Multiple sequence alignment - TraesCS1A01G358600

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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 TraesCS1A01G358600 chr1A 100.000 3624 0 0 850 4473 540339754 540336131 0.000000e+00 6693.0
1 TraesCS1A01G358600 chr1A 100.000 485 0 0 1 485 540340603 540340119 0.000000e+00 896.0
2 TraesCS1A01G358600 chr1D 92.205 2027 88 24 850 2816 445075716 445073700 0.000000e+00 2804.0
3 TraesCS1A01G358600 chr1D 94.943 1661 59 13 2829 4473 445073724 445072073 0.000000e+00 2579.0
4 TraesCS1A01G358600 chr1D 84.756 492 35 18 1 485 445076244 445075786 1.470000e-124 457.0
5 TraesCS1A01G358600 chr1B 90.847 1770 90 29 997 2723 605935625 605933885 0.000000e+00 2305.0
6 TraesCS1A01G358600 chr1B 92.162 1531 93 13 2962 4473 605933883 605932361 0.000000e+00 2137.0
7 TraesCS1A01G358600 chr1B 83.439 471 32 24 14 454 605936603 605936149 3.240000e-106 396.0
8 TraesCS1A01G358600 chr6B 90.751 173 16 0 2504 2676 98982790 98982618 9.680000e-57 231.0
9 TraesCS1A01G358600 chrUn 90.230 174 17 0 2503 2676 20932899 20933072 1.250000e-55 228.0
10 TraesCS1A01G358600 chr2D 90.196 51 4 1 1319 1368 61743 61693 1.040000e-06 65.8
11 TraesCS1A01G358600 chr2A 90.196 51 4 1 1319 1368 279346 279396 1.040000e-06 65.8
12 TraesCS1A01G358600 chr2A 95.000 40 0 2 1312 1349 86379757 86379796 1.340000e-05 62.1
13 TraesCS1A01G358600 chr7A 92.857 42 3 0 1319 1360 22332594 22332553 1.340000e-05 62.1
14 TraesCS1A01G358600 chr7A 90.476 42 4 0 1319 1360 21814837 21814796 6.250000e-04 56.5
15 TraesCS1A01G358600 chr7A 86.538 52 5 2 1319 1370 22140643 22140594 6.250000e-04 56.5
16 TraesCS1A01G358600 chr4A 92.857 42 3 0 1319 1360 711880262 711880303 1.340000e-05 62.1


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 TraesCS1A01G358600 chr1A 540336131 540340603 4472 True 3794.500000 6693 100.000000 1 4473 2 chr1A.!!$R1 4472
1 TraesCS1A01G358600 chr1D 445072073 445076244 4171 True 1946.666667 2804 90.634667 1 4473 3 chr1D.!!$R1 4472
2 TraesCS1A01G358600 chr1B 605932361 605936603 4242 True 1612.666667 2305 88.816000 14 4473 3 chr1B.!!$R1 4459

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
889 1215 0.399091 CCATAGCCACCTCCCTCTCA 60.399 60.0 0.00 0.0 0.00 3.27 F
1466 1827 0.652592 CGATCTGTGGATTTCCGTGC 59.347 55.0 0.00 0.0 39.43 5.34 F
2265 2641 0.101399 CAGTAGGCGCTAGGTGACAG 59.899 60.0 7.64 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 2077 0.738762 CATGAGAGGAGCACACCACG 60.739 60.0 0.00 0.0 0.0 4.94 R
3427 3841 0.108019 GGGGTTTCAAGTCGACCACT 59.892 55.0 13.01 0.0 34.0 4.00 R
3683 4098 0.317160 CTGTACACTGACGGCAAGGA 59.683 55.0 0.00 0.0 0.0 3.36 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
