Multiple sequence alignment - TraesCS1D01G282600

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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 TraesCS1D01G282600 chr1D 100.000 3918 0 0 1 3918 379913733 379909816 0.000000e+00 7236.0
1 TraesCS1D01G282600 chr1D 78.125 1120 185 43 1618 2695 381019449 381020550 0.000000e+00 656.0
2 TraesCS1D01G282600 chr1B 93.894 3341 131 38 1 3303 509904080 509900775 0.000000e+00 4972.0
3 TraesCS1D01G282600 chr1B 77.679 1120 190 41 1618 2695 510809232 510810333 2.570000e-176 628.0
4 TraesCS1D01G282600 chr1B 86.752 468 51 8 3441 3903 509900155 509899694 9.710000e-141 510.0
5 TraesCS1D01G282600 chr1A 91.921 3565 194 42 411 3917 480936494 480932966 0.000000e+00 4902.0
6 TraesCS1D01G282600 chr1A 77.937 1115 184 46 1618 2695 481674397 481675486 1.190000e-179 640.0
7 TraesCS1D01G282600 chr1A 83.411 428 28 12 1 427 480936903 480936518 1.340000e-94 357.0
8 TraesCS1D01G282600 chr3A 83.007 971 145 13 1735 2696 608751173 608752132 0.000000e+00 861.0
9 TraesCS1D01G282600 chr3A 74.734 1223 235 51 1735 2910 608347365 608346170 2.740000e-131 479.0
10 TraesCS1D01G282600 chr3D 82.305 972 150 16 1735 2696 465510082 465511041 0.000000e+00 822.0
11 TraesCS1D01G282600 chr3D 75.144 1215 223 56 1735 2910 465027152 465025978 7.560000e-137 497.0
12 TraesCS1D01G282600 chr3B 81.668 971 158 15 1735 2696 618870681 618871640 0.000000e+00 789.0
13 TraesCS1D01G282600 chr3B 75.549 1002 188 43 1735 2698 618442175 618441193 1.290000e-119 440.0
14 TraesCS1D01G282600 chr4A 76.295 1004 178 48 1735 2704 104410506 104409529 7.610000e-132 481.0
15 TraesCS1D01G282600 chr4A 94.872 39 2 0 2001 2039 139546463 139546501 1.180000e-05 62.1
16 TraesCS1D01G282600 chr4B 83.838 99 13 2 2249 2344 412106532 412106434 1.500000e-14 91.6


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 TraesCS1D01G282600 chr1D 379909816 379913733 3917 True 7236.0 7236 100.000 1 3918 1 chr1D.!!$R1 3917
1 TraesCS1D01G282600 chr1D 381019449 381020550 1101 False 656.0 656 78.125 1618 2695 1 chr1D.!!$F1 1077
2 TraesCS1D01G282600 chr1B 509899694 509904080 4386 True 2741.0 4972 90.323 1 3903 2 chr1B.!!$R1 3902
3 TraesCS1D01G282600 chr1B 510809232 510810333 1101 False 628.0 628 77.679 1618 2695 1 chr1B.!!$F1 1077
4 TraesCS1D01G282600 chr1A 480932966 480936903 3937 True 2629.5 4902 87.666 1 3917 2 chr1A.!!$R1 3916
