Multiple sequence alignment - TraesCS2A01G079700

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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 TraesCS2A01G079700 chr2A 100.000 4148 0 0 1 4148 36055044 36059191 0.000000e+00 7661.0
1 TraesCS2A01G079700 chr2A 92.671 805 40 9 1231 2033 44039618 44038831 0.000000e+00 1142.0
2 TraesCS2A01G079700 chr2A 92.913 254 6 3 3545 3798 44037111 44036870 3.940000e-95 359.0
3 TraesCS2A01G079700 chr2A 87.898 314 22 8 3798 4103 44032701 44032396 5.100000e-94 355.0
4 TraesCS2A01G079700 chr2A 89.286 196 11 6 3376 3564 36122066 36122258 1.930000e-58 237.0
5 TraesCS2A01G079700 chr2A 86.022 93 7 5 3952 4042 737450668 737450580 1.230000e-15 95.3
6 TraesCS2A01G079700 chr2B 93.250 2948 159 13 1 2934 54552404 54555325 0.000000e+00 4305.0
7 TraesCS2A01G079700 chr2B 89.620 1079 51 16 2934 3981 54555361 54556409 0.000000e+00 1315.0
8 TraesCS2A01G079700 chr2D 90.713 2961 187 40 1 2934 32805862 32808761 0.000000e+00 3864.0
9 TraesCS2A01G079700 chr2D 86.475 1220 77 32 2934 4104 32808795 32809975 0.000000e+00 1258.0
10 TraesCS2A01G079700 chr6D 91.795 195 16 0 396 590 400556158 400556352 5.280000e-69 272.0
11 TraesCS2A01G079700 chrUn 88.265 196 10 9 3376 3564 280375537 280375348 5.400000e-54 222.0
12 TraesCS2A01G079700 chrUn 84.043 94 7 6 3952 4043 154526096 154526183 2.660000e-12 84.2
13 TraesCS2A01G079700 chrUn 88.406 69 6 2 3952 4018 201360633 201360701 9.560000e-12 82.4
14 TraesCS2A01G079700 chrUn 88.406 69 6 2 3952 4018 400257785 400257853 9.560000e-12 82.4
15 TraesCS2A01G079700 chr6A 86.170 94 7 5 3952 4043 560466511 560466422 3.410000e-16 97.1
16 TraesCS2A01G079700 chr6A 85.106 94 10 4 3952 4043 560352410 560352319 4.420000e-15 93.5
17 TraesCS2A01G079700 chr6A 85.106 94 10 4 3952 4043 560393759 560393668 4.420000e-15 93.5
18 TraesCS2A01G079700 chr6A 83.505 97 12 4 3952 4046 560511026 560510932 2.050000e-13 87.9
19 TraesCS2A01G079700 chr1B 83.158 95 16 0 341 435 561547848 561547754 2.050000e-13 87.9
20 TraesCS2A01G079700 chr1B 82.105 95 17 0 341 435 561546774 561546680 9.560000e-12 82.4


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 TraesCS2A01G079700 chr2A 36055044 36059191 4147 False 7661.0 7661 100.000 1 4148 1 chr2A.!!$F1 4147
1 TraesCS2A01G079700 chr2A 44036870 44039618 2748 True 750.5 1142 92.792 1231 3798 2 chr2A.!!$R3 2567
2 TraesCS2A01G079700 chr2B 54552404 54556409 4005 False 2810.0 4305 91.435 1 3981 2 chr2B.!!$F1 3980
3 TraesCS2A01G079700 chr2D 32805862 32809975 4113 False 2561.0 3864 88.594 1 4104 2 chr2D.!!$F1 4103

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
279 280 0.524862 TTGACGCGGTAGAAGGTCTC 59.475 55.0 12.47 0.00 0.00 3.36 F
