Multiple sequence alignment - TraesCS4A01G040500

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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 TraesCS4A01G040500 chr4A 100.000 4434 0 0 1 4434 34021192 34025625 0.000000e+00 8189.0
1 TraesCS4A01G040500 chr4D 93.355 3010 120 31 9 2976 432742671 432745642 0.000000e+00 4377.0
2 TraesCS4A01G040500 chr4D 89.346 1314 59 40 3169 4433 432745920 432747201 0.000000e+00 1576.0
3 TraesCS4A01G040500 chr4D 83.111 225 22 10 2975 3189 432745679 432745897 1.630000e-44 191.0
4 TraesCS4A01G040500 chr4B 90.224 1115 83 18 943 2039 530525445 530524339 0.000000e+00 1432.0
5 TraesCS4A01G040500 chr4B 88.584 946 70 14 2063 2982 530524342 530523409 0.000000e+00 1114.0
6 TraesCS4A01G040500 chr4B 87.529 874 65 28 2980 3824 530523349 530522491 0.000000e+00 970.0
7 TraesCS4A01G040500 chr4B 78.941 869 117 19 16 857 530526305 530525476 8.440000e-147 531.0
8 TraesCS4A01G040500 chr4B 88.739 222 17 6 1483 1703 14582963 14583177 9.460000e-67 265.0
9 TraesCS4A01G040500 chr4B 84.186 215 11 10 4234 4433 530522127 530521921 2.110000e-43 187.0
10 TraesCS4A01G040500 chr1D 88.636 88 2 3 3654 3734 17648568 17648482 2.820000e-17 100.0
11 TraesCS4A01G040500 chr1D 77.368 190 9 14 3494 3674 17648732 17648568 1.020000e-11 82.4


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 TraesCS4A01G040500 chr4A 34021192 34025625 4433 False 8189.0 8189 100.0000 1 4434 1 chr4A.!!$F1 4433
1 TraesCS4A01G040500 chr4D 432742671 432747201 4530 False 2048.0 4377 88.6040 9 4433 3 chr4D.!!$F1 4424
2 TraesCS4A01G040500 chr4B 530521921 530526305 4384 True 846.8 1432 85.8928 16 4433 5 chr4B.!!$R1 4417

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
51 52 0.318445 AGCGAGTGTCACCGTTGTAC 60.318 55.000 13.14 0.0 0.0 2.90 F
1113 1151 0.911769 TTCAGGCATCCGGTCAATCT 59.088 50.000 0.00 0.0 0.0 2.40 F
1645 1686 2.079158 CACGATGCTTCAGGTGTTCAT 58.921 47.619 0.08 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 2059 0.608640 AGCGGACACTGGACTAAAGG 59.391 55.0 0.00 0.00 0.00 3.11 R
3042 3193 0.250295 ACACCGACCATGGACAGTTG 60.250 55.0 21.47 11.56 0.00 3.16 R
3512 3726 0.679640 AGGCTGACACCGAGAGAGAG 60.680 60.0 0.00 0.00 33.69 3.20 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
49 50 1.299926 GAGCGAGTGTCACCGTTGT 60.300 57.895 13.14 2.20 0.00 3.32
51 52 0.318445 AGCGAGTGTCACCGTTGTAC 60.318 55.000 13.14 0.00 0.00 2.90
52 53 1.280206 GCGAGTGTCACCGTTGTACC 61.280 60.000 13.14 0.00 0.00 3.34
106 108 4.035792 CCAAACTACCAATCGTTGTGTTCA 59.964 41.667 0.00 0.00 30.39 3.18
256 258 2.546899 AGTTGGTACCTACATGGCTGA 58.453 47.619 25.29 0.00 40.22 4.26
313 315 1.539388 TGCCCTGAAGTAATTGTTGCG 59.461 47.619 0.00 0.00 0.00 4.85
398 400 9.853555 CTAATATAGAGTTGCTATTCTCACCAG 57.146 37.037 0.00 0.00 40.30 4.00
