Multiple sequence alignment - TraesCS2B01G545300

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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 TraesCS2B01G545300 chr2B 100.000 3533 0 0 1 3533 742173743 742170211 0.000000e+00 6525.0
1 TraesCS2B01G545300 chr2B 89.758 1904 159 22 661 2535 742110633 742108737 0.000000e+00 2403.0
2 TraesCS2B01G545300 chr2B 90.541 444 36 5 5 444 6041217 6041658 1.830000e-162 582.0
3 TraesCS2B01G545300 chr2B 89.111 450 41 5 4 450 760745802 760745358 1.430000e-153 553.0
4 TraesCS2B01G545300 chr2B 89.744 429 35 7 18 444 476379532 476379953 1.120000e-149 540.0
5 TraesCS2B01G545300 chr2B 86.916 107 13 1 2879 2984 579382230 579382124 6.200000e-23 119.0
6 TraesCS2B01G545300 chr2B 94.340 53 3 0 454 506 6042705 6042757 8.130000e-12 82.4
7 TraesCS2B01G545300 chr2B 91.379 58 5 0 452 509 36399490 36399433 2.920000e-11 80.5
8 TraesCS2B01G545300 chr2B 100.000 31 0 0 2627 2657 742108659 742108629 1.370000e-04 58.4
9 TraesCS2B01G545300 chr2D 93.711 2433 77 29 502 2886 608578903 608576499 0.000000e+00 3576.0
10 TraesCS2B01G545300 chr2D 91.376 1890 139 7 678 2545 608559721 608557834 0.000000e+00 2566.0
11 TraesCS2B01G545300 chr2D 92.760 442 21 5 2971 3405 608576356 608575919 2.310000e-176 628.0
12 TraesCS2B01G545300 chr2D 93.798 129 8 0 3405 3533 608574086 608573958 1.000000e-45 195.0
13 TraesCS2B01G545300 chr2D 94.643 56 3 0 451 506 130088557 130088612 1.750000e-13 87.9
14 TraesCS2B01G545300 chr2A 90.492 2356 171 30 502 2811 740143549 740141201 0.000000e+00 3061.0
15 TraesCS2B01G545300 chr2A 90.280 2356 176 30 502 2811 740119361 740117013 0.000000e+00 3033.0
16 TraesCS2B01G545300 chr2A 91.525 2065 148 15 502 2546 740079517 740077460 0.000000e+00 2819.0
17 TraesCS2B01G545300 chr2A 92.614 352 25 1 94 444 503472995 503473346 4.070000e-139 505.0
18 TraesCS2B01G545300 chr2A 84.956 226 11 6 2983 3203 740141076 740140869 1.290000e-49 207.0
19 TraesCS2B01G545300 chr2A 90.968 155 9 1 2983 3132 740116888 740116734 1.660000e-48 204.0
20 TraesCS2B01G545300 chr2A 92.453 106 7 1 2881 2985 710790676 710790781 2.200000e-32 150.0
21 TraesCS2B01G545300 chr7A 86.441 1947 222 26 745 2658 29009522 29007585 0.000000e+00 2095.0
22 TraesCS2B01G545300 chr7A 89.981 1607 159 1 1000 2604 563246816 563245210 0.000000e+00 2074.0
23 TraesCS2B01G545300 chr7A 87.387 111 13 1 2879 2988 8939321 8939431 3.700000e-25 126.0
24 TraesCS2B01G545300 chr7A 92.857 56 4 0 454 509 299325823 299325768 8.130000e-12 82.4
25 TraesCS2B01G545300 chr7D 89.436 1666 164 7 1000 2656 497320719 497319057 0.000000e+00 2091.0
26 TraesCS2B01G545300 chr4B 91.628 430 35 1 18 447 575831178 575830750 8.440000e-166 593.0
27 TraesCS2B01G545300 chr4B 91.163 430 37 1 18 447 575856142 575855714 1.830000e-162 582.0
