Multiple sequence alignment - TraesCS2A01G108600

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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 TraesCS2A01G108600 chr2A 100.000 3136 0 0 1 3136 60712807 60709672 0.000000e+00 5792.0
1 TraesCS2A01G108600 chr2A 95.944 1430 36 8 1708 3135 60249051 60247642 0.000000e+00 2300.0
2 TraesCS2A01G108600 chr2A 93.386 635 42 0 1557 2191 59724435 59725069 0.000000e+00 941.0
3 TraesCS2A01G108600 chr2A 85.784 816 61 27 773 1545 59723253 59724056 0.000000e+00 813.0
4 TraesCS2A01G108600 chr2A 79.834 481 68 19 1025 1494 59728433 59727971 1.080000e-84 324.0
5 TraesCS2A01G108600 chr2A 83.857 223 28 8 1000 1218 60195812 60195594 4.100000e-49 206.0
6 TraesCS2A01G108600 chr2A 83.857 223 28 8 1000 1218 60609831 60609613 4.100000e-49 206.0
7 TraesCS2A01G108600 chr2A 86.885 122 9 5 3018 3136 69212577 69212694 2.540000e-26 130.0
8 TraesCS2A01G108600 chr2B 89.738 1715 126 30 773 2449 94034594 94032892 0.000000e+00 2146.0
9 TraesCS2A01G108600 chr2B 88.662 1570 101 35 773 2273 93111730 93113291 0.000000e+00 1842.0
10 TraesCS2A01G108600 chr2B 90.111 1436 94 26 790 2187 94225207 94223782 0.000000e+00 1821.0
11 TraesCS2A01G108600 chr2B 88.889 1233 105 15 989 2191 93440498 93441728 0.000000e+00 1489.0
12 TraesCS2A01G108600 chr2B 90.193 571 34 6 1 551 94035317 94034749 0.000000e+00 725.0
13 TraesCS2A01G108600 chr2B 87.260 573 27 9 1 551 94225936 94225388 2.070000e-171 612.0
14 TraesCS2A01G108600 chr2B 79.834 481 69 18 1025 1494 93139344 93138881 3.020000e-85 326.0
15 TraesCS2A01G108600 chr2B 81.115 323 34 14 255 558 93111246 93111560 1.880000e-57 233.0
16 TraesCS2A01G108600 chr2B 87.500 184 22 1 1310 1492 93700771 93700588 8.810000e-51 211.0
17 TraesCS2A01G108600 chr2B 78.171 339 53 18 890 1221 93934702 93934378 2.470000e-46 196.0
18 TraesCS2A01G108600 chr2B 91.753 97 8 0 3040 3136 12283482 12283578 5.460000e-28 135.0
19 TraesCS2A01G108600 chr2B 81.761 159 17 4 2193 2350 94223725 94223578 4.250000e-24 122.0
20 TraesCS2A01G108600 chr2B 89.796 49 0 4 711 754 93438997 93439045 1.210000e-04 58.4
21 TraesCS2A01G108600 chr2D 90.139 1653 110 29 836 2454 60139127 60137494 0.000000e+00 2100.0
22 TraesCS2A01G108600 chr2D 87.595 1572 113 34 773 2273 59726863 59728423 0.000000e+00 1748.0
23 TraesCS2A01G108600 chr2D 91.623 573 23 9 1 551 60139908 60139339 0.000000e+00 769.0
24 TraesCS2A01G108600 chr2D 84.195 677 63 27 854 1503 59845410 59846069 4.440000e-173 617.0
25 TraesCS2A01G108600 chr2D 75.679 773 154 27 1379 2136 59724710 59725463 3.850000e-94 355.0
26 TraesCS2A01G108600 chr2D 76.812 345 59 17 884 1221 60108893 60108563 1.160000e-39 174.0
27 TraesCS2A01G108600 chr2D 85.443 158 21 2 2451 2607 63400556 63400400 2.500000e-36 163.0
28 TraesCS2A01G108600 chr1A 75.044 565 112 24 1571 2113 299267823 299268380 5.230000e-58 235.0
