Multiple sequence alignment - TraesCS1B01G325300

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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 TraesCS1B01G325300 chr1B 100.000 3203 0 0 1 3203 551034481 551031279 0.000000e+00 5915.0
1 TraesCS1B01G325300 chr1D 96.362 2611 83 6 1 2603 409069504 409066898 0.000000e+00 4285.0
2 TraesCS1B01G325300 chr1D 90.543 497 19 11 2715 3203 409066901 409066425 1.620000e-177 632.0
3 TraesCS1B01G325300 chr1D 81.113 503 80 9 1493 1992 409068241 409067751 3.870000e-104 388.0
4 TraesCS1B01G325300 chr1D 93.600 125 7 1 2596 2720 207187162 207187285 5.460000e-43 185.0
5 TraesCS1B01G325300 chr1D 81.152 191 26 7 530 715 456031669 456031484 9.260000e-31 145.0
6 TraesCS1B01G325300 chr1A 95.408 2613 87 9 1 2603 505284969 505282380 0.000000e+00 4130.0
7 TraesCS1B01G325300 chr1A 92.025 489 17 11 2715 3203 505282383 505281917 0.000000e+00 667.0
8 TraesCS1B01G325300 chr1A 80.517 503 83 9 1493 1992 505283725 505283235 3.900000e-99 372.0
9 TraesCS1B01G325300 chr1A 79.186 221 29 15 288 497 549605281 549605495 1.550000e-28 137.0
10 TraesCS1B01G325300 chr3B 84.142 1236 163 18 489 1705 747746086 747744865 0.000000e+00 1166.0
11 TraesCS1B01G325300 chr3B 78.462 715 123 15 1493 2207 747745317 747744634 3.790000e-119 438.0
12 TraesCS1B01G325300 chr3B 95.763 118 5 0 2600 2717 332925532 332925649 1.170000e-44 191.0
13 TraesCS1B01G325300 chrUn 81.542 1284 156 45 498 1746 108328176 108329413 0.000000e+00 983.0
14 TraesCS1B01G325300 chrUn 87.596 653 79 2 824 1474 134246288 134245636 0.000000e+00 756.0
15 TraesCS1B01G325300 chrUn 87.289 653 81 2 824 1474 65140588 65139936 0.000000e+00 745.0
16 TraesCS1B01G325300 chrUn 78.451 891 133 27 1745 2601 65140151 65139286 7.870000e-146 527.0
17 TraesCS1B01G325300 chrUn 82.617 512 86 1 1745 2253 134245851 134245340 1.750000e-122 449.0
18 TraesCS1B01G325300 chrUn 82.682 358 30 13 4 351 134246765 134246430 4.040000e-74 289.0
19 TraesCS1B01G325300 chrUn 79.511 327 16 25 2317 2601 108329743 108330060 5.460000e-43 185.0
20 TraesCS1B01G325300 chrUn 88.535 157 10 5 633 788 134246435 134246286 1.960000e-42 183.0
21 TraesCS1B01G325300 chrUn 74.950 499 63 29 2718 3200 134244982 134244530 4.250000e-39 172.0
22 TraesCS1B01G325300 chr4B 85.732 792 102 9 557 1343 625962288 625963073 0.000000e+00 826.0
23 TraesCS1B01G325300 chr4B 82.222 765 109 11 798 1549 665915456 665914706 4.510000e-178 634.0
24 TraesCS1B01G325300 chr4B 83.699 638 79 9 825 1460 666572874 666572260 2.140000e-161 579.0
25 TraesCS1B01G325300 chr4B 82.192 511 86 3 1745 2251 666572461 666571952 4.910000e-118 435.0
26 TraesCS1B01G325300 chr4B 83.292 407 50 10 1093 1498 625995987 625996376 3.040000e-95 359.0
27 TraesCS1B01G325300 chr4B 83.714 350 33 13 4 351 666573344 666573017 3.100000e-80 309.0
28 TraesCS1B01G325300 chr4B 86.857 175 14 6 2433 2601 666571775 666571604 1.520000e-43 187.0