419 421 6.719370 ACCAGCAAAATGTGGAAGAACTAATA 59.281 34.615 0.00 0.00 37.27 0.98
461 463 2.939103 GCCAGCTAGGTTGAGTACATTG 59.061 50.000 0.00 0.00 40.61 2.82
466 468 2.200373 AGGTTGAGTACATTGGGTGC 57.800 50.000 0.00 0.00 0.00 5.01
498 518 9.162764 TGTTTGCTCTTTCATATAGTCTTTACC 57.837 33.333 0.00 0.00 0.00 2.85
499 519 8.613482 GTTTGCTCTTTCATATAGTCTTTACCC 58.387 37.037 0.00 0.00 0.00 3.69
612 632 4.081087 TGTGGGAGCATACTAAGAAACTCC 60.081 45.833 0.00 0.00 42.42 3.85
618 638 6.239458 GGAGCATACTAAGAAACTCCTAGCAT 60.239 42.308 0.00 0.00 40.45 3.79
625 645 8.870075 ACTAAGAAACTCCTAGCATTTTCAAT 57.130 30.769 0.00 0.00 31.57 2.57
746 767 4.799564 TTCATATTTCACAAAGGTGGGC 57.200 40.909 0.00 0.00 45.32 5.36
899 937 9.485206 TGTAGAATGAGAAGTTGTTAAACTACC 57.515 33.333 0.00 0.00 46.15 3.18
928 966 6.697455 GGAAAACCATTTCAGAGAAAGTTGAC 59.303 38.462 3.97 0.00 45.53 3.18
1113 1151 0.911769 TTCAGGCATCCGGTCAATCT 59.088 50.000 0.00 0.00 0.00 2.40
1206 1244 3.565902 GCCTTGGTATATTTCACTCTGGC 59.434 47.826 0.00 0.00 0.00 4.85
1276 1314 7.903431 CGTACTATTTATGCACCAGTTCTTTTC 59.097 37.037 0.00 0.00 0.00 2.29
1277 1315 7.759489 ACTATTTATGCACCAGTTCTTTTCA 57.241 32.000 0.00 0.00 0.00 2.69
1391 1429 6.983906 TCAGATCATTCCAACTAGCTCATA 57.016 37.500 0.00 0.00 0.00 2.15
1394 1432 6.145209 CAGATCATTCCAACTAGCTCATAACG 59.855 42.308 0.00 0.00 0.00 3.18
1563 1604 5.679734 ATAGCGCTTATTTTGACCATCAG 57.320 39.130 18.68 0.00 0.00 2.90
1565 1606 8.119629 TAATAGCGCTTATTTTGACCATCAGGT 61.120 37.037 18.68 0.00 40.75 4.00
1588 1629 5.752892 TTTTGTGGTTGTAATGCGACTAA 57.247 34.783 0.00 0.00 0.00 2.24
1589 1630 5.950758 TTTGTGGTTGTAATGCGACTAAT 57.049 34.783 0.00 0.00 0.00 1.73
1591 1632 4.570930 TGTGGTTGTAATGCGACTAATGA 58.429 39.130 0.00 0.00 0.00 2.57
1592 1633 5.182487 TGTGGTTGTAATGCGACTAATGAT 58.818 37.500 0.00 0.00 0.00 2.45
1597 1638 7.931407 TGGTTGTAATGCGACTAATGATATCTT 59.069 33.333 3.98 0.00 0.00 2.40
1628 1669 6.357980 CAGTATCATAGCAATTTAGCACACG 58.642 40.000 0.00 0.00 36.85 4.49
1645 1686 2.079158 CACGATGCTTCAGGTGTTCAT 58.921 47.619 0.08 0.00 0.00 2.57
1703 1752 6.494835 TCCATCATGTACTCATATGTGCTACT 59.505 38.462 1.90 0.00 32.47 2.57
1704 1753 6.589139 CCATCATGTACTCATATGTGCTACTG 59.411 42.308 1.90 6.62 32.47 2.74
1732 1781 7.171508 TGCTGTTATTAGCTCATATTGCTACAC 59.828 37.037 6.68 5.67 44.01 2.90
1986 2039 5.830457 TGTAGACCCATCTCTTAGACATGAG 59.170 44.000 0.00 0.00 36.29 2.90
2057 2119 5.035168 AGAGGATGGATATTTAGGGCTCT 57.965 43.478 0.00 0.00 0.00 4.09
2205 2272 2.290641 ACTGTCCTCGTGCAAATCAAAC 59.709 45.455 0.00 0.00 0.00 2.93
2266 2340 6.655078 ACATTGTAGTCTGATTGCCTTTTT 57.345 33.333 0.00 0.00 0.00 1.94
2333 2407 2.172505 ACATGATTATCCCACAAGCGGA 59.827 45.455 0.00 0.00 0.00 5.54
2390 2464 8.782144 GGTTTCAGATTCAGGAGATCAATATTC 58.218 37.037 0.00 0.00 0.00 1.75
