Multiple sequence alignment - TraesCS6A01G329000

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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 TraesCS6A01G329000 chr6A 100.000 2306 0 0 1 2306 562471462 562469157 0.000000e+00 4259.0
1 TraesCS6A01G329000 chr6A 85.856 1209 92 41 584 1730 562250436 562251627 0.000000e+00 1212.0
2 TraesCS6A01G329000 chr6A 81.268 1404 121 67 210 1532 562271221 562272563 0.000000e+00 1005.0
3 TraesCS6A01G329000 chr6A 85.429 700 40 22 741 1383 562400759 562400065 0.000000e+00 671.0
4 TraesCS6A01G329000 chr6A 81.862 827 76 33 883 1674 562487978 562487191 1.500000e-176 628.0
5 TraesCS6A01G329000 chr6A 88.981 363 25 6 166 519 562249640 562249996 3.520000e-118 435.0
6 TraesCS6A01G329000 chr6A 84.228 298 17 17 421 718 562402220 562401953 1.760000e-66 263.0
7 TraesCS6A01G329000 chr6A 88.360 189 17 3 2068 2252 562251979 562252166 2.980000e-54 222.0
8 TraesCS6A01G329000 chr6A 82.955 176 26 4 2003 2176 49738628 49738801 3.070000e-34 156.0
9 TraesCS6A01G329000 chr6A 78.710 155 14 11 663 799 562488261 562488108 4.080000e-13 86.1
10 TraesCS6A01G329000 chr6D 84.834 1721 119 50 106 1730 418883832 418882158 0.000000e+00 1602.0
11 TraesCS6A01G329000 chr6D 81.204 1229 98 60 210 1383 418770714 418769564 0.000000e+00 867.0
12 TraesCS6A01G329000 chr6D 82.527 847 87 26 614 1412 418893102 418892269 0.000000e+00 688.0
13 TraesCS6A01G329000 chr6D 89.847 522 29 7 883 1383 418732867 418733385 0.000000e+00 649.0
14 TraesCS6A01G329000 chr6D 83.651 630 53 31 162 778 418732204 418732796 4.330000e-152 547.0
15 TraesCS6A01G329000 chr6D 82.892 415 44 13 1902 2306 418882134 418881737 4.720000e-92 348.0
16 TraesCS6A01G329000 chr6D 81.959 194 28 6 2005 2193 29138775 29138584 8.530000e-35 158.0
17 TraesCS6A01G329000 chr6D 89.130 92 9 1 7 98 224801570 224801660 1.870000e-21 113.0
18 TraesCS6A01G329000 chr6D 95.000 60 2 1 1832 1890 108483209 108483268 2.440000e-15 93.5
19 TraesCS6A01G329000 chr6B 84.072 1601 134 57 219 1730 631535623 631534055 0.000000e+00 1432.0
20 TraesCS6A01G329000 chr6B 83.740 1556 121 52 162 1678 631741837 631740375 0.000000e+00 1351.0
21 TraesCS6A01G329000 chr6B 83.267 1261 107 51 159 1383 631192565 631193757 0.000000e+00 1064.0
22 TraesCS6A01G329000 chr6B 83.757 905 84 37 807 1681 631844098 631843227 0.000000e+00 798.0
23 TraesCS6A01G329000 chr6B 85.467 578 52 18 833 1383 631246235 631245663 7.150000e-160 573.0
24 TraesCS6A01G329000 chr6B 84.533 375 37 14 200 566 631846280 631845919 3.650000e-93 351.0
25 TraesCS6A01G329000 chr6B 78.061 588 53 39 210 784 631247038 631246514 3.720000e-78 302.0
26 TraesCS6A01G329000 chr6B 84.694 196 26 4 2060 2252 631523816 631523622 2.340000e-45 193.0
27 TraesCS6A01G329000 chr6B 89.011 91 10 0 7 97 706121459 706121549 1.870000e-21 113.0
28 TraesCS6A01G329000 chr6B 95.000 60 2 1 1832 1890 633613110 633613169 2.440000e-15 93.5
29 TraesCS6A01G329000 chr5A 82.215 298 46 7 1985 2279 546690795 546690502 1.370000e-62 250.0
30 TraesCS6A01G329000 chr4B 83.012 259 40 4 1979 2234 123461097 123461354 4.950000e-57 231.0
31 TraesCS6A01G329000 chr4B 88.542 96 11 0 2 97 536836408 536836313 1.450000e-22 117.0
32 TraesCS6A01G329000 chr4B 95.000 60 2 1 1832 1890 495481640 495481581 2.440000e-15 93.5
33 TraesCS6A01G329000 chr2B 85.024 207 27 4 1987 2191 358634507 358634303 8.350000e-50 207.0
34 TraesCS6A01G329000 chrUn 94.355 124 7 0 1718 1841 86483185 86483062 8.410000e-45 191.0
35 TraesCS6A01G329000 chrUn 94.355 124 7 0 1718 1841 186186282 186186405 8.410000e-45 191.0
36 TraesCS6A01G329000 chrUn 94.355 124 7 0 1718 1841 221557218 221557095 8.410000e-45 191.0
37 TraesCS6A01G329000 chrUn 94.355 124 7 0 1718 1841 270846862 270846985 8.410000e-45 191.0
38 TraesCS6A01G329000 chrUn 94.355 124 7 0 1718 1841 349949502 349949625 8.410000e-45 191.0
39 TraesCS6A01G329000 chrUn 94.355 124 7 0 1718 1841 385378403 385378526 8.410000e-45 191.0
40 TraesCS6A01G329000 chrUn 95.000 60 2 1 1832 1890 217905669 217905728 2.440000e-15 93.5
41 TraesCS6A01G329000 chrUn 95.000 60 2 1 1832 1890 430768506 430768565 2.440000e-15 93.5
42 TraesCS6A01G329000 chr4D 94.355 124 7 0 1718 1841 123343219 123343096 8.410000e-45 191.0
43 TraesCS6A01G329000 chr4D 94.355 124 7 0 1718 1841 123557672 123557549 8.410000e-45 191.0
44 TraesCS6A01G329000 chr1D 94.355 124 7 0 1718 1841 185750662 185750785 8.410000e-45 191.0
45 TraesCS6A01G329000 chr5B 83.626 171 25 3 2022 2190 299025264 299025433 8.530000e-35 158.0
46 TraesCS6A01G329000 chr5B 76.259 139 26 4 2149 2285 608539976 608540109 1.480000e-07 67.6
47 TraesCS6A01G329000 chr3B 82.162 185 30 3 2005 2187 582409802 582409619 3.070000e-34 156.0
48 TraesCS6A01G329000 chr3A 91.753 97 8 0 2 98 57564501 57564597 4.000000e-28 135.0
49 TraesCS6A01G329000 chr2A 90.722 97 9 0 2 98 280533804 280533900 1.860000e-26 130.0
50 TraesCS6A01G329000 chr2A 87.500 96 11 1 7 102 718981790 718981884 2.420000e-20 110.0
51 TraesCS6A01G329000 chr3D 88.660 97 11 0 2 98 324422920 324423016 4.020000e-23 119.0
52 TraesCS6A01G329000 chr3D 95.000 60 2 1 1832 1890 501840371 501840312 2.440000e-15 93.5
53 TraesCS6A01G329000 chr5D 80.503 159 24 3 2130 2285 169969680 169969834 5.210000e-22 115.0
54 TraesCS6A01G329000 chr5D 83.019 106 11 5 1979 2081 69073988 69074089 3.160000e-14 89.8
55 TraesCS6A01G329000 chr1B 89.011 91 10 0 7 97 398962941 398962851 1.870000e-21 113.0