29 TraesCS1B01G325300 chr4B 79.151 259 37 8 2718 2967 666571605 666571355 2.560000e-36 163.0
30 TraesCS1B01G325300 chr4B 85.430 151 16 4 636 786 666573020 666572876 5.530000e-33 152.0
31 TraesCS1B01G325300 chr4B 77.154 267 42 9 2718 2973 625997724 625997982 1.550000e-28 137.0
32 TraesCS1B01G325300 chr4B 84.286 140 9 4 2475 2601 625997586 625997725 1.210000e-24 124.0
33 TraesCS1B01G325300 chr4B 81.395 129 24 0 1817 1945 625963431 625963559 4.370000e-19 106.0
34 TraesCS1B01G325300 chr4B 93.878 49 3 0 2553 2601 665961641 665961593 1.230000e-09 75.0
35 TraesCS1B01G325300 chr5A 87.354 514 62 2 798 1308 705897366 705896853 1.280000e-163 586.0
36 TraesCS1B01G325300 chr5B 95.000 120 6 0 2600 2719 202064989 202064870 4.220000e-44 189.0
37 TraesCS1B01G325300 chr2A 95.726 117 5 0 2600 2716 16356295 16356179 4.220000e-44 189.0
38 TraesCS1B01G325300 chr4A 94.262 122 7 0 2598 2719 658949233 658949112 1.520000e-43 187.0
39 TraesCS1B01G325300 chr2D 92.366 131 10 0 2590 2720 95519532 95519662 1.520000e-43 187.0
40 TraesCS1B01G325300 chr2D 94.262 122 7 0 2597 2718 189521487 189521608 1.520000e-43 187.0
41 TraesCS1B01G325300 chr2B 94.958 119 6 0 2599 2717 142446756 142446638 1.520000e-43 187.0
42 TraesCS1B01G325300 chr4D 94.215 121 7 0 2599 2719 72256247 72256127 5.460000e-43 185.0
43 TraesCS1B01G325300 chr7A 87.755 49 6 0 2563 2611 213836271 213836223 1.240000e-04 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 TraesCS1B01G325300 chr1B 551031279 551034481 3202 True 5915.000000 5915 100.000000 1 3203 1 chr1B.!!$R1 3202
1 TraesCS1B01G325300 chr1D 409066425 409069504 3079 True 1768.333333 4285 89.339333 1 3203 3 chr1D.!!$R2 3202
2 TraesCS1B01G325300 chr1A 505281917 505284969 3052 True 1723.000000 4130 89.316667 1 3203 3 chr1A.!!$R1 3202
3 TraesCS1B01G325300 chr3B 747744634 747746086 1452 True 802.000000 1166 81.302000 489 2207 2 chr3B.!!$R1 1718
4 TraesCS1B01G325300 chrUn 65139286 65140588 1302 True 636.000000 745 82.870000 824 2601 2 chrUn.!!$R1 1777
5 TraesCS1B01G325300 chrUn 108328176 108330060 1884 False 584.000000 983 80.526500 498 2601 2 chrUn.!!$F1 2103
6 TraesCS1B01G325300 chrUn 134244530 134246765 2235 True 369.800000 756 83.276000 4 3200 5 chrUn.!!$R2 3196
7 TraesCS1B01G325300 chr4B 665914706 665915456 750 True 634.000000 634 82.222000 798 1549 1 chr4B.!!$R1 751
8 TraesCS1B01G325300 chr4B 625962288 625963559 1271 False 466.000000 826 83.563500 557 1945 2 chr4B.!!$F1 1388
9 TraesCS1B01G325300 chr4B 666571355 666573344 1989 True 304.166667 579 83.507167 4 2967 6 chr4B.!!$R3 2963
10 TraesCS1B01G325300 chr4B 625995987 625997982 1995 False 206.666667 359 81.577333 1093 2973 3 chr4B.!!$F2 1880
11 TraesCS1B01G325300 chr5A 705896853 705897366 513 True 586.000000 586 87.354000 798 1308 1 chr5A.!!$R1 510

