Multiple sequence alignment - TraesCS3D01G122300

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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 TraesCS3D01G122300 chr3D 100.000 5224 0 0 4387 9610 79638794 79633571 0.000000e+00 9648
1 TraesCS3D01G122300 chr3D 100.000 4080 0 0 1 4080 79643180 79639101 0.000000e+00 7535
2 TraesCS3D01G122300 chr3B 95.864 4110 118 29 1 4080 126014010 126009923 0.000000e+00 6601
3 TraesCS3D01G122300 chr3B 97.001 1667 28 6 6149 7815 126007688 126006044 0.000000e+00 2782
4 TraesCS3D01G122300 chr3B 88.485 1841 120 44 7814 9610 126005885 126004093 0.000000e+00 2141
5 TraesCS3D01G122300 chr3B 97.892 854 18 0 5139 5992 126008969 126008116 0.000000e+00 1478
6 TraesCS3D01G122300 chr3B 96.748 738 15 3 4402 5138 126009739 126009010 0.000000e+00 1221
7 TraesCS3D01G122300 chr3B 89.195 435 41 4 3592 4023 279754616 279754185 1.100000e-148 538
8 TraesCS3D01G122300 chr3B 94.697 132 4 1 6036 6167 126008115 126007987 1.640000e-47 202
9 TraesCS3D01G122300 chr3B 90.345 145 9 4 2953 3095 397324953 397325094 1.650000e-42 185
10 TraesCS3D01G122300 chr3A 98.132 2998 51 2 5139 8132 93902624 93899628 0.000000e+00 5221
11 TraesCS3D01G122300 chr3A 95.141 2161 85 10 647 2794 93907432 93905279 0.000000e+00 3391
12 TraesCS3D01G122300 chr3A 94.051 1496 60 18 8131 9610 93899368 93897886 0.000000e+00 2242
13 TraesCS3D01G122300 chr3A 97.481 1310 16 9 2785 4080 93904830 93903524 0.000000e+00 2220
14 TraesCS3D01G122300 chr3A 95.957 742 12 6 4400 5138 93903507 93902781 0.000000e+00 1188
15 TraesCS3D01G122300 chr3A 94.753 648 31 3 10 657 93909516 93908872 0.000000e+00 1005
16 TraesCS3D01G122300 chr5A 81.407 1350 194 37 6666 7997 44267971 44266661 0.000000e+00 1050
17 TraesCS3D01G122300 chr5A 85.007 747 94 14 5154 5890 44269239 44268501 0.000000e+00 743
18 TraesCS3D01G122300 chr5A 89.423 208 22 0 4398 4605 44270234 44270027 7.400000e-66 263
19 TraesCS3D01G122300 chr5B 81.005 1353 195 40 6666 7997 57964056 57962745 0.000000e+00 1018
20 TraesCS3D01G122300 chr5B 85.067 750 94 13 5154 5886 57965289 57964541 0.000000e+00 749
21 TraesCS3D01G122300 chr5B 88.995 209 23 0 4397 4605 57966298 57966090 9.570000e-65 259
22 TraesCS3D01G122300 chr5D 80.471 1316 210 35 6697 7997 55416737 55415454 0.000000e+00 963
23 TraesCS3D01G122300 chr5D 84.348 575 71 14 5154 5718 55528548 55527983 6.560000e-151 545
24 TraesCS3D01G122300 chr5D 75.963 753 134 26 1482 2210 55533066 55532337 2.570000e-90 344
25 TraesCS3D01G122300 chr5D 78.571 294 49 11 3183 3474 55531529 55531248 2.130000e-41 182
26 TraesCS3D01G122300 chr5D 88.652 141 12 4 2863 3001 55531858 55531720 1.660000e-37 169
27 TraesCS3D01G122300 chr4B 88.764 445 43 5 3592 4033 338505154 338505594 1.100000e-148 538
