Multiple sequence alignment - TraesCS6D01G249700

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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 TraesCS6D01G249700 chr6D 100.000 3599 0 0 1 3599 353037756 353041354 0.000000e+00 6647
1 TraesCS6D01G249700 chr6A 92.262 3050 94 38 1 2977 489512683 489509703 0.000000e+00 4194
2 TraesCS6D01G249700 chr6A 86.813 455 41 11 3030 3469 489509701 489509251 1.160000e-134 490
3 TraesCS6D01G249700 chr6A 82.836 134 21 1 3468 3599 445574964 445574831 6.310000e-23 119
4 TraesCS6D01G249700 chr6B 95.224 2031 60 18 766 2767 525556855 525554833 0.000000e+00 3179
5 TraesCS6D01G249700 chr6B 87.942 481 33 15 1 477 525557550 525557091 8.790000e-151 544
6 TraesCS6D01G249700 chr6B 86.184 456 43 14 3030 3469 525554697 525554246 3.250000e-130 475
7 TraesCS6D01G249700 chr6B 88.500 200 6 4 555 737 525557049 525556850 3.620000e-55 226
8 TraesCS6D01G249700 chr1D 84.328 134 18 3 3468 3599 479580685 479580553 1.050000e-25 128
9 TraesCS6D01G249700 chr5A 88.235 102 12 0 3479 3580 705490795 705490896 4.880000e-24 122
10 TraesCS6D01G249700 chr2B 85.124 121 16 2 3479 3599 32126714 32126832 4.880000e-24 122
11 TraesCS6D01G249700 chr2B 85.149 101 15 0 3479 3579 161937365 161937465 1.770000e-18 104
12 TraesCS6D01G249700 chr2B 81.203 133 22 3 3469 3599 665834640 665834771 1.770000e-18 104
13 TraesCS6D01G249700 chr7A 84.800 125 13 5 3468 3588 184579169 184579291 1.760000e-23 121
14 TraesCS6D01G249700 chr2A 87.379 103 12 1 3479 3581 20591203 20591102 2.270000e-22 117
15 TraesCS6D01G249700 chr3D 88.372 86 10 0 3484 3569 156890239 156890154 1.770000e-18 104


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 TraesCS6D01G249700 chr6D 353037756 353041354 3598 False 6647 6647 100.0000 1 3599 1 chr6D.!!$F1 3598
1 TraesCS6D01G249700 chr6A 489509251 489512683 3432 True 2342 4194 89.5375 1 3469 2 chr6A.!!$R2 3468
2 TraesCS6D01G249700 chr6B 525554246 525557550 3304 True 1106 3179 89.4625 1 3469 4 chr6B.!!$R1 3468

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
861 906 0.100503 CCCACCGATTTTGGCGATTC 59.899 55.0 0.0 0.0 32.13 2.52 F
1962 2055 0.320421 TAGTGCTTTCGTCCTGGTGC 60.320 55.0 0.0 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 2178 0.322008 CCTTGTCCAGCCTCACCTTC 60.322 60.0 0.0 0.0 0.00 3.46 R
3028 3131 0.034089 GCTGGTTGGAGGTGCCTTAT 60.034 55.0 0.0 0.0 37.63 1.73 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
57 60 9.886132 GGGAAAATGTCTTAGTAAGTTGATCTA 57.114 33.333 9.71 0.00 0.00 1.98
63 66 8.418597 TGTCTTAGTAAGTTGATCTAGTTGGT 57.581 34.615 9.71 0.00 0.00 3.67
183 186 9.692749 TTCTGTATGTTATCGGTCTAATTCATC 57.307 33.333 0.00 0.00 0.00 2.92
190 193 7.546316 TGTTATCGGTCTAATTCATCGTCAAAA 59.454 33.333 0.00 0.00 0.00 2.44
243 247 3.245371 TGGAAAGCAGGAGGATTGAATGT 60.245 43.478 0.00 0.00 0.00 2.71
270 274 6.003950 CAGGGAAAGGAACTGAAAATGTAGA 58.996 40.000 0.00 0.00 40.86 2.59
280 284 9.346725 GGAACTGAAAATGTAGAACATCAAATC 57.653 33.333 0.00 0.00 37.97 2.17
320 324 6.920817 TGTTGTATCTCTGTCAATAACTCGT 58.079 36.000 0.00 0.00 0.00 4.18
363 368 0.674895 GCGGCAGAATTGACTCCACT 60.675 55.000 0.00 0.00 0.00 4.00
364 369 1.813513 CGGCAGAATTGACTCCACTT 58.186 50.000 0.00 0.00 0.00 3.16
451 456 7.775120 AGCAGAGAGATTTTTCAAAGTTCAAA 58.225 30.769 0.00 0.00 0.00 2.69
466 472 0.255890 TCAAAGACCCCCATAGCTGC 59.744 55.000 0.00 0.00 0.00 5.25
485 513 3.321497 TGCGGTGGCATTTGTTTAATTC 58.679 40.909 0.00 0.00 46.21 2.17
488 516 3.584834 GGTGGCATTTGTTTAATTCGCT 58.415 40.909 0.00 0.00 0.00 4.93
492 520 3.584834 GCATTTGTTTAATTCGCTGGGT 58.415 40.909 0.00 0.00 0.00 4.51
499 527 3.926821 TTAATTCGCTGGGTGGTTTTC 57.073 42.857 0.00 0.00 0.00 2.29
501 529 1.247567 ATTCGCTGGGTGGTTTTCAG 58.752 50.000 0.00 0.00 0.00 3.02
691 736 1.830086 ACCTTTTTGTTTGTACGCGC 58.170 45.000 5.73 0.00 0.00 6.86
736 781 2.200170 AAATTTCTCCGCAGCCGCAC 62.200 55.000 0.00 0.00 38.40 5.34
802 847 3.660669 ACTGGATAAAGAGAAACCCCCAA 59.339 43.478 0.00 0.00 0.00 4.12
861 906 0.100503 CCCACCGATTTTGGCGATTC 59.899 55.000 0.00 0.00 32.13 2.52
983 1051 2.289756 GCTCCGAGAAAAACCCTCTTCT 60.290 50.000 0.00 0.00 34.58 2.85
1491 1575 4.150454 CCTCCCTCCCTCCTCGCT 62.150 72.222 0.00 0.00 0.00 4.93
1771 1864 0.593128 GCAGTCGTCTGTTGCCATTT 59.407 50.000 11.28 0.00 43.05 2.32
1962 2055 0.320421 TAGTGCTTTCGTCCTGGTGC 60.320 55.000 0.00 0.00 0.00 5.01
1972 2065 1.134401 CGTCCTGGTGCATTGAGGTAT 60.134 52.381 8.11 0.00 0.00 2.73
