Multiple sequence alignment - TraesCS7D01G524700

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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 TraesCS7D01G524700 chr7D 100.000 4501 0 0 1 4501 620489046 620493546 0.000000e+00 8312.0
1 TraesCS7D01G524700 chr7D 84.962 399 53 6 4085 4482 30923642 30923250 9.070000e-107 398.0
2 TraesCS7D01G524700 chr7A 92.525 2515 140 27 389 2888 714598548 714596067 0.000000e+00 3559.0
3 TraesCS7D01G524700 chr7A 92.120 1472 89 15 3019 4487 714595837 714594390 0.000000e+00 2050.0
4 TraesCS7D01G524700 chr7A 91.940 397 30 2 1 396 714599072 714598677 5.090000e-154 555.0
5 TraesCS7D01G524700 chr7A 83.891 329 41 10 4150 4475 129281264 129281583 2.030000e-78 303.0
6 TraesCS7D01G524700 chr7A 86.290 124 14 3 273 396 714598705 714598585 1.020000e-26 132.0
7 TraesCS7D01G524700 chr7B 95.111 1759 79 7 697 2452 716261627 716263381 0.000000e+00 2765.0
8 TraesCS7D01G524700 chr7B 89.454 1356 70 29 2902 4217 716263946 716265268 0.000000e+00 1644.0
9 TraesCS7D01G524700 chr7B 95.465 441 20 0 2445 2885 716263441 716263881 0.000000e+00 704.0
10 TraesCS7D01G524700 chr7B 89.698 398 37 4 1 396 716260969 716261364 5.200000e-139 505.0
11 TraesCS7D01G524700 chr7B 87.500 184 21 1 389 570 716261401 716261584 1.270000e-50 211.0
12 TraesCS7D01G524700 chr7B 89.565 115 9 1 3896 4010 716265896 716266007 4.690000e-30 143.0
13 TraesCS7D01G524700 chr7B 83.495 103 15 2 253 355 716261317 716261417 1.330000e-15 95.3
14 TraesCS7D01G524700 chr7B 100.000 29 0 0 3847 3875 710487084 710487056 2.000000e-03 54.7
15 TraesCS7D01G524700 chr7B 100.000 28 0 0 3847 3874 19099676 19099649 8.000000e-03 52.8
16 TraesCS7D01G524700 chr5D 87.624 404 38 9 4085 4479 439413061 439413461 4.100000e-125 459.0
17 TraesCS7D01G524700 chr5D 85.250 400 37 16 4088 4478 323846577 323846191 4.220000e-105 392.0
18 TraesCS7D01G524700 chr1D 86.732 407 39 13 4088 4485 80875423 80875023 5.350000e-119 438.0
19 TraesCS7D01G524700 chr3D 86.567 402 38 10 4088 4478 592963453 592963057 3.220000e-116 429.0
20 TraesCS7D01G524700 chr4B 86.364 396 42 7 4085 4470 414269375 414269768 5.380000e-114 422.0
21 TraesCS7D01G524700 chr1A 84.236 406 53 9 4085 4481 405685209 405685612 7.060000e-103 385.0


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 TraesCS7D01G524700 chr7D 620489046 620493546 4500 False 8312.000000 8312 100.000000 1 4501 1 chr7D.!!$F1 4500
1 TraesCS7D01G524700 chr7A 714594390 714599072 4682 True 1574.000000 3559 90.718750 1 4487 4 chr7A.!!$R1 4486
2 TraesCS7D01G524700 chr7B 716260969 716266007 5038 False 866.757143 2765 90.041143 1 4217 7 chr7B.!!$F1 4216

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
113 114 0.543277 TCCAGTAGCTGCCCATTCTG 59.457 55.000 0.00 0.0 0.00 3.02 F
374 468 0.607762 TTGCTGCGGCCTATGTTTCA 60.608 50.000 16.57 0.0 37.74 2.69 F
