Multiple sequence alignment - TraesCS7A01G511300

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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 TraesCS7A01G511300 chr7A 100.000 6680 0 0 1 6680 698848082 698854761 0.000000e+00 12336
1 TraesCS7A01G511300 chr7A 98.202 4839 72 5 1854 6680 698762899 698767734 0.000000e+00 8440
2 TraesCS7A01G511300 chr7A 98.198 3940 56 6 2754 6680 699020776 699024713 0.000000e+00 6868
3 TraesCS7A01G511300 chr7A 97.028 1548 42 4 3 1549 699018090 699019634 0.000000e+00 2601
4 TraesCS7A01G511300 chr7A 95.767 1559 52 5 3 1549 698761345 698762901 0.000000e+00 2501
5 TraesCS7A01G511300 chr7A 96.916 908 23 1 1854 2756 699019632 699020539 0.000000e+00 1517
6 TraesCS7A01G511300 chr7D 93.014 4838 269 17 1854 6680 606700437 606705216 0.000000e+00 6998
7 TraesCS7A01G511300 chr7D 91.494 917 30 17 523 1417 606699461 606700351 0.000000e+00 1218
8 TraesCS7A01G511300 chr7D 90.571 700 45 7 867 1549 607505527 607504832 0.000000e+00 907
9 TraesCS7A01G511300 chr7D 89.119 386 38 2 1854 2239 607504834 607504453 1.690000e-130 477
10 TraesCS7A01G511300 chr7D 85.013 387 34 6 6161 6547 141230795 141230433 8.180000e-99 372
11 TraesCS7A01G511300 chrUn 94.040 4564 245 14 2138 6680 92707977 92703420 0.000000e+00 6896
12 TraesCS7A01G511300 chrUn 91.108 4195 321 26 1986 6156 33119432 33123598 0.000000e+00 5633
13 TraesCS7A01G511300 chrUn 88.809 831 45 15 747 1549 33118267 33119077 0.000000e+00 976
14 TraesCS7A01G511300 chrUn 87.500 656 34 15 544 1177 92708681 92708052 0.000000e+00 713
15 TraesCS7A01G511300 chrUn 91.220 205 12 6 514 714 33118064 33118266 2.370000e-69 274
16 TraesCS7A01G511300 chr7B 92.983 4646 282 18 2073 6680 691022456 691027095 0.000000e+00 6734
17 TraesCS7A01G511300 chr7B 87.125 1033 72 24 544 1550 690915321 690916318 0.000000e+00 1114
18 TraesCS7A01G511300 chr7B 94.035 637 32 1 913 1549 691021726 691022356 0.000000e+00 961
19 TraesCS7A01G511300 chr7B 88.440 718 68 8 2774 3478 690916685 690917400 0.000000e+00 852
20 TraesCS7A01G511300 chr7B 88.215 577 26 12 544 1103 690948788 690949339 0.000000e+00 651
21 TraesCS7A01G511300 chr7B 90.972 432 37 2 6250 6680 650132142 650131712 1.250000e-161 580
22 TraesCS7A01G511300 chr7B 94.574 258 13 1 1854 2111 691022354 691022610 1.350000e-106 398
23 TraesCS7A01G511300 chr3B 90.392 4340 358 27 1854 6165 760055274 760050966 0.000000e+00 5650
24 TraesCS7A01G511300 chr3B 88.916 830 47 17 747 1549 760056083 760055272 0.000000e+00 981
25 TraesCS7A01G511300 chr3B 87.500 520 46 7 6161 6680 436511338 436511838 3.470000e-162 582
26 TraesCS7A01G511300 chr3B 90.575 435 40 1 6247 6680 661541451 661541885 5.810000e-160 575
27 TraesCS7A01G511300 chr3B 95.820 311 13 0 1545 1855 416957977 416957667 2.780000e-138 503
28 TraesCS7A01G511300 chr3B 92.308 195 10 4 523 714 760056276 760056084 8.540000e-69 272
29 TraesCS7A01G511300 chr3A 90.675 3957 323 25 1986 5916 704694756 704690820 0.000000e+00 5221
30 TraesCS7A01G511300 chr3A 90.397 3957 334 22 1986 5916 704780520 704776584 0.000000e+00 5160
31 TraesCS7A01G511300 chr3A 89.889 3956 335 28 1986 5916 704840576 704836661 0.000000e+00 5029
32 TraesCS7A01G511300 chr3A 90.955 3372 280 15 2803 6156 704578363 704581727 0.000000e+00 4514
33 TraesCS7A01G511300 chr3A 87.299 1055 60 27 523 1549 704570859 704571867 0.000000e+00 1138
34 TraesCS7A01G511300 chr3A 89.638 801 47 14 770 1549 704695905 704695120 0.000000e+00 987
35 TraesCS7A01G511300 chr3A 88.889 828 44 14 747 1549 704781801 704780997 0.000000e+00 976
36 TraesCS7A01G511300 chr3A 88.527 828 47 17 747 1549 704841745 704840941 0.000000e+00 959
37 TraesCS7A01G511300 chr3A 94.408 304 16 1 1552 1854 16171761 16171458 3.650000e-127 466
38 TraesCS7A01G511300 chr3A 87.335 379 39 2 1854 2223 704571865 704572243 6.190000e-115 425
39 TraesCS7A01G511300 chr3A 91.282 195 14 3 523 714 704696114 704695920 5.140000e-66 263
40 TraesCS7A01G511300 chr4D 90.577 520 45 4 3 521 294458237 294458753 0.000000e+00 686
41 TraesCS7A01G511300 chr4D 88.973 526 50 8 3 525 62472544 62473064 1.570000e-180 643
42 TraesCS7A01G511300 chr2D 90.057 523 44 8 3 523 628952466 628951950 0.000000e+00 671
43 TraesCS7A01G511300 chr2D 89.313 524 49 6 3 523 641228940 641229459 0.000000e+00 651
44 TraesCS7A01G511300 chr3D 89.866 523 46 7 3 523 596987775 596987258 0.000000e+00 665
45 TraesCS7A01G511300 chr6D 89.293 523 51 5 3 523 54567706 54567187 0.000000e+00 651
46 TraesCS7A01G511300 chr1D 88.783 526 52 7 3 526 272332655 272332135 7.310000e-179 638
47 TraesCS7A01G511300 chr2A 88.100 521 55 6 6161 6680 694758322 694758836 4.430000e-171 612
48 TraesCS7A01G511300 chr2A 97.368 304 8 0 1552 1855 92423267 92423570 9.930000e-143 518
49 TraesCS7A01G511300 chr2B 90.972 432 38 1 6250 6680 592808066 592807635 1.250000e-161 580
50 TraesCS7A01G511300 chr5A 97.030 303 9 0 1552 1854 126694878 126694576 1.660000e-140 510
51 TraesCS7A01G511300 chr5A 97.030 303 9 0 1552 1854 643331135 643331437 1.660000e-140 510
52 TraesCS7A01G511300 chr5A 86.506 415 38 12 6162 6576 546150526 546150130 2.210000e-119 440
53 TraesCS7A01G511300 chr4B 96.141 311 11 1 1546 1855 433962042 433962352 2.150000e-139 507
54 TraesCS7A01G511300 chr4A 96.700 303 10 0 1552 1854 538933073 538932771 7.730000e-139 505
