Multiple sequence alignment - TraesCS4D01G325800

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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 TraesCS4D01G325800 chr4D 100.000 3145 0 0 1 3145 485765510 485762366 0.000000e+00 5808.0
1 TraesCS4D01G325800 chr4D 84.451 1730 146 73 596 2246 485684112 485682427 0.000000e+00 1591.0
2 TraesCS4D01G325800 chr4D 91.111 315 27 1 2832 3145 478256616 478256302 2.900000e-115 425.0
3 TraesCS4D01G325800 chr4B 87.705 2009 158 30 662 2607 619659801 619657819 0.000000e+00 2259.0
4 TraesCS4D01G325800 chr4B 85.882 1870 130 59 669 2445 619788288 619786460 0.000000e+00 1868.0
5 TraesCS4D01G325800 chr4B 85.334 1616 141 54 583 2144 619590364 619588791 0.000000e+00 1583.0
6 TraesCS4D01G325800 chr4B 90.048 1045 68 13 1232 2257 619774639 619773612 0.000000e+00 1321.0
7 TraesCS4D01G325800 chr4B 91.781 949 60 2 1232 2174 619935509 619934573 0.000000e+00 1304.0
8 TraesCS4D01G325800 chr4B 90.513 917 57 14 352 1238 619936453 619935537 0.000000e+00 1184.0
9 TraesCS4D01G325800 chr4B 85.792 549 58 7 2287 2827 619934476 619933940 5.890000e-157 564.0
10 TraesCS4D01G325800 chr4B 95.294 255 12 0 87 341 619938304 619938050 3.780000e-109 405.0
11 TraesCS4D01G325800 chr4B 95.111 225 11 0 2603 2827 619648305 619648081 3.860000e-94 355.0
12 TraesCS4D01G325800 chr5A 86.898 1641 113 51 583 2155 666589263 666587657 0.000000e+00 1746.0
13 TraesCS4D01G325800 chr5A 84.848 1617 150 59 583 2144 666526005 666524429 0.000000e+00 1541.0
14 TraesCS4D01G325800 chr5A 92.520 1016 56 8 1232 2235 666683440 666682433 0.000000e+00 1437.0
15 TraesCS4D01G325800 chr5A 92.342 888 55 7 362 1238 666684353 666683468 0.000000e+00 1251.0
16 TraesCS4D01G325800 chr5A 90.172 814 66 5 1232 2038 666656776 666655970 0.000000e+00 1048.0
17 TraesCS4D01G325800 chr5A 87.755 539 51 8 2286 2823 666679686 666679162 1.600000e-172 616.0
18 TraesCS4D01G325800 chr5A 82.479 605 46 29 669 1238 666657383 666656804 2.840000e-130 475.0
19 TraesCS4D01G325800 chr5A 91.797 256 17 4 86 341 666686217 666685966 1.390000e-93 353.0
20 TraesCS4D01G325800 chr5A 97.561 41 1 0 50 90 666686268 666686228 1.560000e-08 71.3
21 TraesCS4D01G325800 chr2D 91.720 314 24 2 2832 3145 476964592 476964281 4.820000e-118 435.0
22 TraesCS4D01G325800 chr2D 91.720 314 24 2 2832 3145 476967435 476967124 4.820000e-118 435.0
23 TraesCS4D01G325800 chr2D 91.720 314 25 1 2832 3145 476968383 476968071 4.820000e-118 435.0
