Multiple sequence alignment - TraesCS6B01G259000

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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 TraesCS6B01G259000 chr6B 100.000 4756 0 0 1 4756 467446950 467451705 0.000000e+00 8783.0
1 TraesCS6B01G259000 chr6B 86.014 143 20 0 2807 2949 504586218 504586360 2.290000e-33 154.0
2 TraesCS6B01G259000 chr6B 94.286 35 1 1 4691 4725 704153050 704153017 9.000000e-03 52.8
3 TraesCS6B01G259000 chr6A 93.138 1982 63 24 581 2523 414878729 414876782 0.000000e+00 2839.0
4 TraesCS6B01G259000 chr6A 91.160 1742 109 23 3030 4756 414876228 414874517 0.000000e+00 2322.0
5 TraesCS6B01G259000 chr6A 95.914 465 12 2 2544 3001 414876796 414876332 0.000000e+00 747.0
6 TraesCS6B01G259000 chr6A 90.037 542 33 12 1 531 414879259 414878728 0.000000e+00 682.0
7 TraesCS6B01G259000 chr6A 85.714 140 20 0 2813 2952 456750647 456750508 1.070000e-31 148.0
8 TraesCS6B01G259000 chr6D 93.754 1553 58 21 2544 4069 302039029 302040569 0.000000e+00 2294.0
9 TraesCS6B01G259000 chr6D 91.296 1505 40 27 326 1783 302036446 302037906 0.000000e+00 1969.0
10 TraesCS6B01G259000 chr6D 94.163 771 20 5 1776 2523 302038275 302039043 0.000000e+00 1151.0
11 TraesCS6B01G259000 chr6D 90.930 430 33 5 4060 4485 302050392 302050819 1.480000e-159 573.0
12 TraesCS6B01G259000 chr6D 94.182 275 9 2 44 313 302035428 302035700 3.420000e-111 412.0
13 TraesCS6B01G259000 chr6D 86.525 141 17 2 2813 2952 318953105 318952966 2.290000e-33 154.0
14 TraesCS6B01G259000 chr6D 93.333 60 4 0 1 60 302033960 302034019 6.560000e-14 89.8
15 TraesCS6B01G259000 chr2D 92.739 303 22 0 1423 1725 480325215 480324913 5.650000e-119 438.0
16 TraesCS6B01G259000 chr2D 91.333 300 26 0 1426 1725 480181350 480181051 1.230000e-110 411.0
17 TraesCS6B01G259000 chr2D 87.227 321 36 3 1001 1317 480181671 480181352 1.260000e-95 361.0
18 TraesCS6B01G259000 chr2D 87.625 299 37 0 1423 1721 159574132 159574430 9.800000e-92 348.0
19 TraesCS6B01G259000 chr2D 84.321 287 42 3 1031 1314 159573844 159574130 1.300000e-70 278.0
20 TraesCS6B01G259000 chr2D 91.216 148 13 0 2806 2953 480180551 480180404 8.070000e-48 202.0
21 TraesCS6B01G259000 chr2D 88.742 151 16 1 2807 2957 159575980 159576129 2.920000e-42 183.0
22 TraesCS6B01G259000 chr2D 92.079 101 7 1 3641 3740 480323768 480323668 1.780000e-29 141.0
23 TraesCS6B01G259000 chr2D 93.258 89 6 0 3644 3732 480179671 480179583 1.070000e-26 132.0
24 TraesCS6B01G259000 chr2B 91.935 310 25 0 1423 1732 563184639 563184330 7.310000e-118 435.0
25 TraesCS6B01G259000 chr2B 90.333 300 29 0 1426 1725 563046120 563045821 1.240000e-105 394.0
26 TraesCS6B01G259000 chr2B 86.916 321 37 3 1001 1317 563046441 563046122 5.850000e-94 355.0
