Multiple sequence alignment - TraesCS7D01G022800

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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 TraesCS7D01G022800 chr7D 100.000 3985 0 0 1 3985 10713779 10717763 0.000000e+00 7360
1 TraesCS7D01G022800 chr7D 81.818 484 57 14 1588 2068 63071052 63071507 1.050000e-100 377
2 TraesCS7D01G022800 chr7A 91.688 3080 153 43 1 3007 9753559 9756608 0.000000e+00 4174
3 TraesCS7D01G022800 chr7A 88.778 900 52 19 3090 3985 9756714 9757568 0.000000e+00 1057
4 TraesCS7D01G022800 chr7A 81.237 485 59 17 1588 2068 639220811 639221267 2.930000e-96 363
5 TraesCS7D01G022800 chr4A 92.033 1343 67 16 699 2018 728087856 728086531 0.000000e+00 1851
6 TraesCS7D01G022800 chr4A 90.275 1018 40 30 2010 2998 728086333 728085346 0.000000e+00 1277
7 TraesCS7D01G022800 chr4A 96.302 676 22 1 1 673 728088529 728087854 0.000000e+00 1107
8 TraesCS7D01G022800 chr4A 88.375 886 55 25 3129 3985 728085212 728084346 0.000000e+00 1022
9 TraesCS7D01G022800 chr6D 82.526 475 52 14 1597 2068 435556737 435557183 4.830000e-104 388
10 TraesCS7D01G022800 chr4D 81.799 478 56 20 1597 2071 452006859 452006410 4.860000e-99 372
11 TraesCS7D01G022800 chr3A 81.875 480 52 18 1597 2071 555171888 555171439 4.860000e-99 372
12 TraesCS7D01G022800 chr2B 84.881 377 36 12 1673 2035 56001853 56002222 1.050000e-95 361
13 TraesCS7D01G022800 chr2B 92.810 153 10 1 2529 2680 510167747 510167595 1.860000e-53 220
14 TraesCS7D01G022800 chr1D 81.532 444 51 18 1588 2028 393065196 393065611 1.770000e-88 337
15 TraesCS7D01G022800 chr1D 80.603 464 57 20 1588 2047 477539023 477539457 1.070000e-85 327
16 TraesCS7D01G022800 chr1D 80.388 464 58 22 1588 2047 392993546 392993980 4.970000e-84 322
17 TraesCS7D01G022800 chr1D 78.744 414 57 13 1624 2034 476038506 476038121 8.550000e-62 248


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 TraesCS7D01G022800 chr7D 10713779 10717763 3984 False 7360.00 7360 100.00000 1 3985 1 chr7D.!!$F1 3984
1 TraesCS7D01G022800 chr7A 9753559 9757568 4009 False 2615.50 4174 90.23300 1 3985 2 chr7A.!!$F2 3984
2 TraesCS7D01G022800 chr4A 728084346 728088529 4183 True 1314.25 1851 91.74625 1 3985 4 chr4A.!!$R1 3984

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
773 788 1.135699 GGTGCGCAATTTGCTCGATG 61.136 55.0 14.00 4.53 42.25 3.84 F
1313 1345 0.304098 GTCGCTGATCATGAGCTTGC 59.696 55.0 12.92 14.66 34.03 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2452 2739 0.179037 TCGACGTATGGACCGGATCT 60.179 55.0 9.46 0.00 0.00 2.75 R
