Multiple sequence alignment - TraesCS1D01G308600

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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 TraesCS1D01G308600 chr1D 100.000 4128 0 0 1 4128 404493479 404489352 0.000000e+00 7624.0
1 TraesCS1D01G308600 chr1B 94.043 3794 149 35 231 3988 544133286 544129534 0.000000e+00 5683.0
2 TraesCS1D01G308600 chr1B 94.059 101 6 0 4028 4128 544113509 544113409 1.990000e-33 154.0
3 TraesCS1D01G308600 chr1B 84.058 138 10 1 72 197 544133504 544133367 5.600000e-24 122.0
4 TraesCS1D01G308600 chr1B 96.491 57 2 0 3 59 544133552 544133496 1.220000e-15 95.3
5 TraesCS1D01G308600 chr1A 94.246 2833 117 18 1284 4093 499981450 499978641 0.000000e+00 4287.0
6 TraesCS1D01G308600 chr1A 84.599 1448 128 45 1 1390 499982809 499981399 0.000000e+00 1351.0


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 TraesCS1D01G308600 chr1D 404489352 404493479 4127 True 7624.000000 7624 100.000000 1 4128 1 chr1D.!!$R1 4127
1 TraesCS1D01G308600 chr1B 544129534 544133552 4018 True 1966.766667 5683 91.530667 3 3988 3 chr1B.!!$R2 3985
2 TraesCS1D01G308600 chr1A 499978641 499982809 4168 True 2819.000000 4287 89.422500 1 4093 2 chr1A.!!$R1 4092

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
120 121 0.320683 CATTGTCTGTCGCCTGTGGA 60.321 55.0 0.0 0.0 0.00 4.02 F
550 635 0.678048 GTTCAGTTAGCAGCCTGGGG 60.678 60.0 0.0 0.0 0.00 4.96 F
1459 1605 0.677731 AGATGGTGTGGGACAATGCG 60.678 55.0 0.0 0.0 44.16 4.73 F
2007 2165 2.688446 TCGCCTGGTCACTAATACTCTG 59.312 50.0 0.0 0.0 0.00 3.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1152 1249 1.879575 TCCCACTCCCTACAGGATTG 58.120 55.000 0.00 0.00 46.33 2.67 R
1987 2145 2.427453 ACAGAGTATTAGTGACCAGGCG 59.573 50.000 0.00 0.00 0.00 5.52 R
3026 3200 1.526917 CTTGATCCCATGGGCCGAC 60.527 63.158 27.41 16.19 34.68 4.79 R
3506 3682 1.505098 TCCCAGATCTATGGCAGAGGA 59.495 52.381 9.58 0.00 39.17 3.71 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
30 31 1.748500 GCTCCTCTCTTGCCTTGCC 60.749 63.158 0.00 0.00 0.00 4.52
33 34 2.045131 CCTCTCTTGCCTTGCCAGC 61.045 63.158 0.00 0.00 0.00 4.85
61 62 6.877322 TGAGCCTAGTTAGTGTGAATTTTACC 59.123 38.462 0.00 0.00 0.00 2.85
66 67 5.861727 AGTTAGTGTGAATTTTACCGACCT 58.138 37.500 0.00 0.00 0.00 3.85
106 107 3.522750 AGCTTCTCCTGAGATTCCATTGT 59.477 43.478 0.00 0.00 37.29 2.71
111 112 4.161189 TCTCCTGAGATTCCATTGTCTGTC 59.839 45.833 0.00 0.00 31.41 3.51
120 121 0.320683 CATTGTCTGTCGCCTGTGGA 60.321 55.000 0.00 0.00 0.00 4.02
