Multiple sequence alignment - TraesCS6B01G130800

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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 TraesCS6B01G130800 chr6B 100.000 4683 0 0 1 4683 127329935 127325253 0.000000e+00 8648
1 TraesCS6B01G130800 chr6D 92.558 2983 140 48 1715 4683 56852188 56849274 0.000000e+00 4204
2 TraesCS6B01G130800 chr6D 88.227 1410 65 34 531 1860 56853432 56852044 0.000000e+00 1591
3 TraesCS6B01G130800 chr6D 77.667 403 58 11 134 507 53580394 53580793 2.840000e-52 217
4 TraesCS6B01G130800 chr6D 98.529 68 0 1 20 86 56853792 56853725 8.230000e-23 119
5 TraesCS6B01G130800 chr6A 91.075 2252 123 29 781 2990 71454318 71452103 0.000000e+00 2974
6 TraesCS6B01G130800 chr6A 94.730 1651 86 1 3032 4682 71452017 71450368 0.000000e+00 2566
7 TraesCS6B01G130800 chr6A 85.824 783 73 24 1 761 71455455 71454689 0.000000e+00 797
8 TraesCS6B01G130800 chr6A 78.649 459 59 19 84 507 612996491 612996945 7.720000e-68 268
9 TraesCS6B01G130800 chr2D 82.367 431 56 13 93 507 155987371 155987797 1.600000e-94 357
10 TraesCS6B01G130800 chr2D 78.158 467 67 18 79 516 646367493 646367953 9.990000e-67 265
11 TraesCS6B01G130800 chr2A 82.135 431 56 14 93 507 542470858 542470433 2.680000e-92 350
12 TraesCS6B01G130800 chr3D 80.995 442 61 15 84 507 277780893 277781329 3.490000e-86 329
13 TraesCS6B01G130800 chr1A 81.350 311 51 7 85 392 570903905 570903599 3.620000e-61 246
14 TraesCS6B01G130800 chr1A 78.710 310 61 5 85 392 265438318 265438624 7.950000e-48 202


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 TraesCS6B01G130800 chr6B 127325253 127329935 4682 True 8648.000000 8648 100.000000 1 4683 1 chr6B.!!$R1 4682
1 TraesCS6B01G130800 chr6D 56849274 56853792 4518 True 1971.333333 4204 93.104667 20 4683 3 chr6D.!!$R1 4663
2 TraesCS6B01G130800 chr6A 71450368 71455455 5087 True 2112.333333 2974 90.543000 1 4682 3 chr6A.!!$R1 4681

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
483 526 0.032130 GATGCTACCGCTTCGATCCA 59.968 55.0 0.00 0.00 36.97 3.41 F
683 736 0.240945 AAAGTCCAAATGAAGCCGCG 59.759 50.0 0.00 0.00 0.00 6.46 F
1821 2316 0.460987 CCGTGTCATTGAGAGGCTCC 60.461 60.0 11.71 3.35 0.00 4.70 F
2598 3098 0.815095 TCGCAGCTACGATCAGGAAA 59.185 50.0 4.55 0.00 37.09 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2213 2710 0.745845 CGTCAGGGAGAAATGCTGGG 60.746 60.000 0.0 0.0 0.00 4.45 R
2502 3002 1.376424 CTCCAGCACCACGCATTCT 60.376 57.895 0.0 0.0 46.13 2.40 R
2796 3296 0.251033 TCTTCTTCGTCTCCGGTGGA 60.251 55.000 0.0 0.0 33.95 4.02 R