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
879 938 2.871182 TTGTTGCGGTTAATGTGCAA 57.129 40.0 7.59 7.59 45.54 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2602 3626 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.2 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
38 39 8.427902 TCAGCATATGTGATACTTATCTCCTT 57.572 34.615 4.29 0.00 33.88 3.36
86 88 7.312657 TCATTTGCTGTAAACAATTTTGCAA 57.687 28.000 0.00 0.00 36.94 4.08
101 103 8.746530 ACAATTTTGCAATGTCATCTTCTCTAT 58.253 29.630 0.00 0.00 0.00 1.98
161 164 6.974965 AGATAGCTGTTTCTTTCACTTTTGG 58.025 36.000 0.00 0.00 0.00 3.28
247 259 4.238514 GGTCGTGATCAGCCTTATATGAC 58.761 47.826 0.00 0.00 0.00 3.06
760 794 3.181445 TGACAACATAGCCCAAACAGTCT 60.181 43.478 0.00 0.00 0.00 3.24
857 916 9.476202 CAACTATTATCATCGTGGAACTTGATA 57.524 33.333 0.00 0.00 38.06 2.15
879 938 2.871182 TTGTTGCGGTTAATGTGCAA 57.129 40.000 7.59 7.59 45.54 4.08
945 1004 8.647143 ATTCTTTTCATTTACAGTTTGGTGTG 57.353 30.769 0.00 0.00 31.46 3.82
1037 1100 9.212641 TGTCAAAATCAACTGTTCAAATTTTCA 57.787 25.926 11.72 7.83 29.54 2.69
1215 1285 3.307480 GCACCCTGGAGTACTACAACATT 60.307 47.826 9.61 0.00 0.00 2.71
1360 1431 4.764823 AGGCAAAGATTTACGATGAAACCA 59.235 37.500 0.00 0.00 0.00 3.67
1361 1432 4.857037 GGCAAAGATTTACGATGAAACCAC 59.143 41.667 0.00 0.00 0.00 4.16
1363 1434 4.939509 AAGATTTACGATGAAACCACCG 57.060 40.909 0.00 0.00 0.00 4.94
1407 1478 0.973632 TCTTTGCTGGGAACGAGCTA 59.026 50.000 4.95 0.00 36.07 3.32
1475 1546 3.684788 ACACTTCATATTGTGTTCCGCTC 59.315 43.478 0.00 0.00 43.88 5.03
1572 2121 8.277720 AGGGAGAAGATAGTCTATACAGTGTA 57.722 38.462 5.24 5.24 0.00 2.90
1605 2154 2.214376 TTGATGAAACCGGCATTCCT 57.786 45.000 15.72 7.85 0.00 3.36
1618 2167 0.617413 CATTCCTCCAGGCAGACAGT 59.383 55.000 0.00 0.00 34.44 3.55
1642 2191 1.074405 TCATCTTTGCTGGGAAGCAGT 59.926 47.619 0.16 0.00 46.21 4.40
1670 2219 3.052082 CCGCACCTTGGCTGACTG 61.052 66.667 0.00 0.00 0.00 3.51
1713 2262 4.834496 ACCATTCATCTTGTGGTGTTTCAT 59.166 37.500 0.00 0.00 44.21 2.57
1728 2277 0.602638 TTCATGGCCTCACGTGTCAC 60.603 55.000 16.51 5.69 0.00 3.67
1732 2281 1.373497 GGCCTCACGTGTCACAGAG 60.373 63.158 16.51 13.06 0.00 3.35
1923 2713 0.108138 GCACCTTGGCTGACTACGAT 60.108 55.000 0.00 0.00 0.00 3.73
1959 2749 0.667993 CCCTTCATGTTGTGTTGCGT 59.332 50.000 0.00 0.00 0.00 5.24
1996 2786 1.956477 GAGGTGGGATGCGCATATTTT 59.044 47.619 25.40 0.00 0.00 1.82
2096 2886 4.193826 TCTACTCTGAGTTGTGCATTCC 57.806 45.455 16.53 0.00 0.00 3.01
2112 2902 3.492353 CCCCCGGACCATCAGCAT 61.492 66.667 0.73 0.00 0.00 3.79
2151 2941 3.247424 CCCCCTGGCTGAAGAGATA 57.753 57.895 0.00 0.00 0.00 1.98
2247 3051 1.691976 TGGTGGTGGTGTTAGTGAGAG 59.308 52.381 0.00 0.00 0.00 3.20
2277 3088 2.351455 GGTAGAGGCTGAGTTTGAAGC 58.649 52.381 0.00 0.00 38.76 3.86
2376 3225 1.209128 AACAAGAGTCACTCGCAACG 58.791 50.000 0.00 0.00 35.36 4.10
