Multiple sequence alignment - TraesCS1D01G091700

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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 TraesCS1D01G091700 chr1D 100.000 4151 0 0 1 4151 78068422 78064272 0.000000e+00 7666.0
1 TraesCS1D01G091700 chr1D 79.397 199 36 5 3217 3412 420882962 420883158 7.240000e-28 135.0
2 TraesCS1D01G091700 chr1A 93.697 2491 124 10 701 3186 105302221 105304683 0.000000e+00 3699.0
3 TraesCS1D01G091700 chr1A 91.762 1845 118 15 1374 3186 109416955 109415113 0.000000e+00 2534.0
4 TraesCS1D01G091700 chr1A 92.685 957 33 9 3216 4151 463948999 463949939 0.000000e+00 1345.0
5 TraesCS1D01G091700 chr1A 93.182 396 22 3 729 1121 109420560 109420167 1.000000e-160 577.0
6 TraesCS1D01G091700 chr1A 93.891 311 13 3 331 641 109422429 109422125 8.130000e-127 464.0
7 TraesCS1D01G091700 chr1A 90.343 321 22 7 382 698 105301655 105301970 2.990000e-111 412.0
8 TraesCS1D01G091700 chr1A 86.804 341 37 7 1 335 504426727 504427065 1.410000e-99 374.0
9 TraesCS1D01G091700 chr1A 91.270 252 8 7 1125 1374 109419879 109419640 8.600000e-87 331.0
10 TraesCS1D01G091700 chr1A 87.943 282 29 4 3818 4094 541433766 541434047 1.110000e-85 327.0
11 TraesCS1D01G091700 chr1A 93.827 81 1 2 729 807 109421044 109420966 7.290000e-23 119.0
12 TraesCS1D01G091700 chr1B 95.321 2116 75 11 1112 3217 121715776 121713675 0.000000e+00 3338.0
13 TraesCS1D01G091700 chr1B 88.831 1146 72 30 1 1116 121717060 121715941 0.000000e+00 1356.0
14 TraesCS1D01G091700 chr1B 89.937 477 21 14 491 950 121564358 121563892 1.290000e-164 590.0
15 TraesCS1D01G091700 chr1B 85.657 502 46 11 1 494 121565122 121564639 4.790000e-139 505.0
16 TraesCS1D01G091700 chr1B 84.229 279 28 11 3816 4087 666026296 666026027 1.480000e-64 257.0
17 TraesCS1D01G091700 chr1B 74.572 409 74 23 3215 3604 666027002 666026605 7.190000e-33 152.0
18 TraesCS1D01G091700 chr3B 92.113 1699 134 0 1476 3174 736311062 736312760 0.000000e+00 2396.0
19 TraesCS1D01G091700 chr3B 91.281 1709 149 0 1466 3174 736325052 736326760 0.000000e+00 2331.0
20 TraesCS1D01G091700 chr3B 76.612 791 101 44 429 1178 736324088 736324835 3.950000e-95 359.0
21 TraesCS1D01G091700 chr3B 83.946 299 31 10 3796 4086 22796465 22796754 1.900000e-68 270.0
22 TraesCS1D01G091700 chr3B 84.167 120 8 5 498 607 736253607 736253725 5.680000e-19 106.0
23 TraesCS1D01G091700 chr3B 89.706 68 2 2 425 489 736253487 736253552 9.560000e-12 82.4
24 TraesCS1D01G091700 chr3B 91.837 49 3 1 1402 1449 736325041 736325089 2.680000e-07 67.6
25 TraesCS1D01G091700 chr3B 84.286 70 7 3 1384 1449 736311020 736311089 9.630000e-07 65.8
