Multiple sequence alignment - TraesCS5D01G178300

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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 TraesCS5D01G178300 chr5D 100.000 3702 0 0 1 3702 277728855 277725154 0.000000e+00 6837.0
1 TraesCS5D01G178300 chr5B 90.839 2838 141 56 641 3391 315910263 315907458 0.000000e+00 3690.0
2 TraesCS5D01G178300 chr5B 90.232 604 45 9 7 599 315918864 315918264 0.000000e+00 776.0
3 TraesCS5D01G178300 chr5B 95.122 41 1 1 3647 3687 398348886 398348925 3.090000e-06 63.9
4 TraesCS5D01G178300 chr5A 91.546 2626 123 32 842 3391 367100333 367097731 0.000000e+00 3528.0
5 TraesCS5D01G178300 chr5A 87.828 838 66 20 1 822 367101227 367100410 0.000000e+00 950.0
6 TraesCS5D01G178300 chr5A 89.888 89 4 4 3546 3630 367097727 367097640 3.910000e-20 110.0
7 TraesCS5D01G178300 chr3B 86.923 130 17 0 3395 3524 201533228 201533357 2.980000e-31 147.0
8 TraesCS5D01G178300 chr3B 93.182 44 2 1 3640 3682 781369833 781369790 3.090000e-06 63.9
9 TraesCS5D01G178300 chr1A 85.124 121 18 0 3395 3515 355335069 355334949 1.400000e-24 124.0
10 TraesCS5D01G178300 chr1A 91.837 49 2 1 3634 3682 391251023 391251069 2.390000e-07 67.6
11 TraesCS5D01G178300 chr1A 91.111 45 4 0 3647 3691 497318183 497318139 1.110000e-05 62.1
12 TraesCS5D01G178300 chr6B 97.619 42 0 1 3647 3688 37927446 37927406 1.840000e-08 71.3
13 TraesCS5D01G178300 chr4A 95.455 44 2 0 3647 3690 580898446 580898489 1.840000e-08 71.3
14 TraesCS5D01G178300 chr7B 95.349 43 2 0 3640 3682 63564790 63564748 6.630000e-08 69.4
15 TraesCS5D01G178300 chr2D 95.349 43 2 0 3647 3689 6673584 6673542 6.630000e-08 69.4
16 TraesCS5D01G178300 chr3A 91.489 47 4 0 3640 3686 100961591 100961637 8.580000e-07 65.8


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 TraesCS5D01G178300 chr5D 277725154 277728855 3701 True 6837.000000 6837 100.000 1 3702 1 chr5D.!!$R1 3701
1 TraesCS5D01G178300 chr5B 315907458 315910263 2805 True 3690.000000 3690 90.839 641 3391 1 chr5B.!!$R1 2750
2 TraesCS5D01G178300 chr5B 315918264 315918864 600 True 776.000000 776 90.232 7 599 1 chr5B.!!$R2 592
3 TraesCS5D01G178300 chr5A 367097640 367101227 3587 True 1529.333333 3528 89.754 1 3630 3 chr5A.!!$R1 3629

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
707 722 0.596859 GATAGCTAACCGGTCGTGCC 60.597 60.0 8.04 0.0 0.0 5.01 F
1814 1942 0.872388 GCTTCATCCCGTCGTTTGTT 59.128 50.0 0.00 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1992 2120 0.882927 TCTTTGCGAGGTTCCCAACG 60.883 55.0 0.0 0.0 0.0 4.10 R
3667 3837 0.259938 TTACCTACTCCCTCCGTCCC 59.740 60.0 0.0 0.0 0.0 4.46 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
22 23 2.248248 ACCGAACTCTTGACCATCTCA 58.752 47.619 0.00 0.00 0.00 3.27
59 60 3.062042 CAAAGTACGAGGGGTGTAACAC 58.938 50.000 0.00 0.00 41.97 3.32
104 105 4.860881 CCCTCGGGGCCTAGCAGA 62.861 72.222 0.84 0.00 35.35 4.26
109 110 3.798511 GGGGCCTAGCAGACCACC 61.799 72.222 0.84 0.00 0.00 4.61
127 128 0.827925 CCGCATGGCTAGGTCTCCTA 60.828 60.000 0.00 0.00 34.61 2.94
134 135 2.312140 TGGCTAGGTCTCCTAACTCAGT 59.688 50.000 0.00 0.00 35.49 3.41
196 197 0.761802 GGTGAGGCCCAAGATCTAGG 59.238 60.000 0.00 0.88 0.00 3.02
225 226 3.863142 ACCGACTAGGACACATGTAAC 57.137 47.619 0.00 0.00 45.00 2.50
226 227 3.428532 ACCGACTAGGACACATGTAACT 58.571 45.455 0.00 0.00 45.00 2.24
268 271 1.452108 GTGGGACCATGGCTAGTGC 60.452 63.158 13.04 0.00 38.76 4.40
292 295 6.457934 GCAGACACACCAAATCATAGATTCAG 60.458 42.308 0.00 0.00 0.00 3.02
307 310 9.672673 TCATAGATTCAGTATCTCGATACATCA 57.327 33.333 16.81 3.22 44.58 3.07
341 344 6.884295 TCCATTGTAACCTCTTCATACAAAGG 59.116 38.462 11.07 11.07 44.08 3.11
360 363 3.759581 AGGCATCCATACCATCAATCAC 58.240 45.455 0.00 0.00 0.00 3.06
363 366 4.525487 GGCATCCATACCATCAATCACAAT 59.475 41.667 0.00 0.00 0.00 2.71
393 396 5.538118 CATGCGTAACATATTACCTCCAGA 58.462 41.667 0.00 0.00 37.94 3.86
430 433 4.090819 ACCTGGGTAAAAACTTTGTGTGT 58.909 39.130 0.00 0.00 0.00 3.72
446 449 3.504906 TGTGTGTTTTTGTTTCGGGTACA 59.495 39.130 0.00 0.00 0.00 2.90
457 460 1.187974 TCGGGTACATTCGGTCATGT 58.812 50.000 0.00 2.13 40.61 3.21
472 475 3.392882 GTCATGTGCATCACCATATCGA 58.607 45.455 0.00 0.00 32.73 3.59
494 497 3.253921 ACTTTAATGCGGGTTTGTACACC 59.746 43.478 0.00 0.00 35.88 4.16
599 611 5.435686 AATTCAACCTAGGTCTACATGCA 57.564 39.130 16.64 0.00 0.00 3.96
600 612 3.887621 TCAACCTAGGTCTACATGCAC 57.112 47.619 16.64 0.00 0.00 4.57
602 614 3.580895 TCAACCTAGGTCTACATGCACAA 59.419 43.478 16.64 0.00 0.00 3.33
603 615 4.041075 TCAACCTAGGTCTACATGCACAAA 59.959 41.667 16.64 0.00 0.00 2.83
604 616 4.844349 ACCTAGGTCTACATGCACAAAT 57.156 40.909 9.21 0.00 0.00 2.32
605 617 5.950544 ACCTAGGTCTACATGCACAAATA 57.049 39.130 9.21 0.00 0.00 1.40
606 618 6.308015 ACCTAGGTCTACATGCACAAATAA 57.692 37.500 9.21 0.00 0.00 1.40
607 619 6.900194 ACCTAGGTCTACATGCACAAATAAT 58.100 36.000 9.21 0.00 0.00 1.28