2410 3287 1.318576 GGGGTTTCTGTGAAGGTGTG 58.681 55.000 0.00 0.00 0.00 3.82
2601 3625 9.847224 TCTTTTCAGAATCCCTAAACCATATAC 57.153 33.333 0.00 0.00 0.00 1.47
2602 3626 9.853177 CTTTTCAGAATCCCTAAACCATATACT 57.147 33.333 0.00 0.00 0.00 2.12
2603 3627 9.847224 TTTTCAGAATCCCTAAACCATATACTC 57.153 33.333 0.00 0.00 0.00 2.59
2604 3628 7.554959 TCAGAATCCCTAAACCATATACTCC 57.445 40.000 0.00 0.00 0.00 3.85
2605 3629 6.500751 TCAGAATCCCTAAACCATATACTCCC 59.499 42.308 0.00 0.00 0.00 4.30
2606 3630 6.502158 CAGAATCCCTAAACCATATACTCCCT 59.498 42.308 0.00 0.00 0.00 4.20
2607 3631 6.731448 AGAATCCCTAAACCATATACTCCCTC 59.269 42.308 0.00 0.00 0.00 4.30
2608 3632 4.759953 TCCCTAAACCATATACTCCCTCC 58.240 47.826 0.00 0.00 0.00 4.30
2609 3633 3.514309 CCCTAAACCATATACTCCCTCCG 59.486 52.174 0.00 0.00 0.00 4.63
2610 3634 4.158015 CCTAAACCATATACTCCCTCCGT 58.842 47.826 0.00 0.00 0.00 4.69
2611 3635 4.220163 CCTAAACCATATACTCCCTCCGTC 59.780 50.000 0.00 0.00 0.00 4.79
2612 3636 2.305858 ACCATATACTCCCTCCGTCC 57.694 55.000 0.00 0.00 0.00 4.79
2613 3637 1.174783 CCATATACTCCCTCCGTCCG 58.825 60.000 0.00 0.00 0.00 4.79
2614 3638 1.174783 CATATACTCCCTCCGTCCGG 58.825 60.000 0.00 0.00 0.00 5.14
2615 3639 1.070604 ATATACTCCCTCCGTCCGGA 58.929 55.000 0.00 0.00 42.90 5.14
2616 3640 0.846015 TATACTCCCTCCGTCCGGAA 59.154 55.000 5.23 0.00 44.66 4.30
2617 3641 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
2618 3642 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
2619 3643 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
2620 3644 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
2621 3645 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
2622 3646 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
2623 3647 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
2624 3648 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
2625 3649 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
2626 3650 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
2627 3651 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
2628 3652 3.700539 TCCGTCCGGAAATACTTGTCATA 59.299 43.478 5.23 0.00 42.05 2.15
2629 3653 4.160065 TCCGTCCGGAAATACTTGTCATAA 59.840 41.667 5.23 0.00 42.05 1.90
2630 3654 4.871557 CCGTCCGGAAATACTTGTCATAAA 59.128 41.667 5.23 0.00 37.50 1.40
2631 3655 5.352016 CCGTCCGGAAATACTTGTCATAAAA 59.648 40.000 5.23 0.00 37.50 1.52
2632 3656 6.128227 CCGTCCGGAAATACTTGTCATAAAAA 60.128 38.462 5.23 0.00 37.50 1.94
2633 3657 7.414762 CCGTCCGGAAATACTTGTCATAAAAAT 60.415 37.037 5.23 0.00 37.50 1.82
2634 3658 7.428183 CGTCCGGAAATACTTGTCATAAAAATG 59.572 37.037 5.23 0.00 0.00 2.32
2635 3659 7.220108 GTCCGGAAATACTTGTCATAAAAATGC 59.780 37.037 5.23 0.00 0.00 3.56
2636 3660 7.032580 CCGGAAATACTTGTCATAAAAATGCA 58.967 34.615 0.00 0.00 0.00 3.96
2637 3661 7.706179 CCGGAAATACTTGTCATAAAAATGCAT 59.294 33.333 0.00 0.00 0.00 3.96