56 TraesCS6A01G329000 chr1B 79.592 147 21 7 2140 2285 633960525 633960663 1.890000e-16 97.1
57 TraesCS6A01G329000 chr1B 95.000 60 2 1 1832 1890 461438121 461438180 2.440000e-15 93.5
58 TraesCS6A01G329000 chr1B 95.000 60 2 1 1832 1890 619197311 619197252 2.440000e-15 93.5
59 TraesCS6A01G329000 chr7B 87.368 95 12 0 4 98 667373777 667373871 2.420000e-20 110.0
60 TraesCS6A01G329000 chr7D 95.000 60 2 1 1832 1890 382114071 382114130 2.440000e-15 93.5


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G329000 chr6A 562469157 562471462 2305 True 4259.00 4259 100.000000 1 2306 1 chr6A.!!$R1 2305
1 TraesCS6A01G329000 chr6A 562271221 562272563 1342 False 1005.00 1005 81.268000 210 1532 1 chr6A.!!$F2 1322
2 TraesCS6A01G329000 chr6A 562249640 562252166 2526 False 623.00 1212 87.732333 166 2252 3 chr6A.!!$F3 2086
3 TraesCS6A01G329000 chr6A 562400065 562402220 2155 True 467.00 671 84.828500 421 1383 2 chr6A.!!$R2 962
4 TraesCS6A01G329000 chr6A 562487191 562488261 1070 True 357.05 628 80.286000 663 1674 2 chr6A.!!$R3 1011
5 TraesCS6A01G329000 chr6D 418881737 418883832 2095 True 975.00 1602 83.863000 106 2306 2 chr6D.!!$R4 2200
6 TraesCS6A01G329000 chr6D 418769564 418770714 1150 True 867.00 867 81.204000 210 1383 1 chr6D.!!$R2 1173
7 TraesCS6A01G329000 chr6D 418892269 418893102 833 True 688.00 688 82.527000 614 1412 1 chr6D.!!$R3 798
8 TraesCS6A01G329000 chr6D 418732204 418733385 1181 False 598.00 649 86.749000 162 1383 2 chr6D.!!$F3 1221
9 TraesCS6A01G329000 chr6B 631534055 631535623 1568 True 1432.00 1432 84.072000 219 1730 1 chr6B.!!$R2 1511
10 TraesCS6A01G329000 chr6B 631740375 631741837 1462 True 1351.00 1351 83.740000 162 1678 1 chr6B.!!$R3 1516
11 TraesCS6A01G329000 chr6B 631192565 631193757 1192 False 1064.00 1064 83.267000 159 1383 1 chr6B.!!$F1 1224
12 TraesCS6A01G329000 chr6B 631843227 631846280 3053 True 574.50 798 84.145000 200 1681 2 chr6B.!!$R5 1481
13 TraesCS6A01G329000 chr6B 631245663 631247038 1375 True 437.50 573 81.764000 210 1383 2 chr6B.!!$R4 1173

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
70 71 0.106318 ATCTCCCAAATGCAGAGGCC 60.106 55.0 0.0 0.0 40.13 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1836 5511 0.107897 ACACGTTCCACTGTGCAGAA 60.108 50.0 6.17 0.0 39.71 3.02 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
55 56 8.906636 ATTAATAAAATGATCGCATGCATCTC 57.093 30.769 19.57 11.05 34.26 2.75
56 57 3.637998 AAAATGATCGCATGCATCTCC 57.362 42.857 19.57 2.12 34.26 3.71
57 58 1.531423 AATGATCGCATGCATCTCCC 58.469 50.000 19.57 0.65 34.26 4.30
58 59 0.399075 ATGATCGCATGCATCTCCCA 59.601 50.000 19.57 6.58 32.31 4.37
59 60 0.180878 TGATCGCATGCATCTCCCAA 59.819 50.000 19.57 1.41 0.00 4.12
60 61 1.311859 GATCGCATGCATCTCCCAAA 58.688 50.000 19.57 0.00 0.00 3.28
61 62 1.884579 GATCGCATGCATCTCCCAAAT 59.115 47.619 19.57 0.00 0.00 2.32
62 63 1.026584 TCGCATGCATCTCCCAAATG 58.973 50.000 19.57 0.00 0.00 2.32
68 69 1.030457 GCATCTCCCAAATGCAGAGG 58.970 55.000 3.35 0.00 46.93 3.69
69 70 1.030457 CATCTCCCAAATGCAGAGGC 58.970 55.000 0.00 0.00 41.68 4.70
70 71 0.106318 ATCTCCCAAATGCAGAGGCC 60.106 55.000 0.00 0.00 40.13 5.19
71 72 2.045045 TCCCAAATGCAGAGGCCG 60.045 61.111 0.00 0.00 40.13 6.13
72 73 3.142838 CCCAAATGCAGAGGCCGG 61.143 66.667 0.00 0.00 40.13 6.13
73 74 3.142838 CCAAATGCAGAGGCCGGG 61.143 66.667 2.18 0.00 40.13 5.73
74 75 3.142838 CAAATGCAGAGGCCGGGG 61.143 66.667 2.18 0.00 40.13 5.73
75 76 3.338250 AAATGCAGAGGCCGGGGA 61.338 61.111 2.18 0.00 40.13 4.81
76 77 2.693871 AAATGCAGAGGCCGGGGAT 61.694 57.895 2.18 0.00 40.13 3.85
77 78 2.631012 AAATGCAGAGGCCGGGGATC 62.631 60.000 2.18 0.00 40.13 3.36
79 80 3.564218 GCAGAGGCCGGGGATCAT 61.564 66.667 2.18 0.00 0.00 2.45
80 81 2.746359 CAGAGGCCGGGGATCATC 59.254 66.667 2.18 0.00 0.00 2.92
81 82 2.527875 AGAGGCCGGGGATCATCC 60.528 66.667 2.18 0.00 35.23 3.51
82 83 4.008933 GAGGCCGGGGATCATCCG 62.009 72.222 16.76 16.76 46.43 4.18
86 87 3.560251 CCGGGGATCATCCGCCTT 61.560 66.667 14.99 0.00 45.71 4.35
87 88 2.510906 CGGGGATCATCCGCCTTT 59.489 61.111 14.99 0.00 45.71 3.11
88 89 1.152963 CGGGGATCATCCGCCTTTT 60.153 57.895 14.99 0.00 45.71 2.27
89 90 1.166531 CGGGGATCATCCGCCTTTTC 61.167 60.000 14.99 0.00 45.71 2.29
90 91 0.183731 GGGGATCATCCGCCTTTTCT 59.816 55.000 9.73 0.00 43.03 2.52
91 92 1.420138 GGGGATCATCCGCCTTTTCTA 59.580 52.381 9.73 0.00 43.03 2.10
92 93 2.158667 GGGGATCATCCGCCTTTTCTAA 60.159 50.000 9.73 0.00 43.03 2.10
93 94 3.551846 GGGATCATCCGCCTTTTCTAAA 58.448 45.455 0.00 0.00 37.43 1.85
94 95 3.951680 GGGATCATCCGCCTTTTCTAAAA 59.048 43.478 0.00 0.00 37.43 1.52
95 96 4.401202 GGGATCATCCGCCTTTTCTAAAAA 59.599 41.667 0.00 0.00 37.43 1.94
142 143 2.766263 TGAAATACAGCCCACGAGAGAT 59.234 45.455 0.00 0.00 0.00 2.75
143 144 2.898729 AATACAGCCCACGAGAGATG 57.101 50.000 0.00 0.00 0.00 2.90
159 160 4.583871 AGAGATGAACCATGTTTGAGACC 58.416 43.478 0.00 0.00 0.00 3.85
160 161 4.288105 AGAGATGAACCATGTTTGAGACCT 59.712 41.667 0.00 0.00 0.00 3.85
176 195 7.645058 TTGAGACCTCAACAAAGAAAGAAAT 57.355 32.000 8.27 0.00 43.90 2.17
200 219 3.758425 TGCCTAAACCTAGTTCCCAAAC 58.242 45.455 0.00 0.00 35.50 2.93
213 232 1.512156 CCCAAACCCGAACAGGAACG 61.512 60.000 0.00 0.00 45.00 3.95
305 326 4.620332 CGACCAATTTAATTGCCACCATGT 60.620 41.667 11.82 3.16 38.92 3.21
320 349 3.562973 CACCATGTATCAACATCTCCTGC 59.437 47.826 0.00 0.00 44.70 4.85
369 398 2.125310 CAACGTGCCTATCCGCCA 60.125 61.111 0.00 0.00 0.00 5.69
378 407 4.569023 TATCCGCCAGCTCGCACG 62.569 66.667 3.68 0.00 0.00 5.34