1377 1521 1.135460 GCTCATTCTTTGGTGCTCTGC 60.135 52.381 0.00 0.0 0.00 4.26 F
3077 3400 0.109723 ACGTGGCATGGTTTACAGGT 59.890 50.000 12.05 0.0 32.37 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1450 1594 1.124780 TGTTCCGAAGTGAACCCTGA 58.875 50.000 1.84 0.00 43.17 3.86 R
1692 1836 1.668294 CTCTGCGGACAGTTGGACT 59.332 57.895 0.00 0.00 44.77 3.85 R
3323 3646 0.531200 GGACACCTCGGTCGATCTTT 59.469 55.000 0.00 0.00 38.70 2.52 R
4165 4502 1.128878 TGTGCACGTGTGTACACAAAC 59.871 47.619 29.44 20.62 46.67 2.93 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
17 18 4.838486 GCGCTCGGGTCTCGTCTG 62.838 72.222 0.00 0.00 40.32 3.51
59 60 1.090052 CCGAGTCGAGGATTTTGGGC 61.090 60.000 15.64 0.00 0.00 5.36
67 68 2.270923 GAGGATTTTGGGCGAAATTGC 58.729 47.619 0.00 0.00 29.75 3.56
88 89 3.073678 CCGTCTGAATCATGGTTCACAA 58.926 45.455 17.53 6.15 34.58 3.33
111 112 2.104792 TGTATCCAGTAGCTGCCCATTC 59.895 50.000 0.00 0.00 0.00 2.67
112 113 1.516110 ATCCAGTAGCTGCCCATTCT 58.484 50.000 0.00 0.00 0.00 2.40
113 114 0.543277 TCCAGTAGCTGCCCATTCTG 59.457 55.000 0.00 0.00 0.00 3.02
197 199 2.644676 GGAGTAGATGAGGTTTTGGGC 58.355 52.381 0.00 0.00 0.00 5.36
315 317 8.718102 TTAGGTTTGATGAGTTGCTATAAGTC 57.282 34.615 0.00 0.00 0.00 3.01
320 322 7.834068 TTGATGAGTTGCTATAAGTCAGTTC 57.166 36.000 0.00 0.00 33.58 3.01
321 323 7.175347 TGATGAGTTGCTATAAGTCAGTTCT 57.825 36.000 0.00 0.00 33.58 3.01
322 324 7.615403 TGATGAGTTGCTATAAGTCAGTTCTT 58.385 34.615 0.00 0.00 33.58 2.52
337 339 4.523173 TCAGTTCTTGTAGATGTTCCGAGT 59.477 41.667 0.00 0.00 0.00 4.18
343 345 5.417894 TCTTGTAGATGTTCCGAGTGTATGT 59.582 40.000 0.00 0.00 0.00 2.29
345 347 6.762702 TGTAGATGTTCCGAGTGTATGTTA 57.237 37.500 0.00 0.00 0.00 2.41
374 468 0.607762 TTGCTGCGGCCTATGTTTCA 60.608 50.000 16.57 0.00 37.74 2.69
417 555 2.095718 GGAAATATTCGCCCTCGATTGC 60.096 50.000 0.00 0.00 45.04 3.56
497 635 7.279981 TGCTATACGTATGTCTCTTTTGCAATT 59.720 33.333 18.37 0.00 0.00 2.32
503 641 9.691362 ACGTATGTCTCTTTTGCAATTAAAAAT 57.309 25.926 0.00 0.00 0.00 1.82
504 642 9.941991 CGTATGTCTCTTTTGCAATTAAAAATG 57.058 29.630 0.00 0.00 0.00 2.32
538 676 1.272807 TACCCAGTACCAGGTTGCTC 58.727 55.000 9.55 0.00 37.59 4.26
549 689 2.832129 CCAGGTTGCTCCTACTAGAACA 59.168 50.000 0.00 0.00 46.24 3.18
550 690 3.118956 CCAGGTTGCTCCTACTAGAACAG 60.119 52.174 0.00 0.00 46.24 3.16
592 732 6.453926 AGCAAGGCAATTTGATTTGTTTTT 57.546 29.167 0.00 0.00 0.00 1.94
616 756 9.817809 TTTCCTACATCTGCTTGTACTATAAAG 57.182 33.333 0.00 0.00 0.00 1.85
658 798 5.215252 TCAGACCCTTTTGAGTTGTAGAG 57.785 43.478 0.00 0.00 0.00 2.43
660 800 5.365605 TCAGACCCTTTTGAGTTGTAGAGAA 59.634 40.000 0.00 0.00 0.00 2.87
721 864 7.168804 GGTAGACAAAGTGTGTACTTACTGAAC 59.831 40.741 13.42 0.00 46.14 3.18
