Multiple sequence alignment - TraesCS3D01G252300

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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 TraesCS3D01G252300 chr3D 100.000 3712 0 0 1 3712 352950826 352947115 0.000000e+00 6855.0
1 TraesCS3D01G252300 chr3A 92.449 3059 141 24 435 3438 471818882 471815859 0.000000e+00 4287.0
2 TraesCS3D01G252300 chr3B 94.467 2259 74 22 855 3079 452104984 452102743 0.000000e+00 3432.0
3 TraesCS3D01G252300 chr3B 87.794 893 90 7 1 886 452105876 452104996 0.000000e+00 1027.0
4 TraesCS3D01G252300 chr3B 85.957 235 26 5 3113 3343 452102740 452102509 1.030000e-60 244.0
5 TraesCS3D01G252300 chr3B 95.349 43 2 0 3341 3383 452102435 452102393 6.650000e-08 69.4
6 TraesCS3D01G252300 chr7A 77.551 196 35 8 478 671 610371152 610370964 3.920000e-20 110.0
7 TraesCS3D01G252300 chr2A 75.568 176 30 7 511 684 431068877 431068713 1.430000e-09 75.0
8 TraesCS3D01G252300 chr1A 81.609 87 16 0 27 113 558974774 558974688 5.140000e-09 73.1
9 TraesCS3D01G252300 chr6D 97.143 35 1 0 283 317 357776461 357776427 4.000000e-05 60.2


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 TraesCS3D01G252300 chr3D 352947115 352950826 3711 True 6855.0 6855 100.00000 1 3712 1 chr3D.!!$R1 3711
1 TraesCS3D01G252300 chr3A 471815859 471818882 3023 True 4287.0 4287 92.44900 435 3438 1 chr3A.!!$R1 3003
2 TraesCS3D01G252300 chr3B 452102393 452105876 3483 True 1193.1 3432 90.89175 1 3383 4 chr3B.!!$R1 3382

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
707 715 0.098200 CGACTTGACGGACGCATCTA 59.902 55.000 0.0 0.0 0.0 1.98 F
2178 2243 1.003696 AGCTTTTACACTCTGCCCTCC 59.996 52.381 0.0 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2424 2489 0.107017 GCCCAAGCTCAGATGGCTTA 60.107 55.0 7.82 0.0 46.59 3.09 R
3673 3874 0.032615 AACAACCCTGTGGAGGCAAA 60.033 50.0 0.00 0.0 38.17 3.68 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
72 73 1.228644 TCTTCCTCGTCGGAACCCA 60.229 57.895 5.10 0.00 46.80 4.51
79 80 1.447838 CGTCGGAACCCATGACCTG 60.448 63.158 0.00 0.00 0.00 4.00
86 87 0.762418 AACCCATGACCTGAACGTCA 59.238 50.000 0.00 0.00 46.36 4.35
103 104 2.675772 ACCGGTCGAGGTGAGGTC 60.676 66.667 0.00 0.00 44.07 3.85
125 126 3.480225 GATAGACGTGGACGGGCGG 62.480 68.421 0.00 0.00 44.95 6.13
153 154 1.227853 AAGGTGGTTGTGCGACTCC 60.228 57.895 0.00 0.00 0.00 3.85
182 183 2.575993 CTCTGTCGTGAGGGCTGG 59.424 66.667 0.00 0.00 0.00 4.85
184 185 4.007644 CTGTCGTGAGGGCTGGCA 62.008 66.667 2.88 0.00 0.00 4.92
203 204 3.151022 GGCCTCCCTCGTCCTCTG 61.151 72.222 0.00 0.00 0.00 3.35
214 215 4.074526 TCCTCTGCCTCGCACTGC 62.075 66.667 0.00 0.00 33.79 4.40
236 237 1.302511 ACGCCTCACATCCACAACC 60.303 57.895 0.00 0.00 0.00 3.77
241 242 1.478471 CCTCACATCCACAACCCAACA 60.478 52.381 0.00 0.00 0.00 3.33
253 254 0.836400 ACCCAACACCTCGACTCCAT 60.836 55.000 0.00 0.00 0.00 3.41
255 256 1.137086 CCCAACACCTCGACTCCATAG 59.863 57.143 0.00 0.00 0.00 2.23
259 260 1.076923 ACCTCGACTCCATAGCGGT 60.077 57.895 0.00 0.00 35.57 5.68
276 277 3.379445 TCGGGTCGTGAGGGAAGC 61.379 66.667 0.00 0.00 0.00 3.86
280 281 2.047179 GTCGTGAGGGAAGCCACC 60.047 66.667 0.00 0.00 0.00 4.61
357 358 3.360340 GCACCAGGCAGCAGTCAC 61.360 66.667 0.00 0.00 43.97 3.67
396 397 4.803426 CACGTGCCTCGAGCCTCC 62.803 72.222 6.99 0.00 42.71 4.30
416 417 2.591429 CGCCGGCATATCCAAGCA 60.591 61.111 28.98 0.00 34.34 3.91
426 427 3.797865 GCATATCCAAGCACCATTTGAGC 60.798 47.826 0.00 0.00 0.00 4.26
501 508 3.884774 ACGCAAGGGACAAGGCCA 61.885 61.111 5.01 0.00 46.39 5.36
552 560 2.347114 CACTGCCCGACATGTCCA 59.653 61.111 20.03 11.20 0.00 4.02
558 566 1.589630 CCCGACATGTCCAAGACGA 59.410 57.895 20.03 0.00 34.95 4.20
559 567 0.736325 CCCGACATGTCCAAGACGAC 60.736 60.000 20.03 0.00 34.95 4.34
568 576 0.824595 TCCAAGACGACCGGAGTTCA 60.825 55.000 9.46 0.00 0.00 3.18
593 601 0.182299 GAGGAGCTTGGGGATGAAGG 59.818 60.000 0.00 0.00 0.00 3.46
603 611 1.522900 GGGATGAAGGGGATTGGAGA 58.477 55.000 0.00 0.00 0.00 3.71
618 626 2.182827 TGGAGAGGAATGGAGTGACTG 58.817 52.381 0.00 0.00 0.00 3.51
664 672 4.164204 TGGATGAATATATGTGGGGTCGA 58.836 43.478 0.00 0.00 0.00 4.20
672 680 2.032071 GTGGGGTCGAAGTGGGTG 59.968 66.667 0.00 0.00 0.00 4.61
692 700 3.083997 GGTGGGCCTGATCCGACT 61.084 66.667 4.53 0.00 35.50 4.18
707 715 0.098200 CGACTTGACGGACGCATCTA 59.902 55.000 0.00 0.00 0.00 1.98
725 733 5.006165 GCATCTAAGCGTCATTATATCTGCC 59.994 44.000 0.00 0.00 0.00 4.85
726 734 5.073311 TCTAAGCGTCATTATATCTGCCC 57.927 43.478 0.00 0.00 0.00 5.36
729 737 2.371841 AGCGTCATTATATCTGCCCCAA 59.628 45.455 0.00 0.00 0.00 4.12
734 742 6.765989 GCGTCATTATATCTGCCCCAATTATA 59.234 38.462 0.00 0.00 0.00 0.98
735 743 7.282224 GCGTCATTATATCTGCCCCAATTATAA 59.718 37.037 0.00 0.00 0.00 0.98
773 781 1.301716 GGTCAGCTCAGGCGTTTGA 60.302 57.895 0.00 0.00 44.37 2.69
868 876 1.405121 GGCTCGGTTCGGTTGTAGATT 60.405 52.381 0.00 0.00 0.00 2.40
928 979 5.826737 TGTGGTTTTCTTCCGGTTGTAATAA 59.173 36.000 0.00 0.00 0.00 1.40
936 987 1.059549 CCGGTTGTAATAACGCGTGAC 59.940 52.381 14.98 9.77 0.00 3.67
1869 1934 1.526887 GCATCGATCCCTCAACCCA 59.473 57.895 0.00 0.00 0.00 4.51
2148 2213 2.502080 GAGACGCACGAGGTCACG 60.502 66.667 0.00 0.00 36.87 4.35
2178 2243 1.003696 AGCTTTTACACTCTGCCCTCC 59.996 52.381 0.00 0.00 0.00 4.30
