Multiple sequence alignment - TraesCS1D01G379700

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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 TraesCS1D01G379700 chr1D 100.000 3701 0 0 1 3701 455758848 455762548 0.000000e+00 6835.0
1 TraesCS1D01G379700 chr1D 94.444 180 7 3 2473 2650 115018580 115018758 1.310000e-69 274.0
2 TraesCS1D01G379700 chr1A 91.523 2489 131 31 1 2456 549300447 549302888 0.000000e+00 3354.0
3 TraesCS1D01G379700 chr1A 92.265 1073 53 14 2651 3701 549302897 549303961 0.000000e+00 1495.0
4 TraesCS1D01G379700 chr1B 92.088 1719 88 17 1 1682 626096613 626098320 0.000000e+00 2377.0
5 TraesCS1D01G379700 chr1B 91.608 846 49 7 2649 3487 626099121 626099951 0.000000e+00 1149.0
6 TraesCS1D01G379700 chr1B 91.754 667 33 7 1708 2365 626098397 626099050 0.000000e+00 907.0
7 TraesCS1D01G379700 chr1B 94.706 170 9 0 3489 3658 626100036 626100205 7.880000e-67 265.0
8 TraesCS1D01G379700 chr1B 100.000 29 0 0 3673 3701 626100204 626100232 2.000000e-03 54.7
9 TraesCS1D01G379700 chr6D 95.977 174 7 0 2477 2650 45503525 45503352 2.180000e-72 283.0
10 TraesCS1D01G379700 chr2D 96.471 170 6 0 2487 2656 5108110 5107941 7.830000e-72 281.0
11 TraesCS1D01G379700 chr2D 93.443 183 12 0 2468 2650 650869232 650869050 4.710000e-69 272.0
12 TraesCS1D01G379700 chr2D 82.906 117 19 1 1937 2052 527547518 527547634 1.820000e-18 104.0
13 TraesCS1D01G379700 chr2D 100.000 29 0 0 2470 2498 555111864 555111892 2.000000e-03 54.7
14 TraesCS1D01G379700 chr7D 96.450 169 6 0 2486 2654 416957168 416957000 2.810000e-71 279.0
15 TraesCS1D01G379700 chr5D 96.450 169 6 0 2484 2652 432167256 432167424 2.810000e-71 279.0
16 TraesCS1D01G379700 chr3D 96.988 166 5 0 2486 2651 346313694 346313529 2.810000e-71 279.0
17 TraesCS1D01G379700 chr2B 93.548 186 8 3 2467 2650 161144189 161144006 1.310000e-69 274.0
18 TraesCS1D01G379700 chr2B 82.906 117 19 1 1937 2052 624892073 624892189 1.820000e-18 104.0
19 TraesCS1D01G379700 chr3A 92.553 188 13 1 2465 2651 682364448 682364635 6.090000e-68 268.0


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 TraesCS1D01G379700 chr1D 455758848 455762548 3700 False 6835.00 6835 100.0000 1 3701 1 chr1D.!!$F2 3700
1 TraesCS1D01G379700 chr1A 549300447 549303961 3514 False 2424.50 3354 91.8940 1 3701 2 chr1A.!!$F1 3700
2 TraesCS1D01G379700 chr1B 626096613 626100232 3619 False 950.54 2377 94.0312 1 3701 5 chr1B.!!$F1 3700

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
274 275 0.613260 ATTCTGCCTTGCTGTACGGA 59.387 50.0 5.68 0.0 0.0 4.69 F
1182 1226 0.606401 CCGAAAGAGCTGGCCAAGAA 60.606 55.0 7.01 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1645 1702 0.949397 TGCTGTGCTCTTTGAAGCTG 59.051 50.0 0.0 0.0 42.94 4.24 R
3062 3187 0.326927 TCCGGAACCCAGAATTCCAC 59.673 55.0 0.0 0.0 45.15 4.02 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
86 87 2.946329 TGCTTTGTTACGTGTTGTCCAT 59.054 40.909 0.00 0.00 0.00 3.41
182 183 3.076621 TCGCAGCTCAGATTTTGACATT 58.923 40.909 0.00 0.00 0.00 2.71
194 195 3.913548 TTTGACATTTGGACATCACGG 57.086 42.857 0.00 0.00 0.00 4.94
243 244 2.796383 GCCGTAGCAGTCAGTGTGATAG 60.796 54.545 0.00 0.00 39.53 2.08
274 275 0.613260 ATTCTGCCTTGCTGTACGGA 59.387 50.000 5.68 0.00 0.00 4.69
278 279 1.131126 CTGCCTTGCTGTACGGATTTG 59.869 52.381 5.68 0.00 0.00 2.32
282 283 3.340034 CCTTGCTGTACGGATTTGGTTA 58.660 45.455 5.68 0.00 0.00 2.85
367 370 7.544566 AGCAATCTTTTGACAAAGCATATTCTG 59.455 33.333 10.58 1.26 39.56 3.02
600 623 7.334858 TGGTTGTTGCCTTAAGAAAAGAAAAT 58.665 30.769 3.36 0.00 0.00 1.82
641 667 3.507233 GTCTGGGAGAAATGCAAATGTCA 59.493 43.478 0.00 0.00 0.00 3.58
642 668 4.159135 GTCTGGGAGAAATGCAAATGTCAT 59.841 41.667 0.00 0.00 0.00 3.06
643 669 5.357878 GTCTGGGAGAAATGCAAATGTCATA 59.642 40.000 0.00 0.00 0.00 2.15
644 670 5.951148 TCTGGGAGAAATGCAAATGTCATAA 59.049 36.000 0.00 0.00 0.00 1.90
645 671 6.436847 TCTGGGAGAAATGCAAATGTCATAAA 59.563 34.615 0.00 0.00 0.00 1.40
646 672 6.397272 TGGGAGAAATGCAAATGTCATAAAC 58.603 36.000 0.00 0.00 0.00 2.01
647 673 6.211184 TGGGAGAAATGCAAATGTCATAAACT 59.789 34.615 0.00 0.00 0.00 2.66
648 674 6.753744 GGGAGAAATGCAAATGTCATAAACTC 59.246 38.462 0.00 0.00 0.00 3.01
669 695 8.480643 AACTCATAATAGCTCGTAATAATGCC 57.519 34.615 0.00 0.00 0.00 4.40
734 764 3.262151 TGTGGACCTCGGTTGAAATATGA 59.738 43.478 0.00 0.00 0.00 2.15
735 765 4.258543 GTGGACCTCGGTTGAAATATGAA 58.741 43.478 0.00 0.00 0.00 2.57
