Multiple sequence alignment - TraesCS5B01G221000

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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 TraesCS5B01G221000 chr5B 100.000 2655 0 0 1 2655 395677764 395675110 0.000000e+00 4903.0
1 TraesCS5B01G221000 chr5B 100.000 53 0 0 1138 1190 395676582 395676530 6.050000e-17 99.0
2 TraesCS5B01G221000 chr5B 100.000 53 0 0 1183 1235 395676627 395676575 6.050000e-17 99.0
3 TraesCS5B01G221000 chr7B 95.057 971 31 4 1183 2144 400625856 400624894 0.000000e+00 1511.0
4 TraesCS5B01G221000 chr7B 90.383 967 67 11 1196 2144 61273693 61274651 0.000000e+00 1247.0
5 TraesCS5B01G221000 chr7B 91.574 902 36 9 304 1198 400626664 400625796 0.000000e+00 1208.0
6 TraesCS5B01G221000 chr7B 86.395 860 70 11 301 1140 61272679 61273511 0.000000e+00 896.0
7 TraesCS5B01G221000 chr7B 93.548 527 30 4 2129 2655 512892051 512891529 0.000000e+00 782.0
8 TraesCS5B01G221000 chr7B 93.957 513 30 1 2143 2655 187080007 187080518 0.000000e+00 774.0
9 TraesCS5B01G221000 chr7B 93.007 286 20 0 1 286 523794150 523794435 4.090000e-113 418.0
10 TraesCS5B01G221000 chr1B 94.088 981 40 4 1178 2140 635780454 635781434 0.000000e+00 1474.0
11 TraesCS5B01G221000 chr1B 85.881 857 74 14 304 1140 113801270 113800441 0.000000e+00 869.0
12 TraesCS5B01G221000 chr1B 93.195 529 32 4 2128 2655 404462856 404462331 0.000000e+00 774.0
13 TraesCS5B01G221000 chr1B 88.387 620 31 9 286 888 635779816 635780411 0.000000e+00 708.0
14 TraesCS5B01G221000 chr1B 92.191 461 36 0 1681 2141 113799821 113799361 0.000000e+00 652.0
15 TraesCS5B01G221000 chr1B 82.439 615 60 25 1196 1789 113800259 113799672 6.600000e-136 494.0
16 TraesCS5B01G221000 chr1B 92.683 287 20 1 1 286 357447795 357447509 1.900000e-111 412.0
17 TraesCS5B01G221000 chr1B 92.308 286 21 1 1 286 619086213 619086497 3.180000e-109 405.0
18 TraesCS5B01G221000 chr1B 98.113 106 2 0 1093 1198 635780415 635780520 4.510000e-43 185.0
19 TraesCS5B01G221000 chr2D 92.396 960 42 9 1198 2141 584836712 584835768 0.000000e+00 1339.0
20 TraesCS5B01G221000 chr2D 83.639 709 69 25 445 1140 584837569 584836895 8.070000e-175 623.0
21 TraesCS5B01G221000 chr2D 100.000 46 0 0 1153 1198 584836712 584836667 4.710000e-13 86.1
22 TraesCS5B01G221000 chr3B 89.551 957 54 16 1201 2140 795282940 795282013 0.000000e+00 1171.0
23 TraesCS5B01G221000 chr3B 93.548 527 32 2 2129 2655 491216135 491215611 0.000000e+00 784.0
24 TraesCS5B01G221000 chr3B 94.152 513 29 1 2143 2655 487197204 487196693 0.000000e+00 780.0
25 TraesCS5B01G221000 chr3B 92.817 529 34 4 2128 2655 604976307 604976832 0.000000e+00 763.0
26 TraesCS5B01G221000 chr3B 85.477 723 68 14 428 1140 582974161 582973466 0.000000e+00 719.0
27 TraesCS5B01G221000 chr3B 85.875 623 55 16 304 921 795283555 795282961 1.340000e-177 632.0
28 TraesCS5B01G221000 chr3B 88.983 236 14 5 323 547 582974409 582974175 5.600000e-72 281.0
29 TraesCS5B01G221000 chr5A 90.487 883 54 8 1265 2141 355770901 355771759 0.000000e+00 1138.0
30 TraesCS5B01G221000 chr5A 83.697 871 87 25 290 1140 355769864 355770699 0.000000e+00 771.0
31 TraesCS5B01G221000 chr7A 90.524 802 50 10 1209 1993 109759588 109758796 0.000000e+00 1037.0
32 TraesCS5B01G221000 chr7A 87.048 857 64 16 304 1140 109760564 109759735 0.000000e+00 924.0
33 TraesCS5B01G221000 chr7A 93.651 63 4 0 643 705 109760050 109759988 7.820000e-16 95.3
34 TraesCS5B01G221000 chr4B 91.277 642 52 3 1501 2140 493801786 493801147 0.000000e+00 872.0
35 TraesCS5B01G221000 chr4B 94.358 514 27 2 2143 2655 371953761 371953249 0.000000e+00 787.0
36 TraesCS5B01G221000 chr4B 91.216 296 23 3 2 295 554102472 554102178 1.480000e-107 399.0
37 TraesCS5B01G221000 chr6D 84.375 864 87 26 301 1140 118741352 118742191 0.000000e+00 804.0
38 TraesCS5B01G221000 chr6D 85.185 621 42 21 1196 1789 118742372 118742969 2.280000e-165 592.0
39 TraesCS5B01G221000 chr6D 92.857 280 19 1 7 286 439060811 439060533 3.180000e-109 405.0
40 TraesCS5B01G221000 chr6D 97.917 48 1 0 1151 1198 118742372 118742419 1.690000e-12 84.2
41 TraesCS5B01G221000 chr5D 93.548 527 32 2 2129 2655 344709096 344709620 0.000000e+00 784.0
42 TraesCS5B01G221000 chr6B 93.169 527 33 3 2129 2655 387046906 387047429 0.000000e+00 771.0
43 TraesCS5B01G221000 chr6B 92.958 284 16 3 4 286 257853223 257853503 6.840000e-111 411.0
44 TraesCS5B01G221000 chr6B 92.334 287 20 2 1 286 301040086 301039801 8.850000e-110 407.0
45 TraesCS5B01G221000 chr2B 91.622 561 31 2 1587 2146 600997228 600996683 0.000000e+00 761.0
46 TraesCS5B01G221000 chr2B 92.933 283 20 0 1 283 500372563 500372845 1.900000e-111 412.0
