Multiple sequence alignment - TraesCS1B01G226000

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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 TraesCS1B01G226000 chr1B 100.000 3320 0 0 1 3320 405907518 405904199 0.000000e+00 6131.0
1 TraesCS1B01G226000 chr1B 84.706 340 43 4 1991 2321 406037238 406037577 6.870000e-87 331.0
2 TraesCS1B01G226000 chr1B 86.979 192 25 0 1534 1725 405525542 405525351 2.010000e-52 217.0
3 TraesCS1B01G226000 chr1D 95.312 1792 49 9 1442 3220 300718921 300717152 0.000000e+00 2811.0
4 TraesCS1B01G226000 chr1D 91.502 859 52 11 549 1397 300719768 300718921 0.000000e+00 1162.0
5 TraesCS1B01G226000 chr1D 90.426 564 25 7 9 556 300720476 300719926 0.000000e+00 715.0
6 TraesCS1B01G226000 chr1D 83.429 350 47 5 1981 2321 300859818 300860165 6.910000e-82 315.0
7 TraesCS1B01G226000 chr1D 86.458 192 26 0 1534 1725 300326303 300326112 9.330000e-51 211.0
8 TraesCS1B01G226000 chr1A 91.654 1905 80 32 1442 3317 375113226 375111372 0.000000e+00 2564.0
9 TraesCS1B01G226000 chr1A 93.424 806 33 6 603 1397 375114022 375113226 0.000000e+00 1177.0
10 TraesCS1B01G226000 chr1A 89.912 565 26 9 9 559 375114689 375114142 0.000000e+00 699.0
11 TraesCS1B01G226000 chr1A 84.571 350 43 5 1981 2321 375468969 375469316 1.480000e-88 337.0
12 TraesCS1B01G226000 chr1A 87.097 186 24 0 1534 1719 374690176 374689991 9.330000e-51 211.0
13 TraesCS1B01G226000 chr4B 83.578 341 44 4 1990 2318 659329680 659329340 3.220000e-80 309.0
14 TraesCS1B01G226000 chr4B 82.781 151 21 5 2135 2283 659521548 659521695 2.690000e-26 130.0
15 TraesCS1B01G226000 chr5A 82.402 358 45 6 1979 2318 694760236 694760593 2.500000e-76 296.0
16 TraesCS1B01G226000 chr5A 81.564 179 30 3 2135 2312 693673605 693673429 9.600000e-31 145.0
17 TraesCS1B01G226000 chr5A 87.500 104 13 0 1277 1380 693674683 693674580 1.620000e-23 121.0
18 TraesCS1B01G226000 chr5A 91.071 56 5 0 1121 1176 693674746 693674691 3.550000e-10 76.8
19 TraesCS1B01G226000 chr4D 80.802 349 46 7 1991 2318 508501905 508502253 1.530000e-63 254.0
20 TraesCS1B01G226000 chr4D 80.447 179 32 3 2135 2312 508431517 508431341 2.080000e-27 134.0
21 TraesCS1B01G226000 chr4D 88.462 104 12 0 1277 1380 508432609 508432506 3.480000e-25 126.0
22 TraesCS1B01G226000 chrUn 86.364 176 24 0 1550 1725 76409314 76409489 3.380000e-45 193.0
23 TraesCS1B01G226000 chr6D 86.364 176 24 0 1550 1725 15551144 15550969 3.380000e-45 193.0
24 TraesCS1B01G226000 chr6D 86.364 176 24 0 1550 1725 15586362 15586187 3.380000e-45 193.0
25 TraesCS1B01G226000 chr6D 78.042 337 50 13 1997 2312 276456215 276455882 1.220000e-44 191.0
26 TraesCS1B01G226000 chr6A 86.364 176 24 0 1550 1725 16338192 16338367 3.380000e-45 193.0
27 TraesCS1B01G226000 chr6A 84.298 121 14 4 1268 1385 399722247 399722365 2.710000e-21 113.0
