Multiple sequence alignment - TraesCS7A01G270300

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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 TraesCS7A01G270300 chr7A 100.000 5210 0 0 1 5210 277734278 277729069 0.000000e+00 9622.0
1 TraesCS7A01G270300 chr7A 100.000 108 0 0 4970 5077 694064015 694063908 3.180000e-47 200.0
2 TraesCS7A01G270300 chr7A 97.222 36 1 0 39 74 140651958 140651923 1.570000e-05 62.1
3 TraesCS7A01G270300 chr7D 92.147 4992 221 70 42 4948 257513235 257518140 0.000000e+00 6889.0
4 TraesCS7A01G270300 chr7D 90.526 190 6 5 4760 4948 570232928 570232750 1.870000e-59 241.0
5 TraesCS7A01G270300 chr7D 93.077 130 7 1 5076 5203 257518153 257518282 6.890000e-44 189.0
6 TraesCS7A01G270300 chr7D 94.915 118 4 2 4960 5077 423304966 423305081 3.200000e-42 183.0
7 TraesCS7A01G270300 chr7D 100.000 35 0 0 41 75 156005881 156005847 1.210000e-06 65.8
8 TraesCS7A01G270300 chr7D 100.000 31 0 0 45 75 89889758 89889728 2.030000e-04 58.4
9 TraesCS7A01G270300 chr7B 91.763 4395 217 47 633 4948 236781903 236786231 0.000000e+00 5976.0
10 TraesCS7A01G270300 chr7B 99.115 113 0 1 4966 5077 735980196 735980084 8.850000e-48 202.0
11 TraesCS7A01G270300 chr7B 98.198 111 2 0 4970 5080 750444583 750444693 1.480000e-45 195.0
12 TraesCS7A01G270300 chr7B 97.143 35 1 0 4 38 612890494 612890460 5.630000e-05 60.2
13 TraesCS7A01G270300 chr6D 91.765 170 11 3 4246 4412 431160835 431160666 3.140000e-57 233.0
14 TraesCS7A01G270300 chr6D 100.000 30 0 0 40 69 46945333 46945362 7.290000e-04 56.5
15 TraesCS7A01G270300 chr6D 94.286 35 2 0 40 74 56298568 56298534 3.000000e-03 54.7
16 TraesCS7A01G270300 chr4B 91.071 168 10 3 4248 4410 178081269 178081102 6.790000e-54 222.0
17 TraesCS7A01G270300 chr4B 100.000 31 0 0 45 75 645312914 645312884 2.030000e-04 58.4
18 TraesCS7A01G270300 chr1B 91.463 164 9 5 4255 4414 314565697 314565535 2.440000e-53 220.0
19 TraesCS7A01G270300 chr1B 86.170 188 17 7 4236 4419 152449985 152450167 1.480000e-45 195.0
20 TraesCS7A01G270300 chr2A 90.964 166 10 4 4255 4415 70985586 70985751 8.780000e-53 219.0
21 TraesCS7A01G270300 chr2A 100.000 35 0 0 40 74 472249126 472249160 1.210000e-06 65.8
22 TraesCS7A01G270300 chr2A 89.130 46 4 1 30 74 11920241 11920196 7.290000e-04 56.5
23 TraesCS7A01G270300 chr6B 90.000 170 14 3 4246 4412 650598707 650598538 3.160000e-52 217.0
24 TraesCS7A01G270300 chr6B 88.889 171 13 6 4250 4415 132353413 132353582 6.840000e-49 206.0
25 TraesCS7A01G270300 chr2D 89.205 176 12 6 4248 4418 524963805 524963632 4.090000e-51 213.0
26 TraesCS7A01G270300 chr2D 97.248 109 3 0 4969 5077 326217585 326217477 8.910000e-43 185.0
27 TraesCS7A01G270300 chr2D 100.000 33 0 0 42 74 74764288 74764256 1.570000e-05 62.1
28 TraesCS7A01G270300 chr1D 89.881 168 13 3 4251 4414 463382068 463381901 4.090000e-51 213.0
29 TraesCS7A01G270300 chr6A 99.115 113 0 1 4966 5077 499656183 499656071 8.850000e-48 202.0
30 TraesCS7A01G270300 chr6A 100.000 32 0 0 40 71 596527244 596527275 5.630000e-05 60.2
31 TraesCS7A01G270300 chr5A 98.246 114 2 0 4964 5077 585213308 585213421 3.180000e-47 200.0
32 TraesCS7A01G270300 chr5A 94.872 39 1 1 37 74 8232971 8232933 5.630000e-05 60.2
33 TraesCS7A01G270300 chr3A 99.099 111 1 0 4970 5080 46996208 46996318 3.180000e-47 200.0
34 TraesCS7A01G270300 chr3A 97.143 35 1 0 40 74 55840385 55840351 5.630000e-05 60.2
35 TraesCS7A01G270300 chr5B 91.111 135 9 3 4945 5077 711156322 711156455 4.150000e-41 180.0
36 TraesCS7A01G270300 chr4A 95.000 40 1 1 37 75 181805600 181805639 1.570000e-05 62.1
37 TraesCS7A01G270300 chr5D 100.000 32 0 0 42 73 366763363 366763394 5.630000e-05 60.2
38 TraesCS7A01G270300 chr5D 96.970 33 1 0 42 74 424938762 424938794 7.290000e-04 56.5
39 TraesCS7A01G270300 chr5D 96.970 33 1 0 40 72 444850168 444850200 7.290000e-04 56.5
40 TraesCS7A01G270300 chr5D 100.000 30 0 0 42 71 444850493 444850522 7.290000e-04 56.5
41 TraesCS7A01G270300 chr5D 90.244 41 2 2 30 69 243298898 243298937 9.000000e-03 52.8
42 TraesCS7A01G270300 chr1A 94.872 39 1 1 37 75 202090743 202090780 5.630000e-05 60.2
43 TraesCS7A01G270300 chr1A 97.143 35 1 0 42 76 550112257 550112223 5.630000e-05 60.2
44 TraesCS7A01G270300 chr4D 97.059 34 1 0 42 75 88117028 88117061 2.030000e-04 58.4
45 TraesCS7A01G270300 chr4D 97.059 34 0 1 37 69 63909205 63909172 7.290000e-04 56.5
46 TraesCS7A01G270300 chr4D 100.000 30 0 0 40 69 126895174 126895203 7.290000e-04 56.5
47 TraesCS7A01G270300 chr4D 97.059 34 0 1 37 69 449827231 449827198 7.290000e-04 56.5
48 TraesCS7A01G270300 chr4D 97.059 34 0 1 37 69 501974527 501974494 7.290000e-04 56.5
49 TraesCS7A01G270300 chr4D 100.000 29 0 0 41 69 108913591 108913619 3.000000e-03 54.7
50 TraesCS7A01G270300 chr4D 96.774 31 1 0 42 72 57223614 57223584 9.000000e-03 52.8
51 TraesCS7A01G270300 chr3D 97.059 34 1 0 42 75 48440285 48440252 2.030000e-04 58.4
52 TraesCS7A01G270300 chrUn 97.059 34 0 1 37 69 129538979 129539012 7.290000e-04 56.5
53 TraesCS7A01G270300 chrUn 100.000 30 0 0 46 75 348144649 348144620 7.290000e-04 56.5
