Multiple sequence alignment - TraesCS4A01G403600

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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 TraesCS4A01G403600 chr4A 100.000 3400 0 0 1 3400 677114554 677111155 0.000000e+00 6279.0
1 TraesCS4A01G403600 chr4A 83.274 281 31 8 2439 2703 413641093 413641373 9.420000e-61 244.0
2 TraesCS4A01G403600 chr4A 82.437 279 32 9 2442 2703 489110685 489110963 9.490000e-56 228.0
3 TraesCS4A01G403600 chr7D 91.731 2999 180 26 421 3364 59162969 59159984 0.000000e+00 4102.0
4 TraesCS4A01G403600 chr7D 92.874 435 27 2 1 431 59163430 59162996 2.230000e-176 628.0
5 TraesCS4A01G403600 chr7A 91.798 2926 181 29 421 3304 63759568 63756660 0.000000e+00 4019.0
6 TraesCS4A01G403600 chr7A 75.910 1648 316 50 488 2101 93898228 93899828 0.000000e+00 769.0
7 TraesCS4A01G403600 chr7A 75.712 1651 321 49 488 2110 94131076 94132674 0.000000e+00 754.0
8 TraesCS4A01G403600 chr7A 77.291 1255 246 21 868 2101 94186552 94187788 0.000000e+00 702.0
9 TraesCS4A01G403600 chr7A 76.555 1254 257 19 868 2101 94217761 94218997 0.000000e+00 652.0
10 TraesCS4A01G403600 chr7A 91.784 426 31 2 10 431 63760020 63759595 1.050000e-164 590.0
11 TraesCS4A01G403600 chr7A 85.053 281 26 8 2439 2703 192071312 192071592 4.320000e-69 272.0
12 TraesCS4A01G403600 chr2A 81.000 300 24 13 2437 2703 637911724 637912023 1.240000e-49 207.0
13 TraesCS4A01G403600 chr2A 97.297 37 1 0 2989 3025 12094458 12094494 2.830000e-06 63.9
14 TraesCS4A01G403600 chr5A 80.537 298 25 13 2439 2703 110117606 110117309 7.440000e-47 198.0
15 TraesCS4A01G403600 chr5A 100.000 31 0 0 2992 3022 88648955 88648985 1.320000e-04 58.4
16 TraesCS4A01G403600 chr3D 80.496 282 35 12 2439 2703 418229848 418230126 7.440000e-47 198.0
17 TraesCS4A01G403600 chr1A 87.805 164 18 2 2542 2703 16272102 16272265 1.250000e-44 191.0
18 TraesCS4A01G403600 chr1A 82.394 142 10 9 2439 2565 126785949 126786090 3.590000e-20 110.0
19 TraesCS4A01G403600 chr4B 90.278 72 6 1 2495 2565 528898418 528898347 3.610000e-15 93.5
20 TraesCS4A01G403600 chr3B 90.909 55 5 0 2439 2493 726466816 726466762 1.310000e-09 75.0
21 TraesCS4A01G403600 chr5B 92.857 42 3 0 2992 3033 34897009 34896968 1.020000e-05 62.1
22 TraesCS4A01G403600 chr1D 92.857 42 3 0 2992 3033 363617548 363617589 1.020000e-05 62.1
23 TraesCS4A01G403600 chr6B 92.683 41 3 0 2999 3039 565639158 565639118 3.660000e-05 60.2
24 TraesCS4A01G403600 chr6B 100.000 28 0 0 2999 3026 514479845 514479872 6.000000e-03 52.8
25 TraesCS4A01G403600 chr3A 94.737 38 2 0 2995 3032 690192259 690192222 3.660000e-05 60.2
26 TraesCS4A01G403600 chr7B 100.000 31 0 0 2995 3025 382751634 382751604 1.320000e-04 58.4