2638 3662 9.729023 CGGAAATACTTGTCATAAAAATGCATA 57.271 29.630 0.00 0.00 0.00 3.14
2691 3715 6.576662 TCTAGATACATCCATTTCTCCGAC 57.423 41.667 0.00 0.00 0.00 4.79
2692 3716 6.068670 TCTAGATACATCCATTTCTCCGACA 58.931 40.000 0.00 0.00 0.00 4.35
2693 3717 5.614324 AGATACATCCATTTCTCCGACAA 57.386 39.130 0.00 0.00 0.00 3.18
2694 3718 5.605534 AGATACATCCATTTCTCCGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
2695 3719 3.703001 ACATCCATTTCTCCGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
2696 3720 4.819105 ACATCCATTTCTCCGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
2697 3721 5.359194 ACATCCATTTCTCCGACAAGTAT 57.641 39.130 0.00 0.00 0.00 2.12
2698 3722 5.745227 ACATCCATTTCTCCGACAAGTATT 58.255 37.500 0.00 0.00 0.00 1.89
2699 3723 6.180472 ACATCCATTTCTCCGACAAGTATTT 58.820 36.000 0.00 0.00 0.00 1.40
2700 3724 6.316390 ACATCCATTTCTCCGACAAGTATTTC 59.684 38.462 0.00 0.00 0.00 2.17
2701 3725 4.868171 TCCATTTCTCCGACAAGTATTTCG 59.132 41.667 0.00 0.00 34.93 3.46
2740 3764 4.695396 AGATGCAGAGCAAAGATAGACAG 58.305 43.478 0.00 0.00 43.62 3.51
2773 3797 1.133575 CCAATCACCAGGGCTGATCAT 60.134 52.381 0.00 0.00 0.00 2.45
2786 3810 4.082026 GGGCTGATCATTACAACTTTTGCT 60.082 41.667 0.00 0.00 0.00 3.91
2810 3834 5.426689 TGTCTCCTGCATCAAATTACTCT 57.573 39.130 0.00 0.00 0.00 3.24
2811 3835 6.544928 TGTCTCCTGCATCAAATTACTCTA 57.455 37.500 0.00 0.00 0.00 2.43
2812 3836 7.129457 TGTCTCCTGCATCAAATTACTCTAT 57.871 36.000 0.00 0.00 0.00 1.98
2813 3837 7.568349 TGTCTCCTGCATCAAATTACTCTATT 58.432 34.615 0.00 0.00 0.00 1.73
2814 3838 7.712639 TGTCTCCTGCATCAAATTACTCTATTC 59.287 37.037 0.00 0.00 0.00 1.75
2828 3852 5.690464 ACTCTATTCAAGGAGAGCACATT 57.310 39.130 0.00 0.00 42.56 2.71
2912 3950 4.329638 TCTGCCTTCAATGGGGAATAAA 57.670 40.909 0.00 0.00 0.00 1.40
2913 3951 4.882559 TCTGCCTTCAATGGGGAATAAAT 58.117 39.130 0.00 0.00 0.00 1.40
2914 3952 6.024563 TCTGCCTTCAATGGGGAATAAATA 57.975 37.500 0.00 0.00 0.00 1.40
2915 3953 6.439487 TCTGCCTTCAATGGGGAATAAATAA 58.561 36.000 0.00 0.00 0.00 1.40
2992 4036 9.635520 TGTAACTGAAGCTCATTAAACTACTAC 57.364 33.333 0.00 0.00 0.00 2.73
2993 4037 9.857957 GTAACTGAAGCTCATTAAACTACTACT 57.142 33.333 0.00 0.00 0.00 2.57
2994 4038 8.764524 AACTGAAGCTCATTAAACTACTACTG 57.235 34.615 0.00 0.00 0.00 2.74
2995 4039 7.897864 ACTGAAGCTCATTAAACTACTACTGT 58.102 34.615 0.00 0.00 0.00 3.55
2996 4040 9.021807 ACTGAAGCTCATTAAACTACTACTGTA 57.978 33.333 0.00 0.00 0.00 2.74
3049 4094 3.317993 CCTGTGGTGGTTACTTTCCTTTG 59.682 47.826 0.00 0.00 0.00 2.77
3061 4106 2.859165 TTCCTTTGCTGGTACTCTGG 57.141 50.000 0.00 0.00 0.00 3.86
3074 4119 3.756963 GGTACTCTGGAAACAATTGGTCC 59.243 47.826 18.85 18.85 42.06 4.46
3112 4159 4.380233 CGGTCGTACCTTGAGTTCAGTTAT 60.380 45.833 3.15 0.00 35.66 1.89
3113 4160 5.476614 GGTCGTACCTTGAGTTCAGTTATT 58.523 41.667 0.00 0.00 34.73 1.40