54 TraesCS7A01G270300 chrUn 100.000 28 0 0 42 69 96355281 96355308 9.000000e-03 52.8
55 TraesCS7A01G270300 chrUn 100.000 28 0 0 42 69 293303306 293303279 9.000000e-03 52.8
56 TraesCS7A01G270300 chrUn 100.000 28 0 0 42 69 293308703 293308676 9.000000e-03 52.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G270300 chr7A 277729069 277734278 5209 True 9622 9622 100.000 1 5210 1 chr7A.!!$R2 5209
1 TraesCS7A01G270300 chr7D 257513235 257518282 5047 False 3539 6889 92.612 42 5203 2 chr7D.!!$F2 5161
2 TraesCS7A01G270300 chr7B 236781903 236786231 4328 False 5976 5976 91.763 633 4948 1 chr7B.!!$F1 4315

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
842 868 0.104120 AACTATCACAGCGGCGCATA 59.896 50.000 35.02 20.65 0.0 3.14 F
1802 1879 0.251297 CACATCACTTTGCCTCCCCA 60.251 55.000 0.00 0.00 0.0 4.96 F
1808 1885 2.532715 TTTGCCTCCCCAGCTCCT 60.533 61.111 0.00 0.00 0.0 3.69 F
3144 3225 0.250510 GCCCTGCCCAAGCTACTATC 60.251 60.000 0.00 0.00 40.8 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1957 2034 1.060729 TAAGGCAGGCAACACCAGTA 58.939 50.0 0.00 0.00 43.14 2.74 R
3145 3226 0.538057 CCTTGCAGGGCTTCAAGTGA 60.538 55.0 0.13 0.00 38.33 3.41 R
3686 3786 1.666054 ACCTCAAACGTTAACGCCAA 58.334 45.0 27.07 9.94 44.43 4.52 R
4875 5003 0.113190 ACAAAAGGGAGGCCTTCAGG 59.887 55.0 14.70 0.00 38.53 3.86 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
18 19 3.045518 TCGTGCCTACCAGAGTTCA 57.954 52.632 0.00 0.00 0.00 3.18
19 20 1.334160 TCGTGCCTACCAGAGTTCAA 58.666 50.000 0.00 0.00 0.00 2.69
20 21 1.272490 TCGTGCCTACCAGAGTTCAAG 59.728 52.381 0.00 0.00 0.00 3.02
21 22 1.000955 CGTGCCTACCAGAGTTCAAGT 59.999 52.381 0.00 0.00 0.00 3.16
22 23 2.689646 GTGCCTACCAGAGTTCAAGTC 58.310 52.381 0.00 0.00 0.00 3.01
23 24 2.300437 GTGCCTACCAGAGTTCAAGTCT 59.700 50.000 0.00 0.00 0.00 3.24
24 25 2.563179 TGCCTACCAGAGTTCAAGTCTC 59.437 50.000 0.00 0.00 0.00 3.36
25 26 2.563179 GCCTACCAGAGTTCAAGTCTCA 59.437 50.000 0.00 0.00 34.73 3.27
26 27 3.367910 GCCTACCAGAGTTCAAGTCTCAG 60.368 52.174 0.00 0.00 34.73 3.35
27 28 4.082845 CCTACCAGAGTTCAAGTCTCAGA 58.917 47.826 0.00 0.00 34.73 3.27
28 29 4.082463 CCTACCAGAGTTCAAGTCTCAGAC 60.082 50.000 0.00 0.00 34.73 3.51
29 30 3.571590 ACCAGAGTTCAAGTCTCAGACT 58.428 45.455 0.00 0.00 45.64 3.24
38 39 2.810439 AGTCTCAGACTTGACACTGC 57.190 50.000 0.00 0.00 40.28 4.40
39 40 1.342819 AGTCTCAGACTTGACACTGCC 59.657 52.381 0.00 0.00 40.28 4.85
40 41 1.342819 GTCTCAGACTTGACACTGCCT 59.657 52.381 0.00 0.00 34.57 4.75
46 47 4.130118 CAGACTTGACACTGCCTTTTAGT 58.870 43.478 0.00 0.00 0.00 2.24
83 84 1.521423 GTCGACTATGAAATTCGGCCG 59.479 52.381 22.12 22.12 31.15 6.13
84 85 1.406180 TCGACTATGAAATTCGGCCGA 59.594 47.619 27.28 27.28 33.50 5.54
86 87 2.546778 GACTATGAAATTCGGCCGACA 58.453 47.619 31.19 23.24 0.00 4.35
97 98 1.514087 GGCCGACAGTCCGATTGTA 59.486 57.895 0.00 0.00 0.00 2.41
102 103 2.322161 CGACAGTCCGATTGTAAACGT 58.678 47.619 0.00 0.00 0.00 3.99
126 127 9.965748 CGTTTTCTTTTAACAAATGTTGAACAT 57.034 25.926 4.72 4.72 41.31 2.71
186 187 8.546597 AATGTACAAATGTTTATGGGAAAAGC 57.453 30.769 0.00 0.00 0.00 3.51
247 249 8.150909 CCATGTACTTTAAAAATGTTAAACGCG 58.849 33.333 3.53 3.53 0.00 6.01
260 262 7.979115 ATGTTAAACGCGCATATAAATGTTT 57.021 28.000 5.73 9.52 35.38 2.83
261 263 7.425915 TGTTAAACGCGCATATAAATGTTTC 57.574 32.000 5.73 0.00 35.38 2.78
262 264 6.469595 TGTTAAACGCGCATATAAATGTTTCC 59.530 34.615 5.73 2.64 35.38 3.13
263 265 4.624336 AACGCGCATATAAATGTTTCCA 57.376 36.364 5.73 0.00 35.38 3.53
264 266 4.624336 ACGCGCATATAAATGTTTCCAA 57.376 36.364 5.73 0.00 35.38 3.53
533 536 6.400568 ACCGAGAAAGAAACGAAATATACCA 58.599 36.000 0.00 0.00 0.00 3.25
555 558 7.213678 ACCAGTGAAAAACAAAGAAAGAACAA 58.786 30.769 0.00 0.00 0.00 2.83
611 616 7.921786 TGAAACATAAAAGTCACATAGAGGG 57.078 36.000 0.00 0.00 0.00 4.30
676 682 0.464373 ATGCACGAATACAGGCTGGG 60.464 55.000 20.34 4.93 0.00 4.45
690 696 1.269998 GGCTGGGCTAGTACTGTATCG 59.730 57.143 5.39 0.00 0.00 2.92
731 737 3.310246 GAGACTTTATTCGATCTCGCCC 58.690 50.000 0.00 0.00 39.60 6.13
755 761 0.803117 CGAGATATAGCTCCCGCGAA 59.197 55.000 8.23 0.00 42.32 4.70
812 838 4.332819 GGCAAACCATTGTGCTACTACTAG 59.667 45.833 0.00 0.00 40.70 2.57
813 839 4.935808 GCAAACCATTGTGCTACTACTAGT 59.064 41.667 0.00 0.00 38.85 2.57
814 840 6.103997 GCAAACCATTGTGCTACTACTAGTA 58.896 40.000 1.89 1.89 38.85 1.82
815 841 6.255887 GCAAACCATTGTGCTACTACTAGTAG 59.744 42.308 25.30 25.30 43.08 2.57
816 842 6.466885 AACCATTGTGCTACTACTAGTAGG 57.533 41.667 29.05 16.06 46.31 3.18
817 843 4.341520 ACCATTGTGCTACTACTAGTAGGC 59.658 45.833 29.05 23.64 46.31 3.93
818 844 4.585162 CCATTGTGCTACTACTAGTAGGCT 59.415 45.833 29.05 14.85 46.31 4.58
819 845 5.768662 CCATTGTGCTACTACTAGTAGGCTA 59.231 44.000 29.05 15.15 46.31 3.93
842 868 0.104120 AACTATCACAGCGGCGCATA 59.896 50.000 35.02 20.65 0.00 3.14
928 981 4.098349 ACGAACATATGGTACGCTTTCCTA 59.902 41.667 7.80 0.00 0.00 2.94
987 1040 7.110810 TCTTTATCTTTCTCTCTCCTACACGA 58.889 38.462 0.00 0.00 0.00 4.35
1017 1070 3.014604 ACCGAAACACTTTCTCTCTCG 57.985 47.619 0.00 0.00 37.52 4.04
