Multiple sequence alignment - TraesCS1B01G327900

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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 TraesCS1B01G327900 chr1B 100.000 2600 0 0 1 2600 553977918 553980517 0.000000e+00 4802.0
1 TraesCS1B01G327900 chr1A 90.813 1132 68 16 681 1797 507552468 507553578 0.000000e+00 1482.0
2 TraesCS1B01G327900 chr1A 92.009 851 28 10 974 1791 507555581 507556424 0.000000e+00 1158.0
3 TraesCS1B01G327900 chr1A 83.105 657 44 31 1817 2431 507556415 507557046 1.060000e-148 536.0
4 TraesCS1B01G327900 chr1A 93.023 215 15 0 2 216 507548590 507548804 5.400000e-82 315.0
5 TraesCS1B01G327900 chr1A 92.437 119 6 2 681 796 507555386 507555504 1.600000e-37 167.0
6 TraesCS1B01G327900 chr1D 89.957 697 63 1 1000 1696 411058980 411059669 0.000000e+00 893.0
7 TraesCS1B01G327900 chr1D 86.425 744 45 19 1817 2526 411059810 411060531 0.000000e+00 763.0
8 TraesCS1B01G327900 chr1D 82.801 657 81 10 1 627 411057924 411058578 2.260000e-155 558.0
9 TraesCS1B01G327900 chr1D 80.030 666 85 17 1122 1782 411063575 411064197 1.420000e-122 449.0
10 TraesCS1B01G327900 chr1D 91.126 293 17 6 681 970 411058694 411058980 3.140000e-104 388.0
11 TraesCS1B01G327900 chr1D 90.110 91 4 2 1711 1796 411059734 411059824 2.110000e-21 113.0
12 TraesCS1B01G327900 chr7D 79.430 316 56 8 243 557 577917217 577916910 5.640000e-52 215.0
13 TraesCS1B01G327900 chr7D 77.134 328 64 5 240 567 81092491 81092175 2.060000e-41 180.0
14 TraesCS1B01G327900 chr3B 84.247 146 23 0 269 414 525193460 525193315 2.700000e-30 143.0
15 TraesCS1B01G327900 chr5D 86.275 102 14 0 247 348 404479361 404479260 7.610000e-21 111.0
16 TraesCS1B01G327900 chr7A 88.710 62 7 0 269 330 35627264 35627203 2.770000e-10 76.8
17 TraesCS1B01G327900 chr7A 76.800 125 28 1 277 401 126057520 126057643 4.640000e-08 69.4
18 TraesCS1B01G327900 chr7B 90.741 54 5 0 277 330 84132025 84131972 3.590000e-09 73.1


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 TraesCS1B01G327900 chr1B 553977918 553980517 2599 False 4802.000000 4802 100.0000 1 2600 1 chr1B.!!$F1 2599
1 TraesCS1B01G327900 chr1A 507548590 507557046 8456 False 731.600000 1482 90.2774 2 2431 5 chr1A.!!$F1 2429
2 TraesCS1B01G327900 chr1D 411057924 411064197 6273 False 527.333333 893 86.7415 1 2526 6 chr1D.!!$F1 2525

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
461 3605 0.60613 TCGATATGGCGGCGGTAGTA 60.606 55.0 9.78 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1927 8029 0.045002 CGTGAATCAATCGACGCGAC 60.045 55.0 15.93 5.54 39.18 5.19 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
53 54 1.995626 GCCTTCCCTCTACCTGCCA 60.996 63.158 0.00 0.00 0.00 4.92
70 71 1.897423 CACTATGACTGCCGGTGGA 59.103 57.895 1.90 0.00 0.00 4.02
