Multiple sequence alignment - TraesCS5D01G431800

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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 TraesCS5D01G431800 chr5D 100.000 4016 0 0 1 4016 488348856 488344841 0.000000e+00 7417.0
1 TraesCS5D01G431800 chr5D 91.139 316 17 6 1348 1662 537938719 537939024 6.210000e-113 418.0
2 TraesCS5D01G431800 chr5D 96.825 189 5 1 3372 3559 6266948 6267136 8.380000e-82 315.0
3 TraesCS5D01G431800 chr5D 96.825 189 5 1 3372 3559 329158944 329159132 8.380000e-82 315.0
4 TraesCS5D01G431800 chr5D 96.825 189 5 1 3372 3559 503300936 503300748 8.380000e-82 315.0
5 TraesCS5D01G431800 chr5D 98.000 50 1 0 9 58 488348799 488348750 1.990000e-13 87.9
6 TraesCS5D01G431800 chr5D 98.000 50 1 0 58 107 488348848 488348799 1.990000e-13 87.9
7 TraesCS5D01G431800 chr5B 87.913 2515 149 58 889 3325 601330319 601327882 0.000000e+00 2817.0
8 TraesCS5D01G431800 chr5B 89.774 753 36 15 58 782 601331251 601330512 0.000000e+00 926.0
9 TraesCS5D01G431800 chr5B 88.214 543 48 10 3472 4014 601327522 601326996 5.660000e-178 634.0
10 TraesCS5D01G431800 chr5B 97.354 189 4 1 3372 3559 538681230 538681042 1.800000e-83 320.0
11 TraesCS5D01G431800 chr5B 93.846 65 2 2 3261 3323 601328014 601327950 3.300000e-16 97.1
12 TraesCS5D01G431800 chr5A 90.337 1956 90 46 1348 3257 609203578 609201676 0.000000e+00 2473.0
13 TraesCS5D01G431800 chr5A 86.494 770 41 25 58 782 609205010 609204259 0.000000e+00 787.0
14 TraesCS5D01G431800 chr5A 83.307 623 37 32 779 1349 609204214 609203607 2.770000e-141 512.0
15 TraesCS5D01G431800 chr5A 94.620 316 13 2 3255 3569 609196649 609196337 1.680000e-133 486.0
16 TraesCS5D01G431800 chr5A 87.113 194 17 2 3728 3913 609196305 609196112 3.140000e-51 213.0
17 TraesCS5D01G431800 chr5A 93.443 61 4 0 3954 4014 609196112 609196052 1.540000e-14 91.6
18 TraesCS5D01G431800 chr2B 85.943 1309 142 25 1396 2696 445495205 445493931 0.000000e+00 1360.0
19 TraesCS5D01G431800 chr2B 91.026 234 13 5 999 1231 346735614 346735840 3.900000e-80 309.0
20 TraesCS5D01G431800 chr7B 84.377 1261 136 41 1448 2696 723894122 723892911 0.000000e+00 1181.0
21 TraesCS5D01G431800 chr7B 91.266 229 13 4 997 1224 625272090 625272312 5.040000e-79 305.0
22 TraesCS5D01G431800 chr4B 84.140 1261 139 41 1448 2696 600369238 600368027 0.000000e+00 1164.0
23 TraesCS5D01G431800 chr4B 96.825 189 5 1 3372 3559 308647438 308647626 8.380000e-82 315.0
24 TraesCS5D01G431800 chrUn 84.060 1261 139 43 1448 2696 41814682 41813472 0.000000e+00 1158.0
25 TraesCS5D01G431800 chrUn 95.385 130 6 0 3557 3686 182429105 182429234 1.460000e-49 207.0
26 TraesCS5D01G431800 chrUn 94.161 137 6 2 3557 3693 231556683 231556549 1.460000e-49 207.0
27 TraesCS5D01G431800 chrUn 94.161 137 6 2 3557 3693 273331444 273331578 1.460000e-49 207.0
28 TraesCS5D01G431800 chrUn 94.161 137 6 2 3557 3693 312036920 312036786 1.460000e-49 207.0
29 TraesCS5D01G431800 chrUn 94.161 137 6 2 3557 3693 414425724 414425590 1.460000e-49 207.0
30 TraesCS5D01G431800 chrUn 93.478 92 5 1 3678 3769 231556602 231556512 7.000000e-28 135.0
31 TraesCS5D01G431800 chrUn 93.478 92 5 1 3678 3769 273331525 273331615 7.000000e-28 135.0
32 TraesCS5D01G431800 chrUn 93.478 92 5 1 3678 3769 312036839 312036749 7.000000e-28 135.0
33 TraesCS5D01G431800 chr2D 90.506 316 19 6 1348 1662 42603957 42604262 1.340000e-109 407.0
34 TraesCS5D01G431800 chr2D 90.506 316 19 6 1348 1662 200393791 200394096 1.340000e-109 407.0
35 TraesCS5D01G431800 chr2D 91.703 229 12 4 997 1224 200393446 200393668 1.080000e-80 311.0
36 TraesCS5D01G431800 chr2D 96.154 130 5 0 3557 3686 18025323 18025452 3.140000e-51 213.0
37 TraesCS5D01G431800 chr2D 94.161 137 6 2 3557 3693 291700900 291701034 1.460000e-49 207.0
38 TraesCS5D01G431800 chr2D 93.478 92 5 1 3678 3769 18025404 18025494 7.000000e-28 135.0
39 TraesCS5D01G431800 chr2D 93.478 92 5 1 3678 3769 291700981 291701071 7.000000e-28 135.0
40 TraesCS5D01G431800 chr4D 90.190 316 20 6 1348 1662 153051589 153051894 6.250000e-108 401.0
41 TraesCS5D01G431800 chr4D 96.825 189 5 1 3372 3559 19877489 19877301 8.380000e-82 315.0
42 TraesCS5D01G431800 chr4D 90.678 236 14 3 997 1231 153051244 153051472 1.400000e-79 307.0
43 TraesCS5D01G431800 chr1D 90.190 316 20 6 1348 1662 239784802 239785107 6.250000e-108 401.0
44 TraesCS5D01G431800 chr1D 93.013 229 9 2 997 1224 239784456 239784678 1.080000e-85 327.0
45 TraesCS5D01G431800 chr1D 96.825 189 5 1 3372 3559 254444068 254443880 8.380000e-82 315.0
46 TraesCS5D01G431800 chr7A 91.903 247 16 4 1348 1594 151359615 151359857 3.840000e-90 342.0
47 TraesCS5D01G431800 chr7A 91.498 247 17 4 1348 1594 578331740 578331498 1.790000e-88 337.0
48 TraesCS5D01G431800 chr3B 98.413 189 2 1 3372 3559 101911149 101911337 8.320000e-87 331.0
49 TraesCS5D01G431800 chr3B 91.266 229 13 4 997 1224 62349472 62349694 5.040000e-79 305.0
50 TraesCS5D01G431800 chr3B 93.478 92 5 1 3678 3769 5997218 5997128 7.000000e-28 135.0
51 TraesCS5D01G431800 chr3A 90.830 229 14 4 997 1224 611009377 611009599 2.350000e-77 300.0
52 TraesCS5D01G431800 chr7D 94.161 137 6 2 3557 3693 6945583 6945717 1.460000e-49 207.0
53 TraesCS5D01G431800 chr7D 93.478 92 5 1 3678 3769 6945664 6945754 7.000000e-28 135.0
54 TraesCS5D01G431800 chr6D 94.161 137 6 2 3557 3693 458914837 458914703 1.460000e-49 207.0