47 TraesCS5B01G221000 chr2B 92.361 288 17 4 1 286 57702055 57702339 3.180000e-109 405.0
48 TraesCS5B01G221000 chr2B 90.837 251 12 6 304 544 600997472 600997223 2.550000e-85 326.0


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 TraesCS5B01G221000 chr5B 395675110 395677764 2654 True 1700.333333 4903 100.000000 1 2655 3 chr5B.!!$R1 2654
1 TraesCS5B01G221000 chr7B 400624894 400626664 1770 True 1359.500000 1511 93.315500 304 2144 2 chr7B.!!$R2 1840
2 TraesCS5B01G221000 chr7B 61272679 61274651 1972 False 1071.500000 1247 88.389000 301 2144 2 chr7B.!!$F3 1843
3 TraesCS5B01G221000 chr7B 512891529 512892051 522 True 782.000000 782 93.548000 2129 2655 1 chr7B.!!$R1 526
4 TraesCS5B01G221000 chr7B 187080007 187080518 511 False 774.000000 774 93.957000 2143 2655 1 chr7B.!!$F1 512
5 TraesCS5B01G221000 chr1B 635779816 635781434 1618 False 789.000000 1474 93.529333 286 2140 3 chr1B.!!$F2 1854
6 TraesCS5B01G221000 chr1B 404462331 404462856 525 True 774.000000 774 93.195000 2128 2655 1 chr1B.!!$R2 527
7 TraesCS5B01G221000 chr1B 113799361 113801270 1909 True 671.666667 869 86.837000 304 2141 3 chr1B.!!$R3 1837
8 TraesCS5B01G221000 chr2D 584835768 584837569 1801 True 682.700000 1339 92.011667 445 2141 3 chr2D.!!$R1 1696
9 TraesCS5B01G221000 chr3B 795282013 795283555 1542 True 901.500000 1171 87.713000 304 2140 2 chr3B.!!$R4 1836
10 TraesCS5B01G221000 chr3B 491215611 491216135 524 True 784.000000 784 93.548000 2129 2655 1 chr3B.!!$R2 526
11 TraesCS5B01G221000 chr3B 487196693 487197204 511 True 780.000000 780 94.152000 2143 2655 1 chr3B.!!$R1 512
12 TraesCS5B01G221000 chr3B 604976307 604976832 525 False 763.000000 763 92.817000 2128 2655 1 chr3B.!!$F1 527
13 TraesCS5B01G221000 chr3B 582973466 582974409 943 True 500.000000 719 87.230000 323 1140 2 chr3B.!!$R3 817
14 TraesCS5B01G221000 chr5A 355769864 355771759 1895 False 954.500000 1138 87.092000 290 2141 2 chr5A.!!$F1 1851
15 TraesCS5B01G221000 chr7A 109758796 109760564 1768 True 685.433333 1037 90.407667 304 1993 3 chr7A.!!$R1 1689
16 TraesCS5B01G221000 chr4B 493801147 493801786 639 True 872.000000 872 91.277000 1501 2140 1 chr4B.!!$R2 639
17 TraesCS5B01G221000 chr4B 371953249 371953761 512 True 787.000000 787 94.358000 2143 2655 1 chr4B.!!$R1 512
18 TraesCS5B01G221000 chr6D 118741352 118742969 1617 False 493.400000 804 89.159000 301 1789 3 chr6D.!!$F1 1488
19 TraesCS5B01G221000 chr5D 344709096 344709620 524 False 784.000000 784 93.548000 2129 2655 1 chr5D.!!$F1 526
20 TraesCS5B01G221000 chr6B 387046906 387047429 523 False 771.000000 771 93.169000 2129 2655 1 chr6B.!!$F2 526
21 TraesCS5B01G221000 chr2B 600996683 600997472 789 True 543.500000 761 91.229500 304 2146 2 chr2B.!!$R1 1842

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
702 897 0.03213 TACAGATGAAGATCGGCGCC 59.968 55.0 19.07 19.07 33.34 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1684 2092 4.154176 CAGCCCATGGAATATTGGAATCA 58.846 43.478 15.22 0.0 34.81 2.57 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
19 20 4.391869 CCGATGGGGAGCATCATG 57.608 61.111 0.00 0.00 38.47 3.07
20 21 1.303074 CCGATGGGGAGCATCATGG 60.303 63.158 0.00 0.00 38.47 3.66
21 22 1.756665 CGATGGGGAGCATCATGGA 59.243 57.895 0.00 0.00 36.25 3.41
22 23 0.109153 CGATGGGGAGCATCATGGAA 59.891 55.000 0.00 0.00 36.25 3.53
23 24 1.271762 CGATGGGGAGCATCATGGAAT 60.272 52.381 0.00 0.00 36.25 3.01
24 25 2.816712 CGATGGGGAGCATCATGGAATT 60.817 50.000 0.00 0.00 36.25 2.17
25 26 2.076207 TGGGGAGCATCATGGAATTG 57.924 50.000 0.00 0.00 36.25 2.32
26 27 1.335145 GGGGAGCATCATGGAATTGG 58.665 55.000 0.00 0.00 36.25 3.16
27 28 0.677842 GGGAGCATCATGGAATTGGC 59.322 55.000 0.00 0.00 36.25 4.52
28 29 0.313043 GGAGCATCATGGAATTGGCG 59.687 55.000 0.00 0.00 36.25 5.69
29 30 1.311859 GAGCATCATGGAATTGGCGA 58.688 50.000 0.00 0.00 33.17 5.54
30 31 1.884579 GAGCATCATGGAATTGGCGAT 59.115 47.619 0.00 0.00 33.17 4.58
31 32 1.611977 AGCATCATGGAATTGGCGATG 59.388 47.619 0.00 0.00 37.20 3.84
32 33 1.336517 GCATCATGGAATTGGCGATGG 60.337 52.381 0.00 0.00 35.18 3.51
33 34 2.232399 CATCATGGAATTGGCGATGGA 58.768 47.619 0.00 0.00 31.80 3.41
34 35 1.971481 TCATGGAATTGGCGATGGAG 58.029 50.000 0.00 0.00 0.00 3.86
35 36 1.490069 TCATGGAATTGGCGATGGAGA 59.510 47.619 0.00 0.00 0.00 3.71
36 37 2.107031 TCATGGAATTGGCGATGGAGAT 59.893 45.455 0.00 0.00 0.00 2.75
37 38 1.971481 TGGAATTGGCGATGGAGATG 58.029 50.000 0.00 0.00 0.00 2.90
38 39 1.212688 TGGAATTGGCGATGGAGATGT 59.787 47.619 0.00 0.00 0.00 3.06
39 40 1.605710 GGAATTGGCGATGGAGATGTG 59.394 52.381 0.00 0.00 0.00 3.21
