Multiple sequence alignment - TraesCS6D01G272700

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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 TraesCS6D01G272700 chr6D 100.000 5038 0 0 424 5461 381526007 381520970 0.000000e+00 9304.0
1 TraesCS6D01G272700 chr6D 100.000 115 0 0 1 115 381526430 381526316 4.290000e-51 213.0
2 TraesCS6D01G272700 chr6D 81.347 193 28 6 4844 5033 330171762 330171949 3.410000e-32 150.0
3 TraesCS6D01G272700 chr6D 87.037 108 13 1 5233 5340 409716996 409716890 2.670000e-23 121.0
4 TraesCS6D01G272700 chr6B 91.140 3352 155 76 546 3819 570141406 570138119 0.000000e+00 4414.0
5 TraesCS6D01G272700 chr6B 88.653 802 55 18 4010 4808 570137969 570137201 0.000000e+00 944.0
6 TraesCS6D01G272700 chr6B 88.905 676 49 20 4801 5460 570136403 570135738 0.000000e+00 809.0
7 TraesCS6D01G272700 chr6A 93.998 2849 108 29 748 3568 522744256 522741443 0.000000e+00 4255.0
8 TraesCS6D01G272700 chr6A 88.668 856 59 22 3960 4808 522740850 522740026 0.000000e+00 1009.0
9 TraesCS6D01G272700 chr6A 88.038 627 35 16 4864 5452 522740022 522739398 0.000000e+00 706.0
10 TraesCS6D01G272700 chr6A 94.444 216 8 3 3617 3832 522741062 522740851 4.080000e-86 329.0
11 TraesCS6D01G272700 chr6A 95.890 146 5 1 577 722 522744698 522744554 9.150000e-58 235.0
12 TraesCS6D01G272700 chr6A 94.595 111 5 1 426 535 522745089 522744979 2.620000e-38 171.0
13 TraesCS6D01G272700 chr1B 81.790 324 51 8 4683 5002 109241391 109241072 1.170000e-66 265.0
14 TraesCS6D01G272700 chr2B 94.444 126 7 0 3834 3959 273871566 273871691 1.550000e-45 195.0
15 TraesCS6D01G272700 chr2B 76.000 200 30 17 1110 1302 731890180 731890368 2.710000e-13 87.9
16 TraesCS6D01G272700 chr2A 93.182 132 9 0 3834 3965 690241708 690241577 1.550000e-45 195.0
17 TraesCS6D01G272700 chr7B 93.077 130 9 0 3836 3965 470313153 470313024 2.010000e-44 191.0
18 TraesCS6D01G272700 chr7A 92.481 133 10 0 3836 3968 439786389 439786521 2.010000e-44 191.0
19 TraesCS6D01G272700 chr5A 92.537 134 9 1 3834 3966 569715177 569715310 2.010000e-44 191.0
20 TraesCS6D01G272700 chr4B 85.714 182 25 1 1653 1833 558045266 558045447 2.010000e-44 191.0
21 TraesCS6D01G272700 chr4B 93.651 126 8 0 3834 3959 54992546 54992671 7.220000e-44 189.0
22 TraesCS6D01G272700 chr1A 93.701 127 8 0 3836 3962 435066022 435066148 2.010000e-44 191.0
23 TraesCS6D01G272700 chr1A 93.651 126 8 0 3834 3959 70415388 70415513 7.220000e-44 189.0
24 TraesCS6D01G272700 chr4D 85.165 182 26 1 1653 1833 446138452 446138633 9.340000e-43 185.0
25 TraesCS6D01G272700 chr4A 85.165 182 26 1 1653 1833 21219399 21219218 9.340000e-43 185.0
26 TraesCS6D01G272700 chr1D 91.111 135 12 0 3828 3962 336556671 336556805 3.360000e-42 183.0
27 TraesCS6D01G272700 chr3A 85.455 110 16 0 5230 5339 4319504 4319613 1.240000e-21 115.0
28 TraesCS6D01G272700 chr3A 84.545 110 17 0 5230 5339 3260305 3260414 5.780000e-20 110.0
29 TraesCS6D01G272700 chr3A 74.689 241 52 9 1115 1352 516806112 516805878 1.250000e-16 99.0
30 TraesCS6D01G272700 chr3B 74.274 241 53 9 1115 1352 523156901 523156667 5.820000e-15 93.5


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 TraesCS6D01G272700 chr6D 381520970 381526430 5460 True 4758.500000 9304 100.0000 1 5461 2 chr6D.!!$R2 5460
1 TraesCS6D01G272700 chr6B 570135738 570141406 5668 True 2055.666667 4414 89.5660 546 5460 3 chr6B.!!$R1 4914
2 TraesCS6D01G272700 chr6A 522739398 522745089 5691 True 1117.500000 4255 92.6055 426 5452 6 chr6A.!!$R1 5026

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
84 85 0.099613 CTCCGACATCACTCCGACAG 59.900 60.0 0.0 0.0 0.00 3.51 F
86 87 0.179161 CCGACATCACTCCGACAGAC 60.179 60.0 0.0 0.0 0.00 3.51 F
98 99 0.249322 CGACAGACGAACCACCTTGT 60.249 55.0 0.0 0.0 45.77 3.16 F
1843 2390 0.313987 CACGTCAGTCAGCCACACTA 59.686 55.0 0.0 0.0 0.00 2.74 F
2853 3423 0.250513 GGAAGGTGGACAAGCTCGAT 59.749 55.0 0.0 0.0 34.84 3.59 F
3958 4886 1.368374 AGATTTTTGGGACGGAGGGA 58.632 50.0 0.0 0.0 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2046 2596 0.520404 TGTACTTCTCACGAGGCGAC 59.480 55.000 0.00 0.00 0.00 5.19 R
2054 2604 7.684937 TCTAGTTTCCTACTGTACTTCTCAC 57.315 40.000 0.00 0.00 37.73 3.51 R
2095 2647 2.684843 CCGCCTCTTGCTCTGTTGC 61.685 63.158 0.00 0.00 38.05 4.17 R
3185 3756 2.261671 CAGGTAGCTCGCGTTGGT 59.738 61.111 5.77 8.91 0.00 3.67 R
4217 5145 0.108329 ACACGCAGATACCCGGAAAG 60.108 55.000 0.73 0.00 0.00 2.62 R
4844 6585 4.002982 TGAAGCCATGTCATCACAACTAC 58.997 43.478 0.00 0.00 35.64 2.73 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 5.772825 ATGCAGTAATTTCTTGTGTGTGT 57.227 34.783 0.00 0.00 0.00 3.72
52 53 4.919206 TGCAGTAATTTCTTGTGTGTGTG 58.081 39.130 0.00 0.00 0.00 3.82
53 54 3.730715 GCAGTAATTTCTTGTGTGTGTGC 59.269 43.478 0.00 0.00 0.00 4.57
54 55 3.968096 CAGTAATTTCTTGTGTGTGTGCG 59.032 43.478 0.00 0.00 0.00 5.34
55 56 1.838913 AATTTCTTGTGTGTGTGCGC 58.161 45.000 0.00 0.00 0.00 6.09
56 57 0.316937 ATTTCTTGTGTGTGTGCGCG 60.317 50.000 0.00 0.00 0.00 6.86
57 58 2.911439 TTTCTTGTGTGTGTGCGCGC 62.911 55.000 27.26 27.26 36.27 6.86
