Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007551.1 Hibiscus syriacus cultivar Beakdansim tig00021168_pilon, whole genome shotgun sequence
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: 68894
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Found at i:17 original size:7 final size:7
Alignment explanation
Indices: 1--2529 Score: 3954
Period size: 7 Copynumber: 376.1 Consensus size: 7
1 CTAAA-C
1 CTAAACC
7 CTAAACC
1 CTAAACC
14 CTAAACC
1 CTAAACC
21 CTAAACC
1 CTAAACC
28 CT-AA-C
1 CTAAACC
33 CTAAACC
1 CTAAACC
40 CTAAA-C
1 CTAAACC
46 CTAAACC
1 CTAAACC
53 CTAAACC
1 CTAAACC
60 CTAAACC
1 CTAAACC
67 CTAAACC
1 CTAAACC
74 CTAAACC
1 CTAAACC
81 CTAAACC
1 CTAAACC
88 CTAAACC
1 CTAAACC
95 CT--ACC
1 CTAAACC
100 CTAAACC
1 CTAAACC
107 CT-AACC
1 CTAAACC
113 CTAAACC
1 CTAAACC
120 CTAAA-C
1 CTAAACC
126 CTAAACC
1 CTAAACC
133 CTAAACC
1 CTAAACC
140 CTAAACC
1 CTAAACC
147 CTAAACC
1 CTAAACC
154 CTAAA-C
1 CTAAACC
*
160 CT-CACC
1 CTAAACC
166 CTAAACC
1 CTAAACC
173 CTAAACC
1 CTAAACC
180 CTAAACC
1 CTAAACC
187 CTAAACC
1 CTAAACC
194 CTAAACC
1 CTAAACC
201 CTAAAACC
1 CT-AAACC
209 CTAAACC
1 CTAAACC
216 CT-AACC
1 CTAAACC
222 CTAAACC
1 CTAAACC
229 CTAAACC
1 CTAAACC
236 CTAAACC
1 CTAAACC
243 CTAAACC
1 CTAAACC
250 CTAAACC
1 CTAAACC
257 CTAAACC
1 CTAAACC
264 CTAAA-C
1 CTAAACC
270 CTAAACC
1 CTAAACC
277 CTAAACC
1 CTAAACC
284 CTAAACC
1 CTAAACC
291 CT-AACC
1 CTAAACC
297 CTAAACC
1 CTAAACC
304 CTAAA-C
1 CTAAACC
310 C-AGAACC
1 CTA-AACC
317 CT-AACC
1 CTAAACC
323 CTAAAACC
1 CT-AAACC
331 CTAAACC
1 CTAAACC
338 CTAAACC
1 CTAAACC
345 CTAAACC
1 CTAAACC
352 CT-AACC
1 CTAAACC
358 CT--ACC
1 CTAAACC
363 CT-AA-C
1 CTAAACC
368 CTAAACC
1 CTAAACC
375 C-AAA-C
1 CTAAACC
380 CTAAACC
1 CTAAACC
*
387 C-CAA-C
1 CTAAACC
392 CTAAACC
1 CTAAACC
399 CTAAACC
1 CTAAACC
406 CTAAACC
1 CTAAACC
413 CTAAACC
1 CTAAACC
420 CTAAACC
1 CTAAACC
427 CTAAACC
1 CTAAACC
434 CTAAACC
1 CTAAACC
441 CTAAA-C
1 CTAAACC
447 CTAAACC
1 CTAAACC
454 CTAAACC
1 CTAAACC
461 CTAAACC
1 CTAAACC
468 CTAAAACC
1 CT-AAACC
476 CTAAACC
1 CTAAACC
483 CTAAACC
1 CTAAACC
490 CT-AA-C
1 CTAAACC
495 CT-AACC
1 CTAAACC
501 CT-AACC
1 CTAAACC
507 CTAAACC
1 CTAAACC
514 CT-AA-C
1 CTAAACC
519 CTAAACC
1 CTAAACC
526 CTAAACC
1 CTAAACC
533 CTAAACC
1 CTAAACC
540 CTAAACC
1 CTAAACC
547 CTAAACC
1 CTAAACC
554 CTAAACC
1 CTAAACC
561 CT---CC
1 CTAAACC
565 CTAAACC
1 CTAAACC
572 CTAAACC
1 CTAAACC
579 CTAAACC
1 CTAAACC
586 CT-AACC
1 CTAAACC
592 CTAAACC
1 CTAAACC
599 CT-AACC
1 CTAAACC
605 CT-AACC
1 CTAAACC
611 CTAAACC
1 CTAAACC
618 CT-AACC
1 CTAAACC
624 CTAAA-C
1 CTAAACC
630 CTAAACC
1 CTAAACC
637 CT-AA-C
1 CTAAACC
642 CTAAACC
1 CTAAACC
649 CT-AA-C
1 CTAAACC
654 CT-AACC
1 CTAAACC
660 CTAAACC
1 CTAAACC
667 CTAAACC
1 CTAAACC
674 CTAAACC
1 CTAAACC
681 CTAAACC
1 CTAAACC
688 CTAAACC
1 CTAAACC
695 CTAAAACC
1 CT-AAACC
703 CTAAACC
1 CTAAACC
710 CT-AACC
1 CTAAACC
716 CTAAACC
1 CTAAACC
723 CTAAACC
1 CTAAACC
730 CT-AACC
1 CTAAACC
736 CTAAACC
1 CTAAACC
743 CTAACACC
1 CTAA-ACC
751 CTAAACC
1 CTAAACC
758 CT-AACC
1 CTAAACC
764 CTAAACC
1 CTAAACC
771 CTAAACC
1 CTAAACC
778 CT-AACC
1 CTAAACC
784 CTAAACC
1 CTAAACC
791 CTAAACC
1 CTAAACC
798 CTAAACC
1 CTAAACC
805 CTAAACC
1 CTAAACC
812 CTAAACC
1 CTAAACC
819 CTAAACC
1 CTAAACC
826 CTAAA-C
1 CTAAACC
832 CTAAACC
1 CTAAACC
839 CTAAACC
1 CTAAACC
846 CTAAACC
1 CTAAACC
853 CTAAA-C
1 CTAAACC
859 CTAAACC
1 CTAAACC
866 CTAAACC
1 CTAAACC
873 CTAAACC
1 CTAAACC
880 CTAAACC
1 CTAAACC
887 CTAAACC
1 CTAAACC
894 CT-AACC
1 CTAAACC
900 CTTAAACC
1 C-TAAACC
908 CTAAACC
1 CTAAACC
915 CTAAACC
1 CTAAACC
922 CTAAACC
1 CTAAACC
929 CTAAACC
1 CTAAACC
936 CTAAACC
1 CTAAACC
943 CTAAA-C
1 CTAAACC
949 CTAAACC
1 CTAAACC
*
956 CTCAACC
1 CTAAACC
963 CTAAACC
1 CTAAACC
970 CT-AACC
1 CTAAACC
976 CTAAACC
1 CTAAACC
983 CTAAACC
1 CTAAACC
990 CTAAA-C
1 CTAAACC
996 CTAAACC
1 CTAAACC
1003 CTAAACC
1 CTAAACC
1010 CTAAACC
1 CTAAACC
1017 CTAAACC
1 CTAAACC
1024 CTAAACC
1 CTAAACC
1031 CT-AACC
1 CTAAACC
1037 CTAAACC
1 CTAAACC
1044 CT--ACC
1 CTAAACC
1049 CTAAACC
1 CTAAACC
1056 CTAAACC
1 CTAAACC
1063 CTAAACC
1 CTAAACC
1070 CTAAACC
1 CTAAACC
1077 CTAAACC
1 CTAAACC
1084 CTAAACC
1 CTAAACC
1091 CTAAACC
1 CTAAACC
*
1098 CTCAACC
1 CTAAACC
1105 CTAAACC
1 CTAAACC
1112 CTAAAAACC
1 CT--AAACC
1121 CTAAACC
1 CTAAACC
1128 CTAAA-C
1 CTAAACC
1134 CTAAACC
1 CTAAACC
1141 CTAAACC
1 CTAAACC
*
1148 CTCAACC
1 CTAAACC
1155 CTAAACC
1 CTAAACC
1162 CTAAACC
1 CTAAACC
1169 CT-AACC
1 CTAAACC
1175 CT-AACC
1 CTAAACC
1181 CTAAACC
1 CTAAACC
1188 CTAAACC
1 CTAAACC
*
1195 C-CAACC
1 CTAAACC
1201 CTAAACC
1 CTAAACC
1208 CTAAACC
1 CTAAACC
*
1215 CTACACC
1 CTAAACC
1222 CTAAA-C
1 CTAAACC
1228 CTAAACC
1 CTAAACC
1235 CT--A-C
1 CTAAACC
1239 CTAAACC
1 CTAAACC
1246 CTAAACC
1 CTAAACC
1253 CTAAACC
