Multiple sequence alignment - TraesCS1B01G130100

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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 TraesCS1B01G130100 chr1B 100.000 3115 0 0 1 3115 160663546 160666660 0.000000e+00 5753.0
1 TraesCS1B01G130100 chr1B 100.000 1108 0 0 3419 4526 160666964 160668071 0.000000e+00 2047.0
2 TraesCS1B01G130100 chr1B 96.622 296 6 4 1 292 31094233 31094528 5.260000e-134 488.0
3 TraesCS1B01G130100 chr1B 82.683 410 57 5 4023 4422 114438893 114438488 7.200000e-93 351.0
4 TraesCS1B01G130100 chr1B 93.496 123 8 0 1706 1828 132937016 132936894 2.780000e-42 183.0
5 TraesCS1B01G130100 chr1A 94.550 1266 53 8 1822 3079 107094723 107095980 0.000000e+00 1941.0
6 TraesCS1B01G130100 chr1A 95.181 830 33 4 880 1703 107093895 107094723 0.000000e+00 1304.0
7 TraesCS1B01G130100 chr1A 89.370 508 25 12 3419 3926 107096077 107096555 2.990000e-171 612.0
8 TraesCS1B01G130100 chr1D 93.745 1263 56 10 1822 3079 106323453 106322209 0.000000e+00 1873.0
9 TraesCS1B01G130100 chr1D 93.742 831 37 8 881 1703 106324276 106323453 0.000000e+00 1232.0
10 TraesCS1B01G130100 chr1D 90.678 472 21 8 3422 3870 106322109 106321638 1.390000e-169 606.0
11 TraesCS1B01G130100 chr1D 96.259 294 7 4 1 290 17252528 17252821 3.170000e-131 479.0
12 TraesCS1B01G130100 chr1D 76.648 531 80 16 4023 4518 476374199 476374720 2.090000e-63 254.0
13 TraesCS1B01G130100 chr1D 93.182 88 6 0 3856 3943 106297668 106297581 3.670000e-26 130.0
14 TraesCS1B01G130100 chr6B 90.035 572 54 3 309 879 235772934 235772365 0.000000e+00 737.0
15 TraesCS1B01G130100 chr6B 96.622 296 6 4 1 292 43277933 43278228 5.260000e-134 488.0
16 TraesCS1B01G130100 chr6B 95.960 297 6 6 1 292 717509613 717509318 1.140000e-130 477.0
17 TraesCS1B01G130100 chr6B 86.997 323 35 7 560 879 235777732 235777414 1.550000e-94 357.0
18 TraesCS1B01G130100 chr6B 80.178 449 63 13 3938 4384 447998215 447998639 3.400000e-81 313.0
19 TraesCS1B01G130100 chr6D 88.328 574 60 6 309 880 78846088 78846656 0.000000e+00 682.0
20 TraesCS1B01G130100 chr6D 87.267 322 34 6 560 879 78841256 78841572 1.200000e-95 361.0
21 TraesCS1B01G130100 chr5D 86.934 574 67 8 309 879 88352901 88352333 4.940000e-179 638.0
22 TraesCS1B01G130100 chr5D 81.548 775 91 21 943 1702 230016571 230017308 3.900000e-165 592.0
23 TraesCS1B01G130100 chr5D 84.402 577 65 21 309 879 264915181 264915738 1.110000e-150 544.0
24 TraesCS1B01G130100 chr5D 84.556 518 44 20 2564 3076 230018361 230018847 8.810000e-132 481.0
25 TraesCS1B01G130100 chr5D 95.623 297 7 6 1 291 89496118 89496414 5.300000e-129 472.0
26 TraesCS1B01G130100 chr5D 80.841 642 84 15 1823 2455 230017310 230017921 6.860000e-128 468.0
27 TraesCS1B01G130100 chr5D 81.910 398 58 7 4044 4429 454726369 454725974 1.570000e-84 324.0
28 TraesCS1B01G130100 chr5D 87.562 201 16 7 3419 3617 230018949 230019142 1.640000e-54 224.0
29 TraesCS1B01G130100 chr5D 90.769 130 11 1 1704 1833 364050534 364050406 6.020000e-39 172.0
30 TraesCS1B01G130100 chr2A 86.972 568 71 3 312 879 82881660 82881096 1.780000e-178 636.0
31 TraesCS1B01G130100 chr2A 83.252 412 55 8 4023 4424 137931063 137930656 2.570000e-97 366.0
32 TraesCS1B01G130100 chr2A 86.378 323 37 6 559 879 82970959 82970642 3.350000e-91 346.0
33 TraesCS1B01G130100 chr2A 79.762 504 74 13 4044 4524 4621601 4621103 1.560000e-89 340.0
34 TraesCS1B01G130100 chr2A 81.546 401 62 6 4033 4424 59318827 59318430 2.030000e-83 320.0
35 TraesCS1B01G130100 chr5A 81.039 770 113 19 943 1702 326721457 326720711 2.350000e-162 582.0
36 TraesCS1B01G130100 chr5A 81.591 641 82 15 1823 2455 326720709 326720097 8.740000e-137 497.0
37 TraesCS1B01G130100 chr5A 80.664 512 44 23 2567 3076 326719620 326719162 3.350000e-91 346.0
38 TraesCS1B01G130100 chr5A 79.567 416 74 4 4023 4429 475717291 475716878 2.060000e-73 287.0
39 TraesCS1B01G130100 chr5A 87.437 199 15 8 3422 3617 326719059 326718868 2.120000e-53 220.0
40 TraesCS1B01G130100 chr5A 89.831 59 6 0 1442 1500 313883887 313883945 4.860000e-10 76.8
41 TraesCS1B01G130100 chr4A 84.896 576 77 9 309 880 544399470 544398901 1.410000e-159 573.0
42 TraesCS1B01G130100 chr2B 96.959 296 4 5 1 292 543170331 543170625 4.070000e-135 492.0
43 TraesCS1B01G130100 chr2B 96.633 297 4 6 1 292 747234622 747234327 5.260000e-134 488.0
44 TraesCS1B01G130100 chr2B 81.593 364 58 7 4023 4384 452910639 452910283 4.430000e-75 292.0
45 TraesCS1B01G130100 chr2B 92.683 123 9 0 1704 1826 677806497 677806375 1.290000e-40 178.0
46 TraesCS1B01G130100 chr2D 96.610 295 6 4 1 291 637665208 637665502 1.890000e-133 486.0
47 TraesCS1B01G130100 chr2D 93.388 121 8 0 1704 1824 605712267 605712387 3.600000e-41 180.0
48 TraesCS1B01G130100 chr3D 95.932 295 8 4 1 291 511351211 511351505 4.100000e-130 475.0
49 TraesCS1B01G130100 chr3D 83.029 383 51 7 4044 4416 588201348 588200970 7.250000e-88 335.0
50 TraesCS1B01G130100 chr3D 80.984 305 55 3 4023 4325 467476831 467477134 5.850000e-59 239.0
51 TraesCS1B01G130100 chr3D 92.742 124 8 1 1704 1827 579756383 579756505 1.290000e-40 178.0
52 TraesCS1B01G130100 chr3A 84.399 391 48 6 4044 4424 31828849 31828462 5.530000e-99 372.0
53 TraesCS1B01G130100 chr4B 79.245 530 68 18 4023 4518 481491750 481491229 9.380000e-87 331.0
54 TraesCS1B01G130100 chr3B 82.153 353 58 3 4033 4384 458163872 458163524 9.520000e-77 298.0
55 TraesCS1B01G130100 chr3B 91.406 128 11 0 1704 1831 51247229 51247356 4.650000e-40 176.0