40 41 2.292267 GAATTGGCGATGGAGATGTGT 58.708 47.619 0.00 0.00 0.00 3.72
41 42 2.425143 ATTGGCGATGGAGATGTGTT 57.575 45.000 0.00 0.00 0.00 3.32
42 43 1.452110 TTGGCGATGGAGATGTGTTG 58.548 50.000 0.00 0.00 0.00 3.33
43 44 0.392863 TGGCGATGGAGATGTGTTGG 60.393 55.000 0.00 0.00 0.00 3.77
44 45 0.392998 GGCGATGGAGATGTGTTGGT 60.393 55.000 0.00 0.00 0.00 3.67
45 46 0.729116 GCGATGGAGATGTGTTGGTG 59.271 55.000 0.00 0.00 0.00 4.17
46 47 1.675714 GCGATGGAGATGTGTTGGTGA 60.676 52.381 0.00 0.00 0.00 4.02
47 48 2.910199 CGATGGAGATGTGTTGGTGAT 58.090 47.619 0.00 0.00 0.00 3.06
48 49 2.610833 CGATGGAGATGTGTTGGTGATG 59.389 50.000 0.00 0.00 0.00 3.07
49 50 3.679639 CGATGGAGATGTGTTGGTGATGA 60.680 47.826 0.00 0.00 0.00 2.92
50 51 3.057969 TGGAGATGTGTTGGTGATGAC 57.942 47.619 0.00 0.00 0.00 3.06
51 52 2.002586 GGAGATGTGTTGGTGATGACG 58.997 52.381 0.00 0.00 0.00 4.35
52 53 2.353704 GGAGATGTGTTGGTGATGACGA 60.354 50.000 0.00 0.00 0.00 4.20
53 54 3.325870 GAGATGTGTTGGTGATGACGAA 58.674 45.455 0.00 0.00 0.00 3.85
54 55 3.329386 AGATGTGTTGGTGATGACGAAG 58.671 45.455 0.00 0.00 0.00 3.79
55 56 2.900716 TGTGTTGGTGATGACGAAGA 57.099 45.000 0.00 0.00 0.00 2.87
56 57 3.401033 TGTGTTGGTGATGACGAAGAT 57.599 42.857 0.00 0.00 0.00 2.40
57 58 3.325870 TGTGTTGGTGATGACGAAGATC 58.674 45.455 0.00 0.00 0.00 2.75
58 59 2.345641 GTGTTGGTGATGACGAAGATCG 59.654 50.000 0.00 0.00 46.93 3.69
59 60 2.230266 TGTTGGTGATGACGAAGATCGA 59.770 45.455 6.78 0.00 43.74 3.59
60 61 3.250744 GTTGGTGATGACGAAGATCGAA 58.749 45.455 6.78 0.00 43.74 3.71
61 62 3.150848 TGGTGATGACGAAGATCGAAG 57.849 47.619 6.78 0.00 43.74 3.79
62 63 2.752903 TGGTGATGACGAAGATCGAAGA 59.247 45.455 6.78 0.00 43.74 2.87
63 64 3.381590 TGGTGATGACGAAGATCGAAGAT 59.618 43.478 6.78 0.00 43.74 2.40
64 65 3.978217 GGTGATGACGAAGATCGAAGATC 59.022 47.826 6.78 2.02 43.74 2.75
65 66 3.978217 GTGATGACGAAGATCGAAGATCC 59.022 47.826 6.78 0.00 43.74 3.36
66 67 3.004839 TGATGACGAAGATCGAAGATCCC 59.995 47.826 6.78 0.00 43.74 3.85
67 68 1.681793 TGACGAAGATCGAAGATCCCC 59.318 52.381 6.78 0.00 43.74 4.81
68 69 1.000052 GACGAAGATCGAAGATCCCCC 60.000 57.143 6.78 0.00 43.74 5.40
69 70 1.333177 CGAAGATCGAAGATCCCCCT 58.667 55.000 6.43 0.00 43.74 4.79
70 71 1.271102 CGAAGATCGAAGATCCCCCTC 59.729 57.143 6.43 0.00 43.74 4.30
71 72 2.604139 GAAGATCGAAGATCCCCCTCT 58.396 52.381 6.43 0.00 45.12 3.69
72 73 2.302587 AGATCGAAGATCCCCCTCTC 57.697 55.000 6.43 0.00 45.12 3.20
73 74 1.203125 AGATCGAAGATCCCCCTCTCC 60.203 57.143 6.43 0.00 45.12 3.71
74 75 0.540830 ATCGAAGATCCCCCTCTCCG 60.541 60.000 0.00 0.00 45.12 4.63
75 76 2.203771 CGAAGATCCCCCTCTCCGG 61.204 68.421 0.00 0.00 0.00 5.14
76 77 1.233369 GAAGATCCCCCTCTCCGGA 59.767 63.158 2.93 2.93 33.16 5.14
77 78 0.830023 GAAGATCCCCCTCTCCGGAG 60.830 65.000 26.32 26.32 39.18 4.63
78 79 2.920384 GATCCCCCTCTCCGGAGC 60.920 72.222 27.39 6.13 38.21 4.70
79 80 4.565850 ATCCCCCTCTCCGGAGCC 62.566 72.222 27.39 0.00 38.21 4.70
84 85 3.009115 CCTCTCCGGAGCCCCAAA 61.009 66.667 27.39 7.39 38.21 3.28
85 86 2.269241 CTCTCCGGAGCCCCAAAC 59.731 66.667 27.39 0.00 32.43 2.93
86 87 3.665675 CTCTCCGGAGCCCCAAACG 62.666 68.421 27.39 0.19 32.43 3.60
90 91 4.016706 CGGAGCCCCAAACGGACT 62.017 66.667 0.00 0.00 0.00 3.85
91 92 2.046217 GGAGCCCCAAACGGACTC 60.046 66.667 0.00 0.00 0.00 3.36
92 93 2.046217 GAGCCCCAAACGGACTCC 60.046 66.667 0.00 0.00 0.00 3.85
93 94 2.852075 AGCCCCAAACGGACTCCA 60.852 61.111 0.00 0.00 0.00 3.86
94 95 2.359975 GCCCCAAACGGACTCCAG 60.360 66.667 0.00 0.00 0.00 3.86
95 96 2.890766 GCCCCAAACGGACTCCAGA 61.891 63.158 0.00 0.00 0.00 3.86
96 97 1.991230 CCCCAAACGGACTCCAGAT 59.009 57.895 0.00 0.00 0.00 2.90
97 98 0.107654 CCCCAAACGGACTCCAGATC 60.108 60.000 0.00 0.00 0.00 2.75
98 99 0.905357 CCCAAACGGACTCCAGATCT 59.095 55.000 0.00 0.00 0.00 2.75
99 100 2.108168 CCCAAACGGACTCCAGATCTA 58.892 52.381 0.00 0.00 0.00 1.98
100 101 2.101582 CCCAAACGGACTCCAGATCTAG 59.898 54.545 0.00 0.00 0.00 2.43
101 102 2.482142 CCAAACGGACTCCAGATCTAGC 60.482 54.545 0.00 0.00 0.00 3.42
102 103 1.404843 AACGGACTCCAGATCTAGCC 58.595 55.000 0.00 0.00 0.00 3.93
103 104 0.553819 ACGGACTCCAGATCTAGCCT 59.446 55.000 0.00 0.00 0.00 4.58
104 105 1.243902 CGGACTCCAGATCTAGCCTC 58.756 60.000 0.00 0.00 0.00 4.70
105 106 1.627864 GGACTCCAGATCTAGCCTCC 58.372 60.000 0.00 0.00 0.00 4.30
106 107 1.627864 GACTCCAGATCTAGCCTCCC 58.372 60.000 0.00 0.00 0.00 4.30
107 108 0.178975 ACTCCAGATCTAGCCTCCCG 60.179 60.000 0.00 0.00 0.00 5.14
108 109 0.111446 CTCCAGATCTAGCCTCCCGA 59.889 60.000 0.00 0.00 0.00 5.14
