Multiple sequence alignment - TraesCS6A01G261200

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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 TraesCS6A01G261200 chr6A 100.000 6200 0 0 1 6200 484607202 484613401 0.000000e+00 11450.0
1 TraesCS6A01G261200 chr6A 81.713 432 73 6 1237 1665 617657087 617657515 7.640000e-94 355.0
2 TraesCS6A01G261200 chr6A 95.918 49 2 0 2794 2842 484610044 484610092 5.150000e-11 80.5
3 TraesCS6A01G261200 chr6D 92.254 2879 114 37 14 2842 344206628 344209447 0.000000e+00 3980.0
4 TraesCS6A01G261200 chr6D 92.716 2169 103 22 3923 6060 344210385 344212529 0.000000e+00 3079.0
5 TraesCS6A01G261200 chr6D 96.687 483 14 1 2843 3325 344209399 344209879 0.000000e+00 802.0
6 TraesCS6A01G261200 chr6D 97.046 474 10 3 3323 3795 344209919 344210389 0.000000e+00 795.0
7 TraesCS6A01G261200 chr6D 80.831 433 75 8 1237 1665 472358927 472358499 3.580000e-87 333.0
8 TraesCS6A01G261200 chr6B 92.999 1257 37 15 527 1745 519719659 519720902 0.000000e+00 1786.0
9 TraesCS6A01G261200 chr6B 95.303 1022 42 5 2843 3860 519722100 519723119 0.000000e+00 1616.0
10 TraesCS6A01G261200 chr6B 94.519 967 27 9 3858 4806 519723404 519724362 0.000000e+00 1469.0
11 TraesCS6A01G261200 chr6B 92.206 834 38 8 2025 2842 519721326 519722148 0.000000e+00 1155.0
12 TraesCS6A01G261200 chr6B 90.523 612 29 7 4970 5562 519724650 519725251 0.000000e+00 782.0
13 TraesCS6A01G261200 chr6B 90.730 507 45 2 5555 6060 519726658 519727163 0.000000e+00 675.0
14 TraesCS6A01G261200 chr6B 80.370 433 77 8 1237 1665 717076860 717076432 7.750000e-84 322.0
15 TraesCS6A01G261200 chr6B 95.312 128 6 0 1826 1953 519720932 519721059 2.930000e-48 204.0
16 TraesCS6A01G261200 chr6B 97.391 115 2 1 4853 4967 519724363 519724476 1.760000e-45 195.0
17 TraesCS6A01G261200 chr2D 86.519 586 72 6 1162 1744 564095584 564095003 6.780000e-179 638.0
18 TraesCS6A01G261200 chr2D 88.710 248 26 2 4429 4676 564092574 564092329 1.010000e-77 302.0
19 TraesCS6A01G261200 chr2D 92.647 68 4 1 2843 2910 591958865 591958931 5.120000e-16 97.1
20 TraesCS6A01G261200 chr2B 86.395 588 69 10 1162 1744 675356270 675355689 3.150000e-177 632.0
21 TraesCS6A01G261200 chr2B 86.567 268 32 4 4410 4676 675353256 675352992 6.080000e-75 292.0
22 TraesCS6A01G261200 chr2B 100.000 28 0 0 2816 2843 461093118 461093091 1.100000e-02 52.8
23 TraesCS6A01G261200 chr2A 89.286 504 54 0 1241 1744 704776761 704776258 3.150000e-177 632.0
24 TraesCS6A01G261200 chr2A 91.139 79 5 2 2844 2922 726424246 726424322 8.500000e-19 106.0
25 TraesCS6A01G261200 chr2A 86.154 65 9 0 2778 2842 726424229 726424293 3.100000e-08 71.3
26 TraesCS6A01G261200 chr5B 78.821 458 87 10 1280 1732 153503435 153502983 3.630000e-77 300.0
27 TraesCS6A01G261200 chr5B 94.737 38 2 0 5577 5614 133017180 133017217 6.710000e-05 60.2
28 TraesCS6A01G261200 chr4B 76.493 268 45 15 1474 1732 22275807 22275549 5.040000e-26 130.0
29 TraesCS6A01G261200 chr3B 90.816 98 8 1 5877 5974 14253697 14253601 5.040000e-26 130.0
30 TraesCS6A01G261200 chr4D 76.296 270 42 18 1474 1732 12409216 12409474 2.350000e-24 124.0
31 TraesCS6A01G261200 chr3D 95.000 80 3 1 2842 2921 370115720 370115798 2.350000e-24 124.0
32 TraesCS6A01G261200 chr3D 92.857 56 4 0 2787 2842 370115714 370115769 1.430000e-11 82.4
33 TraesCS6A01G261200 chr3A 95.000 80 3 1 2843 2922 151644761 151644683 2.350000e-24 124.0
34 TraesCS6A01G261200 chr3A 88.636 88 4 3 6095 6179 468975315 468975399 1.100000e-17 102.0
35 TraesCS6A01G261200 chr3A 94.340 53 3 0 2790 2842 151644765 151644713 1.430000e-11 82.4
36 TraesCS6A01G261200 chr5D 83.898 118 17 2 5823 5939 310667979 310668095 1.830000e-20 111.0
37 TraesCS6A01G261200 chr5D 92.405 79 5 1 2843 2921 414025493 414025416 1.830000e-20 111.0
38 TraesCS6A01G261200 chr1D 95.455 66 2 1 2843 2908 474351128 474351192 3.060000e-18 104.0
39 TraesCS6A01G261200 chr1D 93.443 61 1 3 2785 2842 474351117 474351177 3.080000e-13 87.9
40 TraesCS6A01G261200 chr7D 92.308 65 4 1 2846 2910 461144010 461143947 2.380000e-14 91.6
41 TraesCS6A01G261200 chr7D 90.566 53 3 1 2791 2841 478456281 478456229 1.120000e-07 69.4
42 TraesCS6A01G261200 chr5A 89.231 65 7 0 5875 5939 404176133 404176197 1.430000e-11 82.4
43 TraesCS6A01G261200 chr1B 92.105 38 3 0 2806 2843 635535225 635535262 3.000000e-03 54.7


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 TraesCS6A01G261200 chr6A 484607202 484613401 6199 False 5765.25 11450 97.959000 1 6200 2 chr6A.!!$F2 6199
1 TraesCS6A01G261200 chr6D 344206628 344212529 5901 False 2164.00 3980 94.675750 14 6060 4 chr6D.!!$F1 6046
2 TraesCS6A01G261200 chr6B 519719659 519727163 7504 False 985.25 1786 93.622875 527 6060 8 chr6B.!!$F1 5533
3 TraesCS6A01G261200 chr2D 564092329 564095584 3255 True 470.00 638 87.614500 1162 4676 2 chr2D.!!$R1 3514
4 TraesCS6A01G261200 chr2B 675352992 675356270 3278 True 462.00 632 86.481000 1162 4676 2 chr2B.!!$R2 3514
5 TraesCS6A01G261200 chr2A 704776258 704776761 503 True 632.00 632 89.286000 1241 1744 1 chr2A.!!$R1 503

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
392 396 0.243636 GCCCGTATGCAACAAAGCTT 59.756 50.000 0.00 0.00 34.99 3.74 F
467 476 0.901124 AAGCCTCTCTGCCTACACTG 59.099 55.000 0.00 0.00 0.00 3.66 F
1746 1802 0.318441 TCTTCAAGCCTGGTGAGTCG 59.682 55.000 0.00 0.00 0.00 4.18 F