27 TraesCS6B01G259000 chr2B 85.017 287 40 2 1031 1314 216708491 216708777 6.020000e-74 289.0
28 TraesCS6B01G259000 chr2B 89.865 148 15 0 2807 2954 216710516 216710663 1.750000e-44 191.0
29 TraesCS6B01G259000 chr2B 92.079 101 7 1 3641 3740 563182882 563182782 1.780000e-29 141.0
30 TraesCS6B01G259000 chr2B 93.258 89 6 0 3644 3732 563043975 563043887 1.070000e-26 132.0
31 TraesCS6B01G259000 chr2A 90.968 310 28 0 1423 1732 622853424 622853115 7.360000e-113 418.0
32 TraesCS6B01G259000 chr2A 90.429 303 29 0 1423 1725 622747736 622747434 2.670000e-107 399.0
33 TraesCS6B01G259000 chr2A 87.888 322 34 3 1001 1318 622748054 622747734 1.620000e-99 374.0
34 TraesCS6B01G259000 chr2A 87.267 322 36 4 1001 1318 622853742 622853422 3.500000e-96 363.0
35 TraesCS6B01G259000 chr2A 85.366 287 39 3 1031 1314 170602949 170603235 1.290000e-75 294.0
36 TraesCS6B01G259000 chr2A 87.838 148 18 0 2807 2954 170604806 170604953 1.760000e-39 174.0
37 TraesCS6B01G259000 chr2A 93.258 89 6 0 3644 3732 622746081 622745993 1.070000e-26 132.0
38 TraesCS6B01G259000 chr7D 94.444 36 2 0 4315 4350 417937702 417937667 6.650000e-04 56.5


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 TraesCS6B01G259000 chr6B 467446950 467451705 4755 False 8783.000000 8783 100.00000 1 4756 1 chr6B.!!$F1 4755
1 TraesCS6B01G259000 chr6A 414874517 414879259 4742 True 1647.500000 2839 92.56225 1 4756 4 chr6A.!!$R2 4755
2 TraesCS6B01G259000 chr6D 302033960 302040569 6609 False 1183.160000 2294 93.34560 1 4069 5 chr6D.!!$F2 4068
3 TraesCS6B01G259000 chr2D 480323668 480325215 1547 True 289.500000 438 92.40900 1423 3740 2 chr2D.!!$R2 2317
4 TraesCS6B01G259000 chr2D 480179583 480181671 2088 True 276.500000 411 90.75850 1001 3732 4 chr2D.!!$R1 2731
5 TraesCS6B01G259000 chr2D 159573844 159576129 2285 False 269.666667 348 86.89600 1031 2957 3 chr2D.!!$F1 1926
6 TraesCS6B01G259000 chr2B 563043887 563046441 2554 True 293.666667 394 90.16900 1001 3732 3 chr2B.!!$R1 2731
7 TraesCS6B01G259000 chr2B 563182782 563184639 1857 True 288.000000 435 92.00700 1423 3740 2 chr2B.!!$R2 2317
8 TraesCS6B01G259000 chr2B 216708491 216710663 2172 False 240.000000 289 87.44100 1031 2954 2 chr2B.!!$F1 1923
9 TraesCS6B01G259000 chr2A 622853115 622853742 627 True 390.500000 418 89.11750 1001 1732 2 chr2A.!!$R2 731
10 TraesCS6B01G259000 chr2A 622745993 622748054 2061 True 301.666667 399 90.52500 1001 3732 3 chr2A.!!$R1 2731
11 TraesCS6B01G259000 chr2A 170602949 170604953 2004 False 234.000000 294 86.60200 1031 2954 2 chr2A.!!$F1 1923

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
123 1549 0.399806 GGAGGAGAAGGGGAGAGCAT 60.400 60.0 0.00 0.0 0.00 3.79 F
837 3027 0.764369 ATCAATCTGCCTCCCCGCTA 60.764 55.0 0.00 0.0 0.00 4.26 F
1358 3559 0.179113 TCTTCTCGCGCATGCATACA 60.179 50.0 19.57 0.0 42.97 2.29 F