109 110 0.780637 TCCAGATCTAGCCTCCCGAT 59.219 55.000 0.00 0.00 0.00 4.18
110 111 0.894141 CCAGATCTAGCCTCCCGATG 59.106 60.000 0.00 0.00 0.00 3.84
111 112 1.548809 CCAGATCTAGCCTCCCGATGA 60.549 57.143 0.00 0.00 0.00 2.92
112 113 2.242926 CAGATCTAGCCTCCCGATGAA 58.757 52.381 0.00 0.00 0.00 2.57
113 114 2.230992 CAGATCTAGCCTCCCGATGAAG 59.769 54.545 0.00 0.00 0.00 3.02
114 115 2.109128 AGATCTAGCCTCCCGATGAAGA 59.891 50.000 0.00 0.00 0.00 2.87
115 116 2.454336 TCTAGCCTCCCGATGAAGAA 57.546 50.000 0.00 0.00 0.00 2.52
116 117 2.032620 TCTAGCCTCCCGATGAAGAAC 58.967 52.381 0.00 0.00 0.00 3.01
117 118 1.757118 CTAGCCTCCCGATGAAGAACA 59.243 52.381 0.00 0.00 0.00 3.18
118 119 0.539051 AGCCTCCCGATGAAGAACAG 59.461 55.000 0.00 0.00 0.00 3.16
119 120 0.462759 GCCTCCCGATGAAGAACAGG 60.463 60.000 0.00 0.00 0.00 4.00
120 121 1.195115 CCTCCCGATGAAGAACAGGA 58.805 55.000 0.00 0.00 0.00 3.86
121 122 1.137872 CCTCCCGATGAAGAACAGGAG 59.862 57.143 0.00 0.00 37.86 3.69
122 123 2.103373 CTCCCGATGAAGAACAGGAGA 58.897 52.381 0.00 0.00 39.40 3.71
123 124 2.697751 CTCCCGATGAAGAACAGGAGAT 59.302 50.000 0.00 0.00 39.40 2.75
124 125 2.432146 TCCCGATGAAGAACAGGAGATG 59.568 50.000 0.00 0.00 0.00 2.90
125 126 2.484417 CCCGATGAAGAACAGGAGATGG 60.484 54.545 0.00 0.00 0.00 3.51
126 127 2.208431 CGATGAAGAACAGGAGATGGC 58.792 52.381 0.00 0.00 0.00 4.40
127 128 2.208431 GATGAAGAACAGGAGATGGCG 58.792 52.381 0.00 0.00 0.00 5.69
128 129 0.250234 TGAAGAACAGGAGATGGCGG 59.750 55.000 0.00 0.00 0.00 6.13
129 130 1.078143 AAGAACAGGAGATGGCGGC 60.078 57.895 0.00 0.00 0.00 6.53
130 131 1.841302 AAGAACAGGAGATGGCGGCA 61.841 55.000 16.34 16.34 0.00 5.69
131 132 1.817099 GAACAGGAGATGGCGGCAG 60.817 63.158 19.29 4.81 0.00 4.85
132 133 3.984193 AACAGGAGATGGCGGCAGC 62.984 63.158 20.74 20.74 44.18 5.25
133 134 4.172512 CAGGAGATGGCGGCAGCT 62.173 66.667 30.93 30.93 44.37 4.24
134 135 3.859414 AGGAGATGGCGGCAGCTC 61.859 66.667 39.74 39.74 44.37 4.09
144 145 3.749064 GGCAGCTCCGTCTCGTGA 61.749 66.667 0.00 0.00 0.00 4.35
145 146 2.258591 GCAGCTCCGTCTCGTGAA 59.741 61.111 0.00 0.00 0.00 3.18
146 147 1.372997 GCAGCTCCGTCTCGTGAAA 60.373 57.895 0.00 0.00 0.00 2.69
147 148 1.618640 GCAGCTCCGTCTCGTGAAAC 61.619 60.000 0.00 0.00 0.00 2.78
148 149 0.318699 CAGCTCCGTCTCGTGAAACA 60.319 55.000 0.00 0.00 35.74 2.83
149 150 0.318784 AGCTCCGTCTCGTGAAACAC 60.319 55.000 0.00 0.00 35.74 3.32
165 166 6.543736 GTGAAACACGATAATTCTTTCTCCC 58.456 40.000 0.00 0.00 36.32 4.30
166 167 6.371825 GTGAAACACGATAATTCTTTCTCCCT 59.628 38.462 0.00 0.00 36.32 4.20
167 168 6.371548 TGAAACACGATAATTCTTTCTCCCTG 59.628 38.462 0.00 0.00 0.00 4.45
168 169 5.677319 ACACGATAATTCTTTCTCCCTGA 57.323 39.130 0.00 0.00 0.00 3.86
169 170 6.240549 ACACGATAATTCTTTCTCCCTGAT 57.759 37.500 0.00 0.00 0.00 2.90
170 171 6.653989 ACACGATAATTCTTTCTCCCTGATT 58.346 36.000 0.00 0.00 0.00 2.57
171 172 7.112779 ACACGATAATTCTTTCTCCCTGATTT 58.887 34.615 0.00 0.00 0.00 2.17
172 173 7.066284 ACACGATAATTCTTTCTCCCTGATTTG 59.934 37.037 0.00 0.00 0.00 2.32
173 174 7.066284 CACGATAATTCTTTCTCCCTGATTTGT 59.934 37.037 0.00 0.00 0.00 2.83
174 175 7.611855 ACGATAATTCTTTCTCCCTGATTTGTT 59.388 33.333 0.00 0.00 0.00 2.83
175 176 8.462016 CGATAATTCTTTCTCCCTGATTTGTTT 58.538 33.333 0.00 0.00 0.00 2.83
178 179 8.667076 AATTCTTTCTCCCTGATTTGTTTTTG 57.333 30.769 0.00 0.00 0.00 2.44
179 180 7.416964 TTCTTTCTCCCTGATTTGTTTTTGA 57.583 32.000 0.00 0.00 0.00 2.69
180 181 7.416964 TCTTTCTCCCTGATTTGTTTTTGAA 57.583 32.000 0.00 0.00 0.00 2.69
181 182 7.846066 TCTTTCTCCCTGATTTGTTTTTGAAA 58.154 30.769 0.00 0.00 0.00 2.69
182 183 8.317679 TCTTTCTCCCTGATTTGTTTTTGAAAA 58.682 29.630 0.00 0.00 0.00 2.29
183 184 9.112725 CTTTCTCCCTGATTTGTTTTTGAAAAT 57.887 29.630 0.00 0.00 0.00 1.82
186 187 9.709495 TCTCCCTGATTTGTTTTTGAAAATATG 57.291 29.630 0.00 0.00 0.00 1.78
187 188 8.845413 TCCCTGATTTGTTTTTGAAAATATGG 57.155 30.769 0.00 0.00 0.00 2.74
188 189 8.435982 TCCCTGATTTGTTTTTGAAAATATGGT 58.564 29.630 0.00 0.00 0.00 3.55
189 190 9.717942 CCCTGATTTGTTTTTGAAAATATGGTA 57.282 29.630 0.00 0.00 0.00 3.25
203 204 8.714179 TGAAAATATGGTATTTTATAGCGTCGG 58.286 33.333 7.45 0.00 32.03 4.79
204 205 8.611654 AAAATATGGTATTTTATAGCGTCGGT 57.388 30.769 1.19 1.19 30.30 4.69
205 206 8.611654 AAATATGGTATTTTATAGCGTCGGTT 57.388 30.769 0.65 0.00 0.00 4.44
206 207 8.611654 AATATGGTATTTTATAGCGTCGGTTT 57.388 30.769 0.65 0.00 0.00 3.27
207 208 5.721876 TGGTATTTTATAGCGTCGGTTTG 57.278 39.130 0.65 0.00 0.00 2.93
208 209 5.417811 TGGTATTTTATAGCGTCGGTTTGA 58.582 37.500 0.65 0.00 0.00 2.69
209 210 5.521010 TGGTATTTTATAGCGTCGGTTTGAG 59.479 40.000 0.65 0.00 0.00 3.02