135 136 3.054875 CCTGTGGATGGATGTGAGAAGAA 60.055 47.826 0.00 0.00 0.00 2.52
143 144 4.503910 TGGATGTGAGAAGAACGGTATTG 58.496 43.478 0.00 0.00 0.00 1.90
348 412 2.484264 GACCTGTAGCGTGAATTTTGCT 59.516 45.455 5.52 5.52 42.58 3.91
410 476 4.268884 GTCTAGTGACTTCGATTGGCATTC 59.731 45.833 0.00 0.00 39.94 2.67
527 612 3.478857 TTTTGTCGTCCTACCATGTGT 57.521 42.857 0.00 0.00 0.00 3.72
528 613 2.448926 TTGTCGTCCTACCATGTGTG 57.551 50.000 0.00 0.00 0.00 3.82
529 614 1.334160 TGTCGTCCTACCATGTGTGT 58.666 50.000 0.00 0.00 0.00 3.72
530 615 1.689813 TGTCGTCCTACCATGTGTGTT 59.310 47.619 0.00 0.00 0.00 3.32
550 635 0.678048 GTTCAGTTAGCAGCCTGGGG 60.678 60.000 0.00 0.00 0.00 4.96
569 655 5.147032 TGGGGTGAATTTGTCTTCTTCATT 58.853 37.500 0.00 0.00 32.05 2.57
585 671 7.506938 TCTTCTTCATTTGATTTGGAGAGGTTT 59.493 33.333 0.00 0.00 30.47 3.27
723 820 8.291740 TCTGTTGTGTCAATATTGTCTTTCATG 58.708 33.333 14.97 0.00 0.00 3.07
728 825 8.628280 TGTGTCAATATTGTCTTTCATGTTCAA 58.372 29.630 14.97 0.00 0.00 2.69
809 906 5.061920 ACTTACCAACTTCTCGACATCTC 57.938 43.478 0.00 0.00 0.00 2.75
847 944 3.861840 TCGGGATTTCATGAACTGTCTC 58.138 45.455 7.89 6.10 0.00 3.36
900 997 3.334691 TGCTCAGTGTGCTGTATTTACC 58.665 45.455 17.38 0.00 43.05 2.85
1200 1297 4.582656 CGTCTAAGATGGACCTCTGATCTT 59.417 45.833 9.17 9.17 39.31 2.40
1383 1529 9.928236 AATTTCGTTTATTTTGTTGGTTCATTG 57.072 25.926 0.00 0.00 0.00 2.82
1459 1605 0.677731 AGATGGTGTGGGACAATGCG 60.678 55.000 0.00 0.00 44.16 4.73
1614 1772 3.497640 GCTGCATATCTCAGGTCATGAAC 59.502 47.826 1.26 1.26 37.52 3.18
1615 1773 4.743045 GCTGCATATCTCAGGTCATGAACT 60.743 45.833 7.68 7.68 37.52 3.01
1617 1775 4.162888 TGCATATCTCAGGTCATGAACTGT 59.837 41.667 34.03 21.07 45.99 3.55
1618 1776 5.121811 GCATATCTCAGGTCATGAACTGTT 58.878 41.667 34.03 23.47 45.99 3.16
1619 1777 6.127083 TGCATATCTCAGGTCATGAACTGTTA 60.127 38.462 34.03 24.80 45.99 2.41
1832 1990 7.564793 TGAAGTACACAAGGTATAATGCATCT 58.435 34.615 0.00 0.00 33.76 2.90
1834 1992 6.291377 AGTACACAAGGTATAATGCATCTGG 58.709 40.000 0.00 0.00 33.76 3.86
2007 2165 2.688446 TCGCCTGGTCACTAATACTCTG 59.312 50.000 0.00 0.00 0.00 3.35
2593 2761 9.635404 CCCATTCTACTAAACCATTATTTACCA 57.365 33.333 0.00 0.00 0.00 3.25
2635 2803 6.040504 GGTTCCTTGTAAATGACTTTGTCCTT 59.959 38.462 0.00 0.00 0.00 3.36
2642 2810 3.837213 ATGACTTTGTCCTTGATTGCG 57.163 42.857 0.00 0.00 0.00 4.85
2652 2820 7.624360 TTGTCCTTGATTGCGTCTTATTAAT 57.376 32.000 0.00 0.00 0.00 1.40
2653 2821 7.015226 TGTCCTTGATTGCGTCTTATTAATG 57.985 36.000 0.00 0.00 0.00 1.90
