Multiple sequence alignment - TraesCS3D01G253200

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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 TraesCS3D01G253200 chr3D 100.000 2318 0 0 1 2318 354621006 354618689 0.000000e+00 4281.0
1 TraesCS3D01G253200 chr3A 96.053 912 20 6 1411 2318 473212481 473211582 0.000000e+00 1471.0
2 TraesCS3D01G253200 chr3A 92.147 573 28 4 1 556 473216707 473216135 0.000000e+00 793.0
3 TraesCS3D01G253200 chr3A 93.118 465 30 1 830 1294 473213177 473212715 0.000000e+00 680.0
4 TraesCS3D01G253200 chr3A 82.684 231 19 9 556 783 473213393 473213181 3.930000e-43 185.0
5 TraesCS3D01G253200 chr3A 98.684 76 1 0 1337 1412 473212718 473212643 4.020000e-28 135.0
6 TraesCS3D01G253200 chr3A 87.500 48 6 0 1471 1518 158203516 158203563 3.220000e-04 56.5
7 TraesCS3D01G253200 chr3B 95.708 862 25 7 1467 2318 455062826 455061967 0.000000e+00 1376.0
8 TraesCS3D01G253200 chr3B 90.783 792 48 9 1 787 455066071 455065300 0.000000e+00 1035.0
9 TraesCS3D01G253200 chr3B 94.028 653 28 3 829 1480 455065301 455064659 0.000000e+00 979.0
10 TraesCS3D01G253200 chr2D 97.674 43 1 0 1474 1516 445896310 445896352 8.880000e-10 75.0
11 TraesCS3D01G253200 chr2D 86.792 53 5 2 1466 1516 371786923 371786871 8.950000e-05 58.4
12 TraesCS3D01G253200 chr7A 95.122 41 2 0 1476 1516 572872152 572872112 5.350000e-07 65.8
13 TraesCS3D01G253200 chr7B 86.207 58 7 1 1462 1518 658189905 658189962 6.920000e-06 62.1
14 TraesCS3D01G253200 chr1A 89.583 48 5 0 1469 1516 392778747 392778700 6.920000e-06 62.1
15 TraesCS3D01G253200 chr1B 89.130 46 5 0 1471 1516 658624078 658624123 8.950000e-05 58.4


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 TraesCS3D01G253200 chr3D 354618689 354621006 2317 True 4281.0 4281 100.000000 1 2318 1 chr3D.!!$R1 2317
1 TraesCS3D01G253200 chr3A 473211582 473216707 5125 True 652.8 1471 92.537200 1 2318 5 chr3A.!!$R1 2317
2 TraesCS3D01G253200 chr3B 455061967 455066071 4104 True 1130.0 1376 93.506333 1 2318 3 chr3B.!!$R1 2317

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
827 3595 0.108186 AAATCGATCTGTGCAGCCGA 60.108 50.0 14.77 14.77 37.52 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1669 6503 0.958382 TTGTGATGGCTGTTACGGGC 60.958 55.0 11.01 11.01 35.76 6.13 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
73 91 3.009805 GGTCCTACCTTTGGTGGTTACAT 59.990 47.826 0.00 0.00 41.22 2.29
74 92 4.007659 GTCCTACCTTTGGTGGTTACATG 58.992 47.826 0.00 0.00 41.22 3.21
75 93 3.653836 TCCTACCTTTGGTGGTTACATGT 59.346 43.478 2.69 2.69 41.22 3.21
80 100 4.141344 ACCTTTGGTGGTTACATGTAGTGT 60.141 41.667 5.56 0.00 38.63 3.55
99 119 7.824289 TGTAGTGTAGAAATGCTGCTTAAGATT 59.176 33.333 6.67 0.00 0.00 2.40
120 140 7.234355 AGATTTCTTCCTGTTAAACCATGTCT 58.766 34.615 0.00 0.00 0.00 3.41
176 197 2.306805 TCATGCTTTCCAGGTCAGTGAT 59.693 45.455 0.00 0.00 0.00 3.06
185 206 7.418025 GCTTTCCAGGTCAGTGATAACTACTAT 60.418 40.741 0.00 0.00 0.00 2.12
389 410 6.189859 AGGTTGAATATGATGAATGGTGTGT 58.810 36.000 0.00 0.00 0.00 3.72
390 411 6.095860 AGGTTGAATATGATGAATGGTGTGTG 59.904 38.462 0.00 0.00 0.00 3.82
