Multiple sequence alignment - TraesCS3B01G191800

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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 TraesCS3B01G191800 chr3B 100.000 2409 0 0 1 2409 204847813 204850221 0.000000e+00 4449.0
1 TraesCS3B01G191800 chr3B 87.558 434 50 2 1 433 203346212 203345782 1.290000e-137 499.0
2 TraesCS3B01G191800 chr3B 87.558 434 50 3 1 433 221912945 221912515 1.290000e-137 499.0
3 TraesCS3B01G191800 chr3B 87.327 434 51 4 1 433 215105265 215104835 5.980000e-136 494.0
4 TraesCS3B01G191800 chr3B 92.308 78 6 0 1740 1817 204849473 204849550 7.040000e-21 111.0
5 TraesCS3B01G191800 chr3B 92.308 78 6 0 1661 1738 204849552 204849629 7.040000e-21 111.0
6 TraesCS3B01G191800 chr3B 95.238 42 2 0 1625 1666 798603566 798603525 1.550000e-07 67.6
7 TraesCS3B01G191800 chr3D 89.314 1647 98 31 1 1619 142997700 142999296 0.000000e+00 1995.0
8 TraesCS3B01G191800 chr3D 87.879 594 60 7 1741 2330 142999302 142999887 0.000000e+00 688.0
9 TraesCS3B01G191800 chr3D 87.558 434 50 2 1 433 141411075 141410645 1.290000e-137 499.0
10 TraesCS3B01G191800 chr3D 87.356 435 51 3 1 434 149205549 149205118 1.660000e-136 496.0
11 TraesCS3B01G191800 chr3D 87.126 435 52 3 1 434 147335553 147335984 7.740000e-135 490.0
12 TraesCS3B01G191800 chr3D 88.312 77 3 1 1662 1738 142999302 142999372 1.190000e-13 87.9
13 TraesCS3B01G191800 chr3D 97.500 40 1 0 1629 1668 537315310 537315271 4.300000e-08 69.4
14 TraesCS3B01G191800 chr3D 83.607 61 8 2 2159 2217 519343268 519343208 3.350000e-04 56.5
15 TraesCS3B01G191800 chr3A 89.274 1501 87 28 1 1461 162751682 162753148 0.000000e+00 1812.0
16 TraesCS3B01G191800 chr3A 88.018 434 48 2 1 433 159832474 159832044 5.940000e-141 510.0
17 TraesCS3B01G191800 chr3A 84.483 522 63 8 1824 2330 162753578 162754096 1.290000e-137 499.0
18 TraesCS3B01G191800 chr3A 87.558 434 50 3 1 433 166923907 166923477 1.290000e-137 499.0
19 TraesCS3B01G191800 chr3A 90.968 155 6 5 1467 1619 162753270 162753418 4.060000e-48 202.0
20 TraesCS3B01G191800 chr3A 91.837 49 4 0 1630 1678 722232515 722232563 4.300000e-08 69.4
21 TraesCS3B01G191800 chr3A 95.238 42 2 0 1625 1666 41003396 41003437 1.550000e-07 67.6
22 TraesCS3B01G191800 chr6D 81.600 125 17 5 2117 2238 367086063 367085942 5.480000e-17 99.0
23 TraesCS3B01G191800 chr6A 95.349 43 2 0 1625 1667 540836390 540836348 4.300000e-08 69.4
24 TraesCS3B01G191800 chr7B 95.238 42 2 0 1625 1666 57611045 57611086 1.550000e-07 67.6
25 TraesCS3B01G191800 chr5B 95.238 42 2 0 1625 1666 45195138 45195097 1.550000e-07 67.6
26 TraesCS3B01G191800 chr2A 93.478 46 2 1 1629 1674 469811436 469811480 1.550000e-07 67.6
27 TraesCS3B01G191800 chr5A 93.182 44 1 1 1629 1672 481940725 481940684 2.000000e-06 63.9
28 TraesCS3B01G191800 chr7A 82.812 64 9 2 2185 2247 663175737 663175675 3.350000e-04 56.5


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 TraesCS3B01G191800 chr3B 204847813 204850221 2408 False 1557.000000 4449 94.872000 1 2409 3 chr3B.!!$F1 2408
1 TraesCS3B01G191800 chr3D 142997700 142999887 2187 False 923.633333 1995 88.501667 1 2330 3 chr3D.!!$F2 2329
2 TraesCS3B01G191800 chr3A 162751682 162754096 2414 False 837.666667 1812 88.241667 1 2330 3 chr3A.!!$F3 2329

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
919 956 0.040692 GGTTTCGGTTTCGGACTTGC 60.041 55.0 0.0 0.0 36.95 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2338 2622 0.036306 CCACCTTTCTACCACGCCTT 59.964 55.0 0.0 0.0 0.0 4.35 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
69 72 1.429463 CTTAAGCGGCACTCGAACTT 58.571 50.000 1.45 0.00 42.43 2.66
100 103 1.649271 GGCAATCCCAGTCTCCCCAT 61.649 60.000 0.00 0.00 0.00 4.00
109 112 1.134788 CAGTCTCCCCATGTAACGACC 60.135 57.143 0.00 0.00 0.00 4.79
224 228 3.432588 CGTCGACGTCCTCCTGCT 61.433 66.667 29.08 0.00 34.11 4.24
262 266 1.227943 GCAGAACTGGGTCAGCACA 60.228 57.895 3.99 0.00 34.37 4.57
403 407 2.963371 GTCGCCTCGAAGTCCACT 59.037 61.111 0.00 0.00 37.72 4.00
433 437 2.175878 AGTCGAAATCTTGCTGCAGT 57.824 45.000 16.64 0.00 0.00 4.40
522 548 2.517450 GGATCGCCTCGCAAACTCG 61.517 63.158 0.00 0.00 0.00 4.18
531 557 2.434359 GCAAACTCGAGACCGGGG 60.434 66.667 21.68 3.30 41.49 5.73
552 578 4.383770 GGGAAACTCGGGATTGAATCAGTA 60.384 45.833 7.56 0.00 0.00 2.74
555 581 3.733337 ACTCGGGATTGAATCAGTATGC 58.267 45.455 7.56 0.00 34.76 3.14
557 583 1.800586 CGGGATTGAATCAGTATGCGG 59.199 52.381 7.56 0.00 34.76 5.69
561 587 4.130118 GGATTGAATCAGTATGCGGAAGT 58.870 43.478 7.56 0.00 34.76 3.01
562 588 5.297547 GGATTGAATCAGTATGCGGAAGTA 58.702 41.667 7.56 0.00 34.76 2.24
608 635 2.386064 TTAAAGCCACGCACCGGAGT 62.386 55.000 9.46 1.54 0.00 3.85
640 667 2.618709 GGAGGCGAAATCGGATTCATTT 59.381 45.455 3.28 0.00 40.23 2.32
641 668 3.066760 GGAGGCGAAATCGGATTCATTTT 59.933 43.478 3.28 0.00 40.23 1.82
642 669 4.032703 AGGCGAAATCGGATTCATTTTG 57.967 40.909 3.28 0.00 40.23 2.44