2602 2974 0.107456 ACCTGTTCTGAGCAGTGTGG 59.893 55.000 18.32 8.09 32.41 4.17 F
3173 3555 2.622436 AGAAGATGGCTTTGCGAGTAC 58.378 47.619 0.00 0.00 33.61 2.73 F
3224 3606 2.751259 CCATGTGCAGCAGTGAAGTTAT 59.249 45.455 0.00 0.00 0.00 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 1802 0.104671 TTTGTTGCCTTGCCTGAAGC 59.895 50.000 0.00 0.0 44.14 3.86 R
1972 2029 1.099456 AGTAGGGTAGGAACAGGGGT 58.901 55.000 0.00 0.0 0.00 4.95 R
2809 3189 3.678056 TCATAGTGTCAAAAGGCGTCT 57.322 42.857 0.00 0.0 0.00 4.18 R
3876 4902 0.898320 TTCCTACTCAGCTGACAGGC 59.102 55.000 25.54 0.0 0.00 4.85 R
4877 5997 0.965363 AAGGTTTATGCACCCAGGCG 60.965 55.000 0.00 0.0 37.58 5.52 R
5203 6508 0.744874 GCAGTGTCCCGTATAGCAGA 59.255 55.000 0.00 0.0 0.00 4.26 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
48 49 8.374464 CTTTTTGAAAAGCGCAAACAATTTTA 57.626 26.923 11.47 0.00 38.95 1.52
240 244 5.852827 TCAAATTTCTGAACAATTGGGACC 58.147 37.500 10.83 0.00 0.00 4.46
246 250 1.177401 GAACAATTGGGACCAGAGGC 58.823 55.000 10.83 0.00 0.00 4.70
283 287 5.782893 TTCCTTTTGAAACATGTCCGAAT 57.217 34.783 0.00 0.00 0.00 3.34
284 288 5.119931 TCCTTTTGAAACATGTCCGAATG 57.880 39.130 0.00 3.40 0.00 2.67
298 302 5.309638 TGTCCGAATGTTTGATGTTTAGGA 58.690 37.500 0.00 0.00 0.00 2.94
299 303 5.943416 TGTCCGAATGTTTGATGTTTAGGAT 59.057 36.000 0.00 0.00 0.00 3.24
314 318 0.337428 AGGATTGGATGGCTGGCTTT 59.663 50.000 2.00 0.00 0.00 3.51
316 320 1.477553 GATTGGATGGCTGGCTTTCA 58.522 50.000 2.00 0.00 0.00 2.69
321 325 2.175284 TGGATGGCTGGCTTTCATATCA 59.825 45.455 2.00 0.00 0.00 2.15
328 332 2.868583 CTGGCTTTCATATCACTGTCCG 59.131 50.000 0.00 0.00 0.00 4.79
330 334 1.258982 GCTTTCATATCACTGTCCGCG 59.741 52.381 0.00 0.00 0.00 6.46
331 335 1.860950 CTTTCATATCACTGTCCGCGG 59.139 52.381 22.12 22.12 0.00 6.46
336 340 0.393944 TATCACTGTCCGCGGACTCT 60.394 55.000 46.72 33.15 44.80 3.24
337 341 1.251527 ATCACTGTCCGCGGACTCTT 61.252 55.000 46.72 32.31 44.80 2.85
338 342 1.444553 CACTGTCCGCGGACTCTTC 60.445 63.158 46.72 28.72 44.80 2.87
339 343 2.182030 CTGTCCGCGGACTCTTCC 59.818 66.667 46.72 28.03 44.80 3.46
355 359 3.815401 CTCTTCCGGACATGTCTGTTTTT 59.185 43.478 28.57 0.00 35.14 1.94
368 372 1.338655 CTGTTTTTGGGGTACGGTTGG 59.661 52.381 0.00 0.00 0.00 3.77
370 374 1.610038 GTTTTTGGGGTACGGTTGGAG 59.390 52.381 0.00 0.00 0.00 3.86
392 396 0.243636 GCCCGTATGCAACAAAGCTT 59.756 50.000 0.00 0.00 34.99 3.74
393 397 1.732405 GCCCGTATGCAACAAAGCTTC 60.732 52.381 0.00 0.00 34.99 3.86
394 398 1.812571 CCCGTATGCAACAAAGCTTCT 59.187 47.619 0.00 0.00 34.99 2.85
395 399 3.006940 CCCGTATGCAACAAAGCTTCTA 58.993 45.455 0.00 0.00 34.99 2.10
396 400 3.438781 CCCGTATGCAACAAAGCTTCTAA 59.561 43.478 0.00 0.00 34.99 2.10
397 401 4.083003 CCCGTATGCAACAAAGCTTCTAAA 60.083 41.667 0.00 0.00 34.99 1.85
398 402 5.457140 CCGTATGCAACAAAGCTTCTAAAA 58.543 37.500 0.00 0.00 34.99 1.52
445 450 2.115291 GGCCATCTCTTTCCCACGC 61.115 63.158 0.00 0.00 0.00 5.34
467 476 0.901124 AAGCCTCTCTGCCTACACTG 59.099 55.000 0.00 0.00 0.00 3.66
472 481 3.357203 CCTCTCTGCCTACACTGTCTTA 58.643 50.000 0.00 0.00 0.00 2.10
480 489 3.194968 GCCTACACTGTCTTAGTTGCCTA 59.805 47.826 0.00 0.00 37.60 3.93
482 491 5.352284 CCTACACTGTCTTAGTTGCCTATG 58.648 45.833 0.00 0.00 37.60 2.23
484 493 5.483685 ACACTGTCTTAGTTGCCTATGAA 57.516 39.130 0.00 0.00 37.60 2.57
485 494 6.054860 ACACTGTCTTAGTTGCCTATGAAT 57.945 37.500 0.00 0.00 37.60 2.57
487 496 7.796054 ACACTGTCTTAGTTGCCTATGAATAT 58.204 34.615 0.00 0.00 37.60 1.28
510 519 4.952704 GCCCTCTCTGAAGGCTTC 57.047 61.111 20.27 20.27 43.62 3.86
523 532 3.932089 TGAAGGCTTCTGTTTGCAAAAAC 59.068 39.130 26.26 3.59 0.00 2.43
577 588 2.859165 TGTGGGAGAAAACTAGCCAG 57.141 50.000 0.00 0.00 0.00 4.85
621 632 1.131126 CTAGCCAACATTTCCTGCACG 59.869 52.381 0.00 0.00 0.00 5.34
645 656 1.001020 ATCTTTGCATCCGTGGCCA 60.001 52.632 0.00 0.00 0.00 5.36
646 657 1.033746 ATCTTTGCATCCGTGGCCAG 61.034 55.000 5.11 0.00 0.00 4.85
648 659 2.203972 CTTTGCATCCGTGGCCAGTG 62.204 60.000 5.11 0.51 0.00 3.66
694 709 1.395635 TGTATATCCAGTCCGTGCGT 58.604 50.000 0.00 0.00 0.00 5.24
813 863 4.154347 CCGCCTCCAGCTCACTCC 62.154 72.222 0.00 0.00 40.39 3.85
835 885 4.697756 TCCCGAGGCCGCAACAAG 62.698 66.667 7.44 0.00 0.00 3.16
944 997 1.768077 CCCTAGCCTAGCCAGCCTT 60.768 63.158 0.00 0.00 0.00 4.35
951 1004 3.391665 CTAGCCAGCCTTGACCCCG 62.392 68.421 0.00 0.00 0.00 5.73
1125 1178 3.032609 GATGCCGATGCCGACTCG 61.033 66.667 0.00 0.00 38.22 4.18
1398 1454 1.890552 AGCTCATCACCAAGGAGGAT 58.109 50.000 0.00 0.00 41.22 3.24
1746 1802 0.318441 TCTTCAAGCCTGGTGAGTCG 59.682 55.000 0.00 0.00 0.00 4.18
1751 1807 1.758440 AAGCCTGGTGAGTCGCTTCA 61.758 55.000 3.25 0.00 36.92 3.02
1753 1809 1.079543 CCTGGTGAGTCGCTTCAGG 60.080 63.158 12.74 12.74 38.96 3.86
1755 1811 2.343758 GGTGAGTCGCTTCAGGCA 59.656 61.111 3.25 0.00 41.91 4.75
1834 1890 2.270352 TTGAGATCACAACCACCCAC 57.730 50.000 1.02 0.00 0.00 4.61
1963 2020 2.875296 TGCAACAAATAGGAGCCACTT 58.125 42.857 0.00 0.00 0.00 3.16
1964 2021 3.230134 TGCAACAAATAGGAGCCACTTT 58.770 40.909 0.00 0.00 0.00 2.66
1965 2022 4.402829 TGCAACAAATAGGAGCCACTTTA 58.597 39.130 0.00 0.00 0.00 1.85
1966 2023 4.830046 TGCAACAAATAGGAGCCACTTTAA 59.170 37.500 0.00 0.00 0.00 1.52
1969 2026 6.516693 GCAACAAATAGGAGCCACTTTAAACT 60.517 38.462 0.00 0.00 0.00 2.66
2273 2638 3.316308 GGGCAGGTAGAGCATTATGTTTG 59.684 47.826 0.00 0.00 0.00 2.93
