Multiple sequence alignment - TraesCS4D01G136000

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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 TraesCS4D01G136000 chr4D 100.000 3950 0 0 1 3950 122260561 122256612 0.000000e+00 7295.0
1 TraesCS4D01G136000 chr4D 87.050 278 25 3 3675 3950 489733691 489733959 1.780000e-78 303.0
2 TraesCS4D01G136000 chr4D 84.321 287 25 10 3671 3950 489728411 489728684 3.030000e-66 263.0
3 TraesCS4D01G136000 chr4D 93.491 169 11 0 3342 3510 489728245 489728413 6.550000e-63 252.0
4 TraesCS4D01G136000 chr4D 92.529 174 7 1 441 614 332789642 332789809 1.100000e-60 244.0
5 TraesCS4D01G136000 chr4D 94.326 141 6 1 2957 3095 489733351 489733491 8.600000e-52 215.0
6 TraesCS4D01G136000 chr4D 92.958 142 7 2 2957 3095 489728074 489728215 1.860000e-48 204.0
7 TraesCS4D01G136000 chr4D 81.416 113 15 4 155 267 491349834 491349728 1.960000e-13 87.9
8 TraesCS4D01G136000 chr4A 96.949 2917 62 8 614 3520 448102942 448105841 0.000000e+00 4868.0
9 TraesCS4D01G136000 chr4A 93.919 296 14 1 3659 3950 448105922 448106217 1.010000e-120 444.0
10 TraesCS4D01G136000 chr4A 86.207 87 12 0 1132 1218 447777162 447777248 1.170000e-15 95.3
11 TraesCS4D01G136000 chr4B 96.361 2913 69 7 614 3510 185870009 185867118 0.000000e+00 4758.0
12 TraesCS4D01G136000 chr4B 95.117 471 12 6 4 471 112932583 112932121 0.000000e+00 732.0
13 TraesCS4D01G136000 chr4B 96.429 280 10 0 3671 3950 185867120 185866841 2.780000e-126 462.0
14 TraesCS4D01G136000 chr4B 96.651 209 7 0 2632 2840 131369587 131369795 8.120000e-92 348.0
15 TraesCS4D01G136000 chr4B 97.423 194 4 1 421 614 112932120 112931928 2.940000e-86 329.0
16 TraesCS4D01G136000 chr4B 95.489 133 4 1 2975 3105 628068131 628068263 1.110000e-50 211.0
17 TraesCS4D01G136000 chr4B 87.912 182 12 3 3671 3851 628068444 628068616 5.170000e-49 206.0
18 TraesCS4D01G136000 chr6D 89.885 524 29 14 95 612 48116919 48117424 0.000000e+00 652.0
19 TraesCS4D01G136000 chr6D 96.386 166 6 0 3508 3673 243032890 243033055 1.400000e-69 274.0
20 TraesCS4D01G136000 chr6D 96.364 165 6 0 3508 3672 293177404 293177240 5.030000e-69 272.0
21 TraesCS4D01G136000 chr5D 87.666 527 38 12 95 615 155409942 155409437 4.400000e-164 588.0
22 TraesCS4D01G136000 chr5D 83.673 98 10 4 155 252 136549183 136549274 1.960000e-13 87.9
23 TraesCS4D01G136000 chr5D 87.037 54 7 0 1429 1482 457998904 457998851 1.190000e-05 62.1
24 TraesCS4D01G136000 chr1B 86.056 502 23 17 102 598 187555896 187555437 2.740000e-136 496.0
25 TraesCS4D01G136000 chr1B 88.076 369 29 9 249 615 560950672 560951027 1.310000e-114 424.0
26 TraesCS4D01G136000 chr7B 74.161 983 225 26 1825 2788 88246338 88247310 8.010000e-102 381.0