2424 2489 4.566545 TTATCGCATTCGCAATGGAATT 57.433 36.364 9.81 0.00 39.31 2.17
2676 2741 5.065474 GGGAATCCACATTGATTTGCAAATG 59.935 40.000 28.67 17.93 40.48 2.32
2677 2742 5.875910 GGAATCCACATTGATTTGCAAATGA 59.124 36.000 28.67 18.51 40.48 2.57
2678 2743 6.036735 GGAATCCACATTGATTTGCAAATGAG 59.963 38.462 28.67 16.43 40.48 2.90
2760 2829 4.826733 TCAGTGTGTATGGTTCAAAGCATT 59.173 37.500 12.18 0.00 44.02 3.56
2822 2892 7.688372 AGACTTGTGTTATGCTAAATCATTCG 58.312 34.615 0.00 0.00 0.00 3.34
2842 2912 2.223377 CGAGTACCCTTGTGTTTTGAGC 59.777 50.000 0.00 0.00 0.00 4.26
2863 2934 5.989477 AGCTTATACTATGTGGCTTTGTCA 58.011 37.500 0.00 0.00 0.00 3.58
2867 2938 7.857885 GCTTATACTATGTGGCTTTGTCAATTC 59.142 37.037 0.00 0.00 0.00 2.17
2897 2968 9.685276 ACATTCACCATTGTTTCATCTAGAATA 57.315 29.630 0.00 0.00 35.83 1.75
2959 3054 6.047870 CCTAATGCTGCTATCATATGAGGTC 58.952 44.000 11.78 3.10 0.00 3.85
2964 3059 4.489810 CTGCTATCATATGAGGTCGGTTC 58.510 47.826 11.78 0.00 0.00 3.62
3000 3110 4.793201 ACTTGGATGTTCTTATTAGGCCC 58.207 43.478 0.00 0.00 0.00 5.80
3004 3114 5.837829 TGGATGTTCTTATTAGGCCCTTTT 58.162 37.500 0.00 0.00 0.00 2.27
3084 3196 1.133945 GGCATCCTCTCCCTCCTTTTC 60.134 57.143 0.00 0.00 0.00 2.29
3090 3202 4.986783 TCCTCTCCCTCCTTTTCTTTTTC 58.013 43.478 0.00 0.00 0.00 2.29
3125 3246 4.852134 AATCACTGCATTTGTGCACTTA 57.148 36.364 19.41 6.15 40.23 2.24
3126 3247 5.395682 AATCACTGCATTTGTGCACTTAT 57.604 34.783 19.41 8.39 40.23 1.73
3139 3260 6.554334 TGTGCACTTATTGTTAACTTCCTC 57.446 37.500 19.41 0.00 0.00 3.71
3143 3264 5.446073 GCACTTATTGTTAACTTCCTCGCTC 60.446 44.000 7.22 0.00 0.00 5.03
3224 3349 3.937814 TGTTAGATGTCAGCCGATGTTT 58.062 40.909 0.00 0.00 0.00 2.83
3225 3350 4.323417 TGTTAGATGTCAGCCGATGTTTT 58.677 39.130 0.00 0.00 0.00 2.43
3270 3395 1.438651 TGTGTGCCTAAACTCATCGC 58.561 50.000 0.00 0.00 0.00 4.58
3278 3403 2.874701 CCTAAACTCATCGCATTCCTGG 59.125 50.000 0.00 0.00 0.00 4.45
3293 3418 1.143684 TCCTGGCCTGGAATGATAAGC 59.856 52.381 27.83 0.00 32.39 3.09
3403 3604 1.692411 ACAGAGTTCCCTTGCAAACC 58.308 50.000 0.00 0.00 0.00 3.27
3410 3611 1.153756 CCCTTGCAAACCCTGGAGT 59.846 57.895 0.00 0.00 0.00 3.85
3439 3640 3.057969 TCTGTGGCCAGACACTAATTG 57.942 47.619 5.11 0.00 42.80 2.32
3440 3641 2.086869 CTGTGGCCAGACACTAATTGG 58.913 52.381 5.11 0.00 41.50 3.16
3443 3644 1.075374 TGGCCAGACACTAATTGGCTT 59.925 47.619 0.00 0.00 43.43 4.35
3444 3645 1.474077 GGCCAGACACTAATTGGCTTG 59.526 52.381 13.71 0.00 43.43 4.01
3445 3646 1.474077 GCCAGACACTAATTGGCTTGG 59.526 52.381 7.44 0.00 43.43 3.61
3446 3647 2.879756 GCCAGACACTAATTGGCTTGGA 60.880 50.000 7.44 0.00 43.43 3.53
3447 3648 2.749621 CCAGACACTAATTGGCTTGGAC 59.250 50.000 0.00 0.00 43.43 4.02
3448 3649 3.560025 CCAGACACTAATTGGCTTGGACT 60.560 47.826 0.00 0.00 43.43 3.85
3449 3650 4.074970 CAGACACTAATTGGCTTGGACTT 58.925 43.478 0.00 0.00 43.43 3.01
3450 3651 4.154918 CAGACACTAATTGGCTTGGACTTC 59.845 45.833 0.00 0.00 43.43 3.01
3451 3652 4.072131 GACACTAATTGGCTTGGACTTCA 58.928 43.478 0.00 0.00 0.00 3.02
3452 3653 4.666512 ACACTAATTGGCTTGGACTTCAT 58.333 39.130 0.00 0.00 0.00 2.57
3453 3654 4.460382 ACACTAATTGGCTTGGACTTCATG 59.540 41.667 0.00 0.00 0.00 3.07
3454 3655 4.019174 ACTAATTGGCTTGGACTTCATGG 58.981 43.478 0.00 0.00 0.00 3.66
3455 3656 2.905415 ATTGGCTTGGACTTCATGGA 57.095 45.000 0.00 0.00 0.00 3.41
3456 3657 2.673775 TTGGCTTGGACTTCATGGAA 57.326 45.000 0.00 0.00 0.00 3.53
3457 3658 1.909700 TGGCTTGGACTTCATGGAAC 58.090 50.000 0.00 0.00 0.00 3.62
3458 3659 1.425066 TGGCTTGGACTTCATGGAACT 59.575 47.619 0.00 0.00 0.00 3.01
3459 3660 2.158475 TGGCTTGGACTTCATGGAACTT 60.158 45.455 0.00 0.00 0.00 2.66
3460 3661 2.489722 GGCTTGGACTTCATGGAACTTC 59.510 50.000 0.00 0.00 0.00 3.01
3461 3662 2.489722 GCTTGGACTTCATGGAACTTCC 59.510 50.000 0.20 0.20 36.96 3.46
3462 3663 3.812167 GCTTGGACTTCATGGAACTTCCT 60.812 47.826 9.31 0.00 37.46 3.36
3463 3664 3.703001 TGGACTTCATGGAACTTCCTC 57.297 47.619 9.31 0.00 37.46 3.71
3464 3665 3.251484 TGGACTTCATGGAACTTCCTCT 58.749 45.455 9.31 0.00 37.46 3.69
3465 3666 3.008375 TGGACTTCATGGAACTTCCTCTG 59.992 47.826 9.31 6.93 37.46 3.35
3466 3667 3.261897 GGACTTCATGGAACTTCCTCTGA 59.738 47.826 9.31 8.96 37.46 3.27
3467 3668 4.080638 GGACTTCATGGAACTTCCTCTGAT 60.081 45.833 9.31 0.00 37.46 2.90
3468 3669 4.841422 ACTTCATGGAACTTCCTCTGATG 58.159 43.478 9.31 14.09 37.46 3.07
3469 3670 4.533707 ACTTCATGGAACTTCCTCTGATGA 59.466 41.667 21.12 14.44 37.46 2.92
3470 3671 4.750021 TCATGGAACTTCCTCTGATGAG 57.250 45.455 9.31 0.00 37.46 2.90
3471 3672 4.099633 TCATGGAACTTCCTCTGATGAGT 58.900 43.478 9.31 0.00 37.46 3.41
3472 3673 3.969287 TGGAACTTCCTCTGATGAGTG 57.031 47.619 9.31 0.00 37.46 3.51
3473 3674 3.510459 TGGAACTTCCTCTGATGAGTGA 58.490 45.455 9.31 0.00 37.46 3.41
3474 3675 3.903714 TGGAACTTCCTCTGATGAGTGAA 59.096 43.478 9.31 0.00 37.46 3.18
3475 3676 4.020751 TGGAACTTCCTCTGATGAGTGAAG 60.021 45.833 9.31 15.74 44.22 3.02
3477 3678 4.533919 ACTTCCTCTGATGAGTGAAGTG 57.466 45.455 19.20 5.98 46.51 3.16
3478 3679 3.260740 CTTCCTCTGATGAGTGAAGTGC 58.739 50.000 12.10 0.00 39.71 4.40
3479 3680 1.552337 TCCTCTGATGAGTGAAGTGCC 59.448 52.381 0.00 0.00 38.61 5.01
3480 3681 1.277273 CCTCTGATGAGTGAAGTGCCA 59.723 52.381 0.00 0.00 38.61 4.92
3481 3682 2.619147 CTCTGATGAGTGAAGTGCCAG 58.381 52.381 0.00 0.00 35.67 4.85
