Multiple sequence alignment - TraesCS7B01G012300

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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 TraesCS7B01G012300 chr7B 100.000 5292 0 0 1 5292 8363004 8368295 0.000000e+00 9773.0
1 TraesCS7B01G012300 chr7B 93.803 355 14 6 5 353 699820893 699821245 1.310000e-145 527.0
2 TraesCS7B01G012300 chr7B 88.095 168 16 3 4412 4576 8365636 8365802 4.180000e-46 196.0
3 TraesCS7B01G012300 chr7B 88.095 168 16 3 2633 2799 8367415 8367579 4.180000e-46 196.0
4 TraesCS7B01G012300 chr7A 95.462 2402 45 9 1082 3420 71047118 71049518 0.000000e+00 3773.0
5 TraesCS7B01G012300 chr7A 97.561 1886 34 4 3418 5292 71049819 71051703 0.000000e+00 3217.0
6 TraesCS7B01G012300 chr7A 91.092 2043 132 25 801 2803 58641209 58643241 0.000000e+00 2719.0
7 TraesCS7B01G012300 chr7A 88.694 1884 125 35 3445 5292 58832463 58834294 0.000000e+00 2218.0
8 TraesCS7B01G012300 chr7A 90.041 1687 110 18 3039 4687 58804494 58806160 0.000000e+00 2132.0
9 TraesCS7B01G012300 chr7A 96.497 571 13 4 347 915 71046531 71047096 0.000000e+00 937.0
10 TraesCS7B01G012300 chr7A 82.345 776 99 22 3496 4258 58376388 58377138 1.610000e-179 640.0
11 TraesCS7B01G012300 chr7A 83.615 592 90 3 1651 2240 58643532 58644118 2.790000e-152 549.0
12 TraesCS7B01G012300 chr7A 94.085 355 18 3 1 353 21753983 21754336 2.170000e-148 536.0
13 TraesCS7B01G012300 chr7A 86.486 481 52 10 915 1391 58375863 58376334 2.830000e-142 516.0
14 TraesCS7B01G012300 chr7A 88.557 402 43 2 3040 3441 58375971 58376369 7.970000e-133 484.0
15 TraesCS7B01G012300 chr7A 86.396 419 46 4 941 1359 58804416 58804823 1.050000e-121 448.0
16 TraesCS7B01G012300 chr7A 83.991 431 56 4 3837 4267 58642234 58642651 8.260000e-108 401.0
17 TraesCS7B01G012300 chr7A 88.690 168 17 2 2633 2799 71050821 71050987 2.500000e-48 204.0
18 TraesCS7B01G012300 chr7D 89.045 2136 121 36 2446 4507 54719389 54717293 0.000000e+00 2543.0
19 TraesCS7B01G012300 chr7D 92.341 1632 99 10 840 2447 54722071 54720442 0.000000e+00 2298.0
20 TraesCS7B01G012300 chr7D 89.238 1273 94 14 3039 4272 55088155 55086887 0.000000e+00 1552.0
21 TraesCS7B01G012300 chr7D 93.684 665 24 4 4646 5292 54717297 54716633 0.000000e+00 979.0
22 TraesCS7B01G012300 chr7D 81.872 844 93 29 3451 4272 54597843 54597038 0.000000e+00 656.0
23 TraesCS7B01G012300 chr7D 83.249 591 63 19 807 1387 54598426 54597862 1.310000e-140 510.0
24 TraesCS7B01G012300 chr7D 84.688 529 48 13 4390 4912 55086590 55086089 1.020000e-136 497.0
25 TraesCS7B01G012300 chr7D 83.269 520 73 7 845 1362 55088327 55087820 2.890000e-127 466.0
26 TraesCS7B01G012300 chr7D 81.588 554 97 3 1760 2313 54597502 54596954 2.250000e-123 453.0
27 TraesCS7B01G012300 chr7D 86.318 402 52 2 3040 3441 54598221 54597823 8.140000e-118 435.0
28 TraesCS7B01G012300 chr7D 85.176 425 50 4 3846 4270 54721076 54720665 1.760000e-114 424.0
29 TraesCS7B01G012300 chr7D 81.312 503 78 9 1787 2275 55087341 55086841 1.380000e-105 394.0
30 TraesCS7B01G012300 chr7D 87.291 299 38 0 1064 1362 54718751 54718453 5.070000e-90 342.0
