Multiple sequence alignment - TraesCS5A01G266600

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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 TraesCS5A01G266600 chr5A 100.000 4741 0 0 1 4741 478017934 478013194 0.000000e+00 8756.0
1 TraesCS5A01G266600 chr5A 97.321 112 3 0 4075 4186 27736994 27736883 1.740000e-44 191.0
2 TraesCS5A01G266600 chr5A 91.489 47 2 2 4695 4741 57056135 57056179 3.960000e-06 63.9
3 TraesCS5A01G266600 chr5D 90.363 3943 181 95 72 3898 377486962 377483103 0.000000e+00 4992.0
4 TraesCS5A01G266600 chr5D 90.250 400 26 4 4302 4697 377482824 377482434 1.180000e-140 510.0
5 TraesCS5A01G266600 chr5D 92.053 151 9 3 3931 4078 377483105 377482955 4.810000e-50 209.0
6 TraesCS5A01G266600 chr5D 100.000 38 0 0 28 65 377487022 377486985 2.370000e-08 71.3
7 TraesCS5A01G266600 chr5D 97.222 36 1 0 4706 4741 474813163 474813198 1.420000e-05 62.1
8 TraesCS5A01G266600 chr5B 89.826 2182 87 58 188 2287 450772954 450770826 0.000000e+00 2675.0
9 TraesCS5A01G266600 chr5B 90.914 1717 72 43 2422 4078 450770760 450769068 0.000000e+00 2230.0
10 TraesCS5A01G266600 chr5B 90.838 382 23 4 4334 4711 450767532 450767159 7.080000e-138 501.0
11 TraesCS5A01G266600 chr5B 94.828 116 5 1 4071 4186 278886872 278886986 3.770000e-41 180.0
12 TraesCS5A01G266600 chr5B 84.236 203 12 11 1 183 450773274 450773072 3.770000e-41 180.0
13 TraesCS5A01G266600 chr5B 90.909 77 4 3 2311 2387 450770835 450770762 3.020000e-17 100.0
14 TraesCS5A01G266600 chr2D 94.054 185 10 1 4454 4637 119299346 119299530 3.610000e-71 279.0
15 TraesCS5A01G266600 chr2A 93.514 185 11 1 4454 4637 121225120 121225304 1.680000e-69 274.0
16 TraesCS5A01G266600 chr2A 92.562 121 9 0 4080 4200 602770455 602770575 1.750000e-39 174.0
17 TraesCS5A01G266600 chr2A 100.000 34 0 0 4708 4741 740347622 740347589 3.960000e-06 63.9
18 TraesCS5A01G266600 chr2B 92.432 185 13 1 4454 4637 171461315 171461499 3.640000e-66 263.0
19 TraesCS5A01G266600 chr7D 96.429 112 4 0 4075 4186 248393401 248393512 8.100000e-43 185.0
20 TraesCS5A01G266600 chr4A 97.248 109 3 0 4078 4186 381227049 381226941 8.100000e-43 185.0
21 TraesCS5A01G266600 chr4A 93.548 124 6 2 4064 4186 381221449 381221327 2.910000e-42 183.0
22 TraesCS5A01G266600 chr3A 94.828 116 5 1 4071 4186 46169215 46169101 3.770000e-41 180.0
23 TraesCS5A01G266600 chr3A 93.023 43 3 0 4697 4739 597235349 597235307 3.960000e-06 63.9
24 TraesCS5A01G266600 chr6A 92.126 127 8 2 4067 4192 130415766 130415891 1.360000e-40 178.0
25 TraesCS5A01G266600 chr6A 100.000 33 0 0 4709 4741 615960537 615960505 1.420000e-05 62.1
26 TraesCS5A01G266600 chr7A 92.562 121 9 0 4071 4191 15083292 15083172 1.750000e-39 174.0
27 TraesCS5A01G266600 chrUn 97.222 36 1 0 4702 4737 296339904 296339869 1.420000e-05 62.1
28 TraesCS5A01G266600 chr1B 97.222 36 1 0 4702 4737 21383422 21383457 1.420000e-05 62.1
29 TraesCS5A01G266600 chr1B 97.222 36 1 0 4702 4737 21390212 21390247 1.420000e-05 62.1
30 TraesCS5A01G266600 chr1D 92.857 42 1 2 4700 4741 100826499 100826460 5.120000e-05 60.2


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 TraesCS5A01G266600 chr5A 478013194 478017934 4740 True 8756.000 8756 100.0000 1 4741 1 chr5A.!!$R2 4740
1 TraesCS5A01G266600 chr5D 377482434 377487022 4588 True 1445.575 4992 93.1665 28 4697 4 chr5D.!!$R1 4669
2 TraesCS5A01G266600 chr5B 450767159 450773274 6115 True 1137.200 2675 89.3446 1 4711 5 chr5B.!!$R1 4710

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
770 957 0.106419 AAAACGCCCCTGAGAAACCA 60.106 50.0 0.0 0.0 0.00 3.67 F
771 958 0.537371 AAACGCCCCTGAGAAACCAG 60.537 55.0 0.0 0.0 0.00 4.00 F
2292 2576 0.179004 TTGTTGCTGTGGTAGGTGGG 60.179 55.0 0.0 0.0 0.00 4.61 F
2728 3044 0.383949 GTCCGCTTTGGTTTTGCTGA 59.616 50.0 0.0 0.0 39.52 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1915 2111 0.105039 GGCGGTAACTCTGATGGAGG 59.895 60.0 0.00 0.0 45.83 4.30 R
2387 2690 0.309302 CGGCTAGAGATGACACTCGG 59.691 60.0 0.00 0.0 41.25 4.63 R
3254 3571 0.037232 GGGTCTTCTTCGTCCCAGTG 60.037 60.0 0.00 0.0 39.68 3.66 R
3892 4239 0.177141 AGAGAGAGAGAGGGACGTCG 59.823 60.0 9.92 0.0 0.00 5.12 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
65 75 2.162809 TGTGTGCTGCTATGCTTTGATG 59.837 45.455 0.00 0.00 0.00 3.07
70 96 2.681848 GCTGCTATGCTTTGATGAGTGT 59.318 45.455 0.00 0.00 0.00 3.55
104 130 1.219124 GATGCTCCTGTCGCCTTCA 59.781 57.895 0.00 0.00 0.00 3.02
107 133 1.522580 GCTCCTGTCGCCTTCATCC 60.523 63.158 0.00 0.00 0.00 3.51
128 155 3.057596 CCGCTTGCTGGTAAAATCTGAAA 60.058 43.478 0.00 0.00 0.00 2.69
226 366 2.512515 GTCTGACATGGGCGGCTC 60.513 66.667 9.56 0.00 0.00 4.70
238 378 0.167470 GGCGGCTCGTTTAAAACCTC 59.833 55.000 0.00 0.00 0.00 3.85
248 388 8.724229 GGCTCGTTTAAAACCTCTTATTTTAGA 58.276 33.333 0.00 0.00 34.04 2.10
335 480 5.503634 TCCATCACTCTTTCATCCAGAAA 57.496 39.130 0.00 0.00 43.71 2.52
366 513 3.497640 ACGGTAGATATGCACTCGTAGAC 59.502 47.826 0.00 0.00 0.00 2.59