500 521 8.947055 ATTATTGGCTTTCCACATTAATTGTC 57.053 30.769 0.00 0.00 43.33 3.18
530 552 0.250467 TGCTTGGAGTTGGAGTGCTC 60.250 55.000 0.00 0.00 0.00 4.26
548 570 2.742053 GCTCCTGATGCGTGTTTTTCTA 59.258 45.455 0.00 0.00 0.00 2.10
564 3328 5.794687 TTTTCTATTACACATGTGCTCGG 57.205 39.130 25.68 12.05 0.00 4.63
568 3332 2.078849 TTACACATGTGCTCGGTGAG 57.921 50.000 25.68 0.00 36.42 3.51
595 3360 8.774586 GTGCTAACTTATATCAACTGGGTATTG 58.225 37.037 0.00 0.00 0.00 1.90
608 3373 1.084289 GGTATTGTGCGTGGGAACTC 58.916 55.000 0.00 0.00 0.00 3.01
635 3400 8.801715 AGTATGCAACTTGTATTTGTCTTTTG 57.198 30.769 0.00 0.00 33.35 2.44
636 3401 7.867403 AGTATGCAACTTGTATTTGTCTTTTGG 59.133 33.333 0.00 0.00 33.35 3.28
637 3402 5.971763 TGCAACTTGTATTTGTCTTTTGGT 58.028 33.333 0.00 0.00 0.00 3.67
638 3403 6.402222 TGCAACTTGTATTTGTCTTTTGGTT 58.598 32.000 0.00 0.00 0.00 3.67
639 3404 7.548097 TGCAACTTGTATTTGTCTTTTGGTTA 58.452 30.769 0.00 0.00 0.00 2.85
640 3405 8.200792 TGCAACTTGTATTTGTCTTTTGGTTAT 58.799 29.630 0.00 0.00 0.00 1.89
641 3406 8.699749 GCAACTTGTATTTGTCTTTTGGTTATC 58.300 33.333 0.00 0.00 0.00 1.75
642 3407 9.743057 CAACTTGTATTTGTCTTTTGGTTATCA 57.257 29.630 0.00 0.00 0.00 2.15
643 3408 9.965824 AACTTGTATTTGTCTTTTGGTTATCAG 57.034 29.630 0.00 0.00 0.00 2.90
644 3409 9.349713 ACTTGTATTTGTCTTTTGGTTATCAGA 57.650 29.630 0.00 0.00 0.00 3.27
647 3412 8.739039 TGTATTTGTCTTTTGGTTATCAGATGG 58.261 33.333 0.00 0.00 0.00 3.51
648 3413 6.588719 TTTGTCTTTTGGTTATCAGATGGG 57.411 37.500 0.00 0.00 0.00 4.00
649 3414 4.016444 TGTCTTTTGGTTATCAGATGGGC 58.984 43.478 0.00 0.00 0.00 5.36
650 3415 4.016444 GTCTTTTGGTTATCAGATGGGCA 58.984 43.478 0.00 0.00 0.00 5.36
666 3431 4.519540 TGGGCATTACTTTTTCTTCTGC 57.480 40.909 0.00 0.00 0.00 4.26
674 3439 2.737252 ACTTTTTCTTCTGCCGATCGTC 59.263 45.455 15.09 0.47 0.00 4.20
675 3440 2.743636 TTTTCTTCTGCCGATCGTCT 57.256 45.000 15.09 0.00 0.00 4.18
687 3454 2.597305 CCGATCGTCTTACGGTTTCTTG 59.403 50.000 15.09 0.00 42.81 3.02
688 3455 2.027688 CGATCGTCTTACGGTTTCTTGC 59.972 50.000 7.03 0.00 42.81 4.01
693 3460 3.432252 CGTCTTACGGTTTCTTGCTTCAT 59.568 43.478 0.00 0.00 38.08 2.57
712 3479 6.518200 GCTTCATCCTTTGAATTGGTTGGTTA 60.518 38.462 0.00 0.00 43.30 2.85
744 3511 5.418840 ACGTGAGCATCCAAGGAAATTTAAT 59.581 36.000 0.00 0.00 0.00 1.40
779 3547 5.616488 TTTAACAGTCAAAATCTACGCCC 57.384 39.130 0.00 0.00 0.00 6.13
786 3554 4.163458 AGTCAAAATCTACGCCCTATGGAA 59.837 41.667 0.00 0.00 0.00 3.53
787 3555 5.063880 GTCAAAATCTACGCCCTATGGAAT 58.936 41.667 0.00 0.00 0.00 3.01
788 3556 5.179555 GTCAAAATCTACGCCCTATGGAATC 59.820 44.000 0.00 0.00 0.00 2.52
789 3557 3.594603 AATCTACGCCCTATGGAATCG 57.405 47.619 0.00 0.00 0.00 3.34
790 3558 0.601558 TCTACGCCCTATGGAATCGC 59.398 55.000 0.00 0.00 0.00 4.58
792 3560 2.029073 CGCCCTATGGAATCGCGT 59.971 61.111 5.77 0.00 38.12 6.01
793 3561 2.310233 CGCCCTATGGAATCGCGTG 61.310 63.158 5.77 0.00 38.12 5.34
794 3562 2.607892 GCCCTATGGAATCGCGTGC 61.608 63.158 5.77 0.00 0.00 5.34
795 3563 1.227527 CCCTATGGAATCGCGTGCA 60.228 57.895 5.77 0.00 0.00 4.57
796 3564 1.498865 CCCTATGGAATCGCGTGCAC 61.499 60.000 6.82 6.82 0.00 4.57