3026 3200 2.762327 CCAGGGTTTGAATCCCATCTTG 59.238 50.000 13.51 3.19 46.82 3.02
3055 3229 2.619931 TGGGATCAAGAACTCTGTCCA 58.380 47.619 0.00 0.00 0.00 4.02
3076 3250 2.550830 AGACCAACATATGCGATCCC 57.449 50.000 1.58 0.00 0.00 3.85
3176 3351 6.779860 ACACTTGTGAGTTATTAACCTCCAT 58.220 36.000 7.83 0.00 32.54 3.41
3299 3474 2.054687 TGTCGTTGTCGTATTTCGCT 57.945 45.000 0.00 0.00 39.67 4.93
3494 3670 7.108194 TCAGTTCAGTCATTGAATCTGCTTAT 58.892 34.615 7.28 0.00 46.85 1.73
3602 3778 4.378046 GCATTTACGAGGTTGGTTGTACTG 60.378 45.833 0.00 0.00 0.00 2.74
3729 3924 0.179059 TCACAAGTTCGGCAGAGCAA 60.179 50.000 3.27 0.00 0.00 3.91
3765 3960 3.866651 AGTGGTGCTCAGAATCACATAC 58.133 45.455 0.00 4.04 35.04 2.39
3766 3961 2.939103 GTGGTGCTCAGAATCACATACC 59.061 50.000 0.00 0.00 35.04 2.73
3767 3962 2.571202 TGGTGCTCAGAATCACATACCA 59.429 45.455 0.00 0.00 35.04 3.25
3768 3963 2.939103 GGTGCTCAGAATCACATACCAC 59.061 50.000 5.21 0.00 35.04 4.16
3769 3964 3.369892 GGTGCTCAGAATCACATACCACT 60.370 47.826 5.21 0.00 35.04 4.00
3770 3965 4.256920 GTGCTCAGAATCACATACCACTT 58.743 43.478 0.00 0.00 33.63 3.16
3771 3966 4.697352 GTGCTCAGAATCACATACCACTTT 59.303 41.667 0.00 0.00 33.63 2.66
3772 3967 4.696877 TGCTCAGAATCACATACCACTTTG 59.303 41.667 0.00 0.00 0.00 2.77
3773 3968 4.095483 GCTCAGAATCACATACCACTTTGG 59.905 45.833 0.00 0.00 45.02 3.28
3787 3982 3.132824 CCACTTTGGTTGAGAAAGCCTTT 59.867 43.478 0.00 0.00 34.33 3.11
3930 4130 0.247185 ATTTTGCCGTTCATGCCAGG 59.753 50.000 0.00 0.00 0.00 4.45
3946 4146 3.772572 TGCCAGGTAATAACTCACAGCTA 59.227 43.478 0.00 0.00 0.00 3.32
4062 4262 4.535781 TGTTTGGATTGAGGGATATGGTG 58.464 43.478 0.00 0.00 0.00 4.17
4085 4285 1.000060 TGCAGCTCAAAGCCATGTTTC 60.000 47.619 0.00 0.00 43.77 2.78
4086 4286 1.271656 GCAGCTCAAAGCCATGTTTCT 59.728 47.619 0.00 0.00 43.77 2.52
4089 4289 3.739300 CAGCTCAAAGCCATGTTTCTTTG 59.261 43.478 18.53 18.53 43.77 2.77
4097 4297 5.587388 AGCCATGTTTCTTTGATATGTGG 57.413 39.130 0.00 0.00 0.00 4.17
4098 4298 4.403432 AGCCATGTTTCTTTGATATGTGGG 59.597 41.667 0.00 0.00 0.00 4.61
4099 4299 4.402155 GCCATGTTTCTTTGATATGTGGGA 59.598 41.667 0.00 0.00 0.00 4.37
4100 4300 5.679638 GCCATGTTTCTTTGATATGTGGGAC 60.680 44.000 0.00 0.00 0.00 4.46
4101 4301 5.418524 CCATGTTTCTTTGATATGTGGGACA 59.581 40.000 0.00 0.00 0.00 4.02
4102 4302 6.405065 CCATGTTTCTTTGATATGTGGGACAG 60.405 42.308 0.00 0.00 41.80 3.51
4103 4303 5.009631 TGTTTCTTTGATATGTGGGACAGG 58.990 41.667 0.00 0.00 41.80 4.00
4104 4304 3.931907 TCTTTGATATGTGGGACAGGG 57.068 47.619 0.00 0.00 41.80 4.45