1 CTAAACC
1260 CT-AACC
1 CTAAACC
1266 CTAAACC
1 CTAAACC
1273 CTAAACC
1 CTAAACC
1280 CTAAACC
1 CTAAACC
1287 CTAAACC
1 CTAAACC
1294 CTAAACC
1 CTAAACC
1301 CTAAA-C
1 CTAAACC
1307 CTAAACC
1 CTAAACC
1314 CTAAACC
1 CTAAACC
1321 CTAAACC
1 CTAAACC
1328 CTAAACC
1 CTAAACC
1335 CTAAACC
1 CTAAACC
1342 CTAAAACCC
1 CT-AAA-CC
1351 CT-AACC
1 CTAAACC
1357 CTAAACC
1 CTAAACC
1364 CTAAACC
1 CTAAACC
1371 CTAAA-C
1 CTAAACC
1377 CTAAACC
1 CTAAACC
1384 CTAAACC
1 CTAAACC
1391 CTAAACC
1 CTAAACC
1398 CTAAACC
1 CTAAACC
1405 CT-AACC
1 CTAAACC
1411 CTAAACC
1 CTAAACC
1418 C-AAACC
1 CTAAACC
1424 CT-AACC
1 CTAAACC
1430 CTAAACC
1 CTAAACC
1437 CTAAA-C
1 CTAAACC
1443 CTAAACC
1 CTAAACC
1450 CTAAACC
1 CTAAACC
1457 CTAAACC
1 CTAAACC
1464 CTAAACC
1 CTAAACC
1471 CTAAACC
1 CTAAACC
1478 CTAAACC
1 CTAAACC
1485 CTAAACC
1 CTAAACC
1492 CTAAACC
1 CTAAACC
1499 CT-AACC
1 CTAAACC
1505 CTAAA-C
1 CTAAACC
1511 CTAAA-C
1 CTAAACC
1517 C-AAACC
1 CTAAACC
1523 CTAAACC
1 CTAAACC
1530 CTAAA-C
1 CTAAACC
1536 CT-AACC
1 CTAAACC
1542 CTAAACC
1 CTAAACC
1549 CTAAACC
1 CTAAACC
1556 CTAAACC
1 CTAAACC
1563 CT-AACC
1 CTAAACC
1569 CTAAA-C
1 CTAAACC
1575 CTAAA-C
1 CTAAACC
1581 CTAAACC
1 CTAAACC
1588 CT-AACC
1 CTAAACC
1594 CTAAACC
1 CTAAACC
1601 CTAAA-C
1 CTAAACC
1607 CT-AACC
1 CTAAACC
1613 CTAAACC
1 CTAAACC
1620 CTAAACC
1 CTAAACC
1627 CTAAACC
1 CTAAACC
1634 CTAAACC
1 CTAAACC
1641 CTAAACC
1 CTAAACC
1648 CTAAACC
1 CTAAACC
1655 CTAAACC
1 CTAAACC
1662 CTAAACC
1 CTAAACC
1669 CTAAACC
1 CTAAACC
1676 CTAAA-C
1 CTAAACC
1682 CT-AACC
1 CTAAACC
1688 CTAAACC
1 CTAAACC
1695 CTAAACC
1 CTAAACC
1702 CTAAACC
1 CTAAACC
1709 CTAAA-C
1 CTAAACC
1715 CT-AA-C
1 CTAAACC
1720 CTAAACC
1 CTAAACC
1727 CTAAACC
1 CTAAACC
1734 CTAAACC
1 CTAAACC
1741 CTAAACC
1 CTAAACC
1748 CTAAAACC
1 CT-AAACC
1756 CTAAACCC
1 CTAAA-CC
1764 TCTAAA-C
1 -CTAAACC
1771 CTAAAACC
1 CT-AAACC
1779 CTAAA-C
1 CTAAACC
1785 C-AAACC
1 CTAAACC
1791 CTAAACC
1 CTAAACC
1798 CT-AACC
1 CTAAACC
1804 CTAAACC
1 CTAAACC
1811 CT-AACC
1 CTAAACC
1817 CTAAACC
1 CTAAACC
1824 CTAAACC
1 CTAAACC
1831 CTAAA-C
1 CTAAACC
1837 CTAAA-C
1 CTAAACC
1843 CTAAACC
1 CTAAACC
1850 CT-AACC
1 CTAAACC
1856 CTAAACC
1 CTAAACC
1863 CTAAACC
1 CTAAACC
1870 CTAAA-C
1 CTAAACC
1876 CT--ACC
1 CTAAACC
1881 CTAAACC
1 CTAAACC
1888 CTAAACC
1 CTAAACC
1895 CTAAACC
1 CTAAACC
1902 CT-AACC
1 CTAAACC
1908 CTAAA-C
1 CTAAACC
1914 CTAAACC
1 CTAAACC
1921 CTAAACC
1 CTAAACC
1928 CTAAACC
1 CTAAACC
1935 CTAAACC
1 CTAAACC
1942 CTAAACC
1 CTAAACC
1949 CTAAACC
1 CTAAACC
1956 CTAAACC
1 CTAAACC
1963 CTAAACC
1 CTAAACC
1970 CTAAACC
1 CTAAACC
1977 CT-AACC
1 CTAAACC
1983 CTAAACC
1 CTAAACC
1990 CTAAACC
1 CTAAACC
1997 CTAAACC
1 CTAAACC
2004 CTAAACC
1 CTAAACC
2011 CTAAACC
1 CTAAACC
2018 CTAAACC
1 CTAAACC
2025 CTAAACC
1 CTAAACC
2032 CTAAAACC
1 CT-AAACC
2040 CTAAACC
1 CTAAACC
2047 CTAAACC
1 CTAAACC
2054 CTAAA-C
1 CTAAACC
2060 CTAAACC
1 CTAAACC
2067 CTAAACC
1 CTAAACC
2074 CTAAACC
1 CTAAACC
2081 CTAAACC
1 CTAAACC
2088 CTAAA-C
1 CTAAACC
2094 CT-AACC
1 CTAAACC
2100 CTAAA-C
1 CTAAACC
2106 CT-AACC
1 CTAAACC
2112 CTAAACC
1 CTAAACC
2119 CTAAACC
1 CTAAACC
2126 CTAAA-C
1 CTAAACC
2132 CTAAACC
1 CTAAACC
2139 CTAAACC
1 CTAAACC
2146 CTAAACC
1 CTAAACC
2153 CTAAACC
1 CTAAACC
2160 CTAAACC
1 CTAAACC
2167 CTAAACC
1 CTAAACC
2174 CTAAACC
1 CTAAACC
2181 CTAAACC
1 CTAAACC
2188 CTAAACC
1 CTAAACC
2195 CTAAACC
1 CTAAACC
2202 CTAAACC
1 CTAAACC
2209 CT-AACC
1 CTAAACC
2215 CTAAACC
1 CTAAACC
2222 CTAAACC
1 CTAAACC
2229 CT-AACC
1 CTAAACC
2235 CTAAACC
1 CTAAACC
2242 CTAAA-C
1 CTAAACC
2248 CTAAACC
1 CTAAACC
2255 CTAAACC
1 CTAAACC
2262 CTAAACC
1 CTAAACC
2269 CTAAACC
1 CTAAACC
2276 CTAAACC
1 CTAAACC
2283 CTAAA-C
1 CTAAACC
2289 C-AAACC
1 CTAAACC
2295 CTAAA-C
1 CTAAACC
2301 CTAAA-C
1 CTAAACC
2307 CTAAACC
1 CTAAACC
2314 CTAAACC
1 CTAAACC
2321 CT-AACC
1 CTAAACC
*
2327 CTAACCAAC
1 CTAA--ACC
2336 CTAAACC
1 CTAAACC
2343 CTAAA-C
1 CTAAACC
2349 CTAAACC
1 CTAAACC
2356 CT-AACC
1 CTAAACC
2362 CT-AACC
1 CTAAACC
2368 CTAAACC
1 CTAAACC
2375 CTAAACC
1 CTAAACC
2382 CTAAACC
1 CTAAACC
2389 CTAAACC
1 CTAAACC
2396 CTAAAACC
1 CT-AAACC
2404 CTAAACC
1 CTAAACC
2411 CTAAACC
1 CTAAACC
2418 CTAAACC
1 CTAAACC
2425 CTAAACC
1 CTAAACC
2432 CTAAACC
1 CTAAACC
2439 CTAAACC
1 CTAAACC
2446 CTAAACC
1 CTAAACC
2453 CTAAACC
1 CTAAACC
2460 CTAAACC
1 CTAAACC
2467 CTAAACC
1 CTAAACC
2474 CTAAACC
1 CTAAACC
2481 CTAAA-C
1 CTAAACC
2487 CTAAACC
1 CTAAACC
2494 CTAAACC
1 CTAAACC
2501 CTAAACC
1 CTAAACC
2508 CTAAACC
1 CTAAACC
2515 CTAAACC
1 CTAAACC
2522 CTAAACC
1 CTAAACC
2529 C
1 C
2530 CGAGAGCCCG
Statistics
Matches: 2378, Mismatches: 16, Indels: 257
0.90 0.01 0.10
Matches are distributed among these distances:
4 8 0.00
5 71 0.03
6 489 0.21
7 1720 0.72
8 68 0.03
9 22 0.01
ACGTcount: A:0.42, C:0.43, G:0.00, T:0.15