1030 1083 2.099405 CTCTCTCGCCCTTCTTTCTCT 58.901 52.381 0.00 0.00 0.00 3.10
1071 1124 4.083862 AAGACTTCGCCTCGCCCC 62.084 66.667 0.00 0.00 0.00 5.80
1347 1421 3.379445 CCCAGACTACGGCGGTGT 61.379 66.667 13.24 9.54 0.00 4.16
1487 1561 6.625520 CGTGGTTAGTGGTAGTTTTGGTTTTT 60.626 38.462 0.00 0.00 0.00 1.94
1572 1646 2.335933 AGCGGGTTTAGCCTATATGGT 58.664 47.619 0.00 0.00 38.35 3.55
1576 1650 3.751518 GGGTTTAGCCTATATGGTGGTG 58.248 50.000 0.00 0.00 38.35 4.17
1621 1695 3.436577 AGATCGATACCCGTACCAGAT 57.563 47.619 0.00 0.00 39.75 2.90
1622 1696 3.082548 AGATCGATACCCGTACCAGATG 58.917 50.000 0.00 0.00 39.75 2.90
1710 1786 3.945921 TCAAGAACGATACCGAGAGATGT 59.054 43.478 0.00 0.00 39.50 3.06
1765 1842 6.038356 GTGGTAAATCTGCTGATTGGATTTG 58.962 40.000 18.27 0.00 41.62 2.32
1802 1879 0.251297 CACATCACTTTGCCTCCCCA 60.251 55.000 0.00 0.00 0.00 4.96
1808 1885 2.532715 TTTGCCTCCCCAGCTCCT 60.533 61.111 0.00 0.00 0.00 3.69
1824 1901 5.280011 CCAGCTCCTTTACTAGAGGAAACAA 60.280 44.000 0.00 0.00 42.50 2.83
1853 1930 5.489792 TGTACTCTTCAAATCTGGCTCTT 57.510 39.130 0.00 0.00 0.00 2.85
1957 2034 5.076182 TGTGTGGATCAATGGTGTGTAATT 58.924 37.500 0.00 0.00 0.00 1.40
2010 2088 6.533730 TGGAGTTCTCATGACAGTTAAATGT 58.466 36.000 8.54 8.54 35.68 2.71
2065 2143 6.939730 TGTTAGTGTGCTTCCATATTTTCTCA 59.060 34.615 0.00 0.00 0.00 3.27
2092 2170 8.789825 TGTAATTATGCCCTTTTTACGACTTA 57.210 30.769 0.00 0.00 0.00 2.24
2363 2443 9.236006 ACATAATTATTCTGAGCACTTGTCTTT 57.764 29.630 0.00 0.00 0.00 2.52
2830 2910 9.206690 TCCATTTATTTTATATGCCCTGACAAA 57.793 29.630 0.00 0.00 0.00 2.83
2855 2935 4.403113 TGCTTGTTCAATATGATGCACCAT 59.597 37.500 0.00 0.00 0.00 3.55
2856 2936 5.105269 TGCTTGTTCAATATGATGCACCATT 60.105 36.000 0.00 0.00 0.00 3.16
3003 3084 5.925509 ACACGTATGTATATTCTGCCCTTT 58.074 37.500 0.00 0.00 37.26 3.11
3144 3225 0.250510 GCCCTGCCCAAGCTACTATC 60.251 60.000 0.00 0.00 40.80 2.08
3145 3226 1.428869 CCCTGCCCAAGCTACTATCT 58.571 55.000 0.00 0.00 40.80 1.98
3300 3381 6.612456 TGCATTCCCCATTAATTTCTTCTCAT 59.388 34.615 0.00 0.00 0.00 2.90
3362 3443 9.278978 TGTTGTACTTTCTTTGTGCAATATCTA 57.721 29.630 0.00 0.00 40.79 1.98
3364 3445 9.502091 TTGTACTTTCTTTGTGCAATATCTACT 57.498 29.630 0.00 0.00 35.68 2.57
3424 3505 3.403038 ACCTTAGCTGGCATTAATAGCG 58.597 45.455 0.00 0.00 42.10 4.26
3461 3542 0.945743 TGCGCTGCGATAATGCTAGG 60.946 55.000 28.07 0.00 35.36 3.02
3540 3621 7.624549 TGCAATCTTGGTTCTAGAGATTAGTT 58.375 34.615 4.39 0.00 37.88 2.24
3542 3623 8.951243 GCAATCTTGGTTCTAGAGATTAGTTTT 58.049 33.333 4.39 0.00 37.88 2.43
3609 3706 2.808543 GTCGATGTATCCTTGCCAATCC 59.191 50.000 0.00 0.00 0.00 3.01
3653 3750 6.407202 ACTGTATCTCTTTTCCTATGCGTTT 58.593 36.000 0.00 0.00 0.00 3.60
3686 3786 3.087031 CACACCTGAATTCTTGATGGCT 58.913 45.455 7.05 0.00 0.00 4.75
3982 4082 1.303317 GGGTTCGTCAGCCCATGTT 60.303 57.895 0.00 0.00 44.23 2.71
4042 4142 7.582667 TGTTCAGTATCCATTAGATTCTCGA 57.417 36.000 0.00 0.00 36.33 4.04
4105 4205 1.074319 TTGTTATCTCGCGGCGTGAC 61.074 55.000 26.57 16.36 32.42 3.67
4261 4361 7.676683 TGTATATATCCTTTATGCTCCCTCC 57.323 40.000 0.00 0.00 0.00 4.30
4279 4379 7.059202 TCCCTCCGTTTCTAAATATAAGTCC 57.941 40.000 0.00 0.00 0.00 3.85
4382 4493 9.771534 CTAGTCCCTTATTGGAATCTCTAAAAG 57.228 37.037 0.00 0.00 35.80 2.27
4383 4494 7.578203 AGTCCCTTATTGGAATCTCTAAAAGG 58.422 38.462 0.00 0.00 35.80 3.11
4426 4537 3.403038 GAGTACATGTGGTTGCTCTGTT 58.597 45.455 9.11 0.00 31.61 3.16
4430 4541 2.878406 ACATGTGGTTGCTCTGTTGTAC 59.122 45.455 0.00 0.00 0.00 2.90
4477 4588 5.873146 AACTCTAGTGTAGAATTAGGGGC 57.127 43.478 0.00 0.00 33.75 5.80
4516 4627 2.045143 TTGCATGCCTGGCGATCA 60.045 55.556 16.68 8.28 0.00 2.92
4561 4672 8.733458 TCATGAACTCTAAATTGAAGGATTGTG 58.267 33.333 0.00 0.00 0.00 3.33
4593 4704 1.280457 ATGACCAAGTCCACTCTCCC 58.720 55.000 0.00 0.00 0.00 4.30
4595 4706 1.280457 GACCAAGTCCACTCTCCCAT 58.720 55.000 0.00 0.00 0.00 4.00
4665 4776 0.678950 TGTCTCGTGCATCAGGAACA 59.321 50.000 0.00 0.00 0.00 3.18
4666 4777 1.069978 TGTCTCGTGCATCAGGAACAA 59.930 47.619 0.00 0.00 0.00 2.83
4667 4778 1.461127 GTCTCGTGCATCAGGAACAAC 59.539 52.381 0.00 0.00 0.00 3.32
4668 4779 1.069978 TCTCGTGCATCAGGAACAACA 59.930 47.619 0.00 0.00 0.00 3.33
4684 4795 6.891908 AGGAACAACATAGTTGGCAATATCTT 59.108 34.615 13.71 0.00 0.00 2.40
4686 4797 6.455360 ACAACATAGTTGGCAATATCTTGG 57.545 37.500 13.71 0.00 32.72 3.61
4742 4867 1.190643 CAGGGTTGGTTTGTTGGTGT 58.809 50.000 0.00 0.00 0.00 4.16
4743 4868 1.134848 CAGGGTTGGTTTGTTGGTGTG 60.135 52.381 0.00 0.00 0.00 3.82
4744 4869 1.187087 GGGTTGGTTTGTTGGTGTGA 58.813 50.000 0.00 0.00 0.00 3.58
4745 4870 1.550976 GGGTTGGTTTGTTGGTGTGAA 59.449 47.619 0.00 0.00 0.00 3.18
4746 4871 2.418060 GGGTTGGTTTGTTGGTGTGAAG 60.418 50.000 0.00 0.00 0.00 3.02
4747 4872 2.232696 GGTTGGTTTGTTGGTGTGAAGT 59.767 45.455 0.00 0.00 0.00 3.01
4748 4873 3.444388 GGTTGGTTTGTTGGTGTGAAGTA 59.556 43.478 0.00 0.00 0.00 2.24
4749 4874 4.439563 GGTTGGTTTGTTGGTGTGAAGTAG 60.440 45.833 0.00 0.00 0.00 2.57