432 580 0.109597 GTCAGCCAGCGAACCAAATG 60.110 55.000 0.00 0.00 0.00 2.32
442 594 0.240945 GAACCAAATGGACACCGCTG 59.759 55.000 6.42 0.00 38.94 5.18
465 617 6.584488 TGGCCAGATTCAAATAATTTCCATG 58.416 36.000 0.00 0.00 0.00 3.66
467 619 5.467735 GCCAGATTCAAATAATTTCCATGCC 59.532 40.000 0.00 0.00 0.00 4.40
524 676 1.959042 TCCGACGGTCAGATACTACC 58.041 55.000 14.79 0.00 0.00 3.18
525 677 1.210234 TCCGACGGTCAGATACTACCA 59.790 52.381 14.79 0.00 35.35 3.25
526 678 1.332997 CCGACGGTCAGATACTACCAC 59.667 57.143 5.48 0.00 35.35 4.16
597 775 0.317436 TTGTAACCTTGCGCGCTTTG 60.317 50.000 33.29 21.31 0.00 2.77
660 839 2.608759 GGGGGCAGTATGGGCATT 59.391 61.111 0.00 0.00 35.86 3.56
769 956 0.596577 GAAAACGCCCCTGAGAAACC 59.403 55.000 0.00 0.00 0.00 3.27
770 957 0.106419 AAAACGCCCCTGAGAAACCA 60.106 50.000 0.00 0.00 0.00 3.67
771 958 0.537371 AAACGCCCCTGAGAAACCAG 60.537 55.000 0.00 0.00 0.00 4.00
879 1066 2.158667 AGGAAAAGGAAAAGGCTGACGA 60.159 45.455 0.00 0.00 0.00 4.20
880 1067 2.031069 GGAAAAGGAAAAGGCTGACGAC 60.031 50.000 0.00 0.00 0.00 4.34
881 1068 1.226746 AAAGGAAAAGGCTGACGACG 58.773 50.000 0.00 0.00 0.00 5.12
884 1074 1.005394 GAAAAGGCTGACGACGGGA 60.005 57.895 0.00 0.00 0.00 5.14
908 1098 1.838073 AATTTGACGGAGGAGGGCGT 61.838 55.000 0.00 0.00 0.00 5.68
947 1137 3.883744 CTGAGACGGCACCACCACC 62.884 68.421 0.00 0.00 39.03 4.61
1395 1591 5.850557 TCGGGTAAAACGATTATACTCCA 57.149 39.130 0.00 0.00 35.12 3.86
1396 1592 5.835257 TCGGGTAAAACGATTATACTCCAG 58.165 41.667 0.00 0.00 35.12 3.86
1397 1593 5.360714 TCGGGTAAAACGATTATACTCCAGT 59.639 40.000 0.00 0.00 35.12 4.00
1398 1594 6.545666 TCGGGTAAAACGATTATACTCCAGTA 59.454 38.462 0.00 0.00 35.12 2.74
1401 1597 8.200120 GGGTAAAACGATTATACTCCAGTAGTT 58.800 37.037 0.00 0.00 39.80 2.24
1431 1627 3.003585 ACCGATAAAACCACCGTTTGAAC 59.996 43.478 0.00 0.00 41.42 3.18
1438 1634 0.951558 CCACCGTTTGAACTGAAGGG 59.048 55.000 0.00 0.00 37.88 3.95
1889 2085 4.668118 TTCGGCCCCGTGTTCGAC 62.668 66.667 6.61 0.00 40.74 4.20
1915 2111 3.141767 ACAGGAGAGCCAGGTAAAAAC 57.858 47.619 0.00 0.00 36.29 2.43
1958 2159 2.266055 CTGCCCGTCTTGTCCCTC 59.734 66.667 0.00 0.00 0.00 4.30
1962 2173 2.359967 CCCGTCTTGTCCCTCCTCC 61.360 68.421 0.00 0.00 0.00 4.30
1986 2197 2.036098 TCGGCCGGAGTAGGTCAA 59.964 61.111 27.83 0.00 35.10 3.18
1987 2198 1.607178 TCGGCCGGAGTAGGTCAAA 60.607 57.895 27.83 0.00 35.10 2.69
1988 2199 1.186917 TCGGCCGGAGTAGGTCAAAA 61.187 55.000 27.83 0.00 35.10 2.44
1990 2201 0.323957 GGCCGGAGTAGGTCAAAACT 59.676 55.000 5.05 0.00 35.58 2.66
1991 2202 1.675116 GGCCGGAGTAGGTCAAAACTC 60.675 57.143 5.05 0.00 41.16 3.01
1992 2203 1.992170 CCGGAGTAGGTCAAAACTCG 58.008 55.000 0.00 0.00 42.51 4.18
1993 2204 1.271656 CCGGAGTAGGTCAAAACTCGT 59.728 52.381 0.00 0.00 42.51 4.18
1994 2205 2.325761 CGGAGTAGGTCAAAACTCGTG 58.674 52.381 0.00 0.00 42.51 4.35
2000 2223 5.052481 AGTAGGTCAAAACTCGTGTTTACC 58.948 41.667 20.05 20.05 44.70 2.85
2007 2230 0.395312 ACTCGTGTTTACCAGGGGTG 59.605 55.000 0.00 0.00 41.03 4.61
2056 2279 1.269051 GGTGAAAACCAAAGAGCACGG 60.269 52.381 0.00 0.00 0.00 4.94
2070 2293 2.012237 CACGGAGCATGTCAGATGC 58.988 57.895 0.00 0.00 44.85 3.91
2075 2298 4.651867 GCATGTCAGATGCTGGGT 57.348 55.556 0.00 0.00 41.52 4.51
2076 2299 2.401967 GCATGTCAGATGCTGGGTC 58.598 57.895 0.00 0.00 41.52 4.46
2077 2300 1.099879 GCATGTCAGATGCTGGGTCC 61.100 60.000 0.00 0.00 41.52 4.46
2078 2301 0.465097 CATGTCAGATGCTGGGTCCC 60.465 60.000 0.00 0.00 31.51 4.46
2079 2302 0.915872 ATGTCAGATGCTGGGTCCCA 60.916 55.000 11.11 11.11 31.51 4.37
2080 2303 1.078143 GTCAGATGCTGGGTCCCAC 60.078 63.158 6.47 4.99 31.51 4.61
2081 2304 2.273449 CAGATGCTGGGTCCCACC 59.727 66.667 6.47 0.17 37.60 4.61
2095 2318 2.890474 CACCCTCGCGCGCTTAAT 60.890 61.111 30.48 7.78 0.00 1.40
2216 2484 0.248539 GATCTACGTGACCGGAGCAC 60.249 60.000 9.46 15.31 45.07 4.40
2288 2572 2.030007 CCATGTTTGTTGCTGTGGTAGG 60.030 50.000 0.00 0.00 0.00 3.18
2289 2573 2.428544 TGTTTGTTGCTGTGGTAGGT 57.571 45.000 0.00 0.00 0.00 3.08
2291 2575 1.336755 GTTTGTTGCTGTGGTAGGTGG 59.663 52.381 0.00 0.00 0.00 4.61
2292 2576 0.179004 TTGTTGCTGTGGTAGGTGGG 60.179 55.000 0.00 0.00 0.00 4.61
2293 2577 1.349542 TGTTGCTGTGGTAGGTGGGT 61.350 55.000 0.00 0.00 0.00 4.51
2295 2579 2.359975 GCTGTGGTAGGTGGGTGC 60.360 66.667 0.00 0.00 0.00 5.01
2382 2685 4.500716 GGGAGAAATTCTTTGCCGTTCAAA 60.501 41.667 0.00 1.09 42.01 2.69
2411 2714 0.463833 TGTCATCTCTAGCCGAGCGA 60.464 55.000 0.00 0.00 39.70 4.93
2417 2720 0.587285 CTCTAGCCGAGCGATAACGT 59.413 55.000 0.00 0.00 41.98 3.99
2455 2758 2.483441 TCTCTCGCGGAAGAGAAGG 58.517 57.895 21.35 1.09 46.76 3.46
2484 2790 4.112341 CTGCTTTCTGCGGGCTGC 62.112 66.667 12.43 12.43 46.63 5.25
2609 2918 2.749044 ATGCCGCCTCAACAGCAG 60.749 61.111 0.00 0.00 38.89 4.24
2640 2949 0.663867 CTCGAGATGCTGCGGAGATG 60.664 60.000 8.65 0.00 0.00 2.90
