Multiple sequence alignment - TraesCS1A01G117400

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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 TraesCS1A01G117400 chr1A 100.000 2866 0 0 1 2866 124788429 124785564 0.000000e+00 5293
1 TraesCS1A01G117400 chr1A 83.333 396 48 10 1157 1543 124181598 124181212 1.630000e-92 350
2 TraesCS1A01G117400 chr1A 81.510 384 29 17 1169 1510 124190156 124189773 7.820000e-71 278
3 TraesCS1A01G117400 chr1B 88.699 1929 107 55 2 1876 175277007 175275136 0.000000e+00 2252
4 TraesCS1A01G117400 chr1B 82.258 558 51 21 1832 2345 175274291 175273738 3.390000e-119 438
5 TraesCS1A01G117400 chr1B 85.530 387 38 9 1157 1534 174763499 174763122 3.460000e-104 388
6 TraesCS1A01G117400 chr1B 82.821 390 30 14 1169 1522 174784265 174783877 5.960000e-82 315
7 TraesCS1A01G117400 chr1B 84.848 165 11 2 1851 2001 175274318 175274154 1.380000e-33 154
8 TraesCS1A01G117400 chr1D 88.142 1577 86 35 458 1971 114314376 114312838 0.000000e+00 1783
9 TraesCS1A01G117400 chr1D 88.227 671 27 14 1832 2472 114312936 114312288 0.000000e+00 754
10 TraesCS1A01G117400 chr1D 88.075 478 33 13 1 461 114316220 114315750 1.940000e-151 545
11 TraesCS1A01G117400 chr1D 85.606 396 42 8 1157 1543 114065154 114064765 4.450000e-108 401
12 TraesCS1A01G117400 chr1D 83.733 375 28 12 1169 1510 114083632 114083258 9.900000e-85 324
13 TraesCS1A01G117400 chr1D 90.345 145 8 1 2635 2773 114312278 114312134 4.880000e-43 185
14 TraesCS1A01G117400 chr2D 100.000 153 0 0 2477 2629 398728224 398728072 1.680000e-72 283
15 TraesCS1A01G117400 chr4B 100.000 152 0 0 2477 2628 73100639 73100488 6.050000e-72 281
16 TraesCS1A01G117400 chr3B 99.338 151 1 0 2478 2628 612035638 612035788 1.010000e-69 274
17 TraesCS1A01G117400 chr4A 100.000 147 0 0 2477 2623 639055006 639055152 3.640000e-69 272
18 TraesCS1A01G117400 chr4A 98.039 153 2 1 2478 2629 2399665 2399817 6.090000e-67 265
19 TraesCS1A01G117400 chr5A 98.675 151 2 0 2478 2628 678573976 678573826 4.710000e-68 268
20 TraesCS1A01G117400 chr5A 98.675 151 2 0 2478 2628 685875103 685875253 4.710000e-68 268
21 TraesCS1A01G117400 chr6B 95.000 140 7 0 2478 2617 594438525 594438386 1.340000e-53 220
22 TraesCS1A01G117400 chr5B 94.483 145 4 2 2478 2622 358616930 358617070 1.340000e-53 220
23 TraesCS1A01G117400 chr3D 94.949 99 5 0 1400 1498 86237179 86237277 3.820000e-34 156


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 TraesCS1A01G117400 chr1A 124785564 124788429 2865 True 5293.00 5293 100.000000 1 2866 1 chr1A.!!$R3 2865
1 TraesCS1A01G117400 chr1B 175273738 175277007 3269 True 948.00 2252 85.268333 2 2345 3 chr1B.!!$R3 2343
2 TraesCS1A01G117400 chr1D 114312134 114316220 4086 True 816.75 1783 88.697250 1 2773 4 chr1D.!!$R3 2772

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
108 110 0.394565 GCCTGCGAAGGGTCATCTAT 59.605 55.0 12.68 0.0 0.0 1.98 F
978 2394 0.468648 CGTTTATCCACTCCTCCCCC 59.531 60.0 0.00 0.0 0.0 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1150 2572 0.108329 ATCGGTTAGCTCGGTGTTGG 60.108 55.0 0.00 0.0 0.0 3.77 R
2776 5224 0.035439 CGTAGTTGGCCAGGAATGGT 60.035 55.0 5.11 0.0 0.0 3.55 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
36 37 1.202452 TGCTCTCATGACAGGCATACG 60.202 52.381 0.00 0.00 34.82 3.06
39 40 2.099405 TCTCATGACAGGCATACGACA 58.901 47.619 0.00 0.00 34.82 4.35
40 41 2.159240 TCTCATGACAGGCATACGACAC 60.159 50.000 0.00 0.00 34.82 3.67
68 70 5.684550 TGGTATAGTACGAGCACATACAG 57.315 43.478 0.00 0.00 0.00 2.74
74 76 9.970243 GTATAGTACGAGCACATACAGTAATAG 57.030 37.037 0.00 0.00 0.00 1.73
108 110 0.394565 GCCTGCGAAGGGTCATCTAT 59.605 55.000 12.68 0.00 0.00 1.98
144 146 2.173126 TATGGGAAATGCAAAGGGGG 57.827 50.000 0.00 0.00 0.00 5.40
214 229 6.511121 CGGTAATATTACTCATGTGTTGTGCC 60.511 42.308 21.86 3.01 34.16 5.01
217 232 4.771590 ATTACTCATGTGTTGTGCCAAG 57.228 40.909 5.63 0.00 0.00 3.61
230 248 2.640332 TGTGCCAAGGTGGTATTCACTA 59.360 45.455 0.00 0.00 45.38 2.74
252 270 1.131315 GATCTTTCTGCCGGCAAGTTC 59.869 52.381 32.09 23.40 0.00 3.01
273 291 8.824756 AGTTCTATCTACCAGAAACATCTACA 57.175 34.615 0.00 0.00 33.95 2.74
337 356 6.070136 GGGATAAGGATGGAGTAATAAGACCC 60.070 46.154 0.00 0.00 0.00 4.46
338 357 6.500751 GGATAAGGATGGAGTAATAAGACCCA 59.499 42.308 0.00 0.00 0.00 4.51
339 358 7.017254 GGATAAGGATGGAGTAATAAGACCCAA 59.983 40.741 0.00 0.00 0.00 4.12
563 1962 7.198306 TCGTTAGAAAATTGGGAGAGAAAAC 57.802 36.000 0.00 0.00 0.00 2.43
589 1989 0.530431 GGTGGGCTGCAACTTTTGTG 60.530 55.000 0.50 0.00 0.00 3.33
640 2040 1.151668 GTGCATCTCTCGTGTGCTTT 58.848 50.000 0.00 0.00 39.52 3.51
666 2066 5.675970 CACGGATTGTGTTTGTTACTGTAG 58.324 41.667 0.00 0.00 43.88 2.74
707 2109 2.028748 ACATTGCTGCAACAAAGATCCC 60.029 45.455 18.51 0.00 32.27 3.85
714 2116 1.672881 GCAACAAAGATCCCAGATCCG 59.327 52.381 0.99 0.00 0.00 4.18
893 2307 3.403057 CCACGCAACGGTCACTCG 61.403 66.667 0.00 0.00 0.00 4.18
899 2313 3.851955 AACGGTCACTCGGTGAGT 58.148 55.556 6.94 0.00 43.57 3.41
940 2354 2.124085 ACCTTCCCACCGGATCCA 59.876 61.111 9.46 0.00 38.24 3.41
978 2394 0.468648 CGTTTATCCACTCCTCCCCC 59.531 60.000 0.00 0.00 0.00 5.40
979 2395 0.468648 GTTTATCCACTCCTCCCCCG 59.531 60.000 0.00 0.00 0.00 5.73