643 670 3.443681 AGGCGAAATCGGATTCATTTTGT 59.556 39.130 3.28 0.00 40.23 2.83
644 671 4.082245 AGGCGAAATCGGATTCATTTTGTT 60.082 37.500 3.28 0.00 40.23 2.83
656 683 7.459604 CGGATTCATTTTGTTTTCGTAATCGTG 60.460 37.037 0.00 0.00 38.33 4.35
659 686 3.589061 TTTGTTTTCGTAATCGTGCGT 57.411 38.095 0.00 0.00 38.33 5.24
666 693 2.047750 TAATCGTGCGTGCAGGCA 60.048 55.556 28.89 28.89 41.45 4.75
702 729 3.934391 GACCTGGCAACCGACCTCG 62.934 68.421 0.00 0.00 39.44 4.63
706 733 2.264794 GGCAACCGACCTCGTGAT 59.735 61.111 0.00 0.00 37.74 3.06
715 742 1.796982 CGACCTCGTGATGAGCTTCTG 60.797 57.143 0.00 0.00 43.82 3.02
737 764 4.024387 TGCGCTTTGGTAAGAACAGTTAAG 60.024 41.667 9.73 0.00 32.92 1.85
740 767 5.334879 CGCTTTGGTAAGAACAGTTAAGCAT 60.335 40.000 12.86 0.00 37.25 3.79
741 768 6.128391 CGCTTTGGTAAGAACAGTTAAGCATA 60.128 38.462 12.86 2.08 37.25 3.14
742 769 7.414098 CGCTTTGGTAAGAACAGTTAAGCATAT 60.414 37.037 12.86 0.00 37.25 1.78
916 953 1.672363 GTTTGGTTTCGGTTTCGGACT 59.328 47.619 0.00 0.00 36.95 3.85
918 955 1.301423 TGGTTTCGGTTTCGGACTTG 58.699 50.000 0.00 0.00 36.95 3.16
919 956 0.040692 GGTTTCGGTTTCGGACTTGC 60.041 55.000 0.00 0.00 36.95 4.01
952 990 3.196913 TTCGCACACGCACCTACGA 62.197 57.895 0.00 0.00 39.84 3.43
964 1002 2.768492 CCTACGAAGGGCGCTACGT 61.768 63.158 19.80 19.80 46.04 3.57
966 1004 0.041488 CTACGAAGGGCGCTACGTAG 60.041 60.000 26.18 26.18 46.91 3.51
999 1037 0.891449 GAGGAGCCGGAGATCGATCA 60.891 60.000 26.47 0.00 42.43 2.92
1004 1042 0.318441 GCCGGAGATCGATCAATGGA 59.682 55.000 26.47 0.00 42.43 3.41
1011 1049 0.979665 ATCGATCAATGGAGGCGGAT 59.020 50.000 0.00 0.00 0.00 4.18
1014 1052 1.517242 GATCAATGGAGGCGGATGAC 58.483 55.000 0.00 0.00 0.00 3.06
1149 1193 3.064987 GCGCGTCTCTTCCTGGCTA 62.065 63.158 8.43 0.00 0.00 3.93
1225 1269 3.120511 GCTTAGACTTTGGTTTCTCTGCG 60.121 47.826 0.00 0.00 0.00 5.18
1229 1273 1.202486 ACTTTGGTTTCTCTGCGTCGA 60.202 47.619 0.00 0.00 0.00 4.20
1233 1277 1.202486 TGGTTTCTCTGCGTCGACTTT 60.202 47.619 14.70 0.00 0.00 2.66
1235 1279 2.348591 GGTTTCTCTGCGTCGACTTTTG 60.349 50.000 14.70 0.00 0.00 2.44
1236 1280 2.218953 TTCTCTGCGTCGACTTTTGT 57.781 45.000 14.70 0.00 0.00 2.83
1237 1281 1.767289 TCTCTGCGTCGACTTTTGTC 58.233 50.000 14.70 0.00 45.55 3.18
1269 1313 2.605823 CGTGAGTGTGTCTCTGAACTCC 60.606 54.545 4.49 0.00 43.13 3.85
1280 1324 6.540551 GTGTCTCTGAACTCCTTTTTCTCTTT 59.459 38.462 0.00 0.00 0.00 2.52
1387 1431 0.400213 TCAAGGTCATCCGCTGGTTT 59.600 50.000 0.00 0.00 39.05 3.27
1412 1456 2.056985 CAGATCCCCTGCTAGGCTC 58.943 63.158 0.00 0.00 35.89 4.70
1413 1457 1.532794 AGATCCCCTGCTAGGCTCG 60.533 63.158 0.00 0.00 32.73 5.03
1435 1479 4.322049 CGTCAATTGTCCTTCTGGAGTAGT 60.322 45.833 5.13 0.00 44.16 2.73
1451 1495 9.871238 TCTGGAGTAGTAAATGTTGTTATCTTC 57.129 33.333 0.00 0.00 0.00 2.87
1503 1665 4.887071 ACGAGAGGCCAGAGATATGATATC 59.113 45.833 5.01 4.27 0.00 1.63
1536 1698 2.429610 GCTTCCCACGTCTCACCTAATA 59.570 50.000 0.00 0.00 0.00 0.98
1539 1701 5.671493 CTTCCCACGTCTCACCTAATAAAT 58.329 41.667 0.00 0.00 0.00 1.40
1540 1702 6.684613 GCTTCCCACGTCTCACCTAATAAATA 60.685 42.308 0.00 0.00 0.00 1.40
1541 1703 6.795144 TCCCACGTCTCACCTAATAAATAA 57.205 37.500 0.00 0.00 0.00 1.40
1543 1705 7.270047 TCCCACGTCTCACCTAATAAATAAAG 58.730 38.462 0.00 0.00 0.00 1.85
1544 1706 6.018180 CCCACGTCTCACCTAATAAATAAAGC 60.018 42.308 0.00 0.00 0.00 3.51
1545 1707 6.292168 CCACGTCTCACCTAATAAATAAAGCG 60.292 42.308 0.00 0.00 0.00 4.68
1546 1708 6.474427 CACGTCTCACCTAATAAATAAAGCGA 59.526 38.462 0.00 0.00 0.00 4.93
1547 1709 6.474751 ACGTCTCACCTAATAAATAAAGCGAC 59.525 38.462 0.00 0.00 0.00 5.19
1548 1710 6.344780 CGTCTCACCTAATAAATAAAGCGACG 60.345 42.308 0.00 0.00 33.37 5.12
1619 1781 4.698201 TTCATGACCCTGACACAACTTA 57.302 40.909 0.00 0.00 0.00 2.24
1620 1782 4.908601 TCATGACCCTGACACAACTTAT 57.091 40.909 0.00 0.00 0.00 1.73
1621 1783 4.578871 TCATGACCCTGACACAACTTATG 58.421 43.478 0.00 0.00 0.00 1.90
1622 1784 4.041567 TCATGACCCTGACACAACTTATGT 59.958 41.667 0.00 0.00 45.34 2.29
1623 1785 5.247337 TCATGACCCTGACACAACTTATGTA 59.753 40.000 0.00 0.00 41.46 2.29
1624 1786 5.755409 TGACCCTGACACAACTTATGTAT 57.245 39.130 0.00 0.00 41.46 2.29
1625 1787 5.487433 TGACCCTGACACAACTTATGTATG 58.513 41.667 0.00 0.00 41.46 2.39
1626 1788 5.012664 TGACCCTGACACAACTTATGTATGT 59.987 40.000 0.00 0.00 41.46 2.29
1627 1789 6.211785 TGACCCTGACACAACTTATGTATGTA 59.788 38.462 0.21 0.00 41.46 2.29
1628 1790 6.403878 ACCCTGACACAACTTATGTATGTAC 58.596 40.000 0.00 0.00 41.46 2.90
1629 1791 6.014070 ACCCTGACACAACTTATGTATGTACA 60.014 38.462 0.00 0.00 41.46 2.90
1631 1793 7.552687 CCCTGACACAACTTATGTATGTACATT 59.447 37.037 14.77 0.00 43.99 2.71
1632 1794 8.946085 CCTGACACAACTTATGTATGTACATTT 58.054 33.333 14.77 2.42 43.99 2.32
1653 1815 9.620660 ACATTTTGATAACAAGTATTTTCGGAC 57.379 29.630 0.00 0.00 37.32 4.79
1654 1816 8.785101 CATTTTGATAACAAGTATTTTCGGACG 58.215 33.333 0.00 0.00 37.32 4.79
1655 1817 6.411630 TTGATAACAAGTATTTTCGGACGG 57.588 37.500 0.00 0.00 0.00 4.79