2398 2763 3.081061 TGATGCAGTATTGAAAGGCGTT 58.919 40.909 0.00 0.00 0.00 4.84
2428 2793 1.771255 GATAGTGATCCCTGGCCTGTT 59.229 52.381 3.32 0.00 0.00 3.16
2529 2894 6.540438 TCTATGTTAGTTACTTCCACCAGG 57.460 41.667 0.00 0.00 0.00 4.45
2564 2936 5.076873 TGTTTCTTAATTCAGGTCCTTGGG 58.923 41.667 0.00 0.00 0.00 4.12
2602 2974 0.107456 ACCTGTTCTGAGCAGTGTGG 59.893 55.000 18.32 8.09 32.41 4.17
2661 3033 4.571580 AGCACAACATTGTTTTGGTTGATG 59.428 37.500 13.15 6.42 43.41 3.07
2673 3045 9.912634 TTGTTTTGGTTGATGAGAAATAAGATC 57.087 29.630 0.00 0.00 0.00 2.75
2674 3046 9.300681 TGTTTTGGTTGATGAGAAATAAGATCT 57.699 29.630 0.00 0.00 0.00 2.75
2795 3175 7.823635 TGTACCTGTTATTATCTAGTCCCTCT 58.176 38.462 0.00 0.00 0.00 3.69
2796 3176 7.724506 TGTACCTGTTATTATCTAGTCCCTCTG 59.275 40.741 0.00 0.00 0.00 3.35
2797 3177 6.684538 ACCTGTTATTATCTAGTCCCTCTGT 58.315 40.000 0.00 0.00 0.00 3.41
2798 3178 7.823635 ACCTGTTATTATCTAGTCCCTCTGTA 58.176 38.462 0.00 0.00 0.00 2.74
2799 3179 8.457757 ACCTGTTATTATCTAGTCCCTCTGTAT 58.542 37.037 0.00 0.00 0.00 2.29
2800 3180 8.962679 CCTGTTATTATCTAGTCCCTCTGTATC 58.037 40.741 0.00 0.00 0.00 2.24
2801 3181 9.521841 CTGTTATTATCTAGTCCCTCTGTATCA 57.478 37.037 0.00 0.00 0.00 2.15
2802 3182 9.877222 TGTTATTATCTAGTCCCTCTGTATCAA 57.123 33.333 0.00 0.00 0.00 2.57
2810 3190 9.575868 TCTAGTCCCTCTGTATCAAACTATAAG 57.424 37.037 0.00 0.00 0.00 1.73
2811 3191 9.575868 CTAGTCCCTCTGTATCAAACTATAAGA 57.424 37.037 0.00 0.00 0.00 2.10
2812 3192 8.240267 AGTCCCTCTGTATCAAACTATAAGAC 57.760 38.462 0.00 0.00 0.00 3.01
2813 3193 7.013464 AGTCCCTCTGTATCAAACTATAAGACG 59.987 40.741 0.00 0.00 0.00 4.18
2814 3194 5.921408 CCCTCTGTATCAAACTATAAGACGC 59.079 44.000 0.00 0.00 0.00 5.19
2815 3195 5.921408 CCTCTGTATCAAACTATAAGACGCC 59.079 44.000 0.00 0.00 0.00 5.68
2816 3196 6.239064 CCTCTGTATCAAACTATAAGACGCCT 60.239 42.308 0.00 0.00 0.00 5.52
2817 3197 7.108841 TCTGTATCAAACTATAAGACGCCTT 57.891 36.000 0.00 0.00 36.43 4.35
2818 3198 7.553334 TCTGTATCAAACTATAAGACGCCTTT 58.447 34.615 0.00 0.00 33.94 3.11
2819 3199 8.038944 TCTGTATCAAACTATAAGACGCCTTTT 58.961 33.333 0.00 0.00 33.94 2.27
2820 3200 7.970384 TGTATCAAACTATAAGACGCCTTTTG 58.030 34.615 0.00 0.00 33.94 2.44
2821 3201 7.820386 TGTATCAAACTATAAGACGCCTTTTGA 59.180 33.333 0.00 0.00 32.17 2.69
2822 3202 6.476243 TCAAACTATAAGACGCCTTTTGAC 57.524 37.500 0.00 0.00 33.94 3.18
2823 3203 5.992829 TCAAACTATAAGACGCCTTTTGACA 59.007 36.000 0.00 0.00 33.94 3.58
2824 3204 5.857822 AACTATAAGACGCCTTTTGACAC 57.142 39.130 0.00 0.00 33.94 3.67
2825 3205 5.148651 ACTATAAGACGCCTTTTGACACT 57.851 39.130 0.00 0.00 33.94 3.55
2826 3206 6.276832 ACTATAAGACGCCTTTTGACACTA 57.723 37.500 0.00 0.00 33.94 2.74
2827 3207 6.875076 ACTATAAGACGCCTTTTGACACTAT 58.125 36.000 0.00 0.00 33.94 2.12
2828 3208 6.757010 ACTATAAGACGCCTTTTGACACTATG 59.243 38.462 0.00 0.00 33.94 2.23
2829 3209 3.678056 AGACGCCTTTTGACACTATGA 57.322 42.857 0.00 0.00 0.00 2.15
2830 3210 4.207891 AGACGCCTTTTGACACTATGAT 57.792 40.909 0.00 0.00 0.00 2.45
2831 3211 5.339008 AGACGCCTTTTGACACTATGATA 57.661 39.130 0.00 0.00 0.00 2.15
2832 3212 5.352284 AGACGCCTTTTGACACTATGATAG 58.648 41.667 0.00 0.00 0.00 2.08
2833 3213 5.086104 ACGCCTTTTGACACTATGATAGT 57.914 39.130 0.00 0.00 40.28 2.12
2973 3355 8.586744 GGGGAAAACAAACCATTTAGTATGTAA 58.413 33.333 0.00 0.00 0.00 2.41
3172 3554 3.334583 AAGAAGATGGCTTTGCGAGTA 57.665 42.857 0.00 0.00 33.61 2.59
3173 3555 2.622436 AGAAGATGGCTTTGCGAGTAC 58.378 47.619 0.00 0.00 33.61 2.73
3224 3606 2.751259 CCATGTGCAGCAGTGAAGTTAT 59.249 45.455 0.00 0.00 0.00 1.89
3386 4118 9.936759 TGTTGACTTATTGTGACACTATATTCA 57.063 29.630 9.99 11.92 0.00 2.57
3845 4583 6.227298 TCTTAGCTTCTGACTATGAAAGGG 57.773 41.667 0.00 0.00 0.00 3.95
4198 5230 2.876550 GTTCAGTTTTGTCTTAGCCGGT 59.123 45.455 1.90 0.00 0.00 5.28
4832 5952 6.693315 TCTATGGCCTTTAAATTGTGCTAC 57.307 37.500 3.32 0.00 0.00 3.58
4833 5953 6.184068 TCTATGGCCTTTAAATTGTGCTACA 58.816 36.000 3.32 0.00 0.00 2.74
4835 5955 5.070770 TGGCCTTTAAATTGTGCTACATG 57.929 39.130 3.32 0.00 0.00 3.21
4836 5956 3.865164 GGCCTTTAAATTGTGCTACATGC 59.135 43.478 0.00 0.00 43.25 4.06
4837 5957 4.381932 GGCCTTTAAATTGTGCTACATGCT 60.382 41.667 0.00 0.00 43.37 3.79
4838 5958 5.163561 GGCCTTTAAATTGTGCTACATGCTA 60.164 40.000 0.00 0.00 43.37 3.49
4839 5959 6.461509 GGCCTTTAAATTGTGCTACATGCTAT 60.462 38.462 0.00 0.00 43.37 2.97
4840 5960 7.255451 GGCCTTTAAATTGTGCTACATGCTATA 60.255 37.037 0.00 0.00 43.37 1.31
4841 5961 7.805071 GCCTTTAAATTGTGCTACATGCTATAG 59.195 37.037 0.00 0.00 43.37 1.31
4842 5962 7.805071 CCTTTAAATTGTGCTACATGCTATAGC 59.195 37.037 18.18 18.18 44.48 2.97
4843 5963 8.450578 TTTAAATTGTGCTACATGCTATAGCT 57.549 30.769 24.61 8.18 44.52 3.32
4844 5964 9.554395 TTTAAATTGTGCTACATGCTATAGCTA 57.446 29.630 24.61 12.11 44.52 3.32
4845 5965 9.725019 TTAAATTGTGCTACATGCTATAGCTAT 57.275 29.630 24.61 11.77 44.52 2.97
4846 5966 7.840342 AATTGTGCTACATGCTATAGCTATC 57.160 36.000 24.61 6.37 44.52 2.08
4877 5997 8.146412 TCCTAGTTCCTAAAACAAGACTGTAAC 58.854 37.037 0.00 0.00 33.45 2.50
4899 6019 2.524306 CCTGGGTGCATAAACCTTCAA 58.476 47.619 0.00 0.00 40.35 2.69
4962 6082 2.498167 AGATGCTCGCCAAATGATACC 58.502 47.619 0.00 0.00 0.00 2.73
4963 6083 2.158769 AGATGCTCGCCAAATGATACCA 60.159 45.455 0.00 0.00 0.00 3.25
4964 6084 2.346766 TGCTCGCCAAATGATACCAT 57.653 45.000 0.00 0.00 33.66 3.55