797 3565 0.809636 CCTATGGAATCGCGTGCACA 60.810 55.000 18.64 2.07 0.00 4.57
798 3566 1.220529 CTATGGAATCGCGTGCACAT 58.779 50.000 18.64 9.94 0.00 3.21
799 3567 0.936600 TATGGAATCGCGTGCACATG 59.063 50.000 18.64 8.39 0.00 3.21
800 3568 0.744057 ATGGAATCGCGTGCACATGA 60.744 50.000 18.64 13.97 0.00 3.07
801 3569 0.952984 TGGAATCGCGTGCACATGAA 60.953 50.000 18.64 0.00 0.00 2.57
802 3570 0.167908 GGAATCGCGTGCACATGAAA 59.832 50.000 18.64 0.00 0.00 2.69
803 3571 1.202177 GGAATCGCGTGCACATGAAAT 60.202 47.619 18.64 7.12 0.00 2.17
804 3572 2.518949 GAATCGCGTGCACATGAAATT 58.481 42.857 18.64 8.47 0.00 1.82
805 3573 1.898938 ATCGCGTGCACATGAAATTG 58.101 45.000 18.64 0.00 0.00 2.32
806 3574 0.728803 TCGCGTGCACATGAAATTGC 60.729 50.000 18.64 8.32 39.33 3.56
807 3575 1.697770 GCGTGCACATGAAATTGCG 59.302 52.632 18.64 0.00 41.96 4.85
808 3576 0.728803 GCGTGCACATGAAATTGCGA 60.729 50.000 18.64 0.00 41.96 5.10
809 3577 1.684142 CGTGCACATGAAATTGCGAA 58.316 45.000 18.64 0.00 41.96 4.70
810 3578 2.049959 CGTGCACATGAAATTGCGAAA 58.950 42.857 18.64 0.00 41.96 3.46
811 3579 2.662637 CGTGCACATGAAATTGCGAAAT 59.337 40.909 18.64 0.00 41.96 2.17
812 3580 3.241426 CGTGCACATGAAATTGCGAAATC 60.241 43.478 18.64 0.00 41.96 2.17
813 3581 2.916089 TGCACATGAAATTGCGAAATCG 59.084 40.909 0.00 0.00 41.96 3.34
814 3582 3.170505 GCACATGAAATTGCGAAATCGA 58.829 40.909 7.06 0.00 43.02 3.59
815 3583 3.792956 GCACATGAAATTGCGAAATCGAT 59.207 39.130 7.06 0.00 43.02 3.59
816 3584 4.085924 GCACATGAAATTGCGAAATCGATC 60.086 41.667 7.06 0.00 43.02 3.69
817 3585 5.268544 CACATGAAATTGCGAAATCGATCT 58.731 37.500 7.06 0.00 43.02 2.75
818 3586 5.170803 CACATGAAATTGCGAAATCGATCTG 59.829 40.000 7.06 0.00 43.02 2.90
819 3587 4.944962 TGAAATTGCGAAATCGATCTGT 57.055 36.364 7.06 0.00 43.02 3.41
820 3588 4.650985 TGAAATTGCGAAATCGATCTGTG 58.349 39.130 7.06 0.00 43.02 3.66
821 3589 2.744787 ATTGCGAAATCGATCTGTGC 57.255 45.000 7.06 1.50 43.02 4.57
822 3590 1.437625 TTGCGAAATCGATCTGTGCA 58.562 45.000 7.06 4.38 43.02 4.57
823 3591 1.001624 TGCGAAATCGATCTGTGCAG 58.998 50.000 7.06 0.00 43.02 4.41
824 3592 0.315706 GCGAAATCGATCTGTGCAGC 60.316 55.000 7.06 0.00 43.02 5.25
825 3593 0.302890 CGAAATCGATCTGTGCAGCC 59.697 55.000 0.00 0.00 43.02 4.85
826 3594 0.302890 GAAATCGATCTGTGCAGCCG 59.697 55.000 0.00 7.23 0.00 5.52
827 3595 0.108186 AAATCGATCTGTGCAGCCGA 60.108 50.000 14.77 14.77 37.52 5.54
828 3596 0.108186 AATCGATCTGTGCAGCCGAA 60.108 50.000 15.79 5.28 37.03 4.30
897 3665 0.609406 GGAGCCAAACCCACTCTTCC 60.609 60.000 0.00 0.00 0.00 3.46
984 3752 3.067461 CCACAATTTCACCGAAGAAACCA 59.933 43.478 4.70 0.00 40.03 3.67
985 3753 4.440802 CCACAATTTCACCGAAGAAACCAA 60.441 41.667 4.70 0.00 40.03 3.67
993 3761 2.303175 CCGAAGAAACCAAAAGACCCA 58.697 47.619 0.00 0.00 0.00 4.51
995 3763 2.293399 CGAAGAAACCAAAAGACCCAGG 59.707 50.000 0.00 0.00 0.00 4.45
1063 3831 4.717629 CGAAGCCGTCGTCCAGCA 62.718 66.667 0.00 0.00 45.09 4.41
1132 3900 2.558795 GCGGATATAGAGCCTGACAAGA 59.441 50.000 0.00 0.00 0.00 3.02
1148 3916 0.179073 AAGATCAAGGGCGACATCCG 60.179 55.000 0.00 0.00 42.21 4.18
