Multiple sequence alignment - TraesCS2D01G277800

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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 TraesCS2D01G277800 chr2D 100.000 3431 0 0 1 3431 348189060 348192490 0.000000e+00 6336.0
1 TraesCS2D01G277800 chr2D 97.714 175 4 0 1576 1750 554128376 554128202 5.560000e-78 302.0
2 TraesCS2D01G277800 chr2D 94.595 37 2 0 705 741 410814610 410814646 1.330000e-04 58.4
3 TraesCS2D01G277800 chr2A 95.178 1659 46 12 1782 3431 461702581 461700948 0.000000e+00 2590.0
4 TraesCS2D01G277800 chr2A 91.263 847 35 11 744 1576 461703470 461702649 0.000000e+00 1118.0
5 TraesCS2D01G277800 chr2A 95.187 187 8 1 1576 1761 746757158 746756972 9.310000e-76 294.0
6 TraesCS2D01G277800 chr2A 89.498 219 16 2 1538 1749 587332896 587332678 1.570000e-68 270.0
7 TraesCS2D01G277800 chr2A 97.561 41 1 0 701 741 496571397 496571357 1.710000e-08 71.3
8 TraesCS2D01G277800 chr2B 92.668 1473 64 17 1722 3168 413446622 413448076 0.000000e+00 2082.0
9 TraesCS2D01G277800 chr2B 93.560 854 36 6 746 1581 413445792 413446644 0.000000e+00 1254.0
10 TraesCS2D01G277800 chr2B 96.241 266 10 0 3166 3431 413448169 413448434 1.460000e-118 436.0
11 TraesCS2D01G277800 chr2B 88.076 369 24 11 1 352 138110363 138110728 1.470000e-113 420.0
12 TraesCS2D01G277800 chr5D 90.871 723 49 10 29 741 460037687 460038402 0.000000e+00 953.0
13 TraesCS2D01G277800 chr5A 88.594 754 67 11 1 741 638290757 638291504 0.000000e+00 898.0
14 TraesCS2D01G277800 chr5A 95.833 192 4 4 1557 1744 382566612 382566803 1.200000e-79 307.0
15 TraesCS2D01G277800 chr3D 87.533 754 73 14 2 740 26278256 26277509 0.000000e+00 852.0
16 TraesCS2D01G277800 chr3D 97.778 45 1 0 1538 1582 523157428 523157384 1.020000e-10 78.7
17 TraesCS2D01G277800 chr3B 86.243 756 82 12 2 741 90847396 90846647 0.000000e+00 800.0
18 TraesCS2D01G277800 chr3B 80.861 674 65 31 1 663 769188442 769187822 4.010000e-129 472.0
19 TraesCS2D01G277800 chr3B 83.230 322 36 13 340 660 769160941 769161245 2.610000e-71 279.0
20 TraesCS2D01G277800 chr5B 82.553 619 87 16 30 635 415105408 415106018 3.030000e-145 525.0
21 TraesCS2D01G277800 chr7D 87.879 462 23 10 1 450 126020586 126020146 2.360000e-141 512.0
22 TraesCS2D01G277800 chr7A 89.260 419 29 9 1 407 283143242 283143656 8.490000e-141 510.0
23 TraesCS2D01G277800 chr7A 94.872 39 2 0 703 741 604225594 604225632 1.030000e-05 62.1
24 TraesCS2D01G277800 chr7A 92.500 40 2 1 703 741 33009644 33009605 4.780000e-04 56.5
25 TraesCS2D01G277800 chr1B 80.563 710 74 38 2 699 518908073 518907416 3.980000e-134 488.0
26 TraesCS2D01G277800 chr1B 95.109 184 8 1 1579 1761 476874907 476874724 4.330000e-74 289.0
27 TraesCS2D01G277800 chr1B 92.857 56 3 1 1520 1575 454362807 454362861 2.840000e-11 80.5
28 TraesCS2D01G277800 chr1A 84.054 370 48 9 377 740 535033858 535033494 2.530000e-91 346.0
29 TraesCS2D01G277800 chr1A 86.645 307 27 10 1 297 535034494 535034192 9.180000e-86 327.0
30 TraesCS2D01G277800 chr4D 98.810 168 2 0 1579 1746 22433569 22433736 2.000000e-77 300.0
31 TraesCS2D01G277800 chr4B 98.235 170 3 0 1577 1746 488893288 488893119 7.200000e-77 298.0
32 TraesCS2D01G277800 chr6D 98.225 169 3 0 1579 1747 392897139 392896971 2.590000e-76 296.0
33 TraesCS2D01G277800 chr1D 97.674 172 4 0 1579 1750 331539265 331539436 2.590000e-76 296.0
34 TraesCS2D01G277800 chr1D 87.500 64 5 3 1514 1575 463164444 463164506 1.710000e-08 71.3


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 TraesCS2D01G277800 chr2D 348189060 348192490 3430 False 6336.000000 6336 100.000000 1 3431 1 chr2D.!!$F1 3430
1 TraesCS2D01G277800 chr2A 461700948 461703470 2522 True 1854.000000 2590 93.220500 744 3431 2 chr2A.!!$R4 2687
2 TraesCS2D01G277800 chr2B 413445792 413448434 2642 False 1257.333333 2082 94.156333 746 3431 3 chr2B.!!$F2 2685
3 TraesCS2D01G277800 chr5D 460037687 460038402 715 False 953.000000 953 90.871000 29 741 1 chr5D.!!$F1 712
