Multiple sequence alignment - TraesCS5D01G208300

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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 TraesCS5D01G208300 chr5D 100.000 6778 0 0 1 6778 314835848 314842625 0.000000e+00 12517.0
1 TraesCS5D01G208300 chr5B 96.385 5533 145 21 633 6139 362810209 362815712 0.000000e+00 9058.0
2 TraesCS5D01G208300 chr5B 92.481 665 31 9 6132 6778 362815871 362816534 0.000000e+00 933.0
3 TraesCS5D01G208300 chr5B 93.474 567 23 8 66 623 362809550 362810111 0.000000e+00 830.0
4 TraesCS5D01G208300 chr5B 100.000 31 0 0 37 67 362809475 362809505 2.640000e-04 58.4
5 TraesCS5D01G208300 chr5A 97.085 3980 97 8 633 4600 408837596 408841568 0.000000e+00 6689.0
6 TraesCS5D01G208300 chr5A 96.063 1778 43 11 4598 6358 408841684 408843451 0.000000e+00 2870.0
7 TraesCS5D01G208300 chr5A 96.927 423 11 2 6358 6778 408843575 408843997 0.000000e+00 708.0
8 TraesCS5D01G208300 chr5A 95.498 311 5 4 315 623 408837193 408837496 7.900000e-134 488.0
9 TraesCS5D01G208300 chr5A 91.416 233 10 7 15 241 408836965 408837193 1.840000e-80 311.0


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 TraesCS5D01G208300 chr5D 314835848 314842625 6777 False 12517.00 12517 100.0000 1 6778 1 chr5D.!!$F1 6777
1 TraesCS5D01G208300 chr5B 362809475 362816534 7059 False 2719.85 9058 95.5850 37 6778 4 chr5B.!!$F1 6741
2 TraesCS5D01G208300 chr5A 408836965 408843997 7032 False 2213.20 6689 95.3978 15 6778 5 chr5A.!!$F1 6763

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
625 687 0.108329 CCGGTGCGGTAATGTCTTCT 60.108 55.000 0.00 0.0 42.73 2.85 F
628 690 1.135199 GGTGCGGTAATGTCTTCTCGA 60.135 52.381 0.00 0.0 0.00 4.04 F
1830 1997 2.039418 CCACGGACCATTGGAGAGATA 58.961 52.381 10.37 0.0 34.46 1.98 F
1925 2092 1.264826 TCTTTTGAAAACGGTAGGCGC 59.735 47.619 0.00 0.0 0.00 6.53 F
3134 3315 0.893270 TCCCAACAAACAGATGCCCG 60.893 55.000 0.00 0.0 0.00 6.13 F
3318 3499 1.000955 GGTGGTCTCGACTTGTGTGAT 59.999 52.381 0.00 0.0 0.00 3.06 F
4346 4528 0.681175 GTGCTGTGCCCTTCCATTTT 59.319 50.000 0.00 0.0 0.00 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1516 1683 1.764134 ACCAACTCCGTCCTTGTACAA 59.236 47.619 8.28 8.28 0.00 2.41 R
1925 2092 1.881973 CCAATGGGCGATGTGGAATAG 59.118 52.381 0.00 0.00 32.54 1.73 R
3115 3296 0.893270 CGGGCATCTGTTTGTTGGGA 60.893 55.000 0.00 0.00 0.00 4.37 R
3300 3481 1.000843 CCATCACACAAGTCGAGACCA 59.999 52.381 0.00 0.00 0.00 4.02 R