28 TraesCS2B01G545300 chr4B 88.816 456 42 2 4 450 36613285 36612830 5.150000e-153 551.0
29 TraesCS2B01G545300 chr4B 93.103 58 4 0 452 509 575830675 575830618 6.280000e-13 86.1
30 TraesCS2B01G545300 chr4B 93.103 58 4 0 452 509 575855639 575855582 6.280000e-13 86.1
31 TraesCS2B01G545300 chr1B 89.755 449 43 3 1 447 92348783 92349230 3.960000e-159 571.0
32 TraesCS2B01G545300 chr1B 76.071 280 44 16 682 941 50900375 50900651 1.330000e-24 124.0
33 TraesCS2B01G545300 chr1B 75.540 278 46 15 682 941 50950277 50950550 2.230000e-22 117.0
34 TraesCS2B01G545300 chr5D 93.593 359 20 3 94 450 378672221 378671864 1.870000e-147 532.0
35 TraesCS2B01G545300 chr5D 92.157 357 24 4 94 447 488839688 488840043 5.270000e-138 501.0
36 TraesCS2B01G545300 chr5B 95.652 92 4 0 4 95 316375420 316375329 7.900000e-32 148.0
37 TraesCS2B01G545300 chr5B 86.239 109 14 1 2878 2985 672122391 672122283 2.230000e-22 117.0
38 TraesCS2B01G545300 chr1A 95.604 91 4 0 5 95 566353922 566353832 2.840000e-31 147.0
39 TraesCS2B01G545300 chr6B 87.273 110 13 1 2877 2985 705717440 705717331 1.330000e-24 124.0
40 TraesCS2B01G545300 chr6B 83.636 110 17 1 2879 2987 718239887 718239778 6.240000e-18 102.0
41 TraesCS2B01G545300 chr3D 87.850 107 12 1 2879 2984 66306953 66307059 1.330000e-24 124.0
42 TraesCS2B01G545300 chr6D 86.364 110 10 4 2879 2985 379228384 379228491 8.010000e-22 115.0
43 TraesCS2B01G545300 chr6D 96.364 55 2 0 452 506 83570453 83570507 1.350000e-14 91.6
44 TraesCS2B01G545300 chr6A 84.615 117 17 1 2870 2985 262946608 262946724 8.010000e-22 115.0
45 TraesCS2B01G545300 chr4A 96.429 56 1 1 452 506 578934394 578934449 1.350000e-14 91.6
46 TraesCS2B01G545300 chr3A 93.333 45 3 0 465 509 695773229 695773185 2.280000e-07 67.6


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 TraesCS2B01G545300 chr2B 742170211 742173743 3532 True 6525.000000 6525 100.0000 1 3533 1 chr2B.!!$R3 3532
1 TraesCS2B01G545300 chr2B 742108629 742110633 2004 True 1230.700000 2403 94.8790 661 2657 2 chr2B.!!$R5 1996
2 TraesCS2B01G545300 chr2B 6041217 6042757 1540 False 332.200000 582 92.4405 5 506 2 chr2B.!!$F2 501
3 TraesCS2B01G545300 chr2D 608557834 608559721 1887 True 2566.000000 2566 91.3760 678 2545 1 chr2D.!!$R1 1867
4 TraesCS2B01G545300 chr2D 608573958 608578903 4945 True 1466.333333 3576 93.4230 502 3533 3 chr2D.!!$R2 3031
5 TraesCS2B01G545300 chr2A 740077460 740079517 2057 True 2819.000000 2819 91.5250 502 2546 1 chr2A.!!$R1 2044
6 TraesCS2B01G545300 chr2A 740140869 740143549 2680 True 1634.000000 3061 87.7240 502 3203 2 chr2A.!!$R3 2701
7 TraesCS2B01G545300 chr2A 740116734 740119361 2627 True 1618.500000 3033 90.6240 502 3132 2 chr2A.!!$R2 2630
8 TraesCS2B01G545300 chr7A 29007585 29009522 1937 True 2095.000000 2095 86.4410 745 2658 1 chr7A.!!$R1 1913
