Multiple sequence alignment - TraesCS2D01G123300

Loading Multiple Alignment...

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 TraesCS2D01G123300 chr2D 100.000 4042 0 0 1 4042 72169395 72173436 0.000000e+00 7465.0
1 TraesCS2D01G123300 chr2D 90.299 134 10 1 3869 3999 524087238 524087371 5.370000e-39 172.0
2 TraesCS2D01G123300 chr2B 90.092 1625 120 26 12 1629 108903895 108905485 0.000000e+00 2071.0
3 TraesCS2D01G123300 chr2B 88.339 1415 86 46 2220 3610 108906194 108907553 0.000000e+00 1626.0
4 TraesCS2D01G123300 chr2B 91.414 594 38 7 1628 2219 108905568 108906150 0.000000e+00 802.0
5 TraesCS2D01G123300 chr2B 89.412 340 26 5 408 743 779218251 779218584 1.740000e-113 420.0
6 TraesCS2D01G123300 chr2B 88.529 340 29 5 408 743 270834381 270834714 1.750000e-108 403.0
7 TraesCS2D01G123300 chr2A 94.494 1344 62 6 880 2219 70984217 70985552 0.000000e+00 2061.0
8 TraesCS2D01G123300 chr2A 92.439 1111 51 12 2219 3307 70985756 70986855 0.000000e+00 1555.0
9 TraesCS2D01G123300 chr2A 91.530 673 30 10 3381 4042 70986859 70987515 0.000000e+00 902.0
10 TraesCS2D01G123300 chr2A 89.310 580 40 11 1 564 70983349 70983922 0.000000e+00 708.0
11 TraesCS2D01G123300 chr2A 83.333 78 11 1 3575 3652 729178531 729178606 2.020000e-08 71.3
12 TraesCS2D01G123300 chr5B 89.412 340 26 5 408 743 655868043 655868376 1.740000e-113 420.0
13 TraesCS2D01G123300 chr5B 89.118 340 27 5 408 743 515117705 515117372 8.080000e-112 414.0
14 TraesCS2D01G123300 chr3B 89.118 340 27 5 408 743 706296587 706296254 8.080000e-112 414.0
15 TraesCS2D01G123300 chr3B 88.529 340 29 5 408 743 760865608 760865275 1.750000e-108 403.0
16 TraesCS2D01G123300 chrUn 88.824 340 28 5 408 743 88594941 88595274 3.760000e-110 409.0
17 TraesCS2D01G123300 chrUn 86.705 173 16 5 1623 1789 312812011 312811840 6.900000e-43 185.0
18 TraesCS2D01G123300 chrUn 86.705 173 16 5 1623 1789 397496499 397496328 6.900000e-43 185.0
19 TraesCS2D01G123300 chr1B 88.824 340 28 5 408 743 163907692 163907359 3.760000e-110 409.0
20 TraesCS2D01G123300 chr1B 88.988 336 27 5 412 743 78835045 78834716 1.350000e-109 407.0
21 TraesCS2D01G123300 chr7B 89.691 291 20 3 3719 3999 591294293 591294003 2.970000e-96 363.0
22 TraesCS2D01G123300 chr7B 82.979 94 14 1 3577 3670 120364077 120363986 2.590000e-12 84.2
23 TraesCS2D01G123300 chr6A 87.129 303 20 11 3757 4042 49088070 49087770 3.900000e-85 326.0
24 TraesCS2D01G123300 chr6A 85.000 200 13 6 3509 3700 49088263 49088073 1.920000e-43 187.0
25 TraesCS2D01G123300 chr7A 86.705 173 16 5 1623 1789 628966110 628965939 6.900000e-43 185.0