1656 1818 5.722263 TGATAACAAGTATTTTCGGACGGA 58.278 37.500 0.00 0.00 0.00 4.69
1657 1819 5.808540 TGATAACAAGTATTTTCGGACGGAG 59.191 40.000 0.00 0.00 0.00 4.63
1658 1820 2.968675 ACAAGTATTTTCGGACGGAGG 58.031 47.619 0.00 0.00 0.00 4.30
1659 1821 2.564062 ACAAGTATTTTCGGACGGAGGA 59.436 45.455 0.00 0.00 0.00 3.71
1660 1822 3.007182 ACAAGTATTTTCGGACGGAGGAA 59.993 43.478 0.00 0.00 0.00 3.36
1661 1823 3.521947 AGTATTTTCGGACGGAGGAAG 57.478 47.619 0.00 0.00 0.00 3.46
1662 1824 2.830321 AGTATTTTCGGACGGAGGAAGT 59.170 45.455 0.00 0.00 0.00 3.01
1663 1825 4.019174 AGTATTTTCGGACGGAGGAAGTA 58.981 43.478 0.00 0.00 0.00 2.24
1664 1826 4.648307 AGTATTTTCGGACGGAGGAAGTAT 59.352 41.667 0.00 0.00 0.00 2.12
1665 1827 2.953466 TTTCGGACGGAGGAAGTATG 57.047 50.000 0.00 0.00 0.00 2.39
1666 1828 1.843368 TTCGGACGGAGGAAGTATGT 58.157 50.000 0.00 0.00 0.00 2.29
1667 1829 2.715749 TCGGACGGAGGAAGTATGTA 57.284 50.000 0.00 0.00 0.00 2.29
1668 1830 3.219176 TCGGACGGAGGAAGTATGTAT 57.781 47.619 0.00 0.00 0.00 2.29
1669 1831 3.144506 TCGGACGGAGGAAGTATGTATC 58.855 50.000 0.00 0.00 0.00 2.24
1670 1832 3.147629 CGGACGGAGGAAGTATGTATCT 58.852 50.000 0.00 0.00 0.00 1.98
1671 1833 3.568853 CGGACGGAGGAAGTATGTATCTT 59.431 47.826 0.00 0.00 0.00 2.40
1672 1834 4.556898 CGGACGGAGGAAGTATGTATCTTG 60.557 50.000 0.00 0.00 0.00 3.02
1673 1835 4.583489 GGACGGAGGAAGTATGTATCTTGA 59.417 45.833 0.00 0.00 0.00 3.02
1674 1836 5.068723 GGACGGAGGAAGTATGTATCTTGAA 59.931 44.000 0.00 0.00 0.00 2.69
1675 1837 6.406624 GGACGGAGGAAGTATGTATCTTGAAA 60.407 42.308 0.00 0.00 0.00 2.69
1676 1838 6.942976 ACGGAGGAAGTATGTATCTTGAAAA 58.057 36.000 0.00 0.00 0.00 2.29
1677 1839 7.391620 ACGGAGGAAGTATGTATCTTGAAAAA 58.608 34.615 0.00 0.00 0.00 1.94
1678 1840 8.047310 ACGGAGGAAGTATGTATCTTGAAAAAT 58.953 33.333 0.00 0.00 0.00 1.82
1679 1841 8.552034 CGGAGGAAGTATGTATCTTGAAAAATC 58.448 37.037 0.00 0.00 0.00 2.17
1680 1842 8.552034 GGAGGAAGTATGTATCTTGAAAAATCG 58.448 37.037 0.00 0.00 0.00 3.34
1681 1843 9.314321 GAGGAAGTATGTATCTTGAAAAATCGA 57.686 33.333 0.00 0.00 0.00 3.59
1682 1844 9.838339 AGGAAGTATGTATCTTGAAAAATCGAT 57.162 29.630 0.00 0.00 0.00 3.59
1683 1845 9.869844 GGAAGTATGTATCTTGAAAAATCGATG 57.130 33.333 0.00 0.00 0.00 3.84
1686 1848 9.823647 AGTATGTATCTTGAAAAATCGATGACT 57.176 29.630 0.00 0.00 0.00 3.41
1690 1852 9.599866 TGTATCTTGAAAAATCGATGACTATGT 57.400 29.630 0.00 0.00 0.00 2.29
1702 1864 9.561270 AATCGATGACTATGTTATGTAGATTCG 57.439 33.333 0.00 0.00 0.00 3.34
1703 1865 8.095937 TCGATGACTATGTTATGTAGATTCGT 57.904 34.615 0.00 0.00 0.00 3.85
1704 1866 9.211485 TCGATGACTATGTTATGTAGATTCGTA 57.789 33.333 0.00 0.00 0.00 3.43
1705 1867 9.989869 CGATGACTATGTTATGTAGATTCGTAT 57.010 33.333 0.00 0.00 0.00 3.06
1723 1885 9.653287 GATTCGTATATGAATCTGGATGGTTAA 57.347 33.333 28.93 0.00 46.87 2.01
1725 1887 9.839817 TTCGTATATGAATCTGGATGGTTAAAA 57.160 29.630 3.14 0.00 0.00 1.52
1726 1888 9.489084 TCGTATATGAATCTGGATGGTTAAAAG 57.511 33.333 0.00 0.00 0.00 2.27
1727 1889 8.721478 CGTATATGAATCTGGATGGTTAAAAGG 58.279 37.037 0.00 0.00 0.00 3.11
1728 1890 9.014297 GTATATGAATCTGGATGGTTAAAAGGG 57.986 37.037 0.00 0.00 0.00 3.95
1729 1891 4.609301 TGAATCTGGATGGTTAAAAGGGG 58.391 43.478 0.00 0.00 0.00 4.79
1730 1892 4.293634 TGAATCTGGATGGTTAAAAGGGGA 59.706 41.667 0.00 0.00 0.00 4.81
1731 1893 4.965283 ATCTGGATGGTTAAAAGGGGAA 57.035 40.909 0.00 0.00 0.00 3.97
1732 1894 4.750833 TCTGGATGGTTAAAAGGGGAAA 57.249 40.909 0.00 0.00 0.00 3.13
1733 1895 4.412843 TCTGGATGGTTAAAAGGGGAAAC 58.587 43.478 0.00 0.00 0.00 2.78
1734 1896 3.158676 TGGATGGTTAAAAGGGGAAACG 58.841 45.455 0.00 0.00 0.00 3.60
1735 1897 3.181431 TGGATGGTTAAAAGGGGAAACGA 60.181 43.478 0.00 0.00 0.00 3.85
1736 1898 3.827876 GGATGGTTAAAAGGGGAAACGAA 59.172 43.478 0.00 0.00 0.00 3.85
1737 1899 4.321452 GGATGGTTAAAAGGGGAAACGAAC 60.321 45.833 0.00 0.00 0.00 3.95
1738 1900 3.900971 TGGTTAAAAGGGGAAACGAACT 58.099 40.909 0.00 0.00 0.00 3.01
1739 1901 5.046288 TGGTTAAAAGGGGAAACGAACTA 57.954 39.130 0.00 0.00 0.00 2.24
1751 1913 6.460814 GGGGAAACGAACTAGTATCTACCTTC 60.461 46.154 0.00 0.00 0.00 3.46
1779 1941 9.823647 AAAATCGATGACTATGTTCTGTAGATT 57.176 29.630 0.00 0.00 0.00 2.40
1780 1942 9.469807 AAATCGATGACTATGTTCTGTAGATTC 57.530 33.333 0.00 0.00 0.00 2.52
1781 1943 6.971602 TCGATGACTATGTTCTGTAGATTCC 58.028 40.000 0.00 0.00 0.00 3.01
1782 1944 6.773200 TCGATGACTATGTTCTGTAGATTCCT 59.227 38.462 0.00 0.00 0.00 3.36
1783 1945 7.937394 TCGATGACTATGTTCTGTAGATTCCTA 59.063 37.037 0.00 0.00 0.00 2.94
1784 1946 8.735315 CGATGACTATGTTCTGTAGATTCCTAT 58.265 37.037 0.00 0.00 0.00 2.57
1812 1974 5.283876 TCTGGATGGTTAAAAGGGGAAAT 57.716 39.130 0.00 0.00 0.00 2.17
1875 2142 4.739716 GGTGCAACACATTTTGTAGTCTTG 59.260 41.667 0.00 0.00 37.51 3.02
1883 2150 6.886459 ACACATTTTGTAGTCTTGGCATCTAT 59.114 34.615 0.00 0.00 36.32 1.98
1911 2191 4.425520 GACCTCTCAAACGTCTAATCAGG 58.574 47.826 0.00 0.00 0.00 3.86