27 TraesCS4D01G136000 chr7B 73.865 991 229 26 1825 2794 87173309 87172328 6.240000e-98 368.0
28 TraesCS4D01G136000 chr7B 96.407 167 6 0 3506 3672 595441892 595442058 3.890000e-70 276.0
29 TraesCS4D01G136000 chr7B 78.873 213 31 11 75 279 285571522 285571316 8.910000e-27 132.0
30 TraesCS4D01G136000 chr7B 87.037 54 7 0 1429 1482 87173726 87173673 1.190000e-05 62.1
31 TraesCS4D01G136000 chr7B 87.037 54 7 0 1429 1482 88245927 88245980 1.190000e-05 62.1
32 TraesCS4D01G136000 chr7A 74.108 981 229 22 1825 2788 127608376 127609348 8.010000e-102 381.0
33 TraesCS4D01G136000 chr7A 87.037 54 7 0 1429 1482 127607956 127608009 1.190000e-05 62.1
34 TraesCS4D01G136000 chr7D 73.040 1135 275 27 1825 2939 126682749 126683872 4.820000e-99 372.0
35 TraesCS4D01G136000 chr7D 73.899 908 209 23 1907 2794 126506249 126505350 4.890000e-89 339.0
36 TraesCS4D01G136000 chr7D 87.037 54 7 0 1429 1482 88363050 88362997 1.190000e-05 62.1
37 TraesCS4D01G136000 chr7D 87.037 54 7 0 1429 1482 126506745 126506692 1.190000e-05 62.1
38 TraesCS4D01G136000 chr2A 90.476 252 13 5 108 354 66292102 66291857 4.920000e-84 322.0
39 TraesCS4D01G136000 chr5A 86.786 280 28 2 3671 3950 671183081 671183351 1.780000e-78 303.0
40 TraesCS4D01G136000 chr5A 95.858 169 7 0 3504 3672 458198874 458199042 1.400000e-69 274.0
41 TraesCS4D01G136000 chr5A 95.833 168 7 0 3505 3672 435637332 435637165 5.030000e-69 272.0
42 TraesCS4D01G136000 chr5A 84.211 285 28 9 3671 3950 671177074 671177346 1.090000e-65 261.0
43 TraesCS4D01G136000 chr5A 92.982 171 10 1 3342 3510 671176906 671177076 8.480000e-62 248.0
44 TraesCS4D01G136000 chr5A 92.529 174 7 1 441 614 469907794 469907627 1.100000e-60 244.0
45 TraesCS4D01G136000 chr5A 90.323 186 11 2 441 625 592852401 592852580 1.830000e-58 237.0
46 TraesCS4D01G136000 chr5A 90.857 175 10 1 441 615 532848232 532848400 3.070000e-56 230.0
47 TraesCS4D01G136000 chr5A 91.228 171 10 3 3342 3510 671182916 671183083 1.100000e-55 228.0
48 TraesCS4D01G136000 chr5A 91.558 154 8 2 2957 3105 671176739 671176892 1.440000e-49 207.0
49 TraesCS4D01G136000 chr5A 91.667 144 7 2 2957 3095 671182741 671182884 1.120000e-45 195.0
50 TraesCS4D01G136000 chr3D 96.450 169 6 0 3505 3673 566854559 566854727 3.010000e-71 279.0
51 TraesCS4D01G136000 chr3D 87.037 54 7 0 1429 1482 538375082 538375029 1.190000e-05 62.1
52 TraesCS4D01G136000 chr2B 95.294 170 7 1 3508 3677 208426581 208426749 6.510000e-68 268.0
53 TraesCS4D01G136000 chr2B 95.783 166 7 0 3507 3672 560444440 560444275 6.510000e-68 268.0
54 TraesCS4D01G136000 chrUn 95.238 168 8 0 3505 3672 382102448 382102281 2.340000e-67 267.0
55 TraesCS4D01G136000 chrUn 84.694 98 9 4 155 252 27011318 27011409 4.200000e-15 93.5
56 TraesCS4D01G136000 chr6A 90.857 175 10 3 441 615 436477858 436478026 3.070000e-56 230.0