42 45 3.350612 GCGCGTGCAAAGGGTACA 61.351 61.111 17.66 0.00 42.15 2.90
66 69 0.678048 AGAGGCCATTTTGTCTCCGC 60.678 55.000 5.01 0.00 0.00 5.54
135 145 1.860950 CAAAGCAGAGCATACGCGTAT 59.139 47.619 25.54 25.54 45.49 3.06
139 149 1.190323 GCAGAGCATACGCGTATCAAC 59.810 52.381 28.10 19.56 45.49 3.18
150 160 0.655733 CGTATCAACGCATCCCCAAC 59.344 55.000 0.00 0.00 43.12 3.77
156 166 1.847798 AACGCATCCCCAACCTAGCA 61.848 55.000 0.00 0.00 0.00 3.49
188 198 2.229784 CCCTGCCACATTTCTTCTCAAC 59.770 50.000 0.00 0.00 0.00 3.18
199 209 2.766313 TCTTCTCAACAACACCATCCG 58.234 47.619 0.00 0.00 0.00 4.18
214 226 1.550130 ATCCGTTTCCCCTCGAGCAA 61.550 55.000 6.99 0.00 0.00 3.91
240 252 2.359598 GCAAGTGACAAACGTACGTTG 58.640 47.619 32.31 25.74 38.47 4.10
260 272 3.313274 GTTGAAAACGAAGCGAGTGAA 57.687 42.857 0.00 0.00 36.92 3.18
307 324 1.210155 GTGACAAATCAGCACGGGC 59.790 57.895 0.00 0.00 34.75 6.13
342 370 2.983592 GGGTGGCAGAAACCGTGG 60.984 66.667 0.00 0.00 38.70 4.94
343 371 2.983592 GGTGGCAGAAACCGTGGG 60.984 66.667 0.00 0.00 0.00 4.61
414 442 4.969196 CGCAGCAGACACACCGGT 62.969 66.667 0.00 0.00 0.00 5.28
877 915 4.593125 CCAGCAGCCCCCATAGCC 62.593 72.222 0.00 0.00 0.00 3.93
885 923 2.039405 CCCCATAGCCACCTCCCT 60.039 66.667 0.00 0.00 0.00 4.20
889 1215 0.399091 CCATAGCCACCTCCCTCTCA 60.399 60.000 0.00 0.00 0.00 3.27
938 1264 4.090057 GTGCGGTGCGGCTCTTTC 62.090 66.667 0.00 0.00 0.00 2.62
945 1271 1.672356 TGCGGCTCTTTCTTGCCTC 60.672 57.895 0.00 0.00 46.42 4.70
971 1298 4.731612 AGTCGGCTGCTGCTGTCG 62.732 66.667 24.51 24.51 45.38 4.35
973 1300 4.724602 TCGGCTGCTGCTGTCGTC 62.725 66.667 27.87 3.73 45.38 4.20
994 1321 2.702592 TTCGTTTCAGTTCACCAGGT 57.297 45.000 0.00 0.00 0.00 4.00
995 1322 2.702592 TCGTTTCAGTTCACCAGGTT 57.297 45.000 0.00 0.00 0.00 3.50
999 1349 3.139077 GTTTCAGTTCACCAGGTTCGAT 58.861 45.455 0.00 0.00 0.00 3.59
1405 1765 2.807107 CCCCTCGGATTCATCGCCA 61.807 63.158 0.00 0.00 0.00 5.69
1466 1827 0.652592 CGATCTGTGGATTTCCGTGC 59.347 55.000 0.00 0.00 39.43 5.34
1467 1828 0.652592 GATCTGTGGATTTCCGTGCG 59.347 55.000 0.00 0.00 39.43 5.34
1641 2002 2.743928 GAGGTGTCAGGGCTTGCG 60.744 66.667 0.00 0.00 0.00 4.85
1737 2098 0.322648 TGGTGTGCTCCTCTCATGTG 59.677 55.000 0.00 0.00 0.00 3.21
1776 2137 0.457443 ATTCTCGCATCGTGCTCTCA 59.543 50.000 8.07 0.00 42.25 3.27
1809 2170 2.161211 GCCTGTTGCTCTCTCAATTGAC 59.839 50.000 3.38 0.00 36.87 3.18
1856 2227 3.149196 GGTATTGGTACAGCATCCATGG 58.851 50.000 4.97 4.97 42.39 3.66
1919 2290 4.880537 AGGAAGGATGAGCGCGCG 62.881 66.667 28.44 28.44 0.00 6.86
1958 2329 1.478105 GGCAAGGTCATCCAATGGAAC 59.522 52.381 5.89 0.00 34.34 3.62
2009 2380 2.287915 GTCACGATCCATTGGTATGCAC 59.712 50.000 1.86 0.00 0.00 4.57