3751 4306 0.324368 ATCTCTACCTGGCACCGACA 60.324 55.000 0.0 0.0 0.00 4.35 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
97 99 1.173913 AAATCAAAGGGGCGTGCTAC 58.826 50.000 0.00 0.00 0.00 3.58
156 158 1.448540 CGAGCCGTCAGATTTGCCT 60.449 57.895 0.00 0.00 0.00 4.75
175 177 2.279502 TTATCAAGCGAGCCGAGCGT 62.280 55.000 0.00 0.00 40.04 5.07
176 178 2.936829 TATCAAGCGAGCCGAGCGTG 62.937 60.000 5.50 5.50 43.59 5.34
188 190 1.373497 GAGCGTGTCTCCACCACTG 60.373 63.158 0.00 0.00 38.41 3.66
194 196 0.463654 TGTCTCCACCACTGCAACAC 60.464 55.000 0.00 0.00 0.00 3.32
197 199 2.203139 CCACCACTGCAACACGGA 60.203 61.111 0.00 0.00 0.00 4.69
330 353 2.480224 CAACTGTGTTCTGGTTGCAG 57.520 50.000 0.00 0.00 34.85 4.41
341 364 2.627699 TCTGGTTGCAGAAAATTCCCAC 59.372 45.455 0.00 0.00 0.00 4.61
363 386 5.967088 CACGGTAGAGGTTTTGTTGTAAAAC 59.033 40.000 6.70 6.70 38.90 2.43
374 397 4.757799 TGTTGTAAAACATGACCCATCG 57.242 40.909 0.00 0.00 0.00 3.84
379 402 5.172934 TGTAAAACATGACCCATCGTAGAC 58.827 41.667 0.00 0.00 42.51 2.59
384 407 1.182667 TGACCCATCGTAGACCACTG 58.817 55.000 0.00 0.00 42.51 3.66
394 417 2.725203 TAGACCACTGCAACACCGCC 62.725 60.000 0.00 0.00 0.00 6.13
412 455 3.349006 CCTGTTGCAGAAGCGCGT 61.349 61.111 8.43 0.00 46.23 6.01
470 513 3.161450 GGGAGGTGGCGGATGCTA 61.161 66.667 0.00 0.00 42.25 3.49
483 526 0.032130 GATGCTACCGCTTCGATCCA 59.968 55.000 0.00 0.00 36.97 3.41
520 564 7.967890 AAGCTTTTCCCAAAATCAAACTATG 57.032 32.000 0.00 0.00 0.00 2.23
551 595 8.665685 CAGTTTATATCTTTTAAAGCACGTCCT 58.334 33.333 0.00 0.00 0.00 3.85
577 622 8.830201 AATAAAGCAGCTCTCACATAAGATAG 57.170 34.615 0.00 0.00 0.00 2.08
595 640 6.084749 AGATAGCCTTCCTTCCTTCAAAAT 57.915 37.500 0.00 0.00 0.00 1.82
678 731 3.052036 CACCGCAAAAGTCCAAATGAAG 58.948 45.455 0.00 0.00 0.00 3.02
679 732 2.061028 CCGCAAAAGTCCAAATGAAGC 58.939 47.619 0.00 0.00 0.00 3.86
680 733 2.061028 CGCAAAAGTCCAAATGAAGCC 58.939 47.619 0.00 0.00 0.00 4.35
681 734 2.061028 GCAAAAGTCCAAATGAAGCCG 58.939 47.619 0.00 0.00 0.00 5.52
682 735 2.061028 CAAAAGTCCAAATGAAGCCGC 58.939 47.619 0.00 0.00 0.00 6.53
683 736 0.240945 AAAGTCCAAATGAAGCCGCG 59.759 50.000 0.00 0.00 0.00 6.46
738 799 7.827236 TGATAAGTTTGTTTAATCCCTCGATGT 59.173 33.333 0.00 0.00 0.00 3.06
756 818 3.913548 TGTGCATTGTTTAACAGCGAT 57.086 38.095 0.00 0.00 0.00 4.58
764 826 4.409718 TGTTTAACAGCGATATAGCCCA 57.590 40.909 3.99 0.00 38.01 5.36
950 1369 2.467838 CTCGACATTGATCGCAGTCAT 58.532 47.619 10.54 0.00 41.97 3.06
979 1398 6.484643 CAGATCTTTTGTCTTGGTCTTTCTGA 59.515 38.462 0.00 0.00 0.00 3.27
992 1411 3.187432 GTCTTTCTGAGTAGCTGGTTTGC 59.813 47.826 0.00 0.00 0.00 3.68