28 TraesCS1B01G226000 chr3B 85.950 121 12 4 1268 1385 766631535 766631653 1.250000e-24 124.0
29 TraesCS1B01G226000 chr3B 73.754 301 55 15 1992 2268 6118431 6118731 2.730000e-16 97.1
30 TraesCS1B01G226000 chr3D 86.087 115 12 3 1268 1380 575726148 575726260 1.620000e-23 121.0
31 TraesCS1B01G226000 chr6B 85.000 120 13 4 1268 1384 438386658 438386541 2.090000e-22 117.0
32 TraesCS1B01G226000 chr3A 85.217 115 13 3 1268 1380 711218118 711218230 7.530000e-22 115.0
33 TraesCS1B01G226000 chr4A 100.000 31 0 0 3270 3300 159296915 159296945 1.290000e-04 58.4
34 TraesCS1B01G226000 chr2D 100.000 28 0 0 3270 3297 626109424 626109451 6.000000e-03 52.8


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 TraesCS1B01G226000 chr1B 405904199 405907518 3319 True 6131.000000 6131 100.000000 1 3320 1 chr1B.!!$R2 3319
1 TraesCS1B01G226000 chr1D 300717152 300720476 3324 True 1562.666667 2811 92.413333 9 3220 3 chr1D.!!$R2 3211
2 TraesCS1B01G226000 chr1A 375111372 375114689 3317 True 1480.000000 2564 91.663333 9 3317 3 chr1A.!!$R2 3308


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
135 139 0.033642 TACGTGATTCGGTGGTTGCA 59.966 50.0 0.0 0.0 44.69 4.08 F
988 1293 0.165511 CACAAGCTCGAAGAAGCAGC 59.834 55.0 0.0 0.0 34.09 5.25 F
1500 1823 0.546122 TGGAGCTGGTGAAACAGTGT 59.454 50.0 0.0 0.0 39.98 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1837 2166 0.033920 GTCCCAGTTAAACCGGTCGT 59.966 55.0 8.04 0.7 0.0 4.34 R
1947 2279 0.035176 GCAACCCATGTGCCATTGTT 59.965 50.0 0.00 0.0 0.0 2.83 R
2603 2951 0.191064 ACTGAGGGAGGGACAACAGA 59.809 55.0 0.00 0.0 0.0 3.41 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
119 123 1.129251 TCTACGCAACTTCGTCCTACG 59.871 52.381 0.00 0.00 43.15 3.51
133 137 1.067425 TCCTACGTGATTCGGTGGTTG 60.067 52.381 0.00 0.00 44.69 3.77
134 138 0.719465 CTACGTGATTCGGTGGTTGC 59.281 55.000 0.00 0.00 44.69 4.17
135 139 0.033642 TACGTGATTCGGTGGTTGCA 59.966 50.000 0.00 0.00 44.69 4.08
136 140 1.227999 ACGTGATTCGGTGGTTGCAG 61.228 55.000 0.00 0.00 44.69 4.41
137 141 0.948623 CGTGATTCGGTGGTTGCAGA 60.949 55.000 0.00 0.00 35.71 4.26
138 142 0.798776 GTGATTCGGTGGTTGCAGAG 59.201 55.000 0.00 0.00 0.00 3.35
139 143 0.684535 TGATTCGGTGGTTGCAGAGA 59.315 50.000 0.00 0.00 0.00 3.10
140 144 1.079503 GATTCGGTGGTTGCAGAGAC 58.920 55.000 0.00 0.00 0.00 3.36
141 145 0.396435 ATTCGGTGGTTGCAGAGACA 59.604 50.000 0.00 0.00 0.00 3.41
142 146 0.531974 TTCGGTGGTTGCAGAGACAC 60.532 55.000 0.00 0.00 0.00 3.67
175 179 3.313526 CAGGTTGGTTCCGATGATTGATC 59.686 47.826 0.00 0.00 0.00 2.92
326 340 8.934507 AAAGAGAATACGATTTTCCAGAGTAG 57.065 34.615 0.00 0.00 0.00 2.57
327 341 7.648039 AGAGAATACGATTTTCCAGAGTAGT 57.352 36.000 0.00 0.00 0.00 2.73
328 342 8.749026 AGAGAATACGATTTTCCAGAGTAGTA 57.251 34.615 0.00 0.00 0.00 1.82