78 79 4.649705 TGCCGGTGGAGGGAAGGA 62.650 66.667 1.90 0.00 0.00 3.36
139 140 5.599999 AGAGTGTTTTAGTCCTCGCATAT 57.400 39.130 0.00 0.00 0.00 1.78
146 147 7.545965 GTGTTTTAGTCCTCGCATATATAGCAT 59.454 37.037 7.58 0.00 0.00 3.79
160 161 1.681486 TAGCATTCGGGCGGATGACA 61.681 55.000 0.00 0.00 39.27 3.58
182 183 5.163612 ACACTTCTTCTTCAAGTTTGCCTTC 60.164 40.000 0.00 0.00 31.40 3.46
197 198 1.383523 CCTTCCGGCCTTTGATTCTC 58.616 55.000 0.00 0.00 0.00 2.87
231 232 2.118313 TCTGGATGTAGTCGACGGAA 57.882 50.000 10.46 0.00 0.00 4.30
248 272 1.004200 AACTCCAACGGCGGTAAGG 60.004 57.895 13.24 2.69 0.00 2.69
267 291 1.458445 GGTTAGGTTTTCTCGTCGTGC 59.542 52.381 0.00 0.00 0.00 5.34
283 3427 1.599518 TGCGGCGAGATTTGGTGTT 60.600 52.632 12.98 0.00 0.00 3.32
350 3494 1.563924 TAGGGCGCTGTTCTTTAGGA 58.436 50.000 14.51 0.00 0.00 2.94
371 3515 0.778815 CACGTGCACGAAGACTTCTC 59.221 55.000 42.94 0.00 43.02 2.87
373 3517 0.660595 CGTGCACGAAGACTTCTCGT 60.661 55.000 34.93 5.04 43.02 4.18
401 3545 1.405821 CGATAAGGTCAAGTCGGCTCT 59.594 52.381 0.00 0.00 0.00 4.09
402 3546 2.617308 CGATAAGGTCAAGTCGGCTCTA 59.383 50.000 0.00 0.00 0.00 2.43
403 3547 3.548415 CGATAAGGTCAAGTCGGCTCTAC 60.548 52.174 0.00 0.00 0.00 2.59
407 3551 2.239150 AGGTCAAGTCGGCTCTACTAGA 59.761 50.000 0.00 0.00 0.00 2.43
421 3565 1.353804 CTAGAGGAGCGACGACAGC 59.646 63.158 0.00 0.00 0.00 4.40
461 3605 0.606130 TCGATATGGCGGCGGTAGTA 60.606 55.000 9.78 0.00 0.00 1.82
464 3608 1.271656 GATATGGCGGCGGTAGTAGTT 59.728 52.381 9.78 0.00 0.00 2.24
473 3617 2.607771 GGCGGTAGTAGTTGTTTCGTGA 60.608 50.000 0.00 0.00 0.00 4.35
493 3644 5.502058 CGTGATCTGAGAATCTTGATGCAAC 60.502 44.000 0.00 0.00 34.92 4.17
500 3651 8.671921 TCTGAGAATCTTGATGCAACTTTTATC 58.328 33.333 0.00 0.00 34.92 1.75
526 3677 5.827797 TGTTTGAGATGCTTTGTACTTCCTT 59.172 36.000 0.00 0.00 0.00 3.36
527 3678 6.017109 TGTTTGAGATGCTTTGTACTTCCTTC 60.017 38.462 0.00 0.00 0.00 3.46
531 3682 5.491982 AGATGCTTTGTACTTCCTTCGAAT 58.508 37.500 0.00 0.00 0.00 3.34
591 3743 5.453567 AAAAGCTCCAAATGGACACTAAC 57.546 39.130 0.00 0.00 39.78 2.34
603 3755 3.181453 TGGACACTAACCGGACATTTGAA 60.181 43.478 9.46 0.00 0.00 2.69
621 3773 2.287547 TGAAGGACGAAATTTGCTGTGC 60.288 45.455 0.00 0.00 0.00 4.57
627 3779 1.798283 GAAATTTGCTGTGCATGCCA 58.202 45.000 16.68 11.79 38.76 4.92
650 3832 2.423898 GGCTGGCTGCATGCAGAAT 61.424 57.895 44.02 0.00 46.30 2.40
677 3859 5.454966 TCCTACAGTGATGGCTAGTTATCA 58.545 41.667 0.00 6.88 0.00 2.15
678 3860 5.536538 TCCTACAGTGATGGCTAGTTATCAG 59.463 44.000 10.18 4.54 34.25 2.90
679 3861 5.303078 CCTACAGTGATGGCTAGTTATCAGT 59.697 44.000 10.18 10.56 37.43 3.41
716 3930 5.957132 ACAGGGCATTAATCATGGAGTTAT 58.043 37.500 0.00 0.00 32.81 1.89
781 3998 3.743269 CGCAATAACCCCTCCGACTAAAT 60.743 47.826 0.00 0.00 0.00 1.40