926 931 0.890683 CAATGGGAGCCAGTGGAAAC 59.109 55.0 15.20 2.57 44.60 2.78 F
2111 2130 0.742505 TGATGCTGCAAGGCTTATGC 59.257 50.0 6.36 0.90 44.08 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1753 1772 0.320374 GATCACCCTCGTTCACACCA 59.680 55.0 0.0 0.0 0.00 4.17 R
2517 3290 0.318869 TGTGCATTTTCAGCAAGCGG 60.319 50.0 0.0 0.0 44.64 5.52 R
3449 4329 0.035881 TGGCACAGGCTCTCAAGAAG 59.964 55.0 0.0 0.0 40.87 2.85 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
52 53 3.283684 TTGAACCGCTGGTTGCCG 61.284 61.111 16.02 0.00 46.95 5.69
279 280 0.524862 TTGACGCGGTAGAAGGTCTC 59.475 55.000 12.47 0.00 0.00 3.36
502 503 1.745864 GGAGACGAGCTCGAGGTCA 60.746 63.158 40.58 0.00 44.91 4.02
804 805 4.528674 CGCAAGGTGGGAGATGAG 57.471 61.111 0.00 0.00 31.21 2.90
868 872 2.550101 GGCCATGGCGCAATCTCTC 61.550 63.158 29.90 9.36 43.06 3.20
924 929 2.079088 TGCAATGGGAGCCAGTGGAA 62.079 55.000 15.20 0.00 45.85 3.53
926 931 0.890683 CAATGGGAGCCAGTGGAAAC 59.109 55.000 15.20 2.57 44.60 2.78
955 960 1.881252 CGAACCCGAAGCCCATACG 60.881 63.158 0.00 0.00 38.22 3.06
958 969 2.124901 CCCGAAGCCCATACGCAA 60.125 61.111 0.00 0.00 0.00 4.85
964 975 2.753849 GCCCATACGCAAGCCCAA 60.754 61.111 0.00 0.00 45.62 4.12
1523 1539 6.496565 TCCTATCCAGATCTCCTTGAGAATTC 59.503 42.308 0.00 0.00 42.27 2.17
1578 1595 1.755008 CCTCCTCCGACTCTGGGTC 60.755 68.421 0.00 0.00 41.28 4.46
1809 1828 3.565764 TGAAGCTCATCTTGGTATGGG 57.434 47.619 0.00 0.00 34.56 4.00
1827 1846 1.562008 GGGAAAAGGAGAAGCTAGCCT 59.438 52.381 12.13 1.38 0.00 4.58
1879 1898 4.009370 AGAGCCAGTAGAAAGAACAACC 57.991 45.455 0.00 0.00 0.00 3.77
1902 1921 2.783135 TGCTCGAATTCCTGAAAAGCT 58.217 42.857 0.00 0.00 0.00 3.74
2054 2073 2.420022 AGTGCAATCGTTTATCAGGTGC 59.580 45.455 0.00 0.00 0.00 5.01
2085 2104 5.103290 TGGCTTTTATTGACGTTCTGTTC 57.897 39.130 0.00 0.00 0.00 3.18
2101 2120 2.486592 CTGTTCAAGATGTGATGCTGCA 59.513 45.455 4.13 4.13 35.70 4.41
2111 2130 0.742505 TGATGCTGCAAGGCTTATGC 59.257 50.000 6.36 0.90 44.08 3.14
2183 2432 3.646715 TGTGGGGCTGTGGGTAGC 61.647 66.667 0.00 0.00 42.94 3.58
2312 2566 5.174395 AGTTCTGTGTGATCTACTTGCATC 58.826 41.667 0.00 0.00 0.00 3.91
2313 2567 3.774066 TCTGTGTGATCTACTTGCATCG 58.226 45.455 0.00 0.00 0.00 3.84
2332 2590 6.989759 TGCATCGTGTTAGGTCATATTGTTAT 59.010 34.615 0.00 0.00 0.00 1.89
2334 2592 7.798516 GCATCGTGTTAGGTCATATTGTTATTG 59.201 37.037 0.00 0.00 0.00 1.90
2356 2614 8.948853 ATTGTCAACACTTTGTTAATATGTCG 57.051 30.769 0.00 0.00 38.77 4.35
2517 3290 1.686052 TCCCACCATCTGCAACAAAAC 59.314 47.619 0.00 0.00 0.00 2.43
2539 3312 2.409975 GCTTGCTGAAAATGCACATGT 58.590 42.857 0.00 0.00 40.40 3.21
2540 3313 2.410730 GCTTGCTGAAAATGCACATGTC 59.589 45.455 0.00 0.00 40.40 3.06