2739 2825 7.712205 GCTGATTAAATTCCATTGCCACTTTAT 59.288 33.333 0.00 0.00 0.00 1.40
2840 2926 5.580691 TGTAATCTTTACAGCGATTGGACTG 59.419 40.000 0.00 0.00 39.86 3.51
2951 3039 4.205065 GCAGCCTAATCATCTGCTAGAT 57.795 45.455 6.24 0.00 46.93 1.98
2956 3044 7.201626 GCAGCCTAATCATCTGCTAGATATTTG 60.202 40.741 6.24 0.00 46.93 2.32
2966 3054 8.579006 CATCTGCTAGATATTTGAGAAGTCTCT 58.421 37.037 9.63 0.00 37.24 3.10
3007 3158 2.812499 GCATTCAGCATGGGCCAG 59.188 61.111 13.78 5.44 44.79 4.85
3057 3208 2.169832 AGTTCAACTGTCCATGGTCG 57.830 50.000 12.58 5.53 0.00 4.79
3061 3212 0.250295 CAACTGTCCATGGTCGGTGT 60.250 55.000 21.99 10.86 0.00 4.16
3066 3217 1.695242 TGTCCATGGTCGGTGTAGTTT 59.305 47.619 12.58 0.00 0.00 2.66
3071 3222 3.756434 CCATGGTCGGTGTAGTTTCATTT 59.244 43.478 2.57 0.00 0.00 2.32
3089 3240 6.968131 TCATTTCTTGTCCAGATAAAGTCG 57.032 37.500 0.00 0.00 0.00 4.18
3091 3242 7.608153 TCATTTCTTGTCCAGATAAAGTCGTA 58.392 34.615 0.00 0.00 0.00 3.43
3092 3243 7.759886 TCATTTCTTGTCCAGATAAAGTCGTAG 59.240 37.037 0.00 0.00 0.00 3.51
3123 3274 8.975663 ATGAGATTCTTGTCATGTACATCAAT 57.024 30.769 5.07 0.00 38.10 2.57
3125 3276 9.889128 TGAGATTCTTGTCATGTACATCAATTA 57.111 29.630 5.07 0.55 38.10 1.40
3167 3329 4.969484 TCCTGAGGTCCTTAAAAACTGAC 58.031 43.478 0.00 0.00 0.00 3.51
3229 3435 2.383855 CTCCCGGAGTCTCTCAAGATT 58.616 52.381 0.73 0.00 33.08 2.40
3298 3504 2.739287 CGCCTGCGAAACCCGTTA 60.739 61.111 5.43 0.00 42.83 3.18
3384 3590 0.035056 CCCGTGAAAGAGCCCATTCT 60.035 55.000 0.00 0.00 0.00 2.40
3396 3602 2.241685 AGCCCATTCTGAGCTCTTCATT 59.758 45.455 16.19 0.00 34.68 2.57
3436 3642 1.064611 TCGCTCAAGAGTAGGTAGCCT 60.065 52.381 0.00 0.00 37.71 4.58
3438 3644 1.202475 GCTCAAGAGTAGGTAGCCTGC 60.202 57.143 0.00 0.00 36.48 4.85
3450 3656 2.415512 GGTAGCCTGCGTAACTTTTGAG 59.584 50.000 0.00 0.00 0.00 3.02
3468 3674 4.365514 TGAGACCAAGTTGGCTAATTCA 57.634 40.909 22.25 14.41 42.67 2.57
3477 3683 2.718107 GCTAATTCAGGCAGCGGC 59.282 61.111 0.00 0.00 40.13 6.53
3506 3720 2.156098 TGGACGGTGCCAGTTAATTTC 58.844 47.619 0.00 0.00 33.10 2.17
3512 3726 3.619038 CGGTGCCAGTTAATTTCTCTCTC 59.381 47.826 0.00 0.00 0.00 3.20
3599 3819 1.271163 CCCCGTGAAAAGAGTGGCTAA 60.271 52.381 0.00 0.00 0.00 3.09
3661 3881 2.128507 CGCTCCCTCCCTGTACTCC 61.129 68.421 0.00 0.00 0.00 3.85
3726 3946 8.908903 TCTATCTATTCTTTCAGTTCAGTCTCC 58.091 37.037 0.00 0.00 0.00 3.71
3727 3947 7.732222 ATCTATTCTTTCAGTTCAGTCTCCT 57.268 36.000 0.00 0.00 0.00 3.69
3728 3948 7.164230 TCTATTCTTTCAGTTCAGTCTCCTC 57.836 40.000 0.00 0.00 0.00 3.71
3729 3949 6.951198 TCTATTCTTTCAGTTCAGTCTCCTCT 59.049 38.462 0.00 0.00 0.00 3.69
3730 3950 8.110271 TCTATTCTTTCAGTTCAGTCTCCTCTA 58.890 37.037 0.00 0.00 0.00 2.43
3731 3951 6.582677 TTCTTTCAGTTCAGTCTCCTCTAG 57.417 41.667 0.00 0.00 0.00 2.43
