Multiple sequence alignment - TraesCS6A01G395000

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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 TraesCS6A01G395000 chr6A 100.000 7119 0 0 1 7119 608112133 608119251 0.000000e+00 13147.0
1 TraesCS6A01G395000 chr6D 94.413 6264 161 66 931 7119 461449445 461455594 0.000000e+00 9454.0
2 TraesCS6A01G395000 chr6D 90.450 733 31 18 3 727 461448645 461449346 0.000000e+00 929.0
3 TraesCS6A01G395000 chr6B 94.271 4800 154 37 2367 7119 703284764 703289489 0.000000e+00 7228.0
4 TraesCS6A01G395000 chr6B 92.194 1358 50 32 1040 2367 703283402 703284733 0.000000e+00 1869.0
5 TraesCS6A01G395000 chr6B 89.050 968 64 20 3 937 703281943 703282901 0.000000e+00 1162.0
6 TraesCS6A01G395000 chrUn 84.175 297 47 0 5330 5626 93449296 93449000 9.040000e-74 289.0
7 TraesCS6A01G395000 chrUn 84.507 213 30 3 2004 2213 93453549 93453337 2.600000e-49 207.0
8 TraesCS6A01G395000 chr7B 84.175 297 47 0 5330 5626 743145591 743145887 9.040000e-74 289.0
9 TraesCS6A01G395000 chr7B 76.327 490 105 9 4516 5001 743144521 743145003 1.190000e-62 252.0
10 TraesCS6A01G395000 chr7B 83.099 213 33 2 2004 2213 743142071 743142283 2.620000e-44 191.0
11 TraesCS6A01G395000 chr4D 85.714 56 6 2 328 382 502723713 502723659 2.770000e-04 58.4
12 TraesCS6A01G395000 chr2D 100.000 29 0 0 338 366 584864788 584864816 4.000000e-03 54.7
13 TraesCS6A01G395000 chr4B 100.000 28 0 0 338 365 523631186 523631213 1.300000e-02 52.8
14 TraesCS6A01G395000 chr2B 100.000 28 0 0 338 365 758140597 758140624 1.300000e-02 52.8


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 TraesCS6A01G395000 chr6A 608112133 608119251 7118 False 13147.000000 13147 100.000000 1 7119 1 chr6A.!!$F1 7118
1 TraesCS6A01G395000 chr6D 461448645 461455594 6949 False 5191.500000 9454 92.431500 3 7119 2 chr6D.!!$F1 7116
2 TraesCS6A01G395000 chr6B 703281943 703289489 7546 False 3419.666667 7228 91.838333 3 7119 3 chr6B.!!$F1 7116
3 TraesCS6A01G395000 chr7B 743142071 743145887 3816 False 244.000000 289 81.200333 2004 5626 3 chr7B.!!$F1 3622

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
995 1412 0.768221 AGGAAGGCAGGTCCAGTTGA 60.768 55.0 4.92 0.0 37.65 3.18 F
1645 2136 0.606944 TCCGTTTTTCCCGTGGGATG 60.607 55.0 8.81 0.0 44.74 3.51 F
3425 4085 0.107214 GGGGATGTCATCGAAAGGCA 60.107 55.0 6.74 0.0 0.00 4.75 F
4394 5059 0.247736 AAGCTCTCGAAGGCGTCAAT 59.752 50.0 0.55 0.0 38.98 2.57 F
5267 6101 0.254462 CCTGCCTTCTCTTTCTCCCC 59.746 60.0 0.00 0.0 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2576 3162 0.328926 TGCTCATCACATCTGCCCAA 59.671 50.0 0.00 0.00 0.00 4.12 R
3433 4093 0.037590 CCCCATCCGTTCCAACTGAA 59.962 55.0 0.00 0.00 0.00 3.02 R
5083 5907 0.112995 TCTGCTTGCCAACCCTGAAT 59.887 50.0 0.00 0.00 0.00 2.57 R
5460 6400 0.104120 CGATGGGCTTGACGATGGTA 59.896 55.0 0.00 0.00 0.00 3.25 R
6138 7078 0.176680 AAGCGATGAACCGATCAGCT 59.823 50.0 5.19 3.01 42.36 4.24 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
34 35 5.156608 TGACATCACATTCTCACACAGAT 57.843 39.130 0.00 0.00 0.00 2.90
37 38 6.071165 TGACATCACATTCTCACACAGATACT 60.071 38.462 0.00 0.00 0.00 2.12
