Multiple sequence alignment - TraesCS5D01G106700

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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 TraesCS5D01G106700 chr5D 100.000 7125 0 0 1 7125 120347355 120340231 0.000000e+00 13158.0
1 TraesCS5D01G106700 chr5B 94.441 7159 270 55 45 7125 133600569 133593461 0.000000e+00 10898.0
2 TraesCS5D01G106700 chr5B 89.542 153 14 2 2385 2537 208523451 208523301 7.290000e-45 193.0
3 TraesCS5D01G106700 chr5A 94.577 5182 186 34 1337 6470 130541710 130536576 0.000000e+00 7925.0
4 TraesCS5D01G106700 chr5A 91.439 1355 51 25 27 1340 130543120 130541790 0.000000e+00 1799.0
5 TraesCS5D01G106700 chr5A 96.135 621 20 1 6505 7125 130536577 130535961 0.000000e+00 1011.0
6 TraesCS5D01G106700 chr2B 87.500 192 10 3 1339 1520 615943239 615943052 7.240000e-50 209.0
7 TraesCS5D01G106700 chr7D 90.968 155 11 3 2385 2537 152649421 152649268 9.370000e-49 206.0
8 TraesCS5D01G106700 chr7D 90.972 144 12 1 2394 2537 442281462 442281320 7.290000e-45 193.0
9 TraesCS5D01G106700 chr7A 90.909 154 13 1 2385 2537 579808527 579808374 9.370000e-49 206.0
10 TraesCS5D01G106700 chr7A 89.677 155 13 3 2385 2538 512336368 512336520 2.030000e-45 195.0
11 TraesCS5D01G106700 chr7A 91.667 48 2 2 5812 5858 25522301 25522255 1.660000e-06 65.8
12 TraesCS5D01G106700 chr7A 91.667 48 2 2 5812 5858 25545313 25545267 1.660000e-06 65.8
13 TraesCS5D01G106700 chr7A 92.857 42 2 1 5814 5854 31860285 31860326 7.720000e-05 60.2
14 TraesCS5D01G106700 chrUn 86.979 192 11 3 1339 1520 86509210 86509397 3.370000e-48 204.0
15 TraesCS5D01G106700 chrUn 86.979 192 11 3 1339 1520 260202925 260203112 3.370000e-48 204.0
16 TraesCS5D01G106700 chrUn 86.979 192 11 3 1339 1520 270908420 270908607 3.370000e-48 204.0
17 TraesCS5D01G106700 chrUn 86.979 192 11 3 1339 1520 282363894 282364081 3.370000e-48 204.0
18 TraesCS5D01G106700 chrUn 86.979 192 11 3 1339 1520 397470670 397470857 3.370000e-48 204.0
19 TraesCS5D01G106700 chrUn 91.579 95 8 0 4375 4469 55797773 55797679 1.610000e-26 132.0
20 TraesCS5D01G106700 chrUn 93.750 48 2 1 5812 5858 119058220 119058267 3.570000e-08 71.3
21 TraesCS5D01G106700 chrUn 92.683 41 2 1 5815 5854 45562710 45562750 2.780000e-04 58.4
22 TraesCS5D01G106700 chr7B 90.968 155 9 5 2385 2537 114501745 114501594 3.370000e-48 204.0
23 TraesCS5D01G106700 chr7B 93.333 45 2 1 5813 5856 747593624 747593668 1.660000e-06 65.8
24 TraesCS5D01G106700 chr6B 86.979 192 11 3 1339 1520 596621125 596620938 3.370000e-48 204.0
25 TraesCS5D01G106700 chr4D 86.979 192 11 3 1339 1520 123424516 123424329 3.370000e-48 204.0
26 TraesCS5D01G106700 chr4D 90.526 95 9 0 4375 4469 138280217 138280123 7.500000e-25 126.0
27 TraesCS5D01G106700 chr3A 86.154 195 12 4 1335 1518 227656350 227656160 5.640000e-46 196.0
28 TraesCS5D01G106700 chr1D 89.542 153 16 0 2385 2537 111003373 111003525 2.030000e-45 195.0
29 TraesCS5D01G106700 chr6A 83.951 162 12 3 1339 1490 608882434 608882591 7.450000e-30 143.0
