Multiple sequence alignment - TraesCS5B01G188800

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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 TraesCS5B01G188800 chr5B 100.000 3509 0 0 1 3509 340718084 340721592 0.000000e+00 6481.0
1 TraesCS5B01G188800 chr5A 92.380 2651 124 38 886 3509 396706952 396709551 0.000000e+00 3705.0
2 TraesCS5B01G188800 chr5A 92.401 579 22 7 3 577 396706393 396706953 0.000000e+00 806.0
3 TraesCS5B01G188800 chr5D 94.740 1882 67 9 1 1872 299419588 299421447 0.000000e+00 2898.0
4 TraesCS5B01G188800 chr5D 90.536 1680 97 25 1871 3509 299422914 299424572 0.000000e+00 2165.0
5 TraesCS5B01G188800 chr2A 85.132 417 57 4 2086 2498 41462840 41462425 4.190000e-114 422.0
6 TraesCS5B01G188800 chr2B 84.416 385 59 1 2086 2470 63783369 63782986 9.190000e-101 377.0
7 TraesCS5B01G188800 chr7B 100.000 28 0 0 82 109 727396556 727396529 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 TraesCS5B01G188800 chr5B 340718084 340721592 3508 False 6481.0 6481 100.0000 1 3509 1 chr5B.!!$F1 3508
1 TraesCS5B01G188800 chr5A 396706393 396709551 3158 False 2255.5 3705 92.3905 3 3509 2 chr5A.!!$F1 3506
2 TraesCS5B01G188800 chr5D 299419588 299424572 4984 False 2531.5 2898 92.6380 1 3509 2 chr5D.!!$F1 3508

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
621 626 0.250793 ATTTATCGACGTGGGTGCCA 59.749 50.000 0.0 0.0 0.00 4.92 F
805 810 1.003545 CGTTCAGACACTTGGCACTTG 60.004 52.381 0.0 0.0 0.00 3.16 F
2193 3672 0.529378 CCAATGACAAAGCAGAGGCC 59.471 55.000 0.0 0.0 42.56 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1965 3444 0.376152 GCACATCAGGCTCAATGTCG 59.624 55.0 8.67 6.77 33.92 4.35 R
2319 3798 1.255667 TAGTGCCAGGGACGTTCTCC 61.256 60.0 5.28 0.00 38.55 3.71 R
3424 4963 0.400213 TGTGTTTGAGCTCCCCGATT 59.600 50.0 12.15 0.00 0.00 3.34 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
28 29 4.473520 TTGCGGGCTAGCCTGAGC 62.474 66.667 41.09 34.30 45.10 4.26
43 44 3.181503 GCCTGAGCTGTCATGTATTTGTG 60.182 47.826 0.00 0.00 35.50 3.33
69 70 6.183360 TGGCTGTATCTCTCCATAGTTTGTAC 60.183 42.308 0.00 0.00 0.00 2.90
90 91 8.292444 TGTACGTTTATTTAAGCTACTCCCTA 57.708 34.615 0.00 0.00 0.00 3.53
104 105 6.099269 AGCTACTCCCTACGATCCAAAATAAA 59.901 38.462 0.00 0.00 0.00 1.40
106 107 7.095187 GCTACTCCCTACGATCCAAAATAAATG 60.095 40.741 0.00 0.00 0.00 2.32
