Multiple sequence alignment - TraesCS4A01G085000

Loading Multiple Alignment...

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 TraesCS4A01G085000 chr4A 100.000 4473 0 0 1 4473 89624463 89619991 0.000000e+00 8261.0
1 TraesCS4A01G085000 chr4D 89.311 3499 195 86 123 3529 374830428 374833839 0.000000e+00 4224.0
2 TraesCS4A01G085000 chr4D 85.388 657 68 11 3797 4438 374836596 374837239 0.000000e+00 656.0
3 TraesCS4A01G085000 chr4B 90.643 2736 137 41 959 3631 461734397 461737076 0.000000e+00 3524.0
4 TraesCS4A01G085000 chr4B 82.746 852 88 14 3644 4473 461739118 461739932 0.000000e+00 704.0
5 TraesCS4A01G085000 chr4B 83.761 585 50 23 20 582 461733093 461733654 3.090000e-141 512.0
6 TraesCS4A01G085000 chr4B 86.047 387 32 15 578 961 461733680 461734047 3.240000e-106 396.0
7 TraesCS4A01G085000 chr6B 82.301 226 40 0 2932 3157 173818079 173817854 3.530000e-46 196.0
8 TraesCS4A01G085000 chr2B 83.582 201 28 4 2957 3155 459421223 459421026 2.750000e-42 183.0
9 TraesCS4A01G085000 chr3A 86.275 51 7 0 3819 3869 674594988 674595038 6.250000e-04 56.5
10 TraesCS4A01G085000 chr5B 100.000 28 0 0 509 536 430378210 430378183 8.000000e-03 52.8


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 TraesCS4A01G085000 chr4A 89619991 89624463 4472 True 8261 8261 100.00000 1 4473 1 chr4A.!!$R1 4472
1 TraesCS4A01G085000 chr4D 374830428 374837239 6811 False 2440 4224 87.34950 123 4438 2 chr4D.!!$F1 4315
2 TraesCS4A01G085000 chr4B 461733093 461739932 6839 False 1284 3524 85.79925 20 4473 4 chr4B.!!$F1 4453

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
621 701 0.035317 AACTCTGAATCACCGCAGCA 59.965 50.000 0.00 0.00 32.27 4.41 F
638 718 0.389687 GCAGCAGGTGAGAGTGAGAC 60.390 60.000 3.02 0.00 0.00 3.36 F
915 1005 1.134491 GGTGGGACTTTGGATCCTACG 60.134 57.143 14.23 5.66 46.03 3.51 F
1493 1958 1.134995 TCATCGAGCACTACTGCAAGG 60.135 52.381 0.00 0.00 46.97 3.61 F
2348 2834 0.663688 GCAGAGGCTTGCTGATGATG 59.336 55.000 7.35 0.00 40.89 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2190 2676 0.034059 ACCTCAAGCTGTTCGACAGG 59.966 55.0 14.19 3.36 46.01 4.00 R
2212 2698 0.602060 GACCTCGGAAGTTTCGGTCT 59.398 55.0 3.17 0.00 40.67 3.85 R
2341 2827 0.832626 ACCGGCTCATGTCATCATCA 59.167 50.0 0.00 0.00 31.15 3.07 R
3374 3905 0.392998 CCCCACGTCTGATTTCCCAG 60.393 60.0 0.00 0.00 35.55 4.45 R
3941 9010 0.101759 CGGAGAGTATTTTCGGGCGA 59.898 55.0 0.00 0.00 0.00 5.54 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
24 25 7.303634 GATTGTAATTTGTATCGTGTCTGGT 57.696 36.000 0.00 0.00 0.00 4.00
25 26 7.681939 ATTGTAATTTGTATCGTGTCTGGTT 57.318 32.000 0.00 0.00 0.00 3.67
26 27 7.499321 TTGTAATTTGTATCGTGTCTGGTTT 57.501 32.000 0.00 0.00 0.00 3.27
27 28 7.499321 TGTAATTTGTATCGTGTCTGGTTTT 57.501 32.000 0.00 0.00 0.00 2.43
28 29 7.932335 TGTAATTTGTATCGTGTCTGGTTTTT 58.068 30.769 0.00 0.00 0.00 1.94
117 132 5.163754 CGCCATGATATGATGTAGTACGAGA 60.164 44.000 1.35 0.00 0.00 4.04
118 133 6.261859 GCCATGATATGATGTAGTACGAGAG 58.738 44.000 1.35 0.00 0.00 3.20
120 135 7.065923 GCCATGATATGATGTAGTACGAGAGTA 59.934 40.741 1.35 0.00 46.88 2.59
201 223 3.606065 CTCGGTCCGTGTCGTGTCC 62.606 68.421 11.88 0.00 0.00 4.02
309 339 4.480958 GCCGAGCGAACGATTATTATAC 57.519 45.455 0.00 0.00 35.09 1.47
311 341 4.030306 GCCGAGCGAACGATTATTATACAG 59.970 45.833 0.00 0.00 35.09 2.74
312 342 5.388111 CCGAGCGAACGATTATTATACAGA 58.612 41.667 0.00 0.00 35.09 3.41
314 344 6.527023 CCGAGCGAACGATTATTATACAGAAT 59.473 38.462 0.00 0.00 35.09 2.40
315 345 7.695201 CCGAGCGAACGATTATTATACAGAATA 59.305 37.037 0.00 0.00 35.09 1.75
349 391 4.287552 TGACCTAGGACTGATTAGGGAAC 58.712 47.826 17.98 0.00 40.63 3.62
408 453 3.118454 CACGGTGGCGCTGGTAAG 61.118 66.667 7.64 0.00 0.00 2.34
497 544 0.625316 ATGGCATGGCTAGTGGTTGA 59.375 50.000 21.08 0.00 0.00 3.18
515 562 1.691434 TGATTGGTTGGACCTTTTGCC 59.309 47.619 0.00 0.00 39.58 4.52
520 567 1.152860 TTGGACCTTTTGCCGCTGA 60.153 52.632 0.00 0.00 0.00 4.26
553 604 3.243401 ACGCCAAGAAGGTTCATTTGTTC 60.243 43.478 0.00 0.00 40.61 3.18
585 665 7.981102 TGGCAAAATCAAAATCATCAATCAA 57.019 28.000 0.00 0.00 0.00 2.57
591 671 9.649167 AAAATCAAAATCATCAATCAAGAGACC 57.351 29.630 0.00 0.00 0.00 3.85