518 573 2.683933 TGCCCCTCCTTCTCCGTC 60.684 66.667 0.00 0.00 0.00 4.79
529 584 0.394488 TTCTCCGTCGCCATCTCTCT 60.394 55.000 0.00 0.00 0.00 3.10
737 3552 3.680786 CGACACACCAGAGGCCGA 61.681 66.667 0.00 0.00 0.00 5.54
739 3554 3.941657 GACACACCAGAGGCCGAGC 62.942 68.421 0.00 0.00 0.00 5.03
746 3561 2.196229 AGAGGCCGAGCTCCGTAT 59.804 61.111 8.47 0.00 36.31 3.06
879 4369 1.917336 AACCACACCGAACCACACCT 61.917 55.000 0.00 0.00 0.00 4.00
880 4370 1.597027 CCACACCGAACCACACCTC 60.597 63.158 0.00 0.00 0.00 3.85
881 4371 1.145156 CACACCGAACCACACCTCA 59.855 57.895 0.00 0.00 0.00 3.86
937 4455 0.976641 CTCTTAGCACCACCACCAGA 59.023 55.000 0.00 0.00 0.00 3.86
1412 4997 0.179094 TCGTTTGTTGAGCACCGAGT 60.179 50.000 0.00 0.00 0.00 4.18
1448 5043 0.975556 TACATCTGCCTGCCGGAGAA 60.976 55.000 5.05 0.00 30.92 2.87
1576 5228 1.477558 GCAGGTATAGCACAGGCCAAT 60.478 52.381 5.01 0.00 42.56 3.16
1641 5312 4.469657 TGATGAAACCAGTAGGCTTTTGT 58.530 39.130 0.00 0.00 39.06 2.83
1648 5321 7.120579 TGAAACCAGTAGGCTTTTGTATATGTG 59.879 37.037 0.00 0.00 39.06 3.21
1730 5405 0.804989 CAACGCTGATCTCCAAACCC 59.195 55.000 0.00 0.00 0.00 4.11
1731 5406 0.693049 AACGCTGATCTCCAAACCCT 59.307 50.000 0.00 0.00 0.00 4.34
1732 5407 0.250513 ACGCTGATCTCCAAACCCTC 59.749 55.000 0.00 0.00 0.00 4.30
1734 5409 1.092345 GCTGATCTCCAAACCCTCGC 61.092 60.000 0.00 0.00 0.00 5.03
1735 5410 0.539051 CTGATCTCCAAACCCTCGCT 59.461 55.000 0.00 0.00 0.00 4.93
1736 5411 0.984230 TGATCTCCAAACCCTCGCTT 59.016 50.000 0.00 0.00 0.00 4.68
1737 5412 1.066143 TGATCTCCAAACCCTCGCTTC 60.066 52.381 0.00 0.00 0.00 3.86
1738 5413 1.208293 GATCTCCAAACCCTCGCTTCT 59.792 52.381 0.00 0.00 0.00 2.85
1739 5414 1.056660 TCTCCAAACCCTCGCTTCTT 58.943 50.000 0.00 0.00 0.00 2.52
1742 5417 0.517316 CCAAACCCTCGCTTCTTTCG 59.483 55.000 0.00 0.00 0.00 3.46
1743 5418 1.508632 CAAACCCTCGCTTCTTTCGA 58.491 50.000 0.00 0.00 34.52 3.71
1746 5421 0.895530 ACCCTCGCTTCTTTCGATCA 59.104 50.000 0.00 0.00 35.25 2.92
1747 5422 1.482593 ACCCTCGCTTCTTTCGATCAT 59.517 47.619 0.00 0.00 35.25 2.45
1749 5424 2.541762 CCCTCGCTTCTTTCGATCATTC 59.458 50.000 0.00 0.00 35.25 2.67
1750 5425 2.541762 CCTCGCTTCTTTCGATCATTCC 59.458 50.000 0.00 0.00 35.25 3.01
1751 5426 3.452474 CTCGCTTCTTTCGATCATTCCT 58.548 45.455 0.00 0.00 35.25 3.36
1752 5427 3.190079 TCGCTTCTTTCGATCATTCCTG 58.810 45.455 0.00 0.00 0.00 3.86
1753 5428 2.286067 CGCTTCTTTCGATCATTCCTGC 60.286 50.000 0.00 0.00 0.00 4.85
1754 5429 2.941720 GCTTCTTTCGATCATTCCTGCT 59.058 45.455 0.00 0.00 0.00 4.24
1755 5430 4.122776 GCTTCTTTCGATCATTCCTGCTA 58.877 43.478 0.00 0.00 0.00 3.49
1756 5431 4.572389 GCTTCTTTCGATCATTCCTGCTAA 59.428 41.667 0.00 0.00 0.00 3.09
1757 5432 5.065218 GCTTCTTTCGATCATTCCTGCTAAA 59.935 40.000 0.00 0.00 0.00 1.85
1758 5433 6.403636 GCTTCTTTCGATCATTCCTGCTAAAA 60.404 38.462 0.00 0.00 0.00 1.52
1759 5434 6.422776 TCTTTCGATCATTCCTGCTAAAAC 57.577 37.500 0.00 0.00 0.00 2.43
1760 5435 5.937540 TCTTTCGATCATTCCTGCTAAAACA 59.062 36.000 0.00 0.00 0.00 2.83
1761 5436 5.801350 TTCGATCATTCCTGCTAAAACAG 57.199 39.130 0.00 0.00 37.42 3.16
1762 5437 4.832248 TCGATCATTCCTGCTAAAACAGT 58.168 39.130 0.00 0.00 35.83 3.55
1763 5438 5.245531 TCGATCATTCCTGCTAAAACAGTT 58.754 37.500 0.00 0.00 35.83 3.16
1764 5439 5.122239 TCGATCATTCCTGCTAAAACAGTTG 59.878 40.000 0.00 0.00 35.83 3.16
1765 5440 5.644644 GATCATTCCTGCTAAAACAGTTGG 58.355 41.667 0.00 0.00 35.83 3.77
1766 5441 3.255642 TCATTCCTGCTAAAACAGTTGGC 59.744 43.478 0.00 0.00 35.83 4.52
1767 5442 2.356665 TCCTGCTAAAACAGTTGGCA 57.643 45.000 8.09 8.09 35.83 4.92
1768 5443 2.660572 TCCTGCTAAAACAGTTGGCAA 58.339 42.857 0.00 0.00 35.83 4.52
1769 5444 3.230134 TCCTGCTAAAACAGTTGGCAAT 58.770 40.909 1.92 0.00 35.83 3.56
1770 5445 3.005684 TCCTGCTAAAACAGTTGGCAATG 59.994 43.478 1.92 5.69 35.83 2.82
1771 5446 3.005684 CCTGCTAAAACAGTTGGCAATGA 59.994 43.478 1.92 0.00 35.83 2.57
1772 5447 3.976169 TGCTAAAACAGTTGGCAATGAC 58.024 40.909 1.92 0.00 0.00 3.06
1773 5448 3.636300 TGCTAAAACAGTTGGCAATGACT 59.364 39.130 1.92 0.00 0.00 3.41
1774 5449 4.229876 GCTAAAACAGTTGGCAATGACTC 58.770 43.478 1.92 0.00 0.00 3.36
1775 5450 4.261572 GCTAAAACAGTTGGCAATGACTCA 60.262 41.667 1.92 0.00 0.00 3.41
1776 5451 4.942761 AAAACAGTTGGCAATGACTCAT 57.057 36.364 1.92 0.00 0.00 2.90
1777 5452 4.942761 AAACAGTTGGCAATGACTCATT 57.057 36.364 1.92 0.00 34.04 2.57
1791 5466 8.906636 CAATGACTCATTGGAAACTTCTATTG 57.093 34.615 20.15 0.00 45.03 1.90
1792 5467 7.636150 ATGACTCATTGGAAACTTCTATTGG 57.364 36.000 0.00 0.00 0.00 3.16
1793 5468 6.778821 TGACTCATTGGAAACTTCTATTGGA 58.221 36.000 0.00 0.00 0.00 3.53
1794 5469 7.405292 TGACTCATTGGAAACTTCTATTGGAT 58.595 34.615 0.00 0.00 0.00 3.41
1795 5470 7.554118 TGACTCATTGGAAACTTCTATTGGATC 59.446 37.037 0.00 0.00 0.00 3.36
1796 5471 7.637511 ACTCATTGGAAACTTCTATTGGATCT 58.362 34.615 0.00 0.00 0.00 2.75
1797 5472 7.555554 ACTCATTGGAAACTTCTATTGGATCTG 59.444 37.037 0.00 0.00 0.00 2.90
1798 5473 6.830324 TCATTGGAAACTTCTATTGGATCTGG 59.170 38.462 0.00 0.00 0.00 3.86
1799 5474 5.116084 TGGAAACTTCTATTGGATCTGGG 57.884 43.478 0.00 0.00 0.00 4.45
1800 5475 4.788075 TGGAAACTTCTATTGGATCTGGGA 59.212 41.667 0.00 0.00 0.00 4.37
1801 5476 5.104360 TGGAAACTTCTATTGGATCTGGGAG 60.104 44.000 0.00 0.00 0.00 4.30
1802 5477 5.131142 GGAAACTTCTATTGGATCTGGGAGA 59.869 44.000 0.00 0.00 0.00 3.71
1803 5478 6.353082 GGAAACTTCTATTGGATCTGGGAGAA 60.353 42.308 0.00 0.00 0.00 2.87