38 39 7.122650 TGACATCACATTCTCACACAGATACTA 59.877 37.037 0.00 0.00 0.00 1.82
122 125 9.750125 ATTTGTCTCTTGTCTATTTTTGTTTCC 57.250 29.630 0.00 0.00 0.00 3.13
228 233 3.386726 CAGAGGACGGGGATAATAACACA 59.613 47.826 0.00 0.00 0.00 3.72
281 289 7.876896 TTCTATTTTTATTTCCACAAACGCC 57.123 32.000 0.00 0.00 0.00 5.68
285 293 6.591313 TTTTTATTTCCACAAACGCCTTTC 57.409 33.333 0.00 0.00 0.00 2.62
428 476 7.588143 TGTTCACAGGTTTAAACAATTGTTG 57.412 32.000 23.93 12.90 38.44 3.33
682 740 8.517878 ACATGTTGAGGAAAATGTTCATAAGAG 58.482 33.333 0.00 0.00 35.25 2.85
745 804 3.313249 TGGCACAATATCTTTCATGAGCG 59.687 43.478 0.00 0.00 31.92 5.03
761 820 3.371168 TGAGCGATTTTTGAAGTGTTGC 58.629 40.909 0.00 0.00 0.00 4.17
812 871 1.956629 ATGCGGCGGTAGCTTGTAGT 61.957 55.000 9.78 0.00 44.37 2.73
830 889 3.439857 AGTGATTTGGTGGTAGCATGT 57.560 42.857 0.00 0.00 0.00 3.21
854 913 4.130118 GCTTGTAGTGATTGGGATACTGG 58.870 47.826 0.00 0.00 0.00 4.00
855 914 4.708177 CTTGTAGTGATTGGGATACTGGG 58.292 47.826 0.00 0.00 0.00 4.45
950 1009 4.440525 GCATCTCAAACATACACCCATTGG 60.441 45.833 0.00 0.00 37.80 3.16
952 1011 5.506730 TCTCAAACATACACCCATTGGTA 57.493 39.130 1.20 0.00 45.57 3.25
995 1412 0.768221 AGGAAGGCAGGTCCAGTTGA 60.768 55.000 4.92 0.00 37.65 3.18
1049 1506 3.391382 CCCTCACTCCCGACCACC 61.391 72.222 0.00 0.00 0.00 4.61
1050 1507 3.391382 CCTCACTCCCGACCACCC 61.391 72.222 0.00 0.00 0.00 4.61
1052 1509 2.283676 TCACTCCCGACCACCCTC 60.284 66.667 0.00 0.00 0.00 4.30
1053 1510 2.283966 CACTCCCGACCACCCTCT 60.284 66.667 0.00 0.00 0.00 3.69
1054 1511 2.283966 ACTCCCGACCACCCTCTG 60.284 66.667 0.00 0.00 0.00 3.35
1056 1513 4.316823 TCCCGACCACCCTCTGCT 62.317 66.667 0.00 0.00 0.00 4.24
1058 1515 3.775654 CCGACCACCCTCTGCTCC 61.776 72.222 0.00 0.00 0.00 4.70
1060 1517 2.284995 GACCACCCTCTGCTCCCT 60.285 66.667 0.00 0.00 0.00 4.20
1357 1826 4.214327 CGCGCCTCTCCTCCTTCC 62.214 72.222 0.00 0.00 0.00 3.46
1408 1880 2.563050 CTTCGAGGAGCACGCCATCA 62.563 60.000 0.00 0.00 0.00 3.07
1411 1883 2.045926 AGGAGCACGCCATCAACC 60.046 61.111 0.00 0.00 0.00 3.77
1412 1884 2.359850 GGAGCACGCCATCAACCA 60.360 61.111 0.00 0.00 0.00 3.67
1413 1885 2.401766 GGAGCACGCCATCAACCAG 61.402 63.158 0.00 0.00 0.00 4.00
1612 2103 1.003580 ACGTGCATGTCCATTCTCCTT 59.996 47.619 5.51 0.00 0.00 3.36
1613 2104 1.667724 CGTGCATGTCCATTCTCCTTC 59.332 52.381 0.00 0.00 0.00 3.46
1614 2105 2.679059 CGTGCATGTCCATTCTCCTTCT 60.679 50.000 0.00 0.00 0.00 2.85
1615 2106 3.350833 GTGCATGTCCATTCTCCTTCTT 58.649 45.455 0.00 0.00 0.00 2.52
1616 2107 3.376546 GTGCATGTCCATTCTCCTTCTTC 59.623 47.826 0.00 0.00 0.00 2.87
1617 2108 3.265221 TGCATGTCCATTCTCCTTCTTCT 59.735 43.478 0.00 0.00 0.00 2.85
1645 2136 0.606944 TCCGTTTTTCCCGTGGGATG 60.607 55.000 8.81 0.00 44.74 3.51
1654 2145 2.172483 CCCGTGGGATGGATCGATCC 62.172 65.000 33.41 33.41 41.82 3.36
1807 2306 4.307032 AAGCCACATCCACATTCTTAGT 57.693 40.909 0.00 0.00 0.00 2.24
1835 2337 2.094803 TGCATGGTAGCATTTTGAACCG 60.095 45.455 4.25 0.00 40.11 4.44
1850 2352 2.034053 TGAACCGTTGTCATTTCCTTGC 59.966 45.455 0.00 0.00 0.00 4.01