2048 2420 9.619316 TGTACAATGTGTTGCTATTTTTCATAC 57.381 29.630 0.00 0.00 38.96 2.39
2057 2429 2.153680 ATTTTTCATACGACACGCGC 57.846 45.000 5.73 0.00 46.04 6.86
2062 2434 0.317519 TCATACGACACGCGCCATAG 60.318 55.000 5.73 0.00 46.04 2.23
2064 2436 0.946528 ATACGACACGCGCCATAGTA 59.053 50.000 5.73 5.20 46.04 1.82
2069 2444 0.750850 ACACGCGCCATAGTAAGGAT 59.249 50.000 5.73 0.00 0.00 3.24
2097 2472 5.490213 CGTTGAGTTTGAAACTGTAGTCAC 58.510 41.667 16.25 0.00 43.03 3.67
2125 2500 8.924691 GCAACTTCAAAGTATGATGCAAAATTA 58.075 29.630 10.79 0.00 38.36 1.40
2231 2607 7.427895 GGAGTTATTTCTCGTTAGTCGTTACTC 59.572 40.741 0.00 0.00 40.80 2.59
2265 2641 0.101399 CAGTAGGCGCTAGGTGACAG 59.899 60.000 7.64 0.00 0.00 3.51
2270 2646 1.079819 GCGCTAGGTGACAGCAGAA 60.080 57.895 7.50 0.00 39.04 3.02
2274 2650 0.603569 CTAGGTGACAGCAGAACGGT 59.396 55.000 7.50 0.00 0.00 4.83
2280 2656 0.666577 GACAGCAGAACGGTTAGCGT 60.667 55.000 2.83 2.83 0.00 5.07
2348 2724 1.438651 ACGTAATCATGCTTGCGTGT 58.561 45.000 21.64 1.37 44.04 4.49
2372 2748 4.038162 GCTTAGGTGAGAACCGTGAGATAT 59.962 45.833 0.00 0.00 34.28 1.63
2727 3126 3.671702 GCTGTCTGCCTCAATTTTGCTAC 60.672 47.826 0.00 0.00 35.15 3.58
2739 3138 5.641636 TCAATTTTGCTACTAATCGTGCTGA 59.358 36.000 0.00 0.00 0.00 4.26
2759 3158 5.125100 TGATGAACTTGCAAAATGAGGTC 57.875 39.130 0.00 0.00 0.00 3.85
2789 3188 9.136323 TGTAGCTCTGATAGAATCAAGTATGAA 57.864 33.333 0.00 0.00 39.49 2.57
2790 3189 9.624697 GTAGCTCTGATAGAATCAAGTATGAAG 57.375 37.037 0.00 0.00 39.49 3.02
2791 3190 8.476064 AGCTCTGATAGAATCAAGTATGAAGA 57.524 34.615 0.00 0.00 39.49 2.87
2793 3192 9.142515 GCTCTGATAGAATCAAGTATGAAGATG 57.857 37.037 0.00 0.00 39.49 2.90
2795 3194 9.978044 TCTGATAGAATCAAGTATGAAGATGTG 57.022 33.333 0.00 0.00 39.49 3.21
2796 3195 9.978044 CTGATAGAATCAAGTATGAAGATGTGA 57.022 33.333 0.00 0.00 39.49 3.58
2812 3211 9.559732 TGAAGATGTGATTAAGAAAAGAAGACA 57.440 29.630 0.00 0.00 0.00 3.41
2813 3212 9.818796 GAAGATGTGATTAAGAAAAGAAGACAC 57.181 33.333 0.00 0.00 0.00 3.67
2814 3213 8.329203 AGATGTGATTAAGAAAAGAAGACACC 57.671 34.615 0.00 0.00 0.00 4.16
2815 3214 8.160106 AGATGTGATTAAGAAAAGAAGACACCT 58.840 33.333 0.00 0.00 0.00 4.00
2816 3215 9.436957 GATGTGATTAAGAAAAGAAGACACCTA 57.563 33.333 0.00 0.00 0.00 3.08
2817 3216 8.603242 TGTGATTAAGAAAAGAAGACACCTAC 57.397 34.615 0.00 0.00 0.00 3.18
2818 3217 8.429641 TGTGATTAAGAAAAGAAGACACCTACT 58.570 33.333 0.00 0.00 0.00 2.57
2819 3218 9.924650 GTGATTAAGAAAAGAAGACACCTACTA 57.075 33.333 0.00 0.00 0.00 1.82
2825 3224 7.548967 AGAAAAGAAGACACCTACTAGTATGC 58.451 38.462 2.33 0.00 0.00 3.14
2826 3225 6.852420 AAAGAAGACACCTACTAGTATGCA 57.148 37.500 2.33 0.00 0.00 3.96