26 TraesCS1D01G091700 chr3D 91.941 1700 135 2 1476 3174 554216954 554218652 0.000000e+00 2379.0
27 TraesCS1D01G091700 chr3D 91.124 1735 143 7 1449 3174 554328805 554330537 0.000000e+00 2340.0
28 TraesCS1D01G091700 chr3D 86.686 338 39 5 1 333 446195741 446195405 1.820000e-98 370.0
29 TraesCS1D01G091700 chr3D 80.569 211 9 17 424 607 554177460 554177665 2.600000e-27 134.0
30 TraesCS1D01G091700 chr3D 80.569 211 9 17 424 607 554223666 554223871 2.600000e-27 134.0
31 TraesCS1D01G091700 chr3D 80.383 209 12 13 425 607 554169643 554169848 9.360000e-27 132.0
32 TraesCS1D01G091700 chr3D 92.453 53 3 1 1397 1448 554318347 554318399 1.600000e-09 75.0
33 TraesCS1D01G091700 chr3D 84.286 70 7 3 1384 1449 554216912 554216981 9.630000e-07 65.8
34 TraesCS1D01G091700 chr3A 91.583 1699 143 0 1476 3174 690785062 690786760 0.000000e+00 2346.0
35 TraesCS1D01G091700 chr3A 90.867 1730 154 2 1449 3174 690896653 690898382 0.000000e+00 2316.0
36 TraesCS1D01G091700 chr3A 92.435 542 21 8 3218 3756 37316011 37315487 0.000000e+00 756.0
37 TraesCS1D01G091700 chr3A 80.476 210 10 16 424 607 690795542 690795746 9.360000e-27 132.0
38 TraesCS1D01G091700 chr3A 75.916 191 17 15 424 588 690884580 690884767 2.070000e-08 71.3
39 TraesCS1D01G091700 chr7D 98.079 885 10 2 3273 4151 177103326 177102443 0.000000e+00 1533.0
40 TraesCS1D01G091700 chr7D 87.798 336 31 8 1 331 557086743 557086413 6.510000e-103 385.0
41 TraesCS1D01G091700 chr7D 87.975 316 30 7 31 340 613792589 613792902 2.360000e-97 366.0
42 TraesCS1D01G091700 chr4D 95.962 941 11 6 3217 4151 497453126 497454045 0.000000e+00 1502.0
43 TraesCS1D01G091700 chr4D 86.471 340 33 9 2 334 480521072 480520739 1.100000e-95 361.0
44 TraesCS1D01G091700 chrUn 81.949 975 94 39 3231 4151 105289512 105288566 0.000000e+00 750.0
45 TraesCS1D01G091700 chrUn 87.202 336 36 6 1 331 86715469 86715136 3.920000e-100 375.0
46 TraesCS1D01G091700 chrUn 87.538 329 34 6 1 324 298165402 298165076 1.410000e-99 374.0
47 TraesCS1D01G091700 chr7B 88.184 347 31 9 1 340 746667305 746666962 5.000000e-109 405.0
48 TraesCS1D01G091700 chr7B 87.353 340 33 5 1 333 489547485 489547149 8.420000e-102 381.0
49 TraesCS1D01G091700 chr7A 85.507 345 33 8 3818 4148 448446454 448446795 1.100000e-90 344.0
50 TraesCS1D01G091700 chr4A 86.879 282 32 5 3818 4094 724401426 724401707 1.120000e-80 311.0
51 TraesCS1D01G091700 chr2B 82.209 163 21 6 3216 3375 140217596 140217439 2.600000e-27 134.0
52 TraesCS1D01G091700 chr5B 80.233 172 29 4 3215 3385 626817828 626817995 1.570000e-24 124.0
53 TraesCS1D01G091700 chr5B 80.347 173 27 5 3215 3385 626825557 626825724 1.570000e-24 124.0
