Multiple sequence alignment - TraesCS2D01G262300

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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 TraesCS2D01G262300 chr2D 100.000 5452 0 0 1 5452 318559468 318554017 0.000000e+00 10069.0
1 TraesCS2D01G262300 chr2D 87.974 923 83 17 1 902 87417485 87416570 0.000000e+00 1064.0
2 TraesCS2D01G262300 chr2D 79.212 914 113 47 1 899 159341795 159340944 1.030000e-156 564.0
3 TraesCS2D01G262300 chr2D 90.361 332 28 2 1 331 394533866 394534194 3.020000e-117 433.0
4 TraesCS2D01G262300 chr2D 86.523 371 36 6 4 366 621591087 621590723 3.960000e-106 396.0
5 TraesCS2D01G262300 chr2D 88.199 322 27 8 1 321 152874765 152874454 1.850000e-99 374.0
6 TraesCS2D01G262300 chr2D 86.520 319 33 8 1 318 506938429 506938738 5.230000e-90 342.0
7 TraesCS2D01G262300 chr2D 86.799 303 36 2 3 304 310898670 310898969 8.750000e-88 335.0
8 TraesCS2D01G262300 chr2A 95.481 3231 106 22 2243 5452 412508785 412511996 0.000000e+00 5121.0
9 TraesCS2D01G262300 chr2A 87.727 660 37 18 896 1520 412507282 412507932 0.000000e+00 730.0
10 TraesCS2D01G262300 chr2A 88.971 408 33 7 1737 2141 412508155 412508553 1.360000e-135 494.0
11 TraesCS2D01G262300 chr2A 90.722 97 5 4 1651 1743 753776457 753776361 5.730000e-25 126.0
12 TraesCS2D01G262300 chr2B 95.418 3230 109 20 2243 5452 387080094 387076884 0.000000e+00 5108.0
13 TraesCS2D01G262300 chr2B 94.409 465 17 4 899 1357 387081676 387081215 0.000000e+00 706.0
14 TraesCS2D01G262300 chr2B 88.889 405 34 7 1740 2142 387080720 387080325 6.350000e-134 488.0
15 TraesCS2D01G262300 chr2B 88.571 105 6 4 2140 2238 387080243 387080139 7.420000e-24 122.0
16 TraesCS2D01G262300 chr4D 91.290 907 60 15 1 902 91080134 91079242 0.000000e+00 1219.0
17 TraesCS2D01G262300 chr5D 87.500 920 84 20 1 899 435666877 435667786 0.000000e+00 1033.0
18 TraesCS2D01G262300 chr5D 85.856 905 95 17 1 899 410504200 410505077 0.000000e+00 931.0
19 TraesCS2D01G262300 chr5D 85.022 928 90 31 1 899 542619031 542619938 0.000000e+00 898.0
20 TraesCS2D01G262300 chr5D 86.812 690 75 10 1 688 309674226 309674901 0.000000e+00 756.0
21 TraesCS2D01G262300 chr5D 94.382 89 4 1 1655 1742 223649978 223649890 9.530000e-28 135.0
22 TraesCS2D01G262300 chr5A 87.296 921 92 16 1 899 535585383 535584466 0.000000e+00 1029.0
23 TraesCS2D01G262300 chr7B 85.145 929 97 23 5 901 261979616 261980535 0.000000e+00 913.0
24 TraesCS2D01G262300 chr7B 92.308 91 6 1 1651 1740 732633470 732633560 1.590000e-25 128.0
25 TraesCS2D01G262300 chr3D 84.770 847 95 17 11 836 434952675 434953508 0.000000e+00 819.0
26 TraesCS2D01G262300 chr4A 94.565 92 4 1 1652 1742 697982984 697983075 2.050000e-29 141.0
27 TraesCS2D01G262300 chr4A 93.478 92 5 1 1655 1745 200089249 200089158 9.530000e-28 135.0
28 TraesCS2D01G262300 chr3B 93.750 96 2 4 1655 1748 472309439 472309346 2.050000e-29 141.0
29 TraesCS2D01G262300 chr6B 93.548 93 5 1 1651 1742 172636306 172636214 2.650000e-28 137.0
30 TraesCS2D01G262300 chr7D 93.333 90 5 1 1655 1743 579751264 579751353 1.230000e-26 132.0
31 TraesCS2D01G262300 chr4B 93.333 90 5 1 1653 1741 607437508 607437419 1.230000e-26 132.0
32 TraesCS2D01G262300 chr5B 96.875 32 1 0 1219 1250 426586144 426586175 3.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G262300 chr2D 318554017 318559468 5451 True 10069 10069 100.000000 1 5452 1 chr2D.!!$R4 5451
1 TraesCS2D01G262300 chr2D 87416570 87417485 915 True 1064 1064 87.974000 1 902 1 chr2D.!!$R1 901
2 TraesCS2D01G262300 chr2D 159340944 159341795 851 True 564 564 79.212000 1 899 1 chr2D.!!$R3 898
3 TraesCS2D01G262300 chr2A 412507282 412511996 4714 False 2115 5121 90.726333 896 5452 3 chr2A.!!$F1 4556
4 TraesCS2D01G262300 chr2B 387076884 387081676 4792 True 1606 5108 91.821750 899 5452 4 chr2B.!!$R1 4553
5 TraesCS2D01G262300 chr4D 91079242 91080134 892 True 1219 1219 91.290000 1 902 1 chr4D.!!$R1 901
6 TraesCS2D01G262300 chr5D 435666877 435667786 909 False 1033 1033 87.500000 1 899 1 chr5D.!!$F3 898
7 TraesCS2D01G262300 chr5D 410504200 410505077 877 False 931 931 85.856000 1 899 1 chr5D.!!$F2 898
8 TraesCS2D01G262300 chr5D 542619031 542619938 907 False 898 898 85.022000 1 899 1 chr5D.!!$F4 898
9 TraesCS2D01G262300 chr5D 309674226 309674901 675 False 756 756 86.812000 1 688 1 chr5D.!!$F1 687
10 TraesCS2D01G262300 chr5A 535584466 535585383 917 True 1029 1029 87.296000 1 899 1 chr5A.!!$R1 898
11 TraesCS2D01G262300 chr7B 261979616 261980535 919 False 913 913 85.145000 5 901 1 chr7B.!!$F1 896
12 TraesCS2D01G262300 chr3D 434952675 434953508 833 False 819 819 84.770000 11 836 1 chr3D.!!$F1 825

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