2827 3226 6.458232 AAGAAGACACCTACTAGTATGCAG 57.542 41.667 2.33 0.37 0.00 4.41
2831 3230 5.450453 AGACACCTACTAGTATGCAGATGT 58.550 41.667 2.33 0.00 0.00 3.06
2888 3287 5.665916 AACCATCTTTTATGGAAGCAAGG 57.334 39.130 10.90 0.00 41.64 3.61
2940 3350 2.749466 GCAGCTTGGACCATGGCTAATA 60.749 50.000 13.04 0.00 33.43 0.98
2951 3361 3.008049 CCATGGCTAATACCTGGTCCTAC 59.992 52.174 0.63 0.00 0.00 3.18
2994 3404 4.847198 TGTGCCACTCAAATCTGATGTAT 58.153 39.130 0.00 0.00 0.00 2.29
2995 3405 4.637091 TGTGCCACTCAAATCTGATGTATG 59.363 41.667 0.00 0.00 0.00 2.39
3055 3468 9.145865 GAACCTATGATAGCTAAGCTGATTTAC 57.854 37.037 0.00 0.00 40.10 2.01
3062 3475 2.030946 GCTAAGCTGATTTACCTGTGCG 59.969 50.000 0.00 0.00 0.00 5.34
3126 3540 2.827322 TGGAACTGGAAATTGCTGATGG 59.173 45.455 0.00 0.00 0.00 3.51
3163 3577 2.957402 TGAAGCCATACATCATCCCC 57.043 50.000 0.00 0.00 0.00 4.81
3226 3640 1.147824 CCTCATTCTGGCCAGCGAT 59.852 57.895 28.91 20.30 0.00 4.58
3307 3721 1.745087 CAGTGGCACAAGAACAACAGT 59.255 47.619 21.41 0.00 44.16 3.55
3325 3739 0.429736 GTGTCACAACATCGTCGTCG 59.570 55.000 0.00 0.00 37.81 5.12
3346 3760 2.053244 GATGGAGGTGATGGATCCACT 58.947 52.381 18.99 9.74 45.53 4.00
3427 3841 6.675413 AGCCAGGACAATATAACCGTAATA 57.325 37.500 0.00 0.00 0.00 0.98
3448 3862 1.368579 GGTCGACTTGAAACCCCGA 59.631 57.895 16.46 0.00 0.00 5.14
3631 4046 5.175859 TCTCTGTTTTCCGTTCATATGGTC 58.824 41.667 2.13 0.00 0.00 4.02
3632 4047 4.900684 TCTGTTTTCCGTTCATATGGTCA 58.099 39.130 2.13 0.00 0.00 4.02
3636 4051 6.210078 TGTTTTCCGTTCATATGGTCAAAAC 58.790 36.000 2.13 11.14 37.50 2.43
3646 4061 5.357878 TCATATGGTCAAAACATTCTCCAGC 59.642 40.000 2.13 0.00 0.00 4.85
3653 4068 0.400213 AACATTCTCCAGCCGGTCAA 59.600 50.000 1.90 0.00 0.00 3.18
3663 4078 0.678048 AGCCGGTCAATTTCAGCCTC 60.678 55.000 1.90 0.00 0.00 4.70
3677 4092 3.145551 CCTCAAGCCCTGGCATGC 61.146 66.667 9.90 9.90 44.88 4.06
3683 4098 2.993264 GCCCTGGCATGCTGTGTT 60.993 61.111 18.92 0.00 41.49 3.32
3740 4157 2.169789 CCAAGCGGCTGAGATGACG 61.170 63.158 1.81 0.00 42.16 4.35
3903 4320 2.990066 AGCCTAGAAATTCTCGGTGG 57.010 50.000 14.00 7.43 32.38 4.61
3954 4371 8.675504 TCTTCTACTACTGTGCTACAAGAATAC 58.324 37.037 0.00 0.00 0.00 1.89
3973 4390 1.063867 ACATACACCCTAGAGCGAGGT 60.064 52.381 0.00 0.00 34.45 3.85
4086 4503 2.276116 GCTCTCCACCGTGTCCTCA 61.276 63.158 0.00 0.00 0.00 3.86
4092 4509 0.874390 CCACCGTGTCCTCAATGTTG 59.126 55.000 0.00 0.00 0.00 3.33
4353 4798 4.681744 TGAAATCAACACTTCAAACAGCC 58.318 39.130 0.00 0.00 0.00 4.85
4354 4799 4.159321 TGAAATCAACACTTCAAACAGCCA 59.841 37.500 0.00 0.00 0.00 4.75
4355 4800 4.734398 AATCAACACTTCAAACAGCCAA 57.266 36.364 0.00 0.00 0.00 4.52