1063 2480 0.609957 ATACACCCACCGTCTCGTCA 60.610 55.000 0.00 0.00 0.00 4.35
1078 2495 4.149046 GTCTCGTCACATTTCACAAGTCTC 59.851 45.833 0.00 0.00 0.00 3.36
1079 2496 3.049912 TCGTCACATTTCACAAGTCTCG 58.950 45.455 0.00 0.00 0.00 4.04
1081 2498 3.121328 CGTCACATTTCACAAGTCTCGTC 60.121 47.826 0.00 0.00 0.00 4.20
1083 2500 4.270084 GTCACATTTCACAAGTCTCGTCAA 59.730 41.667 0.00 0.00 0.00 3.18
1087 2509 3.364889 TTCACAAGTCTCGTCAATCGT 57.635 42.857 0.00 0.00 40.80 3.73
1127 2549 3.324108 GGTTACCCACCCAGCCGA 61.324 66.667 0.00 0.00 40.19 5.54
1150 2572 0.731855 AGCTTTCGACCGAAGCGTAC 60.732 55.000 13.19 0.00 35.24 3.67
1152 2574 0.387622 CTTTCGACCGAAGCGTACCA 60.388 55.000 4.99 0.00 35.38 3.25
1153 2575 0.031857 TTTCGACCGAAGCGTACCAA 59.968 50.000 4.99 0.00 35.38 3.67
1154 2576 0.664166 TTCGACCGAAGCGTACCAAC 60.664 55.000 0.18 0.00 0.00 3.77
1537 2970 1.040339 GCCACCAACCAACCAACTCA 61.040 55.000 0.00 0.00 0.00 3.41
1589 3022 1.381327 TCTGGATCTCCCCGTGGTC 60.381 63.158 0.00 0.00 34.29 4.02
1594 3027 3.310860 ATCTCCCCGTGGTCGTTGC 62.311 63.158 0.00 0.00 35.01 4.17
1629 3065 2.043227 GTTCTAGTCATGGAGGGAGGG 58.957 57.143 0.00 0.00 0.00 4.30
1647 3083 0.973496 GGGTGGTCAGAGGAGAGGAC 60.973 65.000 0.00 0.00 0.00 3.85
1730 3166 4.425520 CCGGTCTTGTTTTGCTTTTGTAA 58.574 39.130 0.00 0.00 0.00 2.41
1732 3168 5.522097 CCGGTCTTGTTTTGCTTTTGTAATT 59.478 36.000 0.00 0.00 0.00 1.40
1760 3218 2.009042 GCTCAGACCCAGATGTTTCGG 61.009 57.143 0.00 0.00 0.00 4.30
1764 3222 1.697432 AGACCCAGATGTTTCGGTTCA 59.303 47.619 0.00 0.00 0.00 3.18
1800 3259 3.294214 GCCACATTGGATTGGAGATCTT 58.706 45.455 0.00 0.00 40.96 2.40
1830 3289 1.141019 GCCAGATCTGCCGTCGTAA 59.859 57.895 17.76 0.00 0.00 3.18
1926 4228 9.574516 ACCTAAATATCAGTTAATTGTGGATCC 57.425 33.333 4.20 4.20 0.00 3.36
1932 4280 4.693566 TCAGTTAATTGTGGATCCGAACAC 59.306 41.667 7.39 0.00 38.08 3.32
1935 4283 2.577606 ATTGTGGATCCGAACACCAA 57.422 45.000 7.39 3.54 36.80 3.67
1944 4292 5.588648 TGGATCCGAACACCAATTATTTCTC 59.411 40.000 7.39 0.00 0.00 2.87
1982 4344 3.272574 TGATCTGAAGACCATTGAGCC 57.727 47.619 0.00 0.00 0.00 4.70
2049 4450 5.298777 CGTAGGTTAGGGATAATATCGGGAG 59.701 48.000 0.00 0.00 0.00 4.30
2105 4506 5.127845 TGTCTTCTTAAACAACAATTGGCCA 59.872 36.000 0.00 0.00 34.12 5.36
2124 4526 5.103728 TGGCCAGACCCATCAATTTATCTAA 60.104 40.000 0.00 0.00 37.83 2.10
2125 4527 5.241728 GGCCAGACCCATCAATTTATCTAAC 59.758 44.000 0.00 0.00 0.00 2.34
2126 4528 6.064717 GCCAGACCCATCAATTTATCTAACT 58.935 40.000 0.00 0.00 0.00 2.24
2128 4530 7.885399 GCCAGACCCATCAATTTATCTAACTAT 59.115 37.037 0.00 0.00 0.00 2.12
2129 4531 9.224267 CCAGACCCATCAATTTATCTAACTATG 57.776 37.037 0.00 0.00 0.00 2.23
2133 4535 7.387948 ACCCATCAATTTATCTAACTATGACGC 59.612 37.037 0.00 0.00 0.00 5.19
2218 4631 2.094099 CACAAAGGCACAAACTTGTTGC 59.906 45.455 0.00 1.13 39.91 4.17
2239 4652 3.259064 CGTTCGATTGGGTGAACTACAT 58.741 45.455 3.92 0.00 41.74 2.29
2370 4807 1.033746 AATCCATCGGCCAGCTTGTG 61.034 55.000 2.24 0.00 0.00 3.33
2415 4856 2.653726 TCCAGCGAATTTATGTGCCAT 58.346 42.857 0.00 0.00 0.00 4.40
2418 4859 4.081752 TCCAGCGAATTTATGTGCCATTTT 60.082 37.500 0.00 0.00 0.00 1.82
2436 4877 6.627065 GCCATTTTGTAATGTAAAGCCTGCTA 60.627 38.462 0.00 0.00 39.62 3.49
2458 4900 2.803492 GCCGGATGATTCTAAAGCGAGT 60.803 50.000 5.05 0.00 0.00 4.18
2460 4902 2.219674 CGGATGATTCTAAAGCGAGTGC 59.780 50.000 0.00 0.00 43.24 4.40
2472 4914 1.227380 CGAGTGCTGGGATAGTGGC 60.227 63.158 0.00 0.00 0.00 5.01
2473 4915 1.147153 GAGTGCTGGGATAGTGGCC 59.853 63.158 0.00 0.00 0.00 5.36
2475 4917 2.687200 TGCTGGGATAGTGGCCGT 60.687 61.111 0.00 0.00 0.00 5.68
2476 4918 1.382009 TGCTGGGATAGTGGCCGTA 60.382 57.895 0.00 0.00 0.00 4.02
2478 4920 1.362717 CTGGGATAGTGGCCGTACG 59.637 63.158 8.69 8.69 0.00 3.67
2479 4921 2.083835 CTGGGATAGTGGCCGTACGG 62.084 65.000 30.06 30.06 38.57 4.02
2480 4922 1.829533 GGGATAGTGGCCGTACGGA 60.830 63.158 37.62 17.07 37.50 4.69
2481 4923 1.394266 GGGATAGTGGCCGTACGGAA 61.394 60.000 37.62 21.58 37.50 4.30
2482 4924 0.249197 GGATAGTGGCCGTACGGAAC 60.249 60.000 37.62 30.38 37.50 3.62
2483 4925 0.743097 GATAGTGGCCGTACGGAACT 59.257 55.000 37.62 34.50 37.45 3.01
2484 4926 1.949525 GATAGTGGCCGTACGGAACTA 59.050 52.381 33.89 33.89 39.01 2.24
2485 4927 1.094785 TAGTGGCCGTACGGAACTAC 58.905 55.000 37.62 25.95 35.95 2.73
2486 4928 0.610232 AGTGGCCGTACGGAACTACT 60.610 55.000 37.62 27.63 37.50 2.57
2487 4929 0.457337 GTGGCCGTACGGAACTACTG 60.457 60.000 37.62 9.06 37.50 2.74
2488 4930 0.608856 TGGCCGTACGGAACTACTGA 60.609 55.000 37.62 10.09 37.50 3.41
2489 4931 0.100146 GGCCGTACGGAACTACTGAG 59.900 60.000 37.62 7.49 37.50 3.35
2490 4932 0.525029 GCCGTACGGAACTACTGAGC 60.525 60.000 37.62 14.03 37.50 4.26
2491 4933 0.806868 CCGTACGGAACTACTGAGCA 59.193 55.000 30.64 0.00 37.50 4.26
2492 4934 1.202154 CCGTACGGAACTACTGAGCAG 60.202 57.143 30.64 0.00 37.50 4.24
2493 4935 1.794437 CGTACGGAACTACTGAGCAGC 60.794 57.143 7.57 0.00 0.00 5.25
2494 4936 0.815734 TACGGAACTACTGAGCAGCC 59.184 55.000 0.00 0.00 0.00 4.85
2495 4937 1.517257 CGGAACTACTGAGCAGCCG 60.517 63.158 0.00 0.00 0.00 5.52
2496 4938 1.890894 GGAACTACTGAGCAGCCGA 59.109 57.895 0.00 0.00 0.00 5.54
2497 4939 0.458716 GGAACTACTGAGCAGCCGAC 60.459 60.000 0.00 0.00 0.00 4.79