24 TraesCS4D01G325800 chr2D 91.429 315 24 3 2832 3145 476965540 476965228 2.240000e-116 429.0
25 TraesCS4D01G325800 chr2D 91.401 314 26 1 2832 3145 476966488 476966176 2.240000e-116 429.0
26 TraesCS4D01G325800 chr5D 91.883 308 25 0 2836 3143 220670706 220670399 6.230000e-117 431.0
27 TraesCS4D01G325800 chr1D 91.401 314 27 0 2832 3145 28576684 28576997 6.230000e-117 431.0
28 TraesCS4D01G325800 chr1D 95.833 48 2 0 1 48 204991805 204991758 9.350000e-11 78.7
29 TraesCS4D01G325800 chr1D 95.833 48 1 1 1 48 50866411 50866365 3.360000e-10 76.8
30 TraesCS4D01G325800 chr3D 91.139 316 25 3 2832 3145 409020186 409019872 2.900000e-115 425.0
31 TraesCS4D01G325800 chr3D 97.917 48 1 0 1 48 582884496 582884543 2.010000e-12 84.2
32 TraesCS4D01G325800 chr6D 97.917 48 1 0 1 48 427226713 427226760 2.010000e-12 84.2
33 TraesCS4D01G325800 chr4A 97.917 48 1 0 1 48 248870482 248870435 2.010000e-12 84.2
34 TraesCS4D01G325800 chr1B 97.917 48 1 0 1 48 173116232 173116185 2.010000e-12 84.2
35 TraesCS4D01G325800 chr6A 95.833 48 1 1 1 48 9360692 9360738 3.360000e-10 76.8
36 TraesCS4D01G325800 chr2A 95.833 48 1 1 1 48 163044425 163044471 3.360000e-10 76.8
37 TraesCS4D01G325800 chr1A 95.833 48 1 1 1 48 554032915 554032869 3.360000e-10 76.8


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 TraesCS4D01G325800 chr4D 485762366 485765510 3144 True 5808.00 5808 100.0000 1 3145 1 chr4D.!!$R3 3144
1 TraesCS4D01G325800 chr4D 485682427 485684112 1685 True 1591.00 1591 84.4510 596 2246 1 chr4D.!!$R2 1650
2 TraesCS4D01G325800 chr4B 619657819 619659801 1982 True 2259.00 2259 87.7050 662 2607 1 chr4B.!!$R3 1945
3 TraesCS4D01G325800 chr4B 619786460 619788288 1828 True 1868.00 1868 85.8820 669 2445 1 chr4B.!!$R5 1776
4 TraesCS4D01G325800 chr4B 619588791 619590364 1573 True 1583.00 1583 85.3340 583 2144 1 chr4B.!!$R1 1561
5 TraesCS4D01G325800 chr4B 619773612 619774639 1027 True 1321.00 1321 90.0480 1232 2257 1 chr4B.!!$R4 1025
6 TraesCS4D01G325800 chr4B 619933940 619938304 4364 True 864.25 1304 90.8450 87 2827 4 chr4B.!!$R6 2740
7 TraesCS4D01G325800 chr5A 666587657 666589263 1606 True 1746.00 1746 86.8980 583 2155 1 chr5A.!!$R2 1572
8 TraesCS4D01G325800 chr5A 666524429 666526005 1576 True 1541.00 1541 84.8480 583 2144 1 chr5A.!!$R1 1561
9 TraesCS4D01G325800 chr5A 666655970 666657383 1413 True 761.50 1048 86.3255 669 2038 2 chr5A.!!$R3 1369
10 TraesCS4D01G325800 chr5A 666679162 666686268 7106 True 745.66 1437 92.3950 50 2823 5 chr5A.!!$R4 2773