223 224 4.184629 CCCTTCACCTCTGATTTAAGTCG 58.815 47.826 0.00 0.00 0.00 4.18
264 265 9.143631 CTTATTTCTTTCACAATTCACCAATCC 57.856 33.333 0.00 0.00 0.00 3.01
267 268 3.913548 TTCACAATTCACCAATCCGTG 57.086 42.857 0.00 0.00 34.93 4.94
362 363 8.472007 TGTCTTATGGTAACTGGTTTTGAAAT 57.528 30.769 0.00 0.00 37.61 2.17
365 366 9.308000 TCTTATGGTAACTGGTTTTGAAATCAT 57.692 29.630 0.00 0.00 37.61 2.45
370 371 6.423604 GGTAACTGGTTTTGAAATCATTGTGG 59.576 38.462 0.00 0.00 0.00 4.17
565 570 6.755206 AGTTTAGCACGCCATATATCTGTAA 58.245 36.000 0.00 0.00 0.00 2.41
621 626 0.250793 ATTTATCGACGTGGGTGCCA 59.749 50.000 0.00 0.00 0.00 4.92
634 639 2.102578 GGGTGCCATGCTTTCACTTAT 58.897 47.619 0.00 0.00 0.00 1.73
643 648 6.032094 CCATGCTTTCACTTATTGTGTGATC 58.968 40.000 0.00 0.00 46.27 2.92
785 790 4.833380 TGGTAGCCAGATAATCAGTAGGTC 59.167 45.833 0.00 0.00 0.00 3.85
805 810 1.003545 CGTTCAGACACTTGGCACTTG 60.004 52.381 0.00 0.00 0.00 3.16
879 884 7.678947 ATCTGATGTCAGTTTGGAACTTTAG 57.321 36.000 9.65 0.00 44.12 1.85
959 964 6.034363 CAGTCGACATTTATGACTTCACTGAG 59.966 42.308 19.50 0.00 40.83 3.35
1179 1184 2.174764 CTAGACGTCCGATGTGAAACG 58.825 52.381 13.01 0.00 42.39 3.60
1182 1187 1.385743 GACGTCCGATGTGAAACGAAG 59.614 52.381 3.51 0.00 42.39 3.79
1185 1190 1.385743 GTCCGATGTGAAACGAAGACG 59.614 52.381 0.00 0.00 42.39 4.18
1192 1197 3.374745 TGTGAAACGAAGACGAAGGTAC 58.625 45.455 0.00 0.00 42.39 3.34
1197 1202 2.775890 ACGAAGACGAAGGTACTCTCA 58.224 47.619 0.00 0.00 39.97 3.27
1276 1283 7.206687 TGAAAAACACTTACAATGTTCCCATC 58.793 34.615 0.00 0.00 39.36 3.51
1700 1711 9.753674 TTAATCCAAAGGAGAAGATTTGTATGT 57.246 29.630 0.00 0.00 34.05 2.29
1904 3383 5.954752 ACAGAGAATATCTTGACTGACCTGA 59.045 40.000 0.00 0.00 35.47 3.86
1938 3417 5.887214 TGTAGGCAATGTCTATGTATGGT 57.113 39.130 0.00 0.00 0.00 3.55
1965 3444 5.871524 TGAGATTGTGCAAACTCTGATAGTC 59.128 40.000 18.41 0.00 39.86 2.59
1998 3477 1.028330 ATGTGCATGTCAAGAGGGCG 61.028 55.000 0.00 0.00 0.00 6.13
2021 3500 3.562182 TGAATGAGATCAATGCAGGCAT 58.438 40.909 0.00 0.00 38.46 4.40
2024 3503 2.021457 TGAGATCAATGCAGGCATGTG 58.979 47.619 7.64 8.46 36.68 3.21
2033 3512 1.679153 TGCAGGCATGTGCTAATGATG 59.321 47.619 9.44 3.04 44.32 3.07
2038 3517 5.597806 CAGGCATGTGCTAATGATGATTTT 58.402 37.500 4.84 0.00 41.70 1.82