9 TraesCS2B01G545300 chr7A 563245210 563246816 1606 True 2074.000000 2074 89.9810 1000 2604 1 chr7A.!!$R3 1604
10 TraesCS2B01G545300 chr7D 497319057 497320719 1662 True 2091.000000 2091 89.4360 1000 2656 1 chr7D.!!$R1 1656
11 TraesCS2B01G545300 chr4B 575830618 575831178 560 True 339.550000 593 92.3655 18 509 2 chr4B.!!$R2 491
12 TraesCS2B01G545300 chr4B 575855582 575856142 560 True 334.050000 582 92.1330 18 509 2 chr4B.!!$R3 491

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
646 1709 0.034337 ACGAACGGCACCACATAACT 59.966 50.000 0.0 0.0 0.0 2.24 F
1041 2177 1.004918 CACGTCCTTCTCCGCCTTT 60.005 57.895 0.0 0.0 0.0 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1524 2660 1.737735 CGTGACGAGCATTGCCTCA 60.738 57.895 0.0 1.15 0.0 3.86 R
2972 4237 0.038744 TCGAAACCTACTCCCTCCGT 59.961 55.000 0.0 0.00 0.0 4.69 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.070018 CAACTAGTCTTCCTGCCAACTG 58.930 50.000 0.00 0.00 0.00 3.16
34 35 2.821378 TCCTGCCAACTGAACATCAATG 59.179 45.455 0.00 0.00 0.00 2.82
60 61 6.987404 TGTGTGCAACTAGACTACATTACAAA 59.013 34.615 0.00 0.00 38.04 2.83
65 66 9.448438 TGCAACTAGACTACATTACAAATCAAT 57.552 29.630 0.00 0.00 0.00 2.57
135 136 4.458397 CACTACTAGATAGTTGGTCGGGA 58.542 47.826 0.00 0.00 41.71 5.14
152 153 4.519730 GTCGGGATAGTAGACTAGTTGCAT 59.480 45.833 0.00 0.00 32.58 3.96
155 156 6.946583 TCGGGATAGTAGACTAGTTGCATATT 59.053 38.462 0.00 0.00 0.00 1.28
288 289 7.442364 CAGTACTTTAGTTGCACCATATAGCAT 59.558 37.037 0.00 0.00 40.94 3.79
289 290 7.993183 AGTACTTTAGTTGCACCATATAGCATT 59.007 33.333 0.00 0.00 40.94 3.56
342 345 1.502231 CCATGCGGGATCTAGTTTCG 58.498 55.000 0.00 0.00 40.01 3.46
345 348 2.288961 TGCGGGATCTAGTTTCGAAC 57.711 50.000 0.00 0.00 0.00 3.95
365 368 2.223829 ACATCTCGTCACGATGAATCCC 60.224 50.000 7.79 0.00 40.47 3.85
564 1624 0.118952 AAAACCATCCATGCCCCCTT 59.881 50.000 0.00 0.00 0.00 3.95
590 1652 4.581824 AGTCCGGAGTATATGCGTAGAAAA 59.418 41.667 10.98 0.00 41.89 2.29
640 1703 1.400500 CCAATTAACGAACGGCACCAC 60.400 52.381 0.00 0.00 0.00 4.16
641 1704 1.264557 CAATTAACGAACGGCACCACA 59.735 47.619 0.00 0.00 0.00 4.17
646 1709 0.034337 ACGAACGGCACCACATAACT 59.966 50.000 0.00 0.00 0.00 2.24
653 1716 2.629051 GGCACCACATAACTGGTCTAC 58.371 52.381 0.00 0.00 43.15 2.59
666 1729 1.210234 TGGTCTACTCGGACGTATCCA 59.790 52.381 0.00 0.00 46.67 3.41
832 1911 2.474112 TCCACCTATATATTCCCCGCC 58.526 52.381 0.00 0.00 0.00 6.13
833 1912 1.489230 CCACCTATATATTCCCCGCCC 59.511 57.143 0.00 0.00 0.00 6.13
915 2026 1.375908 CTCCGGCAGCAAAGCTACA 60.376 57.895 0.00 0.00 36.40 2.74
949 2060 4.588528 TCATTAAGCCAAGCCTTCTTTGTT 59.411 37.500 0.00 0.00 0.00 2.83
950 2061 5.070313 TCATTAAGCCAAGCCTTCTTTGTTT 59.930 36.000 0.00 0.00 0.00 2.83