927 1071 1.881973 TCTGTTGGTGCATTGAGAAGC 59.118 47.619 0.00 0.00 0.00 3.86
935 1079 1.151668 GCATTGAGAAGCGACACTGT 58.848 50.000 0.00 0.00 0.00 3.55
936 1080 1.136141 GCATTGAGAAGCGACACTGTG 60.136 52.381 6.19 6.19 0.00 3.66
1081 1225 1.521010 CGGACAGGCTCAGATGCTG 60.521 63.158 0.00 0.00 0.00 4.41
1233 1377 2.088104 TTCTCGACTCTGGCCCATAT 57.912 50.000 0.00 0.00 0.00 1.78
1254 1398 1.445871 GCACTTTCGTCGGGGTTTAT 58.554 50.000 0.00 0.00 0.00 1.40
1318 1462 7.333672 ACGATAACCTCTTCAACCATCTTAAAC 59.666 37.037 0.00 0.00 0.00 2.01
1335 1479 3.842732 AAACGTAATTGCTAACCTGGC 57.157 42.857 0.00 0.00 0.00 4.85
1377 1521 1.135460 GCTCATTCTTTGGTGCTCTGC 60.135 52.381 0.00 0.00 0.00 4.26
1408 1552 4.019174 CCCTGTTTCACTTGCCTGATAAT 58.981 43.478 0.00 0.00 0.00 1.28
1411 1555 5.163683 CCTGTTTCACTTGCCTGATAATGAG 60.164 44.000 0.00 0.00 0.00 2.90
1450 1594 8.721133 ATTTACTTCTTCCCTGGTTTGTATTT 57.279 30.769 0.00 0.00 0.00 1.40
1459 1603 4.148838 CCTGGTTTGTATTTCAGGGTTCA 58.851 43.478 0.00 0.00 42.12 3.18
1482 1626 5.976534 CACTTCGGAACAAAATTCAATGTCA 59.023 36.000 0.00 0.00 0.00 3.58
1524 1668 4.694509 GCATATGAAGCTACAGAAGATGGG 59.305 45.833 6.97 0.00 0.00 4.00
1540 1684 4.798882 AGATGGGTTCTTCTCTATCGTCT 58.201 43.478 0.00 0.00 0.00 4.18
1692 1836 1.340017 GCCACTGGAGAAGTATTGGCA 60.340 52.381 5.54 0.00 42.49 4.92
1858 2002 5.256474 CACTGGGGAGACATTTGTAGATTT 58.744 41.667 0.00 0.00 0.00 2.17
1880 2024 4.647611 TGTGGAAGTTCGATGTTATGGTT 58.352 39.130 0.00 0.00 0.00 3.67
1903 2047 8.054081 GGTTATTCCATATGCTTATGCGCATTT 61.054 37.037 30.42 8.81 42.24 2.32
1925 2069 9.520204 CATTTAGTTGGCAAAATATACCTTCAG 57.480 33.333 0.00 0.00 0.00 3.02
1953 2097 6.657541 TCACCACCTGGAAGTTTAATATTGTC 59.342 38.462 0.00 0.00 38.94 3.18
1954 2098 5.949952 ACCACCTGGAAGTTTAATATTGTCC 59.050 40.000 0.00 0.00 38.94 4.02
2072 2217 1.850998 GGGCTGTAAGGGGGTAGAAAT 59.149 52.381 0.00 0.00 0.00 2.17
2162 2308 9.929180 CAGTTCTGCTATATTTATTAGGTAGCA 57.071 33.333 5.42 5.42 43.74 3.49
2169 2315 9.930693 GCTATATTTATTAGGTAGCACTGAAGT 57.069 33.333 0.00 0.00 38.08 3.01
2193 2339 8.938883 AGTGAAGAGCTTGATAATTATTAGGGA 58.061 33.333 0.00 0.00 0.00 4.20
2299 2452 7.246674 TGTTATGGCTCAGTTCGATTAATTC 57.753 36.000 0.00 0.00 0.00 2.17
2301 2454 4.214986 TGGCTCAGTTCGATTAATTCCA 57.785 40.909 0.00 0.00 0.00 3.53
2348 2501 6.859017 AGTAAAACAATGTTATTTAGCCCCG 58.141 36.000 0.00 0.00 0.00 5.73
2371 2524 5.389620 CGCTGATTCATCACTTCATGATAGC 60.390 44.000 0.00 0.00 46.96 2.97
2421 2574 9.990360 TTTGTCTTGTATGACTATGAGTAACAA 57.010 29.630 0.00 0.00 37.79 2.83
2443 2598 6.095440 ACAAATATGATGGTACTTGCCACTTC 59.905 38.462 0.00 0.00 41.94 3.01
2478 2702 5.048364 CGTGGGACCAAATGAAGATTGTTAA 60.048 40.000 0.00 0.00 0.00 2.01
2755 2979 4.483311 CCCTCGTAGTGTAAGTTTCTCAC 58.517 47.826 0.00 0.00 0.00 3.51