3257 3625 0.034059 AAGACTGACAGGCTGAACGG 59.966 55.0 23.66 20.13 30.77 4.44 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
97 98 5.579511 GCAAATCAAATCATGAGGACCAAAG 59.420 40.000 0.09 0.00 42.53 2.77
117 118 6.127647 CCAAAGCTATGCAATTCTTAGGTTGA 60.128 38.462 8.94 0.00 40.21 3.18
483 494 7.060633 CGATTTGATTTGGACTTAAAGAAACGG 59.939 37.037 0.00 0.00 0.00 4.44
521 532 1.637553 AGACAGTGGGCATTGGATCTT 59.362 47.619 0.00 0.00 0.00 2.40
522 533 2.019984 GACAGTGGGCATTGGATCTTC 58.980 52.381 0.00 0.00 0.00 2.87
543 554 2.795329 GAACTTTCTCATGGGAAGGCA 58.205 47.619 16.85 0.00 0.00 4.75
572 583 5.427481 CCTAAATTGGTCCTTGTAGGTCCTA 59.573 44.000 9.80 0.00 42.97 2.94
605 617 6.286758 TCATGCCAAAATTTTCAGTGCTAAA 58.713 32.000 0.00 0.00 0.00 1.85
716 731 4.389374 CAGAGCCTTACTTTGTTCCTTCA 58.611 43.478 0.00 0.00 0.00 3.02
734 749 4.083110 CCTTCACACTGTGCAATAAAGAGG 60.083 45.833 7.90 1.10 32.98 3.69
752 767 1.415659 AGGCAGCTATTCGATTCAGCT 59.584 47.619 9.44 9.44 46.36 4.24
773 788 1.135699 GGTGCGCAATTTGCTCGATG 61.136 55.000 14.00 4.53 42.25 3.84
853 868 1.678728 CGGGCCATGTTTTAGCTCTCA 60.679 52.381 4.39 0.00 0.00 3.27
954 969 5.838521 ACCCCTATAAAAACCATGGCATAAG 59.161 40.000 13.04 0.00 0.00 1.73
1008 1034 1.464997 GACGGACTGAAAATGTGGAGC 59.535 52.381 0.00 0.00 0.00 4.70
1235 1261 3.986277 AGCAAAGGCAAAAACAGATCAG 58.014 40.909 0.00 0.00 44.61 2.90
1307 1339 3.317603 TTTCACTGTCGCTGATCATGA 57.682 42.857 0.00 0.00 0.00 3.07
1308 1340 2.573941 TCACTGTCGCTGATCATGAG 57.426 50.000 0.09 0.00 0.00 2.90
1310 1342 0.822811 ACTGTCGCTGATCATGAGCT 59.177 50.000 12.92 0.00 34.03 4.09
1313 1345 0.304098 GTCGCTGATCATGAGCTTGC 59.696 55.000 12.92 14.66 34.03 4.01
1314 1346 1.149964 TCGCTGATCATGAGCTTGCG 61.150 55.000 30.66 30.66 39.85 4.85
1381 1414 5.640189 AAGATCACTGCTGAAATCTTTGG 57.360 39.130 14.59 0.00 25.92 3.28
1382 1415 4.914983 AGATCACTGCTGAAATCTTTGGA 58.085 39.130 0.00 0.00 0.00 3.53
1394 1427 5.945784 TGAAATCTTTGGATACCTGTTCCTG 59.054 40.000 0.00 0.00 34.17 3.86
1463 1496 1.007038 GGAGTACACGACCGCAACA 60.007 57.895 0.00 0.00 0.00 3.33
1586 1619 5.769662 AGTCATTTTCTTACATGCAGGTCAA 59.230 36.000 7.56 0.15 0.00 3.18
1842 1904 4.679662 CTTTACGGACCACATCGATAAGT 58.320 43.478 0.00 0.00 0.00 2.24
1844 1906 2.097036 ACGGACCACATCGATAAGTGA 58.903 47.619 15.44 0.00 37.97 3.41
1845 1907 2.693591 ACGGACCACATCGATAAGTGAT 59.306 45.455 15.44 0.05 37.97 3.06
1846 1908 3.887110 ACGGACCACATCGATAAGTGATA 59.113 43.478 15.44 0.00 37.97 2.15
1847 1909 4.340097 ACGGACCACATCGATAAGTGATAA 59.660 41.667 15.44 0.00 37.97 1.75
1918 1982 8.749499 GTGAATCAGAATCAAACACTTTTTCAG 58.251 33.333 0.00 0.00 0.00 3.02
