Multiple sequence alignment - TraesCS2A01G309600

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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 TraesCS2A01G309600 chr2A 100.000 4614 0 0 1 4614 532858157 532862770 0.000000e+00 8521.0
1 TraesCS2A01G309600 chr2A 100.000 2942 0 0 4939 7880 532863095 532866036 0.000000e+00 5433.0
2 TraesCS2A01G309600 chr2A 93.846 65 4 0 5818 5882 642931068 642931132 1.810000e-16 99.0
3 TraesCS2A01G309600 chr2D 94.602 4557 164 37 1 4490 394790634 394795175 0.000000e+00 6977.0
4 TraesCS2A01G309600 chr2D 96.158 1718 50 11 6172 7880 394797095 394798805 0.000000e+00 2793.0
5 TraesCS2A01G309600 chr2D 97.558 860 17 2 5418 6273 394796239 394797098 0.000000e+00 1469.0
6 TraesCS2A01G309600 chr2D 98.504 468 7 0 4953 5420 394795741 394796208 0.000000e+00 826.0
7 TraesCS2A01G309600 chr2D 95.161 124 6 0 4491 4614 394795214 394795337 6.240000e-46 196.0
8 TraesCS2A01G309600 chr2B 95.289 2165 44 13 2255 4405 467863228 467865348 0.000000e+00 3380.0
9 TraesCS2A01G309600 chr2B 95.351 1893 64 13 5955 7837 467869309 467871187 0.000000e+00 2987.0
10 TraesCS2A01G309600 chr2B 91.251 1623 71 31 677 2256 467861473 467863067 0.000000e+00 2145.0
11 TraesCS2A01G309600 chr2B 93.961 977 25 13 5011 5959 467866062 467867032 0.000000e+00 1447.0
12 TraesCS2A01G309600 chr2B 88.525 854 66 19 1 840 467860288 467861123 0.000000e+00 1005.0
13 TraesCS2A01G309600 chr2B 97.059 136 4 0 4355 4490 467865347 467865482 6.150000e-56 230.0
14 TraesCS2A01G309600 chr2B 95.082 122 6 0 4491 4612 467865521 467865642 8.070000e-45 193.0
15 TraesCS2A01G309600 chr2B 77.778 234 34 12 278 503 467861130 467861353 2.310000e-25 128.0
16 TraesCS2A01G309600 chr2B 98.182 55 1 0 4945 4999 467866016 467866070 6.510000e-16 97.1
17 TraesCS2A01G309600 chr1D 83.459 133 22 0 1 133 8100123 8099991 2.990000e-24 124.0
18 TraesCS2A01G309600 chr1D 92.754 69 5 0 5814 5882 438328505 438328437 5.030000e-17 100.0
19 TraesCS2A01G309600 chr7D 82.500 120 19 2 5 122 80797434 80797315 3.890000e-18 104.0
20 TraesCS2A01G309600 chr7B 82.645 121 18 3 1 120 243913026 243913144 3.890000e-18 104.0
21 TraesCS2A01G309600 chr7B 81.513 119 19 3 5 122 457808241 457808125 2.340000e-15 95.3
22 TraesCS2A01G309600 chr7A 93.846 65 4 0 5818 5882 350426628 350426692 1.810000e-16 99.0
23 TraesCS2A01G309600 chr6B 93.846 65 4 0 5818 5882 486853604 486853540 1.810000e-16 99.0
24 TraesCS2A01G309600 chr6B 93.846 65 4 0 5818 5882 626047660 626047596 1.810000e-16 99.0
25 TraesCS2A01G309600 chr4B 93.846 65 4 0 5818 5882 115099452 115099388 1.810000e-16 99.0
26 TraesCS2A01G309600 chr3B 93.846 65 4 0 5818 5882 290321129 290321193 1.810000e-16 99.0
27 TraesCS2A01G309600 chr4D 81.667 120 19 3 5 122 474919746 474919864 6.510000e-16 97.1
28 TraesCS2A01G309600 chr5A 80.833 120 21 2 5 122 489685750 489685869 8.420000e-15 93.5
29 TraesCS2A01G309600 chr5A 80.833 120 21 2 5 122 489685902 489686021 8.420000e-15 93.5