56 TraesCS1B01G130100 chrUn 81.593 364 59 8 4023 4384 78171867 78171510 1.230000e-75 294.0
57 TraesCS1B01G130100 chr5B 77.419 527 84 10 4023 4517 657394418 657394941 9.590000e-72 281.0
58 TraesCS1B01G130100 chr5B 91.525 59 4 1 1442 1500 263525553 263525610 3.750000e-11 80.5
59 TraesCS1B01G130100 chr7B 81.588 277 38 9 4159 4424 691277288 691277562 2.740000e-52 217.0
60 TraesCS1B01G130100 chr4D 94.167 120 7 0 1704 1823 357529162 357529043 2.780000e-42 183.0
61 TraesCS1B01G130100 chr4D 94.167 120 7 0 1704 1823 465674443 465674324 2.780000e-42 183.0
62 TraesCS1B01G130100 chr7A 90.769 130 11 1 1704 1833 615329736 615329608 6.020000e-39 172.0


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 TraesCS1B01G130100 chr1B 160663546 160668071 4525 False 3900.000000 5753 100.000000 1 4526 2 chr1B.!!$F2 4525
1 TraesCS1B01G130100 chr1A 107093895 107096555 2660 False 1285.666667 1941 93.033667 880 3926 3 chr1A.!!$F1 3046
2 TraesCS1B01G130100 chr1D 106321638 106324276 2638 True 1237.000000 1873 92.721667 881 3870 3 chr1D.!!$R2 2989
3 TraesCS1B01G130100 chr1D 476374199 476374720 521 False 254.000000 254 76.648000 4023 4518 1 chr1D.!!$F2 495
4 TraesCS1B01G130100 chr6B 235772365 235772934 569 True 737.000000 737 90.035000 309 879 1 chr6B.!!$R1 570
5 TraesCS1B01G130100 chr6D 78846088 78846656 568 False 682.000000 682 88.328000 309 880 1 chr6D.!!$F2 571
6 TraesCS1B01G130100 chr5D 88352333 88352901 568 True 638.000000 638 86.934000 309 879 1 chr5D.!!$R1 570
7 TraesCS1B01G130100 chr5D 264915181 264915738 557 False 544.000000 544 84.402000 309 879 1 chr5D.!!$F2 570
8 TraesCS1B01G130100 chr5D 230016571 230019142 2571 False 441.250000 592 83.626750 943 3617 4 chr5D.!!$F3 2674
9 TraesCS1B01G130100 chr2A 82881096 82881660 564 True 636.000000 636 86.972000 312 879 1 chr2A.!!$R3 567
10 TraesCS1B01G130100 chr5A 326718868 326721457 2589 True 411.250000 582 82.682750 943 3617 4 chr5A.!!$R2 2674
11 TraesCS1B01G130100 chr4A 544398901 544399470 569 True 573.000000 573 84.896000 309 880 1 chr4A.!!$R1 571
12 TraesCS1B01G130100 chr4B 481491229 481491750 521 True 331.000000 331 79.245000 4023 4518 1 chr4B.!!$R1 495
13 TraesCS1B01G130100 chr5B 657394418 657394941 523 False 281.000000 281 77.419000 4023 4517 1 chr5B.!!$F2 494

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
721 726 0.035439 CTTACCTTCCACGGCACCAT 60.035 55.000 0.00 0.0 0.0 3.55 F
802 807 0.325390 AACCCTAGTCCTCCCCTTCG 60.325 60.000 0.00 0.0 0.0 3.79 F
961 969 0.615331 AGCCAGCCGAAATCTCTTGA 59.385 50.000 0.00 0.0 0.0 3.02 F
2056 2091 1.402968 CCATTTGGCCTCTCATGTTCG 59.597 52.381 3.32 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2065 2100 0.673644 ACAGAAAGGCATCCGGTTCG 60.674 55.000 0.0 0.0 31.04 3.95 R
2151 2186 0.745845 CTATCCACACAGCAGCACCC 60.746 60.000 0.0 0.0 0.00 4.61 R
2346 2393 1.490490 ACTGTTTCTGGAAGTGGCTGA 59.510 47.619 0.0 0.0 33.76 4.26 R
3877 4468 0.038744 ACTACTTCCTCCGTCCCGAA 59.961 55.000 0.0 0.0 0.00 4.30 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
138 139 8.450578 AGAATGTGTATGAAGAAAAGTTGACA 57.549 30.769 0.00 0.00 0.00 3.58
139 140 8.345565 AGAATGTGTATGAAGAAAAGTTGACAC 58.654 33.333 0.00 0.00 37.15 3.67
140 141 6.371809 TGTGTATGAAGAAAAGTTGACACC 57.628 37.500 0.00 0.00 36.06 4.16
141 142 5.883115 TGTGTATGAAGAAAAGTTGACACCA 59.117 36.000 0.00 0.00 36.06 4.17
142 143 6.375736 TGTGTATGAAGAAAAGTTGACACCAA 59.624 34.615 0.00 0.00 36.06 3.67
143 144 7.094162 TGTGTATGAAGAAAAGTTGACACCAAA 60.094 33.333 0.00 0.00 36.06 3.28
144 145 7.757624 GTGTATGAAGAAAAGTTGACACCAAAA 59.242 33.333 0.00 0.00 33.49 2.44
145 146 8.307483 TGTATGAAGAAAAGTTGACACCAAAAA 58.693 29.630 0.00 0.00 33.49 1.94
305 306 3.665745 ATGTTCTCCAACACATTTGCC 57.334 42.857 0.00 0.00 45.47 4.52
306 307 1.336440 TGTTCTCCAACACATTTGCCG 59.664 47.619 0.00 0.00 37.61 5.69
307 308 0.958091 TTCTCCAACACATTTGCCGG 59.042 50.000 0.00 0.00 0.00 6.13
345 346 0.614697 TCTCAGGAATGGAGGCGTCA 60.615 55.000 8.91 0.00 33.18 4.35
377 378 1.305201 GTGGAACAAGACGCAAAGGA 58.695 50.000 0.00 0.00 44.16 3.36
396 397 2.565841 GATGTACCAGTGGCAATCCTC 58.434 52.381 9.78 0.00 0.00 3.71
416 417 0.317770 CAAACACGTTGGCGCAAGAT 60.318 50.000 10.83 0.00 42.83 2.40
588 592 1.612442 ACTACCCCTGACATGCCGT 60.612 57.895 0.00 0.00 0.00 5.68
601 605 4.006357 GCCGTCCCCACGTACCAA 62.006 66.667 0.00 0.00 45.17 3.67
617 621 1.068417 CAACAACGACGGACCAGGA 59.932 57.895 0.00 0.00 0.00 3.86
619 623 2.432628 CAACGACGGACCAGGAGC 60.433 66.667 0.00 0.00 0.00 4.70
709 713 4.466726 CCAGCCAAGACTACTACTTACCTT 59.533 45.833 0.00 0.00 0.00 3.50
714 719 5.392811 CCAAGACTACTACTTACCTTCCACG 60.393 48.000 0.00 0.00 0.00 4.94
721 726 0.035439 CTTACCTTCCACGGCACCAT 60.035 55.000 0.00 0.00 0.00 3.55
777 782 2.073101 GGCTACCTCCTTCCCCTGG 61.073 68.421 0.00 0.00 0.00 4.45
792 797 1.677637 CCTGGCTCCGAACCCTAGTC 61.678 65.000 0.00 0.00 0.00 2.59
795 800 1.393487 GGCTCCGAACCCTAGTCCTC 61.393 65.000 0.00 0.00 0.00 3.71
798 803 1.761271 CCGAACCCTAGTCCTCCCC 60.761 68.421 0.00 0.00 0.00 4.81
802 807 0.325390 AACCCTAGTCCTCCCCTTCG 60.325 60.000 0.00 0.00 0.00 3.79
804 809 2.134933 CCTAGTCCTCCCCTTCGCC 61.135 68.421 0.00 0.00 0.00 5.54
805 810 1.381327 CTAGTCCTCCCCTTCGCCA 60.381 63.158 0.00 0.00 0.00 5.69
806 811 0.760945 CTAGTCCTCCCCTTCGCCAT 60.761 60.000 0.00 0.00 0.00 4.40