54 TraesCS1D01G091700 chr5B 79.747 158 28 3 3215 3371 623152904 623153058 1.220000e-20 111.0
55 TraesCS1D01G091700 chr5B 89.231 65 2 3 425 486 566695074 566695136 4.450000e-10 76.8
56 TraesCS1D01G091700 chr2A 88.421 95 10 1 3217 3310 174436342 174436436 3.390000e-21 113.0


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 TraesCS1D01G091700 chr1D 78064272 78068422 4150 True 7666.0 7666 100.000000 1 4151 1 chr1D.!!$R1 4150
1 TraesCS1D01G091700 chr1A 105301655 105304683 3028 False 2055.5 3699 92.020000 382 3186 2 chr1A.!!$F4 2804
2 TraesCS1D01G091700 chr1A 463948999 463949939 940 False 1345.0 1345 92.685000 3216 4151 1 chr1A.!!$F1 935
3 TraesCS1D01G091700 chr1A 109415113 109422429 7316 True 805.0 2534 92.786400 331 3186 5 chr1A.!!$R1 2855
4 TraesCS1D01G091700 chr1B 121713675 121717060 3385 True 2347.0 3338 92.076000 1 3217 2 chr1B.!!$R2 3216
5 TraesCS1D01G091700 chr1B 121563892 121565122 1230 True 547.5 590 87.797000 1 950 2 chr1B.!!$R1 949
6 TraesCS1D01G091700 chr1B 666026027 666027002 975 True 204.5 257 79.400500 3215 4087 2 chr1B.!!$R3 872
7 TraesCS1D01G091700 chr3B 736311020 736312760 1740 False 1230.9 2396 88.199500 1384 3174 2 chr3B.!!$F3 1790
8 TraesCS1D01G091700 chr3B 736324088 736326760 2672 False 919.2 2331 86.576667 429 3174 3 chr3B.!!$F4 2745
9 TraesCS1D01G091700 chr3D 554328805 554330537 1732 False 2340.0 2340 91.124000 1449 3174 1 chr3D.!!$F5 1725
10 TraesCS1D01G091700 chr3D 554216912 554218652 1740 False 1222.4 2379 88.113500 1384 3174 2 chr3D.!!$F6 1790
11 TraesCS1D01G091700 chr3A 690785062 690786760 1698 False 2346.0 2346 91.583000 1476 3174 1 chr3A.!!$F1 1698
12 TraesCS1D01G091700 chr3A 690896653 690898382 1729 False 2316.0 2316 90.867000 1449 3174 1 chr3A.!!$F4 1725
13 TraesCS1D01G091700 chr3A 37315487 37316011 524 True 756.0 756 92.435000 3218 3756 1 chr3A.!!$R1 538
14 TraesCS1D01G091700 chr7D 177102443 177103326 883 True 1533.0 1533 98.079000 3273 4151 1 chr7D.!!$R1 878
15 TraesCS1D01G091700 chr4D 497453126 497454045 919 False 1502.0 1502 95.962000 3217 4151 1 chr4D.!!$F1 934
16 TraesCS1D01G091700 chrUn 105288566 105289512 946 True 750.0 750 81.949000 3231 4151 1 chrUn.!!$R2 920

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
608 923 0.450482 CGGCGCAACGAAAAGTAGTG 60.450 55.0 10.83 0.0 35.47 2.74 F
609 924 0.584876 GGCGCAACGAAAAGTAGTGT 59.415 50.0 10.83 0.0 0.00 3.55 F
685 1410 0.758123 AAGCCTCATCTCTAGCCAGC 59.242 55.0 0.00 0.0 0.00 4.85 F
1951 7305 0.179051 TAACTTTGCCGACAACCCGT 60.179 50.0 0.00 0.0 34.87 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1428 6689 0.037326 GGTTCATCTCGTGCACCTGA 60.037 55.0 12.15 10.07 40.51 3.86 R
