Multiple sequence alignment - TraesCS7D01G204300

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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 TraesCS7D01G204300 chr7D 100.000 2812 0 0 1 2812 162189977 162192788 0.000000e+00 5193.0
1 TraesCS7D01G204300 chr7D 89.820 501 45 5 1109 1603 162629173 162629673 3.050000e-179 638.0
2 TraesCS7D01G204300 chr7D 90.329 486 41 4 1109 1589 162219333 162219817 1.420000e-177 632.0
3 TraesCS7D01G204300 chr1D 93.878 1127 63 3 1690 2811 433412321 433411196 0.000000e+00 1694.0
4 TraesCS7D01G204300 chr5B 93.116 1133 71 3 1684 2811 339092816 339091686 0.000000e+00 1653.0
5 TraesCS7D01G204300 chr5D 92.750 1131 74 4 1686 2811 493683014 493681887 0.000000e+00 1628.0
6 TraesCS7D01G204300 chr2B 92.511 1135 77 4 1683 2811 51893479 51894611 0.000000e+00 1618.0
7 TraesCS7D01G204300 chr2B 72.812 320 69 11 304 610 667130586 667130900 2.980000e-15 93.5
8 TraesCS7D01G204300 chr5A 92.233 1133 72 7 1684 2811 568897207 568896086 0.000000e+00 1591.0
9 TraesCS7D01G204300 chr5A 93.053 1094 67 4 1690 2778 638077642 638076553 0.000000e+00 1591.0
10 TraesCS7D01G204300 chr5A 92.021 1128 79 7 1690 2811 13095011 13093889 0.000000e+00 1574.0
11 TraesCS7D01G204300 chr3A 91.989 1136 79 8 1679 2808 456384418 456383289 0.000000e+00 1583.0
12 TraesCS7D01G204300 chr3A 80.795 151 25 4 305 452 734747807 734747956 6.370000e-22 115.0
13 TraesCS7D01G204300 chr2A 91.652 1138 84 8 1679 2811 686199700 686198569 0.000000e+00 1565.0
14 TraesCS7D01G204300 chr7B 91.086 976 66 14 637 1608 124235951 124236909 0.000000e+00 1301.0
15 TraesCS7D01G204300 chr7B 83.623 806 93 26 808 1606 124141037 124141810 0.000000e+00 721.0
16 TraesCS7D01G204300 chr7B 87.455 558 59 4 1098 1652 124536563 124537112 1.420000e-177 632.0
17 TraesCS7D01G204300 chr7B 82.190 758 86 33 844 1580 124548554 124549283 8.610000e-170 606.0
18 TraesCS7D01G204300 chr7B 87.103 535 50 12 1112 1643 124360321 124360839 3.120000e-164 588.0
19 TraesCS7D01G204300 chr7B 92.486 173 13 0 470 642 124235566 124235738 6.020000e-62 248.0
20 TraesCS7D01G204300 chr7B 87.435 191 15 4 629 810 124137275 124137465 7.890000e-51 211.0
21 TraesCS7D01G204300 chr7B 89.041 73 7 1 959 1031 124137620 124137691 3.860000e-14 89.8
22 TraesCS7D01G204300 chr7A 83.702 1129 116 32 571 1647 163234494 163235606 0.000000e+00 1003.0
23 TraesCS7D01G204300 chr7A 91.948 621 39 3 1055 1675 163299667 163300276 0.000000e+00 859.0
24 TraesCS7D01G204300 chr7A 88.613 483 45 6 1109 1581 163364604 163365086 1.880000e-161 579.0