3732 3952 5.636123 TCTTTCAGTTCAGTCTCCTCTAGT 58.364 41.667 0.00 0.00 0.00 2.57
3766 3990 4.141228 TCGTACCTGATATCTTCCTCCTGT 60.141 45.833 3.98 0.00 0.00 4.00
3767 3991 4.585162 CGTACCTGATATCTTCCTCCTGTT 59.415 45.833 3.98 0.00 0.00 3.16
3772 3996 5.344743 TGATATCTTCCTCCTGTTGTCAC 57.655 43.478 3.98 0.00 0.00 3.67
3863 4106 2.768527 TCAGCAGTAAATCAGCTAGCCT 59.231 45.455 12.13 0.00 36.78 4.58
3866 4109 2.216898 CAGTAAATCAGCTAGCCTGCC 58.783 52.381 12.13 0.00 41.50 4.85
3872 4115 1.525535 CAGCTAGCCTGCCATGTCC 60.526 63.158 12.13 0.00 34.21 4.02
3874 4133 1.150081 GCTAGCCTGCCATGTCCAT 59.850 57.895 2.29 0.00 0.00 3.41
3881 4140 0.596577 CTGCCATGTCCATATGCAGC 59.403 55.000 14.30 0.00 38.30 5.25
3883 4142 0.879765 GCCATGTCCATATGCAGCTC 59.120 55.000 0.00 0.00 0.00 4.09
3887 4146 0.179076 TGTCCATATGCAGCTCACCG 60.179 55.000 0.00 0.00 0.00 4.94
3904 4171 2.028130 ACCGCATGTGGTTTTCTGAAA 58.972 42.857 25.40 0.00 39.99 2.69
3906 4173 2.293122 CCGCATGTGGTTTTCTGAAAGA 59.707 45.455 17.59 0.00 44.68 2.52
3940 4209 2.223665 GGCTCTAAATGAAGGCACATGC 60.224 50.000 0.00 0.00 41.14 4.06
3968 4237 2.829741 AGTTGAGCTGAGGTTGAGAC 57.170 50.000 0.00 0.00 0.00 3.36
3990 4259 2.232941 CGGAAGTCAGTAAAGGTGGCTA 59.767 50.000 0.00 0.00 0.00 3.93
3993 4265 3.963428 AGTCAGTAAAGGTGGCTACAG 57.037 47.619 1.52 0.00 0.00 2.74
4047 4319 2.681976 GCATCTCAGCCATACAGGTGTT 60.682 50.000 0.00 0.00 40.61 3.32
4053 4325 1.937546 GCCATACAGGTGTTGCAGCC 61.938 60.000 0.00 0.00 40.61 4.85
4109 4387 1.213296 GCCCACCAAAGGATAGGAGA 58.787 55.000 0.00 0.00 0.00 3.71
4110 4388 1.564348 GCCCACCAAAGGATAGGAGAA 59.436 52.381 0.00 0.00 0.00 2.87
4141 4419 2.604686 AGGGAAGGACAGCGAGCA 60.605 61.111 0.00 0.00 0.00 4.26
4142 4420 2.435059 GGGAAGGACAGCGAGCAC 60.435 66.667 0.00 0.00 0.00 4.40
4187 4465 1.144936 GCCCCAGTCTCCAATCTCG 59.855 63.158 0.00 0.00 0.00 4.04
4194 4472 1.664659 AGTCTCCAATCTCGTCGTACG 59.335 52.381 9.53 9.53 44.19 3.67
4195 4473 1.396301 GTCTCCAATCTCGTCGTACGT 59.604 52.381 16.05 0.00 43.14 3.57
4196 4474 2.604914 GTCTCCAATCTCGTCGTACGTA 59.395 50.000 16.05 0.00 43.14 3.57
4295 4576 3.615709 AAAGCCAAAGCCACGCCC 61.616 61.111 0.00 0.00 41.25 6.13
4296 4577 4.912395 AAGCCAAAGCCACGCCCA 62.912 61.111 0.00 0.00 41.25 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.192317 GGGAAATGTAATCGAGTCTTGCT 58.808 43.478 0.00 0.00 0.00 3.91
1 2 3.312697 GGGGAAATGTAATCGAGTCTTGC 59.687 47.826 0.00 0.00 0.00 4.01
2 3 4.770795 AGGGGAAATGTAATCGAGTCTTG 58.229 43.478 0.00 0.00 0.00 3.02
3 4 4.469945 TGAGGGGAAATGTAATCGAGTCTT 59.530 41.667 0.00 0.00 0.00 3.01
4 5 4.030913 TGAGGGGAAATGTAATCGAGTCT 58.969 43.478 0.00 0.00 0.00 3.24
5 6 4.141914 ACTGAGGGGAAATGTAATCGAGTC 60.142 45.833 0.00 0.00 0.00 3.36