31 TraesCS7B01G012300 chr7D 91.803 122 5 5 4388 4507 54596747 54596629 1.180000e-36 165.0
32 TraesCS7B01G012300 chr7D 78.857 175 19 6 2633 2806 55086568 55086411 9.380000e-18 102.0
33 TraesCS7B01G012300 chr7D 95.918 49 2 0 801 849 54732878 54732830 4.390000e-11 80.5
34 TraesCS7B01G012300 chr2A 94.167 360 17 4 1 357 12648979 12648621 3.600000e-151 545.0
35 TraesCS7B01G012300 chr5B 94.085 355 13 6 5 353 676247312 676247664 2.810000e-147 532.0
36 TraesCS7B01G012300 chr5B 93.768 353 16 6 5 355 542698321 542698669 4.690000e-145 525.0
37 TraesCS7B01G012300 chr5B 100.000 28 0 0 1105 1132 540734641 540734668 1.000000e-02 52.8
38 TraesCS7B01G012300 chrUn 93.557 357 15 6 5 355 4345932 4345578 4.690000e-145 525.0
39 TraesCS7B01G012300 chrUn 93.557 357 15 6 5 355 131818520 131818874 4.690000e-145 525.0
40 TraesCS7B01G012300 chrUn 93.557 357 15 6 5 355 378240272 378239918 4.690000e-145 525.0
41 TraesCS7B01G012300 chrUn 93.277 357 16 6 5 355 123975057 123974703 2.180000e-143 520.0
42 TraesCS7B01G012300 chr1D 79.514 288 40 16 2322 2600 426179882 426179605 2.520000e-43 187.0


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 TraesCS7B01G012300 chr7B 8363004 8368295 5291 False 3388.333333 9773 92.063333 1 5292 3 chr7B.!!$F2 5291
1 TraesCS7B01G012300 chr7A 58832463 58834294 1831 False 2218.000000 2218 88.694000 3445 5292 1 chr7A.!!$F2 1847
2 TraesCS7B01G012300 chr7A 71046531 71051703 5172 False 2032.750000 3773 94.552500 347 5292 4 chr7A.!!$F6 4945
3 TraesCS7B01G012300 chr7A 58804416 58806160 1744 False 1290.000000 2132 88.218500 941 4687 2 chr7A.!!$F5 3746
4 TraesCS7B01G012300 chr7A 58641209 58644118 2909 False 1223.000000 2719 86.232667 801 4267 3 chr7A.!!$F4 3466
5 TraesCS7B01G012300 chr7A 58375863 58377138 1275 False 546.666667 640 85.796000 915 4258 3 chr7A.!!$F3 3343
6 TraesCS7B01G012300 chr7D 54716633 54722071 5438 True 1317.200000 2543 89.507400 840 5292 5 chr7D.!!$R3 4452
7 TraesCS7B01G012300 chr7D 55086089 55088327 2238 True 602.200000 1552 83.472800 845 4912 5 chr7D.!!$R4 4067
8 TraesCS7B01G012300 chr7D 54596629 54598426 1797 True 443.800000 656 84.966000 807 4507 5 chr7D.!!$R2 3700

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
110 111 0.030101 GAGGCGATGAGGACGAGAAG 59.970 60.000 0.0 0.0 0.00 2.85 F
171 172 0.109504 GGCTTATTCGCGCCAAAACA 60.110 50.000 0.0 0.0 45.59 2.83 F
1685 1728 0.039527 GGCGTCGAACCAAAATTGCT 60.040 50.000 0.0 0.0 0.00 3.91 F
2685 3821 0.237235 TTTGGCTCGATGTGTTTCGC 59.763 50.000 0.0 0.0 38.97 4.70 F
3071 4228 1.345089 CCAGATGATCTCCTGCTCCTG 59.655 57.143 0.0 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1044 1051 0.398381 GGACCAGGAGCAGGAGATCT 60.398 60.000 0.00 0.0 0.00 2.75 R
1856 1899 1.075748 GGGAAGCAGGGCATCCATT 60.076 57.895 13.68 0.0 46.70 3.16 R
3618 5116 1.490574 CCCTAGGAGGACTGAGTTGG 58.509 60.000 11.48 0.0 37.67 3.77 R
3729 5230 0.396060 GCCTTTTTGGTGGCCATTGA 59.604 50.000 9.72 0.0 43.11 2.57 R
4839 6656 0.321919 TGCTGAAGGGATGCAGTGTC 60.322 55.000 0.00 0.0 34.66 3.67 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
37 38 2.699073 CGTGAGGCATCAATGGAGG 58.301 57.895 0.92 0.00 37.14 4.30
