Multiple sequence alignment - TraesCS1B01G051800

Loading Multiple Alignment...

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 TraesCS1B01G051800 chr1B 100.000 5052 0 0 1 5052 31966260 31971311 0.000000e+00 9330.0
1 TraesCS1B01G051800 chr1B 94.907 4712 195 29 368 5052 32058313 32063006 0.000000e+00 7330.0
2 TraesCS1B01G051800 chr1B 89.808 1197 78 18 3128 4308 31908313 31909481 0.000000e+00 1495.0
3 TraesCS1B01G051800 chr1B 88.519 1263 95 17 3799 5052 31911122 31912343 0.000000e+00 1483.0
4 TraesCS1B01G051800 chr1B 92.843 489 27 3 2311 2791 31907672 31908160 0.000000e+00 702.0
5 TraesCS1B01G051800 chr1B 92.111 431 22 9 167 589 31905294 31905720 9.360000e-167 597.0
6 TraesCS1B01G051800 chr1B 93.199 397 23 2 1303 1696 31906728 31907123 9.430000e-162 580.0
7 TraesCS1B01G051800 chr1B 89.245 437 32 6 669 1105 31905722 31906143 2.680000e-147 532.0
8 TraesCS1B01G051800 chr1B 79.635 712 109 22 3822 4513 32085864 32086559 3.540000e-131 479.0
9 TraesCS1B01G051800 chr1B 87.843 255 21 6 3464 3708 32065322 32065576 1.780000e-74 291.0
10 TraesCS1B01G051800 chr1B 87.500 256 22 6 3463 3708 31972376 31972631 2.300000e-73 287.0
11 TraesCS1B01G051800 chr1B 87.209 258 21 7 3463 3708 31913591 31913848 2.980000e-72 283.0
12 TraesCS1B01G051800 chr1B 79.733 449 46 18 4610 5051 32067506 32067916 2.980000e-72 283.0
13 TraesCS1B01G051800 chr1B 82.687 335 31 14 4665 4999 31909788 31910095 6.440000e-69 272.0
14 TraesCS1B01G051800 chr1B 86.100 259 22 8 3463 3708 32085613 32085870 3.000000e-67 267.0
15 TraesCS1B01G051800 chr1B 87.879 231 21 2 134 357 32058025 32058255 1.080000e-66 265.0
16 TraesCS1B01G051800 chr1B 78.619 449 51 17 4610 5051 31974581 31974991 6.490000e-64 255.0
17 TraesCS1B01G051800 chr1B 83.537 164 21 5 4836 4997 32084077 32084236 1.130000e-31 148.0
18 TraesCS1B01G051800 chr1B 92.208 77 6 0 1096 1172 31967277 31967353 5.350000e-20 110.0
19 TraesCS1B01G051800 chr1B 92.208 77 6 0 1018 1094 31967355 31967431 5.350000e-20 110.0
20 TraesCS1B01G051800 chr1B 90.909 77 7 0 1096 1172 32058973 32059049 2.490000e-18 104.0
21 TraesCS1B01G051800 chr1B 96.667 60 1 1 598 657 32058603 32058545 1.160000e-16 99.0
22 TraesCS1B01G051800 chr1D 91.245 1839 122 21 2838 4654 19901145 19902966 0.000000e+00 2468.0
23 TraesCS1B01G051800 chr1D 93.540 1548 80 11 1303 2840 19899580 19901117 0.000000e+00 2287.0
24 TraesCS1B01G051800 chr1D 87.676 1282 93 34 33 1304 19898180 19899406 0.000000e+00 1432.0
25 TraesCS1B01G051800 chr1D 92.405 79 6 0 1018 1096 19899202 19899280 4.130000e-21 113.0
26 TraesCS1B01G051800 chr1D 88.710 62 5 2 222 282 485879367 485879427 1.950000e-09 75.0