55 TraesCS5D01G431800 chr6B 97.500 80 1 1 3678 3757 320247512 320247590 7.000000e-28 135.0


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 TraesCS5D01G431800 chr5D 488344841 488348856 4015 True 2530.933333 7417 98.666667 1 4016 3 chr5D.!!$R2 4015
1 TraesCS5D01G431800 chr5B 601326996 601331251 4255 True 1118.525000 2817 89.936750 58 4014 4 chr5B.!!$R2 3956
2 TraesCS5D01G431800 chr5A 609201676 609205010 3334 True 1257.333333 2473 86.712667 58 3257 3 chr5A.!!$R2 3199
3 TraesCS5D01G431800 chr5A 609196052 609196649 597 True 263.533333 486 91.725333 3255 4014 3 chr5A.!!$R1 759
4 TraesCS5D01G431800 chr2B 445493931 445495205 1274 True 1360.000000 1360 85.943000 1396 2696 1 chr2B.!!$R1 1300
5 TraesCS5D01G431800 chr7B 723892911 723894122 1211 True 1181.000000 1181 84.377000 1448 2696 1 chr7B.!!$R1 1248
6 TraesCS5D01G431800 chr4B 600368027 600369238 1211 True 1164.000000 1164 84.140000 1448 2696 1 chr4B.!!$R1 1248
7 TraesCS5D01G431800 chrUn 41813472 41814682 1210 True 1158.000000 1158 84.060000 1448 2696 1 chrUn.!!$R1 1248
8 TraesCS5D01G431800 chr2D 200393446 200394096 650 False 359.000000 407 91.104500 997 1662 2 chr2D.!!$F3 665
9 TraesCS5D01G431800 chr4D 153051244 153051894 650 False 354.000000 401 90.434000 997 1662 2 chr4D.!!$F1 665
10 TraesCS5D01G431800 chr1D 239784456 239785107 651 False 364.000000 401 91.601500 997 1662 2 chr1D.!!$F1 665

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
663 705 0.038709 GATGGAAGCTCCTCGATCCG 60.039 60.0 0.00 0.0 37.46 4.18 F
871 989 0.041839 CAGTCTTCACACAGCAACGC 60.042 55.0 0.00 0.0 0.00 4.84 F
874 992 0.249114 TCTTCACACAGCAACGCGTA 60.249 50.0 14.46 0.0 0.00 4.42 F
1322 1527 0.516877 CGGTGTGCTTGTATGTGGTG 59.483 55.0 0.00 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 2010 1.067821 GACCATCTCTGCCTAACCTCG 59.932 57.143 0.00 0.00 0.00 4.63 R
2510 2838 1.788258 TCTTCAAGAGCTGCGACTTG 58.212 50.000 24.96 24.96 43.03 3.16 R
2770 3168 2.401583 ACCTGATCAACTTATGCGCA 57.598 45.000 14.96 14.96 0.00 6.09 R
3232 3638 0.698238 TGCAGGGTAGCATTCCAGTT 59.302 50.000 0.00 0.00 40.11 3.16 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.912634 ATTTGTATTATGCTATTGTTATGTGGC 57.087 29.630 0.00 0.00 0.00 5.01
27 28 8.457238 TTGTATTATGCTATTGTTATGTGGCA 57.543 30.769 0.00 0.00 0.00 4.92
28 29 8.098220 TGTATTATGCTATTGTTATGTGGCAG 57.902 34.615 0.00 0.00 33.23 4.85
29 30 3.996150 ATGCTATTGTTATGTGGCAGC 57.004 42.857 0.00 0.00 33.23 5.25
30 31 3.003394 TGCTATTGTTATGTGGCAGCT 57.997 42.857 0.00 0.00 0.00 4.24
31 32 2.945008 TGCTATTGTTATGTGGCAGCTC 59.055 45.455 0.00 0.00 0.00 4.09
32 33 2.032549 GCTATTGTTATGTGGCAGCTCG 60.033 50.000 0.00 0.00 0.00 5.03
33 34 0.734889 ATTGTTATGTGGCAGCTCGC 59.265 50.000 0.00 0.00 41.28 5.03
34 35 0.605050 TTGTTATGTGGCAGCTCGCA 60.605 50.000 9.78 1.14 45.17 5.10
35 36 0.392863 TGTTATGTGGCAGCTCGCAT 60.393 50.000 12.68 12.68 45.17 4.73
36 37 0.305922 GTTATGTGGCAGCTCGCATC 59.694 55.000 11.75 1.23 45.17 3.91
37 38 0.107752 TTATGTGGCAGCTCGCATCA 60.108 50.000 11.75 6.03 45.17 3.07
38 39 0.107752 TATGTGGCAGCTCGCATCAA 60.108 50.000 11.75 0.00 45.17 2.57
39 40 1.374343 ATGTGGCAGCTCGCATCAAG 61.374 55.000 9.78 0.00 45.17 3.02
40 41 2.437180 TGGCAGCTCGCATCAAGG 60.437 61.111 9.78 0.00 45.17 3.61
41 42 3.207669 GGCAGCTCGCATCAAGGG 61.208 66.667 9.78 0.00 45.17 3.95
42 43 3.885521 GCAGCTCGCATCAAGGGC 61.886 66.667 3.64 0.00 41.79 5.19
43 44 2.437180 CAGCTCGCATCAAGGGCA 60.437 61.111 0.00 0.00 0.00 5.36
44 45 2.124819 AGCTCGCATCAAGGGCAG 60.125 61.111 0.00 0.00 0.00 4.85
45 46 3.885521 GCTCGCATCAAGGGCAGC 61.886 66.667 0.00 0.00 0.00 5.25
46 47 3.207669 CTCGCATCAAGGGCAGCC 61.208 66.667 1.26 1.26 0.00 4.85
47 48 3.982316 CTCGCATCAAGGGCAGCCA 62.982 63.158 15.19 0.00 0.00 4.75
48 49 3.063704 CGCATCAAGGGCAGCCAA 61.064 61.111 15.19 0.00 0.00 4.52
49 50 2.420568 CGCATCAAGGGCAGCCAAT 61.421 57.895 15.19 0.00 0.00 3.16
50 51 1.102809 CGCATCAAGGGCAGCCAATA 61.103 55.000 15.19 0.00 0.00 1.90
51 52 0.386838 GCATCAAGGGCAGCCAATAC 59.613 55.000 15.19 0.00 0.00 1.89
52 53 1.035139 CATCAAGGGCAGCCAATACC 58.965 55.000 15.19 0.00 0.00 2.73
53 54 0.630673 ATCAAGGGCAGCCAATACCA 59.369 50.000 15.19 0.00 0.00 3.25
54 55 0.407528 TCAAGGGCAGCCAATACCAA 59.592 50.000 15.19 0.00 0.00 3.67
55 56 0.532115 CAAGGGCAGCCAATACCAAC 59.468 55.000 15.19 0.00 0.00 3.77
56 57 0.114168 AAGGGCAGCCAATACCAACA 59.886 50.000 15.19 0.00 0.00 3.33
74 75 7.275888 ACCAACATATGCTATTGTTATGTGG 57.724 36.000 1.58 0.00 36.83 4.17
78 79 3.996150 ATGCTATTGTTATGTGGCAGC 57.004 42.857 0.00 0.00 33.23 5.25
81 82 2.032549 GCTATTGTTATGTGGCAGCTCG 60.033 50.000 0.00 0.00 0.00 5.03
228 236 7.500720 TCATCGACAATATAGAAACGGAGTA 57.499 36.000 0.00 0.00 45.00 2.59
229 237 7.582352 TCATCGACAATATAGAAACGGAGTAG 58.418 38.462 0.00 0.00 45.00 2.57
242 250 8.620116 AGAAACGGAGTAGGTATCTATTCTAC 57.380 38.462 5.60 0.00 45.00 2.59
245 253 7.233389 ACGGAGTAGGTATCTATTCTACGTA 57.767 40.000 8.72 0.00 41.94 3.57
246 254 7.671302 ACGGAGTAGGTATCTATTCTACGTAA 58.329 38.462 8.72 0.00 41.94 3.18
247 255 8.150945 ACGGAGTAGGTATCTATTCTACGTAAA 58.849 37.037 8.72 0.00 41.94 2.01
275 308 2.260844 TGTTCAGTTGAAGGAGCCAG 57.739 50.000 0.00 0.00 34.27 4.85
350 392 2.573869 CTCGCCTCTTCTTCCGCA 59.426 61.111 0.00 0.00 0.00 5.69
351 393 1.518133 CTCGCCTCTTCTTCCGCAG 60.518 63.158 0.00 0.00 0.00 5.18
352 394 3.191539 CGCCTCTTCTTCCGCAGC 61.192 66.667 0.00 0.00 0.00 5.25