1940 2008 2.233271 AGCTAAGTTGCATTGCACACT 58.767 42.857 11.66 14.42 38.71 3.55
1947 2015 1.900245 TGCATTGCACACTCATGAGT 58.100 45.000 22.89 22.89 36.29 3.41
2138 2413 2.852075 GTCCCTCACCCACCACCA 60.852 66.667 0.00 0.00 0.00 4.17
2141 2416 2.854032 CCTCACCCACCACCACCT 60.854 66.667 0.00 0.00 0.00 4.00
2447 2734 1.972752 TCTACTGCGTACGTGGGCA 60.973 57.895 17.90 13.60 37.63 5.36
2463 2750 3.822192 CACGCGAGATCCGGTCCA 61.822 66.667 15.93 0.00 39.04 4.02
2464 2751 2.833582 ACGCGAGATCCGGTCCAT 60.834 61.111 15.93 0.00 39.04 3.41
2479 2779 1.948145 GTCCATACGTCGACTCCTGAT 59.052 52.381 14.70 0.00 0.00 2.90
2481 2781 1.001268 CCATACGTCGACTCCTGATGG 60.001 57.143 14.70 13.77 0.00 3.51
2491 2791 4.709886 TCGACTCCTGATGGTTAAAGATGA 59.290 41.667 0.00 0.00 34.23 2.92
2508 2808 9.723601 TTAAAGATGAAAGATTTTGATTTGGGG 57.276 29.630 0.00 0.00 0.00 4.96
2509 2809 7.557875 AAGATGAAAGATTTTGATTTGGGGA 57.442 32.000 0.00 0.00 0.00 4.81
2510 2810 7.744678 AGATGAAAGATTTTGATTTGGGGAT 57.255 32.000 0.00 0.00 0.00 3.85
2511 2811 8.154420 AGATGAAAGATTTTGATTTGGGGATT 57.846 30.769 0.00 0.00 0.00 3.01
2743 3047 5.447818 CCACTCTCTGAACACTGTTGTTTTC 60.448 44.000 0.00 0.00 46.43 2.29
2812 3126 9.148104 GAATTGTCGATTGATCTGATGATGATA 57.852 33.333 0.00 0.00 32.19 2.15
2813 3127 9.668497 AATTGTCGATTGATCTGATGATGATAT 57.332 29.630 0.00 0.00 32.19 1.63
2814 3128 8.475331 TTGTCGATTGATCTGATGATGATATG 57.525 34.615 0.00 0.00 32.19 1.78
2815 3129 7.039882 TGTCGATTGATCTGATGATGATATGG 58.960 38.462 0.00 0.00 32.19 2.74
2972 3292 2.666190 GACGTGGCAGAGCAGCAA 60.666 61.111 0.00 0.00 35.83 3.91
2978 3298 2.107903 GGCAGAGCAGCAAGAGAGC 61.108 63.158 0.00 0.00 35.83 4.09
2997 3349 1.789464 GCGTGTGACTCTGAACTGAAG 59.211 52.381 0.00 0.00 0.00 3.02
3014 3368 9.046296 TGAACTGAAGTTTTGAACTAGAGAATC 57.954 33.333 0.00 0.00 41.91 2.52
3033 3387 8.364129 GAGAATCTGATGGACTGAAACTAATC 57.636 38.462 0.00 0.00 0.00 1.75
3035 3389 8.324306 AGAATCTGATGGACTGAAACTAATCAA 58.676 33.333 0.00 0.00 0.00 2.57
3040 3403 7.676004 TGATGGACTGAAACTAATCAACACTA 58.324 34.615 0.00 0.00 0.00 2.74
3067 3430 6.925610 CGTAGGAAATTTGGATGAGAATGA 57.074 37.500 0.00 0.00 0.00 2.57
3068 3431 6.952743 CGTAGGAAATTTGGATGAGAATGAG 58.047 40.000 0.00 0.00 0.00 2.90
3069 3432 6.763135 CGTAGGAAATTTGGATGAGAATGAGA 59.237 38.462 0.00 0.00 0.00 3.27
3070 3433 7.443575 CGTAGGAAATTTGGATGAGAATGAGAT 59.556 37.037 0.00 0.00 0.00 2.75
3071 3434 7.584122 AGGAAATTTGGATGAGAATGAGATG 57.416 36.000 0.00 0.00 0.00 2.90
3072 3435 7.124052 AGGAAATTTGGATGAGAATGAGATGT 58.876 34.615 0.00 0.00 0.00 3.06
3073 3436 7.618512 AGGAAATTTGGATGAGAATGAGATGTT 59.381 33.333 0.00 0.00 0.00 2.71