1429 6690 0.320683 TGGTTCATCTCGTGCACCTG 60.321 55.0 12.15 4.21 43.59 4.00 R
2400 7762 0.465460 GGCCAGTGAGGTTGTTGTGA 60.465 55.0 0.00 0.00 40.61 3.58 R
3320 8684 1.051812 CCAGAAGCCAGGTCGGATAT 58.948 55.0 0.00 0.00 36.56 1.63 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
92 100 9.793259 TCTTCTAAAATGTCTAATTGTGGTTCT 57.207 29.630 0.00 0.00 0.00 3.01
95 103 9.349713 TCTAAAATGTCTAATTGTGGTTCTTGT 57.650 29.630 0.00 0.00 0.00 3.16
103 111 9.366216 GTCTAATTGTGGTTCTTGTTTTCTTTT 57.634 29.630 0.00 0.00 0.00 2.27
111 119 5.869344 GGTTCTTGTTTTCTTTTGTCTTGCT 59.131 36.000 0.00 0.00 0.00 3.91
216 224 4.333372 GGCCGAAATTGAAATGCAAATGAT 59.667 37.500 0.00 0.00 40.48 2.45
247 258 1.411612 CCCTAAGTTTAGCGGATCGGT 59.588 52.381 1.93 0.00 41.50 4.69
254 265 2.062971 TTAGCGGATCGGTTAGGTCT 57.937 50.000 1.93 0.00 38.83 3.85
270 281 2.441750 AGGTCTGGCCAAAACTTAGTGA 59.558 45.455 7.01 0.00 40.61 3.41
305 320 8.788325 ATATAAGCCTTTTACTTCGTCAACTT 57.212 30.769 0.00 0.00 0.00 2.66
316 331 3.553828 TCGTCAACTTATTGGGGATCC 57.446 47.619 1.92 1.92 36.39 3.36
360 375 3.115892 GCCGACCGATTTGCGTGA 61.116 61.111 0.00 0.00 38.67 4.35
466 481 1.871772 GCGCACTGCACTTTCTCAT 59.128 52.632 0.30 0.00 45.45 2.90
502 814 5.502153 AGTCTCGTCGCTTAATTCATAGT 57.498 39.130 0.00 0.00 0.00 2.12
608 923 0.450482 CGGCGCAACGAAAAGTAGTG 60.450 55.000 10.83 0.00 35.47 2.74
609 924 0.584876 GGCGCAACGAAAAGTAGTGT 59.415 50.000 10.83 0.00 0.00 3.55
610 925 1.794116 GGCGCAACGAAAAGTAGTGTA 59.206 47.619 10.83 0.00 0.00 2.90
658 1383 1.078426 CCCCTTCACATCACGGTCC 60.078 63.158 0.00 0.00 0.00 4.46
681 1406 2.697751 TCCTTGAAGCCTCATCTCTAGC 59.302 50.000 0.00 0.00 0.00 3.42
683 1408 2.165357 TGAAGCCTCATCTCTAGCCA 57.835 50.000 0.00 0.00 0.00 4.75
684 1409 2.037901 TGAAGCCTCATCTCTAGCCAG 58.962 52.381 0.00 0.00 0.00 4.85
685 1410 0.758123 AAGCCTCATCTCTAGCCAGC 59.242 55.000 0.00 0.00 0.00 4.85
686 1411 1.120795 AGCCTCATCTCTAGCCAGCC 61.121 60.000 0.00 0.00 0.00 4.85
687 1412 1.120795 GCCTCATCTCTAGCCAGCCT 61.121 60.000 0.00 0.00 0.00 4.58
688 1413 1.825242 GCCTCATCTCTAGCCAGCCTA 60.825 57.143 0.00 0.00 0.00 3.93
839 2878 4.188462 TGTCGATCGCTTGGTTTGATTAT 58.812 39.130 11.09 0.00 0.00 1.28
931 2977 1.965643 TCAGGCTTTGCAAAAGCATCT 59.034 42.857 24.87 15.79 44.71 2.90
1181 3705 6.264518 ACTTCATGGTAGGTTTAACTTTGGTG 59.735 38.462 0.00 0.00 0.00 4.17
1182 3706 5.074115 TCATGGTAGGTTTAACTTTGGTGG 58.926 41.667 0.00 0.00 0.00 4.61
1183 3707 4.792513 TGGTAGGTTTAACTTTGGTGGA 57.207 40.909 0.00 0.00 0.00 4.02
1184 3708 4.721132 TGGTAGGTTTAACTTTGGTGGAG 58.279 43.478 0.00 0.00 0.00 3.86
1185 3709 4.166531 TGGTAGGTTTAACTTTGGTGGAGT 59.833 41.667 0.00 0.00 0.00 3.85