4105 4305 3.459828 TCTTTGATATGTGGGACAGGGA 58.540 45.455 0.00 0.00 41.80 4.20
4106 4306 3.849574 TCTTTGATATGTGGGACAGGGAA 59.150 43.478 0.00 0.00 41.80 3.97
4107 4307 4.478317 TCTTTGATATGTGGGACAGGGAAT 59.522 41.667 0.00 0.00 41.80 3.01
4108 4308 3.862877 TGATATGTGGGACAGGGAATG 57.137 47.619 0.00 0.00 41.80 2.67
4109 4309 3.392730 TGATATGTGGGACAGGGAATGA 58.607 45.455 0.00 0.00 41.80 2.57
4110 4310 3.392285 TGATATGTGGGACAGGGAATGAG 59.608 47.826 0.00 0.00 41.80 2.90
4111 4311 0.921896 ATGTGGGACAGGGAATGAGG 59.078 55.000 0.00 0.00 41.80 3.86
4112 4312 0.475632 TGTGGGACAGGGAATGAGGT 60.476 55.000 0.00 0.00 41.80 3.85
4113 4313 0.035056 GTGGGACAGGGAATGAGGTG 60.035 60.000 0.00 0.00 41.80 4.00
4114 4314 0.178876 TGGGACAGGGAATGAGGTGA 60.179 55.000 0.00 0.00 0.00 4.02
4115 4315 0.253327 GGGACAGGGAATGAGGTGAC 59.747 60.000 0.00 0.00 0.00 3.67
4117 4317 1.630878 GGACAGGGAATGAGGTGACTT 59.369 52.381 0.00 0.00 44.43 3.01
4118 4318 2.040412 GGACAGGGAATGAGGTGACTTT 59.960 50.000 0.00 0.00 44.43 2.66
4119 4319 3.263425 GGACAGGGAATGAGGTGACTTTA 59.737 47.826 0.00 0.00 44.43 1.85
4120 4320 4.508662 GACAGGGAATGAGGTGACTTTAG 58.491 47.826 0.00 0.00 44.43 1.85
4121 4321 3.910627 ACAGGGAATGAGGTGACTTTAGT 59.089 43.478 0.00 0.00 44.43 2.24
4122 4322 5.091552 ACAGGGAATGAGGTGACTTTAGTA 58.908 41.667 0.00 0.00 44.43 1.82
4123 4323 5.546499 ACAGGGAATGAGGTGACTTTAGTAA 59.454 40.000 0.00 0.00 44.43 2.24
4124 4324 5.875359 CAGGGAATGAGGTGACTTTAGTAAC 59.125 44.000 0.00 0.00 44.43 2.50
4125 4325 4.868734 GGGAATGAGGTGACTTTAGTAACG 59.131 45.833 0.00 0.00 44.43 3.18
4126 4326 4.868734 GGAATGAGGTGACTTTAGTAACGG 59.131 45.833 0.00 0.00 44.43 4.44
4127 4327 3.308438 TGAGGTGACTTTAGTAACGGC 57.692 47.619 0.00 0.00 44.43 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 0.818296 ACTAACTAGGCTCACCGCTG 59.182 55.000 0.00 0.00 42.76 5.18
33 34 1.816835 TCACACTAACTAGGCTCACCG 59.183 52.381 0.00 0.00 42.76 4.94
61 62 1.204941 AGAAAATCCACTCCGAGGTCG 59.795 52.381 0.00 0.00 39.44 4.79
66 67 1.066143 GCTCCAGAAAATCCACTCCGA 60.066 52.381 0.00 0.00 0.00 4.55
92 93 2.606725 GCGACAGACAATGGAATCTCAG 59.393 50.000 0.00 0.00 0.00 3.35
106 107 0.977627 ATCCATCCACAGGCGACAGA 60.978 55.000 0.00 0.00 0.00 3.41
111 112 0.812811 CTCACATCCATCCACAGGCG 60.813 60.000 0.00 0.00 0.00 5.52
120 121 5.104941 TCAATACCGTTCTTCTCACATCCAT 60.105 40.000 0.00 0.00 0.00 3.41
135 136 1.971357 CTCCCTGCCTATCAATACCGT 59.029 52.381 0.00 0.00 0.00 4.83
143 144 1.333177 ACGTGATCTCCCTGCCTATC 58.667 55.000 0.00 0.00 0.00 2.08
