Multiple sequence alignment - TraesCS6B01G251800

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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 TraesCS6B01G251800 chr6B 100.000 4040 0 0 1 4040 451924073 451928112 0.000000e+00 7461.0
1 TraesCS6B01G251800 chr6B 78.539 438 78 14 1 430 664262419 664261990 1.430000e-69 274.0
2 TraesCS6B01G251800 chr6B 76.940 451 87 14 5 446 544792652 544792210 1.450000e-59 241.0
3 TraesCS6B01G251800 chr6A 90.657 3179 167 47 1 3121 432510371 432513477 0.000000e+00 4106.0
4 TraesCS6B01G251800 chr6A 96.383 470 13 3 3573 4040 432519283 432519750 0.000000e+00 771.0
5 TraesCS6B01G251800 chr6A 94.681 188 7 2 3153 3338 432513609 432513795 5.110000e-74 289.0
6 TraesCS6B01G251800 chr6A 89.121 239 11 4 3375 3598 432519041 432519279 2.380000e-72 283.0
7 TraesCS6B01G251800 chr6A 77.574 437 80 17 5 432 76746286 76746713 8.670000e-62 248.0
8 TraesCS6B01G251800 chr6A 77.015 335 69 7 5 334 771085 770754 6.900000e-43 185.0
9 TraesCS6B01G251800 chr6A 97.778 45 1 0 3335 3379 432513845 432513889 1.200000e-10 78.7
10 TraesCS6B01G251800 chr6A 100.000 33 0 0 3126 3158 432513499 432513531 1.210000e-05 62.1
11 TraesCS6B01G251800 chr6D 90.913 2212 106 31 283 2449 291151953 291149792 0.000000e+00 2883.0
12 TraesCS6B01G251800 chr6D 94.045 890 29 9 2470 3338 291149727 291148841 0.000000e+00 1328.0
13 TraesCS6B01G251800 chr6D 91.429 490 15 9 3578 4040 291148387 291147898 0.000000e+00 647.0
14 TraesCS6B01G251800 chr6D 96.296 270 10 0 1 270 291152486 291152217 1.030000e-120 444.0
15 TraesCS6B01G251800 chr6D 96.899 129 4 0 3445 3573 291148554 291148426 2.450000e-52 217.0
16 TraesCS6B01G251800 chr6D 96.552 87 3 0 3338 3424 291148788 291148702 1.170000e-30 145.0
17 TraesCS6B01G251800 chr5A 78.414 454 81 15 1 446 671096020 671096464 3.070000e-71 279.0
18 TraesCS6B01G251800 chr5A 91.667 48 4 0 3155 3202 667304880 667304833 2.610000e-07 67.6
19 TraesCS6B01G251800 chr5A 94.872 39 2 0 3157 3195 582384183 582384145 1.210000e-05 62.1
20 TraesCS6B01G251800 chr7A 77.181 447 88 12 5 444 38231444 38231005 8.670000e-62 248.0
21 TraesCS6B01G251800 chr5D 77.546 432 80 15 7 430 483092964 483092542 1.120000e-60 244.0
22 TraesCS6B01G251800 chr5D 94.872 39 2 0 3157 3195 462076911 462076873 1.210000e-05 62.1
23 TraesCS6B01G251800 chr4D 93.333 45 3 0 3158 3202 486932213 486932169 2.610000e-07 67.6
24 TraesCS6B01G251800 chr2B 90.385 52 4 1 3377 3428 608447112 608447062 2.610000e-07 67.6