11 TraesCS4D01G325800 chr2D 476964281 476968383 4102 True 432.60 435 91.5980 2832 3145 5 chr2D.!!$R1 313

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
290 308 0.878416 GGCAACGCTAACATGTCCAA 59.122 50.000 0.0 0.0 0.0 3.53 F
969 2678 2.027325 CAGCAAGACAAGCACAGCA 58.973 52.632 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1219 2978 1.702886 CTCACTGCGACGATGTTCTT 58.297 50.0 0.0 0.0 0.0 2.52 R
2828 7400 0.250901 AGGAGCCAAAACATCGCACT 60.251 50.0 0.0 0.0 0.0 4.40 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 7.696992 GTGGTGATCCAGTTTATAAGGAAAA 57.303 36.000 0.00 0.00 45.24 2.29
25 26 7.535997 GTGGTGATCCAGTTTATAAGGAAAAC 58.464 38.462 0.00 0.00 45.24 2.43
26 27 6.661805 TGGTGATCCAGTTTATAAGGAAAACC 59.338 38.462 14.11 14.11 39.55 3.27
27 28 6.183360 GGTGATCCAGTTTATAAGGAAAACCG 60.183 42.308 9.26 0.00 37.51 4.44
28 29 6.596497 GTGATCCAGTTTATAAGGAAAACCGA 59.404 38.462 0.00 0.00 37.51 4.69
29 30 7.120138 GTGATCCAGTTTATAAGGAAAACCGAA 59.880 37.037 0.00 0.00 37.51 4.30
30 31 7.832187 TGATCCAGTTTATAAGGAAAACCGAAT 59.168 33.333 0.00 0.00 37.51 3.34
31 32 7.619964 TCCAGTTTATAAGGAAAACCGAATC 57.380 36.000 0.00 0.00 37.51 2.52
32 33 6.314400 TCCAGTTTATAAGGAAAACCGAATCG 59.686 38.462 0.00 0.00 37.51 3.34
33 34 6.314400 CCAGTTTATAAGGAAAACCGAATCGA 59.686 38.462 3.36 0.00 37.51 3.59
34 35 7.148373 CCAGTTTATAAGGAAAACCGAATCGAA 60.148 37.037 3.36 0.00 37.51 3.71
35 36 8.231837 CAGTTTATAAGGAAAACCGAATCGAAA 58.768 33.333 3.36 0.00 37.51 3.46
36 37 8.785946 AGTTTATAAGGAAAACCGAATCGAAAA 58.214 29.630 3.36 0.00 37.51 2.29
37 38 8.843733 GTTTATAAGGAAAACCGAATCGAAAAC 58.156 33.333 3.36 0.00 31.94 2.43
38 39 3.909776 AGGAAAACCGAATCGAAAACC 57.090 42.857 3.36 1.11 0.00 3.27
39 40 3.483421 AGGAAAACCGAATCGAAAACCT 58.517 40.909 3.36 3.52 0.00 3.50
40 41 3.887110 AGGAAAACCGAATCGAAAACCTT 59.113 39.130 3.36 0.00 0.00 3.50
41 42 5.065235 AGGAAAACCGAATCGAAAACCTTA 58.935 37.500 3.36 0.00 0.00 2.69
42 43 5.532032 AGGAAAACCGAATCGAAAACCTTAA 59.468 36.000 3.36 0.00 0.00 1.85
43 44 6.039605 AGGAAAACCGAATCGAAAACCTTAAA 59.960 34.615 3.36 0.00 0.00 1.52
44 45 6.142798 GGAAAACCGAATCGAAAACCTTAAAC 59.857 38.462 3.36 0.00 0.00 2.01
45 46 5.754543 AACCGAATCGAAAACCTTAAACA 57.245 34.783 3.36 0.00 0.00 2.83
46 47 5.754543 ACCGAATCGAAAACCTTAAACAA 57.245 34.783 3.36 0.00 0.00 2.83
47 48 6.134040 ACCGAATCGAAAACCTTAAACAAA 57.866 33.333 3.36 0.00 0.00 2.83
48 49 6.562518 ACCGAATCGAAAACCTTAAACAAAA 58.437 32.000 3.36 0.00 0.00 2.44