4332 4514 1.799544 CTTGCAAAATGGAAGGGCAC 58.200 50.000 0.00 0.00 41.35 5.01 R
4362 4544 2.438434 GAAGGGATGGTGTGGCGG 60.438 66.667 0.00 0.00 0.00 6.13 R
6307 6796 0.036388 TCGACTGAGTTGGGCATTCC 60.036 55.000 0.00 0.00 0.00 3.01 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
17 18 3.450115 AGTACTGCCGTCGAGCCC 61.450 66.667 0.00 0.00 0.00 5.19
18 19 3.755628 GTACTGCCGTCGAGCCCA 61.756 66.667 0.00 0.00 0.00 5.36
19 20 2.758327 TACTGCCGTCGAGCCCAT 60.758 61.111 0.00 0.00 0.00 4.00
20 21 2.355986 TACTGCCGTCGAGCCCATT 61.356 57.895 0.00 0.00 0.00 3.16
21 22 2.292794 TACTGCCGTCGAGCCCATTC 62.293 60.000 0.00 0.00 0.00 2.67
31 32 1.735376 GAGCCCATTCATGCCAGCAG 61.735 60.000 0.00 0.00 0.00 4.24
118 166 0.665670 CGGCTATCTCCAGCACATCG 60.666 60.000 0.00 0.00 43.67 3.84
119 167 0.390860 GGCTATCTCCAGCACATCGT 59.609 55.000 0.00 0.00 43.67 3.73
154 204 2.972153 AAACCCTGGTCTCCCTCTAT 57.028 50.000 0.00 0.00 0.00 1.98
178 229 0.178846 TCCCCATTTCCCCTCACTCA 60.179 55.000 0.00 0.00 0.00 3.41
193 244 2.523168 TCACTGCGTCCACCTCCA 60.523 61.111 0.00 0.00 0.00 3.86
330 383 2.106074 GTGATGCGGGCAATCACGA 61.106 57.895 15.30 0.00 35.89 4.35
331 384 1.815003 TGATGCGGGCAATCACGAG 60.815 57.895 0.00 0.00 0.00 4.18
576 636 4.605967 CGCGCGCCTCTCTCTCTC 62.606 72.222 27.72 0.00 0.00 3.20
577 637 3.209097 GCGCGCCTCTCTCTCTCT 61.209 66.667 23.24 0.00 0.00 3.10
578 638 3.022287 CGCGCCTCTCTCTCTCTC 58.978 66.667 0.00 0.00 0.00 3.20
579 639 1.523711 CGCGCCTCTCTCTCTCTCT 60.524 63.158 0.00 0.00 0.00 3.10
580 640 1.498865 CGCGCCTCTCTCTCTCTCTC 61.499 65.000 0.00 0.00 0.00 3.20
623 685 4.609995 CCGGTGCGGTAATGTCTT 57.390 55.556 0.00 0.00 42.73 3.01
624 686 2.380081 CCGGTGCGGTAATGTCTTC 58.620 57.895 0.00 0.00 42.73 2.87
625 687 0.108329 CCGGTGCGGTAATGTCTTCT 60.108 55.000 0.00 0.00 42.73 2.85
626 688 1.278238 CGGTGCGGTAATGTCTTCTC 58.722 55.000 0.00 0.00 0.00 2.87
627 689 1.278238 GGTGCGGTAATGTCTTCTCG 58.722 55.000 0.00 0.00 0.00 4.04
628 690 1.135199 GGTGCGGTAATGTCTTCTCGA 60.135 52.381 0.00 0.00 0.00 4.04
629 691 2.481449 GGTGCGGTAATGTCTTCTCGAT 60.481 50.000 0.00 0.00 0.00 3.59
630 692 2.789893 GTGCGGTAATGTCTTCTCGATC 59.210 50.000 0.00 0.00 0.00 3.69
631 693 2.223735 TGCGGTAATGTCTTCTCGATCC 60.224 50.000 0.00 0.00 0.00 3.36
633 695 2.288273 CGGTAATGTCTTCTCGATCCCC 60.288 54.545 0.00 0.00 0.00 4.81
634 696 2.698797 GGTAATGTCTTCTCGATCCCCA 59.301 50.000 0.00 0.00 0.00 4.96
635 697 3.325135 GGTAATGTCTTCTCGATCCCCAT 59.675 47.826 0.00 0.00 0.00 4.00
