Multiple sequence alignment - TraesCS6A01G242700

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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 TraesCS6A01G242700 chr6A 100.000 3608 0 0 1 3608 454545362 454548969 0.000000e+00 6663.0
1 TraesCS6A01G242700 chr6D 95.234 2287 59 14 647 2911 316563871 316566129 0.000000e+00 3574.0
2 TraesCS6A01G242700 chr6D 94.015 518 27 2 137 650 316563326 316563843 0.000000e+00 782.0
3 TraesCS6A01G242700 chr6D 89.677 465 34 8 2986 3440 316566126 316566586 6.720000e-162 580.0
4 TraesCS6A01G242700 chr6D 90.769 65 4 2 2913 2977 267524392 267524330 6.420000e-13 86.1
5 TraesCS6A01G242700 chr6B 94.510 2277 77 24 647 2911 507796317 507794077 0.000000e+00 3469.0
6 TraesCS6A01G242700 chr6B 94.432 431 18 5 2986 3412 507794080 507793652 0.000000e+00 658.0
7 TraesCS6A01G242700 chr6B 89.362 517 31 11 143 650 507796846 507796345 2.360000e-176 628.0
8 TraesCS6A01G242700 chr7D 87.719 114 14 0 32 145 595590530 595590643 2.260000e-27 134.0
9 TraesCS6A01G242700 chr7D 87.931 58 7 0 3473 3530 412101586 412101643 6.460000e-08 69.4
10 TraesCS6A01G242700 chr1A 85.965 114 15 1 31 144 474770437 474770325 1.760000e-23 121.0
11 TraesCS6A01G242700 chr3A 87.500 96 11 1 32 127 158592630 158592536 3.810000e-20 110.0
12 TraesCS6A01G242700 chr3A 91.071 56 5 0 3477 3532 652579679 652579624 3.860000e-10 76.8
13 TraesCS6A01G242700 chr2A 81.897 116 20 1 32 147 226459584 226459470 2.970000e-16 97.1
14 TraesCS6A01G242700 chr2A 82.979 94 16 0 3444 3537 21236625 21236718 6.420000e-13 86.1
15 TraesCS6A01G242700 chr2A 80.460 87 17 0 3446 3532 631797235 631797149 2.320000e-07 67.6
16 TraesCS6A01G242700 chr3D 85.882 85 12 0 3446 3530 140523648 140523564 1.380000e-14 91.6
17 TraesCS6A01G242700 chr3D 96.970 33 1 0 1734 1766 351287637 351287669 5.030000e-04 56.5
18 TraesCS6A01G242700 chr3B 89.706 68 7 0 3463 3530 398630018 398629951 1.780000e-13 87.9
19 TraesCS6A01G242700 chr3B 89.231 65 4 3 2913 2977 128675169 128675108 1.070000e-10 78.7
20 TraesCS6A01G242700 chr3B 100.000 34 0 0 3498 3531 10104215 10104248 3.010000e-06 63.9
21 TraesCS6A01G242700 chr1B 92.063 63 4 1 2916 2978 220741188 220741249 1.780000e-13 87.9
22 TraesCS6A01G242700 chr1B 89.552 67 6 1 2912 2978 657164316 657164381 2.310000e-12 84.2
23 TraesCS6A01G242700 chr4D 84.884 86 12 1 3446 3530 134688688 134688603 6.420000e-13 86.1
24 TraesCS6A01G242700 chr7A 89.394 66 5 2 2913 2978 549866242 549866305 8.300000e-12 82.4
25 TraesCS6A01G242700 chr7A 100.000 28 0 0 1 28 7704957 7704930 7.000000e-03 52.8
26 TraesCS6A01G242700 chr2D 90.476 63 4 2 2915 2977 117240185 117240245 8.300000e-12 82.4
27 TraesCS6A01G242700 chr2D 89.231 65 4 3 2913 2977 380976265 380976326 1.070000e-10 78.7
28 TraesCS6A01G242700 chr2D 100.000 35 0 0 32 66 388057568 388057602 8.360000e-07 65.8
29 TraesCS6A01G242700 chr7B 89.062 64 5 2 2915 2978 235838926 235838987 1.070000e-10 78.7
30 TraesCS6A01G242700 chr2B 89.231 65 4 3 2914 2978 544489330 544489391 1.070000e-10 78.7
31 TraesCS6A01G242700 chr5D 97.222 36 1 0 3495 3530 478209328 478209363 1.080000e-05 62.1


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 TraesCS6A01G242700 chr6A 454545362 454548969 3607 False 6663.000000 6663 100.000000 1 3608 1 chr6A.!!$F1 3607
1 TraesCS6A01G242700 chr6D 316563326 316566586 3260 False 1645.333333 3574 92.975333 137 3440 3 chr6D.!!$F1 3303
2 TraesCS6A01G242700 chr6B 507793652 507796846 3194 True 1585.000000 3469 92.768000 143 3412 3 chr6B.!!$R1 3269

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
38 39 0.108281 GAGGGAGGGCGTTTGTAGTC 60.108 60.000 0.00 0.00 0.00 2.59 F
45 46 0.109781 GGCGTTTGTAGTCGTCGGTA 60.110 55.000 0.00 0.00 0.00 4.02 F
346 351 0.659427 TTAGTATCGTCCGCGGTCAG 59.341 55.000 27.15 17.35 38.89 3.51 F
939 1007 2.552819 TAGCTCGGAATCGGAGGCG 61.553 63.158 17.59 0.00 36.95 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1941 2009 1.135053 GTCTTGTAGAGGCTCCGGAAC 60.135 57.143 11.71 0.0 0.00 3.62 R
1998 2066 1.226717 GCGTCTCACCTCGTCCATC 60.227 63.158 0.00 0.0 0.00 3.51 R
2196 2264 2.359230 ACCTTGCCGCTCTGCTTC 60.359 61.111 0.00 0.0 0.00 3.86 R
2824 2892 2.103042 GTAGGAGGCAGCGCAGTTG 61.103 63.158 11.47 0.0 43.28 3.16 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
17 18 4.206697 AATTTTGCCCGGCTCCAA 57.793 50.000 11.61 0.89 0.00 3.53
18 19 1.671166 AATTTTGCCCGGCTCCAAC 59.329 52.632 11.61 0.00 0.00 3.77
19 20 2.153547 AATTTTGCCCGGCTCCAACG 62.154 55.000 11.61 0.00 0.00 4.10
20 21 3.776347 TTTTGCCCGGCTCCAACGA 62.776 57.895 11.61 0.00 0.00 3.85
21 22 4.697756 TTGCCCGGCTCCAACGAG 62.698 66.667 11.61 0.00 39.33 4.18
34 35 3.239253 ACGAGGGAGGGCGTTTGT 61.239 61.111 0.00 0.00 37.48 2.83
35 36 1.909781 ACGAGGGAGGGCGTTTGTA 60.910 57.895 0.00 0.00 37.48 2.41
36 37 1.153628 CGAGGGAGGGCGTTTGTAG 60.154 63.158 0.00 0.00 0.00 2.74
37 38 1.885163 CGAGGGAGGGCGTTTGTAGT 61.885 60.000 0.00 0.00 0.00 2.73
38 39 0.108281 GAGGGAGGGCGTTTGTAGTC 60.108 60.000 0.00 0.00 0.00 2.59
39 40 1.447314 GGGAGGGCGTTTGTAGTCG 60.447 63.158 0.00 0.00 0.00 4.18
40 41 1.291272 GGAGGGCGTTTGTAGTCGT 59.709 57.895 0.00 0.00 0.00 4.34
41 42 0.735287 GGAGGGCGTTTGTAGTCGTC 60.735 60.000 0.00 0.00 0.00 4.20
42 43 1.069378 GAGGGCGTTTGTAGTCGTCG 61.069 60.000 0.00 0.00 32.22 5.12
