Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold870
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5862
ACGTcount: A:0.37, C:0.37, G:0.13, T:0.14
Found at i:471 original size:6 final size:7
Alignment explanation
Indices: 23--3559 Score: 1750
Period size: 7 Copynumber: 481.4 Consensus size: 7
13 ACGAGTAAAG
23 CCCGAAA
1 CCCGAAA
30 CCCCGAAA
1 -CCCGAAA
38 CCTCGAAA
1 CC-CGAAA
46 CCCGAAA
1 CCCGAAA
*
53 CCCGAATT
1 CCCGAA-A
***
61 GGAGAAAA
1 CCCG-AAA
69 CCCGAAA
1 CCCGAAA
76 CCCGAGAAAA
1 CCC--G-AAA
86 CCCGAAA
1 CCCGAAA
93 CCCGAAA
1 CCCGAAA
100 CCCGAAAA
1 CCCG-AAA
108 CCCGGGGAAA
1 CCC---GAAA
118 CCC-AAA
1 CCCGAAA
124 CCCGAAAA
1 CCCG-AAA
132 CCCGAAAAA
1 CCCG--AAA
141 CCCGAGAATA
1 CCC--GAA-A
151 CCCG-AA
1 CCCGAAA
157 CCCGGAGATAA
1 CCC---GA-AA
168 CCCGAAA
1 CCCGAAA
175 CCCGGAAA
1 CCC-GAAA
183 CCCGAAAA
1 CCCG-AAA
191 CCCTGAAA
1 CCC-GAAA
*
199 CCGGAAA
1 CCCGAAA
206 CGCCGGAAA
1 C-CC-GAAA
215 CCCGAAA
1 CCCGAAA
222 CCCG--A
1 CCCGAAA
227 CCCGATAAA
1 CCCG--AAA
236 TCCCTGAAA
1 -CCC-GAAA
*
245 CCCGCAA
1 CCCGAAA
252 CCC-AAA
1 CCCGAAA
**
258 CCCGGCCA
1 CCC-GAAA
266 CTCCGGATAA
1 C-CC-GA-AA
276 CCGGCCGAAA
1 -C--CCGAAA
286 CCCGAAA
1 CCCGAAA
*
293 CCCCTGGCAA
1 -CCC--GAAA
303 CCCGAAA
1 CCCGAAA
310 CCCGAAA
1 CCCGAAA
***
317 CGAAAAAA
1 C-CCGAAA
325 CCCGACCAA
1 CCCGA--AA
334 CCCGAATA
1 CCCGAA-A
342 CCCGAAAA
1 CCCG-AAA
**
350 TCCTAAAA
1 -CCCGAAA
358 CCCGAAAA
1 CCCG-AAA
366 CCCGAAAATA
1 CCCG--AA-A
376 CCCGAAA
1 CCCGAAA
383 CCCGAAA
1 CCCGAAA
*
390 CTCCGGAAC
1 C-CC-GAAA
399 CTCCGAAA
1 C-CCGAAA
407 TCCCTTGCCATAA
1 -CCC--G--A-AA
420 CCCGAAA
1 CCCGAAA
427 CCTCGAAA
1 CC-CGAAA
435 CCCGGGAAA
1 CCC--GAAA
444 CCTCGAAA
1 CC-CGAAA
452 CCCGAAA
1 CCCGAAA
459 CCCGAAA
1 CCCGAAA
466 -CCGAAA
1 CCCGAAA
472 CCCGAATA
1 CCCGAA-A
*
480 CCCGCAA
1 CCCGAAA
487 CCTCTGAAAA
1 CC-C-G-AAA
*
497 CCCTAAA
1 CCCGAAA
504 -CCGAAAA
1 CCCG-AAA
*
511 CCCGCAA
1 CCCGAAA
518 CCCGAATA
1 CCCGAA-A
526 CCCGAAA
1 CCCGAAA
533 CCCGAAA
1 CCCGAAA
540 -CCGATAA
1 CCCGA-AA
547 -CCGAAA
1 CCCGAAA
553 CCCGAAA
1 CCCGAAA
560 CCTCGAAA
1 CC-CGAAA
568 CCCGAAAA
1 CCCG-AAA
*
576 TCCTGAAAA
1 -CCCG-AAA
585 TCCCGAAA
1 -CCCGAAA
593 CCCCGGAAA
1 -CCC-GAAA
602 CCCCGAAA
1 -CCCGAAA
*
610 CCCGCAA
1 CCCGAAA
617 CCTCGAAAA
1 CC-CG-AAA
*
626 CCCGAAC
1 CCCGAAA
633 CCCGAAA
1 CCCGAAA
640 CCCGAAA
1 CCCGAAA
*
647 GCCGAAA
1 CCCGAAA
654 CCCGAAA
1 CCCGAAA
661 CCCGAAA
1 CCCGAAA
*
668 CCGGAAA
1 CCCGAAA
*
675 CCCGACA
1 CCCGAAA
*
682 -CCGCAA
1 CCCGAAA
688 CCCGAAA
1 CCCGAAA
695 CCCGTATAA
1 CCCG-A-AA
**
704 -CCGTGGA
1 CCCG-AAA
711 CCCAGAACA
1 CCC-GAA-A
720 CCC-AAA
1 CCCGAAA
726 CCCGCAAA
1 CCCG-AAA
734 CCCGACAA
1 CCCGA-AA
742 CCTCTGAAA
1 CC-C-GAAA
751 CCCGAAA
1 CCCGAAA
758 CCCGAAA
1 CCCGAAA
765 CCCGAAA
1 CCCGAAA
*
772 CCCGCAA
1 CCCGAAA
*
779 CCCTAAA
1 CCCGAAA
*
786 TCCCG-AC
1 -CCCGAAA
793 CCCTGGAAA
1 CCC--GAAA
802 CCCGATGAA
1 CCCGA--AA
811 CCCGATAA
1 CCCGA-AA
*
819 -CCTAAA
1 CCCGAAA
825 CCCGAAA
1 CCCGAAA
832 TCTCCTGAAA
1 -C-CC-GAAA
842 CCCGATAA
1 CCCGA-AA
850 CCCGTATAA
1 CCCG-A-AA
859 CCCGGAAA
1 CCC-GAAA
*
867 CCCGCAA
1 CCCGAAA
874 CCTCGAAA
1 CC-CGAAA
*
882 CCCG-CA
1 CCCGAAA
888 CTCCGAAA
1 C-CCGAAA
*
896 CCCGCAA
1 CCCGAAA
903 CCCGAAA
1 CCCGAAA
910 CCCGAAAA
1 CCCG-AAA
918 CCCGGAAA
1 CCC-GAAA
926 CCCGTGGAAA
1 CCC---GAAA
936 CCCGAAAA
1 CCCG-AAA
944 CCCGAAAA
1 CCCG-AAA
952 CCCGACGAA
1 CCCGA--AA
961 CCCGAAA
1 CCCGAAA
968 -CCGAAA
1 CCCGAAA
974 CCCGAAA
1 CCCGAAA
*
981 -CCGACA
1 CCCGAAA
987 CCCGAAA
1 CCCGAAA
*
994 CCC-AAC
1 CCCGAAA
*
1000 CCCGACA
1 CCCGAAA
*
1007 CCCGAAC
1 CCCGAAA
1014 CCTCGAAA
1 CC-CGAAA
1022 -CCGAAA
1 CCCGAAA
1028 CCCGAAA
1 CCCGAAA
1035 CCCGAAA
1 CCCGAAA
1042 CCCGAAA
1 CCCGAAA
1049 CCC-AAA
1 CCCGAAA
1055 CCCGAAA
1 CCCGAAA
*
1062 CCCGAAC
1 CCCGAAA
1069 CCCGAAA
1 CCCGAAA
1076 CCCGCGGAAA
1 -CC-C-GAAA
*
1086 CCCGCAA
1 CCCGAAA
1093 CCCGAAA
1 CCCGAAA
*
1100 CCCGCAA
1 CCCGAAA
1107 CCCG-AA
1 CCCGAAA
1113 -CCGAAA
1 CCCGAAA
1119 CCTCCGAAA
1 -C-CCGAAA
1128 -CCGTAAA
1 CCCG-AAA
1135 CCCCGATAAA
1 -CCCG--AAA
1145 CCCTGACAA
1 CCC-GA-AA
*
1154 CCAGAAA
1 CCCGAAA
1161 CCCGAAAA
1 CCCG-AAA
1169 CCCGTAAACAA
1 CCCG---A-AA
1180 CCCGAAAA
1 CCCG-AAA
1188 CCCG-AA
1 CCCGAAA
1194 CCCGAAA
1 CCCGAAA
1201 CCCTGAAA
1 CCC-GAAA
1209 CCCGGAAA
1 CCC-GAAA