636 698 3.760580 AATGTCTTCTCGATCCCCATC 57.239 47.619 0.00 0.00 0.00 3.51
638 700 2.752030 TGTCTTCTCGATCCCCATCTT 58.248 47.619 0.00 0.00 0.00 2.40
639 701 3.910989 TGTCTTCTCGATCCCCATCTTA 58.089 45.455 0.00 0.00 0.00 2.10
645 800 2.965831 CTCGATCCCCATCTTACCTGAA 59.034 50.000 0.00 0.00 0.00 3.02
952 1119 4.339530 GGTTCTCCAGGATAAATGAAAGCC 59.660 45.833 0.00 0.00 0.00 4.35
975 1142 2.689983 AGCTTATGCACCTTATTGTGGC 59.310 45.455 3.16 0.00 42.74 5.01
1395 1562 3.002348 GTGTTGCTTCAGTACCAGTTGAC 59.998 47.826 0.00 0.00 0.00 3.18
1516 1683 3.287867 AGCCATTTGATCAGAATCCGT 57.712 42.857 0.00 0.00 0.00 4.69
1624 1791 6.155221 GGTCAGTCTATATCAAGATGCCCATA 59.845 42.308 0.00 0.00 0.00 2.74
1830 1997 2.039418 CCACGGACCATTGGAGAGATA 58.961 52.381 10.37 0.00 34.46 1.98
1925 2092 1.264826 TCTTTTGAAAACGGTAGGCGC 59.735 47.619 0.00 0.00 0.00 6.53
1969 2136 4.803452 TCACCCTTGAACCTCTTCATTTT 58.197 39.130 0.00 0.00 36.26 1.82
1980 2147 8.602424 TGAACCTCTTCATTTTATCCTTCACTA 58.398 33.333 0.00 0.00 31.00 2.74
2040 2207 7.895759 ACTGTTTGGCATCACATTATTAGTTT 58.104 30.769 0.87 0.00 0.00 2.66
2441 2610 3.321497 TGTTTGCCTGTTTTGTTCACAC 58.679 40.909 0.00 0.00 0.00 3.82
2695 2865 5.695816 TCAACCAGTCATTTTTATTTGCTGC 59.304 36.000 0.00 0.00 0.00 5.25
2808 2979 4.430007 GAACCAGCGTGTATCAGTATCAA 58.570 43.478 0.00 0.00 0.00 2.57
2904 3075 4.730949 TGTTCTACTCCATTCCCTTACG 57.269 45.455 0.00 0.00 0.00 3.18
3023 3194 7.116061 TGTTTTCACTTTTCACTTTTCAAGC 57.884 32.000 0.00 0.00 0.00 4.01
3134 3315 0.893270 TCCCAACAAACAGATGCCCG 60.893 55.000 0.00 0.00 0.00 6.13
3145 3326 4.060038 ACAGATGCCCGTAATTCACTAG 57.940 45.455 0.00 0.00 0.00 2.57
3300 3481 6.801575 TCGAAAAATAACAGCTTTTCTTGGT 58.198 32.000 5.13 0.00 38.72 3.67
3318 3499 1.000955 GGTGGTCTCGACTTGTGTGAT 59.999 52.381 0.00 0.00 0.00 3.06
3399 3580 5.301805 GGATGATTTCCATAATCCCACGTTT 59.698 40.000 0.00 0.00 44.74 3.60
3421 3602 8.861101 CGTTTCCTGTAATTCTCTAACAGTTAG 58.139 37.037 13.53 13.53 39.17 2.34
3425 3606 6.981559 CCTGTAATTCTCTAACAGTTAGCTCC 59.018 42.308 14.73 0.78 39.17 4.70
3445 3626 5.529060 GCTCCATCTTTGTTCCCTAACTATG 59.471 44.000 0.00 0.00 36.51 2.23
3510 3691 6.811253 ACAACTTTCCGACATGCTAAAATA 57.189 33.333 0.00 0.00 0.00 1.40
3753 3934 2.588439 GCCCTCTGCAGATGAGCA 59.412 61.111 18.63 0.00 43.35 4.26
3918 4099 9.271828 CACCTTGTTTATTTTGGCTAGATTTTT 57.728 29.630 0.00 0.00 0.00 1.94
4265 4447 6.656270 TCTTCGTACTACTGGTCTTCACATAA 59.344 38.462 0.00 0.00 0.00 1.90