608 620 6.767902 ACCTAGGTCTACATGCACAAATAATG 59.232 38.462 9.21 0.00 0.00 1.90
609 621 6.767902 CCTAGGTCTACATGCACAAATAATGT 59.232 38.462 0.00 0.00 45.34 2.71
610 622 7.931407 CCTAGGTCTACATGCACAAATAATGTA 59.069 37.037 0.00 0.00 41.46 2.29
617 629 7.792374 ACATGCACAAATAATGTAGACCTAG 57.208 36.000 0.00 0.00 41.46 3.02
618 630 6.767902 ACATGCACAAATAATGTAGACCTAGG 59.232 38.462 7.41 7.41 41.46 3.02
619 631 6.308015 TGCACAAATAATGTAGACCTAGGT 57.692 37.500 16.26 16.26 41.46 3.08
632 644 3.394606 AGACCTAGGTTGAGCAAAAGGAA 59.605 43.478 17.53 0.00 0.00 3.36
636 648 5.602561 ACCTAGGTTGAGCAAAAGGAAAAAT 59.397 36.000 9.21 0.00 0.00 1.82
700 715 6.049149 TCATCTTTTTGAGATAGCTAACCGG 58.951 40.000 0.00 0.00 43.32 5.28
707 722 0.596859 GATAGCTAACCGGTCGTGCC 60.597 60.000 8.04 0.00 0.00 5.01
727 746 1.459592 CGAACCCTGAAATCACACGTC 59.540 52.381 0.00 0.00 0.00 4.34
737 756 6.963242 CCTGAAATCACACGTCAATATTCAAG 59.037 38.462 0.00 0.00 0.00 3.02
748 767 8.177663 CACGTCAATATTCAAGCTTAGATTTGT 58.822 33.333 0.00 0.00 0.00 2.83
854 905 1.745232 ATTTATGGAAGCGCCGTGAA 58.255 45.000 2.29 2.72 40.66 3.18
896 985 1.591327 CACAGCGGCCCAACAAAAC 60.591 57.895 0.00 0.00 0.00 2.43
897 986 1.756561 ACAGCGGCCCAACAAAACT 60.757 52.632 0.00 0.00 0.00 2.66
1032 1127 3.740495 CTCCTCTCTAGCGGCCCCA 62.740 68.421 0.00 0.00 0.00 4.96
1307 1402 2.813908 GGCCGAGGTAACGCACTG 60.814 66.667 0.00 0.00 46.39 3.66
1308 1403 2.260434 GCCGAGGTAACGCACTGA 59.740 61.111 0.00 0.00 46.39 3.41
1474 1569 9.573133 CATGTTCTTGTTGTTATTTATTCCCTC 57.427 33.333 0.00 0.00 0.00 4.30
1475 1570 8.117813 TGTTCTTGTTGTTATTTATTCCCTCC 57.882 34.615 0.00 0.00 0.00 4.30
1476 1571 6.995511 TCTTGTTGTTATTTATTCCCTCCG 57.004 37.500 0.00 0.00 0.00 4.63
1478 1573 6.596497 TCTTGTTGTTATTTATTCCCTCCGTC 59.404 38.462 0.00 0.00 0.00 4.79
1546 1672 1.382522 AGCCTGATGTATGCAAACCG 58.617 50.000 0.00 0.00 0.00 4.44
1555 1683 1.917336 TATGCAAACCGGGGAGGGAC 61.917 60.000 6.32 0.00 46.96 4.46
1641 1769 3.365832 GTGATGAATTGCTTGCCGTATG 58.634 45.455 0.00 0.00 0.00 2.39
1643 1771 3.065233 TGATGAATTGCTTGCCGTATGTC 59.935 43.478 0.00 0.00 0.00 3.06
1675 1803 6.024552 TCTCACTAAAATGATTGTTTGCCC 57.975 37.500 0.00 0.00 0.00 5.36
1691 1819 2.639065 TGCCCGATAATTTCACAGGTC 58.361 47.619 0.00 0.00 0.00 3.85
1814 1942 0.872388 GCTTCATCCCGTCGTTTGTT 59.128 50.000 0.00 0.00 0.00 2.83
1815 1943 1.265905 GCTTCATCCCGTCGTTTGTTT 59.734 47.619 0.00 0.00 0.00 2.83
1905 2033 9.511272 GAGGTTGGAGGTAGAAAAATTAAAGTA 57.489 33.333 0.00 0.00 0.00 2.24
1992 2120 3.072211 GGACAGCCAGTACAAGGTTTAC 58.928 50.000 6.29 0.00 0.00 2.01
1998 2126 2.809696 CCAGTACAAGGTTTACGTTGGG 59.190 50.000 16.74 6.97 43.66 4.12
2001 2129 4.024641 CAGTACAAGGTTTACGTTGGGAAC 60.025 45.833 16.74 12.15 43.66 3.62
2173 2301 5.334569 GCTGCGGTTTCTACTTTCAACAATA 60.335 40.000 0.00 0.00 0.00 1.90
2280 2410 7.750903 GCAGACTATGGTTTCAAAAGTTGATAC 59.249 37.037 3.76 3.76 39.84 2.24
2284 2414 3.312973 TGGTTTCAAAAGTTGATACGCGT 59.687 39.130 19.17 19.17 40.91 6.01
2288 2418 3.644823 TCAAAAGTTGATACGCGTCAGA 58.355 40.909 18.63 0.00 34.08 3.27
2408 2538 5.816258 GCCTAGACTACTGGTCAAATTTACC 59.184 44.000 0.00 8.89 46.72 2.85
2452 2582 3.965379 TCACACCCGAGTTTGCTATTA 57.035 42.857 0.00 0.00 0.00 0.98
2519 2649 6.287589 TCCCAAGCAAACAACTTTTTCTTA 57.712 33.333 0.00 0.00 0.00 2.10
2565 2695 1.322442 GCATGGCTCTTGGGTTATCC 58.678 55.000 0.00 0.00 0.00 2.59
2733 2863 6.016024 CAGAAATTTCACATTGGAGTCAAGGA 60.016 38.462 19.99 0.00 37.99 3.36
2891 3024 2.028130 TGATTGTCAAGCCCGTTGTTT 58.972 42.857 0.00 0.00 37.43 2.83
2903 3036 3.377172 GCCCGTTGTTTATATGAAGCAGT 59.623 43.478 0.00 0.00 0.00 4.40
2916 3049 4.364415 TGAAGCAGTTGTTGTTTACCAC 57.636 40.909 0.00 0.00 29.60 4.16
2934 3067 5.999205 ACCACCATTTCTAAATGATTGCA 57.001 34.783 15.37 0.00 46.72 4.08
2939 3072 6.814644 CACCATTTCTAAATGATTGCACATGT 59.185 34.615 15.37 0.00 46.72 3.21
2969 3102 6.528423 CGTGGTTTATTCACTTTGTTGTTGAA 59.472 34.615 0.00 0.00 33.31 2.69
2989 3135 7.171167 TGTTGAAGTTTGCATCAAATTGTATGG 59.829 33.333 2.14 0.00 37.31 2.74
2994 3140 6.650390 AGTTTGCATCAAATTGTATGGTTTCC 59.350 34.615 0.00 0.00 35.74 3.13
3002 3154 5.649782 AATTGTATGGTTTCCAGCAAGAG 57.350 39.130 11.71 0.00 36.75 2.85
3003 3155 3.788227 TGTATGGTTTCCAGCAAGAGT 57.212 42.857 0.00 0.00 36.75 3.24
3024 3176 9.893305 AAGAGTGTTTTATTTTTCAAGGATACG 57.107 29.630 0.00 0.00 46.39 3.06
3052 3204 2.030946 GCTGGACGCATCAGAAACATAC 59.969 50.000 4.71 0.00 38.92 2.39
3076 3228 0.947244 CAAGACCGTTTTGCTGCTCT 59.053 50.000 0.00 0.00 0.00 4.09
3080 3233 1.129437 GACCGTTTTGCTGCTCTGATC 59.871 52.381 0.00 0.00 0.00 2.92
3083 3236 1.135859 CGTTTTGCTGCTCTGATCCAC 60.136 52.381 0.00 0.00 0.00 4.02
3100 3253 7.121168 TCTGATCCACGATTTAGCTTTTGAATT 59.879 33.333 0.00 0.00 0.00 2.17
3104 3257 4.851014 CACGATTTAGCTTTTGAATTCGCA 59.149 37.500 9.86 0.00 33.79 5.10
3113 3266 4.498323 GCTTTTGAATTCGCATGATGAGAC 59.502 41.667 0.00 0.00 0.00 3.36