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 TraesCS2A01G309600 chr2A 532858157 532866036 7879 False 6977.000000 8521 100.000000 1 7880 2 chr2A.!!$F2 7879
1 TraesCS2A01G309600 chr2D 394790634 394798805 8171 False 2452.200000 6977 96.396600 1 7880 5 chr2D.!!$F1 7879
2 TraesCS2A01G309600 chr2B 467860288 467871187 10899 False 1290.233333 3380 92.497556 1 7837 9 chr2B.!!$F1 7836

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
553 566 0.031585 GGACGCCAAACTTGTTTCCC 59.968 55.000 0.00 0.0 0.00 3.97 F
1163 1712 0.109597 GCGCCTTCTGATTTGGTGTG 60.110 55.000 0.00 0.0 34.19 3.82 F
2087 2675 0.744874 TAGAGGAATCGGGTTCTGCG 59.255 55.000 0.36 0.0 37.01 5.18 F
3466 4235 1.202651 GCACGGCCTGGTAGACATATT 60.203 52.381 0.00 0.0 0.00 1.28 F
4103 4877 2.040813 TCCTGCTTTTCAGATTCCTGCT 59.959 45.455 0.00 0.0 45.72 4.24 F
5640 6600 1.125711 AGCGTGGTTACCTCCCTGTT 61.126 55.000 2.07 0.0 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1391 1953 0.517316 CTAACTGCCAGTTTCACCGC 59.483 55.000 16.40 0.0 39.51 5.68 R
2906 3657 1.774856 AGTGAACTAAACCTGGTGGCT 59.225 47.619 0.00 0.0 36.63 4.75 R
3838 4612 0.820482 TGAGGGCAATGGCATGATCG 60.820 55.000 9.51 0.0 43.71 3.69 R
5397 6323 1.961394 CTGGCCATCCCATCATTTGAG 59.039 52.381 5.51 0.0 44.33 3.02 R
5842 6802 2.048601 TCCGAAACAAGTTGGGGTAGA 58.951 47.619 7.96 0.0 35.83 2.59 R
6883 10225 0.538287 AGGTGCAAGTTCCTTCTGCC 60.538 55.000 0.00 0.0 0.00 4.85 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
67 68 9.525826 AGAGGAACATAAAAATCTTGAAGATGT 57.474 29.630 8.68 0.00 34.65 3.06
155 156 2.969806 CTGTTGCTGCGCCGTTCAT 61.970 57.895 4.18 0.00 0.00 2.57
185 186 6.073167 TCCAACGTCGTGCTAATTGATTTTTA 60.073 34.615 0.00 0.00 0.00 1.52
377 380 7.333528 TCCATAATTCACATGTAGCCTTTTC 57.666 36.000 0.00 0.00 0.00 2.29
502 506 9.125026 AGAACTCTGACATACAAAAATGAGTTT 57.875 29.630 0.00 0.00 38.34 2.66
553 566 0.031585 GGACGCCAAACTTGTTTCCC 59.968 55.000 0.00 0.00 0.00 3.97
554 567 0.741915 GACGCCAAACTTGTTTCCCA 59.258 50.000 0.00 0.00 0.00 4.37
555 568 0.744281 ACGCCAAACTTGTTTCCCAG 59.256 50.000 0.00 0.00 0.00 4.45
556 569 0.744281 CGCCAAACTTGTTTCCCAGT 59.256 50.000 0.00 0.00 0.00 4.00
557 570 1.950909 CGCCAAACTTGTTTCCCAGTA 59.049 47.619 0.00 0.00 0.00 2.74
558 571 2.287368 CGCCAAACTTGTTTCCCAGTAC 60.287 50.000 0.00 0.00 0.00 2.73
559 572 2.956333 GCCAAACTTGTTTCCCAGTACT 59.044 45.455 0.00 0.00 0.00 2.73
571 584 4.026424 TCCCAGTACTAGTAGGGTCCTA 57.974 50.000 21.11 5.12 42.12 2.94
599 622 6.628919 AGTACAAAACCGCATAACTCTTTT 57.371 33.333 0.00 0.00 0.00 2.27
606 629 7.506328 AAACCGCATAACTCTTTTCTTTAGT 57.494 32.000 0.00 0.00 0.00 2.24
612 635 8.230486 CGCATAACTCTTTTCTTTAGTCACATT 58.770 33.333 0.00 0.00 0.00 2.71
640 663 4.634012 TCACTAGGCAAACCAGTGTATT 57.366 40.909 11.69 0.00 41.75 1.89
657 680 6.538381 CAGTGTATTTGCTTTTGGTTTTCCTT 59.462 34.615 0.00 0.00 41.38 3.36