1804 5479 5.885449 ACTTCTATTGGATCTGGGAGAAG 57.115 43.478 18.31 18.31 43.51 2.85
1805 5480 5.533112 ACTTCTATTGGATCTGGGAGAAGA 58.467 41.667 23.03 5.67 41.49 2.87
1806 5481 5.966935 ACTTCTATTGGATCTGGGAGAAGAA 59.033 40.000 23.03 10.98 41.49 2.52
1807 5482 6.099557 ACTTCTATTGGATCTGGGAGAAGAAG 59.900 42.308 23.03 18.12 41.49 2.85
1808 5483 5.781827 TCTATTGGATCTGGGAGAAGAAGA 58.218 41.667 0.00 0.00 0.00 2.87
1809 5484 6.205298 TCTATTGGATCTGGGAGAAGAAGAA 58.795 40.000 0.00 0.00 0.00 2.52
1810 5485 5.786121 ATTGGATCTGGGAGAAGAAGAAA 57.214 39.130 0.00 0.00 0.00 2.52
1811 5486 4.559862 TGGATCTGGGAGAAGAAGAAAC 57.440 45.455 0.00 0.00 0.00 2.78
1812 5487 3.264450 TGGATCTGGGAGAAGAAGAAACC 59.736 47.826 0.00 0.00 0.00 3.27
1813 5488 3.371059 GGATCTGGGAGAAGAAGAAACCC 60.371 52.174 0.00 0.00 40.79 4.11
1814 5489 2.701551 TCTGGGAGAAGAAGAAACCCA 58.298 47.619 0.00 0.00 46.74 4.51
1817 5492 4.034285 TGGGAGAAGAAGAAACCCAATC 57.966 45.455 0.00 0.00 46.06 2.67
1818 5493 3.397618 TGGGAGAAGAAGAAACCCAATCA 59.602 43.478 0.00 0.00 46.06 2.57
1819 5494 4.141041 TGGGAGAAGAAGAAACCCAATCAA 60.141 41.667 0.00 0.00 46.06 2.57
1820 5495 5.019470 GGGAGAAGAAGAAACCCAATCAAT 58.981 41.667 0.00 0.00 40.20 2.57
1821 5496 5.105595 GGGAGAAGAAGAAACCCAATCAATG 60.106 44.000 0.00 0.00 40.20 2.82
1833 5508 4.771114 CCAATCAATGGGTAGGTAGTCA 57.229 45.455 0.00 0.00 46.27 3.41
1834 5509 5.110814 CCAATCAATGGGTAGGTAGTCAA 57.889 43.478 0.00 0.00 46.27 3.18
1835 5510 5.694995 CCAATCAATGGGTAGGTAGTCAAT 58.305 41.667 0.00 0.00 46.27 2.57
1836 5511 6.129179 CCAATCAATGGGTAGGTAGTCAATT 58.871 40.000 0.00 0.00 46.27 2.32
1837 5512 6.607198 CCAATCAATGGGTAGGTAGTCAATTT 59.393 38.462 0.00 0.00 46.27 1.82
1838 5513 7.201821 CCAATCAATGGGTAGGTAGTCAATTTC 60.202 40.741 0.00 0.00 46.27 2.17
1839 5514 6.636454 TCAATGGGTAGGTAGTCAATTTCT 57.364 37.500 0.00 0.00 0.00 2.52
1840 5515 6.414732 TCAATGGGTAGGTAGTCAATTTCTG 58.585 40.000 0.00 0.00 0.00 3.02
1841 5516 4.216411 TGGGTAGGTAGTCAATTTCTGC 57.784 45.455 0.00 0.00 0.00 4.26
1842 5517 3.585289 TGGGTAGGTAGTCAATTTCTGCA 59.415 43.478 0.00 0.00 0.00 4.41
1843 5518 3.939592 GGGTAGGTAGTCAATTTCTGCAC 59.060 47.826 0.00 0.00 0.00 4.57
1844 5519 4.564821 GGGTAGGTAGTCAATTTCTGCACA 60.565 45.833 0.00 0.00 0.00 4.57
1845 5520 4.631813 GGTAGGTAGTCAATTTCTGCACAG 59.368 45.833 0.00 0.00 0.00 3.66
1846 5521 4.357918 AGGTAGTCAATTTCTGCACAGT 57.642 40.909 0.00 0.00 0.00 3.55
1847 5522 4.067896 AGGTAGTCAATTTCTGCACAGTG 58.932 43.478 0.00 0.00 0.00 3.66
1848 5523 3.189287 GGTAGTCAATTTCTGCACAGTGG 59.811 47.826 1.84 0.00 0.00 4.00
1849 5524 3.213206 AGTCAATTTCTGCACAGTGGA 57.787 42.857 1.84 0.00 0.00 4.02
1850 5525 3.554934 AGTCAATTTCTGCACAGTGGAA 58.445 40.909 1.84 0.00 0.00 3.53
1851 5526 3.316308 AGTCAATTTCTGCACAGTGGAAC 59.684 43.478 1.84 0.00 0.00 3.62
1852 5527 2.290367 TCAATTTCTGCACAGTGGAACG 59.710 45.455 1.84 0.00 45.86 3.95
1853 5528 1.967319 ATTTCTGCACAGTGGAACGT 58.033 45.000 1.84 0.00 45.86 3.99
1854 5529 1.013596 TTTCTGCACAGTGGAACGTG 58.986 50.000 1.84 0.00 45.86 4.49
1855 5530 0.107897 TTCTGCACAGTGGAACGTGT 60.108 50.000 1.84 0.00 45.86 4.49
1856 5531 0.747852 TCTGCACAGTGGAACGTGTA 59.252 50.000 1.84 0.00 45.86 2.90
1857 5532 1.137282 TCTGCACAGTGGAACGTGTAA 59.863 47.619 1.84 0.00 45.86 2.41
1858 5533 1.260561 CTGCACAGTGGAACGTGTAAC 59.739 52.381 1.84 0.00 45.86 2.50
1859 5534 0.584876 GCACAGTGGAACGTGTAACC 59.415 55.000 1.84 0.00 45.86 2.85
1860 5535 1.223187 CACAGTGGAACGTGTAACCC 58.777 55.000 0.00 0.00 45.86 4.11
1861 5536 0.249573 ACAGTGGAACGTGTAACCCG 60.250 55.000 0.00 0.00 45.86 5.28
1862 5537 1.301165 AGTGGAACGTGTAACCCGC 60.301 57.895 0.00 0.00 45.86 6.13
1863 5538 2.030862 TGGAACGTGTAACCCGCC 59.969 61.111 0.00 0.00 0.00 6.13
1864 5539 2.344872 GGAACGTGTAACCCGCCT 59.655 61.111 0.00 0.00 0.00 5.52
1865 5540 2.030958 GGAACGTGTAACCCGCCTG 61.031 63.158 0.00 0.00 0.00 4.85
1866 5541 2.667199 AACGTGTAACCCGCCTGC 60.667 61.111 0.00 0.00 0.00 4.85
1867 5542 3.173167 AACGTGTAACCCGCCTGCT 62.173 57.895 0.00 0.00 0.00 4.24
1868 5543 3.118454 CGTGTAACCCGCCTGCTG 61.118 66.667 0.00 0.00 0.00 4.41
1869 5544 2.032071 GTGTAACCCGCCTGCTGT 59.968 61.111 0.00 0.00 0.00 4.40
1870 5545 2.033194 GTGTAACCCGCCTGCTGTC 61.033 63.158 0.00 0.00 0.00 3.51
1871 5546 2.436115 GTAACCCGCCTGCTGTCC 60.436 66.667 0.00 0.00 0.00 4.02
1872 5547 2.925706 TAACCCGCCTGCTGTCCA 60.926 61.111 0.00 0.00 0.00 4.02
1873 5548 2.521451 TAACCCGCCTGCTGTCCAA 61.521 57.895 0.00 0.00 0.00 3.53
1874 5549 2.463589 TAACCCGCCTGCTGTCCAAG 62.464 60.000 0.00 0.00 0.00 3.61
1875 5550 4.335647 CCCGCCTGCTGTCCAAGT 62.336 66.667 0.00 0.00 0.00 3.16
1876 5551 2.743928 CCGCCTGCTGTCCAAGTC 60.744 66.667 0.00 0.00 0.00 3.01
1877 5552 2.031012 CGCCTGCTGTCCAAGTCA 59.969 61.111 0.00 0.00 0.00 3.41
1878 5553 1.597854 CGCCTGCTGTCCAAGTCAA 60.598 57.895 0.00 0.00 0.00 3.18
1879 5554 1.845809 CGCCTGCTGTCCAAGTCAAC 61.846 60.000 0.00 0.00 0.00 3.18
1880 5555 1.518903 GCCTGCTGTCCAAGTCAACC 61.519 60.000 0.00 0.00 0.00 3.77
1881 5556 0.179020 CCTGCTGTCCAAGTCAACCA 60.179 55.000 0.00 0.00 0.00 3.67
1882 5557 0.947244 CTGCTGTCCAAGTCAACCAC 59.053 55.000 0.00 0.00 0.00 4.16
1883 5558 0.546122 TGCTGTCCAAGTCAACCACT 59.454 50.000 0.00 0.00 36.64 4.00
1884 5559 0.947244 GCTGTCCAAGTCAACCACTG 59.053 55.000 0.00 0.00 34.56 3.66
1885 5560 1.475034 GCTGTCCAAGTCAACCACTGA 60.475 52.381 0.00 0.00 34.56 3.41
1886 5561 2.917933 CTGTCCAAGTCAACCACTGAA 58.082 47.619 0.00 0.00 35.22 3.02