1947 2227 0.037232 CGGACAGGTGAAAGGAGGAC 60.037 60.000 0.00 0.00 0.00 3.85
1981 2261 0.029300 CACAACCCTCACTTTGTGCG 59.971 55.000 1.80 0.00 44.42 5.34
1991 2271 0.889186 ACTTTGTGCGGACATGTCCC 60.889 55.000 34.05 26.65 46.96 4.46
1996 2276 1.003696 TGTGCGGACATGTCCCATAAA 59.996 47.619 34.05 19.87 46.96 1.40
2013 2293 7.393515 GTCCCATAAATCCACAAATCCCTATAC 59.606 40.741 0.00 0.00 0.00 1.47
2028 2308 5.473273 TCCCTATACCCAACTCATATGTGT 58.527 41.667 4.59 4.59 0.00 3.72
2049 2330 1.978580 GGAGGATATGGGATGTTCGGT 59.021 52.381 0.00 0.00 0.00 4.69
2056 2338 0.912487 TGGGATGTTCGGTAGCCCTT 60.912 55.000 8.78 0.00 44.16 3.95
2080 2362 2.635787 TAGGATGCGGCCTACCTCGT 62.636 60.000 11.72 0.00 39.50 4.18
2086 2368 1.751927 CGGCCTACCTCGTACCACT 60.752 63.158 0.00 0.00 0.00 4.00
2090 2372 2.344025 GCCTACCTCGTACCACTTTTG 58.656 52.381 0.00 0.00 0.00 2.44
2091 2373 2.289257 GCCTACCTCGTACCACTTTTGT 60.289 50.000 0.00 0.00 0.00 2.83
2092 2374 3.582780 CCTACCTCGTACCACTTTTGTC 58.417 50.000 0.00 0.00 0.00 3.18
2093 2375 3.257624 CCTACCTCGTACCACTTTTGTCT 59.742 47.826 0.00 0.00 0.00 3.41
2096 2378 4.124970 ACCTCGTACCACTTTTGTCTTTC 58.875 43.478 0.00 0.00 0.00 2.62
2097 2379 4.141779 ACCTCGTACCACTTTTGTCTTTCT 60.142 41.667 0.00 0.00 0.00 2.52
2098 2380 4.814771 CCTCGTACCACTTTTGTCTTTCTT 59.185 41.667 0.00 0.00 0.00 2.52
2139 2422 7.878547 TCATATGCATTTGACTGGACAATTA 57.121 32.000 14.89 0.00 0.00 1.40
2146 2429 4.993705 TTGACTGGACAATTAGGAAGGT 57.006 40.909 0.00 0.00 0.00 3.50
2152 2435 5.546499 ACTGGACAATTAGGAAGGTTGTAGA 59.454 40.000 0.00 0.00 36.30 2.59
2156 2439 6.301169 ACAATTAGGAAGGTTGTAGAGGAG 57.699 41.667 0.00 0.00 34.55 3.69
2199 2482 3.740141 ATGAAGACTCAAAACGGACACGT 60.740 43.478 0.00 0.00 45.41 4.49
2247 2531 5.482175 ACGGATGTTTGGGGATCAAAATTAA 59.518 36.000 0.00 0.00 45.74 1.40
2254 2538 6.942163 TTGGGGATCAAAATTAACCAATCA 57.058 33.333 0.00 0.00 32.10 2.57
2257 2541 7.583024 TTGGGGATCAAAATTAACCAATCATGG 60.583 37.037 0.00 0.00 41.64 3.66
2293 2577 1.969923 CAATCTTTGGGTTGGCCTCAA 59.030 47.619 3.32 0.53 34.45 3.02
2320 2604 2.317609 CCTTGACGAGGCGGTGTTG 61.318 63.158 0.00 0.00 39.09 3.33
2330 2614 3.126171 CGAGGCGGTGTTGATGAAATTAA 59.874 43.478 0.00 0.00 0.00 1.40
2331 2615 4.378978 CGAGGCGGTGTTGATGAAATTAAA 60.379 41.667 0.00 0.00 0.00 1.52
2332 2616 4.805219 AGGCGGTGTTGATGAAATTAAAC 58.195 39.130 0.00 0.00 0.00 2.01
2333 2617 4.279671 AGGCGGTGTTGATGAAATTAAACA 59.720 37.500 0.00 0.00 32.81 2.83
2334 2618 4.384547 GGCGGTGTTGATGAAATTAAACAC 59.615 41.667 8.61 8.61 45.65 3.32
2335 2619 4.979197 GCGGTGTTGATGAAATTAAACACA 59.021 37.500 16.61 0.00 46.95 3.72
2336 2620 5.633182 GCGGTGTTGATGAAATTAAACACAT 59.367 36.000 16.61 0.00 46.95 3.21
2337 2621 6.145371 GCGGTGTTGATGAAATTAAACACATT 59.855 34.615 16.61 0.00 46.95 2.71
2338 2622 7.327275 GCGGTGTTGATGAAATTAAACACATTA 59.673 33.333 16.61 0.00 46.95 1.90
2339 2623 9.186323 CGGTGTTGATGAAATTAAACACATTAA 57.814 29.630 16.61 0.00 46.95 1.40
2342 2626 9.202273 TGTTGATGAAATTAAACACATTAAGGC 57.798 29.630 0.00 0.00 36.94 4.35
2343 2627 8.372521 GTTGATGAAATTAAACACATTAAGGCG 58.627 33.333 0.00 0.00 36.94 5.52
2344 2628 7.598278 TGATGAAATTAAACACATTAAGGCGT 58.402 30.769 0.00 0.00 36.94 5.68
2345 2629 7.540400 TGATGAAATTAAACACATTAAGGCGTG 59.460 33.333 0.00 0.00 36.94 5.34
2346 2630 6.153067 TGAAATTAAACACATTAAGGCGTGG 58.847 36.000 7.22 0.00 36.94 4.94
2347 2631 5.715434 AATTAAACACATTAAGGCGTGGT 57.285 34.783 7.22 0.00 36.94 4.16
2348 2632 6.821031 AATTAAACACATTAAGGCGTGGTA 57.179 33.333 7.22 0.00 36.94 3.25
2349 2633 5.866335 TTAAACACATTAAGGCGTGGTAG 57.134 39.130 7.22 0.00 37.45 3.18
2350 2634 3.688694 AACACATTAAGGCGTGGTAGA 57.311 42.857 7.22 0.00 37.45 2.59
2351 2635 3.688694 ACACATTAAGGCGTGGTAGAA 57.311 42.857 7.22 0.00 37.45 2.10
2352 2636 4.010667 ACACATTAAGGCGTGGTAGAAA 57.989 40.909 7.22 0.00 37.45 2.52
2353 2637 4.000988 ACACATTAAGGCGTGGTAGAAAG 58.999 43.478 7.22 0.00 37.45 2.62
2354 2638 3.374058 CACATTAAGGCGTGGTAGAAAGG 59.626 47.826 0.00 0.00 0.00 3.11
2355 2639 3.008704 ACATTAAGGCGTGGTAGAAAGGT 59.991 43.478 0.00 0.00 0.00 3.50
2356 2640 2.754946 TAAGGCGTGGTAGAAAGGTG 57.245 50.000 0.00 0.00 0.00 4.00
2357 2641 0.036306 AAGGCGTGGTAGAAAGGTGG 59.964 55.000 0.00 0.00 0.00 4.61
2358 2642 2.038837 GGCGTGGTAGAAAGGTGGC 61.039 63.158 0.00 0.00 0.00 5.01
2359 2643 2.038837 GCGTGGTAGAAAGGTGGCC 61.039 63.158 0.00 0.00 0.00 5.36
2360 2644 1.373435 CGTGGTAGAAAGGTGGCCA 59.627 57.895 0.00 0.00 0.00 5.36
2361 2645 0.250553 CGTGGTAGAAAGGTGGCCAA 60.251 55.000 7.24 0.00 0.00 4.52
2362 2646 1.244816 GTGGTAGAAAGGTGGCCAAC 58.755 55.000 14.82 14.82 0.00 3.77
2373 2657 2.074099 TGGCCAACCAGCTATGTCA 58.926 52.632 0.61 0.00 42.67 3.58
2374 2658 0.322456 TGGCCAACCAGCTATGTCAC 60.322 55.000 0.61 0.00 42.67 3.67
2375 2659 1.369091 GGCCAACCAGCTATGTCACG 61.369 60.000 0.00 0.00 35.26 4.35
2376 2660 0.673644 GCCAACCAGCTATGTCACGT 60.674 55.000 0.00 0.00 0.00 4.49