25 TraesCS6B01G251800 chr2A 90.385 52 4 1 3377 3428 660512218 660512168 2.610000e-07 67.6
26 TraesCS6B01G251800 chr2D 88.462 52 5 1 3377 3428 516706832 516706782 1.210000e-05 62.1


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 TraesCS6B01G251800 chr6B 451924073 451928112 4039 False 7461.00 7461 100.000000 1 4040 1 chr6B.!!$F1 4039
1 TraesCS6B01G251800 chr6A 432510371 432513889 3518 False 1133.95 4106 95.779000 1 3379 4 chr6A.!!$F2 3378
2 TraesCS6B01G251800 chr6A 432519041 432519750 709 False 527.00 771 92.752000 3375 4040 2 chr6A.!!$F3 665
3 TraesCS6B01G251800 chr6D 291147898 291152486 4588 True 944.00 2883 94.355667 1 4040 6 chr6D.!!$R1 4039

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
922 1193 0.176219 AACTCGACCAAACCACACGA 59.824 50.000 0.0 0.0 0.00 4.35 F
924 1195 0.859232 CTCGACCAAACCACACGAAG 59.141 55.000 0.0 0.0 32.85 3.79 F
946 1217 1.203250 GGAAACCCAAATTCCCTCCCA 60.203 52.381 0.0 0.0 40.41 4.37 F
1250 1524 1.341531 CCATCGTAATCCTTCTCCGCT 59.658 52.381 0.0 0.0 0.00 5.52 F
2551 2899 0.609957 TTGGCACTGAAGCTGATGGG 60.610 55.000 0.0 0.0 34.17 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2221 2525 0.166814 GCAGGAGTCGCATTCACAAC 59.833 55.000 0.0 0.0 0.00 3.32 R
2222 2526 0.250252 TGCAGGAGTCGCATTCACAA 60.250 50.000 0.0 0.0 33.55 3.33 R
2223 2527 1.370810 TGCAGGAGTCGCATTCACA 59.629 52.632 0.0 0.0 33.55 3.58 R
2921 3270 2.863809 TCAGAAAAGCTCAAAGGTCCC 58.136 47.619 0.0 0.0 0.00 4.46 R
3458 4090 0.826062 GGCCCTGTTTGGATTGGATG 59.174 55.000 0.0 0.0 38.35 3.51 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
78 79 7.768240 ACGAATTTAAGGTGGTGGAAAATATC 58.232 34.615 0.00 0.00 0.00 1.63
125 126 7.489160 AGTTATGTCGAGCATTGTGTATAAGA 58.511 34.615 5.94 0.00 38.94 2.10
145 146 4.091549 AGATAGGTTACGGTTGGACTTGA 58.908 43.478 0.00 0.00 0.00 3.02
158 159 2.059541 GGACTTGAAGTCGTACTGTGC 58.940 52.381 18.13 0.00 45.96 4.57
172 173 1.001815 ACTGTGCGTAAACATGGCAAC 60.002 47.619 0.00 0.00 38.58 4.17
236 237 7.511028 TCATATATAACATGGGGTAGACACACA 59.489 37.037 0.00 0.00 0.00 3.72
244 245 3.391626 TGGGGTAGACACACAATGTAACA 59.608 43.478 0.00 0.00 43.56 2.41
273 274 5.746307 AACATAATAGCACATGCACTCAG 57.254 39.130 6.64 0.00 45.16 3.35
275 276 2.048444 AATAGCACATGCACTCAGGG 57.952 50.000 6.64 0.00 45.16 4.45
288 540 0.534412 CTCAGGGAAGCTGACGACAT 59.466 55.000 0.00 0.00 0.00 3.06
300 552 1.841663 GACGACATGTGCCAGCGTTT 61.842 55.000 1.15 0.00 35.09 3.60