58 59 4.962122 CTTGTGTGTGTGCGCGCC 62.962 66.667 30.77 20.33 34.96 6.53
61 62 4.962122 GTGTGTGTGCGCGCCTTG 62.962 66.667 30.77 0.00 0.00 3.61
63 64 3.342627 GTGTGTGCGCGCCTTGTA 61.343 61.111 30.77 6.23 0.00 2.41
64 65 2.358125 TGTGTGCGCGCCTTGTAT 60.358 55.556 30.77 0.00 0.00 2.29
65 66 2.387445 TGTGTGCGCGCCTTGTATC 61.387 57.895 30.77 12.10 0.00 2.24
66 67 2.100631 GTGTGCGCGCCTTGTATCT 61.101 57.895 30.77 0.00 0.00 1.98
67 68 1.809619 TGTGCGCGCCTTGTATCTC 60.810 57.895 30.77 7.88 0.00 2.75
68 69 2.202878 TGCGCGCCTTGTATCTCC 60.203 61.111 30.77 0.00 0.00 3.71
69 70 3.330853 GCGCGCCTTGTATCTCCG 61.331 66.667 23.24 0.00 0.00 4.63
70 71 2.411701 CGCGCCTTGTATCTCCGA 59.588 61.111 0.00 0.00 0.00 4.55
71 72 1.944676 CGCGCCTTGTATCTCCGAC 60.945 63.158 0.00 0.00 0.00 4.79
72 73 1.141019 GCGCCTTGTATCTCCGACA 59.859 57.895 0.00 0.00 0.00 4.35
73 74 0.249489 GCGCCTTGTATCTCCGACAT 60.249 55.000 0.00 0.00 0.00 3.06
74 75 1.772182 CGCCTTGTATCTCCGACATC 58.228 55.000 0.00 0.00 0.00 3.06
75 76 1.067060 CGCCTTGTATCTCCGACATCA 59.933 52.381 0.00 0.00 0.00 3.07
76 77 2.474816 GCCTTGTATCTCCGACATCAC 58.525 52.381 0.00 0.00 0.00 3.06
77 78 2.101582 GCCTTGTATCTCCGACATCACT 59.898 50.000 0.00 0.00 0.00 3.41
78 79 3.797184 GCCTTGTATCTCCGACATCACTC 60.797 52.174 0.00 0.00 0.00 3.51
79 80 3.243569 CCTTGTATCTCCGACATCACTCC 60.244 52.174 0.00 0.00 0.00 3.85
80 81 1.947456 TGTATCTCCGACATCACTCCG 59.053 52.381 0.00 0.00 0.00 4.63
81 82 2.219458 GTATCTCCGACATCACTCCGA 58.781 52.381 0.00 0.00 0.00 4.55
82 83 1.025812 ATCTCCGACATCACTCCGAC 58.974 55.000 0.00 0.00 0.00 4.79
83 84 0.322187 TCTCCGACATCACTCCGACA 60.322 55.000 0.00 0.00 0.00 4.35
84 85 0.099613 CTCCGACATCACTCCGACAG 59.900 60.000 0.00 0.00 0.00 3.51
85 86 0.322187 TCCGACATCACTCCGACAGA 60.322 55.000 0.00 0.00 0.00 3.41
86 87 0.179161 CCGACATCACTCCGACAGAC 60.179 60.000 0.00 0.00 0.00 3.51
87 88 0.521450 CGACATCACTCCGACAGACG 60.521 60.000 0.00 0.00 42.18 4.18
88 89 0.803117 GACATCACTCCGACAGACGA 59.197 55.000 0.00 0.00 45.77 4.20
89 90 1.199327 GACATCACTCCGACAGACGAA 59.801 52.381 0.00 0.00 45.77 3.85
90 91 1.068472 ACATCACTCCGACAGACGAAC 60.068 52.381 0.00 0.00 45.77 3.95
91 92 0.526662 ATCACTCCGACAGACGAACC 59.473 55.000 0.00 0.00 45.77 3.62
92 93 0.820482 TCACTCCGACAGACGAACCA 60.820 55.000 0.00 0.00 45.77 3.67
93 94 0.663568 CACTCCGACAGACGAACCAC 60.664 60.000 0.00 0.00 45.77 4.16
94 95 1.080705 CTCCGACAGACGAACCACC 60.081 63.158 0.00 0.00 45.77 4.61
95 96 1.524863 CTCCGACAGACGAACCACCT 61.525 60.000 0.00 0.00 45.77 4.00
96 97 1.111116 TCCGACAGACGAACCACCTT 61.111 55.000 0.00 0.00 45.77 3.50
97 98 0.944311 CCGACAGACGAACCACCTTG 60.944 60.000 0.00 0.00 45.77 3.61
98 99 0.249322 CGACAGACGAACCACCTTGT 60.249 55.000 0.00 0.00 45.77 3.16
99 100 1.001048 CGACAGACGAACCACCTTGTA 60.001 52.381 0.00 0.00 45.77 2.41
100 101 2.352421 CGACAGACGAACCACCTTGTAT 60.352 50.000 0.00 0.00 45.77 2.29
101 102 3.251571 GACAGACGAACCACCTTGTATC 58.748 50.000 0.00 0.00 0.00 2.24
102 103 2.897969 ACAGACGAACCACCTTGTATCT 59.102 45.455 0.00 0.00 0.00 1.98
103 104 3.056749 ACAGACGAACCACCTTGTATCTC 60.057 47.826 0.00 0.00 0.00 2.75
104 105 2.496470 AGACGAACCACCTTGTATCTCC 59.504 50.000 0.00 0.00 0.00 3.71
105 106 1.203994 ACGAACCACCTTGTATCTCCG 59.796 52.381 0.00 0.00 0.00 4.63
106 107 1.475280 CGAACCACCTTGTATCTCCGA 59.525 52.381 0.00 0.00 0.00 4.55
107 108 2.734492 CGAACCACCTTGTATCTCCGAC 60.734 54.545 0.00 0.00 0.00 4.79
108 109 1.933021 ACCACCTTGTATCTCCGACA 58.067 50.000 0.00 0.00 0.00 4.35
109 110 2.467880 ACCACCTTGTATCTCCGACAT 58.532 47.619 0.00 0.00 0.00 3.06
110 111 2.431057 ACCACCTTGTATCTCCGACATC 59.569 50.000 0.00 0.00 0.00 3.06
111 112 2.430694 CCACCTTGTATCTCCGACATCA 59.569 50.000 0.00 0.00 0.00 3.07
112 113 3.448686 CACCTTGTATCTCCGACATCAC 58.551 50.000 0.00 0.00 0.00 3.06
113 114 3.131223 CACCTTGTATCTCCGACATCACT 59.869 47.826 0.00 0.00 0.00 3.41
114 115 3.381908 ACCTTGTATCTCCGACATCACTC 59.618 47.826 0.00 0.00 0.00 3.51
455 456 2.442188 CGAACTAGGCAACGGCGAC 61.442 63.158 16.62 1.71 46.39 5.19
484 485 1.278238 GCGAACCACCTTGTATCTCG 58.722 55.000 0.00 0.00 0.00 4.04
485 486 1.922570 CGAACCACCTTGTATCTCGG 58.077 55.000 0.00 0.00 0.00 4.63
532 538 3.386078 TGCTCTCTCTCTCTCTCTCTCTC 59.614 52.174 0.00 0.00 0.00 3.20
533 539 3.640967 GCTCTCTCTCTCTCTCTCTCTCT 59.359 52.174 0.00 0.00 0.00 3.10
534 540 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
535 541 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
536 542 5.462240 TCTCTCTCTCTCTCTCTCTCTCAT 58.538 45.833 0.00 0.00 0.00 2.90
537 543 6.614657 TCTCTCTCTCTCTCTCTCTCTCATA 58.385 44.000 0.00 0.00 0.00 2.15
538 544 6.491745 TCTCTCTCTCTCTCTCTCTCTCATAC 59.508 46.154 0.00 0.00 0.00 2.39
539 545 6.136155 TCTCTCTCTCTCTCTCTCTCATACA 58.864 44.000 0.00 0.00 0.00 2.29
540 546 6.784473 TCTCTCTCTCTCTCTCTCTCATACAT 59.216 42.308 0.00 0.00 0.00 2.29
541 547 7.950124 TCTCTCTCTCTCTCTCTCTCATACATA 59.050 40.741 0.00 0.00 0.00 2.29
542 548 7.896811 TCTCTCTCTCTCTCTCTCATACATAC 58.103 42.308 0.00 0.00 0.00 2.39