43 44 2.090524 GGGCGTTTGTAGTCGTCGG 61.091 63.158 0.00 0.00 32.22 4.79
44 45 1.372128 GGCGTTTGTAGTCGTCGGT 60.372 57.895 0.00 0.00 0.00 4.69
45 46 0.109781 GGCGTTTGTAGTCGTCGGTA 60.110 55.000 0.00 0.00 0.00 4.02
46 47 1.253999 GCGTTTGTAGTCGTCGGTAG 58.746 55.000 0.00 0.00 0.00 3.18
47 48 1.135972 GCGTTTGTAGTCGTCGGTAGA 60.136 52.381 0.00 0.00 0.00 2.59
48 49 2.476854 GCGTTTGTAGTCGTCGGTAGAT 60.477 50.000 0.00 0.00 0.00 1.98
49 50 3.096461 CGTTTGTAGTCGTCGGTAGATG 58.904 50.000 0.00 0.00 34.75 2.90
50 51 3.432782 GTTTGTAGTCGTCGGTAGATGG 58.567 50.000 0.00 0.00 34.23 3.51
51 52 2.408271 TGTAGTCGTCGGTAGATGGT 57.592 50.000 0.00 0.00 34.23 3.55
52 53 2.283298 TGTAGTCGTCGGTAGATGGTC 58.717 52.381 0.00 0.00 34.23 4.02
53 54 2.093288 TGTAGTCGTCGGTAGATGGTCT 60.093 50.000 0.00 0.00 34.23 3.85
54 55 2.996249 AGTCGTCGGTAGATGGTCTA 57.004 50.000 0.00 0.00 34.23 2.59
55 56 2.559440 AGTCGTCGGTAGATGGTCTAC 58.441 52.381 8.29 8.29 46.50 2.59
73 74 6.837471 GTCTACGGACCTGGATCTAATATT 57.163 41.667 0.00 0.00 36.53 1.28
74 75 7.229581 GTCTACGGACCTGGATCTAATATTT 57.770 40.000 0.00 0.00 36.53 1.40
75 76 8.345724 GTCTACGGACCTGGATCTAATATTTA 57.654 38.462 0.00 0.00 36.53 1.40
76 77 8.968969 GTCTACGGACCTGGATCTAATATTTAT 58.031 37.037 0.00 0.00 36.53 1.40
77 78 9.543231 TCTACGGACCTGGATCTAATATTTATT 57.457 33.333 0.00 0.00 0.00 1.40
265 270 6.550108 AGAGATATACACACGGTAGGTTTGAT 59.450 38.462 0.00 0.00 34.92 2.57
276 281 7.148590 ACACGGTAGGTTTGATTAACGAATTAC 60.149 37.037 0.00 0.00 37.64 1.89
330 335 1.918609 GCTTTGTCGCGGACTAGTTAG 59.081 52.381 6.13 0.00 33.15 2.34
333 338 4.732938 GCTTTGTCGCGGACTAGTTAGTAT 60.733 45.833 6.13 0.00 36.50 2.12
335 340 2.541346 TGTCGCGGACTAGTTAGTATCG 59.459 50.000 6.13 8.98 36.50 2.92
346 351 0.659427 TTAGTATCGTCCGCGGTCAG 59.341 55.000 27.15 17.35 38.89 3.51
382 390 3.543537 CGGGAGGAGGAGGTCATG 58.456 66.667 0.00 0.00 0.00 3.07
472 480 7.332182 AGGAAGCTCGACAAATACTAAAAGAAG 59.668 37.037 0.00 0.00 0.00 2.85
586 594 6.294620 GCCTAATCGCCATTAGACTAGTACTT 60.295 42.308 12.14 0.00 43.07 2.24
913 981 3.681897 GTGTCTGTCATCTCGCTTCATTT 59.318 43.478 0.00 0.00 0.00 2.32
915 983 4.180057 GTCTGTCATCTCGCTTCATTTCT 58.820 43.478 0.00 0.00 0.00 2.52
917 985 5.458452 GTCTGTCATCTCGCTTCATTTCTAG 59.542 44.000 0.00 0.00 0.00 2.43
918 986 5.126222 TCTGTCATCTCGCTTCATTTCTAGT 59.874 40.000 0.00 0.00 0.00 2.57
919 987 5.344066 TGTCATCTCGCTTCATTTCTAGTC 58.656 41.667 0.00 0.00 0.00 2.59
939 1007 2.552819 TAGCTCGGAATCGGAGGCG 61.553 63.158 17.59 0.00 36.95 5.52
941 1009 4.951963 CTCGGAATCGGAGGCGCC 62.952 72.222 21.89 21.89 36.95 6.53
981 1049 7.386299 GTGATCCTGCTACAGAATTATAACCTG 59.614 40.741 12.62 12.62 32.44 4.00
1869 1937 4.742201 GAGAACCTGCGCGCCTCA 62.742 66.667 30.77 9.42 0.00 3.86
2196 2264 2.551270 GCGTTCGTGGACAAGCTG 59.449 61.111 0.00 0.00 0.00 4.24
2618 2686 1.296867 CGTCATGACCAAATCGCGC 60.297 57.895 20.03 0.00 0.00 6.86
2627 2695 3.057876 TGACCAAATCGCGCAGTAAATTT 60.058 39.130 8.75 0.00 0.00 1.82
2674 2742 1.359459 CTTTCGTTAGTCGGCAGGGC 61.359 60.000 0.00 0.00 40.32 5.19
2711 2779 8.481132 GAAAATATCTCATTTCCATCGTTTCG 57.519 34.615 0.00 0.00 30.98 3.46
2712 2780 7.553881 AAATATCTCATTTCCATCGTTTCGT 57.446 32.000 0.00 0.00 0.00 3.85
2781 2849 3.060272 CGTGACATAATTGATCAGGCGAC 60.060 47.826 0.00 0.00 0.00 5.19
2822 2890 3.932089 ACAATGTTTTGTTCACCACTTGC 59.068 39.130 0.00 0.00 43.57 4.01
2823 2891 2.270275 TGTTTTGTTCACCACTTGCG 57.730 45.000 0.00 0.00 0.00 4.85
2824 2892 0.920664 GTTTTGTTCACCACTTGCGC 59.079 50.000 0.00 0.00 0.00 6.09
2825 2893 0.528017 TTTTGTTCACCACTTGCGCA 59.472 45.000 5.66 5.66 0.00 6.09
2826 2894 0.528017 TTTGTTCACCACTTGCGCAA 59.472 45.000 23.48 23.48 0.00 4.85
2827 2895 0.179150 TTGTTCACCACTTGCGCAAC 60.179 50.000 21.02 8.31 0.00 4.17
2828 2896 1.029408 TGTTCACCACTTGCGCAACT 61.029 50.000 21.02 7.73 0.00 3.16
2829 2897 0.592247 GTTCACCACTTGCGCAACTG 60.592 55.000 21.02 19.93 0.00 3.16
2851 2919 1.115467 CTGCCTCCTACTCGTTCCAT 58.885 55.000 0.00 0.00 0.00 3.41
2907 2975 3.664107 CATTCTCCAAAACAGAGACCGA 58.336 45.455 0.00 0.00 40.05 4.69
2908 2976 4.256920 CATTCTCCAAAACAGAGACCGAT 58.743 43.478 0.00 0.00 40.05 4.18
2909 2977 4.351874 TTCTCCAAAACAGAGACCGATT 57.648 40.909 0.00 0.00 40.05 3.34
2910 2978 3.926616 TCTCCAAAACAGAGACCGATTC 58.073 45.455 0.00 0.00 35.46 2.52
2911 2979 3.578716 TCTCCAAAACAGAGACCGATTCT 59.421 43.478 0.00 0.00 35.46 2.40
2912 2980 4.040461 TCTCCAAAACAGAGACCGATTCTT 59.960 41.667 0.00 0.00 35.46 2.52
2913 2981 4.714632 TCCAAAACAGAGACCGATTCTTT 58.285 39.130 0.00 0.00 33.22 2.52
2914 2982 5.130350 TCCAAAACAGAGACCGATTCTTTT 58.870 37.500 0.00 0.00 33.22 2.27
2915 2983 5.592688 TCCAAAACAGAGACCGATTCTTTTT 59.407 36.000 0.00 0.00 33.22 1.94
2938 3006 7.591006 TTTTCTCTTAAGAATACGCAATCGT 57.409 32.000 6.63 0.00 43.35 3.73
2939 3007 6.569228 TTCTCTTAAGAATACGCAATCGTG 57.431 37.500 6.63 0.00 41.80 4.35
2940 3008 6.097356 TTCTCTTAAGAATACGCAATCGTGT 58.903 36.000 6.63 0.00 41.80 4.49
2941 3009 7.252708 TTCTCTTAAGAATACGCAATCGTGTA 58.747 34.615 6.63 0.00 41.80 2.90
2956 3024 9.177304 CGCAATCGTGTATCTTAGTTTTATAGA 57.823 33.333 0.00 0.00 0.00 1.98
2960 3028 9.694137 ATCGTGTATCTTAGTTTTATAGAAGGC 57.306 33.333 0.00 0.00 0.00 4.35
2961 3029 8.689061 TCGTGTATCTTAGTTTTATAGAAGGCA 58.311 33.333 0.00 0.00 0.00 4.75