55 TraesCS7A01G511300 chr1A 95.364 302 13 1 1552 1852 66338662 66338963 4.690000e-131 479
56 TraesCS7A01G511300 chr1A 93.651 315 17 3 1544 1856 432622539 432622226 1.010000e-127 468


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 TraesCS7A01G511300 chr7A 698848082 698854761 6679 False 12336.000000 12336 100.000000 1 6680 1 chr7A.!!$F1 6679
1 TraesCS7A01G511300 chr7A 698761345 698767734 6389 False 5470.500000 8440 96.984500 3 6680 2 chr7A.!!$F2 6677
2 TraesCS7A01G511300 chr7A 699018090 699024713 6623 False 3662.000000 6868 97.380667 3 6680 3 chr7A.!!$F3 6677
3 TraesCS7A01G511300 chr7D 606699461 606705216 5755 False 4108.000000 6998 92.254000 523 6680 2 chr7D.!!$F1 6157
4 TraesCS7A01G511300 chr7D 607504453 607505527 1074 True 692.000000 907 89.845000 867 2239 2 chr7D.!!$R2 1372
5 TraesCS7A01G511300 chrUn 92703420 92708681 5261 True 3804.500000 6896 90.770000 544 6680 2 chrUn.!!$R1 6136
6 TraesCS7A01G511300 chrUn 33118064 33123598 5534 False 2294.333333 5633 90.379000 514 6156 3 chrUn.!!$F1 5642
7 TraesCS7A01G511300 chr7B 691021726 691027095 5369 False 2697.666667 6734 93.864000 913 6680 3 chr7B.!!$F3 5767
8 TraesCS7A01G511300 chr7B 690915321 690917400 2079 False 983.000000 1114 87.782500 544 3478 2 chr7B.!!$F2 2934
9 TraesCS7A01G511300 chr7B 690948788 690949339 551 False 651.000000 651 88.215000 544 1103 1 chr7B.!!$F1 559
10 TraesCS7A01G511300 chr3B 760050966 760056276 5310 True 2301.000000 5650 90.538667 523 6165 3 chr3B.!!$R2 5642
11 TraesCS7A01G511300 chr3B 436511338 436511838 500 False 582.000000 582 87.500000 6161 6680 1 chr3B.!!$F1 519
12 TraesCS7A01G511300 chr3A 704578363 704581727 3364 False 4514.000000 4514 90.955000 2803 6156 1 chr3A.!!$F1 3353
13 TraesCS7A01G511300 chr3A 704776584 704781801 5217 True 3068.000000 5160 89.643000 747 5916 2 chr3A.!!$R3 5169
14 TraesCS7A01G511300 chr3A 704836661 704841745 5084 True 2994.000000 5029 89.208000 747 5916 2 chr3A.!!$R4 5169
15 TraesCS7A01G511300 chr3A 704690820 704696114 5294 True 2157.000000 5221 90.531667 523 5916 3 chr3A.!!$R2 5393
16 TraesCS7A01G511300 chr3A 704570859 704572243 1384 False 781.500000 1138 87.317000 523 2223 2 chr3A.!!$F2 1700
17 TraesCS7A01G511300 chr4D 294458237 294458753 516 False 686.000000 686 90.577000 3 521 1 chr4D.!!$F2 518
18 TraesCS7A01G511300 chr4D 62472544 62473064 520 False 643.000000 643 88.973000 3 525 1 chr4D.!!$F1 522
19 TraesCS7A01G511300 chr2D 628951950 628952466 516 True 671.000000 671 90.057000 3 523 1 chr2D.!!$R1 520
20 TraesCS7A01G511300 chr2D 641228940 641229459 519 False 651.000000 651 89.313000 3 523 1 chr2D.!!$F1 520
21 TraesCS7A01G511300 chr3D 596987258 596987775 517 True 665.000000 665 89.866000 3 523 1 chr3D.!!$R1 520
22 TraesCS7A01G511300 chr6D 54567187 54567706 519 True 651.000000 651 89.293000 3 523 1 chr6D.!!$R1 520
23 TraesCS7A01G511300 chr1D 272332135 272332655 520 True 638.000000 638 88.783000 3 526 1 chr1D.!!$R1 523
24 TraesCS7A01G511300 chr2A 694758322 694758836 514 False 612.000000 612 88.100000 6161 6680 1 chr2A.!!$F2 519

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
253 269 0.109964 TTAGCATTGTTTCGCCACGC 60.110 50.000 0.00 0.00 0.00 5.34 F
346 362 1.439693 CGCGGCAAAAACGATTCGT 60.440 52.632 5.75 5.75 43.97 3.85 F
1329 1400 2.126618 GTCATCACCGACGTGCGA 60.127 61.111 0.00 0.00 44.57 5.10 F
1748 1870 0.037046 CTTTGCTTTCCCCATGCCAC 60.037 55.000 0.00 0.00 0.00 5.01 F
1752 1874 0.176449 GCTTTCCCCATGCCACAATC 59.824 55.000 0.00 0.00 0.00 2.67 F
1791 1913 0.260816 AGGGATGCAATGGACATGCT 59.739 50.000 0.00 0.00 44.14 3.79 F
1852 1974 1.485066 TCCTACGAATCAAAGAGGCCC 59.515 52.381 0.00 0.00 0.00 5.80 F
1853 1975 1.486726 CCTACGAATCAAAGAGGCCCT 59.513 52.381 0.00 0.00 0.00 5.19 F
5388 6783 1.421268 TGCTTCACACCCTTCAGACAT 59.579 47.619 0.00 0.00 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1729 1851 0.037046 GTGGCATGGGGAAAGCAAAG 60.037 55.000 0.00 0.0 0.00 2.77 R
1733 1855 0.176449 GATTGTGGCATGGGGAAAGC 59.824 55.000 0.00 0.0 0.00 3.51 R
3224 4598 1.270826 CCGTCCAGTGCTCGATGATAT 59.729 52.381 6.73 0.0 0.00 1.63 R
3661 5044 2.202566 GGTCAAAGTGCCTATAGACGC 58.797 52.381 0.00 0.0 0.00 5.19 R
3850 5234 7.160049 TGAACATGTTGCCATATGTTTTTGAT 58.840 30.769 17.58 0.0 44.88 2.57 R
3895 5279 1.667236 TCGCTGATGTGGCTTATTGG 58.333 50.000 0.00 0.0 0.00 3.16 R
4264 5649 2.656560 ACCTGTAGATGACTCGCAAC 57.343 50.000 0.00 0.0 0.00 4.17 R
5459 6854 7.665559 TCATTAAGAGGTTGCTGATTAAGTGTT 59.334 33.333 0.00 0.0 0.00 3.32 R
6366 7768 0.979665 TGGACTCTCCTTGGCTTCAG 59.020 55.000 0.00 0.0 37.46 3.02 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
25 26 3.522731 CTGGAGACGGCGAGAGGG 61.523 72.222 16.62 0.00 0.00 4.30
56 61 2.654877 GGAGAAAGGTGGCGTCGA 59.345 61.111 0.00 0.00 0.00 4.20
243 259 1.508088 GCGGCAGCTTTAGCATTGT 59.492 52.632 0.00 0.00 45.16 2.71
253 269 0.109964 TTAGCATTGTTTCGCCACGC 60.110 50.000 0.00 0.00 0.00 5.34
275 291 1.994507 AACGAGGCGATGAGGACGAG 61.995 60.000 0.00 0.00 0.00 4.18
346 362 1.439693 CGCGGCAAAAACGATTCGT 60.440 52.632 5.75 5.75 43.97 3.85
756 786 2.680352 TCTGGAGTCTGGACCGCC 60.680 66.667 0.00 0.89 0.00 6.13
1329 1400 2.126618 GTCATCACCGACGTGCGA 60.127 61.111 0.00 0.00 44.57 5.10
1374 1445 2.790791 CCTCGAGCTCATCCGCCTT 61.791 63.158 15.40 0.00 0.00 4.35