756 786 5.548056 TGAAAATCTCCAGTTAACCCTCTCT 59.452 40.000 0.88 0.00 0.00 3.10
796 826 9.630098 CAAAGTTCAAATAGATTGCACACTTAT 57.370 29.630 0.00 0.00 37.59 1.73
801 831 8.662781 TCAAATAGATTGCACACTTATCCTAC 57.337 34.615 0.00 0.00 38.98 3.18
805 835 5.371526 AGATTGCACACTTATCCTACCATG 58.628 41.667 0.00 0.00 0.00 3.66
1071 1112 2.350964 GCTTAGTCTAGGCGATCTTCCG 60.351 54.545 0.00 0.00 0.00 4.30
1072 1113 2.924757 TAGTCTAGGCGATCTTCCGA 57.075 50.000 0.00 0.00 0.00 4.55
1140 1184 2.023414 AAGACCACGACGACCTTGCA 62.023 55.000 0.00 0.00 0.00 4.08
1175 1219 4.522971 GGCTACCGAAAGAGCTGG 57.477 61.111 0.00 0.00 38.79 4.85
1182 1226 0.606401 CCGAAAGAGCTGGCCAAGAA 60.606 55.000 7.01 0.00 0.00 2.52
1227 1274 1.540267 CGGAGGGAGAAGATAGCGAT 58.460 55.000 0.00 0.00 0.00 4.58
1238 1285 0.801251 GATAGCGATGAAGCATGCCC 59.199 55.000 15.66 7.45 40.15 5.36
1296 1343 4.385825 CCTCTGCACAAACAGGTAAGTTA 58.614 43.478 0.00 0.00 38.26 2.24
1326 1373 2.295349 CCTGCAGAACAAGCTGTTGAAT 59.705 45.455 17.39 0.00 41.28 2.57
1397 1453 6.530534 GCTCGTAGCTTCTGTCTGTAAAATTA 59.469 38.462 0.00 0.00 38.45 1.40
1494 1551 1.144716 TGGATGGCAGAGCATCGAC 59.855 57.895 0.00 0.00 42.67 4.20
1541 1598 2.195727 TGCATATGGAGGTTCCTGTGA 58.804 47.619 4.56 0.00 37.46 3.58
1573 1630 3.729108 TGATGAGGAAGGTTCAGAGGAT 58.271 45.455 0.00 0.00 0.00 3.24
1643 1700 4.220821 AGGAACAATCTGCGTTTCTAGAGA 59.779 41.667 0.00 0.00 30.11 3.10
1645 1702 3.516615 ACAATCTGCGTTTCTAGAGAGC 58.483 45.455 8.61 8.61 0.00 4.09
1682 1739 0.178068 CACGCTAACCCTGGTATGCT 59.822 55.000 10.37 0.00 0.00 3.79
1683 1740 1.411246 CACGCTAACCCTGGTATGCTA 59.589 52.381 10.37 0.00 0.00 3.49
1684 1741 2.037251 CACGCTAACCCTGGTATGCTAT 59.963 50.000 10.37 0.00 0.00 2.97
1685 1742 2.037251 ACGCTAACCCTGGTATGCTATG 59.963 50.000 10.37 0.93 0.00 2.23
1686 1743 2.427506 GCTAACCCTGGTATGCTATGC 58.572 52.381 6.31 0.00 0.00 3.14
1687 1744 2.224523 GCTAACCCTGGTATGCTATGCA 60.225 50.000 0.00 0.00 44.86 3.96
1688 1745 3.747388 GCTAACCCTGGTATGCTATGCAA 60.747 47.826 0.00 0.00 43.62 4.08
1689 1746 3.600448 AACCCTGGTATGCTATGCAAT 57.400 42.857 0.00 0.00 43.62 3.56
1690 1747 4.722526 AACCCTGGTATGCTATGCAATA 57.277 40.909 0.00 0.00 43.62 1.90
1691 1748 4.934797 ACCCTGGTATGCTATGCAATAT 57.065 40.909 0.00 0.00 43.62 1.28
1733 1843 4.785346 AAGTGGATGATGTAGCTGGATT 57.215 40.909 0.00 0.00 0.00 3.01
1734 1844 4.348863 AGTGGATGATGTAGCTGGATTC 57.651 45.455 0.00 0.00 0.00 2.52
1752 1862 7.558161 TGGATTCATTCATTCGGCATATATC 57.442 36.000 0.00 0.00 0.00 1.63
1850 1960 6.599638 AGAAGAGCCAGGTATGTAACAAAATC 59.400 38.462 0.00 0.00 0.00 2.17
1871 1981 5.945144 TCTATACACCAGTAGTTTTCCCC 57.055 43.478 0.00 0.00 32.86 4.81
1872 1982 5.596763 TCTATACACCAGTAGTTTTCCCCT 58.403 41.667 0.00 0.00 32.86 4.79
1873 1983 6.027482 TCTATACACCAGTAGTTTTCCCCTT 58.973 40.000 0.00 0.00 32.86 3.95
1874 1984 3.965470 ACACCAGTAGTTTTCCCCTTT 57.035 42.857 0.00 0.00 0.00 3.11
1876 1986 3.958147 ACACCAGTAGTTTTCCCCTTTTG 59.042 43.478 0.00 0.00 0.00 2.44
1877 1987 4.211920 CACCAGTAGTTTTCCCCTTTTGA 58.788 43.478 0.00 0.00 0.00 2.69
1878 1988 4.278419 CACCAGTAGTTTTCCCCTTTTGAG 59.722 45.833 0.00 0.00 0.00 3.02
1900 2010 5.846203 AGTTTTGATGTCACCATTTTCCAG 58.154 37.500 0.00 0.00 0.00 3.86
1914 2024 2.440539 TTCCAGAACAGAAGAGCGAC 57.559 50.000 0.00 0.00 0.00 5.19
1930 2044 6.073327 AGAGCGACGAAATCTAACATCATA 57.927 37.500 0.00 0.00 0.00 2.15
1937 2051 9.872791 CGACGAAATCTAACATCATATTTATCG 57.127 33.333 0.00 0.00 0.00 2.92
2089 2203 4.507710 GCTCTACAATCTGAATCACCACA 58.492 43.478 0.00 0.00 0.00 4.17
2101 2215 0.034756 TCACCACATGTCTGGGTTCG 59.965 55.000 3.65 0.00 35.34 3.95
2102 2216 1.302511 ACCACATGTCTGGGTTCGC 60.303 57.895 7.24 0.00 35.34 4.70
2140 2254 1.423721 CTCATCATGTGACGCCACCG 61.424 60.000 0.00 0.00 42.53 4.94
2334 2451 8.836413 TCATGTTGCCTAAGTTATGTAAATAGC 58.164 33.333 0.00 0.00 0.00 2.97
2342 2459 9.046296 CCTAAGTTATGTAAATAGCCTCTTGTG 57.954 37.037 0.00 0.00 0.00 3.33
2371 2488 6.569780 TGTCACCAGTGATGTACATACATAC 58.430 40.000 8.71 6.17 46.20 2.39
2372 2489 6.153680 TGTCACCAGTGATGTACATACATACA 59.846 38.462 8.71 0.00 46.20 2.29
2373 2490 7.147742 TGTCACCAGTGATGTACATACATACAT 60.148 37.037 8.71 0.00 46.20 2.29
2374 2491 8.357402 GTCACCAGTGATGTACATACATACATA 58.643 37.037 8.71 0.00 46.20 2.29
2375 2492 8.357402 TCACCAGTGATGTACATACATACATAC 58.643 37.037 8.71 3.26 46.20 2.39
2376 2493 7.326063 CACCAGTGATGTACATACATACATACG 59.674 40.741 8.71 0.00 46.20 3.06