4965 6085 3.483808 TGCTCGCCAAATGATACCATA 57.516 42.857 0.00 0.00 31.59 2.74
4967 6087 3.752747 TGCTCGCCAAATGATACCATATG 59.247 43.478 0.00 0.00 31.59 1.78
4968 6088 3.127548 GCTCGCCAAATGATACCATATGG 59.872 47.826 20.68 20.68 42.17 2.74
4992 6282 6.201806 GGTGCAATGATAGACAAGTACATCTC 59.798 42.308 0.00 0.00 0.00 2.75
5024 6314 6.177610 TGTCACTGTAGAACCTTTGAACTTT 58.822 36.000 0.00 0.00 0.00 2.66
5046 6351 0.245813 TGTGTTGCTGCTTGTTTGCA 59.754 45.000 0.00 0.00 41.05 4.08
5058 6363 3.676646 GCTTGTTTGCAATAGAGCTTTGG 59.323 43.478 16.58 0.00 33.65 3.28
5148 6453 3.053019 TGATGACAAAGGGCAATATGGGA 60.053 43.478 0.00 0.00 0.00 4.37
5203 6508 8.427276 TGAATATAAGCATGACTGAATGAGACT 58.573 33.333 0.00 0.00 0.00 3.24
5338 6643 7.744068 TGTATGGGGGAAATCTCCTATATCTTT 59.256 37.037 8.45 0.00 42.05 2.52
5339 6644 7.669677 ATGGGGGAAATCTCCTATATCTTTT 57.330 36.000 0.00 0.00 42.05 2.27
5504 6813 2.032681 GGGTCACTGGCAGGTCAC 59.967 66.667 20.34 11.46 0.00 3.67
5545 6854 5.650266 CGGTCTTCTCATACTGGCTCTATAT 59.350 44.000 0.00 0.00 0.00 0.86
5642 8366 1.600485 GTTTGACACGTCGGATTTGGT 59.400 47.619 0.00 0.00 0.00 3.67
5677 8401 5.050769 CCAGCTGACACAACATATATTCGTC 60.051 44.000 17.39 0.00 0.00 4.20
5685 8428 6.015688 ACACAACATATATTCGTCCCGTATCT 60.016 38.462 0.00 0.00 0.00 1.98
5737 8481 2.154462 CACTTGGTCAAACCCTAGCTG 58.846 52.381 0.00 0.00 37.50 4.24
5764 8508 0.040204 CCACTTGGCCCCAAATCTCT 59.960 55.000 0.00 0.00 35.33 3.10
5778 8522 4.256920 CAAATCTCTGTTCCGGTGATCTT 58.743 43.478 0.00 0.00 0.00 2.40
5798 8543 1.617018 CGGCCTTCTCTGGGACATCA 61.617 60.000 0.00 0.00 38.20 3.07
5801 8546 1.767681 GCCTTCTCTGGGACATCATCT 59.232 52.381 0.00 0.00 38.20 2.90
5828 8573 3.471244 GACGAGGAGGCGATGGTCG 62.471 68.421 0.00 0.00 43.89 4.79
5863 8608 3.681835 GAGTGTGGCCGACCGAGT 61.682 66.667 0.00 0.00 39.70 4.18
5865 8610 2.280592 GTGTGGCCGACCGAGTTT 60.281 61.111 0.00 0.00 39.70 2.66
5947 8692 3.450115 GGCTCGAGGCACGTACCT 61.450 66.667 31.94 7.16 45.04 3.08
5981 8726 2.966309 GCGGTGAGGTCCTTTTGCG 61.966 63.158 0.00 0.00 0.00 4.85
6024 8769 4.708421 GGTGTATGAGTGTTGTAGGGACTA 59.292 45.833 0.00 0.00 41.75 2.59
6060 8805 2.994643 AAACAAAGGGTGCGGGAGGG 62.995 60.000 0.00 0.00 0.00 4.30
6107 8852 4.115199 CCCGCCCCCAAAGAGGAG 62.115 72.222 0.00 0.00 41.22 3.69
6108 8853 3.009115 CCGCCCCCAAAGAGGAGA 61.009 66.667 0.00 0.00 41.22 3.71
6109 8854 2.602676 CCGCCCCCAAAGAGGAGAA 61.603 63.158 0.00 0.00 41.22 2.87
6110 8855 1.078143 CGCCCCCAAAGAGGAGAAG 60.078 63.158 0.00 0.00 41.22 2.85
6111 8856 1.304617 GCCCCCAAAGAGGAGAAGG 59.695 63.158 0.00 0.00 41.22 3.46
6112 8857 1.208165 GCCCCCAAAGAGGAGAAGGA 61.208 60.000 0.00 0.00 41.22 3.36
6113 8858 0.915364 CCCCCAAAGAGGAGAAGGAG 59.085 60.000 0.00 0.00 41.22 3.69
6114 8859 0.915364 CCCCAAAGAGGAGAAGGAGG 59.085 60.000 0.00 0.00 41.22 4.30
6115 8860 1.555765 CCCCAAAGAGGAGAAGGAGGA 60.556 57.143 0.00 0.00 41.22 3.71
6116 8861 1.557371 CCCAAAGAGGAGAAGGAGGAC 59.443 57.143 0.00 0.00 41.22 3.85
6117 8862 2.260822 CCAAAGAGGAGAAGGAGGACA 58.739 52.381 0.00 0.00 41.22 4.02
6118 8863 2.639839 CCAAAGAGGAGAAGGAGGACAA 59.360 50.000 0.00 0.00 41.22 3.18
6119 8864 3.265479 CCAAAGAGGAGAAGGAGGACAAT 59.735 47.826 0.00 0.00 41.22 2.71
6120 8865 4.260170 CAAAGAGGAGAAGGAGGACAATG 58.740 47.826 0.00 0.00 0.00 2.82
6121 8866 3.481559 AGAGGAGAAGGAGGACAATGA 57.518 47.619 0.00 0.00 0.00 2.57
6122 8867 3.103742 AGAGGAGAAGGAGGACAATGAC 58.896 50.000 0.00 0.00 0.00 3.06
6123 8868 3.103742 GAGGAGAAGGAGGACAATGACT 58.896 50.000 0.00 0.00 0.00 3.41
6124 8869 2.836981 AGGAGAAGGAGGACAATGACTG 59.163 50.000 0.00 0.00 0.00 3.51
6125 8870 2.093235 GGAGAAGGAGGACAATGACTGG 60.093 54.545 0.00 0.00 0.00 4.00
6126 8871 2.569404 GAGAAGGAGGACAATGACTGGT 59.431 50.000 0.00 0.00 0.00 4.00
6127 8872 2.982488 AGAAGGAGGACAATGACTGGTT 59.018 45.455 0.00 0.00 0.00 3.67
6128 8873 2.867109 AGGAGGACAATGACTGGTTG 57.133 50.000 0.00 0.00 0.00 3.77
6129 8874 1.352352 AGGAGGACAATGACTGGTTGG 59.648 52.381 0.00 0.00 0.00 3.77
6130 8875 1.614317 GGAGGACAATGACTGGTTGGG 60.614 57.143 0.00 0.00 0.00 4.12
6131 8876 0.251341 AGGACAATGACTGGTTGGGC 60.251 55.000 0.00 0.00 0.00 5.36
6132 8877 0.539438 GGACAATGACTGGTTGGGCA 60.539 55.000 0.00 0.00 0.00 5.36
6133 8878 0.883833 GACAATGACTGGTTGGGCAG 59.116 55.000 0.00 0.00 0.00 4.85
6134 8879 1.181098 ACAATGACTGGTTGGGCAGC 61.181 55.000 0.00 0.00 0.00 5.25
6135 8880 0.896940 CAATGACTGGTTGGGCAGCT 60.897 55.000 0.00 0.00 0.00 4.24
6136 8881 0.610232 AATGACTGGTTGGGCAGCTC 60.610 55.000 0.00 0.00 0.00 4.09
6137 8882 2.360475 GACTGGTTGGGCAGCTCC 60.360 66.667 0.00 0.00 0.00 4.70
6138 8883 4.335647 ACTGGTTGGGCAGCTCCG 62.336 66.667 0.00 0.00 34.94 4.63
6159 8904 2.470196 CGATGAGCAGATTTGGCTTG 57.530 50.000 0.00 0.00 42.78 4.01
6160 8905 2.011947 CGATGAGCAGATTTGGCTTGA 58.988 47.619 0.00 0.00 42.78 3.02
6161 8906 2.617308 CGATGAGCAGATTTGGCTTGAT 59.383 45.455 0.00 0.00 42.78 2.57
6162 8907 3.303857 CGATGAGCAGATTTGGCTTGATC 60.304 47.826 0.00 0.00 42.78 2.92
6163 8908 2.372264 TGAGCAGATTTGGCTTGATCC 58.628 47.619 0.00 0.00 42.78 3.36
6164 8909 2.291089 TGAGCAGATTTGGCTTGATCCA 60.291 45.455 0.00 0.00 42.78 3.41
6165 8910 2.957006 GAGCAGATTTGGCTTGATCCAT 59.043 45.455 0.00 0.00 42.78 3.41
6166 8911 3.371965 AGCAGATTTGGCTTGATCCATT 58.628 40.909 0.00 0.00 38.81 3.16