2670 2980 6.371809 TTTCTTCTACGCTTTCATTTGTGT 57.628 33.333 0.00 0.00 0.00 3.72
2723 3039 0.684805 TGTGGGTCCGCTTTGGTTTT 60.685 50.000 2.07 0.00 39.52 2.43
2725 3041 1.300620 GGGTCCGCTTTGGTTTTGC 60.301 57.895 0.00 0.00 39.52 3.68
2726 3042 1.739667 GGTCCGCTTTGGTTTTGCT 59.260 52.632 0.00 0.00 39.52 3.91
2727 3043 0.597377 GGTCCGCTTTGGTTTTGCTG 60.597 55.000 0.00 0.00 39.52 4.41
2728 3044 0.383949 GTCCGCTTTGGTTTTGCTGA 59.616 50.000 0.00 0.00 39.52 4.26
2729 3045 0.667993 TCCGCTTTGGTTTTGCTGAG 59.332 50.000 0.00 0.00 39.52 3.35
2730 3046 0.940991 CCGCTTTGGTTTTGCTGAGC 60.941 55.000 0.00 0.00 0.00 4.26
3182 3499 2.892425 GCGGAGAAGCGGGACATG 60.892 66.667 0.00 0.00 0.00 3.21
3275 3592 2.227089 CTGGGACGAAGAAGACCCGG 62.227 65.000 0.00 0.00 44.70 5.73
3278 3595 1.980772 GACGAAGAAGACCCGGGGA 60.981 63.158 27.92 0.00 0.00 4.81
3380 3697 1.080025 GAAGGACAACGGGGACTCG 60.080 63.158 0.00 0.00 0.00 4.18
3710 4030 2.115911 CAGGTCGGAGAGGTCCTCG 61.116 68.421 13.41 2.57 42.89 4.63
3731 4051 4.091939 TCGTCGAGGCGAGGAGGA 62.092 66.667 7.97 0.00 43.93 3.71
3746 4067 1.549170 GGAGGAAGGAAGTAGTCGCAA 59.451 52.381 0.00 0.00 0.00 4.85
3747 4068 2.417515 GGAGGAAGGAAGTAGTCGCAAG 60.418 54.545 0.00 0.00 0.00 4.01
3748 4069 1.066787 AGGAAGGAAGTAGTCGCAAGC 60.067 52.381 0.00 0.00 37.18 4.01
3767 4099 1.200484 GCTAGATGTAGCCGGTAGAGC 59.800 57.143 10.75 0.00 45.37 4.09
3775 4110 1.307097 AGCCGGTAGAGCTTACGTAG 58.693 55.000 1.90 0.00 37.24 3.51
3881 4228 3.250744 ACGACATGTTGTAATCGGACTG 58.749 45.455 17.45 0.00 38.88 3.51
3892 4239 2.853731 ATCGGACTGACAGATCGAAC 57.146 50.000 21.34 0.00 33.53 3.95
3894 4241 0.446616 CGGACTGACAGATCGAACGA 59.553 55.000 10.08 0.00 0.00 3.85
3903 4250 0.392729 AGATCGAACGACGTCCCTCT 60.393 55.000 10.58 0.00 43.13 3.69
3905 4252 0.392729 ATCGAACGACGTCCCTCTCT 60.393 55.000 10.58 0.00 43.13 3.10
3908 4255 0.728542 GAACGACGTCCCTCTCTCTC 59.271 60.000 10.58 0.00 0.00 3.20
3909 4256 0.325602 AACGACGTCCCTCTCTCTCT 59.674 55.000 10.58 0.00 0.00 3.10
3910 4257 0.108041 ACGACGTCCCTCTCTCTCTC 60.108 60.000 10.58 0.00 0.00 3.20
3911 4258 0.177141 CGACGTCCCTCTCTCTCTCT 59.823 60.000 10.58 0.00 0.00 3.10
3912 4259 1.805120 CGACGTCCCTCTCTCTCTCTC 60.805 61.905 10.58 0.00 0.00 3.20
3913 4260 1.485066 GACGTCCCTCTCTCTCTCTCT 59.515 57.143 3.51 0.00 0.00 3.10
3914 4261 1.913419 ACGTCCCTCTCTCTCTCTCTT 59.087 52.381 0.00 0.00 0.00 2.85
3915 4262 2.307686 ACGTCCCTCTCTCTCTCTCTTT 59.692 50.000 0.00 0.00 0.00 2.52
3916 4263 2.943033 CGTCCCTCTCTCTCTCTCTTTC 59.057 54.545 0.00 0.00 0.00 2.62
3917 4264 3.370527 CGTCCCTCTCTCTCTCTCTTTCT 60.371 52.174 0.00 0.00 0.00 2.52
3918 4265 4.200092 GTCCCTCTCTCTCTCTCTTTCTC 58.800 52.174 0.00 0.00 0.00 2.87
3919 4266 3.118408 TCCCTCTCTCTCTCTCTTTCTCG 60.118 52.174 0.00 0.00 0.00 4.04
3988 4355 2.659897 GCGAGCTGCATCCGGTAG 60.660 66.667 0.00 0.00 45.45 3.18
4064 4434 9.195411 CTCTGAAATAAGCAAATGCAACTTTTA 57.805 29.630 8.28 0.00 45.16 1.52
4088 4458 7.901283 ATTTTTCTAGTCTACTACTCCCTCC 57.099 40.000 0.00 0.00 39.80 4.30
4089 4459 4.686191 TTCTAGTCTACTACTCCCTCCG 57.314 50.000 0.00 0.00 39.80 4.63
4090 4460 3.652055 TCTAGTCTACTACTCCCTCCGT 58.348 50.000 0.00 0.00 39.80 4.69
4091 4461 4.036518 TCTAGTCTACTACTCCCTCCGTT 58.963 47.826 0.00 0.00 39.80 4.44
4092 4462 3.280197 AGTCTACTACTCCCTCCGTTC 57.720 52.381 0.00 0.00 30.33 3.95
4093 4463 2.092484 AGTCTACTACTCCCTCCGTTCC 60.092 54.545 0.00 0.00 30.33 3.62
4094 4464 1.918262 TCTACTACTCCCTCCGTTCCA 59.082 52.381 0.00 0.00 0.00 3.53
4095 4465 2.309755 TCTACTACTCCCTCCGTTCCAA 59.690 50.000 0.00 0.00 0.00 3.53
4096 4466 2.019807 ACTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
4097 4467 2.547990 ACTACTCCCTCCGTTCCAAAT 58.452 47.619 0.00 0.00 0.00 2.32
4098 4468 2.910977 ACTACTCCCTCCGTTCCAAATT 59.089 45.455 0.00 0.00 0.00 1.82
4101 4471 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
4102 4472 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
4103 4473 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
4104 4474 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
4108 4478 1.722464 CGTTCCAAATTACTCGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
4109 4479 2.222508 CGTTCCAAATTACTCGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
4110 4480 2.991190 GTTCCAAATTACTCGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
4111 4481 3.306917 TCCAAATTACTCGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
4112 4482 3.655486 TCCAAATTACTCGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
4114 4484 5.412640 TCCAAATTACTCGTCGCAGAAATA 58.587 37.500 0.00 0.00 39.69 1.40
4115 4485 5.518847 TCCAAATTACTCGTCGCAGAAATAG 59.481 40.000 0.00 0.00 39.69 1.73
4116 4486 5.518847 CCAAATTACTCGTCGCAGAAATAGA 59.481 40.000 0.00 0.00 39.69 1.98
4117 4487 6.201044 CCAAATTACTCGTCGCAGAAATAGAT 59.799 38.462 0.00 0.00 39.69 1.98
4119 4489 3.784701 ACTCGTCGCAGAAATAGATGT 57.215 42.857 0.00 0.00 39.69 3.06