4332 4514 3.122613 TGTTTCGTTTTTGCTTTGTGCTG 59.877 39.130 0.00 0.00 43.37 4.41
4346 4528 0.681175 GTGCTGTGCCCTTCCATTTT 59.319 50.000 0.00 0.00 0.00 1.82
4362 4544 7.970614 CCTTCCATTTTGCAAGTTAGATACTTC 59.029 37.037 0.00 0.00 45.29 3.01
4534 4716 4.286291 ACCGAGGAATAGTTGGACTTTTCT 59.714 41.667 9.87 0.00 36.71 2.52
4711 5011 7.067494 GTGCAGAGAACCTAATACCAATTGAAT 59.933 37.037 7.12 0.00 0.00 2.57
4864 5164 5.007626 GCCGCATGATCAGATTACAGTTTTA 59.992 40.000 0.09 0.00 0.00 1.52
5057 5357 5.298989 TGAACTTCTACTGCCTTGGTAAA 57.701 39.130 0.00 0.00 0.00 2.01
5274 5574 7.975174 ACTCGAAAGGGATGATCATCGATGAT 61.975 42.308 35.11 35.11 42.27 2.45
5373 5673 0.615331 CCTATCAGCCACACCACAGT 59.385 55.000 0.00 0.00 0.00 3.55
5621 5922 2.813474 GCGTGCTATGTGTCGCCA 60.813 61.111 0.00 0.00 42.33 5.69
5813 6114 0.104671 GGCAGAGGATCAGAGTGCTC 59.895 60.000 0.00 0.00 37.82 4.26
5883 6184 3.269538 TGAAGTTGTTCCTCGGAAACA 57.730 42.857 0.00 0.00 35.75 2.83
5884 6185 3.611970 TGAAGTTGTTCCTCGGAAACAA 58.388 40.909 0.00 4.34 35.75 2.83
6046 6348 3.475566 TGGAGTCTATTGCTATGCACC 57.524 47.619 0.00 0.00 38.71 5.01
6088 6390 1.535462 CCACCGCAGTTTGGTTAGAAG 59.465 52.381 0.00 0.00 37.72 2.85
6146 6616 4.207165 ACATGTACCAAGCTTGTTCTTGT 58.793 39.130 24.35 20.88 41.29 3.16
6148 6618 5.127031 ACATGTACCAAGCTTGTTCTTGTTT 59.873 36.000 24.35 0.42 41.29 2.83
6150 6620 6.031751 TGTACCAAGCTTGTTCTTGTTTTT 57.968 33.333 24.35 0.00 41.29 1.94
6297 6786 4.250464 CCTTGTTGGTAATGAGCTCGTAA 58.750 43.478 9.33 0.00 0.00 3.18
6307 6796 5.597813 AATGAGCTCGTAAAAGTTGTCTG 57.402 39.130 9.33 0.00 0.00 3.51
6381 6994 2.579860 ACCTTGAGGAAGAGGCATCAAT 59.420 45.455 0.00 0.00 37.84 2.57
6537 7150 8.470002 AGCATCAAAACTACTCCAAAATAATCC 58.530 33.333 0.00 0.00 0.00 3.01
6633 7246 9.618890 CAAATTCTATTTGGATGAGTAGAGGAA 57.381 33.333 4.59 0.00 0.00 3.36
6640 7253 5.541953 TGGATGAGTAGAGGAATCACATG 57.458 43.478 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.450115 GGGCTCGACGGCAGTACT 61.450 66.667 9.90 0.00 40.61 2.73
1 2 2.573609 AATGGGCTCGACGGCAGTAC 62.574 60.000 9.90 0.00 40.61 2.73
2 3 2.292794 GAATGGGCTCGACGGCAGTA 62.293 60.000 9.90 0.00 40.61 2.74
3 4 3.665675 GAATGGGCTCGACGGCAGT 62.666 63.158 9.90 0.00 40.61 4.40
4 5 2.892425 GAATGGGCTCGACGGCAG 60.892 66.667 9.90 0.00 40.61 4.85
6 7 2.203070 ATGAATGGGCTCGACGGC 60.203 61.111 0.00 0.00 37.49 5.68
7 8 2.537560 GCATGAATGGGCTCGACGG 61.538 63.158 0.00 0.00 0.00 4.79