26 TraesCS2D01G123300 chr7A 80.392 102 12 3 3557 3652 678949339 678949438 2.020000e-08 71.3
27 TraesCS2D01G123300 chr5A 86.705 173 16 5 1623 1789 31626328 31626157 6.900000e-43 185.0
28 TraesCS2D01G123300 chr5A 86.705 173 16 5 1623 1789 31744310 31744139 6.900000e-43 185.0
29 TraesCS2D01G123300 chr5A 86.705 173 16 5 1623 1789 31833519 31833348 6.900000e-43 185.0
30 TraesCS2D01G123300 chr5A 86.705 173 16 5 1623 1789 31933605 31933434 6.900000e-43 185.0
31 TraesCS2D01G123300 chr5D 76.994 326 59 7 3728 4040 424937798 424938120 5.370000e-39 172.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G123300 chr2D 72169395 72173436 4041 False 7465.000000 7465 100.000000 1 4042 1 chr2D.!!$F1 4041
1 TraesCS2D01G123300 chr2B 108903895 108907553 3658 False 1499.666667 2071 89.948333 12 3610 3 chr2B.!!$F3 3598
2 TraesCS2D01G123300 chr2A 70983349 70987515 4166 False 1306.500000 2061 91.943250 1 4042 4 chr2A.!!$F2 4041

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
626 651 0.184451 AGGATGCAGCGATTTGGGAT 59.816 50.0 0.0 0.0 0.00 3.85 F
1118 1178 0.249657 GAGCCTCTGTATTCTGGCCG 60.250 60.0 0.0 0.0 45.94 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1614 0.109342 AGCAACACCTGGGAGACAAG 59.891 55.0 0.00 0.00 0.0 3.16 R
3058 3441 1.269166 CAGATCTGTACGACGTTGGC 58.731 55.0 14.95 0.12 0.0 4.52 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
180 193 2.551355 TTCGTTCTCTCGATCTGCAG 57.449 50.000 7.63 7.63 39.57 4.41
231 244 0.747255 ATCTGTAGCCGATGCGTCTT 59.253 50.000 4.05 0.00 44.33 3.01
238 251 1.736645 CCGATGCGTCTTGTTCGGT 60.737 57.895 4.05 0.00 44.65 4.69
357 380 0.320697 GCCGAGTGTCCCTGTAGTTT 59.679 55.000 0.00 0.00 0.00 2.66
358 381 1.547372 GCCGAGTGTCCCTGTAGTTTA 59.453 52.381 0.00 0.00 0.00 2.01
457 480 5.641209 AGACTGTTCTGTGCATCTCAATTAC 59.359 40.000 0.00 0.00 0.00 1.89
482 505 1.158434 GTTTATTTCGTCCCCGTGCA 58.842 50.000 0.00 0.00 35.01 4.57
491 514 2.032528 CCCCGTGCAGTGTCATGT 59.967 61.111 0.00 0.00 0.00 3.21
529 553 1.238439 CTGTCATGTCCAGCGGTTTT 58.762 50.000 0.00 0.00 0.00 2.43
530 554 0.950836 TGTCATGTCCAGCGGTTTTG 59.049 50.000 0.00 0.00 0.00 2.44
548 572 6.096695 GGTTTTGTTTCTGTTGCTGAACTTA 58.903 36.000 0.00 0.00 32.79 2.24
552 576 9.862371 TTTTGTTTCTGTTGCTGAACTTAAATA 57.138 25.926 0.00 0.00 32.79 1.40
572 596 9.555727 TTAAATAACATTGCTAGGATGGAGTAC 57.444 33.333 0.00 0.00 0.00 2.73
575 599 5.028549 ACATTGCTAGGATGGAGTACAAG 57.971 43.478 0.00 0.00 0.00 3.16
626 651 0.184451 AGGATGCAGCGATTTGGGAT 59.816 50.000 0.00 0.00 0.00 3.85
628 653 1.410153 GGATGCAGCGATTTGGGATTT 59.590 47.619 0.00 0.00 0.00 2.17