2095 3574 9.956720 GCAGCAAAACATATACTAGATGATTTT 57.043 29.630 0.00 0.00 29.74 1.82
2193 3672 0.529378 CCAATGACAAAGCAGAGGCC 59.471 55.000 0.00 0.00 42.56 5.19
2310 3789 0.885196 GTCTGAGAGACAGCGTCCTT 59.115 55.000 5.29 0.00 44.45 3.36
2319 3798 2.097038 CAGCGTCCTTGCCTTCTCG 61.097 63.158 0.00 0.00 34.65 4.04
2337 3816 2.584391 GGAGAACGTCCCTGGCACT 61.584 63.158 0.00 0.00 39.88 4.40
2343 3822 2.125512 GTCCCTGGCACTACTGCG 60.126 66.667 0.00 0.00 45.31 5.18
2346 3825 1.003839 CCCTGGCACTACTGCGAAA 60.004 57.895 0.00 0.00 45.31 3.46
2415 3894 1.009997 AGATTGGGGCCTCATCCAAA 58.990 50.000 5.88 0.00 44.94 3.28
2510 3989 3.964031 CTCCAGGCCAATACTCTCTAAGT 59.036 47.826 5.01 0.00 42.33 2.24
2512 3991 3.706594 CCAGGCCAATACTCTCTAAGTGA 59.293 47.826 5.01 0.00 39.11 3.41
2513 3992 4.202202 CCAGGCCAATACTCTCTAAGTGAG 60.202 50.000 5.01 0.00 43.96 3.51
2571 4051 7.172875 AGAGTTGTGAAGTTCTTCATCATTCAG 59.827 37.037 16.55 0.00 33.02 3.02
2649 4129 8.462143 AATTTATCTACGTGTGTGAACTACTG 57.538 34.615 0.00 0.00 0.00 2.74
2677 4157 9.308318 GTTAAGTTGTGAATTTTACATGGTGTT 57.692 29.630 0.00 0.00 0.00 3.32
2682 4165 8.751335 GTTGTGAATTTTACATGGTGTTAACTG 58.249 33.333 7.22 0.00 0.00 3.16
2690 4173 4.828829 ACATGGTGTTAACTGCTACCTAC 58.171 43.478 12.56 0.00 34.32 3.18
2754 4237 2.173569 AGCCAGATTCCTGAATGGTACC 59.826 50.000 4.43 4.43 43.02 3.34
2845 4328 2.086054 TGGTGTTTGTGTTTTGTGCC 57.914 45.000 0.00 0.00 0.00 5.01
2866 4367 5.065988 TGCCGAGTTTATCTTATTGGCTTTC 59.934 40.000 4.09 0.00 41.73 2.62
2881 4382 2.935042 GCTTTCGAGCCCTTTTCTTTC 58.065 47.619 0.00 0.00 0.00 2.62
2882 4383 2.665794 GCTTTCGAGCCCTTTTCTTTCG 60.666 50.000 0.00 0.00 0.00 3.46
2883 4384 1.519408 TTCGAGCCCTTTTCTTTCGG 58.481 50.000 0.00 0.00 32.52 4.30
2888 4389 2.162408 GAGCCCTTTTCTTTCGGTCATG 59.838 50.000 0.00 0.00 0.00 3.07
2923 4424 3.378427 AGTTGTTCTCAGAAAGTGGCAAC 59.622 43.478 8.97 8.97 34.93 4.17
2939 4440 2.028748 GGCAACAGCAGATTTTGATGGT 60.029 45.455 0.00 0.00 45.83 3.55
2940 4441 3.248266 GCAACAGCAGATTTTGATGGTC 58.752 45.455 0.00 0.00 39.33 4.02
2943 4444 1.402968 CAGCAGATTTTGATGGTCCCG 59.597 52.381 0.00 0.00 39.52 5.14
2955 4456 0.676466 TGGTCCCGTCATGTGAATGC 60.676 55.000 0.00 0.00 0.00 3.56
2975 4476 4.316375 GCAAATTGCTACAATTGCAGTG 57.684 40.909 11.19 2.95 45.61 3.66