56 57 8.905850 TCGAAAACCTTAAACAAAACCTATCTT 58.094 29.630 0.00 0.00 0.00 2.40
158 174 6.477688 CCCAATGTTGAATATGTGAGCATTTC 59.522 38.462 0.00 0.00 36.58 2.17
290 308 0.878416 GGCAACGCTAACATGTCCAA 59.122 50.000 0.00 0.00 0.00 3.53
310 328 7.770433 TGTCCAAATCAATTGATAGTAGTCCAG 59.230 37.037 21.00 3.93 41.85 3.86
347 365 2.322355 CCTGTCATAAGGGCACAGAG 57.678 55.000 2.29 0.00 40.07 3.35
396 2017 2.226962 TCTTAGGTACGGTGAAGGCT 57.773 50.000 0.00 0.00 0.00 4.58
425 2046 6.492087 TGGTTCGGTGAAAGGATAAAATTTCT 59.508 34.615 0.00 0.00 36.57 2.52
449 2070 7.922278 TCTGTTATTGCAATAAAGCATCAATCC 59.078 33.333 28.75 15.13 45.19 3.01
465 2086 2.819608 CAATCCGTTGAACAGACCCAAT 59.180 45.455 0.00 0.00 37.53 3.16
474 2095 3.631686 TGAACAGACCCAATGTGTTGAAG 59.368 43.478 0.00 0.00 44.49 3.02
501 2144 2.436417 TCAGCAGATGCAAGGTAAACC 58.564 47.619 7.68 0.00 45.16 3.27
657 2311 3.188048 GCCAAGAACAGACTCTGAATGTG 59.812 47.826 13.25 5.55 35.18 3.21
822 2480 2.357517 AGCACCGGTCGCTTTCTG 60.358 61.111 21.19 3.15 35.82 3.02
969 2678 2.027325 CAGCAAGACAAGCACAGCA 58.973 52.632 0.00 0.00 0.00 4.41
1207 2966 4.502016 TGGTACGTTACACACAAGAACAA 58.498 39.130 0.00 0.00 0.00 2.83
1208 2967 4.329528 TGGTACGTTACACACAAGAACAAC 59.670 41.667 0.00 0.00 0.00 3.32
1209 2968 4.329528 GGTACGTTACACACAAGAACAACA 59.670 41.667 0.00 0.00 0.00 3.33
1210 2969 5.163874 GGTACGTTACACACAAGAACAACAA 60.164 40.000 0.00 0.00 0.00 2.83
1219 2978 5.689514 CACACAAGAACAACAACTTCAAACA 59.310 36.000 0.00 0.00 0.00 2.83
1224 2983 7.169140 ACAAGAACAACAACTTCAAACAAGAAC 59.831 33.333 0.00 0.00 0.00 3.01
1228 2987 5.799936 ACAACAACTTCAAACAAGAACATCG 59.200 36.000 0.00 0.00 0.00 3.84
1631 3425 4.288398 AGATTGAGGAGATGAAGCAGAGA 58.712 43.478 0.00 0.00 0.00 3.10
1634 3428 3.639952 TGAGGAGATGAAGCAGAGATCA 58.360 45.455 0.00 0.00 0.00 2.92
1760 3581 1.292941 CCTCCTCCTCCTCCTCCTCA 61.293 65.000 0.00 0.00 0.00 3.86
1764 3585 0.476338 CTCCTCCTCCTCCTCATCGA 59.524 60.000 0.00 0.00 0.00 3.59
1765 3586 0.183971 TCCTCCTCCTCCTCATCGAC 59.816 60.000 0.00 0.00 0.00 4.20
1794 3615 3.245948 GACAACAGCAGCAGCCACG 62.246 63.158 0.00 0.00 43.56 4.94
1795 3616 2.974148 CAACAGCAGCAGCCACGA 60.974 61.111 0.00 0.00 43.56 4.35
1796 3617 2.974698 AACAGCAGCAGCCACGAC 60.975 61.111 0.00 0.00 43.56 4.34
1856 3677 4.430765 ATGGTCACCGTCGCGTCC 62.431 66.667 5.77 0.00 0.00 4.79
2248 6752 0.806868 TACGAACCTAGACGCCAGTG 59.193 55.000 0.00 0.00 0.00 3.66
2277 6781 7.151999 TGTTTGACATGACAGTTTGTAACTT 57.848 32.000 0.00 0.00 40.46 2.66