4 TraesCS2D01G277800 chr5A 638290757 638291504 747 False 898.000000 898 88.594000 1 741 1 chr5A.!!$F2 740
5 TraesCS2D01G277800 chr3D 26277509 26278256 747 True 852.000000 852 87.533000 2 740 1 chr3D.!!$R1 738
6 TraesCS2D01G277800 chr3B 90846647 90847396 749 True 800.000000 800 86.243000 2 741 1 chr3B.!!$R1 739
7 TraesCS2D01G277800 chr3B 769187822 769188442 620 True 472.000000 472 80.861000 1 663 1 chr3B.!!$R2 662
8 TraesCS2D01G277800 chr5B 415105408 415106018 610 False 525.000000 525 82.553000 30 635 1 chr5B.!!$F1 605
9 TraesCS2D01G277800 chr1B 518907416 518908073 657 True 488.000000 488 80.563000 2 699 1 chr1B.!!$R2 697
10 TraesCS2D01G277800 chr1A 535033494 535034494 1000 True 336.500000 346 85.349500 1 740 2 chr1A.!!$R1 739

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
766 1104 0.175760 ATGGACGGTGTCGAAGATGG 59.824 55.000 0.0 0.0 40.67 3.51 F
1272 1629 0.673022 CAGCTTGGGTGTCTGCTCTC 60.673 60.000 0.0 0.0 33.03 3.20 F
1592 1962 1.064091 AGGTACTACTCCCTCCGTTCC 60.064 57.143 0.0 0.0 36.02 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1727 2097 1.064091 GGTACTACTCCCTCCGTTCCT 60.064 57.143 0.00 0.0 0.00 3.36 R
2227 2632 1.372501 ACCATTGGACCAACCTAGCT 58.627 50.000 9.67 0.0 39.86 3.32 R
2822 3238 1.696063 ATGATTTTCCATGCCCTCCG 58.304 50.000 0.00 0.0 0.00 4.63 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
61 73 8.070769 GTGTCATTTGAAAAGTCTTCTACCTTC 58.929 37.037 0.00 0.00 0.00 3.46
72 84 7.736447 AGTCTTCTACCTTCTGAAAAATGTG 57.264 36.000 0.00 0.00 0.00 3.21
78 90 8.547967 TCTACCTTCTGAAAAATGTGATGTAC 57.452 34.615 0.00 0.00 0.00 2.90
139 157 8.132362 TGCGTTGTATTAAGAAAAGTGTTCATT 58.868 29.630 0.00 0.00 0.00 2.57
276 303 9.045223 GCTCTTTAAAAAGGTTCATGTGATTTT 57.955 29.630 2.77 0.00 36.67 1.82
389 706 3.318557 GGACTAGGAGTACGCAATAGCTT 59.681 47.826 0.00 0.00 39.10 3.74
390 707 4.518211 GGACTAGGAGTACGCAATAGCTTA 59.482 45.833 0.00 0.00 39.10 3.09
498 831 2.105477 GTGTGGTGGCCTAGATCATCAT 59.895 50.000 3.32 0.00 0.00 2.45
499 832 2.779430 TGTGGTGGCCTAGATCATCATT 59.221 45.455 3.32 0.00 0.00 2.57
555 888 0.539438 TGGACACCTTTGACCATGGC 60.539 55.000 13.04 5.35 41.88 4.40
560 893 2.225242 ACACCTTTGACCATGGCCAATA 60.225 45.455 14.76 5.09 0.00 1.90
572 908 1.631388 TGGCCAATAAAGACGGGAAGA 59.369 47.619 0.61 0.00 0.00 2.87
644 980 4.463050 ACCTGTGAAGGGGTTCAAATAA 57.537 40.909 0.00 0.00 32.04 1.40
660 996 7.870445 GGTTCAAATAAATAACTTGGACTTGCA 59.130 33.333 0.00 0.00 30.59 4.08
663 999 9.823647 TCAAATAAATAACTTGGACTTGCAAAA 57.176 25.926 0.00 0.00 0.00 2.44
668 1004 2.466846 ACTTGGACTTGCAAAAGGGTT 58.533 42.857 12.08 0.00 0.00 4.11
723 1061 4.686191 TTTCTTTCCCATTGCAACACAT 57.314 36.364 0.00 0.00 0.00 3.21
758 1096 5.290400 GCTAGTAGTTTTAATGGACGGTGTC 59.710 44.000 0.00 0.00 0.00 3.67
766 1104 0.175760 ATGGACGGTGTCGAAGATGG 59.824 55.000 0.00 0.00 40.67 3.51
777 1115 1.754803 TCGAAGATGGCCTAATCACGT 59.245 47.619 3.32 0.00 33.55 4.49
881 1237 1.336755 ACCCAAACGCTAACTTGCAAG 59.663 47.619 24.84 24.84 0.00 4.01
884 1240 1.780860 CAAACGCTAACTTGCAAGCAC 59.219 47.619 26.27 11.86 38.70 4.40
886 1242 0.868406 ACGCTAACTTGCAAGCACTC 59.132 50.000 26.27 12.08 38.70 3.51
887 1243 1.151668 CGCTAACTTGCAAGCACTCT 58.848 50.000 26.27 3.26 38.70 3.24
888 1244 1.127582 CGCTAACTTGCAAGCACTCTC 59.872 52.381 26.27 9.70 38.70 3.20
890 1246 2.771089 CTAACTTGCAAGCACTCTCCA 58.229 47.619 26.27 2.03 0.00 3.86
891 1247 1.602311 AACTTGCAAGCACTCTCCAG 58.398 50.000 26.27 0.00 0.00 3.86
893 1249 1.584380 CTTGCAAGCACTCTCCAGCC 61.584 60.000 14.65 0.00 0.00 4.85
894 1250 2.033141 GCAAGCACTCTCCAGCCA 59.967 61.111 0.00 0.00 0.00 4.75
895 1251 1.601759 GCAAGCACTCTCCAGCCAA 60.602 57.895 0.00 0.00 0.00 4.52
896 1252 1.174712 GCAAGCACTCTCCAGCCAAA 61.175 55.000 0.00 0.00 0.00 3.28
897 1253 1.321474 CAAGCACTCTCCAGCCAAAA 58.679 50.000 0.00 0.00 0.00 2.44
898 1254 1.682854 CAAGCACTCTCCAGCCAAAAA 59.317 47.619 0.00 0.00 0.00 1.94
899 1255 1.322442 AGCACTCTCCAGCCAAAAAC 58.678 50.000 0.00 0.00 0.00 2.43