3482 3683 1.973515 TCTGATGAGTGAAGTGCCAGT 59.026 47.619 0.00 0.00 0.00 4.00
3483 3684 2.028658 TCTGATGAGTGAAGTGCCAGTC 60.029 50.000 0.00 0.00 37.10 3.51
3484 3685 1.002430 TGATGAGTGAAGTGCCAGTCC 59.998 52.381 0.00 0.00 36.04 3.85
3485 3686 1.277557 GATGAGTGAAGTGCCAGTCCT 59.722 52.381 0.00 0.00 36.04 3.85
3486 3687 0.394192 TGAGTGAAGTGCCAGTCCTG 59.606 55.000 0.00 0.00 36.04 3.86
3487 3688 0.394565 GAGTGAAGTGCCAGTCCTGT 59.605 55.000 0.00 0.00 31.89 4.00
3488 3689 0.394565 AGTGAAGTGCCAGTCCTGTC 59.605 55.000 0.00 0.00 0.00 3.51
3489 3690 0.946221 GTGAAGTGCCAGTCCTGTCG 60.946 60.000 0.00 0.00 0.00 4.35
3490 3691 1.367840 GAAGTGCCAGTCCTGTCGT 59.632 57.895 0.00 0.00 0.00 4.34
3491 3692 0.946221 GAAGTGCCAGTCCTGTCGTG 60.946 60.000 0.00 0.00 0.00 4.35
3492 3693 2.357517 GTGCCAGTCCTGTCGTGG 60.358 66.667 0.00 0.00 0.00 4.94
3493 3694 2.523168 TGCCAGTCCTGTCGTGGA 60.523 61.111 0.00 0.00 32.60 4.02
3499 3700 4.988716 TCCTGTCGTGGACCGGCT 62.989 66.667 0.00 0.00 43.10 5.52
3500 3701 4.436998 CCTGTCGTGGACCGGCTC 62.437 72.222 0.00 0.00 43.10 4.70
3501 3702 4.436998 CTGTCGTGGACCGGCTCC 62.437 72.222 14.17 14.17 43.10 4.70
3505 3706 4.367023 CGTGGACCGGCTCCGAAA 62.367 66.667 10.28 0.00 43.03 3.46
3506 3707 2.267961 GTGGACCGGCTCCGAAAT 59.732 61.111 10.28 0.00 43.03 2.17
3507 3708 1.814169 GTGGACCGGCTCCGAAATC 60.814 63.158 10.28 4.48 43.03 2.17
3508 3709 1.987855 TGGACCGGCTCCGAAATCT 60.988 57.895 10.28 0.00 43.03 2.40
3509 3710 1.221021 GGACCGGCTCCGAAATCTT 59.779 57.895 10.28 0.00 42.83 2.40
3510 3711 1.090052 GGACCGGCTCCGAAATCTTG 61.090 60.000 10.28 0.00 42.83 3.02
3511 3712 0.108329 GACCGGCTCCGAAATCTTGA 60.108 55.000 10.28 0.00 42.83 3.02
3512 3713 0.108138 ACCGGCTCCGAAATCTTGAG 60.108 55.000 10.28 0.00 42.83 3.02
3513 3714 0.108138 CCGGCTCCGAAATCTTGAGT 60.108 55.000 10.28 0.00 42.83 3.41
3514 3715 1.676014 CCGGCTCCGAAATCTTGAGTT 60.676 52.381 10.28 0.00 42.83 3.01
3515 3716 1.661112 CGGCTCCGAAATCTTGAGTTC 59.339 52.381 1.35 1.27 42.83 3.01
3516 3717 2.010497 GGCTCCGAAATCTTGAGTTCC 58.990 52.381 5.42 0.00 0.00 3.62
3517 3718 2.355209 GGCTCCGAAATCTTGAGTTCCT 60.355 50.000 5.42 0.00 0.00 3.36
3518 3719 2.933260 GCTCCGAAATCTTGAGTTCCTC 59.067 50.000 5.42 0.00 0.00 3.71
3519 3720 3.526534 CTCCGAAATCTTGAGTTCCTCC 58.473 50.000 5.42 0.00 0.00 4.30
3520 3721 2.903784 TCCGAAATCTTGAGTTCCTCCA 59.096 45.455 5.42 0.00 0.00 3.86
3521 3722 3.519510 TCCGAAATCTTGAGTTCCTCCAT 59.480 43.478 5.42 0.00 0.00 3.41
3522 3723 3.624861 CCGAAATCTTGAGTTCCTCCATG 59.375 47.826 5.42 0.00 0.00 3.66
3523 3724 3.064545 CGAAATCTTGAGTTCCTCCATGC 59.935 47.826 5.42 0.00 0.00 4.06
3524 3725 4.268359 GAAATCTTGAGTTCCTCCATGCT 58.732 43.478 0.00 0.00 0.00 3.79
3525 3726 4.313020 AATCTTGAGTTCCTCCATGCTT 57.687 40.909 0.00 0.00 0.00 3.91
3526 3727 3.340814 TCTTGAGTTCCTCCATGCTTC 57.659 47.619 0.00 0.00 0.00 3.86
3527 3728 2.909006 TCTTGAGTTCCTCCATGCTTCT 59.091 45.455 0.00 0.00 0.00 2.85
3528 3729 3.328931 TCTTGAGTTCCTCCATGCTTCTT 59.671 43.478 0.00 0.00 0.00 2.52
3529 3730 3.340814 TGAGTTCCTCCATGCTTCTTC 57.659 47.619 0.00 0.00 0.00 2.87
3530 3731 2.909006 TGAGTTCCTCCATGCTTCTTCT 59.091 45.455 0.00 0.00 0.00 2.85
3531 3732 3.328931 TGAGTTCCTCCATGCTTCTTCTT 59.671 43.478 0.00 0.00 0.00 2.52
3532 3733 4.202503 TGAGTTCCTCCATGCTTCTTCTTT 60.203 41.667 0.00 0.00 0.00 2.52
3533 3734 4.734266 AGTTCCTCCATGCTTCTTCTTTT 58.266 39.130 0.00 0.00 0.00 2.27
3534 3735 5.880901 AGTTCCTCCATGCTTCTTCTTTTA 58.119 37.500 0.00 0.00 0.00 1.52
3535 3736 6.488715 AGTTCCTCCATGCTTCTTCTTTTAT 58.511 36.000 0.00 0.00 0.00 1.40
3536 3737 6.950619 AGTTCCTCCATGCTTCTTCTTTTATT 59.049 34.615 0.00 0.00 0.00 1.40
3537 3738 8.109634 AGTTCCTCCATGCTTCTTCTTTTATTA 58.890 33.333 0.00 0.00 0.00 0.98
3538 3739 8.907885 GTTCCTCCATGCTTCTTCTTTTATTAT 58.092 33.333 0.00 0.00 0.00 1.28
3539 3740 9.479549 TTCCTCCATGCTTCTTCTTTTATTATT 57.520 29.630 0.00 0.00 0.00 1.40
3565 3766 8.140112 AGTCAATATAGTCTCAAAAGTCCAGT 57.860 34.615 0.00 0.00 0.00 4.00
3566 3767 8.598041 AGTCAATATAGTCTCAAAAGTCCAGTT 58.402 33.333 0.00 0.00 0.00 3.16
3567 3768 8.874816 GTCAATATAGTCTCAAAAGTCCAGTTC 58.125 37.037 0.00 0.00 0.00 3.01
3568 3769 8.041323 TCAATATAGTCTCAAAAGTCCAGTTCC 58.959 37.037 0.00 0.00 0.00 3.62
3569 3770 7.741554 ATATAGTCTCAAAAGTCCAGTTCCT 57.258 36.000 0.00 0.00 0.00 3.36
3570 3771 4.078639 AGTCTCAAAAGTCCAGTTCCTG 57.921 45.455 0.00 0.00 0.00 3.86
3571 3772 3.456277 AGTCTCAAAAGTCCAGTTCCTGT 59.544 43.478 0.00 0.00 0.00 4.00
3572 3773 4.080299 AGTCTCAAAAGTCCAGTTCCTGTT 60.080 41.667 0.00 0.00 0.00 3.16
3573 3774 4.640647 GTCTCAAAAGTCCAGTTCCTGTTT 59.359 41.667 0.00 0.00 0.00 2.83
3574 3775 4.881850 TCTCAAAAGTCCAGTTCCTGTTTC 59.118 41.667 0.00 0.00 0.00 2.78
3575 3776 4.855340 TCAAAAGTCCAGTTCCTGTTTCT 58.145 39.130 0.00 0.00 0.00 2.52
3576 3777 5.261216 TCAAAAGTCCAGTTCCTGTTTCTT 58.739 37.500 0.00 0.00 0.00 2.52
3577 3778 5.125417 TCAAAAGTCCAGTTCCTGTTTCTTG 59.875 40.000 0.00 0.00 0.00 3.02
3578 3779 3.214696 AGTCCAGTTCCTGTTTCTTGG 57.785 47.619 0.00 0.00 0.00 3.61
3579 3780 2.777692 AGTCCAGTTCCTGTTTCTTGGA 59.222 45.455 0.00 0.00 0.00 3.53
3580 3781 3.395941 AGTCCAGTTCCTGTTTCTTGGAT 59.604 43.478 0.00 0.00 31.76 3.41
3581 3782 3.753797 GTCCAGTTCCTGTTTCTTGGATC 59.246 47.826 0.00 0.00 31.76 3.36
