Multiple sequence alignment - TraesCS7A01G134700

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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 TraesCS7A01G134700 chr7A 100.000 8102 0 0 1 8102 87302605 87310706 0.000000e+00 14962.0
1 TraesCS7A01G134700 chr7A 99.497 596 3 0 7507 8102 87320367 87320962 0.000000e+00 1085.0
2 TraesCS7A01G134700 chr7D 97.346 5200 97 18 2325 7506 85908680 85913856 0.000000e+00 8800.0
3 TraesCS7A01G134700 chr7D 90.566 2067 109 32 126 2148 85906365 85908389 0.000000e+00 2658.0
4 TraesCS7A01G134700 chr7D 90.256 195 16 1 2143 2337 85908467 85908658 1.350000e-62 252.0
5 TraesCS7A01G134700 chr7D 94.737 76 4 0 1962 2037 41157603 41157528 1.430000e-22 119.0
6 TraesCS7A01G134700 chr7B 96.047 4452 136 24 3071 7506 35081949 35086376 0.000000e+00 7210.0
7 TraesCS7A01G134700 chr7B 88.342 1158 59 26 706 1796 35078237 35079385 0.000000e+00 1321.0
8 TraesCS7A01G134700 chr7B 95.317 662 20 6 2325 2978 35081284 35081942 0.000000e+00 1040.0
9 TraesCS7A01G134700 chr7B 90.796 565 24 15 1794 2337 35080705 35081262 0.000000e+00 730.0
10 TraesCS7A01G134700 chr7B 90.307 423 26 7 302 712 35076663 35077082 2.570000e-149 540.0
11 TraesCS7A01G134700 chr7B 82.703 185 16 9 126 310 35076343 35076511 5.070000e-32 150.0
12 TraesCS7A01G134700 chr5B 99.832 596 1 0 7507 8102 368586063 368586658 0.000000e+00 1096.0
13 TraesCS7A01G134700 chr5B 99.664 596 2 0 7507 8102 368575987 368576582 0.000000e+00 1090.0
14 TraesCS7A01G134700 chr6B 99.664 596 2 0 7507 8102 506228569 506229164 0.000000e+00 1090.0
15 TraesCS7A01G134700 chr6B 99.497 597 2 1 7507 8102 506218352 506218948 0.000000e+00 1085.0
16 TraesCS7A01G134700 chr4A 99.664 596 1 1 7507 8102 697545166 697544572 0.000000e+00 1088.0
17 TraesCS7A01G134700 chr4A 99.497 597 2 1 7506 8102 697555246 697554651 0.000000e+00 1085.0
18 TraesCS7A01G134700 chr4A 93.421 76 5 0 1962 2037 647198759 647198834 6.650000e-21 113.0
19 TraesCS7A01G134700 chr3A 99.497 597 2 1 7507 8102 167784856 167785452 0.000000e+00 1085.0
20 TraesCS7A01G134700 chr3A 99.497 596 3 0 7507 8102 188327558 188328153 0.000000e+00 1085.0
21 TraesCS7A01G134700 chr3D 95.000 180 9 0 3833 4012 193390458 193390279 4.790000e-72 283.0
22 TraesCS7A01G134700 chr3D 79.769 173 18 7 1865 2037 422748719 422748564 8.600000e-20 110.0
23 TraesCS7A01G134700 chrUn 94.413 179 10 0 3833 4011 189405805 189405627 8.010000e-70 276.0
24 TraesCS7A01G134700 chrUn 93.548 186 10 1 3826 4011 251410744 251410927 8.010000e-70 276.0
25 TraesCS7A01G134700 chrUn 94.413 179 10 0 3833 4011 405354554 405354376 8.010000e-70 276.0
26 TraesCS7A01G134700 chrUn 93.548 186 10 1 3826 4011 452187711 452187894 8.010000e-70 276.0
27 TraesCS7A01G134700 chr6D 94.413 179 10 0 3833 4011 124530844 124530666 8.010000e-70 276.0
28 TraesCS7A01G134700 chr1D 93.548 186 10 1 3826 4011 141318407 141318590 8.010000e-70 276.0
29 TraesCS7A01G134700 chr1D 94.231 52 3 0 7070 7121 244199692 244199743 6.740000e-11 80.5
30 TraesCS7A01G134700 chr1A 89.474 57 5 1 1968 2024 335027575 335027520 4.060000e-08 71.3


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 TraesCS7A01G134700 chr7A 87302605 87310706 8101 False 14962.000000 14962 100.000000 1 8102 1 chr7A.!!$F1 8101
1 TraesCS7A01G134700 chr7A 87320367 87320962 595 False 1085.000000 1085 99.497000 7507 8102 1 chr7A.!!$F2 595
2 TraesCS7A01G134700 chr7D 85906365 85913856 7491 False 3903.333333 8800 92.722667 126 7506 3 chr7D.!!$F1 7380
3 TraesCS7A01G134700 chr7B 35076343 35086376 10033 False 1831.833333 7210 90.585333 126 7506 6 chr7B.!!$F1 7380
4 TraesCS7A01G134700 chr5B 368586063 368586658 595 False 1096.000000 1096 99.832000 7507 8102 1 chr5B.!!$F2 595
5 TraesCS7A01G134700 chr5B 368575987 368576582 595 False 1090.000000 1090 99.664000 7507 8102 1 chr5B.!!$F1 595
6 TraesCS7A01G134700 chr6B 506228569 506229164 595 False 1090.000000 1090 99.664000 7507 8102 1 chr6B.!!$F2 595
7 TraesCS7A01G134700 chr6B 506218352 506218948 596 False 1085.000000 1085 99.497000 7507 8102 1 chr6B.!!$F1 595
8 TraesCS7A01G134700 chr4A 697544572 697545166 594 True 1088.000000 1088 99.664000 7507 8102 1 chr4A.!!$R1 595
9 TraesCS7A01G134700 chr4A 697554651 697555246 595 True 1085.000000 1085 99.497000 7506 8102 1 chr4A.!!$R2 596
10 TraesCS7A01G134700 chr3A 167784856 167785452 596 False 1085.000000 1085 99.497000 7507 8102 1 chr3A.!!$F1 595
11 TraesCS7A01G134700 chr3A 188327558 188328153 595 False 1085.000000 1085 99.497000 7507 8102 1 chr3A.!!$F2 595

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
105 106 0.251916 CAGACCGATGCTTAACCCCA 59.748 55.000 0.00 0.0 0.00 4.96 F
109 110 1.005450 ACCGATGCTTAACCCCATTGT 59.995 47.619 0.00 0.0 0.00 2.71 F