1041 2177 1.004918 CACGTCCTTCTCCGCCTTT 60.005 57.895 0.00 0.00 0.00 3.11
1794 2930 2.819019 TGGTCTTGTGCCAACATATGTG 59.181 45.455 9.63 3.84 35.83 3.21
1931 3067 1.271856 TGTATCTGCCCGGAGTTTCA 58.728 50.000 0.73 0.00 0.00 2.69
2007 3143 0.807496 GGCTTCTCACATGCCTTGAC 59.193 55.000 0.00 0.00 41.36 3.18
2053 3189 1.442857 CACCGACTGAGCGACTCAC 60.443 63.158 5.59 0.00 35.39 3.51
2061 3197 0.250945 TGAGCGACTCACTGGAGACT 60.251 55.000 5.59 0.00 44.26 3.24
2193 3329 2.657296 CGCACCTATGGTACCGCG 60.657 66.667 13.84 13.84 38.75 6.46
2356 3492 1.107114 GGAGAAGGATGCTGACGAGA 58.893 55.000 0.00 0.00 0.00 4.04
2394 3530 5.047566 TGGAGAATCTGAACAAAACTGGA 57.952 39.130 0.00 0.00 33.73 3.86
2547 3683 3.386726 TGGATTAAGTGGACGGACCTATG 59.613 47.826 0.00 0.00 39.86 2.23
2577 3713 6.073003 CCAAAAGTTCTAGGAGCTACACAAAG 60.073 42.308 0.00 0.00 0.00 2.77
2660 3814 3.606687 ACATGTGGTTCTTATTCCGACC 58.393 45.455 0.00 0.00 0.00 4.79
2664 3818 1.134907 TGGTTCTTATTCCGACCGAGC 60.135 52.381 0.00 0.00 34.90 5.03
2680 3834 7.547019 TCCGACCGAGCGTATATATATAATAGG 59.453 40.741 3.96 6.33 0.00 2.57
2681 3835 7.178741 CGACCGAGCGTATATATATAATAGGC 58.821 42.308 3.96 14.81 33.41 3.93
2784 3952 1.079127 AGTGACGAATCCTTGCCCG 60.079 57.895 0.00 0.00 0.00 6.13
2812 3980 8.573885 GCATCTCAATCAATCAAGAAATGGATA 58.426 33.333 0.00 0.00 0.00 2.59
2815 3983 9.074576 TCTCAATCAATCAAGAAATGGATATGG 57.925 33.333 0.00 0.00 0.00 2.74
2816 3984 8.999905 TCAATCAATCAAGAAATGGATATGGA 57.000 30.769 0.00 0.00 0.00 3.41
2817 3985 9.596308 TCAATCAATCAAGAAATGGATATGGAT 57.404 29.630 0.00 0.00 0.00 3.41
2846 4077 7.274447 TCCATTTCGTAATAAGTTATTCGGGT 58.726 34.615 11.41 3.96 0.00 5.28
2886 4117 2.302157 CTCCGTTGGTTTCTACTCCCTT 59.698 50.000 0.00 0.00 0.00 3.95
2887 4118 2.301009 TCCGTTGGTTTCTACTCCCTTC 59.699 50.000 0.00 0.00 0.00 3.46
2888 4119 2.038033 CCGTTGGTTTCTACTCCCTTCA 59.962 50.000 0.00 0.00 0.00 3.02
2891 4122 4.760204 CGTTGGTTTCTACTCCCTTCATTT 59.240 41.667 0.00 0.00 0.00 2.32
2892 4123 5.334879 CGTTGGTTTCTACTCCCTTCATTTG 60.335 44.000 0.00 0.00 0.00 2.32
2893 4124 5.576563 TGGTTTCTACTCCCTTCATTTGA 57.423 39.130 0.00 0.00 0.00 2.69
2896 4127 7.010160 TGGTTTCTACTCCCTTCATTTGAAAT 58.990 34.615 0.00 0.00 33.07 2.17
2899 4130 9.841880 GTTTCTACTCCCTTCATTTGAAATTAC 57.158 33.333 0.00 0.00 33.07 1.89
2900 4131 9.807921 TTTCTACTCCCTTCATTTGAAATTACT 57.192 29.630 0.00 0.00 33.07 2.24
2901 4132 9.807921 TTCTACTCCCTTCATTTGAAATTACTT 57.192 29.630 0.00 0.00 33.07 2.24
2904 4135 7.886338 ACTCCCTTCATTTGAAATTACTTGTC 58.114 34.615 0.00 0.00 33.07 3.18
2907 4138 9.581289 TCCCTTCATTTGAAATTACTTGTCTTA 57.419 29.630 0.00 0.00 33.07 2.10
2955 4220 8.818141 AAATACGACTAGATACATCCATTGTG 57.182 34.615 0.00 0.00 39.48 3.33
2956 4221 4.621991 ACGACTAGATACATCCATTGTGC 58.378 43.478 0.00 0.00 39.48 4.57