2377 2661 1.078709 CCAACCAGCTATGTCACGTG 58.921 55.000 9.94 9.94 0.00 4.49
2378 2662 1.078709 CAACCAGCTATGTCACGTGG 58.921 55.000 17.00 0.00 0.00 4.94
2379 2663 0.673644 AACCAGCTATGTCACGTGGC 60.674 55.000 14.58 14.58 0.00 5.01
2380 2664 2.167219 CCAGCTATGTCACGTGGCG 61.167 63.158 16.50 2.04 0.00 5.69
2381 2665 2.509336 AGCTATGTCACGTGGCGC 60.509 61.111 16.50 12.99 0.00 6.53
2382 2666 2.813474 GCTATGTCACGTGGCGCA 60.813 61.111 16.50 12.65 0.00 6.09
2383 2667 2.173669 GCTATGTCACGTGGCGCAT 61.174 57.895 16.50 18.23 0.00 4.73
2384 2668 0.874175 GCTATGTCACGTGGCGCATA 60.874 55.000 16.50 18.36 0.00 3.14
2385 2669 0.852777 CTATGTCACGTGGCGCATAC 59.147 55.000 16.50 6.87 0.00 2.39
2386 2670 0.458260 TATGTCACGTGGCGCATACT 59.542 50.000 16.50 0.00 0.00 2.12
2387 2671 1.083806 ATGTCACGTGGCGCATACTG 61.084 55.000 16.50 8.20 0.00 2.74
2388 2672 2.125713 TCACGTGGCGCATACTGG 60.126 61.111 17.00 2.76 0.00 4.00
2389 2673 2.434185 CACGTGGCGCATACTGGT 60.434 61.111 10.83 0.00 0.00 4.00
2390 2674 2.032634 CACGTGGCGCATACTGGTT 61.033 57.895 10.83 0.00 0.00 3.67
2391 2675 2.032634 ACGTGGCGCATACTGGTTG 61.033 57.895 10.83 0.00 0.00 3.77
2392 2676 2.749865 CGTGGCGCATACTGGTTGG 61.750 63.158 10.83 0.00 0.00 3.77
2393 2677 2.749839 TGGCGCATACTGGTTGGC 60.750 61.111 10.83 0.00 0.00 4.52
2394 2678 3.518068 GGCGCATACTGGTTGGCC 61.518 66.667 10.83 0.00 0.00 5.36
2395 2679 3.876198 GCGCATACTGGTTGGCCG 61.876 66.667 0.30 0.00 37.67 6.13
2396 2680 2.435938 CGCATACTGGTTGGCCGT 60.436 61.111 0.00 0.00 37.67 5.68
2397 2681 2.749865 CGCATACTGGTTGGCCGTG 61.750 63.158 0.00 0.00 37.67 4.94
2398 2682 2.406616 GCATACTGGTTGGCCGTGG 61.407 63.158 0.00 0.00 37.67 4.94
2399 2683 1.002624 CATACTGGTTGGCCGTGGT 60.003 57.895 0.00 0.00 37.67 4.16
2400 2684 1.002624 ATACTGGTTGGCCGTGGTG 60.003 57.895 0.00 0.00 37.67 4.17
2401 2685 1.485294 ATACTGGTTGGCCGTGGTGA 61.485 55.000 0.00 0.00 37.67 4.02
2402 2686 1.697082 TACTGGTTGGCCGTGGTGAA 61.697 55.000 0.00 0.00 37.67 3.18
2403 2687 1.826054 CTGGTTGGCCGTGGTGAAA 60.826 57.895 0.00 0.00 37.67 2.69
2404 2688 1.379977 TGGTTGGCCGTGGTGAAAA 60.380 52.632 0.00 0.00 37.67 2.29
2405 2689 0.970937 TGGTTGGCCGTGGTGAAAAA 60.971 50.000 0.00 0.00 37.67 1.94
2406 2690 0.249280 GGTTGGCCGTGGTGAAAAAG 60.249 55.000 0.00 0.00 0.00 2.27
2407 2691 0.458260 GTTGGCCGTGGTGAAAAAGT 59.542 50.000 0.00 0.00 0.00 2.66
2408 2692 1.134936 GTTGGCCGTGGTGAAAAAGTT 60.135 47.619 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 72 2.361483 ATTGCCGCACCATGCTCA 60.361 55.556 0.00 0.00 42.25 4.26
125 128 2.514824 GGCAGGGACCAAGCGATC 60.515 66.667 0.00 0.00 0.00 3.69
224 228 3.399181 GGACCTCACCGGCATCCA 61.399 66.667 0.00 0.00 35.61 3.41
334 338 1.661821 GATCATCGAGTTCCCCGCG 60.662 63.158 0.00 0.00 37.75 6.46
403 407 5.867716 GCAAGATTTCGACTACTTCTTGGTA 59.132 40.000 16.93 0.00 42.13 3.25
522 548 2.577593 CCGAGTTTCCCCGGTCTC 59.422 66.667 0.00 0.00 40.78 3.36
531 557 5.277538 GCATACTGATTCAATCCCGAGTTTC 60.278 44.000 0.00 0.00 0.00 2.78
552 578 2.167662 CCCTGGTTTTTACTTCCGCAT 58.832 47.619 0.00 0.00 0.00 4.73
555 581 0.519961 CGCCCTGGTTTTTACTTCCG 59.480 55.000 0.00 0.00 0.00 4.30
557 583 0.242825 GCCGCCCTGGTTTTTACTTC 59.757 55.000 0.00 0.00 41.21 3.01
561 587 1.001887 ATCGCCGCCCTGGTTTTTA 60.002 52.632 0.00 0.00 41.21 1.52
562 588 2.282887 ATCGCCGCCCTGGTTTTT 60.283 55.556 0.00 0.00 41.21 1.94
608 635 4.501071 GATTTCGCCTCCTACAGTGTTTA 58.499 43.478 0.00 0.00 0.00 2.01
640 667 2.893837 CACGCACGATTACGAAAACAA 58.106 42.857 0.00 0.00 42.66 2.83
641 668 1.397441 GCACGCACGATTACGAAAACA 60.397 47.619 0.00 0.00 42.66 2.83
642 669 1.235695 GCACGCACGATTACGAAAAC 58.764 50.000 0.00 0.00 42.66 2.43
643 670 0.859882 TGCACGCACGATTACGAAAA 59.140 45.000 0.00 0.00 42.66 2.29
644 671 0.436913 CTGCACGCACGATTACGAAA 59.563 50.000 0.00 0.00 42.66 3.46
659 686 4.408821 GATCCGGGTGTGCCTGCA 62.409 66.667 0.00 0.00 39.86 4.41
702 729 4.198625 AGCGCAGAAGCTCATCAC 57.801 55.556 11.47 0.00 45.67 3.06
715 742 4.464112 CTTAACTGTTCTTACCAAAGCGC 58.536 43.478 0.00 0.00 32.36 5.92
737 764 5.278463 CCACAGCCTTTGGTATGTTATATGC 60.278 44.000 0.00 0.00 0.00 3.14
740 767 5.444744 ACCACAGCCTTTGGTATGTTATA 57.555 39.130 0.00 0.00 46.01 0.98
741 768 4.316025 ACCACAGCCTTTGGTATGTTAT 57.684 40.909 0.00 0.00 46.01 1.89
742 769 3.799432 ACCACAGCCTTTGGTATGTTA 57.201 42.857 0.00 0.00 46.01 2.41
849 884 2.664851 CGAACTGCCAGCACCGAA 60.665 61.111 0.00 0.00 0.00 4.30
916 953 2.306847 GAACTGGGAAGTTGGAAGCAA 58.693 47.619 0.00 0.00 31.35 3.91
918 955 0.875059 CGAACTGGGAAGTTGGAAGC 59.125 55.000 0.00 0.00 30.62 3.86
919 956 0.875059 GCGAACTGGGAAGTTGGAAG 59.125 55.000 5.00 0.00 30.62 3.46
952 990 1.252904 TGTTCCTACGTAGCGCCCTT 61.253 55.000 17.41 0.00 0.00 3.95
956 994 1.408474 CGGTTGTTCCTACGTAGCGC 61.408 60.000 17.41 0.00 0.00 5.92
961 999 1.005394 CAGCCGGTTGTTCCTACGT 60.005 57.895 10.61 0.00 0.00 3.57
964 1002 1.550130 CCTCCAGCCGGTTGTTCCTA 61.550 60.000 17.69 0.00 0.00 2.94