2541 3314 3.859627 GCTTGCTGAAAATGCACATGTCT 60.860 43.478 0.00 0.00 40.40 3.41
2542 3315 3.291809 TGCTGAAAATGCACATGTCTG 57.708 42.857 0.00 0.00 35.31 3.51
2543 3316 2.029739 TGCTGAAAATGCACATGTCTGG 60.030 45.455 0.00 0.00 35.31 3.86
2544 3317 2.029649 GCTGAAAATGCACATGTCTGGT 60.030 45.455 0.00 0.00 0.00 4.00
2545 3318 3.553508 GCTGAAAATGCACATGTCTGGTT 60.554 43.478 0.00 0.00 0.00 3.67
2547 3320 3.384146 TGAAAATGCACATGTCTGGTTGT 59.616 39.130 0.00 0.00 0.00 3.32
2548 3321 3.648339 AAATGCACATGTCTGGTTGTC 57.352 42.857 0.00 0.00 0.00 3.18
2549 3322 1.159285 ATGCACATGTCTGGTTGTCG 58.841 50.000 0.00 0.00 0.00 4.35
2550 3323 0.105778 TGCACATGTCTGGTTGTCGA 59.894 50.000 0.00 0.00 0.00 4.20
2553 3326 2.609491 GCACATGTCTGGTTGTCGACTA 60.609 50.000 17.92 6.32 0.00 2.59
2554 3327 3.849911 CACATGTCTGGTTGTCGACTAT 58.150 45.455 17.92 0.00 0.00 2.12
2555 3328 3.859961 CACATGTCTGGTTGTCGACTATC 59.140 47.826 17.92 10.47 0.00 2.08
2556 3329 2.913777 TGTCTGGTTGTCGACTATCG 57.086 50.000 17.92 6.46 42.10 2.92
2557 3330 2.156917 TGTCTGGTTGTCGACTATCGT 58.843 47.619 17.92 0.00 41.35 3.73
2624 3411 8.425577 AATCCAGTTTAGTATTGATCGTCTTG 57.574 34.615 0.00 0.00 0.00 3.02
2636 3423 5.418310 TGATCGTCTTGAAGGTTGTTTTC 57.582 39.130 0.00 0.00 0.00 2.29
2646 3434 1.480545 AGGTTGTTTTCTGGGTTGCAC 59.519 47.619 0.00 0.00 0.00 4.57
2647 3435 1.480545 GGTTGTTTTCTGGGTTGCACT 59.519 47.619 0.00 0.00 0.00 4.40
2673 3461 2.996621 GCAGTATTCCTGATCGTATGCC 59.003 50.000 0.00 0.00 44.49 4.40
2769 3560 0.618968 ACGAAAGGAGGATGAGGCCT 60.619 55.000 3.86 3.86 42.17 5.19
2852 3643 1.804601 GAAGGGGTTGACAAGTACGG 58.195 55.000 0.00 0.00 0.00 4.02
2854 3645 2.014010 AGGGGTTGACAAGTACGGTA 57.986 50.000 0.00 0.00 0.00 4.02
2879 3670 6.281405 TCTTTTCTCGCTCTTACTTTTCACT 58.719 36.000 0.00 0.00 0.00 3.41
2963 3793 1.293498 CTGCTGCTGAAGGTACGGT 59.707 57.895 0.00 0.00 0.00 4.83
2965 3795 0.970640 TGCTGCTGAAGGTACGGTAA 59.029 50.000 0.00 0.00 0.00 2.85
3090 3966 0.537188 ACGTCCGAGGCTGAAATGAT 59.463 50.000 0.00 0.00 0.00 2.45
3100 3976 2.424956 GGCTGAAATGATGGTTCCTGTC 59.575 50.000 0.00 0.00 0.00 3.51
3133 4009 3.924114 TGAAGGACAAGTTCAGGAACA 57.076 42.857 14.06 0.00 43.47 3.18
3150 4026 1.072266 ACATGGGGAGGCACTAACAA 58.928 50.000 0.00 0.00 41.55 2.83
3151 4027 1.004745 ACATGGGGAGGCACTAACAAG 59.995 52.381 0.00 0.00 41.55 3.16
3165 4041 2.610438 AACAAGGAATGTGCCTGGAT 57.390 45.000 0.00 0.00 42.99 3.41
3194 4070 1.491670 CATTCGGCCGAGTAGACATG 58.508 55.000 29.20 22.83 0.00 3.21
3215 4091 0.736325 CCGGCACATATAGTAGGCGC 60.736 60.000 0.00 0.00 41.92 6.53
3282 4158 4.340381 GCATGAGATATCTTGCCCTTTTGT 59.660 41.667 15.70 0.00 35.54 2.83
3301 4177 2.028876 GTTGGTTGTTGCAACCCTACT 58.971 47.619 26.14 0.00 39.54 2.57