30 TraesCS5D01G106700 chr4A 88.776 98 11 0 4372 4469 418077448 418077545 3.490000e-23 121.0
31 TraesCS5D01G106700 chr3B 92.857 42 2 1 5815 5855 802705111 802705152 7.720000e-05 60.2
32 TraesCS5D01G106700 chr4B 90.909 44 3 1 5812 5854 616769053 616769096 2.780000e-04 58.4


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 TraesCS5D01G106700 chr5D 120340231 120347355 7124 True 13158.000000 13158 100.000000 1 7125 1 chr5D.!!$R1 7124
1 TraesCS5D01G106700 chr5B 133593461 133600569 7108 True 10898.000000 10898 94.441000 45 7125 1 chr5B.!!$R1 7080
2 TraesCS5D01G106700 chr5A 130535961 130543120 7159 True 3578.333333 7925 94.050333 27 7125 3 chr5A.!!$R1 7098

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
475 508 0.390472 CTTCTCCCTTGGTGAGCGTC 60.390 60.0 0.00 0.0 0.00 5.19 F
1933 2084 0.953727 GCCTGTCAAATGTGAGTGCA 59.046 50.0 0.00 0.0 33.27 4.57 F
2833 2985 0.106708 GCAGTGGACCTGACAACTGA 59.893 55.0 12.00 0.0 44.49 3.41 F
3049 3204 0.247736 TTTGTTTGCCGCAGTTTGGT 59.752 45.0 0.00 0.0 0.00 3.67 F
4556 4718 0.875908 GCAGTGTGCACTTCTCGTGA 60.876 55.0 19.41 0.0 46.81 4.35 F
4985 5179 0.028242 CAGTAGAGCGTGCGTCTAGG 59.972 60.0 0.00 0.0 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2001 2152 2.158971 GCCCTGAAACAAACCAATGTGT 60.159 45.455 0.00 0.0 32.81 3.72 R
2997 3152 0.032017 ATCGGGCAGAGGAGGTTAGT 60.032 55.000 0.00 0.0 0.00 2.24 R
4503 4662 0.039527 AAAATGGGAACGCAACTCGC 60.040 50.000 0.00 0.0 43.23 5.03 R
4901 5095 2.165030 GGGAGCACATTTGTTGAGATGG 59.835 50.000 0.00 0.0 0.00 3.51 R
5649 5852 1.153147 GGGGATCGTCCTTGCCTTC 60.153 63.158 4.41 0.0 36.57 3.46 R
6798 7033 1.221840 CCTGCTGCAAGGTATCGGT 59.778 57.895 3.02 0.0 32.17 4.69 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
76 84 0.865769 GTGTGTTTGGAGCGTGTAGG 59.134 55.000 0.00 0.00 0.00 3.18
165 185 1.680522 GAGATCCTTCCTGCAGGCGA 61.681 60.000 28.91 21.64 33.35 5.54
166 186 1.227497 GATCCTTCCTGCAGGCGAG 60.227 63.158 28.91 24.93 33.35 5.03
167 187 2.657102 GATCCTTCCTGCAGGCGAGG 62.657 65.000 33.09 33.09 38.67 4.63
370 398 2.359107 CATCGCCAGTGCCAGTGT 60.359 61.111 0.00 0.00 0.00 3.55
419 447 1.995376 TTTTGCTTCCTGTTCCTCCC 58.005 50.000 0.00 0.00 0.00 4.30
454 482 1.270518 TGCAGCACTTCTCCTGTTCTC 60.271 52.381 0.00 0.00 0.00 2.87
465 493 1.152271 TCCTGTTCTCCCTTCTCCCTT 59.848 52.381 0.00 0.00 0.00 3.95
475 508 0.390472 CTTCTCCCTTGGTGAGCGTC 60.390 60.000 0.00 0.00 0.00 5.19
489 525 3.467119 CGTCCGTTCGGTTGAGCG 61.467 66.667 11.04 0.00 46.81 5.03
495 531 3.562869 GTTCGGTTGAGCGAATTCG 57.437 52.632 23.34 23.34 43.27 3.34
538 575 5.135191 TCCCTCTCCATCTCTCTTTGATCTA 59.865 44.000 0.00 0.00 0.00 1.98
611 662 1.145738 AGGAATGTGGCTGTTCTTGGT 59.854 47.619 0.00 0.00 0.00 3.67
663 717 5.046014 CCCTTGATTCTTCTTCTCTTCCTGA 60.046 44.000 0.00 0.00 0.00 3.86
710 767 2.961531 TTTTCACCCCATTCCTTCGA 57.038 45.000 0.00 0.00 0.00 3.71
739 796 4.098654 TGTTTTTCTTGCTCGAAATCCCAA 59.901 37.500 2.61 0.00 33.33 4.12