3582 3783 3.394274 TCCAGTTCCTGTTTCTTGGATCA 59.606 43.478 0.00 0.00 31.76 2.92
3583 3784 4.141274 TCCAGTTCCTGTTTCTTGGATCAA 60.141 41.667 0.00 0.00 31.76 2.57
3584 3785 4.022849 CCAGTTCCTGTTTCTTGGATCAAC 60.023 45.833 0.00 0.00 31.76 3.18
3585 3786 3.815401 AGTTCCTGTTTCTTGGATCAACG 59.185 43.478 0.00 0.00 31.76 4.10
3586 3787 2.778299 TCCTGTTTCTTGGATCAACGG 58.222 47.619 0.00 0.00 0.00 4.44
3587 3788 2.370519 TCCTGTTTCTTGGATCAACGGA 59.629 45.455 0.00 0.00 0.00 4.69
3588 3789 3.146066 CCTGTTTCTTGGATCAACGGAA 58.854 45.455 0.00 0.00 0.00 4.30
3589 3790 3.058224 CCTGTTTCTTGGATCAACGGAAC 60.058 47.826 0.00 0.00 0.00 3.62
3590 3791 3.815401 CTGTTTCTTGGATCAACGGAACT 59.185 43.478 0.00 0.00 0.00 3.01
3591 3792 3.813166 TGTTTCTTGGATCAACGGAACTC 59.187 43.478 0.00 0.00 0.00 3.01
3592 3793 3.762407 TTCTTGGATCAACGGAACTCA 57.238 42.857 0.00 0.00 0.00 3.41
3593 3794 3.981071 TCTTGGATCAACGGAACTCAT 57.019 42.857 0.00 0.00 0.00 2.90
3594 3795 3.861840 TCTTGGATCAACGGAACTCATC 58.138 45.455 0.00 0.00 0.00 2.92
3595 3796 2.691409 TGGATCAACGGAACTCATCC 57.309 50.000 0.00 0.00 45.57 3.51
3615 3816 5.587388 TCCAAAAAGCTGGATGAATGATC 57.413 39.130 0.00 0.00 40.71 2.92
3616 3817 5.018149 TCCAAAAAGCTGGATGAATGATCA 58.982 37.500 0.00 0.00 40.71 2.92
3617 3818 5.126545 TCCAAAAAGCTGGATGAATGATCAG 59.873 40.000 0.09 0.00 40.71 2.90
3618 3819 5.126545 CCAAAAAGCTGGATGAATGATCAGA 59.873 40.000 0.09 0.00 39.39 3.27
3619 3820 5.831702 AAAAGCTGGATGAATGATCAGAC 57.168 39.130 0.09 0.00 39.39 3.51
3620 3821 3.109044 AGCTGGATGAATGATCAGACG 57.891 47.619 0.09 0.00 39.39 4.18
3621 3822 2.141517 GCTGGATGAATGATCAGACGG 58.858 52.381 0.09 0.00 39.39 4.79
3622 3823 2.224137 GCTGGATGAATGATCAGACGGA 60.224 50.000 0.09 0.00 39.39 4.69
3623 3824 3.556633 GCTGGATGAATGATCAGACGGAT 60.557 47.826 0.09 0.00 39.39 4.18
3624 3825 4.639334 CTGGATGAATGATCAGACGGATT 58.361 43.478 0.09 0.00 39.39 3.01
3625 3826 5.039920 TGGATGAATGATCAGACGGATTT 57.960 39.130 0.09 0.00 39.39 2.17
3626 3827 4.818005 TGGATGAATGATCAGACGGATTTG 59.182 41.667 0.09 0.00 39.39 2.32
3627 3828 4.214971 GGATGAATGATCAGACGGATTTGG 59.785 45.833 0.09 0.00 39.39 3.28
3628 3829 4.220693 TGAATGATCAGACGGATTTGGT 57.779 40.909 0.09 0.00 36.00 3.67
3629 3830 4.588899 TGAATGATCAGACGGATTTGGTT 58.411 39.130 0.09 0.00 36.00 3.67
3630 3831 5.009631 TGAATGATCAGACGGATTTGGTTT 58.990 37.500 0.09 0.00 36.00 3.27
3631 3832 5.123820 TGAATGATCAGACGGATTTGGTTTC 59.876 40.000 0.09 0.00 36.00 2.78
3632 3833 3.343617 TGATCAGACGGATTTGGTTTCC 58.656 45.455 0.00 0.00 36.00 3.13
3633 3834 2.940994 TCAGACGGATTTGGTTTCCA 57.059 45.000 0.00 0.00 32.45 3.53
3634 3835 3.216187 TCAGACGGATTTGGTTTCCAA 57.784 42.857 0.00 0.00 42.29 3.53
3647 3848 5.200368 TGGTTTCCAAATCTTCTTTCAGC 57.800 39.130 0.00 0.00 0.00 4.26
3648 3849 4.039124 TGGTTTCCAAATCTTCTTTCAGCC 59.961 41.667 0.00 0.00 0.00 4.85
3649 3850 4.229876 GTTTCCAAATCTTCTTTCAGCCG 58.770 43.478 0.00 0.00 0.00 5.52
3650 3851 2.436417 TCCAAATCTTCTTTCAGCCGG 58.564 47.619 0.00 0.00 0.00 6.13
3651 3852 1.135286 CCAAATCTTCTTTCAGCCGGC 60.135 52.381 21.89 21.89 0.00 6.13
3652 3853 1.541147 CAAATCTTCTTTCAGCCGGCA 59.459 47.619 31.54 5.56 0.00 5.69
3653 3854 1.909700 AATCTTCTTTCAGCCGGCAA 58.090 45.000 31.54 12.95 0.00 4.52
3654 3855 1.457346 ATCTTCTTTCAGCCGGCAAG 58.543 50.000 31.54 23.19 0.00 4.01
3655 3856 1.211190 CTTCTTTCAGCCGGCAAGC 59.789 57.895 31.54 0.00 0.00 4.01
3656 3857 1.228245 TTCTTTCAGCCGGCAAGCT 60.228 52.632 31.54 4.11 46.45 3.74
3657 3858 1.237285 TTCTTTCAGCCGGCAAGCTC 61.237 55.000 31.54 0.00 42.61 4.09
3658 3859 1.673665 CTTTCAGCCGGCAAGCTCT 60.674 57.895 31.54 2.66 42.61 4.09
3659 3860 1.228245 TTTCAGCCGGCAAGCTCTT 60.228 52.632 31.54 1.71 42.61 2.85
3660 3861 1.518056 TTTCAGCCGGCAAGCTCTTG 61.518 55.000 31.54 16.59 42.61 3.02
3661 3862 3.437795 CAGCCGGCAAGCTCTTGG 61.438 66.667 31.54 1.87 42.61 3.61
3662 3863 3.958860 AGCCGGCAAGCTCTTGGT 61.959 61.111 31.54 0.00 39.48 3.67
3663 3864 2.985847 GCCGGCAAGCTCTTGGTT 60.986 61.111 24.80 0.00 40.74 3.67
3664 3865 2.982744 GCCGGCAAGCTCTTGGTTC 61.983 63.158 24.80 0.00 40.74 3.62
3665 3866 1.302832 CCGGCAAGCTCTTGGTTCT 60.303 57.895 11.15 0.00 40.74 3.01
3666 3867 0.890996 CCGGCAAGCTCTTGGTTCTT 60.891 55.000 11.15 0.00 40.74 2.52
3667 3868 0.519077 CGGCAAGCTCTTGGTTCTTC 59.481 55.000 11.15 0.00 40.74 2.87
3668 3869 1.609208 GGCAAGCTCTTGGTTCTTCA 58.391 50.000 11.15 0.00 40.74 3.02
3669 3870 1.956477 GGCAAGCTCTTGGTTCTTCAA 59.044 47.619 11.15 0.00 40.74 2.69
3670 3871 2.362077 GGCAAGCTCTTGGTTCTTCAAA 59.638 45.455 11.15 0.00 40.74 2.69
3671 3872 3.006217 GGCAAGCTCTTGGTTCTTCAAAT 59.994 43.478 11.15 0.00 40.74 2.32
3672 3873 4.218417 GGCAAGCTCTTGGTTCTTCAAATA 59.782 41.667 11.15 0.00 40.74 1.40
3673 3874 5.105595 GGCAAGCTCTTGGTTCTTCAAATAT 60.106 40.000 11.15 0.00 40.74 1.28
3674 3875 6.393171 GCAAGCTCTTGGTTCTTCAAATATT 58.607 36.000 11.15 0.00 40.74 1.28
3675 3876 6.870439 GCAAGCTCTTGGTTCTTCAAATATTT 59.130 34.615 11.15 0.00 40.74 1.40
3676 3877 7.148689 GCAAGCTCTTGGTTCTTCAAATATTTG 60.149 37.037 20.13 20.13 40.74 2.32
3677 3878 6.393171 AGCTCTTGGTTCTTCAAATATTTGC 58.607 36.000 21.15 8.42 38.05 3.68
3678 3879 5.578336 GCTCTTGGTTCTTCAAATATTTGCC 59.422 40.000 21.15 16.31 38.05 4.52
3679 3880 6.573094 GCTCTTGGTTCTTCAAATATTTGCCT 60.573 38.462 21.15 0.00 38.05 4.75