543 549 6.687604 TCTCTCTCTCTCTCTCATACATACG 58.312 44.000 0.00 0.00 0.00 3.06
544 550 5.234752 TCTCTCTCTCTCTCATACATACGC 58.765 45.833 0.00 0.00 0.00 4.42
555 561 5.480422 TCTCATACATACGCATATGGTTCCT 59.520 40.000 4.61 0.00 42.32 3.36
805 1347 4.929808 TCTTGAGGAATCTTTACAAGCGAC 59.070 41.667 0.00 0.00 38.13 5.19
816 1358 0.391661 ACAAGCGACCGAATCAGCAT 60.392 50.000 0.00 0.00 31.70 3.79
918 1465 2.870411 ACCAGTCCTCGAAAACTTTTCG 59.130 45.455 24.56 24.56 42.74 3.46
940 1487 1.272490 TCGACCCAGATGTTGTGAGTC 59.728 52.381 0.00 0.00 0.00 3.36
951 1498 2.126424 GTGAGTCGTGACGCCTCC 60.126 66.667 13.69 1.35 36.20 4.30
1099 1646 1.899437 GCCGTTCCTCCACATCCTCA 61.899 60.000 0.00 0.00 0.00 3.86
1212 1759 1.610554 GCTACCTGTTCCCGTGCCTA 61.611 60.000 0.00 0.00 0.00 3.93
1355 1902 7.009179 CCATCATGGGACTATGTAAGTACAT 57.991 40.000 8.88 8.88 41.38 2.29
1363 1910 9.596308 TGGGACTATGTAAGTACATATACATGT 57.404 33.333 20.39 2.69 45.19 3.21
1382 1929 4.564110 GATGTACCCAGGCCGCCC 62.564 72.222 5.55 0.00 0.00 6.13
1457 2004 4.850347 ACGTTGTACAGACTCTAGCTTT 57.150 40.909 0.00 0.00 0.00 3.51
1677 2224 1.235281 GGGCTTCGTGGTGGACTTTC 61.235 60.000 0.00 0.00 0.00 2.62
1843 2390 0.313987 CACGTCAGTCAGCCACACTA 59.686 55.000 0.00 0.00 0.00 2.74
1860 2407 7.015389 AGCCACACTATCCTCCTTAATTAGTAC 59.985 40.741 0.00 0.00 0.00 2.73
1892 2439 5.627499 TGTATTTGATCTGACAAGGTTGC 57.373 39.130 0.00 0.00 0.00 4.17
1974 2521 2.617274 GGTTCTCGGGTGTTGCTGC 61.617 63.158 0.00 0.00 0.00 5.25
2054 2604 6.971184 TCTCTTTTAAAGTTATAGTCGCCTCG 59.029 38.462 4.53 0.00 0.00 4.63
2095 2647 9.503427 GGAAACTAGATTTGATATTTGTTTCGG 57.497 33.333 0.00 0.00 41.34 4.30
2170 2722 0.732880 CGTCGCTCATCGTTGGAAGT 60.733 55.000 0.00 0.00 39.67 3.01
2220 2772 1.942657 CCATGGCATCGAAGTGGTAAG 59.057 52.381 0.00 0.00 0.00 2.34
2268 2821 5.897377 ATTACTCCTTCCGTTCCAAAATG 57.103 39.130 0.00 0.00 0.00 2.32
2440 2996 2.073101 GTAAGCCCCCTCCTCCTGG 61.073 68.421 0.00 0.00 0.00 4.45
2445 3001 4.825679 CCCCTCCTCCTGGGTCCC 62.826 77.778 0.00 0.00 43.09 4.46
2457 3013 1.080025 GGGTCCCGACTTCAGTTCG 60.080 63.158 0.00 0.00 0.00 3.95
2459 3015 0.388263 GGTCCCGACTTCAGTTCGTC 60.388 60.000 0.00 0.00 0.00 4.20
2560 3130 1.145803 GTCCAAGAACTACCACGTGC 58.854 55.000 10.91 0.00 0.00 5.34
2853 3423 0.250513 GGAAGGTGGACAAGCTCGAT 59.749 55.000 0.00 0.00 34.84 3.59
2953 3524 2.224314 TGCTATCAGCTGTATCGAGTCG 59.776 50.000 14.67 6.09 42.97 4.18
2958 3529 1.671328 CAGCTGTATCGAGTCGGAAGA 59.329 52.381 13.54 0.00 38.16 2.87
3000 3571 2.094894 GCATGATGTGTTGACCTCGAAG 59.905 50.000 0.00 0.00 0.00 3.79
3185 3756 1.447838 GACGCGCCCATCTTCTTCA 60.448 57.895 5.73 0.00 0.00 3.02
3379 3959 7.613551 TTCAAAATATACTACTCCCTCCTCC 57.386 40.000 0.00 0.00 0.00 4.30
3381 3961 5.698369 AAATATACTACTCCCTCCTCCCA 57.302 43.478 0.00 0.00 0.00 4.37
3386 3966 2.643304 ACTACTCCCTCCTCCCAAAAAC 59.357 50.000 0.00 0.00 0.00 2.43
3449 4032 7.654022 ACAAAGTTTATTTTGGAACAGAGGA 57.346 32.000 3.85 0.00 42.39 3.71
3463 4046 9.581289 TTGGAACAGAGGAAGTAAAATTTATGA 57.419 29.630 0.00 0.00 42.39 2.15
3606 4534 5.440234 ACGTGAGTGTACCTATCATCATC 57.560 43.478 0.00 0.00 46.97 2.92
3607 4535 4.023963 ACGTGAGTGTACCTATCATCATCG 60.024 45.833 0.00 0.00 46.97 3.84
3608 4536 4.613850 CGTGAGTGTACCTATCATCATCGG 60.614 50.000 0.00 0.00 0.00 4.18
3609 4537 4.519350 GTGAGTGTACCTATCATCATCGGA 59.481 45.833 0.00 0.00 0.00 4.55
3610 4538 5.184096 GTGAGTGTACCTATCATCATCGGAT 59.816 44.000 0.00 0.00 0.00 4.18
3630 4558 6.773200 TCGGATGATACATGATAGGATCTACC 59.227 42.308 0.00 0.00 39.35 3.18
3639 4567 7.448420 ACATGATAGGATCTACCATGAAACTG 58.552 38.462 14.30 0.00 42.04 3.16
3779 4707 2.802816 GTGGTGAGTTGTTCTAGCACTG 59.197 50.000 0.00 0.00 38.22 3.66
3782 4710 4.202357 TGGTGAGTTGTTCTAGCACTGATT 60.202 41.667 0.00 0.00 0.00 2.57
3829 4757 2.489938 TCTTTTGCACCGGCTCTTAT 57.510 45.000 0.00 0.00 41.91 1.73
3833 4761 5.865085 TCTTTTGCACCGGCTCTTATATAT 58.135 37.500 0.00 0.00 41.91 0.86
3834 4762 5.700832 TCTTTTGCACCGGCTCTTATATATG 59.299 40.000 0.00 0.00 41.91 1.78
3835 4763 4.617253 TTGCACCGGCTCTTATATATGT 57.383 40.909 0.00 0.00 41.91 2.29
3836 4764 5.731957 TTGCACCGGCTCTTATATATGTA 57.268 39.130 0.00 0.00 41.91 2.29
3837 4765 5.068234 TGCACCGGCTCTTATATATGTAC 57.932 43.478 0.00 0.00 41.91 2.90
3840 4768 5.805994 GCACCGGCTCTTATATATGTACTTC 59.194 44.000 0.00 0.00 36.96 3.01
3841 4769 6.331061 CACCGGCTCTTATATATGTACTTCC 58.669 44.000 0.00 0.00 0.00 3.46
3842 4770 6.153000 CACCGGCTCTTATATATGTACTTCCT 59.847 42.308 0.00 0.00 0.00 3.36
3843 4771 6.377712 ACCGGCTCTTATATATGTACTTCCTC 59.622 42.308 0.00 0.00 0.00 3.71
3844 4772 6.183360 CCGGCTCTTATATATGTACTTCCTCC 60.183 46.154 0.00 0.00 0.00 4.30
3845 4773 6.377429 CGGCTCTTATATATGTACTTCCTCCA 59.623 42.308 0.00 0.00 0.00 3.86
3846 4774 7.068839 CGGCTCTTATATATGTACTTCCTCCAT 59.931 40.741 0.00 0.00 0.00 3.41
3847 4775 8.417884 GGCTCTTATATATGTACTTCCTCCATC 58.582 40.741 0.00 0.00 0.00 3.51
3848 4776 8.417884 GCTCTTATATATGTACTTCCTCCATCC 58.582 40.741 0.00 0.00 0.00 3.51
3849 4777 8.840200 TCTTATATATGTACTTCCTCCATCCC 57.160 38.462 0.00 0.00 0.00 3.85