1200 3724 7.600231 TTGGTGGAGTATATATTGTCCGTAA 57.400 36.000 8.00 2.53 31.05 3.18
1325 3901 8.387813 ACTATAGCTTTGCTACTCCTATCTACT 58.612 37.037 0.00 0.00 44.24 2.57
1326 3902 5.782893 AGCTTTGCTACTCCTATCTACTG 57.217 43.478 0.00 0.00 36.99 2.74
1434 6695 8.498054 AGTAGTTGATTAATGATGTTCAGGTG 57.502 34.615 0.00 0.00 0.00 4.00
1435 6696 6.199937 AGTTGATTAATGATGTTCAGGTGC 57.800 37.500 0.00 0.00 0.00 5.01
1436 6697 5.711506 AGTTGATTAATGATGTTCAGGTGCA 59.288 36.000 0.00 0.00 0.00 4.57
1437 6698 5.565592 TGATTAATGATGTTCAGGTGCAC 57.434 39.130 8.80 8.80 0.00 4.57
1438 6699 4.094739 TGATTAATGATGTTCAGGTGCACG 59.905 41.667 11.45 0.00 0.00 5.34
1439 6700 2.183478 AATGATGTTCAGGTGCACGA 57.817 45.000 11.45 0.00 0.00 4.35
1440 6701 1.730501 ATGATGTTCAGGTGCACGAG 58.269 50.000 11.45 5.75 0.00 4.18
1441 6702 0.678950 TGATGTTCAGGTGCACGAGA 59.321 50.000 11.45 8.30 0.00 4.04
1442 6703 1.276138 TGATGTTCAGGTGCACGAGAT 59.724 47.619 11.45 0.70 0.00 2.75
1443 6704 1.662629 GATGTTCAGGTGCACGAGATG 59.337 52.381 11.45 7.17 0.00 2.90
1444 6705 0.678950 TGTTCAGGTGCACGAGATGA 59.321 50.000 11.45 9.47 0.00 2.92
1445 6706 1.069978 TGTTCAGGTGCACGAGATGAA 59.930 47.619 11.45 14.70 0.00 2.57
1446 6707 1.461127 GTTCAGGTGCACGAGATGAAC 59.539 52.381 25.99 25.99 41.88 3.18
1451 6712 2.363788 GTGCACGAGATGAACCACTA 57.636 50.000 0.00 0.00 29.07 2.74
1881 7235 1.048724 ACGTCCCCATCATCATCGGT 61.049 55.000 0.00 0.00 0.00 4.69
1938 7292 1.001633 AGGATGCACGACGGTAACTTT 59.998 47.619 0.00 0.00 0.00 2.66
1951 7305 0.179051 TAACTTTGCCGACAACCCGT 60.179 50.000 0.00 0.00 34.87 5.28
2350 7712 1.456705 AACAATGGGTTGCCGGTGT 60.457 52.632 1.90 0.00 38.60 4.16
2400 7762 2.093658 CACCATGCCGTCCTACTACTTT 60.094 50.000 0.00 0.00 0.00 2.66
2460 7822 1.516386 CGTTCCCATGGACGTCGAG 60.516 63.158 15.22 1.38 0.00 4.04
2652 8015 1.542187 GCCTGTACACGGAGGACCTT 61.542 60.000 13.57 0.00 0.00 3.50
2682 8045 0.108520 CACCGCACCCGTACAACTAT 60.109 55.000 0.00 0.00 0.00 2.12
2778 8141 2.232941 GAGATTCCGGTACAACACCTCA 59.767 50.000 0.00 0.00 46.19 3.86
3202 8565 5.801380 ACGTACTTATGAAAGTTGGGTCAT 58.199 37.500 0.00 0.00 43.60 3.06
3320 8684 0.553819 GCTCTCCCTCTCCTGGACTA 59.446 60.000 0.00 0.00 0.00 2.59
3515 8897 5.127845 CCCAGCAGATAGAGACAAGAAACTA 59.872 44.000 0.00 0.00 0.00 2.24
3859 9378 9.194972 TCTTCTGACTCTATATCTTCAACACAT 57.805 33.333 0.00 0.00 0.00 3.21
3916 9437 1.600957 GCATCCTTCGTCATCCATGTG 59.399 52.381 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 47 8.814038 AAGATATCCAACTTTCATAACTGCTT 57.186 30.769 0.00 0.00 0.00 3.91
91 99 7.031975 AGAAGAGCAAGACAAAAGAAAACAAG 58.968 34.615 0.00 0.00 0.00 3.16