613 693 4.761739 CCTGCCAAAGTAAACTCTGAATCA 59.238 41.667 0.00 0.00 0.00 2.57
615 695 4.518970 TGCCAAAGTAAACTCTGAATCACC 59.481 41.667 0.00 0.00 0.00 4.02
619 699 3.589988 AGTAAACTCTGAATCACCGCAG 58.410 45.455 0.00 0.00 0.00 5.18
620 700 1.160137 AAACTCTGAATCACCGCAGC 58.840 50.000 0.00 0.00 32.27 5.25
621 701 0.035317 AACTCTGAATCACCGCAGCA 59.965 50.000 0.00 0.00 32.27 4.41
622 702 0.390866 ACTCTGAATCACCGCAGCAG 60.391 55.000 0.00 0.00 32.27 4.24
623 703 1.703438 CTCTGAATCACCGCAGCAGC 61.703 60.000 0.00 0.00 37.42 5.25
624 704 2.032376 TGAATCACCGCAGCAGCA 59.968 55.556 0.82 0.00 42.27 4.41
625 705 1.978712 CTGAATCACCGCAGCAGCAG 61.979 60.000 0.82 0.00 42.27 4.24
626 706 2.749044 AATCACCGCAGCAGCAGG 60.749 61.111 0.82 6.18 42.27 4.85
627 707 3.557903 AATCACCGCAGCAGCAGGT 62.558 57.895 10.83 10.83 44.52 4.00
630 710 4.694233 ACCGCAGCAGCAGGTGAG 62.694 66.667 12.93 8.84 45.95 3.51
631 711 4.383861 CCGCAGCAGCAGGTGAGA 62.384 66.667 12.93 0.00 45.95 3.27
638 718 0.389687 GCAGCAGGTGAGAGTGAGAC 60.390 60.000 3.02 0.00 0.00 3.36
649 729 2.093106 AGAGTGAGACGTGGACATACC 58.907 52.381 0.00 0.00 39.54 2.73
666 746 5.979993 ACATACCAATGTACGTATTCACCA 58.020 37.500 0.00 0.00 44.66 4.17
676 756 1.468520 CGTATTCACCAGCCAAGTTGG 59.531 52.381 18.17 18.17 41.55 3.77
732 814 2.735134 CGAATAGGCTGCGGTAATAACC 59.265 50.000 0.00 0.00 42.95 2.85
805 887 2.046892 TCCTCTGCAGGCGCTTTC 60.047 61.111 15.13 0.00 40.12 2.62
819 901 2.912366 CGCTTTCCCGTGTAACTTTTC 58.088 47.619 0.00 0.00 31.75 2.29
915 1005 1.134491 GGTGGGACTTTGGATCCTACG 60.134 57.143 14.23 5.66 46.03 3.51
916 1006 1.829222 GTGGGACTTTGGATCCTACGA 59.171 52.381 14.23 0.00 37.88 3.43
917 1007 1.829222 TGGGACTTTGGATCCTACGAC 59.171 52.381 14.23 3.43 36.40 4.34
918 1008 2.108970 GGGACTTTGGATCCTACGACT 58.891 52.381 14.23 0.00 36.40 4.18
928 1018 3.558958 GGATCCTACGACTCCTACCCTAC 60.559 56.522 3.84 0.00 0.00 3.18
940 1030 2.238898 CCTACCCTACTCCCCAAAACAG 59.761 54.545 0.00 0.00 0.00 3.16
945 1035 3.267031 CCCTACTCCCCAAAACAGAAGAT 59.733 47.826 0.00 0.00 0.00 2.40
1022 1464 1.139947 CGCCTTCGTCCTCTTCTCC 59.860 63.158 0.00 0.00 0.00 3.71
1029 1471 3.443145 TCGTCCTCTTCTCCTCTCTTT 57.557 47.619 0.00 0.00 0.00 2.52
1030 1472 3.768878 TCGTCCTCTTCTCCTCTCTTTT 58.231 45.455 0.00 0.00 0.00 2.27
1031 1473 3.759618 TCGTCCTCTTCTCCTCTCTTTTC 59.240 47.826 0.00 0.00 0.00 2.29
1032 1474 3.761752 CGTCCTCTTCTCCTCTCTTTTCT 59.238 47.826 0.00 0.00 0.00 2.52
1033 1475 4.219725 CGTCCTCTTCTCCTCTCTTTTCTT 59.780 45.833 0.00 0.00 0.00 2.52
1094 1536 2.104170 GGAGAGAAAGAGACGACCCAT 58.896 52.381 0.00 0.00 0.00 4.00
1095 1537 2.100087 GGAGAGAAAGAGACGACCCATC 59.900 54.545 0.00 0.00 0.00 3.51
1096 1538 2.755655 GAGAGAAAGAGACGACCCATCA 59.244 50.000 0.00 0.00 0.00 3.07
1103 1545 4.221422 ACGACCCATCATCGCCCG 62.221 66.667 0.00 0.00 43.46 6.13
1127 1575 2.743928 GTCCAGCGTCAAGGCCAG 60.744 66.667 5.01 0.00 0.00 4.85
1363 1819 4.344968 GCCATACAAGCCCCTAATCAAATT 59.655 41.667 0.00 0.00 0.00 1.82
1369 1834 6.466812 ACAAGCCCCTAATCAAATTTTCAAG 58.533 36.000 0.00 0.00 0.00 3.02
1410 1875 4.210093 TGACACCGAACGGCGTGT 62.210 61.111 15.70 6.54 39.32 4.49
1411 1876 3.698463 GACACCGAACGGCGTGTG 61.698 66.667 22.44 22.44 42.76 3.82
1412 1877 4.517815 ACACCGAACGGCGTGTGT 62.518 61.111 23.58 23.58 44.11 3.72
1413 1878 3.995669 CACCGAACGGCGTGTGTG 61.996 66.667 15.70 17.26 39.32 3.82
1454 1919 1.142748 GTCATGGAGGAGGACAGCG 59.857 63.158 0.00 0.00 35.35 5.18
1493 1958 1.134995 TCATCGAGCACTACTGCAAGG 60.135 52.381 0.00 0.00 46.97 3.61
1510 1975 2.041686 GGTCCTCGTCGAGCACTCT 61.042 63.158 15.63 0.00 0.00 3.24
1570 2043 2.900546 TCTCTTGGTTTCTCCTCTGACC 59.099 50.000 0.00 0.00 37.07 4.02
1571 2044 1.618837 TCTTGGTTTCTCCTCTGACCG 59.381 52.381 0.00 0.00 34.90 4.79
1572 2045 1.344763 CTTGGTTTCTCCTCTGACCGT 59.655 52.381 0.00 0.00 34.90 4.83
1573 2046 2.297698 TGGTTTCTCCTCTGACCGTA 57.702 50.000 0.00 0.00 34.90 4.02
1575 2048 1.135460 GGTTTCTCCTCTGACCGTACG 60.135 57.143 8.69 8.69 0.00 3.67
1636 2119 3.444805 AGAGAGTGCGGCGAGGAC 61.445 66.667 12.98 3.16 41.95 3.85
1748 2231 4.524318 TCGGCCGGGAATTCGAGC 62.524 66.667 27.83 2.01 0.00 5.03
1857 2343 4.947147 CGGGTGGTGGTGGTGGTG 62.947 72.222 0.00 0.00 0.00 4.17