3851 4779 8.982471 TTATATATGTACTTCCTCCATCCCAA 57.018 34.615 0.00 0.00 0.00 4.12
3852 4780 7.888514 ATATATGTACTTCCTCCATCCCAAA 57.111 36.000 0.00 0.00 0.00 3.28
3853 4781 4.946160 ATGTACTTCCTCCATCCCAAAA 57.054 40.909 0.00 0.00 0.00 2.44
3854 4782 4.946160 TGTACTTCCTCCATCCCAAAAT 57.054 40.909 0.00 0.00 0.00 1.82
3856 4784 5.650283 TGTACTTCCTCCATCCCAAAATTT 58.350 37.500 0.00 0.00 0.00 1.82
3857 4785 6.081356 TGTACTTCCTCCATCCCAAAATTTT 58.919 36.000 0.00 0.00 0.00 1.82
3858 4786 6.556874 TGTACTTCCTCCATCCCAAAATTTTT 59.443 34.615 0.00 0.00 0.00 1.94
3860 4788 5.369404 ACTTCCTCCATCCCAAAATTTTTGT 59.631 36.000 18.05 0.31 0.00 2.83
3861 4789 5.482163 TCCTCCATCCCAAAATTTTTGTC 57.518 39.130 18.05 0.00 0.00 3.18
3862 4790 5.154418 TCCTCCATCCCAAAATTTTTGTCT 58.846 37.500 18.05 2.68 0.00 3.41
3865 4793 7.291182 TCCTCCATCCCAAAATTTTTGTCTTAA 59.709 33.333 18.05 2.49 0.00 1.85
3866 4794 7.936301 CCTCCATCCCAAAATTTTTGTCTTAAA 59.064 33.333 18.05 2.42 0.00 1.52
3867 4795 9.506018 CTCCATCCCAAAATTTTTGTCTTAAAT 57.494 29.630 18.05 2.94 0.00 1.40
3868 4796 9.859152 TCCATCCCAAAATTTTTGTCTTAAATT 57.141 25.926 18.05 0.00 36.91 1.82
3916 4844 9.379791 AGTTACATTTTAGTGTTAGATACAGCC 57.620 33.333 0.00 0.00 37.45 4.85
3917 4845 6.903883 ACATTTTAGTGTTAGATACAGCCG 57.096 37.500 0.00 0.00 37.45 5.52
3918 4846 6.403878 ACATTTTAGTGTTAGATACAGCCGT 58.596 36.000 0.00 0.00 37.45 5.68
3919 4847 7.549839 ACATTTTAGTGTTAGATACAGCCGTA 58.450 34.615 0.00 0.00 37.45 4.02
3920 4848 8.202137 ACATTTTAGTGTTAGATACAGCCGTAT 58.798 33.333 0.00 0.00 41.16 3.06
3936 4864 8.405418 ACAGCCGTATCTAGACAAATATAAGA 57.595 34.615 0.00 0.00 0.00 2.10
3937 4865 8.298140 ACAGCCGTATCTAGACAAATATAAGAC 58.702 37.037 0.00 0.00 0.00 3.01
3938 4866 8.297426 CAGCCGTATCTAGACAAATATAAGACA 58.703 37.037 0.00 0.00 0.00 3.41
3939 4867 8.857098 AGCCGTATCTAGACAAATATAAGACAA 58.143 33.333 0.00 0.00 0.00 3.18
3940 4868 9.130312 GCCGTATCTAGACAAATATAAGACAAG 57.870 37.037 0.00 0.00 0.00 3.16
3952 4880 9.289303 CAAATATAAGACAAGATTTTTGGGACG 57.711 33.333 0.00 0.00 0.00 4.79
3953 4881 5.897377 ATAAGACAAGATTTTTGGGACGG 57.103 39.130 0.00 0.00 0.00 4.79
3954 4882 3.502123 AGACAAGATTTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
3955 4883 3.412386 AGACAAGATTTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
3956 4884 2.488153 GACAAGATTTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
3957 4885 1.818674 CAAGATTTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
3958 4886 1.368374 AGATTTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
3968 4896 4.818447 TGGGACGGAGGGAGTAATATAAA 58.182 43.478 0.00 0.00 0.00 1.40
4019 4947 8.770828 CCTGTAAAAGAAATAGTCGTTTCTGAA 58.229 33.333 2.97 0.00 45.18 3.02
4030 4958 3.185797 GTCGTTTCTGAAAACCGCTACAT 59.814 43.478 4.09 0.00 41.46 2.29
4131 5059 5.523552 TGCACATGAAGAATATTCAGGTACG 59.476 40.000 17.56 0.00 40.85 3.67
4134 5062 5.523916 ACATGAAGAATATTCAGGTACGCAC 59.476 40.000 17.56 0.00 40.98 5.34
4150 5078 8.273557 CAGGTACGCACTAAATATAAACATGTC 58.726 37.037 0.00 0.00 0.00 3.06
4159 5087 9.396022 ACTAAATATAAACATGTCCAACTCAGG 57.604 33.333 0.00 0.00 0.00 3.86
4166 5094 2.452600 TGTCCAACTCAGGCCTTTTT 57.547 45.000 0.00 0.00 0.00 1.94
4195 5123 4.632153 ACATGTACAACTGAGACCTTGTC 58.368 43.478 0.00 0.00 32.77 3.18
4211 5139 4.281688 ACCTTGTCCAACTCAATTTGATGG 59.718 41.667 11.33 11.33 29.84 3.51
4217 5145 3.445096 CCAACTCAATTTGATGGGAGGTC 59.555 47.826 10.11 0.00 0.00 3.85
4273 5205 1.794222 CTCGAACCAATTGTCGGGC 59.206 57.895 15.83 0.00 0.00 6.13
4287 5219 2.045926 GGGCTGACCGACTGCATT 60.046 61.111 11.65 0.00 43.62 3.56
4289 5221 1.375908 GGCTGACCGACTGCATTGA 60.376 57.895 11.65 0.00 43.62 2.57
4295 5227 0.973632 ACCGACTGCATTGAGTGGTA 59.026 50.000 0.00 0.00 30.34 3.25
4385 5317 0.725686 TCGACGACGAGTGGATCTTC 59.274 55.000 5.75 0.00 43.81 2.87
4403 5335 2.738521 CAGAAGGTGGGTGACGCG 60.739 66.667 3.53 3.53 0.00 6.01
4624 5558 8.045176 AGTGTTTCCTTTGCTTCTATATTCAC 57.955 34.615 0.00 0.00 0.00 3.18
4637 5571 3.845781 ATATTCACGGATCAAGTGGCT 57.154 42.857 17.02 9.52 39.86 4.75
4638 5572 4.955811 ATATTCACGGATCAAGTGGCTA 57.044 40.909 17.02 10.92 39.86 3.93
4639 5573 3.627395 ATTCACGGATCAAGTGGCTAA 57.373 42.857 17.02 7.75 39.86 3.09
4640 5574 3.627395 TTCACGGATCAAGTGGCTAAT 57.373 42.857 17.02 0.00 39.86 1.73
4641 5575 3.627395 TCACGGATCAAGTGGCTAATT 57.373 42.857 17.02 0.00 39.86 1.40
4642 5576 4.746535 TCACGGATCAAGTGGCTAATTA 57.253 40.909 17.02 0.00 39.86 1.40
4643 5577 5.092554 TCACGGATCAAGTGGCTAATTAA 57.907 39.130 17.02 0.00 39.86 1.40
4644 5578 5.116180 TCACGGATCAAGTGGCTAATTAAG 58.884 41.667 17.02 0.00 39.86 1.85
4645 5579 4.273480 CACGGATCAAGTGGCTAATTAAGG 59.727 45.833 11.41 0.00 36.06 2.69
4646 5580 4.163458 ACGGATCAAGTGGCTAATTAAGGA 59.837 41.667 0.00 0.00 0.00 3.36
4647 5581 4.752101 CGGATCAAGTGGCTAATTAAGGAG 59.248 45.833 0.00 0.00 0.00 3.69
4648 5582 5.453339 CGGATCAAGTGGCTAATTAAGGAGA 60.453 44.000 0.00 0.00 0.00 3.71
4649 5583 6.538263 GGATCAAGTGGCTAATTAAGGAGAT 58.462 40.000 0.00 0.00 0.00 2.75