27 TraesCS1B01G051800 chr1D 92.857 42 3 0 586 627 267424804 267424763 1.520000e-05 62.1
28 TraesCS1B01G051800 chr1A 89.733 1763 135 24 2909 4638 21338587 21340336 0.000000e+00 2211.0
29 TraesCS1B01G051800 chr1A 89.218 1419 85 20 1303 2716 21336491 21337846 0.000000e+00 1711.0
30 TraesCS1B01G051800 chr1A 87.812 681 43 18 1 657 21335177 21335841 0.000000e+00 761.0
31 TraesCS1B01G051800 chr1A 86.067 445 39 11 653 1096 21335800 21336222 1.660000e-124 457.0
32 TraesCS1B01G051800 chr1A 91.228 171 12 2 1103 1273 21336151 21336318 3.930000e-56 230.0
33 TraesCS1B01G051800 chr6D 90.587 988 71 16 1742 2719 50777517 50776542 0.000000e+00 1290.0
34 TraesCS1B01G051800 chr6D 85.492 386 47 5 2847 3227 50776084 50775703 1.320000e-105 394.0
35 TraesCS1B01G051800 chr6D 81.548 504 56 19 3213 3692 50775191 50774701 1.030000e-101 381.0
36 TraesCS1B01G051800 chr6D 91.398 93 8 0 1106 1198 50779800 50779708 1.480000e-25 128.0
37 TraesCS1B01G051800 chr6D 92.754 69 5 0 1028 1096 50779800 50779732 3.220000e-17 100.0
38 TraesCS1B01G051800 chr6B 89.767 987 77 16 1742 2719 120646175 120647146 0.000000e+00 1242.0
39 TraesCS1B01G051800 chr6B 83.221 447 43 17 3272 3692 120649122 120649562 1.030000e-101 381.0
40 TraesCS1B01G051800 chr6B 85.897 312 33 6 2909 3212 120647842 120648150 6.310000e-84 322.0
41 TraesCS1B01G051800 chr6B 92.045 88 7 0 1106 1193 120644787 120644874 1.910000e-24 124.0
42 TraesCS1B01G051800 chr6B 87.500 72 8 1 586 657 708113785 708113715 1.170000e-11 82.4
43 TraesCS1B01G051800 chr6B 97.297 37 1 0 586 622 189580873 189580909 4.220000e-06 63.9
44 TraesCS1B01G051800 chr6A 89.624 983 77 12 1742 2719 64258295 64259257 0.000000e+00 1227.0
45 TraesCS1B01G051800 chr6A 85.751 386 45 8 2847 3227 64259720 64260100 2.830000e-107 399.0
46 TraesCS1B01G051800 chr6A 81.799 478 57 16 3233 3692 64260881 64261346 1.720000e-99 374.0
47 TraesCS1B01G051800 chr6A 78.261 598 70 22 3863 4403 64261406 64262000 3.770000e-86 329.0
48 TraesCS1B01G051800 chr6A 92.473 93 7 0 1106 1198 64255499 64255591 3.170000e-27 134.0
49 TraesCS1B01G051800 chr6A 92.754 69 5 0 1028 1096 64255499 64255567 3.220000e-17 100.0
50 TraesCS1B01G051800 chr7D 89.045 995 80 16 1742 2719 66826381 66825399 0.000000e+00 1206.0
51 TraesCS1B01G051800 chr7D 84.960 379 36 7 2847 3223 66824485 66824126 1.030000e-96 364.0
52 TraesCS1B01G051800 chr7D 77.410 695 96 31 3746 4403 66823154 66822484 1.730000e-94 357.0
53 TraesCS1B01G051800 chr7D 85.667 300 22 9 3213 3497 66823720 66823427 3.820000e-76 296.0
54 TraesCS1B01G051800 chr7D 80.282 213 17 10 1106 1298 66829055 66828848 2.450000e-28 137.0
55 TraesCS1B01G051800 chr7D 94.118 68 4 0 1028 1095 66829055 66828988 2.490000e-18 104.0