4121 4491 5.440234 ACTCGTCGCAGAAATAGATGTAT 57.560 39.130 0.00 0.00 39.69 2.29
4122 4492 5.453648 ACTCGTCGCAGAAATAGATGTATC 58.546 41.667 0.00 0.00 39.69 2.24
4125 4495 7.041303 ACTCGTCGCAGAAATAGATGTATCTAA 60.041 37.037 5.75 0.00 39.88 2.10
4126 4496 7.645402 TCGTCGCAGAAATAGATGTATCTAAA 58.355 34.615 5.75 0.00 39.88 1.85
4127 4497 8.132995 TCGTCGCAGAAATAGATGTATCTAAAA 58.867 33.333 5.75 0.00 39.88 1.52
4128 4498 8.208560 CGTCGCAGAAATAGATGTATCTAAAAC 58.791 37.037 5.75 1.59 39.88 2.43
4129 4499 9.250624 GTCGCAGAAATAGATGTATCTAAAACT 57.749 33.333 5.75 3.48 39.88 2.66
4159 4529 7.473735 ACATCTAGATACATCCATACCTGTG 57.526 40.000 4.54 0.00 0.00 3.66
4160 4530 7.241628 ACATCTAGATACATCCATACCTGTGA 58.758 38.462 4.54 0.00 0.00 3.58
4161 4531 7.177568 ACATCTAGATACATCCATACCTGTGAC 59.822 40.741 4.54 0.00 0.00 3.67
4163 4533 7.066781 TCTAGATACATCCATACCTGTGACAA 58.933 38.462 0.00 0.00 0.00 3.18
4164 4534 6.166984 AGATACATCCATACCTGTGACAAG 57.833 41.667 0.00 0.00 0.00 3.16
4166 4536 6.839134 AGATACATCCATACCTGTGACAAGTA 59.161 38.462 0.00 0.00 0.00 2.24
4167 4537 5.755409 ACATCCATACCTGTGACAAGTAA 57.245 39.130 0.00 0.00 0.00 2.24
4168 4538 6.313519 ACATCCATACCTGTGACAAGTAAT 57.686 37.500 0.00 0.00 0.00 1.89
4173 4543 5.872617 CCATACCTGTGACAAGTAATTCGAA 59.127 40.000 0.00 0.00 0.00 3.71
4174 4544 6.370442 CCATACCTGTGACAAGTAATTCGAAA 59.630 38.462 0.00 0.00 0.00 3.46
4175 4545 5.668558 ACCTGTGACAAGTAATTCGAAAC 57.331 39.130 0.00 0.00 0.00 2.78
4177 4547 4.377022 CCTGTGACAAGTAATTCGAAACGG 60.377 45.833 0.00 0.00 0.00 4.44
4178 4548 4.370049 TGTGACAAGTAATTCGAAACGGA 58.630 39.130 0.00 0.00 0.00 4.69
4181 4551 4.449743 TGACAAGTAATTCGAAACGGAAGG 59.550 41.667 0.00 0.00 0.00 3.46
4182 4552 4.634199 ACAAGTAATTCGAAACGGAAGGA 58.366 39.130 0.00 0.00 0.00 3.36
4183 4553 4.689345 ACAAGTAATTCGAAACGGAAGGAG 59.311 41.667 0.00 0.00 0.00 3.69
4185 4555 5.649782 AGTAATTCGAAACGGAAGGAGTA 57.350 39.130 0.00 0.00 0.00 2.59
4188 4558 5.649782 AATTCGAAACGGAAGGAGTAGTA 57.350 39.130 0.00 0.00 0.00 1.82
4189 4559 4.691860 TTCGAAACGGAAGGAGTAGTAG 57.308 45.455 0.00 0.00 0.00 2.57
4190 4560 3.679389 TCGAAACGGAAGGAGTAGTAGT 58.321 45.455 0.00 0.00 0.00 2.73
4197 5815 5.814481 ACGGAAGGAGTAGTAGTAAAGAGT 58.186 41.667 0.00 0.00 0.00 3.24
4206 5824 9.018582 GGAGTAGTAGTAAAGAGTAAGGTCAAA 57.981 37.037 0.00 0.00 0.00 2.69
4208 5826 8.510505 AGTAGTAGTAAAGAGTAAGGTCAAACG 58.489 37.037 0.00 0.00 0.00 3.60
4209 5827 7.282332 AGTAGTAAAGAGTAAGGTCAAACGT 57.718 36.000 0.00 0.00 0.00 3.99
4213 5831 4.411256 AAGAGTAAGGTCAAACGTCCAA 57.589 40.909 0.00 0.00 0.00 3.53
4214 5832 4.618920 AGAGTAAGGTCAAACGTCCAAT 57.381 40.909 0.00 0.00 0.00 3.16
4224 5844 5.277825 GTCAAACGTCCAATGATCAAACAA 58.722 37.500 0.00 0.00 0.00 2.83
4230 5850 9.487790 AAACGTCCAATGATCAAACAAAAATAT 57.512 25.926 0.00 0.00 0.00 1.28
4232 5852 9.567848 ACGTCCAATGATCAAACAAAAATATAC 57.432 29.630 0.00 0.00 0.00 1.47
4233 5853 9.787532 CGTCCAATGATCAAACAAAAATATACT 57.212 29.630 0.00 0.00 0.00 2.12
4236 5856 9.236691 CCAATGATCAAACAAAAATATACTCCG 57.763 33.333 0.00 0.00 0.00 4.63
4237 5857 9.787532 CAATGATCAAACAAAAATATACTCCGT 57.212 29.630 0.00 0.00 0.00 4.69
4271 5891 6.715347 AAACCAAAGAGTATGCTTGAAAGT 57.285 33.333 0.00 0.00 0.00 2.66
4272 5892 6.715347 AACCAAAGAGTATGCTTGAAAGTT 57.285 33.333 0.00 0.00 0.00 2.66
4291 5911 4.704965 AGTTCTACAAAACCTCACACTCC 58.295 43.478 0.00 0.00 0.00 3.85
4292 5912 3.380479 TCTACAAAACCTCACACTCCG 57.620 47.619 0.00 0.00 0.00 4.63
4293 5913 2.696707 TCTACAAAACCTCACACTCCGT 59.303 45.455 0.00 0.00 0.00 4.69
4294 5914 1.949465 ACAAAACCTCACACTCCGTC 58.051 50.000 0.00 0.00 0.00 4.79
4295 5915 0.859232 CAAAACCTCACACTCCGTCG 59.141 55.000 0.00 0.00 0.00 5.12
4296 5916 0.462789 AAAACCTCACACTCCGTCGT 59.537 50.000 0.00 0.00 0.00 4.34
4297 5917 0.462789 AAACCTCACACTCCGTCGTT 59.537 50.000 0.00 0.00 0.00 3.85
4298 5918 0.031721 AACCTCACACTCCGTCGTTC 59.968 55.000 0.00 0.00 0.00 3.95
4299 5919 1.080705 CCTCACACTCCGTCGTTCC 60.081 63.158 0.00 0.00 0.00 3.62
4300 5920 1.442184 CTCACACTCCGTCGTTCCG 60.442 63.158 0.00 0.00 0.00 4.30
4301 5921 2.126417 CTCACACTCCGTCGTTCCGT 62.126 60.000 0.00 0.00 0.00 4.69
4302 5922 1.728426 CACACTCCGTCGTTCCGTC 60.728 63.158 0.00 0.00 0.00 4.79
4328 5948 1.492133 CCCCACTGATGTGAGGTGGT 61.492 60.000 9.93 0.00 46.30 4.16
4332 6026 0.321671 ACTGATGTGAGGTGGTTCCG 59.678 55.000 0.00 0.00 41.99 4.30
4348 6042 3.251004 GGTTCCGATGAGAAATGGCATAC 59.749 47.826 0.00 0.00 0.00 2.39
4396 6092 0.802494 AAGCACGAATACAAAGGGCG 59.198 50.000 0.00 0.00 0.00 6.13
4409 6105 4.221422 GGGCGCGTCTGGCAGATA 62.221 66.667 21.84 0.00 43.84 1.98
4410 6106 2.202878 GGCGCGTCTGGCAGATAA 60.203 61.111 21.84 0.00 43.84 1.75
4411 6107 2.526120 GGCGCGTCTGGCAGATAAC 61.526 63.158 21.84 11.95 43.84 1.89
4412 6108 1.809619 GCGCGTCTGGCAGATAACA 60.810 57.895 21.84 0.00 43.84 2.41
4415 6111 1.726853 GCGTCTGGCAGATAACAAGT 58.273 50.000 21.84 0.00 42.87 3.16