1286 4054 0.107312 GACTGGACAGCTGATGGCAT 60.107 55.000 23.35 0.00 39.54 4.40
1294 4108 3.340727 GCTGATGGCATTTCACAGC 57.659 52.632 19.14 19.14 44.88 4.40
1303 4117 2.817901 GCATTTCACAGCCATCAATCC 58.182 47.619 0.00 0.00 0.00 3.01
1304 4118 2.166870 GCATTTCACAGCCATCAATCCA 59.833 45.455 0.00 0.00 0.00 3.41
1305 4119 3.737047 GCATTTCACAGCCATCAATCCAG 60.737 47.826 0.00 0.00 0.00 3.86
1306 4120 2.133281 TTCACAGCCATCAATCCAGG 57.867 50.000 0.00 0.00 0.00 4.45
1307 4121 1.288188 TCACAGCCATCAATCCAGGA 58.712 50.000 0.00 0.00 0.00 3.86
1308 4122 1.634973 TCACAGCCATCAATCCAGGAA 59.365 47.619 0.00 0.00 0.00 3.36
1309 4123 1.747355 CACAGCCATCAATCCAGGAAC 59.253 52.381 0.00 0.00 0.00 3.62
1310 4124 1.019673 CAGCCATCAATCCAGGAACG 58.980 55.000 0.00 0.00 0.00 3.95
1311 4125 0.911769 AGCCATCAATCCAGGAACGA 59.088 50.000 0.00 0.00 0.00 3.85
1312 4126 1.017387 GCCATCAATCCAGGAACGAC 58.983 55.000 0.00 0.00 0.00 4.34
1313 4127 1.678728 GCCATCAATCCAGGAACGACA 60.679 52.381 0.00 0.00 0.00 4.35
1314 4128 2.009774 CCATCAATCCAGGAACGACAC 58.990 52.381 0.00 0.00 0.00 3.67
1315 4129 2.355108 CCATCAATCCAGGAACGACACT 60.355 50.000 0.00 0.00 0.00 3.55
1316 4130 2.455674 TCAATCCAGGAACGACACTG 57.544 50.000 0.00 0.00 34.54 3.66
1317 4131 1.967779 TCAATCCAGGAACGACACTGA 59.032 47.619 0.00 0.00 36.86 3.41
1318 4132 2.567169 TCAATCCAGGAACGACACTGAT 59.433 45.455 0.00 0.00 36.86 2.90
1319 4133 3.767131 TCAATCCAGGAACGACACTGATA 59.233 43.478 0.00 0.00 36.86 2.15
1320 4134 4.405680 TCAATCCAGGAACGACACTGATAT 59.594 41.667 0.00 0.00 36.86 1.63
1321 4135 3.801114 TCCAGGAACGACACTGATATG 57.199 47.619 0.00 0.00 36.86 1.78
1322 4136 3.361786 TCCAGGAACGACACTGATATGA 58.638 45.455 0.00 0.00 36.86 2.15
1323 4137 3.130516 TCCAGGAACGACACTGATATGAC 59.869 47.826 0.00 0.00 36.86 3.06
1324 4138 3.131223 CCAGGAACGACACTGATATGACT 59.869 47.826 0.00 0.00 36.86 3.41
1325 4139 4.108336 CAGGAACGACACTGATATGACTG 58.892 47.826 0.00 0.00 36.86 3.51
1326 4140 3.131223 AGGAACGACACTGATATGACTGG 59.869 47.826 0.00 0.00 0.00 4.00
1327 4141 3.119101 GGAACGACACTGATATGACTGGT 60.119 47.826 0.00 0.00 0.00 4.00
1328 4142 4.097437 GGAACGACACTGATATGACTGGTA 59.903 45.833 0.00 0.00 0.00 3.25
1329 4143 5.393787 GGAACGACACTGATATGACTGGTAA 60.394 44.000 0.00 0.00 0.00 2.85
1330 4144 4.995124 ACGACACTGATATGACTGGTAAC 58.005 43.478 0.00 0.00 0.00 2.50
1331 4145 4.142227 ACGACACTGATATGACTGGTAACC 60.142 45.833 0.00 0.00 0.00 2.85
1332 4146 4.142249 CGACACTGATATGACTGGTAACCA 60.142 45.833 0.00 0.00 0.00 3.67
1333 4147 5.451937 CGACACTGATATGACTGGTAACCAT 60.452 44.000 0.00 0.00 30.82 3.55
1334 4148 5.918608 ACACTGATATGACTGGTAACCATC 58.081 41.667 0.00 0.00 30.82 3.51
1335 4149 5.663106 ACACTGATATGACTGGTAACCATCT 59.337 40.000 0.00 0.00 30.82 2.90
1336 4150 6.839134 ACACTGATATGACTGGTAACCATCTA 59.161 38.462 0.00 0.00 30.82 1.98
1337 4151 7.148641 CACTGATATGACTGGTAACCATCTAC 58.851 42.308 0.00 0.00 30.82 2.59
1338 4152 6.839134 ACTGATATGACTGGTAACCATCTACA 59.161 38.462 0.00 0.00 30.82 2.74
1339 4153 7.014711 ACTGATATGACTGGTAACCATCTACAG 59.985 40.741 0.00 0.00 30.82 2.74