3132 3285 2.036556 CGCTTTCAAATGCGTTCAGT 57.963 45.000 13.08 0.00 44.44 3.41
3134 3287 2.601979 CGCTTTCAAATGCGTTCAGTGA 60.602 45.455 13.08 0.00 44.44 3.41
3190 3343 5.959618 AAATGTTAGCCTTACTGTTCCAC 57.040 39.130 0.00 0.00 0.00 4.02
3211 3364 7.327975 TCCACGAATATTCACAAGTTGATAGT 58.672 34.615 15.57 0.00 32.84 2.12
3225 3378 3.992943 TGATAGTTTCAACCGGTGGAT 57.007 42.857 13.82 0.00 0.00 3.41
3247 3407 7.987458 TGGATGGAACTGTATATGTTTTCTCTC 59.013 37.037 0.00 0.00 0.00 3.20
3264 3424 9.780413 GTTTTCTCTCCTGAAATGCTATAAAAG 57.220 33.333 0.00 0.00 36.07 2.27
3312 3472 0.831307 AAGTTATCGACCAGAGGGGC 59.169 55.000 0.00 0.00 42.05 5.80
3314 3474 1.002403 TTATCGACCAGAGGGGCCA 59.998 57.895 4.39 0.00 40.10 5.36
3324 3484 4.720443 AGGGGCCAGGGGGTGATT 62.720 66.667 4.39 0.00 36.17 2.57
3327 3487 3.672503 GGCCAGGGGGTGATTGGT 61.673 66.667 0.00 0.00 36.17 3.67
3360 3527 8.740123 TTACCATTTCTTCTGAAAACACACTA 57.260 30.769 0.00 0.00 44.22 2.74
3391 3558 7.954788 AGAAAATGAGAGTGAACAGAACTAC 57.045 36.000 0.00 0.00 0.00 2.73
3392 3559 7.500992 AGAAAATGAGAGTGAACAGAACTACA 58.499 34.615 0.00 0.00 0.00 2.74
3394 3561 5.791336 ATGAGAGTGAACAGAACTACACA 57.209 39.130 0.00 0.00 35.97 3.72
3395 3562 5.592104 TGAGAGTGAACAGAACTACACAA 57.408 39.130 0.00 0.00 35.97 3.33
3396 3563 6.161855 TGAGAGTGAACAGAACTACACAAT 57.838 37.500 0.00 0.00 35.97 2.71
3397 3564 6.582636 TGAGAGTGAACAGAACTACACAATT 58.417 36.000 0.00 0.00 35.97 2.32
3398 3565 7.722363 TGAGAGTGAACAGAACTACACAATTA 58.278 34.615 0.00 0.00 35.97 1.40
3399 3566 8.367911 TGAGAGTGAACAGAACTACACAATTAT 58.632 33.333 0.00 0.00 35.97 1.28
3400 3567 9.856488 GAGAGTGAACAGAACTACACAATTATA 57.144 33.333 0.00 0.00 35.97 0.98
3401 3568 9.862371 AGAGTGAACAGAACTACACAATTATAG 57.138 33.333 0.00 0.00 35.97 1.31
3402 3569 9.088512 GAGTGAACAGAACTACACAATTATAGG 57.911 37.037 0.00 0.00 35.97 2.57
3403 3570 8.594550 AGTGAACAGAACTACACAATTATAGGT 58.405 33.333 0.00 0.00 35.97 3.08
3404 3571 9.216117 GTGAACAGAACTACACAATTATAGGTT 57.784 33.333 0.00 0.00 34.05 3.50
3405 3572 9.431887 TGAACAGAACTACACAATTATAGGTTC 57.568 33.333 0.00 0.00 0.00 3.62
3406 3573 9.654663 GAACAGAACTACACAATTATAGGTTCT 57.345 33.333 0.00 0.00 0.00 3.01
3408 3575 9.654663 ACAGAACTACACAATTATAGGTTCTTC 57.345 33.333 0.00 0.00 0.00 2.87
3409 3576 9.877178 CAGAACTACACAATTATAGGTTCTTCT 57.123 33.333 0.00 0.00 0.00 2.85
3413 3580 8.697292 ACTACACAATTATAGGTTCTTCTCTCC 58.303 37.037 0.00 0.00 0.00 3.71
3414 3581 7.496346 ACACAATTATAGGTTCTTCTCTCCA 57.504 36.000 0.00 0.00 0.00 3.86
3415 3582 8.095452 ACACAATTATAGGTTCTTCTCTCCAT 57.905 34.615 0.00 0.00 0.00 3.41
3416 3583 8.207545 ACACAATTATAGGTTCTTCTCTCCATC 58.792 37.037 0.00 0.00 0.00 3.51
3417 3584 7.383572 CACAATTATAGGTTCTTCTCTCCATCG 59.616 40.741 0.00 0.00 0.00 3.84
3418 3585 7.287927 ACAATTATAGGTTCTTCTCTCCATCGA 59.712 37.037 0.00 0.00 0.00 3.59
3419 3586 7.841282 ATTATAGGTTCTTCTCTCCATCGAA 57.159 36.000 0.00 0.00 0.00 3.71
3420 3587 7.655521 TTATAGGTTCTTCTCTCCATCGAAA 57.344 36.000 0.00 0.00 0.00 3.46
3421 3588 4.195225 AGGTTCTTCTCTCCATCGAAAC 57.805 45.455 0.00 0.00 0.00 2.78
3422 3589 3.578716 AGGTTCTTCTCTCCATCGAAACA 59.421 43.478 0.00 0.00 0.00 2.83
3423 3590 4.040461 AGGTTCTTCTCTCCATCGAAACAA 59.960 41.667 0.00 0.00 0.00 2.83
3424 3591 4.938226 GGTTCTTCTCTCCATCGAAACAAT 59.062 41.667 0.00 0.00 0.00 2.71
3425 3592 6.070767 AGGTTCTTCTCTCCATCGAAACAATA 60.071 38.462 0.00 0.00 0.00 1.90
3426 3593 6.256757 GGTTCTTCTCTCCATCGAAACAATAG 59.743 42.308 0.00 0.00 0.00 1.73
3427 3594 5.907207 TCTTCTCTCCATCGAAACAATAGG 58.093 41.667 0.00 0.00 0.00 2.57
3428 3595 4.672587 TCTCTCCATCGAAACAATAGGG 57.327 45.455 0.00 0.00 0.00 3.53
3429 3596 4.030913 TCTCTCCATCGAAACAATAGGGT 58.969 43.478 0.00 0.00 0.00 4.34
3430 3597 4.099573 TCTCTCCATCGAAACAATAGGGTC 59.900 45.833 0.00 0.00 0.00 4.46
3431 3598 3.772572 TCTCCATCGAAACAATAGGGTCA 59.227 43.478 0.00 0.00 0.00 4.02
3432 3599 4.408921 TCTCCATCGAAACAATAGGGTCAT 59.591 41.667 0.00 0.00 0.00 3.06
3433 3600 5.104527 TCTCCATCGAAACAATAGGGTCATT 60.105 40.000 0.00 0.00 0.00 2.57
3434 3601 6.099125 TCTCCATCGAAACAATAGGGTCATTA 59.901 38.462 0.00 0.00 0.00 1.90
3435 3602 6.837312 TCCATCGAAACAATAGGGTCATTAT 58.163 36.000 0.00 0.00 0.00 1.28
3436 3603 6.710295 TCCATCGAAACAATAGGGTCATTATG 59.290 38.462 0.00 0.00 0.00 1.90
3437 3604 6.373779 CATCGAAACAATAGGGTCATTATGC 58.626 40.000 0.00 0.00 0.00 3.14
3438 3605 5.680619 TCGAAACAATAGGGTCATTATGCT 58.319 37.500 0.00 0.00 0.00 3.79
3439 3606 6.119536 TCGAAACAATAGGGTCATTATGCTT 58.880 36.000 0.00 0.00 0.00 3.91
3440 3607 7.276658 TCGAAACAATAGGGTCATTATGCTTA 58.723 34.615 0.00 0.00 0.00 3.09
3441 3608 7.936847 TCGAAACAATAGGGTCATTATGCTTAT 59.063 33.333 0.00 0.00 0.00 1.73
3442 3609 8.567948 CGAAACAATAGGGTCATTATGCTTATT 58.432 33.333 0.00 0.00 0.00 1.40
3446 3613 9.507329 ACAATAGGGTCATTATGCTTATTACTG 57.493 33.333 0.00 0.00 0.00 2.74