900 1256 1.032014 GCACTCTCCAGCCAAAAACA 58.968 50.000 0.00 0.00 0.00 2.83
901 1257 1.615392 GCACTCTCCAGCCAAAAACAT 59.385 47.619 0.00 0.00 0.00 2.71
946 1302 2.113860 TCATTCGCCTTTCCTTCCTG 57.886 50.000 0.00 0.00 0.00 3.86
958 1315 1.447643 CTTCCTGCCCCTACCGATG 59.552 63.158 0.00 0.00 0.00 3.84
980 1337 1.271379 CCTTTTCCTAAACCAACGCCC 59.729 52.381 0.00 0.00 0.00 6.13
1006 1363 2.124570 CTCCCCTTGCCATGGACG 60.125 66.667 18.40 1.78 0.00 4.79
1262 1619 1.341383 GGTGATGATTCCAGCTTGGGT 60.341 52.381 2.86 0.00 38.32 4.51
1272 1629 0.673022 CAGCTTGGGTGTCTGCTCTC 60.673 60.000 0.00 0.00 33.03 3.20
1295 1656 7.757173 TCTCGTTTAATTCTGAGTGAGAGATTG 59.243 37.037 0.00 0.00 30.18 2.67
1340 1702 5.416947 GCTTCTTAATTTGGTCTACTCCGA 58.583 41.667 0.00 0.00 0.00 4.55
1344 1706 7.649533 TCTTAATTTGGTCTACTCCGATGTA 57.350 36.000 0.00 0.00 0.00 2.29
1373 1735 6.442112 AGAAAAGTTTCAGCTTCAAGTATGC 58.558 36.000 6.56 0.00 39.61 3.14
1374 1736 5.772825 AAAGTTTCAGCTTCAAGTATGCA 57.227 34.783 0.00 0.00 0.00 3.96
1375 1737 5.972107 AAGTTTCAGCTTCAAGTATGCAT 57.028 34.783 3.79 3.79 0.00 3.96
1376 1738 7.452880 AAAGTTTCAGCTTCAAGTATGCATA 57.547 32.000 1.16 1.16 0.00 3.14
1377 1739 6.428385 AGTTTCAGCTTCAAGTATGCATAC 57.572 37.500 26.26 26.26 0.00 2.39
1552 1922 4.681744 TCTGTTCATTGAACTGCCAAAAC 58.318 39.130 25.49 2.33 42.39 2.43
1577 1947 8.628280 ACGTCTTATATTTAGGAACAGAGGTAC 58.372 37.037 0.00 0.00 0.00 3.34
1583 1953 8.709272 ATATTTAGGAACAGAGGTACTACTCC 57.291 38.462 0.00 0.00 41.55 3.85
1584 1954 3.385314 AGGAACAGAGGTACTACTCCC 57.615 52.381 0.00 0.00 41.55 4.30
1585 1955 2.927685 AGGAACAGAGGTACTACTCCCT 59.072 50.000 0.00 0.00 41.55 4.20
1586 1956 3.053470 AGGAACAGAGGTACTACTCCCTC 60.053 52.174 0.00 0.00 46.34 4.30
1590 1960 2.433662 GAGGTACTACTCCCTCCGTT 57.566 55.000 0.00 0.00 41.55 4.44
1591 1961 2.296792 GAGGTACTACTCCCTCCGTTC 58.703 57.143 0.00 0.00 41.55 3.95
1592 1962 1.064091 AGGTACTACTCCCTCCGTTCC 60.064 57.143 0.00 0.00 36.02 3.62
1593 1963 1.064091 GGTACTACTCCCTCCGTTCCT 60.064 57.143 0.00 0.00 0.00 3.36
1594 1964 2.173569 GGTACTACTCCCTCCGTTCCTA 59.826 54.545 0.00 0.00 0.00 2.94
1595 1965 3.372025 GGTACTACTCCCTCCGTTCCTAA 60.372 52.174 0.00 0.00 0.00 2.69
1596 1966 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
1597 1967 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
1598 1968 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
1599 1969 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
1600 1970 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
1601 1971 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
1602 1972 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
1603 1973 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
1604 1974 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
1605 1975 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
1606 1976 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
1607 1977 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
1608 1978 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
1609 1979 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
1626 1996 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
1627 1997 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
1641 2011 2.979814 TGGACTACCACATTCGGATG 57.020 50.000 0.88 0.88 41.77 3.51
1643 2013 3.367321 TGGACTACCACATTCGGATGTA 58.633 45.455 9.54 0.00 44.55 2.29
1644 2014 3.964688 TGGACTACCACATTCGGATGTAT 59.035 43.478 9.54 3.42 44.55 2.29
1645 2015 5.141910 TGGACTACCACATTCGGATGTATA 58.858 41.667 9.54 4.49 44.55 1.47
1646 2016 5.778241 TGGACTACCACATTCGGATGTATAT 59.222 40.000 9.54 0.35 44.55 0.86
1647 2017 6.949463 TGGACTACCACATTCGGATGTATATA 59.051 38.462 9.54 1.59 44.55 0.86
1648 2018 7.122204 TGGACTACCACATTCGGATGTATATAG 59.878 40.741 9.54 13.12 44.55 1.31
1649 2019 7.338703 GGACTACCACATTCGGATGTATATAGA 59.661 40.741 20.24 2.13 44.55 1.98