1973 2066 2.102420 CGTCCTGGTGCATTGAGGTATA 59.898 50.000 8.11 0.00 0.00 1.47
1974 2067 3.244215 CGTCCTGGTGCATTGAGGTATAT 60.244 47.826 8.11 0.00 0.00 0.86
1975 2068 4.718961 GTCCTGGTGCATTGAGGTATATT 58.281 43.478 8.11 0.00 0.00 1.28
1976 2069 5.510690 CGTCCTGGTGCATTGAGGTATATTA 60.511 44.000 8.11 0.00 0.00 0.98
1977 2070 6.476378 GTCCTGGTGCATTGAGGTATATTAT 58.524 40.000 8.11 0.00 0.00 1.28
2035 2131 6.978343 TGATGTTTTAGGAATCTAACCACG 57.022 37.500 0.00 0.00 35.40 4.94
2038 2134 8.262227 TGATGTTTTAGGAATCTAACCACGTAT 58.738 33.333 0.00 0.00 35.40 3.06
2082 2178 1.519455 GCGTCCTGAGGAATGGTCG 60.519 63.158 0.96 3.02 37.78 4.79
2089 2185 1.550524 CTGAGGAATGGTCGAAGGTGA 59.449 52.381 0.00 0.00 0.00 4.02
2221 2317 2.615447 TCGGTCGTGGTGAGATATACAC 59.385 50.000 4.53 4.53 37.51 2.90
2614 2715 5.836898 ACTGCATGATGGGATGATTGTAATT 59.163 36.000 0.00 0.00 0.00 1.40
2615 2716 6.091718 TGCATGATGGGATGATTGTAATTG 57.908 37.500 0.00 0.00 0.00 2.32
2616 2717 5.011227 TGCATGATGGGATGATTGTAATTGG 59.989 40.000 0.00 0.00 0.00 3.16
2619 2720 4.894705 TGATGGGATGATTGTAATTGGTGG 59.105 41.667 0.00 0.00 0.00 4.61
2632 2733 4.647564 AATTGGTGGAGTCTCATGTTCT 57.352 40.909 1.47 0.00 0.00 3.01
2638 2739 3.131400 GTGGAGTCTCATGTTCTAGTCCC 59.869 52.174 1.47 0.00 31.53 4.46
2703 2805 1.271163 CCTGTTCCGGGCACTTCTAAA 60.271 52.381 0.00 0.00 0.00 1.85
2813 2915 7.797121 ATTTCCTAATTCTTTGGTGAACCAT 57.203 32.000 2.34 0.00 46.97 3.55
2850 2952 8.567948 CAGAGAAACTTTAGCTTTGTTGGATAA 58.432 33.333 0.00 0.00 0.00 1.75
2876 2978 9.804758 AAGATACCTAGTTTTATGAGTTCTTCG 57.195 33.333 0.00 0.00 0.00 3.79
2877 2979 9.186837 AGATACCTAGTTTTATGAGTTCTTCGA 57.813 33.333 0.00 0.00 0.00 3.71
2878 2980 9.235537 GATACCTAGTTTTATGAGTTCTTCGAC 57.764 37.037 0.00 0.00 0.00 4.20
2879 2981 7.229581 ACCTAGTTTTATGAGTTCTTCGACT 57.770 36.000 0.00 0.00 0.00 4.18
2880 2982 7.314393 ACCTAGTTTTATGAGTTCTTCGACTC 58.686 38.462 0.00 0.00 44.97 3.36
2881 2983 6.752815 CCTAGTTTTATGAGTTCTTCGACTCC 59.247 42.308 2.89 0.00 44.29 3.85
2882 2984 6.347859 AGTTTTATGAGTTCTTCGACTCCT 57.652 37.500 2.89 0.00 44.29 3.69
2883 2985 6.760291 AGTTTTATGAGTTCTTCGACTCCTT 58.240 36.000 2.89 0.00 44.29 3.36
2884 2986 6.647067 AGTTTTATGAGTTCTTCGACTCCTTG 59.353 38.462 2.89 0.00 44.29 3.61
2885 2987 5.977489 TTATGAGTTCTTCGACTCCTTGA 57.023 39.130 2.89 0.00 44.29 3.02
2889 2991 4.341235 TGAGTTCTTCGACTCCTTGAGAAA 59.659 41.667 0.00 0.00 44.29 2.52
2985 3088 9.833179 ATCTGATGGTATAAATTTTGGGATCAT 57.167 29.630 0.00 0.00 0.00 2.45
2986 3089 9.081204 TCTGATGGTATAAATTTTGGGATCATG 57.919 33.333 0.00 0.00 0.00 3.07
2987 3090 8.780616 TGATGGTATAAATTTTGGGATCATGT 57.219 30.769 0.00 0.00 0.00 3.21
2988 3091 9.874195 TGATGGTATAAATTTTGGGATCATGTA 57.126 29.630 0.00 0.00 0.00 2.29
2992 3095 9.840427 GGTATAAATTTTGGGATCATGTAATCG 57.160 33.333 0.00 0.00 0.00 3.34
3000 3103 8.492673 TTTGGGATCATGTAATCGAATATAGC 57.507 34.615 0.00 0.00 0.00 2.97
3001 3104 7.181569 TGGGATCATGTAATCGAATATAGCA 57.818 36.000 0.00 0.00 0.00 3.49
3002 3105 7.619965 TGGGATCATGTAATCGAATATAGCAA 58.380 34.615 0.00 0.00 0.00 3.91
3003 3106 8.100164 TGGGATCATGTAATCGAATATAGCAAA 58.900 33.333 0.00 0.00 0.00 3.68
3004 3107 8.391106 GGGATCATGTAATCGAATATAGCAAAC 58.609 37.037 0.00 0.00 0.00 2.93
3005 3108 9.155975 GGATCATGTAATCGAATATAGCAAACT 57.844 33.333 0.00 0.00 0.00 2.66
3006 3109 9.964253 GATCATGTAATCGAATATAGCAAACTG 57.036 33.333 0.00 0.00 0.00 3.16
3007 3110 8.310406 TCATGTAATCGAATATAGCAAACTGG 57.690 34.615 0.00 0.00 0.00 4.00
3008 3111 7.931407 TCATGTAATCGAATATAGCAAACTGGT 59.069 33.333 0.00 0.00 0.00 4.00
3009 3112 9.203421 CATGTAATCGAATATAGCAAACTGGTA 57.797 33.333 0.00 0.00 34.60 3.25
3010 3113 9.772973 ATGTAATCGAATATAGCAAACTGGTAA 57.227 29.630 0.00 0.00 33.73 2.85
3011 3114 9.256477 TGTAATCGAATATAGCAAACTGGTAAG 57.744 33.333 0.00 0.00 33.73 2.34
3012 3115 7.730364 AATCGAATATAGCAAACTGGTAAGG 57.270 36.000 0.00 0.00 33.73 2.69
3013 3116 6.229936 TCGAATATAGCAAACTGGTAAGGT 57.770 37.500 0.00 0.00 33.73 3.50
3014 3117 6.646267 TCGAATATAGCAAACTGGTAAGGTT 58.354 36.000 0.00 0.00 33.73 3.50
3015 3118 7.107542 TCGAATATAGCAAACTGGTAAGGTTT 58.892 34.615 0.00 0.00 37.37 3.27
3023 3126 6.046885 CAAACTGGTAAGGTTTGCAAAATG 57.953 37.500 14.67 1.08 44.11 2.32
3024 3127 5.606348 AACTGGTAAGGTTTGCAAAATGA 57.394 34.783 14.67 0.00 0.00 2.57
3025 3128 5.806654 ACTGGTAAGGTTTGCAAAATGAT 57.193 34.783 14.67 3.46 0.00 2.45
3026 3129 5.783111 ACTGGTAAGGTTTGCAAAATGATC 58.217 37.500 14.67 0.34 0.00 2.92