2342 6881 9.629878 TGTCAAACTTCAGGGTAAAAATAGTTA 57.370 29.630 0.00 0.00 0.00 2.24
2377 6916 3.262420 AGAATGTCTGTGGTGCGAATAC 58.738 45.455 0.00 0.00 0.00 1.89
2545 7117 0.105246 AGGAAACCATTGTGGGCCAA 60.105 50.000 8.40 0.00 43.37 4.52
2607 7179 1.096386 TTTGGCACACCGGTGTACAC 61.096 55.000 38.32 28.74 46.95 2.90
2608 7180 2.109387 GGCACACCGGTGTACACA 59.891 61.111 38.32 0.00 46.95 3.72
2616 7188 3.998341 ACACCGGTGTACACATTTGTATC 59.002 43.478 38.23 6.46 42.90 2.24
2617 7189 3.061563 CACCGGTGTACACATTTGTATCG 59.938 47.826 26.95 17.07 40.40 2.92
2618 7190 3.056678 ACCGGTGTACACATTTGTATCGA 60.057 43.478 26.51 0.00 40.40 3.59
2619 7191 4.116961 CCGGTGTACACATTTGTATCGAT 58.883 43.478 26.51 2.16 40.40 3.59
2637 7209 2.203153 GGACAATATGCCGCCGGT 60.203 61.111 4.45 0.00 0.00 5.28
2650 7222 0.806884 CGCCGGTATCGCCTTTTACA 60.807 55.000 1.90 0.00 34.25 2.41
2795 7367 8.897809 GTCGATGTTTGAAAATTTAATCAACGA 58.102 29.630 5.06 8.26 35.42 3.85
2827 7399 9.444600 TTCAACTATTTAAGCTAAACTTCGGAT 57.555 29.630 0.00 0.00 39.97 4.18
2831 7403 9.530633 ACTATTTAAGCTAAACTTCGGATAGTG 57.469 33.333 0.00 0.00 39.97 2.74
2832 7404 6.657836 TTTAAGCTAAACTTCGGATAGTGC 57.342 37.500 0.00 0.00 39.97 4.40
2833 7405 2.810650 AGCTAAACTTCGGATAGTGCG 58.189 47.619 0.00 0.00 0.00 5.34
2834 7406 2.426024 AGCTAAACTTCGGATAGTGCGA 59.574 45.455 0.00 0.00 38.78 5.10
2849 7421 1.810151 GTGCGATGTTTTGGCTCCTAA 59.190 47.619 0.00 0.00 0.00 2.69
2863 7435 3.325135 GGCTCCTAAGTGCATATGTACCT 59.675 47.826 18.92 10.03 34.10 3.08
2927 8447 1.354101 AAATCCCGCGGGTATATCCA 58.646 50.000 41.57 23.06 38.11 3.41
2940 8460 6.333416 CGGGTATATCCAGACATTCTATGTG 58.667 44.000 2.20 0.00 40.03 3.21
2966 9432 3.061563 GCACAAAGTTTCGGTGAAAAACC 59.938 43.478 9.60 0.00 46.60 3.27
2984 9450 5.687770 AAACCAAATTATTTGTGGCTTGC 57.312 34.783 15.40 0.00 38.98 4.01
2988 9454 4.562394 CCAAATTATTTGTGGCTTGCGTAG 59.438 41.667 15.40 0.00 38.98 3.51
2997 11358 4.320023 TGTGGCTTGCGTAGAAAAGATAA 58.680 39.130 0.00 0.00 0.00 1.75
3005 11366 7.750903 GCTTGCGTAGAAAAGATAAAGAAATGT 59.249 33.333 0.00 0.00 0.00 2.71
3094 11455 1.405105 TCACTGAAAGCTTTGTGCACC 59.595 47.619 18.30 0.99 45.94 5.01
3106 11467 2.877097 TGTGCACCCACATAGAATGT 57.123 45.000 15.69 0.00 46.51 2.71
3123 11484 0.818852 TGTCCGGATATACACGCGGA 60.819 55.000 7.81 0.00 0.00 5.54
3130 11491 4.208355 CGGATATACACGCGGAATTTTTG 58.792 43.478 12.47 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 6.661805 GGTTTTCCTTATAAACTGGATCACCA 59.338 38.462 11.75 0.00 39.40 4.17