4356 4801 3.502191 TCAACACTTCAAACAGCCAAC 57.498 42.857 0.00 0.00 0.00 3.77
4357 4802 2.159448 TCAACACTTCAAACAGCCAACG 60.159 45.455 0.00 0.00 0.00 4.10
4358 4803 0.738389 ACACTTCAAACAGCCAACGG 59.262 50.000 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 45 3.321968 GGAGACAAAATGGCCTCTGTTTT 59.678 43.478 3.32 3.67 0.00 2.43
60 63 0.321298 GGTTTGTAAGGCAGCGGAGA 60.321 55.000 0.00 0.00 0.00 3.71
66 69 0.515564 CGTTCGGGTTTGTAAGGCAG 59.484 55.000 0.00 0.00 0.00 4.85
116 119 2.128035 GATACGCGTATGCTCTGCTTT 58.872 47.619 34.66 9.03 39.65 3.51
117 120 1.067060 TGATACGCGTATGCTCTGCTT 59.933 47.619 34.66 9.84 39.65 3.91
135 145 0.251916 CTAGGTTGGGGATGCGTTGA 59.748 55.000 0.00 0.00 0.00 3.18
139 149 1.819632 GTGCTAGGTTGGGGATGCG 60.820 63.158 0.00 0.00 0.00 4.73
163 173 0.901580 AAGAAATGTGGCAGGGCTGG 60.902 55.000 0.00 0.00 0.00 4.85
164 174 0.529378 GAAGAAATGTGGCAGGGCTG 59.471 55.000 0.00 0.00 0.00 4.85
165 175 0.407139 AGAAGAAATGTGGCAGGGCT 59.593 50.000 0.00 0.00 0.00 5.19
166 176 0.813821 GAGAAGAAATGTGGCAGGGC 59.186 55.000 0.00 0.00 0.00 5.19
188 198 0.251165 AGGGGAAACGGATGGTGTTG 60.251 55.000 0.00 0.00 0.00 3.33
214 226 3.586100 ACGTTTGTCACTTGCCTTTTT 57.414 38.095 0.00 0.00 0.00 1.94
240 252 3.313274 TTCACTCGCTTCGTTTTCAAC 57.687 42.857 0.00 0.00 0.00 3.18
260 272 9.986833 GCTTTTTCTTTCAACAACATACATTTT 57.013 25.926 0.00 0.00 0.00 1.82
307 324 0.321298 CCCCCGTACACTTGTTCAGG 60.321 60.000 0.00 0.00 0.00 3.86
343 371 2.862674 TTATGTCTTGTCGCCCCGGC 62.863 60.000 0.00 0.00 37.85 6.13
397 425 4.969196 ACCGGTGTGTCTGCTGCG 62.969 66.667 6.12 0.00 0.00 5.18
414 442 0.038526 GTCTTGTTCTCGCTTCCGGA 60.039 55.000 0.00 0.00 34.56 5.14
861 899 3.812544 TGGCTATGGGGGCTGCTG 61.813 66.667 0.00 0.00 0.00 4.41
871 909 0.755686 GTGAGAGGGAGGTGGCTATG 59.244 60.000 0.00 0.00 0.00 2.23
877 915 0.686112 GAGGAGGTGAGAGGGAGGTG 60.686 65.000 0.00 0.00 0.00 4.00
922 1248 3.825160 AAGAAAGAGCCGCACCGCA 62.825 57.895 0.00 0.00 0.00 5.69
923 1249 3.050275 AAGAAAGAGCCGCACCGC 61.050 61.111 0.00 0.00 0.00 5.68
924 1250 2.863153 CAAGAAAGAGCCGCACCG 59.137 61.111 0.00 0.00 0.00 4.94
925 1251 2.563427 GCAAGAAAGAGCCGCACC 59.437 61.111 0.00 0.00 0.00 5.01
926 1252 2.563427 GGCAAGAAAGAGCCGCAC 59.437 61.111 0.00 0.00 41.70 5.34
931 1257 1.172175 CCAAGGAGGCAAGAAAGAGC 58.828 55.000 0.00 0.00 0.00 4.09
968 1294 3.302286 GGTGAACTGAAACGAAAGACGAC 60.302 47.826 0.00 0.00 45.77 4.34
971 1298 3.002348 CCTGGTGAACTGAAACGAAAGAC 59.998 47.826 0.00 0.00 0.00 3.01
973 1300 2.943033 ACCTGGTGAACTGAAACGAAAG 59.057 45.455 0.00 0.00 0.00 2.62
1086 1442 3.227276 CCGTCCCCGAGATCCAGG 61.227 72.222 0.00 0.00 35.63 4.45
1311 1667 4.452733 GCGAAGAGGTGGGACGGG 62.453 72.222 0.00 0.00 0.00 5.28