379 399 0.859882 CACAGCTCATAGCATCAGCG 59.140 55.000 1.22 0.00 45.56 5.18
434 454 2.813908 GCATGTCCACGACCGTCC 60.814 66.667 0.00 0.00 0.00 4.79
437 457 1.605451 ATGTCCACGACCGTCCTCA 60.605 57.895 0.00 0.00 0.00 3.86
439 459 1.183030 TGTCCACGACCGTCCTCAAT 61.183 55.000 0.00 0.00 0.00 2.57
442 462 1.374125 CACGACCGTCCTCAATGCA 60.374 57.895 0.00 0.00 0.00 3.96
533 566 2.798680 CGAGCTTTGCTACATCTACGT 58.201 47.619 0.00 0.00 39.88 3.57
538 571 6.183360 CGAGCTTTGCTACATCTACGTAAAAA 60.183 38.462 0.00 0.00 39.88 1.94
584 883 3.625764 GCTTATGCGGTCTGATTTGGTTA 59.374 43.478 0.00 0.00 0.00 2.85
585 884 4.095782 GCTTATGCGGTCTGATTTGGTTAA 59.904 41.667 0.00 0.00 0.00 2.01
595 894 8.748582 CGGTCTGATTTGGTTAAAAGTAAAAAC 58.251 33.333 0.00 0.00 0.00 2.43
596 895 8.748582 GGTCTGATTTGGTTAAAAGTAAAAACG 58.251 33.333 0.00 0.00 0.00 3.60
601 900 4.846509 TGGTTAAAAGTAAAAACGGCTCG 58.153 39.130 0.00 0.00 0.00 5.03
633 932 4.156008 CGTAAAATTCAAGGGGAAGGTGAG 59.844 45.833 0.00 0.00 39.30 3.51
683 982 9.395707 GTAACATCATATCTAAGAGGTTACGTG 57.604 37.037 12.33 0.00 45.67 4.49
756 1055 1.898938 CATGCAATGTGTAACTGCCG 58.101 50.000 0.00 0.00 40.20 5.69
757 1056 1.468127 CATGCAATGTGTAACTGCCGA 59.532 47.619 0.00 0.00 40.20 5.54
758 1057 1.819928 TGCAATGTGTAACTGCCGAT 58.180 45.000 0.00 0.00 38.04 4.18
806 1105 1.305802 TCCCGTAGCCATGTGACCT 60.306 57.895 0.00 0.00 0.00 3.85
896 1195 5.429109 TGCCTATAAATACCCCGGCAATATA 59.571 40.000 0.00 0.00 43.81 0.86
930 1233 1.607628 CATCAAAGCATAGCTCAGCCC 59.392 52.381 6.68 0.00 38.25 5.19
931 1234 0.914644 TCAAAGCATAGCTCAGCCCT 59.085 50.000 6.68 0.00 38.25 5.19
988 1293 0.165511 CACAAGCTCGAAGAAGCAGC 59.834 55.000 0.00 0.00 34.09 5.25
997 1302 2.229543 TCGAAGAAGCAGCGGTACTTTA 59.770 45.455 0.90 0.00 0.00 1.85
1089 1397 1.740296 CGCCGGGAACTTCAACGAT 60.740 57.895 2.18 0.00 0.00 3.73
1248 1567 6.487689 TGATCGTTTGTGTAATAACATGCA 57.512 33.333 0.00 0.00 38.08 3.96
1251 1570 7.332182 TGATCGTTTGTGTAATAACATGCAGTA 59.668 33.333 0.00 0.00 38.08 2.74
1287 1606 3.587933 GGTGCGTGCGGGTTCAAA 61.588 61.111 0.00 0.00 0.00 2.69
1359 1678 1.125093 TCTTCAAGGACGGCAAGGGA 61.125 55.000 0.00 0.00 0.00 4.20
1426 1745 8.801882 TTTTCATGACGAGGGTTATTATTTCT 57.198 30.769 0.00 0.00 0.00 2.52
1427 1746 8.801882 TTTCATGACGAGGGTTATTATTTCTT 57.198 30.769 0.00 0.00 0.00 2.52
1428 1747 9.893634 TTTCATGACGAGGGTTATTATTTCTTA 57.106 29.630 0.00 0.00 0.00 2.10
1429 1748 9.893634 TTCATGACGAGGGTTATTATTTCTTAA 57.106 29.630 0.00 0.00 0.00 1.85
1430 1749 9.893634 TCATGACGAGGGTTATTATTTCTTAAA 57.106 29.630 0.00 0.00 0.00 1.52
1470 1789 3.754586 TTGGTGCTTTGCCCCTGCT 62.755 57.895 0.00 0.00 38.71 4.24
1493 1816 1.547675 GGTGGAAATGGAGCTGGTGAA 60.548 52.381 0.00 0.00 0.00 3.18
1500 1823 0.546122 TGGAGCTGGTGAAACAGTGT 59.454 50.000 0.00 0.00 39.98 3.55
1640 1963 2.289592 AGTACCACTTCGACCTGAGT 57.710 50.000 0.00 0.00 0.00 3.41