1150 2515 0.321122 CCCACTCAAGTCACTCCTGC 60.321 60.000 0.00 0.0 0.00 4.85 F
2241 5089 0.451783 CGGCTCAATTTTTCTCCCCG 59.548 55.000 0.00 0.0 0.00 5.73 F
2282 5130 2.892784 AGCTAGCAAAGTATCCCGTC 57.107 50.000 18.83 0.0 0.00 4.79 F
2287 5135 3.350219 AGCAAAGTATCCCGTCATGTT 57.650 42.857 0.00 0.0 0.00 2.71 F
3597 6523 4.022589 ACTTCAACAGCACATTCTTCATGG 60.023 41.667 0.00 0.0 37.17 3.66 F
4696 7626 1.117994 TTTGAATTGTGGCCAGCACA 58.882 45.000 5.11 0.0 0.00 4.57 F
5963 8893 0.692756 TGGGGAGGAACACTGTGACA 60.693 55.000 15.86 0.0 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1148 2513 0.183492 AGCCAAGTGTCCTTCTTGCA 59.817 50.000 0.00 0.00 40.35 4.08 R
2055 4817 0.927767 GGAGGAGAGGAGTACCCAGA 59.072 60.000 3.60 0.00 37.41 3.86 R
3119 6043 0.319405 ATGCAGAGCAAACCAAAGGC 59.681 50.000 0.00 0.00 43.62 4.35 R
3828 6758 1.163420 CCAGCGTTTGGTGCAGTACA 61.163 55.000 0.00 0.00 42.41 2.90 R
4177 7107 6.950619 AGTTCTGATAGAAGGCCAAAAGATTT 59.049 34.615 5.01 0.00 34.42 2.17 R
4696 7626 6.229936 AGTGCTTCCATTGCATGAAATTAT 57.770 33.333 0.00 0.00 42.69 1.28 R
5233 8163 0.397941 CCTTCTTGCTGTCTGGACCA 59.602 55.000 0.00 0.00 0.00 4.02 R
6307 9242 0.322322 TTGTTCATACGGGGCGTCTT 59.678 50.000 0.00 0.00 41.54 3.01 R
7245 10184 1.277557 CTGTGCAGTTCTCTTAGGCCT 59.722 52.381 11.78 11.78 0.00 5.19 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
24 25 7.498070 CAAGAAAATCGGTGAGCTAATTTTC 57.502 36.000 17.09 17.09 43.50 2.29
27 28 6.817765 AAAATCGGTGAGCTAATTTTCTGA 57.182 33.333 0.00 0.00 27.88 3.27
28 29 6.817765 AAATCGGTGAGCTAATTTTCTGAA 57.182 33.333 0.00 0.00 0.00 3.02
29 30 6.817765 AATCGGTGAGCTAATTTTCTGAAA 57.182 33.333 0.00 0.00 0.00 2.69
30 31 6.817765 ATCGGTGAGCTAATTTTCTGAAAA 57.182 33.333 17.04 17.04 34.41 2.29
31 32 6.241207 TCGGTGAGCTAATTTTCTGAAAAG 57.759 37.500 19.14 8.48 33.22 2.27
32 33 5.995282 TCGGTGAGCTAATTTTCTGAAAAGA 59.005 36.000 19.14 9.99 33.22 2.52
33 34 6.485313 TCGGTGAGCTAATTTTCTGAAAAGAA 59.515 34.615 19.14 9.85 33.22 2.52
34 35 6.798959 CGGTGAGCTAATTTTCTGAAAAGAAG 59.201 38.462 19.14 17.80 33.22 2.85
35 36 6.584184 GGTGAGCTAATTTTCTGAAAAGAAGC 59.416 38.462 27.72 27.72 40.01 3.86
36 37 6.584184 GTGAGCTAATTTTCTGAAAAGAAGCC 59.416 38.462 29.44 24.20 40.31 4.35
37 38 6.491403 TGAGCTAATTTTCTGAAAAGAAGCCT 59.509 34.615 29.44 22.30 40.31 4.58
38 39 7.665559 TGAGCTAATTTTCTGAAAAGAAGCCTA 59.334 33.333 29.44 22.03 40.31 3.93
39 40 8.049655 AGCTAATTTTCTGAAAAGAAGCCTAG 57.950 34.615 29.44 19.11 40.31 3.02
40 41 7.121907 AGCTAATTTTCTGAAAAGAAGCCTAGG 59.878 37.037 29.44 3.67 40.31 3.02
41 42 7.121315 GCTAATTTTCTGAAAAGAAGCCTAGGA 59.879 37.037 26.19 3.97 36.68 2.94
42 43 7.839680 AATTTTCTGAAAAGAAGCCTAGGAA 57.160 32.000 14.75 0.00 33.22 3.36
43 44 7.839680 ATTTTCTGAAAAGAAGCCTAGGAAA 57.160 32.000 14.75 0.00 33.22 3.13
44 45 6.635030 TTTCTGAAAAGAAGCCTAGGAAAC 57.365 37.500 14.75 1.96 0.00 2.78
45 46 4.652822 TCTGAAAAGAAGCCTAGGAAACC 58.347 43.478 14.75 0.00 0.00 3.27
46 47 3.759086 CTGAAAAGAAGCCTAGGAAACCC 59.241 47.826 14.75 0.00 0.00 4.11
47 48 3.397955 TGAAAAGAAGCCTAGGAAACCCT 59.602 43.478 14.75 0.00 37.84 4.34
48 49 4.141018 TGAAAAGAAGCCTAGGAAACCCTT 60.141 41.667 14.75 5.54 35.26 3.95
49 50 3.722908 AAGAAGCCTAGGAAACCCTTC 57.277 47.619 14.75 14.81 35.26 3.46
63 64 2.696989 CCCTTCCAATGGGCAAAATC 57.303 50.000 0.00 0.00 37.99 2.17
64 65 1.210234 CCCTTCCAATGGGCAAAATCC 59.790 52.381 0.00 0.00 37.99 3.01
65 66 1.907936 CCTTCCAATGGGCAAAATCCA 59.092 47.619 0.00 0.00 38.82 3.41
66 67 2.355007 CCTTCCAATGGGCAAAATCCAC 60.355 50.000 0.00 0.00 37.08 4.02
67 68 2.021262 TCCAATGGGCAAAATCCACA 57.979 45.000 0.00 0.00 37.08 4.17
68 69 2.549082 TCCAATGGGCAAAATCCACAT 58.451 42.857 0.00 0.00 37.08 3.21
69 70 2.911636 TCCAATGGGCAAAATCCACATT 59.088 40.909 0.00 0.00 37.08 2.71
70 71 4.099633 TCCAATGGGCAAAATCCACATTA 58.900 39.130 0.00 0.00 37.08 1.90
71 72 4.533707 TCCAATGGGCAAAATCCACATTAA 59.466 37.500 0.00 0.00 37.08 1.40
72 73 5.013495 TCCAATGGGCAAAATCCACATTAAA 59.987 36.000 0.00 0.00 37.08 1.52
73 74 5.709164 CCAATGGGCAAAATCCACATTAAAA 59.291 36.000 0.00 0.00 37.08 1.52
74 75 6.208204 CCAATGGGCAAAATCCACATTAAAAA 59.792 34.615 0.00 0.00 37.08 1.94
94 95 6.737254 AAAAACAATTCGATACAGACCGAT 57.263 33.333 0.00 0.00 34.58 4.18
95 96 5.718649 AAACAATTCGATACAGACCGATG 57.281 39.130 0.00 0.00 34.58 3.84
96 97 3.123804 ACAATTCGATACAGACCGATGC 58.876 45.455 0.00 0.00 34.58 3.91
97 98 3.181475 ACAATTCGATACAGACCGATGCT 60.181 43.478 0.00 0.00 34.58 3.79
98 99 3.735237 ATTCGATACAGACCGATGCTT 57.265 42.857 0.00 0.00 34.58 3.91
99 100 4.848562 ATTCGATACAGACCGATGCTTA 57.151 40.909 0.00 0.00 34.58 3.09
100 101 4.642445 TTCGATACAGACCGATGCTTAA 57.358 40.909 0.00 0.00 34.58 1.85
