Multiple sequence alignment - TraesCS4A01G112600

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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 TraesCS4A01G112600 chr4A 100.000 3228 0 0 1 3228 137169904 137166677 0.000000e+00 5962.0
1 TraesCS4A01G112600 chr4A 83.249 394 50 11 1551 1942 137178601 137178222 6.630000e-92 348.0
2 TraesCS4A01G112600 chr4A 78.586 495 64 24 998 1479 137175493 137175028 4.070000e-74 289.0
3 TraesCS4A01G112600 chr4A 92.800 125 8 1 1362 1485 136927964 136927840 2.560000e-41 180.0
4 TraesCS4A01G112600 chr4A 83.908 174 26 2 1564 1735 137174998 137174825 7.160000e-37 165.0
5 TraesCS4A01G112600 chr4A 76.677 313 57 13 963 1261 136928305 136927995 3.330000e-35 159.0
6 TraesCS4A01G112600 chr4B 88.174 1632 112 38 884 2478 413871068 413872655 0.000000e+00 1869.0
7 TraesCS4A01G112600 chr4B 91.985 811 55 6 1 806 413870200 413871005 0.000000e+00 1129.0
8 TraesCS4A01G112600 chr4B 90.375 800 57 14 2444 3228 413872661 413873455 0.000000e+00 1033.0
9 TraesCS4A01G112600 chr4B 77.569 691 98 36 998 1662 413859725 413860384 6.580000e-97 364.0
10 TraesCS4A01G112600 chr4B 89.062 128 8 3 1360 1485 414188090 414188213 1.550000e-33 154.0
11 TraesCS4A01G112600 chr4D 89.450 1109 70 18 884 1976 335893147 335894224 0.000000e+00 1356.0
12 TraesCS4A01G112600 chr4D 88.803 902 64 12 1 887 335892238 335893117 0.000000e+00 1072.0
13 TraesCS4A01G112600 chr4D 86.226 726 61 17 1973 2682 335894466 335895168 0.000000e+00 750.0
14 TraesCS4A01G112600 chr4D 88.967 426 32 8 2670 3082 335895317 335895740 2.220000e-141 512.0
15 TraesCS4A01G112600 chr4D 83.249 394 50 11 1551 1942 335781525 335781904 6.630000e-92 348.0
16 TraesCS4A01G112600 chr4D 90.000 160 13 1 3069 3228 335896564 335896720 1.520000e-48 204.0
17 TraesCS4A01G112600 chr4D 88.095 126 12 3 1362 1485 336118250 336118374 2.600000e-31 147.0
18 TraesCS4A01G112600 chr4D 80.114 176 33 2 1087 1261 336118019 336118193 2.610000e-26 130.0
19 TraesCS4A01G112600 chr2D 80.702 114 21 1 2564 2676 467066684 467066797 1.600000e-13 87.9
20 TraesCS4A01G112600 chr2A 79.508 122 11 8 2409 2517 607916364 607916484 1.240000e-09 75.0
21 TraesCS4A01G112600 chr2A 97.436 39 0 1 2407 2445 550870793 550870830 7.480000e-07 65.8
22 TraesCS4A01G112600 chr6B 97.436 39 0 1 2407 2445 18723369 18723406 7.480000e-07 65.8