335 587 6.590292 GTGTGCAGTATTATAGCGGTATCAAT 59.410 38.462 10.99 11.26 0.00 2.57
336 588 7.758076 GTGTGCAGTATTATAGCGGTATCAATA 59.242 37.037 10.99 10.40 0.00 1.90
353 605 3.321111 TCAATAGGGAGAAGCGTCCATAC 59.679 47.826 0.00 0.00 35.74 2.39
361 613 1.264749 AAGCGTCCATACTCAGGCCA 61.265 55.000 5.01 0.00 0.00 5.36
362 614 1.521681 GCGTCCATACTCAGGCCAC 60.522 63.158 5.01 0.00 0.00 5.01
364 616 0.249120 CGTCCATACTCAGGCCACAA 59.751 55.000 5.01 0.00 0.00 3.33
376 628 3.502164 GCCACAAGGATGTAGCCAT 57.498 52.632 0.00 0.00 38.11 4.40
405 657 8.279970 TCGATGAACCTCATTAACAAATCATT 57.720 30.769 0.00 0.00 37.20 2.57
433 686 4.707030 TGCCTTGTTGATTGCTTGATAG 57.293 40.909 0.00 0.00 0.00 2.08
474 727 6.877322 GCACCTTAGATTAGTTCTAACACCAA 59.123 38.462 0.00 0.00 41.10 3.67
482 736 6.930667 TTAGTTCTAACACCAACCTTGTTC 57.069 37.500 0.00 0.00 38.21 3.18
483 737 5.112129 AGTTCTAACACCAACCTTGTTCT 57.888 39.130 0.00 0.00 38.21 3.01
533 789 2.282251 AGCCGTGTCTCCGACAGA 60.282 61.111 0.00 0.00 43.57 3.41
547 803 0.179108 GACAGACCTTCCGGGATTCG 60.179 60.000 0.00 0.00 38.76 3.34
592 848 6.641062 CATTCGTTTAGATTCGACTGGATTC 58.359 40.000 0.00 0.00 34.67 2.52
630 887 7.782049 AGTTTCTACATGTCCTTATCGATGAA 58.218 34.615 8.54 0.00 0.00 2.57
693 953 7.013655 AGTGGAACAGATTTTGCATATGTATCC 59.986 37.037 4.29 2.01 41.80 2.59
820 1080 2.814341 CACCAGCTCAGCTCAGCG 60.814 66.667 3.13 0.00 44.82 5.18
861 1121 1.065701 CCGGACCGACTCTTATCACTG 59.934 57.143 17.49 0.00 0.00 3.66
922 1193 0.176219 AACTCGACCAAACCACACGA 59.824 50.000 0.00 0.00 0.00 4.35
923 1194 0.176219 ACTCGACCAAACCACACGAA 59.824 50.000 0.00 0.00 32.85 3.85
924 1195 0.859232 CTCGACCAAACCACACGAAG 59.141 55.000 0.00 0.00 32.85 3.79
946 1217 1.203250 GGAAACCCAAATTCCCTCCCA 60.203 52.381 0.00 0.00 40.41 4.37
1250 1524 1.341531 CCATCGTAATCCTTCTCCGCT 59.658 52.381 0.00 0.00 0.00 5.52
1279 1553 3.546020 CGCCCGTAGTCATTTTGCTATTG 60.546 47.826 0.00 0.00 0.00 1.90
1284 1558 5.753438 CCGTAGTCATTTTGCTATTGCTCTA 59.247 40.000 0.00 0.00 40.48 2.43
1313 1587 3.907894 CCGAATTTTCCGGTTCAGAAA 57.092 42.857 0.00 0.00 41.91 2.52
1511 1786 3.037851 AGTGGCATCCTAGTCTCATCA 57.962 47.619 0.00 0.00 0.00 3.07
1556 1831 7.963465 GTGTTAGCTTGGAGTTCTATTTAAAGC 59.037 37.037 0.00 0.00 39.01 3.51
1558 1833 6.749923 AGCTTGGAGTTCTATTTAAAGCTG 57.250 37.500 6.23 0.00 45.18 4.24
1768 2072 2.870411 GTTAGAGTTGTGCAAACCGAGT 59.130 45.455 0.00 0.00 0.00 4.18
1789 2093 4.039124 AGTTTCAAATGCCAAAATCGTCCT 59.961 37.500 0.00 0.00 0.00 3.85