788 4005 1.133884 CCCTCCGACTAAATTTCCCCC 60.134 57.143 0.00 0.00 0.00 5.40
796 4013 4.102681 CGACTAAATTTCCCCCATAGAGGT 59.897 45.833 0.00 0.00 34.66 3.85
797 4014 5.377478 GACTAAATTTCCCCCATAGAGGTG 58.623 45.833 0.00 0.00 34.66 4.00
802 4019 2.769602 TCCCCCATAGAGGTGAGTAC 57.230 55.000 0.00 0.00 34.66 2.73
803 4020 2.224077 TCCCCCATAGAGGTGAGTACT 58.776 52.381 0.00 0.00 34.66 2.73
804 4021 3.410136 TCCCCCATAGAGGTGAGTACTA 58.590 50.000 0.00 0.00 34.66 1.82
805 4022 3.995077 TCCCCCATAGAGGTGAGTACTAT 59.005 47.826 0.00 0.00 34.66 2.12
806 4023 4.422592 TCCCCCATAGAGGTGAGTACTATT 59.577 45.833 0.00 0.00 34.66 1.73
807 4024 5.618284 TCCCCCATAGAGGTGAGTACTATTA 59.382 44.000 0.00 0.00 34.66 0.98
808 4025 5.715753 CCCCCATAGAGGTGAGTACTATTAC 59.284 48.000 0.00 0.00 34.66 1.89
809 4026 6.468945 CCCCCATAGAGGTGAGTACTATTACT 60.469 46.154 0.00 0.00 37.13 2.24
937 4156 0.928229 CGGCGAGTTGTATGCTTACC 59.072 55.000 0.00 0.00 0.00 2.85
995 4214 1.589630 CGTGTGATCGTGGGGAAGA 59.410 57.895 0.00 0.00 0.00 2.87
1018 4237 4.752879 TGAAGCGCCGTACCCAGC 62.753 66.667 2.29 0.00 0.00 4.85
1332 4551 4.204891 CGCGTGGATTTCGTCGGC 62.205 66.667 0.00 0.00 0.00 5.54
1347 4566 1.800315 CGGCTACAACGTCCTGTCG 60.800 63.158 0.00 0.00 0.00 4.35
1429 4648 1.677552 GTGACGGTCATGGGGAACT 59.322 57.895 14.78 0.00 0.00 3.01
1482 4701 4.697756 TGGCGCGGGGTGAAGAAG 62.698 66.667 8.83 0.00 0.00 2.85
1492 4711 2.994995 TGAAGAAGGCCGAGCGGA 60.995 61.111 13.94 0.00 37.50 5.54
1605 7651 4.245660 TCAAGTGCTTGAAGTAATCGGAG 58.754 43.478 11.72 0.00 45.56 4.63
1607 7653 2.234908 AGTGCTTGAAGTAATCGGAGCT 59.765 45.455 0.00 0.00 39.35 4.09
1628 7674 1.134037 TGTAAGCCGGTTCACCTTTGT 60.134 47.619 1.90 0.00 0.00 2.83
1629 7675 1.951602 GTAAGCCGGTTCACCTTTGTT 59.048 47.619 1.90 0.00 0.00 2.83
1630 7676 2.351706 AAGCCGGTTCACCTTTGTTA 57.648 45.000 1.90 0.00 0.00 2.41
1631 7677 2.351706 AGCCGGTTCACCTTTGTTAA 57.648 45.000 1.90 0.00 0.00 2.01
1632 7678 2.227194 AGCCGGTTCACCTTTGTTAAG 58.773 47.619 1.90 0.00 0.00 1.85
1633 7679 2.158726 AGCCGGTTCACCTTTGTTAAGA 60.159 45.455 1.90 0.00 32.92 2.10
1634 7680 2.031420 GCCGGTTCACCTTTGTTAAGAC 60.031 50.000 1.90 0.00 32.92 3.01
1674 7721 5.586243 GCAGCTTTTGGATCACTAATCTACA 59.414 40.000 0.00 0.00 34.56 2.74
1792 7894 8.756486 GGTGTACATACCCCAAATTTATTAGT 57.244 34.615 0.00 0.00 34.56 2.24
1793 7895 9.850198 GGTGTACATACCCCAAATTTATTAGTA 57.150 33.333 0.00 0.00 34.56 1.82
1801 7903 8.762481 ACCCCAAATTTATTAGTATCAGTTCC 57.238 34.615 0.00 0.00 0.00 3.62
1802 7904 7.501225 ACCCCAAATTTATTAGTATCAGTTCCG 59.499 37.037 0.00 0.00 0.00 4.30
1803 7905 7.501225 CCCCAAATTTATTAGTATCAGTTCCGT 59.499 37.037 0.00 0.00 0.00 4.69
1804 7906 8.899771 CCCAAATTTATTAGTATCAGTTCCGTT 58.100 33.333 0.00 0.00 0.00 4.44