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 TraesCS4A01G403600 chr4A 677111155 677114554 3399 True 6279.0 6279 100.0000 1 3400 1 chr4A.!!$R1 3399
1 TraesCS4A01G403600 chr7D 59159984 59163430 3446 True 2365.0 4102 92.3025 1 3364 2 chr7D.!!$R1 3363
2 TraesCS4A01G403600 chr7A 63756660 63760020 3360 True 2304.5 4019 91.7910 10 3304 2 chr7A.!!$R1 3294
3 TraesCS4A01G403600 chr7A 93898228 93899828 1600 False 769.0 769 75.9100 488 2101 1 chr7A.!!$F1 1613
4 TraesCS4A01G403600 chr7A 94131076 94132674 1598 False 754.0 754 75.7120 488 2110 1 chr7A.!!$F2 1622
5 TraesCS4A01G403600 chr7A 94186552 94187788 1236 False 702.0 702 77.2910 868 2101 1 chr7A.!!$F3 1233
6 TraesCS4A01G403600 chr7A 94217761 94218997 1236 False 652.0 652 76.5550 868 2101 1 chr7A.!!$F4 1233

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
410 415 0.254178 AGGATGTGGATGTGCTCACC 59.746 55.0 0.0 0.0 33.29 4.02 F
1392 1453 0.485099 ACCCAGGTATGGTGGCAAAA 59.515 50.0 0.0 0.0 46.10 2.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1521 1582 0.247814 GAATCACGCTTGCACCATCG 60.248 55.0 0.0 0.0 0.00 3.84 R
3243 3360 0.030908 GCCTACGATAACGCAGCTCT 59.969 55.0 0.0 0.0 43.96 4.09 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
60 61 4.488770 TCTTGGAATTTGGCCCTAAAACT 58.511 39.130 0.00 0.00 0.00 2.66
76 77 6.946009 CCCTAAAACTCAAATGGAAGGAGTAA 59.054 38.462 0.00 0.00 40.80 2.24
189 190 5.046735 CCCTCTTATGGAGTAGATGACATGG 60.047 48.000 0.00 0.00 40.30 3.66
388 393 5.067023 CCCCTAATTTCTCAATGCTCTTGAC 59.933 44.000 0.00 0.00 0.00 3.18
410 415 0.254178 AGGATGTGGATGTGCTCACC 59.746 55.000 0.00 0.00 33.29 4.02
433 475 5.406780 CCTAGCAGCGATTTAATGGTTCTAG 59.593 44.000 0.00 0.00 0.00 2.43
757 807 5.175859 ACAATTGGACCTAACATGAGTACG 58.824 41.667 10.83 0.00 0.00 3.67
842 892 3.141272 ACAAGTTTTATGGTCCTTGGGGA 59.859 43.478 0.00 0.00 38.84 4.81
998 1059 9.308000 AGGTTTGTTTGTCATTATAGGATTTGA 57.692 29.630 0.00 0.00 0.00 2.69
1029 1090 1.638679 GGGGTAGGCGGTTGGGTATT 61.639 60.000 0.00 0.00 0.00 1.89
1121 1182 1.153369 CCGACCTCAACGCCATCAT 60.153 57.895 0.00 0.00 0.00 2.45
1238 1299 0.744414 GCAGCACCGCTAGGAAATCA 60.744 55.000 0.00 0.00 36.40 2.57
1240 1301 2.292267 CAGCACCGCTAGGAAATCAAT 58.708 47.619 0.00 0.00 36.40 2.57
1264 1325 3.253432 CACTAAGAAGGAAACAAGTGCCC 59.747 47.826 0.00 0.00 0.00 5.36
1272 1333 1.526464 GAAACAAGTGCCCAAATTGCG 59.474 47.619 0.00 0.00 0.00 4.85
1308 1369 2.158957 GGTGGCTCGACTTGATATGGAA 60.159 50.000 0.00 0.00 0.00 3.53
1329 1390 3.946824 ACATGGGATGGAGGATAAGAGT 58.053 45.455 0.00 0.00 33.60 3.24
1392 1453 0.485099 ACCCAGGTATGGTGGCAAAA 59.515 50.000 0.00 0.00 46.10 2.44
1462 1523 4.702612 AGCTCTTCAATGAACTCTCTCGTA 59.297 41.667 0.00 0.00 0.00 3.43