2823 3047 4.990257 TGGCGTATTCTACTACAACTGTC 58.010 43.478 0.00 0.00 0.00 3.51
2836 3060 6.946340 ACTACAACTGTCCATGACATTATGA 58.054 36.000 0.00 0.00 41.94 2.15
2838 3062 6.688637 ACAACTGTCCATGACATTATGATG 57.311 37.500 0.00 0.00 41.94 3.07
2928 3201 9.624697 TTCATTTATGAAATAATAATGAGGCGC 57.375 29.630 0.00 0.00 43.26 6.53
2938 3211 0.465097 AATGAGGCGCCTCTGAATGG 60.465 55.000 46.04 0.00 43.12 3.16
2940 3213 1.340399 TGAGGCGCCTCTGAATGGAT 61.340 55.000 46.04 17.58 43.12 3.41
3005 3299 6.872628 TTGCAAAATAATTTGGATGTTGCA 57.127 29.167 11.59 11.59 44.81 4.08
3006 3300 6.872628 TGCAAAATAATTTGGATGTTGCAA 57.127 29.167 12.78 0.00 44.81 4.08
3007 3301 7.268199 TGCAAAATAATTTGGATGTTGCAAA 57.732 28.000 12.78 0.00 44.81 3.68
3009 3303 8.358148 TGCAAAATAATTTGGATGTTGCAAAAT 58.642 25.926 12.78 0.40 44.81 1.82
3010 3304 9.837525 GCAAAATAATTTGGATGTTGCAAAATA 57.162 25.926 0.95 0.00 44.93 1.40
3016 3310 8.851541 AATTTGGATGTTGCAAAATAAGATGT 57.148 26.923 0.95 0.00 40.92 3.06
3017 3311 7.655236 TTTGGATGTTGCAAAATAAGATGTG 57.345 32.000 0.95 0.00 34.76 3.21
3022 3345 6.278172 TGTTGCAAAATAAGATGTGGCATA 57.722 33.333 0.00 0.00 0.00 3.14
3034 3357 5.387788 AGATGTGGCATATAAAATCCAGCA 58.612 37.500 0.00 0.00 0.00 4.41
3040 3363 7.450944 TGTGGCATATAAAATCCAGCAATCATA 59.549 33.333 0.00 0.00 0.00 2.15
3043 3366 7.093814 GGCATATAAAATCCAGCAATCATACCA 60.094 37.037 0.00 0.00 0.00 3.25
3048 3371 4.987963 ATCCAGCAATCATACCATCAGA 57.012 40.909 0.00 0.00 0.00 3.27
3049 3372 4.776435 TCCAGCAATCATACCATCAGAA 57.224 40.909 0.00 0.00 0.00 3.02
3052 3375 6.131264 TCCAGCAATCATACCATCAGAAAAT 58.869 36.000 0.00 0.00 0.00 1.82
3075 3398 1.518325 TGACGTGGCATGGTTTACAG 58.482 50.000 12.05 0.00 0.00 2.74
3076 3399 0.802494 GACGTGGCATGGTTTACAGG 59.198 55.000 12.05 0.00 0.00 4.00
3077 3400 0.109723 ACGTGGCATGGTTTACAGGT 59.890 50.000 12.05 0.00 32.37 4.00
3078 3401 1.243902 CGTGGCATGGTTTACAGGTT 58.756 50.000 0.00 0.00 32.37 3.50
3079 3402 1.199097 CGTGGCATGGTTTACAGGTTC 59.801 52.381 0.00 0.00 32.37 3.62
3117 3440 4.281688 CCCTTGATGAGTTTTGGTTGTGAT 59.718 41.667 0.00 0.00 0.00 3.06
3134 3457 5.132897 TGTGATGCAGTGGGTTAAAATTC 57.867 39.130 0.00 0.00 0.00 2.17
3140 3463 4.021544 TGCAGTGGGTTAAAATTCATCACC 60.022 41.667 0.00 0.00 0.00 4.02
3141 3464 4.732784 CAGTGGGTTAAAATTCATCACCG 58.267 43.478 0.00 0.00 0.00 4.94
3144 3467 3.192422 TGGGTTAAAATTCATCACCGCTG 59.808 43.478 0.00 0.00 0.00 5.18
3197 3520 2.893489 CCTTGTTTTTGCTAAGCCCTCT 59.107 45.455 0.00 0.00 0.00 3.69
3323 3646 5.835819 AGAGATGAGGTATTCCGATCTCAAA 59.164 40.000 23.43 0.00 46.01 2.69
3440 3763 3.741476 GGCCCTGCTGTTTCGCTG 61.741 66.667 0.00 0.00 0.00 5.18
3446 3769 0.320247 CTGCTGTTTCGCTGAGAGGT 60.320 55.000 0.00 0.00 0.00 3.85
3511 3834 1.611673 GCAGATGTAACAGGTGCCAGT 60.612 52.381 0.00 0.00 0.00 4.00
3519 3842 1.192146 ACAGGTGCCAGTGGTATCGT 61.192 55.000 11.74 6.61 0.00 3.73