848 853 4.787135 TGTATCCCAGATAATTGCCACA 57.213 40.909 0.00 0.00 0.00 4.17
862 867 3.111853 TGCCACAGCTTAATAGATCCG 57.888 47.619 0.00 0.00 40.80 4.18
864 869 2.061773 CCACAGCTTAATAGATCCGCG 58.938 52.381 0.00 0.00 0.00 6.46
961 969 0.615331 AGCCAGCCGAAATCTCTTGA 59.385 50.000 0.00 0.00 0.00 3.02
1469 1489 1.947456 GGGGACGATCCAAATGTAAGC 59.053 52.381 6.41 0.00 38.64 3.09
1472 1492 2.614057 GGACGATCCAAATGTAAGCTGG 59.386 50.000 0.00 0.00 36.28 4.85
1478 1498 1.832998 CCAAATGTAAGCTGGCCCATT 59.167 47.619 0.00 0.00 0.00 3.16
1617 1641 2.568623 AGAGTGGTAGCAAACAAGGG 57.431 50.000 0.00 0.00 0.00 3.95
1695 1726 9.015146 AGAAGTAAAAGGGATATACCTGGAATT 57.985 33.333 7.45 1.22 40.87 2.17
1703 1734 6.566480 AGGGATATACCTGGAATTGGTACATT 59.434 38.462 5.39 0.00 42.12 2.71
1704 1735 6.884836 GGGATATACCTGGAATTGGTACATTC 59.115 42.308 0.00 0.00 42.12 2.67
1705 1736 6.884836 GGATATACCTGGAATTGGTACATTCC 59.115 42.308 15.06 15.06 42.12 3.01
1706 1737 2.999331 ACCTGGAATTGGTACATTCCG 58.001 47.619 16.26 12.08 43.74 4.30
1707 1738 2.307686 ACCTGGAATTGGTACATTCCGT 59.692 45.455 16.26 9.01 43.74 4.69
1708 1739 2.943033 CCTGGAATTGGTACATTCCGTC 59.057 50.000 16.26 0.00 43.74 4.79
1709 1740 2.943033 CTGGAATTGGTACATTCCGTCC 59.057 50.000 16.26 6.56 43.74 4.79
1710 1741 2.294979 GGAATTGGTACATTCCGTCCC 58.705 52.381 8.72 0.00 39.30 4.46
1711 1742 2.356330 GGAATTGGTACATTCCGTCCCA 60.356 50.000 8.72 0.00 39.30 4.37
1712 1743 3.349022 GAATTGGTACATTCCGTCCCAA 58.651 45.455 0.00 0.00 46.54 4.12
1713 1744 2.953284 TTGGTACATTCCGTCCCAAA 57.047 45.000 0.00 0.00 40.40 3.28
1714 1745 2.953284 TGGTACATTCCGTCCCAAAA 57.047 45.000 0.00 0.00 29.02 2.44
1715 1746 3.443145 TGGTACATTCCGTCCCAAAAT 57.557 42.857 0.00 0.00 29.02 1.82
1716 1747 3.768878 TGGTACATTCCGTCCCAAAATT 58.231 40.909 0.00 0.00 29.02 1.82
1717 1748 3.759618 TGGTACATTCCGTCCCAAAATTC 59.240 43.478 0.00 0.00 29.02 2.17
1718 1749 4.014406 GGTACATTCCGTCCCAAAATTCT 58.986 43.478 0.00 0.00 0.00 2.40
1719 1750 4.095932 GGTACATTCCGTCCCAAAATTCTC 59.904 45.833 0.00 0.00 0.00 2.87
1720 1751 2.747446 ACATTCCGTCCCAAAATTCTCG 59.253 45.455 0.00 0.00 0.00 4.04
1721 1752 2.554370 TTCCGTCCCAAAATTCTCGT 57.446 45.000 0.00 0.00 0.00 4.18
1722 1753 2.088950 TCCGTCCCAAAATTCTCGTC 57.911 50.000 0.00 0.00 0.00 4.20
1723 1754 1.621814 TCCGTCCCAAAATTCTCGTCT 59.378 47.619 0.00 0.00 0.00 4.18
1724 1755 2.038033 TCCGTCCCAAAATTCTCGTCTT 59.962 45.455 0.00 0.00 0.00 3.01
1725 1756 2.415512 CCGTCCCAAAATTCTCGTCTTC 59.584 50.000 0.00 0.00 0.00 2.87
1726 1757 3.064207 CGTCCCAAAATTCTCGTCTTCA 58.936 45.455 0.00 0.00 0.00 3.02
1727 1758 3.496884 CGTCCCAAAATTCTCGTCTTCAA 59.503 43.478 0.00 0.00 0.00 2.69
1728 1759 4.154195 CGTCCCAAAATTCTCGTCTTCAAT 59.846 41.667 0.00 0.00 0.00 2.57
1729 1760 5.334879 CGTCCCAAAATTCTCGTCTTCAATT 60.335 40.000 0.00 0.00 0.00 2.32
1730 1761 6.447162 GTCCCAAAATTCTCGTCTTCAATTT 58.553 36.000 0.00 0.00 32.30 1.82
1731 1762 6.363357 GTCCCAAAATTCTCGTCTTCAATTTG 59.637 38.462 0.00 0.00 31.56 2.32
1732 1763 6.040391 TCCCAAAATTCTCGTCTTCAATTTGT 59.960 34.615 0.00 0.00 31.56 2.83
1733 1764 6.701400 CCCAAAATTCTCGTCTTCAATTTGTT 59.299 34.615 0.00 0.00 31.56 2.83
1734 1765 7.224557 CCCAAAATTCTCGTCTTCAATTTGTTT 59.775 33.333 0.00 0.00 31.56 2.83
1735 1766 9.243637 CCAAAATTCTCGTCTTCAATTTGTTTA 57.756 29.630 0.00 0.00 31.56 2.01
1737 1768 9.796120 AAAATTCTCGTCTTCAATTTGTTTACA 57.204 25.926 0.00 0.00 31.56 2.41
1738 1769 9.965824 AAATTCTCGTCTTCAATTTGTTTACAT 57.034 25.926 0.00 0.00 30.29 2.29
1742 1773 8.717821 TCTCGTCTTCAATTTGTTTACATAAGG 58.282 33.333 0.00 0.00 0.00 2.69
1743 1774 8.610248 TCGTCTTCAATTTGTTTACATAAGGA 57.390 30.769 0.00 0.00 0.00 3.36
1744 1775 9.226606 TCGTCTTCAATTTGTTTACATAAGGAT 57.773 29.630 0.00 0.00 0.00 3.24
1745 1776 9.277565 CGTCTTCAATTTGTTTACATAAGGATG 57.722 33.333 0.00 0.00 39.16 3.51
1814 1845 8.494016 AATCTAAGACAAGAATTTTAGGACGG 57.506 34.615 0.00 0.00 0.00 4.79
1815 1846 7.235935 TCTAAGACAAGAATTTTAGGACGGA 57.764 36.000 0.00 0.00 0.00 4.69
1816 1847 7.321153 TCTAAGACAAGAATTTTAGGACGGAG 58.679 38.462 0.00 0.00 0.00 4.63
1817 1848 4.833390 AGACAAGAATTTTAGGACGGAGG 58.167 43.478 0.00 0.00 0.00 4.30
1818 1849 4.530946 AGACAAGAATTTTAGGACGGAGGA 59.469 41.667 0.00 0.00 0.00 3.71
1819 1850 5.012768 AGACAAGAATTTTAGGACGGAGGAA 59.987 40.000 0.00 0.00 0.00 3.36
1820 1851 5.246307 ACAAGAATTTTAGGACGGAGGAAG 58.754 41.667 0.00 0.00 0.00 3.46
1821 1852 5.221864 ACAAGAATTTTAGGACGGAGGAAGT 60.222 40.000 0.00 0.00 0.00 3.01
1849 1880 7.977789 TGCTTAGACTGTGTTTATCAATGAA 57.022 32.000 0.00 0.00 0.00 2.57
1906 1937 3.010584 AGACAACAGCCAATCCCTAACAT 59.989 43.478 0.00 0.00 0.00 2.71
1907 1938 4.227300 AGACAACAGCCAATCCCTAACATA 59.773 41.667 0.00 0.00 0.00 2.29
1937 1970 3.866066 GCATATGGATAGTGGTCGCATGT 60.866 47.826 4.56 0.00 0.00 3.21
2012 2047 2.037251 TGTGTGGAAGGAACTGCTAGTC 59.963 50.000 0.00 0.00 40.86 2.59
2056 2091 1.402968 CCATTTGGCCTCTCATGTTCG 59.597 52.381 3.32 0.00 0.00 3.95
2065 2100 4.467084 TCATGTTCGGGGCGAGCC 62.467 66.667 5.37 5.37 36.32 4.70
2150 2185 6.127786 GCATCTATTGCCTCTCACTTCTTTTT 60.128 38.462 0.00 0.00 46.15 1.94
2151 2186 6.808008 TCTATTGCCTCTCACTTCTTTTTG 57.192 37.500 0.00 0.00 0.00 2.44
2667 3191 8.312564 AGTCCATTAAGTACACTTAGGAAGTTC 58.687 37.037 10.21 0.00 40.46 3.01
2830 3354 2.027192 TCATCTACCTGCCACAACCTTC 60.027 50.000 0.00 0.00 0.00 3.46
2875 3399 2.165030 CCAAGAAATCCAGAATTGCGCT 59.835 45.455 9.73 0.00 0.00 5.92