3027 3130 5.539955 ACTGGTAAGGTTTGCAAAATGATCT 59.460 36.000 14.67 4.15 0.00 2.75
3028 3131 6.719370 ACTGGTAAGGTTTGCAAAATGATCTA 59.281 34.615 14.67 2.56 0.00 1.98
3059 3162 3.820467 CTCCAACCAGCATTGTGTTCTTA 59.180 43.478 0.00 0.00 0.00 2.10
3064 3167 2.553602 CCAGCATTGTGTTCTTAGTGCA 59.446 45.455 0.00 0.00 35.17 4.57
3150 3253 2.719739 AGTTTGATGCACAGGAGGATG 58.280 47.619 0.00 0.00 0.00 3.51
3161 3264 4.395625 CACAGGAGGATGCATATTGTCAT 58.604 43.478 0.00 0.00 0.00 3.06
3212 3336 5.808042 AGCCAAATTATATGCTAGATGCG 57.192 39.130 0.00 0.00 46.63 4.73
3219 3343 0.037882 TATGCTAGATGCGCAGGAGC 60.038 55.000 25.76 25.76 46.63 4.70
3245 3372 3.370840 AAGTTTGATGGCATCCAGCTA 57.629 42.857 23.92 2.54 41.01 3.32
3258 3385 4.158394 GCATCCAGCTATTGACCTTTGAAA 59.842 41.667 0.00 0.00 41.15 2.69
3265 3392 7.315142 CAGCTATTGACCTTTGAAAGCATTAA 58.685 34.615 0.00 0.00 0.00 1.40
3300 3427 6.161855 TCAGCTCCAGAAATGTCGTTATAT 57.838 37.500 0.00 0.00 0.00 0.86
3452 3585 7.759886 TGGTACAATTTTTCATTGTTCGTCAAA 59.240 29.630 5.57 0.00 41.81 2.69
3453 3586 8.265998 GGTACAATTTTTCATTGTTCGTCAAAG 58.734 33.333 5.57 0.00 41.81 2.77
3459 3592 1.545582 CATTGTTCGTCAAAGGGCCAT 59.454 47.619 6.18 0.00 39.62 4.40
3469 3602 2.309755 TCAAAGGGCCATGTGAGAATCT 59.690 45.455 6.07 0.00 34.92 2.40
3470 3603 2.686915 CAAAGGGCCATGTGAGAATCTC 59.313 50.000 0.00 2.75 34.92 2.75
3471 3604 0.467384 AGGGCCATGTGAGAATCTCG 59.533 55.000 6.18 0.00 34.92 4.04
3472 3605 0.465705 GGGCCATGTGAGAATCTCGA 59.534 55.000 4.39 0.00 34.92 4.04
3473 3606 1.134401 GGGCCATGTGAGAATCTCGAA 60.134 52.381 4.39 0.00 34.92 3.71
3474 3607 2.632377 GGCCATGTGAGAATCTCGAAA 58.368 47.619 5.73 0.00 34.92 3.46
3475 3608 3.209410 GGCCATGTGAGAATCTCGAAAT 58.791 45.455 5.73 0.00 34.92 2.17
3476 3609 4.380531 GGCCATGTGAGAATCTCGAAATA 58.619 43.478 5.73 0.00 34.92 1.40
3477 3610 4.450419 GGCCATGTGAGAATCTCGAAATAG 59.550 45.833 5.73 0.00 34.92 1.73
3478 3611 5.053145 GCCATGTGAGAATCTCGAAATAGT 58.947 41.667 5.73 0.00 34.92 2.12
3479 3612 5.525378 GCCATGTGAGAATCTCGAAATAGTT 59.475 40.000 5.73 0.00 34.92 2.24
3480 3613 6.037610 GCCATGTGAGAATCTCGAAATAGTTT 59.962 38.462 5.73 0.00 34.92 2.66
3481 3614 7.625553 CCATGTGAGAATCTCGAAATAGTTTC 58.374 38.462 5.73 0.00 34.92 2.78
3482 3615 7.278646 CCATGTGAGAATCTCGAAATAGTTTCA 59.721 37.037 5.73 0.00 36.18 2.69
3483 3616 7.582435 TGTGAGAATCTCGAAATAGTTTCAC 57.418 36.000 5.73 6.37 36.18 3.18
3484 3617 6.590292 TGTGAGAATCTCGAAATAGTTTCACC 59.410 38.462 5.73 0.00 36.18 4.02
3485 3618 6.036191 GTGAGAATCTCGAAATAGTTTCACCC 59.964 42.308 5.73 0.00 36.18 4.61
3486 3619 5.429130 AGAATCTCGAAATAGTTTCACCCC 58.571 41.667 3.66 0.00 39.63 4.95
3487 3620 3.241067 TCTCGAAATAGTTTCACCCCG 57.759 47.619 3.66 0.00 39.63 5.73
3488 3621 1.664151 CTCGAAATAGTTTCACCCCGC 59.336 52.381 3.66 0.00 39.63 6.13
3489 3622 1.276989 TCGAAATAGTTTCACCCCGCT 59.723 47.619 3.66 0.00 39.63 5.52
3490 3623 2.081462 CGAAATAGTTTCACCCCGCTT 58.919 47.619 3.66 0.00 39.63 4.68
3491 3624 2.486592 CGAAATAGTTTCACCCCGCTTT 59.513 45.455 3.66 0.00 39.63 3.51
3492 3625 3.685756 CGAAATAGTTTCACCCCGCTTTA 59.314 43.478 3.66 0.00 39.63 1.85
3493 3626 4.334481 CGAAATAGTTTCACCCCGCTTTAT 59.666 41.667 3.66 0.00 39.63 1.40
3494 3627 5.524646 CGAAATAGTTTCACCCCGCTTTATA 59.475 40.000 3.66 0.00 39.63 0.98
3495 3628 6.204108 CGAAATAGTTTCACCCCGCTTTATAT 59.796 38.462 3.66 0.00 39.63 0.86
3496 3629 7.385752 CGAAATAGTTTCACCCCGCTTTATATA 59.614 37.037 3.66 0.00 39.63 0.86
3497 3630 9.227777 GAAATAGTTTCACCCCGCTTTATATAT 57.772 33.333 0.00 0.00 39.45 0.86
3514 3647 9.744468 CTTTATATATAAAGCAACCACCAAACC 57.256 33.333 25.10 0.00 41.69 3.27
3515 3648 8.824756 TTATATATAAAGCAACCACCAAACCA 57.175 30.769 2.56 0.00 0.00 3.67
3516 3649 7.726033 ATATATAAAGCAACCACCAAACCAA 57.274 32.000 0.00 0.00 0.00 3.67
3517 3650 2.689553 AAAGCAACCACCAAACCAAG 57.310 45.000 0.00 0.00 0.00 3.61
3518 3651 1.567357 AAGCAACCACCAAACCAAGT 58.433 45.000 0.00 0.00 0.00 3.16
3519 3652 2.445682 AGCAACCACCAAACCAAGTA 57.554 45.000 0.00 0.00 0.00 2.24
3520 3653 2.028876 AGCAACCACCAAACCAAGTAC 58.971 47.619 0.00 0.00 0.00 2.73
3521 3654 1.751924 GCAACCACCAAACCAAGTACA 59.248 47.619 0.00 0.00 0.00 2.90
3522 3655 2.480587 GCAACCACCAAACCAAGTACAC 60.481 50.000 0.00 0.00 0.00 2.90
3523 3656 1.670791 ACCACCAAACCAAGTACACG 58.329 50.000 0.00 0.00 0.00 4.49
3524 3657 0.948678 CCACCAAACCAAGTACACGG 59.051 55.000 0.00 0.00 0.00 4.94
3525 3658 0.309612 CACCAAACCAAGTACACGGC 59.690 55.000 0.00 0.00 0.00 5.68