1472 1533 3.586470 ACTCTCTCGTATCCATGAGGT 57.414 47.619 0.00 0.00 38.21 3.85
1652 1713 2.200081 ACACCATATGCCTTCCACTCT 58.800 47.619 0.00 0.00 0.00 3.24
1663 1724 4.202295 TGCCTTCCACTCTGCTAATATCAG 60.202 45.833 0.00 0.00 0.00 2.90
1668 1729 3.070734 CCACTCTGCTAATATCAGCACCT 59.929 47.826 0.00 0.00 46.41 4.00
1726 1790 3.384146 ACAAGTGTTCCATGTTGCATCAA 59.616 39.130 0.75 0.00 0.00 2.57
1767 1831 1.957113 GCTTCCCAGCTACAAGGCATT 60.957 52.381 0.00 0.00 43.51 3.56
1787 1851 5.799213 CATTCCTAATCAGGTACAGGATCC 58.201 45.833 2.48 2.48 43.18 3.36
1795 1859 1.742768 GTACAGGATCCGCCTCCAG 59.257 63.158 5.98 0.00 46.97 3.86
1804 1871 2.117156 CCGCCTCCAGCAGATTTGG 61.117 63.158 0.00 0.00 44.04 3.28
1921 1988 6.728411 TCTCCACTATTGGTCTACTCAAGTA 58.272 40.000 0.00 0.00 44.35 2.24
1927 1994 4.948341 TTGGTCTACTCAAGTAGCAACA 57.052 40.909 11.56 7.51 45.69 3.33
1955 2022 1.379710 TGGATGACCCATTTGGCCG 60.380 57.895 0.00 0.00 40.82 6.13
2001 2068 3.875727 CAGATCAACAGCTCTACAATGGG 59.124 47.826 0.00 0.00 0.00 4.00
2023 2090 4.445879 GGTTTCTAGGGATGGATGGTTACC 60.446 50.000 0.00 0.00 0.00 2.85
2025 2092 5.427857 TTCTAGGGATGGATGGTTACCTA 57.572 43.478 2.07 0.00 0.00 3.08
2041 2108 6.021672 GGTTACCTAGGCTATAATGGTACCT 58.978 44.000 14.36 0.00 33.59 3.08
2117 2184 0.034767 TCTCCTGGCAAGCAAGATGG 60.035 55.000 0.00 0.00 0.00 3.51
2265 2332 4.888326 AAGCACCATTCAAGGCAATAAA 57.112 36.364 0.00 0.00 0.00 1.40
2266 2333 5.425196 AAGCACCATTCAAGGCAATAAAT 57.575 34.783 0.00 0.00 0.00 1.40
2293 2368 7.166851 GGTATTCCATGTCTCAGATCATGAAT 58.833 38.462 15.09 13.92 42.52 2.57
2432 2507 4.510711 ACTCTCTGCGAATATTGCAATCAG 59.489 41.667 16.86 16.02 42.70 2.90
2433 2508 3.811497 TCTCTGCGAATATTGCAATCAGG 59.189 43.478 16.86 10.31 42.70 3.86
2493 2568 9.840427 GGGTTGAACAATATAAAATCCATATCG 57.160 33.333 0.00 0.00 0.00 2.92
2553 2648 3.866703 TTGTGTCCATGTCCAAACCTA 57.133 42.857 0.00 0.00 0.00 3.08
2619 2714 6.431198 AACACAACGTTCACATAAACTCTT 57.569 33.333 0.00 0.00 29.27 2.85
2675 2770 6.036083 CACTTATGGAAATCAACGTCCACTAG 59.964 42.308 0.00 0.00 46.53 2.57
2734 2830 2.661176 AGGTGGACCTTCCCAGATTA 57.339 50.000 0.00 0.00 46.09 1.75
2789 2890 9.815936 CTTTTGATTGAAATTAACTGATTTGGC 57.184 29.630 0.00 0.00 29.75 4.52
2824 2925 9.767228 ATTACTAATTACATTGCGTATGTACCA 57.233 29.630 10.11 0.02 46.69 3.25
2825 2926 9.767228 TTACTAATTACATTGCGTATGTACCAT 57.233 29.630 10.11 2.02 46.69 3.55
2826 2927 8.083462 ACTAATTACATTGCGTATGTACCATG 57.917 34.615 10.11 0.00 46.69 3.66
2827 2928 6.935741 AATTACATTGCGTATGTACCATGT 57.064 33.333 10.11 2.57 46.69 3.21
2828 2929 5.977171 TTACATTGCGTATGTACCATGTC 57.023 39.130 10.11 0.00 46.69 3.06