1217 CCCGATAAA
1 CCCG--AAA
1226 TCCTCGAAA
1 -CC-CGAAA
1235 CCCGAAA
1 CCCGAAA
*
1242 CTCCGATA
1 C-CCGAAA
1250 CCCGAAA
1 CCCGAAA
1257 CGCCGAAA
1 C-CCGAAA
1265 TCGCCGAAA
1 -C-CCGAAA
1274 CCCGATAA
1 CCCGA-AA
*
1282 CCCGAAC
1 CCCGAAA
*
1289 CCCGAGA
1 CCCGAAA
* *
1296 CCGGAAG
1 CCCGAAA
*
1303 CACGAAA
1 CCCGAAA
* *
1310 CTCTGCAA
1 C-CCGAAA
1318 CCCGAAA
1 CCCGAAA
1325 CCCGAAAA
1 CCCG-AAA
1333 CCCAGAAA
1 CCC-GAAA
1341 CCC-AAA
1 CCCGAAA
* *
1347 CGACGCACA
1 C-CCG-AAA
1356 CCCG-AA
1 CCCGAAA
1362 CCCGAAA
1 CCCGAAA
*
1369 -CCGCAA
1 CCCGAAA
1375 CCCGAAGA
1 CCCGAA-A
1383 CCCCGAAA
1 -CCCGAAA
1391 CCCGAAA
1 CCCGAAA
1398 CCCGATAA
1 CCCGA-AA
*
1406 CCAGAAA
1 CCCGAAA
*
1413 ACCGAAA
1 CCCGAAA
1420 CCCGAAAA
1 CCCG-AAA
1428 CCCGAAA
1 CCCGAAA
*
1435 CCCGCAA
1 CCCGAAA
1442 CCCGAAA
1 CCCGAAA
1449 CCCGAAAA
1 CCCG-AAA
*
1457 CCCTAAAA
1 CCC-GAAA
**
1465 CCCGCCA
1 CCCGAAA
1472 CCCGAAA
1 CCCGAAA
1479 CCCCG-AA
1 -CCCGAAA
1486 CCCGAAA
1 CCCGAAA
1493 CCCGAAA
1 CCCGAAA
1500 CCCGAGAAA
1 CCC--GAAA
1509 CCCGAATA
1 CCCGAA-A
1517 CCCGATAA
1 CCCGA-AA
1525 --CGAAA
1 CCCGAAA
1530 CCTCG-AA
1 CC-CGAAA
1537 CTCCGAAA
1 C-CCGAAA
1545 CCTTCGAAA
1 CC--CGAAA
1554 TCCCGAAA
1 -CCCGAAA
1562 CCCGAAA
1 CCCGAAA
*
1569 CCCGAAC
1 CCCGAAA
1576 CCCG-AA
1 CCCGAAA
1582 -CCGAAA
1 CCCGAAA
1588 CCCG-AA
1 CCCGAAA
*
1594 CCGGGAAAA
1 CC-CG-AAA
1603 CCCCGAAA
1 -CCCGAAA
1611 -CCGAAA
1 CCCGAAA
1617 CCCG-AA
1 CCCGAAA
1623 CCCGAAA
1 CCCGAAA
1630 CCCGAAA
1 CCCGAAA
1637 CCCGAAA
1 CCCGAAA
1644 CCCGAAA
1 CCCGAAA
1651 CCCGAAA
1 CCCGAAA
*
1658 CCCGACA
1 CCCGAAA
1665 CTCCGAAA
1 C-CCGAAA
1673 CCCCGAAA
1 -CCCGAAA
*
1681 TCCGAAA
1 CCCGAAA
*
1688 CCTGGAAA
1 CC-CGAAA
*
1696 -CAGCAAA
1 CCCG-AAA
1703 -CCGAAA
1 CCCGAAA
1709 -CCGAAA
1 CCCGAAA
1715 CCTCGAAA
1 CC-CGAAA
1723 CCCGAAA
1 CCCGAAA
1730 CCCTGAAA
1 CCC-GAAA
*
1738 CCGTGTAAA
1 CC-CG-AAA
1747 CTCGCTGTAAA
1 C-C-C-G-AAA
1758 CCCGAAA
1 CCCGAAA
1765 CTCCGAAA
1 C-CCGAAA
1773 CCGCGTAAA
1 CC-CG-AAA
*
1782 CTCTCGCGAACG
1 --C-C-CGAA-A
1794 CCCGGAATA
1 CCC-GAA-A
*
1803 CCCGCAA
1 CCCGAAA
*
1810 CCCGCAA
1 CCCGAAA
*
1817 CCCGTACA
1 CCCG-AAA
1825 CCCGGAAA
1 CCC-GAAA
1833 CCCTGAAA
1 CCC-GAAA
1841 -CCGAAA
1 CCCGAAA
1847 CCCG-AA
1 CCCGAAA
*
1853 CCTGTAAA
1 CCCG-AAA
1861 TCCTCG-AA
1 -CC-CGAAA
1869 CCCGTGGATAA
1 CCC---GA-AA
1880 CCCGTCAAA
1 CCCG--AAA
1889 CCCGAACA
1 CCCGAA-A
1897 CCCCGAAA
1 -CCCGAAA
1905 -CCGAAAA
1 CCCG-AAA
*
1912 CCGGAACA
1 CCCGAA-A
1920 CCCGAAA
1 CCCGAAA
1927 CCCGGATAA
1 CCC-GA-AA
1936 CCCGAAA
1 CCCGAAA
1943 CCCGAAA
1 CCCGAAA
1950 -CCGAATA
1 CCCGAA-A
1957 CCCGAAA
1 CCCGAAA
*
1964 CCCGCAA
1 CCCGAAA
1971 CCCGAAA
1 CCCGAAA
1978 -CCGAAA
1 CCCGAAA
1984 CCCGAGAA
1 CCCGA-AA
1992 CCCCGAAA
1 -CCCGAAA
2000 CCCCGAAA
1 -CCCGAAA
2008 -CC-AAA
1 CCCGAAA
2013 GCCCCGCAAA
1 --CCCG-AAA
2023 CCCGAAA
1 CCCGAAA
2030 CCCGAAA
1 CCCGAAA
2037 CCCG-AA
1 CCCGAAA
2043 CACCGAAA
1 C-CCGAAA
2051 CCCGGAAA
1 CCC-GAAA
2059 CCCGTTAAA
1 CCCG--AAA
2068 CCCGAAGAA
1 CCCG-A-AA
2077 GCCCGAGAA
1 -CCCGA-AA
2086 -CCGAAA
1 CCCGAAA
*
2092 CCTC-ACA
1 CC-CGAAA
*
2099 CCTGTAAAA
1 CCCG--AAA
2108 CTCCGCAAA
1 C-CCG-AAA
*
2117 CGCCAGACA
1 C-CC-GAAA
2126 CCCGAAA
1 CCCGAAA
*
2133 -CCGACTAC
1 CCCGA--AA
2141 CCCGAAA
1 CCCGAAA
2148 CCCG-AA
1 CCCGAAA
2154 -CCG-AA
1 CCCGAAA
2159 CCCGAAAA
1 CCCG-AAA
2167 CCCGAAAA
1 CCCG-AAA
2175 CCCG-AA
1 CCCGAAA
2181 -CCGAAAA
1 CCCG-AAA
2188 CTCCGAAA
1 C-CCGAAA
2196 CCCGAAA
1 CCCGAAA
2203 GCCCG-AA
1 -CCCGAAA
2210 CCCGAAA
1 CCCGAAA
2217 CCCCGAAA
1 -CCCGAAA
2225 CCCCGAAA
1 -CCCGAAA
2233 CTCTCGGAAA
1 C-C-C-GAAA
*
2243 CCCGCAA
1 CCCGAAA
2250 -CCGAAA
1 CCCGAAA
2256 CCCGAAA
1 CCCGAAA
2263 -CCGAAA
1 CCCGAAA
*
2269 CCCCAAA
1 CCCGAAA
*
2276 CCCCAAAA
1 -CCCGAAA
*
2284 CCCCAAA
1 CCCGAAA
*
2291 GCCCATAAA
1 -CCC-GAAA
*
2300 CCCCAGAA
1 CCCGA-AA
2308 CTCC-AAA
1 C-CCGAAA
2315 CCCCGAAA
1 -CCCGAAA
*
2323 GCACGATAA
1 -CCCGA-AA
*
2332 CCCCAAAA
1 -CCCGAAA
*
2340 CTCCCAAA
1 C-CCGAAA
*
2348 CCCCAAA
1 CCCGAAA
*
2355 GCCCCATAA
1 -CCCGA-AA
2364 CCCCGAAA
1 -CCCGAAA
2372 TCTCCCGCAATTA
1 ---CCCG-AA--A
*
2385 TCTCCCAAGAA
1 ---CCCGA-AA
*
2396 CCCCAAA
1 CCCGAAA
*
2403 CCCCAAA
1 CCCGAAA
*
2410 CCCCAAA
1 CCCGAAA
2417 CCC-AAA
1 CCCGAAA
*
2423 CCCCAAA
1 CCCGAAA
2430 CCC-AAA
1 CCCGAAA
2436 CCC-AAA
1 CCCGAAA
*
2442 CCCCAAA