3526 3659 0.820482 ACCAAACCAAGTACACGGCC 60.820 55.000 0.00 0.00 0.00 6.13
3527 3660 1.572447 CAAACCAAGTACACGGCCG 59.428 57.895 26.86 26.86 0.00 6.13
3528 3661 0.881159 CAAACCAAGTACACGGCCGA 60.881 55.000 35.90 6.51 0.00 5.54
3529 3662 0.179051 AAACCAAGTACACGGCCGAA 60.179 50.000 35.90 14.32 0.00 4.30
3530 3663 0.881600 AACCAAGTACACGGCCGAAC 60.882 55.000 35.90 25.10 0.00 3.95
3531 3664 2.377310 CCAAGTACACGGCCGAACG 61.377 63.158 35.90 21.75 40.31 3.95
3532 3665 1.372004 CAAGTACACGGCCGAACGA 60.372 57.895 35.90 11.21 37.61 3.85
3533 3666 0.734942 CAAGTACACGGCCGAACGAT 60.735 55.000 35.90 16.97 37.61 3.73
3534 3667 0.734942 AAGTACACGGCCGAACGATG 60.735 55.000 35.90 22.07 37.61 3.84
3535 3668 2.507547 TACACGGCCGAACGATGC 60.508 61.111 35.90 0.00 37.61 3.91
3536 3669 3.284133 TACACGGCCGAACGATGCA 62.284 57.895 35.90 6.87 37.61 3.96
3537 3670 2.766875 TACACGGCCGAACGATGCAA 62.767 55.000 35.90 8.23 37.61 4.08
3538 3671 3.118454 ACGGCCGAACGATGCAAG 61.118 61.111 35.90 0.00 37.61 4.01
3539 3672 2.813474 CGGCCGAACGATGCAAGA 60.813 61.111 24.07 0.00 35.47 3.02
3540 3673 2.173669 CGGCCGAACGATGCAAGAT 61.174 57.895 24.07 0.00 35.47 2.40
3541 3674 1.353103 GGCCGAACGATGCAAGATG 59.647 57.895 0.00 0.00 0.00 2.90
3542 3675 1.353103 GCCGAACGATGCAAGATGG 59.647 57.895 0.00 0.00 0.00 3.51
3543 3676 1.369091 GCCGAACGATGCAAGATGGT 61.369 55.000 0.00 0.00 0.00 3.55
3544 3677 0.374758 CCGAACGATGCAAGATGGTG 59.625 55.000 0.00 0.00 0.00 4.17
3545 3678 1.358877 CGAACGATGCAAGATGGTGA 58.641 50.000 0.00 0.00 0.00 4.02
3546 3679 1.325640 CGAACGATGCAAGATGGTGAG 59.674 52.381 0.00 0.00 0.00 3.51
3547 3680 1.667724 GAACGATGCAAGATGGTGAGG 59.332 52.381 0.00 0.00 0.00 3.86
3548 3681 0.615331 ACGATGCAAGATGGTGAGGT 59.385 50.000 0.00 0.00 0.00 3.85
3549 3682 1.831106 ACGATGCAAGATGGTGAGGTA 59.169 47.619 0.00 0.00 0.00 3.08
3550 3683 2.159043 ACGATGCAAGATGGTGAGGTAG 60.159 50.000 0.00 0.00 0.00 3.18
3551 3684 2.216898 GATGCAAGATGGTGAGGTAGC 58.783 52.381 0.00 0.00 0.00 3.58
3552 3685 0.253044 TGCAAGATGGTGAGGTAGCC 59.747 55.000 0.00 0.00 0.00 3.93
3553 3686 0.464554 GCAAGATGGTGAGGTAGCCC 60.465 60.000 0.00 0.00 0.00 5.19
3554 3687 1.207791 CAAGATGGTGAGGTAGCCCT 58.792 55.000 0.00 0.00 46.66 5.19
3564 3697 0.466922 AGGTAGCCCTCATGCAATGC 60.467 55.000 0.00 0.00 46.21 3.56
3565 3698 1.458639 GGTAGCCCTCATGCAATGCC 61.459 60.000 1.53 0.00 46.21 4.40
3566 3699 1.526686 TAGCCCTCATGCAATGCCG 60.527 57.895 1.53 0.00 46.21 5.69
3567 3700 1.981951 TAGCCCTCATGCAATGCCGA 61.982 55.000 1.53 0.00 46.21 5.54
3568 3701 2.198287 GCCCTCATGCAATGCCGAT 61.198 57.895 1.53 0.00 46.21 4.18
3569 3702 0.890542 GCCCTCATGCAATGCCGATA 60.891 55.000 1.53 0.00 46.21 2.92
3570 3703 0.877071 CCCTCATGCAATGCCGATAC 59.123 55.000 1.53 0.00 46.21 2.24
3571 3704 1.544093 CCCTCATGCAATGCCGATACT 60.544 52.381 1.53 0.00 46.21 2.12
3572 3705 2.289631 CCCTCATGCAATGCCGATACTA 60.290 50.000 1.53 0.00 46.21 1.82
3573 3706 2.998670 CCTCATGCAATGCCGATACTAG 59.001 50.000 1.53 0.00 46.21 2.57
3574 3707 2.998670 CTCATGCAATGCCGATACTAGG 59.001 50.000 1.53 0.00 46.21 3.02
3575 3708 2.632512 TCATGCAATGCCGATACTAGGA 59.367 45.455 1.53 0.00 46.21 2.94
3576 3709 3.261643 TCATGCAATGCCGATACTAGGAT 59.738 43.478 1.53 0.00 46.21 3.24
3577 3710 4.466015 TCATGCAATGCCGATACTAGGATA 59.534 41.667 1.53 0.00 46.21 2.59
3578 3711 4.882842 TGCAATGCCGATACTAGGATAA 57.117 40.909 1.53 0.00 0.00 1.75
3579 3712 4.566004 TGCAATGCCGATACTAGGATAAC 58.434 43.478 1.53 0.00 0.00 1.89
3580 3713 3.933332 GCAATGCCGATACTAGGATAACC 59.067 47.826 0.00 0.00 0.00 2.85
3581 3714 4.174009 CAATGCCGATACTAGGATAACCG 58.826 47.826 0.00 0.00 41.83 4.44
3582 3715 2.165167 TGCCGATACTAGGATAACCGG 58.835 52.381 8.83 8.83 41.83 5.28
3583 3716 2.224843 TGCCGATACTAGGATAACCGGA 60.225 50.000 15.90 1.05 41.83 5.14
3584 3717 2.821969 GCCGATACTAGGATAACCGGAA 59.178 50.000 15.90 0.00 41.83 4.30
3585 3718 3.366781 GCCGATACTAGGATAACCGGAAC 60.367 52.174 15.90 0.00 41.83 3.62
3586 3719 3.822735 CCGATACTAGGATAACCGGAACA 59.177 47.826 9.46 0.00 41.83 3.18
3587 3720 4.320788 CCGATACTAGGATAACCGGAACAC 60.321 50.000 9.46 0.00 41.83 3.32
3588 3721 4.612259 CGATACTAGGATAACCGGAACACG 60.612 50.000 9.46 0.00 41.83 4.49
3589 3722 2.450476 ACTAGGATAACCGGAACACGT 58.550 47.619 9.46 1.08 42.24 4.49
3590 3723 3.620488 ACTAGGATAACCGGAACACGTA 58.380 45.455 9.46 2.28 42.24 3.57
3591 3724 3.629398 ACTAGGATAACCGGAACACGTAG 59.371 47.826 9.46 13.75 42.24 3.51
3592 3725 2.726821 AGGATAACCGGAACACGTAGA 58.273 47.619 9.46 0.00 42.24 2.59