2377 2494 7.013942 ACCAGTGATGTACATACATACATACGT 59.986 37.037 8.71 0.00 46.20 3.57
2378 2495 8.508875 CCAGTGATGTACATACATACATACGTA 58.491 37.037 8.71 0.00 46.20 3.57
2400 2517 3.815401 AGAAAGGAGTCGAAAACCATGTG 59.185 43.478 0.00 0.00 0.00 3.21
2402 2519 4.345859 AAGGAGTCGAAAACCATGTGTA 57.654 40.909 0.00 0.00 0.00 2.90
2423 2541 9.903682 TGTGTACATCTACTTTGTAAACTCTAC 57.096 33.333 0.00 0.00 38.22 2.59
2456 2576 7.576236 CCATTTTTATAACGGTAGATGAGCTG 58.424 38.462 0.00 0.00 0.00 4.24
2457 2577 7.441157 CCATTTTTATAACGGTAGATGAGCTGA 59.559 37.037 0.00 0.00 0.00 4.26
2458 2578 8.491152 CATTTTTATAACGGTAGATGAGCTGAG 58.509 37.037 0.00 0.00 0.00 3.35
2459 2579 3.651803 ATAACGGTAGATGAGCTGAGC 57.348 47.619 0.00 0.00 0.00 4.26
2471 2591 2.928694 GAGCTGAGCTCGCTTATACTC 58.071 52.381 26.17 13.78 45.85 2.59
2472 2592 1.611491 AGCTGAGCTCGCTTATACTCC 59.389 52.381 21.97 0.00 30.62 3.85
2473 2593 1.336424 GCTGAGCTCGCTTATACTCCC 60.336 57.143 19.01 0.00 0.00 4.30
2474 2594 2.235016 CTGAGCTCGCTTATACTCCCT 58.765 52.381 9.64 0.00 0.00 4.20
2475 2595 2.625790 CTGAGCTCGCTTATACTCCCTT 59.374 50.000 9.64 0.00 0.00 3.95
2476 2596 2.623889 TGAGCTCGCTTATACTCCCTTC 59.376 50.000 9.64 0.00 0.00 3.46
2477 2597 1.609555 AGCTCGCTTATACTCCCTTCG 59.390 52.381 0.00 0.00 0.00 3.79
2478 2598 1.337387 GCTCGCTTATACTCCCTTCGT 59.663 52.381 0.00 0.00 0.00 3.85
2479 2599 2.223758 GCTCGCTTATACTCCCTTCGTT 60.224 50.000 0.00 0.00 0.00 3.85
2480 2600 3.630101 CTCGCTTATACTCCCTTCGTTC 58.370 50.000 0.00 0.00 0.00 3.95
2481 2601 2.360165 TCGCTTATACTCCCTTCGTTCC 59.640 50.000 0.00 0.00 0.00 3.62
2482 2602 2.361438 CGCTTATACTCCCTTCGTTCCT 59.639 50.000 0.00 0.00 0.00 3.36
2483 2603 3.567164 CGCTTATACTCCCTTCGTTCCTA 59.433 47.826 0.00 0.00 0.00 2.94
2484 2604 4.037208 CGCTTATACTCCCTTCGTTCCTAA 59.963 45.833 0.00 0.00 0.00 2.69
2485 2605 5.450965 CGCTTATACTCCCTTCGTTCCTAAA 60.451 44.000 0.00 0.00 0.00 1.85
2486 2606 6.522946 GCTTATACTCCCTTCGTTCCTAAAT 58.477 40.000 0.00 0.00 0.00 1.40
2487 2607 7.522725 CGCTTATACTCCCTTCGTTCCTAAATA 60.523 40.741 0.00 0.00 0.00 1.40
2488 2608 7.598118 GCTTATACTCCCTTCGTTCCTAAATAC 59.402 40.741 0.00 0.00 0.00 1.89
2489 2609 8.773033 TTATACTCCCTTCGTTCCTAAATACT 57.227 34.615 0.00 0.00 0.00 2.12
2490 2610 5.595257 ACTCCCTTCGTTCCTAAATACTC 57.405 43.478 0.00 0.00 0.00 2.59
2491 2611 4.405036 ACTCCCTTCGTTCCTAAATACTCC 59.595 45.833 0.00 0.00 0.00 3.85
2492 2612 3.708121 TCCCTTCGTTCCTAAATACTCCC 59.292 47.826 0.00 0.00 0.00 4.30
2493 2613 3.710165 CCCTTCGTTCCTAAATACTCCCT 59.290 47.826 0.00 0.00 0.00 4.20
2494 2614 4.202233 CCCTTCGTTCCTAAATACTCCCTC 60.202 50.000 0.00 0.00 0.00 4.30
2495 2615 4.202233 CCTTCGTTCCTAAATACTCCCTCC 60.202 50.000 0.00 0.00 0.00 4.30
2496 2616 2.954318 TCGTTCCTAAATACTCCCTCCG 59.046 50.000 0.00 0.00 0.00 4.63
2497 2617 2.692041 CGTTCCTAAATACTCCCTCCGT 59.308 50.000 0.00 0.00 0.00 4.69
2498 2618 3.131755 CGTTCCTAAATACTCCCTCCGTT 59.868 47.826 0.00 0.00 0.00 4.44
2499 2619 4.382362 CGTTCCTAAATACTCCCTCCGTTT 60.382 45.833 0.00 0.00 0.00 3.60
2500 2620 5.114780 GTTCCTAAATACTCCCTCCGTTTC 58.885 45.833 0.00 0.00 0.00 2.78
2501 2621 4.617593 TCCTAAATACTCCCTCCGTTTCT 58.382 43.478 0.00 0.00 0.00 2.52
2502 2622 5.769835 TCCTAAATACTCCCTCCGTTTCTA 58.230 41.667 0.00 0.00 0.00 2.10
2503 2623 6.197168 TCCTAAATACTCCCTCCGTTTCTAA 58.803 40.000 0.00 0.00 0.00 2.10
2504 2624 6.669154 TCCTAAATACTCCCTCCGTTTCTAAA 59.331 38.462 0.00 0.00 0.00 1.85
2505 2625 7.346436 TCCTAAATACTCCCTCCGTTTCTAAAT 59.654 37.037 0.00 0.00 0.00 1.40
2506 2626 8.645110 CCTAAATACTCCCTCCGTTTCTAAATA 58.355 37.037 0.00 0.00 0.00 1.40
2507 2627 9.473640 CTAAATACTCCCTCCGTTTCTAAATAC 57.526 37.037 0.00 0.00 0.00 1.89
2508 2628 7.672122 AATACTCCCTCCGTTTCTAAATACT 57.328 36.000 0.00 0.00 0.00 2.12
2509 2629 7.672122 ATACTCCCTCCGTTTCTAAATACTT 57.328 36.000 0.00 0.00 0.00 2.24
2510 2630 5.731591 ACTCCCTCCGTTTCTAAATACTTG 58.268 41.667 0.00 0.00 0.00 3.16
2511 2631 5.247792 ACTCCCTCCGTTTCTAAATACTTGT 59.752 40.000 0.00 0.00 0.00 3.16
2512 2632 5.727434 TCCCTCCGTTTCTAAATACTTGTC 58.273 41.667 0.00 0.00 0.00 3.18
2513 2633 5.482878 TCCCTCCGTTTCTAAATACTTGTCT 59.517 40.000 0.00 0.00 0.00 3.41
2514 2634 6.013984 TCCCTCCGTTTCTAAATACTTGTCTT 60.014 38.462 0.00 0.00 0.00 3.01
2515 2635 6.653740 CCCTCCGTTTCTAAATACTTGTCTTT 59.346 38.462 0.00 0.00 0.00 2.52
2516 2636 7.148457 CCCTCCGTTTCTAAATACTTGTCTTTC 60.148 40.741 0.00 0.00 0.00 2.62