1858 2344 4.596585 GGGTGGTGGTGGTGGTGG 62.597 72.222 0.00 0.00 0.00 4.61
1859 2345 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
1860 2346 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
1861 2347 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.00 0.00 4.61
1862 2348 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
1863 2349 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
2005 2491 3.277211 TTGCTCGACTTCCCCGACG 62.277 63.158 0.00 0.00 32.18 5.12
2019 2505 3.462678 GACGGCCCAGGAGAGGTC 61.463 72.222 0.00 0.00 0.00 3.85
2074 2560 5.630264 TCTTGTTCATGCGAATTTTGTGATG 59.370 36.000 0.00 0.00 32.61 3.07
2075 2561 5.118642 TGTTCATGCGAATTTTGTGATGA 57.881 34.783 0.00 0.00 32.61 2.92
2076 2562 5.155643 TGTTCATGCGAATTTTGTGATGAG 58.844 37.500 0.00 0.00 32.61 2.90
2078 2564 5.823209 TCATGCGAATTTTGTGATGAGAT 57.177 34.783 0.00 0.00 0.00 2.75
2079 2565 6.923928 TCATGCGAATTTTGTGATGAGATA 57.076 33.333 0.00 0.00 0.00 1.98
2080 2566 7.500720 TCATGCGAATTTTGTGATGAGATAT 57.499 32.000 0.00 0.00 0.00 1.63
2081 2567 7.933396 TCATGCGAATTTTGTGATGAGATATT 58.067 30.769 0.00 0.00 0.00 1.28
2082 2568 8.071967 TCATGCGAATTTTGTGATGAGATATTC 58.928 33.333 0.00 0.00 0.00 1.75
2146 2632 3.582647 TCTGGGATGCAGAGTAAACAGAA 59.417 43.478 0.00 0.00 31.51 3.02
2154 2640 6.060028 TGCAGAGTAAACAGAATGAACAAC 57.940 37.500 0.00 0.00 39.69 3.32
2162 2648 5.520376 AACAGAATGAACAACCCAAGAAG 57.480 39.130 0.00 0.00 39.69 2.85
2212 2698 1.138069 TGTCGAACAGCTTGAGGTCAA 59.862 47.619 0.00 0.00 0.00 3.18
2235 2721 1.270147 CCGAAACTTCCGAGGTCAGTT 60.270 52.381 4.40 4.40 31.90 3.16
2314 2800 2.253603 GGCGAGAAATTCAATGTGTGC 58.746 47.619 0.00 0.00 0.00 4.57
2319 2805 2.028748 AGAAATTCAATGTGTGCCAGGC 60.029 45.455 3.66 3.66 0.00 4.85
2341 2827 2.610233 AGGAGGCAGAGGCTTGCT 60.610 61.111 17.11 7.21 42.93 3.91
2348 2834 0.663688 GCAGAGGCTTGCTGATGATG 59.336 55.000 7.35 0.00 40.89 3.07
2374 2860 4.675029 CGGTCGAACCTTGCCCGT 62.675 66.667 0.00 0.00 35.66 5.28
2524 3010 3.787001 GAGTCGCAGGGGAAGGGG 61.787 72.222 0.00 0.00 0.00 4.79
2596 3082 4.373116 GCAACCGAGCGGGAGACA 62.373 66.667 14.07 0.00 39.97 3.41
2668 3154 2.356313 AGCGACAAGAGCACGGTG 60.356 61.111 3.15 3.15 36.45 4.94
2702 3188 4.664677 ACGCACCAGCACGAGACC 62.665 66.667 0.00 0.00 42.27 3.85
2911 3412 3.068881 CCCAACGGCTCAGGAGAA 58.931 61.111 0.00 0.00 0.00 2.87
3185 3698 3.760035 AGGAGCAGGTGTACGGCG 61.760 66.667 4.80 4.80 45.49 6.46
3260 3773 2.103042 GTGCGCACCAGGAGATGAC 61.103 63.158 30.12 0.00 0.00 3.06
3261 3774 2.887568 GCGCACCAGGAGATGACG 60.888 66.667 0.30 0.00 0.00 4.35
3476 4007 8.327429 GTGAGTAAATTGTCCATTGTTTTGTTG 58.673 33.333 0.00 0.00 0.00 3.33
3480 4011 6.419980 AATTGTCCATTGTTTTGTTGTGTG 57.580 33.333 0.00 0.00 0.00 3.82
3481 4012 4.527509 TGTCCATTGTTTTGTTGTGTGT 57.472 36.364 0.00 0.00 0.00 3.72
3487 4018 4.458951 TTGTTTTGTTGTGTGTTGCAAC 57.541 36.364 22.83 22.83 44.50 4.17
3500 4031 1.028905 TTGCAACGGGAGGAGTTTTG 58.971 50.000 0.00 0.00 0.00 2.44
3501 4032 1.285950 GCAACGGGAGGAGTTTTGC 59.714 57.895 0.00 0.00 36.14 3.68
3502 4033 1.574428 CAACGGGAGGAGTTTTGCG 59.426 57.895 0.00 0.00 0.00 4.85
3503 4034 1.147600 AACGGGAGGAGTTTTGCGT 59.852 52.632 0.00 0.00 0.00 5.24
3504 4035 1.164041 AACGGGAGGAGTTTTGCGTG 61.164 55.000 0.00 0.00 0.00 5.34
3535 4066 4.115199 AGGCCGAGATGGGTTGCC 62.115 66.667 0.00 0.00 42.48 4.52
3538 4069 2.409870 GCCGAGATGGGTTGCCTTG 61.410 63.158 0.00 0.00 38.63 3.61
3545 6583 1.259840 ATGGGTTGCCTTGGATGCAC 61.260 55.000 0.00 0.00 38.72 4.57
3548 6586 0.319813 GGTTGCCTTGGATGCACAAC 60.320 55.000 9.74 9.74 38.72 3.32
3554 6592 2.295909 GCCTTGGATGCACAACTGTTTA 59.704 45.455 0.00 0.00 0.00 2.01
3592 6630 0.249868 TCGGCTGGTTTGTCAGTCAG 60.250 55.000 0.00 0.00 39.17 3.51
3619 6657 2.009051 CGCATTTGTGATGGTGAGCTA 58.991 47.619 0.00 0.00 0.00 3.32
3628 8665 0.031716 ATGGTGAGCTAGAGCCTGGA 60.032 55.000 0.00 0.00 43.38 3.86
3629 8666 0.685785 TGGTGAGCTAGAGCCTGGAG 60.686 60.000 0.00 0.00 43.38 3.86
3630 8667 0.396417 GGTGAGCTAGAGCCTGGAGA 60.396 60.000 0.00 0.00 43.38 3.71
3649 8718 2.432628 CTGGCTGGACGAACCGAC 60.433 66.667 0.00 0.00 42.61 4.79
3656 8725 2.733593 GACGAACCGACGCTGCTT 60.734 61.111 0.00 0.00 36.70 3.91
3700 8769 5.725362 GCAATAATAGCCTCGAGGAATACT 58.275 41.667 35.69 23.17 37.39 2.12