101 102 3.961182 TCGATACAGACCGATGCTTAAC 58.039 45.455 0.00 0.00 0.00 2.01
102 103 3.050619 CGATACAGACCGATGCTTAACC 58.949 50.000 0.00 0.00 0.00 2.85
103 104 2.973694 TACAGACCGATGCTTAACCC 57.026 50.000 0.00 0.00 0.00 4.11
104 105 0.252197 ACAGACCGATGCTTAACCCC 59.748 55.000 0.00 0.00 0.00 4.95
105 106 0.251916 CAGACCGATGCTTAACCCCA 59.748 55.000 0.00 0.00 0.00 4.96
106 107 1.134098 CAGACCGATGCTTAACCCCAT 60.134 52.381 0.00 0.00 0.00 4.00
107 108 1.564348 AGACCGATGCTTAACCCCATT 59.436 47.619 0.00 0.00 0.00 3.16
108 109 1.676006 GACCGATGCTTAACCCCATTG 59.324 52.381 0.00 0.00 0.00 2.82
109 110 1.005450 ACCGATGCTTAACCCCATTGT 59.995 47.619 0.00 0.00 0.00 2.71
110 111 1.405105 CCGATGCTTAACCCCATTGTG 59.595 52.381 0.00 0.00 0.00 3.33
111 112 2.091541 CGATGCTTAACCCCATTGTGT 58.908 47.619 0.00 0.00 0.00 3.72
112 113 3.275143 CGATGCTTAACCCCATTGTGTA 58.725 45.455 0.00 0.00 0.00 2.90
113 114 3.692101 CGATGCTTAACCCCATTGTGTAA 59.308 43.478 0.00 0.00 0.00 2.41
114 115 4.156922 CGATGCTTAACCCCATTGTGTAAA 59.843 41.667 0.00 0.00 0.00 2.01
115 116 5.336055 CGATGCTTAACCCCATTGTGTAAAA 60.336 40.000 0.00 0.00 0.00 1.52
116 117 5.203060 TGCTTAACCCCATTGTGTAAAAC 57.797 39.130 0.00 0.00 0.00 2.43
117 118 4.039366 TGCTTAACCCCATTGTGTAAAACC 59.961 41.667 0.00 0.00 0.00 3.27
118 119 4.039366 GCTTAACCCCATTGTGTAAAACCA 59.961 41.667 0.00 0.00 0.00 3.67
119 120 5.453480 GCTTAACCCCATTGTGTAAAACCAA 60.453 40.000 0.00 0.00 0.00 3.67
120 121 6.555463 TTAACCCCATTGTGTAAAACCAAA 57.445 33.333 0.00 0.00 0.00 3.28
121 122 5.437191 AACCCCATTGTGTAAAACCAAAA 57.563 34.783 0.00 0.00 0.00 2.44
122 123 5.029807 ACCCCATTGTGTAAAACCAAAAG 57.970 39.130 0.00 0.00 0.00 2.27
123 124 4.141597 ACCCCATTGTGTAAAACCAAAAGG 60.142 41.667 0.00 0.00 0.00 3.11
124 125 3.812609 CCCATTGTGTAAAACCAAAAGGC 59.187 43.478 0.00 0.00 0.00 4.35
142 143 7.201812 CCAAAAGGCATATAGCTTGTTATCACA 60.202 37.037 0.00 0.00 44.79 3.58
143 144 8.355169 CAAAAGGCATATAGCTTGTTATCACAT 58.645 33.333 0.00 0.00 44.79 3.21
209 211 6.174720 TCATAATCCAGTAACTGATGGGAC 57.825 41.667 0.00 0.00 37.19 4.46
266 268 4.481463 AGCAACACGCAATAAACAATACC 58.519 39.130 0.00 0.00 46.13 2.73
297 299 2.676342 GTGGCAGTAATAGACAAACCGG 59.324 50.000 0.00 0.00 0.00 5.28
377 539 2.500098 GGCAGTGGACAGTGACCTATAA 59.500 50.000 12.89 0.00 33.63 0.98
402 566 5.644977 TGTCTCATAGACTGTCGTTTCAT 57.355 39.130 8.42 0.00 45.27 2.57
403 567 6.753107 TGTCTCATAGACTGTCGTTTCATA 57.247 37.500 8.42 0.00 45.27 2.15
405 569 7.027760 TGTCTCATAGACTGTCGTTTCATAAC 58.972 38.462 8.42 0.00 45.27 1.89
649 821 2.752354 TGGTGCTTTGGGTGATTATTCG 59.248 45.455 0.00 0.00 0.00 3.34
669 841 2.097202 CGTTGCTTATGCTAGTCGATGC 60.097 50.000 1.96 0.00 40.48 3.91
670 842 2.154854 TGCTTATGCTAGTCGATGCC 57.845 50.000 1.96 0.00 40.48 4.40
672 844 1.702886 CTTATGCTAGTCGATGCCGG 58.297 55.000 0.00 0.00 36.24 6.13
692 864 2.349755 GGAAGCACGGTGCCCTTA 59.650 61.111 28.14 0.00 46.52 2.69
693 865 1.745489 GGAAGCACGGTGCCCTTAG 60.745 63.158 28.14 0.00 46.52 2.18
700 872 2.167662 CACGGTGCCCTTAGGAAAAAT 58.832 47.619 0.00 0.00 33.47 1.82
742 2075 3.191371 ACTTTTCGAAATCACATCTGGCC 59.809 43.478 12.12 0.00 0.00 5.36
743 2076 2.787473 TTCGAAATCACATCTGGCCT 57.213 45.000 3.32 0.00 0.00 5.19
772 2105 6.953520 TCAGATCAACCAACTCCCATAATTTT 59.046 34.615 0.00 0.00 0.00 1.82
777 2110 7.891561 TCAACCAACTCCCATAATTTTAGTTG 58.108 34.615 0.00 0.00 44.15 3.16
805 2138 1.202794 TGCTGACACCTGAATGCTCAA 60.203 47.619 0.00 0.00 0.00 3.02
836 2171 1.342174 CCATGCATGAAACCCTATGCC 59.658 52.381 28.31 0.00 46.91 4.40
844 2179 4.764050 TGAAACCCTATGCCGAAAGATA 57.236 40.909 0.00 0.00 0.00 1.98
848 2183 6.042781 TGAAACCCTATGCCGAAAGATAGTAT 59.957 38.462 0.00 0.00 0.00 2.12
851 2186 4.466370 CCCTATGCCGAAAGATAGTATGGA 59.534 45.833 0.00 0.00 0.00 3.41
854 2189 2.035449 TGCCGAAAGATAGTATGGACCG 59.965 50.000 0.00 0.00 0.00 4.79
984 2324 7.931275 AGGTAAAGCTCTAACAGAAAACTTTG 58.069 34.615 0.00 0.00 30.00 2.77
986 2326 7.012989 GGTAAAGCTCTAACAGAAAACTTTGGA 59.987 37.037 0.00 0.00 30.00 3.53
1065 2430 2.315925 TCAATCTGAGATGCCCGTTC 57.684 50.000 0.00 0.00 0.00 3.95
1148 2513 1.343069 GACCCACTCAAGTCACTCCT 58.657 55.000 0.00 0.00 33.08 3.69
1150 2515 0.321122 CCCACTCAAGTCACTCCTGC 60.321 60.000 0.00 0.00 0.00 4.85
1152 2517 1.202687 CCACTCAAGTCACTCCTGCAA 60.203 52.381 0.00 0.00 0.00 4.08
1153 2518 2.141517 CACTCAAGTCACTCCTGCAAG 58.858 52.381 0.00 0.00 0.00 4.01
1154 2519 2.042464 ACTCAAGTCACTCCTGCAAGA 58.958 47.619 0.00 0.00 34.07 3.02
1155 2520 2.435805 ACTCAAGTCACTCCTGCAAGAA 59.564 45.455 0.00 0.00 34.07 2.52
1170 2535 2.289694 GCAAGAAGGACACTTGGCTCTA 60.290 50.000 0.00 0.00 43.12 2.43