1887 5562 3.480470 CTGTCCAAGTCAACCACTGAAT 58.520 45.455 0.00 0.00 35.22 2.57
1888 5563 3.885297 CTGTCCAAGTCAACCACTGAATT 59.115 43.478 0.00 0.00 42.96 2.17
1889 5564 4.277476 TGTCCAAGTCAACCACTGAATTT 58.723 39.130 0.00 0.00 39.25 1.82
1890 5565 4.709397 TGTCCAAGTCAACCACTGAATTTT 59.291 37.500 0.00 0.00 39.25 1.82
1891 5566 5.186797 TGTCCAAGTCAACCACTGAATTTTT 59.813 36.000 0.00 0.00 39.25 1.94
1917 5592 1.202879 ACAGCGGAGAAAACCAATCCA 60.203 47.619 0.00 0.00 32.31 3.41
1918 5593 2.094675 CAGCGGAGAAAACCAATCCAT 58.905 47.619 0.00 0.00 32.31 3.41
1924 5599 3.375299 GGAGAAAACCAATCCATCGACAG 59.625 47.826 0.00 0.00 33.08 3.51
1925 5600 4.253685 GAGAAAACCAATCCATCGACAGA 58.746 43.478 0.00 0.00 0.00 3.41
1932 5607 2.522836 ATCCATCGACAGAGATGCAC 57.477 50.000 0.00 0.00 44.86 4.57
1938 5613 1.216444 GACAGAGATGCACGAGCCA 59.784 57.895 1.39 0.00 41.13 4.75
1955 5630 1.086696 CCAACCATCCAACTGTAGCG 58.913 55.000 0.00 0.00 0.00 4.26
1956 5631 1.610624 CCAACCATCCAACTGTAGCGT 60.611 52.381 0.00 0.00 0.00 5.07
1968 5653 3.667360 ACTGTAGCGTAAACCGGATTTT 58.333 40.909 9.46 0.84 36.94 1.82
1970 5655 4.627035 ACTGTAGCGTAAACCGGATTTTAC 59.373 41.667 9.46 13.00 38.21 2.01
1976 5661 7.381766 AGCGTAAACCGGATTTTACTTAATT 57.618 32.000 19.69 4.41 39.05 1.40
1996 5681 9.755064 CTTAATTAGACGATTTTCATCAAACGT 57.245 29.630 0.00 0.00 35.89 3.99
2016 5701 7.784633 AACGTGACCAAATTCATCAAAATTT 57.215 28.000 0.00 0.00 38.95 1.82
2042 5728 9.187996 TGGATAGAAAATAGACAAAATCATGCA 57.812 29.630 0.00 0.00 0.00 3.96
2072 5912 7.251704 AGCATGCAAATATGTCTACTACAAC 57.748 36.000 21.98 0.00 42.70 3.32
2118 5958 8.804688 TTAACCGGATGTTCAATAAGTTTTTG 57.195 30.769 9.46 0.03 38.42 2.44
2149 5989 8.675705 TTGATTATGTTATCCCACACATACTG 57.324 34.615 0.00 0.00 35.94 2.74
2152 5992 4.502105 TGTTATCCCACACATACTGCAT 57.498 40.909 0.00 0.00 0.00 3.96
2193 6033 3.954200 TGTATGTGCATGAATGGTCTGT 58.046 40.909 0.00 0.00 0.00 3.41
2195 6035 1.441738 TGTGCATGAATGGTCTGTCG 58.558 50.000 0.00 0.00 0.00 4.35
2204 6044 4.968197 GGTCTGTCGTGTGACCTC 57.032 61.111 13.31 0.00 46.65 3.85
2211 6051 3.072211 CTGTCGTGTGACCTCTACTACA 58.928 50.000 0.00 0.00 44.86 2.74
2215 6055 5.884232 TGTCGTGTGACCTCTACTACATTAT 59.116 40.000 0.00 0.00 44.86 1.28
2235 6075 2.202851 CAGCTCGTGCAGGCTAGG 60.203 66.667 12.58 0.00 42.74 3.02
2238 6078 4.135153 CTCGTGCAGGCTAGGCGT 62.135 66.667 11.10 0.00 0.00 5.68
2239 6079 4.435436 TCGTGCAGGCTAGGCGTG 62.435 66.667 11.10 10.55 45.60 5.34
2240 6080 4.742201 CGTGCAGGCTAGGCGTGT 62.742 66.667 11.10 0.00 44.79 4.49
2241 6081 2.577059 GTGCAGGCTAGGCGTGTA 59.423 61.111 11.10 6.55 44.79 2.90
2243 6083 1.680989 TGCAGGCTAGGCGTGTAGA 60.681 57.895 11.10 0.00 44.79 2.59
2245 6085 1.066587 CAGGCTAGGCGTGTAGAGC 59.933 63.158 11.10 0.00 39.23 4.09
2247 6087 0.970937 AGGCTAGGCGTGTAGAGCAA 60.971 55.000 11.10 0.00 36.63 3.91
2251 6091 2.893637 CTAGGCGTGTAGAGCAACAAT 58.106 47.619 0.00 0.00 36.08 2.71
2252 6092 2.185004 AGGCGTGTAGAGCAACAATT 57.815 45.000 0.00 0.00 36.08 2.32
2266 6106 6.373774 AGAGCAACAATTAATGAGTGAAGGAG 59.626 38.462 0.00 0.00 0.00 3.69
2268 6108 6.072286 AGCAACAATTAATGAGTGAAGGAGTG 60.072 38.462 0.00 0.00 0.00 3.51
2279 6119 5.702670 TGAGTGAAGGAGTGAATCAATCAAC 59.297 40.000 12.86 5.25 42.88 3.18
2300 6140 6.595326 TCAACATGTACATTAAGAAGAGGCAG 59.405 38.462 5.37 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 9.350357 GAGATGCATGCGATCATTTTATTAATT 57.650 29.630 23.23 6.43 0.00 1.40
30 31 7.972277 GGAGATGCATGCGATCATTTTATTAAT 59.028 33.333 23.23 5.30 0.00 1.40
31 32 7.307694 GGAGATGCATGCGATCATTTTATTAA 58.692 34.615 23.23 0.93 0.00 1.40
32 33 6.127925 GGGAGATGCATGCGATCATTTTATTA 60.128 38.462 23.23 1.32 0.00 0.98
33 34 5.336213 GGGAGATGCATGCGATCATTTTATT 60.336 40.000 23.23 8.37 0.00 1.40
34 35 4.157289 GGGAGATGCATGCGATCATTTTAT 59.843 41.667 23.23 6.91 0.00 1.40
35 36 3.503363 GGGAGATGCATGCGATCATTTTA 59.497 43.478 23.23 2.61 0.00 1.52
36 37 2.295349 GGGAGATGCATGCGATCATTTT 59.705 45.455 23.23 9.68 0.00 1.82
37 38 1.884579 GGGAGATGCATGCGATCATTT 59.115 47.619 23.23 5.86 0.00 2.32
38 39 1.202842 TGGGAGATGCATGCGATCATT 60.203 47.619 23.23 10.47 0.00 2.57
39 40 0.399075 TGGGAGATGCATGCGATCAT 59.601 50.000 23.23 9.75 0.00 2.45
40 41 0.180878 TTGGGAGATGCATGCGATCA 59.819 50.000 23.23 10.77 0.00 2.92
41 42 1.311859 TTTGGGAGATGCATGCGATC 58.688 50.000 14.09 16.08 0.00 3.69
42 43 1.611977 CATTTGGGAGATGCATGCGAT 59.388 47.619 14.09 7.77 0.00 4.58
43 44 1.026584 CATTTGGGAGATGCATGCGA 58.973 50.000 14.09 2.48 0.00 5.10
44 45 0.596600 GCATTTGGGAGATGCATGCG 60.597 55.000 14.09 0.00 46.96 4.73
45 46 3.284197 GCATTTGGGAGATGCATGC 57.716 52.632 11.82 11.82 46.96 4.06
49 50 1.030457 CCTCTGCATTTGGGAGATGC 58.970 55.000 1.66 2.31 43.58 3.91
50 51 1.030457 GCCTCTGCATTTGGGAGATG 58.970 55.000 1.66 0.00 43.58 2.90
51 52 0.106318 GGCCTCTGCATTTGGGAGAT 60.106 55.000 0.00 0.00 43.58 2.75
52 53 1.304282 GGCCTCTGCATTTGGGAGA 59.696 57.895 0.00 0.00 42.24 3.71
53 54 2.117156 CGGCCTCTGCATTTGGGAG 61.117 63.158 0.00 0.00 40.13 4.30
54 55 2.045045 CGGCCTCTGCATTTGGGA 60.045 61.111 0.00 0.00 40.13 4.37
55 56 3.142838 CCGGCCTCTGCATTTGGG 61.143 66.667 0.00 0.00 40.13 4.12
56 57 3.142838 CCCGGCCTCTGCATTTGG 61.143 66.667 0.00 0.00 40.13 3.28
57 58 2.916527 ATCCCCGGCCTCTGCATTTG 62.917 60.000 0.00 0.00 40.13 2.32
58 59 2.631012 GATCCCCGGCCTCTGCATTT 62.631 60.000 0.00 0.00 40.13 2.32
59 60 3.099170 ATCCCCGGCCTCTGCATT 61.099 61.111 0.00 0.00 40.13 3.56