3114 4161 6.623549 CGGTCGTACCTTGAGTTCAGTTATTA 60.624 42.308 3.15 0.00 35.66 0.98
3158 4205 7.775093 TGGGATCATTCATCTTAGTTACCTTTG 59.225 37.037 0.00 0.00 0.00 2.77
3189 4245 3.733684 GCGTTTCAAACCAGAAGCTCAAA 60.734 43.478 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 6.244552 ACCAGCAAAATCATCTAGATCTCA 57.755 37.500 1.03 0.00 35.39 3.27
86 88 9.689976 CAACTCGATTTATAGAGAAGATGACAT 57.310 33.333 6.82 0.00 37.87 3.06
101 103 7.722795 TGAACACTTCAATCAACTCGATTTA 57.277 32.000 0.00 0.00 41.83 1.40
247 259 5.529060 GGAAGACCTTCAAGTTGCTATATGG 59.471 44.000 11.38 0.00 41.20 2.74
622 645 8.630917 CGAGAATCCTACAGATTAGTCCTTTTA 58.369 37.037 0.00 0.00 45.52 1.52
819 878 1.975660 AATAGTTGGTGTTGCACGGT 58.024 45.000 0.00 0.00 34.83 4.83
857 916 3.722147 TGCACATTAACCGCAACAAATT 58.278 36.364 0.00 0.00 31.46 1.82
945 1004 7.871853 TCTTAGACACAAGGCTTTCATTAAAC 58.128 34.615 0.00 0.00 0.00 2.01
1215 1285 0.539669 TGAGCGTGGACTCTTCCTCA 60.540 55.000 0.00 0.00 43.31 3.86
1407 1478 1.302285 CAAGGTGCAGCCATCCTCT 59.698 57.895 13.29 0.00 40.61 3.69
1475 1546 1.226802 CCATCTCTCTGACACGCCG 60.227 63.158 0.00 0.00 0.00 6.46
1572 2121 6.018016 CGGTTTCATCAAAAATCTTTGCCTTT 60.018 34.615 0.00 0.00 41.53 3.11
1605 2154 0.469892 TGAGACACTGTCTGCCTGGA 60.470 55.000 16.69 0.00 43.53 3.86
1618 2167 2.877300 GCTTCCCAGCAAAGATGAGACA 60.877 50.000 0.00 0.00 46.49 3.41
1642 2191 4.424711 GGTGCGGCCATCCTCCAA 62.425 66.667 2.24 0.00 37.17 3.53
1670 2219 1.838913 AGTTTCGTTGTGCACATTGC 58.161 45.000 22.39 12.93 45.29 3.56
1687 2236 4.640771 ACACCACAAGATGAATGGTAGT 57.359 40.909 0.00 0.00 45.11 2.73
1688 2237 5.473162 TGAAACACCACAAGATGAATGGTAG 59.527 40.000 0.00 0.00 45.11 3.18
1713 2262 2.087462 CTCTGTGACACGTGAGGCCA 62.087 60.000 25.01 11.25 0.00 5.36
1728 2277 1.381928 GCATGTGCATCCCACCTCTG 61.382 60.000 0.00 0.00 44.01 3.35
1959 2749 4.056125 CTCTGCCTCGTGACGCCA 62.056 66.667 0.00 0.00 0.00 5.69
1996 2786 1.401318 TTCCCGTTCACCGTCCTGAA 61.401 55.000 0.00 0.00 33.66 3.02
2096 2886 2.111878 GATGCTGATGGTCCGGGG 59.888 66.667 0.00 0.00 0.00 5.73
2112 2902 2.363018 CCGCCCTGGTCAGAGAGA 60.363 66.667 0.00 0.00 0.00 3.10
2151 2941 0.670546 CAAGGGTGCACGAACGAGAT 60.671 55.000 11.45 0.00 0.00 2.75
2247 3051 0.750182 AGCCTCTACCGAGTCTGAGC 60.750 60.000 0.00 0.00 35.43 4.26
2376 3225 1.217244 CCCCACCTACGTACACAGC 59.783 63.158 0.00 0.00 0.00 4.40
2410 3287 0.792640 CACGGTGACATCAAGTGCTC 59.207 55.000 0.74 0.00 32.77 4.26
2601 3625 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
2602 3626 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
2603 3627 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
2604 3628 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
2605 3629 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
2606 3630 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