1421 4398 6.253946 TGTACTCTGATCTATGTCTCTCCA 57.746 41.667 0.00 0.00 0.00 3.86
1427 4404 8.004215 ACTCTGATCTATGTCTCTCCAATAGTT 58.996 37.037 0.00 0.00 0.00 2.24
1481 4459 3.245052 GGGCAGCAAATATGATACTCCCT 60.245 47.826 0.00 0.00 30.21 4.20
1482 4460 4.401925 GGCAGCAAATATGATACTCCCTT 58.598 43.478 0.00 0.00 0.00 3.95
1485 4463 5.300286 GCAGCAAATATGATACTCCCTTTGT 59.700 40.000 0.00 0.00 0.00 2.83
1486 4464 6.183360 GCAGCAAATATGATACTCCCTTTGTT 60.183 38.462 0.00 0.00 0.00 2.83
1496 6326 8.348285 TGATACTCCCTTTGTTCCAAAATAAG 57.652 34.615 0.00 0.00 0.00 1.73
1503 6333 3.907894 TGTTCCAAAATAAGTGTCGCC 57.092 42.857 0.00 0.00 0.00 5.54
1599 6433 1.933181 GCAAATTGGCGGGCTAATTTC 59.067 47.619 20.33 13.44 42.44 2.17
1669 6503 1.207593 CTCGCTTGCAAGGAAACCG 59.792 57.895 27.10 20.38 0.00 4.44
1682 6516 3.479127 AAACCGCCCGTAACAGCCA 62.479 57.895 0.00 0.00 0.00 4.75
1787 6624 3.040147 ACACCAGGACGTCAGTAATTG 57.960 47.619 18.91 8.54 0.00 2.32
1789 6626 1.975680 ACCAGGACGTCAGTAATTGGT 59.024 47.619 18.91 16.02 35.16 3.67
1824 6661 4.880120 TCTACACTACCTACACGAGATTGG 59.120 45.833 0.00 0.00 0.00 3.16
2035 6872 3.517500 ACAAAAAGAGGAAAAGCCCACAA 59.482 39.130 0.00 0.00 37.37 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 91 6.697395 TCTTAAGCAGCATTTCTACACTACA 58.303 36.000 0.00 0.00 0.00 2.74
74 92 7.778470 ATCTTAAGCAGCATTTCTACACTAC 57.222 36.000 0.00 0.00 0.00 2.73
75 93 8.792830 AAATCTTAAGCAGCATTTCTACACTA 57.207 30.769 0.00 0.00 0.00 2.74
80 100 7.831193 AGGAAGAAATCTTAAGCAGCATTTCTA 59.169 33.333 21.23 0.00 42.26 2.10
99 119 5.073144 AGGAGACATGGTTTAACAGGAAGAA 59.927 40.000 0.00 0.00 0.00 2.52
157 178 4.018960 AGTTATCACTGACCTGGAAAGCAT 60.019 41.667 0.00 0.00 0.00 3.79
176 197 5.832060 GGTCAAGTCAGGCCTATAGTAGTTA 59.168 44.000 3.98 0.00 0.00 2.24
185 206 0.324943 GCTTGGTCAAGTCAGGCCTA 59.675 55.000 3.98 0.00 40.45 3.93
357 378 9.293404 CATTCATCATATTCAACCTCCATACTT 57.707 33.333 0.00 0.00 0.00 2.24
389 410 0.250858 ACTTGTGCCAGTATGCAGCA 60.251 50.000 0.00 0.00 43.02 4.41
390 411 0.883833 AACTTGTGCCAGTATGCAGC 59.116 50.000 0.00 0.00 43.02 5.25
500 521 1.952296 ACTCCAAGCAACTCAGCAAAG 59.048 47.619 0.00 0.00 36.85 2.77
530 552 6.021596 GTGTAATAGAAAAACACGCATCAGG 58.978 40.000 0.00 0.00 34.72 3.86
548 570 2.621338 CTCACCGAGCACATGTGTAAT 58.379 47.619 26.01 13.20 0.00 1.89
564 3328 6.480320 CCAGTTGATATAAGTTAGCACCTCAC 59.520 42.308 0.00 0.00 0.00 3.51
568 3332 5.681639 ACCCAGTTGATATAAGTTAGCACC 58.318 41.667 0.00 0.00 0.00 5.01
595 3360 1.732259 CATACTTGAGTTCCCACGCAC 59.268 52.381 0.00 0.00 31.62 5.34
623 3388 7.147915 GCCCATCTGATAACCAAAAGACAAATA 60.148 37.037 0.00 0.00 0.00 1.40
630 3395 5.603170 AATGCCCATCTGATAACCAAAAG 57.397 39.130 0.00 0.00 0.00 2.27
633 3398 5.387113 AGTAATGCCCATCTGATAACCAA 57.613 39.130 0.00 0.00 0.00 3.67
634 3399 5.387113 AAGTAATGCCCATCTGATAACCA 57.613 39.130 0.00 0.00 0.00 3.67
635 3400 6.715347 AAAAGTAATGCCCATCTGATAACC 57.285 37.500 0.00 0.00 0.00 2.85
636 3401 8.000780 AGAAAAAGTAATGCCCATCTGATAAC 57.999 34.615 0.00 0.00 0.00 1.89
637 3402 8.593945 AAGAAAAAGTAATGCCCATCTGATAA 57.406 30.769 0.00 0.00 0.00 1.75