Consensus pattern (7 bp):
CTAAACC
Found at i:2546 original size:7 final size:7
Alignment explanation
Indices: 2536--2826 Score: 407
Period size: 7 Copynumber: 45.1 Consensus size: 7
2526 ACCCCGAGAG
2536 CCCGAGC
1 CCCGAGC
2543 CCCGAGC
1 CCCGAGC
2550 CCCGAG-
1 CCCGAGC
2556 CCCGAG-
1 CCCGAGC
2562 CCCGAG-
1 CCCGAGC
2568 CCCGAGC
1 CCCGAGC
2575 CCCGAG-
1 CCCGAGC
2581 CCCGAG-
1 CCCGAGC
2587 CCCGAG-
1 CCCGAGC
2593 CCCGAGC
1 CCCGAGC
2600 CCCGAG-
1 CCCGAGC
2606 CCCGAGC
1 CCCGAGC
2613 CCCGAGC
1 CCCGAGC
2620 CCCGAG-
1 CCCGAGC
2626 CCCGAGC
1 CCCGAGC
2633 CCCGA--
1 CCCGAGC
2638 CCCGAG-
1 CCCGAGC
2644 CCCGAG-
1 CCCGAGC
2650 CCCGAG-
1 CCCGAGC
2656 -CCGAG-
1 CCCGAGC
2661 CCCGAGC
1 CCCGAGC
2668 CCC--GC
1 CCCGAGC
2673 CCCGAGC
1 CCCGAGC
2680 CCCGAGC
1 CCCGAGC
2687 CCCGAGC
1 CCCGAGC
2694 CCCGAGC
1 CCCGAGC
2701 CCCGAGC
1 CCCGAGC
2708 CCCGAGC
1 CCCGAGC
2715 CCCGAGC
1 CCCGAGC
2722 CCCGAGC
1 CCCGAGC
2729 CCCGAGC
1 CCCGAGC
2736 CCCGAGC
1 CCCGAGC
2743 CCCGAG-
1 CCCGAGC
2749 CCCGAG-
1 CCCGAGC
2755 CCCGAGC
1 CCCGAGC
2762 CCCGAG-
1 CCCGAGC
2768 CCCGAGC
1 CCCGAGC
2775 CCCGAG-
1 CCCGAGC
2781 CCCGAG-
1 CCCGAGC
2787 CCCGAGC
1 CCCGAGC
2794 CCCGAGC
1 CCCGAGC
2801 CCCGAG-
1 CCCGAGC
2807 CCCGAG-
1 CCCGAGC
2813 CCCGAG-
1 CCCGAGC
2819 CCCGAGC
1 CCCGAGC
2826 C
1 C
2827 AGACCCCAGA
Statistics
Matches: 271, Mismatches: 0, Indels: 26
0.91 0.00 0.09
Matches are distributed among these distances:
5 15 0.06
6 113 0.42
7 143 0.53
ACGTcount: A:0.15, C:0.55, G:0.30, T:0.00
Consensus pattern (7 bp):
CCCGAGC
Found at i:2551 original size:13 final size:13
Alignment explanation
Indices: 2533--2826 Score: 398
Period size: 13 Copynumber: 22.8 Consensus size: 13
2523 TAAACCCCGA
2533 GAGCCCGAGCCCC
1 GAGCCCGAGCCCC
2546 GAGCCCCGAG-CCC
1 GAG-CCCGAGCCCC
2559 GAGCCCGAG-CCC
1 GAGCCCGAGCCCC
2571 GAGCCCCGAG-CCC
1 GAG-CCCGAGCCCC
2584 GAGCCCGAG-CCC
1 GAGCCCGAGCCCC
2596 GAGCCCCGAG-CCC
1 GAG-CCCGAGCCCC
2609 GAGCCCCGAGCCCC
1 GAG-CCCGAGCCCC
2623 GAGCCCGAGCCCC
1 GAGCCCGAGCCCC
2636 GA-CCCGAG-CCC
1 GAGCCCGAGCCCC
2647 GAGCCCGAG--CC
1 GAGCCCGAGCCCC
2658 GAGCCCGAGCCCC
1 GAGCCCGAGCCCC
*
2671 G-CCCCGAGCCCC
1 GAGCCCGAGCCCC
2683 GAGCCCCGAGCCCC
1 GAG-CCCGAGCCCC
2697 GAGCCCCGAGCCCC
1 GAG-CCCGAGCCCC
2711 GAGCCCCGAGCCCC
1 GAG-CCCGAGCCCC
2725 GAGCCCCGAGCCCC
1 GAG-CCCGAGCCCC
2739 GAGCCCCGAG-CCC
1 GAG-CCCGAGCCCC
2752 GAGCCCGAGCCCC
1 GAGCCCGAGCCCC
2765 GAGCCCGAGCCCC
1 GAGCCCGAGCCCC
2778 GAGCCCGAG-CCC
1 GAGCCCGAGCCCC
2790 GAGCCCCGAGCCCC
1 GAG-CCCGAGCCCC
2804 GAGCCCGAG-CCC
1 GAGCCCGAGCCCC
2816 GAGCCCGAGCC
1 GAGCCCGAGCC
2827 AGACCCCAGA
Statistics
Matches: 266, Mismatches: 2, Indels: 26
0.90 0.01 0.09
Matches are distributed among these distances:
11 16 0.06
12 71 0.27
13 99 0.37
14 80 0.30
ACGTcount: A:0.15, C:0.54, G:0.31, T:0.00
Consensus pattern (13 bp):
GAGCCCGAGCCCC
Found at i:2837 original size:7 final size:7
Alignment explanation
Indices: 2825--2900 Score: 70
Period size: 7 Copynumber: 11.4 Consensus size: 7
2815 CGAGCCCGAG
2825 CCAGACC
1 CCAGACC
2832 CCAGACC
1 CCAGACC
2839 CCAGA-C
1 CCAGACC
2845 CCAGACC
1 CCAGACC
*
2852 CCCGACC
1 CCAGACC
2859 CC-GA-C
1 CCAGACC
2864 CCAGACC
1 CCAGACC
*
2871 CCCGA-C
1 CCAGACC
*
2877 CCGGACC
1 CCAGACC
*
2884 CCGGACC
1 CCAGACC
* *
2891 ACGGACC
1 CCAGACC
2898 CCA
1 CCA
2901 AACAACAAGT
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
5 3 0.05
6 15 0.25
7 41 0.69
ACGTcount: A:0.24, C:0.58, G:0.18, T:0.00
Consensus pattern (7 bp):
CCAGACC
Found at i:2849 original size:13 final size:13
Alignment explanation
Indices: 2825--2900 Score: 66
Period size: 13 Copynumber: 5.8 Consensus size: 13
2815 CGAGCCCGAG
2825 CCAGACCCCAGACC
1 CCAGACCCCAGA-C
2839 CCAGA-CCCAGACC
1 CCAGACCCCAGA-C
*
2852 CCCGACCCC-GAC
1 CCAGACCCCAGAC
*
2864 CCAGACCCCCGAC
1 CCAGACCCCAGAC
* *
2877 CCGGACCCCGGAC
1 CCAGACCCCAGAC
*
2890 CACGGACCCCA
1 C-CAGACCCCA
2901 AACAACAAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
12 9 0.17
13 29 0.54
14 16 0.30
ACGTcount: A:0.24, C:0.58, G:0.18, T:0.00
Consensus pattern (13 bp):
CCAGACCCCAGAC
Found at i:5068 original size:7 final size:7
Alignment explanation
Indices: 4944--5067 Score: 140
Period size: 7 Copynumber: 17.7 Consensus size: 7
4934 AAGAAGCTTT
4944 AACCCTA
1 AACCCTA
4951 AACCCTA
1 AACCCTA
4958 AACCCTA
1 AACCCTA
4965 AACCCTA
1 AACCCTA
4972 AACCCTA
1 AACCCTA
4979 AACCCTA
1 AACCCTA
**
4986 AACCCCG
1 AACCCTA
4993 AACCCTA
1 AACCCTA
*
5000 AACCCTG
1 AACCCTA
*
5007 AACCCTG
1 AACCCTA
5014 AACCCTA
1 AACCCTA
**
5021 AACCCCG
1 AACCCTA
*
5028 AACCCTG
1 AACCCTA
**
5035 AACCCCG
1 AACCCTA
*
5042 AACCCCA
1 AACCCTA
*
5049 AACCCCA
1 AACCCTA
*
5056 AACCCCA
1 AACCCTA
5063 AACCC
1 AACCC
5068 CGATCAACAA
Statistics