1810 2114 5.703592 TCCTAAAATAAATATGCGCGTCCAT 59.296 36.000 4.79 6.18 0.00 3.41
1826 2130 3.671433 CGTCCATTGAATGCTTGTCTTGG 60.671 47.826 0.00 0.00 0.00 3.61
1840 2144 3.135225 TGTCTTGGGTCGTGTTTGTATG 58.865 45.455 0.00 0.00 0.00 2.39
2012 2316 8.349245 ACTGATCTGAGACTTGTTCTATATTCG 58.651 37.037 6.60 0.00 33.22 3.34
2013 2317 7.142021 TGATCTGAGACTTGTTCTATATTCGC 58.858 38.462 0.00 0.00 33.22 4.70
2014 2318 6.701145 TCTGAGACTTGTTCTATATTCGCT 57.299 37.500 0.00 0.00 33.22 4.93
2015 2319 7.101652 TCTGAGACTTGTTCTATATTCGCTT 57.898 36.000 0.00 0.00 33.22 4.68
2016 2320 6.975197 TCTGAGACTTGTTCTATATTCGCTTG 59.025 38.462 0.00 0.00 33.22 4.01
2017 2321 5.520288 TGAGACTTGTTCTATATTCGCTTGC 59.480 40.000 0.00 0.00 33.22 4.01
2018 2322 5.665459 AGACTTGTTCTATATTCGCTTGCT 58.335 37.500 0.00 0.00 30.17 3.91
2046 2350 9.928236 GCTTGTTTCAAGCACAAATAAATTTTA 57.072 25.926 23.67 0.00 42.56 1.52
2069 2373 3.952323 TGTGATACTAGGGTGCTGTAGAC 59.048 47.826 0.00 0.00 0.00 2.59
2078 2382 1.684983 GGTGCTGTAGACGCCCTAATA 59.315 52.381 0.00 0.00 0.00 0.98
2079 2383 2.299297 GGTGCTGTAGACGCCCTAATAT 59.701 50.000 0.00 0.00 0.00 1.28
2080 2384 3.508793 GGTGCTGTAGACGCCCTAATATA 59.491 47.826 0.00 0.00 0.00 0.86
2154 2458 8.843885 ACACTTATAAGTTTTCCTAAGGTGAC 57.156 34.615 15.60 0.00 37.08 3.67
2173 2477 5.406175 GGTGACATTCAAATTGTGTTCATGG 59.594 40.000 0.00 0.00 0.00 3.66
2219 2523 1.531149 GTGTTCCATTCCGTGACTGTG 59.469 52.381 0.00 0.00 0.00 3.66
2220 2524 1.414550 TGTTCCATTCCGTGACTGTGA 59.585 47.619 0.00 0.00 0.00 3.58
2221 2525 2.069273 GTTCCATTCCGTGACTGTGAG 58.931 52.381 0.00 0.00 0.00 3.51
2222 2526 1.338107 TCCATTCCGTGACTGTGAGT 58.662 50.000 0.00 0.00 0.00 3.41
2223 2527 1.691976 TCCATTCCGTGACTGTGAGTT 59.308 47.619 0.00 0.00 0.00 3.01
2224 2528 1.800586 CCATTCCGTGACTGTGAGTTG 59.199 52.381 0.00 0.00 0.00 3.16
2429 2733 5.368256 AAAGCTGTAGCAAGATTTCTGTG 57.632 39.130 6.65 0.00 45.16 3.66
2468 2772 7.981102 AAAGAAGTCAAAACATAGTACTCCC 57.019 36.000 0.00 0.00 0.00 4.30
2472 2820 6.287589 AGTCAAAACATAGTACTCCCTCTG 57.712 41.667 0.00 0.00 0.00 3.35
2475 2823 7.453752 AGTCAAAACATAGTACTCCCTCTGTAA 59.546 37.037 0.00 0.00 0.00 2.41
2551 2899 0.609957 TTGGCACTGAAGCTGATGGG 60.610 55.000 0.00 0.00 34.17 4.00
2572 2920 4.941263 GGGCACTGTCTTATCACACATTTA 59.059 41.667 0.00 0.00 0.00 1.40
2853 3201 4.926238 CGTATCTTCCAGAGAATATGTGGC 59.074 45.833 0.00 0.00 42.23 5.01
2856 3204 2.890808 TCCAGAGAATATGTGGCGTC 57.109 50.000 0.00 0.00 42.23 5.19