5 TraesCS1D01G282600 chr1A 481674397 481675486 1089 False 640.0 640 77.937 1618 2695 1 chr1A.!!$F1 1077
6 TraesCS1D01G282600 chr3A 608751173 608752132 959 False 861.0 861 83.007 1735 2696 1 chr3A.!!$F1 961
7 TraesCS1D01G282600 chr3A 608346170 608347365 1195 True 479.0 479 74.734 1735 2910 1 chr3A.!!$R1 1175
8 TraesCS1D01G282600 chr3D 465510082 465511041 959 False 822.0 822 82.305 1735 2696 1 chr3D.!!$F1 961
9 TraesCS1D01G282600 chr3D 465025978 465027152 1174 True 497.0 497 75.144 1735 2910 1 chr3D.!!$R1 1175
10 TraesCS1D01G282600 chr3B 618870681 618871640 959 False 789.0 789 81.668 1735 2696 1 chr3B.!!$F1 961
11 TraesCS1D01G282600 chr3B 618441193 618442175 982 True 440.0 440 75.549 1735 2698 1 chr3B.!!$R1 963
12 TraesCS1D01G282600 chr4A 104409529 104410506 977 True 481.0 481 76.295 1735 2704 1 chr4A.!!$R1 969

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
343 351 0.388907 TCCGTCGACATTTTCCGTCC 60.389 55.0 17.16 0.0 0.0 4.79 F
1562 1636 0.037046 CCACTGCCCTCCATTTTTGC 60.037 55.0 0.00 0.0 0.0 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 1823 0.658536 GAGCTTGAACGTGCTGTTGC 60.659 55.0 2.46 0.0 42.09 4.17 R
2996 3154 0.323629 TCCTCGACCACCACCAAATC 59.676 55.0 0.00 0.0 0.00 2.17 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
88 89 4.615912 GCCACCATATTGAATTATCGGTGC 60.616 45.833 0.00 0.00 40.86 5.01
93 94 1.948104 TTGAATTATCGGTGCGAGGG 58.052 50.000 0.00 0.00 39.91 4.30
94 95 0.531974 TGAATTATCGGTGCGAGGGC 60.532 55.000 0.00 0.00 39.91 5.19
104 105 4.468689 GCGAGGGCAGGGGTACAC 62.469 72.222 0.00 0.00 39.62 2.90
190 191 2.618241 TCTGCAACAGTTTGTCCACATC 59.382 45.455 0.00 0.00 34.90 3.06
198 199 4.287067 ACAGTTTGTCCACATCCAGACTAT 59.713 41.667 0.00 0.00 34.02 2.12
200 201 6.013725 ACAGTTTGTCCACATCCAGACTATTA 60.014 38.462 0.00 0.00 34.02 0.98
208 209 4.970611 CACATCCAGACTATTAAGACGACG 59.029 45.833 0.00 0.00 0.00 5.12
210 211 4.611310 TCCAGACTATTAAGACGACGTG 57.389 45.455 4.58 0.00 0.00 4.49
211 212 3.376234 TCCAGACTATTAAGACGACGTGG 59.624 47.826 4.58 0.00 0.00 4.94
226 234 1.361668 CGTGGAAACTCCTGCATCGG 61.362 60.000 0.00 0.00 37.46 4.18
257 265 5.172687 TGGTGTTCTGCATGGAGTTAATA 57.827 39.130 14.43 0.00 0.00 0.98
258 266 4.941263 TGGTGTTCTGCATGGAGTTAATAC 59.059 41.667 14.43 10.02 0.00 1.89
259 267 5.186198 GGTGTTCTGCATGGAGTTAATACT 58.814 41.667 14.43 0.00 37.31 2.12
260 268 5.648092 GGTGTTCTGCATGGAGTTAATACTT 59.352 40.000 14.43 0.00 33.84 2.24