25 TraesCS7D01G204300 chr7A 82.267 547 77 10 1 530 163298758 163299301 3.300000e-124 455.0
26 TraesCS7D01G204300 chr7A 87.980 391 21 13 626 1014 163299302 163299668 3.330000e-119 438.0
27 TraesCS7D01G204300 chr7A 81.905 210 25 9 808 1012 163372301 163372502 6.230000e-37 165.0
28 TraesCS7D01G204300 chr7A 81.928 83 14 1 360 441 163234240 163234322 5.030000e-08 69.4


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 TraesCS7D01G204300 chr7D 162189977 162192788 2811 False 5193.0 5193 100.000000 1 2812 1 chr7D.!!$F1 2811
1 TraesCS7D01G204300 chr7D 162629173 162629673 500 False 638.0 638 89.820000 1109 1603 1 chr7D.!!$F3 494
2 TraesCS7D01G204300 chr1D 433411196 433412321 1125 True 1694.0 1694 93.878000 1690 2811 1 chr1D.!!$R1 1121
3 TraesCS7D01G204300 chr5B 339091686 339092816 1130 True 1653.0 1653 93.116000 1684 2811 1 chr5B.!!$R1 1127
4 TraesCS7D01G204300 chr5D 493681887 493683014 1127 True 1628.0 1628 92.750000 1686 2811 1 chr5D.!!$R1 1125
5 TraesCS7D01G204300 chr2B 51893479 51894611 1132 False 1618.0 1618 92.511000 1683 2811 1 chr2B.!!$F1 1128
6 TraesCS7D01G204300 chr5A 568896086 568897207 1121 True 1591.0 1591 92.233000 1684 2811 1 chr5A.!!$R2 1127
7 TraesCS7D01G204300 chr5A 638076553 638077642 1089 True 1591.0 1591 93.053000 1690 2778 1 chr5A.!!$R3 1088
8 TraesCS7D01G204300 chr5A 13093889 13095011 1122 True 1574.0 1574 92.021000 1690 2811 1 chr5A.!!$R1 1121
9 TraesCS7D01G204300 chr3A 456383289 456384418 1129 True 1583.0 1583 91.989000 1679 2808 1 chr3A.!!$R1 1129
10 TraesCS7D01G204300 chr2A 686198569 686199700 1131 True 1565.0 1565 91.652000 1679 2811 1 chr2A.!!$R1 1132
11 TraesCS7D01G204300 chr7B 124235566 124236909 1343 False 774.5 1301 91.786000 470 1608 2 chr7B.!!$F5 1138
12 TraesCS7D01G204300 chr7B 124536563 124537112 549 False 632.0 632 87.455000 1098 1652 1 chr7B.!!$F2 554
13 TraesCS7D01G204300 chr7B 124548554 124549283 729 False 606.0 606 82.190000 844 1580 1 chr7B.!!$F3 736
14 TraesCS7D01G204300 chr7B 124360321 124360839 518 False 588.0 588 87.103000 1112 1643 1 chr7B.!!$F1 531
15 TraesCS7D01G204300 chr7B 124137275 124141810 4535 False 340.6 721 86.699667 629 1606 3 chr7B.!!$F4 977
16 TraesCS7D01G204300 chr7A 163298758 163300276 1518 False 584.0 859 87.398333 1 1675 3 chr7A.!!$F4 1674
17 TraesCS7D01G204300 chr7A 163234240 163235606 1366 False 536.2 1003 82.815000 360 1647 2 chr7A.!!$F3 1287

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
62 63 0.034186 TGGACTTTGGGCTATGCAGG 60.034 55.0 0.0 0.0 0.00 4.85 F