1436 1514 5.990996 TCAATCCAAAGTCCAATTTTTGAGC 59.009 36.000 2.56 0.00 36.61 4.26
1550 1672 3.057245 GCAGCGTGTGAGATCCTATATGA 60.057 47.826 0.00 0.00 0.00 2.15
1551 1673 4.731720 CAGCGTGTGAGATCCTATATGAG 58.268 47.826 0.00 0.00 0.00 2.90
1552 1674 4.217334 CAGCGTGTGAGATCCTATATGAGT 59.783 45.833 0.00 0.00 0.00 3.41
1553 1675 4.457603 AGCGTGTGAGATCCTATATGAGTC 59.542 45.833 0.00 0.00 0.00 3.36
1554 1676 4.457603 GCGTGTGAGATCCTATATGAGTCT 59.542 45.833 0.00 0.00 0.00 3.24
1555 1677 5.391523 GCGTGTGAGATCCTATATGAGTCTC 60.392 48.000 0.00 0.00 36.67 3.36
1556 1678 5.937540 CGTGTGAGATCCTATATGAGTCTCT 59.062 44.000 0.65 1.47 36.98 3.10
1557 1679 6.429692 CGTGTGAGATCCTATATGAGTCTCTT 59.570 42.308 0.65 0.00 36.98 2.85
1558 1680 7.040755 CGTGTGAGATCCTATATGAGTCTCTTT 60.041 40.741 0.65 0.00 36.98 2.52
1559 1681 8.081633 GTGTGAGATCCTATATGAGTCTCTTTG 58.918 40.741 0.65 0.00 36.98 2.77
1560 1682 8.001292 TGTGAGATCCTATATGAGTCTCTTTGA 58.999 37.037 0.65 0.00 36.98 2.69
1561 1683 9.023962 GTGAGATCCTATATGAGTCTCTTTGAT 57.976 37.037 0.65 0.00 36.98 2.57
1562 1684 9.599056 TGAGATCCTATATGAGTCTCTTTGATT 57.401 33.333 0.65 0.00 36.98 2.57
1564 1686 9.599056 AGATCCTATATGAGTCTCTTTGATTCA 57.401 33.333 0.65 0.00 43.83 2.57
1596 1718 9.989296 TCTTTATAGGATTTTTGAAGGATTGGA 57.011 29.630 0.00 0.00 0.00 3.53
1626 1748 5.190992 GGAATTTTTCCTACGTTGGTTGT 57.809 39.130 15.74 0.00 46.57 3.32
1627 1749 5.593968 GGAATTTTTCCTACGTTGGTTGTT 58.406 37.500 15.74 5.49 46.57 2.83
1628 1750 6.044046 GGAATTTTTCCTACGTTGGTTGTTT 58.956 36.000 15.74 5.09 46.57 2.83
1629 1751 6.019398 GGAATTTTTCCTACGTTGGTTGTTTG 60.019 38.462 15.74 0.00 46.57 2.93
1630 1752 5.640189 TTTTTCCTACGTTGGTTGTTTGA 57.360 34.783 15.74 0.00 0.00 2.69
1631 1753 5.838531 TTTTCCTACGTTGGTTGTTTGAT 57.161 34.783 15.74 0.00 0.00 2.57
1632 1754 5.838531 TTTCCTACGTTGGTTGTTTGATT 57.161 34.783 15.74 0.00 0.00 2.57
1633 1755 5.427036 TTCCTACGTTGGTTGTTTGATTC 57.573 39.130 15.74 0.00 0.00 2.52
1634 1756 3.495377 TCCTACGTTGGTTGTTTGATTCG 59.505 43.478 15.74 0.00 0.00 3.34
1635 1757 3.249080 CCTACGTTGGTTGTTTGATTCGT 59.751 43.478 7.97 0.00 0.00 3.85
1636 1758 4.448395 CCTACGTTGGTTGTTTGATTCGTA 59.552 41.667 7.97 0.00 0.00 3.43
1637 1759 4.461992 ACGTTGGTTGTTTGATTCGTAG 57.538 40.909 0.00 0.00 0.00 3.51
1638 1760 3.249080 ACGTTGGTTGTTTGATTCGTAGG 59.751 43.478 0.00 0.00 0.00 3.18
1639 1761 3.495377 CGTTGGTTGTTTGATTCGTAGGA 59.505 43.478 0.00 0.00 0.00 2.94
1640 1762 4.153475 CGTTGGTTGTTTGATTCGTAGGAT 59.847 41.667 0.00 0.00 0.00 3.24
1641 1763 5.334569 CGTTGGTTGTTTGATTCGTAGGATT 60.335 40.000 0.00 0.00 0.00 3.01
1642 1764 6.128499 CGTTGGTTGTTTGATTCGTAGGATTA 60.128 38.462 0.00 0.00 0.00 1.75
1643 1765 7.571613 CGTTGGTTGTTTGATTCGTAGGATTAA 60.572 37.037 0.00 0.00 0.00 1.40
1644 1766 7.747155 TGGTTGTTTGATTCGTAGGATTAAA 57.253 32.000 0.00 0.00 0.00 1.52
1645 1767 8.343168 TGGTTGTTTGATTCGTAGGATTAAAT 57.657 30.769 0.00 0.00 0.00 1.40
1646 1768 8.455682 TGGTTGTTTGATTCGTAGGATTAAATC 58.544 33.333 0.00 0.00 0.00 2.17
1647 1769 8.674607 GGTTGTTTGATTCGTAGGATTAAATCT 58.325 33.333 0.00 0.00 0.00 2.40
1650 1772 9.226606 TGTTTGATTCGTAGGATTAAATCTTGT 57.773 29.630 0.00 0.00 0.00 3.16
1653 1775 9.542462 TTGATTCGTAGGATTAAATCTTGTAGG 57.458 33.333 0.00 0.00 0.00 3.18
1654 1776 8.920174 TGATTCGTAGGATTAAATCTTGTAGGA 58.080 33.333 0.00 0.00 0.00 2.94
1655 1777 9.930693 GATTCGTAGGATTAAATCTTGTAGGAT 57.069 33.333 0.00 0.00 0.00 3.24
1706 1828 8.421249 AAATTTCACAGGAATTCTAACATCCA 57.579 30.769 5.23 0.00 35.62 3.41
1707 1829 6.817765 TTTCACAGGAATTCTAACATCCAC 57.182 37.500 5.23 0.00 35.62 4.02
1708 1830 5.762179 TCACAGGAATTCTAACATCCACT 57.238 39.130 5.23 0.00 35.62 4.00
1709 1831 5.734720 TCACAGGAATTCTAACATCCACTC 58.265 41.667 5.23 0.00 35.62 3.51
1710 1832 4.878397 CACAGGAATTCTAACATCCACTCC 59.122 45.833 5.23 0.00 35.62 3.85
1711 1833 4.536090 ACAGGAATTCTAACATCCACTCCA 59.464 41.667 5.23 0.00 35.62 3.86
1712 1834 5.014123 ACAGGAATTCTAACATCCACTCCAA 59.986 40.000 5.23 0.00 35.62 3.53
1713 1835 5.355350 CAGGAATTCTAACATCCACTCCAAC 59.645 44.000 5.23 0.00 35.62 3.77
1714 1836 4.640647 GGAATTCTAACATCCACTCCAACC 59.359 45.833 5.23 0.00 33.30 3.77
1715 1837 5.501156 GAATTCTAACATCCACTCCAACCT 58.499 41.667 0.00 0.00 0.00 3.50
1716 1838 4.553330 TTCTAACATCCACTCCAACCTC 57.447 45.455 0.00 0.00 0.00 3.85
1717 1839 3.791320 TCTAACATCCACTCCAACCTCT 58.209 45.455 0.00 0.00 0.00 3.69
1718 1840 4.168101 TCTAACATCCACTCCAACCTCTT 58.832 43.478 0.00 0.00 0.00 2.85
1719 1841 2.867109 ACATCCACTCCAACCTCTTG 57.133 50.000 0.00 0.00 0.00 3.02
1740 1862 4.193826 GGAAGAAATCCTTTGCTTTCCC 57.806 45.455 0.00 0.00 45.56 3.97
1741 1863 3.055819 GGAAGAAATCCTTTGCTTTCCCC 60.056 47.826 0.00 0.00 45.56 4.81
1742 1864 3.258722 AGAAATCCTTTGCTTTCCCCA 57.741 42.857 0.00 0.00 32.90 4.96
1743 1865 3.794911 AGAAATCCTTTGCTTTCCCCAT 58.205 40.909 0.00 0.00 32.90 4.00
1744 1866 3.516700 AGAAATCCTTTGCTTTCCCCATG 59.483 43.478 0.00 0.00 32.90 3.66
1745 1867 1.197812 ATCCTTTGCTTTCCCCATGC 58.802 50.000 0.00 0.00 0.00 4.06
1746 1868 0.904394 TCCTTTGCTTTCCCCATGCC 60.904 55.000 0.00 0.00 0.00 4.40
1747 1869 1.193462 CCTTTGCTTTCCCCATGCCA 61.193 55.000 0.00 0.00 0.00 4.92
1748 1870 0.037046 CTTTGCTTTCCCCATGCCAC 60.037 55.000 0.00 0.00 0.00 5.01
1749 1871 0.762082 TTTGCTTTCCCCATGCCACA 60.762 50.000 0.00 0.00 0.00 4.17