1910 2415 5.726980 AGATCTAGATCATGGTTCTCTGC 57.273 43.478 29.83 3.64 40.22 4.26
2239 2747 1.132453 CATGCCAACATCACAGCTGAG 59.868 52.381 23.35 13.75 32.87 3.35
2251 2782 7.144000 ACATCACAGCTGAGAAAAAGAATTTC 58.856 34.615 23.35 0.00 37.28 2.17
2334 2874 4.508861 CCAACTCAAATGCAAACAGAAAGG 59.491 41.667 0.00 0.00 0.00 3.11
2340 2880 6.347696 TCAAATGCAAACAGAAAGGAATTGT 58.652 32.000 0.00 0.00 0.00 2.71
2344 2884 8.538409 AATGCAAACAGAAAGGAATTGTTATC 57.462 30.769 0.00 0.00 34.18 1.75
2419 2990 1.918293 CTGCCCACTGTCCACCCTA 60.918 63.158 0.00 0.00 0.00 3.53
2434 3005 1.904537 ACCCTAAACAAGACTACGGGG 59.095 52.381 0.00 0.00 38.59 5.73
2464 3035 1.139095 GTAAGTCGTCTGCCCTCGG 59.861 63.158 0.00 0.00 0.00 4.63
2683 3269 6.893005 AGTAGTGGGTAATCCTATCTATCTGC 59.107 42.308 0.00 0.00 36.20 4.26
2699 3285 7.421530 TCTATCTGCTGTTTCAAAGTTGTAC 57.578 36.000 0.00 0.00 0.00 2.90
2767 3353 5.182001 GGTATATTTAGTGGGCATGCTCTTG 59.818 44.000 20.42 0.00 0.00 3.02
2812 3402 5.929058 TTATCTGTTCAGATGCTGAGAGT 57.071 39.130 21.15 0.09 41.75 3.24
2874 3464 2.548480 GACTTCGCAAACCAGTAAGCTT 59.452 45.455 3.48 3.48 0.00 3.74
2878 3468 1.069227 CGCAAACCAGTAAGCTTGACC 60.069 52.381 9.86 0.00 0.00 4.02
2929 3519 0.390472 CCCTCCGCAGTCTTCTTGAC 60.390 60.000 0.00 0.00 45.67 3.18
2967 3557 3.744660 TGTGGCCTTCTTCTTCTTCTTC 58.255 45.455 3.32 0.00 0.00 2.87
2969 3559 4.141390 TGTGGCCTTCTTCTTCTTCTTCTT 60.141 41.667 3.32 0.00 0.00 2.52
2971 3561 4.349342 TGGCCTTCTTCTTCTTCTTCTTCT 59.651 41.667 3.32 0.00 0.00 2.85
2972 3562 5.163152 TGGCCTTCTTCTTCTTCTTCTTCTT 60.163 40.000 3.32 0.00 0.00 2.52
3102 3742 6.653273 AGCGAATCGATATCATGGTTATTG 57.347 37.500 6.91 0.00 0.00 1.90
3137 3777 0.236711 CAGCTGCTTTGGTCGAACTG 59.763 55.000 0.00 0.00 0.00 3.16
3159 3799 6.128172 ACTGACACTTGTCTTCTGTTCTTTTG 60.128 38.462 10.63 0.00 44.99 2.44
3425 4085 0.107214 GGGGATGTCATCGAAAGGCA 60.107 55.000 6.74 0.00 0.00 4.75
3428 4088 2.564771 GGATGTCATCGAAAGGCATGA 58.435 47.619 12.31 0.00 0.00 3.07
3429 4089 3.144506 GGATGTCATCGAAAGGCATGAT 58.855 45.455 12.31 0.00 31.71 2.45
3430 4090 3.058432 GGATGTCATCGAAAGGCATGATG 60.058 47.826 12.31 0.00 40.61 3.07
3483 4143 1.745489 GCAACCTCCCCGACATGAC 60.745 63.158 0.00 0.00 0.00 3.06
3766 4426 2.352519 GGACCTAACTCTGACGTTGACC 60.353 54.545 0.00 0.00 0.00 4.02
4062 4723 4.396166 CAGGTATTTGCCCAAGTAGAGTTG 59.604 45.833 0.00 0.00 0.00 3.16
4080 4745 3.074538 AGTTGGCCATCTACCTTTTCAGT 59.925 43.478 14.90 0.00 0.00 3.41
4108 4773 8.589335 ACACAAGTGAACTAACTTACTGTATG 57.411 34.615 7.28 0.00 38.34 2.39
4110 4775 9.042008 CACAAGTGAACTAACTTACTGTATGTT 57.958 33.333 19.03 19.03 38.34 2.71
4111 4776 9.609346 ACAAGTGAACTAACTTACTGTATGTTT 57.391 29.630 19.90 6.67 38.34 2.83
4112 4777 9.864034 CAAGTGAACTAACTTACTGTATGTTTG 57.136 33.333 19.90 19.37 38.34 2.93
4127 4792 2.507484 TGTTTGTGGAATCTCAGGCTG 58.493 47.619 8.58 8.58 0.00 4.85
4361 5026 1.261238 CCTCCCTGCTTCTTCTCCGT 61.261 60.000 0.00 0.00 0.00 4.69
4394 5059 0.247736 AAGCTCTCGAAGGCGTCAAT 59.752 50.000 0.55 0.00 38.98 2.57
4429 5094 3.439857 TCATCAGCCTAGGTTTGCTTT 57.560 42.857 11.31 0.00 35.12 3.51