884 941 2.234414 CACTCCACCAAATCCCCATTTG 59.766 50.000 1.16 1.16 46.01 2.32
921 979 4.553323 ACTGATTTCTTGCATTGACTTGC 58.447 39.130 0.00 0.00 43.07 4.01
923 981 3.321396 TGATTTCTTGCATTGACTTGCCA 59.679 39.130 0.00 0.00 42.06 4.92
1066 1124 8.761689 ACACCTCTCATTTTGGCAATTATTAAT 58.238 29.630 0.00 0.00 0.00 1.40
1074 1132 6.729690 TTTGGCAATTATTAATCTCCTGGG 57.270 37.500 0.00 0.00 0.00 4.45
1144 1202 3.627577 CACTGGGTTTGCATATGGTACTC 59.372 47.826 4.56 0.00 0.00 2.59
1166 1224 3.594134 GAGTGATGGTTTCTGGTGAGAG 58.406 50.000 0.00 0.00 0.00 3.20
1209 1270 3.746492 GGACTGTACCATGTTCAGACAAC 59.254 47.826 13.37 0.00 39.66 3.32
1407 1558 4.566759 TGCTTACTTCGAATGAAATCCTCG 59.433 41.667 0.00 0.00 32.66 4.63
1411 1562 3.619038 ACTTCGAATGAAATCCTCGCTTC 59.381 43.478 0.00 0.00 32.66 3.86
1557 1708 7.943079 ATTTGGTGACATGTGATCTAATGAA 57.057 32.000 1.15 0.00 42.32 2.57
1559 1710 7.943079 TTGGTGACATGTGATCTAATGAAAT 57.057 32.000 1.15 0.00 42.32 2.17
1560 1711 7.943079 TGGTGACATGTGATCTAATGAAATT 57.057 32.000 1.15 0.00 36.13 1.82
1627 1778 8.177013 GCAAATTTAAATTTAAGGAGCCACATG 58.823 33.333 22.44 9.98 36.52 3.21
1933 2084 0.953727 GCCTGTCAAATGTGAGTGCA 59.046 50.000 0.00 0.00 33.27 4.57
1952 2103 2.417933 GCATCTGTGCCTGAAGTACTTG 59.582 50.000 14.14 0.00 45.76 3.16
1988 2139 6.630071 AGTTTTGGTATATTTGTGGCACATC 58.370 36.000 22.73 7.84 44.52 3.06
1994 2145 5.536161 GGTATATTTGTGGCACATCTGGATT 59.464 40.000 22.73 5.09 44.52 3.01
2000 2151 4.136796 TGTGGCACATCTGGATTATAAGC 58.863 43.478 17.96 0.00 44.52 3.09
2001 2152 4.136796 GTGGCACATCTGGATTATAAGCA 58.863 43.478 13.86 0.00 44.52 3.91
2212 2363 9.708092 ACAACCTAAACTATGAACTCTTAACTC 57.292 33.333 0.00 0.00 0.00 3.01
2315 2466 2.365293 AGTTTTTGGTGGTGATTCTGGC 59.635 45.455 0.00 0.00 0.00 4.85
2347 2498 6.862209 TGTTGGATGATACAAAGGTAATTGC 58.138 36.000 0.00 0.00 33.52 3.56
2389 2540 5.435707 TGGACTCCCTACTAGGAAATACTCT 59.564 44.000 3.36 0.00 37.67 3.24
2450 2601 8.712363 CAATATGGACTACATACGGAATGAAAG 58.288 37.037 6.98 6.39 44.41 2.62
2547 2699 5.888982 ACGGAGGGAGTATCATGTTATTT 57.111 39.130 0.00 0.00 36.25 1.40
2552 2704 3.502211 GGGAGTATCATGTTATTTGGCGG 59.498 47.826 0.00 0.00 36.25 6.13
2817 2969 1.223417 CTTTGGGCCGCTTTTTGCAG 61.223 55.000 0.00 0.00 43.06 4.41
2833 2985 0.106708 GCAGTGGACCTGACAACTGA 59.893 55.000 12.00 0.00 44.49 3.41
2834 2986 1.475034 GCAGTGGACCTGACAACTGAA 60.475 52.381 12.00 0.00 44.49 3.02
2835 2987 2.213499 CAGTGGACCTGACAACTGAAC 58.787 52.381 3.34 0.00 44.49 3.18
3031 3186 3.199071 TGCCCGATAGATTACACAACCTT 59.801 43.478 0.00 0.00 39.76 3.50
3039 3194 4.944048 AGATTACACAACCTTTGTTTGCC 58.056 39.130 0.00 0.00 43.23 4.52
3049 3204 0.247736 TTTGTTTGCCGCAGTTTGGT 59.752 45.000 0.00 0.00 0.00 3.67
3137 3295 3.548745 AGTATTGAGTGCTATGCTGCA 57.451 42.857 4.13 4.13 41.05 4.41
3217 3375 2.069430 TGGCCACACAGTGACCAGA 61.069 57.895 7.81 0.00 40.94 3.86
3339 3497 8.483758 TCCTTTGAACTATAAGTAAGTCATCCC 58.516 37.037 0.00 0.00 0.00 3.85