6 7 3.775316 ACTGAGGGGAAATGTAATCGAGT 59.225 43.478 0.00 0.00 0.00 4.18
7 8 4.408182 ACTGAGGGGAAATGTAATCGAG 57.592 45.455 0.00 0.00 0.00 4.04
8 9 4.513442 CAACTGAGGGGAAATGTAATCGA 58.487 43.478 0.00 0.00 0.00 3.59
9 10 3.627577 CCAACTGAGGGGAAATGTAATCG 59.372 47.826 0.00 0.00 0.00 3.34
10 11 4.855340 TCCAACTGAGGGGAAATGTAATC 58.145 43.478 0.00 0.00 0.00 1.75
11 12 4.860022 CTCCAACTGAGGGGAAATGTAAT 58.140 43.478 0.00 0.00 37.45 1.89
12 13 3.561313 GCTCCAACTGAGGGGAAATGTAA 60.561 47.826 0.00 0.00 41.73 2.41
13 14 2.026262 GCTCCAACTGAGGGGAAATGTA 60.026 50.000 0.00 0.00 41.73 2.29
14 15 1.272147 GCTCCAACTGAGGGGAAATGT 60.272 52.381 0.00 0.00 41.73 2.71
49 50 5.612261 ACTGAACTAAACCCCCTAAAAGGTA 59.388 40.000 0.00 0.00 34.45 3.08
51 52 4.994282 ACTGAACTAAACCCCCTAAAAGG 58.006 43.478 0.00 0.00 34.30 3.11
52 53 6.239204 CCAAACTGAACTAAACCCCCTAAAAG 60.239 42.308 0.00 0.00 0.00 2.27
87 89 4.630069 GCTATGAACACAACGATTGGTAGT 59.370 41.667 0.00 0.00 34.12 2.73
88 90 4.629634 TGCTATGAACACAACGATTGGTAG 59.370 41.667 0.00 0.00 34.12 3.18
89 91 4.390603 GTGCTATGAACACAACGATTGGTA 59.609 41.667 0.00 0.00 37.96 3.25
90 92 3.188460 GTGCTATGAACACAACGATTGGT 59.812 43.478 0.00 0.00 37.96 3.67
91 93 3.426159 GGTGCTATGAACACAACGATTGG 60.426 47.826 0.00 0.00 39.87 3.16
92 94 3.188254 TGGTGCTATGAACACAACGATTG 59.812 43.478 0.00 0.00 39.87 2.67
93 95 3.407698 TGGTGCTATGAACACAACGATT 58.592 40.909 0.00 0.00 39.87 3.34
94 96 3.052455 TGGTGCTATGAACACAACGAT 57.948 42.857 0.00 0.00 39.87 3.73
106 108 6.180472 AGTAAACAAACTGCTATGGTGCTAT 58.820 36.000 0.00 0.00 0.00 2.97
256 258 6.202937 CAGCAACAAAAATTCAACAATGCAT 58.797 32.000 0.00 0.00 33.89 3.96
313 315 5.406780 CCGCATAATCCTTCAATCTACAGTC 59.593 44.000 0.00 0.00 0.00 3.51
386 388 4.701651 TCCACATTTTGCTGGTGAGAATAG 59.298 41.667 0.00 0.00 34.52 1.73
398 400 9.638239 TCAAATATTAGTTCTTCCACATTTTGC 57.362 29.630 0.00 0.00 0.00 3.68
419 421 4.534103 GGCTGGATCTACCCTCTATCAAAT 59.466 45.833 0.00 0.00 38.00 2.32
436 438 0.545309 ACTCAACCTAGCTGGCTGGA 60.545 55.000 7.51 0.00 40.22 3.86
438 440 1.550524 TGTACTCAACCTAGCTGGCTG 59.449 52.381 5.25 0.00 40.22 4.85
466 468 7.775120 ACTATATGAAAGAGCAAACAAATGGG 58.225 34.615 0.00 0.00 0.00 4.00
495 515 4.371681 AGAGGCTCTAATTTGAAGGGGTA 58.628 43.478 17.09 0.00 0.00 3.69
496 516 3.193782 AGAGGCTCTAATTTGAAGGGGT 58.806 45.455 17.09 0.00 0.00 4.95
498 518 7.629437 GCTTTTAAGAGGCTCTAATTTGAAGGG 60.629 40.741 19.07 3.88 0.00 3.95
499 519 7.254137 GCTTTTAAGAGGCTCTAATTTGAAGG 58.746 38.462 19.07 6.81 0.00 3.46
612 632 8.674263 ATCTCTGGACTAATTGAAAATGCTAG 57.326 34.615 0.00 0.00 0.00 3.42
618 638 9.745018 ATCTGAAATCTCTGGACTAATTGAAAA 57.255 29.630 0.00 0.00 0.00 2.29
625 645 7.070074 GGTAGGAATCTGAAATCTCTGGACTAA 59.930 40.741 0.00 0.00 0.00 2.24
722 743 5.723295 CCCACCTTTGTGAAATATGAAAGG 58.277 41.667 0.00 0.00 46.71 3.11