3593 3726 3.091545 AGGATAACCGGAACACGTAGAA 58.908 45.455 9.46 0.00 42.24 2.10
3594 3727 3.119352 AGGATAACCGGAACACGTAGAAC 60.119 47.826 9.46 0.00 42.24 3.01
3595 3728 6.446254 AGGATAACCGGAACACGTAGAACG 62.446 50.000 9.46 0.00 43.88 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 41 8.418597 ACCAACTAGATCAACTTACTAAGACA 57.581 34.615 0.00 0.00 0.00 3.41
183 186 9.289303 CACCCTTTATGAGATTTAATTTTGACG 57.711 33.333 0.00 0.00 0.00 4.35
243 247 0.850100 TTCAGTTCCTTTCCCTGCCA 59.150 50.000 0.00 0.00 0.00 4.92
270 274 4.096382 GCCATCAGTTACCGATTTGATGTT 59.904 41.667 11.12 0.00 35.77 2.71
280 284 2.487762 ACAACATTGCCATCAGTTACCG 59.512 45.455 0.00 0.00 0.00 4.02
320 324 5.012239 AGAAGGCAGAAGATGTTTATTGCA 58.988 37.500 8.98 0.00 33.42 4.08
421 426 3.947868 TGAAAAATCTCTCTGCTCCTGG 58.052 45.455 0.00 0.00 0.00 4.45
466 472 2.344142 GCGAATTAAACAAATGCCACCG 59.656 45.455 0.00 0.00 0.00 4.94
485 513 0.250295 TCTCTGAAAACCACCCAGCG 60.250 55.000 0.00 0.00 0.00 5.18
488 516 3.699038 CAGTTTTCTCTGAAAACCACCCA 59.301 43.478 23.72 0.00 40.10 4.51
492 520 2.357637 CGCCAGTTTTCTCTGAAAACCA 59.642 45.455 23.72 0.00 40.10 3.67
499 527 1.264288 GAACACCGCCAGTTTTCTCTG 59.736 52.381 0.00 0.00 33.23 3.35
501 529 0.234884 CGAACACCGCCAGTTTTCTC 59.765 55.000 0.59 0.00 33.73 2.87
557 585 4.276431 GGACACGTTTGAACTTGGGAAATA 59.724 41.667 5.52 0.00 32.98 1.40
703 748 5.174943 CGGAGAAATTTCCCTTTTGTTTTCG 59.825 40.000 14.61 0.00 33.46 3.46
736 781 3.912907 CTGGGTAGCGTAGGGCCG 61.913 72.222 0.00 0.00 45.17 6.13
745 790 4.162690 CGTGGAGGCCTGGGTAGC 62.163 72.222 12.00 0.00 0.00 3.58
1762 1855 1.202222 CGGCATCTCAGAAATGGCAAC 60.202 52.381 10.70 0.00 46.81 4.17
1771 1864 2.125552 CAACGCCGGCATCTCAGA 60.126 61.111 28.98 0.00 0.00 3.27
1824 1917 0.661187 CGGCGCCATTAATCATGTGC 60.661 55.000 28.98 6.27 33.55 4.57
1954 2047 6.702449 ATAATATACCTCAATGCACCAGGA 57.298 37.500 13.21 0.00 0.00 3.86
2020 2116 8.467963 TTCACATATACGTGGTTAGATTCCTA 57.532 34.615 0.00 0.00 37.50 2.94
2038 2134 8.593842 CGCAAATTGCTTCAAATTATTCACATA 58.406 29.630 16.42 0.00 42.25 2.29
2066 2162 1.134670 CCTTCGACCATTCCTCAGGAC 60.135 57.143 0.00 0.00 0.00 3.85
2082 2178 0.322008 CCTTGTCCAGCCTCACCTTC 60.322 60.000 0.00 0.00 0.00 3.46
2089 2185 1.821061 CGTCTCACCTTGTCCAGCCT 61.821 60.000 0.00 0.00 0.00 4.58
2221 2317 6.783708 ACAGTAGATAGAAGAACTCAAGGG 57.216 41.667 0.00 0.00 0.00 3.95
2469 2565 5.425196 TTGTCATCATCTCCAACATCTGA 57.575 39.130 0.00 0.00 0.00 3.27
2602 2698 6.115446 TGAGACTCCACCAATTACAATCATC 58.885 40.000 0.00 0.00 0.00 2.92
2614 2715 3.764434 GACTAGAACATGAGACTCCACCA 59.236 47.826 0.00 0.00 0.00 4.17
2615 2716 3.131400 GGACTAGAACATGAGACTCCACC 59.869 52.174 0.00 0.00 0.00 4.61
2616 2717 3.131400 GGGACTAGAACATGAGACTCCAC 59.869 52.174 0.00 0.00 0.00 4.02
2619 2720 4.274147 TCAGGGACTAGAACATGAGACTC 58.726 47.826 0.00 0.00 36.02 3.36
2632 2733 3.173965 CCACTTCTTCCTTCAGGGACTA 58.826 50.000 0.00 0.00 45.03 2.59
2638 2739 1.538950 GCAAGCCACTTCTTCCTTCAG 59.461 52.381 0.00 0.00 0.00 3.02
2703 2805 4.620332 GCAGCTCTGTGACAAGTTAGATCT 60.620 45.833 0.00 0.00 0.00 2.75
2813 2915 8.648693 AGCTAAAGTTTCTCTGAAAAGGTAGTA 58.351 33.333 0.00 0.00 0.00 1.82
2850 2952 9.804758 CGAAGAACTCATAAAACTAGGTATCTT 57.195 33.333 0.00 0.00 0.00 2.40
2869 2971 7.653767 TTAATTTCTCAAGGAGTCGAAGAAC 57.346 36.000 0.00 0.00 39.69 3.01
2870 2972 8.848474 AATTAATTTCTCAAGGAGTCGAAGAA 57.152 30.769 0.00 0.00 39.69 2.52
2871 2973 8.721478 CAAATTAATTTCTCAAGGAGTCGAAGA 58.279 33.333 10.53 0.00 0.00 2.87
2872 2974 8.721478 TCAAATTAATTTCTCAAGGAGTCGAAG 58.279 33.333 10.53 0.00 0.00 3.79
2873 2975 8.615878 TCAAATTAATTTCTCAAGGAGTCGAA 57.384 30.769 10.53 0.00 0.00 3.71
2874 2976 8.615878 TTCAAATTAATTTCTCAAGGAGTCGA 57.384 30.769 10.53 0.00 0.00 4.20
2875 2977 8.721478 TCTTCAAATTAATTTCTCAAGGAGTCG 58.279 33.333 10.53 0.00 0.00 4.18
2878 2980 9.351570 GCTTCTTCAAATTAATTTCTCAAGGAG 57.648 33.333 18.25 18.25 0.00 3.69
2879 2981 8.023128 CGCTTCTTCAAATTAATTTCTCAAGGA 58.977 33.333 10.53 7.34 0.00 3.36
2880 2982 7.809806 ACGCTTCTTCAAATTAATTTCTCAAGG 59.190 33.333 10.53 0.00 0.00 3.61
2881 2983 8.633408 CACGCTTCTTCAAATTAATTTCTCAAG 58.367 33.333 10.53 12.21 0.00 3.02
2882 2984 8.134895 ACACGCTTCTTCAAATTAATTTCTCAA 58.865 29.630 10.53 3.92 0.00 3.02
2883 2985 7.648142 ACACGCTTCTTCAAATTAATTTCTCA 58.352 30.769 10.53 0.00 0.00 3.27
2884 2986 8.017946 AGACACGCTTCTTCAAATTAATTTCTC 58.982 33.333 10.53 0.00 0.00 2.87