28 TraesCS3D01G122300 chr4B 78.673 211 28 6 4647 4856 281898532 281898338 3.640000e-24 124
29 TraesCS3D01G122300 chr7B 87.865 445 47 4 3592 4033 195989820 195990260 5.150000e-142 516
30 TraesCS3D01G122300 chr2B 75.163 1377 191 84 1490 2763 103415354 103414026 8.610000e-140 508
31 TraesCS3D01G122300 chr4A 87.844 436 47 3 3592 4024 671921582 671922014 3.100000e-139 507
32 TraesCS3D01G122300 chr1B 92.118 203 11 4 4437 4636 363223719 363223919 2.040000e-71 281
33 TraesCS3D01G122300 chr6A 89.041 146 11 4 2953 3096 197863442 197863584 9.920000e-40 176
34 TraesCS3D01G122300 chr1A 81.858 226 24 6 4647 4871 62478729 62478938 3.570000e-39 174
35 TraesCS3D01G122300 chr6B 78.673 211 28 6 4647 4856 319826135 319825941 3.640000e-24 124


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 TraesCS3D01G122300 chr3D 79633571 79643180 9609 True 8591.500000 9648 100.000000 1 9610 2 chr3D.!!$R1 9609
1 TraesCS3D01G122300 chr3B 126004093 126014010 9917 True 2404.166667 6601 95.114500 1 9610 6 chr3B.!!$R2 9609
2 TraesCS3D01G122300 chr3A 93897886 93909516 11630 True 2544.500000 5221 95.919167 10 9610 6 chr3A.!!$R1 9600
3 TraesCS3D01G122300 chr5A 44266661 44270234 3573 True 685.333333 1050 85.279000 4398 7997 3 chr5A.!!$R1 3599
4 TraesCS3D01G122300 chr5B 57962745 57966298 3553 True 675.333333 1018 85.022333 4397 7997 3 chr5B.!!$R1 3600
5 TraesCS3D01G122300 chr5D 55415454 55416737 1283 True 963.000000 963 80.471000 6697 7997 1 chr5D.!!$R1 1300
6 TraesCS3D01G122300 chr5D 55527983 55533066 5083 True 310.000000 545 81.883500 1482 5718 4 chr5D.!!$R2 4236
7 TraesCS3D01G122300 chr2B 103414026 103415354 1328 True 508.000000 508 75.163000 1490 2763 1 chr2B.!!$R1 1273

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
783 2240 0.110104 CCATTCAGGGAGAGGCATCC 59.890 60.000 0.00 0.32 38.76 3.51 F
1765 3247 0.617820 TTGACCCTGAGACCCCTAGC 60.618 60.000 0.00 0.00 0.00 3.42 F
2274 3792 2.932614 CCTGGTCATTCACGAGACATTC 59.067 50.000 0.00 0.00 36.50 2.67 F
2802 4871 3.848272 AAATCTTGTATGGTGTTGCCG 57.152 42.857 0.00 0.00 41.21 5.69 F
3586 6736 4.946160 TGATTTGGTCCTTTACAGGGAT 57.054 40.909 0.00 0.00 41.25 3.85 F
5324 8960 2.012673 GCAGGTCTTGATGCTGTAAGG 58.987 52.381 0.00 0.00 39.38 2.69 F
5556 9208 2.163613 TGCGTGGTATGTGACACTAGAG 59.836 50.000 7.20 0.00 35.51 2.43 F
6775 10822 1.072116 CACATGGCCGCAAAATGTCG 61.072 55.000 2.75 0.00 32.27 4.35 F
8404 12880 1.200716 TCCTCGTGTATGGTTGTCGTC 59.799 52.381 0.00 0.00 0.00 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 3463 0.179113 AAGGTGGTTTTGTGCTTGCG 60.179 50.000 0.00 0.00 0.00 4.85 R
3586 6736 1.074084 TCCCAATTCACAAGGCGGTAA 59.926 47.619 0.00 0.00 0.00 2.85 R