746 767 6.754675 AGGAAACTGAAAAATGTGTTAAACCG 59.245 34.615 0.00 0.00 41.13 4.44
871 909 8.958119 AGTTTAACAACTTCTCATTCTACACA 57.042 30.769 0.00 0.00 40.66 3.72
899 937 3.674997 TCTCTGAAATGGTTTTCCCGAG 58.325 45.455 0.00 7.80 40.49 4.63
928 966 6.891624 TCAGAAAGATCAACAATTGAGAACG 58.108 36.000 13.59 0.00 43.98 3.95
988 1026 8.160765 TGTCCTTAGTTTCATATTCCTTCACAA 58.839 33.333 0.00 0.00 0.00 3.33
1113 1151 6.494666 AGATAAACCGGAGTATCATTTGGA 57.505 37.500 22.58 0.00 36.25 3.53
1206 1244 8.322906 TCTGACACAAATAAGTACCTTCAATG 57.677 34.615 0.00 0.00 0.00 2.82
1222 1260 6.151691 GCTTAAAAAGATGCATCTGACACAA 58.848 36.000 29.34 17.40 37.19 3.33
1227 1265 5.858049 CGTTTGCTTAAAAAGATGCATCTGA 59.142 36.000 29.34 12.66 37.19 3.27
1276 1314 8.975439 CCAAACAGAAATGAGAAAAGAAGAATG 58.025 33.333 0.00 0.00 0.00 2.67
1277 1315 8.699130 ACCAAACAGAAATGAGAAAAGAAGAAT 58.301 29.630 0.00 0.00 0.00 2.40
1300 1338 6.128499 CGTGTTGGATTTATAACTCGAAACCA 60.128 38.462 13.06 0.00 42.79 3.67
1391 1429 7.172703 GCCTATTGATAGTTAACATTAGCCGTT 59.827 37.037 8.61 0.00 0.00 4.44
1394 1432 7.361286 GCAGCCTATTGATAGTTAACATTAGCC 60.361 40.741 8.61 0.00 0.00 3.93
1415 1453 4.201920 GGTACATAAAAGTAAGCTGCAGCC 60.202 45.833 34.39 19.70 43.38 4.85
1563 1604 3.487942 GTCGCATTACAACCACAAAAACC 59.512 43.478 0.00 0.00 0.00 3.27
1565 1606 4.640789 AGTCGCATTACAACCACAAAAA 57.359 36.364 0.00 0.00 0.00 1.94
1573 1614 9.586150 CAAAGATATCATTAGTCGCATTACAAC 57.414 33.333 5.32 0.00 0.00 3.32
1575 1616 7.095229 GGCAAAGATATCATTAGTCGCATTACA 60.095 37.037 5.32 0.00 0.00 2.41
1588 1629 6.191657 TGATACTGGTGGCAAAGATATCAT 57.808 37.500 5.32 0.00 0.00 2.45
1589 1630 5.628797 TGATACTGGTGGCAAAGATATCA 57.371 39.130 5.32 10.64 0.00 2.15
1591 1632 6.176183 GCTATGATACTGGTGGCAAAGATAT 58.824 40.000 5.52 0.96 0.00 1.63
1592 1633 5.071653 TGCTATGATACTGGTGGCAAAGATA 59.928 40.000 5.52 0.00 0.00 1.98
1597 1638 3.643199 TTGCTATGATACTGGTGGCAA 57.357 42.857 0.00 0.00 36.16 4.52
1628 1669 4.764172 ACTAGATGAACACCTGAAGCATC 58.236 43.478 0.00 0.00 36.49 3.91
1672 1713 8.039538 CACATATGAGTACATGATGGAGCTTAT 58.960 37.037 10.38 0.00 37.87 1.73
1703 1752 5.049198 GCAATATGAGCTAATAACAGCAGCA 60.049 40.000 0.00 0.00 44.35 4.41
1704 1753 5.180868 AGCAATATGAGCTAATAACAGCAGC 59.819 40.000 12.62 0.00 44.35 5.25
1843 1894 2.644299 TCCCTCAAAATCAAGAGAGGCA 59.356 45.455 0.00 0.00 44.95 4.75
2006 2059 0.608640 AGCGGACACTGGACTAAAGG 59.391 55.000 0.00 0.00 0.00 3.11
2079 2141 4.079787 AGCAGACCCAATTGGAATAAGCTA 60.080 41.667 26.60 0.00 37.39 3.32
2086 2148 1.962807 CACAAGCAGACCCAATTGGAA 59.037 47.619 26.60 0.00 37.39 3.53
2205 2272 5.530915 TCTGTACTCCACAAAAATTGTCCAG 59.469 40.000 0.00 0.00 43.23 3.86
2390 2464 1.200716 TCTAAGCACGTCGTACCAAGG 59.799 52.381 0.00 0.00 0.00 3.61