2958 4223 4.556699 CGACTAGATACATCCATTGTGCGA 60.557 45.833 0.00 0.00 39.48 5.10
2959 4224 4.621991 ACTAGATACATCCATTGTGCGAC 58.378 43.478 0.00 0.00 39.48 5.19
2960 4225 3.541996 AGATACATCCATTGTGCGACA 57.458 42.857 0.00 0.00 39.48 4.35
2962 4227 3.811497 AGATACATCCATTGTGCGACATG 59.189 43.478 0.00 0.00 39.48 3.21
2963 4228 1.825090 ACATCCATTGTGCGACATGT 58.175 45.000 0.00 0.00 37.11 3.21
2965 4230 3.342719 ACATCCATTGTGCGACATGTAA 58.657 40.909 0.00 0.00 37.11 2.41
2968 4233 4.614555 TCCATTGTGCGACATGTAATTC 57.385 40.909 0.00 0.00 0.00 2.17
2969 4234 3.376859 TCCATTGTGCGACATGTAATTCC 59.623 43.478 0.00 0.00 0.00 3.01
2970 4235 3.353524 CATTGTGCGACATGTAATTCCG 58.646 45.455 0.00 0.00 0.00 4.30
2972 4237 2.689646 TGTGCGACATGTAATTCCGAA 58.310 42.857 0.00 0.00 0.00 4.30
2974 4239 1.656594 TGCGACATGTAATTCCGAACG 59.343 47.619 0.00 0.00 0.00 3.95
2975 4240 1.005347 GCGACATGTAATTCCGAACGG 60.005 52.381 6.94 6.94 0.00 4.44
2976 4241 2.532235 CGACATGTAATTCCGAACGGA 58.468 47.619 12.04 12.04 43.52 4.69
2977 4242 2.534349 CGACATGTAATTCCGAACGGAG 59.466 50.000 15.34 5.60 46.06 4.63
2978 4243 2.864343 GACATGTAATTCCGAACGGAGG 59.136 50.000 15.34 0.00 46.06 4.30
2979 4244 2.210116 CATGTAATTCCGAACGGAGGG 58.790 52.381 15.34 0.00 46.06 4.30
2990 4279 0.893447 AACGGAGGGAGTAGGTTTCG 59.107 55.000 0.00 0.00 0.00 3.46
3214 4509 1.000145 GCAAAGGAGGAACGATCGAC 59.000 55.000 24.34 14.73 0.00 4.20
3222 4517 2.163010 GAGGAACGATCGACCTGTGTAA 59.837 50.000 30.74 0.00 33.89 2.41
3227 4522 4.182693 ACGATCGACCTGTGTAATTTCA 57.817 40.909 24.34 0.00 0.00 2.69
3241 4536 9.764870 CTGTGTAATTTCATGTTTGAGTATGAG 57.235 33.333 0.00 0.00 35.01 2.90
3307 4602 7.553044 AGTTCCTAGAGGCAATATTTTGTACAC 59.447 37.037 0.00 0.00 35.17 2.90
3313 4608 7.081976 AGAGGCAATATTTTGTACACGTTTTC 58.918 34.615 0.00 0.00 35.17 2.29
3327 4622 1.647702 CGTTTTCTAAGCGTCCGACTC 59.352 52.381 0.00 0.00 0.00 3.36
3333 4628 0.524862 TAAGCGTCCGACTCCTTGAC 59.475 55.000 10.08 0.00 0.00 3.18
3335 4630 2.952245 CGTCCGACTCCTTGACGT 59.048 61.111 0.00 0.00 44.96 4.34
3336 4631 1.154263 CGTCCGACTCCTTGACGTC 60.154 63.158 9.11 9.11 44.96 4.34
3337 4632 1.575576 CGTCCGACTCCTTGACGTCT 61.576 60.000 17.92 0.00 44.96 4.18
3338 4633 1.446907 GTCCGACTCCTTGACGTCTA 58.553 55.000 17.92 8.49 32.34 2.59
3339 4634 1.397692 GTCCGACTCCTTGACGTCTAG 59.602 57.143 18.52 18.52 32.34 2.43
3368 4663 6.430451 CACTCGAAAAGTATCAAAACAGCTT 58.570 36.000 0.00 0.00 36.07 3.74
3376 4671 8.962884 AAAGTATCAAAACAGCTTGGATTTTT 57.037 26.923 0.00 0.00 0.00 1.94
3379 4674 5.612725 TCAAAACAGCTTGGATTTTTCCT 57.387 34.783 0.00 0.00 0.00 3.36
3388 4683 1.186200 GGATTTTTCCTGGAGCCCAC 58.814 55.000 0.00 0.00 0.00 4.61
3391 4686 0.260230 TTTTTCCTGGAGCCCACACA 59.740 50.000 0.00 0.00 0.00 3.72