3074 3437 7.705325 GGAAATTTGGATGAGAATGAGATGTTG 59.295 37.037 0.00 0.00 0.00 3.33
3075 3438 7.713734 AATTTGGATGAGAATGAGATGTTGT 57.286 32.000 0.00 0.00 0.00 3.32
3076 3439 6.505044 TTTGGATGAGAATGAGATGTTGTG 57.495 37.500 0.00 0.00 0.00 3.33
3077 3440 5.425196 TGGATGAGAATGAGATGTTGTGA 57.575 39.130 0.00 0.00 0.00 3.58
3078 3441 5.997843 TGGATGAGAATGAGATGTTGTGAT 58.002 37.500 0.00 0.00 0.00 3.06
3079 3442 5.820947 TGGATGAGAATGAGATGTTGTGATG 59.179 40.000 0.00 0.00 0.00 3.07
3080 3443 5.821470 GGATGAGAATGAGATGTTGTGATGT 59.179 40.000 0.00 0.00 0.00 3.06
3081 3444 6.318144 GGATGAGAATGAGATGTTGTGATGTT 59.682 38.462 0.00 0.00 0.00 2.71
3082 3445 6.490566 TGAGAATGAGATGTTGTGATGTTG 57.509 37.500 0.00 0.00 0.00 3.33
3083 3446 5.999600 TGAGAATGAGATGTTGTGATGTTGT 59.000 36.000 0.00 0.00 0.00 3.32
3084 3447 6.072893 TGAGAATGAGATGTTGTGATGTTGTG 60.073 38.462 0.00 0.00 0.00 3.33
3085 3448 5.182570 AGAATGAGATGTTGTGATGTTGTGG 59.817 40.000 0.00 0.00 0.00 4.17
3086 3449 2.553602 TGAGATGTTGTGATGTTGTGGC 59.446 45.455 0.00 0.00 0.00 5.01
3087 3450 1.888512 AGATGTTGTGATGTTGTGGCC 59.111 47.619 0.00 0.00 0.00 5.36
3088 3451 1.612950 GATGTTGTGATGTTGTGGCCA 59.387 47.619 0.00 0.00 0.00 5.36
3097 3460 3.008923 TGATGTTGTGGCCAGTGATCTTA 59.991 43.478 5.11 0.00 0.00 2.10
3106 3469 4.019411 TGGCCAGTGATCTTAACATGAGAA 60.019 41.667 0.00 0.00 0.00 2.87
3129 3492 2.433604 GAGATGCTCTGGTGAAGATGGA 59.566 50.000 0.00 0.00 33.29 3.41
3150 3513 7.186570 TGGAGATGAACTATGAGATGTTGAA 57.813 36.000 0.00 0.00 0.00 2.69
3162 3525 4.939439 TGAGATGTTGAATGATGGTGTCAG 59.061 41.667 0.00 0.00 40.92 3.51
3163 3526 5.169992 AGATGTTGAATGATGGTGTCAGA 57.830 39.130 0.00 0.00 40.92 3.27
3164 3527 5.752650 AGATGTTGAATGATGGTGTCAGAT 58.247 37.500 0.00 0.00 40.92 2.90
3165 3528 5.821470 AGATGTTGAATGATGGTGTCAGATC 59.179 40.000 0.00 0.00 40.92 2.75
3196 3562 1.801242 TAGGATCCCTGATTTGGCGA 58.199 50.000 8.55 0.00 34.61 5.54
3197 3563 1.143813 AGGATCCCTGATTTGGCGAT 58.856 50.000 8.55 0.00 29.57 4.58
3203 3571 2.503765 TCCCTGATTTGGCGATTCACTA 59.496 45.455 0.00 0.00 0.00 2.74
3225 3593 0.665068 TGTCGTTCGTTCATGTCCGG 60.665 55.000 0.00 0.00 0.00 5.14
3249 3617 1.951130 CAATGGTCGATCTCCGGCG 60.951 63.158 0.00 0.00 45.31 6.46
3250 3618 2.125326 AATGGTCGATCTCCGGCGA 61.125 57.895 9.30 0.00 45.31 5.54
3252 3620 4.632458 GGTCGATCTCCGGCGAGC 62.632 72.222 9.30 14.06 45.31 5.03
3253 3621 3.587933 GTCGATCTCCGGCGAGCT 61.588 66.667 9.30 0.00 37.18 4.09
3254 3622 3.586961 TCGATCTCCGGCGAGCTG 61.587 66.667 9.30 1.86 39.14 4.24
3255 3623 3.586961 CGATCTCCGGCGAGCTGA 61.587 66.667 9.30 0.53 35.94 4.26