29 TraesCS2A01G108600 chr1A 80.822 219 42 0 1000 1218 299261508 299261726 4.160000e-39 172.0
30 TraesCS2A01G108600 chr1D 76.786 336 66 11 884 1218 247867897 247867573 8.940000e-41 178.0
31 TraesCS2A01G108600 chr1D 90.196 102 6 3 3039 3136 393758222 393758121 2.540000e-26 130.0
32 TraesCS2A01G108600 chr5D 91.089 101 6 2 3039 3136 363327423 363327323 1.960000e-27 134.0
33 TraesCS2A01G108600 chr5D 85.593 118 12 3 3022 3136 544282489 544282374 5.490000e-23 119.0
34 TraesCS2A01G108600 chr4A 90.196 102 6 3 3039 3136 113866285 113866184 2.540000e-26 130.0
35 TraesCS2A01G108600 chr7A 88.785 107 8 3 3034 3136 700680116 700680010 9.130000e-26 128.0
36 TraesCS2A01G108600 chr3B 84.252 127 11 7 3014 3136 707421220 707421099 7.110000e-22 115.0
37 TraesCS2A01G108600 chr7B 96.875 32 0 1 2397 2427 690909867 690909836 6.000000e-03 52.8
38 TraesCS2A01G108600 chr5A 96.774 31 1 0 2397 2427 620387073 620387043 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 TraesCS2A01G108600 chr2A 60709672 60712807 3135 True 5792.000000 5792 100.000000 1 3136 1 chr2A.!!$R5 3135
1 TraesCS2A01G108600 chr2A 60247642 60249051 1409 True 2300.000000 2300 95.944000 1708 3135 1 chr2A.!!$R3 1427
2 TraesCS2A01G108600 chr2A 59723253 59725069 1816 False 877.000000 941 89.585000 773 2191 2 chr2A.!!$F2 1418
3 TraesCS2A01G108600 chr2B 94032892 94035317 2425 True 1435.500000 2146 89.965500 1 2449 2 chr2B.!!$R4 2448
4 TraesCS2A01G108600 chr2B 93111246 93113291 2045 False 1037.500000 1842 84.888500 255 2273 2 chr2B.!!$F2 2018
5 TraesCS2A01G108600 chr2B 94223578 94225936 2358 True 851.666667 1821 86.377333 1 2350 3 chr2B.!!$R5 2349
6 TraesCS2A01G108600 chr2B 93438997 93441728 2731 False 773.700000 1489 89.342500 711 2191 2 chr2B.!!$F3 1480
7 TraesCS2A01G108600 chr2D 60137494 60139908 2414 True 1434.500000 2100 90.881000 1 2454 2 chr2D.!!$R3 2453
8 TraesCS2A01G108600 chr2D 59724710 59728423 3713 False 1051.500000 1748 81.637000 773 2273 2 chr2D.!!$F2 1500
9 TraesCS2A01G108600 chr2D 59845410 59846069 659 False 617.000000 617 84.195000 854 1503 1 chr2D.!!$F1 649
10 TraesCS2A01G108600 chr1A 299267823 299268380 557 False 235.000000 235 75.044000 1571 2113 1 chr1A.!!$F2 542

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
887 2286 0.036858 TCGTCATGTGCCGGAAATGA 60.037 50.0 5.05 7.93 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2832 5916 0.244721 GCAAAGGCCCTGATGTGTTC 59.755 55.0 0.0 0.0 0.0 3.18 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
206 213 3.618690 ATTTGCAGTCTCTAGTGGGAC 57.381 47.619 0.00 0.00 0.00 4.46
220 227 7.177216 TCTCTAGTGGGACGAACTATTTGTTTA 59.823 37.037 0.00 0.00 39.30 2.01
323 358 6.462500 ACGATGGAGAAAGATAGATGAATGG 58.538 40.000 0.00 0.00 0.00 3.16
355 394 1.620822 ACCACTTGCTTCAACCATCC 58.379 50.000 0.00 0.00 0.00 3.51