269 277 9.325198 TGCATGGAGTTAATACTTAATACAGTG 57.675 33.333 0.00 0.00 33.84 3.66
270 278 9.326413 GCATGGAGTTAATACTTAATACAGTGT 57.674 33.333 0.00 0.00 33.84 3.55
306 314 5.399991 ACATCATATTGCCTGGGATGAAAT 58.600 37.500 13.16 0.00 38.87 2.17
322 330 7.147966 TGGGATGAAATTGTTGATCATCTTCTG 60.148 37.037 13.93 0.00 45.54 3.02
324 332 6.829229 TGAAATTGTTGATCATCTTCTGCT 57.171 33.333 0.00 0.00 0.00 4.24
327 335 2.897436 TGTTGATCATCTTCTGCTCCG 58.103 47.619 0.00 0.00 0.00 4.63
334 342 1.107114 ATCTTCTGCTCCGTCGACAT 58.893 50.000 17.16 0.00 0.00 3.06
340 348 1.011968 TGCTCCGTCGACATTTTCCG 61.012 55.000 17.16 0.00 0.00 4.30
343 351 0.388907 TCCGTCGACATTTTCCGTCC 60.389 55.000 17.16 0.00 0.00 4.79
347 355 0.393448 TCGACATTTTCCGTCCACCA 59.607 50.000 0.00 0.00 0.00 4.17
348 356 0.515564 CGACATTTTCCGTCCACCAC 59.484 55.000 0.00 0.00 0.00 4.16
349 357 1.600023 GACATTTTCCGTCCACCACA 58.400 50.000 0.00 0.00 0.00 4.17
350 358 2.159382 GACATTTTCCGTCCACCACAT 58.841 47.619 0.00 0.00 0.00 3.21
351 359 2.556622 GACATTTTCCGTCCACCACATT 59.443 45.455 0.00 0.00 0.00 2.71
358 366 2.568062 TCCGTCCACCACATTAAGCTTA 59.432 45.455 0.86 0.86 0.00 3.09
437 479 4.920376 TCCAAGTCTCGCAAAAAGAAAAG 58.080 39.130 0.00 0.00 0.00 2.27
439 481 3.990318 AGTCTCGCAAAAAGAAAAGGG 57.010 42.857 0.00 0.00 0.00 3.95
486 528 1.411394 CAAGACATGCCTGCGTTTTG 58.589 50.000 0.00 0.00 0.00 2.44
674 716 1.672356 GGGCCAATGGATCCGATCG 60.672 63.158 8.51 8.51 0.00 3.69
781 823 1.407437 CCCAGCCAACCACTATGACTC 60.407 57.143 0.00 0.00 0.00 3.36
848 895 2.549349 CCGGCCGTTTATATAGCCACTT 60.549 50.000 26.12 0.00 46.08 3.16
980 1037 1.103398 AGTTGAAGTGTGGCCAGCAC 61.103 55.000 23.11 23.11 37.13 4.40
982 1039 3.357079 GAAGTGTGGCCAGCACGG 61.357 66.667 23.77 0.00 41.36 4.94
1017 1074 0.470766 CAATGGCAATGGGAATGGGG 59.529 55.000 0.00 0.00 0.00 4.96
1018 1075 0.342665 AATGGCAATGGGAATGGGGA 59.657 50.000 0.00 0.00 0.00 4.81
1019 1076 0.569204 ATGGCAATGGGAATGGGGAT 59.431 50.000 0.00 0.00 0.00 3.85
1020 1077 0.398806 TGGCAATGGGAATGGGGATG 60.399 55.000 0.00 0.00 0.00 3.51
1021 1078 1.123246 GGCAATGGGAATGGGGATGG 61.123 60.000 0.00 0.00 0.00 3.51
1022 1079 1.123246 GCAATGGGAATGGGGATGGG 61.123 60.000 0.00 0.00 0.00 4.00
1023 1080 0.265553 CAATGGGAATGGGGATGGGT 59.734 55.000 0.00 0.00 0.00 4.51
1024 1081 1.502910 CAATGGGAATGGGGATGGGTA 59.497 52.381 0.00 0.00 0.00 3.69
1025 1082 1.460218 ATGGGAATGGGGATGGGTAG 58.540 55.000 0.00 0.00 0.00 3.18