2517 2637 7.603024 CCTCCGTTTCTAAATACTTGTCTTTCT 59.397 37.037 0.00 0.00 0.00 2.52
2518 2638 9.635520 CTCCGTTTCTAAATACTTGTCTTTCTA 57.364 33.333 0.00 0.00 0.00 2.10
2519 2639 9.635520 TCCGTTTCTAAATACTTGTCTTTCTAG 57.364 33.333 0.00 0.00 0.00 2.43
2520 2640 8.870879 CCGTTTCTAAATACTTGTCTTTCTAGG 58.129 37.037 0.00 0.00 0.00 3.02
2521 2641 8.381387 CGTTTCTAAATACTTGTCTTTCTAGGC 58.619 37.037 0.00 0.00 0.00 3.93
2522 2642 9.216117 GTTTCTAAATACTTGTCTTTCTAGGCA 57.784 33.333 0.00 0.00 33.22 4.75
2523 2643 9.959721 TTTCTAAATACTTGTCTTTCTAGGCAT 57.040 29.630 0.00 0.00 35.56 4.40
2524 2644 9.959721 TTCTAAATACTTGTCTTTCTAGGCATT 57.040 29.630 0.00 0.00 35.56 3.56
2525 2645 9.959721 TCTAAATACTTGTCTTTCTAGGCATTT 57.040 29.630 0.00 0.00 35.56 2.32
2527 2647 8.635765 AAATACTTGTCTTTCTAGGCATTTCA 57.364 30.769 0.00 0.00 35.56 2.69
2528 2648 8.635765 AATACTTGTCTTTCTAGGCATTTCAA 57.364 30.769 0.00 0.00 35.56 2.69
2529 2649 6.959639 ACTTGTCTTTCTAGGCATTTCAAA 57.040 33.333 0.00 0.00 35.56 2.69
2530 2650 7.530426 ACTTGTCTTTCTAGGCATTTCAAAT 57.470 32.000 0.00 0.00 35.56 2.32
2531 2651 7.373493 ACTTGTCTTTCTAGGCATTTCAAATG 58.627 34.615 5.68 5.68 35.56 2.32
2532 2652 7.231317 ACTTGTCTTTCTAGGCATTTCAAATGA 59.769 33.333 14.65 0.00 35.56 2.57
2533 2653 6.913170 TGTCTTTCTAGGCATTTCAAATGAC 58.087 36.000 14.65 11.48 29.10 3.06
2534 2654 6.716628 TGTCTTTCTAGGCATTTCAAATGACT 59.283 34.615 22.35 22.35 41.04 3.41
2535 2655 7.882791 TGTCTTTCTAGGCATTTCAAATGACTA 59.117 33.333 22.19 22.19 38.54 2.59
2536 2656 8.897752 GTCTTTCTAGGCATTTCAAATGACTAT 58.102 33.333 23.50 4.64 38.80 2.12
2537 2657 9.113838 TCTTTCTAGGCATTTCAAATGACTATC 57.886 33.333 23.50 1.52 38.80 2.08
2538 2658 8.806429 TTTCTAGGCATTTCAAATGACTATCA 57.194 30.769 23.50 12.23 38.80 2.15
2539 2659 7.792374 TCTAGGCATTTCAAATGACTATCAC 57.208 36.000 23.50 0.15 38.80 3.06
2540 2660 7.337938 TCTAGGCATTTCAAATGACTATCACA 58.662 34.615 23.50 5.75 38.80 3.58
2541 2661 7.994911 TCTAGGCATTTCAAATGACTATCACAT 59.005 33.333 23.50 1.77 38.80 3.21
2542 2662 9.276590 CTAGGCATTTCAAATGACTATCACATA 57.723 33.333 23.50 4.36 38.80 2.29
2543 2663 7.934457 AGGCATTTCAAATGACTATCACATAC 58.066 34.615 17.52 0.00 35.20 2.39
2544 2664 6.852853 GGCATTTCAAATGACTATCACATACG 59.147 38.462 14.65 0.00 0.00 3.06
2545 2665 6.852853 GCATTTCAAATGACTATCACATACGG 59.147 38.462 14.65 0.00 0.00 4.02
2546 2666 7.254761 GCATTTCAAATGACTATCACATACGGA 60.255 37.037 14.65 0.00 0.00 4.69
2547 2667 8.777413 CATTTCAAATGACTATCACATACGGAT 58.223 33.333 3.82 0.00 0.00 4.18
2548 2668 7.713764 TTCAAATGACTATCACATACGGATG 57.286 36.000 5.94 5.94 39.16 3.51
2550 2670 7.947282 TCAAATGACTATCACATACGGATGTA 58.053 34.615 14.23 2.61 44.82 2.29
2551 2671 8.585018 TCAAATGACTATCACATACGGATGTAT 58.415 33.333 14.23 10.02 44.82 2.29
2592 2712 7.036220 AGTGTAGATTCACTCATTTTACTCCG 58.964 38.462 0.00 0.00 44.07 4.63
2593 2713 6.812160 GTGTAGATTCACTCATTTTACTCCGT 59.188 38.462 0.00 0.00 35.68 4.69
2594 2714 7.972277 GTGTAGATTCACTCATTTTACTCCGTA 59.028 37.037 0.00 0.00 35.68 4.02
2595 2715 8.692710 TGTAGATTCACTCATTTTACTCCGTAT 58.307 33.333 0.00 0.00 0.00 3.06
2596 2716 8.969267 GTAGATTCACTCATTTTACTCCGTATG 58.031 37.037 0.00 0.00 0.00 2.39
2597 2717 7.556844 AGATTCACTCATTTTACTCCGTATGT 58.443 34.615 0.00 0.00 0.00 2.29
2598 2718 8.692710 AGATTCACTCATTTTACTCCGTATGTA 58.307 33.333 0.00 0.00 0.00 2.29
2599 2719 8.873215 ATTCACTCATTTTACTCCGTATGTAG 57.127 34.615 0.00 0.00 0.00 2.74
2600 2720 7.400599 TCACTCATTTTACTCCGTATGTAGT 57.599 36.000 0.00 0.00 0.00 2.73
2601 2721 7.478322 TCACTCATTTTACTCCGTATGTAGTC 58.522 38.462 0.00 0.00 0.00 2.59
2602 2722 7.121611 TCACTCATTTTACTCCGTATGTAGTCA 59.878 37.037 0.00 0.00 0.00 3.41
2603 2723 7.220300 CACTCATTTTACTCCGTATGTAGTCAC 59.780 40.741 0.00 0.00 0.00 3.67
2604 2724 7.122353 ACTCATTTTACTCCGTATGTAGTCACT 59.878 37.037 0.00 0.00 0.00 3.41
2605 2725 7.833786 TCATTTTACTCCGTATGTAGTCACTT 58.166 34.615 0.00 0.00 0.00 3.16
2606 2726 7.758076 TCATTTTACTCCGTATGTAGTCACTTG 59.242 37.037 0.00 0.00 0.00 3.16
2607 2727 6.579666 TTTACTCCGTATGTAGTCACTTGT 57.420 37.500 0.00 0.00 0.00 3.16
2608 2728 6.579666 TTACTCCGTATGTAGTCACTTGTT 57.420 37.500 0.00 0.00 0.00 2.83
2609 2729 4.806330 ACTCCGTATGTAGTCACTTGTTG 58.194 43.478 0.00 0.00 0.00 3.33
2610 2730 4.521639 ACTCCGTATGTAGTCACTTGTTGA 59.478 41.667 0.00 0.00 0.00 3.18
2611 2731 5.010314 ACTCCGTATGTAGTCACTTGTTGAA 59.990 40.000 0.00 0.00 35.39 2.69
2612 2732 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