353 395 2.821810 GCCTCTTCTTCCGCAGCC 60.822 66.667 0.00 0.00 0.00 4.85
354 396 2.510238 CCTCTTCTTCCGCAGCCG 60.510 66.667 0.00 0.00 0.00 5.52
355 397 3.191539 CTCTTCTTCCGCAGCCGC 61.192 66.667 0.00 0.00 0.00 6.53
356 398 4.760047 TCTTCTTCCGCAGCCGCC 62.760 66.667 0.00 0.00 33.11 6.13
663 705 0.038709 GATGGAAGCTCCTCGATCCG 60.039 60.000 0.00 0.00 37.46 4.18
707 752 6.540438 TTCTTTAGGGCTTTCTCTATCGAA 57.460 37.500 0.00 0.00 0.00 3.71
731 795 3.956744 AGGCCCAGCTTAACTTAGAAAG 58.043 45.455 0.00 0.00 0.00 2.62
732 796 3.587506 AGGCCCAGCTTAACTTAGAAAGA 59.412 43.478 0.00 0.00 0.00 2.52
733 797 4.042934 AGGCCCAGCTTAACTTAGAAAGAA 59.957 41.667 0.00 0.00 0.00 2.52
855 973 4.070552 GCCGTCGCCCTCTTCAGT 62.071 66.667 0.00 0.00 0.00 3.41
857 975 2.344203 CCGTCGCCCTCTTCAGTCT 61.344 63.158 0.00 0.00 0.00 3.24
858 976 1.587054 CGTCGCCCTCTTCAGTCTT 59.413 57.895 0.00 0.00 0.00 3.01
861 979 0.603569 TCGCCCTCTTCAGTCTTCAC 59.396 55.000 0.00 0.00 0.00 3.18
862 980 0.318441 CGCCCTCTTCAGTCTTCACA 59.682 55.000 0.00 0.00 0.00 3.58
863 981 1.802069 GCCCTCTTCAGTCTTCACAC 58.198 55.000 0.00 0.00 0.00 3.82
864 982 1.070758 GCCCTCTTCAGTCTTCACACA 59.929 52.381 0.00 0.00 0.00 3.72
866 984 2.411904 CCTCTTCAGTCTTCACACAGC 58.588 52.381 0.00 0.00 0.00 4.40
867 985 2.224137 CCTCTTCAGTCTTCACACAGCA 60.224 50.000 0.00 0.00 0.00 4.41
868 986 3.461061 CTCTTCAGTCTTCACACAGCAA 58.539 45.455 0.00 0.00 0.00 3.91
869 987 3.198068 TCTTCAGTCTTCACACAGCAAC 58.802 45.455 0.00 0.00 0.00 4.17
870 988 1.570813 TCAGTCTTCACACAGCAACG 58.429 50.000 0.00 0.00 0.00 4.10
871 989 0.041839 CAGTCTTCACACAGCAACGC 60.042 55.000 0.00 0.00 0.00 4.84
872 990 1.083401 GTCTTCACACAGCAACGCG 60.083 57.895 3.53 3.53 0.00 6.01
873 991 1.520564 TCTTCACACAGCAACGCGT 60.521 52.632 5.58 5.58 0.00 6.01
874 992 0.249114 TCTTCACACAGCAACGCGTA 60.249 50.000 14.46 0.00 0.00 4.42
959 1127 3.394836 GAAGCGCCCACCCTCTCT 61.395 66.667 2.29 0.00 0.00 3.10
960 1128 3.672295 GAAGCGCCCACCCTCTCTG 62.672 68.421 2.29 0.00 0.00 3.35
961 1129 4.704103 AGCGCCCACCCTCTCTGA 62.704 66.667 2.29 0.00 0.00 3.27
962 1130 4.459089 GCGCCCACCCTCTCTGAC 62.459 72.222 0.00 0.00 0.00 3.51
963 1131 3.775654 CGCCCACCCTCTCTGACC 61.776 72.222 0.00 0.00 0.00 4.02
964 1132 3.775654 GCCCACCCTCTCTGACCG 61.776 72.222 0.00 0.00 0.00 4.79
965 1133 3.775654 CCCACCCTCTCTGACCGC 61.776 72.222 0.00 0.00 0.00 5.68
966 1134 4.135153 CCACCCTCTCTGACCGCG 62.135 72.222 0.00 0.00 0.00 6.46
967 1135 4.135153 CACCCTCTCTGACCGCGG 62.135 72.222 26.86 26.86 0.00 6.46
1322 1527 0.516877 CGGTGTGCTTGTATGTGGTG 59.483 55.000 0.00 0.00 0.00 4.17
1341 1550 3.756434 GGTGAAATTTCTGGTGATTCCGA 59.244 43.478 18.64 0.00 39.52 4.55
1350 1588 2.939103 CTGGTGATTCCGAGGACATTTC 59.061 50.000 0.00 0.00 39.52 2.17
1378 1616 7.209475 GGTGAAATGACCTCAAAATTCTCAAA 58.791 34.615 0.00 0.00 32.69 2.69
1385 1623 4.218417 ACCTCAAAATTCTCAAACCGGATG 59.782 41.667 9.46 7.12 0.00 3.51
1473 1712 2.227865 CGTGGGAAGGTAATTGTGTTGG 59.772 50.000 0.00 0.00 0.00 3.77
1505 1744 0.914417 TGAGGCTAGGAGGTTTGGGG 60.914 60.000 0.00 0.00 0.00 4.96
1538 1779 3.906014 TCGAATTCCGAGCTAGATCAG 57.094 47.619 8.99 0.00 43.23 2.90
1666 1910 4.262463 CCCACTTCTGCACTTGAGTTAGTA 60.262 45.833 0.00 0.00 0.00 1.82
1667 1911 5.482908 CCACTTCTGCACTTGAGTTAGTAT 58.517 41.667 0.00 0.00 0.00 2.12
1668 1912 6.351033 CCCACTTCTGCACTTGAGTTAGTATA 60.351 42.308 0.00 0.00 0.00 1.47
1669 1913 7.268586 CCACTTCTGCACTTGAGTTAGTATAT 58.731 38.462 0.00 0.00 0.00 0.86
1732 2001 1.009060 TGGTGATCCCCTAGGCTTGTA 59.991 52.381 2.05 0.00 0.00 2.41
1752 2021 2.148446 TAAGGCTACGAGGTTAGGCA 57.852 50.000 7.03 0.00 40.80 4.75
1768 2045 5.529060 GGTTAGGCAGAGATGGTCTAAATTG 59.471 44.000 0.00 0.00 34.53 2.32
1773 2050 6.320672 AGGCAGAGATGGTCTAAATTGATTTG 59.679 38.462 0.00 0.00 32.51 2.32
1778 2055 6.633856 AGATGGTCTAAATTGATTTGCAACC 58.366 36.000 0.00 0.00 39.78 3.77
1805 2082 1.745087 AGCCAGGAATTATTGTGTGCG 59.255 47.619 0.00 0.00 0.00 5.34
1835 2124 7.622713 AGGATCAGATTATCTATTTCAGCTGG 58.377 38.462 15.13 0.00 0.00 4.85
1857 2154 5.589855 TGGTATTGTGATATGCTTGTTCTGG 59.410 40.000 0.00 0.00 0.00 3.86
1870 2169 4.455877 GCTTGTTCTGGTGTATGCTTAAGT 59.544 41.667 4.02 0.00 0.00 2.24
1943 2243 1.412343 ACCAAGTGTGCAACCATTTCC 59.588 47.619 0.00 0.00 34.36 3.13
2052 2374 4.916983 TTTGTTTGGTGATCTTGTCTGG 57.083 40.909 0.00 0.00 0.00 3.86
2061 2383 3.368236 GTGATCTTGTCTGGTTACTTCGC 59.632 47.826 0.00 0.00 0.00 4.70
2351 2678 8.368668 ACACTTTAGTTTGCTACTCTTAGATGT 58.631 33.333 0.00 0.00 38.33 3.06
2510 2838 1.202940 GGAATGTATGCCCTCCCTTCC 60.203 57.143 0.00 0.00 0.00 3.46
2637 2965 0.731514 CATGCCAAGCAAGCAACTCG 60.732 55.000 0.00 0.00 44.83 4.18
2658 2986 4.877823 TCGCAAAATTAGCTGACATGATCT 59.122 37.500 0.00 0.00 0.00 2.75
2700 3098 6.238593 GGTTGCCTTAGAAAGCATTGATCTAG 60.239 42.308 0.00 0.00 39.11 2.43
2703 3101 7.564793 TGCCTTAGAAAGCATTGATCTAGTTA 58.435 34.615 0.00 0.00 33.08 2.24
2736 3134 3.905784 AGTTGTTTGCTTGCATTAGAGC 58.094 40.909 1.00 1.00 39.33 4.09
2737 3135 3.318839 AGTTGTTTGCTTGCATTAGAGCA 59.681 39.130 6.71 6.71 46.37 4.26
2752 3150 3.191078 AGAGCAGGTCATATGCAAGTC 57.809 47.619 1.66 0.00 46.31 3.01
2759 3157 5.352569 GCAGGTCATATGCAAGTCCATATAC 59.647 44.000 0.00 0.00 43.31 1.47
2761 3159 6.936335 CAGGTCATATGCAAGTCCATATACAA 59.064 38.462 0.00 0.00 36.52 2.41
2762 3160 7.609146 CAGGTCATATGCAAGTCCATATACAAT 59.391 37.037 0.00 0.00 36.52 2.71