2901 3425 4.513198 TTAACCAGTTATGCCAGTTTGC 57.487 40.909 0.00 0.00 0.00 3.68
2908 3434 2.989166 GTTATGCCAGTTTGCTTCAAGC 59.011 45.455 1.04 1.04 42.82 4.01
2979 3507 2.627515 TAGCTGAGTGAATCCATGGC 57.372 50.000 6.96 0.00 0.00 4.40
2989 3517 0.975887 AATCCATGGCGTGCCTTTTT 59.024 45.000 12.84 0.00 36.94 1.94
3088 3651 5.661458 CGAAAGGTATGGTCACTTGTATCT 58.339 41.667 0.00 0.00 0.00 1.98
3097 3660 5.330233 TGGTCACTTGTATCTCCAGAGTTA 58.670 41.667 0.00 0.00 0.00 2.24
3533 4096 8.870116 AGTAGTAACCAATGAGTGATATATGCA 58.130 33.333 0.00 0.00 0.00 3.96
3547 4110 0.533531 TATGCATCCTTGAGCAGCCG 60.534 55.000 0.19 0.00 44.94 5.52
3550 4113 2.437359 ATCCTTGAGCAGCCGCAC 60.437 61.111 0.00 0.00 42.27 5.34
3576 4139 8.501580 CAGACTACCATGTTATCTGCAATATTG 58.498 37.037 11.27 11.27 31.14 1.90
3677 4253 5.811399 TGGTAAGCAATCCAAACTATTCG 57.189 39.130 0.00 0.00 0.00 3.34
3678 4254 4.638421 TGGTAAGCAATCCAAACTATTCGG 59.362 41.667 0.00 0.00 0.00 4.30
3679 4255 4.879545 GGTAAGCAATCCAAACTATTCGGA 59.120 41.667 0.00 0.00 0.00 4.55
3761 4352 0.170339 GGATGGTTGTACGCTTTGCC 59.830 55.000 0.00 0.00 0.00 4.52
3827 4418 0.318784 GCACTATCCGCCCTAACTCG 60.319 60.000 0.00 0.00 0.00 4.18
3831 4422 2.224967 ACTATCCGCCCTAACTCGGTAT 60.225 50.000 0.47 0.00 45.44 2.73
3837 4428 2.223572 CGCCCTAACTCGGTATTACGTT 60.224 50.000 0.00 0.00 34.94 3.99
3881 4472 3.734776 GGGAACGTTTCTACATTTCGG 57.265 47.619 6.53 0.00 0.00 4.30
3882 4473 2.417586 GGGAACGTTTCTACATTTCGGG 59.582 50.000 6.53 0.00 0.00 5.14
3883 4474 3.328505 GGAACGTTTCTACATTTCGGGA 58.671 45.455 0.46 0.00 0.00 5.14
3884 4475 3.124128 GGAACGTTTCTACATTTCGGGAC 59.876 47.826 0.46 0.00 0.00 4.46
3911 4502 5.415701 AGGAAGTAGTATTTGTTGCATGTGG 59.584 40.000 0.00 0.00 0.00 4.17
3926 4517 0.040058 TGTGGCTGATCAAGGGCAAT 59.960 50.000 12.05 0.00 39.60 3.56
3927 4518 1.188863 GTGGCTGATCAAGGGCAATT 58.811 50.000 12.05 0.00 39.60 2.32
3928 4519 2.291475 TGTGGCTGATCAAGGGCAATTA 60.291 45.455 12.05 1.30 39.60 1.40
3929 4520 2.360165 GTGGCTGATCAAGGGCAATTAG 59.640 50.000 12.05 0.00 39.60 1.73
3930 4521 2.241941 TGGCTGATCAAGGGCAATTAGA 59.758 45.455 8.54 0.00 35.13 2.10
3931 4522 3.117398 TGGCTGATCAAGGGCAATTAGAT 60.117 43.478 8.54 0.00 35.13 1.98
3932 4523 4.104579 TGGCTGATCAAGGGCAATTAGATA 59.895 41.667 8.54 0.00 35.13 1.98
3933 4524 5.072741 GGCTGATCAAGGGCAATTAGATAA 58.927 41.667 7.62 0.00 0.00 1.75
3934 4525 5.048434 GGCTGATCAAGGGCAATTAGATAAC 60.048 44.000 7.62 0.00 0.00 1.89
3935 4526 5.767168 GCTGATCAAGGGCAATTAGATAACT 59.233 40.000 0.00 0.00 0.00 2.24
3936 4527 6.936900 GCTGATCAAGGGCAATTAGATAACTA 59.063 38.462 0.00 0.00 0.00 2.24
3937 4528 7.095017 GCTGATCAAGGGCAATTAGATAACTAC 60.095 40.741 0.00 0.00 0.00 2.73
3938 4529 7.224297 TGATCAAGGGCAATTAGATAACTACC 58.776 38.462 0.00 0.00 0.00 3.18
3939 4530 6.824958 TCAAGGGCAATTAGATAACTACCT 57.175 37.500 0.00 0.00 0.00 3.08
3940 4531 7.208064 TCAAGGGCAATTAGATAACTACCTT 57.792 36.000 0.00 0.00 33.36 3.50
3941 4532 7.054124 TCAAGGGCAATTAGATAACTACCTTG 58.946 38.462 15.03 15.03 42.62 3.61
3942 4533 6.576778 AGGGCAATTAGATAACTACCTTGT 57.423 37.500 0.00 0.00 30.57 3.16
3943 4534 6.357367 AGGGCAATTAGATAACTACCTTGTG 58.643 40.000 0.00 0.00 30.57 3.33
3944 4535 5.531287 GGGCAATTAGATAACTACCTTGTGG 59.469 44.000 0.00 0.00 39.83 4.17
3953 4544 2.934369 ACCTTGTGGTGGGCATGT 59.066 55.556 0.00 0.00 46.51 3.21
3954 4545 1.531365 ACCTTGTGGTGGGCATGTG 60.531 57.895 0.00 0.00 46.51 3.21
3955 4546 1.531365 CCTTGTGGTGGGCATGTGT 60.531 57.895 0.00 0.00 0.00 3.72
3956 4547 1.526575 CCTTGTGGTGGGCATGTGTC 61.527 60.000 0.00 0.00 0.00 3.67
3957 4548 1.526575 CTTGTGGTGGGCATGTGTCC 61.527 60.000 0.00 0.00 41.09 4.02
3958 4549 2.005606 TTGTGGTGGGCATGTGTCCT 62.006 55.000 5.12 0.00 41.34 3.85
3959 4550 1.675641 GTGGTGGGCATGTGTCCTC 60.676 63.158 5.12 1.05 41.34 3.71
3960 4551 2.436646 GGTGGGCATGTGTCCTCG 60.437 66.667 5.12 0.00 41.34 4.63
3961 4552 2.662596 GTGGGCATGTGTCCTCGA 59.337 61.111 5.12 0.00 41.34 4.04
3962 4553 1.448540 GTGGGCATGTGTCCTCGAG 60.449 63.158 5.13 5.13 41.34 4.04
3963 4554 1.913262 TGGGCATGTGTCCTCGAGT 60.913 57.895 12.31 0.00 41.34 4.18
3964 4555 1.296715 GGGCATGTGTCCTCGAGTT 59.703 57.895 12.31 0.00 36.72 3.01
3965 4556 0.741221 GGGCATGTGTCCTCGAGTTC 60.741 60.000 12.31 4.45 36.72 3.01
3966 4557 0.247736 GGCATGTGTCCTCGAGTTCT 59.752 55.000 12.31 0.00 0.00 3.01
3967 4558 1.354040 GCATGTGTCCTCGAGTTCTG 58.646 55.000 12.31 0.00 0.00 3.02
3968 4559 1.354040 CATGTGTCCTCGAGTTCTGC 58.646 55.000 12.31 0.00 0.00 4.26
3969 4560 0.247736 ATGTGTCCTCGAGTTCTGCC 59.752 55.000 12.31 0.00 0.00 4.85
3970 4561 1.444553 GTGTCCTCGAGTTCTGCCG 60.445 63.158 12.31 0.00 0.00 5.69
3971 4562 1.901948 TGTCCTCGAGTTCTGCCGT 60.902 57.895 12.31 0.00 0.00 5.68
3972 4563 1.289380 GTCCTCGAGTTCTGCCGTT 59.711 57.895 12.31 0.00 0.00 4.44
3973 4564 1.009389 GTCCTCGAGTTCTGCCGTTG 61.009 60.000 12.31 0.00 0.00 4.10
3974 4565 2.383527 CCTCGAGTTCTGCCGTTGC 61.384 63.158 12.31 0.00 38.26 4.17
3975 4566 2.720758 CTCGAGTTCTGCCGTTGCG 61.721 63.158 3.62 0.00 41.78 4.85
3976 4567 2.733218 CGAGTTCTGCCGTTGCGA 60.733 61.111 0.00 0.00 41.78 5.10
3977 4568 2.853914 GAGTTCTGCCGTTGCGAC 59.146 61.111 0.00 0.00 41.78 5.19
3986 4577 3.990806 CGTTGCGACGGCGTTTGA 61.991 61.111 19.10 0.00 45.32 2.69
3987 4578 2.554272 GTTGCGACGGCGTTTGAT 59.446 55.556 16.19 0.00 44.10 2.57