445 485 8.279970 TCACATACATTAAAGTGCTAGCAAAT 57.720 30.769 21.29 12.77 32.25 2.32
452 492 6.885952 TTAAAGTGCTAGCAAATGTACCAA 57.114 33.333 21.29 3.06 0.00 3.67
531 575 1.133976 GCACATATCTGGCCAGGAACT 60.134 52.381 32.23 16.58 43.88 3.01
550 594 0.109179 TGCGGCAATTTCACAGCATC 60.109 50.000 0.00 0.00 0.00 3.91
558 602 4.440103 GCAATTTCACAGCATCGATCAATC 59.560 41.667 0.00 0.00 0.00 2.67
560 604 6.206498 CAATTTCACAGCATCGATCAATCAT 58.794 36.000 0.00 0.00 0.00 2.45
561 605 7.357303 CAATTTCACAGCATCGATCAATCATA 58.643 34.615 0.00 0.00 0.00 2.15
563 607 4.563061 TCACAGCATCGATCAATCATAGG 58.437 43.478 0.00 0.00 0.00 2.57
565 609 3.007723 ACAGCATCGATCAATCATAGGCT 59.992 43.478 0.00 0.00 32.11 4.58
569 613 5.128335 AGCATCGATCAATCATAGGCTCATA 59.872 40.000 0.00 0.00 27.58 2.15
571 615 6.571605 CATCGATCAATCATAGGCTCATAGT 58.428 40.000 0.00 0.00 0.00 2.12
572 616 7.682981 GCATCGATCAATCATAGGCTCATAGTA 60.683 40.741 0.00 0.00 0.00 1.82
573 617 7.888250 TCGATCAATCATAGGCTCATAGTAT 57.112 36.000 0.00 0.00 0.00 2.12
574 618 8.980481 TCGATCAATCATAGGCTCATAGTATA 57.020 34.615 0.00 0.00 0.00 1.47
575 619 9.579932 TCGATCAATCATAGGCTCATAGTATAT 57.420 33.333 0.00 0.00 0.00 0.86
613 661 4.808077 CACATAGTGCATCTCATTGACC 57.192 45.455 0.00 0.00 0.00 4.02
615 663 2.602257 TAGTGCATCTCATTGACCGG 57.398 50.000 0.00 0.00 0.00 5.28
617 665 1.451927 TGCATCTCATTGACCGGCC 60.452 57.895 0.00 0.00 0.00 6.13
619 667 1.153369 CATCTCATTGACCGGCCGT 60.153 57.895 26.12 12.57 0.00 5.68
620 668 1.144057 ATCTCATTGACCGGCCGTC 59.856 57.895 26.12 21.00 42.33 4.79
651 699 9.851686 AAAATATAAACTGCACATCTATCTCCA 57.148 29.630 0.00 0.00 0.00 3.86
652 700 9.851686 AAATATAAACTGCACATCTATCTCCAA 57.148 29.630 0.00 0.00 0.00 3.53
653 701 9.499479 AATATAAACTGCACATCTATCTCCAAG 57.501 33.333 0.00 0.00 0.00 3.61
655 703 2.770802 ACTGCACATCTATCTCCAAGCT 59.229 45.455 0.00 0.00 0.00 3.74
660 721 7.617329 ACTGCACATCTATCTCCAAGCTATATA 59.383 37.037 0.00 0.00 0.00 0.86
691 763 8.645730 TCGTAGTAGTAGAACTTAGTCATCTG 57.354 38.462 0.00 0.00 0.00 2.90
692 764 8.473219 TCGTAGTAGTAGAACTTAGTCATCTGA 58.527 37.037 0.00 0.00 0.00 3.27
693 765 8.757789 CGTAGTAGTAGAACTTAGTCATCTGAG 58.242 40.741 0.00 0.00 34.12 3.35
695 767 8.726870 AGTAGTAGAACTTAGTCATCTGAGAC 57.273 38.462 0.00 0.00 38.81 3.36
696 768 6.671614 AGTAGAACTTAGTCATCTGAGACG 57.328 41.667 0.00 0.00 43.24 4.18
699 771 6.334102 AGAACTTAGTCATCTGAGACGTTT 57.666 37.500 0.00 0.00 43.24 3.60
700 772 6.153067 AGAACTTAGTCATCTGAGACGTTTG 58.847 40.000 0.00 0.00 43.24 2.93
701 773 5.707242 ACTTAGTCATCTGAGACGTTTGA 57.293 39.130 0.00 0.00 43.24 2.69
702 774 6.085555 ACTTAGTCATCTGAGACGTTTGAA 57.914 37.500 0.00 0.00 43.24 2.69
704 776 3.321497 AGTCATCTGAGACGTTTGAAGC 58.679 45.455 0.00 0.00 43.24 3.86
705 777 3.059884 GTCATCTGAGACGTTTGAAGCA 58.940 45.455 0.00 0.00 0.00 3.91