665 688 4.142160 GCTTTTGGTTTTCCTTGTCACTCT 60.142 41.667 0.00 0.00 41.38 3.24
672 695 6.183361 TGGTTTTCCTTGTCACTCTACCAATA 60.183 38.462 0.00 0.00 41.38 1.90
696 719 2.676342 GTGACATCGCCTCCGTAATTTT 59.324 45.455 0.00 0.00 35.54 1.82
699 722 2.936498 ACATCGCCTCCGTAATTTTCTG 59.064 45.455 0.00 0.00 35.54 3.02
706 729 4.620567 GCCTCCGTAATTTTCTGGCAAAAT 60.621 41.667 0.00 0.00 38.79 1.82
710 733 7.275560 CCTCCGTAATTTTCTGGCAAAATAAAG 59.724 37.037 0.00 0.00 30.38 1.85
773 1301 5.488341 TCTTTACGAAAGGAATTGAGAGGG 58.512 41.667 0.00 0.00 39.01 4.30
801 1330 4.745649 ACGAAGAGAAGATAAAACGGGAG 58.254 43.478 0.00 0.00 0.00 4.30
816 1345 1.675641 GGAGGCACAGCGGTTCATT 60.676 57.895 0.00 0.00 0.00 2.57
922 1466 2.348998 GGCCCAGGTGTCAGTGAG 59.651 66.667 0.00 0.00 0.00 3.51
958 1502 2.185310 CTCCCTCCCCCGAAACTGTG 62.185 65.000 0.00 0.00 0.00 3.66
1148 1697 2.653953 TTTAGGCCCGTATCTGCGCC 62.654 60.000 4.18 0.00 41.96 6.53
1156 1705 1.539065 CCGTATCTGCGCCTTCTGATT 60.539 52.381 4.18 0.00 0.00 2.57
1163 1712 0.109597 GCGCCTTCTGATTTGGTGTG 60.110 55.000 0.00 0.00 34.19 3.82
1273 1832 2.102588 AGCAGAGTTTGACTACCGTTGT 59.897 45.455 0.00 0.00 0.00 3.32
1286 1845 1.677576 ACCGTTGTCGAGTCAGTAACA 59.322 47.619 0.00 0.00 39.71 2.41
1288 1850 3.243636 ACCGTTGTCGAGTCAGTAACATT 60.244 43.478 0.00 0.00 39.71 2.71
1348 1910 1.275291 AGTGGACAGGACCATTACGTG 59.725 52.381 0.00 0.00 42.17 4.49
1360 1922 1.933853 CATTACGTGTAGGCTTGAGGC 59.066 52.381 0.00 0.00 41.43 4.70
1391 1953 6.472163 GGATTTGGTTTGTGTGATAATAAGCG 59.528 38.462 0.00 0.00 0.00 4.68
1397 1959 2.198406 GTGTGATAATAAGCGCGGTGA 58.802 47.619 13.41 3.90 0.00 4.02
1431 1993 5.808366 AGAGAGTTGTTCCTGTCACATTA 57.192 39.130 0.00 0.00 0.00 1.90
1433 1995 7.482169 AGAGAGTTGTTCCTGTCACATTATA 57.518 36.000 0.00 0.00 0.00 0.98
1434 1996 8.083828 AGAGAGTTGTTCCTGTCACATTATAT 57.916 34.615 0.00 0.00 0.00 0.86
1435 1997 9.201989 AGAGAGTTGTTCCTGTCACATTATATA 57.798 33.333 0.00 0.00 0.00 0.86
1436 1998 9.988815 GAGAGTTGTTCCTGTCACATTATATAT 57.011 33.333 0.00 0.00 0.00 0.86
1549 2111 9.553064 ACATTAGAGAAATGAATCATGTACTCC 57.447 33.333 15.45 4.68 46.81 3.85
1550 2112 9.775854 CATTAGAGAAATGAATCATGTACTCCT 57.224 33.333 15.45 9.33 46.81 3.69
1614 2202 5.749596 TTGTGTAATTCTTGTCCAGTGTG 57.250 39.130 0.00 0.00 0.00 3.82
1730 2318 3.793144 CCAAGCTCGGCTTCACGC 61.793 66.667 7.99 0.00 46.77 5.34
1781 2369 6.040391 GGATCAAGGGAGATAGATATTCGAGG 59.960 46.154 0.00 0.00 0.00 4.63
1849 2437 1.771255 AGCCTCAGAGGTGTTTCTGTT 59.229 47.619 18.37 0.00 43.96 3.16
1884 2472 1.946768 TCTTTTTCCAGGACTTGTGCG 59.053 47.619 0.00 0.00 0.00 5.34
1907 2495 4.731773 GCCTGATTCATGGCTTTCTTAACG 60.732 45.833 15.64 0.00 45.26 3.18
1930 2518 6.072673 ACGATTTCTTGATTTTAGGTGGACAC 60.073 38.462 0.00 0.00 0.00 3.67
1931 2519 6.072728 CGATTTCTTGATTTTAGGTGGACACA 60.073 38.462 4.69 0.00 0.00 3.72
1940 2528 2.331451 GTGGACACAAAGCCACGC 59.669 61.111 0.00 0.00 44.39 5.34
2078 2666 4.909696 TCTCTCAAGCTTAGAGGAATCG 57.090 45.455 22.16 10.47 40.77 3.34