1788 2114 3.254060 CCTACCTGAACGATGAACAGTG 58.746 50.000 0.00 0.00 0.00 3.66
1836 2165 2.416162 GCCCAACAAAACTTTCACGACA 60.416 45.455 0.00 0.00 0.00 4.35
1837 2166 3.839293 CCCAACAAAACTTTCACGACAA 58.161 40.909 0.00 0.00 0.00 3.18
1947 2279 2.679837 CGGCTCGGTTACAGACTAAGTA 59.320 50.000 0.00 0.00 0.00 2.24
1975 2307 1.274167 CACATGGGTTGCTGATTGCTT 59.726 47.619 0.00 0.00 43.37 3.91
2028 2360 2.261671 CCCGGTCTCAAGGTGACG 59.738 66.667 0.00 0.00 35.45 4.35
2166 2498 4.552365 ATGCGCGAGTCATGGGGG 62.552 66.667 12.10 0.00 0.00 5.40
2169 2501 3.461773 CGCGAGTCATGGGGGTCT 61.462 66.667 0.00 0.00 0.00 3.85
2298 2630 2.955881 GCCCAGCACCTTCTACCGT 61.956 63.158 0.00 0.00 0.00 4.83
2377 2715 4.822685 TGCATTGGCTTGATTTGGTATT 57.177 36.364 0.00 0.00 41.91 1.89
2385 2723 7.385778 TGGCTTGATTTGGTATTTGTACTAC 57.614 36.000 0.00 0.00 0.00 2.73
2412 2754 3.688694 TCGTTTTGCATGGGTACTACT 57.311 42.857 0.00 0.00 0.00 2.57
2603 2951 4.968259 TGTTTGTGTGTACTCCTGCTTAT 58.032 39.130 0.00 0.00 0.00 1.73
2606 2954 4.456280 TGTGTGTACTCCTGCTTATCTG 57.544 45.455 0.00 0.00 0.00 2.90
2617 2965 1.559682 TGCTTATCTGTTGTCCCTCCC 59.440 52.381 0.00 0.00 0.00 4.30
2672 3020 5.887598 TCAGTTCGTATTGCCCTAGTACTTA 59.112 40.000 0.00 0.00 0.00 2.24
2696 3044 0.808125 ACTTGATTATGCGCGCCAAA 59.192 45.000 30.77 22.60 0.00 3.28
2704 3052 2.124011 ATGCGCGCCAAAGATTAATG 57.876 45.000 30.77 0.00 0.00 1.90
2705 3053 1.090728 TGCGCGCCAAAGATTAATGA 58.909 45.000 30.77 0.71 0.00 2.57
2711 3060 2.450160 GCCAAAGATTAATGAACGCCG 58.550 47.619 0.00 0.00 0.00 6.46
2718 3067 3.951680 AGATTAATGAACGCCGGGAATTT 59.048 39.130 2.18 0.00 0.00 1.82
2720 3069 0.530288 AATGAACGCCGGGAATTTGG 59.470 50.000 2.18 0.00 0.00 3.28
2770 3119 2.093447 CGGCCAGTGGAAATTCTACTCT 60.093 50.000 15.20 0.00 35.96 3.24
2794 3143 1.607628 CCGGTAGATTCGACGATCCTT 59.392 52.381 0.00 0.00 0.00 3.36
3003 3352 3.103738 CGTTCGTTCTATAACCGTCAGG 58.896 50.000 0.00 0.00 45.13 3.86
3053 3404 4.787598 TCGGAGTAACTTTTACACGAGAC 58.212 43.478 10.09 0.00 0.00 3.36
3054 3405 3.601211 CGGAGTAACTTTTACACGAGACG 59.399 47.826 0.00 0.00 0.00 4.18
3055 3406 4.611355 CGGAGTAACTTTTACACGAGACGA 60.611 45.833 0.00 0.00 0.00 4.20
3057 3408 5.334414 GGAGTAACTTTTACACGAGACGAGA 60.334 44.000 0.00 0.00 0.00 4.04
3091 3442 3.532542 GCCGCCTAAAAGTTCACTCTAT 58.467 45.455 0.00 0.00 0.00 1.98
3092 3443 3.556365 GCCGCCTAAAAGTTCACTCTATC 59.444 47.826 0.00 0.00 0.00 2.08
3093 3444 4.680975 GCCGCCTAAAAGTTCACTCTATCT 60.681 45.833 0.00 0.00 0.00 1.98
3094 3445 5.451520 GCCGCCTAAAAGTTCACTCTATCTA 60.452 44.000 0.00 0.00 0.00 1.98
3095 3446 6.570692 CCGCCTAAAAGTTCACTCTATCTAA 58.429 40.000 0.00 0.00 0.00 2.10
3096 3447 6.697892 CCGCCTAAAAGTTCACTCTATCTAAG 59.302 42.308 0.00 0.00 0.00 2.18