1290 1743 4.796231 CCGTTCGTGCTCCCCTCG 62.796 72.222 0.00 0.00 0.00 4.63
1315 1768 4.082523 GGCGGCTGCTCCAGTACA 62.083 66.667 18.85 0.00 42.25 2.90
1323 1776 1.248785 TGCTCCAGTACAGGACGGTC 61.249 60.000 2.26 0.00 33.19 4.79
1330 1783 2.044555 TACAGGACGGTCTCGCTGG 61.045 63.158 14.57 0.72 40.63 4.85
1659 2114 1.813178 GTCACACATCCGTCTCTCTCA 59.187 52.381 0.00 0.00 0.00 3.27
1678 2133 2.169352 TCATCTAGCTTCCTCCTTGCAC 59.831 50.000 0.00 0.00 0.00 4.57
1683 2138 0.612744 GCTTCCTCCTTGCACTCTCT 59.387 55.000 0.00 0.00 0.00 3.10
1691 2146 0.972134 CTTGCACTCTCTCTCCACCA 59.028 55.000 0.00 0.00 0.00 4.17
1752 2247 1.674057 GCTAGGTAGCCGCCATGAT 59.326 57.895 0.00 0.00 43.39 2.45
1784 2279 6.928520 AGCTTCCAAGATTAACATTTTCTGG 58.071 36.000 0.00 0.00 0.00 3.86
1785 2280 6.721208 AGCTTCCAAGATTAACATTTTCTGGA 59.279 34.615 0.00 0.00 0.00 3.86
1787 2282 7.872483 GCTTCCAAGATTAACATTTTCTGGAAA 59.128 33.333 0.00 0.00 31.96 3.13
1821 2316 0.460987 CCGTGTCATTGAGAGGCTCC 60.461 60.000 11.71 3.35 0.00 4.70
1897 2392 1.068541 GGGTTCGTGCACATTTTCTCC 60.069 52.381 18.64 8.41 0.00 3.71
1913 2408 8.160106 ACATTTTCTCCACATCTTAGTCTTTCT 58.840 33.333 0.00 0.00 0.00 2.52
1922 2417 7.605691 CCACATCTTAGTCTTTCTGATGAACTT 59.394 37.037 8.05 0.00 38.21 2.66
1923 2418 8.997323 CACATCTTAGTCTTTCTGATGAACTTT 58.003 33.333 8.05 0.00 38.21 2.66
1957 2454 5.041287 TCAAACTCAATAGAGGCGTAATCG 58.959 41.667 0.00 0.00 46.44 3.34
1971 2468 3.928211 CGTAATCGCATGAACTTTGGAG 58.072 45.455 0.00 0.00 0.00 3.86
2002 2499 9.673454 AAAACTTCTTTTGTTATACAATCCGTC 57.327 29.630 0.00 0.00 38.00 4.79
2003 2500 7.972832 ACTTCTTTTGTTATACAATCCGTCA 57.027 32.000 0.00 0.00 38.00 4.35
2012 2509 7.693020 TGTTATACAATCCGTCAATGTTCATG 58.307 34.615 0.00 0.00 0.00 3.07
2013 2510 7.550906 TGTTATACAATCCGTCAATGTTCATGA 59.449 33.333 0.00 0.00 0.00 3.07
2014 2511 4.952262 ACAATCCGTCAATGTTCATGAG 57.048 40.909 0.00 0.00 0.00 2.90
2015 2512 4.326826 ACAATCCGTCAATGTTCATGAGT 58.673 39.130 0.00 0.00 0.00 3.41
2016 2513 4.761739 ACAATCCGTCAATGTTCATGAGTT 59.238 37.500 0.00 0.00 0.00 3.01
2017 2514 5.106555 ACAATCCGTCAATGTTCATGAGTTC 60.107 40.000 0.00 0.00 0.00 3.01
2018 2515 4.001618 TCCGTCAATGTTCATGAGTTCA 57.998 40.909 0.00 0.00 0.00 3.18
2021 2518 4.633126 CCGTCAATGTTCATGAGTTCATCT 59.367 41.667 0.00 0.00 33.61 2.90
2022 2519 5.812127 CCGTCAATGTTCATGAGTTCATCTA 59.188 40.000 0.00 0.00 33.61 1.98
2023 2520 6.481313 CCGTCAATGTTCATGAGTTCATCTAT 59.519 38.462 0.00 0.00 33.61 1.98
2024 2521 7.307042 CCGTCAATGTTCATGAGTTCATCTATC 60.307 40.741 0.00 0.00 33.61 2.08
2025 2522 7.223387 CGTCAATGTTCATGAGTTCATCTATCA 59.777 37.037 0.00 0.00 33.61 2.15