1288 2658 4.562757 CCTTTCCTGGTAAGTTCATGACGA 60.563 45.833 11.48 0.00 0.00 4.20
1337 2707 6.168270 ACTTGTAAGTCTTTCTCTGCTTCT 57.832 37.500 0.00 0.00 32.86 2.85
1338 2708 6.587273 ACTTGTAAGTCTTTCTCTGCTTCTT 58.413 36.000 0.00 0.00 32.86 2.52
1339 2709 6.704050 ACTTGTAAGTCTTTCTCTGCTTCTTC 59.296 38.462 0.00 0.00 32.86 2.87
1340 2710 6.412362 TGTAAGTCTTTCTCTGCTTCTTCT 57.588 37.500 0.00 0.00 0.00 2.85
1341 2711 6.821388 TGTAAGTCTTTCTCTGCTTCTTCTT 58.179 36.000 0.00 0.00 0.00 2.52
1342 2712 6.926272 TGTAAGTCTTTCTCTGCTTCTTCTTC 59.074 38.462 0.00 0.00 0.00 2.87
1343 2713 5.806654 AGTCTTTCTCTGCTTCTTCTTCT 57.193 39.130 0.00 0.00 0.00 2.85
1344 2714 6.173427 AGTCTTTCTCTGCTTCTTCTTCTT 57.827 37.500 0.00 0.00 0.00 2.52
1345 2715 6.223120 AGTCTTTCTCTGCTTCTTCTTCTTC 58.777 40.000 0.00 0.00 0.00 2.87
1386 2759 1.826385 TGCTTGCCTTCCTTTAGAGC 58.174 50.000 0.00 0.00 0.00 4.09
1391 2764 2.187958 TGCCTTCCTTTAGAGCAGCTA 58.812 47.619 0.00 0.00 0.00 3.32
1397 2770 3.431415 TCCTTTAGAGCAGCTACTGTGA 58.569 45.455 0.00 0.00 33.43 3.58
1412 2785 4.944619 ACTGTGAGTGTTCATCTTCTCA 57.055 40.909 0.00 0.00 35.39 3.27
1424 2797 5.152623 TCATCTTCTCAAGAAATGGTCGT 57.847 39.130 11.52 0.00 41.63 4.34
1516 2889 2.125147 TACTGGAGCATGGCGCAC 60.125 61.111 10.83 0.00 46.13 5.34
1539 2912 9.515020 GCACTAGATATAGATTATGCTCAGAAC 57.485 37.037 0.33 0.00 0.00 3.01
1552 2925 2.933056 GCTCAGAACCTTCTACCTGCAC 60.933 54.545 0.00 0.00 35.34 4.57
1666 3091 3.368571 GGTGGTGAGCTTGCTGGC 61.369 66.667 0.00 0.00 0.00 4.85
1843 4590 1.078848 ATCTTCGTCCTGGTGCTGC 60.079 57.895 0.00 0.00 0.00 5.25
1914 4661 2.333938 GTGTTGTGCTGCTGCTGG 59.666 61.111 17.00 0.00 40.48 4.85
2016 4778 0.976641 GTGAGTGATCCTGGTGGTGA 59.023 55.000 0.00 0.00 34.23 4.02
2042 4804 3.764658 GCTGATTGCAGAGAGAGCT 57.235 52.632 0.00 0.00 45.17 4.09
2043 4805 1.292061 GCTGATTGCAGAGAGAGCTG 58.708 55.000 0.00 0.00 45.17 4.24
2148 4912 9.871238 TTGATACTGAAGTTCTTAATGAGTACC 57.129 33.333 4.17 0.00 0.00 3.34
2191 5038 4.317488 AGGTTGCCATGTTATTGCAAAAG 58.683 39.130 1.71 0.00 45.59 2.27
2222 5070 7.945033 TGACAGGAAAAAGCATGTTTATTTC 57.055 32.000 15.12 15.12 32.30 2.17
2241 5089 0.451783 CGGCTCAATTTTTCTCCCCG 59.548 55.000 0.00 0.00 0.00 5.73
2245 5093 3.119602 GGCTCAATTTTTCTCCCCGTAAC 60.120 47.826 0.00 0.00 0.00 2.50
2282 5130 2.892784 AGCTAGCAAAGTATCCCGTC 57.107 50.000 18.83 0.00 0.00 4.79
2287 5135 3.350219 AGCAAAGTATCCCGTCATGTT 57.650 42.857 0.00 0.00 0.00 2.71
2295 5143 5.118990 AGTATCCCGTCATGTTTGAGATTG 58.881 41.667 0.00 0.00 30.85 2.67
2320 5168 6.148480 GCGGCATTTAGAATCAGTTATCTCAT 59.852 38.462 0.00 0.00 0.00 2.90
2890 5814 7.783119 TGTCTTCCTGCCTTAGACAAGTATATA 59.217 37.037 0.00 0.00 43.72 0.86
3051 5975 5.976458 AGAAAATTTGCAGTTCTGTTCCAA 58.024 33.333 0.00 0.00 30.48 3.53
3053 5977 6.536224 AGAAAATTTGCAGTTCTGTTCCAAAG 59.464 34.615 0.00 0.00 30.48 2.77
3084 6008 7.939782 TGAAACTGTAAAAGCATTTCTCATCA 58.060 30.769 0.00 0.00 37.28 3.07
3119 6043 4.589216 TTTCTTTCAATGAAGTGGCCTG 57.411 40.909 3.32 0.00 0.00 4.85
3242 6166 8.562892 GCATTTAGTGTCTACCTCGTAATACTA 58.437 37.037 0.00 0.00 0.00 1.82
3597 6523 4.022589 ACTTCAACAGCACATTCTTCATGG 60.023 41.667 0.00 0.00 37.17 3.66
4177 7107 9.284968 GAAATAGCTTAAATGGCTCAATACCTA 57.715 33.333 0.00 0.00 40.74 3.08
4407 7337 8.739972 CATAAAACCTGCCTAATAGTGAAAGTT 58.260 33.333 0.00 0.00 0.00 2.66
4696 7626 1.117994 TTTGAATTGTGGCCAGCACA 58.882 45.000 5.11 0.00 0.00 4.57
4981 7911 2.565391 TCCAGGTTCGTTCAGCAAGATA 59.435 45.455 0.00 0.00 0.00 1.98
5064 7994 5.300286 AGGACTCTGAACATTTTTCAACCAG 59.700 40.000 0.00 0.00 0.00 4.00
5149 8079 1.234821 AGCGTTTTTCATGGCGAGAA 58.765 45.000 0.00 0.00 0.00 2.87
5566 8496 5.475719 TGTAGTGTAGTGTATTGCCAGAAC 58.524 41.667 0.00 0.00 0.00 3.01
5963 8893 0.692756 TGGGGAGGAACACTGTGACA 60.693 55.000 15.86 0.00 0.00 3.58
6101 9031 0.965363 AGCGTGCAATTTTCCCCGAT 60.965 50.000 0.00 0.00 0.00 4.18
6146 9076 4.053983 TCATGCTCATCGATCAAGTAAGC 58.946 43.478 0.00 0.00 0.00 3.09
6147 9077 3.525268 TGCTCATCGATCAAGTAAGCA 57.475 42.857 0.00 1.64 36.04 3.91
6148 9078 4.063998 TGCTCATCGATCAAGTAAGCAT 57.936 40.909 0.00 0.00 33.67 3.79
6149 9079 5.200368 TGCTCATCGATCAAGTAAGCATA 57.800 39.130 0.00 0.00 33.67 3.14
6152 9082 5.636965 GCTCATCGATCAAGTAAGCATACAT 59.363 40.000 0.00 0.00 34.29 2.29
6175 9110 6.528537 TTACGGAACTGCTTATAAGTACCA 57.471 37.500 13.91 3.13 0.00 3.25
6288 9223 9.740710 ATAATTAATATGGGCAGAAGTTAGGTC 57.259 33.333 0.00 0.00 0.00 3.85
6300 9235 6.578023 CAGAAGTTAGGTCCTTAGAATGGAG 58.422 44.000 0.00 0.00 33.78 3.86
6307 9242 5.538877 AGGTCCTTAGAATGGAGGATGTTA 58.461 41.667 0.00 0.00 43.54 2.41
6313 9248 3.798202 AGAATGGAGGATGTTAAGACGC 58.202 45.455 0.00 0.00 0.00 5.19