1287 1344 3.953775 ACCTTCCACTGGCACGGG 61.954 66.667 0.00 0.00 40.47 5.28
1552 1626 2.608988 CCTCCACTCCACTGCCCT 60.609 66.667 0.00 0.00 0.00 5.19
1562 1636 0.037046 CCACTGCCCTCCATTTTTGC 60.037 55.000 0.00 0.00 0.00 3.68
1575 1649 0.457509 TTTTTGCCACTGTGTGTGCG 60.458 50.000 7.08 0.00 44.92 5.34
1576 1650 1.308783 TTTTGCCACTGTGTGTGCGA 61.309 50.000 7.08 0.29 44.92 5.10
1578 1652 2.588877 GCCACTGTGTGTGCGACT 60.589 61.111 7.08 0.00 44.92 4.18
1580 1654 1.227234 CCACTGTGTGTGCGACTCA 60.227 57.895 7.08 0.00 44.92 3.41
1581 1655 0.601046 CCACTGTGTGTGCGACTCAT 60.601 55.000 7.08 0.00 44.92 2.90
1583 1657 1.988467 CACTGTGTGTGCGACTCATAG 59.012 52.381 0.00 10.92 40.06 2.23
1586 1660 1.611491 TGTGTGTGCGACTCATAGTCA 59.389 47.619 7.75 0.00 45.30 3.41
1587 1661 2.231235 TGTGTGTGCGACTCATAGTCAT 59.769 45.455 7.75 0.00 45.30 3.06
1588 1662 2.854777 GTGTGTGCGACTCATAGTCATC 59.145 50.000 7.75 0.00 45.30 2.92
1589 1663 2.112522 GTGTGCGACTCATAGTCATCG 58.887 52.381 7.75 0.00 45.30 3.84
1590 1664 2.014128 TGTGCGACTCATAGTCATCGA 58.986 47.619 7.75 0.00 45.30 3.59
1592 1666 3.230355 GTGCGACTCATAGTCATCGATC 58.770 50.000 0.00 0.00 45.30 3.69
1593 1667 2.096218 TGCGACTCATAGTCATCGATCG 60.096 50.000 9.36 9.36 45.30 3.69
1594 1668 2.157863 GCGACTCATAGTCATCGATCGA 59.842 50.000 21.86 21.86 45.30 3.59
1595 1669 3.723542 GCGACTCATAGTCATCGATCGAG 60.724 52.174 23.84 14.92 45.30 4.04
1596 1670 3.430556 CGACTCATAGTCATCGATCGAGT 59.569 47.826 23.84 11.97 45.30 4.18
1780 1873 1.663379 CGGGAGGACGTACATGCTGA 61.663 60.000 0.00 0.00 0.00 4.26
2038 2146 3.129502 CCGCCGTCCTCGAGTACA 61.130 66.667 12.31 0.00 39.71 2.90
2316 2463 0.948623 CGTTCGTGATGCCCAAGACA 60.949 55.000 0.00 0.00 33.08 3.41
2720 2867 1.881057 AACCAACCACCACCCCACTT 61.881 55.000 0.00 0.00 0.00 3.16
2739 2886 0.819259 TGCTGGCTCAACTGTTGACC 60.819 55.000 18.69 21.69 35.46 4.02
3056 3226 1.684983 CCTGAATGAATGATGTGCCCC 59.315 52.381 0.00 0.00 0.00 5.80
3081 3251 7.010460 CCTTTTTGTGATGTTTGGTTTTCTCTC 59.990 37.037 0.00 0.00 0.00 3.20
3088 3258 2.543777 TTGGTTTTCTCTCGGACAGG 57.456 50.000 0.00 0.00 0.00 4.00
3125 3297 8.453238 TGGTGTAACTGTAAACATGTAAACAT 57.547 30.769 12.19 3.63 36.74 2.71
3143 3315 5.467035 AACATGTAAACAAGTTCCATGGG 57.533 39.130 13.02 0.00 33.09 4.00
3151 3323 1.779061 AAGTTCCATGGGTGGCGTCT 61.779 55.000 13.02 0.00 45.63 4.18
3221 3393 0.777446 TTTTCCTTCTCACCCCTGGG 59.223 55.000 5.50 5.50 42.03 4.45