3989 7143 2.092968 GGGATCCACTAACACAGCATCA 60.093 50.000 15.23 0.00 0.00 3.07 R
4395 7549 2.192624 GCAAAACGAGCACACAACAAT 58.807 42.857 0.00 0.00 0.00 2.71 R
5396 9039 0.535780 TCTGCAAGAGGTGGCACTTG 60.536 55.000 18.45 14.93 38.67 3.16 R
6383 10402 1.617322 AAAAGGGCGGAAGTTTCTCC 58.383 50.000 0.00 0.00 0.00 3.71 R
7495 11546 2.025510 AGAATCTTTGGGCTGAGGAAGG 60.026 50.000 0.00 0.00 0.00 3.46 R
8409 12888 0.389426 ACGTGCGATAACACTGGGAC 60.389 55.000 0.00 0.00 38.45 4.46 R
9510 14035 2.981350 GCGGTCCTGGCGGAAAAA 60.981 61.111 0.00 0.00 42.08 1.94 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
166 167 6.380995 GTGTCAGAACATCAAATTGCACATA 58.619 36.000 0.00 0.00 37.81 2.29
207 208 1.847506 TGCTCCATGGTCAGGGTGT 60.848 57.895 12.58 0.00 33.26 4.16
219 220 0.944386 CAGGGTGTTTGACCTTCACG 59.056 55.000 0.00 0.00 45.33 4.35
415 416 2.158813 TGTAGCCATCGATCTTTTCCCC 60.159 50.000 0.00 0.00 0.00 4.81
416 417 0.918983 AGCCATCGATCTTTTCCCCA 59.081 50.000 0.00 0.00 0.00 4.96
422 423 0.543749 CGATCTTTTCCCCAGCCTCT 59.456 55.000 0.00 0.00 0.00 3.69
430 431 4.821589 CCCAGCCTCTTCCGCGAC 62.822 72.222 8.23 0.00 0.00 5.19
481 482 1.452108 GGCATCCTTGGTTCTCGGG 60.452 63.158 0.00 0.00 0.00 5.14
574 575 4.302455 GGATGTGATCTCAACCGAGTATG 58.698 47.826 8.14 0.00 40.44 2.39
615 616 6.403964 GGAGTTTAGGTATTAGGGTTTTTGCG 60.404 42.308 0.00 0.00 0.00 4.85
675 2126 1.628846 GGCTCAAGGAGGGAGTTGTTA 59.371 52.381 0.00 0.00 34.83 2.41
703 2159 1.437397 ACTCAAGGGGGAACGGTTTA 58.563 50.000 0.00 0.00 0.00 2.01
704 2160 1.990327 ACTCAAGGGGGAACGGTTTAT 59.010 47.619 0.00 0.00 0.00 1.40
782 2239 3.721793 CCATTCAGGGAGAGGCATC 57.278 57.895 0.00 0.00 0.00 3.91
783 2240 0.110104 CCATTCAGGGAGAGGCATCC 59.890 60.000 0.00 0.32 38.76 3.51
844 2303 2.564771 CCACATGTCAGTGTCACACTT 58.435 47.619 8.05 0.00 42.59 3.16
958 2417 2.664851 TCCGCAACGTCCAAGCAG 60.665 61.111 0.00 0.00 0.00 4.24
1023 2482 4.446413 AAGGTAACCCCGCGCTCG 62.446 66.667 5.56 0.00 38.74 5.03
1167 2626 1.225745 CGCGACGGCAGTTCAATTC 60.226 57.895 0.00 0.00 39.92 2.17
1311 2771 1.440145 GAAGGTATGCTTGGCCGAGC 61.440 60.000 34.66 34.66 43.00 5.03
1367 2827 2.025921 GTGTTGTTGTTCGTTTTGACGC 59.974 45.455 0.00 0.00 0.00 5.19
1411 2871 1.175983 TCCCGAATTGGTTGTGTGGC 61.176 55.000 0.00 0.00 35.15 5.01
1454 2914 5.607477 TGTTAGAAACTACAGGTTCAGTGG 58.393 41.667 9.57 0.00 37.12 4.00
1459 2919 4.618920 AACTACAGGTTCAGTGGTAAGG 57.381 45.455 0.00 0.00 31.69 2.69
1470 2934 9.239551 AGGTTCAGTGGTAAGGTAAAATTATTC 57.760 33.333 0.00 0.00 0.00 1.75
1506 2970 4.035675 GGAAAAGATCGCTTATGGGTTGAG 59.964 45.833 0.00 0.00 32.98 3.02
1507 2971 3.914426 AAGATCGCTTATGGGTTGAGT 57.086 42.857 0.00 0.00 31.07 3.41
1646 3115 1.168714 GGAGATGGGTTTGTGCTGAC 58.831 55.000 0.00 0.00 0.00 3.51