633 740 0.753262 CCTGTAGTTGCGGCCTCTAT 59.247 55.0 0.00 0.0 0.00 1.98 F
1374 1570 0.398381 ATCCCACTCCTCCTCTCTGC 60.398 60.0 0.00 0.0 0.00 4.26 F
1734 2095 0.258484 TACGTTATGGGACGGAGGGA 59.742 55.0 0.00 0.0 46.77 4.20 F
2573 3070 0.661020 CGAAACGGAGGCAAAAGTGT 59.339 50.0 0.00 0.0 0.00 3.55 F
2953 3475 0.037590 AATGGCAGCGGTGTTCCTAA 59.962 50.0 17.07 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1436 1682 0.040204 AAGAGGATGGCAAAGGTGGG 59.960 55.0 0.0 0.0 0.00 4.61 R
2817 3339 0.546507 TGGATGCCTGGAGGTACACA 60.547 55.0 0.0 0.0 37.57 3.72 R
2844 3366 0.736672 GGACCGAAAAGAGAGCCGAC 60.737 60.0 0.0 0.0 0.00 4.79 R
4364 4887 0.684535 TGATGAACAGGAGAACGGCA 59.315 50.0 0.0 0.0 0.00 5.69 R
4922 5445 2.352421 CCGTCGTAGTTGATCCTGTTGT 60.352 50.0 0.0 0.0 0.00 3.32 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
33 35 1.070105 GTTGACGTACCCTGCCACA 59.930 57.895 0.00 0.00 0.00 4.17
245 264 2.434359 GCTCCTCCCCGTTTCGTG 60.434 66.667 0.00 0.00 0.00 4.35
267 286 1.965754 GCCGAAGACAGAGCCAGGAT 61.966 60.000 0.00 0.00 0.00 3.24
270 289 1.205655 CGAAGACAGAGCCAGGATTCA 59.794 52.381 0.00 0.00 0.00 2.57
324 396 2.203788 TGAAGACGGAGCCAGGGT 60.204 61.111 0.00 0.00 0.00 4.34
630 737 2.820037 GCCTGTAGTTGCGGCCTC 60.820 66.667 0.00 0.00 37.86 4.70
631 738 2.982130 CCTGTAGTTGCGGCCTCT 59.018 61.111 0.00 0.00 0.00 3.69
632 739 1.956629 GCCTGTAGTTGCGGCCTCTA 61.957 60.000 0.00 0.00 37.86 2.43
633 740 0.753262 CCTGTAGTTGCGGCCTCTAT 59.247 55.000 0.00 0.00 0.00 1.98
634 741 1.139058 CCTGTAGTTGCGGCCTCTATT 59.861 52.381 0.00 0.00 0.00 1.73
635 742 2.420129 CCTGTAGTTGCGGCCTCTATTT 60.420 50.000 0.00 0.00 0.00 1.40
638 749 3.687698 TGTAGTTGCGGCCTCTATTTTTC 59.312 43.478 0.00 0.00 0.00 2.29
649 762 7.644157 GCGGCCTCTATTTTTCTTTAAGTATTG 59.356 37.037 0.00 0.00 0.00 1.90
702 816 3.871594 GCCTAAGTAATGTCATGTTCGCT 59.128 43.478 0.00 0.00 0.00 4.93
779 909 5.847111 AAAAATATTAAAGACGCCTCCCC 57.153 39.130 0.00 0.00 0.00 4.81
780 910 4.513406 AAATATTAAAGACGCCTCCCCA 57.487 40.909 0.00 0.00 0.00 4.96
844 975 1.689352 CGATTTTAGCGCCGGTTCGT 61.689 55.000 2.29 0.00 0.00 3.85
851 982 4.367023 CGCCGGTTCGTCCCAAGA 62.367 66.667 1.90 0.00 0.00 3.02
934 1065 4.980592 TGCCCTGTCCTCCCTGCA 62.981 66.667 0.00 0.00 0.00 4.41
947 1078 1.239968 CCCTGCACTTGCTTGACCTC 61.240 60.000 2.33 0.00 42.66 3.85
949 1080 1.228245 TGCACTTGCTTGACCTCCC 60.228 57.895 2.33 0.00 42.66 4.30
953 1084 2.032528 TTGCTTGACCTCCCGCTG 59.967 61.111 0.00 0.00 0.00 5.18
955 1086 4.400961 GCTTGACCTCCCGCTGCT 62.401 66.667 0.00 0.00 0.00 4.24
956 1087 2.125350 CTTGACCTCCCGCTGCTC 60.125 66.667 0.00 0.00 0.00 4.26
957 1088 3.672295 CTTGACCTCCCGCTGCTCC 62.672 68.421 0.00 0.00 0.00 4.70
972 1103 1.506309 GCTCCACACGCACATCACAA 61.506 55.000 0.00 0.00 0.00 3.33
993 1128 1.023513 GCACAAGCTACCTGCAGAGG 61.024 60.000 17.39 2.02 45.94 3.69
1016 1151 1.303282 GAATGGGCGAAGAAGGGGT 59.697 57.895 0.00 0.00 0.00 4.95
1042 1177 1.198094 TCCGTTGCTGGATGGGAAGA 61.198 55.000 0.00 0.00 31.53 2.87
1312 1447 2.544267 GCGCTCATGGTACCAATTCTAC 59.456 50.000 20.76 5.84 0.00 2.59
1357 1492 8.447924 TTCTTCTCCATTGATTTGATCTGATC 57.552 34.615 10.72 10.72 0.00 2.92
1374 1570 0.398381 ATCCCACTCCTCCTCTCTGC 60.398 60.000 0.00 0.00 0.00 4.26
1432 1678 7.462571 ACAATGTTTACCTACCATCTTTTCC 57.537 36.000 0.00 0.00 0.00 3.13
1436 1682 5.475564 TGTTTACCTACCATCTTTTCCTTGC 59.524 40.000 0.00 0.00 0.00 4.01
1437 1683 3.087370 ACCTACCATCTTTTCCTTGCC 57.913 47.619 0.00 0.00 0.00 4.52
1439 1685 2.291540 CCTACCATCTTTTCCTTGCCCA 60.292 50.000 0.00 0.00 0.00 5.36
1451 1697 1.891722 CTTGCCCACCTTTGCCATCC 61.892 60.000 0.00 0.00 0.00 3.51
1458 1704 2.622452 CCACCTTTGCCATCCTCTTCAT 60.622 50.000 0.00 0.00 0.00 2.57
1459 1705 3.371917 CCACCTTTGCCATCCTCTTCATA 60.372 47.826 0.00 0.00 0.00 2.15
1486 1732 1.273267 TGCCACCACTCCATAGTCTCT 60.273 52.381 0.00 0.00 31.97 3.10
1487 1733 1.410882 GCCACCACTCCATAGTCTCTC 59.589 57.143 0.00 0.00 31.97 3.20
1498 1744 4.657504 TCCATAGTCTCTCCATTGCTCAAT 59.342 41.667 0.00 0.00 0.00 2.57
1509 1755 3.524541 CATTGCTCAATTAAGTTGCCCC 58.475 45.455 0.00 0.00 37.74 5.80
1511 1757 2.170166 TGCTCAATTAAGTTGCCCCTG 58.830 47.619 0.00 0.00 37.74 4.45
1512 1758 2.171003 GCTCAATTAAGTTGCCCCTGT 58.829 47.619 0.00 0.00 37.74 4.00
1513 1759 2.164422 GCTCAATTAAGTTGCCCCTGTC 59.836 50.000 0.00 0.00 37.74 3.51
1515 1761 4.019174 CTCAATTAAGTTGCCCCTGTCAT 58.981 43.478 0.00 0.00 37.74 3.06
1516 1762 5.186256 TCAATTAAGTTGCCCCTGTCATA 57.814 39.130 0.00 0.00 37.74 2.15
1517 1763 5.192927 TCAATTAAGTTGCCCCTGTCATAG 58.807 41.667 0.00 0.00 37.74 2.23
1518 1764 5.045213 TCAATTAAGTTGCCCCTGTCATAGA 60.045 40.000 0.00 0.00 37.74 1.98
1519 1765 2.789409 AAGTTGCCCCTGTCATAGAC 57.211 50.000 0.00 0.00 0.00 2.59