2613 2733 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
2614 2734 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
2615 2735 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
2616 2736 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
2617 2737 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
2618 2738 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
2626 2746 9.996554 TCACTTGTTGAAATCTCTATAAAGACA 57.003 29.630 0.00 0.00 0.00 3.41
2644 2764 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
2645 2765 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2646 2766 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2647 2767 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2712 2832 7.913674 AAGTTGATTTGGCTTTGTGTAAAAA 57.086 28.000 0.00 0.00 0.00 1.94
2763 2884 1.131126 GTGTCATCCTGGCAATTGTCG 59.869 52.381 5.42 0.29 31.67 4.35
2765 2886 1.031571 TCATCCTGGCAATTGTCGGC 61.032 55.000 13.63 0.00 0.00 5.54
2803 2924 2.595124 TGTGTACCAGTCACAGTGTG 57.405 50.000 17.53 17.53 40.26 3.82
2853 2974 0.320683 TGTGACCCAATGACTCTGCG 60.321 55.000 0.00 0.00 0.00 5.18
2919 3040 4.269363 GCAAATTACAATCATTGAGGCTGC 59.731 41.667 3.79 2.78 0.00 5.25
2930 3051 0.616891 TGAGGCTGCATCACTGTCAT 59.383 50.000 13.56 0.00 0.00 3.06
2931 3052 1.297664 GAGGCTGCATCACTGTCATC 58.702 55.000 9.73 0.00 0.00 2.92
2934 3055 1.445871 GCTGCATCACTGTCATCACA 58.554 50.000 0.00 0.00 0.00 3.58
2974 3095 6.587608 GGAGAATTTGCCAGTTATGAAACTTG 59.412 38.462 0.00 0.00 43.60 3.16
3062 3187 5.722263 TGGCCAAATAATCAAACTGATGTG 58.278 37.500 0.61 0.00 37.15 3.21
3136 3265 3.069016 CACCTGTCACCTAAGTGTACACA 59.931 47.826 27.06 7.31 44.83 3.72
3157 3289 8.429739 ACACAACGTTAAAATTATGTCGATTG 57.570 30.769 0.00 0.00 0.00 2.67
3213 3348 2.270352 TGCAGAGGGTTAGGTGTTTG 57.730 50.000 0.00 0.00 0.00 2.93
3384 3519 1.841919 AGATGTGTCTGATGGCCATGA 59.158 47.619 26.56 15.37 32.13 3.07
3402 3537 3.961480 TGACCAACTTGTCATCGATCT 57.039 42.857 0.00 0.00 40.22 2.75
3434 3569 5.967674 GTGATTTAGTTCATGGAAATGAGCG 59.032 40.000 0.00 0.00 36.96 5.03
3437 3572 1.098050 GTTCATGGAAATGAGCGCCT 58.902 50.000 2.29 0.00 31.46 5.52
3468 3607 3.248024 CTCCAGGGGTATAGCCATGTTA 58.752 50.000 28.23 17.62 39.65 2.41
3502 3724 4.602340 AACATACACGTATCATCTCCCC 57.398 45.455 0.00 0.00 0.00 4.81
3592 3814 4.232221 CACACTTTTCCATGTCAAGCATC 58.768 43.478 0.00 0.00 35.19 3.91
3643 3870 2.894126 GAGACAAGGGAAGAGACACAGA 59.106 50.000 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 6.850752 TGTGACAATCTGGAGTCTAATGTA 57.149 37.500 0.00 0.00 35.81 2.29
182 183 1.695242 AGTTGGTACCGTGATGTCCAA 59.305 47.619 7.57 0.00 36.08 3.53
194 195 7.668492 CCTATGGAAATAGGAGTAGTTGGTAC 58.332 42.308 5.97 0.00 45.08 3.34
600 623 6.042093 CCCAGACATTAGGAAGCTATAAGACA 59.958 42.308 0.00 0.00 0.00 3.41
621 644 4.730949 ATGACATTTGCATTTCTCCCAG 57.269 40.909 0.00 0.00 0.00 4.45
643 669 8.936864 GGCATTATTACGAGCTATTATGAGTTT 58.063 33.333 0.00 0.00 0.00 2.66
644 670 7.549488 GGGCATTATTACGAGCTATTATGAGTT 59.451 37.037 0.00 0.00 0.00 3.01
645 671 7.042335 GGGCATTATTACGAGCTATTATGAGT 58.958 38.462 0.00 0.00 0.00 3.41
646 672 6.480320 GGGGCATTATTACGAGCTATTATGAG 59.520 42.308 0.00 0.00 0.00 2.90
647 673 6.156256 AGGGGCATTATTACGAGCTATTATGA 59.844 38.462 0.00 0.00 0.00 2.15
648 674 6.349300 AGGGGCATTATTACGAGCTATTATG 58.651 40.000 0.00 0.00 0.00 1.90
702 732 3.263425 ACCGAGGTCCACAAAACTATCAT 59.737 43.478 0.00 0.00 0.00 2.45
734 764 7.757242 ATAGAGAGGGTTAACTGGAGATTTT 57.243 36.000 5.42 0.00 0.00 1.82
735 765 8.855804 TTATAGAGAGGGTTAACTGGAGATTT 57.144 34.615 5.42 0.00 0.00 2.17
769 799 6.449698 AGTGTGCAATCTATTTGAACTTTGG 58.550 36.000 0.00 0.00 43.44 3.28
814 844 6.666678 TCATCTCTCCTGCTATTCCAATTTT 58.333 36.000 0.00 0.00 0.00 1.82
816 846 5.901413 TCATCTCTCCTGCTATTCCAATT 57.099 39.130 0.00 0.00 0.00 2.32
834 875 9.347240 CCCATCAACCTCCAATATTATATCATC 57.653 37.037 0.00 0.00 0.00 2.92
886 927 8.832521 TGATTAAGTATCAAAGAACACGTTTGT 58.167 29.630 0.00 0.00 40.29 2.83
937 978 5.527214 CGGCCAATCAAGTAAGTAATCATCA 59.473 40.000 2.24 0.00 0.00 3.07
1071 1112 0.108585 TGTTGGCCTTCACTGGAGTC 59.891 55.000 3.32 0.00 0.00 3.36
1072 1113 0.179018 GTGTTGGCCTTCACTGGAGT 60.179 55.000 18.72 0.00 0.00 3.85
1140 1184 1.673168 CCGTTACTCGTAGCCCTAGT 58.327 55.000 0.00 0.00 37.94 2.57
1175 1219 3.796844 GCTTGTTCTCTGGTTTTCTTGGC 60.797 47.826 0.00 0.00 0.00 4.52