2087 2675 0.744874 TAGAGGAATCGGGTTCTGCG 59.255 55.000 0.36 0.00 37.01 5.18
2295 3045 4.883083 TGAAACTGTCATGTCCTGTACTC 58.117 43.478 0.00 0.00 0.00 2.59
2342 3092 2.028936 CATGTTGTTGCACGGGACA 58.971 52.632 0.00 0.00 0.00 4.02
2619 3370 6.942976 ACTGGTCAAAGAATATTACTTCGGA 58.057 36.000 0.00 0.00 0.00 4.55
2733 3484 6.992063 ATATTGTTAACAGTCTCTTGGCTG 57.008 37.500 6.91 0.00 38.58 4.85
2906 3657 8.200120 TGTTGTCATTTCCAATGAATACAACAA 58.800 29.630 21.34 11.25 44.77 2.83
2973 3724 4.002267 TGCAGCTAATGTTTCGAAATCG 57.998 40.909 14.69 0.00 41.45 3.34
3304 4073 4.019174 AGGATAGTGGATTGTTGCAAAGG 58.981 43.478 0.00 0.00 0.00 3.11
3466 4235 1.202651 GCACGGCCTGGTAGACATATT 60.203 52.381 0.00 0.00 0.00 1.28
3491 4260 4.766891 ACAGGATTACATCACAAACAAGGG 59.233 41.667 0.00 0.00 0.00 3.95
3644 4414 2.364002 GTTTATTTGGGCAGTGTGGTGT 59.636 45.455 0.00 0.00 0.00 4.16
3645 4415 2.373335 TATTTGGGCAGTGTGGTGTT 57.627 45.000 0.00 0.00 0.00 3.32
3682 4452 5.182760 ACAATCTTCTCAGACATTTCTTGGC 59.817 40.000 0.00 0.00 0.00 4.52
3691 4461 4.336433 CAGACATTTCTTGGCGGTTATGAT 59.664 41.667 0.00 0.00 38.94 2.45
3781 4555 9.145865 GGCAGATAATTGTAGATAAGAGCTTAC 57.854 37.037 0.00 0.00 0.00 2.34
4103 4877 2.040813 TCCTGCTTTTCAGATTCCTGCT 59.959 45.455 0.00 0.00 45.72 4.24
4214 4988 6.814043 TCTTGACATCATCAGATACTTCCAG 58.186 40.000 0.00 0.00 38.99 3.86
4215 4989 6.608808 TCTTGACATCATCAGATACTTCCAGA 59.391 38.462 0.00 0.00 38.99 3.86
4219 4993 7.713942 TGACATCATCAGATACTTCCAGAAATG 59.286 37.037 0.00 0.00 31.88 2.32
4228 5002 2.291411 ACTTCCAGAAATGCCTGCTCAT 60.291 45.455 0.00 0.00 32.97 2.90
4470 5293 5.299279 TCCTGAACAAATCACAAGGTTTCTC 59.701 40.000 0.00 0.00 33.47 2.87
4578 5439 4.456566 AGCTGGCAAAATGCTTTTAATTGG 59.543 37.500 2.00 0.00 44.28 3.16
5188 6114 5.667626 TGGAGCTCTTAATCTTATTGGAGGT 59.332 40.000 14.64 0.00 34.85 3.85
5332 6258 6.365970 AACTGAGAACTAATCTGTCATGGT 57.634 37.500 0.00 0.00 38.96 3.55
5397 6323 3.403038 TCTGCAAAAAGGTAGAGCTGTC 58.597 45.455 0.00 0.00 0.00 3.51
5400 6326 3.181455 TGCAAAAAGGTAGAGCTGTCTCA 60.181 43.478 0.00 0.00 41.81 3.27
5450 6409 7.708752 AGAATCGATTTCCTGTAGAAGATTGAC 59.291 37.037 12.81 0.00 35.40 3.18
5640 6600 1.125711 AGCGTGGTTACCTCCCTGTT 61.126 55.000 2.07 0.00 0.00 3.16
5825 6785 6.228273 TGACTAAACGCTTTTGAGATCTTG 57.772 37.500 0.00 0.00 0.00 3.02
5839 6799 2.373169 AGATCTTGTGGGTTTCAGCTCA 59.627 45.455 0.00 0.00 0.00 4.26
5842 6802 2.092429 TCTTGTGGGTTTCAGCTCAAGT 60.092 45.455 7.23 0.00 35.35 3.16
5942 6905 3.926821 TGGATTTGTAAACCGCTTTCC 57.073 42.857 0.00 0.00 0.00 3.13
6413 9755 8.752187 ACTTGTCTAAATATGCATTTTCCACAT 58.248 29.630 3.54 0.00 35.88 3.21
6438 9780 2.764010 AGAATACTGGTGCCGTGTATCA 59.236 45.455 7.00 0.00 0.00 2.15
6446 9788 0.390603 TGCCGTGTATCAACCCTTCG 60.391 55.000 0.00 0.00 0.00 3.79
6483 9825 1.352114 TAATACTCGCGCGCAAAAGT 58.648 45.000 32.61 29.17 0.00 2.66