23 TraesCS4A01G112600 chr2B 97.436 39 0 1 2407 2445 514346500 514346463 7.480000e-07 65.8
24 TraesCS4A01G112600 chr5A 91.489 47 2 2 2404 2448 448293374 448293328 2.690000e-06 63.9
25 TraesCS4A01G112600 chr3B 97.368 38 0 1 2407 2444 819010791 819010827 2.690000e-06 63.9


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 TraesCS4A01G112600 chr4A 137166677 137169904 3227 True 5962.000000 5962 100.000000 1 3228 1 chr4A.!!$R1 3227
1 TraesCS4A01G112600 chr4A 137174825 137178601 3776 True 267.333333 348 81.914333 998 1942 3 chr4A.!!$R3 944
2 TraesCS4A01G112600 chr4B 413870200 413873455 3255 False 1343.666667 1869 90.178000 1 3228 3 chr4B.!!$F3 3227
3 TraesCS4A01G112600 chr4B 413859725 413860384 659 False 364.000000 364 77.569000 998 1662 1 chr4B.!!$F1 664
4 TraesCS4A01G112600 chr4D 335892238 335896720 4482 False 778.800000 1356 88.689200 1 3228 5 chr4D.!!$F2 3227

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
967 1020 0.179097 GACCTTCGTCTCTGCATCCC 60.179 60.0 0.0 0.0 35.99 3.85 F
1821 3975 0.102120 TTGGCACTTTGTTTGCTCCG 59.898 50.0 0.0 0.0 40.07 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2021 4423 0.179142 GCTACGAAGTCCCCGAAGTC 60.179 60.0 0.00 0.00 43.93 3.01 R
3151 6621 0.958822 CCCAAAACCGGTGAAAGAGG 59.041 55.0 8.52 4.73 0.00 3.69 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
32 33 2.192175 GGTAACCGAGCATGGGGG 59.808 66.667 0.00 0.00 38.89 5.40
39 40 0.323360 CCGAGCATGGGGGAAAAGAA 60.323 55.000 0.00 0.00 0.00 2.52
93 94 2.291217 GGAGAAAGGGGACAAGAGCAAT 60.291 50.000 0.00 0.00 0.00 3.56
143 144 3.441496 ACAACCACTTGACTTGCATTG 57.559 42.857 0.00 0.00 0.00 2.82
187 190 3.702048 CCGCGGAGGAGGTTTGGA 61.702 66.667 24.07 0.00 45.00 3.53
226 229 1.541310 TAGTGACAAGGCTCCCGGTG 61.541 60.000 0.00 0.00 0.00 4.94
239 242 2.433491 CGGTGCGGACGGATTCAA 60.433 61.111 9.03 0.00 0.00 2.69
244 247 2.004017 GTGCGGACGGATTCAAATACA 58.996 47.619 0.00 0.00 0.00 2.29
266 271 5.357032 ACATCTTTTTCAAGAAGTGTTCGGT 59.643 36.000 0.00 0.00 42.53 4.69
310 315 2.547855 GCCAAATCTTTTGCCTCCGTTT 60.548 45.455 0.00 0.00 0.00 3.60
423 428 2.802247 GCCAGCAGAAAACATGGTTTTC 59.198 45.455 21.04 21.04 38.36 2.29
495 501 0.323542 TTCCTCCGAGAGTCCTGGTC 60.324 60.000 0.00 0.00 0.00 4.02
636 642 5.301805 CCACTTCCTTTGAGGTTTTGTATGT 59.698 40.000 0.00 0.00 36.53 2.29