3731 3890 7.479980 TGATGCATGTTAATGGTTACTTAAGC 58.520 34.615 2.46 0.00 34.09 3.09
3801 3960 3.531207 CCCATCGCCTCGAGCAGA 61.531 66.667 6.99 8.74 44.04 4.26
3939 4098 2.086094 CTGGTTCATATGTGCACAGCA 58.914 47.619 25.84 15.70 35.60 4.41
4104 4263 7.331193 CGATTACTACAAAGAAAGTAAGCCACT 59.669 37.037 5.27 0.00 40.01 4.00
4171 4330 4.378459 CCGATTGTGTTCTAAGGAAGCAAC 60.378 45.833 0.00 0.00 33.59 4.17
4289 4448 3.369546 AAACCATGTACAAAGTGCAGC 57.630 42.857 0.00 0.00 30.87 5.25
4291 4450 1.881973 ACCATGTACAAAGTGCAGCTG 59.118 47.619 10.11 10.11 30.87 4.24
4293 4452 2.294233 CCATGTACAAAGTGCAGCTGTT 59.706 45.455 16.64 0.00 30.87 3.16
4328 4487 3.585289 TCCACAGGCCAACTAGTTATCAA 59.415 43.478 8.04 0.00 0.00 2.57
4336 4495 9.778741 CAGGCCAACTAGTTATCAAATTATCTA 57.221 33.333 8.04 0.00 0.00 1.98
4503 4662 4.685924 AGCATTTTCTTGTGTCACTTTGG 58.314 39.130 4.27 0.00 0.00 3.28
4545 4704 5.649557 TGAACAAATATTATGGCAGTGTGC 58.350 37.500 0.00 0.00 44.08 4.57
4556 4718 0.875908 GCAGTGTGCACTTCTCGTGA 60.876 55.000 19.41 0.00 46.81 4.35
4558 4720 2.926586 GCAGTGTGCACTTCTCGTGATA 60.927 50.000 19.41 0.00 46.81 2.15
4566 4728 5.232414 GTGCACTTCTCGTGATATAAAGACC 59.768 44.000 10.32 0.00 46.81 3.85
4574 4736 5.345702 TCGTGATATAAAGACCTTCAACGG 58.654 41.667 0.00 0.00 0.00 4.44
4730 4922 6.446318 TCAATTGCCTGTACTGAAACATTTC 58.554 36.000 0.00 0.00 37.69 2.17
4779 4973 4.190001 AGATGCATCACTGAACATGTCTC 58.810 43.478 27.81 0.00 0.00 3.36
4808 5002 6.931838 TCTGTAGGTTGAAGTATTAGTGGTG 58.068 40.000 0.00 0.00 0.00 4.17
4985 5179 0.028242 CAGTAGAGCGTGCGTCTAGG 59.972 60.000 0.00 0.00 0.00 3.02
5146 5343 2.995482 CGTAAGTGACGCGCATCC 59.005 61.111 5.73 0.00 46.27 3.51
5217 5420 1.730501 TCTTGCAGCCGAAAGATCAG 58.269 50.000 0.00 0.00 0.00 2.90
5238 5441 2.204059 AGCAAGAGGACAGGGGCT 60.204 61.111 0.00 0.00 0.00 5.19
5272 5475 0.749454 CATGGCCAGAACTGTAGCCC 60.749 60.000 13.05 5.74 45.14 5.19
5545 5748 1.140652 AGAAGATAGCAGGCTTGGAGC 59.859 52.381 0.00 0.00 41.46 4.70
5580 5783 0.320771 CCAACAGCCTGTCTAACGCT 60.321 55.000 0.00 0.00 0.00 5.07
5649 5852 4.570663 GTCGCGGATGAGACCCGG 62.571 72.222 6.13 0.00 46.55 5.73
5698 5901 6.052405 TGATGATTTTGGCTGCCTTTATTT 57.948 33.333 21.03 0.00 0.00 1.40
5699 5902 7.180322 TGATGATTTTGGCTGCCTTTATTTA 57.820 32.000 21.03 1.46 0.00 1.40
5848 6061 9.807921 AAAAATGTCTTATATTATGGGACGGAT 57.192 29.630 0.00 0.00 0.00 4.18
5863 6077 6.131264 TGGGACGGATGAGTACTTAGAATAA 58.869 40.000 0.00 0.00 0.00 1.40
5953 6169 2.257207 AGAGTCTCCCAAAATCGTCCA 58.743 47.619 0.00 0.00 0.00 4.02
5970 6186 5.120399 TCGTCCAACACTTCATACACTTTT 58.880 37.500 0.00 0.00 0.00 2.27
5999 6215 3.246699 GTGTAGCGAGCTGTAACACAAAA 59.753 43.478 19.04 0.00 40.08 2.44
6022 6238 4.162320 AGAACTCTGTTCCTGAACACTCAA 59.838 41.667 8.58 0.00 45.42 3.02
6061 6281 3.516586 TCAGGTTGAGGTGTTCCATCTA 58.483 45.455 0.00 0.00 35.89 1.98
6094 6314 1.589196 GACGGCGGAAGGAAGATCG 60.589 63.158 13.24 0.00 0.00 3.69
6135 6358 7.509546 CCTCATAATCCTTAGTAGCCAAAAGA 58.490 38.462 0.00 0.00 0.00 2.52