638 3403 8.055181 AGAAGAAAAAGTAATGCCCATCTGATA 58.945 33.333 0.00 0.00 0.00 2.15
639 3404 6.894103 AGAAGAAAAAGTAATGCCCATCTGAT 59.106 34.615 0.00 0.00 0.00 2.90
640 3405 6.151648 CAGAAGAAAAAGTAATGCCCATCTGA 59.848 38.462 0.00 0.00 33.11 3.27
641 3406 6.327934 CAGAAGAAAAAGTAATGCCCATCTG 58.672 40.000 0.00 0.00 0.00 2.90
642 3407 5.105595 GCAGAAGAAAAAGTAATGCCCATCT 60.106 40.000 0.00 0.00 0.00 2.90
643 3408 5.105063 GCAGAAGAAAAAGTAATGCCCATC 58.895 41.667 0.00 0.00 0.00 3.51
644 3409 4.081476 GGCAGAAGAAAAAGTAATGCCCAT 60.081 41.667 1.87 0.00 44.67 4.00
645 3410 3.258123 GGCAGAAGAAAAAGTAATGCCCA 59.742 43.478 1.87 0.00 44.67 5.36
646 3411 3.849911 GGCAGAAGAAAAAGTAATGCCC 58.150 45.455 1.87 0.00 44.67 5.36
647 3412 3.190535 TCGGCAGAAGAAAAAGTAATGCC 59.809 43.478 3.24 3.24 46.44 4.40
648 3413 4.419522 TCGGCAGAAGAAAAAGTAATGC 57.580 40.909 0.00 0.00 0.00 3.56
649 3414 5.163854 ACGATCGGCAGAAGAAAAAGTAATG 60.164 40.000 20.98 0.00 0.00 1.90
650 3415 4.935808 ACGATCGGCAGAAGAAAAAGTAAT 59.064 37.500 20.98 0.00 0.00 1.89
666 3431 2.556534 AGAAACCGTAAGACGATCGG 57.443 50.000 20.98 2.21 46.05 4.18
674 3439 4.003648 AGGATGAAGCAAGAAACCGTAAG 58.996 43.478 0.00 0.00 0.00 2.34
675 3440 4.015872 AGGATGAAGCAAGAAACCGTAA 57.984 40.909 0.00 0.00 0.00 3.18
693 3460 6.800072 ACTTTAACCAACCAATTCAAAGGA 57.200 33.333 0.00 0.00 0.00 3.36
712 3479 4.876107 CCTTGGATGCTCACGTAATACTTT 59.124 41.667 0.00 0.00 0.00 2.66
720 3487 2.496899 ATTTCCTTGGATGCTCACGT 57.503 45.000 0.00 0.00 0.00 4.49
744 3511 2.952978 ACTGTTAAATTGTTCCGTGGCA 59.047 40.909 0.00 0.00 0.00 4.92
779 3547 1.070376 CATGTGCACGCGATTCCATAG 60.070 52.381 15.93 1.61 0.00 2.23
786 3554 1.898938 CAATTTCATGTGCACGCGAT 58.101 45.000 15.93 0.00 0.00 4.58
787 3555 0.728803 GCAATTTCATGTGCACGCGA 60.729 50.000 15.93 8.20 40.58 5.87
788 3556 1.697770 GCAATTTCATGTGCACGCG 59.302 52.632 13.13 3.53 40.58 6.01
789 3557 0.728803 TCGCAATTTCATGTGCACGC 60.729 50.000 13.13 5.68 40.94 5.34
790 3558 1.684142 TTCGCAATTTCATGTGCACG 58.316 45.000 13.13 0.00 40.94 5.34
791 3559 3.241426 CGATTTCGCAATTTCATGTGCAC 60.241 43.478 10.75 10.75 40.94 4.57
792 3560 2.916089 CGATTTCGCAATTTCATGTGCA 59.084 40.909 6.80 0.00 40.94 4.57
793 3561 3.170505 TCGATTTCGCAATTTCATGTGC 58.829 40.909 0.00 0.00 39.60 4.57
794 3562 5.170803 CAGATCGATTTCGCAATTTCATGTG 59.829 40.000 0.00 0.00 39.60 3.21
795 3563 5.163723 ACAGATCGATTTCGCAATTTCATGT 60.164 36.000 0.00 0.00 39.60 3.21
796 3564 5.170803 CACAGATCGATTTCGCAATTTCATG 59.829 40.000 0.00 0.00 39.60 3.07
797 3565 5.268544 CACAGATCGATTTCGCAATTTCAT 58.731 37.500 0.00 0.00 39.60 2.57
798 3566 4.650985 CACAGATCGATTTCGCAATTTCA 58.349 39.130 0.00 0.00 39.60 2.69
799 3567 3.479949 GCACAGATCGATTTCGCAATTTC 59.520 43.478 0.00 0.00 39.60 2.17
800 3568 3.119884 TGCACAGATCGATTTCGCAATTT 60.120 39.130 0.00 0.00 39.60 1.82
801 3569 2.419673 TGCACAGATCGATTTCGCAATT 59.580 40.909 0.00 0.00 39.60 2.32
802 3570 2.009051 TGCACAGATCGATTTCGCAAT 58.991 42.857 0.00 0.00 39.60 3.56
803 3571 1.394572 CTGCACAGATCGATTTCGCAA 59.605 47.619 0.00 0.00 39.60 4.85
804 3572 1.001624 CTGCACAGATCGATTTCGCA 58.998 50.000 0.00 4.41 39.60 5.10