2874 2988 0.402504 ATCGGCCACCAACTAACCAA 59.597 50.000 2.24 0.00 0.00 3.67
2945 3059 9.675464 AATTTCCAGAAATACATGCAAAATCAT 57.325 25.926 6.07 0.00 39.88 2.45
2946 3060 9.675464 ATTTCCAGAAATACATGCAAAATCATT 57.325 25.926 3.80 0.00 39.08 2.57
2947 3061 8.706492 TTCCAGAAATACATGCAAAATCATTC 57.294 30.769 0.00 0.00 0.00 2.67
2948 3062 8.070034 TCCAGAAATACATGCAAAATCATTCT 57.930 30.769 0.00 0.00 0.00 2.40
2989 3104 1.351017 CCATGTACAGGAACACCAGGT 59.649 52.381 9.54 0.00 30.75 4.00
3004 3119 5.381757 ACACCAGGTGTAGCTTGAAAAATA 58.618 37.500 24.77 0.00 45.56 1.40
3038 3153 2.301009 GGGACGGAAAGAGTAGGAACAA 59.699 50.000 0.00 0.00 0.00 2.83
3056 3171 5.333875 GGAACAAGAAAATTAGCTCGAACGT 60.334 40.000 0.00 0.00 0.00 3.99
3057 3172 5.265407 ACAAGAAAATTAGCTCGAACGTC 57.735 39.130 0.00 0.00 0.00 4.34
3060 3175 1.992170 AAATTAGCTCGAACGTCGCT 58.008 45.000 14.69 14.69 40.21 4.93
3066 3181 1.342082 GCTCGAACGTCGCTTTGCTA 61.342 55.000 0.00 0.00 40.21 3.49
3081 3196 1.443852 TGCTACATCCCCATGCCATA 58.556 50.000 0.00 0.00 32.57 2.74
3088 3204 1.228367 CCCCATGCCATAGTGCTCC 60.228 63.158 0.00 0.00 0.00 4.70
3102 3218 2.970974 GCTCCTGTTCTTGCGTGCC 61.971 63.158 0.00 0.00 0.00 5.01
3105 3221 1.893808 CCTGTTCTTGCGTGCCTGT 60.894 57.895 0.00 0.00 0.00 4.00
3142 3258 0.318022 TGCTTTGCATTGTCGTGCTG 60.318 50.000 0.00 0.00 45.27 4.41
3162 3278 4.998400 TGCGCTGCCTTGCCGTTA 62.998 61.111 9.73 0.00 0.00 3.18
3164 3280 3.051392 GCGCTGCCTTGCCGTTAAT 62.051 57.895 0.00 0.00 0.00 1.40
3167 3283 0.243636 GCTGCCTTGCCGTTAATTGT 59.756 50.000 0.00 0.00 0.00 2.71
3170 3286 1.810151 TGCCTTGCCGTTAATTGTCTC 59.190 47.619 0.00 0.00 0.00 3.36
3171 3287 1.132453 GCCTTGCCGTTAATTGTCTCC 59.868 52.381 0.00 0.00 0.00 3.71
3173 3289 2.432444 CTTGCCGTTAATTGTCTCCCA 58.568 47.619 0.00 0.00 0.00 4.37
3180 3297 3.564225 CGTTAATTGTCTCCCATTAGCCC 59.436 47.826 0.00 0.00 0.00 5.19
3184 3301 0.253160 TGTCTCCCATTAGCCCCTGT 60.253 55.000 0.00 0.00 0.00 4.00
3203 3320 1.470996 TTGCACCTTGGGGTCAATGC 61.471 55.000 0.00 0.00 45.41 3.56
3209 3326 1.152860 TTGGGGTCAATGCGTGTGT 60.153 52.632 0.00 0.00 0.00 3.72
3210 3327 1.451337 TTGGGGTCAATGCGTGTGTG 61.451 55.000 0.00 0.00 0.00 3.82
3211 3328 2.625823 GGGGTCAATGCGTGTGTGG 61.626 63.158 0.00 0.00 0.00 4.17
3212 3329 1.599518 GGGTCAATGCGTGTGTGGA 60.600 57.895 0.00 0.00 0.00 4.02
3213 3330 1.169661 GGGTCAATGCGTGTGTGGAA 61.170 55.000 0.00 0.00 0.00 3.53
3214 3331 0.665835 GGTCAATGCGTGTGTGGAAA 59.334 50.000 0.00 0.00 0.00 3.13
3215 3332 1.066303 GGTCAATGCGTGTGTGGAAAA 59.934 47.619 0.00 0.00 0.00 2.29
3216 3333 2.384382 GTCAATGCGTGTGTGGAAAAG 58.616 47.619 0.00 0.00 0.00 2.27
3217 3334 1.130955 CAATGCGTGTGTGGAAAAGC 58.869 50.000 0.00 0.00 0.00 3.51