2498 4940 0.243907 GAACTACTGAGCAGCCGACA 59.756 55.000 0.00 0.00 0.00 4.35
2499 4941 0.038159 AACTACTGAGCAGCCGACAC 60.038 55.000 0.00 0.00 0.00 3.67
2500 4942 1.153745 CTACTGAGCAGCCGACACC 60.154 63.158 0.00 0.00 0.00 4.16
2501 4943 2.564553 CTACTGAGCAGCCGACACCC 62.565 65.000 0.00 0.00 0.00 4.61
2502 4944 4.007644 CTGAGCAGCCGACACCCA 62.008 66.667 0.00 0.00 0.00 4.51
2503 4945 4.314440 TGAGCAGCCGACACCCAC 62.314 66.667 0.00 0.00 0.00 4.61
2504 4946 4.008933 GAGCAGCCGACACCCACT 62.009 66.667 0.00 0.00 0.00 4.00
2505 4947 4.320456 AGCAGCCGACACCCACTG 62.320 66.667 0.00 0.00 0.00 3.66
2511 4953 4.308458 CGACACCCACTGGCCGAA 62.308 66.667 0.00 0.00 33.59 4.30
2512 4954 2.668550 GACACCCACTGGCCGAAC 60.669 66.667 0.00 0.00 33.59 3.95
2513 4955 3.469863 GACACCCACTGGCCGAACA 62.470 63.158 0.00 0.00 33.59 3.18
2514 4956 2.034066 CACCCACTGGCCGAACAT 59.966 61.111 0.00 0.00 33.59 2.71
2515 4957 1.603455 CACCCACTGGCCGAACATT 60.603 57.895 0.00 0.00 33.59 2.71
2516 4958 1.603455 ACCCACTGGCCGAACATTG 60.603 57.895 0.00 0.00 33.59 2.82
2517 4959 2.342650 CCCACTGGCCGAACATTGG 61.343 63.158 0.00 8.17 39.95 3.16
2518 4960 1.303236 CCACTGGCCGAACATTGGA 60.303 57.895 9.15 0.00 42.06 3.53
2519 4961 1.586154 CCACTGGCCGAACATTGGAC 61.586 60.000 9.15 0.00 42.06 4.02
2520 4962 1.671054 ACTGGCCGAACATTGGACG 60.671 57.895 0.00 0.00 37.30 4.79
2521 4963 1.375396 CTGGCCGAACATTGGACGA 60.375 57.895 0.00 0.00 37.30 4.20
2522 4964 0.744414 CTGGCCGAACATTGGACGAT 60.744 55.000 0.00 0.00 37.30 3.73
2523 4965 1.024046 TGGCCGAACATTGGACGATG 61.024 55.000 0.00 0.00 37.30 3.84
2524 4966 1.062525 GCCGAACATTGGACGATGC 59.937 57.895 0.00 0.28 0.00 3.91
2525 4967 1.369091 GCCGAACATTGGACGATGCT 61.369 55.000 0.00 0.00 0.00 3.79
2526 4968 1.086696 CCGAACATTGGACGATGCTT 58.913 50.000 0.00 0.00 0.00 3.91
2527 4969 1.468520 CCGAACATTGGACGATGCTTT 59.531 47.619 0.00 0.00 0.00 3.51
2528 4970 2.508867 CGAACATTGGACGATGCTTTG 58.491 47.619 0.00 0.00 0.00 2.77
2529 4971 2.159430 CGAACATTGGACGATGCTTTGA 59.841 45.455 0.00 0.00 0.00 2.69
2530 4972 3.181507 CGAACATTGGACGATGCTTTGAT 60.182 43.478 0.00 0.00 0.00 2.57
2531 4973 4.346129 GAACATTGGACGATGCTTTGATC 58.654 43.478 0.00 0.00 0.00 2.92
2532 4974 2.684881 ACATTGGACGATGCTTTGATCC 59.315 45.455 0.00 0.00 0.00 3.36
2533 4975 2.488204 TTGGACGATGCTTTGATCCA 57.512 45.000 0.00 6.91 37.68 3.41
2534 4976 2.028420 TGGACGATGCTTTGATCCAG 57.972 50.000 0.00 0.00 34.50 3.86
2535 4977 0.659957 GGACGATGCTTTGATCCAGC 59.340 55.000 6.99 6.99 37.82 4.85
2536 4978 0.302890 GACGATGCTTTGATCCAGCG 59.697 55.000 5.92 5.92 45.30 5.18
2537 4979 1.091771 ACGATGCTTTGATCCAGCGG 61.092 55.000 11.12 5.52 44.23 5.52
2538 4980 1.091771 CGATGCTTTGATCCAGCGGT 61.092 55.000 8.95 1.67 40.45 5.68
2539 4981 0.659957 GATGCTTTGATCCAGCGGTC 59.340 55.000 8.95 6.51 40.45 4.79
2540 4982 1.091771 ATGCTTTGATCCAGCGGTCG 61.092 55.000 8.95 0.00 40.45 4.79
2541 4983 2.464459 GCTTTGATCCAGCGGTCGG 61.464 63.158 0.00 0.00 0.00 4.79
2542 4984 2.435938 TTTGATCCAGCGGTCGGC 60.436 61.111 0.00 0.00 44.05 5.54
2543 4985 3.969250 TTTGATCCAGCGGTCGGCC 62.969 63.158 0.00 0.00 45.17 6.13
2545 4987 4.593864 GATCCAGCGGTCGGCCTC 62.594 72.222 3.66 0.00 45.17 4.70
2551 4993 4.083862 GCGGTCGGCCTCCTCTTT 62.084 66.667 3.66 0.00 34.80 2.52
2552 4994 2.125512 CGGTCGGCCTCCTCTTTG 60.126 66.667 3.66 0.00 0.00 2.77
2553 4995 2.943978 CGGTCGGCCTCCTCTTTGT 61.944 63.158 3.66 0.00 0.00 2.83
2554 4996 1.376037 GGTCGGCCTCCTCTTTGTG 60.376 63.158 0.00 0.00 0.00 3.33
2555 4997 1.671742 GTCGGCCTCCTCTTTGTGA 59.328 57.895 0.00 0.00 0.00 3.58
2556 4998 0.670854 GTCGGCCTCCTCTTTGTGAC 60.671 60.000 0.00 0.00 0.00 3.67
2557 4999 1.118965 TCGGCCTCCTCTTTGTGACA 61.119 55.000 0.00 0.00 0.00 3.58
2558 5000 0.036010 CGGCCTCCTCTTTGTGACAT 60.036 55.000 0.00 0.00 0.00 3.06
2559 5001 1.457346 GGCCTCCTCTTTGTGACATG 58.543 55.000 0.00 0.00 0.00 3.21
2560 5002 0.807496 GCCTCCTCTTTGTGACATGC 59.193 55.000 0.00 0.00 0.00 4.06
2561 5003 1.883638 GCCTCCTCTTTGTGACATGCA 60.884 52.381 0.00 0.00 0.00 3.96
2562 5004 2.719739 CCTCCTCTTTGTGACATGCAT 58.280 47.619 0.00 0.00 0.00 3.96
2563 5005 2.422479 CCTCCTCTTTGTGACATGCATG 59.578 50.000 25.09 25.09 0.00 4.06
2564 5006 3.079578 CTCCTCTTTGTGACATGCATGT 58.920 45.455 31.82 31.82 45.16 3.21
2565 5007 4.256110 CTCCTCTTTGTGACATGCATGTA 58.744 43.478 31.45 14.49 41.95 2.29
2566 5008 4.002982 TCCTCTTTGTGACATGCATGTAC 58.997 43.478 31.45 25.74 41.95 2.90
2567 5009 3.181517 CCTCTTTGTGACATGCATGTACG 60.182 47.826 31.45 14.10 41.95 3.67
2568 5010 2.741517 TCTTTGTGACATGCATGTACGG 59.258 45.455 31.45 19.70 41.95 4.02
2569 5011 2.177394 TTGTGACATGCATGTACGGT 57.823 45.000 31.45 9.56 41.95 4.83
2570 5012 1.720805 TGTGACATGCATGTACGGTC 58.279 50.000 31.45 18.92 41.95 4.79
2571 5013 1.001406 TGTGACATGCATGTACGGTCA 59.999 47.619 31.45 21.25 41.95 4.02
2572 5014 1.660607 GTGACATGCATGTACGGTCAG 59.339 52.381 31.45 2.62 41.95 3.51
2573 5015 1.548269 TGACATGCATGTACGGTCAGA 59.452 47.619 31.45 6.29 41.95 3.27
2574 5016 2.168313 TGACATGCATGTACGGTCAGAT 59.832 45.455 31.45 5.52 41.95 2.90
2575 5017 2.797156 GACATGCATGTACGGTCAGATC 59.203 50.000 31.45 11.80 41.95 2.75