3447 3614 9.725019 CAATAGGGTCATTATGCTTATTACTGA 57.275 33.333 0.00 0.00 0.00 3.41
3449 3616 9.726438 ATAGGGTCATTATGCTTATTACTGAAC 57.274 33.333 0.00 0.00 0.00 3.18
3450 3617 7.806180 AGGGTCATTATGCTTATTACTGAACT 58.194 34.615 0.00 0.00 0.00 3.01
3451 3618 8.275040 AGGGTCATTATGCTTATTACTGAACTT 58.725 33.333 0.00 0.00 0.00 2.66
3452 3619 8.345565 GGGTCATTATGCTTATTACTGAACTTG 58.654 37.037 0.00 0.00 0.00 3.16
3453 3620 8.893727 GGTCATTATGCTTATTACTGAACTTGT 58.106 33.333 0.00 0.00 0.00 3.16
3461 3628 9.719355 TGCTTATTACTGAACTTGTTGAATAGA 57.281 29.630 0.00 0.00 0.00 1.98
3512 3679 9.967451 TTTTATTATAGGTTGAACTGATCACCA 57.033 29.630 0.00 0.00 37.92 4.17
3514 3681 6.867519 TTATAGGTTGAACTGATCACCAGA 57.132 37.500 0.00 0.00 45.78 3.86
3515 3682 5.762179 ATAGGTTGAACTGATCACCAGAA 57.238 39.130 0.00 0.00 45.78 3.02
3516 3683 4.013267 AGGTTGAACTGATCACCAGAAG 57.987 45.455 0.00 0.00 45.78 2.85
3517 3684 3.648067 AGGTTGAACTGATCACCAGAAGA 59.352 43.478 0.00 0.00 45.78 2.87
3518 3685 4.103153 AGGTTGAACTGATCACCAGAAGAA 59.897 41.667 0.00 0.00 45.78 2.52
3519 3686 4.453819 GGTTGAACTGATCACCAGAAGAAG 59.546 45.833 0.00 0.00 45.78 2.85
3520 3687 5.300752 GTTGAACTGATCACCAGAAGAAGA 58.699 41.667 0.00 0.00 45.78 2.87
3521 3688 5.551305 TGAACTGATCACCAGAAGAAGAA 57.449 39.130 0.00 0.00 45.78 2.52
3522 3689 6.119240 TGAACTGATCACCAGAAGAAGAAT 57.881 37.500 0.00 0.00 45.78 2.40
3523 3690 6.537355 TGAACTGATCACCAGAAGAAGAATT 58.463 36.000 0.00 0.00 45.78 2.17
3524 3691 7.000472 TGAACTGATCACCAGAAGAAGAATTT 59.000 34.615 0.00 0.00 45.78 1.82
3525 3692 8.156820 TGAACTGATCACCAGAAGAAGAATTTA 58.843 33.333 0.00 0.00 45.78 1.40
3526 3693 7.913674 ACTGATCACCAGAAGAAGAATTTAC 57.086 36.000 0.00 0.00 45.78 2.01
3527 3694 6.591834 ACTGATCACCAGAAGAAGAATTTACG 59.408 38.462 0.00 0.00 45.78 3.18
3528 3695 5.351465 TGATCACCAGAAGAAGAATTTACGC 59.649 40.000 0.00 0.00 0.00 4.42
3529 3696 4.637276 TCACCAGAAGAAGAATTTACGCA 58.363 39.130 0.00 0.00 0.00 5.24
3530 3697 5.060506 TCACCAGAAGAAGAATTTACGCAA 58.939 37.500 0.00 0.00 0.00 4.85
3555 3722 8.140112 AGTACTGAACTGAGGAAATACTGAAT 57.860 34.615 0.00 0.00 36.93 2.57
3562 3729 9.841880 GAACTGAGGAAATACTGAATTTAAACC 57.158 33.333 0.00 0.00 37.93 3.27
3567 3734 8.575649 AGGAAATACTGAATTTAAACCGTCAT 57.424 30.769 0.00 0.00 37.93 3.06
3600 3767 4.037690 GCATGCGAGGCAAAACTAATAAG 58.962 43.478 0.00 0.00 43.62 1.73
3628 3798 7.777095 AGAGTCAGAACGCTAGATAGAAAAAT 58.223 34.615 0.00 0.00 33.35 1.82
3629 3799 8.904834 AGAGTCAGAACGCTAGATAGAAAAATA 58.095 33.333 0.00 0.00 33.35 1.40
3631 3801 9.303537 AGTCAGAACGCTAGATAGAAAAATAAC 57.696 33.333 0.00 0.00 0.00 1.89
3632 3802 8.541312 GTCAGAACGCTAGATAGAAAAATAACC 58.459 37.037 0.00 0.00 0.00 2.85
3633 3803 8.255206 TCAGAACGCTAGATAGAAAAATAACCA 58.745 33.333 0.00 0.00 0.00 3.67
3634 3804 8.328864 CAGAACGCTAGATAGAAAAATAACCAC 58.671 37.037 0.00 0.00 0.00 4.16
3635 3805 8.258708 AGAACGCTAGATAGAAAAATAACCACT 58.741 33.333 0.00 0.00 0.00 4.00
3636 3806 8.421673 AACGCTAGATAGAAAAATAACCACTC 57.578 34.615 0.00 0.00 0.00 3.51
3637 3807 6.985059 ACGCTAGATAGAAAAATAACCACTCC 59.015 38.462 0.00 0.00 0.00 3.85
3638 3808 6.424207 CGCTAGATAGAAAAATAACCACTCCC 59.576 42.308 0.00 0.00 0.00 4.30
3639 3809 7.510407 GCTAGATAGAAAAATAACCACTCCCT 58.490 38.462 0.00 0.00 0.00 4.20
3640 3810 8.648693 GCTAGATAGAAAAATAACCACTCCCTA 58.351 37.037 0.00 0.00 0.00 3.53
3673 3843 4.950434 AACGTTTTACATTATGGGACGG 57.050 40.909 0.00 0.00 33.74 4.79
3674 3844 4.205065 ACGTTTTACATTATGGGACGGA 57.795 40.909 13.17 0.00 33.74 4.69
3675 3845 4.186159 ACGTTTTACATTATGGGACGGAG 58.814 43.478 13.17 0.00 33.74 4.63
3676 3846 3.558418 CGTTTTACATTATGGGACGGAGG 59.442 47.826 0.00 0.00 0.00 4.30
3677 3847 3.849563 TTTACATTATGGGACGGAGGG 57.150 47.619 0.00 0.00 0.00 4.30
3678 3848 2.779429 TACATTATGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
3679 3849 1.424638 ACATTATGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
3680 3850 1.344087 ACATTATGGGACGGAGGGAGT 60.344 52.381 0.00 0.00 0.00 3.85
3681 3851 2.090943 ACATTATGGGACGGAGGGAGTA 60.091 50.000 0.00 0.00 0.00 2.59
3682 3852 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
3683 3853 0.481567 TATGGGACGGAGGGAGTAGG 59.518 60.000 0.00 0.00 0.00 3.18
3684 3854 1.591280 ATGGGACGGAGGGAGTAGGT 61.591 60.000 0.00 0.00 0.00 3.08
3685 3855 0.920763 TGGGACGGAGGGAGTAGGTA 60.921 60.000 0.00 0.00 0.00 3.08
3686 3856 0.259938 GGGACGGAGGGAGTAGGTAA 59.740 60.000 0.00 0.00 0.00 2.85
3687 3857 1.397672 GGACGGAGGGAGTAGGTAAC 58.602 60.000 0.00 0.00 0.00 2.50
3688 3858 1.341383 GGACGGAGGGAGTAGGTAACA 60.341 57.143 0.00 0.00 41.41 2.41
3689 3859 2.450476 GACGGAGGGAGTAGGTAACAA 58.550 52.381 0.00 0.00 41.41 2.83
3690 3860 3.029570 GACGGAGGGAGTAGGTAACAAT 58.970 50.000 0.00 0.00 41.41 2.71
3691 3861 4.210331 GACGGAGGGAGTAGGTAACAATA 58.790 47.826 0.00 0.00 41.41 1.90
3692 3862 3.956848 ACGGAGGGAGTAGGTAACAATAC 59.043 47.826 0.00 0.00 41.41 1.89