3097 3448 6.199342 CGCCTAAAAGTTCACTCTATCTAAGC 59.801 42.308 0.00 0.00 0.00 3.09
3098 3449 7.269316 GCCTAAAAGTTCACTCTATCTAAGCT 58.731 38.462 0.00 0.00 0.00 3.74
3099 3450 7.223777 GCCTAAAAGTTCACTCTATCTAAGCTG 59.776 40.741 0.00 0.00 0.00 4.24
3100 3451 7.708752 CCTAAAAGTTCACTCTATCTAAGCTGG 59.291 40.741 0.00 0.00 0.00 4.85
3101 3452 4.664150 AGTTCACTCTATCTAAGCTGGC 57.336 45.455 0.00 0.00 0.00 4.85
3191 3545 0.323999 TACTGGCGCTAACCTCTCCA 60.324 55.000 7.64 0.00 0.00 3.86
3238 3592 5.617528 TGTTGTCCACTTAAACTACTCCA 57.382 39.130 0.00 0.00 0.00 3.86
3241 3595 7.057894 TGTTGTCCACTTAAACTACTCCAAAT 58.942 34.615 0.00 0.00 0.00 2.32
3242 3596 7.012894 TGTTGTCCACTTAAACTACTCCAAATG 59.987 37.037 0.00 0.00 0.00 2.32
3243 3597 6.597562 TGTCCACTTAAACTACTCCAAATGT 58.402 36.000 0.00 0.00 0.00 2.71
3245 3599 8.212312 TGTCCACTTAAACTACTCCAAATGTAA 58.788 33.333 0.00 0.00 0.00 2.41
3246 3600 8.718734 GTCCACTTAAACTACTCCAAATGTAAG 58.281 37.037 0.00 0.00 0.00 2.34
3247 3601 8.653191 TCCACTTAAACTACTCCAAATGTAAGA 58.347 33.333 0.00 0.00 0.00 2.10
3248 3602 8.718734 CCACTTAAACTACTCCAAATGTAAGAC 58.281 37.037 0.00 0.00 0.00 3.01
3249 3603 9.490379 CACTTAAACTACTCCAAATGTAAGACT 57.510 33.333 0.00 0.00 0.00 3.24
3253 3607 7.981102 AACTACTCCAAATGTAAGACTTTCC 57.019 36.000 0.00 0.00 0.00 3.13
3254 3608 7.074653 ACTACTCCAAATGTAAGACTTTCCA 57.925 36.000 0.00 0.00 0.00 3.53
3255 3609 7.690256 ACTACTCCAAATGTAAGACTTTCCAT 58.310 34.615 0.00 0.00 0.00 3.41
3257 3611 7.839680 ACTCCAAATGTAAGACTTTCCATTT 57.160 32.000 14.85 14.85 37.86 2.32
3258 3612 7.886338 ACTCCAAATGTAAGACTTTCCATTTC 58.114 34.615 16.57 0.00 35.84 2.17
3259 3613 7.505585 ACTCCAAATGTAAGACTTTCCATTTCA 59.494 33.333 16.57 9.63 35.84 2.69
3260 3614 8.421249 TCCAAATGTAAGACTTTCCATTTCAT 57.579 30.769 16.57 2.05 35.84 2.57
3261 3615 9.527157 TCCAAATGTAAGACTTTCCATTTCATA 57.473 29.630 16.57 7.71 35.84 2.15
3287 3641 7.448748 AAATGTAAGACTTTTCGGCTGTTAT 57.551 32.000 0.00 0.00 0.00 1.89
3293 3647 3.395639 ACTTTTCGGCTGTTATCGACAA 58.604 40.909 0.00 0.00 37.93 3.18
3295 3649 2.004583 TTCGGCTGTTATCGACAAGG 57.995 50.000 0.00 0.00 37.93 3.61
3301 3655 3.326747 GCTGTTATCGACAAGGTCAAGT 58.673 45.455 0.00 0.00 37.93 3.16
3302 3656 3.368236 GCTGTTATCGACAAGGTCAAGTC 59.632 47.826 0.00 0.00 37.93 3.01
3310 3664 0.032952 CAAGGTCAAGTCGGTTCCGA 59.967 55.000 10.00 10.00 36.02 4.55
3317 3671 3.128242 GTCAAGTCGGTTCCGATAGAAGA 59.872 47.826 16.87 8.50 40.65 2.87
3318 3672 3.377485 TCAAGTCGGTTCCGATAGAAGAG 59.623 47.826 16.87 4.38 40.65 2.85
3319 3673 1.677052 AGTCGGTTCCGATAGAAGAGC 59.323 52.381 16.87 2.09 40.65 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.617308 GCTGCTACCTGATAGTACGTGA 59.383 50.000 0.00 0.00 32.90 4.35
1 2 2.357952 TGCTGCTACCTGATAGTACGTG 59.642 50.000 0.00 0.00 32.90 4.49
2 3 2.651455 TGCTGCTACCTGATAGTACGT 58.349 47.619 0.00 0.00 32.90 3.57