2026 2523 8.886719 GTCAATGTTCATGAGTTCATCTATCAA 58.113 33.333 0.00 0.00 33.61 2.57
2033 2530 6.925718 TCATGAGTTCATCTATCAATCCGAAC 59.074 38.462 0.00 0.00 33.61 3.95
2036 2533 3.660501 TCATCTATCAATCCGAACCCG 57.339 47.619 0.00 0.00 0.00 5.28
2038 2535 1.410004 TCTATCAATCCGAACCCGCT 58.590 50.000 0.00 0.00 0.00 5.52
2040 2537 2.169769 TCTATCAATCCGAACCCGCTTT 59.830 45.455 0.00 0.00 0.00 3.51
2043 2540 1.538075 TCAATCCGAACCCGCTTTTTC 59.462 47.619 0.00 0.00 0.00 2.29
2046 2543 1.161843 TCCGAACCCGCTTTTTCATC 58.838 50.000 0.00 0.00 0.00 2.92
2050 2547 2.095263 CGAACCCGCTTTTTCATCATGT 60.095 45.455 0.00 0.00 0.00 3.21
2051 2548 3.611530 CGAACCCGCTTTTTCATCATGTT 60.612 43.478 0.00 0.00 0.00 2.71
2052 2549 4.378978 CGAACCCGCTTTTTCATCATGTTA 60.379 41.667 0.00 0.00 0.00 2.41
2053 2550 5.650543 GAACCCGCTTTTTCATCATGTTAT 58.349 37.500 0.00 0.00 0.00 1.89
2054 2551 4.997565 ACCCGCTTTTTCATCATGTTATG 58.002 39.130 0.00 0.00 0.00 1.90
2055 2552 4.704540 ACCCGCTTTTTCATCATGTTATGA 59.295 37.500 0.00 0.00 44.55 2.15
2056 2553 5.184864 ACCCGCTTTTTCATCATGTTATGAA 59.815 36.000 5.87 5.87 43.50 2.57
2057 2554 5.516339 CCCGCTTTTTCATCATGTTATGAAC 59.484 40.000 8.85 0.00 43.69 3.18
2256 2753 2.686106 GGAGCCCCGTTCCACCTA 60.686 66.667 0.00 0.00 33.06 3.08
2462 2959 4.468689 GCCCCTGCGACTACCACC 62.469 72.222 0.00 0.00 0.00 4.61
2502 3002 2.050350 CGACGGCCAGGTAGAGGAA 61.050 63.158 2.24 0.00 0.00 3.36
2598 3098 0.815095 TCGCAGCTACGATCAGGAAA 59.185 50.000 4.55 0.00 37.09 3.13
2695 3195 1.133823 ACACTGCCCATGAACTGAACA 60.134 47.619 0.00 0.00 0.00 3.18
2711 3211 2.569853 TGAACAATCGTGGGGACTATGT 59.430 45.455 0.00 0.00 0.00 2.29
2951 3458 4.385358 AACCAAGATGAACACCACAAAC 57.615 40.909 0.00 0.00 0.00 2.93
2976 3483 5.925506 TTTACTATGAACCGAGGTCATCA 57.074 39.130 7.58 0.00 0.00 3.07
3003 3544 4.335082 TGTCGAAATTTGGCATTCGTAG 57.665 40.909 18.04 0.00 46.28 3.51
3011 3552 7.061673 CGAAATTTGGCATTCGTAGATTGAAAA 59.938 33.333 12.30 0.00 42.47 2.29
3013 3554 5.957842 TTGGCATTCGTAGATTGAAAAGT 57.042 34.783 0.00 0.00 39.96 2.66
3097 3649 2.280389 AGGCAGCACGGCATATCG 60.280 61.111 0.00 0.00 44.47 2.92
3176 3728 1.138859 TCGAATCGGTGGATTGCTCAT 59.861 47.619 1.76 0.00 42.86 2.90
3184 3736 0.252761 TGGATTGCTCATCGAAGCCA 59.747 50.000 6.64 0.00 41.77 4.75
3418 3970 3.241530 TTCAGGGTGCCGTGCTCT 61.242 61.111 6.08 0.00 0.00 4.09
3559 4111 0.615331 TCCAGGAGTGCCTTGATGTC 59.385 55.000 0.00 0.00 43.90 3.06
3562 4114 1.078848 GGAGTGCCTTGATGTCGCT 60.079 57.895 0.00 0.00 0.00 4.93
3586 4138 2.031012 CTGCCAGCGTCCTCAACA 59.969 61.111 0.00 0.00 0.00 3.33
