCAAGCATTACGAAATTTATTGCCTAC 59.087 33.333 0.00 0.00 0.00 3.18
1730 2157 7.990917 TCAAGCATTACGAAATTTATTGCCTA 58.009 30.769 0.00 0.00 0.00 3.93
1731 2158 6.862209 TCAAGCATTACGAAATTTATTGCCT 58.138 32.000 0.00 0.00 0.00 4.75
1732 2159 7.434897 TCATCAAGCATTACGAAATTTATTGCC 59.565 33.333 0.00 0.00 0.00 4.52
1733 2160 8.338985 TCATCAAGCATTACGAAATTTATTGC 57.661 30.769 0.00 0.00 0.00 3.56
1819 2246 8.939201 TGTCACACAAATGTAATGAACAAATT 57.061 26.923 2.30 0.00 42.70 1.82
1928 2355 6.652481 TCCATGTCATCTTTCAGAAGAAGTTC 59.348 38.462 0.00 0.00 44.61 3.01
2071 2501 4.321452 CCTGCATCACAACAGTTAAGCAAT 60.321 41.667 0.00 0.00 31.76 3.56
2130 2560 7.951591 TCCTTCTTGATTAAAGGTTTTCCAAG 58.048 34.615 0.00 0.00 42.28 3.61
2205 2635 5.772825 TCTAAAAGCAGCTGAATGTTTGT 57.227 34.783 20.43 0.80 0.00 2.83
2230 2660 9.606631 AACTACCTCTGATGAAGATATTTCAAC 57.393 33.333 4.99 3.88 33.29 3.18
2280 2710 7.153985 AGAGAAATTTGAGACTTCTGTCAGAG 58.846 38.462 2.12 0.64 45.20 3.35
2337 2767 6.396450 TGCATAGCAAAAACATTTAGATGCA 58.604 32.000 0.00 0.00 43.43 3.96
2437 2867 5.409826 GTCTTTGTCTGACAACAAGATAGGG 59.590 44.000 21.95 5.40 37.90 3.53
2593 3023 3.942748 TGAAATACCGGTACTTGCATTCC 59.057 43.478 18.55 0.00 0.00 3.01
2598 3028 5.107065 GCATATCTGAAATACCGGTACTTGC 60.107 44.000 18.55 7.20 0.00 4.01
2620 3054 7.365028 GGACCATCTCAATGTATATCCATAGCA 60.365 40.741 0.00 0.00 0.00 3.49
2691 3125 4.454161 CCCATTGTATCAAGTCGTGTTTCA 59.546 41.667 0.00 0.00 0.00 2.69
2699 3133 7.141363 GCATTGTATTCCCATTGTATCAAGTC 58.859 38.462 0.00 0.00 0.00 3.01
2704 3138 6.366877 GCATTGCATTGTATTCCCATTGTATC 59.633 38.462 10.11 0.00 0.00 2.24
2732 3166 4.354071 TTGACACATATTCCATTGTGCG 57.646 40.909 3.13 0.00 45.59 5.34
2827 3261 4.232221 CAAGCACCATTTGTCATCTGAAC 58.768 43.478 0.00 0.00 0.00 3.18
3131 3565 5.511545 GCCACGGAACTCCTGATTCTATAAT 60.512 44.000 0.00 0.00 0.00 1.28
3134 3568 2.103263 GCCACGGAACTCCTGATTCTAT 59.897 50.000 0.00 0.00 0.00 1.98
3272 3706 0.463620 TTCTGGTTGGGCTGCAAAAC 59.536 50.000 0.50 5.06 0.00 2.43
3340 3774 0.253044 TCAACTGATAGGCCACCTGC 59.747 55.000 5.01 0.00 34.61 4.85
3366 3800 5.427378 TCAGAGATAAAAATGCGATCACCA 58.573 37.500 0.00 0.00 0.00 4.17
3489 3923 1.198713 TTTGCAGGCCTTCAAACCAA 58.801 45.000 24.30 4.83 0.00 3.67
3567 4001 3.057315 ACTTGGCAGATTCAAATTCACCG 60.057 43.478 0.00 0.00 0.00 4.94
3621 4055 9.533831 TCCACTATATATAGACAATCTTCAGCA 57.466 33.333 23.70 0.00 34.50 4.41
3645 4079 7.499232 CCATTATGGATAATTACCTCCGAATCC 59.501 40.741 5.05 0.00 40.96 3.01
3783 4241 2.301346 ACAAGACAAAGGAACAGCAGG 58.699 47.619 0.00 0.00 0.00 4.85
3928 4413 8.678199 CCTTTCTTATTGAAGACTGGATAAACC 58.322 37.037 0.00 0.00 41.52 3.27
3949 4434 2.290577 ACTCCAGATGCCACTTCCTTTC 60.291 50.000 0.00 0.00 0.00 2.62
3961 4446 7.664731 AGCTTATCAATAATCCAACTCCAGATG 59.335 37.037 0.00 0.00 0.00 2.90
3962 4447 7.753630 AGCTTATCAATAATCCAACTCCAGAT 58.246 34.615 0.00 0.00 0.00 2.90
4081 4566 9.603921 ACTAATAAATCGTCCTCGGAAATTTTA 57.396 29.630 10.86 5.79 37.69 1.52
4116 4601 4.904251 AGATGAATAGAGGCACATACCTGT 59.096 41.667 0.00 0.00 41.32 4.00
4292 4778 3.693085 CAGGTTGAGCTGTGCAGATTTAT 59.307 43.478 3.02 0.00 0.00 1.40
4390 4902 2.436646 GCAGCCTGGTGCACGTAT 60.437 61.111 15.83 0.00 43.41 3.06