2887 3236 4.951254 TCAGAAATGTTAGTTGTGTCGGA 58.049 39.130 0.00 0.00 0.00 4.55
2921 3270 5.414360 TCTAGACATAAGTTTGCTCAGCAG 58.586 41.667 0.00 0.00 40.61 4.24
2974 3323 9.665719 ACAAATTTTGTTCCACTAGTTTCAATT 57.334 25.926 8.97 0.00 42.22 2.32
3043 3392 3.904136 AAGCTGTTGCATGTTCAGTAC 57.096 42.857 12.67 0.00 42.74 2.73
3052 3401 6.072728 TGTTGCATGTTCAGTACTTATGTTCC 60.073 38.462 0.00 0.00 0.00 3.62
3085 3434 0.309922 CCAGTGTGCTGAAAGTGCAG 59.690 55.000 0.00 0.00 45.28 4.41
3121 3471 7.165460 AGGTAGTTGTAAATTGGCAATAACC 57.835 36.000 14.05 10.47 34.89 2.85
3124 3474 5.478407 AGTTGTAAATTGGCAATAACCTGC 58.522 37.500 14.05 7.77 41.85 4.85
3161 3611 8.408601 ACTTGTGCATTTTGATATACTCCATTC 58.591 33.333 0.00 0.00 0.00 2.67
3214 3664 5.280654 AGTCAAATTTGGTTGCAGATGTT 57.719 34.783 17.90 0.00 0.00 2.71
3252 3702 8.908786 ATCTCTCTGTTTGTGTTCTTAAATCA 57.091 30.769 0.00 0.00 0.00 2.57
3308 3760 9.635520 ATGAACACATCTCATTTTCAAATTCTC 57.364 29.630 0.00 0.00 28.91 2.87
3391 3896 4.664150 TTTGAAACTAAGGCCCTGTTTG 57.336 40.909 18.87 3.59 34.55 2.93
3411 3916 9.612620 CTGTTTGGATTGAGTGTAAAATTAGTC 57.387 33.333 0.00 0.00 0.00 2.59
3418 3923 6.109156 TGAGTGTAAAATTAGTCTGCTCCA 57.891 37.500 0.00 0.00 0.00 3.86
3573 4205 3.448660 GCATTTTGGAGCCTGGTTTCTAT 59.551 43.478 0.00 0.00 0.00 1.98
3574 4206 4.644685 GCATTTTGGAGCCTGGTTTCTATA 59.355 41.667 0.00 0.00 0.00 1.31
3575 4207 5.127031 GCATTTTGGAGCCTGGTTTCTATAA 59.873 40.000 0.00 0.00 0.00 0.98
3577 4209 6.584185 TTTTGGAGCCTGGTTTCTATAAAC 57.416 37.500 0.00 0.00 43.58 2.01
3578 4210 5.514500 TTGGAGCCTGGTTTCTATAAACT 57.486 39.130 4.01 0.00 43.76 2.66
3579 4211 6.630203 TTGGAGCCTGGTTTCTATAAACTA 57.370 37.500 4.01 0.00 43.76 2.24
3580 4212 6.824958 TGGAGCCTGGTTTCTATAAACTAT 57.175 37.500 4.01 0.00 43.76 2.12
3582 4214 8.326765 TGGAGCCTGGTTTCTATAAACTATAA 57.673 34.615 4.01 0.00 43.76 0.98
3583 4215 8.429641 TGGAGCCTGGTTTCTATAAACTATAAG 58.570 37.037 4.01 0.00 43.76 1.73
3585 4217 9.478768 GAGCCTGGTTTCTATAAACTATAAGTC 57.521 37.037 4.01 0.00 43.76 3.01
3587 4219 9.478768 GCCTGGTTTCTATAAACTATAAGTCTC 57.521 37.037 4.01 0.00 43.76 3.36
3933 4627 7.017551 ACTGCCCATATCAATATCTACTTTCCA 59.982 37.037 0.00 0.00 0.00 3.53
4010 4704 1.580845 CTGAGCCAACGAAGCCAAGG 61.581 60.000 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 2.604046 AGTAAGCTTCACATAGGCGG 57.396 50.000 0.00 0.00 0.00 6.13
125 126 4.285260 ACTTCAAGTCCAACCGTAACCTAT 59.715 41.667 0.00 0.00 0.00 2.57
145 146 3.082698 TGTTTACGCACAGTACGACTT 57.917 42.857 0.00 0.00 34.56 3.01