2607 3631 2.373540 TGACAAGTATTTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
2608 3632 6.411630 TTTTATGACAAGTATTTCCGGACG 57.588 37.500 1.83 0.00 0.00 4.79
2609 3633 7.220108 GCATTTTTATGACAAGTATTTCCGGAC 59.780 37.037 1.83 0.00 0.00 4.79
2610 3634 7.094162 TGCATTTTTATGACAAGTATTTCCGGA 60.094 33.333 0.00 0.00 0.00 5.14
2611 3635 7.032580 TGCATTTTTATGACAAGTATTTCCGG 58.967 34.615 0.00 0.00 0.00 5.14
2612 3636 8.633075 ATGCATTTTTATGACAAGTATTTCCG 57.367 30.769 0.00 0.00 0.00 4.30
2665 3689 8.908903 GTCGGAGAAATGGATGTATCTAGATAT 58.091 37.037 15.43 1.62 39.69 1.63
2666 3690 7.888546 TGTCGGAGAAATGGATGTATCTAGATA 59.111 37.037 8.44 8.44 39.69 1.98
2667 3691 6.721668 TGTCGGAGAAATGGATGTATCTAGAT 59.278 38.462 10.73 10.73 39.69 1.98
2668 3692 6.068670 TGTCGGAGAAATGGATGTATCTAGA 58.931 40.000 0.00 0.00 39.69 2.43
2669 3693 6.332735 TGTCGGAGAAATGGATGTATCTAG 57.667 41.667 0.00 0.00 39.69 2.43
2670 3694 6.323996 ACTTGTCGGAGAAATGGATGTATCTA 59.676 38.462 0.00 0.00 39.69 1.98
2671 3695 5.129485 ACTTGTCGGAGAAATGGATGTATCT 59.871 40.000 0.00 0.00 39.69 1.98
2672 3696 5.360591 ACTTGTCGGAGAAATGGATGTATC 58.639 41.667 0.00 0.00 39.69 2.24
2673 3697 5.359194 ACTTGTCGGAGAAATGGATGTAT 57.641 39.130 0.00 0.00 39.69 2.29
2674 3698 4.819105 ACTTGTCGGAGAAATGGATGTA 57.181 40.909 0.00 0.00 39.69 2.29
2675 3699 3.703001 ACTTGTCGGAGAAATGGATGT 57.297 42.857 0.00 0.00 39.69 3.06
2676 3700 6.510157 CGAAATACTTGTCGGAGAAATGGATG 60.510 42.308 0.00 0.00 39.69 3.51
2677 3701 5.523916 CGAAATACTTGTCGGAGAAATGGAT 59.476 40.000 0.00 0.00 39.69 3.41
2678 3702 4.868171 CGAAATACTTGTCGGAGAAATGGA 59.132 41.667 0.00 0.00 39.69 3.41
2679 3703 5.143916 CGAAATACTTGTCGGAGAAATGG 57.856 43.478 0.00 0.00 39.69 3.16
2688 3712 1.135315 TCCGTCCCGAAATACTTGTCG 60.135 52.381 0.00 0.00 37.01 4.35
2689 3713 2.537401 CTCCGTCCCGAAATACTTGTC 58.463 52.381 0.00 0.00 0.00 3.18
2690 3714 1.206371 CCTCCGTCCCGAAATACTTGT 59.794 52.381 0.00 0.00 0.00 3.16
2691 3715 1.472728 CCCTCCGTCCCGAAATACTTG 60.473 57.143 0.00 0.00 0.00 3.16
2692 3716 0.828677 CCCTCCGTCCCGAAATACTT 59.171 55.000 0.00 0.00 0.00 2.24
2693 3717 0.032813 TCCCTCCGTCCCGAAATACT 60.033 55.000 0.00 0.00 0.00 2.12
2694 3718 0.388294 CTCCCTCCGTCCCGAAATAC 59.612 60.000 0.00 0.00 0.00 1.89
2695 3719 0.032813 ACTCCCTCCGTCCCGAAATA 60.033 55.000 0.00 0.00 0.00 1.40
2696 3720 0.032813 TACTCCCTCCGTCCCGAAAT 60.033 55.000 0.00 0.00 0.00 2.17
2697 3721 0.967380 GTACTCCCTCCGTCCCGAAA 60.967 60.000 0.00 0.00 0.00 3.46
2698 3722 1.379044 GTACTCCCTCCGTCCCGAA 60.379 63.158 0.00 0.00 0.00 4.30
2699 3723 0.982852 TAGTACTCCCTCCGTCCCGA 60.983 60.000 0.00 0.00 0.00 5.14
2700 3724 0.534652 CTAGTACTCCCTCCGTCCCG 60.535 65.000 0.00 0.00 0.00 5.14
2701 3725 0.842635 TCTAGTACTCCCTCCGTCCC 59.157 60.000 0.00 0.00 0.00 4.46
2702 3726 2.506444 CATCTAGTACTCCCTCCGTCC 58.494 57.143 0.00 0.00 0.00 4.79