2962 3030 8.969267 CGTGTATCTTAGTTTTATAGAAGGCAG 58.031 37.037 0.00 0.00 0.00 4.85
2978 3046 7.617041 AGAAGGCAGAAATATGTACAAGAAC 57.383 36.000 0.00 0.00 0.00 3.01
2979 3047 6.599638 AGAAGGCAGAAATATGTACAAGAACC 59.400 38.462 0.00 0.00 0.00 3.62
2980 3048 5.815581 AGGCAGAAATATGTACAAGAACCA 58.184 37.500 0.00 0.00 0.00 3.67
2981 3049 6.426587 AGGCAGAAATATGTACAAGAACCAT 58.573 36.000 0.00 0.00 0.00 3.55
2982 3050 6.891908 AGGCAGAAATATGTACAAGAACCATT 59.108 34.615 0.00 0.00 0.00 3.16
2983 3051 7.067494 AGGCAGAAATATGTACAAGAACCATTC 59.933 37.037 0.00 0.00 0.00 2.67
2984 3052 7.196331 GCAGAAATATGTACAAGAACCATTCC 58.804 38.462 0.00 0.00 0.00 3.01
3006 3074 1.651737 TCCATTCCCTCCGACAAAGA 58.348 50.000 0.00 0.00 0.00 2.52
3017 3085 6.211986 TCCCTCCGACAAAGAGTAGAATTTTA 59.788 38.462 0.00 0.00 0.00 1.52
3080 3151 6.093219 ACATCAGTCATCAGCTTAATCACAAC 59.907 38.462 0.00 0.00 0.00 3.32
3262 3336 8.037723 ACCTCCCTTTTTAGTCTTTTACTACA 57.962 34.615 0.00 0.00 40.48 2.74
3273 3347 9.578576 TTAGTCTTTTACTACAACCAGTCTAGA 57.421 33.333 0.00 0.00 40.48 2.43
3288 3362 8.653036 ACCAGTCTAGAGTAGTTTTTCAGTAT 57.347 34.615 0.00 0.00 0.00 2.12
3332 3409 6.672266 TCTTCAGTGGTAGAGAAATCAACT 57.328 37.500 0.00 0.00 0.00 3.16
3406 3483 4.515191 AGCAAATTAATACGTGCATCGGAT 59.485 37.500 16.59 7.03 46.04 4.18
3421 3498 5.065090 TGCATCGGATTATGACTGACAAAAG 59.935 40.000 0.00 0.00 0.00 2.27
3429 3509 3.281727 TGACTGACAAAAGAAGTGGCT 57.718 42.857 0.00 0.00 0.00 4.75
3430 3510 2.945008 TGACTGACAAAAGAAGTGGCTG 59.055 45.455 0.00 0.00 0.00 4.85
3440 3520 4.510167 AAGAAGTGGCTGCTATGGTTAT 57.490 40.909 0.00 0.00 0.00 1.89
3441 3521 5.630415 AAGAAGTGGCTGCTATGGTTATA 57.370 39.130 0.00 0.00 0.00 0.98
3442 3522 5.630415 AGAAGTGGCTGCTATGGTTATAA 57.370 39.130 0.00 0.00 0.00 0.98
3443 3523 6.001449 AGAAGTGGCTGCTATGGTTATAAA 57.999 37.500 0.00 0.00 0.00 1.40
3444 3524 5.823045 AGAAGTGGCTGCTATGGTTATAAAC 59.177 40.000 0.00 0.00 0.00 2.01
3445 3525 5.373812 AGTGGCTGCTATGGTTATAAACT 57.626 39.130 1.50 0.00 0.00 2.66
3446 3526 6.494666 AGTGGCTGCTATGGTTATAAACTA 57.505 37.500 1.50 0.00 0.00 2.24
3447 3527 6.289064 AGTGGCTGCTATGGTTATAAACTAC 58.711 40.000 1.50 0.00 0.00 2.73
3448 3528 6.099845 AGTGGCTGCTATGGTTATAAACTACT 59.900 38.462 1.50 0.00 0.00 2.57
3449 3529 6.766467 GTGGCTGCTATGGTTATAAACTACTT 59.234 38.462 1.50 0.00 0.00 2.24
3450 3530 6.990349 TGGCTGCTATGGTTATAAACTACTTC 59.010 38.462 1.50 0.00 0.00 3.01
3451 3531 6.427242 GGCTGCTATGGTTATAAACTACTTCC 59.573 42.308 1.50 0.00 0.00 3.46
3452 3532 7.217906 GCTGCTATGGTTATAAACTACTTCCT 58.782 38.462 1.50 0.00 0.00 3.36
3453 3533 7.715686 GCTGCTATGGTTATAAACTACTTCCTT 59.284 37.037 1.50 0.00 0.00 3.36
3454 3534 9.614792 CTGCTATGGTTATAAACTACTTCCTTT 57.385 33.333 1.50 0.00 0.00 3.11
3455 3535 9.391006 TGCTATGGTTATAAACTACTTCCTTTG 57.609 33.333 1.50 0.00 0.00 2.77
3456 3536 9.392259 GCTATGGTTATAAACTACTTCCTTTGT 57.608 33.333 1.50 0.00 0.00 2.83
3458 3538 8.803397 ATGGTTATAAACTACTTCCTTTGTCC 57.197 34.615 1.50 0.00 0.00 4.02
3459 3539 7.170277 TGGTTATAAACTACTTCCTTTGTCCC 58.830 38.462 1.50 0.00 0.00 4.46
3460 3540 6.314648 GGTTATAAACTACTTCCTTTGTCCCG 59.685 42.308 0.00 0.00 0.00 5.14
3461 3541 2.180432 AACTACTTCCTTTGTCCCGC 57.820 50.000 0.00 0.00 0.00 6.13
3462 3542 1.053424 ACTACTTCCTTTGTCCCGCA 58.947 50.000 0.00 0.00 0.00 5.69
3463 3543 1.418637 ACTACTTCCTTTGTCCCGCAA 59.581 47.619 0.00 0.00 34.87 4.85
3464 3544 2.039879 ACTACTTCCTTTGTCCCGCAAT 59.960 45.455 0.00 0.00 36.89 3.56
3465 3545 1.247567 ACTTCCTTTGTCCCGCAATG 58.752 50.000 0.00 0.00 36.89 2.82
3466 3546 1.247567 CTTCCTTTGTCCCGCAATGT 58.752 50.000 0.00 0.00 36.89 2.71
3467 3547 2.224670 ACTTCCTTTGTCCCGCAATGTA 60.225 45.455 0.00 0.00 36.89 2.29
3468 3548 2.570415 TCCTTTGTCCCGCAATGTAA 57.430 45.000 0.00 0.00 36.89 2.41
3469 3549 2.432444 TCCTTTGTCCCGCAATGTAAG 58.568 47.619 0.00 0.00 36.89 2.34
3470 3550 2.159382 CCTTTGTCCCGCAATGTAAGT 58.841 47.619 0.00 0.00 36.89 2.24
3471 3551 2.556622 CCTTTGTCCCGCAATGTAAGTT 59.443 45.455 0.00 0.00 36.89 2.66
3472 3552 3.564511 CTTTGTCCCGCAATGTAAGTTG 58.435 45.455 0.00 0.00 36.89 3.16
3473 3553 2.264005 TGTCCCGCAATGTAAGTTGT 57.736 45.000 0.00 0.00 0.00 3.32
3474 3554 2.577700 TGTCCCGCAATGTAAGTTGTT 58.422 42.857 0.00 0.00 0.00 2.83
3475 3555 2.952978 TGTCCCGCAATGTAAGTTGTTT 59.047 40.909 0.00 0.00 0.00 2.83
3476 3556 3.381908 TGTCCCGCAATGTAAGTTGTTTT 59.618 39.130 0.00 0.00 0.00 2.43
3477 3557 4.142138 TGTCCCGCAATGTAAGTTGTTTTT 60.142 37.500 0.00 0.00 0.00 1.94
3478 3558 4.443063 GTCCCGCAATGTAAGTTGTTTTTC 59.557 41.667 0.00 0.00 0.00 2.29
3479 3559 3.738791 CCCGCAATGTAAGTTGTTTTTCC 59.261 43.478 0.00 0.00 0.00 3.13
3480 3560 4.363999 CCGCAATGTAAGTTGTTTTTCCA 58.636 39.130 0.00 0.00 0.00 3.53
3481 3561 4.806247 CCGCAATGTAAGTTGTTTTTCCAA 59.194 37.500 0.00 0.00 0.00 3.53
3482 3562 5.051106 CCGCAATGTAAGTTGTTTTTCCAAG 60.051 40.000 0.00 0.00 0.00 3.61
3483 3563 5.556194 CGCAATGTAAGTTGTTTTTCCAAGC 60.556 40.000 0.00 0.00 0.00 4.01
3484 3564 5.523552 GCAATGTAAGTTGTTTTTCCAAGCT 59.476 36.000 0.00 0.00 0.00 3.74
3485 3565 6.699642 GCAATGTAAGTTGTTTTTCCAAGCTA 59.300 34.615 0.00 0.00 0.00 3.32
3486 3566 7.223777 GCAATGTAAGTTGTTTTTCCAAGCTAA 59.776 33.333 0.00 0.00 0.00 3.09
3487 3567 9.092876 CAATGTAAGTTGTTTTTCCAAGCTAAA 57.907 29.630 0.00 0.00 0.00 1.85
3488 3568 8.642908 ATGTAAGTTGTTTTTCCAAGCTAAAC 57.357 30.769 2.67 2.67 33.50 2.01