348 412 5.323581 TCCACAACAAATGAATCTGGATGA 58.676 37.500 0.00 0.00 0.00 2.92
514 599 3.472652 TGAACAACACACATGGTAGGAC 58.527 45.455 0.00 0.00 0.00 3.85
527 612 2.221169 CAGGCTGCTAACTGAACAACA 58.779 47.619 0.00 0.00 36.86 3.33
528 613 1.537202 CCAGGCTGCTAACTGAACAAC 59.463 52.381 9.56 0.00 36.86 3.32
529 614 1.545428 CCCAGGCTGCTAACTGAACAA 60.545 52.381 9.56 0.00 36.86 2.83
530 615 0.036732 CCCAGGCTGCTAACTGAACA 59.963 55.000 9.56 0.00 36.86 3.18
569 655 9.312904 AGATGAATTTAAACCTCTCCAAATCAA 57.687 29.630 0.00 0.00 0.00 2.57
681 778 4.404073 ACAACAGAGCACCATAACCAAAAA 59.596 37.500 0.00 0.00 0.00 1.94
682 779 3.957497 ACAACAGAGCACCATAACCAAAA 59.043 39.130 0.00 0.00 0.00 2.44
723 820 2.029918 AGCAAAGAGGGCGAAATTGAAC 60.030 45.455 0.00 0.00 36.08 3.18
728 825 3.751479 AAAAAGCAAAGAGGGCGAAAT 57.249 38.095 0.00 0.00 36.08 2.17
760 857 8.857694 TCCTGGTTTATACTTAAAAGGACTTG 57.142 34.615 0.00 0.00 32.81 3.16
809 906 7.621428 AATCCCGATCAGCATATTTATCTTG 57.379 36.000 0.00 0.00 0.00 3.02
900 997 5.046910 ACATATCAAGTTGACGGCAAAAG 57.953 39.130 4.55 0.00 35.42 2.27
992 1089 4.898320 ACTTGTCATACACATGAGCAAGA 58.102 39.130 22.38 0.00 43.66 3.02
1107 1204 4.511826 CCACCGAAAGCTCCAATATTACTC 59.488 45.833 0.00 0.00 0.00 2.59
1152 1249 1.879575 TCCCACTCCCTACAGGATTG 58.120 55.000 0.00 0.00 46.33 2.67
1200 1297 3.669536 TGCATCCACAAAACGACTATGA 58.330 40.909 0.00 0.00 0.00 2.15
1315 1461 5.486526 ACAAGCAGAATGAACCAACAAAAA 58.513 33.333 0.00 0.00 39.69 1.94
1383 1529 2.887152 AGGTTCATGAGAAACCAAGCAC 59.113 45.455 15.76 0.00 42.60 4.40
1459 1605 4.631813 CACCAAAGTGCAGGTTCTAGATAC 59.368 45.833 0.00 0.00 37.14 2.24
1614 1772 6.458342 GGGAAGAGAAACTTGTGTGTTAACAG 60.458 42.308 8.98 0.00 39.13 3.16
1615 1773 5.355910 GGGAAGAGAAACTTGTGTGTTAACA 59.644 40.000 3.59 3.59 39.13 2.41
1616 1774 5.220989 GGGGAAGAGAAACTTGTGTGTTAAC 60.221 44.000 0.00 0.00 39.13 2.01
1617 1775 4.885325 GGGGAAGAGAAACTTGTGTGTTAA 59.115 41.667 0.00 0.00 39.13 2.01
1618 1776 4.080243 TGGGGAAGAGAAACTTGTGTGTTA 60.080 41.667 0.00 0.00 39.13 2.41
1619 1777 3.288092 GGGGAAGAGAAACTTGTGTGTT 58.712 45.455 0.00 0.00 39.13 3.32
1832 1990 8.298729 TGATACCAATACATTAACAAATGCCA 57.701 30.769 0.00 0.00 33.57 4.92
1834 1992 9.964303 TGATGATACCAATACATTAACAAATGC 57.036 29.630 0.00 0.00 33.57 3.56
1861 2019 2.486472 AGGTGTTGCTCCTGAAGATG 57.514 50.000 0.00 0.00 33.62 2.90
1987 2145 2.427453 ACAGAGTATTAGTGACCAGGCG 59.573 50.000 0.00 0.00 0.00 5.52
2007 2165 5.734855 TCTACACAAGCAACAAGAGAAAC 57.265 39.130 0.00 0.00 0.00 2.78