3693 3863 3.956199 CGGAGGGAGTAGGTAACAATACA 59.044 47.826 0.00 0.00 41.41 2.29
3694 3864 4.037684 CGGAGGGAGTAGGTAACAATACAG 59.962 50.000 0.00 0.00 41.41 2.74
3695 3865 5.206587 GGAGGGAGTAGGTAACAATACAGA 58.793 45.833 0.00 0.00 41.41 3.41
3696 3866 5.659971 GGAGGGAGTAGGTAACAATACAGAA 59.340 44.000 0.00 0.00 41.41 3.02
3697 3867 6.155737 GGAGGGAGTAGGTAACAATACAGAAA 59.844 42.308 0.00 0.00 41.41 2.52
3698 3868 6.944096 AGGGAGTAGGTAACAATACAGAAAC 58.056 40.000 0.00 0.00 41.41 2.78
3699 3869 6.499350 AGGGAGTAGGTAACAATACAGAAACA 59.501 38.462 0.00 0.00 41.41 2.83
3700 3870 6.817140 GGGAGTAGGTAACAATACAGAAACAG 59.183 42.308 0.00 0.00 41.41 3.16
3701 3871 7.384477 GGAGTAGGTAACAATACAGAAACAGT 58.616 38.462 0.00 0.00 41.41 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.417924 CCCTGAGATGGTCAAGAGTTCG 60.418 54.545 0.00 0.00 33.60 3.95
22 23 3.182152 ACTTTGTACCATCAGTAGCCCT 58.818 45.455 0.00 0.00 0.00 5.19
59 60 3.577389 GGGTCAACTTCCCATCTGG 57.423 57.895 0.00 0.00 44.05 3.86
109 110 1.040646 TTAGGAGACCTAGCCATGCG 58.959 55.000 0.00 0.00 37.42 4.73
117 118 4.399483 ACCAACTGAGTTAGGAGACCTA 57.601 45.455 16.89 0.00 34.61 3.08
127 128 2.832733 GAGTAGGCCTACCAACTGAGTT 59.167 50.000 34.54 16.26 39.06 3.01
134 135 3.912248 CCTTCTAGAGTAGGCCTACCAA 58.088 50.000 34.54 20.91 39.06 3.67
157 158 0.403655 TTGTATGCCAAGCTGGTGGA 59.596 50.000 8.71 0.00 41.65 4.02
225 226 1.261238 AAAGGGAGACGAGGCCTGAG 61.261 60.000 12.00 6.64 0.00 3.35
226 227 0.040646 TAAAGGGAGACGAGGCCTGA 59.959 55.000 12.00 0.00 0.00 3.86
268 271 6.596888 ACTGAATCTATGATTTGGTGTGTCTG 59.403 38.462 0.00 0.00 0.00 3.51
307 310 9.159254 TGAAGAGGTTACAATGGAGTATCATAT 57.841 33.333 0.00 0.00 36.25 1.78
341 344 5.717078 ATTGTGATTGATGGTATGGATGC 57.283 39.130 0.00 0.00 0.00 3.91
363 366 8.215926 AGGTAATATGTTACGCATGCTTTTAA 57.784 30.769 17.13 7.59 40.89 1.52
403 406 5.126384 CACAAAGTTTTTACCCAGGTTCAGA 59.874 40.000 0.00 0.00 0.00 3.27
405 408 4.773149 ACACAAAGTTTTTACCCAGGTTCA 59.227 37.500 0.00 0.00 0.00 3.18
430 433 3.631227 ACCGAATGTACCCGAAACAAAAA 59.369 39.130 0.00 0.00 0.00 1.94
435 438 2.083167 TGACCGAATGTACCCGAAAC 57.917 50.000 0.00 0.00 0.00 2.78
446 449 1.339920 TGGTGATGCACATGACCGAAT 60.340 47.619 13.50 0.00 46.28 3.34
457 460 5.049474 GCATTAAAGTCGATATGGTGATGCA 60.049 40.000 11.57 0.00 36.92 3.96
472 475 3.253921 GGTGTACAAACCCGCATTAAAGT 59.746 43.478 0.00 0.00 33.79 2.66
599 611 7.048512 GCTCAACCTAGGTCTACATTATTTGT 58.951 38.462 16.64 0.00 42.62 2.83
600 612 7.047891 TGCTCAACCTAGGTCTACATTATTTG 58.952 38.462 16.64 5.70 0.00 2.32
602 614 6.808321 TGCTCAACCTAGGTCTACATTATT 57.192 37.500 16.64 0.00 0.00 1.40
603 615 6.808321 TTGCTCAACCTAGGTCTACATTAT 57.192 37.500 16.64 0.00 0.00 1.28
604 616 6.614694 TTTGCTCAACCTAGGTCTACATTA 57.385 37.500 16.64 0.00 0.00 1.90
605 617 5.499004 TTTGCTCAACCTAGGTCTACATT 57.501 39.130 16.64 0.00 0.00 2.71
606 618 5.491982 CTTTTGCTCAACCTAGGTCTACAT 58.508 41.667 16.64 0.00 0.00 2.29
607 619 4.262894 CCTTTTGCTCAACCTAGGTCTACA 60.263 45.833 16.64 8.78 0.00 2.74
608 620 4.020485 TCCTTTTGCTCAACCTAGGTCTAC 60.020 45.833 16.64 6.06 0.00 2.59
609 621 4.164981 TCCTTTTGCTCAACCTAGGTCTA 58.835 43.478 16.64 5.38 0.00 2.59
610 622 2.979678 TCCTTTTGCTCAACCTAGGTCT 59.020 45.455 16.64 2.62 0.00 3.85
611 623 3.418684 TCCTTTTGCTCAACCTAGGTC 57.581 47.619 16.64 2.75 0.00 3.85
612 624 3.876309 TTCCTTTTGCTCAACCTAGGT 57.124 42.857 9.21 9.21 0.00 3.08
613 625 5.529581 TTTTTCCTTTTGCTCAACCTAGG 57.470 39.130 7.41 7.41 0.00 3.02
614 626 8.522830 TGATATTTTTCCTTTTGCTCAACCTAG 58.477 33.333 0.00 0.00 0.00 3.02
615 627 8.415950 TGATATTTTTCCTTTTGCTCAACCTA 57.584 30.769 0.00 0.00 0.00 3.08
616 628 7.233348 TCTGATATTTTTCCTTTTGCTCAACCT 59.767 33.333 0.00 0.00 0.00 3.50
617 629 7.378181 TCTGATATTTTTCCTTTTGCTCAACC 58.622 34.615 0.00 0.00 0.00 3.77
618 630 8.084684 ACTCTGATATTTTTCCTTTTGCTCAAC 58.915 33.333 0.00 0.00 0.00 3.18
619 631 8.084073 CACTCTGATATTTTTCCTTTTGCTCAA 58.916 33.333 0.00 0.00 0.00 3.02
632 644 8.463930 TTTTGTCTTGGACACTCTGATATTTT 57.536 30.769 0.00 0.00 42.60 1.82
666 681 4.213270 TCTCAAAAAGATGATTTCACGCGT 59.787 37.500 5.58 5.58 0.00 6.01
707 722 1.459592 GACGTGTGATTTCAGGGTTCG 59.540 52.381 0.00 0.00 0.00 3.95
709 724 2.631160 TGACGTGTGATTTCAGGGTT 57.369 45.000 0.00 0.00 0.00 4.11
710 725 2.631160 TTGACGTGTGATTTCAGGGT 57.369 45.000 0.00 0.00 0.00 4.34
711 726 5.353956 TGAATATTGACGTGTGATTTCAGGG 59.646 40.000 0.00 0.00 0.00 4.45
737 756 5.860716 CAGCTGAAAAGGAACAAATCTAAGC 59.139 40.000 8.42 0.00 0.00 3.09
748 767 1.888512 GCATCCACAGCTGAAAAGGAA 59.111 47.619 23.35 7.18 31.17 3.36
833 854 2.088423 TCACGGCGCTTCCATAAATTT 58.912 42.857 6.90 0.00 34.01 1.82
836 857 0.800012 GTTCACGGCGCTTCCATAAA 59.200 50.000 6.90 0.00 34.01 1.40
837 858 0.320858 TGTTCACGGCGCTTCCATAA 60.321 50.000 6.90 0.00 34.01 1.90
838 859 0.739462 CTGTTCACGGCGCTTCCATA 60.739 55.000 6.90 0.00 34.01 2.74