6167 8912 3.773119 AGCAGATTTGGCTTGATCCATTT 59.227 39.130 0.00 0.00 38.81 2.32
6168 8913 4.224370 AGCAGATTTGGCTTGATCCATTTT 59.776 37.500 0.00 0.00 38.81 1.82
6169 8914 4.331717 GCAGATTTGGCTTGATCCATTTTG 59.668 41.667 0.00 0.00 35.77 2.44
6170 8915 5.484715 CAGATTTGGCTTGATCCATTTTGT 58.515 37.500 0.00 0.00 35.77 2.83
6171 8916 5.350365 CAGATTTGGCTTGATCCATTTTGTG 59.650 40.000 0.00 0.00 35.77 3.33
6172 8917 4.686191 TTTGGCTTGATCCATTTTGTGT 57.314 36.364 0.00 0.00 35.77 3.72
6173 8918 3.940209 TGGCTTGATCCATTTTGTGTC 57.060 42.857 0.00 0.00 0.00 3.67
6174 8919 3.499338 TGGCTTGATCCATTTTGTGTCT 58.501 40.909 0.00 0.00 0.00 3.41
6175 8920 3.896888 TGGCTTGATCCATTTTGTGTCTT 59.103 39.130 0.00 0.00 0.00 3.01
6176 8921 4.022068 TGGCTTGATCCATTTTGTGTCTTC 60.022 41.667 0.00 0.00 0.00 2.87
6177 8922 4.161333 GCTTGATCCATTTTGTGTCTTCG 58.839 43.478 0.00 0.00 0.00 3.79
6178 8923 4.083324 GCTTGATCCATTTTGTGTCTTCGA 60.083 41.667 0.00 0.00 0.00 3.71
6179 8924 5.611796 TTGATCCATTTTGTGTCTTCGAG 57.388 39.130 0.00 0.00 0.00 4.04
6180 8925 3.436704 TGATCCATTTTGTGTCTTCGAGC 59.563 43.478 0.00 0.00 0.00 5.03
6181 8926 2.844946 TCCATTTTGTGTCTTCGAGCA 58.155 42.857 0.00 0.00 0.00 4.26
6182 8927 2.548057 TCCATTTTGTGTCTTCGAGCAC 59.452 45.455 9.09 9.09 36.26 4.40
6183 8928 2.350772 CCATTTTGTGTCTTCGAGCACC 60.351 50.000 12.20 0.00 34.94 5.01
6184 8929 0.934496 TTTTGTGTCTTCGAGCACCG 59.066 50.000 12.20 0.00 40.25 4.94
6185 8930 0.179094 TTTGTGTCTTCGAGCACCGT 60.179 50.000 12.20 0.00 39.75 4.83
6186 8931 0.874175 TTGTGTCTTCGAGCACCGTG 60.874 55.000 12.20 0.00 39.75 4.94
6187 8932 1.007734 GTGTCTTCGAGCACCGTGA 60.008 57.895 1.65 0.00 39.75 4.35
6188 8933 1.007734 TGTCTTCGAGCACCGTGAC 60.008 57.895 1.65 14.50 40.33 3.67
6189 8934 1.007734 GTCTTCGAGCACCGTGACA 60.008 57.895 1.65 0.00 39.99 3.58
6190 8935 0.596600 GTCTTCGAGCACCGTGACAA 60.597 55.000 1.65 0.00 39.99 3.18
6191 8936 0.103390 TCTTCGAGCACCGTGACAAA 59.897 50.000 1.65 0.00 39.75 2.83
6192 8937 0.508641 CTTCGAGCACCGTGACAAAG 59.491 55.000 1.65 0.00 39.75 2.77
6193 8938 0.103390 TTCGAGCACCGTGACAAAGA 59.897 50.000 1.65 0.00 39.75 2.52
6194 8939 0.317160 TCGAGCACCGTGACAAAGAT 59.683 50.000 1.65 0.00 39.75 2.40
6195 8940 0.439985 CGAGCACCGTGACAAAGATG 59.560 55.000 1.65 0.00 0.00 2.90
6196 8941 0.166814 GAGCACCGTGACAAAGATGC 59.833 55.000 1.65 0.00 0.00 3.91
6197 8942 1.210155 GCACCGTGACAAAGATGCC 59.790 57.895 1.65 0.00 0.00 4.40
6198 8943 1.514678 GCACCGTGACAAAGATGCCA 61.515 55.000 1.65 0.00 0.00 4.92
6199 8944 0.950836 CACCGTGACAAAGATGCCAA 59.049 50.000 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
213 217 9.305925 GTCCCAATTGTTCAGAAATTTGATATC 57.694 33.333 4.43 0.00 0.00 1.63
219 223 5.602145 TCTGGTCCCAATTGTTCAGAAATTT 59.398 36.000 4.43 0.00 0.00 1.82
225 229 2.440409 CCTCTGGTCCCAATTGTTCAG 58.560 52.381 4.43 6.49 0.00 3.02
227 231 1.177401 GCCTCTGGTCCCAATTGTTC 58.823 55.000 4.43 0.00 0.00 3.18
232 236 3.411517 CGGGCCTCTGGTCCCAAT 61.412 66.667 0.84 0.00 46.44 3.16
240 244 0.821711 TTGAACAAACCGGGCCTCTG 60.822 55.000 6.32 0.00 0.00 3.35
246 250 3.744238 AAGGAATTTGAACAAACCGGG 57.256 42.857 6.32 0.00 32.51 5.73
283 287 5.105392 GCCATCCAATCCTAAACATCAAACA 60.105 40.000 0.00 0.00 0.00 2.83
284 288 5.127682 AGCCATCCAATCCTAAACATCAAAC 59.872 40.000 0.00 0.00 0.00 2.93
298 302 2.170012 ATGAAAGCCAGCCATCCAAT 57.830 45.000 0.00 0.00 0.00 3.16
299 303 2.824689 TATGAAAGCCAGCCATCCAA 57.175 45.000 0.00 0.00 0.00 3.53
314 318 0.384309 GTCCGCGGACAGTGATATGA 59.616 55.000 44.88 12.24 44.02 2.15
330 334 1.134965 CAGACATGTCCGGAAGAGTCC 60.135 57.143 22.21 4.47 41.01 3.85
331 335 1.546476 ACAGACATGTCCGGAAGAGTC 59.454 52.381 22.21 18.62 32.99 3.36
336 340 2.621055 CCAAAAACAGACATGTCCGGAA 59.379 45.455 22.21 0.00 39.29 4.30
337 341 2.226330 CCAAAAACAGACATGTCCGGA 58.774 47.619 22.21 0.00 39.29 5.14
338 342 1.269448 CCCAAAAACAGACATGTCCGG 59.731 52.381 22.21 16.72 39.29 5.14
339 343 1.269448 CCCCAAAAACAGACATGTCCG 59.731 52.381 22.21 14.96 39.29 4.79
340 344 2.316108 ACCCCAAAAACAGACATGTCC 58.684 47.619 22.21 4.75 39.29 4.02
341 345 3.058501 CGTACCCCAAAAACAGACATGTC 60.059 47.826 18.47 18.47 39.29 3.06
342 346 2.882137 CGTACCCCAAAAACAGACATGT 59.118 45.455 0.00 0.00 43.15 3.21
343 347 2.227865 CCGTACCCCAAAAACAGACATG 59.772 50.000 0.00 0.00 0.00 3.21
344 348 2.158579 ACCGTACCCCAAAAACAGACAT 60.159 45.455 0.00 0.00 0.00 3.06
345 349 1.212441 ACCGTACCCCAAAAACAGACA 59.788 47.619 0.00 0.00 0.00 3.41
346 350 1.971481 ACCGTACCCCAAAAACAGAC 58.029 50.000 0.00 0.00 0.00 3.51
355 359 1.906105 GCATCTCCAACCGTACCCCA 61.906 60.000 0.00 0.00 0.00 4.96
368 372 1.378531 TTGTTGCATACGGGCATCTC 58.621 50.000 0.00 0.00 44.48 2.75
370 374 1.798813 GCTTTGTTGCATACGGGCATC 60.799 52.381 0.00 0.66 44.48 3.91
394 398 9.752961 GCCATTTTGGAGTTACTTTTAGTTTTA 57.247 29.630 0.00 0.00 40.96 1.52
395 399 8.482943 AGCCATTTTGGAGTTACTTTTAGTTTT 58.517 29.630 0.00 0.00 40.96 2.43
396 400 8.018537 AGCCATTTTGGAGTTACTTTTAGTTT 57.981 30.769 0.00 0.00 40.96 2.66
397 401 7.597288 AGCCATTTTGGAGTTACTTTTAGTT 57.403 32.000 0.00 0.00 40.96 2.24
398 402 7.521585 CGAAGCCATTTTGGAGTTACTTTTAGT 60.522 37.037 0.00 0.00 40.96 2.24
458 463 2.347731 GGCAACTAAGACAGTGTAGGC 58.652 52.381 0.00 0.00 37.63 3.93
480 489 6.753913 TCAGAGAGGGCTAAACATATTCAT 57.246 37.500 0.00 0.00 0.00 2.57
482 491 5.994668 CCTTCAGAGAGGGCTAAACATATTC 59.005 44.000 0.00 0.00 32.94 1.75