4650 5584 7.001073 GGATCAAGTGGCTAATTAAGGAGATT 58.999 38.462 0.00 0.00 0.00 2.40
4651 5585 7.174080 GGATCAAGTGGCTAATTAAGGAGATTC 59.826 40.741 0.00 0.00 0.00 2.52
4652 5586 7.200434 TCAAGTGGCTAATTAAGGAGATTCT 57.800 36.000 0.00 0.00 0.00 2.40
4653 5587 7.275920 TCAAGTGGCTAATTAAGGAGATTCTC 58.724 38.462 5.03 5.03 0.00 2.87
4654 5588 6.814954 AGTGGCTAATTAAGGAGATTCTCA 57.185 37.500 15.36 0.00 31.08 3.27
4655 5589 7.200434 AGTGGCTAATTAAGGAGATTCTCAA 57.800 36.000 15.36 2.04 31.08 3.02
4656 5590 7.633789 AGTGGCTAATTAAGGAGATTCTCAAA 58.366 34.615 15.36 6.86 31.08 2.69
4657 5591 8.109634 AGTGGCTAATTAAGGAGATTCTCAAAA 58.890 33.333 15.36 6.54 31.08 2.44
4658 5592 8.739972 GTGGCTAATTAAGGAGATTCTCAAAAA 58.260 33.333 15.36 6.22 31.08 1.94
4693 5627 2.638363 AGGAGGCTCGAAAAGGTTTAGT 59.362 45.455 8.69 0.00 0.00 2.24
4788 5724 8.179509 ACCATCTAGTTGTACTCCATATGTAC 57.820 38.462 1.24 0.00 40.27 2.90
5034 6787 4.275936 CCCCTCGTCAGGCAAAATAAATAG 59.724 45.833 0.00 0.00 38.72 1.73
5068 6821 6.803154 ACTGAGTAATAGAAAACCAGCAAC 57.197 37.500 0.00 0.00 0.00 4.17
5084 6865 5.527582 ACCAGCAACATAATTCTACCGAATC 59.472 40.000 0.00 0.00 38.89 2.52
5086 6867 4.211374 AGCAACATAATTCTACCGAATCGC 59.789 41.667 0.00 0.00 38.89 4.58
5108 6889 5.515626 CGCTGTTACGTTTAAAGATCTAGCT 59.484 40.000 0.00 0.00 0.00 3.32
5133 6914 7.489160 TGCTAAGTATGAATATCAAGACGTGT 58.511 34.615 0.00 0.00 0.00 4.49
5196 6978 4.530161 AGGTTGTAAGAGAGAGTGCAAGAT 59.470 41.667 0.00 0.00 0.00 2.40
5325 7107 6.882140 TGCATTAACCATTAATAGATACCCCG 59.118 38.462 0.00 0.00 34.22 5.73
5448 7232 5.095490 GGCTTGAACGATACCTTTTTCATG 58.905 41.667 0.00 0.00 0.00 3.07
5453 7237 9.410556 CTTGAACGATACCTTTTTCATGAAAAT 57.589 29.630 29.13 19.10 39.69 1.82
5455 7239 9.190858 TGAACGATACCTTTTTCATGAAAATTG 57.809 29.630 29.13 24.13 39.69 2.32
5456 7240 9.191995 GAACGATACCTTTTTCATGAAAATTGT 57.808 29.630 29.13 27.32 39.69 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 9.177608 ACACACACAAGAAATTACTGCATATAT 57.822 29.630 0.00 0.00 0.00 0.86
26 27 8.450180 CACACACACAAGAAATTACTGCATATA 58.550 33.333 0.00 0.00 0.00 0.86
27 28 7.307694 CACACACACAAGAAATTACTGCATAT 58.692 34.615 0.00 0.00 0.00 1.78
28 29 6.667370 CACACACACAAGAAATTACTGCATA 58.333 36.000 0.00 0.00 0.00 3.14
29 30 5.522456 CACACACACAAGAAATTACTGCAT 58.478 37.500 0.00 0.00 0.00 3.96
30 31 4.733230 GCACACACACAAGAAATTACTGCA 60.733 41.667 0.00 0.00 0.00 4.41
31 32 3.730715 GCACACACACAAGAAATTACTGC 59.269 43.478 0.00 0.00 0.00 4.40
32 33 3.968096 CGCACACACACAAGAAATTACTG 59.032 43.478 0.00 0.00 0.00 2.74
33 34 3.548014 GCGCACACACACAAGAAATTACT 60.548 43.478 0.30 0.00 0.00 2.24
34 35 2.719046 GCGCACACACACAAGAAATTAC 59.281 45.455 0.30 0.00 0.00 1.89
35 36 2.601029 CGCGCACACACACAAGAAATTA 60.601 45.455 8.75 0.00 0.00 1.40
36 37 1.838913 GCGCACACACACAAGAAATT 58.161 45.000 0.30 0.00 0.00 1.82
37 38 0.316937 CGCGCACACACACAAGAAAT 60.317 50.000 8.75 0.00 0.00 2.17
38 39 1.061729 CGCGCACACACACAAGAAA 59.938 52.632 8.75 0.00 0.00 2.52
39 40 2.706432 CGCGCACACACACAAGAA 59.294 55.556 8.75 0.00 0.00 2.52
40 41 3.935872 GCGCGCACACACACAAGA 61.936 61.111 29.10 0.00 0.00 3.02
41 42 4.962122 GGCGCGCACACACACAAG 62.962 66.667 34.42 0.00 0.00 3.16
44 45 4.962122 CAAGGCGCGCACACACAC 62.962 66.667 34.42 13.69 0.00 3.82
46 47 2.563086 GATACAAGGCGCGCACACAC 62.563 60.000 34.42 15.34 0.00 3.82
47 48 2.358125 ATACAAGGCGCGCACACA 60.358 55.556 34.42 13.83 0.00 3.72
48 49 2.025359 GAGATACAAGGCGCGCACAC 62.025 60.000 34.42 16.19 0.00 3.82
49 50 1.809619 GAGATACAAGGCGCGCACA 60.810 57.895 34.42 12.64 0.00 4.57
50 51 2.526120 GGAGATACAAGGCGCGCAC 61.526 63.158 34.42 21.95 0.00 5.34
51 52 2.202878 GGAGATACAAGGCGCGCA 60.203 61.111 34.42 12.78 0.00 6.09
52 53 3.330853 CGGAGATACAAGGCGCGC 61.331 66.667 25.94 25.94 0.00 6.86
53 54 1.944676 GTCGGAGATACAAGGCGCG 60.945 63.158 0.00 0.00 40.67 6.86
54 55 0.249489 ATGTCGGAGATACAAGGCGC 60.249 55.000 0.00 0.00 40.67 6.53
55 56 1.067060 TGATGTCGGAGATACAAGGCG 59.933 52.381 0.00 0.00 40.67 5.52
56 57 2.101582 AGTGATGTCGGAGATACAAGGC 59.898 50.000 0.00 0.00 40.67 4.35
57 58 3.243569 GGAGTGATGTCGGAGATACAAGG 60.244 52.174 0.00 0.00 40.67 3.61
58 59 3.549019 CGGAGTGATGTCGGAGATACAAG 60.549 52.174 0.00 0.00 40.67 3.16
59 60 2.357952 CGGAGTGATGTCGGAGATACAA 59.642 50.000 0.00 0.00 40.67 2.41
60 61 1.947456 CGGAGTGATGTCGGAGATACA 59.053 52.381 0.00 0.00 40.67 2.29
61 62 2.031857 GTCGGAGTGATGTCGGAGATAC 60.032 54.545 0.00 0.00 40.67 2.24
62 63 2.219458 GTCGGAGTGATGTCGGAGATA 58.781 52.381 0.00 0.00 40.67 1.98
63 64 1.025812 GTCGGAGTGATGTCGGAGAT 58.974 55.000 0.00 0.00 40.67 2.75
64 65 0.322187 TGTCGGAGTGATGTCGGAGA 60.322 55.000 0.00 0.00 0.00 3.71
65 66 0.099613 CTGTCGGAGTGATGTCGGAG 59.900 60.000 0.00 0.00 0.00 4.63
66 67 0.322187 TCTGTCGGAGTGATGTCGGA 60.322 55.000 0.00 0.00 0.00 4.55
67 68 0.179161 GTCTGTCGGAGTGATGTCGG 60.179 60.000 0.00 0.00 0.00 4.79
68 69 0.521450 CGTCTGTCGGAGTGATGTCG 60.521 60.000 0.00 0.00 35.71 4.35
69 70 0.803117 TCGTCTGTCGGAGTGATGTC 59.197 55.000 0.00 0.00 40.32 3.06