8 9 2.537560 GGCATGAATGGGCTCGACG 61.538 63.158 0.00 0.00 0.00 5.12
9 10 1.442526 CTGGCATGAATGGGCTCGAC 61.443 60.000 0.00 0.00 0.00 4.20
10 11 1.153107 CTGGCATGAATGGGCTCGA 60.153 57.895 0.00 0.00 0.00 4.04
11 12 2.842256 GCTGGCATGAATGGGCTCG 61.842 63.158 0.00 0.00 0.00 5.03
12 13 1.735376 CTGCTGGCATGAATGGGCTC 61.735 60.000 0.00 0.00 0.00 4.70
13 14 1.756950 CTGCTGGCATGAATGGGCT 60.757 57.895 0.00 0.00 0.00 5.19
14 15 1.324740 TTCTGCTGGCATGAATGGGC 61.325 55.000 0.00 0.00 0.00 5.36
15 16 0.458669 GTTCTGCTGGCATGAATGGG 59.541 55.000 0.00 0.00 0.00 4.00
16 17 1.135199 GTGTTCTGCTGGCATGAATGG 60.135 52.381 0.00 0.00 0.00 3.16
17 18 1.816835 AGTGTTCTGCTGGCATGAATG 59.183 47.619 0.00 0.00 0.00 2.67
18 19 2.211250 AGTGTTCTGCTGGCATGAAT 57.789 45.000 0.00 0.00 0.00 2.57
19 20 1.610038 CAAGTGTTCTGCTGGCATGAA 59.390 47.619 0.00 0.23 0.00 2.57
20 21 1.241165 CAAGTGTTCTGCTGGCATGA 58.759 50.000 0.00 0.00 0.00 3.07
21 22 0.242825 CCAAGTGTTCTGCTGGCATG 59.757 55.000 0.00 0.00 0.00 4.06
103 150 1.067669 GCTGACGATGTGCTGGAGATA 59.932 52.381 0.00 0.00 0.00 1.98
118 166 0.944386 TTTTTCTCGCAGGTGCTGAC 59.056 50.000 0.00 0.00 39.32 3.51
119 167 0.944386 GTTTTTCTCGCAGGTGCTGA 59.056 50.000 0.00 0.00 39.32 4.26
154 204 2.783510 GTGAGGGGAAATGGGGAATAGA 59.216 50.000 0.00 0.00 0.00 1.98
193 244 0.172803 CTCTACTGTTTAGCGGCGGT 59.827 55.000 18.21 18.21 0.00 5.68
201 252 2.923605 GCGGCGACAACTCTACTGTTTA 60.924 50.000 12.98 0.00 0.00 2.01
260 313 1.248785 TGAGCTCGGGTGTGGTAGTC 61.249 60.000 9.64 0.00 0.00 2.59
263 316 2.632544 CGTGAGCTCGGGTGTGGTA 61.633 63.158 9.64 0.00 0.00 3.25
430 488 3.246112 CAGGTCCAACCCCCGTCA 61.246 66.667 0.00 0.00 39.75 4.35
623 685 2.177016 TCAGGTAAGATGGGGATCGAGA 59.823 50.000 0.00 0.00 0.00 4.04
624 686 2.598565 TCAGGTAAGATGGGGATCGAG 58.401 52.381 0.00 0.00 0.00 4.04
625 687 2.767644 TCAGGTAAGATGGGGATCGA 57.232 50.000 0.00 0.00 0.00 3.59
626 688 3.580458 AGATTCAGGTAAGATGGGGATCG 59.420 47.826 0.00 0.00 0.00 3.69
627 689 5.163152 ACAAGATTCAGGTAAGATGGGGATC 60.163 44.000 0.00 0.00 0.00 3.36
628 690 4.728860 ACAAGATTCAGGTAAGATGGGGAT 59.271 41.667 0.00 0.00 0.00 3.85
629 691 4.111577 ACAAGATTCAGGTAAGATGGGGA 58.888 43.478 0.00 0.00 0.00 4.81
630 692 4.080356 TGACAAGATTCAGGTAAGATGGGG 60.080 45.833 0.00 0.00 0.00 4.96
631 693 5.102953 TGACAAGATTCAGGTAAGATGGG 57.897 43.478 0.00 0.00 0.00 4.00
633 695 6.596888 ACACATGACAAGATTCAGGTAAGATG 59.403 38.462 0.00 0.00 38.43 2.90