3680 3881 6.924111 TCTTGGTTCTTCAAATATTTGCCTC 58.076 36.000 21.15 10.37 38.05 4.70
3681 3882 5.659440 TGGTTCTTCAAATATTTGCCTCC 57.341 39.130 21.15 17.17 38.05 4.30
3682 3883 5.083122 TGGTTCTTCAAATATTTGCCTCCA 58.917 37.500 21.15 18.97 38.05 3.86
3683 3884 5.047377 TGGTTCTTCAAATATTTGCCTCCAC 60.047 40.000 21.15 13.50 38.05 4.02
3684 3885 5.047377 GGTTCTTCAAATATTTGCCTCCACA 60.047 40.000 21.15 1.77 38.05 4.17
3685 3886 5.902613 TCTTCAAATATTTGCCTCCACAG 57.097 39.130 21.15 9.24 38.05 3.66
3686 3887 4.706476 TCTTCAAATATTTGCCTCCACAGG 59.294 41.667 21.15 5.21 43.82 4.00
3687 3888 3.364549 TCAAATATTTGCCTCCACAGGG 58.635 45.455 21.15 0.00 40.75 4.45
3688 3889 3.099141 CAAATATTTGCCTCCACAGGGT 58.901 45.455 14.96 0.00 40.75 4.34
3689 3890 3.473113 AATATTTGCCTCCACAGGGTT 57.527 42.857 0.00 0.00 40.75 4.11
3690 3891 2.214376 TATTTGCCTCCACAGGGTTG 57.786 50.000 0.00 0.00 40.75 3.77
3691 3892 0.188342 ATTTGCCTCCACAGGGTTGT 59.812 50.000 0.00 0.00 40.75 3.32
3692 3893 0.032615 TTTGCCTCCACAGGGTTGTT 60.033 50.000 0.00 0.00 40.75 2.83
3693 3894 0.754957 TTGCCTCCACAGGGTTGTTG 60.755 55.000 0.00 0.00 40.75 3.33
3694 3895 1.903404 GCCTCCACAGGGTTGTTGG 60.903 63.158 0.00 0.00 40.75 3.77
3695 3896 1.903404 CCTCCACAGGGTTGTTGGC 60.903 63.158 0.00 0.00 35.89 4.52
3696 3897 1.152777 CTCCACAGGGTTGTTGGCA 60.153 57.895 0.00 0.00 34.62 4.92
3697 3898 0.540365 CTCCACAGGGTTGTTGGCAT 60.540 55.000 0.00 0.00 34.62 4.40
3698 3899 0.827089 TCCACAGGGTTGTTGGCATG 60.827 55.000 0.00 0.00 34.62 4.06
3699 3900 1.005867 CACAGGGTTGTTGGCATGC 60.006 57.895 9.90 9.90 34.62 4.06
3700 3901 1.457267 ACAGGGTTGTTGGCATGCA 60.457 52.632 21.36 2.54 32.28 3.96
3701 3902 0.832983 ACAGGGTTGTTGGCATGCAT 60.833 50.000 21.36 0.00 32.28 3.96
3702 3903 0.322322 CAGGGTTGTTGGCATGCATT 59.678 50.000 21.36 0.00 0.00 3.56
3703 3904 0.609662 AGGGTTGTTGGCATGCATTC 59.390 50.000 21.36 9.05 0.00 2.67
3704 3905 0.391528 GGGTTGTTGGCATGCATTCC 60.392 55.000 21.36 8.62 0.00 3.01
3705 3906 0.391528 GGTTGTTGGCATGCATTCCC 60.392 55.000 21.36 9.39 0.00 3.97
3706 3907 0.609662 GTTGTTGGCATGCATTCCCT 59.390 50.000 21.36 0.00 0.00 4.20
3707 3908 1.002315 GTTGTTGGCATGCATTCCCTT 59.998 47.619 21.36 0.00 0.00 3.95
3708 3909 1.350071 TGTTGGCATGCATTCCCTTT 58.650 45.000 21.36 0.00 0.00 3.11
3709 3910 1.275856 TGTTGGCATGCATTCCCTTTC 59.724 47.619 21.36 0.00 0.00 2.62
3710 3911 1.551883 GTTGGCATGCATTCCCTTTCT 59.448 47.619 21.36 0.00 0.00 2.52
3711 3912 1.477553 TGGCATGCATTCCCTTTCTC 58.522 50.000 21.36 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 2.555547 GGGCATGTAAGATGGCGGC 61.556 63.158 0.00 0.00 44.39 6.53
35 36 0.466922 AGCAGGGCATGTAAGATGGC 60.467 55.000 0.00 2.04 42.96 4.40
86 87 1.845627 TAGACCTCACCTCGACCGGT 61.846 60.000 6.92 6.92 37.93 5.28
103 104 1.068472 GCCCGTCCACGTCTATCATAG 60.068 57.143 0.00 0.00 37.74 2.23
125 126 0.967380 CAACCACCTTGGATGAGGCC 60.967 60.000 0.00 0.00 42.23 5.19
127 128 1.538047 CACAACCACCTTGGATGAGG 58.462 55.000 9.27 0.00 42.23 3.86
182 183 4.554036 GGACGAGGGAGGCCATGC 62.554 72.222 5.01 0.00 0.00 4.06
184 185 2.444895 GAGGACGAGGGAGGCCAT 60.445 66.667 5.01 0.00 0.00 4.40
214 215 4.758251 TGGATGTGAGGCGTGCCG 62.758 66.667 5.02 0.00 41.95 5.69
219 220 2.040544 GGGTTGTGGATGTGAGGCG 61.041 63.158 0.00 0.00 0.00 5.52
225 226 0.555769 AGGTGTTGGGTTGTGGATGT 59.444 50.000 0.00 0.00 0.00 3.06
227 228 0.250727 CGAGGTGTTGGGTTGTGGAT 60.251 55.000 0.00 0.00 0.00 3.41
236 237 1.471676 GCTATGGAGTCGAGGTGTTGG 60.472 57.143 0.00 0.00 0.00 3.77
241 242 1.076923 ACCGCTATGGAGTCGAGGT 60.077 57.895 0.00 0.00 42.00 3.85
253 254 3.129502 CTCACGACCCGACCGCTA 61.130 66.667 0.00 0.00 0.00 4.26
259 260 3.379445 GCTTCCCTCACGACCCGA 61.379 66.667 0.00 0.00 0.00 5.14
276 277 0.108138 GAGTCGGAGGTCAATGGTGG 60.108 60.000 0.00 0.00 0.00 4.61
308 309 0.320946 AATGGTACGGTGTTCCCACG 60.321 55.000 0.00 0.00 42.80 4.94
321 322 1.301623 CGCAACCCCTCCAATGGTA 59.698 57.895 0.00 0.00 33.52 3.25
324 325 3.451894 GCCGCAACCCCTCCAATG 61.452 66.667 0.00 0.00 0.00 2.82
375 376 2.355837 GCTCGAGGCACGTGAACA 60.356 61.111 22.23 0.00 43.13 3.18
376 377 3.112709 GGCTCGAGGCACGTGAAC 61.113 66.667 31.94 11.38 44.01 3.18
396 397 2.591429 TTGGATATGCCGGCGCTG 60.591 61.111 23.90 9.96 40.66 5.18
401 402 0.538057 ATGGTGCTTGGATATGCCGG 60.538 55.000 0.00 0.00 40.66 6.13
406 407 2.620115 CGCTCAAATGGTGCTTGGATAT 59.380 45.455 0.00 0.00 33.89 1.63
407 408 2.016318 CGCTCAAATGGTGCTTGGATA 58.984 47.619 0.00 0.00 33.89 2.59
416 417 2.046314 CCCGACCGCTCAAATGGT 60.046 61.111 0.00 0.00 42.42 3.55
475 476 2.266055 CCCTTGCGTGGAGGAGAC 59.734 66.667 2.93 0.00 36.33 3.36
501 508 1.893801 GATCCCCGATCCGTCAACTAT 59.106 52.381 0.00 0.00 33.37 2.12
552 560 1.664306 GGTGAACTCCGGTCGTCTT 59.336 57.895 0.00 0.00 0.00 3.01
568 576 2.685380 CCCAAGCTCCTCTCCGGT 60.685 66.667 0.00 0.00 0.00 5.28
593 601 2.131023 ACTCCATTCCTCTCCAATCCC 58.869 52.381 0.00 0.00 0.00 3.85
603 611 0.178861 ACCCCAGTCACTCCATTCCT 60.179 55.000 0.00 0.00 0.00 3.36
618 626 1.749258 GCACTCCGGATCAAACCCC 60.749 63.158 3.57 0.00 0.00 4.95
664 672 2.440599 GCCCACCATCACCCACTT 59.559 61.111 0.00 0.00 0.00 3.16
672 680 2.111878 CGGATCAGGCCCACCATC 59.888 66.667 0.00 0.00 39.06 3.51
692 700 3.044809 GCTTAGATGCGTCCGTCAA 57.955 52.632 1.23 0.00 0.00 3.18