685 710 1.202336 GCAGCTGAATGCCATGTTACC 60.202 52.381 20.43 0.00 44.23 2.85
712 771 5.630680 GTCATGTTAGTTTTGTTGCATCCTG 59.369 40.000 0.00 0.00 0.00 3.86
716 775 5.301551 TGTTAGTTTTGTTGCATCCTGATGT 59.698 36.000 8.79 0.00 40.80 3.06
720 779 4.443913 TTTGTTGCATCCTGATGTCATG 57.556 40.909 8.79 0.00 40.80 3.07
731 791 6.801539 TCCTGATGTCATGTTTAGTTGTTC 57.198 37.500 0.00 0.00 0.00 3.18
743 803 7.766219 TGTTTAGTTGTTCTCTGTTACTGAC 57.234 36.000 0.00 0.00 0.00 3.51
769 829 5.611374 TGAGAAATTACATAGCTAGCCCAC 58.389 41.667 12.13 0.00 0.00 4.61
849 909 4.096382 CGAAGCAAGGCCTGTATTATTGTT 59.904 41.667 5.69 0.00 0.00 2.83
852 912 5.505780 AGCAAGGCCTGTATTATTGTTGTA 58.494 37.500 5.69 0.00 0.00 2.41
861 921 9.706691 GCCTGTATTATTGTTGTATCTAGCTTA 57.293 33.333 0.00 0.00 0.00 3.09
874 934 7.500992 TGTATCTAGCTTAAATCTGGAACTGG 58.499 38.462 0.00 0.00 0.00 4.00
875 935 5.359194 TCTAGCTTAAATCTGGAACTGGG 57.641 43.478 0.00 0.00 0.00 4.45
878 938 3.092301 GCTTAAATCTGGAACTGGGCTT 58.908 45.455 0.00 0.00 0.00 4.35
929 989 0.819259 GCTGAAACACTGCTGGGTGA 60.819 55.000 0.00 0.00 40.13 4.02
952 1012 6.209192 TGATTTGCAATGTCCTGTTACTTCAT 59.791 34.615 0.00 0.00 0.00 2.57
1115 1175 4.440880 CTTTGAGAGCCTCTGTATTCTGG 58.559 47.826 0.00 0.00 0.00 3.86
1118 1178 0.249657 GAGCCTCTGTATTCTGGCCG 60.250 60.000 0.00 0.00 45.94 6.13
1124 1184 3.181465 CCTCTGTATTCTGGCCGTGTATT 60.181 47.826 0.00 0.00 0.00 1.89
1131 1191 2.496111 TCTGGCCGTGTATTTTCGTTT 58.504 42.857 0.00 0.00 0.00 3.60
1268 1328 3.262420 CTGCATGTCAACTGGTACCTAC 58.738 50.000 14.36 4.42 0.00 3.18
1274 1334 4.901868 TGTCAACTGGTACCTACATTTCC 58.098 43.478 14.36 0.00 0.00 3.13
1275 1335 3.930848 GTCAACTGGTACCTACATTTCCG 59.069 47.826 14.36 0.00 0.00 4.30
1277 1337 4.040706 TCAACTGGTACCTACATTTCCGTT 59.959 41.667 14.36 0.30 0.00 4.44
1278 1338 4.198028 ACTGGTACCTACATTTCCGTTC 57.802 45.455 14.36 0.00 0.00 3.95
1279 1339 3.055602 ACTGGTACCTACATTTCCGTTCC 60.056 47.826 14.36 0.00 0.00 3.62
1284 1344 2.026542 ACCTACATTTCCGTTCCCCTTC 60.027 50.000 0.00 0.00 0.00 3.46
1288 1348 0.323451 ATTTCCGTTCCCCTTCCAGC 60.323 55.000 0.00 0.00 0.00 4.85
1298 1358 0.250295 CCCTTCCAGCACAGACGAAA 60.250 55.000 0.00 0.00 0.00 3.46
1301 1361 1.466167 CTTCCAGCACAGACGAAATGG 59.534 52.381 0.00 0.00 0.00 3.16
1302 1362 0.684535 TCCAGCACAGACGAAATGGA 59.315 50.000 0.00 0.00 34.54 3.41
1312 1372 3.123621 CAGACGAAATGGACTGTGCTTAC 59.876 47.826 0.00 0.00 0.00 2.34
1318 1378 1.128200 TGGACTGTGCTTACTGGTGT 58.872 50.000 0.00 0.00 0.00 4.16
1320 1380 1.070134 GGACTGTGCTTACTGGTGTGA 59.930 52.381 0.00 0.00 0.00 3.58