60 61 3.564218 GATCCCCGGCCTCTGCAT 61.564 66.667 0.00 0.00 40.13 3.96
62 63 3.543536 GATGATCCCCGGCCTCTGC 62.544 68.421 0.00 0.00 0.00 4.26
63 64 2.746359 GATGATCCCCGGCCTCTG 59.254 66.667 0.00 0.00 0.00 3.35
64 65 2.527875 GGATGATCCCCGGCCTCT 60.528 66.667 0.00 0.00 0.00 3.69
65 66 4.008933 CGGATGATCCCCGGCCTC 62.009 72.222 5.78 0.00 43.05 4.70
69 70 2.624674 AAAAGGCGGATGATCCCCGG 62.625 60.000 20.60 0.00 46.55 5.73
71 72 0.183731 AGAAAAGGCGGATGATCCCC 59.816 55.000 5.78 8.30 31.13 4.81
72 73 2.930826 TAGAAAAGGCGGATGATCCC 57.069 50.000 5.78 0.00 31.13 3.85
73 74 5.576447 TTTTTAGAAAAGGCGGATGATCC 57.424 39.130 0.08 0.08 0.00 3.36
93 94 7.872113 TGGGTTGCAGACAATTTTTATTTTT 57.128 28.000 0.00 0.00 38.27 1.94
94 95 7.772757 TCTTGGGTTGCAGACAATTTTTATTTT 59.227 29.630 1.13 0.00 38.27 1.82
95 96 7.278875 TCTTGGGTTGCAGACAATTTTTATTT 58.721 30.769 1.13 0.00 38.27 1.40
96 97 6.825610 TCTTGGGTTGCAGACAATTTTTATT 58.174 32.000 1.13 0.00 38.27 1.40
97 98 6.418057 TCTTGGGTTGCAGACAATTTTTAT 57.582 33.333 1.13 0.00 38.27 1.40
98 99 5.860941 TCTTGGGTTGCAGACAATTTTTA 57.139 34.783 1.13 0.00 38.27 1.52
99 100 4.751767 TCTTGGGTTGCAGACAATTTTT 57.248 36.364 1.13 0.00 38.27 1.94
100 101 4.344679 TCATCTTGGGTTGCAGACAATTTT 59.655 37.500 1.13 0.00 38.27 1.82
101 102 3.896888 TCATCTTGGGTTGCAGACAATTT 59.103 39.130 1.13 0.00 38.27 1.82
102 103 3.499338 TCATCTTGGGTTGCAGACAATT 58.501 40.909 1.13 0.00 38.27 2.32
103 104 3.159213 TCATCTTGGGTTGCAGACAAT 57.841 42.857 1.13 0.00 38.27 2.71
104 105 2.655090 TCATCTTGGGTTGCAGACAA 57.345 45.000 0.00 0.00 0.00 3.18
113 114 2.311542 TGGGCTGTATTTCATCTTGGGT 59.688 45.455 0.00 0.00 0.00 4.51
142 143 3.855255 TGAGGTCTCAAACATGGTTCA 57.145 42.857 0.00 0.00 36.53 3.18
176 195 2.712087 TGGGAACTAGGTTTAGGCAACA 59.288 45.455 0.00 0.00 37.07 3.33
200 219 1.066716 TGGATTACGTTCCTGTTCGGG 60.067 52.381 7.76 0.00 36.68 5.14
213 232 0.470341 GGAGCCACCCTCTGGATTAC 59.530 60.000 0.00 0.00 39.48 1.89
369 398 2.715532 TTTCTTGAGCCGTGCGAGCT 62.716 55.000 7.15 7.15 45.23 4.09
378 407 3.321968 AGGTGGAATTGTTTTCTTGAGCC 59.678 43.478 0.00 0.00 0.00 4.70
518 573 1.064946 GACGGACAGAGAGATGGCG 59.935 63.158 0.00 0.00 0.00 5.69
529 584 0.601576 CGATGTGGTTTGGACGGACA 60.602 55.000 0.00 0.00 0.00 4.02
575 1019 4.603946 GATGGGTAGGTCGGCGGC 62.604 72.222 7.21 4.32 0.00 6.53
728 3529 2.136196 GATACGGAGCTCGGCCTCTG 62.136 65.000 20.22 0.00 44.45 3.35
756 3573 3.245315 CGCTGCCTGTACGTACGC 61.245 66.667 20.18 17.89 0.00 4.42
824 4301 4.521256 GGTGGTTTTTATAGGAGTTGCACA 59.479 41.667 0.00 0.00 0.00 4.57
870 4347 0.474184 CCAAGGAGTGAGGTGTGGTT 59.526 55.000 0.00 0.00 0.00 3.67
879 4369 2.379972 GTAGCTAGAGCCAAGGAGTGA 58.620 52.381 0.00 0.00 43.38 3.41
880 4370 1.410882 GGTAGCTAGAGCCAAGGAGTG 59.589 57.143 0.00 0.00 43.38 3.51
881 4371 1.289530 AGGTAGCTAGAGCCAAGGAGT 59.710 52.381 0.00 0.00 43.38 3.85
989 4507 1.341877 CCCCTTGCATGATGGTGGTAA 60.342 52.381 0.00 0.00 0.00 2.85
991 4509 1.000739 CCCCTTGCATGATGGTGGT 59.999 57.895 0.00 0.00 0.00 4.16
1303 4871 2.001361 GCGAACGAGTAGGCCTGCTA 62.001 60.000 24.59 0.00 0.00 3.49
1426 5011 0.396556 TCCGGCAGGCAGATGTACTA 60.397 55.000 0.00 0.00 37.47 1.82
1536 5183 2.688958 GCTCTCACCGGTAACTGACTAT 59.311 50.000 6.87 0.00 0.00 2.12
1688 5363 3.458487 GAGATGCCCTAACTTCCCCTTTA 59.542 47.826 0.00 0.00 0.00 1.85
1735 5410 7.361201 CTGTTTTAGCAGGAATGATCGAAAGAA 60.361 37.037 0.00 0.00 36.89 2.52
1736 5411 6.092670 CTGTTTTAGCAGGAATGATCGAAAGA 59.907 38.462 0.00 0.00 37.40 2.52
1737 5412 6.128172 ACTGTTTTAGCAGGAATGATCGAAAG 60.128 38.462 0.00 0.00 40.59 2.62
1738 5413 5.705441 ACTGTTTTAGCAGGAATGATCGAAA 59.295 36.000 0.00 0.00 40.59 3.46
1739 5414 5.245531 ACTGTTTTAGCAGGAATGATCGAA 58.754 37.500 0.00 0.00 40.59 3.71
1742 5417 5.644644 CCAACTGTTTTAGCAGGAATGATC 58.355 41.667 0.00 0.00 40.59 2.92
1743 5418 4.082026 GCCAACTGTTTTAGCAGGAATGAT 60.082 41.667 0.00 0.00 40.59 2.45
1746 5421 3.230134 TGCCAACTGTTTTAGCAGGAAT 58.770 40.909 5.76 0.00 40.59 3.01
1747 5422 2.660572 TGCCAACTGTTTTAGCAGGAA 58.339 42.857 5.76 0.00 40.59 3.36
1749 5424 3.005684 TCATTGCCAACTGTTTTAGCAGG 59.994 43.478 8.93 6.91 40.59 4.85
1750 5425 3.983344 GTCATTGCCAACTGTTTTAGCAG 59.017 43.478 8.93 0.00 41.92 4.24
1751 5426 3.636300 AGTCATTGCCAACTGTTTTAGCA 59.364 39.130 5.76 5.76 0.00 3.49
1752 5427 4.229876 GAGTCATTGCCAACTGTTTTAGC 58.770 43.478 0.00 0.00 0.00 3.09
1753 5428 5.437289 TGAGTCATTGCCAACTGTTTTAG 57.563 39.130 0.00 0.00 0.00 1.85
1754 5429 6.215121 CAATGAGTCATTGCCAACTGTTTTA 58.785 36.000 28.11 0.00 43.38 1.52
1755 5430 4.942761 ATGAGTCATTGCCAACTGTTTT 57.057 36.364 0.00 0.00 0.00 2.43
1756 5431 4.501915 CCAATGAGTCATTGCCAACTGTTT 60.502 41.667 31.96 1.20 46.73 2.83
1757 5432 3.006110 CCAATGAGTCATTGCCAACTGTT 59.994 43.478 31.96 1.70 46.73 3.16
1758 5433 2.559668 CCAATGAGTCATTGCCAACTGT 59.440 45.455 31.96 1.60 46.73 3.55
1759 5434 2.821378 TCCAATGAGTCATTGCCAACTG 59.179 45.455 31.96 20.56 46.73 3.16
1760 5435 3.159213 TCCAATGAGTCATTGCCAACT 57.841 42.857 31.96 3.03 46.73 3.16
1761 5436 3.940209 TTCCAATGAGTCATTGCCAAC 57.060 42.857 31.96 0.00 46.73 3.77
1762 5437 3.896888 AGTTTCCAATGAGTCATTGCCAA 59.103 39.130 31.96 24.42 46.73 4.52
1763 5438 3.499338 AGTTTCCAATGAGTCATTGCCA 58.501 40.909 31.96 20.98 46.73 4.92
1764 5439 4.219288 AGAAGTTTCCAATGAGTCATTGCC 59.781 41.667 31.96 20.95 46.73 4.52
1765 5440 5.382618 AGAAGTTTCCAATGAGTCATTGC 57.617 39.130 31.96 21.33 46.73 3.56
1767 5442 7.890127 TCCAATAGAAGTTTCCAATGAGTCATT 59.110 33.333 12.75 12.75 34.04 2.57