6653 9995 8.802267 CCACTCTTTTGAATTTAGGGACAAATA 58.198 33.333 0.00 0.00 33.38 1.40
6654 9996 9.846248 CACTCTTTTGAATTTAGGGACAAATAG 57.154 33.333 0.00 0.00 33.38 1.73
6655 9997 9.588096 ACTCTTTTGAATTTAGGGACAAATAGT 57.412 29.630 0.00 0.00 33.38 2.12
6670 10012 8.204836 GGGACAAATAGTAATAGAGAAAGCTGA 58.795 37.037 0.00 0.00 0.00 4.26
6731 10073 8.448008 TCTATTTTCCAATAGGTGCTTATCCAT 58.552 33.333 2.84 0.00 41.66 3.41
6734 10076 5.233083 TCCAATAGGTGCTTATCCATCAG 57.767 43.478 0.00 0.00 35.89 2.90
6739 10081 3.658725 AGGTGCTTATCCATCAGGTACT 58.341 45.455 0.00 0.00 43.88 2.73
6867 10209 3.771216 AGAATTTGCACCTCAACCAGAT 58.229 40.909 0.00 0.00 33.73 2.90
6886 10228 4.641541 CAGATGGTGAAATGTAGAATGGCA 59.358 41.667 0.00 0.00 0.00 4.92
6925 10267 9.415008 ACCTATGCATACAACCATAAAATACAA 57.585 29.630 1.16 0.00 0.00 2.41
6926 10268 9.677567 CCTATGCATACAACCATAAAATACAAC 57.322 33.333 1.16 0.00 0.00 3.32
6950 10294 1.019805 GCAGTAGGAAGACGGGCAAC 61.020 60.000 0.00 0.00 0.00 4.17
6988 10333 7.567458 AGGCAATATTGTTATTTCAATGGCTT 58.433 30.769 16.61 0.00 37.40 4.35
7120 10468 3.424962 GCAATTTCGCTGTCTGAACTACC 60.425 47.826 0.00 0.00 0.00 3.18
7159 10507 5.364446 ACACAATCCGGGAGTACAATACATA 59.636 40.000 0.00 0.00 0.00 2.29
7252 10600 6.402222 AGATCTGGTGCTACTTTTAAGTCAG 58.598 40.000 0.00 0.89 40.37 3.51
7453 10801 2.158943 GGATACAAGGGGTTCTTCCTCG 60.159 54.545 0.00 0.00 42.70 4.63
7459 10807 0.246910 GGGGTTCTTCCTCGACTCAC 59.753 60.000 0.00 0.00 36.25 3.51
7602 10950 1.133407 CGACACAAGAGCTACTCCTCC 59.867 57.143 0.00 0.00 32.17 4.30
7787 11135 0.969894 ACGAGTGGAGGACCTGAAAG 59.030 55.000 0.00 0.00 37.04 2.62
7837 11188 0.741221 GTCCTGGAACATCAGACGGC 60.741 60.000 0.00 0.00 38.20 5.68
7868 11219 3.391049 GTGCGGTAATAAGATGGAGGTC 58.609 50.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 7.009179 TGTTCCTCTTCAACATCTAGTGATT 57.991 36.000 0.00 0.00 0.00 2.57
35 36 9.130661 TCAAGATTTTTATGTTCCTCTTCAACA 57.869 29.630 0.00 0.00 38.12 3.33
67 68 2.058595 GCGAGCTAGGGGGACTTCA 61.059 63.158 0.00 0.00 0.00 3.02
155 156 2.442212 TAGCACGACGTTGGATTTCA 57.558 45.000 7.90 0.00 0.00 2.69
414 418 7.759489 ACCTTGACAAACAGCTCATTTTATA 57.241 32.000 0.00 0.00 0.00 0.98
424 428 2.223782 TGATGCAACCTTGACAAACAGC 60.224 45.455 0.00 0.00 0.00 4.40
473 477 9.208022 CTCATTTTTGTATGTCAGAGTTCTACA 57.792 33.333 0.00 0.00 0.00 2.74
508 512 9.612620 CTATCGAGAATAACCCATTTTTATTGC 57.387 33.333 0.00 0.00 30.79 3.56
511 515 9.503399 GTCCTATCGAGAATAACCCATTTTTAT 57.497 33.333 0.00 0.00 0.00 1.40
519 532 2.352519 GGCGTCCTATCGAGAATAACCC 60.353 54.545 0.00 0.00 0.00 4.11
553 566 8.993404 ACTTTAATAGGACCCTACTAGTACTG 57.007 38.462 5.39 0.00 28.99 2.74
555 568 9.853177 TGTACTTTAATAGGACCCTACTAGTAC 57.147 37.037 19.16 19.16 36.83 2.73
557 570 9.774071 TTTGTACTTTAATAGGACCCTACTAGT 57.226 33.333 0.00 0.00 36.83 2.57
571 584 8.331730 AGAGTTATGCGGTTTTGTACTTTAAT 57.668 30.769 0.00 0.00 0.00 1.40
606 629 6.647334 TTGCCTAGTGAAAAATGAATGTGA 57.353 33.333 0.00 0.00 0.00 3.58