3756 8825 8.999431 GTATTTCTTCTTGAACCATCACACTTA 58.001 33.333 0.00 0.00 34.61 2.24
3759 8828 5.991606 TCTTCTTGAACCATCACACTTACAG 59.008 40.000 0.00 0.00 34.61 2.74
3771 8840 2.092914 ACACTTACAGGCTAGGGCATTC 60.093 50.000 0.00 0.00 40.87 2.67
3782 8851 3.810896 GGCATTCCCAACGCGACC 61.811 66.667 15.93 0.00 0.00 4.79
3783 8852 2.746277 GCATTCCCAACGCGACCT 60.746 61.111 15.93 0.00 0.00 3.85
3784 8853 2.332654 GCATTCCCAACGCGACCTT 61.333 57.895 15.93 0.00 0.00 3.50
3785 8854 1.794222 CATTCCCAACGCGACCTTC 59.206 57.895 15.93 0.00 0.00 3.46
3786 8855 0.953471 CATTCCCAACGCGACCTTCA 60.953 55.000 15.93 0.00 0.00 3.02
3787 8856 0.250553 ATTCCCAACGCGACCTTCAA 60.251 50.000 15.93 0.00 0.00 2.69
3788 8857 0.882927 TTCCCAACGCGACCTTCAAG 60.883 55.000 15.93 0.00 0.00 3.02
3789 8858 2.325082 CCCAACGCGACCTTCAAGG 61.325 63.158 15.93 0.22 42.49 3.61
3790 8859 2.556287 CAACGCGACCTTCAAGGC 59.444 61.111 15.93 0.00 39.63 4.35
3793 8862 3.479269 CGCGACCTTCAAGGCGTC 61.479 66.667 17.86 11.20 43.36 5.19
3794 8863 3.119096 GCGACCTTCAAGGCGTCC 61.119 66.667 17.86 3.19 39.63 4.79
3795 8864 2.809601 CGACCTTCAAGGCGTCCG 60.810 66.667 2.20 0.00 39.63 4.79
3816 8885 1.001974 CAAACATGAGGACCGAGGTGA 59.998 52.381 0.00 0.00 0.00 4.02
3822 8891 0.609681 GAGGACCGAGGTGAGTCTGT 60.610 60.000 0.00 0.00 33.39 3.41
3832 8901 1.897137 TGAGTCTGTGGACGCGTCT 60.897 57.895 35.50 16.71 46.29 4.18
3839 8908 2.108157 TGGACGCGTCTGCTTGTT 59.892 55.556 35.50 0.00 39.65 2.83
3910 8979 3.508762 GGATCGTCGTCACATACTTGTT 58.491 45.455 0.00 0.00 32.34 2.83
3919 8988 2.158534 TCACATACTTGTTTGGCACCCT 60.159 45.455 0.00 0.00 32.34 4.34
3941 9010 2.041755 GGTCCCACCTCAAAATCCTCTT 59.958 50.000 0.00 0.00 34.73 2.85
3952 9021 2.420058 AATCCTCTTCGCCCGAAAAT 57.580 45.000 4.58 0.00 33.34 1.82
3987 9056 4.150897 AGCGGTCACCACACATTTATAT 57.849 40.909 0.00 0.00 0.00 0.86
4023 9092 2.260434 GCGGACGTAGCTCCACAA 59.740 61.111 8.09 0.00 0.00 3.33
4031 9100 0.453390 GTAGCTCCACAAGGCATTGC 59.547 55.000 11.69 0.00 40.27 3.56
4035 9104 0.963962 CTCCACAAGGCATTGCTGTT 59.036 50.000 11.69 0.00 40.27 3.16
4047 9116 3.441572 GCATTGCTGTTGGTTAGAGTGAT 59.558 43.478 0.16 0.00 0.00 3.06
4050 9119 2.224499 TGCTGTTGGTTAGAGTGATGCA 60.224 45.455 0.00 0.00 0.00 3.96
4058 9127 1.262417 TAGAGTGATGCAACCGGACA 58.738 50.000 9.46 3.23 0.00 4.02
4065 9134 4.280019 GCAACCGGACAAGGGGGT 62.280 66.667 9.46 0.00 34.99 4.95
4067 9136 3.576259 AACCGGACAAGGGGGTGG 61.576 66.667 9.46 0.00 33.47 4.61
4086 9155 4.117372 GTCGCTTCAACGCCGACG 62.117 66.667 0.00 0.00 41.32 5.12
4141 9210 0.321653 GATTGAAGTGAGGTGCCCGT 60.322 55.000 0.00 0.00 0.00 5.28
4181 9264 0.748729 TCGTCCACACCACAAAACCC 60.749 55.000 0.00 0.00 0.00 4.11
4204 9287 0.108424 CTGCTCCTCTTTGTCTCCGG 60.108 60.000 0.00 0.00 0.00 5.14
4205 9288 0.832135 TGCTCCTCTTTGTCTCCGGT 60.832 55.000 0.00 0.00 0.00 5.28
4207 9290 0.969894 CTCCTCTTTGTCTCCGGTGT 59.030 55.000 0.00 0.00 0.00 4.16
4221 9304 4.675404 GTGTTCACCACCTCTCCG 57.325 61.111 0.00 0.00 38.18 4.63
4222 9305 1.668151 GTGTTCACCACCTCTCCGC 60.668 63.158 0.00 0.00 38.18 5.54
4223 9306 1.837051 TGTTCACCACCTCTCCGCT 60.837 57.895 0.00 0.00 0.00 5.52
4224 9307 1.079750 GTTCACCACCTCTCCGCTC 60.080 63.158 0.00 0.00 0.00 5.03
4225 9308 2.283529 TTCACCACCTCTCCGCTCC 61.284 63.158 0.00 0.00 0.00 4.70
4226 9309 2.681778 CACCACCTCTCCGCTCCT 60.682 66.667 0.00 0.00 0.00 3.69
4227 9310 2.363147 ACCACCTCTCCGCTCCTC 60.363 66.667 0.00 0.00 0.00 3.71
4244 9327 1.283029 CCTCTCCATCTTTGCTTCCCA 59.717 52.381 0.00 0.00 0.00 4.37
4249 9332 4.018506 TCTCCATCTTTGCTTCCCACATAA 60.019 41.667 0.00 0.00 0.00 1.90
4286 9371 0.871722 CCGATGTTGCCAAAGTCGAA 59.128 50.000 12.58 0.00 34.46 3.71
4293 9378 2.612212 GTTGCCAAAGTCGAAGTTCTCA 59.388 45.455 0.56 0.00 0.00 3.27
4299 9384 2.839486 AGTCGAAGTTCTCAATGCCA 57.161 45.000 0.56 0.00 0.00 4.92
4300 9385 3.126001 AGTCGAAGTTCTCAATGCCAA 57.874 42.857 0.56 0.00 0.00 4.52
4303 9388 3.189287 GTCGAAGTTCTCAATGCCAACAT 59.811 43.478 0.56 0.00 38.49 2.71
4325 9410 2.786495 GCGGCTTCGGATCTCCTCA 61.786 63.158 0.00 0.00 0.00 3.86
4326 9411 2.045280 CGGCTTCGGATCTCCTCAT 58.955 57.895 0.00 0.00 0.00 2.90
4376 9461 1.806461 TATCTGCGGCCATCGACCTC 61.806 60.000 2.24 0.00 42.43 3.85