2339 5081 0.311165 TCGCTCGATTAGGCACTAGC 59.689 55.0 0.00 0.0 44.25 3.42 F
3407 8274 0.178843 ATCCCTACCACACCCACCTT 60.179 55.0 0.00 0.0 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1185 3379 0.389948 GGTCGGACTGGTGCTTGTAG 60.390 60.000 8.23 0.00 0.00 2.74 R
1909 4528 6.346678 CGCTAAGTCAAAAGAGTTAAGGACAC 60.347 42.308 0.00 0.00 0.00 3.67 R
2927 7132 0.393537 GTCATCCCAGGCCTTGTCAG 60.394 60.000 0.00 0.00 0.00 3.51 R
3734 8672 0.178903 AGTTGCTCCTGTAGGACCCA 60.179 55.000 0.00 0.00 39.78 4.51 R
4235 9174 0.320374 CGGGATCCATTAGGCGCTAA 59.680 55.000 15.23 4.47 33.74 3.09 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
40 41 2.545526 CGATGGTTCATGATTTCTCCGG 59.454 50.000 0.00 0.00 0.00 5.14
42 43 3.931907 TGGTTCATGATTTCTCCGGAT 57.068 42.857 3.57 0.00 0.00 4.18
84 1510 1.478105 AGCCGGGATTCAAATTTCTGC 59.522 47.619 2.18 0.00 0.00 4.26
95 1521 3.796178 TCAAATTTCTGCAGCACGTTTTC 59.204 39.130 9.47 0.00 0.00 2.29
104 1530 2.966309 GCACGTTTTCTGCGAGGGG 61.966 63.158 0.00 0.00 0.00 4.79
108 1534 1.377333 GTTTTCTGCGAGGGGGAGG 60.377 63.158 0.00 0.00 34.34 4.30
112 1538 2.364317 CTGCGAGGGGGAGGAGAA 60.364 66.667 0.00 0.00 0.00 2.87
113 1539 2.364317 TGCGAGGGGGAGGAGAAG 60.364 66.667 0.00 0.00 0.00 2.85
115 1541 2.444895 CGAGGGGGAGGAGAAGGG 60.445 72.222 0.00 0.00 0.00 3.95
117 1543 2.543637 AGGGGGAGGAGAAGGGGA 60.544 66.667 0.00 0.00 0.00 4.81
119 1545 2.647949 GGGGGAGGAGAAGGGGAGA 61.648 68.421 0.00 0.00 0.00 3.71
121 1547 1.764454 GGGAGGAGAAGGGGAGAGC 60.764 68.421 0.00 0.00 0.00 4.09
122 1548 1.002274 GGAGGAGAAGGGGAGAGCA 59.998 63.158 0.00 0.00 0.00 4.26
123 1549 0.399806 GGAGGAGAAGGGGAGAGCAT 60.400 60.000 0.00 0.00 0.00 3.79
124 1550 1.133009 GGAGGAGAAGGGGAGAGCATA 60.133 57.143 0.00 0.00 0.00 3.14
249 1684 3.561143 TGTCCTTGTTTGCTATTGGTGT 58.439 40.909 0.00 0.00 0.00 4.16
304 1739 9.541884 TGGATAAGCATGTATATACTGAACCTA 57.458 33.333 13.89 0.36 0.00 3.08
373 2542 5.184892 AGAGATAGGACTGCCAAATTGTT 57.815 39.130 0.00 0.00 36.29 2.83
404 2573 4.214758 GTCGGCACCACAGTAAAAGTTATT 59.785 41.667 0.00 0.00 0.00 1.40
416 2585 7.393234 ACAGTAAAAGTTATTTGGAGCTGCATA 59.607 33.333 9.39 4.42 0.00 3.14
417 2586 8.408601 CAGTAAAAGTTATTTGGAGCTGCATAT 58.591 33.333 9.39 12.75 0.00 1.78
418 2587 8.408601 AGTAAAAGTTATTTGGAGCTGCATATG 58.591 33.333 18.91 0.00 0.00 1.78
419 2588 4.843220 AGTTATTTGGAGCTGCATATGC 57.157 40.909 21.09 21.09 42.50 3.14
487 2657 1.544724 TCTGCAAACCCATGCTAACC 58.455 50.000 0.67 0.00 46.54 2.85
489 2659 1.247419 TGCAAACCCATGCTAACCCG 61.247 55.000 0.67 0.00 46.54 5.28
490 2660 1.944234 GCAAACCCATGCTAACCCGG 61.944 60.000 0.00 0.00 43.06 5.73
491 2661 1.680989 AAACCCATGCTAACCCGGC 60.681 57.895 0.00 0.00 0.00 6.13