1330 1390 4.268884 GCTTACTGGTGTGATCGATTTCTC 59.731 45.833 0.00 0.00 0.00 2.87
1439 1499 0.530870 GCTGGAGCGGATGGTACTTC 60.531 60.000 0.00 0.00 0.00 3.01
1440 1500 0.824109 CTGGAGCGGATGGTACTTCA 59.176 55.000 0.00 0.00 0.00 3.02
1554 1614 2.139118 GCCTCACTGACAGTTCACTTC 58.861 52.381 5.04 0.00 0.00 3.01
1688 1833 5.589855 ACAGTTCATTTGACACTGATCACAA 59.410 36.000 20.04 0.00 37.02 3.33
1752 1897 2.594962 CCGTGCTGTTGTCGTCCAC 61.595 63.158 0.00 0.00 0.00 4.02
1795 1940 4.563374 GCAAGGGTAATGCTTTGGAAACAT 60.563 41.667 0.00 0.00 39.63 2.71
1843 1988 3.188492 TGTGCATGCTTGTTTGTCAAAG 58.812 40.909 20.33 0.00 35.48 2.77
1962 2107 2.979678 ACTAAGTTTGAAGAGCCTGGGA 59.020 45.455 0.00 0.00 0.00 4.37
1985 2130 9.498176 GGGATTGTGAACTTTAGTCTACTTTTA 57.502 33.333 0.00 0.00 0.00 1.52
2003 2148 9.827411 CTACTTTTAGATAAACCTGTTGCTTTC 57.173 33.333 0.00 0.00 0.00 2.62
2004 2149 8.232913 ACTTTTAGATAAACCTGTTGCTTTCA 57.767 30.769 0.00 0.00 0.00 2.69
2005 2150 8.691797 ACTTTTAGATAAACCTGTTGCTTTCAA 58.308 29.630 0.00 0.00 0.00 2.69
2006 2151 9.696917 CTTTTAGATAAACCTGTTGCTTTCAAT 57.303 29.630 0.00 0.00 34.29 2.57
2245 2595 6.676990 ATGATATGCTCAGTATCACCTGAA 57.323 37.500 0.00 0.00 40.78 3.02
2468 2824 7.583762 GCAGTATTGTTTTGCTTCATGTTTTTC 59.416 33.333 0.00 0.00 35.05 2.29
2505 2861 2.731976 GCGTGTTACCTTCACAGAAGAG 59.268 50.000 8.26 1.89 35.79 2.85
2512 2868 6.776116 TGTTACCTTCACAGAAGAGACTCTTA 59.224 38.462 17.71 0.00 36.73 2.10
2599 2955 2.228103 AGAGCATTCAGTTGTGCATGTG 59.772 45.455 0.00 0.00 43.63 3.21
2643 2999 1.673168 CTAGCCAATCTTCCAGTGCC 58.327 55.000 0.00 0.00 0.00 5.01
2665 3021 5.819901 GCCTGCTTGTCTATCTGTAAATTCT 59.180 40.000 0.00 0.00 0.00 2.40
2714 3093 5.682659 AGCTGCTCATTCTATTCAGAACAT 58.317 37.500 0.00 0.00 43.50 2.71
2801 3182 2.957402 TTTCAGGTGGACATGAGCTT 57.043 45.000 0.00 0.00 37.97 3.74
2891 3272 3.650647 TGGTTGCTCCAATCTGGTC 57.349 52.632 0.00 0.00 44.12 4.02
2912 3293 5.338463 GGTCCTAGTTGCCTATCTGTTTTCT 60.338 44.000 0.00 0.00 0.00 2.52
3052 3435 2.968574 TCCAGGGCTAAGATGTCATCTC 59.031 50.000 15.75 3.82 39.08 2.75
3054 3437 2.702478 CAGGGCTAAGATGTCATCTCCA 59.298 50.000 15.75 6.39 39.08 3.86
3058 3441 2.546795 GCTAAGATGTCATCTCCACCGG 60.547 54.545 15.75 0.00 39.08 5.28
3164 3547 1.507562 TAGTGTGCACCATTCGTGTG 58.492 50.000 15.69 0.00 44.97 3.82
3208 3591 6.265196 TGAACTTTATCACTGTCATTTGGCTT 59.735 34.615 0.00 0.00 0.00 4.35
3229 3612 1.853319 GAGTTGCGTGACTGGAACG 59.147 57.895 6.28 0.70 43.94 3.95
3322 3708 6.871844 ACGAGAGAGATTTCAGATTTCATCA 58.128 36.000 0.00 0.00 0.00 3.07
3445 3842 7.121315 AGCTACTTTTATCTGTTTGGAATGGTC 59.879 37.037 0.00 0.00 0.00 4.02