56 TraesCS1B01G051800 chr7A 90.401 573 46 8 2152 2719 73807268 73807836 0.000000e+00 745.0
57 TraesCS1B01G051800 chr7A 86.842 418 41 9 1742 2154 73806767 73807175 5.960000e-124 455.0
58 TraesCS1B01G051800 chr7A 86.316 380 42 6 2847 3223 73808301 73808673 6.090000e-109 405.0
59 TraesCS1B01G051800 chr7A 76.177 701 97 41 3743 4403 73846895 73847565 6.350000e-79 305.0
60 TraesCS1B01G051800 chr7A 82.927 287 30 8 3224 3497 73809090 73809370 1.820000e-59 241.0
61 TraesCS1B01G051800 chr7A 83.420 193 20 6 3538 3722 73846786 73846974 8.700000e-38 169.0
62 TraesCS1B01G051800 chr7A 97.368 38 1 0 1303 1340 73805790 73805827 1.170000e-06 65.8
63 TraesCS1B01G051800 chr5A 93.617 47 3 0 581 627 535566893 535566939 2.520000e-08 71.3
64 TraesCS1B01G051800 chrUn 92.857 42 3 0 586 627 233268584 233268543 1.520000e-05 62.1
65 TraesCS1B01G051800 chr2B 100.000 28 0 0 631 658 66724844 66724817 9.000000e-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 TraesCS1B01G051800 chr1B 31966260 31971311 5051 False 9330.000000 9330 100.000000 1 5052 1 chr1B.!!$F1 5051
1 TraesCS1B01G051800 chr1B 32058025 32063006 4981 False 3797.500000 7330 91.393000 134 5052 2 chr1B.!!$F6 4918
2 TraesCS1B01G051800 chr1B 31905294 31913848 8554 False 743.000000 1495 89.452625 167 5052 8 chr1B.!!$F3 4885
3 TraesCS1B01G051800 chr1B 32084077 32086559 2482 False 298.000000 479 83.090667 3463 4997 3 chr1B.!!$F8 1534
4 TraesCS1B01G051800 chr1B 32065322 32067916 2594 False 287.000000 291 83.788000 3464 5051 2 chr1B.!!$F7 1587
5 TraesCS1B01G051800 chr1B 31972376 31974991 2615 False 271.000000 287 83.059500 3463 5051 2 chr1B.!!$F5 1588
6 TraesCS1B01G051800 chr1D 19898180 19902966 4786 False 1575.000000 2468 91.216500 33 4654 4 chr1D.!!$F2 4621
7 TraesCS1B01G051800 chr1A 21335177 21340336 5159 False 1074.000000 2211 88.811600 1 4638 5 chr1A.!!$F1 4637
8 TraesCS1B01G051800 chr6D 50774701 50779800 5099 True 458.600000 1290 88.355800 1028 3692 5 chr6D.!!$R1 2664
9 TraesCS1B01G051800 chr6B 120644787 120649562 4775 False 517.250000 1242 87.732500 1106 3692 4 chr6B.!!$F2 2586
10 TraesCS1B01G051800 chr6A 64255499 64262000 6501 False 427.166667 1227 86.777000 1028 4403 6 chr6A.!!$F1 3375
11 TraesCS1B01G051800 chr7D 66822484 66829055 6571 True 410.666667 1206 85.247000 1028 4403 6 chr7D.!!$R1 3375
12 TraesCS1B01G051800 chr7A 73805790 73809370 3580 False 382.360000 745 88.770800 1303 3497 5 chr7A.!!$F1 2194
13 TraesCS1B01G051800 chr7A 73846786 73847565 779 False 237.000000 305 79.798500 3538 4403 2 chr7A.!!$F2 865

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
65 67 0.035458 TGTGTGTGTGTGTGTGTGGA 59.965 50.000 0.00 0.00 0.00 4.02 F