2076 2234 3.069158 GCAATGAAGCATAGAAGGGCATT 59.931 43.478 0.00 0.00 0.00 3.56
2538 2698 7.978982 AGAAATCAGATTGTTGGAGTAAATCG 58.021 34.615 0.00 0.00 35.83 3.34
2593 2761 4.355889 AGGAACCCACCCAAGTATAACTTT 59.644 41.667 0.00 0.00 36.03 2.66
2635 2803 7.624360 AAGAACCATTAATAAGACGCAATCA 57.376 32.000 0.00 0.00 0.00 2.57
2652 2820 5.669477 AGTGCAAGCAAAATAAAAGAACCA 58.331 33.333 0.00 0.00 0.00 3.67
2653 2821 7.889589 ATAGTGCAAGCAAAATAAAAGAACC 57.110 32.000 0.00 0.00 0.00 3.62
2714 2887 2.823747 ACGAAAATTTAGGTTGGCTCCC 59.176 45.455 0.00 0.00 0.00 4.30
3026 3200 1.526917 CTTGATCCCATGGGCCGAC 60.527 63.158 27.41 16.19 34.68 4.79
3055 3229 3.214328 GGGATCGCATATGTTGGTCTTT 58.786 45.455 4.64 0.00 0.00 2.52
3150 3325 6.708949 TGGAGGTTAATAACTCACAAGTGTTC 59.291 38.462 2.96 0.00 35.36 3.18
3158 3333 6.867662 CATCCATGGAGGTTAATAACTCAC 57.132 41.667 21.33 0.00 39.02 3.51
3176 3351 2.281002 CATGCGATCGGCCATCCA 60.281 61.111 18.30 5.22 42.61 3.41
3377 3552 4.858935 TGTTTCTTGCTACATGTTTCAGC 58.141 39.130 2.30 8.03 35.82 4.26
3494 3670 7.241628 TCTATGGCAGAGGAGTCAATATAAGA 58.758 38.462 9.58 0.00 0.00 2.10
3506 3682 1.505098 TCCCAGATCTATGGCAGAGGA 59.495 52.381 9.58 0.00 39.17 3.71
3563 3739 4.833478 AAATGCAGAGTCATCCAGTAGT 57.167 40.909 0.00 0.00 0.00 2.73
3602 3778 3.826729 GACTATCCCCCAATATGGCAAAC 59.173 47.826 0.00 0.00 35.79 2.93
3729 3924 2.821969 CACCACTAGCATTGAAAGCCTT 59.178 45.455 0.00 0.00 0.00 4.35
3765 3960 2.310538 AGGCTTTCTCAACCAAAGTGG 58.689 47.619 0.00 0.00 45.02 4.00
3766 3961 4.114794 CAAAGGCTTTCTCAACCAAAGTG 58.885 43.478 10.08 0.00 33.96 3.16
3767 3962 3.132824 CCAAAGGCTTTCTCAACCAAAGT 59.867 43.478 10.08 0.00 33.96 2.66
3768 3963 3.132824 ACCAAAGGCTTTCTCAACCAAAG 59.867 43.478 10.08 0.00 34.47 2.77
3769 3964 3.103742 ACCAAAGGCTTTCTCAACCAAA 58.896 40.909 10.08 0.00 0.00 3.28
3770 3965 2.745968 ACCAAAGGCTTTCTCAACCAA 58.254 42.857 10.08 0.00 0.00 3.67
3771 3966 2.430332 CAACCAAAGGCTTTCTCAACCA 59.570 45.455 10.08 0.00 0.00 3.67
3772 3967 2.693074 TCAACCAAAGGCTTTCTCAACC 59.307 45.455 10.08 0.00 0.00 3.77
3773 3968 3.632145 TCTCAACCAAAGGCTTTCTCAAC 59.368 43.478 10.08 0.00 0.00 3.18
3774 3969 3.897239 TCTCAACCAAAGGCTTTCTCAA 58.103 40.909 10.08 0.00 0.00 3.02
3775 3970 3.576078 TCTCAACCAAAGGCTTTCTCA 57.424 42.857 10.08 0.00 0.00 3.27
3776 3971 4.918810 TTTCTCAACCAAAGGCTTTCTC 57.081 40.909 10.08 0.00 0.00 2.87
3777 3972 5.675684 TTTTTCTCAACCAAAGGCTTTCT 57.324 34.783 10.08 0.00 0.00 2.52