1750 1872 0.762082 TTGCTTTCCCCATGCCACAA 60.762 50.000 0.00 0.00 0.00 3.33
1751 1873 0.544833 TGCTTTCCCCATGCCACAAT 60.545 50.000 0.00 0.00 0.00 2.71
1752 1874 0.176449 GCTTTCCCCATGCCACAATC 59.824 55.000 0.00 0.00 0.00 2.67
1753 1875 1.559368 CTTTCCCCATGCCACAATCA 58.441 50.000 0.00 0.00 0.00 2.57
1754 1876 1.901159 CTTTCCCCATGCCACAATCAA 59.099 47.619 0.00 0.00 0.00 2.57
1755 1877 2.021262 TTCCCCATGCCACAATCAAA 57.979 45.000 0.00 0.00 0.00 2.69
1756 1878 1.265236 TCCCCATGCCACAATCAAAC 58.735 50.000 0.00 0.00 0.00 2.93
1757 1879 0.975135 CCCCATGCCACAATCAAACA 59.025 50.000 0.00 0.00 0.00 2.83
1758 1880 1.347050 CCCCATGCCACAATCAAACAA 59.653 47.619 0.00 0.00 0.00 2.83
1759 1881 2.224475 CCCCATGCCACAATCAAACAAA 60.224 45.455 0.00 0.00 0.00 2.83
1760 1882 2.807392 CCCATGCCACAATCAAACAAAC 59.193 45.455 0.00 0.00 0.00 2.93
1761 1883 3.494749 CCCATGCCACAATCAAACAAACT 60.495 43.478 0.00 0.00 0.00 2.66
1762 1884 3.742369 CCATGCCACAATCAAACAAACTC 59.258 43.478 0.00 0.00 0.00 3.01
1763 1885 4.370049 CATGCCACAATCAAACAAACTCA 58.630 39.130 0.00 0.00 0.00 3.41
1764 1886 4.462508 TGCCACAATCAAACAAACTCAA 57.537 36.364 0.00 0.00 0.00 3.02
1765 1887 4.825422 TGCCACAATCAAACAAACTCAAA 58.175 34.783 0.00 0.00 0.00 2.69
1766 1888 5.426504 TGCCACAATCAAACAAACTCAAAT 58.573 33.333 0.00 0.00 0.00 2.32
1767 1889 6.577103 TGCCACAATCAAACAAACTCAAATA 58.423 32.000 0.00 0.00 0.00 1.40
1768 1890 6.478344 TGCCACAATCAAACAAACTCAAATAC 59.522 34.615 0.00 0.00 0.00 1.89
1769 1891 6.478344 GCCACAATCAAACAAACTCAAATACA 59.522 34.615 0.00 0.00 0.00 2.29
1770 1892 7.010923 GCCACAATCAAACAAACTCAAATACAA 59.989 33.333 0.00 0.00 0.00 2.41
1771 1893 9.044150 CCACAATCAAACAAACTCAAATACAAT 57.956 29.630 0.00 0.00 0.00 2.71
1775 1897 9.927668 AATCAAACAAACTCAAATACAATAGGG 57.072 29.630 0.00 0.00 0.00 3.53
1776 1898 8.698973 TCAAACAAACTCAAATACAATAGGGA 57.301 30.769 0.00 0.00 0.00 4.20
1777 1899 9.308000 TCAAACAAACTCAAATACAATAGGGAT 57.692 29.630 0.00 0.00 0.00 3.85
1778 1900 9.357652 CAAACAAACTCAAATACAATAGGGATG 57.642 33.333 0.00 0.00 0.00 3.51
1779 1901 7.100458 ACAAACTCAAATACAATAGGGATGC 57.900 36.000 0.00 0.00 0.00 3.91
1780 1902 6.663093 ACAAACTCAAATACAATAGGGATGCA 59.337 34.615 0.00 0.00 0.00 3.96
1781 1903 7.178274 ACAAACTCAAATACAATAGGGATGCAA 59.822 33.333 0.00 0.00 0.00 4.08
1782 1904 7.902920 AACTCAAATACAATAGGGATGCAAT 57.097 32.000 0.00 0.00 0.00 3.56
1783 1905 7.281040 ACTCAAATACAATAGGGATGCAATG 57.719 36.000 0.00 0.00 0.00 2.82
1784 1906 6.266103 ACTCAAATACAATAGGGATGCAATGG 59.734 38.462 0.00 0.00 0.00 3.16
1785 1907 6.372104 TCAAATACAATAGGGATGCAATGGA 58.628 36.000 0.00 0.00 0.00 3.41
1786 1908 6.265196 TCAAATACAATAGGGATGCAATGGAC 59.735 38.462 0.00 0.00 0.00 4.02
1787 1909 3.668141 ACAATAGGGATGCAATGGACA 57.332 42.857 0.00 0.00 0.00 4.02
1788 1910 4.188937 ACAATAGGGATGCAATGGACAT 57.811 40.909 0.00 0.00 0.00 3.06
1789 1911 3.893200 ACAATAGGGATGCAATGGACATG 59.107 43.478 0.00 0.00 0.00 3.21
1790 1912 1.985473 TAGGGATGCAATGGACATGC 58.015 50.000 0.00 0.00 44.08 4.06
1791 1913 0.260816 AGGGATGCAATGGACATGCT 59.739 50.000 0.00 0.00 44.14 3.79
1792 1914 1.496001 AGGGATGCAATGGACATGCTA 59.504 47.619 0.00 0.00 44.14 3.49
1793 1915 2.109480 AGGGATGCAATGGACATGCTAT 59.891 45.455 0.00 0.00 44.14 2.97
1794 1916 2.895404 GGGATGCAATGGACATGCTATT 59.105 45.455 0.00 0.00 44.14 1.73
1795 1917 3.322828 GGGATGCAATGGACATGCTATTT 59.677 43.478 0.00 0.00 44.14 1.40
1796 1918 4.553323 GGATGCAATGGACATGCTATTTC 58.447 43.478 0.00 0.00 44.14 2.17
1797 1919 4.038282 GGATGCAATGGACATGCTATTTCA 59.962 41.667 0.00 0.00 44.14 2.69
1798 1920 5.452216 GGATGCAATGGACATGCTATTTCAA 60.452 40.000 0.00 0.00 44.14 2.69
1799 1921 5.601583 TGCAATGGACATGCTATTTCAAT 57.398 34.783 0.00 0.00 44.14 2.57
1800 1922 5.593968 TGCAATGGACATGCTATTTCAATC 58.406 37.500 0.00 0.00 44.14 2.67
1801 1923 4.986659 GCAATGGACATGCTATTTCAATCC 59.013 41.667 0.00 0.00 40.64 3.01
1802 1924 5.221382 GCAATGGACATGCTATTTCAATCCT 60.221 40.000 0.00 0.00 40.64 3.24
1803 1925 6.016024 GCAATGGACATGCTATTTCAATCCTA 60.016 38.462 0.00 0.00 40.64 2.94
1804 1926 7.365741 CAATGGACATGCTATTTCAATCCTAC 58.634 38.462 0.00 0.00 0.00 3.18
1805 1927 5.056480 TGGACATGCTATTTCAATCCTACG 58.944 41.667 0.00 0.00 0.00 3.51
1806 1928 5.057149 GGACATGCTATTTCAATCCTACGT 58.943 41.667 0.00 0.00 0.00 3.57
1807 1929 5.527582 GGACATGCTATTTCAATCCTACGTT 59.472 40.000 0.00 0.00 0.00 3.99
1808 1930 6.038271 GGACATGCTATTTCAATCCTACGTTT 59.962 38.462 0.00 0.00 0.00 3.60
1809 1931 7.391148 ACATGCTATTTCAATCCTACGTTTT 57.609 32.000 0.00 0.00 0.00 2.43
1810 1932 7.826690 ACATGCTATTTCAATCCTACGTTTTT 58.173 30.769 0.00 0.00 0.00 1.94
1811 1933 7.968405 ACATGCTATTTCAATCCTACGTTTTTC 59.032 33.333 0.00 0.00 0.00 2.29
1812 1934 6.848451 TGCTATTTCAATCCTACGTTTTTCC 58.152 36.000 0.00 0.00 0.00 3.13
1813 1935 6.657541 TGCTATTTCAATCCTACGTTTTTCCT 59.342 34.615 0.00 0.00 0.00 3.36
1814 1936 7.825270 TGCTATTTCAATCCTACGTTTTTCCTA 59.175 33.333 0.00 0.00 0.00 2.94
1815 1937 8.837389 GCTATTTCAATCCTACGTTTTTCCTAT 58.163 33.333 0.00 0.00 0.00 2.57
1818 1940 7.619964 TTCAATCCTACGTTTTTCCTATTCC 57.380 36.000 0.00 0.00 0.00 3.01
1819 1941 6.954232 TCAATCCTACGTTTTTCCTATTCCT 58.046 36.000 0.00 0.00 0.00 3.36
1820 1942 6.821665 TCAATCCTACGTTTTTCCTATTCCTG 59.178 38.462 0.00 0.00 0.00 3.86