2576 5018 2.168313 ACATGCATGTACGGTCAGATCA 59.832 45.455 30.50 0.00 39.68 2.92
2577 5019 2.584492 TGCATGTACGGTCAGATCAG 57.416 50.000 0.00 0.00 0.00 2.90
2578 5020 1.824852 TGCATGTACGGTCAGATCAGT 59.175 47.619 0.00 0.00 0.00 3.41
2579 5021 3.020984 TGCATGTACGGTCAGATCAGTA 58.979 45.455 0.00 0.00 0.00 2.74
2580 5022 3.066760 TGCATGTACGGTCAGATCAGTAG 59.933 47.826 0.00 0.00 0.00 2.57
2581 5023 3.633235 CATGTACGGTCAGATCAGTAGC 58.367 50.000 0.00 0.00 0.00 3.58
2582 5024 2.718563 TGTACGGTCAGATCAGTAGCA 58.281 47.619 0.00 0.00 0.00 3.49
2583 5025 3.288092 TGTACGGTCAGATCAGTAGCAT 58.712 45.455 0.00 0.00 0.00 3.79
2584 5026 3.315470 TGTACGGTCAGATCAGTAGCATC 59.685 47.826 0.00 0.00 0.00 3.91
2585 5027 1.335182 ACGGTCAGATCAGTAGCATCG 59.665 52.381 0.00 0.00 0.00 3.84
2586 5028 1.335182 CGGTCAGATCAGTAGCATCGT 59.665 52.381 0.00 0.00 0.00 3.73
2587 5029 2.603412 CGGTCAGATCAGTAGCATCGTC 60.603 54.545 0.00 0.00 0.00 4.20
2588 5030 2.287909 GGTCAGATCAGTAGCATCGTCC 60.288 54.545 0.00 0.00 0.00 4.79
2589 5031 2.359214 GTCAGATCAGTAGCATCGTCCA 59.641 50.000 0.00 0.00 0.00 4.02
2590 5032 2.620585 TCAGATCAGTAGCATCGTCCAG 59.379 50.000 0.00 0.00 0.00 3.86
2591 5033 2.620585 CAGATCAGTAGCATCGTCCAGA 59.379 50.000 0.00 0.00 0.00 3.86
2592 5034 2.621055 AGATCAGTAGCATCGTCCAGAC 59.379 50.000 0.00 0.00 0.00 3.51
2593 5035 1.834188 TCAGTAGCATCGTCCAGACA 58.166 50.000 0.00 0.00 0.00 3.41
2594 5036 2.379005 TCAGTAGCATCGTCCAGACAT 58.621 47.619 0.00 0.00 0.00 3.06
2595 5037 2.359214 TCAGTAGCATCGTCCAGACATC 59.641 50.000 0.00 0.00 0.00 3.06
2596 5038 1.335182 AGTAGCATCGTCCAGACATCG 59.665 52.381 0.00 0.00 0.00 3.84
2597 5039 0.668535 TAGCATCGTCCAGACATCGG 59.331 55.000 0.00 0.00 0.00 4.18
2598 5040 2.240500 GCATCGTCCAGACATCGGC 61.241 63.158 0.00 0.00 0.00 5.54
2599 5041 1.439228 CATCGTCCAGACATCGGCT 59.561 57.895 0.00 0.00 0.00 5.52
2600 5042 0.873312 CATCGTCCAGACATCGGCTG 60.873 60.000 0.00 0.00 0.00 4.85
2601 5043 2.635229 ATCGTCCAGACATCGGCTGC 62.635 60.000 0.00 0.00 32.06 5.25
2602 5044 2.265739 GTCCAGACATCGGCTGCA 59.734 61.111 0.50 0.00 32.06 4.41
2603 5045 2.103042 GTCCAGACATCGGCTGCAC 61.103 63.158 0.50 0.00 32.06 4.57
2604 5046 2.046988 CCAGACATCGGCTGCACA 60.047 61.111 0.50 0.00 32.06 4.57
2605 5047 2.393768 CCAGACATCGGCTGCACAC 61.394 63.158 0.50 0.00 32.06 3.82
2606 5048 2.046892 AGACATCGGCTGCACACC 60.047 61.111 0.50 0.00 0.00 4.16
2621 5063 3.706287 CACCGTCGTGTGTATAGCA 57.294 52.632 5.89 0.00 35.10 3.49
2622 5064 1.545759 CACCGTCGTGTGTATAGCAG 58.454 55.000 5.89 0.00 35.10 4.24
2623 5065 0.179145 ACCGTCGTGTGTATAGCAGC 60.179 55.000 0.00 0.00 0.00 5.25
2624 5066 1.200474 CCGTCGTGTGTATAGCAGCG 61.200 60.000 0.00 0.00 0.00 5.18
2625 5067 1.798368 CGTCGTGTGTATAGCAGCGC 61.798 60.000 0.00 0.00 0.00 5.92
2626 5068 0.525668 GTCGTGTGTATAGCAGCGCT 60.526 55.000 2.64 2.64 43.41 5.92
2627 5069 0.248498 TCGTGTGTATAGCAGCGCTC 60.248 55.000 7.13 2.24 40.44 5.03
2628 5070 1.209275 CGTGTGTATAGCAGCGCTCC 61.209 60.000 7.13 0.00 40.44 4.70
2629 5071 0.876342 GTGTGTATAGCAGCGCTCCC 60.876 60.000 7.13 0.57 40.44 4.30
2630 5072 1.661821 GTGTATAGCAGCGCTCCCG 60.662 63.158 7.13 0.00 40.44 5.14
2633 5075 0.386985 GTATAGCAGCGCTCCCGTAC 60.387 60.000 7.13 5.33 40.44 3.67
2643 5085 1.679680 CGCTCCCGTACTCTATTCCAA 59.320 52.381 0.00 0.00 0.00 3.53
2691 5133 1.064060 GATTGATGCTTACCGGTGTGC 59.936 52.381 19.93 21.04 0.00 4.57
2736 5184 5.659079 AGCATCCTACTAGAAAGCTTACACT 59.341 40.000 0.00 2.63 29.91 3.55
2749 5197 1.822990 CTTACACTGGAGGGCTTCGTA 59.177 52.381 0.00 0.00 0.00 3.43
2773 5221 1.578206 GCAACAGTTTCGGGAGAGCC 61.578 60.000 0.00 0.00 41.75 4.70
2783 5231 4.666105 GGAGAGCCCAACCATTCC 57.334 61.111 0.00 0.00 34.14 3.01
2784 5232 2.002625 GGAGAGCCCAACCATTCCT 58.997 57.895 0.00 0.00 34.14 3.36
2785 5233 0.394899 GGAGAGCCCAACCATTCCTG 60.395 60.000 0.00 0.00 34.14 3.86
2786 5234 3.752271 GGAGAGCCCAACCATTCCTGG 62.752 61.905 0.00 0.00 40.87 4.45
2795 5243 2.780595 CCATTCCTGGCCAACTACG 58.219 57.895 7.01 0.00 35.23 3.51
2796 5244 0.251916 CCATTCCTGGCCAACTACGA 59.748 55.000 7.01 0.00 35.23 3.43
2797 5245 1.656652 CATTCCTGGCCAACTACGAG 58.343 55.000 7.01 0.00 0.00 4.18
2798 5246 1.066143 CATTCCTGGCCAACTACGAGT 60.066 52.381 7.01 0.00 0.00 4.18
2799 5247 1.927487 TTCCTGGCCAACTACGAGTA 58.073 50.000 7.01 0.00 0.00 2.59
2800 5248 1.471119 TCCTGGCCAACTACGAGTAG 58.529 55.000 7.01 8.58 39.04 2.57
2801 5249 0.179108 CCTGGCCAACTACGAGTAGC 60.179 60.000 7.01 0.00 36.66 3.58
2802 5250 0.530744 CTGGCCAACTACGAGTAGCA 59.469 55.000 7.01 0.00 36.66 3.49
2803 5251 0.245539 TGGCCAACTACGAGTAGCAC 59.754 55.000 0.61 0.00 36.66 4.40
2804 5252 0.531200 GGCCAACTACGAGTAGCACT 59.469 55.000 9.94 0.00 36.66 4.40
2805 5253 1.469423 GGCCAACTACGAGTAGCACTC 60.469 57.143 9.94 6.31 41.71 3.51
2806 5254 1.201647 GCCAACTACGAGTAGCACTCA 59.798 52.381 9.94 0.00 45.30 3.41
2807 5255 2.352421 GCCAACTACGAGTAGCACTCAA 60.352 50.000 9.94 3.80 45.30 3.02
2808 5256 3.243336 CCAACTACGAGTAGCACTCAAC 58.757 50.000 9.94 0.00 45.30 3.18
2809 5257 3.305131 CCAACTACGAGTAGCACTCAACA 60.305 47.826 9.94 1.40 45.30 3.33
2810 5258 4.486090 CAACTACGAGTAGCACTCAACAT 58.514 43.478 9.94 2.64 45.30 2.71
2811 5259 4.358494 ACTACGAGTAGCACTCAACATC 57.642 45.455 9.94 0.00 45.30 3.06