1666 3143 2.477972 TTCGTCGTCTGCAGGCTCAG 62.478 60.000 17.70 7.09 35.46 3.35
1765 3247 0.617820 TTGACCCTGAGACCCCTAGC 60.618 60.000 0.00 0.00 0.00 3.42
2195 3702 5.297776 GCTTCATATTGGTCATGCACTTACT 59.702 40.000 0.00 0.00 0.00 2.24
2274 3792 2.932614 CCTGGTCATTCACGAGACATTC 59.067 50.000 0.00 0.00 36.50 2.67
2579 4135 5.187381 GGGTTCTAGGCCCAGTTAGTATATC 59.813 48.000 15.60 0.00 45.40 1.63
2582 4138 7.309928 GGTTCTAGGCCCAGTTAGTATATCTTC 60.310 44.444 0.00 0.00 0.00 2.87
2802 4871 3.848272 AAATCTTGTATGGTGTTGCCG 57.152 42.857 0.00 0.00 41.21 5.69
2821 4890 9.163899 TGTTGCCGAATGTAGTTATTTTGTATA 57.836 29.630 0.00 0.00 0.00 1.47
2836 4905 7.944729 ATTTTGTATAGACTTCAACCTGCAT 57.055 32.000 0.00 0.00 0.00 3.96
3030 5101 6.264970 TCATCTTCTCCTGTGTCAGATCATAG 59.735 42.308 0.00 0.00 32.44 2.23
3586 6736 4.946160 TGATTTGGTCCTTTACAGGGAT 57.054 40.909 0.00 0.00 41.25 3.85
3989 7143 5.242838 TGGCCGAAAACTCAAAATAATCTGT 59.757 36.000 0.00 0.00 0.00 3.41
4047 7201 6.330514 TGGGGCTGTCAAGGTATGTTATAATA 59.669 38.462 0.00 0.00 0.00 0.98
4048 7202 7.018149 TGGGGCTGTCAAGGTATGTTATAATAT 59.982 37.037 0.12 0.12 0.00 1.28
4541 7695 3.007182 AGGTGCACAATTTGAAGGAATGG 59.993 43.478 20.43 0.00 0.00 3.16
5324 8960 2.012673 GCAGGTCTTGATGCTGTAAGG 58.987 52.381 0.00 0.00 39.38 2.69
5396 9039 7.104290 ACAGGTATCTTCTTTTGCCTAGTTAC 58.896 38.462 0.00 0.00 0.00 2.50
5556 9208 2.163613 TGCGTGGTATGTGACACTAGAG 59.836 50.000 7.20 0.00 35.51 2.43
5900 9552 4.351192 ACGACACAAATGTTTTTCTCTGC 58.649 39.130 0.00 0.00 39.95 4.26
6219 10238 2.295349 CCATTTGCCTCTACATGCCATC 59.705 50.000 0.00 0.00 0.00 3.51
6383 10402 8.808529 CACTATAAGTTTTCCAGATACTCGTTG 58.191 37.037 0.00 0.00 0.00 4.10
6645 10666 6.368516 TCCGAAACTACTTATTTAACCAACCG 59.631 38.462 0.00 0.00 0.00 4.44
6775 10822 1.072116 CACATGGCCGCAAAATGTCG 61.072 55.000 2.75 0.00 32.27 4.35
6841 10888 4.639310 GGTACGACACTTGAAGATCTCCTA 59.361 45.833 0.00 0.00 0.00 2.94
7172 11223 3.243636 GGGCAAGCTTGGTGATCATTATG 60.244 47.826 27.10 0.00 0.00 1.90
7237 11288 4.202121 TGCAAATGGATACTCTCGGTACTC 60.202 45.833 0.00 0.00 32.72 2.59
7288 11339 5.419542 TCATTAGAAGCATACAAGTTCGCT 58.580 37.500 0.00 0.00 35.90 4.93
7495 11546 1.375268 AGAAGAACTCTGGCAGCGC 60.375 57.895 10.34 0.00 31.12 5.92
7527 11578 4.212004 GCCCAAAGATTCTTGCAGAAAAAC 59.788 41.667 0.00 0.35 37.82 2.43
8246 12722 2.100087 TGACTGTTCGACTGCTGTTGTA 59.900 45.455 10.46 0.00 0.00 2.41
8387 12863 2.696187 GTTCTCTCCCGCTAAAGATCCT 59.304 50.000 0.00 0.00 0.00 3.24
8389 12865 1.268352 CTCTCCCGCTAAAGATCCTCG 59.732 57.143 0.00 0.00 0.00 4.63
8404 12880 1.200716 TCCTCGTGTATGGTTGTCGTC 59.799 52.381 0.00 0.00 0.00 4.20
8409 12888 2.591148 CGTGTATGGTTGTCGTCGTTAG 59.409 50.000 0.00 0.00 0.00 2.34