805 3573 0.315706 GCTGCACAGATCGATTTCGC 60.316 55.000 0.00 0.00 39.60 4.70
806 3574 0.302890 GGCTGCACAGATCGATTTCG 59.697 55.000 0.00 0.00 41.45 3.46
807 3575 0.302890 CGGCTGCACAGATCGATTTC 59.697 55.000 0.00 0.00 0.00 2.17
808 3576 0.108186 TCGGCTGCACAGATCGATTT 60.108 50.000 0.00 0.00 33.33 2.17
809 3577 0.108186 TTCGGCTGCACAGATCGATT 60.108 50.000 14.14 0.00 36.28 3.34
810 3578 0.108186 TTTCGGCTGCACAGATCGAT 60.108 50.000 14.14 0.00 36.28 3.59
811 3579 0.320334 TTTTCGGCTGCACAGATCGA 60.320 50.000 0.50 7.09 35.23 3.59
812 3580 0.095935 CTTTTCGGCTGCACAGATCG 59.904 55.000 0.50 4.80 0.00 3.69
813 3581 1.129437 GACTTTTCGGCTGCACAGATC 59.871 52.381 0.50 0.00 0.00 2.75
814 3582 1.160137 GACTTTTCGGCTGCACAGAT 58.840 50.000 0.50 0.00 0.00 2.90
815 3583 1.221466 CGACTTTTCGGCTGCACAGA 61.221 55.000 0.50 0.00 41.89 3.41
816 3584 1.205064 CGACTTTTCGGCTGCACAG 59.795 57.895 0.50 0.00 41.89 3.66
817 3585 0.602638 ATCGACTTTTCGGCTGCACA 60.603 50.000 0.50 0.00 45.90 4.57
818 3586 0.517316 AATCGACTTTTCGGCTGCAC 59.483 50.000 0.50 0.00 45.90 4.57
819 3587 0.796312 GAATCGACTTTTCGGCTGCA 59.204 50.000 0.50 0.00 45.90 4.41
820 3588 0.097150 GGAATCGACTTTTCGGCTGC 59.903 55.000 0.00 0.00 45.90 5.25
821 3589 1.726853 AGGAATCGACTTTTCGGCTG 58.273 50.000 0.00 0.00 45.90 4.85
822 3590 2.076863 CAAGGAATCGACTTTTCGGCT 58.923 47.619 0.00 0.00 45.90 5.52
823 3591 1.130561 CCAAGGAATCGACTTTTCGGC 59.869 52.381 0.00 0.00 45.90 5.54
824 3592 2.415512 GTCCAAGGAATCGACTTTTCGG 59.584 50.000 0.00 0.00 45.90 4.30
826 3594 2.159693 GCGTCCAAGGAATCGACTTTTC 60.160 50.000 3.61 0.00 0.00 2.29
827 3595 1.804748 GCGTCCAAGGAATCGACTTTT 59.195 47.619 3.61 0.00 0.00 2.27
828 3596 1.439679 GCGTCCAAGGAATCGACTTT 58.560 50.000 3.61 0.00 0.00 2.66
984 3752 1.079073 CATGCCCCCTGGGTCTTTT 59.921 57.895 12.71 0.00 46.51 2.27
985 3753 2.155197 GACATGCCCCCTGGGTCTTT 62.155 60.000 12.71 0.00 46.51 2.52
993 3761 3.402681 CCGACTGACATGCCCCCT 61.403 66.667 0.00 0.00 0.00 4.79
1116 3884 4.590647 CCCTTGATCTTGTCAGGCTCTATA 59.409 45.833 0.00 0.00 38.29 1.31
1132 3900 2.505982 CCGGATGTCGCCCTTGAT 59.494 61.111 0.00 0.00 37.59 2.57
1257 4025 0.250295 CTGTCCAGTCCAAGCCGAAA 60.250 55.000 0.00 0.00 0.00 3.46
1286 4054 2.041485 TCCTGGATTGATGGCTGTGAAA 59.959 45.455 0.00 0.00 0.00 2.69
1294 4108 2.009774 GTGTCGTTCCTGGATTGATGG 58.990 52.381 0.00 0.00 0.00 3.51
1295 4109 2.674852 CAGTGTCGTTCCTGGATTGATG 59.325 50.000 0.00 0.00 0.00 3.07
1296 4110 2.567169 TCAGTGTCGTTCCTGGATTGAT 59.433 45.455 0.00 0.00 0.00 2.57
1297 4111 1.967779 TCAGTGTCGTTCCTGGATTGA 59.032 47.619 0.00 0.00 0.00 2.57
1298 4112 2.455674 TCAGTGTCGTTCCTGGATTG 57.544 50.000 0.00 0.00 0.00 2.67
1299 4113 4.405680 TCATATCAGTGTCGTTCCTGGATT 59.594 41.667 0.00 0.00 0.00 3.01
1300 4114 3.960755 TCATATCAGTGTCGTTCCTGGAT 59.039 43.478 0.00 0.00 0.00 3.41
1301 4115 3.130516 GTCATATCAGTGTCGTTCCTGGA 59.869 47.826 0.00 0.00 0.00 3.86
1302 4116 3.131223 AGTCATATCAGTGTCGTTCCTGG 59.869 47.826 0.00 0.00 0.00 4.45
1303 4117 4.108336 CAGTCATATCAGTGTCGTTCCTG 58.892 47.826 0.00 0.00 0.00 3.86