3656 4211 3.556004 GCAGGAGGTAGCTGATAACCATC 60.556 52.174 0.00 1.36 38.30 3.51
3769 4324 1.076014 TGTCGGTGCCAGGTAGAGA 59.924 57.895 0.00 0.00 0.00 3.10
3802 4357 6.545504 TCTGCAGATTCACTTTGTAACTTC 57.454 37.500 13.74 0.00 0.00 3.01
3803 4358 6.054941 TCTGCAGATTCACTTTGTAACTTCA 58.945 36.000 13.74 0.00 0.00 3.02
3881 4436 9.155975 ACTTGAAGAGTATTTTACATGCAGTAG 57.844 33.333 0.00 0.00 36.65 2.57
3971 4526 5.952347 TGGCTTCAGTAGATCAGTTAAGAGA 59.048 40.000 0.00 0.00 0.00 3.10
4045 4600 3.362281 TCATACAACACGAATTTCGCG 57.638 42.857 18.24 11.77 45.12 5.87
4075 4630 3.640029 ACCCATGGTAGTAATCTGGTACG 59.360 47.826 11.73 0.00 32.11 3.67
4095 4650 6.543831 GGTACGGTCCTAATACAGTTCTAAGA 59.456 42.308 0.00 0.00 0.00 2.10
4097 4652 6.421485 ACGGTCCTAATACAGTTCTAAGAGA 58.579 40.000 0.00 0.00 0.00 3.10
4160 4715 0.105964 CAATCCCTCGCCGGTAATCA 59.894 55.000 1.90 0.00 0.00 2.57
4656 5213 6.560003 ATCTGTACCATAACCTTGTCATGA 57.440 37.500 0.00 0.00 0.00 3.07
4682 5239 2.880890 CTGCAGGAAAGCAAACACTAGT 59.119 45.455 5.57 0.00 45.13 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 108 6.100004 GCTGGTCTTTTAAAAAGATAAGCCC 58.900 40.000 6.10 5.35 34.35 5.19
137 139 2.401195 GCAAATCTGACGGCTCGC 59.599 61.111 0.00 0.00 0.00 5.03
138 140 1.021390 AAGGCAAATCTGACGGCTCG 61.021 55.000 0.00 0.00 34.77 5.03
156 158 1.588932 CGCTCGGCTCGCTTGATAA 60.589 57.895 0.00 0.00 0.00 1.75
175 177 0.463654 GTGTTGCAGTGGTGGAGACA 60.464 55.000 0.00 0.00 38.70 3.41
176 178 1.498865 CGTGTTGCAGTGGTGGAGAC 61.499 60.000 0.00 0.00 0.00 3.36
194 196 6.789262 AGAAATAATTCTGCAACAAGATCCG 58.211 36.000 0.00 0.00 44.25 4.18
274 276 8.027440 GCAACAAAACCTCAATTGCAAATATA 57.973 30.769 1.71 0.00 44.01 0.86
276 278 6.297694 GCAACAAAACCTCAATTGCAAATA 57.702 33.333 1.71 0.00 44.01 1.40
278 280 4.612932 GCAACAAAACCTCAATTGCAAA 57.387 36.364 1.71 0.00 44.01 3.68
281 283 4.612932 TTTGCAACAAAACCTCAATTGC 57.387 36.364 0.00 0.00 44.66 3.56
330 353 3.345508 ACCTCTACCGTGGGAATTTTC 57.654 47.619 0.00 0.00 0.00 2.29
341 364 6.121613 TGTTTTACAACAAAACCTCTACCG 57.878 37.500 9.43 0.00 40.10 4.02
363 386 1.757118 AGTGGTCTACGATGGGTCATG 59.243 52.381 0.00 0.00 0.00 3.07
374 397 1.566018 GCGGTGTTGCAGTGGTCTAC 61.566 60.000 0.00 0.00 34.15 2.59
384 407 3.977244 CAACAGGGGCGGTGTTGC 61.977 66.667 15.09 0.00 46.03 4.17
394 417 4.093952 CGCGCTTCTGCAACAGGG 62.094 66.667 5.56 4.85 39.64 4.45
395 418 2.770587 GAACGCGCTTCTGCAACAGG 62.771 60.000 5.73 0.00 39.64 4.00
396 419 1.439365 GAACGCGCTTCTGCAACAG 60.439 57.895 5.73 0.00 39.64 3.16
412 455 1.448893 GGGTTCGCATACTGCCGAA 60.449 57.895 0.00 0.00 41.12 4.30