6136 6359 7.993183 CCTCATAATCCTTAGTAGCCAAAAGAA 59.007 37.037 0.00 0.00 0.00 2.52
6137 6360 8.964476 TCATAATCCTTAGTAGCCAAAAGAAG 57.036 34.615 0.00 0.00 0.00 2.85
6257 6480 5.751243 AACAATAGGTTCTGTGTGTGAAC 57.249 39.130 0.00 0.00 42.00 3.18
6287 6510 7.929785 GGTGCTTCATGGATTGATATTTGAAAT 59.070 33.333 0.00 0.00 33.34 2.17
6391 6616 1.805345 CTTGCTTTCTCAGTGAGCTGG 59.195 52.381 15.72 8.24 42.78 4.85
6571 6803 0.398318 AGAAGGTGGGTCAGCAGTTC 59.602 55.000 0.00 0.00 33.95 3.01
6577 6809 0.681733 TGGGTCAGCAGTTCAGTCTC 59.318 55.000 0.00 0.00 0.00 3.36
6667 6899 4.527816 ACAATTGTTATCACAAGCCCACAT 59.472 37.500 4.92 0.00 46.25 3.21
6668 6900 4.989279 ATTGTTATCACAAGCCCACATC 57.011 40.909 0.00 0.00 46.25 3.06
6669 6901 3.431673 TGTTATCACAAGCCCACATCA 57.568 42.857 0.00 0.00 0.00 3.07
6670 6902 3.081061 TGTTATCACAAGCCCACATCAC 58.919 45.455 0.00 0.00 0.00 3.06
6724 6956 4.940046 ACACCATAGATGAAAGTGAAGCAG 59.060 41.667 0.00 0.00 32.76 4.24
6750 6982 4.986034 ACACATTACTTTTCATCGTCGTCA 59.014 37.500 0.00 0.00 0.00 4.35
6753 6985 5.291128 ACATTACTTTTCATCGTCGTCATCC 59.709 40.000 0.00 0.00 0.00 3.51
6771 7003 1.264288 TCCTCGTCGTCATCATCATCG 59.736 52.381 0.00 0.00 0.00 3.84
6798 7033 1.000646 TGGCAAGGCAGCATCATCA 60.001 52.632 0.00 0.00 35.83 3.07
7119 7354 1.674322 TTGGTTGCTAGCTTCGGCC 60.674 57.895 17.23 10.83 43.01 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.583765 CTCTTAAAAATACACTACTACTCCCAC 57.416 37.037 0.00 0.00 0.00 4.61
1 2 8.255905 GCTCTTAAAAATACACTACTACTCCCA 58.744 37.037 0.00 0.00 0.00 4.37
2 3 7.434602 CGCTCTTAAAAATACACTACTACTCCC 59.565 40.741 0.00 0.00 0.00 4.30
3 4 7.043524 GCGCTCTTAAAAATACACTACTACTCC 60.044 40.741 0.00 0.00 0.00 3.85
4 5 7.487189 TGCGCTCTTAAAAATACACTACTACTC 59.513 37.037 9.73 0.00 0.00 2.59
5 6 7.318141 TGCGCTCTTAAAAATACACTACTACT 58.682 34.615 9.73 0.00 0.00 2.57
6 7 7.515957 TGCGCTCTTAAAAATACACTACTAC 57.484 36.000 9.73 0.00 0.00 2.73
7 8 7.816031 ACTTGCGCTCTTAAAAATACACTACTA 59.184 33.333 9.73 0.00 0.00 1.82
8 9 6.649557 ACTTGCGCTCTTAAAAATACACTACT 59.350 34.615 9.73 0.00 0.00 2.57
9 10 6.828672 ACTTGCGCTCTTAAAAATACACTAC 58.171 36.000 9.73 0.00 0.00 2.73
10 11 7.041644 ACAACTTGCGCTCTTAAAAATACACTA 60.042 33.333 9.73 0.00 0.00 2.74
11 12 5.941948 ACTTGCGCTCTTAAAAATACACT 57.058 34.783 9.73 0.00 0.00 3.55
12 13 5.912955 ACAACTTGCGCTCTTAAAAATACAC 59.087 36.000 9.73 0.00 0.00 2.90
13 14 6.067263 ACAACTTGCGCTCTTAAAAATACA 57.933 33.333 9.73 0.00 0.00 2.29
14 15 7.201240 GCTTACAACTTGCGCTCTTAAAAATAC 60.201 37.037 9.73 0.00 0.00 1.89
15 16 6.799925 GCTTACAACTTGCGCTCTTAAAAATA 59.200 34.615 9.73 0.00 0.00 1.40
16 17 5.629435 GCTTACAACTTGCGCTCTTAAAAAT 59.371 36.000 9.73 0.00 0.00 1.82
17 18 4.973663 GCTTACAACTTGCGCTCTTAAAAA 59.026 37.500 9.73 0.00 0.00 1.94
18 19 4.533222 GCTTACAACTTGCGCTCTTAAAA 58.467 39.130 9.73 0.00 0.00 1.52
19 20 3.363575 CGCTTACAACTTGCGCTCTTAAA 60.364 43.478 9.73 0.00 43.08 1.52
20 21 2.156891 CGCTTACAACTTGCGCTCTTAA 59.843 45.455 9.73 0.00 43.08 1.85