707 715 2.371841 TGGGGCAGATATAATGACGCTT 59.628 45.455 10.54 0.00 39.29 4.68
722 730 8.664992 TCTCATATGTAGTTTATAATTGGGGCA 58.335 33.333 1.90 0.00 0.00 5.36
723 731 9.167311 CTCTCATATGTAGTTTATAATTGGGGC 57.833 37.037 1.90 0.00 0.00 5.80
729 737 9.935241 CAGCACCTCTCATATGTAGTTTATAAT 57.065 33.333 1.90 0.00 0.00 1.28
734 742 4.471386 ACCAGCACCTCTCATATGTAGTTT 59.529 41.667 1.90 0.00 0.00 2.66
735 743 4.033709 ACCAGCACCTCTCATATGTAGTT 58.966 43.478 1.90 0.00 0.00 2.24
739 747 2.433604 CTGACCAGCACCTCTCATATGT 59.566 50.000 1.90 0.00 0.00 2.29
849 857 1.925185 GAATCTACAACCGAACCGAGC 59.075 52.381 0.00 0.00 0.00 5.03
850 858 3.436496 GAGAATCTACAACCGAACCGAG 58.564 50.000 0.00 0.00 0.00 4.63
851 859 3.498927 GAGAATCTACAACCGAACCGA 57.501 47.619 0.00 0.00 0.00 4.69
936 987 6.293462 CCTTTTCTTTAAGGTTTCTCTCCACG 60.293 42.308 0.00 0.00 39.89 4.94
939 990 7.225011 TCTCCTTTTCTTTAAGGTTTCTCTCC 58.775 38.462 0.00 0.00 44.19 3.71
971 1030 8.359642 AGCGTACCAAGGATACGTTTATTTATA 58.640 33.333 16.63 0.00 45.65 0.98
1743 1808 2.039624 ACCTCCCGGATGAGCACT 59.960 61.111 0.73 0.00 0.00 4.40
1869 1934 2.069273 CCAACGTCGATGAGCTTCTTT 58.931 47.619 12.58 0.00 0.00 2.52
2148 2213 4.457257 AGAGTGTAAAAGCTGCAGAAATCC 59.543 41.667 20.43 0.00 0.00 3.01
2178 2243 1.236616 TGGCATTGTTCAGCACGGAG 61.237 55.000 0.00 0.00 0.00 4.63
2424 2489 0.107017 GCCCAAGCTCAGATGGCTTA 60.107 55.000 7.82 0.00 46.59 3.09
2760 2829 6.007076 TGGTAAACTGAGTGCCATCATAAAA 58.993 36.000 0.00 0.00 0.00 1.52
2822 2892 3.477530 AGCTCAAAACACAAGGGTACTC 58.522 45.455 0.00 0.00 0.00 2.59
2842 2912 8.892723 TGAATTGACAAAGCCACATAGTATAAG 58.107 33.333 0.00 0.00 0.00 1.73
2863 2934 7.443477 TGAAACAATGGTGAATGTCATGAATT 58.557 30.769 0.00 0.00 0.00 2.17
2867 2938 6.627243 AGATGAAACAATGGTGAATGTCATG 58.373 36.000 0.00 0.00 0.00 3.07
2897 2968 9.688091 AAAAACAAGTAATACAAATTTTGGGGT 57.312 25.926 13.42 0.94 34.12 4.95
2959 3054 4.952262 AGTCATCAAACATCATGAACCG 57.048 40.909 0.00 0.00 30.76 4.44
2964 3059 6.203808 ACATCCAAGTCATCAAACATCATG 57.796 37.500 0.00 0.00 0.00 3.07
3004 3114 7.492524 TGCACCAAACATTACTGATACAAAAA 58.507 30.769 0.00 0.00 0.00 1.94
3009 3121 6.435430 TGATGCACCAAACATTACTGATAC 57.565 37.500 0.00 0.00 0.00 2.24
3084 3196 4.654091 TTTGAAGACAGGGCAGAAAAAG 57.346 40.909 0.00 0.00 0.00 2.27
3090 3202 2.486982 CAGTGATTTGAAGACAGGGCAG 59.513 50.000 0.00 0.00 0.00 4.85
3125 3246 4.464597 AGAGAGAGCGAGGAAGTTAACAAT 59.535 41.667 8.61 0.00 0.00 2.71
3126 3247 3.827302 AGAGAGAGCGAGGAAGTTAACAA 59.173 43.478 8.61 0.00 0.00 2.83
3139 3260 2.866156 TGTGTTTCAAACAGAGAGAGCG 59.134 45.455 2.26 0.00 43.10 5.03
3224 3349 8.815565 TCTAATTGGGCAACTAAATGATGTAA 57.184 30.769 0.00 0.00 41.93 2.41
3225 3350 8.995027 ATCTAATTGGGCAACTAAATGATGTA 57.005 30.769 0.00 0.00 41.93 2.29
3278 3403 3.128589 TGTTTTCGCTTATCATTCCAGGC 59.871 43.478 0.00 0.00 0.00 4.85
3293 3418 2.607180 CCTTTTTGTTGGGCTGTTTTCG 59.393 45.455 0.00 0.00 0.00 3.46
3321 3446 8.664669 AATGGTAACTTGGATTTGAAACCTAT 57.335 30.769 0.00 0.00 37.61 2.57
3322 3447 7.947890 AGAATGGTAACTTGGATTTGAAACCTA 59.052 33.333 0.00 0.00 37.61 3.08
3324 3449 6.868339 CAGAATGGTAACTTGGATTTGAAACC 59.132 38.462 0.00 0.00 37.61 3.27
3325 3450 7.433680 ACAGAATGGTAACTTGGATTTGAAAC 58.566 34.615 0.00 0.00 43.62 2.78
3426 3627 2.749621 GTCCAAGCCAATTAGTGTCTGG 59.250 50.000 0.00 0.00 0.00 3.86
3428 3629 4.202461 TGAAGTCCAAGCCAATTAGTGTCT 60.202 41.667 0.00 0.00 0.00 3.41
3438 3639 1.425066 AGTTCCATGAAGTCCAAGCCA 59.575 47.619 0.00 0.00 0.00 4.75
3439 3640 2.206576 AGTTCCATGAAGTCCAAGCC 57.793 50.000 0.00 0.00 0.00 4.35
3440 3641 2.489722 GGAAGTTCCATGAAGTCCAAGC 59.510 50.000 17.44 0.00 36.28 4.01
3441 3642 4.006319 GAGGAAGTTCCATGAAGTCCAAG 58.994 47.826 23.87 0.00 39.61 3.61
3442 3643 3.652869 AGAGGAAGTTCCATGAAGTCCAA 59.347 43.478 23.87 0.00 39.61 3.53
3443 3644 3.008375 CAGAGGAAGTTCCATGAAGTCCA 59.992 47.826 23.87 0.00 39.61 4.02
3444 3645 3.261897 TCAGAGGAAGTTCCATGAAGTCC 59.738 47.826 23.87 0.00 39.61 3.85
3445 3646 4.543590 TCAGAGGAAGTTCCATGAAGTC 57.456 45.455 23.87 11.15 39.61 3.01
3446 3647 4.533707 TCATCAGAGGAAGTTCCATGAAGT 59.466 41.667 25.18 13.00 39.61 3.01
3447 3648 5.095145 TCATCAGAGGAAGTTCCATGAAG 57.905 43.478 25.18 21.95 39.61 3.02
3448 3649 4.533707 ACTCATCAGAGGAAGTTCCATGAA 59.466 41.667 25.18 14.10 46.44 2.57
3449 3650 4.081254 CACTCATCAGAGGAAGTTCCATGA 60.081 45.833 24.18 24.18 46.44 3.07
3450 3651 4.081254 TCACTCATCAGAGGAAGTTCCATG 60.081 45.833 23.87 20.04 46.44 3.66
3451 3652 4.099633 TCACTCATCAGAGGAAGTTCCAT 58.900 43.478 23.87 9.19 46.44 3.41
3452 3653 3.510459 TCACTCATCAGAGGAAGTTCCA 58.490 45.455 23.87 3.25 46.44 3.53
3453 3654 4.502962 CTTCACTCATCAGAGGAAGTTCC 58.497 47.826 14.54 14.54 46.44 3.62
3457 3658 3.260740 GCACTTCACTCATCAGAGGAAG 58.739 50.000 15.70 15.70 46.44 3.46
3458 3659 2.027745 GGCACTTCACTCATCAGAGGAA 60.028 50.000 0.00 0.00 46.44 3.36
3459 3660 1.552337 GGCACTTCACTCATCAGAGGA 59.448 52.381 0.00 0.00 46.44 3.71
3460 3661 1.277273 TGGCACTTCACTCATCAGAGG 59.723 52.381 0.00 0.00 46.44 3.69
3462 3663 1.973515 ACTGGCACTTCACTCATCAGA 59.026 47.619 0.00 0.00 0.00 3.27
3463 3664 2.344950 GACTGGCACTTCACTCATCAG 58.655 52.381 0.00 0.00 0.00 2.90
3464 3665 1.002430 GGACTGGCACTTCACTCATCA 59.998 52.381 0.00 0.00 0.00 3.07