43 44 2.412605 GCATCAATGGAGGCTGACC 58.587 57.895 0.00 0.00 46.80 4.02
44 45 1.442526 GCATCAATGGAGGCTGACCG 61.443 60.000 0.00 0.00 46.80 4.79
45 46 0.816825 CATCAATGGAGGCTGACCGG 60.817 60.000 0.00 0.00 42.76 5.28
46 47 2.615227 ATCAATGGAGGCTGACCGGC 62.615 60.000 0.00 0.00 42.76 6.13
47 48 4.473520 AATGGAGGCTGACCGGCG 62.474 66.667 0.00 0.00 44.22 6.46
73 74 4.424566 CGCGGCAGCTTTGGCATT 62.425 61.111 7.38 0.00 42.32 3.56
74 75 2.812178 GCGGCAGCTTTGGCATTG 60.812 61.111 0.00 0.00 41.70 2.82
75 76 2.964174 CGGCAGCTTTGGCATTGA 59.036 55.556 0.46 0.00 41.70 2.57
76 77 1.514087 CGGCAGCTTTGGCATTGAT 59.486 52.632 0.46 0.00 41.70 2.57
77 78 0.108520 CGGCAGCTTTGGCATTGATT 60.109 50.000 0.46 0.00 41.70 2.57
78 79 1.648504 GGCAGCTTTGGCATTGATTC 58.351 50.000 0.00 0.00 41.70 2.52
79 80 1.066716 GGCAGCTTTGGCATTGATTCA 60.067 47.619 0.00 0.00 41.70 2.57
80 81 1.997606 GCAGCTTTGGCATTGATTCAC 59.002 47.619 0.00 0.00 41.70 3.18
81 82 2.613691 CAGCTTTGGCATTGATTCACC 58.386 47.619 0.00 0.00 41.70 4.02
82 83 1.203052 AGCTTTGGCATTGATTCACCG 59.797 47.619 0.00 0.00 41.70 4.94
83 84 1.632422 CTTTGGCATTGATTCACCGC 58.368 50.000 0.00 0.00 0.00 5.68
84 85 0.109365 TTTGGCATTGATTCACCGCG 60.109 50.000 0.00 0.00 0.00 6.46
85 86 1.932011 TTGGCATTGATTCACCGCGG 61.932 55.000 26.86 26.86 0.00 6.46
86 87 2.408835 GCATTGATTCACCGCGGG 59.591 61.111 31.76 18.67 0.00 6.13
87 88 2.112198 GCATTGATTCACCGCGGGA 61.112 57.895 31.76 20.83 0.00 5.14
88 89 1.653094 GCATTGATTCACCGCGGGAA 61.653 55.000 31.76 27.61 0.00 3.97
89 90 0.808125 CATTGATTCACCGCGGGAAA 59.192 50.000 31.76 22.80 0.00 3.13
90 91 0.808755 ATTGATTCACCGCGGGAAAC 59.191 50.000 31.76 25.31 0.00 2.78
101 102 4.110493 GGGAAACGAGGCGATGAG 57.890 61.111 0.00 0.00 0.00 2.90
102 103 1.521681 GGGAAACGAGGCGATGAGG 60.522 63.158 0.00 0.00 0.00 3.86
103 104 1.515954 GGAAACGAGGCGATGAGGA 59.484 57.895 0.00 0.00 0.00 3.71
104 105 0.806492 GGAAACGAGGCGATGAGGAC 60.806 60.000 0.00 0.00 0.00 3.85
105 106 1.140407 GAAACGAGGCGATGAGGACG 61.140 60.000 0.00 0.00 0.00 4.79
106 107 1.592400 AAACGAGGCGATGAGGACGA 61.592 55.000 0.00 0.00 0.00 4.20
107 108 1.994507 AACGAGGCGATGAGGACGAG 61.995 60.000 0.00 0.00 0.00 4.18
108 109 2.180862 CGAGGCGATGAGGACGAGA 61.181 63.158 0.00 0.00 0.00 4.04
109 110 1.715862 CGAGGCGATGAGGACGAGAA 61.716 60.000 0.00 0.00 0.00 2.87
110 111 0.030101 GAGGCGATGAGGACGAGAAG 59.970 60.000 0.00 0.00 0.00 2.85
111 112 1.066587 GGCGATGAGGACGAGAAGG 59.933 63.158 0.00 0.00 0.00 3.46
112 113 1.066587 GCGATGAGGACGAGAAGGG 59.933 63.158 0.00 0.00 0.00 3.95
113 114 1.736586 CGATGAGGACGAGAAGGGG 59.263 63.158 0.00 0.00 0.00 4.79
114 115 1.443828 GATGAGGACGAGAAGGGGC 59.556 63.158 0.00 0.00 0.00 5.80
115 116 2.356818 GATGAGGACGAGAAGGGGCG 62.357 65.000 0.00 0.00 0.00 6.13
116 117 2.754658 GAGGACGAGAAGGGGCGA 60.755 66.667 0.00 0.00 0.00 5.54
117 118 2.756283 AGGACGAGAAGGGGCGAG 60.756 66.667 0.00 0.00 0.00 5.03
118 119 2.754658 GGACGAGAAGGGGCGAGA 60.755 66.667 0.00 0.00 0.00 4.04
119 120 2.490685 GACGAGAAGGGGCGAGAC 59.509 66.667 0.00 0.00 0.00 3.36
120 121 3.398353 GACGAGAAGGGGCGAGACG 62.398 68.421 0.00 0.00 0.00 4.18