2985 4486 2.223641 ACAATTGCAGTGCACACTCTTG 60.224 45.455 19.58 17.23 40.20 3.02
2998 4499 4.035324 GCACACTCTTGATTCCTGATGATG 59.965 45.833 0.00 0.00 0.00 3.07
3060 4561 7.992608 TCAATACAGTTTATCAGGCATGTATGT 59.007 33.333 0.00 0.00 34.87 2.29
3061 4562 9.271828 CAATACAGTTTATCAGGCATGTATGTA 57.728 33.333 0.00 1.06 34.87 2.29
3062 4563 8.833231 ATACAGTTTATCAGGCATGTATGTAC 57.167 34.615 0.00 0.00 33.74 2.90
3063 4564 6.649155 ACAGTTTATCAGGCATGTATGTACA 58.351 36.000 0.00 0.00 40.98 2.90
3064 4565 6.538742 ACAGTTTATCAGGCATGTATGTACAC 59.461 38.462 0.00 0.00 39.30 2.90
3065 4566 6.538381 CAGTTTATCAGGCATGTATGTACACA 59.462 38.462 0.00 0.00 39.30 3.72
3066 4567 7.065683 CAGTTTATCAGGCATGTATGTACACAA 59.934 37.037 0.00 0.00 39.30 3.33
3067 4568 6.918892 TTATCAGGCATGTATGTACACAAC 57.081 37.500 0.00 0.00 39.30 3.32
3078 4579 7.826260 TGTATGTACACAACTACACATGATG 57.174 36.000 0.00 0.00 33.78 3.07
3095 4596 3.753815 TGATGAAGATTGGTCTTGTGCA 58.246 40.909 0.00 0.00 44.57 4.57
3136 4642 2.300433 TGCTTGTGACAATGCAACTCT 58.700 42.857 16.22 0.00 32.12 3.24
3146 4652 2.072874 ATGCAACTCTGGTGCCCTGT 62.073 55.000 5.09 0.00 0.00 4.00
3147 4653 2.263741 GCAACTCTGGTGCCCTGTG 61.264 63.158 0.00 0.00 0.00 3.66
3149 4655 0.466189 CAACTCTGGTGCCCTGTGTT 60.466 55.000 10.55 10.55 38.84 3.32
3150 4656 0.258774 AACTCTGGTGCCCTGTGTTT 59.741 50.000 10.55 0.93 36.35 2.83
3171 4686 4.643387 GGCACCAGGTTCGCAGGT 62.643 66.667 4.37 0.00 35.65 4.00
3203 4718 4.256090 GTTGGGCATGGCGATCGC 62.256 66.667 31.52 31.52 41.06 4.58
3217 4732 2.333389 GATCGCGTATCGGACTTGAT 57.667 50.000 5.77 0.00 39.05 2.57
3228 4743 1.001974 CGGACTTGATGTTGAGACCCA 59.998 52.381 0.00 0.00 0.00 4.51
3284 4799 2.343163 CTTCCCGTAGCTCCGCAGAG 62.343 65.000 0.00 0.00 43.57 3.35
3355 4872 9.978044 ACCGATCAAAAATAACTACTCCTATAC 57.022 33.333 0.00 0.00 0.00 1.47
3382 4901 4.799564 ACACTGACCAAAACACAAACAT 57.200 36.364 0.00 0.00 0.00 2.71
3387 4906 3.123050 GACCAAAACACAAACATGCTCC 58.877 45.455 0.00 0.00 0.00 4.70
3403 4922 2.957680 TGCTCCAGATTTTGTGCTTCAA 59.042 40.909 0.00 0.00 0.00 2.69
3430 4969 1.203065 GCGTCCGTAAGTTAATCGGG 58.797 55.000 10.95 0.00 43.75 5.14
3431 4970 1.843992 CGTCCGTAAGTTAATCGGGG 58.156 55.000 10.95 2.25 43.75 5.73
3432 4971 1.405105 CGTCCGTAAGTTAATCGGGGA 59.595 52.381 10.95 0.00 43.75 4.81