1520 1766 1.958288 AGTTGCCCCTGTCATAGACT 58.042 50.000 0.00 0.00 33.15 3.24
1521 1767 1.556911 AGTTGCCCCTGTCATAGACTG 59.443 52.381 0.00 0.00 33.15 3.51
1522 1768 0.911769 TTGCCCCTGTCATAGACTGG 59.088 55.000 14.05 14.05 46.58 4.00
1530 1776 2.692557 CTGTCATAGACTGGACCAGAGG 59.307 54.545 28.56 7.75 35.18 3.69
1531 1777 2.043115 TGTCATAGACTGGACCAGAGGT 59.957 50.000 28.56 13.48 33.99 3.85
1532 1778 3.268595 TGTCATAGACTGGACCAGAGGTA 59.731 47.826 28.56 15.14 32.34 3.08
1533 1779 3.633065 GTCATAGACTGGACCAGAGGTAC 59.367 52.174 28.56 13.24 35.25 3.34
1534 1780 7.056862 TGTCATAGACTGGACCAGAGGTACT 62.057 48.000 28.56 18.09 37.45 2.73
1535 1781 8.769083 TGTCATAGACTGGACCAGAGGTACTC 62.769 50.000 28.56 13.49 44.17 2.59
1556 1802 6.363065 ACTCAAACATATGCTCCATCATTCT 58.637 36.000 1.58 0.00 0.00 2.40
1562 1808 7.741027 ACATATGCTCCATCATTCTTTGTAG 57.259 36.000 1.58 0.00 0.00 2.74
1563 1809 7.285566 ACATATGCTCCATCATTCTTTGTAGT 58.714 34.615 1.58 0.00 0.00 2.73
1565 1811 9.445878 CATATGCTCCATCATTCTTTGTAGTAT 57.554 33.333 0.00 0.00 0.00 2.12
1566 1812 7.976135 ATGCTCCATCATTCTTTGTAGTATC 57.024 36.000 0.00 0.00 0.00 2.24
1567 1813 6.888105 TGCTCCATCATTCTTTGTAGTATCA 58.112 36.000 0.00 0.00 0.00 2.15
1568 1814 7.512130 TGCTCCATCATTCTTTGTAGTATCAT 58.488 34.615 0.00 0.00 0.00 2.45
1569 1815 7.994911 TGCTCCATCATTCTTTGTAGTATCATT 59.005 33.333 0.00 0.00 0.00 2.57
1570 1816 8.844244 GCTCCATCATTCTTTGTAGTATCATTT 58.156 33.333 0.00 0.00 0.00 2.32
1589 1835 6.586344 TCATTTACTAGATCTGCCTCCAAAG 58.414 40.000 5.18 0.00 0.00 2.77
1593 1839 4.033709 ACTAGATCTGCCTCCAAAGCTAA 58.966 43.478 5.18 0.00 0.00 3.09
1599 1845 6.891908 AGATCTGCCTCCAAAGCTAAAATAAA 59.108 34.615 0.00 0.00 0.00 1.40
1600 1846 7.562821 AGATCTGCCTCCAAAGCTAAAATAAAT 59.437 33.333 0.00 0.00 0.00 1.40
1601 1847 6.866480 TCTGCCTCCAAAGCTAAAATAAATG 58.134 36.000 0.00 0.00 0.00 2.32
1602 1848 6.663093 TCTGCCTCCAAAGCTAAAATAAATGA 59.337 34.615 0.00 0.00 0.00 2.57
1606 1967 7.063426 GCCTCCAAAGCTAAAATAAATGAACAC 59.937 37.037 0.00 0.00 0.00 3.32
1607 1968 8.306761 CCTCCAAAGCTAAAATAAATGAACACT 58.693 33.333 0.00 0.00 0.00 3.55
1649 2010 6.479331 GTCTATAGTGGTTACCTAAGCTTTGC 59.521 42.308 3.20 0.00 34.93 3.68
1656 2017 7.336176 AGTGGTTACCTAAGCTTTGCTAAATAC 59.664 37.037 3.20 3.98 38.25 1.89
1657 2018 7.336176 GTGGTTACCTAAGCTTTGCTAAATACT 59.664 37.037 3.20 0.00 38.25 2.12
1658 2019 7.551617 TGGTTACCTAAGCTTTGCTAAATACTC 59.448 37.037 3.20 0.00 38.25 2.59
1659 2020 7.012138 GGTTACCTAAGCTTTGCTAAATACTCC 59.988 40.741 3.20 0.00 38.25 3.85
1660 2021 5.437946 ACCTAAGCTTTGCTAAATACTCCC 58.562 41.667 3.20 0.00 38.25 4.30
1661 2022 5.191921 ACCTAAGCTTTGCTAAATACTCCCT 59.808 40.000 3.20 0.00 38.25 4.20
1662 2023 5.760743 CCTAAGCTTTGCTAAATACTCCCTC 59.239 44.000 3.20 0.00 38.25 4.30
1663 2024 4.157849 AGCTTTGCTAAATACTCCCTCC 57.842 45.455 0.00 0.00 36.99 4.30
1664 2025 2.872858 GCTTTGCTAAATACTCCCTCCG 59.127 50.000 0.00 0.00 0.00 4.63
1665 2026 3.681874 GCTTTGCTAAATACTCCCTCCGT 60.682 47.826 0.00 0.00 0.00 4.69
1666 2027 3.814005 TTGCTAAATACTCCCTCCGTC 57.186 47.619 0.00 0.00 0.00 4.79
1667 2028 2.037144 TGCTAAATACTCCCTCCGTCC 58.963 52.381 0.00 0.00 0.00 4.79
1668 2029 1.343789 GCTAAATACTCCCTCCGTCCC 59.656 57.143 0.00 0.00 0.00 4.46
1669 2030 2.674420 CTAAATACTCCCTCCGTCCCA 58.326 52.381 0.00 0.00 0.00 4.37
1670 2031 2.191981 AAATACTCCCTCCGTCCCAT 57.808 50.000 0.00 0.00 0.00 4.00
1671 2032 3.339713 AAATACTCCCTCCGTCCCATA 57.660 47.619 0.00 0.00 0.00 2.74
1672 2033 3.339713 AATACTCCCTCCGTCCCATAA 57.660 47.619 0.00 0.00 0.00 1.90
1673 2034 3.562108 ATACTCCCTCCGTCCCATAAT 57.438 47.619 0.00 0.00 0.00 1.28
1674 2035 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
1675 2036 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
1676 2037 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
1677 2038 2.563179 CTCCCTCCGTCCCATAATGTAG 59.437 54.545 0.00 0.00 0.00 2.74
1678 2039 1.623811 CCCTCCGTCCCATAATGTAGG 59.376 57.143 0.00 0.00 0.00 3.18
1679 2040 2.605257 CCTCCGTCCCATAATGTAGGA 58.395 52.381 0.00 0.00 0.00 2.94
1680 2041 2.299297 CCTCCGTCCCATAATGTAGGAC 59.701 54.545 0.00 0.00 45.49 3.85
1712 2073 7.864307 GATACTAGTGTAGTGTCAAAAACGT 57.136 36.000 5.39 0.00 43.73 3.99
1713 2074 7.864307 ATACTAGTGTAGTGTCAAAAACGTC 57.136 36.000 5.39 0.00 39.81 4.34
1714 2075 5.045872 ACTAGTGTAGTGTCAAAAACGTCC 58.954 41.667 0.00 0.00 37.69 4.79
1715 2076 4.133013 AGTGTAGTGTCAAAAACGTCCT 57.867 40.909 0.00 0.00 0.00 3.85
1716 2077 5.266733 AGTGTAGTGTCAAAAACGTCCTA 57.733 39.130 0.00 0.00 0.00 2.94
1717 2078 5.045872 AGTGTAGTGTCAAAAACGTCCTAC 58.954 41.667 0.00 0.00 31.73 3.18
1730 2091 3.901087 TCCTACGTTATGGGACGGA 57.099 52.632 0.00 0.00 46.77 4.69