6386 9322 6.514048 CGCTCACATAGTTGACTCATATGAGA 60.514 42.308 34.16 14.14 44.74 3.27
6633 9569 1.677966 AGCTGAGCTTACCCGTCGA 60.678 57.895 0.00 0.00 33.89 4.20
6935 9874 2.616376 GTGGTGCTGTGACACAATGTTA 59.384 45.455 10.02 0.00 42.55 2.41
6944 9883 9.660180 TGCTGTGACACAATGTTATACTTATAA 57.340 29.630 10.02 0.00 0.00 0.98
7176 10115 6.563422 TGCTTGGCATGTAATATCTTGAAAC 58.437 36.000 2.12 0.00 31.71 2.78
7245 10184 6.056884 ACAGATAAGTTAACCAACCAACGAA 58.943 36.000 0.88 0.00 35.05 3.85
7431 10370 7.607991 TCAATCTAGATGAAGTGGTTTTCCTTC 59.392 37.037 5.86 0.00 41.38 3.46
7441 10380 6.248569 AGTGGTTTTCCTTCAGAAGTTAGA 57.751 37.500 9.41 0.00 41.38 2.10
7480 10420 4.912317 AGCAATGATCATATGGAGCTCT 57.088 40.909 14.64 0.00 31.67 4.09
7486 10426 5.573337 TGATCATATGGAGCTCTACATCG 57.427 43.478 14.64 5.06 35.38 3.84
7487 10427 4.400567 TGATCATATGGAGCTCTACATCGG 59.599 45.833 14.64 5.71 35.38 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.498070 GAAAATTAGCTCACCGATTTTCTTG 57.502 36.000 16.54 0.00 41.65 3.02
3 4 6.842163 TCAGAAAATTAGCTCACCGATTTTC 58.158 36.000 16.30 16.30 43.59 2.29
4 5 6.817765 TCAGAAAATTAGCTCACCGATTTT 57.182 33.333 0.00 0.00 35.18 1.82
5 6 6.817765 TTCAGAAAATTAGCTCACCGATTT 57.182 33.333 0.00 0.00 0.00 2.17
6 7 6.817765 TTTCAGAAAATTAGCTCACCGATT 57.182 33.333 0.00 0.00 0.00 3.34
7 8 6.655003 TCTTTTCAGAAAATTAGCTCACCGAT 59.345 34.615 8.81 0.00 0.00 4.18
8 9 5.995282 TCTTTTCAGAAAATTAGCTCACCGA 59.005 36.000 8.81 0.00 0.00 4.69
9 10 6.241207 TCTTTTCAGAAAATTAGCTCACCG 57.759 37.500 8.81 0.00 0.00 4.94
10 11 6.584184 GCTTCTTTTCAGAAAATTAGCTCACC 59.416 38.462 22.79 5.87 38.63 4.02
11 12 6.584184 GGCTTCTTTTCAGAAAATTAGCTCAC 59.416 38.462 25.90 15.05 38.63 3.51
12 13 6.491403 AGGCTTCTTTTCAGAAAATTAGCTCA 59.509 34.615 25.90 2.26 38.63 4.26
13 14 6.918626 AGGCTTCTTTTCAGAAAATTAGCTC 58.081 36.000 25.90 20.03 38.63 4.09
14 15 6.907853 AGGCTTCTTTTCAGAAAATTAGCT 57.092 33.333 25.90 16.66 38.63 3.32
15 16 7.121315 TCCTAGGCTTCTTTTCAGAAAATTAGC 59.879 37.037 22.36 22.36 38.63 3.09
16 17 8.567285 TCCTAGGCTTCTTTTCAGAAAATTAG 57.433 34.615 8.81 9.93 38.63 1.73
17 18 8.934023 TTCCTAGGCTTCTTTTCAGAAAATTA 57.066 30.769 8.81 0.00 38.63 1.40
18 19 7.839680 TTCCTAGGCTTCTTTTCAGAAAATT 57.160 32.000 8.81 0.00 38.63 1.82
19 20 7.255977 GGTTTCCTAGGCTTCTTTTCAGAAAAT 60.256 37.037 8.81 0.00 38.63 1.82
20 21 6.040504 GGTTTCCTAGGCTTCTTTTCAGAAAA 59.959 38.462 2.96 8.09 38.63 2.29
21 22 5.535030 GGTTTCCTAGGCTTCTTTTCAGAAA 59.465 40.000 2.96 0.00 38.63 2.52
22 23 5.070685 GGTTTCCTAGGCTTCTTTTCAGAA 58.929 41.667 2.96 0.00 36.62 3.02
23 24 4.506802 GGGTTTCCTAGGCTTCTTTTCAGA 60.507 45.833 2.96 0.00 0.00 3.27
24 25 3.759086 GGGTTTCCTAGGCTTCTTTTCAG 59.241 47.826 2.96 0.00 0.00 3.02
25 26 3.397955 AGGGTTTCCTAGGCTTCTTTTCA 59.602 43.478 2.96 0.00 42.75 2.69
26 27 4.035612 AGGGTTTCCTAGGCTTCTTTTC 57.964 45.455 2.96 0.00 42.75 2.29
27 28 4.408276 GAAGGGTTTCCTAGGCTTCTTTT 58.592 43.478 15.21 2.93 44.07 2.27
28 29 4.035612 GAAGGGTTTCCTAGGCTTCTTT 57.964 45.455 15.21 4.32 44.07 2.52
29 30 3.722908 GAAGGGTTTCCTAGGCTTCTT 57.277 47.619 15.21 9.48 44.07 2.52
45 46 1.907936 TGGATTTTGCCCATTGGAAGG 59.092 47.619 3.62 0.00 0.00 3.46
46 47 2.302445 TGTGGATTTTGCCCATTGGAAG 59.698 45.455 3.62 0.00 35.91 3.46
47 48 2.333069 TGTGGATTTTGCCCATTGGAA 58.667 42.857 3.62 0.00 35.91 3.53
48 49 2.021262 TGTGGATTTTGCCCATTGGA 57.979 45.000 3.62 0.00 35.91 3.53
49 50 3.353370 AATGTGGATTTTGCCCATTGG 57.647 42.857 0.00 0.00 35.91 3.16
50 51 6.814506 TTTTAATGTGGATTTTGCCCATTG 57.185 33.333 0.00 0.00 35.91 2.82
71 72 6.542852 CATCGGTCTGTATCGAATTGTTTTT 58.457 36.000 0.00 0.00 42.59 1.94
72 73 5.447279 GCATCGGTCTGTATCGAATTGTTTT 60.447 40.000 0.00 0.00 42.59 2.43
73 74 4.034048 GCATCGGTCTGTATCGAATTGTTT 59.966 41.667 0.00 0.00 42.59 2.83
74 75 3.555956 GCATCGGTCTGTATCGAATTGTT 59.444 43.478 0.00 0.00 42.59 2.83
75 76 3.123804 GCATCGGTCTGTATCGAATTGT 58.876 45.455 0.00 0.00 42.59 2.71
76 77 3.384668 AGCATCGGTCTGTATCGAATTG 58.615 45.455 0.00 0.00 42.59 2.32
77 78 3.735237 AGCATCGGTCTGTATCGAATT 57.265 42.857 0.00 0.00 42.59 2.17
78 79 3.735237 AAGCATCGGTCTGTATCGAAT 57.265 42.857 0.00 0.00 42.59 3.34
79 80 4.357142 GTTAAGCATCGGTCTGTATCGAA 58.643 43.478 0.00 0.00 42.59 3.71
80 81 3.243301 GGTTAAGCATCGGTCTGTATCGA 60.243 47.826 0.00 0.00 43.69 3.59
81 82 3.050619 GGTTAAGCATCGGTCTGTATCG 58.949 50.000 0.00 0.00 0.00 2.92
82 83 3.391049 GGGTTAAGCATCGGTCTGTATC 58.609 50.000 7.03 0.00 0.00 2.24
83 84 2.104281 GGGGTTAAGCATCGGTCTGTAT 59.896 50.000 7.03 0.00 0.00 2.29
84 85 1.483415 GGGGTTAAGCATCGGTCTGTA 59.517 52.381 7.03 0.00 0.00 2.74
85 86 0.252197 GGGGTTAAGCATCGGTCTGT 59.748 55.000 7.03 0.00 0.00 3.41