4750 4875 4.223556 TGGTTTGTTGGTGTGAAGTAGA 57.776 40.909 0.00 0.00 0.00 2.59
4751 4876 4.787551 TGGTTTGTTGGTGTGAAGTAGAT 58.212 39.130 0.00 0.00 0.00 1.98
4752 4877 4.819630 TGGTTTGTTGGTGTGAAGTAGATC 59.180 41.667 0.00 0.00 0.00 2.75
4753 4878 4.215613 GGTTTGTTGGTGTGAAGTAGATCC 59.784 45.833 0.00 0.00 0.00 3.36
4754 4879 3.695830 TGTTGGTGTGAAGTAGATCCC 57.304 47.619 0.00 0.00 0.00 3.85
4755 4880 2.304761 TGTTGGTGTGAAGTAGATCCCC 59.695 50.000 0.00 0.00 0.00 4.81
4756 4881 2.572104 GTTGGTGTGAAGTAGATCCCCT 59.428 50.000 0.00 0.00 0.00 4.79
4757 4882 2.187958 TGGTGTGAAGTAGATCCCCTG 58.812 52.381 0.00 0.00 0.00 4.45
4868 4996 9.019764 GTTCGTTTATTCACATTTCCCAATATG 57.980 33.333 0.00 0.00 0.00 1.78
4869 4997 8.512966 TCGTTTATTCACATTTCCCAATATGA 57.487 30.769 0.00 0.00 0.00 2.15
4871 4999 8.405531 CGTTTATTCACATTTCCCAATATGAGT 58.594 33.333 0.00 0.00 27.43 3.41
4872 5000 9.520204 GTTTATTCACATTTCCCAATATGAGTG 57.480 33.333 0.00 0.00 27.43 3.51
4873 5001 6.720112 ATTCACATTTCCCAATATGAGTGG 57.280 37.500 0.00 0.00 27.43 4.00
4874 5002 5.191727 TCACATTTCCCAATATGAGTGGT 57.808 39.130 0.00 0.00 34.01 4.16
4875 5003 5.192927 TCACATTTCCCAATATGAGTGGTC 58.807 41.667 0.00 0.00 34.01 4.02
4876 5004 4.339247 CACATTTCCCAATATGAGTGGTCC 59.661 45.833 0.00 0.00 34.01 4.46
4877 5005 4.230502 ACATTTCCCAATATGAGTGGTCCT 59.769 41.667 0.00 0.00 34.01 3.85
4878 5006 3.931907 TTCCCAATATGAGTGGTCCTG 57.068 47.619 0.00 0.00 34.01 3.86
4879 5007 3.129262 TCCCAATATGAGTGGTCCTGA 57.871 47.619 0.00 0.00 34.01 3.86
4882 5010 3.434167 CCCAATATGAGTGGTCCTGAAGG 60.434 52.174 0.00 0.00 34.01 3.46
4915 5048 4.862574 TGTCTTATATGTGCTCGTTGTCAC 59.137 41.667 0.00 0.00 0.00 3.67
4948 5081 8.834004 ACCCTGTAAGATCAGTACTTATTGTA 57.166 34.615 0.00 0.00 34.07 2.41
4949 5082 8.693625 ACCCTGTAAGATCAGTACTTATTGTAC 58.306 37.037 0.00 0.00 44.00 2.90
4979 5112 9.667107 TTGTTGTTTCTTTATATACTCCCTCTG 57.333 33.333 0.00 0.00 0.00 3.35
4980 5113 8.822805 TGTTGTTTCTTTATATACTCCCTCTGT 58.177 33.333 0.00 0.00 0.00 3.41
4981 5114 9.668497 GTTGTTTCTTTATATACTCCCTCTGTT 57.332 33.333 0.00 0.00 0.00 3.16
4982 5115 9.886132 TTGTTTCTTTATATACTCCCTCTGTTC 57.114 33.333 0.00 0.00 0.00 3.18
4983 5116 9.042450 TGTTTCTTTATATACTCCCTCTGTTCA 57.958 33.333 0.00 0.00 0.00 3.18
4984 5117 9.315525 GTTTCTTTATATACTCCCTCTGTTCAC 57.684 37.037 0.00 0.00 0.00 3.18
4985 5118 8.840200 TTCTTTATATACTCCCTCTGTTCACT 57.160 34.615 0.00 0.00 0.00 3.41
4986 5119 8.840200 TCTTTATATACTCCCTCTGTTCACTT 57.160 34.615 0.00 0.00 0.00 3.16
4987 5120 9.268282 TCTTTATATACTCCCTCTGTTCACTTT 57.732 33.333 0.00 0.00 0.00 2.66
4988 5121 9.892130 CTTTATATACTCCCTCTGTTCACTTTT 57.108 33.333 0.00 0.00 0.00 2.27
4994 5127 7.554959 ACTCCCTCTGTTCACTTTTATAAGA 57.445 36.000 0.00 0.00 35.30 2.10
4995 5128 7.387643 ACTCCCTCTGTTCACTTTTATAAGAC 58.612 38.462 0.00 0.00 35.30 3.01
4996 5129 6.708285 TCCCTCTGTTCACTTTTATAAGACC 58.292 40.000 0.00 0.00 35.30 3.85
4997 5130 6.500751 TCCCTCTGTTCACTTTTATAAGACCT 59.499 38.462 0.00 0.00 35.30 3.85
4998 5131 7.017254 TCCCTCTGTTCACTTTTATAAGACCTT 59.983 37.037 0.00 0.00 35.30 3.50
4999 5132 7.334671 CCCTCTGTTCACTTTTATAAGACCTTC 59.665 40.741 0.00 0.00 35.30 3.46
5000 5133 7.878127 CCTCTGTTCACTTTTATAAGACCTTCA 59.122 37.037 0.00 0.00 35.30 3.02
5001 5134 9.273016 CTCTGTTCACTTTTATAAGACCTTCAA 57.727 33.333 0.00 0.00 35.30 2.69
5002 5135 9.273016 TCTGTTCACTTTTATAAGACCTTCAAG 57.727 33.333 0.00 0.00 35.30 3.02
5003 5136 9.273016 CTGTTCACTTTTATAAGACCTTCAAGA 57.727 33.333 0.00 0.00 35.30 3.02
5004 5137 9.793259 TGTTCACTTTTATAAGACCTTCAAGAT 57.207 29.630 0.00 0.00 35.30 2.40
5017 5150 8.503458 AGACCTTCAAGATATTTCAGACAATG 57.497 34.615 0.00 0.00 0.00 2.82
5018 5151 8.105829 AGACCTTCAAGATATTTCAGACAATGT 58.894 33.333 0.00 0.00 0.00 2.71
5019 5152 9.383519 GACCTTCAAGATATTTCAGACAATGTA 57.616 33.333 0.00 0.00 0.00 2.29
5020 5153 9.167311 ACCTTCAAGATATTTCAGACAATGTAC 57.833 33.333 0.00 0.00 0.00 2.90
5021 5154 9.166173 CCTTCAAGATATTTCAGACAATGTACA 57.834 33.333 0.00 0.00 0.00 2.90
5028 5161 8.970691 ATATTTCAGACAATGTACAAAACAGC 57.029 30.769 0.00 0.00 42.70 4.40
5029 5162 4.829064 TCAGACAATGTACAAAACAGCC 57.171 40.909 0.00 0.00 42.70 4.85
5030 5163 3.568007 TCAGACAATGTACAAAACAGCCC 59.432 43.478 0.00 0.00 42.70 5.19
5031 5164 3.317711 CAGACAATGTACAAAACAGCCCA 59.682 43.478 0.00 0.00 42.70 5.36
5032 5165 4.022068 CAGACAATGTACAAAACAGCCCAT 60.022 41.667 0.00 0.00 42.70 4.00
5033 5166 4.588528 AGACAATGTACAAAACAGCCCATT 59.411 37.500 0.00 0.00 42.70 3.16
5034 5167 5.070313 AGACAATGTACAAAACAGCCCATTT 59.930 36.000 0.00 0.00 42.70 2.32
5035 5168 5.679601 ACAATGTACAAAACAGCCCATTTT 58.320 33.333 0.00 0.00 42.70 1.82
5037 5170 5.543507 ATGTACAAAACAGCCCATTTTGA 57.456 34.783 19.09 3.50 45.75 2.69
5038 5171 4.942852 TGTACAAAACAGCCCATTTTGAG 58.057 39.130 19.09 1.00 45.75 3.02
5039 5172 2.837498 ACAAAACAGCCCATTTTGAGC 58.163 42.857 19.09 0.00 45.75 4.26
5040 5173 2.435437 ACAAAACAGCCCATTTTGAGCT 59.565 40.909 19.09 0.00 45.75 4.09
5045 5178 1.542492 AGCCCATTTTGAGCTGTCTG 58.458 50.000 0.00 0.00 34.99 3.51