706 778 3.494626 GTCATCTGAGACGTTTGAAGCAA 59.505 43.478 0.00 0.00 0.00 3.91
707 779 3.494626 TCATCTGAGACGTTTGAAGCAAC 59.505 43.478 0.00 0.00 0.00 4.17
709 781 2.866156 TCTGAGACGTTTGAAGCAACTG 59.134 45.455 0.00 0.00 0.00 3.16
770 882 3.243643 GCAACTGTTGATTTGACACTTGC 59.756 43.478 23.81 0.56 38.59 4.01
771 883 3.715628 ACTGTTGATTTGACACTTGCC 57.284 42.857 0.00 0.00 0.00 4.52
887 2286 0.036858 TCGTCATGTGCCGGAAATGA 60.037 50.000 5.05 7.93 0.00 2.57
949 3511 0.376152 GCATTGCATCCAGTGTCTCG 59.624 55.000 3.15 0.00 31.88 4.04
950 3512 2.008543 GCATTGCATCCAGTGTCTCGA 61.009 52.381 3.15 0.00 31.88 4.04
955 3517 1.202313 GCATCCAGTGTCTCGACCTAC 60.202 57.143 0.00 0.00 0.00 3.18
961 3523 2.035449 CAGTGTCTCGACCTACCACAAA 59.965 50.000 0.00 0.00 0.00 2.83
963 3525 3.323979 AGTGTCTCGACCTACCACAAATT 59.676 43.478 0.00 0.00 0.00 1.82
964 3526 3.678548 GTGTCTCGACCTACCACAAATTC 59.321 47.826 0.00 0.00 0.00 2.17
965 3527 3.322541 TGTCTCGACCTACCACAAATTCA 59.677 43.478 0.00 0.00 0.00 2.57
967 3529 3.322541 TCTCGACCTACCACAAATTCACA 59.677 43.478 0.00 0.00 0.00 3.58
969 3531 4.647611 TCGACCTACCACAAATTCACAAT 58.352 39.130 0.00 0.00 0.00 2.71
971 3533 6.231951 TCGACCTACCACAAATTCACAATTA 58.768 36.000 0.00 0.00 0.00 1.40
972 3534 6.711194 TCGACCTACCACAAATTCACAATTAA 59.289 34.615 0.00 0.00 0.00 1.40
975 3537 7.657336 ACCTACCACAAATTCACAATTAAGTG 58.343 34.615 0.45 0.45 40.85 3.16
976 3538 7.504238 ACCTACCACAAATTCACAATTAAGTGA 59.496 33.333 10.35 1.43 46.12 3.41
985 3547 5.431420 TCACAATTAAGTGACGTTGCATT 57.569 34.783 10.35 0.00 43.18 3.56
986 3548 5.826586 TCACAATTAAGTGACGTTGCATTT 58.173 33.333 10.35 0.00 43.18 2.32
988 3550 5.685068 CACAATTAAGTGACGTTGCATTTGA 59.315 36.000 10.35 0.00 42.05 2.69
989 3551 5.914635 ACAATTAAGTGACGTTGCATTTGAG 59.085 36.000 10.35 0.00 0.00 3.02
991 3553 1.597742 AGTGACGTTGCATTTGAGCT 58.402 45.000 0.00 0.00 34.99 4.09
992 3554 2.766313 AGTGACGTTGCATTTGAGCTA 58.234 42.857 0.00 0.00 34.99 3.32
993 3555 2.738846 AGTGACGTTGCATTTGAGCTAG 59.261 45.455 0.00 0.00 34.99 3.42
994 3556 1.464608 TGACGTTGCATTTGAGCTAGC 59.535 47.619 6.62 6.62 34.99 3.42
995 3557 1.734465 GACGTTGCATTTGAGCTAGCT 59.266 47.619 19.45 19.45 34.99 3.32
998 3569 3.190079 CGTTGCATTTGAGCTAGCTAGA 58.810 45.455 25.15 6.30 34.99 2.43
1083 3657 1.860853 GTCGCCGACGTTCTACGAC 60.861 63.158 15.18 15.18 46.05 4.34
1117 3691 1.078848 GCTCTGGCGACCATCAAGT 60.079 57.895 0.00 0.00 30.82 3.16
1188 3762 2.434884 CGGCTGCACTTCCACGAT 60.435 61.111 0.50 0.00 0.00 3.73
1222 3799 8.758829 TCCAAGTAAGCTCTTCAAATACATAGA 58.241 33.333 0.00 0.00 0.00 1.98
1247 3832 2.051345 GGCACGCACCTGTTTTCG 60.051 61.111 0.00 0.00 0.00 3.46
1259 3844 2.602660 CCTGTTTTCGTTGCAGTTTTGG 59.397 45.455 0.00 0.00 0.00 3.28
1262 3847 4.058817 TGTTTTCGTTGCAGTTTTGGTTT 58.941 34.783 0.00 0.00 0.00 3.27
1269 3854 4.489523 CGTTGCAGTTTTGGTTTGTAAACG 60.490 41.667 1.80 0.00 39.77 3.60