1650 2020 8.053026 ACTACCACATTCGGATGTATATAGAC 57.947 38.462 20.24 0.00 44.55 2.59
1651 2021 6.911250 ACCACATTCGGATGTATATAGACA 57.089 37.500 9.54 2.07 44.55 3.41
1652 2022 7.482169 ACCACATTCGGATGTATATAGACAT 57.518 36.000 12.70 12.70 44.55 3.06
1653 2023 7.323420 ACCACATTCGGATGTATATAGACATG 58.677 38.462 17.40 6.38 44.55 3.21
1654 2024 7.039011 ACCACATTCGGATGTATATAGACATGT 60.039 37.037 17.40 6.99 44.55 3.21
1655 2025 7.819415 CCACATTCGGATGTATATAGACATGTT 59.181 37.037 17.40 0.00 44.55 2.71
1656 2026 9.208022 CACATTCGGATGTATATAGACATGTTT 57.792 33.333 17.40 0.00 44.55 2.83
1657 2027 9.778741 ACATTCGGATGTATATAGACATGTTTT 57.221 29.630 17.40 0.00 44.51 2.43
1672 2042 8.764524 AGACATGTTTTAGAGTGTAGATTCAC 57.235 34.615 0.00 0.00 38.46 3.18
1683 2053 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
1684 2054 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
1685 2055 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
1686 2056 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
1687 2057 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
1688 2058 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
1689 2059 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
1690 2060 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
1691 2061 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
1692 2062 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
1693 2063 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
1694 2064 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
1695 2065 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
1696 2066 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
1697 2067 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
1698 2068 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
1699 2069 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
1700 2070 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
1701 2071 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
1702 2072 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
1703 2073 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
1704 2074 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
1705 2075 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
1706 2076 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
1707 2077 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
1708 2078 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
1709 2079 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
1710 2080 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
1711 2081 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
1712 2082 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
1713 2083 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
1714 2084 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
1715 2085 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
1716 2086 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
1717 2087 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
1718 2088 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
1719 2089 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
1720 2090 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
1721 2091 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
1734 2104 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
1735 2105 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
1736 2106 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
1737 2107 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
1738 2108 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
1739 2109 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
1740 2110 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
1741 2111 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
1742 2112 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
1749 2119 2.173569 GGAACGGAGGGAGTAGTACCTA 59.826 54.545 0.00 0.00 37.18 3.08