2885 2987 7.875971 AGACACGCTTCTTCAAATTAATTTCT 58.124 30.769 10.53 0.00 0.00 2.52
2889 2991 6.653320 TGGTAGACACGCTTCTTCAAATTAAT 59.347 34.615 0.00 0.00 0.00 1.40
2943 3046 6.271857 ACCATCAGATAATGTTCATCTAGGCT 59.728 38.462 0.00 0.00 31.48 4.58
2976 3079 7.619965 TGCTATATTCGATTACATGATCCCAA 58.380 34.615 0.00 0.00 0.00 4.12
2977 3080 7.181569 TGCTATATTCGATTACATGATCCCA 57.818 36.000 0.00 0.00 0.00 4.37
2978 3081 8.391106 GTTTGCTATATTCGATTACATGATCCC 58.609 37.037 0.00 0.00 0.00 3.85
2979 3082 9.155975 AGTTTGCTATATTCGATTACATGATCC 57.844 33.333 0.00 0.00 0.00 3.36
2980 3083 9.964253 CAGTTTGCTATATTCGATTACATGATC 57.036 33.333 0.00 0.00 0.00 2.92
2981 3084 8.939929 CCAGTTTGCTATATTCGATTACATGAT 58.060 33.333 0.00 0.00 0.00 2.45
2982 3085 7.931407 ACCAGTTTGCTATATTCGATTACATGA 59.069 33.333 0.00 0.00 0.00 3.07
2983 3086 8.087982 ACCAGTTTGCTATATTCGATTACATG 57.912 34.615 0.00 0.00 0.00 3.21
2984 3087 9.772973 TTACCAGTTTGCTATATTCGATTACAT 57.227 29.630 0.00 0.00 0.00 2.29
2985 3088 9.256477 CTTACCAGTTTGCTATATTCGATTACA 57.744 33.333 0.00 0.00 0.00 2.41
2986 3089 8.709646 CCTTACCAGTTTGCTATATTCGATTAC 58.290 37.037 0.00 0.00 0.00 1.89
2987 3090 8.426489 ACCTTACCAGTTTGCTATATTCGATTA 58.574 33.333 0.00 0.00 0.00 1.75
2988 3091 7.280356 ACCTTACCAGTTTGCTATATTCGATT 58.720 34.615 0.00 0.00 0.00 3.34
2989 3092 6.827727 ACCTTACCAGTTTGCTATATTCGAT 58.172 36.000 0.00 0.00 0.00 3.59
2990 3093 6.229936 ACCTTACCAGTTTGCTATATTCGA 57.770 37.500 0.00 0.00 0.00 3.71
2991 3094 6.920569 AACCTTACCAGTTTGCTATATTCG 57.079 37.500 0.00 0.00 0.00 3.34
3001 3104 5.983540 TCATTTTGCAAACCTTACCAGTTT 58.016 33.333 12.39 0.00 37.93 2.66
3002 3105 5.606348 TCATTTTGCAAACCTTACCAGTT 57.394 34.783 12.39 0.00 0.00 3.16
3003 3106 5.539955 AGATCATTTTGCAAACCTTACCAGT 59.460 36.000 12.39 0.00 0.00 4.00
3004 3107 6.029346 AGATCATTTTGCAAACCTTACCAG 57.971 37.500 12.39 0.00 0.00 4.00
3005 3108 7.716799 ATAGATCATTTTGCAAACCTTACCA 57.283 32.000 12.39 0.00 0.00 3.25
3006 3109 9.736023 CTTATAGATCATTTTGCAAACCTTACC 57.264 33.333 12.39 0.16 0.00 2.85
3007 3110 9.736023 CCTTATAGATCATTTTGCAAACCTTAC 57.264 33.333 12.39 4.21 0.00 2.34
3008 3111 8.413229 GCCTTATAGATCATTTTGCAAACCTTA 58.587 33.333 12.39 0.00 0.00 2.69
3009 3112 7.093377 TGCCTTATAGATCATTTTGCAAACCTT 60.093 33.333 12.39 0.00 0.00 3.50
3010 3113 6.380846 TGCCTTATAGATCATTTTGCAAACCT 59.619 34.615 12.39 6.88 0.00 3.50
3011 3114 6.476706 GTGCCTTATAGATCATTTTGCAAACC 59.523 38.462 12.39 0.00 0.00 3.27
3012 3115 6.476706 GGTGCCTTATAGATCATTTTGCAAAC 59.523 38.462 12.39 0.00 0.00 2.93
3013 3116 6.380846 AGGTGCCTTATAGATCATTTTGCAAA 59.619 34.615 8.05 8.05 0.00 3.68
3014 3117 5.893255 AGGTGCCTTATAGATCATTTTGCAA 59.107 36.000 0.00 0.00 0.00 4.08
3015 3118 5.448654 AGGTGCCTTATAGATCATTTTGCA 58.551 37.500 0.00 0.00 0.00 4.08
3016 3119 5.048434 GGAGGTGCCTTATAGATCATTTTGC 60.048 44.000 0.00 0.00 0.00 3.68
3017 3120 6.064060 TGGAGGTGCCTTATAGATCATTTTG 58.936 40.000 0.00 0.00 37.63 2.44
3018 3121 6.266131 TGGAGGTGCCTTATAGATCATTTT 57.734 37.500 0.00 0.00 37.63 1.82
3019 3122 5.912149 TGGAGGTGCCTTATAGATCATTT 57.088 39.130 0.00 0.00 37.63 2.32
3020 3123 5.456763 GGTTGGAGGTGCCTTATAGATCATT 60.457 44.000 0.00 0.00 37.63 2.57
3021 3124 4.042187 GGTTGGAGGTGCCTTATAGATCAT 59.958 45.833 0.00 0.00 37.63 2.45
3022 3125 3.391296 GGTTGGAGGTGCCTTATAGATCA 59.609 47.826 0.00 0.00 37.63 2.92
3023 3126 3.391296 TGGTTGGAGGTGCCTTATAGATC 59.609 47.826 0.00 0.00 37.63 2.75
3024 3127 3.392616 CTGGTTGGAGGTGCCTTATAGAT 59.607 47.826 0.00 0.00 37.63 1.98
3025 3128 2.771943 CTGGTTGGAGGTGCCTTATAGA 59.228 50.000 0.00 0.00 37.63 1.98
3026 3129 2.746472 GCTGGTTGGAGGTGCCTTATAG 60.746 54.545 0.00 0.00 37.63 1.31
3027 3130 1.211949 GCTGGTTGGAGGTGCCTTATA 59.788 52.381 0.00 0.00 37.63 0.98
3028 3131 0.034089 GCTGGTTGGAGGTGCCTTAT 60.034 55.000 0.00 0.00 37.63 1.73
3059 3162 6.266558 TCAAACAACTGGGTTAATAATGCACT 59.733 34.615 0.00 0.00 0.00 4.40
3064 3167 8.700973 ACAAGTTCAAACAACTGGGTTAATAAT 58.299 29.630 0.00 0.00 0.00 1.28
3114 3217 8.629158 TGCATCAAACTTAACTACATCAAACTT 58.371 29.630 0.00 0.00 0.00 2.66
3115 3218 8.076178 GTGCATCAAACTTAACTACATCAAACT 58.924 33.333 0.00 0.00 0.00 2.66
3116 3219 7.860373 TGTGCATCAAACTTAACTACATCAAAC 59.140 33.333 0.00 0.00 0.00 2.93
3117 3220 7.935520 TGTGCATCAAACTTAACTACATCAAA 58.064 30.769 0.00 0.00 0.00 2.69
3118 3221 7.308529 CCTGTGCATCAAACTTAACTACATCAA 60.309 37.037 0.00 0.00 0.00 2.57
3119 3222 6.149308 CCTGTGCATCAAACTTAACTACATCA 59.851 38.462 0.00 0.00 0.00 3.07