1848 7950 9.988815 ATTAGTATCAGTGAAGATTATGTGTCC 57.011 33.333 0.00 0.00 0.00 4.02
1852 7954 6.990341 TCAGTGAAGATTATGTGTCCATTG 57.010 37.500 0.00 0.00 32.29 2.82
1856 7958 7.765819 CAGTGAAGATTATGTGTCCATTGTCTA 59.234 37.037 0.00 0.00 32.29 2.59
1889 7991 4.573201 TGTCTCTTTACCCTTTCACGTTTG 59.427 41.667 0.00 0.00 0.00 2.93
1891 7993 5.065602 GTCTCTTTACCCTTTCACGTTTGTT 59.934 40.000 0.00 0.00 0.00 2.83
1892 7994 5.295045 TCTCTTTACCCTTTCACGTTTGTTC 59.705 40.000 0.00 0.00 0.00 3.18
1893 7995 5.187687 TCTTTACCCTTTCACGTTTGTTCT 58.812 37.500 0.00 0.00 0.00 3.01
1894 7996 5.295045 TCTTTACCCTTTCACGTTTGTTCTC 59.705 40.000 0.00 0.00 0.00 2.87
1895 7997 2.993937 ACCCTTTCACGTTTGTTCTCA 58.006 42.857 0.00 0.00 0.00 3.27
1896 7998 2.681344 ACCCTTTCACGTTTGTTCTCAC 59.319 45.455 0.00 0.00 0.00 3.51
1907 8009 8.279800 TCACGTTTGTTCTCACTGTTATTATTG 58.720 33.333 0.00 0.00 0.00 1.90
1913 8015 5.592104 TCTCACTGTTATTATTGGAGCGA 57.408 39.130 0.00 0.00 0.00 4.93
1927 8029 4.875544 TGGAGCGATCGGAATTTTTAAG 57.124 40.909 18.30 0.00 0.00 1.85
1932 8034 3.269310 CGATCGGAATTTTTAAGTCGCG 58.731 45.455 7.38 0.00 0.00 5.87
1962 8064 2.176045 TCACGGCAAGAGATTCCAGTA 58.824 47.619 0.00 0.00 0.00 2.74
2031 8134 2.548904 AGCTAGTAACGAGCCGTAGATG 59.451 50.000 0.62 0.00 39.99 2.90
2074 8177 3.782443 GCGGGTGGAGGTAGGGTG 61.782 72.222 0.00 0.00 0.00 4.61
2095 8205 1.153667 CGGCACTTGAGAGGAGAGC 60.154 63.158 0.00 0.00 0.00 4.09
2105 8215 3.003763 AGGAGAGCGGTGGGGTTC 61.004 66.667 0.00 0.00 0.00 3.62
2115 8225 2.154074 GTGGGGTTCAGAGGGGTGT 61.154 63.158 0.00 0.00 0.00 4.16
2181 8291 1.699656 CTGAGATTCGGGCAGCGTTG 61.700 60.000 0.00 0.00 0.00 4.10
2192 8302 1.565156 GCAGCGTTGTGTCAATCCGA 61.565 55.000 0.00 0.00 0.00 4.55
2315 8456 1.221466 CGAAGCGAAACTGCTCCACA 61.221 55.000 0.00 0.00 46.60 4.17
2322 8463 1.461127 GAAACTGCTCCACACACGATC 59.539 52.381 0.00 0.00 0.00 3.69
2391 8532 3.189285 TGTCAGTCATATGCATGTCACG 58.811 45.455 10.16 0.00 33.57 4.35
2444 8585 4.409218 GCCGTGACGCAGGTACGA 62.409 66.667 0.00 0.00 40.01 3.43
2449 8590 0.452987 GTGACGCAGGTACGACCATA 59.547 55.000 6.78 0.00 41.95 2.74
2451 8592 1.752498 TGACGCAGGTACGACCATATT 59.248 47.619 6.78 0.00 41.95 1.28
2452 8593 2.223641 TGACGCAGGTACGACCATATTC 60.224 50.000 6.78 0.11 41.95 1.75
2453 8594 1.268896 ACGCAGGTACGACCATATTCG 60.269 52.381 6.78 0.00 41.95 3.34
2460 8601 2.805277 CGACCATATTCGTACCGCC 58.195 57.895 0.00 0.00 34.16 6.13
2461 8602 1.000233 CGACCATATTCGTACCGCCG 61.000 60.000 0.00 0.00 34.16 6.46
2462 8603 1.280206 GACCATATTCGTACCGCCGC 61.280 60.000 0.00 0.00 0.00 6.53
2463 8604 1.006571 CCATATTCGTACCGCCGCT 60.007 57.895 0.00 0.00 0.00 5.52
2481 8624 3.117794 CGCTGTTGCCATGGATAAATTG 58.882 45.455 18.40 4.81 35.36 2.32
2485 8628 5.292589 GCTGTTGCCATGGATAAATTGAAAG 59.707 40.000 18.40 0.00 0.00 2.62