612 635 4.892934 ACTGGTTTGCCTAGTGAAAAATGA 59.107 37.500 0.00 0.00 35.27 2.57
640 663 4.020662 AGTGACAAGGAAAACCAAAAGCAA 60.021 37.500 0.00 0.00 0.00 3.91
665 688 2.626266 AGGCGATGTCACGATATTGGTA 59.374 45.455 0.00 0.00 35.09 3.25
672 695 1.099295 TACGGAGGCGATGTCACGAT 61.099 55.000 0.00 0.00 35.09 3.73
696 719 8.303876 GTCAATTTAGGACTTTATTTTGCCAGA 58.696 33.333 0.00 0.00 32.54 3.86
699 722 7.088272 ACGTCAATTTAGGACTTTATTTTGCC 58.912 34.615 0.00 0.00 33.11 4.52
706 729 6.105397 AGGTGACGTCAATTTAGGACTTTA 57.895 37.500 21.95 0.00 33.11 1.85
710 733 6.161381 TCTAAAGGTGACGTCAATTTAGGAC 58.839 40.000 35.43 20.23 37.65 3.85
716 1244 3.581332 TCCCTCTAAAGGTGACGTCAATT 59.419 43.478 21.95 17.32 41.59 2.32
801 1330 0.387239 GAACAATGAACCGCTGTGCC 60.387 55.000 0.00 0.00 0.00 5.01
816 1345 1.336440 CACGTGGCAAATTCCTGAACA 59.664 47.619 7.95 0.00 0.00 3.18
922 1466 2.433318 GCGAGCAGTGGGAGTGTC 60.433 66.667 0.00 0.00 0.00 3.67
927 1471 4.704103 AGGGAGCGAGCAGTGGGA 62.704 66.667 0.00 0.00 0.00 4.37
1115 1659 0.454196 CCTAAACAATTTCGGCCGGG 59.546 55.000 27.83 10.58 0.00 5.73
1148 1697 1.197721 GCCGACACACCAAATCAGAAG 59.802 52.381 0.00 0.00 0.00 2.85
1156 1705 3.637911 ATTATTAGGCCGACACACCAA 57.362 42.857 0.00 0.00 0.00 3.67
1163 1712 1.193874 CGCGGAAATTATTAGGCCGAC 59.806 52.381 14.77 7.57 44.43 4.79
1273 1832 5.220989 CGATTCCCTAATGTTACTGACTCGA 60.221 44.000 0.00 0.00 29.76 4.04
1286 1845 3.545703 CAAGAGCAACCGATTCCCTAAT 58.454 45.455 0.00 0.00 0.00 1.73
1288 1850 1.209504 CCAAGAGCAACCGATTCCCTA 59.790 52.381 0.00 0.00 0.00 3.53
1322 1884 1.507140 TGGTCCTGTCCACTCACTTT 58.493 50.000 0.00 0.00 31.96 2.66
1348 1910 2.946785 TCCTACTAGCCTCAAGCCTAC 58.053 52.381 0.00 0.00 45.47 3.18
1360 1922 8.786826 TTATCACACAAACCAAATCCTACTAG 57.213 34.615 0.00 0.00 0.00 2.57
1362 1924 9.747898 TTATTATCACACAAACCAAATCCTACT 57.252 29.630 0.00 0.00 0.00 2.57
1391 1953 0.517316 CTAACTGCCAGTTTCACCGC 59.483 55.000 16.40 0.00 39.51 5.68
1397 1959 4.423625 ACAACTCTCTAACTGCCAGTTT 57.576 40.909 16.40 0.07 39.51 2.66
1547 2109 2.371179 AGACGGATCGGAGTGTATAGGA 59.629 50.000 7.35 0.00 0.00 2.94
1548 2110 2.780714 AGACGGATCGGAGTGTATAGG 58.219 52.381 7.35 0.00 0.00 2.57
1549 2111 4.313282 TGTAGACGGATCGGAGTGTATAG 58.687 47.826 7.35 0.00 0.00 1.31
1550 2112 4.341366 TGTAGACGGATCGGAGTGTATA 57.659 45.455 7.35 0.00 0.00 1.47
1551 2113 3.204306 TGTAGACGGATCGGAGTGTAT 57.796 47.619 7.35 0.00 0.00 2.29
1552 2114 2.696989 TGTAGACGGATCGGAGTGTA 57.303 50.000 7.35 0.00 0.00 2.90
1609 2197 6.183360 TGGCACAAAATAAGAAACATCACACT 60.183 34.615 0.00 0.00 31.92 3.55
1781 2369 3.868077 CAGAAGGGATCAATTCACGAGTC 59.132 47.826 10.66 0.00 30.81 3.36
1849 2437 7.362920 CCTGGAAAAAGAGTTGACTCAAGAAAA 60.363 37.037 13.20 0.00 45.21 2.29
1907 2495 7.214467 TGTGTCCACCTAAAATCAAGAAATC 57.786 36.000 0.00 0.00 0.00 2.17
1930 2518 1.752501 CGATACCTCGCGTGGCTTTG 61.753 60.000 26.14 13.81 38.20 2.77