484 493 5.559148 CCTTCAGAGAGGGCTAAACATAT 57.441 43.478 0.00 0.00 32.94 1.78
599 610 3.343617 GTGCAGGAAATGTTGGCTAGTA 58.656 45.455 0.00 0.00 0.00 1.82
601 612 1.131126 CGTGCAGGAAATGTTGGCTAG 59.869 52.381 0.00 0.00 0.00 3.42
621 632 1.667724 CACGGATGCAAAGATCCAGTC 59.332 52.381 4.99 0.00 42.01 3.51
709 724 0.602638 TCTGCTGCGTTTCCGTTGAT 60.603 50.000 0.00 0.00 36.15 2.57
890 943 4.785453 GGCTTGGCTCGGACAGGG 62.785 72.222 0.00 0.00 0.00 4.45
951 1004 0.671251 CATCTACCTGAGGCTCCGAC 59.329 60.000 12.86 0.00 0.00 4.79
1106 1159 4.592192 AGTCGGCATCGGCATCGG 62.592 66.667 0.00 0.00 44.51 4.18
1107 1160 3.032609 GAGTCGGCATCGGCATCG 61.033 66.667 0.00 0.00 44.51 3.84
1108 1161 3.032609 CGAGTCGGCATCGGCATC 61.033 66.667 4.10 0.00 44.51 3.91
1398 1454 4.794439 CGGCGCACATCCTCGACA 62.794 66.667 10.83 0.00 32.26 4.35
1746 1802 0.104671 TTTGTTGCCTTGCCTGAAGC 59.895 50.000 0.00 0.00 44.14 3.86
1751 1807 5.034852 AGTTAAATTTTGTTGCCTTGCCT 57.965 34.783 0.00 0.00 0.00 4.75
1753 1809 5.527214 AGGAAGTTAAATTTTGTTGCCTTGC 59.473 36.000 0.00 0.00 0.00 4.01
1755 1811 6.765989 GGAAGGAAGTTAAATTTTGTTGCCTT 59.234 34.615 11.66 11.66 34.94 4.35
1834 1890 9.778741 TTTTTGCCTCCATAGTAGTATATCTTG 57.221 33.333 0.00 0.00 0.00 3.02
1963 2020 2.424793 AGGAACAGGGGTGGAGTTTAA 58.575 47.619 0.00 0.00 0.00 1.52
1964 2021 2.127651 AGGAACAGGGGTGGAGTTTA 57.872 50.000 0.00 0.00 0.00 2.01
1965 2022 1.703513 GTAGGAACAGGGGTGGAGTTT 59.296 52.381 0.00 0.00 0.00 2.66
1966 2023 1.359168 GTAGGAACAGGGGTGGAGTT 58.641 55.000 0.00 0.00 0.00 3.01
1969 2026 1.229723 GGGTAGGAACAGGGGTGGA 60.230 63.158 0.00 0.00 0.00 4.02
1971 2028 1.201424 GTAGGGTAGGAACAGGGGTG 58.799 60.000 0.00 0.00 0.00 4.61
1972 2029 1.099456 AGTAGGGTAGGAACAGGGGT 58.901 55.000 0.00 0.00 0.00 4.95
1973 2030 3.142407 AGATAGTAGGGTAGGAACAGGGG 59.858 52.174 0.00 0.00 0.00 4.79
2398 2763 6.716628 GCCAGGGATCACTATCAAAATCAATA 59.283 38.462 0.00 0.00 33.41 1.90
2428 2793 7.795047 TGAGATCCTTTGCACTATCAGAAATA 58.205 34.615 0.00 0.00 0.00 1.40
2522 2887 1.209019 CAAGATCTGGAGTCCTGGTGG 59.791 57.143 15.43 0.00 0.00 4.61
2529 2894 8.553459 TGAATTAAGAAACAAGATCTGGAGTC 57.447 34.615 3.42 0.40 0.00 3.36
2564 2936 7.849804 ACAGGTATCAGAACAACATATTCAC 57.150 36.000 0.00 0.00 0.00 3.18
2689 3069 6.070656 AGAAATTGAGGTTTCCATGAGTCAA 58.929 36.000 0.00 0.00 38.55 3.18
2690 3070 5.634118 AGAAATTGAGGTTTCCATGAGTCA 58.366 37.500 0.00 0.00 38.55 3.41
2691 3071 7.687941 TTAGAAATTGAGGTTTCCATGAGTC 57.312 36.000 0.00 0.00 38.55 3.36
2788 3168 7.140048 CGTCTTATAGTTTGATACAGAGGGAC 58.860 42.308 0.00 0.00 0.00 4.46
2795 3175 7.820386 TCAAAAGGCGTCTTATAGTTTGATACA 59.180 33.333 0.94 0.00 32.01 2.29
2796 3176 8.114905 GTCAAAAGGCGTCTTATAGTTTGATAC 58.885 37.037 14.81 3.14 31.51 2.24
2797 3177 7.820386 TGTCAAAAGGCGTCTTATAGTTTGATA 59.180 33.333 14.81 10.64 31.51 2.15
2798 3178 6.653320 TGTCAAAAGGCGTCTTATAGTTTGAT 59.347 34.615 14.81 0.00 31.51 2.57
2799 3179 5.992829 TGTCAAAAGGCGTCTTATAGTTTGA 59.007 36.000 0.94 6.19 32.01 2.69
2800 3180 6.073222 AGTGTCAAAAGGCGTCTTATAGTTTG 60.073 38.462 0.94 3.51 32.01 2.93
2801 3181 5.995897 AGTGTCAAAAGGCGTCTTATAGTTT 59.004 36.000 0.94 0.00 32.01 2.66
2802 3182 5.548406 AGTGTCAAAAGGCGTCTTATAGTT 58.452 37.500 0.94 0.00 32.01 2.24
2803 3183 5.148651 AGTGTCAAAAGGCGTCTTATAGT 57.851 39.130 0.94 0.00 32.01 2.12
2804 3184 6.978659 TCATAGTGTCAAAAGGCGTCTTATAG 59.021 38.462 0.94 0.00 32.01 1.31
2805 3185 6.869695 TCATAGTGTCAAAAGGCGTCTTATA 58.130 36.000 0.94 0.00 32.01 0.98
2806 3186 5.730550 TCATAGTGTCAAAAGGCGTCTTAT 58.269 37.500 0.94 0.00 32.01 1.73
2807 3187 5.142061 TCATAGTGTCAAAAGGCGTCTTA 57.858 39.130 0.94 0.00 32.01 2.10
2808 3188 4.002906 TCATAGTGTCAAAAGGCGTCTT 57.997 40.909 0.00 0.00 34.07 3.01
2809 3189 3.678056 TCATAGTGTCAAAAGGCGTCT 57.322 42.857 0.00 0.00 0.00 4.18
2810 3190 5.109903 ACTATCATAGTGTCAAAAGGCGTC 58.890 41.667 0.00 0.00 37.69 5.19
2811 3191 5.086104 ACTATCATAGTGTCAAAAGGCGT 57.914 39.130 0.00 0.00 37.69 5.68
2823 3203 9.477484 GATACGGATTTTTGACACTATCATAGT 57.523 33.333 0.00 0.00 37.11 2.12
2824 3204 9.476202 TGATACGGATTTTTGACACTATCATAG 57.524 33.333 0.00 0.00 37.11 2.23
2825 3205 9.825109 TTGATACGGATTTTTGACACTATCATA 57.175 29.630 0.00 0.00 37.11 2.15
2826 3206 8.731275 TTGATACGGATTTTTGACACTATCAT 57.269 30.769 0.00 0.00 37.11 2.45
2827 3207 8.554835 TTTGATACGGATTTTTGACACTATCA 57.445 30.769 0.00 0.00 34.65 2.15
2837 3217 9.659830 GCGTCTTATATTTTGATACGGATTTTT 57.340 29.630 0.00 0.00 0.00 1.94
2838 3218 8.287503 GGCGTCTTATATTTTGATACGGATTTT 58.712 33.333 0.00 0.00 0.00 1.82
2839 3219 7.660208 AGGCGTCTTATATTTTGATACGGATTT 59.340 33.333 0.00 0.00 0.00 2.17
2840 3220 7.159372 AGGCGTCTTATATTTTGATACGGATT 58.841 34.615 0.00 0.00 0.00 3.01
2841 3221 6.698380 AGGCGTCTTATATTTTGATACGGAT 58.302 36.000 0.00 0.00 0.00 4.18
2842 3222 6.092955 AGGCGTCTTATATTTTGATACGGA 57.907 37.500 0.00 0.00 0.00 4.69
2843 3223 6.780706 AAGGCGTCTTATATTTTGATACGG 57.219 37.500 0.00 0.00 0.00 4.02
2891 3272 9.745880 TCCTTCTGTATCAAAATATAAGACGTC 57.254 33.333 7.70 7.70 0.00 4.34
3172 3554 6.305411 ACTATAGGATCAGCTAAAGGTACGT 58.695 40.000 4.43 0.00 0.00 3.57
3173 3555 6.821031 ACTATAGGATCAGCTAAAGGTACG 57.179 41.667 4.43 0.00 0.00 3.67
3224 3606 9.602568 TTATAACGACTATAAAGCAAATGGACA 57.397 29.630 0.00 0.00 30.87 4.02