21 22 1.724623 CGCTTACAACTTGCGCTCTTA 59.275 47.619 9.73 0.00 43.08 2.10
22 23 0.512952 CGCTTACAACTTGCGCTCTT 59.487 50.000 9.73 0.00 43.08 2.85
23 24 2.153913 CGCTTACAACTTGCGCTCT 58.846 52.632 9.73 0.00 43.08 4.09
24 25 4.725758 CGCTTACAACTTGCGCTC 57.274 55.556 9.73 0.00 43.08 5.03
76 84 0.388391 TTAAATGTTGCGCTGGCTGC 60.388 50.000 9.73 6.26 40.82 5.25
89 97 7.639039 TCGTCCTAAATGCTGCTAATTAAATG 58.361 34.615 0.00 0.00 0.00 2.32
165 185 3.224007 ATGCCCTTTTGGACCGCCT 62.224 57.895 0.00 0.00 44.07 5.52
166 186 2.679996 ATGCCCTTTTGGACCGCC 60.680 61.111 0.00 0.00 44.07 6.13
167 187 2.573340 CATGCCCTTTTGGACCGC 59.427 61.111 0.00 0.00 44.07 5.68
168 188 1.606313 ACCATGCCCTTTTGGACCG 60.606 57.895 0.00 0.00 44.07 4.79
169 189 0.541764 TCACCATGCCCTTTTGGACC 60.542 55.000 0.00 0.00 44.07 4.46
362 384 0.837691 AGGATCCACTGACACTGGCA 60.838 55.000 15.82 0.00 0.00 4.92
370 398 2.800516 GAGCGAGAGGATCCACTGA 58.199 57.895 17.19 0.00 33.66 3.41
403 431 3.068881 CGGGAGGAACAGGAAGCA 58.931 61.111 0.00 0.00 0.00 3.91
419 447 2.580867 GCACGAGCTACCTCTGCG 60.581 66.667 0.00 0.00 34.75 5.18
454 482 1.301293 GCTCACCAAGGGAGAAGGG 59.699 63.158 0.00 0.00 34.24 3.95
465 493 4.351938 CCGAACGGACGCTCACCA 62.352 66.667 7.53 0.00 37.50 4.17
489 525 9.271738 GATTCATCAGAAAAGAAGAACGAATTC 57.728 33.333 0.00 0.00 37.29 2.17
495 531 6.883756 AGAGGGATTCATCAGAAAAGAAGAAC 59.116 38.462 0.00 0.00 37.29 3.01
587 638 1.707427 AGAACAGCCACATTCCTTCCT 59.293 47.619 0.00 0.00 0.00 3.36
622 673 1.202818 AGGGACACCAGCTCTTGTTTC 60.203 52.381 0.00 0.00 40.13 2.78
710 767 7.116805 GGATTTCGAGCAAGAAAAACAAATCAT 59.883 33.333 10.00 0.00 42.52 2.45
739 796 1.340697 GGGGGTAAATTTGCCTCGTCT 60.341 52.381 22.53 0.00 33.74 4.18
921 979 0.982852 TATCCCCTGTCACCTGCTGG 60.983 60.000 8.29 8.29 39.83 4.85
923 981 2.795291 TATATCCCCTGTCACCTGCT 57.205 50.000 0.00 0.00 0.00 4.24
1066 1124 2.103153 ATCGAATAAGGCCCAGGAGA 57.897 50.000 0.00 0.00 0.00 3.71
1074 1132 6.430451 CAATTGGTACTGAATCGAATAAGGC 58.570 40.000 0.00 0.00 0.00 4.35
1144 1202 2.029020 TCTCACCAGAAACCATCACTCG 60.029 50.000 0.00 0.00 0.00 4.18
1166 1224 7.596621 CAGTCCATTAAAAGAAAGAAAGAAGCC 59.403 37.037 0.00 0.00 0.00 4.35
1209 1270 9.027129 CATTTCACAAAATTATATCAGCACTGG 57.973 33.333 0.00 0.00 32.69 4.00
1407 1558 6.441777 CGTTTTCGCTTATGCTTAGTGAAGC 61.442 44.000 2.69 2.69 46.58 3.86
1627 1778 4.334481 AGGCTAACCGCACATTACAAATAC 59.666 41.667 0.00 0.00 42.76 1.89
1754 1905 6.034591 CAGCCATGAAAGATAAAAGAGCAAG 58.965 40.000 0.00 0.00 0.00 4.01
1933 2084 5.423610 AGATACAAGTACTTCAGGCACAGAT 59.576 40.000 4.77 0.00 0.00 2.90
1971 2122 6.639632 AATCCAGATGTGCCACAAATATAC 57.360 37.500 0.00 0.00 0.00 1.47
1988 2139 6.455360 AACCAATGTGTGCTTATAATCCAG 57.545 37.500 0.00 0.00 0.00 3.86
1994 2145 7.043961 TGAAACAAACCAATGTGTGCTTATA 57.956 32.000 0.00 0.00 32.51 0.98
2000 2151 3.456280 CCCTGAAACAAACCAATGTGTG 58.544 45.455 0.00 0.00 35.69 3.82
2001 2152 2.158971 GCCCTGAAACAAACCAATGTGT 60.159 45.455 0.00 0.00 32.81 3.72