3274 3446 5.582665 GCTAGCCAGGCTATGTACATTTATC 59.417 44.000 22.14 2.18 40.54 1.75
3352 3526 6.516739 TTACAGAAATGTTGTTGTGGTGAA 57.483 33.333 0.00 0.00 0.00 3.18
3365 3539 1.040646 TGGTGAAGTTCGCTGAGAGT 58.959 50.000 15.69 0.00 0.00 3.24
3382 3556 4.696877 TGAGAGTGCATGACAAATCGAATT 59.303 37.500 0.00 0.00 0.00 2.17
3392 3996 7.148771 GCATGACAAATCGAATTGTTTTCATGA 60.149 33.333 30.95 11.43 43.31 3.07
3430 4034 5.774690 TGTGAGGATGGCAATTTTCTTTAGT 59.225 36.000 0.00 0.00 0.00 2.24
3472 4129 2.818751 AATCTAAATTGGGCCGTCCA 57.181 45.000 0.00 0.00 45.43 4.02
3501 4159 0.759346 ATAAATCCTCCGAGCGCCTT 59.241 50.000 2.29 0.00 0.00 4.35
3516 4174 2.051941 CCTTGGCCTGCACACAATT 58.948 52.632 3.32 0.00 0.00 2.32
3551 4212 2.719376 GCAGGAGCACCTCAAACAA 58.281 52.632 0.00 0.00 45.94 2.83
3576 4239 4.664677 GCGTCGTGGAGGCACACT 62.665 66.667 10.02 0.00 42.14 3.55
3581 4244 1.878070 CGTGGAGGCACACTACGTA 59.122 57.895 10.02 0.00 46.75 3.57
3588 4251 0.677842 GGCACACTACGTATAGGGGG 59.322 60.000 0.00 0.00 38.40 5.40
3648 4311 1.940758 CACTTGTTGTGCACGCAGC 60.941 57.895 13.13 2.65 45.96 5.25
3672 4335 0.675837 CACCAGTGTGCAGGGATCAG 60.676 60.000 0.00 0.00 35.31 2.90
3679 4342 2.439156 GCAGGGATCAGCCGCTTT 60.439 61.111 0.00 0.00 37.63 3.51
3684 4347 1.244019 GGGATCAGCCGCTTTGTTGT 61.244 55.000 0.00 0.00 37.63 3.32
3692 4355 1.593196 CCGCTTTGTTGTCCTCTTCA 58.407 50.000 0.00 0.00 0.00 3.02
3738 4401 1.590238 CATCTTTAGCAACGCTCTCCG 59.410 52.381 0.00 0.00 40.44 4.63
3758 4421 1.073025 ACAATGGACCTGCGCTTCA 59.927 52.632 9.73 0.00 0.00 3.02
3760 4423 0.813184 CAATGGACCTGCGCTTCATT 59.187 50.000 9.73 1.83 0.00 2.57
3769 4432 3.576356 CGCTTCATTGCCGCGGAT 61.576 61.111 33.48 12.32 42.88 4.18
3770 4433 2.243957 CGCTTCATTGCCGCGGATA 61.244 57.895 33.48 16.62 42.88 2.59
3771 4434 1.279840 GCTTCATTGCCGCGGATAC 59.720 57.895 33.48 12.57 0.00 2.24
3772 4435 1.436195 GCTTCATTGCCGCGGATACA 61.436 55.000 33.48 15.63 0.00 2.29
3773 4436 0.304705 CTTCATTGCCGCGGATACAC 59.695 55.000 33.48 11.67 0.00 2.90
3774 4437 0.107897 TTCATTGCCGCGGATACACT 60.108 50.000 33.48 9.01 0.00 3.55
3823 4491 2.103538 GTATGGTCGCGCTTCCGA 59.896 61.111 5.56 0.00 36.29 4.55
3842 4510 2.525629 TCACCTTCACCGGGCTCA 60.526 61.111 6.32 0.00 0.00 4.26
3846 4514 1.672356 CCTTCACCGGGCTCAACTG 60.672 63.158 6.32 0.00 0.00 3.16
3856 4524 1.069090 GCTCAACTGGTCCGTCACA 59.931 57.895 0.00 0.00 0.00 3.58
3872 4540 1.081376 ACACTCTTCTCGTTCGCGG 60.081 57.895 6.13 0.00 41.70 6.46