1 CCCGAAA
2449 CCC-AAA
1 CCCGAAA
2455 CCC-AAA
1 CCCGAAA
*
2461 CCCCAAA
1 CCCGAAA
*
2468 CCCCAAA
1 CCCGAAA
*
2475 CCCCAAA
1 CCCGAAA
*
2482 CCCCAATAA
1 -CCCGA-AA
*
2491 CCCCAAA
1 CCCGAAA
*
2498 CCCCAAAA
1 -CCCGAAA
*
2506 CCCCAAA
1 CCCGAAA
*
2513 CCCCAAA
1 CCCGAAA
*
2520 CCCCAAA
1 CCCGAAA
*
2527 CCCCAAAA
1 -CCCGAAA
2535 CCC-AAA
1 CCCGAAA
*
2541 CCCCAAA
1 CCCGAAA
*
2548 CCCCAAA
1 CCCGAAA
*
2555 CCCCAAA
1 CCCGAAA
*
2562 CCCCAAA
1 CCCGAAA
*
2569 CCCCAAA
1 CCCGAAA
*
2576 CCCCAAA
1 CCCGAAA
2583 CCC-AAA
1 CCCGAAA
*
2589 CCCCAAA
1 CCCGAAA
*
2596 CCCCAAA
1 CCCGAAA
*
2603 CCCCAAA
1 CCCGAAA
*
2610 CCCCAAA
1 CCCGAAA
*
2617 CCCCAAA
1 CCCGAAA
*
2624 CCCCAAA
1 CCCGAAA
*
2631 CCCCAAA
1 CCCGAAA
*
2638 CCCCAAA
1 CCCGAAA
**
2645 CCCCCAA
1 CCCGAAA
*
2652 CCCCAAA
1 CCCGAAA
*
2659 CCCCAAA
1 CCCGAAA
*
2666 CCCCAAA
1 CCCGAAA
*
2673 CCC-CAA
1 CCCGAAA
*
2679 CCCCAAA
1 CCCGAAA
2686 CCC-AAA
1 CCCGAAA
*
2692 CCCCAAA
1 CCCGAAA
*
2699 CCC-CAA
1 CCCGAAA
*
2705 CCCCAAA
1 CCCGAAA
*
2712 CCCCCAAA
1 -CCCGAAA
*
2720 CCCCAAA
1 CCCGAAA
*
2727 CCCCAAA
1 CCCGAAA
*
2734 CCCCAAA
1 CCCGAAA
*
2741 CCCAAAA
1 CCCGAAA
*
2748 CCCCAAA
1 CCCGAAA
*
2755 CCCCAAA
1 CCCGAAA
*
2762 CCCCAAA
1 CCCGAAA
*
2769 CCCCAAA
1 CCCGAAA
*
2776 CCCCAAA
1 CCCGAAA
*
2783 CCCCAAA
1 CCCGAAA
*
2790 CCCCAAA
1 CCCGAAA
2797 CCC-AAA
1 CCCGAAA
*
2803 CCCCCAAA
1 -CCCGAAA
*
2811 CCCCCAAA
1 -CCCGAAA
*
2819 CCCCAAA
1 CCCGAAA
2826 CCC--AA
1 CCCGAAA
*
2831 CCCCAAA
1 CCCGAAA
*
2838 CCCCAAA
1 CCCGAAA
*
2845 CCCCAAAA
1 -CCCGAAA
*
2853 CCCCAAA
1 CCCGAAA
*
2860 CCCCAAAA
1 -CCCGAAA
*
2868 CCCCAAA
1 CCCGAAA
*
2875 CCCCAAA
1 CCCGAAA
2882 CACC-AAA
1 C-CCGAAA
*
2889 CCC-CAA
1 CCCGAAA
*
2895 CCCCAAA
1 CCCGAAA
*
2902 CCCCAAA
1 CCCGAAA
*
2909 CCC-CAA
1 CCCGAAA
*
2915 CCCCAAA
1 CCCGAAA
*
2922 CCCCAAAA
1 -CCCGAAA
*
2930 CCCCAAA
1 CCCGAAA
2937 CCC-AAA
1 CCCGAAA
*
2943 CCCCAAA
1 CCCGAAA
*
2950 CCCCAAA
1 CCCGAAA
*
2957 CCCCAAA
1 CCCGAAA
*
2964 CCCCAAA
1 CCCGAAA
*
2971 CCCCAAA
1 CCCGAAA
*
2978 CCCCAAA
1 CCCGAAA
*
2985 CCCCAAA
1 CCCGAAA
*
2992 CCCCAAA
1 CCCGAAA
*
2999 CCCCAAA
1 CCCGAAA
*
3006 CCCCAAA
1 CCCGAAA
*
3013 CCCCAAA
1 CCCGAAA
*
3020 CCCCAAA
1 CCCGAAA
*
3027 CCCCAAA
1 CCCGAAA
*
3034 CCCCAAA
1 CCCGAAA
*
3041 CCCAAAA
1 CCCGAAA
*
3048 CAC-AAA
1 CCCGAAA
*
3054 CCCCAAA
1 CCCGAAA
3061 CCC-AAA
1 CCCGAAA
*
3067 CCCCAAA
1 CCCGAAA
*
3074 CCCCAAA
1 CCCGAAA
3081 CCC-AAA
1 CCCGAAA
*
3087 CCCCAAA
1 CCCGAAA
*
3094 CCCCAAA
1 CCCGAAA
*
3101 CCCCAAA
1 CCCGAAA
*
3108 CCCCAAA
1 CCCGAAA
*
3115 CCCCAAA
1 CCCGAAA
3122 CCC-AAA
1 CCCGAAA
*
3128 CCCCAAA
1 CCCGAAA
*
3135 CCCCAAA
1 CCCGAAA
3142 CCC-AAA
1 CCCGAAA
3148 CCC-AAA
1 CCCGAAA
*
3154 CCCCAAA
1 CCCGAAA
*
3161 CCC-CAA
1 CCCGAAA
*
3167 CCCCAAA
1 CCCGAAA
*
3174 CCCCAAAA
1 -CCCGAAA
*
3182 CCCCAAA
1 CCCGAAA
3189 CCC---A
1 CCCGAAA
*
3193 CCCCAAA
1 CCCGAAA
*
3200 CCC-CAA
1 CCCGAAA
*
3206 CCC-CAA
1 CCCGAAA
*
3212 CCCCAAA
1 CCCGAAA
3219 CCC-AAA
1 CCCGAAA
*
3225 CCCCAAA
1 CCCGAAA
*
3232 CCCCAAA
1 CCCGAAA
3239 -CC--AA
1 CCCGAAA
*
3243 CCCCAAA
1 CCCGAAA
*
3250 CCCAAAA
1 CCCGAAA
*
3257 CCCCAAA
1 CCCGAAA
*
3264 CCCCAAA
1 CCCGAAA
*
3271 CCCCAAA
1 CCCGAAA
3278 CCC--AA
1 CCCGAAA
3283 CCC-AAA
1 CCCGAAA
3289 CCC-AAA
1 CCCGAAA
3295 CCC-AAA
1 CCCGAAA
*
3301 CCCCAAA
1 CCCGAAA
3308 CCC-AAA
1 CCCGAAA
*
3314 CCCCAAA
1 CCCGAAA
*
3321 CCCCAAA
1 CCCGAAA
*
3328 CCCCAAA
1 CCCGAAA
3335 CCC-AAA
1 CCCGAAA
*
3341 CCC-CAA
1 CCCGAAA
*
3347 CCCCAAA
1 CCCGAAA
*
3354 CCCCAAA
1 CCCGAAA
*
3361 CCCCAAA
1 CCCGAAA
*
3368 CCCCAAA
1 CCCGAAA
*
3375 CCCCAAA
1 CCCGAAA
3382 CCC-AAA
1 CCCGAAA
*
3388 CCCCAAA
1 CCCGAAA
*
3395 CCCCAAA
1 CCCGAAA
3402 CCC-AAA
1 CCCGAAA
*
3408 CCCCAAA
1 CCCGAAA
3415 CCC-AAA
1 CCCGAAA
*
3421 CCCCAAA
1 CCCGAAA
*
3428 CCCCAAA
1 CCCGAAA
*
3435 CCCCAAA
1 CCCGAAA
3442 CCC-AAA
1 CCCGAAA
*
3448 CCCCAAA
1 CCCGAAA
*
3455 CCCCAAA
1 CCCGAAA
*
3462 CCCCAAA
1 CCCGAAA
*
3469 CCC-CAA
1 CCCGAAA
3475 CCC-AAA
1 CCCGAAA
*
3481 CCCCAAA
1 CCCGAAA
*
3488 CCCCAAA
1 CCCGAAA
*
3495 CCC-CAA
1 CCCGAAA
*
3501 CCCTTAAAA
1 CCC--GAAA
3510 CCC-AAA
1 CCCGAAA
*
3516 CCCCAAA
1 CCCGAAA
*
3523 CCC-CAA
1 CCCGAAA
*
3529 CCCCAAA
1 CCCGAAA
*
3536 CCCCAAA
1 CCCGAAA
*
3543 CCCAAAA
1 CCCGAAA
*
3550 CCCCAAA
1 CCCGAAA
3557 CCC
1 CCC
3560 CAAAAACCCC
Statistics