2614 2688 6.758254 CCTTTTGGAATAAACAGTTGACCAT 58.242 36.000 0.00 0.00 44.07 3.55
2695 2781 2.620115 CAGCAAGAATGATGGCCGTAAT 59.380 45.455 0.00 0.00 39.28 1.89
2820 2906 3.197766 TCCAGTCCAATCGCTGTAAAGAT 59.802 43.478 0.00 0.00 0.00 2.40
2840 2926 8.024145 TCTTTTCCTAATCTATCAAGGTCTCC 57.976 38.462 0.00 0.00 0.00 3.71
2951 3039 8.964476 AACTGAAAACAGAGACTTCTCAAATA 57.036 30.769 8.93 0.00 45.21 1.40
2956 3044 9.491934 GTTTAAAACTGAAAACAGAGACTTCTC 57.508 33.333 0.00 0.00 43.17 2.87
2966 3054 7.604164 TGCAATTCCTGTTTAAAACTGAAAACA 59.396 29.630 0.00 0.00 41.86 2.83
3042 3193 0.250295 ACACCGACCATGGACAGTTG 60.250 55.000 21.47 11.56 0.00 3.16
3043 3194 1.275291 CTACACCGACCATGGACAGTT 59.725 52.381 21.47 4.82 0.00 3.16
3044 3195 0.895530 CTACACCGACCATGGACAGT 59.104 55.000 21.47 8.21 0.00 3.55
3045 3196 0.895530 ACTACACCGACCATGGACAG 59.104 55.000 21.47 7.42 0.00 3.51
3046 3197 1.344065 AACTACACCGACCATGGACA 58.656 50.000 21.47 0.00 0.00 4.02
3057 3208 5.763204 TCTGGACAAGAAATGAAACTACACC 59.237 40.000 0.00 0.00 29.54 4.16
3061 3212 9.793259 ACTTTATCTGGACAAGAAATGAAACTA 57.207 29.630 0.00 0.00 38.79 2.24
3066 3217 6.464222 ACGACTTTATCTGGACAAGAAATGA 58.536 36.000 0.00 0.00 38.79 2.57
3071 3222 6.657966 TCTTCTACGACTTTATCTGGACAAGA 59.342 38.462 0.00 0.00 39.94 3.02
3089 3240 9.160496 ACATGACAAGAATCTCATTTCTTCTAC 57.840 33.333 0.00 0.00 42.58 2.59
3091 3242 9.160496 GTACATGACAAGAATCTCATTTCTTCT 57.840 33.333 0.00 0.00 42.58 2.85
3092 3243 8.939929 TGTACATGACAAGAATCTCATTTCTTC 58.060 33.333 0.00 0.00 42.58 2.87
3127 3278 8.646900 ACCTCAGGAAAACAAGCAAAAATAATA 58.353 29.630 0.00 0.00 0.00 0.98
3128 3279 7.508687 ACCTCAGGAAAACAAGCAAAAATAAT 58.491 30.769 0.00 0.00 0.00 1.28
3130 3281 6.462347 GGACCTCAGGAAAACAAGCAAAAATA 60.462 38.462 0.00 0.00 0.00 1.40
3131 3282 5.357742 ACCTCAGGAAAACAAGCAAAAAT 57.642 34.783 0.00 0.00 0.00 1.82
3134 3285 2.693074 GGACCTCAGGAAAACAAGCAAA 59.307 45.455 0.00 0.00 0.00 3.68
3136 3287 1.494721 AGGACCTCAGGAAAACAAGCA 59.505 47.619 0.00 0.00 0.00 3.91
3137 3288 2.278332 AGGACCTCAGGAAAACAAGC 57.722 50.000 0.00 0.00 0.00 4.01
3138 3289 6.709018 TTTTAAGGACCTCAGGAAAACAAG 57.291 37.500 0.00 0.00 0.00 3.16
3139 3290 6.666113 AGTTTTTAAGGACCTCAGGAAAACAA 59.334 34.615 22.80 0.00 37.74 2.83
3167 3329 6.350194 GCACCTGTAGGAAAAAGGGATAAAAG 60.350 42.308 4.64 0.00 38.94 2.27
3223 3429 2.112815 GCCGACCGGGGAAATCTTG 61.113 63.158 6.32 0.00 35.78 3.02
3298 3504 1.485895 GAGATGGAGGAGAAGCAGCTT 59.514 52.381 7.60 7.60 0.00 3.74
3384 3590 4.019051 TGGATTTCCTCAATGAAGAGCTCA 60.019 41.667 17.77 0.00 36.14 4.26
3396 3602 1.377202 GCGGTGCTGGATTTCCTCA 60.377 57.895 0.00 0.00 36.82 3.86
3436 3642 3.537580 ACTTGGTCTCAAAAGTTACGCA 58.462 40.909 0.00 0.00 32.75 5.24
3438 3644 4.788521 GCCAACTTGGTCTCAAAAGTTACG 60.789 45.833 9.63 0.00 43.09 3.18