2812 5260 3.756963 ACTACGAGTAGCACTCAACATCA 59.243 43.478 9.94 0.00 45.30 3.07
2813 5261 3.223423 ACGAGTAGCACTCAACATCAG 57.777 47.619 14.09 2.16 45.30 2.90
2814 5262 2.558795 ACGAGTAGCACTCAACATCAGT 59.441 45.455 14.09 2.63 45.30 3.41
2815 5263 3.756963 ACGAGTAGCACTCAACATCAGTA 59.243 43.478 14.09 0.00 45.30 2.74
2816 5264 4.142578 ACGAGTAGCACTCAACATCAGTAG 60.143 45.833 14.09 0.00 45.30 2.57
2817 5265 4.142578 CGAGTAGCACTCAACATCAGTAGT 60.143 45.833 14.09 0.00 45.30 2.73
2818 5266 5.064834 CGAGTAGCACTCAACATCAGTAGTA 59.935 44.000 14.09 0.00 45.30 1.82
2819 5267 6.197364 AGTAGCACTCAACATCAGTAGTAC 57.803 41.667 0.00 0.00 0.00 2.73
2820 5268 5.946972 AGTAGCACTCAACATCAGTAGTACT 59.053 40.000 0.00 0.00 0.00 2.73
2821 5269 7.888839 GAGTAGCACTCAACATCAGTAGTACTG 60.889 44.444 22.16 22.16 44.56 2.74
2822 5270 4.524714 AGCACTCAACATCAGTAGTACTGT 59.475 41.667 25.83 13.23 46.03 3.55
2823 5271 5.710567 AGCACTCAACATCAGTAGTACTGTA 59.289 40.000 25.83 15.16 46.03 2.74
2824 5272 6.378564 AGCACTCAACATCAGTAGTACTGTAT 59.621 38.462 25.83 16.48 46.03 2.29
2825 5273 6.693545 GCACTCAACATCAGTAGTACTGTATC 59.306 42.308 25.83 4.82 46.03 2.24
2826 5274 7.415765 GCACTCAACATCAGTAGTACTGTATCT 60.416 40.741 25.83 10.10 46.03 1.98
2827 5275 9.110502 CACTCAACATCAGTAGTACTGTATCTA 57.889 37.037 25.83 10.13 46.03 1.98
2828 5276 9.854668 ACTCAACATCAGTAGTACTGTATCTAT 57.145 33.333 25.83 11.84 46.03 1.98
2855 5303 8.693120 AAGATGAGATACAATCAATTCATGCT 57.307 30.769 0.00 0.00 0.00 3.79
2856 5304 8.325421 AGATGAGATACAATCAATTCATGCTC 57.675 34.615 0.00 0.00 0.00 4.26
2857 5305 8.158132 AGATGAGATACAATCAATTCATGCTCT 58.842 33.333 0.00 0.00 0.00 4.09
2858 5306 9.433153 GATGAGATACAATCAATTCATGCTCTA 57.567 33.333 0.00 0.00 0.00 2.43
2859 5307 9.788889 ATGAGATACAATCAATTCATGCTCTAA 57.211 29.630 0.00 0.00 0.00 2.10
2860 5308 9.049523 TGAGATACAATCAATTCATGCTCTAAC 57.950 33.333 0.00 0.00 0.00 2.34
2861 5309 8.969260 AGATACAATCAATTCATGCTCTAACA 57.031 30.769 0.00 0.00 0.00 2.41
2862 5310 9.399797 AGATACAATCAATTCATGCTCTAACAA 57.600 29.630 0.00 0.00 0.00 2.83
2863 5311 9.443283 GATACAATCAATTCATGCTCTAACAAC 57.557 33.333 0.00 0.00 0.00 3.32
2864 5312 7.458409 ACAATCAATTCATGCTCTAACAACT 57.542 32.000 0.00 0.00 0.00 3.16
2865 5313 8.565896 ACAATCAATTCATGCTCTAACAACTA 57.434 30.769 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 6.997239 TGTGCTCGTACTATACCATATAGG 57.003 41.667 7.58 0.00 45.67 2.57
68 70 7.750903 GCAGGCATCGAATAAATTTCCTATTAC 59.249 37.037 0.00 0.00 0.00 1.89
74 76 3.003275 TCGCAGGCATCGAATAAATTTCC 59.997 43.478 0.00 0.00 32.53 3.13
108 110 6.288941 TCCCATAATTGTCACTTTCGACTA 57.711 37.500 0.00 0.00 36.82 2.59
144 146 0.388391 CTGGCTAGCTCGCTAGATGC 60.388 60.000 25.63 13.49 46.56 3.91
214 229 7.989741 AGAAAGATCATAGTGAATACCACCTTG 59.010 37.037 0.00 0.00 46.87 3.61
217 232 6.203723 GCAGAAAGATCATAGTGAATACCACC 59.796 42.308 0.00 0.00 46.87 4.61
230 248 1.340405 ACTTGCCGGCAGAAAGATCAT 60.340 47.619 30.75 5.40 0.00 2.45
273 291 1.543690 GGGCTGCCCAGGGAATTAT 59.456 57.895 32.46 0.00 44.65 1.28
305 324 0.695347 CCATCCTTATCCCTGCCCTC 59.305 60.000 0.00 0.00 0.00 4.30
337 356 2.296190 GCCTTTGACCCCTACTTTGTTG 59.704 50.000 0.00 0.00 0.00 3.33
338 357 2.594131 GCCTTTGACCCCTACTTTGTT 58.406 47.619 0.00 0.00 0.00 2.83
339 358 1.203013 GGCCTTTGACCCCTACTTTGT 60.203 52.381 0.00 0.00 0.00 2.83
500 1899 1.525197 GTCGTCGAAGCATTTGTGACA 59.475 47.619 0.00 0.00 36.58 3.58
563 1962 3.899981 TTGCAGCCCACCAGCTACG 62.900 63.158 0.00 0.00 42.61 3.51
589 1989 4.980805 TTCACGCCTCACACGGGC 62.981 66.667 0.00 0.00 45.57 6.13
651 2051 5.354792 TGGTTTCACCTACAGTAACAAACAC 59.645 40.000 0.00 0.00 39.58 3.32
707 2109 2.295629 TGAGCATCTAGAAGCGGATCTG 59.704 50.000 13.87 0.00 34.92 2.90
714 2116 4.333913 TCTTGGATGAGCATCTAGAAGC 57.666 45.455 12.00 12.00 37.92 3.86
893 2307 3.623060 TCCGTTACGTGATACTACTCACC 59.377 47.826 3.52 0.00 42.06 4.02
897 2311 4.142381 GGGTTTCCGTTACGTGATACTACT 60.142 45.833 3.52 0.00 0.00 2.57
899 2313 4.370364 GGGTTTCCGTTACGTGATACTA 57.630 45.455 3.52 0.00 0.00 1.82
1000 2416 2.488347 CGGGGTGGTGGGGAATTTATAG 60.488 54.545 0.00 0.00 0.00 1.31
1063 2480 4.150627 CGATTGACGAGACTTGTGAAATGT 59.849 41.667 0.00 0.00 45.77 2.71
1078 2495 1.188769 GCGAGAGACGACGATTGACG 61.189 60.000 0.00 3.17 45.77 4.35
1079 2496 0.862283 GGCGAGAGACGACGATTGAC 60.862 60.000 0.00 0.00 45.77 3.18
1081 2498 3.984241 GGCGAGAGACGACGATTG 58.016 61.111 0.00 0.00 45.77 2.67
1111 2533 1.376812 CTTCGGCTGGGTGGGTAAC 60.377 63.158 0.00 0.00 0.00 2.50
1112 2534 1.128809 TTCTTCGGCTGGGTGGGTAA 61.129 55.000 0.00 0.00 0.00 2.85
1119 2541 1.639298 CGAAAGCTTCTTCGGCTGGG 61.639 60.000 11.85 0.00 43.51 4.45
1127 2549 1.149148 GCTTCGGTCGAAAGCTTCTT 58.851 50.000 12.09 0.00 33.34 2.52
1140 2562 2.377310 CGGTGTTGGTACGCTTCGG 61.377 63.158 0.00 0.00 35.12 4.30
1150 2572 0.108329 ATCGGTTAGCTCGGTGTTGG 60.108 55.000 0.00 0.00 0.00 3.77
1152 2574 0.108329 CCATCGGTTAGCTCGGTGTT 60.108 55.000 5.90 0.00 37.06 3.32
1153 2575 1.515954 CCATCGGTTAGCTCGGTGT 59.484 57.895 5.90 0.00 37.06 4.16
1154 2576 1.883084 GCCATCGGTTAGCTCGGTG 60.883 63.158 0.00 0.00 38.35 4.94
1320 2751 1.446366 GATGTAGTCGGCCTTCCCC 59.554 63.158 0.00 0.00 0.00 4.81