3525 3848 0.535335 GCCAGTGGTATCGTCCAAGA 59.465 55.000 11.74 0.00 39.34 3.02
3526 3849 1.139058 GCCAGTGGTATCGTCCAAGAT 59.861 52.381 11.74 0.00 39.34 2.40
3527 3850 2.803492 GCCAGTGGTATCGTCCAAGATC 60.803 54.545 11.74 0.00 39.34 2.75
3552 3875 5.387788 TCATCATCCCCTTGATTAATGGTG 58.612 41.667 0.00 0.00 34.09 4.17
3607 3930 4.366267 TCTTCTTCTCCAGGGCTTCTATT 58.634 43.478 0.00 0.00 0.00 1.73
3694 4019 5.069501 AGAATAGGTAGGTGTCGTTTGTC 57.930 43.478 0.00 0.00 0.00 3.18
3699 4024 0.598158 TAGGTGTCGTTTGTCGTGCC 60.598 55.000 0.00 0.00 40.80 5.01
3763 4089 7.663493 CCCCTGCAGGAATTTTAATTTTAACAA 59.337 33.333 34.91 0.00 38.24 2.83
3825 4152 4.141688 CCCAGGAGGAGTAACTTATTGACC 60.142 50.000 0.00 0.00 38.24 4.02
4117 4454 0.179034 GAAGGCCGAGCTCCAATGAT 60.179 55.000 8.47 0.00 0.00 2.45
4165 4502 6.383871 CGTAGCGCGAAAAATTCTAAATTTG 58.616 36.000 12.10 0.00 44.77 2.32
4172 4509 7.843686 CGCGAAAAATTCTAAATTTGTTTGTGT 59.156 29.630 0.00 0.00 0.00 3.72
4224 4561 8.304202 TGTGCAAAAATTCACAACATTATACC 57.696 30.769 0.00 0.00 39.91 2.73
4237 4574 7.219917 CACAACATTATACCTTTAAATGTGGCG 59.780 37.037 6.40 0.00 41.67 5.69
4275 4612 6.517605 ACAAATACACATTTTAAAACGGGCT 58.482 32.000 1.97 0.00 31.82 5.19
4350 4687 6.973474 ACCACATTTTTCGACGAAATTTAACA 59.027 30.769 22.62 5.01 31.34 2.41
4360 4697 5.452302 CGACGAAATTTAACATGATCTTGCC 59.548 40.000 8.45 0.00 0.00 4.52
4381 4718 7.609760 TGCCGAATACATATATGTTTCCATC 57.390 36.000 22.90 12.78 41.97 3.51
4475 4814 1.821332 GGCCTCCAGAAATCCGCAG 60.821 63.158 0.00 0.00 0.00 5.18
4487 4826 3.512033 AATCCGCAGTCTGAGAAGTAC 57.488 47.619 3.32 0.00 0.00 2.73
4488 4827 2.201921 TCCGCAGTCTGAGAAGTACT 57.798 50.000 3.32 0.00 0.00 2.73
4489 4828 2.085320 TCCGCAGTCTGAGAAGTACTC 58.915 52.381 3.32 0.00 45.11 2.59
4491 4830 2.088423 CGCAGTCTGAGAAGTACTCCT 58.912 52.381 3.32 0.00 44.34 3.69
4492 4831 3.271729 CGCAGTCTGAGAAGTACTCCTA 58.728 50.000 3.32 0.00 44.34 2.94
4493 4832 3.880490 CGCAGTCTGAGAAGTACTCCTAT 59.120 47.826 3.32 0.00 44.34 2.57
4494 4833 4.336993 CGCAGTCTGAGAAGTACTCCTATT 59.663 45.833 3.32 0.00 44.34 1.73
4495 4834 5.163602 CGCAGTCTGAGAAGTACTCCTATTT 60.164 44.000 3.32 0.00 44.34 1.40
4496 4835 6.270064 GCAGTCTGAGAAGTACTCCTATTTC 58.730 44.000 3.32 0.00 44.34 2.17
4498 4837 7.681065 GCAGTCTGAGAAGTACTCCTATTTCTC 60.681 44.444 3.32 11.49 42.26 2.87
4499 4838 7.338196 CAGTCTGAGAAGTACTCCTATTTCTCA 59.662 40.741 17.55 17.55 46.04 3.27
4500 4839 7.891183 AGTCTGAGAAGTACTCCTATTTCTCAA 59.109 37.037 18.60 10.38 46.77 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.943340 CTTCTCCTAAGCGGCAAATCC 59.057 52.381 1.45 0.00 0.00 3.01
59 60 3.357021 CATGATTCAGACGGCAATTTCG 58.643 45.455 0.00 0.00 0.00 3.46
67 68 2.698803 TGTGAACCATGATTCAGACGG 58.301 47.619 1.60 0.00 39.25 4.79