158 159 2.032377 ACAACTCGTTGCCATGTTTACG 60.032 45.455 9.55 4.84 44.03 3.18
244 245 9.288576 AGTGCATGTGCTATTATGTTAACATAT 57.711 29.630 25.09 17.77 42.66 1.78
256 257 1.561076 TCCCTGAGTGCATGTGCTATT 59.439 47.619 6.55 0.00 42.66 1.73
273 274 1.639298 GCACATGTCGTCAGCTTCCC 61.639 60.000 0.00 0.00 0.00 3.97
275 276 0.950555 TGGCACATGTCGTCAGCTTC 60.951 55.000 0.00 0.00 0.00 3.86
288 540 3.215568 CACCCAAACGCTGGCACA 61.216 61.111 0.00 0.00 44.90 4.57
300 552 4.584518 CTGCACACTGGCCACCCA 62.585 66.667 0.00 0.00 39.32 4.51
335 587 2.092049 TGAGTATGGACGCTTCTCCCTA 60.092 50.000 0.00 0.00 0.00 3.53
336 588 1.342076 TGAGTATGGACGCTTCTCCCT 60.342 52.381 0.00 0.00 0.00 4.20
353 605 2.322355 CTACATCCTTGTGGCCTGAG 57.678 55.000 3.32 0.00 36.53 3.35
361 613 3.009723 CGAACAATGGCTACATCCTTGT 58.990 45.455 0.00 0.00 35.94 3.16
362 614 3.270027 TCGAACAATGGCTACATCCTTG 58.730 45.455 0.00 0.00 35.94 3.61
364 616 3.134623 TCATCGAACAATGGCTACATCCT 59.865 43.478 0.00 0.00 35.94 3.24
375 627 7.447374 TTGTTAATGAGGTTCATCGAACAAT 57.553 32.000 18.52 0.00 41.94 2.71
376 628 6.869315 TTGTTAATGAGGTTCATCGAACAA 57.131 33.333 18.52 18.52 43.11 2.83
405 657 2.288334 GCAATCAACAAGGCATGACACA 60.288 45.455 0.00 0.00 0.00 3.72
411 663 4.708421 ACTATCAAGCAATCAACAAGGCAT 59.292 37.500 0.00 0.00 0.00 4.40
433 686 2.488545 AGGTGCATATCGATCTACCGAC 59.511 50.000 0.00 0.00 41.70 4.79
474 727 1.102978 GCACACCAACAGAACAAGGT 58.897 50.000 0.00 0.00 33.91 3.50
482 736 1.027357 AGAGCAAAGCACACCAACAG 58.973 50.000 0.00 0.00 0.00 3.16
483 737 2.221169 CTAGAGCAAAGCACACCAACA 58.779 47.619 0.00 0.00 0.00 3.33
547 803 2.481568 GCACCAGAAACCTAAACGTACC 59.518 50.000 0.00 0.00 0.00 3.34
548 804 3.132925 TGCACCAGAAACCTAAACGTAC 58.867 45.455 0.00 0.00 0.00 3.67
551 807 3.666902 CGAATGCACCAGAAACCTAAACG 60.667 47.826 0.00 0.00 0.00 3.60
563 819 3.369756 GTCGAATCTAAACGAATGCACCA 59.630 43.478 0.00 0.00 40.12 4.17
592 848 4.124238 TGTAGAAACTCTGAAAACCACGG 58.876 43.478 0.00 0.00 0.00 4.94
637 894 1.541233 CCAGCATATTGTCGTCTCCCC 60.541 57.143 0.00 0.00 0.00 4.81
638 895 1.139058 ACCAGCATATTGTCGTCTCCC 59.861 52.381 0.00 0.00 0.00 4.30
729 989 7.088905 CCGCCTTATGTTTACTATTCGATACT 58.911 38.462 0.00 0.00 0.00 2.12
730 990 6.865205 ACCGCCTTATGTTTACTATTCGATAC 59.135 38.462 0.00 0.00 0.00 2.24
731 991 6.985117 ACCGCCTTATGTTTACTATTCGATA 58.015 36.000 0.00 0.00 0.00 2.92
733 993 5.068198 AGACCGCCTTATGTTTACTATTCGA 59.932 40.000 0.00 0.00 0.00 3.71