378 395 0.105964 TGGTTGTTGCTCTGCTACGT 59.894 50.0 0.0 0.0 37.12 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1628 5584 0.106769 TTTGGACTCCAACAGCAGCA 60.107 50.0 10.25 0.00 43.82 4.41 R
2348 6311 0.104487 TTCGGCGGCGGATTGTATTA 59.896 50.0 31.73 5.41 0.00 0.98 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
43 44 4.144727 AGTCCTCCCGCCTCCGAT 62.145 66.667 0.00 0.00 36.29 4.18
47 48 3.917760 CTCCCGCCTCCGATGGAC 61.918 72.222 0.00 0.00 36.29 4.02
53 54 1.452108 GCCTCCGATGGACTTTGGG 60.452 63.158 0.00 0.00 0.00 4.12
55 56 1.604378 CTCCGATGGACTTTGGGCT 59.396 57.895 0.00 0.00 0.00 5.19
56 57 0.830648 CTCCGATGGACTTTGGGCTA 59.169 55.000 0.00 0.00 0.00 3.93
59 60 0.947244 CGATGGACTTTGGGCTATGC 59.053 55.000 0.00 0.00 0.00 3.14
62 63 0.034186 TGGACTTTGGGCTATGCAGG 60.034 55.000 0.00 0.00 0.00 4.85
67 68 2.476852 TTTGGGCTATGCAGGTGCGA 62.477 55.000 0.00 0.00 45.83 5.10
68 69 2.124736 GGGCTATGCAGGTGCGAA 60.125 61.111 0.00 0.00 45.83 4.70
99 100 2.768344 CACCCCGCCAGGAGGTAT 60.768 66.667 8.67 0.00 38.49 2.73
109 110 3.356837 GGAGGTATCCCGCTCTCG 58.643 66.667 0.00 0.00 40.03 4.04
112 113 0.311477 GAGGTATCCCGCTCTCGTTC 59.689 60.000 0.00 0.00 35.12 3.95
115 116 1.952296 GGTATCCCGCTCTCGTTCTTA 59.048 52.381 0.00 0.00 0.00 2.10
124 125 3.724751 CGCTCTCGTTCTTATTAGGTTCG 59.275 47.826 0.00 0.00 0.00 3.95
131 132 4.797349 CGTTCTTATTAGGTTCGGTGTCTC 59.203 45.833 0.00 0.00 0.00 3.36
138 139 0.106149 GGTTCGGTGTCTCAGTTGGT 59.894 55.000 0.00 0.00 0.00 3.67
156 157 2.858622 TGCTATGTGGCAGCAACTC 58.141 52.632 0.43 0.00 45.71 3.01
169 170 0.321122 GCAACTCTGTCCCTCAGTGG 60.321 60.000 0.00 0.00 43.97 4.00
194 195 7.886338 GGAATAACATCCCTCACATTTAATCC 58.114 38.462 0.00 0.00 33.05 3.01
200 201 3.140144 TCCCTCACATTTAATCCCATCCC 59.860 47.826 0.00 0.00 0.00 3.85
203 204 3.815401 CTCACATTTAATCCCATCCCGAC 59.185 47.826 0.00 0.00 0.00 4.79
239 241 0.386352 CAAGTGCATGTGAAGGCGTG 60.386 55.000 0.00 0.00 0.00 5.34
244 246 0.671781 GCATGTGAAGGCGTGTCTCT 60.672 55.000 0.00 0.00 0.00 3.10
245 247 1.073964 CATGTGAAGGCGTGTCTCTG 58.926 55.000 0.00 0.00 0.00 3.35
253 256 1.574925 GCGTGTCTCTGTCGACTCA 59.425 57.895 17.92 1.79 35.00 3.41
267 270 2.745100 CTCACGGGAGTCGGTCGA 60.745 66.667 6.49 0.00 44.67 4.20
269 272 0.812811 CTCACGGGAGTCGGTCGATA 60.813 60.000 6.49 0.00 44.67 2.92
275 278 3.686726 ACGGGAGTCGGTCGATATTATAC 59.313 47.826 0.00 0.00 40.62 1.47
276 279 3.937706 CGGGAGTCGGTCGATATTATACT 59.062 47.826 0.00 0.00 34.75 2.12
278 281 5.106396 CGGGAGTCGGTCGATATTATACTTT 60.106 44.000 0.00 0.00 34.75 2.66