1314 1670 3.644399 GACGGCGAAGAGGTGGGAC 62.644 68.421 16.62 0.00 0.00 4.46
1467 1828 4.980805 TTGGACACCTGCGCGACC 62.981 66.667 12.10 0.00 0.00 4.79
1641 2002 4.838486 CCGTCGACGAGCCTGCTC 62.838 72.222 37.65 9.11 43.02 4.26
1716 2077 0.738762 CATGAGAGGAGCACACCACG 60.739 60.000 0.00 0.00 0.00 4.94
1809 2170 2.297315 TGCTCGCATATCTACCTTCTGG 59.703 50.000 0.00 0.00 39.83 3.86
1856 2227 9.476202 GCATAATTAATCAGATTAACCCCAAAC 57.524 33.333 16.42 2.28 37.53 2.93
1919 2290 2.203126 CCCGCAGCCTCAATCCTC 60.203 66.667 0.00 0.00 0.00 3.71
2048 2420 1.206745 CCTTACTATGGCGCGTGTCG 61.207 60.000 8.43 0.00 42.12 4.35
2057 2429 3.386726 TCAACGGGTGATCCTTACTATGG 59.613 47.826 0.00 0.00 0.00 2.74
2062 2434 3.329929 AACTCAACGGGTGATCCTTAC 57.670 47.619 0.00 0.00 35.07 2.34
2064 2436 2.105821 TCAAACTCAACGGGTGATCCTT 59.894 45.455 0.00 0.00 35.07 3.36
2069 2444 2.680841 CAGTTTCAAACTCAACGGGTGA 59.319 45.455 0.00 0.00 40.46 4.02
2097 2472 5.050644 TGCATCATACTTTGAAGTTGCTG 57.949 39.130 15.33 10.37 38.93 4.41
2125 2500 1.975680 ACTATCACACCGGACCAAAGT 59.024 47.619 9.46 0.90 0.00 2.66
2127 2502 1.002659 CCACTATCACACCGGACCAAA 59.997 52.381 9.46 0.00 0.00 3.28
2231 2607 3.311596 GCCTACTGCTTAAAATGGTACCG 59.688 47.826 7.57 0.00 36.87 4.02
2274 2650 2.264813 CTAGGCACGCTTAAACGCTAA 58.735 47.619 0.00 0.00 36.19 3.09
2280 2656 4.195308 CGCCTAGGCACGCTTAAA 57.805 55.556 32.47 0.00 42.06 1.52
2348 2724 1.272490 CTCACGGTTCTCACCTAAGCA 59.728 52.381 0.00 0.00 41.64 3.91
2669 3066 1.135960 GCCAAGAGAATAGAGGGGCT 58.864 55.000 0.00 0.00 37.00 5.19
2727 3126 3.371898 TGCAAGTTCATCAGCACGATTAG 59.628 43.478 0.00 0.00 29.21 1.73
2739 3138 5.534207 TTGACCTCATTTTGCAAGTTCAT 57.466 34.783 0.00 0.00 0.00 2.57
2759 3158 8.659925 ACTTGATTCTATCAGAGCTACATTTG 57.340 34.615 0.00 0.00 40.94 2.32
2789 3188 8.160106 AGGTGTCTTCTTTTCTTAATCACATCT 58.840 33.333 0.00 0.00 0.00 2.90
2790 3189 8.329203 AGGTGTCTTCTTTTCTTAATCACATC 57.671 34.615 0.00 0.00 0.00 3.06
2791 3190 9.220767 GTAGGTGTCTTCTTTTCTTAATCACAT 57.779 33.333 0.00 0.00 0.00 3.21
2793 3192 8.834749 AGTAGGTGTCTTCTTTTCTTAATCAC 57.165 34.615 0.00 0.00 0.00 3.06
2799 3198 8.035984 GCATACTAGTAGGTGTCTTCTTTTCTT 58.964 37.037 15.45 0.00 0.00 2.52
2800 3199 7.178628 TGCATACTAGTAGGTGTCTTCTTTTCT 59.821 37.037 15.45 0.00 0.00 2.52
2801 3200 7.321153 TGCATACTAGTAGGTGTCTTCTTTTC 58.679 38.462 15.45 0.00 0.00 2.29
2802 3201 7.178628 TCTGCATACTAGTAGGTGTCTTCTTTT 59.821 37.037 15.45 0.00 0.00 2.27
2803 3202 6.663953 TCTGCATACTAGTAGGTGTCTTCTTT 59.336 38.462 15.45 0.00 0.00 2.52
2804 3203 6.188407 TCTGCATACTAGTAGGTGTCTTCTT 58.812 40.000 15.45 0.00 0.00 2.52
2805 3204 5.756918 TCTGCATACTAGTAGGTGTCTTCT 58.243 41.667 15.45 0.00 0.00 2.85