4561 5074 4.757657 TGTGTATGCCGAAACAATAACAGT 59.242 37.500 0.00 0.00 0.00 3.55
4585 5098 2.813754 CACAGTTGACCCATGGTACTTG 59.186 50.000 11.73 4.00 35.25 3.16
4593 5106 1.075482 CCAGCCACAGTTGACCCAT 59.925 57.895 0.00 0.00 0.00 4.00
4629 5142 2.488153 CCAAACAGCTAGGTAGGTTTGC 59.512 50.000 22.81 0.00 45.26 3.68
4638 5151 3.350833 AGAAGATTGCCAAACAGCTAGG 58.649 45.455 0.00 0.00 0.00 3.02
4803 5316 4.002906 ACCTTCGCATCACTTTAACTCA 57.997 40.909 0.00 0.00 0.00 3.41
5294 5807 5.084519 AGGAATAATGAATCCATGCAGCAT 58.915 37.500 0.52 0.52 38.23 3.79
5650 6187 2.263077 CTGAAGGCACAGCTAGTTACG 58.737 52.381 0.00 0.00 0.00 3.18
5735 6272 4.614555 TTTGGAGCTTATGTATTGTGCG 57.385 40.909 0.00 0.00 0.00 5.34
6053 6590 7.604549 TCACAATGCATAAAGATGTTGTGAAT 58.395 30.769 20.23 0.00 46.03 2.57
6057 6594 8.836268 AAATTCACAATGCATAAAGATGTTGT 57.164 26.923 0.00 0.00 34.33 3.32
6335 6872 7.661847 GTCTTGTTTTAAGAGAGGGAAGAATCA 59.338 37.037 0.00 0.00 0.00 2.57
6492 7171 0.318441 TCACTGCTTTCTGGTCCTCG 59.682 55.000 0.00 0.00 0.00 4.63
6587 7266 4.282957 GCTTCATGATGACTAGATCCCTCA 59.717 45.833 12.54 0.00 0.00 3.86
6692 7371 3.713858 AAGTGATGCTGATCTCGAGAG 57.286 47.619 21.52 8.54 0.00 3.20
6828 7507 2.827921 GACTGCCTGAAATGGGTTGAAT 59.172 45.455 0.00 0.00 0.00 2.57
6929 7609 5.529430 TCCTCGATTCTCAGACAAGTATCTC 59.471 44.000 0.00 0.00 0.00 2.75
7131 7812 3.317150 GAAACTTTTGCCTCCATTTCGG 58.683 45.455 0.00 0.00 0.00 4.30
7152 7833 8.830580 TCTTCTTCTTAATTAATTGATGAGGCG 58.169 33.333 11.05 2.67 0.00 5.52
7205 7886 4.767928 TGTATTTGTATTGGTTTTCGCCCT 59.232 37.500 0.00 0.00 0.00 5.19
7229 7910 3.378911 TTGTGAGTAGTTCGCATGTGA 57.621 42.857 4.45 4.45 45.20 3.58
7296 7977 3.696548 TGTGAGTGTTTGTTATTGTGCCA 59.303 39.130 0.00 0.00 0.00 4.92
7297 7979 4.041723 GTGTGAGTGTTTGTTATTGTGCC 58.958 43.478 0.00 0.00 0.00 5.01
7304 7986 9.182933 GTGTTTTAAAAGTGTGAGTGTTTGTTA 57.817 29.630 0.00 0.00 0.00 2.41
7312 7994 7.164230 TCCATTGTGTTTTAAAAGTGTGAGT 57.836 32.000 0.00 0.00 0.00 3.41
7339 8021 0.391597 GTCGAGTGTTCCTGTTGGGA 59.608 55.000 0.00 0.00 43.41 4.37
7378 8061 0.323633 TGTCTTCGACCGTCCCCATA 60.324 55.000 0.00 0.00 0.00 2.74
7406 8089 1.643868 CGCCGCTGCTTAAATGGACA 61.644 55.000 0.00 0.00 34.43 4.02
7407 8090 1.062525 CGCCGCTGCTTAAATGGAC 59.937 57.895 0.00 0.00 34.43 4.02
7443 8126 1.098050 GCATAGGCAAGAAGTGTGGG 58.902 55.000 0.00 0.00 40.72 4.61
7479 8162 2.289195 ACGGGCAAAAATCGAGACTGTA 60.289 45.455 0.00 0.00 0.00 2.74
7482 8165 1.535462 CAACGGGCAAAAATCGAGACT 59.465 47.619 0.00 0.00 0.00 3.24
7483 8166 1.265905 ACAACGGGCAAAAATCGAGAC 59.734 47.619 0.00 0.00 0.00 3.36
7504 8187 1.966451 CACCCTGACGAACAAGGCC 60.966 63.158 0.00 0.00 33.64 5.19
7520 8203 1.730547 GCACGGTGATTGCTTGCAC 60.731 57.895 13.29 0.00 37.00 4.57
7612 8295 2.939460 AAGCAAGTGTGTTGACAACC 57.061 45.000 15.59 7.71 32.49 3.77
7619 8303 4.887071 TGAGGTTGATAAAGCAAGTGTGTT 59.113 37.500 0.00 0.00 0.00 3.32
7654 8338 0.178953 AGAACATTGGGCAAGTGGCT 60.179 50.000 4.74 0.00 44.01 4.75
7655 8339 0.681175 AAGAACATTGGGCAAGTGGC 59.319 50.000 0.00 0.00 43.74 5.01


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

AutoCloner maintained by Alex Coulton.