3489 3569 7.832769 TGTAAGTTGTTTTTCCAAGCTAAACT 58.167 30.769 9.75 0.00 33.92 2.66
3490 3570 8.958506 TGTAAGTTGTTTTTCCAAGCTAAACTA 58.041 29.630 9.75 0.96 33.92 2.24
3491 3571 9.447040 GTAAGTTGTTTTTCCAAGCTAAACTAG 57.553 33.333 9.75 0.00 33.92 2.57
3492 3572 7.640597 AGTTGTTTTTCCAAGCTAAACTAGT 57.359 32.000 9.75 0.00 33.92 2.57
3493 3573 8.063200 AGTTGTTTTTCCAAGCTAAACTAGTT 57.937 30.769 1.12 1.12 33.92 2.24
3494 3574 8.528643 AGTTGTTTTTCCAAGCTAAACTAGTTT 58.471 29.630 23.58 23.58 33.92 2.66
3495 3575 8.592155 GTTGTTTTTCCAAGCTAAACTAGTTTG 58.408 33.333 27.40 18.47 43.80 2.93
3496 3576 6.754675 TGTTTTTCCAAGCTAAACTAGTTTGC 59.245 34.615 27.40 25.25 43.13 3.68
3497 3577 6.458232 TTTTCCAAGCTAAACTAGTTTGCA 57.542 33.333 27.40 10.43 43.13 4.08
3498 3578 6.458232 TTTCCAAGCTAAACTAGTTTGCAA 57.542 33.333 27.40 15.93 43.13 4.08
3499 3579 6.458232 TTCCAAGCTAAACTAGTTTGCAAA 57.542 33.333 27.40 8.05 43.13 3.68
3500 3580 6.458232 TCCAAGCTAAACTAGTTTGCAAAA 57.542 33.333 27.40 9.05 43.13 2.44
3501 3581 6.868622 TCCAAGCTAAACTAGTTTGCAAAAA 58.131 32.000 27.40 8.37 43.13 1.94
3502 3582 6.754675 TCCAAGCTAAACTAGTTTGCAAAAAC 59.245 34.615 27.40 2.88 43.13 2.43
3503 3583 6.291585 CCAAGCTAAACTAGTTTGCAAAAACG 60.292 38.462 27.40 7.34 43.13 3.60
3504 3584 5.886992 AGCTAAACTAGTTTGCAAAAACGT 58.113 33.333 27.40 7.99 37.71 3.99
3505 3585 5.969435 AGCTAAACTAGTTTGCAAAAACGTC 59.031 36.000 27.40 0.55 37.71 4.34
3506 3586 5.969435 GCTAAACTAGTTTGCAAAAACGTCT 59.031 36.000 27.40 8.91 37.71 4.18
3507 3587 6.471198 GCTAAACTAGTTTGCAAAAACGTCTT 59.529 34.615 27.40 6.22 37.71 3.01
3508 3588 7.641020 GCTAAACTAGTTTGCAAAAACGTCTTA 59.359 33.333 27.40 7.00 37.71 2.10
3509 3589 7.730067 AAACTAGTTTGCAAAAACGTCTTAC 57.270 32.000 19.94 0.00 37.71 2.34
3510 3590 6.425577 ACTAGTTTGCAAAAACGTCTTACA 57.574 33.333 14.67 0.00 37.71 2.41
3511 3591 7.023197 ACTAGTTTGCAAAAACGTCTTACAT 57.977 32.000 14.67 0.00 37.71 2.29
3512 3592 7.477494 ACTAGTTTGCAAAAACGTCTTACATT 58.523 30.769 14.67 0.00 37.71 2.71
3513 3593 8.614346 ACTAGTTTGCAAAAACGTCTTACATTA 58.386 29.630 14.67 0.00 37.71 1.90
3514 3594 9.607285 CTAGTTTGCAAAAACGTCTTACATTAT 57.393 29.630 14.67 0.00 37.71 1.28
3515 3595 8.280909 AGTTTGCAAAAACGTCTTACATTATG 57.719 30.769 14.67 0.00 37.71 1.90
3516 3596 8.132362 AGTTTGCAAAAACGTCTTACATTATGA 58.868 29.630 14.67 0.00 37.71 2.15
3517 3597 8.417176 GTTTGCAAAAACGTCTTACATTATGAG 58.583 33.333 14.67 0.00 0.00 2.90
3518 3598 7.428282 TGCAAAAACGTCTTACATTATGAGA 57.572 32.000 0.00 0.00 0.00 3.27
3519 3599 8.039603 TGCAAAAACGTCTTACATTATGAGAT 57.960 30.769 0.00 0.00 0.00 2.75
3520 3600 9.157104 TGCAAAAACGTCTTACATTATGAGATA 57.843 29.630 0.00 0.00 0.00 1.98
3521 3601 9.638300 GCAAAAACGTCTTACATTATGAGATAG 57.362 33.333 0.00 0.00 0.00 2.08
3524 3604 9.751542 AAAACGTCTTACATTATGAGATAGAGG 57.248 33.333 0.00 4.49 0.00 3.69
3525 3605 7.455641 ACGTCTTACATTATGAGATAGAGGG 57.544 40.000 0.00 0.00 0.00 4.30
3526 3606 7.232188 ACGTCTTACATTATGAGATAGAGGGA 58.768 38.462 0.00 0.00 0.00 4.20
3527 3607 7.392113 ACGTCTTACATTATGAGATAGAGGGAG 59.608 40.741 0.00 0.00 0.00 4.30
3528 3608 7.392113 CGTCTTACATTATGAGATAGAGGGAGT 59.608 40.741 0.00 0.00 0.00 3.85
3529 3609 9.742144 GTCTTACATTATGAGATAGAGGGAGTA 57.258 37.037 0.00 0.00 0.00 2.59
3530 3610 9.967451 TCTTACATTATGAGATAGAGGGAGTAG 57.033 37.037 0.00 0.00 0.00 2.57
3531 3611 9.967451 CTTACATTATGAGATAGAGGGAGTAGA 57.033 37.037 0.00 0.00 0.00 2.59
3534 3614 9.661954 ACATTATGAGATAGAGGGAGTAGAAAA 57.338 33.333 0.00 0.00 0.00 2.29
3538 3618 6.821388 TGAGATAGAGGGAGTAGAAAATTGC 58.179 40.000 0.00 0.00 0.00 3.56
3539 3619 6.613271 TGAGATAGAGGGAGTAGAAAATTGCT 59.387 38.462 0.00 0.00 0.00 3.91
3540 3620 7.061566 AGATAGAGGGAGTAGAAAATTGCTC 57.938 40.000 0.00 0.00 0.00 4.26
3541 3621 6.613271 AGATAGAGGGAGTAGAAAATTGCTCA 59.387 38.462 0.00 0.00 0.00 4.26
3542 3622 4.837972 AGAGGGAGTAGAAAATTGCTCAC 58.162 43.478 0.00 0.00 0.00 3.51
3543 3623 3.600388 AGGGAGTAGAAAATTGCTCACG 58.400 45.455 0.00 0.00 36.57 4.35
3544 3624 3.260884 AGGGAGTAGAAAATTGCTCACGA 59.739 43.478 0.00 0.00 36.57 4.35
3545 3625 4.000988 GGGAGTAGAAAATTGCTCACGAA 58.999 43.478 0.00 0.00 0.00 3.85
3546 3626 4.093556 GGGAGTAGAAAATTGCTCACGAAG 59.906 45.833 0.00 0.00 0.00 3.79
3547 3627 4.929808 GGAGTAGAAAATTGCTCACGAAGA 59.070 41.667 0.00 0.00 0.00 2.87
3563 3643 7.525688 TCACGAAGAGATGACAATATGAAAC 57.474 36.000 0.00 0.00 0.00 2.78
3564 3644 7.323420 TCACGAAGAGATGACAATATGAAACT 58.677 34.615 0.00 0.00 0.00 2.66
3565 3645 7.276438 TCACGAAGAGATGACAATATGAAACTG 59.724 37.037 0.00 0.00 0.00 3.16
3566 3646 6.036517 ACGAAGAGATGACAATATGAAACTGC 59.963 38.462 0.00 0.00 0.00 4.40
3567 3647 6.257411 CGAAGAGATGACAATATGAAACTGCT 59.743 38.462 0.00 0.00 0.00 4.24
3568 3648 7.201591 CGAAGAGATGACAATATGAAACTGCTT 60.202 37.037 0.00 0.00 0.00 3.91
3569 3649 7.551035 AGAGATGACAATATGAAACTGCTTC 57.449 36.000 0.00 0.00 34.31 3.86
3571 3651 7.065563 AGAGATGACAATATGAAACTGCTTCAC 59.934 37.037 0.00 0.00 46.80 3.18
3572 3652 6.656270 AGATGACAATATGAAACTGCTTCACA 59.344 34.615 0.00 0.00 46.80 3.58
3573 3653 6.000891 TGACAATATGAAACTGCTTCACAC 57.999 37.500 0.00 0.00 46.80 3.82
3574 3654 5.530543 TGACAATATGAAACTGCTTCACACA 59.469 36.000 0.00 0.00 46.80 3.72
3575 3655 5.762045 ACAATATGAAACTGCTTCACACAC 58.238 37.500 0.00 0.00 46.80 3.82