Matches: 106, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 106 1.00
ACGTcount: A:0.38, C:0.48, G:0.05, T:0.09
Consensus pattern (7 bp):
AACCCTA
Found at i:7156 original size:21 final size:21
Alignment explanation
Indices: 7130--7268 Score: 170
Period size: 21 Copynumber: 6.6 Consensus size: 21
7120 AAGAAGCTTT
* *
7130 AACCCTAAACCCTAAACCCTA
1 AACCCTAAACCCCAAACCCTG
* *
7151 AACCCTAAACCCTAAACCCTA
1 AACCCTAAACCCCAAACCCTG
* *
7172 AACCCTAAACCCTAAACCCCG
1 AACCCTAAACCCCAAACCCTG
*
7193 AACCCTAAACCCCGAACCCTG
1 AACCCTAAACCCCAAACCCTG
*
7214 AACCCTAAACCCCGAACCCTG
1 AACCCTAAACCCCAAACCCTG
** *
7235 AACCCCGAACCCCAAACCCCG
1 AACCCTAAACCCCAAACCCTG
*
7256 AACCCCAAACCCC
1 AACCCTAAACCCC
7269 GATCAACAAG
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 108 1.00
ACGTcount: A:0.37, C:0.49, G:0.05, T:0.09
Consensus pattern (21 bp):
AACCCTAAACCCCAAACCCTG
Found at i:7268 original size:7 final size:7
Alignment explanation
Indices: 7130--7267 Score: 150
Period size: 7 Copynumber: 19.7 Consensus size: 7
7120 AAGAAGCTTT
7130 AACCCTA
1 AACCCTA
7137 AACCCTA
1 AACCCTA
7144 AACCCTA
1 AACCCTA
7151 AACCCTA
1 AACCCTA
7158 AACCCTA
1 AACCCTA
7165 AACCCTA
1 AACCCTA
7172 AACCCTA
1 AACCCTA
7179 AACCCTA
1 AACCCTA
**
7186 AACCCCG
1 AACCCTA
7193 AACCCTA
1 AACCCTA
**
7200 AACCCCG
1 AACCCTA
*
7207 AACCCTG
1 AACCCTA
7214 AACCCTA
1 AACCCTA
**
7221 AACCCCG
1 AACCCTA
*
7228 AACCCTG
1 AACCCTA
**
7235 AACCCCG
1 AACCCTA
*
7242 AACCCCA
1 AACCCTA
**
7249 AACCCCG
1 AACCCTA
*
7256 AACCCCA
1 AACCCTA
7263 AACCC
1 AACCC
7268 CGATCAACAA
Statistics
Matches: 116, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 116 1.00
ACGTcount: A:0.38, C:0.49, G:0.05, T:0.09
Consensus pattern (7 bp):
AACCCTA
Found at i:9492 original size:7 final size:7
Alignment explanation
Indices: 9340--9491 Score: 169
Period size: 7 Copynumber: 21.7 Consensus size: 7
9330 AAGAAGCTTT
9340 AACCCTA
1 AACCCTA
9347 AACCCTA
1 AACCCTA
9354 AACCCTA
1 AACCCTA
9361 AACCCTA
1 AACCCTA
9368 AACCCTA
1 AACCCTA
9375 AACCCTA
1 AACCCTA
9382 AACCCTA
1 AACCCTA
9389 AACCCTA
1 AACCCTA
9396 AACCCTA
1 AACCCTA
9403 AACCCTA
1 AACCCTA
**
9410 AACCCCG
1 AACCCTA
9417 AACCCTA
1 AACCCTA
**
9424 AACCCCG
1 AACCCTA
*
9431 AACCCTG
1 AACCCTA
*
9438 AACCATA
1 AACCCTA
**
9445 AACCCCG
1 AACCCTA
*
9452 AACCCTG
1 AACCCTA
**
9459 AACCCCG
1 AACCCTA
*
9466 AACCCCA
1 AACCCTA
**
9473 AACCCCG
1 AACCCTA
*
9480 AACCCCA
1 AACCCTA
9487 AACCC
1 AACCC
9492 CGATCAACAA
Statistics
Matches: 128, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 128 1.00
ACGTcount: A:0.39, C:0.47, G:0.05, T:0.09
Consensus pattern (7 bp):
AACCCTA
Found at i:11694 original size:7 final size:7
Alignment explanation
Indices: 11563--11693 Score: 129
Period size: 7 Copynumber: 18.7 Consensus size: 7
11553 AAGAAGCTTT
11563 AACCCTA
1 AACCCTA
11570 AACCCTA
1 AACCCTA
11577 AACCCTA
1 AACCCTA
11584 AACCCTA
1 AACCCTA
11591 AACCCTA
1 AACCCTA
11598 AACCCTA
1 AACCCTA
11605 AACCCTA
1 AACCCTA
11612 AACCCTA
1 AACCCTA
**
11619 AACCCCG
1 AACCCTA
*
11626 AACCCTG
1 AACCCTA
*
11633 AA-CCTCG
1 AACCCT-A
*
11640 AACCCTG
1 AACCCTA
*
11647 AACCCTG
1 AACCCTA
**
11654 AACCCCG
1 AACCCTA
*
11661 AACCCTG
1 AACCCTA
*
11668 AACCCCA
1 AACCCTA
**
11675 AACCCCG
1 AACCCTA
*
11682 AACCCCA
1 AACCCTA
11689 AACCC
1 AACCC
11694 CGATCAACAA
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
6 3 0.03
7 107 0.95
8 3 0.03
ACGTcount: A:0.37, C:0.47, G:0.06, T:0.10
Consensus pattern (7 bp):
AACCCTA
Found at i:13907 original size:7 final size:7
Alignment explanation
Indices: 13768--13906 Score: 145
Period size: 7 Copynumber: 19.7 Consensus size: 7
13758 AAGAAGCTTT
13768 AACCCTA
1 AACCCTA
13775 AACCCTA
1 AACCCTA
13782 AACCCTA
1 AACCCTA
13789 AACCCTA
1 AACCCTA
13796 AACCCTA
1 AACCCTA
13803 AACCCTA
1 AACCCTA
**
13810 AACCCCCG
1 AA-CCCTA
13818 AACCCTA
1 AACCCTA
*
13825 AACCCTG
1 AACCCTA
13832 AACCCTA
1 AACCCTA
*
13839 AATCCC-G
1 AA-CCCTA
**
13846 AACCCCG
1 AACCCTA
**
13853 AACCCCG
1 AACCCTA
*
13860 AACCCTG
1 AACCCTA
*
13867 AACCCTG
1 AACCCTA
13874 AACCCTA
1 AACCCTA
*
13881 AACCCCA
1 AACCCTA
13888 AACCCTA
1 AACCCTA
*
13895 AACCCCA
1 AACCCTA
13902 AACCC
1 AACCC
13907 CGAACAACAA
Statistics
Matches: 117, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
6 3 0.03
7 106 0.91
8 8 0.07
ACGTcount: A:0.37, C:0.47, G:0.05, T:0.10
Consensus pattern (7 bp):
AACCCTA
Found at i:15989 original size:7 final size:7
Alignment explanation
Indices: 15977--16051 Score: 123
Period size: 7 Copynumber: 10.7 Consensus size: 7
15967 AAGAAGCTTT
15977 AACCCTA
1 AACCCTA
15984 AACCCTA
1 AACCCTA
15991 AACCCTA
1 AACCCTA
15998 AACCCTA
1 AACCCTA
16005 AACCCTA
1 AACCCTA
*
16012 AACACTA
1 AACCCTA
16019 AACCCTA
1 AACCCTA
**
16026 AACCCCG
1 AACCCTA
16033 AACCCTA