1768 5443 7.405292 TCCAATAGAAGTTTCCAATGAGTCAT 58.595 34.615 0.00 0.00 0.00 3.06
1769 5444 6.778821 TCCAATAGAAGTTTCCAATGAGTCA 58.221 36.000 0.00 0.00 0.00 3.41
1770 5445 7.772757 AGATCCAATAGAAGTTTCCAATGAGTC 59.227 37.037 0.00 0.00 0.00 3.36
1771 5446 7.555554 CAGATCCAATAGAAGTTTCCAATGAGT 59.444 37.037 0.00 0.00 0.00 3.41
1772 5447 7.013083 CCAGATCCAATAGAAGTTTCCAATGAG 59.987 40.741 0.00 0.00 0.00 2.90
1773 5448 6.830324 CCAGATCCAATAGAAGTTTCCAATGA 59.170 38.462 0.00 0.00 0.00 2.57
1774 5449 6.040166 CCCAGATCCAATAGAAGTTTCCAATG 59.960 42.308 0.00 0.00 0.00 2.82
1775 5450 6.068853 TCCCAGATCCAATAGAAGTTTCCAAT 60.069 38.462 0.00 0.00 0.00 3.16
1776 5451 5.252863 TCCCAGATCCAATAGAAGTTTCCAA 59.747 40.000 0.00 0.00 0.00 3.53
1777 5452 4.788075 TCCCAGATCCAATAGAAGTTTCCA 59.212 41.667 0.00 0.00 0.00 3.53
1778 5453 5.131142 TCTCCCAGATCCAATAGAAGTTTCC 59.869 44.000 0.00 0.00 0.00 3.13
1779 5454 6.240549 TCTCCCAGATCCAATAGAAGTTTC 57.759 41.667 0.00 0.00 0.00 2.78
1780 5455 6.445139 TCTTCTCCCAGATCCAATAGAAGTTT 59.555 38.462 17.92 0.00 40.38 2.66
1781 5456 5.966935 TCTTCTCCCAGATCCAATAGAAGTT 59.033 40.000 17.92 0.00 40.38 2.66
1782 5457 5.533112 TCTTCTCCCAGATCCAATAGAAGT 58.467 41.667 17.92 0.00 40.38 3.01
1783 5458 6.326064 TCTTCTTCTCCCAGATCCAATAGAAG 59.674 42.308 14.71 14.71 40.69 2.85
1784 5459 6.205298 TCTTCTTCTCCCAGATCCAATAGAA 58.795 40.000 0.00 0.00 0.00 2.10
1785 5460 5.781827 TCTTCTTCTCCCAGATCCAATAGA 58.218 41.667 0.00 0.00 0.00 1.98
1786 5461 6.491714 TTCTTCTTCTCCCAGATCCAATAG 57.508 41.667 0.00 0.00 0.00 1.73
1787 5462 6.353082 GGTTTCTTCTTCTCCCAGATCCAATA 60.353 42.308 0.00 0.00 0.00 1.90
1788 5463 5.504853 GTTTCTTCTTCTCCCAGATCCAAT 58.495 41.667 0.00 0.00 0.00 3.16
1789 5464 4.263506 GGTTTCTTCTTCTCCCAGATCCAA 60.264 45.833 0.00 0.00 0.00 3.53
1790 5465 3.264450 GGTTTCTTCTTCTCCCAGATCCA 59.736 47.826 0.00 0.00 0.00 3.41
1791 5466 3.371059 GGGTTTCTTCTTCTCCCAGATCC 60.371 52.174 0.00 0.00 38.15 3.36
1792 5467 3.264450 TGGGTTTCTTCTTCTCCCAGATC 59.736 47.826 0.00 0.00 42.52 2.75
1793 5468 3.260205 TGGGTTTCTTCTTCTCCCAGAT 58.740 45.455 0.00 0.00 42.52 2.90
1794 5469 2.701551 TGGGTTTCTTCTTCTCCCAGA 58.298 47.619 0.00 0.00 42.52 3.86
1795 5470 3.508845 TTGGGTTTCTTCTTCTCCCAG 57.491 47.619 0.00 0.00 46.93 4.45
1796 5471 3.397618 TGATTGGGTTTCTTCTTCTCCCA 59.602 43.478 0.00 0.00 45.20 4.37
1797 5472 4.034285 TGATTGGGTTTCTTCTTCTCCC 57.966 45.455 0.00 0.00 38.68 4.30
1798 5473 5.105595 CCATTGATTGGGTTTCTTCTTCTCC 60.106 44.000 0.00 0.00 42.33 3.71
1799 5474 5.958955 CCATTGATTGGGTTTCTTCTTCTC 58.041 41.667 0.00 0.00 42.33 2.87
1800 5475 5.990120 CCATTGATTGGGTTTCTTCTTCT 57.010 39.130 0.00 0.00 42.33 2.85
1812 5487 4.771114 TGACTACCTACCCATTGATTGG 57.229 45.455 0.00 0.00 46.00 3.16
1813 5488 7.557719 AGAAATTGACTACCTACCCATTGATTG 59.442 37.037 0.00 0.00 0.00 2.67
1814 5489 7.557719 CAGAAATTGACTACCTACCCATTGATT 59.442 37.037 0.00 0.00 0.00 2.57
1815 5490 7.056635 CAGAAATTGACTACCTACCCATTGAT 58.943 38.462 0.00 0.00 0.00 2.57
1816 5491 6.414732 CAGAAATTGACTACCTACCCATTGA 58.585 40.000 0.00 0.00 0.00 2.57
1817 5492 5.066505 GCAGAAATTGACTACCTACCCATTG 59.933 44.000 0.00 0.00 0.00 2.82
1818 5493 5.193679 GCAGAAATTGACTACCTACCCATT 58.806 41.667 0.00 0.00 0.00 3.16
1819 5494 4.227300 TGCAGAAATTGACTACCTACCCAT 59.773 41.667 0.00 0.00 0.00 4.00
1820 5495 3.585289 TGCAGAAATTGACTACCTACCCA 59.415 43.478 0.00 0.00 0.00 4.51
1821 5496 3.939592 GTGCAGAAATTGACTACCTACCC 59.060 47.826 0.00 0.00 0.00 3.69
1822 5497 4.575885 TGTGCAGAAATTGACTACCTACC 58.424 43.478 0.00 0.00 0.00 3.18
1823 5498 5.120830 CACTGTGCAGAAATTGACTACCTAC 59.879 44.000 6.17 0.00 0.00 3.18
1824 5499 5.237815 CACTGTGCAGAAATTGACTACCTA 58.762 41.667 6.17 0.00 0.00 3.08
1825 5500 4.067896 CACTGTGCAGAAATTGACTACCT 58.932 43.478 6.17 0.00 0.00 3.08
1826 5501 3.189287 CCACTGTGCAGAAATTGACTACC 59.811 47.826 6.17 0.00 0.00 3.18
1827 5502 4.065088 TCCACTGTGCAGAAATTGACTAC 58.935 43.478 6.17 0.00 0.00 2.73
1828 5503 4.350368 TCCACTGTGCAGAAATTGACTA 57.650 40.909 6.17 0.00 0.00 2.59
1829 5504 3.213206 TCCACTGTGCAGAAATTGACT 57.787 42.857 6.17 0.00 0.00 3.41
1830 5505 3.632189 GTTCCACTGTGCAGAAATTGAC 58.368 45.455 6.17 0.00 0.00 3.18
1831 5506 2.290367 CGTTCCACTGTGCAGAAATTGA 59.710 45.455 6.17 0.00 0.00 2.57
1832 5507 2.033299 ACGTTCCACTGTGCAGAAATTG 59.967 45.455 6.17 0.00 0.00 2.32
1833 5508 2.033299 CACGTTCCACTGTGCAGAAATT 59.967 45.455 6.17 0.00 0.00 1.82
1834 5509 1.603802 CACGTTCCACTGTGCAGAAAT 59.396 47.619 6.17 0.00 0.00 2.17
1835 5510 1.013596 CACGTTCCACTGTGCAGAAA 58.986 50.000 6.17 0.00 0.00 2.52
1836 5511 0.107897 ACACGTTCCACTGTGCAGAA 60.108 50.000 6.17 0.00 39.71 3.02
1837 5512 0.747852 TACACGTTCCACTGTGCAGA 59.252 50.000 6.17 0.00 39.71 4.26
1838 5513 1.260561 GTTACACGTTCCACTGTGCAG 59.739 52.381 1.29 0.00 39.71 4.41
1839 5514 1.292061 GTTACACGTTCCACTGTGCA 58.708 50.000 1.29 0.00 39.71 4.57
1840 5515 0.584876 GGTTACACGTTCCACTGTGC 59.415 55.000 1.29 0.00 39.71 4.57
1841 5516 1.223187 GGGTTACACGTTCCACTGTG 58.777 55.000 0.00 0.00 41.81 3.66
1842 5517 0.249573 CGGGTTACACGTTCCACTGT 60.250 55.000 0.00 0.00 0.00 3.55
1843 5518 1.562575 GCGGGTTACACGTTCCACTG 61.563 60.000 9.27 0.00 0.00 3.66
1844 5519 1.301165 GCGGGTTACACGTTCCACT 60.301 57.895 9.27 0.00 0.00 4.00
1845 5520 2.319841 GGCGGGTTACACGTTCCAC 61.320 63.158 9.27 0.00 0.00 4.02
1846 5521 2.030862 GGCGGGTTACACGTTCCA 59.969 61.111 9.27 0.00 0.00 3.53