984 1126 2.048127 GCCTCCTCGTTGTTCGCT 60.048 61.111 0.00 0.00 39.67 4.93 F
1512 3226 1.165270 GCTGCCAAATCGTTACTGGT 58.835 50.000 0.00 0.00 32.46 4.00 F
2685 8138 1.055849 TGTCTAGGTGCAGGCTGAAA 58.944 50.000 20.86 1.81 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1512 3226 0.391597 GTCAAGGTGAACCGACCAGA 59.608 55.0 0.00 0.0 42.08 3.86 R
2343 7785 0.957395 ATGTTGTTCCTGCAGCTCCG 60.957 55.0 8.66 0.0 0.00 4.63 R
3420 11400 0.099259 TCGTCACGGCATAAGTACGG 59.901 55.0 0.00 0.0 0.00 4.02 R
4661 16249 0.726827 CGAATGTAGCGGCAATGTGT 59.273 50.0 1.45 0.0 0.00 3.72 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
65 67 0.035458 TGTGTGTGTGTGTGTGTGGA 59.965 50.000 0.00 0.00 0.00 4.02
69 71 3.002246 GTGTGTGTGTGTGTGTGGATAAG 59.998 47.826 0.00 0.00 0.00 1.73
122 125 9.727627 CCATTCTCAAGATTAAATTTCTACTGC 57.272 33.333 0.00 0.00 0.00 4.40
262 291 3.243201 GGAAGTGACCTTTGCAAAGAGTG 60.243 47.826 35.25 22.71 38.28 3.51
443 530 5.246981 TGTCTTCTTGATCCATTCCTGTT 57.753 39.130 0.00 0.00 0.00 3.16
449 536 5.384336 TCTTGATCCATTCCTGTTTGTTCA 58.616 37.500 0.00 0.00 0.00 3.18
451 538 6.323482 TCTTGATCCATTCCTGTTTGTTCAAA 59.677 34.615 0.00 0.00 0.00 2.69
452 539 6.669125 TGATCCATTCCTGTTTGTTCAAAT 57.331 33.333 1.33 0.00 0.00 2.32
453 540 7.773489 TGATCCATTCCTGTTTGTTCAAATA 57.227 32.000 1.33 0.00 0.00 1.40
454 541 7.829725 TGATCCATTCCTGTTTGTTCAAATAG 58.170 34.615 12.75 12.75 0.00 1.73
455 542 6.588719 TCCATTCCTGTTTGTTCAAATAGG 57.411 37.500 24.93 24.93 40.94 2.57
457 544 5.245977 CCATTCCTGTTTGTTCAAATAGGGT 59.754 40.000 27.85 19.25 40.27 4.34
458 545 5.782893 TTCCTGTTTGTTCAAATAGGGTG 57.217 39.130 27.85 12.60 40.27 4.61
460 547 5.070001 TCCTGTTTGTTCAAATAGGGTGAG 58.930 41.667 27.85 12.09 40.27 3.51
462 549 5.182001 CCTGTTTGTTCAAATAGGGTGAGAG 59.818 44.000 23.89 5.84 37.39 3.20
463 550 4.518970 TGTTTGTTCAAATAGGGTGAGAGC 59.481 41.667 1.33 0.00 0.00 4.09
464 551 4.365514 TTGTTCAAATAGGGTGAGAGCA 57.634 40.909 0.00 0.00 0.00 4.26
466 553 4.724399 TGTTCAAATAGGGTGAGAGCAAA 58.276 39.130 0.00 0.00 0.00 3.68
515 603 4.045636 ACTTTTGGTCATGTGTTCTTGC 57.954 40.909 0.00 0.00 0.00 4.01
577 665 8.562892 GTGTATTCCAATGATATGTTCTTGAGG 58.437 37.037 0.00 0.00 0.00 3.86
631 719 5.422214 GTCTTTTTAGAGACTCCATGGGA 57.578 43.478 13.02 0.00 42.18 4.37
633 721 5.877564 GTCTTTTTAGAGACTCCATGGGAAG 59.122 44.000 13.02 5.29 42.18 3.46
635 723 5.422214 TTTTAGAGACTCCATGGGAAGTC 57.578 43.478 20.88 20.88 33.36 3.01
637 725 2.745968 AGAGACTCCATGGGAAGTCTC 58.254 52.381 35.36 35.36 45.79 3.36
640 728 4.282496 GAGACTCCATGGGAAGTCTCTAA 58.718 47.826 35.16 8.77 44.21 2.10
642 730 5.094387 AGACTCCATGGGAAGTCTCTAAAA 58.906 41.667 23.98 0.00 36.33 1.52