3256 3624 2.334653 GATCTCCGGCGAGCTGAG 59.665 66.667 9.30 6.50 35.94 3.35
3257 3625 3.839642 GATCTCCGGCGAGCTGAGC 62.840 68.421 9.30 0.00 35.94 4.26
3263 3631 4.742201 GGCGAGCTGAGCCGTTCA 62.742 66.667 13.32 0.00 45.58 3.18
3269 3637 2.345244 CTGAGCCGTTCAGCCTGT 59.655 61.111 0.00 0.00 46.30 4.00
3270 3638 1.739562 CTGAGCCGTTCAGCCTGTC 60.740 63.158 0.00 0.00 46.30 3.51
3271 3639 2.343758 GAGCCGTTCAGCCTGTCA 59.656 61.111 0.00 0.00 0.00 3.58
3272 3640 1.739562 GAGCCGTTCAGCCTGTCAG 60.740 63.158 0.00 0.00 0.00 3.51
3273 3641 2.031163 GCCGTTCAGCCTGTCAGT 59.969 61.111 0.00 0.00 0.00 3.41
3274 3642 2.029844 GCCGTTCAGCCTGTCAGTC 61.030 63.158 0.00 0.00 0.00 3.51
3275 3643 1.668294 CCGTTCAGCCTGTCAGTCT 59.332 57.895 0.00 0.00 0.00 3.24
3276 3644 0.034059 CCGTTCAGCCTGTCAGTCTT 59.966 55.000 0.00 0.00 0.00 3.01
3316 3691 2.990479 GTCCTCCATTGACGGGCT 59.010 61.111 0.00 0.00 0.00 5.19
3317 3692 1.450312 GTCCTCCATTGACGGGCTG 60.450 63.158 0.00 0.00 0.00 4.85
3355 3738 3.610114 GCTCATAAATAACCATGGCGCAG 60.610 47.826 13.04 0.00 0.00 5.18
3391 3774 0.387878 GATCGAGGTAGCATGGCGAG 60.388 60.000 0.00 0.00 34.25 5.03
3393 3776 2.490148 CGAGGTAGCATGGCGAGGA 61.490 63.158 0.00 0.00 0.00 3.71
3431 3814 4.094646 ATCACGTCCATGGCGGCA 62.095 61.111 25.35 16.34 33.14 5.69
3432 3815 4.758251 TCACGTCCATGGCGGCAG 62.758 66.667 25.35 17.13 33.14 4.85
3892 4281 3.003763 GTGGAAGGGCGAGGAGGT 61.004 66.667 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 7.814587 AGTTTTTCAACCTAAGAATTGCATAGC 59.185 33.333 0.00 0.00 32.70 2.97
385 396 4.336532 ACAAAAATCGTGCGGAGAATAC 57.663 40.909 0.00 0.00 0.00 1.89
483 494 5.238214 ACTGTCTCTTCTTTGATGAGCAAAC 59.762 40.000 0.00 0.00 41.37 2.93
521 532 2.615493 GCCTTCCCATGAGAAAGTTCGA 60.615 50.000 0.00 0.00 0.00 3.71
522 533 1.740025 GCCTTCCCATGAGAAAGTTCG 59.260 52.381 0.00 0.00 0.00 3.95
543 554 4.692523 ACAAGGACCAATTTAGGGGAAT 57.307 40.909 0.00 0.00 0.00 3.01
557 568 3.593096 CCGTTTTAGGACCTACAAGGAC 58.407 50.000 17.73 5.62 37.67 3.85
716 731 2.816087 CTGCCTCTTTATTGCACAGTGT 59.184 45.455 1.61 0.00 0.00 3.55
773 788 5.121454 TGAATAATTGTGGAAAATTTGCCGC 59.879 36.000 20.35 20.35 32.16 6.53
853 868 0.802994 TCGTTTTCGCACACGTGACT 60.803 50.000 25.01 0.00 43.73 3.41
893 908 3.648528 GGAAAATGGCATCCGAAGC 57.351 52.632 0.00 0.00 0.00 3.86
898 913 0.395724 AGGTCCGGAAAATGGCATCC 60.396 55.000 5.23 0.00 0.00 3.51
954 969 4.801891 TCTGATGAGCAATTTGTTTCTGC 58.198 39.130 0.00 0.00 36.29 4.26
969 984 2.295629 GTCTGCCTCGATGATCTGATGA 59.704 50.000 0.00 0.00 0.00 2.92
1235 1261 2.805845 CAGCTGCTTTTATCACCATGC 58.194 47.619 0.00 0.00 0.00 4.06