1733 2094 2.811307 TACGTTATGGGACGGAGGG 58.189 57.895 0.00 0.00 46.77 4.30
1734 2095 0.258484 TACGTTATGGGACGGAGGGA 59.742 55.000 0.00 0.00 46.77 4.20
1735 2096 1.041447 ACGTTATGGGACGGAGGGAG 61.041 60.000 2.39 0.00 46.77 4.30
1736 2097 1.041447 CGTTATGGGACGGAGGGAGT 61.041 60.000 0.00 0.00 39.27 3.85
1737 2098 1.751733 CGTTATGGGACGGAGGGAGTA 60.752 57.143 0.00 0.00 39.27 2.59
1738 2099 1.685517 GTTATGGGACGGAGGGAGTAC 59.314 57.143 0.00 0.00 0.00 2.73
1743 2104 1.962100 GGGACGGAGGGAGTACATTAG 59.038 57.143 0.00 0.00 0.00 1.73
1786 2147 4.305539 TGGCTTCTCAATCTTGGATTGA 57.694 40.909 18.10 18.10 36.67 2.57
1823 2185 3.242936 GCTTTTCACGAGCTTTGGTGTAA 60.243 43.478 11.65 7.21 37.18 2.41
1832 2194 4.669197 CGAGCTTTGGTGTAAAAGGAATCG 60.669 45.833 0.00 0.00 37.58 3.34
1846 2208 1.949525 GGAATCGTAGCCATTGCACAT 59.050 47.619 0.00 0.00 41.13 3.21
1853 2215 3.809279 CGTAGCCATTGCACATGATTAGA 59.191 43.478 0.00 0.00 41.13 2.10
1861 2223 6.474427 CCATTGCACATGATTAGATTGTGAAC 59.526 38.462 0.00 0.00 42.59 3.18
1878 2240 6.317789 TGTGAACATGCTTTCTTAAAGGAG 57.682 37.500 0.00 0.00 42.23 3.69
1926 2288 9.725019 AACTGACATGATATTCTTTCAGTGTTA 57.275 29.630 10.90 0.00 42.17 2.41
1943 2305 6.544197 TCAGTGTTAGGTTATTTTGCAGTCAA 59.456 34.615 0.00 0.00 0.00 3.18
1944 2306 7.067615 TCAGTGTTAGGTTATTTTGCAGTCAAA 59.932 33.333 0.00 0.00 40.17 2.69
1950 2312 2.825861 ATTTTGCAGTCAAAGGGCAG 57.174 45.000 0.00 0.00 42.50 4.85
1954 2316 3.712016 TTGCAGTCAAAGGGCAGTATA 57.288 42.857 0.00 0.00 38.97 1.47
1958 2320 4.010349 GCAGTCAAAGGGCAGTATAAACT 58.990 43.478 0.00 0.00 35.91 2.66
1967 2329 4.412199 AGGGCAGTATAAACTTCCAGCATA 59.588 41.667 0.00 0.00 40.49 3.14
1970 2332 5.467063 GGCAGTATAAACTTCCAGCATAGAC 59.533 44.000 0.00 0.00 38.74 2.59
2060 2422 7.935405 ACCAGACAAATTCTAAAACCCCTATA 58.065 34.615 0.00 0.00 31.12 1.31
2061 2423 8.566109 ACCAGACAAATTCTAAAACCCCTATAT 58.434 33.333 0.00 0.00 31.12 0.86
2062 2424 8.850156 CCAGACAAATTCTAAAACCCCTATATG 58.150 37.037 0.00 0.00 31.12 1.78
2063 2425 9.408648 CAGACAAATTCTAAAACCCCTATATGT 57.591 33.333 0.00 0.00 31.12 2.29
2104 2466 4.749245 AAATGTGTCGCTTTAGTCCTTG 57.251 40.909 0.00 0.00 0.00 3.61
2117 2479 5.734855 TTAGTCCTTGCGCATTTATTCTC 57.265 39.130 12.75 0.00 0.00 2.87
2119 2481 3.624861 AGTCCTTGCGCATTTATTCTCAG 59.375 43.478 12.75 1.12 0.00 3.35
2125 2489 5.475273 TGCGCATTTATTCTCAGAAAGAG 57.525 39.130 5.66 0.00 46.14 2.85
2175 2623 1.266718 GGAAACATCGAAGTGCAGCAA 59.733 47.619 0.00 0.00 0.00 3.91
2184 2632 7.312154 ACATCGAAGTGCAGCAAAAATTTATA 58.688 30.769 0.00 0.00 0.00 0.98
2185 2633 7.485913 ACATCGAAGTGCAGCAAAAATTTATAG 59.514 33.333 0.00 0.00 0.00 1.31
2188 2642 6.251376 CGAAGTGCAGCAAAAATTTATAGTCC 59.749 38.462 0.00 0.00 0.00 3.85
2238 2692 3.181517 CCATGCTGTGTCATTTCAGTACG 60.182 47.826 0.00 0.00 34.57 3.67
2240 2694 3.057019 TGCTGTGTCATTTCAGTACGTC 58.943 45.455 0.00 0.00 34.57 4.34
2301 2795 1.204467 AGTGTGTTGTGGTTGCAAAGG 59.796 47.619 0.00 0.00 0.00 3.11
2306 2800 3.628487 GTGTTGTGGTTGCAAAGGTAGTA 59.372 43.478 0.00 0.00 0.00 1.82
2310 2804 4.720046 TGTGGTTGCAAAGGTAGTATTGA 58.280 39.130 0.00 0.00 0.00 2.57
2323 2817 7.366847 AGGTAGTATTGACTGTGAAGCATAT 57.633 36.000 0.00 0.00 36.28 1.78
2329 2823 8.140628 AGTATTGACTGTGAAGCATATAGTCAG 58.859 37.037 11.90 0.00 45.70 3.51
2334 2828 5.128499 ACTGTGAAGCATATAGTCAGCTCTT 59.872 40.000 0.00 0.00 37.70 2.85
2335 2829 5.595885 TGTGAAGCATATAGTCAGCTCTTC 58.404 41.667 0.00 0.00 37.70 2.87
2347 2841 4.039032 GTCAGCTCTTCAGTATACTTCGC 58.961 47.826 1.56 1.97 0.00 4.70
2430 2927 3.129287 CCCAATGTAGACAGATTTGCACC 59.871 47.826 0.00 0.00 0.00 5.01
2439 2936 1.067354 CAGATTTGCACCTGCCCTTTC 60.067 52.381 0.00 0.00 41.18 2.62
2471 2968 5.380043 CCAGGAATTAAGCATATGTCAGGT 58.620 41.667 4.29 0.00 0.00 4.00
2561 3058 8.902040 ACTAGTACTACTATTTTTCGAAACGG 57.098 34.615 10.79 3.80 29.08 4.44
2562 3059 8.730680 ACTAGTACTACTATTTTTCGAAACGGA 58.269 33.333 10.79 0.00 29.08 4.69
2563 3060 9.219497 CTAGTACTACTATTTTTCGAAACGGAG 57.781 37.037 10.79 9.96 29.08 4.63
2564 3061 7.031975 AGTACTACTATTTTTCGAAACGGAGG 58.968 38.462 10.79 3.11 0.00 4.30
2565 3062 4.628766 ACTACTATTTTTCGAAACGGAGGC 59.371 41.667 10.79 0.00 0.00 4.70
2566 3063 3.404899 ACTATTTTTCGAAACGGAGGCA 58.595 40.909 10.79 0.00 0.00 4.75
2567 3064 3.816523 ACTATTTTTCGAAACGGAGGCAA 59.183 39.130 10.79 0.42 0.00 4.52
2568 3065 3.719173 ATTTTTCGAAACGGAGGCAAA 57.281 38.095 10.79 0.00 0.00 3.68
2573 3070 0.661020 CGAAACGGAGGCAAAAGTGT 59.339 50.000 0.00 0.00 0.00 3.55
2614 3135 7.581213 TTCTTCAGCCTTGAATTTTCAACTA 57.419 32.000 1.66 0.00 42.19 2.24
2625 3146 9.462174 CTTGAATTTTCAACTATGCAACAGTTA 57.538 29.630 14.64 2.93 41.88 2.24