3120 3223 6.371548 TCCTGTGCATCAAACTTAACTACATC 59.628 38.462 0.00 0.00 0.00 3.06
3121 3224 6.237901 TCCTGTGCATCAAACTTAACTACAT 58.762 36.000 0.00 0.00 0.00 2.29
3122 3225 5.616270 TCCTGTGCATCAAACTTAACTACA 58.384 37.500 0.00 0.00 0.00 2.74
3123 3226 5.122396 CCTCCTGTGCATCAAACTTAACTAC 59.878 44.000 0.00 0.00 0.00 2.73
3124 3227 5.012664 TCCTCCTGTGCATCAAACTTAACTA 59.987 40.000 0.00 0.00 0.00 2.24
3125 3228 4.074970 CCTCCTGTGCATCAAACTTAACT 58.925 43.478 0.00 0.00 0.00 2.24
3126 3229 4.072131 TCCTCCTGTGCATCAAACTTAAC 58.928 43.478 0.00 0.00 0.00 2.01
3127 3230 4.365514 TCCTCCTGTGCATCAAACTTAA 57.634 40.909 0.00 0.00 0.00 1.85
3128 3231 4.264253 CATCCTCCTGTGCATCAAACTTA 58.736 43.478 0.00 0.00 0.00 2.24
3129 3232 2.957402 TCCTCCTGTGCATCAAACTT 57.043 45.000 0.00 0.00 0.00 2.66
3130 3233 2.719739 CATCCTCCTGTGCATCAAACT 58.280 47.619 0.00 0.00 0.00 2.66
3212 3336 5.734503 GCCATCAAACTTTTATAGCTCCTGC 60.735 44.000 0.00 0.00 40.05 4.85
3219 3343 6.040166 AGCTGGATGCCATCAAACTTTTATAG 59.960 38.462 7.06 0.00 44.23 1.31
3220 3344 5.893255 AGCTGGATGCCATCAAACTTTTATA 59.107 36.000 7.06 0.00 44.23 0.98
3221 3345 4.713321 AGCTGGATGCCATCAAACTTTTAT 59.287 37.500 7.06 0.00 44.23 1.40
3222 3346 4.088634 AGCTGGATGCCATCAAACTTTTA 58.911 39.130 7.06 0.00 44.23 1.52
3245 3372 7.054491 ACAGTTAATGCTTTCAAAGGTCAAT 57.946 32.000 0.00 0.00 0.00 2.57
3258 3385 6.118170 AGCTGATATGACAACAGTTAATGCT 58.882 36.000 0.00 0.00 34.60 3.79
3265 3392 3.771479 TCTGGAGCTGATATGACAACAGT 59.229 43.478 0.00 0.00 34.60 3.55
3300 3427 6.611613 ATCACAACCAGACATTTCTAGAGA 57.388 37.500 0.00 0.00 0.00 3.10
3431 3564 6.648502 CCCTTTGACGAACAATGAAAAATTG 58.351 36.000 0.00 0.00 38.36 2.32
3432 3565 5.236263 GCCCTTTGACGAACAATGAAAAATT 59.764 36.000 0.00 0.00 38.36 1.82
3452 3585 0.467384 CGAGATTCTCACATGGCCCT 59.533 55.000 13.88 0.00 0.00 5.19
3453 3586 0.465705 TCGAGATTCTCACATGGCCC 59.534 55.000 13.88 0.00 0.00 5.80
3459 3592 6.590292 GGTGAAACTATTTCGAGATTCTCACA 59.410 38.462 13.88 0.00 42.55 3.58
3469 3602 1.276989 AGCGGGGTGAAACTATTTCGA 59.723 47.619 0.00 0.00 42.55 3.71
3470 3603 1.734163 AGCGGGGTGAAACTATTTCG 58.266 50.000 0.00 0.00 42.55 3.46
3471 3604 5.830000 ATAAAGCGGGGTGAAACTATTTC 57.170 39.130 0.00 0.00 40.08 2.17
3475 3608 9.715121 CTTTATATATAAAGCGGGGTGAAACTA 57.285 33.333 25.10 0.00 41.69 2.24
3476 3609 8.617290 CTTTATATATAAAGCGGGGTGAAACT 57.383 34.615 25.10 0.00 41.69 2.66
3489 3622 9.256228 TGGTTTGGTGGTTGCTTTATATATAAA 57.744 29.630 15.47 15.47 0.00 1.40
3490 3623 8.824756 TGGTTTGGTGGTTGCTTTATATATAA 57.175 30.769 0.81 0.81 0.00 0.98
3491 3624 8.824756 TTGGTTTGGTGGTTGCTTTATATATA 57.175 30.769 0.00 0.00 0.00 0.86
3492 3625 7.398904 ACTTGGTTTGGTGGTTGCTTTATATAT 59.601 33.333 0.00 0.00 0.00 0.86
3493 3626 6.722129 ACTTGGTTTGGTGGTTGCTTTATATA 59.278 34.615 0.00 0.00 0.00 0.86
3494 3627 5.542251 ACTTGGTTTGGTGGTTGCTTTATAT 59.458 36.000 0.00 0.00 0.00 0.86
3495 3628 4.896482 ACTTGGTTTGGTGGTTGCTTTATA 59.104 37.500 0.00 0.00 0.00 0.98
3496 3629 3.709141 ACTTGGTTTGGTGGTTGCTTTAT 59.291 39.130 0.00 0.00 0.00 1.40
3497 3630 3.100671 ACTTGGTTTGGTGGTTGCTTTA 58.899 40.909 0.00 0.00 0.00 1.85
3498 3631 1.905894 ACTTGGTTTGGTGGTTGCTTT 59.094 42.857 0.00 0.00 0.00 3.51
3499 3632 1.567357 ACTTGGTTTGGTGGTTGCTT 58.433 45.000 0.00 0.00 0.00 3.91
3500 3633 2.028876 GTACTTGGTTTGGTGGTTGCT 58.971 47.619 0.00 0.00 0.00 3.91
3501 3634 1.751924 TGTACTTGGTTTGGTGGTTGC 59.248 47.619 0.00 0.00 0.00 4.17
3502 3635 2.223386 CGTGTACTTGGTTTGGTGGTTG 60.223 50.000 0.00 0.00 0.00 3.77
3503 3636 2.018515 CGTGTACTTGGTTTGGTGGTT 58.981 47.619 0.00 0.00 0.00 3.67
3504 3637 1.670791 CGTGTACTTGGTTTGGTGGT 58.329 50.000 0.00 0.00 0.00 4.16
3505 3638 0.948678 CCGTGTACTTGGTTTGGTGG 59.051 55.000 0.00 0.00 0.00 4.61
3506 3639 0.309612 GCCGTGTACTTGGTTTGGTG 59.690 55.000 5.95 0.00 0.00 4.17
3507 3640 0.820482 GGCCGTGTACTTGGTTTGGT 60.820 55.000 0.00 0.00 0.00 3.67
3508 3641 1.847890 CGGCCGTGTACTTGGTTTGG 61.848 60.000 19.50 0.00 0.00 3.28
3509 3642 0.881159 TCGGCCGTGTACTTGGTTTG 60.881 55.000 27.15 0.00 0.00 2.93
3510 3643 0.179051 TTCGGCCGTGTACTTGGTTT 60.179 50.000 27.15 0.00 0.00 3.27
3511 3644 0.881600 GTTCGGCCGTGTACTTGGTT 60.882 55.000 27.15 0.00 0.00 3.67
3512 3645 1.301165 GTTCGGCCGTGTACTTGGT 60.301 57.895 27.15 0.00 0.00 3.67
3513 3646 2.377310 CGTTCGGCCGTGTACTTGG 61.377 63.158 27.15 5.99 0.00 3.61
3514 3647 0.734942 ATCGTTCGGCCGTGTACTTG 60.735 55.000 27.15 9.34 0.00 3.16
3515 3648 0.734942 CATCGTTCGGCCGTGTACTT 60.735 55.000 27.15 9.22 0.00 2.24