634 696 6.715280 ACACATGACAAGATTCAGGTAAGAT 58.285 36.000 0.00 0.00 38.43 2.40
635 697 6.114187 ACACATGACAAGATTCAGGTAAGA 57.886 37.500 0.00 0.00 38.43 2.10
636 698 7.148407 GGTTACACATGACAAGATTCAGGTAAG 60.148 40.741 0.00 0.00 38.43 2.34
638 700 6.170506 GGTTACACATGACAAGATTCAGGTA 58.829 40.000 0.00 0.00 38.43 3.08
639 701 5.003804 GGTTACACATGACAAGATTCAGGT 58.996 41.667 0.00 0.00 41.08 4.00
765 920 1.757682 TTGGGCAACGGTATTCCATC 58.242 50.000 0.00 0.00 37.60 3.51
819 985 6.906678 TCATACGAAAGCATGAAAAATGATCG 59.093 34.615 0.00 0.00 40.74 3.69
952 1119 4.023707 GCCACAATAAGGTGCATAAGCTAG 60.024 45.833 0.00 0.00 42.74 3.42
1395 1562 4.103785 ACAATATCCCCTTCTGTGATCTGG 59.896 45.833 0.00 0.00 0.00 3.86
1516 1683 1.764134 ACCAACTCCGTCCTTGTACAA 59.236 47.619 8.28 8.28 0.00 2.41
1540 1707 6.127140 GGTACACCAATATTCTCAGTACCACT 60.127 42.308 20.45 0.00 45.67 4.00
1624 1791 6.414732 TGTTAGGACGAAAATCATCAGGAAT 58.585 36.000 0.00 0.00 0.00 3.01
1830 1997 4.039609 CCCTCTTGAACCTTGCTTTTCAAT 59.960 41.667 0.00 0.00 40.16 2.57
1925 2092 1.881973 CCAATGGGCGATGTGGAATAG 59.118 52.381 0.00 0.00 32.54 1.73
1969 2136 5.423931 TGTACAGCCATGTTAGTGAAGGATA 59.576 40.000 0.00 0.00 41.01 2.59
1980 2147 9.801873 GTAATAATTTTGATGTACAGCCATGTT 57.198 29.630 8.95 1.80 41.01 2.71
2009 2176 4.462508 TGTGATGCCAAACAGTTCAAAA 57.537 36.364 0.00 0.00 0.00 2.44
2040 2207 4.453136 GGAAAAACTACACGGTAGCATCAA 59.547 41.667 10.00 0.00 0.00 2.57
2134 2303 8.431222 TCATTCACCCAAAATTTCAGAATTCTT 58.569 29.630 4.86 0.00 34.44 2.52
2363 2532 3.245122 TGAACATAGGGGTTTGGTTCTCC 60.245 47.826 0.00 0.00 38.82 3.71
2640 2810 7.815068 CAGAATATGCAGAAGTATAGGTACACC 59.185 40.741 0.00 0.00 33.09 4.16
2695 2865 3.740397 CCACAGCCACACGCATGG 61.740 66.667 1.08 1.08 43.26 3.66
2808 2979 9.515226 GTTGACTAACCTGATAGATAGAGAGAT 57.485 37.037 0.00 0.00 0.00 2.75
2904 3075 1.574702 GGTTAGCAGGACGGCACAAC 61.575 60.000 0.00 1.12 35.83 3.32
3023 3194 4.913335 AAGGATAGCATGCAAGATGTTG 57.087 40.909 21.98 0.00 36.67 3.33
3111 3292 3.244526 GGGCATCTGTTTGTTGGGAAAAT 60.245 43.478 0.00 0.00 0.00 1.82
3115 3296 0.893270 CGGGCATCTGTTTGTTGGGA 60.893 55.000 0.00 0.00 0.00 4.37
3161 3342 8.670135 CAGAAACACCCGAATACATAAACATTA 58.330 33.333 0.00 0.00 0.00 1.90
3300 3481 1.000843 CCATCACACAAGTCGAGACCA 59.999 52.381 0.00 0.00 0.00 4.02
3318 3499 4.408596 TGTTCAGGTGTATCATATCTGCCA 59.591 41.667 0.00 0.00 0.00 4.92
3399 3580 7.147880 GGAGCTAACTGTTAGAGAATTACAGGA 60.148 40.741 27.14 0.00 42.70 3.86