522 2693 5.832060 GCCCCTAGATAAAGGTCGCTATATA 59.168 44.000 0.00 0.00 34.56 0.86
523 2694 6.494146 GCCCCTAGATAAAGGTCGCTATATAT 59.506 42.308 0.00 0.00 34.56 0.86
544 2715 2.892852 TCCTTTCTTTTGCCATCACTGG 59.107 45.455 0.00 0.00 46.17 4.00
545 2716 2.629617 CCTTTCTTTTGCCATCACTGGT 59.370 45.455 0.00 0.00 45.10 4.00
567 2754 5.645497 GGTGATGAGTTACTTGAGAAGCAAT 59.355 40.000 0.00 0.00 35.59 3.56
571 2758 4.692625 TGAGTTACTTGAGAAGCAATGAGC 59.307 41.667 0.00 0.00 46.19 4.26
837 3027 0.764369 ATCAATCTGCCTCCCCGCTA 60.764 55.000 0.00 0.00 0.00 4.26
1212 3409 2.677524 CAGTCCGACCCCACCGTA 60.678 66.667 0.00 0.00 0.00 4.02
1350 3551 1.080501 CTGGTTCTCTTCTCGCGCA 60.081 57.895 8.75 0.00 0.00 6.09
1357 3558 0.506080 CTCTTCTCGCGCATGCATAC 59.494 55.000 19.57 5.35 42.97 2.39
1358 3559 0.179113 TCTTCTCGCGCATGCATACA 60.179 50.000 19.57 0.00 42.97 2.29
1359 3560 0.863799 CTTCTCGCGCATGCATACAT 59.136 50.000 19.57 0.00 42.97 2.29
1360 3561 2.061028 CTTCTCGCGCATGCATACATA 58.939 47.619 19.57 0.00 42.97 2.29
1364 3565 1.792367 TCGCGCATGCATACATAACTC 59.208 47.619 19.57 0.00 42.97 3.01
1367 3568 2.485426 GCGCATGCATACATAACTCCAT 59.515 45.455 19.57 0.00 42.15 3.41
1403 3609 2.776312 TTCGTGTGAGACTGACTGTC 57.224 50.000 0.00 0.00 45.67 3.51
1408 3614 2.030363 GTGTGAGACTGACTGTCCTCTG 60.030 54.545 5.17 0.00 46.46 3.35
1909 4528 1.566018 GCTGGGAAAGTCGTTGACCG 61.566 60.000 0.00 0.00 32.18 4.79
2040 4674 6.220201 TGAAGTTAATTGCTGGTAAAAAGCC 58.780 36.000 0.00 0.00 40.06 4.35
2051 4685 7.059788 TGCTGGTAAAAAGCCATTATCAGATA 58.940 34.615 14.75 3.97 41.80 1.98
2197 4939 2.738587 TTTTAGTGGACCTGTGCCAA 57.261 45.000 0.00 0.00 37.12 4.52
2199 4941 2.738587 TTAGTGGACCTGTGCCAAAA 57.261 45.000 0.00 0.00 37.12 2.44
2339 5081 0.311165 TCGCTCGATTAGGCACTAGC 59.689 55.000 0.00 0.00 44.25 3.42
2460 5583 2.225467 GCAGAAGTCCAGGGATAATGC 58.775 52.381 0.00 0.00 0.00 3.56
2517 5741 3.434940 ACCATCCCTTTCTGGTTACAC 57.565 47.619 0.00 0.00 43.21 2.90
2927 7132 2.670414 GAGCTGCTGTCATCTACAACAC 59.330 50.000 7.01 0.00 37.74 3.32
2928 7133 2.301296 AGCTGCTGTCATCTACAACACT 59.699 45.455 0.00 0.00 37.74 3.55
3067 7862 2.034558 ACTTGGCTTTGGTCACAAATCG 59.965 45.455 0.00 0.00 44.91 3.34
3132 7975 7.972832 TCACACGGGATATATTTGATTAACC 57.027 36.000 0.00 0.00 0.00 2.85
3216 8059 7.807977 ATCAGGATAATATTGCAAACGAACT 57.192 32.000 1.71 0.00 0.00 3.01
3407 8274 0.178843 ATCCCTACCACACCCACCTT 60.179 55.000 0.00 0.00 0.00 3.50
3422 8289 2.615493 CCACCTTAAAGATGCTCCGTGT 60.615 50.000 0.00 0.00 0.00 4.49
3762 8700 1.000955 ACAGGAGCAACTAAGTCACCG 59.999 52.381 0.00 0.00 0.00 4.94
3809 8747 3.133721 AGATATGTGCGAAGAAGAAGGCT 59.866 43.478 0.00 0.00 0.00 4.58
3840 8778 0.461870 ATGCGCTATGGTTGCTCGAA 60.462 50.000 9.73 0.00 0.00 3.71