4 5 6.713276 TCGGTTTTCCTTATAAACTGGATCA 58.287 36.000 0.00 0.00 40.57 2.92
5 6 7.619964 TTCGGTTTTCCTTATAAACTGGATC 57.380 36.000 0.00 0.00 40.57 3.36
6 7 7.012044 CGATTCGGTTTTCCTTATAAACTGGAT 59.988 37.037 0.00 0.00 40.91 3.41
7 8 6.314400 CGATTCGGTTTTCCTTATAAACTGGA 59.686 38.462 0.00 0.00 40.57 3.86
8 9 6.314400 TCGATTCGGTTTTCCTTATAAACTGG 59.686 38.462 6.18 0.00 40.57 4.00
9 10 7.298507 TCGATTCGGTTTTCCTTATAAACTG 57.701 36.000 6.18 0.00 41.20 3.16
10 11 7.910441 TTCGATTCGGTTTTCCTTATAAACT 57.090 32.000 6.18 0.00 36.12 2.66
11 12 8.843733 GTTTTCGATTCGGTTTTCCTTATAAAC 58.156 33.333 6.18 0.00 37.95 2.01
12 13 8.022550 GGTTTTCGATTCGGTTTTCCTTATAAA 58.977 33.333 6.18 0.00 37.95 1.40
13 14 7.391275 AGGTTTTCGATTCGGTTTTCCTTATAA 59.609 33.333 6.18 0.00 37.95 0.98
14 15 6.880529 AGGTTTTCGATTCGGTTTTCCTTATA 59.119 34.615 6.18 0.00 37.95 0.98
15 16 5.708697 AGGTTTTCGATTCGGTTTTCCTTAT 59.291 36.000 6.18 0.00 37.95 1.73
16 17 5.065235 AGGTTTTCGATTCGGTTTTCCTTA 58.935 37.500 6.18 0.00 37.95 2.69
17 18 3.887110 AGGTTTTCGATTCGGTTTTCCTT 59.113 39.130 6.18 0.00 37.95 3.36
18 19 3.483421 AGGTTTTCGATTCGGTTTTCCT 58.517 40.909 6.18 5.72 37.95 3.36
19 20 3.909776 AGGTTTTCGATTCGGTTTTCC 57.090 42.857 6.18 3.63 0.00 3.13
20 21 6.692249 TGTTTAAGGTTTTCGATTCGGTTTTC 59.308 34.615 6.18 0.00 0.00 2.29
21 22 6.562518 TGTTTAAGGTTTTCGATTCGGTTTT 58.437 32.000 6.18 0.00 0.00 2.43
22 23 6.134040 TGTTTAAGGTTTTCGATTCGGTTT 57.866 33.333 6.18 0.00 0.00 3.27
23 24 5.754543 TGTTTAAGGTTTTCGATTCGGTT 57.245 34.783 6.18 0.00 0.00 4.44
24 25 5.754543 TTGTTTAAGGTTTTCGATTCGGT 57.245 34.783 6.18 0.00 0.00 4.69
25 26 6.074729 GGTTTTGTTTAAGGTTTTCGATTCGG 60.075 38.462 6.18 0.00 0.00 4.30
26 27 6.693978 AGGTTTTGTTTAAGGTTTTCGATTCG 59.306 34.615 0.00 0.00 0.00 3.34
27 28 7.997107 AGGTTTTGTTTAAGGTTTTCGATTC 57.003 32.000 0.00 0.00 0.00 2.52
28 29 9.687210 GATAGGTTTTGTTTAAGGTTTTCGATT 57.313 29.630 0.00 0.00 0.00 3.34
29 30 9.074576 AGATAGGTTTTGTTTAAGGTTTTCGAT 57.925 29.630 0.00 0.00 0.00 3.59
30 31 8.454570 AGATAGGTTTTGTTTAAGGTTTTCGA 57.545 30.769 0.00 0.00 0.00 3.71
359 1980 6.890268 ACCTAAGAAACAAAGTTTCTCCTGTT 59.110 34.615 21.31 10.87 37.75 3.16
373 1994 3.555586 GCCTTCACCGTACCTAAGAAACA 60.556 47.826 0.00 0.00 0.00 2.83
374 1995 2.998670 GCCTTCACCGTACCTAAGAAAC 59.001 50.000 0.00 0.00 0.00 2.78
396 2017 1.070105 CCTTTCACCGAACCACCGA 59.930 57.895 0.00 0.00 0.00 4.69