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 TraesCS4D01G136000 chr4D 122256612 122260561 3949 True 7295.000000 7295 100.000000 1 3950 1 chr4D.!!$R1 3949
1 TraesCS4D01G136000 chr4D 489733351 489733959 608 False 259.000000 303 90.688000 2957 3950 2 chr4D.!!$F3 993
2 TraesCS4D01G136000 chr4D 489728074 489728684 610 False 239.666667 263 90.256667 2957 3950 3 chr4D.!!$F2 993
3 TraesCS4D01G136000 chr4A 448102942 448106217 3275 False 2656.000000 4868 95.434000 614 3950 2 chr4A.!!$F2 3336
4 TraesCS4D01G136000 chr4B 185866841 185870009 3168 True 2610.000000 4758 96.395000 614 3950 2 chr4B.!!$R2 3336
5 TraesCS4D01G136000 chr4B 112931928 112932583 655 True 530.500000 732 96.270000 4 614 2 chr4B.!!$R1 610
6 TraesCS4D01G136000 chr6D 48116919 48117424 505 False 652.000000 652 89.885000 95 612 1 chr6D.!!$F1 517
7 TraesCS4D01G136000 chr5D 155409437 155409942 505 True 588.000000 588 87.666000 95 615 1 chr5D.!!$R1 520
8 TraesCS4D01G136000 chr7B 88245927 88247310 1383 False 221.550000 381 80.599000 1429 2788 2 chr7B.!!$F2 1359
9 TraesCS4D01G136000 chr7B 87172328 87173726 1398 True 215.050000 368 80.451000 1429 2794 2 chr7B.!!$R2 1365
10 TraesCS4D01G136000 chr7A 127607956 127609348 1392 False 221.550000 381 80.572500 1429 2788 2 chr7A.!!$F1 1359
11 TraesCS4D01G136000 chr7D 126682749 126683872 1123 False 372.000000 372 73.040000 1825 2939 1 chr7D.!!$F1 1114
12 TraesCS4D01G136000 chr7D 126505350 126506745 1395 True 200.550000 339 80.468000 1429 2794 2 chr7D.!!$R2 1365
13 TraesCS4D01G136000 chr5A 671182741 671183351 610 False 242.000000 303 89.893667 2957 3950 3 chr5A.!!$F5 993
14 TraesCS4D01G136000 chr5A 671176739 671177346 607 False 238.666667 261 89.583667 2957 3950 3 chr5A.!!$F4 993

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
716 788 2.375174 TGGTTGTTCCTGCTATCTTGGT 59.625 45.455 0.00 0.0 37.07 3.67 F
1562 1688 1.376609 CGAAGCATTAGTGGTGGGGC 61.377 60.000 0.00 0.0 35.94 5.80 F
2571 2715 1.496934 CATTTTTCTTGGCGCGGTTT 58.503 45.000 8.83 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1988 2117 1.375908 TGCTTCGCCATGAGTGACC 60.376 57.895 0.0 0.0 33.78 4.02 R
2812 2956 1.376466 GGCTCTTGACCTTGCCTGA 59.624 57.895 0.0 0.0 41.92 3.86 R
3658 3827 0.109412 CACACGTACTCCCTCCGTTC 60.109 60.000 0.0 0.0 31.46 3.95 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
62 65 7.273815 GTCTTGTTTTCTTAGAGATGGAGTACG 59.726 40.741 0.00 0.00 0.00 3.67
192 199 3.054139 TCCTGAGCTCAAATAATGGCAGT 60.054 43.478 18.85 0.00 0.00 4.40
193 200 4.164030 TCCTGAGCTCAAATAATGGCAGTA 59.836 41.667 18.85 0.00 0.00 2.74
194 201 4.883585 CCTGAGCTCAAATAATGGCAGTAA 59.116 41.667 18.85 0.00 0.00 2.24