4428 9513 3.795688 ATCATATTGTCCTCCGGCAAT 57.204 42.857 9.54 9.54 38.63 3.56
4443 9528 3.334691 CGGCAATGAGGAGTAACAGAAA 58.665 45.455 0.00 0.00 0.00 2.52
4445 9530 3.125316 GGCAATGAGGAGTAACAGAAACG 59.875 47.826 0.00 0.00 0.00 3.60
4448 9540 1.336517 TGAGGAGTAACAGAAACGCCG 60.337 52.381 0.00 0.00 41.23 6.46
4465 9557 2.359850 GCACGGAGGTGGCAATCA 60.360 61.111 0.00 0.00 44.54 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.303634 ACCAGACACGATACAAATTACAATC 57.696 36.000 0.00 0.00 0.00 2.67
3 4 7.499321 AAAACCAGACACGATACAAATTACA 57.501 32.000 0.00 0.00 0.00 2.41
117 132 1.741770 CCCGCTCGCTTTTGCTACT 60.742 57.895 0.00 0.00 44.80 2.57
118 133 2.750888 CCCCGCTCGCTTTTGCTAC 61.751 63.158 0.00 0.00 44.80 3.58
119 134 2.435938 CCCCGCTCGCTTTTGCTA 60.436 61.111 0.00 0.00 44.80 3.49
120 135 4.329545 TCCCCGCTCGCTTTTGCT 62.330 61.111 0.00 0.00 44.80 3.91
121 136 3.804193 CTCCCCGCTCGCTTTTGC 61.804 66.667 0.00 0.00 43.23 3.68
122 137 3.127533 CCTCCCCGCTCGCTTTTG 61.128 66.667 0.00 0.00 0.00 2.44
123 138 4.410400 CCCTCCCCGCTCGCTTTT 62.410 66.667 0.00 0.00 0.00 2.27
314 344 9.042450 TCAGTCCTAGGTCAGATAATTTGTTTA 57.958 33.333 9.08 0.00 0.00 2.01
315 345 7.918076 TCAGTCCTAGGTCAGATAATTTGTTT 58.082 34.615 9.08 0.00 0.00 2.83
318 355 9.703892 CTAATCAGTCCTAGGTCAGATAATTTG 57.296 37.037 12.95 0.00 0.00 2.32
330 372 3.563223 TCGTTCCCTAATCAGTCCTAGG 58.437 50.000 0.82 0.82 35.39 3.02
331 373 4.208746 ACTCGTTCCCTAATCAGTCCTAG 58.791 47.826 0.00 0.00 0.00 3.02
332 374 4.246712 ACTCGTTCCCTAATCAGTCCTA 57.753 45.455 0.00 0.00 0.00 2.94
333 375 3.103080 ACTCGTTCCCTAATCAGTCCT 57.897 47.619 0.00 0.00 0.00 3.85
334 376 3.952967 ACTACTCGTTCCCTAATCAGTCC 59.047 47.826 0.00 0.00 0.00 3.85
349 391 2.860735 GTGATGCCTTGCTTACTACTCG 59.139 50.000 0.00 0.00 0.00 4.18
408 453 2.162408 GGGTGATGTCTTGCTTAGTTGC 59.838 50.000 0.00 0.00 0.00 4.17
409 454 3.189287 GTGGGTGATGTCTTGCTTAGTTG 59.811 47.826 0.00 0.00 0.00 3.16
410 455 3.412386 GTGGGTGATGTCTTGCTTAGTT 58.588 45.455 0.00 0.00 0.00 2.24
411 456 2.290323 GGTGGGTGATGTCTTGCTTAGT 60.290 50.000 0.00 0.00 0.00 2.24
412 457 2.359900 GGTGGGTGATGTCTTGCTTAG 58.640 52.381 0.00 0.00 0.00 2.18
413 458 1.004277 GGGTGGGTGATGTCTTGCTTA 59.996 52.381 0.00 0.00 0.00 3.09
414 459 0.251341 GGGTGGGTGATGTCTTGCTT 60.251 55.000 0.00 0.00 0.00 3.91
415 460 1.380302 GGGTGGGTGATGTCTTGCT 59.620 57.895 0.00 0.00 0.00 3.91
421 466 3.567579 CTTGCCGGGTGGGTGATGT 62.568 63.158 2.18 0.00 38.44 3.06
497 544 0.678950 CGGCAAAAGGTCCAACCAAT 59.321 50.000 0.00 0.00 41.95 3.16
515 562 2.222931 TGGCGTCGATTATTTTTCAGCG 60.223 45.455 0.00 0.00 0.00 5.18
520 567 4.457949 ACCTTCTTGGCGTCGATTATTTTT 59.542 37.500 0.00 0.00 40.22 1.94
569 620 6.127814 GCAGGTCTCTTGATTGATGATTTTGA 60.128 38.462 0.00 0.00 0.00 2.69
585 665 3.648545 AGAGTTTACTTTGGCAGGTCTCT 59.351 43.478 0.00 3.46 0.00 3.10
591 671 5.335191 GGTGATTCAGAGTTTACTTTGGCAG 60.335 44.000 1.18 0.00 0.00 4.85
613 693 4.694233 CTCACCTGCTGCTGCGGT 62.694 66.667 21.31 20.81 43.76 5.68
615 695 2.814341 CTCTCACCTGCTGCTGCG 60.814 66.667 11.21 5.84 43.34 5.18
619 699 0.389687 GTCTCACTCTCACCTGCTGC 60.390 60.000 0.00 0.00 0.00 5.25
620 700 0.109365 CGTCTCACTCTCACCTGCTG 60.109 60.000 0.00 0.00 0.00 4.41
621 701 0.538516 ACGTCTCACTCTCACCTGCT 60.539 55.000 0.00 0.00 0.00 4.24
622 702 0.387878 CACGTCTCACTCTCACCTGC 60.388 60.000 0.00 0.00 0.00 4.85
623 703 0.242286 CCACGTCTCACTCTCACCTG 59.758 60.000 0.00 0.00 0.00 4.00
624 704 0.110678 TCCACGTCTCACTCTCACCT 59.889 55.000 0.00 0.00 0.00 4.00
625 705 0.241481 GTCCACGTCTCACTCTCACC 59.759 60.000 0.00 0.00 0.00 4.02
626 706 0.952280 TGTCCACGTCTCACTCTCAC 59.048 55.000 0.00 0.00 0.00 3.51
627 707 1.911057 ATGTCCACGTCTCACTCTCA 58.089 50.000 0.00 0.00 0.00 3.27
628 708 2.097791 GGTATGTCCACGTCTCACTCTC 59.902 54.545 0.00 0.00 35.97 3.20
629 709 2.093106 GGTATGTCCACGTCTCACTCT 58.907 52.381 0.00 0.00 35.97 3.24
630 710 1.816835 TGGTATGTCCACGTCTCACTC 59.183 52.381 0.00 0.00 41.93 3.51
631 711 1.919240 TGGTATGTCCACGTCTCACT 58.081 50.000 0.00 0.00 41.93 3.41
638 718 2.883574 ACGTACATTGGTATGTCCACG 58.116 47.619 10.39 10.39 44.46 4.94
649 729 3.266636 TGGCTGGTGAATACGTACATTG 58.733 45.455 0.00 0.00 0.00 2.82