121 122 3.132139 CGAGAAGGGGCGAGACGA 61.132 66.667 0.00 0.00 0.00 4.20
122 123 2.802106 GAGAAGGGGCGAGACGAG 59.198 66.667 0.00 0.00 0.00 4.18
123 124 3.418744 GAGAAGGGGCGAGACGAGC 62.419 68.421 0.00 0.00 0.00 5.03
167 168 3.871574 GCGGCTTATTCGCGCCAA 61.872 61.111 0.00 0.00 46.62 4.52
168 169 2.788581 CGGCTTATTCGCGCCAAA 59.211 55.556 0.00 0.00 46.62 3.28
169 170 1.135731 CGGCTTATTCGCGCCAAAA 59.864 52.632 0.00 0.00 46.62 2.44
170 171 1.131618 CGGCTTATTCGCGCCAAAAC 61.132 55.000 0.00 0.00 46.62 2.43
171 172 0.109504 GGCTTATTCGCGCCAAAACA 60.110 50.000 0.00 0.00 45.59 2.83
172 173 1.259316 GCTTATTCGCGCCAAAACAG 58.741 50.000 0.00 0.00 0.00 3.16
173 174 1.401018 GCTTATTCGCGCCAAAACAGT 60.401 47.619 0.00 0.00 0.00 3.55
174 175 2.920647 GCTTATTCGCGCCAAAACAGTT 60.921 45.455 0.00 0.00 0.00 3.16
175 176 2.604969 TATTCGCGCCAAAACAGTTC 57.395 45.000 0.00 0.00 0.00 3.01
176 177 0.385473 ATTCGCGCCAAAACAGTTCG 60.385 50.000 0.00 0.00 0.00 3.95
177 178 2.975167 TTCGCGCCAAAACAGTTCGC 62.975 55.000 0.00 6.96 42.05 4.70
178 179 2.729491 GCGCCAAAACAGTTCGCC 60.729 61.111 0.00 0.00 39.91 5.54
179 180 2.050442 CGCCAAAACAGTTCGCCC 60.050 61.111 0.00 0.00 0.00 6.13
180 181 2.338620 GCCAAAACAGTTCGCCCC 59.661 61.111 0.00 0.00 0.00 5.80
181 182 2.642700 CCAAAACAGTTCGCCCCG 59.357 61.111 0.00 0.00 0.00 5.73
182 183 2.642700 CAAAACAGTTCGCCCCGG 59.357 61.111 0.00 0.00 0.00 5.73
183 184 3.292159 AAAACAGTTCGCCCCGGC 61.292 61.111 0.00 0.00 37.85 6.13
248 249 4.056125 GCTGTTTTCGGCCCAGGC 62.056 66.667 0.00 0.00 45.68 4.85
259 260 3.518068 CCCAGGCCGGCGAAAATC 61.518 66.667 22.54 4.96 0.00 2.17
260 261 3.876198 CCAGGCCGGCGAAAATCG 61.876 66.667 22.54 2.78 43.89 3.34
265 266 3.573491 CCGGCGAAAATCGGGCTC 61.573 66.667 9.30 0.00 42.32 4.70
266 267 3.573491 CGGCGAAAATCGGGCTCC 61.573 66.667 0.00 0.00 40.84 4.70
267 268 2.124695 GGCGAAAATCGGGCTCCT 60.125 61.111 1.64 0.00 40.84 3.69
268 269 2.472909 GGCGAAAATCGGGCTCCTG 61.473 63.158 1.64 0.00 40.84 3.86
269 270 2.472909 GCGAAAATCGGGCTCCTGG 61.473 63.158 1.64 0.00 40.84 4.45
270 271 1.819632 CGAAAATCGGGCTCCTGGG 60.820 63.158 0.00 0.00 36.00 4.45
271 272 1.453928 GAAAATCGGGCTCCTGGGG 60.454 63.158 0.00 0.00 0.00 4.96
272 273 2.911221 GAAAATCGGGCTCCTGGGGG 62.911 65.000 0.00 0.00 0.00 5.40
280 281 4.087892 CTCCTGGGGGCACGACTG 62.088 72.222 0.00 0.00 0.00 3.51
289 290 3.284449 GCACGACTGGGCCGTTTT 61.284 61.111 0.00 0.00 38.29 2.43
290 291 2.841160 GCACGACTGGGCCGTTTTT 61.841 57.895 0.00 0.00 38.29 1.94
386 387 1.411246 GGGGGAAAACAACTTGTGACC 59.589 52.381 0.00 0.20 0.00 4.02
400 401 2.712709 TGTGACCGAAAACCTTCACAA 58.287 42.857 0.86 0.00 44.09 3.33
404 405 3.103007 GACCGAAAACCTTCACAAAACG 58.897 45.455 0.00 0.00 0.00 3.60
450 451 3.546724 TCGTCACAAGGGTTTTCATCAA 58.453 40.909 0.00 0.00 0.00 2.57
555 556 2.294074 TCTTTGTTTGTGAGGGGAACG 58.706 47.619 0.00 0.00 0.00 3.95
562 563 0.682852 TGTGAGGGGAACGAACGAAT 59.317 50.000 0.14 0.00 0.00 3.34
705 706 6.048509 GGGGTTGTATAAATGCAAATTCTGG 58.951 40.000 0.00 0.00 34.26 3.86
997 1004 4.215399 CCAAAGCTAGGTTTTCGTGAATCA 59.785 41.667 17.04 0.00 0.00 2.57