86 87 0.251916 TGGGGTTAAGCATCGGTCTG 59.748 55.000 7.03 0.00 0.00 3.51
87 88 1.213296 ATGGGGTTAAGCATCGGTCT 58.787 50.000 7.03 0.00 0.00 3.85
88 89 1.676006 CAATGGGGTTAAGCATCGGTC 59.324 52.381 7.03 0.00 0.00 4.79
89 90 1.005450 ACAATGGGGTTAAGCATCGGT 59.995 47.619 7.03 0.00 0.00 4.69
90 91 1.405105 CACAATGGGGTTAAGCATCGG 59.595 52.381 7.03 0.00 0.00 4.18
91 92 2.091541 ACACAATGGGGTTAAGCATCG 58.908 47.619 7.03 0.00 0.00 3.84
92 93 5.652994 TTTACACAATGGGGTTAAGCATC 57.347 39.130 7.03 0.00 0.00 3.91
93 94 5.279758 GGTTTTACACAATGGGGTTAAGCAT 60.280 40.000 7.03 0.00 0.00 3.79
94 95 4.039366 GGTTTTACACAATGGGGTTAAGCA 59.961 41.667 7.03 0.00 0.00 3.91
95 96 4.039366 TGGTTTTACACAATGGGGTTAAGC 59.961 41.667 0.00 0.00 0.00 3.09
96 97 5.793030 TGGTTTTACACAATGGGGTTAAG 57.207 39.130 0.00 0.00 0.00 1.85
97 98 6.555463 TTTGGTTTTACACAATGGGGTTAA 57.445 33.333 0.00 0.00 0.00 2.01
98 99 6.408206 CCTTTTGGTTTTACACAATGGGGTTA 60.408 38.462 0.00 0.00 34.07 2.85
99 100 5.432645 CTTTTGGTTTTACACAATGGGGTT 58.567 37.500 0.00 0.00 0.00 4.11
100 101 4.141597 CCTTTTGGTTTTACACAATGGGGT 60.142 41.667 0.00 0.00 34.07 4.95
101 102 4.384940 CCTTTTGGTTTTACACAATGGGG 58.615 43.478 0.00 0.00 34.07 4.96
102 103 3.812609 GCCTTTTGGTTTTACACAATGGG 59.187 43.478 0.00 0.00 42.99 4.00
103 104 4.446371 TGCCTTTTGGTTTTACACAATGG 58.554 39.130 0.00 0.00 42.99 3.16
104 105 7.903995 ATATGCCTTTTGGTTTTACACAATG 57.096 32.000 0.00 0.00 42.99 2.82
105 106 7.763985 GCTATATGCCTTTTGGTTTTACACAAT 59.236 33.333 0.00 0.00 42.99 2.71
106 107 7.039363 AGCTATATGCCTTTTGGTTTTACACAA 60.039 33.333 0.00 0.00 44.23 3.33
107 108 6.435904 AGCTATATGCCTTTTGGTTTTACACA 59.564 34.615 0.00 0.00 44.23 3.72
108 109 6.863275 AGCTATATGCCTTTTGGTTTTACAC 58.137 36.000 0.00 0.00 44.23 2.90
109 110 7.039363 ACAAGCTATATGCCTTTTGGTTTTACA 60.039 33.333 0.00 0.00 44.23 2.41
110 111 7.320399 ACAAGCTATATGCCTTTTGGTTTTAC 58.680 34.615 0.00 0.00 44.23 2.01
111 112 7.475137 ACAAGCTATATGCCTTTTGGTTTTA 57.525 32.000 0.00 0.00 44.23 1.52
112 113 6.358974 ACAAGCTATATGCCTTTTGGTTTT 57.641 33.333 0.00 0.00 44.23 2.43
113 114 6.358974 AACAAGCTATATGCCTTTTGGTTT 57.641 33.333 0.00 0.00 44.23 3.27
114 115 7.341769 TGATAACAAGCTATATGCCTTTTGGTT 59.658 33.333 0.00 0.00 44.23 3.67
115 116 6.833416 TGATAACAAGCTATATGCCTTTTGGT 59.167 34.615 0.00 0.00 44.23 3.67
116 117 7.141363 GTGATAACAAGCTATATGCCTTTTGG 58.859 38.462 0.00 0.00 44.23 3.28
117 118 7.706159 TGTGATAACAAGCTATATGCCTTTTG 58.294 34.615 0.00 0.00 44.23 2.44
118 119 7.880160 TGTGATAACAAGCTATATGCCTTTT 57.120 32.000 0.00 0.00 44.23 2.27
119 120 7.040201 CCATGTGATAACAAGCTATATGCCTTT 60.040 37.037 0.00 0.00 44.23 3.11
120 121 6.432162 CCATGTGATAACAAGCTATATGCCTT 59.568 38.462 0.00 0.00 44.23 4.35
121 122 5.942236 CCATGTGATAACAAGCTATATGCCT 59.058 40.000 0.00 0.00 44.23 4.75
122 123 5.939883 TCCATGTGATAACAAGCTATATGCC 59.060 40.000 0.00 0.00 44.23 4.40
123 124 7.335171 TCATCCATGTGATAACAAGCTATATGC 59.665 37.037 0.00 0.00 35.28 3.14
124 125 8.782339 TCATCCATGTGATAACAAGCTATATG 57.218 34.615 0.00 0.00 30.56 1.78
184 186 7.054124 GTCCCATCAGTTACTGGATTATGAAA 58.946 38.462 12.79 0.00 34.24 2.69
185 187 6.157820 TGTCCCATCAGTTACTGGATTATGAA 59.842 38.462 12.79 0.00 34.24 2.57
186 188 5.665360 TGTCCCATCAGTTACTGGATTATGA 59.335 40.000 12.79 0.05 34.24 2.15
187 189 5.928976 TGTCCCATCAGTTACTGGATTATG 58.071 41.667 12.79 8.44 34.24 1.90
188 190 5.455326 GCTGTCCCATCAGTTACTGGATTAT 60.455 44.000 12.79 0.00 37.70 1.28
189 191 4.141711 GCTGTCCCATCAGTTACTGGATTA 60.142 45.833 12.79 0.00 37.70 1.75
190 192 3.370953 GCTGTCCCATCAGTTACTGGATT 60.371 47.826 12.79 0.00 37.70 3.01
191 193 2.171448 GCTGTCCCATCAGTTACTGGAT 59.829 50.000 12.79 2.33 37.70 3.41
192 194 1.555075 GCTGTCCCATCAGTTACTGGA 59.445 52.381 12.79 0.00 37.70 3.86
193 195 1.278985 TGCTGTCCCATCAGTTACTGG 59.721 52.381 12.79 0.00 37.70 4.00
194 196 2.744202 GTTGCTGTCCCATCAGTTACTG 59.256 50.000 5.94 5.94 37.70 2.74
195 197 2.371841 TGTTGCTGTCCCATCAGTTACT 59.628 45.455 0.00 0.00 37.70 2.24
196 198 2.778299 TGTTGCTGTCCCATCAGTTAC 58.222 47.619 0.00 0.00 37.70 2.50
197 199 3.411446 CTTGTTGCTGTCCCATCAGTTA 58.589 45.455 0.00 0.00 37.70 2.24
198 200 2.233271 CTTGTTGCTGTCCCATCAGTT 58.767 47.619 0.00 0.00 37.70 3.16
199 201 1.901591 CTTGTTGCTGTCCCATCAGT 58.098 50.000 0.00 0.00 37.70 3.41
200 202 0.524862 GCTTGTTGCTGTCCCATCAG 59.475 55.000 0.00 0.00 38.95 2.90
222 224 6.383726 TGCTCCCTGGCAAATTCTATTTTATT 59.616 34.615 0.00 0.00 39.43 1.40
266 268 8.437360 TGTCTATTACTGCCACTCAATTATTG 57.563 34.615 0.00 0.00 0.00 1.90
297 299 2.560542 TGACCATGGCACCACAAATTAC 59.439 45.455 13.04 0.00 0.00 1.89
402 566 6.989155 ATAGTCGAATATGTTCCCTGGTTA 57.011 37.500 4.29 0.00 0.00 2.85