3988 4579 1.509162 GTTGCGACGGCGTTTGATC 60.509 57.895 16.19 0.00 44.10 2.92
3989 4580 2.673114 TTGCGACGGCGTTTGATCC 61.673 57.895 16.19 0.00 44.10 3.36
3990 4581 3.115892 GCGACGGCGTTTGATCCA 61.116 61.111 16.19 0.00 40.36 3.41
3991 4582 3.081133 CGACGGCGTTTGATCCAG 58.919 61.111 16.19 0.00 0.00 3.86
3992 4583 2.785258 GACGGCGTTTGATCCAGC 59.215 61.111 16.19 0.00 0.00 4.85
3993 4584 3.083600 GACGGCGTTTGATCCAGCG 62.084 63.158 16.19 0.00 0.00 5.18
3996 4587 4.520846 GCGTTTGATCCAGCGCCG 62.521 66.667 15.74 0.00 43.52 6.46
3997 4588 3.864686 CGTTTGATCCAGCGCCGG 61.865 66.667 2.25 2.25 0.00 6.13
3998 4589 4.179579 GTTTGATCCAGCGCCGGC 62.180 66.667 19.07 19.07 40.37 6.13
3999 4590 4.713735 TTTGATCCAGCGCCGGCA 62.714 61.111 28.98 6.55 43.41 5.69
4026 4617 4.709250 CCTTGGAAGGTAATCTAAGAGCC 58.291 47.826 2.46 0.00 39.49 4.70
4027 4618 4.410555 CCTTGGAAGGTAATCTAAGAGCCT 59.589 45.833 2.46 0.00 39.49 4.58
4028 4619 5.454045 CCTTGGAAGGTAATCTAAGAGCCTC 60.454 48.000 2.46 0.00 39.49 4.70
4031 4622 3.596940 AGGTAATCTAAGAGCCTCGGA 57.403 47.619 0.00 0.00 0.00 4.55
4037 4628 3.377253 TCTAAGAGCCTCGGAAGGTAA 57.623 47.619 0.00 0.00 45.34 2.85
4042 4633 3.912248 AGAGCCTCGGAAGGTAATCTAA 58.088 45.455 0.00 0.00 45.34 2.10
4054 4645 3.388024 AGGTAATCTAAGAGCGGATGCAA 59.612 43.478 0.00 0.00 46.23 4.08
4063 4654 0.968405 AGCGGATGCAAATTGTGGTT 59.032 45.000 0.00 0.00 46.23 3.67
4081 4672 2.754552 GGTTTGCATTAGTGGCATCTGA 59.245 45.455 0.00 0.00 41.58 3.27
4111 4702 2.151202 GATCATGTGTTGGGTTCGTGT 58.849 47.619 0.00 0.00 0.00 4.49
4131 4722 1.783071 TACGTGGATGGCAGGTATGA 58.217 50.000 0.00 0.00 0.00 2.15
4139 4730 3.073650 GGATGGCAGGTATGATTTCCTCT 59.926 47.826 0.00 0.00 30.91 3.69
4142 4733 3.134458 GGCAGGTATGATTTCCTCTTCG 58.866 50.000 0.00 0.00 30.91 3.79
4144 4735 3.804873 GCAGGTATGATTTCCTCTTCGAC 59.195 47.826 0.00 0.00 30.91 4.20
4145 4736 4.045104 CAGGTATGATTTCCTCTTCGACG 58.955 47.826 0.00 0.00 30.91 5.12
4146 4737 3.700038 AGGTATGATTTCCTCTTCGACGT 59.300 43.478 0.00 0.00 0.00 4.34
4148 4739 4.267928 GGTATGATTTCCTCTTCGACGTTG 59.732 45.833 0.00 0.00 0.00 4.10
4149 4740 2.066262 TGATTTCCTCTTCGACGTTGC 58.934 47.619 0.00 0.00 0.00 4.17
4154 4746 0.039074 CCTCTTCGACGTTGCAGTCT 60.039 55.000 2.26 0.00 38.90 3.24
4164 4756 0.755327 GTTGCAGTCTTGTGGGGGTT 60.755 55.000 0.00 0.00 0.00 4.11
4190 4782 1.202758 TCTGGAGTTTGATGGCGTGTT 60.203 47.619 0.00 0.00 0.00 3.32
4201 4793 2.898343 GCGTGTTCGGGGTGTTGT 60.898 61.111 0.00 0.00 37.56 3.32
4229 4821 4.624024 GTCTGATTCGTTCAACGGTAATGA 59.376 41.667 10.69 1.13 42.81 2.57
4233 4825 6.904498 TGATTCGTTCAACGGTAATGATTTT 58.096 32.000 10.69 0.00 42.81 1.82
4262 4857 0.108019 GAACCACTTTGGAGGTCCGT 59.892 55.000 0.00 0.00 40.96 4.69
4266 4861 2.173143 ACCACTTTGGAGGTCCGTAAAA 59.827 45.455 0.00 0.00 40.96 1.52
4275 4870 5.197451 TGGAGGTCCGTAAAATTGCATATT 58.803 37.500 0.00 0.00 39.43 1.28
4306 4901 2.338620 CGTCGAGCTTGGGTGTGA 59.661 61.111 0.00 0.00 0.00 3.58
4315 4910 1.271597 GCTTGGGTGTGAAGGTGATCT 60.272 52.381 0.00 0.00 0.00 2.75
4318 4913 1.774254 TGGGTGTGAAGGTGATCTGTT 59.226 47.619 0.00 0.00 0.00 3.16
4360 4955 2.111384 CTAGTGTGGTACCAGAGGCAT 58.889 52.381 16.93 3.05 0.00 4.40
4369 4964 2.665000 CAGAGGCATGTGACGGGT 59.335 61.111 0.00 0.00 0.00 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 113 9.554395 TGTCAACTTTTCTTCATACACATTCTA 57.446 29.630 0.00 0.00 0.00 2.10
113 114 8.345565 GTGTCAACTTTTCTTCATACACATTCT 58.654 33.333 0.00 0.00 36.77 2.40
114 115 7.591426 GGTGTCAACTTTTCTTCATACACATTC 59.409 37.037 0.00 0.00 38.13 2.67
115 116 7.068103 TGGTGTCAACTTTTCTTCATACACATT 59.932 33.333 0.00 0.00 38.13 2.71
116 117 6.545666 TGGTGTCAACTTTTCTTCATACACAT 59.454 34.615 0.00 0.00 38.13 3.21
117 118 5.883115 TGGTGTCAACTTTTCTTCATACACA 59.117 36.000 0.00 0.00 38.13 3.72
118 119 6.371809 TGGTGTCAACTTTTCTTCATACAC 57.628 37.500 0.00 0.00 36.20 2.90
119 120 7.397892 TTTGGTGTCAACTTTTCTTCATACA 57.602 32.000 0.00 0.00 31.78 2.29
120 121 8.696410 TTTTTGGTGTCAACTTTTCTTCATAC 57.304 30.769 0.00 0.00 31.78 2.39
284 285 3.552684 CGGCAAATGTGTTGGAGAACATT 60.553 43.478 0.00 0.00 46.35 2.71
285 286 2.030007 CGGCAAATGTGTTGGAGAACAT 60.030 45.455 0.00 0.00 43.95 2.71
286 287 1.336440 CGGCAAATGTGTTGGAGAACA 59.664 47.619 0.00 0.00 39.88 3.18
287 288 1.335872 CCGGCAAATGTGTTGGAGAAC 60.336 52.381 0.00 0.00 0.00 3.01
288 289 0.958091 CCGGCAAATGTGTTGGAGAA 59.042 50.000 0.00 0.00 0.00 2.87
289 290 0.179004 ACCGGCAAATGTGTTGGAGA 60.179 50.000 0.00 0.00 0.00 3.71
290 291 0.039256 CACCGGCAAATGTGTTGGAG 60.039 55.000 0.00 0.00 0.00 3.86
291 292 2.037053 CACCGGCAAATGTGTTGGA 58.963 52.632 0.00 0.00 0.00 3.53
292 293 1.664333 GCACCGGCAAATGTGTTGG 60.664 57.895 0.00 0.00 40.72 3.77
293 294 0.940519 CAGCACCGGCAAATGTGTTG 60.941 55.000 0.00 0.00 44.61 3.33
294 295 1.363443 CAGCACCGGCAAATGTGTT 59.637 52.632 0.00 0.00 44.61 3.32
295 296 3.041701 CAGCACCGGCAAATGTGT 58.958 55.556 0.00 0.00 44.61 3.72
296 297 2.431260 GCAGCACCGGCAAATGTG 60.431 61.111 0.00 0.00 44.61 3.21
297 298 4.041917 CGCAGCACCGGCAAATGT 62.042 61.111 0.00 0.00 44.61 2.71
298 299 3.951655 GACGCAGCACCGGCAAATG 62.952 63.158 0.00 0.00 44.61 2.32
299 300 3.737172 GACGCAGCACCGGCAAAT 61.737 61.111 0.00 0.00 44.61 2.32
317 318 2.909006 TCCATTCCTGAGAGAAGTGCTT 59.091 45.455 0.00 0.00 0.00 3.91
328 329 0.036388 GTTGACGCCTCCATTCCTGA 60.036 55.000 0.00 0.00 0.00 3.86