1 AACCCTA
16040 AACCCTA
1 AACCCTA
16047 AACCC
1 AACCC
16052 GAACCCCGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 62 1.00
ACGTcount: A:0.43, C:0.44, G:0.01, T:0.12
Consensus pattern (7 bp):
AACCCTA
Found at i:18157 original size:7 final size:7
Alignment explanation
Indices: 18142--18259 Score: 103
Period size: 7 Copynumber: 16.7 Consensus size: 7
18132 AAGAAGCTTT
18142 AACCCTA
1 AACCCTA
*
18149 AATCCTA
1 AACCCTA
18156 AACCCTA
1 AACCCTA
18163 AACCCTA
1 AACCCTA
18170 AACCCTA
1 AACCCTA
**
18177 AACCCCCG
1 AA-CCCTA
18185 AACCCTA
1 AACCCTA
*
18192 AACCCCA
1 AACCCTA
*
18199 AACCCCA
1 AACCCTA
*
18206 AACCCCA
1 AACCCTA
**
18213 AACCCCG
1 AACCCTA
*
18220 AA-CCTCG
1 AACCCT-A
*
18227 AACCCCA
1 AACCCTA
*
18234 AACCCCA
1 AACCCTA
18241 AACCCTA
1 AACCCTA
*
18248 AACCCCA
1 AACCCTA
18255 AACCC
1 AACCC
18260 CGAACAACAA
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
6 2 0.02
7 86 0.91
8 7 0.07
ACGTcount: A:0.40, C:0.50, G:0.03, T:0.08
Consensus pattern (7 bp):
AACCCTA
Found at i:18260 original size:7 final size:7
Alignment explanation
Indices: 18155--18260 Score: 122
Period size: 7 Copynumber: 15.0 Consensus size: 7
18145 CCTAAATCCT
*
18155 AAACCCT
1 AAACCCC
*
18162 AAACCCT
1 AAACCCC
*
18169 AAACCCT
1 AAACCCC
18176 AAACCCCC
1 AAA-CCCC
* *
18184 GAACCCT
1 AAACCCC
18191 AAACCCC
1 AAACCCC
18198 AAACCCC
1 AAACCCC
18205 AAACCCC
1 AAACCCC
18212 AAACCCC
1 AAACCCC
* *
18219 GAACCTC
1 AAACCCC
*
18226 GAACCCC
1 AAACCCC
18233 AAACCCC
1 AAACCCC
*
18240 AAACCCT
1 AAACCCC
18247 AAACCCC
1 AAACCCC
18254 AAACCCC
1 AAACCCC
18261 GAACAACAAG
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
7 82 0.94
8 5 0.06
ACGTcount: A:0.40, C:0.52, G:0.03, T:0.06
Consensus pattern (7 bp):
AAACCCC
Found at i:20351 original size:7 final size:7
Alignment explanation
Indices: 20336--20453 Score: 103
Period size: 7 Copynumber: 16.7 Consensus size: 7
20326 AAGAAGCTTT
20336 AACCCTA
1 AACCCTA
*
20343 AATCCTA
1 AACCCTA
20350 AACCCTA
1 AACCCTA
20357 AACCCTA
1 AACCCTA
20364 AACCCTA
1 AACCCTA
**
20371 AACCCCCG
1 AA-CCCTA
20379 AACCCTA
1 AACCCTA
*
20386 AACCCCA
1 AACCCTA
*
20393 AACCCCA
1 AACCCTA
*
20400 AACCCCA
1 AACCCTA
**
20407 AACCCCG
1 AACCCTA
*
20414 AA-CCTCG
1 AACCCT-A
*
20421 AACCCCA
1 AACCCTA
*
20428 AACCCCA
1 AACCCTA
20435 AACCCTA
1 AACCCTA
*
20442 AACCCCA
1 AACCCTA
20449 AACCC
1 AACCC
20454 CGAACAACAA
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
6 2 0.02
7 86 0.91
8 7 0.07
ACGTcount: A:0.40, C:0.50, G:0.03, T:0.08
Consensus pattern (7 bp):
AACCCTA
Found at i:20454 original size:7 final size:7
Alignment explanation
Indices: 20349--20454 Score: 122
Period size: 7 Copynumber: 15.0 Consensus size: 7
20339 CCTAAATCCT
*
20349 AAACCCT
1 AAACCCC
*
20356 AAACCCT
1 AAACCCC
*
20363 AAACCCT
1 AAACCCC
20370 AAACCCCC
1 AAA-CCCC
* *
20378 GAACCCT
1 AAACCCC
20385 AAACCCC
1 AAACCCC
20392 AAACCCC
1 AAACCCC
20399 AAACCCC
1 AAACCCC
20406 AAACCCC
1 AAACCCC
* *
20413 GAACCTC
1 AAACCCC
*
20420 GAACCCC
1 AAACCCC
20427 AAACCCC
1 AAACCCC
*
20434 AAACCCT
1 AAACCCC
20441 AAACCCC
1 AAACCCC
20448 AAACCCC
1 AAACCCC
20455 GAACAACAAG
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
7 82 0.94
8 5 0.06
ACGTcount: A:0.40, C:0.52, G:0.03, T:0.06
Consensus pattern (7 bp):
AAACCCC
Found at i:22546 original size:7 final size:7
Alignment explanation
Indices: 22531--22648 Score: 103
Period size: 7 Copynumber: 16.7 Consensus size: 7
22521 AAGAAGCTTT
22531 AACCCTA
1 AACCCTA
*
22538 AATCCTA
1 AACCCTA
22545 AACCCTA
1 AACCCTA
22552 AACCCTA
1 AACCCTA
22559 AACCCTA
1 AACCCTA
**
22566 AACCCCCG
1 AA-CCCTA
22574 AACCCTA
1 AACCCTA
*
22581 AACCCCA
1 AACCCTA
*
22588 AACCCCA
1 AACCCTA
*
22595 AACCCCA
1 AACCCTA
**
22602 AACCCCG
1 AACCCTA
*
22609 AA-CCTCG
1 AACCCT-A
*
22616 AACCCCA
1 AACCCTA
*
22623 AACCCCA
1 AACCCTA
22630 AACCCTA
1 AACCCTA
*
22637 AACCCCA
1 AACCCTA
22644 AACCC
1 AACCC
22649 CGAACAACAA
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
6 2 0.02
7 86 0.91
8 7 0.07
ACGTcount: A:0.40, C:0.50, G:0.03, T:0.08
Consensus pattern (7 bp):
AACCCTA
Found at i:22649 original size:7 final size:7
Alignment explanation
Indices: 22544--22649 Score: 122
Period size: 7 Copynumber: 15.0 Consensus size: 7
22534 CCTAAATCCT
*
22544 AAACCCT
1 AAACCCC
*
22551 AAACCCT
1 AAACCCC
*
22558 AAACCCT
1 AAACCCC
22565 AAACCCCC
1 AAA-CCCC
* *
22573 GAACCCT
1 AAACCCC
22580 AAACCCC
1 AAACCCC
22587 AAACCCC
1 AAACCCC
22594 AAACCCC
1 AAACCCC
22601 AAACCCC
1 AAACCCC
* *
22608 GAACCTC
1 AAACCCC
*
22615 GAACCCC
1 AAACCCC
22622 AAACCCC
1 AAACCCC
*
22629 AAACCCT
1 AAACCCC
22636 AAACCCC
1 AAACCCC
22643 AAACCCC
1 AAACCCC
22650 GAACAACAAG
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
7 82 0.94
8 5 0.06