2763 3161 8.166061 AGGTCATATGCAAGTCCATATACAATT 58.834 33.333 0.00 0.00 36.52 2.32
2764 3162 9.448438 GGTCATATGCAAGTCCATATACAATTA 57.552 33.333 0.00 0.00 36.52 1.40
2772 3170 9.559958 GCAAGTCCATATACAATTATATGTTGC 57.440 33.333 15.45 15.45 42.91 4.17
2773 3171 9.759259 CAAGTCCATATACAATTATATGTTGCG 57.241 33.333 9.67 0.00 43.27 4.85
2774 3172 7.974675 AGTCCATATACAATTATATGTTGCGC 58.025 34.615 0.00 0.00 43.27 6.09
2775 3173 7.606073 AGTCCATATACAATTATATGTTGCGCA 59.394 33.333 5.66 5.66 43.27 6.09
2776 3174 8.397906 GTCCATATACAATTATATGTTGCGCAT 58.602 33.333 12.75 0.00 43.27 4.73
2777 3175 9.606631 TCCATATACAATTATATGTTGCGCATA 57.393 29.630 12.75 3.62 43.27 3.14
3030 3431 3.009033 ACTGGTGAGCAAAGCCTATACAA 59.991 43.478 0.00 0.00 0.00 2.41
3054 3455 6.299805 AGAGACTTCCAATGTACTAATGCA 57.700 37.500 0.00 0.00 0.00 3.96
3127 3529 3.971150 AGTTCGAGAGTTCAGAGTTGTG 58.029 45.455 0.00 0.00 0.00 3.33
3147 3549 7.448469 AGTTGTGACCTAAATTCAATAAGCTGT 59.552 33.333 0.00 0.00 0.00 4.40
3148 3550 7.144722 TGTGACCTAAATTCAATAAGCTGTG 57.855 36.000 0.00 0.00 0.00 3.66
3149 3551 6.030228 GTGACCTAAATTCAATAAGCTGTGC 58.970 40.000 0.00 0.00 0.00 4.57
3175 3577 1.003718 GTGGAGGTTCTTGACGGGG 60.004 63.158 0.00 0.00 0.00 5.73
3203 3609 1.601166 GGAGCCGTTGTTACAAACCT 58.399 50.000 0.00 0.00 0.00 3.50
3204 3610 1.265905 GGAGCCGTTGTTACAAACCTG 59.734 52.381 0.00 0.00 0.00 4.00
3205 3611 2.215196 GAGCCGTTGTTACAAACCTGA 58.785 47.619 0.00 0.00 0.00 3.86
3206 3612 2.614983 GAGCCGTTGTTACAAACCTGAA 59.385 45.455 0.00 0.00 0.00 3.02
3207 3613 3.018149 AGCCGTTGTTACAAACCTGAAA 58.982 40.909 0.00 0.00 0.00 2.69
3208 3614 3.634910 AGCCGTTGTTACAAACCTGAAAT 59.365 39.130 0.00 0.00 0.00 2.17
3209 3615 4.098807 AGCCGTTGTTACAAACCTGAAATT 59.901 37.500 0.00 0.00 0.00 1.82
3210 3616 4.443063 GCCGTTGTTACAAACCTGAAATTC 59.557 41.667 0.00 0.00 0.00 2.17
3211 3617 4.979815 CCGTTGTTACAAACCTGAAATTCC 59.020 41.667 0.00 0.00 0.00 3.01
3212 3618 5.450688 CCGTTGTTACAAACCTGAAATTCCA 60.451 40.000 0.00 0.00 0.00 3.53
3213 3619 5.685511 CGTTGTTACAAACCTGAAATTCCAG 59.314 40.000 0.00 0.00 0.00 3.86
3214 3620 5.195001 TGTTACAAACCTGAAATTCCAGC 57.805 39.130 0.00 0.00 32.97 4.85
3215 3621 4.892934 TGTTACAAACCTGAAATTCCAGCT 59.107 37.500 0.00 0.00 32.97 4.24
3216 3622 5.362430 TGTTACAAACCTGAAATTCCAGCTT 59.638 36.000 0.00 0.00 32.97 3.74
3217 3623 6.547880 TGTTACAAACCTGAAATTCCAGCTTA 59.452 34.615 0.00 0.00 32.97 3.09
3218 3624 7.232534 TGTTACAAACCTGAAATTCCAGCTTAT 59.767 33.333 0.00 0.00 32.97 1.73
3219 3625 6.272822 ACAAACCTGAAATTCCAGCTTATC 57.727 37.500 0.00 0.00 32.97 1.75
3220 3626 6.012745 ACAAACCTGAAATTCCAGCTTATCT 58.987 36.000 0.00 0.00 32.97 1.98
3221 3627 6.071728 ACAAACCTGAAATTCCAGCTTATCTG 60.072 38.462 0.00 0.00 42.49 2.90
3222 3628 5.184892 ACCTGAAATTCCAGCTTATCTGT 57.815 39.130 0.00 0.00 41.25 3.41
3223 3629 6.313519 ACCTGAAATTCCAGCTTATCTGTA 57.686 37.500 0.00 0.00 41.25 2.74
3224 3630 6.721318 ACCTGAAATTCCAGCTTATCTGTAA 58.279 36.000 0.00 0.00 41.25 2.41
3225 3631 6.825721 ACCTGAAATTCCAGCTTATCTGTAAG 59.174 38.462 0.00 0.00 41.25 2.34
3239 3645 8.547967 CTTATCTGTAAGCTGTTAAACTGGAA 57.452 34.615 0.00 0.00 31.63 3.53
3240 3646 9.167311 CTTATCTGTAAGCTGTTAAACTGGAAT 57.833 33.333 0.00 0.00 31.63 3.01
3241 3647 6.801539 TCTGTAAGCTGTTAAACTGGAATG 57.198 37.500 0.00 0.00 0.00 2.67
3242 3648 5.181245 TCTGTAAGCTGTTAAACTGGAATGC 59.819 40.000 0.00 0.00 0.00 3.56
3243 3649 5.070001 TGTAAGCTGTTAAACTGGAATGCT 58.930 37.500 0.00 0.00 0.00 3.79
3244 3650 6.234920 TGTAAGCTGTTAAACTGGAATGCTA 58.765 36.000 0.00 0.00 0.00 3.49
3245 3651 5.629079 AAGCTGTTAAACTGGAATGCTAC 57.371 39.130 0.00 0.00 0.00 3.58
3246 3652 4.010349 AGCTGTTAAACTGGAATGCTACC 58.990 43.478 0.00 0.00 0.00 3.18
3247 3653 3.128764 GCTGTTAAACTGGAATGCTACCC 59.871 47.826 0.00 0.00 0.00 3.69
3248 3654 4.589908 CTGTTAAACTGGAATGCTACCCT 58.410 43.478 0.00 0.00 0.00 4.34
3249 3655 4.331968 TGTTAAACTGGAATGCTACCCTG 58.668 43.478 0.00 0.00 0.00 4.45
3250 3656 1.839424 AAACTGGAATGCTACCCTGC 58.161 50.000 0.00 0.00 0.00 4.85
3252 3658 0.698238 ACTGGAATGCTACCCTGCAA 59.302 50.000 0.00 0.00 46.61 4.08
3253 3659 1.285962 ACTGGAATGCTACCCTGCAAT 59.714 47.619 0.00 0.00 46.61 3.56
3337 3969 3.253921 GCAATGTACTATGATGCATGCCA 59.746 43.478 16.68 7.22 37.00 4.92
3448 4085 1.692411 GGGTATTGTGGCATTCCCTC 58.308 55.000 0.00 0.00 32.89 4.30
3474 4111 3.390967 TCCATTCCGGAGCATCTTAATCA 59.609 43.478 3.34 0.00 39.64 2.57
3517 4214 9.595823 CAAAGAAAAATTCCATTATCAGCTCAT 57.404 29.630 0.00 0.00 0.00 2.90
3562 4259 4.687948 CGATCTAGCAATCATGGAATTCGT 59.312 41.667 0.00 0.00 0.00 3.85
3577 4274 8.656849 CATGGAATTCGTTATGCTATAAGGTAC 58.343 37.037 0.00 0.00 0.00 3.34
3585 4282 7.870954 TCGTTATGCTATAAGGTACCAATTCAG 59.129 37.037 15.94 5.48 0.00 3.02
3586 4283 7.360101 CGTTATGCTATAAGGTACCAATTCAGC 60.360 40.741 15.94 15.30 0.00 4.26
3630 4356 4.342665 CAGTGGGAGTCCCTATCTACTTTC 59.657 50.000 28.73 6.59 45.70 2.62
3663 4389 4.312052 GGCTTTGCCGGTACATCA 57.688 55.556 1.90 0.00 39.62 3.07
3664 4390 2.793831 GGCTTTGCCGGTACATCAT 58.206 52.632 1.90 0.00 39.62 2.45
3665 4391 1.961793 GGCTTTGCCGGTACATCATA 58.038 50.000 1.90 0.00 39.62 2.15
3666 4392 2.504367 GGCTTTGCCGGTACATCATAT 58.496 47.619 1.90 0.00 39.62 1.78
3667 4393 2.884639 GGCTTTGCCGGTACATCATATT 59.115 45.455 1.90 0.00 39.62 1.28
3668 4394 3.304659 GGCTTTGCCGGTACATCATATTG 60.305 47.826 1.90 0.00 39.62 1.90