8415 12894 1.668047 GGTTGTCGTCGTTAGTCCCAG 60.668 57.143 0.00 0.00 0.00 4.45
8419 12898 1.000938 GTCGTCGTTAGTCCCAGTGTT 60.001 52.381 0.00 0.00 0.00 3.32
8420 12899 2.226437 GTCGTCGTTAGTCCCAGTGTTA 59.774 50.000 0.00 0.00 0.00 2.41
8421 12900 3.084039 TCGTCGTTAGTCCCAGTGTTAT 58.916 45.455 0.00 0.00 0.00 1.89
8422 12901 3.127548 TCGTCGTTAGTCCCAGTGTTATC 59.872 47.826 0.00 0.00 0.00 1.75
8423 12902 3.432782 GTCGTTAGTCCCAGTGTTATCG 58.567 50.000 0.00 0.00 0.00 2.92
8425 12904 2.416296 CGTTAGTCCCAGTGTTATCGCA 60.416 50.000 0.00 0.00 0.00 5.10
8426 12905 2.928116 GTTAGTCCCAGTGTTATCGCAC 59.072 50.000 0.00 0.00 39.51 5.34
8432 12911 1.319374 CCAGTGTTATCGCACGTAACG 59.681 52.381 3.90 3.90 43.61 3.18
8628 13111 1.985473 AACTGGCAATGCTTGAGTCA 58.015 45.000 4.82 0.00 0.00 3.41
8646 13129 5.478332 TGAGTCAGCTCTCTGTTTCTATTGA 59.522 40.000 4.26 0.00 42.13 2.57
8647 13130 6.154192 TGAGTCAGCTCTCTGTTTCTATTGAT 59.846 38.462 4.26 0.00 42.13 2.57
8648 13131 6.945218 AGTCAGCTCTCTGTTTCTATTGATT 58.055 36.000 0.00 0.00 41.10 2.57
8753 13237 6.872020 ACAGAAAATTCAAATGGAGCAATGAG 59.128 34.615 0.00 0.00 0.00 2.90
8892 13380 8.441312 AATTTCTGCATTCAATTTGAACTTGT 57.559 26.923 13.80 0.00 39.45 3.16
8894 13382 6.146601 TCTGCATTCAATTTGAACTTGTCA 57.853 33.333 13.80 10.32 39.45 3.58
8895 13383 5.978919 TCTGCATTCAATTTGAACTTGTCAC 59.021 36.000 13.80 0.00 39.45 3.67
8898 13408 6.256104 TGCATTCAATTTGAACTTGTCACTTG 59.744 34.615 13.80 6.60 39.45 3.16
8935 13445 5.959618 AAGTGTAGAAAGGGCAACAATAC 57.040 39.130 0.00 0.00 39.74 1.89
8937 13447 3.749609 GTGTAGAAAGGGCAACAATACGT 59.250 43.478 0.00 0.00 39.74 3.57
8961 13471 3.302415 GCAGAAACGCAAAACCACATTTC 60.302 43.478 0.00 0.00 0.00 2.17
9021 13535 6.028146 TCATGATTCAATGACAACAAAGGG 57.972 37.500 0.00 0.00 31.58 3.95
9022 13536 4.255833 TGATTCAATGACAACAAAGGGC 57.744 40.909 0.00 0.00 0.00 5.19
9038 13554 3.078891 AGGGCTGCTTCTTAGAAAAGG 57.921 47.619 0.00 0.00 33.22 3.11
9042 13558 4.765339 GGGCTGCTTCTTAGAAAAGGTAAA 59.235 41.667 0.00 0.00 33.22 2.01
9091 13610 7.177392 AGCCACTCTGCTAAAAATAGAACAATT 59.823 33.333 0.00 0.00 40.56 2.32
9141 13660 1.879380 TGCGAGAGGGAAAATGTGTTG 59.121 47.619 0.00 0.00 0.00 3.33
9200 13719 6.531594 AGTCGAAGCCAAAAAGAAAAAGAAAG 59.468 34.615 0.00 0.00 0.00 2.62
9510 14035 7.646884 ACAAAAATGGAGGAGAGAGGATAAAT 58.353 34.615 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.465705 TCGGCATGAGGTGAGATTCC 59.534 55.000 0.00 0.00 0.00 3.01
104 105 1.534595 CTCTGCCTCAAACACTTCAGC 59.465 52.381 0.00 0.00 0.00 4.26
207 208 2.828877 CACCACTACGTGAAGGTCAAA 58.171 47.619 0.00 0.00 35.23 2.69
219 220 0.953960 CCGTTCCCAAGCACCACTAC 60.954 60.000 0.00 0.00 0.00 2.73
246 247 0.609957 CAAGTTGGCCATCCTGCTCA 60.610 55.000 6.09 0.00 0.00 4.26