3385 4117 7.238571 GGGTAACGTCAGTACATTATTTGTTG 58.761 38.462 0.00 0.00 37.30 3.33
3386 4118 6.372381 GGGGTAACGTCAGTACATTATTTGTT 59.628 38.462 0.00 0.00 37.30 2.83
3860 4598 1.545582 CAGGCCCACAAATACCAAGTG 59.454 52.381 0.00 0.00 0.00 3.16
3876 4902 0.898320 TTCCTACTCAGCTGACAGGC 59.102 55.000 25.54 0.00 0.00 4.85
4198 5230 1.967319 AAAAGCTTTGGAGTCGAGCA 58.033 45.000 13.54 0.00 38.85 4.26
4759 5879 4.326600 ACCTACCCTACTACATGTGTGA 57.673 45.455 9.11 0.00 0.00 3.58
4832 5952 7.287061 ACTAGGACTAGGATAGCTATAGCATG 58.713 42.308 26.07 9.97 44.39 4.06
4833 5953 7.460214 ACTAGGACTAGGATAGCTATAGCAT 57.540 40.000 26.07 16.62 44.39 3.79
4835 5955 6.769341 GGAACTAGGACTAGGATAGCTATAGC 59.231 46.154 17.33 17.33 44.39 2.97
4836 5956 8.097791 AGGAACTAGGACTAGGATAGCTATAG 57.902 42.308 6.13 3.25 39.11 1.31
4837 5957 9.571823 TTAGGAACTAGGACTAGGATAGCTATA 57.428 37.037 6.13 0.00 42.44 1.31
4838 5958 6.980795 AGGAACTAGGACTAGGATAGCTAT 57.019 41.667 5.76 5.76 39.11 2.97
4839 5959 7.885209 TTAGGAACTAGGACTAGGATAGCTA 57.115 40.000 10.81 0.00 42.44 3.32
4840 5960 6.783517 TTAGGAACTAGGACTAGGATAGCT 57.216 41.667 10.81 0.00 42.44 3.32
4841 5961 7.287235 TGTTTTAGGAACTAGGACTAGGATAGC 59.713 40.741 10.81 0.00 42.44 2.97
4842 5962 8.763984 TGTTTTAGGAACTAGGACTAGGATAG 57.236 38.462 10.81 0.00 44.25 2.08
4843 5963 9.198475 CTTGTTTTAGGAACTAGGACTAGGATA 57.802 37.037 10.81 0.00 44.25 2.59
4844 5964 7.899709 TCTTGTTTTAGGAACTAGGACTAGGAT 59.100 37.037 10.81 0.00 44.25 3.24
4845 5965 7.178097 GTCTTGTTTTAGGAACTAGGACTAGGA 59.822 40.741 10.81 0.00 44.25 2.94
4846 5966 7.178805 AGTCTTGTTTTAGGAACTAGGACTAGG 59.821 40.741 10.81 0.00 44.25 3.02
4877 5997 0.965363 AAGGTTTATGCACCCAGGCG 60.965 55.000 0.00 0.00 37.58 5.52
4899 6019 9.160496 CTGTAGACATTTTCAATAGAGAGCTTT 57.840 33.333 0.00 0.00 0.00 3.51
4962 6082 6.872628 ACTTGTCTATCATTGCACCATATG 57.127 37.500 0.00 0.00 0.00 1.78
4963 6083 7.508687 TGTACTTGTCTATCATTGCACCATAT 58.491 34.615 0.00 0.00 0.00 1.78
4964 6084 6.883744 TGTACTTGTCTATCATTGCACCATA 58.116 36.000 0.00 0.00 0.00 2.74
4965 6085 5.744171 TGTACTTGTCTATCATTGCACCAT 58.256 37.500 0.00 0.00 0.00 3.55
4967 6087 6.051717 AGATGTACTTGTCTATCATTGCACC 58.948 40.000 0.00 0.00 0.00 5.01
4968 6088 6.758416 TGAGATGTACTTGTCTATCATTGCAC 59.242 38.462 7.32 0.00 0.00 4.57
4992 6282 7.730364 AAGGTTCTACAGTGACAAATTAGTG 57.270 36.000 0.00 0.00 0.00 2.74
5024 6314 2.811855 CAAACAAGCAGCAACACATCA 58.188 42.857 0.00 0.00 0.00 3.07
5046 6351 4.035675 GCGCAATTAGACCAAAGCTCTATT 59.964 41.667 0.30 0.00 0.00 1.73
5058 6363 2.996621 AGACAGACAAGCGCAATTAGAC 59.003 45.455 11.47 0.00 0.00 2.59
5148 6453 3.251484 TCTCATTGTTCTCCTCCCAACT 58.749 45.455 0.00 0.00 0.00 3.16
5203 6508 0.744874 GCAGTGTCCCGTATAGCAGA 59.255 55.000 0.00 0.00 0.00 4.26
5243 6548 0.605319 ATGCCCACACGTACAACTGG 60.605 55.000 0.00 0.00 0.00 4.00
5338 6643 5.362143 TGAACATTTCATTCCCAGTTCACAA 59.638 36.000 0.00 0.00 40.01 3.33
5339 6644 4.892345 TGAACATTTCATTCCCAGTTCACA 59.108 37.500 0.00 0.00 40.01 3.58
5375 6680 9.545105 AAACATTGCAGAAATCAATAGAAACAA 57.455 25.926 0.00 0.00 33.27 2.83
5491 6800 1.270550 GGATTTTGTGACCTGCCAGTG 59.729 52.381 0.00 0.00 0.00 3.66
5498 6807 3.644861 GGTCGGGATTTTGTGACCT 57.355 52.632 3.09 0.00 45.86 3.85
5504 6813 1.935933 CCGTCTAGGTCGGGATTTTG 58.064 55.000 15.90 0.00 43.68 2.44
5524 6833 7.039434 CCAACATATAGAGCCAGTATGAGAAGA 60.039 40.741 0.00 0.00 39.69 2.87
5527 6836 5.481824 CCCAACATATAGAGCCAGTATGAGA 59.518 44.000 0.00 0.00 39.69 3.27
5545 6854 2.203337 GTGCCAGTCAGCCCAACA 60.203 61.111 0.00 0.00 0.00 3.33
5677 8401 0.979665 ATCCAGGATGCAGATACGGG 59.020 55.000 0.00 0.00 31.97 5.28
5685 8428 2.421952 GCTAGGTTTGATCCAGGATGCA 60.422 50.000 6.70 1.97 31.97 3.96
5737 8481 2.034221 GGCCAAGTGGAGTGGACC 59.966 66.667 0.00 0.00 38.35 4.46
5778 8522 1.306141 ATGTCCCAGAGAAGGCCGA 60.306 57.895 0.00 0.00 0.00 5.54
5798 8543 2.502492 CCTCGTCCCCGCATGAGAT 61.502 63.158 0.00 0.00 31.82 2.75
5801 8546 3.147595 CTCCTCGTCCCCGCATGA 61.148 66.667 0.00 0.00 0.00 3.07
5863 8608 0.322456 CCAGCCGGATCAACTCCAAA 60.322 55.000 5.05 0.00 45.24 3.28
5865 8610 1.198094 TTCCAGCCGGATCAACTCCA 61.198 55.000 5.05 0.00 45.24 3.86
5876 8621 2.051804 GACGCAATGGATTCCAGCCG 62.052 60.000 11.78 14.49 36.75 5.52
5880 8625 2.112198 GCCGACGCAATGGATTCCA 61.112 57.895 8.08 8.08 34.25 3.53
5981 8726 4.424711 TGCACCGAAGATGGGGCC 62.425 66.667 4.31 0.00 0.00 5.80
6090 8835 4.115199 CTCCTCTTTGGGGGCGGG 62.115 72.222 0.00 0.00 36.20 6.13
6091 8836 2.543067 CTTCTCCTCTTTGGGGGCGG 62.543 65.000 0.00 0.00 36.78 6.13
6092 8837 1.078143 CTTCTCCTCTTTGGGGGCG 60.078 63.158 0.00 0.00 36.78 6.13
6093 8838 1.208165 TCCTTCTCCTCTTTGGGGGC 61.208 60.000 0.00 0.00 36.78 5.80
6094 8839 0.915364 CTCCTTCTCCTCTTTGGGGG 59.085 60.000 0.00 0.00 36.78 5.40
6095 8840 0.915364 CCTCCTTCTCCTCTTTGGGG 59.085 60.000 0.00 0.00 37.77 4.96
6096 8841 1.557371 GTCCTCCTTCTCCTCTTTGGG 59.443 57.143 0.00 0.00 36.20 4.12
6097 8842 2.260822 TGTCCTCCTTCTCCTCTTTGG 58.739 52.381 0.00 0.00 37.10 3.28
6098 8843 4.019860 TCATTGTCCTCCTTCTCCTCTTTG 60.020 45.833 0.00 0.00 0.00 2.77
6099 8844 4.019771 GTCATTGTCCTCCTTCTCCTCTTT 60.020 45.833 0.00 0.00 0.00 2.52
6100 8845 3.517500 GTCATTGTCCTCCTTCTCCTCTT 59.482 47.826 0.00 0.00 0.00 2.85
6101 8846 3.103742 GTCATTGTCCTCCTTCTCCTCT 58.896 50.000 0.00 0.00 0.00 3.69
6102 8847 3.103742 AGTCATTGTCCTCCTTCTCCTC 58.896 50.000 0.00 0.00 0.00 3.71