197 199 4.381932 GCCTATTCCCCAACAACTCAATTG 60.382 45.833 0.00 0.00 44.60 2.32
271 273 7.951530 ACCTAAGATTTTGCTTGAAAACATG 57.048 32.000 0.00 0.00 36.35 3.21
315 317 4.623167 CACTCGGAACATCTACAAGAACTG 59.377 45.833 0.00 0.00 0.00 3.16
320 322 5.651530 ACATACACTCGGAACATCTACAAG 58.348 41.667 0.00 0.00 0.00 3.16
321 323 5.654603 ACATACACTCGGAACATCTACAA 57.345 39.130 0.00 0.00 0.00 2.41
322 324 5.654603 AACATACACTCGGAACATCTACA 57.345 39.130 0.00 0.00 0.00 2.74
337 339 6.155827 GCAGCAAAACATTTCCTAACATACA 58.844 36.000 0.00 0.00 0.00 2.29
343 345 2.609244 GCCGCAGCAAAACATTTCCTAA 60.609 45.455 0.00 0.00 39.53 2.69
345 347 0.319813 GCCGCAGCAAAACATTTCCT 60.320 50.000 0.00 0.00 39.53 3.36
417 555 2.794910 ACAATCGTGTCTCTGTTTGACG 59.205 45.455 0.00 0.00 37.26 4.35
497 635 6.660094 GGTAACCTACACCATCACCATTTTTA 59.340 38.462 0.00 0.00 36.01 1.52
549 689 4.072839 GCTTGGTGCTTTTAGGTTCTACT 58.927 43.478 0.00 0.00 38.95 2.57
550 690 3.818773 TGCTTGGTGCTTTTAGGTTCTAC 59.181 43.478 0.00 0.00 43.37 2.59
592 732 8.534954 ACTTTATAGTACAAGCAGATGTAGGA 57.465 34.615 0.00 0.00 36.51 2.94
680 820 7.719633 ACTTTGTCTACCATGTAACACAGAATT 59.280 33.333 0.00 0.00 0.00 2.17
685 825 5.525745 CACACTTTGTCTACCATGTAACACA 59.474 40.000 0.00 0.00 0.00 3.72
686 826 5.526111 ACACACTTTGTCTACCATGTAACAC 59.474 40.000 0.00 0.00 29.79 3.32
721 864 2.033049 GCAGGAGAGCTGCATGTATTTG 59.967 50.000 1.02 0.00 46.19 2.32
757 900 9.408648 GTCATATTTTATCTTTCCTTCCTTCCA 57.591 33.333 0.00 0.00 0.00 3.53
758 901 9.408648 TGTCATATTTTATCTTTCCTTCCTTCC 57.591 33.333 0.00 0.00 0.00 3.46
927 1071 8.239681 TGTTATCTAAGAAAATCACAGTGTCG 57.760 34.615 0.00 0.00 0.00 4.35
935 1079 7.439356 CGCCTCATCTGTTATCTAAGAAAATCA 59.561 37.037 0.00 0.00 0.00 2.57
936 1080 7.653713 TCGCCTCATCTGTTATCTAAGAAAATC 59.346 37.037 0.00 0.00 0.00 2.17
1117 1261 1.455383 CCATTTACATGCTCCCCGGC 61.455 60.000 0.00 0.00 0.00 6.13
1119 1263 1.785041 CGCCATTTACATGCTCCCCG 61.785 60.000 0.00 0.00 0.00 5.73
1254 1398 4.028490 GGTCCACCGTGCCCATCA 62.028 66.667 0.00 0.00 0.00 3.07
1318 1462 2.942376 TGATGCCAGGTTAGCAATTACG 59.058 45.455 0.00 0.00 44.83 3.18
1335 1479 8.031277 TGAGCATAGTACTAATGCATAGTGATG 58.969 37.037 25.65 12.22 44.64 3.07
1353 1497 4.035324 CAGAGCACCAAAGAATGAGCATAG 59.965 45.833 0.00 0.00 33.83 2.23
1377 1521 1.152777 TGAAACAGGGCAGTGTGGG 60.153 57.895 0.00 0.00 0.00 4.61
1408 1552 5.491070 AGTAAATAATCACTGCAGTGCTCA 58.509 37.500 36.76 23.33 45.25 4.26
1411 1555 6.428385 AGAAGTAAATAATCACTGCAGTGC 57.572 37.500 36.76 22.05 45.25 4.40
1450 1594 1.124780 TGTTCCGAAGTGAACCCTGA 58.875 50.000 1.84 0.00 43.17 3.86
1459 1603 6.142818 TGACATTGAATTTTGTTCCGAAGT 57.857 33.333 0.00 0.00 0.00 3.01
1482 1626 4.277515 TGCTTTCTTCAGTACATCAGCT 57.722 40.909 0.00 0.00 0.00 4.24
1524 1668 4.142359 TGCTTGGAGACGATAGAGAAGAAC 60.142 45.833 0.00 0.00 41.38 3.01