643 731 5.548056 AGACTCCATGGGAAGTCTCTAAAAA 59.452 40.000 23.98 0.00 36.33 1.94
646 734 5.805728 TCCATGGGAAGTCTCTAAAAAGAC 58.194 41.667 13.02 0.00 44.96 3.01
775 902 7.509318 TGGTCTGTATACTTGCATACCTAATCT 59.491 37.037 4.17 0.00 36.22 2.40
862 996 3.883489 GGGTTTGTATAATGAGTGCCCTC 59.117 47.826 0.00 0.00 38.27 4.30
864 998 2.526304 TGTATAATGAGTGCCCTCGC 57.474 50.000 0.00 0.00 40.85 5.03
878 1012 2.735134 GCCCTCGCGTTGTATAATTAGG 59.265 50.000 5.77 0.38 0.00 2.69
963 1105 2.551459 CCAAAGCATCCATCCGATCTTC 59.449 50.000 0.00 0.00 0.00 2.87
984 1126 2.048127 GCCTCCTCGTTGTTCGCT 60.048 61.111 0.00 0.00 39.67 4.93
992 1134 2.970324 GTTGTTCGCTGTCGCCCA 60.970 61.111 0.00 0.00 35.26 5.36
1045 1187 4.056125 CCGCCTCTGACGTGCTGA 62.056 66.667 0.00 0.00 0.00 4.26
1089 1231 2.352805 CTCTCCAAAGCCCGCCTT 59.647 61.111 0.00 0.00 34.51 4.35
1100 1242 2.347490 CCGCCTTAGGTGCACTGT 59.653 61.111 17.98 7.16 0.00 3.55
1172 1531 2.747855 CAAAGCCCGCCTCAGGTC 60.748 66.667 0.00 0.00 0.00 3.85
1420 2549 4.450419 CAGTTTTGTTGTGCTTTTTGGACA 59.550 37.500 0.00 0.00 45.26 4.02
1461 2590 2.354259 CTTGGCCAAAACTTTTGTGCA 58.646 42.857 20.91 0.00 0.00 4.57
1512 3226 1.165270 GCTGCCAAATCGTTACTGGT 58.835 50.000 0.00 0.00 32.46 4.00
1595 3309 9.618890 CCTGAAAATCTAAGATGACCTTCATAA 57.381 33.333 0.00 0.00 37.20 1.90
1720 3434 3.753272 GGCACTCAACTTCTTGCAATCTA 59.247 43.478 0.00 0.00 36.66 1.98
1726 3440 2.565841 ACTTCTTGCAATCTATCCGCC 58.434 47.619 0.00 0.00 0.00 6.13
1870 6738 8.630054 TTCTTTATGGTATAGTGCACTTGTTT 57.370 30.769 27.06 10.37 0.00 2.83
1994 6862 3.320826 GCCAACACTTTCAACCAGGTATT 59.679 43.478 0.00 0.00 0.00 1.89
2343 7785 1.453155 CCATGTGGGCTACAAGTGTC 58.547 55.000 8.05 0.00 43.77 3.67
2369 7811 3.056607 GCTGCAGGAACAACATTATTGGT 60.057 43.478 17.12 0.00 0.00 3.67
2416 7858 3.427573 TGCCTGTACTTGCTCTACACTA 58.572 45.455 8.34 0.00 0.00 2.74
2455 7907 5.186409 ACGGTCACTGTAGTTGGTATAATGT 59.814 40.000 0.00 0.00 0.00 2.71
2685 8138 1.055849 TGTCTAGGTGCAGGCTGAAA 58.944 50.000 20.86 1.81 0.00 2.69
2686 8139 1.419762 TGTCTAGGTGCAGGCTGAAAA 59.580 47.619 20.86 0.00 0.00 2.29
2751 8508 1.734388 GAGTTTTGCCACCGCCTTGT 61.734 55.000 0.00 0.00 0.00 3.16
2998 9637 2.440409 CTATTTCCTGCTGGCTTGTGT 58.560 47.619 4.42 0.00 0.00 3.72
3023 9662 1.213296 AGGCCATATCAGACCCGTTT 58.787 50.000 5.01 0.00 0.00 3.60
3037 9676 4.339814 AGACCCGTTTGAATAAAAGCAACA 59.660 37.500 0.00 0.00 0.00 3.33
3038 9677 5.010617 AGACCCGTTTGAATAAAAGCAACAT 59.989 36.000 0.00 0.00 0.00 2.71
3327 11307 9.793259 TCTGGTCCTTATTTTTATCATGATACC 57.207 33.333 15.10 11.68 0.00 2.73
3337 11317 1.227943 CATGATACCGGTGGGCAGG 60.228 63.158 19.93 10.35 36.48 4.85