1182 1226 6.016777 CAGTTTCTATGCTTGTTCTCTGGTTT 60.017 38.462 0.00 0.00 0.00 3.27
1191 1235 2.744202 CTCCGCAGTTTCTATGCTTGTT 59.256 45.455 0.00 0.00 41.61 2.83
1227 1274 1.675310 CAGTTCGGGGCATGCTTCA 60.675 57.895 18.92 0.00 0.00 3.02
1238 1285 1.739562 GCTCTGACAGGCAGTTCGG 60.740 63.158 2.23 0.00 45.14 4.30
1296 1343 3.505293 GCTTGTTCTGCAGGATTCTCTTT 59.495 43.478 15.13 0.00 0.00 2.52
1494 1551 1.284982 CGGTGACAAAGACCTCGCTG 61.285 60.000 0.00 0.00 0.00 5.18
1541 1598 2.030027 TCCTCATCAACTCCCTGTGT 57.970 50.000 0.00 0.00 0.00 3.72
1573 1630 2.040278 CCTTCCACCTCCATTGTCTTCA 59.960 50.000 0.00 0.00 0.00 3.02
1643 1700 1.236628 CTGTGCTCTTTGAAGCTGCT 58.763 50.000 0.00 0.00 42.94 4.24
1645 1702 0.949397 TGCTGTGCTCTTTGAAGCTG 59.051 50.000 0.00 0.00 42.94 4.24
1723 1833 3.058639 GCCGAATGAATGAATCCAGCTAC 60.059 47.826 0.00 0.00 0.00 3.58
1733 1843 5.189539 TCCTGGATATATGCCGAATGAATGA 59.810 40.000 1.35 0.00 0.00 2.57
1734 1844 5.430886 TCCTGGATATATGCCGAATGAATG 58.569 41.667 1.35 0.00 0.00 2.67
1752 1862 4.557496 GCTAAACAGCTCTTTTGTTCCTGG 60.557 45.833 0.00 0.00 37.77 4.45
1850 1960 5.952347 AGGGGAAAACTACTGGTGTATAG 57.048 43.478 0.00 0.00 0.00 1.31
1900 2010 3.246619 AGATTTCGTCGCTCTTCTGTTC 58.753 45.455 0.00 0.00 0.00 3.18
1914 2024 9.680946 CTGCGATAAATATGATGTTAGATTTCG 57.319 33.333 0.00 0.00 0.00 3.46
1937 2051 1.633852 CTGCTTCAGCTTCGTCCTGC 61.634 60.000 0.00 0.00 42.66 4.85
2064 2178 3.181475 GGTGATTCAGATTGTAGAGCGGA 60.181 47.826 0.00 0.00 0.00 5.54
2089 2203 2.047274 CGTGGCGAACCCAGACAT 60.047 61.111 0.00 0.00 46.54 3.06
2265 2382 2.019951 ACGTCACAATGTCGCCGAC 61.020 57.895 10.96 10.96 32.42 4.79
2334 2451 3.443681 ACTGGTGACAAAAACACAAGAGG 59.556 43.478 9.06 0.00 40.55 3.69
2342 2459 5.493133 TGTACATCACTGGTGACAAAAAC 57.507 39.130 5.52 2.14 43.11 2.43
2371 2488 5.287992 GGTTTTCGACTCCTTTCTACGTATG 59.712 44.000 0.00 0.00 0.00 2.39
2372 2489 5.047802 TGGTTTTCGACTCCTTTCTACGTAT 60.048 40.000 0.00 0.00 0.00 3.06
2373 2490 4.278170 TGGTTTTCGACTCCTTTCTACGTA 59.722 41.667 0.00 0.00 0.00 3.57
2374 2491 3.068590 TGGTTTTCGACTCCTTTCTACGT 59.931 43.478 0.00 0.00 0.00 3.57
2375 2492 3.645884 TGGTTTTCGACTCCTTTCTACG 58.354 45.455 0.00 0.00 0.00 3.51
2376 2493 4.995487 ACATGGTTTTCGACTCCTTTCTAC 59.005 41.667 0.00 0.00 0.00 2.59
2377 2494 4.994852 CACATGGTTTTCGACTCCTTTCTA 59.005 41.667 0.00 0.00 0.00 2.10
2378 2495 3.815401 CACATGGTTTTCGACTCCTTTCT 59.185 43.478 0.00 0.00 0.00 2.52
2423 2541 8.885722 TCTACCGTTATAAAAATGGCTAAACTG 58.114 33.333 0.00 0.00 0.00 3.16
2434 2554 6.479001 GCTCAGCTCATCTACCGTTATAAAAA 59.521 38.462 0.00 0.00 0.00 1.94
2456 2576 2.350964 CGAAGGGAGTATAAGCGAGCTC 60.351 54.545 2.73 2.73 0.00 4.09
2457 2577 1.609555 CGAAGGGAGTATAAGCGAGCT 59.390 52.381 0.00 0.00 0.00 4.09
2458 2578 1.337387 ACGAAGGGAGTATAAGCGAGC 59.663 52.381 0.00 0.00 0.00 5.03
2459 2579 3.550436 GGAACGAAGGGAGTATAAGCGAG 60.550 52.174 0.00 0.00 0.00 5.03
2461 2581 2.361438 AGGAACGAAGGGAGTATAAGCG 59.639 50.000 0.00 0.00 0.00 4.68
2462 2582 5.526506 TTAGGAACGAAGGGAGTATAAGC 57.473 43.478 0.00 0.00 0.00 3.09
2463 2583 8.858094 AGTATTTAGGAACGAAGGGAGTATAAG 58.142 37.037 0.00 0.00 0.00 1.73
2464 2584 8.773033 AGTATTTAGGAACGAAGGGAGTATAA 57.227 34.615 0.00 0.00 0.00 0.98
2465 2585 7.449704 GGAGTATTTAGGAACGAAGGGAGTATA 59.550 40.741 0.00 0.00 0.00 1.47
2466 2586 6.267242 GGAGTATTTAGGAACGAAGGGAGTAT 59.733 42.308 0.00 0.00 0.00 2.12
2467 2587 5.595952 GGAGTATTTAGGAACGAAGGGAGTA 59.404 44.000 0.00 0.00 0.00 2.59
2468 2588 4.405036 GGAGTATTTAGGAACGAAGGGAGT 59.595 45.833 0.00 0.00 0.00 3.85
2469 2589 4.202233 GGGAGTATTTAGGAACGAAGGGAG 60.202 50.000 0.00 0.00 0.00 4.30
2470 2590 3.708121 GGGAGTATTTAGGAACGAAGGGA 59.292 47.826 0.00 0.00 0.00 4.20
2471 2591 3.710165 AGGGAGTATTTAGGAACGAAGGG 59.290 47.826 0.00 0.00 0.00 3.95
2472 2592 4.202233 GGAGGGAGTATTTAGGAACGAAGG 60.202 50.000 0.00 0.00 0.00 3.46
2473 2593 4.499357 CGGAGGGAGTATTTAGGAACGAAG 60.499 50.000 0.00 0.00 0.00 3.79
2474 2594 3.382546 CGGAGGGAGTATTTAGGAACGAA 59.617 47.826 0.00 0.00 0.00 3.85
2475 2595 2.954318 CGGAGGGAGTATTTAGGAACGA 59.046 50.000 0.00 0.00 0.00 3.85
2476 2596 2.692041 ACGGAGGGAGTATTTAGGAACG 59.308 50.000 0.00 0.00 0.00 3.95
2477 2597 4.750021 AACGGAGGGAGTATTTAGGAAC 57.250 45.455 0.00 0.00 0.00 3.62
2478 2598 5.028131 AGAAACGGAGGGAGTATTTAGGAA 58.972 41.667 0.00 0.00 0.00 3.36
2479 2599 4.617593 AGAAACGGAGGGAGTATTTAGGA 58.382 43.478 0.00 0.00 0.00 2.94