3 4 3.253432 TGATGCTGCTACCTGATAGTACG 59.747 47.826 0.00 0.00 32.90 3.67
4 5 4.855715 TGATGCTGCTACCTGATAGTAC 57.144 45.455 0.00 0.00 32.90 2.73
5 6 5.305386 ACAATGATGCTGCTACCTGATAGTA 59.695 40.000 0.00 0.00 32.90 1.82
6 7 4.102210 ACAATGATGCTGCTACCTGATAGT 59.898 41.667 0.00 0.00 32.90 2.12
7 8 4.451435 CACAATGATGCTGCTACCTGATAG 59.549 45.833 0.00 0.00 0.00 2.08
119 123 0.798776 CTCTGCAACCACCGAATCAC 59.201 55.000 0.00 0.00 0.00 3.06
133 137 1.194772 GTTTAACAGGCGTGTCTCTGC 59.805 52.381 13.21 0.00 35.08 4.26
134 138 2.476619 CTGTTTAACAGGCGTGTCTCTG 59.523 50.000 16.62 0.00 42.35 3.35
135 139 2.755650 CTGTTTAACAGGCGTGTCTCT 58.244 47.619 16.62 0.00 42.35 3.10
175 179 1.879796 GCCTGACTGACTCTTGTTGGG 60.880 57.143 0.00 0.00 0.00 4.12
326 340 4.971220 GCTAGAAAGAGATACGCACAGTAC 59.029 45.833 0.00 0.00 38.29 2.73
327 341 4.638865 TGCTAGAAAGAGATACGCACAGTA 59.361 41.667 0.00 0.00 40.03 2.74
328 342 3.444034 TGCTAGAAAGAGATACGCACAGT 59.556 43.478 0.00 0.00 0.00 3.55
369 389 1.738432 CCTGCTCTCGCTGATGCTA 59.262 57.895 0.00 0.00 37.28 3.49
379 399 2.439104 CCCTACCTGCCCTGCTCTC 61.439 68.421 0.00 0.00 0.00 3.20
546 579 6.202762 CCGCATAAGCTCATACATAAGTTTCA 59.797 38.462 0.00 0.00 39.10 2.69
547 580 6.202954 ACCGCATAAGCTCATACATAAGTTTC 59.797 38.462 0.00 0.00 39.10 2.78
559 755 2.938451 CAAATCAGACCGCATAAGCTCA 59.062 45.455 0.00 0.00 39.10 4.26
567 866 3.886505 ACTTTTAACCAAATCAGACCGCA 59.113 39.130 0.00 0.00 0.00 5.69
568 867 4.499037 ACTTTTAACCAAATCAGACCGC 57.501 40.909 0.00 0.00 0.00 5.68
569 868 8.748582 GTTTTTACTTTTAACCAAATCAGACCG 58.251 33.333 0.00 0.00 0.00 4.79
584 883 1.001048 GCCCGAGCCGTTTTTACTTTT 60.001 47.619 0.00 0.00 0.00 2.27
585 884 0.594602 GCCCGAGCCGTTTTTACTTT 59.405 50.000 0.00 0.00 0.00 2.66
613 912 4.199002 ACTCACCTTCCCCTTGAATTTT 57.801 40.909 0.00 0.00 31.06 1.82
656 955 9.352191 ACGTAACCTCTTAGATATGATGTTACT 57.648 33.333 19.65 11.51 0.00 2.24
667 966 3.438183 ACACCCACGTAACCTCTTAGAT 58.562 45.455 0.00 0.00 0.00 1.98
668 967 2.880443 ACACCCACGTAACCTCTTAGA 58.120 47.619 0.00 0.00 0.00 2.10
669 968 3.428589 GCTACACCCACGTAACCTCTTAG 60.429 52.174 0.00 0.00 0.00 2.18
681 980 2.295909 TGAGCAAAAATGCTACACCCAC 59.704 45.455 2.89 0.00 46.36 4.61
683 982 3.578688 CTTGAGCAAAAATGCTACACCC 58.421 45.455 2.89 0.00 46.36 4.61
754 1053 4.592192 ATCACGGCTCGGCATCGG 62.592 66.667 0.00 0.00 36.95 4.18
755 1054 2.094126 GAAATCACGGCTCGGCATCG 62.094 60.000 0.00 0.00 37.82 3.84
756 1055 0.811616 AGAAATCACGGCTCGGCATC 60.812 55.000 0.00 0.00 0.00 3.91
757 1056 0.811616 GAGAAATCACGGCTCGGCAT 60.812 55.000 0.00 0.00 0.00 4.40
758 1057 1.447838 GAGAAATCACGGCTCGGCA 60.448 57.895 0.00 0.00 0.00 5.69
806 1105 1.762419 GACGACGTGCTTTGTGTAGA 58.238 50.000 4.58 0.00 0.00 2.59
896 1195 4.202461 TGCTTTGATGTTCTGGGAGTAACT 60.202 41.667 0.00 0.00 0.00 2.24