839 860 2.031919 TGTTCACGGCGCTTCCAT 59.968 55.556 6.90 0.00 34.01 3.41
854 905 2.282251 TCGGAGGACGTGCTCTGT 60.282 61.111 35.57 6.01 44.69 3.41
971 1066 3.827898 CGGCTGGAGAGGACGGAC 61.828 72.222 0.00 0.00 0.00 4.79
1307 1402 2.286872 AGAGCAGCACTACATTGCATC 58.713 47.619 0.00 0.00 45.62 3.91
1308 1403 2.414994 AGAGCAGCACTACATTGCAT 57.585 45.000 0.00 0.00 45.62 3.96
1348 1443 0.255890 ATTCGATCTTGGGGTGGGTG 59.744 55.000 0.00 0.00 0.00 4.61
1373 1468 1.836383 ATTCGTTATCGCGACCAGAC 58.164 50.000 12.93 6.94 40.85 3.51
1460 1555 5.434408 AGGTTGACGGAGGGAATAAATAAC 58.566 41.667 0.00 0.00 0.00 1.89
1463 1558 3.118000 GGAGGTTGACGGAGGGAATAAAT 60.118 47.826 0.00 0.00 0.00 1.40
1467 1562 1.614241 CGGAGGTTGACGGAGGGAAT 61.614 60.000 0.00 0.00 0.00 3.01
1546 1672 1.821088 ATGATAGTTGGTCCCTCCCC 58.179 55.000 0.00 0.00 34.77 4.81
1669 1797 3.426615 ACCTGTGAAATTATCGGGCAAA 58.573 40.909 0.00 0.00 0.00 3.68
1675 1803 7.713764 TCATACATGACCTGTGAAATTATCG 57.286 36.000 0.00 0.00 38.92 2.92
1691 1819 5.920840 CCGACCACTATACTTGTCATACATG 59.079 44.000 0.00 0.00 0.00 3.21
1837 1965 1.736126 CAAACGCTCACTCATGCATCT 59.264 47.619 0.00 0.00 0.00 2.90
1851 1979 3.061965 ACAATCAAAGCACAAACAAACGC 59.938 39.130 0.00 0.00 0.00 4.84
1905 2033 5.221722 TGGTAAGAAGCTCTCTGTCACATTT 60.222 40.000 0.00 0.00 33.37 2.32
1992 2120 0.882927 TCTTTGCGAGGTTCCCAACG 60.883 55.000 0.00 0.00 0.00 4.10
1998 2126 2.612212 TGTCACTTTCTTTGCGAGGTTC 59.388 45.455 0.00 0.00 0.00 3.62
2001 2129 2.599848 CGTTGTCACTTTCTTTGCGAGG 60.600 50.000 0.00 0.00 0.00 4.63
2004 2132 1.329292 TCCGTTGTCACTTTCTTTGCG 59.671 47.619 0.00 0.00 0.00 4.85
2088 2216 1.425448 CCCTTGGACTTTGGAGTTCCT 59.575 52.381 0.00 0.00 35.88 3.36
2173 2301 4.981806 TTGTGCAAAAGAAGCTTACTGT 57.018 36.364 0.00 0.00 0.00 3.55
2378 2508 5.854010 TGACCAGTAGTCTAGGCATTAAG 57.146 43.478 0.00 0.00 46.46 1.85
2473 2603 3.864921 GCGGTCTACCACTTCACTTTGAT 60.865 47.826 0.00 0.00 35.14 2.57
2565 2695 3.005261 TGTGGGACAAAATTTCATGTCGG 59.995 43.478 14.03 0.00 45.39 4.79
2566 2696 4.229096 CTGTGGGACAAAATTTCATGTCG 58.771 43.478 14.03 0.73 45.39 4.35
2567 2697 5.200368 ACTGTGGGACAAAATTTCATGTC 57.800 39.130 12.64 12.64 44.16 3.06
2733 2863 5.723887 ACAGGTGTTCTCCAAGATATTCTCT 59.276 40.000 0.00 0.00 34.96 3.10
2858 2991 6.091713 GGCTTGACAATCAAAATTCTTCCATG 59.908 38.462 0.00 0.00 35.73 3.66
2891 3024 7.094549 GGTGGTAAACAACAACTGCTTCATATA 60.095 37.037 0.00 0.00 36.56 0.86
2916 3049 7.229228 CACATGTGCAATCATTTAGAAATGG 57.771 36.000 13.94 1.45 44.51 3.16
2934 3067 1.533625 ATAAACCACGCTGCACATGT 58.466 45.000 0.00 0.00 0.00 3.21
2939 3072 1.890876 AGTGAATAAACCACGCTGCA 58.109 45.000 0.00 0.00 39.38 4.41
2945 3078 7.544217 ACTTCAACAACAAAGTGAATAAACCAC 59.456 33.333 0.00 0.00 34.52 4.16
2969 3102 6.650390 GGAAACCATACAATTTGATGCAAACT 59.350 34.615 2.79 0.00 36.13 2.66
2989 3135 7.770801 AAAATAAAACACTCTTGCTGGAAAC 57.229 32.000 0.00 0.00 0.00 2.78
2994 3140 7.706179 TCCTTGAAAAATAAAACACTCTTGCTG 59.294 33.333 0.00 0.00 0.00 4.41
3002 3154 8.077386 TGGACGTATCCTTGAAAAATAAAACAC 58.923 33.333 0.00 0.00 46.43 3.32
3003 3155 8.167605 TGGACGTATCCTTGAAAAATAAAACA 57.832 30.769 0.00 0.00 46.43 2.83
3052 3204 2.872028 GCAAAACGGTCTTGCTGTG 58.128 52.632 11.76 0.00 44.66 3.66
3076 3228 6.757897 ATTCAAAAGCTAAATCGTGGATCA 57.242 33.333 0.00 0.00 0.00 2.92
3080 3233 4.262976 GCGAATTCAAAAGCTAAATCGTGG 59.737 41.667 6.22 0.00 0.00 4.94
3083 3236 5.738693 TCATGCGAATTCAAAAGCTAAATCG 59.261 36.000 6.22 0.97 0.00 3.34
3100 3253 1.280982 GAAAGCGTCTCATCATGCGA 58.719 50.000 0.00 0.00 33.13 5.10
3104 3257 4.025015 GCATTTGAAAGCGTCTCATCAT 57.975 40.909 0.00 0.00 0.00 2.45
3181 3334 5.305585 ACTTGTGAATATTCGTGGAACAGT 58.694 37.500 10.80 6.57 41.80 3.55
3182 3335 5.862924 ACTTGTGAATATTCGTGGAACAG 57.137 39.130 10.80 6.07 41.80 3.16
3183 3336 5.760743 TCAACTTGTGAATATTCGTGGAACA 59.239 36.000 10.80 6.26 30.82 3.18
3188 3341 9.478019 GAAACTATCAACTTGTGAATATTCGTG 57.522 33.333 10.80 3.68 40.50 4.35
3189 3342 9.214957 TGAAACTATCAACTTGTGAATATTCGT 57.785 29.630 10.80 0.00 40.50 3.85
3211 3364 1.144093 AGTTCCATCCACCGGTTGAAA 59.856 47.619 13.02 0.00 0.00 2.69
3219 3372 6.828785 AGAAAACATATACAGTTCCATCCACC 59.171 38.462 0.00 0.00 0.00 4.61
3225 3378 7.180229 TCAGGAGAGAAAACATATACAGTTCCA 59.820 37.037 0.00 0.00 0.00 3.53
3247 3407 5.888161 AGGTGTCCTTTTATAGCATTTCAGG 59.112 40.000 0.00 0.00 0.00 3.86
3281 3441 5.163457 TGGTCGATAACTTGATGCTACATGA 60.163 40.000 0.00 0.00 0.00 3.07
3282 3442 5.049828 TGGTCGATAACTTGATGCTACATG 58.950 41.667 0.00 0.00 0.00 3.21
3312 3472 1.522900 ATCTACCAATCACCCCCTGG 58.477 55.000 0.00 0.00 36.24 4.45
3314 3474 4.692523 AAAAATCTACCAATCACCCCCT 57.307 40.909 0.00 0.00 0.00 4.79
3336 3502 8.740123 TTAGTGTGTTTTCAGAAGAAATGGTA 57.260 30.769 0.00 0.00 42.90 3.25
3348 3514 6.928979 TTTCTTCGGATTAGTGTGTTTTCA 57.071 33.333 0.00 0.00 0.00 2.69