ACGTcount: A:0.40, C:0.52, G:0.03, T:0.06
Consensus pattern (7 bp):
AAACCCC
Found at i:24741 original size:7 final size:7
Alignment explanation
Indices: 24725--24890 Score: 242
Period size: 7 Copynumber: 23.7 Consensus size: 7
24715 AAGAAGCTTT
24725 AACCCTA
1 AACCCTA
*
24732 AACTCTA
1 AACCCTA
24739 AACCCTA
1 AACCCTA
24746 AACCCTA
1 AACCCTA
24753 AACCCTA
1 AACCCTA
*
24760 AAGCCTA
1 AACCCTA
24767 AACCCTA
1 AACCCTA
*
24774 ACCCCTA
1 AACCCTA
24781 AACCCTA
1 AACCCTA
*
24788 AACCATA
1 AACCCTA
24795 AACCCTA
1 AACCCTA
*
24802 AACCCTT
1 AACCCTA
24809 AACCCTA
1 AACCCTA
*
24816 AACCTTA
1 AACCCTA
24823 AACCCTA
1 AACCCTA
24830 AACCCTA
1 AACCCTA
24837 AACCCTA
1 AACCCTA
*
24844 AACCTTA
1 AACCCTA
24851 AACCCTA
1 AACCCTA
*
24858 AACCCCA
1 AACCCTA
*
24865 AACCCCA
1 AACCCTA
*
24872 AACCCCA
1 AACCCTA
24879 AACCCTA
1 AACCCTA
24886 AACCC
1 AACCC
24891 CGGACCTCGA
Statistics
Matches: 143, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 143 1.00
ACGTcount: A:0.42, C:0.43, G:0.01, T:0.14
Consensus pattern (7 bp):
AACCCTA
Found at i:24903 original size:28 final size:28
Alignment explanation
Indices: 24738--24918 Score: 148
Period size: 28 Copynumber: 6.5 Consensus size: 28
24728 CCTAAACTCT
* * * *
24738 AAACCCTAAACCCTAAACCCTAAAGCCT
1 AAACCCTAAACCCCAAACCCCAAACCCC
* **
24766 AAACCCT-AACCCCTAAACCCTAAACCAT
1 AAACCCTAAACCCC-AAACCCCAAACCCC
** * **
24794 AAACCCTAAACCCTTAACCCTAAACCTT
1 AAACCCTAAACCCCAAACCCCAAACCCC
* * **
24822 AAACCCTAAACCCTAAACCCTAAACCTT
1 AAACCCTAAACCCCAAACCCCAAACCCC
24850 AAACCCTAAACCCCAAACCCCAAACCCC
1 AAACCCTAAACCCCAAACCCCAAACCCC
** * *
24878 AAACCCTAAACCCCGGACCTCGAACCCC
1 AAACCCTAAACCCCAAACCCCAAACCCC
* *
24906 GAACCCTGAACCC
1 AAACCCTAAACCC
24919 TGAACCCTGA
Statistics
Matches: 134, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
27 5 0.04
28 124 0.93
29 5 0.04
ACGTcount: A:0.40, C:0.44, G:0.03, T:0.13
Consensus pattern (28 bp):
AAACCCTAAACCCCAAACCCCAAACCCC
Found at i:24908 original size:7 final size:7
Alignment explanation
Indices: 24858--24937 Score: 70
Period size: 7 Copynumber: 11.4 Consensus size: 7
24848 TTAAACCCTA
*
24858 AACCCCA
1 AACCCCG
*
24865 AACCCCA
1 AACCCCG
*
24872 AACCCCA
1 AACCCCG
**
24879 AACCCTA
1 AACCCCG
24886 AACCCCG
1 AACCCCG
* *
24893 GACCTCG
1 AACCCCG
24900 AACCCCG
1 AACCCCG
*
24907 AACCCTG
1 AACCCCG
*
24914 AACCCTG
1 AACCCCG
*
24921 AACCCTG
1 AACCCCG
24928 AACCCCG
1 AACCCCG
24935 AAC
1 AAC
24938 AACAAGTCTA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 64 1.00
ACGTcount: A:0.34, C:0.50, G:0.10, T:0.06
Consensus pattern (7 bp):
AACCCCG
Found at i:24916 original size:14 final size:14
Alignment explanation
Indices: 24725--24937 Score: 124
Period size: 14 Copynumber: 15.2 Consensus size: 14
24715 AAGAAGCTTT
* **
24725 AACCCTAAACTCTA
1 AACCCTAAACCCCG
**
24739 AACCCTAAACCCTA
1 AACCCTAAACCCCG
* **
24753 AACCCTAAAGCCTA
1 AACCCTAAACCCCG
*
24767 AACCCT-AACCCCTA
1 AACCCTAAACCCC-G
***
24781 AACCCTAAACCATA
1 AACCCTAAACCCCG
**
24795 AACCCTAAACCCTT
1 AACCCTAAACCCCG
***
24809 AACCCTAAACCTTA
1 AACCCTAAACCCCG
**
24823 AACCCTAAACCCTA
1 AACCCTAAACCCCG
***
24837 AACCCTAAACCTTA
1 AACCCTAAACCCCG
*
24851 AACCCTAAACCCCA
1 AACCCTAAACCCCG
* *
24865 AACCCCAAACCCCA
1 AACCCTAAACCCCG
24879 AACCCTAAACCCCG
1 AACCCTAAACCCCG
* *
24893 GA-CCTCGAACCCCG
1 AACCCT-AAACCCCG
* *
24907 AACCCTGAACCCTG
1 AACCCTAAACCCCG
*
24921 AACCCTGAACCCCG
1 AACCCTAAACCCCG
24935 AAC
1 AAC
24938 AACAAGTCTA
Statistics
Matches: 173, Mismatches: 22, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
13 7 0.04
14 159 0.92
15 7 0.04
ACGTcount: A:0.39, C:0.44, G:0.04, T:0.13
Consensus pattern (14 bp):
AACCCTAAACCCCG
Found at i:27023 original size:7 final size:7
Alignment explanation
Indices: 27007--27171 Score: 226
Period size: 7 Copynumber: 23.7 Consensus size: 7
26997 AAGAAGCTTT
27007 AACCCTA
1 AACCCTA
*
27014 AACTCTA
1 AACCCTA
27021 AACCCTA
1 AACCCTA
27028 AACCCT-
1 AACCCTA
27034 AACCCTA
1 AACCCTA
27041 AACCCTA
1 AACCCTA
*
27048 AAGCCTA
1 AACCCTA
27055 AACCCTA
1 AACCCTA
*
27062 ACCCCTA
1 AACCCTA
27069 AACCCTA
1 AACCCTA
*
27076 AACCATA
1 AACCCTA
27083 AACCCTA
1 AACCCTA
*
27090 AACCCTT
1 AACCCTA
27097 AACCCT-
1 AACCCTA
27103 AACCCTTA
1 AACCC-TA
27111 AACCCTA
1 AACCCTA
27118 AACCCTA
1 AACCCTA
*
27125 AACCTTA
1 AACCCTA
27132 AACCCTA
1 AACCCTA
*
27139 AACCCCA
1 AACCCTA
*
27146 AACCCCA
1 AACCCTA
*
27153 AACCCCA
1 AACCCTA
27160 AACCCTA
1 AACCCTA
27167 AACCC
1 AACCC
27172 GACCCCGAAC
Statistics
Matches: 142, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
6 11 0.08
7 126 0.89
8 5 0.04
ACGTcount: A:0.41, C:0.44, G:0.01, T:0.15
Consensus pattern (7 bp):
AACCCTA
Found at i:27183 original size:7 final size:7
Alignment explanation