3355 4231 2.427506 CACCTTTCTCTTGTACAGGGC 58.572 52.381 5.01 0.00 0.00 5.19
3438 4318 7.551617 TGAGGTATGTGATTATGATGATGATGC 59.448 37.037 0.00 0.00 0.00 3.91
3440 4320 6.827251 GGTATGTGATTATGATGATGATGCCT 59.173 38.462 0.00 0.00 0.00 4.75
3441 4321 6.759497 ATGTGATTATGATGATGATGCCTG 57.241 37.500 0.00 0.00 0.00 4.85
3443 4323 4.014406 TGATTATGATGATGATGCCTGGC 58.986 43.478 12.87 12.87 0.00 4.85
3444 4324 3.801307 TTATGATGATGATGCCTGGCT 57.199 42.857 21.03 5.22 0.00 4.75
3446 4326 0.549469 TGATGATGATGCCTGGCTGT 59.451 50.000 21.03 8.62 0.00 4.40
3447 4327 1.770061 TGATGATGATGCCTGGCTGTA 59.230 47.619 21.03 6.01 0.00 2.74
3449 4329 0.179037 TGATGATGCCTGGCTGTAGC 60.179 55.000 21.03 8.91 41.14 3.58
3450 4330 0.108207 GATGATGCCTGGCTGTAGCT 59.892 55.000 21.03 0.00 41.70 3.32
3452 4332 0.107508 TGATGCCTGGCTGTAGCTTC 60.108 55.000 21.03 6.00 41.70 3.86
3453 4333 0.179936 GATGCCTGGCTGTAGCTTCT 59.820 55.000 21.03 0.00 41.70 2.85
3454 4334 0.622665 ATGCCTGGCTGTAGCTTCTT 59.377 50.000 21.03 0.00 41.70 2.52
3455 4335 0.321919 TGCCTGGCTGTAGCTTCTTG 60.322 55.000 21.03 0.00 41.70 3.02
3482 4362 4.015084 CCTGTGCCATTCTTCTTCTTCAT 58.985 43.478 0.00 0.00 0.00 2.57
3484 4364 4.914983 TGTGCCATTCTTCTTCTTCATCT 58.085 39.130 0.00 0.00 0.00 2.90
3485 4365 5.319453 TGTGCCATTCTTCTTCTTCATCTT 58.681 37.500 0.00 0.00 0.00 2.40
3689 4601 6.055588 GCATCTCCCTTAATTAGCACTGTAA 58.944 40.000 0.00 0.00 0.00 2.41
3763 4676 1.067669 GCTGAGGACGCATGTGATCTA 59.932 52.381 14.43 0.00 0.00 1.98
3764 4677 2.861750 GCTGAGGACGCATGTGATCTAG 60.862 54.545 14.43 5.71 0.00 2.43
3765 4678 1.683385 TGAGGACGCATGTGATCTAGG 59.317 52.381 14.43 0.00 0.00 3.02
3766 4679 1.957177 GAGGACGCATGTGATCTAGGA 59.043 52.381 14.43 0.00 0.00 2.94
3767 4680 1.959985 AGGACGCATGTGATCTAGGAG 59.040 52.381 14.43 0.00 0.00 3.69
3768 4681 1.683917 GGACGCATGTGATCTAGGAGT 59.316 52.381 14.43 0.00 0.00 3.85
3831 4744 0.745468 TTGTACCAAACCCAAACGGC 59.255 50.000 0.00 0.00 33.26 5.68
3857 4770 1.018148 CTCTAGATCGTCCGTGCAGT 58.982 55.000 0.00 0.00 0.00 4.40
3858 4771 0.733150 TCTAGATCGTCCGTGCAGTG 59.267 55.000 0.00 0.00 0.00 3.66
3859 4772 0.867753 CTAGATCGTCCGTGCAGTGC 60.868 60.000 8.58 8.58 0.00 4.40
3879 4800 2.553962 CATGAACGGACATGCACCA 58.446 52.632 10.21 0.00 40.54 4.17
3926 4847 5.254339 TGTTTGTTTGTGTATGCATGTGA 57.746 34.783 10.16 0.00 0.00 3.58
3930 4851 4.388485 TGTTTGTGTATGCATGTGAGTCT 58.612 39.130 10.16 0.00 0.00 3.24
3944 4865 9.176460 TGCATGTGAGTCTAAAATCAATGATTA 57.824 29.630 9.09 0.00 31.46 1.75
3985 4906 4.083537 TGCGTGGTTGATTCTGTAATGAAC 60.084 41.667 0.00 0.00 38.16 3.18
4007 4928 9.872757 TGAACGATTGTAAGAACTTGTTAATTC 57.127 29.630 0.00 0.00 0.00 2.17
4094 5018 2.238521 GGATTTTCTGCTTGGGACACA 58.761 47.619 0.00 0.00 39.29 3.72