3865 8803 2.026262 ACACCTTTGTCCTGTTCAGTGT 60.026 45.455 0.00 0.00 32.64 3.55
3870 8808 0.673985 TGTCCTGTTCAGTGTCTCCG 59.326 55.000 0.00 0.00 0.00 4.63
3982 8920 1.642728 TGTTTGCTTGCTGCTGTTTG 58.357 45.000 0.00 0.00 43.37 2.93
4032 8970 6.969473 CGCTCTATGTACTCATGTATGTATGG 59.031 42.308 0.00 0.00 35.70 2.74
4052 8990 4.598022 TGGATGCATGTGGAGAATTTGTA 58.402 39.130 2.46 0.00 0.00 2.41
4127 9066 3.788227 TCCACAGCTTCCATTAACTGT 57.212 42.857 0.00 0.00 43.92 3.55
4143 9082 8.410141 CCATTAACTGTTTTTAGAACCAAGACA 58.590 33.333 0.00 0.00 0.00 3.41
4235 9174 7.566760 TTGGCGAATGTTATGTATTTCATCT 57.433 32.000 0.00 0.00 37.91 2.90
4240 9179 7.475565 GCGAATGTTATGTATTTCATCTTAGCG 59.524 37.037 0.00 0.00 37.91 4.26
4253 9192 1.623811 TCTTAGCGCCTAATGGATCCC 59.376 52.381 9.90 0.00 34.57 3.85
4258 9197 2.358737 CCTAATGGATCCCGCGCC 60.359 66.667 9.90 0.00 34.57 6.53
4259 9198 2.425592 CTAATGGATCCCGCGCCA 59.574 61.111 9.90 2.29 38.78 5.69
4260 9199 1.669115 CTAATGGATCCCGCGCCAG 60.669 63.158 9.90 0.00 37.64 4.85
4293 9232 2.033065 CGCATTGCTGTGATCTAAGAGC 60.033 50.000 7.12 0.00 34.71 4.09
4294 9233 2.941064 GCATTGCTGTGATCTAAGAGCA 59.059 45.455 0.16 1.20 39.66 4.26
4299 9238 2.857152 GCTGTGATCTAAGAGCAAGTCG 59.143 50.000 0.00 0.00 26.97 4.18
4303 9242 2.166459 TGATCTAAGAGCAAGTCGTGGG 59.834 50.000 0.00 0.00 0.00 4.61
4312 9251 1.227853 AAGTCGTGGGCTGTGGTTC 60.228 57.895 0.00 0.00 0.00 3.62
4426 9366 8.630917 TCAAAATTGTTCATGAATTGCCAAAAT 58.369 25.926 12.12 2.55 0.00 1.82
4555 9495 9.278734 GGAATATTTGAGATTTCGACAAAGTTC 57.721 33.333 12.75 12.75 37.04 3.01
4557 9497 9.612620 AATATTTGAGATTTCGACAAAGTTCAC 57.387 29.630 4.72 0.00 37.04 3.18
4558 9498 6.677781 TTTGAGATTTCGACAAAGTTCACT 57.322 33.333 0.00 0.00 0.00 3.41
4562 9502 7.796838 TGAGATTTCGACAAAGTTCACTAATG 58.203 34.615 0.00 0.00 0.00 1.90
4595 9535 7.462731 TGTTCATGATTTCAAAACTTGTTTGC 58.537 30.769 0.00 0.00 31.15 3.68
4596 9536 6.271396 TCATGATTTCAAAACTTGTTTGCG 57.729 33.333 0.00 0.00 0.00 4.85
4598 9538 6.533012 TCATGATTTCAAAACTTGTTTGCGAA 59.467 30.769 0.00 3.95 0.00 4.70
4602 9542 7.691463 TGATTTCAAAACTTGTTTGCGAATTTG 59.309 29.630 0.00 4.08 0.00 2.32
4603 9543 6.712241 TTCAAAACTTGTTTGCGAATTTGA 57.288 29.167 7.89 7.89 34.55 2.69
4604 9544 6.900568 TCAAAACTTGTTTGCGAATTTGAT 57.099 29.167 7.89 0.00 32.26 2.57
4605 9545 7.301068 TCAAAACTTGTTTGCGAATTTGATT 57.699 28.000 7.89 0.00 32.26 2.57
4607 9547 8.233190 TCAAAACTTGTTTGCGAATTTGATTTT 58.767 25.926 7.89 2.19 32.26 1.82
4608 9548 8.848528 CAAAACTTGTTTGCGAATTTGATTTTT 58.151 25.926 0.00 0.00 0.00 1.94
4609 9549 8.599876 AAACTTGTTTGCGAATTTGATTTTTC 57.400 26.923 0.00 0.00 0.00 2.29
4610 9550 7.538303 ACTTGTTTGCGAATTTGATTTTTCT 57.462 28.000 0.00 0.00 0.00 2.52
4611 9551 7.973601 ACTTGTTTGCGAATTTGATTTTTCTT 58.026 26.923 0.00 0.00 0.00 2.52