4664 6364 4.142578 ACACGCACACAACACTTGAATAAA 60.143 37.500 0.00 0.00 0.00 1.40
4711 6413 3.181367 CGTGCGGACGTAGGTACT 58.819 61.111 22.12 0.00 40.91 2.73
4712 6414 1.061570 CGTGCGGACGTAGGTACTC 59.938 63.158 22.12 0.00 40.91 2.59
4713 6415 1.431036 GTGCGGACGTAGGTACTCC 59.569 63.158 0.00 0.00 41.75 3.85
4714 6416 1.750399 TGCGGACGTAGGTACTCCC 60.750 63.158 0.00 0.00 41.75 4.30
4716 6418 1.443322 GCGGACGTAGGTACTCCCTC 61.443 65.000 0.00 0.00 44.81 4.30
4717 6419 0.817229 CGGACGTAGGTACTCCCTCC 60.817 65.000 0.00 0.00 44.81 4.30
4719 6421 4.972875 CGTAGGTACTCCCTCCGT 57.027 61.111 0.00 0.00 44.81 4.69
4720 6422 3.181526 CGTAGGTACTCCCTCCGTT 57.818 57.895 0.00 0.00 44.81 4.44
4721 6423 1.467920 CGTAGGTACTCCCTCCGTTT 58.532 55.000 0.00 0.00 44.81 3.60
4722 6424 1.403323 CGTAGGTACTCCCTCCGTTTC 59.597 57.143 0.00 0.00 44.81 2.78
4723 6425 2.450476 GTAGGTACTCCCTCCGTTTCA 58.550 52.381 0.00 0.00 44.81 2.69
4724 6426 2.019807 AGGTACTCCCTCCGTTTCAA 57.980 50.000 0.00 0.00 40.71 2.69
4725 6427 2.332117 AGGTACTCCCTCCGTTTCAAA 58.668 47.619 0.00 0.00 40.71 2.69
4726 6428 2.910977 AGGTACTCCCTCCGTTTCAAAT 59.089 45.455 0.00 0.00 40.71 2.32
4727 6429 3.329814 AGGTACTCCCTCCGTTTCAAATT 59.670 43.478 0.00 0.00 40.71 1.82
4728 6430 4.533311 AGGTACTCCCTCCGTTTCAAATTA 59.467 41.667 0.00 0.00 40.71 1.40
4729 6431 4.633126 GGTACTCCCTCCGTTTCAAATTAC 59.367 45.833 0.00 0.00 0.00 1.89
4730 6432 4.635699 ACTCCCTCCGTTTCAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
4731 6433 4.576879 ACTCCCTCCGTTTCAAATTACTC 58.423 43.478 0.00 0.00 0.00 2.59
4732 6434 3.592059 TCCCTCCGTTTCAAATTACTCG 58.408 45.455 0.00 0.00 0.00 4.18
4733 6435 3.007182 TCCCTCCGTTTCAAATTACTCGT 59.993 43.478 0.00 0.00 0.00 4.18
4734 6436 3.370061 CCCTCCGTTTCAAATTACTCGTC 59.630 47.826 0.00 0.00 0.00 4.20
4735 6437 3.060363 CCTCCGTTTCAAATTACTCGTCG 59.940 47.826 0.00 0.00 0.00 5.12
4736 6438 3.641648 TCCGTTTCAAATTACTCGTCGT 58.358 40.909 0.00 0.00 0.00 4.34
4737 6439 4.793071 TCCGTTTCAAATTACTCGTCGTA 58.207 39.130 0.00 0.00 0.00 3.43
4738 6440 4.853196 TCCGTTTCAAATTACTCGTCGTAG 59.147 41.667 0.00 0.00 0.00 3.51
4739 6441 4.853196 CCGTTTCAAATTACTCGTCGTAGA 59.147 41.667 0.00 0.00 0.00 2.59
4740 6442 5.343058 CCGTTTCAAATTACTCGTCGTAGAA 59.657 40.000 0.00 0.00 39.69 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 9.477484 CTTACTGTTGAAGACTGTTACATAACT 57.523 33.333 3.58 0.00 40.42 2.24
9 10 9.472361 TCTTACTGTTGAAGACTGTTACATAAC 57.528 33.333 0.00 0.00 40.42 1.89
65 75 6.637658 GCATCGACTCCTTAAATACTACACTC 59.362 42.308 0.00 0.00 0.00 3.51
104 130 2.684881 CAGATTTTACCAGCAAGCGGAT 59.315 45.455 9.31 0.00 0.00 4.18
107 133 3.829886 TTCAGATTTTACCAGCAAGCG 57.170 42.857 0.00 0.00 0.00 4.68
128 155 2.868253 GCCGGATGCAAAGGTTAGT 58.132 52.632 5.05 0.00 40.77 2.24
206 346 2.124983 CCGCCCATGTCAGACCAG 60.125 66.667 0.00 0.00 0.00 4.00
253 393 4.221924 AGCACACCAAGTTTTAAACCAACT 59.778 37.500 4.01 0.00 35.94 3.16
274 415 5.845391 AGTAGTGAGTTCAGGATTCTAGC 57.155 43.478 0.00 0.00 0.00 3.42
308 449 6.385176 TCTGGATGAAAGAGTGATGGAAGTAT 59.615 38.462 0.00 0.00 0.00 2.12
310 451 4.533707 TCTGGATGAAAGAGTGATGGAAGT 59.466 41.667 0.00 0.00 0.00 3.01
311 452 5.095145 TCTGGATGAAAGAGTGATGGAAG 57.905 43.478 0.00 0.00 0.00 3.46
312 453 5.503634 TTCTGGATGAAAGAGTGATGGAA 57.496 39.130 0.00 0.00 0.00 3.53
335 480 5.303078 AGTGCATATCTACCGTCAATCTTCT 59.697 40.000 0.00 0.00 0.00 2.85
336 481 5.533482 AGTGCATATCTACCGTCAATCTTC 58.467 41.667 0.00 0.00 0.00 2.87
366 513 4.520492 ACCTCCTGTTTTACTGCAAATGAG 59.480 41.667 0.00 0.00 0.00 2.90
418 566 0.240945 GTGTCCATTTGGTTCGCTGG 59.759 55.000 0.00 0.00 36.34 4.85
432 580 3.628646 AATCTGGCCAGCGGTGTCC 62.629 63.158 28.91 11.31 0.00 4.02
442 594 5.467735 GCATGGAAATTATTTGAATCTGGCC 59.532 40.000 0.00 0.00 0.00 5.36
465 617 1.109323 ACACTGCAAACTTCCAGGGC 61.109 55.000 0.00 0.00 35.92 5.19
467 619 1.392589 ACACACTGCAAACTTCCAGG 58.607 50.000 0.00 0.00 33.43 4.45
510 662 2.025155 AGCAGTGGTAGTATCTGACCG 58.975 52.381 0.00 0.00 38.69 4.79
526 678 4.005650 TGAGCTAAACTGATCCAAAGCAG 58.994 43.478 0.00 0.00 44.61 4.24
597 775 2.216750 TACCGTTAGCCTGACGTGCC 62.217 60.000 8.27 0.00 38.77 5.01
646 825 0.817634 TGCGTAATGCCCATACTGCC 60.818 55.000 0.00 0.00 45.60 4.85
647 826 0.588252 CTGCGTAATGCCCATACTGC 59.412 55.000 0.00 0.00 45.60 4.40
660 839 2.124901 CGGGCCAATTCCTGCGTA 60.125 61.111 4.39 0.00 0.00 4.42
891 1081 2.920912 ACGCCCTCCTCCGTCAAA 60.921 61.111 0.00 0.00 31.00 2.69
908 1098 2.457794 GGTAGGTTCCCTCCCCCA 59.542 66.667 0.00 0.00 34.61 4.96
955 1145 2.278531 GCTCTCTCGCGAGGAAGC 60.279 66.667 32.56 32.56 37.86 3.86
956 1146 1.226547 GTGCTCTCTCGCGAGGAAG 60.227 63.158 33.98 28.83 37.86 3.46
957 1147 2.878429 GTGCTCTCTCGCGAGGAA 59.122 61.111 33.98 21.30 37.86 3.36
958 1148 3.500642 CGTGCTCTCTCGCGAGGA 61.501 66.667 33.98 26.60 41.99 3.71
959 1149 4.544689 CCGTGCTCTCTCGCGAGG 62.545 72.222 33.98 24.14 41.99 4.63