280 283 7.470900 GGGAGTCGGTCGATATTATACTTTAG 58.529 42.308 0.00 0.00 0.00 1.85
281 284 7.120432 GGGAGTCGGTCGATATTATACTTTAGT 59.880 40.741 0.00 0.00 0.00 2.24
334 351 8.783093 CATGTGTTTACAGTTTTGATCCTTCTA 58.217 33.333 0.00 0.00 40.79 2.10
335 352 8.740123 TGTGTTTACAGTTTTGATCCTTCTAA 57.260 30.769 0.00 0.00 31.91 2.10
337 354 9.612620 GTGTTTACAGTTTTGATCCTTCTAATG 57.387 33.333 0.00 0.00 0.00 1.90
341 358 7.596749 ACAGTTTTGATCCTTCTAATGTACG 57.403 36.000 0.00 0.00 0.00 3.67
342 359 7.383687 ACAGTTTTGATCCTTCTAATGTACGA 58.616 34.615 0.00 0.00 0.00 3.43
378 395 0.105964 TGGTTGTTGCTCTGCTACGT 59.894 50.000 0.00 0.00 37.12 3.57
389 406 1.411246 TCTGCTACGTTGGTCTTGTGT 59.589 47.619 0.00 0.00 0.00 3.72
395 412 1.202440 ACGTTGGTCTTGTGTCGCTTA 60.202 47.619 0.00 0.00 0.00 3.09
396 413 1.455786 CGTTGGTCTTGTGTCGCTTAG 59.544 52.381 0.00 0.00 0.00 2.18
397 414 1.194772 GTTGGTCTTGTGTCGCTTAGC 59.805 52.381 0.00 0.00 0.00 3.09
408 426 4.201841 TGTGTCGCTTAGCATGATGAATTG 60.202 41.667 4.70 0.00 0.00 2.32
441 459 7.012607 TCTACTATAATAAGGTTTACCCGGCT 58.987 38.462 0.00 0.00 38.74 5.52
445 463 0.904394 TAAGGTTTACCCGGCTCCGT 60.904 55.000 7.59 0.00 38.74 4.69
449 467 0.392060 GTTTACCCGGCTCCGTTGAT 60.392 55.000 7.59 0.00 37.81 2.57
458 476 0.955428 GCTCCGTTGATGAAGTGGCA 60.955 55.000 0.00 0.00 0.00 4.92
472 490 3.052455 AGTGGCAATGACGACAACATA 57.948 42.857 0.00 0.00 0.00 2.29
498 517 8.414003 ACATTCGTCTCACTCTATTGCTTATAA 58.586 33.333 0.00 0.00 0.00 0.98
531 550 4.649267 TGGTTCATGGACCTGATTGTAA 57.351 40.909 24.02 0.00 40.47 2.41
553 597 9.499479 TGTAATTTTTGTTAACTACGGTATCCA 57.501 29.630 7.22 0.00 0.00 3.41
695 983 2.245096 GAAATCAGCACATGCGTGAAC 58.755 47.619 14.17 3.78 46.80 3.18
697 985 1.638388 ATCAGCACATGCGTGAACCG 61.638 55.000 14.17 0.00 46.80 4.44
722 1020 2.969628 AAGCCGATGGAGAGTACAAG 57.030 50.000 0.00 0.00 0.00 3.16
755 1055 5.990386 GGTCCTATAAGATTTTTCTCCGGAC 59.010 44.000 0.00 0.00 37.16 4.79
762 1062 0.245539 TTTTTCTCCGGACGATCGCT 59.754 50.000 16.60 2.00 0.00 4.93
774 1083 1.588932 GATCGCTGCACGGAATCGA 60.589 57.895 0.00 0.00 43.89 3.59
866 1221 0.443869 CGTCGAAATTGTCCTGCTGG 59.556 55.000 2.58 2.58 0.00 4.85
877 1232 3.970410 CTGCTGGCCCTGGACCAA 61.970 66.667 2.53 0.00 36.56 3.67
910 1271 1.153549 GCCAGAGACCGCGAAGAAT 60.154 57.895 8.23 0.00 0.00 2.40
918 1279 1.376683 CCGCGAAGAATCACCCCAA 60.377 57.895 8.23 0.00 0.00 4.12
1016 4942 6.608808 CACCTCCTAATCCATCAATTTCCTTT 59.391 38.462 0.00 0.00 0.00 3.11
1043 4969 0.523072 CAACACAAGCCCCGATCAAG 59.477 55.000 0.00 0.00 0.00 3.02