4612 9552 7.904461 ACTTGTTTGCGAATTTGATTTTTCTTG 59.096 29.630 0.00 0.00 0.00 3.02
4613 9553 6.713520 TGTTTGCGAATTTGATTTTTCTTGG 58.286 32.000 0.00 0.00 0.00 3.61
4614 9554 4.988708 TGCGAATTTGATTTTTCTTGGC 57.011 36.364 0.00 0.00 0.00 4.52
4615 9555 4.375272 TGCGAATTTGATTTTTCTTGGCA 58.625 34.783 0.00 0.00 0.00 4.92
4616 9556 4.813161 TGCGAATTTGATTTTTCTTGGCAA 59.187 33.333 0.00 0.00 0.00 4.52
4617 9557 5.295292 TGCGAATTTGATTTTTCTTGGCAAA 59.705 32.000 0.00 0.00 33.59 3.68
4619 9559 6.857451 GCGAATTTGATTTTTCTTGGCAAAAT 59.143 30.769 0.00 0.00 36.69 1.82
4662 9602 8.964420 TCAAGAAATGTTTATGAATTCGGAAC 57.036 30.769 0.04 6.26 0.00 3.62
4700 9640 3.201726 ACATCGGCGTGAATTTGAAAG 57.798 42.857 6.85 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.173708 ATCGGTGGTCGCTTTCTCTC 59.826 55.000 0.00 0.00 39.05 3.20
40 41 1.885871 GGTCTGGCCTTTGTGCATC 59.114 57.895 3.32 0.00 0.00 3.91
84 1510 1.205064 CCTCGCAGAAAACGTGCTG 59.795 57.895 8.49 8.49 38.88 4.41
95 1521 2.364317 TTCTCCTCCCCCTCGCAG 60.364 66.667 0.00 0.00 0.00 5.18
104 1530 0.399806 ATGCTCTCCCCTTCTCCTCC 60.400 60.000 0.00 0.00 0.00 4.30
108 1534 2.029470 CGTGATATGCTCTCCCCTTCTC 60.029 54.545 0.00 0.00 0.00 2.87
112 1538 1.333177 GACGTGATATGCTCTCCCCT 58.667 55.000 0.00 0.00 0.00 4.79
113 1539 1.040646 TGACGTGATATGCTCTCCCC 58.959 55.000 0.00 0.00 0.00 4.81
115 1541 2.159240 TGTGTGACGTGATATGCTCTCC 60.159 50.000 0.00 0.00 0.00 3.71
117 1543 2.736719 GCTGTGTGACGTGATATGCTCT 60.737 50.000 0.00 0.00 0.00 4.09
119 1545 1.205655 AGCTGTGTGACGTGATATGCT 59.794 47.619 0.00 0.00 0.00 3.79
121 1547 2.222886 GCAAGCTGTGTGACGTGATATG 60.223 50.000 0.00 0.00 0.00 1.78
122 1548 2.002586 GCAAGCTGTGTGACGTGATAT 58.997 47.619 0.00 0.00 0.00 1.63
123 1549 1.270041 TGCAAGCTGTGTGACGTGATA 60.270 47.619 0.00 0.00 0.00 2.15
124 1550 0.532640 TGCAAGCTGTGTGACGTGAT 60.533 50.000 0.00 0.00 0.00 3.06
249 1684 4.940046 GGAGATGCTCAGAAACTTGATTGA 59.060 41.667 0.00 0.00 31.08 2.57
352 2521 4.034510 CGAACAATTTGGCAGTCCTATCTC 59.965 45.833 0.78 0.00 0.00 2.75
373 2542 2.599281 TGGTGCCGACTTCTCCGA 60.599 61.111 0.00 0.00 0.00 4.55
490 2660 1.335145 TTATCTAGGGGCGTGTAGGC 58.665 55.000 0.00 0.00 45.91 3.93
491 2661 2.299297 CCTTTATCTAGGGGCGTGTAGG 59.701 54.545 0.00 0.00 0.00 3.18
522 2693 3.512724 CCAGTGATGGCAAAAGAAAGGAT 59.487 43.478 0.00 0.00 0.00 3.24
523 2694 2.892852 CCAGTGATGGCAAAAGAAAGGA 59.107 45.455 0.00 0.00 0.00 3.36
544 2715 6.369890 TCATTGCTTCTCAAGTAACTCATCAC 59.630 38.462 0.00 0.00 38.22 3.06
545 2716 6.466812 TCATTGCTTCTCAAGTAACTCATCA 58.533 36.000 0.00 0.00 38.22 3.07
837 3027 1.172812 GGCTCGAGTTTGGCCTGTTT 61.173 55.000 15.13 0.00 42.31 2.83
1185 3379 0.389948 GGTCGGACTGGTGCTTGTAG 60.390 60.000 8.23 0.00 0.00 2.74