425 2046 6.696583 CGGATTGATGCTTTATTGCAATAACA 59.303 34.615 27.44 22.86 46.61 2.41
449 2070 1.946768 ACACATTGGGTCTGTTCAACG 59.053 47.619 0.00 0.00 0.00 4.10
465 2086 2.634453 TGCTGATCTCTCCTTCAACACA 59.366 45.455 0.00 0.00 0.00 3.72
474 2095 2.485903 CTTGCATCTGCTGATCTCTCC 58.514 52.381 2.65 0.00 42.66 3.71
501 2144 6.634436 GTGAATTCTTTAGTGCACTTTCACAG 59.366 38.462 34.00 19.37 40.67 3.66
657 2311 1.659098 CGTCATCCTTGTTCGGCTTAC 59.341 52.381 0.00 0.00 0.00 2.34
759 2413 0.727398 GTGCCGGCTTTACTTAGCAG 59.273 55.000 29.70 0.00 43.02 4.24
969 2678 1.513158 CTCCAAGTGCTCGATCGGT 59.487 57.895 16.41 0.00 0.00 4.69
1028 2758 1.403814 GTCCTGATCGACCTCCATGA 58.596 55.000 0.00 0.00 0.00 3.07
1122 2852 2.839486 TGATGTCGAAGTGGAGCTTT 57.161 45.000 0.00 0.00 37.59 3.51
1207 2966 5.560966 ACGATGTTCTTGTTTGAAGTTGT 57.439 34.783 0.00 0.00 0.00 3.32
1208 2967 4.666176 CGACGATGTTCTTGTTTGAAGTTG 59.334 41.667 0.00 0.00 0.00 3.16
1209 2968 4.785341 GCGACGATGTTCTTGTTTGAAGTT 60.785 41.667 0.00 0.00 0.00 2.66
1210 2969 3.303132 GCGACGATGTTCTTGTTTGAAGT 60.303 43.478 0.00 0.00 0.00 3.01
1219 2978 1.702886 CTCACTGCGACGATGTTCTT 58.297 50.000 0.00 0.00 0.00 2.52
1385 3173 3.083349 CTCCGGATGGCCCTGTCA 61.083 66.667 3.57 0.00 34.14 3.58
1613 3407 3.637694 CTGATCTCTGCTTCATCTCCTCA 59.362 47.826 0.00 0.00 0.00 3.86
1631 3425 2.360350 CCACCGTTGCTGCCTGAT 60.360 61.111 0.00 0.00 0.00 2.90
1634 3428 3.246112 TACCCACCGTTGCTGCCT 61.246 61.111 0.00 0.00 0.00 4.75
1777 3598 3.282157 CGTGGCTGCTGCTGTTGT 61.282 61.111 15.64 0.00 39.59 3.32
1798 3619 4.647615 CTATCCTGGGCGCGTCCG 62.648 72.222 26.87 19.37 34.94 4.79
1799 3620 4.971125 GCTATCCTGGGCGCGTCC 62.971 72.222 26.05 26.05 0.00 4.79
1812 3633 2.419297 CGTCTGCTTCCTTCTTGGCTAT 60.419 50.000 0.00 0.00 35.26 2.97
1856 3677 4.700365 TGCGGCAGAGACGACGTG 62.700 66.667 4.58 0.00 35.20 4.49
2046 3870 3.258372 TCATTTAGCCAGTCGAACACTCT 59.742 43.478 0.00 0.00 30.26 3.24
2176 4007 6.064717 ACCATCTACTCTGCTTCAAGTTTTT 58.935 36.000 0.00 0.00 0.00 1.94
2248 6752 6.092748 ACAAACTGTCATGTCAAACAAAGAC 58.907 36.000 0.00 8.31 37.57 3.01
2277 6781 5.300034 CCATAAGTTGATTCATTGCAGGCTA 59.700 40.000 0.00 0.00 0.00 3.93
2362 6901 2.029739 TCTTTCGTATTCGCACCACAGA 60.030 45.455 0.00 0.00 36.96 3.41
2417 6965 6.880484 TCCTCGCATACCTCTTTAATGTTTA 58.120 36.000 0.00 0.00 0.00 2.01
2419 6967 5.353394 TCCTCGCATACCTCTTTAATGTT 57.647 39.130 0.00 0.00 0.00 2.71
2429 6977 0.261991 TCTCCCTTCCTCGCATACCT 59.738 55.000 0.00 0.00 0.00 3.08