2650 3171 5.319043 TGTTTCCATCCCTTCAGTTTACT 57.681 39.130 0.00 0.00 0.00 2.24
2654 3175 6.636454 TTCCATCCCTTCAGTTTACTACAT 57.364 37.500 0.00 0.00 0.00 2.29
2664 3185 8.031277 CCTTCAGTTTACTACATAACCTTACGT 58.969 37.037 0.00 0.00 0.00 3.57
2673 3194 8.284945 ACTACATAACCTTACGTCAATACAGA 57.715 34.615 0.00 0.00 0.00 3.41
2674 3195 8.910944 ACTACATAACCTTACGTCAATACAGAT 58.089 33.333 0.00 0.00 0.00 2.90
2814 3336 1.375908 ACAGGTGTACCGCATGCTG 60.376 57.895 17.13 12.36 42.08 4.41
2817 3339 2.046314 GTGTACCGCATGCTGGGT 60.046 61.111 25.35 22.59 40.35 4.51
2844 3366 0.107268 TCCAGGCATCCATCATCACG 59.893 55.000 0.00 0.00 0.00 4.35
2859 3381 0.386858 TCACGTCGGCTCTCTTTTCG 60.387 55.000 0.00 0.00 0.00 3.46
2952 3474 0.392461 GAATGGCAGCGGTGTTCCTA 60.392 55.000 17.07 0.00 0.00 2.94
2953 3475 0.037590 AATGGCAGCGGTGTTCCTAA 59.962 50.000 17.07 0.00 0.00 2.69
3063 3585 1.004440 GTTCTCGCTCCTGCCACTT 60.004 57.895 0.00 0.00 35.36 3.16
3150 3672 2.423926 TGTCAACTTCGCTGTCTCTC 57.576 50.000 0.00 0.00 0.00 3.20
3344 3866 9.166173 CCATTCATTGATCGCCTCTTAATATAA 57.834 33.333 0.00 0.00 0.00 0.98
3789 4312 1.516110 ATGAGCTGGGAGCAGGTAAT 58.484 50.000 0.00 0.00 45.56 1.89
3930 4453 3.064545 GTGAGGCAGTGATAAGTGCATTC 59.935 47.826 12.14 9.01 41.75 2.67
4019 4542 8.826765 AGGTTAGTTCAATGGATCTCTCTAAAA 58.173 33.333 0.00 0.00 0.00 1.52
4028 4551 8.449397 CAATGGATCTCTCTAAAAGTGTTTCAG 58.551 37.037 0.00 0.00 0.00 3.02
4050 4573 3.826729 GCCTTATTGTTTCAGGTGAAGGT 59.173 43.478 0.00 0.00 35.45 3.50
4117 4640 2.985847 GGTTGGCAGCACCTGGTC 60.986 66.667 3.14 0.00 40.22 4.02
4364 4887 0.678048 GCGGTCTCCTTTGCCAGAAT 60.678 55.000 0.00 0.00 0.00 2.40
4556 5079 1.134946 GCAACATACCCTGAACATGCC 59.865 52.381 0.00 0.00 0.00 4.40
4723 5246 9.334693 GAGTTCAGAAATATGTTTGTTTGCTAG 57.665 33.333 0.00 0.00 0.00 3.42
4765 5288 2.949644 TGCTGACTAACTAGCGATGCTA 59.050 45.455 0.00 0.00 42.74 3.49
4922 5445 1.975680 ACTAACCCTCGCTTCCAGAAA 59.024 47.619 0.00 0.00 0.00 2.52
5024 5551 0.806492 GTCTTCGATGCGTCTTCCCC 60.806 60.000 4.05 0.00 0.00 4.81
5178 5705 2.814336 GCGAAGAAGAACCATCCAAGTT 59.186 45.455 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
131 150 1.448540 CTCGGCCTTGACGCTGAAT 60.449 57.895 0.00 0.00 43.45 2.57
245 264 0.739112 CTGGCTCTGTCTTCGGCTTC 60.739 60.000 0.00 0.00 0.00 3.86
459 558 2.426425 GTCGTCGTCGCTGTCGTT 60.426 61.111 0.00 0.00 36.96 3.85
534 633 2.104170 GTCGTCCTTCTCCTCCTTCAT 58.896 52.381 0.00 0.00 0.00 2.57
702 816 6.349280 CGGGACAAAGATTCAGCTAAAATTCA 60.349 38.462 0.00 0.00 0.00 2.57
844 975 1.729284 GTAAAATCGCCGTCTTGGGA 58.271 50.000 0.00 0.00 38.63 4.37
851 982 3.790177 GGCTCGTAAAATCGCCGT 58.210 55.556 0.00 0.00 32.22 5.68
934 1065 2.032681 GCGGGAGGTCAAGCAAGT 59.967 61.111 0.00 0.00 0.00 3.16
953 1084 1.506309 TTGTGATGTGCGTGTGGAGC 61.506 55.000 0.00 0.00 0.00 4.70
955 1086 0.943673 CTTTGTGATGTGCGTGTGGA 59.056 50.000 0.00 0.00 0.00 4.02
956 1087 0.661187 GCTTTGTGATGTGCGTGTGG 60.661 55.000 0.00 0.00 0.00 4.17
957 1088 0.029167 TGCTTTGTGATGTGCGTGTG 59.971 50.000 0.00 0.00 0.00 3.82
962 1093 1.134226 GCTTGTGCTTTGTGATGTGC 58.866 50.000 0.00 0.00 36.03 4.57
982 1113 0.343372 ATTCCCTCCCTCTGCAGGTA 59.657 55.000 15.13 0.00 38.30 3.08
993 1128 0.464554 CTTCTTCGCCCATTCCCTCC 60.465 60.000 0.00 0.00 0.00 4.30
1016 1151 1.617018 ATCCAGCAACGGAGCAGCTA 61.617 55.000 0.00 0.00 38.88 3.32
1042 1177 1.142748 CGCTTCTCCTCGCCTTGAT 59.857 57.895 0.00 0.00 0.00 2.57
1312 1447 9.790344 AGAAGAAGGATGAGACAAAATATATGG 57.210 33.333 0.00 0.00 0.00 2.74
1324 1459 6.572182 AATCAATGGAGAAGAAGGATGAGA 57.428 37.500 0.00 0.00 0.00 3.27
1357 1492 2.063378 GGCAGAGAGGAGGAGTGGG 61.063 68.421 0.00 0.00 0.00 4.61
1389 1585 2.034053 TGTTTTCGATGCAAACAGGGAC 59.966 45.455 9.30 0.00 38.84 4.46
1397 1593 5.837437 AGGTAAACATTGTTTTCGATGCAA 58.163 33.333 19.15 0.00 43.54 4.08
1432 1678 1.593265 GATGGCAAAGGTGGGCAAG 59.407 57.895 0.00 0.00 44.40 4.01
1436 1682 0.040204 AAGAGGATGGCAAAGGTGGG 59.960 55.000 0.00 0.00 0.00 4.61
1437 1683 1.272092 TGAAGAGGATGGCAAAGGTGG 60.272 52.381 0.00 0.00 0.00 4.61
1439 1685 4.803329 ATATGAAGAGGATGGCAAAGGT 57.197 40.909 0.00 0.00 0.00 3.50
1451 1697 5.882557 AGTGGTGGCAGTAAAATATGAAGAG 59.117 40.000 0.00 0.00 0.00 2.85
1458 1704 4.584638 ATGGAGTGGTGGCAGTAAAATA 57.415 40.909 0.00 0.00 0.00 1.40
1459 1705 2.969821 TGGAGTGGTGGCAGTAAAAT 57.030 45.000 0.00 0.00 0.00 1.82
1486 1732 3.195396 GGGCAACTTAATTGAGCAATGGA 59.805 43.478 0.00 0.00 41.23 3.41
1487 1733 3.524541 GGGCAACTTAATTGAGCAATGG 58.475 45.455 0.00 0.00 41.23 3.16
1498 1744 3.844211 AGTCTATGACAGGGGCAACTTAA 59.156 43.478 0.46 0.00 34.60 1.85
1509 1755 2.692557 CCTCTGGTCCAGTCTATGACAG 59.307 54.545 18.65 5.93 34.60 3.51