92 100 6.924111 AGAAGAGCAAGACAAAAGAAAACAA 58.076 32.000 0.00 0.00 0.00 2.83
93 101 6.515272 AGAAGAGCAAGACAAAAGAAAACA 57.485 33.333 0.00 0.00 0.00 2.83
111 119 9.851686 ATAATTCACCATGTATTTGCTAGAAGA 57.148 29.630 0.00 0.00 0.00 2.87
169 177 8.611757 GCCATTGAAACACATTTCTTTACTTTT 58.388 29.630 1.82 0.00 44.02 2.27
172 180 6.223120 GGCCATTGAAACACATTTCTTTACT 58.777 36.000 0.00 0.00 44.02 2.24
173 181 5.118510 CGGCCATTGAAACACATTTCTTTAC 59.881 40.000 2.24 0.00 44.02 2.01
174 182 5.010112 TCGGCCATTGAAACACATTTCTTTA 59.990 36.000 2.24 0.00 44.02 1.85
222 230 4.320348 CGATCCGCTAAACTTAGGGAGTAG 60.320 50.000 13.49 0.00 43.92 2.57
223 231 3.567164 CGATCCGCTAAACTTAGGGAGTA 59.433 47.826 13.49 1.88 43.92 2.59
224 232 2.361438 CGATCCGCTAAACTTAGGGAGT 59.639 50.000 13.49 3.61 43.92 3.85
225 233 2.288273 CCGATCCGCTAAACTTAGGGAG 60.288 54.545 13.49 5.72 43.92 4.30
226 234 1.684983 CCGATCCGCTAAACTTAGGGA 59.315 52.381 13.49 10.67 43.92 4.20
228 236 2.884894 ACCGATCCGCTAAACTTAGG 57.115 50.000 0.00 0.00 0.00 2.69
233 244 2.100418 AGACCTAACCGATCCGCTAAAC 59.900 50.000 0.00 0.00 0.00 2.01
238 249 1.067582 CCAGACCTAACCGATCCGC 59.932 63.158 0.00 0.00 0.00 5.54
239 250 1.067582 GCCAGACCTAACCGATCCG 59.932 63.158 0.00 0.00 0.00 4.18
247 258 4.103469 TCACTAAGTTTTGGCCAGACCTAA 59.897 41.667 5.11 0.00 40.22 2.69
294 309 3.877508 GGATCCCCAATAAGTTGACGAAG 59.122 47.826 0.00 0.00 37.53 3.79
296 311 2.159014 CGGATCCCCAATAAGTTGACGA 60.159 50.000 6.06 0.00 37.53 4.20
297 312 2.210116 CGGATCCCCAATAAGTTGACG 58.790 52.381 6.06 0.00 37.53 4.35
298 313 3.277142 ACGGATCCCCAATAAGTTGAC 57.723 47.619 6.06 0.00 37.53 3.18
299 314 4.717778 TCTAACGGATCCCCAATAAGTTGA 59.282 41.667 6.06 1.30 37.53 3.18
300 315 5.031066 TCTAACGGATCCCCAATAAGTTG 57.969 43.478 6.06 0.00 35.05 3.16
301 316 4.720273 ACTCTAACGGATCCCCAATAAGTT 59.280 41.667 6.06 5.20 0.00 2.66
302 317 4.296056 ACTCTAACGGATCCCCAATAAGT 58.704 43.478 6.06 0.37 0.00 2.24
303 318 4.957684 ACTCTAACGGATCCCCAATAAG 57.042 45.455 6.06 0.00 0.00 1.73
304 319 4.685030 GCAACTCTAACGGATCCCCAATAA 60.685 45.833 6.06 0.00 0.00 1.40
305 320 3.181458 GCAACTCTAACGGATCCCCAATA 60.181 47.826 6.06 0.00 0.00 1.90
316 331 4.715527 AGTACTTAGGGCAACTCTAACG 57.284 45.455 0.00 0.00 0.00 3.18
360 375 1.338973 GCGTTCATGAATGGGCATCAT 59.661 47.619 25.29 0.00 38.02 2.45
466 481 1.000486 AGACTTCCTCTAGCCGGCA 60.000 57.895 31.54 14.00 0.00 5.69
502 814 5.056480 AGACAATGACAAAGTCAATCGTGA 58.944 37.500 3.74 0.00 45.96 4.35
608 923 2.550978 AGCATCATTGGCACGTACTAC 58.449 47.619 0.00 0.00 0.00 2.73
609 924 2.979814 AGCATCATTGGCACGTACTA 57.020 45.000 0.00 0.00 0.00 1.82