3357 3524 6.936279 TCACTCTCATTTTCTTCGGATTAGT 58.064 36.000 0.00 0.00 0.00 2.24
3360 3527 5.997746 TGTTCACTCTCATTTTCTTCGGATT 59.002 36.000 0.00 0.00 0.00 3.01
3391 3558 7.383572 CGATGGAGAGAAGAACCTATAATTGTG 59.616 40.741 0.00 0.00 0.00 3.33
3392 3559 7.287927 TCGATGGAGAGAAGAACCTATAATTGT 59.712 37.037 0.00 0.00 0.00 2.71
3394 3561 7.841282 TCGATGGAGAGAAGAACCTATAATT 57.159 36.000 0.00 0.00 0.00 1.40
3395 3562 7.841282 TTCGATGGAGAGAAGAACCTATAAT 57.159 36.000 0.00 0.00 0.00 1.28
3396 3563 7.123697 TGTTTCGATGGAGAGAAGAACCTATAA 59.876 37.037 0.00 0.00 0.00 0.98
3397 3564 6.605995 TGTTTCGATGGAGAGAAGAACCTATA 59.394 38.462 0.00 0.00 0.00 1.31
3398 3565 5.422331 TGTTTCGATGGAGAGAAGAACCTAT 59.578 40.000 0.00 0.00 0.00 2.57
3399 3566 4.770531 TGTTTCGATGGAGAGAAGAACCTA 59.229 41.667 0.00 0.00 0.00 3.08
3400 3567 3.578716 TGTTTCGATGGAGAGAAGAACCT 59.421 43.478 0.00 0.00 0.00 3.50
3401 3568 3.926616 TGTTTCGATGGAGAGAAGAACC 58.073 45.455 0.00 0.00 0.00 3.62
3402 3569 6.256757 CCTATTGTTTCGATGGAGAGAAGAAC 59.743 42.308 0.00 0.00 0.00 3.01
3403 3570 6.341316 CCTATTGTTTCGATGGAGAGAAGAA 58.659 40.000 0.00 0.00 0.00 2.52
3404 3571 5.163405 CCCTATTGTTTCGATGGAGAGAAGA 60.163 44.000 0.00 0.00 0.00 2.87
3405 3572 5.053145 CCCTATTGTTTCGATGGAGAGAAG 58.947 45.833 0.00 0.00 0.00 2.85
3406 3573 4.469945 ACCCTATTGTTTCGATGGAGAGAA 59.530 41.667 0.00 0.00 0.00 2.87
3407 3574 4.030913 ACCCTATTGTTTCGATGGAGAGA 58.969 43.478 0.00 0.00 0.00 3.10
3408 3575 4.141937 TGACCCTATTGTTTCGATGGAGAG 60.142 45.833 0.00 0.00 0.00 3.20
3409 3576 3.772572 TGACCCTATTGTTTCGATGGAGA 59.227 43.478 0.00 0.00 0.00 3.71
3410 3577 4.137116 TGACCCTATTGTTTCGATGGAG 57.863 45.455 0.00 0.00 0.00 3.86
3411 3578 4.771114 ATGACCCTATTGTTTCGATGGA 57.229 40.909 0.00 0.00 0.00 3.41
3412 3579 6.568462 GCATAATGACCCTATTGTTTCGATGG 60.568 42.308 0.00 0.00 0.00 3.51
3413 3580 6.205464 AGCATAATGACCCTATTGTTTCGATG 59.795 38.462 0.00 0.00 0.00 3.84
3414 3581 6.299141 AGCATAATGACCCTATTGTTTCGAT 58.701 36.000 0.00 0.00 0.00 3.59
3415 3582 5.680619 AGCATAATGACCCTATTGTTTCGA 58.319 37.500 0.00 0.00 0.00 3.71
3416 3583 6.377327 AAGCATAATGACCCTATTGTTTCG 57.623 37.500 0.00 0.00 0.00 3.46
3420 3587 9.507329 CAGTAATAAGCATAATGACCCTATTGT 57.493 33.333 0.00 0.00 0.00 2.71
3421 3588 9.725019 TCAGTAATAAGCATAATGACCCTATTG 57.275 33.333 0.00 0.00 0.00 1.90
3423 3590 9.726438 GTTCAGTAATAAGCATAATGACCCTAT 57.274 33.333 0.00 0.00 28.18 2.57
3424 3591 8.934697 AGTTCAGTAATAAGCATAATGACCCTA 58.065 33.333 0.00 0.00 28.18 3.53
3425 3592 7.806180 AGTTCAGTAATAAGCATAATGACCCT 58.194 34.615 0.00 0.00 28.18 4.34
3426 3593 8.345565 CAAGTTCAGTAATAAGCATAATGACCC 58.654 37.037 0.00 0.00 28.18 4.46
3427 3594 8.893727 ACAAGTTCAGTAATAAGCATAATGACC 58.106 33.333 0.00 0.00 28.18 4.02
3435 3602 9.719355 TCTATTCAACAAGTTCAGTAATAAGCA 57.281 29.630 0.00 0.00 0.00 3.91
3486 3653 9.967451 TGGTGATCAGTTCAACCTATAATAAAA 57.033 29.630 0.00 0.00 41.74 1.52
3487 3654 9.613428 CTGGTGATCAGTTCAACCTATAATAAA 57.387 33.333 0.00 0.00 41.74 1.40
3488 3655 8.988060 TCTGGTGATCAGTTCAACCTATAATAA 58.012 33.333 0.00 0.00 41.74 1.40
3489 3656 8.547481 TCTGGTGATCAGTTCAACCTATAATA 57.453 34.615 0.00 0.00 41.74 0.98
3490 3657 7.437713 TCTGGTGATCAGTTCAACCTATAAT 57.562 36.000 0.00 0.00 41.74 1.28
3491 3658 6.867519 TCTGGTGATCAGTTCAACCTATAA 57.132 37.500 0.00 0.00 41.74 0.98
3492 3659 6.667848 TCTTCTGGTGATCAGTTCAACCTATA 59.332 38.462 0.00 0.00 41.74 1.31
3493 3660 5.485353 TCTTCTGGTGATCAGTTCAACCTAT 59.515 40.000 0.00 0.00 41.74 2.57
3494 3661 4.838423 TCTTCTGGTGATCAGTTCAACCTA 59.162 41.667 0.00 0.00 41.74 3.08
3495 3662 3.648067 TCTTCTGGTGATCAGTTCAACCT 59.352 43.478 0.00 0.00 41.74 3.50
3496 3663 4.008074 TCTTCTGGTGATCAGTTCAACC 57.992 45.455 0.00 0.00 41.74 3.77
3497 3664 5.300752 TCTTCTTCTGGTGATCAGTTCAAC 58.699 41.667 0.00 0.00 42.83 3.18
3498 3665 5.551305 TCTTCTTCTGGTGATCAGTTCAA 57.449 39.130 0.00 0.00 43.76 2.69
3499 3666 5.551305 TTCTTCTTCTGGTGATCAGTTCA 57.449 39.130 0.00 0.00 43.76 3.18
3500 3667 7.446001 AAATTCTTCTTCTGGTGATCAGTTC 57.554 36.000 0.00 0.00 43.76 3.01
3501 3668 7.118390 CGTAAATTCTTCTTCTGGTGATCAGTT 59.882 37.037 0.00 0.00 43.76 3.16
3502 3669 6.591834 CGTAAATTCTTCTTCTGGTGATCAGT 59.408 38.462 0.00 0.00 43.76 3.41
3503 3670 6.456181 GCGTAAATTCTTCTTCTGGTGATCAG 60.456 42.308 0.00 0.00 44.68 2.90
3504 3671 5.351465 GCGTAAATTCTTCTTCTGGTGATCA 59.649 40.000 0.00 0.00 0.00 2.92
3505 3672 5.351465 TGCGTAAATTCTTCTTCTGGTGATC 59.649 40.000 0.00 0.00 0.00 2.92
3506 3673 5.245531 TGCGTAAATTCTTCTTCTGGTGAT 58.754 37.500 0.00 0.00 0.00 3.06
3507 3674 4.637276 TGCGTAAATTCTTCTTCTGGTGA 58.363 39.130 0.00 0.00 0.00 4.02
3508 3675 5.049405 ACTTGCGTAAATTCTTCTTCTGGTG 60.049 40.000 0.00 0.00 0.00 4.17
3509 3676 5.063880 ACTTGCGTAAATTCTTCTTCTGGT 58.936 37.500 0.00 0.00 0.00 4.00
3510 3677 5.613358 ACTTGCGTAAATTCTTCTTCTGG 57.387 39.130 0.00 0.00 0.00 3.86