1304 3923 4.941873 AGTTAACCATGCTGCTTAACTACC 59.058 41.667 17.81 0.00 38.40 3.18
1338 3957 1.661509 CGCGTCTGTTCTGCTGTCA 60.662 57.895 0.00 0.00 0.00 3.58
1374 3993 1.202371 GCTATCCCGAACGTGATGTCA 60.202 52.381 2.82 0.00 0.00 3.58
1437 4056 0.399454 AGACCATGTGCAAGCAGACT 59.601 50.000 0.00 0.00 0.00 3.24
1534 4154 2.029380 CGTGATCACCACCAAGTAGACA 60.029 50.000 20.03 0.00 42.76 3.41
1552 4532 0.734889 CAGGCTAATTTGCTCACCCG 59.265 55.000 11.61 0.00 0.00 5.28
1561 4547 1.198094 TTGCTCACCCGGGATTCTCA 61.198 55.000 32.02 15.06 0.00 3.27
1601 4606 2.168496 CCTTCGTGGACAGTTCCTCTA 58.832 52.381 0.00 0.00 43.31 2.43
1676 4681 1.108776 CCCCATTCTTCGACCTCGTA 58.891 55.000 0.00 0.00 40.80 3.43
1964 4984 3.023949 GCTCCTGCACTCCGACCAT 62.024 63.158 0.00 0.00 39.41 3.55
2141 5168 3.430790 GCTCCAAGGTGAATTAATTGGGC 60.431 47.826 5.17 3.68 42.05 5.36
2649 5731 4.819105 AATACATCGGTCTTGAGGAACA 57.181 40.909 0.00 0.00 0.00 3.18
2674 5756 1.810030 GGATTCAGTGGACGCGGTC 60.810 63.158 12.47 5.53 0.00 4.79
2731 5813 0.874390 GTTTGAGCATCCGAACAGCA 59.126 50.000 0.00 0.00 32.49 4.41
2758 5842 4.516135 CTGATGCAGCAGCGCACG 62.516 66.667 20.45 0.01 46.56 5.34
2782 5866 1.160137 GGCCAGTGAACACATCAGAC 58.840 55.000 0.00 0.00 39.19 3.51
2799 5883 4.133820 TCAGACGCAAAAGATTTCAAGGA 58.866 39.130 0.00 0.00 0.00 3.36
2808 5892 6.633856 CAAAAGATTTCAAGGAATCGGGATT 58.366 36.000 0.00 0.00 40.22 3.01
2815 5899 3.138283 TCAAGGAATCGGGATTAGGCATT 59.862 43.478 0.00 0.00 0.00 3.56
2816 5900 3.146104 AGGAATCGGGATTAGGCATTG 57.854 47.619 0.00 0.00 0.00 2.82
2819 5903 3.476552 GAATCGGGATTAGGCATTGTGA 58.523 45.455 0.00 0.00 0.00 3.58
2820 5904 3.576078 ATCGGGATTAGGCATTGTGAA 57.424 42.857 0.00 0.00 0.00 3.18
2821 5905 2.917933 TCGGGATTAGGCATTGTGAAG 58.082 47.619 0.00 0.00 0.00 3.02
2822 5906 1.334869 CGGGATTAGGCATTGTGAAGC 59.665 52.381 0.00 0.00 0.00 3.86
2824 5908 2.288666 GGATTAGGCATTGTGAAGCGA 58.711 47.619 0.00 0.00 0.00 4.93
2844 5928 2.414994 AGCAGATGAACACATCAGGG 57.585 50.000 11.79 3.57 42.53 4.45
2906 5990 3.632145 GTGAAGTCAATGTGAAAGGGTGT 59.368 43.478 0.00 0.00 0.00 4.16
2993 6077 1.359848 AACTTGGCTTACGCAGATCG 58.640 50.000 0.00 0.00 45.38 3.69
3038 6122 9.336171 GATAGTTTATTCTTCTTCTCATTGCCT 57.664 33.333 0.00 0.00 0.00 4.75
3039 6123 9.692325 ATAGTTTATTCTTCTTCTCATTGCCTT 57.308 29.630 0.00 0.00 0.00 4.35
3069 6153 1.006102 AGTACAGACGCAAGCGCTT 60.006 52.632 18.98 18.98 44.19 4.68
3077 6161 2.668457 AGACGCAAGCGCTTATATATGC 59.332 45.455 24.55 20.44 44.19 3.14
3112 6196 1.881641 TATGAACGCACACACGCACG 61.882 55.000 0.00 0.00 36.19 5.34
3113 6197 4.643385 GAACGCACACACGCACGG 62.643 66.667 0.00 0.00 36.19 4.94
3135 6219 3.368531 GCCTATTCCTATAAGCACCTCCG 60.369 52.174 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
206 213 5.788531 CGAGCAAAGGTAAACAAATAGTTCG 59.211 40.000 0.00 0.00 40.26 3.95