345 346 0.387565 GTTCCACCGGCAAATGTGTT 59.612 50.000 0.00 0.00 0.00 3.32
377 378 1.212935 GGAGGATTGCCACTGGTACAT 59.787 52.381 0.00 0.00 34.69 2.29
426 427 1.271597 ACCTGGACTTGCTCAACCATC 60.272 52.381 0.00 0.00 0.00 3.51
430 431 2.224305 ACTGTACCTGGACTTGCTCAAC 60.224 50.000 0.00 0.00 0.00 3.18
432 433 1.344438 CACTGTACCTGGACTTGCTCA 59.656 52.381 0.00 0.00 0.00 4.26
478 479 2.592993 CGGCCTTGTTCTCCCAGGA 61.593 63.158 0.00 0.00 0.00 3.86
487 488 3.050275 GAAGAGCGCGGCCTTGTT 61.050 61.111 8.83 0.00 0.00 2.83
588 592 1.069427 CGTTGTTGGTACGTGGGGA 59.931 57.895 0.00 0.00 34.47 4.81
601 605 3.048602 CTCCTGGTCCGTCGTTGT 58.951 61.111 0.00 0.00 0.00 3.32
639 643 0.250901 ACTCTTGCGTTGGCCTTGAT 60.251 50.000 3.32 0.00 38.85 2.57
640 644 1.148273 ACTCTTGCGTTGGCCTTGA 59.852 52.632 3.32 0.00 38.85 3.02
709 713 3.716195 CCTGGATGGTGCCGTGGA 61.716 66.667 0.00 0.00 0.00 4.02
714 719 1.348008 TGGATCTCCTGGATGGTGCC 61.348 60.000 0.00 0.00 34.33 5.01
721 726 1.132913 CCTCTGGATGGATCTCCTGGA 60.133 57.143 0.00 0.00 36.20 3.86
777 782 1.393487 GGAGGACTAGGGTTCGGAGC 61.393 65.000 0.00 0.00 0.00 4.70
792 797 0.611896 ACAAAATGGCGAAGGGGAGG 60.612 55.000 0.00 0.00 0.00 4.30
795 800 1.540267 TACACAAAATGGCGAAGGGG 58.460 50.000 0.00 0.00 0.00 4.79
798 803 4.335082 TTCGATACACAAAATGGCGAAG 57.665 40.909 0.00 0.00 36.33 3.79
802 807 4.500477 GCTTGATTCGATACACAAAATGGC 59.500 41.667 0.00 0.00 0.00 4.40
804 809 6.803320 ACAAGCTTGATTCGATACACAAAATG 59.197 34.615 32.50 0.00 0.00 2.32
805 810 6.913170 ACAAGCTTGATTCGATACACAAAAT 58.087 32.000 32.50 0.70 0.00 1.82
806 811 6.312399 ACAAGCTTGATTCGATACACAAAA 57.688 33.333 32.50 0.00 0.00 2.44
848 853 1.613925 TGCTCGCGGATCTATTAAGCT 59.386 47.619 6.13 0.00 0.00 3.74
862 867 0.315568 CCCTGATAGGTACTGCTCGC 59.684 60.000 0.00 0.00 41.52 5.03
864 869 2.036604 GCTTCCCTGATAGGTACTGCTC 59.963 54.545 0.00 0.00 41.52 4.26
992 1001 2.467826 GGGTTCTGCATCTCAGCGC 61.468 63.158 0.00 0.00 42.56 5.92
998 1007 0.179936 GCTGCTAGGGTTCTGCATCT 59.820 55.000 0.00 0.00 36.07 2.90
1407 1427 5.356882 TGCACTGAAAGAAAACGAATAGG 57.643 39.130 0.00 0.00 37.43 2.57
1469 1489 3.117738 AGAGAGAATTGGTAATGGGCCAG 60.118 47.826 13.78 0.00 37.31 4.85
1472 1492 4.098501 CCAAAGAGAGAATTGGTAATGGGC 59.901 45.833 0.00 0.00 40.96 5.36
1670 1701 9.067986 CAATTCCAGGTATATCCCTTTTACTTC 57.932 37.037 0.00 0.00 36.75 3.01
1703 1734 1.621814 AGACGAGAATTTTGGGACGGA 59.378 47.619 0.00 0.00 0.00 4.69
1704 1735 2.094762 AGACGAGAATTTTGGGACGG 57.905 50.000 0.00 0.00 0.00 4.79
1705 1736 3.064207 TGAAGACGAGAATTTTGGGACG 58.936 45.455 0.00 0.00 0.00 4.79
1706 1737 5.629079 ATTGAAGACGAGAATTTTGGGAC 57.371 39.130 0.00 0.00 0.00 4.46
1707 1738 6.040391 ACAAATTGAAGACGAGAATTTTGGGA 59.960 34.615 0.00 0.00 28.93 4.37
1708 1739 6.215845 ACAAATTGAAGACGAGAATTTTGGG 58.784 36.000 0.00 0.00 28.93 4.12
1709 1740 7.698836 AACAAATTGAAGACGAGAATTTTGG 57.301 32.000 0.00 0.00 28.93 3.28
1711 1742 9.796120 TGTAAACAAATTGAAGACGAGAATTTT 57.204 25.926 0.00 0.00 28.93 1.82
1712 1743 9.965824 ATGTAAACAAATTGAAGACGAGAATTT 57.034 25.926 0.00 0.00 31.03 1.82
1716 1747 8.717821 CCTTATGTAAACAAATTGAAGACGAGA 58.282 33.333 0.00 0.00 0.00 4.04
1717 1748 8.717821 TCCTTATGTAAACAAATTGAAGACGAG 58.282 33.333 0.00 0.00 0.00 4.18
1718 1749 8.610248 TCCTTATGTAAACAAATTGAAGACGA 57.390 30.769 0.00 0.00 0.00 4.20
1719 1750 9.277565 CATCCTTATGTAAACAAATTGAAGACG 57.722 33.333 0.00 0.00 0.00 4.18
1788 1819 8.947115 CCGTCCTAAAATTCTTGTCTTAGATTT 58.053 33.333 0.00 0.00 0.00 2.17
1789 1820 8.319146 TCCGTCCTAAAATTCTTGTCTTAGATT 58.681 33.333 0.00 0.00 0.00 2.40
1790 1821 7.848128 TCCGTCCTAAAATTCTTGTCTTAGAT 58.152 34.615 0.00 0.00 0.00 1.98
1791 1822 7.235935 TCCGTCCTAAAATTCTTGTCTTAGA 57.764 36.000 0.00 0.00 0.00 2.10
1792 1823 6.535508 CCTCCGTCCTAAAATTCTTGTCTTAG 59.464 42.308 0.00 0.00 0.00 2.18
1793 1824 6.211986 TCCTCCGTCCTAAAATTCTTGTCTTA 59.788 38.462 0.00 0.00 0.00 2.10
1794 1825 5.012768 TCCTCCGTCCTAAAATTCTTGTCTT 59.987 40.000 0.00 0.00 0.00 3.01
1795 1826 4.530946 TCCTCCGTCCTAAAATTCTTGTCT 59.469 41.667 0.00 0.00 0.00 3.41
1796 1827 4.828829 TCCTCCGTCCTAAAATTCTTGTC 58.171 43.478 0.00 0.00 0.00 3.18
1797 1828 4.903045 TCCTCCGTCCTAAAATTCTTGT 57.097 40.909 0.00 0.00 0.00 3.16
1798 1829 5.246307 ACTTCCTCCGTCCTAAAATTCTTG 58.754 41.667 0.00 0.00 0.00 3.02
1799 1830 5.500546 ACTTCCTCCGTCCTAAAATTCTT 57.499 39.130 0.00 0.00 0.00 2.52
1800 1831 6.809976 ATACTTCCTCCGTCCTAAAATTCT 57.190 37.500 0.00 0.00 0.00 2.40
1801 1832 7.678927 GCAAATACTTCCTCCGTCCTAAAATTC 60.679 40.741 0.00 0.00 0.00 2.17
1802 1833 6.095021 GCAAATACTTCCTCCGTCCTAAAATT 59.905 38.462 0.00 0.00 0.00 1.82
1803 1834 5.589050 GCAAATACTTCCTCCGTCCTAAAAT 59.411 40.000 0.00 0.00 0.00 1.82
1804 1835 4.939439 GCAAATACTTCCTCCGTCCTAAAA 59.061 41.667 0.00 0.00 0.00 1.52
1805 1836 4.224370 AGCAAATACTTCCTCCGTCCTAAA 59.776 41.667 0.00 0.00 0.00 1.85
1806 1837 3.773119 AGCAAATACTTCCTCCGTCCTAA 59.227 43.478 0.00 0.00 0.00 2.69
1807 1838 3.371965 AGCAAATACTTCCTCCGTCCTA 58.628 45.455 0.00 0.00 0.00 2.94
1808 1839 2.188817 AGCAAATACTTCCTCCGTCCT 58.811 47.619 0.00 0.00 0.00 3.85
1809 1840 2.693267 AGCAAATACTTCCTCCGTCC 57.307 50.000 0.00 0.00 0.00 4.79
1810 1841 4.804665 GTCTAAGCAAATACTTCCTCCGTC 59.195 45.833 0.00 0.00 0.00 4.79
1811 1842 4.466726 AGTCTAAGCAAATACTTCCTCCGT 59.533 41.667 0.00 0.00 0.00 4.69
1812 1843 4.806247 CAGTCTAAGCAAATACTTCCTCCG 59.194 45.833 0.00 0.00 0.00 4.63