2487 8630 6.767456 TGTTGCCATGGATAAATTGAAAGTT 58.233 32.000 18.40 0.00 0.00 2.66
2493 8636 9.822185 GCCATGGATAAATTGAAAGTTAATCTT 57.178 29.630 18.40 0.00 38.10 2.40
2520 8663 1.066430 GCCCGTATGTCAGAGGAACAA 60.066 52.381 0.00 0.00 0.00 2.83
2541 8691 2.545537 GTGGAACCCTTCTCGAAAGT 57.454 50.000 0.00 0.00 0.00 2.66
2542 8692 3.672767 GTGGAACCCTTCTCGAAAGTA 57.327 47.619 0.00 0.00 0.00 2.24
2543 8693 4.203654 GTGGAACCCTTCTCGAAAGTAT 57.796 45.455 0.00 0.00 0.00 2.12
2544 8694 4.576879 GTGGAACCCTTCTCGAAAGTATT 58.423 43.478 0.00 0.00 0.00 1.89
2546 8696 6.346896 GTGGAACCCTTCTCGAAAGTATTAT 58.653 40.000 0.00 0.00 0.00 1.28
2547 8697 6.479331 GTGGAACCCTTCTCGAAAGTATTATC 59.521 42.308 0.00 0.00 0.00 1.75
2549 8699 7.093024 TGGAACCCTTCTCGAAAGTATTATCTT 60.093 37.037 0.00 0.00 0.00 2.40
2550 8700 7.438757 GGAACCCTTCTCGAAAGTATTATCTTC 59.561 40.741 0.00 0.00 0.00 2.87
2551 8701 6.818233 ACCCTTCTCGAAAGTATTATCTTCC 58.182 40.000 0.00 0.00 0.00 3.46
2552 8702 6.183360 ACCCTTCTCGAAAGTATTATCTTCCC 60.183 42.308 0.00 0.00 0.00 3.97
2553 8703 5.921408 CCTTCTCGAAAGTATTATCTTCCCG 59.079 44.000 0.00 0.00 0.00 5.14
2555 8705 6.069684 TCTCGAAAGTATTATCTTCCCGTC 57.930 41.667 0.00 0.00 0.00 4.79
2556 8706 5.826737 TCTCGAAAGTATTATCTTCCCGTCT 59.173 40.000 0.00 0.00 0.00 4.18
2557 8707 6.320672 TCTCGAAAGTATTATCTTCCCGTCTT 59.679 38.462 0.00 0.00 0.00 3.01
2559 8709 7.646314 TCGAAAGTATTATCTTCCCGTCTTAG 58.354 38.462 0.00 0.00 0.00 2.18
2568 8750 2.743636 TCCCGTCTTAGCAAACTCAG 57.256 50.000 0.00 0.00 0.00 3.35
2578 8760 0.169009 GCAAACTCAGCCACGAATCC 59.831 55.000 0.00 0.00 0.00 3.01
2593 8775 5.981315 CCACGAATCCTAAATAAGCGAAGTA 59.019 40.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 0.181350 GAGGGAAGGCGAATCCACAT 59.819 55.000 8.84 0.00 38.80 3.21
53 54 1.330655 CCTCCACCGGCAGTCATAGT 61.331 60.000 0.00 0.00 0.00 2.12
78 79 3.217231 CGTAGGCACGGGGATTCT 58.783 61.111 0.00 0.00 44.59 2.40
139 140 1.067142 GTCATCCGCCCGAATGCTATA 60.067 52.381 0.00 0.00 0.00 1.31
146 147 1.079405 GAAGTGTCATCCGCCCGAA 60.079 57.895 0.00 0.00 0.00 4.30
160 161 4.339530 GGAAGGCAAACTTGAAGAAGAAGT 59.660 41.667 0.00 0.00 40.21 3.01
182 183 0.811616 CGAGGAGAATCAAAGGCCGG 60.812 60.000 0.00 0.00 36.25 6.13
190 191 4.600692 TGAACAAACTCGAGGAGAATCA 57.399 40.909 18.41 12.26 36.25 2.57
197 198 3.319137 TCCAGATGAACAAACTCGAGG 57.681 47.619 18.41 1.00 0.00 4.63
231 232 1.761500 AACCTTACCGCCGTTGGAGT 61.761 55.000 0.00 0.00 0.00 3.85
248 272 2.850441 GCACGACGAGAAAACCTAAC 57.150 50.000 0.00 0.00 0.00 2.34
267 291 1.006832 CCTAACACCAAATCTCGCCG 58.993 55.000 0.00 0.00 0.00 6.46
283 3427 4.590647 CCTTGAATAGATCTGGAGCACCTA 59.409 45.833 5.18 0.00 37.04 3.08
330 3474 1.903860 TCCTAAAGAACAGCGCCCTAA 59.096 47.619 2.29 0.00 0.00 2.69