3576 3656 4.668576 ATATGAAACTGCTTCACACACG 57.331 40.909 0.00 0.00 46.80 4.49
3577 3657 2.017138 TGAAACTGCTTCACACACGA 57.983 45.000 0.00 0.00 39.20 4.35
3578 3658 1.663643 TGAAACTGCTTCACACACGAC 59.336 47.619 0.00 0.00 39.20 4.34
3579 3659 1.663643 GAAACTGCTTCACACACGACA 59.336 47.619 0.00 0.00 33.86 4.35
3580 3660 1.953559 AACTGCTTCACACACGACAT 58.046 45.000 0.00 0.00 0.00 3.06
3581 3661 1.220529 ACTGCTTCACACACGACATG 58.779 50.000 0.00 0.00 0.00 3.21
3582 3662 0.514255 CTGCTTCACACACGACATGG 59.486 55.000 0.00 0.00 0.00 3.66
3583 3663 0.179059 TGCTTCACACACGACATGGT 60.179 50.000 0.00 0.00 0.00 3.55
3584 3664 0.944386 GCTTCACACACGACATGGTT 59.056 50.000 0.00 0.00 0.00 3.67
3585 3665 1.333619 GCTTCACACACGACATGGTTT 59.666 47.619 0.00 0.00 0.00 3.27
3586 3666 2.854424 GCTTCACACACGACATGGTTTG 60.854 50.000 0.00 0.00 0.00 2.93
3587 3667 0.660488 TCACACACGACATGGTTTGC 59.340 50.000 0.00 0.00 0.00 3.68
3588 3668 0.380024 CACACACGACATGGTTTGCA 59.620 50.000 0.00 0.00 0.00 4.08
3589 3669 0.380378 ACACACGACATGGTTTGCAC 59.620 50.000 0.00 0.00 0.00 4.57
3590 3670 0.317770 CACACGACATGGTTTGCACC 60.318 55.000 0.00 0.00 44.56 5.01
3607 3687 1.922570 ACCATCTGTGAACGATACGC 58.077 50.000 0.00 0.00 0.00 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.291383 CGTTGGAGCCGGGCAAAA 61.291 61.111 23.09 9.35 0.00 2.44
3 4 4.257654 TCGTTGGAGCCGGGCAAA 62.258 61.111 23.09 9.73 0.00 3.68
4 5 4.697756 CTCGTTGGAGCCGGGCAA 62.698 66.667 23.09 3.66 32.61 4.52
8 9 4.148825 CTCCCTCGTTGGAGCCGG 62.149 72.222 0.00 0.00 45.13 6.13
14 15 3.546714 AAACGCCCTCCCTCGTTGG 62.547 63.158 0.70 0.00 46.56 3.77
15 16 2.032071 AAACGCCCTCCCTCGTTG 59.968 61.111 0.70 0.00 46.56 4.10
17 18 1.885163 CTACAAACGCCCTCCCTCGT 61.885 60.000 0.00 0.00 41.06 4.18
18 19 1.153628 CTACAAACGCCCTCCCTCG 60.154 63.158 0.00 0.00 0.00 4.63
19 20 0.108281 GACTACAAACGCCCTCCCTC 60.108 60.000 0.00 0.00 0.00 4.30
20 21 1.885163 CGACTACAAACGCCCTCCCT 61.885 60.000 0.00 0.00 0.00 4.20
21 22 1.447314 CGACTACAAACGCCCTCCC 60.447 63.158 0.00 0.00 0.00 4.30
22 23 0.735287 GACGACTACAAACGCCCTCC 60.735 60.000 0.00 0.00 0.00 4.30
23 24 1.069378 CGACGACTACAAACGCCCTC 61.069 60.000 0.00 0.00 0.00 4.30
24 25 1.080974 CGACGACTACAAACGCCCT 60.081 57.895 0.00 0.00 0.00 5.19
25 26 2.090524 CCGACGACTACAAACGCCC 61.091 63.158 0.00 0.00 0.00 6.13
26 27 0.109781 TACCGACGACTACAAACGCC 60.110 55.000 0.00 0.00 0.00 5.68
27 28 1.135972 TCTACCGACGACTACAAACGC 60.136 52.381 0.00 0.00 0.00 4.84
28 29 2.880822 TCTACCGACGACTACAAACG 57.119 50.000 0.00 0.00 0.00 3.60
29 30 3.119708 ACCATCTACCGACGACTACAAAC 60.120 47.826 0.00 0.00 0.00 2.93
30 31 3.084039 ACCATCTACCGACGACTACAAA 58.916 45.455 0.00 0.00 0.00 2.83
31 32 2.679837 GACCATCTACCGACGACTACAA 59.320 50.000 0.00 0.00 0.00 2.41
32 33 2.093288 AGACCATCTACCGACGACTACA 60.093 50.000 0.00 0.00 0.00 2.74
33 34 2.559440 AGACCATCTACCGACGACTAC 58.441 52.381 0.00 0.00 0.00 2.73
34 35 2.996249 AGACCATCTACCGACGACTA 57.004 50.000 0.00 0.00 0.00 2.59
35 36 2.559440 GTAGACCATCTACCGACGACT 58.441 52.381 0.00 0.00 42.61 4.18
36 37 1.260033 CGTAGACCATCTACCGACGAC 59.740 57.143 9.80 0.00 44.89 4.34
37 38 1.575244 CGTAGACCATCTACCGACGA 58.425 55.000 9.80 0.00 44.89 4.20
38 39 0.585357 CCGTAGACCATCTACCGACG 59.415 60.000 9.80 1.99 44.89 5.12
39 40 1.601430 GTCCGTAGACCATCTACCGAC 59.399 57.143 16.37 16.37 44.89 4.79
40 41 1.959042 GTCCGTAGACCATCTACCGA 58.041 55.000 9.80 6.67 44.89 4.69
50 51 6.837471 AATATTAGATCCAGGTCCGTAGAC 57.163 41.667 0.00 0.00 42.73 2.59
51 52 9.543231 AATAAATATTAGATCCAGGTCCGTAGA 57.457 33.333 0.00 0.00 0.00 2.59
249 254 3.989167 TCGTTAATCAAACCTACCGTGTG 59.011 43.478 0.00 0.00 34.33 3.82
276 281 6.275494 AGTACGGGATTAAAATGGTTTTGG 57.725 37.500 0.00 0.00 34.19 3.28
330 335 2.654404 GCTGACCGCGGACGATAC 60.654 66.667 35.90 12.64 43.93 2.24
346 351 1.730547 GTTTGGATGCGTGCACTGC 60.731 57.895 21.49 21.49 0.00 4.40
549 557 2.041966 CGATTAGGCGTGCGTAGTTAG 58.958 52.381 0.00 0.00 0.00 2.34
586 594 0.179192 GCGGTGTCGATGTACGTACA 60.179 55.000 29.15 29.15 43.13 2.90
688 729 3.522731 CAGAGAGAGACCCGGCGG 61.523 72.222 21.46 21.46 0.00 6.13
689 730 2.752238 ACAGAGAGAGACCCGGCG 60.752 66.667 0.00 0.00 0.00 6.46
694 735 2.202544 CGCGCACAGAGAGAGACC 60.203 66.667 8.75 0.00 0.00 3.85
889 957 2.257894 GAAGCGAGATGACAGACACAG 58.742 52.381 0.00 0.00 0.00 3.66
913 981 2.133553 CGATTCCGAGCTACGACTAGA 58.866 52.381 0.00 0.00 45.77 2.43
915 983 1.202568 TCCGATTCCGAGCTACGACTA 60.203 52.381 7.07 0.00 45.77 2.59
917 985 0.041135 CTCCGATTCCGAGCTACGAC 60.041 60.000 7.07 0.00 45.77 4.34
918 986 1.164662 CCTCCGATTCCGAGCTACGA 61.165 60.000 7.07 0.00 45.77 3.43
919 987 1.283181 CCTCCGATTCCGAGCTACG 59.717 63.158 0.00 0.00 42.18 3.51
941 1009 0.029567 GATCACCTACTCGACCGCAG 59.970 60.000 0.00 0.00 0.00 5.18
942 1010 1.381928 GGATCACCTACTCGACCGCA 61.382 60.000 0.00 0.00 0.00 5.69
944 1012 0.663688 CAGGATCACCTACTCGACCG 59.336 60.000 0.00 0.00 45.94 4.79
945 1013 0.386113 GCAGGATCACCTACTCGACC 59.614 60.000 0.00 0.00 45.94 4.79
946 1014 1.394618 AGCAGGATCACCTACTCGAC 58.605 55.000 0.00 0.00 45.94 4.20
969 1037 6.183360 CCTCCGTCAACAACAGGTTATAATTC 60.183 42.308 0.00 0.00 37.72 2.17
981 1049 3.967715 GGCTCCTCCGTCAACAAC 58.032 61.111 0.00 0.00 0.00 3.32
1494 1562 4.270153 AGGAGACCTGCCCACCCA 62.270 66.667 0.00 0.00 29.57 4.51