1821 1943 5.750352 TCCTACGTTTTTCCTATTCCTGT 57.250 39.130 0.00 0.00 0.00 4.00
1822 1944 5.484715 TCCTACGTTTTTCCTATTCCTGTG 58.515 41.667 0.00 0.00 0.00 3.66
1823 1945 5.012354 TCCTACGTTTTTCCTATTCCTGTGT 59.988 40.000 0.00 0.00 0.00 3.72
1824 1946 5.704053 CCTACGTTTTTCCTATTCCTGTGTT 59.296 40.000 0.00 0.00 0.00 3.32
1825 1947 6.206048 CCTACGTTTTTCCTATTCCTGTGTTT 59.794 38.462 0.00 0.00 0.00 2.83
1826 1948 6.459670 ACGTTTTTCCTATTCCTGTGTTTT 57.540 33.333 0.00 0.00 0.00 2.43
1827 1949 6.869695 ACGTTTTTCCTATTCCTGTGTTTTT 58.130 32.000 0.00 0.00 0.00 1.94
1828 1950 6.754675 ACGTTTTTCCTATTCCTGTGTTTTTG 59.245 34.615 0.00 0.00 0.00 2.44
1829 1951 6.292114 CGTTTTTCCTATTCCTGTGTTTTTGC 60.292 38.462 0.00 0.00 0.00 3.68
1830 1952 5.860941 TTTCCTATTCCTGTGTTTTTGCA 57.139 34.783 0.00 0.00 0.00 4.08
1831 1953 5.860941 TTCCTATTCCTGTGTTTTTGCAA 57.139 34.783 0.00 0.00 0.00 4.08
1832 1954 6.418057 TTCCTATTCCTGTGTTTTTGCAAT 57.582 33.333 0.00 0.00 0.00 3.56
1833 1955 6.024552 TCCTATTCCTGTGTTTTTGCAATC 57.975 37.500 0.00 0.00 0.00 2.67
1834 1956 5.047377 TCCTATTCCTGTGTTTTTGCAATCC 60.047 40.000 0.00 0.00 0.00 3.01
1835 1957 4.961438 ATTCCTGTGTTTTTGCAATCCT 57.039 36.364 0.00 0.00 0.00 3.24
1836 1958 6.152661 CCTATTCCTGTGTTTTTGCAATCCTA 59.847 38.462 0.00 0.00 0.00 2.94
1837 1959 4.846779 TCCTGTGTTTTTGCAATCCTAC 57.153 40.909 0.00 0.00 0.00 3.18
1838 1960 3.252215 TCCTGTGTTTTTGCAATCCTACG 59.748 43.478 0.00 0.00 0.00 3.51
1839 1961 3.252215 CCTGTGTTTTTGCAATCCTACGA 59.748 43.478 0.00 0.00 0.00 3.43
1840 1962 4.261405 CCTGTGTTTTTGCAATCCTACGAA 60.261 41.667 0.00 0.00 0.00 3.85
1841 1963 5.446143 TGTGTTTTTGCAATCCTACGAAT 57.554 34.783 0.00 0.00 0.00 3.34
1842 1964 5.457140 TGTGTTTTTGCAATCCTACGAATC 58.543 37.500 0.00 0.00 0.00 2.52
1843 1965 5.009110 TGTGTTTTTGCAATCCTACGAATCA 59.991 36.000 0.00 0.00 0.00 2.57
1844 1966 5.918011 GTGTTTTTGCAATCCTACGAATCAA 59.082 36.000 0.00 0.00 0.00 2.57
1845 1967 6.419413 GTGTTTTTGCAATCCTACGAATCAAA 59.581 34.615 0.00 0.00 0.00 2.69
1846 1968 6.640499 TGTTTTTGCAATCCTACGAATCAAAG 59.360 34.615 0.00 0.00 0.00 2.77
1847 1969 6.567687 TTTTGCAATCCTACGAATCAAAGA 57.432 33.333 0.00 0.00 0.00 2.52
1848 1970 5.801350 TTGCAATCCTACGAATCAAAGAG 57.199 39.130 0.00 0.00 0.00 2.85
1849 1971 4.191544 TGCAATCCTACGAATCAAAGAGG 58.808 43.478 0.00 0.00 0.00 3.69
1850 1972 3.002759 GCAATCCTACGAATCAAAGAGGC 59.997 47.826 0.00 0.00 0.00 4.70
1851 1973 2.981859 TCCTACGAATCAAAGAGGCC 57.018 50.000 0.00 0.00 0.00 5.19
1852 1974 1.485066 TCCTACGAATCAAAGAGGCCC 59.515 52.381 0.00 0.00 0.00 5.80
1853 1975 1.486726 CCTACGAATCAAAGAGGCCCT 59.513 52.381 0.00 0.00 0.00 5.19
1854 1976 2.698797 CCTACGAATCAAAGAGGCCCTA 59.301 50.000 0.00 0.00 0.00 3.53
1855 1977 3.325135 CCTACGAATCAAAGAGGCCCTAT 59.675 47.826 0.00 0.00 0.00 2.57
1856 1978 4.527038 CCTACGAATCAAAGAGGCCCTATA 59.473 45.833 0.00 0.00 0.00 1.31
1857 1979 5.187967 CCTACGAATCAAAGAGGCCCTATAT 59.812 44.000 0.00 0.00 0.00 0.86
1858 1980 4.899502 ACGAATCAAAGAGGCCCTATATG 58.100 43.478 0.00 0.00 0.00 1.78
2107 2483 5.631119 TCTATCTAACCATCCGTCTGATCA 58.369 41.667 0.00 0.00 0.00 2.92
2269 3351 4.142622 ACAAACATGGATAGCACGTGATTG 60.143 41.667 22.23 10.54 40.95 2.67
2430 3516 4.566759 CGATGGGCGTATTTATGGACTATG 59.433 45.833 0.00 0.00 34.64 2.23
2831 4194 7.741785 TCATTCTCCTTAAAGTTGTTACTCCA 58.258 34.615 0.00 0.00 31.99 3.86
3131 4495 5.384063 AATTACGCATGTCAATTGTCCAA 57.616 34.783 5.13 0.00 0.00 3.53
3134 4498 1.978097 CGCATGTCAATTGTCCAAACG 59.022 47.619 5.13 8.04 0.00 3.60
3446 4822 6.265649 CCTAGTATGCTAGAGAAACTTGGCTA 59.734 42.308 18.42 0.00 45.77 3.93
3850 5234 1.897423 CCAGTGCGTACCCATGAGA 59.103 57.895 0.00 0.00 0.00 3.27
3895 5279 3.895041 TCAAAGGTGGAGAAATCCCAAAC 59.105 43.478 0.00 0.00 35.12 2.93
4264 5649 4.892345 TGGATCACCTCAGTAGAGAGAATG 59.108 45.833 0.00 0.00 44.98 2.67
4581 5975 7.776107 TCGATGATCATCCATCTTATACCTTC 58.224 38.462 26.30 1.37 40.46 3.46
5204 6599 6.855763 AATGAAAAGGCACCATTCATAAGA 57.144 33.333 16.43 0.00 41.58 2.10
5388 6783 1.421268 TGCTTCACACCCTTCAGACAT 59.579 47.619 0.00 0.00 0.00 3.06
5459 6854 3.696051 GCATTGTTCCTATGCAAGAAGGA 59.304 43.478 10.82 10.82 45.93 3.36
5543 6938 9.350357 GATGATATATTTTCCAACATGCATGTC 57.650 33.333 31.45 14.87 40.80 3.06
6345 7747 1.419387 GCTTCATAGATGAGTGGGGCT 59.581 52.381 0.00 0.00 38.19 5.19
6362 7764 4.663120 TGGGGCTATATCTTTAGGCTTTCA 59.337 41.667 0.00 0.60 42.68 2.69
6366 7768 5.004448 GCTATATCTTTAGGCTTTCACCCC 58.996 45.833 0.00 0.00 0.00 4.95
6367 7769 5.221945 GCTATATCTTTAGGCTTTCACCCCT 60.222 44.000 0.00 0.00 35.22 4.79
6385 7787 0.979665 CTGAAGCCAAGGAGAGTCCA 59.020 55.000 0.00 0.00 39.61 4.02
6640 8043 0.533308 CCCCGTTGTCTTGTCCGAAA 60.533 55.000 0.00 0.00 0.00 3.46
6662 8065 3.328050 ACGGACCAAAGGAAATCTCTCTT 59.672 43.478 0.00 0.00 0.00 2.85
6666 8069 5.513962 GGACCAAAGGAAATCTCTCTTGAGT 60.514 44.000 0.00 0.00 40.98 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.227999 CGCCGTCTCCAGCTCAAAAA 61.228 55.000 0.00 0.00 0.00 1.94
1 2 1.667830 CGCCGTCTCCAGCTCAAAA 60.668 57.895 0.00 0.00 0.00 2.44
25 26 2.040359 CTCCCCCTTCCTCCCTCC 60.040 72.222 0.00 0.00 0.00 4.30
56 61 2.920645 CGCACAGAGTCTCCACCGT 61.921 63.158 0.00 0.00 0.00 4.83
90 95 1.626825 GCCTATATAAAGCCGACCCCA 59.373 52.381 0.00 0.00 0.00 4.96