5046 5179 1.074405 AGCCCATTTTGAGCTGTCTGA 59.926 47.619 0.00 0.00 34.99 3.27
5047 5180 1.888512 GCCCATTTTGAGCTGTCTGAA 59.111 47.619 0.00 0.00 0.00 3.02
5048 5181 2.297033 GCCCATTTTGAGCTGTCTGAAA 59.703 45.455 0.00 0.00 0.00 2.69
5049 5182 3.056322 GCCCATTTTGAGCTGTCTGAAAT 60.056 43.478 0.00 0.00 0.00 2.17
5050 5183 4.491676 CCCATTTTGAGCTGTCTGAAATG 58.508 43.478 0.00 0.57 37.04 2.32
5051 5184 4.219070 CCCATTTTGAGCTGTCTGAAATGA 59.781 41.667 13.84 0.00 38.18 2.57
5052 5185 5.159209 CCATTTTGAGCTGTCTGAAATGAC 58.841 41.667 13.84 0.00 38.18 3.06
5053 5186 5.048224 CCATTTTGAGCTGTCTGAAATGACT 60.048 40.000 13.84 0.00 38.18 3.41
5054 5187 6.444633 CATTTTGAGCTGTCTGAAATGACTT 58.555 36.000 0.00 0.00 38.18 3.01
5055 5188 7.308770 CCATTTTGAGCTGTCTGAAATGACTTA 60.309 37.037 13.84 0.00 38.18 2.24
5056 5189 6.545504 TTTGAGCTGTCTGAAATGACTTAC 57.454 37.500 0.00 0.00 37.79 2.34
5057 5190 5.213891 TGAGCTGTCTGAAATGACTTACA 57.786 39.130 0.00 0.00 37.79 2.41
5058 5191 5.610398 TGAGCTGTCTGAAATGACTTACAA 58.390 37.500 0.00 0.00 37.79 2.41
5059 5192 6.054941 TGAGCTGTCTGAAATGACTTACAAA 58.945 36.000 0.00 0.00 37.79 2.83
5060 5193 6.542005 TGAGCTGTCTGAAATGACTTACAAAA 59.458 34.615 0.00 0.00 37.79 2.44
5061 5194 6.963796 AGCTGTCTGAAATGACTTACAAAAG 58.036 36.000 0.00 0.00 37.79 2.27
5063 5196 6.634436 GCTGTCTGAAATGACTTACAAAAGTG 59.366 38.462 0.00 0.00 46.09 3.16
5064 5197 7.467267 GCTGTCTGAAATGACTTACAAAAGTGA 60.467 37.037 0.00 0.00 46.09 3.41
5065 5198 8.275015 TGTCTGAAATGACTTACAAAAGTGAA 57.725 30.769 0.00 0.00 46.09 3.18
5066 5199 8.181573 TGTCTGAAATGACTTACAAAAGTGAAC 58.818 33.333 0.00 0.00 46.09 3.18
5067 5200 7.373441 GTCTGAAATGACTTACAAAAGTGAACG 59.627 37.037 0.00 0.00 46.09 3.95
5068 5201 6.491394 TGAAATGACTTACAAAAGTGAACGG 58.509 36.000 0.00 0.00 46.09 4.44
5069 5202 6.316640 TGAAATGACTTACAAAAGTGAACGGA 59.683 34.615 0.00 0.00 46.09 4.69
5070 5203 5.924475 ATGACTTACAAAAGTGAACGGAG 57.076 39.130 0.00 0.00 46.09 4.63
5071 5204 4.124238 TGACTTACAAAAGTGAACGGAGG 58.876 43.478 0.00 0.00 46.09 4.30
5072 5205 3.473625 ACTTACAAAAGTGAACGGAGGG 58.526 45.455 0.00 0.00 44.40 4.30
5073 5206 3.135167 ACTTACAAAAGTGAACGGAGGGA 59.865 43.478 0.00 0.00 44.40 4.20
5074 5207 2.256117 ACAAAAGTGAACGGAGGGAG 57.744 50.000 0.00 0.00 0.00 4.30
5123 5258 1.200716 CATGTCTGAATGCCCACACAC 59.799 52.381 0.00 0.00 0.00 3.82
5127 5262 0.673333 CTGAATGCCCACACACGCTA 60.673 55.000 0.00 0.00 0.00 4.26
5136 5271 2.548067 CCCACACACGCTAGAAAACTCT 60.548 50.000 0.00 0.00 0.00 3.24
5138 5273 3.059597 CCACACACGCTAGAAAACTCTTG 60.060 47.826 0.00 0.00 0.00 3.02
5188 5323 8.611757 GCAGAAATGAAACTGTTGGTTATTTTT 58.388 29.630 0.00 0.00 37.12 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.272490 CTTGAACTCTGGTAGGCACGA 59.728 52.381 0.00 0.00 0.00 4.35
1 2 1.000955 ACTTGAACTCTGGTAGGCACG 59.999 52.381 0.00 0.00 0.00 5.34
2 3 2.300437 AGACTTGAACTCTGGTAGGCAC 59.700 50.000 0.00 0.00 0.00 5.01
3 4 2.563179 GAGACTTGAACTCTGGTAGGCA 59.437 50.000 0.00 0.00 0.00 4.75
4 5 2.563179 TGAGACTTGAACTCTGGTAGGC 59.437 50.000 0.00 0.00 35.66 3.93
5 6 4.082463 GTCTGAGACTTGAACTCTGGTAGG 60.082 50.000 5.12 0.00 35.23 3.18
6 7 4.764823 AGTCTGAGACTTGAACTCTGGTAG 59.235 45.833 9.77 0.00 40.28 3.18
7 8 4.730966 AGTCTGAGACTTGAACTCTGGTA 58.269 43.478 9.77 0.00 40.28 3.25
8 9 3.571590 AGTCTGAGACTTGAACTCTGGT 58.428 45.455 9.77 0.00 40.28 4.00
20 21 1.342819 AGGCAGTGTCAAGTCTGAGAC 59.657 52.381 3.98 3.98 44.34 3.36
21 22 1.709578 AGGCAGTGTCAAGTCTGAGA 58.290 50.000 0.00 0.00 34.02 3.27
22 23 2.540265 AAGGCAGTGTCAAGTCTGAG 57.460 50.000 0.00 0.00 34.02 3.35
23 24 3.281727 AAAAGGCAGTGTCAAGTCTGA 57.718 42.857 0.00 0.00 34.02 3.27
24 25 4.024556 CACTAAAAGGCAGTGTCAAGTCTG 60.025 45.833 0.00 0.00 38.86 3.51
25 26 4.130118 CACTAAAAGGCAGTGTCAAGTCT 58.870 43.478 0.00 0.00 38.86 3.24
26 27 3.251004 CCACTAAAAGGCAGTGTCAAGTC 59.749 47.826 0.00 0.00 41.52 3.01
27 28 3.214328 CCACTAAAAGGCAGTGTCAAGT 58.786 45.455 0.00 0.00 41.52 3.16
28 29 2.554032 CCCACTAAAAGGCAGTGTCAAG 59.446 50.000 0.00 0.00 41.52 3.02
29 30 2.173782 TCCCACTAAAAGGCAGTGTCAA 59.826 45.455 0.00 0.00 41.52 3.18
30 31 1.771854 TCCCACTAAAAGGCAGTGTCA 59.228 47.619 0.00 0.00 41.52 3.58
31 32 2.427506 CTCCCACTAAAAGGCAGTGTC 58.572 52.381 2.54 0.00 41.52 3.67
32 33 1.073923 CCTCCCACTAAAAGGCAGTGT 59.926 52.381 2.54 0.00 41.52 3.55
33 34 1.351017 TCCTCCCACTAAAAGGCAGTG 59.649 52.381 0.00 0.00 42.52 3.66
34 35 1.630878 CTCCTCCCACTAAAAGGCAGT 59.369 52.381 0.00 0.00 0.00 4.40
35 36 1.909302 TCTCCTCCCACTAAAAGGCAG 59.091 52.381 0.00 0.00 0.00 4.85
36 37 1.628846 GTCTCCTCCCACTAAAAGGCA 59.371 52.381 0.00 0.00 0.00 4.75
37 38 1.405661 CGTCTCCTCCCACTAAAAGGC 60.406 57.143 0.00 0.00 0.00 4.35
38 39 1.900486 ACGTCTCCTCCCACTAAAAGG 59.100 52.381 0.00 0.00 0.00 3.11
39 40 3.586892 GAACGTCTCCTCCCACTAAAAG 58.413 50.000 0.00 0.00 0.00 2.27
40 41 2.301009 GGAACGTCTCCTCCCACTAAAA 59.699 50.000 8.87 0.00 41.61 1.52
83 84 4.720530 AAACGTTTACAATCGGACTGTC 57.279 40.909 12.83 0.00 0.00 3.51
84 85 4.812626 AGAAAACGTTTACAATCGGACTGT 59.187 37.500 15.03 0.00 0.00 3.55