323 358 0.454196 AAGTGGTTGGTCGTGCAAAC 59.546 50.000 0.00 0.00 0.00 2.93
336 375 1.620822 GGATGGTTGAAGCAAGTGGT 58.379 50.000 0.00 0.00 0.00 4.16
355 394 1.473677 TCATGGGCTGAGATTTTTGCG 59.526 47.619 0.00 0.00 0.00 4.85
445 485 1.338294 CCTACGTGGTGCATTGGTACA 60.338 52.381 0.00 0.00 0.00 2.90
476 516 4.613622 CGCGAAACAAGATCATGGTTCTTT 60.614 41.667 22.43 5.72 43.37 2.52
531 575 0.109179 GATGCTGTGAAATTGCCGCA 60.109 50.000 0.00 0.00 0.00 5.69
537 581 5.823209 TGATTGATCGATGCTGTGAAATT 57.177 34.783 0.54 0.00 0.00 1.82
539 583 5.467735 CCTATGATTGATCGATGCTGTGAAA 59.532 40.000 0.54 0.00 0.00 2.69
540 584 4.992951 CCTATGATTGATCGATGCTGTGAA 59.007 41.667 0.54 0.00 0.00 3.18
563 607 8.777865 TTTTCACATGGCTATATACTATGAGC 57.222 34.615 12.34 1.34 0.00 4.26
569 613 8.156820 TGTGCTATTTTCACATGGCTATATACT 58.843 33.333 0.00 0.00 39.29 2.12
597 645 0.745845 GCCGGTCAATGAGATGCACT 60.746 55.000 1.90 0.00 0.00 4.40
600 648 2.537560 CGGCCGGTCAATGAGATGC 61.538 63.158 20.10 0.00 0.00 3.91
603 651 2.577059 GACGGCCGGTCAATGAGA 59.423 61.111 31.76 0.00 45.36 3.27
610 658 1.445871 ATTTTAACTGACGGCCGGTC 58.554 50.000 31.76 23.40 46.27 4.79
612 660 5.295045 AGTTTATATTTTAACTGACGGCCGG 59.705 40.000 31.76 14.78 33.55 6.13
613 661 6.354039 AGTTTATATTTTAACTGACGGCCG 57.646 37.500 26.86 26.86 33.55 6.13
642 690 9.990360 CGATAGAGTATATAGCTTGGAGATAGA 57.010 37.037 0.00 0.00 39.76 1.98
643 691 9.772973 ACGATAGAGTATATAGCTTGGAGATAG 57.227 37.037 0.00 0.00 41.38 2.08
660 721 9.965824 GACTAAGTTCTACTACTACGATAGAGT 57.034 37.037 0.00 0.00 41.38 3.24
688 760 2.866156 CAGTTGCTTCAAACGTCTCAGA 59.134 45.455 0.00 0.00 35.13 3.27
690 762 2.351418 CACAGTTGCTTCAAACGTCTCA 59.649 45.455 0.00 0.00 35.13 3.27
691 763 2.607635 TCACAGTTGCTTCAAACGTCTC 59.392 45.455 0.00 0.00 35.13 3.36
692 764 2.627945 TCACAGTTGCTTCAAACGTCT 58.372 42.857 0.00 0.00 35.13 4.18
693 765 3.398954 TTCACAGTTGCTTCAAACGTC 57.601 42.857 0.00 0.00 35.13 4.34
695 767 5.088739 GGATATTCACAGTTGCTTCAAACG 58.911 41.667 0.00 0.00 35.13 3.60
696 768 5.402398 GGGATATTCACAGTTGCTTCAAAC 58.598 41.667 0.00 0.00 0.00 2.93
699 771 3.270027 CGGGATATTCACAGTTGCTTCA 58.730 45.455 0.00 0.00 0.00 3.02
700 772 3.270877 ACGGGATATTCACAGTTGCTTC 58.729 45.455 0.00 0.00 0.00 3.86
701 773 3.350219 ACGGGATATTCACAGTTGCTT 57.650 42.857 0.00 0.00 0.00 3.91
702 774 3.009723 CAACGGGATATTCACAGTTGCT 58.990 45.455 4.13 0.00 31.59 3.91
704 776 4.875536 TCATCAACGGGATATTCACAGTTG 59.124 41.667 8.92 8.92 36.43 3.16
705 777 5.097742 TCATCAACGGGATATTCACAGTT 57.902 39.130 0.00 0.00 33.95 3.16
706 778 4.753516 TCATCAACGGGATATTCACAGT 57.246 40.909 0.00 0.00 33.95 3.55
707 779 5.528690 ACAATCATCAACGGGATATTCACAG 59.471 40.000 0.00 0.00 33.95 3.66
709 781 5.527214 TCACAATCATCAACGGGATATTCAC 59.473 40.000 0.00 0.00 33.95 3.18
770 882 0.892755 AACTTGTGCATGCATGGAGG 59.107 50.000 25.64 18.63 0.00 4.30