2806 3205 6.039941 ACATCTGCATACTAGTAGGTGTCTTC 59.960 42.308 15.45 0.00 40.86 2.87
2807 3206 5.894393 ACATCTGCATACTAGTAGGTGTCTT 59.106 40.000 15.45 0.00 40.86 3.01
2808 3207 5.300539 CACATCTGCATACTAGTAGGTGTCT 59.699 44.000 15.45 0.00 42.52 3.41
2809 3208 5.299531 TCACATCTGCATACTAGTAGGTGTC 59.700 44.000 15.45 0.65 42.52 3.67
2810 3209 5.201243 TCACATCTGCATACTAGTAGGTGT 58.799 41.667 15.45 9.58 44.76 4.16
2811 3210 5.774498 TCACATCTGCATACTAGTAGGTG 57.226 43.478 15.45 8.97 38.18 4.00
2812 3211 6.985653 AATCACATCTGCATACTAGTAGGT 57.014 37.500 15.45 0.00 0.00 3.08
2813 3212 8.031864 CCTTAATCACATCTGCATACTAGTAGG 58.968 40.741 10.20 10.20 0.00 3.18
2814 3213 8.797438 TCCTTAATCACATCTGCATACTAGTAG 58.203 37.037 8.85 0.00 0.00 2.57
2815 3214 8.706322 TCCTTAATCACATCTGCATACTAGTA 57.294 34.615 4.77 4.77 0.00 1.82
2816 3215 7.603180 TCCTTAATCACATCTGCATACTAGT 57.397 36.000 0.00 0.00 0.00 2.57
2817 3216 8.893219 TTTCCTTAATCACATCTGCATACTAG 57.107 34.615 0.00 0.00 0.00 2.57
2818 3217 8.704668 TCTTTCCTTAATCACATCTGCATACTA 58.295 33.333 0.00 0.00 0.00 1.82
2819 3218 7.568349 TCTTTCCTTAATCACATCTGCATACT 58.432 34.615 0.00 0.00 0.00 2.12
2820 3219 7.792374 TCTTTCCTTAATCACATCTGCATAC 57.208 36.000 0.00 0.00 0.00 2.39
2821 3220 8.049117 ACTTCTTTCCTTAATCACATCTGCATA 58.951 33.333 0.00 0.00 0.00 3.14
2822 3221 6.888632 ACTTCTTTCCTTAATCACATCTGCAT 59.111 34.615 0.00 0.00 0.00 3.96
2823 3222 6.240894 ACTTCTTTCCTTAATCACATCTGCA 58.759 36.000 0.00 0.00 0.00 4.41
2824 3223 6.372659 TGACTTCTTTCCTTAATCACATCTGC 59.627 38.462 0.00 0.00 0.00 4.26
2825 3224 7.148340 GGTGACTTCTTTCCTTAATCACATCTG 60.148 40.741 0.00 0.00 37.34 2.90
2826 3225 6.881602 GGTGACTTCTTTCCTTAATCACATCT 59.118 38.462 0.00 0.00 37.34 2.90
2827 3226 6.881602 AGGTGACTTCTTTCCTTAATCACATC 59.118 38.462 0.00 0.00 37.44 3.06
2831 3230 5.003804 GCAGGTGACTTCTTTCCTTAATCA 58.996 41.667 0.00 0.00 40.21 2.57
2888 3287 2.778299 TGCATGACACAAGGTACCTTC 58.222 47.619 24.73 13.99 33.42 3.46
2940 3350 4.062490 ACAGATACAAGTAGGACCAGGT 57.938 45.455 0.00 0.00 0.00 4.00
2994 3404 6.761242 CCTATGATGTTGTCCGAGTATTTTCA 59.239 38.462 0.00 0.00 0.00 2.69
2995 3405 6.202954 CCCTATGATGTTGTCCGAGTATTTTC 59.797 42.308 0.00 0.00 0.00 2.29
3004 3417 5.611374 ACTAAATCCCTATGATGTTGTCCG 58.389 41.667 0.00 0.00 32.68 4.79
3055 3468 3.057596 ACAAATGTTATCCAACGCACAGG 60.058 43.478 0.00 0.00 37.48 4.00
3062 3475 7.826690 ACAAGTATGGACAAATGTTATCCAAC 58.173 34.615 0.00 0.00 45.47 3.77
3107 3521 3.841643 CACCATCAGCAATTTCCAGTTC 58.158 45.455 0.00 0.00 0.00 3.01
3126 3540 1.067142 TCAAGTATCGGTCACCTGCAC 60.067 52.381 0.00 0.00 0.00 4.57
3163 3577 4.496840 GGAACAACCGTAACTTCTGGTTTG 60.497 45.833 0.00 0.00 43.23 2.93