341 3485 2.029739 TCGTGCACGTGATCCTAAAGAA 60.030 45.455 35.74 11.63 40.80 2.52
350 3494 1.000163 AGAAGTCTTCGTGCACGTGAT 60.000 47.619 35.74 20.90 40.80 3.06
371 3515 3.692791 TGACCTTATCGATGACAGACG 57.307 47.619 8.54 0.00 0.00 4.18
373 3517 4.201920 CGACTTGACCTTATCGATGACAGA 60.202 45.833 8.54 0.00 36.70 3.41
401 3545 1.937278 CTGTCGTCGCTCCTCTAGTA 58.063 55.000 0.00 0.00 0.00 1.82
402 3546 1.370587 GCTGTCGTCGCTCCTCTAGT 61.371 60.000 0.00 0.00 0.00 2.57
403 3547 1.353804 GCTGTCGTCGCTCCTCTAG 59.646 63.158 0.00 0.00 0.00 2.43
407 3551 4.104417 GTCGCTGTCGTCGCTCCT 62.104 66.667 0.00 0.00 36.96 3.69
445 3589 1.000506 CAACTACTACCGCCGCCATAT 59.999 52.381 0.00 0.00 0.00 1.78
447 3591 1.143183 CAACTACTACCGCCGCCAT 59.857 57.895 0.00 0.00 0.00 4.40
461 3605 5.788450 AGATTCTCAGATCACGAAACAACT 58.212 37.500 0.00 0.00 0.00 3.16
464 3608 5.783111 TCAAGATTCTCAGATCACGAAACA 58.217 37.500 0.00 0.00 0.00 2.83
473 3617 7.463961 AAAAGTTGCATCAAGATTCTCAGAT 57.536 32.000 0.00 0.00 0.00 2.90
493 3644 8.752766 ACAAAGCATCTCAAACATGATAAAAG 57.247 30.769 0.00 0.00 0.00 2.27
500 3651 6.072286 AGGAAGTACAAAGCATCTCAAACATG 60.072 38.462 0.00 0.00 0.00 3.21
551 3702 9.882996 GGAGCTTTTTATTTCCTTTGAAAAATG 57.117 29.630 0.00 0.00 43.37 2.32
552 3703 9.625747 TGGAGCTTTTTATTTCCTTTGAAAAAT 57.374 25.926 0.00 0.00 43.37 1.82
558 3709 7.661027 TCCATTTGGAGCTTTTTATTTCCTTTG 59.339 33.333 0.00 0.00 39.78 2.77
563 3715 7.154656 AGTGTCCATTTGGAGCTTTTTATTTC 58.845 34.615 0.00 0.00 46.49 2.17
591 3743 1.803334 TTCGTCCTTCAAATGTCCGG 58.197 50.000 0.00 0.00 0.00 5.14
603 3755 1.317613 TGCACAGCAAATTTCGTCCT 58.682 45.000 0.00 0.00 34.76 3.85
627 3779 2.827190 CATGCAGCCAGCCACGAT 60.827 61.111 0.00 0.00 44.83 3.73
650 3832 0.618680 AGCCATCACTGTAGGAGGCA 60.619 55.000 12.96 0.00 44.34 4.75
677 3859 1.002087 CCTGTTTGTTCGCCTCCTACT 59.998 52.381 0.00 0.00 0.00 2.57
678 3860 1.439679 CCTGTTTGTTCGCCTCCTAC 58.560 55.000 0.00 0.00 0.00 3.18
679 3861 0.323629 CCCTGTTTGTTCGCCTCCTA 59.676 55.000 0.00 0.00 0.00 2.94
716 3930 0.801872 CACGCGTGATCAATTCCCAA 59.198 50.000 34.93 0.00 0.00 4.12
781 3998 2.661176 ACTCACCTCTATGGGGGAAA 57.339 50.000 0.00 0.00 38.45 3.13
805 4022 9.066892 TGGAAACTCGTAGTAGAAAACTAGTAA 57.933 33.333 0.00 0.00 41.42 2.24
806 4023 8.621532 TGGAAACTCGTAGTAGAAAACTAGTA 57.378 34.615 0.00 0.00 41.42 1.82
807 4024 7.516198 TGGAAACTCGTAGTAGAAAACTAGT 57.484 36.000 0.00 0.00 41.42 2.57
808 4025 7.701501 GGATGGAAACTCGTAGTAGAAAACTAG 59.298 40.741 0.00 0.00 41.42 2.57
809 4026 7.542025 GGATGGAAACTCGTAGTAGAAAACTA 58.458 38.462 0.00 0.00 39.80 2.24
822 4039 2.945315 CGACTCGGATGGAAACTCG 58.055 57.895 0.00 0.00 0.00 4.18
937 4156 1.416813 GATCTGCGAACGGTGCTCAG 61.417 60.000 0.00 0.00 0.00 3.35
947 4166 4.161295 CCCCTGCGGATCTGCGAA 62.161 66.667 21.30 4.18 37.81 4.70