1931 2519 1.518572 CGATACCTCGCGTGGCTTT 60.519 57.895 26.14 11.61 38.20 3.51
1940 2528 4.673441 AGACAACAGAAATCGATACCTCG 58.327 43.478 0.00 0.00 46.41 4.63
2078 2666 1.966451 CACCTTCACCGCAGAACCC 60.966 63.158 0.00 0.00 0.00 4.11
2087 2675 4.035675 GTGCTTTATATGCTCACCTTCACC 59.964 45.833 0.00 0.00 0.00 4.02
2169 2757 8.658499 AATTTCTGGGAGTATATTAACACGAC 57.342 34.615 0.00 0.00 0.00 4.34
2295 3045 2.597455 ACCACCCTGTTTCCTGAAATG 58.403 47.619 0.00 0.00 32.36 2.32
2733 3484 7.024768 TGTAACTTTTGCTACAATTATTCGGC 58.975 34.615 0.00 0.00 29.14 5.54
2906 3657 1.774856 AGTGAACTAAACCTGGTGGCT 59.225 47.619 0.00 0.00 36.63 4.75
2973 3724 8.976986 AGACAATTCAATAAAGACAAAGCATC 57.023 30.769 0.00 0.00 0.00 3.91
3130 3899 7.070447 AGAGTCACAGAAGCTATCCATGAAATA 59.930 37.037 0.00 0.00 0.00 1.40
3138 3907 7.870445 CCTATTTAAGAGTCACAGAAGCTATCC 59.130 40.741 0.00 0.00 0.00 2.59
3304 4073 2.224113 CCAATGGTATTGCAGCCCAATC 60.224 50.000 5.33 0.00 42.99 2.67
3466 4235 6.432783 CCCTTGTTTGTGATGTAATCCTGTTA 59.567 38.462 0.00 0.00 44.73 2.41
3491 4260 4.782019 TGTGATGAAAATTGTAGGTGCC 57.218 40.909 0.00 0.00 0.00 5.01
3644 4414 9.809096 CTGAGAAGATTGTATTACTAGCTTGAA 57.191 33.333 12.35 0.00 30.43 2.69
3645 4415 9.190317 TCTGAGAAGATTGTATTACTAGCTTGA 57.810 33.333 12.35 2.83 30.43 3.02
3713 4483 4.402155 GGGATGGTCATGCAGATGTAAAAA 59.598 41.667 4.93 0.00 0.00 1.94
3714 4484 3.953612 GGGATGGTCATGCAGATGTAAAA 59.046 43.478 4.93 0.00 0.00 1.52
3838 4612 0.820482 TGAGGGCAATGGCATGATCG 60.820 55.000 9.51 0.00 43.71 3.69
4103 4877 4.518970 AGGCGCTTCATTTTTAAGTTCTGA 59.481 37.500 7.64 0.00 0.00 3.27
4157 4931 3.935203 TGAGTACAAATAAGCAGCTGAGC 59.065 43.478 20.43 2.01 0.00 4.26
4214 4988 1.358046 GCGGATGAGCAGGCATTTC 59.642 57.895 0.00 0.00 37.05 2.17
4215 4989 2.123428 GGCGGATGAGCAGGCATTT 61.123 57.895 0.00 0.00 39.27 2.32
4219 4993 2.439156 AAAGGCGGATGAGCAGGC 60.439 61.111 0.00 0.00 39.27 4.85
4228 5002 0.321653 GCCTCAGAAAGAAAGGCGGA 60.322 55.000 0.00 0.00 45.55 5.54
4417 5240 5.221621 ACCACTTGGGAATTGTTTAACATGG 60.222 40.000 0.00 2.96 41.15 3.66
4470 5293 8.777865 TCTGTTGAAGATAGACAACTATTTGG 57.222 34.615 0.00 0.00 44.25 3.28
4499 5360 3.252944 CACAGTGACACATGCATTGGTAA 59.747 43.478 8.59 0.00 0.00 2.85
4938 5799 4.437390 GGGTCATACGAGCAAAAATGAGTG 60.437 45.833 0.00 0.00 41.62 3.51
4939 5800 3.689649 GGGTCATACGAGCAAAAATGAGT 59.310 43.478 0.00 0.00 41.62 3.41
4940 5801 3.689161 TGGGTCATACGAGCAAAAATGAG 59.311 43.478 0.00 0.00 41.62 2.90
4941 5802 3.438781 GTGGGTCATACGAGCAAAAATGA 59.561 43.478 0.00 0.00 41.62 2.57
4942 5803 3.190327 TGTGGGTCATACGAGCAAAAATG 59.810 43.478 0.00 0.00 41.62 2.32
4943 5804 3.417101 TGTGGGTCATACGAGCAAAAAT 58.583 40.909 0.00 0.00 41.62 1.82
5188 6114 6.054941 CCATAAGCGGCCATATAATGTATCA 58.945 40.000 2.24 0.00 0.00 2.15
5332 6258 5.878116 CCGATGAAAGTTGGGAACAGTATTA 59.122 40.000 0.00 0.00 44.54 0.98
5397 6323 1.961394 CTGGCCATCCCATCATTTGAG 59.039 52.381 5.51 0.00 44.33 3.02