1044 1051 2.525124 ATGGACGGACCTGCAACCA 61.525 57.895 0.00 0.00 39.86 3.67
1387 1394 1.070914 TGTTGCGGTATGACAACCTCA 59.929 47.619 3.66 1.85 44.38 3.86
1553 1596 2.669569 CCTGGTGGTGTTGGCTCG 60.670 66.667 0.00 0.00 0.00 5.03
1634 1677 2.634940 TCCTCAAGAACCTCAACCTCAG 59.365 50.000 0.00 0.00 0.00 3.35
1647 1690 0.773644 ACCTCAGCAATGGTCACCTT 59.226 50.000 0.00 0.00 29.18 3.50
1681 1724 1.862602 GCCTGGCGTCGAACCAAAAT 61.863 55.000 1.35 0.00 36.56 1.82
1685 1728 0.039527 GGCGTCGAACCAAAATTGCT 60.040 50.000 0.00 0.00 0.00 3.91
1707 1750 5.511729 GCTGTGCGGTTTAGATTTGATAAAC 59.488 40.000 0.97 0.97 40.71 2.01
1711 1754 7.081976 GTGCGGTTTAGATTTGATAAACAACT 58.918 34.615 9.91 0.00 42.37 3.16
1916 1959 4.729918 GCAGGTGTGGGAGGCAGG 62.730 72.222 0.00 0.00 0.00 4.85
1920 1963 2.439156 GTGTGGGAGGCAGGCATC 60.439 66.667 0.00 0.00 0.00 3.91
2130 2173 4.597507 AGAGACAAGATGTTCACCCCTTTA 59.402 41.667 0.00 0.00 0.00 1.85
2134 2177 4.772100 ACAAGATGTTCACCCCTTTATTGG 59.228 41.667 0.00 0.00 0.00 3.16
2157 2200 0.901114 AGTCAATGCCATTGCTGCCA 60.901 50.000 12.62 0.00 40.05 4.92
2396 2443 5.530915 TGATTTACCTGCACATACTAATGCC 59.469 40.000 0.00 0.00 41.33 4.40
2576 3678 8.868522 AGAAGAACAATGAAACATGGAATCTA 57.131 30.769 0.00 0.00 0.00 1.98
2685 3821 0.237235 TTTGGCTCGATGTGTTTCGC 59.763 50.000 0.00 0.00 38.97 4.70
2726 3866 2.904434 ACGTCCCTCCAGTTTCAATAGT 59.096 45.455 0.00 0.00 0.00 2.12
3071 4228 1.345089 CCAGATGATCTCCTGCTCCTG 59.655 57.143 0.00 0.00 0.00 3.86
3271 4428 3.918220 CGACGATTGCTGGCGCTC 61.918 66.667 7.64 0.00 36.97 5.03
3540 5038 3.692406 GGTGTCCTCCTCGGCGTT 61.692 66.667 6.85 0.00 0.00 4.84
3729 5230 1.479709 CTCGAGACCCTTGACCTCAT 58.520 55.000 6.58 0.00 0.00 2.90
3942 5493 3.618997 GCGGATGGTAGAAGAACTTTCCA 60.619 47.826 0.00 0.00 36.48 3.53
3961 5512 2.569404 CCAGTTCAAGGTCTAGGAAGCT 59.431 50.000 0.00 0.00 0.00 3.74
4232 5785 0.320421 CGAGTGGTTTCCGTCATGGT 60.320 55.000 0.00 0.00 39.52 3.55
4839 6656 1.523154 TAGCCCTTGCAAAAGTGGCG 61.523 55.000 17.92 5.40 46.67 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 0.816825 CTCCATTGATGCCTCACGGG 60.817 60.000 6.75 4.77 38.36 5.28
18 19 0.816825 CCTCCATTGATGCCTCACGG 60.817 60.000 0.00 0.00 0.00 4.94
19 20 1.442526 GCCTCCATTGATGCCTCACG 61.443 60.000 0.00 0.00 0.00 4.35
20 21 0.106819 AGCCTCCATTGATGCCTCAC 60.107 55.000 0.00 0.00 33.08 3.51
21 22 0.106868 CAGCCTCCATTGATGCCTCA 60.107 55.000 0.00 0.00 33.08 3.86
22 23 0.182061 TCAGCCTCCATTGATGCCTC 59.818 55.000 0.00 0.00 33.08 4.70
23 24 0.106819 GTCAGCCTCCATTGATGCCT 60.107 55.000 0.00 0.00 33.08 4.75
24 25 1.105759 GGTCAGCCTCCATTGATGCC 61.106 60.000 0.00 0.00 33.08 4.40
25 26 1.442526 CGGTCAGCCTCCATTGATGC 61.443 60.000 0.00 0.00 32.84 3.91
26 27 0.816825 CCGGTCAGCCTCCATTGATG 60.817 60.000 0.00 0.00 0.00 3.07
27 28 1.528824 CCGGTCAGCCTCCATTGAT 59.471 57.895 0.00 0.00 0.00 2.57
28 29 2.989639 CCGGTCAGCCTCCATTGA 59.010 61.111 0.00 0.00 0.00 2.57
29 30 2.825836 GCCGGTCAGCCTCCATTG 60.826 66.667 1.90 0.00 0.00 2.82
30 31 4.473520 CGCCGGTCAGCCTCCATT 62.474 66.667 1.90 0.00 0.00 3.16