3421 3602 3.956744 AGTTAGGGAACAAAGATGGAGC 58.043 45.455 0.00 0.00 38.10 4.70
3425 3606 8.883731 CAGTAACATAGTTAGGGAACAAAGATG 58.116 37.037 0.00 0.00 38.10 2.90
3470 3651 7.549488 GGAAAGTTGTTTTCTCAGCTATAGCTA 59.451 37.037 26.45 9.30 45.75 3.32
3510 3691 7.992754 AGTTGCAGAAAGAAGAATGTTCTAT 57.007 32.000 0.00 0.00 36.28 1.98
3753 3934 6.981762 TTTCTTCACAAACATGTGCATTTT 57.018 29.167 0.00 0.00 39.49 1.82
3826 4007 6.604171 ACCAAGGTGATGCATCTATGATTTA 58.396 36.000 26.32 1.49 0.00 1.40
3871 4052 7.434492 AGGTGGTGACATTTATCTAATAGACG 58.566 38.462 0.00 0.00 46.14 4.18
4051 4232 9.793259 AGTTCTGATAAAGTTAAAACTCCATCA 57.207 29.630 14.03 14.03 38.57 3.07
4265 4447 3.832527 ACAACTTCATTACCTGCACCTT 58.167 40.909 0.00 0.00 0.00 3.50
4332 4514 1.799544 CTTGCAAAATGGAAGGGCAC 58.200 50.000 0.00 0.00 41.35 5.01
4362 4544 2.438434 GAAGGGATGGTGTGGCGG 60.438 66.667 0.00 0.00 0.00 6.13
4392 4574 5.580691 TGAAGCATGGAATACTACAAACTCG 59.419 40.000 0.00 0.00 0.00 4.18
4564 4746 8.402326 AGTTTTCGTAAAAAGAAACCAATGAC 57.598 30.769 0.00 0.00 37.33 3.06
4711 5011 5.245751 TCTTTCTTGCAATCTTTATGGCCAA 59.754 36.000 10.96 0.00 30.07 4.52
4864 5164 6.114187 TGTCACAAGAGTTAGGTTCATGAT 57.886 37.500 0.00 0.00 0.00 2.45
5115 5415 9.877178 GAGAAGAGAATGAAATAGAGTTACCAA 57.123 33.333 0.00 0.00 0.00 3.67
5621 5922 1.283029 CCCTTCATGTCCACCATCTGT 59.717 52.381 0.00 0.00 0.00 3.41
5813 6114 2.370281 TTGTAGCCTCTTCAAGCTCG 57.630 50.000 0.00 0.00 40.56 5.03
5840 6141 2.317609 CCACTTCTGAACGCCCGTG 61.318 63.158 0.00 1.07 0.00 4.94
6046 6348 4.755123 GGACAACGGGGAATTACATCATAG 59.245 45.833 0.00 0.00 0.00 2.23
6088 6390 1.936547 GACCAAGATCTGAATGCCGAC 59.063 52.381 0.00 0.00 0.00 4.79
6177 6650 4.279671 ACATTTTGACATACGGGCAAGAAA 59.720 37.500 0.00 0.00 0.00 2.52
6242 6729 2.447443 TGCATCAACGAGACTCCTACT 58.553 47.619 0.00 0.00 0.00 2.57
6297 6786 2.380064 TGGGCATTCCAGACAACTTT 57.620 45.000 0.00 0.00 41.46 2.66
6307 6796 0.036388 TCGACTGAGTTGGGCATTCC 60.036 55.000 0.00 0.00 0.00 3.01
6469 7082 0.175989 CTTAGAGGCGTTGTCTCCCC 59.824 60.000 0.00 0.00 34.41 4.81
6537 7150 6.662414 AAAATGAGCTTGCATGATGATTTG 57.338 33.333 14.17 0.00 0.00 2.32
6633 7246 4.283978 TGAAATTGTTCCTTGGCATGTGAT 59.716 37.500 0.00 0.00 32.28 3.06
6640 7253 4.692228 TCTTTGTGAAATTGTTCCTTGGC 58.308 39.130 0.00 0.00 32.28 4.52


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

AutoCloner maintained by Alex Coulton.