70 71 1.068472 GTTCGTCTGTCGGAGTGATGT 60.068 52.381 0.00 0.00 40.32 3.06
71 72 1.618861 GTTCGTCTGTCGGAGTGATG 58.381 55.000 0.00 0.00 40.32 3.07
72 73 0.526662 GGTTCGTCTGTCGGAGTGAT 59.473 55.000 0.00 0.00 40.32 3.06
73 74 0.820482 TGGTTCGTCTGTCGGAGTGA 60.820 55.000 0.00 0.00 40.32 3.41
74 75 0.663568 GTGGTTCGTCTGTCGGAGTG 60.664 60.000 0.00 0.00 40.32 3.51
75 76 1.658673 GTGGTTCGTCTGTCGGAGT 59.341 57.895 0.00 0.00 40.32 3.85
76 77 1.080705 GGTGGTTCGTCTGTCGGAG 60.081 63.158 0.00 0.00 40.32 4.63
77 78 1.111116 AAGGTGGTTCGTCTGTCGGA 61.111 55.000 0.00 0.00 40.32 4.55
78 79 0.944311 CAAGGTGGTTCGTCTGTCGG 60.944 60.000 0.00 0.00 40.32 4.79
79 80 0.249322 ACAAGGTGGTTCGTCTGTCG 60.249 55.000 0.00 0.00 41.41 4.35
80 81 2.806608 TACAAGGTGGTTCGTCTGTC 57.193 50.000 0.00 0.00 0.00 3.51
81 82 2.897969 AGATACAAGGTGGTTCGTCTGT 59.102 45.455 0.00 0.00 0.00 3.41
82 83 3.512680 GAGATACAAGGTGGTTCGTCTG 58.487 50.000 0.00 0.00 0.00 3.51
83 84 2.496470 GGAGATACAAGGTGGTTCGTCT 59.504 50.000 0.00 0.00 0.00 4.18
84 85 2.734492 CGGAGATACAAGGTGGTTCGTC 60.734 54.545 0.00 0.00 0.00 4.20
85 86 1.203994 CGGAGATACAAGGTGGTTCGT 59.796 52.381 0.00 0.00 0.00 3.85
86 87 1.475280 TCGGAGATACAAGGTGGTTCG 59.525 52.381 0.00 0.00 0.00 3.95
87 88 2.232941 TGTCGGAGATACAAGGTGGTTC 59.767 50.000 0.00 0.00 40.67 3.62
88 89 2.253610 TGTCGGAGATACAAGGTGGTT 58.746 47.619 0.00 0.00 40.67 3.67
89 90 1.933021 TGTCGGAGATACAAGGTGGT 58.067 50.000 0.00 0.00 40.67 4.16
90 91 2.430694 TGATGTCGGAGATACAAGGTGG 59.569 50.000 0.00 0.00 40.67 4.61
91 92 3.131223 AGTGATGTCGGAGATACAAGGTG 59.869 47.826 0.00 0.00 40.67 4.00
92 93 3.366396 AGTGATGTCGGAGATACAAGGT 58.634 45.455 0.00 0.00 40.67 3.50
93 94 3.971150 GAGTGATGTCGGAGATACAAGG 58.029 50.000 0.00 0.00 40.67 3.61
423 424 4.450419 GCCTAGTTCGATGGATCAATTCTG 59.550 45.833 0.00 0.00 0.00 3.02
424 425 4.101585 TGCCTAGTTCGATGGATCAATTCT 59.898 41.667 0.00 0.00 0.00 2.40
455 456 4.953868 TGGTTCGCCGGTGTGTCG 62.954 66.667 16.01 3.10 41.18 4.35
466 467 1.475280 TCCGAGATACAAGGTGGTTCG 59.525 52.381 0.00 0.00 0.00 3.95
532 538 5.724328 AGGAACCATATGCGTATGTATGAG 58.276 41.667 21.60 10.43 36.72 2.90
533 539 5.738619 AGGAACCATATGCGTATGTATGA 57.261 39.130 21.60 0.00 36.72 2.15
534 540 8.492673 AATTAGGAACCATATGCGTATGTATG 57.507 34.615 21.60 11.05 36.72 2.39
537 543 9.515226 AATTAATTAGGAACCATATGCGTATGT 57.485 29.630 21.60 6.93 36.72 2.29
541 547 9.569122 AGTAAATTAATTAGGAACCATATGCGT 57.431 29.630 0.01 0.00 0.00 5.24
566 572 8.667076 AATCCTTTTTCATCAAAACAAAGGAG 57.333 30.769 15.06 0.00 42.78 3.69
568 574 8.344831 GGAAATCCTTTTTCATCAAAACAAAGG 58.655 33.333 3.05 3.05 36.67 3.11
572 578 7.334090 TGTGGAAATCCTTTTTCATCAAAACA 58.666 30.769 0.44 0.00 32.94 2.83
573 579 7.784633 TGTGGAAATCCTTTTTCATCAAAAC 57.215 32.000 0.44 0.00 32.94 2.43
639 886 9.100554 CGATCGATTCACCTAGATAACTACTAT 57.899 37.037 10.26 0.00 0.00 2.12
712 976 6.070881 ACACATGTGCTTATCTTTCTCTCTCT 60.071 38.462 25.68 0.00 0.00 3.10
713 977 6.035866 CACACATGTGCTTATCTTTCTCTCTC 59.964 42.308 25.68 0.00 39.39 3.20
714 978 5.873712 CACACATGTGCTTATCTTTCTCTCT 59.126 40.000 25.68 0.00 39.39 3.10
715 979 5.871524 TCACACATGTGCTTATCTTTCTCTC 59.128 40.000 25.68 0.00 45.25 3.20
716 980 5.798132 TCACACATGTGCTTATCTTTCTCT 58.202 37.500 25.68 0.00 45.25 3.10
805 1347 1.376543 ACTCTGCAATGCTGATTCGG 58.623 50.000 14.95 6.43 36.06 4.30
918 1465 2.093973 ACTCACAACATCTGGGTCGATC 60.094 50.000 0.00 0.00 0.00 3.69
940 1487 1.883084 GCATAAGGGAGGCGTCACG 60.883 63.158 8.91 0.00 0.00 4.35
951 1498 0.940126 GTCCACGAGCATGCATAAGG 59.060 55.000 21.98 15.93 0.00 2.69
1099 1646 3.710722 CTCCTTCAGGTGGGCGCT 61.711 66.667 7.64 0.00 36.34 5.92
1212 1759 2.997315 TAGCACGGCAGCCACTCT 60.997 61.111 13.30 6.90 34.23 3.24
1353 1900 6.341316 GCCTGGGTACATCTACATGTATATG 58.659 44.000 22.87 22.87 45.38 1.78
1355 1902 4.775780 GGCCTGGGTACATCTACATGTATA 59.224 45.833 5.91 0.00 45.38 1.47
1362 1909 1.069258 GCGGCCTGGGTACATCTAC 59.931 63.158 0.00 0.00 0.00 2.59
1363 1910 2.138179 GGCGGCCTGGGTACATCTA 61.138 63.158 12.87 0.00 0.00 1.98
1364 1911 3.480133 GGCGGCCTGGGTACATCT 61.480 66.667 12.87 0.00 0.00 2.90
1457 2004 3.462678 TATACCAGCGCCGGCACA 61.463 61.111 28.98 0.00 43.41 4.57
1843 2390 9.939424 AGTAGAAGTGTACTAATTAAGGAGGAT 57.061 33.333 0.00 0.00 31.14 3.24
1860 2407 8.763049 TGTCAGATCAAATACAAGTAGAAGTG 57.237 34.615 0.00 0.00 0.00 3.16
1974 2521 4.201792 CGAGTCATGAGCAGAAAAATGAGG 60.202 45.833 0.00 0.00 30.00 3.86
2046 2596 0.520404 TGTACTTCTCACGAGGCGAC 59.480 55.000 0.00 0.00 0.00 5.19
2054 2604 7.684937 TCTAGTTTCCTACTGTACTTCTCAC 57.315 40.000 0.00 0.00 37.73 3.51
2095 2647 2.684843 CCGCCTCTTGCTCTGTTGC 61.685 63.158 0.00 0.00 38.05 4.17
2113 2665 0.178990 ACACCCAGAAGAACTTGGGC 60.179 55.000 9.40 0.00 39.14 5.36
2118 2670 1.122019 AGCCGACACCCAGAAGAACT 61.122 55.000 0.00 0.00 0.00 3.01
2120 2672 1.371183 CAGCCGACACCCAGAAGAA 59.629 57.895 0.00 0.00 0.00 2.52
2155 2707 1.079503 GGACACTTCCAACGATGAGC 58.920 55.000 0.00 0.00 42.30 4.26
2170 2722 1.272258 TGGATGAGGTACACGAGGACA 60.272 52.381 0.00 0.00 0.00 4.02