1391 1587 2.416431 CGGTTCGGGTAAACTACTGGAG 60.416 54.545 0.00 0.00 0.00 3.86
1393 1589 1.545582 TCGGTTCGGGTAAACTACTGG 59.454 52.381 0.00 0.00 0.00 4.00
1395 1591 5.659440 TTTATCGGTTCGGGTAAACTACT 57.341 39.130 0.00 0.00 0.00 2.57
1396 1592 5.063438 GGTTTTATCGGTTCGGGTAAACTAC 59.937 44.000 0.00 0.00 0.00 2.73
1397 1593 5.175127 GGTTTTATCGGTTCGGGTAAACTA 58.825 41.667 0.00 0.00 0.00 2.24
1398 1594 4.002982 GGTTTTATCGGTTCGGGTAAACT 58.997 43.478 0.00 0.00 0.00 2.66
1401 1597 3.333804 GTGGTTTTATCGGTTCGGGTAA 58.666 45.455 0.00 0.00 0.00 2.85
1404 1600 1.089112 GGTGGTTTTATCGGTTCGGG 58.911 55.000 0.00 0.00 0.00 5.14
1431 1627 1.812571 CGGTGAATGGTTTCCCTTCAG 59.187 52.381 6.72 0.00 32.27 3.02
1438 1634 2.202298 CGCGCGGTGAATGGTTTC 60.202 61.111 24.84 0.00 0.00 2.78
1530 1726 6.309494 GTCCTGTCACAAGTAAAAACAAAACC 59.691 38.462 0.00 0.00 0.00 3.27
1889 2085 1.684386 CCTGGCTCTCCTGTAGCTGG 61.684 65.000 0.00 0.00 39.97 4.85
1915 2111 0.105039 GGCGGTAACTCTGATGGAGG 59.895 60.000 0.00 0.00 45.83 4.30
1950 2151 1.609501 CGGTGAGGAGGAGGGACAA 60.610 63.158 0.00 0.00 0.00 3.18
1976 2187 5.176406 GGTAAACACGAGTTTTGACCTACTC 59.824 44.000 16.04 0.00 45.32 2.59
1977 2188 5.052481 GGTAAACACGAGTTTTGACCTACT 58.948 41.667 16.04 0.00 45.32 2.57
1978 2189 4.810491 TGGTAAACACGAGTTTTGACCTAC 59.190 41.667 22.61 12.55 45.32 3.18
1979 2190 5.021033 TGGTAAACACGAGTTTTGACCTA 57.979 39.130 22.61 12.03 45.32 3.08
1980 2191 3.875134 CTGGTAAACACGAGTTTTGACCT 59.125 43.478 22.61 2.32 45.32 3.85
1981 2192 3.002965 CCTGGTAAACACGAGTTTTGACC 59.997 47.826 16.04 17.29 45.32 4.02
1983 2194 3.207778 CCCTGGTAAACACGAGTTTTGA 58.792 45.455 16.04 0.00 45.32 2.69
1987 2198 1.134228 ACCCCTGGTAAACACGAGTT 58.866 50.000 0.00 0.00 40.40 3.01
1988 2199 0.395312 CACCCCTGGTAAACACGAGT 59.605 55.000 0.00 0.00 32.11 4.18
1990 2201 1.129917 TTCACCCCTGGTAAACACGA 58.870 50.000 0.00 0.00 32.11 4.35
1991 2202 1.970092 TTTCACCCCTGGTAAACACG 58.030 50.000 0.00 0.00 32.11 4.49
1992 2203 2.033675 CGTTTTCACCCCTGGTAAACAC 59.966 50.000 10.59 0.00 32.11 3.32
1993 2204 2.092538 TCGTTTTCACCCCTGGTAAACA 60.093 45.455 10.59 0.00 32.11 2.83
1994 2205 2.551032 CTCGTTTTCACCCCTGGTAAAC 59.449 50.000 0.00 2.83 32.11 2.01
2000 2223 1.303317 CCCCTCGTTTTCACCCCTG 60.303 63.158 0.00 0.00 0.00 4.45
2007 2230 2.229784 TCTACGTTCTCCCCTCGTTTTC 59.770 50.000 0.00 0.00 38.69 2.29
2081 2304 1.004277 CCTAGATTAAGCGCGCGAGG 61.004 60.000 37.18 24.30 0.00 4.63
2082 2305 0.317938 ACCTAGATTAAGCGCGCGAG 60.318 55.000 37.18 19.04 0.00 5.03
2083 2306 0.594028 CACCTAGATTAAGCGCGCGA 60.594 55.000 37.18 13.84 0.00 5.87
2084 2307 0.870307 ACACCTAGATTAAGCGCGCG 60.870 55.000 28.44 28.44 0.00 6.86
2085 2308 1.258197 GAACACCTAGATTAAGCGCGC 59.742 52.381 26.66 26.66 0.00 6.86
2086 2309 1.517276 CGAACACCTAGATTAAGCGCG 59.483 52.381 0.00 0.00 0.00 6.86
2087 2310 2.534757 GACGAACACCTAGATTAAGCGC 59.465 50.000 0.00 0.00 0.00 5.92
2088 2311 3.114065 GGACGAACACCTAGATTAAGCG 58.886 50.000 0.00 0.00 0.00 4.68
2089 2312 3.114065 CGGACGAACACCTAGATTAAGC 58.886 50.000 0.00 0.00 0.00 3.09
2090 2313 4.096081 AGACGGACGAACACCTAGATTAAG 59.904 45.833 0.00 0.00 0.00 1.85
2091 2314 4.012374 AGACGGACGAACACCTAGATTAA 58.988 43.478 0.00 0.00 0.00 1.40
2092 2315 3.614092 AGACGGACGAACACCTAGATTA 58.386 45.455 0.00 0.00 0.00 1.75
2093 2316 2.422832 GAGACGGACGAACACCTAGATT 59.577 50.000 0.00 0.00 0.00 2.40
2094 2317 2.015587 GAGACGGACGAACACCTAGAT 58.984 52.381 0.00 0.00 0.00 1.98
2095 2318 1.271001 TGAGACGGACGAACACCTAGA 60.271 52.381 0.00 0.00 0.00 2.43
2382 2685 0.613292 AGAGATGACACTCGGTGGCT 60.613 55.000 10.62 2.41 42.96 4.75
2387 2690 0.309302 CGGCTAGAGATGACACTCGG 59.691 60.000 0.00 0.00 41.25 4.63
2417 2720 0.385598 CACGAGCTCGAACGAACAGA 60.386 55.000 40.58 0.00 43.02 3.41
2455 2758 3.636381 CAGAAAGCAGCAACTTTTCTCC 58.364 45.455 4.73 0.00 39.93 3.71
2680 2990 7.064016 ACAGCACGTGAATAAACAACAAAAATT 59.936 29.630 22.23 0.00 0.00 1.82
2723 3039 2.979649 CTCTCCTGCAGCTCAGCA 59.020 61.111 8.66 0.00 41.50 4.41
2725 3041 2.202770 CGCTCTCCTGCAGCTCAG 60.203 66.667 8.66 3.61 42.49 3.35
2726 3042 2.677875 TCGCTCTCCTGCAGCTCA 60.678 61.111 8.66 0.00 34.45 4.26
2727 3043 2.104729 CTCGCTCTCCTGCAGCTC 59.895 66.667 8.66 0.00 34.45 4.09
2728 3044 2.679642 ACTCGCTCTCCTGCAGCT 60.680 61.111 8.66 0.00 34.45 4.24
2729 3045 2.202730 GACTCGCTCTCCTGCAGC 60.203 66.667 8.66 0.00 0.00 5.25
2730 3046 1.369839 TACGACTCGCTCTCCTGCAG 61.370 60.000 6.78 6.78 0.00 4.41
2843 3160 2.346365 CAGAGCAGCAGCAGGTCA 59.654 61.111 18.12 0.00 45.49 4.02
3180 3497 2.123077 CTCCGCCTCCTCCTCCAT 60.123 66.667 0.00 0.00 0.00 3.41
3182 3499 2.520741 CTCTCCGCCTCCTCCTCC 60.521 72.222 0.00 0.00 0.00 4.30
3254 3571 0.037232 GGGTCTTCTTCGTCCCAGTG 60.037 60.000 0.00 0.00 39.68 3.66
3257 3574 2.280552 CCGGGTCTTCTTCGTCCCA 61.281 63.158 0.00 0.00 39.87 4.37
3275 3592 2.046217 GAGTTCTTGCCGGGTCCC 60.046 66.667 2.18 0.00 0.00 4.46