3433 4972 2.542411 CGTCCGTAAGTTAATCGGGGAG 60.542 54.545 10.95 1.74 43.75 4.30
3434 4973 1.410153 TCCGTAAGTTAATCGGGGAGC 59.590 52.381 10.95 0.00 43.75 4.70
3435 4974 1.411612 CCGTAAGTTAATCGGGGAGCT 59.588 52.381 4.42 0.00 40.49 4.09
3436 4975 2.545322 CCGTAAGTTAATCGGGGAGCTC 60.545 54.545 4.71 4.71 40.49 4.09
3437 4976 2.100252 CGTAAGTTAATCGGGGAGCTCA 59.900 50.000 17.19 0.00 0.00 4.26
3438 4977 3.429822 CGTAAGTTAATCGGGGAGCTCAA 60.430 47.826 17.19 0.00 0.00 3.02
3439 4978 3.713826 AAGTTAATCGGGGAGCTCAAA 57.286 42.857 17.19 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 3.503363 ACAGCCACACAAATACATGACAG 59.497 43.478 0.00 0.00 0.00 3.51
43 44 4.946478 AACTATGGAGAGATACAGCCAC 57.054 45.455 0.00 0.00 32.42 5.01
69 70 6.498304 TCGTAGGGAGTAGCTTAAATAAACG 58.502 40.000 0.00 0.00 0.00 3.60
90 91 3.370104 TGGGGCATTTATTTTGGATCGT 58.630 40.909 0.00 0.00 0.00 3.73
223 224 2.044123 ATAAGCTAAGTGCAGTGGGC 57.956 50.000 10.01 10.01 45.94 5.36
264 265 4.651994 CTTTGCCAGAATAACTAAGCACG 58.348 43.478 0.00 0.00 36.99 5.34
267 268 4.156739 ACAGCTTTGCCAGAATAACTAAGC 59.843 41.667 0.00 0.00 36.98 3.09
362 363 5.408880 AAATTCATGATGCACCACAATGA 57.591 34.783 0.00 0.00 0.00 2.57
365 366 6.283544 ACATAAATTCATGATGCACCACAA 57.716 33.333 0.00 0.00 0.00 3.33
398 403 2.980568 ACAAGTTGAAACGGTGAGACA 58.019 42.857 10.54 0.00 0.00 3.41
406 411 9.666626 TTTGTAATACCATTACAAGTTGAAACG 57.333 29.630 18.65 0.00 43.25 3.60
611 616 2.267351 TGAAAGCATGGCACCCACG 61.267 57.895 0.00 0.00 35.80 4.94
615 620 3.056607 ACAATAAGTGAAAGCATGGCACC 60.057 43.478 0.00 0.00 33.14 5.01
634 639 9.906660 GTACAAAAAGGAATTATGATCACACAA 57.093 29.630 0.00 0.00 0.00 3.33
711 716 9.500785 CCAAATGTTGGTAAATGGTTTAGATTT 57.499 29.630 0.00 0.00 45.93 2.17
785 790 1.003545 CAAGTGCCAAGTGTCTGAACG 60.004 52.381 0.00 0.00 0.00 3.95
793 798 0.250901 AGCCTACCAAGTGCCAAGTG 60.251 55.000 0.00 0.00 0.00 3.16
824 829 3.641437 GTATGCAACAGCAGACCAAAA 57.359 42.857 4.03 0.00 42.92 2.44
879 884 6.603201 TCATCATCCAAGGATAACCAAACTTC 59.397 38.462 0.40 0.00 38.94 3.01
1179 1184 8.325421 TGATATATGAGAGTACCTTCGTCTTC 57.675 38.462 0.00 0.00 0.00 2.87
1182 1187 8.270080 TGATGATATATGAGAGTACCTTCGTC 57.730 38.462 0.00 0.00 0.00 4.20
1276 1283 4.703897 TGTAGAACAGAGAAAACACCCAG 58.296 43.478 0.00 0.00 0.00 4.45