981 4200 1.198094 TGGCTTCTTCCCCACGATCA 61.198 55.000 0.00 0.00 0.00 2.92
995 4214 2.106683 GTACGGCGCTTCATGGCTT 61.107 57.895 6.90 0.00 0.00 4.35
1347 4566 2.688794 GCTCAGCTTGCTGCAGTCC 61.689 63.158 16.64 0.00 45.94 3.85
1418 4637 3.006061 ATGGACGAGTTCCCCATGA 57.994 52.632 0.00 0.00 45.17 3.07
1590 7636 6.337853 CTTACAAGCTCCGATTACTTCAAG 57.662 41.667 0.00 0.00 0.00 3.02
1607 7653 1.950909 CAAAGGTGAACCGGCTTACAA 59.049 47.619 0.00 0.00 42.08 2.41
1628 7674 4.322801 GCTGGTCCTGCTCTTAAGTCTTAA 60.323 45.833 13.24 4.97 0.00 1.85
1629 7675 3.195825 GCTGGTCCTGCTCTTAAGTCTTA 59.804 47.826 13.24 0.00 0.00 2.10
1630 7676 2.027653 GCTGGTCCTGCTCTTAAGTCTT 60.028 50.000 13.24 0.00 0.00 3.01
1631 7677 1.552792 GCTGGTCCTGCTCTTAAGTCT 59.447 52.381 13.24 0.00 0.00 3.24
1632 7678 1.276421 TGCTGGTCCTGCTCTTAAGTC 59.724 52.381 20.19 0.00 0.00 3.01
1633 7679 1.277557 CTGCTGGTCCTGCTCTTAAGT 59.722 52.381 20.19 0.00 0.00 2.24
1634 7680 2.011046 GCTGCTGGTCCTGCTCTTAAG 61.011 57.143 20.19 10.66 0.00 1.85
1690 7737 8.674263 TGATGAGTAGCCTAACTAGTAGTAAC 57.326 38.462 2.50 0.00 34.49 2.50
1744 7841 3.245284 CGGACGGAAATACATAGTTGCTG 59.755 47.826 0.00 0.00 0.00 4.41
1822 7924 9.988815 GGACACATAATCTTCACTGATACTAAT 57.011 33.333 0.00 0.00 0.00 1.73
1832 7934 6.992063 AGACAATGGACACATAATCTTCAC 57.008 37.500 0.00 0.00 35.94 3.18
1875 7977 2.681344 GTGAGAACAAACGTGAAAGGGT 59.319 45.455 0.00 0.00 0.00 4.34
1878 7980 4.600012 ACAGTGAGAACAAACGTGAAAG 57.400 40.909 0.00 0.00 0.00 2.62
1881 7983 7.956420 ATAATAACAGTGAGAACAAACGTGA 57.044 32.000 0.00 0.00 0.00 4.35
1889 7991 5.810587 TCGCTCCAATAATAACAGTGAGAAC 59.189 40.000 0.00 0.00 0.00 3.01
1891 7993 5.592104 TCGCTCCAATAATAACAGTGAGA 57.408 39.130 0.00 0.00 0.00 3.27
1892 7994 5.117745 CGATCGCTCCAATAATAACAGTGAG 59.882 44.000 0.26 0.00 0.00 3.51
1893 7995 4.982295 CGATCGCTCCAATAATAACAGTGA 59.018 41.667 0.26 0.00 0.00 3.41
1894 7996 4.150627 CCGATCGCTCCAATAATAACAGTG 59.849 45.833 10.32 0.00 0.00 3.66
1895 7997 4.038763 TCCGATCGCTCCAATAATAACAGT 59.961 41.667 10.32 0.00 0.00 3.55
1896 7998 4.556233 TCCGATCGCTCCAATAATAACAG 58.444 43.478 10.32 0.00 0.00 3.16
1907 8009 4.550255 CGACTTAAAAATTCCGATCGCTCC 60.550 45.833 10.32 0.00 0.00 4.70
1913 8015 3.241868 CGACGCGACTTAAAAATTCCGAT 60.242 43.478 15.93 0.00 0.00 4.18
1927 8029 0.045002 CGTGAATCAATCGACGCGAC 60.045 55.000 15.93 5.54 39.18 5.19
1932 8034 1.999735 TCTTGCCGTGAATCAATCGAC 59.000 47.619 0.00 0.00 0.00 4.20
1988 8090 1.961277 CCTTGTCAGTGACGCCACC 60.961 63.158 18.17 0.00 44.22 4.61
2003 8106 1.477295 GCTCGTTACTAGCTCACCCTT 59.523 52.381 1.43 0.00 37.01 3.95
2074 8177 3.672295 CTCCTCTCAAGTGCCGGCC 62.672 68.421 26.77 15.80 0.00 6.13
2095 8205 3.717294 CCCCTCTGAACCCCACCG 61.717 72.222 0.00 0.00 0.00 4.94