1394 1427 2.506472 GGGCCGAGGATTCCACTC 59.494 66.667 5.29 0.00 0.00 3.51
1463 1496 1.210155 GCCGAAAGTCGCAGCAAAT 59.790 52.632 0.00 0.00 38.82 2.32
1586 1619 8.267894 ACATAGTAGGATATGAAACTTTGCACT 58.732 33.333 0.00 0.00 36.76 4.40
1691 1751 1.963515 GGGTCTTGGTGCATTTCAAGT 59.036 47.619 19.58 0.00 40.67 3.16
1746 1808 9.696917 GTGGTAGATTTGATGAAAACAGATTTT 57.303 29.630 0.00 0.00 40.83 1.82
1769 1831 7.412853 GTTCAGTTCAAGATGCTATTATGTGG 58.587 38.462 0.00 0.00 0.00 4.17
1888 1952 6.263516 AGTGTTTGATTCTGATTCACATGG 57.736 37.500 0.00 0.00 0.00 3.66
1918 1982 2.982470 GTGTGCAATGCAACTTAGCTTC 59.018 45.455 10.44 0.00 41.47 3.86
1994 2062 8.761689 ACCTAGCACAAATTATGGATGAAATTT 58.238 29.630 0.00 0.00 36.08 1.82
2138 2413 2.930562 GAGGCAGGTGGTGGAGGT 60.931 66.667 0.00 0.00 0.00 3.85
2141 2416 4.954118 ACGGAGGCAGGTGGTGGA 62.954 66.667 0.00 0.00 0.00 4.02
2177 2464 4.704103 TCCGGTGCTGCTCCTCCT 62.704 66.667 17.64 0.00 0.00 3.69
2178 2465 4.154347 CTCCGGTGCTGCTCCTCC 62.154 72.222 17.64 6.46 0.00 4.30
2447 2734 1.527611 TATGGACCGGATCTCGCGT 60.528 57.895 9.46 0.00 37.59 6.01
2450 2737 0.237761 GACGTATGGACCGGATCTCG 59.762 60.000 9.46 7.70 38.88 4.04
2451 2738 0.237761 CGACGTATGGACCGGATCTC 59.762 60.000 9.46 0.00 0.00 2.75
2452 2739 0.179037 TCGACGTATGGACCGGATCT 60.179 55.000 9.46 0.00 0.00 2.75
2459 2746 1.376543 TCAGGAGTCGACGTATGGAC 58.623 55.000 10.46 5.91 33.94 4.02
2460 2747 1.947456 CATCAGGAGTCGACGTATGGA 59.053 52.381 10.46 6.20 0.00 3.41
2461 2748 1.001268 CCATCAGGAGTCGACGTATGG 60.001 57.143 10.46 14.82 36.89 2.74
2462 2749 1.676529 ACCATCAGGAGTCGACGTATG 59.323 52.381 10.46 10.02 38.69 2.39
2463 2750 2.054232 ACCATCAGGAGTCGACGTAT 57.946 50.000 10.46 0.00 38.69 3.06
2464 2751 1.830279 AACCATCAGGAGTCGACGTA 58.170 50.000 10.46 0.00 38.69 3.57
2491 2791 9.016438 CAAATCAATCCCCAAATCAAAATCTTT 57.984 29.630 0.00 0.00 0.00 2.52
2504 2804 5.514484 CCAAATCCAAACAAATCAATCCCCA 60.514 40.000 0.00 0.00 0.00 4.96
2507 2807 7.926674 AATCCAAATCCAAACAAATCAATCC 57.073 32.000 0.00 0.00 0.00 3.01
2508 2808 8.238631 CCAAATCCAAATCCAAACAAATCAATC 58.761 33.333 0.00 0.00 0.00 2.67
2509 2809 7.309316 GCCAAATCCAAATCCAAACAAATCAAT 60.309 33.333 0.00 0.00 0.00 2.57
2510 2810 6.016443 GCCAAATCCAAATCCAAACAAATCAA 60.016 34.615 0.00 0.00 0.00 2.57
2511 2811 5.472820 GCCAAATCCAAATCCAAACAAATCA 59.527 36.000 0.00 0.00 0.00 2.57
2784 3098 6.145048 CATCATCAGATCAATCGACAATTCGA 59.855 38.462 0.00 0.00 45.06 3.71
2812 3126 2.336088 GCACGCTGCAAACACCAT 59.664 55.556 0.00 0.00 44.26 3.55
2972 3292 1.268352 GTTCAGAGTCACACGCTCTCT 59.732 52.381 0.00 0.00 40.97 3.10