1357 3558 5.890424 TGATGCATGCATATGGAGTTATG 57.110 39.130 32.27 0.00 38.08 1.90
1358 3559 6.451064 CATGATGCATGCATATGGAGTTAT 57.549 37.500 32.27 9.77 38.08 1.89
1359 3560 5.890424 CATGATGCATGCATATGGAGTTA 57.110 39.130 32.27 7.66 38.08 2.24
1360 3561 4.783764 CATGATGCATGCATATGGAGTT 57.216 40.909 32.27 9.74 38.08 3.01
1385 3586 0.952280 GGACAGTCAGTCTCACACGA 59.048 55.000 2.17 0.00 46.72 4.35
1386 3587 0.955178 AGGACAGTCAGTCTCACACG 59.045 55.000 2.17 0.00 46.72 4.49
1403 3609 2.159043 ACCTATGCATCGTGAACAGAGG 60.159 50.000 0.19 3.33 46.03 3.69
1408 3614 1.933853 GTCCACCTATGCATCGTGAAC 59.066 52.381 22.28 12.73 0.00 3.18
1541 3751 1.376466 GCTCTGGAAGCCCTTGACA 59.624 57.895 0.00 0.00 45.92 3.58
1909 4528 6.346678 CGCTAAGTCAAAAGAGTTAAGGACAC 60.347 42.308 0.00 0.00 0.00 3.67
2051 4685 7.227512 GCACTGGTAGCAGAAATTGAGTATATT 59.772 37.037 27.87 0.00 0.00 1.28
2538 5809 7.118390 TGTTTGAAAATTGTGTAACCAGTTTGG 59.882 33.333 0.00 0.00 45.02 3.28
2539 5810 8.023050 TGTTTGAAAATTGTGTAACCAGTTTG 57.977 30.769 0.00 0.00 29.65 2.93
2545 5816 8.272866 GCATACTTGTTTGAAAATTGTGTAACC 58.727 33.333 0.00 0.00 34.36 2.85
2548 5819 8.629158 AGAGCATACTTGTTTGAAAATTGTGTA 58.371 29.630 0.00 0.00 0.00 2.90
2623 5894 7.819900 AGATGTTACTTTTAGGTGAGCTGTAAG 59.180 37.037 0.00 0.35 0.00 2.34
2629 5900 7.900782 TTGTAGATGTTACTTTTAGGTGAGC 57.099 36.000 0.00 0.00 0.00 4.26
2927 7132 0.393537 GTCATCCCAGGCCTTGTCAG 60.394 60.000 0.00 0.00 0.00 3.51
2928 7133 1.685224 GTCATCCCAGGCCTTGTCA 59.315 57.895 0.00 0.00 0.00 3.58
2999 7296 6.640518 CCATTGCTTAACTGTAGGAAGTCTA 58.359 40.000 0.00 0.00 0.00 2.59
3000 7297 5.491982 CCATTGCTTAACTGTAGGAAGTCT 58.508 41.667 0.00 0.00 0.00 3.24
3001 7298 4.095036 GCCATTGCTTAACTGTAGGAAGTC 59.905 45.833 0.00 0.00 33.53 3.01
3006 7683 6.449635 TTTATGCCATTGCTTAACTGTAGG 57.550 37.500 0.00 0.00 36.98 3.18
3017 7694 8.767478 AGCTGATAAATATTTTATGCCATTGC 57.233 30.769 5.91 2.58 38.26 3.56
3067 7862 4.034975 AGTTATCAAGTACTAGTCGACCGC 59.965 45.833 13.01 0.00 0.00 5.68
3187 8030 9.500785 TCGTTTGCAATATTATCCTGATTATGA 57.499 29.630 0.00 0.00 0.00 2.15
3216 8059 5.369685 TTGCAATATCTTCGAAAGCAACA 57.630 34.783 0.00 0.00 35.81 3.33
3329 8174 6.338146 TGTCATGCATAACCTAAGTGAGTAC 58.662 40.000 0.00 0.00 0.00 2.73
3407 8274 6.399743 TGTTATGTTACACGGAGCATCTTTA 58.600 36.000 0.00 0.00 33.73 1.85
3734 8672 0.178903 AGTTGCTCCTGTAGGACCCA 60.179 55.000 0.00 0.00 39.78 4.51
3840 8778 2.291282 TGAACAGGACAAAGGTGTTGGT 60.291 45.455 0.00 0.00 38.41 3.67
3843 8781 3.016736 CACTGAACAGGACAAAGGTGTT 58.983 45.455 6.76 0.00 38.41 3.32
3865 8803 1.554617 TGATGATGCAAAGACCGGAGA 59.445 47.619 9.46 0.00 0.00 3.71
3870 8808 2.846039 CAGCTGATGATGCAAAGACC 57.154 50.000 8.42 0.00 0.00 3.85