210 211 5.050567 GGTATTTTATAGCGTCGGTTTGAGG 60.051 44.000 0.65 0.00 35.56 3.86
211 212 2.589798 TTATAGCGTCGGTTTGAGGG 57.410 50.000 0.65 0.00 33.05 4.30
212 213 1.477553 TATAGCGTCGGTTTGAGGGT 58.522 50.000 0.65 0.00 44.60 4.34
213 214 0.175073 ATAGCGTCGGTTTGAGGGTC 59.825 55.000 0.65 0.00 41.84 4.46
214 215 1.180456 TAGCGTCGGTTTGAGGGTCA 61.180 55.000 0.65 0.00 41.84 4.02
215 216 2.027625 GCGTCGGTTTGAGGGTCAG 61.028 63.158 0.00 0.00 33.05 3.51
216 217 2.027625 CGTCGGTTTGAGGGTCAGC 61.028 63.158 0.00 0.00 0.00 4.26
217 218 2.027625 GTCGGTTTGAGGGTCAGCG 61.028 63.158 0.00 0.00 0.00 5.18
218 219 2.742372 CGGTTTGAGGGTCAGCGG 60.742 66.667 0.00 0.00 0.00 5.52
219 220 2.359975 GGTTTGAGGGTCAGCGGG 60.360 66.667 0.00 0.00 0.00 6.13
220 221 2.359975 GTTTGAGGGTCAGCGGGG 60.360 66.667 0.00 0.00 0.00 5.73
221 222 4.344865 TTTGAGGGTCAGCGGGGC 62.345 66.667 0.00 0.00 0.00 5.80
426 435 1.746171 CGGTCTGATCGGTCCTACTGA 60.746 57.143 14.76 0.00 37.97 3.41
533 688 0.101399 CCTCCTCACCTCACGATTCG 59.899 60.000 4.14 4.14 0.00 3.34
544 699 1.666553 ACGATTCGCAGGAACGCAA 60.667 52.632 5.86 0.00 34.37 4.85
689 884 4.547367 GGCGCGCCCCTTACAGAT 62.547 66.667 39.89 0.00 0.00 2.90
690 885 3.272334 GCGCGCCCCTTACAGATG 61.272 66.667 23.24 0.00 0.00 2.90
691 886 2.499205 CGCGCCCCTTACAGATGA 59.501 61.111 0.00 0.00 0.00 2.92
692 887 1.153449 CGCGCCCCTTACAGATGAA 60.153 57.895 0.00 0.00 0.00 2.57
693 888 1.154205 CGCGCCCCTTACAGATGAAG 61.154 60.000 0.00 0.00 0.00 3.02
694 889 0.178068 GCGCCCCTTACAGATGAAGA 59.822 55.000 0.00 0.00 0.00 2.87
695 890 1.202698 GCGCCCCTTACAGATGAAGAT 60.203 52.381 0.00 0.00 0.00 2.40
696 891 2.760374 CGCCCCTTACAGATGAAGATC 58.240 52.381 0.00 0.00 0.00 2.75
697 892 2.760374 GCCCCTTACAGATGAAGATCG 58.240 52.381 0.00 0.00 33.34 3.69
698 893 2.548920 GCCCCTTACAGATGAAGATCGG 60.549 54.545 0.00 0.00 33.34 4.18
699 894 2.548920 CCCCTTACAGATGAAGATCGGC 60.549 54.545 0.00 0.00 33.34 5.54
700 895 2.398498 CCTTACAGATGAAGATCGGCG 58.602 52.381 0.00 0.00 33.34 6.46
701 896 1.789464 CTTACAGATGAAGATCGGCGC 59.211 52.381 0.00 0.00 33.34 6.53
702 897 0.032130 TACAGATGAAGATCGGCGCC 59.968 55.000 19.07 19.07 33.34 6.53
703 898 1.958205 CAGATGAAGATCGGCGCCC 60.958 63.158 23.46 7.02 33.34 6.13
704 899 2.666526 GATGAAGATCGGCGCCCC 60.667 66.667 23.46 10.66 0.00 5.80
705 900 4.256180 ATGAAGATCGGCGCCCCC 62.256 66.667 23.46 10.25 0.00 5.40
1041 1242 0.911769 TCCATCACCACTCATCACCC 59.088 55.000 0.00 0.00 0.00 4.61
1044 1245 0.253347 ATCACCACTCATCACCCCCT 60.253 55.000 0.00 0.00 0.00 4.79
1075 1276 2.430921 CTGTTCGTCGGCTCGCTT 60.431 61.111 0.00 0.00 0.00 4.68
1203 1576 8.623903 TGTATTATTGCTATCTGCTCTTTTTGG 58.376 33.333 0.00 0.00 43.37 3.28
1204 1577 7.651027 ATTATTGCTATCTGCTCTTTTTGGT 57.349 32.000 0.00 0.00 43.37 3.67
1205 1578 5.990120 ATTGCTATCTGCTCTTTTTGGTT 57.010 34.783 0.00 0.00 43.37 3.67
1206 1579 5.789643 TTGCTATCTGCTCTTTTTGGTTT 57.210 34.783 0.00 0.00 43.37 3.27
1207 1580 5.789643 TGCTATCTGCTCTTTTTGGTTTT 57.210 34.783 0.00 0.00 43.37 2.43
1208 1581 6.160576 TGCTATCTGCTCTTTTTGGTTTTT 57.839 33.333 0.00 0.00 43.37 1.94
1209 1582 7.283625 TGCTATCTGCTCTTTTTGGTTTTTA 57.716 32.000 0.00 0.00 43.37 1.52
1210 1583 7.895759 TGCTATCTGCTCTTTTTGGTTTTTAT 58.104 30.769 0.00 0.00 43.37 1.40
1211 1584 8.028938 TGCTATCTGCTCTTTTTGGTTTTTATC 58.971 33.333 0.00 0.00 43.37 1.75
1212 1585 8.028938 GCTATCTGCTCTTTTTGGTTTTTATCA 58.971 33.333 0.00 0.00 38.95 2.15
1215 1588 8.592105 TCTGCTCTTTTTGGTTTTTATCATTG 57.408 30.769 0.00 0.00 0.00 2.82
1216 1589 8.203485 TCTGCTCTTTTTGGTTTTTATCATTGT 58.797 29.630 0.00 0.00 0.00 2.71
1217 1590 8.364129 TGCTCTTTTTGGTTTTTATCATTGTC 57.636 30.769 0.00 0.00 0.00 3.18
1218 1591 7.984050 TGCTCTTTTTGGTTTTTATCATTGTCA 59.016 29.630 0.00 0.00 0.00 3.58
1219 1592 8.825745 GCTCTTTTTGGTTTTTATCATTGTCAA 58.174 29.630 0.00 0.00 0.00 3.18
1588 1979 0.251209 GGGACCAGGTGAAGGGAAAC 60.251 60.000 0.00 0.00 0.00 2.78
1667 2075 4.222145 TCAAGTACTAAGTGATGGTGGTCC 59.778 45.833 0.00 0.00 0.00 4.46
1684 2092 1.066257 CCGCTGTTTGCTGCTTGTT 59.934 52.632 0.00 0.00 40.11 2.83
1902 2313 8.988064 TTACTTTGTGTCAGATATGACTCTTC 57.012 34.615 20.42 9.49 39.41 2.87
2041 2473 8.631480 AGACCGAATAGTTAAGAACCAAAAAT 57.369 30.769 0.00 0.00 0.00 1.82
2254 2687 6.817765 TTCCGAGAACTTTTATTTCTGCAT 57.182 33.333 0.00 0.00 33.30 3.96
2391 2825 2.496470 GTTGGAGACGTATCAACTCCCT 59.504 50.000 12.92 0.00 46.57 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.605257 CAATTCCATGATGCTCCCCAT 58.395 47.619 0.00 0.00 36.70 4.00