3669 4395 3.563808 GCTTTGCCGGTACATCATATTGA 59.436 43.478 1.90 0.00 0.00 2.57
3670 4396 4.216257 GCTTTGCCGGTACATCATATTGAT 59.784 41.667 1.90 0.00 37.65 2.57
3671 4397 5.278463 GCTTTGCCGGTACATCATATTGATT 60.278 40.000 1.90 0.00 34.28 2.57
3672 4398 6.707440 TTTGCCGGTACATCATATTGATTT 57.293 33.333 1.90 0.00 34.28 2.17
3673 4399 5.687770 TGCCGGTACATCATATTGATTTG 57.312 39.130 1.90 0.00 34.28 2.32
3674 4400 5.372373 TGCCGGTACATCATATTGATTTGA 58.628 37.500 1.90 0.00 34.28 2.69
3675 4401 5.238432 TGCCGGTACATCATATTGATTTGAC 59.762 40.000 1.90 0.00 34.28 3.18
3676 4402 5.238432 GCCGGTACATCATATTGATTTGACA 59.762 40.000 1.90 0.00 34.28 3.58
3677 4403 6.658831 CCGGTACATCATATTGATTTGACAC 58.341 40.000 0.00 0.00 34.28 3.67
3678 4404 6.483307 CCGGTACATCATATTGATTTGACACT 59.517 38.462 0.00 0.00 34.28 3.55
3679 4405 7.012327 CCGGTACATCATATTGATTTGACACTT 59.988 37.037 0.00 0.00 34.28 3.16
3680 4406 8.064222 CGGTACATCATATTGATTTGACACTTC 58.936 37.037 0.00 0.00 34.28 3.01
3681 4407 8.345565 GGTACATCATATTGATTTGACACTTCC 58.654 37.037 0.00 0.00 34.28 3.46
3682 4408 9.113838 GTACATCATATTGATTTGACACTTCCT 57.886 33.333 0.00 0.00 34.28 3.36
3683 4409 8.585471 ACATCATATTGATTTGACACTTCCTT 57.415 30.769 0.00 0.00 34.28 3.36
3684 4410 9.685276 ACATCATATTGATTTGACACTTCCTTA 57.315 29.630 0.00 0.00 34.28 2.69
3685 4411 9.941664 CATCATATTGATTTGACACTTCCTTAC 57.058 33.333 0.00 0.00 34.28 2.34
3686 4412 9.911788 ATCATATTGATTTGACACTTCCTTACT 57.088 29.630 0.00 0.00 32.13 2.24
3687 4413 9.166173 TCATATTGATTTGACACTTCCTTACTG 57.834 33.333 0.00 0.00 0.00 2.74
3688 4414 6.824305 ATTGATTTGACACTTCCTTACTGG 57.176 37.500 0.00 0.00 37.10 4.00
3689 4415 4.072131 TGATTTGACACTTCCTTACTGGC 58.928 43.478 0.00 0.00 35.26 4.85
3690 4416 3.857157 TTTGACACTTCCTTACTGGCT 57.143 42.857 0.00 0.00 35.26 4.75
3691 4417 3.857157 TTGACACTTCCTTACTGGCTT 57.143 42.857 0.00 0.00 35.26 4.35
3692 4418 3.857157 TGACACTTCCTTACTGGCTTT 57.143 42.857 0.00 0.00 35.26 3.51
3693 4419 3.476552 TGACACTTCCTTACTGGCTTTG 58.523 45.455 0.00 0.00 35.26 2.77
3694 4420 2.226674 GACACTTCCTTACTGGCTTTGC 59.773 50.000 0.00 0.00 35.26 3.68
3713 4439 7.205297 GCTTTGCCAGTACATCATATTGATTT 58.795 34.615 0.00 0.00 34.28 2.17
3759 4485 1.238439 CATTGCTTCCAGGACAACGT 58.762 50.000 0.00 0.00 0.00 3.99
3760 4486 1.608590 CATTGCTTCCAGGACAACGTT 59.391 47.619 0.00 0.00 0.00 3.99
3775 4501 5.473796 ACAACGTTGAGTATTCGTGTTTT 57.526 34.783 33.66 3.81 37.85 2.43
3891 4625 8.009974 CAGGGTAATTTATCTTTCGCTAATTCG 58.990 37.037 0.00 0.00 0.00 3.34
3900 4634 1.745232 TCGCTAATTCGCAAATGGGT 58.255 45.000 2.63 0.00 0.00 4.51
3902 4636 1.559831 GCTAATTCGCAAATGGGTGC 58.440 50.000 0.00 0.00 41.32 5.01
3906 4640 2.229690 ATTCGCAAATGGGTGCTGCC 62.230 55.000 0.00 0.00 42.62 4.85
3919 4653 0.464036 TGCTGCCTACTATCAACCCG 59.536 55.000 0.00 0.00 0.00 5.28
3921 4655 1.120530 CTGCCTACTATCAACCCGGT 58.879 55.000 0.00 0.00 0.00 5.28
3931 4665 0.032403 TCAACCCGGTACAACAGACG 59.968 55.000 0.00 0.00 0.00 4.18
3935 4669 1.364901 CCGGTACAACAGACGGTGT 59.635 57.895 0.00 0.00 43.24 4.16
3967 4701 5.164620 TCAAAGAGTGGTTATGCAGATCA 57.835 39.130 0.00 0.00 0.00 2.92
3983 4717 3.869832 CAGATCATTCAGTGAACATCGCT 59.130 43.478 7.96 0.00 40.97 4.93
4014 4748 7.527457 AGTAATTTCGTTCATCAAACTTAGCC 58.473 34.615 0.00 0.00 35.59 3.93
4015 4749 4.398549 TTTCGTTCATCAAACTTAGCCG 57.601 40.909 0.00 0.00 35.59 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 8.907885 TGCCACATAACAATAGCATAATACAAA 58.092 29.630 0.00 0.00 0.00 2.83
4 5 7.023575 GCTGCCACATAACAATAGCATAATAC 58.976 38.462 0.00 0.00 0.00 1.89
6 7 5.771666 AGCTGCCACATAACAATAGCATAAT 59.228 36.000 0.00 0.00 32.42 1.28
7 8 5.132502 AGCTGCCACATAACAATAGCATAA 58.867 37.500 0.00 0.00 32.42 1.90
8 9 4.717877 AGCTGCCACATAACAATAGCATA 58.282 39.130 0.00 0.00 32.42 3.14
9 10 3.559069 AGCTGCCACATAACAATAGCAT 58.441 40.909 0.00 0.00 32.42 3.79
10 11 2.945008 GAGCTGCCACATAACAATAGCA 59.055 45.455 0.00 0.00 32.42 3.49
11 12 2.032549 CGAGCTGCCACATAACAATAGC 60.033 50.000 0.00 0.00 0.00 2.97
12 13 2.032549 GCGAGCTGCCACATAACAATAG 60.033 50.000 0.00 0.00 37.76 1.73
13 14 1.939934 GCGAGCTGCCACATAACAATA 59.060 47.619 0.00 0.00 37.76 1.90
14 15 0.734889 GCGAGCTGCCACATAACAAT 59.265 50.000 0.00 0.00 37.76 2.71
15 16 0.605050 TGCGAGCTGCCACATAACAA 60.605 50.000 0.00 0.00 45.60 2.83
16 17 0.392863 ATGCGAGCTGCCACATAACA 60.393 50.000 0.00 0.00 45.60 2.41
17 18 0.305922 GATGCGAGCTGCCACATAAC 59.694 55.000 0.00 0.00 45.60 1.89
18 19 0.107752 TGATGCGAGCTGCCACATAA 60.108 50.000 0.00 0.00 45.60 1.90
19 20 0.107752 TTGATGCGAGCTGCCACATA 60.108 50.000 0.00 0.00 45.60 2.29
20 21 1.374343 CTTGATGCGAGCTGCCACAT 61.374 55.000 0.00 0.00 45.60 3.21
21 22 2.032376 TTGATGCGAGCTGCCACA 59.968 55.556 0.00 0.00 45.60 4.17
22 23 2.758089 CCTTGATGCGAGCTGCCAC 61.758 63.158 0.00 0.00 45.60 5.01
23 24 2.437180 CCTTGATGCGAGCTGCCA 60.437 61.111 0.00 0.00 45.60 4.92
24 25 3.207669 CCCTTGATGCGAGCTGCC 61.208 66.667 0.00 0.00 45.60 4.85
25 26 3.885521 GCCCTTGATGCGAGCTGC 61.886 66.667 0.00 0.00 46.70 5.25
26 27 2.437180 TGCCCTTGATGCGAGCTG 60.437 61.111 0.00 0.00 0.00 4.24
27 28 2.124819 CTGCCCTTGATGCGAGCT 60.125 61.111 0.00 0.00 0.00 4.09
28 29 3.885521 GCTGCCCTTGATGCGAGC 61.886 66.667 0.00 0.00 0.00 5.03
29 30 3.207669 GGCTGCCCTTGATGCGAG 61.208 66.667 7.66 0.00 0.00 5.03