735 995 8.828688 AATAGACCGCCTTATGTTTACTATTC 57.171 34.615 0.00 0.00 0.00 1.75
736 996 9.623000 AAAATAGACCGCCTTATGTTTACTATT 57.377 29.630 0.00 0.00 32.06 1.73
747 1007 6.394025 ACAAAACAAAAATAGACCGCCTTA 57.606 33.333 0.00 0.00 0.00 2.69
749 1009 4.929819 ACAAAACAAAAATAGACCGCCT 57.070 36.364 0.00 0.00 0.00 5.52
941 1212 3.028130 GGAGAGGTAGAGAAGTTGGGAG 58.972 54.545 0.00 0.00 0.00 4.30
946 1217 1.476477 GCCGGAGAGGTAGAGAAGTT 58.524 55.000 5.05 0.00 43.70 2.66
1250 1524 0.974010 ATGACTACGGGCGGGAAAGA 60.974 55.000 0.00 0.00 0.00 2.52
1279 1553 4.965119 AAATTCGGTTCACCATTAGAGC 57.035 40.909 0.00 0.00 35.14 4.09
1284 1558 2.230266 CCGGAAAATTCGGTTCACCATT 59.770 45.455 0.00 0.00 42.33 3.16
1313 1587 9.908152 GTGTAGTAAGCTAAAATGACCAAAAAT 57.092 29.630 0.00 0.00 0.00 1.82
1488 1763 4.342378 TGATGAGACTAGGATGCCACTAAC 59.658 45.833 0.00 0.00 0.00 2.34
1511 1786 8.175716 GCTAACACTTCTAAAATACGCAAGAAT 58.824 33.333 0.00 0.00 43.62 2.40
1591 1866 2.095059 CCTAAAATGCAAACGCAGCTCT 60.095 45.455 0.00 0.00 44.13 4.09
1615 1917 1.367471 CTCGTGCAACTCAGGTCCA 59.633 57.895 0.00 0.00 31.75 4.02
1768 2072 4.599047 AGGACGATTTTGGCATTTGAAA 57.401 36.364 0.00 0.00 0.00 2.69
1789 2093 6.960468 TCAATGGACGCGCATATTTATTTTA 58.040 32.000 5.73 0.00 0.00 1.52
1810 2114 1.879380 CGACCCAAGACAAGCATTCAA 59.121 47.619 0.00 0.00 0.00 2.69
1826 2130 7.133513 TGATTGTTTTACATACAAACACGACC 58.866 34.615 0.00 0.00 42.48 4.79
1859 2163 7.850935 ATAGACCGTCTGATCCCTAAATAAA 57.149 36.000 11.52 0.00 0.00 1.40
1994 2298 5.751028 AGCAAGCGAATATAGAACAAGTCTC 59.249 40.000 0.00 0.00 37.84 3.36
2011 2315 1.519758 CTTGAAACAAGCAAGCAAGCG 59.480 47.619 0.00 0.00 36.66 4.68
2046 2350 4.585162 GTCTACAGCACCCTAGTATCACAT 59.415 45.833 0.00 0.00 0.00 3.21
2154 2458 6.690530 AGGTACCATGAACACAATTTGAATG 58.309 36.000 15.94 0.00 0.00 2.67
2173 2477 4.429108 TGCAAGCAAAAACAGAAAGGTAC 58.571 39.130 0.00 0.00 0.00 3.34
2219 2523 1.728971 CAGGAGTCGCATTCACAACTC 59.271 52.381 0.00 0.00 37.90 3.01
2220 2524 1.800805 CAGGAGTCGCATTCACAACT 58.199 50.000 0.00 0.00 0.00 3.16
2221 2525 0.166814 GCAGGAGTCGCATTCACAAC 59.833 55.000 0.00 0.00 0.00 3.32
2222 2526 0.250252 TGCAGGAGTCGCATTCACAA 60.250 50.000 0.00 0.00 33.55 3.33
2223 2527 1.370810 TGCAGGAGTCGCATTCACA 59.629 52.632 0.00 0.00 33.55 3.58
2224 2528 4.284123 TGCAGGAGTCGCATTCAC 57.716 55.556 0.00 0.00 33.55 3.18
2246 2550 9.185192 GAACAATAAAATGAAGGTTTGTCTCAG 57.815 33.333 0.00 0.00 0.00 3.35