1692 1836 1.668294 CTCTGCGGACAGTTGGACT 59.332 57.895 0.00 0.00 44.77 3.85
1858 2002 4.280436 ACCATAACATCGAACTTCCACA 57.720 40.909 0.00 0.00 0.00 4.17
1903 2047 8.644374 AAACTGAAGGTATATTTTGCCAACTA 57.356 30.769 0.00 0.00 31.27 2.24
1925 2069 5.784578 ATTAAACTTCCAGGTGGTGAAAC 57.215 39.130 0.00 0.00 36.34 2.78
1953 2097 4.719273 AGAAGATAAGGAACTGAGGAAGGG 59.281 45.833 0.00 0.00 40.86 3.95
1954 2098 5.423610 TCAGAAGATAAGGAACTGAGGAAGG 59.576 44.000 0.00 0.00 40.86 3.46
2162 2308 9.678260 AATAATTATCAAGCTCTTCACTTCAGT 57.322 29.630 0.00 0.00 0.00 3.41
2189 2335 6.159398 ACTCCATGACTATTCAAGAAATCCCT 59.841 38.462 0.00 0.00 34.61 4.20
2348 2501 5.469084 TGCTATCATGAAGTGATGAATCAGC 59.531 40.000 0.00 0.00 46.85 4.26
2421 2574 6.006275 AGAAGTGGCAAGTACCATCATATT 57.994 37.500 0.00 0.00 43.01 1.28
2478 2702 8.725148 TGCAACATACAACAAACAAAGAAAAAT 58.275 25.926 0.00 0.00 0.00 1.82
2755 2979 7.339212 TGTCAGGTCAATTTATTTACATGGGAG 59.661 37.037 0.00 0.00 0.00 4.30
2874 3098 8.250332 TGCTGGGTGATAAATCTTAATTTTGAC 58.750 33.333 0.00 0.00 36.49 3.18
2878 3102 9.822185 GAAATGCTGGGTGATAAATCTTAATTT 57.178 29.630 0.00 0.00 38.61 1.82
2889 3135 7.894753 TTCATAAATGAAATGCTGGGTGATA 57.105 32.000 2.91 0.00 43.26 2.15
2922 3195 0.681733 TATCCATTCAGAGGCGCCTC 59.318 55.000 43.08 43.08 43.03 4.70
2927 3200 8.045507 TCAGATATCAATTATCCATTCAGAGGC 58.954 37.037 5.32 0.00 37.96 4.70
2928 3201 9.955102 TTCAGATATCAATTATCCATTCAGAGG 57.045 33.333 5.32 0.00 37.96 3.69
2981 3254 7.450124 TGCAACATCCAAATTATTTTGCAAT 57.550 28.000 9.67 0.00 43.37 3.56
2994 3288 6.164876 CCACATCTTATTTTGCAACATCCAA 58.835 36.000 0.00 0.00 0.00 3.53
3001 3295 9.881649 TTTTATATGCCACATCTTATTTTGCAA 57.118 25.926 0.00 0.00 0.00 4.08
3007 3301 8.526147 GCTGGATTTTATATGCCACATCTTATT 58.474 33.333 0.00 0.00 0.00 1.40
3009 3303 7.003482 TGCTGGATTTTATATGCCACATCTTA 58.997 34.615 0.00 0.00 0.00 2.10
3010 3304 5.834742 TGCTGGATTTTATATGCCACATCTT 59.165 36.000 0.00 0.00 0.00 2.40
3011 3305 5.387788 TGCTGGATTTTATATGCCACATCT 58.612 37.500 0.00 0.00 0.00 2.90
3012 3306 5.710513 TGCTGGATTTTATATGCCACATC 57.289 39.130 0.00 0.00 0.00 3.06
3013 3307 6.268158 TGATTGCTGGATTTTATATGCCACAT 59.732 34.615 0.00 0.00 0.00 3.21
3016 3310 6.921486 ATGATTGCTGGATTTTATATGCCA 57.079 33.333 0.00 0.00 0.00 4.92
3017 3311 7.093814 TGGTATGATTGCTGGATTTTATATGCC 60.094 37.037 0.00 0.00 0.00 4.40
3022 3345 7.946219 TCTGATGGTATGATTGCTGGATTTTAT 59.054 33.333 0.00 0.00 0.00 1.40
3034 3357 8.400947 CGTCAAGAATTTTCTGATGGTATGATT 58.599 33.333 0.00 0.00 37.65 2.57
3040 3363 4.216257 CCACGTCAAGAATTTTCTGATGGT 59.784 41.667 12.43 5.84 37.65 3.55
3043 3366 3.820467 TGCCACGTCAAGAATTTTCTGAT 59.180 39.130 0.00 0.00 37.65 2.90
3048 3371 2.627699 ACCATGCCACGTCAAGAATTTT 59.372 40.909 0.00 0.00 0.00 1.82