Indices: 27139--27209 Score: 74
Period size: 7 Copynumber: 10.4 Consensus size: 7
27129 TTAAACCCTA
*
27139 AACCCCA
1 AACCCCG
*
27146 AACCCCA
1 AACCCCG
27153 AACCCC-
1 AACCCCG
* *
27159 AAACCCT
1 AACCCCG
*
27166 AAACCCG
1 AACCCCG
27173 -ACCCCG
1 AACCCCG
27179 AACCCCG
1 AACCCCG
*
27186 AACCCTG
1 AACCCCG
27193 AACCCCG
1 AACCCCG
27200 AACCCCG
1 AACCCCG
27207 AAC
1 AAC
27210 AACAAGTCTA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
6 10 0.18
7 47 0.82
ACGTcount: A:0.35, C:0.54, G:0.08, T:0.03
Consensus pattern (7 bp):
AACCCCG
Found at i:27204 original size:33 final size:33
Alignment explanation
Indices: 27140--27204 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 33
27130 TAAACCCTAA
*
27140 ACCCCAAACCCCAAACCCCAAACCCTAAACCCG
1 ACCCCAAACCCCAAACCCCAAACCCCAAACCCG
* * ** *
27173 ACCCCGAACCCCGAACCCTGAACCCCGAACCC
1 ACCCCAAACCCCAAACCCCAAACCCCAAACCC
27205 CGAACAACAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.34, C:0.55, G:0.08, T:0.03
Consensus pattern (33 bp):
ACCCCAAACCCCAAACCCCAAACCCCAAACCCG
Found at i:29301 original size:7 final size:7
Alignment explanation
Indices: 29280--29494 Score: 196
Period size: 7 Copynumber: 30.7 Consensus size: 7
29270 AAGAAGCTTT
29280 AACCCTA
1 AACCCTA
*
29287 AACTCTA
1 AACCCTA
*
29294 AATCCTA
1 AACCCTA
29301 AACCCTA
1 AACCCTA
29308 AACCCTA
1 AACCCTA
29315 AACCCTA
1 AACCCTA
*
29322 AAGCCTA
1 AACCCTA
*
29329 AAGCCTA
1 AACCCTA
29336 AACCCTA
1 AACCCTA
*
29343 ACCCCTA
1 AACCCTA
29350 AACCCTA
1 AACCCTA
*
29357 AACCATA
1 AACCCTA
29364 AACCCTA
1 AACCCTA
*
29371 AACCCTT
1 AACCCTA
*
29378 AACCCTT
1 AACCCTA
*
29385 AACCCTT
1 AACCCTA
29392 AACCCTA
1 AACCCTA
*
29399 AACCTTA
1 AACCCTA
*
29406 AACCCCA
1 AACCCTA
*
29413 AACCCCA
1 AACCCTA
*
29420 AACCCCA
1 AACCCTA
**
29427 AACCCCG
1 AACCCTA
**
29434 AACCCCG
1 AACCCTA
**
29441 AACCCCG
1 AACCCTA
*
29448 AACCCTG
1 AACCCTA
*
29455 AACCCTG
1 AACCCTA
**
29462 AACCCCG
1 AACCCTA
*
29469 AACCCCA
1 AACCCTA
*
29476 AACCCTG
1 AACCCTA
*
29483 AACCCTG
1 AACCCTA
29490 AACCC
1 AACCC
29495 CGAACAACAA
Statistics
Matches: 187, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 187 1.00
ACGTcount: A:0.38, C:0.45, G:0.05, T:0.13
Consensus pattern (7 bp):
AACCCTA
Found at i:31569 original size:7 final size:7
Alignment explanation
Indices: 31557--31756 Score: 242
Period size: 7 Copynumber: 28.7 Consensus size: 7
31547 TTATCAAAAG
31557 AACCCTA
1 AACCCTA
31564 AACCCTA
1 AACCCTA
31571 AACCCTA
1 AACCCTA
*
31578 AAGCCTA
1 AACCCTA
31585 AACCCTA
1 AACCCTA
*
31592 ACCCCTA
1 AACCCTA
*
31599 AACCATA
1 AACCCTA
*
31606 AACCATA
1 AACCCTA
31613 AACCCTA
1 AACCCTA
*
31620 AACCCTT
1 AACCCTA
*
31627 AA-CCTT
1 AACCCTA
31633 AACCCTA
1 AACCCTA
31640 AACCCTA
1 AACCCTA
31647 AACCCTA
1 AACCCTA
*
31654 AACCCCA
1 AACCCTA
31661 AACCCTA
1 AACCCTA
31668 AACCCTA
1 AACCCTA
31675 AACCCTA
1 AACCCTA
31682 AACCCTA
1 AACCCTA
31689 AACCCTA
1 AACCCTA
31696 AACCCTA
1 AACCCTA
*
31703 AA-CCTCG
1 AACCCT-A
*
31710 AACCCCA
1 AACCCTA
**
31717 AACCCCG
1 AACCCTA
*
31724 AACCCCA
1 AACCCTA
*
31731 AACCCCA
1 AACCCTA
*
31738 AACCCTG
1 AACCCTA
*
31745 AACCCTG
1 AACCCTA
31752 AACCC
1 AACCC
31757 CGAACAACAA
Statistics
Matches: 173, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
6 9 0.05
7 162 0.94
8 2 0.01
ACGTcount: A:0.41, C:0.45, G:0.03, T:0.12
Consensus pattern (7 bp):
AACCCTA
Found at i:34024 original size:22 final size:21
Alignment explanation
Indices: 33982--34021 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
33972 GAGTTTATTT
*
33982 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
34003 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
34022 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:35706 original size:11 final size:11
Alignment explanation
Indices: 35684--35719 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
35674 GTTTTATGCT
35684 TTCTCT-TTGA
1 TTCTCTCTTGA
35694 TTCTCTCTTGA
1 TTCTCTCTTGA
35705 TTCTCTCTTGA
1 TTCTCTCTTGA
35716 TTCT
1 TTCT
35720 AGTTGATTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.08, C:0.25, G:0.08, T:0.58
Consensus pattern (11 bp):
TTCTCTCTTGA
Found at i:35725 original size:21 final size:21
Alignment explanation
Indices: 35684--35727 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35674 GTTTTATGCT
*
35684 TTCTCTTTGATTCTCTCTTGA
1 TTCTCTTTGATTCTCACTTGA
*
35705 TTCTCTCTTGATTCT-AGTTGA
1 TTCTCT-TTGATTCTCACTTGA
35726 TT
1 TT
35728 GTTATTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.11, C:0.20, G:0.11, T:0.57
Consensus pattern (21 bp):
TTCTCTTTGATTCTCACTTGA
Found at i:35986 original size:18 final size:17
Alignment explanation
Indices: 35932--35980 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
35922 TTGGACCCTT
* *