2212 2363 2.289882 TGAGGGCTGTGAACTTGATCAG 60.290 50.000 0.00 0.00 0.00 2.90
2264 2415 2.438254 CCTACAATGGCTGCCGCA 60.438 61.111 14.98 0.00 38.10 5.69
2347 2498 7.305474 GGAGTCCATAACAACACATAAAACTG 58.695 38.462 3.60 0.00 0.00 3.16
2444 2595 4.949856 AGTGTGTTTGTTCACTCCTTTCAT 59.050 37.500 0.00 0.00 40.28 2.57
2450 2601 5.124936 ACCTTTTAGTGTGTTTGTTCACTCC 59.875 40.000 1.08 0.00 42.77 3.85
2547 2699 5.703592 GGTATAATCATAATGTCAACCGCCA 59.296 40.000 0.00 0.00 0.00 5.69
2588 2740 5.065731 CCATGTAAGCTTCTCCAGATTCAAC 59.934 44.000 0.00 0.00 31.87 3.18
2687 2839 5.303078 AGTGAGCTACAAGAGGTATACCATG 59.697 44.000 23.87 19.58 35.50 3.66
2817 2969 2.325583 TGTTCAGTTGTCAGGTCCAC 57.674 50.000 0.00 0.00 0.00 4.02
2833 2985 6.343716 TCAAGCCACATTCATGTATTTGTT 57.656 33.333 0.00 0.00 39.39 2.83
2834 2986 5.981088 TCAAGCCACATTCATGTATTTGT 57.019 34.783 0.00 0.00 39.39 2.83
2835 2987 7.933396 TCTATCAAGCCACATTCATGTATTTG 58.067 34.615 0.00 0.00 39.39 2.32
2997 3152 0.032017 ATCGGGCAGAGGAGGTTAGT 60.032 55.000 0.00 0.00 0.00 2.24
2998 3153 1.889829 CTATCGGGCAGAGGAGGTTAG 59.110 57.143 0.00 0.00 0.00 2.34
3031 3186 0.179124 GACCAAACTGCGGCAAACAA 60.179 50.000 3.44 0.00 0.00 2.83
3039 3194 3.666902 CGGTATTGAAAGACCAAACTGCG 60.667 47.826 7.56 0.00 40.26 5.18
3137 3295 9.739276 TCTGTCAGGTCAAATGAATATTTAACT 57.261 29.630 0.00 0.00 34.81 2.24
3339 3497 4.569966 CACAGGATTCTTCGGAATTCAGAG 59.430 45.833 7.93 3.63 43.87 3.35
3731 3890 7.818446 CCATACCATCTGACAAGAAGATAGATG 59.182 40.741 0.00 0.00 42.59 2.90
3801 3960 4.290093 TCCACATAGAGCTCCACTACAAT 58.710 43.478 10.93 0.00 0.00 2.71
3872 4031 6.294361 TGTTAGGCATAAAGTGAGAGCTTA 57.706 37.500 0.00 0.00 0.00 3.09
4104 4263 8.829373 TCATAAGAGAGGCAAGCATATATCTA 57.171 34.615 0.00 0.00 0.00 1.98
4289 4448 6.037172 GCCTGTGGAAGTATTATACACAACAG 59.963 42.308 19.81 19.81 37.03 3.16
4291 4450 5.296035 GGCCTGTGGAAGTATTATACACAAC 59.704 44.000 5.11 3.29 37.03 3.32
4293 4452 4.471747 TGGCCTGTGGAAGTATTATACACA 59.528 41.667 3.32 0.00 35.76 3.72
4350 4509 5.516090 TGAATCGTCTTTTGCTTGGTTAAC 58.484 37.500 0.00 0.00 0.00 2.01
4363 4522 2.496899 AACCCTGCATGAATCGTCTT 57.503 45.000 0.00 0.00 0.00 3.01
4503 4662 0.039527 AAAATGGGAACGCAACTCGC 60.040 50.000 0.00 0.00 43.23 5.03
4512 4671 8.611757 GCCATAATATTTGTTCAAAATGGGAAC 58.388 33.333 19.43 0.00 43.78 3.62
4516 4675 8.605746 CACTGCCATAATATTTGTTCAAAATGG 58.394 33.333 16.21 16.21 36.53 3.16
4556 4718 4.497291 TGCCCGTTGAAGGTCTTTATAT 57.503 40.909 0.00 0.00 0.00 0.86
4558 4720 2.817844 GTTGCCCGTTGAAGGTCTTTAT 59.182 45.455 0.00 0.00 0.00 1.40
4566 4728 3.670627 GCTGATAAAGTTGCCCGTTGAAG 60.671 47.826 0.00 0.00 0.00 3.02
4574 4736 2.989422 ACAACGCTGATAAAGTTGCC 57.011 45.000 7.37 0.00 46.41 4.52
4779 4973 9.234384 CACTAATACTTCAACCTACAGATAACG 57.766 37.037 0.00 0.00 0.00 3.18
4808 5002 2.422276 AAGAATGGTCGTTTTGCAGC 57.578 45.000 0.00 0.00 0.00 5.25
4901 5095 2.165030 GGGAGCACATTTGTTGAGATGG 59.835 50.000 0.00 0.00 0.00 3.51