253 269 1.138883 TCCTCATCGCCTCGTTTCG 59.861 57.895 0.00 0.00 0.00 3.46
275 291 4.796231 TCGCTTCTCGCCGCTTCC 62.796 66.667 0.00 0.00 38.27 3.46
332 348 1.063412 GCCGGACGAATCGTTTTTGC 61.063 55.000 10.45 7.23 41.37 3.68
513 533 5.316167 TGGACACAAATGTTAGAGCATCTT 58.684 37.500 0.00 0.00 41.02 2.40
626 652 4.600576 TGTCTGCTTGTGCCGCGA 62.601 61.111 8.23 0.00 38.71 5.87
734 764 0.973496 GGTCCAGACTCCAGAGGTCC 60.973 65.000 0.00 0.00 34.56 4.46
756 786 1.650528 AGGGAAGGAGTGGAAGTCTG 58.349 55.000 0.00 0.00 36.25 3.51
1329 1400 2.124736 CCGTCCATGTCCGGCATT 60.125 61.111 8.42 0.00 37.43 3.56
1374 1445 0.687427 TGACGGGCAGATCCATCTCA 60.687 55.000 0.00 0.00 34.22 3.27
1436 1514 7.621428 ATTGTCAGTGTTCATGGATAGAAAG 57.379 36.000 0.00 0.00 0.00 2.62
1570 1692 9.989296 TCCAATCCTTCAAAAATCCTATAAAGA 57.011 29.630 0.00 0.00 0.00 2.52
1605 1727 6.752815 TCAAACAACCAACGTAGGAAAAATTC 59.247 34.615 0.00 0.00 0.00 2.17
1606 1728 6.631962 TCAAACAACCAACGTAGGAAAAATT 58.368 32.000 0.00 0.00 0.00 1.82
1607 1729 6.210287 TCAAACAACCAACGTAGGAAAAAT 57.790 33.333 0.00 0.00 0.00 1.82
1608 1730 5.640189 TCAAACAACCAACGTAGGAAAAA 57.360 34.783 0.00 0.00 0.00 1.94
1609 1731 5.838531 ATCAAACAACCAACGTAGGAAAA 57.161 34.783 0.00 0.00 0.00 2.29
1610 1732 5.504337 CGAATCAAACAACCAACGTAGGAAA 60.504 40.000 0.00 0.00 0.00 3.13
1611 1733 4.024725 CGAATCAAACAACCAACGTAGGAA 60.025 41.667 0.00 0.00 0.00 3.36
1612 1734 3.495377 CGAATCAAACAACCAACGTAGGA 59.505 43.478 0.00 0.00 0.00 2.94
1613 1735 3.249080 ACGAATCAAACAACCAACGTAGG 59.751 43.478 0.00 0.00 0.00 3.18
1614 1736 4.461992 ACGAATCAAACAACCAACGTAG 57.538 40.909 0.00 0.00 0.00 3.51
1615 1737 4.448395 CCTACGAATCAAACAACCAACGTA 59.552 41.667 0.00 0.00 34.70 3.57
1616 1738 3.249080 CCTACGAATCAAACAACCAACGT 59.751 43.478 0.00 0.00 36.71 3.99
1617 1739 3.495377 TCCTACGAATCAAACAACCAACG 59.505 43.478 0.00 0.00 0.00 4.10
1618 1740 5.622770 ATCCTACGAATCAAACAACCAAC 57.377 39.130 0.00 0.00 0.00 3.77
1619 1741 7.747155 TTAATCCTACGAATCAAACAACCAA 57.253 32.000 0.00 0.00 0.00 3.67
1620 1742 7.747155 TTTAATCCTACGAATCAAACAACCA 57.253 32.000 0.00 0.00 0.00 3.67
1621 1743 8.674607 AGATTTAATCCTACGAATCAAACAACC 58.325 33.333 0.78 0.00 32.35 3.77
1624 1746 9.226606 ACAAGATTTAATCCTACGAATCAAACA 57.773 29.630 0.78 0.00 32.35 2.83
1627 1749 9.542462 CCTACAAGATTTAATCCTACGAATCAA 57.458 33.333 0.78 0.00 32.35 2.57
1628 1750 8.920174 TCCTACAAGATTTAATCCTACGAATCA 58.080 33.333 0.78 0.00 32.35 2.57
1629 1751 9.930693 ATCCTACAAGATTTAATCCTACGAATC 57.069 33.333 0.78 0.00 0.00 2.52
1680 1802 9.527157 TGGATGTTAGAATTCCTGTGAAATTTA 57.473 29.630 0.65 0.00 33.32 1.40
1681 1803 8.306761 GTGGATGTTAGAATTCCTGTGAAATTT 58.693 33.333 0.65 0.00 33.32 1.82
1682 1804 7.671398 AGTGGATGTTAGAATTCCTGTGAAATT 59.329 33.333 0.65 0.00 33.32 1.82
1683 1805 7.177878 AGTGGATGTTAGAATTCCTGTGAAAT 58.822 34.615 0.65 0.00 33.32 2.17
1684 1806 6.542821 AGTGGATGTTAGAATTCCTGTGAAA 58.457 36.000 0.65 0.00 33.32 2.69
1685 1807 6.126863 AGTGGATGTTAGAATTCCTGTGAA 57.873 37.500 0.65 0.00 34.33 3.18
1686 1808 5.338381 GGAGTGGATGTTAGAATTCCTGTGA 60.338 44.000 0.65 0.00 0.00 3.58
1687 1809 4.878397 GGAGTGGATGTTAGAATTCCTGTG 59.122 45.833 0.65 0.00 0.00 3.66
1688 1810 4.536090 TGGAGTGGATGTTAGAATTCCTGT 59.464 41.667 0.65 0.00 0.00 4.00
1689 1811 5.102953 TGGAGTGGATGTTAGAATTCCTG 57.897 43.478 0.65 0.00 0.00 3.86
1690 1812 5.501156 GTTGGAGTGGATGTTAGAATTCCT 58.499 41.667 0.65 0.00 0.00 3.36
1691 1813 4.640647 GGTTGGAGTGGATGTTAGAATTCC 59.359 45.833 0.65 0.00 0.00 3.01
1692 1814 5.501156 AGGTTGGAGTGGATGTTAGAATTC 58.499 41.667 0.00 0.00 0.00 2.17
1693 1815 5.251700 AGAGGTTGGAGTGGATGTTAGAATT 59.748 40.000 0.00 0.00 0.00 2.17
1694 1816 4.785376 AGAGGTTGGAGTGGATGTTAGAAT 59.215 41.667 0.00 0.00 0.00 2.40
1695 1817 4.168101 AGAGGTTGGAGTGGATGTTAGAA 58.832 43.478 0.00 0.00 0.00 2.10
1696 1818 3.791320 AGAGGTTGGAGTGGATGTTAGA 58.209 45.455 0.00 0.00 0.00 2.10
1697 1819 4.256920 CAAGAGGTTGGAGTGGATGTTAG 58.743 47.826 0.00 0.00 0.00 2.34
1698 1820 4.286297 CAAGAGGTTGGAGTGGATGTTA 57.714 45.455 0.00 0.00 0.00 2.41
1699 1821 3.146104 CAAGAGGTTGGAGTGGATGTT 57.854 47.619 0.00 0.00 0.00 2.71
1700 1822 2.867109 CAAGAGGTTGGAGTGGATGT 57.133 50.000 0.00 0.00 0.00 3.06
1709 1831 5.279156 CAAAGGATTTCTTCCAAGAGGTTGG 60.279 44.000 0.00 0.00 45.96 3.77
1719 1841 3.055819 GGGGAAAGCAAAGGATTTCTTCC 60.056 47.826 5.56 4.65 46.09 3.46
1720 1842 3.578282 TGGGGAAAGCAAAGGATTTCTTC 59.422 43.478 5.56 0.41 46.09 2.87
1721 1843 3.586429 TGGGGAAAGCAAAGGATTTCTT 58.414 40.909 5.56 0.00 46.09 2.52
1722 1844 3.258722 TGGGGAAAGCAAAGGATTTCT 57.741 42.857 5.56 0.00 46.09 2.52
1723 1845 3.865446 CATGGGGAAAGCAAAGGATTTC 58.135 45.455 0.00 0.00 46.11 2.17
1724 1846 2.026915 GCATGGGGAAAGCAAAGGATTT 60.027 45.455 0.00 0.00 40.26 2.17
1725 1847 1.556451 GCATGGGGAAAGCAAAGGATT 59.444 47.619 0.00 0.00 0.00 3.01
1726 1848 1.197812 GCATGGGGAAAGCAAAGGAT 58.802 50.000 0.00 0.00 0.00 3.24
1727 1849 0.904394 GGCATGGGGAAAGCAAAGGA 60.904 55.000 0.00 0.00 0.00 3.36
1728 1850 1.193462 TGGCATGGGGAAAGCAAAGG 61.193 55.000 0.00 0.00 0.00 3.11
1729 1851 0.037046 GTGGCATGGGGAAAGCAAAG 60.037 55.000 0.00 0.00 0.00 2.77
1730 1852 0.762082 TGTGGCATGGGGAAAGCAAA 60.762 50.000 0.00 0.00 0.00 3.68