86 87 5.996669 AAGAAAACGTTTACAATCGGACT 57.003 34.783 15.03 0.00 0.00 3.85
169 170 6.211184 TGATGTCTGCTTTTCCCATAAACATT 59.789 34.615 0.00 0.00 0.00 2.71
245 247 9.061610 GTATACATTGGAAACATTTATATGCGC 57.938 33.333 0.00 0.00 42.32 6.09
279 281 9.480053 GTCTACCTTTTACATACACTTTGTACA 57.520 33.333 0.00 0.00 35.42 2.90
430 433 8.994429 TGTTTTCATACACAGTTTTGAACATT 57.006 26.923 0.00 0.00 0.00 2.71
431 434 8.465999 TCTGTTTTCATACACAGTTTTGAACAT 58.534 29.630 0.00 0.00 41.16 2.71
441 444 8.830580 TCTTTCTTTCTCTGTTTTCATACACAG 58.169 33.333 0.00 0.00 41.65 3.66
511 514 7.274904 TCACTGGTATATTTCGTTTCTTTCTCG 59.725 37.037 0.00 0.00 0.00 4.04
530 533 6.754193 TGTTCTTTCTTTGTTTTTCACTGGT 58.246 32.000 0.00 0.00 0.00 4.00
604 609 3.432326 GCTGTTGATTCGGTTCCCTCTAT 60.432 47.826 0.00 0.00 0.00 1.98
611 616 0.095417 GCTCGCTGTTGATTCGGTTC 59.905 55.000 0.00 0.00 0.00 3.62
619 624 2.357881 CTGCTGGCTCGCTGTTGA 60.358 61.111 1.45 0.00 0.00 3.18
690 696 1.135575 CGCCTGAAAGATTTCCTGTGC 60.136 52.381 3.00 0.60 36.36 4.57
750 756 1.756375 GCCAGCTGAGTATGTTCGCG 61.756 60.000 17.39 0.00 0.00 5.87
755 761 0.914644 ATGGTGCCAGCTGAGTATGT 59.085 50.000 17.39 0.00 0.00 2.29
838 864 4.201851 GCCGTGATCCAATATCATGTATGC 60.202 45.833 6.49 0.64 34.20 3.14
842 868 2.553028 GGGCCGTGATCCAATATCATGT 60.553 50.000 0.00 0.00 34.20 3.21
928 981 2.029964 ACGTGGCGGTCGATTGTT 59.970 55.556 0.00 0.00 0.00 2.83
987 1040 1.134610 AGTGTTTCGGTTTGGTCTCGT 60.135 47.619 0.00 0.00 0.00 4.18
1017 1070 1.082690 CGAGCAAGAGAAAGAAGGGC 58.917 55.000 0.00 0.00 0.00 5.19
1083 1136 4.554363 CTCGTAGGCTCACGCGGG 62.554 72.222 12.47 6.51 41.67 6.13
1198 1254 3.117175 CTGCGCAATGGTAGCTGCC 62.117 63.158 14.87 14.87 35.01 4.85
1572 1646 5.830799 ATGATAATGCTGGAGTATCACCA 57.169 39.130 19.02 0.97 42.79 4.17
1576 1650 6.638610 AGTGCTATGATAATGCTGGAGTATC 58.361 40.000 9.30 9.30 33.09 2.24
1710 1786 4.394920 ACTCGAGTTTTTCAAGTCTGCAAA 59.605 37.500 13.58 0.00 30.88 3.68
1802 1879 6.435292 TTTGTTTCCTCTAGTAAAGGAGCT 57.565 37.500 0.00 0.00 43.65 4.09
1824 1901 8.270744 AGCCAGATTTGAAGAGTACATCTATTT 58.729 33.333 0.00 0.00 37.23 1.40
1853 1930 3.753272 GCTCTGACCAAAATTGAGCTACA 59.247 43.478 0.00 0.00 44.52 2.74
1933 2010 3.159213 ACACACCATTGATCCACACAT 57.841 42.857 0.00 0.00 0.00 3.21
1957 2034 1.060729 TAAGGCAGGCAACACCAGTA 58.939 50.000 0.00 0.00 43.14 2.74
2010 2088 9.463902 AGAGAAGTTAGAGTAGCTACATACAAA 57.536 33.333 25.28 9.37 0.00 2.83
2065 2143 8.288689 AGTCGTAAAAAGGGCATAATTACAAT 57.711 30.769 7.47 0.00 0.00 2.71
2363 2443 6.472887 AGCACAAGAACAAGGCTAAAGTATA 58.527 36.000 0.00 0.00 32.09 1.47
2455 2535 2.647299 ACTCATTCCACCACCAACCATA 59.353 45.455 0.00 0.00 0.00 2.74
2620 2700 2.775032 TACGTGAAACCTCCCTGCGC 62.775 60.000 0.00 0.00 0.00 6.09
2623 2703 1.831736 AGGATACGTGAAACCTCCCTG 59.168 52.381 0.00 0.00 46.39 4.45
2697 2777 4.929211 TGGTGTGACATCAAAGAATACTCG 59.071 41.667 0.00 0.00 0.00 4.18
2830 2910 4.142315 GGTGCATCATATTGAACAAGCAGT 60.142 41.667 0.00 0.00 29.48 4.40
2855 2935 9.521503 CGAGATGATACACTTCTAAATTCTCAA 57.478 33.333 0.00 0.00 33.96 3.02
2856 2936 7.649705 GCGAGATGATACACTTCTAAATTCTCA 59.350 37.037 0.00 0.00 33.96 3.27
2905 2986 7.575909 CGGAATATATCTGTAGTGGAGAAGGTG 60.576 44.444 0.00 0.00 0.00 4.00
3144 3225 0.879765 CTTGCAGGGCTTCAAGTGAG 59.120 55.000 0.00 0.00 36.01 3.51
3145 3226 0.538057 CCTTGCAGGGCTTCAAGTGA 60.538 55.000 0.13 0.00 38.33 3.41
3177 3258 6.785191 ACTACATAATCCAAATCTGCAAACG 58.215 36.000 0.00 0.00 0.00 3.60
3289 3370 5.717078 TCAAAGCAAGCATGAGAAGAAAT 57.283 34.783 0.00 0.00 0.00 2.17
3300 3381 4.057432 GCTTACCAATTTCAAAGCAAGCA 58.943 39.130 9.45 0.00 43.00 3.91
3362 3443 4.494091 AAGCACAATCTACCTATGCAGT 57.506 40.909 0.00 0.00 38.79 4.40
3364 3445 5.368145 CCTAAAGCACAATCTACCTATGCA 58.632 41.667 0.00 0.00 38.79 3.96
3456 3537 9.678260 AATCATGGTCTGAATAAATATCCTAGC 57.322 33.333 0.00 0.00 37.44 3.42
3540 3621 9.661563 AACGTATAGATGGTCAAATGACTAAAA 57.338 29.630 12.87 0.00 44.20 1.52
3542 3623 7.223971 GCAACGTATAGATGGTCAAATGACTAA 59.776 37.037 12.87 3.23 44.20 2.24
3543 3624 6.700081 GCAACGTATAGATGGTCAAATGACTA 59.300 38.462 12.87 7.74 44.20 2.59
3653 3750 4.824479 TTCAGGTGTGAGCATTAGATCA 57.176 40.909 0.00 0.00 37.94 2.92
3686 3786 1.666054 ACCTCAAACGTTAACGCCAA 58.334 45.000 27.07 9.94 44.43 4.52
3896 3996 3.065786 AGGTTCGATCGCTCGTATAAACA 59.934 43.478 11.09 0.00 45.25 2.83
3982 4082 1.329292 CGTCCTTTTCACGCTTTCACA 59.671 47.619 0.00 0.00 0.00 3.58
4042 4142 1.669115 GCAGACACACATGCGACCT 60.669 57.895 0.00 0.00 31.87 3.85
4105 4205 7.282585 TGATAAAAGACTGATATTGTCTGGGG 58.717 38.462 11.44 0.00 43.16 4.96
4253 4353 6.522946 ACTTATATTTAGAAACGGAGGGAGC 58.477 40.000 0.00 0.00 0.00 4.70
4382 4493 5.541484 TCCCTCCGTTCCTAAATATAAGTCC 59.459 44.000 0.00 0.00 0.00 3.85
4383 4494 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
4426 4537 1.361197 TGGGGAGAGGTGATCAGTACA 59.639 52.381 0.00 0.00 0.00 2.90
4430 4541 0.326048 AGGTGGGGAGAGGTGATCAG 60.326 60.000 0.00 0.00 0.00 2.90
4477 4588 8.370940 TGCAACTCTGAATTATAATAGGAGAGG 58.629 37.037 21.21 15.32 31.61 3.69