2335 2639 5.047164 TGCCATAATCTGAAACACTGCAAAT 60.047 36.000 0.00 0.00 0.00 2.32
2336 2640 4.280425 TGCCATAATCTGAAACACTGCAAA 59.720 37.500 0.00 0.00 0.00 3.68
2337 2641 3.825585 TGCCATAATCTGAAACACTGCAA 59.174 39.130 0.00 0.00 0.00 4.08
2338 2642 3.419943 TGCCATAATCTGAAACACTGCA 58.580 40.909 0.00 0.00 0.00 4.41
2409 2713 3.341823 CCACAGAAATCTTGCTACAGCT 58.658 45.455 2.44 0.00 42.66 4.24
2449 2753 5.780793 ACAGAGGGAGTACTATGTTTTGACT 59.219 40.000 0.00 0.00 39.70 3.41
2450 2754 6.038997 ACAGAGGGAGTACTATGTTTTGAC 57.961 41.667 0.00 0.00 39.70 3.18
2451 2755 7.786046 TTACAGAGGGAGTACTATGTTTTGA 57.214 36.000 0.00 0.00 39.70 2.69
2453 2757 8.431910 TCTTTACAGAGGGAGTACTATGTTTT 57.568 34.615 0.00 0.00 39.70 2.43
2454 2758 8.068892 CTCTTTACAGAGGGAGTACTATGTTT 57.931 38.462 0.00 0.00 39.70 2.83
2455 2759 7.648039 CTCTTTACAGAGGGAGTACTATGTT 57.352 40.000 0.00 0.00 39.70 2.71
2551 2899 7.710907 TCCTATAAATGTGTGATAAGACAGTGC 59.289 37.037 0.00 0.00 0.00 4.40
2572 2920 4.104897 GGCTTAGGTTTCTCCCATTCCTAT 59.895 45.833 0.00 0.00 36.75 2.57
2921 3270 2.863809 TCAGAAAAGCTCAAAGGTCCC 58.136 47.619 0.00 0.00 0.00 4.46
3043 3392 6.268617 TGGAGTATCAGATCAGGGAACATAAG 59.731 42.308 0.00 0.00 36.25 1.73
3052 3401 3.492309 GCACACTGGAGTATCAGATCAGG 60.492 52.174 0.00 0.00 38.11 3.86
3121 3471 3.059166 GCACAAGTTTAACCAATGGCAG 58.941 45.455 0.00 0.00 0.00 4.85
3124 3474 6.259608 TCAAAATGCACAAGTTTAACCAATGG 59.740 34.615 0.00 0.00 0.00 3.16
3187 3637 4.892934 TCTGCAACCAAATTTGACTTAGGT 59.107 37.500 19.86 4.78 0.00 3.08
3202 3652 4.072131 TGACCTTTCTAACATCTGCAACC 58.928 43.478 0.00 0.00 0.00 3.77
3214 3664 7.451877 ACAAACAGAGAGATACTGACCTTTCTA 59.548 37.037 0.00 0.00 38.55 2.10
3252 3702 1.311859 ATGCGCATCATCCAATTCGT 58.688 45.000 19.28 0.00 0.00 3.85
3391 3896 7.201652 GGAGCAGACTAATTTTACACTCAATCC 60.202 40.741 0.00 0.00 0.00 3.01
3411 3916 6.428159 AACTTGAGTTAAATACTGTGGAGCAG 59.572 38.462 0.00 0.00 42.71 4.24
3458 4090 0.826062 GGCCCTGTTTGGATTGGATG 59.174 55.000 0.00 0.00 38.35 3.51
3550 4182 1.620323 GAAACCAGGCTCCAAAATGCT 59.380 47.619 0.00 0.00 0.00 3.79
3596 4263 3.885484 AGCTGTGTCGATTTTTGTCTG 57.115 42.857 0.00 0.00 0.00 3.51
3600 4267 7.518161 TCAAGTAATAGCTGTGTCGATTTTTG 58.482 34.615 0.00 0.00 0.00 2.44
3784 4478 5.429762 TCTCCTGGGTAGAACATGAATGAAT 59.570 40.000 0.00 0.00 0.00 2.57
4010 4704 1.334869 CTTAATGTCATCGGCCAAGGC 59.665 52.381 2.24 1.52 41.06 4.35


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

AutoCloner maintained by Alex Coulton.