1511 1757 2.741145 ACCTCTGGTCCAGTCTATGAC 58.259 52.381 18.65 0.00 32.61 3.06
1512 1758 3.528078 AGTACCTCTGGTCCAGTCTATGA 59.472 47.826 18.65 0.00 37.09 2.15
1513 1759 3.886505 GAGTACCTCTGGTCCAGTCTATG 59.113 52.174 18.65 6.56 37.09 2.23
1515 1761 2.917600 TGAGTACCTCTGGTCCAGTCTA 59.082 50.000 18.65 4.12 37.09 2.59
1516 1762 1.711375 TGAGTACCTCTGGTCCAGTCT 59.289 52.381 18.65 10.07 37.09 3.24
1517 1763 2.217510 TGAGTACCTCTGGTCCAGTC 57.782 55.000 18.65 8.23 37.09 3.51
1518 1764 2.633481 GTTTGAGTACCTCTGGTCCAGT 59.367 50.000 18.65 3.08 37.09 4.00
1519 1765 2.632996 TGTTTGAGTACCTCTGGTCCAG 59.367 50.000 13.21 13.21 37.09 3.86
1520 1766 2.684943 TGTTTGAGTACCTCTGGTCCA 58.315 47.619 0.00 0.00 37.09 4.02
1521 1767 3.983044 ATGTTTGAGTACCTCTGGTCC 57.017 47.619 0.00 0.00 37.09 4.46
1522 1768 4.811557 GCATATGTTTGAGTACCTCTGGTC 59.188 45.833 4.29 0.00 37.09 4.02
1523 1769 4.471386 AGCATATGTTTGAGTACCTCTGGT 59.529 41.667 4.29 0.00 40.16 4.00
1524 1770 5.028549 AGCATATGTTTGAGTACCTCTGG 57.971 43.478 4.29 0.00 0.00 3.86
1525 1771 5.053145 GGAGCATATGTTTGAGTACCTCTG 58.947 45.833 4.29 0.00 0.00 3.35
1526 1772 4.716784 TGGAGCATATGTTTGAGTACCTCT 59.283 41.667 4.29 0.00 0.00 3.69
1527 1773 5.023533 TGGAGCATATGTTTGAGTACCTC 57.976 43.478 4.29 0.00 0.00 3.85
1528 1774 5.130975 TGATGGAGCATATGTTTGAGTACCT 59.869 40.000 4.29 0.00 0.00 3.08
1529 1775 5.368145 TGATGGAGCATATGTTTGAGTACC 58.632 41.667 4.29 0.00 0.00 3.34
1530 1776 7.443575 AGAATGATGGAGCATATGTTTGAGTAC 59.556 37.037 4.29 0.00 0.00 2.73
1531 1777 7.512130 AGAATGATGGAGCATATGTTTGAGTA 58.488 34.615 4.29 0.00 0.00 2.59
1532 1778 6.363065 AGAATGATGGAGCATATGTTTGAGT 58.637 36.000 4.29 0.00 0.00 3.41
1533 1779 6.879276 AGAATGATGGAGCATATGTTTGAG 57.121 37.500 4.29 0.00 0.00 3.02
1534 1780 7.123098 ACAAAGAATGATGGAGCATATGTTTGA 59.877 33.333 4.29 0.00 31.78 2.69
1535 1781 7.262772 ACAAAGAATGATGGAGCATATGTTTG 58.737 34.615 4.29 5.24 32.55 2.93
1536 1782 7.414222 ACAAAGAATGATGGAGCATATGTTT 57.586 32.000 4.29 0.00 0.00 2.83
1537 1783 7.776969 ACTACAAAGAATGATGGAGCATATGTT 59.223 33.333 4.29 0.00 30.15 2.71
1556 1802 9.982651 GGCAGATCTAGTAAATGATACTACAAA 57.017 33.333 0.00 0.00 0.00 2.83
1562 1808 7.233389 TGGAGGCAGATCTAGTAAATGATAC 57.767 40.000 0.00 0.00 0.00 2.24
1563 1809 7.855784 TTGGAGGCAGATCTAGTAAATGATA 57.144 36.000 0.00 0.00 0.00 2.15
1565 1811 6.560003 TTTGGAGGCAGATCTAGTAAATGA 57.440 37.500 0.00 0.00 0.00 2.57
1566 1812 5.238214 GCTTTGGAGGCAGATCTAGTAAATG 59.762 44.000 0.00 0.00 0.00 2.32
1567 1813 5.131809 AGCTTTGGAGGCAGATCTAGTAAAT 59.868 40.000 0.00 0.00 0.00 1.40
1568 1814 4.471386 AGCTTTGGAGGCAGATCTAGTAAA 59.529 41.667 0.00 0.00 0.00 2.01
1569 1815 4.033709 AGCTTTGGAGGCAGATCTAGTAA 58.966 43.478 0.00 0.00 0.00 2.24
1570 1816 3.647636 AGCTTTGGAGGCAGATCTAGTA 58.352 45.455 0.00 0.00 0.00 1.82
1571 1817 2.476199 AGCTTTGGAGGCAGATCTAGT 58.524 47.619 0.00 0.00 0.00 2.57
1572 1818 4.679373 TTAGCTTTGGAGGCAGATCTAG 57.321 45.455 0.00 0.00 0.00 2.43
1581 1827 8.306761 AGTGTTCATTTATTTTAGCTTTGGAGG 58.693 33.333 0.00 0.00 0.00 4.30
1623 1984 7.633116 GCAAAGCTTAGGTAACCACTATAGACT 60.633 40.741 6.78 0.00 37.17 3.24
1628 1989 5.437191 AGCAAAGCTTAGGTAACCACTAT 57.563 39.130 0.00 0.00 33.89 2.12
1638 1999 5.685728 AGGGAGTATTTAGCAAAGCTTAGG 58.314 41.667 0.00 0.00 40.44 2.69
1649 2010 2.674420 TGGGACGGAGGGAGTATTTAG 58.326 52.381 0.00 0.00 0.00 1.85
1656 2017 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
1657 2018 2.605257 CTACATTATGGGACGGAGGGA 58.395 52.381 0.00 0.00 0.00 4.20
1658 2019 1.623811 CCTACATTATGGGACGGAGGG 59.376 57.143 0.00 0.00 0.00 4.30
1659 2020 2.605257 TCCTACATTATGGGACGGAGG 58.395 52.381 0.00 0.00 31.72 4.30
1686 2047 7.922278 ACGTTTTTGACACTACACTAGTATCAA 59.078 33.333 0.00 0.02 46.91 2.57
1687 2048 7.428020 ACGTTTTTGACACTACACTAGTATCA 58.572 34.615 0.00 0.00 40.20 2.15
1688 2049 7.061557 GGACGTTTTTGACACTACACTAGTATC 59.938 40.741 0.00 0.00 37.23 2.24
1689 2050 6.865205 GGACGTTTTTGACACTACACTAGTAT 59.135 38.462 0.00 0.00 37.23 2.12
1690 2051 6.039717 AGGACGTTTTTGACACTACACTAGTA 59.960 38.462 0.00 0.00 37.23 1.82
1691 2052 5.045872 GGACGTTTTTGACACTACACTAGT 58.954 41.667 0.00 0.00 40.28 2.57
1692 2053 5.287226 AGGACGTTTTTGACACTACACTAG 58.713 41.667 0.00 0.00 0.00 2.57
1693 2054 5.266733 AGGACGTTTTTGACACTACACTA 57.733 39.130 0.00 0.00 0.00 2.74
1694 2055 4.133013 AGGACGTTTTTGACACTACACT 57.867 40.909 0.00 0.00 0.00 3.55
1695 2056 4.085415 CGTAGGACGTTTTTGACACTACAC 60.085 45.833 0.00 0.00 36.74 2.90
1696 2057 4.043750 CGTAGGACGTTTTTGACACTACA 58.956 43.478 0.00 0.00 36.74 2.74
1697 2058 4.619931 CGTAGGACGTTTTTGACACTAC 57.380 45.455 0.00 0.00 36.74 2.73
1711 2072 1.336125 CTCCGTCCCATAACGTAGGAC 59.664 57.143 13.98 13.98 45.49 3.85