5400 6326 2.292389 TGAACTGGCCATCCCATCATTT 60.292 45.455 5.51 0.00 44.33 2.32
5825 6785 2.262423 AGACTTGAGCTGAAACCCAC 57.738 50.000 0.00 0.00 0.00 4.61
5839 6799 3.473625 CGAAACAAGTTGGGGTAGACTT 58.526 45.455 7.96 0.00 36.58 3.01
5842 6802 2.048601 TCCGAAACAAGTTGGGGTAGA 58.951 47.619 7.96 0.00 35.83 2.59
6101 9345 6.455360 ACATAAAGCCATAACACTGGAATG 57.545 37.500 0.00 0.00 38.69 2.67
6407 9749 4.947388 GGCACCAGTATTCTTTTATGTGGA 59.053 41.667 0.00 0.00 0.00 4.02
6413 9755 4.010667 ACACGGCACCAGTATTCTTTTA 57.989 40.909 0.00 0.00 0.00 1.52
6423 9765 1.024579 GGGTTGATACACGGCACCAG 61.025 60.000 0.00 0.00 0.00 4.00
6438 9780 7.576861 TTTAGAAAAGAAATGTCGAAGGGTT 57.423 32.000 0.00 0.00 0.00 4.11
6532 9874 9.379770 TCATGAAATGGAGGTAGTCTATAATGA 57.620 33.333 0.00 0.00 46.73 2.57
6623 9965 5.768164 TCCCTAAATTCAAAAGAGTGGACAC 59.232 40.000 0.00 0.00 0.00 3.67
6670 10012 9.895138 AATAAAATGAAGGAGCAGCATAAAAAT 57.105 25.926 0.00 0.00 0.00 1.82
6731 10073 3.769739 ATTGTCAGCAACAGTACCTGA 57.230 42.857 0.00 0.12 39.58 3.86
6734 10076 3.146066 TGGAATTGTCAGCAACAGTACC 58.854 45.455 0.00 0.00 39.58 3.34
6739 10081 5.301551 ACATTAGTTGGAATTGTCAGCAACA 59.698 36.000 0.00 0.00 37.44 3.33
6867 10209 4.299586 TCTGCCATTCTACATTTCACCA 57.700 40.909 0.00 0.00 0.00 4.17
6882 10224 0.823356 GGTGCAAGTTCCTTCTGCCA 60.823 55.000 0.00 0.00 0.00 4.92
6883 10225 0.538287 AGGTGCAAGTTCCTTCTGCC 60.538 55.000 0.00 0.00 0.00 4.85
6900 10242 9.677567 GTTGTATTTTATGGTTGTATGCATAGG 57.322 33.333 6.67 0.00 0.00 2.57
6914 10256 8.942338 TCCTACTGCTACTGTTGTATTTTATG 57.058 34.615 0.00 0.00 0.00 1.90
6920 10262 5.163642 CGTCTTCCTACTGCTACTGTTGTAT 60.164 44.000 0.00 0.00 0.00 2.29
6921 10263 4.155462 CGTCTTCCTACTGCTACTGTTGTA 59.845 45.833 0.00 0.00 0.00 2.41
6922 10264 3.057456 CGTCTTCCTACTGCTACTGTTGT 60.057 47.826 0.00 0.00 0.00 3.32
6923 10265 3.502920 CGTCTTCCTACTGCTACTGTTG 58.497 50.000 0.00 0.00 0.00 3.33
6925 10267 2.093106 CCGTCTTCCTACTGCTACTGT 58.907 52.381 0.00 0.00 0.00 3.55
6926 10268 1.405821 CCCGTCTTCCTACTGCTACTG 59.594 57.143 0.00 0.00 0.00 2.74
6927 10269 1.765230 CCCGTCTTCCTACTGCTACT 58.235 55.000 0.00 0.00 0.00 2.57
6975 10320 4.889409 GTGAGGATCCAAGCCATTGAAATA 59.111 41.667 15.82 0.00 38.83 1.40
6988 10333 0.698238 CAAAGGTGGGTGAGGATCCA 59.302 55.000 15.82 0.00 0.00 3.41
7139 10487 5.048224 CGTCTATGTATTGTACTCCCGGATT 60.048 44.000 0.73 0.00 0.00 3.01
7142 10490 3.057736 CCGTCTATGTATTGTACTCCCGG 60.058 52.174 0.00 0.00 0.00 5.73
7252 10600 3.698029 TGAGAAAAGAACAGCACAAGC 57.302 42.857 0.00 0.00 42.56 4.01
7453 10801 0.890996 CCTTGTTGGGCTGGTGAGTC 60.891 60.000 0.00 0.00 0.00 3.36
7778 11126 3.128589 TGCTGTTGTGTTTCTTTCAGGTC 59.871 43.478 0.00 0.00 0.00 3.85
7787 11135 2.111756 CTTCGCTTGCTGTTGTGTTTC 58.888 47.619 0.00 0.00 0.00 2.78
7837 11188 0.379669 ATTACCGCACCGTCGTCTAG 59.620 55.000 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.