4097 5021 4.262592 GGATTTTCTGCTTGGGACACATTT 60.263 41.667 0.00 0.00 39.29 2.32
4099 5023 1.619654 TCTGCTTGGGACACATTTGG 58.380 50.000 0.00 0.00 39.29 3.28
4100 5024 0.037975 CTGCTTGGGACACATTTGGC 60.038 55.000 0.00 0.00 39.29 4.52
4103 5027 1.202627 GCTTGGGACACATTTGGCAAA 60.203 47.619 16.01 16.01 39.29 3.68
4104 5028 2.758009 CTTGGGACACATTTGGCAAAG 58.242 47.619 18.61 12.33 39.29 2.77
4105 5029 1.047002 TGGGACACATTTGGCAAAGG 58.953 50.000 21.73 21.73 28.57 3.11
4106 5030 0.321346 GGGACACATTTGGCAAAGGG 59.679 55.000 26.01 18.49 28.57 3.95
4107 5031 0.321346 GGACACATTTGGCAAAGGGG 59.679 55.000 23.83 23.83 28.57 4.79
4108 5032 0.320683 GACACATTTGGCAAAGGGGC 60.321 55.000 25.15 14.74 43.73 5.80
4116 5040 3.134127 GCAAAGGGGCCTGCTACG 61.134 66.667 0.84 0.00 35.62 3.51
4117 5041 3.134127 CAAAGGGGCCTGCTACGC 61.134 66.667 0.84 0.00 0.00 4.42
4118 5042 3.646715 AAAGGGGCCTGCTACGCA 61.647 61.111 0.84 0.00 36.92 5.24
4119 5043 2.983879 AAAGGGGCCTGCTACGCAT 61.984 57.895 0.84 0.00 38.13 4.73
4120 5044 2.893682 AAAGGGGCCTGCTACGCATC 62.894 60.000 0.84 0.00 38.13 3.91
4121 5045 4.937431 GGGGCCTGCTACGCATCC 62.937 72.222 0.84 0.00 38.13 3.51
4122 5046 4.175337 GGGCCTGCTACGCATCCA 62.175 66.667 0.84 0.00 38.13 3.41
4123 5047 2.897350 GGCCTGCTACGCATCCAC 60.897 66.667 0.00 0.00 38.13 4.02
4124 5048 2.897350 GCCTGCTACGCATCCACC 60.897 66.667 0.00 0.00 38.13 4.61
4125 5049 2.586079 CCTGCTACGCATCCACCG 60.586 66.667 0.00 0.00 38.13 4.94
4126 5050 2.586079 CTGCTACGCATCCACCGG 60.586 66.667 0.00 0.00 38.13 5.28
4127 5051 4.830765 TGCTACGCATCCACCGGC 62.831 66.667 0.00 0.00 31.71 6.13
4128 5052 4.530857 GCTACGCATCCACCGGCT 62.531 66.667 0.00 0.00 0.00 5.52
4129 5053 2.586079 CTACGCATCCACCGGCTG 60.586 66.667 0.00 0.00 0.00 4.85
4130 5054 3.071837 TACGCATCCACCGGCTGA 61.072 61.111 0.00 0.00 0.00 4.26
4131 5055 2.369257 CTACGCATCCACCGGCTGAT 62.369 60.000 0.00 0.00 0.00 2.90
4132 5056 1.110518 TACGCATCCACCGGCTGATA 61.111 55.000 0.00 0.00 0.00 2.15
4133 5057 1.004560 CGCATCCACCGGCTGATAT 60.005 57.895 0.00 0.00 0.00 1.63
4134 5058 0.603707 CGCATCCACCGGCTGATATT 60.604 55.000 0.00 0.00 0.00 1.28
4135 5059 1.609208 GCATCCACCGGCTGATATTT 58.391 50.000 0.00 0.00 0.00 1.40
4136 5060 1.956477 GCATCCACCGGCTGATATTTT 59.044 47.619 0.00 0.00 0.00 1.82
4137 5061 2.362077 GCATCCACCGGCTGATATTTTT 59.638 45.455 0.00 0.00 0.00 1.94
4138 5062 3.796504 GCATCCACCGGCTGATATTTTTG 60.797 47.826 0.00 0.00 0.00 2.44
4139 5063 3.358111 TCCACCGGCTGATATTTTTGA 57.642 42.857 0.00 0.00 0.00 2.69
4140 5064 3.691575 TCCACCGGCTGATATTTTTGAA 58.308 40.909 0.00 0.00 0.00 2.69
4141 5065 4.082845 TCCACCGGCTGATATTTTTGAAA 58.917 39.130 0.00 0.00 0.00 2.69
4142 5066 4.157656 TCCACCGGCTGATATTTTTGAAAG 59.842 41.667 0.00 0.00 0.00 2.62