1814 2212 9.289303 GGTGCAATACTTGACATAAGTTTATTG 57.711 33.333 0.00 9.37 33.00 1.90
1815 2213 9.840427 GTGCAATACTTGACATAAGTTTATTGT 57.160 29.630 12.90 0.00 32.69 2.71
1817 2215 9.503427 GCAATACTTGACATAAGTTTATTGTCC 57.497 33.333 12.90 0.72 32.69 4.02
1818 2216 9.702726 CAATACTTGACATAAGTTTATTGTCCG 57.297 33.333 9.48 5.27 28.77 4.79
1819 2217 6.178239 ACTTGACATAAGTTTATTGTCCGC 57.822 37.500 9.48 0.00 0.00 5.54
1820 2218 5.703592 ACTTGACATAAGTTTATTGTCCGCA 59.296 36.000 9.48 0.00 0.00 5.69
1821 2219 5.539582 TGACATAAGTTTATTGTCCGCAC 57.460 39.130 9.48 0.00 0.00 5.34
1855 2260 3.920231 AGCCTGAAGATGATGCTACAA 57.080 42.857 0.00 0.00 0.00 2.41
1880 2285 5.133941 TGTAATGCCCGCCTTTATAATTCA 58.866 37.500 0.00 0.00 0.00 2.57
1991 2396 4.938226 CAGAGGAATTAGTTGGGAACAGAC 59.062 45.833 0.00 0.00 44.54 3.51
2177 2582 6.553953 TGTTGCTCAGGTACTATGGAAATA 57.446 37.500 0.00 0.00 36.02 1.40
2226 2631 9.190317 TGATCATTATCTGTTGTCTAGTGTACT 57.810 33.333 0.00 0.00 32.93 2.73
2229 2634 8.622157 TCATTATCTGTTGTCTAGTGTACTAGC 58.378 37.037 13.02 9.40 44.24 3.42
2230 2635 8.625651 CATTATCTGTTGTCTAGTGTACTAGCT 58.374 37.037 13.02 0.00 44.24 3.32
2231 2636 9.848710 ATTATCTGTTGTCTAGTGTACTAGCTA 57.151 33.333 13.02 0.00 44.24 3.32
2232 2637 7.795482 ATCTGTTGTCTAGTGTACTAGCTAG 57.205 40.000 19.44 19.44 44.24 3.42
2233 2638 6.114089 TCTGTTGTCTAGTGTACTAGCTAGG 58.886 44.000 24.35 7.13 44.24 3.02
2234 2639 5.813383 TGTTGTCTAGTGTACTAGCTAGGT 58.187 41.667 24.35 12.43 44.24 3.08
2449 2863 8.873215 AAAATAACATAGGTGATGAGTACTCG 57.127 34.615 17.85 3.01 39.06 4.18
2450 2864 4.920640 AACATAGGTGATGAGTACTCGG 57.079 45.455 17.85 2.00 39.06 4.63
2652 3067 6.321945 TGGCTAGATAACTACGTACATCCAAA 59.678 38.462 0.00 0.00 0.00 3.28
3118 3557 5.221722 TGCAACAGGATAAGAGAAGTTGAGT 60.222 40.000 0.00 0.00 38.80 3.41
3119 3558 5.703130 GCAACAGGATAAGAGAAGTTGAGTT 59.297 40.000 0.00 0.00 38.80 3.01
3120 3559 6.348050 GCAACAGGATAAGAGAAGTTGAGTTG 60.348 42.308 0.00 0.00 38.80 3.16
3121 3560 6.672266 ACAGGATAAGAGAAGTTGAGTTGA 57.328 37.500 0.00 0.00 0.00 3.18
3122 3561 6.696411 ACAGGATAAGAGAAGTTGAGTTGAG 58.304 40.000 0.00 0.00 0.00 3.02
3142 3581 2.230266 AGCACCAAAGTTTTGTCGTGTT 59.770 40.909 12.40 6.66 34.74 3.32
3293 3827 3.307379 GTCACTTGGCGAGGTTCTT 57.693 52.632 6.71 0.00 0.00 2.52
3312 3846 5.447624 TCTTCGAGTTCACAATACACTGA 57.552 39.130 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 56 9.670719 CATTTTTCAGAAGGTAGAAGACTTTTC 57.329 33.333 0.00 0.00 0.00 2.29
389 706 1.618837 GTGTGACAGCTGTCCTTCCTA 59.381 52.381 37.23 19.54 44.15 2.94
390 707 0.394565 GTGTGACAGCTGTCCTTCCT 59.605 55.000 37.23 7.46 44.15 3.36
544 877 3.192422 CGTCTTTATTGGCCATGGTCAAA 59.808 43.478 34.01 20.36 43.25 2.69
545 878 2.752354 CGTCTTTATTGGCCATGGTCAA 59.248 45.455 32.71 32.71 44.19 3.18
555 888 4.216411 TCCTTCTTCCCGTCTTTATTGG 57.784 45.455 0.00 0.00 0.00 3.16
560 893 4.042435 TGGTTTATCCTTCTTCCCGTCTTT 59.958 41.667 0.00 0.00 37.07 2.52
572 908 5.067273 TCATTCGTGTTGTGGTTTATCCTT 58.933 37.500 0.00 0.00 37.07 3.36
644 980 4.653801 ACCCTTTTGCAAGTCCAAGTTATT 59.346 37.500 0.00 0.00 0.00 1.40
660 996 6.670695 ATAAGCATGACTCAAAACCCTTTT 57.329 33.333 0.00 0.00 0.00 2.27
663 999 4.463891 CCAATAAGCATGACTCAAAACCCT 59.536 41.667 0.00 0.00 0.00 4.34
668 1004 4.883585 CCTAGCCAATAAGCATGACTCAAA 59.116 41.667 0.00 0.00 34.23 2.69
676 1012 3.803186 ATGCTCCTAGCCAATAAGCAT 57.197 42.857 2.48 2.48 45.76 3.79
741 1079 3.742369 TCTTCGACACCGTCCATTAAAAC 59.258 43.478 0.00 0.00 37.05 2.43
742 1080 3.992643 TCTTCGACACCGTCCATTAAAA 58.007 40.909 0.00 0.00 37.05 1.52
758 1096 2.225068 ACGTGATTAGGCCATCTTCG 57.775 50.000 5.01 11.72 0.00 3.79
766 1104 4.686554 GGAATCAGATGTACGTGATTAGGC 59.313 45.833 14.53 6.18 42.26 3.93
802 1140 4.143242 CGTGGTCATTCGCATCTGATTATC 60.143 45.833 0.00 0.00 0.00 1.75
881 1237 1.032014 TGTTTTTGGCTGGAGAGTGC 58.968 50.000 0.00 0.00 0.00 4.40
884 1240 3.568538 CGAAATGTTTTTGGCTGGAGAG 58.431 45.455 0.00 0.00 0.00 3.20