2480 2600 6.475596 TTAGAAACGGAGGGAGTATTTAGG 57.524 41.667 0.00 0.00 0.00 2.69
2481 2601 9.473640 GTATTTAGAAACGGAGGGAGTATTTAG 57.526 37.037 0.00 0.00 0.00 1.85
2482 2602 9.205513 AGTATTTAGAAACGGAGGGAGTATTTA 57.794 33.333 0.00 0.00 0.00 1.40
2483 2603 8.087303 AGTATTTAGAAACGGAGGGAGTATTT 57.913 34.615 0.00 0.00 0.00 1.40
2484 2604 7.672122 AGTATTTAGAAACGGAGGGAGTATT 57.328 36.000 0.00 0.00 0.00 1.89
2485 2605 7.125356 ACAAGTATTTAGAAACGGAGGGAGTAT 59.875 37.037 0.00 0.00 0.00 2.12
2486 2606 6.438425 ACAAGTATTTAGAAACGGAGGGAGTA 59.562 38.462 0.00 0.00 0.00 2.59
2487 2607 5.247792 ACAAGTATTTAGAAACGGAGGGAGT 59.752 40.000 0.00 0.00 0.00 3.85
2488 2608 5.731591 ACAAGTATTTAGAAACGGAGGGAG 58.268 41.667 0.00 0.00 0.00 4.30
2489 2609 5.482878 AGACAAGTATTTAGAAACGGAGGGA 59.517 40.000 0.00 0.00 0.00 4.20
2490 2610 5.731591 AGACAAGTATTTAGAAACGGAGGG 58.268 41.667 0.00 0.00 0.00 4.30
2491 2611 7.603024 AGAAAGACAAGTATTTAGAAACGGAGG 59.397 37.037 0.00 0.00 0.00 4.30
2492 2612 8.535690 AGAAAGACAAGTATTTAGAAACGGAG 57.464 34.615 0.00 0.00 0.00 4.63
2493 2613 9.635520 CTAGAAAGACAAGTATTTAGAAACGGA 57.364 33.333 0.00 0.00 0.00 4.69
2494 2614 8.870879 CCTAGAAAGACAAGTATTTAGAAACGG 58.129 37.037 0.00 0.00 0.00 4.44
2495 2615 8.381387 GCCTAGAAAGACAAGTATTTAGAAACG 58.619 37.037 0.00 0.00 0.00 3.60
2496 2616 9.216117 TGCCTAGAAAGACAAGTATTTAGAAAC 57.784 33.333 0.00 0.00 0.00 2.78
2497 2617 9.959721 ATGCCTAGAAAGACAAGTATTTAGAAA 57.040 29.630 0.00 0.00 0.00 2.52
2498 2618 9.959721 AATGCCTAGAAAGACAAGTATTTAGAA 57.040 29.630 0.00 0.00 0.00 2.10
2499 2619 9.959721 AAATGCCTAGAAAGACAAGTATTTAGA 57.040 29.630 0.00 0.00 0.00 2.10
2501 2621 9.733556 TGAAATGCCTAGAAAGACAAGTATTTA 57.266 29.630 0.00 0.00 0.00 1.40
2502 2622 8.635765 TGAAATGCCTAGAAAGACAAGTATTT 57.364 30.769 0.00 0.00 0.00 1.40
2503 2623 8.635765 TTGAAATGCCTAGAAAGACAAGTATT 57.364 30.769 0.00 0.00 0.00 1.89
2504 2624 8.635765 TTTGAAATGCCTAGAAAGACAAGTAT 57.364 30.769 0.00 0.00 0.00 2.12
2505 2625 8.514594 CATTTGAAATGCCTAGAAAGACAAGTA 58.485 33.333 4.82 0.00 0.00 2.24
2506 2626 6.959639 TTTGAAATGCCTAGAAAGACAAGT 57.040 33.333 0.00 0.00 0.00 3.16
2507 2627 7.540055 GTCATTTGAAATGCCTAGAAAGACAAG 59.460 37.037 12.86 0.00 0.00 3.16
2508 2628 7.231317 AGTCATTTGAAATGCCTAGAAAGACAA 59.769 33.333 12.86 0.00 0.00 3.18
2509 2629 6.716628 AGTCATTTGAAATGCCTAGAAAGACA 59.283 34.615 12.86 0.00 0.00 3.41
2510 2630 7.150783 AGTCATTTGAAATGCCTAGAAAGAC 57.849 36.000 12.86 3.23 0.00 3.01
2511 2631 9.113838 GATAGTCATTTGAAATGCCTAGAAAGA 57.886 33.333 13.20 0.00 0.00 2.52
2512 2632 8.896744 TGATAGTCATTTGAAATGCCTAGAAAG 58.103 33.333 13.20 0.00 0.00 2.62
2513 2633 8.677300 GTGATAGTCATTTGAAATGCCTAGAAA 58.323 33.333 13.20 0.91 0.00 2.52
2514 2634 7.828717 TGTGATAGTCATTTGAAATGCCTAGAA 59.171 33.333 13.20 2.99 0.00 2.10
2515 2635 7.337938 TGTGATAGTCATTTGAAATGCCTAGA 58.662 34.615 13.20 1.78 0.00 2.43
2516 2636 7.558161 TGTGATAGTCATTTGAAATGCCTAG 57.442 36.000 13.20 0.00 0.00 3.02
2517 2637 9.056005 GTATGTGATAGTCATTTGAAATGCCTA 57.944 33.333 10.59 10.59 0.00 3.93
2518 2638 7.254898 CGTATGTGATAGTCATTTGAAATGCCT 60.255 37.037 12.86 9.73 0.00 4.75
2519 2639 6.852853 CGTATGTGATAGTCATTTGAAATGCC 59.147 38.462 12.86 1.61 0.00 4.40
2520 2640 6.852853 CCGTATGTGATAGTCATTTGAAATGC 59.147 38.462 12.86 8.33 0.00 3.56
2521 2641 8.141835 TCCGTATGTGATAGTCATTTGAAATG 57.858 34.615 11.54 11.54 0.00 2.32
2522 2642 8.777413 CATCCGTATGTGATAGTCATTTGAAAT 58.223 33.333 0.00 0.00 0.00 2.17
2523 2643 7.768582 ACATCCGTATGTGATAGTCATTTGAAA 59.231 33.333 0.00 0.00 44.79 2.69
2524 2644 7.272244 ACATCCGTATGTGATAGTCATTTGAA 58.728 34.615 0.00 0.00 44.79 2.69
2525 2645 6.816136 ACATCCGTATGTGATAGTCATTTGA 58.184 36.000 0.00 0.00 44.79 2.69
2526 2646 8.650714 CATACATCCGTATGTGATAGTCATTTG 58.349 37.037 3.56 0.00 46.70 2.32
2527 2647 8.763049 CATACATCCGTATGTGATAGTCATTT 57.237 34.615 3.56 0.00 46.70 2.32
2568 2688 6.812160 ACGGAGTAAAATGAGTGAATCTACAC 59.188 38.462 0.00 0.00 41.94 2.90
2569 2689 6.931838 ACGGAGTAAAATGAGTGAATCTACA 58.068 36.000 0.00 0.00 41.94 2.74
2585 2705 7.255555 TTCAACAAGTGACTACATACGGAGTAA 60.256 37.037 0.00 0.00 41.03 2.24
2586 2706 6.207221 TTCAACAAGTGACTACATACGGAGTA 59.793 38.462 0.00 0.00 41.66 2.59
2587 2707 5.010314 TTCAACAAGTGACTACATACGGAGT 59.990 40.000 0.00 0.00 39.84 3.85
2588 2708 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
2589 2709 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