1517 1524 3.248024 ACTGGACAGACAAGGGATGTAA 58.752 45.455 6.29 0.00 44.12 2.41
1904 3383 5.307204 ACATTGCCTACAACATTTGCAAAT 58.693 33.333 18.99 18.99 44.17 2.32
1938 3417 8.043113 ACTATCAGAGTTTGCACAATCTCATAA 58.957 33.333 18.75 7.93 38.79 1.90
1965 3444 0.376152 GCACATCAGGCTCAATGTCG 59.624 55.000 8.67 6.77 33.92 4.35
1998 3477 3.568430 TGCCTGCATTGATCTCATTCATC 59.432 43.478 0.00 0.00 0.00 2.92
2021 3500 9.577110 GATTGAAAGAAAATCATCATTAGCACA 57.423 29.630 0.00 0.00 34.73 4.57
2024 3503 9.028185 GTGGATTGAAAGAAAATCATCATTAGC 57.972 33.333 0.00 0.00 36.03 3.09
2033 3512 9.512435 CTGATGTATGTGGATTGAAAGAAAATC 57.488 33.333 0.00 0.00 34.00 2.17
2038 3517 9.904198 TTAATCTGATGTATGTGGATTGAAAGA 57.096 29.630 0.00 0.00 0.00 2.52
2095 3574 6.718388 CAAAAGATAATTCTGAGCACGCATA 58.282 36.000 0.00 0.00 30.72 3.14
2193 3672 7.290857 TCGTTTAATCTGGAGAATCTTTTCG 57.709 36.000 0.00 0.00 36.93 3.46
2310 3789 1.585006 GACGTTCTCCGAGAAGGCA 59.415 57.895 24.26 0.00 42.16 4.75
2319 3798 1.255667 TAGTGCCAGGGACGTTCTCC 61.256 60.000 5.28 0.00 38.55 3.71
2337 3816 3.056179 TGTCCATGATGTCTTTCGCAGTA 60.056 43.478 0.00 0.00 0.00 2.74
2343 3822 4.946157 AGAACCATGTCCATGATGTCTTTC 59.054 41.667 8.82 2.55 41.20 2.62
2346 3825 3.371273 CCAGAACCATGTCCATGATGTCT 60.371 47.826 8.82 5.45 41.20 3.41
2379 3858 4.455533 CCAATCTCTTTCATGGTGTCGAAA 59.544 41.667 0.00 0.00 0.00 3.46
2415 3894 2.092914 GGGGATGAACACCGAAGAAGAT 60.093 50.000 0.00 0.00 29.82 2.40
2510 3989 3.117888 GCTATCCTTTTCCATGACCCTCA 60.118 47.826 0.00 0.00 0.00 3.86
2512 3991 3.126453 AGCTATCCTTTTCCATGACCCT 58.874 45.455 0.00 0.00 0.00 4.34
2513 3992 3.584733 AGCTATCCTTTTCCATGACCC 57.415 47.619 0.00 0.00 0.00 4.46
2516 3995 5.441718 ACAGAAGCTATCCTTTTCCATGA 57.558 39.130 0.00 0.00 32.78 3.07
2608 4088 3.418684 AAATTACTCACGACCTTGCCT 57.581 42.857 0.00 0.00 0.00 4.75
2649 4129 6.639279 ACCATGTAAAATTCACAACTTAACGC 59.361 34.615 0.00 0.00 0.00 4.84
2677 4157 8.414003 CAAGTCTGATTATGTAGGTAGCAGTTA 58.586 37.037 0.00 0.00 0.00 2.24
2682 4165 5.601662 TGCAAGTCTGATTATGTAGGTAGC 58.398 41.667 0.00 0.00 0.00 3.58
2690 4173 4.275196 CCACTCCATGCAAGTCTGATTATG 59.725 45.833 0.00 0.00 0.00 1.90
2726 4209 5.163581 CCATTCAGGAATCTGGCTAAACTTG 60.164 44.000 0.00 0.00 41.23 3.16
2821 4304 5.450688 GGCACAAAACACAAACACCATAGTA 60.451 40.000 0.00 0.00 0.00 1.82