1052 4978 1.227497 CCCGATCAAGGCAGAGCTC 60.227 63.158 5.27 5.27 0.00 4.09
1073 4999 1.458588 CCTCCCCTACAGCTCCCTC 60.459 68.421 0.00 0.00 0.00 4.30
1171 5121 4.814294 GAGCCGACGGTTCGCCAT 62.814 66.667 15.24 0.00 44.43 4.40
1503 5453 4.722700 GCAAGGGAAGGCTCGCCA 62.723 66.667 11.02 0.00 38.92 5.69
1610 5566 8.497554 CGTAGTAGAGTAGCCTGAGTAATTTAG 58.502 40.741 0.00 0.00 0.00 1.85
1628 5584 2.999185 AGGGTCCATGGAAATGTGTT 57.001 45.000 18.20 0.00 0.00 3.32
1664 5620 1.608590 CAAATTGTTGACCCACTCGCT 59.391 47.619 0.00 0.00 36.83 4.93
1668 5624 0.531974 TGTTGACCCACTCGCTTGTC 60.532 55.000 0.00 0.00 0.00 3.18
1675 5631 2.600769 ACTCGCTTGTCCCCGTCT 60.601 61.111 0.00 0.00 0.00 4.18
1676 5632 2.182030 CTCGCTTGTCCCCGTCTC 59.818 66.667 0.00 0.00 0.00 3.36
1677 5633 3.358076 CTCGCTTGTCCCCGTCTCC 62.358 68.421 0.00 0.00 0.00 3.71
1678 5634 4.452733 CGCTTGTCCCCGTCTCCC 62.453 72.222 0.00 0.00 0.00 4.30
1679 5635 3.003763 GCTTGTCCCCGTCTCCCT 61.004 66.667 0.00 0.00 0.00 4.20
1680 5636 2.982130 CTTGTCCCCGTCTCCCTG 59.018 66.667 0.00 0.00 0.00 4.45
1681 5637 1.609501 CTTGTCCCCGTCTCCCTGA 60.610 63.158 0.00 0.00 0.00 3.86
1708 5664 4.442375 TGTTTTTGAACGAAGGCTCAAA 57.558 36.364 0.00 0.00 40.16 2.69
1770 5726 4.040755 AGGATTACAGGACTGCCACTTAT 58.959 43.478 0.00 0.00 36.29 1.73
1780 5736 5.705905 AGGACTGCCACTTATAACAAGAAAC 59.294 40.000 0.00 0.00 36.29 2.78
1813 5769 7.484641 GCGAAAATAAAGATACATTGTGCTCAA 59.515 33.333 3.31 3.31 37.98 3.02
1845 5801 3.932710 TCGAAGGCATAGAACAATGTCAC 59.067 43.478 0.00 0.00 33.79 3.67
1865 5821 1.062525 GAACGCCGCTATGCCAAAG 59.937 57.895 0.00 0.00 0.00 2.77
1928 5884 4.035091 GTGCATGTTTTGTGTCACTGACTA 59.965 41.667 10.54 0.00 33.15 2.59
2074 6035 1.895131 GAATTCCCAAGCAGCCAAAGA 59.105 47.619 0.00 0.00 0.00 2.52
2191 6153 1.792118 AACGAAGGCGCTGAAAACCC 61.792 55.000 7.64 0.00 42.48 4.11
2209 6172 2.586792 CCGGAGAAGGCCAAGAGG 59.413 66.667 5.01 0.00 38.23 3.69
2221 6184 0.395311 CCAAGAGGATGCAGCACCAT 60.395 55.000 3.51 0.00 36.89 3.55
2250 6213 5.148502 GGTCAAGGATAGGAGTCTCCATAA 58.851 45.833 21.26 6.37 39.61 1.90
2251 6214 5.782845 GGTCAAGGATAGGAGTCTCCATAAT 59.217 44.000 21.26 10.89 39.61 1.28
2266 6229 3.497103 CATAATCCATGGCACCAGAGA 57.503 47.619 6.96 0.00 0.00 3.10
2318 6281 2.529136 CCCTCCACACCTGGACCA 60.529 66.667 0.00 0.00 42.15 4.02
2348 6311 2.762887 TGCCGAAGATGAAGATCAGACT 59.237 45.455 0.00 0.00 0.00 3.24
2363 6326 1.792949 CAGACTAATACAATCCGCCGC 59.207 52.381 0.00 0.00 0.00 6.53