3420 11400 1.560505 ACCACATTTCATGGCCCTTC 58.439 50.000 0.00 0.00 41.31 3.46
3505 11509 7.724951 GGTTATTACCAGATCTACCTAGTGTCT 59.275 40.741 0.00 0.00 44.36 3.41
3534 11663 8.460831 AAATGTTACGGCTTTTACATTGATTC 57.539 30.769 0.00 0.00 40.14 2.52
3811 11948 8.296713 TCCATTTGCTTCTACTTGTAACAAATC 58.703 33.333 0.00 0.00 34.88 2.17
3890 12028 3.456277 GGGTCTAACATCTGGATGGTTCT 59.544 47.826 14.06 0.42 42.91 3.01
4066 15349 4.274147 ACCAATGAGACTAGTGAGATCGT 58.726 43.478 0.00 0.00 0.00 3.73
4097 15386 3.123620 GTTGCTGAGCTGCGGGAG 61.124 66.667 5.83 0.00 35.36 4.30
4485 16061 5.084818 TGATAATGTAGGTATGGGATGCG 57.915 43.478 0.00 0.00 0.00 4.73
4519 16095 3.176297 CCCAAGTTAGGGCCACCA 58.824 61.111 6.18 0.00 43.10 4.17
4677 16265 2.113860 AAGACACATTGCCGCTACAT 57.886 45.000 0.00 0.00 0.00 2.29
4693 16281 1.573108 ACATTCGACTGGATGGGACT 58.427 50.000 7.74 0.00 0.00 3.85
4734 16322 2.193447 CCTCGATTACCATGTGTGACG 58.807 52.381 0.00 0.00 0.00 4.35
4735 16323 2.416836 CCTCGATTACCATGTGTGACGT 60.417 50.000 0.00 0.00 0.00 4.34
4756 16346 5.700832 ACGTGTGTTGATTATCAGTTGATGT 59.299 36.000 4.90 0.00 36.05 3.06
4773 16363 1.007502 GTCGCAATTTGCTGGCACA 60.008 52.632 18.57 0.00 42.25 4.57
4774 16364 1.007502 TCGCAATTTGCTGGCACAC 60.008 52.632 18.57 0.00 42.25 3.82
4832 16423 7.037438 GGTTTTGATTTCACATGATAGTGCAT 58.963 34.615 0.00 0.00 39.35 3.96
4865 16456 7.148355 CCAAGATGGCTATTGCAAAATTTTT 57.852 32.000 1.71 0.00 41.91 1.94
5018 16614 1.269166 GTCCAAGCATACGTCAGTCG 58.731 55.000 0.00 0.00 46.00 4.18
5035 16631 0.541063 TCGTACACAAGCTCCCTCCA 60.541 55.000 0.00 0.00 0.00 3.86
5036 16632 0.537188 CGTACACAAGCTCCCTCCAT 59.463 55.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.732571 CACACACACACTGTTCCACC 59.267 55.000 0.00 0.00 0.00 4.61
65 67 2.037251 ACACAACCAGCGTCTGACTTAT 59.963 45.455 6.21 0.00 32.44 1.73
69 71 1.014352 AAACACAACCAGCGTCTGAC 58.986 50.000 8.20 0.00 32.44 3.51
115 118 6.265196 ACAACCAAATTGAGATTTGCAGTAGA 59.735 34.615 6.39 0.00 46.94 2.59
116 119 6.449698 ACAACCAAATTGAGATTTGCAGTAG 58.550 36.000 6.39 0.00 46.94 2.57
117 120 6.403866 ACAACCAAATTGAGATTTGCAGTA 57.596 33.333 6.39 0.00 46.94 2.74
118 121 5.280654 ACAACCAAATTGAGATTTGCAGT 57.719 34.783 6.39 2.72 46.94 4.40
119 122 5.754406 TCAACAACCAAATTGAGATTTGCAG 59.246 36.000 6.39 2.24 46.94 4.41
120 123 5.668471 TCAACAACCAAATTGAGATTTGCA 58.332 33.333 6.39 0.00 46.94 4.08
121 124 6.601741 TTCAACAACCAAATTGAGATTTGC 57.398 33.333 6.39 0.00 46.94 3.68
262 291 6.161381 TGTTCGAAATCACTAGTTAAGGGTC 58.839 40.000 0.00 0.00 0.00 4.46
393 477 0.953727 GACTTGACTTGCATGCACCA 59.046 50.000 22.58 15.75 0.00 4.17
443 530 4.365514 TGCTCTCACCCTATTTGAACAA 57.634 40.909 0.00 0.00 0.00 2.83