195 202 5.533903 CCTGAGCTCAAATAATGGCAGTAAT 59.466 40.000 18.85 0.00 0.00 1.89
196 203 6.712095 CCTGAGCTCAAATAATGGCAGTAATA 59.288 38.462 18.85 0.00 0.00 0.98
261 268 2.730672 CTGTTCTAGGTGCGCGCAC 61.731 63.158 46.90 46.90 45.49 5.34
281 288 4.785561 GCACCATTTTTGTGAAAAACAACG 59.214 37.500 0.00 0.00 44.97 4.10
288 295 6.771188 TTTTGTGAAAAACAACGTTCATGT 57.229 29.167 0.00 0.00 44.97 3.21
295 302 3.691049 AACAACGTTCATGTTGGTCTG 57.309 42.857 14.85 0.00 46.43 3.51
716 788 2.375174 TGGTTGTTCCTGCTATCTTGGT 59.625 45.455 0.00 0.00 37.07 3.67
738 810 5.863935 GGTGCTTTCATAATGAAAAGGACAC 59.136 40.000 19.68 17.21 44.69 3.67
1029 1116 4.069232 CGCGAGGAGTTGCTGGGA 62.069 66.667 0.00 0.00 0.00 4.37
1097 1184 2.202932 CATTCCTCCGTCGCCCTG 60.203 66.667 0.00 0.00 0.00 4.45
1261 1348 3.327757 TGATGCCAAGAACTTACTGTCCT 59.672 43.478 0.00 0.00 0.00 3.85
1562 1688 1.376609 CGAAGCATTAGTGGTGGGGC 61.377 60.000 0.00 0.00 35.94 5.80
1612 1741 2.450502 AGGAAGTGGTGGGCAGGT 60.451 61.111 0.00 0.00 0.00 4.00
1988 2117 3.805928 TGGGAGCCAGGTGTACAG 58.194 61.111 0.00 0.00 0.00 2.74
2571 2715 1.496934 CATTTTTCTTGGCGCGGTTT 58.503 45.000 8.83 0.00 0.00 3.27
2812 2956 3.807209 GCCGATTATCACTAAGGTGGCAT 60.807 47.826 0.00 0.00 43.17 4.40
2892 3036 4.052518 CTGCAGGGGTGGAAGGGG 62.053 72.222 5.57 0.00 0.00 4.79
3220 3384 4.025015 GCAGATGTTTATGTGCTTCCAG 57.975 45.455 2.58 0.00 46.76 3.86
3494 3661 5.895636 TGGTTAAAGGTTACATGCATCTG 57.104 39.130 0.00 0.00 0.00 2.90
3520 3689 1.272872 TGGCTACTACTCCCTCCGTTT 60.273 52.381 0.00 0.00 0.00 3.60
3521 3690 1.408340 GGCTACTACTCCCTCCGTTTC 59.592 57.143 0.00 0.00 0.00 2.78
3522 3691 2.377073 GCTACTACTCCCTCCGTTTCT 58.623 52.381 0.00 0.00 0.00 2.52
3525 3694 4.400567 GCTACTACTCCCTCCGTTTCTAAA 59.599 45.833 0.00 0.00 0.00 1.85
3528 3697 7.039853 GCTACTACTCCCTCCGTTTCTAAATAT 60.040 40.741 0.00 0.00 0.00 1.28
3529 3698 9.512588 CTACTACTCCCTCCGTTTCTAAATATA 57.487 37.037 0.00 0.00 0.00 0.86
3530 3699 8.406730 ACTACTCCCTCCGTTTCTAAATATAG 57.593 38.462 0.00 0.00 0.00 1.31
3534 3703 6.379579 TCCCTCCGTTTCTAAATATAGGTCT 58.620 40.000 0.00 0.00 0.00 3.85
3535 3704 6.842807 TCCCTCCGTTTCTAAATATAGGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3536 3705 7.346436 TCCCTCCGTTTCTAAATATAGGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3537 3706 7.656542 CCCTCCGTTTCTAAATATAGGTCTTTC 59.343 40.741 0.00 0.00 0.00 2.62
3538 3707 8.422566 CCTCCGTTTCTAAATATAGGTCTTTCT 58.577 37.037 0.00 0.00 0.00 2.52
3553 3722 7.736447 AGGTCTTTCTAGTGATTTCAACAAG 57.264 36.000 0.00 0.00 0.00 3.16
3554 3723 7.283329 AGGTCTTTCTAGTGATTTCAACAAGT 58.717 34.615 0.00 0.00 0.00 3.16
3555 3724 7.227512 AGGTCTTTCTAGTGATTTCAACAAGTG 59.772 37.037 0.00 0.00 0.00 3.16