886 1242 2.061028 GCGAAATGTTTTTGGCTGGAG 58.939 47.619 0.00 0.00 41.66 3.86
887 1243 2.147436 GCGAAATGTTTTTGGCTGGA 57.853 45.000 0.00 0.00 41.66 3.86
891 1247 3.184379 GGAAGAAGCGAAATGTTTTTGGC 59.816 43.478 0.00 0.00 44.23 4.52
893 1249 4.209080 GGTGGAAGAAGCGAAATGTTTTTG 59.791 41.667 0.00 0.00 0.00 2.44
894 1250 4.368315 GGTGGAAGAAGCGAAATGTTTTT 58.632 39.130 0.00 0.00 0.00 1.94
895 1251 3.243737 GGGTGGAAGAAGCGAAATGTTTT 60.244 43.478 0.00 0.00 0.00 2.43
896 1252 2.296190 GGGTGGAAGAAGCGAAATGTTT 59.704 45.455 0.00 0.00 0.00 2.83
897 1253 1.886542 GGGTGGAAGAAGCGAAATGTT 59.113 47.619 0.00 0.00 0.00 2.71
898 1254 1.202879 TGGGTGGAAGAAGCGAAATGT 60.203 47.619 0.00 0.00 0.00 2.71
899 1255 1.200020 GTGGGTGGAAGAAGCGAAATG 59.800 52.381 0.00 0.00 0.00 2.32
900 1256 1.073923 AGTGGGTGGAAGAAGCGAAAT 59.926 47.619 0.00 0.00 0.00 2.17
901 1257 0.472471 AGTGGGTGGAAGAAGCGAAA 59.528 50.000 0.00 0.00 0.00 3.46
946 1302 0.255033 AAAAGGTCATCGGTAGGGGC 59.745 55.000 0.00 0.00 0.00 5.80
958 1315 2.030540 GGCGTTGGTTTAGGAAAAGGTC 60.031 50.000 0.00 0.00 0.00 3.85
980 1337 2.045131 GCAAGGGGAGAGCAAGCAG 61.045 63.158 0.00 0.00 0.00 4.24
1262 1619 5.134202 TCAGAATTAAACGAGAGCAGACA 57.866 39.130 0.00 0.00 0.00 3.41
1272 1629 6.091305 TGCAATCTCTCACTCAGAATTAAACG 59.909 38.462 0.00 0.00 0.00 3.60
1328 1689 2.730934 AGCTACATCGGAGTAGACCA 57.269 50.000 16.13 0.00 43.24 4.02
1340 1702 7.445402 TGAAGCTGAAACTTTTCTAAGCTACAT 59.555 33.333 13.88 3.09 42.31 2.29
1344 1706 6.319911 ACTTGAAGCTGAAACTTTTCTAAGCT 59.680 34.615 9.61 9.61 43.89 3.74
1373 1735 8.587111 CATAAGCAGTATACAGTATTGCGTATG 58.413 37.037 23.97 23.97 44.38 2.39
1374 1736 8.520351 TCATAAGCAGTATACAGTATTGCGTAT 58.480 33.333 14.91 14.91 39.06 3.06
1375 1737 7.878036 TCATAAGCAGTATACAGTATTGCGTA 58.122 34.615 12.50 12.50 39.63 4.42
1376 1738 6.745116 TCATAAGCAGTATACAGTATTGCGT 58.255 36.000 5.50 10.01 39.63 5.24
1377 1739 7.637709 TTCATAAGCAGTATACAGTATTGCG 57.362 36.000 5.50 0.00 39.63 4.85
1542 1912 7.107542 TCCTAAATATAAGACGTTTTGGCAGT 58.892 34.615 0.83 0.00 30.97 4.40
1552 1922 8.848182 AGTACCTCTGTTCCTAAATATAAGACG 58.152 37.037 0.00 0.00 0.00 4.18
1577 1947 6.667558 AATATTTAGGAACGGAGGGAGTAG 57.332 41.667 0.00 0.00 0.00 2.57
1581 1951 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
1582 1952 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
1583 1953 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
1600 1970 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
1601 1971 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
1605 1975 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
1606 1976 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
1607 1977 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
1608 1978 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
1609 1979 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
1610 1980 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
1611 1981 7.396540 AATGTGGTAGTCCATTTGAAATCTC 57.603 36.000 0.00 0.00 46.20 2.75
1612 1982 6.094048 CGAATGTGGTAGTCCATTTGAAATCT 59.906 38.462 0.00 0.00 46.20 2.40
1613 1983 6.258160 CGAATGTGGTAGTCCATTTGAAATC 58.742 40.000 0.00 0.00 46.20 2.17
1614 1984 5.125417 CCGAATGTGGTAGTCCATTTGAAAT 59.875 40.000 0.00 0.00 46.20 2.17
1615 1985 4.457603 CCGAATGTGGTAGTCCATTTGAAA 59.542 41.667 0.00 0.00 46.20 2.69
1616 1986 4.006989 CCGAATGTGGTAGTCCATTTGAA 58.993 43.478 0.00 0.00 46.20 2.69
1617 1987 3.262151 TCCGAATGTGGTAGTCCATTTGA 59.738 43.478 0.00 0.00 46.20 2.69
1618 1988 3.605634 TCCGAATGTGGTAGTCCATTTG 58.394 45.455 0.00 0.00 46.20 2.32
1619 1989 3.992943 TCCGAATGTGGTAGTCCATTT 57.007 42.857 0.00 0.00 46.20 2.32
1620 1990 3.199946 ACATCCGAATGTGGTAGTCCATT 59.800 43.478 0.00 0.00 44.51 3.16
1621 1991 2.771943 ACATCCGAATGTGGTAGTCCAT 59.228 45.455 0.00 0.00 44.51 3.41
1622 1992 2.184533 ACATCCGAATGTGGTAGTCCA 58.815 47.619 0.00 0.00 44.51 4.02
1623 1993 2.981859 ACATCCGAATGTGGTAGTCC 57.018 50.000 0.00 0.00 44.51 3.85