424 467 0.313043 ACGTGTACAGTGAGGGTTCG 59.687 55.000 0.00 0.00 0.00 3.95
434 477 1.070821 CCTGCATGACACGTGTACAG 58.929 55.000 23.44 23.35 0.00 2.74
476 519 2.431454 CCATCACCCGGTGGATCGA 61.431 63.158 17.76 0.00 37.72 3.59
483 526 0.696501 AAAGCTTACCATCACCCGGT 59.303 50.000 0.00 0.00 40.73 5.28
520 564 8.786028 GTGCTTTAAAAGATATAAACTGTTCGC 58.214 33.333 0.00 0.00 0.00 4.70
551 595 9.920133 CTATCTTATGTGAGAGCTGCTTTATTA 57.080 33.333 2.53 0.00 0.00 0.98
577 622 4.560128 GTTGATTTTGAAGGAAGGAAGGC 58.440 43.478 0.00 0.00 0.00 4.35
659 712 2.061028 GCTTCATTTGGACTTTTGCGG 58.939 47.619 0.00 0.00 0.00 5.69
683 736 4.779733 TCGCCCTCTCTGTCCCCC 62.780 72.222 0.00 0.00 0.00 5.40
692 753 4.160329 TCAGGTTATTATCATCGCCCTCT 58.840 43.478 0.00 0.00 0.00 3.69
693 754 4.537135 TCAGGTTATTATCATCGCCCTC 57.463 45.455 0.00 0.00 0.00 4.30
738 799 5.277779 GGCTATATCGCTGTTAAACAATGCA 60.278 40.000 0.00 0.00 0.00 3.96
756 818 0.325860 ACGGTGGAAGGTGGGCTATA 60.326 55.000 0.00 0.00 0.00 1.31
950 1369 4.103153 AGACCAAGACAAAAGATCTGTGGA 59.897 41.667 0.00 0.00 32.84 4.02
979 1398 1.302511 CCACCGCAAACCAGCTACT 60.303 57.895 0.00 0.00 0.00 2.57
992 1411 2.829914 CCATCACCATGCCCACCG 60.830 66.667 0.00 0.00 0.00 4.94
1032 1464 3.181967 CTGAAGCCGCCGAGAACG 61.182 66.667 0.00 0.00 39.43 3.95
1098 1530 3.673597 TCGTGCCCTCCTCCTCCT 61.674 66.667 0.00 0.00 0.00 3.69
1099 1531 3.462678 GTCGTGCCCTCCTCCTCC 61.463 72.222 0.00 0.00 0.00 4.30
1100 1532 3.827898 CGTCGTGCCCTCCTCCTC 61.828 72.222 0.00 0.00 0.00 3.71
1101 1533 4.361971 TCGTCGTGCCCTCCTCCT 62.362 66.667 0.00 0.00 0.00 3.69
1203 1656 4.994471 CAGACCTGCACCAGCGCA 62.994 66.667 11.47 0.00 46.23 6.09
1619 2072 3.726144 GGAGGGCCTTGCAGAGCT 61.726 66.667 7.89 0.00 0.00 4.09
1659 2114 2.433970 GAGTGCAAGGAGGAAGCTAGAT 59.566 50.000 0.00 0.00 0.00 1.98
1678 2133 5.654650 AGTAGTTTGTATGGTGGAGAGAGAG 59.345 44.000 0.00 0.00 0.00 3.20
1683 2138 5.655532 GGAGTAGTAGTTTGTATGGTGGAGA 59.344 44.000 0.00 0.00 0.00 3.71
1691 2146 7.363617 GGCTGTACAAGGAGTAGTAGTTTGTAT 60.364 40.741 0.00 0.00 36.82 2.29
1752 2247 7.118496 TGTTAATCTTGGAAGCTTTTTGGAA 57.882 32.000 0.00 0.00 0.00 3.53
1784 2279 1.068748 CGGCCTGCATGCATAGATTTC 60.069 52.381 22.97 6.09 0.00 2.17
1785 2280 0.956633 CGGCCTGCATGCATAGATTT 59.043 50.000 22.97 0.00 0.00 2.17
1787 2282 0.887836 CACGGCCTGCATGCATAGAT 60.888 55.000 22.97 3.18 0.00 1.98
1821 2316 3.461773 ACGGGGTGGCAGATCTCG 61.462 66.667 0.00 3.60 0.00 4.04
1885 2380 5.645497 AGACTAAGATGTGGAGAAAATGTGC 59.355 40.000 0.00 0.00 0.00 4.57
1897 2392 8.545229 AAGTTCATCAGAAAGACTAAGATGTG 57.455 34.615 0.00 0.00 37.80 3.21