30 31 2.842188 ATTGGCTGCCCTTGATGCGA 62.842 55.000 17.53 0.00 0.00 5.10
31 32 1.102809 TATTGGCTGCCCTTGATGCG 61.103 55.000 17.53 0.00 0.00 4.73
32 33 0.386838 GTATTGGCTGCCCTTGATGC 59.613 55.000 17.53 5.13 0.00 3.91
33 34 1.035139 GGTATTGGCTGCCCTTGATG 58.965 55.000 17.53 0.00 0.00 3.07
34 35 0.630673 TGGTATTGGCTGCCCTTGAT 59.369 50.000 17.53 7.62 0.00 2.57
35 36 0.407528 TTGGTATTGGCTGCCCTTGA 59.592 50.000 17.53 0.00 0.00 3.02
36 37 0.532115 GTTGGTATTGGCTGCCCTTG 59.468 55.000 17.53 0.00 0.00 3.61
37 38 0.114168 TGTTGGTATTGGCTGCCCTT 59.886 50.000 17.53 5.93 0.00 3.95
38 39 0.336048 ATGTTGGTATTGGCTGCCCT 59.664 50.000 17.53 6.14 0.00 5.19
39 40 2.065899 TATGTTGGTATTGGCTGCCC 57.934 50.000 17.53 0.00 0.00 5.36
40 41 2.288395 GCATATGTTGGTATTGGCTGCC 60.288 50.000 12.87 12.87 0.00 4.85
41 42 2.624838 AGCATATGTTGGTATTGGCTGC 59.375 45.455 4.29 0.00 33.29 5.25
49 50 7.040755 GCCACATAACAATAGCATATGTTGGTA 60.041 37.037 4.29 4.79 42.21 3.25
50 51 6.239008 GCCACATAACAATAGCATATGTTGGT 60.239 38.462 4.29 2.56 39.89 3.67
51 52 6.151691 GCCACATAACAATAGCATATGTTGG 58.848 40.000 4.29 5.84 39.89 3.77
52 53 6.737118 TGCCACATAACAATAGCATATGTTG 58.263 36.000 4.29 3.91 39.89 3.33
53 54 6.515531 GCTGCCACATAACAATAGCATATGTT 60.516 38.462 4.29 0.08 37.99 2.71
54 55 5.048504 GCTGCCACATAACAATAGCATATGT 60.049 40.000 4.29 0.00 40.04 2.29
55 56 5.182570 AGCTGCCACATAACAATAGCATATG 59.817 40.000 0.00 0.00 34.08 1.78
56 57 5.319453 AGCTGCCACATAACAATAGCATAT 58.681 37.500 0.00 0.00 32.42 1.78
81 82 1.227943 TATTGGCTGCCCTCGATGC 60.228 57.895 17.53 0.38 0.00 3.91
88 89 0.746659 GATGTTGGTATTGGCTGCCC 59.253 55.000 17.53 0.00 0.00 5.36
95 96 4.943705 AGCACTTGTAGGATGTTGGTATTG 59.056 41.667 0.00 0.00 0.00 1.90
180 181 4.019174 CCTGCACACCTGATTTCCTAATT 58.981 43.478 0.00 0.00 0.00 1.40
185 189 1.541588 GAACCTGCACACCTGATTTCC 59.458 52.381 0.00 0.00 0.00 3.13
246 254 7.255277 GCTCCTTCAACTGAACATAGAGTTTTT 60.255 37.037 0.00 0.00 41.51 1.94
247 255 6.205658 GCTCCTTCAACTGAACATAGAGTTTT 59.794 38.462 0.00 0.00 41.51 2.43
250 258 4.323104 GGCTCCTTCAACTGAACATAGAGT 60.323 45.833 0.00 0.00 0.00 3.24
252 260 3.582647 TGGCTCCTTCAACTGAACATAGA 59.417 43.478 0.00 0.00 0.00 1.98
253 261 3.937706 CTGGCTCCTTCAACTGAACATAG 59.062 47.826 0.00 0.00 0.00 2.23
254 262 3.307691 CCTGGCTCCTTCAACTGAACATA 60.308 47.826 0.00 0.00 0.00 2.29
255 263 2.553904 CCTGGCTCCTTCAACTGAACAT 60.554 50.000 0.00 0.00 0.00 2.71
256 264 1.202806 CCTGGCTCCTTCAACTGAACA 60.203 52.381 0.00 0.00 0.00 3.18
275 308 1.198759 TCTCACTTACCCCAGTGCCC 61.199 60.000 0.00 0.00 43.51 5.36
381 423 4.760047 GCTTGAGAAGGCCGCCGA 62.760 66.667 3.05 0.00 0.00 5.54
557 599 4.129737 CGGAAGAAGGAGCGCCGA 62.130 66.667 2.29 0.00 44.43 5.54
678 720 2.820197 AGAAAGCCCTAAAGAAAAGCCG 59.180 45.455 0.00 0.00 0.00 5.52
682 724 6.942976 TCGATAGAGAAAGCCCTAAAGAAAA 58.057 36.000 0.00 0.00 42.67 2.29
707 752 2.642807 TCTAAGTTAAGCTGGGCCTTGT 59.357 45.455 4.53 0.00 0.00 3.16
731 795 6.759497 TTGGGCTTCTAGCTTAATTTCTTC 57.241 37.500 0.00 0.00 41.99 2.87
732 796 7.539034 TTTTGGGCTTCTAGCTTAATTTCTT 57.461 32.000 0.00 0.00 41.99 2.52
733 797 7.539034 TTTTTGGGCTTCTAGCTTAATTTCT 57.461 32.000 0.00 0.00 41.99 2.52
854 972 1.083401 CGCGTTGCTGTGTGAAGAC 60.083 57.895 0.00 0.00 0.00 3.01
855 973 0.249114 TACGCGTTGCTGTGTGAAGA 60.249 50.000 20.78 0.00 33.91 2.87
857 975 1.722464 GTATACGCGTTGCTGTGTGAA 59.278 47.619 20.78 0.00 33.91 3.18
858 976 1.336056 TGTATACGCGTTGCTGTGTGA 60.336 47.619 20.78 0.00 33.91 3.58
861 979 1.201877 GGTTGTATACGCGTTGCTGTG 60.202 52.381 20.78 0.00 0.00 3.66
862 980 1.073177 GGTTGTATACGCGTTGCTGT 58.927 50.000 20.78 1.21 0.00 4.40
863 981 1.072391 TGGTTGTATACGCGTTGCTG 58.928 50.000 20.78 0.00 0.00 4.41
864 982 1.073177 GTGGTTGTATACGCGTTGCT 58.927 50.000 20.78 5.37 0.00 3.91
866 984 0.367548 CGGTGGTTGTATACGCGTTG 59.632 55.000 20.78 0.00 0.00 4.10
867 985 0.243365 TCGGTGGTTGTATACGCGTT 59.757 50.000 20.78 8.23 0.00 4.84
868 986 0.243365 TTCGGTGGTTGTATACGCGT 59.757 50.000 19.17 19.17 0.00 6.01
869 987 1.322338 CTTTCGGTGGTTGTATACGCG 59.678 52.381 3.53 3.53 0.00 6.01
870 988 1.061566 GCTTTCGGTGGTTGTATACGC 59.938 52.381 0.00 0.00 0.00 4.42
871 989 2.093152 GTGCTTTCGGTGGTTGTATACG 59.907 50.000 0.00 0.00 0.00 3.06
872 990 3.068560 TGTGCTTTCGGTGGTTGTATAC 58.931 45.455 0.00 0.00 0.00 1.47
873 991 3.404224 TGTGCTTTCGGTGGTTGTATA 57.596 42.857 0.00 0.00 0.00 1.47
874 992 2.264005 TGTGCTTTCGGTGGTTGTAT 57.736 45.000 0.00 0.00 0.00 2.29
919 1082 2.747855 CGAGAGCTTGGGTTGGGC 60.748 66.667 0.00 0.00 0.00 5.36
920 1083 0.955919 GTTCGAGAGCTTGGGTTGGG 60.956 60.000 0.00 0.00 0.00 4.12
921 1084 0.035458 AGTTCGAGAGCTTGGGTTGG 59.965 55.000 0.00 0.00 0.00 3.77
922 1085 1.433534 GAGTTCGAGAGCTTGGGTTG 58.566 55.000 0.00 0.00 0.00 3.77
923 1086 0.038159 CGAGTTCGAGAGCTTGGGTT 60.038 55.000 0.00 0.00 43.02 4.11
1322 1527 4.095036 GTCCTCGGAATCACCAGAAATTTC 59.905 45.833 10.33 10.33 38.90 2.17
1350 1588 1.904287 TTTGAGGTCATTTCACCCCG 58.096 50.000 0.00 0.00 37.09 5.73
1378 1616 0.836400 ACTCACCAACTCCATCCGGT 60.836 55.000 0.00 0.00 0.00 5.28
1385 1623 3.945285 TCAAAACAGAACTCACCAACTCC 59.055 43.478 0.00 0.00 0.00 3.85
1473 1712 4.020485 TCCTAGCCTCAAACTAAAGTGGAC 60.020 45.833 0.00 0.00 0.00 4.02
1505 1744 4.566759 TCGGAATTCGACAGATCATTTCAC 59.433 41.667 0.00 0.00 43.74 3.18
1529 1770 3.399440 ACTATTGCTGCCTGATCTAGC 57.601 47.619 0.00 0.00 37.93 3.42