3556 3725 7.226720 GGTCTTTCTAGTGATTTCAACAAGTGA 59.773 37.037 0.00 0.00 0.00 3.41
3557 3726 8.064814 GTCTTTCTAGTGATTTCAACAAGTGAC 58.935 37.037 0.00 0.00 35.39 3.67
3558 3727 7.987458 TCTTTCTAGTGATTTCAACAAGTGACT 59.013 33.333 0.00 0.00 35.39 3.41
3559 3728 9.261180 CTTTCTAGTGATTTCAACAAGTGACTA 57.739 33.333 0.00 0.00 35.39 2.59
3560 3729 8.589335 TTCTAGTGATTTCAACAAGTGACTAC 57.411 34.615 0.00 0.00 35.39 2.73
3561 3730 7.722363 TCTAGTGATTTCAACAAGTGACTACA 58.278 34.615 0.00 0.00 35.39 2.74
3562 3731 8.367911 TCTAGTGATTTCAACAAGTGACTACAT 58.632 33.333 0.00 0.00 35.39 2.29
3563 3732 9.639601 CTAGTGATTTCAACAAGTGACTACATA 57.360 33.333 0.00 0.00 35.39 2.29
3564 3733 8.311650 AGTGATTTCAACAAGTGACTACATAC 57.688 34.615 0.00 0.00 35.39 2.39
3565 3734 7.116376 AGTGATTTCAACAAGTGACTACATACG 59.884 37.037 0.00 0.00 35.39 3.06
3566 3735 6.367695 TGATTTCAACAAGTGACTACATACGG 59.632 38.462 0.00 0.00 35.39 4.02
3567 3736 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
3568 3737 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
3569 3738 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
3576 3745 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
3580 3749 6.112734 ACTACATACGGAGCAAAATGAATGA 58.887 36.000 0.00 0.00 0.00 2.57
3586 3755 6.124088 ACGGAGCAAAATGAATGAATCTAC 57.876 37.500 0.00 0.00 0.00 2.59
3588 3757 5.967674 CGGAGCAAAATGAATGAATCTACAC 59.032 40.000 0.00 0.00 0.00 2.90
3589 3758 6.183360 CGGAGCAAAATGAATGAATCTACACT 60.183 38.462 0.00 0.00 0.00 3.55
3592 3761 9.102757 GAGCAAAATGAATGAATCTACACTCTA 57.897 33.333 0.00 0.00 0.00 2.43
3620 3789 9.901172 AGTATGTCTATATACATCCGTATGTGA 57.099 33.333 3.56 0.00 45.99 3.58
3624 3793 9.901172 TGTCTATATACATCCGTATGTGATAGT 57.099 33.333 17.08 3.55 45.99 2.12
3626 3795 9.557061 TCTATATACATCCGTATGTGATAGTCC 57.443 37.037 17.08 0.00 45.99 3.85
3627 3796 9.338622 CTATATACATCCGTATGTGATAGTCCA 57.661 37.037 3.56 0.00 45.99 4.02
3628 3797 8.768501 ATATACATCCGTATGTGATAGTCCAT 57.231 34.615 3.56 0.00 45.99 3.41
3629 3798 5.808366 ACATCCGTATGTGATAGTCCATT 57.192 39.130 0.00 0.00 44.79 3.16
3631 3800 5.991606 ACATCCGTATGTGATAGTCCATTTG 59.008 40.000 0.00 0.00 44.79 2.32
3632 3801 5.862678 TCCGTATGTGATAGTCCATTTGA 57.137 39.130 0.00 0.00 0.00 2.69
3633 3802 6.228616 TCCGTATGTGATAGTCCATTTGAA 57.771 37.500 0.00 0.00 0.00 2.69
3634 3803 6.645306 TCCGTATGTGATAGTCCATTTGAAA 58.355 36.000 0.00 0.00 0.00 2.69
3635 3804 7.279615 TCCGTATGTGATAGTCCATTTGAAAT 58.720 34.615 0.00 0.00 0.00 2.17
3636 3805 7.441157 TCCGTATGTGATAGTCCATTTGAAATC 59.559 37.037 0.00 0.00 0.00 2.17
3637 3806 7.442364 CCGTATGTGATAGTCCATTTGAAATCT 59.558 37.037 0.00 0.00 0.00 2.40
3638 3807 8.491152 CGTATGTGATAGTCCATTTGAAATCTC 58.509 37.037 0.00 0.00 0.00 2.75