3800 3995 7.565398 TCTGATCTTTTACTAGCTATGGTCCTT 59.435 37.037 0.00 0.00 0.00 3.36
3841 4039 4.344679 TCGAGTAAACAAAAGGAGTACCCA 59.655 41.667 3.60 0.00 37.41 4.51
3930 4130 5.968387 AACGCATAGCTGTGAGTTATTAC 57.032 39.130 26.45 1.10 39.75 1.89
3946 4146 3.126001 TCTGTTCTTCCAGAAACGCAT 57.874 42.857 0.00 0.00 38.49 4.73
3965 4165 6.617105 GCAAATGCTTTGATGCTAACAGTTTC 60.617 38.462 11.34 0.00 43.26 2.78
3994 4194 8.734386 CAAAATAGTTGCCTAGAAGAGAATGTT 58.266 33.333 0.00 0.00 0.00 2.71
4027 4227 7.391275 CCTCAATCCAAACATTGCCTTAAAAAT 59.609 33.333 0.00 0.00 34.26 1.82
4029 4229 6.229733 CCTCAATCCAAACATTGCCTTAAAA 58.770 36.000 0.00 0.00 34.26 1.52
4031 4231 4.222588 CCCTCAATCCAAACATTGCCTTAA 59.777 41.667 0.00 0.00 34.26 1.85
4032 4232 3.768757 CCCTCAATCCAAACATTGCCTTA 59.231 43.478 0.00 0.00 34.26 2.69
4062 4262 1.203994 ACATGGCTTTGAGCTGCAATC 59.796 47.619 1.02 0.00 41.99 2.67
4085 4285 3.931907 TCCCTGTCCCACATATCAAAG 57.068 47.619 0.00 0.00 0.00 2.77
4086 4286 4.229353 TCATTCCCTGTCCCACATATCAAA 59.771 41.667 0.00 0.00 0.00 2.69
4089 4289 3.244700 CCTCATTCCCTGTCCCACATATC 60.245 52.174 0.00 0.00 0.00 1.63
4090 4290 2.713167 CCTCATTCCCTGTCCCACATAT 59.287 50.000 0.00 0.00 0.00 1.78
4091 4291 2.126882 CCTCATTCCCTGTCCCACATA 58.873 52.381 0.00 0.00 0.00 2.29
4092 4292 0.921896 CCTCATTCCCTGTCCCACAT 59.078 55.000 0.00 0.00 0.00 3.21
4093 4293 0.475632 ACCTCATTCCCTGTCCCACA 60.476 55.000 0.00 0.00 0.00 4.17
4094 4294 0.035056 CACCTCATTCCCTGTCCCAC 60.035 60.000 0.00 0.00 0.00 4.61
4095 4295 0.178876 TCACCTCATTCCCTGTCCCA 60.179 55.000 0.00 0.00 0.00 4.37
4096 4296 0.253327 GTCACCTCATTCCCTGTCCC 59.747 60.000 0.00 0.00 0.00 4.46
4097 4297 1.280457 AGTCACCTCATTCCCTGTCC 58.720 55.000 0.00 0.00 0.00 4.02
4098 4298 3.425162 AAAGTCACCTCATTCCCTGTC 57.575 47.619 0.00 0.00 0.00 3.51
4099 4299 3.910627 ACTAAAGTCACCTCATTCCCTGT 59.089 43.478 0.00 0.00 0.00 4.00
4100 4300 4.559862 ACTAAAGTCACCTCATTCCCTG 57.440 45.455 0.00 0.00 0.00 4.45
4101 4301 5.337330 CGTTACTAAAGTCACCTCATTCCCT 60.337 44.000 0.00 0.00 0.00 4.20
4102 4302 4.868734 CGTTACTAAAGTCACCTCATTCCC 59.131 45.833 0.00 0.00 0.00 3.97
4103 4303 4.868734 CCGTTACTAAAGTCACCTCATTCC 59.131 45.833 0.00 0.00 0.00 3.01
4104 4304 4.329256 GCCGTTACTAAAGTCACCTCATTC 59.671 45.833 0.00 0.00 0.00 2.67
4105 4305 4.251268 GCCGTTACTAAAGTCACCTCATT 58.749 43.478 0.00 0.00 0.00 2.57
4106 4306 3.858247 GCCGTTACTAAAGTCACCTCAT 58.142 45.455 0.00 0.00 0.00 2.90
4107 4307 3.308438 GCCGTTACTAAAGTCACCTCA 57.692 47.619 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.