3465 3666 1.277557 AGGACTGGCACTTCACTCATC 59.722 52.381 0.00 0.00 0.00 2.92
3466 3667 1.002888 CAGGACTGGCACTTCACTCAT 59.997 52.381 0.00 0.00 0.00 2.90
3467 3668 0.394192 CAGGACTGGCACTTCACTCA 59.606 55.000 0.00 0.00 0.00 3.41
3468 3669 0.394565 ACAGGACTGGCACTTCACTC 59.605 55.000 4.14 0.00 34.19 3.51
3469 3670 0.394565 GACAGGACTGGCACTTCACT 59.605 55.000 0.00 0.00 38.82 3.41
3470 3671 0.946221 CGACAGGACTGGCACTTCAC 60.946 60.000 5.93 0.00 38.95 3.18
3471 3672 1.367471 CGACAGGACTGGCACTTCA 59.633 57.895 5.93 0.00 38.95 3.02
3472 3673 0.946221 CACGACAGGACTGGCACTTC 60.946 60.000 5.93 0.00 38.95 3.01
3473 3674 1.069765 CACGACAGGACTGGCACTT 59.930 57.895 5.93 0.00 38.95 3.16
3474 3675 2.737180 CACGACAGGACTGGCACT 59.263 61.111 5.93 0.00 38.95 4.40
3475 3676 2.357517 CCACGACAGGACTGGCAC 60.358 66.667 5.93 0.00 38.95 5.01
3476 3677 2.523168 TCCACGACAGGACTGGCA 60.523 61.111 5.93 0.00 38.95 4.92
3491 3692 1.090052 CAAGATTTCGGAGCCGGTCC 61.090 60.000 9.29 6.55 42.85 4.46
3492 3693 0.108329 TCAAGATTTCGGAGCCGGTC 60.108 55.000 9.29 5.57 40.25 4.79
3493 3694 0.108138 CTCAAGATTTCGGAGCCGGT 60.108 55.000 9.29 0.00 40.25 5.28
3494 3695 0.108138 ACTCAAGATTTCGGAGCCGG 60.108 55.000 9.29 0.00 40.25 6.13
3495 3696 1.661112 GAACTCAAGATTTCGGAGCCG 59.339 52.381 1.74 1.74 41.35 5.52
3496 3697 2.010497 GGAACTCAAGATTTCGGAGCC 58.990 52.381 0.00 0.00 31.88 4.70
3497 3698 2.979240 AGGAACTCAAGATTTCGGAGC 58.021 47.619 0.00 0.00 31.88 4.70
3512 3713 6.765915 ATAAAAGAAGAAGCATGGAGGAAC 57.234 37.500 0.00 0.00 0.00 3.62
3513 3714 9.479549 AATAATAAAAGAAGAAGCATGGAGGAA 57.520 29.630 0.00 0.00 0.00 3.36
3539 3740 9.256228 ACTGGACTTTTGAGACTATATTGACTA 57.744 33.333 0.00 0.00 0.00 2.59
3540 3741 8.140112 ACTGGACTTTTGAGACTATATTGACT 57.860 34.615 0.00 0.00 0.00 3.41
3541 3742 8.779354 AACTGGACTTTTGAGACTATATTGAC 57.221 34.615 0.00 0.00 0.00 3.18
3542 3743 8.041323 GGAACTGGACTTTTGAGACTATATTGA 58.959 37.037 0.00 0.00 0.00 2.57
3543 3744 8.043710 AGGAACTGGACTTTTGAGACTATATTG 58.956 37.037 0.00 0.00 37.18 1.90
3544 3745 8.152023 AGGAACTGGACTTTTGAGACTATATT 57.848 34.615 0.00 0.00 37.18 1.28
3545 3746 7.741554 AGGAACTGGACTTTTGAGACTATAT 57.258 36.000 0.00 0.00 37.18 0.86
3563 3764 3.815401 CGTTGATCCAAGAAACAGGAACT 59.185 43.478 0.00 0.00 43.88 3.01
3564 3765 3.058224 CCGTTGATCCAAGAAACAGGAAC 60.058 47.826 0.00 0.00 37.48 3.62
3565 3766 3.146066 CCGTTGATCCAAGAAACAGGAA 58.854 45.455 0.00 0.00 37.48 3.36
3566 3767 2.370519 TCCGTTGATCCAAGAAACAGGA 59.629 45.455 0.00 0.00 38.50 3.86
3567 3768 2.778299 TCCGTTGATCCAAGAAACAGG 58.222 47.619 0.00 0.00 0.00 4.00
3568 3769 3.815401 AGTTCCGTTGATCCAAGAAACAG 59.185 43.478 0.00 0.00 0.00 3.16
3569 3770 3.813166 GAGTTCCGTTGATCCAAGAAACA 59.187 43.478 0.00 0.00 0.00 2.83
3570 3771 3.813166 TGAGTTCCGTTGATCCAAGAAAC 59.187 43.478 0.00 0.00 0.00 2.78
3571 3772 4.079980 TGAGTTCCGTTGATCCAAGAAA 57.920 40.909 0.00 0.00 0.00 2.52
3572 3773 3.762407 TGAGTTCCGTTGATCCAAGAA 57.238 42.857 0.00 0.00 0.00 2.52
3573 3774 3.369471 GGATGAGTTCCGTTGATCCAAGA 60.369 47.826 0.00 0.00 33.93 3.02
3574 3775 2.939103 GGATGAGTTCCGTTGATCCAAG 59.061 50.000 0.00 0.00 33.93 3.61
3575 3776 2.985896 GGATGAGTTCCGTTGATCCAA 58.014 47.619 0.00 0.00 33.93 3.53
3576 3777 2.691409 GGATGAGTTCCGTTGATCCA 57.309 50.000 0.00 0.00 33.93 3.41
3585 3786 3.157087 TCCAGCTTTTTGGATGAGTTCC 58.843 45.455 0.00 0.00 42.24 3.62
3594 3795 5.126545 TCTGATCATTCATCCAGCTTTTTGG 59.873 40.000 0.00 0.00 39.70 3.28
3595 3796 6.034591 GTCTGATCATTCATCCAGCTTTTTG 58.965 40.000 0.00 0.00 0.00 2.44
3596 3797 5.163683 CGTCTGATCATTCATCCAGCTTTTT 60.164 40.000 0.00 0.00 0.00 1.94
3597 3798 4.334759 CGTCTGATCATTCATCCAGCTTTT 59.665 41.667 0.00 0.00 0.00 2.27
3598 3799 3.875727 CGTCTGATCATTCATCCAGCTTT 59.124 43.478 0.00 0.00 0.00 3.51
3599 3800 3.464907 CGTCTGATCATTCATCCAGCTT 58.535 45.455 0.00 0.00 0.00 3.74
3600 3801 2.224233 CCGTCTGATCATTCATCCAGCT 60.224 50.000 0.00 0.00 0.00 4.24
3601 3802 2.141517 CCGTCTGATCATTCATCCAGC 58.858 52.381 0.00 0.00 0.00 4.85
3602 3803 3.740631 TCCGTCTGATCATTCATCCAG 57.259 47.619 0.00 0.00 0.00 3.86
3603 3804 4.694760 AATCCGTCTGATCATTCATCCA 57.305 40.909 0.00 0.00 31.61 3.41
3604 3805 4.214971 CCAAATCCGTCTGATCATTCATCC 59.785 45.833 0.00 0.00 31.61 3.51
3605 3806 4.818546 ACCAAATCCGTCTGATCATTCATC 59.181 41.667 0.00 0.00 31.61 2.92
3606 3807 4.785301 ACCAAATCCGTCTGATCATTCAT 58.215 39.130 0.00 0.00 31.61 2.57
3607 3808 4.220693 ACCAAATCCGTCTGATCATTCA 57.779 40.909 0.00 0.00 31.61 2.57
3608 3809 5.449177 GGAAACCAAATCCGTCTGATCATTC 60.449 44.000 0.00 0.00 31.61 2.67
3609 3810 4.399303 GGAAACCAAATCCGTCTGATCATT 59.601 41.667 0.00 0.00 31.61 2.57
3610 3811 3.947834 GGAAACCAAATCCGTCTGATCAT 59.052 43.478 0.00 0.00 31.61 2.45
3611 3812 3.244735 TGGAAACCAAATCCGTCTGATCA 60.245 43.478 0.00 0.00 39.98 2.92
3612 3813 3.343617 TGGAAACCAAATCCGTCTGATC 58.656 45.455 0.00 0.00 39.98 2.92
3613 3814 3.433306 TGGAAACCAAATCCGTCTGAT 57.567 42.857 0.00 0.00 39.98 2.90
3614 3815 2.940994 TGGAAACCAAATCCGTCTGA 57.059 45.000 0.00 0.00 39.98 3.27
3624 3825 5.453198 GGCTGAAAGAAGATTTGGAAACCAA 60.453 40.000 0.00 0.00 37.80 3.67
3625 3826 4.039124 GGCTGAAAGAAGATTTGGAAACCA 59.961 41.667 0.00 0.00 34.07 3.67
3626 3827 4.560128 GGCTGAAAGAAGATTTGGAAACC 58.440 43.478 0.00 0.00 34.07 3.27