3218 3335 0.317770 AATGCGTGTGTGGAAAAGCG 60.318 50.000 0.00 0.00 0.00 4.68
3221 3338 2.018544 CGTGTGTGGAAAAGCGGAA 58.981 52.632 0.00 0.00 0.00 4.30
3229 3346 0.881796 GGAAAAGCGGAAACAGAGGG 59.118 55.000 0.00 0.00 0.00 4.30
3237 3354 0.036294 GGAAACAGAGGGTTCGAGGG 60.036 60.000 0.00 0.00 39.29 4.30
3242 3359 1.041437 CAGAGGGTTCGAGGGGATAC 58.959 60.000 0.00 0.00 0.00 2.24
3243 3360 0.635009 AGAGGGTTCGAGGGGATACA 59.365 55.000 0.00 0.00 39.74 2.29
3254 3371 0.750850 GGGGATACAGAGCTGCGTTA 59.249 55.000 0.00 0.00 39.74 3.18
3314 3431 0.614979 ACGTGGAGGTAGTGGCTGAT 60.615 55.000 0.00 0.00 0.00 2.90
3315 3432 1.341679 ACGTGGAGGTAGTGGCTGATA 60.342 52.381 0.00 0.00 0.00 2.15
3322 3439 0.317938 GTAGTGGCTGATAGCGTCGG 60.318 60.000 0.00 0.00 43.62 4.79
3356 3473 3.367910 GCTGTGAGAGGAGTAAGTTGAGG 60.368 52.174 0.00 0.00 0.00 3.86
3364 3481 5.947566 AGAGGAGTAAGTTGAGGAGACTAAC 59.052 44.000 0.00 0.00 44.43 2.34
3365 3482 5.642165 AGGAGTAAGTTGAGGAGACTAACA 58.358 41.667 0.00 0.00 44.43 2.41
3366 3483 6.075984 AGGAGTAAGTTGAGGAGACTAACAA 58.924 40.000 0.00 0.00 44.43 2.83
3367 3484 6.209788 AGGAGTAAGTTGAGGAGACTAACAAG 59.790 42.308 0.00 0.00 44.43 3.16
3368 3485 6.015265 GGAGTAAGTTGAGGAGACTAACAAGT 60.015 42.308 0.00 0.00 44.43 3.16
3369 3486 6.983984 AGTAAGTTGAGGAGACTAACAAGTC 58.016 40.000 0.00 0.00 44.43 3.01
3370 3487 5.871396 AAGTTGAGGAGACTAACAAGTCA 57.129 39.130 8.16 0.00 44.43 3.41
3371 3488 6.426646 AAGTTGAGGAGACTAACAAGTCAT 57.573 37.500 8.16 0.00 44.43 3.06
3372 3489 6.426646 AGTTGAGGAGACTAACAAGTCATT 57.573 37.500 8.16 0.00 44.43 2.57
3373 3490 6.831976 AGTTGAGGAGACTAACAAGTCATTT 58.168 36.000 8.16 0.00 44.43 2.32
3374 3491 7.963532 AGTTGAGGAGACTAACAAGTCATTTA 58.036 34.615 8.16 0.00 44.43 1.40
3375 3492 8.429641 AGTTGAGGAGACTAACAAGTCATTTAA 58.570 33.333 8.16 0.00 44.43 1.52
3376 3493 9.220767 GTTGAGGAGACTAACAAGTCATTTAAT 57.779 33.333 8.16 0.00 44.43 1.40
3377 3494 8.777865 TGAGGAGACTAACAAGTCATTTAATG 57.222 34.615 8.16 0.00 44.43 1.90
3378 3495 8.593679 TGAGGAGACTAACAAGTCATTTAATGA 58.406 33.333 3.20 3.20 44.43 2.57
3379 3496 9.092876 GAGGAGACTAACAAGTCATTTAATGAG 57.907 37.037 8.00 0.00 44.43 2.90
3380 3497 8.043710 AGGAGACTAACAAGTCATTTAATGAGG 58.956 37.037 8.00 4.07 38.57 3.86
3381 3498 8.041323 GGAGACTAACAAGTCATTTAATGAGGA 58.959 37.037 8.00 0.00 40.53 3.71
3382 3499 9.092876 GAGACTAACAAGTCATTTAATGAGGAG 57.907 37.037 8.00 3.75 40.53 3.69
3383 3500 8.816894 AGACTAACAAGTCATTTAATGAGGAGA 58.183 33.333 8.00 0.00 40.53 3.71
3384 3501 9.606631 GACTAACAAGTCATTTAATGAGGAGAT 57.393 33.333 8.00 0.00 40.53 2.75