1712 2073 1.683943 CTCCGTCCCATAACGTAGGA 58.316 55.000 3.41 0.00 41.01 2.94
1713 2074 0.672342 CCTCCGTCCCATAACGTAGG 59.328 60.000 0.00 0.00 41.46 3.18
1714 2075 0.672342 CCCTCCGTCCCATAACGTAG 59.328 60.000 0.00 0.00 41.01 3.51
1715 2076 0.258484 TCCCTCCGTCCCATAACGTA 59.742 55.000 0.00 0.00 41.01 3.57
1716 2077 1.000739 TCCCTCCGTCCCATAACGT 59.999 57.895 0.00 0.00 41.01 3.99
1717 2078 1.041447 ACTCCCTCCGTCCCATAACG 61.041 60.000 0.00 0.00 42.24 3.18
1718 2079 1.685517 GTACTCCCTCCGTCCCATAAC 59.314 57.143 0.00 0.00 0.00 1.89
1719 2080 1.288633 TGTACTCCCTCCGTCCCATAA 59.711 52.381 0.00 0.00 0.00 1.90
1720 2081 0.928505 TGTACTCCCTCCGTCCCATA 59.071 55.000 0.00 0.00 0.00 2.74
1721 2082 0.264955 ATGTACTCCCTCCGTCCCAT 59.735 55.000 0.00 0.00 0.00 4.00
1722 2083 0.042131 AATGTACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
1723 2084 1.962100 CTAATGTACTCCCTCCGTCCC 59.038 57.143 0.00 0.00 0.00 4.46
1724 2085 2.664015 ACTAATGTACTCCCTCCGTCC 58.336 52.381 0.00 0.00 0.00 4.79
1725 2086 5.278858 CCATAACTAATGTACTCCCTCCGTC 60.279 48.000 0.00 0.00 33.34 4.79
1726 2087 4.587684 CCATAACTAATGTACTCCCTCCGT 59.412 45.833 0.00 0.00 33.34 4.69
1727 2088 4.587684 ACCATAACTAATGTACTCCCTCCG 59.412 45.833 0.00 0.00 33.34 4.63
1728 2089 5.365895 ACACCATAACTAATGTACTCCCTCC 59.634 44.000 0.00 0.00 33.34 4.30
1729 2090 6.481434 ACACCATAACTAATGTACTCCCTC 57.519 41.667 0.00 0.00 33.34 4.30
1730 2091 7.983166 TTACACCATAACTAATGTACTCCCT 57.017 36.000 0.00 0.00 33.34 4.20
1731 2092 9.052759 CATTTACACCATAACTAATGTACTCCC 57.947 37.037 0.00 0.00 33.34 4.30
1732 2093 9.826574 TCATTTACACCATAACTAATGTACTCC 57.173 33.333 0.00 0.00 33.34 3.85
1734 2095 9.309516 CGTCATTTACACCATAACTAATGTACT 57.690 33.333 0.00 0.00 33.34 2.73
1735 2096 8.060090 GCGTCATTTACACCATAACTAATGTAC 58.940 37.037 0.00 0.00 33.34 2.90
1736 2097 7.764901 TGCGTCATTTACACCATAACTAATGTA 59.235 33.333 0.00 0.00 33.34 2.29
1737 2098 6.596106 TGCGTCATTTACACCATAACTAATGT 59.404 34.615 0.00 0.00 33.34 2.71
1738 2099 7.010697 TGCGTCATTTACACCATAACTAATG 57.989 36.000 0.00 0.00 35.15 1.90
1743 2104 5.514914 CCATTTGCGTCATTTACACCATAAC 59.485 40.000 0.00 0.00 0.00 1.89
1786 2147 4.272748 GTGAAAAGCCTCAAGTAAACGTCT 59.727 41.667 0.00 0.00 0.00 4.18
1823 2185 2.423538 GTGCAATGGCTACGATTCCTTT 59.576 45.455 0.00 0.00 41.91 3.11
1832 2194 5.954296 ATCTAATCATGTGCAATGGCTAC 57.046 39.130 0.00 0.00 41.91 3.58
1846 2208 7.692460 AGAAAGCATGTTCACAATCTAATCA 57.308 32.000 0.00 0.00 0.00 2.57
1853 2215 7.231317 TCTCCTTTAAGAAAGCATGTTCACAAT 59.769 33.333 0.00 0.00 37.18 2.71
1926 2288 3.006859 GCCCTTTGACTGCAAAATAACCT 59.993 43.478 0.00 0.00 42.96 3.50
1933 2295 2.356665 TACTGCCCTTTGACTGCAAA 57.643 45.000 0.00 0.00 41.47 3.68
1950 2312 7.982354 AGAAGTGTCTATGCTGGAAGTTTATAC 59.018 37.037 0.00 0.00 30.18 1.47
1954 2316 5.234466 AGAAGTGTCTATGCTGGAAGTTT 57.766 39.130 0.00 0.00 30.18 2.66
1958 2320 6.061441 TCAAAAAGAAGTGTCTATGCTGGAA 58.939 36.000 0.00 0.00 32.16 3.53
2066 2428 8.822855 CGACACATTTTAGGTGCTAACATATAA 58.177 33.333 0.00 0.00 39.87 0.98
2067 2429 7.042321 GCGACACATTTTAGGTGCTAACATATA 60.042 37.037 0.00 0.00 39.87 0.86
2068 2430 6.238374 GCGACACATTTTAGGTGCTAACATAT 60.238 38.462 0.00 0.00 39.87 1.78
2069 2431 5.064198 GCGACACATTTTAGGTGCTAACATA 59.936 40.000 0.00 0.00 39.87 2.29
2070 2432 4.142687 GCGACACATTTTAGGTGCTAACAT 60.143 41.667 0.00 0.00 39.87 2.71
2071 2433 3.187637 GCGACACATTTTAGGTGCTAACA 59.812 43.478 0.00 0.00 39.87 2.41
2072 2434 3.435671 AGCGACACATTTTAGGTGCTAAC 59.564 43.478 0.00 0.00 39.87 2.34
2073 2435 3.670625 AGCGACACATTTTAGGTGCTAA 58.329 40.909 0.00 0.00 39.87 3.09
2074 2436 3.328382 AGCGACACATTTTAGGTGCTA 57.672 42.857 0.00 0.00 39.87 3.49
2075 2437 2.185004 AGCGACACATTTTAGGTGCT 57.815 45.000 0.00 0.00 39.87 4.40
2086 2448 1.508632 GCAAGGACTAAAGCGACACA 58.491 50.000 0.00 0.00 0.00 3.72
2117 2479 1.462670 GCGCAAGGACTTCTCTTTCTG 59.537 52.381 0.30 0.00 38.28 3.02
2119 2481 1.512926 TGCGCAAGGACTTCTCTTTC 58.487 50.000 8.16 0.00 38.28 2.62
2125 2489 2.704725 TTTGAATGCGCAAGGACTTC 57.295 45.000 17.11 14.30 44.26 3.01
2201 2655 2.470821 GCATGGCATTGCTTTCATCTC 58.529 47.619 8.82 0.00 39.57 2.75
2238 2692 5.698545 GCCATGAATATAGGAGTTGACTGAC 59.301 44.000 0.00 0.00 0.00 3.51
2240 2694 5.862845 AGCCATGAATATAGGAGTTGACTG 58.137 41.667 0.00 0.00 0.00 3.51
2272 2766 4.585955 ACCACAACACACTACTACTGAG 57.414 45.455 0.00 0.00 0.00 3.35
2279 2773 3.434637 CTTTGCAACCACAACACACTAC 58.565 45.455 0.00 0.00 0.00 2.73
2301 2795 9.400638 GACTATATGCTTCACAGTCAATACTAC 57.599 37.037 0.00 0.00 36.48 2.73
2306 2800 5.757320 GCTGACTATATGCTTCACAGTCAAT 59.243 40.000 4.49 0.00 43.55 2.57