1803 1871 2.583319 AGCACGATGGCGATGTCG 60.583 61.111 0.00 0.00 43.13 4.35
1941 2009 1.135053 GTCTTGTAGAGGCTCCGGAAC 60.135 57.143 11.71 0.00 0.00 3.62
1998 2066 1.226717 GCGTCTCACCTCGTCCATC 60.227 63.158 0.00 0.00 0.00 3.51
2196 2264 2.359230 ACCTTGCCGCTCTGCTTC 60.359 61.111 0.00 0.00 0.00 3.86
2627 2695 9.826574 ATTGTTTGTCTCTACAGTACAAAACTA 57.173 29.630 11.50 0.00 42.79 2.24
2644 2712 5.844396 CCGACTAACGAAAGAATTGTTTGTC 59.156 40.000 5.14 7.52 45.77 3.18
2674 2742 3.793559 AGATATTTTCCTGGAACCGACG 58.206 45.455 9.04 0.00 0.00 5.12
2708 2776 3.983666 TCGAAACGAAAACGAAAACGAA 58.016 36.364 0.00 0.00 31.06 3.85
2709 2777 3.631388 TCGAAACGAAAACGAAAACGA 57.369 38.095 0.00 0.00 31.06 3.85
2710 2778 3.417025 GCATCGAAACGAAAACGAAAACG 60.417 43.478 0.00 0.00 39.99 3.60
2711 2779 3.479232 TGCATCGAAACGAAAACGAAAAC 59.521 39.130 0.00 0.00 39.99 2.43
2712 2780 3.681855 TGCATCGAAACGAAAACGAAAA 58.318 36.364 0.00 0.00 39.99 2.29
2781 2849 2.423185 TGTGGTCAAAACACTCAAGCTG 59.577 45.455 0.00 0.00 39.52 4.24
2824 2892 2.103042 GTAGGAGGCAGCGCAGTTG 61.103 63.158 11.47 0.00 43.28 3.16
2825 2893 2.232298 GAGTAGGAGGCAGCGCAGTT 62.232 60.000 11.47 0.00 0.00 3.16
2826 2894 2.681778 AGTAGGAGGCAGCGCAGT 60.682 61.111 11.47 0.00 0.00 4.40
2827 2895 2.105930 GAGTAGGAGGCAGCGCAG 59.894 66.667 11.47 1.31 0.00 5.18
2828 2896 3.826754 CGAGTAGGAGGCAGCGCA 61.827 66.667 11.47 0.00 0.00 6.09
2829 2897 3.358076 AACGAGTAGGAGGCAGCGC 62.358 63.158 0.00 0.00 0.00 5.92
2930 2998 9.177304 TCTATAAAACTAAGATACACGATTGCG 57.823 33.333 0.00 0.00 44.79 4.85
2934 3002 9.694137 GCCTTCTATAAAACTAAGATACACGAT 57.306 33.333 0.00 0.00 0.00 3.73
2935 3003 8.689061 TGCCTTCTATAAAACTAAGATACACGA 58.311 33.333 0.00 0.00 0.00 4.35
2936 3004 8.867112 TGCCTTCTATAAAACTAAGATACACG 57.133 34.615 0.00 0.00 0.00 4.49
2952 3020 9.331282 GTTCTTGTACATATTTCTGCCTTCTAT 57.669 33.333 0.00 0.00 0.00 1.98
2953 3021 7.769044 GGTTCTTGTACATATTTCTGCCTTCTA 59.231 37.037 0.00 0.00 0.00 2.10
2954 3022 6.599638 GGTTCTTGTACATATTTCTGCCTTCT 59.400 38.462 0.00 0.00 0.00 2.85
2955 3023 6.374333 TGGTTCTTGTACATATTTCTGCCTTC 59.626 38.462 0.00 0.00 0.00 3.46
2956 3024 6.245408 TGGTTCTTGTACATATTTCTGCCTT 58.755 36.000 0.00 0.00 0.00 4.35
2957 3025 5.815581 TGGTTCTTGTACATATTTCTGCCT 58.184 37.500 0.00 0.00 0.00 4.75
2958 3026 6.699575 ATGGTTCTTGTACATATTTCTGCC 57.300 37.500 0.00 0.00 0.00 4.85
2959 3027 7.148086 TGGAATGGTTCTTGTACATATTTCTGC 60.148 37.037 0.00 0.00 0.00 4.26
2960 3028 8.279970 TGGAATGGTTCTTGTACATATTTCTG 57.720 34.615 0.00 0.00 0.00 3.02
2961 3029 9.479549 AATGGAATGGTTCTTGTACATATTTCT 57.520 29.630 0.00 0.00 0.00 2.52
2962 3030 9.736023 GAATGGAATGGTTCTTGTACATATTTC 57.264 33.333 0.00 0.00 0.00 2.17
2963 3031 8.695456 GGAATGGAATGGTTCTTGTACATATTT 58.305 33.333 0.00 0.00 0.00 1.40
2964 3032 7.838696 TGGAATGGAATGGTTCTTGTACATATT 59.161 33.333 0.00 0.00 0.00 1.28
2965 3033 7.353525 TGGAATGGAATGGTTCTTGTACATAT 58.646 34.615 0.00 0.00 0.00 1.78
2966 3034 6.726379 TGGAATGGAATGGTTCTTGTACATA 58.274 36.000 0.00 0.00 0.00 2.29
2967 3035 5.579047 TGGAATGGAATGGTTCTTGTACAT 58.421 37.500 0.00 0.00 0.00 2.29
2968 3036 4.991776 TGGAATGGAATGGTTCTTGTACA 58.008 39.130 0.00 0.00 0.00 2.90
2969 3037 6.405842 GGAATGGAATGGAATGGTTCTTGTAC 60.406 42.308 0.00 0.00 0.00 2.90
2970 3038 5.656416 GGAATGGAATGGAATGGTTCTTGTA 59.344 40.000 0.00 0.00 0.00 2.41
2971 3039 4.467438 GGAATGGAATGGAATGGTTCTTGT 59.533 41.667 0.00 0.00 0.00 3.16
2972 3040 4.141869 GGGAATGGAATGGAATGGTTCTTG 60.142 45.833 0.00 0.00 0.00 3.02
2973 3041 4.033009 GGGAATGGAATGGAATGGTTCTT 58.967 43.478 0.00 0.00 0.00 2.52
2974 3042 3.273084 AGGGAATGGAATGGAATGGTTCT 59.727 43.478 0.00 0.00 0.00 3.01
2975 3043 3.638627 GAGGGAATGGAATGGAATGGTTC 59.361 47.826 0.00 0.00 0.00 3.62
2976 3044 3.630828 GGAGGGAATGGAATGGAATGGTT 60.631 47.826 0.00 0.00 0.00 3.67
2977 3045 2.091111 GGAGGGAATGGAATGGAATGGT 60.091 50.000 0.00 0.00 0.00 3.55
2978 3046 2.601905 GGAGGGAATGGAATGGAATGG 58.398 52.381 0.00 0.00 0.00 3.16
2979 3047 2.158623 TCGGAGGGAATGGAATGGAATG 60.159 50.000 0.00 0.00 0.00 2.67
2980 3048 2.135189 TCGGAGGGAATGGAATGGAAT 58.865 47.619 0.00 0.00 0.00 3.01
2981 3049 1.211949 GTCGGAGGGAATGGAATGGAA 59.788 52.381 0.00 0.00 0.00 3.53
2982 3050 0.837272 GTCGGAGGGAATGGAATGGA 59.163 55.000 0.00 0.00 0.00 3.41
2983 3051 0.546122 TGTCGGAGGGAATGGAATGG 59.454 55.000 0.00 0.00 0.00 3.16
2984 3052 2.418368 TTGTCGGAGGGAATGGAATG 57.582 50.000 0.00 0.00 0.00 2.67
3017 3085 4.152759 CGACGTTAATGTTACATGGGTTGT 59.847 41.667 0.98 0.00 42.62 3.32
3080 3151 9.993454 TCAGAACCATTCATAAGATATTCAGAG 57.007 33.333 0.00 0.00 0.00 3.35
3164 3235 1.079819 ACTCCGAGTGTTGCCATCG 60.080 57.895 0.00 0.00 36.24 3.84
3168 3239 0.951040 CTTCCACTCCGAGTGTTGCC 60.951 60.000 23.83 0.00 44.50 4.52
3262 3336 7.362802 ACTGAAAAACTACTCTAGACTGGTT 57.637 36.000 0.00 0.00 0.00 3.67
3273 3347 8.671028 ACACGTGAAAAATACTGAAAAACTACT 58.329 29.630 25.01 0.00 0.00 2.57
3406 3483 5.239306 CAGCCACTTCTTTTGTCAGTCATAA 59.761 40.000 0.00 0.00 0.00 1.90
3407 3484 4.756642 CAGCCACTTCTTTTGTCAGTCATA 59.243 41.667 0.00 0.00 0.00 2.15
3412 3489 1.952296 AGCAGCCACTTCTTTTGTCAG 59.048 47.619 0.00 0.00 0.00 3.51
3421 3498 5.823045 AGTTTATAACCATAGCAGCCACTTC 59.177 40.000 0.00 0.00 0.00 3.01