Matches: 2975, Mismatches: 221, Indels: 667
0.77 0.06 0.17
Matches are distributed among these distances:
4 6 0.00
5 36 0.01
6 413 0.14
7 1476 0.50
8 607 0.20
9 286 0.10
10 94 0.03
11 36 0.01
12 11 0.00
13 10 0.00
ACGTcount: A:0.41, C:0.46, G:0.10, T:0.04
Consensus pattern (7 bp):
CCCGAAA
Found at i:942 original size:26 final size:26
Alignment explanation
Indices: 906--955 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
896 CCCGCAACCC
*
906 GAAACCCGAAAACCCGGAAACCCGTG
1 GAAACCCGAAAACCCGAAAACCCGTG
932 GAAACCCGAAAACCCGAAAACCCG
1 GAAACCCGAAAACCCGAAAACCCG
956 ACGAACCCGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.42, C:0.36, G:0.20, T:0.02
Consensus pattern (26 bp):
GAAACCCGAAAACCCGAAAACCCGTG
Found at i:1030 original size:132 final size:125
Alignment explanation
Indices: 890--1739 Score: 334
Period size: 124 Copynumber: 6.4 Consensus size: 125
880 AACCCGCACT
*
890 CCGAAACCCGCAACCCGAAACCCGAAAACCCGGAAACCCGTGGAAACCCGAAAACCCGAAAACCC
1 CCGAAACCCGAAACCCGAAACCCG-AAACCC--AAACCC---GAAACCCG-AAACCCG-AAACCC
955 GAC-G-AACCCG-AAACCGAAACCCG-AAACCGACACCCGAAACCCAACCCCGACACCCGAACCC
58 G-CGGAAACCCGCAAACCGAAACCCGCAAACCGA-A-CCGAAACCCAACCCCGACACCCGAACCC
1016 TCGAAA
120 TCGAAA
*
1022 CCGAAACCCGAAACCCGAAACCCGAAACCCAAACCCGAAACCCGAACCCCGAAACCCGCGGAAAC
1 CCGAAACCCGAAACCCGAAACCCGAAACCCAAACCCGAAACCCGAAACCCGAAACCCGCGGAAAC
* * * *
1087 CCGCAACCCGAAACCCGCAACCCGAACCGAAACCTCCGAA-ACCGTAAACCCCGATAAACCCT-G
66 CCGCAAACCGAAACCCGCAAACCGAACCGAAA-C-CC-AACCCCG-ACA-CCCG---AACCCTCG
1150 ACAA
123 A-AA
*
1154 CCAGAAACCCGAAAACCCGTAAACAACCCGAAAACCCGAACCCGAAACCCTGAAACCCGGAAACC
1 CC-GAAACCCG-AAACCCG---A-AACCCG-AAACCCAAACCCGAAACCC-GAAACCC-GAAACC
** * * *
1219 CG-ATAAATCCTCG-AAACCCGAAACTCCG-ATACCCGAAACGCCGAAATCGCCGAAACCCGATA
57 CGCGGAAA-CC-CGCAAA-CCGAAAC-CCGCA-AACCG-AA--CCGAAA-C-CC-AACCCCGA-C
*
1281 ACCCGAACCC-CGAGA
110 ACCCGAACCCTCGAAA
* * * * * *
1296 CCGGAAGCACGAAACTCTGCAACCCGAAACCCGAAAACCCAGAAACCC-AAACGACG-CACACC-
1 CC-GAAACCCGAAAC-CCGAAACCCGAAACCC--AAACCC-GAAACCCGAAAC-CCGAAAC-CCG
* * * * **
1358 C-G-AACCCG-AAACCGCAACCCG-AAGACC---CCGAAACCCGAAACCCGATAACCAGAAAAC-
59 CGGAAACCCGCAAACCGAAACCCGCAA-ACCGAACCGAAACCC-AACCCCGA-CACCCGAACCCT
1415 CGAAA
121 CGAAA
* * **
1420 CCCGAAAACCCGAAACCCGCAACCCGAAACCCGAAAACCCTAAAACCCGCCACCCGAAACCC-C-
1 -CCG-AAACCCGAAACCCGAAACCCGAAACCC--AAACCC-GAAACCCGAAACCCGAAACCCGCG
* ** *
1483 G-AACCCG-AAACCCGAAACCCGAGAAACCCGAATACCCGATAACGAAACCTCGA-ACTCCGAAA
61 GAAACCCGCAAA-CCGAAACCCG-CAAA-CCG-A-A-CCGA-AACCCAACCCCGACAC-CCG-AA
*
1545 CCTTCGAAA
117 CCCTCGAAA
* * *
1554 TCCCGAAACCCGAAACCCGAACCCCG-AACCGAAACCCG-AACCGGGAAAACCCCGAAA--C-C-
1 --CCGAAACCCGAAACCCGAAACCCGAAACCCAAACCCGAAACC-CG-AAA-CCCGAAACCCGCG
* *
1613 GAAACCCG-AACCCGAAACCCG-AAACCCGAAACCCGAAACCCGAAACCCGACACTCCGAAACCC
61 GAAACCCGCAAACCGAAACCCGCAAA-CCG-AA-CCGAAACCC-AACCCCGACAC-CCG-AACCC
1676 -CGAAA
120 TCGAAA
* * *
1681 TCCGAAACCTGGAAA-CAGCAAA-CCGAAACCGAAACCTCGAAACCCGAAACCCTGAAACC
1 -CCGAAACC-CGAAACCCG-AAACCCGAAACCCAAACC-CGAAACCCGAAACCC-GAAACC
1740 GTGTAAACTC
Statistics
Matches: 578, Mismatches: 66, Indels: 151
0.73 0.08 0.19
Matches are distributed among these distances:
123 1 0.00
124 77 0.13
125 43 0.07
126 48 0.08
127 55 0.10
128 27 0.05
129 18 0.03
130 14 0.02
131 26 0.04
132 48 0.08
133 30 0.05
134 39 0.07
135 6 0.01
136 2 0.00
137 9 0.02
138 19 0.03
139 24 0.04
140 16 0.03
141 16 0.03
142 21 0.04
143 15 0.03
144 2 0.00
146 17 0.03
147 5 0.01
ACGTcount: A:0.40, C:0.41, G:0.15, T:0.04
Consensus pattern (125 bp):
CCGAAACCCGAAACCCGAAACCCGAAACCCAAACCCGAAACCCGAAACCCGAAACCCGCGGAAAC
CCGCAAACCGAAACCCGCAAACCGAACCGAAACCCAACCCCGACACCCGAACCCTCGAAA
Found at i:1201 original size:40 final size:38
Alignment explanation
Indices: 442--1689 Score: 217
Period size: 37 Copynumber: 33.7 Consensus size: 38
432 AAACCCGGGA
442 AACCTCGAAACCCGAAACCCG-AAA--CCG--AAACCCG
1 AACC-CGAAACCCGAAACCCGTAAACCCCGATAAACCCG
*
476 AATACCCGCAACCTCTGAAAACCC-TAAA--CCGA-AAACCCG
1 -A-ACCCGAAACC-C-G-AAACCCGTAAACCCCGATAAACCCG
515 CAACCCGAATACCCGAAACCCG-AAA--CCGAT-AA-CCG
1 -AACCCGAA-ACCCGAAACCCGTAAACCCCGATAAACCCG
* * *
550 AAACCCGAAACCTCGAAACCCGAAAATCCTGA-AAATCCCG
1 -AACCCGAAACC-CGAAACCCGTAAACCCCGATAAA-CCCG
* *
590 AAACCCCGGAAACCCCGAAACCCG-CAACCTCGA-AAACCCG