2978 3298 3.085443 ACTTCAGTTCAGAGTCACACG 57.915 47.619 0.00 0.00 0.00 4.49
2997 3349 7.821846 AGTCCATCAGATTCTCTAGTTCAAAAC 59.178 37.037 0.00 0.00 0.00 2.43
3014 3368 6.652481 AGTGTTGATTAGTTTCAGTCCATCAG 59.348 38.462 0.00 0.00 0.00 2.90
3020 3374 7.758528 ACGGTATAGTGTTGATTAGTTTCAGTC 59.241 37.037 0.00 0.00 0.00 3.51
3031 3385 7.497909 CCAAATTTCCTACGGTATAGTGTTGAT 59.502 37.037 0.00 0.00 0.00 2.57
3033 3387 6.819649 TCCAAATTTCCTACGGTATAGTGTTG 59.180 38.462 0.00 0.00 0.00 3.33
3035 3389 6.549433 TCCAAATTTCCTACGGTATAGTGT 57.451 37.500 0.00 0.00 0.00 3.55
3040 3403 6.494666 TCTCATCCAAATTTCCTACGGTAT 57.505 37.500 0.00 0.00 0.00 2.73
3065 3428 2.553602 GCCACAACATCACAACATCTCA 59.446 45.455 0.00 0.00 0.00 3.27
3066 3429 2.095059 GGCCACAACATCACAACATCTC 60.095 50.000 0.00 0.00 0.00 2.75
3067 3430 1.888512 GGCCACAACATCACAACATCT 59.111 47.619 0.00 0.00 0.00 2.90
3068 3431 1.612950 TGGCCACAACATCACAACATC 59.387 47.619 0.00 0.00 0.00 3.06
3069 3432 1.614903 CTGGCCACAACATCACAACAT 59.385 47.619 0.00 0.00 0.00 2.71
3070 3433 1.031235 CTGGCCACAACATCACAACA 58.969 50.000 0.00 0.00 0.00 3.33
3071 3434 1.032014 ACTGGCCACAACATCACAAC 58.968 50.000 0.00 0.00 0.00 3.32
3072 3435 1.031235 CACTGGCCACAACATCACAA 58.969 50.000 0.00 0.00 0.00 3.33
3073 3436 0.182299 TCACTGGCCACAACATCACA 59.818 50.000 0.00 0.00 0.00 3.58
3074 3437 1.470098 GATCACTGGCCACAACATCAC 59.530 52.381 0.00 0.00 0.00 3.06
3075 3438 1.352017 AGATCACTGGCCACAACATCA 59.648 47.619 0.00 0.00 0.00 3.07
3076 3439 2.119801 AGATCACTGGCCACAACATC 57.880 50.000 0.00 0.84 0.00 3.06
3077 3440 2.592102 AAGATCACTGGCCACAACAT 57.408 45.000 0.00 0.00 0.00 2.71
3078 3441 3.146066 GTTAAGATCACTGGCCACAACA 58.854 45.455 0.00 0.00 0.00 3.33
3079 3442 3.146066 TGTTAAGATCACTGGCCACAAC 58.854 45.455 0.00 0.00 0.00 3.32
3080 3443 3.500448 TGTTAAGATCACTGGCCACAA 57.500 42.857 0.00 0.00 0.00 3.33
3081 3444 3.008923 TCATGTTAAGATCACTGGCCACA 59.991 43.478 0.00 0.00 0.00 4.17
3082 3445 3.609853 TCATGTTAAGATCACTGGCCAC 58.390 45.455 0.00 0.00 0.00 5.01
3083 3446 3.519107 TCTCATGTTAAGATCACTGGCCA 59.481 43.478 4.71 4.71 0.00 5.36
3084 3447 4.142609 TCTCATGTTAAGATCACTGGCC 57.857 45.455 0.00 0.00 0.00 5.36
3085 3448 5.819379 TCATTCTCATGTTAAGATCACTGGC 59.181 40.000 0.00 0.00 0.00 4.85
3086 3449 7.270779 TCTCATTCTCATGTTAAGATCACTGG 58.729 38.462 0.00 0.00 0.00 4.00
3087 3450 8.766151 CATCTCATTCTCATGTTAAGATCACTG 58.234 37.037 0.00 0.00 0.00 3.66
3088 3451 7.441760 GCATCTCATTCTCATGTTAAGATCACT 59.558 37.037 0.00 0.00 0.00 3.41
3129 3492 9.274206 CATCATTCAACATCTCATAGTTCATCT 57.726 33.333 0.00 0.00 0.00 2.90