3429 3509 9.391006 CAAAGGAAGTAGTTTATAACCATAGCA 57.609 33.333 0.00 0.00 0.00 3.49
3430 3510 9.392259 ACAAAGGAAGTAGTTTATAACCATAGC 57.608 33.333 0.00 0.00 0.00 2.97
3440 3520 3.071312 TGCGGGACAAAGGAAGTAGTTTA 59.929 43.478 0.00 0.00 0.00 2.01
3441 3521 2.158726 TGCGGGACAAAGGAAGTAGTTT 60.159 45.455 0.00 0.00 0.00 2.66
3442 3522 1.418637 TGCGGGACAAAGGAAGTAGTT 59.581 47.619 0.00 0.00 0.00 2.24
3443 3523 1.053424 TGCGGGACAAAGGAAGTAGT 58.947 50.000 0.00 0.00 0.00 2.73
3444 3524 2.178912 TTGCGGGACAAAGGAAGTAG 57.821 50.000 0.00 0.00 34.56 2.57
3445 3525 2.224670 ACATTGCGGGACAAAGGAAGTA 60.225 45.455 0.00 0.00 42.86 2.24
3446 3526 1.247567 CATTGCGGGACAAAGGAAGT 58.752 50.000 0.00 0.00 42.86 3.01
3447 3527 1.247567 ACATTGCGGGACAAAGGAAG 58.752 50.000 0.00 0.00 42.86 3.46
3448 3528 2.570415 TACATTGCGGGACAAAGGAA 57.430 45.000 0.00 0.00 42.86 3.36
3449 3529 2.224670 ACTTACATTGCGGGACAAAGGA 60.225 45.455 0.00 0.00 42.86 3.36
3450 3530 2.159382 ACTTACATTGCGGGACAAAGG 58.841 47.619 0.00 0.00 42.86 3.11
3451 3531 3.004315 ACAACTTACATTGCGGGACAAAG 59.996 43.478 0.00 0.00 42.86 2.77
3452 3532 2.952978 ACAACTTACATTGCGGGACAAA 59.047 40.909 0.00 0.00 42.86 2.83
3453 3533 2.577700 ACAACTTACATTGCGGGACAA 58.422 42.857 0.00 0.00 44.01 3.18
3454 3534 2.264005 ACAACTTACATTGCGGGACA 57.736 45.000 0.00 0.00 32.47 4.02
3455 3535 3.636282 AAACAACTTACATTGCGGGAC 57.364 42.857 0.00 0.00 32.47 4.46
3456 3536 4.500035 GGAAAAACAACTTACATTGCGGGA 60.500 41.667 0.00 0.00 32.47 5.14
3457 3537 3.738791 GGAAAAACAACTTACATTGCGGG 59.261 43.478 0.00 0.00 32.47 6.13
3458 3538 4.363999 TGGAAAAACAACTTACATTGCGG 58.636 39.130 0.00 0.00 32.47 5.69
3459 3539 5.556194 GCTTGGAAAAACAACTTACATTGCG 60.556 40.000 0.00 0.00 32.47 4.85
3460 3540 5.523552 AGCTTGGAAAAACAACTTACATTGC 59.476 36.000 0.00 0.00 32.47 3.56
3461 3541 8.641499 TTAGCTTGGAAAAACAACTTACATTG 57.359 30.769 0.00 0.00 35.59 2.82
3462 3542 9.093970 GTTTAGCTTGGAAAAACAACTTACATT 57.906 29.630 0.00 0.00 34.12 2.71
3463 3543 8.474831 AGTTTAGCTTGGAAAAACAACTTACAT 58.525 29.630 10.76 0.00 35.93 2.29
3464 3544 7.832769 AGTTTAGCTTGGAAAAACAACTTACA 58.167 30.769 10.76 0.00 35.93 2.41
3465 3545 9.447040 CTAGTTTAGCTTGGAAAAACAACTTAC 57.553 33.333 10.76 0.00 35.93 2.34
3466 3546 9.181061 ACTAGTTTAGCTTGGAAAAACAACTTA 57.819 29.630 10.76 0.00 35.93 2.24
3467 3547 8.063200 ACTAGTTTAGCTTGGAAAAACAACTT 57.937 30.769 10.76 0.00 35.93 2.66
3468 3548 7.640597 ACTAGTTTAGCTTGGAAAAACAACT 57.359 32.000 10.76 0.00 35.93 3.16
3469 3549 8.592155 CAAACTAGTTTAGCTTGGAAAAACAAC 58.408 33.333 20.15 0.00 35.93 3.32
3470 3550 7.276878 GCAAACTAGTTTAGCTTGGAAAAACAA 59.723 33.333 20.15 0.00 35.93 2.83
3471 3551 6.754675 GCAAACTAGTTTAGCTTGGAAAAACA 59.245 34.615 20.15 0.00 35.93 2.83
3472 3552 6.754675 TGCAAACTAGTTTAGCTTGGAAAAAC 59.245 34.615 27.56 0.00 33.60 2.43
3473 3553 6.868622 TGCAAACTAGTTTAGCTTGGAAAAA 58.131 32.000 27.56 13.23 33.60 1.94
3474 3554 6.458232 TGCAAACTAGTTTAGCTTGGAAAA 57.542 33.333 27.56 13.70 33.60 2.29
3475 3555 6.458232 TTGCAAACTAGTTTAGCTTGGAAA 57.542 33.333 27.56 17.80 38.60 3.13
3476 3556 6.458232 TTTGCAAACTAGTTTAGCTTGGAA 57.542 33.333 27.56 19.07 39.38 3.53
3477 3557 6.458232 TTTTGCAAACTAGTTTAGCTTGGA 57.542 33.333 27.56 15.48 33.60 3.53
3478 3558 6.291585 CGTTTTTGCAAACTAGTTTAGCTTGG 60.292 38.462 27.56 15.90 40.31 3.61
3479 3559 6.252655 ACGTTTTTGCAAACTAGTTTAGCTTG 59.747 34.615 27.56 17.15 40.31 4.01
3480 3560 6.327154 ACGTTTTTGCAAACTAGTTTAGCTT 58.673 32.000 27.56 7.41 40.31 3.74
3481 3561 5.886992 ACGTTTTTGCAAACTAGTTTAGCT 58.113 33.333 27.56 13.70 40.31 3.32
3482 3562 5.969435 AGACGTTTTTGCAAACTAGTTTAGC 59.031 36.000 20.15 22.58 40.31 3.09
3483 3563 7.964545 AAGACGTTTTTGCAAACTAGTTTAG 57.035 32.000 20.15 14.94 40.31 1.85
3484 3564 8.449397 TGTAAGACGTTTTTGCAAACTAGTTTA 58.551 29.630 20.15 3.59 40.31 2.01
3485 3565 7.306953 TGTAAGACGTTTTTGCAAACTAGTTT 58.693 30.769 15.22 15.22 40.31 2.66
3486 3566 6.844254 TGTAAGACGTTTTTGCAAACTAGTT 58.156 32.000 12.39 1.12 40.31 2.24
3487 3567 6.425577 TGTAAGACGTTTTTGCAAACTAGT 57.574 33.333 12.39 11.55 40.31 2.57
3488 3568 7.908193 AATGTAAGACGTTTTTGCAAACTAG 57.092 32.000 12.39 8.30 40.31 2.57
3489 3569 9.388346 CATAATGTAAGACGTTTTTGCAAACTA 57.612 29.630 12.39 0.00 40.31 2.24
3490 3570 8.132362 TCATAATGTAAGACGTTTTTGCAAACT 58.868 29.630 12.39 2.08 40.31 2.66
3491 3571 8.276060 TCATAATGTAAGACGTTTTTGCAAAC 57.724 30.769 12.39 0.58 39.24 2.93
3492 3572 8.346300 TCTCATAATGTAAGACGTTTTTGCAAA 58.654 29.630 8.05 8.05 0.00 3.68
3493 3573 7.866729 TCTCATAATGTAAGACGTTTTTGCAA 58.133 30.769 0.00 0.00 0.00 4.08
3494 3574 7.428282 TCTCATAATGTAAGACGTTTTTGCA 57.572 32.000 0.00 1.87 0.00 4.08
3495 3575 9.638300 CTATCTCATAATGTAAGACGTTTTTGC 57.362 33.333 0.00 0.00 0.00 3.68
3498 3578 9.751542 CCTCTATCTCATAATGTAAGACGTTTT 57.248 33.333 0.00 0.00 0.00 2.43
3499 3579 8.361139 CCCTCTATCTCATAATGTAAGACGTTT 58.639 37.037 0.00 0.00 0.00 3.60
3500 3580 7.724506 TCCCTCTATCTCATAATGTAAGACGTT 59.275 37.037 0.00 0.00 0.00 3.99
3501 3581 7.232188 TCCCTCTATCTCATAATGTAAGACGT 58.768 38.462 0.00 0.00 0.00 4.34
3502 3582 7.392113 ACTCCCTCTATCTCATAATGTAAGACG 59.608 40.741 0.00 0.00 0.00 4.18
3503 3583 8.644374 ACTCCCTCTATCTCATAATGTAAGAC 57.356 38.462 0.00 0.00 0.00 3.01
3504 3584 9.967451 CTACTCCCTCTATCTCATAATGTAAGA 57.033 37.037 0.00 0.00 0.00 2.10