3049 3372 2.238521 ACCATGCCACGTCAAGAATTT 58.761 42.857 0.00 0.00 0.00 1.82
3052 3375 1.686355 AAACCATGCCACGTCAAGAA 58.314 45.000 0.00 0.00 0.00 2.52
3102 3425 3.374745 CACTGCATCACAACCAAAACTC 58.625 45.455 0.00 0.00 0.00 3.01
3104 3427 2.472816 CCACTGCATCACAACCAAAAC 58.527 47.619 0.00 0.00 0.00 2.43
3117 3440 4.021544 GGTGATGAATTTTAACCCACTGCA 60.022 41.667 0.00 0.00 0.00 4.41
3141 3464 2.256461 CAAAGCTTCCGCCACAGC 59.744 61.111 0.00 0.00 36.60 4.40
3144 3467 3.595108 GACGCAAAGCTTCCGCCAC 62.595 63.158 16.49 7.46 36.60 5.01
3149 3472 4.546570 AGTAATTTTGACGCAAAGCTTCC 58.453 39.130 0.00 0.00 34.72 3.46
3190 3513 1.211457 CTCCAATTAGCACAGAGGGCT 59.789 52.381 0.00 0.00 45.18 5.19
3197 3520 6.115446 CCATTAAGAGTCTCCAATTAGCACA 58.885 40.000 0.00 0.00 0.00 4.57
3323 3646 0.531200 GGACACCTCGGTCGATCTTT 59.469 55.000 0.00 0.00 38.70 2.52
3440 3763 4.803426 CTCACGCCGGCACCTCTC 62.803 72.222 28.98 0.00 0.00 3.20
3511 3834 4.588528 TGATGATGATCTTGGACGATACCA 59.411 41.667 0.00 0.00 38.24 3.25
3519 3842 3.605879 AGGGGATGATGATGATCTTGGA 58.394 45.455 0.00 0.00 0.00 3.53
3525 3848 6.895756 CCATTAATCAAGGGGATGATGATGAT 59.104 38.462 12.02 0.00 39.90 2.45
3526 3849 6.183361 ACCATTAATCAAGGGGATGATGATGA 60.183 38.462 12.02 0.00 40.01 2.92
3527 3850 6.014647 ACCATTAATCAAGGGGATGATGATG 58.985 40.000 0.00 0.00 40.01 3.07
3552 3875 3.679389 TGTGCCTCTCCATTCTTTCTTC 58.321 45.455 0.00 0.00 0.00 2.87
3607 3930 6.325993 TCAAAGTCTTCATGATGGGGATTA 57.674 37.500 8.60 0.00 0.00 1.75
3783 4110 7.149972 TCCTGGGGCCATTATTATACCATATA 58.850 38.462 4.39 0.00 0.00 0.86
3784 4111 5.982534 TCCTGGGGCCATTATTATACCATAT 59.017 40.000 4.39 0.00 0.00 1.78
3801 4128 4.037927 TCAATAAGTTACTCCTCCTGGGG 58.962 47.826 0.00 0.00 40.50 4.96
3825 4152 1.404035 TGTATGGAGTCCACGACATCG 59.596 52.381 15.86 0.00 46.33 3.84
3858 4185 6.424812 GTCAGAATAGCACACATACATGCATA 59.575 38.462 0.00 0.00 44.59 3.14
3859 4186 5.237996 GTCAGAATAGCACACATACATGCAT 59.762 40.000 0.00 0.00 44.59 3.96
3860 4187 4.571984 GTCAGAATAGCACACATACATGCA 59.428 41.667 0.00 0.00 44.59 3.96
3861 4188 4.813161 AGTCAGAATAGCACACATACATGC 59.187 41.667 0.00 0.00 42.39 4.06
4023 4356 2.773661 AGGTGCATGTGGACTGATGATA 59.226 45.455 4.67 0.00 36.56 2.15
4158 4495 5.512082 GCACGTGTGTACACAAACAAATTTA 59.488 36.000 29.44 0.45 46.75 1.40
4165 4502 1.128878 TGTGCACGTGTGTACACAAAC 59.871 47.619 29.44 20.62 46.67 2.93
4172 4509 4.443913 AGTATACATGTGCACGTGTGTA 57.556 40.909 41.46 36.88 44.97 2.90
4249 4586 6.643360 GCCCGTTTTAAAATGTGTATTTGTCT 59.357 34.615 16.89 0.00 36.65 3.41
4350 4687 9.453572 AAACATATATGTATTCGGCAAGATCAT 57.546 29.630 18.56 0.00 40.80 2.45
4475 4814 7.633193 TGAGAAATAGGAGTACTTCTCAGAC 57.367 40.000 7.05 0.00 45.43 3.51


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

AutoCloner maintained by Alex Coulton.