1731 1853 0.762082 TTGTGGCATGGGGAAAGCAA 60.762 50.000 0.00 0.00 0.00 3.91
1732 1854 0.544833 ATTGTGGCATGGGGAAAGCA 60.545 50.000 0.00 0.00 0.00 3.91
1733 1855 0.176449 GATTGTGGCATGGGGAAAGC 59.824 55.000 0.00 0.00 0.00 3.51
1734 1856 1.559368 TGATTGTGGCATGGGGAAAG 58.441 50.000 0.00 0.00 0.00 2.62
1735 1857 2.021262 TTGATTGTGGCATGGGGAAA 57.979 45.000 0.00 0.00 0.00 3.13
1736 1858 1.622811 GTTTGATTGTGGCATGGGGAA 59.377 47.619 0.00 0.00 0.00 3.97
1737 1859 1.265236 GTTTGATTGTGGCATGGGGA 58.735 50.000 0.00 0.00 0.00 4.81
1738 1860 0.975135 TGTTTGATTGTGGCATGGGG 59.025 50.000 0.00 0.00 0.00 4.96
1739 1861 2.807392 GTTTGTTTGATTGTGGCATGGG 59.193 45.455 0.00 0.00 0.00 4.00
1740 1862 3.731089 AGTTTGTTTGATTGTGGCATGG 58.269 40.909 0.00 0.00 0.00 3.66
1741 1863 4.370049 TGAGTTTGTTTGATTGTGGCATG 58.630 39.130 0.00 0.00 0.00 4.06
1742 1864 4.669206 TGAGTTTGTTTGATTGTGGCAT 57.331 36.364 0.00 0.00 0.00 4.40
1743 1865 4.462508 TTGAGTTTGTTTGATTGTGGCA 57.537 36.364 0.00 0.00 0.00 4.92
1744 1866 5.989551 ATTTGAGTTTGTTTGATTGTGGC 57.010 34.783 0.00 0.00 0.00 5.01
1745 1867 8.417780 TTGTATTTGAGTTTGTTTGATTGTGG 57.582 30.769 0.00 0.00 0.00 4.17
1749 1871 9.927668 CCCTATTGTATTTGAGTTTGTTTGATT 57.072 29.630 0.00 0.00 0.00 2.57
1750 1872 9.308000 TCCCTATTGTATTTGAGTTTGTTTGAT 57.692 29.630 0.00 0.00 0.00 2.57
1751 1873 8.698973 TCCCTATTGTATTTGAGTTTGTTTGA 57.301 30.769 0.00 0.00 0.00 2.69
1752 1874 9.357652 CATCCCTATTGTATTTGAGTTTGTTTG 57.642 33.333 0.00 0.00 0.00 2.93
1753 1875 8.034804 GCATCCCTATTGTATTTGAGTTTGTTT 58.965 33.333 0.00 0.00 0.00 2.83
1754 1876 7.178274 TGCATCCCTATTGTATTTGAGTTTGTT 59.822 33.333 0.00 0.00 0.00 2.83
1755 1877 6.663093 TGCATCCCTATTGTATTTGAGTTTGT 59.337 34.615 0.00 0.00 0.00 2.83
1756 1878 7.099266 TGCATCCCTATTGTATTTGAGTTTG 57.901 36.000 0.00 0.00 0.00 2.93
1757 1879 7.716799 TTGCATCCCTATTGTATTTGAGTTT 57.283 32.000 0.00 0.00 0.00 2.66
1758 1880 7.201938 CCATTGCATCCCTATTGTATTTGAGTT 60.202 37.037 0.00 0.00 0.00 3.01
1759 1881 6.266103 CCATTGCATCCCTATTGTATTTGAGT 59.734 38.462 0.00 0.00 0.00 3.41
1760 1882 6.491062 TCCATTGCATCCCTATTGTATTTGAG 59.509 38.462 0.00 0.00 0.00 3.02
1761 1883 6.265196 GTCCATTGCATCCCTATTGTATTTGA 59.735 38.462 0.00 0.00 0.00 2.69
1762 1884 6.040729 TGTCCATTGCATCCCTATTGTATTTG 59.959 38.462 0.00 0.00 0.00 2.32
1763 1885 6.135454 TGTCCATTGCATCCCTATTGTATTT 58.865 36.000 0.00 0.00 0.00 1.40
1764 1886 5.704354 TGTCCATTGCATCCCTATTGTATT 58.296 37.500 0.00 0.00 0.00 1.89
1765 1887 5.323382 TGTCCATTGCATCCCTATTGTAT 57.677 39.130 0.00 0.00 0.00 2.29
1766 1888 4.787135 TGTCCATTGCATCCCTATTGTA 57.213 40.909 0.00 0.00 0.00 2.41
1767 1889 3.668141 TGTCCATTGCATCCCTATTGT 57.332 42.857 0.00 0.00 0.00 2.71
1768 1890 3.305813 GCATGTCCATTGCATCCCTATTG 60.306 47.826 0.00 0.00 0.00 1.90
1769 1891 2.895404 GCATGTCCATTGCATCCCTATT 59.105 45.455 0.00 0.00 0.00 1.73
1770 1892 2.109480 AGCATGTCCATTGCATCCCTAT 59.891 45.455 0.00 0.00 0.00 2.57
1771 1893 1.496001 AGCATGTCCATTGCATCCCTA 59.504 47.619 0.00 0.00 0.00 3.53
1772 1894 0.260816 AGCATGTCCATTGCATCCCT 59.739 50.000 0.00 0.00 0.00 4.20
1773 1895 1.985473 TAGCATGTCCATTGCATCCC 58.015 50.000 0.00 0.00 0.00 3.85
1774 1896 4.038282 TGAAATAGCATGTCCATTGCATCC 59.962 41.667 0.00 0.00 0.00 3.51
1775 1897 5.190992 TGAAATAGCATGTCCATTGCATC 57.809 39.130 0.00 0.00 0.00 3.91
1776 1898 5.601583 TTGAAATAGCATGTCCATTGCAT 57.398 34.783 0.00 0.00 0.00 3.96
1777 1899 5.452216 GGATTGAAATAGCATGTCCATTGCA 60.452 40.000 0.00 0.00 0.00 4.08
1778 1900 4.986659 GGATTGAAATAGCATGTCCATTGC 59.013 41.667 0.00 0.00 0.00 3.56
1779 1901 6.401047 AGGATTGAAATAGCATGTCCATTG 57.599 37.500 0.00 0.00 0.00 2.82
1780 1902 6.205464 CGTAGGATTGAAATAGCATGTCCATT 59.795 38.462 0.00 0.00 0.00 3.16
1781 1903 5.702670 CGTAGGATTGAAATAGCATGTCCAT 59.297 40.000 0.00 0.00 0.00 3.41
1782 1904 5.056480 CGTAGGATTGAAATAGCATGTCCA 58.944 41.667 0.00 0.00 0.00 4.02
1783 1905 5.057149 ACGTAGGATTGAAATAGCATGTCC 58.943 41.667 0.00 0.00 0.00 4.02
1784 1906 6.604735 AACGTAGGATTGAAATAGCATGTC 57.395 37.500 0.00 0.00 0.00 3.06
1785 1907 7.391148 AAAACGTAGGATTGAAATAGCATGT 57.609 32.000 0.00 0.00 0.00 3.21
1786 1908 7.432252 GGAAAAACGTAGGATTGAAATAGCATG 59.568 37.037 0.00 0.00 0.00 4.06
1787 1909 7.339466 AGGAAAAACGTAGGATTGAAATAGCAT 59.661 33.333 0.00 0.00 0.00 3.79
1788 1910 6.657541 AGGAAAAACGTAGGATTGAAATAGCA 59.342 34.615 0.00 0.00 0.00 3.49
1789 1911 7.085052 AGGAAAAACGTAGGATTGAAATAGC 57.915 36.000 0.00 0.00 0.00 2.97
1792 1914 8.683615 GGAATAGGAAAAACGTAGGATTGAAAT 58.316 33.333 0.00 0.00 0.00 2.17
1793 1915 7.886446 AGGAATAGGAAAAACGTAGGATTGAAA 59.114 33.333 0.00 0.00 0.00 2.69
1794 1916 7.335924 CAGGAATAGGAAAAACGTAGGATTGAA 59.664 37.037 0.00 0.00 0.00 2.69
1795 1917 6.821665 CAGGAATAGGAAAAACGTAGGATTGA 59.178 38.462 0.00 0.00 0.00 2.57
1796 1918 6.598064 ACAGGAATAGGAAAAACGTAGGATTG 59.402 38.462 0.00 0.00 0.00 2.67
1797 1919 6.598064 CACAGGAATAGGAAAAACGTAGGATT 59.402 38.462 0.00 0.00 0.00 3.01
1798 1920 6.113411 CACAGGAATAGGAAAAACGTAGGAT 58.887 40.000 0.00 0.00 0.00 3.24
1799 1921 5.012354 ACACAGGAATAGGAAAAACGTAGGA 59.988 40.000 0.00 0.00 0.00 2.94
1800 1922 5.243207 ACACAGGAATAGGAAAAACGTAGG 58.757 41.667 0.00 0.00 0.00 3.18
1801 1923 6.796705 AACACAGGAATAGGAAAAACGTAG 57.203 37.500 0.00 0.00 0.00 3.51
1802 1924 7.571080 AAAACACAGGAATAGGAAAAACGTA 57.429 32.000 0.00 0.00 0.00 3.57