3516 3649 1.153901 CATCGTTCGGCCGTGTACT 60.154 57.895 27.15 5.71 0.00 2.73
3517 3650 2.795389 GCATCGTTCGGCCGTGTAC 61.795 63.158 27.15 19.67 0.00 2.90
3518 3651 2.507547 GCATCGTTCGGCCGTGTA 60.508 61.111 27.15 9.28 0.00 2.90
3519 3652 4.673298 TGCATCGTTCGGCCGTGT 62.673 61.111 27.15 4.81 0.00 4.49
3520 3653 3.367051 CTTGCATCGTTCGGCCGTG 62.367 63.158 27.15 16.97 0.00 4.94
3521 3654 2.852495 ATCTTGCATCGTTCGGCCGT 62.852 55.000 27.15 1.01 0.00 5.68
3522 3655 2.173669 ATCTTGCATCGTTCGGCCG 61.174 57.895 22.12 22.12 0.00 6.13
3523 3656 1.353103 CATCTTGCATCGTTCGGCC 59.647 57.895 0.00 0.00 0.00 6.13
3524 3657 1.353103 CCATCTTGCATCGTTCGGC 59.647 57.895 0.00 0.00 0.00 5.54
3525 3658 0.374758 CACCATCTTGCATCGTTCGG 59.625 55.000 0.00 0.00 0.00 4.30
3526 3659 1.325640 CTCACCATCTTGCATCGTTCG 59.674 52.381 0.00 0.00 0.00 3.95
3527 3660 1.667724 CCTCACCATCTTGCATCGTTC 59.332 52.381 0.00 0.00 0.00 3.95
3528 3661 1.003580 ACCTCACCATCTTGCATCGTT 59.996 47.619 0.00 0.00 0.00 3.85
3529 3662 0.615331 ACCTCACCATCTTGCATCGT 59.385 50.000 0.00 0.00 0.00 3.73
3530 3663 2.477825 CTACCTCACCATCTTGCATCG 58.522 52.381 0.00 0.00 0.00 3.84
3531 3664 2.216898 GCTACCTCACCATCTTGCATC 58.783 52.381 0.00 0.00 0.00 3.91
3532 3665 1.133976 GGCTACCTCACCATCTTGCAT 60.134 52.381 0.00 0.00 0.00 3.96
3533 3666 0.253044 GGCTACCTCACCATCTTGCA 59.747 55.000 0.00 0.00 0.00 4.08
3534 3667 0.464554 GGGCTACCTCACCATCTTGC 60.465 60.000 0.00 0.00 0.00 4.01
3535 3668 1.207791 AGGGCTACCTCACCATCTTG 58.792 55.000 0.00 0.00 46.95 3.02
3536 3669 3.740364 AGGGCTACCTCACCATCTT 57.260 52.632 0.00 0.00 46.95 2.40
3546 3679 1.458639 GGCATTGCATGAGGGCTACC 61.459 60.000 11.39 0.00 34.04 3.18
3547 3680 1.789078 CGGCATTGCATGAGGGCTAC 61.789 60.000 11.39 0.00 34.04 3.58
3548 3681 1.526686 CGGCATTGCATGAGGGCTA 60.527 57.895 11.39 0.00 34.04 3.93
3549 3682 2.635787 ATCGGCATTGCATGAGGGCT 62.636 55.000 11.39 0.00 34.04 5.19
3550 3683 0.890542 TATCGGCATTGCATGAGGGC 60.891 55.000 11.39 0.00 0.00 5.19
3551 3684 0.877071 GTATCGGCATTGCATGAGGG 59.123 55.000 11.39 0.00 0.00 4.30
3552 3685 1.888215 AGTATCGGCATTGCATGAGG 58.112 50.000 11.39 0.00 0.00 3.86
3553 3686 2.998670 CCTAGTATCGGCATTGCATGAG 59.001 50.000 11.39 0.00 0.00 2.90
3554 3687 2.632512 TCCTAGTATCGGCATTGCATGA 59.367 45.455 11.39 8.09 0.00 3.07
3555 3688 3.044235 TCCTAGTATCGGCATTGCATG 57.956 47.619 11.39 2.27 0.00 4.06
3556 3689 3.988976 ATCCTAGTATCGGCATTGCAT 57.011 42.857 11.39 0.00 0.00 3.96
3557 3690 4.562757 GGTTATCCTAGTATCGGCATTGCA 60.563 45.833 11.39 0.00 0.00 4.08
3558 3691 3.933332 GGTTATCCTAGTATCGGCATTGC 59.067 47.826 0.00 0.00 0.00 3.56
3559 3692 4.174009 CGGTTATCCTAGTATCGGCATTG 58.826 47.826 0.00 0.00 0.00 2.82
3560 3693 3.194968 CCGGTTATCCTAGTATCGGCATT 59.805 47.826 0.00 0.00 0.00 3.56
3561 3694 2.758979 CCGGTTATCCTAGTATCGGCAT 59.241 50.000 0.00 0.00 0.00 4.40
3562 3695 2.165167 CCGGTTATCCTAGTATCGGCA 58.835 52.381 0.00 0.00 0.00 5.69
3563 3696 2.440409 TCCGGTTATCCTAGTATCGGC 58.560 52.381 0.00 0.00 36.40 5.54
3564 3697 3.822735 TGTTCCGGTTATCCTAGTATCGG 59.177 47.826 0.00 0.00 37.61 4.18
3565 3698 4.612259 CGTGTTCCGGTTATCCTAGTATCG 60.612 50.000 0.00 0.00 0.00 2.92
3566 3699 4.276926 ACGTGTTCCGGTTATCCTAGTATC 59.723 45.833 0.00 0.00 42.24 2.24
3567 3700 4.210331 ACGTGTTCCGGTTATCCTAGTAT 58.790 43.478 0.00 0.00 42.24 2.12
3568 3701 3.620488 ACGTGTTCCGGTTATCCTAGTA 58.380 45.455 0.00 0.00 42.24 1.82
3569 3702 2.450476 ACGTGTTCCGGTTATCCTAGT 58.550 47.619 0.00 0.00 42.24 2.57
3570 3703 3.879295 TCTACGTGTTCCGGTTATCCTAG 59.121 47.826 0.00 0.00 42.24 3.02
3571 3704 3.884895 TCTACGTGTTCCGGTTATCCTA 58.115 45.455 0.00 0.00 42.24 2.94
3572 3705 2.726821 TCTACGTGTTCCGGTTATCCT 58.273 47.619 0.00 0.00 42.24 3.24
3573 3706 3.182182 GTTCTACGTGTTCCGGTTATCC 58.818 50.000 0.00 0.00 42.24 2.59
3574 3707 2.848302 CGTTCTACGTGTTCCGGTTATC 59.152 50.000 0.00 0.00 42.24 1.75
3575 3708 2.867429 CGTTCTACGTGTTCCGGTTAT 58.133 47.619 0.00 0.00 42.24 1.89
3576 3709 1.665735 GCGTTCTACGTGTTCCGGTTA 60.666 52.381 0.00 0.00 44.73 2.85
3577 3710 0.940991 GCGTTCTACGTGTTCCGGTT 60.941 55.000 0.00 0.00 44.73 4.44
3578 3711 1.372128 GCGTTCTACGTGTTCCGGT 60.372 57.895 0.00 0.00 44.73 5.28
3579 3712 1.372004 TGCGTTCTACGTGTTCCGG 60.372 57.895 0.00 0.00 44.73 5.14
3580 3713 1.771044 GTGCGTTCTACGTGTTCCG 59.229 57.895 0.00 0.00 44.73 4.30


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

AutoCloner maintained by Alex Coulton.