637 643 6.488683 CCACTTCCTTTGAGGTTTTGTATGTA 59.511 38.462 0.00 0.00 36.53 2.29
638 644 7.176690 CCACTTCCTTTGAGGTTTTGTATGTAT 59.823 37.037 0.00 0.00 36.53 2.29
654 660 8.662781 TTGTATGTATTTTGCTAGCTTCTAGG 57.337 34.615 17.23 0.00 0.00 3.02
802 809 7.687941 AACAAGGTTCATTAGATTGTGTAGG 57.312 36.000 0.00 0.00 34.50 3.18
819 838 0.554305 AGGACACCCTTTCCGGTTTT 59.446 50.000 0.00 0.00 40.78 2.43
826 845 0.670239 CCTTTCCGGTTTTGCATGGC 60.670 55.000 0.00 0.00 0.00 4.40
834 853 2.497173 TTTTGCATGGCCACACGCT 61.497 52.632 20.74 0.00 36.61 5.07
875 894 7.979444 TGGAGTAATTCTAGTTTGACCTTTG 57.021 36.000 0.00 0.00 0.00 2.77
967 1020 0.179097 GACCTTCGTCTCTGCATCCC 60.179 60.000 0.00 0.00 35.99 3.85
1005 3117 1.982073 GAGGAGCGAAAACCATGGCG 61.982 60.000 13.04 8.51 0.00 5.69
1006 3118 2.332654 GGAGCGAAAACCATGGCGT 61.333 57.895 13.04 0.00 0.00 5.68
1122 3255 3.959449 TGGAGCTCTACTACGAGTCTCTA 59.041 47.826 14.64 0.00 35.94 2.43
1194 3327 3.532155 GGACTCCTCGATGCCGCT 61.532 66.667 0.00 0.00 35.37 5.52
1263 3396 0.391528 CCATCACATGTCAGGTGCGA 60.392 55.000 12.74 0.00 36.22 5.10
1282 3415 3.483734 CGACATCGCTGCACTATAGTAG 58.516 50.000 4.74 1.49 0.00 2.57
1315 3451 0.890996 GCTGGGTTTCTGAGGTGTGG 60.891 60.000 0.00 0.00 0.00 4.17
1330 3466 3.449018 AGGTGTGGATTAGCACTGTCTAG 59.551 47.826 0.00 0.00 36.03 2.43
1339 3475 6.095720 GGATTAGCACTGTCTAGTTACTGACT 59.904 42.308 13.15 0.00 42.55 3.41
1347 3483 6.097839 ACTGTCTAGTTACTGACTTGTTTGGA 59.902 38.462 13.15 0.00 39.86 3.53
1441 3585 2.358737 CTCAACACCGTGGAGGCC 60.359 66.667 3.03 0.00 46.52 5.19
1481 3625 3.202906 CCGGACGTGGTAATTCATTCAT 58.797 45.455 0.00 0.00 0.00 2.57
1482 3626 3.625764 CCGGACGTGGTAATTCATTCATT 59.374 43.478 0.00 0.00 0.00 2.57
1483 3627 4.260620 CCGGACGTGGTAATTCATTCATTC 60.261 45.833 0.00 0.00 0.00 2.67
1484 3628 4.331443 CGGACGTGGTAATTCATTCATTCA 59.669 41.667 0.00 0.00 0.00 2.57
1485 3629 5.163804 CGGACGTGGTAATTCATTCATTCAA 60.164 40.000 0.00 0.00 0.00 2.69
1604 3752 2.093890 TGTGCATTTCGGCTTCATCAT 58.906 42.857 0.00 0.00 34.04 2.45
1726 3874 2.360350 AGCATGGCCACAAGGTCG 60.360 61.111 8.16 0.00 44.71 4.79
1727 3875 2.672996 GCATGGCCACAAGGTCGT 60.673 61.111 8.16 0.00 44.71 4.34
1729 3877 2.040544 CATGGCCACAAGGTCGTCC 61.041 63.158 8.16 0.00 44.71 4.79
1730 3878 3.605749 ATGGCCACAAGGTCGTCCG 62.606 63.158 8.16 0.00 44.71 4.79