449 536 5.416952 CACTCAATTTGCTCTCACCCTATTT 59.583 40.000 0.00 0.00 0.00 1.40
451 538 4.225942 TCACTCAATTTGCTCTCACCCTAT 59.774 41.667 0.00 0.00 0.00 2.57
452 539 3.582647 TCACTCAATTTGCTCTCACCCTA 59.417 43.478 0.00 0.00 0.00 3.53
453 540 2.373169 TCACTCAATTTGCTCTCACCCT 59.627 45.455 0.00 0.00 0.00 4.34
454 541 2.783135 TCACTCAATTTGCTCTCACCC 58.217 47.619 0.00 0.00 0.00 4.61
455 542 5.181748 ACTATCACTCAATTTGCTCTCACC 58.818 41.667 0.00 0.00 0.00 4.02
515 603 3.941483 CCTGGTTGCCTAATTACACAGAG 59.059 47.826 0.00 0.00 0.00 3.35
682 770 6.183361 ACTCCCTCCATTCCTACGTATAAGTA 60.183 42.308 0.00 0.00 0.00 2.24
690 778 6.607004 ATTATTACTCCCTCCATTCCTACG 57.393 41.667 0.00 0.00 0.00 3.51
691 779 8.541234 CCTAATTATTACTCCCTCCATTCCTAC 58.459 40.741 0.00 0.00 0.00 3.18
775 902 5.323371 GCACTAATTGCCATCTTTGGTTA 57.677 39.130 0.00 0.00 46.63 2.85
862 996 1.802365 GGGCCCTAATTATACAACGCG 59.198 52.381 17.04 3.53 0.00 6.01
864 998 3.181448 ACCAGGGCCCTAATTATACAACG 60.181 47.826 28.13 7.24 0.00 4.10
878 1012 1.424638 TATTAGAGAGCACCAGGGCC 58.575 55.000 0.00 0.00 0.00 5.80
941 1083 1.492176 AGATCGGATGGATGCTTTGGT 59.508 47.619 0.00 0.00 34.82 3.67
963 1105 3.952628 GAACAACGAGGAGGCCGGG 62.953 68.421 2.18 0.00 0.00 5.73
1089 1231 2.646175 GGAGGCGACAGTGCACCTA 61.646 63.158 14.63 0.00 36.28 3.08
1229 1609 6.054295 AGCCACAAGAACTGAAGATCATATC 58.946 40.000 0.00 0.00 0.00 1.63
1235 1615 6.944862 AGAATTTAGCCACAAGAACTGAAGAT 59.055 34.615 0.00 0.00 0.00 2.40
1420 2549 5.171339 AGCTCTAACATTTCAGGACATGT 57.829 39.130 0.00 0.00 35.00 3.21
1461 2590 4.018870 TCTGCTATCTAGGATCTCCATCGT 60.019 45.833 0.00 0.00 38.89 3.73
1512 3226 0.391597 GTCAAGGTGAACCGACCAGA 59.608 55.000 0.00 0.00 42.08 3.86
1595 3309 9.297037 AGTTAAATGCTAGTTCACTTTTACCAT 57.703 29.630 0.00 0.00 0.00 3.55
1678 3392 9.807649 GAGTGCCATTACAATTTATGAAATCTT 57.192 29.630 0.00 0.00 0.00 2.40
1720 3434 8.958060 ACTCATATATATTACCATAGGCGGAT 57.042 34.615 0.00 0.00 0.00 4.18
1847 6714 7.754924 CCAAAACAAGTGCACTATACCATAAAG 59.245 37.037 22.01 3.64 0.00 1.85
1850 6717 5.124776 GCCAAAACAAGTGCACTATACCATA 59.875 40.000 22.01 0.00 0.00 2.74
1851 6718 4.082245 GCCAAAACAAGTGCACTATACCAT 60.082 41.667 22.01 0.00 0.00 3.55
1852 6719 3.254657 GCCAAAACAAGTGCACTATACCA 59.745 43.478 22.01 0.00 0.00 3.25
1854 6721 4.497473 TGCCAAAACAAGTGCACTATAC 57.503 40.909 22.01 4.80 0.00 1.47
1855 6722 4.339530 TGTTGCCAAAACAAGTGCACTATA 59.660 37.500 22.01 0.00 32.63 1.31
1856 6723 3.131933 TGTTGCCAAAACAAGTGCACTAT 59.868 39.130 22.01 8.94 32.63 2.12
1870 6738 3.978193 AGCCCCCGATGTTGCCAA 61.978 61.111 0.00 0.00 0.00 4.52
2050 6926 7.754069 TTTCAAGAATGTGAACACAATGAAC 57.246 32.000 11.60 2.90 45.41 3.18