1532 1773 2.422519 CCCAACTATTGCTGCCTGATCT 60.423 50.000 0.00 0.00 0.00 2.75
1538 1779 1.256812 AACACCCAACTATTGCTGCC 58.743 50.000 0.00 0.00 0.00 4.85
1732 2001 2.628657 CTGCCTAACCTCGTAGCCTTAT 59.371 50.000 0.00 0.00 0.00 1.73
1741 2010 1.067821 GACCATCTCTGCCTAACCTCG 59.932 57.143 0.00 0.00 0.00 4.63
1752 2021 7.363268 GGTTGCAAATCAATTTAGACCATCTCT 60.363 37.037 0.00 0.00 36.99 3.10
1768 2045 2.231964 TGGCTTGATCAGGTTGCAAATC 59.768 45.455 0.00 0.70 0.00 2.17
1773 2050 2.187073 CCTGGCTTGATCAGGTTGC 58.813 57.895 6.70 5.29 44.97 4.17
1778 2055 5.359009 ACACAATAATTCCTGGCTTGATCAG 59.641 40.000 0.00 0.00 0.00 2.90
1832 2121 6.238566 CCAGAACAAGCATATCACAATACCAG 60.239 42.308 0.00 0.00 0.00 4.00
1833 2122 5.589855 CCAGAACAAGCATATCACAATACCA 59.410 40.000 0.00 0.00 0.00 3.25
1834 2123 5.590259 ACCAGAACAAGCATATCACAATACC 59.410 40.000 0.00 0.00 0.00 2.73
1835 2124 6.094048 ACACCAGAACAAGCATATCACAATAC 59.906 38.462 0.00 0.00 0.00 1.89
1857 2154 6.313744 ACTTCCAACAACTTAAGCATACAC 57.686 37.500 1.29 0.00 0.00 2.90
1935 2235 6.603201 AGATAACATGTGAAATCGGAAATGGT 59.397 34.615 0.00 0.00 0.00 3.55
1943 2243 8.655970 TCTGTAACAAGATAACATGTGAAATCG 58.344 33.333 0.00 0.00 0.00 3.34
2052 2374 2.070262 ACCACGTAAGGCGAAGTAAC 57.930 50.000 0.00 0.00 44.77 2.50
2061 2383 2.172851 TAACCTGCAACCACGTAAGG 57.827 50.000 0.00 0.00 46.39 2.69
2327 2654 8.808092 AGACATCTAAGAGTAGCAAACTAAAGT 58.192 33.333 0.00 0.00 39.07 2.66
2351 2678 8.668353 GCATTCAGATAACATTTACTCAACAGA 58.332 33.333 0.00 0.00 0.00 3.41
2426 2754 2.409948 ACACCTGAGCATAAGCCTTC 57.590 50.000 0.00 0.00 43.56 3.46
2510 2838 1.788258 TCTTCAAGAGCTGCGACTTG 58.212 50.000 24.96 24.96 43.03 3.16
2637 2965 5.888105 ACAGATCATGTCAGCTAATTTTGC 58.112 37.500 0.00 0.00 37.75 3.68
2658 2986 3.373439 GCAACCAAAAAGCAATGTGAACA 59.627 39.130 0.00 0.00 0.00 3.18
2703 3101 9.703892 TGCAAGCAAACAACTATACAAATAAAT 57.296 25.926 0.00 0.00 0.00 1.40
2707 3105 9.357652 CTAATGCAAGCAAACAACTATACAAAT 57.642 29.630 0.00 0.00 0.00 2.32
2736 3134 6.466812 TGTATATGGACTTGCATATGACCTG 58.533 40.000 6.97 0.00 0.00 4.00
2737 3135 6.686484 TGTATATGGACTTGCATATGACCT 57.314 37.500 6.97 0.00 0.00 3.85
2759 3157 8.732413 ATCAACTTATGCGCAACATATAATTG 57.268 30.769 17.11 13.45 40.93 2.32
2761 3159 8.098220 TGATCAACTTATGCGCAACATATAAT 57.902 30.769 17.11 3.77 40.93 1.28
2762 3160 7.307930 CCTGATCAACTTATGCGCAACATATAA 60.308 37.037 17.11 7.26 40.93 0.98
2763 3161 6.147656 CCTGATCAACTTATGCGCAACATATA 59.852 38.462 17.11 0.00 40.93 0.86
2764 3162 5.049198 CCTGATCAACTTATGCGCAACATAT 60.049 40.000 17.11 0.00 40.93 1.78
2766 3164 3.065786 CCTGATCAACTTATGCGCAACAT 59.934 43.478 17.11 0.00 43.18 2.71
2768 3166 2.420022 ACCTGATCAACTTATGCGCAAC 59.580 45.455 17.11 0.00 0.00 4.17
2770 3168 2.401583 ACCTGATCAACTTATGCGCA 57.598 45.000 14.96 14.96 0.00 6.09
2771 3169 2.792542 GCAACCTGATCAACTTATGCGC 60.793 50.000 0.00 0.00 0.00 6.09
2772 3170 2.419673 TGCAACCTGATCAACTTATGCG 59.580 45.455 0.00 0.00 35.40 4.73
2773 3171 4.096833 TCATGCAACCTGATCAACTTATGC 59.903 41.667 0.00 4.44 0.00 3.14
2774 3172 5.220989 CCTCATGCAACCTGATCAACTTATG 60.221 44.000 0.00 0.00 0.00 1.90
2775 3173 4.885907 CCTCATGCAACCTGATCAACTTAT 59.114 41.667 0.00 0.00 0.00 1.73
2776 3174 4.019411 TCCTCATGCAACCTGATCAACTTA 60.019 41.667 0.00 0.00 0.00 2.24
2777 3175 3.087031 CCTCATGCAACCTGATCAACTT 58.913 45.455 0.00 0.00 0.00 2.66
3030 3431 6.711277 TGCATTAGTACATTGGAAGTCTCTT 58.289 36.000 0.00 0.00 0.00 2.85
3054 3455 2.289694 GGTCACAGCACACCATCTAGTT 60.290 50.000 0.00 0.00 32.33 2.24
3127 3529 6.261118 CAGCACAGCTTATTGAATTTAGGTC 58.739 40.000 0.00 0.00 36.40 3.85
3147 3549 2.603473 ACCTCCACGGTAGCAGCA 60.603 61.111 0.00 0.00 46.73 4.41
3214 3620 8.547967 TTCCAGTTTAACAGCTTACAGATAAG 57.452 34.615 0.00 0.00 40.83 1.73
3215 3621 8.946085 CATTCCAGTTTAACAGCTTACAGATAA 58.054 33.333 0.00 0.00 0.00 1.75
3216 3622 7.065803 GCATTCCAGTTTAACAGCTTACAGATA 59.934 37.037 0.00 0.00 0.00 1.98
3217 3623 6.127897 GCATTCCAGTTTAACAGCTTACAGAT 60.128 38.462 0.00 0.00 0.00 2.90
3218 3624 5.181245 GCATTCCAGTTTAACAGCTTACAGA 59.819 40.000 0.00 0.00 0.00 3.41
3219 3625 5.182001 AGCATTCCAGTTTAACAGCTTACAG 59.818 40.000 0.00 0.00 0.00 2.74
3220 3626 5.070001 AGCATTCCAGTTTAACAGCTTACA 58.930 37.500 0.00 0.00 0.00 2.41
3221 3627 5.629079 AGCATTCCAGTTTAACAGCTTAC 57.371 39.130 0.00 0.00 0.00 2.34
3222 3628 5.646360 GGTAGCATTCCAGTTTAACAGCTTA 59.354 40.000 0.00 0.00 32.70 3.09
3223 3629 4.459337 GGTAGCATTCCAGTTTAACAGCTT 59.541 41.667 0.00 0.00 32.70 3.74
3224 3630 4.010349 GGTAGCATTCCAGTTTAACAGCT 58.990 43.478 0.00 0.00 35.06 4.24
3225 3631 3.128764 GGGTAGCATTCCAGTTTAACAGC 59.871 47.826 0.00 0.00 0.00 4.40
3226 3632 4.396166 CAGGGTAGCATTCCAGTTTAACAG 59.604 45.833 0.00 0.00 0.00 3.16
3227 3633 4.331968 CAGGGTAGCATTCCAGTTTAACA 58.668 43.478 0.00 0.00 0.00 2.41
3228 3634 3.128764 GCAGGGTAGCATTCCAGTTTAAC 59.871 47.826 0.00 0.00 0.00 2.01
3229 3635 3.245087 TGCAGGGTAGCATTCCAGTTTAA 60.245 43.478 0.00 0.00 40.11 1.52
3230 3636 2.307392 TGCAGGGTAGCATTCCAGTTTA 59.693 45.455 0.00 0.00 40.11 2.01
3231 3637 1.075374 TGCAGGGTAGCATTCCAGTTT 59.925 47.619 0.00 0.00 40.11 2.66
3232 3638 0.698238 TGCAGGGTAGCATTCCAGTT 59.302 50.000 0.00 0.00 40.11 3.16
3233 3639 0.698238 TTGCAGGGTAGCATTCCAGT 59.302 50.000 0.00 0.00 45.19 4.00
3234 3640 1.679680 CATTGCAGGGTAGCATTCCAG 59.320 52.381 0.00 0.00 45.19 3.86