3393 4688 0.038166 TTTCCTGGAGCCCACACATC 59.962 55.000 0.00 0.00 0.00 3.06
3416 6544 1.153369 CATCTACACCCACCGCTGG 60.153 63.158 0.00 0.00 37.29 4.85
3430 6558 4.431131 CTGGCCGCATGGGGAAGT 62.431 66.667 31.50 0.00 35.78 3.01
3435 6563 1.524621 CCGCATGGGGAAGTAGCAG 60.525 63.158 23.98 0.00 0.00 4.24
3439 6567 1.308216 ATGGGGAAGTAGCAGCCCT 60.308 57.895 0.00 0.00 41.72 5.19
3453 6581 2.308690 CAGCCCTACTAGTACTCCCAC 58.691 57.143 0.00 0.00 0.00 4.61
3479 6607 3.728373 AACCAGTCCCCCATCCGC 61.728 66.667 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.623811 TGGCAGGAAGACTAGTTGGAC 59.376 52.381 0.00 0.00 0.00 4.02
2 3 2.039084 AGTTGGCAGGAAGACTAGTTGG 59.961 50.000 0.00 0.00 0.00 3.77
24 25 3.968649 AGTTGCACACACATTGATGTTC 58.031 40.909 0.00 0.00 39.39 3.18
34 35 5.924254 TGTAATGTAGTCTAGTTGCACACAC 59.076 40.000 0.00 0.00 0.00 3.82
60 61 7.604549 TGCACAGACATTGATGTTTAATTGAT 58.395 30.769 0.00 0.00 41.95 2.57
65 66 6.389830 AGTTGCACAGACATTGATGTTTAA 57.610 33.333 0.00 0.00 41.95 1.52
79 80 2.826128 TGTCCCTAGTCTAGTTGCACAG 59.174 50.000 6.15 0.00 0.00 3.66
152 153 9.675464 CAACCTACCAACCATAAGAACTTAATA 57.325 33.333 0.00 0.00 0.00 0.98
155 156 5.941647 GCAACCTACCAACCATAAGAACTTA 59.058 40.000 0.00 0.00 0.00 2.24
161 162 4.434713 GTTGCAACCTACCAACCATAAG 57.565 45.455 19.15 0.00 36.27 1.73
224 225 3.896648 ACTACATGGTGCAACTTTTCG 57.103 42.857 2.04 0.00 36.74 3.46
225 226 5.941948 AGTACTACATGGTGCAACTTTTC 57.058 39.130 2.04 0.00 36.74 2.29
342 345 3.487574 GGATTCATCGTGACGAGATGTTC 59.512 47.826 14.71 9.20 44.20 3.18
345 348 2.223805 TGGGATTCATCGTGACGAGATG 60.224 50.000 14.71 8.10 44.95 2.90
354 357 0.611200 TTCACCGTGGGATTCATCGT 59.389 50.000 0.00 0.00 0.00 3.73
365 368 1.790755 TCAGATCCGTTTTCACCGTG 58.209 50.000 0.00 0.00 0.00 4.94
429 432 8.532977 GTGTTACTCACATTTATTTTGGCATT 57.467 30.769 0.00 0.00 45.51 3.56
447 1429 5.236478 GCTTGTTACTCACATGTGTGTTACT 59.764 40.000 32.63 17.63 45.76 2.24
564 1624 2.854963 ACGCATATACTCCGGACTACA 58.145 47.619 0.00 0.00 0.00 2.74
596 1658 1.464997 CCGTCTGGCTGCTAAAGTTTC 59.535 52.381 0.00 0.00 0.00 2.78
640 1703 2.681848 ACGTCCGAGTAGACCAGTTATG 59.318 50.000 0.00 0.00 32.91 1.90
641 1704 2.996631 ACGTCCGAGTAGACCAGTTAT 58.003 47.619 0.00 0.00 32.91 1.89
646 1709 1.959042 GGATACGTCCGAGTAGACCA 58.041 55.000 0.00 0.00 34.13 4.02
666 1729 3.890756 TGGTCAACATGTGCTTTCAATCT 59.109 39.130 0.00 0.00 0.00 2.40
769 1836 2.668632 GCGTTGGATGGGTCCTGA 59.331 61.111 0.00 0.00 45.32 3.86
832 1911 4.082245 GTGAATGGAGTTGGTATTTGGTGG 60.082 45.833 0.00 0.00 0.00 4.61
833 1912 4.082245 GGTGAATGGAGTTGGTATTTGGTG 60.082 45.833 0.00 0.00 0.00 4.17
915 2026 4.778213 TGGCTTAATGAAGTGGAGCTAT 57.222 40.909 0.00 0.00 34.90 2.97
1074 2210 1.613317 ATGCACGGACATCTTCGGGA 61.613 55.000 0.00 0.00 30.32 5.14