988 1293 3.118738 AGAGGAGCCATGTTAAAGTACCG 60.119 47.826 0.00 0.00 0.00 4.02
997 1302 1.339151 GGACGAAAGAGGAGCCATGTT 60.339 52.381 0.00 0.00 0.00 2.71
1217 1530 9.006215 GTTATTACACAAACGATCAATTAAGCC 57.994 33.333 0.00 0.00 0.00 4.35
1248 1567 3.873361 CACCTGAATGCACATCGATTACT 59.127 43.478 0.00 0.00 0.00 2.24
1251 1570 2.019249 CCACCTGAATGCACATCGATT 58.981 47.619 0.00 0.00 0.00 3.34
1287 1606 1.228190 AGGGGTACTGGTTGGTGTTT 58.772 50.000 0.00 0.00 0.00 2.83
1359 1678 3.083349 TGGTAGCAGGAGCCGCAT 61.083 61.111 0.00 0.00 43.56 4.73
1400 1719 9.238368 AGAAATAATAACCCTCGTCATGAAAAA 57.762 29.630 0.00 0.00 0.00 1.94
1401 1720 8.801882 AGAAATAATAACCCTCGTCATGAAAA 57.198 30.769 0.00 0.00 0.00 2.29
1402 1721 8.801882 AAGAAATAATAACCCTCGTCATGAAA 57.198 30.769 0.00 0.00 0.00 2.69
1403 1722 9.893634 TTAAGAAATAATAACCCTCGTCATGAA 57.106 29.630 0.00 0.00 0.00 2.57
1404 1723 9.893634 TTTAAGAAATAATAACCCTCGTCATGA 57.106 29.630 0.00 0.00 0.00 3.07
1430 1749 3.372822 ACAATATGGCGATCGTCGTTTTT 59.627 39.130 20.95 11.44 42.81 1.94
1431 1750 2.933906 ACAATATGGCGATCGTCGTTTT 59.066 40.909 20.95 15.53 42.81 2.43
1432 1751 2.546778 ACAATATGGCGATCGTCGTTT 58.453 42.857 20.95 9.61 42.81 3.60
1433 1752 2.218953 ACAATATGGCGATCGTCGTT 57.781 45.000 20.95 10.02 42.81 3.85
1434 1753 1.858458 CAACAATATGGCGATCGTCGT 59.142 47.619 19.61 19.61 42.81 4.34
1435 1754 1.192312 CCAACAATATGGCGATCGTCG 59.808 52.381 15.94 2.37 43.89 5.12
1436 1755 2.032894 CACCAACAATATGGCGATCGTC 60.033 50.000 13.98 13.98 44.75 4.20
1437 1756 1.939934 CACCAACAATATGGCGATCGT 59.060 47.619 17.81 0.00 44.75 3.73
1438 1757 1.334059 GCACCAACAATATGGCGATCG 60.334 52.381 11.69 11.69 44.75 3.69
1439 1758 1.949525 AGCACCAACAATATGGCGATC 59.050 47.619 0.00 0.00 44.75 3.69
1440 1759 2.057137 AGCACCAACAATATGGCGAT 57.943 45.000 0.00 0.00 44.75 4.58
1441 1760 1.832883 AAGCACCAACAATATGGCGA 58.167 45.000 0.00 0.00 44.75 5.54
1444 1763 2.620242 GGCAAAGCACCAACAATATGG 58.380 47.619 0.00 0.00 46.38 2.74
1470 1789 0.251297 CCAGCTCCATTTCCACCACA 60.251 55.000 0.00 0.00 0.00 4.17
1493 1816 7.116948 CGATCAGAAGTCAAGATTAACACTGTT 59.883 37.037 0.00 0.00 0.00 3.16
1836 2165 0.758123 TCCCAGTTAAACCGGTCGTT 59.242 50.000 8.04 1.06 35.70 3.85
1837 2166 0.033920 GTCCCAGTTAAACCGGTCGT 59.966 55.000 8.04 0.70 0.00 4.34
1947 2279 0.035176 GCAACCCATGTGCCATTGTT 59.965 50.000 0.00 0.00 0.00 2.83
2028 2360 2.358737 CCCTGCTCCACGTGGAAC 60.359 66.667 35.36 31.31 44.91 3.62
2166 2498 1.068250 GTCCAGCCGCCAGATAGAC 59.932 63.158 0.00 0.00 0.00 2.59
2169 2501 2.134287 GGAGTCCAGCCGCCAGATA 61.134 63.158 3.60 0.00 0.00 1.98
2298 2630 1.204704 CAGCTGTACTGGACGATGGAA 59.795 52.381 5.25 0.00 43.19 3.53
2377 2715 4.393680 GCAAAACGATCCATGGTAGTACAA 59.606 41.667 12.58 0.00 0.00 2.41