1624 1994 8.182881 GTCTATATACATCCGAATGTGGTAGTC 58.817 40.741 0.00 0.00 45.72 2.59
1625 1995 7.668469 TGTCTATATACATCCGAATGTGGTAGT 59.332 37.037 0.00 0.00 45.72 2.73
1626 1996 8.051901 TGTCTATATACATCCGAATGTGGTAG 57.948 38.462 0.00 0.00 45.72 3.18
1627 1997 8.466798 CATGTCTATATACATCCGAATGTGGTA 58.533 37.037 0.00 0.00 45.72 3.25
1628 1998 6.911250 TGTCTATATACATCCGAATGTGGT 57.089 37.500 0.00 0.00 45.72 4.16
1629 1999 7.323420 ACATGTCTATATACATCCGAATGTGG 58.677 38.462 0.00 0.00 45.72 4.17
1630 2000 8.763049 AACATGTCTATATACATCCGAATGTG 57.237 34.615 0.00 0.00 45.72 3.21
1646 2016 9.856488 GTGAATCTACACTCTAAAACATGTCTA 57.144 33.333 0.00 0.00 37.73 2.59
1647 2017 8.589338 AGTGAATCTACACTCTAAAACATGTCT 58.411 33.333 0.00 0.00 46.36 3.41
1648 2018 8.764524 AGTGAATCTACACTCTAAAACATGTC 57.235 34.615 0.00 0.00 46.36 3.06
1661 2031 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
1662 2032 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
1663 2033 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
1664 2034 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
1665 2035 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
1666 2036 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
1667 2037 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
1668 2038 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
1669 2039 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
1670 2040 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
1671 2041 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
1672 2042 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
1673 2043 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
1674 2044 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
1675 2045 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
1676 2046 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
1677 2047 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
1678 2048 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
1679 2049 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
1680 2050 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
1681 2051 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
1682 2052 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
1683 2053 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
1684 2054 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
1685 2055 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
1687 2057 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
1688 2058 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
1689 2059 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
1690 2060 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
1691 2061 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
1692 2062 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
1693 2063 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
1694 2064 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
1695 2065 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
1708 2078 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
1709 2079 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
1710 2080 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
1711 2081 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
1712 2082 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
1713 2083 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
1714 2084 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
1715 2085 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
1716 2086 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
1717 2087 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
1718 2088 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
1719 2089 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
1720 2090 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