652 732 2.300723 ACTTGGCTGGTGAATACGTACA 59.699 45.455 0.00 0.00 0.00 2.90
653 733 2.968675 ACTTGGCTGGTGAATACGTAC 58.031 47.619 0.00 0.00 0.00 3.67
655 735 2.151202 CAACTTGGCTGGTGAATACGT 58.849 47.619 0.00 0.00 0.00 3.57
656 736 1.468520 CCAACTTGGCTGGTGAATACG 59.531 52.381 0.00 0.00 0.00 3.06
683 763 0.855349 CTGATATTCCACGCAGTCGC 59.145 55.000 0.00 0.00 41.61 5.19
699 781 1.968493 GCCTATTCGTATGGACCCTGA 59.032 52.381 0.00 0.00 0.00 3.86
700 782 1.971357 AGCCTATTCGTATGGACCCTG 59.029 52.381 0.00 0.00 0.00 4.45
732 814 2.492088 TGGAAGTAGATCGTGGTCACAG 59.508 50.000 1.90 0.00 0.00 3.66
770 852 6.054295 CAGAGGAGAATATCAAAAGGGTCAG 58.946 44.000 0.00 0.00 0.00 3.51
772 854 4.819088 GCAGAGGAGAATATCAAAAGGGTC 59.181 45.833 0.00 0.00 0.00 4.46
805 887 1.796459 CTGACGGAAAAGTTACACGGG 59.204 52.381 0.00 0.00 0.00 5.28
808 890 3.553105 ACGAACTGACGGAAAAGTTACAC 59.447 43.478 0.00 0.00 36.77 2.90
819 901 0.859232 CTGGTCAAACGAACTGACGG 59.141 55.000 0.00 0.00 43.45 4.79
915 1005 0.932211 TGGGGAGTAGGGTAGGAGTC 59.068 60.000 0.00 0.00 0.00 3.36
916 1006 1.400941 TTGGGGAGTAGGGTAGGAGT 58.599 55.000 0.00 0.00 0.00 3.85
917 1007 2.504585 GTTTTGGGGAGTAGGGTAGGAG 59.495 54.545 0.00 0.00 0.00 3.69
918 1008 2.157973 TGTTTTGGGGAGTAGGGTAGGA 60.158 50.000 0.00 0.00 0.00 2.94
928 1018 3.503748 GTGTGATCTTCTGTTTTGGGGAG 59.496 47.826 0.00 0.00 0.00 4.30
940 1030 3.069289 TGTGATGTGCTGTGTGATCTTC 58.931 45.455 0.00 0.00 0.00 2.87
945 1035 1.541015 GGACTGTGATGTGCTGTGTGA 60.541 52.381 0.00 0.00 0.00 3.58
1014 1456 5.393027 CGAGGAAGAAAAGAGAGGAGAAGAG 60.393 48.000 0.00 0.00 0.00 2.85
1022 1464 2.615869 CAGGCGAGGAAGAAAAGAGAG 58.384 52.381 0.00 0.00 0.00 3.20
1331 1787 0.530870 GCTTGTATGGCGGAGGAGAC 60.531 60.000 0.00 0.00 0.00 3.36
1369 1834 2.435410 CCGTACGGCAAGGGGAAC 60.435 66.667 23.44 0.00 0.00 3.62
1394 1859 3.698463 CACACGCCGTTCGGTGTC 61.698 66.667 24.34 2.74 45.99 3.67
1468 1933 2.736978 CAGTAGTGCTCGATGATGTCC 58.263 52.381 0.00 0.00 0.00 4.02
1570 2043 0.247814 ATCTCACGCCGTAACGTACG 60.248 55.000 15.01 15.01 46.34 3.67
1571 2044 1.842546 GAATCTCACGCCGTAACGTAC 59.157 52.381 0.00 0.00 46.34 3.67
1572 2045 1.739466 AGAATCTCACGCCGTAACGTA 59.261 47.619 0.00 0.00 46.34 3.57
1575 2048 5.063060 ACAAATTAGAATCTCACGCCGTAAC 59.937 40.000 0.00 0.00 0.00 2.50
1613 2096 2.806856 CGCCGCACTCTCTGAATGC 61.807 63.158 0.00 0.00 35.96 3.56
1774 2257 0.528924 CTACCGTGGGATTGACGACA 59.471 55.000 0.00 0.00 39.21 4.35
1857 2343 4.394712 CAGCTCCGGTCCACCACC 62.395 72.222 0.00 0.00 42.69 4.61
1858 2344 4.394712 CCAGCTCCGGTCCACCAC 62.395 72.222 0.00 0.00 35.14 4.16
1861 2347 2.198304 AAATCCCAGCTCCGGTCCAC 62.198 60.000 0.00 0.00 0.00 4.02
1862 2348 0.619255 TAAATCCCAGCTCCGGTCCA 60.619 55.000 0.00 0.00 0.00 4.02
1863 2349 0.544697 TTAAATCCCAGCTCCGGTCC 59.455 55.000 0.00 0.00 0.00 4.46
2019 2505 1.588082 GCTGCAACCAACCTGATGG 59.412 57.895 0.00 0.00 46.38 3.51
2049 2535 5.771469 TCACAAAATTCGCATGAACAAGAT 58.229 33.333 0.00 0.00 36.81 2.40
2075 2561 6.572119 GCCGACTGAATCATGAGAGAATATCT 60.572 42.308 0.09 0.00 42.61 1.98
2076 2562 5.576384 GCCGACTGAATCATGAGAGAATATC 59.424 44.000 0.09 0.00 0.00 1.63
2078 2564 4.342092 TGCCGACTGAATCATGAGAGAATA 59.658 41.667 0.09 0.00 0.00 1.75
2079 2565 3.133542 TGCCGACTGAATCATGAGAGAAT 59.866 43.478 0.09 0.00 0.00 2.40
2080 2566 2.497273 TGCCGACTGAATCATGAGAGAA 59.503 45.455 0.09 0.00 0.00 2.87
2081 2567 2.102578 TGCCGACTGAATCATGAGAGA 58.897 47.619 0.09 0.00 0.00 3.10
2082 2568 2.591571 TGCCGACTGAATCATGAGAG 57.408 50.000 0.09 0.00 0.00 3.20
2091 2577 3.402110 CCATAGCATTATGCCGACTGAA 58.598 45.455 14.10 0.00 46.52 3.02
2114 2600 5.314718 TCTGCATCCCAGATCACATAAAT 57.685 39.130 0.00 0.00 45.44 1.40
2115 2601 4.776435 TCTGCATCCCAGATCACATAAA 57.224 40.909 0.00 0.00 45.44 1.40
2125 2611 3.616956 TCTGTTTACTCTGCATCCCAG 57.383 47.619 0.00 0.00 43.17 4.45
2146 2632 1.963515 GCACCTTCTTGGGTTGTTCAT 59.036 47.619 0.00 0.00 41.11 2.57
2176 2662 4.697756 CAGGTTTCTCGGCCGGCA 62.698 66.667 30.85 9.40 0.00 5.69
2183 2669 0.784778 GCTGTTCGACAGGTTTCTCG 59.215 55.000 14.19 0.00 46.01 4.04
2190 2676 0.034059 ACCTCAAGCTGTTCGACAGG 59.966 55.000 14.19 3.36 46.01 4.00