4516 4627 7.523293 TCATGACCACTTTGACATTTAACAT 57.477 32.000 0.00 0.00 0.00 2.71
4561 4672 6.127647 TGGACTTGGTCATTCAAATATGCTTC 60.128 38.462 0.14 0.00 33.68 3.86
4593 4704 5.893687 TGGCAACTTCTATGCAAATACATG 58.106 37.500 0.00 0.00 45.60 3.21
4595 4706 5.418524 ACATGGCAACTTCTATGCAAATACA 59.581 36.000 0.00 0.00 45.60 2.29
4652 4763 4.379813 CCAACTATGTTGTTCCTGATGCAC 60.380 45.833 9.20 0.00 0.00 4.57
4665 4776 7.068226 GGTTACCAAGATATTGCCAACTATGTT 59.932 37.037 12.08 0.00 0.00 2.71
4666 4777 6.546034 GGTTACCAAGATATTGCCAACTATGT 59.454 38.462 12.08 0.00 0.00 2.29
4667 4778 6.772716 AGGTTACCAAGATATTGCCAACTATG 59.227 38.462 3.51 0.00 0.00 2.23
4668 4779 6.911308 AGGTTACCAAGATATTGCCAACTAT 58.089 36.000 3.51 3.12 0.00 2.12
4684 4795 7.667635 TCAATCAAACACATATGAAGGTTACCA 59.332 33.333 10.38 0.10 0.00 3.25
4686 4797 9.722056 GATCAATCAAACACATATGAAGGTTAC 57.278 33.333 10.38 0.00 0.00 2.50
4742 4867 3.757947 TGAGACAGGGGATCTACTTCA 57.242 47.619 0.00 0.00 0.00 3.02
4743 4868 3.323403 CCATGAGACAGGGGATCTACTTC 59.677 52.174 0.00 0.00 30.99 3.01
4744 4869 3.051803 TCCATGAGACAGGGGATCTACTT 60.052 47.826 0.00 0.00 35.84 2.24
4745 4870 2.520120 TCCATGAGACAGGGGATCTACT 59.480 50.000 0.00 0.00 35.84 2.57
4746 4871 2.964209 TCCATGAGACAGGGGATCTAC 58.036 52.381 0.00 0.00 35.84 2.59
4747 4872 3.051803 ACTTCCATGAGACAGGGGATCTA 60.052 47.826 0.00 0.00 35.84 1.98
4748 4873 2.293452 ACTTCCATGAGACAGGGGATCT 60.293 50.000 0.00 0.00 35.84 2.75
4749 4874 2.122768 ACTTCCATGAGACAGGGGATC 58.877 52.381 0.00 0.00 35.84 3.36
4750 4875 2.277008 ACTTCCATGAGACAGGGGAT 57.723 50.000 0.00 0.00 35.84 3.85
4751 4876 2.044492 ACTACTTCCATGAGACAGGGGA 59.956 50.000 0.00 0.00 35.84 4.81
4752 4877 2.472029 ACTACTTCCATGAGACAGGGG 58.528 52.381 0.00 0.00 35.84 4.79
4753 4878 3.772025 AGAACTACTTCCATGAGACAGGG 59.228 47.826 0.00 0.00 36.56 4.45
4754 4879 5.654650 AGTAGAACTACTTCCATGAGACAGG 59.345 44.000 8.47 0.00 43.35 4.00
4755 4880 6.375736 TCAGTAGAACTACTTCCATGAGACAG 59.624 42.308 11.21 0.00 43.35 3.51
4756 4881 6.246163 TCAGTAGAACTACTTCCATGAGACA 58.754 40.000 11.21 0.00 43.35 3.41
4757 4882 6.761099 TCAGTAGAACTACTTCCATGAGAC 57.239 41.667 11.21 0.00 43.35 3.36
4837 4965 9.397280 TGGGAAATGTGAATAAACGAACATATA 57.603 29.630 0.00 0.00 33.04 0.86
4840 4968 6.582677 TGGGAAATGTGAATAAACGAACAT 57.417 33.333 0.00 0.00 34.79 2.71
4842 4970 9.019764 CATATTGGGAAATGTGAATAAACGAAC 57.980 33.333 0.00 0.00 0.00 3.95
4843 4971 8.961634 TCATATTGGGAAATGTGAATAAACGAA 58.038 29.630 0.00 0.00 29.23 3.85
4845 4973 8.405531 ACTCATATTGGGAAATGTGAATAAACG 58.594 33.333 0.61 0.00 31.43 3.60
4873 5001 0.405973 AAAAGGGAGGCCTTCAGGAC 59.594 55.000 14.70 0.00 46.16 3.85
4874 5002 0.405585 CAAAAGGGAGGCCTTCAGGA 59.594 55.000 14.70 0.00 37.39 3.86
4875 5003 0.113190 ACAAAAGGGAGGCCTTCAGG 59.887 55.000 14.70 0.00 38.53 3.86
4876 5004 1.074566 AGACAAAAGGGAGGCCTTCAG 59.925 52.381 14.70 0.00 0.00 3.02
4877 5005 1.149101 AGACAAAAGGGAGGCCTTCA 58.851 50.000 14.70 0.00 0.00 3.02
4878 5006 2.294449 AAGACAAAAGGGAGGCCTTC 57.706 50.000 6.77 3.67 0.00 3.46
4879 5007 5.044105 ACATATAAGACAAAAGGGAGGCCTT 60.044 40.000 6.77 0.00 0.00 4.35
4882 5010 4.036852 GCACATATAAGACAAAAGGGAGGC 59.963 45.833 0.00 0.00 0.00 4.70
4915 5048 9.303116 AGTACTGATCTTACAGGGTATAATCAG 57.697 37.037 17.80 17.80 42.61 2.90
4953 5086 9.667107 CAGAGGGAGTATATAAAGAAACAACAA 57.333 33.333 0.00 0.00 0.00 2.83
4957 5090 9.042450 TGAACAGAGGGAGTATATAAAGAAACA 57.958 33.333 0.00 0.00 0.00 2.83
4958 5091 9.315525 GTGAACAGAGGGAGTATATAAAGAAAC 57.684 37.037 0.00 0.00 0.00 2.78
4959 5092 9.268282 AGTGAACAGAGGGAGTATATAAAGAAA 57.732 33.333 0.00 0.00 0.00 2.52
4960 5093 8.840200 AGTGAACAGAGGGAGTATATAAAGAA 57.160 34.615 0.00 0.00 0.00 2.52
4961 5094 8.840200 AAGTGAACAGAGGGAGTATATAAAGA 57.160 34.615 0.00 0.00 0.00 2.52
4962 5095 9.892130 AAAAGTGAACAGAGGGAGTATATAAAG 57.108 33.333 0.00 0.00 0.00 1.85
4968 5101 9.268282 TCTTATAAAAGTGAACAGAGGGAGTAT 57.732 33.333 0.00 0.00 34.13 2.12
4969 5102 8.529476 GTCTTATAAAAGTGAACAGAGGGAGTA 58.471 37.037 0.00 0.00 34.13 2.59
4970 5103 7.387643 GTCTTATAAAAGTGAACAGAGGGAGT 58.612 38.462 0.00 0.00 34.13 3.85
4971 5104 6.819146 GGTCTTATAAAAGTGAACAGAGGGAG 59.181 42.308 0.00 0.00 34.13 4.30
4972 5105 6.500751 AGGTCTTATAAAAGTGAACAGAGGGA 59.499 38.462 0.00 0.00 34.13 4.20
4973 5106 6.712276 AGGTCTTATAAAAGTGAACAGAGGG 58.288 40.000 0.00 0.00 34.13 4.30
4974 5107 7.878127 TGAAGGTCTTATAAAAGTGAACAGAGG 59.122 37.037 0.00 0.00 34.13 3.69
4975 5108 8.833231 TGAAGGTCTTATAAAAGTGAACAGAG 57.167 34.615 0.00 0.00 34.13 3.35
4976 5109 9.273016 CTTGAAGGTCTTATAAAAGTGAACAGA 57.727 33.333 0.00 0.00 34.13 3.41
4977 5110 9.273016 TCTTGAAGGTCTTATAAAAGTGAACAG 57.727 33.333 0.00 0.00 34.13 3.16
4978 5111 9.793259 ATCTTGAAGGTCTTATAAAAGTGAACA 57.207 29.630 0.00 0.00 34.13 3.18
4991 5124 8.954350 CATTGTCTGAAATATCTTGAAGGTCTT 58.046 33.333 0.00 0.00 0.00 3.01
4992 5125 8.105829 ACATTGTCTGAAATATCTTGAAGGTCT 58.894 33.333 0.00 0.00 0.00 3.85
4993 5126 8.273780 ACATTGTCTGAAATATCTTGAAGGTC 57.726 34.615 0.00 0.00 0.00 3.85