2703 3727 1.881324 GCATCTAGTACTCCCTCCGTC 59.119 57.143 0.00 0.00 0.00 4.79
2704 3728 1.214673 TGCATCTAGTACTCCCTCCGT 59.785 52.381 0.00 0.00 0.00 4.69
2705 3729 1.883275 CTGCATCTAGTACTCCCTCCG 59.117 57.143 0.00 0.00 0.00 4.63
2706 3730 3.153919 CTCTGCATCTAGTACTCCCTCC 58.846 54.545 0.00 0.00 0.00 4.30
2707 3731 2.556622 GCTCTGCATCTAGTACTCCCTC 59.443 54.545 0.00 0.00 0.00 4.30
2708 3732 2.091610 TGCTCTGCATCTAGTACTCCCT 60.092 50.000 0.00 0.00 31.71 4.20
2709 3733 2.311463 TGCTCTGCATCTAGTACTCCC 58.689 52.381 0.00 0.00 31.71 4.30
2710 3734 4.098654 TCTTTGCTCTGCATCTAGTACTCC 59.901 45.833 0.00 0.00 38.76 3.85
2711 3735 5.255710 TCTTTGCTCTGCATCTAGTACTC 57.744 43.478 0.00 0.00 38.76 2.59
2712 3736 5.867903 ATCTTTGCTCTGCATCTAGTACT 57.132 39.130 0.00 0.00 38.76 2.73
2713 3737 6.861055 GTCTATCTTTGCTCTGCATCTAGTAC 59.139 42.308 0.00 0.00 38.76 2.73
2714 3738 6.547510 TGTCTATCTTTGCTCTGCATCTAGTA 59.452 38.462 0.00 0.00 38.76 1.82
2715 3739 5.362143 TGTCTATCTTTGCTCTGCATCTAGT 59.638 40.000 0.00 0.00 38.76 2.57
2740 3764 3.274288 GGTGATTGGTGAAGATCTCCAC 58.726 50.000 2.98 2.98 39.48 4.02
2773 3797 5.678616 GCAGGAGACAAAGCAAAAGTTGTAA 60.679 40.000 0.00 0.00 38.07 2.41
2786 3810 6.240894 AGAGTAATTTGATGCAGGAGACAAA 58.759 36.000 0.00 0.00 36.82 2.83
2810 3834 3.691118 GTGCAATGTGCTCTCCTTGAATA 59.309 43.478 1.43 0.00 45.31 1.75
2811 3835 2.490903 GTGCAATGTGCTCTCCTTGAAT 59.509 45.455 1.43 0.00 45.31 2.57
2812 3836 1.881973 GTGCAATGTGCTCTCCTTGAA 59.118 47.619 1.43 0.00 45.31 2.69
2813 3837 1.202794 TGTGCAATGTGCTCTCCTTGA 60.203 47.619 1.43 0.00 45.31 3.02
2814 3838 1.241165 TGTGCAATGTGCTCTCCTTG 58.759 50.000 1.43 0.00 45.31 3.61
2828 3852 4.759693 AGTCTTACATCCGAAATTTGTGCA 59.240 37.500 0.00 0.00 0.00 4.57
2912 3950 7.657023 AGTTACTTTGGTCGATACCTCTTAT 57.343 36.000 0.00 0.00 46.91 1.73
2913 3951 8.579850 TTAGTTACTTTGGTCGATACCTCTTA 57.420 34.615 0.00 0.00 46.91 2.10
2914 3952 5.997384 AGTTACTTTGGTCGATACCTCTT 57.003 39.130 0.00 0.00 46.91 2.85
2915 3953 7.657023 ATTAGTTACTTTGGTCGATACCTCT 57.343 36.000 0.00 0.00 46.91 3.69
2992 4036 6.166984 AGGGTGTGTATGAATGATCTACAG 57.833 41.667 0.00 0.00 0.00 2.74
2993 4037 7.202001 CCTTAGGGTGTGTATGAATGATCTACA 60.202 40.741 0.00 0.00 0.00 2.74
2994 4038 7.155328 CCTTAGGGTGTGTATGAATGATCTAC 58.845 42.308 0.00 0.00 0.00 2.59
2995 4039 6.239600 GCCTTAGGGTGTGTATGAATGATCTA 60.240 42.308 0.00 0.00 34.45 1.98
2996 4040 5.455326 GCCTTAGGGTGTGTATGAATGATCT 60.455 44.000 0.00 0.00 34.45 2.75
3049 4094 3.191371 CCAATTGTTTCCAGAGTACCAGC 59.809 47.826 4.43 0.00 0.00 4.85
3061 4106 6.644592 TGATCAAATTTCGGACCAATTGTTTC 59.355 34.615 4.43 0.23 0.00 2.78
3074 4119 4.258935 ACGACCGAATGATCAAATTTCG 57.741 40.909 18.61 18.61 41.31 3.46
3169 4225 4.363138 CCTTTGAGCTTCTGGTTTGAAAC 58.637 43.478 0.00 0.00 0.00 2.78


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

AutoCloner maintained by Alex Coulton.