4143 5067 4.157656 CCACCGGCTGATATTTTTGAAAGA 59.842 41.667 0.00 0.00 0.00 2.52
4144 5068 5.163519 CCACCGGCTGATATTTTTGAAAGAT 60.164 40.000 0.00 0.00 0.00 2.40
4145 5069 5.973565 CACCGGCTGATATTTTTGAAAGATC 59.026 40.000 0.00 2.08 0.00 2.75
4146 5070 5.652014 ACCGGCTGATATTTTTGAAAGATCA 59.348 36.000 0.00 9.52 0.00 2.92
4147 5071 6.183360 ACCGGCTGATATTTTTGAAAGATCAG 60.183 38.462 23.50 23.50 40.05 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 4.899239 GAGATGGCCGACGCAGGG 62.899 72.222 0.00 0.00 36.38 4.45
58 59 4.147449 CAGGAGATGGCCGACGCA 62.147 66.667 0.00 0.00 36.38 5.24
390 391 3.461773 GCCTCCTGCGCCTACTCA 61.462 66.667 4.18 0.00 0.00 3.41
480 481 2.815298 CTCGAGCTCGTCTCCGTCC 61.815 68.421 33.33 0.00 38.62 4.79
482 483 2.820479 CCTCGAGCTCGTCTCCGT 60.820 66.667 33.33 0.00 38.62 4.69
621 622 3.955101 CCTCGCCGCTCTACTCCG 61.955 72.222 0.00 0.00 0.00 4.63
801 802 1.700368 CTGGTCCTCCTCCTCCTCA 59.300 63.158 0.00 0.00 34.23 3.86
804 805 2.766229 GCCTGGTCCTCCTCCTCC 60.766 72.222 0.00 0.00 34.23 4.30
868 872 0.038801 TGAGCTTCAGTGAGTGAGCG 60.039 55.000 9.16 0.00 36.21 5.03
924 929 2.281276 GTTCGGCCCAACTCCGTT 60.281 61.111 5.92 0.00 46.49 4.44
944 949 2.481471 GGGCTTGCGTATGGGCTTC 61.481 63.158 1.64 0.00 0.00 3.86
955 960 4.056125 GGCTCGGTTTGGGCTTGC 62.056 66.667 0.00 0.00 0.00 4.01
958 969 3.897122 TTGGGCTCGGTTTGGGCT 61.897 61.111 0.00 0.00 0.00 5.19
964 975 2.203437 GTTGGGTTGGGCTCGGTT 60.203 61.111 0.00 0.00 0.00 4.44
1347 1361 3.827898 CTCTCCCACTCGGCGTCC 61.828 72.222 6.85 0.00 0.00 4.79
1434 1448 2.737376 GTGTCCTGGTCGGCGTTC 60.737 66.667 6.85 1.15 0.00 3.95
1523 1539 4.539726 TCCATGGAAATTCTGAGATTGGG 58.460 43.478 13.46 0.00 0.00 4.12
1578 1595 5.871524 TCTCAAAACGAGATCAGAATTCAGG 59.128 40.000 8.44 0.00 46.18 3.86
1617 1636 8.250332 ACAAAATTGCGTTAATGGAGATGTAAT 58.750 29.630 0.00 0.00 0.00 1.89
1753 1772 0.320374 GATCACCCTCGTTCACACCA 59.680 55.000 0.00 0.00 0.00 4.17
1806 1825 1.282157 GGCTAGCTTCTCCTTTTCCCA 59.718 52.381 15.72 0.00 0.00 4.37
1809 1828 2.421775 GCAAGGCTAGCTTCTCCTTTTC 59.578 50.000 15.72 0.12 38.08 2.29
1827 1846 4.001248 CGCAATCCTCTTGGGCAA 57.999 55.556 0.00 0.00 34.39 4.52
1902 1921 1.652012 GTTGCTGCGCTTGTTACCA 59.348 52.632 9.73 0.00 0.00 3.25
1920 1939 2.643232 GCTTGCTCCTTGCCCTTGG 61.643 63.158 0.00 0.00 42.00 3.61
1924 1943 2.109126 CGTAGCTTGCTCCTTGCCC 61.109 63.158 0.00 0.00 42.00 5.36
2054 2073 5.977129 ACGTCAATAAAAGCCAAAGTGAAAG 59.023 36.000 0.00 0.00 0.00 2.62
2085 2104 1.469251 GCCTTGCAGCATCACATCTTG 60.469 52.381 0.00 0.00 0.00 3.02
2101 2120 4.625311 GCAATTTAAACACGCATAAGCCTT 59.375 37.500 0.00 0.00 37.52 4.35
2312 2566 8.192068 TGACAATAACAATATGACCTAACACG 57.808 34.615 0.00 0.00 0.00 4.49