4477 5142 2.042259 TTTGCCTCATCGCCTGCAG 61.042 57.895 6.78 6.78 34.81 4.41
4584 5251 1.807814 GGGGGATGACTGTCTACCAT 58.192 55.000 19.25 3.46 0.00 3.55
4959 5632 0.951558 ATCTGTCAAACCGCAACACC 59.048 50.000 0.00 0.00 0.00 4.16
5008 5681 1.205055 CCTGGGAAGGTAAGGTCTCC 58.795 60.000 0.00 0.00 0.00 3.71
5026 5699 5.112686 GTCTCCCTCATCTGTGTATTGAAC 58.887 45.833 0.00 0.00 0.00 3.18
5044 5717 3.054139 TGAACATCTCATTTCCTGGGGAG 60.054 47.826 0.00 0.00 31.21 4.30
5075 5899 3.935203 CAGCTCATCTCGGTGTTTATGTT 59.065 43.478 0.00 0.00 0.00 2.71
5076 5900 4.393062 CAGCTCATCTCGGTGTTTATGTTT 59.607 41.667 0.00 0.00 0.00 2.83
5077 5901 5.003804 AGCTCATCTCGGTGTTTATGTTTT 58.996 37.500 0.00 0.00 0.00 2.43
5078 5902 5.122396 AGCTCATCTCGGTGTTTATGTTTTC 59.878 40.000 0.00 0.00 0.00 2.29
5079 5903 5.106712 GCTCATCTCGGTGTTTATGTTTTCA 60.107 40.000 0.00 0.00 0.00 2.69
5080 5904 6.403636 GCTCATCTCGGTGTTTATGTTTTCAT 60.404 38.462 0.00 0.00 43.60 2.57
5081 5905 7.447374 TCATCTCGGTGTTTATGTTTTCATT 57.553 32.000 0.00 0.00 41.25 2.57
5082 5906 7.526608 TCATCTCGGTGTTTATGTTTTCATTC 58.473 34.615 0.00 0.00 41.25 2.67
5083 5907 6.869315 TCTCGGTGTTTATGTTTTCATTCA 57.131 33.333 0.00 0.00 41.25 2.57
5267 6101 0.254462 CCTGCCTTCTCTTTCTCCCC 59.746 60.000 0.00 0.00 0.00 4.81
5418 6358 4.292178 GCCTCGGGGATGAGCTCG 62.292 72.222 4.80 0.00 34.56 5.03
5431 6371 2.202946 GCTCGCTGGCCTACTTCC 60.203 66.667 3.32 0.00 0.00 3.46
5460 6400 2.615493 GGACACCATCGACCACTTCAAT 60.615 50.000 0.00 0.00 0.00 2.57
5587 6527 4.910585 CGGGCATCGGCTACACCC 62.911 72.222 0.00 0.00 40.87 4.61
5628 6568 1.014564 GCTCCGCACAACTGGTACTC 61.015 60.000 0.00 0.00 0.00 2.59
5638 6578 4.036734 CACAACTGGTACTCAAACATGCTT 59.963 41.667 0.00 0.00 0.00 3.91
5639 6579 4.275936 ACAACTGGTACTCAAACATGCTTC 59.724 41.667 0.00 0.00 0.00 3.86
5659 6599 7.322664 TGCTTCCATTCCTCAATTGTATTTTC 58.677 34.615 5.13 0.00 0.00 2.29
5723 6663 4.207955 AGATTGCTCATCATTGCTCATGT 58.792 39.130 0.00 0.00 33.75 3.21
5948 6888 0.179004 ACCAAACACCCGATTGCTCA 60.179 50.000 0.00 0.00 0.00 4.26
6155 7095 0.807667 ACAGCTGATCGGTTCATCGC 60.808 55.000 23.35 0.00 32.72 4.58
6232 7172 1.399440 CACAGCATGCATGAGGTGTAC 59.601 52.381 30.64 10.38 43.83 2.90
6264 7207 7.607250 ACAGATTTACCTTTTTGTTGTTGTGA 58.393 30.769 0.00 0.00 0.00 3.58
6403 7350 1.581934 TCACTTGTTGCCTTCAGTCG 58.418 50.000 0.00 0.00 0.00 4.18
6405 7352 0.468226 ACTTGTTGCCTTCAGTCGGA 59.532 50.000 0.00 0.00 0.00 4.55
6515 7462 8.354426 CCATTCATCATCATACTTGCACATAAA 58.646 33.333 0.00 0.00 0.00 1.40
6562 7509 7.235812 AGTTAAACTAGAGGTTCAGAAGGTCAT 59.764 37.037 0.00 0.00 37.12 3.06
6591 7538 7.261325 TCAATATCTTTGTTCTCTTCTCTCGG 58.739 38.462 0.00 0.00 0.00 4.63
6592 7539 7.122799 TCAATATCTTTGTTCTCTTCTCTCGGA 59.877 37.037 0.00 0.00 0.00 4.55
6593 7540 5.730296 ATCTTTGTTCTCTTCTCTCGGAA 57.270 39.130 0.00 0.00 0.00 4.30
6628 7575 6.267471 TGGACAAGAAAGGATAAAGCACAAAT 59.733 34.615 0.00 0.00 0.00 2.32
6709 7656 3.578716 AGAACTTAGCAGCTTGTACTCCA 59.421 43.478 0.00 0.00 0.00 3.86
6770 7717 2.322658 TCGGTAAGGAGGTGACAGTTT 58.677 47.619 0.00 0.00 0.00 2.66
6771 7718 2.701951 TCGGTAAGGAGGTGACAGTTTT 59.298 45.455 0.00 0.00 0.00 2.43