6103 8848 2.836981 CAGTCATTGTCCTCCTTCTCCT 59.163 50.000 0.00 0.00 0.00 3.69
6104 8849 2.093235 CCAGTCATTGTCCTCCTTCTCC 60.093 54.545 0.00 0.00 0.00 3.71
6105 8850 2.569404 ACCAGTCATTGTCCTCCTTCTC 59.431 50.000 0.00 0.00 0.00 2.87
6106 8851 2.625639 ACCAGTCATTGTCCTCCTTCT 58.374 47.619 0.00 0.00 0.00 2.85
6107 8852 3.077359 CAACCAGTCATTGTCCTCCTTC 58.923 50.000 0.00 0.00 0.00 3.46
6108 8853 2.224867 CCAACCAGTCATTGTCCTCCTT 60.225 50.000 0.00 0.00 0.00 3.36
6109 8854 1.352352 CCAACCAGTCATTGTCCTCCT 59.648 52.381 0.00 0.00 0.00 3.69
6110 8855 1.614317 CCCAACCAGTCATTGTCCTCC 60.614 57.143 0.00 0.00 0.00 4.30
6111 8856 1.826385 CCCAACCAGTCATTGTCCTC 58.174 55.000 0.00 0.00 0.00 3.71
6112 8857 0.251341 GCCCAACCAGTCATTGTCCT 60.251 55.000 0.00 0.00 0.00 3.85
6113 8858 0.539438 TGCCCAACCAGTCATTGTCC 60.539 55.000 0.00 0.00 0.00 4.02
6114 8859 0.883833 CTGCCCAACCAGTCATTGTC 59.116 55.000 0.00 0.00 0.00 3.18
6115 8860 1.181098 GCTGCCCAACCAGTCATTGT 61.181 55.000 0.00 0.00 35.28 2.71
6116 8861 0.896940 AGCTGCCCAACCAGTCATTG 60.897 55.000 0.00 0.00 35.28 2.82
6117 8862 0.610232 GAGCTGCCCAACCAGTCATT 60.610 55.000 0.00 0.00 35.28 2.57
6118 8863 1.001641 GAGCTGCCCAACCAGTCAT 60.002 57.895 0.00 0.00 35.28 3.06
6119 8864 2.431683 GAGCTGCCCAACCAGTCA 59.568 61.111 0.00 0.00 35.28 3.41
6120 8865 2.360475 GGAGCTGCCCAACCAGTC 60.360 66.667 0.00 0.00 35.28 3.51
6121 8866 4.335647 CGGAGCTGCCCAACCAGT 62.336 66.667 0.00 0.00 35.28 4.00
6134 8879 0.531532 AAATCTGCTCATCGCCGGAG 60.532 55.000 5.05 0.00 38.05 4.63
6135 8880 0.811219 CAAATCTGCTCATCGCCGGA 60.811 55.000 5.05 0.00 38.05 5.14
6136 8881 1.645455 CAAATCTGCTCATCGCCGG 59.355 57.895 0.00 0.00 38.05 6.13
6137 8882 1.645455 CCAAATCTGCTCATCGCCG 59.355 57.895 0.00 0.00 38.05 6.46
6138 8883 1.099879 AGCCAAATCTGCTCATCGCC 61.100 55.000 0.00 0.00 38.05 5.54
6139 8884 0.737219 AAGCCAAATCTGCTCATCGC 59.263 50.000 0.00 0.00 38.34 4.58
6140 8885 2.011947 TCAAGCCAAATCTGCTCATCG 58.988 47.619 0.00 0.00 38.34 3.84
6141 8886 3.004524 GGATCAAGCCAAATCTGCTCATC 59.995 47.826 0.00 0.00 38.34 2.92
6142 8887 2.957006 GGATCAAGCCAAATCTGCTCAT 59.043 45.455 0.00 0.00 38.34 2.90
6143 8888 2.291089 TGGATCAAGCCAAATCTGCTCA 60.291 45.455 0.00 0.00 38.34 4.26
6144 8889 2.372264 TGGATCAAGCCAAATCTGCTC 58.628 47.619 0.00 0.00 38.34 4.26
6145 8890 2.519771 TGGATCAAGCCAAATCTGCT 57.480 45.000 0.00 0.00 41.89 4.24
6146 8891 3.814005 AATGGATCAAGCCAAATCTGC 57.186 42.857 0.00 0.00 42.16 4.26
6147 8892 5.350365 CACAAAATGGATCAAGCCAAATCTG 59.650 40.000 0.00 0.00 42.16 2.90
6148 8893 5.012354 ACACAAAATGGATCAAGCCAAATCT 59.988 36.000 0.00 0.00 42.16 2.40
6149 8894 5.240121 ACACAAAATGGATCAAGCCAAATC 58.760 37.500 0.00 0.00 42.16 2.17
6150 8895 5.012354 AGACACAAAATGGATCAAGCCAAAT 59.988 36.000 0.00 0.00 42.16 2.32
6151 8896 4.344679 AGACACAAAATGGATCAAGCCAAA 59.655 37.500 0.00 0.00 42.16 3.28
6152 8897 3.896888 AGACACAAAATGGATCAAGCCAA 59.103 39.130 0.00 0.00 42.16 4.52
6153 8898 3.499338 AGACACAAAATGGATCAAGCCA 58.501 40.909 0.00 0.00 43.23 4.75
6154 8899 4.488879 GAAGACACAAAATGGATCAAGCC 58.511 43.478 0.00 0.00 0.00 4.35
6155 8900 4.083324 TCGAAGACACAAAATGGATCAAGC 60.083 41.667 0.00 0.00 0.00 4.01
6156 8901 5.611796 TCGAAGACACAAAATGGATCAAG 57.388 39.130 0.00 0.00 0.00 3.02
6157 8902 4.083324 GCTCGAAGACACAAAATGGATCAA 60.083 41.667 0.00 0.00 0.00 2.57
6158 8903 3.436704 GCTCGAAGACACAAAATGGATCA 59.563 43.478 0.00 0.00 0.00 2.92
6159 8904 3.436704 TGCTCGAAGACACAAAATGGATC 59.563 43.478 0.00 0.00 0.00 3.36
6160 8905 3.189287 GTGCTCGAAGACACAAAATGGAT 59.811 43.478 7.75 0.00 38.05 3.41
6161 8906 2.548057 GTGCTCGAAGACACAAAATGGA 59.452 45.455 7.75 0.00 38.05 3.41
6162 8907 2.350772 GGTGCTCGAAGACACAAAATGG 60.351 50.000 13.09 0.00 39.22 3.16
6163 8908 2.662791 CGGTGCTCGAAGACACAAAATG 60.663 50.000 13.09 0.00 42.43 2.32
6164 8909 1.531149 CGGTGCTCGAAGACACAAAAT 59.469 47.619 13.09 0.00 42.43 1.82
6165 8910 0.934496 CGGTGCTCGAAGACACAAAA 59.066 50.000 13.09 0.00 42.43 2.44
6166 8911 0.179094 ACGGTGCTCGAAGACACAAA 60.179 50.000 13.09 0.00 42.43 2.83
6167 8912 0.874175 CACGGTGCTCGAAGACACAA 60.874 55.000 13.09 0.00 42.43 3.33
6168 8913 1.299850 CACGGTGCTCGAAGACACA 60.300 57.895 13.09 0.00 42.43 3.72
6169 8914 1.007734 TCACGGTGCTCGAAGACAC 60.008 57.895 2.51 4.70 42.43 3.67
6170 8915 1.007734 GTCACGGTGCTCGAAGACA 60.008 57.895 2.51 0.00 42.32 3.41
6171 8916 0.596600 TTGTCACGGTGCTCGAAGAC 60.597 55.000 2.51 16.02 42.71 3.01
6172 8917 0.103390 TTTGTCACGGTGCTCGAAGA 59.897 50.000 2.51 2.46 42.43 2.87
6173 8918 0.508641 CTTTGTCACGGTGCTCGAAG 59.491 55.000 2.51 10.21 42.43 3.79
6174 8919 0.103390 TCTTTGTCACGGTGCTCGAA 59.897 50.000 2.51 4.75 42.43 3.71
6175 8920 0.317160 ATCTTTGTCACGGTGCTCGA 59.683 50.000 2.51 0.00 42.43 4.04
6176 8921 0.439985 CATCTTTGTCACGGTGCTCG 59.560 55.000 2.51 0.00 45.88 5.03
6177 8922 0.166814 GCATCTTTGTCACGGTGCTC 59.833 55.000 2.51 0.00 0.00 4.26
6178 8923 1.237285 GGCATCTTTGTCACGGTGCT 61.237 55.000 2.51 0.00 33.38 4.40
6179 8924 1.210155 GGCATCTTTGTCACGGTGC 59.790 57.895 2.51 0.00 0.00 5.01
6180 8925 0.950836 TTGGCATCTTTGTCACGGTG 59.049 50.000 0.56 0.56 37.14 4.94
6181 8926 3.412722 TTGGCATCTTTGTCACGGT 57.587 47.368 0.00 0.00 37.14 4.83


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

AutoCloner maintained by Alex Coulton.