1504 2935 1.306226 GTGGCTGGTCCTCCTAGGT 60.306 63.158 9.08 0.00 36.53 3.08
1513 2944 2.200337 GGTTGGTTGGTGGCTGGTC 61.200 63.158 0.00 0.00 0.00 4.02
1514 2945 2.123468 GGTTGGTTGGTGGCTGGT 60.123 61.111 0.00 0.00 0.00 4.00
1517 2950 0.755327 GAGTTGGTTGGTTGGTGGCT 60.755 55.000 0.00 0.00 0.00 4.75
1594 3027 0.905357 AGAACATCAAGGACTCCCGG 59.095 55.000 0.00 0.00 37.58 5.73
1595 3028 2.761208 ACTAGAACATCAAGGACTCCCG 59.239 50.000 0.00 0.00 37.58 5.14
1629 3065 1.316706 CGTCCTCTCCTCTGACCACC 61.317 65.000 0.00 0.00 0.00 4.61
1647 3083 2.633481 CCCTAAAACTAGATCCCCTCCG 59.367 54.545 0.00 0.00 0.00 4.63
1730 3166 4.353777 TCTGGGTCTGAGCTTGTACTAAT 58.646 43.478 6.83 0.00 0.00 1.73
1732 3168 3.451402 TCTGGGTCTGAGCTTGTACTA 57.549 47.619 6.83 0.00 0.00 1.82
1747 3205 2.185004 ACTGAACCGAAACATCTGGG 57.815 50.000 0.00 0.00 0.00 4.45
1748 3206 2.484264 GGAACTGAACCGAAACATCTGG 59.516 50.000 0.00 0.00 0.00 3.86
1760 3218 2.540973 GGCAACAAAGTCGGAACTGAAC 60.541 50.000 0.00 0.00 35.36 3.18
1800 3259 3.691118 GCAGATCTGGCAAATGTAACTGA 59.309 43.478 23.89 0.00 0.00 3.41
1919 4221 5.357032 AGAAATAATTGGTGTTCGGATCCAC 59.643 40.000 13.41 3.70 0.00 4.02
1926 4228 6.254281 AGGTTGAGAAATAATTGGTGTTCG 57.746 37.500 0.00 0.00 0.00 3.95
1971 4333 1.760192 AATCAGCAGGCTCAATGGTC 58.240 50.000 0.00 0.00 0.00 4.02
1982 4344 1.226859 CATGGCGGCAAATCAGCAG 60.227 57.895 18.31 0.00 37.64 4.24
2049 4450 1.202114 TCCAGAATCAAACAATGGCGC 59.798 47.619 0.00 0.00 0.00 6.53
2124 4526 2.426024 ACCTACGTTGATGCGTCATAGT 59.574 45.455 9.96 14.57 44.55 2.12
2125 4527 3.079960 ACCTACGTTGATGCGTCATAG 57.920 47.619 9.96 8.61 44.55 2.23
2126 4528 3.243168 GGTACCTACGTTGATGCGTCATA 60.243 47.826 9.96 0.00 44.55 2.15
2128 4530 1.135315 GGTACCTACGTTGATGCGTCA 60.135 52.381 3.97 3.97 44.55 4.35
2129 4531 1.135315 TGGTACCTACGTTGATGCGTC 60.135 52.381 14.36 0.00 44.55 5.19
2131 4533 1.274596 GTGGTACCTACGTTGATGCG 58.725 55.000 14.36 0.00 37.94 4.73
2133 4535 1.203052 ACCGTGGTACCTACGTTGATG 59.797 52.381 25.10 16.39 39.76 3.07
2218 4631 2.679450 TGTAGTTCACCCAATCGAACG 58.321 47.619 0.00 0.00 44.94 3.95
2239 4652 5.588958 AGATTCATCAGTTCATCGAGACA 57.411 39.130 0.00 0.00 0.00 3.41
2388 4829 4.758674 CACATAAATTCGCTGGATCATCCT 59.241 41.667 4.96 0.00 37.46 3.24
2415 4856 5.105917 GGCTAGCAGGCTTTACATTACAAAA 60.106 40.000 18.24 0.00 37.85 2.44
2418 4859 3.541632 GGCTAGCAGGCTTTACATTACA 58.458 45.455 18.24 0.00 37.85 2.41
2436 4877 1.412710 TCGCTTTAGAATCATCCGGCT 59.587 47.619 0.00 0.00 0.00 5.52
2458 4900 1.382009 TACGGCCACTATCCCAGCA 60.382 57.895 2.24 0.00 0.00 4.41
2460 4902 1.362717 CGTACGGCCACTATCCCAG 59.637 63.158 7.57 0.00 0.00 4.45
2472 4914 0.806868 TGCTCAGTAGTTCCGTACGG 59.193 55.000 28.66 28.66 0.00 4.02
2473 4915 1.794437 GCTGCTCAGTAGTTCCGTACG 60.794 57.143 8.69 8.69 0.00 3.67
2475 4917 0.815734 GGCTGCTCAGTAGTTCCGTA 59.184 55.000 0.00 0.00 0.00 4.02
2476 4918 1.592223 GGCTGCTCAGTAGTTCCGT 59.408 57.895 0.00 0.00 0.00 4.69
2478 4920 0.458716 GTCGGCTGCTCAGTAGTTCC 60.459 60.000 0.00 0.00 0.00 3.62
2479 4921 0.243907 TGTCGGCTGCTCAGTAGTTC 59.756 55.000 0.00 0.00 0.00 3.01
2480 4922 0.038159 GTGTCGGCTGCTCAGTAGTT 60.038 55.000 0.00 0.00 0.00 2.24
2481 4923 1.587054 GTGTCGGCTGCTCAGTAGT 59.413 57.895 0.00 0.00 0.00 2.73
2482 4924 1.153745 GGTGTCGGCTGCTCAGTAG 60.154 63.158 0.00 0.00 0.00 2.57
2483 4925 2.646175 GGGTGTCGGCTGCTCAGTA 61.646 63.158 0.00 0.00 0.00 2.74
2484 4926 4.008933 GGGTGTCGGCTGCTCAGT 62.009 66.667 0.00 0.00 0.00 3.41
2485 4927 4.007644 TGGGTGTCGGCTGCTCAG 62.008 66.667 0.00 0.00 0.00 3.35
2486 4928 4.314440 GTGGGTGTCGGCTGCTCA 62.314 66.667 0.00 0.00 0.00 4.26
2487 4929 4.008933 AGTGGGTGTCGGCTGCTC 62.009 66.667 0.00 0.00 0.00 4.26
2488 4930 4.320456 CAGTGGGTGTCGGCTGCT 62.320 66.667 0.00 0.00 0.00 4.24
2494 4936 4.308458 TTCGGCCAGTGGGTGTCG 62.308 66.667 12.15 0.00 36.17 4.35
2495 4937 2.668550 GTTCGGCCAGTGGGTGTC 60.669 66.667 12.15 0.00 36.17 3.67
2496 4938 2.351924 AATGTTCGGCCAGTGGGTGT 62.352 55.000 12.15 0.00 36.17 4.16
2497 4939 1.603455 AATGTTCGGCCAGTGGGTG 60.603 57.895 12.15 0.00 36.17 4.61
2498 4940 1.603455 CAATGTTCGGCCAGTGGGT 60.603 57.895 12.15 0.00 36.17 4.51
2499 4941 2.342650 CCAATGTTCGGCCAGTGGG 61.343 63.158 12.15 0.00 44.70 4.61
2500 4942 3.277133 CCAATGTTCGGCCAGTGG 58.723 61.111 4.20 4.20 43.31 4.00
2501 4943 1.875963 GTCCAATGTTCGGCCAGTG 59.124 57.895 2.24 0.00 0.00 3.66
2502 4944 1.671054 CGTCCAATGTTCGGCCAGT 60.671 57.895 2.24 0.00 0.00 4.00
2503 4945 0.744414 ATCGTCCAATGTTCGGCCAG 60.744 55.000 2.24 0.00 0.00 4.85
2504 4946 1.024046 CATCGTCCAATGTTCGGCCA 61.024 55.000 2.24 0.00 0.00 5.36
2505 4947 1.721487 CATCGTCCAATGTTCGGCC 59.279 57.895 0.00 0.00 0.00 6.13
2506 4948 1.062525 GCATCGTCCAATGTTCGGC 59.937 57.895 0.00 0.00 0.00 5.54
2507 4949 1.086696 AAGCATCGTCCAATGTTCGG 58.913 50.000 0.00 0.00 0.00 4.30
2508 4950 2.159430 TCAAAGCATCGTCCAATGTTCG 59.841 45.455 0.00 0.00 0.00 3.95
2509 4951 3.829886 TCAAAGCATCGTCCAATGTTC 57.170 42.857 0.00 0.00 0.00 3.18
2510 4952 3.129287 GGATCAAAGCATCGTCCAATGTT 59.871 43.478 0.00 0.00 0.00 2.71
2511 4953 2.684881 GGATCAAAGCATCGTCCAATGT 59.315 45.455 0.00 0.00 0.00 2.71
2512 4954 2.684374 TGGATCAAAGCATCGTCCAATG 59.316 45.455 0.00 0.00 36.12 2.82