6772 7719 3.896888 TCGGTAAGGAGGTGACAGTTTTA 59.103 43.478 0.00 0.00 0.00 1.52
6865 7815 3.775654 GACCTGAGACCCGGCCAG 61.776 72.222 2.24 0.00 0.00 4.85
6923 7873 2.525629 TTCACGTCCTGCCCCTGA 60.526 61.111 0.00 0.00 0.00 3.86
7007 7957 3.831637 AGGTTGTTGCAGCCCCCA 61.832 61.111 0.00 0.00 35.27 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.662234 AGAATGTGATGTCATGAAAGATTGGT 59.338 34.615 0.00 0.00 0.00 3.67
1 2 7.096884 AGAATGTGATGTCATGAAAGATTGG 57.903 36.000 0.00 0.00 0.00 3.16
34 35 3.450904 GGACATAGATGCCCCCATAGTA 58.549 50.000 0.00 0.00 0.00 1.82
37 38 1.668826 GGGACATAGATGCCCCCATA 58.331 55.000 2.52 0.00 43.94 2.74
38 39 2.479562 GGGACATAGATGCCCCCAT 58.520 57.895 2.52 0.00 43.94 4.00
212 217 5.431179 AGTTTCTGTGTTATTATCCCCGT 57.569 39.130 0.00 0.00 0.00 5.28
265 273 3.891324 CGAAAGGCGTTTGTGGAAATAA 58.109 40.909 9.48 0.00 34.64 1.40
267 275 2.415697 CGAAAGGCGTTTGTGGAAAT 57.584 45.000 9.48 0.00 34.64 2.17
279 287 7.408921 CGTGAACAATTTTACAATACGAAAGGC 60.409 37.037 0.00 0.00 0.00 4.35
281 289 7.112287 TGCGTGAACAATTTTACAATACGAAAG 59.888 33.333 0.00 0.00 0.00 2.62
285 293 5.219768 GCTGCGTGAACAATTTTACAATACG 60.220 40.000 0.00 0.00 0.00 3.06
663 721 7.325660 TGATGCTCTTATGAACATTTTCCTC 57.674 36.000 0.00 0.00 30.04 3.71
682 740 6.901887 CACACATAGACTCGTAAATTTGATGC 59.098 38.462 0.00 0.00 0.00 3.91
693 751 3.808466 ATGCATCACACATAGACTCGT 57.192 42.857 0.00 0.00 0.00 4.18
694 752 4.784394 GCAAATGCATCACACATAGACTCG 60.784 45.833 0.00 0.00 41.59 4.18
735 794 5.830912 ACACTTCAAAAATCGCTCATGAAA 58.169 33.333 0.00 0.00 30.37 2.69
745 804 3.789224 ACGTTCGCAACACTTCAAAAATC 59.211 39.130 0.00 0.00 0.00 2.17
793 852 1.227263 CTACAAGCTACCGCCGCAT 60.227 57.895 0.00 0.00 36.60 4.73
812 871 3.278574 GCTACATGCTACCACCAAATCA 58.721 45.455 0.00 0.00 38.95 2.57
830 889 5.070446 CCAGTATCCCAATCACTACAAGCTA 59.930 44.000 0.00 0.00 0.00 3.32
843 902 2.126882 CTGATGGACCCAGTATCCCAA 58.873 52.381 0.00 0.00 35.12 4.12
854 913 4.460948 ACATTTTGCATTCTGATGGACC 57.539 40.909 0.00 0.00 32.96 4.46
855 914 5.232463 ACAACATTTTGCATTCTGATGGAC 58.768 37.500 0.00 0.00 36.00 4.02
922 981 3.428045 GGTGTATGTTTGAGATGCTTGCC 60.428 47.826 0.00 0.00 0.00 4.52
971 1385 1.002011 GGACCTGCCTTCCTTCCAC 60.002 63.158 0.00 0.00 0.00 4.02
995 1412 1.068753 CGCGCCTCCTTCATCTGAT 59.931 57.895 0.00 0.00 0.00 2.90
1024 1441 3.775654 GGAGTGAGGGCAGACGGG 61.776 72.222 0.00 0.00 0.00 5.28
1035 1452 2.283676 GAGGGTGGTCGGGAGTGA 60.284 66.667 0.00 0.00 0.00 3.41
1037 1454 2.283966 CAGAGGGTGGTCGGGAGT 60.284 66.667 0.00 0.00 0.00 3.85
1038 1455 3.775654 GCAGAGGGTGGTCGGGAG 61.776 72.222 0.00 0.00 0.00 4.30
1049 1506 3.044894 AGAAATAGGAAGGGAGCAGAGG 58.955 50.000 0.00 0.00 0.00 3.69
1050 1507 3.743899 GCAGAAATAGGAAGGGAGCAGAG 60.744 52.174 0.00 0.00 0.00 3.35
1052 1509 2.172293 AGCAGAAATAGGAAGGGAGCAG 59.828 50.000 0.00 0.00 0.00 4.24
1053 1510 2.171448 GAGCAGAAATAGGAAGGGAGCA 59.829 50.000 0.00 0.00 0.00 4.26
1054 1511 2.437651 AGAGCAGAAATAGGAAGGGAGC 59.562 50.000 0.00 0.00 0.00 4.70
1056 1513 3.041946 GGAGAGCAGAAATAGGAAGGGA 58.958 50.000 0.00 0.00 0.00 4.20