3639 3808 9.553064 GTATGTGATAGTCCATTTGAAATCTCT 57.447 33.333 0.00 0.00 0.00 3.10
3642 3811 9.958180 TGTGATAGTCCATTTGAAATCTCTAAA 57.042 29.630 0.00 0.00 0.00 1.85
3648 3817 9.579932 AGTCCATTTGAAATCTCTAAAAAGACT 57.420 29.630 0.00 0.00 0.00 3.24
3673 3842 1.755179 TTAGGAACGGAGGGAGTACG 58.245 55.000 0.00 0.00 0.00 3.67
3817 3999 4.889832 AAGTTGACTGCTTCTGAAGTTG 57.110 40.909 17.97 13.06 30.68 3.16
3941 4123 5.176958 CGGACAGTTAAACTAACCTTGTGAG 59.823 44.000 2.85 0.00 39.47 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.149129 ACAAGATTTCACAAGACTTTTCCC 57.851 37.500 0.00 0.00 0.00 3.97
1 2 8.479313 AAAACAAGATTTCACAAGACTTTTCC 57.521 30.769 0.00 0.00 0.00 3.13
62 65 4.946478 ATTGCTACTCCCTATCTGTGTC 57.054 45.455 0.00 0.00 0.00 3.67
106 109 8.491045 TGAAAAATTGGGAGAACCTAGAATTT 57.509 30.769 0.00 0.00 41.11 1.82
281 288 8.306761 AGAATATTTTTCCAGACCAACATGAAC 58.693 33.333 0.00 0.00 0.00 3.18
288 295 8.713708 TGGTTTAGAATATTTTTCCAGACCAA 57.286 30.769 0.00 0.00 30.10 3.67
364 371 9.567776 TTTCTCAAAGAACTAACATTCATGGTA 57.432 29.630 0.00 0.00 33.26 3.25
522 584 9.725019 TCATCCCATCTGTGTAATAAATATCAC 57.275 33.333 0.00 0.00 0.00 3.06
686 758 5.606348 AGCAGGAACAACCAAAATTTACA 57.394 34.783 0.00 0.00 42.04 2.41
687 759 7.602753 AGATAGCAGGAACAACCAAAATTTAC 58.397 34.615 0.00 0.00 42.04 2.01
688 760 7.775053 AGATAGCAGGAACAACCAAAATTTA 57.225 32.000 0.00 0.00 42.04 1.40
689 761 6.670695 AGATAGCAGGAACAACCAAAATTT 57.329 33.333 0.00 0.00 42.04 1.82
690 762 6.458210 CAAGATAGCAGGAACAACCAAAATT 58.542 36.000 0.00 0.00 42.04 1.82
691 763 5.047092 CCAAGATAGCAGGAACAACCAAAAT 60.047 40.000 0.00 0.00 42.04 1.82
692 764 4.280677 CCAAGATAGCAGGAACAACCAAAA 59.719 41.667 0.00 0.00 42.04 2.44
693 765 3.826157 CCAAGATAGCAGGAACAACCAAA 59.174 43.478 0.00 0.00 42.04 3.28
694 766 3.181434 ACCAAGATAGCAGGAACAACCAA 60.181 43.478 0.00 0.00 42.04 3.67
695 767 2.375174 ACCAAGATAGCAGGAACAACCA 59.625 45.455 0.00 0.00 42.04 3.67
716 788 5.698832 CGTGTCCTTTTCATTATGAAAGCA 58.301 37.500 18.09 13.45 45.77 3.91
738 810 3.716006 CGAACACACCTGGCAGCG 61.716 66.667 9.56 4.69 0.00 5.18
860 947 2.104967 CAAATGGACATGGCTGATGGT 58.895 47.619 0.00 0.00 36.23 3.55
1013 1100 2.435059 GTCCCAGCAACTCCTCGC 60.435 66.667 0.00 0.00 0.00 5.03
1029 1116 1.271597 GGCTCCATGTGTTCCTTCAGT 60.272 52.381 0.00 0.00 0.00 3.41
1125 1212 3.384467 TCAGAATGCGAGTGATGTATGGA 59.616 43.478 0.00 0.00 34.76 3.41
1261 1348 2.741985 CATGTCGCCACCTTCGCA 60.742 61.111 0.00 0.00 0.00 5.10
1714 1843 1.822990 CTCCATGGTGATTTGCAGCTT 59.177 47.619 12.58 0.00 45.14 3.74
1988 2117 1.375908 TGCTTCGCCATGAGTGACC 60.376 57.895 0.00 0.00 33.78 4.02
2571 2715 1.827399 AAAAGAAGAGCGCCTCCCGA 61.827 55.000 2.29 0.00 40.02 5.14