2313 2567 9.769093 GTTGACAATAACAATATGACCTAACAC 57.231 33.333 0.00 0.00 0.00 3.32
2332 2590 7.853437 CACGACATATTAACAAAGTGTTGACAA 59.147 33.333 3.90 0.00 41.30 3.18
2334 2592 6.302313 GCACGACATATTAACAAAGTGTTGAC 59.698 38.462 3.90 0.00 41.30 3.18
2356 2614 5.448360 GCAGAGAACATCAAAATAGGAGCAC 60.448 44.000 0.00 0.00 0.00 4.40
2388 2646 7.566879 AGAAAACAGATATGAGATCCCTACACT 59.433 37.037 0.00 0.00 0.00 3.55
2517 3290 0.318869 TGTGCATTTTCAGCAAGCGG 60.319 50.000 0.00 0.00 44.64 5.52
2553 3326 8.357402 AGTTAAACTGCCAAATTTAAAGACGAT 58.643 29.630 0.00 0.00 33.31 3.73
2554 3327 7.708998 AGTTAAACTGCCAAATTTAAAGACGA 58.291 30.769 0.00 0.00 33.31 4.20
2555 3328 7.860872 AGAGTTAAACTGCCAAATTTAAAGACG 59.139 33.333 0.00 0.00 33.31 4.18
2556 3329 8.968242 CAGAGTTAAACTGCCAAATTTAAAGAC 58.032 33.333 0.00 0.00 33.31 3.01
2624 3411 2.167487 TGCAACCCAGAAAACAACCTTC 59.833 45.455 0.00 0.00 0.00 3.46
2673 3461 2.478370 CCACTGCATTTACAAGATGGCG 60.478 50.000 0.00 0.00 0.00 5.69
2769 3560 3.078196 TATGGAACTGCGGGCGGA 61.078 61.111 6.47 0.00 0.00 5.54
2852 3643 8.163516 GTGAAAAGTAAGAGCGAGAAAAGATAC 58.836 37.037 0.00 0.00 0.00 2.24
2854 3645 6.931840 AGTGAAAAGTAAGAGCGAGAAAAGAT 59.068 34.615 0.00 0.00 0.00 2.40
2879 3670 4.543689 TCTAGGGGAGCTCTATTTTCGAA 58.456 43.478 14.64 0.00 0.00 3.71
2963 3793 3.073798 TGATGTCCTTCCAGTTGCCTTTA 59.926 43.478 0.00 0.00 0.00 1.85
2965 3795 1.425066 TGATGTCCTTCCAGTTGCCTT 59.575 47.619 0.00 0.00 0.00 4.35
3059 3935 2.023223 CGGACGTGGTACAAACCCG 61.023 63.158 0.00 0.00 46.16 5.28
3100 3976 0.758734 TCCTTCATATCCACCTGCGG 59.241 55.000 0.00 0.00 0.00 5.69
3133 4009 0.625849 CCTTGTTAGTGCCTCCCCAT 59.374 55.000 0.00 0.00 0.00 4.00
3150 4026 2.374504 CTCCATATCCAGGCACATTCCT 59.625 50.000 0.00 0.00 36.78 3.36
3151 4027 2.553904 CCTCCATATCCAGGCACATTCC 60.554 54.545 0.00 0.00 0.00 3.01
3184 4060 0.530744 TGTGCCGGACATGTCTACTC 59.469 55.000 24.50 14.70 0.00 2.59
3194 4070 1.402456 CGCCTACTATATGTGCCGGAC 60.402 57.143 5.05 0.46 0.00 4.79
3215 4091 9.750125 TTTGCCGCTCTATAATCTATATACATG 57.250 33.333 0.00 0.00 0.00 3.21
3282 4158 2.445682 AGTAGGGTTGCAACAACCAA 57.554 45.000 29.55 13.83 42.03 3.67
3301 4177 1.480212 CCCTCACACCACACCTGCTA 61.480 60.000 0.00 0.00 0.00 3.49
3355 4231 3.428725 GCTAGCAGAGATATCCCACATCG 60.429 52.174 10.63 0.00 0.00 3.84
3438 4318 1.552337 TCTCAAGAAGCTACAGCCAGG 59.448 52.381 0.00 0.00 43.38 4.45
3440 4320 1.066573 GCTCTCAAGAAGCTACAGCCA 60.067 52.381 0.00 0.00 43.38 4.75
3441 4321 1.650825 GCTCTCAAGAAGCTACAGCC 58.349 55.000 0.00 0.00 43.38 4.85
3443 4323 2.233431 ACAGGCTCTCAAGAAGCTACAG 59.767 50.000 0.00 0.00 0.00 2.74
3444 4324 2.028658 CACAGGCTCTCAAGAAGCTACA 60.029 50.000 0.00 0.00 0.00 2.74