1058 1515 3.432890 GGTGGAGAGCAGAAATAGGAAGG 60.433 52.174 0.00 0.00 0.00 3.46
1060 1517 3.055094 GTGGTGGAGAGCAGAAATAGGAA 60.055 47.826 0.00 0.00 0.00 3.36
1133 1602 4.764771 TGGCTGGCATTGGGAGGC 62.765 66.667 0.00 0.00 0.00 4.70
1408 1880 2.968206 GCCGTAGTCGTCCTGGTT 59.032 61.111 0.00 0.00 35.01 3.67
1411 1883 4.189188 CCCGCCGTAGTCGTCCTG 62.189 72.222 0.00 0.00 35.01 3.86
1612 2103 5.758784 GGAAAAACGGAGAAGAAGAAGAAGA 59.241 40.000 0.00 0.00 0.00 2.87
1613 2104 5.049336 GGGAAAAACGGAGAAGAAGAAGAAG 60.049 44.000 0.00 0.00 0.00 2.85
1614 2105 4.820173 GGGAAAAACGGAGAAGAAGAAGAA 59.180 41.667 0.00 0.00 0.00 2.52
1615 2106 4.386711 GGGAAAAACGGAGAAGAAGAAGA 58.613 43.478 0.00 0.00 0.00 2.87
1616 2107 3.186613 CGGGAAAAACGGAGAAGAAGAAG 59.813 47.826 0.00 0.00 0.00 2.85
1617 2108 3.135994 CGGGAAAAACGGAGAAGAAGAA 58.864 45.455 0.00 0.00 0.00 2.52
1645 2136 1.338337 ACACACGAGATGGATCGATCC 59.662 52.381 33.41 33.41 45.56 3.36
1654 2145 1.401905 TCGGAGATCACACACGAGATG 59.598 52.381 0.00 0.00 0.00 2.90
1658 2149 1.202143 CGAATCGGAGATCACACACGA 60.202 52.381 0.00 0.00 45.12 4.35
1659 2150 1.191944 CGAATCGGAGATCACACACG 58.808 55.000 0.00 0.00 45.12 4.49
1783 2282 4.961438 AAGAATGTGGATGTGGCTTTTT 57.039 36.364 0.00 0.00 0.00 1.94
1807 2306 5.651576 TCAAAATGCTACCATGCAGAATGTA 59.348 36.000 0.00 0.00 46.71 2.29
1835 2337 6.790285 AATGATTTGCAAGGAAATGACAAC 57.210 33.333 4.23 0.00 0.00 3.32
1850 2352 8.160603 TCGTTGATCGAATTGAAAATGATTTG 57.839 30.769 0.00 0.00 45.98 2.32
2208 2716 1.203038 TGTTGGCATGGGTTGATGAGT 60.203 47.619 0.00 0.00 0.00 3.41
2312 2851 5.350633 TCCTTTCTGTTTGCATTTGAGTTG 58.649 37.500 0.00 0.00 0.00 3.16
2419 2990 2.354805 GCAGATCCCCGTAGTCTTGTTT 60.355 50.000 0.00 0.00 0.00 2.83
2434 3005 3.253416 GACTTACGGGTCGCAGATC 57.747 57.895 0.00 0.00 40.67 2.75
2464 3035 9.399403 GATGAAACTGTGGAAATTTAGAAGTTC 57.601 33.333 0.00 0.00 34.92 3.01
2576 3162 0.328926 TGCTCATCACATCTGCCCAA 59.671 50.000 0.00 0.00 0.00 4.12
2683 3269 6.912591 GTGATGGAAGTACAACTTTGAAACAG 59.087 38.462 0.00 0.00 38.80 3.16
2699 3285 2.094258 CGATCAACGGTTGTGATGGAAG 59.906 50.000 19.47 2.19 38.46 3.46
2767 3353 2.395690 CGAGCAATCGACCGCAAC 59.604 61.111 10.26 3.58 34.64 4.17
2812 3402 2.161855 CCTGCAAAAGCACACCTGATA 58.838 47.619 0.00 0.00 0.00 2.15
2874 3464 2.289882 CCTCTGCAATGAGAAGTGGTCA 60.290 50.000 4.59 0.00 36.23 4.02
2878 3468 3.331478 ACTCCTCTGCAATGAGAAGTG 57.669 47.619 12.31 0.00 30.44 3.16
2967 3557 4.694982 GCAGGGAAGAAGAAGAAGAAGAAG 59.305 45.833 0.00 0.00 0.00 2.85
2969 3559 3.648067 TGCAGGGAAGAAGAAGAAGAAGA 59.352 43.478 0.00 0.00 0.00 2.87
2971 3561 3.244700 CCTGCAGGGAAGAAGAAGAAGAA 60.245 47.826 26.14 0.00 37.23 2.52
2972 3562 2.304180 CCTGCAGGGAAGAAGAAGAAGA 59.696 50.000 26.14 0.00 37.23 2.87
3102 3742 1.581447 CTGCGGCTTCCAAAAGGAC 59.419 57.895 0.00 0.00 32.79 3.85
3137 3777 6.024049 CACAAAAGAACAGAAGACAAGTGTC 58.976 40.000 3.12 3.12 45.08 3.67
3425 4085 2.086869 CGTTCCAACTGAAGGCATCAT 58.913 47.619 0.00 0.00 37.44 2.45
3428 4088 0.400213 TCCGTTCCAACTGAAGGCAT 59.600 50.000 0.00 0.00 37.49 4.40