2212 2698 0.602060 GACCTCGGAAGTTTCGGTCT 59.398 55.000 3.17 0.00 40.67 3.85
2235 2721 1.135402 CCGATGACATGACACTGACGA 60.135 52.381 0.00 0.00 0.00 4.20
2296 2782 3.495193 CTGGCACACATTGAATTTCTCG 58.505 45.455 0.00 0.00 0.00 4.04
2319 2805 4.527583 GCCTCTGCCTCCTCTGCG 62.528 72.222 0.00 0.00 0.00 5.18
2341 2827 0.832626 ACCGGCTCATGTCATCATCA 59.167 50.000 0.00 0.00 31.15 3.07
2348 2834 1.810030 GGTTCGACCGGCTCATGTC 60.810 63.158 0.00 0.00 0.00 3.06
2374 2860 1.959508 GCCTTCTCCTCTGCTCTCTGA 60.960 57.143 0.00 0.00 0.00 3.27
2668 3154 1.732308 GTCCGACCATACCGAGGAC 59.268 63.158 0.00 0.00 43.55 3.85
2800 3286 4.722700 CTGTTGTGGGGAGGCCGG 62.723 72.222 0.00 0.00 0.00 6.13
2810 3296 0.951040 GAGGCCGTTCTCCTGTTGTG 60.951 60.000 0.00 0.00 33.24 3.33
2972 3485 4.840005 GGCTCTGTACTGGCCGGC 62.840 72.222 21.18 21.18 36.37 6.13
3033 3546 3.170810 GAGCTCTCGTACGCCTCGG 62.171 68.421 11.24 0.00 0.00 4.63
3260 3773 1.865865 ACTGCTGTACCAAACTGACG 58.134 50.000 0.00 0.00 0.00 4.35
3261 3774 3.724374 TGTACTGCTGTACCAAACTGAC 58.276 45.455 25.51 6.09 46.19 3.51
3373 3904 1.026718 CCCACGTCTGATTTCCCAGC 61.027 60.000 0.00 0.00 34.28 4.85
3374 3905 0.392998 CCCCACGTCTGATTTCCCAG 60.393 60.000 0.00 0.00 35.55 4.45
3422 3953 4.647564 ATGAGTCAATGACCCTCACTTT 57.352 40.909 10.12 0.00 38.00 2.66
3458 3989 5.486526 ACACACAACAAAACAATGGACAAT 58.513 33.333 0.00 0.00 0.00 2.71
3476 4007 1.507141 CTCCTCCCGTTGCAACACAC 61.507 60.000 28.01 3.05 0.00 3.82
3480 4011 1.029681 AAAACTCCTCCCGTTGCAAC 58.970 50.000 19.89 19.89 0.00 4.17
3481 4012 1.028905 CAAAACTCCTCCCGTTGCAA 58.971 50.000 0.00 0.00 0.00 4.08
3487 4018 2.325082 CCACGCAAAACTCCTCCCG 61.325 63.158 0.00 0.00 0.00 5.14
3500 4031 2.052237 CAAGAACACACGCCACGC 60.052 61.111 0.00 0.00 0.00 5.34
3501 4032 1.564622 CTCAAGAACACACGCCACG 59.435 57.895 0.00 0.00 0.00 4.94
3502 4033 1.941812 CCTCAAGAACACACGCCAC 59.058 57.895 0.00 0.00 0.00 5.01
3503 4034 1.891919 GCCTCAAGAACACACGCCA 60.892 57.895 0.00 0.00 0.00 5.69
3504 4035 2.617274 GGCCTCAAGAACACACGCC 61.617 63.158 0.00 0.00 0.00 5.68
3535 4066 5.125100 ACATAAACAGTTGTGCATCCAAG 57.875 39.130 0.00 0.00 29.32 3.61
3538 4069 3.674753 GCAACATAAACAGTTGTGCATCC 59.325 43.478 7.74 0.00 46.09 3.51
3545 6583 3.061271 GTGCGTTGCAACATAAACAGTTG 60.061 43.478 28.01 9.57 46.86 3.16
3548 6586 2.467305 GTGTGCGTTGCAACATAAACAG 59.533 45.455 28.01 11.68 41.47 3.16
3554 6592 0.455410 AGTTGTGTGCGTTGCAACAT 59.545 45.000 28.01 0.60 43.31 2.71
3592 6630 1.621107 CATCACAAATGCGTGCTTCC 58.379 50.000 0.00 0.00 36.80 3.46
3619 6657 3.397906 GCCAGTTCTCCAGGCTCT 58.602 61.111 0.00 0.00 44.92 4.09
3628 8665 1.371558 GGTTCGTCCAGCCAGTTCT 59.628 57.895 0.00 0.00 35.97 3.01
3629 8666 2.027625 CGGTTCGTCCAGCCAGTTC 61.028 63.158 1.14 0.00 35.57 3.01
3630 8667 2.030562 CGGTTCGTCCAGCCAGTT 59.969 61.111 1.14 0.00 35.57 3.16
3639 8676 2.733593 AAGCAGCGTCGGTTCGTC 60.734 61.111 0.00 0.00 0.00 4.20
3649 8718 1.153901 CCAGGCAAATCAAGCAGCG 60.154 57.895 0.00 0.00 0.00 5.18
3656 8725 2.827322 CCTCAAATCACCAGGCAAATCA 59.173 45.455 0.00 0.00 0.00 2.57
3679 8748 7.540474 TGAAGTATTCCTCGAGGCTATTATT 57.460 36.000 27.39 15.73 46.93 1.40
3680 8749 7.726033 ATGAAGTATTCCTCGAGGCTATTAT 57.274 36.000 27.39 15.38 46.93 1.28
3681 8750 7.159322 GATGAAGTATTCCTCGAGGCTATTA 57.841 40.000 27.39 11.85 46.93 0.98
3700 8769 9.500785 TGGATTGTAATATAATTGAGCGATGAA 57.499 29.630 0.00 0.00 0.00 2.57
3719 8788 4.569719 AGAAGAAATACGGGTGGATTGT 57.430 40.909 0.00 0.00 0.00 2.71
3771 8840 2.325082 CCTTGAAGGTCGCGTTGGG 61.325 63.158 5.77 0.00 0.00 4.12
3773 8842 2.556287 GCCTTGAAGGTCGCGTTG 59.444 61.111 13.58 0.00 37.80 4.10
3774 8843 3.041940 CGCCTTGAAGGTCGCGTT 61.042 61.111 13.58 0.00 39.78 4.84
3777 8846 3.119096 GGACGCCTTGAAGGTCGC 61.119 66.667 21.82 15.93 38.06 5.19
3778 8847 2.809601 CGGACGCCTTGAAGGTCG 60.810 66.667 20.79 20.79 37.80 4.79
3779 8848 3.119096 GCGGACGCCTTGAAGGTC 61.119 66.667 13.58 3.10 37.80 3.85
3780 8849 2.951475 TTTGCGGACGCCTTGAAGGT 62.951 55.000 13.58 0.00 37.80 3.50
3781 8850 2.258013 TTTGCGGACGCCTTGAAGG 61.258 57.895 14.61 6.92 41.09 3.46
3782 8851 1.082104 GTTTGCGGACGCCTTGAAG 60.082 57.895 14.61 0.00 41.09 3.02
3783 8852 1.169661 ATGTTTGCGGACGCCTTGAA 61.170 50.000 14.61 0.00 41.09 2.69