3535 3933 2.684843 CGGTCTCCTTTGCTGCTGC 61.685 63.158 8.89 8.89 40.20 5.25
3652 4050 0.235926 GCCAACTTGTTCGTGCTCTC 59.764 55.000 0.00 0.00 0.00 3.20
3698 4096 2.414594 GGATTCAGCGGCAATGGC 59.585 61.111 1.45 0.00 40.13 4.40
3718 4121 1.453762 GCCAGCCATCTGCCATCTTC 61.454 60.000 0.00 0.00 42.71 2.87
3741 4144 2.815647 CAGCCCGTTCTTCCTCGC 60.816 66.667 0.00 0.00 0.00 5.03
3792 4195 0.323542 ATCCTCTCCGACGGTGTCTT 60.324 55.000 14.79 0.00 0.00 3.01
3797 4200 2.432628 CCGACGGTGTCTTGCTCC 60.433 66.667 5.48 0.00 0.00 4.70
3809 4212 1.291877 CTTGCTCCGACAACCCTTCG 61.292 60.000 0.00 0.00 36.20 3.79
3832 4235 0.259938 GGGACCCCGACTACTTCCTA 59.740 60.000 0.00 0.00 0.00 2.94
3837 4240 1.000496 CCCCGACTACTTCCTAATCGC 60.000 57.143 0.00 0.00 0.00 4.58
3872 4275 0.514255 CATTGATATGGGACGCGCAG 59.486 55.000 5.73 2.42 0.00 5.18
3917 4320 4.129737 CCTCGCCACCACGATCGT 62.130 66.667 16.60 16.60 42.02 3.73
3918 4321 2.579787 CTCGCCACCACGATCGTC 60.580 66.667 19.84 5.75 42.02 4.20
3919 4322 4.470170 TCGCCACCACGATCGTCG 62.470 66.667 19.84 18.27 46.93 5.12
3929 4332 2.385315 CACGATCGTCGATAGCAACAT 58.615 47.619 19.84 0.00 43.74 2.71
3960 4363 3.712881 GACGTGCTGCCACCGTTC 61.713 66.667 0.00 2.12 38.79 3.95
4014 4420 2.629617 AGACTGTTGCATTTTTGGGAGG 59.370 45.455 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
138 151 2.735151 TCGCAGACCTAGATTTCTGGA 58.265 47.619 14.30 9.10 39.81 3.86
223 236 2.066262 CTAACACCGAACAAGACGCAT 58.934 47.619 0.00 0.00 0.00 4.73
224 237 1.067364 TCTAACACCGAACAAGACGCA 59.933 47.619 0.00 0.00 0.00 5.24
231 244 1.673626 GGCCGAATCTAACACCGAACA 60.674 52.381 0.00 0.00 0.00 3.18
238 251 2.202824 CCGCGGCCGAATCTAACA 60.203 61.111 33.48 0.00 36.29 2.41
357 380 1.199615 TCACCGCATCCTCCAACATA 58.800 50.000 0.00 0.00 0.00 2.29
358 381 0.548031 ATCACCGCATCCTCCAACAT 59.452 50.000 0.00 0.00 0.00 2.71
482 505 8.641541 AGGATGAAACAAAATTAACATGACACT 58.358 29.630 0.00 0.00 0.00 3.55
517 540 1.404035 ACAGAAACAAAACCGCTGGAC 59.596 47.619 1.50 0.00 0.00 4.02
529 553 8.462811 TGTTATTTAAGTTCAGCAACAGAAACA 58.537 29.630 0.00 0.00 34.60 2.83
530 554 8.850454 TGTTATTTAAGTTCAGCAACAGAAAC 57.150 30.769 0.00 0.00 34.60 2.78
548 572 7.573710 TGTACTCCATCCTAGCAATGTTATTT 58.426 34.615 0.00 0.00 0.00 1.40
552 576 5.045578 ACTTGTACTCCATCCTAGCAATGTT 60.046 40.000 0.00 0.00 0.00 2.71
557 581 5.127194 CAGTAACTTGTACTCCATCCTAGCA 59.873 44.000 0.00 0.00 0.00 3.49
572 596 5.151632 ACGCAAACACTTACAGTAACTTG 57.848 39.130 0.00 0.00 0.00 3.16
575 599 3.243643 ACGACGCAAACACTTACAGTAAC 59.756 43.478 0.00 0.00 0.00 2.50