3429 4089 0.400213 ATCCGTTCCAACTGAAGGCA 59.600 50.000 0.00 0.00 37.49 4.75
3430 4090 0.804989 CATCCGTTCCAACTGAAGGC 59.195 55.000 0.00 0.00 37.49 4.35
3433 4093 0.037590 CCCCATCCGTTCCAACTGAA 59.962 55.000 0.00 0.00 0.00 3.02
3434 4094 1.682849 CCCCATCCGTTCCAACTGA 59.317 57.895 0.00 0.00 0.00 3.41
3435 4095 2.046285 GCCCCATCCGTTCCAACTG 61.046 63.158 0.00 0.00 0.00 3.16
3436 4096 2.231380 AGCCCCATCCGTTCCAACT 61.231 57.895 0.00 0.00 0.00 3.16
3483 4143 1.404851 GGTTCTCTTCAAGGGAGCTCG 60.405 57.143 7.83 0.00 0.00 5.03
3541 4201 2.024176 GCATCTTCTTGCCGGTCTTA 57.976 50.000 1.90 0.00 36.60 2.10
3766 4426 2.935201 CAAGATCTTCTTCTTGCTCCCG 59.065 50.000 4.57 0.00 44.30 5.14
4062 4723 5.007682 TGTAAACTGAAAAGGTAGATGGCC 58.992 41.667 0.00 0.00 0.00 5.36
4096 4761 7.936847 TGAGATTCCACAAACATACAGTAAGTT 59.063 33.333 0.00 0.00 0.00 2.66
4100 4765 6.406370 CCTGAGATTCCACAAACATACAGTA 58.594 40.000 0.00 0.00 0.00 2.74
4101 4766 5.248640 CCTGAGATTCCACAAACATACAGT 58.751 41.667 0.00 0.00 0.00 3.55
4102 4767 4.095483 GCCTGAGATTCCACAAACATACAG 59.905 45.833 0.00 0.00 0.00 2.74
4106 4771 3.087031 CAGCCTGAGATTCCACAAACAT 58.913 45.455 0.00 0.00 0.00 2.71
4107 4772 2.507484 CAGCCTGAGATTCCACAAACA 58.493 47.619 0.00 0.00 0.00 2.83
4108 4773 1.815003 CCAGCCTGAGATTCCACAAAC 59.185 52.381 0.00 0.00 0.00 2.93
4110 4775 0.322816 GCCAGCCTGAGATTCCACAA 60.323 55.000 0.00 0.00 0.00 3.33
4111 4776 1.300963 GCCAGCCTGAGATTCCACA 59.699 57.895 0.00 0.00 0.00 4.17
4112 4777 0.747283 CTGCCAGCCTGAGATTCCAC 60.747 60.000 0.00 0.00 0.00 4.02
4127 4792 0.445436 CTTTCGACATGTCTGCTGCC 59.555 55.000 22.95 0.00 0.00 4.85
4394 5059 4.454678 GCTGATGAACAACCATGGAGATA 58.545 43.478 21.47 0.00 0.00 1.98
4429 5094 1.879380 CCGTTCTGCATTTGAGGTTGA 59.121 47.619 0.00 0.00 0.00 3.18
4477 5142 5.705609 TTGTTTTAGTCAGGGAGAATTGC 57.294 39.130 0.00 0.00 0.00 3.56
4584 5251 2.696775 TCCACCTTCTTTACTGGACCA 58.303 47.619 0.00 0.00 0.00 4.02
4797 5464 2.103373 CCTCCTCTGGACGAAGATTCA 58.897 52.381 0.00 0.00 0.00 2.57
4959 5632 3.482232 CTGCCTAAGGATGCCGGGG 62.482 68.421 2.18 0.00 0.00 5.73
5008 5681 6.343703 TGAGATGTTCAATACACAGATGAGG 58.656 40.000 0.00 0.00 40.19 3.86
5026 5699 3.201708 AGAACTCCCCAGGAAATGAGATG 59.798 47.826 0.00 0.00 0.00 2.90
5044 5717 2.481104 CCGAGATGAGCTGGAGAAGAAC 60.481 54.545 0.00 0.00 0.00 3.01
5056 5730 6.480524 TGAAAACATAAACACCGAGATGAG 57.519 37.500 0.00 0.00 0.00 2.90
5075 5899 3.237746 TGCCAACCCTGAATGAATGAAA 58.762 40.909 0.00 0.00 0.00 2.69
5076 5900 2.886913 TGCCAACCCTGAATGAATGAA 58.113 42.857 0.00 0.00 0.00 2.57
5077 5901 2.601240 TGCCAACCCTGAATGAATGA 57.399 45.000 0.00 0.00 0.00 2.57
5078 5902 2.675889 GCTTGCCAACCCTGAATGAATG 60.676 50.000 0.00 0.00 0.00 2.67
5079 5903 1.551883 GCTTGCCAACCCTGAATGAAT 59.448 47.619 0.00 0.00 0.00 2.57
5080 5904 0.968405 GCTTGCCAACCCTGAATGAA 59.032 50.000 0.00 0.00 0.00 2.57
5081 5905 0.178967 TGCTTGCCAACCCTGAATGA 60.179 50.000 0.00 0.00 0.00 2.57
5082 5906 0.245539 CTGCTTGCCAACCCTGAATG 59.754 55.000 0.00 0.00 0.00 2.67
5083 5907 0.112995 TCTGCTTGCCAACCCTGAAT 59.887 50.000 0.00 0.00 0.00 2.57
5267 6101 4.172505 GGTCAGCTAGATATGCAGATTCG 58.827 47.826 0.00 0.00 0.00 3.34