1731 3879 4.309950 GGCCACAAGGTCGTCCGT 62.310 66.667 0.00 0.00 39.05 4.69
1734 3882 1.666872 CCACAAGGTCGTCCGTTCC 60.667 63.158 0.00 0.00 39.05 3.62
1736 3884 2.135581 ACAAGGTCGTCCGTTCCCA 61.136 57.895 0.00 0.00 39.05 4.37
1737 3885 1.295423 CAAGGTCGTCCGTTCCCAT 59.705 57.895 0.00 0.00 39.05 4.00
1738 3886 1.019278 CAAGGTCGTCCGTTCCCATG 61.019 60.000 0.00 0.00 39.05 3.66
1739 3887 2.798148 AAGGTCGTCCGTTCCCATGC 62.798 60.000 0.00 0.00 39.05 4.06
1740 3888 2.818274 GTCGTCCGTTCCCATGCC 60.818 66.667 0.00 0.00 0.00 4.40
1741 3889 4.444838 TCGTCCGTTCCCATGCCG 62.445 66.667 0.00 0.00 0.00 5.69
1761 3909 3.078560 GCGCCTGCGTTGTAGTAC 58.921 61.111 13.57 0.00 42.09 2.73
1764 3912 0.668096 CGCCTGCGTTGTAGTACCAA 60.668 55.000 2.83 0.00 34.35 3.67
1788 3939 7.928307 ATCGCATACATTTTATGGCTAGATT 57.072 32.000 0.00 0.00 33.60 2.40
1789 3940 7.132694 TCGCATACATTTTATGGCTAGATTG 57.867 36.000 0.00 0.00 33.60 2.67
1791 3942 6.348786 CGCATACATTTTATGGCTAGATTGCT 60.349 38.462 0.00 0.00 33.60 3.91
1792 3943 6.805271 GCATACATTTTATGGCTAGATTGCTG 59.195 38.462 0.00 0.00 33.60 4.41
1793 3944 7.308770 GCATACATTTTATGGCTAGATTGCTGA 60.309 37.037 0.00 0.00 33.60 4.26
1794 3945 6.382869 ACATTTTATGGCTAGATTGCTGAC 57.617 37.500 0.00 0.00 33.60 3.51
1795 3946 6.125029 ACATTTTATGGCTAGATTGCTGACT 58.875 36.000 0.00 0.00 33.60 3.41
1821 3975 0.102120 TTGGCACTTTGTTTGCTCCG 59.898 50.000 0.00 0.00 40.07 4.63
1863 4017 0.865218 GAGACAGACAGATGCGCTCG 60.865 60.000 9.73 3.43 0.00 5.03
1933 4087 0.730155 TACGACGTAAGCAACAGCCG 60.730 55.000 4.96 0.00 45.62 5.52
1942 4096 1.375268 GCAACAGCCGCTCTTCTCT 60.375 57.895 0.00 0.00 0.00 3.10
1944 4098 1.074752 CAACAGCCGCTCTTCTCTTC 58.925 55.000 0.00 0.00 0.00 2.87
1951 4105 3.070748 GCCGCTCTTCTCTTCTTCTTTT 58.929 45.455 0.00 0.00 0.00 2.27
1953 4107 4.328712 GCCGCTCTTCTCTTCTTCTTTTAG 59.671 45.833 0.00 0.00 0.00 1.85
1955 4109 5.575218 CCGCTCTTCTCTTCTTCTTTTAGAC 59.425 44.000 0.00 0.00 0.00 2.59
2015 4417 6.650390 TCTTGAATTGTGATGAGATCGTTTGA 59.350 34.615 0.00 0.00 0.00 2.69
2021 4423 4.872124 TGTGATGAGATCGTTTGATTCAGG 59.128 41.667 0.00 0.00 34.09 3.86
2093 4495 4.440880 TCCAAAGATTTGCCAACACAAAG 58.559 39.130 0.00 0.00 42.45 2.77
2119 4521 1.082117 GCCGTGACTATCCAACCGTG 61.082 60.000 0.00 0.00 0.00 4.94
2122 4524 1.359848 GTGACTATCCAACCGTGCAG 58.640 55.000 0.00 0.00 0.00 4.41