3446 4326 1.066573 GCACAGGCTCTCAAGAAGCTA 60.067 52.381 0.00 0.00 36.96 3.32
3447 4327 0.321475 GCACAGGCTCTCAAGAAGCT 60.321 55.000 0.00 0.00 36.96 3.74
3449 4329 0.035881 TGGCACAGGCTCTCAAGAAG 59.964 55.000 0.00 0.00 40.87 2.85
3450 4330 2.144952 TGGCACAGGCTCTCAAGAA 58.855 52.632 0.00 0.00 40.87 2.52
3482 4362 4.813750 TGATGATGCAGACAGAAGAAGA 57.186 40.909 0.00 0.00 0.00 2.87
3484 4364 5.585047 CAGATTGATGATGCAGACAGAAGAA 59.415 40.000 0.00 0.00 0.00 2.52
3485 4365 5.116882 CAGATTGATGATGCAGACAGAAGA 58.883 41.667 0.00 0.00 0.00 2.87
3614 4526 1.472480 CTATCAAACCTGCCAAACCGG 59.528 52.381 0.00 0.00 38.11 5.28
3677 4589 4.080919 TCTGCATCCACTTACAGTGCTAAT 60.081 41.667 0.00 0.00 44.63 1.73
3689 4601 6.127054 TGCTTAACTACTAATCTGCATCCACT 60.127 38.462 0.00 0.00 0.00 4.00
3763 4676 5.370875 ACAGAGACGTAAGGTATACTCCT 57.629 43.478 2.25 0.00 46.39 3.69
3764 4677 6.127786 ACAAACAGAGACGTAAGGTATACTCC 60.128 42.308 2.25 0.00 46.39 3.85
3765 4678 6.850555 ACAAACAGAGACGTAAGGTATACTC 58.149 40.000 2.25 0.00 46.39 2.59
3766 4679 6.830873 ACAAACAGAGACGTAAGGTATACT 57.169 37.500 2.25 0.00 46.39 2.12
3767 4680 7.620806 GCAAACAAACAGAGACGTAAGGTATAC 60.621 40.741 0.00 0.00 46.39 1.47
3768 4681 6.366877 GCAAACAAACAGAGACGTAAGGTATA 59.633 38.462 0.00 0.00 46.39 1.47
3831 4744 3.495377 CACGGACGATCTAGAGTTCTAGG 59.505 52.174 14.47 3.63 44.60 3.02
3857 4770 3.176661 CATGTCCGTTCATGCGCA 58.823 55.556 14.96 14.96 38.65 6.09
3864 4784 0.602638 TCTGTGGTGCATGTCCGTTC 60.603 55.000 0.00 0.00 0.00 3.95
3944 4865 1.202651 GCAGGGCGGACACTATTACAT 60.203 52.381 0.00 0.00 0.00 2.29
3969 4890 9.430623 TCTTACAATCGTTCATTACAGAATCAA 57.569 29.630 0.00 0.00 0.00 2.57
4099 5023 3.134127 CGTAGCAGGCCCCTTTGC 61.134 66.667 6.59 6.59 40.57 3.68
4112 5036 2.369257 ATCAGCCGGTGGATGCGTAG 62.369 60.000 1.90 0.00 39.19 3.51
4113 5037 1.110518 TATCAGCCGGTGGATGCGTA 61.111 55.000 17.06 0.00 39.19 4.42
4114 5038 1.758440 ATATCAGCCGGTGGATGCGT 61.758 55.000 17.06 4.04 39.19 5.24
4115 5039 0.603707 AATATCAGCCGGTGGATGCG 60.604 55.000 17.06 0.00 39.19 4.73
4116 5040 1.609208 AAATATCAGCCGGTGGATGC 58.391 50.000 17.06 0.00 39.19 3.91
4117 5041 3.631686 TCAAAAATATCAGCCGGTGGATG 59.368 43.478 17.06 6.11 40.92 3.51
4118 5042 3.897239 TCAAAAATATCAGCCGGTGGAT 58.103 40.909 1.90 9.31 0.00 3.41
4119 5043 3.358111 TCAAAAATATCAGCCGGTGGA 57.642 42.857 1.90 0.55 0.00 4.02
4120 5044 4.157656 TCTTTCAAAAATATCAGCCGGTGG 59.842 41.667 1.90 0.00 0.00 4.61
4121 5045 5.309323 TCTTTCAAAAATATCAGCCGGTG 57.691 39.130 1.90 0.00 0.00 4.94
4122 5046 5.652014 TGATCTTTCAAAAATATCAGCCGGT 59.348 36.000 1.90 0.00 0.00 5.28
4123 5047 6.135290 TGATCTTTCAAAAATATCAGCCGG 57.865 37.500 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.