1847 5522 2.030958 CAGGCGGGTTACACGTTCC 61.031 63.158 9.27 1.78 0.00 3.62
1848 5523 2.674084 GCAGGCGGGTTACACGTTC 61.674 63.158 9.27 1.45 0.00 3.95
1849 5524 2.667199 GCAGGCGGGTTACACGTT 60.667 61.111 9.27 0.00 0.00 3.99
1850 5525 3.622826 AGCAGGCGGGTTACACGT 61.623 61.111 9.27 0.00 0.00 4.49
1851 5526 3.118454 CAGCAGGCGGGTTACACG 61.118 66.667 1.26 1.26 0.00 4.49
1852 5527 2.032071 ACAGCAGGCGGGTTACAC 59.968 61.111 0.00 0.00 0.00 2.90
1853 5528 2.345991 GACAGCAGGCGGGTTACA 59.654 61.111 0.00 0.00 0.00 2.41
1854 5529 2.436115 GGACAGCAGGCGGGTTAC 60.436 66.667 0.00 0.00 0.00 2.50
1855 5530 2.463589 CTTGGACAGCAGGCGGGTTA 62.464 60.000 0.00 0.00 0.00 2.85
1856 5531 3.850098 CTTGGACAGCAGGCGGGTT 62.850 63.158 0.00 0.00 0.00 4.11
1857 5532 4.335647 CTTGGACAGCAGGCGGGT 62.336 66.667 0.00 0.00 0.00 5.28
1858 5533 4.335647 ACTTGGACAGCAGGCGGG 62.336 66.667 0.00 0.00 0.00 6.13
1859 5534 2.743928 GACTTGGACAGCAGGCGG 60.744 66.667 0.00 0.00 0.00 6.13
1860 5535 1.597854 TTGACTTGGACAGCAGGCG 60.598 57.895 0.00 0.00 0.00 5.52
1861 5536 1.518903 GGTTGACTTGGACAGCAGGC 61.519 60.000 0.00 0.00 0.00 4.85
1862 5537 0.179020 TGGTTGACTTGGACAGCAGG 60.179 55.000 0.00 0.00 0.00 4.85
1863 5538 0.947244 GTGGTTGACTTGGACAGCAG 59.053 55.000 0.00 0.00 0.00 4.24
1864 5539 0.546122 AGTGGTTGACTTGGACAGCA 59.454 50.000 0.00 0.00 0.00 4.41
1865 5540 0.947244 CAGTGGTTGACTTGGACAGC 59.053 55.000 0.00 0.00 29.75 4.40
1866 5541 2.620251 TCAGTGGTTGACTTGGACAG 57.380 50.000 0.00 0.00 29.75 3.51
1867 5542 3.576078 ATTCAGTGGTTGACTTGGACA 57.424 42.857 0.00 0.00 34.94 4.02
1868 5543 4.918810 AAATTCAGTGGTTGACTTGGAC 57.081 40.909 0.00 0.00 34.94 4.02
1869 5544 5.930837 AAAAATTCAGTGGTTGACTTGGA 57.069 34.783 0.00 0.00 34.94 3.53
1888 5563 4.035909 GGTTTTCTCCGCTGTAGACAAAAA 59.964 41.667 0.00 0.00 0.00 1.94
1889 5564 3.562557 GGTTTTCTCCGCTGTAGACAAAA 59.437 43.478 0.00 0.00 0.00 2.44
1890 5565 3.135994 GGTTTTCTCCGCTGTAGACAAA 58.864 45.455 0.00 0.00 0.00 2.83
1891 5566 2.103432 TGGTTTTCTCCGCTGTAGACAA 59.897 45.455 0.00 0.00 0.00 3.18
1892 5567 1.689813 TGGTTTTCTCCGCTGTAGACA 59.310 47.619 0.00 0.00 0.00 3.41
1893 5568 2.450609 TGGTTTTCTCCGCTGTAGAC 57.549 50.000 0.00 0.00 0.00 2.59
1894 5569 3.596214 GATTGGTTTTCTCCGCTGTAGA 58.404 45.455 0.00 0.00 0.00 2.59
1895 5570 2.678336 GGATTGGTTTTCTCCGCTGTAG 59.322 50.000 0.00 0.00 0.00 2.74
1896 5571 2.039216 TGGATTGGTTTTCTCCGCTGTA 59.961 45.455 0.00 0.00 31.36 2.74
1897 5572 1.202879 TGGATTGGTTTTCTCCGCTGT 60.203 47.619 0.00 0.00 31.36 4.40
1898 5573 1.533625 TGGATTGGTTTTCTCCGCTG 58.466 50.000 0.00 0.00 31.36 5.18
1900 5575 1.064060 CGATGGATTGGTTTTCTCCGC 59.936 52.381 0.00 0.00 31.36 5.54
1917 5592 0.248825 GCTCGTGCATCTCTGTCGAT 60.249 55.000 4.26 0.00 39.41 3.59
1918 5593 1.137614 GCTCGTGCATCTCTGTCGA 59.862 57.895 4.26 0.00 39.41 4.20
1924 5599 0.745845 ATGGTTGGCTCGTGCATCTC 60.746 55.000 12.07 0.00 41.91 2.75
1925 5600 0.745845 GATGGTTGGCTCGTGCATCT 60.746 55.000 12.07 0.00 41.91 2.90
1932 5607 0.606401 ACAGTTGGATGGTTGGCTCG 60.606 55.000 0.00 0.00 0.00 5.03
1938 5613 3.688694 TTACGCTACAGTTGGATGGTT 57.311 42.857 0.00 0.00 0.00 3.67
1955 5630 9.906111 CGTCTAATTAAGTAAAATCCGGTTTAC 57.094 33.333 16.23 16.23 42.05 2.01
1956 5631 9.868277 TCGTCTAATTAAGTAAAATCCGGTTTA 57.132 29.630 0.00 0.00 0.00 2.01
1970 5655 9.755064 ACGTTTGATGAAAATCGTCTAATTAAG 57.245 29.630 1.69 0.00 33.31 1.85
1976 5661 5.119588 GGTCACGTTTGATGAAAATCGTCTA 59.880 40.000 0.00 0.00 35.08 2.59
2016 5701 9.187996 TGCATGATTTTGTCTATTTTCTATCCA 57.812 29.630 0.00 0.00 0.00 3.41
2044 5730 9.559732 TGTAGTAGACATATTTGCATGCTATTT 57.440 29.630 20.33 1.39 31.20 1.40
2059 5745 9.640963 GAGTTGAACTATTGTTGTAGTAGACAT 57.359 33.333 0.00 0.00 38.07 3.06
2072 5912 8.169268 GGTTAATCTCGTTGAGTTGAACTATTG 58.831 37.037 0.00 0.00 0.00 1.90
2118 5958 8.849168 TGTGTGGGATAACATAATCAATTCATC 58.151 33.333 0.00 0.00 31.49 2.92
2149 5989 2.751259 TGTTGGATGAAGCTCAAGATGC 59.249 45.455 0.00 0.00 0.00 3.91
2152 5992 4.401022 ACATTGTTGGATGAAGCTCAAGA 58.599 39.130 0.00 0.00 0.00 3.02
2193 6033 6.037940 GTCATAATGTAGTAGAGGTCACACGA 59.962 42.308 0.00 0.00 0.00 4.35
2195 6035 7.096884 TGTCATAATGTAGTAGAGGTCACAC 57.903 40.000 0.00 0.00 0.00 3.82
2204 6044 4.677378 GCACGAGCTGTCATAATGTAGTAG 59.323 45.833 0.00 0.00 37.91 2.57
2211 6051 1.945387 CCTGCACGAGCTGTCATAAT 58.055 50.000 6.36 0.00 42.74 1.28
2215 6055 2.218037 CTAGCCTGCACGAGCTGTCA 62.218 60.000 6.36 0.00 40.28 3.58
2235 6075 5.163854 ACTCATTAATTGTTGCTCTACACGC 60.164 40.000 0.00 0.00 0.00 5.34
2237 6077 7.364522 TCACTCATTAATTGTTGCTCTACAC 57.635 36.000 0.00 0.00 0.00 2.90
2238 6078 7.119699 CCTTCACTCATTAATTGTTGCTCTACA 59.880 37.037 0.00 0.00 0.00 2.74
2239 6079 7.334421 TCCTTCACTCATTAATTGTTGCTCTAC 59.666 37.037 0.00 0.00 0.00 2.59
2240 6080 7.394016 TCCTTCACTCATTAATTGTTGCTCTA 58.606 34.615 0.00 0.00 0.00 2.43
2241 6081 6.240894 TCCTTCACTCATTAATTGTTGCTCT 58.759 36.000 0.00 0.00 0.00 4.09
2243 6083 6.006449 ACTCCTTCACTCATTAATTGTTGCT 58.994 36.000 0.00 0.00 0.00 3.91
2245 6085 7.439157 TCACTCCTTCACTCATTAATTGTTG 57.561 36.000 0.00 0.00 0.00 3.33
2247 6087 7.884877 TGATTCACTCCTTCACTCATTAATTGT 59.115 33.333 0.00 0.00 0.00 2.71
2251 6091 8.102676 TGATTGATTCACTCCTTCACTCATTAA 58.897 33.333 1.99 0.00 28.01 1.40
2252 6092 7.623630 TGATTGATTCACTCCTTCACTCATTA 58.376 34.615 1.99 0.00 28.01 1.90
2279 6119 7.615582 TTTCTGCCTCTTCTTAATGTACATG 57.384 36.000 9.63 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.