1721 2091 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
1722 2092 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
1723 2093 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
1724 2094 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
1725 2095 3.372025 GGTACTACTCCCTCCGTTCCTAA 60.372 52.174 0.00 0.00 0.00 2.69
1726 2096 2.173569 GGTACTACTCCCTCCGTTCCTA 59.826 54.545 0.00 0.00 0.00 2.94
1727 2097 1.064091 GGTACTACTCCCTCCGTTCCT 60.064 57.143 0.00 0.00 0.00 3.36
1728 2098 1.064091 AGGTACTACTCCCTCCGTTCC 60.064 57.143 0.00 0.00 36.02 3.62
1729 2099 2.433662 AGGTACTACTCCCTCCGTTC 57.566 55.000 0.00 0.00 36.02 3.95
1730 2100 4.533001 ATTAGGTACTACTCCCTCCGTT 57.467 45.455 0.00 0.00 42.67 4.44
1731 2101 5.629125 CTTATTAGGTACTACTCCCTCCGT 58.371 45.833 0.00 0.00 42.67 4.69
1732 2102 4.458642 GCTTATTAGGTACTACTCCCTCCG 59.541 50.000 0.00 0.00 42.67 4.63
1733 2103 5.643176 AGCTTATTAGGTACTACTCCCTCC 58.357 45.833 0.00 0.00 42.67 4.30
1734 2104 8.703378 TTAAGCTTATTAGGTACTACTCCCTC 57.297 38.462 7.08 0.00 42.67 4.30
1735 2105 9.671862 AATTAAGCTTATTAGGTACTACTCCCT 57.328 33.333 7.08 0.00 42.67 4.20
1740 2110 9.650539 GGCCTAATTAAGCTTATTAGGTACTAC 57.349 37.037 30.38 22.01 45.30 2.73
1741 2111 8.526147 CGGCCTAATTAAGCTTATTAGGTACTA 58.474 37.037 30.38 11.53 45.30 1.82
1742 2112 7.234166 TCGGCCTAATTAAGCTTATTAGGTACT 59.766 37.037 30.38 11.74 45.30 2.73
1749 2119 8.154856 TGTCTTATCGGCCTAATTAAGCTTATT 58.845 33.333 7.08 0.48 0.00 1.40
1803 2201 5.621329 GCCAAAGTGCGGACAATAAACTTAT 60.621 40.000 10.52 0.00 31.09 1.73
1814 2212 2.383527 CGAGAGCCAAAGTGCGGAC 61.384 63.158 0.00 0.00 36.02 4.79
1815 2213 2.048222 CGAGAGCCAAAGTGCGGA 60.048 61.111 0.00 0.00 36.02 5.54
1817 2215 1.630244 CTTCCGAGAGCCAAAGTGCG 61.630 60.000 0.00 0.00 36.02 5.34
1818 2216 1.916697 GCTTCCGAGAGCCAAAGTGC 61.917 60.000 0.00 0.00 36.66 4.40
1819 2217 2.166270 GCTTCCGAGAGCCAAAGTG 58.834 57.895 0.00 0.00 36.66 3.16
1820 2218 4.703703 GCTTCCGAGAGCCAAAGT 57.296 55.556 0.00 0.00 36.66 2.66
1855 2260 6.266558 TGAATTATAAAGGCGGGCATTACAAT 59.733 34.615 3.78 0.55 0.00 2.71
1880 2285 1.400494 GCGCAACAAGGGATAAATCGT 59.600 47.619 0.30 0.00 0.00 3.73
2019 2424 3.748048 CCTTTCGATCTGAAGAAGCACAA 59.252 43.478 6.53 0.00 37.99 3.33
2177 2582 1.922057 TGGATCACGCCCATCCAAT 59.078 52.632 7.87 0.00 45.73 3.16
2226 2631 2.557869 ACCATTGGACCAACCTAGCTA 58.442 47.619 9.67 0.00 39.86 3.32
2227 2632 1.372501 ACCATTGGACCAACCTAGCT 58.627 50.000 9.67 0.00 39.86 3.32
2228 2633 2.215942 AACCATTGGACCAACCTAGC 57.784 50.000 9.67 0.00 39.86 3.42
2229 2634 6.659824 AGTTATAACCATTGGACCAACCTAG 58.340 40.000 9.67 1.08 39.86 3.02
2230 2635 6.645884 AGTTATAACCATTGGACCAACCTA 57.354 37.500 9.67 0.00 39.86 3.08
2231 2636 5.530176 AGTTATAACCATTGGACCAACCT 57.470 39.130 9.67 0.00 39.86 3.50
2232 2637 6.209788 TCAAAGTTATAACCATTGGACCAACC 59.790 38.462 22.04 0.00 39.54 3.77
2233 2638 7.222000 TCAAAGTTATAACCATTGGACCAAC 57.778 36.000 22.04 7.73 31.15 3.77
2234 2639 7.287927 TGTTCAAAGTTATAACCATTGGACCAA 59.712 33.333 25.67 9.92 35.49 3.67
2470 2884 9.260002 GAGAAGAATGAACTAAATCATCCTCTC 57.740 37.037 0.00 0.00 39.08 3.20
2822 3238 1.696063 ATGATTTTCCATGCCCTCCG 58.304 50.000 0.00 0.00 0.00 4.63
2971 3388 2.882324 CCTTTCTACTGAAGGCGTCTC 58.118 52.381 1.41 0.00 33.28 3.36
3118 3557 2.490115 ACGACAAAACTTTGGTGCTCAA 59.510 40.909 7.09 0.00 42.34 3.02
3119 3558 2.088423 ACGACAAAACTTTGGTGCTCA 58.912 42.857 7.09 0.00 42.34 4.26
3120 3559 2.159435 ACACGACAAAACTTTGGTGCTC 60.159 45.455 7.09 0.00 42.34 4.26
3121 3560 1.816224 ACACGACAAAACTTTGGTGCT 59.184 42.857 7.09 0.00 42.34 4.40
3122 3561 2.271821 ACACGACAAAACTTTGGTGC 57.728 45.000 7.09 0.00 42.34 5.01
3142 3581 3.726291 TTCATCATCGGCGATAAGTGA 57.274 42.857 23.53 21.38 0.00 3.41
3293 3827 3.572682 AGGTCAGTGTATTGTGAACTCGA 59.427 43.478 0.00 0.00 35.80 4.04
3312 3846 2.283388 CACATGCCAGGCCAAGGT 60.283 61.111 9.64 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.