1304 4118 3.131223 CCAGTCATATCAGTGTCGTTCCT 59.869 47.826 0.00 0.00 0.00 3.36
1305 4119 3.119101 ACCAGTCATATCAGTGTCGTTCC 60.119 47.826 0.00 0.00 0.00 3.62
1306 4120 4.111375 ACCAGTCATATCAGTGTCGTTC 57.889 45.455 0.00 0.00 0.00 3.95
1307 4121 5.408356 GTTACCAGTCATATCAGTGTCGTT 58.592 41.667 0.00 0.00 0.00 3.85
1308 4122 4.142227 GGTTACCAGTCATATCAGTGTCGT 60.142 45.833 0.00 0.00 0.00 4.34
1309 4123 4.142249 TGGTTACCAGTCATATCAGTGTCG 60.142 45.833 0.00 0.00 0.00 4.35
1310 4124 5.339008 TGGTTACCAGTCATATCAGTGTC 57.661 43.478 0.00 0.00 0.00 3.67
1311 4125 5.663106 AGATGGTTACCAGTCATATCAGTGT 59.337 40.000 10.74 0.00 36.75 3.55
1312 4126 6.166984 AGATGGTTACCAGTCATATCAGTG 57.833 41.667 10.74 0.00 36.75 3.66
1313 4127 6.839134 TGTAGATGGTTACCAGTCATATCAGT 59.161 38.462 10.74 0.00 36.75 3.41
1314 4128 7.290110 TGTAGATGGTTACCAGTCATATCAG 57.710 40.000 10.74 0.00 36.75 2.90
1315 4129 6.267699 CCTGTAGATGGTTACCAGTCATATCA 59.732 42.308 10.74 2.33 36.75 2.15
1316 4130 6.692486 CCTGTAGATGGTTACCAGTCATATC 58.308 44.000 10.74 1.00 36.75 1.63
1317 4131 5.012148 GCCTGTAGATGGTTACCAGTCATAT 59.988 44.000 10.74 0.00 36.75 1.78
1318 4132 4.344102 GCCTGTAGATGGTTACCAGTCATA 59.656 45.833 10.74 0.00 36.75 2.15
1319 4133 3.134804 GCCTGTAGATGGTTACCAGTCAT 59.865 47.826 10.74 0.00 36.75 3.06
1320 4134 2.500098 GCCTGTAGATGGTTACCAGTCA 59.500 50.000 10.74 5.47 36.75 3.41
1321 4135 2.481449 CGCCTGTAGATGGTTACCAGTC 60.481 54.545 10.74 7.85 36.75 3.51
1322 4136 1.480954 CGCCTGTAGATGGTTACCAGT 59.519 52.381 10.74 2.07 36.75 4.00
1323 4137 1.754803 TCGCCTGTAGATGGTTACCAG 59.245 52.381 10.74 0.00 36.75 4.00
1324 4138 1.479323 GTCGCCTGTAGATGGTTACCA 59.521 52.381 6.53 6.53 38.19 3.25
1325 4139 1.535437 CGTCGCCTGTAGATGGTTACC 60.535 57.143 0.00 0.00 0.00 2.85
1326 4140 1.535437 CCGTCGCCTGTAGATGGTTAC 60.535 57.143 0.00 0.00 39.36 2.50
1327 4141 0.742505 CCGTCGCCTGTAGATGGTTA 59.257 55.000 0.00 0.00 39.36 2.85
1328 4142 1.515954 CCGTCGCCTGTAGATGGTT 59.484 57.895 0.00 0.00 39.36 3.67
1329 4143 3.077519 GCCGTCGCCTGTAGATGGT 62.078 63.158 6.36 0.00 44.51 3.55
1330 4144 2.279517 GCCGTCGCCTGTAGATGG 60.280 66.667 0.39 0.39 45.25 3.51
1351 4165 4.959596 TGAAATCTTCAGCAGCATCTTC 57.040 40.909 0.00 0.00 34.08 2.87
1485 4463 2.768698 TCGGCGACACTTATTTTGGAA 58.231 42.857 4.99 0.00 0.00 3.53
1486 4464 2.459060 TCGGCGACACTTATTTTGGA 57.541 45.000 4.99 0.00 0.00 3.53
1496 6326 4.388790 GTTTTGTACTAAATCGGCGACAC 58.611 43.478 13.76 4.22 0.00 3.67
1503 6333 4.497300 TCCCTCCGTTTTGTACTAAATCG 58.503 43.478 5.78 10.46 0.00 3.34
1599 6433 0.040157 CCATGGTTCACAACAGTGCG 60.040 55.000 2.57 0.00 33.28 5.34
1669 6503 0.958382 TTGTGATGGCTGTTACGGGC 60.958 55.000 11.01 11.01 35.76 6.13
1682 6516 2.159014 GCATGTTGCCCATCATTGTGAT 60.159 45.455 0.00 0.00 35.84 3.06
1787 6624 6.653740 AGGTAGTGTAGAAATTTTAGTGCACC 59.346 38.462 14.63 0.00 0.00 5.01
1789 6626 8.369424 TGTAGGTAGTGTAGAAATTTTAGTGCA 58.631 33.333 0.00 0.00 0.00 4.57
1824 6661 5.467035 ACTAGGATAGAGCAGAGATTTGC 57.533 43.478 0.00 0.00 42.77 3.68
2035 6872 8.184192 CGGCACAAATTTATCTTAGAAACTGAT 58.816 33.333 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.