3226 3640 1.303236 CACGACATCCCAAAGCCCA 60.303 57.895 0.00 0.00 0.00 5.36
3307 3721 0.662077 CCGACGACGATGTTGTGACA 60.662 55.000 9.28 0.00 42.66 3.58
3325 3739 1.072965 GTGGATCCATCACCTCCATCC 59.927 57.143 19.62 0.00 40.96 3.51
3367 3781 1.655329 CCTCGTCAGATAGTCCGCC 59.345 63.158 0.00 0.00 0.00 6.13
3427 3841 0.108019 GGGGTTTCAAGTCGACCACT 59.892 55.000 13.01 0.00 34.00 4.00
3448 3862 7.953493 TGTTAGGAATTATTCTTGGGTTTCCTT 59.047 33.333 7.28 0.00 42.17 3.36
3485 3899 4.744795 AGAAGACCAACTGCTAGTATGG 57.255 45.455 0.00 0.00 31.63 2.74
3605 4019 7.509546 ACCATATGAACGGAAAACAGAGATAT 58.490 34.615 3.65 0.00 0.00 1.63
3610 4024 4.900684 TGACCATATGAACGGAAAACAGA 58.099 39.130 3.65 0.00 0.00 3.41
3619 4034 6.128035 TGGAGAATGTTTTGACCATATGAACG 60.128 38.462 3.65 0.00 0.00 3.95
3631 4046 1.200020 GACCGGCTGGAGAATGTTTTG 59.800 52.381 21.41 0.00 39.21 2.44
3632 4047 1.202879 TGACCGGCTGGAGAATGTTTT 60.203 47.619 21.41 0.00 39.21 2.43
3636 4051 1.755179 AATTGACCGGCTGGAGAATG 58.245 50.000 21.41 0.00 39.21 2.67
3646 4061 1.470098 CTTGAGGCTGAAATTGACCGG 59.530 52.381 0.00 0.00 0.00 5.28
3653 4068 0.324091 CCAGGGCTTGAGGCTGAAAT 60.324 55.000 0.00 0.00 41.46 2.17
3663 4078 2.678934 ACAGCATGCCAGGGCTTG 60.679 61.111 15.66 18.83 45.38 4.01
3677 4092 0.532862 ACTGACGGCAAGGAACACAG 60.533 55.000 0.00 0.00 0.00 3.66
3683 4098 0.317160 CTGTACACTGACGGCAAGGA 59.683 55.000 0.00 0.00 0.00 3.36
3740 4157 8.021396 GGTGACAGAAACATGTTAAATCTTACC 58.979 37.037 12.39 13.86 32.25 2.85
3903 4320 8.854614 ATAGGATGCCATATTAAGAGTGTTTC 57.145 34.615 0.00 0.00 0.00 2.78
3954 4371 1.693627 ACCTCGCTCTAGGGTGTATG 58.306 55.000 2.44 0.00 41.32 2.39
3973 4390 1.601419 CCTTGGGCGAACGAGGAGTA 61.601 60.000 7.15 0.00 43.58 2.59
4086 4503 1.067635 GCAAAGTCGATGCCCAACATT 60.068 47.619 0.00 0.00 39.84 2.71
4092 4509 3.813596 ATCGCAAAGTCGATGCCC 58.186 55.556 4.00 0.00 46.18 5.36
4351 4796 1.065109 AAAACTGTTCGCCGTTGGC 59.935 52.632 0.00 0.00 46.75 4.52
4352 4797 0.378962 TCAAAACTGTTCGCCGTTGG 59.621 50.000 0.00 0.00 0.00 3.77
4353 4798 2.399396 ATCAAAACTGTTCGCCGTTG 57.601 45.000 0.00 0.00 0.00 4.10
4354 4799 3.312973 TGTAATCAAAACTGTTCGCCGTT 59.687 39.130 0.00 0.00 0.00 4.44
4355 4800 2.873472 TGTAATCAAAACTGTTCGCCGT 59.127 40.909 0.00 0.00 0.00 5.68
4356 4801 3.223157 GTGTAATCAAAACTGTTCGCCG 58.777 45.455 0.00 0.00 0.00 6.46
4357 4802 3.561503 GGTGTAATCAAAACTGTTCGCC 58.438 45.455 0.00 0.00 0.00 5.54
4358 4803 3.059461 TCGGTGTAATCAAAACTGTTCGC 60.059 43.478 0.00 0.00 0.00 4.70
4359 4804 4.718858 TCGGTGTAATCAAAACTGTTCG 57.281 40.909 0.00 0.00 0.00 3.95
4360 4805 6.664515 TGAATCGGTGTAATCAAAACTGTTC 58.335 36.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.