3399 3516 8.977267 AATGAGGAGATAAAAGGATGAGAAAG 57.023 34.615 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 6.976934 TTTAGGGCCAAATTCCAAGATATC 57.023 37.500 6.18 0.00 0.00 1.63
60 61 6.542821 ACAATGAGTTACTCCTTCCATTTGA 58.457 36.000 10.10 0.00 0.00 2.69
76 77 4.890088 TCGTGCCTTTACTTACAATGAGT 58.110 39.130 0.00 0.00 0.00 3.41
189 190 6.163135 ACATGCAAATACTCTACTAGGGAC 57.837 41.667 0.00 0.00 0.00 4.46
277 278 3.940209 TGCAACCAAATCCTTTAGCAG 57.060 42.857 0.00 0.00 0.00 4.24
278 279 4.888326 ATTGCAACCAAATCCTTTAGCA 57.112 36.364 0.00 0.00 34.05 3.49
326 327 8.746922 AAGTTTTATTGCAATGTATGACACAG 57.253 30.769 22.27 0.00 41.51 3.66
370 375 4.942483 CCTCAGTCAAGAGCATTGAGAAAT 59.058 41.667 4.75 0.00 37.96 2.17
373 378 3.168292 TCCTCAGTCAAGAGCATTGAGA 58.832 45.455 4.75 0.44 37.96 3.27
388 393 1.208776 TGAGCACATCCACATCCTCAG 59.791 52.381 0.00 0.00 0.00 3.35
410 415 6.216569 TCTAGAACCATTAAATCGCTGCTAG 58.783 40.000 0.00 0.00 0.00 3.42
433 475 3.057019 TGCGCGTATTCACATCCTTATC 58.943 45.455 8.43 0.00 0.00 1.75
690 740 6.652481 AGTGTATGAGAAACTTTGGTGATCAG 59.348 38.462 0.00 0.00 0.00 2.90
757 807 7.369803 TCACTCAAAAGAGTTTCATCTATGC 57.630 36.000 0.00 0.00 32.26 3.14
863 913 9.384764 GATGTATTTCCCTTATATAGAAGTGGC 57.615 37.037 6.38 0.00 0.00 5.01
998 1059 0.252284 CCTACCCCTCCTCGGCATAT 60.252 60.000 0.00 0.00 0.00 1.78
1029 1090 3.326836 TTGTCGTCATGGACATAAGCA 57.673 42.857 5.74 0.00 45.62 3.91
1121 1182 1.912731 TGATAGCAACCCTAGCACCAA 59.087 47.619 0.00 0.00 37.51 3.67
1189 1250 1.077501 CATCGACAATGGGGCCAGT 60.078 57.895 4.39 0.00 0.00 4.00
1238 1299 6.239036 GGCACTTGTTTCCTTCTTAGTGAATT 60.239 38.462 0.00 0.00 36.07 2.17
1240 1301 4.578928 GGCACTTGTTTCCTTCTTAGTGAA 59.421 41.667 0.00 0.00 36.07 3.18
1264 1325 2.651703 CACTTTGTAGTCGCGCAATTTG 59.348 45.455 8.75 0.00 30.26 2.32
1272 1333 1.429463 CCACCTCACTTTGTAGTCGC 58.571 55.000 0.00 0.00 30.26 5.19
1308 1369 3.946824 ACTCTTATCCTCCATCCCATGT 58.053 45.455 0.00 0.00 0.00 3.21
1329 1390 5.882000 CACATGTTGGATGGAGAGTTGATTA 59.118 40.000 0.00 0.00 0.00 1.75
1392 1453 6.591750 TCTTGTTCCTTCGAGAAGATAAGT 57.408 37.500 13.90 0.00 40.79 2.24
1462 1523 3.034635 GGTGTCTAGTGACCTCATGGAT 58.965 50.000 0.00 0.00 42.28 3.41
1472 1533 2.646175 GGCAGCCGGTGTCTAGTGA 61.646 63.158 1.90 0.00 0.00 3.41
1521 1582 0.247814 GAATCACGCTTGCACCATCG 60.248 55.000 0.00 0.00 0.00 3.84
1523 1584 1.246649 TTGAATCACGCTTGCACCAT 58.753 45.000 0.00 0.00 0.00 3.55
1663 1724 1.092921 TCCACGTTGTGTTCAGGTGC 61.093 55.000 0.00 0.00 32.40 5.01
1668 1729 1.088306 GTGGTTCCACGTTGTGTTCA 58.912 50.000 6.22 0.00 0.00 3.18
1726 1790 1.032014 AATTGTGGCGCTGAAGTTGT 58.968 45.000 7.64 0.00 0.00 3.32
1787 1851 0.465097 ATCCAAATCTGCTGGAGGCG 60.465 55.000 0.00 0.00 46.04 5.52