1913 2408 8.763356 GTTTGATGCAACAAATAAAGTTCATCA 58.237 29.630 22.79 12.61 40.91 3.07
1922 2417 9.844790 CTCTATTGAGTTTGATGCAACAAATAA 57.155 29.630 22.79 17.85 40.91 1.40
1923 2418 8.461222 CCTCTATTGAGTTTGATGCAACAAATA 58.539 33.333 22.79 11.26 40.91 1.40
1929 2424 3.374988 CGCCTCTATTGAGTTTGATGCAA 59.625 43.478 3.47 0.00 38.61 4.08
1978 2475 8.385898 TGACGGATTGTATAACAAAAGAAGTT 57.614 30.769 0.00 0.00 41.96 2.66
1979 2476 7.972832 TGACGGATTGTATAACAAAAGAAGT 57.027 32.000 0.00 0.00 41.96 3.01
1980 2477 9.277565 CATTGACGGATTGTATAACAAAAGAAG 57.722 33.333 0.00 0.00 41.96 2.85
1983 2480 8.964420 AACATTGACGGATTGTATAACAAAAG 57.036 30.769 0.00 0.00 41.96 2.27
2000 2497 8.429493 TGATAGATGAACTCATGAACATTGAC 57.571 34.615 0.00 0.00 36.57 3.18
2002 2499 9.880064 GATTGATAGATGAACTCATGAACATTG 57.120 33.333 0.00 0.00 36.57 2.82
2003 2500 9.064706 GGATTGATAGATGAACTCATGAACATT 57.935 33.333 0.00 0.00 36.57 2.71
2012 2509 4.991687 GGGTTCGGATTGATAGATGAACTC 59.008 45.833 3.33 0.00 36.75 3.01
2013 2510 4.501571 CGGGTTCGGATTGATAGATGAACT 60.502 45.833 3.33 0.00 36.75 3.01
2014 2511 3.741344 CGGGTTCGGATTGATAGATGAAC 59.259 47.826 0.00 0.00 36.02 3.18
2015 2512 3.802329 GCGGGTTCGGATTGATAGATGAA 60.802 47.826 0.00 0.00 36.79 2.57
2016 2513 2.288825 GCGGGTTCGGATTGATAGATGA 60.289 50.000 0.00 0.00 36.79 2.92
2017 2514 2.069273 GCGGGTTCGGATTGATAGATG 58.931 52.381 0.00 0.00 36.79 2.90
2018 2515 1.971357 AGCGGGTTCGGATTGATAGAT 59.029 47.619 0.00 0.00 36.79 1.98
2021 2518 2.702592 AAAGCGGGTTCGGATTGATA 57.297 45.000 0.00 0.00 36.79 2.15
2022 2519 1.834188 AAAAGCGGGTTCGGATTGAT 58.166 45.000 0.00 0.00 36.79 2.57
2023 2520 1.538075 GAAAAAGCGGGTTCGGATTGA 59.462 47.619 0.00 0.00 36.79 2.57
2024 2521 1.268352 TGAAAAAGCGGGTTCGGATTG 59.732 47.619 0.00 0.00 36.79 2.67
2025 2522 1.611519 TGAAAAAGCGGGTTCGGATT 58.388 45.000 0.00 0.00 36.79 3.01
2026 2523 1.743394 GATGAAAAAGCGGGTTCGGAT 59.257 47.619 0.00 0.00 36.79 4.18
2033 2530 5.247507 TCATAACATGATGAAAAAGCGGG 57.752 39.130 0.00 0.00 32.84 6.13
2046 2543 5.220796 CTGCACCAGAGATGTTCATAACATG 60.221 44.000 9.86 0.00 42.04 3.21
2050 2547 4.824479 TCTGCACCAGAGATGTTCATAA 57.176 40.909 0.00 0.00 35.39 1.90
2051 2548 6.676990 ATATCTGCACCAGAGATGTTCATA 57.323 37.500 1.91 0.00 44.08 2.15
2052 2549 3.928005 ATCTGCACCAGAGATGTTCAT 57.072 42.857 1.20 0.00 44.08 2.57
2213 2710 0.745845 CGTCAGGGAGAAATGCTGGG 60.746 60.000 0.00 0.00 0.00 4.45
2247 2744 4.752879 TGCGCGCCTAGGTGGAAC 62.753 66.667 30.77 6.42 38.35 3.62
2502 3002 1.376424 CTCCAGCACCACGCATTCT 60.376 57.895 0.00 0.00 46.13 2.40