5418 6358 2.124529 GCCAGGAAGTAGGCCAGC 60.125 66.667 5.01 0.00 45.18 4.85
5431 6371 1.746615 CGATGGTGTCCTTGGCCAG 60.747 63.158 5.11 0.00 35.56 4.85
5460 6400 0.104120 CGATGGGCTTGACGATGGTA 59.896 55.000 0.00 0.00 0.00 3.25
5587 6527 0.813210 GGCTGGAAGAAGATGGCGAG 60.813 60.000 0.00 0.00 34.07 5.03
5628 6568 4.524316 TTGAGGAATGGAAGCATGTTTG 57.476 40.909 0.00 0.00 0.00 2.93
5638 6578 8.469200 GTCATGAAAATACAATTGAGGAATGGA 58.531 33.333 13.59 0.00 0.00 3.41
5639 6579 7.707893 GGTCATGAAAATACAATTGAGGAATGG 59.292 37.037 13.59 0.00 0.00 3.16
5687 6627 2.093973 AGCAATCTACAAGGGAGTGTCG 60.094 50.000 0.00 0.00 32.35 4.35
5723 6663 4.118410 CCACTGCAAACAAAAGCATGTAA 58.882 39.130 0.00 0.00 40.42 2.41
5948 6888 1.156736 GTGTAGCTGCAACCACGAAT 58.843 50.000 5.91 0.00 0.00 3.34
6136 7076 0.807667 GCGATGAACCGATCAGCTGT 60.808 55.000 14.67 0.42 42.36 4.40
6138 7078 0.176680 AAGCGATGAACCGATCAGCT 59.823 50.000 5.19 3.01 42.36 4.24
6139 7079 0.579156 GAAGCGATGAACCGATCAGC 59.421 55.000 0.00 0.00 42.53 4.26
6140 7080 2.215907 AGAAGCGATGAACCGATCAG 57.784 50.000 0.00 0.00 42.53 2.90
6141 7081 2.672961 AAGAAGCGATGAACCGATCA 57.327 45.000 0.00 0.00 43.67 2.92
6142 7082 3.190874 AGAAAGAAGCGATGAACCGATC 58.809 45.455 0.00 0.00 0.00 3.69
6143 7083 3.252974 AGAAAGAAGCGATGAACCGAT 57.747 42.857 0.00 0.00 0.00 4.18
6144 7084 2.743636 AGAAAGAAGCGATGAACCGA 57.256 45.000 0.00 0.00 0.00 4.69
6145 7085 3.433615 AGAAAGAAAGAAGCGATGAACCG 59.566 43.478 0.00 0.00 0.00 4.44
6146 7086 4.693095 AGAGAAAGAAAGAAGCGATGAACC 59.307 41.667 0.00 0.00 0.00 3.62
6155 7095 5.907197 TGTTACGCAGAGAAAGAAAGAAG 57.093 39.130 0.00 0.00 0.00 2.85
6264 7207 5.809001 TCAACATCCTGCTCTTTACATCTT 58.191 37.500 0.00 0.00 0.00 2.40
6403 7350 4.846779 TTTGCACCTCAAATGTTACTCC 57.153 40.909 0.00 0.00 39.58 3.85
6429 7376 6.062095 AGTACAGTACAGCCAGAAACAATTT 58.938 36.000 13.37 0.00 0.00 1.82
6526 7473 8.507524 AACCTCTAGTTTAACTGGAATATTGC 57.492 34.615 12.04 0.00 35.25 3.56
6584 7531 2.813754 CCAAGCATGTTTTTCCGAGAGA 59.186 45.455 0.00 0.00 0.00 3.10
6585 7532 2.813754 TCCAAGCATGTTTTTCCGAGAG 59.186 45.455 0.00 0.00 0.00 3.20
6586 7533 2.552315 GTCCAAGCATGTTTTTCCGAGA 59.448 45.455 0.00 0.00 0.00 4.04
6588 7535 2.302260 TGTCCAAGCATGTTTTTCCGA 58.698 42.857 0.00 0.00 0.00 4.55
6589 7536 2.791383 TGTCCAAGCATGTTTTTCCG 57.209 45.000 0.00 0.00 0.00 4.30
6591 7538 5.234972 CCTTTCTTGTCCAAGCATGTTTTTC 59.765 40.000 2.09 0.00 38.28 2.29
6592 7539 5.104982 TCCTTTCTTGTCCAAGCATGTTTTT 60.105 36.000 2.09 0.00 38.28 1.94
6593 7540 4.405358 TCCTTTCTTGTCCAAGCATGTTTT 59.595 37.500 2.09 0.00 38.28 2.43
6628 7575 4.662966 TGGACTACCCACACTCTAGTAA 57.337 45.455 0.00 0.00 40.82 2.24
6695 7642 2.072298 CTCAAGTGGAGTACAAGCTGC 58.928 52.381 0.00 0.00 38.90 5.25
6709 7656 4.070716 CTCAGTTTCATGGCTTCTCAAGT 58.929 43.478 0.00 0.00 0.00 3.16
6746 7693 2.036733 CTGTCACCTCCTTACCGAAACA 59.963 50.000 0.00 0.00 0.00 2.83
6865 7815 1.920835 AGCTTCACCCTGGAGGACC 60.921 63.158 0.00 0.00 39.89 4.46


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

AutoCloner maintained by Alex Coulton.