3917 4585 1.227556 ATCAACGGCGGACCTATGC 60.228 57.895 13.24 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 2.589157 TTGTGTACCCCTGCCCTCG 61.589 63.158 0.00 0.00 0.00 4.63
93 94 4.013728 TCATAATTGTTGTGTACCCCTGC 58.986 43.478 0.00 0.00 0.00 4.85
94 95 5.496556 TCTCATAATTGTTGTGTACCCCTG 58.503 41.667 0.00 0.00 0.00 4.45
97 98 9.337396 TGATAATCTCATAATTGTTGTGTACCC 57.663 33.333 0.00 0.00 0.00 3.69
190 191 3.376234 TCCACGTCGTCTTAATAGTCTGG 59.624 47.826 0.00 0.00 0.00 3.86
198 199 2.624838 AGGAGTTTCCACGTCGTCTTAA 59.375 45.455 0.00 0.00 39.61 1.85
200 201 1.038280 AGGAGTTTCCACGTCGTCTT 58.962 50.000 0.00 0.00 39.61 3.01
208 209 1.648467 GCCGATGCAGGAGTTTCCAC 61.648 60.000 0.00 0.00 39.61 4.02
210 211 2.115291 GGCCGATGCAGGAGTTTCC 61.115 63.158 0.00 0.00 40.13 3.13
211 212 2.115291 GGGCCGATGCAGGAGTTTC 61.115 63.158 0.00 0.00 40.13 2.78
257 265 4.872691 GCATCTGCTCACACTGTATTAAGT 59.127 41.667 0.00 0.00 38.21 2.24
258 266 4.872124 TGCATCTGCTCACACTGTATTAAG 59.128 41.667 3.53 0.00 42.66 1.85
259 267 4.831107 TGCATCTGCTCACACTGTATTAA 58.169 39.130 3.53 0.00 42.66 1.40
260 268 4.470334 TGCATCTGCTCACACTGTATTA 57.530 40.909 3.53 0.00 42.66 0.98
291 299 3.237746 TCAACAATTTCATCCCAGGCAA 58.762 40.909 0.00 0.00 0.00 4.52
306 314 3.264947 CGGAGCAGAAGATGATCAACAA 58.735 45.455 0.00 0.00 46.49 2.83
322 330 1.012486 ACGGAAAATGTCGACGGAGC 61.012 55.000 11.62 0.00 0.00 4.70
324 332 0.388907 GGACGGAAAATGTCGACGGA 60.389 55.000 11.62 0.00 37.22 4.69
327 335 0.794473 GGTGGACGGAAAATGTCGAC 59.206 55.000 9.11 9.11 42.26 4.20
334 342 2.554893 GCTTAATGTGGTGGACGGAAAA 59.445 45.455 0.00 0.00 0.00 2.29
340 348 3.375299 CAGCTAAGCTTAATGTGGTGGAC 59.625 47.826 7.74 0.00 36.40 4.02
343 351 5.182001 AGTTTCAGCTAAGCTTAATGTGGTG 59.818 40.000 7.74 11.27 36.40 4.17
347 355 6.467677 TGAGAGTTTCAGCTAAGCTTAATGT 58.532 36.000 7.74 0.00 36.40 2.71
348 356 6.974932 TGAGAGTTTCAGCTAAGCTTAATG 57.025 37.500 7.74 9.49 36.40 1.90
376 384 2.058798 GCTAAAAGCAAAAGCCCGTTC 58.941 47.619 0.00 0.00 41.89 3.95
377 385 1.686587 AGCTAAAAGCAAAAGCCCGTT 59.313 42.857 1.22 0.00 45.56 4.44
378 386 1.000274 CAGCTAAAAGCAAAAGCCCGT 60.000 47.619 1.22 0.00 45.56 5.28
380 388 2.558359 TCTCAGCTAAAAGCAAAAGCCC 59.442 45.455 1.22 0.00 45.56 5.19
451 493 7.192232 GCATGTCTTGGAATATCAGTTTCTTC 58.808 38.462 0.00 0.00 0.00 2.87
452 494 6.096001 GGCATGTCTTGGAATATCAGTTTCTT 59.904 38.462 0.00 0.00 0.00 2.52