591 616 1.787012 TCCTCCAACTTAAACGACGC 58.213 50.000 0.00 0.00 0.00 5.19
626 651 1.277557 CAAATCCGGGGCATTTCCAAA 59.722 47.619 0.00 0.00 36.21 3.28
628 653 0.975040 CCAAATCCGGGGCATTTCCA 60.975 55.000 0.00 0.00 36.21 3.53
639 664 1.768870 ACCATCTAGACCCCAAATCCG 59.231 52.381 0.00 0.00 0.00 4.18
685 710 4.346970 TGCAACAAAACTAACATGACACG 58.653 39.130 0.00 0.00 0.00 4.49
712 771 7.426929 ACAGAGAACAACTAAACATGACATC 57.573 36.000 0.00 0.00 0.00 3.06
716 775 8.201464 TCAGTAACAGAGAACAACTAAACATGA 58.799 33.333 0.00 0.00 0.00 3.07
720 779 6.985059 AGGTCAGTAACAGAGAACAACTAAAC 59.015 38.462 0.00 0.00 0.00 2.01
731 791 7.872993 TGTAATTTCTCAAGGTCAGTAACAGAG 59.127 37.037 0.00 0.00 0.00 3.35
743 803 5.703130 GGGCTAGCTATGTAATTTCTCAAGG 59.297 44.000 15.72 0.00 0.00 3.61
769 829 5.621197 TCACCATTTACCACTCAAAATCG 57.379 39.130 0.00 0.00 0.00 3.34
849 909 7.419057 CCCAGTTCCAGATTTAAGCTAGATACA 60.419 40.741 0.00 0.00 0.00 2.29
852 912 5.688766 GCCCAGTTCCAGATTTAAGCTAGAT 60.689 44.000 0.00 0.00 0.00 1.98
861 921 4.388577 AGTAAAGCCCAGTTCCAGATTT 57.611 40.909 0.00 0.00 0.00 2.17
867 927 5.503002 TGGTAATTAGTAAAGCCCAGTTCC 58.497 41.667 0.00 0.00 0.00 3.62
929 989 6.594788 ATGAAGTAACAGGACATTGCAAAT 57.405 33.333 1.71 0.00 0.00 2.32
977 1037 5.806366 TGTGTATGTGATCTGCAATCAAG 57.194 39.130 11.51 0.00 0.00 3.02
1107 1167 3.619929 ACGAAAATACACGGCCAGAATAC 59.380 43.478 2.24 0.00 0.00 1.89
1115 1175 3.817238 ACATCAAACGAAAATACACGGC 58.183 40.909 0.00 0.00 0.00 5.68
1118 1178 9.187455 ACCAATTTACATCAAACGAAAATACAC 57.813 29.630 0.00 0.00 0.00 2.90
1124 1184 6.574350 ACCAACCAATTTACATCAAACGAAA 58.426 32.000 0.00 0.00 0.00 3.46
1131 1191 6.227298 ACAACAACCAACCAATTTACATCA 57.773 33.333 0.00 0.00 0.00 3.07
1181 1241 1.337260 CCTTCCTTGAGTCCAGTGACG 60.337 57.143 0.00 0.00 46.51 4.35
1217 1277 2.661537 TCACCAAGAGCGTGCACG 60.662 61.111 34.01 34.01 43.27 5.34
1244 1304 0.673333 TACCAGTTGACATGCAGCCG 60.673 55.000 0.00 0.00 0.00 5.52
1268 1328 1.463674 CTGGAAGGGGAACGGAAATG 58.536 55.000 0.00 0.00 0.00 2.32
1274 1334 1.672356 CTGTGCTGGAAGGGGAACG 60.672 63.158 0.00 0.00 0.00 3.95
1275 1335 0.606673 GTCTGTGCTGGAAGGGGAAC 60.607 60.000 0.00 0.00 0.00 3.62
1277 1337 2.583441 CGTCTGTGCTGGAAGGGGA 61.583 63.158 0.00 0.00 0.00 4.81
1278 1338 2.046892 CGTCTGTGCTGGAAGGGG 60.047 66.667 0.00 0.00 0.00 4.79
1279 1339 0.250295 TTTCGTCTGTGCTGGAAGGG 60.250 55.000 0.00 0.00 0.00 3.95
1284 1344 0.798776 GTCCATTTCGTCTGTGCTGG 59.201 55.000 0.00 0.00 0.00 4.85
1298 1358 1.699634 ACACCAGTAAGCACAGTCCAT 59.300 47.619 0.00 0.00 0.00 3.41
1301 1361 2.526304 TCACACCAGTAAGCACAGTC 57.474 50.000 0.00 0.00 0.00 3.51