1 -AA-CCC-GAAA-CCCGAAACCCGTAAACCCCGATAAACCCG
*
630 AACCCCGAAACCCGAAAGCCG-AAA-CCCG--AAACCCG
1 AA-CCCGAAACCCGAAACCCGTAAACCCCGATAAACCCG
* * *
665 AAACCGGAAACCCGACA-CCG-CAA-CCCG--AAACCCG
1 -AACCCGAAACCCGAAACCCGTAAACCCCGATAAACCCG
* ** *
699 TATAACCGTGGACCCAGAACACCC--AAA-CCCG-CAAACCCG
1 -A-ACCCG-AAACCC-GAA-ACCCGTAAACCCCGATAAACCCG
738 ACAACCTCTGAAACCCGAAACCCG-AAA-CCCG--AAACCCG
1 --AACC-C-GAAACCCGAAACCCGTAAACCCCGATAAACCCG
* * * *
776 CAACCCTAAATCCCG-ACCCCTGGAAA-CCCGATGAACCCG
1 -AACCCGAAA-CCCGAAACCC-GTAAACCCCGATAAACCCG
* *
815 ATAACCTAAACCCGAAATCTCC-TGAAA-CCCGAT-AACCCG
1 A-ACCCGAAACCCGAAA-C-CCGT-AAACCCCGATAAACCCG
* * * *
854 TA----TAACCCGGAAACCCG-CAACCTCG--AAACCCG
1 AACCCGAAACCC-GAAACCCGTAAACCCCGATAAACCCG
* *
886 CACTCCGAAACCCGCAACCCG-AAA-CCCGA-AAACCCGG
1 AAC-CCGAAACCCGAAACCCGTAAACCCCGATAAACCC-G
* **
923 AAACCCGTGGAAACCCGAAAACCCG-AAAACCCGACGAACCCG
1 -AACCC---GAAACCCG-AAACCCGTAAACCCCGATAAACCCG
* * *
965 AAACCGAAACCCGAAA-CCG-ACA-CCCGAAACCCAACCCCG
1 AACCCGAAACCCGAAACCCGTAAACCCCGATA---AA-CCCG
*
1004 ACACCCGAACCCTCGAAA-CCG-AAA-CCCG--AAACCCG
1 A-ACCCGAAACC-CGAAACCCGTAAACCCCGATAAACCCG
*
1039 AAACCCGAAACCC-AAACCCG-AAA-CCCG--AACCCCG
1 -AACCCGAAACCCGAAACCCGTAAACCCCGATAAACCCG
* *
1073 AAACCCGCGGAAACCCGCAACCCG-AAA-CCCG--CAACCCG
1 -AA-CC-C-GAAACCCGAAACCCGTAAACCCCGATAAACCCG
1111 AA-CCGAAACCTCCGAAA-CCGTAAACCCCGATAAACCCTG
1 AACCCGAAA-C-CCGAAACCCGTAAACCCCGATAAACCC-G
*
1150 ACAACCAGAAACCCGAAAACCCGTAAACAACCCGA-AAACCCG
1 --AACCCGAAACCCG-AAACCCGTAAAC--CCCGATAAACCCG
*
1192 AACCCGAAACCCTGAAACCCGGAAA-CCCGATAAATCCTCG
1 AACCCGAAACCC-GAAACCCGTAAACCCCGATAAA-CC-CG
* * *
1232 AAACCCGAAACTCCGATACCCG-AAACGCCG--AAA-TCG
1 -AACCCGAAAC-CCGAAACCCGTAAACCCCGATAAACCCG
* *
1268 ---CCGAAACCCGATAACCCG--AACCCCG--AGACCGG
1 AACCCGAAACCCGA-AACCCGTAAACCCCGATAAACCCG
* * *
1300 AAGCACGAAACTCTGCAACCCG-AAA-CCCGA-AAACCCAG
1 AA-CCCGAAAC-CCGAAACCCGTAAACCCCGATAAACCC-G
* *
1338 AAACCC-AAACGACGCACACCCG--AA-CCCG--AAA-CCG
1 -AACCCGAAAC-CCG-AAACCCGTAAACCCCGATAAACCCG
*
1372 CAACCCGAAGACCCCGAAACCCG-AAA-CCCGAT-AACCAG
1 -AACCCGAA-A-CCCGAAACCCGTAAACCCCGATAAACCCG
* *
1410 AAAACCGAAACCCGAAAACCCG-AAA-CCCG--CAACCCG
1 -AACCCGAAACCCG-AAACCCGTAAACCCCGATAAACCCG
* ** *
1446 AAACCCGAAAACCCTAAAACCCG-CCA-CCCGA-AACCCCG
1 -AACCCG-AAACCC-GAAACCCGTAAACCCCGATAAACCCG
* *
1484 AACCCGAAACCCGAAACCCG-AGAAACCCGA-ATACCCG
1 AACCCGAAACCCGAAACCCGTA-AACCCCGATAAACCCG
* * *
1521 ATA-ACGAAACCTCG-AACTCCG-AAACCTTCGA-AATCCCG
1 A-ACCCGAAACC-CGAAAC-CCGTAAACC-CCGATAAACCCG
*
1559 AAACCCGAAACCCGAACCCCG--AA--CCG--AAACCCG
1 -AACCCGAAACCCGAAACCCGTAAACCCCGATAAACCCG
*
1592 AACCGGGAAAACCCCGAAA-CCG-AAA-CCCG---AACCCG
1 AACC-CG-AAA-CCCGAAACCCGTAAACCCCGATAAACCCG
1627 AAACCCGAAACCCGAAACCCG-AAA-CCCG--AAACCCG
1 -AACCCGAAACCCGAAACCCGTAAACCCCGATAAACCCG
*
1662 ACACTCCGAAACCCCGAAATCCG-AAACC
1 A-AC-CCGAAA-CCCGAAACCCGTAAACC
1690 TGGAAACAGC
Statistics
Matches: 966, Mismatches: 111, Indels: 269
0.72 0.08 0.20
Matches are distributed among these distances:
31 12 0.01
32 26 0.03
33 26 0.03
34 79 0.08
35 132 0.14
36 130 0.13
37 153 0.16
38 134 0.14
39 82 0.08
40 71 0.07
41 68 0.07
42 35 0.04
43 13 0.01
44 5 0.01
ACGTcount: A:0.39, C:0.41, G:0.15, T:0.05
Consensus pattern (38 bp):
AACCCGAAACCCGAAACCCGTAAACCCCGATAAACCCG
Found at i:1234 original size:48 final size:47
Alignment explanation
Indices: 332--2268 Score: 306
Period size: 44 Copynumber: 42.3 Consensus size: 47
322 AAACCCGACC
* *
332 AACCCGAATACCCGAAAATCC-TAAA-ACCCGAAAACCCGAAAATACCCGA
1 AACCCGAA-ACCCGAAAACCCGTAAACACCCG-AAACCCGAAACT--CCGA
* * *
381 AACCCGAAACTCCGGAACCTCCG-AAATC-CCTTGCCATAACCCGAAAC-CTCGA
1 AACCCGAAAC-CCGAAAAC-CCGTAAA-CACC---CGA-AACCCGAAACTC-CGA
433 AACCCGGGAAACCTCG-AAACCCG--AA-ACCCGAAA-CCGAAAC-CCGA
1 AACCC--GAAACC-CGAAAACCCGTAAACACCCGAAACCCGAAACTCCGA
* *
477 ATACCCGCAACCTCTGAAAACCC-T-AA-A-CCGAAAACCCGCAAC-CCGA
1 A-ACCCGAAACC-C-GAAAACCCGTAAACACCCG-AAACCCGAAACTCCGA
*
523 ATACCCGAAACCCG-AAA-CCG-ATA-A-CCGAAACCCGAAAC-CTCGA
1 A-ACCCGAAACCCGAAAACCCGTAAACACCCGAAACCCGAAACTC-CGA
* *
566 AACCCGAAAATCCTGAAAATCCCG-AAAC-CCCGGAAACCCCGAAAC-CCGC
1 AACCCG-AAA-CCCGAAAA-CCCGTAAACACCC-GAAA-CCCGAAACTCCGA
* *
615 AACCTCGAAAACCCG-AACCCCG--AA-ACCCGAAAGCCGAAAC-CCGA
1 AACC-CG-AAACCCGAAAACCCGTAAACACCCGAAACCCGAAACTCCGA