486 528 1.660560 GCTGACATGATGGTGCACCC 61.661 60.000 32.62 18.79 34.29 4.61
674 716 1.452108 CCGATCTTTCCAGCCACCC 60.452 63.158 0.00 0.00 0.00 4.61
781 823 2.908015 CATGGTAGGGGGTCACCG 59.092 66.667 0.00 0.00 41.60 4.94
848 895 3.447586 GTGACATGAGTAGCTAGGGTTCA 59.552 47.826 0.00 0.00 0.00 3.18
988 1045 1.108776 ATTGCCATTGTGCAGCTAGG 58.891 50.000 0.00 0.00 43.21 3.02
1017 1074 2.279517 CGGCGAGCACTACCCATC 60.280 66.667 0.00 0.00 0.00 3.51
1241 1298 1.064803 TGTTGATGTTGTTGTGGACGC 59.935 47.619 0.00 0.00 0.00 5.19
1488 1545 1.848895 ACGGTAGGGCTTGGGGAAA 60.849 57.895 0.00 0.00 0.00 3.13
1552 1626 2.106566 ACACACAGTGGCAAAAATGGA 58.893 42.857 5.31 0.00 37.94 3.41
1575 1649 4.212425 ACACTCGATCGATGACTATGAGTC 59.788 45.833 19.78 0.00 45.26 3.36
1576 1650 4.130857 ACACTCGATCGATGACTATGAGT 58.869 43.478 19.78 6.65 35.73 3.41
1578 1652 4.691216 CCTACACTCGATCGATGACTATGA 59.309 45.833 19.78 0.00 0.00 2.15
1580 1654 4.452795 CACCTACACTCGATCGATGACTAT 59.547 45.833 19.78 4.14 0.00 2.12
1581 1655 3.808174 CACCTACACTCGATCGATGACTA 59.192 47.826 19.78 5.17 0.00 2.59
1583 1657 2.612672 TCACCTACACTCGATCGATGAC 59.387 50.000 19.78 0.00 0.00 3.06
1586 1660 2.614520 CACTCACCTACACTCGATCGAT 59.385 50.000 19.78 6.61 0.00 3.59
1587 1661 2.007608 CACTCACCTACACTCGATCGA 58.992 52.381 18.32 18.32 0.00 3.59
1588 1662 1.064208 CCACTCACCTACACTCGATCG 59.936 57.143 9.36 9.36 0.00 3.69
1589 1663 2.093106 ACCACTCACCTACACTCGATC 58.907 52.381 0.00 0.00 0.00 3.69
1590 1664 2.217510 ACCACTCACCTACACTCGAT 57.782 50.000 0.00 0.00 0.00 3.59
1592 1666 1.611977 TGAACCACTCACCTACACTCG 59.388 52.381 0.00 0.00 0.00 4.18
1593 1667 3.391049 GTTGAACCACTCACCTACACTC 58.609 50.000 0.00 0.00 32.21 3.51
1594 1668 2.223971 CGTTGAACCACTCACCTACACT 60.224 50.000 0.00 0.00 32.21 3.55
1595 1669 2.132762 CGTTGAACCACTCACCTACAC 58.867 52.381 0.00 0.00 32.21 2.90
1596 1670 1.539496 GCGTTGAACCACTCACCTACA 60.539 52.381 0.00 0.00 32.21 2.74
1730 1823 0.658536 GAGCTTGAACGTGCTGTTGC 60.659 55.000 2.46 0.00 42.09 4.17
2720 2867 2.706636 GTCAACAGTTGAGCCAGCA 58.293 52.632 16.68 0.00 41.01 4.41
2739 2886 1.869774 TACTGCAGCAGTCAACACAG 58.130 50.000 31.58 0.60 41.21 3.66
2996 3154 0.323629 TCCTCGACCACCACCAAATC 59.676 55.000 0.00 0.00 0.00 2.17
3056 3226 7.253750 CGAGAGAAAACCAAACATCACAAAAAG 60.254 37.037 0.00 0.00 0.00 2.27
3143 3315 4.419522 AACATGAATTACAAGACGCCAC 57.580 40.909 0.00 0.00 0.00 5.01