966 1004 2.359975 CCTCCAGCCGGTTGTTCC 60.360 66.667 17.69 0.00 0.00 3.62
1149 1193 2.060980 GCATGAGGGTCGAGGGAGT 61.061 63.158 0.00 0.00 0.00 3.85
1225 1269 1.658994 TGGTGGTGACAAAAGTCGAC 58.341 50.000 7.70 7.70 46.06 4.20
1229 1273 3.314080 CACGTTATGGTGGTGACAAAAGT 59.686 43.478 0.00 0.00 46.06 2.66
1233 1277 2.103432 ACTCACGTTATGGTGGTGACAA 59.897 45.455 0.00 0.00 46.06 3.18
1235 1279 2.066262 CACTCACGTTATGGTGGTGAC 58.934 52.381 0.00 0.00 39.41 3.67
1236 1280 1.689813 ACACTCACGTTATGGTGGTGA 59.310 47.619 15.92 4.33 39.41 4.02
1237 1281 1.798223 CACACTCACGTTATGGTGGTG 59.202 52.381 10.30 10.59 41.12 4.17
1238 1282 1.414919 ACACACTCACGTTATGGTGGT 59.585 47.619 10.69 4.64 38.46 4.16
1239 1283 2.066262 GACACACTCACGTTATGGTGG 58.934 52.381 10.69 4.19 38.46 4.61
1240 1284 2.987149 GAGACACACTCACGTTATGGTG 59.013 50.000 5.83 5.83 44.36 4.17
1241 1285 3.299340 GAGACACACTCACGTTATGGT 57.701 47.619 0.00 0.00 44.36 3.55
1269 1313 3.120649 CGCCGACCTACAAAGAGAAAAAG 60.121 47.826 0.00 0.00 0.00 2.27
1280 1324 4.129737 GCTCAGCGCCGACCTACA 62.130 66.667 2.29 0.00 0.00 2.74
1412 1456 3.045601 ACTCCAGAAGGACAATTGACG 57.954 47.619 13.59 0.00 39.61 4.35
1413 1457 5.153950 ACTACTCCAGAAGGACAATTGAC 57.846 43.478 13.59 5.81 39.61 3.18
1503 1665 1.197721 GTGGGAAGCAGAAACACGATG 59.802 52.381 0.00 0.00 0.00 3.84
1536 1698 2.190981 CTCTACGGCGTCGCTTTATTT 58.809 47.619 19.21 0.00 40.63 1.40
1539 1701 1.430632 CCTCTACGGCGTCGCTTTA 59.569 57.895 19.21 7.60 40.63 1.85
1540 1702 2.181021 CCTCTACGGCGTCGCTTT 59.819 61.111 19.21 6.77 40.63 3.51
1627 1789 9.620660 GTCCGAAAATACTTGTTATCAAAATGT 57.379 29.630 0.00 0.00 32.87 2.71
1628 1790 8.785101 CGTCCGAAAATACTTGTTATCAAAATG 58.215 33.333 0.00 0.00 32.87 2.32
1629 1791 7.966204 CCGTCCGAAAATACTTGTTATCAAAAT 59.034 33.333 0.00 0.00 32.87 1.82
1630 1792 7.172875 TCCGTCCGAAAATACTTGTTATCAAAA 59.827 33.333 0.00 0.00 32.87 2.44
1631 1793 6.649973 TCCGTCCGAAAATACTTGTTATCAAA 59.350 34.615 0.00 0.00 32.87 2.69
1632 1794 6.164876 TCCGTCCGAAAATACTTGTTATCAA 58.835 36.000 0.00 0.00 0.00 2.57
1633 1795 5.722263 TCCGTCCGAAAATACTTGTTATCA 58.278 37.500 0.00 0.00 0.00 2.15
1634 1796 5.233689 CCTCCGTCCGAAAATACTTGTTATC 59.766 44.000 0.00 0.00 0.00 1.75
1635 1797 5.105228 TCCTCCGTCCGAAAATACTTGTTAT 60.105 40.000 0.00 0.00 0.00 1.89
1636 1798 4.220382 TCCTCCGTCCGAAAATACTTGTTA 59.780 41.667 0.00 0.00 0.00 2.41
1637 1799 3.007182 TCCTCCGTCCGAAAATACTTGTT 59.993 43.478 0.00 0.00 0.00 2.83
1638 1800 2.564062 TCCTCCGTCCGAAAATACTTGT 59.436 45.455 0.00 0.00 0.00 3.16
1639 1801 3.241067 TCCTCCGTCCGAAAATACTTG 57.759 47.619 0.00 0.00 0.00 3.16
1640 1802 3.260128 ACTTCCTCCGTCCGAAAATACTT 59.740 43.478 0.00 0.00 0.00 2.24
1641 1803 2.830321 ACTTCCTCCGTCCGAAAATACT 59.170 45.455 0.00 0.00 0.00 2.12
1642 1804 3.242549 ACTTCCTCCGTCCGAAAATAC 57.757 47.619 0.00 0.00 0.00 1.89
1643 1805 4.403432 ACATACTTCCTCCGTCCGAAAATA 59.597 41.667 0.00 0.00 0.00 1.40
1644 1806 3.197116 ACATACTTCCTCCGTCCGAAAAT 59.803 43.478 0.00 0.00 0.00 1.82
1645 1807 2.564062 ACATACTTCCTCCGTCCGAAAA 59.436 45.455 0.00 0.00 0.00 2.29
1646 1808 2.173519 ACATACTTCCTCCGTCCGAAA 58.826 47.619 0.00 0.00 0.00 3.46
1647 1809 1.843368 ACATACTTCCTCCGTCCGAA 58.157 50.000 0.00 0.00 0.00 4.30
1648 1810 2.715749 TACATACTTCCTCCGTCCGA 57.284 50.000 0.00 0.00 0.00 4.55
1649 1811 3.147629 AGATACATACTTCCTCCGTCCG 58.852 50.000 0.00 0.00 0.00 4.79
1650 1812 4.583489 TCAAGATACATACTTCCTCCGTCC 59.417 45.833 0.00 0.00 0.00 4.79
1651 1813 5.769484 TCAAGATACATACTTCCTCCGTC 57.231 43.478 0.00 0.00 0.00 4.79
1652 1814 6.540438 TTTCAAGATACATACTTCCTCCGT 57.460 37.500 0.00 0.00 0.00 4.69
1653 1815 7.843490 TTTTTCAAGATACATACTTCCTCCG 57.157 36.000 0.00 0.00 0.00 4.63
1654 1816 8.552034 CGATTTTTCAAGATACATACTTCCTCC 58.448 37.037 0.00 0.00 0.00 4.30
1655 1817 9.314321 TCGATTTTTCAAGATACATACTTCCTC 57.686 33.333 0.00 0.00 0.00 3.71
1656 1818 9.838339 ATCGATTTTTCAAGATACATACTTCCT 57.162 29.630 0.00 0.00 0.00 3.36
1657 1819 9.869844 CATCGATTTTTCAAGATACATACTTCC 57.130 33.333 0.00 0.00 0.00 3.46
1660 1822 9.823647 AGTCATCGATTTTTCAAGATACATACT 57.176 29.630 0.00 0.00 0.00 2.12
1664 1826 9.599866 ACATAGTCATCGATTTTTCAAGATACA 57.400 29.630 0.00 0.00 0.00 2.29
1676 1838 9.561270 CGAATCTACATAACATAGTCATCGATT 57.439 33.333 0.00 0.00 0.00 3.34
1677 1839 8.731605 ACGAATCTACATAACATAGTCATCGAT 58.268 33.333 0.00 0.00 31.25 3.59
1678 1840 8.095937 ACGAATCTACATAACATAGTCATCGA 57.904 34.615 0.00 0.00 31.25 3.59
1679 1841 9.989869 ATACGAATCTACATAACATAGTCATCG 57.010 33.333 0.00 0.00 0.00 3.84
1699 1861 9.839817 TTTTAACCATCCAGATTCATATACGAA 57.160 29.630 0.00 0.00 0.00 3.85
1700 1862 9.489084 CTTTTAACCATCCAGATTCATATACGA 57.511 33.333 0.00 0.00 0.00 3.43
1701 1863 8.721478 CCTTTTAACCATCCAGATTCATATACG 58.279 37.037 0.00 0.00 0.00 3.06
1702 1864 9.014297 CCCTTTTAACCATCCAGATTCATATAC 57.986 37.037 0.00 0.00 0.00 1.47