2168 4570 1.883084 GGCTACAACTCCGGCGATG 60.883 63.158 9.30 0.00 0.00 3.84
2228 4630 0.379669 GCGGGCTGATGACAATTGAG 59.620 55.000 13.59 0.00 0.00 3.02
2231 4633 2.749076 CGGGCTGATGACAATTGAGAAA 59.251 45.455 13.59 0.00 0.00 2.52
2234 4636 5.107133 GGGCTGATGACAATTGAGAAATTG 58.893 41.667 13.59 9.12 43.77 2.32
2243 4645 3.855689 ATTGAGAAATTGTGCTTCCCG 57.144 42.857 0.00 0.00 0.00 5.14
2244 4646 2.559698 TGAGAAATTGTGCTTCCCGA 57.440 45.000 0.00 0.00 0.00 5.14
2247 4649 0.526211 GAAATTGTGCTTCCCGACCC 59.474 55.000 0.00 0.00 0.00 4.46
2279 4681 6.041523 TCCTGATCATGTCCATATACGTGAAA 59.958 38.462 0.00 0.00 45.79 2.69
2282 4684 7.272244 TGATCATGTCCATATACGTGAAAGTT 58.728 34.615 0.00 0.00 45.79 2.66
2403 4805 3.693411 GGGAAAGCCATTTGCCGA 58.307 55.556 0.00 0.00 45.50 5.54
2454 4857 8.188139 TCCATGGAGCTCGTTTAAAATAAAATC 58.812 33.333 11.44 0.00 0.00 2.17
2552 5002 6.219473 TGTTGTTGTTGAAAAAGTCACACAT 58.781 32.000 0.00 0.00 35.39 3.21
2562 5012 7.416817 TGAAAAAGTCACACATGTTCATACAG 58.583 34.615 0.00 0.00 37.77 2.74
2655 5115 0.698238 ATGGTGGCCAGTACACACAT 59.302 50.000 5.11 0.00 40.54 3.21
2664 5124 2.807967 CCAGTACACACATGGTTCACTG 59.192 50.000 0.00 7.62 37.99 3.66
2838 5470 1.115467 ATCGAGCTCGTCCTCCAAAT 58.885 50.000 33.33 15.66 40.80 2.32
2865 5497 3.764885 ACTCATTTGGCGCACTTTATC 57.235 42.857 10.83 0.00 0.00 1.75
2890 5523 1.620819 TCTCACTGCTCTTGAACCTCC 59.379 52.381 0.00 0.00 0.00 4.30
2942 5575 8.850007 ACTTCTCCTTTTTATGGTAGTCTTTC 57.150 34.615 0.00 0.00 0.00 2.62
2949 5582 7.119262 CCTTTTTATGGTAGTCTTTCATCACGT 59.881 37.037 0.00 0.00 0.00 4.49
3076 6546 7.869429 GGAATGCGATAAAATCCATGAAAATCT 59.131 33.333 0.00 0.00 0.00 2.40
3131 6601 2.031258 TGACGCAAAAGTTGGACTCA 57.969 45.000 0.00 0.00 0.00 3.41
3151 6621 0.535335 TCAACGAGCCCATGTAGTCC 59.465 55.000 0.00 0.00 0.00 3.85
3208 6679 6.701400 GCTATGCCTTGTTTCTTTTCTTTTCA 59.299 34.615 0.00 0.00 0.00 2.69
3209 6680 7.386025 GCTATGCCTTGTTTCTTTTCTTTTCAT 59.614 33.333 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 8.258007 TCGAAGAAGTGGTCATGTATAATCTTT 58.742 33.333 0.00 0.00 0.00 2.52
71 72 0.034960 GCTCTTGTCCCCTTTCTCCC 60.035 60.000 0.00 0.00 0.00 4.30
93 94 6.493115 TGAGCTCATCCCAATTAAAGTCAAAA 59.507 34.615 13.74 0.00 0.00 2.44
143 144 0.523072 AACATCAAGGACGTGCATGC 59.477 50.000 11.82 11.82 0.00 4.06
226 229 3.131396 AGATGTATTTGAATCCGTCCGC 58.869 45.455 0.00 0.00 0.00 5.54