1302 1362 2.610479 CGATCACACCAGTAAGCACAGT 60.610 50.000 0.00 0.00 0.00 3.55
1312 1372 4.248859 ACAAGAGAAATCGATCACACCAG 58.751 43.478 0.00 0.00 0.00 4.00
1318 1378 4.709886 TGGTCCTACAAGAGAAATCGATCA 59.290 41.667 0.00 0.00 0.00 2.92
1320 1380 4.466370 TGTGGTCCTACAAGAGAAATCGAT 59.534 41.667 0.00 0.00 0.00 3.59
1330 1390 3.139077 GGTTGAAGTGTGGTCCTACAAG 58.861 50.000 0.00 0.00 31.36 3.16
1377 1437 1.952296 GCATGGCGGATTTCATCTTCT 59.048 47.619 0.00 0.00 0.00 2.85
1439 1499 5.440610 AGTGAGGCAAGAAGGGTATAAATG 58.559 41.667 0.00 0.00 0.00 2.32
1440 1500 5.717119 AGTGAGGCAAGAAGGGTATAAAT 57.283 39.130 0.00 0.00 0.00 1.40
1554 1614 0.109342 AGCAACACCTGGGAGACAAG 59.891 55.000 0.00 0.00 0.00 3.16
1688 1833 2.022722 AGGGGGATCTGCCATTCAAAAT 60.023 45.455 0.00 0.00 38.95 1.82
1752 1897 0.926155 CAAGATCATCAGCGTCACCG 59.074 55.000 0.00 0.00 37.07 4.94
1843 1988 5.108517 TCTGCAAAAACAACTTCATTCCAC 58.891 37.500 0.00 0.00 0.00 4.02
1942 2087 3.703001 TCCCAGGCTCTTCAAACTTAG 57.297 47.619 0.00 0.00 0.00 2.18
1985 2130 7.288810 TGAATTGAAAGCAACAGGTTTATCT 57.711 32.000 0.00 0.00 36.72 1.98
2007 2152 9.601810 TCCTTTGATATTAACCTCTAGCTATGA 57.398 33.333 0.00 0.00 0.00 2.15
2245 2595 4.023707 GCATCGACTAAGCCAAGCAAATAT 60.024 41.667 0.00 0.00 0.00 1.28
2348 2698 2.355756 GCACCATGGCTACACAATACAG 59.644 50.000 13.04 0.00 0.00 2.74
2468 2824 7.013529 GGTAACACGCTGTATTTTTGAGTTAG 58.986 38.462 0.00 0.00 0.00 2.34
2505 2861 5.673337 TGTGCAACTTCAACATAAGAGTC 57.327 39.130 0.00 0.00 38.04 3.36
2512 2868 4.470334 AACCTTTGTGCAACTTCAACAT 57.530 36.364 0.00 0.00 38.04 2.71
2643 2999 7.224362 CAGGAGAATTTACAGATAGACAAGCAG 59.776 40.741 0.00 0.00 0.00 4.24
2665 3021 3.761752 GGGTTTTTATGTAGCAAGCAGGA 59.238 43.478 0.00 0.00 0.00 3.86
2714 3093 5.076182 TCCAAATCAATGTCAAACAGGCTA 58.924 37.500 0.00 0.00 0.00 3.93
2724 3103 5.766670 TCATGCCTCTATCCAAATCAATGTC 59.233 40.000 0.00 0.00 0.00 3.06
2801 3182 1.795768 CGTTTCCAGTGCTCTTGCTA 58.204 50.000 0.00 0.00 40.48 3.49
2828 3209 1.440353 CTTACCGCAAGCAACACGC 60.440 57.895 0.00 0.00 42.91 5.34
2912 3293 2.485814 GCAAACAACAGTTGGGCAAAAA 59.514 40.909 17.76 0.00 34.12 1.94
3052 3435 4.360964 TACGACGTTGGCCGGTGG 62.361 66.667 5.50 0.00 42.24 4.61
3054 3437 3.562779 CTGTACGACGTTGGCCGGT 62.563 63.158 5.50 0.00 42.24 5.28
3058 3441 1.269166 CAGATCTGTACGACGTTGGC 58.731 55.000 14.95 0.12 0.00 4.52
3164 3547 6.578023 AGTTCAGAGTAGCACATAGGAATTC 58.422 40.000 0.00 0.00 0.00 2.17
3208 3591 0.103390 TTCCAGTCACGCAACTCGAA 59.897 50.000 0.00 0.00 41.67 3.71
3229 3612 1.267806 CCACAAGCACATGACAGAACC 59.732 52.381 0.00 0.00 0.00 3.62