3511 3678 7.116376 TCAGTACTTGCGTAAATTCTTCTTCTG 59.884 37.037 0.00 0.00 0.00 3.02
3512 3679 7.152645 TCAGTACTTGCGTAAATTCTTCTTCT 58.847 34.615 0.00 0.00 0.00 2.85
3513 3680 7.347508 TCAGTACTTGCGTAAATTCTTCTTC 57.652 36.000 0.00 0.00 0.00 2.87
3514 3681 7.441458 AGTTCAGTACTTGCGTAAATTCTTCTT 59.559 33.333 0.00 0.00 31.29 2.52
3515 3682 6.929606 AGTTCAGTACTTGCGTAAATTCTTCT 59.070 34.615 0.00 0.00 31.29 2.85
3516 3683 7.010023 CAGTTCAGTACTTGCGTAAATTCTTC 58.990 38.462 0.00 0.00 33.85 2.87
3517 3684 6.704493 TCAGTTCAGTACTTGCGTAAATTCTT 59.296 34.615 0.00 0.00 33.85 2.52
3518 3685 6.220930 TCAGTTCAGTACTTGCGTAAATTCT 58.779 36.000 0.00 0.00 33.85 2.40
3519 3686 6.401153 CCTCAGTTCAGTACTTGCGTAAATTC 60.401 42.308 0.00 0.00 33.85 2.17
3520 3687 5.408604 CCTCAGTTCAGTACTTGCGTAAATT 59.591 40.000 0.00 0.00 33.85 1.82
3521 3688 4.929808 CCTCAGTTCAGTACTTGCGTAAAT 59.070 41.667 0.00 0.00 33.85 1.40
3522 3689 4.038282 TCCTCAGTTCAGTACTTGCGTAAA 59.962 41.667 0.00 0.00 33.85 2.01
3523 3690 3.570975 TCCTCAGTTCAGTACTTGCGTAA 59.429 43.478 0.00 0.00 33.85 3.18
3524 3691 3.151554 TCCTCAGTTCAGTACTTGCGTA 58.848 45.455 0.00 0.00 33.85 4.42
3525 3692 1.961394 TCCTCAGTTCAGTACTTGCGT 59.039 47.619 0.00 0.00 33.85 5.24
3526 3693 2.724977 TCCTCAGTTCAGTACTTGCG 57.275 50.000 0.00 0.00 33.85 4.85
3527 3694 6.091441 CAGTATTTCCTCAGTTCAGTACTTGC 59.909 42.308 0.00 0.00 33.85 4.01
3528 3695 7.378966 TCAGTATTTCCTCAGTTCAGTACTTG 58.621 38.462 0.00 0.00 33.85 3.16
3529 3696 7.540474 TCAGTATTTCCTCAGTTCAGTACTT 57.460 36.000 0.00 0.00 33.85 2.24
3530 3697 7.540474 TTCAGTATTTCCTCAGTTCAGTACT 57.460 36.000 0.00 0.00 37.68 2.73
3531 3698 8.779354 AATTCAGTATTTCCTCAGTTCAGTAC 57.221 34.615 0.00 0.00 0.00 2.73
3533 3700 9.793259 TTAAATTCAGTATTTCCTCAGTTCAGT 57.207 29.630 0.00 0.00 37.60 3.41
3536 3703 9.841880 GGTTTAAATTCAGTATTTCCTCAGTTC 57.158 33.333 0.00 0.00 37.60 3.01
3537 3704 8.512138 CGGTTTAAATTCAGTATTTCCTCAGTT 58.488 33.333 0.00 0.00 37.60 3.16
3538 3705 7.664318 ACGGTTTAAATTCAGTATTTCCTCAGT 59.336 33.333 0.00 0.00 37.60 3.41
3539 3706 8.040716 ACGGTTTAAATTCAGTATTTCCTCAG 57.959 34.615 0.00 0.00 37.60 3.35
3540 3707 7.662258 TGACGGTTTAAATTCAGTATTTCCTCA 59.338 33.333 0.00 0.00 37.60 3.86
3541 3708 8.036273 TGACGGTTTAAATTCAGTATTTCCTC 57.964 34.615 0.00 0.00 37.60 3.71
3542 3709 7.989416 TGACGGTTTAAATTCAGTATTTCCT 57.011 32.000 0.00 0.00 37.60 3.36
3555 3722 8.380743 TGCTTCTAAGTTTATGACGGTTTAAA 57.619 30.769 0.00 0.00 0.00 1.52
3562 3729 4.267690 TCGCATGCTTCTAAGTTTATGACG 59.732 41.667 17.13 0.00 0.00 4.35
3567 3734 2.936498 GCCTCGCATGCTTCTAAGTTTA 59.064 45.455 17.13 0.00 0.00 2.01
3600 3767 4.992319 TCTATCTAGCGTTCTGACTCTAGC 59.008 45.833 0.04 0.00 39.78 3.42
3649 3819 6.016443 TCCGTCCCATAATGTAAAACGTTTTT 60.016 34.615 29.42 15.16 0.00 1.94
3650 3820 5.472820 TCCGTCCCATAATGTAAAACGTTTT 59.527 36.000 27.65 27.65 0.00 2.43
3651 3821 5.002516 TCCGTCCCATAATGTAAAACGTTT 58.997 37.500 7.96 7.96 0.00 3.60
3652 3822 4.577875 TCCGTCCCATAATGTAAAACGTT 58.422 39.130 0.00 0.00 0.00 3.99
3653 3823 4.186159 CTCCGTCCCATAATGTAAAACGT 58.814 43.478 0.00 0.00 0.00 3.99
3654 3824 3.558418 CCTCCGTCCCATAATGTAAAACG 59.442 47.826 0.00 0.00 0.00 3.60
3655 3825 3.881089 CCCTCCGTCCCATAATGTAAAAC 59.119 47.826 0.00 0.00 0.00 2.43
3656 3826 3.781407 TCCCTCCGTCCCATAATGTAAAA 59.219 43.478 0.00 0.00 0.00 1.52
3657 3827 3.386063 TCCCTCCGTCCCATAATGTAAA 58.614 45.455 0.00 0.00 0.00 2.01
3658 3828 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
3659 3829 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
3660 3830 1.344087 ACTCCCTCCGTCCCATAATGT 60.344 52.381 0.00 0.00 0.00 2.71
3661 3831 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
3662 3832 2.492940 CCTACTCCCTCCGTCCCATAAT 60.493 54.545 0.00 0.00 0.00 1.28
3663 3833 1.133262 CCTACTCCCTCCGTCCCATAA 60.133 57.143 0.00 0.00 0.00 1.90
3664 3834 0.481567 CCTACTCCCTCCGTCCCATA 59.518 60.000 0.00 0.00 0.00 2.74
3665 3835 1.233369 CCTACTCCCTCCGTCCCAT 59.767 63.158 0.00 0.00 0.00 4.00
3666 3836 0.920763 TACCTACTCCCTCCGTCCCA 60.921 60.000 0.00 0.00 0.00 4.37
3667 3837 0.259938 TTACCTACTCCCTCCGTCCC 59.740 60.000 0.00 0.00 0.00 4.46
3668 3838 1.341383 TGTTACCTACTCCCTCCGTCC 60.341 57.143 0.00 0.00 0.00 4.79
3669 3839 2.134789 TGTTACCTACTCCCTCCGTC 57.865 55.000 0.00 0.00 0.00 4.79
3670 3840 2.610438 TTGTTACCTACTCCCTCCGT 57.390 50.000 0.00 0.00 0.00 4.69
3671 3841 3.956199 TGTATTGTTACCTACTCCCTCCG 59.044 47.826 0.00 0.00 0.00 4.63
3672 3842 5.206587 TCTGTATTGTTACCTACTCCCTCC 58.793 45.833 0.00 0.00 0.00 4.30
3673 3843 6.786967 TTCTGTATTGTTACCTACTCCCTC 57.213 41.667 0.00 0.00 0.00 4.30
3674 3844 6.499350 TGTTTCTGTATTGTTACCTACTCCCT 59.501 38.462 0.00 0.00 0.00 4.20
3675 3845 6.704310 TGTTTCTGTATTGTTACCTACTCCC 58.296 40.000 0.00 0.00 0.00 4.30
3676 3846 7.384477 ACTGTTTCTGTATTGTTACCTACTCC 58.616 38.462 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.