2409 6372 0.976641 TTGAGCACTTCCCTGACGAT 59.023 50.000 0.00 0.00 0.00 3.73
2449 6412 4.351938 CCAAGGTGCCGTCGTCGA 62.352 66.667 2.98 0.00 39.71 4.20
2689 6653 2.028190 CGCGGATCGGAGCAGATT 59.972 61.111 4.16 0.00 33.78 2.40
2725 6689 1.480954 GATTCTCCAAGGTACAGCCGA 59.519 52.381 0.00 0.00 43.70 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.007387 GTGGCGTCAAAGGGCAAAG 60.007 57.895 0.00 0.00 40.19 2.77
26 27 4.144727 ATCGGAGGCGGGAGGACT 62.145 66.667 0.00 0.00 35.84 3.85
30 31 3.917760 GTCCATCGGAGGCGGGAG 61.918 72.222 0.00 0.00 29.39 4.30
31 32 3.976490 AAGTCCATCGGAGGCGGGA 62.976 63.158 0.00 0.00 29.39 5.14
35 36 1.452108 CCCAAAGTCCATCGGAGGC 60.452 63.158 0.00 0.00 29.39 4.70
38 39 1.140852 CATAGCCCAAAGTCCATCGGA 59.859 52.381 0.00 0.00 0.00 4.55
42 43 1.410648 CCTGCATAGCCCAAAGTCCAT 60.411 52.381 0.00 0.00 0.00 3.41
43 44 0.034186 CCTGCATAGCCCAAAGTCCA 60.034 55.000 0.00 0.00 0.00 4.02
46 47 0.967380 GCACCTGCATAGCCCAAAGT 60.967 55.000 0.00 0.00 41.59 2.66
47 48 1.811860 GCACCTGCATAGCCCAAAG 59.188 57.895 0.00 0.00 41.59 2.77
53 54 1.153369 TCCTTCGCACCTGCATAGC 60.153 57.895 0.00 0.00 42.21 2.97
55 56 1.220749 GGTCCTTCGCACCTGCATA 59.779 57.895 0.00 0.00 42.21 3.14
56 57 2.045926 GGTCCTTCGCACCTGCAT 60.046 61.111 0.00 0.00 42.21 3.96
59 60 2.125912 CGAGGTCCTTCGCACCTG 60.126 66.667 0.00 0.00 44.87 4.00
67 68 3.003763 GTGAGGGGCGAGGTCCTT 61.004 66.667 0.00 0.00 32.74 3.36
81 82 3.326385 ATACCTCCTGGCGGGGTGA 62.326 63.158 13.58 0.00 35.97 4.02
99 100 2.621998 CCTAATAAGAACGAGAGCGGGA 59.378 50.000 0.00 0.00 43.17 5.14
101 102 3.712091 ACCTAATAAGAACGAGAGCGG 57.288 47.619 0.00 0.00 43.17 5.52
102 103 3.724751 CGAACCTAATAAGAACGAGAGCG 59.275 47.826 0.00 0.00 44.79 5.03
109 110 5.717119 TGAGACACCGAACCTAATAAGAAC 58.283 41.667 0.00 0.00 0.00 3.01
112 113 5.326200 ACTGAGACACCGAACCTAATAAG 57.674 43.478 0.00 0.00 0.00 1.73
115 116 3.306780 CCAACTGAGACACCGAACCTAAT 60.307 47.826 0.00 0.00 0.00 1.73
124 125 2.289694 ACATAGCACCAACTGAGACACC 60.290 50.000 0.00 0.00 0.00 4.16
131 132 0.806868 CTGCCACATAGCACCAACTG 59.193 55.000 0.00 0.00 38.00 3.16
169 170 7.039714 GGGATTAAATGTGAGGGATGTTATTCC 60.040 40.741 0.00 0.00 34.83 3.01
177 178 4.202716 GGGATGGGATTAAATGTGAGGGAT 60.203 45.833 0.00 0.00 0.00 3.85
185 186 3.120321 TCGTCGGGATGGGATTAAATG 57.880 47.619 0.00 0.00 0.00 2.32
221 222 0.819259 ACACGCCTTCACATGCACTT 60.819 50.000 0.00 0.00 0.00 3.16
239 241 0.954449 TCCCGTGAGTCGACAGAGAC 60.954 60.000 19.50 7.22 42.86 3.36
253 256 2.260844 TAATATCGACCGACTCCCGT 57.739 50.000 0.00 0.00 36.31 5.28