3176 3542 2.338809 TCGCCAAATCAGGGATCCTAT 58.661 47.619 12.58 0.15 29.64 2.57
3182 3548 1.281867 AGTGAATCGCCAAATCAGGGA 59.718 47.619 0.00 0.00 0.00 4.20
3191 3557 1.203758 ACGACACATAGTGAATCGCCA 59.796 47.619 3.88 0.00 36.14 5.69
3192 3558 1.922570 ACGACACATAGTGAATCGCC 58.077 50.000 3.88 0.00 36.14 5.54
3193 3559 2.035674 CGAACGACACATAGTGAATCGC 60.036 50.000 3.88 0.00 36.14 4.58
3196 3562 4.552355 TGAACGAACGACACATAGTGAAT 58.448 39.130 3.88 0.00 36.96 2.57
3197 3563 3.967401 TGAACGAACGACACATAGTGAA 58.033 40.909 3.88 0.00 36.96 3.18
3203 3571 2.066262 GGACATGAACGAACGACACAT 58.934 47.619 0.00 1.30 0.00 3.21
3225 3593 2.989840 CGGAGATCGACCATTGCTAATC 59.010 50.000 11.37 0.00 42.43 1.75
3256 3624 2.029844 GACTGACAGGCTGAACGGC 61.030 63.158 23.66 6.64 38.75 5.68
3257 3625 0.034059 AAGACTGACAGGCTGAACGG 59.966 55.000 23.66 20.13 30.77 4.44
3258 3626 1.143305 CAAGACTGACAGGCTGAACG 58.857 55.000 23.66 10.58 30.77 3.95
3259 3627 1.517242 CCAAGACTGACAGGCTGAAC 58.483 55.000 23.66 14.82 30.77 3.18
3260 3628 0.397941 CCCAAGACTGACAGGCTGAA 59.602 55.000 23.66 8.02 30.77 3.02
3261 3629 2.061220 CCCAAGACTGACAGGCTGA 58.939 57.895 23.66 0.00 30.77 4.26
3262 3630 1.673665 GCCCAAGACTGACAGGCTG 60.674 63.158 12.78 14.16 40.57 4.85
3263 3631 1.495579 ATGCCCAAGACTGACAGGCT 61.496 55.000 4.48 4.48 44.19 4.58
3264 3632 1.001641 ATGCCCAAGACTGACAGGC 60.002 57.895 7.51 3.10 44.13 4.85
3265 3633 0.679002 CCATGCCCAAGACTGACAGG 60.679 60.000 7.51 0.00 0.00 4.00
3266 3634 1.310933 GCCATGCCCAAGACTGACAG 61.311 60.000 0.00 0.00 0.00 3.51
3267 3635 1.303561 GCCATGCCCAAGACTGACA 60.304 57.895 0.00 0.00 0.00 3.58
3268 3636 2.048603 GGCCATGCCCAAGACTGAC 61.049 63.158 0.00 0.00 44.06 3.51
3269 3637 2.356278 GGCCATGCCCAAGACTGA 59.644 61.111 0.00 0.00 44.06 3.41
3314 3689 0.454620 CTCGTACGTGGAGTGACAGC 60.455 60.000 16.05 0.00 0.00 4.40
3316 3691 0.887836 AGCTCGTACGTGGAGTGACA 60.888 55.000 16.05 0.00 34.00 3.58
3317 3692 0.179194 GAGCTCGTACGTGGAGTGAC 60.179 60.000 16.05 0.00 34.00 3.67
3322 3698 5.276270 GTTATTTATGAGCTCGTACGTGGA 58.724 41.667 15.35 0.00 0.00 4.02
3355 3738 3.414700 CGTGCAGGAGCGTGGTTC 61.415 66.667 0.00 0.00 46.23 3.62
3391 3774 2.815647 CGCGTCCTCCTTGCTTCC 60.816 66.667 0.00 0.00 0.00 3.46
3415 3798 4.758251 CTGCCGCCATGGACGTGA 62.758 66.667 18.40 6.30 42.00 4.35
3581 3970 3.519930 GCGTCGGAGGAGAGGGAC 61.520 72.222 1.18 0.00 0.00 4.46
3740 4129 4.498520 TAGAGCTCCGTGCAGCGC 62.499 66.667 10.93 0.00 44.82 5.92


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

AutoCloner maintained by Alex Coulton.