2513 4955 2.947652 CTGGATCAAAGCATCGTCCAAT 59.052 45.455 0.00 0.00 38.41 3.16
2514 4956 2.358957 CTGGATCAAAGCATCGTCCAA 58.641 47.619 0.00 0.00 38.41 3.53
2515 4957 2.013563 GCTGGATCAAAGCATCGTCCA 61.014 52.381 13.25 0.00 40.52 4.02
2516 4958 0.659957 GCTGGATCAAAGCATCGTCC 59.340 55.000 13.25 0.00 40.52 4.79
2517 4959 0.302890 CGCTGGATCAAAGCATCGTC 59.697 55.000 17.02 0.00 40.86 4.20
2518 4960 1.091771 CCGCTGGATCAAAGCATCGT 61.092 55.000 17.02 0.00 40.86 3.73
2519 4961 1.091771 ACCGCTGGATCAAAGCATCG 61.092 55.000 17.02 8.06 40.86 3.84
2520 4962 0.659957 GACCGCTGGATCAAAGCATC 59.340 55.000 17.02 11.03 40.86 3.91
2521 4963 1.091771 CGACCGCTGGATCAAAGCAT 61.092 55.000 17.02 6.74 40.86 3.79
2522 4964 1.741401 CGACCGCTGGATCAAAGCA 60.741 57.895 17.02 0.00 40.86 3.91
2523 4965 2.464459 CCGACCGCTGGATCAAAGC 61.464 63.158 9.09 9.09 37.31 3.51
2524 4966 2.464459 GCCGACCGCTGGATCAAAG 61.464 63.158 0.00 0.00 0.00 2.77
2525 4967 2.435938 GCCGACCGCTGGATCAAA 60.436 61.111 0.00 0.00 0.00 2.69
2526 4968 4.467084 GGCCGACCGCTGGATCAA 62.467 66.667 0.00 0.00 37.74 2.57
2528 4970 4.593864 GAGGCCGACCGCTGGATC 62.594 72.222 0.00 0.00 42.76 3.36
2534 4976 4.083862 AAAGAGGAGGCCGACCGC 62.084 66.667 15.33 15.33 42.76 5.68
2535 4977 2.125512 CAAAGAGGAGGCCGACCG 60.126 66.667 14.56 0.00 42.76 4.79
2536 4978 1.376037 CACAAAGAGGAGGCCGACC 60.376 63.158 13.01 13.01 0.00 4.79
2537 4979 0.670854 GTCACAAAGAGGAGGCCGAC 60.671 60.000 0.00 0.00 0.00 4.79
2538 4980 1.118965 TGTCACAAAGAGGAGGCCGA 61.119 55.000 0.00 0.00 0.00 5.54
2539 4981 0.036010 ATGTCACAAAGAGGAGGCCG 60.036 55.000 0.00 0.00 0.00 6.13
2540 4982 1.457346 CATGTCACAAAGAGGAGGCC 58.543 55.000 0.00 0.00 0.00 5.19
2541 4983 0.807496 GCATGTCACAAAGAGGAGGC 59.193 55.000 0.00 0.00 0.00 4.70
2542 4984 2.189594 TGCATGTCACAAAGAGGAGG 57.810 50.000 0.00 0.00 0.00 4.30
2543 4985 3.079578 ACATGCATGTCACAAAGAGGAG 58.920 45.455 26.61 0.00 35.87 3.69
2544 4986 3.144657 ACATGCATGTCACAAAGAGGA 57.855 42.857 26.61 0.00 35.87 3.71
2545 4987 3.181517 CGTACATGCATGTCACAAAGAGG 60.182 47.826 34.54 17.14 41.97 3.69
2546 4988 3.181517 CCGTACATGCATGTCACAAAGAG 60.182 47.826 34.54 16.79 41.97 2.85
2547 4989 2.741517 CCGTACATGCATGTCACAAAGA 59.258 45.455 34.54 13.77 41.97 2.52
2548 4990 2.483877 ACCGTACATGCATGTCACAAAG 59.516 45.455 34.54 19.01 41.97 2.77
2549 4991 2.482336 GACCGTACATGCATGTCACAAA 59.518 45.455 34.54 15.32 41.97 2.83
2550 4992 2.073056 GACCGTACATGCATGTCACAA 58.927 47.619 34.54 15.72 41.97 3.33
2551 4993 1.001406 TGACCGTACATGCATGTCACA 59.999 47.619 34.54 22.81 41.97 3.58
2552 4994 1.660607 CTGACCGTACATGCATGTCAC 59.339 52.381 34.54 25.90 41.97 3.67
2553 4995 1.548269 TCTGACCGTACATGCATGTCA 59.452 47.619 34.54 23.58 41.97 3.58
2554 4996 2.293677 TCTGACCGTACATGCATGTC 57.706 50.000 34.54 23.28 41.97 3.06
2555 4997 2.168313 TGATCTGACCGTACATGCATGT 59.832 45.455 33.20 33.20 44.48 3.21
2556 4998 2.798847 CTGATCTGACCGTACATGCATG 59.201 50.000 25.09 25.09 0.00 4.06
2557 4999 2.432146 ACTGATCTGACCGTACATGCAT 59.568 45.455 6.60 0.00 0.00 3.96
2558 5000 1.824852 ACTGATCTGACCGTACATGCA 59.175 47.619 6.60 0.00 0.00 3.96
2559 5001 2.586258 ACTGATCTGACCGTACATGC 57.414 50.000 6.60 0.00 0.00 4.06
2560 5002 3.066760 TGCTACTGATCTGACCGTACATG 59.933 47.826 6.60 0.00 0.00 3.21
2561 5003 3.288092 TGCTACTGATCTGACCGTACAT 58.712 45.455 6.60 0.00 0.00 2.29
2562 5004 2.718563 TGCTACTGATCTGACCGTACA 58.281 47.619 6.60 0.00 0.00 2.90
2563 5005 3.607310 CGATGCTACTGATCTGACCGTAC 60.607 52.174 6.60 0.00 0.00 3.67
2564 5006 2.548480 CGATGCTACTGATCTGACCGTA 59.452 50.000 6.60 0.00 0.00 4.02
2565 5007 1.335182 CGATGCTACTGATCTGACCGT 59.665 52.381 6.60 0.00 0.00 4.83
2566 5008 1.335182 ACGATGCTACTGATCTGACCG 59.665 52.381 6.60 3.37 0.00 4.79
2567 5009 2.287909 GGACGATGCTACTGATCTGACC 60.288 54.545 6.60 0.00 0.00 4.02
2568 5010 2.359214 TGGACGATGCTACTGATCTGAC 59.641 50.000 6.60 0.00 0.00 3.51
2569 5011 2.620585 CTGGACGATGCTACTGATCTGA 59.379 50.000 6.60 0.00 0.00 3.27
2570 5012 2.620585 TCTGGACGATGCTACTGATCTG 59.379 50.000 0.00 0.00 0.00 2.90
2571 5013 2.621055 GTCTGGACGATGCTACTGATCT 59.379 50.000 0.00 0.00 0.00 2.75
2572 5014 2.359214 TGTCTGGACGATGCTACTGATC 59.641 50.000 0.00 0.00 0.00 2.92
2573 5015 2.379005 TGTCTGGACGATGCTACTGAT 58.621 47.619 0.00 0.00 0.00 2.90
2574 5016 1.834188 TGTCTGGACGATGCTACTGA 58.166 50.000 0.00 0.00 0.00 3.41
2575 5017 2.736978 GATGTCTGGACGATGCTACTG 58.263 52.381 0.00 0.00 0.00 2.74
2576 5018 1.335182 CGATGTCTGGACGATGCTACT 59.665 52.381 0.00 0.00 0.00 2.57
2577 5019 1.600663 CCGATGTCTGGACGATGCTAC 60.601 57.143 0.00 0.00 0.00 3.58
2578 5020 0.668535 CCGATGTCTGGACGATGCTA 59.331 55.000 0.00 0.00 0.00 3.49
2579 5021 1.439228 CCGATGTCTGGACGATGCT 59.561 57.895 0.00 0.00 0.00 3.79
2580 5022 2.240500 GCCGATGTCTGGACGATGC 61.241 63.158 0.00 0.00 0.00 3.91
2581 5023 0.873312 CAGCCGATGTCTGGACGATG 60.873 60.000 0.00 0.00 0.00 3.84
2582 5024 1.439228 CAGCCGATGTCTGGACGAT 59.561 57.895 0.00 0.00 0.00 3.73
2583 5025 2.885113 CAGCCGATGTCTGGACGA 59.115 61.111 0.00 0.00 0.00 4.20
2584 5026 2.887568 GCAGCCGATGTCTGGACG 60.888 66.667 0.00 0.00 32.41 4.79
2585 5027 2.103042 GTGCAGCCGATGTCTGGAC 61.103 63.158 0.00 0.00 43.61 4.02