610 925 2.979814 TAGCATCATTGGCACGTACT 57.020 45.000 0.00 0.00 0.00 2.73
658 1383 3.910568 AGAGATGAGGCTTCAAGGAAG 57.089 47.619 1.33 1.67 42.03 3.46
684 1409 8.517056 GGCTATTACTATTAGCTAGCTATAGGC 58.483 40.741 26.25 26.25 39.60 3.93
685 1410 9.575868 TGGCTATTACTATTAGCTAGCTATAGG 57.424 37.037 24.69 17.92 36.06 2.57
688 1413 8.364142 GCATGGCTATTACTATTAGCTAGCTAT 58.636 37.037 24.69 16.33 37.17 2.97
730 2764 1.546589 AACCTTGTGGCATGGGCATG 61.547 55.000 0.00 0.00 43.71 4.06
731 2765 1.229272 AACCTTGTGGCATGGGCAT 60.229 52.632 0.00 0.00 43.71 4.40
732 2766 2.200930 AACCTTGTGGCATGGGCA 59.799 55.556 0.00 0.00 43.71 5.36
733 2767 2.658422 CAACCTTGTGGCATGGGC 59.342 61.111 0.00 0.00 36.63 5.36
734 2768 2.658422 GCAACCTTGTGGCATGGG 59.342 61.111 0.00 0.00 31.84 4.00
735 2769 2.259204 CGCAACCTTGTGGCATGG 59.741 61.111 0.00 0.00 30.74 3.66
839 2878 2.616797 TTTGCAACCGCTGACCAGGA 62.617 55.000 0.00 0.00 39.64 3.86
887 2931 4.739735 GCTGTGGCCTATTTATACACTCGT 60.740 45.833 3.32 0.00 33.44 4.18
926 2972 0.450983 GCTGCTCAGTGGAAAGATGC 59.549 55.000 0.00 0.00 0.00 3.91
931 2977 0.106708 AACTCGCTGCTCAGTGGAAA 59.893 50.000 10.17 0.00 39.31 3.13
1143 3667 6.823182 CCTACCATGAAGTGATCAACAACATA 59.177 38.462 0.00 0.00 42.54 2.29
1181 3705 9.298774 GCTACAATTACGGACAATATATACTCC 57.701 37.037 0.00 0.00 0.00 3.85
1182 3706 9.850628 TGCTACAATTACGGACAATATATACTC 57.149 33.333 0.00 0.00 0.00 2.59
1200 3724 7.754924 CCAAAGTTAAACGAATCATGCTACAAT 59.245 33.333 0.00 0.00 0.00 2.71
1325 3901 8.106247 AGGAATCGCAAAAAGAAAGTTATACA 57.894 30.769 0.00 0.00 0.00 2.29
1410 6671 7.148255 TGCACCTGAACATCATTAATCAACTAC 60.148 37.037 0.00 0.00 0.00 2.73
1411 6672 6.883756 TGCACCTGAACATCATTAATCAACTA 59.116 34.615 0.00 0.00 0.00 2.24
1412 6673 5.711506 TGCACCTGAACATCATTAATCAACT 59.288 36.000 0.00 0.00 0.00 3.16
1413 6674 5.801947 GTGCACCTGAACATCATTAATCAAC 59.198 40.000 5.22 0.00 0.00 3.18
1414 6675 5.391843 CGTGCACCTGAACATCATTAATCAA 60.392 40.000 12.15 0.00 0.00 2.57
1415 6676 4.094739 CGTGCACCTGAACATCATTAATCA 59.905 41.667 12.15 0.00 0.00 2.57
1416 6677 4.332543 TCGTGCACCTGAACATCATTAATC 59.667 41.667 12.15 0.00 0.00 1.75
1417 6678 4.260985 TCGTGCACCTGAACATCATTAAT 58.739 39.130 12.15 0.00 0.00 1.40
1418 6679 3.669536 TCGTGCACCTGAACATCATTAA 58.330 40.909 12.15 0.00 0.00 1.40
1419 6680 3.056179 TCTCGTGCACCTGAACATCATTA 60.056 43.478 12.15 0.00 0.00 1.90
1420 6681 2.079158 CTCGTGCACCTGAACATCATT 58.921 47.619 12.15 0.00 0.00 2.57
1421 6682 1.276138 TCTCGTGCACCTGAACATCAT 59.724 47.619 12.15 0.00 0.00 2.45
1422 6683 0.678950 TCTCGTGCACCTGAACATCA 59.321 50.000 12.15 0.00 0.00 3.07
1423 6684 1.662629 CATCTCGTGCACCTGAACATC 59.337 52.381 12.15 0.00 0.00 3.06