1795 1859 1.936547 GTCCTCGACATCCAAATCTGC 59.063 52.381 0.00 0.00 32.09 4.26
1804 1871 5.251601 GGGCTTATATAGTCCTCGACATC 57.748 47.826 0.00 0.00 45.74 3.06
1955 2022 2.827921 AGAGCAAAACCCCATTGATCAC 59.172 45.455 0.00 0.00 43.68 3.06
2001 2068 4.412528 AGGTAACCATCCATCCCTAGAAAC 59.587 45.833 0.00 0.00 37.17 2.78
2023 2090 8.280084 TCCTACATAGGTACCATTATAGCCTAG 58.720 40.741 15.94 0.32 44.02 3.02
2025 2092 6.896307 GTCCTACATAGGTACCATTATAGCCT 59.104 42.308 15.94 0.00 44.02 4.58
2041 2108 9.615660 ATTACCCATAGAAGATTGTCCTACATA 57.384 33.333 0.00 0.00 0.00 2.29
2248 2315 5.760484 ACCAATTTATTGCCTTGAATGGT 57.240 34.783 0.00 0.00 36.48 3.55
2266 2333 7.365831 TTCATGATCTGAGACATGGAATACCAA 60.366 37.037 19.75 8.51 41.59 3.67
2416 2491 1.337703 TGGCCTGATTGCAATATTCGC 59.662 47.619 12.97 11.31 0.00 4.70
2493 2568 2.664081 CCTGGGTGGGCAGAGACTC 61.664 68.421 0.00 0.00 0.00 3.36
2495 2570 1.779061 TTTCCTGGGTGGGCAGAGAC 61.779 60.000 0.00 0.00 36.20 3.36
2522 2617 1.403814 TGGACACAATTTTTCGCCCA 58.596 45.000 0.00 0.00 0.00 5.36
2531 2626 3.575805 AGGTTTGGACATGGACACAATT 58.424 40.909 0.00 0.00 0.00 2.32
2553 2648 4.909695 TGAGAGGACATGATGGATACCATT 59.090 41.667 0.00 0.00 45.26 3.16
2599 2694 5.120399 TGGAAGAGTTTATGTGAACGTTGT 58.880 37.500 5.00 0.00 34.74 3.32
2619 2714 1.634973 TGCCATGAGGTGAAGAATGGA 59.365 47.619 4.74 0.00 41.84 3.41
2719 2815 4.779993 ACTTGATAATCTGGGAAGGTCC 57.220 45.455 0.00 0.00 35.23 4.46
2756 2852 9.492973 CAGTTAATTTCAATCAAAAGGGATGTT 57.507 29.630 0.00 0.00 0.00 2.71
2823 2924 7.015226 TCAGTAAACAGTTCACTTTGACATG 57.985 36.000 0.00 0.00 0.00 3.21
2824 2925 7.807977 ATCAGTAAACAGTTCACTTTGACAT 57.192 32.000 0.00 0.00 0.00 3.06
2825 2926 7.624360 AATCAGTAAACAGTTCACTTTGACA 57.376 32.000 0.00 0.00 0.00 3.58
2826 2927 8.911247 AAAATCAGTAAACAGTTCACTTTGAC 57.089 30.769 0.00 0.00 0.00 3.18
2827 2928 9.567848 GAAAAATCAGTAAACAGTTCACTTTGA 57.432 29.630 0.00 0.00 0.00 2.69
2828 2929 9.573133 AGAAAAATCAGTAAACAGTTCACTTTG 57.427 29.630 0.00 0.00 0.00 2.77
2856 2970 0.535553 GTTGGTTAGTTGGTGGCCGA 60.536 55.000 0.00 0.00 0.00 5.54
2874 2988 7.125792 AGATTTATAGAGGTGGACAATTCGT 57.874 36.000 0.00 0.00 0.00 3.85
2934 3048 7.064134 CACATGCTTGTTAGAATGATTTTGCAT 59.936 33.333 1.83 0.00 39.49 3.96
2971 3086 2.054799 ACACCTGGTGTTCCTGTACAT 58.945 47.619 26.28 0.00 45.08 2.29
3004 3119 8.881262 ACTCTTTCCGTCCCATAATATAAGAAT 58.119 33.333 0.00 0.00 0.00 2.40
3023 3138 9.004717 AGCTAATTTTCTTGTTCCTACTCTTTC 57.995 33.333 0.00 0.00 0.00 2.62
3038 3153 2.344741 GCGACGTTCGAGCTAATTTTCT 59.655 45.455 10.82 0.00 43.74 2.52
3056 3171 0.546122 ATGGGGATGTAGCAAAGCGA 59.454 50.000 0.00 0.00 0.00 4.93