403 567 5.888982 ATAGTCGAATATGTTCCCTGGTT 57.111 39.130 4.29 0.00 0.00 3.67
405 569 7.170393 TGATATAGTCGAATATGTTCCCTGG 57.830 40.000 15.30 0.00 0.00 4.45
533 697 6.969473 GCTGATGCTATACTTTGAAAAGGTTC 59.031 38.462 7.65 0.00 35.23 3.62
534 698 6.434028 TGCTGATGCTATACTTTGAAAAGGTT 59.566 34.615 7.65 0.00 37.44 3.50
536 700 6.441093 TGCTGATGCTATACTTTGAAAAGG 57.559 37.500 7.65 0.00 39.01 3.11
537 701 9.049523 TCTATGCTGATGCTATACTTTGAAAAG 57.950 33.333 1.22 1.22 39.84 2.27
538 702 8.830580 GTCTATGCTGATGCTATACTTTGAAAA 58.169 33.333 0.00 0.00 40.48 2.29
539 703 8.206867 AGTCTATGCTGATGCTATACTTTGAAA 58.793 33.333 0.00 0.00 40.48 2.69
540 704 7.730084 AGTCTATGCTGATGCTATACTTTGAA 58.270 34.615 0.00 0.00 40.48 2.69
541 705 7.295322 AGTCTATGCTGATGCTATACTTTGA 57.705 36.000 0.00 0.00 40.48 2.69
542 706 7.959689 AAGTCTATGCTGATGCTATACTTTG 57.040 36.000 0.00 0.00 40.48 2.77
545 709 9.703892 CTTTTAAGTCTATGCTGATGCTATACT 57.296 33.333 0.00 0.00 40.48 2.12
546 710 9.482627 ACTTTTAAGTCTATGCTGATGCTATAC 57.517 33.333 0.00 0.00 35.65 1.47
548 712 7.989741 ACACTTTTAAGTCTATGCTGATGCTAT 59.010 33.333 0.00 0.00 37.08 2.97
613 785 3.149436 GCACCATGCATGTATTCGTTT 57.851 42.857 24.58 0.00 44.26 3.60
625 797 0.609662 AATCACCCAAAGCACCATGC 59.390 50.000 0.00 0.00 45.46 4.06
649 821 2.221981 GGCATCGACTAGCATAAGCAAC 59.778 50.000 8.36 0.00 45.49 4.17
669 841 4.760047 CACCGTGCTTCCCTCCGG 62.760 72.222 0.00 0.00 45.72 5.14
692 864 3.832490 GTGTTAGAGCCCCAATTTTTCCT 59.168 43.478 0.00 0.00 0.00 3.36
693 865 3.056107 GGTGTTAGAGCCCCAATTTTTCC 60.056 47.826 0.00 0.00 0.00 3.13
700 872 4.341199 TGGGTGTTAGAGCCCCAA 57.659 55.556 0.00 0.00 45.38 4.12
742 2075 6.425210 TGGGAGTTGGTTGATCTGATATAG 57.575 41.667 0.00 0.00 0.00 1.31
743 2076 8.504811 TTATGGGAGTTGGTTGATCTGATATA 57.495 34.615 0.00 0.00 0.00 0.86
772 2105 4.283467 AGGTGTCAGCATAGTGTTCAACTA 59.717 41.667 4.59 0.00 45.47 2.24
777 2110 3.319137 TCAGGTGTCAGCATAGTGTTC 57.681 47.619 4.59 0.00 0.00 3.18
805 2138 1.005097 TCATGCATGGAAAGAGCCAGT 59.995 47.619 25.97 0.00 42.15 4.00
836 2171 9.073368 CATTTATACGGTCCATACTATCTTTCG 57.927 37.037 0.00 0.00 0.00 3.46
844 2179 4.967084 TGGCATTTATACGGTCCATACT 57.033 40.909 0.00 0.00 0.00 2.12
848 2183 3.389656 TCTCATGGCATTTATACGGTCCA 59.610 43.478 0.00 0.00 0.00 4.02
851 2186 7.450074 TCTAAATCTCATGGCATTTATACGGT 58.550 34.615 0.00 0.00 0.00 4.83
955 2294 9.086758 AGTTTTCTGTTAGAGCTTTACCTACTA 57.913 33.333 0.00 0.00 0.00 1.82
963 2302 7.588497 ATCCAAAGTTTTCTGTTAGAGCTTT 57.412 32.000 0.00 0.00 0.00 3.51
984 2324 1.230212 CCTTTGGGCTGGGGTATCC 59.770 63.158 0.00 0.00 0.00 2.59
986 2326 3.438822 CCCTTTGGGCTGGGGTAT 58.561 61.111 0.00 0.00 39.76 2.73
1015 2355 5.867174 CACGTACTTCATGGTGACTAATTGA 59.133 40.000 0.00 0.00 32.23 2.57
1016 2356 5.063438 CCACGTACTTCATGGTGACTAATTG 59.937 44.000 0.00 0.00 32.23 2.32
1017 2357 5.175859 CCACGTACTTCATGGTGACTAATT 58.824 41.667 0.00 0.00 32.23 1.40
1018 2358 4.382685 CCCACGTACTTCATGGTGACTAAT 60.383 45.833 0.00 0.00 32.23 1.73
1019 2359 3.056393 CCCACGTACTTCATGGTGACTAA 60.056 47.826 0.00 0.00 32.23 2.24
1020 2360 2.494471 CCCACGTACTTCATGGTGACTA 59.506 50.000 0.00 0.00 32.23 2.59
1065 2430 6.986817 AGTCCATTTGTCTCGTTATATCTTGG 59.013 38.462 0.00 0.00 0.00 3.61
1148 2513 0.183492 AGCCAAGTGTCCTTCTTGCA 59.817 50.000 0.00 0.00 40.35 4.08
1150 2515 2.557920 AGAGCCAAGTGTCCTTCTTG 57.442 50.000 0.00 0.00 41.06 3.02
1152 2517 2.027653 GCTTAGAGCCAAGTGTCCTTCT 60.028 50.000 0.00 0.00 34.48 2.85
1153 2518 2.027653 AGCTTAGAGCCAAGTGTCCTTC 60.028 50.000 0.00 0.00 43.77 3.46
1154 2519 1.981495 AGCTTAGAGCCAAGTGTCCTT 59.019 47.619 0.00 0.00 43.77 3.36
1155 2520 1.650528 AGCTTAGAGCCAAGTGTCCT 58.349 50.000 0.00 0.00 43.77 3.85
1186 2551 4.489737 TGTTAGAAGAAGACTGGGAGGAA 58.510 43.478 0.00 0.00 0.00 3.36
1337 2707 6.825721 AGTGAAGCAAAGAAGAAGAAGAAGAA 59.174 34.615 0.00 0.00 0.00 2.52
1338 2708 6.352516 AGTGAAGCAAAGAAGAAGAAGAAGA 58.647 36.000 0.00 0.00 0.00 2.87
1339 2709 6.616774 AGTGAAGCAAAGAAGAAGAAGAAG 57.383 37.500 0.00 0.00 0.00 2.85
1340 2710 6.599244 TCAAGTGAAGCAAAGAAGAAGAAGAA 59.401 34.615 0.00 0.00 0.00 2.52
1341 2711 6.115446 TCAAGTGAAGCAAAGAAGAAGAAGA 58.885 36.000 0.00 0.00 0.00 2.87
1342 2712 6.369059 TCAAGTGAAGCAAAGAAGAAGAAG 57.631 37.500 0.00 0.00 0.00 2.85
1343 2713 6.949352 ATCAAGTGAAGCAAAGAAGAAGAA 57.051 33.333 0.00 0.00 0.00 2.52
1344 2714 6.732154 CAATCAAGTGAAGCAAAGAAGAAGA 58.268 36.000 0.00 0.00 0.00 2.87
1345 2715 5.401674 GCAATCAAGTGAAGCAAAGAAGAAG 59.598 40.000 4.73 0.00 31.95 2.85
1386 2759 4.185467 AGATGAACACTCACAGTAGCTG 57.815 45.455 0.00 0.00 33.30 4.24
1391 2764 4.944619 TGAGAAGATGAACACTCACAGT 57.055 40.909 0.00 0.00 35.01 3.55