1813 1844 5.582665 CACAGTCTAAGCAAATACTTCCTCC 59.417 44.000 0.00 0.00 0.00 4.30
1814 1845 6.166982 ACACAGTCTAAGCAAATACTTCCTC 58.833 40.000 0.00 0.00 0.00 3.71
1815 1846 6.115448 ACACAGTCTAAGCAAATACTTCCT 57.885 37.500 0.00 0.00 0.00 3.36
1816 1847 6.803154 AACACAGTCTAAGCAAATACTTCC 57.197 37.500 0.00 0.00 0.00 3.46
1817 1848 9.974750 GATAAACACAGTCTAAGCAAATACTTC 57.025 33.333 0.00 0.00 0.00 3.01
1818 1849 9.502091 TGATAAACACAGTCTAAGCAAATACTT 57.498 29.630 0.00 0.00 0.00 2.24
1819 1850 9.502091 TTGATAAACACAGTCTAAGCAAATACT 57.498 29.630 0.00 0.00 0.00 2.12
1849 1880 7.151976 GGTGTAAGCTAACCAACAATCAAAAT 58.848 34.615 8.00 0.00 36.41 1.82
1906 1937 7.019656 ACCACTATCCATATGCATTGACATA 57.980 36.000 3.54 3.24 36.96 2.29
1907 1938 5.884322 ACCACTATCCATATGCATTGACAT 58.116 37.500 3.54 2.30 0.00 3.06
2012 2047 5.236047 GCCAGTAGCTACTCATGATGAAAAG 59.764 44.000 23.68 7.83 38.99 2.27
2065 2100 0.673644 ACAGAAAGGCATCCGGTTCG 60.674 55.000 0.00 0.00 31.04 3.95
2142 2177 1.410153 ACAGCAGCACCCAAAAAGAAG 59.590 47.619 0.00 0.00 0.00 2.85
2150 2185 1.487850 TATCCACACAGCAGCACCCA 61.488 55.000 0.00 0.00 0.00 4.51
2151 2186 0.745845 CTATCCACACAGCAGCACCC 60.746 60.000 0.00 0.00 0.00 4.61
2259 2301 4.332819 GGGATGACATGTTTCTTTACTCCG 59.667 45.833 0.00 0.00 0.00 4.63
2277 2319 6.779539 AGCATCTAAGATTTAAAAGGGGGATG 59.220 38.462 14.12 14.12 0.00 3.51
2280 2322 6.641169 GAGCATCTAAGATTTAAAAGGGGG 57.359 41.667 0.00 0.00 0.00 5.40
2346 2393 1.490490 ACTGTTTCTGGAAGTGGCTGA 59.510 47.619 0.00 0.00 33.76 4.26
2493 2540 1.606668 GGTCACGCAATCCTCAACAAA 59.393 47.619 0.00 0.00 0.00 2.83
2730 3254 5.011023 ACAGTGCAAGATGTCGATCCATATA 59.989 40.000 0.00 0.00 0.00 0.86
2830 3354 5.136816 TCAACATGAATGGATTGTGTTGG 57.863 39.130 18.14 7.85 45.79 3.77
2875 3399 8.410141 GCAAACTGGCATAACTGGTTAAATATA 58.590 33.333 0.00 0.00 0.00 0.86
2908 3434 7.719483 ACAATGGAATTATAAACAGCCATGAG 58.281 34.615 10.58 9.49 36.34 2.90
2948 3476 5.282055 TCACTCAGCTATGGAACCATAAG 57.718 43.478 13.51 10.54 38.30 1.73
2989 3517 1.774217 AGCCTTGTGGACCTGGGAA 60.774 57.895 0.00 0.00 34.57 3.97
2990 3518 2.121963 AGCCTTGTGGACCTGGGA 60.122 61.111 0.00 0.00 34.57 4.37
3533 4096 2.437359 GTGCGGCTGCTCAAGGAT 60.437 61.111 20.27 0.00 43.34 3.24
3547 4110 3.557595 GCAGATAACATGGTAGTCTGTGC 59.442 47.826 21.23 11.94 38.75 4.57
3550 4113 8.501580 CAATATTGCAGATAACATGGTAGTCTG 58.498 37.037 18.41 18.41 39.35 3.51
3576 4139 2.263077 CATCGTCTGACCAGTTAGTGC 58.737 52.381 1.55 0.00 0.00 4.40
3648 4220 2.355197 TGGATTGCTTACCATGTCACG 58.645 47.619 0.00 0.00 0.00 4.35
3698 4289 1.237285 ATGACGCCAACTTGACAGGC 61.237 55.000 0.00 0.00 44.89 4.85
3761 4352 7.173907 CCAGATTTTTATGCCTAGTATGACTGG 59.826 40.741 0.00 0.00 33.24 4.00
3827 4418 7.731720 TGTGCGCATATTATAAACGTAATACC 58.268 34.615 15.91 0.00 31.37 2.73
3831 4422 8.762426 TGTAATGTGCGCATATTATAAACGTAA 58.238 29.630 32.96 14.15 34.39 3.18
3837 4428 7.413548 CCCGATTGTAATGTGCGCATATTATAA 60.414 37.037 33.93 33.93 33.01 0.98
3874 4465 0.249398 ACTTCCTCCGTCCCGAAATG 59.751 55.000 0.00 0.00 0.00 2.32
3875 4466 1.755380 CTACTTCCTCCGTCCCGAAAT 59.245 52.381 0.00 0.00 0.00 2.17
3876 4467 1.180029 CTACTTCCTCCGTCCCGAAA 58.820 55.000 0.00 0.00 0.00 3.46
3877 4468 0.038744 ACTACTTCCTCCGTCCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
3878 4469 0.911769 TACTACTTCCTCCGTCCCGA 59.088 55.000 0.00 0.00 0.00 5.14
3879 4470 1.978454 ATACTACTTCCTCCGTCCCG 58.022 55.000 0.00 0.00 0.00 5.14
3880 4471 3.450096 ACAAATACTACTTCCTCCGTCCC 59.550 47.826 0.00 0.00 0.00 4.46
3881 4472 4.732672 ACAAATACTACTTCCTCCGTCC 57.267 45.455 0.00 0.00 0.00 4.79
3882 4473 4.329256 GCAACAAATACTACTTCCTCCGTC 59.671 45.833 0.00 0.00 0.00 4.79
3883 4474 4.251268 GCAACAAATACTACTTCCTCCGT 58.749 43.478 0.00 0.00 0.00 4.69
3884 4475 4.250464 TGCAACAAATACTACTTCCTCCG 58.750 43.478 0.00 0.00 0.00 4.63
3885 4476 5.648092 ACATGCAACAAATACTACTTCCTCC 59.352 40.000 0.00 0.00 0.00 4.30
3911 4502 5.767168 AGTTATCTAATTGCCCTTGATCAGC 59.233 40.000 0.00 0.00 0.00 4.26
3937 4528 1.526575 GACACATGCCCACCACAAGG 61.527 60.000 0.00 0.00 42.21 3.61
3938 4529 1.526575 GGACACATGCCCACCACAAG 61.527 60.000 0.00 0.00 0.00 3.16
3939 4530 1.530419 GGACACATGCCCACCACAA 60.530 57.895 0.00 0.00 0.00 3.33
3940 4531 2.115052 GGACACATGCCCACCACA 59.885 61.111 0.00 0.00 0.00 4.17
3941 4532 1.675641 GAGGACACATGCCCACCAC 60.676 63.158 0.00 0.00 0.00 4.16
3942 4533 2.756400 GAGGACACATGCCCACCA 59.244 61.111 0.00 0.00 0.00 4.17
3943 4534 2.436646 CGAGGACACATGCCCACC 60.437 66.667 0.00 0.00 0.00 4.61
3944 4535 1.448540 CTCGAGGACACATGCCCAC 60.449 63.158 3.91 0.00 0.00 4.61
3945 4536 1.480212 AACTCGAGGACACATGCCCA 61.480 55.000 18.41 0.00 0.00 5.36
3946 4537 0.741221 GAACTCGAGGACACATGCCC 60.741 60.000 18.41 0.00 0.00 5.36
3947 4538 0.247736 AGAACTCGAGGACACATGCC 59.752 55.000 18.41 0.00 0.00 4.40
3948 4539 1.354040 CAGAACTCGAGGACACATGC 58.646 55.000 18.41 0.00 0.00 4.06
3949 4540 1.354040 GCAGAACTCGAGGACACATG 58.646 55.000 18.41 7.57 0.00 3.21
3950 4541 0.247736 GGCAGAACTCGAGGACACAT 59.752 55.000 18.41 0.00 0.00 3.21
3951 4542 1.666011 GGCAGAACTCGAGGACACA 59.334 57.895 18.41 0.00 0.00 3.72
3952 4543 1.444553 CGGCAGAACTCGAGGACAC 60.445 63.158 18.41 4.93 0.00 3.67
3953 4544 1.461091 AACGGCAGAACTCGAGGACA 61.461 55.000 18.41 0.00 0.00 4.02
3954 4545 1.009389 CAACGGCAGAACTCGAGGAC 61.009 60.000 18.41 10.09 0.00 3.85