771 883 1.990799 CAACTTGTGCATGCATGGAG 58.009 50.000 25.64 22.04 0.00 3.86
795 2178 1.918868 CTCTTTTGCGGGGCCGTTAC 61.919 60.000 0.00 0.00 42.09 2.50
928 2343 0.330604 AGACACTGGATGCAATGCCT 59.669 50.000 1.53 0.00 31.31 4.75
940 2366 1.244816 TGTGGTAGGTCGAGACACTG 58.755 55.000 5.55 0.00 33.44 3.66
949 3511 7.807907 CACTTAATTGTGAATTTGTGGTAGGTC 59.192 37.037 0.00 0.00 40.12 3.85
950 3512 7.504238 TCACTTAATTGTGAATTTGTGGTAGGT 59.496 33.333 0.00 0.00 43.08 3.08
955 3517 6.205784 ACGTCACTTAATTGTGAATTTGTGG 58.794 36.000 0.51 0.00 46.77 4.17
961 3523 5.431420 TGCAACGTCACTTAATTGTGAAT 57.569 34.783 0.51 0.00 46.77 2.57
963 3525 5.431420 AATGCAACGTCACTTAATTGTGA 57.569 34.783 0.00 0.00 43.72 3.58
964 3526 5.685068 TCAAATGCAACGTCACTTAATTGTG 59.315 36.000 0.00 0.00 39.15 3.33
965 3527 5.826586 TCAAATGCAACGTCACTTAATTGT 58.173 33.333 0.00 0.00 0.00 2.71
967 3529 4.917415 GCTCAAATGCAACGTCACTTAATT 59.083 37.500 0.00 0.00 0.00 1.40
969 3531 3.563808 AGCTCAAATGCAACGTCACTTAA 59.436 39.130 0.00 0.00 34.99 1.85
971 3533 1.949525 AGCTCAAATGCAACGTCACTT 59.050 42.857 0.00 0.00 34.99 3.16
972 3534 1.597742 AGCTCAAATGCAACGTCACT 58.402 45.000 0.00 0.00 34.99 3.41
975 3537 1.734465 AGCTAGCTCAAATGCAACGTC 59.266 47.619 12.68 0.00 34.99 4.34
976 3538 1.813513 AGCTAGCTCAAATGCAACGT 58.186 45.000 12.68 0.00 34.99 3.99
978 3540 3.935203 TGTCTAGCTAGCTCAAATGCAAC 59.065 43.478 23.26 9.25 34.99 4.17
979 3541 4.206477 TGTCTAGCTAGCTCAAATGCAA 57.794 40.909 23.26 0.00 34.99 4.08
980 3542 3.893326 TGTCTAGCTAGCTCAAATGCA 57.107 42.857 23.26 10.07 34.99 3.96
981 3543 3.497640 CCATGTCTAGCTAGCTCAAATGC 59.502 47.826 23.26 7.53 0.00 3.56
984 3546 2.158900 GGCCATGTCTAGCTAGCTCAAA 60.159 50.000 23.26 4.54 0.00 2.69
985 3547 1.414181 GGCCATGTCTAGCTAGCTCAA 59.586 52.381 23.26 7.79 0.00 3.02
986 3548 1.043816 GGCCATGTCTAGCTAGCTCA 58.956 55.000 23.26 14.09 0.00 4.26
988 3550 1.133199 AGAGGCCATGTCTAGCTAGCT 60.133 52.381 23.12 23.12 0.00 3.32
989 3551 1.337118 AGAGGCCATGTCTAGCTAGC 58.663 55.000 16.35 6.62 0.00 3.42
991 3553 1.957177 CGAAGAGGCCATGTCTAGCTA 59.043 52.381 5.01 0.00 0.00 3.32
992 3554 0.749649 CGAAGAGGCCATGTCTAGCT 59.250 55.000 5.01 0.00 0.00 3.32
993 3555 0.461961 ACGAAGAGGCCATGTCTAGC 59.538 55.000 5.01 0.00 0.00 3.42
994 3556 2.028130 AGACGAAGAGGCCATGTCTAG 58.972 52.381 5.01 0.00 38.09 2.43
995 3557 2.025155 GAGACGAAGAGGCCATGTCTA 58.975 52.381 5.01 0.00 39.83 2.59
998 3569 2.145397 TAGAGACGAAGAGGCCATGT 57.855 50.000 5.01 0.00 0.00 3.21
1081 3655 3.400590 GTTCGGGCACGTCGTGTC 61.401 66.667 25.18 23.44 41.85 3.67
1107 3681 2.100631 CACGGCGGACTTGATGGTC 61.101 63.158 13.24 0.00 35.66 4.02
1188 3762 2.037251 AGAGCTTACTTGGACGAAGCAA 59.963 45.455 8.41 0.00 46.46 3.91
1247 3832 4.722627 GCGTTTACAAACCAAAACTGCAAC 60.723 41.667 0.00 0.00 36.29 4.17