2812 2956 1.376466 GGCTCTTGACCTTGCCTGA 59.624 57.895 0.00 0.00 41.92 3.86
3021 3176 8.417176 CGAAATTTAAGATGTTTGAAGGAAACG 58.583 33.333 0.00 0.00 46.15 3.60
3220 3384 8.994429 TGAGATAACTGAAGAAGAAGAATGAC 57.006 34.615 0.00 0.00 0.00 3.06
3290 3457 8.765219 CACTGAATTTATTGGTCCTCTTATACG 58.235 37.037 0.00 0.00 0.00 3.06
3494 3661 2.431419 GAGGGAGTAGTAGCCAGTTTCC 59.569 54.545 0.00 0.00 0.00 3.13
3528 3697 8.429641 ACTTGTTGAAATCACTAGAAAGACCTA 58.570 33.333 0.00 0.00 0.00 3.08
3529 3698 7.227512 CACTTGTTGAAATCACTAGAAAGACCT 59.772 37.037 0.00 0.00 0.00 3.85
3530 3699 7.226720 TCACTTGTTGAAATCACTAGAAAGACC 59.773 37.037 0.00 0.00 0.00 3.85
3534 3703 9.042008 GTAGTCACTTGTTGAAATCACTAGAAA 57.958 33.333 0.00 0.00 35.39 2.52
3535 3704 8.201464 TGTAGTCACTTGTTGAAATCACTAGAA 58.799 33.333 0.00 0.00 35.39 2.10
3536 3705 7.722363 TGTAGTCACTTGTTGAAATCACTAGA 58.278 34.615 0.00 0.00 35.39 2.43
3537 3706 7.946655 TGTAGTCACTTGTTGAAATCACTAG 57.053 36.000 0.00 0.00 35.39 2.57
3538 3707 9.419297 GTATGTAGTCACTTGTTGAAATCACTA 57.581 33.333 0.00 0.00 35.39 2.74
3539 3708 7.116376 CGTATGTAGTCACTTGTTGAAATCACT 59.884 37.037 0.00 0.00 35.39 3.41
3540 3709 7.227461 CGTATGTAGTCACTTGTTGAAATCAC 58.773 38.462 0.00 0.00 35.39 3.06
3541 3710 6.367695 CCGTATGTAGTCACTTGTTGAAATCA 59.632 38.462 0.00 0.00 35.39 2.57
3542 3711 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
3543 3712 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
3544 3713 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
3545 3714 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
3546 3715 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
3547 3716 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
3548 3717 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
3549 3718 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
3550 3719 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
3551 3720 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
3552 3721 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
3553 3722 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
3554 3723 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
3555 3724 6.257849 TCATTCATTTTGCTCCGTATGTAGTC 59.742 38.462 0.00 0.00 0.00 2.59
3556 3725 6.112734 TCATTCATTTTGCTCCGTATGTAGT 58.887 36.000 0.00 0.00 0.00 2.73
3557 3726 6.603237 TCATTCATTTTGCTCCGTATGTAG 57.397 37.500 0.00 0.00 0.00 2.74
3558 3727 6.993786 TTCATTCATTTTGCTCCGTATGTA 57.006 33.333 0.00 0.00 0.00 2.29
3559 3728 5.895636 TTCATTCATTTTGCTCCGTATGT 57.104 34.783 0.00 0.00 0.00 2.29
3560 3729 6.732154 AGATTCATTCATTTTGCTCCGTATG 58.268 36.000 0.00 0.00 0.00 2.39
3561 3730 6.949352 AGATTCATTCATTTTGCTCCGTAT 57.051 33.333 0.00 0.00 0.00 3.06