3450 3656 2.164422 GCCTGAATTAGCCAACTTGGTC 59.836 50.000 9.63 2.34 40.46 4.02
3506 3720 2.093711 TGACACCGAGAGAGAGAGAGAG 60.094 54.545 0.00 0.00 0.00 3.20
3512 3726 0.679640 AGGCTGACACCGAGAGAGAG 60.680 60.000 0.00 0.00 33.69 3.20
3599 3819 4.371624 TCACCCAAATCACATCTGTCTT 57.628 40.909 0.00 0.00 0.00 3.01
3661 3881 3.955291 CTGGCCGACAGTCTATCAG 57.045 57.895 0.00 0.00 42.42 2.90
3702 3922 8.830915 AGGAGACTGAACTGAAAGAATAGATA 57.169 34.615 0.00 0.00 41.13 1.98
3703 3923 7.619302 AGAGGAGACTGAACTGAAAGAATAGAT 59.381 37.037 0.00 0.00 44.43 1.98
3726 3946 2.925724 ACGATGAGACAGGGACTAGAG 58.074 52.381 0.00 0.00 36.02 2.43
3727 3947 3.433314 GGTACGATGAGACAGGGACTAGA 60.433 52.174 0.00 0.00 36.02 2.43
3728 3948 2.879646 GGTACGATGAGACAGGGACTAG 59.120 54.545 0.00 0.00 36.02 2.57
3729 3949 2.508716 AGGTACGATGAGACAGGGACTA 59.491 50.000 0.00 0.00 36.02 2.59
3730 3950 1.285373 AGGTACGATGAGACAGGGACT 59.715 52.381 0.00 0.00 43.88 3.85
3731 3951 1.405821 CAGGTACGATGAGACAGGGAC 59.594 57.143 0.00 0.00 0.00 4.46
3732 3952 1.283905 TCAGGTACGATGAGACAGGGA 59.716 52.381 0.00 0.00 0.00 4.20
3766 3990 1.842052 AGCATGCATGGATGTGACAA 58.158 45.000 27.34 0.00 0.00 3.18
3767 3991 1.474879 CAAGCATGCATGGATGTGACA 59.525 47.619 27.34 0.00 0.00 3.58
3772 3996 2.267426 CAACACAAGCATGCATGGATG 58.733 47.619 27.34 21.79 0.00 3.51
3832 4075 5.724328 TGATTTACTGCTGAACTAGACTGG 58.276 41.667 0.00 0.00 0.00 4.00
3863 4106 0.184211 AGCTGCATATGGACATGGCA 59.816 50.000 0.00 11.27 33.50 4.92
3866 4109 1.878088 GGTGAGCTGCATATGGACATG 59.122 52.381 4.56 0.00 0.00 3.21
3887 4146 4.022068 TCCATCTTTCAGAAAACCACATGC 60.022 41.667 0.00 0.00 0.00 4.06
3904 4171 3.313811 AGCCTACACTGCTCCATCT 57.686 52.632 0.00 0.00 32.41 2.90
3963 4232 2.561419 CCTTTACTGACTTCCGGTCTCA 59.439 50.000 0.00 0.00 44.74 3.27
3964 4233 2.561858 ACCTTTACTGACTTCCGGTCTC 59.438 50.000 0.00 0.00 44.74 3.36
3965 4234 2.299297 CACCTTTACTGACTTCCGGTCT 59.701 50.000 0.00 0.00 44.74 3.85
3966 4235 2.612221 CCACCTTTACTGACTTCCGGTC 60.612 54.545 0.00 0.00 44.70 4.79
3967 4236 1.346722 CCACCTTTACTGACTTCCGGT 59.653 52.381 0.00 0.00 38.16 5.28
3968 4237 1.944430 GCCACCTTTACTGACTTCCGG 60.944 57.143 0.00 0.00 0.00 5.14
4109 4387 0.705253 TCCCTCCTCGTCCTTCTCTT 59.295 55.000 0.00 0.00 0.00 2.85
4110 4388 0.705253 TTCCCTCCTCGTCCTTCTCT 59.295 55.000 0.00 0.00 0.00 3.10
4194 4472 2.098770 CCCTGGAGCTGTACTACGTTAC 59.901 54.545 0.00 0.00 27.93 2.50
4195 4473 2.372264 CCCTGGAGCTGTACTACGTTA 58.628 52.381 0.00 0.00 27.93 3.18
4196 4474 1.183549 CCCTGGAGCTGTACTACGTT 58.816 55.000 0.00 0.00 27.93 3.99
4303 4584 3.039588 AACGTACGCAGGTTGCCG 61.040 61.111 16.72 0.00 41.12 5.69


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

AutoCloner maintained by Alex Coulton.