1424 6685 1.276138 TCATCTCGTGCACCTGAACAT 59.724 47.619 12.15 0.00 0.00 2.71
1425 6686 0.678950 TCATCTCGTGCACCTGAACA 59.321 50.000 12.15 0.00 0.00 3.18
1426 6687 1.461127 GTTCATCTCGTGCACCTGAAC 59.539 52.381 22.48 22.48 39.00 3.18
1427 6688 1.608025 GGTTCATCTCGTGCACCTGAA 60.608 52.381 12.15 12.20 40.51 3.02
1428 6689 0.037326 GGTTCATCTCGTGCACCTGA 60.037 55.000 12.15 10.07 40.51 3.86
1429 6690 0.320683 TGGTTCATCTCGTGCACCTG 60.321 55.000 12.15 4.21 43.59 4.00
1430 6691 0.320771 GTGGTTCATCTCGTGCACCT 60.321 55.000 12.15 0.00 43.59 4.00
1431 6692 0.320771 AGTGGTTCATCTCGTGCACC 60.321 55.000 12.15 0.00 43.52 5.01
1432 6693 2.363788 TAGTGGTTCATCTCGTGCAC 57.636 50.000 6.82 6.82 0.00 4.57
1433 6694 3.056179 TCAATAGTGGTTCATCTCGTGCA 60.056 43.478 0.00 0.00 0.00 4.57
1434 6695 3.307242 GTCAATAGTGGTTCATCTCGTGC 59.693 47.826 0.00 0.00 0.00 5.34
1435 6696 3.865745 GGTCAATAGTGGTTCATCTCGTG 59.134 47.826 0.00 0.00 0.00 4.35
1436 6697 3.513912 TGGTCAATAGTGGTTCATCTCGT 59.486 43.478 0.00 0.00 0.00 4.18
1437 6698 4.123497 TGGTCAATAGTGGTTCATCTCG 57.877 45.455 0.00 0.00 0.00 4.04
1438 6699 6.115446 TGATTGGTCAATAGTGGTTCATCTC 58.885 40.000 0.00 0.00 0.00 2.75
1439 6700 6.065976 TGATTGGTCAATAGTGGTTCATCT 57.934 37.500 0.00 0.00 0.00 2.90
1440 6701 6.757897 TTGATTGGTCAATAGTGGTTCATC 57.242 37.500 0.00 0.00 39.36 2.92
1463 6724 9.512588 GGACCTGAACATCATTAATCAGATAAT 57.487 33.333 3.34 0.00 41.38 1.28
1467 6728 6.115446 GTGGACCTGAACATCATTAATCAGA 58.885 40.000 3.34 0.00 41.38 3.27
1468 6729 5.007039 CGTGGACCTGAACATCATTAATCAG 59.993 44.000 0.00 0.00 39.16 2.90
1881 7235 2.917227 TCGAGCTGCCACCACTCA 60.917 61.111 0.00 0.00 0.00 3.41
1951 7305 2.024868 CGTTGATGGTCGCCGACAA 61.025 57.895 20.08 8.50 33.68 3.18
2283 7645 4.157120 CCGCGGGAATCGAACCCT 62.157 66.667 20.10 0.00 44.72 4.34
2400 7762 0.465460 GGCCAGTGAGGTTGTTGTGA 60.465 55.000 0.00 0.00 40.61 3.58
2460 7822 1.226717 CGTGAAGTAGAGGCGCTCC 60.227 63.158 7.64 0.00 0.00 4.70
2529 7891 2.341101 AATGGTCTCGCGACTCCGT 61.341 57.895 3.71 9.28 40.10 4.69
2550 7912 0.967662 CATTGTTCATGGTGGCCACA 59.032 50.000 35.78 22.39 35.80 4.17
2735 8098 0.394938 TAGCTTGGTCGCCTTGAACA 59.605 50.000 0.00 0.00 44.41 3.18
2778 8141 2.699846 GCTCTGGAAGATGATCTCCACT 59.300 50.000 8.81 0.00 45.62 4.00
3202 8565 9.444600 GTAGACAGACCCTAACATAAAAATTCA 57.555 33.333 0.00 0.00 0.00 2.57
3320 8684 1.051812 CCAGAAGCCAGGTCGGATAT 58.948 55.000 0.00 0.00 36.56 1.63
3515 8897 4.640201 ACAGCACCGTTCAATTTAGCATAT 59.360 37.500 0.00 0.00 0.00 1.78
3970 9491 5.593095 CCTACCCCCTCTATTTTTAACTTGC 59.407 44.000 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.