3235 3641 1.005805 ACATTGCAGGGTAGCATTCCA 59.994 47.619 0.00 0.00 45.19 3.53
3236 3642 1.767759 ACATTGCAGGGTAGCATTCC 58.232 50.000 0.00 0.00 45.19 3.01
3237 3643 4.136796 TCATACATTGCAGGGTAGCATTC 58.863 43.478 5.87 0.00 45.19 2.67
3238 3644 4.169059 TCATACATTGCAGGGTAGCATT 57.831 40.909 5.87 0.00 45.19 3.56
3239 3645 3.862877 TCATACATTGCAGGGTAGCAT 57.137 42.857 5.87 0.00 45.19 3.79
3240 3646 3.117926 ACATCATACATTGCAGGGTAGCA 60.118 43.478 5.87 0.00 43.99 3.49
3241 3647 3.480470 ACATCATACATTGCAGGGTAGC 58.520 45.455 5.87 0.00 0.00 3.58
3242 3648 6.054941 TGTTACATCATACATTGCAGGGTAG 58.945 40.000 5.87 0.22 0.00 3.18
3243 3649 5.995446 TGTTACATCATACATTGCAGGGTA 58.005 37.500 2.53 2.53 0.00 3.69
3244 3650 4.854173 TGTTACATCATACATTGCAGGGT 58.146 39.130 0.00 0.00 0.00 4.34
3245 3651 5.125257 TGTTGTTACATCATACATTGCAGGG 59.875 40.000 0.00 0.00 0.00 4.45
3246 3652 6.193514 TGTTGTTACATCATACATTGCAGG 57.806 37.500 0.00 0.00 0.00 4.85
3247 3653 7.474190 TCATGTTGTTACATCATACATTGCAG 58.526 34.615 8.38 0.00 43.07 4.41
3248 3654 7.388460 TCATGTTGTTACATCATACATTGCA 57.612 32.000 8.38 0.00 43.07 4.08
3249 3655 8.686397 TTTCATGTTGTTACATCATACATTGC 57.314 30.769 8.38 0.00 43.07 3.56
3253 3659 9.018582 TGGAATTTCATGTTGTTACATCATACA 57.981 29.630 8.38 0.00 43.07 2.29
3337 3969 9.656040 GATCAGACTATTCTCAAAGATGCATAT 57.344 33.333 0.00 0.00 0.00 1.78
3562 4259 7.513856 TGCTGAATTGGTACCTTATAGCATAA 58.486 34.615 19.93 3.39 34.14 1.90
3630 4356 2.990066 AGCCAGTAAGAAGGGAATCG 57.010 50.000 0.00 0.00 0.00 3.34
3655 4381 8.345565 GGAAGTGTCAAATCAATATGATGTACC 58.654 37.037 0.00 0.00 37.15 3.34
3656 4382 9.113838 AGGAAGTGTCAAATCAATATGATGTAC 57.886 33.333 0.00 0.00 37.15 2.90
3657 4383 9.685276 AAGGAAGTGTCAAATCAATATGATGTA 57.315 29.630 0.00 0.00 37.15 2.29
3658 4384 8.585471 AAGGAAGTGTCAAATCAATATGATGT 57.415 30.769 0.00 0.00 37.15 3.06
3659 4385 9.941664 GTAAGGAAGTGTCAAATCAATATGATG 57.058 33.333 0.00 0.00 37.15 3.07
3660 4386 9.911788 AGTAAGGAAGTGTCAAATCAATATGAT 57.088 29.630 0.00 0.00 39.09 2.45
3661 4387 9.166173 CAGTAAGGAAGTGTCAAATCAATATGA 57.834 33.333 0.00 0.00 0.00 2.15
3662 4388 8.400947 CCAGTAAGGAAGTGTCAAATCAATATG 58.599 37.037 0.00 0.00 41.22 1.78
3663 4389 7.067494 GCCAGTAAGGAAGTGTCAAATCAATAT 59.933 37.037 0.00 0.00 41.22 1.28
3664 4390 6.374333 GCCAGTAAGGAAGTGTCAAATCAATA 59.626 38.462 0.00 0.00 41.22 1.90
3665 4391 5.183904 GCCAGTAAGGAAGTGTCAAATCAAT 59.816 40.000 0.00 0.00 41.22 2.57
3666 4392 4.518970 GCCAGTAAGGAAGTGTCAAATCAA 59.481 41.667 0.00 0.00 41.22 2.57
3667 4393 4.072131 GCCAGTAAGGAAGTGTCAAATCA 58.928 43.478 0.00 0.00 41.22 2.57
3668 4394 4.327680 AGCCAGTAAGGAAGTGTCAAATC 58.672 43.478 0.00 0.00 41.22 2.17
3669 4395 4.373156 AGCCAGTAAGGAAGTGTCAAAT 57.627 40.909 0.00 0.00 41.22 2.32
3670 4396 3.857157 AGCCAGTAAGGAAGTGTCAAA 57.143 42.857 0.00 0.00 41.22 2.69
3671 4397 3.857157 AAGCCAGTAAGGAAGTGTCAA 57.143 42.857 0.00 0.00 41.22 3.18
3672 4398 3.476552 CAAAGCCAGTAAGGAAGTGTCA 58.523 45.455 0.00 0.00 41.22 3.58
3673 4399 2.226674 GCAAAGCCAGTAAGGAAGTGTC 59.773 50.000 0.00 0.00 41.22 3.67
3674 4400 2.230660 GCAAAGCCAGTAAGGAAGTGT 58.769 47.619 0.00 0.00 41.22 3.55
3675 4401 2.997485 GCAAAGCCAGTAAGGAAGTG 57.003 50.000 0.00 0.00 41.22 3.16
3686 4412 7.141539 ATCAATATGATGTACTGGCAAAGCCA 61.142 38.462 10.68 10.68 45.71 4.75
3687 4413 5.242393 ATCAATATGATGTACTGGCAAAGCC 59.758 40.000 0.00 0.00 41.76 4.35
3688 4414 5.756195 TCAATATGATGTACTGGCAAAGC 57.244 39.130 0.00 0.00 0.00 3.51
3689 4415 8.407832 TCAAATCAATATGATGTACTGGCAAAG 58.592 33.333 0.00 0.00 37.15 2.77
3690 4416 8.190122 GTCAAATCAATATGATGTACTGGCAAA 58.810 33.333 0.00 0.00 37.15 3.68
3691 4417 7.338957 TGTCAAATCAATATGATGTACTGGCAA 59.661 33.333 0.00 0.00 37.15 4.52
3692 4418 6.827762 TGTCAAATCAATATGATGTACTGGCA 59.172 34.615 0.00 0.00 37.15 4.92
3693 4419 7.012704 AGTGTCAAATCAATATGATGTACTGGC 59.987 37.037 0.00 0.00 37.15 4.85
3694 4420 8.442632 AGTGTCAAATCAATATGATGTACTGG 57.557 34.615 0.00 0.00 37.15 4.00
3695 4421 9.926751 GAAGTGTCAAATCAATATGATGTACTG 57.073 33.333 0.00 0.00 37.15 2.74
3696 4422 9.113838 GGAAGTGTCAAATCAATATGATGTACT 57.886 33.333 0.00 0.00 37.15 2.73
3697 4423 9.113838 AGGAAGTGTCAAATCAATATGATGTAC 57.886 33.333 0.00 0.00 37.15 2.90
3713 4439 6.061441 TGAAAGAAAGCATAAGGAAGTGTCA 58.939 36.000 0.00 0.00 0.00 3.58
3759 4485 5.525745 TGAAGCAGAAAACACGAATACTCAA 59.474 36.000 0.00 0.00 0.00 3.02
3760 4486 5.053811 TGAAGCAGAAAACACGAATACTCA 58.946 37.500 0.00 0.00 0.00 3.41
3775 4501 1.516161 GTGCACTCACATGAAGCAGA 58.484 50.000 10.32 0.00 42.66 4.26
3814 4540 0.701731 TGGTTTATCCCACCCAGGTG 59.298 55.000 10.00 10.00 45.02 4.00
3891 4625 0.967380 AGTAGGCAGCACCCATTTGC 60.967 55.000 0.00 0.00 43.34 3.68
3900 4634 0.464036 CGGGTTGATAGTAGGCAGCA 59.536 55.000 0.00 0.00 0.00 4.41
3902 4636 1.120530 ACCGGGTTGATAGTAGGCAG 58.879 55.000 6.32 0.00 0.00 4.85
3906 4640 4.400251 TCTGTTGTACCGGGTTGATAGTAG 59.600 45.833 4.31 0.00 0.00 2.57
3919 4653 6.591062 TGAATTATTACACCGTCTGTTGTACC 59.409 38.462 0.00 0.00 33.91 3.34
3921 4655 8.035984 TGATGAATTATTACACCGTCTGTTGTA 58.964 33.333 0.00 0.00 33.91 2.41
3931 4665 8.281212 ACCACTCTTTGATGAATTATTACACC 57.719 34.615 0.00 0.00 0.00 4.16
3967 4701 1.995484 CACGAGCGATGTTCACTGAAT 59.005 47.619 0.00 0.00 0.00 2.57
3983 4717 4.811908 TGATGAACGAAATTACTCCACGA 58.188 39.130 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.