2268 2821 3.744238 AACACCAAATTGGCACCTTAC 57.256 42.857 12.67 0.00 42.67 2.34
2326 2882 2.810887 GGCGGACGACGGGTTTAC 60.811 66.667 0.00 0.00 44.51 2.01
2431 2987 2.760385 GTCGGGACCCAGGAGGAG 60.760 72.222 12.15 0.00 39.89 3.69
2440 2996 0.388263 GACGAACTGAAGTCGGGACC 60.388 60.000 0.00 0.00 0.00 4.46
2445 3001 0.039074 AGCAGGACGAACTGAAGTCG 60.039 55.000 13.73 0.00 40.97 4.18
2457 3013 1.338484 TGTGATGAGCTCAAGCAGGAC 60.338 52.381 22.50 11.15 45.16 3.85
2459 3015 1.467734 GTTGTGATGAGCTCAAGCAGG 59.532 52.381 22.50 0.00 45.16 4.85
2560 3130 2.224079 CGACCATCTCCTTGTTGTTGTG 59.776 50.000 0.00 0.00 0.00 3.33
2953 3524 2.430465 TGCATGCTTCTGACTTCTTCC 58.570 47.619 20.33 0.00 0.00 3.46
3000 3571 4.436050 CGACCTGAAAGATACACACAATGC 60.436 45.833 0.00 0.00 34.07 3.56
3185 3756 2.261671 CAGGTAGCTCGCGTTGGT 59.738 61.111 5.77 8.91 0.00 3.67
3377 3957 4.340617 AGTTGAGTCACTTGTTTTTGGGA 58.659 39.130 0.00 0.00 0.00 4.37
3378 3958 4.718940 AGTTGAGTCACTTGTTTTTGGG 57.281 40.909 0.00 0.00 0.00 4.12
3379 3959 7.420184 AAAAAGTTGAGTCACTTGTTTTTGG 57.580 32.000 0.00 0.00 37.07 3.28
3449 4032 9.979578 TTGCATGTGAGTTCATAAATTTTACTT 57.020 25.926 0.00 0.00 0.00 2.24
3571 4188 8.260818 AGGTACACTCACGTTCTTATAGTACTA 58.739 37.037 4.77 4.77 32.28 1.82
3604 4532 7.450014 GGTAGATCCTATCATGTATCATCCGAT 59.550 40.741 0.00 0.00 35.50 4.18
3605 4533 6.773200 GGTAGATCCTATCATGTATCATCCGA 59.227 42.308 0.00 0.00 0.00 4.55
3606 4534 6.547510 TGGTAGATCCTATCATGTATCATCCG 59.452 42.308 0.00 0.00 37.07 4.18
3607 4535 7.904558 TGGTAGATCCTATCATGTATCATCC 57.095 40.000 0.00 0.00 37.07 3.51
3608 4536 9.140874 TCATGGTAGATCCTATCATGTATCATC 57.859 37.037 20.35 0.00 37.20 2.92
3609 4537 9.498039 TTCATGGTAGATCCTATCATGTATCAT 57.502 33.333 20.35 1.59 37.20 2.45
3610 4538 8.899887 TTCATGGTAGATCCTATCATGTATCA 57.100 34.615 20.35 5.22 37.20 2.15
3611 4539 9.593134 GTTTCATGGTAGATCCTATCATGTATC 57.407 37.037 20.35 10.91 37.20 2.24
3612 4540 9.331466 AGTTTCATGGTAGATCCTATCATGTAT 57.669 33.333 20.35 8.01 37.20 2.29
3613 4541 8.588472 CAGTTTCATGGTAGATCCTATCATGTA 58.412 37.037 20.35 12.43 37.20 2.29
3614 4542 7.071698 ACAGTTTCATGGTAGATCCTATCATGT 59.928 37.037 20.35 5.51 37.20 3.21
3615 4543 7.448420 ACAGTTTCATGGTAGATCCTATCATG 58.552 38.462 16.95 16.95 37.23 3.07
3630 4558 7.495606 TCACTATTGCCATAGTACAGTTTCATG 59.504 37.037 9.95 0.00 43.37 3.07
3639 4567 5.928839 CCAGATGTCACTATTGCCATAGTAC 59.071 44.000 9.95 9.37 43.37 2.73
3797 4725 6.077838 CGGTGCAAAAGAAAGAACATAGTAC 58.922 40.000 0.00 0.00 0.00 2.73
3798 4726 5.180492 CCGGTGCAAAAGAAAGAACATAGTA 59.820 40.000 0.00 0.00 0.00 1.82
3799 4727 4.023193 CCGGTGCAAAAGAAAGAACATAGT 60.023 41.667 0.00 0.00 0.00 2.12
3829 4757 7.699709 TTTTGGGATGGAGGAAGTACATATA 57.300 36.000 0.00 0.00 0.00 0.86
3833 4761 4.946160 ATTTTGGGATGGAGGAAGTACA 57.054 40.909 0.00 0.00 0.00 2.90
3834 4762 6.605471 AAAATTTTGGGATGGAGGAAGTAC 57.395 37.500 1.75 0.00 0.00 2.73
3835 4763 6.556874 ACAAAAATTTTGGGATGGAGGAAGTA 59.443 34.615 20.79 0.00 0.00 2.24
3836 4764 5.369404 ACAAAAATTTTGGGATGGAGGAAGT 59.631 36.000 20.79 0.00 0.00 3.01
3837 4765 5.868454 ACAAAAATTTTGGGATGGAGGAAG 58.132 37.500 20.79 0.00 0.00 3.46
3840 4768 5.488262 AGACAAAAATTTTGGGATGGAGG 57.512 39.130 20.79 0.00 0.00 4.30
3841 4769 8.900983 TTTAAGACAAAAATTTTGGGATGGAG 57.099 30.769 20.79 0.00 0.00 3.86
3842 4770 9.859152 AATTTAAGACAAAAATTTTGGGATGGA 57.141 25.926 20.79 5.16 33.78 3.41
3890 4818 9.379791 GGCTGTATCTAACACTAAAATGTAACT 57.620 33.333 0.00 0.00 33.45 2.24
3891 4819 8.325997 CGGCTGTATCTAACACTAAAATGTAAC 58.674 37.037 0.00 0.00 33.45 2.50
3892 4820 8.036575 ACGGCTGTATCTAACACTAAAATGTAA 58.963 33.333 0.00 0.00 33.45 2.41
3893 4821 7.549839 ACGGCTGTATCTAACACTAAAATGTA 58.450 34.615 0.00 0.00 33.45 2.29
3895 4823 6.903883 ACGGCTGTATCTAACACTAAAATG 57.096 37.500 0.00 0.00 33.45 2.32
3910 4838 9.511272 TCTTATATTTGTCTAGATACGGCTGTA 57.489 33.333 8.08 8.08 34.45 2.74
3912 4840 8.297426 TGTCTTATATTTGTCTAGATACGGCTG 58.703 37.037 0.00 0.00 0.00 4.85
3914 4842 9.130312 CTTGTCTTATATTTGTCTAGATACGGC 57.870 37.037 0.00 0.00 0.00 5.68
3926 4854 9.289303 CGTCCCAAAAATCTTGTCTTATATTTG 57.711 33.333 0.00 0.00 0.00 2.32
3927 4855 8.466798 CCGTCCCAAAAATCTTGTCTTATATTT 58.533 33.333 0.00 0.00 0.00 1.40
3929 4857 7.343357 TCCGTCCCAAAAATCTTGTCTTATAT 58.657 34.615 0.00 0.00 0.00 0.86
3930 4858 6.713276 TCCGTCCCAAAAATCTTGTCTTATA 58.287 36.000 0.00 0.00 0.00 0.98
3931 4859 5.566469 TCCGTCCCAAAAATCTTGTCTTAT 58.434 37.500 0.00 0.00 0.00 1.73
3932 4860 4.975631 TCCGTCCCAAAAATCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
3933 4861 3.821033 CTCCGTCCCAAAAATCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
3934 4862 3.412386 CTCCGTCCCAAAAATCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
3935 4863 2.488153 CCTCCGTCCCAAAAATCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
3936 4864 2.514803 CCTCCGTCCCAAAAATCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
3937 4865 1.818674 CCCTCCGTCCCAAAAATCTTG 59.181 52.381 0.00 0.00 0.00 3.02