3562 3731 6.821160 TGTAGATTCATTCATTTTGCTCCGTA 59.179 34.615 0.00 0.00 0.00 4.02
3563 3732 5.647658 TGTAGATTCATTCATTTTGCTCCGT 59.352 36.000 0.00 0.00 0.00 4.69
3564 3733 5.967674 GTGTAGATTCATTCATTTTGCTCCG 59.032 40.000 0.00 0.00 0.00 4.63
3565 3734 7.066766 AGAGTGTAGATTCATTCATTTTGCTCC 59.933 37.037 0.00 0.00 0.00 4.70
3566 3735 7.983307 AGAGTGTAGATTCATTCATTTTGCTC 58.017 34.615 0.00 0.00 0.00 4.26
3567 3736 7.934855 AGAGTGTAGATTCATTCATTTTGCT 57.065 32.000 0.00 0.00 0.00 3.91
3604 3773 8.589701 AATGGACTATCACATACGGATGTATA 57.410 34.615 14.23 10.59 44.82 1.47
3613 3782 9.553064 AGAGATTTCAAATGGACTATCACATAC 57.447 33.333 0.00 0.00 0.00 2.39
3640 3809 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
3641 3810 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
3642 3811 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3643 3812 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3644 3813 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
3645 3814 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
3646 3815 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3647 3816 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3648 3817 6.207417 CGTACTCCCTCCGTTCCTAAATATAA 59.793 42.308 0.00 0.00 0.00 0.98
3649 3818 5.707298 CGTACTCCCTCCGTTCCTAAATATA 59.293 44.000 0.00 0.00 0.00 0.86
3650 3819 4.522022 CGTACTCCCTCCGTTCCTAAATAT 59.478 45.833 0.00 0.00 0.00 1.28
3651 3820 3.885297 CGTACTCCCTCCGTTCCTAAATA 59.115 47.826 0.00 0.00 0.00 1.40
3652 3821 2.692041 CGTACTCCCTCCGTTCCTAAAT 59.308 50.000 0.00 0.00 0.00 1.40
3653 3822 2.094675 CGTACTCCCTCCGTTCCTAAA 58.905 52.381 0.00 0.00 0.00 1.85
3654 3823 1.004745 ACGTACTCCCTCCGTTCCTAA 59.995 52.381 0.00 0.00 0.00 2.69
3655 3824 0.620556 ACGTACTCCCTCCGTTCCTA 59.379 55.000 0.00 0.00 0.00 2.94
3656 3825 0.964358 CACGTACTCCCTCCGTTCCT 60.964 60.000 0.00 0.00 31.46 3.36
3657 3826 1.246737 ACACGTACTCCCTCCGTTCC 61.247 60.000 0.00 0.00 31.46 3.62
3658 3827 0.109412 CACACGTACTCCCTCCGTTC 60.109 60.000 0.00 0.00 31.46 3.95
3659 3828 0.538057 TCACACGTACTCCCTCCGTT 60.538 55.000 0.00 0.00 31.46 4.44
3660 3829 0.959372 CTCACACGTACTCCCTCCGT 60.959 60.000 0.00 0.00 34.71 4.69
3661 3830 1.801332 CTCACACGTACTCCCTCCG 59.199 63.158 0.00 0.00 0.00 4.63
3662 3831 0.966370 AGCTCACACGTACTCCCTCC 60.966 60.000 0.00 0.00 0.00 4.30
3673 3842 6.500684 TCCTGAAAATTGATTAGCTCACAC 57.499 37.500 0.00 0.00 32.17 3.82
3710 3880 7.039784 AGCACTAGCAGGTAAAATCATTGAAAA 60.040 33.333 0.00 0.00 45.49 2.29
3817 3999 3.373439 GCATTCTGTCCTTGTCTGATCAC 59.627 47.826 0.00 0.00 0.00 3.06
3876 4058 2.289945 ACACATGGACAAAGAGAGGCTC 60.290 50.000 6.34 6.34 0.00 4.70


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

AutoCloner maintained by Alex Coulton.