* *
659 AACCCGAAA-CCGGAAACCCG---ACA-CCGCAACCCGAAAC-CCGTA
1 AACCCGAAACCCGAAAACCCGTAAACACCCGAAACCCGAAACTCCG-A
** * *
701 TAA-CCGTGGACCCAGAACACCC---AA-ACCCGCAAACCCGACAACCTCTGA
1 -AACCCG-AAACCC-GAAAACCCGTAAACACCCG-AAACCCGA-AA-CTCCGA
* *
749 AACCCGAAACCCG-AAACCCG--AA-ACCCGCAACCCTAAA-TCCCG-
1 AACCCGAAACCCGAAAACCCGTAAACACCCGAAACCCGAAACT-CCGA
* * *
791 ACCCCTGGAAACCCGATGAACCCGATAACCTAAACCCGAAATCTCCTGAAAC-CCGA
1 AACCC--GAAACCCGA-AAACCCG-TAA---ACACCCGAAA-C-CC-GAAACTCCGA
* * * *
847 TAACCCGTATAACCCGGAAACCCG-CAAC-CTCGAAACCCG-CACTCCGA
1 -AACCCG-A-AACCCGAAAACCCGTAAACACCCGAAACCCGAAACTCCGA
* *
894 AACCCGCAACCCG-AAACCCG-AAA-ACCCGGAAACCCG----T-GGA
1 AACCCGAAACCCGAAAACCCGTAAACACCC-GAAACCCGAAACTCCGA
*
934 AACCCGAAAACCCGAAAACCCG-ACGA-ACCCGAAA-CCGAAAC-CCGA
1 AACCCG-AAACCCGAAAACCCGTA-AACACCCGAAACCCGAAACTCCGA
* * *
979 AA-CCGACACCCG-AAACCC---AAC-CCCGACACCCG-AACCCTCGA
1 AACCCGAAACCCGAAAACCCGTAAACACCCGAAACCCGAAACTC-CGA
1020 AA-CCGAAACCCG-AAACCCG--AA-ACCCGAAACCC-AAAC-CCGA
1 AACCCGAAACCCGAAAACCCGTAAACACCCGAAACCCGAAACTCCGA
* ** * *
1060 AACCCGAACCCCG-AAACCCGCGGAA-ACCCGCAACCCGAAAC-CCGC
1 AACCCGAAACCCGAAAACCCG-TAAACACCCGAAACCCGAAACTCCGA
*
1105 AACCCG-AA-CCGAAACCTCCG--AA-A-CCGTAAACCCCGATAAAC-CCTGA
1 AACCCGAAACCCGAAAAC-CCGTAAACACCCG-AAA-CCCG--AAACTCC-GA
*
1151 CAACCAGAAACCCGAAAACCCGTAAACAACCCGAAAACCCG-AAC-CCGA
1 -AACCCGAAACCCGAAAACCCGTAAAC-ACCCG-AAACCCGAAACTCCGA
* *
1199 AACCCTGAAACCCGGAAACCCGATAAATC-CTCGAAACCCGAAACTCCGA
1 AACCC-GAAACCCGAAAACCCG-TAAA-CACCCGAAACCCGAAACTCCGA
* * *
1248 TACCCGAAACGCCGAAATCGCCG--AA-ACCCGATAACCCG-AACCCCGA
1 AACCCGAAAC-CCGAAAAC-CCGTAAACACCCGA-AACCCGAAACTCCGA
* * * * * **
1294 GACCGGAAGCACG-AAACTC-TGCA-ACCCGAAACCCGAAAAC-CCAGA
1 AACCCGAAACCCGAAAACCCGTAAACACCCGAAACCCG-AAACTCC-GA
* * * * * * *
1339 AACCC-AAACGACGCACACCCG-AACCCGAAACCGCAACCCGAAGACCCCGA
1 AACCCGAAAC-CCGAAAACCCGTAA-AC--ACCCGAAACCCGAA-ACTCCGA
* *
1389 AACCCGAAACCCGATAACCAG-AAA-A-CCGAAACCCGAAAAC-CCGA
1 AACCCGAAACCCGAAAACCCGTAAACACCCGAAACCCG-AAACTCCGA
* * **
1433 AACCCGCAACCCG-AAACCCG-AAA-ACCCTAAAACCCGCCAC-CCGA
1 AACCCGAAACCCGAAAACCCGTAAACACCC-GAAACCCGAAACTCCGA
*
1477 AACCCCG-AACCCG-AAACCCG-AAAC-CCGAGAAACCCGAATAC-CCGA
1 AA-CCCGAAACCCGAAAACCCGTAAACACC-CGAAACCCGAA-ACTCCGA
*
1522 TAA--CGAAACCTCG--AACTCCG-AAAC-CTTCGAAATCCCGAAAC-CCGA
1 -AACCCGAAACC-CGAAAAC-CCGTAAACAC-CCGAAA-CCCGAAACTCCGA
* * *
1567 AACCCGAACCCCG--AA-CCG--AA-ACCCG-AACCGGGAAAACCCCGA
1 AACCCGAAACCCGAAAACCCGTAAACACCCGAAACC-CG-AAACTCCGA
1609 AA-CCGAAACCCG--AACCCG--AA-ACCCGAAACCCGAAAC-CCGA
1 AACCCGAAACCCGAAAACCCGTAAACACCCGAAACCCGAAACTCCGA
* * *
1649 AACCCGAAACCCG-ACACTCCG-AAAC-CCCGAAATCCGAAAC-CTGGA
1 AACCCGAAACCCGAAAAC-CCGTAAACACCCGAAACCCGAAACTC-CGA
* *
1694 AA-CAGCAAA-CCG-AAA-CCG-AAAC-CTCGAAACCCGAAAC-CCTGA
1 AACCCG-AAACCCGAAAACCCGTAAACACCCGAAACCCGAAACTCC-GA
* * *
1736 AACCGTGTAAACTCGCTGTAAACCCG-AAAC-TCCGAAACCGCGTAAACTCTCGCGA
1 AACC-CG-AAAC-C-C-GAAAACCCGTAAACACCCGAAACC-CG-AAA--CTC-CGA
* * * *
1791 ACGCCCGGAATACCCG-CAACCCG--CA-ACCCGTACACCCGGAAAC-CCTGA
1 A-ACCC-GAA-ACCCGAAAACCCGTAAACACCCG-AAACCC-GAAACTCC-GA
* *
1839 AA-CCGAAACCCG--AACCTGTAAATC-CTCG-AACCCGTGGATAAC-CCGTCA
1 AACCCGAAACCCGAAAACCCGTAAA-CACCCGAAACCC---GA-AACTCCG--A
*
1887 AACCCGAACACCCCG-AAA-CCG-AAA-ACCGGAACACCCGAAAC-CCGGA
1 AACCCGAA-A-CCCGAAAACCCGTAAACACCCGAA-ACCCGAAACTCC-GA
* *
1933 TAACCCGAAACCCG-AAA-CCG--AATACCCGAAACCCGCAAC-CCGA
1 -AACCCGAAACCCGAAAACCCGTAAACACCCGAAACCCGAAACTCCGA
* *
1976 AA-CCGAAACCCGAGAACCCCG-AAAC-CCCGAAA-CC-AAAGCCCCGCA
1 AACCCGAAACCCGA-AAACCCGTAAACACCCGAAACCCGAAA-CTCCG-A
2021 AACCCGAAACCCG-AAACCCG--AACA-CCGAAACCCGGAAAC-CCGTTA
1 AACCCGAAACCCGAAAACCCGTAAACACCCGAAACCC-GAAACTCCG--A
* * * *
2066 AACCCGAAGAAGCCCGAGAA-CCG-AAAC-CTC-ACACCTGTAAAACTCCGCA
1 AACCCG-A-AA-CCCGAAAACCCGTAAACACCCGAAACCCG--AAACTCCG-A
* *
2115 AACGCCAGACACCCG-AAA-CCG-ACTAC-CCCGAAACCCG-AA--CCG-
1 AAC-CC-GAAACCCGAAAACCCGTA-AACACCCGAAACCCGAAACTCCGA
* *
2157 AACCCGAAAACCCGAAAACCCGAACCGAAAACTCCGAAACCCGAAAGC-CCG-
1 AACCCG-AAACCCGAAAACCCGTA---AACAC-CCGAAACCCGAAA-CTCCGA
* * * *
2208 AACCCGAAACCCCGAAACCCCG-AAACTCTCGGAAACCCGCAA--CCGA
1 AACCCGAAA-CCCGAAAACCCGTAAACAC-CCGAAACCCGAAACTCCGA
2254 AACCCGAAA-CCGAAA
1 AACCCGAAACCCGAAA
2269 CCCCAAACCC
Statistics