1803 1925 6.459670 AAAACACAGGAATAGGAAAAACGT 57.540 33.333 0.00 0.00 0.00 3.99
1804 1926 6.292114 GCAAAAACACAGGAATAGGAAAAACG 60.292 38.462 0.00 0.00 0.00 3.60
1805 1927 6.536941 TGCAAAAACACAGGAATAGGAAAAAC 59.463 34.615 0.00 0.00 0.00 2.43
1806 1928 6.644347 TGCAAAAACACAGGAATAGGAAAAA 58.356 32.000 0.00 0.00 0.00 1.94
1807 1929 6.227298 TGCAAAAACACAGGAATAGGAAAA 57.773 33.333 0.00 0.00 0.00 2.29
1808 1930 5.860941 TGCAAAAACACAGGAATAGGAAA 57.139 34.783 0.00 0.00 0.00 3.13
1809 1931 5.860941 TTGCAAAAACACAGGAATAGGAA 57.139 34.783 0.00 0.00 0.00 3.36
1810 1932 5.047377 GGATTGCAAAAACACAGGAATAGGA 60.047 40.000 1.71 0.00 0.00 2.94
1811 1933 5.047092 AGGATTGCAAAAACACAGGAATAGG 60.047 40.000 1.71 0.00 0.00 2.57
1812 1934 6.029346 AGGATTGCAAAAACACAGGAATAG 57.971 37.500 1.71 0.00 0.00 1.73
1813 1935 6.348950 CGTAGGATTGCAAAAACACAGGAATA 60.349 38.462 1.71 0.00 0.00 1.75
1814 1936 4.961438 AGGATTGCAAAAACACAGGAAT 57.039 36.364 1.71 0.00 0.00 3.01
1815 1937 4.261405 CGTAGGATTGCAAAAACACAGGAA 60.261 41.667 1.71 0.00 0.00 3.36
1816 1938 3.252215 CGTAGGATTGCAAAAACACAGGA 59.748 43.478 1.71 0.00 0.00 3.86
1817 1939 3.252215 TCGTAGGATTGCAAAAACACAGG 59.748 43.478 1.71 0.00 0.00 4.00
1818 1940 4.481930 TCGTAGGATTGCAAAAACACAG 57.518 40.909 1.71 0.00 0.00 3.66
1819 1941 4.902443 TTCGTAGGATTGCAAAAACACA 57.098 36.364 1.71 0.00 0.00 3.72
1820 1942 5.457140 TGATTCGTAGGATTGCAAAAACAC 58.543 37.500 1.71 0.00 0.00 3.32
1821 1943 5.697473 TGATTCGTAGGATTGCAAAAACA 57.303 34.783 1.71 0.00 0.00 2.83
1822 1944 6.861055 TCTTTGATTCGTAGGATTGCAAAAAC 59.139 34.615 1.71 0.00 0.00 2.43
1823 1945 6.976088 TCTTTGATTCGTAGGATTGCAAAAA 58.024 32.000 1.71 0.00 0.00 1.94
1824 1946 6.349280 CCTCTTTGATTCGTAGGATTGCAAAA 60.349 38.462 1.71 0.00 0.00 2.44
1825 1947 5.123820 CCTCTTTGATTCGTAGGATTGCAAA 59.876 40.000 1.71 0.00 0.00 3.68
1826 1948 4.635765 CCTCTTTGATTCGTAGGATTGCAA 59.364 41.667 0.00 0.00 0.00 4.08
1827 1949 4.191544 CCTCTTTGATTCGTAGGATTGCA 58.808 43.478 0.00 0.00 0.00 4.08
1828 1950 3.002759 GCCTCTTTGATTCGTAGGATTGC 59.997 47.826 0.00 0.00 0.00 3.56
1829 1951 3.561725 GGCCTCTTTGATTCGTAGGATTG 59.438 47.826 0.00 0.00 0.00 2.67
1830 1952 3.433740 GGGCCTCTTTGATTCGTAGGATT 60.434 47.826 0.84 0.00 0.00 3.01
1831 1953 2.104963 GGGCCTCTTTGATTCGTAGGAT 59.895 50.000 0.84 0.00 0.00 3.24
1832 1954 1.485066 GGGCCTCTTTGATTCGTAGGA 59.515 52.381 0.84 0.00 0.00 2.94
1833 1955 1.486726 AGGGCCTCTTTGATTCGTAGG 59.513 52.381 0.00 0.00 0.00 3.18
1834 1956 2.990066 AGGGCCTCTTTGATTCGTAG 57.010 50.000 0.00 0.00 0.00 3.51
1835 1957 5.542635 ACATATAGGGCCTCTTTGATTCGTA 59.457 40.000 10.74 0.00 0.00 3.43
1836 1958 4.348168 ACATATAGGGCCTCTTTGATTCGT 59.652 41.667 10.74 0.00 0.00 3.85
1837 1959 4.899502 ACATATAGGGCCTCTTTGATTCG 58.100 43.478 10.74 0.00 0.00 3.34
1838 1960 6.410540 CCTACATATAGGGCCTCTTTGATTC 58.589 44.000 10.74 0.00 44.06 2.52
1839 1961 6.013293 GTCCTACATATAGGGCCTCTTTGATT 60.013 42.308 10.74 0.00 46.20 2.57
1840 1962 5.485708 GTCCTACATATAGGGCCTCTTTGAT 59.514 44.000 10.74 0.00 46.20 2.57
1841 1963 4.838986 GTCCTACATATAGGGCCTCTTTGA 59.161 45.833 10.74 0.00 46.20 2.69
1842 1964 5.153950 GTCCTACATATAGGGCCTCTTTG 57.846 47.826 10.74 8.75 46.20 2.77
1854 1976 9.052759 GTGGTTTCATAAAATCGTCCTACATAT 57.947 33.333 0.00 0.00 0.00 1.78
1855 1977 8.041919 TGTGGTTTCATAAAATCGTCCTACATA 58.958 33.333 0.00 0.00 0.00 2.29
1856 1978 6.882140 TGTGGTTTCATAAAATCGTCCTACAT 59.118 34.615 0.00 0.00 0.00 2.29
1857 1979 6.231951 TGTGGTTTCATAAAATCGTCCTACA 58.768 36.000 0.00 0.00 0.00 2.74
1858 1980 6.730960 TGTGGTTTCATAAAATCGTCCTAC 57.269 37.500 0.00 0.00 0.00 3.18
2084 2460 5.631119 TGATCAGACGGATGGTTAGATAGA 58.369 41.667 0.00 0.00 36.00 1.98
2107 2483 0.716591 TCCTACCCCAGTCACCATCT 59.283 55.000 0.00 0.00 0.00 2.90
2269 3351 8.831715 ATTAAAAACAACAATTGGGATCTCAC 57.168 30.769 10.83 0.00 34.12 3.51
2304 3386 8.634444 CATGTCTCTAGCCTACTAAACACTATT 58.366 37.037 0.00 0.00 0.00 1.73
3131 4495 8.392612 CGGTGATAGTTTCCATAAATTAACGTT 58.607 33.333 5.88 5.88 0.00 3.99
3134 4498 8.068380 GCTCGGTGATAGTTTCCATAAATTAAC 58.932 37.037 0.00 0.00 0.00 2.01
3224 4598 1.270826 CCGTCCAGTGCTCGATGATAT 59.729 52.381 6.73 0.00 0.00 1.63
3661 5044 2.202566 GGTCAAAGTGCCTATAGACGC 58.797 52.381 0.00 0.00 0.00 5.19
3850 5234 7.160049 TGAACATGTTGCCATATGTTTTTGAT 58.840 30.769 17.58 0.00 44.88 2.57
3895 5279 1.667236 TCGCTGATGTGGCTTATTGG 58.333 50.000 0.00 0.00 0.00 3.16
4264 5649 2.656560 ACCTGTAGATGACTCGCAAC 57.343 50.000 0.00 0.00 0.00 4.17
5459 6854 7.665559 TCATTAAGAGGTTGCTGATTAAGTGTT 59.334 33.333 0.00 0.00 0.00 3.32
5543 6938 9.582223 GTACAAATGAGAAAAGTTCTTACTTCG 57.418 33.333 0.00 0.00 43.74 3.79
6002 7401 8.828751 ACAAGTTTATCCCAGGTATAAAGTGTA 58.171 33.333 5.77 0.00 34.32 2.90
6132 7532 6.659745 TGTCTTTAGTTGTGGCTTCTAGTA 57.340 37.500 0.00 0.00 0.00 1.82
6362 7764 1.151810 TCTCCTTGGCTTCAGGGGT 60.152 57.895 0.00 0.00 38.11 4.95
6366 7768 0.979665 TGGACTCTCCTTGGCTTCAG 59.020 55.000 0.00 0.00 37.46 3.02
6367 7769 1.434188 TTGGACTCTCCTTGGCTTCA 58.566 50.000 0.00 0.00 37.46 3.02
6385 7787 1.286553 TGGTGTGAGGACCCACTTTTT 59.713 47.619 12.53 0.00 37.89 1.94
6640 8043 2.907042 AGAGAGATTTCCTTTGGTCCGT 59.093 45.455 0.00 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.