2105 8215 1.038130 CCGTCCTAGACACCCCTCTG 61.038 65.000 0.00 0.00 32.09 3.35
2177 8287 1.459592 GGTCTTCGGATTGACACAACG 59.540 52.381 11.79 0.00 35.11 4.10
2181 8291 2.932614 CAGATGGTCTTCGGATTGACAC 59.067 50.000 11.79 4.61 35.11 3.67
2192 8302 0.322277 CAGCTGGTGCAGATGGTCTT 60.322 55.000 5.57 0.00 43.16 3.01
2315 8456 3.675225 CAGATCGTTCACAAAGATCGTGT 59.325 43.478 6.55 0.00 43.87 4.49
2322 8463 2.660094 CGTGCACAGATCGTTCACAAAG 60.660 50.000 18.64 0.00 41.29 2.77
2391 8532 2.296471 TGAGGTCTTTTCGACAGGAGAC 59.704 50.000 7.69 7.69 44.68 3.36
2431 8572 1.395635 ATATGGTCGTACCTGCGTCA 58.604 50.000 5.77 0.00 39.58 4.35
2433 8574 1.268896 CGAATATGGTCGTACCTGCGT 60.269 52.381 5.77 0.00 39.58 5.24
2481 8624 3.426292 GGGCAGCGTCAAGATTAACTTTC 60.426 47.826 0.00 0.00 36.61 2.62
2485 8628 0.373716 CGGGCAGCGTCAAGATTAAC 59.626 55.000 0.00 0.00 0.00 2.01
2487 8630 0.818938 TACGGGCAGCGTCAAGATTA 59.181 50.000 0.00 0.00 0.00 1.75
2493 8636 2.183300 GACATACGGGCAGCGTCA 59.817 61.111 0.00 0.00 0.00 4.35
2520 8663 1.348036 CTTTCGAGAAGGGTTCCACCT 59.652 52.381 0.00 0.00 44.56 4.00
2534 8684 6.461110 AAGACGGGAAGATAATACTTTCGA 57.539 37.500 0.00 0.00 34.12 3.71
2537 8687 7.120923 TGCTAAGACGGGAAGATAATACTTT 57.879 36.000 0.00 0.00 0.00 2.66
2538 8688 6.726490 TGCTAAGACGGGAAGATAATACTT 57.274 37.500 0.00 0.00 0.00 2.24
2539 8689 6.726490 TTGCTAAGACGGGAAGATAATACT 57.274 37.500 0.00 0.00 0.00 2.12
2540 8690 6.985059 AGTTTGCTAAGACGGGAAGATAATAC 59.015 38.462 0.00 0.00 0.00 1.89
2541 8691 7.120923 AGTTTGCTAAGACGGGAAGATAATA 57.879 36.000 0.00 0.00 0.00 0.98
2542 8692 5.990668 AGTTTGCTAAGACGGGAAGATAAT 58.009 37.500 0.00 0.00 0.00 1.28
2543 8693 5.046878 TGAGTTTGCTAAGACGGGAAGATAA 60.047 40.000 0.00 0.00 0.00 1.75
2544 8694 4.464951 TGAGTTTGCTAAGACGGGAAGATA 59.535 41.667 0.00 0.00 0.00 1.98
2546 8696 2.631062 TGAGTTTGCTAAGACGGGAAGA 59.369 45.455 0.00 0.00 0.00 2.87
2547 8697 2.996621 CTGAGTTTGCTAAGACGGGAAG 59.003 50.000 0.00 0.00 0.00 3.46
2549 8699 1.337823 GCTGAGTTTGCTAAGACGGGA 60.338 52.381 0.00 0.00 0.00 5.14
2550 8700 1.079503 GCTGAGTTTGCTAAGACGGG 58.920 55.000 0.00 0.00 0.00 5.28
2551 8701 1.079503 GGCTGAGTTTGCTAAGACGG 58.920 55.000 0.00 0.00 0.00 4.79
2552 8702 1.461127 GTGGCTGAGTTTGCTAAGACG 59.539 52.381 0.00 0.00 33.60 4.18
2553 8703 1.461127 CGTGGCTGAGTTTGCTAAGAC 59.539 52.381 0.00 0.00 31.35 3.01
2555 8705 1.795768 TCGTGGCTGAGTTTGCTAAG 58.204 50.000 0.00 0.00 0.00 2.18
2556 8706 2.248280 TTCGTGGCTGAGTTTGCTAA 57.752 45.000 0.00 0.00 0.00 3.09
2557 8707 2.346803 GATTCGTGGCTGAGTTTGCTA 58.653 47.619 0.00 0.00 0.00 3.49
2559 8709 0.169009 GGATTCGTGGCTGAGTTTGC 59.831 55.000 0.00 0.00 0.00 3.68
2568 8750 3.128349 TCGCTTATTTAGGATTCGTGGC 58.872 45.455 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.