Matches: 1480, Mismatches: 169, Indels: 483
0.69 0.08 0.23
Matches are distributed among these distances:
39 12 0.01
40 27 0.02
41 118 0.08
42 131 0.09
43 111 0.08
44 230 0.16
45 187 0.13
46 135 0.09
47 93 0.06
48 86 0.06
49 95 0.06
50 90 0.06
51 53 0.04
52 33 0.02
53 19 0.01
54 21 0.01
55 13 0.01
56 16 0.01
57 10 0.01
ACGTcount: A:0.39, C:0.41, G:0.15, T:0.05
Consensus pattern (47 bp):
AACCCGAAACCCGAAAACCCGTAAACACCCGAAACCCGAAACTCCGA
Found at i:3560 original size:7 final size:7
Alignment explanation
Indices: 2253--3591 Score: 1876
Period size: 7 Copynumber: 193.3 Consensus size: 7
2243 CCCGCAACCG
*
2253 AAACCCG
1 AAACCCC
*
2260 AAA-CCG
1 AAACCCC
2266 AAACCCC
1 AAACCCC
2273 AAACCCC
1 AAACCCC
2280 AAAACCCC
1 -AAACCCC
*
2288 AAAGCCCAT
1 AAA-CCC-C
2297 AAACCCC
1 AAACCCC
*
2304 AGAACTCC
1 A-AACCCC
2312 AAACCCC
1 AAACCCC
* *
2319 GAAAGCACG
1 -AAA-CCCC
2328 ATAACCCC
1 A-AACCCC
2336 AAAACTCCC
1 -AAAC-CCC
2345 AAACCCC
1 AAACCCC
2352 AAAGCCCC
1 AAA-CCCC
2360 ATAACCCC
1 A-AACCCC
2368 GAAATCTCCCGC
1 -AAA---CCC-C
2380 AATTATCTCCC
1 AA--A-C-CCC
2391 AAGAACCCC
1 -A-AACCCC
2400 AAACCCC
1 AAACCCC
2407 AAACCCC
1 AAACCCC
2414 AAA-CCC
1 AAACCCC
2420 AAACCCC
1 AAACCCC
2427 AAA-CCC
1 AAACCCC
2433 AAA-CCC
1 AAACCCC
2439 AAACCCC
1 AAACCCC
2446 AAA-CCC
1 AAACCCC
2452 AAA-CCC
1 AAACCCC
2458 AAACCCC
1 AAACCCC
2465 AAACCCC
1 AAACCCC
2472 AAACCCC
1 AAACCCC
2479 AAACCCC
1 AAACCCC
2486 AATAACCCC
1 -A-AACCCC
2495 AAACCCC
1 AAACCCC
2502 AAAACCCC
1 -AAACCCC
2510 AAACCCC
1 AAACCCC
2517 AAACCCC
1 AAACCCC
2524 AAACCCC
1 AAACCCC
*
2531 AAAACCC
1 AAACCCC
2538 AAACCCC
1 AAACCCC
2545 AAACCCC
1 AAACCCC
2552 AAACCCC
1 AAACCCC
2559 AAACCCC
1 AAACCCC
2566 AAACCCC
1 AAACCCC
2573 AAACCCC
1 AAACCCC
2580 AAA-CCC
1 AAACCCC
2586 AAACCCC
1 AAACCCC
2593 AAACCCC
1 AAACCCC
2600 AAACCCC
1 AAACCCC
2607 AAACCCC
1 AAACCCC
2614 AAACCCC
1 AAACCCC
2621 AAACCCC
1 AAACCCC
2628 AAACCCC
1 AAACCCC
2635 AAACCCC
1 AAACCCC
2642 AAACCCC
1 AAACCCC
*
2649 CAACCCC
1 AAACCCC
2656 AAACCCC
1 AAACCCC
2663 AAACCCC
1 AAACCCC
2670 AAACCCC
1 AAACCCC
2677 -AACCCC
1 AAACCCC
2683 AAA-CCC
1 AAACCCC
2689 AAACCCC
1 AAACCCC
2696 AAACCCC
1 AAACCCC
2703 -AACCCC
1 AAACCCC
2709 AAACCCCC
1 AAA-CCCC
2717 AAACCCC
1 AAACCCC
2724 AAACCCC
1 AAACCCC
2731 AAACCCC
1 AAACCCC
*
2738 AAACCCA
1 AAACCCC
2745 AAACCCC
1 AAACCCC
2752 AAACCCC
1 AAACCCC
2759 AAACCCC
1 AAACCCC
2766 AAACCCC
1 AAACCCC
2773 AAACCCC
1 AAACCCC
2780 AAACCCC
1 AAACCCC
2787 AAACCCC
1 AAACCCC
2794 AAA-CCC
1 AAACCCC
2800 AAACCCCC
1 AAA-CCCC
2808 AAACCCCC
1 AAA-CCCC
2816 AAACCCC
1 AAACCCC
2823 AAA-CCC
1 AAACCCC
2829 -AACCCC
1 AAACCCC
2835 AAACCCC
1 AAACCCC
2842 AAACCCC
1 AAACCCC
2849 AAAACCCC
1 -AAACCCC
2857 AAACCCC
1 AAACCCC
2864 AAAACCCC
1 -AAACCCC
2872 AAACCCC
1 AAACCCC
*
2879 AAACACC
1 AAACCCC
2886 AAACCCC
1 AAACCCC
2893 -AACCCC
1 AAACCCC
2899 AAACCCC
1 AAACCCC
2906 AAACCCC
1 AAACCCC
2913 -AACCCC
1 AAACCCC
2919 AAACCCC
1 AAACCCC
2926 AAAACCCC
1 -AAACCCC
2934 AAA-CCC
1 AAACCCC
2940 AAACCCC
1 AAACCCC
2947 AAACCCC
1 AAACCCC
2954 AAACCCC
1 AAACCCC
2961 AAACCCC
1 AAACCCC
2968 AAACCCC
1 AAACCCC
2975 AAACCCC
1 AAACCCC
2982 AAACCCC
1 AAACCCC
2989 AAACCCC
1 AAACCCC
2996 AAACCCC
1 AAACCCC
3003 AAACCCC
1 AAACCCC
3010 AAACCCC
1 AAACCCC
3017 AAACCCC
1 AAACCCC
3024 AAACCCC
1 AAACCCC
3031 AAACCCC
1 AAACCCC
3038 AAA-CCC
1 AAACCCC
* *
3044 AAAACAC
1 AAACCCC
3051 AAACCCC
1 AAACCCC
3058 AAA-CCC
1 AAACCCC
3064 AAACCCC
1 AAACCCC
3071 AAACCCC
1 AAACCCC
3078 AAA-CCC
1 AAACCCC
3084 AAACCCC
1 AAACCCC
3091 AAACCCC
1 AAACCCC
3098 AAACCCC
1 AAACCCC
3105 AAACCCC
1 AAACCCC
3112 AAACCCC
1 AAACCCC
3119 AAA-CCC
1 AAACCCC
3125 AAACCCC
1 AAACCCC
3132 AAACCCC
1 AAACCCC
3139 AAA-CCC
1 AAACCCC
3145 AAA-CCC
1 AAACCCC
3151 AAACCCC
1 AAACCCC
3158 AAACCCC
1 AAACCCC
3165 -AACCCC
1 AAACCCC
3171 AAACCCC
1 AAACCCC
3178 AAAACCCC
1 -AAACCCC
3186 AAA-CCC
1 AAACCCC
3192 --ACCCC
1 AAACCCC
3197 AAACCCC
1 AAACCCC
3204 -AACCCC
1 AAACCCC
3210 -AACCCC
1 AAACCCC
3216 AAA-CCC
1 AAACCCC
3222 AAACCCC
1 AAACCCC
3229 AAACCCC
1 AAACCCC
3236 AAA--CC
1 AAACCCC
3241 -AACCCC
1 AAACCCC
*
3247 AAACCCA
1 AAACCCC
3254 AAACCCC
1 AAACCCC
3261 AAACCCC
1 AAACCCC
3268 AAACCCC
1 AAACCCC
3275 AAA-CCC
1 AAACCCC
3281 -AA-CCC
1 AAACCCC
3286 AAA-CCC