35932 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
35950 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
35968 AGTGCATTCGATG
1 AGTGCA-TCGATG
35981 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:36051 original size:46 final size:45
Alignment explanation
Indices: 35949--36056 Score: 146
Period size: 45 Copynumber: 2.4 Consensus size: 45
35939 CGGTGCACTA
*
35949 AGAGTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCC
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCC
* **
35994 AGAGTGTATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATTC
1 AGAGTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCC
*
36040 TGAGTGCATCGATGCAT
1 AGAGTGCATCGATGCAT
36057 AGTATGTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
45 30 0.55
46 22 0.40
47 3 0.05
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (45 bp):
AGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCC
Found at i:36087 original size:65 final size:64
Alignment explanation
Indices: 36001--36141 Score: 171
Period size: 64 Copynumber: 2.2 Consensus size: 64
35991 GCCAGAGTGT
* *
36001 ATCGATGCATCAAATGCATTCGATGTTTTCATAAAATTC-TGAGTGCATCGATGCATAG-TAT-G
1 ATCGGTGCATCAAATGCATTCGATG-TTTAAT-AAATTCATG-GTGCATCGATGCATAGCT-TGG
36063 TGC
62 TGC
* ** *
36066 ATCGGTGCATGAAATGCATTCGATGTTTAATTTATTCATGGTGCATCGATGCATGGCTTGGTGC
1 ATCGGTGCATCAAATGCATTCGATGTTTAATAAATTCATGGTGCATCGATGCATAGCTTGGTGC
36130 ATCGGTGCATCA
1 ATCGGTGCATCA
36142 CTCTGAAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
63 20 0.30
64 23 0.35
65 23 0.35
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (64 bp):
ATCGGTGCATCAAATGCATTCGATGTTTAATAAATTCATGGTGCATCGATGCATAGCTTGGTGC
Found at i:37152 original size:47 final size:47
Alignment explanation
Indices: 37080--37266 Score: 331
Period size: 47 Copynumber: 4.0 Consensus size: 47
37070 GACTTTCATA
*
37080 AAAGCTTTGGATTGTTCAGAGTTTGGATTAATAGTAAAGAAGCCAAT-
1 AAAGCTTTGGATGGTTCAGAGTTTGGATTAATAGTAAAGAAGCC-ATC
*
37127 AATGCTTTGGATGGTTCAGAGTTTGGATTAATAGTAAAGAAGCCATC
1 AAAGCTTTGGATGGTTCAGAGTTTGGATTAATAGTAAAGAAGCCATC
*
37174 AAAGCTTTGGATGGTTCAGATTTTGGATTAATAGTAAAGAAGCCATC
1 AAAGCTTTGGATGGTTCAGAGTTTGGATTAATAGTAAAGAAGCCATC
37221 AAAGCTTTGGATGGTTCAGAGTTTGGATTAATAGTAAAGAAGCCAT
1 AAAGCTTTGGATGGTTCAGAGTTTGGATTAATAGTAAAGAAGCCAT
37267 GTTGTTGTCC
Statistics
Matches: 134, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
46 2 0.01
47 132 0.99
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.32
Consensus pattern (47 bp):
AAAGCTTTGGATGGTTCAGAGTTTGGATTAATAGTAAAGAAGCCATC
Found at i:47078 original size:17 final size:17
Alignment explanation
Indices: 47031--47079 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 17
47021 TTCAGAATTT
47031 AACGCGAACTTGAAATA
1 AACGCGAACTTGAAATA
*
47048 AATCGTAACGAACTTGGAATA
1 AA-CG---CGAACTTGAAATA
47069 AACGCGAACTT
1 AACGCGAACTT
47080 TGATTATCGC
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
17 9 0.33
18 2 0.07
20 2 0.07
21 14 0.52
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.20
Consensus pattern (17 bp):
AACGCGAACTTGAAATA
Found at i:48817 original size:12 final size:12
Alignment explanation
Indices: 48800--48838 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
48790 TCCCTCTTCC
*
48800 TCCTCTCCCCCT
1 TCCTCTCCCTCT
*
48812 TCCTCTACCTCT
1 TCCTCTCCCTCT
*
48824 CCCTCTCCCTCT
1 TCCTCTCCCTCT
48836 TCC
1 TCC
48839 CCTTCCTCGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.03, C:0.62, G:0.00, T:0.36
Consensus pattern (12 bp):
TCCTCTCCCTCT
Found at i:48834 original size:18 final size:18
Alignment explanation
Indices: 48801--48835 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
48791 CCCTCTTCCT
*
48801 CCTCTCCCCCTTCCTCTA
1 CCTCTCCCCCTCCCTCTA
*
48819 CCTCTCCCTCTCCCTCT
1 CCTCTCCCCCTCCCTCT
48836 TCCCCTTCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.63, G:0.00, T:0.34
Consensus pattern (18 bp):
CCTCTCCCCCTCCCTCTA
Found at i:53140 original size:40 final size:40
Alignment explanation
Indices: 53085--53160 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
53075 GAAAAGTAGT
*
53085 TTTGCTTTGAGTAGGATATATTGGATCTATATTTTTCTAC
1 TTTGCTTTGAGTAGGATATACTGGATCTATATTTTTCTAC
* *
53125 TTTGCTTTGAGTAGGATTTACTGGATCTGTATTTTT
1 TTTGCTTTGAGTAGGATATACTGGATCTATATTTTT
53161 TTCATTATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.20, C:0.09, G:0.20, T:0.51
Consensus pattern (40 bp):
TTTGCTTTGAGTAGGATATACTGGATCTATATTTTTCTAC
Found at i:63873 original size:2 final size:2
Alignment explanation
Indices: 63868--63903 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
63858 AAAAAAAATG
63868 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63904 GTGATATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.