2310 2804 4.648762 AGAGCTGACTATATGCTTCACAGT 59.351 41.667 0.00 0.00 37.16 3.55
2323 2817 5.007823 GCGAAGTATACTGAAGAGCTGACTA 59.992 44.000 6.06 0.00 0.00 2.59
2347 2841 8.355169 AGCCTGACAAACATTTGCATATTATAG 58.645 33.333 4.25 0.00 41.79 1.31
2361 2855 1.429930 TGGTCCTAGCCTGACAAACA 58.570 50.000 0.00 0.00 34.36 2.83
2404 2901 5.104151 TGCAAATCTGTCTACATTGGGGATA 60.104 40.000 0.00 0.00 0.00 2.59
2408 2905 3.129287 GGTGCAAATCTGTCTACATTGGG 59.871 47.826 0.00 0.00 0.00 4.12
2430 2927 1.147153 GGATCCGGAGAAAGGGCAG 59.853 63.158 11.34 0.00 0.00 4.85
2439 2936 2.551071 GCTTAATTCCTGGGATCCGGAG 60.551 54.545 11.34 3.98 30.67 4.63
2471 2968 5.301551 ACCATGTGCTGTGTTTATTCTGAAA 59.698 36.000 0.00 0.00 0.00 2.69
2550 3047 2.424246 ACTTTTGCCTCCGTTTCGAAAA 59.576 40.909 13.10 0.00 0.00 2.29
2551 3048 2.018515 ACTTTTGCCTCCGTTTCGAAA 58.981 42.857 6.47 6.47 0.00 3.46
2553 3050 0.941542 CACTTTTGCCTCCGTTTCGA 59.058 50.000 0.00 0.00 0.00 3.71
2554 3051 0.661020 ACACTTTTGCCTCCGTTTCG 59.339 50.000 0.00 0.00 0.00 3.46
2555 3052 2.876550 ACTACACTTTTGCCTCCGTTTC 59.123 45.455 0.00 0.00 0.00 2.78
2556 3053 2.927028 ACTACACTTTTGCCTCCGTTT 58.073 42.857 0.00 0.00 0.00 3.60
2557 3054 2.632987 ACTACACTTTTGCCTCCGTT 57.367 45.000 0.00 0.00 0.00 4.44
2558 3055 3.007614 ACATACTACACTTTTGCCTCCGT 59.992 43.478 0.00 0.00 0.00 4.69
2559 3056 3.596214 ACATACTACACTTTTGCCTCCG 58.404 45.455 0.00 0.00 0.00 4.63
2560 3057 4.379499 GCAACATACTACACTTTTGCCTCC 60.379 45.833 0.00 0.00 34.57 4.30
2561 3058 4.455877 AGCAACATACTACACTTTTGCCTC 59.544 41.667 0.00 0.00 40.15 4.70
2562 3059 4.216257 CAGCAACATACTACACTTTTGCCT 59.784 41.667 0.00 0.00 40.15 4.75
2563 3060 4.023193 ACAGCAACATACTACACTTTTGCC 60.023 41.667 0.00 0.00 40.15 4.52
2564 3061 5.108385 ACAGCAACATACTACACTTTTGC 57.892 39.130 0.00 0.00 39.69 3.68
2565 3062 9.677567 AAATTACAGCAACATACTACACTTTTG 57.322 29.630 0.00 0.00 0.00 2.44
2566 3063 9.893305 GAAATTACAGCAACATACTACACTTTT 57.107 29.630 0.00 0.00 0.00 2.27
2567 3064 9.284968 AGAAATTACAGCAACATACTACACTTT 57.715 29.630 0.00 0.00 0.00 2.66
2568 3065 8.848474 AGAAATTACAGCAACATACTACACTT 57.152 30.769 0.00 0.00 0.00 3.16
2600 3097 9.462174 CTAACTGTTGCATAGTTGAAAATTCAA 57.538 29.630 20.85 4.52 44.31 2.69
2650 3171 8.905850 TCATCTGTATTGACGTAAGGTTATGTA 58.094 33.333 0.00 0.00 46.39 2.29
2654 3175 9.661563 AAAATCATCTGTATTGACGTAAGGTTA 57.338 29.630 0.00 0.00 46.39 2.85
2669 3190 9.442047 CTTGGTTTCTCTACTAAAATCATCTGT 57.558 33.333 0.00 0.00 0.00 3.41
2672 3193 8.047310 TCCCTTGGTTTCTCTACTAAAATCATC 58.953 37.037 0.00 0.00 0.00 2.92
2673 3194 7.928873 TCCCTTGGTTTCTCTACTAAAATCAT 58.071 34.615 0.00 0.00 0.00 2.45
2674 3195 7.324388 TCCCTTGGTTTCTCTACTAAAATCA 57.676 36.000 0.00 0.00 0.00 2.57
2797 3319 2.108514 CCAGCATGCGGTACACCTG 61.109 63.158 16.76 4.77 33.09 4.00
2817 3339 0.546507 TGGATGCCTGGAGGTACACA 60.547 55.000 0.00 0.00 37.57 3.72
2844 3366 0.736672 GGACCGAAAAGAGAGCCGAC 60.737 60.000 0.00 0.00 0.00 4.79
2859 3381 2.438795 AGGAGCGAGACGAGGACC 60.439 66.667 0.00 0.00 0.00 4.46
2952 3474 1.280710 TGTGCCGGGATTGTGTATCTT 59.719 47.619 2.18 0.00 33.53 2.40
2953 3475 0.908910 TGTGCCGGGATTGTGTATCT 59.091 50.000 2.18 0.00 33.53 1.98
3063 3585 5.509808 GGGTAATCCCGACATGGAACACA 62.510 52.174 0.00 0.00 43.42 3.72
3150 3672 4.142945 GCGAGCATAATGAAAGATAGCCAG 60.143 45.833 0.00 0.00 0.00 4.85
3344 3866 6.968248 ACCATCATATATTCTCAGTATGGGGT 59.032 38.462 0.00 0.00 37.03 4.95
3702 4225 8.721478 GTCAGCATTGTCAACTTAATCTTCTTA 58.279 33.333 0.00 0.00 0.00 2.10
3703 4226 7.446625 AGTCAGCATTGTCAACTTAATCTTCTT 59.553 33.333 0.00 0.00 0.00 2.52
3704 4227 6.939163 AGTCAGCATTGTCAACTTAATCTTCT 59.061 34.615 0.00 0.00 0.00 2.85
3705 4228 7.138692 AGTCAGCATTGTCAACTTAATCTTC 57.861 36.000 0.00 0.00 0.00 2.87
3789 4312 3.255642 GTGCCTTCTTTGCCTTGTCAATA 59.744 43.478 0.00 0.00 0.00 1.90
3930 4453 2.537625 GAGAAATGGAGTCATCGAAGCG 59.462 50.000 0.00 0.00 32.24 4.68
4019 4542 5.010012 CCTGAAACAATAAGGCTGAAACACT 59.990 40.000 0.00 0.00 0.00 3.55
4028 4551 3.826729 ACCTTCACCTGAAACAATAAGGC 59.173 43.478 0.00 0.00 36.33 4.35
4364 4887 0.684535 TGATGAACAGGAGAACGGCA 59.315 50.000 0.00 0.00 0.00 5.69
4556 5079 2.761208 ACTTGCTACTAGCTACACCCAG 59.239 50.000 9.49 0.00 42.97 4.45
4723 5246 5.522460 AGCAATGTGATATTTTCTGCAATGC 59.478 36.000 0.00 0.00 37.23 3.56
4922 5445 2.352421 CCGTCGTAGTTGATCCTGTTGT 60.352 50.000 0.00 0.00 0.00 3.32
5178 5705 1.909700 CTGGCCAGAAAGCAACCTTA 58.090 50.000 29.88 0.00 0.00 2.69
5340 5870 4.450976 TCTTTATGAACGTGCATGGCTAT 58.549 39.130 19.81 3.80 0.00 2.97
5411 5941 5.422214 AACTATGCTGTTACTAGCTGGTT 57.578 39.130 8.46 0.00 44.01 3.67


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

AutoCloner maintained by Alex Coulton.