415 416 4.116328 TCGTCGCGGAAGAGGCTG 62.116 66.667 6.13 0.00 31.53 4.85
416 417 3.816524 CTCGTCGCGGAAGAGGCT 61.817 66.667 6.13 0.00 35.22 4.58
422 423 1.815003 TCGATACCTCGTCGCGGAA 60.815 57.895 8.55 0.00 45.25 4.30
430 431 0.371301 TTGACGTCGTCGATACCTCG 59.629 55.000 19.81 0.00 46.41 4.63
448 449 1.141053 GATGCCTCCGTTGACCCTATT 59.859 52.381 0.00 0.00 0.00 1.73
631 632 6.405842 CCCTTAATTTTACCATTCTCAGCCAC 60.406 42.308 0.00 0.00 0.00 5.01
692 2148 1.552578 AAGCCCAATAAACCGTTCCC 58.447 50.000 0.00 0.00 0.00 3.97
697 2153 3.349022 TGTTCCTAAGCCCAATAAACCG 58.651 45.455 0.00 0.00 0.00 4.44
703 2159 2.171003 GCACTTGTTCCTAAGCCCAAT 58.829 47.619 0.00 0.00 0.00 3.16
704 2160 1.144913 AGCACTTGTTCCTAAGCCCAA 59.855 47.619 0.00 0.00 0.00 4.12
778 2235 3.451894 CTTTGTGGCCCGGGATGC 61.452 66.667 29.31 13.47 0.00 3.91
779 2236 3.451894 GCTTTGTGGCCCGGGATG 61.452 66.667 29.31 6.12 0.00 3.51
783 2240 3.814268 CATCGCTTTGTGGCCCGG 61.814 66.667 0.00 0.00 0.00 5.73
844 2303 1.968493 GATTAGAGGATACCGTGCCCA 59.032 52.381 0.00 0.00 37.17 5.36
981 2440 1.257750 TGGTGAGAGATCGGGTGGTG 61.258 60.000 0.00 0.00 0.00 4.17
1023 2482 2.029666 CCATCGATGGGAGCGGAC 59.970 66.667 32.99 0.00 44.31 4.79
1161 2620 6.538381 TGATAATAAACAGAGCGCAGAATTGA 59.462 34.615 11.47 0.00 0.00 2.57
1167 2626 3.362401 CGCTGATAATAAACAGAGCGCAG 60.362 47.826 11.47 0.64 37.70 5.18
1311 2771 1.396996 CGAAAGCAAGTAATCACGGGG 59.603 52.381 0.00 0.00 0.00 5.73
1367 2827 3.057596 ACTGGTTGTCAATTACCAATGCG 60.058 43.478 0.00 0.00 43.46 4.73
1411 2871 3.442625 ACATCAGCACAATTCACAGATGG 59.557 43.478 0.00 0.00 36.59 3.51
1470 2934 5.907391 GCGATCTTTTCCCATAAACATAACG 59.093 40.000 0.00 0.00 0.00 3.18
1506 2970 2.222027 AGCCTGCAAGTAGAACAACAC 58.778 47.619 0.00 0.00 0.00 3.32
1507 2971 2.638480 AGCCTGCAAGTAGAACAACA 57.362 45.000 0.00 0.00 0.00 3.33
1646 3115 1.803519 GAGCCTGCAGACGACGAAG 60.804 63.158 17.39 0.00 0.00 3.79
1666 3143 0.539986 TAGGTCCATCCGAAGTTGCC 59.460 55.000 0.00 0.00 41.99 4.52
1765 3247 1.009829 CAAGCGATTTCTTCTCCCCG 58.990 55.000 0.00 0.00 0.00 5.73
1966 3463 0.179113 AAGGTGGTTTTGTGCTTGCG 60.179 50.000 0.00 0.00 0.00 4.85
2129 3636 5.954335 GGTGGTAGAACCTGAAATGAAATG 58.046 41.667 0.00 0.00 39.58 2.32
2195 3702 9.337396 CATAAAATTTACACCTCTATAGCCACA 57.663 33.333 0.00 0.00 0.00 4.17
2622 4221 4.525487 ACACGGTAAGAAACATCTGGTCTA 59.475 41.667 0.00 0.00 0.00 2.59
2821 4890 8.486210 TGTAGAATATAATGCAGGTTGAAGTCT 58.514 33.333 0.00 0.00 0.00 3.24
3586 6736 1.074084 TCCCAATTCACAAGGCGGTAA 59.926 47.619 0.00 0.00 0.00 2.85
3989 7143 2.092968 GGGATCCACTAACACAGCATCA 60.093 50.000 15.23 0.00 0.00 3.07
4386 7540 4.554526 CGAGCACACAACAATAAAAGCTGA 60.555 41.667 0.00 0.00 0.00 4.26