238 241 9.450807 CGAACACTTCTTGAAAAAGATGTATTT 57.549 29.630 6.67 4.43 36.00 1.40
239 242 8.076178 CCGAACACTTCTTGAAAAAGATGTATT 58.924 33.333 6.67 3.14 36.00 1.89
244 247 6.766467 ACTACCGAACACTTCTTGAAAAAGAT 59.234 34.615 0.00 0.00 0.00 2.40
261 265 1.542472 TCGTGCTTGATGACTACCGAA 59.458 47.619 0.00 0.00 0.00 4.30
263 268 1.854743 CATCGTGCTTGATGACTACCG 59.145 52.381 11.81 0.00 46.98 4.02
266 271 3.384467 TCATCCATCGTGCTTGATGACTA 59.616 43.478 17.02 5.88 46.98 2.59
353 358 5.069119 TCTCGCTGTTATGTGATGGATAGTT 59.931 40.000 0.00 0.00 0.00 2.24
423 428 9.898152 ATCTTATCTTTCCCTTTTTAGAGTCAG 57.102 33.333 0.00 0.00 0.00 3.51
495 501 1.399089 CGTAAACCAAGCCATTACCCG 59.601 52.381 0.00 0.00 0.00 5.28
497 503 2.414957 GCACGTAAACCAAGCCATTACC 60.415 50.000 0.00 0.00 0.00 2.85
598 604 4.824289 AGGAAGTGGCTTGCAATTAATTG 58.176 39.130 21.54 21.54 40.66 2.32
636 642 8.534954 TTCTACTCCTAGAAGCTAGCAAAATA 57.465 34.615 18.83 3.27 34.57 1.40
637 643 7.425224 TTCTACTCCTAGAAGCTAGCAAAAT 57.575 36.000 18.83 2.12 34.57 1.82
638 644 6.852420 TTCTACTCCTAGAAGCTAGCAAAA 57.148 37.500 18.83 0.00 34.57 2.44
654 660 1.429463 CAGTGGTGGCGTTTCTACTC 58.571 55.000 0.00 0.00 0.00 2.59
770 777 8.490355 CAATCTAATGAACCTTGTTTCTTTTGC 58.510 33.333 0.00 0.00 0.00 3.68
802 809 0.031585 GCAAAACCGGAAAGGGTGTC 59.968 55.000 9.46 0.00 40.76 3.67
813 832 1.664333 GTGTGGCCATGCAAAACCG 60.664 57.895 9.72 0.00 0.00 4.44
826 845 2.433838 CTCCTCAGCAGCGTGTGG 60.434 66.667 6.61 6.61 33.16 4.17
841 860 7.519032 ACTAGAATTACTCCATGTCTAGCTC 57.481 40.000 12.00 0.00 40.89 4.09
875 894 3.314357 GGTTTATATTGGCGAGGTGGTTC 59.686 47.826 0.00 0.00 0.00 3.62
944 997 1.079750 GCAGAGACGAAGGTCACCC 60.080 63.158 0.00 0.00 45.92 4.61
951 1004 0.179089 CAGGGGATGCAGAGACGAAG 60.179 60.000 0.00 0.00 0.00 3.79
967 1020 1.386525 CCGGTTGATCAATGGGCAGG 61.387 60.000 12.12 5.05 0.00 4.85
1005 3117 2.676471 AAATGGTGCAGGCGGGAC 60.676 61.111 0.00 0.00 37.06 4.46
1006 3118 2.361104 GAAATGGTGCAGGCGGGA 60.361 61.111 0.00 0.00 0.00 5.14
1122 3255 0.620556 ACTGAAATGAGTCGGGGCAT 59.379 50.000 0.00 0.00 0.00 4.40
1194 3327 3.900888 GGAACCAGGGTGAGGTCA 58.099 61.111 0.00 0.00 38.76 4.02
1263 3396 5.306394 TCTACTACTATAGTGCAGCGATGT 58.694 41.667 15.90 4.36 39.81 3.06
1282 3415 1.285078 ACCCAGCCCAAAAGGATCTAC 59.715 52.381 0.00 0.00 38.24 2.59