2510 7082 4.152580 GGTTTCCTCATCGTTCTCAAGTTC 59.847 45.833 0.00 0.00 0.00 3.01
2587 7159 0.393944 TGTACACCGGTGTGCCAAAA 60.394 50.000 43.17 26.43 46.86 2.44
2594 7166 2.335316 ACAAATGTGTACACCGGTGT 57.665 45.000 39.83 39.83 46.87 4.16
2607 7179 6.317088 GGCATATTGTCCATCGATACAAATG 58.683 40.000 15.68 17.80 38.95 2.32
2608 7180 5.122239 CGGCATATTGTCCATCGATACAAAT 59.878 40.000 15.68 9.22 38.95 2.32
2616 7188 1.868997 GGCGGCATATTGTCCATCG 59.131 57.895 3.07 0.00 0.00 3.84
2617 7189 1.577328 CCGGCGGCATATTGTCCATC 61.577 60.000 15.42 0.00 0.00 3.51
2618 7190 1.600636 CCGGCGGCATATTGTCCAT 60.601 57.895 15.42 0.00 0.00 3.41
2619 7191 1.687297 TACCGGCGGCATATTGTCCA 61.687 55.000 28.71 0.00 0.00 4.02
2773 7345 9.410556 CTCCTCGTTGATTAAATTTTCAAACAT 57.589 29.630 6.83 0.00 33.90 2.71
2792 7364 4.870991 GCTTAAATAGTTGAAGCTCCTCGT 59.129 41.667 4.82 0.00 41.89 4.18
2827 7399 1.003118 AGGAGCCAAAACATCGCACTA 59.997 47.619 0.00 0.00 0.00 2.74
2828 7400 0.250901 AGGAGCCAAAACATCGCACT 60.251 50.000 0.00 0.00 0.00 4.40
2829 7401 1.448985 TAGGAGCCAAAACATCGCAC 58.551 50.000 0.00 0.00 0.00 5.34
2830 7402 2.083774 CTTAGGAGCCAAAACATCGCA 58.916 47.619 0.00 0.00 0.00 5.10
2831 7403 2.084546 ACTTAGGAGCCAAAACATCGC 58.915 47.619 0.00 0.00 0.00 4.58
2832 7404 2.159517 GCACTTAGGAGCCAAAACATCG 60.160 50.000 0.00 0.00 0.00 3.84
2833 7405 2.819608 TGCACTTAGGAGCCAAAACATC 59.180 45.455 0.00 0.00 0.00 3.06
2834 7406 2.875296 TGCACTTAGGAGCCAAAACAT 58.125 42.857 0.00 0.00 0.00 2.71
2892 8412 5.674989 CGGGATTTTTGTTCCGAATTTTTG 58.325 37.500 0.00 0.00 44.69 2.44
2940 8460 1.130955 CACCGAAACTTTGTGCATGC 58.869 50.000 11.82 11.82 0.00 4.06
2966 9432 5.398169 TCTACGCAAGCCACAAATAATTTG 58.602 37.500 0.00 0.00 44.11 2.32
2968 9434 5.637006 TTCTACGCAAGCCACAAATAATT 57.363 34.783 0.00 0.00 45.62 1.40
2972 9438 3.568007 TCTTTTCTACGCAAGCCACAAAT 59.432 39.130 0.00 0.00 45.62 2.32
2976 9442 4.939509 TTATCTTTTCTACGCAAGCCAC 57.060 40.909 0.00 0.00 45.62 5.01
3016 11377 7.341256 AGACAATTTCTGATGCCTCATTACAAT 59.659 33.333 0.00 0.00 31.12 2.71
3078 11439 0.459489 GTGGGTGCACAAAGCTTTCA 59.541 50.000 20.43 1.41 45.94 2.69
3083 11444 1.533625 TCTATGTGGGTGCACAAAGC 58.466 50.000 20.43 6.10 45.96 3.51
3094 11455 6.100004 GTGTATATCCGGACATTCTATGTGG 58.900 44.000 6.12 0.00 45.03 4.17
3106 11467 1.250328 ATTCCGCGTGTATATCCGGA 58.750 50.000 6.61 6.61 46.94 5.14


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

AutoCloner maintained by Alex Coulton.