2590 2710 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
2591 2711 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
2592 2712 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
2600 2720 9.996554 TGTCTTTATAGAGATTTCAACAAGTGA 57.003 29.630 0.00 0.00 0.00 3.41
2618 2738 9.338622 CCTCCGTTCCTAAATATTTGTCTTTAT 57.661 33.333 11.05 0.00 0.00 1.40
2619 2739 7.771826 CCCTCCGTTCCTAAATATTTGTCTTTA 59.228 37.037 11.05 0.00 0.00 1.85
2620 2740 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
2621 2741 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2622 2742 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2623 2743 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2624 2744 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2625 2745 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2626 2746 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2627 2747 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
2628 2748 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2629 2749 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2630 2750 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2631 2751 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2632 2752 3.117738 CCTACTACTCCCTCCGTTCCTAA 60.118 52.174 0.00 0.00 0.00 2.69
2633 2753 2.441001 CCTACTACTCCCTCCGTTCCTA 59.559 54.545 0.00 0.00 0.00 2.94
2634 2754 1.214923 CCTACTACTCCCTCCGTTCCT 59.785 57.143 0.00 0.00 0.00 3.36
2635 2755 1.064091 ACCTACTACTCCCTCCGTTCC 60.064 57.143 0.00 0.00 0.00 3.62
2636 2756 2.022934 CACCTACTACTCCCTCCGTTC 58.977 57.143 0.00 0.00 0.00 3.95
2637 2757 1.357079 ACACCTACTACTCCCTCCGTT 59.643 52.381 0.00 0.00 0.00 4.44
2638 2758 0.998145 ACACCTACTACTCCCTCCGT 59.002 55.000 0.00 0.00 0.00 4.69
2639 2759 1.390565 CACACCTACTACTCCCTCCG 58.609 60.000 0.00 0.00 0.00 4.63
2640 2760 1.287146 TCCACACCTACTACTCCCTCC 59.713 57.143 0.00 0.00 0.00 4.30
2641 2761 2.822707 TCCACACCTACTACTCCCTC 57.177 55.000 0.00 0.00 0.00 4.30
2642 2762 3.778622 ATTCCACACCTACTACTCCCT 57.221 47.619 0.00 0.00 0.00 4.20
2643 2763 4.514401 CAAATTCCACACCTACTACTCCC 58.486 47.826 0.00 0.00 0.00 4.30
2644 2764 3.939592 GCAAATTCCACACCTACTACTCC 59.060 47.826 0.00 0.00 0.00 3.85
2645 2765 4.833390 AGCAAATTCCACACCTACTACTC 58.167 43.478 0.00 0.00 0.00 2.59
2646 2766 4.910458 AGCAAATTCCACACCTACTACT 57.090 40.909 0.00 0.00 0.00 2.57
2647 2767 7.042925 CGTAATAGCAAATTCCACACCTACTAC 60.043 40.741 0.00 0.00 0.00 2.73
2712 2832 8.659491 CAAACCACATCATCGATCGATTATATT 58.341 33.333 27.45 12.69 31.62 1.28
2715 2835 5.106948 GCAAACCACATCATCGATCGATTAT 60.107 40.000 27.45 21.87 31.62 1.28
2716 2836 4.211164 GCAAACCACATCATCGATCGATTA 59.789 41.667 27.45 20.54 31.62 1.75
2717 2837 3.002656 GCAAACCACATCATCGATCGATT 59.997 43.478 27.45 12.18 31.62 3.34
2763 2884 6.096001 ACACAAATGGAAATTAGAGATCTGCC 59.904 38.462 0.00 0.00 0.00 4.85
2765 2886 8.616076 GGTACACAAATGGAAATTAGAGATCTG 58.384 37.037 0.00 0.00 0.00 2.90
2853 2974 1.032014 TTGTCCTTTTCAGCCAGCAC 58.968 50.000 0.00 0.00 0.00 4.40
2919 3040 3.805971 ACGCATATGTGATGACAGTGATG 59.194 43.478 22.73 3.29 34.87 3.07
2934 3055 6.147821 GCAAATTCTCCTACACATACGCATAT 59.852 38.462 0.00 0.00 0.00 1.78
2974 3095 0.951558 AATCACGCAACCACCAAGAC 59.048 50.000 0.00 0.00 0.00 3.01
3062 3187 0.326927 TCCGGAACCCAGAATTCCAC 59.673 55.000 0.00 0.00 45.15 4.02
3174 3306 7.801104 TCTGCATATTCCAAGTCCAAACTATA 58.199 34.615 0.00 0.00 33.48 1.31
3175 3307 6.662755 TCTGCATATTCCAAGTCCAAACTAT 58.337 36.000 0.00 0.00 33.48 2.12
3177 3309 4.922206 TCTGCATATTCCAAGTCCAAACT 58.078 39.130 0.00 0.00 37.32 2.66
3187 3322 3.136443 CACCTAACCCTCTGCATATTCCA 59.864 47.826 0.00 0.00 0.00 3.53
3213 3348 4.755411 TCTGAGTTTCATATGTTCGACCC 58.245 43.478 1.90 0.00 0.00 4.46
3326 3461 2.282462 GGACACCCTTGGCACAGG 60.282 66.667 8.28 8.28 42.39 4.00
3384 3519 3.685139 ACAGATCGATGACAAGTTGGT 57.315 42.857 0.54 0.00 0.00 3.67
3426 3561 3.070018 GCATGACTATAGGCGCTCATTT 58.930 45.455 7.64 0.00 0.00 2.32
3429 3564 1.270826 GAGCATGACTATAGGCGCTCA 59.729 52.381 23.30 10.85 44.10 4.26
3434 3569 1.277557 CCCTGGAGCATGACTATAGGC 59.722 57.143 4.43 0.50 32.61 3.93
3437 3572 2.795291 ACCCCTGGAGCATGACTATA 57.205 50.000 0.00 0.00 0.00 1.31
3592 3814 4.143597 CGTAATCGCCAAGCTTATCTTACG 60.144 45.833 17.01 17.01 35.85 3.18
3643 3870 0.178990 GACCTGGCCCTGTCAACTTT 60.179 55.000 14.98 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.