1315 3451 7.090953 AGTCAGTAACTAGACAGTGCTAATC 57.909 40.000 0.00 0.00 36.07 1.75
1330 3466 3.003378 GCACCTCCAAACAAGTCAGTAAC 59.997 47.826 0.00 0.00 0.00 2.50
1339 3475 1.039068 CACCATGCACCTCCAAACAA 58.961 50.000 0.00 0.00 0.00 2.83
1481 3625 4.122046 ACGATGATGAGATGCGAATTGAA 58.878 39.130 0.00 0.00 0.00 2.69
1482 3626 3.721035 ACGATGATGAGATGCGAATTGA 58.279 40.909 0.00 0.00 0.00 2.57
1483 3627 3.739810 AGACGATGATGAGATGCGAATTG 59.260 43.478 0.00 0.00 0.00 2.32
1484 3628 3.986572 GAGACGATGATGAGATGCGAATT 59.013 43.478 0.00 0.00 0.00 2.17
1485 3629 3.255395 AGAGACGATGATGAGATGCGAAT 59.745 43.478 0.00 0.00 0.00 3.34
1596 3744 1.137675 TCCTCCACGCAGATGATGAAG 59.862 52.381 0.00 0.00 0.00 3.02
1604 3752 3.385384 CCAGCTCCTCCACGCAGA 61.385 66.667 0.00 0.00 0.00 4.26
1726 3874 4.778143 AGCGGCATGGGAACGGAC 62.778 66.667 1.45 0.00 0.00 4.79
1727 3875 4.776322 CAGCGGCATGGGAACGGA 62.776 66.667 1.45 0.00 0.00 4.69
1742 3890 1.445410 TACTACAACGCAGGCGCAG 60.445 57.895 14.32 8.92 44.19 5.18
1746 3894 1.664151 GATTGGTACTACAACGCAGGC 59.336 52.381 0.00 0.00 32.39 4.85
1747 3895 1.924524 CGATTGGTACTACAACGCAGG 59.075 52.381 0.00 0.00 32.39 4.85
1757 3905 6.293955 GCCATAAAATGTATGCGATTGGTACT 60.294 38.462 0.00 0.00 0.00 2.73
1761 3909 5.125100 AGCCATAAAATGTATGCGATTGG 57.875 39.130 0.00 0.00 0.00 3.16
1764 3912 7.627088 GCAATCTAGCCATAAAATGTATGCGAT 60.627 37.037 0.00 0.00 0.00 4.58
1788 3939 2.972625 GTGCCAACACTATAGTCAGCA 58.027 47.619 1.26 6.95 43.85 4.41
1933 4087 5.061684 GCGTCTAAAAGAAGAAGAGAAGAGC 59.938 44.000 0.00 0.00 0.00 4.09
1942 4096 3.006967 AGCTCAGGCGTCTAAAAGAAGAA 59.993 43.478 0.00 0.00 44.37 2.52
1944 4098 2.966050 AGCTCAGGCGTCTAAAAGAAG 58.034 47.619 0.00 0.00 44.37 2.85
1951 4105 1.250840 TGCTGAAGCTCAGGCGTCTA 61.251 55.000 12.98 0.00 44.43 2.59
1953 4107 1.449246 ATGCTGAAGCTCAGGCGTC 60.449 57.895 12.98 0.00 44.43 5.19
1955 4109 0.460811 TACATGCTGAAGCTCAGGCG 60.461 55.000 12.98 0.00 44.43 5.52
2015 4417 1.555533 GAAGTCCCCGAAGTCCTGAAT 59.444 52.381 0.00 0.00 0.00 2.57
2021 4423 0.179142 GCTACGAAGTCCCCGAAGTC 60.179 60.000 0.00 0.00 43.93 3.01
2093 4495 3.501458 GATAGTCACGGCCCGGCTC 62.501 68.421 8.57 0.00 0.00 4.70
2143 4545 2.092882 GGAGTTGTAGCCGACACGC 61.093 63.158 0.00 0.00 37.96 5.34
2168 4570 1.349627 CGCCATCATTGAGCACGAC 59.650 57.895 0.00 0.00 0.00 4.34