56 57 4.424566 AATGCCAAAGCTGCCGCG 62.425 61.111 0.00 0.00 42.32 6.46
57 58 2.567564 ATCAATGCCAAAGCTGCCGC 62.568 55.000 0.00 0.00 40.80 6.53
58 59 0.108520 AATCAATGCCAAAGCTGCCG 60.109 50.000 0.00 0.00 40.80 5.69
59 60 1.066716 TGAATCAATGCCAAAGCTGCC 60.067 47.619 0.00 0.00 40.80 4.85
60 61 1.997606 GTGAATCAATGCCAAAGCTGC 59.002 47.619 0.00 0.00 40.80 5.25
61 62 2.613691 GGTGAATCAATGCCAAAGCTG 58.386 47.619 0.00 0.00 40.80 4.24
62 63 1.203052 CGGTGAATCAATGCCAAAGCT 59.797 47.619 0.00 0.00 40.80 3.74
63 64 1.632422 CGGTGAATCAATGCCAAAGC 58.368 50.000 0.00 0.00 40.48 3.51
64 65 1.632422 GCGGTGAATCAATGCCAAAG 58.368 50.000 0.00 0.00 0.00 2.77
65 66 0.109365 CGCGGTGAATCAATGCCAAA 60.109 50.000 0.00 0.00 0.00 3.28
66 67 1.505807 CGCGGTGAATCAATGCCAA 59.494 52.632 0.00 0.00 0.00 4.52
67 68 2.405805 CCGCGGTGAATCAATGCCA 61.406 57.895 19.50 0.00 0.00 4.92
68 69 2.408835 CCGCGGTGAATCAATGCC 59.591 61.111 19.50 0.00 0.00 4.40
69 70 1.653094 TTCCCGCGGTGAATCAATGC 61.653 55.000 26.12 0.00 0.00 3.56
70 71 0.808125 TTTCCCGCGGTGAATCAATG 59.192 50.000 26.12 5.01 0.00 2.82
71 72 0.808755 GTTTCCCGCGGTGAATCAAT 59.191 50.000 26.12 0.00 0.00 2.57
72 73 1.570347 CGTTTCCCGCGGTGAATCAA 61.570 55.000 26.12 9.49 0.00 2.57
73 74 2.030401 CGTTTCCCGCGGTGAATCA 61.030 57.895 26.12 10.19 0.00 2.57
74 75 1.693083 CTCGTTTCCCGCGGTGAATC 61.693 60.000 26.12 21.75 36.19 2.52
75 76 1.740296 CTCGTTTCCCGCGGTGAAT 60.740 57.895 26.12 0.00 36.19 2.57
76 77 2.356553 CTCGTTTCCCGCGGTGAA 60.357 61.111 26.12 22.90 36.19 3.18
77 78 4.367023 CCTCGTTTCCCGCGGTGA 62.367 66.667 26.12 18.17 36.67 4.02
82 83 3.564027 CATCGCCTCGTTTCCCGC 61.564 66.667 0.00 0.00 36.19 6.13
83 84 1.878522 CTCATCGCCTCGTTTCCCG 60.879 63.158 0.00 0.00 38.13 5.14
84 85 1.521681 CCTCATCGCCTCGTTTCCC 60.522 63.158 0.00 0.00 0.00 3.97
85 86 0.806492 GTCCTCATCGCCTCGTTTCC 60.806 60.000 0.00 0.00 0.00 3.13
86 87 1.140407 CGTCCTCATCGCCTCGTTTC 61.140 60.000 0.00 0.00 0.00 2.78
87 88 1.153823 CGTCCTCATCGCCTCGTTT 60.154 57.895 0.00 0.00 0.00 3.60
88 89 1.994507 CTCGTCCTCATCGCCTCGTT 61.995 60.000 0.00 0.00 0.00 3.85
89 90 2.437895 TCGTCCTCATCGCCTCGT 60.438 61.111 0.00 0.00 0.00 4.18
90 91 1.715862 TTCTCGTCCTCATCGCCTCG 61.716 60.000 0.00 0.00 0.00 4.63
91 92 0.030101 CTTCTCGTCCTCATCGCCTC 59.970 60.000 0.00 0.00 0.00 4.70
92 93 1.388065 CCTTCTCGTCCTCATCGCCT 61.388 60.000 0.00 0.00 0.00 5.52
93 94 1.066587 CCTTCTCGTCCTCATCGCC 59.933 63.158 0.00 0.00 0.00 5.54
94 95 1.066587 CCCTTCTCGTCCTCATCGC 59.933 63.158 0.00 0.00 0.00 4.58
95 96 1.736586 CCCCTTCTCGTCCTCATCG 59.263 63.158 0.00 0.00 0.00 3.84
96 97 1.443828 GCCCCTTCTCGTCCTCATC 59.556 63.158 0.00 0.00 0.00 2.92
97 98 2.427245 CGCCCCTTCTCGTCCTCAT 61.427 63.158 0.00 0.00 0.00 2.90
98 99 3.068691 CGCCCCTTCTCGTCCTCA 61.069 66.667 0.00 0.00 0.00 3.86
99 100 2.754658 TCGCCCCTTCTCGTCCTC 60.755 66.667 0.00 0.00 0.00 3.71
100 101 2.756283 CTCGCCCCTTCTCGTCCT 60.756 66.667 0.00 0.00 0.00 3.85
101 102 2.754658 TCTCGCCCCTTCTCGTCC 60.755 66.667 0.00 0.00 0.00 4.79
102 103 2.490685 GTCTCGCCCCTTCTCGTC 59.509 66.667 0.00 0.00 0.00 4.20
103 104 3.441290 CGTCTCGCCCCTTCTCGT 61.441 66.667 0.00 0.00 0.00 4.18