1524 2660 1.737735 CGTGACGAGCATTGCCTCA 60.738 57.895 0.00 1.15 0.00 3.86
1735 2871 2.693069 CATGACCTCGAGAAGCTTTGT 58.307 47.619 15.71 0.14 0.00 2.83
2007 3143 1.795525 CGGACGTAGAGACATGTGCAG 60.796 57.143 1.15 0.00 0.00 4.41
2053 3189 2.885894 GGTACTCCGGATTAGTCTCCAG 59.114 54.545 3.57 0.00 34.78 3.86
2356 3492 2.038269 CCATTAGCACGCGGTTGGT 61.038 57.895 12.47 9.06 0.00 3.67
2394 3530 2.226437 CGTGTGTGCAAGATAAGCCTTT 59.774 45.455 0.00 0.00 0.00 3.11
2547 3683 2.437413 CTCCTAGAACTTTTGGCACCC 58.563 52.381 0.00 0.00 0.00 4.61
2660 3814 7.299787 TCGGCCTATTATATATATACGCTCG 57.700 40.000 0.00 7.81 0.00 5.03
2680 3834 3.251004 CCTTTTACAGCCTTGATATCGGC 59.749 47.826 12.38 12.38 46.65 5.54
2681 3835 4.451900 ACCTTTTACAGCCTTGATATCGG 58.548 43.478 0.00 0.00 0.00 4.18
2784 3952 6.475727 CCATTTCTTGATTGATTGAGATGCAC 59.524 38.462 0.00 0.00 0.00 4.57
2829 3997 8.496707 TCCTTTTGACCCGAATAACTTATTAC 57.503 34.615 0.00 0.00 0.00 1.89
2830 3998 8.323567 ACTCCTTTTGACCCGAATAACTTATTA 58.676 33.333 0.00 0.00 0.00 0.98
2868 4099 3.396260 TGAAGGGAGTAGAAACCAACG 57.604 47.619 0.00 0.00 0.00 4.10
2935 4200 3.670523 CGCACAATGGATGTATCTAGTCG 59.329 47.826 0.00 0.00 41.46 4.18
2937 4202 4.099419 TGTCGCACAATGGATGTATCTAGT 59.901 41.667 0.00 0.00 41.46 2.57
2941 4206 3.561310 ACATGTCGCACAATGGATGTATC 59.439 43.478 0.00 0.00 41.46 2.24
2948 4213 3.694734 GGAATTACATGTCGCACAATGG 58.305 45.455 0.00 0.00 0.00 3.16
2949 4214 3.063316 TCGGAATTACATGTCGCACAATG 59.937 43.478 0.00 0.00 0.00 2.82
2952 4217 2.371910 TCGGAATTACATGTCGCACA 57.628 45.000 0.00 0.00 0.00 4.57
2953 4218 2.534150 CGTTCGGAATTACATGTCGCAC 60.534 50.000 0.00 0.00 0.00 5.34
2954 4219 1.656594 CGTTCGGAATTACATGTCGCA 59.343 47.619 0.00 0.00 0.00 5.10
2955 4220 1.005347 CCGTTCGGAATTACATGTCGC 60.005 52.381 0.00 0.00 0.00 5.19
2956 4221 2.532235 TCCGTTCGGAATTACATGTCG 58.468 47.619 11.66 0.00 0.00 4.35
2958 4223 2.419574 CCCTCCGTTCGGAATTACATGT 60.420 50.000 14.79 2.69 33.41 3.21
2959 4224 2.159014 TCCCTCCGTTCGGAATTACATG 60.159 50.000 14.79 0.00 33.41 3.21
2960 4225 2.102588 CTCCCTCCGTTCGGAATTACAT 59.897 50.000 14.79 0.00 33.41 2.29
2962 4227 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2963 4228 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2965 4230 1.400737 CTACTCCCTCCGTTCGGAAT 58.599 55.000 14.79 2.09 33.41 3.01
2968 4233 0.969409 AACCTACTCCCTCCGTTCGG 60.969 60.000 4.74 4.74 0.00 4.30
2969 4234 0.893447 AAACCTACTCCCTCCGTTCG 59.107 55.000 0.00 0.00 0.00 3.95
2970 4235 1.135170 CGAAACCTACTCCCTCCGTTC 60.135 57.143 0.00 0.00 0.00 3.95
2972 4237 0.038744 TCGAAACCTACTCCCTCCGT 59.961 55.000 0.00 0.00 0.00 4.69
2974 4239 2.140839 TCTCGAAACCTACTCCCTCC 57.859 55.000 0.00 0.00 0.00 4.30
2975 4240 2.362717 CCATCTCGAAACCTACTCCCTC 59.637 54.545 0.00 0.00 0.00 4.30