1703 1865 8.170061 CCCCTTTTAACCATCCAGATTCATATA 58.830 37.037 0.00 0.00 0.00 0.86
1704 1866 7.012607 CCCCTTTTAACCATCCAGATTCATAT 58.987 38.462 0.00 0.00 0.00 1.78
1705 1867 6.161348 TCCCCTTTTAACCATCCAGATTCATA 59.839 38.462 0.00 0.00 0.00 2.15
1706 1868 5.043432 TCCCCTTTTAACCATCCAGATTCAT 60.043 40.000 0.00 0.00 0.00 2.57
1707 1869 4.293634 TCCCCTTTTAACCATCCAGATTCA 59.706 41.667 0.00 0.00 0.00 2.57
1708 1870 4.867086 TCCCCTTTTAACCATCCAGATTC 58.133 43.478 0.00 0.00 0.00 2.52
1709 1871 4.965283 TCCCCTTTTAACCATCCAGATT 57.035 40.909 0.00 0.00 0.00 2.40
1710 1872 4.965283 TTCCCCTTTTAACCATCCAGAT 57.035 40.909 0.00 0.00 0.00 2.90
1711 1873 4.412843 GTTTCCCCTTTTAACCATCCAGA 58.587 43.478 0.00 0.00 0.00 3.86
1712 1874 3.192633 CGTTTCCCCTTTTAACCATCCAG 59.807 47.826 0.00 0.00 0.00 3.86
1713 1875 3.158676 CGTTTCCCCTTTTAACCATCCA 58.841 45.455 0.00 0.00 0.00 3.41
1714 1876 3.423749 TCGTTTCCCCTTTTAACCATCC 58.576 45.455 0.00 0.00 0.00 3.51
1715 1877 4.521639 AGTTCGTTTCCCCTTTTAACCATC 59.478 41.667 0.00 0.00 0.00 3.51
1716 1878 4.476297 AGTTCGTTTCCCCTTTTAACCAT 58.524 39.130 0.00 0.00 0.00 3.55
1717 1879 3.900971 AGTTCGTTTCCCCTTTTAACCA 58.099 40.909 0.00 0.00 0.00 3.67
1718 1880 5.065914 ACTAGTTCGTTTCCCCTTTTAACC 58.934 41.667 0.00 0.00 0.00 2.85
1719 1881 7.821359 AGATACTAGTTCGTTTCCCCTTTTAAC 59.179 37.037 0.00 0.00 0.00 2.01
1720 1882 7.910584 AGATACTAGTTCGTTTCCCCTTTTAA 58.089 34.615 0.00 0.00 0.00 1.52
1721 1883 7.486407 AGATACTAGTTCGTTTCCCCTTTTA 57.514 36.000 0.00 0.00 0.00 1.52
1722 1884 6.370186 AGATACTAGTTCGTTTCCCCTTTT 57.630 37.500 0.00 0.00 0.00 2.27
1723 1885 6.127225 GGTAGATACTAGTTCGTTTCCCCTTT 60.127 42.308 0.00 0.00 0.00 3.11
1724 1886 5.362143 GGTAGATACTAGTTCGTTTCCCCTT 59.638 44.000 0.00 0.00 0.00 3.95
1725 1887 4.892345 GGTAGATACTAGTTCGTTTCCCCT 59.108 45.833 0.00 0.00 0.00 4.79
1726 1888 4.892345 AGGTAGATACTAGTTCGTTTCCCC 59.108 45.833 0.00 0.00 0.00 4.81
1727 1889 6.096001 TGAAGGTAGATACTAGTTCGTTTCCC 59.904 42.308 0.00 0.00 0.00 3.97
1728 1890 7.093322 TGAAGGTAGATACTAGTTCGTTTCC 57.907 40.000 0.00 0.00 0.00 3.13
1729 1891 8.976986 TTTGAAGGTAGATACTAGTTCGTTTC 57.023 34.615 0.00 4.52 0.00 2.78
1730 1892 9.768662 TTTTTGAAGGTAGATACTAGTTCGTTT 57.231 29.630 0.00 0.00 0.00 3.60
1731 1893 9.939802 ATTTTTGAAGGTAGATACTAGTTCGTT 57.060 29.630 0.00 0.00 0.00 3.85
1732 1894 9.583765 GATTTTTGAAGGTAGATACTAGTTCGT 57.416 33.333 0.00 0.00 0.00 3.85
1733 1895 8.744011 CGATTTTTGAAGGTAGATACTAGTTCG 58.256 37.037 0.00 0.00 0.00 3.95
1734 1896 9.798994 TCGATTTTTGAAGGTAGATACTAGTTC 57.201 33.333 0.00 0.00 0.00 3.01
1736 1898 9.751542 CATCGATTTTTGAAGGTAGATACTAGT 57.248 33.333 0.00 0.00 0.00 2.57
1737 1899 9.967346 TCATCGATTTTTGAAGGTAGATACTAG 57.033 33.333 0.00 0.00 0.00 2.57
1738 1900 9.745880 GTCATCGATTTTTGAAGGTAGATACTA 57.254 33.333 0.00 0.00 0.00 1.82
1739 1901 8.478877 AGTCATCGATTTTTGAAGGTAGATACT 58.521 33.333 0.00 0.00 0.00 2.12
1751 1913 9.087424 TCTACAGAACATAGTCATCGATTTTTG 57.913 33.333 0.00 0.00 0.00 2.44
1780 1942 9.236006 CCTTTTAACCATCCAGATTCATATAGG 57.764 37.037 0.00 0.00 0.00 2.57
1781 1943 9.236006 CCCTTTTAACCATCCAGATTCATATAG 57.764 37.037 0.00 0.00 0.00 1.31
1782 1944 8.170061 CCCCTTTTAACCATCCAGATTCATATA 58.830 37.037 0.00 0.00 0.00 0.86
1783 1945 7.012607 CCCCTTTTAACCATCCAGATTCATAT 58.987 38.462 0.00 0.00 0.00 1.78
1784 1946 6.161348 TCCCCTTTTAACCATCCAGATTCATA 59.839 38.462 0.00 0.00 0.00 2.15
1812 1974 6.499172 TCATGTTAACTTTTGCAATCGTTCA 58.501 32.000 14.72 9.82 0.00 3.18
1875 2142 2.231721 GAGAGGTCCGGTTATAGATGCC 59.768 54.545 0.00 0.00 0.00 4.40
1883 2150 1.270550 GACGTTTGAGAGGTCCGGTTA 59.729 52.381 0.00 0.00 37.22 2.85
1911 2191 1.507141 CCGGACAGTGACCAAGTTGC 61.507 60.000 12.19 0.00 0.00 4.17
1947 2227 2.418060 GGTTGTGGTTGGGTGACTTTTG 60.418 50.000 0.00 0.00 0.00 2.44
1991 2271 7.237982 TGGGTATAGGGATTTGTGGATTTATG 58.762 38.462 0.00 0.00 0.00 1.90
1996 2276 4.731929 AGTTGGGTATAGGGATTTGTGGAT 59.268 41.667 0.00 0.00 0.00 3.41
2013 2293 2.505407 TCCTCCACACATATGAGTTGGG 59.495 50.000 10.38 6.52 0.00 4.12
2028 2308 1.977854 CCGAACATCCCATATCCTCCA 59.022 52.381 0.00 0.00 0.00 3.86
2049 2330 1.344438 CGCATCCTACATGAAGGGCTA 59.656 52.381 0.00 0.00 37.24 3.93
2056 2338 3.141409 TAGGCCGCATCCTACATGA 57.859 52.632 0.00 0.00 37.66 3.07
2080 2362 7.931578 TGAAGAAAGAAAGACAAAAGTGGTA 57.068 32.000 0.00 0.00 0.00 3.25
2086 2368 5.128499 TGGGCATGAAGAAAGAAAGACAAAA 59.872 36.000 0.00 0.00 0.00 2.44
2090 2372 4.460382 TGATGGGCATGAAGAAAGAAAGAC 59.540 41.667 0.00 0.00 0.00 3.01
2091 2373 4.665451 TGATGGGCATGAAGAAAGAAAGA 58.335 39.130 0.00 0.00 0.00 2.52
2092 2374 5.395682 TTGATGGGCATGAAGAAAGAAAG 57.604 39.130 0.00 0.00 0.00 2.62
2093 2375 5.481122 TGATTGATGGGCATGAAGAAAGAAA 59.519 36.000 0.00 0.00 0.00 2.52
2096 2378 4.994907 TGATTGATGGGCATGAAGAAAG 57.005 40.909 0.00 0.00 0.00 2.62
2097 2379 6.517697 GCATATGATTGATGGGCATGAAGAAA 60.518 38.462 6.97 0.00 0.00 2.52