5217 5420 2.125350 CCTGTCCTCTTGCTCCGC 60.125 66.667 0.00 0.00 0.00 5.54
5238 5441 1.409064 GCCATGTCAGTCCGAGTATCA 59.591 52.381 0.00 0.00 33.17 2.15
5272 5475 5.218139 GTTGTCAGCATTTTCTTCCTTGAG 58.782 41.667 0.00 0.00 0.00 3.02
5420 5623 1.202855 TCTCTGCCTGCTCTTTGCTTT 60.203 47.619 0.00 0.00 43.37 3.51
5545 5748 1.483595 TTGGACTCCTCCTGTGCCAG 61.484 60.000 0.00 0.00 37.48 4.85
5562 5765 3.217242 AGCGTTAGACAGGCTGTTG 57.783 52.632 22.98 10.53 45.17 3.33
5580 5783 2.590291 ACATTGTCGGCGTGCACA 60.590 55.556 18.64 0.25 0.00 4.57
5649 5852 1.153147 GGGGATCGTCCTTGCCTTC 60.153 63.158 4.41 0.00 36.57 3.46
5698 5901 8.868916 GCAAAACAAACTCAGAACAGAAAAATA 58.131 29.630 0.00 0.00 0.00 1.40
5699 5902 7.603784 AGCAAAACAAACTCAGAACAGAAAAAT 59.396 29.630 0.00 0.00 0.00 1.82
5827 6040 6.724441 ACTCATCCGTCCCATAATATAAGACA 59.276 38.462 0.00 0.00 0.00 3.41
5848 6061 7.279313 GCACCGGAATTTTATTCTAAGTACTCA 59.721 37.037 9.46 0.00 0.00 3.41
5934 6150 2.742589 GTTGGACGATTTTGGGAGACTC 59.257 50.000 0.00 0.00 0.00 3.36
5953 6169 8.559536 CACTATGTCAAAAGTGTATGAAGTGTT 58.440 33.333 9.50 0.00 38.62 3.32
5970 6186 2.092323 ACAGCTCGCTACACTATGTCA 58.908 47.619 0.00 0.00 0.00 3.58
5984 6200 5.294552 ACAGAGTTCTTTTGTGTTACAGCTC 59.705 40.000 0.00 0.00 0.00 4.09
6022 6238 7.503566 TCAACCTGATCAAAAACAGAAAGATCT 59.496 33.333 0.00 0.00 36.82 2.75
6094 6314 3.062466 GGCTTCCTTGGCGTTCCC 61.062 66.667 0.00 0.00 0.00 3.97
6135 6358 2.047179 GAACTCGCCCCGCTTCTT 60.047 61.111 0.00 0.00 0.00 2.52
6136 6359 2.660064 ATGAACTCGCCCCGCTTCT 61.660 57.895 0.00 0.00 0.00 2.85
6137 6360 2.125106 ATGAACTCGCCCCGCTTC 60.125 61.111 0.00 0.00 0.00 3.86
6261 6484 6.395426 TCAAATATCAATCCATGAAGCACC 57.605 37.500 0.00 0.00 42.54 5.01
6287 6510 7.116090 GCTCTCGTCGACTATCTACAGTAAATA 59.884 40.741 14.70 0.00 0.00 1.40
6365 6590 6.179040 AGCTCACTGAGAAAGCAAGAAATAT 58.821 36.000 10.45 0.00 38.51 1.28
6366 6591 5.555017 AGCTCACTGAGAAAGCAAGAAATA 58.445 37.500 10.45 0.00 38.51 1.40
6391 6616 5.855045 TCTAGACAGACAAGGGAAGAAAAC 58.145 41.667 0.00 0.00 0.00 2.43
6571 6803 5.300752 AGTTATTTATGGATGCCGAGACTG 58.699 41.667 0.00 0.00 0.00 3.51
6577 6809 8.783093 TCATTTCTAAGTTATTTATGGATGCCG 58.217 33.333 0.00 0.00 0.00 5.69
6668 6900 7.381408 GCATCATTTATTCAATCATGGTGAGTG 59.619 37.037 6.85 1.31 43.13 3.51
6669 6901 7.287005 AGCATCATTTATTCAATCATGGTGAGT 59.713 33.333 6.85 0.00 30.47 3.41
6670 6902 7.658261 AGCATCATTTATTCAATCATGGTGAG 58.342 34.615 6.85 0.00 30.47 3.51
6724 6956 6.360329 ACGACGATGAAAAGTAATGTGTTTC 58.640 36.000 0.00 0.00 32.92 2.78
6750 6982 2.095516 CGATGATGATGACGACGAGGAT 60.096 50.000 0.00 0.00 0.00 3.24
6753 6985 2.302662 GACGATGATGATGACGACGAG 58.697 52.381 0.00 0.00 0.00 4.18
6771 7003 1.364626 CTGCCTTGCCAGATGACGAC 61.365 60.000 0.00 0.00 34.77 4.34
6798 7033 1.221840 CCTGCTGCAAGGTATCGGT 59.778 57.895 3.02 0.00 32.17 4.69


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

AutoCloner maintained by Alex Coulton.