6 7 1.411930 CCAATTCCATGATGCTCCCCA 60.412 52.381 0.00 0.00 0.00 4.96
7 8 1.335145 CCAATTCCATGATGCTCCCC 58.665 55.000 0.00 0.00 0.00 4.81
8 9 0.677842 GCCAATTCCATGATGCTCCC 59.322 55.000 0.00 0.00 0.00 4.30
9 10 0.313043 CGCCAATTCCATGATGCTCC 59.687 55.000 0.00 0.00 0.00 4.70
10 11 1.311859 TCGCCAATTCCATGATGCTC 58.688 50.000 0.00 0.00 0.00 4.26
11 12 1.611977 CATCGCCAATTCCATGATGCT 59.388 47.619 0.00 0.00 31.15 3.79
12 13 1.336517 CCATCGCCAATTCCATGATGC 60.337 52.381 0.00 0.00 36.09 3.91
13 14 2.228103 CTCCATCGCCAATTCCATGATG 59.772 50.000 0.00 0.00 36.93 3.07
14 15 2.107031 TCTCCATCGCCAATTCCATGAT 59.893 45.455 0.00 0.00 0.00 2.45
15 16 1.490069 TCTCCATCGCCAATTCCATGA 59.510 47.619 0.00 0.00 0.00 3.07
16 17 1.971481 TCTCCATCGCCAATTCCATG 58.029 50.000 0.00 0.00 0.00 3.66
17 18 2.158564 ACATCTCCATCGCCAATTCCAT 60.159 45.455 0.00 0.00 0.00 3.41
18 19 1.212688 ACATCTCCATCGCCAATTCCA 59.787 47.619 0.00 0.00 0.00 3.53
19 20 1.605710 CACATCTCCATCGCCAATTCC 59.394 52.381 0.00 0.00 0.00 3.01
20 21 2.292267 ACACATCTCCATCGCCAATTC 58.708 47.619 0.00 0.00 0.00 2.17
21 22 2.424601 CAACACATCTCCATCGCCAATT 59.575 45.455 0.00 0.00 0.00 2.32
22 23 2.019249 CAACACATCTCCATCGCCAAT 58.981 47.619 0.00 0.00 0.00 3.16
23 24 1.452110 CAACACATCTCCATCGCCAA 58.548 50.000 0.00 0.00 0.00 4.52
24 25 0.392863 CCAACACATCTCCATCGCCA 60.393 55.000 0.00 0.00 0.00 5.69
25 26 0.392998 ACCAACACATCTCCATCGCC 60.393 55.000 0.00 0.00 0.00 5.54
26 27 0.729116 CACCAACACATCTCCATCGC 59.271 55.000 0.00 0.00 0.00 4.58
27 28 2.385013 TCACCAACACATCTCCATCG 57.615 50.000 0.00 0.00 0.00 3.84
28 29 3.624861 GTCATCACCAACACATCTCCATC 59.375 47.826 0.00 0.00 0.00 3.51
29 30 3.614092 GTCATCACCAACACATCTCCAT 58.386 45.455 0.00 0.00 0.00 3.41
30 31 2.612721 CGTCATCACCAACACATCTCCA 60.613 50.000 0.00 0.00 0.00 3.86
31 32 2.002586 CGTCATCACCAACACATCTCC 58.997 52.381 0.00 0.00 0.00 3.71
32 33 2.959516 TCGTCATCACCAACACATCTC 58.040 47.619 0.00 0.00 0.00 2.75
33 34 3.006859 TCTTCGTCATCACCAACACATCT 59.993 43.478 0.00 0.00 0.00 2.90
34 35 3.325870 TCTTCGTCATCACCAACACATC 58.674 45.455 0.00 0.00 0.00 3.06
35 36 3.401033 TCTTCGTCATCACCAACACAT 57.599 42.857 0.00 0.00 0.00 3.21
36 37 2.900716 TCTTCGTCATCACCAACACA 57.099 45.000 0.00 0.00 0.00 3.72
37 38 2.345641 CGATCTTCGTCATCACCAACAC 59.654 50.000 0.00 0.00 34.72 3.32
38 39 2.230266 TCGATCTTCGTCATCACCAACA 59.770 45.455 0.00 0.00 41.35 3.33
39 40 2.876091 TCGATCTTCGTCATCACCAAC 58.124 47.619 0.00 0.00 41.35 3.77
40 41 3.192633 TCTTCGATCTTCGTCATCACCAA 59.807 43.478 0.00 0.00 41.35 3.67
41 42 2.752903 TCTTCGATCTTCGTCATCACCA 59.247 45.455 0.00 0.00 41.35 4.17
42 43 3.422417 TCTTCGATCTTCGTCATCACC 57.578 47.619 0.00 0.00 41.35 4.02
43 44 3.978217 GGATCTTCGATCTTCGTCATCAC 59.022 47.826 4.10 0.00 41.35 3.06
44 45 3.004839 GGGATCTTCGATCTTCGTCATCA 59.995 47.826 4.10 0.00 41.35 3.07
45 46 3.570559 GGGATCTTCGATCTTCGTCATC 58.429 50.000 4.10 0.00 41.35 2.92
46 47 2.297597 GGGGATCTTCGATCTTCGTCAT 59.702 50.000 4.10 0.00 41.35 3.06
47 48 1.681793 GGGGATCTTCGATCTTCGTCA 59.318 52.381 4.10 0.00 41.35 4.35
48 49 1.000052 GGGGGATCTTCGATCTTCGTC 60.000 57.143 4.10 0.00 41.35 4.20
49 50 1.041437 GGGGGATCTTCGATCTTCGT 58.959 55.000 4.10 0.00 41.35 3.85
50 51 1.271102 GAGGGGGATCTTCGATCTTCG 59.729 57.143 4.10 0.00 42.10 3.79
51 52 2.560981 GAGAGGGGGATCTTCGATCTTC 59.439 54.545 4.10 0.00 0.00 2.87
52 53 2.604139 GAGAGGGGGATCTTCGATCTT 58.396 52.381 4.10 0.00 0.00 2.40
53 54 1.203125 GGAGAGGGGGATCTTCGATCT 60.203 57.143 4.10 0.00 0.00 2.75
54 55 1.262417 GGAGAGGGGGATCTTCGATC 58.738 60.000 0.00 0.00 0.00 3.69
55 56 3.466714 GGAGAGGGGGATCTTCGAT 57.533 57.895 0.00 0.00 0.00 3.59
57 58 2.203771 CCGGAGAGGGGGATCTTCG 61.204 68.421 0.00 0.00 46.04 3.79
58 59 0.830023 CTCCGGAGAGGGGGATCTTC 60.830 65.000 28.21 0.00 41.52 2.87
59 60 1.234529 CTCCGGAGAGGGGGATCTT 59.765 63.158 28.21 0.00 41.52 2.40
60 61 2.939298 CTCCGGAGAGGGGGATCT 59.061 66.667 28.21 0.00 41.52 2.75
61 62 2.920384 GCTCCGGAGAGGGGGATC 60.920 72.222 35.69 10.76 42.26 3.36
62 63 4.565850 GGCTCCGGAGAGGGGGAT 62.566 72.222 35.69 0.00 42.26 3.85
67 68 3.009115 TTTGGGGCTCCGGAGAGG 61.009 66.667 35.69 10.61 40.79 3.69
68 69 2.269241 GTTTGGGGCTCCGGAGAG 59.731 66.667 35.69 11.46 43.57 3.20
69 70 3.702048 CGTTTGGGGCTCCGGAGA 61.702 66.667 35.69 11.50 35.24 3.71
70 71 4.778143 CCGTTTGGGGCTCCGGAG 62.778 72.222 27.83 27.83 43.01 4.63
77 78 2.198304 ATCTGGAGTCCGTTTGGGGC 62.198 60.000 4.30 0.00 42.41 5.80
78 79 0.107654 GATCTGGAGTCCGTTTGGGG 60.108 60.000 4.30 0.00 36.01 4.96
79 80 0.905357 AGATCTGGAGTCCGTTTGGG 59.095 55.000 4.30 0.00 35.24 4.12