1 AAACCCC
3292 AAA-CCC
1 AAACCCC
3298 AAACCCC
1 AAACCCC
3305 AAA-CCC
1 AAACCCC
3311 AAACCCC
1 AAACCCC
3318 AAACCCC
1 AAACCCC
3325 AAACCCC
1 AAACCCC
3332 AAA-CCC
1 AAACCCC
3338 AAACCCC
1 AAACCCC
3345 -AACCCC
1 AAACCCC
3351 AAACCCC
1 AAACCCC
3358 AAACCCC
1 AAACCCC
3365 AAACCCC
1 AAACCCC
3372 AAACCCC
1 AAACCCC
3379 AAA-CCC
1 AAACCCC
3385 AAACCCC
1 AAACCCC
3392 AAACCCC
1 AAACCCC
3399 AAA-CCC
1 AAACCCC
3405 AAACCCC
1 AAACCCC
3412 AAA-CCC
1 AAACCCC
3418 AAACCCC
1 AAACCCC
3425 AAACCCC
1 AAACCCC
3432 AAACCCC
1 AAACCCC
3439 AAA-CCC
1 AAACCCC
3445 AAACCCC
1 AAACCCC
3452 AAACCCC
1 AAACCCC
3459 AAACCCC
1 AAACCCC
3466 AAACCCC
1 AAACCCC
3473 -AA-CCC
1 AAACCCC
3478 AAACCCC
1 AAACCCC
3485 AAACCCC
1 AAACCCC
3492 AAACCCC
1 AAACCCC
*
3499 -AACCCTT
1 AAACCC-C
*
3506 AAAACCC
1 AAACCCC
3513 AAACCCC
1 AAACCCC
3520 AAACCCC
1 AAACCCC
3527 -AACCCC
1 AAACCCC
3533 AAACCCC
1 AAACCCC
*
3540 AAACCCA
1 AAACCCC
3547 AAACCCC
1 AAACCCC
3554 AAACCCC
1 AAACCCC
3561 AAAAACCCC
1 --AAACCCC
3570 -AACCCC
1 AAACCCC
3576 AAACCCC
1 AAACCCC
3583 AAACCCC
1 AAACCCC
3590 AA
1 AA
3592 CACGACCCCG
Statistics
Matches: 1229, Mismatches: 28, Indels: 150
0.87 0.02 0.11
Matches are distributed among these distances:
4 3 0.00
5 15 0.01
6 235 0.19
7 824 0.67
8 106 0.09
9 30 0.02
10 1 0.00
11 9 0.01
12 4 0.00
13 2 0.00
ACGTcount: A:0.44, C:0.55, G:0.01, T:0.01
Consensus pattern (7 bp):
AAACCCC
Found at i:3615 original size:7 final size:6
Alignment explanation
Indices: 3594--3693 Score: 128
Period size: 7 Copynumber: 15.5 Consensus size: 6
3584 AACCCCAACA
3594 CGACCC CGACCC CGACCCC CGACCCC CGACCCC CGACCCC CGACCCC CGACCC
1 CGACCC CGACCC CGA-CCC CGA-CCC CGA-CCC CGA-CCC CGA-CCC CGACCC
*
3647 TGACCC CGACCC CGACCC CGACCC CGACCC CGAACCC CGAACCC CGA
1 CGACCC CGACCC CGACCC CGACCC CGACCC CG-ACCC CG-ACCC CGA
3694 ACCTCGAACC
Statistics
Matches: 90, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
6 43 0.48
7 47 0.52
ACGTcount: A:0.18, C:0.65, G:0.16, T:0.01
Consensus pattern (6 bp):
CGACCC
Found at i:3703 original size:21 final size:21
Alignment explanation
Indices: 3673--3768 Score: 59
Period size: 21 Copynumber: 4.5 Consensus size: 21
3663 CCCGACCCCG
* * *
3673 ACCCCGAACCCCGAACCCCGA
1 ACCCCAAACCCCAAACCCCAA
* * *
3694 ACCTCGAACCCCAAAACCCAA
1 ACCCCAAACCCCAAACCCCAA
* *
3715 ACCCCTAAACCCCCAAGCCCAA
1 ACCCC-AAACCCCAAACCCCAA
*
3737 ACCCCCAAGCCCC-AACCCTCAA
1 A-CCCCAAACCCCAAACCC-CAA
* *
3759 GCTCCAAACC
1 ACCCCAAACC
3769 TTAAAACCCT
Statistics
Matches: 59, Mismatches: 13, Indels: 6
0.76 0.17 0.08
Matches are distributed among these distances:
21 32 0.54
22 23 0.39
23 4 0.07
ACGTcount: A:0.34, C:0.54, G:0.07, T:0.04
Consensus pattern (21 bp):
ACCCCAAACCCCAAACCCCAA
Found at i:3724 original size:8 final size:7
Alignment explanation
Indices: 3673--3751 Score: 59
Period size: 7 Copynumber: 11.0 Consensus size: 7
3663 CCCGACCCCG
*
3673 ACCCCGA
1 ACCCCAA
*
3680 ACCCCGA
1 ACCCCAA
*
3687 ACCCCGA
1 ACCCCAA
* *
3694 ACCTCGA
1 ACCCCAA
3701 ACCCCAA
1 ACCCCAA
*
3708 AACCCAA
1 ACCCCAA
3715 ACCCCTAA
1 ACCCC-AA
*
3723 ACCCCCA
1 ACCCCAA
*
3730 AGCCCAA
1 ACCCCAA
3737 ACCCCCAA
1 A-CCCCAA
*
3745 GCCCCAA
1 ACCCCAA
3752 CCCTCAAGCT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
7 48 0.80
8 12 0.20
ACGTcount: A:0.35, C:0.54, G:0.08, T:0.03
Consensus pattern (7 bp):
ACCCCAA
Found at i:3725 original size:22 final size:22
Alignment explanation
Indices: 3700--3751 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
3690 CCGAACCTCG
*
3700 AACCCCAAAACCCAAACCCCTA
1 AACCCCAAAACCCAAACCCCCA
* *
3722 AACCCCCAAGCCCAAACCCCCA
1 AACCCCAAAACCCAAACCCCCA
*
3744 AGCCCCAA
1 AACCCCAA
3752 CCCTCAAGCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.54, G:0.04, T:0.02
Consensus pattern (22 bp):
AACCCCAAAACCCAAACCCCCA
Found at i:3753 original size:14 final size:14
Alignment explanation
Indices: 3722--3765 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
3712 CAAACCCCTA
*
3722 AACCCCCAAGCCCA
1 AACCCCCAAGCCCC
3736 AACCCCCAAGCCCC
1 AACCCCCAAGCCCC
* *
3750 AACCCTCAAGCTCC
1 AACCCCCAAGCCCC
3764 AA
1 AA
3766 ACCTTAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.34, C:0.55, G:0.07, T:0.05
Consensus pattern (14 bp):
AACCCCCAAGCCCC
Done.