2385 2723 2.212869 CCATGCAAAACGATCCATGG 57.787 50.000 4.97 4.97 45.96 3.66
2412 2754 8.950007 ACCTTAATTAATCAAAAACCTCCTCA 57.050 30.769 0.00 0.00 0.00 3.86
2603 2951 0.191064 ACTGAGGGAGGGACAACAGA 59.809 55.000 0.00 0.00 0.00 3.41
2606 2954 0.899019 GAGACTGAGGGAGGGACAAC 59.101 60.000 0.00 0.00 0.00 3.32
2617 2965 3.066621 GGCAGTACTGATGAGAGACTGAG 59.933 52.174 27.08 0.00 38.19 3.35
2696 3044 2.702592 TTCCCGGCGTTCATTAATCT 57.297 45.000 6.01 0.00 0.00 2.40
2704 3052 1.504900 GACCAAATTCCCGGCGTTC 59.495 57.895 6.01 0.00 0.00 3.95
2705 3053 1.974875 GGACCAAATTCCCGGCGTT 60.975 57.895 6.01 0.00 0.00 4.84
2711 3060 3.767711 AGAAAGTCAGGACCAAATTCCC 58.232 45.455 0.00 0.00 36.12 3.97
2718 3067 3.493699 CGTTGGTTAGAAAGTCAGGACCA 60.494 47.826 0.00 0.00 35.52 4.02
2720 3069 3.725490 ACGTTGGTTAGAAAGTCAGGAC 58.275 45.455 0.00 0.00 0.00 3.85
2770 3119 1.452110 TCGTCGAATCTACCGGAACA 58.548 50.000 9.46 0.00 0.00 3.18
2794 3143 1.259609 ATGACGTACCGACCTTTCCA 58.740 50.000 0.00 0.00 0.00 3.53
3003 3352 8.307483 TCATTCACTATCATTAGGTAGCTAAGC 58.693 37.037 18.51 0.00 0.00 3.09
3053 3404 3.257561 CGATGTTGCCGGCTCTCG 61.258 66.667 29.70 23.82 38.88 4.04
3054 3405 3.567797 GCGATGTTGCCGGCTCTC 61.568 66.667 29.70 17.62 0.00 3.20
3091 3442 1.282157 GAAAGGGAAGGCCAGCTTAGA 59.718 52.381 5.01 0.00 35.15 2.10
3092 3443 1.683319 GGAAAGGGAAGGCCAGCTTAG 60.683 57.143 5.01 0.00 35.15 2.18
3093 3444 0.331616 GGAAAGGGAAGGCCAGCTTA 59.668 55.000 5.01 0.00 35.15 3.09
3094 3445 1.077445 GGAAAGGGAAGGCCAGCTT 59.923 57.895 5.01 0.00 35.15 3.74
3095 3446 0.550147 TAGGAAAGGGAAGGCCAGCT 60.550 55.000 5.01 0.00 35.15 4.24
3096 3447 0.331616 TTAGGAAAGGGAAGGCCAGC 59.668 55.000 5.01 0.00 35.15 4.85
3097 3448 1.916181 TCTTAGGAAAGGGAAGGCCAG 59.084 52.381 5.01 0.00 35.15 4.85
3098 3449 2.053747 TCTTAGGAAAGGGAAGGCCA 57.946 50.000 5.01 0.00 35.15 5.36
3099 3450 3.451402 TTTCTTAGGAAAGGGAAGGCC 57.549 47.619 0.00 0.00 36.63 5.19
3191 3545 2.271800 CAAAGACTAGCTCGGCGATTT 58.728 47.619 11.27 2.95 0.00 2.17
3255 3609 9.187455 GCCGAAAAGTCTTACATTTTTATGAAA 57.813 29.630 0.00 0.00 0.00 2.69
3257 3611 8.020819 CAGCCGAAAAGTCTTACATTTTTATGA 58.979 33.333 0.00 0.00 0.00 2.15
3258 3612 7.807907 ACAGCCGAAAAGTCTTACATTTTTATG 59.192 33.333 0.00 0.00 0.00 1.90
3259 3613 7.882179 ACAGCCGAAAAGTCTTACATTTTTAT 58.118 30.769 0.00 0.00 0.00 1.40
3260 3614 7.266922 ACAGCCGAAAAGTCTTACATTTTTA 57.733 32.000 0.00 0.00 0.00 1.52
3261 3615 6.144078 ACAGCCGAAAAGTCTTACATTTTT 57.856 33.333 0.00 0.00 0.00 1.94
3262 3616 5.767816 ACAGCCGAAAAGTCTTACATTTT 57.232 34.783 0.00 0.00 0.00 1.82
3263 3617 5.767816 AACAGCCGAAAAGTCTTACATTT 57.232 34.783 0.00 0.00 0.00 2.32
3293 3647 4.186136 TCGGAACCGACTTGACCT 57.814 55.556 12.04 0.00 44.01 3.85



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

AutoCloner maintained by Alex Coulton.