80 81 2.482142 GCTAGATCTGGAGTCCGTTTGG 60.482 54.545 10.75 0.00 0.00 3.28
81 82 2.482142 GGCTAGATCTGGAGTCCGTTTG 60.482 54.545 10.75 0.00 0.00 2.93
82 83 1.757699 GGCTAGATCTGGAGTCCGTTT 59.242 52.381 10.75 0.00 0.00 3.60
83 84 1.063567 AGGCTAGATCTGGAGTCCGTT 60.064 52.381 10.75 0.00 0.00 4.44
84 85 0.553819 AGGCTAGATCTGGAGTCCGT 59.446 55.000 10.75 0.00 0.00 4.69
85 86 1.243902 GAGGCTAGATCTGGAGTCCG 58.756 60.000 10.75 0.00 0.00 4.79
86 87 1.627864 GGAGGCTAGATCTGGAGTCC 58.372 60.000 10.75 10.45 0.00 3.85
87 88 1.627864 GGGAGGCTAGATCTGGAGTC 58.372 60.000 10.75 5.01 0.00 3.36
88 89 0.178975 CGGGAGGCTAGATCTGGAGT 60.179 60.000 10.75 0.00 0.00 3.85
89 90 0.111446 TCGGGAGGCTAGATCTGGAG 59.889 60.000 10.75 0.00 0.00 3.86
90 91 0.780637 ATCGGGAGGCTAGATCTGGA 59.219 55.000 10.75 0.00 0.00 3.86
91 92 0.894141 CATCGGGAGGCTAGATCTGG 59.106 60.000 5.18 2.94 0.00 3.86
92 93 1.916506 TCATCGGGAGGCTAGATCTG 58.083 55.000 5.18 0.00 0.00 2.90
93 94 2.109128 TCTTCATCGGGAGGCTAGATCT 59.891 50.000 0.00 0.00 0.00 2.75
94 95 2.520069 TCTTCATCGGGAGGCTAGATC 58.480 52.381 0.00 0.00 0.00 2.75
95 96 2.630580 GTTCTTCATCGGGAGGCTAGAT 59.369 50.000 0.00 0.00 0.00 1.98
96 97 2.032620 GTTCTTCATCGGGAGGCTAGA 58.967 52.381 0.00 0.00 0.00 2.43
97 98 1.757118 TGTTCTTCATCGGGAGGCTAG 59.243 52.381 0.00 0.00 0.00 3.42
98 99 1.757118 CTGTTCTTCATCGGGAGGCTA 59.243 52.381 0.00 0.00 0.00 3.93
99 100 0.539051 CTGTTCTTCATCGGGAGGCT 59.461 55.000 0.00 0.00 0.00 4.58
100 101 0.462759 CCTGTTCTTCATCGGGAGGC 60.463 60.000 0.00 0.00 32.26 4.70
101 102 1.195115 TCCTGTTCTTCATCGGGAGG 58.805 55.000 0.00 0.00 34.60 4.30
102 103 2.593346 CTCCTGTTCTTCATCGGGAG 57.407 55.000 5.78 5.78 46.40 4.30
103 104 2.231716 TCTCCTGTTCTTCATCGGGA 57.768 50.000 0.00 0.00 37.52 5.14
104 105 2.484417 CCATCTCCTGTTCTTCATCGGG 60.484 54.545 0.00 0.00 0.00 5.14
105 106 2.831333 CCATCTCCTGTTCTTCATCGG 58.169 52.381 0.00 0.00 0.00 4.18
106 107 2.208431 GCCATCTCCTGTTCTTCATCG 58.792 52.381 0.00 0.00 0.00 3.84
107 108 2.208431 CGCCATCTCCTGTTCTTCATC 58.792 52.381 0.00 0.00 0.00 2.92
108 109 1.134280 CCGCCATCTCCTGTTCTTCAT 60.134 52.381 0.00 0.00 0.00 2.57
109 110 0.250234 CCGCCATCTCCTGTTCTTCA 59.750 55.000 0.00 0.00 0.00 3.02
110 111 1.092345 GCCGCCATCTCCTGTTCTTC 61.092 60.000 0.00 0.00 0.00 2.87
111 112 1.078143 GCCGCCATCTCCTGTTCTT 60.078 57.895 0.00 0.00 0.00 2.52
112 113 2.249413 CTGCCGCCATCTCCTGTTCT 62.249 60.000 0.00 0.00 0.00 3.01
113 114 1.817099 CTGCCGCCATCTCCTGTTC 60.817 63.158 0.00 0.00 0.00 3.18
114 115 2.270205 CTGCCGCCATCTCCTGTT 59.730 61.111 0.00 0.00 0.00 3.16
115 116 4.479993 GCTGCCGCCATCTCCTGT 62.480 66.667 0.00 0.00 0.00 4.00
116 117 4.172512 AGCTGCCGCCATCTCCTG 62.173 66.667 0.00 0.00 36.60 3.86
117 118 3.859414 GAGCTGCCGCCATCTCCT 61.859 66.667 0.00 0.00 36.60 3.69
118 119 4.925861 GGAGCTGCCGCCATCTCC 62.926 72.222 0.00 0.00 44.46 3.71
127 128 2.765250 TTTCACGAGACGGAGCTGCC 62.765 60.000 0.00 0.00 0.00 4.85
128 129 1.372997 TTTCACGAGACGGAGCTGC 60.373 57.895 0.00 0.00 0.00 5.25
129 130 0.318699 TGTTTCACGAGACGGAGCTG 60.319 55.000 0.00 0.00 0.00 4.24
130 131 0.318784 GTGTTTCACGAGACGGAGCT 60.319 55.000 0.00 0.00 0.00 4.09
131 132 2.142641 GTGTTTCACGAGACGGAGC 58.857 57.895 0.00 0.00 0.00 4.70
141 142 6.371825 AGGGAGAAAGAATTATCGTGTTTCAC 59.628 38.462 0.00 0.00 30.92 3.18
142 143 6.371548 CAGGGAGAAAGAATTATCGTGTTTCA 59.628 38.462 0.00 0.00 30.92 2.69
143 144 6.594159 TCAGGGAGAAAGAATTATCGTGTTTC 59.406 38.462 0.00 0.00 0.00 2.78
144 145 6.472887 TCAGGGAGAAAGAATTATCGTGTTT 58.527 36.000 0.00 0.00 0.00 2.83
145 146 6.049955 TCAGGGAGAAAGAATTATCGTGTT 57.950 37.500 0.00 0.00 0.00 3.32
146 147 5.677319 TCAGGGAGAAAGAATTATCGTGT 57.323 39.130 0.00 0.00 0.00 4.49
147 148 7.066284 ACAAATCAGGGAGAAAGAATTATCGTG 59.934 37.037 0.00 0.00 0.00 4.35
148 149 7.112779 ACAAATCAGGGAGAAAGAATTATCGT 58.887 34.615 0.00 0.00 0.00 3.73
149 150 7.559590 ACAAATCAGGGAGAAAGAATTATCG 57.440 36.000 0.00 0.00 0.00 2.92
152 153 9.762933 CAAAAACAAATCAGGGAGAAAGAATTA 57.237 29.630 0.00 0.00 0.00 1.40
153 154 8.485392 TCAAAAACAAATCAGGGAGAAAGAATT 58.515 29.630 0.00 0.00 0.00 2.17
154 155 8.021898 TCAAAAACAAATCAGGGAGAAAGAAT 57.978 30.769 0.00 0.00 0.00 2.40
155 156 7.416964 TCAAAAACAAATCAGGGAGAAAGAA 57.583 32.000 0.00 0.00 0.00 2.52
156 157 7.416964 TTCAAAAACAAATCAGGGAGAAAGA 57.583 32.000 0.00 0.00 0.00 2.52
157 158 8.491331 TTTTCAAAAACAAATCAGGGAGAAAG 57.509 30.769 0.00 0.00 0.00 2.62
160 161 9.709495 CATATTTTCAAAAACAAATCAGGGAGA 57.291 29.630 0.00 0.00 0.00 3.71
161 162 8.938906 CCATATTTTCAAAAACAAATCAGGGAG 58.061 33.333 0.00 0.00 0.00 4.30