3784 8853 1.599518 ATGTTTGCGGACGCCTTGA 60.600 52.632 14.61 0.00 41.09 3.02
3785 8854 1.442520 CATGTTTGCGGACGCCTTG 60.443 57.895 14.61 3.92 41.09 3.61
3786 8855 1.577328 CTCATGTTTGCGGACGCCTT 61.577 55.000 14.61 0.00 41.09 4.35
3787 8856 2.031919 TCATGTTTGCGGACGCCT 59.968 55.556 14.61 0.00 41.09 5.52
3788 8857 2.480555 CTCATGTTTGCGGACGCC 59.519 61.111 14.61 0.00 41.09 5.68
3789 8858 2.032634 TCCTCATGTTTGCGGACGC 61.033 57.895 10.13 10.13 31.75 5.19
3790 8859 1.787847 GTCCTCATGTTTGCGGACG 59.212 57.895 0.00 0.00 45.17 4.79
3792 8861 1.375396 CGGTCCTCATGTTTGCGGA 60.375 57.895 0.00 0.00 34.34 5.54
3793 8862 1.361668 CTCGGTCCTCATGTTTGCGG 61.362 60.000 0.00 0.00 0.00 5.69
3794 8863 1.361668 CCTCGGTCCTCATGTTTGCG 61.362 60.000 0.00 0.00 0.00 4.85
3795 8864 0.321653 ACCTCGGTCCTCATGTTTGC 60.322 55.000 0.00 0.00 0.00 3.68
3816 8885 2.645567 CAGACGCGTCCACAGACT 59.354 61.111 34.08 12.49 41.16 3.24
3822 8891 1.954146 GAACAAGCAGACGCGTCCA 60.954 57.895 34.08 0.00 45.49 4.02
3832 8901 0.886938 TGCGGGATTTCGAACAAGCA 60.887 50.000 0.00 3.06 0.00 3.91
3839 8908 2.036006 CCGGTTTGCGGGATTTCGA 61.036 57.895 0.00 0.00 37.28 3.71
3892 8961 3.054166 CCAAACAAGTATGTGACGACGA 58.946 45.455 0.00 0.00 40.46 4.20
3898 8967 2.158534 AGGGTGCCAAACAAGTATGTGA 60.159 45.455 0.00 0.00 40.46 3.58
3919 8988 1.354368 GAGGATTTTGAGGTGGGACCA 59.646 52.381 0.00 0.00 41.95 4.02
3929 8998 0.611200 TCGGGCGAAGAGGATTTTGA 59.389 50.000 0.00 0.00 0.00 2.69
3941 9010 0.101759 CGGAGAGTATTTTCGGGCGA 59.898 55.000 0.00 0.00 0.00 5.54
3973 9042 4.879545 GGTTGACCGATATAAATGTGTGGT 59.120 41.667 0.00 0.00 0.00 4.16
4014 9083 1.076192 AGCAATGCCTTGTGGAGCT 59.924 52.632 0.00 0.00 34.69 4.09
4023 9092 2.224867 ACTCTAACCAACAGCAATGCCT 60.225 45.455 0.00 0.00 0.00 4.75
4031 9100 3.189287 GGTTGCATCACTCTAACCAACAG 59.811 47.826 0.00 0.00 41.64 3.16
4035 9104 1.338674 CCGGTTGCATCACTCTAACCA 60.339 52.381 0.00 0.00 42.01 3.67
4047 9116 4.278513 CCCCCTTGTCCGGTTGCA 62.279 66.667 0.00 0.00 0.00 4.08
4050 9119 3.576259 CCACCCCCTTGTCCGGTT 61.576 66.667 0.00 0.00 0.00 4.44
4083 9152 3.019545 CTTCTCGATCGCCGCGTC 61.020 66.667 11.09 8.78 38.37 5.19
4086 9155 4.873129 TGGCTTCTCGATCGCCGC 62.873 66.667 11.09 9.50 46.67 6.53
4164 9247 1.029681 GAGGGTTTTGTGGTGTGGAC 58.970 55.000 0.00 0.00 0.00 4.02
4181 9264 2.166254 GGAGACAAAGAGGAGCAGAGAG 59.834 54.545 0.00 0.00 0.00 3.20
4205 9288 1.816863 GAGCGGAGAGGTGGTGAACA 61.817 60.000 0.00 0.00 0.00 3.18
4207 9290 2.283529 GGAGCGGAGAGGTGGTGAA 61.284 63.158 0.00 0.00 0.00 3.18
4218 9301 0.826715 CAAAGATGGAGAGGAGCGGA 59.173 55.000 0.00 0.00 0.00 5.54
4219 9302 0.813210 GCAAAGATGGAGAGGAGCGG 60.813 60.000 0.00 0.00 0.00 5.52
4220 9303 0.177604 AGCAAAGATGGAGAGGAGCG 59.822 55.000 0.00 0.00 0.00 5.03
4221 9304 2.287769 GAAGCAAAGATGGAGAGGAGC 58.712 52.381 0.00 0.00 0.00 4.70
4222 9305 2.421248 GGGAAGCAAAGATGGAGAGGAG 60.421 54.545 0.00 0.00 0.00 3.69
4223 9306 1.561542 GGGAAGCAAAGATGGAGAGGA 59.438 52.381 0.00 0.00 0.00 3.71
4224 9307 1.283029 TGGGAAGCAAAGATGGAGAGG 59.717 52.381 0.00 0.00 0.00 3.69
4225 9308 2.290514 TGTGGGAAGCAAAGATGGAGAG 60.291 50.000 0.00 0.00 0.00 3.20
4226 9309 1.704628 TGTGGGAAGCAAAGATGGAGA 59.295 47.619 0.00 0.00 0.00 3.71
4227 9310 2.205022 TGTGGGAAGCAAAGATGGAG 57.795 50.000 0.00 0.00 0.00 3.86
4244 9327 1.063567 AGCGGAGAGGAGAGGTTATGT 60.064 52.381 0.00 0.00 0.00 2.29
4249 9332 1.379309 GTGAGCGGAGAGGAGAGGT 60.379 63.158 0.00 0.00 0.00 3.85
4286 9371 2.559668 CCACATGTTGGCATTGAGAACT 59.440 45.455 0.00 0.00 39.07 3.01
4299 9384 2.819984 ATCCGAAGCCGCCACATGTT 62.820 55.000 0.00 0.00 0.00 2.71
4300 9385 3.329542 ATCCGAAGCCGCCACATGT 62.330 57.895 0.00 0.00 0.00 3.21
4303 9388 3.371097 GAGATCCGAAGCCGCCACA 62.371 63.158 0.00 0.00 0.00 4.17
4325 9410 0.749454 GCGCCAAGATTCAGACCCAT 60.749 55.000 0.00 0.00 0.00 4.00
4326 9411 1.377202 GCGCCAAGATTCAGACCCA 60.377 57.895 0.00 0.00 0.00 4.51
4354 9439 2.029518 CGATGGCCGCAGATAGCA 59.970 61.111 0.00 0.00 46.13 3.49
4428 9513 1.336517 CGGCGTTTCTGTTACTCCTCA 60.337 52.381 0.00 0.00 0.00 3.86
4448 9540 2.359850 TGATTGCCACCTCCGTGC 60.360 61.111 0.00 0.00 38.79 5.34


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

AutoCloner maintained by Alex Coulton.