3239 3622 2.346766 ACAACAGATCCACAAGCACA 57.653 45.000 0.00 0.00 0.00 4.57
3335 3721 3.441572 GGTGTTGCAAGATGATTGTAGCT 59.558 43.478 0.00 0.00 0.00 3.32
3342 3739 2.756760 GGATGTGGTGTTGCAAGATGAT 59.243 45.455 0.00 0.00 0.00 2.45
3409 3806 1.911057 AAAAGTAGCTGCCCAAGACC 58.089 50.000 0.00 0.00 0.00 3.85
3445 3842 3.930618 TGTTTAGTTTCACTTTGCGTCG 58.069 40.909 0.00 0.00 0.00 5.12
3587 3985 1.371183 CTGGAACGAGGCACTGGAA 59.629 57.895 0.00 0.00 41.55 3.53
3610 4008 3.258228 TTCTGCGTGCTGGCCATCT 62.258 57.895 5.51 0.00 0.00 2.90
3652 4050 1.304052 TTGCCGTCAATTGGGAGGG 60.304 57.895 5.42 3.61 43.88 4.30
3700 4098 1.164662 CGAAGATGGCAGATGGCTGG 61.165 60.000 7.95 0.00 42.53 4.85
3701 4099 1.164662 CCGAAGATGGCAGATGGCTG 61.165 60.000 7.95 0.00 45.13 4.85
3702 4100 1.147824 CCGAAGATGGCAGATGGCT 59.852 57.895 7.95 0.00 44.01 4.75
3792 4195 2.342279 CGAAGGGTTGTCGGAGCA 59.658 61.111 0.00 0.00 34.85 4.26
3797 4200 2.742372 CCTGGCGAAGGGTTGTCG 60.742 66.667 0.00 0.00 43.15 4.35
3809 4212 3.468140 GTAGTCGGGGTCCCTGGC 61.468 72.222 14.14 14.14 34.13 4.85
3856 4259 2.421314 CCTGCGCGTCCCATATCA 59.579 61.111 8.43 0.00 0.00 2.15
3900 4303 4.129737 ACGATCGTGGTGGCGAGG 62.130 66.667 22.06 0.00 44.43 4.63
3901 4304 2.579787 GACGATCGTGGTGGCGAG 60.580 66.667 28.12 0.00 44.43 5.03
3905 4308 0.660595 GCTATCGACGATCGTGGTGG 60.661 60.000 28.12 16.39 41.35 4.61
3908 4311 1.121240 GTTGCTATCGACGATCGTGG 58.879 55.000 28.12 25.01 41.35 4.94
3909 4312 1.822581 TGTTGCTATCGACGATCGTG 58.177 50.000 28.12 17.50 41.35 4.35
3910 4313 2.223502 ACATGTTGCTATCGACGATCGT 60.224 45.455 22.97 22.97 41.35 3.73
3911 4314 2.385315 ACATGTTGCTATCGACGATCG 58.615 47.619 14.80 14.88 42.10 3.69
3912 4315 5.061064 GGAATACATGTTGCTATCGACGATC 59.939 44.000 14.80 1.26 0.00 3.69
3913 4316 4.923871 GGAATACATGTTGCTATCGACGAT 59.076 41.667 15.74 15.74 0.00 3.73
3914 4317 4.202070 TGGAATACATGTTGCTATCGACGA 60.202 41.667 2.30 0.00 0.00 4.20
3915 4318 4.048504 TGGAATACATGTTGCTATCGACG 58.951 43.478 2.30 0.00 0.00 5.12
3916 4319 4.211374 GGTGGAATACATGTTGCTATCGAC 59.789 45.833 2.30 3.50 0.00 4.20
3917 4320 4.377021 GGTGGAATACATGTTGCTATCGA 58.623 43.478 2.30 0.00 0.00 3.59
3918 4321 3.184379 CGGTGGAATACATGTTGCTATCG 59.816 47.826 2.30 0.12 0.00 2.92
3919 4322 4.024893 CACGGTGGAATACATGTTGCTATC 60.025 45.833 2.30 0.00 0.00 2.08
3947 4350 0.953471 GTACATGAACGGTGGCAGCA 60.953 55.000 17.80 0.00 0.00 4.41
3960 4363 1.135315 GCACAGCTTGCCGTACATG 59.865 57.895 9.03 0.00 46.63 3.21
4014 4420 3.728373 ACGGTTGCCATCCCCTCC 61.728 66.667 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.