3627 3828 4.229876 CGGCTGAAAGAAGATTTGGAAAC 58.770 43.478 0.00 0.00 34.07 2.78
3628 3829 3.255642 CCGGCTGAAAGAAGATTTGGAAA 59.744 43.478 0.00 0.00 34.07 3.13
3629 3830 2.819608 CCGGCTGAAAGAAGATTTGGAA 59.180 45.455 0.00 0.00 34.07 3.53
3630 3831 2.436417 CCGGCTGAAAGAAGATTTGGA 58.564 47.619 0.00 0.00 34.07 3.53
3631 3832 1.135286 GCCGGCTGAAAGAAGATTTGG 60.135 52.381 22.15 0.00 34.07 3.28
3632 3833 1.541147 TGCCGGCTGAAAGAAGATTTG 59.459 47.619 29.70 0.00 34.07 2.32
3633 3834 1.909700 TGCCGGCTGAAAGAAGATTT 58.090 45.000 29.70 0.00 34.07 2.17
3634 3835 1.815003 CTTGCCGGCTGAAAGAAGATT 59.185 47.619 29.70 0.00 34.07 2.40
3635 3836 1.457346 CTTGCCGGCTGAAAGAAGAT 58.543 50.000 29.70 0.00 34.07 2.40
3636 3837 1.237285 GCTTGCCGGCTGAAAGAAGA 61.237 55.000 29.70 0.00 34.07 2.87
3637 3838 1.211190 GCTTGCCGGCTGAAAGAAG 59.789 57.895 29.70 21.68 34.07 2.85
3638 3839 1.228245 AGCTTGCCGGCTGAAAGAA 60.228 52.632 29.70 11.48 41.43 2.52
3639 3840 1.672356 GAGCTTGCCGGCTGAAAGA 60.672 57.895 29.70 1.94 43.20 2.52
3640 3841 1.239968 AAGAGCTTGCCGGCTGAAAG 61.240 55.000 29.70 23.19 43.20 2.62
3641 3842 1.228245 AAGAGCTTGCCGGCTGAAA 60.228 52.632 29.70 13.13 43.20 2.69
3642 3843 1.968017 CAAGAGCTTGCCGGCTGAA 60.968 57.895 29.70 13.95 43.20 3.02
3643 3844 2.359107 CAAGAGCTTGCCGGCTGA 60.359 61.111 29.70 15.51 43.20 4.26
3644 3845 3.437795 CCAAGAGCTTGCCGGCTG 61.438 66.667 29.70 21.00 43.20 4.85
3645 3846 3.497884 AACCAAGAGCTTGCCGGCT 62.498 57.895 29.70 6.86 46.11 5.52
3646 3847 2.982744 GAACCAAGAGCTTGCCGGC 61.983 63.158 22.73 22.73 39.16 6.13
3647 3848 0.890996 AAGAACCAAGAGCTTGCCGG 60.891 55.000 0.00 0.00 39.16 6.13
3648 3849 0.519077 GAAGAACCAAGAGCTTGCCG 59.481 55.000 4.72 0.00 39.16 5.69
3649 3850 1.609208 TGAAGAACCAAGAGCTTGCC 58.391 50.000 4.72 0.00 39.16 4.52
3650 3851 3.715628 TTTGAAGAACCAAGAGCTTGC 57.284 42.857 4.72 0.00 39.16 4.01
3651 3852 7.148689 GCAAATATTTGAAGAACCAAGAGCTTG 60.149 37.037 28.33 3.27 40.55 4.01
3652 3853 6.870439 GCAAATATTTGAAGAACCAAGAGCTT 59.130 34.615 28.33 0.00 40.55 3.74
3653 3854 6.393171 GCAAATATTTGAAGAACCAAGAGCT 58.607 36.000 28.33 0.00 40.55 4.09
3654 3855 5.578336 GGCAAATATTTGAAGAACCAAGAGC 59.422 40.000 28.33 10.32 40.55 4.09
3655 3856 6.928520 AGGCAAATATTTGAAGAACCAAGAG 58.071 36.000 28.33 1.23 40.55 2.85
3656 3857 6.071391 GGAGGCAAATATTTGAAGAACCAAGA 60.071 38.462 28.33 0.00 40.55 3.02
3657 3858 6.101997 GGAGGCAAATATTTGAAGAACCAAG 58.898 40.000 28.33 1.90 40.55 3.61
3658 3859 5.541868 TGGAGGCAAATATTTGAAGAACCAA 59.458 36.000 28.33 9.17 40.55 3.67
3659 3860 5.047377 GTGGAGGCAAATATTTGAAGAACCA 60.047 40.000 28.33 22.78 40.55 3.67
3660 3861 5.047377 TGTGGAGGCAAATATTTGAAGAACC 60.047 40.000 28.33 19.36 40.55 3.62
3661 3862 6.024552 TGTGGAGGCAAATATTTGAAGAAC 57.975 37.500 28.33 18.53 40.55 3.01
3662 3863 5.185635 CCTGTGGAGGCAAATATTTGAAGAA 59.814 40.000 28.33 9.08 40.55 2.52
3663 3864 4.706476 CCTGTGGAGGCAAATATTTGAAGA 59.294 41.667 28.33 6.97 40.55 2.87
3664 3865 4.142093 CCCTGTGGAGGCAAATATTTGAAG 60.142 45.833 28.33 13.58 39.84 3.02
3665 3866 3.768757 CCCTGTGGAGGCAAATATTTGAA 59.231 43.478 28.33 7.83 39.84 2.69
3666 3867 3.245586 ACCCTGTGGAGGCAAATATTTGA 60.246 43.478 28.33 7.33 38.17 2.69
3667 3868 3.099141 ACCCTGTGGAGGCAAATATTTG 58.901 45.455 21.54 21.54 38.17 2.32
3668 3869 3.473113 ACCCTGTGGAGGCAAATATTT 57.527 42.857 0.00 0.00 38.17 1.40
3669 3870 3.099141 CAACCCTGTGGAGGCAAATATT 58.901 45.455 0.00 0.00 38.17 1.28
3670 3871 2.042979 ACAACCCTGTGGAGGCAAATAT 59.957 45.455 0.00 0.00 38.17 1.28
3671 3872 1.427368 ACAACCCTGTGGAGGCAAATA 59.573 47.619 0.00 0.00 38.17 1.40
3672 3873 0.188342 ACAACCCTGTGGAGGCAAAT 59.812 50.000 0.00 0.00 38.17 2.32
3673 3874 0.032615 AACAACCCTGTGGAGGCAAA 60.033 50.000 0.00 0.00 38.17 3.68
3674 3875 0.754957 CAACAACCCTGTGGAGGCAA 60.755 55.000 0.00 0.00 38.17 4.52
3675 3876 1.152777 CAACAACCCTGTGGAGGCA 60.153 57.895 0.00 0.00 38.17 4.75
3676 3877 1.903404 CCAACAACCCTGTGGAGGC 60.903 63.158 0.00 0.00 38.17 4.70
3677 3878 1.903404 GCCAACAACCCTGTGGAGG 60.903 63.158 0.00 0.00 39.42 4.30
3678 3879 0.540365 ATGCCAACAACCCTGTGGAG 60.540 55.000 0.00 0.00 35.37 3.86
3679 3880 0.827089 CATGCCAACAACCCTGTGGA 60.827 55.000 0.00 0.00 35.37 4.02
3680 3881 1.667151 CATGCCAACAACCCTGTGG 59.333 57.895 0.00 0.00 35.37 4.17
3681 3882 1.005867 GCATGCCAACAACCCTGTG 60.006 57.895 6.36 0.00 35.37 3.66
3682 3883 0.832983 ATGCATGCCAACAACCCTGT 60.833 50.000 16.68 0.00 37.39 4.00
3683 3884 0.322322 AATGCATGCCAACAACCCTG 59.678 50.000 16.68 0.00 0.00 4.45
3684 3885 0.609662 GAATGCATGCCAACAACCCT 59.390 50.000 16.68 0.00 0.00 4.34
3685 3886 0.391528 GGAATGCATGCCAACAACCC 60.392 55.000 19.82 3.03 0.00 4.11
3686 3887 0.391528 GGGAATGCATGCCAACAACC 60.392 55.000 25.70 2.65 39.85 3.77
3687 3888 0.609662 AGGGAATGCATGCCAACAAC 59.390 50.000 25.70 7.43 43.29 3.32
3688 3889 1.350071 AAGGGAATGCATGCCAACAA 58.650 45.000 25.70 0.00 43.29 2.83
3689 3890 1.275856 GAAAGGGAATGCATGCCAACA 59.724 47.619 25.70 0.00 43.29 3.33
3690 3891 1.551883 AGAAAGGGAATGCATGCCAAC 59.448 47.619 25.70 8.98 43.29 3.77
3691 3892 1.826720 GAGAAAGGGAATGCATGCCAA 59.173 47.619 25.70 0.00 43.29 4.52
3692 3893 1.477553 GAGAAAGGGAATGCATGCCA 58.522 50.000 25.70 3.52 43.29 4.92


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

AutoCloner maintained by Alex Coulton.