2586 5028 2.265739 GTGCAGCCGATGTCTGGA 59.734 61.111 0.00 0.00 32.41 3.86
2587 5029 2.046988 TGTGCAGCCGATGTCTGG 60.047 61.111 0.00 0.00 32.41 3.86
2588 5030 2.393768 GGTGTGCAGCCGATGTCTG 61.394 63.158 0.00 0.00 34.79 3.51
2589 5031 2.046892 GGTGTGCAGCCGATGTCT 60.047 61.111 0.00 0.00 0.00 3.41
2604 5046 0.179145 GCTGCTATACACACGACGGT 60.179 55.000 0.00 0.00 0.00 4.83
2605 5047 1.200474 CGCTGCTATACACACGACGG 61.200 60.000 0.00 0.00 0.00 4.79
2606 5048 1.798368 GCGCTGCTATACACACGACG 61.798 60.000 0.00 0.00 0.00 5.12
2607 5049 0.525668 AGCGCTGCTATACACACGAC 60.526 55.000 10.39 0.00 36.99 4.34
2608 5050 0.248498 GAGCGCTGCTATACACACGA 60.248 55.000 18.48 0.00 39.88 4.35
2609 5051 1.209275 GGAGCGCTGCTATACACACG 61.209 60.000 22.85 0.00 39.88 4.49
2610 5052 0.876342 GGGAGCGCTGCTATACACAC 60.876 60.000 28.44 5.29 39.88 3.82
2611 5053 1.441729 GGGAGCGCTGCTATACACA 59.558 57.895 28.44 0.00 39.88 3.72
2612 5054 1.661821 CGGGAGCGCTGCTATACAC 60.662 63.158 28.44 9.67 39.88 2.90
2613 5055 0.820482 TACGGGAGCGCTGCTATACA 60.820 55.000 28.44 6.99 39.88 2.29
2614 5056 0.386985 GTACGGGAGCGCTGCTATAC 60.387 60.000 28.44 23.84 39.88 1.47
2615 5057 0.536687 AGTACGGGAGCGCTGCTATA 60.537 55.000 28.44 17.42 39.88 1.31
2616 5058 1.797211 GAGTACGGGAGCGCTGCTAT 61.797 60.000 28.44 18.45 39.88 2.97
2617 5059 2.439701 AGTACGGGAGCGCTGCTA 60.440 61.111 28.44 11.40 39.88 3.49
2618 5060 2.888464 TAGAGTACGGGAGCGCTGCT 62.888 60.000 28.44 12.52 43.88 4.24
2619 5061 1.797211 ATAGAGTACGGGAGCGCTGC 61.797 60.000 22.03 22.03 0.00 5.25
2620 5062 0.669077 AATAGAGTACGGGAGCGCTG 59.331 55.000 18.48 2.15 0.00 5.18
2621 5063 0.953003 GAATAGAGTACGGGAGCGCT 59.047 55.000 11.27 11.27 0.00 5.92
2622 5064 0.039346 GGAATAGAGTACGGGAGCGC 60.039 60.000 0.00 0.00 0.00 5.92
2623 5065 1.315690 TGGAATAGAGTACGGGAGCG 58.684 55.000 0.00 0.00 0.00 5.03
2624 5066 3.455327 GTTTGGAATAGAGTACGGGAGC 58.545 50.000 0.00 0.00 0.00 4.70
2625 5067 3.490419 CCGTTTGGAATAGAGTACGGGAG 60.490 52.174 0.00 0.00 43.42 4.30
2626 5068 2.428171 CCGTTTGGAATAGAGTACGGGA 59.572 50.000 0.00 0.00 43.42 5.14
2627 5069 2.817901 CCGTTTGGAATAGAGTACGGG 58.182 52.381 0.00 0.00 43.42 5.28
2629 5071 5.240713 ACTACCGTTTGGAATAGAGTACG 57.759 43.478 0.00 0.00 39.21 3.67
2630 5072 5.359292 AGGACTACCGTTTGGAATAGAGTAC 59.641 44.000 0.00 0.00 41.83 2.73
2633 5075 6.651975 ATAGGACTACCGTTTGGAATAGAG 57.348 41.667 0.00 0.00 41.83 2.43
2643 5085 6.455360 TGATTAACGAATAGGACTACCGTT 57.545 37.500 18.49 18.49 44.22 4.44
2691 5133 1.571460 GCAGCAGAGGAAACACACG 59.429 57.895 0.00 0.00 0.00 4.49
2719 5167 4.710375 CCCTCCAGTGTAAGCTTTCTAGTA 59.290 45.833 3.20 0.00 0.00 1.82
2736 5184 1.686325 GCCATCTACGAAGCCCTCCA 61.686 60.000 0.00 0.00 0.00 3.86
2749 5197 0.400213 TCCCGAAACTGTTGCCATCT 59.600 50.000 0.00 0.00 0.00 2.90
2768 5216 1.693640 CCAGGAATGGTTGGGCTCT 59.306 57.895 0.00 0.00 0.00 4.09
2773 5221 0.542702 AGTTGGCCAGGAATGGTTGG 60.543 55.000 5.11 0.00 37.53 3.77
2774 5222 1.818674 GTAGTTGGCCAGGAATGGTTG 59.181 52.381 5.11 0.00 0.00 3.77
2775 5223 1.613255 CGTAGTTGGCCAGGAATGGTT 60.613 52.381 5.11 0.00 0.00 3.67
2776 5224 0.035439 CGTAGTTGGCCAGGAATGGT 60.035 55.000 5.11 0.00 0.00 3.55
2777 5225 0.251916 TCGTAGTTGGCCAGGAATGG 59.748 55.000 5.11 0.00 0.00 3.16
2778 5226 1.066143 ACTCGTAGTTGGCCAGGAATG 60.066 52.381 5.11 0.51 0.00 2.67
2779 5227 1.276622 ACTCGTAGTTGGCCAGGAAT 58.723 50.000 5.11 0.00 0.00 3.01
2780 5228 1.822990 CTACTCGTAGTTGGCCAGGAA 59.177 52.381 5.11 0.00 0.00 3.36
2781 5229 1.471119 CTACTCGTAGTTGGCCAGGA 58.529 55.000 5.11 0.00 0.00 3.86
2782 5230 0.179108 GCTACTCGTAGTTGGCCAGG 60.179 60.000 5.11 0.00 35.65 4.45
2783 5231 0.530744 TGCTACTCGTAGTTGGCCAG 59.469 55.000 5.11 0.00 35.65 4.85
2784 5232 0.245539 GTGCTACTCGTAGTTGGCCA 59.754 55.000 0.00 0.00 35.65 5.36
2785 5233 0.531200 AGTGCTACTCGTAGTTGGCC 59.469 55.000 0.00 0.00 35.65 5.36
2786 5234 1.910688 GAGTGCTACTCGTAGTTGGC 58.089 55.000 6.02 0.00 35.28 4.52
2795 5243 5.317733 ACTACTGATGTTGAGTGCTACTC 57.682 43.478 8.75 8.75 45.26 2.59
2796 5244 5.946972 AGTACTACTGATGTTGAGTGCTACT 59.053 40.000 0.00 0.00 33.75 2.57
2797 5245 6.197364 AGTACTACTGATGTTGAGTGCTAC 57.803 41.667 0.00 0.00 33.75 3.58
2829 5277 9.788889 AGCATGAATTGATTGTATCTCATCTTA 57.211 29.630 0.00 0.00 0.00 2.10
2830 5278 8.693120 AGCATGAATTGATTGTATCTCATCTT 57.307 30.769 0.00 0.00 0.00 2.40
2831 5279 8.158132 AGAGCATGAATTGATTGTATCTCATCT 58.842 33.333 0.00 0.00 0.00 2.90
2832 5280 8.325421 AGAGCATGAATTGATTGTATCTCATC 57.675 34.615 0.00 0.00 0.00 2.92
2833 5281 9.788889 TTAGAGCATGAATTGATTGTATCTCAT 57.211 29.630 0.00 0.00 0.00 2.90
2834 5282 9.049523 GTTAGAGCATGAATTGATTGTATCTCA 57.950 33.333 0.00 0.00 0.00 3.27
2835 5283 9.049523 TGTTAGAGCATGAATTGATTGTATCTC 57.950 33.333 0.00 0.00 0.00 2.75
2836 5284 8.969260 TGTTAGAGCATGAATTGATTGTATCT 57.031 30.769 0.00 0.00 0.00 1.98
2837 5285 9.443283 GTTGTTAGAGCATGAATTGATTGTATC 57.557 33.333 0.00 0.00 0.00 2.24
2838 5286 9.182214 AGTTGTTAGAGCATGAATTGATTGTAT 57.818 29.630 0.00 0.00 0.00 2.29
2839 5287 8.565896 AGTTGTTAGAGCATGAATTGATTGTA 57.434 30.769 0.00 0.00 0.00 2.41
2840 5288 7.458409 AGTTGTTAGAGCATGAATTGATTGT 57.542 32.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.