1259 3844 0.318360 GCACCCTGGCGTTTACAAAC 60.318 55.000 0.00 0.00 35.59 2.93
1262 3847 1.599518 CTGCACCCTGGCGTTTACA 60.600 57.895 0.00 0.00 36.28 2.41
1269 3854 0.960861 GGTTAACTCTGCACCCTGGC 60.961 60.000 5.42 0.00 0.00 4.85
1338 3957 1.904287 TAGCGTTTTGTTCCATGCCT 58.096 45.000 0.00 0.00 0.00 4.75
1374 3993 3.052081 ACTTCGAAGCCTCGCAGT 58.948 55.556 24.86 4.09 45.03 4.40
1437 4056 2.265739 GATGTGGCGCAGGAGACA 59.734 61.111 10.83 3.68 0.00 3.41
1534 4154 0.394352 CCGGGTGAGCAAATTAGCCT 60.394 55.000 0.00 0.00 34.23 4.58
1552 4532 1.211457 ACTGCACCAGATGAGAATCCC 59.789 52.381 0.00 0.00 35.18 3.85
1561 4547 1.687612 CCTCCCAACTGCACCAGAT 59.312 57.895 0.00 0.00 35.18 2.90
1676 4681 0.396811 CGAAGGACTGGGTGAGGTTT 59.603 55.000 0.00 0.00 0.00 3.27
1861 4866 2.786512 ATTGGCCAGGTTGCGGTCAT 62.787 55.000 5.11 0.00 38.12 3.06
2404 5486 3.375699 AGACATACTCCCTCCGTTTCAT 58.624 45.455 0.00 0.00 0.00 2.57
2647 5729 0.987294 CCACTGAATCCTCTGGGTGT 59.013 55.000 0.00 0.00 0.00 4.16
2649 5731 1.280457 GTCCACTGAATCCTCTGGGT 58.720 55.000 0.00 0.00 0.00 4.51
2674 5756 4.984161 ACAACTTTGAAAGATTTGGCATCG 59.016 37.500 12.53 0.00 0.00 3.84
2731 5813 0.607489 GCTGCATCAGTGTTGAGGGT 60.607 55.000 5.35 0.00 35.71 4.34
2758 5842 0.250901 ATGTGTTCACTGGCCTGGAC 60.251 55.000 14.82 5.49 0.00 4.02
2782 5866 3.853671 CCGATTCCTTGAAATCTTTTGCG 59.146 43.478 0.00 0.00 34.19 4.85
2799 5883 3.576078 TCACAATGCCTAATCCCGATT 57.424 42.857 0.00 0.00 34.93 3.34
2808 5892 1.086696 GCTTCGCTTCACAATGCCTA 58.913 50.000 0.00 0.00 0.00 3.93
2815 5899 1.800586 GTTCATCTGCTTCGCTTCACA 59.199 47.619 0.00 0.00 0.00 3.58
2816 5900 1.800586 TGTTCATCTGCTTCGCTTCAC 59.199 47.619 0.00 0.00 0.00 3.18
2819 5903 1.882912 TGTGTTCATCTGCTTCGCTT 58.117 45.000 0.00 0.00 0.00 4.68
2820 5904 2.005451 GATGTGTTCATCTGCTTCGCT 58.995 47.619 1.58 0.00 44.86 4.93
2821 5905 2.448726 GATGTGTTCATCTGCTTCGC 57.551 50.000 1.58 0.00 44.86 4.70
2830 5914 2.173519 CAAAGGCCCTGATGTGTTCAT 58.826 47.619 0.00 0.00 36.95 2.57
2831 5915 1.619654 CAAAGGCCCTGATGTGTTCA 58.380 50.000 0.00 0.00 0.00 3.18
2832 5916 0.244721 GCAAAGGCCCTGATGTGTTC 59.755 55.000 0.00 0.00 0.00 3.18
2833 5917 2.354902 GCAAAGGCCCTGATGTGTT 58.645 52.632 0.00 0.00 0.00 3.32
2834 5918 4.102113 GCAAAGGCCCTGATGTGT 57.898 55.556 0.00 0.00 0.00 3.72
2906 5990 0.104487 TCCTTTGGTCGCACGTACAA 59.896 50.000 0.00 0.00 0.00 2.41
3069 6153 5.598417 AGGGATGAGTGTATGCGCATATATA 59.402 40.000 31.14 18.91 0.00 0.86
3077 6161 3.942130 TCATAGGGATGAGTGTATGCG 57.058 47.619 0.00 0.00 37.15 4.73
3078 6162 3.990469 CGTTCATAGGGATGAGTGTATGC 59.010 47.826 0.00 0.00 43.03 3.14
3112 6196 3.055021 GGAGGTGCTTATAGGAATAGGCC 60.055 52.174 0.00 0.00 39.34 5.19
3113 6197 3.368531 CGGAGGTGCTTATAGGAATAGGC 60.369 52.174 0.00 0.00 40.24 3.93


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

AutoCloner maintained by Alex Coulton.