2845 4328 6.583912 TCGAAAGCCAATAAGATAAACTCG 57.416 37.500 0.00 0.00 0.00 4.18
2866 4367 0.796927 GACCGAAAGAAAAGGGCTCG 59.203 55.000 0.00 0.00 0.00 5.03
2873 4374 6.430925 ACATCATTCTCATGACCGAAAGAAAA 59.569 34.615 6.69 0.00 42.46 2.29
2874 4375 5.939883 ACATCATTCTCATGACCGAAAGAAA 59.060 36.000 6.69 0.00 42.46 2.52
2875 4376 5.352293 CACATCATTCTCATGACCGAAAGAA 59.648 40.000 6.69 1.94 42.46 2.52
2876 4377 4.872124 CACATCATTCTCATGACCGAAAGA 59.128 41.667 5.44 5.44 42.46 2.52
2877 4378 4.495349 GCACATCATTCTCATGACCGAAAG 60.495 45.833 1.90 0.00 42.46 2.62
2878 4379 3.374988 GCACATCATTCTCATGACCGAAA 59.625 43.478 1.90 0.00 42.46 3.46
2879 4380 2.938451 GCACATCATTCTCATGACCGAA 59.062 45.455 0.00 0.00 42.46 4.30
2880 4381 2.093553 TGCACATCATTCTCATGACCGA 60.094 45.455 0.00 0.00 42.46 4.69
2881 4382 2.282407 TGCACATCATTCTCATGACCG 58.718 47.619 0.00 0.00 42.46 4.79
2882 4383 3.276857 ACTGCACATCATTCTCATGACC 58.723 45.455 0.00 0.00 42.46 4.02
2883 4384 4.155462 ACAACTGCACATCATTCTCATGAC 59.845 41.667 0.00 0.00 42.46 3.06
2888 4389 4.453478 TGAGAACAACTGCACATCATTCTC 59.547 41.667 12.70 12.70 37.50 2.87
2923 4424 1.402968 CGGGACCATCAAAATCTGCTG 59.597 52.381 0.00 0.00 0.00 4.41
2939 4440 1.902938 TTTGCATTCACATGACGGGA 58.097 45.000 0.00 0.00 31.07 5.14
2940 4441 2.924926 CAATTTGCATTCACATGACGGG 59.075 45.455 0.00 0.00 31.07 5.28
2955 4456 3.741856 TGCACTGCAATTGTAGCAATTTG 59.258 39.130 21.76 13.59 42.17 2.32
2975 4476 3.603532 TCATCAGGAATCAAGAGTGTGC 58.396 45.455 0.00 0.00 0.00 4.57
2998 4499 8.219105 GTGCACTTGTACAGTTATACACTTTAC 58.781 37.037 10.32 0.00 38.63 2.01
3060 4561 7.334171 CCAATCTTCATCATGTGTAGTTGTGTA 59.666 37.037 0.00 0.00 0.00 2.90
3061 4562 6.149973 CCAATCTTCATCATGTGTAGTTGTGT 59.850 38.462 0.00 0.00 0.00 3.72
3062 4563 6.149973 ACCAATCTTCATCATGTGTAGTTGTG 59.850 38.462 0.00 0.00 0.00 3.33
3063 4564 6.240894 ACCAATCTTCATCATGTGTAGTTGT 58.759 36.000 0.00 0.00 0.00 3.32
3064 4565 6.596888 AGACCAATCTTCATCATGTGTAGTTG 59.403 38.462 0.00 2.79 0.00 3.16
3065 4566 6.715280 AGACCAATCTTCATCATGTGTAGTT 58.285 36.000 0.00 0.00 0.00 2.24
3066 4567 6.305272 AGACCAATCTTCATCATGTGTAGT 57.695 37.500 0.00 0.00 0.00 2.73
3067 4568 6.596888 ACAAGACCAATCTTCATCATGTGTAG 59.403 38.462 0.00 0.00 43.69 2.74