4387 7541 3.665409 CGAGCACACAACAATAAAAGCTG 59.335 43.478 0.00 0.00 0.00 4.24
4388 7542 3.315191 ACGAGCACACAACAATAAAAGCT 59.685 39.130 0.00 0.00 0.00 3.74
4389 7543 3.628017 ACGAGCACACAACAATAAAAGC 58.372 40.909 0.00 0.00 0.00 3.51
4390 7544 6.402017 CAAAACGAGCACACAACAATAAAAG 58.598 36.000 0.00 0.00 0.00 2.27
4391 7545 5.220303 GCAAAACGAGCACACAACAATAAAA 60.220 36.000 0.00 0.00 0.00 1.52
4392 7546 4.266502 GCAAAACGAGCACACAACAATAAA 59.733 37.500 0.00 0.00 0.00 1.40
4393 7547 3.794028 GCAAAACGAGCACACAACAATAA 59.206 39.130 0.00 0.00 0.00 1.40
4394 7548 3.181496 TGCAAAACGAGCACACAACAATA 60.181 39.130 0.00 0.00 37.02 1.90
4395 7549 2.192624 GCAAAACGAGCACACAACAAT 58.807 42.857 0.00 0.00 0.00 2.71
4777 8239 5.527214 GGCTAGCAAGTTCCAATTTGTTTTT 59.473 36.000 18.24 0.00 0.00 1.94
4778 8240 5.056480 GGCTAGCAAGTTCCAATTTGTTTT 58.944 37.500 18.24 0.00 0.00 2.43
4779 8241 4.344968 AGGCTAGCAAGTTCCAATTTGTTT 59.655 37.500 18.24 0.00 0.00 2.83
4780 8242 3.897505 AGGCTAGCAAGTTCCAATTTGTT 59.102 39.130 18.24 0.00 0.00 2.83
4781 8243 3.500343 AGGCTAGCAAGTTCCAATTTGT 58.500 40.909 18.24 0.00 0.00 2.83
5129 8609 8.362639 TCCAAAACTCAGAACTACGTACTTAAT 58.637 33.333 0.00 0.00 0.00 1.40
5396 9039 0.535780 TCTGCAAGAGGTGGCACTTG 60.536 55.000 18.45 14.93 38.67 3.16
5556 9208 4.022242 CCCAGATCATTCAATTGCTCATCC 60.022 45.833 0.00 0.00 0.00 3.51
6219 10238 2.554032 GTTCAATCAGGACAACACTGGG 59.446 50.000 0.00 0.00 36.62 4.45
6383 10402 1.617322 AAAAGGGCGGAAGTTTCTCC 58.383 50.000 0.00 0.00 0.00 3.71
6579 10598 4.151883 TCCATCCAGAAAAGAAAAGGGTG 58.848 43.478 0.00 0.00 0.00 4.61
6775 10822 6.371809 TCAACAACATTACCAAGTGACTTC 57.628 37.500 0.00 0.00 0.00 3.01
6841 10888 3.517602 GTTGCCTTCTTCCAAACGTTTT 58.482 40.909 11.66 0.00 0.00 2.43
7172 11223 4.793451 CAACAATGGTTGCTGGTGGAGC 62.793 54.545 0.00 0.00 46.98 4.70
7237 11288 2.821969 AGTCTTGCCAATAGCCTTGTTG 59.178 45.455 0.00 0.00 42.71 3.33
7495 11546 2.025510 AGAATCTTTGGGCTGAGGAAGG 60.026 50.000 0.00 0.00 0.00 3.46
7613 11664 6.677781 TTCCACTAAGAAAAGGATATTGCG 57.322 37.500 0.00 0.00 0.00 4.85
8158 12634 7.358600 CCAACATCAAATCAGTGTTTTTCATCG 60.359 37.037 0.00 0.00 34.09 3.84
8246 12722 6.295719 AGGTATACGGACAGATCTTTGTTT 57.704 37.500 0.00 0.00 0.00 2.83
8387 12863 0.592637 ACGACGACAACCATACACGA 59.407 50.000 0.00 0.00 0.00 4.35
8389 12865 3.568538 ACTAACGACGACAACCATACAC 58.431 45.455 0.00 0.00 0.00 2.90
8404 12880 2.190981 GCGATAACACTGGGACTAACG 58.809 52.381 0.00 0.00 0.00 3.18
8409 12888 0.389426 ACGTGCGATAACACTGGGAC 60.389 55.000 0.00 0.00 38.45 4.46
8425 12904 4.448732 GGATAACAAGAAACCACGTTACGT 59.551 41.667 3.95 3.95 42.36 3.57
8426 12905 4.448395 TGGATAACAAGAAACCACGTTACG 59.552 41.667 2.19 2.19 0.00 3.18