2098 2380 5.047590 GCATATGATTGATGGGCATGAAGAA 60.048 40.000 6.97 0.00 0.00 2.52
2139 2422 3.246167 ACCATCTCCTCTACAACCTTCCT 60.246 47.826 0.00 0.00 0.00 3.36
2146 2429 3.877559 CATGCAACCATCTCCTCTACAA 58.122 45.455 0.00 0.00 0.00 2.41
2152 2435 1.399714 CATGCATGCAACCATCTCCT 58.600 50.000 26.68 0.80 0.00 3.69
2174 2457 5.050634 CGTGTCCGTTTTGAGTCTTCATTTA 60.051 40.000 0.00 0.00 32.27 1.40
2212 2495 3.501396 CATCCGTGGATGTGCACC 58.499 61.111 18.76 0.00 44.93 5.01
2266 2550 3.826729 GCCAACCCAAAGATTGTAAGAGT 59.173 43.478 0.00 0.00 0.00 3.24
2276 2560 0.850100 TCTTGAGGCCAACCCAAAGA 59.150 50.000 5.01 1.51 36.66 2.52
2285 2569 2.224159 GGTGGACCTCTTGAGGCCA 61.224 63.158 20.80 20.80 34.41 5.36
2318 2602 8.085296 ACGCCTTAATGTGTTTAATTTCATCAA 58.915 29.630 0.00 0.00 0.00 2.57
2320 2604 7.009174 CCACGCCTTAATGTGTTTAATTTCATC 59.991 37.037 0.00 0.00 34.28 2.92
2330 2614 3.688694 TCTACCACGCCTTAATGTGTT 57.311 42.857 0.00 0.00 34.28 3.32
2331 2615 3.688694 TTCTACCACGCCTTAATGTGT 57.311 42.857 0.00 0.00 34.28 3.72
2332 2616 3.374058 CCTTTCTACCACGCCTTAATGTG 59.626 47.826 0.00 0.00 35.87 3.21
2333 2617 3.008704 ACCTTTCTACCACGCCTTAATGT 59.991 43.478 0.00 0.00 0.00 2.71
2334 2618 3.374058 CACCTTTCTACCACGCCTTAATG 59.626 47.826 0.00 0.00 0.00 1.90
2335 2619 3.606687 CACCTTTCTACCACGCCTTAAT 58.393 45.455 0.00 0.00 0.00 1.40
2336 2620 2.289819 CCACCTTTCTACCACGCCTTAA 60.290 50.000 0.00 0.00 0.00 1.85
2337 2621 1.276989 CCACCTTTCTACCACGCCTTA 59.723 52.381 0.00 0.00 0.00 2.69
2338 2622 0.036306 CCACCTTTCTACCACGCCTT 59.964 55.000 0.00 0.00 0.00 4.35
2339 2623 1.677552 CCACCTTTCTACCACGCCT 59.322 57.895 0.00 0.00 0.00 5.52
2340 2624 2.038837 GCCACCTTTCTACCACGCC 61.039 63.158 0.00 0.00 0.00 5.68
2341 2625 2.038837 GGCCACCTTTCTACCACGC 61.039 63.158 0.00 0.00 0.00 5.34
2342 2626 0.250553 TTGGCCACCTTTCTACCACG 60.251 55.000 3.88 0.00 0.00 4.94
2343 2627 1.244816 GTTGGCCACCTTTCTACCAC 58.755 55.000 3.88 0.00 0.00 4.16
2344 2628 0.111639 GGTTGGCCACCTTTCTACCA 59.888 55.000 3.88 0.00 43.29 3.25
2345 2629 2.957060 GGTTGGCCACCTTTCTACC 58.043 57.895 3.88 4.44 43.29 3.18
2354 2638 0.322456 TGACATAGCTGGTTGGCCAC 60.322 55.000 3.88 0.00 40.46 5.01
2355 2639 0.322456 GTGACATAGCTGGTTGGCCA 60.322 55.000 0.00 0.00 43.73 5.36
2356 2640 1.369091 CGTGACATAGCTGGTTGGCC 61.369 60.000 0.00 0.00 0.00 5.36
2357 2641 0.673644 ACGTGACATAGCTGGTTGGC 60.674 55.000 0.00 0.00 0.00 4.52
2358 2642 1.078709 CACGTGACATAGCTGGTTGG 58.921 55.000 10.90 0.00 0.00 3.77
2359 2643 1.078709 CCACGTGACATAGCTGGTTG 58.921 55.000 19.30 0.00 0.00 3.77
2360 2644 0.673644 GCCACGTGACATAGCTGGTT 60.674 55.000 19.30 0.00 0.00 3.67
2361 2645 1.079127 GCCACGTGACATAGCTGGT 60.079 57.895 19.30 0.00 0.00 4.00
2362 2646 2.167219 CGCCACGTGACATAGCTGG 61.167 63.158 19.30 0.00 0.00 4.85
2363 2647 2.802667 GCGCCACGTGACATAGCTG 61.803 63.158 19.30 8.85 0.00 4.24
2364 2648 2.509336 GCGCCACGTGACATAGCT 60.509 61.111 19.30 0.00 0.00 3.32
2365 2649 0.874175 TATGCGCCACGTGACATAGC 60.874 55.000 19.30 14.44 0.00 2.97
2366 2650 0.852777 GTATGCGCCACGTGACATAG 59.147 55.000 19.30 0.00 0.00 2.23
2367 2651 0.458260 AGTATGCGCCACGTGACATA 59.542 50.000 19.30 17.69 0.00 2.29
2368 2652 1.083806 CAGTATGCGCCACGTGACAT 61.084 55.000 19.30 18.69 0.00 3.06
2369 2653 1.736282 CAGTATGCGCCACGTGACA 60.736 57.895 19.30 12.68 0.00 3.58
2370 2654 2.452813 CCAGTATGCGCCACGTGAC 61.453 63.158 19.30 3.81 31.97 3.67
2371 2655 2.125713 CCAGTATGCGCCACGTGA 60.126 61.111 19.30 0.00 31.97 4.35
2372 2656 2.032634 AACCAGTATGCGCCACGTG 61.033 57.895 9.08 9.08 31.97 4.49
2373 2657 2.032634 CAACCAGTATGCGCCACGT 61.033 57.895 4.18 0.00 31.97 4.49
2374 2658 2.749865 CCAACCAGTATGCGCCACG 61.750 63.158 4.18 0.00 31.97 4.94
2375 2659 3.051392 GCCAACCAGTATGCGCCAC 62.051 63.158 4.18 2.39 31.97 5.01
2376 2660 2.749839 GCCAACCAGTATGCGCCA 60.750 61.111 4.18 0.00 31.97 5.69
2377 2661 3.518068 GGCCAACCAGTATGCGCC 61.518 66.667 4.18 0.00 35.26 6.53
2378 2662 3.876198 CGGCCAACCAGTATGCGC 61.876 66.667 2.24 0.00 34.57 6.09
2379 2663 2.435938 ACGGCCAACCAGTATGCG 60.436 61.111 2.24 0.00 34.57 4.73
2380 2664 2.406616 CCACGGCCAACCAGTATGC 61.407 63.158 2.24 0.00 34.57 3.14
2381 2665 1.002624 ACCACGGCCAACCAGTATG 60.003 57.895 2.24 0.00 34.57 2.39
2382 2666 1.002624 CACCACGGCCAACCAGTAT 60.003 57.895 2.24 0.00 34.57 2.12
2383 2667 1.697082 TTCACCACGGCCAACCAGTA 61.697 55.000 2.24 0.00 34.57 2.74
2384 2668 2.559922 TTTCACCACGGCCAACCAGT 62.560 55.000 2.24 0.00 34.57 4.00
2385 2669 1.388065 TTTTCACCACGGCCAACCAG 61.388 55.000 2.24 0.00 34.57 4.00
2386 2670 0.970937 TTTTTCACCACGGCCAACCA 60.971 50.000 2.24 0.00 34.57 3.67
2387 2671 0.249280 CTTTTTCACCACGGCCAACC 60.249 55.000 2.24 0.00 0.00 3.77
2388 2672 0.458260 ACTTTTTCACCACGGCCAAC 59.542 50.000 2.24 0.00 0.00 3.77
2389 2673 1.187087 AACTTTTTCACCACGGCCAA 58.813 45.000 2.24 0.00 0.00 4.52
2390 2674 2.889200 AACTTTTTCACCACGGCCA 58.111 47.368 2.24 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.