3057 3172 0.664761 CATGGGGATGTAGCAAAGCG 59.335 55.000 0.00 0.00 0.00 4.68
3060 3175 0.334335 TGGCATGGGGATGTAGCAAA 59.666 50.000 0.00 0.00 0.00 3.68
3066 3181 0.178981 GCACTATGGCATGGGGATGT 60.179 55.000 18.10 0.27 0.00 3.06
3081 3196 0.882042 CACGCAAGAACAGGAGCACT 60.882 55.000 0.00 0.00 43.62 4.40
3088 3204 1.280746 CACAGGCACGCAAGAACAG 59.719 57.895 0.00 0.00 43.62 3.16
3119 3235 1.370293 CGACAATGCAAAGCACGCA 60.370 52.632 0.00 0.00 43.04 5.24
3148 3264 0.243636 ACAATTAACGGCAAGGCAGC 59.756 50.000 0.00 0.00 0.00 5.25
3162 3278 2.091665 CAGGGGCTAATGGGAGACAATT 60.092 50.000 0.00 0.00 0.00 2.32
3164 3280 0.918983 CAGGGGCTAATGGGAGACAA 59.081 55.000 0.00 0.00 0.00 3.18
3167 3283 0.918983 CAACAGGGGCTAATGGGAGA 59.081 55.000 0.00 0.00 0.00 3.71
3170 3286 1.000233 TGCAACAGGGGCTAATGGG 60.000 57.895 0.00 0.00 0.00 4.00
3171 3287 1.322538 GGTGCAACAGGGGCTAATGG 61.323 60.000 0.00 0.00 39.98 3.16
3173 3289 0.409484 AAGGTGCAACAGGGGCTAAT 59.591 50.000 3.64 0.00 39.98 1.73
3203 3320 0.378962 TTTCCGCTTTTCCACACACG 59.621 50.000 0.00 0.00 0.00 4.49
3209 3326 1.604604 CCTCTGTTTCCGCTTTTCCA 58.395 50.000 0.00 0.00 0.00 3.53
3210 3327 0.881796 CCCTCTGTTTCCGCTTTTCC 59.118 55.000 0.00 0.00 0.00 3.13
3211 3328 1.605753 ACCCTCTGTTTCCGCTTTTC 58.394 50.000 0.00 0.00 0.00 2.29
3212 3329 1.954382 GAACCCTCTGTTTCCGCTTTT 59.046 47.619 0.00 0.00 37.29 2.27
3213 3330 1.605753 GAACCCTCTGTTTCCGCTTT 58.394 50.000 0.00 0.00 37.29 3.51
3214 3331 0.602905 CGAACCCTCTGTTTCCGCTT 60.603 55.000 0.00 0.00 37.29 4.68
3215 3332 1.004918 CGAACCCTCTGTTTCCGCT 60.005 57.895 0.00 0.00 37.29 5.52
3216 3333 1.005394 TCGAACCCTCTGTTTCCGC 60.005 57.895 0.00 0.00 37.29 5.54
3217 3334 0.389948 CCTCGAACCCTCTGTTTCCG 60.390 60.000 0.00 0.00 37.29 4.30
3218 3335 0.036294 CCCTCGAACCCTCTGTTTCC 60.036 60.000 0.00 0.00 37.29 3.13
3221 3338 0.252742 ATCCCCTCGAACCCTCTGTT 60.253 55.000 0.00 0.00 40.81 3.16
3229 3346 1.067821 CAGCTCTGTATCCCCTCGAAC 59.932 57.143 0.00 0.00 0.00 3.95
3237 3354 2.287668 ACGATAACGCAGCTCTGTATCC 60.288 50.000 0.00 0.00 43.96 2.59
3242 3359 1.759994 CCTACGATAACGCAGCTCTG 58.240 55.000 0.00 0.00 43.96 3.35
3243 3360 0.030908 GCCTACGATAACGCAGCTCT 59.969 55.000 0.00 0.00 43.96 4.09
3254 3371 1.672854 TAGCGCAACTGGCCTACGAT 61.673 55.000 11.47 1.62 40.31 3.73
3305 3422 2.808315 CCGACGCTATCAGCCACT 59.192 61.111 0.00 0.00 38.18 4.00
3314 3431 0.889638 CCTAGAGATGGCCGACGCTA 60.890 60.000 0.00 5.30 34.44 4.26
3315 3432 2.196925 CCTAGAGATGGCCGACGCT 61.197 63.158 0.00 4.26 34.44 5.07
3338 3455 4.043561 AGTCTCCTCAACTTACTCCTCTCA 59.956 45.833 0.00 0.00 0.00 3.27
3374 3491 8.977267 CTTTCTCATCCTTTTATCTCCTCATT 57.023 34.615 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.