104 105 3.114647 CTCGTCTCGCCCCTTCTCG 62.115 68.421 0.00 0.00 0.00 4.04
105 106 2.802106 CTCGTCTCGCCCCTTCTC 59.198 66.667 0.00 0.00 0.00 2.87
106 107 3.453679 GCTCGTCTCGCCCCTTCT 61.454 66.667 0.00 0.00 0.00 2.85
107 108 4.516195 GGCTCGTCTCGCCCCTTC 62.516 72.222 0.00 0.00 41.73 3.46
126 127 3.991051 ACTGCGTCAGGGACACGG 61.991 66.667 10.80 0.00 37.74 4.94
127 128 2.734723 CACTGCGTCAGGGACACG 60.735 66.667 10.80 0.00 36.97 4.49
128 129 2.357517 CCACTGCGTCAGGGACAC 60.358 66.667 10.19 0.00 36.97 3.67
129 130 3.625897 CCCACTGCGTCAGGGACA 61.626 66.667 10.19 0.00 45.80 4.02
153 154 1.259316 CTGTTTTGGCGCGAATAAGC 58.741 50.000 12.10 2.13 0.00 3.09
154 155 2.611974 ACTGTTTTGGCGCGAATAAG 57.388 45.000 12.10 6.68 0.00 1.73
155 156 2.663334 CGAACTGTTTTGGCGCGAATAA 60.663 45.455 12.10 0.00 0.00 1.40
156 157 1.136197 CGAACTGTTTTGGCGCGAATA 60.136 47.619 12.10 0.00 0.00 1.75
157 158 0.385473 CGAACTGTTTTGGCGCGAAT 60.385 50.000 12.10 0.00 0.00 3.34
158 159 1.010574 CGAACTGTTTTGGCGCGAA 60.011 52.632 12.10 0.00 0.00 4.70
159 160 2.629210 CGAACTGTTTTGGCGCGA 59.371 55.556 12.10 0.00 0.00 5.87
160 161 3.091022 GCGAACTGTTTTGGCGCG 61.091 61.111 0.00 0.00 38.24 6.86
161 162 2.729491 GGCGAACTGTTTTGGCGC 60.729 61.111 13.79 13.79 46.20 6.53
162 163 2.050442 GGGCGAACTGTTTTGGCG 60.050 61.111 11.96 5.00 41.72 5.69
163 164 2.338620 GGGGCGAACTGTTTTGGC 59.661 61.111 10.46 10.46 40.35 4.52
164 165 2.642700 CGGGGCGAACTGTTTTGG 59.357 61.111 0.00 0.00 0.00 3.28
165 166 2.642700 CCGGGGCGAACTGTTTTG 59.357 61.111 0.00 0.00 0.00 2.44
166 167 3.292159 GCCGGGGCGAACTGTTTT 61.292 61.111 2.18 0.00 0.00 2.43
229 230 4.404654 CTGGGCCGAAAACAGCGC 62.405 66.667 0.00 0.00 41.90 5.92
230 231 3.737172 CCTGGGCCGAAAACAGCG 61.737 66.667 0.00 0.00 0.00 5.18
231 232 4.056125 GCCTGGGCCGAAAACAGC 62.056 66.667 0.00 0.00 34.56 4.40
242 243 3.518068 GATTTTCGCCGGCCTGGG 61.518 66.667 23.46 6.82 38.63 4.45
243 244 3.876198 CGATTTTCGCCGGCCTGG 61.876 66.667 23.46 7.26 42.50 4.45
244 245 3.876198 CCGATTTTCGCCGGCCTG 61.876 66.667 23.46 8.15 38.82 4.85
248 249 3.573491 GAGCCCGATTTTCGCCGG 61.573 66.667 0.00 0.00 44.94 6.13
249 250 3.573491 GGAGCCCGATTTTCGCCG 61.573 66.667 0.00 0.00 38.82 6.46
250 251 2.124695 AGGAGCCCGATTTTCGCC 60.125 61.111 0.00 0.00 38.82 5.54
251 252 2.472909 CCAGGAGCCCGATTTTCGC 61.473 63.158 0.00 0.00 38.82 4.70
252 253 1.819632 CCCAGGAGCCCGATTTTCG 60.820 63.158 0.00 0.00 40.07 3.46
253 254 1.453928 CCCCAGGAGCCCGATTTTC 60.454 63.158 0.00 0.00 0.00 2.29
254 255 2.683475 CCCCAGGAGCCCGATTTT 59.317 61.111 0.00 0.00 0.00 1.82
255 256 3.420482 CCCCCAGGAGCCCGATTT 61.420 66.667 0.00 0.00 33.47 2.17
263 264 4.087892 CAGTCGTGCCCCCAGGAG 62.088 72.222 0.00 0.00 36.62 3.69
272 273 2.841160 AAAAACGGCCCAGTCGTGC 61.841 57.895 0.00 0.00 45.33 5.34
273 274 3.427670 AAAAACGGCCCAGTCGTG 58.572 55.556 0.00 0.00 45.33 4.35
339 340 1.453669 CCCTTAGGGCATCTCCAGC 59.546 63.158 3.52 0.00 35.35 4.85
350 351 1.422161 CCCCAGATCAGCCCCTTAGG 61.422 65.000 0.00 0.00 39.47 2.69
351 352 1.422161 CCCCCAGATCAGCCCCTTAG 61.422 65.000 0.00 0.00 0.00 2.18