3359 3676 0.396811 AGTCCCCGTTGTCCTTCTTG 59.603 55.000 0.00 0.00 0.00 3.02
3555 3875 2.328099 CGGTGTTCTTCCTGCCTGC 61.328 63.158 0.00 0.00 0.00 4.85
3710 4030 4.517703 CCTCGCCTCGACGACGAC 62.518 72.222 5.75 0.00 43.81 4.34
3731 4051 3.090037 TCTAGCTTGCGACTACTTCCTT 58.910 45.455 0.00 0.00 0.00 3.36
3746 4067 2.785562 CTCTACCGGCTACATCTAGCT 58.214 52.381 0.00 0.00 44.46 3.32
3747 4068 1.200484 GCTCTACCGGCTACATCTAGC 59.800 57.143 0.00 0.00 44.34 3.42
3748 4069 2.785562 AGCTCTACCGGCTACATCTAG 58.214 52.381 0.00 0.00 38.36 2.43
3775 4110 7.942990 AGCTATCACACACTTCCTAATACTAC 58.057 38.462 0.00 0.00 0.00 2.73
3881 4228 0.522915 GGGACGTCGTTCGATCTGTC 60.523 60.000 9.92 12.90 42.86 3.51
3892 4239 0.177141 AGAGAGAGAGAGGGACGTCG 59.823 60.000 9.92 0.00 0.00 5.12
3894 4241 1.580059 AGAGAGAGAGAGAGGGACGT 58.420 55.000 0.00 0.00 0.00 4.34
3903 4250 3.197766 AGAGAGCGAGAAAGAGAGAGAGA 59.802 47.826 0.00 0.00 0.00 3.10
3905 4252 3.197766 AGAGAGAGCGAGAAAGAGAGAGA 59.802 47.826 0.00 0.00 0.00 3.10
3908 4255 2.285220 CGAGAGAGAGCGAGAAAGAGAG 59.715 54.545 0.00 0.00 0.00 3.20
3909 4256 2.276201 CGAGAGAGAGCGAGAAAGAGA 58.724 52.381 0.00 0.00 0.00 3.10
3910 4257 1.268032 GCGAGAGAGAGCGAGAAAGAG 60.268 57.143 0.00 0.00 0.00 2.85
3911 4258 0.730265 GCGAGAGAGAGCGAGAAAGA 59.270 55.000 0.00 0.00 0.00 2.52
3912 4259 3.234368 GCGAGAGAGAGCGAGAAAG 57.766 57.895 0.00 0.00 0.00 2.62
3919 4266 2.958137 CTACGCACGCGAGAGAGAGC 62.958 65.000 19.66 3.82 43.23 4.09
3998 4365 4.228210 TCCACTCTATCCTTTGCTCCAAAT 59.772 41.667 0.00 0.00 32.70 2.32
4001 4368 2.768527 CTCCACTCTATCCTTTGCTCCA 59.231 50.000 0.00 0.00 0.00 3.86
4064 4434 6.546772 CGGAGGGAGTAGTAGACTAGAAAAAT 59.453 42.308 0.00 0.00 39.06 1.82
4078 4448 3.629142 AATTTGGAACGGAGGGAGTAG 57.371 47.619 0.00 0.00 0.00 2.57
4080 4450 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
4081 4451 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
4082 4452 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
4083 4453 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
4084 4454 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
4085 4455 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
4086 4456 2.598589 CGACGAGTAATTTGGAACGGA 58.401 47.619 0.00 0.00 0.00 4.69
4088 4458 1.722464 TGCGACGAGTAATTTGGAACG 59.278 47.619 0.00 0.00 0.00 3.95
4089 4459 2.991190 TCTGCGACGAGTAATTTGGAAC 59.009 45.455 0.00 0.00 0.00 3.62
4090 4460 3.306917 TCTGCGACGAGTAATTTGGAA 57.693 42.857 0.00 0.00 0.00 3.53
4091 4461 3.306917 TTCTGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
4092 4462 4.600012 ATTTCTGCGACGAGTAATTTGG 57.400 40.909 0.00 0.00 0.00 3.28
4093 4463 6.569228 TCTATTTCTGCGACGAGTAATTTG 57.431 37.500 0.00 0.00 0.00 2.32
4094 4464 6.757010 ACATCTATTTCTGCGACGAGTAATTT 59.243 34.615 0.00 0.00 0.00 1.82
4095 4465 6.273825 ACATCTATTTCTGCGACGAGTAATT 58.726 36.000 0.00 0.00 0.00 1.40
4096 4466 5.833082 ACATCTATTTCTGCGACGAGTAAT 58.167 37.500 0.00 2.18 0.00 1.89
4097 4467 5.244785 ACATCTATTTCTGCGACGAGTAA 57.755 39.130 0.00 0.00 0.00 2.24
4098 4468 4.895224 ACATCTATTTCTGCGACGAGTA 57.105 40.909 0.00 0.00 0.00 2.59
4101 4471 5.690997 AGATACATCTATTTCTGCGACGA 57.309 39.130 0.00 0.00 34.85 4.20
4102 4472 7.853377 TTTAGATACATCTATTTCTGCGACG 57.147 36.000 0.00 0.00 39.02 5.12
4103 4473 9.250624 AGTTTTAGATACATCTATTTCTGCGAC 57.749 33.333 0.00 0.00 39.02 5.19
4132 4502 9.775539 ACAGGTATGGATGTATCTAGATGTATT 57.224 33.333 15.79 0.00 0.00 1.89
4134 4504 8.390921 TCACAGGTATGGATGTATCTAGATGTA 58.609 37.037 15.79 4.44 0.00 2.29
4136 4506 7.177392 TGTCACAGGTATGGATGTATCTAGATG 59.823 40.741 15.79 0.00 0.00 2.90
4137 4507 7.241628 TGTCACAGGTATGGATGTATCTAGAT 58.758 38.462 10.73 10.73 0.00 1.98
4138 4508 6.610830 TGTCACAGGTATGGATGTATCTAGA 58.389 40.000 0.00 0.00 0.00 2.43
4139 4509 6.901081 TGTCACAGGTATGGATGTATCTAG 57.099 41.667 0.00 0.00 0.00 2.43
4140 4510 6.839134 ACTTGTCACAGGTATGGATGTATCTA 59.161 38.462 0.00 0.00 0.00 1.98
4142 4512 5.918608 ACTTGTCACAGGTATGGATGTATC 58.081 41.667 0.00 0.00 0.00 2.24
4143 4513 5.957771 ACTTGTCACAGGTATGGATGTAT 57.042 39.130 0.00 0.00 0.00 2.29
4144 4514 6.860790 TTACTTGTCACAGGTATGGATGTA 57.139 37.500 0.00 0.00 0.00 2.29
4145 4515 5.755409 TTACTTGTCACAGGTATGGATGT 57.245 39.130 0.00 0.00 0.00 3.06
4146 4516 6.018751 CGAATTACTTGTCACAGGTATGGATG 60.019 42.308 0.00 0.00 0.00 3.51
4147 4517 6.049149 CGAATTACTTGTCACAGGTATGGAT 58.951 40.000 0.00 0.00 0.00 3.41
4148 4518 5.186215 TCGAATTACTTGTCACAGGTATGGA 59.814 40.000 0.00 0.00 0.00 3.41
4151 4521 6.090358 CGTTTCGAATTACTTGTCACAGGTAT 59.910 38.462 0.00 0.00 0.00 2.73
4152 4522 5.403166 CGTTTCGAATTACTTGTCACAGGTA 59.597 40.000 0.00 0.00 0.00 3.08
4153 4523 4.210537 CGTTTCGAATTACTTGTCACAGGT 59.789 41.667 0.00 0.00 0.00 4.00
4155 4525 4.446385 TCCGTTTCGAATTACTTGTCACAG 59.554 41.667 0.00 0.00 0.00 3.66
4156 4526 4.370049 TCCGTTTCGAATTACTTGTCACA 58.630 39.130 0.00 0.00 0.00 3.58