308 325 7.651808 AGAAGGATCAAAACTGTAAACACATG 58.348 34.615 0.00 0.00 0.00 3.21
309 326 7.823745 AGAAGGATCAAAACTGTAAACACAT 57.176 32.000 0.00 0.00 0.00 3.21
310 327 8.740123 TTAGAAGGATCAAAACTGTAAACACA 57.260 30.769 0.00 0.00 0.00 3.72
320 337 7.760340 AGAGTCGTACATTAGAAGGATCAAAAC 59.240 37.037 0.00 0.00 0.00 2.43
321 338 7.837863 AGAGTCGTACATTAGAAGGATCAAAA 58.162 34.615 0.00 0.00 0.00 2.44
326 343 6.017770 CGAAGAGAGTCGTACATTAGAAGGAT 60.018 42.308 0.00 0.00 36.26 3.24
341 358 1.666311 CCAACACGGACGAAGAGAGTC 60.666 57.143 0.00 0.00 36.56 3.36
342 359 0.314302 CCAACACGGACGAAGAGAGT 59.686 55.000 0.00 0.00 36.56 3.24
354 371 0.592247 GCAGAGCAACAACCAACACG 60.592 55.000 0.00 0.00 0.00 4.49
356 373 1.946768 GTAGCAGAGCAACAACCAACA 59.053 47.619 0.00 0.00 0.00 3.33
378 395 1.202592 TGCTAAGCGACACAAGACCAA 60.203 47.619 0.00 0.00 0.00 3.67
389 406 3.614159 GCAATTCATCATGCTAAGCGA 57.386 42.857 0.00 0.00 39.46 4.93
396 413 3.377485 AGACAGTCAGCAATTCATCATGC 59.623 43.478 2.66 0.00 42.87 4.06
397 414 5.816258 AGTAGACAGTCAGCAATTCATCATG 59.184 40.000 2.66 0.00 0.00 3.07
441 459 1.811965 CATTGCCACTTCATCAACGGA 59.188 47.619 0.00 0.00 0.00 4.69
445 463 2.483877 GTCGTCATTGCCACTTCATCAA 59.516 45.455 0.00 0.00 0.00 2.57
449 467 1.601903 GTTGTCGTCATTGCCACTTCA 59.398 47.619 0.00 0.00 0.00 3.02
472 490 4.727507 AGCAATAGAGTGAGACGAATGT 57.272 40.909 0.00 0.00 0.00 2.71
498 517 2.473816 CATGAACCATGTAGCGACGAT 58.526 47.619 0.00 0.00 37.12 3.73
531 550 9.895138 ATAGTGGATACCGTAGTTAACAAAAAT 57.105 29.630 8.61 0.00 0.00 1.82
612 682 2.366590 CCACTCATCCTGATTCCGATGA 59.633 50.000 11.13 11.13 41.94 2.92
613 683 2.366590 TCCACTCATCCTGATTCCGATG 59.633 50.000 5.03 5.03 37.76 3.84
616 686 2.988010 TTCCACTCATCCTGATTCCG 57.012 50.000 0.00 0.00 0.00 4.30
690 978 1.447314 CGGCTTAGACCCGGTTCAC 60.447 63.158 0.39 0.00 41.99 3.18
691 979 0.974010 ATCGGCTTAGACCCGGTTCA 60.974 55.000 0.39 0.00 45.60 3.18
692 980 0.529992 CATCGGCTTAGACCCGGTTC 60.530 60.000 0.00 0.00 45.60 3.62
695 983 2.088674 CTCCATCGGCTTAGACCCGG 62.089 65.000 0.00 0.00 45.60 5.73
697 985 0.676736 CTCTCCATCGGCTTAGACCC 59.323 60.000 0.00 0.00 0.00 4.46
722 1020 5.541953 AATCTTATAGGACCGGGTTGTAC 57.458 43.478 6.32 0.00 0.00 2.90
755 1055 2.920964 CGATTCCGTGCAGCGATCG 61.921 63.158 11.69 11.69 44.77 3.69
762 1062 2.434185 GGCTGTCGATTCCGTGCA 60.434 61.111 0.00 0.00 37.05 4.57
836 1191 4.980805 TTCGACGTGGTGGCTGCC 62.981 66.667 12.87 12.87 0.00 4.85
866 1221 2.978010 CACGTGTTGGTCCAGGGC 60.978 66.667 7.58 0.00 0.00 5.19