352 353 1.385915 CCCCCAGATCAGCCCCTTA 60.386 63.158 0.00 0.00 0.00 2.69
353 354 2.697644 CCCCCAGATCAGCCCCTT 60.698 66.667 0.00 0.00 0.00 3.95
354 355 2.805827 TTTCCCCCAGATCAGCCCCT 62.806 60.000 0.00 0.00 0.00 4.79
364 365 2.100749 GTCACAAGTTGTTTTCCCCCAG 59.899 50.000 5.57 0.00 0.00 4.45
386 387 4.011058 ACTCGTTTTGTGAAGGTTTTCG 57.989 40.909 0.00 0.00 36.04 3.46
400 401 9.939802 AATAAACTATCACCTAAGAACTCGTTT 57.060 29.630 0.00 0.00 0.00 3.60
431 432 5.514274 TCTTTGATGAAAACCCTTGTGAC 57.486 39.130 0.00 0.00 0.00 3.67
450 451 6.371548 TCACTACAAAAATCTGCGCTAATCTT 59.628 34.615 9.73 0.00 0.00 2.40
555 556 3.907194 CGCCGAAGATCTAGTATTCGTTC 59.093 47.826 18.37 12.08 47.00 3.95
562 563 0.666913 GCCACGCCGAAGATCTAGTA 59.333 55.000 0.00 0.00 0.00 1.82
605 606 4.202461 GGTATATTCATGGCCCACTGAGAA 60.202 45.833 0.00 0.00 0.00 2.87
705 706 5.314923 TCTTGAAGCTACATGGCAAAATC 57.685 39.130 0.00 0.00 34.17 2.17
767 768 2.200081 AGGTGATTGTATGCCCAGACT 58.800 47.619 0.00 0.00 0.00 3.24
997 1004 1.091771 CGCTGGTCTTTCGCCATCAT 61.092 55.000 0.00 0.00 35.19 2.45
1044 1051 0.398381 GGACCAGGAGCAGGAGATCT 60.398 60.000 0.00 0.00 0.00 2.75
1553 1596 3.554692 CAATGTCGACGGCCTCGC 61.555 66.667 11.62 12.99 42.62 5.03
1634 1677 2.545742 GGTTTGTCAAGGTGACCATTGC 60.546 50.000 3.63 3.45 46.40 3.56
1681 1724 2.881513 TCAAATCTAAACCGCACAGCAA 59.118 40.909 0.00 0.00 0.00 3.91
1685 1728 6.561737 TGTTTATCAAATCTAAACCGCACA 57.438 33.333 4.12 0.00 37.97 4.57
1707 1750 1.915614 GCTGCCATGACCACGAGTTG 61.916 60.000 0.00 0.00 0.00 3.16
1711 1754 1.965930 GTTGCTGCCATGACCACGA 60.966 57.895 0.00 0.00 0.00 4.35
1856 1899 1.075748 GGGAAGCAGGGCATCCATT 60.076 57.895 13.68 0.00 46.70 3.16
1916 1959 2.437359 ACTGGCCTTCGCTGATGC 60.437 61.111 3.32 0.00 34.44 3.91
1920 1963 2.032528 TTCCACTGGCCTTCGCTG 59.967 61.111 3.32 0.00 34.44 5.18
2130 2173 2.498481 CAATGGCATTGACTCACCCAAT 59.502 45.455 31.50 0.00 42.83 3.16
2134 2177 1.135199 CAGCAATGGCATTGACTCACC 60.135 52.381 37.23 21.13 42.83 4.02
2157 2200 3.268103 AAACCGCCCGCTCTTCCAT 62.268 57.895 0.00 0.00 0.00 3.41
2196 2239 9.624697 GCATGTTGATGACTTAATTAAACTTGA 57.375 29.630 11.22 0.00 0.00 3.02
2671 3807 2.061773 ACTGAAGCGAAACACATCGAG 58.938 47.619 0.24 0.00 45.48 4.04
2685 3821 7.855904 GGGACGTGCAAATAAATATTACTGAAG 59.144 37.037 9.96 0.00 0.00 3.02
2726 3866 6.316640 TCGTGTTTCTAACAAAATGAGTCCAA 59.683 34.615 0.00 0.00 44.16 3.53
3559 5057 3.822192 CCGATCAGGACGGCGACA 61.822 66.667 16.62 0.00 45.00 4.35
3618 5116 1.490574 CCCTAGGAGGACTGAGTTGG 58.509 60.000 11.48 0.00 37.67 3.77
3729 5230 0.396060 GCCTTTTTGGTGGCCATTGA 59.604 50.000 9.72 0.00 43.11 2.57
3942 5493 3.259625 GTCAGCTTCCTAGACCTTGAACT 59.740 47.826 0.00 0.00 0.00 3.01
3954 5505 1.188219 TTCGCTCAGGTCAGCTTCCT 61.188 55.000 1.68 1.68 37.25 3.36
3961 5512 4.717629 CGGCGTTCGCTCAGGTCA 62.718 66.667 16.40 0.00 0.00 4.02
4621 6436 7.803279 TGATGTGTCTAGTTCTCATATACGT 57.197 36.000 0.00 0.00 0.00 3.57
4839 6656 0.321919 TGCTGAAGGGATGCAGTGTC 60.322 55.000 0.00 0.00 34.66 3.67


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

AutoCloner maintained by Alex Coulton.