4157 4527 4.977741 TCCGTTTCGAATTACTTGTCAC 57.022 40.909 0.00 0.00 0.00 3.67
4159 4529 4.687483 TCCTTCCGTTTCGAATTACTTGTC 59.313 41.667 0.00 0.00 0.00 3.18
4160 4530 4.634199 TCCTTCCGTTTCGAATTACTTGT 58.366 39.130 0.00 0.00 0.00 3.16
4161 4531 4.689345 ACTCCTTCCGTTTCGAATTACTTG 59.311 41.667 0.00 0.00 0.00 3.16
4163 4533 4.532314 ACTCCTTCCGTTTCGAATTACT 57.468 40.909 0.00 0.00 0.00 2.24
4164 4534 5.405797 ACTACTCCTTCCGTTTCGAATTAC 58.594 41.667 0.00 0.00 0.00 1.89
4166 4536 4.532314 ACTACTCCTTCCGTTTCGAATT 57.468 40.909 0.00 0.00 0.00 2.17
4167 4537 4.704057 ACTACTACTCCTTCCGTTTCGAAT 59.296 41.667 0.00 0.00 0.00 3.34
4168 4538 4.074970 ACTACTACTCCTTCCGTTTCGAA 58.925 43.478 0.00 0.00 0.00 3.71
4173 4543 6.244654 ACTCTTTACTACTACTCCTTCCGTT 58.755 40.000 0.00 0.00 0.00 4.44
4174 4544 5.814481 ACTCTTTACTACTACTCCTTCCGT 58.186 41.667 0.00 0.00 0.00 4.69
4175 4545 7.012232 CCTTACTCTTTACTACTACTCCTTCCG 59.988 44.444 0.00 0.00 0.00 4.30
4177 4547 8.806429 ACCTTACTCTTTACTACTACTCCTTC 57.194 38.462 0.00 0.00 0.00 3.46
4178 4548 8.389366 TGACCTTACTCTTTACTACTACTCCTT 58.611 37.037 0.00 0.00 0.00 3.36
4181 4551 9.838975 GTTTGACCTTACTCTTTACTACTACTC 57.161 37.037 0.00 0.00 0.00 2.59
4182 4552 8.510505 CGTTTGACCTTACTCTTTACTACTACT 58.489 37.037 0.00 0.00 0.00 2.57
4183 4553 8.293157 ACGTTTGACCTTACTCTTTACTACTAC 58.707 37.037 0.00 0.00 0.00 2.73
4185 4555 7.282332 ACGTTTGACCTTACTCTTTACTACT 57.718 36.000 0.00 0.00 0.00 2.57
4188 4558 5.069516 TGGACGTTTGACCTTACTCTTTACT 59.930 40.000 0.00 0.00 0.00 2.24
4189 4559 5.291971 TGGACGTTTGACCTTACTCTTTAC 58.708 41.667 0.00 0.00 0.00 2.01
4190 4560 5.534207 TGGACGTTTGACCTTACTCTTTA 57.466 39.130 0.00 0.00 0.00 1.85
4197 5815 4.900684 TGATCATTGGACGTTTGACCTTA 58.099 39.130 0.00 0.00 0.00 2.69
4206 5824 9.567848 GTATATTTTTGTTTGATCATTGGACGT 57.432 29.630 0.00 0.00 0.00 4.34
4251 5871 6.566197 AGAACTTTCAAGCATACTCTTTGG 57.434 37.500 0.00 0.00 0.00 3.28
4262 5882 5.971792 GTGAGGTTTTGTAGAACTTTCAAGC 59.028 40.000 0.00 0.00 30.75 4.01
4265 5885 6.177610 AGTGTGAGGTTTTGTAGAACTTTCA 58.822 36.000 0.00 0.00 0.00 2.69
4266 5886 6.238402 GGAGTGTGAGGTTTTGTAGAACTTTC 60.238 42.308 0.00 0.00 0.00 2.62
4267 5887 5.589050 GGAGTGTGAGGTTTTGTAGAACTTT 59.411 40.000 0.00 0.00 0.00 2.66
4268 5888 5.123936 GGAGTGTGAGGTTTTGTAGAACTT 58.876 41.667 0.00 0.00 0.00 2.66
4269 5889 4.704965 GGAGTGTGAGGTTTTGTAGAACT 58.295 43.478 0.00 0.00 0.00 3.01
4270 5890 3.493503 CGGAGTGTGAGGTTTTGTAGAAC 59.506 47.826 0.00 0.00 0.00 3.01
4271 5891 3.133362 ACGGAGTGTGAGGTTTTGTAGAA 59.867 43.478 0.00 0.00 42.51 2.10
4272 5892 2.696707 ACGGAGTGTGAGGTTTTGTAGA 59.303 45.455 0.00 0.00 42.51 2.59
4300 5920 0.736325 CATCAGTGGGGACGAACGAC 60.736 60.000 0.14 0.00 0.00 4.34
4301 5921 1.183030 ACATCAGTGGGGACGAACGA 61.183 55.000 0.14 0.00 0.00 3.85
4302 5922 1.014044 CACATCAGTGGGGACGAACG 61.014 60.000 0.00 0.00 42.13 3.95
4328 5948 3.476552 GGTATGCCATTTCTCATCGGAA 58.523 45.455 0.00 0.00 34.09 4.30
4332 6026 2.154462 CCGGGTATGCCATTTCTCATC 58.846 52.381 1.04 0.00 36.17 2.92
4348 6042 0.536006 GGAGCTTGATGAATCCCGGG 60.536 60.000 16.85 16.85 0.00 5.73
4396 6092 1.726853 ACTTGTTATCTGCCAGACGC 58.273 50.000 0.00 0.00 38.31 5.19
4404 6100 5.408604 AGGCGAGTTGTTAACTTGTTATCTG 59.591 40.000 7.22 0.00 43.03 2.90
4405 6101 5.548406 AGGCGAGTTGTTAACTTGTTATCT 58.452 37.500 7.22 0.00 43.03 1.98
4406 6102 5.857822 AGGCGAGTTGTTAACTTGTTATC 57.142 39.130 7.22 0.00 43.03 1.75
4407 6103 6.435428 CAAAGGCGAGTTGTTAACTTGTTAT 58.565 36.000 7.22 0.00 43.03 1.89
4408 6104 5.731126 GCAAAGGCGAGTTGTTAACTTGTTA 60.731 40.000 7.22 0.00 43.03 2.41
4409 6105 4.668289 CAAAGGCGAGTTGTTAACTTGTT 58.332 39.130 7.22 0.00 43.03 2.83
4410 6106 3.488553 GCAAAGGCGAGTTGTTAACTTGT 60.489 43.478 7.22 0.00 43.03 3.16
4411 6107 3.042887 GCAAAGGCGAGTTGTTAACTTG 58.957 45.455 7.22 4.88 43.03 3.16
4412 6108 2.034179 GGCAAAGGCGAGTTGTTAACTT 59.966 45.455 7.22 0.00 38.88 2.66
4415 6111 1.335496 GTGGCAAAGGCGAGTTGTTAA 59.665 47.619 0.00 0.00 42.47 2.01
4445 6145 0.179100 TCGCTGCTGTGAGCTATTCC 60.179 55.000 2.33 0.00 42.97 3.01
4555 6255 3.915842 CGTGATCGAGATGCTGAACAGC 61.916 54.545 18.32 18.32 46.26 4.40
4670 6372 2.715046 TGTGCATGCAAAACCCAAAAA 58.285 38.095 24.58 0.00 0.00 1.94
4711 6413 3.007182 ACGAGTAATTTGAAACGGAGGGA 59.993 43.478 0.00 0.00 0.00 4.20
4712 6414 3.332034 ACGAGTAATTTGAAACGGAGGG 58.668 45.455 0.00 0.00 0.00 4.30
4713 6415 3.060363 CGACGAGTAATTTGAAACGGAGG 59.940 47.826 0.00 0.00 0.00 4.30
4714 6416 3.671928 ACGACGAGTAATTTGAAACGGAG 59.328 43.478 0.00 0.00 0.00 4.63
4715 6417 3.641648 ACGACGAGTAATTTGAAACGGA 58.358 40.909 0.00 0.00 0.00 4.69
4716 6418 4.853196 TCTACGACGAGTAATTTGAAACGG 59.147 41.667 0.00 0.00 34.45 4.44
4717 6419 5.980324 TCTACGACGAGTAATTTGAAACG 57.020 39.130 0.00 0.00 34.45 3.60


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

AutoCloner maintained by Alex Coulton.