162 163 8.435982 ACCATATTTTCAAAAACAAATCAGGGA 58.564 29.630 0.00 0.00 0.00 4.20
163 164 8.620116 ACCATATTTTCAAAAACAAATCAGGG 57.380 30.769 0.00 0.00 0.00 4.45
177 178 8.714179 CCGACGCTATAAAATACCATATTTTCA 58.286 33.333 9.28 0.89 33.73 2.69
178 179 8.715088 ACCGACGCTATAAAATACCATATTTTC 58.285 33.333 9.28 0.00 33.73 2.29
179 180 8.611654 ACCGACGCTATAAAATACCATATTTT 57.388 30.769 10.50 10.50 35.62 1.82
180 181 8.611654 AACCGACGCTATAAAATACCATATTT 57.388 30.769 0.00 0.00 0.00 1.40
181 182 8.500773 CAAACCGACGCTATAAAATACCATATT 58.499 33.333 0.00 0.00 0.00 1.28
182 183 7.874016 TCAAACCGACGCTATAAAATACCATAT 59.126 33.333 0.00 0.00 0.00 1.78
183 184 7.208777 TCAAACCGACGCTATAAAATACCATA 58.791 34.615 0.00 0.00 0.00 2.74
184 185 6.050432 TCAAACCGACGCTATAAAATACCAT 58.950 36.000 0.00 0.00 0.00 3.55
185 186 5.417811 TCAAACCGACGCTATAAAATACCA 58.582 37.500 0.00 0.00 0.00 3.25
186 187 5.050567 CCTCAAACCGACGCTATAAAATACC 60.051 44.000 0.00 0.00 0.00 2.73
187 188 5.050567 CCCTCAAACCGACGCTATAAAATAC 60.051 44.000 0.00 0.00 0.00 1.89
188 189 5.051816 CCCTCAAACCGACGCTATAAAATA 58.948 41.667 0.00 0.00 0.00 1.40
189 190 3.875134 CCCTCAAACCGACGCTATAAAAT 59.125 43.478 0.00 0.00 0.00 1.82
190 191 3.264104 CCCTCAAACCGACGCTATAAAA 58.736 45.455 0.00 0.00 0.00 1.52
191 192 2.234414 ACCCTCAAACCGACGCTATAAA 59.766 45.455 0.00 0.00 0.00 1.40
192 193 1.826720 ACCCTCAAACCGACGCTATAA 59.173 47.619 0.00 0.00 0.00 0.98
193 194 1.406539 GACCCTCAAACCGACGCTATA 59.593 52.381 0.00 0.00 0.00 1.31
194 195 0.175073 GACCCTCAAACCGACGCTAT 59.825 55.000 0.00 0.00 0.00 2.97
195 196 1.180456 TGACCCTCAAACCGACGCTA 61.180 55.000 0.00 0.00 0.00 4.26
196 197 2.342648 GACCCTCAAACCGACGCT 59.657 61.111 0.00 0.00 0.00 5.07
197 198 2.027625 CTGACCCTCAAACCGACGC 61.028 63.158 0.00 0.00 0.00 5.19
198 199 2.027625 GCTGACCCTCAAACCGACG 61.028 63.158 0.00 0.00 0.00 5.12
199 200 2.027625 CGCTGACCCTCAAACCGAC 61.028 63.158 0.00 0.00 0.00 4.79
200 201 2.342279 CGCTGACCCTCAAACCGA 59.658 61.111 0.00 0.00 0.00 4.69
201 202 2.742372 CCGCTGACCCTCAAACCG 60.742 66.667 0.00 0.00 0.00 4.44
202 203 2.359975 CCCGCTGACCCTCAAACC 60.360 66.667 0.00 0.00 0.00 3.27
203 204 2.359975 CCCCGCTGACCCTCAAAC 60.360 66.667 0.00 0.00 0.00 2.93
204 205 4.344865 GCCCCGCTGACCCTCAAA 62.345 66.667 0.00 0.00 0.00 2.69
278 279 4.496336 CCCAGGGCTAGGCACAGC 62.496 72.222 19.14 0.00 41.02 4.40
426 435 5.319453 TCGGTCTATATGGTCTATTCGGTT 58.681 41.667 0.00 0.00 0.00 4.44
544 699 1.675641 GAGTGAATTGGCTGCCGGT 60.676 57.895 14.98 1.51 0.00 5.28
616 811 2.123939 CATGGGCATGGGGCGTTA 60.124 61.111 0.00 0.00 46.16 3.18
617 812 4.059304 TCATGGGCATGGGGCGTT 62.059 61.111 0.00 0.00 46.16 4.84
683 878 0.032130 GGCGCCGATCTTCATCTGTA 59.968 55.000 12.58 0.00 0.00 2.74
684 879 1.227380 GGCGCCGATCTTCATCTGT 60.227 57.895 12.58 0.00 0.00 3.41
685 880 1.958205 GGGCGCCGATCTTCATCTG 60.958 63.158 22.54 0.00 0.00 2.90
686 881 2.423446 GGGCGCCGATCTTCATCT 59.577 61.111 22.54 0.00 0.00 2.90
687 882 2.666526 GGGGCGCCGATCTTCATC 60.667 66.667 22.54 2.12 0.00 2.92
688 883 4.256180 GGGGGCGCCGATCTTCAT 62.256 66.667 22.54 0.00 0.00 2.57
702 897 2.037772 CCGATCTTCATCTGTAAGGGGG 59.962 54.545 0.00 0.00 0.00 5.40
703 898 2.548920 GCCGATCTTCATCTGTAAGGGG 60.549 54.545 0.00 0.00 0.00 4.79
704 899 2.760374 GCCGATCTTCATCTGTAAGGG 58.240 52.381 0.00 0.00 0.00 3.95
705 900 2.398498 CGCCGATCTTCATCTGTAAGG 58.602 52.381 0.00 0.00 0.00 2.69
706 901 1.789464 GCGCCGATCTTCATCTGTAAG 59.211 52.381 0.00 0.00 0.00 2.34
707 902 1.538204 GGCGCCGATCTTCATCTGTAA 60.538 52.381 12.58 0.00 0.00 2.41
708 903 0.032130 GGCGCCGATCTTCATCTGTA 59.968 55.000 12.58 0.00 0.00 2.74
1041 1242 3.760580 ACAGAGTTGAAGAAGACAGGG 57.239 47.619 0.00 0.00 0.00 4.45
1044 1245 4.360563 GACGAACAGAGTTGAAGAAGACA 58.639 43.478 0.00 0.00 0.00 3.41
1075 1276 2.270434 AATGAAGGAGGGCAGTAGGA 57.730 50.000 0.00 0.00 0.00 2.94
1588 1979 4.421365 CCACCATGGACCTTGTGG 57.579 61.111 21.47 10.86 40.96 4.17
1684 2092 4.154176 CAGCCCATGGAATATTGGAATCA 58.846 43.478 15.22 0.00 34.81 2.57
1745 2153 4.515191 TGAGAAGATAACAAGCAACACCAC 59.485 41.667 0.00 0.00 0.00 4.16
2254 2687 9.914834 AGCAGAACTACCATGGTATTATTTTTA 57.085 29.630 24.78 1.28 0.00 1.52
2263 2697 6.535540 TGTTTTTAGCAGAACTACCATGGTA 58.464 36.000 23.23 23.23 0.00 3.25
2362 2796 8.410673 AGTTGATACGTCTCCAACATATCTAT 57.589 34.615 21.52 4.80 41.72 1.98
2456 2890 8.056407 ACAAGAGCAAAAGAGTTCTTAAAAGT 57.944 30.769 0.00 0.00 37.02 2.66
2463 2897 6.705863 ATGAAACAAGAGCAAAAGAGTTCT 57.294 33.333 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.