8432 12911 3.758300 CGCATGGATAACAAGAAACCAC 58.242 45.455 0.00 0.00 33.38 4.16
8628 13111 7.170965 TCCAAAATCAATAGAAACAGAGAGCT 58.829 34.615 0.00 0.00 0.00 4.09
8646 13129 8.462589 ACAAAAATGCCATTAGTTTCCAAAAT 57.537 26.923 0.00 0.00 0.00 1.82
8647 13130 7.872113 ACAAAAATGCCATTAGTTTCCAAAA 57.128 28.000 0.00 0.00 0.00 2.44
8648 13131 7.872113 AACAAAAATGCCATTAGTTTCCAAA 57.128 28.000 0.00 0.00 0.00 3.28
8708 13191 3.501828 TGTAAATGTGATCACAGCACCAC 59.498 43.478 30.63 22.18 45.48 4.16
8711 13194 5.611796 TTCTGTAAATGTGATCACAGCAC 57.388 39.130 30.63 25.40 45.48 4.40
8753 13237 3.319122 GGCATATGTGGGAAATTGGAGTC 59.681 47.826 4.29 0.00 0.00 3.36
8801 13285 3.381045 GTCAATTGACACTGACACTCGA 58.619 45.455 29.43 0.00 44.18 4.04
8869 13357 7.010367 GTGACAAGTTCAAATTGAATGCAGAAA 59.990 33.333 11.87 0.00 38.79 2.52
8892 13380 5.013704 ACTTTCCACCCATGTATACAAGTGA 59.986 40.000 24.56 13.95 31.32 3.41
8894 13382 5.222048 ACACTTTCCACCCATGTATACAAGT 60.222 40.000 10.14 5.25 0.00 3.16
8895 13383 5.253330 ACACTTTCCACCCATGTATACAAG 58.747 41.667 10.14 5.28 0.00 3.16
8898 13408 6.229936 TCTACACTTTCCACCCATGTATAC 57.770 41.667 0.00 0.00 0.00 1.47
8935 13445 1.003331 TGGTTTTGCGTTTCTGCTACG 60.003 47.619 0.00 0.00 41.71 3.51
8937 13447 2.017782 TGTGGTTTTGCGTTTCTGCTA 58.982 42.857 0.00 0.00 35.36 3.49
8976 13486 8.917088 CATGACCATTTAAGGACATAAATTCCT 58.083 33.333 0.00 0.00 46.13 3.36
8977 13487 8.912988 TCATGACCATTTAAGGACATAAATTCC 58.087 33.333 0.00 0.00 41.08 3.01
8984 13494 7.959658 TTGAATCATGACCATTTAAGGACAT 57.040 32.000 0.00 0.00 43.22 3.06
8988 13498 7.774134 TGTCATTGAATCATGACCATTTAAGG 58.226 34.615 17.00 0.00 44.73 2.69
8996 13510 5.865552 CCTTTGTTGTCATTGAATCATGACC 59.134 40.000 17.00 0.00 44.73 4.02
8997 13511 5.865552 CCCTTTGTTGTCATTGAATCATGAC 59.134 40.000 14.52 14.52 45.35 3.06
9014 13528 3.508845 TTCTAAGAAGCAGCCCTTTGT 57.491 42.857 3.29 0.00 32.78 2.83
9015 13529 4.321527 CCTTTTCTAAGAAGCAGCCCTTTG 60.322 45.833 3.29 2.47 32.78 2.77
9017 13531 3.181428 ACCTTTTCTAAGAAGCAGCCCTT 60.181 43.478 3.47 3.47 36.19 3.95
9019 13533 2.796557 ACCTTTTCTAAGAAGCAGCCC 58.203 47.619 0.00 0.00 32.92 5.19
9020 13534 5.240844 TGTTTACCTTTTCTAAGAAGCAGCC 59.759 40.000 0.00 0.00 32.92 4.85
9021 13535 6.313744 TGTTTACCTTTTCTAAGAAGCAGC 57.686 37.500 0.00 0.00 32.92 5.25
9022 13536 9.750125 AAATTGTTTACCTTTTCTAAGAAGCAG 57.250 29.630 0.00 0.00 32.92 4.24
9067 13586 7.274250 GCAATTGTTCTATTTTTAGCAGAGTGG 59.726 37.037 7.40 0.00 0.00 4.00
9141 13660 0.038892 CAGACAAATGGCCAGTGCAC 60.039 55.000 13.05 9.40 40.13 4.57
9510 14035 2.981350 GCGGTCCTGGCGGAAAAA 60.981 61.111 0.00 0.00 42.08 1.94


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

AutoCloner maintained by Alex Coulton.