3955 4546 1.289066 CAACGGCAGAACTCGAGGA 59.711 57.895 18.41 0.00 0.00 3.71
3956 4547 2.383527 GCAACGGCAGAACTCGAGG 61.384 63.158 18.41 0.00 40.72 4.63
3957 4548 2.720758 CGCAACGGCAGAACTCGAG 61.721 63.158 11.84 11.84 41.24 4.04
3958 4549 2.733218 CGCAACGGCAGAACTCGA 60.733 61.111 0.00 0.00 41.24 4.04
3959 4550 2.733218 TCGCAACGGCAGAACTCG 60.733 61.111 0.00 0.00 41.24 4.18
3960 4551 2.853914 GTCGCAACGGCAGAACTC 59.146 61.111 0.00 0.00 41.24 3.01
3961 4552 3.036084 CGTCGCAACGGCAGAACT 61.036 61.111 0.00 0.00 45.21 3.01
3970 4561 1.509162 GATCAAACGCCGTCGCAAC 60.509 57.895 0.00 0.00 39.84 4.17
3971 4562 2.673114 GGATCAAACGCCGTCGCAA 61.673 57.895 0.00 0.00 39.84 4.85
3972 4563 3.115892 GGATCAAACGCCGTCGCA 61.116 61.111 0.00 0.00 39.84 5.10
3973 4564 3.083600 CTGGATCAAACGCCGTCGC 62.084 63.158 0.00 0.00 39.84 5.19
3974 4565 3.081133 CTGGATCAAACGCCGTCG 58.919 61.111 0.00 0.00 42.43 5.12
3975 4566 2.785258 GCTGGATCAAACGCCGTC 59.215 61.111 0.00 0.00 0.00 4.79
3976 4567 3.118454 CGCTGGATCAAACGCCGT 61.118 61.111 0.00 0.00 0.00 5.68
3977 4568 4.520846 GCGCTGGATCAAACGCCG 62.521 66.667 6.62 0.00 45.35 6.46
3980 4571 3.864686 CCGGCGCTGGATCAAACG 61.865 66.667 32.31 9.91 0.00 3.60
3981 4572 4.179579 GCCGGCGCTGGATCAAAC 62.180 66.667 39.24 16.18 0.00 2.93
3982 4573 4.713735 TGCCGGCGCTGGATCAAA 62.714 61.111 39.24 14.77 35.36 2.69
3995 4586 2.742372 CTTCCAAGGTCCGTGCCG 60.742 66.667 0.00 0.00 0.00 5.69
3996 4587 2.359975 CCTTCCAAGGTCCGTGCC 60.360 66.667 0.00 0.00 41.41 5.01
4005 4596 5.606505 GAGGCTCTTAGATTACCTTCCAAG 58.393 45.833 7.40 0.00 0.00 3.61
4006 4597 4.099573 CGAGGCTCTTAGATTACCTTCCAA 59.900 45.833 13.50 0.00 0.00 3.53
4007 4598 3.637229 CGAGGCTCTTAGATTACCTTCCA 59.363 47.826 13.50 0.00 0.00 3.53
4008 4599 3.006003 CCGAGGCTCTTAGATTACCTTCC 59.994 52.174 13.50 0.00 0.00 3.46
4009 4600 3.890147 TCCGAGGCTCTTAGATTACCTTC 59.110 47.826 13.50 0.00 0.00 3.46
4010 4601 3.912248 TCCGAGGCTCTTAGATTACCTT 58.088 45.455 13.50 0.00 0.00 3.50
4011 4602 3.596940 TCCGAGGCTCTTAGATTACCT 57.403 47.619 13.50 0.00 0.00 3.08
4012 4603 3.006003 CCTTCCGAGGCTCTTAGATTACC 59.994 52.174 13.50 0.00 35.94 2.85
4013 4604 4.245845 CCTTCCGAGGCTCTTAGATTAC 57.754 50.000 13.50 0.00 35.94 1.89
4026 4617 3.304794 CCGCTCTTAGATTACCTTCCGAG 60.305 52.174 0.00 0.00 0.00 4.63
4027 4618 2.621998 CCGCTCTTAGATTACCTTCCGA 59.378 50.000 0.00 0.00 0.00 4.55
4028 4619 2.621998 TCCGCTCTTAGATTACCTTCCG 59.378 50.000 0.00 0.00 0.00 4.30
4031 4622 3.388024 TGCATCCGCTCTTAGATTACCTT 59.612 43.478 0.00 0.00 39.64 3.50
4037 4628 4.036027 CACAATTTGCATCCGCTCTTAGAT 59.964 41.667 0.00 0.00 39.64 1.98
4042 4633 0.813184 CCACAATTTGCATCCGCTCT 59.187 50.000 0.00 0.00 39.64 4.09
4054 4645 3.070734 TGCCACTAATGCAAACCACAATT 59.929 39.130 0.00 0.00 35.40 2.32
4063 4654 4.334552 TCTTTCAGATGCCACTAATGCAA 58.665 39.130 0.00 0.00 42.92 4.08
4081 4672 4.647853 CCCAACACATGATCCATCATCTTT 59.352 41.667 0.00 0.00 45.23 2.52
4095 4686 1.868498 CGTAACACGAACCCAACACAT 59.132 47.619 0.00 0.00 46.05 3.21
4111 4702 2.112190 TCATACCTGCCATCCACGTAA 58.888 47.619 0.00 0.00 0.00 3.18
4131 4722 2.069273 CTGCAACGTCGAAGAGGAAAT 58.931 47.619 5.05 0.00 46.48 2.17
4139 4730 0.927537 CACAAGACTGCAACGTCGAA 59.072 50.000 0.00 0.00 38.90 3.71
4142 4733 1.507141 CCCCACAAGACTGCAACGTC 61.507 60.000 0.00 0.00 0.00 4.34
4144 4735 2.260869 CCCCCACAAGACTGCAACG 61.261 63.158 0.00 0.00 0.00 4.10
4145 4736 0.755327 AACCCCCACAAGACTGCAAC 60.755 55.000 0.00 0.00 0.00 4.17
4146 4737 0.467290 GAACCCCCACAAGACTGCAA 60.467 55.000 0.00 0.00 0.00 4.08
4148 4739 1.603739 GGAACCCCCACAAGACTGC 60.604 63.158 0.00 0.00 34.14 4.40
4149 4740 0.250901 CTGGAACCCCCACAAGACTG 60.251 60.000 0.00 0.00 40.82 3.51
4154 4746 0.698238 CAGATCTGGAACCCCCACAA 59.302 55.000 15.38 0.00 40.82 3.33
4179 4771 3.632080 ACCCCGAACACGCCATCA 61.632 61.111 0.00 0.00 0.00 3.07
4201 4793 0.970640 TTGAACGAATCAGACCGGGA 59.029 50.000 6.32 0.00 39.77 5.14
4245 4840 1.426751 TTACGGACCTCCAAAGTGGT 58.573 50.000 0.00 0.00 42.59 4.16
4250 4845 3.223435 TGCAATTTTACGGACCTCCAAA 58.777 40.909 0.00 0.00 35.14 3.28
4262 4857 6.349280 GGCTCCATCGCTAATATGCAATTTTA 60.349 38.462 0.00 0.00 0.00 1.52
4266 4861 3.012518 GGCTCCATCGCTAATATGCAAT 58.987 45.455 0.00 0.00 0.00 3.56
4298 4893 1.434188 ACAGATCACCTTCACACCCA 58.566 50.000 0.00 0.00 0.00 4.51
4326 4921 4.012374 CCACACTAGCAACCATCAAAGAT 58.988 43.478 0.00 0.00 0.00 2.40
4327 4922 3.181445 ACCACACTAGCAACCATCAAAGA 60.181 43.478 0.00 0.00 0.00 2.52
4333 4928 1.982226 TGGTACCACACTAGCAACCAT 59.018 47.619 11.60 0.00 32.24 3.55
4337 4932 1.899814 CCTCTGGTACCACACTAGCAA 59.100 52.381 11.60 0.00 35.76 3.91
4343 4938 0.324943 ACATGCCTCTGGTACCACAC 59.675 55.000 11.60 0.96 0.00 3.82
4344 4939 0.324614 CACATGCCTCTGGTACCACA 59.675 55.000 11.60 8.05 0.00 4.17
4360 4955 1.153329 GACACCAACACCCGTCACA 60.153 57.895 0.00 0.00 0.00 3.58
4369 4964 2.997980 TGAAGAAGCTTGACACCAACA 58.002 42.857 2.10 0.00 0.00 3.33
4426 5057 5.221224 CCTGACCAAACTGAACAAATAGCAA 60.221 40.000 0.00 0.00 0.00 3.91
4458 5090 9.427821 CATAAGGATCTAGTATAAGCCACCTAT 57.572 37.037 0.00 0.00 0.00 2.57
4461 5093 7.719871 TCATAAGGATCTAGTATAAGCCACC 57.280 40.000 0.00 0.00 0.00 4.61
4494 5127 3.840890 TTTTGCGTGGAATACATGTCC 57.159 42.857 0.00 0.00 38.39 4.02


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

AutoCloner maintained by Alex Coulton.