3078 4579 2.508526 ACCTGCACAAGACCAATCTTC 58.491 47.619 0.00 0.00 43.69 2.87
3095 4596 4.681781 GCATATTCAGTGTCAGTGCTACCT 60.682 45.833 2.50 0.00 0.00 3.08
3146 4652 1.816183 CGAACCTGGTGCCCTTAAACA 60.816 52.381 0.00 0.00 0.00 2.83
3147 4653 0.879090 CGAACCTGGTGCCCTTAAAC 59.121 55.000 0.00 0.00 0.00 2.01
3149 4655 1.302993 GCGAACCTGGTGCCCTTAA 60.303 57.895 0.00 0.00 0.00 1.85
3150 4656 2.349755 GCGAACCTGGTGCCCTTA 59.650 61.111 0.00 0.00 0.00 2.69
3171 4686 2.517959 CCCAACTTGCTCCATCAGAAA 58.482 47.619 0.00 0.00 0.00 2.52
3203 4718 3.791887 GTCTCAACATCAAGTCCGATACG 59.208 47.826 0.00 0.00 0.00 3.06
3228 4743 4.021925 GGACGCCTGGAACCTGCT 62.022 66.667 0.00 0.00 0.00 4.24
3296 4811 3.820467 CTGAATTAACACTCACCAGGCAA 59.180 43.478 0.00 0.00 0.00 4.52
3346 4861 4.585162 GGTCAGTGTATGCAGTATAGGAGT 59.415 45.833 0.00 0.00 0.00 3.85
3354 4871 3.315191 GTGTTTTGGTCAGTGTATGCAGT 59.685 43.478 0.00 0.00 0.00 4.40
3355 4872 3.314913 TGTGTTTTGGTCAGTGTATGCAG 59.685 43.478 0.00 0.00 0.00 4.41
3382 4901 2.585330 TGAAGCACAAAATCTGGAGCA 58.415 42.857 0.00 0.00 33.86 4.26
3403 4922 0.683412 ACTTACGGACGCCTCCTTTT 59.317 50.000 0.07 0.00 33.79 2.27
3405 4924 1.549203 TAACTTACGGACGCCTCCTT 58.451 50.000 0.07 0.00 33.79 3.36
3406 4925 1.549203 TTAACTTACGGACGCCTCCT 58.451 50.000 0.07 0.00 33.79 3.69
3407 4926 2.467838 GATTAACTTACGGACGCCTCC 58.532 52.381 0.00 0.00 0.00 4.30
3408 4927 2.114825 CGATTAACTTACGGACGCCTC 58.885 52.381 0.00 0.00 0.00 4.70
3424 4963 0.400213 TGTGTTTGAGCTCCCCGATT 59.600 50.000 12.15 0.00 0.00 3.34
3430 4969 2.059541 GTACGTCTGTGTTTGAGCTCC 58.940 52.381 12.15 0.00 0.00 4.70
3431 4970 2.726760 CTGTACGTCTGTGTTTGAGCTC 59.273 50.000 6.82 6.82 0.00 4.09
3432 4971 2.743938 CTGTACGTCTGTGTTTGAGCT 58.256 47.619 0.00 0.00 0.00 4.09
3433 4972 1.192534 GCTGTACGTCTGTGTTTGAGC 59.807 52.381 0.00 0.00 0.00 4.26
3434 4973 2.469826 TGCTGTACGTCTGTGTTTGAG 58.530 47.619 0.00 0.00 0.00 3.02
3435 4974 2.469826 CTGCTGTACGTCTGTGTTTGA 58.530 47.619 0.00 0.00 0.00 2.69
3436 4975 1.526887 CCTGCTGTACGTCTGTGTTTG 59.473 52.381 0.00 0.00 0.00 2.93
3437 4976 1.865865 CCTGCTGTACGTCTGTGTTT 58.134 50.000 0.00 0.00 0.00 2.83
3438 4977 0.600255 GCCTGCTGTACGTCTGTGTT 60.600 55.000 0.00 0.00 0.00 3.32
3439 4978 1.006102 GCCTGCTGTACGTCTGTGT 60.006 57.895 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.