910 1271 2.466186 GGGGGACTTGTTGGGGTGA 61.466 63.158 0.00 0.00 0.00 4.02
1016 4942 1.150536 GGCTTGTGTTGGGTGGAGA 59.849 57.895 0.00 0.00 0.00 3.71
1052 4978 2.446802 GAGCTGTAGGGGAGGGGG 60.447 72.222 0.00 0.00 0.00 5.40
1073 4999 2.390599 CGCGGTGTGGGTTGATGAG 61.391 63.158 0.00 0.00 0.00 2.90
1116 5065 0.174162 GCCATTCTTGCCGCTTGATT 59.826 50.000 0.00 0.00 0.00 2.57
1511 5461 3.009115 GGCCAGCTGTAGGGGACA 61.009 66.667 13.81 0.00 36.35 4.02
1610 5566 1.066929 GCAACACATTTCCATGGACCC 60.067 52.381 15.91 0.00 34.27 4.46
1628 5584 0.106769 TTTGGACTCCAACAGCAGCA 60.107 50.000 10.25 0.00 43.82 4.41
1664 5620 0.546747 AATCAGGGAGACGGGGACAA 60.547 55.000 0.00 0.00 0.00 3.18
1668 5624 3.978876 AAAAATCAGGGAGACGGGG 57.021 52.632 0.00 0.00 0.00 5.73
1708 5664 4.825085 TGTTAATTCAAAGTCGGGCTCTTT 59.175 37.500 0.00 0.00 35.82 2.52
1770 5726 5.821516 TTTCGCTCTTTGGTTTCTTGTTA 57.178 34.783 0.00 0.00 0.00 2.41
1780 5736 9.013490 CAATGTATCTTTATTTTCGCTCTTTGG 57.987 33.333 0.00 0.00 0.00 3.28
1813 5769 5.854010 TCTATGCCTTCGAGTTGTTCTAT 57.146 39.130 0.00 0.00 0.00 1.98
1862 5818 3.370633 GCCTTAGTAGGTTAGCTGGCTTT 60.371 47.826 0.00 0.00 44.00 3.51
1865 5821 1.763545 AGCCTTAGTAGGTTAGCTGGC 59.236 52.381 0.00 2.09 44.00 4.85
1928 5884 0.618968 TTGCCCCTGTTTTTGGTGGT 60.619 50.000 0.00 0.00 0.00 4.16
1954 5915 3.071206 GCGGAGGCAGAGTCAGGA 61.071 66.667 0.00 0.00 39.62 3.86
2018 5979 1.919012 TGAACCACTTCACAGGCCA 59.081 52.632 5.01 0.00 31.00 5.36
2074 6035 1.692411 GTTTGTTCCTGGTGCCTCTT 58.308 50.000 0.00 0.00 0.00 2.85
2191 6153 2.586792 CTCTTGGCCTTCTCCGGG 59.413 66.667 3.32 0.00 0.00 5.73
2221 6184 1.688735 CTCCTATCCTTGACCGATGCA 59.311 52.381 0.00 0.00 0.00 3.96
2250 6213 0.549950 CCTTCTCTGGTGCCATGGAT 59.450 55.000 18.40 0.00 0.00 3.41
2251 6214 1.565390 CCCTTCTCTGGTGCCATGGA 61.565 60.000 18.40 0.00 0.00 3.41
2261 6224 1.403687 GGATCGGGGTCCCTTCTCTG 61.404 65.000 8.15 0.00 31.82 3.35
2318 6281 1.002430 TCATCTTCGGCAACTTGCTCT 59.998 47.619 13.43 0.00 44.28 4.09
2348 6311 0.104487 TTCGGCGGCGGATTGTATTA 59.896 50.000 31.73 5.41 0.00 0.98
2363 6326 2.048503 GAGTCGGTGGTGGTTCGG 60.049 66.667 0.00 0.00 0.00 4.30
2416 6379 0.034863 TTGGTGGCGTAATCCTTCCC 60.035 55.000 0.00 0.00 0.00 3.97
2449 6412 2.419297 GCCTCAGTTCCTCGATTCATGT 60.419 50.000 0.00 0.00 0.00 3.21
2689 6653 2.107041 AATCGGCGTCCACAACCTCA 62.107 55.000 6.85 0.00 0.00 3.86
2725 6689 3.316573 GCAGCAGCTTCCCGTAGGT 62.317 63.158 0.00 0.00 42.41 3.08


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

AutoCloner maintained by Alex Coulton.