3505 3585 9.967451 TCTACTCCCTCTATCTCATAATGTAAG 57.033 37.037 0.00 0.00 0.00 2.34
3508 3588 9.661954 TTTTCTACTCCCTCTATCTCATAATGT 57.338 33.333 0.00 0.00 0.00 2.71
3512 3592 8.589338 GCAATTTTCTACTCCCTCTATCTCATA 58.411 37.037 0.00 0.00 0.00 2.15
3513 3593 7.292120 AGCAATTTTCTACTCCCTCTATCTCAT 59.708 37.037 0.00 0.00 0.00 2.90
3514 3594 6.613271 AGCAATTTTCTACTCCCTCTATCTCA 59.387 38.462 0.00 0.00 0.00 3.27
3515 3595 7.061566 AGCAATTTTCTACTCCCTCTATCTC 57.938 40.000 0.00 0.00 0.00 2.75
3516 3596 6.613271 TGAGCAATTTTCTACTCCCTCTATCT 59.387 38.462 0.00 0.00 0.00 1.98
3517 3597 6.704050 GTGAGCAATTTTCTACTCCCTCTATC 59.296 42.308 0.00 0.00 0.00 2.08
3518 3598 6.587273 GTGAGCAATTTTCTACTCCCTCTAT 58.413 40.000 0.00 0.00 0.00 1.98
3519 3599 5.394224 CGTGAGCAATTTTCTACTCCCTCTA 60.394 44.000 0.00 0.00 0.00 2.43
3520 3600 4.621747 CGTGAGCAATTTTCTACTCCCTCT 60.622 45.833 0.00 0.00 0.00 3.69
3521 3601 3.619038 CGTGAGCAATTTTCTACTCCCTC 59.381 47.826 0.00 0.00 0.00 4.30
3522 3602 3.260884 TCGTGAGCAATTTTCTACTCCCT 59.739 43.478 0.00 0.00 0.00 4.20
3523 3603 3.596214 TCGTGAGCAATTTTCTACTCCC 58.404 45.455 0.00 0.00 0.00 4.30
3524 3604 4.929808 TCTTCGTGAGCAATTTTCTACTCC 59.070 41.667 0.00 0.00 0.00 3.85
3525 3605 5.864474 TCTCTTCGTGAGCAATTTTCTACTC 59.136 40.000 3.89 0.00 42.38 2.59
3526 3606 5.784177 TCTCTTCGTGAGCAATTTTCTACT 58.216 37.500 3.89 0.00 42.38 2.57
3527 3607 6.311445 TCATCTCTTCGTGAGCAATTTTCTAC 59.689 38.462 3.89 0.00 42.38 2.59
3528 3608 6.311445 GTCATCTCTTCGTGAGCAATTTTCTA 59.689 38.462 3.89 0.00 42.38 2.10
3529 3609 5.121454 GTCATCTCTTCGTGAGCAATTTTCT 59.879 40.000 3.89 0.00 42.38 2.52
3530 3610 5.106948 TGTCATCTCTTCGTGAGCAATTTTC 60.107 40.000 3.89 0.00 42.38 2.29
3531 3611 4.756642 TGTCATCTCTTCGTGAGCAATTTT 59.243 37.500 3.89 0.00 42.38 1.82
3532 3612 4.318332 TGTCATCTCTTCGTGAGCAATTT 58.682 39.130 3.89 0.00 42.38 1.82
3533 3613 3.930336 TGTCATCTCTTCGTGAGCAATT 58.070 40.909 3.89 0.00 42.38 2.32
3534 3614 3.599730 TGTCATCTCTTCGTGAGCAAT 57.400 42.857 3.89 0.00 42.38 3.56
3535 3615 3.385193 TTGTCATCTCTTCGTGAGCAA 57.615 42.857 3.89 1.11 42.38 3.91
3536 3616 3.599730 ATTGTCATCTCTTCGTGAGCA 57.400 42.857 3.89 0.00 42.38 4.26
3537 3617 5.284864 TCATATTGTCATCTCTTCGTGAGC 58.715 41.667 3.89 0.00 42.38 4.26
3538 3618 7.490725 AGTTTCATATTGTCATCTCTTCGTGAG 59.509 37.037 2.61 2.61 43.96 3.51
3539 3619 7.276438 CAGTTTCATATTGTCATCTCTTCGTGA 59.724 37.037 0.00 0.00 0.00 4.35
3540 3620 7.397194 CAGTTTCATATTGTCATCTCTTCGTG 58.603 38.462 0.00 0.00 0.00 4.35
3541 3621 6.036517 GCAGTTTCATATTGTCATCTCTTCGT 59.963 38.462 0.00 0.00 0.00 3.85
3542 3622 6.257411 AGCAGTTTCATATTGTCATCTCTTCG 59.743 38.462 0.00 0.00 0.00 3.79
3543 3623 7.551035 AGCAGTTTCATATTGTCATCTCTTC 57.449 36.000 0.00 0.00 0.00 2.87
3544 3624 7.609146 TGAAGCAGTTTCATATTGTCATCTCTT 59.391 33.333 0.00 0.00 40.82 2.85
3545 3625 7.065563 GTGAAGCAGTTTCATATTGTCATCTCT 59.934 37.037 2.68 0.00 46.85 3.10
3546 3626 7.148356 TGTGAAGCAGTTTCATATTGTCATCTC 60.148 37.037 2.68 0.00 46.85 2.75
3547 3627 6.656270 TGTGAAGCAGTTTCATATTGTCATCT 59.344 34.615 2.68 0.00 46.85 2.90
3548 3628 6.744537 GTGTGAAGCAGTTTCATATTGTCATC 59.255 38.462 2.68 0.00 46.85 2.92
3549 3629 6.207221 TGTGTGAAGCAGTTTCATATTGTCAT 59.793 34.615 2.68 0.00 46.85 3.06
3550 3630 5.530543 TGTGTGAAGCAGTTTCATATTGTCA 59.469 36.000 2.68 0.00 46.85 3.58
3551 3631 5.853282 GTGTGTGAAGCAGTTTCATATTGTC 59.147 40.000 2.68 0.00 46.85 3.18
3552 3632 5.560760 CGTGTGTGAAGCAGTTTCATATTGT 60.561 40.000 2.68 0.00 46.85 2.71
3553 3633 4.847757 CGTGTGTGAAGCAGTTTCATATTG 59.152 41.667 2.68 0.00 46.85 1.90
3554 3634 4.754618 TCGTGTGTGAAGCAGTTTCATATT 59.245 37.500 2.68 0.00 46.85 1.28
3555 3635 4.152402 GTCGTGTGTGAAGCAGTTTCATAT 59.848 41.667 2.68 0.00 46.85 1.78
3556 3636 3.493129 GTCGTGTGTGAAGCAGTTTCATA 59.507 43.478 2.68 0.00 46.85 2.15
3557 3637 2.287915 GTCGTGTGTGAAGCAGTTTCAT 59.712 45.455 2.68 0.00 46.85 2.57
3558 3638 1.663643 GTCGTGTGTGAAGCAGTTTCA 59.336 47.619 0.00 0.00 43.40 2.69
3559 3639 1.663643 TGTCGTGTGTGAAGCAGTTTC 59.336 47.619 0.00 0.00 36.29 2.78
3560 3640 1.732941 TGTCGTGTGTGAAGCAGTTT 58.267 45.000 0.00 0.00 0.00 2.66
3561 3641 1.599071 CATGTCGTGTGTGAAGCAGTT 59.401 47.619 0.00 0.00 0.00 3.16
3562 3642 1.220529 CATGTCGTGTGTGAAGCAGT 58.779 50.000 0.00 0.00 0.00 4.40
3563 3643 0.514255 CCATGTCGTGTGTGAAGCAG 59.486 55.000 0.00 0.00 0.00 4.24
3564 3644 0.179059 ACCATGTCGTGTGTGAAGCA 60.179 50.000 0.00 0.00 0.00 3.91
3565 3645 0.944386 AACCATGTCGTGTGTGAAGC 59.056 50.000 0.00 0.00 0.00 3.86
3566 3646 2.854424 GCAAACCATGTCGTGTGTGAAG 60.854 50.000 0.00 0.00 0.00 3.02
3567 3647 1.064803 GCAAACCATGTCGTGTGTGAA 59.935 47.619 0.00 0.00 0.00 3.18
3568 3648 0.660488 GCAAACCATGTCGTGTGTGA 59.340 50.000 0.00 0.00 0.00 3.58
3569 3649 0.380024 TGCAAACCATGTCGTGTGTG 59.620 50.000 0.00 0.00 0.00 3.82
3570 3650 0.380378 GTGCAAACCATGTCGTGTGT 59.620 50.000 0.00 0.00 0.00 3.72
3571 3651 0.317770 GGTGCAAACCATGTCGTGTG 60.318 55.000 0.00 0.00 0.00 3.82
3572 3652 0.749818 TGGTGCAAACCATGTCGTGT 60.750 50.000 0.00 0.00 34.33 4.49
3573 3653 2.028936 TGGTGCAAACCATGTCGTG 58.971 52.632 0.00 0.00 34.33 4.35
3574 3654 4.569279 TGGTGCAAACCATGTCGT 57.431 50.000 0.00 0.00 34.33 4.34
3588 3668 1.922570 GCGTATCGTTCACAGATGGT 58.077 50.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.