3170 3342 9.710900 AATGAAAGAATAACAACATTCCCTTTC 57.289 29.630 0.00 0.00 35.85 2.62
3173 3345 7.099120 GCAATGAAAGAATAACAACATTCCCT 58.901 34.615 0.00 0.00 35.85 4.20
3181 3353 7.440856 GGAAAAGGTGCAATGAAAGAATAACAA 59.559 33.333 0.00 0.00 0.00 2.83
3221 3393 4.278170 TCAACCCAACAATCAACAGATGTC 59.722 41.667 0.00 0.00 0.00 3.06
3288 3460 6.596106 AGCATACGGTTTGATATTGTACACAA 59.404 34.615 0.00 0.00 40.51 3.33
3295 3467 5.989168 TGGTCTAGCATACGGTTTGATATTG 59.011 40.000 2.63 0.00 0.00 1.90
3331 3505 4.462483 ACTTCACCACAACAACATTTCTGT 59.538 37.500 0.00 0.00 37.12 3.41
3352 3526 0.605083 TCATGCACTCTCAGCGAACT 59.395 50.000 0.00 0.00 33.85 3.01
3365 3539 5.981915 TGAAAACAATTCGATTTGTCATGCA 59.018 32.000 22.05 16.59 38.85 3.96
3382 3556 9.376075 ACAACAACATAAATTGTCATGAAAACA 57.624 25.926 0.00 0.00 42.01 2.83
3392 3996 6.690530 CCATCCTCACAACAACATAAATTGT 58.309 36.000 0.00 0.00 44.76 2.71
3447 4051 5.395214 GGACGGCCCAATTTAGATTTTTGAT 60.395 40.000 0.00 0.00 34.14 2.57
3472 4129 4.647611 TCGGAGGATTTATGTTGTTGTGT 58.352 39.130 0.00 0.00 0.00 3.72
3476 4133 2.936498 CGCTCGGAGGATTTATGTTGTT 59.064 45.455 7.20 0.00 0.00 2.83
3501 4159 0.611618 CCCTAATTGTGTGCAGGCCA 60.612 55.000 5.01 0.00 0.00 5.36
3516 4174 2.742116 GCATCACGCCTTCCCCCTA 61.742 63.158 0.00 0.00 32.94 3.53
3548 4206 3.857038 ACGACGCCCAGGTGTTGT 61.857 61.111 16.07 16.07 45.30 3.32
3672 4335 0.238553 GAAGAGGACAACAAAGCGGC 59.761 55.000 0.00 0.00 0.00 6.53
3679 4342 1.202604 GGAACGGTGAAGAGGACAACA 60.203 52.381 0.00 0.00 0.00 3.33
3758 4421 0.596600 CGTAGTGTATCCGCGGCAAT 60.597 55.000 23.51 15.08 0.00 3.56
3760 4423 2.410060 CGTAGTGTATCCGCGGCA 59.590 61.111 23.51 10.59 0.00 5.69
3769 4432 1.812235 TGACGAGCTTCCGTAGTGTA 58.188 50.000 0.00 0.00 43.49 2.90
3770 4433 1.174783 ATGACGAGCTTCCGTAGTGT 58.825 50.000 0.00 0.00 43.49 3.55
3771 4434 1.920574 CAATGACGAGCTTCCGTAGTG 59.079 52.381 0.00 0.00 43.49 2.74
3772 4435 1.544691 ACAATGACGAGCTTCCGTAGT 59.455 47.619 0.00 0.00 43.49 2.73
3773 4436 2.186076 GACAATGACGAGCTTCCGTAG 58.814 52.381 0.00 0.00 43.49 3.51
3774 4437 1.466866 CGACAATGACGAGCTTCCGTA 60.467 52.381 0.00 0.00 43.49 4.02
3842 4510 1.068741 GAAGAGTGTGACGGACCAGTT 59.931 52.381 0.00 0.00 0.00 3.16
3846 4514 0.109689 CGAGAAGAGTGTGACGGACC 60.110 60.000 0.00 0.00 0.00 4.46
3856 4524 2.126424 GCCGCGAACGAGAAGAGT 60.126 61.111 8.23 0.00 43.93 3.24


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

AutoCloner maintained by Alex Coulton.