1397 2770 6.302269 ACCATTTCTTGAGAAGATGAACACT 58.698 36.000 12.99 0.00 37.38 3.55
1412 2785 5.576447 AAGAAAACACACGACCATTTCTT 57.424 34.783 6.10 6.10 42.43 2.52
1424 2797 5.253330 ACAACCTCAGAGAAAGAAAACACA 58.747 37.500 0.00 0.00 0.00 3.72
1539 2912 5.245531 TCATTTAGTTGTGCAGGTAGAAGG 58.754 41.667 0.00 0.00 0.00 3.46
1552 2925 7.657761 ACACTCAGTTTCCTACTCATTTAGTTG 59.342 37.037 0.00 0.00 39.80 3.16
1651 3055 2.281970 CTGCCAGCAAGCTCACCA 60.282 61.111 0.00 0.00 0.00 4.17
1684 3109 1.966451 GCACCACTACCACACAGCC 60.966 63.158 0.00 0.00 0.00 4.85
1817 4564 1.554392 CAGGACGAAGATGAAGCTCG 58.446 55.000 0.00 0.00 0.00 5.03
1819 4566 1.066573 CACCAGGACGAAGATGAAGCT 60.067 52.381 0.00 0.00 0.00 3.74
1849 4596 2.749441 GCAACTCCAGCTCCAGCC 60.749 66.667 0.00 0.00 43.38 4.85
1914 4661 1.202770 AGTAGCACCAACTCCAACCAC 60.203 52.381 0.00 0.00 0.00 4.16
2041 4803 2.691771 CCAGAAGCAGCAGCAGCAG 61.692 63.158 12.92 0.00 45.49 4.24
2042 4804 2.671963 CCAGAAGCAGCAGCAGCA 60.672 61.111 12.92 0.00 45.49 4.41
2043 4805 2.809861 TACCCAGAAGCAGCAGCAGC 62.810 60.000 3.17 0.46 45.49 5.25
2055 4817 0.927767 GGAGGAGAGGAGTACCCAGA 59.072 60.000 3.60 0.00 37.41 3.86
2142 4906 5.977129 CCAAATTCACAACTTGTTGGTACTC 59.023 40.000 16.48 0.00 32.58 2.59
2148 4912 4.370917 CTCCCCAAATTCACAACTTGTTG 58.629 43.478 11.44 11.44 0.00 3.33
2210 5058 6.407475 AAAATTGAGCCGAAATAAACATGC 57.593 33.333 0.00 0.00 0.00 4.06
2222 5070 0.451783 CGGGGAGAAAAATTGAGCCG 59.548 55.000 0.00 0.00 0.00 5.52
2282 5130 2.572191 ATGCCGCAATCTCAAACATG 57.428 45.000 0.00 0.00 0.00 3.21
2287 5135 4.639755 TGATTCTAAATGCCGCAATCTCAA 59.360 37.500 0.00 0.00 0.00 3.02
2295 5143 5.466728 TGAGATAACTGATTCTAAATGCCGC 59.533 40.000 0.00 0.00 0.00 6.53
2663 5579 3.386726 GGCACCCCAATAAAACTAATCCC 59.613 47.826 0.00 0.00 0.00 3.85
2833 5751 6.758886 CCAACTGATACTCCAGTCAAATAGAC 59.241 42.308 0.00 0.00 45.82 2.59
3051 5975 6.463995 TGCTTTTACAGTTTCATGTTCCTT 57.536 33.333 0.00 0.00 34.56 3.36
3053 5977 7.653311 AGAAATGCTTTTACAGTTTCATGTTCC 59.347 33.333 0.00 0.00 34.56 3.62
3091 6015 7.818930 GGCCACTTCATTGAAAGAAAATAATCA 59.181 33.333 0.00 0.00 0.00 2.57
3119 6043 0.319405 ATGCAGAGCAAACCAAAGGC 59.681 50.000 0.00 0.00 43.62 4.35
3828 6758 1.163420 CCAGCGTTTGGTGCAGTACA 61.163 55.000 0.00 0.00 42.41 2.90
4177 7107 6.950619 AGTTCTGATAGAAGGCCAAAAGATTT 59.049 34.615 5.01 0.00 34.42 2.17
4696 7626 6.229936 AGTGCTTCCATTGCATGAAATTAT 57.770 33.333 0.00 0.00 42.69 1.28
4876 7806 3.248363 CAGAAACAATGAGAACGACTGCA 59.752 43.478 0.00 0.00 0.00 4.41
4937 7867 9.104713 TGGAACATCAATGTATATATCAGGACT 57.895 33.333 0.00 0.00 40.80 3.85
5149 8079 1.557099 TATTGGTCGCAGTCTGGAGT 58.443 50.000 1.14 0.00 0.00 3.85
5233 8163 0.397941 CCTTCTTGCTGTCTGGACCA 59.602 55.000 0.00 0.00 0.00 4.02
5514 8444 1.458445 CATCAACTCAGCTGACACACG 59.542 52.381 13.74 5.23 0.00 4.49
5566 8496 4.883585 ACACATATAACATGCACTCCAAGG 59.116 41.667 0.00 0.00 0.00 3.61
5963 8893 1.131303 TTGTCCCACGGATCCCTGTT 61.131 55.000 6.06 0.00 32.73 3.16
5970 8900 2.275418 GCCCATTGTCCCACGGAT 59.725 61.111 0.00 0.00 32.73 4.18
6101 9031 1.296715 GCCAGCTCCTTCGAGGAAA 59.703 57.895 0.00 0.00 45.28 3.13
6146 9076 8.589335 ACTTATAAGCAGTTCCGTAATGTATG 57.411 34.615 12.54 0.00 0.00 2.39
6147 9077 9.688592 GTACTTATAAGCAGTTCCGTAATGTAT 57.311 33.333 12.54 0.00 0.00 2.29
6148 9078 8.137437 GGTACTTATAAGCAGTTCCGTAATGTA 58.863 37.037 12.54 0.00 0.00 2.29
6149 9079 6.982724 GGTACTTATAAGCAGTTCCGTAATGT 59.017 38.462 12.54 0.00 0.00 2.71
6152 9082 6.071447 TGTGGTACTTATAAGCAGTTCCGTAA 60.071 38.462 12.54 0.00 35.07 3.18
6238 9173 2.515926 GTGAGCAACACTGACTGAGA 57.484 50.000 6.77 0.00 45.13 3.27
6288 9223 5.986135 CGTCTTAACATCCTCCATTCTAAGG 59.014 44.000 0.00 0.00 0.00 2.69
6300 9235 0.461135 TACGGGGCGTCTTAACATCC 59.539 55.000 0.00 0.00 41.54 3.51
6307 9242 0.322322 TTGTTCATACGGGGCGTCTT 59.678 50.000 0.00 0.00 41.54 3.01
6313 9248 1.405105 CAAGGCATTGTTCATACGGGG 59.595 52.381 2.19 0.00 0.00 5.73
6386 9322 7.707624 TTCACCTTCAGATTAATCAAGCAAT 57.292 32.000 17.56 0.00 0.00 3.56
6588 9524 2.465813 CACTCCTCCCACTGATCTTCT 58.534 52.381 0.00 0.00 0.00 2.85
6633 9569 3.125316 GCTGCTTATTTTCGTACTGCTGT 59.875 43.478 0.66 0.66 0.00 4.40
6800 9736 7.575720 GCATCTATAAAAGGCACTGTTGAGTTT 60.576 37.037 0.00 0.00 36.07 2.66
6912 9850 1.677576 CATTGTGTCACAGCACCACTT 59.322 47.619 5.67 0.00 38.52 3.16
7000 9939 5.503498 GTGCACACACGTAAAATCAACTAA 58.497 37.500 13.17 0.00 36.98 2.24
7245 10184 1.277557 CTGTGCAGTTCTCTTAGGCCT 59.722 52.381 11.78 11.78 0.00 5.19
7343 10282 6.379703 TCTTGATTTTGGAGTTCCTTTGTTGA 59.620 34.615 0.00 0.00 36.82 3.18
7441 10380 9.618890 ATCATTGCTTTAATCTACACATGTACT 57.381 29.630 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.