3982 8920 5.705905 AGTAAAAGGATAGCACACTTGGAAC 59.294 40.000 0.00 0.00 0.00 3.62
4032 8970 7.259882 TGATTTACAAATTCTCCACATGCATC 58.740 34.615 0.00 0.00 0.00 3.91
4105 9044 3.821033 ACAGTTAATGGAAGCTGTGGAAC 59.179 43.478 0.00 0.00 40.24 3.62
4198 9137 6.371809 ACATTCGCCAATTATATTGACGTT 57.628 33.333 7.73 0.00 0.00 3.99
4199 9138 6.371809 AACATTCGCCAATTATATTGACGT 57.628 33.333 7.73 0.00 0.00 4.34
4214 9153 7.475565 CGCTAAGATGAAATACATAACATTCGC 59.524 37.037 0.00 0.00 39.56 4.70
4223 9162 6.372659 CCATTAGGCGCTAAGATGAAATACAT 59.627 38.462 7.64 0.00 42.47 2.29
4235 9174 0.320374 CGGGATCCATTAGGCGCTAA 59.680 55.000 15.23 4.47 33.74 3.09
4240 9179 3.050275 GCGCGGGATCCATTAGGC 61.050 66.667 15.23 7.44 33.74 3.93
4268 9207 1.215244 AGATCACAGCAATGCGATCG 58.785 50.000 11.69 11.69 39.39 3.69
4293 9232 1.507141 GAACCACAGCCCACGACTTG 61.507 60.000 0.00 0.00 0.00 3.16
4294 9233 1.227853 GAACCACAGCCCACGACTT 60.228 57.895 0.00 0.00 0.00 3.01
4299 9238 0.603065 GAAATGGAACCACAGCCCAC 59.397 55.000 0.00 0.00 32.07 4.61
4303 9242 3.665745 ATTGTGAAATGGAACCACAGC 57.334 42.857 0.00 0.00 41.17 4.40
4312 9251 9.784680 TGAACATTTTTCAAAATTGTGAAATGG 57.215 25.926 21.64 16.24 44.71 3.16
4368 9307 9.083080 AGGAACAGTTTTTAATTTCGTGAAAAG 57.917 29.630 0.00 0.00 33.56 2.27
4370 9309 9.724839 CTAGGAACAGTTTTTAATTTCGTGAAA 57.275 29.630 0.00 0.00 34.46 2.69
4388 9327 9.695526 CATGAACAATTTTGAAATCTAGGAACA 57.304 29.630 0.00 0.00 0.00 3.18
4429 9369 9.814899 ATGTTTCAAATACACTTGAATTTGTGA 57.185 25.926 12.11 0.00 43.12 3.58
4474 9414 8.685427 TCATGAACGTATTTTGAAATCATGGAT 58.315 29.630 16.72 0.00 31.67 3.41
4479 9419 9.905171 TGAAATCATGAACGTATTTTGAAATCA 57.095 25.926 0.00 0.00 0.00 2.57
4529 9469 9.278734 GAACTTTGTCGAAATCTCAAATATTCC 57.721 33.333 0.00 0.00 32.04 3.01
4546 9486 9.736023 ACATTCTTTTCATTAGTGAACTTTGTC 57.264 29.630 0.00 0.00 43.72 3.18
4552 9492 9.897744 TCATGAACATTCTTTTCATTAGTGAAC 57.102 29.630 0.00 0.00 43.72 3.18
4581 9521 6.900568 ATCAAATTCGCAAACAAGTTTTGA 57.099 29.167 0.91 0.00 36.42 2.69
4585 9525 7.973601 AGAAAAATCAAATTCGCAAACAAGTT 58.026 26.923 0.00 0.00 0.00 2.66
4586 9526 7.538303 AGAAAAATCAAATTCGCAAACAAGT 57.462 28.000 0.00 0.00 0.00 3.16
4587 9527 7.373966 CCAAGAAAAATCAAATTCGCAAACAAG 59.626 33.333 0.00 0.00 0.00 3.16
4595 9535 9.875675 TTATTTTGCCAAGAAAAATCAAATTCG 57.124 25.926 0.00 0.00 38.06 3.34
4636 9576 9.405587 GTTCCGAATTCATAAACATTTCTTGAA 57.594 29.630 6.22 5.58 31.40 2.69
4637 9577 8.792633 AGTTCCGAATTCATAAACATTTCTTGA 58.207 29.630 6.22 0.00 0.00 3.02
4638 9578 8.970691 AGTTCCGAATTCATAAACATTTCTTG 57.029 30.769 6.22 0.00 0.00 3.02
4685 9625 4.382754 GTGAACATCTTTCAAATTCACGCC 59.617 41.667 0.00 0.00 39.65 5.68


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

AutoCloner maintained by Alex Coulton.