2343 7785 0.957395 ATGTTGTTCCTGCAGCTCCG 60.957 55.000 8.66 0.00 0.00 4.63
2369 7811 2.223479 GCAAAGAGTCGAACCTTGCAAA 60.223 45.455 16.85 0.00 0.00 3.68
2416 7858 4.819630 AGTGACCGTACACAATTGAAACAT 59.180 37.500 13.59 0.00 42.45 2.71
2455 7907 5.408909 TCGCGATGTTTAGTTCCAATAACAA 59.591 36.000 3.71 0.00 34.54 2.83
2600 8053 2.203480 GGCCCCAACAACTGCTCA 60.203 61.111 0.00 0.00 0.00 4.26
2796 8589 1.762460 GGCAGGCCTAGGCAGTAGA 60.762 63.158 34.09 0.00 44.11 2.59
2921 9560 6.072199 AGAGATAGGAAAGCCATGAAAAGT 57.928 37.500 0.00 0.00 36.29 2.66
2930 9569 5.175127 GCTTATGCTAGAGATAGGAAAGCC 58.825 45.833 0.00 0.00 31.94 4.35
2998 9637 2.054799 GGTCTGATATGGCCTTGGGTA 58.945 52.381 3.32 0.00 0.00 3.69
3038 9677 9.999660 GGTCCAGATGTCTCTACGATATATATA 57.000 37.037 0.00 0.00 0.00 0.86
3268 11216 3.630769 ACATATTGCACAGCTCCATTCAG 59.369 43.478 0.00 0.00 0.00 3.02
3337 11317 1.731160 GTGACACTTCTGATGCTGCTC 59.269 52.381 0.00 0.00 0.00 4.26
3420 11400 0.099259 TCGTCACGGCATAAGTACGG 59.901 55.000 0.00 0.00 0.00 4.02
3505 11509 7.921214 TCAATGTAAAAGCCGTAACATTTTGAA 59.079 29.630 0.00 0.00 39.80 2.69
3534 11663 3.659786 TCGGTACCTGAATCAACAAGTG 58.340 45.455 10.90 0.00 0.00 3.16
3621 11752 2.814919 CAAGTAACCCAACGGCAACATA 59.185 45.455 0.00 0.00 0.00 2.29
3811 11948 5.505173 ACATCTCAAGTTTGACCAAGTTG 57.495 39.130 0.00 0.00 44.43 3.16
4066 15349 2.822561 TCAGCAACACAAAGAACCACAA 59.177 40.909 0.00 0.00 0.00 3.33
4097 15386 3.057456 TCTGTCTAGCACTTTCTTCGTCC 60.057 47.826 0.00 0.00 0.00 4.79
4180 15680 3.833070 CACAGGTACAGGTAAGAAGAGGT 59.167 47.826 0.00 0.00 0.00 3.85
4386 15937 2.816087 CTGCCACAGCTCAACTTTATGT 59.184 45.455 0.00 0.00 40.80 2.29
4387 15938 2.163010 CCTGCCACAGCTCAACTTTATG 59.837 50.000 0.00 0.00 40.80 1.90
4388 15939 2.440409 CCTGCCACAGCTCAACTTTAT 58.560 47.619 0.00 0.00 40.80 1.40
4389 15940 1.545428 CCCTGCCACAGCTCAACTTTA 60.545 52.381 0.00 0.00 40.80 1.85
4485 16061 2.769893 TGGGTAAAACCTTCTACGTGC 58.230 47.619 0.00 0.00 38.64 5.34
4575 16163 5.363562 ACAAGATCAAGAGATACATGCCA 57.636 39.130 0.00 0.00 33.72 4.92
4661 16249 0.726827 CGAATGTAGCGGCAATGTGT 59.273 50.000 1.45 0.00 0.00 3.72
4677 16265 1.001974 CACAAGTCCCATCCAGTCGAA 59.998 52.381 0.00 0.00 0.00 3.71
4734 16322 6.243551 CGACATCAACTGATAATCAACACAC 58.756 40.000 0.00 0.00 32.63 3.82
4735 16323 5.163864 GCGACATCAACTGATAATCAACACA 60.164 40.000 0.00 0.00 32.63 3.72
4832 16423 4.001248 CCATCTTGGCCTCGCAAA 57.999 55.556 3.32 0.00 0.00 3.68
4877 16468 6.594788 ATCATTGCCTTTGTGTCTTTACAT 57.405 33.333 0.00 0.00 38.08 2.29
5018 16614 1.471676 CGATGGAGGGAGCTTGTGTAC 60.472 57.143 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.