4994 5127 9.167311 GTACATTGTCTGAAATATCTTGAAGGT 57.833 33.333 0.00 0.00 0.00 3.50
4995 5128 9.166173 TGTACATTGTCTGAAATATCTTGAAGG 57.834 33.333 0.00 0.00 0.00 3.46
5002 5135 9.065871 GCTGTTTTGTACATTGTCTGAAATATC 57.934 33.333 0.00 0.00 35.85 1.63
5003 5136 8.028938 GGCTGTTTTGTACATTGTCTGAAATAT 58.971 33.333 0.00 0.00 35.85 1.28
5004 5137 7.367285 GGCTGTTTTGTACATTGTCTGAAATA 58.633 34.615 0.00 0.00 35.85 1.40
5005 5138 6.215845 GGCTGTTTTGTACATTGTCTGAAAT 58.784 36.000 0.00 0.00 35.85 2.17
5006 5139 5.451242 GGGCTGTTTTGTACATTGTCTGAAA 60.451 40.000 0.00 0.00 35.85 2.69
5007 5140 4.037446 GGGCTGTTTTGTACATTGTCTGAA 59.963 41.667 0.00 0.00 35.85 3.02
5008 5141 3.568007 GGGCTGTTTTGTACATTGTCTGA 59.432 43.478 0.00 0.00 35.85 3.27
5009 5142 3.317711 TGGGCTGTTTTGTACATTGTCTG 59.682 43.478 0.00 0.00 35.85 3.51
5010 5143 3.561143 TGGGCTGTTTTGTACATTGTCT 58.439 40.909 0.00 0.00 35.85 3.41
5011 5144 4.519540 ATGGGCTGTTTTGTACATTGTC 57.480 40.909 0.00 0.00 35.85 3.18
5012 5145 4.953940 AATGGGCTGTTTTGTACATTGT 57.046 36.364 0.00 0.00 35.85 2.71
5013 5146 5.757320 TCAAAATGGGCTGTTTTGTACATTG 59.243 36.000 19.52 0.00 43.52 2.82
5014 5147 5.923204 TCAAAATGGGCTGTTTTGTACATT 58.077 33.333 19.52 0.00 43.52 2.71
5015 5148 5.540911 CTCAAAATGGGCTGTTTTGTACAT 58.459 37.500 19.52 0.00 43.52 2.29
5016 5149 4.739137 GCTCAAAATGGGCTGTTTTGTACA 60.739 41.667 19.52 0.00 41.63 2.90
5017 5150 3.740832 GCTCAAAATGGGCTGTTTTGTAC 59.259 43.478 19.52 12.95 41.63 2.90
5018 5151 3.988819 GCTCAAAATGGGCTGTTTTGTA 58.011 40.909 19.52 10.81 41.63 2.41
5019 5152 2.837498 GCTCAAAATGGGCTGTTTTGT 58.163 42.857 19.52 0.00 41.63 2.83
5027 5160 1.538047 TCAGACAGCTCAAAATGGGC 58.462 50.000 0.00 0.00 46.33 5.36
5028 5161 4.219070 TCATTTCAGACAGCTCAAAATGGG 59.781 41.667 12.29 0.00 36.21 4.00
5029 5162 5.048224 AGTCATTTCAGACAGCTCAAAATGG 60.048 40.000 12.29 0.00 40.98 3.16
5030 5163 6.010294 AGTCATTTCAGACAGCTCAAAATG 57.990 37.500 0.00 0.00 40.98 2.32
5031 5164 6.645790 AAGTCATTTCAGACAGCTCAAAAT 57.354 33.333 0.00 0.00 40.98 1.82
5032 5165 6.542005 TGTAAGTCATTTCAGACAGCTCAAAA 59.458 34.615 0.00 0.00 40.98 2.44
5033 5166 6.054941 TGTAAGTCATTTCAGACAGCTCAAA 58.945 36.000 0.00 0.00 40.98 2.69
5034 5167 5.610398 TGTAAGTCATTTCAGACAGCTCAA 58.390 37.500 0.00 0.00 40.98 3.02
5035 5168 5.213891 TGTAAGTCATTTCAGACAGCTCA 57.786 39.130 0.00 0.00 40.98 4.26
5036 5169 6.545504 TTTGTAAGTCATTTCAGACAGCTC 57.454 37.500 0.00 0.00 40.98 4.09
5037 5170 6.543831 ACTTTTGTAAGTCATTTCAGACAGCT 59.456 34.615 0.00 0.00 40.60 4.24
5038 5171 6.634436 CACTTTTGTAAGTCATTTCAGACAGC 59.366 38.462 0.00 0.00 42.67 4.40
5039 5172 7.919690 TCACTTTTGTAAGTCATTTCAGACAG 58.080 34.615 0.00 0.00 42.67 3.51
5040 5173 7.857734 TCACTTTTGTAAGTCATTTCAGACA 57.142 32.000 0.00 0.00 42.67 3.41
5041 5174 7.373441 CGTTCACTTTTGTAAGTCATTTCAGAC 59.627 37.037 0.00 0.00 42.67 3.51
5042 5175 7.406553 CGTTCACTTTTGTAAGTCATTTCAGA 58.593 34.615 0.00 0.00 42.67 3.27
5043 5176 6.632834 CCGTTCACTTTTGTAAGTCATTTCAG 59.367 38.462 0.00 0.00 42.67 3.02
5044 5177 6.316640 TCCGTTCACTTTTGTAAGTCATTTCA 59.683 34.615 0.00 0.00 42.67 2.69
5045 5178 6.721321 TCCGTTCACTTTTGTAAGTCATTTC 58.279 36.000 0.00 0.00 42.67 2.17
5046 5179 6.238648 CCTCCGTTCACTTTTGTAAGTCATTT 60.239 38.462 0.00 0.00 42.67 2.32
5047 5180 5.238650 CCTCCGTTCACTTTTGTAAGTCATT 59.761 40.000 0.00 0.00 42.67 2.57
5048 5181 4.755123 CCTCCGTTCACTTTTGTAAGTCAT 59.245 41.667 0.00 0.00 42.67 3.06
5049 5182 4.124238 CCTCCGTTCACTTTTGTAAGTCA 58.876 43.478 0.00 0.00 42.67 3.41
5050 5183 3.497262 CCCTCCGTTCACTTTTGTAAGTC 59.503 47.826 0.00 0.00 42.67 3.01
5051 5184 3.135167 TCCCTCCGTTCACTTTTGTAAGT 59.865 43.478 0.00 0.00 45.40 2.24
5052 5185 3.735591 TCCCTCCGTTCACTTTTGTAAG 58.264 45.455 0.00 0.00 37.40 2.34
5053 5186 3.135167 ACTCCCTCCGTTCACTTTTGTAA 59.865 43.478 0.00 0.00 0.00 2.41
5054 5187 2.701951 ACTCCCTCCGTTCACTTTTGTA 59.298 45.455 0.00 0.00 0.00 2.41
5055 5188 1.489230 ACTCCCTCCGTTCACTTTTGT 59.511 47.619 0.00 0.00 0.00 2.83
5056 5189 2.256117 ACTCCCTCCGTTCACTTTTG 57.744 50.000 0.00 0.00 0.00 2.44
5057 5190 5.952347 ATATACTCCCTCCGTTCACTTTT 57.048 39.130 0.00 0.00 0.00 2.27
5058 5191 5.952347 AATATACTCCCTCCGTTCACTTT 57.048 39.130 0.00 0.00 0.00 2.66
5059 5192 5.424252 TCAAATATACTCCCTCCGTTCACTT 59.576 40.000 0.00 0.00 0.00 3.16
5060 5193 4.960469 TCAAATATACTCCCTCCGTTCACT 59.040 41.667 0.00 0.00 0.00 3.41
5061 5194 5.048507 GTCAAATATACTCCCTCCGTTCAC 58.951 45.833 0.00 0.00 0.00 3.18
5062 5195 4.100498 GGTCAAATATACTCCCTCCGTTCA 59.900 45.833 0.00 0.00 0.00 3.18
5063 5196 4.100498 TGGTCAAATATACTCCCTCCGTTC 59.900 45.833 0.00 0.00 0.00 3.95
5064 5197 4.035112 TGGTCAAATATACTCCCTCCGTT 58.965 43.478 0.00 0.00 0.00 4.44
5065 5198 3.649843 TGGTCAAATATACTCCCTCCGT 58.350 45.455 0.00 0.00 0.00 4.69
5066 5199 4.891992 ATGGTCAAATATACTCCCTCCG 57.108 45.455 0.00 0.00 0.00 4.63
5123 5258 3.654414 ACAGGTCAAGAGTTTTCTAGCG 58.346 45.455 0.00 0.00 31.96 4.26
5138 5273 9.609346 TGCCTAGTAAAATCTTAATAACAGGTC 57.391 33.333 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.