2228 4630 0.526211 GGGTCGGGAAGCACAATTTC 59.474 55.000 0.00 0.00 0.00 2.17
2231 4633 0.322546 GAAGGGTCGGGAAGCACAAT 60.323 55.000 0.00 0.00 0.00 2.71
2234 4636 2.434359 CGAAGGGTCGGGAAGCAC 60.434 66.667 0.00 0.00 43.81 4.40
2247 4649 1.202580 GGACATGATCAGGACCCGAAG 60.203 57.143 15.42 0.00 0.00 3.79
2257 4659 6.816136 ACTTTCACGTATATGGACATGATCA 58.184 36.000 0.00 0.00 0.00 2.92
2279 4681 4.141390 ACAGAAGGATGAAACTGTCCAACT 60.141 41.667 0.00 0.00 38.95 3.16
2403 4805 2.936498 CGTCCTCCATTTAGCATTTCGT 59.064 45.455 0.00 0.00 0.00 3.85
2526 4976 6.535150 TGTGTGACTTTTTCAACAACAACAAA 59.465 30.769 0.00 0.00 35.39 2.83
2528 4978 5.592054 TGTGTGACTTTTTCAACAACAACA 58.408 33.333 0.00 0.00 35.39 3.33
2529 4979 6.145371 ACATGTGTGACTTTTTCAACAACAAC 59.855 34.615 0.00 0.00 35.39 3.32
2531 4981 5.777802 ACATGTGTGACTTTTTCAACAACA 58.222 33.333 0.00 0.00 35.39 3.33
2532 4982 6.364706 TGAACATGTGTGACTTTTTCAACAAC 59.635 34.615 0.00 0.00 35.39 3.32
2535 4985 7.700234 TGTATGAACATGTGTGACTTTTTCAAC 59.300 33.333 0.00 0.00 35.39 3.18
2552 5002 7.509141 AATTTCACACACATCTGTATGAACA 57.491 32.000 0.00 0.00 36.54 3.18
2562 5012 7.140705 TGTCATCTTCAAATTTCACACACATC 58.859 34.615 0.00 0.00 0.00 3.06
2616 5076 7.607223 CCACCATATCCAAATCACAATTTTGTT 59.393 33.333 0.00 0.00 39.91 2.83
2632 5092 1.488812 TGTGTACTGGCCACCATATCC 59.511 52.381 0.00 0.00 30.82 2.59
2635 5095 1.353091 TGTGTGTACTGGCCACCATA 58.647 50.000 0.00 0.00 30.82 2.74
2655 5115 6.154203 TCATGCATTTTTAACAGTGAACCA 57.846 33.333 0.00 0.00 0.00 3.67
2821 5453 1.661112 GAAATTTGGAGGACGAGCTCG 59.339 52.381 33.45 33.45 46.33 5.03
2838 5470 1.271652 TGCGCCAAATGAGTAGGGAAA 60.272 47.619 4.18 0.00 0.00 3.13
2865 5497 3.622163 GGTTCAAGAGCAGTGAGATGATG 59.378 47.826 0.00 0.00 0.00 3.07
2890 5523 5.229921 TGGAGAAGAAAGAAAACACAACG 57.770 39.130 0.00 0.00 0.00 4.10
3104 6574 7.305474 AGTCCAACTTTTGCGTCATTTTATAG 58.695 34.615 0.00 0.00 0.00 1.31
3105 6575 7.041030 TGAGTCCAACTTTTGCGTCATTTTATA 60.041 33.333 0.00 0.00 0.00 0.98
3106 6576 6.084326 AGTCCAACTTTTGCGTCATTTTAT 57.916 33.333 0.00 0.00 0.00 1.40
3131 6601 1.139058 GGACTACATGGGCTCGTTGAT 59.861 52.381 0.00 0.00 0.00 2.57
3151 6621 0.958822 CCCAAAACCGGTGAAAGAGG 59.041 55.000 8.52 4.73 0.00 3.69


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

AutoCloner maintained by Alex Coulton.