2976 4241 2.389715 CCATCTCGAAACCTACTCCCT 58.610 52.381 0.00 0.00 0.00 4.20
2977 4242 1.202545 GCCATCTCGAAACCTACTCCC 60.203 57.143 0.00 0.00 0.00 4.30
2978 4243 1.480954 TGCCATCTCGAAACCTACTCC 59.519 52.381 0.00 0.00 0.00 3.85
2979 4244 2.427453 TCTGCCATCTCGAAACCTACTC 59.573 50.000 0.00 0.00 0.00 2.59
2990 4279 0.809241 CAGCTTCGGTCTGCCATCTC 60.809 60.000 0.00 0.00 34.09 2.75
3156 4450 5.155509 TGGACGCAAATTAAATCGATCAG 57.844 39.130 0.00 0.00 0.00 2.90
3214 4509 8.729756 TCATACTCAAACATGAAATTACACAGG 58.270 33.333 0.00 0.00 0.00 4.00
3222 4517 5.163723 CCACGCTCATACTCAAACATGAAAT 60.164 40.000 0.00 0.00 31.04 2.17
3227 4522 2.009774 GCCACGCTCATACTCAAACAT 58.990 47.619 0.00 0.00 0.00 2.71
3241 4536 1.266989 GATGCCCTAATTAAGCCACGC 59.733 52.381 5.04 0.00 0.00 5.34
3288 4583 6.569179 AAACGTGTACAAAATATTGCCTCT 57.431 33.333 0.00 0.00 40.34 3.69
3307 4602 1.647702 GAGTCGGACGCTTAGAAAACG 59.352 52.381 4.53 0.00 0.00 3.60
3313 4608 0.809385 TCAAGGAGTCGGACGCTTAG 59.191 55.000 11.61 2.44 0.00 2.18
3327 4622 0.531200 GTGGACCCTAGACGTCAAGG 59.469 60.000 19.50 16.76 31.55 3.61
3333 4628 1.171308 TTTCGAGTGGACCCTAGACG 58.829 55.000 0.00 0.00 0.00 4.18
3334 4629 2.561858 ACTTTTCGAGTGGACCCTAGAC 59.438 50.000 0.00 0.00 37.17 2.59
3335 4630 2.885616 ACTTTTCGAGTGGACCCTAGA 58.114 47.619 0.00 0.00 37.17 2.43
3336 4631 4.401519 TGATACTTTTCGAGTGGACCCTAG 59.598 45.833 0.00 0.00 39.48 3.02
3337 4632 4.346730 TGATACTTTTCGAGTGGACCCTA 58.653 43.478 0.00 0.00 39.48 3.53
3338 4633 3.170717 TGATACTTTTCGAGTGGACCCT 58.829 45.455 0.00 0.00 39.48 4.34
3339 4634 3.604875 TGATACTTTTCGAGTGGACCC 57.395 47.619 0.00 0.00 39.48 4.46
3368 4663 0.783206 TGGGCTCCAGGAAAAATCCA 59.217 50.000 0.00 0.00 0.00 3.41
3376 4671 1.538629 TGATGTGTGGGCTCCAGGA 60.539 57.895 0.00 0.00 32.34 3.86
3379 4674 1.985614 CTCTGATGTGTGGGCTCCA 59.014 57.895 0.00 0.00 0.00 3.86
3388 4683 2.169144 TGGGTGTAGATGCTCTGATGTG 59.831 50.000 0.00 0.00 0.00 3.21
3391 4686 1.765314 GGTGGGTGTAGATGCTCTGAT 59.235 52.381 0.00 0.00 0.00 2.90
3393 4688 0.179100 CGGTGGGTGTAGATGCTCTG 60.179 60.000 0.00 0.00 0.00 3.35
3416 6544 2.902343 GCTACTTCCCCATGCGGC 60.902 66.667 0.00 0.00 0.00 6.53
3425 6553 2.668625 ACTAGTAGGGCTGCTACTTCC 58.331 52.381 8.44 0.00 38.44 3.46
3427 6555 4.463070 GAGTACTAGTAGGGCTGCTACTT 58.537 47.826 1.87 0.00 38.44 2.24
3430 6558 2.107901 GGGAGTACTAGTAGGGCTGCTA 59.892 54.545 1.87 0.00 0.00 3.49
3435 6563 2.694109 CAAGTGGGAGTACTAGTAGGGC 59.306 54.545 1.87 0.00 0.00 5.19
3439 6567 5.512298 TGCATACAAGTGGGAGTACTAGTA 58.488 41.667 0.00 0.00 0.00 1.82
3453 6581 1.463674 GGGGACTGGTTGCATACAAG 58.536 55.000 0.00 0.00 36.16 3.16
3479 6607 9.663904 CATTTGTTGTATAATTTAGATGGACCG 57.336 33.333 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.