3938 4866 1.708551 TCCCTCCGTCCCAAAAATCTT 59.291 47.619 0.00 0.00 0.00 2.40
3939 4867 1.282157 CTCCCTCCGTCCCAAAAATCT 59.718 52.381 0.00 0.00 0.00 2.40
3940 4868 1.004394 ACTCCCTCCGTCCCAAAAATC 59.996 52.381 0.00 0.00 0.00 2.17
3941 4869 1.073098 ACTCCCTCCGTCCCAAAAAT 58.927 50.000 0.00 0.00 0.00 1.82
3942 4870 1.732117 TACTCCCTCCGTCCCAAAAA 58.268 50.000 0.00 0.00 0.00 1.94
3943 4871 1.732117 TTACTCCCTCCGTCCCAAAA 58.268 50.000 0.00 0.00 0.00 2.44
3944 4872 1.961133 ATTACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
3945 4873 2.852714 TATTACTCCCTCCGTCCCAA 57.147 50.000 0.00 0.00 0.00 4.12
3946 4874 4.474303 TTATATTACTCCCTCCGTCCCA 57.526 45.455 0.00 0.00 0.00 4.37
3947 4875 5.813513 TTTTATATTACTCCCTCCGTCCC 57.186 43.478 0.00 0.00 0.00 4.46
3948 4876 5.642491 GCATTTTATATTACTCCCTCCGTCC 59.358 44.000 0.00 0.00 0.00 4.79
3949 4877 6.147328 GTGCATTTTATATTACTCCCTCCGTC 59.853 42.308 0.00 0.00 0.00 4.79
3950 4878 5.995897 GTGCATTTTATATTACTCCCTCCGT 59.004 40.000 0.00 0.00 0.00 4.69
3951 4879 5.120208 CGTGCATTTTATATTACTCCCTCCG 59.880 44.000 0.00 0.00 0.00 4.63
3952 4880 5.995897 ACGTGCATTTTATATTACTCCCTCC 59.004 40.000 0.00 0.00 0.00 4.30
3953 4881 7.441458 AGAACGTGCATTTTATATTACTCCCTC 59.559 37.037 0.00 0.00 0.00 4.30
3954 4882 7.280356 AGAACGTGCATTTTATATTACTCCCT 58.720 34.615 0.00 0.00 0.00 4.20
3955 4883 7.492352 AGAACGTGCATTTTATATTACTCCC 57.508 36.000 0.00 0.00 0.00 4.30
3956 4884 8.609176 TCAAGAACGTGCATTTTATATTACTCC 58.391 33.333 0.00 0.00 0.00 3.85
3957 4885 9.982291 TTCAAGAACGTGCATTTTATATTACTC 57.018 29.630 0.00 0.00 0.00 2.59
4030 4958 3.057596 CGGCTGCATAGAAAGAAAAACCA 60.058 43.478 0.50 0.00 0.00 3.67
4131 5059 8.673711 TGAGTTGGACATGTTTATATTTAGTGC 58.326 33.333 0.00 0.00 0.00 4.40
4134 5062 8.345565 GCCTGAGTTGGACATGTTTATATTTAG 58.654 37.037 0.00 0.00 0.00 1.85
4166 5094 5.449862 GGTCTCAGTTGTACATGTTTTGCAA 60.450 40.000 2.30 0.00 0.00 4.08
4168 5096 4.275936 AGGTCTCAGTTGTACATGTTTTGC 59.724 41.667 2.30 0.00 0.00 3.68
4169 5097 6.183360 ACAAGGTCTCAGTTGTACATGTTTTG 60.183 38.462 2.30 0.00 35.10 2.44
4185 5113 4.821805 TCAAATTGAGTTGGACAAGGTCTC 59.178 41.667 0.00 0.00 32.47 3.36
4195 5123 3.434309 ACCTCCCATCAAATTGAGTTGG 58.566 45.455 8.31 8.31 0.00 3.77
4211 5139 1.413077 CAGATACCCGGAAAGACCTCC 59.587 57.143 0.73 0.00 36.31 4.30
4217 5145 0.108329 ACACGCAGATACCCGGAAAG 60.108 55.000 0.73 0.00 0.00 2.62
4273 5205 1.073964 CACTCAATGCAGTCGGTCAG 58.926 55.000 0.00 0.00 0.00 3.51
4278 5210 1.995484 CTGTACCACTCAATGCAGTCG 59.005 52.381 0.00 0.00 0.00 4.18
4287 5219 2.289631 CCAGTGCAATCTGTACCACTCA 60.290 50.000 3.87 0.00 36.47 3.41
4289 5221 1.611673 GCCAGTGCAATCTGTACCACT 60.612 52.381 3.87 0.00 38.97 4.00
4316 5248 3.319137 TTCTTCATCACTTCACTCCCG 57.681 47.619 0.00 0.00 0.00 5.14
4385 5317 2.358737 GCGTCACCCACCTTCTGG 60.359 66.667 0.00 0.00 40.26 3.86
4450 5382 4.260334 GGCAAAAAGAGTTTCACACAATGC 60.260 41.667 0.00 0.00 0.00 3.56
4496 5428 3.350912 GTGTTGTTCTTACACAAGTGCG 58.649 45.455 0.00 0.00 44.08 5.34
4509 5441 4.393062 CCATCACATGTAGAGGTGTTGTTC 59.607 45.833 12.82 0.00 33.60 3.18
4568 5500 0.742505 AGGTTCGACAAGACACGTGA 59.257 50.000 25.01 0.00 0.00 4.35
4601 5533 6.093495 CCGTGAATATAGAAGCAAAGGAAACA 59.907 38.462 0.00 0.00 0.00 2.83
4624 5558 4.703897 TCCTTAATTAGCCACTTGATCCG 58.296 43.478 0.00 0.00 0.00 4.18
4656 5590 5.147767 AGCCTCCTTAATTCACCACTTTTT 58.852 37.500 0.00 0.00 0.00 1.94
4657 5591 4.740902 AGCCTCCTTAATTCACCACTTTT 58.259 39.130 0.00 0.00 0.00 2.27
4658 5592 4.336280 GAGCCTCCTTAATTCACCACTTT 58.664 43.478 0.00 0.00 0.00 2.66
4659 5593 3.619979 CGAGCCTCCTTAATTCACCACTT 60.620 47.826 0.00 0.00 0.00 3.16
4660 5594 2.093447 CGAGCCTCCTTAATTCACCACT 60.093 50.000 0.00 0.00 0.00 4.00
4661 5595 2.093658 TCGAGCCTCCTTAATTCACCAC 60.094 50.000 0.00 0.00 0.00 4.16
4662 5596 2.184533 TCGAGCCTCCTTAATTCACCA 58.815 47.619 0.00 0.00 0.00 4.17
4663 5597 2.981859 TCGAGCCTCCTTAATTCACC 57.018 50.000 0.00 0.00 0.00 4.02
4664 5598 4.095036 CCTTTTCGAGCCTCCTTAATTCAC 59.905 45.833 0.00 0.00 0.00 3.18
4665 5599 4.261801 CCTTTTCGAGCCTCCTTAATTCA 58.738 43.478 0.00 0.00 0.00 2.57
4788 5724 5.399013 CCAGTTCAAAAATACCTTTAGCGG 58.601 41.667 0.00 0.00 0.00 5.52
4844 6585 4.002982 TGAAGCCATGTCATCACAACTAC 58.997 43.478 0.00 0.00 35.64 2.73
5068 6821 5.907197 AACAGCGATTCGGTAGAATTATG 57.093 39.130 10.81 0.00 46.30 1.90
5084 6865 5.515626 AGCTAGATCTTTAAACGTAACAGCG 59.484 40.000 0.00 0.00 37.94 5.18
5086 6867 6.531948 AGCAGCTAGATCTTTAAACGTAACAG 59.468 38.462 0.00 0.00 0.00 3.16
5108 6889 7.489160 ACACGTCTTGATATTCATACTTAGCA 58.511 34.615 0.00 0.00 0.00 3.49
5121 6902 6.015688 ACACCTTTAGAGAACACGTCTTGATA 60.016 38.462 0.00 0.00 36.41 2.15
5301 7083 7.107542 TCGGGGTATCTATTAATGGTTAATGC 58.892 38.462 0.00 0.00 36.56 3.56
5314 7096 8.940397 AATGAAAATCATTTCGGGGTATCTAT 57.060 30.769 0.00 0.00 44.03 1.98
5384 7168 6.087522 TGGCATTTTTACGTACAAAGCATAC 58.912 36.000 20.15 10.58 0.00 2.39


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

AutoCloner maintained by Alex Coulton.