2695 3195 3.109151 TGGTAACATAGTCCCCACGATT 58.891 45.455 0.00 0.00 46.17 3.34
2711 3211 4.141937 CCTCCTCGTCTGAATCATTGGTAA 60.142 45.833 0.00 0.00 0.00 2.85
2796 3296 0.251033 TCTTCTTCGTCTCCGGTGGA 60.251 55.000 0.00 0.00 33.95 4.02
2951 3458 6.761242 TGATGACCTCGGTTCATAGTAAATTG 59.239 38.462 0.00 0.00 0.00 2.32
2976 3483 5.107530 CGAATGCCAAATTTCGACATGTTTT 60.108 36.000 0.00 0.00 45.68 2.43
3003 3544 8.296713 TGGCTCATACACTAAAACTTTTCAATC 58.703 33.333 0.00 0.00 0.00 2.67
3011 3552 5.865085 TCAGTTGGCTCATACACTAAAACT 58.135 37.500 0.00 0.00 0.00 2.66
3013 3554 6.770785 AGTTTCAGTTGGCTCATACACTAAAA 59.229 34.615 0.00 0.00 0.00 1.52
3027 3568 5.817816 ACTGTAGAACAAGAGTTTCAGTTGG 59.182 40.000 0.00 0.00 39.22 3.77
3097 3649 0.469917 TCTTCCGGAATGGCCATCTC 59.530 55.000 21.08 17.61 37.80 2.75
3136 3688 2.203126 GCCCTGATCTTGCCGAGG 60.203 66.667 0.00 0.00 0.00 4.63
3184 3736 2.225467 GTGGAAGAAGAAGCAGCAGTT 58.775 47.619 0.00 0.00 0.00 3.16
3472 4024 1.300620 CTTGACGTCGAAGGTGCCA 60.301 57.895 11.62 0.00 0.00 4.92
3476 4028 1.538950 GAGGTACTTGACGTCGAAGGT 59.461 52.381 22.82 14.68 41.55 3.50
3574 4126 0.957395 CAGCCATTGTTGAGGACGCT 60.957 55.000 0.00 0.00 0.00 5.07
3581 4133 1.675310 CTCCGCCAGCCATTGTTGA 60.675 57.895 0.00 0.00 0.00 3.18
3656 4211 1.893786 AGCTACCACAAGAGCTCCG 59.106 57.895 10.93 4.45 46.08 4.63
3751 4306 0.324368 ATCTCTACCTGGCACCGACA 60.324 55.000 0.00 0.00 0.00 4.35
3757 4312 6.151648 CAGAATTTTGAAATCTCTACCTGGCA 59.848 38.462 0.00 0.00 0.00 4.92
3759 4314 6.151648 TGCAGAATTTTGAAATCTCTACCTGG 59.848 38.462 0.00 0.00 0.00 4.45
3769 4324 8.770828 CAAAGTGAATCTGCAGAATTTTGAAAT 58.229 29.630 22.50 0.00 0.00 2.17
3854 4409 7.810658 ACTGCATGTAAAATACTCTTCAAGTG 58.189 34.615 0.00 0.00 39.11 3.16
3971 4526 3.747529 GCATGCTGCCTTTGTAATTTTGT 59.252 39.130 11.37 0.00 37.42 2.83
3985 4540 1.317431 TGATTGGGTCTGCATGCTGC 61.317 55.000 20.33 13.82 45.29 5.25
4075 4630 7.642082 TGTCTCTTAGAACTGTATTAGGACC 57.358 40.000 0.00 0.00 0.00 4.46
4120 4675 6.671614 TTGACACAGAACAATAAACTCGTT 57.328 33.333 0.00 0.00 0.00 3.85
4160 4715 5.249393 AGTGGAAACTGTCATCAGAATACCT 59.751 40.000 2.17 0.00 43.76 3.08
4256 4811 2.006056 GCTGCCACACTCACTCTGATC 61.006 57.143 0.00 0.00 0.00 2.92
4268 4823 2.032376 TTCTGCGATGCTGCCACA 59.968 55.556 0.00 0.00 0.00 4.17
4507 5063 6.313519 TCTTGCACTCCTATATTTGTCCTT 57.686 37.500 0.00 0.00 0.00 3.36
4614 5171 9.615295 GTACAGATAAAGGATATCGAGTCTTTC 57.385 37.037 7.66 0.00 32.53 2.62
4656 5213 1.113788 TTTGCTTTCCTGCAGCTGTT 58.886 45.000 16.64 0.00 44.27 3.16


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

AutoCloner maintained by Alex Coulton.